Origin IGS: nnnnngactatcagattaagacaggtctttatgaaaaaggtttccttttgaaaaaggcactcttacagattgctagtcaggttaattgacatttttttgaaactataacccgcgtcaggattatcttgtcgtgggtttcttgctgatttgcttattttatactcaatgaaaatcaaagagcaaactaggaaactagccgtaggttgctcaaagcactgctttgaggttgtaaataaggctgacgaagtcagctcaaaacatgtttttgaggttgcggatgaaactgacgaagtcagtaattatatctacggcaaggcgacgttgacgcggtttgaagagattttcgaagagtattattagaaagtatctcagtgatttcctcatctataagcaaaaaacttgaaaaaagtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctgtaatacctctttttctttctatatgaaaatgataacgcaaacattcacttttttcaagttttttgcttatagatgaggaaatcactgagatactttctaataatactcttcgaaaatctcttcaaaccgcgtcaacgtcgccttgccgtagatataattactgacttcgtcagtttcatccgcaacctcaaaaacatgttttgagctgacttcgtcagccttatttacaacctcaaagcagtgctttgagcaacctacggctagtttcctagtttgctctttgattttcattgagtataaaataagcaaatcagcaagaaacccacgacaagataatcctgacgcgggttatagtttcaaaaaaatgtcaattaacctgactagcaatctgtaagagtgcctttttcaaaaggaaacctttttcataaagacctgtcttaatctgatagtcnnnnn Mask Tandem Repeat Region ================================================ nnnnngactatcagattaagacaggtctttatgaaaaaggtttccttttgaaaaaggcactcttacagattgctagtcaggttaattgacatttttttgaaactataacccgcgtcaggattatcttgtcgtgggtttcttgctgatttgcttattttatactcaatgaaaatcaaagagcaaactaggaaactagccgtaggttgctcaaagcactgctttgaggttgtaaataaggctgacgaagtcagctcaaaacatgtttttgaggttgcggatgaaactgacgaagtcagtaattatatctacggcaaggcgacgttgacgcggtttgaagagattttcgaagagtattattagaaagtatctcagtgatttcctcatctataagcaaaaaacttgaaaaaagtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag Find is-nt database================================================ Query_seq: SMT_495:SMT_496|SMT_495:SMT_496:bacterial peptide chain release factor 2 (RF-2):superoxide dismutase, manganese-dependent:->->:430114..430572 459 nnnnngactatcagattaagacaggtctttatgaaaaaggtttccttttgaaaaaggcactcttacagattgctagtcaggttaattgacatttttttgaaactataacccgcgtcaggattatcttgtcgtgggtttcttgctgatttgcttattttatactcaatgaaaatcaaagagcaaactaggaaactagccgtaggttgctcaaagcactgctttgaggttgtaaataaggctgacgaagtcagctcaaaacatgtttttgaggttgcggatgaaactgacgaagtcagtaattatatctacggcaaggcgacgttgacgcggtttgaagagattttcgaagagtattattagaaagtatctcagtgatttcctcatctataagcaaaaaacttgaaaaaagtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_495:SMT_496|SMT_495:SMT_496:bacterial peptide chain release factor 2 (RF-2):superoxide dismutase, manganese-dependent:->->:430114..430572 459 nnnnngactatcagattaagacaggtctttatgaaaaaggtttccttttgaaaaaggcactcttacagattgctagtcaggttaattgacatttttttgaaactataacccgcgtcaggattatcttgtcgtgggtttcttgctgatttgcttattttatactcaatgaaaatcaaagagcaaactaggaaactagccgtaggttgctcaaagcactgctttgaggttgtaaataaggctgacgaagtcagctcaaaacatgtttttgaggttgcggatgaaactgacgaagtcagtaattatatctacggcaaggcgacgttgacgcggtttgaagagattttcgaagagtattattagaaagtatctcagtgatttcctcatctataagcaaaaaacttgaaaaaagtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_495:SMT_496|SMT_495:SMT_496:bacterial peptide chain release factor 2 (RF-2):superoxide dismutase, manganese-dependent:->->:430114..430572 459 nnnnngactatcagattaagacaggtctttatgaaaaaggtttccttttgaaaaaggcactcttacagattgctagtcaggttaattgacatttttttgaaactataacccgcgtcaggattatcttgtcgtgggtttcttgctgatttgcttattttatactcaatgaaaatcaaagagcaaactaggaaactagccgtaggttgctcaaagcactgctttgaggttgtaaataaggctgacgaagtcagctcaaaacatgtttttgaggttgcggatgaaactgacgaagtcagtaattatatctacggcaaggcgacgttgacgcggtttgaagagattttcgaagagtattattagaaagtatctcagtgatttcctcatctataagcaaaaaacttgaaaaaagtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 15 Min: 151 Max: 357 Len: 207 Subject: UniRef90_Q04L28 Cluster: Hypothetical protein; n=2; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 2.0E-24 bit: 113.0 Len: 189 Query Start:166 Query End:354 Subject Strand: null Subject Start: 1 Subject End: 63 ..................................................................................................................................................................... M K I K E Q T R K L A V G C S K H C F E V V N K A D E V S S K H V F E V A D E T D E V S N Y I Y G K A T L T R F E E I F E E Y ......................................................................................................... ..................................................................................................................................................................... M K I K E Q T R K L A A G C S K H C F E V A D K T D E V S S K H G F E V V D E T D E V S N H T Y G K A T L T R I E E I F E E Y ......................................................................................................... Subject: UniRef90_Q04LB4 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 7.0E-24 bit: 111.0 Len: 189 Query Start:166 Query End:354 Subject Strand: null Subject Start: 1 Subject End: 63 ..................................................................................................................................................................... M K I K E Q T R K L A V G C S K H C F E V V N K A D E V S S K H V F E V A D E T D E V S N Y I Y G K A T L T R F E E I F E E Y ......................................................................................................... ..................................................................................................................................................................... M K I K E Q T R K L A A G C S K H C F E V V D R T D E V S S K H C F E V V D E T D E V S N H T Y G R A T M T W F E E I F E E Y ......................................................................................................... Subject: UniRef90_Q04I51 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 4.0E-19 bit: 95.9 Len: 174 Query Start:166 Query End:339 Subject Strand: null Subject Start: 1 Subject End: 58 ..................................................................................................................................................................... M K I K E Q T R K L A V G C S K H C F E V V N K A D E V S S K H V F E V A D E T D E V S N Y I Y G K A T L T R F E E ........................................................................................................................ ..................................................................................................................................................................... M