Origin IGS: gatgataaagtattactgtctgctttcggatgacaaatgtcggcactatatctaatatagaaatgatgccgaatccttcctcaatcagattcagtgacgtgaaaatataacgaagagactgccccgaagtctatgtcgaactccgaggcagcctcttttatcttgggaaaaacgtccttagcctccaaatcgtgcaggctttggccgtactcccatta .........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 taatgggagtacggccaaagcctgcacgatttggaggctaaggacgtttttcccaagataaaagaggctgcctcggagttcgacatagacttcggggcagtctcttcgttatattttcacgtcactgaatctgattgaggaaggattcggcatcatttctatattagatatagtgccgacatttgtcatccgaaagcagacagtaatactttatcatc Mask Tandem Repeat Region ================================================ gatgataaagtattactgtctgctttcggatgacaaatgtcggcactatatctaatatagaaatgatgccgaatccttcctcaatcagattcagtgacgtgaaaatataacgaagagactgccccgaagtctatgtcgaactccgaggcagcctcttttatcttgggaaaaacgtccttagcctccaaatcgtgcaggctttggccgtactcccatta Find is-nt database================================================ Query_seq: PG2171:PG2172|PG2171:PG2172:D-isomer specific 2-hydroxyacid dehydrogenase family protein:hypothetical protein:<-<-:2279063..2279280 218 gatgataaagtattactgtctgctttcggatgacaaatgtcggcactatatctaatatagaaatgatgccgaatccttcctcaatcagattcagtgacgtgaaaatataacgaagagactgccccgaagtctatgtcgaactccgaggcagcctcttttatcttgggaaaaacgtccttagcctccaaatcgtgcaggctttggccgtactcccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2171:PG2172|PG2171:PG2172:D-isomer specific 2-hydroxyacid dehydrogenase family protein:hypothetical protein:<-<-:2279063..2279280 218 gatgataaagtattactgtctgctttcggatgacaaatgtcggcactatatctaatatagaaatgatgccgaatccttcctcaatcagattcagtgacgtgaaaatataacgaagagactgccccgaagtctatgtcgaactccgaggcagcctcttttatcttgggaaaaacgtccttagcctccaaatcgtgcaggctttggccgtactcccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2171:PG2172|PG2171:PG2172:D-isomer specific 2-hydroxyacid dehydrogenase family protein:hypothetical protein:<-<-:2279063..2279280 218 gatgataaagtattactgtctgctttcggatgacaaatgtcggcactatatctaatatagaaatgatgccgaatccttcctcaatcagattcagtgacgtgaaaatataacgaagagactgccccgaagtctatgtcgaactccgaggcagcctcttttatcttgggaaaaacgtccttagcctccaaatcgtgcaggctttggccgtactcccatta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgataaagtattactgtctgctttcggatgacaaatgtcggcactatatctaatatagaaatgatgccgaatccttcctcaatcagattcagtgacgtgaaaatataacgaagagactgccccgaagtctatgtcgaactccgaggcagcctcttttatcttgggaaaaacgtccttagcctccaaatcgtgcaggctttggccgtactcccatta Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 12 End: 107 ........... M T V C F R M T N V G T I S N I E M M P N P S S I R F S D V K I ............................................................................................................... Protein_Len: 38 Strand: - Start: 84 End: 197 ................................................................................... D S E T V H F Y L S S V A G F D I D F E S A A E K I K P F V D K A E L D H M ..................... Protein_Len: 35 Strand: - Start: 2 End: 106 . H Y L I V T Q K R I V F T P V I D L I S I I G F G E E I L N L S T F M ................................................................................................................ gatgataaagtattactgtctgctttcggatgacaaatgtcggcactatatctaatatagaaatgatgccgaatccttcctcaatcagattcagtgacgtgaaaatataacgaagagactgccccgaagtctatgtcgaactccgaggcagcctcttttatcttgggaaaaacgtccttagcctccaaatcgtgcaggctttggccgtactcccatta 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================================================ gatgataaagtattactgtctgctttcggatgacaaatgtcggcactatatctaatatagaaatgatgccgaatccttcctcaatcagattcagtgacgtgaaaatataacgaagagactgccccgaagtctatgtcgaactccgaggcagcctcttttatcttgggaaaaacgtccttagcctccaaatcgtgcaggctttggccgtactcccatta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 61 HP_score: -4.0 Tail_Score: -4.14739 Start: 106 End: 162 Full_Region: ggacgtttttcccaa gataaaagaggctgcctcggagtt cgacata gacttcggggcagtctcttcgttata ttttcacgtcactga .........................................................................................................gataaaagaggctgcctcggagttcgacatagacttcggggcagtctcttcgttata........................................................ TransTerm Strand: - Conf: 80 HP_score: -8.9 Tail_Score: -3.96506 Start: 111 End: 159 Full_Region: cgtttttcccaagat aaaagaggctgcctcggagtt cgacata gacttcggggcagtctcttcg ttatattttcacgtc ..............................................................................................................aaaagaggctgcctcggagttcgacatagacttcggggcagtctcttcg........................................................... TransTerm Strand: + Conf: 79 HP_score: -6.8 Tail_Score: -4.66537 Start: 115 End: 155 Full_Region: TGAAAATATAACGAA GAGACTGCCCCGAAGT CTATGTCGA ACTCCGAGGCAGCCTC TTTTATCTTGGGAAA ..................................................................................................................GAGACTGCCCCGAAGTCTATGTCGAACTCCGAGGCAGCCTC............................................................... TransTerm Strand: - Conf: 100 HP_score: -14.1 Tail_Score: -3.61709 Start: 115 End: 155 Full_Region: tttcccaagataaaa gaggctgcctcggagtt cgacata gacttcggggcagtctc ttcgttatattttca ..................................................................................................................gaggctgcctcggagttcgacatagacttcggggcagtctc............................................................... Find igs database================================================ Query_seq: PG2171:PG2172|PG2171:PG2172:D-isomer specific 2-hydroxyacid dehydrogenase family protein:hypothetical protein:<-<-:2279063..2279280 218 gatgataaagtattactgtctgctttcggatgacaaatgtcggcactatatctaatatagaaatgatgccgaatccttcctcaatcagattcagtgacgtgaaaatataacgaagagactgccccgaagtctatgtcgaactccgaggcagcctcttttatcttgggaaaaacgtccttagcctccaaatcgtgcaggctttggccgtactcccatta Intra-Species Hit: Count: 1 Min: 1 Max: 218 Len: 218 Subject: NC_002950_PG2171_PG2172|D-isomer specific 2-hydroxyacid dehydrogenase family protein:hypothetical protein|NEGATIVE:NEGATIVE|[2279063,2279280]|218 HSP 1 e-value: 1.0E-120 bit: 432.0 Len: 218 Query Start:1 Query End:218 Subject Strand: POSITIVE Subject Start: 1 Subject End: 218 gatgataaagtattactgtctgctttcggatgacaaatgtcggcactatatctaatatagaaatgatgccgaatccttcctcaatcagattcagtgacgtgaaaatataacgaagagactgccccgaagtctatgtcgaactccgaggcagcctcttttatcttgggaaaaacgtccttagcctccaaatcgtgcaggctttggccgtactcccatta gatgataaagtattactgtctgctttcggatgacaaatgtcggcactatatctaatatagaaatgatgccgaatccttcctcaatcagattcagtgacgtgaaaatataacgaagagactgccccgaagtctatgtcgaactccgaggcagcctcttttatcttgggaaaaacgtccttagcctccaaatcgtgcaggctttggccgtactcccatta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAUAAAGUAUUACUGUCUGCUUUCGGAUGACAAAUGUCGGCACUAUAUCUAAUAUAGAAAUGAUGCCGAAUCCUUCCUCAAUCAGAUUCAGUGACGUGAAAAUAUAACGAAGAGACUGCCCCGAAGUCUAUGUCGAACUCCGAGGCAGCCUCUUUUAUCUUGGGAAAAACGUCCUUAGCCUCCAAAUCGUGCAGGCUUUGGCCGUACUCCCAUUA ...((((..(..((((((((((.((..(((.........((((((.(((.((((...)))).))).)))))).....)))..)).))))..))))))..)...........((((((.(((((.((.((((......).))).)).))))).)))))))))).(((((...(((.((..(((((.((.....)).)))))..)).)))..)))))... (-65.24) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGGGAGUACGGCCAAAGCCUGCACGAUUUGGAGGCUAAGGACGUUUUUCCCAAGAUAAAAGAGGCUGCCUCGGAGUUCGACAUAGACUUCGGGGCAGUCUCUUCGUUAUAUUUUCACGUCACUGAAUCUGAUUGAGGAAGGAUUCGGCAUCAUUUCUAUAUUAGAUAUAGUGCCGACAUUUGUCAUCCGAAAGCAGACAGUAAUACUUUAUCAUC ...((((((.(((.((..(((((.((.....)).)))))..)).)))..)))))).((((((.(((((((((((((((((.......)))))))))))))))))...................((((..((((.((..(((.