Origin IGS: tagtcgtcgttcgtgtttatccaaaccccacacaaacgcttgtttcttatagaaaacagcagttacagcaaacgctctcaaaacttattccaacggttttgagagcgtttttctttctgttttctcttgcatttgctaagagaatttattatctttgcactacaactgtattttttttacacgtaaataagaatttctctacacgtaaataaatatttctttacgcgtaagtaaatatttctcta .........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 tagagaaatatttacttacgcgtaaagaaatatttatttacgtgtagagaaattcttatttacgtgtaaaaaaaatacagttgtagtgcaaagataataaattctcttagcaaatgcaagagaaaacagaaagaaaaacgctctcaaaaccgttggaataagttttgagagcgtttgctgtaactgctgttttctataagaaacaagcgtttgtgtggggtttggataaacacgaacgacgacta Mask Tandem Repeat Region ================================================ tagtcgtcgttcgtgtttatccaaaccccacacaaacgcttgtttcttatagaaaacagcagttacagcaaacgctctcaaaacttattccaacggttttgagagcgtttttctttctgttttctcttgcatttgctaagagaatttattatctttgcactacaactgtatttttttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Find is-nt database================================================ Query_seq: PI0578:PI0579|PI0578:PI0579:methyltransferase:hypothetical protein:->->:523314..523558 245 tagtcgtcgttcgtgtttatccaaaccccacacaaacgcttgtttcttatagaaaacagcagttacagcaaacgctctcaaaacttattccaacggttttgagagcgtttttctttctgttttctcttgcatttgctaagagaatttattatctttgcactacaactgtattttttttacacgtaaataagaatttctctacacgtaaataaatatttctttacgcgtaagtaaatatttctcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0578:PI0579|PI0578:PI0579:methyltransferase:hypothetical protein:->->:523314..523558 245 tagtcgtcgttcgtgtttatccaaaccccacacaaacgcttgtttcttatagaaaacagcagttacagcaaacgctctcaaaacttattccaacggttttgagagcgtttttctttctgttttctcttgcatttgctaagagaatttattatctttgcactacaactgtattttttttacacgtaaataagaatttctctacacgtaaataaatatttctttacgcgtaagtaaatatttctcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0578:PI0579|PI0578:PI0579:methyltransferase:hypothetical protein:->->:523314..523558 245 tagtcgtcgttcgtgtttatccaaaccccacacaaacgcttgtttcttatagaaaacagcagttacagcaaacgctctcaaaacttattccaacggttttgagagcgtttttctttctgttttctcttgcatttgctaagagaatttattatctttgcactacaactgtattttttttacacgtaaataagaatttctctacacgtaaataaatatttctttacgcgtaagtaaatatttctcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagtcgtcgttcgtgtttatccaaaccccacacaaacgcttgtttcttatagaaaacagcagttacagcaaacgctctcaaaacttattccaacggttttgagagcgtttttctttctgttttctcttgcatttgctaagagaatttattatctttgcactacaactgtattttttttacacgtaaataagaatttctctacacgtaaataaatatttctttacgcgtaagtaaatatttctcta Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 87 End: 209 ...................................................................................... M P T V L R A F F F L F S L A F A K R I Y Y L C T T T V F F L H V N K N F S T R K .................................... Protein_Len: 32 Strand: - Start: 50 End: 145 ................................................. L F C C N C C V S E F S I G V T K L A N K K R N E R A N A L L M .................................................................................................... tagtcgtcgttcgtgtttatccaaaccccacacaaacgcttgtttcttatagaaaacagcagttacagcaaacgctctcaaaacttattccaacggttttgagagcgtttttctttctgttttctcttgcatttgctaagagaatttattatctttgcactacaactgtattttttttacacgtaaataagaatttctctacacgtaaataaatatttctttacgcgtaagtaaatatttctcta 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================================================ tagtcgtcgttcgtgtttatccaaaccccacacaaacgcttgtttcttatagaaaacagcagttacagcaaacgctctcaaaacttattccaacggttttgagagcgtttttctttctgttttctcttgcatttgctaagagaatttattatctttgcactacaactgtattttttttacacgtaaataagaatttctctacacgtaaataaatatttctttacgcgtaagtaaatatttctcta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.9 