Origin IGS: ttcaatacgctcctattatatagtatagttttttattaaaagtattctacacccttttttaggaaatgtcaataaactaaatggataatttggaagttcagtctgacttacaaaaagaaaaggagttttcactccttttcacagattgaagacaaagtccttataaaagtgtcttctaaagattttaacttcaatctgaagcgaggttatcctcgctttagattaacagttatctgggatacagacactggttccctaagacgactttttaaaaatctgaaacaggcaataagtacaagagttgattcatttgaaatatatgataacgtacgagatgatgtctttactttagctaaagtttttaatgagtatgattcgctcaatattatatttttccaattatctacttatggaggtgaacaattgattcgaattgatttcaatcctaatactttaaaagaatttggtggaatgaaagtatggagacaattaatttaattagtaacaaagaattaattgaaatgggctatcgccctcatacagcaaatgatatcattcatcaggcaagagaattacttgtctcacgaggctatacattttataatcgcaaacgtttgatggttgttccaaaaagtgttgtaaatgagattctaggaactgaggtggcgtaat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attacgccacctcagttcctagaatctcatttacaacactttttggaacaaccatcaaacgtttgcgattataaaatgtatagcctcgtgagacaagtaattctcttgcctgatgaatgatatcatttgctgtatgagggcgatagcccatttcaattaattctttgttactaattaaattaattgtctccatactttcattccaccaaattcttttaaagtattaggattgaaatcaattcgaatcaattgttcacctccataagtagataattggaaaaatataatattgagcgaatcatactcattaaaaactttagctaaagtaaagacatcatctcgtacgttatcatatatttcaaatgaatcaactcttgtacttattgcctgtttcagatttttaaaaagtcgtcttagggaaccagtgtctgtatcccagataactgttaatctaaagcgaggataacctcgcttcagattgaagttaaaatctttagaagacacttttataaggactttgtcttcaatctgtgaaaaggagtgaaaactccttttctttttgtaagtcagactgaacttccaaattatccatttagtttattgacatttcctaaaaaagggtgtagaatacttttaataaaaaactatactatataataggagcgtattgaa Mask Tandem Repeat Region ================================================ ttcaatacgctcctattatatagtatagttttttattaaaagtattctacacccttttttaggaaatgtcaataaactaaatggataatttggaagttcagtctgacttacaaaaagaaaaggagttttcactccttttcacagattgaagacaaagtccttataaaagtgtcttctaaagattttaacttcaatctgaagcgaggttatcctcgctttagattaacagttatctgggatacagacactggttccctaagacgactttttaaaaatctgaaacaggcaataagtacaagagttgattcatttgaaatatatgataacgtacgagatgatgtctttactttagctaaagtttttaatgagtatgattcgctcaatattatatttttccaattatctacttatggaggtgaacaattgattcgaattgatttcaatcctaatactttaaaagaatttggtggaatgaaagtatggagacaattaatttaattagtaacaaagaattaattgaaatgggctatcgccctcatacagcaaatgatatcattcatcaggcaagagaattacttgtctcacgaggctatacattttataatcgcaaacgtttgatggttgttccaaaaagtgttgtaaatgagattctaggaactgaggtggcgtaat Find is-nt database================================================ Query_seq: SSA_0234:SSA_0235|SSA_0234:SSA_0235:hypothetical protein:Integrase/recombinase, phage associated, putative:<-->:229029..229700 672 ttcaatacgctcctattatatagtatagttttttattaaaagtattctacacccttttttaggaaatgtcaataaactaaatggataatttggaagttcagtctgacttacaaaaagaaaaggagttttcactccttttcacagattgaagacaaagtccttataaaagtgtcttctaaagattttaacttcaatctgaagcgaggttatcctcgctttagattaacagttatctgggatacagacactggttccctaagacgactttttaaaaatctgaaacaggcaataagtacaagagttgattcatttgaaatatatgataacgtacgagatgatgtctttactttagctaaagtttttaatgagtatgattcgctcaatattatatttttccaattatctacttatggaggtgaacaattgattcgaattgatttcaatcctaatactttaaaagaatttggtggaatgaaagtatggagacaattaatttaattagtaacaaagaattaattgaaatgggctatcgccctcatacagcaaatgatatcattcatcaggcaagagaattacttgtctcacgaggctatacattttataatcgcaaacgtttgatggttgttccaaaaagtgttgtaaatgagattctaggaactgaggtggcgtaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0234:SSA_0235|SSA_0234:SSA_0235:hypothetical protein:Integrase/recombinase, phage associated, putative:<-->:229029..229700 672 ttcaatacgctcctattatatagtatagttttttattaaaagtattctacacccttttttaggaaatgtcaataaactaaatggataatttggaagttcagtctgacttacaaaaagaaaaggagttttcactccttttcacagattgaagacaaagtccttataaaagtgtcttctaaagattttaacttcaatctgaagcgaggttatcctcgctttagattaacagttatctgggatacagacactggttccctaagacgactttttaaaaatctgaaacaggcaataagtacaagagttgattcatttgaaatatatgataacgtacgagatgatgtctttactttagctaaagtttttaatgagtatgattcgctcaatattatatttttccaattatctacttatggaggtgaacaattgattcgaattgatttcaatcctaatactttaaaagaatttggtggaatgaaagtatggagacaattaatttaattagtaacaaagaattaattgaaatgggctatcgccctcatacagcaaatgatatcattcatcaggcaagagaattacttgtctcacgaggctatacattttataatcgcaaacgtttgatggttgttccaaaaagtgttgtaaatgagattctaggaactgaggtggcgtaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0234:SSA_0235|SSA_0234:SSA_0235:hypothetical protein:Integrase/recombinase, phage associated, putative:<-->:229029..229700 672 