Origin IGS: attatattttcagtctaatcagactgaaaataggtaagatactccttaacactattttttaggcgtaatggacatttggtaggctgatagttccagcctaccaaatgtccattacgccttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaggcgtaatggacatttggtaggctggaactatcagcctaccaaatgtccattacgcctaaaaaatagtgttaaggagtatcttacctattttcagtctgattagactgaaaatataat Mask Tandem Repeat Region ================================================ attatattttcagtctaatcagactgaaaataggtaagatactccttaacactattttttaggcgtaatggacatttggtaggctgatagttccagcctaccaaatgtccattacgccttta Find is-nt database================================================ Query_seq: PI1959:PI1960|PI1959:PI1960:hypothetical protein:hypothetical protein:->->:1918031..1918152 122 attatattttcagtctaatcagactgaaaataggtaagatactccttaacactattttttaggcgtaatggacatttggtaggctgatagttccagcctaccaaatgtccattacgccttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1959:PI1960|PI1959:PI1960:hypothetical protein:hypothetical protein:->->:1918031..1918152 122 attatattttcagtctaatcagactgaaaataggtaagatactccttaacactattttttaggcgtaatggacatttggtaggctgatagttccagcctaccaaatgtccattacgccttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1959:PI1960|PI1959:PI1960:hypothetical protein:hypothetical protein:->->:1918031..1918152 122 attatattttcagtctaatcagactgaaaataggtaagatactccttaacactattttttaggcgtaatggacatttggtaggctgatagttccagcctaccaaatgtccattacgccttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attatattttcagtctaatcagactgaaaataggtaagatactccttaacactattttttaggcgtaatggacatttggtaggctgatagttccagcctaccaaatgtccattacgccttta Predict ORF larger than 30AA ================================================ attatattttcagtctaatcagactgaaaataggtaagatactccttaacactattttttaggcgtaatggacatttggtaggctgatagttccagcctaccaaatgtccattacgccttta 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================================================ attatattttcagtctaatcagactgaaaataggtaagatactccttaacactattttttaggcgtaatggacatttggtaggctgatagttccagcctaccaaatgtccattacgccttta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1959:PI1960|PI1959:PI1960:hypothetical protein:hypothetical protein:->->:1918031..1918152 122 attatattttcagtctaatcagactgaaaataggtaagatactccttaacactattttttaggcgtaatggacatttggtaggctgatagttccagcctaccaaatgtccattacgccttta Intra-Species Hit: Count: 1 Min: 1 Max: 122 Len: 122 Subject: pint_PI1959_PI1960|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1918031,1918152]|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 attatattttcagtctaatcagactgaaaataggtaagatactccttaacactattttttaggcgtaatggacatttggtaggctgatagttccagcctaccaaatgtccattacgccttta attatattttcagtctaatcagactgaaaataggtaagatactccttaacactattttttaggcgtaatggacatttggtaggctgatagttccagcctaccaaatgtccattacgccttta HSP 2 e-value: 7.0E-14 bit: 77.8 Len: 59 Query Start:61 Query End:119 Subject Strand: NEGATIVE Subject Start: 61 Subject End: 119 ............................................................aggcgtaatggacatttggtaggctgatagttccagcctaccaaatgtccattacgcct... ............................................................aggcgtaatggacatttggtaggctggaactatcagcctaccaaatgtccattacgcct... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAUAUUUUCAGUCUAAUCAGACUGAAAAUAGGUAAGAUACUCCUUAACACUAUUUUUUAGGCGUAAUGGACAUUUGGUAGGCUGAUAGUUCCAGCCUACCAAAUGUCCAUUACGCCUUUA ....((((((((((((....))))))))))))..((((......))))............((((((((((((((((((((((((((.......))))))))))))))))))))))))))... (-63.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGGCGUAAUGGACAUUUGGUAGGCUGGAACUAUCAGCCUACCAAAUGUCCAUUACGCCUAAAAAAUAGUGUUAAGGAGUAUCUUACCUAUUUUCAGUCUGAUUAGACUGAAAAUAUAAU ...(((((((((((((((((((((((((((.....)))))))))))))))))))))))))))............((((......))))..((((((((((((....)))))))))))).... (-63.