K I K E Q T R K L A A G C S K H C F E V M D R T D E V S S K H G F E V V D E T D E V S N H T Y G E V K L T W F E E ........................................................................................................................ Subject: UniRef90_Q04I19 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 4.0E-16 bit: 85.9 Len: 144 Query Start:157 Query End:300 Subject Strand: null Subject Start: 5 Subject End: 52 ............................................................................................................................................................ L Y S M K I K E Q T R K L A V G C S K H C F E V V N K A D E V S S K H V F E V A D E T D E V S N ............................................................................................................................................................... ............................................................................................................................................................ L Y S M K I K E Q T R K L A T G C S K H R F E V V D K T D E V S S K H C F E V A D R T D E V S N ............................................................................................................................................................... Subject: UniRef90_Q04I61 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 5.0E-16 bit: 85.5 Len: 204 Query Start:151 Query End:354 Subject Strand: null Subject Start: 21 Subject End: 73 ...................................................................................................................................................... L I L Y S M K I K E Q T R K L A V G C S K H C F E V V N K A D E V S S K H V F E V A D E T D E V S N Y I Y G K A T L T R F E E I F E E Y ......................................................................................................... ...................................................................................................................................................... I F L Y S M K I K V Q T R K L A A G C S K H C F E V V - - - - - - - - - - - - - - - D E T D E V S N H T Y G K A T L T W F E E I F E K Y ......................................................................................................... Subject: UniRef90_Q04LP5 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 4.0E-15 bit: 82.4 Len: 147 Query Start:208 Query End:354 Subject Strand: null Subject Start: 147 Subject End: 195 ............................................................................................................................................................................................................... S K H C F E V V N K A D E V S S K H V F E V A D E T D E V S N Y I Y G K A T L T R F E E I F E E Y ......................................................................................................... ............................................................................................................................................................................................................... S K H C F E V V D R T D E V S S K H C F E V V D R T D E V S N H T H G K A T L T W F E E I F K E Y ......................................................................................................... HSP 2 e-value: 2.0E-14 bit: 80.1 Len: 147 Query Start:154 Query End:300 Subject Strand: null Subject Start: 24 Subject End: 72 ......................................................................................................................................................... I L Y S M K I K E Q T R K L A V G C S K H C F E V V N K A D E V S S K H V F E V A D E T D E V S N ............................................................................................................................................................... ......................................................................................................................................................... V L Y S M K T K E Q T R K L A S G C S K H C F E V V D G T D V V S S K H C F E V V D R T D E V S S ............................................................................................................................................................... Subject: UniRef90_Q04IR5 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 4.0E-14 bit: 79.3 Len: 189 Query Start:166 Query End:354 Subject Strand: null Subject Start: 1 Subject End: 48 ..................................................................................................................................................................... M K I K E Q T R K L A V G C S K H C F E V V N K A D E V S S K H V F E V A D E T D E V S N Y I Y G K A T L T R F E E I F E E Y ......................................................................................................... ..................................................................................................................................................................... M K I K E Q T R K L A A G C S K H C F E V V - - - - - - - - - - - - - - - D E T D E V S N H T Y G K V K L T W F E E I F E E Y ......................................................................................................... Subject: UniRef90_Q04M07 Cluster: Hypothetical protein; n=2; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 5.0E-13 bit: 75.5 Len: 189 Query Start:166 Query End:354 Subject Strand: null Subject Start: 1 Subject End: 48 ..................................................................................................................................................................... M K I K E Q T R K L A V G C S K H C F E V V N K A D E V S S K H V F E V A D E T D E V S N Y I Y G K A T L T R F E E I F E E Y ......................................................................................................... ..................................................................................................................................................................... M