Origin IGS: attttcgataatatatgataatcaaaaaaaagtaaataggcattttaaaaggccgtgtttaatttaaccgcaagaggtgcaaagaacgctaaatattatctataacttatctacaacttatctttacccataaatcggggtttccaaaggggtatcccctttggcagcgcgaggaaaaggg .........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 cccttttcctcgcgctgccaaaggggatacccctttggaaaccccgatttatgggtaaagataagttgtagataagttatagataatatttagcgttctttgcacctcttgcggttaaattaaacacggccttttaaaatgcctatttacttttttttgattatcatatattatcgaaaat Mask Tandem Repeat Region ================================================ attttcgataatatatgataatcaaaaaaaagtaaataggcattttaaaaggccgtgtttaatttaaccgcaagaggtgcaaagaacgctaaatattatctataacttatctacaacttatctttacccataaatcggggtttccaaaggggtatcccctttggcagcgcgaggaaaaggg Find is-nt database================================================ Query_seq: TDE2264:TDE2265|TDE2264:TDE2265:ABC transporter, ATP-binding/permease protein:hypothetical protein:<-->:2302124..2302304 181 attttcgataatatatgataatcaaaaaaaagtaaataggcattttaaaaggccgtgtttaatttaaccgcaagaggtgcaaagaacgctaaatattatctataacttatctacaacttatctttacccataaatcggggtttccaaaggggtatcccctttggcagcgcgaggaaaaggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2264:TDE2265|TDE2264:TDE2265:ABC transporter, ATP-binding/permease protein:hypothetical protein:<-->:2302124..2302304 181 attttcgataatatatgataatcaaaaaaaagtaaataggcattttaaaaggccgtgtttaatttaaccgcaagaggtgcaaagaacgctaaatattatctataacttatctacaacttatctttacccataaatcggggtttccaaaggggtatcccctttggcagcgcgaggaaaaggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2264:TDE2265|TDE2264:TDE2265:ABC transporter, ATP-binding/permease protein:hypothetical protein:<-->:2302124..2302304 181 attttcgataatatatgataatcaaaaaaaagtaaataggcattttaaaaggccgtgtttaatttaaccgcaagaggtgcaaagaacgctaaatattatctataacttatctacaacttatctttacccataaatcggggtttccaaaggggtatcccctttggcagcgcgaggaaaaggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attttcgataatatatgataatcaaaaaaaagtaaataggcattttaaaaggccgtgtttaatttaaccgcaagaggtgcaaagaacgctaaatattatctataacttatctacaacttatctttacccataaatcggggtttccaaaggggtatcccctttggcagcgcgaggaaaaggg Predict ORF larger than 30AA ================================================ attttcgataatatatgataatcaaaaaaaagtaaataggcattttaaaaggccgtgtttaatttaaccgcaagaggtgcaaagaacgctaaatattatctataacttatctacaacttatctttacccataaatcggggtttccaaaggggtatcccctttggcagcgcgaggaaaaggg 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: 83 Start: 8 End: 37 .......ATTTACTTTTTTTTGATTATCATATATTAT................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 15 End: 44 ..............AATGCCTATTTACTTTTTTTTGATTATCAT......................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attttcgataatatatgataatcaaaaaaaagtaaataggcattttaaaaggccgtgtttaatttaaccgcaagaggtgcaaagaacgctaaatattatctataacttatctacaacttatctttacccataaatcggggtttccaaaggggtatcccctttggcagcgcgaggaaaaggg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 73 HP_score: -8.2 Tail_Score: -3.53012 Start: 149 End: 159 Full_Region: ATCGGGGTTTCCAAA GGGG TAT CCCC TTTGGCAGCGCGAGG ....................................................................................................................................................GGGGTATCCCC...................... Find igs database================================================ Query_seq: TDE2264:TDE2265|TDE2264:TDE2265:ABC transporter, ATP-binding/permease protein:hypothetical protein:<-->:2302124..2302304 181 attttcgataatatatgataatcaaaaaaaagtaaataggcattttaaaaggccgtgtttaatttaaccgcaagaggtgcaaagaacgctaaatattatctataacttatctacaacttatctttacccataaatcggggtttccaaaggggtatcccctttggcagcgcgaggaaaaggg Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: NC_002967_TDE2264_TDE2265|ABC transporter, ATP-binding/permease protein:hypothetical protein|NEGATIVE:POSITIVE|[2302124,2302304]|181 HSP 1 e-value: 4.0E-84 bit: 311.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 attttcgataatatatgataatcnnnnnnnngtaaataggcattttaaaaggccgtgtttaatttaaccgcaagaggtgcaaagaacgctaaatattatctataacttatctacaacttatctttacccataaatcggggtttccaaaggggtatcccctttggcagcgcgaggaaaaggg attttcgataatatatgataatcaaaaaaaagtaaataggcattttaaaaggccgtgtttaatttaaccgcaagaggtgcaaagaacgctaaatattatctataacttatctacaacttatctttacccataaatcggggtttccaaaggggtatcccctttggcagcgcgaggaaaaggg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUUCGAUAAUAUAUGAUAAUCAAAAAAAAGUAAAUAGGCAUUUUAAAAGGCCGUGUUUAAUUUAACCGCAAGAGGUGCAAAGAACGCUAAAUAUUAUCUAUAACUUAUCUACAACUUAUCUUUACCCAUAAAUCGGGGUUUCCAAAGGGGUAUCCCCUUUGGCAGCGCGAGGAAAAGGG ......