Origin IGS: taatcaatgaatgtttaaccgcgtaatacaacaagtccgaaaaatatgatatcatatttcaagaaaacagtcgactgatttttccgagtggctcgaacgacattgtatctacgctaaaatcaatttgaaaaatgagaaagaaaatttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaattttctttctcatttttcaaattgattttagcgtagatacaatgtcgttcgagccactcggaaaaatcagtcgactgttttcttgaaatatgatatcatatttttcggacttgttgtattacgcggttaaacattcattgatta Mask Tandem Repeat Region ================================================ taatcaatgaatgtttaaccgcgtaatacaacaagtccgaaaaatatgatatcatatttcaagaaaacagtcgactgatttttccgagtggctcgaacgacattgtatctacgctaaaatcaatttgaaaaatgagaaagaaaatttta Find is-nt database================================================ Query_seq: PI0258:PI0259|PI0258:PI0259:conjugative transposon protein, TraG:conserved protein found in conjugation, TraI:->->:252346..252494 149 taatcaatgaatgtttaaccgcgtaatacaacaagtccgaaaaatatgatatcatatttcaagaaaacagtcgactgatttttccgagtggctcgaacgacattgtatctacgctaaaatcaatttgaaaaatgagaaagaaaatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0258:PI0259|PI0258:PI0259:conjugative transposon protein, TraG:conserved protein found in conjugation, TraI:->->:252346..252494 149 taatcaatgaatgtttaaccgcgtaatacaacaagtccgaaaaatatgatatcatatttcaagaaaacagtcgactgatttttccgagtggctcgaacgacattgtatctacgctaaaatcaatttgaaaaatgagaaagaaaatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0258:PI0259|PI0258:PI0259:conjugative transposon protein, TraG:conserved protein found in conjugation, TraI:->->:252346..252494 149 taatcaatgaatgtttaaccgcgtaatacaacaagtccgaaaaatatgatatcatatttcaagaaaacagtcgactgatttttccgagtggctcgaacgacattgtatctacgctaaaatcaatttgaaaaatgagaaagaaaatttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatcaatgaatgtttaaccgcgtaatacaacaagtccgaaaaatatgatatcatatttcaagaaaacagtcgactgatttttccgagtggctcgaacgacattgtatctacgctaaaatcaatttgaaaaatgagaaagaaaatttta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 56 End: 148 ....................................................... M S R K Q S T D F S E W L E R H C I Y A K I N L K N E K E N F . taatcaatgaatgtttaaccgcgtaatacaacaagtccgaaaaatatgatatcatatttcaagaaaacagtcgactgatttttccgagtggctcgaacgacattgtatctacgctaaaatcaatttgaaaaatgagaaagaaaatttta 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================================================ taatcaatgaatgtttaaccgcgtaatacaacaagtccgaaaaatatgatatcatatttcaagaaaacagtcgactgatttttccgagtggctcgaacgacattgtatctacgctaaaatcaatttgaaaaatgagaaagaaaatttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0258:PI0259|PI0258:PI0259:conjugative transposon protein, TraG:conserved protein found in conjugation, TraI:->->:252346..252494 149 taatcaatgaatgtttaaccgcgtaatacaacaagtccgaaaaatatgatatcatatttcaagaaaacagtcgactgatttttccgagtggctcgaacgacattgtatctacgctaaaatcaatttgaaaaatgagaaagaaaatttta Intra-Species Hit: Count: 1 Min: 1 Max: 149 Len: 149 Subject: pint_PI0258_PI0259|conjugative transposon protein, TraG:conserved protein found in conjugation, TraI|POSITIVE:POSITIVE|[252346,252494]|149 HSP 1 e-value: 2.0E-79 bit: 295.0 Len: 149 Query Start:1 Query End:149 Subject Strand: POSITIVE Subject Start: 1 Subject End: 149 taatcaatgaatgtttaaccgcgtaatacaacaagtccgaaaaatatgatatcatatttcaagaaaacagtcgactgatttttccgagtggctcgaacgacattgtatctacgctaaaatcaatttgaaaaatgagaaagaaaatttta taatcaatgaatgtttaaccgcgtaatacaacaagtccgaaaaatatgatatcatatttcaagaaaacagtcgactgatttttccgagtggctcgaacgacattgtatctacgctaaaatcaatttgaaaaatgagaaagaaaatttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCAAUGAAUGUUUAACCGCGUAAUACAACAAGUCCGAAAAAUAUGAUAUCAUAUUUCAAGAAAACAGUCGACUGAUUUUUCCGAGUGGCUCGAACGACAUUGUAUCUACGCUAAAAUCAAUUUGAAAAAUGAGAAAGAAAAUUUUA ...(((((((...((((...(((((((((((...((.(((.(((((((....)))))))........((.(((...........))).))..))).))....)))))).))))))))).)))..))))..................... (-24.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAUUUUCUUUCUCAUUUUUCAAAUUGAUUUUAGCGUAGAUACAAUGUCGUUCGAGCCACUCGGAAAAAUCAGUCGACUGUUUUCUUGAAAUAUGAUAUCAUAUUUUUCGGACUUGUUGUAUUACGCGGUUAAACAUUCAUUGAUUA .....................