Origin IGS: agtttaaaaaaataacctgacaccattatatataagactctcttgtcttacaattcatggtgtcaggtttctattaatgttttaataatgtttttgttttggccttgcaatgtgggatttacccagcttgcaagacgtttatcttgattta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaatcaagataaacgtcttgcaagctgggtaaatcccacattgcaaggccaaaacaaaaacattattaaaacattaatagaaacctgacaccatgaattgtaagacaagagagtcttatatataatggtgtcaggttatttttttaaact Mask Tandem Repeat Region ================================================ agtttaaaaaaataacctgacaccattatatataagactctcttgtcttacaattcatggtgtcaggtttctattaatgttttaataatgtttttgttttggccttgcaatgtgggatttacccagcttgcaagacgtttatcttgattta Find is-nt database================================================ Query_seq: PI1463:PI1464|PI1463:PI1464:fumarate hydratase, class I:zinc protease:->->:1387130..1387280 151 agtttaaaaaaataacctgacaccattatatataagactctcttgtcttacaattcatggtgtcaggtttctattaatgttttaataatgtttttgttttggccttgcaatgtgggatttacccagcttgcaagacgtttatcttgattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1463:PI1464|PI1463:PI1464:fumarate hydratase, class I:zinc protease:->->:1387130..1387280 151 agtttaaaaaaataacctgacaccattatatataagactctcttgtcttacaattcatggtgtcaggtttctattaatgttttaataatgtttttgttttggccttgcaatgtgggatttacccagcttgcaagacgtttatcttgattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1463:PI1464|PI1463:PI1464:fumarate hydratase, class I:zinc protease:->->:1387130..1387280 151 agtttaaaaaaataacctgacaccattatatataagactctcttgtcttacaattcatggtgtcaggtttctattaatgttttaataatgtttttgttttggccttgcaatgtgggatttacccagcttgcaagacgtttatcttgattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtttaaaaaaataacctgacaccattatatataagactctcttgtcttacaattcatggtgtcaggtttctattaatgttttaataatgtttttgttttggccttgcaatgtgggatttacccagcttgcaagacgtttatcttgattta Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 25 End: 144 ........................ M I Y K T L L S Y N S W C Q V S I N V L I M F L F W P C N V G F T Q L A R R L S ....... agtttaaaaaaataacctgacaccattatatataagactctcttgtcttacaattcatggtgtcaggtttctattaatgttttaataatgtttttgttttggccttgcaatgtgggatttacccagcttgcaagacgtttatcttgattta 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: 86 Start: 25 End: 54 ........................ATTGTAAGACAAGAGAGTCTTATATATAAT................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agtttaaaaaaataacctgacaccattatatataagactctcttgtcttacaattcatggtgtcaggtttctattaatgttttaataatgtttttgttttggccttgcaatgtgggatttacccagcttgcaagacgtttatcttgattta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -10.3 Tail_Score: -4.28371 Start: 16 End: 67 Full_Region: AGTTTAAAAAAATAA CCTGACACCATTATATATAAGAC TCTCTT GTCTTACAATTCATGGTGTCAGG TTTCTATTAATGTTT ...............CCTGACACCATTATATATAAGACTCTCTTGTCTTACAATTCATGGTGTCAGG.................................................................................... TransTerm Strand: - Conf: 83 HP_score: -10.2 Tail_Score: -3.46885 Start: 17 End: 66 Full_Region: aacattaatagaaac ctgacaccatgaattgtaagac aagaga gtcttatatataatggtgtcag gttatttttttaaac ................ctgacaccatgaattgtaagacaagagagtcttatatataatggtgtcag..................................................................................... Find igs database================================================ Query_seq: PI1463:PI1464|PI1463:PI1464:fumarate hydratase, class I:zinc protease:->->:1387130..1387280 151 agtttaaaaaaataacctgacaccattatatataagactctcttgtcttacaattcatggtgtcaggtttctattaatgttttaataatgtttttgttttggccttgcaatgtgggatttacccagcttgcaagacgtttatcttgattta Intra-Species Hit: Count: 1 Min: 13 Max: 151 Len: 139 Subject: pint_PI1463_PI1464|fumarate hydratase, class I:zinc protease|POSITIVE:POSITIVE|[1387130,1387280]|151 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:13 Query End:151 Subject Strand: POSITIVE Subject Start: 13 Subject End: 151 ............taacctgacaccattatatataagactctcttgtcttacaattcatggtgtcaggtttctattaatgttttaataatgtttttgttttggccttgcaatgtgggatttacccagcttgcaagacgtttatcttgattta ............taacctgacaccattatatataagactctcttgtcttacaattcatggtgtcaggtttctattaatgttttaataatgtttttgttttggccttgcaatgtgggatttacccagcttgcaagacgtttatcttgattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACCUGACACCAUUAUAUAUAAGACUCUCUUGUCUUACAAUUCAUGGUGUCAGGUUUCUAUUAAUGUUUUAAUAAUGUUUUUGUUUUGGCCUUGCAAUGUGGGAUUUACCCAGCUUGCAAGACGUUUAUCUUGAUUUA .(((((((((((((......((((((......))))))......)))))))))))))