Origin IGS: tgattgctgaggtgtagagctgattgctgcaacagaccgctgaacacggacaactgaacgctgaataacaattaaataaattatttactgactaattttaatttaaaacatttatcatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatgataaatgttttaaattaaaattagtcagtaaataatttatttaattgttattcagcgttcagttgtccgtgttcagcggtctgttgcagcaatcagctctacacctcagcaatca Mask Tandem Repeat Region ================================================ tgattgctgaggtgtagagctgattgctgcaacagaccgctgaacacggacaactgaacgctgaataacaattaaataaattatttactgactaattttaatttaaaacatttatcatt Find is-nt database================================================ Query_seq: TF0531:TF0532|TF0531:TF0532:hypothetical protein:hypothetical protein:->->:557530..557648 119 tgattgctgaggtgtagagctgattgctgcaacagaccgctgaacacggacaactgaacgctgaataacaattaaataaattatttactgactaattttaatttaaaacatttatcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0531:TF0532|TF0531:TF0532:hypothetical protein:hypothetical protein:->->:557530..557648 119 tgattgctgaggtgtagagctgattgctgcaacagaccgctgaacacggacaactgaacgctgaataacaattaaataaattatttactgactaattttaatttaaaacatttatcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0531:TF0532|TF0531:TF0532:hypothetical protein:hypothetical protein:->->:557530..557648 119 tgattgctgaggtgtagagctgattgctgcaacagaccgctgaacacggacaactgaacgctgaataacaattaaataaattatttactgactaattttaatttaaaacatttatcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgattgctgaggtgtagagctgattgctgcaacagaccgctgaacacggacaactgaacgctgaataacaattaaataaattatttactgactaattttaatttaaaacatttatcatt Predict ORF larger than 30AA ================================================ tgattgctgaggtgtagagctgattgctgcaacagaccgctgaacacggacaactgaacgctgaataacaattaaataaattatttactgactaattttaatttaaaacatttatcatt 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================================================ tgattgctgaggtgtagagctgattgctgcaacagaccgctgaacacggacaactgaacgctgaataacaattaaataaattatttactgactaattttaatttaaaacatttatcatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0531:TF0532|TF0531:TF0532:hypothetical protein:hypothetical protein:->->:557530..557648 119 tgattgctgaggtgtagagctgattgctgcaacagaccgctgaacacggacaactgaacgctgaataacaattaaataaattatttactgactaattttaatttaaaacatttatcatt Intra-Species Hit: Count: 1 Min: 1 Max: 119 Len: 119 Subject: tfor_TF0531_TF0532|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[557530,557648]|119 HSP 1 e-value: 1.0E-61 bit: 236.0 Len: 119 Query Start:1 Query End:119 Subject Strand: POSITIVE Subject Start: 1 Subject End: 119 tgattgctgaggtgtagagctgattgctgcaacagaccgctgaacacggacaactgaacgctgaataacaattaaataaattatttactgactaattttaatttaaaacatttatcatt tgattgctgaggtgtagagctgattgctgcaacagaccgctgaacacggacaactgaacgctgaataacaattaaataaattatttactgactaattttaatttaaaacatttatcatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUGCUGAGGUGUAGAGCUGAUUGCUGCAACAGACCGCUGAACACGGACAACUGAACGCUGAAUAACAAUUAAAUAAAUUAUUUACUGACUAAUUUUAAUUUAAAACAUUUAUCAUU ((((((.((.(((((..(((.....)))....(((....(((....)))....))).)))))...)).))))))..(((((((...............))))))).............. (-14.66) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAUAAAUGUUUUAAAUUAAAAUUAGUCAGUAAAUAAUUUAUUUAAUUGUUAUUCAGCGUUCAGUUGUCCGUGUUCAGCGGUCUGUUGCAGCAAUCAGCUCUACACCUCAGCAAUCA ((((((((.((...(((((((...............)))))))..)).)))))))).........((((...((((..((((((.(((....)))))).)))..))))..))))