Origin IGS: aattttttaggttttacttgcctgtggtaagcaagattgttagtttacaatttgaaagcaaaagtaggcattttaaatggattagacaacaaaaatgaataaaaaaatgtgcccgaaggcacattttgtcagatattcctaaagatgatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatcatctttaggaatatctgacaaaatgtgccttcgggcacatttttttattcatttttgttgtctaatccatttaaaatgcctacttttgctttcaaattgtaaactaacaatcttgcttaccacaggcaagtaaaacctaaaaaatt Mask Tandem Repeat Region ================================================ aattttttaggttttacttgcctgtggtaagcaagattgttagtttacaatttgaaagcaaaagtaggcattttaaatggattagacaacaaaaatgaataaaaaaatgtgcccgaaggcacattttgtcagatattcctaaagatgatta Find is-nt database================================================ Query_seq: PI0030:PI0031|PI0030:PI0031:transcriptional regulator, AsnC family:peptidylprolyl isomerase:->->:35111..35261 151 aattttttaggttttacttgcctgtggtaagcaagattgttagtttacaatttgaaagcaaaagtaggcattttaaatggattagacaacaaaaatgaataaaaaaatgtgcccgaaggcacattttgtcagatattcctaaagatgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0030:PI0031|PI0030:PI0031:transcriptional regulator, AsnC family:peptidylprolyl isomerase:->->:35111..35261 151 aattttttaggttttacttgcctgtggtaagcaagattgttagtttacaatttgaaagcaaaagtaggcattttaaatggattagacaacaaaaatgaataaaaaaatgtgcccgaaggcacattttgtcagatattcctaaagatgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0030:PI0031|PI0030:PI0031:transcriptional regulator, AsnC family:peptidylprolyl isomerase:->->:35111..35261 151 aattttttaggttttacttgcctgtggtaagcaagattgttagtttacaatttgaaagcaaaagtaggcattttaaatggattagacaacaaaaatgaataaaaaaatgtgcccgaaggcacattttgtcagatattcctaaagatgatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattttttaggttttacttgcctgtggtaagcaagattgttagtttacaatttgaaagcaaaagtaggcattttaaatggattagacaacaaaaatgaataaaaaaatgtgcccgaaggcacattttgtcagatattcctaaagatgatta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 17 End: 136 ................ K G T T L L I T L K C N S L L L L C K L H I L C C F H I F F H A R L C M K D S M ............... aattttttaggttttacttgcctgtggtaagcaagattgttagtttacaatttgaaagcaaaagtaggcattttaaatggattagacaacaaaaatgaataaaaaaatgtgcccgaaggcacattttgtcagatattcctaaagatgatta 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================================================ aattttttaggttttacttgcctgtggtaagcaagattgttagtttacaatttgaaagcaaaagtaggcattttaaatggattagacaacaaaaatgaataaaaaaatgtgcccgaaggcacattttgtcagatattcctaaagatgatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 88 HP_score: -9.0 Tail_Score: -4.42619 Start: 108 End: 123 Full_Region: AAATGAATAAAAAAA TGTGCC CGAA GGCACA TTTTGTCAGATATTC ...........................................................................................................TGTGCCCGAAGGCACA............................ Find igs database================================================ Query_seq: PI0030:PI0031|PI0030:PI0031:transcriptional regulator, AsnC family:peptidylprolyl isomerase:->->:35111..35261 151 aattttttaggttttacttgcctgtggtaagcaagattgttagtttacaatttgaaagcaaaagtaggcattttaaatggattagacaacaaaaatgaataaaaaaatgtgcccgaaggcacattttgtcagatattcctaaagatgatta Intra-Species Hit: Count: 1 Min: 1 Max: 151 Len: 151 Subject: pint_PI0030_PI0031|transcriptional regulator, AsnC family:peptidylprolyl isomerase|POSITIVE:POSITIVE|[35111,35261]|151 HSP 1 e-value: 5.0E-68 bit: 258.0 Len: 151 Query Start:1 Query End:151 Subject Strand: POSITIVE Subject Start: 1 Subject End: 151 aattttttaggttttacttgcctgtggtaagcaagattgttagtttacaatttgaaagcaaaagtaggcattttaaatggattagacaacaaaaatgaatnnnnnnntgtgcccgaaggcacattttgtcagatattcctaaagatgatta aattttttaggttttacttgcctgtggtaagcaagattgttagtttacaatttgaaagcaaaagtaggcattttaaatggattagacaacaaaaatgaataaaaaaatgtgcccgaaggcacattttgtcagatattcctaaagatgatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUUUAGGUUUUACUUGCCUGUGGUAAGCAAGAUUGUUAGUUUACAAUUUGAAAGCAAAAGUAGGCAUUUUAAAUGGAUUAGACAACAAAAAUGAAUAAAAAAAUGUGCCCGAAGGCACAUUUUGUCAGAUAUUCCUAAAGAUGAUUA ...((((((((.....((((((...)))))).....(((((.(((((..((((((((((........)).))))))))....))))))))))...(((.....((((((((((....)))))))))).)))......))))))))...... (-37.