Origin IGS: gtcaactcctcaaaggtcaatcagccttattctacaaaaataagaacaagtccaaatctagccgtcagcataaaacacccactagacaagaaaacctgctccacagcacgctaaggctgaaaacaaactcagctggtctagccaactgagccttcactgtctctattata .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tataatagagacagtgaaggctcagttggctagaccagctgagtttgttttcagccttagcgtgctgtggagcaggttttcttgtctagtgggtgttttatgctgacggctagatttggacttgttcttatttttgtagaataaggctgattgacctttgaggagttgac Mask Tandem Repeat Region ================================================ gtcaactcctcaaaggtcaatcagccttattctacaaaaataagaacaagtccaaatctagccgtcagcataaaacacccactagacaagaaaacctgctccacagcacgctaaggctgaaaacaaactcagctggtctagccaactgagccttcactgtctctattata Find is-nt database================================================ Query_seq: SSA_1866:SSA_1867|SSA_1866:SSA_1867:hypothetical protein:ABC-type polar amino acid transport system, ATPase component, putative:<-<-:1862273..1862442 170 gtcaactcctcaaaggtcaatcagccttattctacaaaaataagaacaagtccaaatctagccgtcagcataaaacacccactagacaagaaaacctgctccacagcacgctaaggctgaaaacaaactcagctggtctagccaactgagccttcactgtctctattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1866:SSA_1867|SSA_1866:SSA_1867:hypothetical protein:ABC-type polar amino acid transport system, ATPase component, putative:<-<-:1862273..1862442 170 gtcaactcctcaaaggtcaatcagccttattctacaaaaataagaacaagtccaaatctagccgtcagcataaaacacccactagacaagaaaacctgctccacagcacgctaaggctgaaaacaaactcagctggtctagccaactgagccttcactgtctctattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1866:SSA_1867|SSA_1866:SSA_1867:hypothetical protein:ABC-type polar amino acid transport system, ATPase component, putative:<-<-:1862273..1862442 170 gtcaactcctcaaaggtcaatcagccttattctacaaaaataagaacaagtccaaatctagccgtcagcataaaacacccactagacaagaaaacctgctccacagcacgctaaggctgaaaacaaactcagctggtctagccaactgagccttcactgtctctattata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtcaactcctcaaaggtcaatcagccttattctacaaaaataagaacaagtccaaatctagccgtcagcataaaacacccactagacaagaaaacctgctccacagcacgctaaggctgaaaacaaactcagctggtctagccaactgagccttcactgtctctattata Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 68 End: 169 ................................................................... C L V G V L C S F R S W L V S L S F V F E A P R A L Q A K V T E I M . gtcaactcctcaaaggtcaatcagccttattctacaaaaataagaacaagtccaaatctagccgtcagcataaaacacccactagacaagaaaacctgctccacagcacgctaaggctgaaaacaaactcagctggtctagccaactgagccttcactgtctctattata 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================================================ gtcaactcctcaaaggtcaatcagccttattctacaaaaataagaacaagtccaaatctagccgtcagcataaaacacccactagacaagaaaacctgctccacagcacgctaaggctgaaaacaaactcagctggtctagccaactgagccttcactgtctctattata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1866:SSA_1867|SSA_1866:SSA_1867:hypothetical protein:ABC-type polar amino acid transport system, ATPase component, putative:<-<-:1862273..1862442 170 gtcaactcctcaaaggtcaatcagccttattctacaaaaataagaacaagtccaaatctagccgtcagcataaaacacccactagacaagaaaacctgctccacagcacgctaaggctgaaaacaaactcagctggtctagccaactgagccttcactgtctctattata Intra-Species Hit: Count: 1 Min: 1 Max: 170 Len: 170 Subject: NC_009009_SSA_1866_SSA_1867|hypothetical protein:ABC-type polar amino acid transport system, ATPase component, putative|NEGATIVE:NEGATIVE|[1862273,1862442]|170 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 gtcaactcctcaaaggtcaatcagccttattctacaaaaataagaacaagtccaaatctagccgtcagcataaaacacccactagacaagaaaacctgctccacagcacgctaaggctgaaaacaaactcagctggtctagccaactgagccttcactgtctctattata gtcaactcctcaaaggtcaatcagccttattctacaaaaataagaacaagtccaaatctagccgtcagcataaaacacccactagacaagaaaacctgctccacagcacgctaaggctgaaaacaaactcagctggtctagccaactgagccttcactgtctctattata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCAACUCCUCAAAGGUCAAUCAGCCUUAUUCUACAAAAAUAAGAACAAGUCCAAAUCUAGCCGUCAGCAUAAAACACCCACUAGACAAGAAAACCUGCUCCACAGCACGCUAAGGCUGAAAACAAACUCAGCUGGUCUAGCCAACUGAGCCUUCACUGUCUCUAUUAUA ............((((....(((((((((...........................(((((....................)))))..........((((....))))...))))))))).......(((((.(((.....))).)))))))))................ (-30.35) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAUAGAGACAGUGAAGGCUCAGUUGGCUAGACCAGCUGAGUUUGUUUUCAGCCUUAGCGUGCUGUGGAGCAGGUUUUCUUGUCUAGUGGGUGUUUUAUGCUGACGGCUAGAUUUGGACUUGUUCUUAUUUUUGUAGAAUAAGGCUGAUUGACCUUUGAGGAGUUGAC .....(((((.......((((((((((((.....))))))))))))....(((((((((...(((...(((((((((((....(((((((.(..((.....))...).)))))))..))))))))))).......)))...))))))))).....))))).......... (-57.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1003 110 61 201 152 NC_009009:SSA_1866|5end_hypothetical_protein_1862182..1862412_NEGATIVE 451 157 113 149 104 NC_009009:SSA_0547|5end_Acyl_carrier_protein_synthase,_putative_541991..542221_POSITIVE 429 159 111 66 21 NC_009009:SSA_0375|5end_D-methionine-binding_lipoprotein_(ABC-type_transporter),_putative_364257..364487_POSITIVE 359 107 61 87 38 NC_009009:SSA_1266|5end_crcB-like_protein_1,_putative_1291000..1291230_NEGATIVE 342 134 96 81 40 NC_009009:SSA_1078|5end_hypothetical_protein_1095742..1095972_POSITIVE 342 159 124 36 3 NC_009009:SSA_0489|5end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_489655..489885_POSITIVE 329 146 101 193 150 NC_009009:SSA_0141|5end_Copper_chaperone,_putative_136893..137123_POSITIVE 328 148 107 49 7 NC_009009:SSA_1320|5end_hypothetical_protein_1337194..1337424_NEGATIVE 319 162 126 144 115 NC_009009:SSA_0355|5end_DNA_mismatch_repair_protein,_putative_346847..347077_POSITIVE 313 152 115 213 162 NC_009009:SSA_0102|5end_Kinase,_putative_104035..104265_POSITIVE 312 81 41 60 14 NC_009009:SSA_1892|5end_hypothetical_protein_1889262..1889492_NEGATIVE 312 150 104 175 124 NC_009009:SSA_1618|5end_hypothetical_protein_1621574..1621804_NEGATIVE 311 138 98 44 1 NC_009009:SSA_2257|5end_DNA_mismatch_repair_protein,_putative_2253184..2253414_NEGATIVE 308 159 115 214 151 NC_009009:SSA_0487|5end_Delta-aminolevulinic_acid_dehydratase,_putative_487349..487579_POSITIVE 306 106 63 65 23 NC_009009:SSA_0335|5end_Phosphomevalonate_kinase,_putative_328792..329022_POSITIVE 298 149 103 226 176 NC_009009:SSA_1393|5end_hypothetical_protein_1408773..1409003_NEGATIVE 297 163 128 206 169 NC_009009:SSA_0570|5end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A,_putative_563915..564145_POSITIVE 295 106 62 76 12 NC_009009:SSA_2141|5end_Argininosuccinate_lyase,_putative_2142201..2142431_NEGATIVE 295 120 75 70 23 NC_009009:SSA_1340|5end_Zn/Mn_ABC-type_porter_lipoprotein,_putative_1356372..1356602_NEGATIVE 293 118 78 215 172 NC_009009:SSA_1076|5end_hypothetical_protein_1094227..1094457_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 408 119 74 144 93 NC_009009:SSA_0687|3end_hypothetical_protein_671290..671440_POSITIVE 371 157 123 41 3 NC_009009:SSA_0546|3end_Phospho-2-dehydro-3-deoxyheptonate_aldolase_(DAHP_synthatase),_possibly_tyr-sensitive,_putative_541963..542113_POSITIVE 368 167 121 120 71 NC_009009:SSA_1269|3end_hypothetical_protein_1291970..1292120_NEGATIVE 359 107 61 114 65 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 342 134 96 88 47 NC_009009:SSA_1077|3end_N-acetyl-glucosamine_matabolism,_putative_1095829..1095979_POSITIVE 342 159 124 43 10 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 319 162 126 89 60 NC_009009:SSA_0354|3end_Uncharacterized_membrane_protein_346872..347022_POSITIVE 312 150 104 70 19 NC_009009:SSA_1619|3end_Ribosome_recycling_factor,_putative_1621679..1621829_NEGATIVE 306 106 63 75 33 NC_009009:SSA_0334|3end_Diphosphomevalonate_decarboxylase,_putative_328882..329032_POSITIVE 293 159 116 59 7 NC_009009:SSA_1068|3end_Transcriptional_regulator,_LysR_family_(capsular_polysaccharide_biosynthesis_regulation),_putative_1088367..1088517_POSITIVE 289 144 103 149 110 NC_009009:SSA_0017|3end_Cell_shape_determining_protein_MreC,_putative_23706..23856_POSITIVE 284 160 111 126 69 NC_009009:SSA_1993|3end_Conserved_uncharacterized_protein_1990380..1990530_NEGATIVE 284 150 110 58 14 NC_009009:SSA_0836|3end_SecA-like_protein,_putative_823969..824119_POSITIVE 283 165 123 61 21 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 281 106 68 61 6 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 281 139 94 57 17 NC_009009:SSA_0502|3end_Peptide_ABC_transporter,_permease_protein,_putative_502323..502473_POSITIVE 279 152 114 53 4 NC_009009:SSA_1051|3end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1066808..1066958_POSITIVE 278 118 73 150 102 NC_009009:SSA_1633|3end_FimA_fimbrial_subunit-like_protein,_putative_1634106..1634256_NEGATIVE 278 170 126 124 88 NC_009009:SSA_1036|3end_Deoxyribose-phosphate_aldolase,_putative_1052211..1052361_POSITIVE 276 165 134 145 108 NC_009009:SSA_0684|3end_Fibril-like_structure_subunit_FibA,_putative_668893..669043_POSITIVE