(((((((((((.((.((((...)))).)).))))))).))))....)))..)).)))))))).....))))))... (-81.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 923 140 91 231 182 NC_002950:PG2171|5end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_2278972..2279202_NEGATIVE 412 154 111 119 71 NC_002950:PG2220|5end_hypothetical_protein_2334935..2335165_POSITIVE 384 199 151 202 138 NC_002950:PG1394|5end_hypothetical_protein_1476782..1477012_NEGATIVE 370 155 111 61 20 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 358 154 111 119 71 NC_002950:PG1059|5end_hypothetical_protein_1126495..1126725_NEGATIVE 355 177 135 213 170 NC_002950:PG0165|5end_heat_shock_protein_15_187807..188037_NEGATIVE 355 199 151 181 115 NC_002950:PG0158|5end_competence_protein_F-related_protein_180175..180405_POSITIVE 353 156 119 65 28 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 341 209 161 204 137 NC_002950:PG1533|5end_Toprim_domain_protein_1613761..1613991_NEGATIVE 340 156 115 221 151 NC_002950:PG0143|5end_hydrolase,_carbon-nitrogen_family_166625..166855_NEGATIVE 340 153 112 51 3 NC_002950:PG0018|5end_hypothetical_protein_19648..19878_POSITIVE 339 188 141 221 159 NC_002950:PG0480|5end_precorrin-2_C20-methyltransferase,_putative_521319..521549_NEGATIVE 335 159 111 195 128 NC_002950:PG0095|5end_DNA_mismatch_repair_protein_114763..114993_NEGATIVE 334 187 142 191 130 NC_002950:PG1352|5end_hypothetical_protein_1433150..1433380_NEGATIVE 333 167 122 188 153 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 333 151 111 155 115 NC_002950:PG0221|5end_hypothetical_protein_255834..256064_NEGATIVE 332 165 121 92 34 NC_002950:PG0441|5end_hypothetical_protein_478734..478964_POSITIVE 327 153 111 106 47 NC_002950:PG2043|5end_conserved_hypothetical_protein_TIGR00486_2142218..2142448_POSITIVE 322 162 121 89 38 NC_002950:PG1091|5end_DHH_subfamily_1_protein_1157017..1157247_POSITIVE 322 167 124 64 24 NC_002950:PG0322|5end_serine/threonine_transporter_355708..355938_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 454 168 122 72 18 NC_002950:PG1274|3end_elongation_factor_P_1352489..1352639_POSITIVE 356 210 164 129 77 NC_002950:PG1027|3end_hypothetical_protein_1089197..1089347_NEGATIVE 340 158 114 146 93 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 340 158 114 146 93 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 340 155 112 57 27 NC_002950:PG1055|3end_thiol_protease_1121202..1121352_NEGATIVE 339 188 141 108 46 NC_002950:PG0481|3end_2-amino-3-ketobutyrate_coenzyme_A_ligase_521432..521582_NEGATIVE 338 153 117 47 8 NC_002950:PG0017|3end_sensor_histidine_kinase_19724..19874_POSITIVE 334 187 142 140 79 NC_002950:PG1353|3end_orotate_phosphoribosyltransferase_1433201..1433351_NEGATIVE 334 156 114 61 28 NC_002950:PG1321|3end_formate--tetrahydrofolate_ligase_1399656..1399806_NEGATIVE 334 177 134 63 14 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 333 151 111 76 36 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 332 165 121 88 30 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 326 209 163 113 66 NC_002950:PG0246|3end_hypothetical_protein_281050..281200_NEGATIVE 324 155 111 61 27 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 324 159 112 69 26 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 321 153 111 147 102 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 320 210 162 90 35 NC_002950:PG1171|3end_oxidoreductase,_putative_1251175..1251325_POSITIVE 315 159 111 57 25 NC_002950:PG1028|3end_TPR_domain_protein_1091096..1091246_POSITIVE 313 155 119 28 1 NC_002950:PG1037|3end_hypothetical_protein_1102824..1102974_POSITIVE 312 155 114 132 93 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE