Origin IGS: tctattttcctttaaaattcacactacctctatcatacagttttttgggccaagacgcaatttctttgtcaggaatattatgggtcgctgtggcttcattcaaaatcaggcactaccagccagtcaaaaccgctcccgcctttatttcttggaggttttatgttatgatgaaggatagaaaaaggagagaatc .........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 gattctctcctttttctatccttcatcataacataaaacctccaagaaataaaggcgggagcggttttgactggctggtagtgcctgattttgaatgaagccacagcgacccataatattcctgacaaagaaattgcgtcttggcccaaaaaactgtatgatagaggtagtgtgaattttaaaggaaaataga Mask Tandem Repeat Region ================================================ tctattttcctttaaaattcacactacctctatcatacagttttttgggccaagacgcaatttctttgtcaggaatattatgggtcgctgtggcttcattcaaaatcaggcactaccagccagtcaaaaccgctcccgcctttatttcttggaggttttatgttatgatgaaggatagaaaaaggagagaatc Find is-nt database================================================ Query_seq: SSA_2060:SSA_2061|SSA_2060:SSA_2061:Arabinose efflux permease, putative:Peptide deformylase, putative:<-->:2062494..2062686 193 tctattttcctttaaaattcacactacctctatcatacagttttttgggccaagacgcaatttctttgtcaggaatattatgggtcgctgtggcttcattcaaaatcaggcactaccagccagtcaaaaccgctcccgcctttatttcttggaggttttatgttatgatgaaggatagaaaaaggagagaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2060:SSA_2061|SSA_2060:SSA_2061:Arabinose efflux permease, putative:Peptide deformylase, putative:<-->:2062494..2062686 193 tctattttcctttaaaattcacactacctctatcatacagttttttgggccaagacgcaatttctttgtcaggaatattatgggtcgctgtggcttcattcaaaatcaggcactaccagccagtcaaaaccgctcccgcctttatttcttggaggttttatgttatgatgaaggatagaaaaaggagagaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2060:SSA_2061|SSA_2060:SSA_2061:Arabinose efflux permease, putative:Peptide deformylase, putative:<-->:2062494..2062686 193 tctattttcctttaaaattcacactacctctatcatacagttttttgggccaagacgcaatttctttgtcaggaatattatgggtcgctgtggcttcattcaaaatcaggcactaccagccagtcaaaaccgctcccgcctttatttcttggaggttttatgttatgatgaaggatagaaaaaggagagaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tctattttcctttaaaattcacactacctctatcatacagttttttgggccaagacgcaatttctttgtcaggaatattatgggtcgctgtggcttcattcaaaatcaggcactaccagccagtcaaaaccgctcccgcctttatttcttggaggttttatgttatgatgaaggatagaaaaaggagagaatc Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: + Start: 17 End: 175 ................ M H T T S I I Q F F G P R R N F F V R N I M G R C G F I Q N Q A L P A S Q N R S R L Y F L E V L C Y D E G .................. Protein_Len: 49 Strand: + Start: 45 End: 191 ............................................ M G Q D A I S L S G I L W V A V A S F K I R H Y Q P V K T A P A F I S W R F Y V M M K D R K R R E .. Protein_Len: 36 Strand: - Start: 5 End: 109 .... * K G K F N V S G R D Y L K K P W S A I E K D P I N H T A T A E N L I M .................................................................................... tctattttcctttaaaattcacactacctctatcatacagttttttgggccaagacgcaatttctttgtcaggaatattatgggtcgctgtggcttcattcaaaatcaggcactaccagccagtcaaaaccgctcccgcctttatttcttggaggttttatgttatgatgaaggatagaaaaaggagagaatc 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: 140 End: 169 ...........................................................................................................................................CTTTATTTCTTGGAGGTTTTATGTTATGAT........................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 32 End: 61 ...............................ATTGCGTCTTGGCCCAAAAAACTGTATGAT.................