Origin IGS: aattactccctatatacctctatttacatataacaatctaagttttttttgaaaacaaatctaattaatttttagtttaaactgctacgatgtccattattgttgagggagcattttggagctcacgaaacactaatggctatcaagcaattaagatataattttaaaaataatgagtttttttatttcaagaaaaactttatttttatattaatctcacatttcactttttatattttacaatagaaatcataaaatttctatgatttatttttattttttaaaaataaaaaagttgaataaaatatttctactttttatccaactttttcactataattattattttacttat .........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 ataagtaaaataataattatagtgaaaaagttggataaaaagtagaaatattttattcaacttttttatttttaaaaaataaaaataaatcatagaaattttatgatttctattgtaaaatataaaaagtgaaatgtgagattaatataaaaataaagtttttcttgaaataaaaaaactcattatttttaaaattatatcttaattgcttgatagccattagtgtttcgtgagctccaaaatgctccctcaacaataatggacatcgtagcagtttaaactaaaaattaattagatttgttttcaaaaaaaacttagattgttatatgtaaatagaggtatatagggagtaatt Mask Tandem Repeat Region ================================================ aattactccctatatacctctatttacatataacaatctaagttttttttgaaaacaaatctaattaatttttagtttaaactgctacgatgtccattattgttgagggagcattttggagctcacgaaacactaatggctatcaagcaattaagatataattttaaaaataatgagtttttttatttcaagaaaaactttatttttatattaatctcacatttcactttttatattttacaatagaaatcataaaatttctatgatttatttttattttttaaaaataaaaaagttgaataaaatatttctactttttatccaactttttcactataattattattttacttat Find is-nt database================================================ Query_seq: FN1581:FN1582|FN1581:FN1582:DNA mismatch repair protein mutS:hypothetical protein:<-<-:93322..93676 355 aattactccctatatacctctatttacatataacaatctaagttttttttgaaaacaaatctaattaatttttagtttaaactgctacgatgtccattattgttgagggagcattttggagctcacgaaacactaatggctatcaagcaattaagatataattttaaaaataatgagtttttttatttcaagaaaaactttatttttatattaatctcacatttcactttttatattttacaatagaaatcataaaatttctatgatttatttttattttttaaaaataaaaaagttgaataaaatatttctactttttatccaactttttcactataattattattttacttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1581:FN1582|FN1581:FN1582:DNA mismatch repair protein mutS:hypothetical protein:<-<-:93322..93676 355 aattactccctatatacctctatttacatataacaatctaagttttttttgaaaacaaatctaattaatttttagtttaaactgctacgatgtccattattgttgagggagcattttggagctcacgaaacactaatggctatcaagcaattaagatataattttaaaaataatgagtttttttatttcaagaaaaactttatttttatattaatctcacatttcactttttatattttacaatagaaatcataaaatttctatgatttatttttattttttaaaaataaaaaagttgaataaaatatttctactttttatccaactttttcactataattattattttacttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1581:FN1582|FN1581:FN1582:DNA mismatch repair protein mutS:hypothetical protein:<-<-:93322..93676 355 aattactccctatatacctctatttacatataacaatctaagttttttttgaaaacaaatctaattaatttttagtttaaactgctacgatgtccattattgttgagggagcattttggagctcacgaaacactaatggctatcaagcaattaagatataattttaaaaataatgagtttttttatttcaagaaaaactttatttttatattaatctcacatttcactttttatattttacaatagaaatcataaaatttctatgatttatttttattttttaaaaataaaaaagttgaataaaatatttctactttttatccaactttttcactataattattattttacttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattactccctatatacctctatttacatataacaatctaagttttttttgaaaacaaatctaattaatttttagtttaaactgctacgatgtccattattgttgagggagcattttggagctcacgaaacactaatggctatcaagcaattaagatataattttaaaaataatgagtttttttatttcaagaaaaactttatttttatattaatctcacatttcactttttatattttacaatagaaatcataaaatttctatgatttatttttattttttaaaaataaaaaagttgaataaaatatttctactttttatccaactttttcactataattattattttacttat Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 82 End: 243 ................................................................................. M L R C P L L L R E H F G A H E T L M A I K Q L R Y N F K N N E F F Y F K K N F I F I L I S H F T F Y I L Q ................................................................................................................ Protein_Len: 45 Strand: + Start: 221 End: 355 ............................................................................................................................................................................................................................ M S L F I F Y N R N H K I S M I Y F Y F L K I K K L N K I F L L F I Q L F H Y N Y Y F T Y aattactccctatatacctctatttacatataacaatctaagttttttttgaaaacaaatctaattaatttttagtttaaactgctacgatgtccattattgttgagggagcattttggagctcacgaaacactaatggctatcaagcaattaagatataattttaaaaataatgagtttttttatttcaagaaaaactttatttttatattaatctcacatttcactttttatattttacaatagaaatcataaaatttctatgatttatttttattttttaaaaataaaaaagttgaataaaatatttctactttttatccaactttttcactataattattattttacttat 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: 83 Start: 235 End: 264 ..........................................................................................................................................................................................................................................ATAGAAATTTTATGATTTCTATTGTAAAAT........................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattactccctatatacctctatttacatataacaatctaagttttttttgaaaacaaatctaattaatttttagtttaaactgctacgatgtccattattgttgagggagcattttggagctcacgaaacactaatggctatcaagcaattaagatataattttaaaaataatgagtttttttatttcaagaaaaactttatttttatattaatctcacatttcactttttatattttacaatagaaatcataaaatttctatgatttatttttattttttaaaaataaaaaagttgaataaaatatttctactttttatccaactttttcactataattattattttacttat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 45 HP_score: -3.7 Tail_Score: -3.35433 Start: 244 End: 263 Full_Region: TTTTATATTTTACAA TAGAAAT CATAAA ATTTCTA TGATTTATTTTTATT ...................................................................................................................................................................................................................................................TAGAAATCATAAAATTTCTA............................................................................................ TransTerm Strand: - Conf: 86 HP_score: -4.6 Tail_Score: -5.93252 Start: 295 End: 326 Full_Region: aattatagtgaaaaa gttggataaaaagt agaa atattttattcaac ttttttatttttaaa ......................................................................................................................................................................................................................................................................................................gttggataaaaagtagaaatattttattcaac............................. Find igs database================================================ Query_seq: FN1581:FN1582|FN1581:FN1582:DNA mismatch repair protein mutS:hypothetical protein:<-<-:93322..93676 355 aattactccctatatacctctatttacatataacaatctaagttttttttgaaaacaaatctaattaatttttagtttaaactgctacgatgtccattattgttgagggagcattttggagctcacgaaacactaatggctatcaagcaattaagatataattttaaaaataatgagtttttttatttcaagaaaaactttatttttatattaatctcacatttcactttttatattttacaatagaaatcataaaatttctatgatttatttttattttttaaaaataaaaaagttgaataaaatatttctactttttatccaactttttcactataattattattttacttat Intra-Species Hit: Count: 1 Min: 1 Max: 177 Len: 177 Subject: NC_003454_FN1581_FN1582|DNA mismatch repair protein mutS:hypothetical protein|NEGATIVE:NEGATIVE|[93322,93676]|355 HSP 1 e-value: 2.0E-81 bit: 303.0 Len: 177 Query Start:1 Query End:177 Subject Strand: POSITIVE Subject Start: 1 Subject End: 177 aattactccctatatacctctatttacatataacaatctaagnnnnnnnngaaaacaaatctaattaatttttagtttaaactgctacgatgtccattattgttgagggagcattttggagctcacgaaacactaatggctatcaagcaattaagatataattttaaaaataatgag.................................................................................................................................................................................. aattactccctatatacctctatttacatataacaatctaagttttttttgaaaacaaatctaattaatttttagtttaaactgctacgatgtccattattgttgagggagcattttggagctcacgaaacactaatggctatcaagcaattaagatataattttaaaaataatgag.................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUACUCCCUAUAUACCUCUAUUUACAUAUAACAAUCUAAGUUUUUUUUGAAAACAAAUCUAAUUAAUUUUUAGUUUAAACUGCUACGAUGUCCAUUAUUGUUGAGGGAGCAUUUUGGAGCUCACGAAACACUAAUGGCUAUCAAGCAAUUAAGAUAUAAUUUUAAAAAUAAUGAG .........................................(((.(((((((((....((((..((((........))))..((((..((((.((((((.((((..(.((((........)))).)..)))).)))))).)))).))))....))))....))))))))).)))... (-30.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCAUUAUUUUUAAAAUUAUAUCUUAAUUGCUUGAUAGCCAUUAGUGUUUCGUGAGCUCCAAAAUGCUCCCUCAACAAUAAUGGACAUCGUAGCAGUUUAAACUAAAAAUUAAUUAGAUUUGUUUUCAAAAAAAACUUAGAUUGUUAUAUGUAAAUAGAGGUAUAUAGGGAGUAAUU ...(((((((((.....((((((((..((((..(((..((((((.((((..(.((((........)))).)..)))).))))))..))).((((((((((..((((.......))))....(((((.....))))).))))))))))...))))...))))))))..))))))))). (-37.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 928 130 81 221 172 NC_003454:FN1581|5end_DNA_mismatch_repair_protein_mutS_93231..93461_NEGATIVE 824 140 91 229 179 NC_003454:FN0054|5end_tyrosyl-tRNA_synthetase_690836..691066_POSITIVE 719 140 91 222 168 NC_003454:FN1142|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1791529..1791759_POSITIVE 636 147 101 219 175 NC_003454:FN1995|5end_hypothetical_protein_498245..498475_POSITIVE 610 150 101 215 163 NC_003454:FN1439|5end_Transcriptional_regulator,_DeoR_family_2106428..2106658_POSITIVE 610 150 101 111 59 NC_003454:FN1438|5end_hypothetical_protein_2106324..2106554_POSITIVE 587 130 84 218 169 NC_003454:FN1740|5end_ATP_synthase_subunit_K_238400..238630_NEGATIVE 475 130 81 191 142 NC_003454:FN1351|5end_15_kDa_lipoprotein_precursor_2003372..2003602_NEGATIVE 436 119 74 231 191 NC_003454:FN1731|5end_Anthranilate_synthase_component_II_231037..231267_NEGATIVE 427 130 81 226 181 NC_003454:FN1328|5end_Exodeoxyribonuclease_VII_small_subunit_1983129..1983359_NEGATIVE 317 111 81 230 200 NC_003454:FN1984|5end_Glutaredoxin-like_protein_485487..485717_POSITIVE 313 130 84 231 182 NC_003454:FN0186|5end_Cytochrome_c-type_biogenesis_protein_ccdA_810853..811083_POSITIVE 263 125 81 219 176 NC_003454:FN0220|5end_Autolysin_sensor_kinase_844934..845164_NEGATIVE 248 147 101 196 149 NC_003454:FN0053|5end_Branched-chain_amino_acid_transport_system_carrier_protein_689340..689570_POSITIVE 235 129 82 69 26 NC_003454:FN0077|5end_Ethanolamine_two-component_sensor_kinase_714704..714934_POSITIVE 232 123 82 65 19 NC_003454:FN0363|5end_ATP_synthase_C_chain,_sodium_ion_specific_993703..993933_NEGATIVE 225 125 91 90 47 NC_003454:FN1919|5end_Methyltransferase_415882..416112_NEGATIVE 215 45 1 124 79 NC_003454:FN0659|5end_ABC_transporter_permease_protein_1316391..1316621_NEGATIVE 210 126 81 54 8 NC_003454:FN0954|5end_Hypothetical_cytosolic_protein_1611616..1611846_NEGATIVE 209 140 95 89 43 NC_003454:FN0905|5end_hypothetical_protein_1564086..1564316_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 587 130 84 57 8 NC_003454:FN1741|3end_ATP_synthase_subunit_I_238561..238711_NEGATIVE 586 149 101 64 15 NC_003454:FN1259|3end_Uracil-DNA_glycosylase_1915756..1915906_POSITIVE 551 130 81 58 9 NC_003454:FN0828|3end_ABC_transporter_permease_protein_1489505..1489655_POSITIVE 475 130 81 57 8 NC_003454:FN1352|3end_ABC_transporter_ATP-binding_protein_2003506..2003656_NEGATIVE 401 147 101 71 25 NC_003454:FN1077|3end_hypothetical_protein_1723754..1723904_NEGATIVE 390 159 117 44 2 NC_003454:FN1329|3end_Methyltransferase_1983342..1983492_NEGATIVE 273 168 134 43 1 NC_003454:FN0053|3end_Branched-chain_amino_acid_transport_system_carrier_protein_690694..690844_POSITIVE 248 147 101 67 20 NC_003454:FN0052|3end_Arsenate_reductase_689291..689441_POSITIVE 239 149 133 17 1 NC_003454:FN0222|3end_Melibiose_carrier_protein_848238..848388_POSITIVE 235 129 82 69 26 NC_003454:FN0076|3end_Ethanolamine_two-component_response_regulator_714784..714934_POSITIVE 226 149 109 48 6 NC_003454:FN1260|3end_Sensory_Transduction_Protein_Kinase_1915863..1916013_NEGATIVE 225 125 91 93 50 NC_003454:FN1920|3end_tRNA_(5-methylaminomethyl-2-thiouridylate)_-methyltransferase_415879..416029_NEGATIVE 215 45 1 134 89 NC_003454:FN0660|3end_ABC_transporter_ATP-binding_protein_1316381..1316531_NEGATIVE 209 140 95 51 5 NC_003454:FN0906|3end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+]_1564124..1564274_NEGATIVE 207 47 3 151 101 NC_003454:FN0589|3end_Transcriptional_regulator,_MarR_family_1242833..1242983_POSITIVE 198 130 81 61 3 NC_003454:FN0104|3end_Acetyltransferase_739618..739768_NEGATIVE 193 139 92 123 59 NC_003454:FN0511|3end_D-lactate_dehydrogenase_1161372..1161522_POSITIVE 193 140 92 68 15 NC_003454:FN0344|3end_Methyltransferase_976622..976772_NEGATIVE 189 124 82 141 100 NC_003454:FN0751|3end_L-asparaginase_I_1409721..1409871_NEGATIVE 188 126 82 52 7 NC_003454:FN0025|3end_Hypothetical_exported_24-amino_acid_repeat_protein_664326..664476_POSITIVE