Origin IGS: aatccttacgtttaattaatgcaaaagtacaaaaaagagccgaaagcaccaaattgccatcacttccttttaaaagttactcgctgacaagtctttatatattcttctaaaaccatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatggttttagaagaatatataaagacttgtcagcgagtaacttttaaaaggaagtgatggcaatttggtgctttcggctcttttttgtacttttgcattaattaaacgtaaggatt Mask Tandem Repeat Region ================================================ aatccttacgtttaattaatgcaaaagtacaaaaaagagccgaaagcaccaaattgccatcacttccttttaaaagttactcgctgacaagtctttatatattcttctaaaaccatta Find is-nt database================================================ Query_seq: PI1858:PI1859|PI1858:PI1859:conserved hypothetical protein:conserved hypothetical protein:->->:1805416..1805533 118 aatccttacgtttaattaatgcaaaagtacaaaaaagagccgaaagcaccaaattgccatcacttccttttaaaagttactcgctgacaagtctttatatattcttctaaaaccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1858:PI1859|PI1858:PI1859:conserved hypothetical protein:conserved hypothetical protein:->->:1805416..1805533 118 aatccttacgtttaattaatgcaaaagtacaaaaaagagccgaaagcaccaaattgccatcacttccttttaaaagttactcgctgacaagtctttatatattcttctaaaaccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1858:PI1859|PI1858:PI1859:conserved hypothetical protein:conserved hypothetical protein:->->:1805416..1805533 118 aatccttacgtttaattaatgcaaaagtacaaaaaagagccgaaagcaccaaattgccatcacttccttttaaaagttactcgctgacaagtctttatatattcttctaaaaccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatccttacgtttaattaatgcaaaagtacaaaaaagagccgaaagcaccaaattgccatcacttccttttaaaagttactcgctgacaagtctttatatattcttctaaaaccatta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 15 End: 107 .............. M N A K V Q K R A E S T K L P S L P F K S Y S L T S L Y I F F ........... aatccttacgtttaattaatgcaaaagtacaaaaaagagccgaaagcaccaaattgccatcacttccttttaaaagttactcgctgacaagtctttatatattcttctaaaaccatta 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================================================ aatccttacgtttaattaatgcaaaagtacaaaaaagagccgaaagcaccaaattgccatcacttccttttaaaagttactcgctgacaagtctttatatattcttctaaaaccatta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1858:PI1859|PI1858:PI1859:conserved hypothetical protein:conserved hypothetical protein:->->:1805416..1805533 118 aatccttacgtttaattaatgcaaaagtacaaaaaagagccgaaagcaccaaattgccatcacttccttttaaaagttactcgctgacaagtctttatatattcttctaaaaccatta Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: pint_PI1858_PI1859|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1805416,1805533]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 aatccttacgtttaattaatgcaaaagtacaaaaaagagccgaaagcaccaaattgccatcacttccttttaaaagttactcgctgacaagtctttatatattcttctaaaaccatta aatccttacgtttaattaatgcaaaagtacaaaaaagagccgaaagcaccaaattgccatcacttccttttaaaagttactcgctgacaagtctttatatattcttctaaaaccatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCCUUACGUUUAAUUAAUGCAAAAGUACAAAAAAGAGCCGAAAGCACCAAAUUGCCAUCACUUCCUUUUAAAAGUUACUCGCUGACAAGUCUUUAUAUAUUCUUCUAAAACCAUUA .........((((......(((....)))....(((((...((..(((......)))..))..............((((.....))))...))))).............))))..... ( -7.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGGUUUUAGAAGAAUAUAUAAAGACUUGUCAGCGAGUAACUUUUAAAAGGAAGUGAUGGCAAUUUGGUGCUUUCGGCUCUUUUUUGUACUUUUGCAUUAAUUAAACGUAAGGAUU (((((....((((((...........(((((....))))).......(((((((..(((.((((......)))).)))..)))))))....)))))))))))......(....).... (-19.