..((((((....))))))................(((((((..((((.....))))..)))))))................. (-43.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUCAAGAUAAACGUCUUGCAAGCUGGGUAAAUCCCACAUUGCAAGGCCAAAACAAAAACAUUAUUAAAACAUUAAUAGAAACCUGACACCAUGAAUUGUAAGACAAGAGAGUCUUAUAUAUAAUGGUGUCAGGUUA ...............(((((((((..((((.....))))..))))))))).............(((((((....))))))).(((((((((((((....((((((((......))))))))....))))))))))))). (-52.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 130 91 75 31 pint:PI0942|5end_DNA-binding_protein_HU_874624..874854_POSITIVE 302 127 85 53 9 pint:PI1451|5end_outer_membrane_receptor_proteins,_tonB_dependent_(possibly_iron_transport_related)_1372931..1373161_POSITIVE 289 128 89 75 47 pint:PI1798|5end__elongation_factor_Ts_1731788..1732018_POSITIVE 288 119 77 189 140 pint:PI1722|5end_possible_peptidyl-prolyl_cis-trans_isomerase_1639536..1639766_POSITIVE 288 125 81 83 41 pint:PI1672|5end_conserved_hypothetical_protein;_possible_DNA-binding_protein,_histone-like_family_1587027..1587257_POSITIVE 280 122 92 130 101 pint:PI0985|5end_aspartyl-tRNA_synthetase_910174..910404_POSITIVE 275 128 81 100 45 pint:PI1475|5end_possible_short_chain_dehydrogenase_1397142..1397372_POSITIVE 272 118 75 144 94 pint:PI1563|5end_thiol:disulfide_interchange_protein_dsbD_1480681..1480911_POSITIVE 267 119 77 175 125 pint:PI2133|5end_collagenase_2081106..2081336_POSITIVE 251 127 91 148 105 pint:PI0069|5end_hypothetical_protein_67072..67302_POSITIVE 250 128 82 223 178 pint:PI2123|5end_adenine_phosphoribosyltransferase_2071711..2071941_POSITIVE 250 128 89 116 71 pint:PI0604|5end_O-succinylbenzoic_acid--CoA_ligase_550825..551055_POSITIVE 248 126 87 76 21 pint:PI2130|5end_DNA_polymerase_I_2077980..2078210_POSITIVE 245 119 77 41 1 pint:PI0038|5end_transcriptional_regulator,_LysR_family_39578..39808_POSITIVE 244 127 81 190 143 pint:PI0707|5end_conserved_hypothetical_protein;_possible_integral_membrane_protein_643358..643588_POSITIVE 244 119 76 64 19 pint:PI0207|5end_conserved_hypothetical_protein_199797..200027_POSITIVE 243 125 81 215 162 pint:PI1064|5end_hypothetical_protein_983071..983301_POSITIVE 242 128 82 60 6 pint:PI1860|5end_hypothetical_protein_1805949..1806179_POSITIVE 242 124 83 230 190 pint:PI1529|5end_cytosine/adenosine_deaminase_1449887..1450117_POSITIVE 239 124 89 86 44 pint:PI1431|5end_conserved_hypothetical_protein_1352079..1352309_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 326 130 91 46 2 pint:PI0941|3end_hypothetical_protein_874675..874825_POSITIVE 312 50 2 70 22 pint:PI1463|3end_fumarate_hydratase,_class_I_1387069..1387219_POSITIVE 298 55 25 34 3 pint:PI0421|3end_hypothetical_protein_387774..387924_POSITIVE 267 119 77 128 78 pint:PI2132|3end_hypothetical_protein_2081139..2081289_POSITIVE 259 119 81 118 68 pint:PI1548|3end_conserved_hypothetical_protein_1466886..1467036_POSITIVE 250 128 83 149 101 pint:PI1528|3end_hypothetical_protein_1449878..1450028_POSITIVE 250 128 89 52 7 pint:PI0603|3end_3-dehydroquinate_synthase_550841..550991_POSITIVE 244 127 81 146 99 pint:PI0706|3end_pyridoxal_phosphate_biosynthetic_protein_(4-hydroxythreonine-4-phosphate_dehydrogenase)_643394..643544_POSITIVE 242 128 82 145 91 pint:PI1861|3end_hypothetical_protein_1806114..1806264_POSITIVE 239 127 86 94 43 pint:PI1108|3end_conserved_hypothetical_protein_1032693..1032843_POSITIVE 238 123 82 56 15 pint:PI0132|3end_hypothetical_protein_124519..124669_POSITIVE 233 123 87 139 104 pint:PI0494|3end_hypothetical_protein_455170..455320_POSITIVE 232 120 78 143 96 pint:PI1245|3end_hypothetical_protein_1171492..1171642_POSITIVE 232 120 78 147 100 pint:PI1246|3end_conserved_hypothetical_protein;_possible_lipoprotein_1171496..1171646_POSITIVE 232 126 93 143 113 pint:PI0905|3end_hypothetical_protein_834697..834847_POSITIVE 231 127 84 51 8 pint:PI2111|3end_conserved_hypothetical_protein_2063258..2063408_POSITIVE 228 120 76 140 92 pint:PI1768|3end_conserved_hypothetical_protein_1696639..1696789_POSITIVE 228 118 74 140 95 pint:PI0793|3end_ABC_transporter,_permease_protein_731078..731228_POSITIVE 228 70 27 139 99 pint:PI0616|3end_electron_transfer_flavoprotein,_beta-subunit_566440..566590_POSITIVE 226 119 77 81 35 pint:PI1484|3end_conserved_hypothetical_protein_1405223..1405373_POSITIVE