Origin IGS: tggaaaaatttttattgatgtggtttttgattagtcttctgtagccttggccaagaatataatagtcgtatatcttttggcttcaggcagatttttgggtgatagcagacctttatcggccggtcttgctatcaccctcaatttgtggctttttctcggtttttgtctttattcggaaaaaaacctttatgtgt .........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 acacataaaggtttttttccgaataaagacaaaaaccgagaaaaagccacaaattgagggtgatagcaagaccggccgataaaggtctgctatcacccaaaaatctgcctgaagccaaaagatatacgactattatattcttggccaaggctacagaagactaatcaaaaaccacatcaataaaaatttttcca Mask Tandem Repeat Region ================================================ tggaaaaatttttattgatgtggtttttgattagtcttctgtagccttggccaagaatataatagtcgtatatcttttggcttcaggcagatttttgggtgatagcagacctttatcggccggtcttgctatcaccctcaatttgtggctttttctcggtttttgtctttattcggaaaaaaacctttatgtgt Find is-nt database================================================ Query_seq: PG0687:PG0689|PG0687:PG0689:succinate-semialdehyde dehydrogenase:NAD-dependent 4-hydroxybutyrate dehydrogenase:<-<-:744614..744807 194 tggaaaaatttttattgatgtggtttttgattagtcttctgtagccttggccaagaatataatagtcgtatatcttttggcttcaggcagatttttgggtgatagcagacctttatcggccggtcttgctatcaccctcaatttgtggctttttctcggtttttgtctttattcggaaaaaaacctttatgtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0687:PG0689|PG0687:PG0689:succinate-semialdehyde dehydrogenase:NAD-dependent 4-hydroxybutyrate dehydrogenase:<-<-:744614..744807 194 tggaaaaatttttattgatgtggtttttgattagtcttctgtagccttggccaagaatataatagtcgtatatcttttggcttcaggcagatttttgggtgatagcagacctttatcggccggtcttgctatcaccctcaatttgtggctttttctcggtttttgtctttattcggaaaaaaacctttatgtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0687:PG0689|PG0687:PG0689:succinate-semialdehyde dehydrogenase:NAD-dependent 4-hydroxybutyrate dehydrogenase:<-<-:744614..744807 194 tggaaaaatttttattgatgtggtttttgattagtcttctgtagccttggccaagaatataatagtcgtatatcttttggcttcaggcagatttttgggtgatagcagacctttatcggccggtcttgctatcaccctcaatttgtggctttttctcggtttttgtctttattcggaaaaaaacctttatgtgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tggaaaaatttttattgatgtggtttttgattagtcttctgtagccttggccaagaatataatagtcgtatatcttttggcttcaggcagatttttgggtgatagcagacctttatcggccggtcttgctatcaccctcaatttgtggctttttctcggtttttgtctttattcggaaaaaaacctttatgtgt Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 47 End: 193 .............................................. M A K N I I V V Y L L A S G R F L G D S R P L S A G L A I T L N L W L F L G F C L Y S E K N L Y V . Protein_Len: 41 Strand: + Start: 72 End: 194 ....................................................................... M F W L Q A D F W V I A D L Y R P V L L S P S I C G F F S V F V F I R K K T F M C Protein_Len: 36 Strand: - Start: 34 End: 141 ................................. D E T A K A L F I I T T Y R K A E P L N K P S L L G K D A P R A I V R M ..................................................... Protein_Len: 34 Strand: - Start: 15 End: 116 .............. Q H P K Q N T K Q L R P W S Y L L R I D K P K L C I K P H Y C V K M .............................................................................. tggaaaaatttttattgatgtggtttttgattagtcttctgtagccttggccaagaatataatagtcgtatatcttttggcttcaggcagatttttgggtgatagcagacctttatcggccggtcttgctatcaccctcaatttgtggctttttctcggtttttgtctttattcggaaaaaaacctttatgtgt 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================================================ tggaaaaatttttattgatgtggtttttgattagtcttctgtagccttggccaagaatataatagtcgtatatcttttggcttcaggcagatttttgggtgatagcagacctttatcggccggtcttgctatcaccctcaatttgtggctttttctcggtttttgtctttattcggaaaaaaacctttatgtgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 73 HP_score: -6.9 Tail_Score: -4.10363 Start: 93 End: 141 Full_Region: TGGCTTCAGGCAGAT TTTTGGGTGATAGCAGACC TTTATCGGCC GGTCTTGCTATCACCCTCAA TTTGTGGCTTTTTCT ............................................................................................TTTTGGGTGATAGCAGACCTTTATCGGCCGGTCTTGCTATCACCCTCAA..................................................... TransTerm Strand: + Conf: 85 HP_score: -12.1 Tail_Score: -2.72441 Start: 97 End: 137 Full_Region: TTCAGGCAGATTTTT GGGTGATAGCAGACC TTTATCGGCC GGTCTTGCTATCACCC TCAATTTGTGGCTTT ................................................................................................GGGTGATAGCAGACCTTTATCGGCCGGTCTTGCTATCACCC......................................................... Find igs database================================================ Query_seq: PG0687:PG0689|PG0687:PG0689:succinate-semialdehyde dehydrogenase:NAD-dependent 4-hydroxybutyrate dehydrogenase:<-<-:744614..744807 194 tggaaaaatttttattgatgtggtttttgattagtcttctgtagccttggccaagaatataatagtcgtatatcttttggcttcaggcagatttttgggtgatagcagacctttatcggccggtcttgctatcaccctcaatttgtggctttttctcggtttttgtctttattcggaaaaaaacctttatgtgt Intra-Species Hit: Count: 1 Min: 1 Max: 176 Len: 176 Subject: NC_002950_PG0687_PG0689|succinate-semialdehyde dehydrogenase:NAD-dependent 4-hydroxybutyrate dehydrogenase|NEGATIVE:NEGATIVE|[744614,744807]|194 HSP 1 e-value: 2.0E-95 bit: 349.0 Len: 176 Query Start:1 Query End:176 Subject Strand: POSITIVE Subject Start: 1 Subject End: 176 tggaaaaatttttattgatgtggtttttgattagtcttctgtagccttggccaagaatataatagtcgtatatcttttggcttcaggcagatttttgggtgatagcagacctttatcggccggtcttgctatcaccctcaatttgtggctttttctcggtttttgtctttattcgg.................. tggaaaaatttttattgatgtggtttttgattagtcttctgtagccttggccaagaatataatagtcgtatatcttttggcttcaggcagatttttgggtgatagcagacctttatcggccggtcttgctatcaccctcaatttgtggctttttctcggtttttgtctttattcgg.................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGGAAAAAUUUUUAUUGAUGUGGUUUUUGAUUAGUCUUCUGUAGCCUUGGCCAAGAAUAUAAUAGUCGUAUAUCUUUUGGCUUCAGGCAGAUUUUUGGGUGAUAGCAGACCUUUAUCGGCCGGUCUUGCUAUCACCCUCAAUUUGUGGCUUUUUCUCGGUUUUUGUCUUUAUUCGG ............((..((((........((..((((.......((((.(((((((((((((.......))))).))))))))..))))........(((((((((((((((..........)))).))))))))))).........))))...))........))))..))..... (-48.59) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGAAUAAAGACAAAAACCGAGAAAAAGCCACAAAUUGAGGGUGAUAGCAAGACCGGCCGAUAAAGGUCUGCUAUCACCCAAAAAUCUGCCUGAAGCCAAAAGAUAUACGACUAUUAUAUUCUUGGCCAAGGCUACAGAAGACUAAUCAAAAACCACAUCAAUAAAAAUUUUUCCA ...................(.((((((.......((((((((((((((((.((((..........))))))))))))))).....(((((((...(((((..((((((.......)))))).)))))..))))...)))...................))))).....))))))). (-46.