Origin IGS: acccccctccaaaaataaaaataggtatctcctaaatttatcggtatttaaaataagggctttagaaaaagcctttatttcaatttaccatttaccttaaaatacagattaaaatacaaaaagttacataaaagagccttacttaaaacttattgacaaacaaaaaaaaagaacctataatacttttctgaggttcaaa .........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 tttgaacctcagaaaagtattataggttctttttttttgtttgtcaataagttttaagtaaggctcttttatgtaactttttgtattttaatctgtattttaaggtaaatggtaaattgaaataaaggctttttctaaagcccttattttaaataccgataaatttaggagatacctatttttatttttggaggggggt Mask Tandem Repeat Region ================================================ acccccctccaaaaataaaaataggtatctcctaaatttatcggtatttaaaataagggctttagaaaaagcctttatttcaatttaccatttaccttaaaatacagattaaaatacaaaaagttacataaaagagccttacttaaaacttattgacaaacaaaaaaaaagaacctataatacttttctgaggttcaaa Find is-nt database================================================ Query_seq: TDE0119:TDE0120|TDE0119:TDE0120:flagellar protein FliS:hypothetical protein:<-->:137589..137787 199 acccccctccaaaaataaaaataggtatctcctaaatttatcggtatttaaaataagggctttagaaaaagcctttatttcaatttaccatttaccttaaaatacagattaaaatacaaaaagttacataaaagagccttacttaaaacttattgacaaacaaaaaaaaagaacctataatacttttctgaggttcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0119:TDE0120|TDE0119:TDE0120:flagellar protein FliS:hypothetical protein:<-->:137589..137787 199 acccccctccaaaaataaaaataggtatctcctaaatttatcggtatttaaaataagggctttagaaaaagcctttatttcaatttaccatttaccttaaaatacagattaaaatacaaaaagttacataaaagagccttacttaaaacttattgacaaacaaaaaaaaagaacctataatacttttctgaggttcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0119:TDE0120|TDE0119:TDE0120:flagellar protein FliS:hypothetical protein:<-->:137589..137787 199 acccccctccaaaaataaaaataggtatctcctaaatttatcggtatttaaaataagggctttagaaaaagcctttatttcaatttaccatttaccttaaaatacagattaaaatacaaaaagttacataaaagagccttacttaaaacttattgacaaacaaaaaaaaagaacctataatacttttctgaggttcaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acccccctccaaaaataaaaataggtatctcctaaatttatcggtatttaaaataagggctttagaaaaagcctttatttcaatttaccatttaccttaaaatacagattaaaatacaaaaagttacataaaagagccttacttaaaacttattgacaaacaaaaaaaaagaacctataatacttttctgaggttcaaa Predict ORF larger than 30AA ================================================ acccccctccaaaaataaaaataggtatctcctaaatttatcggtatttaaaataagggctttagaaaaagcctttatttcaatttaccatttaccttaaaatacagattaaaatacaaaaagttacataaaagagccttacttaaaacttattgacaaacaaaaaaaaagaacctataatacttttctgaggttcaaa 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: 152 End: 181 .......................................................................................................................................................ATTGACAAACAAAAAAAAAGAACCTATAAT.................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acccccctccaaaaataaaaataggtatctcctaaatttatcggtatttaaaataagggctttagaaaaagcctttatttcaatttaccatttaccttaaaatacagattaaaatacaaaaagttacataaaagagccttacttaaaacttattgacaaacaaaaaaaaagaacctataatacttttctgaggttcaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 75 HP_score: -3.4 Tail_Score: -5.61881 Start: 22 End: 34 Full_Region: aaataccgataaatt tagg agata ccta tttttatttttggag .....................taggagataccta..................................................................................................................................................................... TransTerm Strand: + Conf: 85 HP_score: -10.0 Tail_Score: -3.72765 Start: 48 End: 83 Full_Region: TAAATTTATCGGTAT TTAAAATAAGGGCTTT AGAA AAAGCCTTTATTTCAA TTTACCATTTACCTT ...............................................TTAAAATAAGGGCTTTAGAAAAAGCCTTTATTTCAA.................................................................................................................... TransTerm