Origin IGS: taggctttcagccctctatcggggaatgctttttcccaacgctttgcttcgctctacattgggctgaattaacgtgccctttcagggcttttacagcgttcagtaatcagtagtcagtaaacaaattaacatctcaacaaccaaacacctcaacgccacgaaagggttagctcgcaaggggtacaagggctgtaagcctgacatcattgaatagtcagggcgggtacacagtgtccgaacgcccccccctccccccttcaaagggagaatttgcagggatgaagctgacaactgacgccccccaacaactaaacagctaaacaaatcaacccaatttgaggtaataatgcttacctttgtacacgtctaaaatcaaatgtaaaaacgt .........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 acgtttttacatttgattttagacgtgtacaaaggtaagcattattacctcaaattgggttgatttgtttagctgtttagttgttggggggcgtcagttgtcagcttcatccctgcaaattctccctttgaaggggggaggggggggcgttcggacactgtgtacccgccctgactattcaatgatgtcaggcttacagcccttgtaccccttgcgagctaaccctttcgtggcgttgaggtgtttggttgttgagatgttaatttgtttactgactactgattactgaacgctgtaaaagccctgaaagggcacgttaattcagcccaatgtagagcgaagcaaagcgttgggaaaaagcattccccgatagagggctgaaagccta Mask Tandem Repeat Region ================================================ taggctttcagccctctatcggggaatgctttttcccaacgctttgcttcgctctacattgggctgaattaacgtgccctttcagggcttttacagcgttcagtaatcagtagtcagtaaacaaattaacatctcaacaaccaaacacctcaacgccacgaaagggttagctcgcaaggggtacaagggctgtaagcctgacatcattgaatagtcagggcgggtacacagtgtccgaacgcccccccctccccccttcaaagggagaatttgcagggatgaagctgacaactgacgccccccaacaactaaacagctaaacaaatcaacccaatttgaggtaataatgcttacctttgtacacgtctaaaatcaaatgtaaaaacgt Find is-nt database================================================ Query_seq: TF0958:TF0959|TF0958:TF0959:conserved hypothetical protein:periplasmic protease:->->:1004970..1005357 388 taggctttcagccctctatcggggaatgctttttcccaacgctttgcttcgctctacattgggctgaattaacgtgccctttcagggcttttacagcgttcagtaatcagtagtcagtaaacaaattaacatctcaacaaccaaacacctcaacgccacgaaagggttagctcgcaaggggtacaagggctgtaagcctgacatcattgaatagtcagggcgggtacacagtgtccgaacgcccccccctccccccttcaaagggagaatttgcagggatgaagctgacaactgacgccccccaacaactaaacagctaaacaaatcaacccaatttgaggtaataatgcttacctttgtacacgtctaaaatcaaatgtaaaaacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0958:TF0959|TF0958:TF0959:conserved hypothetical protein:periplasmic protease:->->:1004970..1005357 388 taggctttcagccctctatcggggaatgctttttcccaacgctttgcttcgctctacattgggctgaattaacgtgccctttcagggcttttacagcgttcagtaatcagtagtcagtaaacaaattaacatctcaacaaccaaacacctcaacgccacgaaagggttagctcgcaaggggtacaagggctgtaagcctgacatcattgaatagtcagggcgggtacacagtgtccgaacgcccccccctccccccttcaaagggagaatttgcagggatgaagctgacaactgacgccccccaacaactaaacagctaaacaaatcaacccaatttgaggtaataatgcttacctttgtacacgtctaaaatcaaatgtaaaaacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0958:TF0959|TF0958:TF0959:conserved hypothetical protein:periplasmic protease:->->:1004970..1005357 388 taggctttcagccctctatcggggaatgctttttcccaacgctttgcttcgctctacattgggctgaattaacgtgccctttcagggcttttacagcgttcagtaatcagtagtcagtaaacaaattaacatctcaacaaccaaacacctcaacgccacgaaagggttagctcgcaaggggtacaagggctgtaagcctgacatcattgaatagtcagggcgggtacacagtgtccgaacgcccccccctccccccttcaaagggagaatttgcagggatgaagctgacaactgacgccccccaacaactaaacagctaaacaaatcaacccaatttgaggtaataatgcttacctttgtacacgtctaaaatcaaatgtaaaaacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taggctttcagccctctatcggggaatgctttttcccaacgctttgcttcgctctacattgggctgaattaacgtgccctttcagggcttttacagcgttcagtaatcagtagtcagtaaacaaattaacatctcaacaaccaaacacctcaacgccacgaaagggttagctcgcaaggggtacaagggctgtaagcctgacatcattgaatagtcagggcgggtacacagtgtccgaacgcccccccctccccccttcaaagggagaatttgcagggatgaagctgacaactgacgccccccaacaactaaacagctaaacaaatcaacccaatttgaggtaataatgcttacctttgtacacgtctaaaatcaaatgtaaaaacgt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 18 End: 110 ................. M G E C F F P T L C F A L H W A E L T C P F R A F T A F S N Q ...................................................................................................................................................................................................................................................................................... Protein_Len: 40 Strand: + Start: 198 End: 317 ..................................................................................................................................................................................................... M T S L N S Q G G Y T V S E R P P L P P S K G E F A G M K L T T D A P Q Q L N S ....................................................................... Protein_Len: 33 Strand: - Start: 218 End: 316 ......................................................................................................................................................................................................................... P P Y V T D S R G G R G G E F P S N A P I F S V V S A G W C S F M ........................................................................ Protein_Len: 60 Strand: - Start: 103 End: 348 ...................................................................................................... A R L P Y L P Q L G S M M S Y D P R T C L T R V G G G G G K L P L I Q L S S A S L Q R G G V V L C S F L D V W N S T I M ........................................ Protein_Len: 31 Strand: - Start: 11 End: 103 .......... G E I P S H K K G V S Q K A R C Q A S N V H G K L A K V A N M ............................................................................................................................................................................................................................................................................................. taggctttcagccctctatcggggaatgctttttcccaacgctttgcttcgctctacattgggctgaattaacgtgccctttcagggcttttacagcgttcagtaatcagtagtcagtaaacaaattaacatctcaacaaccaaacacctcaacgccacgaaagggttagctcgcaaggggtacaagggctgtaagcctgacatcattgaatagtcagggcgggtacacagtgtccgaacgcccccccctccccccttcaaagggagaatttgcagggatgaagctgacaactgacgccccccaacaactaaacagctaaacaaatcaacccaatttgaggtaataatgcttacctttgtacacgtctaaaatcaaatgtaaaaacgt 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================================================ taggctttcagccctctatcggggaatgctttttcccaacgctttgcttcgctctacattgggctgaattaacgtgccctttcagggcttttacagcgttcagtaatcagtagtcagtaaacaaattaacatctcaacaaccaaacacctcaacgccacgaaagggttagctcgcaaggggtacaagggctgtaagcctgacatcattgaatagtcagggcgggtacacagtgtccgaacgcccccccctccccccttcaaagggagaatttgcagggatgaagctgacaactgacgccccccaacaactaaacagctaaacaaatcaacccaatttgaggtaataatgcttacctttgtacacgtctaaaatcaaatgtaaaaacgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 78 HP_score: -9.1 Tail_Score: -4.11484 Start: 76 End: 88 Full_Region: GGGCTGAATTAACGT GCCCT TTC AGGGC TTTTACAGCGTTCAG ...........................................................................GCCCTTTCAGGGC............................................................................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 55 HP_score: -3.3 Tail_Score: -3.88787 Start: 340 End: 355 Full_Region: ATCAACCCAATTTGA GGTAA TAATGC TTACC TTTGTACACGTCTAA ...................................................................................................................................................................................................................................................................................................................................................GGTAATAATGCTTACC................................. Find igs database================================================ Query_seq: TF0958:TF0959|TF0958:TF0959:conserved hypothetical protein:periplasmic protease:->->:1004970..1005357 388 taggctttcagccctctatcggggaatgctttttcccaacgctttgcttcgctctacattgggctgaattaacgtgccctttcagggcttttacagcgttcagtaatcagtagtcagtaaacaaattaacatctcaacaaccaaacacctcaacgccacgaaagggttagctcgcaaggggtacaagggctgtaagcctgacatcattgaatagtcagggcgggtacacagtgtccgaacgcccccccctccccccttcaaagggagaatttgcagggatgaagctgacaactgacgccccccaacaactaaacagctaaacaaatcaacccaatttgaggtaataatgcttacctttgtacacgtctaaaatcaaatgtaaaaacgt Intra-Species Hit: Count: 4 Min: 1 Max: 388 Len: 388 Subject: tfor_TF0958_TF0959|conserved hypothetical protein:periplasmic