Origin IGS: tagaacctccaatgttttaatactatagctgtaactattattgttacatctatagtataagcttttttagatgtaatgtcaatggttacaactaaaattttctaaattcttttatagattttatttgagatttatatatagttctttttttatttacaaattatgaattacacgggtatgtcgaagttgaacattggacactgatctccgattttcaacggtagtatactaatactcttttttttaatataatgtatat .........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 atatacattatattaaaaaaaagagtattagtatactaccgttgaaaatcggagatcagtgtccaatgttcaacttcgacatacccgtgtaattcataatttgtaaataaaaaaagaactatatataaatctcaaataaaatctataaaagaatttagaaaattttagttgtaaccattgacattacatctaaaaaagcttatactatagatgtaacaataatagttacagctatagtattaaaacattggaggttcta Mask Tandem Repeat Region ================================================ tagaacctccaatgttttaatactatagctgtaactattattgttacatctatagtataagcttttttagatgtaatgtcaatggttacaactaaaattttctaaattcttttatagattttatttgagatttatatatagttctttttttatttacaaattatgaattacacgggtatgtcgaagttgaacattggacactgatctccgattttcaacggtagtatactaatactcttttttttaatataatgtatat Find is-nt database================================================ Query_seq: TDE0802:TDE0803|TDE0802:TDE0803:hypothetical protein:hypothetical protein:<-->:825198..825456 259 tagaacctccaatgttttaatactatagctgtaactattattgttacatctatagtataagcttttttagatgtaatgtcaatggttacaactaaaattttctaaattcttttatagattttatttgagatttatatatagttctttttttatttacaaattatgaattacacgggtatgtcgaagttgaacattggacactgatctccgattttcaacggtagtatactaatactcttttttttaatataatgtatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0802:TDE0803|TDE0802:TDE0803:hypothetical protein:hypothetical protein:<-->:825198..825456 259 tagaacctccaatgttttaatactatagctgtaactattattgttacatctatagtataagcttttttagatgtaatgtcaatggttacaactaaaattttctaaattcttttatagattttatttgagatttatatatagttctttttttatttacaaattatgaattacacgggtatgtcgaagttgaacattggacactgatctccgattttcaacggtagtatactaatactcttttttttaatataatgtatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0802:TDE0803|TDE0802:TDE0803:hypothetical protein:hypothetical protein:<-->:825198..825456 259 tagaacctccaatgttttaatactatagctgtaactattattgttacatctatagtataagcttttttagatgtaatgtcaatggttacaactaaaattttctaaattcttttatagattttatttgagatttatatatagttctttttttatttacaaattatgaattacacgggtatgtcgaagttgaacattggacactgatctccgattttcaacggtagtatactaatactcttttttttaatataatgtatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaacctccaatgttttaatactatagctgtaactattattgttacatctatagtataagcttttttagatgtaatgtcaatggttacaactaaaattttctaaattcttttatagattttatttgagatttatatatagttctttttttatttacaaattatgaattacacgggtatgtcgaagttgaacattggacactgatctccgattttcaacggtagtatactaatactcttttttttaatataatgtatat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 3 End: 98 .. F R W H K L V I A T V I I T V D I T Y A K K S T I D I T V V L M ................................................................................................................................................................. tagaacctccaatgttttaatactatagctgtaactattattgttacatctatagtataagcttttttagatgtaatgtcaatggttacaactaaaattttctaaattcttttatagattttatttgagatttatatatagttctttttttatttacaaattatgaattacacgggtatgtcgaagttgaacattggacactgatctccgattttcaacggtagtatactaatactcttttttttaatataatgtatat 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: 89 Start: 54 End: 83 .....................................................ATTGACATTACATCTAAAAAAGCTTATACT................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 224 End: 253 ...............................................................................................................................................................................................................................GTATACTAATACTCTTTTTTTTAATATAAT...... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagaacctccaatgttttaatactatagctgtaactattattgttacatctatagtataagcttttttagatgtaatgtcaatggttacaactaaaattttctaaattcttttatagattttatttgagatttatatatagttctttttttatttacaaattatgaattacacgggtatgtcgaagttgaacattggacactgatctccgattttcaacggtagtatactaatactcttttttttaatataatgtatat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 77 HP_score: -4.6 Tail_Score: -5.13473 Start: 16 End: 62 Full_Region: TAGAACCTCCAATGT TTTAATACTATAGCTGTAACTA TTA TTGTTACATCTATAGTATAAGC TTTTTTAGATGTAAT ...............TTTAATACTATAGCTGTAACTATTATTGTTACATCTATAGTATAAGC..................................................................................................................................................................................................... TransTerm Strand: + Conf: 76 HP_score: -8.1 Tail_Score: -3.66999 Start: 17 End: 61 Full_Region: AGAACCTCCAATGTT TTAATACTATAGCTGTAACTA TTA TTGTTACATCTATAGTATAAG CTTTTTTAGATGTAA ................TTAATACTATAGCTGTAACTATTATTGTTACATCTATAGTATAAG...................................................................................................................................................................................................... TransTerm Strand: + Conf: 76 HP_score: -9.4 Tail_Score: -2.79476 Start: 18 End: 60 Full_Region: GAACCTCCAATGTTT TAATACTATAGCTGTAACTA TTA TTGTTACATCTATAGTATAA GCTTTTTTAGATGTA .................TAATACTATAGCTGTAACTATTATTGTTACATCTATAGTATAA....................................................................................................................................................................................................... TransTerm Strand: - Conf: 74 HP_score: -9.3 Tail_Score: -3.04322 Start: 23 End: 55 Full_Region: ctaaaaaagcttata ctatagatgtaacaa taa tagttacagctatag tattaaaacattgga ......................ctatagatgtaacaataatagttacagctatag............................................................................................................................................................................................................ TransTerm Strand: + Conf: 56 HP_score: -2.9 Tail_Score: -4.51847 Start: 65 End: 97 Full_Region: CTATAGTATAAGCTT TTTTAGATGTAAT GTCAATG GTTACAACTAAAA TTTTCTAAATTCTTT ................................................................TTTTAGATGTAATGTCAATGGTTACAACTAAAA.................................................................................................................................................................. Find igs database================================================ Query_seq: TDE0802:TDE0803|TDE0802:TDE0803:hypothetical protein:hypothetical protein:<-->:825198..825456 259 tagaacctccaatgttttaatactatagctgtaactattattgttacatctatagtataagcttttttagatgtaatgtcaatggttacaactaaaattttctaaattcttttatagattttatttgagatttatatatagttctttttttatttacaaattatgaattacacgggtatgtcgaagttgaacattggacactgatctccgattttcaacggtagtatactaatactcttttttttaatataatgtatat Intra-Species Hit: Count: 1 Min: 1 Max: 237 Len: 237 Subject: NC_002967_TDE0802_TDE0803|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[825198,825456]|259 HSP 1 e-value: 2.0E-47 bit: 190.0 Len: 96 Query Start:1 Query End:96 Subject Strand: POSITIVE Subject Start: 1 Subject End: 96 tagaacctccaatgttttaatactatagctgtaactattattgttacatctatagtataagcttttttagatgtaatgtcaatggttacaactaaa................................................................................................................................................................... tagaacctccaatgttttaatactatagctgtaactattattgttacatctatagtataagcttttttagatgtaatgtcaatggttacaactaaa................................................................................................................................................................... HSP 2 e-value: 1.0E-38 bit: 161.0 Len: 81 Query Start:157 Query End:237 Subject Strand: POSITIVE Subject Start: 157 Subject End: 237 ............................................................................................................................................................caaattatgaattacacgggtatgtcgaagttgaacattggacactgatctccgattttcaacggtagtatactaatactc...................... ............................................................................................................................................................caaattatgaattacacgggtatgtcgaagttgaacattggacactgatctccgattttcaacggtagtatactaatactc...................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAACCUCCAAUGUUUUAAUACUAUAGCUGUAACUAUUAUUGUUACAUCUAUAGUAUAAGCUUUUUUAGAUGUAAUGUCAAUGGUUACAACUAAAAUUUUCUAAAUUCUUUUAUAGAUUUUAUUUGAGAUUUAUAUAUAGUUCUUUUUUUAUUUACAAAUUAUGAAUUACACGGGUAUGUCGAAGUUGAACAUUGGACACUGAUCUCCGAUUUUCAACGGUAGUAUACUAAUACUC (((((........((((..(((((((((.((((((.......)))))).)))))))))))))..((((((.((((((.......)))))).))))))..)))))........((((((((((....))))))))))..((((((....(((......)))....))))))....((((((..(..((((((.((((((........)))))).))))))..)..))))))....... (-54.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGUAUUAGUAUACUACCGUUGAAAAUCGGAGAUCAGUGUCCAAUGUUCAACUUCGACAUACCCGUGUAAUUCAUAAUUUGUAAAUAAAAAAAGAACUAUAUAUAAAUCUCAAAUAAAAUCUAUAAAAGAAUUUAGAAAAUUUUAGUUGUAACCAUUGACAUUACAUCUAAAAAAGCUUAUACUAUAGAUGUAACAAUAAUAGUUACAGCUAUAGUAUUAAAACAUUGGAGGUUCUA (((.(((.(((((.....((((((.((.(((.(....).))).)).))))))....((((....))))...............................))))).))))))................(((((((......((((((.(((((.........))))).))))))......(((((((((.((((((.......)))))).)))))))))...........))))))). (-42.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 744 50 1 141 92 NC_002967:TDE0802|5end_hypothetical_protein_825107..825337_NEGATIVE 357 223 181 158 115 NC_002967:TDE1935|5end_hypothetical_protein_1952994..1953224_POSITIVE 320 217 173 185 144 NC_002967:TDE1612|5end_phosphoribosyl_transferase_domain_protein_1660549..1660779_POSITIVE 268 205 173 231 194 NC_002967:TDE1936|5end_hypothetical_protein_1953086..1953316_POSITIVE 263 220 171 124 81 NC_002967:TDE1362|5end_hypothetical_protein_1400992..1401222_POSITIVE 254 228 183 126 73 NC_002967:TDE1750|5end_hypothetical_protein_1803825..1804055_NEGATIVE 245 210 173 106 64 NC_002967:TDE1845|5end_hypothetical_protein_1875169..1875399_NEGATIVE 245 228 188 121 81 NC_002967:TDE0463|5end_purine_nucleoside_phosphorylase_517183..517413_POSITIVE 243 220 173 145 95 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 240 230 182 71 31 NC_002967:TDE0351|5end_L-lactate_dehydrogenase_395998..396228_NEGATIVE 235 223 189 178 142 NC_002967:TDE1241|5end_HD_domain_protein_1272269..1272499_POSITIVE 232 218 172 185 142 NC_002967:TDE0155|5end_adenylate/guanylate_cyclase_catalytic_domain_protein_180154..180384_NEGATIVE 230 220 173 78 13 NC_002967:TDE2766|5end_motility_protein_A_2820874..2821104_NEGATIVE 230 204 161 155 114 NC_002967:TDE2158|5end_ABC_transporter,_ATP-binding_protein_2191664..2191894_POSITIVE 229 220 171 223 181 NC_002967:TDE1745|5end_hypothetical_protein_1799474..1799704_NEGATIVE 228 217 171 221 178 NC_002967:TDE1311|5end_ABC_transporter,_ATP-binding/permease_protein_1347371..1347601_POSITIVE 226 210 161 102 55 NC_002967:TDE2204|5end_Na+/H+_antiporter_family_protein_2241169..2241399_POSITIVE 225 224 182 163 118 NC_002967:TDE0476|5end_hypothetical_protein_532914..533144_NEGATIVE 221 210 162 83 27 NC_002967:TDE0544|5end_hypothetical_protein_583854..584084_POSITIVE 219 229 205 130 106 NC_002967:TDE0460|5end_transporter,_putative_515942..516172_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 298 215 173 62 15 NC_002967:TDE2515|3end_hypothetical_protein_2540972..2541122_NEGATIVE 277 228 181 114 69 NC_002967:TDE0900|3end_ABC_transporter,_ATP-binding_protein_918692..918842_POSITIVE 268 226 182 144 103 NC_002967:TDE1402|3end_hypothetical_protein_1444515..1444665_POSITIVE 259 212 173 56 12 NC_002967:TDE1934|3end_hypothetical_protein_1952804..1952954_POSITIVE 256 218 173 58 1 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 254 228 183 120 67 NC_002967:TDE1751|3end_ribosomal_protein_L21_1803831..1803981_NEGATIVE 246 215 173 62 15 NC_002967:TDE0945|3end_hypothetical_protein_968320..968470_POSITIVE 245 210 173 106 64 NC_002967:TDE1846|3end_hypothetical_protein_1875169..1875319_NEGATIVE 245 217 171 50 2 NC_002967:TDE0904|3end_hypothetical_protein_922278..922428_NEGATIVE 243 220 173 148 98 NC_002967:TDE2631|3end_peptide_ABC_transporter,_permease_protein,_putative_2672733..2672883_POSITIVE 234 207 171 150 115 NC_002967:TDE1361|3end_hypothetical_protein_1401106..1401256_POSITIVE 230 204 161 143 102 NC_002967:TDE2157|3end_ABC_transporter,_permease_protein,_putative_2191732..2191882_POSITIVE 230 212 171 54 4 NC_002967:TDE0205|3end_adenylate/guanylate_cyclase_catalytic_domain_protein_239688..239838_POSITIVE 228 217 171 110 67 NC_002967:TDE1310|3end_modulator_of_DNA_gyrase_family_protein_1347340..1347490_POSITIVE 225 224 182 107 62 NC_002967:TDE0477|3end_hypothetical_protein_532970..533120_NEGATIVE 219 218 172 84 42 NC_002967:TDE0862|3end_hypothetical_protein_884126..884276_POSITIVE 217 211 172 76 40 NC_002967:TDE0987|3end_oligopeptide/dipeptide_ABC_transporter,_ATP-binding_protein_1015077..1015227_POSITIVE 216 221 182 39 3 NC_002967:TDE2139|3end_hypothetical_protein_2172897..2173047_POSITIVE 216 196 157 137 99 NC_002967:TDE1335|3end_alginate_O-acetylation_protein,_putative_1372368..1372518_POSITIVE 213 211 174 52 17 NC_002967:TDE0463|3end_purine_nucleoside_phosphorylase_517964..518114_POSITIVE