Origin IGS: attaggggaagtacagccggcggagcttcaaggcgtacagccggcaaagcttcgaggcgtacagccagcggagcttcaaggctaaacccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcccctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatataatggtataaaggtttttatgaaactaagaaagaaacagccaaacttatgaagctaaaaaactttaatatagcccagctgcccattatctacggcttttttttgcggcgttctgcttatgatgatgataaacatgaaacagtgcgacagcagcaaaaggcctctcatcaaaaaagagcagttttcaaacaattatccatcat .........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 atgatggataattgtttgaaaactgctcttttttgatgagaggccttttgctgctgtcgcactgtttcatgtttatcatcatcataagcagaacgccgcaaaaaaaagccgtagataatgggcagctgggctatattaaagttttttagcttcataagtttggctgtttctttcttagtttcataaaaacctttataccattatatttgtaggaattatttgaaaaaaatagtaaattagaaaaatatttttataaattggattaaactaaaaatttgataacaatgcgggttcttaggggcgcagcccataagcggaattttggagaaaggaggggttataggggagggtaacaaccaacgcagtttcaaggtcaaacacctttcttccgaaaaaggggtttagccttgaagctccgctggctgtacgcctcgaagctttgccggctgtacgccttgaagctccgccggctgtacttcccctaat Mask Tandem Repeat Region ================================================ attaggggaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntaaacccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcccctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatataatggtataaaggtttttatgaaactaagaaagaaacagccaaacttatgaagctaaaaaactttaatatagcccagctgcccattatctacggcttttttttgcggcgttctgcttatgatgatgataaacatgaaacagtgcgacagcagcaaaaggcctctcatcaaaaaagagcagttttcaaacaattatccatcat Find is-nt database================================================ Query_seq: TDE2312:TDE2313|TDE2312:TDE2313:hypothetical protein:hypothetical protein:-><-:2349110..2349595 486 attaggggaagtacagccggcggagcttcaaggcgtacagccggcaaagcttcgaggcgtacagccagcggagcttcaaggctaaacccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcccctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatataatggtataaaggtttttatgaaactaagaaagaaacagccaaacttatgaagctaaaaaactttaatatagcccagctgcccattatctacggcttttttttgcggcgttctgcttatgatgatgataaacatgaaacagtgcgacagcagcaaaaggcctctcatcaaaaaagagcagttttcaaacaattatccatcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2312:TDE2313|TDE2312:TDE2313:hypothetical protein:hypothetical protein:-><-:2349110..2349595 486 attaggggaagtacagccggcggagcttcaaggcgtacagccggcaaagcttcgaggcgtacagccagcggagcttcaaggctaaacccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcccctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatataatggtataaaggtttttatgaaactaagaaagaaacagccaaacttatgaagctaaaaaactttaatatagcccagctgcccattatctacggcttttttttgcggcgttctgcttatgatgatgataaacatgaaacagtgcgacagcagcaaaaggcctctcatcaaaaaagagcagttttcaaacaattatccatcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2312:TDE2313|TDE2312:TDE2313:hypothetical protein:hypothetical protein:-><-:2349110..2349595 486 attaggggaagtacagccggcggagcttcaaggcgtacagccggcaaagcttcgaggcgtacagccagcggagcttcaaggctaaacccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcccctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatataatggtataaaggtttttatgaaactaagaaagaaacagccaaacttatgaagctaaaaaactttaatatagcccagctgcccattatctacggcttttttttgcggcgttctgcttatgatgatgataaacatgaaacagtgcgacagcagcaaaaggcctctcatcaaaaaagagcagttttcaaacaattatccatcat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attaggggaagtacagccggcggagcttcaaggcgtacagccggcaaagcttcgaggcgtacagccagcggagcttcaaggctaaacccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcccctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatataatggtataaaggtttttatgaaactaagaaagaaacagccaaacttatgaagctaaaaaactttaatatagcccagctgcccattatctacggcttttttttgcggcgttctgcttatgatgatgataaacatgaaacagtgcgacagcagcaaaaggcctctcatcaaaaaagagcagttttcaaacaattatccatcat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 1 End: 189 M R G S T A G G A S R R T A G K A S R R T A S G A S R L N P F F G R K V F D L E T A L V V T L P Y N P S F L Q N S A Y G ......................................................................................................................................................................................................................................................................................................... Protein_Len: 46 Strand: + Start: 110 End: 247 ............................................................................................................. M T L K L R W L L P S P I T P P F S K I P L M G C A P K N P H C Y Q I F S L I Q F I K I F F ............................................................................................................................................................................................................................................... Protein_Len: 51 Strand: + Start: 332 End: 484 ........................................................................................................................................................................................................................................................................................................................................... M