Origin IGS: aaaattgtaaattttatgcaaaaaacacttgatatattgtaaaaatatggtatagttaaagtaaggtctttttaaaagactaaaaatatttaagtttaggtctagcgtcctaaacaaaggagttgttttatgaaagatttattgaacaatgggtttcagcctgtgtctgaaacggagatggtaatggttgaggggggaggaggtgcttcagatatggtaatagatggtgataatcctggagctcaaagaccgacacctccaccacctccttctaatggcggaggatgtggtgatgtaaattggcttgagatgagatagtaactctaattttaggcctcctccttacaattctatattttaattgtaaggaggagttatcgat .........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 atcgataactcctccttacaattaaaatatagaattgtaaggaggaggcctaaaattagagttactatctcatctcaagccaatttacatcaccacatcctccgccattagaaggaggtggtggaggtgtcggtctttgagctccaggattatcaccatctattaccatatctgaagcacctcctcccccctcaaccattaccatctccgtttcagacacaggctgaaacccattgttcaataaatctttcataaaacaactcctttgtttaggacgctagacctaaacttaaatatttttagtcttttaaaaagaccttactttaactataccatatttttacaatatatcaagtgttttttgcataaaatttacaatttt Mask Tandem Repeat Region ================================================ aaaattgtaaattttatgcaaaaaacacttgatatattgtaaaaatatggtatagttaaagtaaggtctttttaaaagactaaaaatatttaagtttaggtctagcgtcctaaacaaaggagttgttttatgaaagatttattgaacaatgggtttcagcctgtgtctgaaacggagatggtaatggttgaggggggaggaggtgcttcagatatggtaatagatggtgataatcctggagctcaaagaccgacacctccaccacctccttctaatggcggaggatgtggtgatgtaaattggcttgagatgagatagtaactctaattttaggcctcctccttacaattctatattttaattgtaaggaggagttatcgat Find is-nt database================================================ Query_seq: TDE0721:TDE0722|TDE0721:TDE0722:hypothetical protein:lipoprotein, putative:->->:758277..758658 382 aaaattgtaaattttatgcaaaaaacacttgatatattgtaaaaatatggtatagttaaagtaaggtctttttaaaagactaaaaatatttaagtttaggtctagcgtcctaaacaaaggagttgttttatgaaagatttattgaacaatgggtttcagcctgtgtctgaaacggagatggtaatggttgaggggggaggaggtgcttcagatatggtaatagatggtgataatcctggagctcaaagaccgacacctccaccacctccttctaatggcggaggatgtggtgatgtaaattggcttgagatgagatagtaactctaattttaggcctcctccttacaattctatattttaattgtaaggaggagttatcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0721:TDE0722|TDE0721:TDE0722:hypothetical protein:lipoprotein, putative:->->:758277..758658 382 aaaattgtaaattttatgcaaaaaacacttgatatattgtaaaaatatggtatagttaaagtaaggtctttttaaaagactaaaaatatttaagtttaggtctagcgtcctaaacaaaggagttgttttatgaaagatttattgaacaatgggtttcagcctgtgtctgaaacggagatggtaatggttgaggggggaggaggtgcttcagatatggtaatagatggtgataatcctggagctcaaagaccgacacctccaccacctccttctaatggcggaggatgtggtgatgtaaattggcttgagatgagatagtaactctaattttaggcctcctccttacaattctatattttaattgtaaggaggagttatcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0721:TDE0722|TDE0721:TDE0722:hypothetical protein:lipoprotein, putative:->->:758277..758658 382 aaaattgtaaattttatgcaaaaaacacttgatatattgtaaaaatatggtatagttaaagtaaggtctttttaaaagactaaaaatatttaagtttaggtctagcgtcctaaacaaaggagttgttttatgaaagatttattgaacaatgggtttcagcctgtgtctgaaacggagatggtaatggttgaggggggaggaggtgcttcagatatggtaatagatggtgataatcctggagctcaaagaccgacacctccaccacctccttctaatggcggaggatgtggtgatgtaaattggcttgagatgagatagtaactctaattttaggcctcctccttacaattctatattttaattgtaaggaggagttatcgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaattgtaaattttatgcaaaaaacacttgatatattgtaaaaatatggtatagttaaagtaaggtctttttaaaagactaaaaatatttaagtttaggtctagcgtcctaaacaaaggagttgttttatgaaagatttattgaacaatgggtttcagcctgtgtctgaaacggagatggtaatggttgaggggggaggaggtgcttcagatatggtaatagatggtgataatcctggagctcaaagaccgacacctccaccacctccttctaatggcggaggatgtggtgatgtaaattggcttgagatgagatagtaactctaattttaggcctcctccttacaattctatattttaattgtaaggaggagttatcgat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 130 End: 315 ................................................................................................................................. M K D L L N N G F Q P V S E T E M V M V E G G G G A S D M V I D G D N P G A Q R P T P P P P P S N G G G C G D V N W L E ................................................................... Protein_Len: 36 Strand: - Start: 275 End: 382 .................................................................................................................................................................................................................................................................................. H R L I H H H L N A Q S S I T V R I K P R R R V I R Y K L Q L S S N D M Protein_Len: 30 Strand: - Start: 211 End: 300 .................................................................................................................................................................................................................. I H Y Y I T I I R S S L S R C R W W R R R I A S S T T I Y M .................................................................................. Protein_Len: 45 Strand: - Start: 131 End: 265 .................................................................................................................................. S L N I S C H T E A Q T Q F P S P L P Q P P L L H K L Y P L L H H Y D Q L E F V S V E V M ..................................................................................................................... Protein_Len: 46 Strand: - Start: 1 End: 138 F N Y I K H L F C K I Y Q L F I T Y N F Y P R K L L S F I N L N L D L T R F L P T T K H F M .................................................................................................................................................................................................................................................... aaaattgtaaattttatgcaaaaaacacttgatatattgtaaaaatatggtatagttaaagtaaggtctttttaaaagactaaaaatatttaagtttaggtctagcgtcctaaacaaaggagttgttttatgaaagatttattgaacaatgggtttcagcctgtgtctgaaacggagatggtaatggttgaggggggaggaggtgcttcagatatggtaatagatggtgataatcctggagctcaaagaccgacacctccaccacctccttctaatggcggaggatgtggtgatgtaaattggcttgagatgagatagtaactctaattttaggcctcctccttacaattctatattttaattgtaaggaggagttatcgat 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================================================ aaaattgtaaattttatgcaaaaaacacttgatatattgtaaaaatatggtatagttaaagtaaggtctttttaaaagactaaaaatatttaagtttaggtctagcgtcctaaacaaaggagttgttttatgaaagatttattgaacaatgggtttcagcctgtgtctgaaacggagatggtaatggttgaggggggaggaggtgcttcagatatggtaatagatggtgataatcctggagctcaaagaccgacacctccaccacctccttctaatggcggaggatgtggtgatgtaaattggcttgagatgagatagtaactctaattttaggcctcctccttacaattctatattttaattgtaaggaggagttatcgat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 48 HP_score: -3.4 Tail_Score: -3.38046 Start: 250 End: 290 Full_Region: agccaatttacatca ccacatcctccgccatt agaagga ggtggtggaggtgtcgg tctttgagctccagg .........................................................................................................................................................................................................................................................ccacatcctccgccattagaaggaggtggtggaggtgtcgg............................................................................................ TransTerm Strand: + Conf: 57 HP_score: -6.7 Tail_Score: -2.66912 Start: 262 End: 290 Full_Region: AGACCGACACCTCCA CCACCTCCTTC TAATGGC GGAGGATGTGG TGATGTAAATTGGCT .....................................................................................................................................................................................................................................................................CCACCTCCTTCTAATGGCGGAGGATGTGG............................................................................................ Find igs database================================================ Query_seq: TDE0721:TDE0722|TDE0721:TDE0722:hypothetical protein:lipoprotein, putative:->->:758277..758658 382 aaaattgtaaattttatgcaaaaaacacttgatatattgtaaaaatatggtatagttaaagtaaggtctttttaaaagactaaaaatatttaagtttaggtctagcgtcctaaacaaaggagttgttttatgaaagatttattgaacaatgggtttcagcctgtgtctgaaacggagatggtaatggttgaggggggaggaggtgcttcagatatggtaatagatggtgataatcctggagctcaaagaccgacacctccaccacctccttctaatggcggaggatgtggtgatgtaaattggcttgagatgagatagtaactctaattttaggcctcctccttacaattctatattttaattgtaaggaggagttatcgat Intra-Species Hit: Count: 2 Min: 1 Max: 382 Len: 382 Subject: NC_002967_TDE0721_TDE0722|hypothetical protein:lipoprotein, putative|POSITIVE:POSITIVE|[758277,758658]|382 HSP 1 e-value: 0.0 bit: 757.0 Len: 382 Query Start:1 Query End:382 Subject Strand: POSITIVE Subject Start: 1 Subject End: 382 aaaattgtaaattttatgcaaaaaacacttgatatattgtaaaaatatggtatagttaaagtaaggtctttttaaaagactaaaaatatttaagtttaggtctagcgtcctaaacaaaggagttgttttatgaaagatttattgaacaatgggtttcagcctgtgtctgaaacggagatggtaatggttgaggggggaggaggtgcttcagatatggtaatagatggtgataatcctggagctcaaagaccgacacctccaccacctccttctaatggcggaggatgtggtgatgtaaattggcttgagatgagatagtaactctaattttaggcctcctccttacaattctatattttaattgtaaggaggagttatcgat aaaattgtaaattttatgcaaaaaacacttgatatattgtaaaaatatggtatagttaaagtaaggtctttttaaaagactaaaaatatttaagtttaggtctagcgtcctaaacaaaggagttgttttatgaaagatttattgaacaatgggtttcagcctgtgtctgaaacggagatggtaatggttgaggggggaggaggtgcttcagatatggtaatagatggtgataatcctggagctcaaagaccgacacctccaccacctccttctaatggcggaggatgtggtgatgtaaattggcttgagatgagatagtaactctaattttaggcctcctccttacaattctatattttaattgtaaggaggagttatcgat Subject: NC_002967_TDE0717_TDE0718|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[752441,753354]|914 HSP 1 e-value: 5.0E-61 bit: 236.0 Len: 175 Query Start:20 Query End:194 Subject Strand: POSITIVE Subject Start: 42 Subject End: 216 ...................aaaaaacacttgatatattgtaaaaatatggtatagttaaagtaaggtctttttaaaagactaaaaatatttaagtttaggtctagcgtcctaaacaaaggagttgttttatgaaagatttattgaacaatgggtttcagcctgtgtctgaaacggagatggtaatggttgaggg............................................................................................................................................................................................ ...................aaaaagcacttgacatattgcaaaagtatggtacacttaaagtaaggtcttttgaaaagcctaaaaatatttaagtttaggtgtaggagcctaaacaaaggagttgttttatgaaagatttattgaacaaagggtttcagcctgtgtctgaaacagagatggtaatggttgaggg............................................................................................................................................................................................ Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUUGUAAAUUUUAUGCAAAAAACACUUGAUAUAUUGUAAAAAUAUGGUAUAGUUAAAGUAAGGUCUUUUUAAAAGACUAAAAAUAUUUAAGUUUAGGUCUAGCGUCCUAAACAAAGGAGUUGUUUUAUGAAAGAUUUAUUGAACAAUGGGUUUCAGCCUGUGUCUGAAACGGAGAUGGUAAUGGUUGAGGGGGGAGGAGGUGCUUCAGAUAUGGUAAUAGAUGGUGAUAAUCCUGGAGCUCAAAGACCGACACCUCCACCACCUCCUUCUAAUGGCGGAGGAUGUGGUGAUGUAAAUUGGCUUGAGAUGAGAUAGUAACUCUAAUUUUAGGCCUCCUCCUUACAAUUCUAUAUUUUAAUUGUAAGGAGGAGUUAUCGAU ......(((((((((...((.(((((((((..(((((..((....))..)))))..........((((((.....))))))............(((((((.(....).)))))))....))).)))))).)).)))))))))..........((((((((....).))))))).....(((((((....((((..(..((..(.(((((((........................))))))).).....))..).))))((((((.((((((.......)))))).)))))).........((((((((((.(((.......))).)))))))))).(((((((((((((.........))))))))))))).))))))).. (-104.36) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGAUAACUCCUCCUUACAAUUAAAAUAUAGAAUUGUAAGGAGGAGGCCUAAAAUUAGAGUUACUAUCUCAUCUCAAGCCAAUUUACAUCACCACAUCCUCCGCCAUUAGAAGGAGGUGGUGGAGGUGUCGGUCUUUGAGCUCCAGGAUUAUCACCAUCUAUUACCAUAUCUGAAGCACCUCCUCCCCCCUCAACCAUUACCAUCUCCGUUUCAGACACAGGCUGAAACCCAUUGUUCAAUAAAUCUUUCAUAAAACAACUCCUUUGUUUAGGACGCUAGACCUAAACUUAAAUAUUUUUAGUCUUUUAAAAAGACCUUACUUUAACUAUACCAUAUUUUUACAAUAUAUCAAGUGUUUUUUGCAUAAAAUUUACAAUUUU ...((((.(((((((((((((((.........)))))))))))))))...........(((.......)))...(((.(((........(((((((.((((.(.......).)))).))))))).((((..((((((.(....).))))))..)))).............((((((((...............................))))))))....)))))).....(((((..((((........................(((((((.(....).))))))).............(((((.....)))))