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tctattttcctttaaaattcacactacctctatcatacagttttttgggccaagacgcaatttctttgtcaggaatattatgggtcgctgtggcttcattcaaaatcaggcactaccagccagtcaaaaccgctcccgcctttatttcttggaggttttatgttatgatgaaggatagaaaaaggagagaatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2060:SSA_2061|SSA_2060:SSA_2061:Arabinose efflux permease, putative:Peptide deformylase, putative:<-->:2062494..2062686 193 tctattttcctttaaaattcacactacctctatcatacagttttttgggccaagacgcaatttctttgtcaggaatattatgggtcgctgtggcttcattcaaaatcaggcactaccagccagtcaaaaccgctcccgcctttatttcttggaggttttatgttatgatgaaggatagaaaaaggagagaatc Intra-Species Hit: Count: 1 Min: 1 Max: 193 Len: 193 Subject: NC_009009_SSA_2060_SSA_2061|Arabinose efflux permease, putative:Peptide deformylase, putative|NEGATIVE:POSITIVE|[2062494,2062686]|193 HSP 1 e-value: 1.0E-105 bit: 383.0 Len: 193 Query Start:1 Query End:193 Subject Strand: POSITIVE Subject Start: 1 Subject End: 193 tctattttcctttaaaattcacactacctctatcatacagttttttgggccaagacgcaatttctttgtcaggaatattatgggtcgctgtggcttcattcaaaatcaggcactaccagccagtcaaaaccgctcccgcctttatttcttggaggttttatgttatgatgaaggatagaaaaaggagagaatc tctattttcctttaaaattcacactacctctatcatacagttttttgggccaagacgcaatttctttgtcaggaatattatgggtcgctgtggcttcattcaaaatcaggcactaccagccagtcaaaaccgctcccgcctttatttcttggaggttttatgttatgatgaaggatagaaaaaggagagaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUAUUUUCCUUUAAAAUUCACACUACCUCUAUCAUACAGUUUUUUGGGCCAAGACGCAAUUUCUUUGUCAGGAAUAUUAUGGGUCGCUGUGGCUUCAUUCAAAAUCAGGCACUACCAGCCAGUCAAAACCGCUCCCGCCUUUAUUUCUUGGAGGUUUUAUGUUAUGAUGAAGGAUAGAAAAAGGAGAGAAUC ....(((((((((..........((((((.(((((((((...(((((.((((.(((.((((((((.....))))))....)).)))....))))..............(((.......)))...)))))........(((((((.....)))))))....)).))))))).))).)))..))))))))).... (-42.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUCUCUCCUUUUUCUAUCCUUCAUCAUAACAUAAAACCUCCAAGAAAUAAAGGCGGGAGCGGUUUUGACUGGCUGGUAGUGCCUGAUUUUGAAUGAAGCCACAGCGACCCAUAAUAUUCCUGACAAAGAAAUUGCGUCUUGGCCCAAAAAACUGUAUGAUAGAGGUAGUGUGAAUUUUAAAGGAAAAUAGA .......((((((..(((.(((..((((((.((.........(((((.....(((((..(.(((((......))))).)..)))))..)))))......((((..(((.....((((.(((........))))))))))..)))).........))))))))..))))))..........))))))....... (-37.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1033 140 91 231 182 NC_009009:SSA_2060|5end_Arabinose_efflux_permease,_putative_2062403..2062633_NEGATIVE 373 138 91 85 34 NC_009009:SSA_0847|5end_6-phosphofructokinase,_putative_833372..833602_POSITIVE 367 120 76 137 86 NC_009009:SSA_2125|5end_Small_primase-like_protein_(Toprim_domain),_putative_2130019..2130249_NEGATIVE 355 126 83 90 46 NC_009009:SSA_1996|5end_DNA-directed_RNA_polymerase_delta_subunit,_putative_1994024..1994254_NEGATIVE 348 138 93 146 102 NC_009009:SSA_1783|5end_Xanthosine_triphosphate_pyrophosphatase_(NTPase/HAM1_family),_putative_1769106..1769336_NEGATIVE 325 147 102 87 42 NC_009009:SSA_0233|5end_Permease,_putative_227203..227433_POSITIVE 318 140 92 217 169 NC_009009:SSA_1770|5end_hypothetical_protein_1758431..1758661_NEGATIVE 316 124 81 71 18 NC_009009:SSA_0031|5end_Glutamine_phosphoribosylpyrophosphate_amidotransferase,_putative_36439..36669_POSITIVE 315 139 102 45 3 