Origin IGS: taattgttcctctatatgtctttttcggaaatcgaataagaacattttatctattccattcagtaatacggcaagggtttaaaagttaaaaaagtaaaaaaacaagacaaacatttggatgtatcaaaaacatgctatacgtttgcagaacaaattttaaagactaaatacaatgaagacaaaaattttaggagggatatttaccctcgtagtgatggtagcggtaagctacggagtggacaaaagtaaaagtatgcgaaatgatgtcaacctctcggatatgacattaagcaatgtagaggcattagcaagcggagaattagcggattgtgagtatggatgctttgctaatggggatggatgttggtgctatgattggtatccttgttacagagaagcaaaatagattgctcataacgctcactctctttggaaaaagattgagcaaagttttttaaattaaatgaatatggagaggacaaaaccctctccatatattatataaaatcgtcaaaaaagaagtattttt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaatacttcttttttgacgattttatataatatatggagagggttttgtcctctccatattcatttaatttaaaaaactttgctcaatctttttccaaagagagtgagcgttatgagcaatctattttgcttctctgtaacaaggataccaatcatagcaccaacatccatccccattagcaaagcatccatactcacaatccgctaattctccgcttgctaatgcctctacattgcttaatgtcatatccgagaggttgacatcatttcgcatacttttacttttgtccactccgtagcttaccgctaccatcactacgagggtaaatatccctcctaaaatttttgtcttcattgtatttagtctttaaaatttgttctgcaaacgtatagcatgtttttgatacatccaaatgtttgtcttgtttttttacttttttaacttttaaacccttgccgtattactgaatggaatagataaaatgttcttattcgatttccgaaaaagacatatagaggaacaatta Mask Tandem Repeat Region ================================================ taattgttcctctatatgtctttttcggaaatcgaataagaacattttatctattccattcagtaatacggcaagggtttaaaagttaaaaaagtaaaaaaacaagacaaacatttggatgtatcaaaaacatgctatacgtttgcagaacaaattttaaagactaaatacaatgaagacaaaaattttaggagggatatttaccctcgtagtgatggtagcggtaagctacggagtggacaaaagtaaaagtatgcgaaatgatgtcaacctctcggatatgacattaagcaatgtagaggcattagcaagcggagaattagcggattgtgagtatggatgctttgctaatggggatggatgttggtgctatgattggtatccttgttacagagaagcaaaatagattgctcataacgctcactctctttggaaaaagattgagcaaagttttttaaattaaatgaatatggagaggacaaaaccctctccatatattatataaaatcgtcaaaaaagaagtattttt Find is-nt database================================================ Query_seq: TF1391:TF1392|TF1391:TF1392:hypothetical protein:conserved hypothetical protein:->->:1464303..1464831 529 taattgttcctctatatgtctttttcggaaatcgaataagaacattttatctattccattcagtaatacggcaagggtttaaaagttaaaaaagtaaaaaaacaagacaaacatttggatgtatcaaaaacatgctatacgtttgcagaacaaattttaaagactaaatacaatgaagacaaaaattttaggagggatatttaccctcgtagtgatggtagcggtaagctacggagtggacaaaagtaaaagtatgcgaaatgatgtcaacctctcggatatgacattaagcaatgtagaggcattagcaagcggagaattagcggattgtgagtatggatgctttgctaatggggatggatgttggtgctatgattggtatccttgttacagagaagcaaaatagattgctcataacgctcactctctttggaaaaagattgagcaaagttttttaaattaaatgaatatggagaggacaaaaccctctccatatattatataaaatcgtcaaaaaagaagtattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1391:TF1392|TF1391:TF1392:hypothetical protein:conserved hypothetical protein:->->:1464303..1464831 529 taattgttcctctatatgtctttttcggaaatcgaataagaacattttatctattccattcagtaatacggcaagggtttaaaagttaaaaaagtaaaaaaacaagacaaacatttggatgtatcaaaaacatgctatacgtttgcagaacaaattttaaagactaaatacaatgaagacaaaaattttaggagggatatttaccctcgtagtgatggtagcggtaagctacggagtggacaaaagtaaaagtatgcgaaatgatgtcaacctctcggatatgacattaagcaatgtagaggcattagcaagcggagaattagcggattgtgagtatggatgctttgctaatggggatggatgttggtgctatgattggtatccttgttacagagaagcaaaatagattgctcataacgctcactctctttggaaaaagattgagcaaagttttttaaattaaatgaatatggagaggacaaaaccctctccatatattatataaaatcgtcaaaaaagaagtattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1391:TF1392|TF1391:TF1392:hypothetical protein:conserved hypothetical protein:->->:1464303..1464831 529 taattgttcctctatatgtctttttcggaaatcgaataagaacattttatctattccattcagtaatacggcaagggtttaaaagttaaaaaagtaaaaaaacaagacaaacatttggatgtatcaaaaacatgctatacgtttgcagaacaaattttaaagactaaatacaatgaagacaaaaattttaggagggatatttaccctcgtagtgatggtagcggtaagctacggagtggacaaaagtaaaagtatgcgaaatgatgtcaacctctcggatatgacattaagcaatgtagaggcattagcaagcggagaattagcggattgtgagtatggatgctttgctaatggggatggatgttggtgctatgattggtatccttgttacagagaagcaaaatagattgctcataacgctcactctctttggaaaaagattgagcaaagttttttaaattaaatgaatatggagaggacaaaaccctctccatatattatataaaatcgtcaaaaaagaagtattttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taattgttcctctatatgtctttttcggaaatcgaataagaacattttatctattccattcagtaatacggcaagggtttaaaagttaaaaaagtaaaaaaacaagacaaacatttggatgtatcaaaaacatgctatacgtttgcagaacaaattttaaagactaaatacaatgaagacaaaaattttaggagggatatttaccctcgtagtgatggtagcggtaagctacggagtggacaaaagtaaaagtatgcgaaatgatgtcaacctctcggatatgacattaagcaatgtagaggcattagcaagcggagaattagcggattgtgagtatggatgctttgctaatggggatggatgttggtgctatgattggtatccttgttacagagaagcaaaatagattgctcataacgctcactctctttggaaaaagattgagcaaagttttttaaattaaatgaatatggagaggacaaaaccctctccatatattatataaaatcgtcaaaaaagaagtattttt Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 