Origin IGS: taaaagaaaagacagttataaaaggtatgacaaagcaaatagaattaataattagcaatacaaataaaatactgttaaataatacaatacagaggagaaagtgtataataaatattaaatcgttaaattcttttaactaatagatttgcttttatcctcatttattagtatatttgcgatgcaaaatctaaataaaaactaaatatgtataataatttaaatgtgaaaattcacgttatgagcacaagttacttagctcttttagcatatatcagtctaatctttaaatattaatttcatatcaaataaaacc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggttttatttgatatgaaattaatatttaaagattagactgatatatgctaaaagagctaagtaacttgtgctcataacgtgaattttcacatttaaattattatacatatttagtttttatttagattttgcatcgcaaatatactaataaatgaggataaaagcaaatctattagttaaaagaatttaacgatttaatatttattatacactttctcctctgtattgtattatttaacagtattttatttgtattgctaattattaattctatttgctttgtcataccttttataactgtcttttctttta Mask Tandem Repeat Region ================================================ taaaagaaaagacagttataaaaggtatgacaaagcaaatagaattaataattagcaatacaaataaaatactgttaaataatacaatacagaggagaaagtgtataataaatattaaatcgttaaattcttttaactaatagatttgcttttatcctcatttattagtatatttgcgatgcaaaatctaaataaaaactaaatatgtataataatttaaatgtgaaaattcacgttatgagcacaagttacttagctcttttagcatatatcagtctaatctttaaatattaatttcatatcaaataaaacc Find is-nt database================================================ Query_seq: PI1695:PI1696|PI1695:PI1696:hypothetical protein:conserved hypothetical protein:->->:1610371..1610683 313 taaaagaaaagacagttataaaaggtatgacaaagcaaatagaattaataattagcaatacaaataaaatactgttaaataatacaatacagaggagaaagtgtataataaatattaaatcgttaaattcttttaactaatagatttgcttttatcctcatttattagtatatttgcgatgcaaaatctaaataaaaactaaatatgtataataatttaaatgtgaaaattcacgttatgagcacaagttacttagctcttttagcatatatcagtctaatctttaaatattaatttcatatcaaataaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1695:PI1696|PI1695:PI1696:hypothetical protein:conserved hypothetical protein:->->:1610371..1610683 313 taaaagaaaagacagttataaaaggtatgacaaagcaaatagaattaataattagcaatacaaataaaatactgttaaataatacaatacagaggagaaagtgtataataaatattaaatcgttaaattcttttaactaatagatttgcttttatcctcatttattagtatatttgcgatgcaaaatctaaataaaaactaaatatgtataataatttaaatgtgaaaattcacgttatgagcacaagttacttagctcttttagcatatatcagtctaatctttaaatattaatttcatatcaaataaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1695:PI1696|PI1695:PI1696:hypothetical protein:conserved hypothetical protein:->->:1610371..1610683 313 taaaagaaaagacagttataaaaggtatgacaaagcaaatagaattaataattagcaatacaaataaaatactgttaaataatacaatacagaggagaaagtgtataataaatattaaatcgttaaattcttttaactaatagatttgcttttatcctcatttattagtatatttgcgatgcaaaatctaaataaaaactaaatatgtataataatttaaatgtgaaaattcacgttatgagcacaagttacttagctcttttagcatatatcagtctaatctttaaatattaatttcatatcaaataaaacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaagaaaagacagttataaaaggtatgacaaagcaaatagaattaataattagcaatacaaataaaatactgttaaataatacaatacagaggagaaagtgtataataaatattaaatcgttaaattcttttaactaatagatttgcttttatcctcatttattagtatatttgcgatgcaaaatctaaataaaaactaaatatgtataataatttaaatgtgaaaattcacgttatgagcacaagttacttagctcttttagcatatatcagtctaatctttaaatattaatttcatatcaaataaaacc Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 18 End: 137 ................. M K G M T K Q I E L I I S N T N K I L L N N T I Q R R K C I I N I K S L N S F N ................................................................................................................................................................................ Protein_Len: 38 Strand: - Start: 2 End: 115 . F S F V T I F P I V F C I S N I I L L V F L I S N F L V I C L L F H I I F M ...................................................................................................................................................................................................... taaaagaaaagacagttataaaaggtatgacaaagcaaatagaattaataattagcaatacaaataaaatactgttaaataatacaatacagaggagaaagtgtataataaatattaaatcgttaaattcttttaactaatagatttgcttttatcctcatttattagtatatttgcgatgcaaaatctaaataaaaactaaatatgtataataatttaaatgtgaaaattcacgttatgagcacaagttacttagctcttttagcatatatcagtctaatctttaaatattaatttcatatcaaataaaacc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 79 End: 108 ..............................................................................TTATACACTTTCTCCTCTGTATTGTATTAT............................