Origin IGS: ctcctttttcctaatactcaatgaaaatcaaagagcaaactagaaaactagccgcaggctgctcaaaacactgttttgaggttgtatataagactgacgaagtcaatcacatatatacggcaaggcgacgttgacgtggtttgaatttgattttcgaagagtataaactcatctgataacaactatcttaccccaatccccaaacaaaaactggacttccttcccaaatgcgcctatctacctcccaaatgcactttttggataaaaaataggcagaacaaacgtcctacctactaaaaatatggtatgaaaggaaattgatgttttactgtcaccctaggcaagcttgggacaaataaatcattgatagcaacctttacgacatcctatttaaagttaattcaatttttaatgtccctgctatttctaagccacctctggtatgatctattcatggtcagaatagataacaccgttctaagttacgattcatagtttttcttacatcctttgtatcaaattattaaat .........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 atttaataatttgatacaaaggatgtaagaaaaactatgaatcgtaacttagaacggtgttatctattctgaccatgaatagatcataccagaggtggcttagaaatagcagggacattaaaaattgaattaactttaaataggatgtcgtaaaggttgctatcaatgatttatttgtcccaagcttgcctagggtgacagtaaaacatcaatttcctttcataccatatttttagtaggtaggacgtttgttctgcctattttttatccaaaaagtgcatttgggaggtagataggcgcatttgggaaggaagtccagtttttgtttggggattggggtaagatagttgttatcagatgagtttatactcttcgaaaatcaaattcaaaccacgtcaacgtcgccttgccgtatatatgtgattgacttcgtcagtcttatatacaacctcaaaacagtgttttgagcagcctgcggctagttttctagtttgctctttgattttcattgagtattaggaaaaaggag Mask Tandem Repeat Region ================================================ ctcctttttcctaatactcaatgaaaatcaaagagcaaactagaaaactagccgcaggctgctcaaaacactgttttgaggttgtatataagactgacgaagtcaatcacatatatacggcaaggcgacgttgacgtggtttgaatttgattttcgaagagtataaactcatctgataacaactatcttaccccaatccccaaacaaaaactggacttccttcccaaatgcgcctatctacctcccaaatgcactttttggataaaaaataggcagaacaaacgtcctacctactaaaaatatggtatgaaaggaaattgatgttttactgtcaccctaggcaagcttgggacaaataaatcattgatagcaacctttacgacatcctatttaaagttaattcaatttttaatgtccctgctatttctaagccacctctggtatgatctattcatggtcagaatagataacaccgttctaagttacgattcatagtttttcttacatcctttgtatcaaattattaaat Find is-nt database================================================ Query_seq: SMT_1200:SMT_1201|SMT_1200:SMT_1201:K06148 ATP-binding cassette, subfamily C, bacterial:hypothetical protein predicted by Glimmer/Critica:<-<-:1163326..1163854 529 ctcctttttcctaatactcaatgaaaatcaaagagcaaactagaaaactagccgcaggctgctcaaaacactgttttgaggttgtatataagactgacgaagtcaatcacatatatacggcaaggcgacgttgacgtggtttgaatttgattttcgaagagtataaactcatctgataacaactatcttaccccaatccccaaacaaaaactggacttccttcccaaatgcgcctatctacctcccaaatgcactttttggataaaaaataggcagaacaaacgtcctacctactaaaaatatggtatgaaaggaaattgatgttttactgtcaccctaggcaagcttgggacaaataaatcattgatagcaacctttacgacatcctatttaaagttaattcaatttttaatgtccctgctatttctaagccacctctggtatgatctattcatggtcagaatagataacaccgttctaagttacgattcatagtttttcttacatcctttgtatcaaattattaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1200:SMT_1201|SMT_1200:SMT_1201:K06148 ATP-binding cassette, subfamily C, bacterial:hypothetical protein predicted by Glimmer/Critica:<-<-:1163326..1163854 529 ctcctttttcctaatactcaatgaaaatcaaagagcaaactagaaaactagccgcaggctgctcaaaacactgttttgaggttgtatataagactgacgaagtcaatcacatatatacggcaaggcgacgttgacgtggtttgaatttgattttcgaagagtataaactcatctgataacaactatcttaccccaatccccaaacaaaaactggacttccttcccaaatgcgcctatctacctcccaaatgcactttttggataaaaaataggcagaacaaacgtcctacctactaaaaatatggtatgaaaggaaattgatgttttactgtcaccctaggcaagcttgggacaaataaatcattgatagcaacctttacgacatcctatttaaagttaattcaatttttaatgtccctgctatttctaagccacctctggtatgatctattcatggtcagaatagataacaccgttctaagttacgattcatagtttttcttacatcctttgtatcaaattattaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1200:SMT_1201|SMT_1200:SMT_1201:K06148 ATP-binding cassette, subfamily C, bacterial:hypothetical protein predicted by Glimmer/Critica:<-<-:1163326..1163854 529 ctcctttttcctaatactcaatgaaaatcaaagagcaaactagaaaactagccgcaggctgctcaaaacactgttttgaggttgtatataagactgacgaagtcaatcacatatatacggcaaggcgacgttgacgtggtttgaatttgattttcgaagagtataaactcatctgataacaactatcttaccccaatccccaaacaaaaactggacttccttcccaaatgcgcctatctacctcccaaatgcactttttggataaaaaataggcagaacaaacgtcctacctactaaaaatatggtatgaaaggaaattgatgttttactgtcaccctaggcaagcttgggacaaataaatcattgatagcaacctttacgacatcctatttaaagttaattcaatttttaatgtccctgctatttctaagccacctctggtatgatctattcatggtcagaatagataacaccgttctaagttacgattcatagtttttcttacatcctttgtatcaaattattaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 10 Min: 3 Max: 187 Len: 185 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: 1.0E-9 bit: 57.0 Len: 87 Query Start:21 Query End:107 Subject Strand: null Subject Start: 1 Subject End: 29 .................... M K I K E Q T R K L A A G C S K H C F E V V Y K T D E V N ...................................................................................................................................................................................................................................................................................................................................................................................................................................... .................... 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 ...................................................................................................................................................................................................................................................................................................................................................................................................................................... HSP 2 e-value: 1.0E-9 bit: 28.1 Len: 39 Query Start:107 Query End:145 Subject Strand: null Subject Start: 45 Subject End: 57 .......................................................................................................... S H I Y G K A T L T W F E ................................................................................................................................................................................................................................................................................................................................................................................................ .......................................................................................................... N H T Y G R A T M T W F 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: 2.0E-9 bit: 63.9 Len: 129 Query Start:3 Query End:131 Subject Strand: null Subject Start: 2 Subject End: 59 .. P F S * Y S M K I K E Q T R K L A A G C - - - - - - - - - - - - - - - S K H C F E V V Y K T D E V N H I Y T A R R R .............................................................................................................................................................................................................................................................................................................................................................................................................. .. P S S 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 I Y T A R R R .............................................................................................................................................................................................................................................................................................................................................................................................................. 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: 3.0E-9 bit: 63.5 Len: 147 Query Start:21 Query End:167 Subject Strand: null Subject Start: 1 Subject End: 49 .................... M K I K E Q T R K L A A G C S K H C F E V V Y K T D E V - N H I Y T A R R R * R G L N L I F E E Y K .......................................................................................................................................................................................................................................................................................................................................................................... .................... 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 K .......................................................................................................................................................................................................................................................................................................................................................................... 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: 7.0E-9 bit: 62.4 Len: 153 Query Start:21 Query End:173 Subject Strand: null Subject Start: 1 Subject End: 51 .................... M K I K E Q T R K L A A G C S K H C F E V V Y K T D E V - N H I Y T A R R R * R G L N L I F E E Y K L I .................................................................................................................................................................................................................................................................................................................................................................... .................... 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 K M M .................................................................................................................................................................................................................................................................................................................................................................... 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: 2.0E-8 bit: 61.2 Len: 150 Query Start:15 Query End:164 Subject Strand: null Subject Start: 24 Subject End: 73 .............. Y S M K I K E Q T R K L A A G C S K H C F E V V Y K T D E V - N H I Y T A R R R * R G L N L I F E E Y ............................................................................................................................................................................................................................................................................................................................................................................. .............. 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_Q04I51 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 3.0E-8 bit: 55.8 Len: 87 Query Start:21 Query End:107 Subject Strand: null Subject Start: 1 Subject End: 29 .................... M K I K E Q T R K L A A G C S K H C F E V V Y K T D E V N ...................................................................................................................................................................................................................................................................................................................................................................................................................................... .................... 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 ...................................................................................................................................................................................................................................................................................................................................................................................................................................... HSP 2 e-value: 3.0E-8 bit: 24.6 Len: 39 Query Start:107 Query End:145 Subject Strand: null Subject Start: 45 Subject End: 57 .......................................................................................................... S H I Y G K A T L T W F E ................................................................................................................................................................................................................................................................................................................................................................................................ .......................................................................................................... N H T Y G E V K L T W F E ................................................................................................................................................................................................................................................................................................................................................................................................ 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: 1.0E-7 bit: 58.5 Len: 147 Query Start:21 Query End:167 Subject Strand: null Subject Start: 1 Subject End: 64 .................... M K I K E Q T R K L A A G C S K H C F E V V Y K T D E V - - - - - - - - - - - - - - - - N H I Y T A R R R * R G L N L I F E E Y K .......................................................................................................................................................................................................................................................................................................................................................................... .................... 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 K .......................................................................................................................................................................................................................................................................................................................................................................... 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: 8.0E-7 bit: 55.5 Len: 147 Query Start:21 Query End:167 Subject Strand: null Subject Start: 1 Subject End: 49 .................... M K I K E Q T R K L A A G C S K H C F E V V Y K T D E V - N H I Y T A R R R * R G L N L I F E E Y K .......................................................................................................................................................................................................................................................................................................................................................................... .................... 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 K .......................................................................................................................................................................................................................................................................................................................................................................... Subject: UniRef90_O05164 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae|Rep: Hypothetical protein - Streptococcus pneumoniae HSP 1 e-value: 9.0E-7 bit: 55.5 Len: 183 Query Start:5 Query End:187 Subject Strand: null Subject Start: 1 Subject End: 47 .... D S C Y Q M S L Y S S K I K F K P R Q R R L A V Y M * L T S S V L Y T T S K Q C F E Q P A A S F L V C S L I F I E Y * E K ...................................................................................................................................................................................................................................................................................................................................................... .... D D L Y D L I L F E N L - - F K P R Q - - - - - - - - - - - - L P 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 K N K ...................................................................................................................................................................................................................................................................................................................................................... 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: 2.0E-6 bit: 52.8 Len: 96 Query Start:21 Query End:116 Subject Strand: null Subject Start: 1 Subject End: 33 .................... M K I K E Q T R K L A A G C S K H C F E V V Y K T D E V - N H I Y ............................................................................................................................................................................................................................................................................................................................................................................................................................. .................... 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 ............................................................................................................................................................................................................................................................................................................................................................................................................................. HSP 2 e-value: 2.0E-6 bit: 21.6 Len: 30 Query Start:107 Query End:136 Subject Strand: null Subject Start: 30 Subject End: 39 .......................................................................................................... S H I Y G K A T L T ......................................................................................................................................................................................................................................................................................................................................................................................................... .......................................................................................................... N H T Y G K A T L T ......................................................................................................................................................................................................................................................................................................................................................................................................... ctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttaccccaatccccaaacaaaaactggacttccttcccaaatgcgcctatctacctcccaaatgcactttttggataaaaaataggcagaacaaacgtcctacctactaaaaatatggtatgaaaggaaattgatgttttactgtcaccctaggcaagcttgggacaaataaatcattgatagcaacctttacgacatcctatttaaagttaattcaatttttaatgtccctgctatttctaagccacctctggtatgatctattcatggtcagaatagataacaccgttctaagttacgattcatagtttttcttacatcctttgtatcaaattattaaat Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 21 End: 131 .................... M K I K E Q T R K L A A G C S K H C F E V V Y K T D E V N H I Y T A R R R .............................................................................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 30 Strand: + Start: 173 End: 262 ............................................................................................................................................................................ M I T T I L P Q S P N K N W T S F P N A P I Y L P N A L F G ........................................................................................................................................................................................................................................................................... Protein_Len: 44 Strand: + Start: 163 End: 294 .................................................................................................................................................................. M N S S D N N Y L T P I P K Q K L D F L P K C A Y L P P K C T F W I K N R Q N K R P T Y ........................................................................................................................................................................................................................................... Protein_Len: 43 Strand: + Start: 364 End: 492 ........................................................................................................................................................................................................................................................................................................................................................................... M I A T F T T S Y L K L I Q F L M S L L F L S H L W Y D L F M V R I D N T V L S Y D S ..................................... Protein_Len: 39 Strand: - Start: 66 End: 182 ................................................................. F V T K L N Y I L S V F D I V Y I R C P S T S T T Q I Q N E F L I F E D S L M ........................