((((..(((.((((((((.(((((((((..((((((.......((((((..(((....))))))))).((((((((....)))))))))))))).)))))))))))))...))))...)))))))... (-29.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 300 105 67 104 55 pint:PI1931|5end_alpha_glycan_phosphorylase,_maltodextrin_phosphorylase_1875456..1875686_POSITIVE 282 96 51 211 160 pint:PI1491|5end_conserved_hypothetical_protein_1409410..1409640_POSITIVE 278 115 71 140 87 pint:PI1639|5end_conserved_hypothetical_protein_1556725..1556955_POSITIVE 267 115 85 40 6 pint:PI2144|5end_hypothetical_protein_2091954..2092184_POSITIVE 265 107 71 215 166 pint:PI0879|5end_hypothetical_protein_813396..813626_POSITIVE 264 115 72 213 160 pint:PI2003|5end_hypothetical_protein_1960823..1961053_POSITIVE 263 119 72 70 25 pint:PI1139|5end_endopeptidase,_endothelin-converting_enzyme_1065216..1065446_POSITIVE 260 100 68 203 176 pint:PI1947|5end_hypothetical_protein_1902534..1902764_POSITIVE 260 101 68 71 41 pint:PI0771|5end_conserved_hypothetical_protein_706524..706754_POSITIVE 260 93 60 117 85 pint:PI0668|5end_peptidyl-prolyl_cis-trans_isomerase_SlyD,_FKBP-type_(peptidylprolyl_isomerase)_610216..610446_POSITIVE 256 115 72 55 22 pint:PI0194|5end_2-amino-3-ketobutyrate_coenzyme_A_ligase_(glycine_C-acetyltransferase)_185804..186034_POSITIVE 254 109 62 142 97 pint:PI1541|5end_hypothetical_protein_1461604..1461834_POSITIVE 249 121 85 117 69 pint:PI1760|5end_hypothetical_protein_1684413..1684643_POSITIVE 245 115 79 194 145 pint:PI0719|5end_conserved_hypothetical_protein_653043..653273_POSITIVE 245 100 59 229 182 pint:PI0373|5end_hypothetical_protein_344293..344523_POSITIVE 245 114 71 155 111 pint:PI0361|5end_hypothetical_protein_333062..333292_POSITIVE 244 115 71 44 6 pint:PI1539|5end_3-phosphoshikimate_1-carboxyvinyltransferase_1459804..1460034_POSITIVE 243 115 76 69 37 pint:PI1116|5end_conserved_hypothetical_protein_1040257..1040487_POSITIVE 242 110 69 61 23 pint:PI2024|5end_hypothetical_protein_1978804..1979034_POSITIVE 241 117 72 116 70 pint:PI0931|5end_hypothetical_protein_862652..862882_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 116 75 41 3 pint:PI1805|3end_TPR_repeat_containing_protein_1740533..1740683_POSITIVE 261 115 85 108 74 pint:PI1356|3end_hypothetical_protein_1273340..1273490_POSITIVE 257 116 87 145 114 pint:PI0524|3end_meso-diaminopimelate_D-dehydrogenase_480849..480999_POSITIVE 246 115 71 134 86 pint:PI1814|3end_hypothetical_protein_1753233..1753383_POSITIVE 243 115 76 63 31 pint:PI1115|3end_conserved_hypothetical_protein_1040331..1040481_POSITIVE 242 110 69 136 98 pint:PI2022|3end_hypothetical_protein_1978959..1979109_POSITIVE 242 100 68 52 3 pint:PI0634|3end_conserved_hypothetical_protein_581121..581271_POSITIVE 241 110 68 62 15 pint:PI0752|3end_conserved_hypothetical_protein_683467..683617_POSITIVE 237 98 53 151 105 pint:PI1622|3end_hypothetical_protein_1547230..1547380_POSITIVE 237 115 85 134 100 pint:PI0670|3end_hypothetical_protein_611280..611430_POSITIVE 236 115 71 142 96 pint:PI1730|3end_hypothetical_protein_1650367..1650517_POSITIVE 236 106 63 140 101 pint:PI0924|3end_possible_glycosyl_hydrolase_855953..856103_POSITIVE 235 115 72 135 97 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 234 114 78 138 93 pint:PI0926|3end_hypothetical_protein_857047..857197_POSITIVE 234 115 85 111 74 pint:PI0560|3end_hypothetical_protein_508910..509060_POSITIVE 233 115 85 35 1 pint:PI0996|3end_hypothetical_protein_920660..920810_POSITIVE 233 115 85 94 60 pint:PI0759|3end_hypothetical_protein_693998..694148_POSITIVE 233 115 71 134 86 pint:PI0689|3end_hypothetical_protein_625877..626027_POSITIVE 233 115 85 134 100 pint:PI0061|3end_hypothetical_protein_60690..60840_POSITIVE 232 101 69 37 7 pint:PI0681|3end_hypothetical_protein_619256..619406_POSITIVE