Origin IGS: agcgcagttatcactttttaacagaattatctttacaaaattttataaaaaaaacgacttgcaattgctgaatataggcagctgcaagtcgtttcgtttagaaatta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taatttctaaacgaaacgacttgcagctgcctatattcagcaattgcaagtcgttttttttataaaattttgtaaagataattctgttaaaaagtgataactgcgct Mask Tandem Repeat Region ================================================ agcgcagttatcactttttaacagaattatctttacaaaattttataaaaaaaacgacttgcaattgctgaatataggcagctgcaagtcgtttcgtttagaaatta Find is-nt database================================================ Query_seq: PI0004:PI0007|PI0004:PI0007:hypothetical protein:hypothetical protein:->->:6450..6556 107 agcgcagttatcactttttaacagaattatctttacaaaattttataaaaaaaacgacttgcaattgctgaatataggcagctgcaagtcgtttcgtttagaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0004:PI0007|PI0004:PI0007:hypothetical protein:hypothetical protein:->->:6450..6556 107 agcgcagttatcactttttaacagaattatctttacaaaattttataaaaaaaacgacttgcaattgctgaatataggcagctgcaagtcgtttcgtttagaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0004:PI0007|PI0004:PI0007:hypothetical protein:hypothetical protein:->->:6450..6556 107 agcgcagttatcactttttaacagaattatctttacaaaattttataaaaaaaacgacttgcaattgctgaatataggcagctgcaagtcgtttcgtttagaaatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcgcagttatcactttttaacagaattatctttacaaaattttataaaaaaaacgacttgcaattgctgaatataggcagctgcaagtcgtttcgtttagaaatta Predict ORF larger than 30AA ================================================ agcgcagttatcactttttaacagaattatctttacaaaattttataaaaaaaacgacttgcaattgctgaatataggcagctgcaagtcgtttcgtttagaaatta 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================================================ agcgcagttatcactttttaacagaattatctttacaaaattttataaaaaaaacgacttgcaattgctgaatataggcagctgcaagtcgtttcgtttagaaatta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -10.9 Tail_Score: -4.06903 Start: 55 End: 91 Full_Region: ATTTTATAAAAAAAA CGACTTGCAATTGCTGA ATA TAGGCAGCTGCAAGTCG TTTCGTTTAGAAATT ......................................................CGACTTGCAATTGCTGAATATAGGCAGCTGCAAGTCG................ Find igs database================================================ Query_seq: PI0004:PI0007|PI0004:PI0007:hypothetical protein:hypothetical protein:->->:6450..6556 107 agcgcagttatcactttttaacagaattatctttacaaaattttataaaaaaaacgacttgcaattgctgaatataggcagctgcaagtcgtttcgtttagaaatta Intra-Species Hit: Count: 1 Min: 1 Max: 107 Len: 107 Subject: pint_PI0004_PI0007|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[6450,6556]|107 HSP 1 e-value: 3.0E-40 bit: 165.0 Len: 107 Query Start:1 Query End:107 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 agcgcagttatcactttttaacagaattatctttacaaaattttatnnnnnnnncgacttgcaattgctgaatataggcagctgcaagtcgtttcgtttagaaatta agcgcagttatcactttttaacagaattatctttacaaaattttataaaaaaaacgacttgcaattgctgaatataggcagctgcaagtcgtttcgtttagaaatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCGCAGUUAUCACUUUUUAACAGAAUUAUCUUUACAAAAUUUUAUAAAAAAAACGACUUGCAAUUGCUGAAUAUAGGCAGCUGCAAGUCGUUUCGUUUAGAAAUUA ......((((........))))................((((((.((((..((((((((((((.(((((.......))))).))))))))))))..)))))))))). (-29.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUUCUAAACGAAACGACUUGCAGCUGCCUAUAUUCAGCAAUUGCAAGUCGUUUUUUUUAUAAAAUUUUGUAAAGAUAAUUCUGUUAAAAAGUGAUAACUGCGCU ...(((.((((.((((((((((((((.(((.........))).)))))))))))))).)))).))).