ttcaatacgctcctattatatagtatagttttttattaaaagtattctacacccttttttaggaaatgtcaataaactaaatggataatttggaagttcagtctgacttacaaaaagaaaaggagttttcactccttttcacagattgaagacaaagtccttataaaagtgtcttctaaagattttaacttcaatctgaagcgaggttatcctcgctttagattaacagttatctgggatacagacactggttccctaagacgactttttaaaaatctgaaacaggcaataagtacaagagttgattcatttgaaatatatgataacgtacgagatgatgtctttactttagctaaagtttttaatgagtatgattcgctcaatattatatttttccaattatctacttatggaggtgaacaattgattcgaattgatttcaatcctaatactttaaaagaatttggtggaatgaaagtatggagacaattaatttaattagtaacaaagaattaattgaaatgggctatcgccctcatacagcaaatgatatcattcatcaggcaagagaattacttgtctcacgaggctatacattttataatcgcaaacgtttgatggttgttccaaaaagtgttgtaaatgagattctaggaactgaggtggcgtaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 9 Min: 220 Max: 668 Len: 449 Subject: UniRef90_Q5LXP7 Cluster: Replication initiator protein; n=4; Streptococcus thermophilus|Rep: Replication initiator protein - Streptococcus thermophilus (strain CNRZ 1066) HSP 1 e-value: 2.0E-43 bit: 177.0 Len: 276 Query Start:220 Query End:495 Subject Strand: null Subject Start: 30 Subject End: 121 ........................................................................................................................................................................................................................... R L T V I W D T D T G S L R R L F K N L K Q A I S T R V D S F E I Y D N V R D D V F T L A K V F N E Y D S L N I I F F Q L S T Y G G E Q L I R I D F N P N T L K E F G G M K V W R Q L I ................................................................................................................................................................................. ........................................................................................................................................................................................................................... R L T V I W D T D T G S L R R I F K N L K Q A I S T R V D S F E I H D N V R D D V F T L A K D F N E Y D S I N I I F F Q L S T Y G G E Q L I R I D F N P N T L K E F D G M K V W R Q L M ................................................................................................................................................................................. Subject: UniRef90_Q03ID0 Cluster: Uncharacterized conserved protein; n=3; Streptococcus thermophilus|Rep: Uncharacterized conserved protein - Streptococcus thermophilus (strain ATCC BAA-491 / LMD-9) HSP 1 e-value: 8.0E-26 bit: 119.0 Len: 177 Query Start:492 Query End:668 Subject Strand: null Subject Start: 4 Subject End: 62 ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... N L I S N K E L I E M G Y R P H T A N D I I H Q A R E L L V S R G Y T F Y N R K R L M V V P K S V V N E I L G T E V A .... ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... N L I S N K E L I E M G Y R P H T A N D I I H Q A R E L L V S R G Y T F Y N R K R L M V V P K S V V N E I L G T E V A .... Subject: UniRef90_Q3DRA7 Cluster: Replication protein; n=1; Streptococcus agalactiae 18RS21|Rep: Replication protein - Streptococcus agalactiae 18RS21 HSP 1 e-value: 3.0E-24 bit: 114.0 Len: 276 Query Start:220 Query End:495 Subject Strand: null Subject Start: 30 Subject End: 120 ........................................................................................................................................................................................................................... R L T V I W D T D T G S L R R L F K N L K Q A I S T R V D S F E I Y D N V R D D V F T L A K V F N E Y D S L N I I F F Q L S T Y G G E Q L I R I D F N P N T L K E F G G M K V W R Q L I ................................................................................................................................................................................. ........................................................................................................................................................................................................................... R L T V I F D S E N Q S L R R I F R E L R K S L D N I I Q E F S I Q E N L R E D Y F T L Y K M I N E - D S I N L I F F Q L S D Y G G Y Q V I R L D