protease|POSITIVE:POSITIVE|[1004970,1005357]|388 HSP 1 e-value: 1.0E-134 bit: 478.0 Len: 241 Query Start:1 Query End:241 Subject Strand: POSITIVE Subject Start: 1 Subject End: 241 taggctttcagccctctatcggggaatgctttttcccaacgctttgcttcgctctacattgggctgaattaacgtgccctttcagggcttttacagcgttcagtaatcagtagtcagtaaacaaattaacatctcaacaaccaaacacctcaacgccacgaaagggttagctcgcaaggggtacaagggctgtaagcctgacatcattgaatagtcagggcgggtacacagtgtccgaacg................................................................................................................................................... taggctttcagccctctatcggggaatgctttttcccaacgctttgcttcgctctacattgggctgaattaacgtgccctttcagggcttttacagcgttcagtaatcagtagtcagtaaacaaattaacatctcaacaaccaaacacctcaacgccacgaaagggttagctcgcaaggggtacaagggctgtaagcctgacatcattgaatagtcagggcgggtacacagtgtccgaacg................................................................................................................................................... HSP 2 e-value: 8.0E-69 bit: 262.0 Len: 132 Query Start:257 Query End:388 Subject Strand: POSITIVE Subject Start: 257 Subject End: 388 ................................................................................................................................................................................................................................................................ttcaaagggagaatttgcagggatgaagctgacaactgacgccccccaacaactaaacagctaaacaaatcaacccaatttgaggtaataatgcttacctttgtacacgtctaaaatcaaatgtaaaaacgt ................................................................................................................................................................................................................................................................ttcaaagggagaatttgcagggatgaagctgacaactgacgccccccaacaactaaacagctaaacaaatcaacccaatttgaggtaataatgcttacctttgtacacgtctaaaatcaaatgtaaaaacgt Subject: tfor_TF2438_TF2439|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2616218,2616519]|302 HSP 1 e-value: 1.0E-21 bit: 105.0 Len: 117 Query Start:31 Query End:147 Subject Strand: POSITIVE Subject Start: 153 Subject End: 269 ..............................ttttcccaacgctttgcttcgctctacattgggctgaattaacgtgccctttcagggcttttacagcgttcagtaatcagtagtcagtaaacaaattaacatctcaacaaccaaaca................................................................................................................................................................................................................................................. ..............................ttttcccaacgcttcgcttcgctacacattgggctgaattaatgcgccctttcagggcttttacagcagtcagtgttcagcggtcagcaaacaaatcaacccctcaacaactaaaca................................................................................................................................................................................................................................................. Subject: tfor_TF1762_TF1763|hypothetical protein:K+-dependent Na+/Ca+ exchanger related-protein|POSITIVE:POSITIVE|[1899709,1900545]|837 HSP 1 e-value: 1.0E-21 bit: 105.0 Len: 69 Query Start:30 Query End:98 Subject Strand: POSITIVE Subject Start: 49 Subject End: 117 .............................tttttcccaacgctttgcttcgctctacattgggctgaattaacgtgccctttcagggcttttacagcg.................................................................................................................................................................................................................................................................................................. .............................tttttcccaacgcttcgcttcgctgcacattgggctgaattaacgcgccctttcagggcttttacagcg.................................................................................................................................................................................................................................................................................................. HSP 