Origin IGS: tgattccctgttcactcctttagctatttctatccgttaaaactgtttaccccagatagaatttgggctgagctccttgcaaggaactcagcccttttagtattcgttaaatagttatccta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taggataactatttaacgaatactaaaagggctgagttccttgcaaggagctcagcccaaattctatctggggtaaacagttttaacggatagaaatagctaaaggagtgaacagggaatca Mask Tandem Repeat Region ================================================ tgattccctgttcactcctttagctatttctatccgttaaaactgtttaccccagatagaatttgggctgagctccttgcaaggaactcagcccttttagtattcgttaaatagttatccta Find is-nt database================================================ Query_seq: PI1243:PI1244|PI1243:PI1244:conserved hypothetical protein:hypothetical protein:->->:1168821..1168942 122 tgattccctgttcactcctttagctatttctatccgttaaaactgtttaccccagatagaatttgggctgagctccttgcaaggaactcagcccttttagtattcgttaaatagttatccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1243:PI1244|PI1243:PI1244:conserved hypothetical protein:hypothetical protein:->->:1168821..1168942 122 tgattccctgttcactcctttagctatttctatccgttaaaactgtttaccccagatagaatttgggctgagctccttgcaaggaactcagcccttttagtattcgttaaatagttatccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1243:PI1244|PI1243:PI1244:conserved hypothetical protein:hypothetical protein:->->:1168821..1168942 122 tgattccctgttcactcctttagctatttctatccgttaaaactgtttaccccagatagaatttgggctgagctccttgcaaggaactcagcccttttagtattcgttaaatagttatccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgattccctgttcactcctttagctatttctatccgttaaaactgtttaccccagatagaatttgggctgagctccttgcaaggaactcagcccttttagtattcgttaaatagttatccta Predict ORF larger than 30AA ================================================ tgattccctgttcactcctttagctatttctatccgttaaaactgtttaccccagatagaatttgggctgagctccttgcaaggaactcagcccttttagtattcgttaaatagttatccta 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================================================ tgattccctgttcactcctttagctatttctatccgttaaaactgtttaccccagatagaatttgggctgagctccttgcaaggaactcagcccttttagtattcgttaaatagttatccta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -16.5 Tail_Score: -4.46404 Start: 65 End: 94 Full_Region: CCCCAGATAGAATTT GGGCTGAGCTCCT TGCA AGGAACTCAGCCC TTTTAGTATTCGTTA ................................................................GGGCTGAGCTCCTTGCAAGGAACTCAGCCC............................ Find igs database================================================ Query_seq: PI1243:PI1244|PI1243:PI1244:conserved hypothetical protein:hypothetical protein:->->:1168821..1168942 122 tgattccctgttcactcctttagctatttctatccgttaaaactgtttaccccagatagaatttgggctgagctccttgcaaggaactcagcccttttagtattcgttaaatagttatccta Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: pint_PI1243_PI1244|conserved hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1168821,1168942]|122 HSP 1 e-value: 2.0E-63 bit: 242.0 Len: 122 Query Start:1 Query End:122 Subject Strand: POSITIVE Subject Start: 1 Subject End: 122 tgattccctgttcactcctttagctatttctatccgttaaaactgtttaccccagatagaatttgggctgagctccttgcaaggaactcagcccttttagtattcgttaaatagttatccta tgattccctgttcactcctttagctatttctatccgttaaaactgtttaccccagatagaatttgggctgagctccttgcaaggaactcagcccttttagtattcgttaaatagttatccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUUCCCUGUUCACUCCUUUAGCUAUUUCUAUCCGUUAAAACUGUUUACCCCAGAUAGAAUUUGGGCUGAGCUCCUUGCAAGGAACUCAGCCCUUUUAGUAUUCGUUAAAUAGUUAUCCUA ....................(((((((((.............((((((.....)))))).....((((((((.((((....)))).))))))))..............)))))))))..... (-30.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGAUAACUAUUUAACGAAUACUAAAAGGGCUGAGUUCCUUGCAAGGAGCUCAGCCCAAAUUCUAUCUGGGGUAAACAGUUUUAACGGAUAGAAAUAGCUAAAGGAGUGAACAGGGAAUCA ...(((..((.....((...........(((((((((((((....)))))))))))))...(((((((((...((((....)))).)))))))))............)).....))