Origin IGS: tcgtatatattattttatgtaaataatcgcttgcgaatatatagaaagtcgttatatgttttggaacagcctcggaaacatgttaaagtgcccgttgcaaacagtttcgacctgttttcatctctgcgttatcgcttgcaaaagtagtgaatgatttcggatttcaatgtttttaaataagaaaatgcacatccgatccgtttttgtgcatatcttcgacgcatgtaaagttctctgttcacaaagaggcaagacattatttcgcattgagtttttaatcgctattttggtcttccggagtccaaccctgaaacttttaagagcatttcattttgggggatgctgtttaatcaatcgcaaaaaatgaagttgttacaaaggaatactcagcgggagaaaagaaaattttccttttttttattttta .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaaataaaaaaaaggaaaattttcttttctcccgctgagtattcctttgtaacaacttcattttttgcgattgattaaacagcatcccccaaaatgaaatgctcttaaaagtttcagggttggactccggaagaccaaaatagcgattaaaaactcaatgcgaaataatgtcttgcctctttgtgaacagagaactttacatgcgtcgaagatatgcacaaaaacggatcggatgtgcattttcttatttaaaaacattgaaatccgaaatcattcactacttttgcaagcgataacgcagagatgaaaacaggtcgaaactgtttgcaacgggcactttaacatgtttccgaggctgttccaaaacatataacgactttctatatattcgcaagcgattatttacataaaataatatatacga Mask Tandem Repeat Region ================================================ tcgtatatattattttatgtaaataatcgcttgcgaatatatagaaagtcgttatatgttttggaacagcctcggaaacatgttaaagtgcccgttgcaaacagtttcgacctgttttcatctctgcgttatcgcttgcaaaagtagtgaatgatttcggatttcaatgtttttaaataagaaaatgcacatccgatccgtttttgtgcatatcttcgacgcatgtaaagttctctgttcacaaagaggcaagacattatttcgcattgagtttttaatcgctattttggtcttccggagtccaaccctgaaacttttaagagcatttcattttgggggatgctgtttaatcaatcgcaaaaaatgaagttgttacaaaggaatactcagcgggagaaaagaaaattttccttttttttattttta Find is-nt database================================================ Query_seq: TF1280:TF1281|TF1280:TF1281:electron transfer flavoprotein, beta subunit:2-dehydro-3-deoxyphosphooctonate aldolase (3-deoxy-D-manno-2-octulosonate-8-phosphate synthase) (KDO-8-phosphate synthetase) (KDO 8-P synthase):->->:1365318..1365743 426 tcgtatatattattttatgtaaataatcgcttgcgaatatatagaaagtcgttatatgttttggaacagcctcggaaacatgttaaagtgcccgttgcaaacagtttcgacctgttttcatctctgcgttatcgcttgcaaaagtagtgaatgatttcggatttcaatgtttttaaataagaaaatgcacatccgatccgtttttgtgcatatcttcgacgcatgtaaagttctctgttcacaaagaggcaagacattatttcgcattgagtttttaatcgctattttggtcttccggagtccaaccctgaaacttttaagagcatttcattttgggggatgctgtttaatcaatcgcaaaaaatgaagttgttacaaaggaatactcagcgggagaaaagaaaattttccttttttttattttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1280:TF1281|TF1280:TF1281:electron transfer flavoprotein, beta subunit:2-dehydro-3-deoxyphosphooctonate aldolase (3-deoxy-D-manno-2-octulosonate-8-phosphate synthase) (KDO-8-phosphate synthetase) (KDO 8-P synthase):->->:1365318..1365743 426 tcgtatatattattttatgtaaataatcgcttgcgaatatatagaaagtcgttatatgttttggaacagcctcggaaacatgttaaagtgcccgttgcaaacagtttcgacctgttttcatctctgcgttatcgcttgcaaaagtagtgaatgatttcggatttcaatgtttttaaataagaaaatgcacatccgatccgtttttgtgcatatcttcgacgcatgtaaagttctctgttcacaaagaggcaagacattatttcgcattgagtttttaatcgctattttggtcttccggagtccaaccctgaaacttttaagagcatttcattttgggggatgctgtttaatcaatcgcaaaaaatgaagttgttacaaaggaatactcagcgggagaaaagaaaattttccttttttttattttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1280:TF1281|TF1280:TF1281:electron transfer flavoprotein, beta subunit:2-dehydro-3-deoxyphosphooctonate aldolase (3-deoxy-D-manno-2-octulosonate-8-phosphate synthase) (KDO-8-phosphate synthetase) (KDO 8-P synthase):->->:1365318..1365743 426 