Origin IGS: tgatctcggcactcgttgtaccttctcaccgtatctgcagaaagcaaaaaatctatgcaaatcatttgcatattcaggattttttcacgaatattgcatgtttaaatcggatgaggtgagatgatgaatgaagatgcatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatgcatcttcattcatcatctcacctcatccgatttaaacatgcaatattcgtgaaaaaatcctgaatatgcaaatgatttgcatagattttttgctttctgcagatacggtgagaaggtacaacgagtgccgagatca Mask Tandem Repeat Region ================================================ tgatctcggcactcgttgtaccttctcaccgtatctgcagaaagcaaaaaatctatgcaaatcatttgcatattcaggattttttcacgaatattgcatgtttaaatcggatgaggtgagatgatgaatgaagatgcatt Find is-nt database================================================ Query_seq: TF1215:TF1216|TF1215:TF1216:haloacid dehalogenase-like hydrolase:possible ECF-family RNA polymerase sigma factor:->->:1303277..1303416 140 tgatctcggcactcgttgtaccttctcaccgtatctgcagaaagcaaaaaatctatgcaaatcatttgcatattcaggattttttcacgaatattgcatgtttaaatcggatgaggtgagatgatgaatgaagatgcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1215:TF1216|TF1215:TF1216:haloacid dehalogenase-like hydrolase:possible ECF-family RNA polymerase sigma factor:->->:1303277..1303416 140 tgatctcggcactcgttgtaccttctcaccgtatctgcagaaagcaaaaaatctatgcaaatcatttgcatattcaggattttttcacgaatattgcatgtttaaatcggatgaggtgagatgatgaatgaagatgcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1215:TF1216|TF1215:TF1216:haloacid dehalogenase-like hydrolase:possible ECF-family RNA polymerase sigma factor:->->:1303277..1303416 140 tgatctcggcactcgttgtaccttctcaccgtatctgcagaaagcaaaaaatctatgcaaatcatttgcatattcaggattttttcacgaatattgcatgtttaaatcggatgaggtgagatgatgaatgaagatgcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatctcggcactcgttgtaccttctcaccgtatctgcagaaagcaaaaaatctatgcaaatcatttgcatattcaggattttttcacgaatattgcatgtttaaatcggatgaggtgagatgatgaatgaagatgcatt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 3 End: 116 .. M S A L V V P S H R I C R K Q K I Y A N H L H I Q D F F T N I A C L N R M R ........................ Protein_Len: 30 Strand: - Start: 3 End: 92 .. D R C E N Y R R V T D A S L L F D I C I M Q M N L I K E R M ................................................ tgatctcggcactcgttgtaccttctcaccgtatctgcagaaagcaaaaaatctatgcaaatcatttgcatattcaggattttttcacgaatattgcatgtttaaatcggatgaggtgagatgatgaatgaagatgcatt 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================================================ tgatctcggcactcgttgtaccttctcaccgtatctgcagaaagcaaaaaatctatgcaaatcatttgcatattcaggattttttcacgaatattgcatgtttaaatcggatgaggtgagatgatgaatgaagatgcatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1215:TF1216|TF1215:TF1216:haloacid dehalogenase-like hydrolase:possible ECF-family RNA polymerase sigma factor:->->:1303277..1303416 140 tgatctcggcactcgttgtaccttctcaccgtatctgcagaaagcaaaaaatctatgcaaatcatttgcatattcaggattttttcacgaatattgcatgtttaaatcggatgaggtgagatgatgaatgaagatgcatt Intra-Species Hit: Count: 1 Min: 1 Max: 140 Len: 140 Subject: tfor_TF1215_TF1216|haloacid dehalogenase-like hydrolase:possible ECF-family RNA polymerase sigma factor|POSITIVE:POSITIVE|[1303277,1303416]|140 HSP 1 e-value: 5.0E-74 bit: 278.0 Len: 140 Query Start:1 Query End:140 Subject Strand: POSITIVE Subject Start: 1 Subject End: 140 tgatctcggcactcgttgtaccttctcaccgtatctgcagaaagcaaaaaatctatgcaaatcatttgcatattcaggattttttcacgaatattgcatgtttaaatcggatgaggtgagatgatgaatgaagatgcatt tgatctcggcactcgttgtaccttctcaccgtatctgcagaaagcaaaaaatctatgcaaatcatttgcatattcaggattttttcacgaatattgcatgtttaaatcggatgaggtgagatgatgaatgaagatgcatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUCUCGGCACUCGUUGUACCUUCUCACCGUAUCUGCAGAAAGCAAAAAAUCUAUGCAAAUCAUUUGCAUAUUCAGGAUUUUUUCACGAAUAUUGCAUGUUUAAAUCGGAUGAGGUGAGAUGAUGAAUGAAGAUGCAUU ........(((((((((.((.(.(((((((.((((((......(.(((((((((((((((.....)))))).....))))))))))..((((((...))))))....)))))).))))))).).)))))).)).)))... (-33.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGCAUCUUCAUUCAUCAUCUCACCUCAUCCGAUUUAAACAUGCAAUAUUCGUGAAAAAAUCCUGAAUAUGCAAAUGAUUUGCAUAGAUUUUUUGCUUUCUGCAGAUACGGUGAGAAGGUACAACGAGUGCCGAGAUCA ..