Origin IGS: taaccttacattaaaggattccctttgtacttttgtactcttattagccataagcgtttgtgtgatttgtgaaagactgttttttcaacctgtagctaaagaatgaaaaaggaaattccaatcacataagtttagggagaaaatgaaaaacaattgttaaactgatttgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acaaatcagtttaacaattgtttttcattttctccctaaacttatgtgattggaatttcctttttcattctttagctacaggttgaaaaaacagtctttcacaaatcacacaaacgcttatggctaataagagtacaaaagtacaaagggaatcctttaatgtaaggtta Mask Tandem Repeat Region ================================================ taaccttacattaaaggattccctttgtacttttgtactcttattagccataagcgtttgtgtgatttgtgaaagactgttttttcaacctgtagctaaagaatgaaaaaggaaattccaatcacataagtttagggagaaaatgaaaaacaattgttaaactgatttgt Find is-nt database================================================ Query_seq: TF1987:TF1989|TF1987:TF1989:hypothetical protein:outer membrane protein, possible TonB dependent receptor:->->:2137793..2137962 170 taaccttacattaaaggattccctttgtacttttgtactcttattagccataagcgtttgtgtgatttgtgaaagactgttttttcaacctgtagctaaagaatgaaaaaggaaattccaatcacataagtttagggagaaaatgaaaaacaattgttaaactgatttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1987:TF1989|TF1987:TF1989:hypothetical protein:outer membrane protein, possible TonB dependent receptor:->->:2137793..2137962 170 taaccttacattaaaggattccctttgtacttttgtactcttattagccataagcgtttgtgtgatttgtgaaagactgttttttcaacctgtagctaaagaatgaaaaaggaaattccaatcacataagtttagggagaaaatgaaaaacaattgttaaactgatttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1987:TF1989|TF1987:TF1989:hypothetical protein:outer membrane protein, possible TonB dependent receptor:->->:2137793..2137962 170 taaccttacattaaaggattccctttgtacttttgtactcttattagccataagcgtttgtgtgatttgtgaaagactgttttttcaacctgtagctaaagaatgaaaaaggaaattccaatcacataagtttagggagaaaatgaaaaacaattgttaaactgatttgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaccttacattaaaggattccctttgtacttttgtactcttattagccataagcgtttgtgtgatttgtgaaagactgttttttcaacctgtagctaaagaatgaaaaaggaaattccaatcacataagtttagggagaaaatgaaaaacaattgttaaactgatttgt Predict ORF larger than 30AA ================================================ taaccttacattaaaggattccctttgtacttttgtactcttattagccataagcgtttgtgtgatttgtgaaagactgttttttcaacctgtagctaaagaatgaaaaaggaaattccaatcacataagtttagggagaaaatgaaaaacaattgttaaactgatttgt 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================================================ taaccttacattaaaggattccctttgtacttttgtactcttattagccataagcgtttgtgtgatttgtgaaagactgttttttcaacctgtagctaaagaatgaaaaaggaaattccaatcacataagtttagggagaaaatgaaaaacaattgttaaactgatttgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1987:TF1989|TF1987:TF1989:hypothetical protein:outer membrane protein, possible TonB dependent receptor:->->:2137793..2137962 170 taaccttacattaaaggattccctttgtacttttgtactcttattagccataagcgtttgtgtgatttgtgaaagactgttttttcaacctgtagctaaagaatgaaaaaggaaattccaatcacataagtttagggagaaaatgaaaaacaattgttaaactgatttgt Intra-Species Hit: Count: 1 Min: 1 Max: 170 Len: 170 Subject: tfor_TF1987_TF1989|hypothetical protein:outer membrane protein, possible TonB dependent receptor|POSITIVE:POSITIVE|[2137793,2137962]|170 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 taaccttacattaaaggattccctttgtacttttgtactcttattagccataagcgtttgtgtgatttgtgaaagactgttttttcaacctgtagctaaagaatgaaaaaggaaattccaatcacataagtttagggagaaaatgaaaaacaattgttaaactgatttgt taaccttacattaaaggattccctttgtacttttgtactcttattagccataagcgtttgtgtgatttgtgaaagactgttttttcaacctgtagctaaagaatgaaaaaggaaattccaatcacataagtttagggagaaaatgaaaaacaattgttaaactgatttgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACCUUACAUUAAAGGAUUCCCUUUGUACUUUUGUACUCUUAUUAGCCAUAAGCGUUUGUGUGAUUUGUGAAAGACUGUUUUUUCAACCUGUAGCUAAAGAAUGAAAAAGGAAAUUCCAAUCACAUAAGUUUAGGGAGAAAAUGAAAAACAAUUGUUAAACUGAUUUGU ...((((......)))).(((((...((((....))))............(((((...(((((((((.(.(((....(.((((((((..((........))..)))))))).)..))))))))))))).))))))))))............................... (-30.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAAUCAGUUUAACAAUUGUUUUUCAUUUUCUCCCUAAACUUAUGUGAUUGGAAUUUCCUUUUUCAUUCUUUAGCUACAGGUUGAAAAAACAGUCUUUCACAAAUCACACAAACGCUUAUGGCUAAUAAGAGUACAAAAGUACAAAGGGAAUCCUUUAAUGUAAGGUUA ......(((((....)))))............(((((...(((((((((((.(((.....(((((((..((........))..))))))).......)))...))))))......((.....))..))))).((((....))))..)))))..((((......))))... (-29.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 92 54 158 109 tfor:TF0782|5end_ThiJ/PfpI_family_protein_835976..836206_POSITIVE 260 90 42 118 55 tfor:TF2443|5end_amidophosphoribosyl-transferase_2620287..2620517_POSITIVE 254 94 53 199 159 tfor:TF1639|5end_conserved_hypothetical_protein_1747652..1747882_POSITIVE 253 41 3 55 15 tfor:TF3053|5end_conserved_hypothetical_protein_3278564..3278794_POSITIVE 251 60 16 209 174 tfor:TF3143|5end_conserved_hypothetical_protein;_possible_membrane_protein_3377465..3377695_POSITIVE 250 96 54 129 75 tfor:TF1975|5end_uridylate_kinase_2121536..2121766_POSITIVE 246 66 21 107 59 tfor:TF1446|5end_hypothetical_protein_1530649..1530879_POSITIVE 244 60 16 65 24 tfor:TF0047|5end_hypothetical_protein_53844..54074_POSITIVE 239 70 21 105 56 tfor:TF1153|5end_pyruvate-formate_lyase-activating_enzyme_1234643..1234873_POSITIVE 238 70 23 117 71 tfor:TF1939|5end_hypothetical_protein_2086299..2086529_POSITIVE 237 63 22 231 183 tfor:TF1348|5end_conserved_hypothetical_protein_1428170..1428400_POSITIVE 236 84 54 207 170 tfor:TF0163|5end_hypothetical_protein_173631..173861_POSITIVE 235 140 96 103 52 tfor:TF0925|5end_hypothetical_protein_961736..961966_POSITIVE 233 76 35 100 58 tfor:TF0343|5end_hypothetical_protein_366502..366732_POSITIVE 232 95 60 222 194 tfor:TF2509|5end_ATP-dependent_clp_protease,_proteolytic_subunit_2687562..2687792_POSITIVE 232 75 44 103 75 tfor:TF0610|5end_conserved_hypothetical_protein;_possible_phosphatidylglycerophosphate_synthase_643460..643690_POSITIVE 229 74 37 65 34 tfor:TF3015|5end_hypothetical_protein_3238430..3238660_POSITIVE 229 98 55 75 25 tfor:TF0803|5end_hypothetical_protein_861045..861275_POSITIVE 228 97 60 164 131 tfor:TF2538|5end_hypothetical_protein_2721840..2722070_POSITIVE 227 59 20 82 43 tfor:TF1538|5end_conserved_hypothetical_protein_1643531..1643761_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 69 21 93 29 tfor:TF0339|3end_hypothetical_protein_363747..363897_POSITIVE 265 85 47 89 52 tfor:TF0815|3end_conserved_hypothetical_protein_873974..874124_POSITIVE 264 92 54 106 57 tfor:TF0781|3end_serine_protease_inhibitor_836004..836154_POSITIVE 253 41 3 65 25 tfor:TF3052|3end_conserved_hypothetical_protein_3278654..3278804_POSITIVE 252 79 45 122 78 tfor:TF0666|3end_conserved_hypothetical_protein_710945..711095_POSITIVE 248 60 19 135 92 tfor:TF2515|3end_outer_membrane_protein,_TonB_dependent_receptor_2694865..2695015_POSITIVE 246 66 21 96 48 tfor:TF1445|3end_RNA_polymerase_sigma_factor_1530718..1530868_POSITIVE 227 64 23 131 93 tfor:TF1657|3end_lauroyl/myristoyl_acyltransferase_1773407..1773557_POSITIVE 225 92 55 79 43 tfor:TF1325|3end_L-fucose_isomerase_1405870..1406020_POSITIVE 223 66 27 133 82 tfor:TF1997|3end_ROK_family_transcriptional_regulator_2152686..2152836_POSITIVE 219 99 56 44 1 tfor:TF2482|3end_hypothetical_protein_2659185..2659335_POSITIVE 217 34 4 57 29 tfor:TF1447|3end_D-ribulose-phosphate-3_epimerase_1531764..1531914_POSITIVE 216 80 33 118 82 tfor:TF2188|3end_conserved_hypothetical_protein_2363535..2363685_POSITIVE 213 70 37 119 92 tfor:TF0259|3end_conserved_hypothetical_protein_290981..291131_POSITIVE 212 98 52 136 80 tfor:TF1289|3end_ribosomal_protein_L11_methyltransferase_1371233..1371383_POSITIVE 210 96 54 66 21 tfor:TF2823|3end_TPR-containing_protein_3014337..3014487_POSITIVE 210 51 20 132 99 tfor:TF1813|3end_peptide_methionine_sulfoxide_reductase_1955293..1955443_POSITIVE 210 119 75 94 55 tfor:TF0960|3end_beta-galactosidase_1010506..1010656_POSITIVE 209 96 54 60 16 tfor:TF1577|3end_hypothetical_protein_1686234..1686384_POSITIVE 208 146 123 94 67 tfor:TF2711|3end_hemolysis_secretion_protein_2886005..2886155_POSITIVE