F N P N S L K E F E G L Q V W R Q I M ................................................................................................................................................................................. Subject: UniRef90_Q3JYW6 Cluster: Hypothetical protein; n=2; Streptococcus agalactiae|Rep: Hypothetical protein - Streptococcus agalactiae serotype Ia HSP 1 e-value: 5.0E-18 bit: 93.6 Len: 180 Query Start:486 Query End:665 Subject Strand: null Subject Start: 2 Subject End: 61 ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... T I N L I S N K E L I E M G Y R P H T A N D I I H Q A R E L L V S R G Y T F Y N R K R L M V V P K S V V N E I L G T E V ....... ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... T N N V M T N K D L I E M G Y R P S T A N H I I H Q A R N L M V E R G Y T F Y D R K R L M V V P R S A V S E V I G L E V ....... Subject: UniRef90_Q93A41 Cluster: Hypothetical protein; n=1; Enterococcus faecalis|Rep: Hypothetical protein - Enterococcus faecalis (Streptococcus faecalis) HSP 1 e-value: 2.0E-6 bit: 55.1 Len: 171 Query Start:498 Query End:668 Subject Strand: null Subject Start: 4 Subject End: 60 ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. I S N K E L I E M G Y R P H T A N D I I H Q A R E L L V S R G Y T F Y N R K R L M V V P K S V V N E I L G T E V A .... ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. V T K K D L I K L G Y G N S F S A D I I K K A K E L M I S K G H T Y Y Q S K K L D R V P Q E A V E E I L G I K L S .... Subject: UniRef90_Q180H3 Cluster: Hypothetical protein; n=1; Clostridium difficile 630|Rep: Hypothetical protein - Clostridium difficile (strain 630) HSP 1 e-value: 2.0E-6 bit: 55.1 Len: 159 Query Start:498 Query End:656 Subject Strand: null Subject Start: 4 Subject End: 56 ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. I S N K E L I E M G Y R P H T A N D I I H Q A R E L L V S R G Y T F Y N R K R L M V V P K S V V N E I L G ................ ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. V T K K D L I E L G Y G T S F A A D I I R E A K K L M I S K G H T Y Y Q S R K L D R V P R E A V E E L L G ................ Subject: UniRef90_Q2BSE7 Cluster: Hypothetical protein; n=2; Lactobacillus reuteri|Rep: Hypothetical protein - Lactobacillus reuteri JCM 1112 HSP 1 e-value: 3.0E-6 bit: 54.7 Len: 162 Query Start:495 Query End:656 Subject Strand: null Subject Start: 4 Subject End: 57 .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. L I S N K E L I E M G Y R P H T A N D I I H Q A R E L L V S R G Y T F Y N R K R L M V V P K S V V N E I L G ................ .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. M V N Y K D L I R L G F K E H Q A R D I I H Q A K I N L V E Q G L P L Y N G K R I G V V P V R A V E K I V G ................ Subject: UniRef90_Q3DRA8 Cluster: Hypothetical protein; n=1; Streptococcus agalactiae 18RS21|Rep: Hypothetical protein - Streptococcus agalactiae 18RS21 HSP 1 e-value: 3.0E-6 bit: 54.3 Len: 156 Query Start:507 Query End:662 Subject Strand: null Subject Start: 10 Subject End: 61 .......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... K E L I E M G Y R P H T A N D I I H Q A R E L L V S R G Y T F Y N R K R L M V V P K S V V N E I L G T E .......... .......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Q E I M D L G F S K W T A Y N I L R Q A K H I M V E R G F D F Y N N K G L G T V P V S V V A E I L G L E .......... Subject: UniRef90_Q3D8W5 Cluster: Hypothetical protein; n=2; Bacilli|Rep: Hypothetical protein - Streptococcus agalactiae COH1 HSP 1 e-value: 4.0E-6 bit: 53.9 Len: 159 Query Start:498 Query End:656 Subject Strand: null Subject Start: 19 Subject End: 71 ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. I S N K E L I E M G Y R P H T A N D I I H Q A R E L L V S R G Y T F Y N R K R L M V V P K S V V N E I L G ................ ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. V T K K D L V E L G Y G T S F S A D I I K K A K E L M I T K G H T Y Y Q S R K L D R V P R E A V E E I L G ................ ttcaatacgctcctattatatagtatagttttttattaaaagtattctacacccttttttaggaaatgtcaataaactaaatggataatttggaagttcagtctgacttacaaaaagaaaaggagttttcactccttttcacagattgaagacaaagtccttataaaagtgtcttctaaagattttaacttcaatctgaagcgaggttatcctcgctttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntaat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 85 End: 495 .................................................................................... M I W K F S L T Y K K K R S F H S F S Q I E D K V L I K V S S K D F N F N L K R G Y P R F R L T V I W D T D T G S L R R ................................................................................................................................................................................. Protein_Len: 33 Strand: + Start: 517 End: 615 .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... M K W A I A L I Q Q M I S F I R Q E N Y L S H E A I H F I I A N V ......................................................... Protein_Len: 60 Strand: + Start: 462 End: 668 ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................. M W W N E S M E T I N L I S N K E L I E M G Y R P H T A N D I I H Q A R E L L V S R G Y T F Y N R K R L M V V P K S V V .... Protein_Len: 39 Strand: - Start: 556 End: 672 ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... E D P L L I V Q R V L S Y M K Y D C V N S P Q E L F H Q L H S E L F Q P P T M Protein_Len: 60 Strand: - Start: 210 End: 389 ................................................................................................................................................................................................................. G R K L N V T I Q S V S V P E R L R S K L F R F C A I L V L T S E N S I Y S L T R S S T K V K A L T K L S Y S E S L I M ........................................................................................................................................................................................................................................................................................... Protein_Len: 38 Strand: - Start: 19 End: 132 .................. I T Y N K I L L I R C G K K P F T L L S F P Y N P L E T Q S V F L F P T K M ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ ttcaatacgctcctattatatagtatagttttttattaaaagtattctacacccttttttaggaaatgtcaataaactaaatggataatttggaagttcagtctgacttacaaaaagaaaaggagttttcactccttttcacagattgaagacaaagtccttataaaagtgtcttctaaagattttaacttcaatctgaagcgaggttatcctcgctttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntaat 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: 89 Start: 44 End: 73 ...........................................ATTGACATTTCCTAAAAAAGGGTGTAGAAT....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 88 Start: 576 End: 605 ...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTTGTCTCACGAGGCTATACATTTTATAAT................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 310 End: 339 .....................................................................................................................................................................................................................................................................................................................TTTGAAATATATGATAACGTACGAGATGAT............................................................................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttcaatacgctcctattatatagtatagttttttattaaaagtattctacacccttttttaggaaatgtcaataaactaaatggataatttggaagttcagtctgacttacaaaaagaaaaggagttttcactccttttcacagattgaagacaaagtccttataaaagtgtcttctaaagattttaacttcaatctgaagcgaggttatcctcgctttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -12.6 Tail_Score: -4.87665 Start: 117 End: 140 Full_Region: ttgtcttcaatctgt gaaaaggagt gaaa actccttttc tttttgtaagtcaga ....................................................................................................................gaaaaggagtgaaaactccttttc.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 72 HP_score: -6.7 Tail_Score: -4.11484 Start: 122 End: 135 Full_Region: CTTACAAAAAGAAAA GGAGT TTTC ACTCC TTTTCACAGATTGAA .........................................................................................................................GGAGTTTTCACTCC......