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 994 130 81 221 172 NC_002950:PG0687|5end_succinate-semialdehyde_dehydrogenase_744523..744753_NEGATIVE 407 127 82 62 12 NC_002950:PG0802|5end_alpha_keto_acid_dehydrogenase_complex,_E3_component,_lipoamide_dehydrogenase_859722..859952_NEGATIVE 393 130 81 62 7 NC_002950:PG0654|5end_hypothetical_protein_706685..706915_NEGATIVE 371 130 84 193 150 NC_002950:PG0201|5end_ribonuclease_P_238770..239000_NEGATIVE 363 139 97 181 146 NC_002950:PG0217|5end_hypothetical_protein_252490..252720_POSITIVE 356 129 82 222 168 NC_002950:PG1162|5end_ATP:cob(I)alamin_adenosyltransferase,_putative_1242039..1242269_NEGATIVE 354 117 75 230 190 NC_002950:PG0376|5end_30S_ribosomal_protein_S9_406399..406629_POSITIVE 349 119 76 46 2 NC_002950:PG2095|5end_lipoprotein,_putative_2200617..2200847_NEGATIVE 348 128 85 138 95 NC_002950:PG0934|5end_hypothetical_protein_994318..994548_NEGATIVE 344 130 81 196 135 NC_002950:PG1098|5end_hypothetical_protein_1167009..1167239_NEGATIVE 342 137 95 175 127 NC_002950:PG1964|5end_bacterial_sugar_transferase_2052910..2053140_POSITIVE 340 149 105 49 1 NC_002950:PG1075|5end_coenzyme_A_transferase,_beta_subunit_1142778..1143008_POSITIVE 334 139 95 60 5 NC_002950:PG1094|5end_phosphomannomutase_1158753..1158983_POSITIVE 333 160 111 159 113 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 332 149 104 79 23 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 331 130 82 77 18 NC_002950:PG1080|5end_3-hydroxyacyl-CoA_dehydrogenase_family_protein_1147366..1147596_POSITIVE 329 140 97 139 94 NC_002950:PG1966|5end_hypothetical_protein_2056924..2057154_NEGATIVE 329 150 105 173 127 NC_002950:PG0871|5end_hypothetical_protein_934836..935066_NEGATIVE 327 150 101 67 26 NC_002950:PG1057|5end_hypothetical_protein_1123419..1123649_POSITIVE 327 158 118 202 149 NC_002950:PG0538|5end_outer_membrane_efflux_protein_589142..589372_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 407 127 82 57 7 NC_002950:PG0803|3end_glucosamine-6-phosphate_deaminase_859727..859877_NEGATIVE 383 156 111 98 37 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 373 130 81 137 89 NC_002950:PG0479|3end_hypothetical_protein_520545..520695_POSITIVE 363 139 97 147 112 NC_002950:PG0216|3end_hypothetical_protein_252536..252686_POSITIVE 346 120 77 145 112 NC_002950:PG0935|3end_4-diphosphocytidyl-2C-methyl-D-erythritol_kinase_994297..994447_NEGATIVE 342 120 73 145 78 NC_002950:PG0275|3end_thioredoxin_family_protein_306955..307105_NEGATIVE 341 140 92 74 15 NC_002950:PG1968|3end_hypothetical_protein_2058460..2058610_NEGATIVE 338 139 98 76 41 NC_002950:PG0507|3end_hypothetical_protein_548190..548340_POSITIVE 331 160 114 117 69 NC_002950:PG0424|3end_hypothetical_protein_463213..463363_POSITIVE 327 150 101 47 6 NC_002950:PG1056|3end_hypothetical_protein_1123479..1123629_POSITIVE 327 149 110 135 99 NC_002950:PG0377|3end_30S_ribosomal_protein_S2_407845..407995_POSITIVE 325 129 81 66 18 NC_002950:PG0375|3end_50S_ribosomal_protein_L13_406469..406619_POSITIVE 319 130 82 122 62 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 316 159 115 132 77 NC_002950:PG1595|3end_ribulose-phosphate_3-epimerase_1673594..1673744_NEGATIVE 315 139 95 125 67 NC_002950:PG0736|3end_ribonuclease_HII_786293..786443_POSITIVE 314 127 85 120 78 NC_002950:PG1896|3end_S-adenosylmethionine_synthetase_1995955..1996105_POSITIVE 313 130 81 123 68 NC_002950:PG0787|3end_hypothetical_protein_837997..838147_POSITIVE 313 130 86 117 66 NC_002950:PG0283|3end_efflux_transporter,_MFP_component,_RND_family_316995..317145_NEGATIVE 310 123 82 42 1 NC_002950:PG2096|3end_hypothetical_protein_2200625..2200775_NEGATIVE 306 126 81 58 5 NC_002950:PG0399|3end_lipoprotein,_putative_435707..435857_NEGATIVE