Origin IGS: tgatgaaaacaaaaattctaagaggggtctttgccctcgcagtgatggtggctgcaggctacggagtgaaccggagcatgcagaaagacaccgatctttcggagatggcgctaagtaatgtggaggccttggcttggtttgaaggaggcgatggcaatggcaatacaataggttgcccaggaggaacttgctctatgactgactcttttggcagatcgtgtacggcatgttgcccttcaggattaaagcctaaatgtgatttgtcatttggtacttgcagttgtgaatgagcatttgagagtcggggcatca .........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 tgatgccccgactctcaaatgctcattcacaactgcaagtaccaaatgacaaatcacatttaggctttaatcctgaagggcaacatgccgtacacgatctgccaaaagagtcagtcatagagcaagttcctcctgggcaacctattgtattgccattgccatcgcctccttcaaaccaagccaaggcctccacattacttagcgccatctccgaaagatcggtgtctttctgcatgctccggttcactccgtagcctgcagccaccatcactgcgagggcaaagacccctcttagaatttttgttttcatca Mask Tandem Repeat Region ================================================ tgatgaaaacaaaaattctaagaggggtctttgccctcgcagtgatggtggctgcaggctacggagtgaaccggagcatgcagaaagacaccgatctttcggagatggcgctaagtaatgtggaggccttggcttggtttgaaggaggcgatggcaatggcaatacaataggttgcccaggaggaacttgctctatgactgactcttttggcagatcgtgtacggcatgttgcccttcaggattaaagcctaaatgtgatttgtcatttggtacttgcagttgtgaatgagcatttgagagtcggggcatca Find is-nt database================================================ Query_seq: TF1382:TF1384|TF1382:TF1384:hypothetical protein:hypothetical protein:->->:1457838..1458149 312 tgatgaaaacaaaaattctaagaggggtctttgccctcgcagtgatggtggctgcaggctacggagtgaaccggagcatgcagaaagacaccgatctttcggagatggcgctaagtaatgtggaggccttggcttggtttgaaggaggcgatggcaatggcaatacaataggttgcccaggaggaacttgctctatgactgactcttttggcagatcgtgtacggcatgttgcccttcaggattaaagcctaaatgtgatttgtcatttggtacttgcagttgtgaatgagcatttgagagtcggggcatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1382:TF1384|TF1382:TF1384:hypothetical protein:hypothetical protein:->->:1457838..1458149 312 tgatgaaaacaaaaattctaagaggggtctttgccctcgcagtgatggtggctgcaggctacggagtgaaccggagcatgcagaaagacaccgatctttcggagatggcgctaagtaatgtggaggccttggcttggtttgaaggaggcgatggcaatggcaatacaataggttgcccaggaggaacttgctctatgactgactcttttggcagatcgtgtacggcatgttgcccttcaggattaaagcctaaatgtgatttgtcatttggtacttgcagttgtgaatgagcatttgagagtcggggcatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1382:TF1384|TF1382:TF1384:hypothetical protein:hypothetical protein:->->:1457838..1458149 312 tgatgaaaacaaaaattctaagaggggtctttgccctcgcagtgatggtggctgcaggctacggagtgaaccggagcatgcagaaagacaccgatctttcggagatggcgctaagtaatgtggaggccttggcttggtttgaaggaggcgatggcaatggcaatacaataggttgcccaggaggaacttgctctatgactgactcttttggcagatcgtgtacggcatgttgcccttcaggattaaagcctaaatgtgatttgtcatttggtacttgcagttgtgaatgagcatttgagagtcggggcatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgatgaaaacaaaaattctaagaggggtctttgccctcgcagtgatggtggctgcaggctacggagtgaaccggagcatgcagaaagacaccgatctttcggagatggcgctaagtaatgtggaggccttggcttggtttgaaggaggcgatggcaatggcaatacaataggttgcccaggaggaacttgctctatgactgactcttttggcagatcgtgtacggcatgttgcccttcaggattaaagcctaaatgtgatttgtcatttggtacttgcagttgtgaatgagcatttgagagtcggggcatca Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 3 End: 287 .. M K T K I L R G V F A L A V M V A A G Y G V N R S M Q K D T D L S E M A L S N V E A L A W F E G G D G N G N T I G C P G ......................... Protein_Len: 60 Strand: - Start: 62 End: 310 ............................................................. A Q N S P P S P L P L V I P Q G P P V Q E I V S E K P L D H V A H Q G E P N F G L H S K D N P V Q L Q S H A N S L R P M .. Protein_Len: 60 Strand: - Start: 1 End: 180 S S F L F E L L P R Q G R L S P P Q L S R L S G S C A S L C R D K P S P A L Y H P P R P K T Q L L R H C H C Y L L N G M .................................................................................................................................... tgatgaaaacaaaaattctaagaggggtctttgccctcgcagtgatggtggctgcaggctacggagtgaaccggagcatgcagaaagacaccgatctttcggagatggcgctaagtaatgtggaggccttggcttggtttgaaggaggcgatggcaatggcaatacaataggttgcccaggaggaacttgctctatgactgactcttttggcagatcgtgtacggcatgttgcccttcaggattaaagcctaaatgtgatttgtcatttggtacttgcagttgtgaatgagcatttgagagtcggggcatca 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================================================ tgatgaaaacaaaaattctaagaggggtctttgccctcgcagtgatggtggctgcaggctacggagtgaaccggagcatgcagaaagacaccgatctttcggagatggcgctaagtaatgtggaggccttggcttggtttgaaggaggcgatggcaatggcaatacaataggttgcccaggaggaacttgctctatgactgactcttttggcagatcgtgtacggcatgttgcccttcaggattaaagcctaaatgtgatttgtcatttggtacttgcagttgtgaatgagcatttgagagtcggggcatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1382:TF1384|TF1382:TF1384:hypothetical protein:hypothetical protein:->->:1457838..1458149 312 tgatgaaaacaaaaattctaagaggggtctttgccctcgcagtgatggtggctgcaggctacggagtgaaccggagcatgcagaaagacaccgatctttcggagatggcgctaagtaatgtggaggccttggcttggtttgaaggaggcgatggcaatggcaatacaataggttgcccaggaggaacttgctctatgactgactcttttggcagatcgtgtacggcatgttgcccttcaggattaaagcctaaatgtgatttgtcatttggtacttgcagttgtgaatgagcatttgagagtcggggcatca Intra-Species Hit: Count: 1 Min: 1 Max: 312 Len: 312 Subject: tfor_TF1382_TF1384|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1457838,1458149]|312 HSP 1 e-value: 1.0E-176 bit: 618.0 Len: 312 Query Start:1 Query End:312 Subject Strand: POSITIVE Subject Start: 1 Subject End: 312 tgatgaaaacaaaaattctaagaggggtctttgccctcgcagtgatggtggctgcaggctacggagtgaaccggagcatgcagaaagacaccgatctttcggagatggcgctaagtaatgtggaggccttggcttggtttgaaggaggcgatggcaatggcaatacaataggttgcccaggaggaacttgctctatgactgactcttttggcagatcgtgtacggcatgttgcccttcaggattaaagcctaaatgtgatttgtcatttggtacttgcagttgtgaatgagcatttgagagtcggggcatca tgatgaaaacaaaaattctaagaggggtctttgccctcgcagtgatggtggctgcaggctacggagtgaaccggagcatgcagaaagacaccgatctttcggagatggcgctaagtaatgtggaggccttggcttggtttgaaggaggcgatggcaatggcaatacaataggttgcccaggaggaacttgctctatgactgactcttttggcagatcgtgtacggcatgttgcccttcaggattaaagcctaaatgtgatttgtcatttggtacttgcagttgtgaatgagcatttgagagtcggggcatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUGAAAACAAAAAUUCUAAGAGGGGUCUUUGCCCUCGCAGUGAUGGUGGCUGCAGGCUACGGAGUGAACCGGAGCAUGCAGAAAGACACCGAUCUUUCGGAGAUGGCGCUAAGUAAUGUGGAGGCCUUGGCUUGGUUUGAAGGAGGCGAUGGCAAUGGCAAUACAAUAGGUUGCCCAGGAGGAACUUGCUCUAUGACUGACUCUUUUGGCAGAUCGUGUACGGCAUGUUGCCCUUCAGGAUUAAAGCCUAAAUGUGAUUUGUCAUUUGGUACUUGCAGUUGUGAAUGAGCAUUUGAGAGUCGGGGCAUCA .((((...............(((((((((((((((.((((......((((.(((((.(((.(((......))).))).))))).....))))..(((((((((.....(((........))).((((....))))..))))))))).)))).)))...((((((.......))))))...)))).)))).))))....(((((((((..(((((..((((.....))))))))).((((.((((.(((.(((((((........)))))))..)))..)))).)))).........)))))))))..)))). (-99.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUGCCCCGACUCUCAAAUGCUCAUUCACAACUGCAAGUACCAAAUGACAAAUCACAUUUAGGCUUUAAUCCUGAAGGGCAACAUGCCGUACACGAUCUGCCAAAAGAGUCAGUCAUAGAGCAAGUUCCUCCUGGGCAACCUAUUGUAUUGCCAUUGCCAUCGCCUCCUUCAAACCAAGCCAAGGCCUCCACAUUACUUAGCGCCAUCUCCGAAAGAUCGGUGUCUUUCUGCAUGCUCCGGUUCACUCCGUAGCCUGCAGCCACCAUCACUGCGAGGGCAAAGACCCCUCUUAGAAUUUUUGUUUUCAUCA .((((....((((((....((.(((((....((.....))....)))))))...........(((....(((.((.(.(((.....))).).)).)))..)))...))))))......(((((((((((......(((((.........))))).(((((.((((...................(((((...........)).)))..........(((.((((.....(((((.(((.(((......))).))).))))).)))))))...)))).)))))............))))..))))))))))). (-75.