(((((...(((....)))..))))).(((.......))). (-26.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 556 39 1 130 92 pint:PI1702|5end_hypothetical_protein_1620587..1620817_POSITIVE 475 38 1 191 154 pint:PI1371|5end_hypothetical_protein_1292359..1292589_POSITIVE 472 40 1 73 34 pint:PI1041|5end_hypothetical_protein_960443..960673_POSITIVE 464 42 1 60 19 pint:PI1540|5end_hypothetical_protein_1461362..1461592_POSITIVE 437 41 1 172 132 pint:PI0867|5end_hypothetical_protein_803859..804089_POSITIVE 437 41 1 89 49 pint:PI0866|5end_hypothetical_protein_803776..804006_POSITIVE 407 41 1 118 78 pint:PI0659|5end_hypothetical_protein_603203..603433_POSITIVE 403 41 1 113 73 pint:PI0089|5end_hypothetical_protein_88162..88392_POSITIVE 394 32 1 231 200 pint:PI0211|5end_hypothetical_protein_204067..204297_POSITIVE 390 40 1 79 40 pint:PI1064|5end_hypothetical_protein_983071..983301_POSITIVE 360 40 1 113 73 pint:PI0568|5end_hypothetical_protein_512950..513180_POSITIVE 355 41 1 132 92 pint:PI2022|5end_hypothetical_protein_1978631..1978861_POSITIVE 355 41 1 86 46 pint:PI2023|5end_hypothetical_protein_1978585..1978815_POSITIVE 345 40 6 35 1 pint:PI1072|5end_hypothetical_protein_990220..990450_POSITIVE 329 40 1 44 5 pint:PI0884|5end_hypothetical_protein_817302..817532_POSITIVE 317 39 7 33 1 pint:PI1308|5end_hypothetical_protein_1223419..1223649_POSITIVE 313 89 41 53 1 pint:PI2145|5end_hypothetical_protein_2092213..2092443_POSITIVE 308 91 51 107 54 pint:PI1476|5end_acyl-CoA_synthase/O-succinylbenzoic_acid-CoA_ligase_1397699..1397929_POSITIVE 303 97 53 174 122 pint:PI1639|5end_conserved_hypothetical_protein_1556725..1556955_POSITIVE 300 96 55 104 38 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 529 42 1 43 2 pint:PI0010|3end_conserved_hypothetical_protein_11679..11829_POSITIVE 373 94 56 39 1 pint:PI0004|3end_hypothetical_protein_6389..6539_POSITIVE 360 40 1 138 98 pint:PI0567|3end_hypothetical_protein_513055..513205_POSITIVE 355 41 1 52 12 pint:PI2021|3end_DNA_repair_protein_1978631..1978781_POSITIVE 330 39 11 31 3 pint:PI1379|3end_hypothetical_protein_1302292..1302442_POSITIVE 322 90 47 44 1 pint:PI1040|3end_8-amino-7-oxononanoate_synthase_960202..960352_POSITIVE 313 89 41 60 8 pint:PI2144|3end_hypothetical_protein_2092300..2092450_POSITIVE 299 96 60 61 15 pint:PI1608|3end_possible_Na+/H+_anti-porter_1536300..1536450_POSITIVE 293 99 53 90 44 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 273 91 54 62 20 pint:PI0719|3end_conserved_hypothetical_protein_654010..654160_POSITIVE 272 92 55 59 2 pint:PI2169|3end_hypothetical_protein_2112325..2112475_POSITIVE 271 39 10 30 1 pint:PI1307|3end_possible_Fe-S_oxidoreductase_1223496..1223646_POSITIVE 269 99 55 74 25 pint:PI1741|3end_lipid-A-disaccharide_synthase_1663856..1664006_POSITIVE 263 97 57 135 104 pint:PI0459|3end_30S_ribosomal_protein_S10_432467..432617_POSITIVE 263 84 55 59 28 pint:PI0249|3end_conserved_hypothetical_protein_247026..247176_POSITIVE 260 97 53 48 5 pint:PI0679|3end_hypothetical_protein_617012..617162_POSITIVE 259 99 55 130 87 pint:PI1382|3end_hypothetical_protein_1304137..1304287_POSITIVE 259 100 55 47 3 pint:PI0094|3end_protoporphyrinogen_oxidase_90511..90661_POSITIVE 255 97 53 82 37 pint:PI0951|3end_hypothetical_protein_885448..885598_POSITIVE 255 99 55 76 38 pint:PI0809|3end_hypothetical_protein_747108..747258_POSITIVE