Origin IGS: aacggctgataccaaaagactccgggcagttaaagctgcctggagcctttagccggaatcttaaaacgccctctacttgactttatagcttttttttgctttactatatgcctc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gaggcatatagtaaagcaaaaaaaagctataaagtcaagtagagggcgttttaagattccggctaaaggctccaggcagctttaactgcccggagtcttttggtatcagccgtt Mask Tandem Repeat Region ================================================ aacggctgataccaaaagactccgggcagttaaagctgcctggagcctttagccggaatcttaaaacgccctctacttgactttatagcttttttttgctttactatatgcctc Find is-nt database================================================ Query_seq: TDE2606:TDE2607|TDE2606:TDE2607:urocanate hydratase:hypothetical protein:->->:2648612..2648725 114 aacggctgataccaaaagactccgggcagttaaagctgcctggagcctttagccggaatcttaaaacgccctctacttgactttatagcttttttttgctttactatatgcctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE2606:TDE2607|TDE2606:TDE2607:urocanate hydratase:hypothetical protein:->->:2648612..2648725 114 aacggctgataccaaaagactccgggcagttaaagctgcctggagcctttagccggaatcttaaaacgccctctacttgactttatagcttttttttgctttactatatgcctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE2606:TDE2607|TDE2606:TDE2607:urocanate hydratase:hypothetical protein:->->:2648612..2648725 114 aacggctgataccaaaagactccgggcagttaaagctgcctggagcctttagccggaatcttaaaacgccctctacttgactttatagcttttttttgctttactatatgcctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacggctgataccaaaagactccgggcagttaaagctgcctggagcctttagccggaatcttaaaacgccctctacttgactttatagcttttttttgctttactatatgcctc Predict ORF larger than 30AA ================================================ aacggctgataccaaaagactccgggcagttaaagctgcctggagcctttagccggaatcttaaaacgccctctacttgactttatagcttttttttgctttactatatgcctc 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: 82 Start: 76 End: 105 ...........................................................................CTTGACTTTATAGCTTTTTTTTGCTTTACT......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacggctgataccaaaagactccgggcagttaaagctgcctggagcctttagccggaatcttaaaacgccctctacttgactttatagcttttttttgctttactatatgcctc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 93 HP_score: -11.4 Tail_Score: -4.34402 Start: 18 End: 47 Full_Region: aagattccggctaaa ggctccaggcag ctttaa ctgcccggagtc ttttggtatcagccg .................ggctccaggcagctttaactgcccggagtc................................................................... Find igs database================================================ Query_seq: TDE2606:TDE2607|TDE2606:TDE2607:urocanate hydratase:hypothetical protein:->->:2648612..2648725 114 aacggctgataccaaaagactccgggcagttaaagctgcctggagcctttagccggaatcttaaaacgccctctacttgactttatagcttttttttgctttactatatgcctc Intra-Species Hit: Count: 1 Min: 1 Max: 114 Len: 114 Subject: NC_002967_TDE2606_TDE2607|urocanate hydratase:hypothetical protein|POSITIVE:POSITIVE|[2648612,2648725]|114 HSP 1 e-value: 2.0E-44 bit: 178.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 aacggctgataccaaaagactccgggcagttaaagctgcctggagcctttagccggaatcttaaaacgccctctacttgactttatagcnnnnnnnngctttactatatgcctc aacggctgataccaaaagactccgggcagttaaagctgcctggagcctttagccggaatcttaaaacgccctctacttgactttatagcttttttttgctttactatatgcctc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACGGCUGAUACCAAAAGACUCCGGGCAGUUAAAGCUGCCUGGAGCCUUUAGCCGGAAUCUUAAAACGCCCUCUACUUGACUUUAUAGCUUUUUUUUGCUUUACUAUAUGCCUC ..(((((((.......((.(((((((((((....))))))))))).)))))))))............................((.(((........))).))........... (-33.01) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGGCAUAUAGUAAAGCAAAAAAAAGCUAUAAAGUCAAGUAGAGGGCGUUUUAAGAUUCCGGCUAAAGGCUCCAGGCAGCUUUAACUGCCCGGAGUCUUUUGGUAUCAGCCGUU ..(((.((((((.............))))))..(((........))).......(((.(((...(((((((((.(((((......))))).)))))))))))).))).)))