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCAUCUUUAGGAAUAUCUGACAAAAUGUGCCUUCGGGCACAUUUUUUUAUUCAUUUUUGUUGUCUAAUCCAUUUAAAAUGCCUACUUUUGCUUUCAAAUUGUAAACUAACAAUCUUGCUUACCACAGGCAAGUAAAACCUAAAAAAUU ........((((((......(((.((((((((((....)))))))))).))).......((((((......(.((((.(((.((........))))).)))).).....)))))).(((((((.....))))))).....))))))..... (-32.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 265 58 11 68 18 pint:PI0302|5end_hypothetical_protein_286325..286555_POSITIVE 260 98 64 204 164 pint:PI1539|5end_3-phosphoshikimate_1-carboxyvinyltransferase_1459804..1460034_POSITIVE 246 140 108 231 187 pint:PI0496|5end_heat_shock_protein_hsp70_(chaperone_protein_dnaK)_456632..456862_POSITIVE 245 145 112 71 34 pint:PI0843|5end_carboxyl-terminal_protease_776145..776375_POSITIVE 238 70 21 38 2 pint:PI0306|5end_conserved_hypothetical_protein_288909..289139_POSITIVE 235 60 15 147 96 pint:PI1516|5end_multidrug_resistance_protein;_HlyD_family_secretion_protein_1434381..1434611_POSITIVE 232 68 21 217 159 pint:PI1721|5end_peptidyl-prolyl_cis-trans_isomerase,_PPIC-type_1638086..1638316_POSITIVE 231 139 93 59 8 pint:PI1760|5end_hypothetical_protein_1684413..1684643_POSITIVE 229 40 14 61 36 pint:PI1547|5end_hypothetical_protein_1465808..1466038_POSITIVE 229 121 83 51 15 pint:PI0572|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_516382..516612_POSITIVE 228 139 107 225 192 pint:PI0925|5end_ribosomal_protein_L11_methyltransferase_855806..856036_POSITIVE 226 150 108 167 122 pint:PI1625|5end_conserved_hypothetical_protein;_possible_phage_transposase_1549316..1549546_POSITIVE 226 69 21 160 110 pint:PI0508|5end_possible_cell_filamentation_protein_466463..466693_POSITIVE 226 150 108 167 122 pint:PI0332|5end_conserved_hypothetical_protein_312600..312830_POSITIVE 224 145 105 193 148 pint:PI1078|5end_conserved_hypothetical_protein_999500..999730_POSITIVE 221 62 29 61 22 pint:PI0627|5end_conserved_hypothetical_protein_575618..575848_POSITIVE 219 129 102 92 63 pint:PI0063|5end_transcriptional_regulator,_GntR_family_63181..63411_POSITIVE 218 140 106 58 33 pint:PI1066|5end_dihydrofolate_reductase_983427..983657_POSITIVE 218 70 23 91 49 pint:PI0199|5end_phosphate_acetyltransferase_189890..190120_POSITIVE 217 49 11 225 186 pint:PI1458|5end_dihydroneopterin_aldolase_1381166..1381396_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 273 68 22 110 68 pint:PI1380|3end_conserved_hypothetical_protein_1303242..1303392_POSITIVE 252 39 2 53 19 pint:PI1743|3end_stationary-phase_survival_protein_1664930..1665080_POSITIVE 234 131 99 51 16 pint:PI0023|3end_internalin-related_protein_28070..28220_POSITIVE 231 139 93 109 58 pint:PI1761|3end_hypothetical_protein_1684543..1684693_POSITIVE 230 120 77 122 66 pint:PI1495|3end_conserved_hypothetical_protein_1417022..1417172_POSITIVE 229 121 83 38 2 pint:PI0571|3end_conserved_hypothetical_protein;_possible_permease_516449..516599_POSITIVE 226 150 108 62 17 pint:PI0331|3end_hypothetical_protein_312575..312725_POSITIVE 224 70 22 53 5 pint:PI0199|3end_phosphate_acetyltransferase_190923..191073_POSITIVE 221 62 29 61 22 pint:PI0626|3end_penicillin-binding_protein,_D-alanyl-D-alanine_carboxypeptidase_575698..575848_POSITIVE 219 36 9 125 98 pint:PI0694|3end_Na+/dicarboxylate_or_sulfate_symporter_631177..631327_POSITIVE 217 132 108 119 90 pint:PI0365|3end_hypothetical_protein_336118..336268_POSITIVE 213 150 107 54 1 pint:PI0175|3end_succinyl-CoA_synthetase_beta_subunit_168233..168383_POSITIVE 212 70 22 134 89 pint:PI1642|3end_conserved_hypothetical_protein_1560439..1560589_POSITIVE 212 145 113 37 1 pint:PI0842|3end_5-formyltetrahydrofolate_cyclo-ligase_776191..776341_POSITIVE 212 70 22 134 89 pint:PI0348|3end_conserved_hypothetical_protein_323211..323361_POSITIVE 208 147 108 35 1 pint:PI2061|3end_type_I_restriction_enzyme_restriction_subunit_2021647..2021797_POSITIVE 208 119 71 113 78 pint:PI0554|3end_hypothetical_protein_504599..504749_POSITIVE 205 60 19 149 109 pint:PI2135|3end_conserved_hypothetical_protein_2083253..2083403_POSITIVE 204 121 107 113 99 pint:PI0539|3end_hypothetical_protein_493728..493878_POSITIVE 201 60 17 67 21 pint:PI0530|3end_possible_membrane-fusion_protein_484757..484907_POSITIVE