2 e-value: 2.0E-7 bit: 58.0 Len: 77 Query Start:128 Query End:204 Subject Strand: POSITIVE Subject Start: 174 Subject End: 250 ...............................................................................................................................aacatctcaacaaccaaacacctcaacgccacgaaagggttagctcgcaaggggtacaagggctgtaagcctgacat........................................................................................................................................................................................ ...............................................................................................................................aacatctcaacacctcaacacctcaacgccccgaaggggttagctcgcccgaggcccaagggctgaaagcccgacat........................................................................................................................................................................................ Subject: tfor_TF2998_TF2999|surface antigen BspA:conserved hypothetical protein|POSITIVE:POSITIVE|[3215212,3215705]|494 HSP 1 e-value: 4.0E-9 bit: 63.9 Len: 80 Query Start:31 Query End:110 Subject Strand: POSITIVE Subject Start: 245 Subject End: 324 ..............................ttttcccaacgctttgcttcgctctacattgggctgaattaacgtgccctttcagggcttttacagcgttcagtaatcag...................................................................................................................................................................................................................................................................................... ..............................ttttcccaacgcttcgcttcgctacgcattgggctgaattattacgccctttcagggctcttacagctgtcagcaatcag...................................................................................................................................................................................................................................................................................... HSP 2 e-value: 2.0E-8 bit: 61.9 Len: 71 Query Start:134 Query End:204 Subject Strand: POSITIVE Subject Start: 333 Subject End: 402 .....................................................................................................................................tcaacaaccaaacacctcaacgccacgaaagggttagctcgcaaggggtacaagggctgtaagcctgacat........................................................................................................................................................................................ .....................................................................................................................................tcaacacctaaacccctcaacgccccgaaggggttagctcgc-atgggcacaagggctgaaagcctgacat........................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGCUUUCAGCCCUCUAUCGGGGAAUGCUUUUUCCCAACGCUUUGCUUCGCUCUACAUUGGGCUGAAUUAACGUGCCCUUUCAGGGCUUUUACAGCGUUCAGUAAUCAGUAGUCAGUAAACAAAUUAACAUCUCAACAACCAAACACCUCAACGCCACGAAAGGGUUAGCUCGCAAGGGGUACAAGGGCUGUAAGCCUGACAUCAUUGAAUAGUCAGGGCGGGUACACAGUGUCCGAACGCCCCCCCCUCCCCCCUUCAAAGGGAGAAUUUGCAGGGAUGAAGCUGACAACUGACGCCCCCCAACAACUAAACAGCUAAACAAAUCAACCCAAUUUGAGGUAAUAAUGCUUACCUUUGUACACGUCUAAAAUCAAAUGUAAAAACGU (((((.((((((((......((((((.....))))))...((........))........)))))))).......((((.....))))...(((.((((.((((..(((((.((......)).......((((((...................(((.(....))))......((((((((.....((((......((((((...........)))))).(((..((...))..)))...))))))))(((((.........)))))...)))).))))))..)))))..)))))))).......................................(((((((......))))))).)))...)))))................... (-105.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGUUUUUACAUUUGAUUUUAGACGUGUACAAAGGUAAGCAUUAUUACCUCAAAUUGGGUUGAUUUGUUUAGCUGUUUAGUUGUUGGGGGGCGUCAGUUGUCAGCUUCAUCCCUGCAAAUUCUCCCUUUGAAGGGGGGAGGGGGGGGCGUUCGGACACUGUGUACCCGCCCUGACUAUUCAAUGAUGUCAGGCUUACAGCCCUUGUACCCCUUGCGAGCUAACCCUUUCGUGGCGUUGAGGUGUUUGGUUGUUGAGAUGUUAAUUUGUUUACUGACUACUGAUUACUGAACGCUGUAAAAGCCCUGAAAGGGCACGUUAAUUCAGCCCAAUGUAGAGCGAAGCAAAGCGUUGGGAAAAAGCAUUCCCCGAUAGAGGGCUGAAAGCCUA .....................