..... (-17.76) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 388 48 1 199 155 tfor:TF0341|5end_conserved_hypothetical_protein_364348..364578_POSITIVE 358 60 11 59 14 tfor:TF1062|5end_glycosyltransferase_1131727..1131957_POSITIVE 356 49 4 190 144 tfor:TF0140|5end_exodeoxyribonuclease_VII,_small_subunit_148203..148433_POSITIVE 351 57 12 50 7 tfor:TF3046|5end_hypothetical_protein_3274948..3275178_POSITIVE 346 50 4 172 128 tfor:TF2276|5end_conserved_hypothetical_protein_2438226..2438456_POSITIVE 345 50 1 106 63 tfor:TF0350|5end_hypothetical_protein_370794..371024_POSITIVE 339 48 3 174 127 tfor:TF2820|5end_argininosuccinate_synthetase_3009876..3010106_POSITIVE 337 63 29 36 4 tfor:TF2245|5end_conserved_hypothetical_protein_2420654..2420884_POSITIVE 333 49 1 88 42 tfor:TF1274|5end_hypothetical_protein_1357621..1357851_POSITIVE 328 50 4 172 132 tfor:TF2439|5end_conserved_hypothetical_protein_2616380..2616610_POSITIVE 328 60 11 79 21 tfor:TF1885|5end_conserved_hypothetical_protein_2037307..2037537_POSITIVE 324 50 4 229 175 tfor:TF1576|5end_hypothetical_protein_1685852..1686082_POSITIVE 322 48 5 66 1 tfor:TF1331|5end_outer_membrane_protein_1409688..1409918_POSITIVE 321 49 2 161 117 tfor:TF0285|5end_conserved_hypothetical_protein_314465..314695_POSITIVE 320 46 1 226 191 tfor:TF0351|5end_hypothetical_protein_370922..371152_POSITIVE 318 50 4 201 163 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 315 40 5 172 137 tfor:TF2171|5end_hypothetical_protein_2345485..2345715_POSITIVE 315 40 5 172 137 tfor:TF2166|5end_hypothetical_protein_2342115..2342345_POSITIVE 310 50 1 151 101 tfor:TF2530|5end_conserved_hypothetical_protein_2711416..2711646_POSITIVE 310 74 33 66 13 tfor:TF0361|5end_hypothetical_protein_379458..379688_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 373 60 11 54 1 tfor:TF2244|3end_possible_mobilization_protein_2420752..2420902_POSITIVE 358 60 11 59 14 tfor:TF1061|3end_glycosyltransferase_1131807..1131957_POSITIVE 328 49 7 77 40 tfor:TF1165|3end_conserved_hypothetical_protein_1245921..1246071_POSITIVE 310 50 1 151 101 tfor:TF2529|3end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_2711496..2711646_POSITIVE 310 74 33 66 13 tfor:TF0360|3end_hypothetical_protein_379538..379688_POSITIVE 300 66 21 150 111 tfor:TF1830|3end_3-isopropylmalate_dehydratase,_large_subunit_1980401..1980551_POSITIVE 296 50 3 79 38 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 292 50 11 76 37 tfor:TF1169|3end_lipoprotein_ABC_transporter,_permease_component_1251573..1251723_POSITIVE 292 50 11 76 37 tfor:TF1166|3end_ABC_transporter,_permease_component_1248603..1248753_POSITIVE 290 46 11 97 57 tfor:TF1720|3end_conserved_hypothetical_protein_1844376..1844526_POSITIVE 288 70 25 63 6 tfor:TF0365|3end_hypothetical_protein_383152..383302_POSITIVE 286 44 9 67 37 tfor:TF1590|3end_hypothetical_protein_1706043..1706193_POSITIVE 286 42 6 38 1 tfor:TF1493|3end_thioredoxin_family_protein_1594066..1594216_POSITIVE 285 62 21 44 4 tfor:TF2767|3end_2-oxoglutarate_synthase,_alpha_subunit_2954151..2954301_POSITIVE 285 70 21 75 22 tfor:TF0023|3end_possible_response_element_in_two_component_regulation_20233..20383_POSITIVE 284 59 20 150 115 tfor:TF2402|3end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2576224..2576374_POSITIVE 283 64 21 143 94 tfor:TF1186|3end_hypothetical_protein_1269815..1269965_POSITIVE 281 39 4 150 116 tfor:TF2449|3end_undecaprenyl_diphosphate_synthase_2626541..2626691_POSITIVE 280 48 4 70 12 tfor:TF2455|3end_conserved_hypothetical_protein;_possible_membrane_protein_2632437..2632587_POSITIVE 280 59 13 131 83 tfor:TF0128|3end_hypothetical_protein_140556..140706_POSITIVE