Origin IGS: acttcacctcttttatttttcctttgtttattatggtatattttgaaaaatgcctttggcctcttttagattgagaagagggagaactcggtttcccactatgatagacagtggctcactatggagtcagcatctaatcaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttgattagatgctgactccatagtgagccactgtctatcatagtgggaaaccgagttctccctcttctcaatctaaaagaggccaaaggcatttttcaaaatataccataataaacaaaggaaaaataaaagaggtgaagt Mask Tandem Repeat Region ================================================ acttcacctcttttatttttcctttgtttattatggtatattttgaaaaatgcctttggcctcttttagattgagaagagggagaactcggtttcccactatgatagacagtggctcactatggagtcagcatctaatcaa Find is-nt database================================================ Query_seq: SSA_2016:SSA_2017|SSA_2016:SSA_2017:Phosphoglycerate mutase, putative:Hypothetical protein (possibly membrane-associated):<-<-:2016384..2016524 141 acttcacctcttttatttttcctttgtttattatggtatattttgaaaaatgcctttggcctcttttagattgagaagagggagaactcggtttcccactatgatagacagtggctcactatggagtcagcatctaatcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_2016:SSA_2017|SSA_2016:SSA_2017:Phosphoglycerate mutase, putative:Hypothetical protein (possibly membrane-associated):<-<-:2016384..2016524 141 acttcacctcttttatttttcctttgtttattatggtatattttgaaaaatgcctttggcctcttttagattgagaagagggagaactcggtttcccactatgatagacagtggctcactatggagtcagcatctaatcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_2016:SSA_2017|SSA_2016:SSA_2017:Phosphoglycerate mutase, putative:Hypothetical protein (possibly membrane-associated):<-<-:2016384..2016524 141 acttcacctcttttatttttcctttgtttattatggtatattttgaaaaatgcctttggcctcttttagattgagaagagggagaactcggtttcccactatgatagacagtggctcactatggagtcagcatctaatcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acttcacctcttttatttttcctttgtttattatggtatattttgaaaaatgcctttggcctcttttagattgagaagagggagaactcggtttcccactatgatagacagtggctcactatggagtcagcatctaatcaa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 50 End: 139 ................................................. M P L A S F R L R R G R T R F P T M I D S G S L W S Q H L I .. acttcacctcttttatttttcctttgtttattatggtatattttgaaaaatgcctttggcctcttttagattgagaagagggagaactcggtttcccactatgatagacagtggctcactatggagtcagcatctaatcaa 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================================================ acttcacctcttttatttttcctttgtttattatggtatattttgaaaaatgcctttggcctcttttagattgagaagagggagaactcggtttcccactatgatagacagtggctcactatggagtcagcatctaatcaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_2016:SSA_2017|SSA_2016:SSA_2017:Phosphoglycerate mutase, putative:Hypothetical protein (possibly membrane-associated):<-<-:2016384..2016524 141 acttcacctcttttatttttcctttgtttattatggtatattttgaaaaatgcctttggcctcttttagattgagaagagggagaactcggtttcccactatgatagacagtggctcactatggagtcagcatctaatcaa Intra-Species Hit: Count: 1 Min: 1 Max: 141 Len: 141 Subject: NC_009009_SSA_2016_SSA_2017|Phosphoglycerate mutase, putative:Hypothetical protein (possibly membrane-associated)|NEGATIVE:NEGATIVE|[2016384, 2016524]|141 HSP 1 e-value: 1.0E-74 bit: 280.0 Len: 141 Query Start:1 Query End:141 Subject Strand: POSITIVE Subject Start: 1 Subject End: 141 acttcacctcttttatttttcctttgtttattatggtatattttgaaaaatgcctttggcctcttttagattgagaagagggagaactcggtttcccactatgatagacagtggctcactatggagtcagcatctaatcaa acttcacctcttttatttttcctttgtttattatggtatattttgaaaaatgcctttggcctcttttagattgagaagagggagaactcggtttcccactatgatagacagtggctcactatggagtcagcatctaatcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUUCACCUCUUUUAUUUUUCCUUUGUUUAUUAUGGUAUAUUUUGAAAAAUGCCUUUGGCCUCUUUUAGAUUGAGAAGAGGGAGAACUCGGUUUCCCACUAUGAUAGACAGUGGCUCACUAUGGAGUCAGCAUCUAAUCAA ........................(((((((((((((....(((((((...(((...)))...))))))).........((((((......))))))))))))))))))).((((((......))))))............ (-30.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGAUUAGAUGCUGACUCCAUAGUGAGCCACUGUCUAUCAUAGUGGGAAACCGAGUUCUCCCUCUUCUCAAUCUAAAAGAGGCCAAAGGCAUUUUUCAAAAUAUACCAUAAUAAACAAAGGAAAAAUAAAAGAGGUGAAGU ((((..((((((((((((....((...(((((((.....)))))))...)).)))))...((((((..........)))))).....))))))).))))....