Origin IGS: cttgcttcctccttagggatattataacagataattacagtaattacaaaatagaataatctttcgacttctcttatcttatttagaatacatcatgggattaagatattcgctaaacacatctcaaatgttaga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tctaacatttgagatgtgtttagcgaatatcttaatcccatgatgtattctaaataagataagagaagtcgaaagattattctattttgtaattactgtaattatctgttataatatccctaaggaggaagcaag Mask Tandem Repeat Region ================================================ cttgcttcctccttagggatattataacagataattacagtaattacaaaatagaataatctttcgacttctcttatcttatttagaatacatcatgggattaagatattcgctaaacacatctcaaatgttaga Find is-nt database================================================ Query_seq: SSA_1456:SSA_1457|SSA_1456:SSA_1457:hypothetical protein:Neopullulanase, putative:<-<-:1462440..1462574 135 cttgcttcctccttagggatattataacagataattacagtaattacaaaatagaataatctttcgacttctcttatcttatttagaatacatcatgggattaagatattcgctaaacacatctcaaatgttaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1456:SSA_1457|SSA_1456:SSA_1457:hypothetical protein:Neopullulanase, putative:<-<-:1462440..1462574 135 cttgcttcctccttagggatattataacagataattacagtaattacaaaatagaataatctttcgacttctcttatcttatttagaatacatcatgggattaagatattcgctaaacacatctcaaatgttaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1456:SSA_1457|SSA_1456:SSA_1457:hypothetical protein:Neopullulanase, putative:<-<-:1462440..1462574 135 cttgcttcctccttagggatattataacagataattacagtaattacaaaatagaataatctttcgacttctcttatcttatttagaatacatcatgggattaagatattcgctaaacacatctcaaatgttaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttgcttcctccttagggatattataacagataattacagtaattacaaaatagaataatctttcgacttctcttatcttatttagaatacatcatgggattaagatattcgctaaacacatctcaaatgttaga Predict ORF larger than 30AA ================================================ cttgcttcctccttagggatattataacagataattacagtaattacaaaatagaataatctttcgacttctcttatcttatttagaatacatcatgggattaagatattcgctaaacacatctcaaatgttaga 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: 90 Start: 21 End: 50 ....................TTTGTAATTACTGTAATTATCTGTTATAAT..................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttgcttcctccttagggatattataacagataattacagtaattacaaaatagaataatctttcgacttctcttatcttatttagaatacatcatgggattaagatattcgctaaacacatctcaaatgttaga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1456:SSA_1457|SSA_1456:SSA_1457:hypothetical protein:Neopullulanase, putative:<-<-:1462440..1462574 135 cttgcttcctccttagggatattataacagataattacagtaattacaaaatagaataatctttcgacttctcttatcttatttagaatacatcatgggattaagatattcgctaaacacatctcaaatgttaga Intra-Species Hit: Count: 1 Min: 1 Max: 135 Len: 135 Subject: NC_009009_SSA_1456_SSA_1457|hypothetical protein:Neopullulanase, putative|NEGATIVE:NEGATIVE|[1462440,1462574]|135 HSP 1 e-value: 4.0E-71 bit: 268.0 Len: 135 Query Start:1 Query End:135 Subject Strand: POSITIVE Subject Start: 1 Subject End: 135 cttgcttcctccttagggatattataacagataattacagtaattacaaaatagaataatctttcgacttctcttatcttatttagaatacatcatgggattaagatattcgctaaacacatctcaaatgttaga cttgcttcctccttagggatattataacagataattacagtaattacaaaatagaataatctttcgacttctcttatcttatttagaatacatcatgggattaagatattcgctaaacacatctcaaatgttaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGCUUCCUCCUUAGGGAUAUUAUAACAGAUAAUUACAGUAAUUACAAAAUAGAAUAAUCUUUCGACUUCUCUUAUCUUAUUUAGAAUACAUCAUGGGAUUAAGAUAUUCGCUAAACACAUCUCAAAUGUUAGA .....(((((....))))).....(((((..((((((...)))))).......(((((.((((......((((.......................))))..))))))))).................))))).. (-12.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAACAUUUGAGAUGUGUUUAGCGAAUAUCUUAAUCCCAUGAUGUAUUCUAAAUAAGAUAAGAGAAGUCGAAAGAUUAUUCUAUUUUGUAAUUACUGUAAUUAUCUGUUAUAAUAUCCCUAAGGAGGAAGCAAG ........(((((((((.........)))))))))........(((.((((..((((((((.(((.((((....)))).)))))))))))......((((((.....))))))............)))).))).. (-24.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 769 130 81 221 172 NC_009009:SSA_1456|5end_hypothetical_protein_1462349..1462579_NEGATIVE 254 48 6 141 95 NC_009009:SSA_1085|5end_Dihydrodipicolinate_reductase,_putative_1102564..1102794_POSITIVE 248 42 3 114 69 NC_009009:SSA_1254|5end_hypothetical_protein_1281484..1281714_NEGATIVE 245 41 7 124 98 NC_009009:SSA_2243|5end_Conserved_uncharacterized_protein_2239341..2239571_NEGATIVE 227 79 51 118 90 NC_009009:SSA_0751|5end_Oligoendopeptidase_F,_putative_732367..732597_POSITIVE 225 43 2 137 91 NC_009009:SSA_0615|5end_RggD,_putative_609195..609425_NEGATIVE 224 126 97 191 165 NC_009009:SSA_0682|5end_Conserved_uncharacterized_protein_663438..663668_POSITIVE 223 101 61 184 141 NC_009009:SSA_2302|5end_Type_IV_fimbrial_biogenesis_protein,_prepilin_cysteine_protease_(C20)_PilD,_putative_2304044..2304274_NEGATIVE 220 123 85 159 122 NC_009009:SSA_1412|5end_hypothetical_protein_1424095..1424325_NEGATIVE 216 100 55 120 80 NC_009009:SSA_0758|5end_Ornithine_acetyltransferase_/_amino-acid_acetyltransferase,_putative_740636..740866_POSITIVE 213 96 55 119 71 NC_009009:SSA_1849|5end_Primosomal_protein_N',_putative_1845649..1845879_NEGATIVE 209 125 83 135 96 NC_009009:SSA_1766|5end_Bacitracin_ABC_transporter,_permease_protein,_putative_1755131..1755361_NEGATIVE 207 103 68 129 95 NC_009009:SSA_0955|5end_Aminopeptidase_N,_putative_958519..958749_POSITIVE 196 97 62 95 64 NC_009009:SSA_2230|5end_Ribonucleotide_reductase,_class_III,_anaerobic,_putative_2231158..2231388_NEGATIVE 194 18 1 23 3 NC_009009:SSA_0882|5end_Phosphoserine_phosphatase,_putative_876903..877133_POSITIVE 194 120 71 159 98 NC_009009:SSA_0398|5end_hypothetical_protein_396452..396682_NEGATIVE 193 34 5 128 96 NC_009009:SSA_0584|5end_hypothetical_protein_575806..576036_POSITIVE 189 76 38 108 61 NC_009009:SSA_1411|5end_Glucose-1-phosphate_thymidylytransferase,_putative_1423960..1424190_NEGATIVE 189 23 4 164 144 NC_009009:SSA_0924|5end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_933738..933968_POSITIVE 188 127 92 182 145 NC_009009:SSA_0978|5end_hypothetical_protein_983736..983966_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 254 48 6 100 54 NC_009009:SSA_1084|3end_Conserved_uncharacterized_protein_1102603..1102753_POSITIVE 248 42 3 142 97 NC_009009:SSA_1255|3end_hypothetical_protein_1281456..1281606_NEGATIVE 223 101 61 115 72 NC_009009:SSA_2303|3end_hypothetical_protein_2304113..2304263_NEGATIVE 216 100 55 102 62 NC_009009:SSA_0757|3end_N-acetyl-gamma-glutamyl-phosphate_reductase,_putative_740698..740848_POSITIVE 213 96 55 58 10 NC_009009:SSA_1850|3end_DNA-directed_RNA_polymerase,_subunit_K/omega,_putative_1845710..1845860_NEGATIVE 209 125 83 116 77 NC_009009:SSA_1767|3end_Bacitracin_ABC_transporter,_ATP-binding_protein,_putative_1755150..1755300_NEGATIVE 204 86 46 98 53 NC_009009:SSA_1939|3end_Acyl_carrier_protein,_putative_1925875..1926025_NEGATIVE 201 74 35 81 46 NC_009009:SSA_1027|3end_hypothetical_protein_1045244..1045394_POSITIVE 201 56 14 143 103 NC_009009:SSA_0642|3end_Type_4_prepilin_peptidase,_putative_629391..629541_NEGATIVE 196 31 1 133 98 NC_009009:SSA_2014|3end_D-alanyl-D-alanine_carboxypeptidase,_putative_2014019..2014169_NEGATIVE 194 120 71 141 80 NC_009009:SSA_0400|3end_hypothetical_protein_396470..396620_NEGATIVE 192 101 62 116 69 NC_009009:SSA_1861|3end_Aminopeptidase_C,_putative_1856568..1856718_NEGATIVE 192 106 64 43 5 NC_009009:SSA_0808|3end_hypothetical_protein_791012..791162_POSITIVE 192 42 1 88 46 NC_009009:SSA_0392|3end_hypothetical_protein_388303..388453_POSITIVE 189 76 38 74 27 NC_009009:SSA_1412|3end_hypothetical_protein_1423994..1424144_NEGATIVE 189 23 4 44 24 NC_009009:SSA_0923|3end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933698..933848_POSITIVE 187 81 60 133 110 NC_009009:SSA_1256|3end_NAD-dependent_deacetylase,_putative_1282357..1282507_NEGATIVE 187 114 71 115 71 NC_009009:SSA_0533|3end_Glycerol_dehydratase_large_subunit_pduC,_putative_530711..530861_POSITIVE 187 43 2 110 69 NC_009009:SSA_0045|3end_hypothetical_protein_50949..51099_POSITIVE 186 99 66 148 115 NC_009009:SSA_2239|3end_Conserved_uncharacterized_cytosolic_protein_2236922..2237072_NEGATIVE