Origin IGS: aagggcataaaatcaactcaaatgcttcaatcagtcatataaattttttatcacggtgataaattatttatataagccaagtctccttgaacatggtaaaatgagaagtaatcttataaaatagaagatttagaattttatccattaaaggagaataa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttattctcctttaatggataaaattctaaatcttctattttataagattacttctcattttaccatgttcaaggagacttggcttatataaataatttatcaccgtgataaaaaatttatatgactgattgaagcatttgagttgattttatgccctt Mask Tandem Repeat Region ================================================ aagggcataaaatcaactcaaatgcttcaatcagtcatataaattttttatcacggtgataaattatttatataagccaagtctccttgaacatggtaaaatgagaagtaatcttataaaatagaagatttagaattttatccattaaaggagaataa Find is-nt database================================================ Query_seq: SSA_0374:SSA_0375|SSA_0374:SSA_0375:Peptide methionine sulfoxide reductase msrA/msrB, putative:D-methionine-binding lipoprotein (ABC-type transporter), putative:->->:364239..364396 158 aagggcataaaatcaactcaaatgcttcaatcagtcatataaattttttatcacggtgataaattatttatataagccaagtctccttgaacatggtaaaatgagaagtaatcttataaaatagaagatttagaattttatccattaaaggagaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0374:SSA_0375|SSA_0374:SSA_0375:Peptide methionine sulfoxide reductase msrA/msrB, putative:D-methionine-binding lipoprotein (ABC-type transporter), putative:->->:364239..364396 158 aagggcataaaatcaactcaaatgcttcaatcagtcatataaattttttatcacggtgataaattatttatataagccaagtctccttgaacatggtaaaatgagaagtaatcttataaaatagaagatttagaattttatccattaaaggagaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0374:SSA_0375|SSA_0374:SSA_0375:Peptide methionine sulfoxide reductase msrA/msrB, putative:D-methionine-binding lipoprotein (ABC-type transporter), putative:->->:364239..364396 158 aagggcataaaatcaactcaaatgcttcaatcagtcatataaattttttatcacggtgataaattatttatataagccaagtctccttgaacatggtaaaatgagaagtaatcttataaaatagaagatttagaattttatccattaaaggagaataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagggcataaaatcaactcaaatgcttcaatcagtcatataaattttttatcacggtgataaattatttatataagccaagtctccttgaacatggtaaaatgagaagtaatcttataaaatagaagatttagaattttatccattaaaggagaataa Predict ORF larger than 30AA ================================================ aagggcataaaatcaactcaaatgcttcaatcagtcatataaattttttatcacggtgataaattatttatataagccaagtctccttgaacatggtaaaatgagaagtaatcttataaaatagaagatttagaattttatccattaaaggagaataa 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================================================ aagggcataaaatcaactcaaatgcttcaatcagtcatataaattttttatcacggtgataaattatttatataagccaagtctccttgaacatggtaaaatgagaagtaatcttataaaatagaagatttagaattttatccattaaaggagaataa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 72 HP_score: -6.7 Tail_Score: -4.14627 Start: 47 End: 63 Full_Region: CAGTCATATAAATTT TTTATCA CGG TGATAAA TTATTTATATAAGCC ..............................................TTTATCACGGTGATAAA............................................................................................... Find igs database================================================ Query_seq: SSA_0374:SSA_0375|SSA_0374:SSA_0375:Peptide methionine sulfoxide reductase