Origin IGS: tataaataaaactttatccaattataccataaattcctgtaaaaaaagtatccttagggtactagatactcatttctccccaacctaattaaaaagggcaaaacttctatcaagcttatatctacacttcttcccttcccgtctgctaaatcatcttcaagttacttctgcaaaatcgagctatctactctggagattactggtcgccttctattcttccttattttaaaaaaaaattacaatgcatactaaaaaaaccccgttttcacggggtttagtgtctgactataattgttatctgggaacggaatcgaa .........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 ttcgattccgttcccagataacaattatagtcagacactaaaccccgtgaaaacggggtttttttagtatgcattgtaatttttttttaaaataaggaagaatagaaggcgaccagtaatctccagagtagatagctcgattttgcagaagtaacttgaagatgatttagcagacgggaagggaagaagtgtagatataagcttgatagaagttttgccctttttaattaggttggggagaaatgagtatctagtaccctaaggatactttttttacaggaatttatggtataattggataaagttttatttata Mask Tandem Repeat Region ================================================ tataaataaaactttatccaattataccataaattcctgtaaaaaaagtatccttagggtactagatactcatttctccccaacctaattaaaaagggcaaaacttctatcaagcttatatctacacttcttcccttcccgtctgctaaatcatcttcaagttacttctgcaaaatcgagctatctactctggagattactggtcgccttctattcttccttattttaaaaaaaaattacaatgcatactaaaaaaaccccgttttcacggggtttagtgtctgactataattgttatctgggaacggaatcgaa Find is-nt database================================================ Query_seq: SSA_1519:SSA_1520|SSA_1519:SSA_1520:Polysaccharide/teichoic acid transporter, putative:Elongation factor Tu, putative:<-<-:1526160..1526474 315 tataaataaaactttatccaattataccataaattcctgtaaaaaaagtatccttagggtactagatactcatttctccccaacctaattaaaaagggcaaaacttctatcaagcttatatctacacttcttcccttcccgtctgctaaatcatcttcaagttacttctgcaaaatcgagctatctactctggagattactggtcgccttctattcttccttattttaaaaaaaaattacaatgcatactaaaaaaaccccgttttcacggggtttagtgtctgactataattgttatctgggaacggaatcgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1519:SSA_1520|SSA_1519:SSA_1520:Polysaccharide/teichoic acid transporter, putative:Elongation factor Tu, putative:<-<-:1526160..1526474 315 tataaataaaactttatccaattataccataaattcctgtaaaaaaagtatccttagggtactagatactcatttctccccaacctaattaaaaagggcaaaacttctatcaagcttatatctacacttcttcccttcccgtctgctaaatcatcttcaagttacttctgcaaaatcgagctatctactctggagattactggtcgccttctattcttccttattttaaaaaaaaattacaatgcatactaaaaaaaccccgttttcacggggtttagtgtctgactataattgttatctgggaacggaatcgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1519:SSA_1520|SSA_1519:SSA_1520:Polysaccharide/teichoic acid transporter, putative:Elongation factor Tu, putative:<-<-:1526160..1526474 315 tataaataaaactttatccaattataccataaattcctgtaaaaaaagtatccttagggtactagatactcatttctccccaacctaattaaaaagggcaaaacttctatcaagcttatatctacacttcttcccttcccgtctgctaaatcatcttcaagttacttctgcaaaatcgagctatctactctggagattactggtcgccttctattcttccttattttaaaaaaaaattacaatgcatactaaaaaaaccccgttttcacggggtttagtgtctgactataattgttatctgggaacggaatcgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tataaataaaactttatccaattataccataaattcctgtaaaaaaagtatccttagggtactagatactcatttctccccaacctaattaaaaagggcaaaacttctatcaagcttatatctacacttcttcccttcccgtctgctaaatcatcttcaagttacttctgcaaaatcgagctatctactctggagattactggtcgccttctattcttccttattttaaaaaaaaattacaatgcatactaaaaaaaccccgttttcacggggtttagtgtctgactataattgttatctgggaacggaatcgaa Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 88 End: 249 ....................................................................................... M K K G K T S I K L I S T L L P F P S A K S S S S Y F C K I E L S T L E I T G R L L F F L I L K K N Y N A Y .................................................................. Protein_Len: 42 Strand: + Start: 150 End: 275 ..................................................................................................................................................... M I F K L L L Q N R A I Y S G D Y W S P S I L P Y F K K K L Q C I L K K P R F H G V ........................................ tataaataaaactttatccaattataccataaattcctgtaaaaaaagtatccttagggtactagatactcatttctccccaacctaattaaaaagggcaaaacttctatcaagcttatatctacacttcttcccttcccgtctgctaaatcatcttcaagttacttctgcaaaatcgagctatctactctggagattactggtcgccttctattcttccttattttaaaaaaaaattacaatgcatactaaaaaaaccccgttttcacggggtttagtgtctgactataattgttatctgggaacggaatcgaa 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================================================ tataaataaaactttatccaattataccataaattcctgtaaaaaaagtatccttagggtactagatactcatttctccccaacctaattaaaaagggcaaaacttctatcaagcttatatctacacttcttcccttcccgtctgctaaatcatcttcaagttacttctgcaaaatcgagctatctactctggagattactggtcgccttctattcttccttattttaaaaaaaaattacaatgcatactaaaaaaaccccgttttcacggggtttagtgtctgactataattgttatctgggaacggaatcgaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 82 HP_score: -4.2 Tail_Score: -5.40474 Start: 48 End: 62 Full_Region: agaaatgagtatcta gtaccc taa ggatac tttttttacaggaat ...............................................gtaccctaaggatac............................................................................................................................................................................................................................................................. TransTerm Strand: + Conf: 41 HP_score: -2.1 Tail_Score: -2.91395 Start: 57 End: 71 Full_Region: AAAAAAGTATCCTTA GGGTA CTAGA TACTC ATTTCTCCCCAACCT ........................................................GGGTACTAGATACTC.................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 87 HP_score: -10.4 Tail_Score: -3.89212 Start: 258 End: 273 Full_Region: TGCATACTAAAAAAA CCCCGT TTTC ACGGGG TTTAGTGTCTGACTA .................................................................................................................................................................................................................................................................CCCCGTTTTCACGGGG.......................................... Find igs database================================================ Query_seq: SSA_1519:SSA_1520|SSA_1519:SSA_1520:Polysaccharide/teichoic acid transporter, putative:Elongation factor Tu, putative:<-<-:1526160..1526474 315 tataaataaaactttatccaattataccataaattcctgtaaaaaaagtatccttagggtactagatactcatttctccccaacctaattaaaaagggcaaaacttctatcaagcttatatctacacttcttcccttcccgtctgctaaatcatcttcaagttacttctgcaaaatcgagctatctactctggagattactggtcgccttctattcttccttattttaaaaaaaaattacaatgcatactaaaaaaaccccgttttcacggggtttagtgtctgactataattgttatctgggaacggaatcgaa Intra-Species Hit: Count: 1 Min: 1 Max: 315 Len: 315 Subject: NC_009009_SSA_1519_SSA_1520|Polysaccharide/teichoic acid transporter, putative:Elongation factor Tu, putative|NEGATIVE:NEGATIVE|[1526160,1526474]|315 HSP 1 e-value: 1.0E-137 bit: 488.0 Len: 315 Query Start:1 Query End:315 Subject Strand: POSITIVE Subject Start: 1 Subject End: 315 