Origin IGS: aattttcttctccttcgacagtgattagatagaataagcttcacttgaacgggcactttcagattggagcagccttgctctctctttgaaaattccttcaaacagcagcaaggtcagcttagaagccaccaactctatattcagccagcttctcagtcagccttttgattttccataatcagcagacagcagcaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgctgctgtctgctgattatggaaaatcaaaaggctgactgagaagctggctgaatatagagttggtggcttctaagctgaccttgctgctgtttgaaggaattttcaaagagagagcaaggctgctccaatctgaaagtgcccgttcaagtgaagcttattctatctaatcactgtcgaaggagaagaaaatt Mask Tandem Repeat Region ================================================ aattttcttctccttcgacagtgattagatagaataagcttcacttgaacgggcactttcagattggagcagccttgctctctctttgaaaattccttcaaacagcagcaaggtcagcttagaagccaccaactctatattcagccagcttctcagtcagccttttgattttccataatcagcagacagcagcaa Find is-nt database================================================ Query_seq: SSA_2099:SSA_2101|SSA_2099:SSA_2101:ABC-type arginine/histidine transporter, permease protein, putative:Amino acid ABC transporter, periplasmic amino acid-binding protein, putative:<-<-:2104404..2104598 195 aattttcttctccttcgacagtgattagatagaataagcttcacttgaacgggcactttcagattggagcagccttgctctctctttgaaaattccttcaaacagcagcaaggtcagcttagaagccaccaactctatattcagccagcttctcagtcagccttttgattttccataatcagcagacagcagcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2099:SSA_2101|SSA_2099:SSA_2101:ABC-type arginine/histidine transporter, permease protein, putative:Amino acid ABC transporter, periplasmic amino acid-binding protein, putative:<-<-:2104404..2104598 195 aattttcttctccttcgacagtgattagatagaataagcttcacttgaacgggcactttcagattggagcagccttgctctctctttgaaaattccttcaaacagcagcaaggtcagcttagaagccaccaactctatattcagccagcttctcagtcagccttttgattttccataatcagcagacagcagcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2099:SSA_2101|SSA_2099:SSA_2101:ABC-type arginine/histidine transporter, permease protein, putative:Amino acid ABC transporter, periplasmic amino acid-binding protein, putative:<-<-:2104404..2104598 195 aattttcttctccttcgacagtgattagatagaataagcttcacttgaacgggcactttcagattggagcagccttgctctctctttgaaaattccttcaaacagcagcaaggtcagcttagaagccaccaactctatattcagccagcttctcagtcagccttttgattttccataatcagcagacagcagcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattttcttctccttcgacagtgattagatagaataagcttcacttgaacgggcactttcagattggagcagccttgctctctctttgaaaattccttcaaacagcagcaaggtcagcttagaagccaccaactctatattcagccagcttctcagtcagccttttgattttccataatcagcagacagcagcaa Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 64 End: 165 ............................................................... M E Q P C S L F E N S F K Q Q Q G Q L R S H Q L Y I Q P A S Q S A F .............................. Protein_Len: 30 Strand: + Start: 86 End: 175 ..................................................................................... M K I P S N S S K V S L E A T N S I F S Q L L S Q P F D F P .................... Protein_Len: 43 Strand: - Start: 28 End: 156 ........................... I S Y A E S S R A S E S Q L L R A R E K F I G E F L L L T L K S A V L E I N L W S R M ....................................... Protein_Len: 33 Strand: - Start: 3 End: 101 .. K R R R R C H N S L I L K V Q V P V K L N S C G Q E R K S F E K M .............................................................................................. aattttcttctccttcgacagtgattagatagaataagcttcacttgaacgggcactttcagattggagcagccttgctctctctttgaaaattccttcaaacagcagcaaggtcagcttagaagccaccaactctatattcagccagcttctcagtcagccttttgattttccataatcagcagacagcagcaa 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================================================ aattttcttctccttcgacagtgattagatagaataagcttcacttgaacgggcactttcagattggagcagccttgctctctctttgaaaattccttcaaacagcagcaaggtcagcttagaagccaccaactctatattcagccagcttctcagtcagccttttgattttccataatcagcagacagcagcaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2099:SSA_2101|SSA_2099:SSA_2101:ABC-type arginine/histidine transporter, permease protein, putative:Amino acid ABC transporter, periplasmic amino acid-binding protein, putative:<-<-:2104404..2104598 195 aattttcttctccttcgacagtgattagatagaataagcttcacttgaacgggcactttcagattggagcagccttgctctctctttgaaaattccttcaaacagcagcaaggtcagcttagaagccaccaactctatattcagccagcttctcagtcagccttttgattttccataatcagcagacagcagcaa Intra-Species Hit: Count: 1 Min: 1 Max: 195 Len: 195 Subject: NC_009009_SSA_2099_SSA_2101|ABC-type arginine/histidine transporter, permease protein, putative:Amino acid ABC transporter, periplasmic amino acid-binding protein, putative|NEGATIVE:NEGATIVE|[2104404,2104598]|195 HSP 1 e-value: 1.0E-106 bit: 387.0 Len: 195 Query Start:1 Query End:195 Subject Strand: POSITIVE Subject Start: 1 Subject End: 195 aattttcttctccttcgacagtgattagatagaataagcttcacttgaacgggcactttcagattggagcagccttgctctctctttgaaaattccttcaaacagcagcaaggtcagcttagaagccaccaactctatattcagccagcttctcagtcagccttttgattttccataatcagcagacagcagcaa aattttcttctccttcgacagtgattagatagaataagcttcacttgaacgggcactttcagattggagcagccttgctctctctttgaaaattccttcaaacagcagcaaggtcagcttagaagccaccaactctatattcagccagcttctcagtcagccttttgattttccataatcagcagacagcagcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUUUCUUCUCCUUCGACAGUGAUUAGAUAGAAUAAGCUUCACUUGAACGGGCACUUUCAGAUUGGAGCAGCCUUGCUCUCUCUUUGAAAAUUCCUUCAAACAGCAGCAAGGUCAGCUUAGAAGCCACCAACUCUAUAUUCAGCCAGCUUCUCAGUCAGCCUUUUGAUUUUCCAUAAUCAGCAGACAGCAGCAA .....................(((....(((((....(((((..(((((.(....).)))))....((((.((((((((..((.((((((......)))))).)).))))))))..)))).))))).......)))))..)))....(((.((..(((.((....(((((......))))))).))))).))).. (-42.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCUGCUGUCUGCUGAUUAUGGAAAAUCAAAAGGCUGACUGAGAAGCUGGCUGAAUAUAGAGUUGGUGGCUUCUAAGCUGACCUUGCUGCUGUUUGAAGGAAUUUUCAAAGAGAGAGCAAGGCUGCUCCAAUCUGAAAGUGCCCGUUCAAGUGAAGCUUAUUCUAUCUAAUCACUGUCGAAGGAGAAGAAAAUU ...((.((.((.((((((((.......(((...((((........))))...)))..(((((((....((((((..(((.(.(((((((.((.(((((((....))))))).))..)))))))).)))......((((........))))...)))))).))))))).))))))..)).)))).))......... (-48.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 972 90 41 181 132 NC_009009:SSA_2099|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2104313..2104543_NEGATIVE 356 80 33 192 122 NC_009009:SSA_0512|5end_Nicotinate-nucleotide--dimethylbenzimidazole_phosphoribosyltransferase,_putative_510439..510669_POSITIVE 354 190 142 47 2 NC_009009:SSA_0403|5end_CAAX_amino_terminal_protease_family,_putative_400475..400705_POSITIVE 338 162 126 135 100 NC_009009:SSA_0066|5end_hypothetical_protein_67602..67832_POSITIVE 333 190 141 141 63 NC_009009:SSA_1798|5end_hypothetical_protein_1780513..1780743_NEGATIVE 331 164 124 48 1 NC_009009:SSA_0793|5end_DNA-entry_nuclease,_putative_774859..775089_POSITIVE 329 90 42 86 32 NC_009009:SSA_2102|5end_Conserved_uncharacterized_protein_2106410..2106640_NEGATIVE 329 110 63 109 59 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 328 160 115 133 82 