Origin IGS: nnnnnctgcataatacattttactcatgaaactattttaccataatttgacttaaattgtaaatcgtttacaaattgataataaaacgaaaaagactgaagaaagctagtaagtaaaacattttcttcaatctctttaaacacttataaataataagccatttagaactagaaatatcataattaggatataacaaaatgtttatcatctataattaggcgcattcttattactattgcttaaccttcagatacttaattatcaacaaaattcccaacaggatgtttagataaaagcccaactgatacgtttttgtcaggatttcccaacttgtccaaagtcgtaccaaatcttctagcgacatgcggaagaaataaccctctgtagcaatccatagaactaaaaagaaataactaccagcagcaagccatttcgtccaccgtttttttagtaggcaagcaatcaagagcgaacagataaagatagctgttacaatagcatgttccatcaaaaaagtaaaaccgtaatagatttccacaaagcgtctaccattatccgcattcgccccttttataaaaggtagtgcaaaacttaaaataaaacagagttccagtatataactttttaagattttcatagtacacctcctataaattgtgaatcccaaagccccctttattggcttataagtcaggagaaagtagctcctacctcatcaataaattggtcaaccctatctacttctattatacgatattggtttactatcatcaagaaaccgctttatttttttagctttttatggtatgataaacaaaatatctaggggaaaacaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgttttcccctagatattttgtttatcataccataaaaagctaaaaaaataaagcggtttcttgatgatagtaaaccaatatcgtataatagaagtagatagggttgaccaatttattgatgaggtaggagctactttctcctgacttataagccaataaagggggctttgggattcacaatttataggaggtgtactatgaaaatcttaaaaagttatatactggaactctgttttattttaagttttgcactaccttttataaaaggggcgaatgcggataatggtagacgctttgtggaaatctattacggttttacttttttgatggaacatgctattgtaacagctatctttatctgttcgctcttgattgcttgcctactaaaaaaacggtggacgaaatggcttgctgctggtagttatttctttttagttctatggattgctacagagggttatttcttccgcatgtcgctagaagatttggtacgactttggacaagttgggaaatcctgacaaaaacgtatcagttgggcttttatctaaacatcctgttgggaattttgttgataattaagtatctgaaggttaagcaatagtaataagaatgcgcctaattatagatgataaacattttgttatatcctaattatgatatttctagttctaaatggcttattatttataagtgtttaaagagattgaagaaaatgttttacttactagctttcttcagtctttttcgttttattatcaatttgtaaacgatttacaatttaagtcaaattatggtaaaatagtttcatgagtaaaatgtattatgcagnnnnn Mask Tandem Repeat Region ================================================ nnnnnctgcataatacattttactcatgaaactattttaccataatttgacttaaattgtaaatcgtttacaaattgataataaaacgaaaaagactgaagaaagctagtaagtaaaacattttcttcaatctctttaaacacttataaataataagccatttagaactagaaatatcataattaggatataacaaaatgtttatcatctataattaggcgcattcttattactattgcttaaccttcagatacttaattatcaacaaaattcccaacaggatgtttagataaaagcccaactgatacgtttttgtcaggatttcccaacttgtccaaagtcgtaccaaatcttctagcgacatgcggaagaaataaccctctgtagcaatccatagaactaaaaagaaataactaccagcagcaagccatttcgtccaccgtttttttagtaggcaagcaatcaagagcgaacagataaagatagctgttacaatagcatgttccatcaaaaaagtaaaaccgtaatagatttccacaaagcgtctaccattatccgcattcgccccttttataaaaggtagtgcaaaacttaaaataaaacagagttccagtatataactttttaagattttcatagtacacctcctataaattgtgaatcccaaagccccctttattggcttataagtcaggagaaagtagctcctacctcatcaataaattggtcaaccctatctacttctattatacgatattggtttactatcatcaagaaaccgctttatttttttagctttttatggtatgataaacaaaatatctaggggaaaacaa Find is-nt database================================================ Query_seq: SMT_1501:SMT_1502|SMT_1501:SMT_1502:recombination protein:pantothenate kinase:->->:1485231..1486066 836 nnnnnctgcataatacattttactcatgaaactattttaccataatttgacttaaattgtaaatcgtttacaaattgataataaaacgaaaaagactgaagaaagctagtaagtaaaacattttcttcaatctctttaaacacttataaataataagccatttagaactagaaatatcataattaggatataacaaaatgtttatcatctataattaggcgcattcttattactattgcttaaccttcagatacttaattatcaacaaaattcccaacaggatgtttagataaaagcccaactgatacgtttttgtcaggatttcccaacttgtccaaagtcgtaccaaatcttctagcgacatgcggaagaaataaccctctgtagcaatccatagaactaaaaagaaataactaccagcagcaagccatttcgtccaccgtttttttagtaggcaagcaatcaagagcgaacagataaagatagctgttacaatagcatgttccatcaaaaaagtaaaaccgtaatagatttccacaaagcgtctaccattatccgcattcgccccttttataaaaggtagtgcaaaacttaaaataaaacagagttccagtatataactttttaagattttcatagtacacctcctataaattgtgaatcccaaagccccctttattggcttataagtcaggagaaagtagctcctacctcatcaataaattggtcaaccctatctacttctattatacgatattggtttactatcatcaagaaaccgctttatttttttagctttttatggtatgataaacaaaatatctaggggaaaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1501:SMT_1502|SMT_1501:SMT_1502:recombination