Origin IGS: gatataagaataataacacgaaaaactcaagttttcaagtagccgatgaaaaatgtacattcagagtacatttttcatcttagagtttgtatcaattctgcctgtgacagaattgaacttcgagttttgcctgacggcaaaacatcgcggaagtaaggctcaaacatcgacaggaggtcgattactgtcaactattgcgatatttttcaaagcttgtctttgaaaaactaggtgtcaaatgcgtacaaggacgtacgcatttgacataaccaccgccgtccatggcagctggggaatgtacatccgtttccgattttcaaacatgcacaa .........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 ttgtgcatgtttgaaaatcggaaacggatgtacattccccagctgccatggacggcggtggttatgtcaaatgcgtacgtccttgtacgcatttgacacctagtttttcaaagacaagctttgaaaaatatcgcaatagttgacagtaatcgacctcctgtcgatgtttgagccttacttccgcgatgttttgccgtcaggcaaaactcgaagttcaattctgtcacaggcagaattgatacaaactctaagatgaaaaatgtactctgaatgtacatttttcatcggctacttgaaaacttgagtttttcgtgttattattcttatatc Mask Tandem Repeat Region ================================================ gatataagaataataacacgaaaaactcaagttttcaagtagccgatgaaaaatgtacattcagagtacatttttcatcttagagtttgtatcaattctgcctgtgacagaattgaacttcgagttttgcctgacggcaaaacatcgcggaagtaaggctcaaacatcgacaggaggtcgattactgtcaactattgcgatatttttcaaagcttgtctttgaaaaactaggtgtcaaatgcgtacaaggacgtacgcatttgacataaccaccgccgtccatggcagctggggaatgtacatccgtttccgattttcaaacatgcacaa Find is-nt database================================================ Query_seq: TDE2492:TDE2493|TDE2492:TDE2493:hypothetical protein:hypothetical protein:<-<-:2516505..2516834 330 gatataagaataataacacgaaaaactcaagttttcaagtagccgatgaaaaatgtacattcagagtacatttttcatcttagagtttgtatcaattctgcctgtgacagaattgaacttcgagttttgcctgacggcaaaacatcgcggaagtaaggctcaaacatcgacaggaggtcgattactgtcaactattgcgatatttttcaaagcttgtctttgaaaaactaggtgtcaaatgcgtacaaggacgtacgcatttgacataaccaccgccgtccatggcagctggggaatgtacatccgtttccgattttcaaacatgcacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2492:TDE2493|TDE2492:TDE2493:hypothetical protein:hypothetical protein:<-<-:2516505..2516834 330 gatataagaataataacacgaaaaactcaagttttcaagtagccgatgaaaaatgtacattcagagtacatttttcatcttagagtttgtatcaattctgcctgtgacagaattgaacttcgagttttgcctgacggcaaaacatcgcggaagtaaggctcaaacatcgacaggaggtcgattactgtcaactattgcgatatttttcaaagcttgtctttgaaaaactaggtgtcaaatgcgtacaaggacgtacgcatttgacataaccaccgccgtccatggcagctggggaatgtacatccgtttccgattttcaaacatgcacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2492:TDE2493|TDE2492:TDE2493:hypothetical protein:hypothetical protein:<-<-:2516505..2516834 330 gatataagaataataacacgaaaaactcaagttttcaagtagccgatgaaaaatgtacattcagagtacatttttcatcttagagtttgtatcaattctgcctgtgacagaattgaacttcgagttttgcctgacggcaaaacatcgcggaagtaaggctcaaacatcgacaggaggtcgattactgtcaactattgcgatatttttcaaagcttgtctttgaaaaactaggtgtcaaatgcgtacaaggacgtacgcatttgacataaccaccgccgtccatggcagctggggaatgtacatccgtttccgattttcaaacatgcacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatataagaataataacacgaaaaactcaagttttcaagtagccgatgaaaaatgtacattcagagtacatttttcatcttagagtttgtatcaattctgcctgtgacagaattgaacttcgagttttgcctgacggcaaaacatcgcggaagtaaggctcaaacatcgacaggaggtcgattactgtcaactattgcgatatttttcaaagcttgtctttgaaaaactaggtgtcaaatgcgtacaaggacgtacgcatttgacataaccaccgccgtccatggcagctggggaatgtacatccgtttccgattttcaaacatgcacaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 46 End: 153 ............................................. M K N V H S E Y I F H L R V C I N S A C D R I E L R V L P D G K T S R K ................................................................................................................................................................................. Protein_Len: 56 Strand: + Start: 53 End: 220 .................................................... M Y I Q S T F F I L E F V S I L P V T E L N F E F C L T A K H R G S K A Q T S T G G R L L S T I A I F F K A C L .............................................................................................................. Protein_Len: 41 Strand: + Start: 144 End: 266 ............................................................................................................................................... M A E V R L K H R Q E V D Y C Q L L R Y F S K L V F E K L G V K C V Q G R T H L T ................................................................ Protein_Len: 30 Strand: + Start: 239 End: 328 .............................................................................................................................................................................................................................................. M R T R T Y A F D I T T A V H G S W G M Y I R F R F S N M H .. Protein_Len: 31 Strand: - Start: 238 End: 330 ............................................................................................................................................................................................................................................. I R V L V Y A N S M V V A T W P L Q P I Y M R K R N E F M C M Protein_Len: 30 Strand: - Start: 231 End: 320 ...................................................................................................................................................................................................................................... T D F A Y L S T R M Q C L W R R G H C S P F T C G N G I K M .......... Protein_Len: 31 Strand: - Start: 191 End: 283 .............................................................................................................................................................................................. S N R Y K E F S T K S F S P T L H T C P R V C K V Y G G G D M ............................................... Protein_Len: 38 Strand: - Start: 78 End: 191 ............................................................................. R L T Q I L E A Q S L I S S R T K G S P L V D R F Y P E F M S L L D I V T M ........................................................................................................................................... gatataagaataataacacgaaaaactcaagttttcaagtagccgatgaaaaatgtacattcagagtacatttttcatcttagagtttgtatcaattctgcctgtgacagaattgaacttcgagttttgcctgacggcaaaacatcgcggaagtaaggctcaaacatcgacaggaggtcgattactgtcaactattgcgatatttttcaaagcttgtctttgaaaaactaggtgtcaaatgcgtacaaggacgtacgcatttgacataaccaccgccgtccatggcagctggggaatgtacatccgtttccgattttcaaacatgcacaa 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: 90 Start: 10 End: 39 .........CTTGAAAACTTGAGTTTTTCGTGTTATTAT................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatataagaataataacacgaaaaactcaagttttcaagtagccgatgaaaaatgtacattcagagtacatttttcatcttagagtttgtatcaattctgcctgtgacagaattgaacttcgagttttgcctgacggcaaaacatcgcggaagtaaggctcaaacatcgacaggaggtcgattactgtcaactattgcgatatttttcaaagcttgtctttgaaaaactaggtgtcaaatgcgtacaaggacgtacgcatttgacataaccaccgccgtccatggcagctggggaatgtacatccgtttccgattttcaaacatgcacaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 41 HP_score: -2.7 Tail_Score: -2.72379 Start: 42 End: 82 Full_Region: aattgatacaaactc taagatgaaaaatgtac tctgaat gtacatttttcatcggc tacttgaaaacttga .........................................taagatgaaaaatgtactctgaatgtacatttttcatcggc........................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 75 HP_score: -10.0 Tail_Score: -3.14528 Start: 47 End: 77 Full_Region: TTTTCAAGTAGCCGA TGAAAAATGTAC ATTCAGA GTACATTTTTCA TCTTAGAGTTTGTAT ..............................................TGAAAAATGTACATTCAGAGTACATTTTTCA............................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 52 HP_score: -3.1 Tail_Score: -3.62478 Start: 165 End: 183 Full_Region: gcaatagttgacagt aatcgac ctcct gtcgatg tttgagccttacttc ....................................................................................................................................................................aatcgacctcctgtcgatg................................................................................................................................................... TransTerm Strand: - Conf: 77 HP_score: -6.2 Tail_Score: -4.56597 Start: 228 End: 269 Full_Region: catggacggcggtgg ttatgtcaaatgcgtacg tcct tgtacgcatttgacacctag tttttcaaagacaag ...................................................................................................................................................................................................................................ttatgtcaaatgcgtacgtccttgtacgcatttgacacctag............................................................. TransTerm