Origin IGS: tataaaaaattataccaaaaaaagggccatttggcacctgcaaacatgggataattttcaaactcaagaacactacttgtcttaaaaatcccatcaaatagagcatcctatcctactgattctttgaaaatggtgaagaaataagaaaaaattgagagaagaaatctttgcatcttccttctctcaacttgcagtttact .........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 agtaaactgcaagttgagagaaggaagatgcaaagatttcttctctcaattttttcttatttcttcaccattttcaaagaatcagtaggataggatgctctatttgatgggatttttaagacaagtagtgttcttgagtttgaaaattatcccatgtttgcaggtgccaaatggccctttttttggtataattttttata Mask Tandem Repeat Region ================================================ tataaaaaattataccaaaaaaagggccatttggcacctgcaaacatgggataattttcaaactcaagaacactacttgtcttaaaaatcccatcaaatagagcatcctatcctactgattctttgaaaatggtgaagaaataagaaaaaattgagagaagaaatctttgcatcttccttctctcaacttgcagtttact Find is-nt database================================================ Query_seq: SMT_1162:SMT_1163|SMT_1162:SMT_1163:ATP-dependent DNA helicase:hypothetical protein:<-<-:1108986..1109185 200 tataaaaaattataccaaaaaaagggccatttggcacctgcaaacatgggataattttcaaactcaagaacactacttgtcttaaaaatcccatcaaatagagcatcctatcctactgattctttgaaaatggtgaagaaataagaaaaaattgagagaagaaatctttgcatcttccttctctcaacttgcagtttact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1162:SMT_1163|SMT_1162:SMT_1163:ATP-dependent DNA helicase:hypothetical protein:<-<-:1108986..1109185 200 tataaaaaattataccaaaaaaagggccatttggcacctgcaaacatgggataattttcaaactcaagaacactacttgtcttaaaaatcccatcaaatagagcatcctatcctactgattctttgaaaatggtgaagaaataagaaaaaattgagagaagaaatctttgcatcttccttctctcaacttgcagtttact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1162:SMT_1163|SMT_1162:SMT_1163:ATP-dependent DNA helicase:hypothetical protein:<-<-:1108986..1109185 200 tataaaaaattataccaaaaaaagggccatttggcacctgcaaacatgggataattttcaaactcaagaacactacttgtcttaaaaatcccatcaaatagagcatcctatcctactgattctttgaaaatggtgaagaaataagaaaaaattgagagaagaaatctttgcatcttccttctctcaacttgcagtttact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tataaaaaattataccaaaaaaagggccatttggcacctgcaaacatgggataattttcaaactcaagaacactacttgtcttaaaaatcccatcaaatagagcatcctatcctactgattctttgaaaatggtgaagaaataagaaaaaattgagagaagaaatctttgcatcttccttctctcaacttgcagtttact Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 9 End: 98 ........ M I P K K G P F G T C K H G I I F K L K N T T C L K N P I K ...................................................................................................... Protein_Len: 35 Strand: - Start: 2 End: 106 . Y F I I G F F P G N P V Q L C P I I K L S L F V V Q R L F G M L Y L M .............................................................................................. tataaaaaattataccaaaaaaagggccatttggcacctgcaaacatgggataattttcaaactcaagaacactacttgtcttaaaaatcccatcaaatagagcatcctatcctactgattctttgaaaatggtgaagaaataagaaaaaattgagagaagaaatctttgcatcttccttctctcaacttgcagtttact 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: 88 Start: 9 End: 38 ........GGTGCCAAATGGCCCTTTTTTTGGTATAAT.................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tataaaaaattataccaaaaaaagggccatttggcacctgcaaacatgggataattttcaaactcaagaacactacttgtcttaaaaatcccatcaaatagagcatcctatcctactgattctttgaaaatggtgaagaaataagaaaaaattgagagaagaaatctttgcatcttccttctctcaacttgcagtttact Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 79 HP_score: -3.7 Tail_Score: -5.59357 Start: 24 End: 37 Full_Region: atcccatgtttgcag gtgcc aaat ggccc tttttttggtataat .......................gtgccaaatggccc................