Origin IGS: ctttatccttaatcactaacttctattttttaatctttataagaaaatgcagatgagacttactctaaagcttgatataagctacttttcagagttcgtctacattgctgagcagcctgataagagccgactccgtcaactcattattttcatcccactcttttttatctattgtttattttaccaaaaaaaaagccaaaagcccatcataagaaaagactttaaaaattttttcaaagtgtttcacaaaggctaaatttttggtaaaatatattcagaataaatttctggaaatagatttaggaggatctt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aagatcctcctaaatctatttccagaaatttattctgaatatattttaccaaaaatttagcctttgtgaaacactttgaaaaaatttttaaagtcttttcttatgatgggcttttggctttttttttggtaaaataaacaatagataaaaaagagtgggatgaaaataatgagttgacggagtcggctcttatcaggctgctcagcaatgtagacgaactctgaaaagtagcttatatcaagctttagagtaagtctcatctgcattttcttataaagattaaaaaatagaagttagtgattaaggataaag Mask Tandem Repeat Region ================================================ ctttatccttaatcactaacttctattttttaatctttataagaaaatgcagatgagacttactctaaagcttgatataagctacttttcagagttcgtctacattgctgagcagcctgataagagccgactccgtcaactcattattttcatcccactcttttttatctattgtttattttaccaaaaaaaaagccaaaagcccatcataagaaaagactttaaaaattttttcaaagtgtttcacaaaggctaaatttttggtaaaatatattcagaataaatttctggaaatagatttaggaggatctt Find is-nt database================================================ Query_seq: SSA_1722:SSA_1723|SSA_1722:SSA_1723:Thymidylate kinase, putative:hypothetical protein:<-->:1708754..1709065 312 ctttatccttaatcactaacttctattttttaatctttataagaaaatgcagatgagacttactctaaagcttgatataagctacttttcagagttcgtctacattgctgagcagcctgataagagccgactccgtcaactcattattttcatcccactcttttttatctattgtttattttaccaaaaaaaaagccaaaagcccatcataagaaaagactttaaaaattttttcaaagtgtttcacaaaggctaaatttttggtaaaatatattcagaataaatttctggaaatagatttaggaggatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1722:SSA_1723|SSA_1722:SSA_1723:Thymidylate kinase, putative:hypothetical protein:<-->:1708754..1709065 312 ctttatccttaatcactaacttctattttttaatctttataagaaaatgcagatgagacttactctaaagcttgatataagctacttttcagagttcgtctacattgctgagcagcctgataagagccgactccgtcaactcattattttcatcccactcttttttatctattgtttattttaccaaaaaaaaagccaaaagcccatcataagaaaagactttaaaaattttttcaaagtgtttcacaaaggctaaatttttggtaaaatatattcagaataaatttctggaaatagatttaggaggatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1722:SSA_1723|SSA_1722:SSA_1723:Thymidylate kinase, putative:hypothetical protein:<-->:1708754..1709065 312 ctttatccttaatcactaacttctattttttaatctttataagaaaatgcagatgagacttactctaaagcttgatataagctacttttcagagttcgtctacattgctgagcagcctgataagagccgactccgtcaactcattattttcatcccactcttttttatctattgtttattttaccaaaaaaaaagccaaaagcccatcataagaaaagactttaaaaattttttcaaagtgtttcacaaaggctaaatttttggtaaaatatattcagaataaatttctggaaatagatttaggaggatctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttatccttaatcactaacttctattttttaatctttataagaaaatgcagatgagacttactctaaagcttgatataagctacttttcagagttcgtctacattgctgagcagcctgataagagccgactccgtcaactcattattttcatcccactcttttttatctattgtttattttaccaaaaaaaaagccaaaagcccatcataagaaaagactttaaaaattttttcaaagtgtttcacaaaggctaaatttttggtaaaatatattcagaataaatttctggaaatagatttaggaggatctt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 105 End: 209 ........................................................................................................ M L S S L I R A D S V N S L F S S H S F L S I V Y F T K K K A K S P S ....................................................................................................... Protein_Len: 60 Strand: + Start: 47 End: 253 .............................................. M Q M R L T L K L D I S Y F S E F V Y I A E Q P D K S R L R Q L I I F I P L F F I Y C L F Y Q K K S Q K P I I R K D F K ........................................................... Protein_Len: 32 Strand: - Start: 179 End: 274 .................................................................................................................................................................................. K V L F F A L L G D Y S F V K F I K E F H K V F A L N K T F Y M ...................................... ctttatccttaatcactaacttctattttttaatctttataagaaaatgcagatgagacttactctaaagcttgatataagctacttttcagagttcgtctacattgctgagcagcctgataagagccgactccgtcaactcattattttcatcccactcttttttatctattgtttattttaccaaaaaaaaagccaaaagcccatcataagaaaagactttaaaaattttttcaaagtgtttcacaaaggctaaatttttggtaaaatatattcagaataaatttctggaaatagatttaggaggatctt 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: 81 Start: 178 End: 207 .................................................................................................................................................................................ATGGGCTTTTGGCTTTTTTTTTGGTAAAAT......................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 209 End: 238 ................................................................................................................................................................................................................TTTGAAAAAATTTTTAAAGTCTTTTCTTAT.......................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 241 End: 270 ................................................................................................................................................................................................................................................GTTTCACAAAGGCTAAATTTTTGGTAAAAT.......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctttatccttaatcactaacttctattttttaatctttataagaaaatgcagatgagacttactctaaagcttgatataagctacttttcagagttcgtctacattgctgagcagcctgataagagccgactccgtcaactcattattttcatcccactcttttttatctattgtttattttaccaaaaaaaaagccaaaagcccatcataagaaaagactttaaaaattttttcaaagtgtttcacaaaggctaaatttttggtaaaatatattcagaataaatttctggaaatagatttaggaggatctt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_1722:SSA_1723|SSA_1722:SSA_1723:Thymidylate kinase, putative:hypothetical protein:<-->:1708754..1709065 312 ctttatccttaatcactaacttctattttttaatctttataagaaaatgcagatgagacttactctaaagcttgatataagctacttttcagagttcgtctacattgctgagcagcctgataagagccgactccgtcaactcattattttcatcccactcttttttatctattgtttattttaccaaaaaaaaagccaaaagcccatcataagaaaagactttaaaaattttttcaaagtgtttcacaaaggctaaatttttggtaaaatatattcagaataaatttctggaaatagatttaggaggatctt Intra-Species Hit: Count: 1 Min: 1 Max: 312 Len: 312 Subject: NC_009009_SSA_1722_SSA_1723|Thymidylate kinase, putative:hypothetical protein|NEGATIVE:POSITIVE|[1708754,1709065]|312 HSP 1 e-value: 1.0E-100 bit: 367.0 Len: 185 Query Start:1 Query End:185 Subject Strand: POSITIVE Subject Start: 1 Subject End: 185 ctttatccttaatcactaacttctattttttaatctttataagaaaatgcagatgagacttactctaaagcttgatataagctacttttcagagttcgtctacattgctgagcagcctgataagagccgactccgtcaactcattattttcatcccactcttttttatctattgtttattttacc............................................................................................................................... ctttatccttaatcactaacttctattttttaatctttataagaaaatgcagatgagacttactctaaagcttgatataagctacttttcagagttcgtctacattgctgagcagcctgataagagccgactccgtcaactcattattttcatcccactcttttttatctattgtttattttacc............................................................................................................................... HSP 2 e-value: 2.0E-26 bit: 121.0 Len: 61 Query Start:252 Query End:312 Subject Strand: POSITIVE Subject Start: 252 Subject End: 312 ...........................................................................................................................................................................................................................................................gctaaatttttggtaaaatatattcagaataaatttctggaaatagatttaggaggatctt ...........................................................................................................................................................................................................................................................gctaaatttttggtaaaatatattcagaataaatttctggaaatagatttaggaggatctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUUAUCCUUAAUCACUAACUUCUAUUUUUUAAUCUUUAUAAGAAAAUGCAGAUGAGACUUACUCUAAAGCUUGAUAUAAGCUACUUUUCAGAGUUCGUCUACAUUGCUGAGCAGCCUGAUAAGAGCCGACUCCGUCAACUCAUUAUUUUCAUCCCACUCUUUUUUAUCUAUUGUUUAUUUUACCAAAAAAAAAGCCAAAAGCCCAUCAUAAGAAAAGACUUUAAAAAUUUUUUCAAAGUGUUUCACAAAGGCUAAAUUUUUGGUAAAAUAUAUUCAGAAUAAAUUUCUGGAAAUAGAUUUAGGAGGAUCUU ..........................................((((((((((.((((((..(((((((((((((...))))))....)).)))))..)))).)))))).((((.((((....)).)).).)))............))))))......(((((....(((((((...((((((((((((((...((((...............(((((((.........)))))))...(((...)))...))))...))))))))))))))..(((((((.....))))))))))))))..)))))...... (-65.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGAUCCUCCUAAAUCUAUUUCCAGAAAUUUAUUCUGAAUAUAUUUUACCAAAAAUUUAGCCUUUGUGAAACACUUUGAAAAAAUUUUUAAAGUCUUUUCUUAUGAUGGGCUUUUGGCUUUUUUUUUGGUAAAAUAAACAAUAGAUAAAAAAGAGUGGGAUGAAAAUAAUGAGUUGACGGAGUCGGCUCUUAUCAGGCUGCUCAGCAAUGUAGACGAACUCUGAAAAGUAGCUUAUAUCAAGCUUUAGAGUAAGUCUCAUCUGCAUUUUCUUAUAAAGAUUAAAAAAUAGAAGUUAGUGAUUAAGGAUAAAG ...((((((((((.(((((((.(((((.....)))))....((((((((((((((...((((...(((...)))...............(((((((..((....)).))))))).))))...))))))))))))))......(((.......(((..(..(((...(((.((((((((...))))))))))))))..)..))).((((((.((((..(((((((.....(((((.....))))))))))))..))))))).)))....))).............)))))))..)))).))....)))).... (-80.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1021 140 91 231 182 NC_009009:SSA_1722|5end_Thymidylate_kinase,_putative_1708663..1708893_NEGATIVE 366 130 83 176 124 NC_009009:SSA_0915|5end_hypothetical_protein_927542..927772_POSITIVE 351 136 92 181 131 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 345 169 124 189 130 NC_009009:SSA_0520|5end_Ethanolamine_ammonia-lyase_light_chain,_putative_519462..519692_POSITIVE 340 143 101 41 2 NC_009009:SSA_0522|5end_Ethanolamine_utilization_protein,_putative_521067..521297_POSITIVE 328 180 131 96 42 NC_009009:SSA_2133|5end_3-methyladenine_DNA_glycosylase,_putative_2136327..2136557_NEGATIVE 321 120 76 212 148 NC_009009:SSA_2074|5end_Preprotein_translocase_subunit_YajC,_putative_2076935..2077165_NEGATIVE 321 134 91 59 10 NC_009009:SSA_0883|5end_Glycerate_kinase,_putative_877560..877790_POSITIVE 319 