Origin IGS: aaatgtggcgtgagaatttttctgttttggagcgaaaattttttgcttcccacacgaaaacgaaaattttctcgccctacgtttttcggagcgtacaataggaaaagtttggtgtgacgtgtgacgtgtcctgaaaaaagctactccatcctgatctgccttgtgcatatttcccttaccatcactatattttctgtagttttgtaccgcttcatcaattaaaaacaacaacaat .........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 attgttgttgtttttaattgatgaagcggtacaaaactacagaaaatatagtgatggtaagggaaatatgcacaaggcagatcaggatggagtagcttttttcaggacacgtcacacgtcacaccaaacttttcctattgtacgctccgaaaaacgtagggcgagaaaattttcgttttcgtgtgggaagcaaaaaattttcgctccaaaacagaaaaattctcacgccacattt Mask Tandem Repeat Region ================================================ aaatgtggcgtgagaatttttctgttttggagcgaaaattttttgcttcccacacgaaaacgaaaattttctcgccctacgtttttcggagcgtacaataggaaaagtttggtgtgacgtgtgacgtgtcctgaaaaaagctactccatcctgatctgccttgtgcatatttcccttaccatcactatattttctgtagttttgtaccgcttcatcaattaaaaacaacaacaat Find is-nt database================================================ Query_seq: PG0732:PG0733|PG0732:PG0733:hypothetical protein:riboflavin synthase subunit alpha:->->:783079..783313 235 aaatgtggcgtgagaatttttctgttttggagcgaaaattttttgcttcccacacgaaaacgaaaattttctcgccctacgtttttcggagcgtacaataggaaaagtttggtgtgacgtgtgacgtgtcctgaaaaaagctactccatcctgatctgccttgtgcatatttcccttaccatcactatattttctgtagttttgtaccgcttcatcaattaaaaacaacaacaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0732:PG0733|PG0732:PG0733:hypothetical protein:riboflavin synthase subunit alpha:->->:783079..783313 235 aaatgtggcgtgagaatttttctgttttggagcgaaaattttttgcttcccacacgaaaacgaaaattttctcgccctacgtttttcggagcgtacaataggaaaagtttggtgtgacgtgtgacgtgtcctgaaaaaagctactccatcctgatctgccttgtgcatatttcccttaccatcactatattttctgtagttttgtaccgcttcatcaattaaaaacaacaacaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0732:PG0733|PG0732:PG0733:hypothetical protein:riboflavin synthase subunit alpha:->->:783079..783313 235 aaatgtggcgtgagaatttttctgttttggagcgaaaattttttgcttcccacacgaaaacgaaaattttctcgccctacgtttttcggagcgtacaataggaaaagtttggtgtgacgtgtgacgtgtcctgaaaaaagctactccatcctgatctgccttgtgcatatttcccttaccatcactatattttctgtagttttgtaccgcttcatcaattaaaaacaacaacaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaatgtggcgtgagaatttttctgttttggagcgaaaattttttgcttcccacacgaaaacgaaaattttctcgccctacgtttttcggagcgtacaataggaaaagtttggtgtgacgtgtgacgtgtcctgaaaaaagctactccatcctgatctgccttgtgcatatttcccttaccatcactatattttctgtagttttgtaccgcttcatcaattaaaaacaacaacaat Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 3 End: 98 .. M W R E N F S V L E R K F F A S H T K T K I F S P Y V F R S V Q ......................................................................................................................................... Protein_Len: 35 Strand: + Start: 10 End: 114 ......... M R I F L F W S E N F L L P T R K R K F S R P T F F G A Y N R K S L V ......................................................................................................................... Protein_Len: 33 Strand: + Start: 121 End: 219 ........................................................................................................................ M T C P E K S Y S I L I C L V H I S L T I T I F S V V L Y R F I N ................ Protein_Len: 32 Strand: - Start: 3 End: 98 .. H P T L I K R N Q L S F K K S G V R F R F N E R G V N K P A Y M ......................................................................................................................................... Protein_Len: 60 Strand: - Start: 1 End: 234 S F S F K R A R R K E S R V I P F T Q H S T H R T R F F A V G D Q D A K H M N G K G D S Y K R Y N Q V A E D I L F L L M . aaatgtggcgtgagaatttttctgttttggagcgaaaattttttgcttcccacacgaaaacgaaaattttctcgccctacgtttttcggagcgtacaataggaaaagtttggtgtgacgtgtgacgtgtcctgaaaaaagctactccatcctgatctgccttgtgcatatttcccttaccatcactatattttctgtagttttgtaccgcttcatcaattaaaaacaacaacaat 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================================================ aaatgtggcgtgagaatttttctgttttggagcgaaaattttttgcttcccacacgaaaacgaaaattttctcgccctacgtttttcggagcgtacaataggaaaagtttggtgtgacgtgtgacgtgtcctgaaaaaagctactccatcctgatctgccttgtgcatatttcccttaccatcactatattttctgtagttttgtaccgcttcatcaattaaaaacaacaacaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0732:PG0733|PG0732:PG0733:hypothetical protein:riboflavin synthase subunit alpha:->->:783079..783313 235 aaatgtggcgtgagaatttttctgttttggagcgaaaattttttgcttcccacacgaaaacgaaaattttctcgccctacgtttttcggagcgtacaataggaaaagtttggtgtgacgtgtgacgtgtcctgaaaaaagctactccatcctgatctgccttgtgcatatttcccttaccatcactatattttctgtagttttgtaccgcttcatcaattaaaaacaacaacaat Intra-Species Hit: Count: 1 Min: 1 Max: 235 Len: 235 Subject: NC_002950_PG0732_PG0733|hypothetical protein:riboflavin synthase subunit alpha|POSITIVE:POSITIVE|[783079,783313]|235 HSP 1 e-value: 1.0E-130 bit: 466.0 Len: 235 Query Start:1 Query End:235 Subject Strand: POSITIVE Subject Start: 1 Subject End: 235 aaatgtggcgtgagaatttttctgttttggagcgaaaattttttgcttcccacacgaaaacgaaaattttctcgccctacgtttttcggagcgtacaataggaaaagtttggtgtgacgtgtgacgtgtcctgaaaaaagctactccatcctgatctgccttgtgcatatttcccttaccatcactatattttctgtagttttgtaccgcttcatcaattaaaaacaacaacaat aaatgtggcgtgagaatttttctgttttggagcgaaaattttttgcttcccacacgaaaacgaaaattttctcgccctacgtttttcggagcgtacaataggaaaagtttggtgtgacgtgtgacgtgtcctgaaaaaagctactccatcctgatctgccttgtgcatatttcccttaccatcactatattttctgtagttttgtaccgcttcatcaattaaaaacaacaacaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUGUGGCGUGAGAAUUUUUCUGUUUUGGAGCGAAAAUUUUUUGCUUCCCACACGAAAACGAAAAUUUUCUCGCCCUACGUUUUUCGGAGCGUACAAUAGGAAAAGUUUGGUGUGACGUGUGACGUGUCCUGAAAAAAGCUACUCCAUCCUGAUCUGCCUUGUGCAUAUUUCCCUUACCAUCACUAUAUUUUCUGUAGUUUUGUACCGCUUCAUCAAUUAAAAACAACAACAAU ((((((((.(((((((.(((((.(((((((((((((.....)))))))).......))))))))))..))))))).))))))))...(((((((((((..((((((...(((((((..(((.((.(((..((......)).))))))))...(((.(((.....))).)))........)).)))))..))))))......))))).))))))