Origin IGS: tagcagccctttcttctgcactgttcacccggcagggcacgcaagagcagacgctctgctgaggtaaatcaaaaacagctatgcccgcacagggcagaaacctatttattaacccgcaaccccaaaggggctgcacaaaattaaacaatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattgtttaattttgtgcagcccctttggggttgcgggttaataaataggtttctgccctgtgcgggcatagctgtttttgatttacctcagcagagcgtctgctcttgcgtgccctgccgggtgaacagtgcagaagaaagggctgcta Mask Tandem Repeat Region ================================================ tagcagccctttcttctgcactgttcacccggcagggcacgcaagagcagacgctctgctgaggtaaatcaaaaacagctatgcccgcacagggcagaaacctatttattaacccgcaaccccaaaggggctgcacaaaattaaacaatt Find is-nt database================================================ Query_seq: PI1227:PI1228|PI1227:PI1228:conserved hypothetical protein; possible DNA-binding protein, histone-like family:conserved hypothetical protein:->->:1149035..1149184 150 tagcagccctttcttctgcactgttcacccggcagggcacgcaagagcagacgctctgctgaggtaaatcaaaaacagctatgcccgcacagggcagaaacctatttattaacccgcaaccccaaaggggctgcacaaaattaaacaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1227:PI1228|PI1227:PI1228:conserved hypothetical protein; possible DNA-binding protein, histone-like family:conserved hypothetical protein:->->:1149035..1149184 150 tagcagccctttcttctgcactgttcacccggcagggcacgcaagagcagacgctctgctgaggtaaatcaaaaacagctatgcccgcacagggcagaaacctatttattaacccgcaaccccaaaggggctgcacaaaattaaacaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1227:PI1228|PI1227:PI1228:conserved hypothetical protein; possible DNA-binding protein, histone-like family:conserved hypothetical protein:->->:1149035..1149184 150 tagcagccctttcttctgcactgttcacccggcagggcacgcaagagcagacgctctgctgaggtaaatcaaaaacagctatgcccgcacagggcagaaacctatttattaacccgcaaccccaaaggggctgcacaaaattaaacaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagcagccctttcttctgcactgttcacccggcagggcacgcaagagcagacgctctgctgaggtaaatcaaaaacagctatgcccgcacagggcagaaacctatttattaacccgcaaccccaaaggggctgcacaaaattaaacaatt Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 16 End: 141 ............... M H C S P G R A R K S R R S A E V N Q K Q L C P H R A E T Y L L T R N P K G A A Q N ......... Protein_Len: 49 Strand: - Start: 2 End: 148 . A A R E E A S N V R C P V C S C V S Q Q P L D F V A I G A C P L F R N I L G C G W L P Q V F N F M .. tagcagccctttcttctgcactgttcacccggcagggcacgcaagagcagacgctctgctgaggtaaatcaaaaacagctatgcccgcacagggcagaaacctatttattaacccgcaaccccaaaggggctgcacaaaattaaacaatt 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================================================ tagcagccctttcttctgcactgttcacccggcagggcacgcaagagcagacgctctgctgaggtaaatcaaaaacagctatgcccgcacagggcagaaacctatttattaacccgcaaccccaaaggggctgcacaaaattaaacaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1227:PI1228|PI1227:PI1228:conserved hypothetical protein; possible DNA-binding protein, histone-like family:conserved hypothetical protein:->->:1149035..1149184 150 tagcagccctttcttctgcactgttcacccggcagggcacgcaagagcagacgctctgctgaggtaaatcaaaaacagctatgcccgcacagggcagaaacctatttattaacccgcaaccccaaaggggctgcacaaaattaaacaatt Intra-Species Hit: Count: 1 Min: 1 Max: 150 Len: 150 Subject: pint_PI1227_PI1228|conserved hypothetical protein; possible DNA-binding protein, histone-like family:conserved hypothetical protein|POSITIVE:POSITIVE|[1149035,1149184]|150 HSP 1 e-value: 5.0E-80 bit: 297.0 Len: 150 Query Start:1 Query End:150 Subject Strand: POSITIVE Subject Start: 1 Subject End: 150 tagcagccctttcttctgcactgttcacccggcagggcacgcaagagcagacgctctgctgaggtaaatcaaaaacagctatgcccgcacagggcagaaacctatttattaacccgcaaccccaaaggggctgcacaaaattaaacaatt tagcagccctttcttctgcactgttcacccggcagggcacgcaagagcagacgctctgctgaggtaaatcaaaaacagctatgcccgcacagggcagaaacctatttattaacccgcaaccccaaaggggctgcacaaaattaaacaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCAGCCCUUUCUUCUGCACUGUUCACCCGGCAGGGCACGCAAGAGCAGACGCUCUGCUGAGGUAAAUCAAAAACAGCUAUGCCCGCACAGGGCAGAAACCUAUUUAUUAACCCGCAACCCCAAAGGGGCUGCACAAAAUUAAACAAUU ..((((((((((....(((.(((((.((((((((((((..((....))....))))))))).)))........)))))...(((((.....)))))...................)))......))))))))))................ (-50.