K L K N F N I A Q L P I I Y G F F L R R S A Y D D D K H E T V R Q Q Q K A S H Q K R A V F K Q L S I .. Protein_Len: 30 Strand: + Start: 396 End: 485 ........................................................................................................................................................................................................................................................................................................................................................................................................... M L M M M I N M K Q C D S S K R P L I K K E Q F S N N Y P S . Protein_Len: 31 Strand: - Start: 372 End: 464 ................................................................................................................................................................................................................................................................................................................................................................................... R R S K K A A N Q K H H H Y V H F L A V A A F P R E D F F L M ...................... Protein_Len: 45 Strand: - Start: 341 End: 475 .................................................................................................................................................................................................................................................................................................................................................... F V K I Y G L Q G N D V A K K Q P T R S I I I I F M F C H S L L L L G R M L F S C N E F M ........... Protein_Len: 31 Strand: - Start: 85 End: 177 .................................................................................... V G K E S S L H K V K F S R Q N N G E G I V G G K E L I G S M ..................................................................................................................................................................................................................................................................................................................... attaggggaagtacagccggcggagcttcaaggcgtacagccggcaaagcttcgaggcgtacagccagcggagcttcaaggctaaacccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcccctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatataatggtataaaggtttttatgaaactaagaaagaaacagccaaacttatgaagctaaaaaactttaatatagcccagctgcccattatctacggcttttttttgcggcgttctgcttatgatgatgataaacatgaaacagtgcgacagcagcaaaaggcctctcatcaaaaaagagcagttttcaaacaattatccatcat 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================================================ attaggggaagtacagccggcggagcttcaaggcgtacagccggcaaagcttcgaggcgtacagccagcggagcttcaaggctaaacccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcccctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatataatggtataaaggtttttatgaaactaagaaagaaacagccaaacttatgaagctaaaaaactttaatatagcccagctgcccattatctacggcttttttttgcggcgttctgcttatgatgatgataaacatgaaacagtgcgacagcagcaaaaggcctctcatcaaaaaagagcagttttcaaacaattatccatcat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 95 HP_score: -12.9 Tail_Score: -3.54158 Start: 69 End: 126 Full_Region: GAGGCGTACAGCCAG CGGAGCTTCAAGGCTAAACCCCTTTTT CGGA AGAAAGGTGTTTGACCTTGAAACTGCG TTGGTTGTTACCCTC ....................................................................CGGAGCTTCAAGGCTAAACCCCTTTTTCGGAAGAAAGGTGTTTGACCTTGAAACTGCG........................................................................................................................................................................................................................................................................................................................................................................ Find igs database================================================ Query_seq: TDE2312:TDE2313|TDE2312:TDE2313:hypothetical protein:hypothetical protein:-><-:2349110..2349595 486 attaggggaagtacagccggcggagcttcaaggcgtacagccggcaaagcttcgaggcgtacagccagcggagcttcaaggctaaacccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcccctaagaacccgcattgttatcaaatttttagtttaatccaatttataaaaatatttttctaatttactatttttttcaaataattcctacaaatataatggtataaaggtttttatgaaactaagaaagaaacagccaaacttatgaagctaaaaaactttaatatagcccagctgcccattatctacggcttttttttgcggcgttctgcttatgatgatgataaacatgaaacagtgcgacagcagcaaaaggcctctcatcaaaaaagagcagttttcaaacaattatccatcat Intra-Species Hit: Count: 2 Min: 1 Max: 486 Len: 486 Subject: NC_002967_TDE2312_TDE2313|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[2349110,2349595]|486 HSP 1 e-value: 1.0E-114 bit: 414.0 Len: 209 Query Start:1 Query End:209 Subject Strand: POSITIVE Subject Start: 1 Subject End: 209 