Origin IGS: gtctttctatatgtagtttaccataaaactagaaccttttccgcaattttactattgaatcatctctaactcaatgaaacaaactgccttattacggcaaccaaaaacagaccttctttataagaaagcctgtttgttttacaaggagtcaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgactccttgtaaaacaaacaggctttcttataaagaaggtctgtttttggttgccgtaataaggcagtttgtttcattgagttagagatgattcaatagtaaaattgcggaaaaggttctagttttatggtaaactacatatagaaagac Mask Tandem Repeat Region ================================================ gtctttctatatgtagtttaccataaaactagaaccttttccgcaattttactattgaatcatctctaactcaatgaaacaaactgccttattacggcaaccaaaaacagaccttctttataagaaagcctgtttgttttacaaggagtcaa Find is-nt database================================================ Query_seq: SSA_1760:SSA_1761|SSA_1760:SSA_1761:hypothetical protein:Hemolysin (containing CBS domains), putative:<-<-:1747375..1747526 152 gtctttctatatgtagtttaccataaaactagaaccttttccgcaattttactattgaatcatctctaactcaatgaaacaaactgccttattacggcaaccaaaaacagaccttctttataagaaagcctgtttgttttacaaggagtcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1760:SSA_1761|SSA_1760:SSA_1761:hypothetical protein:Hemolysin (containing CBS domains), putative:<-<-:1747375..1747526 152 gtctttctatatgtagtttaccataaaactagaaccttttccgcaattttactattgaatcatctctaactcaatgaaacaaactgccttattacggcaaccaaaaacagaccttctttataagaaagcctgtttgttttacaaggagtcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1760:SSA_1761|SSA_1760:SSA_1761:hypothetical protein:Hemolysin (containing CBS domains), putative:<-<-:1747375..1747526 152 gtctttctatatgtagtttaccataaaactagaaccttttccgcaattttactattgaatcatctctaactcaatgaaacaaactgccttattacggcaaccaaaaacagaccttctttataagaaagcctgtttgttttacaaggagtcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtctttctatatgtagtttaccataaaactagaaccttttccgcaattttactattgaatcatctctaactcaatgaaacaaactgccttattacggcaaccaaaaacagaccttctttataagaaagcctgtttgttttacaaggagtcaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 59 End: 151 .......................................................... M I S N S M K Q T A L L R Q P K T D L L Y K K A C L F Y K E S . gtctttctatatgtagtttaccataaaactagaaccttttccgcaattttactattgaatcatctctaactcaatgaaacaaactgccttattacggcaaccaaaaacagaccttctttataagaaagcctgtttgttttacaaggagtcaa 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: 46 End: 75 .............................................ATTGAGTTAGAGATGATTCAATAGTAAAAT............................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtctttctatatgtagtttaccataaaactagaaccttttccgcaattttactattgaatcatctctaactcaatgaaacaaactgccttattacggcaaccaaaaacagaccttctttataagaaagcctgtttgttttacaaggagtcaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 74 HP_score: -5.7 Tail_Score: -4.64861 Start: 108 End: 132 Full_Region: TACGGCAACCAAAAA CAGACCTTCTT TAT AAGAAAGCCTG TTTGTTTTACAAGGA ...........................................................................................................CAGACCTTCTTTATAAGAAAGCCTG.................... Find igs database================================================ Query_seq: SSA_1760:SSA_1761|SSA_1760:SSA_1761:hypothetical protein:Hemolysin (containing CBS domains), putative:<-<-:1747375..1747526 152 gtctttctatatgtagtttaccataaaactagaaccttttccgcaattttactattgaatcatctctaactcaatgaaacaaactgccttattacggcaaccaaaaacagaccttctttataagaaagcctgtttgttttacaaggagtcaa Intra-Species Hit: Count: 1 Min: 1 Max: 152 Len: 152 Subject: NC_009009_SSA_1760_SSA_1761|hypothetical protein:Hemolysin (containing CBS domains), putative|NEGATIVE:NEGATIVE|[1747375,1747526]|152 HSP 1 e-value: 3.0E-81 bit: 301.0 Len: 152 Query Start:1 Query End:152 Subject Strand: POSITIVE Subject Start: 1 Subject End: 152 gtctttctatatgtagtttaccataaaactagaaccttttccgcaattttactattgaatcatctctaactcaatgaaacaaactgccttattacggcaaccaaaaacagaccttctttataagaaagcctgtttgttttacaaggagtcaa gtctttctatatgtagtttaccataaaactagaaccttttccgcaattttactattgaatcatctctaactcaatgaaacaaactgccttattacggcaaccaaaaacagaccttctttataagaaagcctgtttgttttacaaggagtcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCUUUCUAUAUGUAGUUUACCAUAAAACUAGAACCUUUUCCGCAAUUUUACUAUUGAAUCAUCUCUAACUCAAUGAAACAAACUGCCUUAUUACGGCAACCAAAAACAGACCUUCUUUAUAAGAAAGCCUGUUUGUUUUACAAGGAGUCAA ...........(.((((((......)))))).).....((((.((((......)))).................((((((....((((.......)))).....((((((.(.((((.....)))).).))))))))))))...)))).... (-23.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGACUCCUUGUAAAACAAACAGGCUUUCUUAUAAAGAAGGUCUGUUUUUGGUUGCCGUAAUAAGGCAGUUUGUUUCAUUGAGUUAGAGAUGAUUCAAUAGUAAAAUUGCGGAAAAGGUUCUAGUUUUAUGGUAAACUACAUAUAGAAAGAC ....((..(((((....(((((((((((((.....))))))))))))).((((((((((((....(((((((.....(((((((((....)))))))))....))))))).(((....))).....))))))).)))))..)))))..)).. (-40.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 843 130 81 221 172 NC_009009:SSA_1760|5end_hypothetical_protein_1747284..1747514_NEGATIVE 372 113 71 230 194 NC_009009:SSA_0222|5end_PTS_system,_mannose-specific_IID_component,_putative_217217..217447_POSITIVE 288 110 63 52 5 NC_009009:SSA_0879|5end_Cell_division_regulator,_negative_regulator_of_FtsZ_septation_ring_formation,_putative_873632..873862_POSITIVE 243 104 61 194 147 NC_009009:SSA_1179|5end_Carbamoylphosphate_synthase_large_subunit_/_biotin_carboxylase,_putative_1207806..1208036_NEGATIVE 240 150 102 168 126 NC_009009:SSA_1242|5end_Dihydroorotate_dehydrogenase_B,_putative_1267386..1267616_NEGATIVE 239 134 95 54 19 NC_009009:SSA_0087|5end_V-type_sodium_ATPase,_subunit_E,_putative_88329..88559_POSITIVE 237 129 84 209 168 NC_009009:SSA_0688|5end_2,3-bisphosphoglycerate-dependent_phosphoglycerate_mutase,_putative_671360..671590_POSITIVE 233 105 69 166 136 NC_009009:SSA_1332|5end_hypothetical_protein_1347645..1347875_NEGATIVE 232 136 94 162 113 NC_009009:SSA_1957|5end_Glycosyl_transferase_N-acetylglucosaminyltransferase,_putative_1954670..1954900_NEGATIVE 231 74 41 105 68 NC_009009:SSA_0171|5end_Cro-like_transcriptional_repressor,_XRE_family,_putative_168956..169186_NEGATIVE 228 134 95 191 157 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 227 130 84 70 16 NC_009009:SSA_0303|5end_surface_protein_C_296451..296681_POSITIVE 226 143 113 135 105 NC_009009:SSA_0956|5end_surface_protein_D_961223..961453_POSITIVE 224 105 71 35 4 NC_009009:SSA_1648|5end_hypothetical_protein_1647909..1648139_NEGATIVE 224 64 29 70 26 NC_009009:SSA_1367|5end_hypothetical_protein_1383593..1383823_POSITIVE 223 68 30 57 22 NC_009009:SSA_2358|5end_hypothetical_protein_2360497..2360727_NEGATIVE 223 110 62 51 5 NC_009009:SSA_1417|5end_SAM-dependent_methyltransferase,_putative_1427993..1428223_NEGATIVE 221 147 101 216 169 NC_009009:SSA_0744|5end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_726804..727034_NEGATIVE 219 74 32 179 135 NC_009009:SSA_1883|5end_hypothetical_protein_1882302..1882532_NEGATIVE 219 77 40 135 91 NC_009009:SSA_0523|5end_Aldehyde_dehydrogenase,_putative_521637..521867_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 128 84 59 25 NC_009009:SSA_0631|3end_Tryptophan_synthase_beta_chain,_putative_621133..621283_POSITIVE 239 134 95 43 8 NC_009009:SSA_0086|3end_V-type_sodium_ATPase,_subunit_K,_putative_88398..88548_POSITIVE 237 129 84 59 18 NC_009009:SSA_0687|3end_hypothetical_protein_671290..671440_POSITIVE 233 105 69 118 88 NC_009009:SSA_1333|3end_hypothetical_protein_1347693..1347843_NEGATIVE 230 141 103 87 45 NC_009009:SSA_2024|3end_hypothetical_protein_2029105..2029255_NEGATIVE 224 105 71 38 7 NC_009009:SSA_1649|3end_hypothetical_protein_1647906..1648056_NEGATIVE 219 77 40 128 84 NC_009009:SSA_0522|3end_Ethanolamine_utilization_protein,_putative_521710..521860_POSITIVE 217 124 85 77 33 NC_009009:SSA_0772|3end_Histidine-containing_phosphocarrier_protein_of_the_PTS,_putative_752681..752831_POSITIVE 212 68 21 101 41 NC_009009:SSA_0199|3end_GTP_cyclohydrolase_I,_putative_198910..199060_POSITIVE 210 44 3 119 86 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 208 148 112 59 20 NC_009009:SSA_2096|3end_ATP-dependent_protease,_ATP-binding_subunit,_putative_2099557..2099707_NEGATIVE 208 110 63 50 7 NC_009009:SSA_1751|3end_Dextran_glucosidase,_alpha_amylase_family,_putative_1738110..1738260_NEGATIVE 208 50 4 120 76 NC_009009:SSA_1353|3end_hypothetical_protein_1367974..1368124_NEGATIVE 206 66 28 123 87 NC_009009:SSA_2357|3end_50S_ribosomal_protein_L9,_putative_2357985..2358135_NEGATIVE 206 138 95 147 103 NC_009009:SSA_1243|3end_Dihydroorotate_dehydrogenase_electron_transfer_subunit,_putative_1267398..1267548_NEGATIVE 200 45 4 118 67 NC_009009:SSA_1332|3end_hypothetical_protein_1347217..1347367_NEGATIVE 199 130 84 57 12 NC_009009:SSA_0521|3end_Ethanolamine_utilization_protein_EutL,_putative_521131..521281_POSITIVE 198 63 21 77 32 NC_009009:SSA_1923|3end_NADPH-q_uinone_reductase_(modulator_of_drug_activity_B),_putative_1912120..1912270_NEGATIVE 198 115 86 64 29 NC_009009:SSA_0525|3end_Microcompartment_protein,_putative_523842..523992_POSITIVE 197 120 87 145 116 NC_009009:SSA_1745|3end_General_stress_response_protein_CsbD,_putative_1731997..1732147_NEGATIVE