protein:pantothenate kinase:->->:1485231..1486066 836 nnnnnctgcataatacattttactcatgaaactattttaccataatttgacttaaattgtaaatcgtttacaaattgataataaaacgaaaaagactgaagaaagctagtaagtaaaacattttcttcaatctctttaaacacttataaataataagccatttagaactagaaatatcataattaggatataacaaaatgtttatcatctataattaggcgcattcttattactattgcttaaccttcagatacttaattatcaacaaaattcccaacaggatgtttagataaaagcccaactgatacgtttttgtcaggatttcccaacttgtccaaagtcgtaccaaatcttctagcgacatgcggaagaaataaccctctgtagcaatccatagaactaaaaagaaataactaccagcagcaagccatttcgtccaccgtttttttagtaggcaagcaatcaagagcgaacagataaagatagctgttacaatagcatgttccatcaaaaaagtaaaaccgtaatagatttccacaaagcgtctaccattatccgcattcgccccttttataaaaggtagtgcaaaacttaaaataaaacagagttccagtatataactttttaagattttcatagtacacctcctataaattgtgaatcccaaagccccctttattggcttataagtcaggagaaagtagctcctacctcatcaataaattggtcaaccctatctacttctattatacgatattggtttactatcatcaagaaaccgctttatttttttagctttttatggtatgataaacaaaatatctaggggaaaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1501:SMT_1502|SMT_1501:SMT_1502:recombination protein:pantothenate kinase:->->:1485231..1486066 836 nnnnnctgcataatacattttactcatgaaactattttaccataatttgacttaaattgtaaatcgtttacaaattgataataaaacgaaaaagactgaagaaagctagtaagtaaaacattttcttcaatctctttaaacacttataaataataagccatttagaactagaaatatcataattaggatataacaaaatgtttatcatctataattaggcgcattcttattactattgcttaaccttcagatacttaattatcaacaaaattcccaacaggatgtttagataaaagcccaactgatacgtttttgtcaggatttcccaacttgtccaaagtcgtaccaaatcttctagcgacatgcggaagaaataaccctctgtagcaatccatagaactaaaaagaaataactaccagcagcaagccatttcgtccaccgtttttttagtaggcaagcaatcaagagcgaacagataaagatagctgttacaatagcatgttccatcaaaaaagtaaaaccgtaatagatttccacaaagcgtctaccattatccgcattcgccccttttataaaaggtagtgcaaaacttaaaataaaacagagttccagtatataactttttaagattttcatagtacacctcctataaattgtgaatcccaaagccccctttattggcttataagtcaggagaaagtagctcctacctcatcaataaattggtcaaccctatctacttctattatacgatattggtttactatcatcaagaaaccgctttatttttttagctttttatggtatgataaacaaaatatctaggggaaaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 2 Min: 302 Max: 637 Len: 336 Subject: UniRef90_Q04L72 Cluster: Membrane protein, putative; n=2; Streptococcus pneumoniae|Rep: Membrane protein, putative - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 5.0E-48 bit: 193.0 Len: 336 Query Start:302 Query End:637 Subject Strand: null Subject Start: 1 Subject End: 124 ............................................................................................................................................................................................................................................................................................................. M K I L K S Y I L E L C F I L S F A L P F I K G A N A D N G R R F V E I Y Y G F T F L M E H A I V T A I F I C S L L I A C L L K K R W T K - - - - - - - - - - - - W L A A G S Y F F L V L W I A T E G Y F F R M S L E D L V R L W T S W E I L T K T Y Q ....................................................................................................................................................................................................... ............................................................................................................................................................................................................................................................................................................. M K I L K R Y I L E L C F I L S F A L P F I K G A N A D N G R C F V E T Y Y G F T F L M E H A I V T A V F I Y S F L I A F L L K K R W A K W I A A G S Y C F L V L W I A A G S Y C F L V L W I A T E G Y F F R M S L E D L I R L W T S L E I L T Q T Y Q ....................................................................................................................................................................................................... Subject: UniRef90_Q97RH5 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae|Rep: Hypothetical protein - Streptococcus pneumoniae HSP 1 e-value: 3.0E-26 bit: 115.0 Len: 192 Query Start:446 Query End:637 Subject Strand: null Subject Start: 1 Subject End: 64 ............................................................................................................................................................................................................................................................................................................................................................................................................................................................. M K I L K S Y I L E L C F I L S F A L P F I K G A N A D N G R R F V E I Y Y G F T F L M E H A I V T A I F I C S L L I A C L L K ....................................................................................................................................................................................................... ............................................................................................................................................................................................................................................................................................................................................................................................................................................................. M K I L K R Y I L E L C F I L S F A L P F I K G T N A D N G R C F V E T Y Y G F T F L M E H A I V T A V F I C S F L I A F L L K ....................................................................................................................................................................................................... HSP 2 e-value: 3.0E-26 bit: 26.9 Len: 45 Query Start:403 Query End:447 Subject Strand: null Subject Start: 64 Subject End: 78 .................................................................................................................................................................................................................................................................................................................................................................................................................. K N G G R N G L L L V V I S F ..................................................................................................................................................................................................................................................................................................................................................................................................... .................................................................................................................................................................................................................................................................................................................................................................................................................. K N D G R N G L L R V V I A F ..................................................................................................................................................................................................................................................................................................................................................................................................... nnnnnctgcataatacattttactcatgaaactattttaccataatttgacttaaattgtaaatcgtttacaaattgataataaaacgaaaaagactgaagaaagctagtaagtaaaacattttcttcaatctctttaaacacttataaataataagccatttagaactagaaatatcataattaggatataacaaaatgtttatcatctataattaggcgcattcttattactattgcttaaccttcagatacttaattatcaacaaaattcccaacaggatgtttagataaaagcccaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagtacacctcctataaattgtgaatcccaaagccccctttattggcttataagtcaggagaaagtagctcctacctcatcaataaattggtcaaccctatctacttctattatacgatattggtttactatcatcaagaaaccgctttatttttttagctttttatggtatgataaacaaaatatctaggggaaaacaa Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 661 End: 792 .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... M P K P P L L A Y K S G E S S S Y L I N K L V N P I Y F Y Y T I L V Y Y H Q E T A L F F ............................................ Protein_Len: 58 Strand: + Start: 650 End: 823 ......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... M N C E S Q S P L Y W L I S Q E K V A P T S S I N W S T L S T S I I R Y W F T I I K K P L Y F F S F L W Y D K Q N I ............. Protein_Len: 38 Strand: + Start: 723 End: 836 .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. M G Q P Y L L L L Y D I G L L S S R N R F I F L A F Y G M I N K I S R G K Q Protein_Len: 30 Strand: - Start: 555 End: 644 .......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... G C E G R K Y F T T C F K F Y F L T G T Y L K K L N E Y Y M ................................................................................................................................................................................................ Protein_Len: 46 Strand: - Start: 258 End: 395 ................................................................................................................................................................................................................................................................. N D V F N G V P H K S L L G V S V N K D P N G L K D L T T G F R R A V H P L F L G R Y C D M ......................................................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: - Start: 236 End: 694 ........................................................................................................................................................................................................................................... T F G Y Y I E V F R R G N D A N A G K I F P L A F S L I F C L E L I Y S K L I K M T C R R Y I T F G L A G K I P K Y T M .............................................................................................................................................. Protein_Len: 46 Strand: - Start: 71 End: 208 ...................................................................... L N I I F R F L S F F A L L Y F M K K L R K L C K Y I I L W K S S S I D Y N P Y L L I N I M .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 39 Strand: - Start: 27 End: 143 .......................... S V I K G Y N S K F Q L D N V F Q Y Y F S F S Q L F S T L L V N E E I E K F M ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... nnnnnctgcataatacattttactcatgaaactattttaccataatttgacttaaattgtaaatcgtttacaaattgataataaaacgaaaaagactgaagaaagctagtaagtaaaacattttcttcaatctctttaaacacttataaataataagccatttagaactagaaatatcataattaggatataacaaaatgtttatcatctataattaggcgcattcttattactattgcttaaccttcagatacttaattatcaacaaaattcccaacaggatgtttagataaaagcccaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagtacacctcctataaattgtgaatcccaaagccccctttattggcttataagtcaggagaaagtagctcctacctcatcaataaattggtcaaccctatctacttctattatacgatattggtttactatcatcaagaaaccgctttatttttttagctttttatggtatgataaacaaaatatctaggggaaaacaa 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: 85 Start: 746 End: 775 .........