115 End: 246 .................................................................................................................. M D V S K T C Y T F A E Q I L K T K Y N E D K N F R R D I Y P R S D G S G K L R S G Q K ........................................................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 173 End: 403 ............................................................................................................................................................................ M K T K I L G G I F T L V V M V A V S Y G V D K S K S M R N D V N L S D M T L S N V E A L A S G E L A D C E Y G C F A N .............................................................................................................................. Protein_Len: 43 Strand: + Start: 327 End: 455 ...................................................................................................................................................................................................................................................................................................................................... M V S M D A L L M G M D V G A M I G I L V T E K Q N R L L I T L T L F G K R L S K V F .......................................................................... Protein_Len: 48 Strand: - Start: 351 End: 494 .............................................................................................................................................................................................................................................................................................................................................................. H P H I N T S H N T D K N C L L L I S Q E Y R E S E K S F S Q A F N K L N F S Y P S S L V R E M ................................... Protein_Len: 42 Strand: - Start: 323 End: 448 .................................................................................................................................................................................................................................................................................................................................. R I T L I S A K S I P I S T P A I I P I R T V S F C F L N S M V S V R K P F L N L M ................................................................................. Protein_Len: 30 Strand: - Start: 191 End: 280 .............................................................................................................................................................................................. S P Y K G E Y H H Y R Y A V S H V F T F T H S I I D V E R M ......................................................................................................................................................................................................................................................... taattgttcctctatatgtctttttcggaaatcgaataagaacattttatctattccattcagtaatacggcaagggtttaaaagttaaaaaagtaaaaaaacaagacaaacatttggatgtatcaaaaacatgctatacgtttgcagaacaaattttaaagactaaatacaatgaagacaaaaattttaggagggatatttaccctcgtagtgatggtagcggtaagctacggagtggacaaaagtaaaagtatgcgaaatgatgtcaacctctcggatatgacattaagcaatgtagaggcattagcaagcggagaattagcggattgtgagtatggatgctttgctaatggggatggatgttggtgctatgattggtatccttgttacagagaagcaaaatagattgctcataacgctcactctctttggaaaaagattgagcaaagttttttaaattaaatgaatatggagaggacaaaaccctctccatatattatataaaatcgtcaaaaaagaagtattttt 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: 84 Start: 154 End: 183 .........................................................................................................................................................TTTGTCTTCATTGTATTTAGTCTTTAAAAT.......................................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 215 End: 244 ......................................................................................................................................................................................................................TTTGTCCACTCCGTAGCTTACCGCTACCAT............................................................................................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taattgttcctctatatgtctttttcggaaatcgaataagaacattttatctattccattcagtaatacggcaagggtttaaaagttaaaaaagtaaaaaaacaagacaaacatttggatgtatcaaaaacatgctatacgtttgcagaacaaattttaaagactaaatacaatgaagacaaaaattttaggagggatatttaccctcgtagtgatggtagcggtaagctacggagtggacaaaagtaaaagtatgcgaaatgatgtcaacctctcggatatgacattaagcaatgtagaggcattagcaagcggagaattagcggattgtgagtatggatgctttgctaatggggatggatgttggtgctatgattggtatccttgttacagagaagcaaaatagattgctcataacgctcactctctttggaaaaagattgagcaaagttttttaaattaaatgaatatggagaggacaaaaccctctccatatattatataaaatcgtcaaaaaagaagtattttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 47 HP_score: -2.4 Tail_Score: -3.58726 Start: 398 End: 411 Full_Region: gagtgagcgttatga gcaa tctatt ttgc ttctctgtaacaagg .............................................................................................................................................................................................................................................................................................................................................................................................................gcaatctattttgc...................................................................................................................... TransTerm Strand: + Conf: 72 HP_score: -8.4 Tail_Score: -3.50869 Start: 467 End: 497 Full_Region: TTTTTAAATTAAATG AATATGGAGAGG ACAAAAC CCTCTCCATATA TTATATAAAATCGTC ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AATATGGAGAGGACAAAACCCTCTCCATATA................................ TransTerm Strand: - Conf: 95 HP_score: -12.4 Tail_Score: -3.65514 Start: 469 End: 495 Full_Region: cgattttatataata tatggagagggt ttt gtcctctccata ttcatttaatttaaa ....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................tatggagagggttttgtcctctccata.................................. Find igs database================================================ Query_seq: TF1391:TF1392|TF1391:TF1392:hypothetical protein:conserved hypothetical protein:->->:1464303..1464831 529 taattgttcctctatatgtctttttcggaaatcgaataagaacattttatctattccattcagtaatacggcaagggtttaaaagttaaaaaagtaaaaaaacaagacaaacatttggatgtatcaaaaacatgctatacgtttgcagaacaaattttaaagactaaatacaatgaagacaaaaattttaggagggatatttaccctcgtagtgatggtagcggtaagctacggagtggacaaaagtaaaagtatgcgaaatgatgtcaacctctcggatatgacattaagcaatgtagaggcattagcaagcggagaattagcggattgtgagtatggatgctttgctaatggggatggatgttggtgctatgattggtatccttgttacagagaagcaaaatagattgctcataacgctcactctctttggaaaaagattgagcaaagttttttaaattaaatgaatatggagaggacaaaaccctctccatatattatataaaatcgtcaaaaaagaagtattttt Intra-Species Hit: Count: 1 Min: 1 Max: 529 Len: 529 Subject: tfor_TF1391_TF1392|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1464303,1464831]|529 HSP 1 e-value: 0.0 bit: 846.0 Len: 427 Query Start:103 Query End:529 Subject Strand: POSITIVE Subject Start: 103 Subject End: 529 ......................................................................................................caagacaaacatttggatgtatcaaaaacatgctatacgtttgcagaacaaattttaaagactaaatacaatgaagacaaaaattttaggagggatatttaccctcgtagtgatggtagcggtaagctacggagtggacaaaagtaaaagtatgcgaaatgatgtcaacctctcggatatgacattaagcaatgtagaggcattagcaagcggagaattagcggattgtgagtatggatgctttgctaatggggatggatgttggtgctatgattggtatccttgttacagagaagcaaaatagattgctcataacgctcactctctttggaaaaagattgagcaaagttttttaaattaaatgaatatggagaggacaaaaccctctccatatattatataaaatcgtcaaaaaagaagtattttt ......................................................................................................caagacaaacatttggatgtatcaaaaacatgctatacgtttgcagaacaaattttaaagactaaatacaatgaagacaaaaattttaggagggatatttaccctcgtagtgatggtagcggtaagctacggagtggacaaaagtaaaagtatgcgaaatgatgtcaacctctcggatatgacattaagcaatgtagaggcattagcaagcggagaattagcggattgtgagtatggatgctttgctaatggggatggatgttggtgctatgattggtatccttgttacagagaagcaaaatagattgctcataacgctcactctctttggaaaaagattgagcaaagttttttaaattaaatgaatatggagaggacaaaaccctctccatatattatataaaatcgtcaaaaaagaagtattttt HSP 2 e-value: 1.0E-37 bit: 159.0 Len: 80 Query Start:1 Query End:80 Subject Strand: POSITIVE Subject Start: 1 Subject End: 80 taattgttcctctatatgtctttttcggaaatcgaataagaacattttatctattccattcagtaatacggcaagggttt................................................................................................................................................................................................................................................................................................................................................................................................................................................................. taattgttcctctatatgtctttttcggaaatcgaataagaacattttatctattccattcagtaatacggcaagggttt................................................................................................................................................................................................................................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUUGUUCCUCUAUAUGUCUUUUUCGGAAAUCGAAUAAGAACAUUUUAUCUAUUCCAUUCAGUAAUACGGCAAGGGUUUAAAAGUUAAAAAAGUAAAAAAACAAGACAAACAUUUGGAUGUAUCAAAAACAUGCUAUACGUUUGCAGAACAAAUUUUAAAGACUAAAUACAAUGAAGACAAAAAUUUUAGGAGGGAUAUUUACCCUCGUAGUGAUGGUAGCGGUAAGCUACGGAGUGGACAAAAGUAAAAGUAUGCGAAAUGAUGUCAACCUCUCGGAUAUGACAUUAAGCAAUGUAGAGGCAUUAGCAAGCGGAGAAUUAGCGGAUUGUGAGUAUGGAUGCUUUGCUAAUGGGGAUGGAUGUUGGUGCUAUGAUUGGUAUCCUUGUUACAGAGAAGCAAAAUAGAUUGCUCAUAACGCUCACUCUCUUUGGAAAAAGAUUGAGCAAAGUUUUUUAAAUUAAAUGAAUAUGGAGAGGACAAAACCCUCUCCAUAUAUUAUAUAAAAUCGUCAAAAAAGAAGUAUUUUU ...((((((((((((((.((((.((((.....)))).))))...((((.((((((((..(((.((........((..(((((((.........((......))..(.(((((...(((((((.......)))).)))...))))))........)))))))..))..........................(((((.......))))).)).)))..(((((.....))))))))))))).)))).........(((....((((((((.((....))...)))))))).))))))))))))....)))))..((((((((......(((((((((....((.((((((..((..(..(((((..(((......)))..)))))...)..))....)))))).))...))))))))).(((((...(((((....))))).)))))..))))))))...(((.(((((((((((((((.......))))))))))).)))).)))........................ (-124.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUACUUCUUUUUUGACGAUUUUAUAUAAUAUAUGGAGAGGGUUUUGUCCUCUCCAUAUUCAUUUAAUUUAAAAAACUUUGCUCAAUCUUUUUCCAAAGAGAGUGAGCGUUAUGAGCAAUCUAUUUUGCUUCUCUGUAACAAGGAUACCAAUCAUAGCACCAACAUCCAUCCCCAUUAGCAAAGCAUCCAUACUCACAAUCCGCUAAUUCUCCGCUUGCUAAUGCCUCUACAUUGCUUAAUGUCAUAUCCGAGAGGUUGACAUCAUUUCGCAUACUUUUACUUUUGUCCACUCCGUAGCUUACCGCUACCAUCACUACGAGGGUAAAUAUCCCUCCUAAAAUUUUUGUCUUCAUUGUAUUUAGUCUUUAAAAUUUGUUCUGCAAACGUAUAGCAUGUUUUUGAUACAUCCAAAUGUUUGUCUUGUUUUUUUACUUUUUUAACUUUUAAACCCUUGCCGUAUUACUGAAUGGAAUAGAUAAAAUGUUCUUAUUCGAUUUCCGAAAAAGACAUAUAGAGGAACAAUUA ...........((((((((.....(((......((((((((((((.....)))))))))))).....))).))))))))....(((((.((((((....)))))).))))).....((((((......))))))(((((((....(((((.........((...............(((((((((.((............................)))))))))))...............((((((...((....)).))))))......)).....(((((((((((.......(((((.....))))).......))))))))))))))))..........((((((((..(((.((((((((....(((((.((((.(((....))).)))).))))).(((((...(((..