K I K E Q T R K L A A G C S K Q C F E V V - - - - - - - - - - - - - - - D E T D E V S N H T Y G K A K L M W F E E I F E E Y ......................................................................................................... Subject: UniRef90_Q04KB8 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 4.0E-12 bit: 72.8 Len: 189 Query Start:166 Query End:354 Subject Strand: null Subject Start: 1 Subject End: 48 ..................................................................................................................................................................... M K I K E Q T R K L A V G C S K H C F E V V N K A D E V S S K H V F E V A D E T D E V S N Y I Y G K A T L T R F E E I F E E Y ......................................................................................................... ..................................................................................................................................................................... M K I K E Q T R K L A A G Y S K H S F E V V - - - - - - - - - - - - - - - D E T D E V S N H T Y S K A T L T W F E E I F E E Y ......................................................................................................... Subject: UniRef90_Q04IH0 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 2.0E-11 bit: 70.1 Len: 126 Query Start:229 Query End:354 Subject Strand: null Subject Start: 1 Subject End: 42 .................................................................................................................................................................................................................................... V N K A D E V S S K H V F E V A D E T D E V S N Y I Y G K A T L T R F E E I F E E Y ......................................................................................................... .................................................................................................................................................................................................................................... M D E T D E V S S K H V F E V V D E T D E V S N H T Y G K A T L T W F A E I F E E Y ......................................................................................................... Subject: UniRef90_Q04HT0 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 2.0E-9 bit: 63.9 Len: 102 Query Start:159 Query End:260 Subject Strand: null Subject Start: 102 Subject End: 135 .............................................................................................................................................................. C F E L T S S A L F T T S K Q C F E Q P T A S F L V C S L I F I E Y ....................................................................................................................................................................................................... .............................................................................................................................................................. C F E L T S S V S S T T S K Q C F E Q P A A S F L V C S L I F I E Y ....................................................................................................................................................................................................... HSP 2 e-value: 5.0E-6 bit: 52.4 Len: 147 Query Start:207 Query End:353 Subject Strand: null Subject Start: 11 Subject End: 59 .............................................................................................................................................................................................................. Y S S K I S S N R V N V A L P * I * L L X X X X X X X X X X T C F E L T S S A L F T T S K Q C F E .......................................................................................................... .............................................................................................................................................................................................................. Y S S K I S S N H V S V A L P Y V W L L T L S V S F T T S K Q C F E L T S S V S S T T S K L C F E .......................................................................................................... Subject: UniRef90_Q54904 Cluster: NanA gene; n=1; Streptococcus pneumoniae|Rep: NanA gene - Streptococcus pneumoniae HSP 1 e-value: 2.0E-8 bit: 60.5 Len: 105 Query Start:156 Query End:260 Subject Strand: null Subject Start: 64 Subject End: 98 ........................................................................................................................................................... C F E L T S S A L F T T S K Q C F E Q P T A S F L V C S L I F I E Y K ....................................................................................................................................................................................................... ........................................................................................................................................................... C F E L T L S V L S T T S K Q C F E H H A A S F L V C S L I F I E Y K ....................................................................................................................................................................................................... Subject: UniRef90_O05164 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae|Rep: Hypothetical protein - Streptococcus pneumoniae HSP 1 e-value: 2.0E-8 bit: 53.1 Len: 75 Query Start:156 Query End:230 Subject Strand: null Subject Start: 21 Subject End: 45 ........................................................................................................................................................... T T S K Q C F E Q P T A S F L V C S L I F I E Y K ..................................................................................................................................................................................................................................... ........................................................................................................................................................... T