Origin IGS: atgattcgtgtcttttgtcgttttatggtttgctctgcaaatttacataaaaatccgcctgctttcaagcgttatggataaaaaatcaagctttccattctgaatcaacgtttctttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgactttttttgattttatttagggtttatgcctaaacgtttgctttatacacaaacgataatga .........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 tcattatcgtttgtgtataaagcaaacgtttaggcataaaccctaaataaaatcaaaaaaagtcgattcatctcttctcaacaatatacatctgcgcttcggataagaaagaaacgttgattcagaatggaaagcttgattttttatccataacgcttgaaagcaggcggatttttatgtaaatttgcagagcaaaccataaaacgacaaaagacacgaatcat Mask Tandem Repeat Region ================================================ atgattcgtgtcttttgtcgttttatggtttgctctgcaaatttacataaaaatccgcctgctttcaagcgttatggataaaaaatcaagctttccattctgaatcaacgtttctttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgactttttttgattttatttagggtttatgcctaaacgtttgctttatacacaaacgataatga Find is-nt database================================================ Query_seq: TF0480:TF0481|TF0480:TF0481:ornithine carbamoyltransferase:possible anti-sigma factor:->->:499650..499873 224 atgattcgtgtcttttgtcgttttatggtttgctctgcaaatttacataaaaatccgcctgctttcaagcgttatggataaaaaatcaagctttccattctgaatcaacgtttctttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgactttttttgattttatttagggtttatgcctaaacgtttgctttatacacaaacgataatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0480:TF0481|TF0480:TF0481:ornithine carbamoyltransferase:possible anti-sigma factor:->->:499650..499873 224 atgattcgtgtcttttgtcgttttatggtttgctctgcaaatttacataaaaatccgcctgctttcaagcgttatggataaaaaatcaagctttccattctgaatcaacgtttctttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgactttttttgattttatttagggtttatgcctaaacgtttgctttatacacaaacgataatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0480:TF0481|TF0480:TF0481:ornithine carbamoyltransferase:possible anti-sigma factor:->->:499650..499873 224 atgattcgtgtcttttgtcgttttatggtttgctctgcaaatttacataaaaatccgcctgctttcaagcgttatggataaaaaatcaagctttccattctgaatcaacgtttctttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgactttttttgattttatttagggtttatgcctaaacgtttgctttatacacaaacgataatga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgattcgtgtcttttgtcgttttatggtttgctctgcaaatttacataaaaatccgcctgctttcaagcgttatggataaaaaatcaagctttccattctgaatcaacgtttctttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgactttttttgattttatttagggtttatgcctaaacgtttgctttatacacaaacgataatga Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 8 End: 100 ....... M S F V V L W F A L Q I Y I K I R L L S S V M D K K S S F P F ............................................................................................................................ Protein_Len: 34 Strand: + Start: 78 End: 179 ............................................................................. M K N Q A F H S E S T F L S Y P K R R C I L L R R D E S T F F D F I ............................................. Protein_Len: 38 Strand: - Start: 46 End: 159 ............................................. M F I R R S E L T I S L F D L K G N Q I L T E K K D S A C I Y I T S F L H M ................................................................. atgattcgtgtcttttgtcgttttatggtttgctctgcaaatttacataaaaatccgcctgctttcaagcgttatggataaaaaatcaagctttccattctgaatcaacgtttctttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgactttttttgattttatttagggtttatgcctaaacgtttgctttatacacaaacgataatga 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: 82 Start: 40 End: 69 .......................................CTTGAAAGCAGGCGGATTTTTATGTAAATT........................