tataaataaaactttatccaattataccataaattcctgtnnnnnnngtatccttagggtactagatactcatttctccccaacctaattaaaaagggcaaaacttctatcaagcttatatctacacttcttcccttcccgtctgctaaatcatcttcaagttacttctgcaaaatcgagctatctactctggagattactggtcgccttctattcttccttattttnnnnnnnnnttacaatgcatactnnnnnnnccccgttttcacggggtttagtgtctgactataattgttatctgggaacggaatcgaa tataaataaaactttatccaattataccataaattcctgtaaaaaaagtatccttagggtactagatactcatttctccccaacctaattaaaaagggcaaaacttctatcaagcttatatctacacttcttcccttcccgtctgctaaatcatcttcaagttacttctgcaaaatcgagctatctactctggagattactggtcgccttctattcttccttattttaaaaaaaaattacaatgcatactaaaaaaaccccgttttcacggggtttagtgtctgactataattgttatctgggaacggaatcgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAAUAAAACUUUAUCCAAUUAUACCAUAAAUUCCUGUAAAAAAAGUAUCCUUAGGGUACUAGAUACUCAUUUCUCCCCAACCUAAUUAAAAAGGGCAAAACUUCUAUCAAGCUUAUAUCUACACUUCUUCCCUUCCCGUCUGCUAAAUCAUCUUCAAGUUACUUCUGCAAAAUCGAGCUAUCUACUCUGGAGAUUACUGGUCGCCUUCUAUUCUUCCUUAUUUUAAAAAAAAAUUACAAUGCAUACUAAAAAAACCCCGUUUUCACGGGGUUUAGUGUCUGACUAUAAUUGUUAUCUGGGAACGGAAUCGAA .....................................((((.....(((((((...))))))).((((....(((..(((...............)))..)))....))))...........))))....((((.((((((...((......((((((((((.......((........)).....))).)))))))...(((((.................(((((.....)))))........(((((((....(((((((....))))))))))))))..))))).....))....)))))).))))..... (-51.56) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGAUUCCGUUCCCAGAUAACAAUUAUAGUCAGACACUAAACCCCGUGAAAACGGGGUUUUUUUAGUAUGCAUUGUAAUUUUUUUUUAAAAUAAGGAAGAAUAGAAGGCGACCAGUAAUCUCCAGAGUAGAUAGCUCGAUUUUGCAGAAGUAACUUGAAGAUGAUUUAGCAGACGGGAAGGGAAGAAGUGUAGAUAUAAGCUUGAUAGAAGUUUUGCCCUUUUUAAUUAGGUUGGGGAGAAAUGAGUAUCUAGUACCCUAAGGAUACUUUUUUUACAGGAAUUUAUGGUAUAAUUGGAUAAAGUUUUAUUUAUA .....((((.(((((.......((((((..((((..((((((((((((....)))))))....))))).((((..((.(((((((((((...)))))))))))....((.((.......)).)).((((.....)))).))..))))........))))..))))))........))))).))))....((((((((.((((((.......((((..((((..((.....))..))))..))))...(((((((((((.((((....((........))...)))).)))))...)))))))))))))))))))) (-72.06) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 881 100 51 191 142 NC_009009:SSA_1519|5end_Polysaccharide/teichoic_acid_transporter,_putative_1526069..1526299_NEGATIVE 343 147 111 56 7 NC_009009:SSA_2129|5end_Arsenical_resistance_operon_transcription_repressor_(ArsR),_putative_2133308..2133538_NEGATIVE 321 147 108 126 73 NC_009009:SSA_0894|5end_ATP-binding_cassette_protein,_putative_885779..886009_POSITIVE 305 170 122 193 126 NC_009009:SSA_1307|5end_Trk_transporter_membrane-spanning_protein-K+_transport,_putative_1326270..1326500_NEGATIVE 303 140 96 111 55 NC_009009:SSA_0433|5end_Methenyl_tetrahydrofolate_cyclohydrolase,_putative_435654..435884_NEGATIVE 303 288 243 198 147 NC_009009:SSA_0310|5end_hypothetical_protein_305306..305536_POSITIVE 302 209 164 215 176 NC_009009:SSA_1583|5end_6-O-methylguanine-DNA_methyltransferase,_putative_1586026..1586256_NEGATIVE 301 217 173 231 175 NC_009009:SSA_1595|5end_Tellurite_resistance,_putative_1601814..1602044_NEGATIVE 301 230 181 210 144 NC_009009:SSA_0071|5end_N-acetylmannosamine-6-p_hosphate_2-epimerase_1,_putative_75210..75440_POSITIVE 300 189 141 65 7 NC_009009:SSA_0527|5end_Propanediol_utilization_protein_PduL_524625..524855_POSITIVE 294 220 175 144 114 NC_009009:SSA_1254|5end_hypothetical_protein_1281484..1281714_NEGATIVE 288 190 141 52 18 NC_009009:SSA_0923|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_933010..933240_POSITIVE 288 199 152 75 26 NC_009009:SSA_0219|5end_PTS_system,_sugar-specific_enzyme_IIA_component,_putative_215367..215597_POSITIVE 287 159 113 136 78 NC_009009:SSA_0834|5end_Accessory_secretory_protein_Asp2,_putative_819510..819740_POSITIVE 286 224 190 231 196 NC_009009:SSA_1575|5end_Glycosyl_transferase,_putative_1579110..1579340_NEGATIVE 284 281 243 210 179 NC_009009:SSA_2211|5end_Transmembrane_protein,_putative_2212473..2212703_NEGATIVE 284 208 165 167 120 NC_009009:SSA_1550|5end_hypothetical_protein_1552665..1552895_NEGATIVE 282 158 127 215 186 NC_009009:SSA_1250|5end_Conserved_uncharacterized_protein,_putative_1274512..1274742_NEGATIVE 282 168 137 69 36 NC_009009:SSA_0833|5end_Accessory_secretory_protein_Asp1,_putative_817940..818170_POSITIVE 280 171 135 224 180 NC_009009:SSA_0660|5end_Cell_division_protein_DivIVA,_putative_643798..644028_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 342 204 163 110 70 NC_009009:SSA_2166|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_2163873..2164023_NEGATIVE 321 147 108 139 86 NC_009009:SSA_0893|3end_ATP-binding_cassette_transporter-like_protein,_putative_885872..886022_POSITIVE 303 140 96 96 40 NC_009009:SSA_0434|3end_Glutamate_formiminotransferase,_putative_435669..435819_NEGATIVE 292 173 137 129 85 NC_009009:SSA_1297|3end_Nuclease_subunit_of_the_excinuclease_complex,_subunit_C,_putative_1313141..1313291_NEGATIVE 287 159 113 146 88 NC_009009:SSA_0833|3end_Accessory_secretory_protein_Asp1,_putative_819600..819750_POSITIVE 286 80 31 84 30 NC_009009:SSA_0395|3end_6-phospho-beta-glucosidase,_putative_392580..392730_POSITIVE 284 281 243 56 25 NC_009009:SSA_2212|3end_Possible_polysaccharide_transport_protein,_putative_2212627..2212777_NEGATIVE 282 168 137 60 27 NC_009009:SSA_0832|3end_SecY-like_protein,_putative_818011..818161_POSITIVE 282 207 161 68 17 NC_009009:SSA_0470|3end_Precorrin-4_methylase,_putative_473732..473882_POSITIVE 279 218 173 118 82 NC_009009:SSA_2262|3end_Arginyl-tRNA_synthetase,_putative_2260685..2260835_POSITIVE 279 207 161 80 35 NC_009009:SSA_0488|3end_Glutamate-1-semialdehyde_2,1-aminotransferase,_putative_489742..489892_POSITIVE 278 164 127 145 108 NC_009009:SSA_0214|3end_Single-strand_DNA-binding_protein_(conjugal_DNA-protein_transfer_system),_putative_210690..210840_POSITIVE 275 159 114 145 84 NC_009009:SSA_1267|3end_crcB-like_protein_2,_putative_1290973..1291123_NEGATIVE 274 146 103 134 82 NC_009009:SSA_1550|3end_hypothetical_protein_1552228..1552378_NEGATIVE 270 164 128 137 94 NC_009009:SSA_0989|3end_Conserved_protein,_possible_transcriptional_regulator_(sigma-70,_region_4),_putative_991816..991966_POSITIVE 267 171 131 135 96 NC_009009:SSA_2219|3end_UDP-glucose_4-epimerase,_putative_2219967..2220117_NEGATIVE 267 179 134 46 8 NC_009009:SSA_1593|3end_Dipeptidase,_putative_1596390..1596540_NEGATIVE 265 198 151 147 91 NC_009009:SSA_1247|3end_hypothetical_protein_1271222..1271372_NEGATIVE 265 147 104 148 99 NC_009009:SSA_0892|3end_ATP-binding_cassette_lipoprotein,_putative_884578..884728_POSITIVE 265 221 197 101 73 NC_009009:SSA_0087|3end_V-type_sodium_ATPase,_subunit_E,_putative_88999..89149_POSITIVE