(((((((((.((((((................(((..........)))((((((......(((......))).....)))))).....))))))))))..))))).....(((.(((((.(((.......)))(((.(((((((((...))))))))).)))..))))).))).. (-42.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCUUUUCCUCGCGCUGCCAAAGGGGAUACCCCUUUGGAAACCCCGAUUUAUGGGUAAAGAUAAGUUGUAGAUAAGUUAUAGAUAAUAUUUAGCGUUCUUUGCACCUCUUGCGGUUAAAUUAAACACGGCCUUUUAAAAUGCCUAUUUACUUUUUUUUGAUUAUCAUAUAUUAUCGAAAAU .............(((((((((((((...))))))))).....(((......(((((((((...((..((((((............))))))))..))))))).)).....)))............)))).......................((((((((...........)))))))). (-36.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 950 170 121 199 150 NC_002967:TDE1060|5end_hypothetical_protein_1086519..1086749_POSITIVE 864 100 51 191 142 NC_002967:TDE2264|5end_ABC_transporter,_ATP-binding/permease_protein_2302033..2302263_NEGATIVE 777 173 136 117 80 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 694 170 135 231 194 NC_002967:TDE0403|5end_hypothetical_protein_454433..454663_POSITIVE 421 170 121 123 78 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 417 180 140 217 173 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 409 90 48 226 187 NC_002967:TDE1061|5end_ABC_transporter,_ATP-binding/permease_protein,_HlyB_family_1086646..1086876_POSITIVE 394 89 51 217 183 NC_002967:TDE0438|5end_queuine_tRNA-ribosyltransferase_494811..495041_NEGATIVE 371 180 135 59 14 NC_002967:TDE2141|5end_hypothetical_protein_2175768..2175998_NEGATIVE 348 168 122 114 65 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 347 89 52 130 87 NC_002967:TDE2480|5end_heat_shock_protein_90_2505288..2505518_NEGATIVE 341 97 56 158 115 NC_002967:TDE0597|5end_hypothetical_protein_637212..637442_NEGATIVE 338 175 137 96 57 NC_002967:TDE0618|5end_hypothetical_protein_650355..650585_NEGATIVE 338 175 137 224 185 NC_002967:TDE0617|5end_hypothetical_protein_650227..650457_NEGATIVE 337 168 121 216 176 NC_002967:TDE1058|5end_hypothetical_protein_1086366..1086596_NEGATIVE 333 167 142 28 1 NC_002967:TDE0827|5end_hypothetical_protein_848053..848283_NEGATIVE 323 89 50 191 155 NC_002967:TDE2435|5end_hypothetical_protein_2466462..2466692_NEGATIVE 314 180 132 223 173 NC_002967:TDE2419|5end_hypothetical_protein_2444769..2444999_NEGATIVE 314 170 121 59 3 NC_002967:TDE2209|5end_CarB_family_protein_2247589..2247819_POSITIVE 309 168 134 222 184 NC_002967:TDE2595|5end_hypothetical_protein_2631080..2631310_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 574 173 136 53 15 NC_002967:TDE1982|3end_hypothetical_protein_1992511..1992661_NEGATIVE 371 180 157 24 2 NC_002967:TDE0828|3end_glucose-inhibited_division_protein_A_848283..848433_NEGATIVE 347 89 52 66 23 NC_002967:TDE2481|3end_hypothetical_protein_2505352..2505502_NEGATIVE 343 170 146 28 1 NC_002967:TDE1891|3end_hypothetical_protein_1912050..1912200_POSITIVE 339 179 140 102 56 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 314 180 134 75 25 NC_002967:TDE1500|3end_hypothetical_protein_1546763..1546913_NEGATIVE 312 178 137 72 27 NC_002967:TDE0944|3end_hypothetical_protein_967037..967187_POSITIVE 303 180 139 72 35 NC_002967:TDE1055|3end_MATE_efflux_family_protein_1082982..1083132_NEGATIVE 302 175 137 101 52 NC_002967:TDE1066|3end_hypothetical_protein_1094335..1094485_NEGATIVE 297 90 64 54 29 NC_002967:TDE1529|3end_hypothetical_protein_1575067..1575217_POSITIVE 297 89 42 55 7 NC_002967:TDE0974|3end_hypothetical_protein_998875..999025_POSITIVE 293 174 138 151 104 NC_002967:TDE2081|3end_hypothetical_protein_2112529..2112679_POSITIVE 292 173 135 140 101 NC_002967:TDE0859|3end_hypothetical_protein_881106..881256_POSITIVE 284 167 121 143 103 NC_002967:TDE1949|3end_ABC_transporter,_ATP-binding_protein_1964544..1964694_NEGATIVE 282 180 136 129 79 NC_002967:TDE1914|3end_Holliday_junction_DNA_helicase_RuvB_1930889..1931039_NEGATIVE 281 163 127 143 112 NC_002967:TDE2528|3end_hypothetical_protein_2556220..2556370_NEGATIVE 281 160 129 34 3 NC_002967:TDE0026|3end_TraB_family_protein_31826..31976_NEGATIVE 280 173 136 125 62 NC_002967:TDE2205|3end_enoate_reductase,_putative_2242575..2242725_NEGATIVE 280 161 136 64 43 NC_002967:TDE1693|3end_hypothetical_protein_1748438..1748588_NEGATIVE 274 179 135 97 49 NC_002967:TDE2582|3end_GGDEF_domain_protein_2616164..2616314_POSITIVE