Origin IGS: aaagactccttgccgagcacatgctcaatttttttcatacgccttggctacaaagatccaagatattaagactttaatcaactcataggacgtgttcagttagcactgtgattttaaaattatggtcttagcagcttattatatcctcatctttgtatcaagcacgtacagaccttattttaccacaatttcaggcaaaagaaaaaggctgaaaatggcttttttctataaaagtactgaaaatctatttttcttttctatagttgattatagttggctgtcagagttcgttttttccctttcgattcgtcaaataagatggcggtatagccactattcacttttcaaagaggacttcttgctttataataaatacagtgactcatttcaaacatgtaaaggagacaatc .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 gattgtctcctttacatgtttgaaatgagtcactgtatttattataaagcaagaagtcctctttgaaaagtgaatagtggctataccgccatcttatttgacgaatcgaaagggaaaaaacgaactctgacagccaactataatcaactatagaaaagaaaaatagattttcagtacttttatagaaaaaagccattttcagcctttttcttttgcctgaaattgtggtaaaataaggtctgtacgtgcttgatacaaagatgaggatataataagctgctaagaccataattttaaaatcacagtgctaactgaacacgtcctatgagttgattaaagtcttaatatcttggatctttgtagccaaggcgtatgaaaaaaattgagcatgtgctcggcaaggagtcttt Mask Tandem Repeat Region ================================================ aaagactccttgccgagcacatgctcaatttttttcatacgccttggctacaaagatccaagatattaagactttaatcaactcataggacgtgttcagttagcactgtgattttaaaattatggtcttagcagcttattatatcctcatctttgtatcaagcacgtacagaccttattttaccacaatttcaggcaaaagaaaaaggctgaaaatggcttttttctataaaagtactgaaaatctatttttcttttctatagttgattatagttggctgtcagagttcgttttttccctttcgattcgtcaaataagatggcggtatagccactattcacttttcaaagaggacttcttgctttataataaatacagtgactcatttcaaacatgtaaaggagacaatc Find is-nt database================================================ Query_seq: SSA_2049:SSA_2050|SSA_2049:SSA_2050:Polyribonucleotide nucleotidyltransferase, putative:Arabinose efflux permease, putative:<-->:2052985..2053394 410 aaagactccttgccgagcacatgctcaatttttttcatacgccttggctacaaagatccaagatattaagactttaatcaactcataggacgtgttcagttagcactgtgattttaaaattatggtcttagcagcttattatatcctcatctttgtatcaagcacgtacagaccttattttaccacaatttcaggcaaaagaaaaaggctgaaaatggcttttttctataaaagtactgaaaatctatttttcttttctatagttgattatagttggctgtcagagttcgttttttccctttcgattcgtcaaataagatggcggtatagccactattcacttttcaaagaggacttcttgctttataataaatacagtgactcatttcaaacatgtaaaggagacaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2049:SSA_2050|SSA_2049:SSA_2050:Polyribonucleotide nucleotidyltransferase, putative:Arabinose efflux permease, putative:<-->:2052985..2053394 410 aaagactccttgccgagcacatgctcaatttttttcatacgccttggctacaaagatccaagatattaagactttaatcaactcataggacgtgttcagttagcactgtgattttaaaattatggtcttagcagcttattatatcctcatctttgtatcaagcacgtacagaccttattttaccacaatttcaggcaaaagaaaaaggctgaaaatggcttttttctataaaagtactgaaaatctatttttcttttctatagttgattatagttggctgtcagagttcgttttttccctttcgattcgtcaaataagatggcggtatagccactattcacttttcaaagaggacttcttgctttataataaatacagtgactcatttcaaacatgtaaaggagacaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2049:SSA_2050|SSA_2049:SSA_2050:Polyribonucleotide nucleotidyltransferase, putative:Arabinose efflux permease, putative:<-->:2052985..2053394 410 aaagactccttgccgagcacatgctcaatttttttcatacgccttggctacaaagatccaagatattaagactttaatcaactcataggacgtgttcagttagcactgtgattttaaaattatggtcttagcagcttattatatcctcatctttgtatcaagcacgtacagaccttattttaccacaatttcaggcaaaagaaaaaggctgaaaatggcttttttctataaaagtactgaaaatctatttttcttttctatagttgattatagttggctgtcagagttcgttttttccctttcgattcgtcaaataagatggcggtatagccactattcacttttcaaagaggacttcttgctttataataaatacagtgactcatttcaaacatgtaaaggagacaatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagactccttgccgagcacatgctcaatttttttcatacgccttggctacaaagatccaagatattaagactttaatcaactcataggacgtgttcagttagcactgtgattttaaaattatggtcttagcagcttattatatcctcatctttgtatcaagcacgtacagaccttattttaccacaatttcaggcaaaagaaaaaggctgaaaatggcttttttctataaaagtactgaaaatctatttttcttttctatagttgattatagttggctgtcagagttcgttttttccctttcgattcgtcaaataagatggcggtatagccactattcacttttcaaagaggacttcttgctttataataaatacagtgactcatttcaaacatgtaaaggagacaatc Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 119 End: 409 ...................................................................................................................... M M V L A A Y Y I L I F V S S T Y R P Y F T T I S G K R K R L K M A F F Y K S T E N L F F F S I V D Y S W L S E F V F S . aaagactccttgccgagcacatgctcaatttttttcatacgccttggctacaaagatccaagatattaagactttaatcaactcataggacgtgttcagttagcactgtgattttaaaattatggtcttagcagcttattatatcctcatctttgtatcaagcacgtacagaccttattttaccacaatttcaggcaaaagaaaaaggctgaaaatggcttttttctataaaagtactgaaaatctatttttcttttctatagttgattatagttggctgtcagagttcgttttttccctttcgattcgtcaaataagatggcggtatagccactattcacttttcaaagaggacttcttgctttataataaatacagtgactcatttcaaacatgtaaaggagacaatc 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: 86 Start: 341 End: 370 ....................................................................................................................................................................................................................................................................................................................................................CTTTTCAAAGAGGACTTCTTGCTTTATAAT........................................ PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 177 End: 206 ................................................................................................................................................................................TTTTTCTTTTGCCTGAAATTGTGGTAAAAT............................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 363 End: 392 ..........................................................................................................................................................................................................................................................................................................................................................................TTTGAAATGAGTCACTGTATTTATTATAAA.................. PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 113 End: 142 ................................................................................................................TTTAAAATTATGGTCTTAGCAGCTTATTAT............................................................................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaagactccttgccgagcacatgctcaatttttttcatacgccttggctacaaagatccaagatattaagactttaatcaactcataggacgtgttcagttagcactgtgattttaaaattatggtcttagcagcttattatatcctcatctttgtatcaagcacgtacagaccttattttaccacaatttcaggcaaaagaaaaaggctgaaaatggcttttttctataaaagtactgaaaatctatttttcttttctatagttgattatagttggctgtcagagttcgttttttccctttcgattcgtcaaataagatggcggtatagccactattcacttttcaaagaggacttcttgctttataataaatacagtgactcatttcaaacatgtaaaggagacaatc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 60 HP_score: -2.9 Tail_Score: -4.62002 Start: 239 End: 253 Full_Region: TTCTATAAAAGTACT GAAAA TCTAT TTTTC TTTTCTATAGTTGAT ..............................................................................................................................................................................................................................................GAAAATCTATTTTTC............................................................................................................................................................. Find igs database================================================ Query_seq: SSA_2049:SSA_2050|SSA_2049:SSA_2050:Polyribonucleotide nucleotidyltransferase, putative:Arabinose efflux permease, putative:<-->:2052985..2053394 410 aaagactccttgccgagcacatgctcaatttttttcatacgccttggctacaaagatccaagatattaagactttaatcaactcataggacgtgttcagttagcactgtgattttaaaattatggtcttagcagcttattatatcctcatctttgtatcaagcacgtacagaccttattttaccacaatttcaggcaaaagaaaaaggctgaaaatggcttttttctataaaagtactgaaaatctatttttcttttctatagttgattatagttggctgtcagagttcgttttttccctttcgattcgtcaaataagatggcggtatagccactattcacttttcaaagaggacttcttgctttataataaatacagtgactcatttcaaacatgtaaaggagacaatc