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 89 HP_score: -6.7 Tail_Score: -5.35224 Start: 122 End: 135 Full_Region: ttcaatctgtgaaaa ggagt gaaa actcc ttttctttttgtaag .........................................................................................................................ggagtgaaaactcc......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 93 HP_score: -11.4 Tail_Score: -3.50393 Start: 189 End: 229 Full_Region: TTCTAAAGATTTTAA CTTCAATCTGAAGCGAGG TTAT CCTCGCTTTAGATTAACAG TTATCTGGGATACAG ............................................................................................................................................................................................CTTCAATCTGAAGCGAGGTTATCCTCGCTTTAGATTAACAG........................................................................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 89 HP_score: -10.4 Tail_Score: -3.75897 Start: 201 End: 216 Full_Region: TAACTTCAATCTGAA GCGAGG TTAT CCTCGC TTTAGATTAACAGTT ........................................................................................................................................................................................................GCGAGGTTATCCTCGC........................................................................................................................................................................................................................................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: SSA_0234:SSA_0235|SSA_0234:SSA_0235:hypothetical protein:Integrase/recombinase, phage associated, putative:<-->:229029..229700 672 ttcaatacgctcctattatatagtatagttttttattaaaagtattctacacccttttttaggaaatgtcaataaactaaatggataatttggaagttcagtctgacttacaaaaagaaaaggagttttcactccttttcacagattgaagacaaagtccttataaaagtgtcttctaaagattttaacttcaatctgaagcgaggttatcctcgctttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntaat Intra-Species Hit: Count: 1 Min: 1 Max: 219 Len: 219 Subject: NC_009009_SSA_0234_SSA_0235|hypothetical protein:Integrase/recombinase, phage associated, putative|NEGATIVE:POSITIVE|[229029,229700]|672 HSP 1 e-value: 1.0E-120 bit: 434.0 Len: 219 Query Start:1 Query End:219 Subject Strand: POSITIVE Subject Start: 1 Subject End: 219 ttcaatacgctcctattatatagtatagttttttattaaaagtattctacacccttttttaggaaatgtcaataaactaaatggataatttggaagttcagtctgacttacaaaaagaaaaggagttttcactccttttcacagattgaagacaaagtccttataaaagtgtcttctaaagattttaacttcaatctgaagcgaggttatcctcgcttt..................................................................................................................................................................................................................................................................................................................................................................................................................................................................... ttcaatacgctcctattatatagtatagttttttattaaaagtattctacacccttttttaggaaatgtcaataaactaaatggataatttggaagttcagtctgacttacaaaaagaaaaggagttttcactccttttcacagattgaagacaaagtccttataaaagtgtcttctaaagattttaacttcaatctgaagcgaggttatcctcgcttt..................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAAUACGCUCCUAUUAUAUAGUAUAGUUUUUUAUUAAAAGUAUUCUACACCCUUUUUUAGGAAAUGUCAAUAAACUAAAUGGAUAAUUUGGAAGUUCAGUCUGACUUACAAAAAGAAAAGGAGUUUUCACUCCUUUUCACAGAUUGAAGACAAAGUCCUUAUAAAAGUGUCUUCUAAAGAUUUUAACUUCAAUCUGAAGCGAGGUUAUCCUCGCUUU ....................(((.(((.((((.....)))).))).))).((.(((((..((((..((((......((((((.....))))))...(((((((((..((....)).((((((((((....)))))))))).)))))))))))))...))))...))))).)).......(((((........)))))(((((((((....))))))))) (-53.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGCGAGGAUAACCUCGCUUCAGAUUGAAGUUAAAAUCUUUAGAAGACACUUUUAUAAGGACUUUGUCUUCAAUCUGUGAAAAGGAGUGAAAACUCCUUUUCUUUUUGUAAGUCAGACUGAACUUCCAAAUUAUCCAUUUAGUUUAUUGACAUUUCCUAAAAAAGGGUGUAGAAUACUUUUAAUAAAAAACUAUACUAUAUAAUAGGAGCGUAUUGAA .((((((((....))))))))((((((((((.((((.((((((.((((...)))).)))))).)))).)))))))))).((((((((((....)))))))))).........(((((..((((((................)))))))))))..((((((......