T S K Q C F E Q P A A S F L V C S L I F I E Y K ..................................................................................................................................................................................................................................... HSP 2 e-value: 2.0E-8 bit: 27.3 Len: 36 Query Start:322 Query End:357 Subject Strand: null Subject Start: 6 Subject End: 17 ................................................................................................................................................................................................................................................................................................................................. I I L F E N L F K P R Q ...................................................................................................... ................................................................................................................................................................................................................................................................................................................................. L I L F E N L F K P R Q ...................................................................................................... Subject: UniRef90_Q04I45 Cluster: Hypothetical protein; n=2; Streptococcus pneumoniae|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 5.0E-8 bit: 58.9 Len: 162 Query Start:166 Query End:327 Subject Strand: null Subject Start: 1 Subject End: 39 ..................................................................................................................................................................... M K I K E Q T R K L A V G C S K H C F E V V N K A D E V S S K H V F E V A D E T D E V S N Y I Y G K A T L T .................................................................................................................................... ..................................................................................................................................................................... M K I K G Q T R K L A A G C S K Q C F E V M - - - - - - - - - - - - - - - D R T D E V S N H T Y G K A T L T .................................................................................................................................... Subject: UniRef90_Q04N01 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 8.0E-6 bit: 51.6 Len: 102 Query Start:159 Query End:260 Subject Strand: null Subject Start: 15 Subject End: 48 .............................................................................................................................................................. C F E L T S S A L F T T S K Q C F E Q P T A S F L V C S L I F I E Y ....................................................................................................................................................................................................... .............................................................................................................................................................. C F E L T S S V L S T T S K Q C F E Q P V T S F L S D A L V L I A Y ....................................................................................................................................................................................................... nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgacatttttttgaaactataacccgcgtcaggattatcttgtcgtgggtttcttgctgatttgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntagaaagtatctcagtgatttcctcatctataagcaaaaaacttgaaaaaagtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 233 End: 322 ........................................................................................................................................................................................................................................ M R L T K S A Q N M F L R L R M K L T K S V I I S T A R R R ......................................................................................................................................... Protein_Len: 60 Strand: + Start: 148 End: 357 ................................................................................................................................................... M L I L Y S M K I K E Q T R K L A V G C S K H C F E V V N K A D E V S S K H V F E V A D E T D E V S N Y I Y G K A T L T ...................................................................................................... Protein_Len: 31 Strand: + Start: 366 End: 458 ............................................................................................................................................................................................................................................................................................................................................................................. M S V I S S S I S K K L E K S E C L R Y H F H I E R K R G I T . Protein_Len: 33 Strand: - Start: 296 End: 394 ....................................................................................................................................................................................................................................................................................................... Y N Y R R C P S T S A T Q L S K R L T N N S L I E T I E E D I L M ................................................................. Protein_Len: 43 Strand: - Start: 256 End: 384 ............................................................................................................................................................................................................................................................... F M N K L N R I F S V F D T I I D V A L R R Q R P K F L N E F L I I L F Y R L S K R M ........................................................................... Protein_Len: 60 Strand: - Start: 66 End: 296 ................................................................. P N D Q R P N R A S K S I K Y E I F I L S C V L F S A T P Q E F C Q K S T T F L A S S T L E F C T K S T A S S V S S T M ................................................................................................................................................................... nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgacatttttttgaaactataacccgcgtcaggattatcttgtcgtgggtttcttgctgatttgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntagaaagtatctcagtgatttcctcatctataagcaaaaaacttgaaaaaagtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 91 Start: 399 End: 428 ..............................................................................................................................................................................................................................................................................................................................................................................................................CTTGAAAAAAGTGAATGTTTGCGTTATCAT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgacatttttttgaaactataacccgcgtcaggattatcttgtcgtgggtttcttgctgatttgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntagaaagtatctcagtgatttcctcatctataagcaaaaaacttgaaaaaagtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 50 HP_score: -2.1 Tail_Score: -3.84633 Start: 76 End: 90 Full_Region: TCTTACAGATTGCTA GTCAG GTTAA TTGAC ATTTTTTTGAAACTA ...........................................................................GTCAGGTTAATTGAC................................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 88 HP_score: -10.8 Tail_Score: -4.30833 Start: 109 End: 135 Full_Region: TTTTTGAAACTATAA CCCGCGTCAGGA TTA TCTTGTCGTGGG TTTCTTGCTGATTTG ............................................................................................................CCCGCGTCAGGATTATCTTGTCGTGGG.................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 62 HP_score: -3.8 Tail_Score: -4.27062 Start: 178 End: 209 Full_Region: tcaaagcagtgcttt gagcaacctacgg ctagttt cctagtttgctc tttgattttcattga .................................................................................................................................................................................gagcaacctacggctagtttcctagtttgctc.......................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 70 HP_score: -8.3 Tail_Score: -3.35996 Start: 206 End: 226 Full_Region: AACTAGCCGTAGGTT GCTCAAAGC ACT GCTTTGAGG TTGTAAATAAGGCTG .............................................................................................................................................................................................................GCTCAAAGCACTGCTTTGAGG......................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 81 HP_score: -11.8 Tail_Score: -2.61383 Start: 207 End: 225 Full_Region: ACTAGCCGTAGGTTG CTCAAAGC ACT GCTTTGAG GTTGTAAATAAGGCT ..............................................................................................................................................................................................................CTCAAAGCACTGCTTTGAG.......................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 75 HP_score: -10.0 Tail_Score: -2.94708 Start: 238 End: 252 Full_Region: aaaaacatgttttga gctgac ttc gtcagc cttatttacaacctc .............................................................................................................................................................................................................................................gctgacttcgtcagc............................................................................................................................................................................................................... TransTerm Strand: - Conf: 41 HP_score: -2.6 Tail_Score: -2.56715 Start: 251 End: 271 Full_Region: cagtttcatccgcaa cctcaaaa acatg ttttgagc tgacttcgtcagcct ..........................................................................................................................................................................................................................................................cctcaaaaacatgttttgagc............................................................................................................................................................................................ TransTerm Strand: - Conf: 72 HP_score: -7.7 Tail_Score: -3.72695 Start: 284 End: 296 Full_Region: ccgtagatataatta ctgac ttc gtcag tttcatccgcaacct ...........................................................................................................................................................................................................................................................................................ctgacttcgtcag................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_495:SMT_496|SMT_495:SMT_496:bacterial peptide chain release factor 2 (RF-2):superoxide dismutase, manganese-dependent:->->:430114..430572 459 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgacatttttttgaaactataacccgcgtcaggattatcttgtcgtgggtttcttgctgatttgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntagaaagtatctcagtgatttcctcatctataagcaaaaaacttgaaaaaagtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag Intra-Species Hit: Count: 1 Min: 99 Max: 459 Len: 361 Subject: smit_SMT_495_SMT_496|bacterial peptide chain release factor 2 (RF-2):superoxide dismutase, manganese-dependent|POSITIVE:POSITIVE|[430114, 430572]|459 HSP 1 e-value: 2.0E-20 bit: 101.0 Len: 51 Query Start:99 Query End:149 Subject Strand: POSITIVE Subject Start: 99 Subject End: 149 ..................................................................................................gaaactataacccgcgtcaggattatcttgtcgtgggtttcttgctgattt...................................................................................................................................................................................................................................................................................................................... ..................................................................................................gaaactataacccgcgtcaggattatcttgtcgtgggtttcttgctgattt...................................................................................................................................................................................................................................................................................................................... HSP 2 e-value: 2.0E-20 bit: 101.0 Len: 51 Query Start:409 Query End:459 Subject Strand: POSITIVE Subject Start: 409 Subject End: 459 ........................................................................................................................................................................................................................................................................................................................................................................................................................gtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag ........................................................................................................................................................................................................................................................................................................................................................................................................................gtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag HSP 3 e-value: 7.0E-11 bit: 69.9 Len: 35 Query Start:358 Query End:392 Subject Strand: POSITIVE Subject Start: 358 Subject End: 392 .....................................................................................................................................................................................................................................................................................................................................................................tagaaagtatctcagtgatttcctcatctataagc................................................................... .....................................................................................................................................................................................................................................................................................................................................................................tagaaagtatctcagtgatttcctcatctataagc................................................................... Inter-species Hit: Count: 3 Min: 99 Max: 459 Len: 361 Subject: NC_008533_SPD_0666_SPD_0667|DNA polymerase III, delta subunit:superoxide dismutase, manganese-dependent|POSITIVE:POSITIVE|[687400, 687571]|172 HSP 1 e-value: 2.0E-20 bit: 101.0 Len: 51 Query Start:409 Query End:459 Subject Strand: POSITIVE Subject Start: 122 Subject End: 172 ........................................................................................................................................................................................................................................................................................................................................................................................................................gtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag ........................................................................................................................................................................................................................................................................................................................................................................................................................gtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag HSP 2 e-value: 1.0E-15 bit: 85.7 Len: 51 Query Start:99 Query End:149 Subject Strand: POSITIVE Subject Start: 9 Subject End: 59 ..................................................................................................gaaactataacccgcgtcaggattatcttgtcgtgggtttcttgctgattt...................................................................................................................................................................................................................................................................................................................... ..................................................................................................gaaactacaacccgcgtcaggactatcttgtcgtgggtttcttgctgattt...................................................................................................................................................................................................................................................................................................................... HSP 3 e-value: 4.0E-6 bit: 54.0 Len: 35 Query Start:358 Query End:392 Subject Strand: POSITIVE Subject Start: 71 Subject End: 105 .....................................................................................................................................................................................................................................................................................................................................................................tagaaagtatctcagtgatttcctcatctataagc................................................................... .....................................................................................................................................................................................................................................................................................................................................................................tagaaagtatgtcagtgatttccttatctataagc................................................................... Subject: NC_003098_spr0673_spr0674|DNA polymerase III subunit delta:Manganese co-factored superoxide dismutase|POSITIVE:POSITIVE|[679869,680040]|172 HSP 1 e-value: 2.0E-20 bit: 101.0 Len: 51 Query Start:409 Query End:459 Subject Strand: POSITIVE Subject Start: 122 Subject End: 172 ........................................................................................................................................................................................................................................................................................................................................................................................................................gtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag ........................................................................................................................................................................................................................................................................................................................................................................................................................gtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag HSP 2 e-value: 1.0E-15 bit: 85.7 Len: 51 Query Start:99 Query End:149 Subject Strand: POSITIVE Subject Start: 9 Subject End: 59 ..................................................................................................gaaactataacccgcgtcaggattatcttgtcgtgggtttcttgctgattt...................................................................................................................................................................................................................................................................................................................... ..................................................................................................gaaactacaacccgcgtcaggactatcttgtcgtgggtttcttgctgattt...................................................................................................................................................................................................................................................................................................................... HSP 3 e-value: 4.0E-6 bit: 54.0 Len: 35 Query Start:358 Query End:392 Subject Strand: POSITIVE Subject Start: 71 Subject End: 105 .....................................................................................................................................................................................................................................................................................................................................................................tagaaagtatctcagtgatttcctcatctataagc................................................................... .....................................................................................................................................................................................................................................................................................................................................................................tagaaagtatgtcagtgatttccttatctataagc................................................................... Subject: NC_003028_SP_0765_SP_0766|DNA polymerase III subunit delta:superoxide dismutase, manganese-dependent|POSITIVE:POSITIVE|[725208, 725379]|172 HSP 1 e-value: 2.0E-20 bit: 101.0 Len: 51 Query Start:409 Query End:459 Subject Strand: POSITIVE Subject Start: 122 Subject End: 172 ........................................................................................................................................................................................................................................................................................................................................................................................................................gtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag ........................................................................................................................................................................................................................................................................................................................................................................................................................gtgaatgtttgcgttatcattttcatatagaaagaaaaagaggtattacag HSP 2 e-value: 1.0E-15 bit: 85.7 Len: 51 Query Start:99 Query End:149 Subject Strand: POSITIVE Subject Start: 9 Subject End: 59 ..................................................................................................gaaactataacccgcgtcaggattatcttgtcgtgggtttcttgctgattt...................................................................................................................................................................................................................................................................................................................... ..................................................................................................gaaactacaacccgcgtcaggactatcttgtcgtgggtttcttgctgattt...................................................................................................................................................................................................................................................................................................................... HSP 3 e-value: 4.0E-6 bit: 54.0 Len: 35 Query Start:358 Query End:392 Subject Strand: POSITIVE Subject Start: 71 Subject End: 105 .....................................................................................................................................................................................................................................................................................................................................................................tagaaagtatctcagtgatttcctcatctataagc................................................................... .....................................................................................................................................................................................................................................................................................................................................................................tagaaagtatgtcagtgatttccttatctataagc................