Origin IGS: tctttgaaaatcctttaggcagccgcttgtctaaaagaaaagcccttgcagcttaatcaaaaactgcaagggcttttttcttttacttaaattcttaatgtaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattacattaagaatttaagtaaaagaaaaaagcccttgcagtttttgattaagctgcaagggcttttcttttagacaagcggctgcctaaaggattttcaaaga Mask Tandem Repeat Region ================================================ tctttgaaaatcctttaggcagccgcttgtctaaaagaaaagcccttgcagcttaatcaaaaactgcaagggcttttttcttttacttaaattcttaatgtaatt Find is-nt database================================================ Query_seq: TDE1487:TDE1488|TDE1487:TDE1488:conserved hypothetical protein TIGR01033:glyceraldehyde-3-phosphate dehydrogenase, type I:-><-:1531589..1531693 105 tctttgaaaatcctttaggcagccgcttgtctaaaagaaaagcccttgcagcttaatcaaaaactgcaagggcttttttcttttacttaaattcttaatgtaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE1487:TDE1488|TDE1487:TDE1488:conserved hypothetical protein TIGR01033:glyceraldehyde-3-phosphate dehydrogenase, type I:-><-:1531589..1531693 105 tctttgaaaatcctttaggcagccgcttgtctaaaagaaaagcccttgcagcttaatcaaaaactgcaagggcttttttcttttacttaaattcttaatgtaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE1487:TDE1488|TDE1487:TDE1488:conserved hypothetical protein TIGR01033:glyceraldehyde-3-phosphate dehydrogenase, type I:-><-:1531589..1531693 105 tctttgaaaatcctttaggcagccgcttgtctaaaagaaaagcccttgcagcttaatcaaaaactgcaagggcttttttcttttacttaaattcttaatgtaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctttgaaaatcctttaggcagccgcttgtctaaaagaaaagcccttgcagcttaatcaaaaactgcaagggcttttttcttttacttaaattcttaatgtaatt Predict ORF larger than 30AA ================================================ tctttgaaaatcctttaggcagccgcttgtctaaaagaaaagcccttgcagcttaatcaaaaactgcaagggcttttttcttttacttaaattcttaatgtaatt 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================================================ tctttgaaaatcctttaggcagccgcttgtctaaaagaaaagcccttgcagcttaatcaaaaactgcaagggcttttttcttttacttaaattcttaatgtaatt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -15.4 Tail_Score: -4.07568 Start: 37 End: 78 Full_Region: aatttaagtaaaaga aaaaagcccttgcagttt ttgatt aagctgcaagggcttttc ttttagacaagcggc ....................................aaaaagcccttgcagtttttgattaagctgcaagggcttttc........................... TransTerm Strand: + Conf: 100 HP_score: -13.1 Tail_Score: -5.85244 Start: 42 End: 73 Full_Region: TTGTCTAAAAGAAAA GCCCTTGCAGCTT AATCAA AAACTGCAAGGGC TTTTTTCTTTTACTT .........................................GCCCTTGCAGCTTAATCAAAAACTGCAAGGGC................................ TransTerm Strand: - Conf: 100 HP_score: -15.3 Tail_Score: -5.07652 Start: 42 End: 73 Full_Region: aagtaaaagaaaaaa gcccttgcagttt ttgatt aagctgcaagggc ttttcttttagacaa .........................................gcccttgcagtttttgattaagctgcaagggc................................ Find igs database================================================ Query_seq: TDE1487:TDE1488|TDE1487:TDE1488:conserved hypothetical protein TIGR01033:glyceraldehyde-3-phosphate dehydrogenase, type I:-><-:1531589..1531693 105 tctttgaaaatcctttaggcagccgcttgtctaaaagaaaagcccttgcagcttaatcaaaaactgcaagggcttttttcttttacttaaattcttaatgtaatt Intra-Species Hit: Count: 1 Min: 1 Max: 105 Len: 105 Subject: NC_002967_TDE1487_TDE1488|conserved hypothetical protein TIGR01033:glyceraldehyde-3-phosphate dehydrogenase, type I|POSITIVE:NEGATIVE|[1531589,1531693]|105 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 105 Query Start:1 Query End:105 Subject Strand: POSITIVE Subject Start: 1 Subject End: 105 tctttgaaaatcctttaggcagccgcttgtctaaaagaaaagcccttgcagcttaatcaaaaactgcaagggcttttttcttttacttaaattcttaatgtaatt tctttgaaaatcctttaggcagccgcttgtctaaaagaaaagcccttgcagcttaatcaaaaactgcaagggcttttttcttttacttaaattcttaatgtaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUUGAAAAUCCUUUAGGCAGCCGCUUGUCUAAAAGAAAAGCCCUUGCAGCUUAAUCAAAAACUGCAAGGGCUUUUUUCUUUUACUUAAAUUCUUAAUGUAAUU .............(((((((((....))))))))).(((((((((((((((.((......)).)))))))))))))))....((((((((....)))).)))).. (-31.