(((((((..................)))))))......))))))......... (-64.16) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 808 140 91 231 182 NC_009009:SSA_0234|5end_hypothetical_protein_228938..229168_NEGATIVE 257 160 114 181 136 NC_009009:SSA_1770|5end_hypothetical_protein_1758431..1758661_NEGATIVE 253 171 133 182 139 NC_009009:SSA_1436|5end_hypothetical_protein_1443125..1443355_NEGATIVE 253 147 101 106 64 NC_009009:SSA_0477|5end_Cobalamin_biosynthesis_protein_CbiM_(ABC-type_cobalt_transporter),_putative_479223..479453_POSITIVE 245 138 91 221 163 NC_009009:SSA_0341|5end_hypothetical_protein_334731..334961_NEGATIVE 241 64 21 170 121 NC_009009:SSA_1091|5end_Thymidylate_synthase,_putative_1108635..1108865_POSITIVE 235 110 65 62 7 NC_009009:SSA_1920|5end_Phosphotransferase_system,_mannose-specific_EIID,_putative_1909863..1910093_POSITIVE 231 125 82 157 104 NC_009009:SSA_1182|5end_Gid-like_protein,_putative_1210866..1211096_NEGATIVE 225 128 89 202 166 NC_009009:SSA_1833|5end_hypothetical_protein_1822662..1822892_POSITIVE 225 140 92 72 9 NC_009009:SSA_0158|5end_hypothetical_protein_153801..154031_POSITIVE 223 206 168 117 75 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 222 43 8 132 102 NC_009009:SSA_0667|5end_Transcriptional_regulator,_putative_649778..650008_POSITIVE 220 140 97 100 65 NC_009009:SSA_1787|5end_Diaminopimelate_decarboxylase,_putative_1771551..1771781_NEGATIVE 218 71 31 141 111 NC_009009:SSA_0367|5end_hypothetical_protein_358309..358539_POSITIVE 217 139 98 209 165 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 217 210 163 210 163 NC_009009:SSA_1914|5end_hypothetical_protein_1905195..1905425_NEGATIVE 216 120 73 154 103 NC_009009:SSA_1144|5end_Beta-N-acetylhexosaminidase,_putative_1175610..1175840_NEGATIVE 213 136 91 188 132 NC_009009:SSA_2015|5end_Phosphoglycerate_mutase,_putative_2015492..2015722_NEGATIVE 212 124 81 201 152 NC_009009:SSA_0575|5end_Hydrolase,_HAD_superfamily,_putative_569527..569757_POSITIVE 211 139 92 166 119 NC_009009:SSA_1415|5end_Oxidoreductase,_putative_1426508..1426738_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 387 160 113 60 12 NC_009009:SSA_0327|3end_Glycosyltransferase,_putative_320436..320586_POSITIVE 280 130 81 89 38 NC_009009:SSA_1670|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1668637..1668787_NEGATIVE 261 203 172 64 31 NC_009009:SSA_0328|3end_Xaa-Pro_dipeptidyl-peptidase,_putative_320487..320637_NEGATIVE 257 160 114 121 76 NC_009009:SSA_1771|3end_Conserved_DNA_methyltransferase_protein,_putative_1758491..1758641_NEGATIVE 253 147 101 84 42 NC_009009:SSA_0476|3end_Precorrin-2_C20-methyltransferase,_putative_479281..479431_POSITIVE 246 159 111 69 11 NC_009009:SSA_0459|3end_hypothetical_protein_462513..462663_POSITIVE 245 138 91 61 3 NC_009009:SSA_0342|3end_Pyruvate_formate-lyase,_putative_334891..335041_NEGATIVE 241 140 91 88 34 NC_009009:SSA_1731|3end_ATP-dependent_Clp_protease,_proteolytic_subunit,_putative_1716218..1716368_NEGATIVE 241 64 21 65 16 NC_009009:SSA_1090|3end_Glucokinase,_putative_1108610..1108760_POSITIVE 231 125 82 55 2 NC_009009:SSA_1183|3end_hypothetical_protein_1210968..1211118_NEGATIVE 230 68 26 141 92 NC_009009:SSA_0506|3end_Iron-sulfur_cluster-binding_protein,_putative_504430..504580_NEGATIVE 225 128 89 74 38 NC_009009:SSA_1832|3end_hypothetical_protein_1822614..1822764_POSITIVE 225 140 92 68 5 NC_009009:SSA_0157|3end_hypothetical_protein_153877..154027_POSITIVE 223 206 168 124 82 NC_009009:SSA_1651|3end_hypothetical_protein_1649587..1649737_NEGATIVE 217 139 98 73 29 NC_009009:SSA_2244|3end_Arsenate_reductase,_putative_2239477..2239627_NEGATIVE 217 210 163 129 82 NC_009009:SSA_1915|3end_hypothetical_protein_1905276..1905426_NEGATIVE 216 120 73 70 19 NC_009009:SSA_1145|3end_hypothetical_protein_1175694..1175844_NEGATIVE 213 136 91 88 32 NC_009009:SSA_2016|3end_Phosphoglycerate_mutase,_putative_2015592..2015742_NEGATIVE 210 160 122 38 4 NC_009009:SSA_0255|3end_Multiple_antibiotic_resistance_operon_transcription_repressor_(MarR),_putative_247485..247635_NEGATIVE 208 164 129 54 22 NC_009009:SSA_1561|3end_Ribonuclease_III,_putative_1565185..1565335_NEGATIVE