(((((......((.((((((.....((((......)))).....)))))).))(..(((((...((((((..(((((.(((.....(..((((.(...((((((((....)))))))).).))))..)....))))))).)..))).))).)))))..)....))))).(((((.((((((((........(((.(((...((((((((.(((.....((((((..((.(((.((..((((..........))))..))))).))..))))))......))).))))))))...))).......((((((((...((...))...)))))))).....)))..........)))))))).))))).. (-128.67) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 861 90 41 124 75 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 861 90 41 117 68 tfor:TF0539|5end_hypothetical_protein_566884..567114_POSITIVE 824 98 51 185 138 tfor:TF2517|5end_hypothetical_protein_2695089..2695319_POSITIVE 747 90 41 124 75 tfor:TF0534|5end_hypothetical_protein_559509..559739_POSITIVE 742 80 31 103 53 tfor:TF1716|5end_hypothetical_protein_1837442..1837672_POSITIVE 735 70 21 97 44 tfor:TF0679|5end_hypothetical_protein_721155..721385_POSITIVE 733 110 61 220 171 tfor:TF0828|5end_hypothetical_protein_887090..887320_POSITIVE 700 110 61 211 161 tfor:TF2824|5end_nucleoside-transporting_protein_nupG_3014701..3014931_POSITIVE 694 110 61 210 161 tfor:TF1183|5end_hypothetical_protein_1268391..1268621_POSITIVE 688 48 3 183 135 tfor:TF2478|5end_hypothetical_protein_2655375..2655605_POSITIVE 685 89 41 64 15 tfor:TF0678|5end_hypothetical_protein_721103..721333_POSITIVE 650 47 1 189 139 tfor:TF2036|5end_possible_pyruvate_formate-lyase_activating_enzyme_2196302..2196532_POSITIVE 643 98 51 225 178 tfor:TF1184|5end_hypothetical_protein_1269004..1269234_POSITIVE 631 110 61 214 165 tfor:TF1186|5end_hypothetical_protein_1269568..1269798_POSITIVE 630 47 1 84 33 tfor:TF2191|5end_hypothetical_protein_2365934..2366164_POSITIVE 630 47 1 219 168 tfor:TF0823|5end_conserved_hypothetical_protein_880660..880890_POSITIVE 605 50 1 68 13 tfor:TF3107|5end_hypothetical_protein_3338459..3338689_POSITIVE 599 268 221 215 154 tfor:TF0685|5end_hypothetical_protein_730852..731082_POSITIVE 598 79 33 200 143 tfor:TF1406|5end_transposase_1481758..1481988_POSITIVE 575 89 41 78 26 tfor:TF0822|5end_hypothetical_protein_880487..880717_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 747 90 41 54 5 tfor:TF0533|3end_hypothetical_protein_559519..559669_POSITIVE 696 89 41 82 34 tfor:TF2840|3end_hypothetical_protein_3031289..3031439_POSITIVE 665 289 243 59 12 tfor:TF1169|3end_lipoprotein_ABC_transporter,_permease_component_1251573..1251723_POSITIVE 662 110 61 91 42 tfor:TF1182|3end_hypothetical_protein_1268938..1269088_POSITIVE 631 110 61 129 80 tfor:TF1185|3end_hypothetical_protein_1269563..1269713_POSITIVE 605 50 1 137 82 tfor:TF3106|3end_hypothetical_protein_3338608..3338758_POSITIVE 573 289 242 84 45 tfor:TF1588|3end_hypothetical_protein_1702560..1702710_POSITIVE 560 289 242 67 21 tfor:TF1592|3end_hypothetical_protein_1708557..1708707_POSITIVE 555 89 41 61 9 tfor:TF0820|3end_hypothetical_protein_879942..880092_POSITIVE 517 55 20 42 3 tfor:TF0370|3end_hypothetical_protein_386317..386467_POSITIVE 509 289 245 51 6 tfor:TF2171|3end_hypothetical_protein_2345792..2345942_POSITIVE 504 47 1 114 62 tfor:TF2547|3end_hypothetical_protein_2730947..2731097_POSITIVE 497 298 254 69 25 tfor:TF1166|3end_ABC_transporter,_permease_component_1248603..1248753_POSITIVE 491 50 1 144 88 tfor:TF1405|3end_conserved_hypothetical_protein_1481819..1481969_POSITIVE 488 298 251 63 4 tfor:TF1590|3end_hypothetical_protein_1706043..1706193_POSITIVE 459 240 191 133 70 tfor:TF1762|3end_hypothetical_protein_1899648..1899798_POSITIVE 459 240 191 64 1 tfor:TF1761|3end_hypothetical_protein_1899579..1899729_POSITIVE 452 168 122 45 1 tfor:TF1657|3end_lauroyl/myristoyl_acyltransferase_1773407..1773557_POSITIVE 441 330 283 61 15 tfor:TF2839|3end_ATP-dependent_exodeoxyribonuclease_3031035..3031185_POSITIVE 403 227 186 35 3 tfor:TF1839|3end_conserved_hypothetical_protein_1989699..1989849_POSITIVE