tcgtatatattattttatgtaaataatcgcttgcgaatatatagaaagtcgttatatgttttggaacagcctcggaaacatgttaaagtgcccgttgcaaacagtttcgacctgttttcatctctgcgttatcgcttgcaaaagtagtgaatgatttcggatttcaatgtttttaaataagaaaatgcacatccgatccgtttttgtgcatatcttcgacgcatgtaaagttctctgttcacaaagaggcaagacattatttcgcattgagtttttaatcgctattttggtcttccggagtccaaccctgaaacttttaagagcatttcattttgggggatgctgtttaatcaatcgcaaaaaatgaagttgttacaaaggaatactcagcgggagaaaagaaaattttccttttttttattttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcgtatatattattttatgtaaataatcgcttgcgaatatatagaaagtcgttatatgttttggaacagcctcggaaacatgttaaagtgcccgttgcaaacagtttcgacctgttttcatctctgcgttatcgcttgcaaaagtagtgaatgatttcggatttcaatgtttttaaataagaaaatgcacatccgatccgtttttgtgcatatcttcgacgcatgtaaagttctctgttcacaaagaggcaagacattatttcgcattgagtttttaatcgctattttggtcttccggagtccaaccctgaaacttttaagagcatttcattttgggggatgctgtttaatcaatcgcaaaaaatgaagttgttacaaaggaatactcagcgggagaaaagaaaattttccttttttttattttta Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 7 End: 144 ...... M L F Y V N N R L R I Y R K S L Y V L E Q P R K H V K V P V A N S F D L F S S L R Y R L Q K .......................................................................................................................................................................................................................................................................................... Protein_Len: 43 Strand: + Start: 23 End: 151 ...................... M I A C E Y I E S R Y M F W N S L G N M L K C P L Q T V S T C F H L C V I A C K S S E ................................................................................................................................................................................................................................................................................... Protein_Len: 33 Strand: + Start: 177 End: 275 ................................................................................................................................................................................ M R K C T S D P F L C I S S T H V K F S V H K E A R H Y F A L S F ....................................................................................................................................................... Protein_Len: 60 Strand: + Start: 161 End: 364 ................................................................................................................................................................ M S M F L N K K M H I R S V F V H I F D A C K V L C S Q R G K T L F R I E F L I A I L V F R S P T L K L L R A F H F G G .............................................................. Protein_Len: 34 Strand: + Start: 325 End: 426 .................................................................................................................................................................................................................................................................................................................................... M S F W G M L F N Q S Q K M K L L Q R N T Q R E K R K F S F F L F L Protein_Len: 43 Strand: - Start: 132 End: 260 ................................................................................................................................... R K C F Y H I I E S K L T K L Y S F A C G I R K Q A Y R R R M Y L E R N V F L C S M M ...................................................................................................................................................................... Protein_Len: 55 Strand: - Start: 121 End: 285 ........................................................................................................................ R Q T I A Q L L L S H N R I E I N K F L F I C M R D T K T C I K S A H L T R Q E C L P L V N N R M S N K I A M ............................................................................................................................................. tcgtatatattattttatgtaaataatcgcttgcgaatatatagaaagtcgttatatgttttggaacagcctcggaaacatgttaaagtgcccgttgcaaacagtttcgacctgttttcatctctgcgttatcgcttgcaaaagtagtgaatgatttcggatttcaatgtttttaaataagaaaatgcacatccgatccgtttttgtgcatatcttcgacgcatgtaaagttctctgttcacaaagaggcaagacattatttcgcattgagtttttaatcgctattttggtcttccggagtccaaccctgaaacttttaagagcatttcattttgggggatgctgtttaatcaatcgcaaaaaatgaagttgttacaaaggaatactcagcgggagaaaagaaaattttccttttttttattttta 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================================================ tcgtatatattattttatgtaaataatcgcttgcgaatatatagaaagtcgttatatgttttggaacagcctcggaaacatgttaaagtgcccgttgcaaacagtttcgacctgttttcatctctgcgttatcgcttgcaaaagtagtgaatgatttcggatttcaatgtttttaaataagaaaatgcacatccgatccgtttttgtgcatatcttcgacgcatgtaaagttctctgttcacaaagaggcaagacattatttcgcattgagtttttaatcgctattttggtcttccggagtccaaccctgaaacttttaagagcatttcattttgggggatgctgtttaatcaatcgcaaaaaatgaagttgttacaaaggaatactcagcgggagaaaagaaaattttccttttttttattttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 60 HP_score: -2.9 Tail_Score: -4.40159 Start: 396 End: 410 Full_Region: GAATACTCAGCGGGA GAAAA GAAAA TTTTC CTTTTTTTTATTTTT ...........................................................................................................................................................................................................................................................................................................................................................................................................GAAAAGAAAATTTTC................ Find igs database================================================ Query_seq: TF1280:TF1281|TF1280:TF1281:electron transfer flavoprotein, beta subunit:2-dehydro-3-deoxyphosphooctonate aldolase (3-deoxy-D-manno-2-octulosonate-8-phosphate synthase) (KDO-8-phosphate synthetase) (KDO 8-P synthase):->->:1365318..1365743 426 tcgtatatattattttatgtaaataatcgcttgcgaatatatagaaagtcgttatatgttttggaacagcctcggaaacatgttaaagtgcccgttgcaaacagtttcgacctgttttcatctctgcgttatcgcttgcaaaagtagtgaatgatttcggatttcaatgtttttaaataagaaaatgcacatccgatccgtttttgtgcatatcttcgacgcatgtaaagttctctgttcacaaagaggcaagacattatttcgcattgagtttttaatcgctattttggtcttccggagtccaaccctgaaacttttaagagcatttcattttgggggatgctgtttaatcaatcgcaaaaaatgaagttgttacaaaggaatactcagcgggagaaaagaaaattttccttttttttattttta Intra-Species Hit: Count: 1 Min: 1 Max: 411 Len: 411 Subject: tfor_TF1280_TF1281|electron transfer flavoprotein, beta subunit:2-dehydro-3-deoxyphosphooctonate aldolase (3-deoxy-D-manno-2-octulosonate-8-phosphate synthase) (KDO-8-phosphate synthetase) (KDO 8-P synthase)|POSITIVE:POSITIVE|[1365318,1365743]|426 HSP 1 e-value: 0.0 bit: 815.0 Len: 411 Query Start:1 Query End:411 Subject