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUGUUUAAUUUUGUGCAGCCCCUUUGGGGUUGCGGGUUAAUAAAUAGGUUUCUGCCCUGUGCGGGCAUAGCUGUUUUUGAUUUACCUCAGCAGAGCGUCUGCUCUUGCGUGCCCUGCCGGGUGAACAGUGCAGAAGAAAGGGCUGCUA ................(((((((..(((((((...(((((((.((((((.(...(((((.....))))).).)))))))))))))))))))).......(((((.((.(..(((((....)))))..))).))))).....))))))).. (-52.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 453 49 3 191 129 pint:PI0651|5end_HD_superfamily_hydrolase_592270..592500_POSITIVE 410 56 12 75 25 pint:PI1923|5end_conserved_hypothetical_protein_1865560..1865790_POSITIVE 401 65 21 142 98 pint:PI0702|5end_conserved_hypothetical_protein;_possible_tetracenomycin_C_synthesis_protein_homolog_638640..638870_POSITIVE 397 61 21 109 63 pint:PI2029|5end_DNA_topoisomerase_I_1982775..1983005_POSITIVE 384 66 21 166 131 pint:PI1157|5end_hypothetical_protein_1081704..1081934_POSITIVE 379 58 12 152 96 pint:PI0566|5end_enoyl-[acyl-carrier-protein]_reductase_511832..512062_POSITIVE 366 66 25 121 66 pint:PI1381|5end_conserved_hypothetical_protein_1303060..1303290_POSITIVE 361 60 15 123 64 pint:PI1468|5end_conserved_hypothetical_protein;_probable_TPR_domain_protein_1393900..1394130_POSITIVE 360 60 13 73 22 pint:PI1586|5end_possible_HesA/MoeB/ThiF_family_protein_1514372..1514602_POSITIVE 356 66 22 167 117 pint:PI0544|5end_hypoxanthine-guanine_phosphoribosyltransferase_(hypoxanthine_phosphoribosyltransferase)_495645..495875_POSITIVE 356 66 22 76 26 pint:PI0542|5end_hypothetical_protein_495554..495784_POSITIVE 349 50 8 228 182 pint:PI0333|5end_hypothetical_protein_313478..313708_POSITIVE 345 89 43 213 164 pint:PI1755|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1681930..1682160_POSITIVE 345 64 25 50 3 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 343 69 31 84 41 pint:PI0592|5end_DNA_mismatch_repair_protein_540795..541025_POSITIVE 335 66 28 201 155 pint:PI0790|5end_hypothetical_protein_728953..729183_POSITIVE 335 70 27 42 1 pint:PI0692|5end_iron_compound_ABC_transporter,_permease_protein_627350..627580_POSITIVE 330 60 11 80 32 pint:PI1980|5end_conserved_hypothetical_protein_1937470..1937700_POSITIVE 330 59 18 211 159 pint:PI0285|5end_succinyltransferase_protein_270097..270327_POSITIVE 329 50 6 65 9 pint:PI2158|5end_glycosyl_transferase,_group_2_family_protein_2104392..2104622_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 397 61 21 56 10 pint:PI2028|3end_shikimate_kinase_1982802..1982952_POSITIVE 355 59 30 32 2 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 344 44 4 76 32 pint:PI1818|3end_hypothetical_protein_1757270..1757420_POSITIVE 343 60 16 135 84 pint:PI0947|3end_conserved_hypothetical_protein_880709..880859_POSITIVE 338 65 27 64 26 pint:PI1227|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1148974..1149124_POSITIVE 336 49 3 151 93 pint:PI1245|3end_hypothetical_protein_1171492..1171642_POSITIVE 333 50 2 90 32 pint:PI0059|3end_peptide_chain_release_factor_RF-2_58171..58321_POSITIVE 332 49 1 104 48 pint:PI0027|3end_aminopeptidase_C_31756..31906_POSITIVE 330 95 55 96 49 pint:PI1366|3end_conserved_hypothetical_protein;_possible_hydrolase,_HAD_superfamily_1286647..1286797_POSITIVE 329 50 3 127 71 pint:PI0056|3end_conserved_hypothetical_protein;_possible_DNA_uptake_protein_55907..56057_POSITIVE 325 46 1 143 89 pint:PI1572|3end_hypothetical_protein_1498215..1498365_POSITIVE 325 52 22 147 114 pint:PI0543|3end_adenylate_kinase_495722..495872_POSITIVE 324 39 5 36 1 pint:PI0333|3end_hypothetical_protein_313788..313938_POSITIVE 323 57 18 149 100 pint:PI2087|3end_dihydropicolinate_reductase_2044255..2044405_POSITIVE 317 48 5 148 90 pint:PI1715|3end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1632324..1632474_POSITIVE 317 46 10 110 80 pint:PI0171|3end_hypothetical_protein_164085..164235_POSITIVE 317 46 10 61 31 pint:PI0169|3end_hypothetical_protein_164036..164186_POSITIVE 317 54 13 70 23 pint:PI0007|3end_hypothetical_protein_7300..7450_POSITIVE 316 58 13 118 68 pint:PI1722|3end_possible_peptidyl-prolyl_cis-trans_isomerase_1640995..1641145_POSITIVE 316 48 2 149 110 pint:PI1650|3end_N-acetylmuramoyl-L-alanine_amidase_1563901..1564051_POSITIVE