Origin IGS: cagtaaatagagccgatcagtttatcttttagtccgtcgaaagttcactcaattagtgagctgtggaagtgatgggcagagcaagttgtaaaggaaataacttgattatttctggtgcttgcttcctaaaatcctagattaggaattagtaaaaagaaaccgagaggcaatagaaacaggaagttttgacaacttcctgtttttttgacaatttagtagaaaaaagtgtcctttattctgcaggaaagtccttgagaatatagattttttggacaatattttatataatatcaagtatagaaatgatgttttagagtttatgaaatgaaagagtaagggaagaa .........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 ttcttcccttactctttcatttcataaactctaaaacatcatttctatacttgatattatataaaatattgtccaaaaaatctatattctcaaggactttcctgcagaataaaggacacttttttctactaaattgtcaaaaaaacaggaagttgtcaaaacttcctgtttctattgcctctcggtttctttttactaattcctaatctaggattttaggaagcaagcaccagaaataatcaagttatttcctttacaacttgctctgcccatcacttccacagctcactaattgagtgaactttcgacggactaaaagataaactgatcggctctatttactg Mask Tandem Repeat Region ================================================ cagtaaatagagccgatcagtttatcttttagtccgtcgaaagttcactcaattagtgagctgtggaagtgatgggcagagcaagttgtaaaggaaataacttgattatttctggtgcttgcttcctaaaatcctagattaggaattagtaaaaagaaaccgagaggcaatagaaacaggaagttttgacaacttcctgtttttttgacaatttagtagaaaaaagtgtcctttattctgcaggaaagtccttgagaatatagattttttggacaatattttatataatatcaagtatagaaatgatgttttagagtttatgaaatgaaagagtaagggaagaa Find is-nt database================================================ Query_seq: SSA_0829:SSA_0830|SSA_0829:SSA_0830:Platelet-binding glycoprotein:Glycosyltransferase, putative:->->:812226..812569 344 cagtaaatagagccgatcagtttatcttttagtccgtcgaaagttcactcaattagtgagctgtggaagtgatgggcagagcaagttgtaaaggaaataacttgattatttctggtgcttgcttcctaaaatcctagattaggaattagtaaaaagaaaccgagaggcaatagaaacaggaagttttgacaacttcctgtttttttgacaatttagtagaaaaaagtgtcctttattctgcaggaaagtccttgagaatatagattttttggacaatattttatataatatcaagtatagaaatgatgttttagagtttatgaaatgaaagagtaagggaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0829:SSA_0830|SSA_0829:SSA_0830:Platelet-binding glycoprotein:Glycosyltransferase, putative:->->:812226..812569 344 cagtaaatagagccgatcagtttatcttttagtccgtcgaaagttcactcaattagtgagctgtggaagtgatgggcagagcaagttgtaaaggaaataacttgattatttctggtgcttgcttcctaaaatcctagattaggaattagtaaaaagaaaccgagaggcaatagaaacaggaagttttgacaacttcctgtttttttgacaatttagtagaaaaaagtgtcctttattctgcaggaaagtccttgagaatatagattttttggacaatattttatataatatcaagtatagaaatgatgttttagagtttatgaaatgaaagagtaagggaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0829:SSA_0830|SSA_0829:SSA_0830:Platelet-binding glycoprotein:Glycosyltransferase, putative:->->:812226..812569 344 cagtaaatagagccgatcagtttatcttttagtccgtcgaaagttcactcaattagtgagctgtggaagtgatgggcagagcaagttgtaaaggaaataacttgattatttctggtgcttgcttcctaaaatcctagattaggaattagtaaaaagaaaccgagaggcaatagaaacaggaagttttgacaacttcctgtttttttgacaatttagtagaaaaaagtgtcctttattctgcaggaaagtccttgagaatatagattttttggacaatattttatataatatcaagtatagaaatgatgttttagagtttatgaaatgaaagagtaagggaagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagtaaatagagccgatcagtttatcttttagtccgtcgaaagttcactcaattagtgagctgtggaagtgatgggcagagcaagttgtaaaggaaataacttgattatttctggtgcttgcttcctaaaatcctagattaggaattagtaaaaagaaaccgagaggcaatagaaacaggaagttttgacaacttcctgtttttttgacaatttagtagaaaaaagtgtcctttattctgcaggaaagtccttgagaatatagattttttggacaatattttatataatatcaagtatagaaatgatgttttagagtttatgaaatgaaagagtaagggaagaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: - Start: 142 End: 321 ............................................................................................................................................. S