Intra-Species Hit: Count: 1 Min: 1 Max: 410 Len: 410 Subject: NC_009009_SSA_2049_SSA_2050|Polyribonucleotide nucleotidyltransferase, putative:Arabinose efflux permease, putative|NEGATIVE:POSITIVE|[2052985,2053394]|410 HSP 1 e-value: 0.0 bit: 771.0 Len: 410 Query Start:1 Query End:410 Subject Strand: POSITIVE Subject Start: 1 Subject End: 410 aaagactccttgccgagcacatgctcaannnnnnncatacgccttggctacaaagatccaagatattaagactttaatcaactcataggacgtgttcagttagcactgtgattttaaaattatggtcttagcagcttattatatcctcatctttgtatcaagcacgtacagaccttattttaccacaatttcaggcaaaagaaaaaggctgaaaatggcttttttctataaaagtactgaaaatctatttttcttttctatagttgattatagttggctgtcagagttcgttttttccctttcgattcgtcaaataagatggcggtatagccactattcacttttcaaagaggacttcttgctttataataaatacagtgactcatttcaaacatgtaaaggagacaatc aaagactccttgccgagcacatgctcaatttttttcatacgccttggctacaaagatccaagatattaagactttaatcaactcataggacgtgttcagttagcactgtgattttaaaattatggtcttagcagcttattatatcctcatctttgtatcaagcacgtacagaccttattttaccacaatttcaggcaaaagaaaaaggctgaaaatggcttttttctataaaagtactgaaaatctatttttcttttctatagttgattatagttggctgtcagagttcgttttttccctttcgattcgtcaaataagatggcggtatagccactattcacttttcaaagaggacttcttgctttataataaatacagtgactcatttcaaacatgtaaaggagacaatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGACUCCUUGCCGAGCACAUGCUCAAUUUUUUUCAUACGCCUUGGCUACAAAGAUCCAAGAUAUUAAGACUUUAAUCAACUCAUAGGACGUGUUCAGUUAGCACUGUGAUUUUAAAAUUAUGGUCUUAGCAGCUUAUUAUAUCCUCAUCUUUGUAUCAAGCACGUACAGACCUUAUUUUACCACAAUUUCAGGCAAAAGAAAAAGGCUGAAAAUGGCUUUUUUCUAUAAAAGUACUGAAAAUCUAUUUUUCUUUUCUAUAGUUGAUUAUAGUUGGCUGUCAGAGUUCGUUUUUUCCCUUUCGAUUCGUCAAAUAAGAUGGCGGUAUAGCCACUAUUCACUUUUCAAAGAGGACUUCUUGCUUUAUAAUAAAUACAGUGACUCAUUUCAAACAUGUAAAGGAGACAAUC .....(((((((((((((....))))................(((((((....))..))))).......((((.(((((((((.((((((....((((((..((.(((.((((.((((((...(((((..((.((((..((((..........))))..))))..))..)))))..))))))....)))).)))))...(((((((((((......)))))))))))........))))))..............))))))))))))))).))))))).....(((((.......(((((((.((...((..((((.(.((((......))))))))).))...)))))).)))......(((.(((.....))).))))))))..............))))))...... (-89.37) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUUGUCUCCUUUACAUGUUUGAAAUGAGUCACUGUAUUUAUUAUAAAGCAAGAAGUCCUCUUUGAAAAGUGAAUAGUGGCUAUACCGCCAUCUUAUUUGACGAAUCGAAAGGGAAAAAACGAACUCUGACAGCCAACUAUAAUCAACUAUAGAAAAGAAAAAUAGAUUUUCAGUACUUUUAUAGAAAAAAGCCAUUUUCAGCCUUUUUCUUUUGCCUGAAAUUGUGGUAAAAUAAGGUCUGUACGUGCUUGAUACAAAGAUGAGGAUAUAAUAAGCUGCUAAGACCAUAAUUUUAAAAUCACAGUGCUAACUGAACACGUCCUAUGAGUUGAUUAAAGUCUUAAUAUCUUGGAUCUUUGUAGCCAAGGCGUAUGAAAAAAAUUGAGCAUGUGCUCGGCAAGGAGUCUUU ....(.(((((.......(((.....((((.((((.(((((((.............(((..(((((...((((((((((((......)))))..))))).))...)))))..)))......................(((((......)))))........)))))))...)))))))).....)))....(((.......(((((....(((((((.........))))))).)))))..(((((((((..((((((((((.(((((((..((((((.....(((((((............((((....)))).........)))).)))......)).))))))))))).).))))))).((....))...........))..)))))))))..))).))))).)... (-93.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 928 50 1 141 92 NC_009009:SSA_2049|5end_Polyribonucleotide_nucleotidyltransferase,_putative_2052894..2053124_NEGATIVE 354 360 318 42 7 NC_009009:SSA_2270|5end_Aspartyl-tRNA_synthetase,_putative_2272068..2272298_NEGATIVE 352 361 321 55 7 NC_009009:SSA_0983|5end_Conserved_uncharacterized_protein_986086..986316_POSITIVE 347 312 272 186 148 NC_009009:SSA_1511|5end_Glycosyltransferase,_putative_1516697..1516927_NEGATIVE 324 44 1 56 2 NC_009009:SSA_1670|5end_Transcriptional_regulator,_TetR/AcrR_family,_putative_1669248..1669478_NEGATIVE 323 325 281 220 181 