..................))))...))))).))))..(((..((((....))))..)))...... (-82.58) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 345 189 141 76 24 NC_002967:TDE1104|5end_tRNA_pseudouridine_synthase_B_1137786..1138016_NEGATIVE 345 196 151 69 31 NC_002967:TDE0204|5end_glutamyl-tRNA_synthetase_236968..237198_POSITIVE 338 208 161 60 1 NC_002967:TDE0667|5end_FeS_assembly_protein_SufB_704290..704520_POSITIVE 336 238 194 84 29 NC_002967:TDE0054|5end_flagellar_biosynthesis_protein_62384..62614_POSITIVE 335 200 151 213 154 NC_002967:TDE0043|5end_TPR_domain_protein_49688..49918_POSITIVE 334 198 151 78 38 NC_002967:TDE2170|5end_hypothetical_protein_2201749..2201979_NEGATIVE 332 209 161 139 76 NC_002967:TDE0759|5end_hypothetical_protein_799499..799729_NEGATIVE 328 292 261 230 202 NC_002967:TDE1095|5end_alanine_racemase_1129826..1130056_POSITIVE 323 211 173 87 30 NC_002967:TDE2141|5end_hypothetical_protein_2175768..2175998_NEGATIVE 320 208 161 150 101 NC_002967:TDE1847|5end_hypothetical_protein_1875664..1875894_POSITIVE 318 309 266 184 145 NC_002967:TDE2701|5end_hypothetical_protein_2745689..2745919_POSITIVE 314 200 158 149 110 NC_002967:TDE2619|5end_RNA_methyltransferase,_TrmA_family,_putative_2660280..2660510_POSITIVE 313 304 261 47 5 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 310 197 154 136 82 NC_002967:TDE0974|5end_hypothetical_protein_998694..998924_POSITIVE 306 380 332 219 169 NC_002967:TDE2721|5end_helicase_domain_protein_2779605..2779835_NEGATIVE 306 270 234 117 71 NC_002967:TDE1863|5end_Holliday_junction_DNA_helicase_RuvA_1888579..1888809_NEGATIVE 305 304 264 59 23 NC_002967:TDE1499|5end_adenylosuccinate_lyase,_putative_1545266..1545496_POSITIVE 304 206 166 229 194 NC_002967:TDE1962|5end_hypothetical_protein_1975204..1975434_NEGATIVE 302 305 269 193 147 NC_002967:TDE0023|5end_acetyltransferase,_GNAT_family_29419..29649_NEGATIVE 301 304 265 157 113 NC_002967:TDE1005|5end_hypothetical_protein_1030206..1030436_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 409 278 234 140 100 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 345 189 141 61 9 NC_002967:TDE1105|3end_ribosome-binding_factor_A_1137801..1137951_NEGATIVE 345 196 151 79 41 NC_002967:TDE0203|3end_hypothetical_protein_237058..237208_POSITIVE 338 208 161 63 4 NC_002967:TDE0666|3end_FeS_assembly_ATPase_SufC_704373..704523_POSITIVE 336 238 194 87 32 NC_002967:TDE0053|3end_flagellar_biosynthetic_protein_FliR_62467..62617_POSITIVE 334 198 151 50 10 NC_002967:TDE2171|3end_hypothetical_protein_2201777..2201927_NEGATIVE 328 292 261 46 18 NC_002967:TDE1094|3end_hypothetical_protein_1129722..1129872_POSITIVE 325 199 151 102 51 NC_002967:TDE1982|3end_hypothetical_protein_1992511..1992661_NEGATIVE 317 200 153 50 5 NC_002967:TDE2420|3end_DNA-directed_RNA_polymerase_beta'_subunit_2444960..2445110_NEGATIVE 317 380 332 74 28 NC_002967:TDE1669|3end_hemolysin_1723878..1724028_POSITIVE 314 200 158 136 97 NC_002967:TDE2618|3end_PHP_domain_protein_2660347..2660497_POSITIVE 307 200 151 79 29 NC_002967:TDE1008|3end_flagellar_protein,_putative_1032806..1032956_POSITIVE 306 270 234 124 78 NC_002967:TDE1864|3end_crossover_junction_endodeoxyribonuclease_RuvC_1888572..1888722_NEGATIVE 306 237 194 103 54 NC_002967:TDE0189|3end_hypothetical_protein_225672..225822_NEGATIVE 293 200 153 81 31 NC_002967:TDE1839|3end_hypothetical_protein_1870391..1870541_NEGATIVE 290 230 186 55 5 NC_002967:TDE0474|3end_hypothetical_protein_531134..531284_POSITIVE 284 189 151 81 40 NC_002967:TDE1867|3end_hypothetical_protein_1892351..1892501_NEGATIVE 283 214 173 120 80 NC_002967:TDE2025|3end_hypothetical_protein_2051075..2051225_NEGATIVE 281 208 163 57 6 NC_002967:TDE1176|3end_oxygen-independent_coproporphyrinogen_III_oxidase,_putative_1205282..1205432_NEGATIVE 277 273 234 139 100 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE