Origin IGS: tagcaatagaataggctaaatgaaacttaatctttagctttctaatacacaaaaacgataacttcttgtttggaagttatcgtttttgctgtcttttaggagaacaaatatagaaacaagattgatcta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tagatcaatcttgtttctatatttgttctcctaaaagacagcaaaaacgataacttccaaacaagaagttatcgtttttgtgtattagaaagctaaagattaagtttcatttagcctattctattgcta Mask Tandem Repeat Region ================================================ tagcaatagaataggctaaatgaaacttaatctttagctttctaatacacaaaaacgataacttcttgtttggaagttatcgtttttgctgtcttttaggagaacaaatatagaaacaagattgatcta Find is-nt database================================================ Query_seq: SSA_0613:SSA_0614|SSA_0613:SSA_0614:Glucosyltransferase, putative:Transporter, putative:-><-:606694..606822 129 tagcaatagaataggctaaatgaaacttaatctttagctttctaatacacaaaaacgataacttcttgtttggaagttatcgtttttgctgtcttttaggagaacaaatatagaaacaagattgatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0613:SSA_0614|SSA_0613:SSA_0614:Glucosyltransferase, putative:Transporter, putative:-><-:606694..606822 129 tagcaatagaataggctaaatgaaacttaatctttagctttctaatacacaaaaacgataacttcttgtttggaagttatcgtttttgctgtcttttaggagaacaaatatagaaacaagattgatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0613:SSA_0614|SSA_0613:SSA_0614:Glucosyltransferase, putative:Transporter, putative:-><-:606694..606822 129 tagcaatagaataggctaaatgaaacttaatctttagctttctaatacacaaaaacgataacttcttgtttggaagttatcgtttttgctgtcttttaggagaacaaatatagaaacaagattgatcta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagcaatagaataggctaaatgaaacttaatctttagctttctaatacacaaaaacgataacttcttgtttggaagttatcgtttttgctgtcttttaggagaacaaatatagaaacaagattgatcta Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 37 End: 126 .................................... S E L V C F R Y S R T Q F N D N K S D K L L V F I S V L N M ... tagcaatagaataggctaaatgaaacttaatctttagctttctaatacacaaaaacgataacttcttgtttggaagttatcgtttttgctgtcttttaggagaacaaatatagaaacaagattgatcta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagcaatagaataggctaaatgaaacttaatctttagctttctaatacacaaaaacgataacttcttgtttggaagttatcgtttttgctgtcttttaggagaacaaatatagaaacaagattgatcta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -11.7 Tail_Score: -4.07568 Start: 46 End: 93 Full_Region: TCTTTAGCTTTCTAA TACACAAAAACGATAACTTCT TGTTT GGAAGTTATCGTTTTTGCTGTC TTTTAGGAGAACAAA .............................................TACACAAAAACGATAACTTCTTGTTTGGAAGTTATCGTTTTTGCTGTC.................................... TransTerm Strand: - Conf: 100 HP_score: -13.6 Tail_Score: -3.02511 Start: 48 End: 91 Full_Region: tgttctcctaaaaga cagcaaaaacgataacttc caaacaa gaagttatcgtttttgtg tattagaaagctaaa ...............................................cagcaaaaacgataacttccaaacaagaagttatcgtttttgtg...................................... TransTerm Strand: + Conf: 100 HP_score: -10.3 Tail_Score: -4.91573 Start: 56 End: 82 Full_Region: TCTAATACACAAAAA CGATAACTTCT TGTTT GGAAGTTATCG TTTTTGCTGTCTTTT .......................................................CGATAACTTCTTGTTTGGAAGTTATCG............................................... TransTerm Strand: - Conf: 100 HP_score: -9.6 Tail_Score: -5.10064 Start: 56 End: 82 Full_Region: aaaagacagcaaaaa cgataacttc caaacaa gaagttatcg tttttgtgtattaga .......................................................cgataacttccaaacaagaagttatcg............................................... Find igs database================================================ Query_seq: SSA_0613:SSA_0614|SSA_0613:SSA_0614:Glucosyltransferase, putative:Transporter, putative:-><-:606694..606822 129 tagcaatagaataggctaaatgaaacttaatctttagctttctaatacacaaaaacgataacttcttgtttggaagttatcgtttttgctgtcttttaggagaacaaatatagaaacaagattgatcta Intra-Species Hit: Count: 1 Min: 1 Max: 129 Len: 129 Subject: NC_009009_SSA_0613_SSA_0614|Glucosyltransferase, putative:Transporter, putative|POSITIVE:NEGATIVE|[606694,606822]|129 HSP 1 e-value: 2.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 tagcaatagaataggctaaatgaaacttaatctttagctttctaatacacaaaaacgataacttcttgtttggaagttatcgtttttgctgtcttttaggagaacaaatatagaaacaagattgatcta tagcaatagaataggctaaatgaaacttaatctttagctttctaatacacaaaaacgataacttcttgtttggaagttatcgtttttgctgtcttttaggagaacaaatatagaaacaagattgatcta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGCAAUAGAAUAGGCUAAAUGAAACUUAAUCUUUAGCUUUCUAAUACACAAAAACGAUAACUUCUUGUUUGGAAGUUAUCGUUUUUGCUGUCUUUUAGGAGAACAAAUAUAGAAACAAGAUUGAUCUA ......((((...(((((((.((.......)))))))))((((((.((((((((((((((((((((.....))))))))))))))))).)))...))))))........................)))) (-34.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAUCAAUCUUGUUUCUAUAUUUGUUCUCCUAAAAGACAGCAAAAACGAUAACUUCCAAACAAGAAGUUAUCGUUUUUGUGUAUUAGAAAGCUAAAGAUUAAGUUUCAUUUAGCCUAUUCUAUUGCUA .(((.(((...(((....))).))).)))...........(((((((((((((((((.......)))))))))))))))))(((.(((((.((((((((.......)).))))))...))))).))).. (-33.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 315 100 56 85 45 NC_009009:SSA_0623|5end_hypothetical_protein_614512..614742_POSITIVE 285 97 52 85 41 NC_009009:SSA_0257|5end_N-acetylmuramidase/lysin,_putative_248878..249108_POSITIVE 266 97 57 120 74 NC_009009:SSA_2193|5end_ADP-ribose_pyrophosphatase,_putative_2194793..2195023_NEGATIVE 263 99 56 145 97 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 258 92 51 201 154 NC_009009:SSA_0913|5end_Acetyltransferase,_putative_924195..924425_POSITIVE 257 96 57 112 67 NC_009009:SSA_0256|5end_Metalloregulator_ScaR_(Fe/Mn-dependent_transcriptional_repressor),_putative_248699..248929_NEGATIVE 248 101 64 116 73 NC_009009:SSA_0570|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A,_putative_563915..564145_POSITIVE 244 45 2 55 8 NC_009009:SSA_0927|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_936049..936279_POSITIVE 241 120 79 52 21 NC_009009:SSA_0792|5end_hypothetical_protein_774618..774848_POSITIVE 232 101 63 113 77 NC_009009:SSA_1646|5end_hypothetical_protein_1646771..1647001_NEGATIVE 232 110 66 129 73 NC_009009:SSA_1073|5end_Gamma-glutamyl_phosphate_reductase,_putative_1090886..1091116_POSITIVE 230 97 62 149 101 NC_009009:SSA_2201|5end_hypothetical_protein_2201807..2202037_POSITIVE 230 106 76 191 158 NC_009009:SSA_1868|5end_ABC-type_arginine/histidine_transport_system,_permease_component,_putative_1863902..1864132_NEGATIVE 227 97 56 87 46 NC_009009:SSA_1791|5end_Acylphosphatase,_putative_1773676..1773906_POSITIVE 226 100 56 178 128 NC_009009:SSA_0032|5end_Phosphoribosylformylglycinamidine_cyclo-ligase,_putative_37938..38168_POSITIVE 225 103 62 40 4 NC_009009:SSA_0188|5end_hypothetical_protein_190798..191028_POSITIVE 223 104 62 148 101 NC_009009:SSA_0694|5end_Mutator_protein,_putative_677730..677960_POSITIVE 220 89 54 191 151 NC_009009:SSA_1344|5end_Xanthine/uracil_permeases,_putative_1363352..1363582_NEGATIVE 219 101 64 196 163 NC_009009:SSA_0789|5end_Proton-translocating_ATPase,_F1_sector,_epsilon_subunit,_putative_772451..772681_POSITIVE 218 92 56 164 129 NC_009009:SSA_2054|5end_hypothetical_protein_2057899..2058129_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 88 50 41 3 NC_009009:SSA_0613|3end_Glucosyltransferase,_putative_606633..606783_POSITIVE 266 97 57 65 19 NC_009009:SSA_2194|3end_Nicotinamide_mononucleotide_transporter,_putative_2194848..2194998_NEGATIVE 263 99 56 144 96 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 248 101 64 116 73 NC_009009:SSA_0569|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563995..564145_POSITIVE 241 103 62 125 81 NC_009009:SSA_0819|3end_hypothetical_protein_801181..801331_POSITIVE 241 120 79 59 28 NC_009009:SSA_0791|3end_UDP-N-acetylglucosamine-like_protein,_putative_774705..774855_POSITIVE 239 104 65 132 83 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 233 100 58 136 93 NC_009009:SSA_2260|3end_DNA_mismatch_repair_protein_hexA,_putative_2255601..2255751_NEGATIVE 232 101 63 62 26 NC_009009:SSA_1647|3end_hypothetical_protein_1646822..1646972_NEGATIVE 232 73 31 132 87 NC_009009:SSA_1111|3end_Branched-chain_amino_acid_transport_system_II_carrier_protein,_putative_1137940..1138090_POSITIVE 232 110 66 107 51 NC_009009:SSA_1072|3end_Glutamate_5-kinase,_putative_1090944..1091094_POSITIVE 226 100 56 118 68 NC_009009:SSA_0031|3end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_37958..38108_POSITIVE 223 100 51 97 54 NC_009009:SSA_0052|3end_Transcriptional_regulator,_GntR_family,_putative_55942..56092_NEGATIVE 221 97 51 123 66 NC_009009:SSA_0705|3end_hypothetical_protein_690552..690702_NEGATIVE 218 92 56 127 92 NC_009009:SSA_2055|3end_hypothetical_protein_2057936..2058086_NEGATIVE 218 100 51 108 49 NC_009009:SSA_1525|3end_Lyzozyme_M1_(1,4-beta-N-acetylmuramidase),_putative_1533683..1533833_POSITIVE 217 100 61 129 75 NC_009009:SSA_0164|3end_hypothetical_protein_163997..164147_POSITIVE 215 100 62 123 82 NC_009009:SSA_0836|3end_SecA-like_protein,_putative_823969..824119_POSITIVE 214 100 55 127 70 NC_009009:SSA_2324|3end_hypothetical_protein_2328847..2328997_NEGATIVE 213 105 65 138 90 NC_009009:SSA_1576|3end_Catabolite_control_protein_A,_putative_1579177..1579327_NEGATIVE