Strand: - Conf: 79 HP_score: -10.7 Tail_Score: -3.23708 Start: 231 End: 268 Full_Region: atggacggcggtggt tatgtcaaatgcgtacg tcct tgtacgcatttgacacc tagtttttcaaagac ......................................................................................................................................................................................................................................tatgtcaaatgcgtacgtccttgtacgcatttgacacc.............................................................. TransTerm Strand: - Conf: 93 HP_score: -14.2 Tail_Score: -2.53903 Start: 232 End: 267 Full_Region: tggacggcggtggtt atgtcaaatgcgtacg tcct tgtacgcatttgacac ctagtttttcaaaga .......................................................................................................................................................................................................................................atgtcaaatgcgtacgtccttgtacgcatttgacac............................................................... TransTerm Strand: - Conf: 72 HP_score: -8.6 Tail_Score: -3.56836 Start: 240 End: 259 Full_Region: ggtggttatgtcaaa tgcgtacg tcct tgtacgca tttgacacctagttt ...............................................................................................................................................................................................................................................tgcgtacgtccttgtacgca....................................................................... Find igs database================================================ Query_seq: TDE2492:TDE2493|TDE2492:TDE2493:hypothetical protein:hypothetical protein:<-<-:2516505..2516834 330 gatataagaataataacacgaaaaactcaagttttcaagtagccgatgaaaaatgtacattcagagtacatttttcatcttagagtttgtatcaattctgcctgtgacagaattgaacttcgagttttgcctgacggcaaaacatcgcggaagtaaggctcaaacatcgacaggaggtcgattactgtcaactattgcgatatttttcaaagcttgtctttgaaaaactaggtgtcaaatgcgtacaaggacgtacgcatttgacataaccaccgccgtccatggcagctggggaatgtacatccgtttccgattttcaaacatgcacaa Intra-Species Hit: Count: 1 Min: 1 Max: 330 Len: 330 Subject: NC_002967_TDE2492_TDE2493|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[2516505,2516834]|330 HSP 1 e-value: 0.0 bit: 654.0 Len: 330 Query Start:1 Query End:330 Subject Strand: POSITIVE Subject Start: 1 Subject End: 330 gatataagaataataacacgaaaaactcaagttttcaagtagccgatgaaaaatgtacattcagagtacatttttcatcttagagtttgtatcaattctgcctgtgacagaattgaacttcgagttttgcctgacggcaaaacatcgcggaagtaaggctcaaacatcgacaggaggtcgattactgtcaactattgcgatatttttcaaagcttgtctttgaaaaactaggtgtcaaatgcgtacaaggacgtacgcatttgacataaccaccgccgtccatggcagctggggaatgtacatccgtttccgattttcaaacatgcacaa gatataagaataataacacgaaaaactcaagttttcaagtagccgatgaaaaatgtacattcagagtacatttttcatcttagagtttgtatcaattctgcctgtgacagaattgaacttcgagttttgcctgacggcaaaacatcgcggaagtaaggctcaaacatcgacaggaggtcgattactgtcaactattgcgatatttttcaaagcttgtctttgaaaaactaggtgtcaaatgcgtacaaggacgtacgcatttgacataaccaccgccgtccatggcagctggggaatgtacatccgtttccgattttcaaacatgcacaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAUAAGAAUAAUAACACGAAAAACUCAAGUUUUCAAGUAGCCGAUGAAAAAUGUACAUUCAGAGUACAUUUUUCAUCUUAGAGUUUGUAUCAAUUCUGCCUGUGACAGAAUUGAACUUCGAGUUUUGCCUGACGGCAAAACAUCGCGGAAGUAAGGCUCAAACAUCGACAGGAGGUCGAUUACUGUCAACUAUUGCGAUAUUUUUCAAAGCUUGUCUUUGAAAAACUAGGUGUCAAAUGCGUACAAGGACGUACGCAUUUGACAUAACCACCGCCGUCCAUGGCAGCUGGGGAAUGUACAUCCGUUUCCGAUUUUCAAACAUGCACAA ((((((((.........((..(((((....)))))...))....((((((((((((((.......))))))))))))))......)))))))).........((((.((...(((((..(((.((((((((....))))))))...(((((.(((...(((....((((((.....))))))..((((((...((.(((...((((((((((.....))))))))))....(((((((((((((((......)))))))))))))))......))).))...))))))...)))....))).)))))...)))..)))))...)))))). (-109.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGUGCAUGUUUGAAAAUCGGAAACGGAUGUACAUUCCCCAGCUGCCAUGGACGGCGGUGGUUAUGUCAAAUGCGUACGUCCUUGUACGCAUUUGACACCUAGUUUUUCAAAGACAAGCUUUGAAAAAUAUCGCAAUAGUUGACAGUAAUCGACCUCCUGUCGAUGUUUGAGCCUUACUUCCGCGAUGUUUUGCCGUCAGGCAAAACUCGAAGUUCAAUUCUGUCACAGGCAGAAUUGAUACAAACUCUAAGAUGAAAAAUGUACUCUGAAUGUACAUUUUUCAUCGGCUACUUGAAAACUUGAGUUUUUCGUGUUAUUAUUCUUAUAUC .(((((((.........(((....))))))))))....(((.(((((......))))))))...(((((((((((((((....)))))))))))))))....(((((((((((.....)))))))))))...(.((((((.((((...((((((.....)))))).....((((.........(((.((((((((....)))))))))))..((((((((((((.....)))))))))).)).........((((((((((((((.......))))))))))))))))))....((((((....))))))..)))))))))))....... (-115.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 921 140 91 231 182 NC_002967:TDE2492|5end_hypothetical_protein_2516414..2516644_NEGATIVE 576 88 41 173 126 NC_002967:TDE1095|5end_alanine_racemase_1129826..1130056_POSITIVE 565 88 42 215 170 NC_002967:TDE2339|5end_leucyl-tRNA_synthetase_2374845..2375075_POSITIVE 458 88 43 199 155 NC_002967:TDE2549|5end_methyl-accepting_chemotaxis_protein_2573285..2573515_POSITIVE 453 306 268 40 4 NC_002967:TDE2238|5end_hypothetical_protein_2276337..2276567_POSITIVE 451 88 44 119 75 NC_002967:TDE2133|5end_cobalt_transport_protein,_putative_2164323..2164553_NEGATIVE 441 159 113 230 177 NC_002967:TDE2489|5end_peptide_chain_release_factor_1_2512476..2512706_NEGATIVE 429 88 42 101 56 NC_002967:TDE2100|5end_hypothetical_protein_2125370..2125600_POSITIVE 402 319 271 185 116 NC_002967:TDE1808|5end_hypothetical_protein_1845049..1845279_NEGATIVE 371 88 44 231 188 NC_002967:TDE1933|5end_hypothetical_protein_1952611..1952841_NEGATIVE 360 79 31 185 125 NC_002967:TDE2338|5end_hypothetical_protein_2374719..2374949_NEGATIVE 354 308 266 189 140 NC_002967:TDE0594|5end_cysteine_protease_domain,_YopT-type_634805..635035_NEGATIVE 349 313 272 65 12 NC_002967:TDE0360|5end_ABC_transporter,_ATP-binding/permease_protein_405844..406074_NEGATIVE 339 329 283 173 120 NC_002967:TDE0781|5end_30S_ribosomal_protein_S8_812561..812791_POSITIVE 334 318 274 87 43 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 331 160 121 167 123 NC_002967:TDE2224|5end_hypothetical_protein_2264743..2264973_POSITIVE 331 160 121 66 22 NC_002967:TDE2223|5end_hypothetical_protein_2264642..2264872_POSITIVE 328 137 92 160 118 NC_002967:TDE1837|5end_hypothetical_protein_1869946..1870176_NEGATIVE 326 320 272 230 181 NC_002967:TDE0545|5end_hypothetical_protein_584774..585004_POSITIVE 324 150 107 56 12 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 533 305 268 53 17 NC_002967:TDE1094|3end_hypothetical_protein_1129722..1129872_POSITIVE 494 88 41 99 53 NC_002967:TDE2238|3end_hypothetical_protein_2276545..2276695_POSITIVE 458 319 272 79 30 NC_002967:TDE1611|3end_hypothetical_protein_1660434..1660584_POSITIVE 403 298 255 89 43 NC_002967:TDE2482|3end_hypothetical_protein_2505822..2505972_POSITIVE 388 318 271 83 20 NC_002967:TDE1048|3end_30S_ribosomal_protein_S7_1075032..1075182_POSITIVE 385 293 252 88 46 NC_002967:TDE2736|3end_hypothetical_protein_2791702..2791852_NEGATIVE 337 138 94 79 40 NC_002967:TDE1245|3end_hypothetical_protein_1277905..1278055_NEGATIVE 335 291 266 136 107 NC_002967:TDE0595|3end_hypothetical_protein_634838..634988_NEGATIVE 333 79 31 87 27 NC_002967:TDE1056|3end_hypothetical_protein_1085895..1086045_POSITIVE 332 169 121 43 4 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 331 160 121 46 2 NC_002967:TDE2222|3end_hypothetical_protein_2264702..2264852_POSITIVE 331 86 41 129 85 NC_002967:TDE2100|3end_hypothetical_protein_2125572..2125722_POSITIVE 328 137 92 138 96 NC_002967:TDE1838|3end_hypothetical_protein_1869968..1870118_NEGATIVE 322 314 275 121 77 NC_002967:TDE1450|3end_MutS2_family_protein_1497856..1498006_POSITIVE 322 309 273 141 106 NC_002967:TDE0693|3end_phosphomethylpyrimidine_kinase_730831..730981_POSITIVE 321 299 258 73 38 NC_002967:TDE2345|3end_ribosome_recycling_factor_2381946..2382096_NEGATIVE 320 180 135 53 4 NC_002967:TDE1856|3end_radical_SAM_domain_protein_1883956..1884106_POSITIVE 319 318 274 51 2 NC_002967:TDE2763|3end_flagellar_motor_switch_protein_2817737..2817887_NEGATIVE 318 314 273 62 1 NC_002967:TDE0573|3end_hypothetical_protein_604910..605060_POSITIVE 316 311 271 135 108 NC_002967:TDE0956|3end_hypothetical_protein_980330..980480_POSITIVE