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_1162:SMT_1163|SMT_1162:SMT_1163:ATP-dependent DNA helicase:hypothetical protein:<-<-:1108986..1109185 200 tataaaaaattataccaaaaaaagggccatttggcacctgcaaacatgggataattttcaaactcaagaacactacttgtcttaaaaatcccatcaaatagagcatcctatcctactgattctttgaaaatggtgaagaaataagaaaaaattgagagaagaaatctttgcatcttccttctctcaacttgcagtttact Intra-Species Hit: Count: 1 Min: 1 Max: 200 Len: 200 Subject: smit_SMT_1162_SMT_1163|ATP-dependent DNA helicase:hypothetical protein|NEGATIVE:NEGATIVE|[1108986,1109185]|200 HSP 1 e-value: 4.0E-97 bit: 355.0 Len: 200 Query Start:1 Query End:200 Subject Strand: POSITIVE Subject Start: 1 Subject End: 200 tataaaaaattataccnnnnnnngggccatttggcacctgcaaacatgggataattttcaaactcaagaacactacttgtcttaaaaatcccatcaaatagagcatcctatcctactgattctttgaaaatggtgaagaaataagaaaaaattgagagaagaaatctttgcatcttccttctctcaacttgcagtttact tataaaaaattataccaaaaaaagggccatttggcacctgcaaacatgggataattttcaaactcaagaacactacttgtcttaaaaatcccatcaaatagagcatcctatcctactgattctttgaaaatggtgaagaaataagaaaaaattgagagaagaaatctttgcatcttccttctctcaacttgcagtttact Inter-species Hit: Count: 3 Min: 1 Max: 188 Len: 188 Subject: NC_008533_SPD_0704_SPD_0705|hypothetical protein:DnaQ family exonuclease/DinG family helicase, putative|POSITIVE:POSITIVE|[718212,718410]|199 HSP 1 e-value: 6.0E-59 bit: 228.0 Len: 188 Query Start:1 Query End:188 Subject Strand: NEGATIVE Subject Start: 13 Subject End: 199 tataaaaaattataccnnnnnnngggccatttggcacctgcaaacatgggataattttcaaactcaagaacactacttgtcttaaaaatcccatcaaatagagcatcctatcctactgattctttgaaaatggtgaagaaataagaaaaaattgagagaagaaatctttgcatcttccttctctcaac............ tataaaaaattataccaaaaaaagggccatttggcacctgcaaacataggataattttcaaactcaagaacactacttttcttaaaaatcccatcgaatagagcattctagcctgctgatttttttaaaatagtgaagaaatacg-aaaaattgagagaagaaatgtttgcatcttccttctctcaac............ Subject: NC_003098_spr0710_spr0711|hypothetical protein:ATP-dependent DNA helicase|POSITIVE:POSITIVE|[710681,710879]|199 HSP 1 e-value: 6.0E-59 bit: 228.0 Len: 188 Query Start:1 Query End:188 Subject Strand: NEGATIVE Subject Start: 13 Subject End: 199 tataaaaaattataccnnnnnnngggccatttggcacctgcaaacatgggataattttcaaactcaagaacactacttgtcttaaaaatcccatcaaatagagcatcctatcctactgattctttgaaaatggtgaagaaataagaaaaaattgagagaagaaatctttgcatcttccttctctcaac............ tataaaaaattataccaaaaaaagggccatttggcacctgcaaacataggataattttcaaactcaagaacactacttttcttaaaaatcccatcgaatagagcattctagcctgctgatttttttaaaatagtgaagaaatacg-aaaaattgagagaagaaatgtttgcatcttccttctctcaac............ Subject: NC_003028_SP_0801_SP_0802|hypothetical protein:ATP-dependent DNA helicase|POSITIVE:POSITIVE|[755351,755549]|199 HSP 1 e-value: 1.0E-56 bit: 220.0 Len: 188 Query Start:1 Query End:188 Subject Strand: NEGATIVE Subject Start: 13 Subject End: 199 tataaaaaattataccnnnnnnngggccatttggcacctgcaaacatgggataattttcaaactcaagaacactacttgtcttaaaaatcccatcaaatagagcatcctatcctactgattctttgaaaatggtgaagaaataagaaaaaattgagagaagaaatctttgcatcttccttctctcaac............ tataaaaaattataccaaaaaaagggccatttggcacctgcaaacataggataattttcaaactcaagaacactacttttcttaaaaatcccatcgaatagagcattctagcctgctgatttttgtaaaatagtgaagaaatacg-aaaaattgagagaagaaatgtttgcatcttccttctctcaac............ Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAAAAAUUAUACCAAAAAAAGGGCCAUUUGGCACCUGCAAACAUGGGAUAAUUUUCAAACUCAAGAACACUACUUGUCUUAAAAAUCCCAUCAAAUAGAGCAUCCUAUCCUACUGAUUCUUUGAAAAUGGUGAAGAAAUAAGAAAAAAUUGAGAGAAGAAAUCUUUGCAUCUUCCUUCUCUCAAC ............(((((.....((((((....))).)))......(((((((..((((......((((.......))))....)))))))))))....(((((.(((..........))).)))))....)))))................((((((((((................)))))))))). (-36.49) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUGAGAGAAGGAAGAUGCAAAGAUUUCUUCUCUCAAUUUUUUCUUAUUUCUUCACCAUUUUCAAAGAAUCAGUAGGAUAGGAUGCUCUAUUUGAUGGGAUUUUUAAGACAAGUAGUGUUCUUGAGUUUGAAAAUUAUCCCAUGUUUGCAGGUGCCAAAUGGCCCUUUUUUUGGUAUAAUUUUUUAUA ((((((((((((((..(....)..)))))))))))))).....((((......(((.((((((.(((((((.((..((((((....))))))..))..)))))))..)).)))).)))....))))...(((((((((.(((.......(((.(((....)))))).....))).))))))))).... (-47.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 871 70 21 161 112 smit:SMT_1162|5end_ATP-dependent_DNA_helicase_1108895..1109125_NEGATIVE 287 64 24 169 118 smit:SMT_1612|5end_K06024_segregation_and_condensation_protein_B_1600052..1600282_POSITIVE 287 59 11 124 84 smit:SMT_1223|5end_pneumococcal_surface_protein_A_1187780..1188010_NEGATIVE 281 68 25 88 44 smit:SMT_1322|5end_K02075_zinc/manganese_transport_system_permease_protein_1291371..1291601_POSITIVE 274 59 26 104 69 smit:SMT_1947|5end_lysine_decarboxylase_1883113..1883343_NEGATIVE 271 68 26 118 74 smit:SMT_479|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416656..416886_NEGATIVE 271 68 26 118 74 smit:SMT_462|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_401658..401888_NEGATIVE 267 140 91 126 88 smit:SMT_600|5end_ADP-ribose_pyrophosphatase_516307..516537_POSITIVE 264 110 63 81 28 smit:SMT_1184|5end_phosphotransferase_system,_mannose/fructose/N-acetylgalactosamine-specific_component_IIB_1142037..1142267_NEGATIVE 262 49 9 161 125 smit:SMT_1485|5end_exodeoxyribonuclease_1465825..1466055_NEGATIVE 254 50 9 167 121 smit:SMT_773|5end_UDP-N-acetylenolpyruvoylglucosamine_reductase_684365..684595_NEGATIVE 254 51 15 227 189 smit:SMT_219|5end_phosphatidate_cytidylyltransferase_150922..151152_POSITIVE 253 49 23 211 181 smit:SMT_1542|5end_phosphomevalonate_kinase_1527084..1527314_NEGATIVE 251 118 72 122 67 smit:SMT_1870|5end_K07566_putative_translation_factor_1829819..1830049_NEGATIVE 246 50 24 106 75 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 244 70 24 100 55 smit:SMT_1791|5end_hypothetical_protein_1765907..1766137_POSITIVE 244 66 24 90 34 smit:SMT_397|5end_NAD(+)_synthetase_326519..326749_POSITIVE 241 69 22 62 19 smit:SMT_1796|5end_dihydroorotate_dehydrogenase_A_1770816..1771046_NEGATIVE 237 45 9 157 120 smit:SMT_692|5end_hypothetical_protein_603550..603780_NEGATIVE 235 119 71 50 5 smit:SMT_974|5end_DNA-binding_response_regulator_922847..923077_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 287 64 24 150 99 smit:SMT_1611|3end_K05896_segregation_and_condensation_protein_A_1600113..1600263_POSITIVE 281 68 25 95 51 smit:SMT_1321|3end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1291458..1291608_POSITIVE 279 68 23 145 87 smit:SMT_1489|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1470714..1470864_POSITIVE 267 140 91 116 78 smit:SMT_599|3end_glucosamine-1-phosphate_N-acetyltransferase_/_UDP-N-acetylglucosamine_pyrophosphorylase_516377..516527_POSITIVE 264 110 63 84 31 smit:SMT_1185|3end_beta-galactosidase_1142034..1142184_NEGATIVE 254 50 9 53 7 smit:SMT_774|3end_hypothetical_protein_684479..684629_NEGATIVE 251 118 72 138 83 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 246 49 23 57 24 smit:SMT_218|3end_undecaprenyl_pyrophosphate_synthetase_150993..151143_POSITIVE 244 66 24 93 37 smit:SMT_396|3end_putative_nicotinate_phosphoribosyltransferase_326602..326752_POSITIVE 232 53 23 90 63 smit:SMT_914|3end_sucrose-6-phosphate_hydrolase_867673..867823_POSITIVE 229 49 25 140 116 smit:SMT_1847|3end_hypothetical_protein_1812697..1812847_POSITIVE 226 68 22 95 43 smit:SMT_1853|3end_1,4-alpha-glucan_branching_enzyme_1817687..1817837_NEGATIVE 225 53 12 68 19 smit:SMT_520|3end_glutathione_reductase_444881..445031_NEGATIVE 223 117 72 60 13 smit:SMT_1172|3end_hypothetical_protein_1119344..1119494_NEGATIVE 220 49 23 119 95 smit:SMT_1476|3end_thiol_peroxidase_1458728..1458878_NEGATIVE 220 125 87 58 18 smit:SMT_726|3end_ImpB/MucB/SamB_family_protein_630412..630562_NEGATIVE 217 50 22 61 33 smit:SMT_1879|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836567..1836717_NEGATIVE 217 46 20 73 49 smit:SMT_1210|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1170959..1171109_NEGATIVE 216 70 24 44 4 smit:SMT_1747|3end_anthranilate_synthase_component_I_1726832..1726982_POSITIVE 215 60 16 88 41 smit:SMT_1934|3end_homoserine_dehydrogenase_1873150..1873300_POSITIVE