Origin IGS: ccaaggaatatctccattccaatattcctctacaacagtacttggagttccacctgttagaacatcatacgctatattcttgatgcttatttcttcccagccttcaggta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tacctgaaggctgggaagaaataagcatcaagaatatagcgtatgatgttctaacaggtggaactccaagtactgttgtagaggaatattggaatggagatattccttgg Mask Tandem Repeat Region ================================================ ccaaggaatatctccattccaatattcctctacaacagtacttggagttccacctgttagaacatcatacgctatattcttgatgcttatttcttcccagccttcaggta Find is-nt database================================================ Query_seq: TDE0368:TDE0369|TDE0368:TDE0369:type I restriction-modification system, S subunit, putative:type I restriction-modification system, M subunit:<-<-:418336..418445 110 ccaaggaatatctccattccaatattcctctacaacagtacttggagttccacctgttagaacatcatacgctatattcttgatgcttatttcttcccagccttcaggta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0368:TDE0369|TDE0368:TDE0369:type I restriction-modification system, S subunit, putative:type I restriction-modification system, M subunit:<-<-:418336..418445 110 ccaaggaatatctccattccaatattcctctacaacagtacttggagttccacctgttagaacatcatacgctatattcttgatgcttatttcttcccagccttcaggta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0368:TDE0369|TDE0368:TDE0369:type I restriction-modification system, S subunit, putative:type I restriction-modification system, M subunit:<-<-:418336..418445 110 ccaaggaatatctccattccaatattcctctacaacagtacttggagttccacctgttagaacatcatacgctatattcttgatgcttatttcttcccagccttcaggta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccaaggaatatctccattccaatattcctctacaacagtacttggagttccacctgttagaacatcatacgctatattcttgatgcttatttcttcccagccttcaggta Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 8 End: 109 ....... M S P F Q Y S S T T V L G V P P V R T S Y A I F L M L I S S Q P S G . Protein_Len: 30 Strand: - Start: 1 End: 90 W P I D G N W Y E E V V T S P T G G T L V D Y A I N K I S M .................... ccaaggaatatctccattccaatattcctctacaacagtacttggagttccacctgttagaacatcatacgctatattcttgatgcttatttcttcccagccttcaggta 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================================================ ccaaggaatatctccattccaatattcctctacaacagtacttggagttccacctgttagaacatcatacgctatattcttgatgcttatttcttcccagccttcaggta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0368:TDE0369|TDE0368:TDE0369:type I restriction-modification system, S subunit, putative:type I restriction-modification system, M subunit:<-<-:418336..418445 110 ccaaggaatatctccattccaatattcctctacaacagtacttggagttccacctgttagaacatcatacgctatattcttgatgcttatttcttcccagccttcaggta Intra-Species Hit: Count: 1 Min: 1 Max: 110 Len: 110 Subject: NC_002967_TDE0368_TDE0369|type I restriction-modification system, S subunit, putative:type I restriction-modification system, M subunit|NEGATIVE:NEGATIVE|[418336,418445]|110 HSP 1 e-value: 3.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 ccaaggaatatctccattccaatattcctctacaacagtacttggagttccacctgttagaacatcatacgctatattcttgatgcttatttcttcccagccttcaggta ccaaggaatatctccattccaatattcctctacaacagtacttggagttccacctgttagaacatcatacgctatattcttgatgcttatttcttcccagccttcaggta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCAAGGAAUAUCUCCAUUCCAAUAUUCCUCUACAACAGUACUUGGAGUUCCACCUGUUAGAACAUCAUACGCUAUAUUCUUGAUGCUUAUUUCUUCCCAGCCUUCAGGUA ...((((((((..........)))))))).........(((((((((......(((..(((((((((.............))))).....))))...))).))))))))) (-18.82) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UACCUGAAGGCUGGGAAGAAAUAAGCAUCAAGAAUAUAGCGUAUGAUGUUCUAACAGGUGGAACUCCAAGUACUGUUGUAGAGGAAUAUUGGAAUGGAGAUAUUCCUUGG ..(((.......)))........(((((((.............))))))).((((((.(((....)))....))))))..