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 424 241 203 42 7 tfor:TF1589|5end_surface_antigen_BspA_1703189..1703419_POSITIVE 421 79 35 92 39 tfor:TF2039|5end_possible_cell-cycle_regulation_histidine_triad_(HIT)_protein_2199318..2199548_POSITIVE 421 187 144 74 25 tfor:TF1919|5end_hypothetical_protein_2070037..2070267_POSITIVE 417 59 25 231 188 tfor:TF2225|5end_CTn_excision_protein_2394935..2395165_POSITIVE 413 241 203 42 7 tfor:TF1591|5end_surface_antigen_BspA_1706387..1706617_POSITIVE 413 68 23 226 178 tfor:TF1347|5end_conserved_hypothetical_protein_1426171..1426401_POSITIVE 407 77 31 225 171 tfor:TF2226|5end_CTn_excision_protein_2395529..2395759_POSITIVE 407 64 23 147 103 tfor:TF0265|5end_conserved_hypothetical_protein,_Rhs_family_293279..293509_POSITIVE 400 99 51 79 23 tfor:TF1475|5end_glucose-6-phosphate_1-dehydrogenase_1568034..1568264_POSITIVE 400 65 21 185 133 tfor:TF0313|5end_outer_membrane_protein,_TonB_dependent_receptor_338182..338412_POSITIVE 399 78 33 74 26 tfor:TF2038|5end_hypothetical_protein_2198978..2199208_POSITIVE 399 77 31 213 174 tfor:TF1064|5end_ampG_permease_1134004..1134234_POSITIVE 396 110 61 227 170 tfor:TF0119|5end_gluconate_aldolase_130577..130807_POSITIVE 395 77 32 229 179 tfor:TF2177|5end_hypothetical_protein_2349281..2349511_POSITIVE 394 79 32 92 36 tfor:TF3014|5end_oxidoreductase,_short-chain_dehydrogenase/reductase_family_3237623..3237853_POSITIVE 394 80 31 74 19 tfor:TF2309|5end_cysteinyl-tRNA_synthetase_2468892..2469122_POSITIVE 393 70 24 86 35 tfor:TF2357|5end_collagenase_2522561..2522791_POSITIVE 388 80 36 205 150 tfor:TF2926|5end_glycine_hydroxymethyltransferase_3128070..3128300_POSITIVE 386 127 82 213 168 tfor:TF0441|5end_Na+-transporting_NADH:ubiquinone_oxidoreductase,_subunit_3_464614..464844_POSITIVE 384 128 81 61 2 tfor:TF2834|5end_cardiolipin_synthase_3025986..3026216_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 852 63 22 151 110 tfor:TF2027|3end_conserved_hypothetical_protein_2184176..2184326_POSITIVE 421 187 144 62 13 tfor:TF1918|3end_hypothetical_protein_2070105..2070255_POSITIVE 400 99 51 88 32 tfor:TF1474|3end_6-phosphogluconolactonase_1568123..1568273_POSITIVE 395 77 32 53 3 tfor:TF2176|3end_hypothetical_protein_2349185..2349335_POSITIVE 389 77 35 116 69 tfor:TF2013|3end_polysaccharide_deacetylase_2169341..2169491_POSITIVE 384 155 120 132 98 tfor:TF1069|3end_glucokinase_regulatory_protein,_sugar_phosphate_isomerase_domain_1139794..1139944_POSITIVE 381 78 37 149 102 tfor:TF1954|3end_long-chain-fatty-acid--CoA_ligase_2106940..2107090_POSITIVE 381 80 35 80 26 tfor:TF0174|3end_hypothetical_protein_185600..185750_POSITIVE 379 78 33 97 34 tfor:TF0247|3end_conserved_hypothetical_protein_278348..278498_POSITIVE 374 60 13 150 97 tfor:TF0823|3end_conserved_hypothetical_protein_881633..881783_POSITIVE 373 80 32 93 33 tfor:TF2107|3end_hypothetical_protein_2277436..2277586_POSITIVE 372 70 25 151 103 tfor:TF0685|3end_hypothetical_protein_731132..731282_POSITIVE 371 76 31 73 11 tfor:TF1931|3end_ATPase/GTPase_2078622..2078772_POSITIVE 370 68 24 102 53 tfor:TF2909|3end_GTP-binding_protein,_possible_GTP1/OBG_family_3105956..3106106_POSITIVE 370 149 101 106 58 tfor:TF1498|3end_GTP-binding_protein_1598490..1598640_POSITIVE 370 60 12 60 10 tfor:TF0385|3end_conserved_hypothetical_protein_406980..407130_POSITIVE 368 77 31 63 13 tfor:TF0832|3end_conserved_hypothetical_protein_888788..888938_POSITIVE 367 89 47 141 90 tfor:TF2953|3end_possible_TonB-dependent_outer_membrane_receptor_3161501..3161651_POSITIVE 367 70 24 65 15 tfor:TF1465|3end_modulator_of_DNA_gyrase_1555544..1555694_POSITIVE 365 68 22 90 40 tfor:TF2640|3end_hypothetical_protein_2809533..2809683_POSITIVE