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atgattcgtgtcttttgtcgttttatggtttgctctgcaaatttacataaaaatccgcctgctttcaagcgttatggataaaaaatcaagctttccattctgaatcaacgtttctttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgactttttttgattttatttagggtttatgcctaaacgtttgctttatacacaaacgataatga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0480:TF0481|TF0480:TF0481:ornithine carbamoyltransferase:possible anti-sigma factor:->->:499650..499873 224 atgattcgtgtcttttgtcgttttatggtttgctctgcaaatttacataaaaatccgcctgctttcaagcgttatggataaaaaatcaagctttccattctgaatcaacgtttctttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgactttttttgattttatttagggtttatgcctaaacgtttgctttatacacaaacgataatga Intra-Species Hit: Count: 2 Min: 1 Max: 224 Len: 224 Subject: tfor_TF0480_TF0481|ornithine carbamoyltransferase:possible anti-sigma factor|POSITIVE:POSITIVE|[499650,499873]|224 HSP 1 e-value: 1.0E-111 bit: 402.0 Len: 224 Query Start:1 Query End:224 Subject Strand: POSITIVE Subject Start: 1 Subject End: 224 atgattcgtgtcttttgtcgttttatggtttgctctgcaaatttacataaaaatccgcctgctttcaagcgttatggataaaaaatcaagctttccattctgaatcaacgtttctttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgacnnnnnnngattttatttagggtttatgcctaaacgtttgctttatacacaaacgataatga atgattcgtgtcttttgtcgttttatggtttgctctgcaaatttacataaaaatccgcctgctttcaagcgttatggataaaaaatcaagctttccattctgaatcaacgtttctttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgactttttttgattttatttagggtttatgcctaaacgtttgctttatacacaaacgataatga Subject: tfor_TF0489_TF0490|D-xylose-proton symporter:conserved hypothetical protein|POSITIVE:POSITIVE|[513130,513673]|544 HSP 1 e-value: 4.0E-51 bit: 202.0 Len: 145 Query Start:80 Query End:224 Subject Strand: POSITIVE Subject Start: 398 Subject End: 544 ...............................................................................aaaaaatcaagctttccattctgaatcaacgtttcttt-cttatccgaagcgcagatgtatattgttgagaagagatgaatcgac-nnnnnnngattttatttagggtttatgcctaaacgtttgctttatacacaaacgataatga ...............................................................................aaaaaatcaagctttccattctgaatcaacgttttttttcttatccgaagcgcagatgtatattgttgagaagagatgaatcgacttttttttgattttatttagggtttatgcctaaacgtttgctttatatacaaacgataatga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGAUUCGUGUCUUUUGUCGUUUUAUGGUUUGCUCUGCAAAUUUACAUAAAAAUCCGCCUGCUUUCAAGCGUUAUGGAUAAAAAAUCAAGCUUUCCAUUCUGAAUCAACGUUUCUUUCUUAUCCGAAGCGCAGAUGUAUAUUGUUGAGAAGAGAUGAAUCGACUUUUUUUGAUUUUAUUUAGGGUUUAUGCCUAAACGUUUGCUUUAUACACAAACGAUAAUGA .((((((((.((((((....(((((((((((((...))))))...)))))))................(((((.(((((((.(((..((((.(((......))).....)))).))).))))))).)))))...............)))))).))))))))....................((((....))))...((((((.........))))))....... (-45.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAUUAUCGUUUGUGUAUAAAGCAAACGUUUAGGCAUAAACCCUAAAUAAAAUCAAAAAAAGUCGAUUCAUCUCUUCUCAACAAUAUACAUCUGCGCUUCGGAUAAGAAAGAAACGUUGAUUCAGAAUGGAAAGCUUGAUUUUUUAUCCAUAACGCUUGAAAGCAGGCGGAUUUUUAUGUAAAUUUGCAGAGCAAACCAUAAAACGACAAAAGACACGAAUCAU ........((((((((...........(((((((.......))))))).............((((........................((((((.....((((((((((..((.(((..(((.....))).)))))..)))))))))).....(((....)))..)))))).((((((....(((((...))))).)))))).)))).....))))))))... (-44.