... (-36.02) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 398 69 21 58 11 NC_002967:TDE1052|5end_rubredoxin_1078870..1079100_NEGATIVE 388 69 22 223 178 NC_002967:TDE2402|5end_radical_SAM_domain_protein_2427691..2427921_POSITIVE 381 66 21 78 14 NC_002967:TDE1038|5end_hypothetical_protein_1066976..1067206_NEGATIVE 336 60 13 89 25 NC_002967:TDE1294|5end_phosphocarrier_protein_HPr_1332321..1332551_NEGATIVE 333 63 23 41 7 NC_002967:TDE1987|5end_hypothetical_protein_2002312..2002542_POSITIVE 330 70 21 199 149 NC_002967:TDE1027|5end_ribonuclease_III_1057562..1057792_POSITIVE 327 55 17 68 19 NC_002967:TDE2736|5end_hypothetical_protein_2791812..2792042_NEGATIVE 325 70 25 225 180 NC_002967:TDE1214|5end_flagellar_basal_body_protein_1246307..1246537_POSITIVE 323 49 3 204 158 NC_002967:TDE1550|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_1592747..1592977_POSITIVE 322 62 23 47 10 NC_002967:TDE0572|5end_hypothetical_protein_603494..603724_POSITIVE 321 56 12 186 134 NC_002967:TDE2623|5end_hypothetical_protein_2664324..2664554_NEGATIVE 321 69 22 200 157 NC_002967:TDE2268|5end_hypothetical_protein_2304959..2305189_NEGATIVE 320 70 21 64 18 NC_002967:TDE0153|5end_coenzyme_A_disulfide_reductase,_putative_176185..176415_NEGATIVE 319 55 21 221 175 NC_002967:TDE0733|5end_hypothetical_protein_774096..774326_NEGATIVE 316 70 21 194 131 NC_002967:TDE2779|5end_hypothetical_protein_2830425..2830655_NEGATIVE 316 47 4 191 144 NC_002967:TDE2697|5end_3-oxo-5-alpha-steroid_4-dehydrogenase_family_protein_2740260..2740490_POSITIVE 316 47 3 230 182 NC_002967:TDE1143|5end_hypothetical_protein_1181834..1182064_NEGATIVE 311 50 3 205 172 NC_002967:TDE0239|5end_glycine_reductase_complex_protein_GrdD_272982..273212_NEGATIVE 310 69 23 174 123 NC_002967:TDE2399|5end_ribonuclease_P_protein_component_2426160..2426390_NEGATIVE 307 53 14 120 75 NC_002967:TDE2494|5end_hypothetical_protein_2518497..2518727_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 486 50 3 76 36 NC_002967:TDE2606|3end_urocanate_hydratase_2648551..2648701_POSITIVE 356 59 12 143 101 NC_002967:TDE2527|3end_hypothetical_protein_2555449..2555599_NEGATIVE 347 58 11 151 87 NC_002967:TDE1693|3end_hypothetical_protein_1748438..1748588_NEGATIVE 326 58 23 51 10 NC_002967:TDE0824|3end_lipoprotein,_putative_845226..845376_NEGATIVE 326 57 16 39 2 NC_002967:TDE0794|3end_hypothetical_protein_819224..819374_NEGATIVE 325 46 1 148 98 NC_002967:TDE1743|3end_chromate_transport_protein_1797940..1798090_NEGATIVE 321 60 11 60 2 NC_002967:TDE1981|3end_hypothetical_protein_1992437..1992587_POSITIVE 319 70 21 59 19 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 316 70 21 111 48 NC_002967:TDE2780|3end_hypothetical_protein_2830508..2830658_NEGATIVE 305 41 3 89 38 NC_002967:TDE1633|3end_citrate_lyase_acyl_carrier_protein_1682428..1682578_NEGATIVE 305 70 21 137 94 NC_002967:TDE0350|3end_MATE_efflux_family_protein_395019..395169_POSITIVE 304 51 12 82 51 NC_002967:TDE2380|3end_hypothetical_protein_2411062..2411212_POSITIVE 304 55 18 139 103 NC_002967:TDE0068|3end_succinyl-diaminopimelate_desuccinylase_76612..76762_POSITIVE 303 66 22 47 5 NC_002967:TDE0240|3end_glycine_reductase_complex_protein_GrdC_272995..273145_NEGATIVE 302 61 21 80 38 NC_002967:TDE1084|3end_folylpolyglutamate_synthetase,_putative_1114934..1115084_NEGATIVE 301 56 11 76 28 NC_002967:TDE2269|3end_hypothetical_protein_2304931..2305081_NEGATIVE 299 74 37 48 15 NC_002967:TDE2209|3end_CarB_family_protein_2249300..2249450_POSITIVE 299 61 21 53 23 NC_002967:TDE1427|3end_glycosyl_transferase,_group_1_family_protein_1471190..1471340_POSITIVE 297 58 12 70 29 NC_002967:TDE2242|3end_antigen,_putative_2279569..2279719_NEGATIVE 297 47 3 148 112 NC_002967:TDE0105|3end_MTA/SAH_nucleosidase_124732..124882_NEGATIVE