((.((((..........(((((((................((((.((((((.((.....)).))))))))))....(((((((.(((........))).)))))))..))))))).(((((.....))))).)))))) (-34.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 140 95 115 65 tfor:TF2016|5end_hypothetical_protein_2172948..2173178_POSITIVE 310 45 6 68 18 tfor:TF0541|5end_conserved_hypothetical_protein_568473..568703_POSITIVE 303 41 1 58 12 tfor:TF3072|5end_conserved_hypothetical_protein_3295302..3295532_POSITIVE 297 45 3 72 23 tfor:TF1593|5end_hypothetical_protein_1708859..1709089_POSITIVE 294 57 12 112 68 tfor:TF2807|5end_possible_chloride_channel_protein_2996637..2996867_POSITIVE 293 45 2 214 171 tfor:TF2035|5end_conserved_hypothetical_protein_2194665..2194895_POSITIVE 293 45 4 161 118 tfor:TF1507|5end_outer_membrane_receptor,_TonB-dependent_1614536..1614766_POSITIVE 288 40 4 46 6 tfor:TF1604|5end_possible_anti-sigma_factor_1717811..1718041_POSITIVE 287 137 107 89 60 tfor:TF3146|5end_GTP-binding_protein_Obg_3381852..3382082_POSITIVE 287 46 6 211 169 tfor:TF3006|5end_response_regulator,_transcriptional_regulator_RprY_3226360..3226590_POSITIVE 281 137 99 155 118 tfor:TF1228|5end_conserved_hypothetical_protein_1314103..1314333_POSITIVE 276 50 1 72 15 tfor:TF3031|5end_conserved_hypothetical_protein_3254401..3254631_POSITIVE 275 118 76 215 172 tfor:TF1195|5end_hypothetical_protein_1278595..1278825_POSITIVE 274 45 5 204 155 tfor:TF3022|5end_chorismate_synthase_3246136..3246366_POSITIVE 273 45 6 62 12 tfor:TF0248|5end_hypothetical_protein_278249..278479_POSITIVE 270 45 9 55 6 tfor:TF1928|5end_conserved_hypothetical_protein_2075529..2075759_POSITIVE 267 46 4 46 9 tfor:TF1819|5end_cation_efflux_system_AcrB/AcrD/AcrF_family;_ABC_transporter,_ATP-binding/permease_component_1958681..1958911_POSITIVE 267 45 1 119 64 tfor:TF0261|5end_conserved_hypothetical_protein_291784..292014_POSITIVE 266 120 76 190 147 tfor:TF1522|5end_hypothetical_protein_1629531..1629761_POSITIVE 265 47 7 53 18 tfor:TF2398|5end_magnesium_chelatase,_D/I_family_2569549..2569779_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 347 140 95 107 57 tfor:TF2015|3end_N6-adenine-specific_DNA_methylase_2173020..2173170_POSITIVE 303 41 1 58 12 tfor:TF3071|3end_integral_membrane_protein,_possible_MotA/TolQ/ExbB_proton_channel_family_3295382..3295532_POSITIVE 294 57 12 60 16 tfor:TF2805|3end_zinc_protease_2996665..2996815_POSITIVE 292 37 6 132 91 tfor:TF0970|3end_2-keto-3-deoxygluconate_kinase_1021540..1021690_POSITIVE 281 110 68 113 65 tfor:TF2135|3end_conserved_hypothetical_protein_2311635..2311785_POSITIVE 273 45 6 81 31 tfor:TF0247|3end_conserved_hypothetical_protein_278348..278498_POSITIVE 267 46 4 39 2 tfor:TF1818|3end_conserved_hypothetical_protein_1958754..1958904_POSITIVE 264 46 1 67 9 tfor:TF1932|3end_pigmentation_and_extracellular_proteinase_regulator_2079755..2079905_POSITIVE 263 47 3 120 64 tfor:TF2907|3end_CDP-diacylglycerol-serine-O-phosphatidyltransfera_se_3103681..3103831_POSITIVE 260 136 105 106 68 tfor:TF0879|3end_TraG_family_protein_934085..934235_POSITIVE 259 48 1 61 13 tfor:TF1382|3end_hypothetical_protein_1457777..1457927_POSITIVE 259 48 1 57 9 tfor:TF1383|3end_hypothetical_protein_1457773..1457923_POSITIVE 257 130 87 53 17 tfor:TF2409|3end_hypothetical_protein_2584155..2584305_POSITIVE 257 45 13 48 3 tfor:TF1927|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2075602..2075752_POSITIVE 256 136 94 106 65 tfor:TF1437|3end_hypothetical_protein_1522361..1522511_POSITIVE 255 46 1 96 44 tfor:TF2911|3end_hypothetical_protein_3106640..3106790_POSITIVE 253 47 6 62 14 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 253 47 1 125 78 tfor:TF0298|3end_dipeptidase_324868..325018_POSITIVE 252 97 51 119 74 tfor:TF2646|3end_conserved_hypothetical_protein_2816697..2816847_POSITIVE 251 46 3 61 22 tfor:TF0431|3end_hypothetical_protein_452470..452620_POSITIVE