Tail_Score: -5.48623 Start: 73 End: 107 Full_Region: AGCAGTTACAGCAAA CGCTCTCAAAACT TATTCCAAC GGTTTTGAGAGCG TTTTTCTTTCTGTTT ........................................................................CGCTCTCAAAACTTATTCCAACGGTTTTGAGAGCG.......................................................................................................................................... TransTerm Strand: - Conf: 87 HP_score: -10.2 Tail_Score: -3.85092 Start: 73 End: 107 Full_Region: aaacagaaagaaaaa cgctctcaaaac cgttggaataa gttttgagagcg tttgctgtaactgct ........................................................................cgctctcaaaaccgttggaataagttttgagagcg.......................................................................................................................................... TransTerm Strand: + Conf: 71 HP_score: -5.7 Tail_Score: -4.52143 Start: 122 End: 144 Full_Region: GTTTTTCTTTCTGTT TTCTCTTGC ATTT GCTAAGAGAA TTTATTATCTTTGCA .........................................................................................................................TTCTCTTGCATTTGCTAAGAGAA..................................................................................................... Find igs database================================================ Query_seq: PI0578:PI0579|PI0578:PI0579:methyltransferase:hypothetical protein:->->:523314..523558 245 tagtcgtcgttcgtgtttatccaaaccccacacaaacgcttgtttcttatagaaaacagcagttacagcaaacgctctcaaaacttattccaacggttttgagagcgtttttctttctgttttctcttgcatttgctaagagaatttattatctttgcactacaactgtattttttttacacgtaaataagaatttctctacacgtaaataaatatttctttacgcgtaagtaaatatttctcta Intra-Species Hit: Count: 1 Min: 1 Max: 245 Len: 245 Subject: pint_PI0578_PI0579|methyltransferase:hypothetical protein|POSITIVE:POSITIVE|[523314,523558]|245 HSP 1 e-value: 1.0E-122 bit: 438.0 Len: 245 Query Start:1 Query End:245 Subject Strand: POSITIVE Subject Start: 1 Subject End: 245 tagtcgtcgttcgtgtttatccaaaccccacacaaacgcttgtttcttatagaaaacagcagttacagcaaacgctctcaaaacttattccaacggttttgagagcgtttttctttctgttttctcttgcatttgctaagagaatttattatctttgcactacaactgtannnnnnnnacacgtaaataagaatttctctacacgtaaataaatatttctttacgcgtaagtaaatatttctcta tagtcgtcgttcgtgtttatccaaaccccacacaaacgcttgtttcttatagaaaacagcagttacagcaaacgctctcaaaacttattccaacggttttgagagcgtttttctttctgttttctcttgcatttgctaagagaatttattatctttgcactacaactgtattttttttacacgtaaataagaatttctctacacgtaaataaatatttctttacgcgtaagtaaatatttctcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUCGUCGUUCGUGUUUAUCCAAACCCCACACAAACGCUUGUUUCUUAUAGAAAACAGCAGUUACAGCAAACGCUCUCAAAACUUAUUCCAACGGUUUUGAGAGCGUUUUUCUUUCUGUUUUCUCUUGCAUUUGCUAAGAGAAUUUAUUAUCUUUGCACUACAACUGUAUUUUUUUUACACGUAAAUAAGAAUUUCUCUACACGUAAAUAAAUAUUUCUUUACGCGUAAGUAAAUAUUUCUCUA .......((((.((((.............)))).))))((((((((...(((((((..((((((.....((((((((((((((((.........)))))))))))))))).......((..(((((((((....)).)))))))..))...............))))))...)))))))...).))))))).((((((.(((.((((((.((....)).)))))).))))).))))......... (-53.62) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAGAAAUAUUUACUUACGCGUAAAGAAAUAUUUAUUUACGUGUAGAGAAAUUCUUAUUUACGUGUAAAAAAAAUACAGUUGUAGUGCAAAGAUAAUAAAUUCUCUUAGCAAAUGCAAGAGAAAACAGAAAGAAAAACGCUCUCAAAACCGUUGGAAUAAGUUUUGAGAGCGUUUGCUGUAACUGCUGUUUUCUAUAAGAAACAAGCGUUUGUGUGGGGUUUGGAUAAACACGAACGACGACUA (((((((........(((((((((((.....((((.((((....)))).)))).....)))))))))))........((((((((((..............(((((((.((....)))))))))...........(((((((((((((((...........)))))))))))))))))))))))))...)))))))..........((((((((((...((....))..))))))))).)..... (-68.