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 90 47 91 47 pint:PI0564|5end_hypothetical_protein_511537..511767_POSITIVE 275 80 39 46 9 pint:PI1447|5end_probable_OPT_oligopeptide_transporter_protein_1369972..1370202_POSITIVE 270 70 35 44 7 pint:PI0010|5end_conserved_hypothetical_protein_10628..10858_POSITIVE 268 59 21 50 2 pint:PI0843|5end_carboxyl-terminal_protease_776145..776375_POSITIVE 265 50 3 149 102 pint:PI1230|5end_probable_metallo-beta-lactamase_family_protein_1151840..1152070_POSITIVE 262 70 21 174 118 pint:PI1177|5end_hypothtical_protein_1098856..1099086_POSITIVE 257 55 20 143 113 pint:PI1326|5end_Na+-driven_multidrug_efflux_pump_1244182..1244412_POSITIVE 250 77 38 167 118 pint:PI2160|5end_hypothetical_protein_2107270..2107500_POSITIVE 246 71 35 41 5 pint:PI0251|5end_hypothetical_protein_247551..247781_POSITIVE 244 83 41 120 73 pint:PI1136|5end_conserved_hypothetical_protein_1062195..1062425_POSITIVE 235 96 55 46 16 pint:PI1690|5end_transcription_regulator;_possible_Fe2+/Zn2+_uptake_regulation_proteins_1604984..1605214_POSITIVE 233 89 41 96 50 pint:PI0592|5end_DNA_mismatch_repair_protein_540795..541025_POSITIVE 232 99 52 79 19 pint:PI0547|5end_fructose-bisphosphate_aldolase_498376..498606_POSITIVE 230 65 33 49 9 pint:PI1041|5end_hypothetical_protein_960443..960673_POSITIVE 227 65 33 55 15 pint:PI1064|5end_hypothetical_protein_983071..983301_POSITIVE 226 56 20 222 186 pint:PI1437|5end_hypothetical_protein_1356088..1356318_POSITIVE 226 56 20 95 59 pint:PI1436|5end_hypothetical_protein_1355961..1356191_POSITIVE 226 67 39 77 43 pint:PI0009|5end_NAD-dependent_epimerase/dehydratase_family_protein_9653..9883_POSITIVE 225 65 39 151 122 pint:PI1009|5end_cytochrome_c_nitrite_reductase,_large_subunit_929342..929572_POSITIVE 221 70 25 55 14 pint:PI0260|5end_conjugative_transposon_protein,_TraJ_253023..253253_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 90 47 131 87 pint:PI0565|3end_hypothetical_protein_511657..511807_POSITIVE 262 70 21 57 1 pint:PI1176|3end_endonuclease_III_1098819..1098969_POSITIVE 244 83 41 48 1 pint:PI1135|3end_hypothetical_protein_1062203..1062353_POSITIVE 237 41 2 47 4 pint:PI1032|3end_methylmalonyl-CoA_decarboxylase,_alpha_subunit_950162..950312_POSITIVE 229 57 15 76 34 pint:PI0017|3end_thiol-disulfide_isomerase;_thioredoxin_22835..22985_POSITIVE 228 95 54 95 46 pint:PI1713|3end_ABC_transporter,_ATP-binding_protein_1630192..1630342_POSITIVE 228 59 40 16 1 pint:PI0842|3end_5-formyltetrahydrofolate_cyclo-ligase_776191..776341_POSITIVE 225 65 39 60 31 pint:PI1008|3end_cytochrome_c_nitrite_reductase,_small_subunit_929331..929481_POSITIVE 219 77 37 34 2 pint:PI2061|3end_type_I_restriction_enzyme_restriction_subunit_2021647..2021797_POSITIVE 214 96 51 144 107 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 212 93 52 51 8 pint:PI0789|3end_NAD-utilizing_dehydrogenase_728385..728535_POSITIVE 208 87 54 138 104 pint:PI1516|3end_multidrug_resistance_protein;_HlyD_family_secretion_protein_1435693..1435843_POSITIVE 208 69 39 66 35 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 207 64 38 144 122 pint:PI0857|3end_hypothetical_protein_790986..791136_POSITIVE 207 109 80 87 55 pint:PI0358|3end_hypothetical_protein_328105..328255_POSITIVE 206 76 31 122 63 pint:PI1264|3end_hypothetical_protein_1185074..1185224_POSITIVE 205 86 41 43 7 pint:PI1622|3end_hypothetical_protein_1547230..1547380_POSITIVE 204 67 26 147 103 pint:PI0540|3end_conserved_hypothetical_protein_493865..494015_POSITIVE 204 70 29 136 86 pint:PI0140|3end_conserved_hypothetical_protein_132106..132256_POSITIVE 202 64 35 137 109 pint:PI1726|3end_ATP-dependent_DNA_helicase_1645542..1645692_POSITIVE