Origin IGS: taatggtttcatcttttttcatttatatgctacttgttcctctattattgttttataatacgaaaaaatgagataaacttgagggatattgctccattttcgttaaaaagttgtacctttgttcccatattgatttataaaaactaatttgtatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatacaaattagtttttataaatcaatatgggaacaaaggtacaactttttaacgaaaatggagcaatatccctcaagtttatctcattttttcgtattataaaacaataatagaggaacaagtagcatataaatgaaaaaagatgaaaccatta Mask Tandem Repeat Region ================================================ taatggtttcatcttttttcatttatatgctacttgttcctctattattgttttataatacgaaaaaatgagataaacttgagggatattgctccattttcgttaaaaagttgtacctttgttcccatattgatttataaaaactaatttgtatt Find is-nt database================================================ Query_seq: PI1083:PI1084|PI1083:PI1084:TPR-repeat-containing protein:threonyl-tRNA synthetase:->->:1002649..1002803 155 taatggtttcatcttttttcatttatatgctacttgttcctctattattgttttataatacgaaaaaatgagataaacttgagggatattgctccattttcgttaaaaagttgtacctttgttcccatattgatttataaaaactaatttgtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1083:PI1084|PI1083:PI1084:TPR-repeat-containing protein:threonyl-tRNA synthetase:->->:1002649..1002803 155 taatggtttcatcttttttcatttatatgctacttgttcctctattattgttttataatacgaaaaaatgagataaacttgagggatattgctccattttcgttaaaaagttgtacctttgttcccatattgatttataaaaactaatttgtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1083:PI1084|PI1083:PI1084:TPR-repeat-containing protein:threonyl-tRNA synthetase:->->:1002649..1002803 155 taatggtttcatcttttttcatttatatgctacttgttcctctattattgttttataatacgaaaaaatgagataaacttgagggatattgctccattttcgttaaaaagttgtacctttgttcccatattgatttataaaaactaatttgtatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatggtttcatcttttttcatttatatgctacttgttcctctattattgttttataatacgaaaaaatgagataaacttgagggatattgctccattttcgttaaaaagttgtacctttgttcccatattgatttataaaaactaatttgtatt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 25 End: 144 ........................ M C Y L F L Y Y C F I I R K N E I N L R D I A P F S L K S C T F V P I L I Y K N ........... Protein_Len: 33 Strand: - Start: 56 End: 154 ....................................................... L V F F H S L S S P Y Q E M K T L F N Y R Q E W I S K Y F S I Q M . taatggtttcatcttttttcatttatatgctacttgttcctctattattgttttataatacgaaaaaatgagataaacttgagggatattgctccattttcgttaaaaagttgtacctttgttcccatattgatttataaaaactaatttgtatt 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================================================ taatggtttcatcttttttcatttatatgctacttgttcctctattattgttttataatacgaaaaaatgagataaacttgagggatattgctccattttcgttaaaaagttgtacctttgttcccatattgatttataaaaactaatttgtatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1083:PI1084|PI1083:PI1084:TPR-repeat-containing protein:threonyl-tRNA synthetase:->->:1002649..1002803 155 taatggtttcatcttttttcatttatatgctacttgttcctctattattgttttataatacgaaaaaatgagataaacttgagggatattgctccattttcgttaaaaagttgtacctttgttcccatattgatttataaaaactaatttgtatt Intra-Species Hit: Count: 1 Min: 1 Max: 155 Len: 155 Subject: pint_PI1083_PI1084|TPR-repeat-containing protein:threonyl-tRNA synthetase|POSITIVE:POSITIVE|[1002649,1002803]|155 HSP 1 e-value: 6.0E-83 bit: 307.0 Len: 155 Query Start:1 Query End:155 Subject Strand: POSITIVE Subject Start: 1 Subject End: 155 taatggtttcatcttttttcatttatatgctacttgttcctctattattgttttataatacgaaaaaatgagataaacttgagggatattgctccattttcgttaaaaagttgtacctttgttcccatattgatttataaaaactaatttgtatt taatggtttcatcttttttcatttatatgctacttgttcctctattattgttttataatacgaaaaaatgagataaacttgagggatattgctccattttcgttaaaaagttgtacctttgttcccatattgatttataaaaactaatttgtatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGGUUUCAUCUUUUUUCAUUUAUAUGCUACUUGUUCCUCUAUUAUUGUUUUAUAAUACGAAAAAAUGAGAUAAACUUGAGGGAUAUUGCUCCAUUUUCGUUAAAAAGUUGUACCUUUGUUCCCAUAUUGAUUUAUAAAAACUAAUUUGUAUU ....(((..((.((((((..........((....((((((((.....(((((((((...........)))))))))....))))))))..))............)))))).)).)))..................((((((......)))))).. (-22.25) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUACAAAUUAGUUUUUAUAAAUCAAUAUGGGAACAAAGGUACAACUUUUUAACGAAAAUGGAGCAAUAUCCCUCAAGUUUAUCUCAUUUUUUCGUAUUAUAAAACAAUAAUAGAGGAACAAGUAGCAUAUAAAUGAAAAAAGAUGAAACCAUUA ...........