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 557 220 172 195 147 pint:PI0115|5end_hypothetical_protein_108062..108292_POSITIVE 557 220 172 181 133 pint:PI0111|5end_hypothetical_protein_108048..108278_POSITIVE 557 220 172 146 98 pint:PI0112|5end_hypothetical_protein_108013..108243_POSITIVE 501 230 181 150 101 pint:PI0619|5end_hypothetical_protein_569364..569594_POSITIVE 421 234 192 164 122 pint:PI0130|5end_hypothetical_protein_122032..122262_POSITIVE 366 230 181 116 67 pint:PI1450|5end_hypothetical_protein_1372683..1372913_POSITIVE 358 234 193 138 97 pint:PI0312|5end_hypothetical_protein_294591..294821_POSITIVE 351 118 71 192 145 pint:PI1477|5end_TonB-dependent_outer_membrane_receptor_1399734..1399964_POSITIVE 334 130 81 62 7 pint:PI0650|5end_conserved_hypothetical_protein_591617..591847_POSITIVE 315 137 93 155 104 pint:PI1483|5end_hypothetical_protein_1404310..1404540_POSITIVE 312 229 181 130 82 pint:PI0983|5end_hypothetical_protein_909750..909980_POSITIVE 312 70 25 155 108 pint:PI0734|5end_ABC_transporter,_ATP-binding_/_permease_667052..667282_POSITIVE 302 240 198 148 106 pint:PI1673|5end_hypothetical_protein_1587718..1587948_POSITIVE 297 218 180 231 192 pint:PI0172|5end_ISPg3-related_transposase_164262..164492_POSITIVE 291 63 21 129 90 pint:PI1727|5end__ATP-dependent_Clp_protease,_ATP-binding_subunit_1645680..1645910_POSITIVE 289 137 94 185 127 pint:PI0516|5end_ferredoxin,_4Fe-4S_475864..476094_POSITIVE 282 48 2 216 169 pint:PI0226|5end_ABC_transporter,_ATP-binding_/_permease_protein_222110..222340_POSITIVE 282 48 2 144 97 pint:PI0225|5end_conserved_hypothetical_protein_222038..222268_POSITIVE 279 137 94 162 119 pint:PI2140|5end_conserved_hypothetical_protein_2086773..2087003_POSITIVE 275 79 32 230 168 pint:PI0161|5end_possible_TonB_receptor_153364..153594_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 465 230 181 50 1 pint:PI0598|3end_hypothetical_protein_547233..547383_POSITIVE 324 234 201 44 11 pint:PI0808|3end_ISPg3-related_transposase_746457..746607_POSITIVE 279 137 94 61 18 pint:PI2139|3end_cysteinyl-tRNA_synthetase_2086752..2086902_POSITIVE 272 40 1 131 96 pint:PI1633|3end_hypothetical_protein_1552955..1553105_POSITIVE 272 234 200 41 3 pint:PI1461|3end_conserved_hypothetical_protein_1385073..1385223_POSITIVE 272 79 38 54 5 pint:PI0160|3end_conserved_hypothetical_protein_153268..153418_POSITIVE 271 138 92 139 93 pint:PI0674|3end_conserved_hypothetical_protein_616154..616304_POSITIVE 270 240 200 60 20 pint:PI1314|3end_hypothetical_protein_1231423..1231573_POSITIVE 270 234 200 68 34 pint:PI0172|3end_ISPg3-related_transposase_165238..165388_POSITIVE 266 230 181 119 68 pint:PI2105|3end_hypothetical_protein_2059586..2059736_POSITIVE 266 72 37 61 25 pint:PI1010|3end_conserved_hypothetical_protein_932195..932345_POSITIVE 261 138 91 90 41 pint:PI2125|3end_D-tyrosyl-tRNA(Tyr)_deacylase_2074979..2075129_POSITIVE 261 139 93 143 85 pint:PI2034|3end_conserved_hypothetical_protein_1988120..1988270_POSITIVE 258 174 132 146 109 pint:PI2172|3end_hypothetical_protein_2113991..2114141_POSITIVE 258 174 132 119 82 pint:PI2173|3end_hypothetical_protein_2113964..2114114_POSITIVE 258 75 49 119 94 pint:PI1486|3end_alginate_O-acetylation_protein_1407062..1407212_POSITIVE 257 160 111 143 98 pint:PI1742|3end_SpoOJ_regulator_protein_1665670..1665820_POSITIVE 252 48 3 136 94 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 248 132 94 64 21 pint:PI0261|3end_conjugative_transposon_protein,_TraK_254765..254915_POSITIVE 247 140 94 110 57 pint:PI0787|3end_glycosyltransferase_725793..725943_POSITIVE