Origin IGS: taaaagaatgaaaagaaaccagcgagattttattctcgctggtttttcttttccaaggtcataatttctacctatagcaaacaataatttcagtcaatggtgcttctaaaatgggggttttggactggttggcgagataggttatagttttagactatatcaaactctgggaaattccaattatacagaggggggattttctgataagataaaatcaagaaaaattttggaggacgttt .........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 aaacgtcctccaaaatttttcttgattttatcttatcagaaaatcccccctctgtataattggaatttcccagagtttgatatagtctaaaactataacctatctcgccaaccagtccaaaacccccattttagaagcaccattgactgaaattattgtttgctataggtagaaattatgaccttggaaaagaaaaaccagcgagaataaaatctcgctggtttcttttcattctttta Mask Tandem Repeat Region ================================================ taaaagaatgaaaagaaaccagcgagattttattctcgctggtttttcttttccaaggtcataatttctacctatagcaaacaataatttcagtcaatggtgcttctaaaatgggggttttggactggttggcgagataggttatagttttagactatatcaaactctgggaaattccaattatacagaggggggattttctgataagataaaatcaagaaaaattttggaggacgttt Find is-nt database================================================ Query_seq: SSA_0415:SSA_0416|SSA_0415:SSA_0416:Permease, putative:5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase, putative:->->:411791..412029 239 taaaagaatgaaaagaaaccagcgagattttattctcgctggtttttcttttccaaggtcataatttctacctatagcaaacaataatttcagtcaatggtgcttctaaaatgggggttttggactggttggcgagataggttatagttttagactatatcaaactctgggaaattccaattatacagaggggggattttctgataagataaaatcaagaaaaattttggaggacgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0415:SSA_0416|SSA_0415:SSA_0416:Permease, putative:5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase, putative:->->:411791..412029 239 taaaagaatgaaaagaaaccagcgagattttattctcgctggtttttcttttccaaggtcataatttctacctatagcaaacaataatttcagtcaatggtgcttctaaaatgggggttttggactggttggcgagataggttatagttttagactatatcaaactctgggaaattccaattatacagaggggggattttctgataagataaaatcaagaaaaattttggaggacgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0415:SSA_0416|SSA_0415:SSA_0416:Permease, putative:5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase, putative:->->:411791..412029 239 taaaagaatgaaaagaaaccagcgagattttattctcgctggtttttcttttccaaggtcataatttctacctatagcaaacaataatttcagtcaatggtgcttctaaaatgggggttttggactggttggcgagataggttatagttttagactatatcaaactctgggaaattccaattatacagaggggggattttctgataagataaaatcaagaaaaattttggaggacgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaagaatgaaaagaaaccagcgagattttattctcgctggtttttcttttccaaggtcataatttctacctatagcaaacaataatttcagtcaatggtgcttctaaaatgggggttttggactggttggcgagataggttatagttttagactatatcaaactctgggaaattccaattatacagaggggggattttctgataagataaaatcaagaaaaattttggaggacgttt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 125 End: 238 ............................................................................................................................ M V G E I G Y S F R L Y Q T L G N S N Y T E G G F S D K I K S R K I L E D V . Protein_Len: 31 Strand: - Start: 1 End: 93 L L I F L F W R S K I R A P K E K G L D Y N R G I A F L L K M .................................................................................................................................................. taaaagaatgaaaagaaaccagcgagattttattctcgctggtttttcttttccaaggtcataatttctacctatagcaaacaataatttcagtcaatggtgcttctaaaatgggggttttggactggttggcgagataggttatagttttagactatatcaaactctgggaaattccaattatacagaggggggattttctgataagataaaatcaagaaaaattttggaggacgttt 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================================================ taaaagaatgaaaagaaaccagcgagattttattctcgctggtttttcttttccaaggtcataatttctacctatagcaaacaataatttcagtcaatggtgcttctaaaatgggggttttggactggttggcgagataggttatagttttagactatatcaaactctgggaaattccaattatacagaggggggattttctgataagataaaatcaagaaaaattttggaggacgttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -12.5 Tail_Score: -4.81843 Start: 19 End: 42 Full_Region: cttggaaaagaaaaa ccagcgaga ataaaa tctcgctgg tttcttttcattctt ..................ccagcgagaataaaatctcgctgg..................