Origin IGS: gactatacctctttataaagataatactattatatcacaaaatagattcacaatatgatatgcggtacaattcaatggtatgtaagcactttaaaaaagagttattttgctctaaaaatggtataatgaaagaatgacagaaaggaattattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaataattcctttctgtcattctttcattataccatttttagagcaaaataactcttttttaaagtgcttacataccattgaattgtaccgcatatcatattgtgaatctattttgtgatataatagtattatctttataaagaggtatagtc Mask Tandem Repeat Region ================================================ gactatacctctttataaagataatactattatatcacaaaatagattcacaatatgatatgcggtacaattcaatggtatgtaagcactttaaaaaagagttattttgctctaaaaatggtataatgaaagaatgacagaaaggaattattt Find is-nt database================================================ Query_seq: SMT_588:SMT_589|SMT_588:SMT_589:hypothetical protein:hypothetical protein:<-->:505568..505720 153 gactatacctctttataaagataatactattatatcacaaaatagattcacaatatgatatgcggtacaattcaatggtatgtaagcactttaaaaaagagttattttgctctaaaaatggtataatgaaagaatgacagaaaggaattattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_588:SMT_589|SMT_588:SMT_589:hypothetical protein:hypothetical protein:<-->:505568..505720 153 gactatacctctttataaagataatactattatatcacaaaatagattcacaatatgatatgcggtacaattcaatggtatgtaagcactttaaaaaagagttattttgctctaaaaatggtataatgaaagaatgacagaaaggaattattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_588:SMT_589|SMT_588:SMT_589:hypothetical protein:hypothetical protein:<-->:505568..505720 153 gactatacctctttataaagataatactattatatcacaaaatagattcacaatatgatatgcggtacaattcaatggtatgtaagcactttaaaaaagagttattttgctctaaaaatggtataatgaaagaatgacagaaaggaattattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gactatacctctttataaagataatactattatatcacaaaatagattcacaatatgatatgcggtacaattcaatggtatgtaagcactttaaaaaagagttattttgctctaaaaatggtataatgaaagaatgacagaaaggaattattt Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 15 End: 134 .............. M K I I L L Y H K I D S Q Y D M R Y N S M V C K H F K K E L F C S K N G I M K E ................... Protein_Len: 38 Strand: - Start: 38 End: 151 ..................................... L I S E C Y S I R Y L E I T H L C K L F S N N Q E L F P I I F S H C F P I M .. gactatacctctttataaagataatactattatatcacaaaatagattcacaatatgatatgcggtacaattcaatggtatgtaagcactttaaaaaagagttattttgctctaaaaatggtataatgaaagaatgacagaaaggaattattt 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: 12 End: 41 ...........TTTGTGATATAATAGTATTATCTTTATAAA................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gactatacctctttataaagataatactattatatcacaaaatagattcacaatatgatatgcggtacaattcaatggtatgtaagcactttaaaaaagagttattttgctctaaaaatggtataatgaaagaatgacagaaaggaattattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_588:SMT_589|SMT_588:SMT_589:hypothetical protein:hypothetical protein:<-->:505568..505720 153 gactatacctctttataaagataatactattatatcacaaaatagattcacaatatgatatgcggtacaattcaatggtatgtaagcactttaaaaaagagttattttgctctaaaaatggtataatgaaagaatgacagaaaggaattattt Intra-Species Hit: Count: 1 Min: 1 Max: 153 Len: 153 Subject: smit_SMT_588_SMT_589|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[505568,505720]|153 HSP 1 e-value: 9.0E-82 bit: 303.0 Len: 153 Query Start:1 Query End:153 Subject Strand: POSITIVE Subject Start: 1 Subject End: 153 gactatacctctttataaagataatactattatatcacaaaatagattcacaatatgatatgcggtacaattcaatggtatgtaagcactttaaaaaagagttattttgctctaaaaatggtataatgaaagaatgacagaaaggaattattt gactatacctctttataaagataatactattatatcacaaaatagattcacaatatgatatgcggtacaattcaatggtatgtaagcactttaaaaaagagttattttgctctaaaaatggtataatgaaagaatgacagaaaggaattattt Inter-species Hit: Count: 3 Min: 2 Max: 153 Len: 152 Subject: NC_008533_SPD_1332_SPD_1333|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1348295,1348437]|143 HSP 1 e-value: 2.0E-15 bit: 83.8 Len: 74 Query Start:80 Query End:153 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 74 ...............................................................................atgtaagcactttaaaaaagagttattttgctctaaaaatggtataatgaaagaatgacagaaaggaattattt ...............................................................................atgtaagcactttaaaaaagagttattttgtttcaaaaatggtataatgagagaacaatagaaaggaagtattt HSP 2 e-value: 9.0E-8 bit: 58.0 Len: 41 Query Start:2 Query End:42 Subject Strand: NEGATIVE Subject Start: 102 Subject End: 142 .actatacctctttataaagataatactattatatcacaaaa............................................................................................................... .actatacctctgtgtaaagataagactattatatcacaaaa............................................................................................................... Subject: NC_003098_spr1357_spr1358|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1340764,1340906]|143 HSP 1 e-value: 2.0E-15 bit: 83.8 Len: 74 Query Start:80 Query End:153 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 74 ...............................................................................atgtaagcactttaaaaaagagttattttgctctaaaaatggtataatgaaagaatgacagaaaggaattattt ...............................................................................atgtaagcactttaaaaaagagttattttgtttcaaaaatggtataatgagagaacaatagaaaggaagtattt HSP 2 e-value: 9.0E-8 bit: 58.0 Len: 41 Query Start:2 Query End:42 Subject Strand: NEGATIVE Subject Start: 102 Subject End: 142 .actatacctctttataaagataatactattatatcacaaaa............................................................................................................... .actatacctctgtgtaaagataagactattatatcacaaaa............................................................................................................... Subject: NC_003028_SP_1505_SP_1506|membrane protein:hypothetical protein|NEGATIVE:POSITIVE|[1414844,1414986]|143 HSP 1 e-value: 2.0E-15 bit: 83.8 Len: 74 Query Start:80 Query End:153 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 74 ...............................................................................atgtaagcactttaaaaaagagttattttgctctaaaaatggtataatgaaagaatgacagaaaggaattattt ...............................................................................atgtaagcactttaaaaaagagttattttgtttcaaaaatggtataatgagagaacaatagaaaggaagtattt HSP 2 e-value: 9.0E-8 bit: 58.0 Len: 41 Query Start:2 Query End:42 Subject Strand: NEGATIVE Subject Start: 102 Subject End: 142 .actatacctctttataaagataatactattatatcacaaaa............................................................................................................... .actatacctctgtgtaaagataagactattatatcacaaaa............................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAUACCUCUUUAUAAAGAUAAUACUAUUAUAUCACAAAAUAGAUUCACAAUAUGAUAUGCGGUACAAUUCAAUGGUAUGUAAGCACUUUAAAAAAGAGUUAUUUUGCUCUAAAAAUGGUAUAAUGAAAGAAUGACAGAAAGGAAUUAUUU ..((((((......(((((......(((((.........)))))............((((((.((........)).)))))).....)))))....(((((......)))))......))))))............................ (-20.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAAUUCCUUUCUGUCAUUCUUUCAUUAUACCAUUUUUAGAGCAAAAUAACUCUUUUUUAAAGUGCUUACAUACCAUUGAAUUGUACCGCAUAUCAUAUUGUGAAUCUAUUUUGUGAUAUAAUAGUAUUAUCUUUAUAAAGAGGUAUAGU ..........................((((((((.(((((((((((...(((.......)))...)))))..........((...((((...((((((((..(((....)))..))))))))....))))..))....)))))))))))))) (-21.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 802 90 41 182 133 smit:SMT_588|5end_hypothetical_protein_505477..505707_NEGATIVE 254 110 63 58 14 smit:SMT_771|5end_spermidine/putrescine_transport_system_permease_protein_PotB_682183..682413_NEGATIVE 234 90 47 195 142 smit:SMT_153|5end_sensor_histidine_kinase,_putative_101443..101673_POSITIVE 229 145 113 231 190 smit:SMT_1055|5end_transcriptional_regulator,_GntR_family_994752..994982_NEGATIVE 229 145 107 220 173 smit:SMT_847|5end_thioredoxin_reductase_792800..793030_POSITIVE 217 128 81 228 185 smit:SMT_663|5end_phosphate_acetyltransferase_574990..575220_NEGATIVE 216 47 2 145 103 smit:SMT_1633|5end_formate--tetrahydrofolate_ligase_1619240..1619470_POSITIVE 213 145 107 48 1 smit:SMT_1534|5end_signal_peptidase_I_1517218..1517448_POSITIVE 213 133 96 57 22 smit:SMT_127|5end_transcriptional_regulator,_PadR_family_78563..78793_NEGATIVE 210 41 5 133 96 smit:SMT_1965|5end_hypothetical_protein_1897044..1897274_POSITIVE 210 41 5 133 96 smit:SMT_74|5end_hypothetical_protein_2197..2427_NEGATIVE 207 87 63 191 167 smit:SMT_630|5end_phosphoserine_phosphatase_535459..535689_POSITIVE 205 72 33 132 85 smit:SMT_1685|5end_phenylalanyl-tRNA_synthetase_alpha_chain_1668845..1669075_NEGATIVE 198 103 61 66 21 smit:SMT_1019|5end_K03295_cation_efflux_system_protein,_CDF_family_955672..955902_NEGATIVE 197 90 55 101 67 smit:SMT_1020|5end_transcriptional_regulator,_TetR_family_955755..955985_POSITIVE 196 107 61 223 161 smit:SMT_370|5end_acetyltransferase,_GNAT_family_304688..304918_POSITIVE 195 136 98 188 147 smit:SMT_1412|5end_hypothetical_protein_1395522..1395752_POSITIVE 194 146 109 184 136 smit:SMT_958|5end_hypothetical_protein_predicted_by_Glimmer/Critica_905052..905282_POSITIVE 190 99 56 88 53 smit:SMT_1137|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1079267..1079497_NEGATIVE 190 86 44 57 19 smit:SMT_864|5end_K07485_transposase_814322..814552_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 110 63 98 54 smit:SMT_772|3end_spermidine/putrescine_ABC_transporter,_ATP-binding_protein_682143..682293_NEGATIVE 207 87 63 132 108 smit:SMT_629|3end_glycogen_synthase_535480..535630_POSITIVE 191 85 41 151 104 smit:SMT_1801|3end_heavy_metal_translocating_P-type_ATPase_1775408..1775558_POSITIVE 190 99 56 86 51 smit:SMT_1138|3end_hypothetical_protein_1079269..1079419_NEGATIVE 190 86 44 102 64 smit:SMT_863|3end_K07485_transposase_814447..814597_POSITIVE 186 66 25 89 35 smit:SMT_331|3end_endo-beta-N-acetylglucosaminidase_271415..271565_POSITIVE 183 88 59 87 58 smit:SMT_870|3end_hypothetical_protein_817700..817850_NEGATIVE 182 86 46 83 41 smit:SMT_1787|3end_phosphoribosylformylglycinamidine_synthase_1763668..1763818_NEGATIVE 181 113 75 115 78 smit:SMT_739|3end_50S_ribosomal_protein_L7/L12_643274..643424_NEGATIVE 179 110 61 63 11 smit:SMT_1914|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1860324..1860474_POSITIVE 177 92 54 46 8 smit:SMT_790|3end_hypothetical_protein_701093..701243_NEGATIVE 176 88 62 107 82 smit:SMT_520|3end_glutathione_reductase_444881..445031_NEGATIVE 176 109 70 139 101 smit:SMT_228|3end_hypothetical_protein_165093..165243_POSITIVE 176 109 70 139 101 smit:SMT_224|3end_hypothetical_protein_159599..159749_POSITIVE 174 121 100 139 119 smit:SMT_2167|3end_hypothetical_protein_2040711..2040861_POSITIVE 174 121 100 139 119 smit:SMT_2162|3end_hypothetical_protein_2037508..2037658_POSITIVE 174 121 100 139 119 smit:SMT_2157|3end_hypothetical_protein_2031399..2031549_POSITIVE 174 91 60 62 31 smit:SMT_2023|3end_tryptophan_synthase,_alpha_subunit_1939997..1940147_POSITIVE 174 91 60 48 17 smit:SMT_2015|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1932839..1932989_POSITIVE 174 91 60 33 2 smit:SMT_2007|3end_hypothetical_protein_1928147..1928297_POSITIVE