138 91 226 161 NC_009009:SSA_1164|5end_hypothetical_protein_1191138..1191368_NEGATIVE 317 143 109 60 15 NC_009009:SSA_1466|5end_Prephenate_dehydrogenase,_putative_1473111..1473341_NEGATIVE 313 156 112 100 39 NC_009009:SSA_2124|5end_Dehydrogenase,_eukaryotic-like,_putative_2129411..2129641_NEGATIVE 312 110 65 66 13 NC_009009:SSA_0049|5end_Dihydroxyacetone_kinase_(Dak1),_putative_53612..53842_POSITIVE 308 129 90 227 190 NC_009009:SSA_0599|5end_hypothetical_protein_588667..588897_POSITIVE 305 130 85 137 98 NC_009009:SSA_0582|5end_Methylase,_putative_573769..573999_POSITIVE 304 137 100 65 21 NC_009009:SSA_1066|5end_ABC-type_oligopeptide_transport_system,_putative_1084335..1084565_POSITIVE 298 160 113 145 93 NC_009009:SSA_2275|5end_hypothetical_protein_2275590..2275820_NEGATIVE 298 126 81 58 14 NC_009009:SSA_0753|5end_Foldase_protein_prsA_precursor,_putative_734968..735198_POSITIVE 295 137 91 68 24 NC_009009:SSA_1940|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_1927129..1927359_NEGATIVE 293 136 94 61 5 NC_009009:SSA_1805|5end_Primosomal_protein_DnaI,_putative_1789564..1789794_NEGATIVE 293 139 93 207 157 NC_009009:SSA_1704|5end_Conserved_uncharacterized_protein_1696401..1696631_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 180 131 84 30 NC_009009:SSA_2134|3end_hypothetical_protein_2136339..2136489_NEGATIVE 313 156 112 88 27 NC_009009:SSA_2125|3end_Small_primase-like_protein_(Toprim_domain),_putative_2129423..2129573_NEGATIVE 308 157 111 151 100 NC_009009:SSA_1124|3end_Oxidoreductase,_putative_1148547..1148697_NEGATIVE 308 129 90 43 6 NC_009009:SSA_0597|3end_hypothetical_protein_588563..588713_POSITIVE 306 137 96 144 94 NC_009009:SSA_2340|3end_hypothetical_protein_2341539..2341689_NEGATIVE 305 130 85 62 23 NC_009009:SSA_0581|3end_Conserved_uncharacterized_protein_573774..573924_POSITIVE 298 160 113 148 96 NC_009009:SSA_2276|3end_hypothetical_protein_2275587..2275737_NEGATIVE 296 137 93 126 64 NC_009009:SSA_0519|3end_Ethanolamine_ammonia-lyase_large_subunit,_putative_519525..519675_POSITIVE 295 129 85 41 7 NC_009009:SSA_2207|3end_hypothetical_protein_2206868..2207018_NEGATIVE 295 137 91 68 24 NC_009009:SSA_1941|3end_hypothetical_protein_1927129..1927279_NEGATIVE 293 136 94 60 4 NC_009009:SSA_1806|3end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1789565..1789715_NEGATIVE 293 160 111 83 1 NC_009009:SSA_1467|3end_Chorismate_synthase,_putative_1473127..1473277_NEGATIVE 293 127 81 144 90 NC_009009:SSA_0829|3end_Platelet-binding_glycoprotein_812165..812315_POSITIVE 288 137 96 142 91 NC_009009:SSA_0489|3end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_490319..490469_POSITIVE 284 130 81 54 8 NC_009009:SSA_1575|3end_Glycosyl_transferase,_putative_1577932..1578082_NEGATIVE 282 130 85 141 96 NC_009009:SSA_2376|3end_ABC_transporter_with_duplicated_ATPase_domains,_putative_2380188..2380338_POSITIVE 282 148 108 95 38 NC_009009:SSA_0585|3end_hypothetical_protein_577286..577436_POSITIVE 281 170 123 96 48 NC_009009:SSA_2217|3end_Cps9H,_putative_2218086..2218236_NEGATIVE 280 159 111 65 21 NC_009009:SSA_1975|3end_ABC-type_multidrug_transport_system,_ATPase_component,_putative_1970257..1970407_NEGATIVE 279 128 82 136 91 NC_009009:SSA_1139|3end_Pyruvate_dehydrogenase_E1_component_beta_subunit,_putative_1167934..1168084_POSITIVE