N T F L F R S A I S V P L K S L K R N K Q C N L L F F H G K N Q L F T R S F I S K K S L I K Y L I L Y L F S T K S N M ....................... cagtaaatagagccgatcagtttatcttttagtccgtcgaaagttcactcaattagtgagctgtggaagtgatgggcagagcaagttgtaaaggaaataacttgattatttctggtgcttgcttcctaaaatcctagattaggaattagtaaaaagaaaccgagaggcaatagaaacaggaagttttgacaacttcctgtttttttgacaatttagtagaaaaaagtgtcctttattctgcaggaaagtccttgagaatatagattttttggacaatattttatataatatcaagtatagaaatgatgttttagagtttatgaaatgaaagagtaagggaagaa 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: 82 Start: 260 End: 289 ...................................................................................................................................................................................................................................................................ATAGATTTTTTGGACAATATTTTATATAAT....................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cagtaaatagagccgatcagtttatcttttagtccgtcgaaagttcactcaattagtgagctgtggaagtgatgggcagagcaagttgtaaaggaaataacttgattatttctggtgcttgcttcctaaaatcctagattaggaattagtaaaaagaaaccgagaggcaatagaaacaggaagttttgacaacttcctgtttttttgacaatttagtagaaaaaagtgtcctttattctgcaggaaagtccttgagaatatagattttttggacaatattttatataatatcaagtatagaaatgatgttttagagtttatgaaatgaaagagtaagggaagaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 43 HP_score: -2.8 Tail_Score: -3.0663 Start: 82 End: 104 Full_Region: AAGTGATGGGCAGAG CAAGTTGT AAAGGAA ATAACTTG ATTATTTCTGGTGCT .................................................................................CAAGTTGTAAAGGAAATAACTTG................................................................................................................................................................................................................................................ TransTerm Strand: + Conf: 100 HP_score: -10.7 Tail_Score: -5.4477 Start: 177 End: 199 Full_Region: GAGAGGCAATAGAAA CAGGAAGTT TTGAC AACTTCCTG TTTTTTTGACAATTT ................................................................................................................................................................................CAGGAAGTTTTGACAACTTCCTG................................................................................................................................................. TransTerm Strand: - Conf: 95 HP_score: -10.7 Tail_Score: -4.22678 Start: 177 End: 199 Full_Region: aaattgtcaaaaaaa caggaagtt gtcaa aacttcctg tttctattgcctctc ................................................................................................................................................................................caggaagttgtcaaaacttcctg................................................................................................................................................. Find igs database================================================ Query_seq: SSA_0829:SSA_0830|SSA_0829:SSA_0830:Platelet-binding glycoprotein:Glycosyltransferase, putative:->->:812226..812569 344 cagtaaatagagccgatcagtttatcttttagtccgtcgaaagttcactcaattagtgagctgtggaagtgatgggcagagcaagttgtaaaggaaataacttgattatttctggtgcttgcttcctaaaatcctagattaggaattagtaaaaagaaaccgagaggcaatagaaacaggaagttttgacaacttcctgtttttttgacaatttagtagaaaaaagtgtcctttattctgcaggaaagtccttgagaatatagattttttggacaatattttatataatatcaagtatagaaatgatgttttagagtttatgaaatgaaagagtaagggaagaa Intra-Species