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 31 Strand: - Start: 14 End: 106 ............. Y E I F I L S C V L F S A A P Q E F C Q K S T T Y L V S S T M ....................................................................................................................................................................................................................................................................................................................................................................................................................................... ctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttaccccaatccccaaacaaaaactggacttccttcccaaatgcgcctatctacctcccaaatgcactttttggataaaaaataggcagaacaaacgtcctacctactaaaaatatggtatgaaaggaaattgatgttttactgtcaccctaggcaagcttgggacaaataaatcattgatagcaacctttacgacatcctatttaaagttaattcaatttttaatgtccctgctatttctaagccacctctggtatgatctattcatggtcagaatagataacaccgttctaagttacgattcatagtttttcttacatcctttgtatcaaattattaaat Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttaccccaatccccaaacaaaaactggacttccttcccaaatgcgcctatctacctcccaaatgcactttttggataaaaaataggcagaacaaacgtcctacctactaaaaatatggtatgaaaggaaattgatgttttactgtcaccctaggcaagcttgggacaaataaatcattgatagcaacctttacgacatcctatttaaagttaattcaatttttaatgtccctgctatttctaagccacctctggtatgatctattcatggtcagaatagataacaccgttctaagttacgattcatagtttttcttacatcctttgtatcaaattattaaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 76 HP_score: -10.4 Tail_Score: -2.752 Start: 62 End: 80 Full_Region: ACTAGCCGCAGGCTG CTCAAAAC ACT GTTTTGAG GTTGTATATAAGACT .............................................................CTCAAAACACTGTTTTGAG................................................................................................................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -8.2 Tail_Score: -5.24129 Start: 270 End: 293 Full_Region: ataccatatttttag taggtaggac gttt gttctgccta ttttttatccaaaaa .............................................................................................................................................................................................................................................................................taggtaggacgtttgttctgccta............................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 48 HP_score: -3.1 Tail_Score: -3.42621 Start: 439 End: 475 Full_Region: TTTCTAAGCCACCTC TGGTATGATCTATTC ATGGTCA GAATAGATAACACCG TTCTAAGTTACGATT ......................................................................................................................................................................................................................................................................................................................................................................................................................................................TGGTATGATCTATTCATGGTCAGAATAGATAACACCG...................................................... TransTerm Strand: + Conf: 47 HP_score: -4.4 Tail_Score: -2.65091 Start: 440 End: 474 Full_Region: TTCTAAGCCACCTCT GGTATGATCTATTC ATGGTCA GAATAGATAACACC GTTCTAAGTTACGAT .......................................................................................................................................................................................................................................................................................................................................................................................................................................................GGTATGATCTATTCATGGTCAGAATAGATAACACC....................................................... Find igs database================================================ Query_seq: SMT_1200:SMT_1201|SMT_1200:SMT_1201:K06148 ATP-binding cassette, subfamily C, bacterial:hypothetical protein predicted by Glimmer/Critica:<-<-:1163326..1163854 529 ctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttaccccaatccccaaacaaaaactggacttccttcccaaatgcgcctatctacctcccaaatgcactttttggataaaaaataggcagaacaaacgtcctacctactaaaaatatggtatgaaaggaaattgatgttttactgtcaccctaggcaagcttgggacaaataaatcattgatagcaacctttacgacatcctatttaaagttaattcaatttttaatgtccctgctatttctaagccacctctggtatgatctattcatggtcagaatagataacaccgttctaagttacgattcatagtttttcttacatcctttgtatcaaattattaaat Intra-Species Hit: Count: 1 Min: 188 Max: 529 Len: 342 Subject: smit_SMT_1200_SMT_1201|K06148 ATP-binding cassette, subfamily C, bacterial:hypothetical protein predicted by Glimmer/Critica|NEGATIVE:NEGATIVE|[1163326,1163854]|529 HSP 1 e-value: 0.0 bit: 678.0 Len: 342 Query Start:188 Query End:529 Subject Strand: POSITIVE Subject Start: 188 Subject End: 529 ...........................................................................................................................................................................................ttaccccaatccccaaacaaaaactggacttccttcccaaatgcgcctatctacctcccaaatgcactttttggataaaaaataggcagaacaaacgtcctacctactaaaaatatggtatgaaaggaaattgatgttttactgtcaccctaggcaagcttgggacaaataaatcattgatagcaacctttacgacatcctatttaaagttaattcaatttttaatgtccctgctatttctaagccacctctggtatgatctattcatggtcagaatagataacaccgttctaagttacgattcatagtttttcttacatcctttgtatcaaattattaaat ...........................................................................................................................................................................................ttaccccaatccccaaacaaaaactggacttccttcccaaatgcgcctatctacctcccaaatgcactttttggataaaaaataggcagaacaaacgtcctacctactaaaaatatggtatgaaaggaaattgatgttttactgtcaccctaggcaagcttgggacaaataaatcattgatagcaacctttacgacatcctatttaaagttaattcaatttttaatgtccctgctatttctaagccacctctggtatgatctattcatggtcagaatagataacaccgttctaagttacgattcatagtttttcttacatcctttgtatcaaattattaaat Inter-species Hit: Count: 2 Min: 188 Max: 497 Len: 310 Subject: NC_003028_SP_0041_SP_0042|bacteriocin BlpU:competence factor transporting ATP-binding/permease protein ComA|POSITIVE:POSITIVE|[40102,40815]|714 HSP 1 e-value: 1.0E-103 bit: 377.0 Len: 310 Query Start:188 Query End:497 Subject Strand: NEGATIVE Subject Start: 213 Subject End: 521 ...........................................................................................................................................................................................ttaccccaatccccaaacaaaaactggacttccttcccaaatgcgcctatctacctcccaaatgcactttttggataaaaaa-taggcagaacaaacgtcctacctactaaaaatatggtat-gaaaggaaattgatgttttactgtcaccctaggcaagcttgggacaaataaatcattgatagcaacctttacgacatcctatttaaagttaattcaatttttaatgtccctgctatttctaagccacctctggtatgatctattcatggtcagaatagataacaccgttctaagttacgattcatagtt................................ ...........................................................................................................................................................................................ttaccccaatcactaaacaaaaactggacttccttcccaaatgagcctatctccctcccaactgcactttttggataaaaaaataggcagaacaagagtcctgcccactaaaaatatgctattgaaaggaaattgattttttactgtcaccctaggcaagcttgaaacaaataaatcattgatagtaacacttacgacatcctattta---ttacttcaatttctaatgtctctgctatttctaagctacctctggtatgatctattcctagtcagaatagataacaccgttctaaattacgattcatagtt................................ Subject: NC_008533_SPD_0047_SPD_0049|hypothetical protein:competence factor transporting ATP-binding/permease protein ComA|POSITIVE:POSITIVE|[39873,41901]|2029 HSP 1 e-value: 1.0E-71 bit: 272.0 Len: 234 Query Start:264 Query End:497 Subject Strand: NEGATIVE Subject Start: 85 Subject End: 316 .......................................................................................................................................................................................................................................................................aaaaaataggcagaacaaacgtcctacctactaaaaatatggtat-gaaaggaaattgatgttttactgtcaccctaggcaagcttgggacaaataaatcattgatagcaacctttacgacatcctatttaaagttaattcaatttttaatgtccctgctatttctaagccacctctggtatgatctattcatggtcagaatagataacaccgttctaagttacgattcatagtt................................ .......................................................................................................................................................................................................................................................................aaaaaataggcagaacaagagtcctgcccactaaaaatatgctattgaaaggaaaatgattttttactgtcaccctaggcaagcttgaaacaaataaatcattgatagtaacacttacgacatcctattta---ttacttcaatttctaatgtctctgctatttctaagctacctctggtatgatctattcctagtcagaatagataacaccgttctaaattacgattcatagtt................................ HSP 2 e-value: 7.0E-27 bit: 123.0 Len: 82 Query Start:188 Query End:269 Subject Strand: NEGATIVE Subject Start: 1755 Subject End: 1836 ...........................................................................................................................................................................................ttaccccaatccccaaacaaaaactggacttccttcccaaatgcgcctatctacctcccaaatgcactttttggataaaaaa.................................................................................................................................................................................................................................................................... ...........................................................................................................................................................................................ttaccccaatcactaaacaaaaactggacttccttcccaaatgagcctatctccctcccaactgcactttttggataaaaaa.................................................................................................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACCCCAAUCCCCAAACAAAAACUGGACUUCCUUCCCAAAUGCGCCUAUCUACCUCCCAAAUGCACUUUUUGGAUAAAAAAUAGGCAGAACAAACGUCCUACCUACUAAAAAUAUGGUAUGAAAGGAAAUUGAUGUUUUACUGUCACCCUAGGCAAGCUUGGGACAAAUAAAUCAUUGAUAGCAACCUUUACGACAUCCUAUUUAAAGUUAAUUCAAUUUUUAAUGUCCCUGCUAUUUCUAAGCCACCUCUGGUAUGAUCUAUUCAUGGUCAGAAUAGAUAACACCGUUCUAAGUUACGAUUCAUAGUU .......((((....(((......(((.(((.............(((((........(((((.......)))))..........(((((((((....((((..((((((......))))).)..))))......))))...)))))....))))).(((..((((((..((((..(((((.......(((((............))))).....))))).)))).)))))).)))......)))))).....(((...((((((((.......))))))))...))).......)))..))))....... (-56.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUAUGAAUCGUAACUUAGAACGGUGUUAUCUAUUCUGACCAUGAAUAGAUCAUACCAGAGGUGGCUUAGAAAUAGCAGGGACAUUAAAAAUUGAAUUAACUUUAAAUAGGAUGUCGUAAAGGUUGCUAUCAAUGAUUUAUUUGUCCCAAGCUUGCCUAGGGUGACAGUAAAACAUCAAUUUCCUUUCAUACCAUAUUUUUAGUAGGUAGGACGUUUGUUCUGCCUAUUUUUUAUCCAAAAAGUGCAUUUGGGAGGUAGAUAGGCGCAUUUGGGAAGGAAGUCCAGUUUUUGUUUGGGGAUUGGGGUAA ....(((((((((..........(((((.((((((((.......)))))))).)))))...((((((.((....)).....((((((.....(((((.....)))))....)))))).........)))))).)))))))))...(((((((..((((((.(....)................(((..((.....(((((((((((((((((((....)))))))))))).........)))))))....))..)))....))))))..)))))))....(.((((((((((....)))))))))).).. (-85.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 317 189 141 200 146 smit:SMT_1620|5end_hypothetical_protein_1607240..1607470_NEGATIVE 315 190 141 52 8 smit:SMT_1348|5end_exoribonuclease_II_1327502..1327732_NEGATIVE 314 280 231 158 110 smit:SMT_311|5end_3-oxoacyl-_252123..252353_POSITIVE 313 256 219 71 30 smit:SMT_113|5end_hypothetical_protein_61425..61655_POSITIVE 299 70 24 55 8 smit:SMT_2126|5end_indole-3-glycerol_phosphate_synthase_2009107..2009337_POSITIVE 299 70 24 55 8 smit:SMT_1751|5end_indole-3-glycerol_phosphate_synthase_1729012..1729242_POSITIVE 294 276 233 72 12 smit:SMT_1644|5end_3-isopropylmalate_dehydrogenase_1630704..1630934_POSITIVE 272 66 23 146 100 smit:SMT_1188|5end_hypothetical_protein_1146653..1146883_NEGATIVE 264 66 22 199 150 smit:SMT_1296|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1257290..1257520_POSITIVE 262 200 151 122 75 smit:SMT_1901|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1850537..1850767_POSITIVE 262 297 253 83 40 smit:SMT_1840|5end_6-phosphogluconate_dehydrogenase,_decarboxylating_1806285..1806515_NEGATIVE 261 188 145 113 58 smit:SMT_1670|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1658613..1658843_POSITIVE 261 74 31 40 2 smit:SMT_1357|5end_endo-beta-N-acetylglucosaminidase_1336156..1336386_NEGATIVE 257 49 9 84 42 smit:SMT_608|5end_laminin-binding_surface_protein_520757..520987_POSITIVE 256 100 53 225 181 smit:SMT_175|5end_50S_ribosomal_protein_L22_117724..117954_POSITIVE 253 46 4 89 47 smit:SMT_521|5end_K02005_HlyD_family_secretion_protein_445566..445796_POSITIVE 253 168 121 53 11 smit:SMT_215|5end_leucyl-tRNA_synthetase_147045..147275_POSITIVE 251 69 25 122 81 smit:SMT_229|5end_mechanosensitive_ion_channel_165623..165853_NEGATIVE 250 285 248 50 15 smit:SMT_1367|5end_K02237_competence_protein_ComEA_1347522..1347752_NEGATIVE 249 79 50 185 158 smit:SMT_1921|5end_D-alanine-activating_enzyme_1863185..1863415_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 280 231 136 88 smit:SMT_310|3end_3-oxoacyl-_252181..252331_POSITIVE 299 70 24 58 11 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 285 276 236 60 9 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 272 66 23 136 90 smit:SMT_1189|3end_phosphoribosylaminoimidazole_carboxylase_ATPase_subunit_1146663..1146813_NEGATIVE 268 276 232 69 20 smit:SMT_1864|3end_integral_membrane_protein_1827172..1827322_POSITIVE 263 179 132 145 106 smit:SMT_137|3end_hypothetical_protein_88137..88287_NEGATIVE 262 200 151 125 78 smit:SMT_1900|3end_K03710_GntR_family_transcriptional_regulator_1850620..1850770_POSITIVE 257 49 9 63 21 smit:SMT_607|3end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_520816..520966_POSITIVE 254 269 227 135 71 smit:SMT_1124|3end_pyrrolidone-carboxylate_peptidase_1060225..1060375_NEGATIVE 251 69 25 79 38 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE 249 186 149 46 2 smit:SMT_1821|3end_Mg2+_and_Co2+_transporter_1794515..1794665_POSITIVE 248 164 143 124 102 smit:SMT_2042|3end_K04077_chaperonin_GroEL_(Hsp60)_1952960..1953110_NEGATIVE 248 273 239 61 29 smit:SMT_1397|3end_mutator_MutT_protein_1373271..1373421_POSITIVE 247 165 126 145 110 smit:SMT_1539|3end_sensor_histidine_kinase,_putative_1523315..1523465_NEGATIVE 247 165 125 74 39 smit:SMT_1350|3end_multidrug_resistance_efflux_pump_1328026..1328176_NEGATIVE 247 256 212 124 83 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 247 186 145 43 10 smit:SMT_613|3end_dihydrodipicolinate_synthase_524321..524471_POSITIVE 245 262 228 125 96 smit:SMT_1295|3end_transcriptional_regulator_CtsR_1257368..1257518_POSITIVE 239 184 144 132 84 smit:SMT_853|3end_ATP-dependent_endopeptidase_clp_ATP-binding_subunit_ClpX_798053..798203_NEGATIVE 236 48 5 46 1 smit:SMT_1198|3end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1158837..1158987_NEGATIVE