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTTGATGATAGTAAACCAATATCGTATAAT............................................................. PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 34 End: 63 .................................TTTACAATTTAAGTCAAATTATGGTAAAAT..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 782 End: 811 .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTTTATTTTTTTAGCTTTTTATGGTATGAT......................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 569 End: 598 ........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTTATAAAAGGTAGTGCAAAACTTAAAAT.............................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ nnnnnctgcataatacattttactcatgaaactattttaccataatttgacttaaattgtaaatcgtttacaaattgataataaaacgaaaaagactgaagaaagctagtaagtaaaacattttcttcaatctctttaaacacttataaataataagccatttagaactagaaatatcataattaggatataacaaaatgtttatcatctataattaggcgcattcttattactattgcttaaccttcagatacttaattatcaacaaaattcccaacaggatgtttagataaaagcccaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagtacacctcctataaattgtgaatcccaaagccccctttattggcttataagtcaggagaaagtagctcctacctcatcaataaattggtcaaccctatctacttctattatacgatattggtttactatcatcaagaaaccgctttatttttttagctttttatggtatgataaacaaaatatctaggggaaaacaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1501:SMT_1502|SMT_1501:SMT_1502:recombination protein:pantothenate kinase:->->:1485231..1486066 836 nnnnnctgcataatacattttactcatgaaactattttaccataatttgacttaaattgtaaatcgtttacaaattgataataaaacgaaaaagactgaagaaagctagtaagtaaaacattttcttcaatctctttaaacacttataaataataagccatttagaactagaaatatcataattaggatataacaaaatgtttatcatctataattaggcgcattcttattactattgcttaaccttcagatacttaattatcaacaaaattcccaacaggatgtttagataaaagcccaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagtacacctcctataaattgtgaatcccaaagccccctttattggcttataagtcaggagaaagtagctcctacctcatcaataaattggtcaaccctatctacttctattatacgatattggtttactatcatcaagaaaccgctttatttttttagctttttatggtatgataaacaaaatatctaggggaaaacaa Intra-Species Hit: Count: 1 Min: 6 Max: 836 Len: 831 Subject: smit_SMT_1501_SMT_1502|recombination protein:pantothenate kinase|POSITIVE:POSITIVE|[1485231,1486066]|836 HSP 1 e-value: 1.0E-166 bit: 587.0 Len: 296 Query Start:6 Query End:301 Subject Strand: POSITIVE Subject Start: 6 Subject End: 301 .....ctgcataatacattttactcatgaaactattttaccataatttgacttaaattgtaaatcgtttacaaattgataataaaacgaaaaagactgaagaaagctagtaagtaaaacattttcttcaatctctttaaacacttataaataataagccatttagaactagaaatatcataattaggatataacaaaatgtttatcatctataattaggcgcattcttattactattgcttaaccttcagatacttaattatcaacaaaattcccaacaggatgtttagataaaagcccaa....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... .....ctgcataatacattttactcatgaaactattttaccataatttgacttaaattgtaaatcgtttacaaattgataataaaacgaaaaagactgaagaaagctagtaagtaaaacattttcttcaatctctttaaacacttataaataataagccatttagaactagaaatatcataattaggatataacaaaatgtttatcatctataattaggcgcattcttattactattgcttaaccttcagatacttaattatcaacaaaattcccaacaggatgtttagataaaagcccaa....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... HSP 2 e-value: 6.0E-96 bit: 353.0 Len: 199 Query Start:638 Query End:836 Subject Strand: POSITIVE Subject Start: 638 Subject End: 836 .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................agtacacctcctataaattgtgaatcccaaagccccctttattggcttataagtcaggagaaagtagctcctacctcatcaataaattggtcaaccctatctacttctattatacgatattggtttactatcatcaagaaaccgctttannnnnnnagctttttatggtatgataaacaaaatatctaggggaaaacaa .