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_0415:SSA_0416|SSA_0415:SSA_0416:Permease, putative:5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase, putative:->->:411791..412029 239 taaaagaatgaaaagaaaccagcgagattttattctcgctggtttttcttttccaaggtcataatttctacctatagcaaacaataatttcagtcaatggtgcttctaaaatgggggttttggactggttggcgagataggttatagttttagactatatcaaactctgggaaattccaattatacagaggggggattttctgataagataaaatcaagaaaaattttggaggacgttt Intra-Species Hit: Count: 1 Min: 1 Max: 239 Len: 239 Subject: NC_009009_SSA_0415_SSA_0416|Permease, putative:5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase, putative|POSITIVE:POSITIVE|[411791,412029]|239 HSP 1 e-value: 1.0E-133 bit: 474.0 Len: 239 Query Start:1 Query End:239 Subject Strand: POSITIVE Subject Start: 1 Subject End: 239 taaaagaatgaaaagaaaccagcgagattttattctcgctggtttttcttttccaaggtcataatttctacctatagcaaacaataatttcagtcaatggtgcttctaaaatgggggttttggactggttggcgagataggttatagttttagactatatcaaactctgggaaattccaattatacagaggggggattttctgataagataaaatcaagaaaaattttggaggacgttt taaaagaatgaaaagaaaccagcgagattttattctcgctggtttttcttttccaaggtcataatttctacctatagcaaacaataatttcagtcaatggtgcttctaaaatgggggttttggactggttggcgagataggttatagttttagactatatcaaactctgggaaattccaattatacagaggggggattttctgataagataaaatcaagaaaaattttggaggacgttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGAAUGAAAAGAAACCAGCGAGAUUUUAUUCUCGCUGGUUUUUCUUUUCCAAGGUCAUAAUUUCUACCUAUAGCAAACAAUAAUUUCAGUCAAUGGUGCUUCUAAAAUGGGGGUUUUGGACUGGUUGGCGAGAUAGGUUAUAGUUUUAGACUAUAUCAAACUCUGGGAAAUUCCAAUUAUACAGAGGGGGGAUUUUCUGAUAAGAUAAAAUCAAGAAAAAUUUUGGAGGACGUUU .....(((((...((((((((((((((......)))))))))))))).((((((((.(((..((((...((((((.((.(((........(((((......((((((.....))))))....)))))))).))...))))))...))))...)))..((((....((.((((((((((..((......))..))))))))))))...))))...............))))))))))))) (-65.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACGUCCUCCAAAAUUUUUCUUGAUUUUAUCUUAUCAGAAAAUCCCCCCUCUGUAUAAUUGGAAUUUCCCAGAGUUUGAUAUAGUCUAAAACUAUAACCUAUCUCGCCAACCAGUCCAAAACCCCCAUUUUAGAAGCACCAUUGACUGAAAUUAUUGUUUGCUAUAGGUAGAAAUUAUGACCUUGGAAAAGAAAAACCAGCGAGAAUAAAAUCUCGCUGGUUUCUUUUCAUUCUUUUA ....(((.........((((((.(((........)))))))))..(..(((..(((...(((((........(((...(.((((((.....)))))).)....))).........))))).......(((((((...((....)).))))))).......)))...)))..).......)))....((((((((..((((((((((......))))))))))))))))))......... (-49.33) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 145 101 174 125 NC_009009:SSA_0484|5end_Glutamyl-tRNA_reductase,_putative_484492..484722_POSITIVE 317 168 124 60 21 NC_009009:SSA_1683|5end_NrdI_protein,_putative_1677405..1677635_NEGATIVE 314 128 84 210 155 NC_009009:SSA_1583|5end_6-O-methylguanine-DNA_methyltransferase,_putative_1586026..1586256_NEGATIVE 308 131 91 227 185 NC_009009:SSA_0538|5end_PduH_protein,_putative_533794..534024_POSITIVE 307 170 121 173 112 NC_009009:SSA_1806|5end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1790749..1790979_NEGATIVE 303 78 32 67 16 NC_009009:SSA_0199|5end_GTP_cyclohydrolase_I,_putative_198276..198506_POSITIVE 300 138 94 145 88 NC_009009:SSA_2001|5end_Hydroxymethylpyrimidine/phosphomethylpyrimidine_kinase,_putative_1998220..1998450_NEGATIVE 299 133 95 229 177 