Origin IGS: cgtctaagcgtctcataaatttaaatgtgactgagacgccatttaaaatttatgtgcgtcggattctcacagttaaataattgcgttgacaaagccgttacagccgttcttccattctttgaaaagaatgtttaatagacaagaaatctggactagtattggtctggatttttttgtgaatatagaggtcatagctttttgactatgcttcgttataattagaaaaattttaagttttatcaag .........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 cttgataaaacttaaaatttttctaattataacgaagcatagtcaaaaagctatgacctctatattcacaaaaaaatccagaccaatactagtccagatttcttgtctattaaacattcttttcaaagaatggaagaacggctgtaacggctttgtcaacgcaattatttaactgtgagaatccgacgcacataaattttaaatggcgtctcagtcacatttaaatttatgagacgcttagacg Mask Tandem Repeat Region ================================================ cgtctaagcgtctcataaatttaaatgtgactgagacgccatttaaaatttatgtgcgtcggattctcacagttaaataattgcgttgacaaagccgttacagccgttcttccattctttgaaaagaatgtttaatagacaagaaatctggactagtattggtctggatttttttgtgaatatagaggtcatagctttttgactatgcttcgttataattagaaaaattttaagttttatcaag Find is-nt database================================================ Query_seq: SSA_2031:SSA_2032|SSA_2031:SSA_2032:Conserved domain uncharacterized protein:Integrase/recombinase, phage integrase family, putative:->->:2037902..2038145 244 cgtctaagcgtctcataaatttaaatgtgactgagacgccatttaaaatttatgtgcgtcggattctcacagttaaataattgcgttgacaaagccgttacagccgttcttccattctttgaaaagaatgtttaatagacaagaaatctggactagtattggtctggatttttttgtgaatatagaggtcatagctttttgactatgcttcgttataattagaaaaattttaagttttatcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2031:SSA_2032|SSA_2031:SSA_2032:Conserved domain uncharacterized protein:Integrase/recombinase, phage integrase family, putative:->->:2037902..2038145 244 cgtctaagcgtctcataaatttaaatgtgactgagacgccatttaaaatttatgtgcgtcggattctcacagttaaataattgcgttgacaaagccgttacagccgttcttccattctttgaaaagaatgtttaatagacaagaaatctggactagtattggtctggatttttttgtgaatatagaggtcatagctttttgactatgcttcgttataattagaaaaattttaagttttatcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2031:SSA_2032|SSA_2031:SSA_2032:Conserved domain uncharacterized protein:Integrase/recombinase, phage integrase family, putative:->->:2037902..2038145 244 cgtctaagcgtctcataaatttaaatgtgactgagacgccatttaaaatttatgtgcgtcggattctcacagttaaataattgcgttgacaaagccgttacagccgttcttccattctttgaaaagaatgtttaatagacaagaaatctggactagtattggtctggatttttttgtgaatatagaggtcatagctttttgactatgcttcgttataattagaaaaattttaagttttatcaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgtctaagcgtctcataaatttaaatgtgactgagacgccatttaaaatttatgtgcgtcggattctcacagttaaataattgcgttgacaaagccgttacagccgttcttccattctttgaaaagaatgtttaatagacaagaaatctggactagtattggtctggatttttttgtgaatatagaggtcatagctttttgactatgcttcgttataattagaaaaattttaagttttatcaag Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 31 End: 132 .............................. M R R H L K F M C V G F S Q L N N C V D K A V T A V L P F F E K N V ................................................................................................................ Protein_Len: 41 Strand: + Start: 77 End: 199 ............................................................................ M I A L T K P L Q P F F H S L K R M F N R Q E I W T S I G L D F F V N I E V I A F ............................................. Protein_Len: 56 Strand: - Start: 76 End: 243 ........................................................................... I I A N V F G N C G N K W E K F L I N L L C S I Q V L I P R S K K T F I S T M A K Q S H K T I I L F I K L K I M . cgtctaagcgtctcataaatttaaatgtgactgagacgccatttaaaatttatgtgcgtcggattctcacagttaaataattgcgttgacaaagccgttacagccgttcttccattctttgaaaagaatgtttaatagacaagaaatctggactagtattggtctggatttttttgtgaatatagaggtcatagctttttgactatgcttcgttataattagaaaaattttaagttttatcaag 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: 83 Start: 215 End: 244 ......................................................................................................................................................................................................................CTTGATAAAACTTAAAATTTTTCTAATTAT Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgtctaagcgtctcataaatttaaatgtgactgagacgccatttaaaatttatgtgcgtcggattctcacagttaaataattgcgttgacaaagccgttacagccgttcttccattctttgaaaagaatgtttaatagacaagaaatctggactagtattggtctggatttttttgtgaatatagaggtcatagctttttgactatgcttcgttataattagaaaaattttaagttttatcaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 70 HP_score: -7.1 Tail_Score: -3.72576 Start: 113 End: 130 Full_Region: TTACAGCCGTTCTTC CATTCTT TGAA AAGAATG TTTAATAGACAAGAA ................................................................................................................CATTCTTTGAAAAGAATG.................................................................................................................. TransTerm Strand: + Conf: 84 HP_score: -3.7 Tail_Score: -5.65177 Start: 147 End: 168 Full_Region: TTAATAGACAAGAAA TCTGGACTA GTAT TGGTCTGGA TTTTTTTGTGAATAT ..................................................................................................................................................TCTGGACTAGTATTGGTCTGGA............................................................................ Find igs database================================================ Query_seq: SSA_2031:SSA_2032|SSA_2031:SSA_2032:Conserved domain uncharacterized protein:Integrase/recombinase, phage integrase family, putative:->->:2037902..2038145 244 cgtctaagcgtctcataaatttaaatgtgactgagacgccatttaaaatttatgtgcgtcggattctcacagttaaataattgcgttgacaaagccgttacagccgttcttccattctttgaaaagaatgtttaatagacaagaaatctggactagtattggtctggatttttttgtgaatatagaggtcatagctttttgactatgcttcgttataattagaaaaattttaagttttatcaag Intra-Species Hit: Count: 1 Min: 1 Max: 244 Len: 244 Subject: NC_009009_SSA_2031_SSA_2032|Conserved domain uncharacterized protein:Integrase/recombinase, phage integrase family, putative|POSITIVE:POSITIVE|[2037902,2038145]|244 HSP 1 e-value: 1.0E-123 bit: 442.0 Len: 244 Query Start:1 Query End:244 Subject Strand: POSITIVE Subject Start: 1 Subject End: 244 cgtctaagcgtctcataaatttaaatgtgactgagacgccatttaaaatttatgtgcgtcggattctcacagttaaataattgcgttgacaaagccgttacagccgttcttccattctttgaaaagaatgtttaatagacaagaaatctggactagtattggtctggannnnnnngtgaatatagaggtcatagctttttgactatgcttcgttataattagaaaaattttaagttttatcaag cgtctaagcgtctcataaatttaaatgtgactgagacgccatttaaaatttatgtgcgtcggattctcacagttaaataattgcgttgacaaagccgttacagccgttcttccattctttgaaaagaatgtttaatagacaagaaatctggactagtattggtctggatttttttgtgaatatagaggtcatagctttttgactatgcttcgttataattagaaaaattttaagttttatcaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUCUAAGCGUCUCAUAAAUUUAAAUGUGACUGAGACGCCAUUUAAAAUUUAUGUGCGUCGGAUUCUCACAGUUAAAUAAUUGCGUUGACAAAGCCGUUACAGCCGUUCUUCCAUUCUUUGAAAAGAAUGUUUAAUAGACAAGAAAUCUGGACUAGUAUUGGUCUGGAUUUUUUUGUGAAUAUAGAGGUCAUAGCUUUUUGACUAUGCUUCGUUAUAAUUAGAAAAAUUUUAAGUUUUAUCAAG .......((((((((...((......))...)))))))).(((((((((((.((((...(((..((.(.(((((....))))).)..)).....))).))))...((((...(((((((....)))))))........((((((((((..(((((....)))))..)).))))))))))))...((((.((((((.....).))))))))).............)))))))))))......... (-54.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGAUAAAACUUAAAAUUUUUCUAAUUAUAACGAAGCAUAGUCAAAAAGCUAUGACCUCUAUAUUCACAAAAAAAUCCAGACCAAUACUAGUCCAGAUUUCUUGUCUAUUAAACAUUCUUUUCAAAGAAUGGAAGAACGGCUGUAACGGCUUUGUCAACGCAAUUAUUUAACUGUGAGAAUCCGACGCACAUAAAUUUUAAAUGGCGUCUCAGUCACAUUUAAAUUUAUGAGACGCUUAGACG ...........(((((((((.............((.(((((((......)))))).).))....((((((...(((((..(((........)))..))))).((((........(((((((....)))))))...((..(((((...)))))...))...)))).........))))))..............)))))))))..(((((((((................)))))))))