(((((....(((.............)))...)))))..)))..))))))))))))).)))))))))))...((((.((((.....)))).))))..)))))))......... (-112.75) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 403 357 311 200 145 tfor:TF2272|5end_conserved_hypothetical_protein_2436156..2436386_POSITIVE 348 370 323 195 142 tfor:TF1853|5end_homoserine_O-succinyltransferase_2006470..2006700_POSITIVE 341 380 338 81 40 tfor:TF2440|5end_conserved_hypothetical_protein;_possible_DNA_mismatch_repair_protein_2616858..2617088_POSITIVE 340 339 292 182 125 tfor:TF0152|5end_RNA_polymerase_ECF-type_sigma_factor_162021..162251_POSITIVE 338 349 308 203 153 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 338 360 311 170 123 tfor:TF1425|5end_phospho-N-acetylmuramoyl_pentapeptide_transferase_1508600..1508830_POSITIVE 337 236 191 160 100 tfor:TF1547|5end_conserved_hypothetical_protein_1651459..1651689_POSITIVE 337 389 341 114 58 tfor:TF0662|5end_hypothetical_protein_708316..708546_POSITIVE 335 240 191 71 9 tfor:TF2038|5end_hypothetical_protein_2198978..2199208_POSITIVE 333 370 324 187 130 tfor:TF2467|5end_3-dehydroquinate_dehydratase_II_2645827..2646057_POSITIVE 332 314 272 187 149 tfor:TF0426|5end_conserved_hypothetical_protein_444728..444958_POSITIVE 331 248 204 168 120 tfor:TF1810|5end_conserved_hypothetical_protein;_possible_membrane_protein_1950490..1950720_POSITIVE 328 384 342 89 50 tfor:TF0851|5end_helicase_SNF2_family_899486..899716_POSITIVE 328 250 207 80 23 tfor:TF0248|5end_hypothetical_protein_278249..278479_POSITIVE 325 370 322 178 129 tfor:TF0904|5end_conserved_hypothetical_protein_948435..948665_POSITIVE 324 240 191 72 20 tfor:TF2223|5end_CTn_excision__protein_2394247..2394477_POSITIVE 324 235 191 231 183 tfor:TF1586|5end_hypothetical_protein_1690971..1691201_POSITIVE 321 371 331 78 27 tfor:TF2331|5end_conserved_hypothetical_protein_2491073..2491303_POSITIVE 321 370 323 182 132 tfor:TF2187|5end_conserved_hypothetical_protein_2361693..2361923_POSITIVE 321 279 233 160 118 tfor:TF1478|5end_membrane_fusion_efflux_protein_1571101..1571331_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 656 220 173 138 91 tfor:TF2027|3end_conserved_hypothetical_protein_2184176..2184326_POSITIVE 403 357 311 151 96 tfor:TF2271|3end_conserved_hypothetical_protein_2436187..2436337_POSITIVE 353 377 339 136 100 tfor:TF0038|3end_conserved_hypothetical_protein_41213..41363_POSITIVE 351 356 311 66 8 tfor:TF2673|3end_conserved_hypothetical_protein_2848272..2848422_POSITIVE 351 319 271 139 102 tfor:TF2100|3end_hypothetical_protein_2273686..2273836_POSITIVE 341 380 338 73 32 tfor:TF2439|3end_conserved_hypothetical_protein_2616930..2617080_POSITIVE 332 314 272 84 46 tfor:TF0425|3end_outer_membrane_protein_444705..444855_POSITIVE 328 250 207 99 42 tfor:TF0247|3end_conserved_hypothetical_protein_278348..278498_POSITIVE 324 380 331 149 110 tfor:TF0318|3end_outer_membrane_protein,_TonB_dependent_receptor_344301..344451_POSITIVE 321 349 301 57 1 tfor:TF0993|3end_hypothetical_protein_1048782..1048932_POSITIVE 319 380 336 68 18 tfor:TF2332|3end_signal_peptidase_I_2492613..2492763_POSITIVE 317 336 291 66 7 tfor:TF0875|3end_outer_membrane_receptor,_TonB-linked_929251..929401_POSITIVE 316 367 321 146 98 tfor:TF0841|3end_NADH_dehydrogenase/NAD(P)H_nitroreductase_893048..893198_POSITIVE 315 400 354 119 71 tfor:TF2847|3end_hypothetical_protein_3034985..3035135_POSITIVE 315 349 309 46 9 tfor:TF0774|3end_membrane-fusion_protein;_36_kDa_antigen_823730..823880_POSITIVE 313 370 322 147 96 tfor:TF2489|3end_hypothetical_protein_2664698..2664848_POSITIVE 313 354 311 151 117 tfor:TF1424|3end_N-acetylymuramoyl-L-alanine-D-glutamate_ligase_1508674..1508824_POSITIVE 313 399 352 115 67 tfor:TF0874|3end_transposase_926652..926802_POSITIVE 312 237 197 148 105 tfor:TF1808|3end_DNA_processing_protein_subunit_A_1950560..1950710_POSITIVE 311 349 302 97 55 tfor:TF1577|3end_hypothetical_protein_1686234..1686384_POSITIVE