(((((((((......)))))))))...(((.((.((((((.........(((......))).....(((...((...((((((.((((((......))))))))))))..)).)))..........)))))).))..))).... (-20.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 120 73 53 2 pint:PI0327|5end_hypothetical_protein_308791..309021_POSITIVE 262 128 81 91 49 pint:PI0023|5end_internalin-related_protein_25924..26154_POSITIVE 249 120 73 52 2 pint:PI1621|5end_hypothetical_protein_1545424..1545654_POSITIVE 249 125 83 127 85 pint:PI1398|5end_probable_imidazolonepropionase_1319429..1319659_POSITIVE 233 125 83 178 142 pint:PI1632|5end_hypothetical_protein_1552819..1553049_POSITIVE 230 145 101 220 176 pint:PI0539|5end_hypothetical_protein_493406..493636_POSITIVE 225 118 79 179 134 pint:PI0339|5end_hypothetical_protein_315735..315965_POSITIVE 223 59 25 36 3 pint:PI1417|5end_MATE_efflux_family_protein_(Na+-driven_multidrug_efflux_pump)_1336126..1336356_POSITIVE 220 93 55 163 128 pint:PI1889|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-(pentape_ptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_1831411..1831641_POSITIVE 219 125 81 40 1 pint:PI1811|5end_conserved_hypothetical_protein_1749518..1749748_POSITIVE 218 122 84 106 69 pint:PI2094|5end_hypothetical_protein_2049540..2049770_POSITIVE 218 50 3 75 30 pint:PI0959|5end_uridine_kinase_890495..890725_POSITIVE 218 125 81 230 196 pint:PI0409|5end_3-deoxy-D-manno-octulosonic-acid_transferase_(kdotransferase)_374648..374878_POSITIVE 212 127 81 103 57 pint:PI2067|5end_hypothetical_protein_2027760..2027990_POSITIVE 211 42 2 194 157 pint:PI1518|5end_outer_membrane_protein_oprM_precursor,_multidrug_resistance_protein_1438922..1439152_POSITIVE 211 126 81 219 168 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 209 130 82 93 50 pint:PI2047|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diamino_pimelate--D-alanyl-D-alanyl_ligase_1999328..1999558_POSITIVE 208 117 78 181 135 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 207 101 69 213 185 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 206 43 4 142 96 pint:PI1668|5end_conserved_hypothetical_protein_1580692..1580922_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 43 3 71 34 pint:PI0502|3end_conserved_hypothetical_protein;_possible_helicase_463089..463239_POSITIVE 249 125 83 49 7 pint:PI1397|3end_histidine_ammonia-lyase_1319431..1319581_POSITIVE 240 126 81 145 93 pint:PI0301|3end_probable_transposase_285982..286132_POSITIVE 233 125 83 76 40 pint:PI1631|3end_hypothetical_protein_1552797..1552947_POSITIVE 225 45 2 89 38 pint:PI1025|3end_tRNA_modification_GTPase_942232..942382_POSITIVE 225 118 79 77 32 pint:PI0338|3end_hypothetical_protein_315713..315863_POSITIVE 220 93 55 147 112 pint:PI1888|3end_UDP-N-acetylmuramate--L-alanine_ligase_1831475..1831625_POSITIVE 219 115 85 52 22 pint:PI0725|3end_hypothetical_protein_658933..659083_POSITIVE 218 50 3 69 24 pint:PI0958|3end_G:T/U_mismatch-specific_DNA_glycosylase_890569..890719_POSITIVE 218 50 3 133 82 pint:PI0024|3end_hypothetical_protein_28559..28709_POSITIVE 209 120 76 140 96 pint:PI1683|3end_integral_membrane_protein_1600898..1601048_POSITIVE 206 43 4 142 96 pint:PI1667|3end_conserved_hypothetical_protein_1580772..1580922_POSITIVE 206 125 81 143 103 pint:PI1369|3end_alkyl_hydroperoxide_reductase,_subunit__C_1290423..1290573_POSITIVE 206 127 82 133 83 pint:PI1331|3end_conserved_hypothetical_protein_1249463..1249613_POSITIVE 203 129 82 100 48 pint:PI0595|3end_conserved_hypothetical_protein_546406..546556_POSITIVE 203 95 59 79 45 pint:PI0017|3end_thiol-disulfide_isomerase;_thioredoxin_22835..22985_POSITIVE 200 129 81 149 93 pint:PI2030|3end_hypothetical_protein_1986127..1986277_POSITIVE 200 44 4 131 82 pint:PI0745|3end_conserved_hypothetical_protein_675670..675820_POSITIVE 199 122 83 76 47 pint:PI0490|3end_DNA_primase_451090..451240_POSITIVE 199 120 79 75 27 pint:PI0389|3end_integrase_357386..357536_POSITIVE