NC_009009:SSA_0783|5end_Proton-translocating_ATPase,_F0_sector,_subunit_a,_putative_766815..767045_POSITIVE 285 52 11 150 115 NC_009009:SSA_1068|5end_Transcriptional_regulator,_LysR_family_(capsular_polysaccharide_biosynthesis_regulation),_putative_1087355..1087585_POSITIVE 285 128 88 133 101 NC_009009:SSA_0105|5end_Uridine_kinase,_putative_106761..106991_POSITIVE 280 133 91 223 180 NC_009009:SSA_1922|5end_hypothetical_protein_1912106..1912336_NEGATIVE 278 68 23 97 49 NC_009009:SSA_0324|5end_Conserved_uncharacterized_protein_317019..317249_POSITIVE 276 43 14 182 147 NC_009009:SSA_0975|5end_2-isopropylmalate_synthase,_putative_980971..981201_POSITIVE 272 208 163 163 124 NC_009009:SSA_1062|5end_50S_ribosomal_protein_L27,_putative_1078284..1078514_POSITIVE 270 140 95 149 107 NC_009009:SSA_2037|5end_tRNA_(Guanosine-2'-O-)-methyltransferase,_TrmH_family,_putative_2041524..2041754_NEGATIVE 268 77 41 128 95 NC_009009:SSA_1146|5end_Phosphotransferase_system_cellobiose-specific_component_IIA,_putative_1176453..1176683_POSITIVE 267 144 101 68 7 NC_009009:SSA_0008|5end_Transcription-repair_coupling_factor,_putative_5571..5801_POSITIVE 266 142 112 40 3 NC_009009:SSA_2009|5end_Heat_shock_transcription_repressor_HrcA,_putative_2011132..2011362_NEGATIVE 266 60 12 155 108 NC_009009:SSA_0583|5end_Nucleotidyltransferase,_putative_574505..574735_POSITIVE 264 135 94 50 4 NC_009009:SSA_1056|5end_Firmicute_fructose-1,6-bisphosphatase,_putative_1071760..1071990_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 442 53 11 81 39 NC_009009:SSA_0415|3end_Permease,_putative_411730..411880_POSITIVE 345 47 13 78 44 NC_009009:SSA_2135|3end_Transcriptional_repressor,_DeoR_family_(possibly_truncated),_putative_2137474..2137624_POSITIVE 305 47 11 74 38 NC_009009:SSA_2136|3end_50S_ribosomal_protein_L34,_putative_2137507..2137657_NEGATIVE 303 78 32 86 35 NC_009009:SSA_0198|3end_Dihydrofolate_synthetase,_putative_198375..198525_POSITIVE 301 168 125 39 1 NC_009009:SSA_1684|3end_Histidine_kinase,_putative_1677426..1677576_NEGATIVE 300 138 96 149 83 NC_009009:SSA_1367|3end_hypothetical_protein_1383828..1383978_POSITIVE 296 133 94 145 98 NC_009009:SSA_2002|3end_tRNA_pseudouridine_synthase_A,_putative_1998210..1998360_NEGATIVE 285 52 11 60 25 NC_009009:SSA_1067|3end_hypothetical_protein_1087345..1087495_POSITIVE 285 128 88 107 75 NC_009009:SSA_0104|3end_Queuine_tRNA-ribosyltransferase,_putative_106815..106965_POSITIVE 283 133 93 149 103 NC_009009:SSA_1615|3end_Alanine_dehydrogenase,_putative_1619318..1619468_POSITIVE 278 80 31 149 92 NC_009009:SSA_2074|3end_Preprotein_translocase_subunit_YajC,_putative_2076600..2076750_NEGATIVE 276 57 12 108 57 NC_009009:SSA_0506|3end_Iron-sulfur_cluster-binding_protein,_putative_504430..504580_NEGATIVE 276 68 23 75 35 NC_009009:SSA_0392|3end_hypothetical_protein_388303..388453_POSITIVE 267 144 101 75 14 NC_009009:SSA_0006|3end_Peptidyl-tRNA_hydrolase,_putative_5658..5808_POSITIVE 264 59 12 85 34 NC_009009:SSA_2165|3end_ABC-type_oligopeptide_transporter,_periplasmic_component,_putative_2163787..2163937_POSITIVE 264 68 22 81 42 NC_009009:SSA_0934|3end_HydD,_putative_944091..944241_POSITIVE 263 158 111 94 49 NC_009009:SSA_2094|3end_Conserved_uncharacterized_protein_2097990..2098140_NEGATIVE 260 127 82 55 12 NC_009009:SSA_1502|3end_Conserved_uncharacterized_protein_(contains_LysM,_Lysin_motif)_1505782..1505932_NEGATIVE 256 170 124 71 22 NC_009009:SSA_0332|3end_hypothetical_protein_326924..327074_POSITIVE 255 154 112 105 57 NC_009009:SSA_1215|3end_hypothetical_protein_1238247..1238397_POSITIVE