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 616 120 74 132 90 pint:PI1265|5end_hypothetical_protein_1185016..1185246_POSITIVE 611 120 74 132 90 pint:PI0709|5end_possible_IS1249-related_transposase_646467..646697_POSITIVE 591 101 65 189 153 pint:PI0535|5end_hypothetical_protein_489508..489738_POSITIVE 580 110 62 97 56 pint:PI1294|5end_hypothetical_protein_1208490..1208720_POSITIVE 580 110 61 163 121 pint:PI1025|5end_tRNA_modification_GTPase_940752..940982_POSITIVE 552 87 51 217 182 pint:PI1269|5end_conserved_hypothetical_protein;_possible_peptidase_1188147..1188377_POSITIVE 499 99 60 213 180 pint:PI1534|5end_ATPase/GTPase_1453679..1453909_POSITIVE 493 87 44 219 179 pint:PI1267|5end_probable_integrase_1186105..1186335_POSITIVE 487 115 74 127 90 pint:PI1907|5end_possible_IS1249-related_transposase_1851105..1851335_POSITIVE 487 115 74 127 90 pint:PI0840|5end_conserved_hypothetical_protein;_possible_transposase_774227..774457_POSITIVE 487 115 74 127 90 pint:PI0153|5end_IS1249-related_transposase_145930..146160_POSITIVE 467 115 78 127 94 pint:PI1292|5end_conserved_hypothetical_protein_1206106..1206336_POSITIVE 463 87 62 227 202 pint:PI1295|5end_hypothetical_protein_1208636..1208866_POSITIVE 382 113 71 231 196 pint:PI1971|5end_possible_IS1249-related_transposase_1928027..1928257_POSITIVE 382 113 71 231 196 pint:PI1533|5end_conserved_hypothetical_protein;_possible_transposase_1452667..1452897_POSITIVE 382 113 71 231 196 pint:PI0534|5end_conserved_hypothetical_protein;_possible_transposase_488568..488798_POSITIVE 306 102 62 53 8 pint:PI0257|5end_conjugative_transposon_protein,_TraF_249348..249578_POSITIVE 297 110 61 108 53 pint:PI1610|5end_Na+/H+_anti-porter_1536942..1537172_POSITIVE 294 114 75 141 95 pint:PI2154|5end_leucyl-tRNA_synthetase_2099861..2100091_POSITIVE 294 110 61 90 39 pint:PI0094|5end_protoporphyrinogen_oxidase_89571..89801_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 616 120 74 110 68 pint:PI1264|3end_hypothetical_protein_1185074..1185224_POSITIVE 591 101 65 91 55 pint:PI1533|3end_conserved_hypothetical_protein;_possible_transposase_1453589..1453739_POSITIVE 591 101 65 91 55 pint:PI0534|3end_conserved_hypothetical_protein;_possible_transposase_489490..489640_POSITIVE 580 110 61 63 21 pint:PI1024|3end_conserved_hypothetical_protein;_possible_nitroreductase_family_protein_940732..940882_POSITIVE 532 101 65 91 55 pint:PI1971|3end_possible_IS1249-related_transposase_1928949..1929099_POSITIVE 487 115 74 101 64 pint:PI0152|3end_DNA_mismatch_endonuclease_vsr_145984..146134_POSITIVE 466 119 94 30 5 pint:PI1959|3end_hypothetical_protein_1917970..1918120_POSITIVE 447 118 94 73 49 pint:PI0839|3end_conserved_hypothetical_protein_774210..774360_POSITIVE 318 87 42 67 20 pint:PI0787|3end_glycosyltransferase_725793..725943_POSITIVE 294 110 61 90 39 pint:PI0092|3end_regulatory_protein_RecX_89651..89801_POSITIVE 291 109 61 98 41 pint:PI0259|3end_conserved_protein_found_in_conjugation,_TraI_253043..253193_POSITIVE 283 107 63 73 26 pint:PI1455|3end_hypothetical_protein_1378963..1379113_POSITIVE 273 107 61 69 30 pint:PI1777|3end_conserved_hypothetical_protein_1710081..1710231_POSITIVE 273 102 63 45 1 pint:PI0256|3end_conjugative_transposon_protein,_TraE_249420..249570_POSITIVE 269 109 61 144 78 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 268 116 75 62 23 pint:PI1766|3end_sugar_transporter,_possible_glucose/galactose_transporter_1694350..1694500_POSITIVE 268 103 61 100 53 pint:PI0024|3end_hypothetical_protein_28559..28709_POSITIVE 265 107 68 106 65 pint:PI1437|3end_hypothetical_protein_1356407..1356557_POSITIVE 263 120 72 58 8 pint:PI1230|3end_probable_metallo-beta-lactamase_family_protein_1152729..1152879_POSITIVE 262 108 77 94 68 pint:PI1983|3end_possible_xylanase_1940004..1940154_POSITIVE