msrA/msrB, putative:D-methionine-binding lipoprotein (ABC-type transporter), putative:->->:364239..364396 158 aagggcataaaatcaactcaaatgcttcaatcagtcatataaattttttatcacggtgataaattatttatataagccaagtctccttgaacatggtaaaatgagaagtaatcttataaaatagaagatttagaattttatccattaaaggagaataa Intra-Species Hit: Count: 1 Min: 1 Max: 158 Len: 158 Subject: NC_009009_SSA_0374_SSA_0375|Peptide methionine sulfoxide reductase msrA/msrB, putative:D-methionine-binding lipoprotein (ABC-type transporter), putative|POSITIVE:POSITIVE|[364239,364396]|158 HSP 1 e-value: 9.0E-85 bit: 313.0 Len: 158 Query Start:1 Query End:158 Subject Strand: POSITIVE Subject Start: 1 Subject End: 158 aagggcataaaatcaactcaaatgcttcaatcagtcatataaattttttatcacggtgataaattatttatataagccaagtctccttgaacatggtaaaatgagaagtaatcttataaaatagaagatttagaattttatccattaaaggagaataa aagggcataaaatcaactcaaatgcttcaatcagtcatataaattttttatcacggtgataaattatttatataagccaagtctccttgaacatggtaaaatgagaagtaatcttataaaatagaagatttagaattttatccattaaaggagaataa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGGCAUAAAAUCAACUCAAAUGCUUCAAUCAGUCAUAUAAAUUUUUUAUCACGGUGAUAAAUUAUUUAUAUAAGCCAAGUCUCCUUGAACAUGGUAAAAUGAGAAGUAAUCUUAUAAAAUAGAAGAUUUAGAAUUUUAUCCAUUAAAGGAGAAUAA ...(((.................(((......))).((((((((..((((((.....))))))..))))))))..)))...(((((((....((((((((((...((((..(((........)))..))))...)))))).))))..))))))).... (-35.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUUCUCCUUUAAUGGAUAAAAUUCUAAAUCUUCUAUUUUAUAAGAUUACUUCUCAUUUUACCAUGUUCAAGGAGACUUGGCUUAUAUAAAUAAUUUAUCACCGUGAUAAAAAAUUUAUAUGACUGAUUGAAGCAUUUGAGUUGAUUUUAUGCCCUU ....(((((((..((((.((((((.........(((........))).........))))))))))....))))))).(..(.((((((((((..((((((.....))))))..)))))))))))..).....((((..((.....))..)))).... (-30.97) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 262 119 72 207 163 NC_009009:SSA_0043|5end_hypothetical_protein_48801..49031_POSITIVE 240 55 12 92 47 NC_009009:SSA_0129|5end_Translation_initiation_factor_IF-1,_putative_119957..120187_POSITIVE 239 116 75 95 48 NC_009009:SSA_0611|5end_HtpX_protease,_putative_599539..599769_POSITIVE 237 58 13 139 97 NC_009009:SSA_1422|5end_hypothetical_protein_1431555..1431785_NEGATIVE 216 98 52 64 25 NC_009009:SSA_0603|5end_Cobalt_transporter,_putative_591596..591826_POSITIVE 211 59 12 137 80 NC_009009:SSA_1257|5end_hypothetical_protein_1283867..1284097_NEGATIVE 210 60 17 70 15 NC_009009:SSA_1137|5end_Dihydrolipoamide_dehydrogenase,_putative_1164375..1164605_POSITIVE 208 105 76 66 39 NC_009009:SSA_0964|5end_DEAD_RNA_helicase,_putative_974114..974344_NEGATIVE 207 93 53 223 179 NC_009009:SSA_2289|5end_Cadmium_efflux_system_transcriptional_regulator_(ArsR-like),_putative_2291087..2291317_POSITIVE 207 93 53 223 179 NC_009009:SSA_2389|5end_Arsenical_resistance_operon_transcription_repressor,_putative_2032183..2032413_NEGATIVE 207 93 53 193 149 NC_009009:SSA_2387|5end_Arsenical_resistance_operon_transcription_repressor,_putative_2032213..2032443_NEGATIVE 206 118 76 92 49 NC_009009:SSA_1086|5end_TRNA_nucleotidyltransferase,_putative_1103328..1103558_POSITIVE 205 