Origin IGS: tcggaacaagctcaaagaatggtagatttttaatttctatgaagggcacggcggatttgccggccgagaggcggcaaatcctgtgaagataccgttgtacagaacgtacaacggtaaactaaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tttagtttaccgttgtacgttctgtacaacggtatcttcacaggatttgccgcctctcggccggcaaatccgccgtgcccttcatagaaattaaaaatctaccattctttgagcttgttccga Mask Tandem Repeat Region ================================================ tcggaacaagctcaaagaatggtagatttttaatttctatgaagggcacggcggatttgccggccgagaggcggcaaatcctgtgaagataccgttgtacagaacgtacaacggtaaactaaa Find is-nt database================================================ Query_seq: TDE2209:TDE2210|TDE2209:TDE2210:CarB family protein:hypothetical protein:-><-:2249361..2249483 123 tcggaacaagctcaaagaatggtagatttttaatttctatgaagggcacggcggatttgccggccgagaggcggcaaatcctgtgaagataccgttgtacagaacgtacaacggtaaactaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2209:TDE2210|TDE2209:TDE2210:CarB family protein:hypothetical protein:-><-:2249361..2249483 123 tcggaacaagctcaaagaatggtagatttttaatttctatgaagggcacggcggatttgccggccgagaggcggcaaatcctgtgaagataccgttgtacagaacgtacaacggtaaactaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2209:TDE2210|TDE2209:TDE2210:CarB family protein:hypothetical protein:-><-:2249361..2249483 123 tcggaacaagctcaaagaatggtagatttttaatttctatgaagggcacggcggatttgccggccgagaggcggcaaatcctgtgaagataccgttgtacagaacgtacaacggtaaactaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tcggaacaagctcaaagaatggtagatttttaatttctatgaagggcacggcggatttgccggccgagaggcggcaaatcctgtgaagataccgttgtacagaacgtacaacggtaaactaaa Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 26 End: 121 ......................... M F N F Y E G H G G F A G R E A A N P V K I P L Y R T Y N G K L .. tcggaacaagctcaaagaatggtagatttttaatttctatgaagggcacggcggatttgccggccgagaggcggcaaatcctgtgaagataccgttgtacagaacgtacaacggtaaactaaa 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================================================ tcggaacaagctcaaagaatggtagatttttaatttctatgaagggcacggcggatttgccggccgagaggcggcaaatcctgtgaagataccgttgtacagaacgtacaacggtaaactaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE2209:TDE2210|TDE2209:TDE2210:CarB family protein:hypothetical protein:-><-:2249361..2249483 123 tcggaacaagctcaaagaatggtagatttttaatttctatgaagggcacggcggatttgccggccgagaggcggcaaatcctgtgaagataccgttgtacagaacgtacaacggtaaactaaa Intra-Species Hit: Count: 1 Min: 1 Max: 123 Len: 123 Subject: NC_002967_TDE2209_TDE2210|CarB family protein:hypothetical protein|POSITIVE:NEGATIVE|[2249361,2249483]|123 HSP 1 e-value: 6.0E-64 bit: 244.0 Len: 123 Query Start:1 Query End:123 Subject Strand: POSITIVE Subject Start: 1 Subject End: 123 tcggaacaagctcaaagaatggtagatttttaatttctatgaagggcacggcggatttgccggccgagaggcggcaaatcctgtgaagataccgttgtacagaacgtacaacggtaaactaaa tcggaacaagctcaaagaatggtagatttttaatttctatgaagggcacggcggatttgccggccgagaggcggcaaatcctgtgaagataccgttgtacagaacgtacaacggtaaactaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCGGAACAAGCUCAAAGAAUGGUAGAUUUUUAAUUUCUAUGAAGGGCACGGCGGAUUUGCCGGCCGAGAGGCGGCAAAUCCUGUGAAGAUACCGUUGUACAGAACGUACAACGGUAAACUAAA ((...((..((((.....((((.((((.....))))))))...)))).....((((((((((.((....)))))))))))).))...))(((((((((((.....)))))))))))....... (-46.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAGUUUACCGUUGUACGUUCUGUACAACGGUAUCUUCACAGGAUUUGCCGCCUCUCGGCCGGCAAAUCCGCCGUGCCCUUCAUAGAAAUUAAAAAUCUACCAUUCUUUGAGCUUGUUCCGA .......(((((((((((.....)))))))))))....(((.((((((((((((....)).))))))))))...)))...((((.((((...............)))).)))).......... (-40.06) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 444 88 44 109 47 NC_002967:TDE2715|5end_hypothetical_protein_2772668..2772898_POSITIVE 396 75 39 190 141 NC_002967:TDE2103|5end_glycosyl_transferase,_group_2_family_protein_2128393..2128623_NEGATIVE 392 75 44 221 186 NC_002967:TDE1500|5end_hypothetical_protein_1548070..1548300_NEGATIVE 386 100 53 102 59 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 385 76 39 220 164 NC_002967:TDE0848|5end_hypothetical_protein_871269..871499_POSITIVE 382 86 43 45 5 NC_002967:TDE2495|5end_hypothetical_protein_2521053..2521283_NEGATIVE 375 77 40 51 4 NC_002967:TDE1987|5end_hypothetical_protein_2002312..2002542_POSITIVE 366 83 43 212 175 NC_002967:TDE1973|5end_CvpA_family_protein_1987706..1987936_NEGATIVE 354 98 52 186 128 NC_002967:TDE0978|5end_hypothetical_protein_1001868..1002098_POSITIVE 353 85 43 160 105 NC_002967:TDE2404|5end_RNA_polymerase_sigma-54_factor,_putative_2430704..2430934_NEGATIVE 350 90 45 62 16 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 344 76 40 44 2 NC_002967:TDE0781|5end_30S_ribosomal_protein_S8_812561..812791_POSITIVE 344 95 51 76 18 NC_002967:TDE0593|5end_internalin-related_protein_633936..634166_NEGATIVE 343 84 42 68 17 NC_002967:TDE0852|5end_50S_ribosomal_protein_L13_875019..875249_POSITIVE 341 89 43 80 18 NC_002967:TDE1622|5end_hypothetical_protein_1670981..1671211_NEGATIVE 340 90 44 210 158 NC_002967:TDE1592|5end_ABC_transporter,_ATP-binding_protein_1639491..1639721_POSITIVE 338 79 34 68 13 NC_002967:TDE2070|5end_hypothetical_protein_2097035..2097265_POSITIVE 338 82 46 66 21 NC_002967:TDE1042|5end_deoxyuridine_5'triphosphate_nucleotidohydrolase_1070492..1070722_POSITIVE 337 88 41 134 69 NC_002967:TDE2515|5end_hypothetical_protein_2542057..2542287_NEGATIVE 337 77 42 55 12 NC_002967:TDE2448|5end_hypothetical_protein_2477417..2477647_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 426 90 41 58 13 NC_002967:TDE0940|3end_hypothetical_protein_963635..963785_POSITIVE 410 85 47 44 6 NC_002967:TDE2209|3end_CarB_family_protein_2249300..2249450_POSITIVE 396 75 39 58 9 NC_002967:TDE2104|3end_hypothetical_protein_2128525..2128675_NEGATIVE 386 100 53 130 87 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 382 86 43 139 85 NC_002967:TDE0833|3end_lipoprotein,_putative_854097..854247_POSITIVE 364 88 42 65 7 NC_002967:TDE1402|3end_hypothetical_protein_1444515..1444665_POSITIVE 353 85 43 148 93 NC_002967:TDE2405|3end_hypothetical_protein_2430716..2430866_NEGATIVE 353 97 51 87 43 NC_002967:TDE1530|3end_hypothetical_protein_1575096..1575246_NEGATIVE 350 90 45 49 3 NC_002967:TDE0240|3end_glycine_reductase_complex_protein_GrdC_272995..273145_NEGATIVE 341 70 24 150 99 NC_002967:TDE0875|3end_ribosomal_large_subunit_pseudouridine_synthase_B_898273..898423_POSITIVE 336 84 49 38 5 NC_002967:TDE0452|3end_hypothetical_protein_509949..510099_NEGATIVE 335 86 42 60 14 NC_002967:TDE0176|3end_hypothetical_protein_208800..208950_NEGATIVE 331 81 43 78 31 NC_002967:TDE2582|3end_GGDEF_domain_protein_2616164..2616314_POSITIVE 331 85 42 135 83 NC_002967:TDE2239|3end_hypothetical_protein_2276554..2276704_NEGATIVE 328 87 46 146 98 NC_002967:TDE1782|3end_hypothetical_protein_1823304..1823454_NEGATIVE 328 97 51 136 97 NC_002967:TDE0977|3end_hypothetical_protein_1001640..1001790_POSITIVE 327 89 42 47 1 NC_002967:TDE1451|3end_hypothetical_protein_1497850..1498000_NEGATIVE 327 75 34 134 88 NC_002967:TDE0341|3end_ribonucleotide-diphosphate_reductase_alpha_subunit_379589..379739_NEGATIVE 327 96 62 132 103 NC_002967:TDE0012|3end_carbon_starvation_protein_CstA,_putative_17702..17852_POSITIVE 326 86 49 151 102 NC_002967:TDE0959|3end_hypothetical_protein_982365..982515_POSITIVE