((((((((((........)))))))))).. (-25.02) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 897 60 11 151 102 NC_002967:TDE0368|5end_type_I_restriction-modification_system,_S_subunit,_putative_418245..418475_NEGATIVE 301 46 2 54 13 NC_002967:TDE1657|5end_transcription_antitermination_protein_NusB_1707640..1707870_NEGATIVE 294 108 63 121 70 NC_002967:TDE0082|5end_transcriptional_regulator,_MerR_family_94251..94481_NEGATIVE 278 106 71 122 75 NC_002967:TDE0518|5end_hypothetical_protein_565263..565493_NEGATIVE 259 68 24 231 188 NC_002967:TDE1144|5end_hypothetical_protein_1182855..1183085_NEGATIVE 256 110 77 162 133 NC_002967:TDE2570|5end_ribonuclease_HI_2597375..2597605_POSITIVE 256 41 4 121 79 NC_002967:TDE1342|5end_hypothetical_protein_1378442..1378672_POSITIVE 252 35 2 171 140 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 245 104 64 106 69 NC_002967:TDE1329|5end_ATPase,_AAA_family_1363503..1363733_POSITIVE 244 88 41 185 141 NC_002967:TDE1147|5end_hypothetical_protein_1185960..1186190_NEGATIVE 242 50 4 225 162 NC_002967:TDE1564|5end_hypothetical_protein_1616502..1616732_POSITIVE 242 59 18 60 18 NC_002967:TDE0153|5end_coenzyme_A_disulfide_reductase,_putative_176185..176415_NEGATIVE 237 110 63 150 89 NC_002967:TDE2516|5end_hypothetical_protein_2542021..2542251_POSITIVE 236 109 71 121 75 NC_002967:TDE1409|5end_flagellar_filament_outer_layer_protein_FlaA,_putative_1451561..1451791_POSITIVE 236 68 22 218 165 NC_002967:TDE0839|5end_rhodanese-like_domain_protein_859341..859571_NEGATIVE 234 95 51 172 124 NC_002967:TDE0069|5end_conserved_hypothetical_protein_TIGR00238_76551..76781_POSITIVE 231 58 23 217 181 NC_002967:TDE1248|5end_hypothetical_protein_1282596..1282826_POSITIVE 230 108 63 219 157 NC_002967:TDE1213|5end_flagellar_basal_body_rod_protein_1245817..1246047_POSITIVE 229 108 71 171 138 NC_002967:TDE1335|5end_alginate_O-acetylation_protein,_putative_1370816..1371046_POSITIVE 226 110 64 141 87 NC_002967:TDE1113|5end_hypothetical_protein_1148250..1148480_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 108 63 118 67 NC_002967:TDE0083|3end_GTP-binding_protein_EngA_94254..94404_NEGATIVE 270 55 12 56 7 NC_002967:TDE1658|3end_basic_membrane_protein,_putative_1707655..1707805_NEGATIVE 256 41 4 124 82 NC_002967:TDE1341|3end_hypothetical_protein_1378525..1378675_POSITIVE 256 55 15 127 79 NC_002967:TDE0978|3end_hypothetical_protein_1002424..1002574_POSITIVE 248 105 63 129 89 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 236 109 71 99 53 NC_002967:TDE1408|3end_flagellar_filament_outer_layer_protein_FlaA,_putative_1451619..1451769_POSITIVE 236 68 22 140 87 NC_002967:TDE0840|3end_hypothetical_protein_859419..859569_NEGATIVE 229 97 64 151 113 NC_002967:TDE1722|3end_hypothetical_protein_1776518..1776668_POSITIVE 229 108 71 149 116 NC_002967:TDE1334|3end_hypothetical_protein_1370874..1371024_POSITIVE 225 109 64 71 25 NC_002967:TDE1453|3end_alpha-galactosidase_1501516..1501666_POSITIVE 224 46 4 147 93 NC_002967:TDE1563|3end_hypothetical_protein_1616513..1616663_POSITIVE 223 107 63 94 50 NC_002967:TDE1807|3end_hypothetical_protein_1843434..1843584_NEGATIVE 223 63 36 50 25 NC_002967:TDE0796|3end_histidinol_phosphate_phosphatase_HisJ_family_protein_820946..821096_POSITIVE 223 88 50 117 86 NC_002967:TDE0711|3end_hypothetical_protein_745690..745840_NEGATIVE 222 90 48 144 100 NC_002967:TDE0068|3end_succinyl-diaminopimelate_desuccinylase_76612..76762_POSITIVE 221 47 1 124 77 NC_002967:TDE1047|3end_30S_ribosomal_protein_S12_1074551..1074701_POSITIVE 220 88 41 44 11 NC_002967:TDE2312|3end_hypothetical_protein_2349049..2349199_POSITIVE 220 109 61 121 58 NC_002967:TDE1175|3end_chaperonin_GroEL_1203517..1203667_NEGATIVE 219 110 61 109 54 NC_002967:TDE0781|3end_30S_ribosomal_protein_S8_813039..813189_POSITIVE 217 110 63 116 55 NC_002967:TDE1622|3end_hypothetical_protein_1670820..1670970_NEGATIVE