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................agtacacctcctataaattgtgaatcccaaagccccctttattggcttataagtcaggagaaagtagctcctacctcatcaataaattggtcaaccctatctacttctattatacgatattggtttactatcatcaagaaaccgctttatttttttagctttttatggtatgataaacaaaatatctaggggaaaacaa Inter-species Hit: Count: 4 Min: 31 Max: 836 Len: 806 Subject: NC_003028_SP_0840_SP_0841|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[788037,788409]|373 HSP 1 e-value: 5.0E-78 bit: 293.0 Len: 271 Query Start:31 Query End:301 Subject Strand: NEGATIVE Subject Start: 99 Subject End: 370 ..............................actattttaccataatttgacttaaattgtaaatcgtttacaaattgataataaaacgaaaaagactgaagaaagctagtaagtaaaacattttcttcaatctctttaaacacttataaataataagccatttagaactagaaatatcataattaggat-ataacaaaatgtttatcatctataattaggcgcattcttattactattgcttaaccttcagatacttaattatcaacaaaattcccaacaggatgtttagataaaagcccaa....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... ..............................actattttaccataatttgactcaaattgtaaatcgtttacaaattgataataaaacgaaaaagaccgaagaaagcaagtcacgaagccattttcttcaatctctttcaacacttataaataataaaccatttagaactataaatatcacagtccagataaaaacaaaaagtttatcatctataatcaggcagattattatttctattgcttaaccttaaaatactttattatcaacaaaattcctaacaaaatgtttagataaaagcccaa....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Subject: NC_008533_SPD_0734_SPD_0735|hypothetical protein:methyltransferase small domain, putative|POSITIVE:POSITIVE|[747209,747414]|206 HSP 1 e-value: 1.0E-53 bit: 212.0 Len: 190 Query Start:31 Query End:220 Subject Strand: NEGATIVE Subject Start: 13 Subject End: 203 ..............................actattttaccataatttgacttaaattgtaaatcgtttacaaattgataataaaacgaaaaagactgaagaaagctagtaagtaaaacattttcttcaatctctttaaacacttataaataataagccatttagaactagaaatatcataattaggat-ataacaaaatgtttatcatctataattaggc........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ ..............................actattttaccataatttgactcaaattgtaaatcgtttacaaattgataataaaacgaaaaagaccgaagaaagcgagtcacgaagccattttcttcaatctctttcaacacttataaataataaaccatttagaactataaatatcacagtccagataaaaacaaaaagtttatcatctataatcaggc........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ Subject: NC_003098_spr0742_spr0743|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[739678,739883]|206 HSP 1 e-value: 1.0E-53 bit: 212.0 Len: 190 Query Start:31 Query End:220 Subject Strand: NEGATIVE Subject Start: 13 Subject End: 203 ..............................actattttaccataatttgacttaaattgtaaatcgtttacaaattgataataaaacgaaaaagactgaagaaagctagtaagtaaaacattttcttcaatctctttaaacacttataaataataagccatttagaactagaaatatcataattaggat-ataacaaaatgtttatcatctataattaggc........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ ..............................actattttaccataatttgactcaaattgtaaatcgtttacaaattgataataaaacgaaaaagaccgaagaaagcgagtcacgaagccattttcttcaatctctttcaacacttataaataataaaccatttagaactataaatatcacagtccagataaaaacaaaaagtttatcatctataatcaggc........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ Subject: NC_003028_SP_0839_SP_0840|pantothenate kinase:hypothetical protein|NEGATIVE:POSITIVE|[787611,787799]|189 HSP 1 e-value: 4.0E-14 bit: 81.8 Len: 66 Query Start:771 Query End:836 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 66 ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................tcaagaaaccgctttannnnnnnagctttttatggtatgataaacaaaatatctaggggaaaacaa ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................tcaagaaaccgctttatttttttagctttttatggtatgatagacaaaatatctaggggaaaacaa HSP 2 e-value: 2.0E-9 bit: 65.9 Len: 89 Query Start:638 Query End:726 Subject Strand: NEGATIVE Subject Start: 101 Subject End: 189 .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................agtacacctcctataaattgtgaatcccaaagccccctttattggcttataagtcaggagaaagtagctcctacctcatcaataaattg.............................................................................................................. .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................agtacacctcctataagttgtgaactaaaaagccccctttataagcttataaatcagtagaatctatctcctatttcatcaataaattg.............................................................................................