attaggggaagtacagccggcggagcttcaaggcgtacagccggcaaagcttcgaggcgtacagccagcggagcttcaaggctaaacccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcccctaagaacccgcattgttatc..................................................................................................................................................................................................................................................................................... attaggggaagtacagccggcggagcttcaaggcgtacagccggcaaagcttcgaggcgtacagccagcggagcttcaaggctaaacccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcccctaagaacccgcattgttatc..................................................................................................................................................................................................................................................................................... HSP 2 e-value: 1.0E-102 bit: 375.0 Len: 213 Query Start:274 Query End:486 Subject Strand: POSITIVE Subject Start: 274 Subject End: 486 .................................................................................................................................................................................................................................................................................cctacaaatataatggtataaaggtttttatgaaactaagaaagaaacagccaaacttatgaagctaaaaaactttaatatagcccagctgcccattatctacggcnnnnnnnngcggcgttctgcttatgatgatgataaacatgaaacagtgcgacagcagcaaaaggcctctcatcaaaaaagagcagttttcaaacaattatccatcat .................................................................................................................................................................................................................................................................................cctacaaatataatggtataaaggtttttatgaaactaagaaagaaacagccaaacttatgaagctaaaaaactttaatatagcccagctgcccattatctacggcttttttttgcggcgttctgcttatgatgatgataaacatgaaacagtgcgacagcagcaaaaggcctctcatcaaaaaagagcagttttcaaacaattatccatcat Subject: NC_002967_TDE1982_TDE1983|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1993075,1993465]|391 HSP 1 e-value: 1.0E-62 bit: 242.0 Len: 138 Query Start:72 Query End:209 Subject Strand: POSITIVE Subject Start: 1 Subject End: 138 .......................................................................agcttcaaggctaaacccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcccctaagaacccgcattgttatc..................................................................................................................................................................................................................................................................................... .......................................................................agcttcgaggctaagaccctttttcggaagaaaggtgtttgaccttgaaactgcgttggttgttaccctcccctataacccctcctttctccaaaattccgcttatgggctgcgcctctaagaacccgcattgttatc..................................................................................................................................................................................................................................................................................... HSP 2 e-value: 4.0E-28 bit: 127.0 Len: 84 Query Start:274 Query End:357 Subject Strand: POSITIVE Subject Start: 203 Subject End: 286 .................................................................................................................................................................................................................................................................................cctacaaatataatggtataaaggtttttatgaaactaagaaagaaacagccaaacttatgaagctaaaaaactttaatatagc................................................................................................................................. .................................................................................................................................................................................................................................................................................cctacaaatattatggtataaaggtttttatgaaactaagaaataaacagctaaacttatgaagctaaaaaacgttgatatagc................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUAGGGGAAGUACAGCCGGCGGAGCUUCAAGGCGUACAGCCGGCAAAGCUUCGAGGCGUACAGCCAGCGGAGCUUCAAGGCUAAACCCCUUUUUCGGAAGAAAGGUGUUUGACCUUGAAACUGCGUUGGUUGUUACCCUCCCCUAUAACCCCUCCUUUCUCCAAAAUUCCGCUUAUGGGCUGCGCCCCUAAGAACCCGCAUUGUUAUCAAAUUUUUAGUUUAAUCCAAUUUAUAAAAAUAUUUUUCUAAUUUACUAUUUUUUUCAAAUAAUUCCUACAAAUAUAAUGGUAUAAAGGUUUUUAUGAAACUAAGAAAGAAACAGCCAAACUUAUGAAGCUAAAAAACUUUAAUAUAGCCCAGCUGCCCAUUAUCUACGGCUUUUUUUUGCGGCGUUCUGCUUAUGAUGAUGAUAAACAUGAAACAGUGCGACAGCAGCAAAAGGCCUCUCAUCAAAAAAGAGCAGUUUUCAAACAAUUAUCCAUCAU ..((((((.....(((((((((((((((...(((.....)))....))))...((((.((((((((((((.((.(((((((.(((((.((((..((....)))))).))))).))))))).)).))))))))).)))))))...........................))))))....)))))..))))))((((((((((...........(((((((((.........((((((((((.(((........(((((((.........................))))))).))).))))))))))))))))))).((((.((((.......(((((........)))))...((((...))))............)))).)))).))))).)))))....(((((((((((......(((((..(((....))).......((.(((.........))))).)))))......))))).)))))) (-131.81) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGAUGGAUAAUUGUUUGAAAACUGCUCUUUUUUGAUGAGAGGCCUUUUGCUGCUGUCGCACUGUUUCAUGUUUAUCAUCAUCAUAAGCAGAACGCCGCAAAAAAAAGCCGUAGAUAAUGGGCAGCUGGGCUAUAUUAAAGUUUUUUAGCUUCAUAAGUUUGGCUGUUUCUUUCUUAGUUUCAUAAAAACCUUUAUACCAUUAUAUUUGUAGGAAUUAUUUGAAAAAAAUAGUAAAUUAGAAAAAUAUUUUUAUAAAUUGGAUUAAACUAAAAAUUUGAUAACAAUGCGGGUUCUUAGGGGCGCAGCCCAUAAGCGGAAUUUUGGAGAAAGGAGGGGUUAUAGGGGAGGGUAACAACCAACGCAGUUUCAAGGUCAAACACCUUUCUUCCGAAAAAGGGGUUUAGCCUUGAAGCUCCGCUGGCUGUACGCCUCGAAGCUUUGCCGGCUGUACGCCUUGAAGCUCCGCCGGCUGUACUUCCCCUAAU ....................((((.(((((((((..(((((..((.((((..((((.(((.(((.....(((((((.......)))))))((((.(((((.....((((...(((.((..((((((..((((.(((..(((((....))))).)))))))..))))))..)))))..))))........((((((((....(((.(((.(((..(((((((.....)))))))...))).))).)))....))))))..))........................))))))))).)))..)))))))...)))).))..))))).))))))))).)))).(((((((((...(((.(((.((.((((((((((..((((.(((((........))))).))))..)))))))))).)).))).)))..(((.((.((((((...(((.....)))..)))))).))..)))....))))))))).. (-140.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 996 200 151 220 171 NC_002967:TDE1982|5end_hypothetical_protein_1992984..1993214_NEGATIVE 974 60 11 194 145 NC_002967:TDE2309|5end_sigma-54_dependent_transcriptional_regulator,_putative_2348099..2348329_NEGATIVE 637 188 141 227 180 NC_002967:TDE2097|5end_hypothetical_protein_2124741..2124971_NEGATIVE 601 190 141 218 171 NC_002967:TDE2735|5end_surface_antigen,_putative_2790154..2790384_POSITIVE 512 198 151 215 166 NC_002967:TDE2142|5end_methyl-accepting_chemotaxis_protein_2175769..2175999_POSITIVE 499 180 137 228 185 NC_002967:TDE2024|5end_hypothetical_protein_2051021..2051251_NEGATIVE 482 81 41 139 102 NC_002967:TDE2260|5end_hypothetical_protein_2297338..2297568_POSITIVE 471 90 41 231 170 NC_002967:TDE2311|5end_hypothetical_protein_2348238..2348468_POSITIVE 463 159 114 80 37 NC_002967:TDE1892|5end_hypothetical_protein_1912065..1912295_POSITIVE 447 198 153 192 135 NC_002967:TDE0619|5end_methyl-accepting_chemotaxis_protein_650318..650548_POSITIVE 438 190 142 194 149 NC_002967:TDE0741|5end_hypothetical_protein_778158..778388_NEGATIVE 431 59 15 213 156 NC_002967:TDE1846|5end_hypothetical_protein_1875426..1875656_NEGATIVE 425 88 41 103 45 NC_002967:TDE0946|5end_hypothetical_protein_968212..968442_POSITIVE 421 162 124 197 154 NC_002967:TDE2259|5end_hypothetical_protein_2297237..2297467_NEGATIVE 416 88 41 103 45 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 414 66 21 207 145 NC_002967:TDE2251|5end_uracil_permease_2289440..2289670_POSITIVE 412 159 114 96 49 NC_002967:TDE2265|5end_hypothetical_protein_2302165..2302395_POSITIVE 412 159 114 75 28 NC_002967:TDE0402|5end_hypothetical_protein_454352..454582_NEGATIVE 412 159 114 197 150 NC_002967:TDE0401|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_454230..454460_NEGATIVE 403 199 155 210 164 NC_002967:TDE2419|5end_hypothetical_protein_2444769..2444999_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 895 50 1 139 90 NC_002967:TDE2136|3end_hypothetical_protein_2165390..2165540_NEGATIVE 681 110 61 74 28 NC_002967:TDE1893|3end_GTP-binding_protein_LepA_1912212..1912362_NEGATIVE 565 80 32 74 28 NC_002967:TDE1982|3end_hypothetical_protein_1992511..1992661_NEGATIVE 499 157 113 86 43 NC_002967:TDE1564|3end_hypothetical_protein_1616704..1616854_POSITIVE 470 69 21 150 98 NC_002967:TDE2310|3end_hypothetical_protein_2348256..2348406_POSITIVE 450 219 171 48 1 NC_002967:TDE2098|3end_hypothetical_protein_2124951..2125101_NEGATIVE 447 90 41 131 73 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 443 66 21 129 84 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 432 60 11 78 29 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 430 100 51 142 99 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 425 88 41 131 73 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 421 90 41 107 47 NC_002967:TDE2621|3end_hypothetical_protein_2662197..2662347_POSITIVE 416 88 41 131 73 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 414 66 21 96 34 NC_002967:TDE2250|3end_hypothetical_protein_2289409..2289559_POSITIVE 410 220 171 91 29 NC_002967:TDE1981|3end_hypothetical_protein_1992437..1992587_POSITIVE 394 190 141 76 31 NC_002967:TDE1059|3end_hypothetical_protein_1086498..1086648_NEGATIVE 388 420 373 71 25 NC_002967:TDE0134|3end_oxidoreductase,_FAD-dependent_155010..155160_POSITIVE 387 58 14 135 92 NC_002967:TDE0616|3end_hypothetical_protein_650079..650229_POSITIVE 378 57 11 85 32 NC_002967:TDE2630|3end_peptide_ABC_transporter,_permease_protein,_putative_2671912..2672062_POSITIVE 378 90 47 86 39 NC_002967:TDE2135|3end_hypothetical_protein_2165418..2165568_POSITIVE