NC_009009:SSA_1059|5end_hypothetical_protein_1076153..1076383_POSITIVE 328 78 44 40 7 NC_009009:SSA_0937|5end_Arsenate_reductase,_glutaredoxin_family,_putative_946183..946413_POSITIVE 326 84 50 40 8 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 324 166 121 73 32 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 323 80 37 207 165 NC_009009:SSA_0153|5end_hypothetical_protein_148677..148907_POSITIVE 322 159 111 209 151 NC_009009:SSA_2197|5end_hypothetical_protein_2197784..2198014_NEGATIVE 322 159 114 42 5 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 322 119 71 162 108 NC_009009:SSA_1404|5end_hypothetical_protein_1418723..1418953_NEGATIVE 321 159 112 227 184 NC_009009:SSA_1693|5end_Phosphotransferase_system_lactose-specific_component_IIBC,_putative_1686811..1687041_NEGATIVE 321 185 143 186 147 NC_009009:SSA_0245|5end_hypothetical_protein_239136..239366_POSITIVE 320 90 41 168 121 NC_009009:SSA_1650|5end_3-Ketoacyl-ACP_reductase,_putative_1649594..1649824_NEGATIVE 319 185 141 191 139 NC_009009:SSA_2278|5end_Ukp_protein,_putative_2281669..2281899_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 339 178 140 56 16 NC_009009:SSA_0827|3end_Conserved_uncharacterized_cytosolic_protein,_putative_806952..807102_POSITIVE 338 162 126 130 95 NC_009009:SSA_0065|3end_Low_molecular_weight_phosphotyrosine_protein_phosphatase,_putative_67677..67827_POSITIVE 333 190 141 141 63 NC_009009:SSA_1799|3end_Acetyltransferase,_putative_1780513..1780663_NEGATIVE 328 160 115 111 60 NC_009009:SSA_1058|3end_Thiamine_biosynthesis_protein,_putative_1076211..1076361_POSITIVE 322 159 111 151 93 NC_009009:SSA_2198|3end_hypothetical_protein_2197842..2197992_NEGATIVE 322 119 71 127 73 NC_009009:SSA_1405|3end_Copper_homeostasis_protein_CutC,_putative_1418758..1418908_NEGATIVE 321 185 143 140 101 NC_009009:SSA_0244|3end_hypothetical_protein_239170..239320_POSITIVE 319 166 122 148 112 NC_009009:SSA_1956|3end_ABC-type_Fe-S_cluster_assembly_transporter,_ATPase_component,_putative_1952644..1952794_NEGATIVE 319 186 141 118 77 NC_009009:SSA_1138|3end_Pyruvate_dehydrogenase,_TPP-dependent_E1_component_alpha-subunit,_putative_1166884..1167034_POSITIVE 319 120 71 124 64 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 315 97 51 134 80 NC_009009:SSA_0121|3end_hypothetical_protein_115442..115592_POSITIVE 314 190 141 144 104 NC_009009:SSA_1054|3end_CBS_domain_protein,_putative_1070973..1071123_POSITIVE 312 118 75 143 97 NC_009009:SSA_0202|3end_hypothetical_protein_201402..201552_POSITIVE 310 170 124 138 96 NC_009009:SSA_0704|3end_Isocitrate_dehydrogenase_[NADP],_putative_690550..690700_POSITIVE 305 128 96 54 13 NC_009009:SSA_1051|3end_Spermidine/putrescine_ABC_transporter,_spermidine/putrescine-binding_protein,_putative_1066808..1066958_POSITIVE 302 100 52 101 40 NC_009009:SSA_1660|3end_ABC-type_antimicrobial_peptide_transport_system,_ATPase_component,_putative_1656819..1656969_NEGATIVE 299 173 134 33 1 NC_009009:SSA_1034|3end_Conserved_uncharacterized_protein_1050252..1050402_POSITIVE 296 174 132 100 52 NC_009009:SSA_0690|3end_Recombinational_DNA_repair_protein_(RecF_pathway),_putative_675108..675258_POSITIVE 295 81 50 145 120 NC_009009:SSA_0569|3end_Aspartyl/glutamyl-tRNA(Asn/Gln)_amidotransferase_subunit_C,_putative_563995..564145_POSITIVE 294 170 121 77 38 NC_009009:SSA_1495|3end_S-adenosylmethionine_synthetase,_putative_1501019..1501169_NEGATIVE