...... (-44.49) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 384 117 78 38 1 NC_009009:SSA_0871|5end_Cell_division_protein_FtsX,_putative_863621..863851_POSITIVE 327 116 79 183 141 NC_009009:SSA_0198|5end_Dihydrofolate_synthetase,_putative_196901..197131_POSITIVE 314 210 161 114 47 NC_009009:SSA_0861|5end_hypothetical_protein_852977..853207_NEGATIVE 312 140 94 96 56 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 290 111 80 215 181 NC_009009:SSA_0472|5end_Precorrin-3B_C17-methyltransferase,_putative_474780..475010_POSITIVE 286 127 84 49 7 NC_009009:SSA_0086|5end_V-type_sodium_ATPase,_subunit_K,_putative_87839..88069_POSITIVE 280 97 59 87 40 NC_009009:SSA_0575|5end_Hydrolase,_HAD_superfamily,_putative_569527..569757_POSITIVE 276 210 165 115 78 NC_009009:SSA_1577|5end_Proline_dipeptidase,_putative_1580294..1580524_POSITIVE 270 123 81 219 172 NC_009009:SSA_1269|5end_hypothetical_protein_1293352..1293582_NEGATIVE 270 118 81 65 28 NC_009009:SSA_0197|5end_Dihydropteroate_synthase,_putative_195946..196176_POSITIVE 269 121 81 111 69 NC_009009:SSA_2014|5end_D-alanyl-D-alanine_carboxypeptidase,_putative_2014807..2015037_NEGATIVE 269 130 84 64 6 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 264 200 156 223 180 NC_009009:SSA_0025|5end_DNA_repair_protein_recO,_putative_29694..29924_POSITIVE 262 118 81 94 38 NC_009009:SSA_0068|5end_Alcohol-acetaldehyde_dehydrogenase,_putative_70114..70344_POSITIVE 261 208 163 171 127 NC_009009:SSA_1612|5end_Diacylglycerol_kinase,_putative_1616497..1616727_NEGATIVE 260 130 84 68 25 NC_009009:SSA_0635|5end_Indole-3-glycerol_phosphate_synthase,_putative_624388..624618_POSITIVE 258 100 52 137 82 NC_009009:SSA_1254|5end_hypothetical_protein_1281484..1281714_NEGATIVE 257 113 93 61 38 NC_009009:SSA_0323|5end_Flavoprotein,_putative_316799..317029_NEGATIVE 257 109 63 53 2 NC_009009:SSA_0243|5end_Cyclo-nucleotide_phosphodiesterase,_putative_238235..238465_NEGATIVE 256 121 94 212 185 NC_009009:SSA_1401|5end_Transcriptional_regulator_GntR_family_1413062..1413292_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 397 117 77 45 7 NC_009009:SSA_0870|3end_Cell_division_protein_FtsE,_putative_863708..863858_POSITIVE 314 210 161 99 32 NC_009009:SSA_0862|3end_MurM,_putative_852992..853142_NEGATIVE 306 176 141 82 46 NC_009009:SSA_1205|3end_Bta,_putative_1230057..1230207_POSITIVE 290 111 80 138 104 NC_009009:SSA_0471|3end_CbiG_protein,_putative_474783..474933_POSITIVE 287 124 82 99 58 NC_009009:SSA_2209|3end_Penicillin-binding_protein_2A,_putative_2208144..2208294_NEGATIVE 285 189 141 87 37 NC_009009:SSA_1962|3end_Amino_acid_ABC_transporter,_ATP-binding_protein,_putative_1960930..1961080_POSITIVE 283 104 62 144 105 NC_009009:SSA_1418|3end_Conserved_uncharacterized_protein_1428139..1428289_NEGATIVE 280 177 144 88 51 NC_009009:SSA_1487|3end_Conserved_uncharacterized_protein_1493483..1493633_NEGATIVE 270 123 81 95 48 NC_009009:SSA_1270|3end_Flavodoxin_1293476..1293626_NEGATIVE 270 128 83 55 1 NC_009009:SSA_1039|3end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_1055389..1055539_POSITIVE 269 121 81 124 82 NC_009009:SSA_2015|3end_Phosphoglycerate_mutase,_putative_2014794..2014944_NEGATIVE 260 130 84 71 28 NC_009009:SSA_0634|3end_Anthranilate_phosphoribosyltransferase,_putative_624471..624621_POSITIVE 255 130 81 79 27 NC_009009:SSA_1384|3end_hypothetical_protein_1401715..1401865_NEGATIVE 250 180 139 97 52 NC_009009:SSA_0259|3end_Thiol_peroxidase,_putative_253013..253163_NEGATIVE 248 214 171 90 45 NC_009009:SSA_1544|3end_Conserved_uncharacterized_protein_1548314..1548464_NEGATIVE 248 116 83 46 2 NC_009009:SSA_0371|3end_NADP-specific_glutamate_dehydrogenase,_putative_360413..360563_NEGATIVE 248 119 95 143 121 NC_009009:SSA_0263|3end_Zinc_metalloproteinase_in_scaA_5'region,_putative_258246..258396_POSITIVE 246 189 142 125 77 NC_009009:SSA_1471|3end_hypothetical_protein_1476981..1477131_NEGATIVE 245 214 171 102 65 NC_009009:SSA_1220|3end_DNA_gyrase_A_subunit,_putative_1241352..1241502_NEGATIVE 243 100 60 142 105 NC_009009:SSA_1347|3end_PhnA_protein,_putative_1364791..1364941_NEGATIVE