Hit: Count: 1 Min: 1 Max: 344 Len: 344 Subject: NC_009009_SSA_0829_SSA_0830|Platelet-binding glycoprotein:Glycosyltransferase, putative|POSITIVE:POSITIVE|[812226,812569]|344 HSP 1 e-value: 0.0 bit: 640.0 Len: 344 Query Start:1 Query End:344 Subject Strand: POSITIVE Subject Start: 1 Subject End: 344 cagtaaatagagccgatcagtttatcttttagtccgtcgaaagttcactcaattagtgagctgtggaagtgatgggcagagcaagttgtaaaggaaataacttgattatttctggtgcttgcttcctaaaatcctagattaggaattagtaaaaagaaaccgagaggcaatagaaacaggaagttttgacaacttcctgnnnnnnngacaatttagtagaaaaaagtgtcctttattctgcaggaaagtccttgagaatatagattttttggacaatattttatataatatcaagtatagaaatgatgttttagagtttatgaaatgaaagagtaagggaagaa cagtaaatagagccgatcagtttatcttttagtccgtcgaaagttcactcaattagtgagctgtggaagtgatgggcagagcaagttgtaaaggaaataacttgattatttctggtgcttgcttcctaaaatcctagattaggaattagtaaaaagaaaccgagaggcaatagaaacaggaagttttgacaacttcctgtttttttgacaatttagtagaaaaaagtgtcctttattctgcaggaaagtccttgagaatatagattttttggacaatattttatataatatcaagtatagaaatgatgttttagagtttatgaaatgaaagagtaagggaagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUAAAUAGAGCCGAUCAGUUUAUCUUUUAGUCCGUCGAAAGUUCACUCAAUUAGUGAGCUGUGGAAGUGAUGGGCAGAGCAAGUUGUAAAGGAAAUAACUUGAUUAUUUCUGGUGCUUGCUUCCUAAAAUCCUAGAUUAGGAAUUAGUAAAAAGAAACCGAGAGGCAAUAGAAACAGGAAGUUUUGACAACUUCCUGUUUUUUUGACAAUUUAGUAGAAAAAAGUGUCCUUUAUUCUGCAGGAAAGUCCUUGAGAAUAUAGAUUUUUUGGACAAUAUUUUAUAUAAUAUCAAGUAUAGAAAUGAUGUUUUAGAGUUUAUGAAAUGAAAGAGUAAGGGAAGAA .(.(((((...(((..((.(((..((((((.((((((((..((((((((.....)))))))).......)))))))).((((((((......((((((((.....))))))))...)))))))).((((..(((((...))))).))))..))))))))).))..)))...((((((((((((((.....))))))))))))))......))))).)...........(((((((((((.((((......))))....((((((((((..(((((.((((((((((........)))).)))))).))))).)))))))))).......))))))))))).... (-96.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUUCCCUUACUCUUUCAUUUCAUAAACUCUAAAACAUCAUUUCUAUACUUGAUAUUAUAUAAAAUAUUGUCCAAAAAAUCUAUAUUCUCAAGGACUUUCCUGCAGAAUAAAGGACACUUUUUUCUACUAAAUUGUCAAAAAAACAGGAAGUUGUCAAAACUUCCUGUUUCUAUUGCCUCUCGGUUUCUUUUUACUAAUUCCUAAUCUAGGAUUUUAGGAAGCAAGCACCAGAAAUAAUCAAGUUAUUUCCUUUACAACUUGCUCUGCCCAUCACUUCCACAGCUCACUAAUUGAGUGAACUUUCGACGGACUAAAAGAUAAACUGAUCGGCUCUAUUUACUG ..................................................(((((((((((.((((...(((((..........((((((..(((.....)))..))))))..)))))...)))).)).)))..))))))..((((((((((((.....)))))))))))).....(((..((((((((((((..((((.(((((...)))))..))))..((((((.....((((((((...))))))))........))))))....((.((.........(((((.....)))))........)).))...))))))..))))))..)))........... (-64.85) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 337 74 32 197 149 NC_009009:SSA_0299|5end_hypothetical_protein_292759..292989_POSITIVE 318 96 55 175 130 NC_009009:SSA_0604|5end_hypothetical_protein_592451..592681_POSITIVE 315 79 32 176 115 NC_009009:SSA_0760|5end_Acetylornithine_aminotransferase,_putative_742581..742811_POSITIVE 299 150 101 64 13 NC_009009:SSA_0386|5end_Glycine-betaine_ABC_transporter,_ATPase_component,_putative_381455..381685_NEGATIVE 291 106 62 192 155 NC_009009:SSA_1138|5end_Pyruvate_dehydrogenase,_TPP-dependent_E1_component_alpha-subunit,_putative_1165731..1165961_POSITIVE 288 76 34 68 18 NC_009009:SSA_0387|5end_Transcriptional_regulator,_GntR_family,_putative_382343..382573_NEGATIVE 285 79 31 138 95 NC_009009:SSA_1364|5end_hypothetical_protein_1381297..1381527_NEGATIVE 283 60 12 231 177 NC_009009:SSA_1084|5end_Conserved_uncharacterized_protein_1101675..1101905_POSITIVE 