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAACUAUAACCCGCGUCAGGAUUAUCUUGUCGUGGGUUUCUUGCUGAUUUGCUUAUUUUAUACUCAAUGAAAAUCAAAGAGCAAACUAGGAAACUAGCCGUAGGUUGCUCAAAGCACUGCUUUGAGGUUGUAAAUAAGGCUGACGAAGUCAGCUCAAAACAUGUUUUUGAGGUUGCGGAUGAAACUGACGAAGUCAGUAAUUAUAUCUACGGCAAGGCGACGUUGACGCGGUUUGAAGAGAUUUUCGAAGAGUAUUAUUAGAAAGUAUCUCAGUGAUUUCCUCAUCUAUAAGCAAAAAACUUGAAAAAAGUGAAUGUUUGCGUUAUCAUUUUCAUAUAGAAAGAAAAAGAGGUAUUACAG ........((((((((.((((.....)))).))))))))..(..((((..(((((.((..((((((..((((((((......(((((.((....)).(((((((((..((((((((...))))))))............((((((...((((((((((((.....))))))).............)))))...))))))......)))))))))...(((.......))).)))))....))))))))..))))))....)).)))))..))))..)...((((........(((((..((((.....)))).....))))).......(((((.....))))).....))))........ (-109.51) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUAAUACCUCUUUUUCUUUCUAUAUGAAAAUGAUAACGCAAACAUUCACUUUUUUCAAGUUUUUUGCUUAUAGAUGAGGAAAUCACUGAGAUACUUUCUAAUAAUACUCUUCGAAAAUCUCUUCAAACCGCGUCAACGUCGCCUUGCCGUAGAUAUAAUUACUGACUUCGUCAGUUUCAUCCGCAACCUCAAAAACAUGUUUUGAGCUGACUUCGUCAGCCUUAUUUACAACCUCAAAGCAGUGCUUUGAGCAACCUACGGCUAGUUUCCUAGUUUGCUCUUUGAUUUUCAUUGAGUAUAAAAUAAGCAAAUCAGCAAGAAACCCACGACAAGAUAAUCCUGACGCGGGUUAUAGUUUC ((((((..((((......((((.....))))...((((.(((((.....((((.....))))..)))))))))....))))........(((((..((((..............)))))))))......((((((((..((((....(((((((........((((((...))))))............((((((.((.((((((((((((((...)))))).............))))))))))..))))))....)))))))..(((((......(((((..((.....))..)))))........((......))..)))))...))))..(.....).)))))))).)))))).... (-85.75) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 832 120 71 164 115 smit:SMT_1200|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1163235..1163465_NEGATIVE 811 120 71 231 182 smit:SMT_1379|5end_thymidylate_kinase_1357438..1357668_NEGATIVE 802 110 61 169 118 smit:SMT_1602|5end_hypothetical_protein_1592385..1592615_POSITIVE 802 110 61 181 130 smit:SMT_1488|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1467157..1467387_POSITIVE 802 110 61 217 166 smit:SMT_1138|5end_hypothetical_protein_1079547..1079777_NEGATIVE 802 110 61 194 143 smit:SMT_833|5end_hypothetical_protein_predicted_by_Glimmer/Critica_775362..775592_NEGATIVE 802 110 61 178 127 smit:SMT_130|5end_capsular_polysaccharide_biosynthesis_protein_80995..81225_POSITIVE 799 218 171 182 135 smit:SMT_677|5end_DNA_topoisomerase_I_587318..587548_NEGATIVE 751 110 61 203 152 smit:SMT_1810|5end_hypothetical_protein_1785219..1785449_POSITIVE 751 256 211 85 40 smit:SMT_958|5end_hypothetical_protein_predicted_by_Glimmer/Critica_905052..905282_POSITIVE 751 110 61 155 104 smit:SMT_483|5end_transcriptional_activator_TipA,_putative_418827..419057_POSITIVE 747 110 61 164 115 smit:SMT_366|5end_hypothetical_protein_302085..302315_POSITIVE 713 130 81 216 167 smit:SMT_150|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_98787..99017_POSITIVE 707 130 81 181 132 smit:SMT_163|5end_cardiolipin_synthetase_107309..107539_POSITIVE 705 130 81 178 129 smit:SMT_775|5end_alpha-acetolactate_decarboxylase_685972..686202_NEGATIVE 702 110 61 166 115 smit:SMT_1782|5end_hypothetical_protein_1759520..1759750_POSITIVE 699 110 61 168 117 smit:SMT_1963|5end_ribonuclease_BN,_putative_1896462..1896692_NEGATIVE 698 110 61 220 169 smit:SMT_1179|5end_aldose_1-epimerase_1137854..1138084_NEGATIVE 673 260 211 57 7 smit:SMT_2109|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1999099..1999329_NEGATIVE 665 105 64 230 189 smit:SMT_443|5end_hydroxyethylthiazole_kinase_382555..382785_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 857 260 211 95 46 smit:SMT_834|3end_hypothetical_protein_775517..775667_NEGATIVE 849 229 184 64 19 smit:SMT_1471|3end_hypothetical_protein_1453442..1453592_NEGATIVE 829 260 211 95 46 smit:SMT_1477|3end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1459447..1459597_NEGATIVE 814 220 171 55 6 smit:SMT_1912|3end_D-alanyl-D-alanine_carboxypeptidase_1857807..1857957_NEGATIVE 814 256 211 86 41 smit:SMT_1569|3end_dihydroxy-acid_dehydratase_1563068..1563218_POSITIVE 814 220 171 55 6 smit:SMT_868|3end_D-alanyl-D-alanine_carboxypeptidase_816509..816659_NEGATIVE 799 218 171 53 6 smit:SMT_678|3end_K04096_DNA_processing_protein_587447..587597_NEGATIVE 754 258 211 93 46 smit:SMT_915|3end_sucrose_operon_repressor_868619..868769_POSITIVE 750 255 211 72 27 smit:SMT_1487|3end_hypothetical_protein_1467076..1467226_POSITIVE 742 229 185 65 22 smit:SMT_1216|3end_hypothetical_protein_1175969..1176119_POSITIVE 735 256 211 47 2 smit:SMT_1872|3end_K03217_preprotein_translocase_YidC_subunit_1830883..1831033_NEGATIVE 734 256 211 86 41 smit:SMT_1536|3end_trigger_factor_1520636..1520786_NEGATIVE 730 258 211 67 20 smit:SMT_1815|3end_K02035_peptide/nickel_transport_system_substrate-binding_protein_1788899..1789049_NEGATIVE 729 258 211 93 45 smit:SMT_698|3end_uracil_permease_609769..609919_POSITIVE 713 130 81 134 85 smit:SMT_149|3end_hypothetical_protein_predicted_by_Glimmer/Critica_98785..98935_POSITIVE 702 258 211 93 45 smit:SMT_1140|3end_glycogen_phosphorylase_1081316..1081466_NEGATIVE 696 260 211 92 43 smit:SMT_799|3end_hypothetical_protein_707296..707446_NEGATIVE 673 260 211 95 45 smit:SMT_2109|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1999061..1999211_NEGATIVE 673 260 211 95 45 smit:SMT_1180|3end_putative_tagatose-6-phosphate_aldose/ketose_isomerase_1138036..1138186_NEGATIVE 659 260 211 87 38 smit:SMT_764|3end_alanyl-tRNA_synthetase_669495..669645_NEGATIVE