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 135 95 188 152 tfor:TF2789|5end_enoyl-[acyl-carrier-protein]_reductase_2972431..2972661_POSITIVE 317 133 91 48 5 tfor:TF2926|5end_glycine_hydroxymethyltransferase_3128070..3128300_POSITIVE 312 50 1 182 134 tfor:TF2991|5end_conserved_hypothetical_protein_3206316..3206546_POSITIVE 296 77 37 56 7 tfor:TF1349|5end_conserved_hypothetical_protein;_possible_prophage_maintanence_or_virulance_related_1429054..1429284_POSITIVE 296 70 23 224 179 tfor:TF0012|5end_conserved_hypothetical_protein_5512..5742_POSITIVE 290 104 61 84 39 tfor:TF0064|5end_conserved_hypothetical_protein_68419..68649_POSITIVE 287 129 89 207 162 tfor:TF0328|5end_conserved_hypothetical_protein_354182..354412_POSITIVE 283 48 2 72 15 tfor:TF1753|5end_topoisomerase_IV_subunit_A_1888130..1888360_POSITIVE 282 166 128 188 135 tfor:TF2791|5end_GTP-binding_protein_TypA_2975298..2975528_POSITIVE 281 136 91 142 99 tfor:TF1579|5end_hypothetical_protein_1686889..1687119_POSITIVE 278 149 112 91 45 tfor:TF3103|5end_outer_membrane_protein_3332982..3333212_POSITIVE 278 37 1 125 90 tfor:TF1067|5end_conserved_hypothetical_protein_1136867..1137097_POSITIVE 277 136 91 212 168 tfor:TF1591|5end_surface_antigen_BspA_1706387..1706617_POSITIVE 272 104 61 84 39 tfor:TF0066|5end_conserved_hypothetical_protein_70729..70959_POSITIVE 271 60 12 110 61 tfor:TF3129|5end_DNA_methylase_3362477..3362707_POSITIVE 269 58 11 224 185 tfor:TF2990|5end_nicotinate-nucleotide_pyrophosphorylase_3205464..3205694_POSITIVE 268 100 55 59 4 tfor:TF2418|5end_GTP-binding_protein_2597204..2597434_POSITIVE 268 147 104 102 63 tfor:TF0310|5end_conserved_hypothetical_protein_334685..334915_POSITIVE 267 163 124 121 85 tfor:TF3136|5end_Na+-translocating_NADH-quinone_reductase,_subunit_F_3369994..3370224_POSITIVE 267 59 18 181 143 tfor:TF2810|5end_conserved_hypothetical_protein_3000583..3000813_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 104 61 75 30 tfor:TF0063|3end_conserved_hypothetical_protein_68490..68640_POSITIVE 278 37 1 36 1 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 272 166 121 137 99 tfor:TF0684|3end_conserved_hypothetical_protein_730564..730714_POSITIVE 272 104 61 75 30 tfor:TF0065|3end_conserved_hypothetical_protein_70800..70950_POSITIVE 268 147 104 112 73 tfor:TF0309|3end_conserved_hypothetical_protein_334775..334925_POSITIVE 267 163 124 121 85 tfor:TF3135|3end_hypothetical_protein_3370074..3370224_POSITIVE 266 136 96 151 114 tfor:TF1761|3end_hypothetical_protein_1899579..1899729_POSITIVE 265 165 125 73 36 tfor:TF1421|3end_UDP-N-acetylmuramate--alanine_ligase_1504921..1505071_POSITIVE 264 160 114 124 65 tfor:TF2911|3end_hypothetical_protein_3106640..3106790_POSITIVE 263 104 68 74 37 tfor:TF0062|3end_conserved_hypothetical_protein_66180..66330_POSITIVE 260 96 56 45 11 tfor:TF2226|3end_CTn_excision_protein_2395956..2396106_POSITIVE 256 148 106 114 70 tfor:TF0990|3end_hypothetical_protein_1046662..1046812_POSITIVE 256 75 33 74 29 tfor:TF0183|3end_conserved_hypothetical_protein_196567..196717_POSITIVE 255 100 54 75 24 tfor:TF1917|3end_hypothetical_protein_2070244..2070394_POSITIVE 251 36 2 127 93 tfor:TF1897|3end_conserved_hypothetical_protein;_possible_aminopeptidase_2052107..2052257_POSITIVE 250 70 23 67 7 tfor:TF1752|3end_hypothetical_protein_1888172..1888322_POSITIVE 250 129 85 43 5 tfor:TF1040|3end_dihydroorotate_dehydrogenase,_electron_transfer_subunit_1102118..1102268_POSITIVE 249 130 89 124 85 tfor:TF2909|3end_GTP-binding_protein,_possible_GTP1/OBG_family_3105956..3106106_POSITIVE 249 80 54 132 107 tfor:TF0408|3end_possible_gliding_motility-related_lipoprotein_426324..426474_POSITIVE 248 77 34 47 2 tfor:TF2650|3end_succinate_dehydrogenase,_iron-sulfur_subunit_2821806..2821956_POSITIVE