NC_009009:SSA_1459|5end_RNA_methyltransferase,_putative_1467481..1467711_NEGATIVE 313 126 82 78 34 NC_009009:SSA_0463|5end_Cobyrinic_acid_A,C-diamide_synthase,_putative_466865..467095_POSITIVE 312 155 111 184 130 NC_009009:SSA_0175|5end_Penicillin-binding_protein_1B,_putative_172152..172382_POSITIVE 310 72 38 69 31 NC_009009:SSA_1451|5end_Exonuclease_RexA,_putative_1456418..1456648_NEGATIVE 310 67 26 108 65 NC_009009:SSA_0671|5end_Methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase,_putative_654340..654570_POSITIVE 309 150 107 130 71 NC_009009:SSA_0190|5end_hypothetical_protein_191481..191711_POSITIVE 307 102 62 206 159 NC_009009:SSA_1292|5end_hypothetical_protein_1311578..1311808_NEGATIVE 304 169 122 94 35 NC_009009:SSA_1800|5end_UDP-N-acetylmuramate--L-alanine_ligase,_putative_1782371..1782601_NEGATIVE 304 157 111 59 7 NC_009009:SSA_1405|5end_Copper_homeostasis_protein_CutC,_putative_1419393..1419623_NEGATIVE 303 123 86 180 131 NC_009009:SSA_0943|5end_ABC_transporter_membrane-spanning_permease-phosphate_transport,_putative_950846..951076_POSITIVE 302 154 112 163 114 NC_009009:SSA_1040|5end_Sugar_ABC_transporter,_permease_protein,_putative_1055302..1055532_POSITIVE 299 129 81 78 6 NC_009009:SSA_1481|5end_FmtA-like_protein,_putative_1486622..1486852_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 140 92 123 81 NC_009009:SSA_1960|3end_hypothetical_protein_1956571..1956721_NEGATIVE 348 138 93 149 105 NC_009009:SSA_1784|3end_Glutamate_racemase,_putative_1769103..1769253_NEGATIVE 325 147 102 81 36 NC_009009:SSA_0232|3end_hypothetical_protein_227277..227427_POSITIVE 310 72 38 72 34 NC_009009:SSA_1452|3end_Second_subunit_of_major_exonuclease,_putative_1456415..1456565_NEGATIVE 309 150 107 92 33 NC_009009:SSA_0189|3end_Competence_protein_ComGF,_putative_191523..191673_POSITIVE 308 159 115 60 7 NC_009009:SSA_0676|3end_Farnesyl_diphosphate_synthase,_putative_659553..659703_POSITIVE 303 176 131 81 29 NC_009009:SSA_1949|3end_AliA_protein,_putative_1942403..1942553_NEGATIVE 302 89 45 133 95 NC_009009:SSA_2126|3end_hypothetical_protein_2129985..2130135_NEGATIVE 299 159 112 91 42 NC_009009:SSA_1430|3end_Ribonuclease_Z,_putative_1437107..1437257_NEGATIVE 299 159 112 147 99 NC_009009:SSA_0190|3end_hypothetical_protein_191905..192055_POSITIVE 290 139 91 151 100 NC_009009:SSA_1039|3end_Sugar_ABC_transporter,_ATP-binding_protein,_putative_1055389..1055539_POSITIVE 284 137 91 151 108 NC_009009:SSA_2042|3end_hypothetical_protein_2046669..2046819_NEGATIVE 283 139 99 148 103 NC_009009:SSA_0716|3end_Competence_protein,_putative_703710..703860_POSITIVE 282 121 81 133 92 NC_009009:SSA_0221|3end_PTS_system,_mannose-specific_IIC_component,_putative_217295..217445_POSITIVE 281 151 113 48 1 NC_009009:SSA_2308|3end_hypothetical_protein_2309893..2310043_NEGATIVE 281 124 84 64 30 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 279 70 22 55 7 NC_009009:SSA_2142|3end_Argininosuccinate_synthase,_putative_2142216..2142366_NEGATIVE 279 140 92 126 59 NC_009009:SSA_1451|3end_Exonuclease_RexA,_putative_1452744..1452894_NEGATIVE 278 141 108 142 113 NC_009009:SSA_2324|3end_hypothetical_protein_2328847..2328997_NEGATIVE 278 60 18 135 90 NC_009009:SSA_1712|3end_Arsenate_reductase_(ArsC),_glutaredoxin_family,_putative_1699731..1699881_NEGATIVE