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAUUUUACCAUAAUUUGACUUAAAUUGUAAAUCGUUUACAAAUUGAUAAUAAAACGAAAAAGACUGAAGAAAGCUAGUAAGUAAAACAUUUUCUUCAAUCUCUUUAAACACUUAUAAAUAAUAAGCCAUUUAGAACUAGAAAUAUCAUAAUUAGGAUAUAACAAAAUGUUUAUCAUCUAUAAUUAGGCGCAUUCUUAUUACUAUUGCUUAACCUUCAGAUACUUAAUUAUCAACAAAAUUCCCAACAGGAUGUUUAGAUAAAAGCCCAACUGAUACGUUUUUGUCAGGAUUUCCCAACUUGUCCAAAGUCGUACCAAAUCUUCUAGCGACAUGCGGAAGAAAUAACCCUCUGUAGCAAUCCAUAGAACUAAAAAGAAAUAACUACCAGCAGCAAGCCAUUUCGUCCACCGUUUUUUUAGUAGGCAAGCAAUCAAGAGCGAACAGAUAAAGAUAGCUGUUACAAUAGCAUGUUCCAUCAAAAAAGUAAAACCGUAAUAGAUUUCCACAAAGCGUCUACCAUUAUCCGCAUUCGCCCCUUUUAUAAAAGGUAGUGCAAAACUUAAAAUAAAACAGAGUUCCAGUAUAUAACUUUUUAAGAUUUUCAUAGUACACCUCCUAUAAAUUGUGAAUCCCAAAGCCCCCUUUAUUGGCUUAUAAGUCAGGAGAAAGUAGCUCCUACCUCAUCAAUAAAUUGGUCAACCCUAUCUACUUCUAUUAUACGAUAUUGGUUUACUAUCAUCAAGAAACCGCUUUAUUUUUUUAGCUUUUUAUGGUAUGAUAAACAAAAUAUCUAGGGGAAAACAA ...............((((.......((((((.....))))))..(((((((....(......).((((((.((((((((((...(((((((((......(((.((((((..(((((.....)))))...))))))...))).(((((........)))))...)))))))))....((((....))))..........))))))..))))...)))))).......))))))).)))).(((((....((((((((.(((((((((...........))))))))).((((..........))))...(((((((((..((((((.((.....))))))))........(((((........))))).(((((((((..............((..(((........................)))..)).....((((((....(((...(((((((((....))))).))))..))).....((((((.((((((((((.........((.((..((((......(.((((((....((((((..((((.(((((((((((((((.........................))))))).))))....))))))))..))))))..)))))).)..(((((.........)))))...((..(((((.......)))))..))...........))))..)).)).......))))))))........)))))))).............)))))).))))))))).......))))))))).....))))))))..)))))..... (-143.26) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUUUUCCCCUAGAUAUUUUGUUUAUCAUACCAUAAAAAGCUAAAAAAAUAAAGCGGUUUCUUGAUGAUAGUAAACCAAUAUCGUAUAAUAGAAGUAGAUAGGGUUGACCAAUUUAUUGAUGAGGUAGGAGCUACUUUCUCCUGACUUAUAAGCCAAUAAAGGGGGCUUUGGGAUUCACAAUUUAUAGGAGGUGUACUAUGAAAAUCUUAAAAAGUUAUAUACUGGAACUCUGUUUUAUUUUAAGUUUUGCACUACCUUUUAUAAAAGGGGCGAAUGCGGAUAAUGGUAGACGCUUUGUGGAAAUCUAUUACGGUUUUACUUUUUUGAUGGAACAUGCUAUUGUAACAGCUAUCUUUAUCUGUUCGCUCUUGAUUGCUUGCCUACUAAAAAAACGGUGGACGAAAUGGCUUGCUGCUGGUAGUUAUUUCUUUUUAGUUCUAUGGAUUGCUACAGAGGGUUAUUUCUUCCGCAUGUCGCUAGAAGAUUUGGUACGACUUUGGACAAGUUGGGAAAUCCUGACAAAAACGUAUCAGUUGGGCUUUUAUCUAAACAUCCUGUUGGGAAUUUUGUUGAUAAUUAAGUAUCUGAAGGUUAAGCAAUAGUAAUAAGAAUGCGCCUAAUUAUAGAUGAUAAACAUUUUGUUAUAUCCUAAUUAUGAUAUUUCUAGUUCUAAAUGGCUUAUUAUUUAUAAGUGUUUAAAGAGAUUGAAGAAAAUGUUUUACUUACUAGCUUUCUUCAGUCUUUUUCGUUUUAUUAUCAAUUUGUAAACGAUUUACAAUUUAAGUCAAAUUAUGGUAAAAUAGU .............((((.......)))).((((((((((((((...((((((((((((.((((..(((((....((((..((((.(((.......))))))).))))..((..((((((((((((.((((((.......)))))).)))))....)))))))..))..(((((((((.....(((((((........))))))))))))))))..))))).....))))..)))))))))))).)))))).........((((((((.(((((((..((((((((.(((((.......((((...(((((((..(........)..))))))).....))))........))))).)))))))))))))))..((((((((((..((((.......(((((.(((((((((..(((.((((((((....((....)).......)))))))))))..))))))))).)))))..(((((((((...)))))..)))).))))....((..((....))..)).........((((....(((((((((..(((((((.....)))....)))))))))..))))..)))).)).)))))))).(((((((((..((((....(((((((((((((.((((((((((((.......)))))))...........)))))..)))))))))))))))))..((((((((((((((((..(((.........)))))))))))))))))))..)))))))))...)))))))).((((((.....))))))...))))))))