282 79 32 73 7 NC_009009:SSA_2252|5end_hypothetical_protein_2248649..2248879_NEGATIVE 280 95 53 219 175 NC_009009:SSA_1742|5end_Ferrichrome-binding_protein,_putative_1728872..1729102_POSITIVE 280 94 55 226 180 NC_009009:SSA_0205|5end_NisK_(sensor-receptor_histidine_kinase_domain),_putative_202722..202952_POSITIVE 280 143 112 150 112 NC_009009:SSA_0165|5end_hypothetical_protein_163938..164168_POSITIVE 277 51 11 160 122 NC_009009:SSA_2041|5end_Leucine-rich_protein,_putative_2046682..2046912_NEGATIVE 277 76 34 76 15 NC_009009:SSA_1238|5end_hypothetical_protein_1263154..1263384_NEGATIVE 275 76 31 161 127 NC_009009:SSA_1398|5end_Membrane_protein,_hemolysin_III-like,_putative_1410881..1411111_POSITIVE 274 93 56 76 34 NC_009009:SSA_0021|5end_hypothetical_protein_26842..27072_POSITIVE 273 84 41 151 100 NC_009009:SSA_0417|5end_5,10-methylenetetrahydrofolate_reductase,_putative_414280..414510_POSITIVE 271 49 13 223 189 NC_009009:SSA_0522|5end_Ethanolamine_utilization_protein,_putative_521067..521297_POSITIVE 267 77 35 45 1 NC_009009:SSA_2287|5end_50S_ribosomal_protein_L32,_putative_2289821..2290051_POSITIVE 267 83 47 182 136 NC_009009:SSA_1613|5end_hypothetical_protein_1616975..1617205_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 199 152 139 93 NC_009009:SSA_0725|3end_hypothetical_protein_710812..710962_POSITIVE 295 96 52 134 90 NC_009009:SSA_1019|3end_Collagen-binding_surface_protein,_putative_1035377..1035527_POSITIVE 291 84 55 145 111 NC_009009:SSA_0603|3end_Cobalt_transporter,_putative_592512..592662_POSITIVE 285 79 31 83 40 NC_009009:SSA_1365|3end_FmtA-like_protein,_putative_1381352..1381502_NEGATIVE 280 95 53 139 95 NC_009009:SSA_1741|3end_ABC-type_Fe3+-siderophores_transporter,_ATPase_component,_putative_1728872..1729022_POSITIVE 280 143 112 129 91 NC_009009:SSA_0164|3end_hypothetical_protein_163997..164147_POSITIVE 277 76 34 79 18 NC_009009:SSA_1239|3end_hypothetical_protein_1263151..1263301_NEGATIVE 269 68 26 85 38 NC_009009:SSA_2242|3end_hypothetical_protein_2238121..2238271_NEGATIVE 269 209 164 91 37 NC_009009:SSA_1234|3end_5'-nucleotidase,_putative_1257636..1257786_NEGATIVE 266 50 13 63 23 NC_009009:SSA_1244|3end_hypothetical_protein_1268465..1268615_NEGATIVE 265 94 60 61 25 NC_009009:SSA_1212|3end_Ribose-phosphate_pyrophosphokinase_2,_putative_1236437..1236587_POSITIVE 264 80 34 51 2 NC_009009:SSA_0216|3end_Histidine_kinase,_putative_213270..213420_POSITIVE 262 93 56 142 105 NC_009009:SSA_2132|3end_Ure_cluster_protein,_putative_2135665..2135815_POSITIVE 262 84 45 143 110 NC_009009:SSA_0744|3end_S-adenosylmethio_nine:tRNA-ribosyltransferase-isomerase_(queuine_synthetase),_putative_725776..725926_NEGATIVE 260 85 45 47 4 NC_009009:SSA_0497|3end_Nickel_ABC_transporter,_putative_497997..498147_POSITIVE 259 80 38 134 77 NC_009009:SSA_2267|3end_Lactose_operon_transcriptional_repressor,_LacI_family,_putative_2267190..2267340_POSITIVE 259 79 32 146 100 NC_009009:SSA_2190|3end_33_kDa_chaperonin,_putative_2192118..2192268_POSITIVE 259 80 31 137 76 NC_009009:SSA_1659|3end_ABC-type_antimicrobial_peptide_transport_system,_permease_component,_putative_1654831..1654981_NEGATIVE 256 83 43 90 50 NC_009009:SSA_0615|3end_RggD,_putative_608326..608476_NEGATIVE 253 67 21 146 97 NC_009009:SSA_1992|3end_Fructose-bisphosphate_aldolase,_putative_1989091..1989241_NEGATIVE