NC_009009:SSA_0931|5end_hypothetical_protein_940281..940511_POSITIVE 320 320 273 82 34 NC_009009:SSA_0509|5end_Propanediol_utilization_protein,_putative_508024..508254_POSITIVE 296 364 321 179 131 NC_009009:SSA_1925|5end_Seryl-tRNA_synthetase,_putative_1913508..1913738_POSITIVE 296 326 281 131 88 NC_009009:SSA_0533|5end_Glycerol_dehydratase_large_subunit_pduC,_putative_528970..529200_POSITIVE 295 317 272 50 2 NC_009009:SSA_0672|5end_hypothetical_protein_655191..655421_POSITIVE 294 360 312 101 38 NC_009009:SSA_0708|5end_hypothetical_protein_694144..694374_POSITIVE 293 218 175 166 126 NC_009009:SSA_1748|5end_Inorganic_pyrophosphatase/exopolyphosphatase,_putative_1734478..1734708_NEGATIVE 291 48 6 49 2 NC_009009:SSA_1786|5end_Conserved_uncharacterized_protein_1770244..1770474_NEGATIVE 286 325 296 228 202 NC_009009:SSA_2285|5end_hypothetical_protein_2287404..2287634_POSITIVE 285 320 275 215 170 NC_009009:SSA_1448|5end_ATP_phosphoribosyltransferase_regulatory_subunit,_putative_1450817..1451047_NEGATIVE 283 50 3 42 1 NC_009009:SSA_1452|5end_Second_subunit_of_major_exonuclease,_putative_1459696..1459926_NEGATIVE 282 333 292 205 166 NC_009009:SSA_0089|5end_V-type_sodium_ATPase,_subunit_F,_putative_89930..90160_POSITIVE 278 210 162 159 113 NC_009009:SSA_1527|5end_hypothetical_protein_1534587..1534817_POSITIVE 277 310 263 168 119 NC_009009:SSA_2346|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_III,_putative_2348546..2348776_NEGATIVE 276 209 165 164 102 NC_009009:SSA_2066|5end_DNA_polymerase_III_polC-type,_putative_2070137..2070367_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 323 325 281 122 83 NC_009009:SSA_0929|3end_ABC-type_multidrug_transporter,_ATPase_and_permease_components,_putative_940263..940413_POSITIVE 296 326 281 109 66 NC_009009:SSA_0532|3end_Propanediol_utilization_protein_PduB,_putative_529028..529178_POSITIVE 295 317 272 53 5 NC_009009:SSA_0671|3end_Methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase,_putative_655274..655424_POSITIVE 280 197 158 107 61 NC_009009:SSA_0507|3end_hypothetical_protein_506442..506592_POSITIVE 277 310 263 67 18 NC_009009:SSA_2347|3end_Coenzyme_F390_synthetase,_putative_2348647..2348797_NEGATIVE 272 66 22 144 92 NC_009009:SSA_1502|3end_Conserved_uncharacterized_protein_(contains_LysM,_Lysin_motif)_1505782..1505932_NEGATIVE 270 217 188 145 112 NC_009009:SSA_0713|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase,_putative_700028..700178_POSITIVE 269 172 131 127 83 NC_009009:SSA_1364|3end_hypothetical_protein_1380482..1380632_NEGATIVE 268 42 5 54 19 NC_009009:SSA_2308|3end_hypothetical_protein_2309893..2310043_NEGATIVE 268 310 263 80 13 NC_009009:SSA_1447|3end_ATP_phosphoribosyltransferase,_putative_1449187..1449337_NEGATIVE 268 49 3 148 106 NC_009009:SSA_0807|3end_GTP-binding_protein,_putative_790839..790989_POSITIVE 264 49 6 148 100 NC_009009:SSA_0826|3end_hypothetical_protein_805516..805666_POSITIVE 263 52 11 151 117 NC_009009:SSA_2220|3end_Galactosyltransferase,_putative_2220834..2220984_NEGATIVE 263 311 275 149 114 NC_009009:SSA_1449|3end_Histidinol-phosphate/aromatic_aminotransferase_and_cobyric_acid_decarboxylase,_putative_1450873..1451023_NEGATIVE 263 366 322 45 11 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 261 234 193 58 28 NC_009009:SSA_0673|3end_hypothetical_protein_656994..657144_POSITIVE 260 99 54 86 38 NC_009009:SSA_1955|3end_ABC-type_Fe-S_cluster_assembly_transporter,_permease_component,_putative_1951340..1951490_NEGATIVE 259 326 287 144 100 NC_009009:SSA_0484|3end_Glutamyl-tRNA_reductase,_putative_485825..485975_POSITIVE 257 48 3 74 16 NC_009009:SSA_2058|3end_30S_ribosomal_protein_S15,_putative_2060058..2060208_NEGATIVE 257 47 7 134 95 NC_009009:SSA_0046|3end_Adenylosuccinate_lyase,_putative_52269..52419_POSITIVE