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUACAUUAAGAAUUUAAGUAAAAGAAAAAAGCCCUUGCAGUUUUUGAUUAAGCUGCAAGGGCUUUUCUUUUAGACAAGCGGCUGCCUAAAGGAUUUUCAAAGA ..((((.((((....))))))))..((((.(((((((((((((((......))))))))))))))).((((((((.((......)).)))))))).))))..... (-34.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 320 66 22 57 9 NC_002967:TDE0138|5end_alkyldihydroxyacetonephosphate_synthase,_putative_158221..158451_POSITIVE 319 55 17 179 137 NC_002967:TDE1576|5end_tRNA-i(6)A37_modification_enzyme_MiaB_1622778..1623008_POSITIVE 298 56 13 179 138 NC_002967:TDE0797|5end_acylphosphatase_820859..821089_POSITIVE 290 52 18 57 18 NC_002967:TDE0740|5end_hypothetical_protein_775987..776217_POSITIVE 289 77 34 227 185 NC_002967:TDE1097|5end_acetyltransferase,_GNAT_family_1132766..1132996_NEGATIVE 284 53 12 222 188 NC_002967:TDE0573|5end_hypothetical_protein_604681..604911_POSITIVE 278 54 14 151 109 NC_002967:TDE2521|5end_hypothetical_protein_2548074..2548304_NEGATIVE 278 77 42 203 163 NC_002967:TDE0773|5end_30S_ribosomal_protein_S3_809443..809673_POSITIVE 277 50 5 90 30 NC_002967:TDE1536|5end_TPR_domain_protein_1580468..1580698_NEGATIVE 276 52 13 188 136 NC_002967:TDE2219|5end_hypothetical_protein_2260646..2260876_NEGATIVE 274 75 31 160 101 NC_002967:TDE1136|5end_M23/M37_peptidase_domain_protein_1166049..1166279_NEGATIVE 274 54 11 140 105 NC_002967:TDE0860|5end_ribosomal_small_subunit_pseudouridine_synthase_A_881023..881253_POSITIVE 271 58 13 192 143 NC_002967:TDE1948|5end_ABC_transporter,_permease_protein_1964551..1964781_NEGATIVE 270 89 48 74 30 NC_002967:TDE1547|5end_ribonuclease_HII_1591124..1591354_POSITIVE 266 50 13 59 7 NC_002967:TDE0340|5end_fructose-bisphosphate_aldolase_378639..378869_POSITIVE 265 55 11 81 33 NC_002967:TDE2303|5end_hypothetical_protein_2343055..2343285_POSITIVE 264 78 42 230 199 NC_002967:TDE1163|5end_hypothetical_protein_1197930..1198160_NEGATIVE 260 74 43 230 189 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 260 51 12 39 1 NC_002967:TDE0438|5end_queuine_tRNA-ribosyltransferase_494811..495041_NEGATIVE 259 41 1 48 13 NC_002967:TDE2712|5end_hypothetical_protein_2769008..2769238_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 461 79 32 55 6 NC_002967:TDE1487|3end_conserved_hypothetical_protein_TIGR01033_1531528..1531678_POSITIVE 307 49 8 61 16 NC_002967:TDE2571|3end_hypothetical_protein_2597922..2598072_NEGATIVE 285 54 17 151 116 NC_002967:TDE0575|3end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_606252..606402_NEGATIVE 277 50 5 86 26 NC_002967:TDE1537|3end_polyprenyl_synthetase_family_protein_1580472..1580622_NEGATIVE 274 75 31 143 84 NC_002967:TDE1137|3end_hypothetical_protein_1166066..1166216_NEGATIVE 274 54 11 143 108 NC_002967:TDE0859|3end_hypothetical_protein_881106..881256_POSITIVE 273 89 43 97 47 NC_002967:TDE0664|3end_OmpA_family_protein_699728..699878_POSITIVE 270 89 48 74 30 NC_002967:TDE1546|3end_hypothetical_protein_1591204..1591354_POSITIVE 265 55 11 81 33 NC_002967:TDE2302|3end_HD_domain_protein_2343135..2343285_POSITIVE 265 60 11 105 44 NC_002967:TDE2028|3end_OmpA_family_protein_2057019..2057169_POSITIVE 264 90 43 82 39 NC_002967:TDE1084|3end_folylpolyglutamate_synthetase,_putative_1114934..1115084_NEGATIVE 262 50 13 121 89 NC_002967:TDE2717|3end_phosphatidate_cytidylyltransferase,_putative_2773921..2774071_NEGATIVE 259 54 11 133 85 NC_002967:TDE1403|3end_ABC_transporter,_ATP-binding_protein_1444500..1444650_NEGATIVE 256 55 17 86 59 NC_002967:TDE2293|3end_hypothetical_protein_2329325..2329475_NEGATIVE 255 74 35 77 39 NC_002967:TDE1917|3end_cytidylyltransferase_domain_protein_1934764..1934914_NEGATIVE 253 71 36 59 21 NC_002967:TDE2328|3end_efflux_pump_component_MtrF_2366364..2366514_POSITIVE 252 54 13 72 36 NC_002967:TDE0479|3end_hydroxylamine_reductase_535029..535179_NEGATIVE 251 50 16 52 10 NC_002967:TDE0394|3end_oligopeptide/dipeptide_ABC_transporter,_permease_protein_445023..445173_POSITIVE 250 55 21 33 5 NC_002967:TDE2604|3end_hypothetical_protein_2644224..2644374_NEGATIVE 250 52 11 63 14 NC_002967:TDE0123|3end_hypothetical_protein_141543..141693_NEGATIVE