Strand: POSITIVE Subject Start: 1 Subject End: 411 tcgtatatattattttatgtaaataatcgcttgcgaatatatagaaagtcgttatatgttttggaacagcctcggaaacatgttaaagtgcccgttgcaaacagtttcgacctgttttcatctctgcgttatcgcttgcaaaagtagtgaatgatttcggatttcaatgtttttaaataagaaaatgcacatccgatccgtttttgtgcatatcttcgacgcatgtaaagttctctgttcacaaagaggcaagacattatttcgcattgagtttttaatcgctattttggtcttccggagtccaaccctgaaacttttaagagcatttcattttgggggatgctgtttaatcaatcgcaaaaaatgaagttgttacaaaggaatactcagcgggagaaaagaaaattttcc............... tcgtatatattattttatgtaaataatcgcttgcgaatatatagaaagtcgttatatgttttggaacagcctcggaaacatgttaaagtgcccgttgcaaacagtttcgacctgttttcatctctgcgttatcgcttgcaaaagtagtgaatgatttcggatttcaatgtttttaaataagaaaatgcacatccgatccgtttttgtgcatatcttcgacgcatgtaaagttctctgttcacaaagaggcaagacattatttcgcattgagtttttaatcgctattttggtcttccggagtccaaccctgaaacttttaagagcatttcattttgggggatgctgtttaatcaatcgcaaaaaatgaagttgttacaaaggaatactcagcgggagaaaagaaaattttcc............... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGUAUAUAUUAUUUUAUGUAAAUAAUCGCUUGCGAAUAUAUAGAAAGUCGUUAUAUGUUUUGGAACAGCCUCGGAAACAUGUUAAAGUGCCCGUUGCAAACAGUUUCGACCUGUUUUCAUCUCUGCGUUAUCGCUUGCAAAAGUAGUGAAUGAUUUCGGAUUUCAAUGUUUUUAAAUAAGAAAAUGCACAUCCGAUCCGUUUUUGUGCAUAUCUUCGACGCAUGUAAAGUUCUCUGUUCACAAAGAGGCAAGACAUUAUUUCGCAUUGAGUUUUUAAUCGCUAUUUUGGUCUUCCGGAGUCCAACCCUGAAACUUUUAAGAGCAUUUCAUUUUGGGGGAUGCUGUUUAAUCAAUCGCAAAAAAUGAAGUUGUUACAAAGGAAUACUCAGCGGGAGAAAAGAAAAUUUUCC (((((...(((((((.....)))))))....))))).......((((((....(((((((((.((......)).))))))))).......(((((((.....(((((((.......(((((..(((((....))).......))..))))).(((((((((..((((.((..(((((.......(((((((.............)))))))...(((((.((..((((.(((((((........))))....))).))))...)).)))))..)))))..))....))))...)))))))))......)))))))......(((((((((((((..(.(((............))).)..))))))))).)))).............)))))))..........)))))). (-87.73) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGAAAAUUUUCUUUUCUCCCGCUGAGUAUUCCUUUGUAACAACUUCAUUUUUUGCGAUUGAUUAAACAGCAUCCCCCAAAAUGAAAUGCUCUUAAAAGUUUCAGGGUUGGACUCCGGAAGACCAAAAUAGCGAUUAAAAACUCAAUGCGAAAUAAUGUCUUGCCUCUUUGUGAACAGAGAACUUUACAUGCGUCGAAGAUAUGCACAAAAACGGAUCGGAUGUGCAUUUUCUUAUUUAAAAACAUUGAAAUCCGAAAUCAUUCACUACUUUUGCAAGCGAUAACGCAGAGAUGAAAACAGGUCGAAACUGUUUGCAACGGGCACUUUAACAUGUUUCCGAGGCUGUUCCAAAACAUAUAACGACUUUCUAUAUAUUCGCAAGCGAUUAUUUACAUAAAAUAAUAUAUACGA ((....((((((........((((..((.((..((((((.((......)).))))))..)).))..)))).....((((..((((((..........))))))...)))).....)))))))).......((.............((((((...((((...(..((((((....)))))).)...))))..((((...(((((......(((((.(((((.((((............................(((....)))....((.((((..(((....)))........((((((.......)))))))))).))))))...........)))))..)))))......)))))..))))..........))))))....(((((((.....))))))).....)). (-77.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 140 92 209 173 tfor:TF1914|5end_conserved_hypothetical_protein_2066599..2066829_POSITIVE 349 138 91 176 125 tfor:TF3022|5end_chorismate_synthase_3246136..3246366_POSITIVE 342 130 86 201 151 tfor:TF2295|5end_hypothetical_protein_2448164..2448394_POSITIVE 338 138 93 195 149 tfor:TF1252|5end_phosphofructokinase;_pyrophosphate-fructose_6-phosphate_1-phosphotransferase_(probable_beta_subunit)_1334361..1334591_POSITIVE 334 128 85 230 186 tfor:TF1678|5end_periplasmic_protease_1791097..1791327_POSITIVE 330 126 81 138 76 tfor:TF1070|5end_hydrolase_1139704..1139934_POSITIVE 328 240 192 169 121 tfor:TF2256|5end_transfer_region-related_protein,_TraI_2427908..2428138_POSITIVE 326 110 62 60 9 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 317 98 57 42 3 tfor:TF1472|5end_acyl-ACP_thioesterase_1565475..1565705_POSITIVE 316 160 111 123 55 tfor:TF2042|5end_sugar_phosphate_isomerase,_polysialic_acid_capsule_expression_protein_2201647..2201877_POSITIVE 314 130 88 49 1 tfor:TF2294|5end_hypothetical_protein_2448012..2448242_POSITIVE 311 109 63 223 160 tfor:TF1929|5end_conserved_hypothetical_protein_2076049..2076279_POSITIVE 311 139 91 98 44 tfor:TF1927|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2075037..2075267_POSITIVE 311 308 263 212 159 tfor:TF0977|5end_possible_outer_membrane_protein_1027719..1027949_POSITIVE 310 120 71 129 74 tfor:TF1948|5end_conserved_hypothetical_protein_2095942..2096172_POSITIVE 308 139 91 176 138 tfor:TF2259|5end_transfer_region-related_protein,_TraK_2429577..2429807_POSITIVE 307 130 88 73 23 tfor:TF2602|5end_tRNA-(5-methylaminomethyl-2-thiouridylate)_methyltransferase_2775086..2775316_POSITIVE 305 240 194 173 116 tfor:TF1446|5end_hypothetical_protein_1530649..1530879_POSITIVE 304 138 92 173 122 tfor:TF2314|5end_conserved_hypothetical_protein_2473530..2473760_POSITIVE 304 138 91 64 28 tfor:TF0538|5end_hypothetical_protein_566891..567121_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 339 135 91 150 103 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 331 307 261 51 7 tfor:TF2139|3end_hypothetical_protein_2316178..2316328_POSITIVE 330 126 81 148 86 tfor:TF1069|3end_glucokinase_regulatory_protein,_sugar_phosphate_isomerase_domain_1139794..1139944_POSITIVE 328 240 192 142 94 tfor:TF2255|3end_transfer_region-related_protein,_TraH_2427961..2428111_POSITIVE 326 110 62 55 4 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 311 139 91 82 28 tfor:TF1925|3end_hypothetical_protein_2075101..2075251_POSITIVE 310 120 71 130 75 tfor:TF1947|3end_conserved_hypothetical_protein_2096023..2096173_POSITIVE 308 139 91 141 103 tfor:TF2257|3end_transfer_region-related_protein,_TraJ_2429622..2429772_POSITIVE 304 138 92 148 97 tfor:TF2313|3end_SAM-dependent_methyltransferase_2473585..2473735_POSITIVE 304 240 191 149 90 tfor:TF1350|3end_possible_transcriptional_regulator_1430636..1430786_POSITIVE 303 160 120 49 1 tfor:TF2041|3end_conserved_hypothetical_protein_2201653..2201803_POSITIVE 300 160 111 138 81 tfor:TF2843|3end_conserved_hypothetical_protein;_possible_lipoprotein_3033760..3033910_POSITIVE 294 140 93 137 90 tfor:TF1276|3end_acyl-CoA_dehydrogenase_(short_chain_coenzyme_A_dehydrogenase)_1363080..1363230_POSITIVE 292 109 67 93 50 tfor:TF1513|3end_hypothetical_protein_1625450..1625600_POSITIVE 291 160 113 45 10 tfor:TF0521|3end_hypothetical_protein_547895..548045_POSITIVE 290 226 194 137 105 tfor:TF1445|3end_RNA_polymerase_sigma_factor_1530718..1530868_POSITIVE 288 149 115 49 14 tfor:TF0402|3end_conserved_hypothetical_protein_422609..422759_POSITIVE 285 308 264 135 94 tfor:TF1600|3end_uroporphyrinogen-III_synthase_1714817..1714967_POSITIVE 285 160 118 47 6 tfor:TF0826|3end_primosomal_protein_N'_886290..886440_POSITIVE 285 319 281 66 19 tfor:TF0382|3end_transcription_termination_factor_405228..405378_POSITIVE