Strand: + Conf: 83 HP_score: -9.0 Tail_Score: -3.85567 Start: 54 End: 77 Full_Region: TATCGGTATTTAAAA TAAGGGCTTT AGAA AAAGCCTTTA TTTCAATTTACCATT .....................................................TAAGGGCTTTAGAAAAAGCCTTTA.......................................................................................................................... TransTerm Strand: + Conf: 78 HP_score: -7.6 Tail_Score: -4.53439 Start: 58 End: 73 Full_Region: GGTATTTAAAATAAG GGCTTT AGAA AAAGCC TTTATTTCAATTTAC .........................................................GGCTTTAGAAAAAGCC.............................................................................................................................. Find igs database================================================ Query_seq: TDE0119:TDE0120|TDE0119:TDE0120:flagellar protein FliS:hypothetical protein:<-->:137589..137787 199 acccccctccaaaaataaaaataggtatctcctaaatttatcggtatttaaaataagggctttagaaaaagcctttatttcaatttaccatttaccttaaaatacagattaaaatacaaaaagttacataaaagagccttacttaaaacttattgacaaacaaaaaaaaagaacctataatacttttctgaggttcaaa Intra-Species Hit: Count: 1 Min: 1 Max: 199 Len: 199 Subject: NC_002967_TDE0119_TDE0120|flagellar protein FliS:hypothetical protein|NEGATIVE:POSITIVE|[137589,137787]|199 HSP 1 e-value: 8.0E-55 bit: 214.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 108 acccccctccaaaaataaaaataggtatctcctaaatttatcggtatttaaaataagggctttagaaaaagcctttatttcaatttaccatttaccttaaaatacaga........................................................................................... acccccctccaaaaataaaaataggtatctcctaaatttatcggtatttaaaataagggctttagaaaaagcctttatttcaatttaccatttaccttaaaatacaga........................................................................................... HSP 2 e-value: 1.0E-7 bit: 58.0 Len: 29 Query Start:171 Query End:199 Subject Strand: POSITIVE Subject Start: 171 Subject End: 199 ..........................................................................................................................................................................gaacctataatacttttctgaggttcaaa ..........................................................................................................................................................................gaacctataatacttttctgaggttcaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCCCCCUCCAAAAAUAAAAAUAGGUAUCUCCUAAAUUUAUCGGUAUUUAAAAUAAGGGCUUUAGAAAAAGCCUUUAUUUCAAUUUACCAUUUACCUUAAAAUACAGAUUAAAAUACAAAAAGUUACAUAAAAGAGCCUUACUUAAAACUUAUUGACAAACAAAAAAAAAGAACCUAUAAUACUUUUCUGAGGUUCAAA .....((((..((((.....((((((.(((............((((.((.(((((((((((((....))))))))))))).))..))))...........................(((.(((((.....................))))).)))..............))))))))).....))))..))))...... (-33.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGAACCUCAGAAAAGUAUUAUAGGUUCUUUUUUUUUGUUUGUCAAUAAGUUUUAAGUAAGGCUCUUUUAUGUAACUUUUUGUAUUUUAAUCUGUAUUUUAAGGUAAAUGGUAAAUUGAAAUAAAGGCUUUUUCUAAAGCCCUUAUUUUAAAUACCGAUAAAUUUAGGAGAUACCUAUUUUUAUUUUUGGAGGGGGGU ......((((..(((((((..((((((...((((((..(((((((...(((((....(((((.....)))))..)))))....((((((((........))))))))...((((..(((((((((.((((((....)))))).))))))))).)))))))))))..)))))).))))))...))))))).))))..... (-47.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 785 50 1 141 92 NC_002967:TDE0119|5end_flagellar_protein_FliS_137498..137728_NEGATIVE 264 100 55 106 61 NC_002967:TDE2116|5end_hypothetical_protein_2147708..2147938_NEGATIVE 245 65 24 57 17 NC_002967:TDE0071|5end_peptidase,_U32_family_78602..78832_POSITIVE 234 67 21 126 90 NC_002967:TDE1655|5end_hypothetical_protein_1704958..1705188_POSITIVE 234 64 28 33 5 NC_002967:TDE1649|5end_hypothetical_protein_1697437..1697667_NEGATIVE 230 38 1 107 61 NC_002967:TDE1541|5end_metallo-beta-lactamase_family_protein_1584898..1585128_POSITIVE 227 63 23 64 22 NC_002967:TDE2750|5end_GTP-binding_protein_HflX,_truncation_2806033..2806263_POSITIVE 219 45 3 116 63 NC_002967:TDE2059|5end_hypothetical_protein_2086509..2086739_NEGATIVE 214 45 2 123 59 NC_002967:TDE2514|5end_serine/threonine_protein_phosphatase_family_protein_2540532..2540762_NEGATIVE 213 65 27 142 102 NC_002967:TDE0941|5end_NLP/P60_family_protein_964102..964332_NEGATIVE 213 66 21 121 84 NC_002967:TDE0199|5end_hypothetical_protein_234708..234938_NEGATIVE 209 81 53 146 113 NC_002967:TDE1543|5end_conserved_hypothetical_protein_TIGR00247_1586068..1586298_POSITIVE 209 93 55 175 139 NC_002967:TDE0750|5end_magnesium_chelatase,_subunit_D/I_family_790135..790365_NEGATIVE 207 88 42 184 145 NC_002967:TDE2267|5end_HRDC_domain_protein_2304464..2304694_NEGATIVE 207 90 42 172 129 NC_002967:TDE1499|5end_adenylosuccinate_lyase,_putative_1545266..1545496_POSITIVE 205 60 14 221 169 NC_002967:TDE0761|5end_protease_complex-associated_polypeptide_799969..800199_POSITIVE 204 120 80 164 120 NC_002967:TDE1699|5end_hypothetical_protein_1757920..1758150_NEGATIVE 203 139 96 211 172 NC_002967:TDE2072|5end_hypothetical_protein_2098813..2099043_POSITIVE 203 62 24 191 149 NC_002967:TDE1708|5end_apolipoprotein_N-acyltransferase_1764822..1765052_NEGATIVE 202 80 33 161 109 NC_002967:TDE1753|5end_UDP-glucose_4-epimerase_1806540..1806770_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 234 64 28 93 65 NC_002967:TDE1650|3end_ABC_transporter,_ATP-binding_protein_1697377..1697527_NEGATIVE 230 38 1 77 31 NC_002967:TDE1540|3end_hypothetical_protein_1584948..1585098_POSITIVE 209 81 53 126 93 NC_002967:TDE1542|3end_hypothetical_protein_1586128..1586278_POSITIVE 208 77 31 68 18 NC_002967:TDE0479|3end_hydroxylamine_reductase_535029..535179_NEGATIVE 207 90 42 80 37 NC_002967:TDE1498|3end_hypothetical_protein_1545254..1545404_POSITIVE 206 80 31 111 64 NC_002967:TDE1499|3end_adenylosuccinate_lyase,_putative_1546788..1546938_POSITIVE 203 81 53 106 74 NC_002967:TDE1443|3end_RNA_methyltransferase,_TrmH_family,_group_3_1488809..1488959_NEGATIVE 202 80 33 64 12 NC_002967:TDE1754|3end_desulfoferrodoxin/neelaredoxin_1806637..1806787_NEGATIVE 201 44 3 134 105 NC_002967:TDE0866|3end_hypothetical_protein_888629..888779_POSITIVE 200 75 41 61 19 NC_002967:TDE1590|3end_aminotransferase,_DegT/DnrJ/EryC1/StrS_family_1638621..1638771_POSITIVE 200 30 2 36 11 NC_002967:TDE1329|3end_ATPase,_AAA_family_1365346..1365496_POSITIVE 200 150 115 149 112 NC_002967:TDE0654|3end_peptidase,_M20/M25/M40_family_690858..691008_POSITIVE 199 78 57 36 15 NC_002967:TDE2433|3end_treponemal_membrane_protein,_putative_2463265..2463415_POSITIVE 199 131 93 49 16 NC_002967:TDE1341|3end_hypothetical_protein_1378525..1378675_POSITIVE 198 77 36 58 7 NC_002967:TDE1629|3end_dihydrolipoamide_dehydrogenase_1677153..1677303_NEGATIVE 197 49 4 105 70 NC_002967:TDE1301|3end_DNA_repair_protein_RecN_1337431..1337581_NEGATIVE 197 108 62 64 11 NC_002967:TDE0078|3end_glycine_reductase_complex_selenoprotein_GrdB1_88745..88895_NEGATIVE 196 87 41 79 35 NC_002967:TDE2668|3end_serine_hydroxymethyltransferase_2704546..2704696_NEGATIVE 195 67 26 133 75 NC_002967:TDE2607|3end_hypothetical_protein_2649334..2649484_POSITIVE 195 76 37 69 31 NC_002967:TDE0938|3end_hypothetical_protein_960963..961113_NEGATIVE