((((..........................)))).... (-26.57) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 989 130 81 221 172 NC_009009:SSA_2016|5end_Phosphoglycerate_mutase,_putative_2016293..2016523_NEGATIVE 374 116 76 79 32 NC_009009:SSA_0089|5end_V-type_sodium_ATPase,_subunit_F,_putative_89930..90160_POSITIVE 339 93 58 40 6 NC_009009:SSA_0494|5end_ABC-type_dipeptide/oligopeptide/nickel_transport_system,_ATPase_component,_putative_494407..494637_POSITIVE 327 112 76 176 136 NC_009009:SSA_0796|5end_ABC-NBD_transporters_with_duplicated_ATPase_domains,_putative_777085..777315_POSITIVE 323 130 90 161 110 NC_009009:SSA_1798|5end_hypothetical_protein_1780513..1780743_NEGATIVE 317 98 54 60 25 NC_009009:SSA_0427|5end_DNA-binding_transcriptional_activator,_SARP_family,_putative_424497..424727_POSITIVE 310 98 56 144 112 NC_009009:SSA_1260|5end_Phosphopentomutase,_putative_1286963..1287193_NEGATIVE 308 96 51 225 188 NC_009009:SSA_2044|5end_Cysteinyl-tRNA_synthetase,_putative_2048409..2048639_NEGATIVE 305 92 51 137 80 NC_009009:SSA_1791|5end_Acylphosphatase,_putative_1773676..1773906_POSITIVE 299 94 53 202 143 NC_009009:SSA_1658|5end_Cationic_amino_acid_transporter,_putative_1654674..1654904_NEGATIVE 292 98 54 144 96 NC_009009:SSA_1726|5end_ABC_transporter_ATP-binding_protein-branched_chain_amino_acid_transport,_putative_1712467..1712697_NEGATIVE 289 129 88 44 3 NC_009009:SSA_1044|5end_Homoserine_kinase,_putative_1059853..1060083_POSITIVE 287 96 53 185 148 NC_009009:SSA_1466|5end_Prephenate_dehydrogenase,_putative_1473111..1473341_NEGATIVE 287 128 87 193 150 NC_009009:SSA_0838|5end_GtfB,_putative_825406..825636_POSITIVE 285 128 87 154 102 NC_009009:SSA_0897|5end_Two_component_system_histidine_kinase,_putative_888358..888588_POSITIVE 278 131 95 231 182 NC_009009:SSA_1370|5end_CAAX_amino_terminal_protease_family,_putative_1386968..1387198_NEGATIVE 274 131 91 204 155 NC_009009:SSA_1419|5end_hypothetical_protein_1429675..1429905_NEGATIVE 274 98 52 215 163 NC_009009:SSA_1050|5end_ABC_transporter_membrane-spanning_permease-spermidine/putrescine_transport,_putative_1064888..1065118_POSITIVE 270 130 87 135 93 NC_009009:SSA_1997|5end_Membrane_spanning_protein,_putative_1994911..1995141_NEGATIVE 269 132 104 60 35 NC_009009:SSA_1793|5end_Histidine_kinase_(sensor_protein),_putative_1776361..1776591_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 116 76 92 45 NC_009009:SSA_0088|3end_V-type_sodium_ATPase,_subunit_C,_putative_90023..90173_POSITIVE 339 93 58 36 2 NC_009009:SSA_0493|3end_ABC-type_dipeptide/nickel_transport_system,_periplasmic_component,_putative_494483..494633_POSITIVE 327 112 76 76 36 NC_009009:SSA_0795|3end_hypothetical_protein_777065..777215_POSITIVE 317 97 51 104 36 NC_009009:SSA_0397|3end_hypothetical_protein_393992..394142_NEGATIVE 310 98 56 130 98 NC_009009:SSA_1261|3end_Ribose-5-phosphate_isomerase_A,_putative_1286977..1287127_NEGATIVE 292 98 54 144 96 NC_009009:SSA_1727|3end_ABC_transporter_membrane-spanning_permease-branched_chain_amino_acid_transport,_putative_1712467..1712617_NEGATIVE 289 129 88 42 1 NC_009009:SSA_1043|3end_Homoserine_dehydrogenase,_putative_1059931..1060081_POSITIVE 281 127 89 76 30 NC_009009:SSA_0057|3end_Phosphotransferase_system_sugar-specific_EII_component,_putative_61246..61396_POSITIVE 278 131 95 148 99 NC_009009:SSA_1371|3end_FmtA-like_protein,_putative_1387051..1387201_NEGATIVE 269 132 104 76 51 NC_009009:SSA_1794|3end_Two-component_response_transcriptional_regulator_(CheY-like_receiver_and_winged-helix_DNA-binding_domains),_putative_1776345..1776495_NEGATIVE 267 131 91 68 22 NC_009009:SSA_1248|3end_hypothetical_protein_1272355..1272505_NEGATIVE 266 126 87 120 82 NC_009009:SSA_2027|3end_P-type_ATPase-metal/cation_transport_(probably_copper),_putative_2033109..2033259_NEGATIVE 266 100 51 70 14 NC_009009:SSA_1194|3end_Aspartate-semialdehyde_dehydrogenase,_putative_1220113..1220263_NEGATIVE 264 136 91 55 4 NC_009009:SSA_0297|3end_Malolactic_enzyme,_putative_291411..291561_POSITIVE 262 109 61 111 67 NC_009009:SSA_1771|3end_Conserved_DNA_methyltransferase_protein,_putative_1758491..1758641_NEGATIVE 262 135 96 91 50 NC_009009:SSA_1464|3end_3-phosphoshikimate_1-carboxyvinyltransferase,_putative_1470233..1470383_NEGATIVE 262 92 51 149 105 NC_009009:SSA_1375|3end_Multidrug_ABC_transporter,_ATPase_and_permease_components,_putative_1393085..1393235_NEGATIVE 261 117 86 141 106 NC_009009:SSA_1861|3end_Aminopeptidase_C,_putative_1856568..1856718_NEGATIVE 259 89 41 123 68 NC_009009:SSA_2058|3end_30S_ribosomal_protein_S15,_putative_2060058..2060208_NEGATIVE 257 91 52 134 94 NC_009009:SSA_0050|3end_Dihydroxyacetone_kinase,_phosphatase_domain_(Dak2),_putative_55270..55420_POSITIVE