....... (-193.66) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 319 272 208 159 smit:SMT_1244|5end_putative_repressor_protein_1204392..1204622_POSITIVE 322 359 311 62 20 smit:SMT_302|5end_K07444_putative_N6-adenine-specific_DNA_methylase_244808..245038_POSITIVE 318 352 312 188 135 smit:SMT_1328|5end_hypothetical_protein_1304468..1304698_NEGATIVE 299 449 404 117 85 smit:SMT_358|5end_hypothetical_protein_293947..294177_POSITIVE 279 440 391 225 170 smit:SMT_1543|5end_diphosphomevalonate_decarboxylase_1528024..1528254_NEGATIVE 275 544 502 208 166 smit:SMT_534|5end_hypothetical_protein_predicted_by_Glimmer/Critica_453571..453801_POSITIVE 275 544 502 208 166 smit:SMT_531|5end_hypothetical_protein_predicted_by_Glimmer/Critica_452672..452902_POSITIVE 275 544 502 208 166 smit:SMT_527|5end_hypothetical_protein_predicted_by_Glimmer/Critica_451502..451732_POSITIVE 275 544 502 208 166 smit:SMT_511|5end_hypothetical_protein_predicted_by_Glimmer/Critica_439391..439621_POSITIVE 274 640 598 46 1 smit:SMT_1210|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1171051..1171281_NEGATIVE 274 640 598 125 80 smit:SMT_1209|5end_choline_binding_protein_PcpA_1170972..1171202_NEGATIVE 273 430 383 211 176 smit:SMT_857|5end_endo-beta-N-acetylglucosaminidase_802491..802721_NEGATIVE 271 679 638 203 166 smit:SMT_1217|5end_hypothetical_protein_1176603..1176833_NEGATIVE 270 435 391 203 166 smit:SMT_1331|5end_hypothetical_protein_1306236..1306466_NEGATIVE 269 680 637 69 34 smit:SMT_2063|5end_hypothetical_protein_1971792..1972022_NEGATIVE 269 680 637 108 73 smit:SMT_1996|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1921078..1921308_NEGATIVE 269 335 293 34 1 smit:SMT_107|5end_ribose-phosphate_pyrophosphokinase_52402..52632_POSITIVE 268 339 297 67 13 smit:SMT_2030|5end_chromosomal_replication_initiator_protein_DnaA_1945167..1945397_NEGATIVE 268 424 383 190 154 smit:SMT_1506|5end_Cl-channel,_voltage-gated_family_protein_1489986..1490216_NEGATIVE 267 682 642 40 6 smit:SMT_1829|5end_hypothetical_protein_1798156..1798386_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 338 291 141 87 smit:SMT_1530|3end_K07456_DNA_mismatch_repair_protein_MutS2_1513010..1513160_NEGATIVE 336 440 392 72 27 smit:SMT_1806|3end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781644..1781794_POSITIVE 301 353 316 151 108 smit:SMT_608|3end_laminin-binding_surface_protein_521187..521337_POSITIVE 296 539 492 63 13 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 275 544 502 94 52 smit:SMT_533|3end_RNA_binding_protein_453537..453687_POSITIVE 275 544 502 94 52 smit:SMT_530|3end_RNA_binding_protein_452638..452788_POSITIVE 275 544 502 94 52 smit:SMT_526|3end_RNA_binding_protein_451468..451618_POSITIVE 275 544 502 94 52 smit:SMT_510|3end_hypothetical_protein_439357..439507_POSITIVE 274 640 598 138 93 smit:SMT_1210|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1170959..1171109_NEGATIVE 272 290 241 56 13 smit:SMT_593|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_510317..510467_POSITIVE 271 679 638 118 81 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE 269 680 637 63 28 smit:SMT_1997|3end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_1921123..1921273_NEGATIVE 265 689 651 40 7 smit:SMT_1542|3end_phosphomevalonate_kinase_1526077..1526227_NEGATIVE 263 640 591 124 72 smit:SMT_654|3end_K06158_ATP-binding_cassette,_sub-family_F,_member_3_564157..564307_NEGATIVE 262 680 638 58 21 smit:SMT_1066|3end_holo-(acyl_carrier_protein)_synthase_1005859..1006009_POSITIVE 260 340 291 56 3 smit:SMT_541|3end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457120..457270_NEGATIVE 257 460 420 150 114 smit:SMT_507|3end_hypothetical_protein_437638..437788_NEGATIVE 257 460 420 150 114 smit:SMT_504|3end_hypothetical_protein_436207..436357_NEGATIVE 256 699 651 145 89 smit:SMT_1454|3end_cytidine_deaminase_1437497..1437647_NEGATIVE 254 360 311 135 75 smit:SMT_1200|3end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1161076..1161226_NEGATIVE