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 145 End: 174 ................................................................................................................................................TTTGCTTTTATCCTCATTTATTAGTATATT........................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaagaaaagacagttataaaaggtatgacaaagcaaatagaattaataattagcaatacaaataaaatactgttaaataatacaatacagaggagaaagtgtataataaatattaaatcgttaaattcttttaactaatagatttgcttttatcctcatttattagtatatttgcgatgcaaaatctaaataaaaactaaatatgtataataatttaaatgtgaaaattcacgttatgagcacaagttacttagctcttttagcatatatcagtctaatctttaaatattaatttcatatcaaataaaacc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1695:PI1696|PI1695:PI1696:hypothetical protein:conserved hypothetical protein:->->:1610371..1610683 313 taaaagaaaagacagttataaaaggtatgacaaagcaaatagaattaataattagcaatacaaataaaatactgttaaataatacaatacagaggagaaagtgtataataaatattaaatcgttaaattcttttaactaatagatttgcttttatcctcatttattagtatatttgcgatgcaaaatctaaataaaaactaaatatgtataataatttaaatgtgaaaattcacgttatgagcacaagttacttagctcttttagcatatatcagtctaatctttaaatattaatttcatatcaaataaaacc Intra-Species Hit: Count: 1 Min: 1 Max: 313 Len: 313 Subject: pint_PI1695_PI1696|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1610371,1610683]|313 HSP 1 e-value: 1.0E-39 bit: 165.0 Len: 83 Query Start:231 Query End:313 Subject Strand: POSITIVE Subject Start: 231 Subject End: 313 ......................................................................................................................................................................................................................................tcacgttatgagcacaagttacttagctcttttagcatatatcagtctaatctttaaatattaatttcatatcaaataaaacc ......................................................................................................................................................................................................................................tcacgttatgagcacaagttacttagctcttttagcatatatcagtctaatctttaaatattaatttcatatcaaataaaacc HSP 2 e-value: 4.0E-27 bit: 123.0 Len: 62 Query Start:121 Query End:182 Subject Strand: POSITIVE Subject Start: 121 Subject End: 182 ........................................................................................................................cgttaaattcttttaactaatagatttgcttttatcctcatttattagtatatttgcgatgc................................................................................................................................... ........................................................................................................................cgttaaattcttttaactaatagatttgcttttatcctcatttattagtatatttgcgatgc................................................................................................................................... HSP 3 e-value: 2.0E-7 bit: 58.0 Len: 29 Query Start:1 Query End:29 Subject Strand: POSITIVE Subject Start: 1 Subject End: 29 taaaagaaaagacagttataaaaggtatg............................................................................................................................................................................................................................................................................................ taaaagaaaagacagttataaaaggtatg............................................................................................................................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGAAAAGACAGUUAUAAAAGGUAUGACAAAGCAAAUAGAAUUAAUAAUUAGCAAUACAAAUAAAAUACUGUUAAAUAAUACAAUACAGAGGAGAAAGUGUAUAAUAAAUAUUAAAUCGUUAAAUUCUUUUAACUAAUAGAUUUGCUUUUAUCCUCAUUUAUUAGUAUAUUUGCGAUGCAAAAUCUAAAUAAAAACUAAAUAUGUAUAAUAAUUUAAAUGUGAAAAUUCACGUUAUGAGCACAAGUUACUUAGCUCUUUUAGCAUAUAUCAGUCUAAUCUUUAAAUAUUAAUUUCAUAUCAAAUAAAACC ..(((((..((((.((((((.....))))))...(((((((..((((((((((((((...............)))))).............(((((((((((....(((...(((((....((((((....))))))))))).))).)))))).)))))..)))))))).))))))).........................((((((...........(((((((....)))))))..((((............)))).....))))))....))))..)))))............................ (-52.76) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUUUAUUUGAUAUGAAAUUAAUAUUUAAAGAUUAGACUGAUAUAUGCUAAAAGAGCUAAGUAACUUGUGCUCAUAACGUGAAUUUUCACAUUUAAAUUAUUAUACAUAUUUAGUUUUUAUUUAGAUUUUGCAUCGCAAAUAUACUAAUAAAUGAGGAUAAAAGCAAAUCUAUUAGUUAAAAGAAUUUAACGAUUUAAUAUUUAUUAUACACUUUCUCCUCUGUAUUGUAUUAUUUAACAGUAUUUUAUUUGUAUUGCUAAUUAUUAAUUCUAUUUGCUUUGUCAUACCUUUUAUAACUGUCUUUUCUUUUA ((((((((.....)))))))).......(((((..((((.(.((((.((((((.((((((((...)))).)))).....((((....))))...................)))))).((((((.....(((((...)))))......)))))).((((((.(((((((((......((((((....))))))((.((((((.(((..(((((...........(((((((........)))))))......)))))...))).)))))).)).)))))))))...)).)))).)))).).))))..))))).. (-50.23) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 181 146 206 167 pint:PI0240|5end_conserved_hypothetical_protein_238462..238692_POSITIVE 244 275 234 107 64 pint:PI1002|5end_metal_dependent_hydrolase_923842..924072_POSITIVE 242 274 234 216 173 pint:PI1058|5end_possible_FHA_domain_protein_977577..977807_POSITIVE 237 246 211 217 189 pint:PI0674|5end_conserved_hypothetical_protein_613711..613941_POSITIVE 237 246 211 153 125 pint:PI0675|5end_hypothetical_protein_613647..613877_POSITIVE 231 185 143 223 182 pint:PI0455|5end_hypothetical_protein_427361..427591_POSITIVE 222 268 231 45 1 pint:PI2085|5end_conserved_hypothetical_protein_2041100..2041330_POSITIVE 221 190 173 36 19 pint:PI2144|5end_hypothetical_protein_2091954..2092184_POSITIVE 221 190 173 209 192 pint:PI2003|5end_hypothetical_protein_1960823..1961053_POSITIVE 221 190 173 48 31 pint:PI2002|5end_hypothetical_protein_1960662..1960892_POSITIVE 221 190 173 48 31 pint:PI1934|5end_hypothetical_protein_1882363..1882593_POSITIVE 221 190 173 36 19 pint:PI1866|5end_hypothetical_protein_1811693..1811923_POSITIVE 221 276 232 80 44 pint:PI1451|5end_outer_membrane_receptor_proteins,_tonB_dependent_(possibly_iron_transport_related)_1372931..1373161_POSITIVE 221 190 173 48 31 pint:PI1346|5end_hypothetical_protein_1260814..1261044_POSITIVE 221 190 173 56 39 pint:PI1168|5end_hypothetical_protein_1089696..1089926_POSITIVE 221 190 173 48 31 pint:PI1167|5end_hypothetical_protein_1089688..1089918_POSITIVE 221 190 173 36 19 pint:PI1129|5end_hypothetical_protein_1055377..1055607_POSITIVE 221 190 173 20 3 pint:PI0061|5end_hypothetical_protein_60500..60730_POSITIVE 221 190 173 20 3 pint:PI0004|5end_hypothetical_protein_6199..6429_POSITIVE 218 114 89 89 61 pint:PI0611|5end_hypothetical_protein_559387..559617_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 253 181 146 99 60 pint:PI0239|3end_conserved_hypothetical_protein_238435..238585_POSITIVE 244 275 234 107 64 pint:PI1001|3end_hypothetical_protein_923922..924072_POSITIVE 242 274 234 107 64 pint:PI1057|3end_hypothetical_protein_977548..977698_POSITIVE 221 190 173 134 117 pint:PI1922|3end_hypothetical_protein_1865454..1865604_POSITIVE 221 190 173 130 113 pint:PI1340|3end_hypothetical_protein_1256872..1257022_POSITIVE 221 190 173 31 14 pint:PI0996|3end_hypothetical_protein_920660..920810_POSITIVE 221 190 173 90 73 pint:PI0759|3end_hypothetical_protein_693998..694148_POSITIVE 221 190 173 130 113 pint:PI0670|3end_hypothetical_protein_611280..611430_POSITIVE 221 190 173 130 113 pint:PI0061|3end_hypothetical_protein_60690..60840_POSITIVE 221 190 173 130 113 pint:PI0004|3end_hypothetical_protein_6389..6539_POSITIVE 216 273 231 131 82 pint:PI0445|3end_conserved_hypothetical_protein_413359..413509_POSITIVE 215 56 11 68 23 pint:PI1481|3end_hypothetical_protein_1404232..1404382_POSITIVE 214 285 246 133 85 pint:PI0475|3end_50S_ribosomal_protein_L6_440096..440246_POSITIVE 213 278 233 119 71 pint:PI1715|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1632324..1632474_POSITIVE 213 275 231 126 84 pint:PI0348|3end_conserved_hypothetical_protein_323211..323361_POSITIVE 210 275 231 126 84 pint:PI1642|3end_conserved_hypothetical_protein_1560439..1560589_POSITIVE 210 189 173 139 123 pint:PI1601|3end_hypothetical_protein_1530454..1530604_POSITIVE 210 190 155 102 74 pint:PI0866|3end_hypothetical_protein_803993..804143_POSITIVE 209 286 242 109 70 pint:PI0713|3end_hypothetical_protein_650529..650679_POSITIVE 209 246 203 108 61 pint:PI0701|3end_hypothetical_protein_638537..638687_POSITIVE