..))). (-40.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 579 98 53 207 162 pint:PI1058|5end_possible_FHA_domain_protein_977577..977807_POSITIVE 302 107 61 68 15 pint:PI1679|5end_hypothetical_protein_1594744..1594974_POSITIVE 286 95 64 76 42 pint:PI0739|5end_conserved_hypothetical_protein_671794..672024_POSITIVE 281 44 1 202 147 pint:PI2140|5end_conserved_hypothetical_protein_2086773..2087003_POSITIVE 281 116 71 51 5 pint:PI0985|5end_aspartyl-tRNA_synthetase_910174..910404_POSITIVE 278 98 56 231 187 pint:PI1294|5end_hypothetical_protein_1208490..1208720_POSITIVE 278 98 56 195 151 pint:PI1182|5end_hypothetical_protein_1104025..1104255_POSITIVE 277 92 51 228 196 pint:PI2126|5end_conserved_hypothetical_protein_2074907..2075137_POSITIVE 274 106 65 210 162 pint:PI1646|5end_hypothetical_protein_1561954..1562184_POSITIVE 273 94 51 222 178 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 269 92 53 56 14 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 268 80 35 55 5 pint:PI2176|5end_conserved_hypothetical_protein_2116484..2116714_POSITIVE 266 98 51 205 164 pint:PI0977|5end_riboflavin_synthase,_alpha_subunit_904043..904273_POSITIVE 264 94 52 127 72 pint:PI1973|5end_conserved_hypothetical_protein_1930429..1930659_POSITIVE 261 98 51 65 13 pint:PI0593|5end_NAD-specific_glutamate_dehydrogenase_542967..543197_POSITIVE 260 96 51 193 145 pint:PI0815|5end_hypothetical_protein_754475..754705_POSITIVE 258 108 63 157 105 pint:PI1525|5end_CDP-diacylglycerol--serine_O-phosphatidyltransferase_1446758..1446988_POSITIVE 258 79 34 137 91 pint:PI1496|5end_nucleoside_phosphorylase_1417116..1417346_POSITIVE 258 80 33 60 9 pint:PI0774|5end_phosphoserine_aminotransferase_(phosphoserine_transaminase)_709497..709727_POSITIVE 253 99 72 149 112 pint:PI0397|5end_conserved_hypothetical_protein_362406..362636_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 579 98 53 98 53 pint:PI1057|3end_hypothetical_protein_977548..977698_POSITIVE 384 99 69 34 1 pint:PI1243|3end_conserved_hypothetical_protein_1168760..1168910_POSITIVE 352 98 52 101 44 pint:PI1653|3end_hypothetical_protein_1565714..1565864_POSITIVE 346 96 65 31 2 pint:PI0159|3end_hypothetical_protein_152120..152270_POSITIVE 299 105 64 151 111 pint:PI0593|3end_NAD-specific_glutamate_dehydrogenase_544369..544519_POSITIVE 289 94 53 51 5 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 286 95 64 73 39 pint:PI0738|3end_conserved_hypothetical_protein_671871..672021_POSITIVE 284 36 1 140 98 pint:PI0380|3end_conserved_hypothetical_protein_350541..350691_POSITIVE 281 44 1 101 46 pint:PI2139|3end_cysteinyl-tRNA_synthetase_2086752..2086902_POSITIVE 278 98 56 108 64 pint:PI1293|3end_ISPg4-related_transposase_(IS5_family)_1208447..1208597_POSITIVE 278 98 56 108 64 pint:PI1181|3end_ISPg4-related_transposase_(IS5_family)_1104018..1104168_POSITIVE 278 98 56 108 64 pint:PI1085|3end_ISPg4-related_transposase_(IS5_family)_1006499..1006649_POSITIVE 273 99 53 65 24 pint:PI0447|3end_DNA-directed_RNA_polymerase,_beta'_subunit_421755..421905_POSITIVE 272 80 34 119 74 pint:PI1065|3end_hypothetical_protein_983650..983800_POSITIVE 269 92 53 51 9 pint:PI0264|3end_transfer_region-related_protein,_TraN_257371..257521_POSITIVE 264 94 52 121 66 pint:PI1972|3end_hypothetical_protein_1930503..1930653_POSITIVE 260 96 51 64 16 pint:PI0814|3end_conserved_hypothetical_protein_754426..754576_POSITIVE 258 103 67 40 2 pint:PI0984|3end_hypothetical_protein_910144..910294_POSITIVE 255 109 67 139 93 pint:PI2074|3end_conserved_hypothetical_protein_2034375..2034525_POSITIVE 253 99 72 59 22 pint:PI0396|3end_possible_tetracycline_resistance_element_mobilization_regulatory_protein,_C-terminal_fragment_362396..362546_POSITIVE