90 43 177 118 NC_009009:SSA_1642|5end_N-acetylglucosamine-1-phosphate_uridyltransferase,_putative_1644482..1644712_NEGATIVE 205 55 23 180 149 NC_009009:SSA_1423|5end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1433783..1434013_NEGATIVE 204 117 74 194 150 NC_009009:SSA_1683|5end_NrdI_protein,_putative_1677405..1677635_NEGATIVE 203 38 3 72 40 NC_009009:SSA_2334|5end_D-alanine--D-alanyl_carrier_protein_ligase,_putative_2338007..2338237_NEGATIVE 202 121 82 144 97 NC_009009:SSA_0146|5end_DNA_repair_ATPase,_putative_139686..139916_POSITIVE 201 41 2 94 53 NC_009009:SSA_2062|5end_hypothetical_protein_2063521..2063751_NEGATIVE 200 128 85 202 165 NC_009009:SSA_0516|5end_AmiR_two-component_response_regulator_with_transcriptional_antiterminator_output_domain,_putative_514485..514715_POSITIVE 199 100 53 115 81 NC_009009:SSA_1691|5end_Transcriptional_regulator,_XRE_family,_putative_1683281..1683511_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 116 75 93 46 NC_009009:SSA_0610|3end_LemA-like_protein,_putative_599617..599767_POSITIVE 237 58 13 133 91 NC_009009:SSA_1423|3end_Single-stranded_DNA-specific_exonuclease,_5'-3',_putative_1431561..1431711_NEGATIVE 234 114 80 137 93 NC_009009:SSA_0165|3end_hypothetical_protein_164623..164773_POSITIVE 216 98 52 71 32 NC_009009:SSA_0602|3end_ABC-type_cobalt_transport_system,_ATPase_component,_putative_591683..591833_POSITIVE 215 87 51 131 91 NC_009009:SSA_1056|3end_Firmicute_fructose-1,6-bisphosphatase,_putative_1073750..1073900_POSITIVE 212 60 16 149 108 NC_009009:SSA_1821|3end_Acetyltransferase_(N-acetylase_of_ribosomal_proteins),_putative_1810047..1810197_NEGATIVE 211 59 12 146 89 NC_009009:SSA_1258|3end_Purine_nucleoside_phosphorylase,_family_1,_putative_1283858..1284008_NEGATIVE 208 105 76 145 118 NC_009009:SSA_0965|3end_Oxidoreductase,_putative_974035..974185_NEGATIVE 206 118 76 95 52 NC_009009:SSA_1085|3end_Dihydrodipicolinate_reductase,_putative_1103411..1103561_POSITIVE 205 55 23 74 43 NC_009009:SSA_1424|3end_Hydrolase,_putative_1433889..1434039_NEGATIVE 203 38 3 52 20 NC_009009:SSA_2335|3end_D-Ala-teichoic_acid_biosynthesis_protein,_putative_2338027..2338177_NEGATIVE 199 100 53 102 68 NC_009009:SSA_1690|3end_hypothetical_protein_1683348..1683498_POSITIVE 198 87 43 140 93 NC_009009:SSA_0926|3end_Histone_acetyltransferase_HPA2,_putative_935961..936111_POSITIVE 197 73 37 54 18 NC_009009:SSA_0374|3end_Peptide_methionine_sulfoxide_reductase_msrA/msrB,_putative_364178..364328_POSITIVE 196 41 3 52 22 NC_009009:SSA_1409|3end_DTDP-glucose-4,6-dehydratase,_putative_1421209..1421359_NEGATIVE 194 60 14 55 9 NC_009009:SSA_1608|3end_hypothetical_protein_1613283..1613433_NEGATIVE 192 86 54 47 21 NC_009009:SSA_2176|3end_hypothetical_protein_2174269..2174419_NEGATIVE 192 90 50 49 1 NC_009009:SSA_1643|3end_hypothetical_protein_1644610..1644760_NEGATIVE 192 38 2 41 2 NC_009009:SSA_0203|3end_hypothetical_protein_202124..202274_POSITIVE 189 62 37 77 52 NC_009009:SSA_1869|3end_ATP-dependent_RNA_helicase,_putative_1864152..1864302_NEGATIVE