...................... (-55.21) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGUUGUUGUUUUUAAUUGAUGAAGCGGUACAAAACUACAGAAAAUAUAGUGAUGGUAAGGGAAAUAUGCACAAGGCAGAUCAGGAUGGAGUAGCUUUUUUCAGGACACGUCACACGUCACACCAAACUUUUCCUAUUGUACGCUCCGAAAAACGUAGGGCGAGAAAAUUUUCGUUUUCGUGUGGGAAGCAAAAAAUUUUCGCUCCAAAACAGAAAAAUUCUCACGCCACAUUU .((((.(..(((((........)))))..)))))...............((((.((((..(((((...(((.....)))........((((((...........((..(((.....)))....))..................(((((.(...(((.(((((((((....)))))))))))).).)).)))...........))))))...........)))))..)))))))). (-46.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 510 50 1 61 14 NC_002950:PG1799|5end_hypothetical_protein_1894499..1894729_POSITIVE 468 94 55 127 84 NC_002950:PG1980|5end_hypothetical_protein_2067930..2068160_NEGATIVE 457 90 41 87 38 NC_002950:PG2064|5end_hypothetical_protein_2160550..2160780_POSITIVE 430 103 61 47 7 NC_002950:PG0524|5end_hypothetical_protein_568599..568829_POSITIVE 429 80 32 113 65 NC_002950:PG0174|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_197628..197858_NEGATIVE 366 34 1 138 105 NC_002950:PG2063|5end_hypothetical_protein_2160596..2160826_NEGATIVE 361 44 1 169 127 NC_002950:PG0081|5end_hypothetical_protein_93805..94035_POSITIVE 353 90 41 88 41 NC_002950:PG0313|5end_hypothetical_protein_347366..347596_POSITIVE 348 45 1 144 106 NC_002950:PG0661|5end_hypothetical_protein_709853..710083_NEGATIVE 335 93 52 157 110 NC_002950:PG1645|5end_ISPg5,_transposase_Orf1_1726062..1726292_NEGATIVE 335 46 1 144 92 NC_002950:PG0132|5end_hypothetical_protein_152879..153109_POSITIVE 320 89 41 118 79 NC_002950:PG1617|5end_hypothetical_protein_1697755..1697985_NEGATIVE 316 159 111 63 11 NC_002950:PG0010|5end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpC_8775..9005_POSITIVE 307 93 55 69 22 NC_002950:PG1126|5end_uracil_permease_1202933..1203163_NEGATIVE 304 50 1 105 56 NC_002950:PG0007|5end_hypothetical_protein_6913..7143_NEGATIVE 303 120 71 91 36 NC_002950:PG1199|5end_hypothetical_protein_1276893..1277123_POSITIVE 297 174 138 181 144 NC_002950:PG0271|5end_single-stranded_binding_protein_303842..304072_POSITIVE 293 162 127 69 26 NC_002950:PG1429|5end_hypothetical_protein_1515113..1515343_NEGATIVE 293 162 127 160 117 NC_002950:PG1428|5end_riboflavin_synthase_subunit_beta_1515022..1515252_NEGATIVE 291 216 174 115 77 NC_002950:PG0165|5end_heat_shock_protein_15_187807..188037_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 362 49 1 62 7 NC_002950:PG0732|3end_hypothetical_protein_783018..783168_POSITIVE 358 80 31 51 9 NC_002950:PG0542|3end_hypothetical_protein_595377..595527_NEGATIVE 307 128 86 138 94 NC_002950:PG1977|3end_hypothetical_protein_2064687..2064837_NEGATIVE 303 120 71 87 32 NC_002950:PG1198|3end_hypothetical_protein_1276969..1277119_POSITIVE 298 160 111 87 28 NC_002950:PG0793|3end_fructose-1,6-bisphosphatase_846335..846485_POSITIVE 297 174 138 130 93 NC_002950:PG0270|3end_redox-sensitive_transcriptional_activator_OxyR_303871..304021_POSITIVE 294 90 41 66 16 NC_002950:PG1626|3end_hypothetical_protein_1710486..1710636_POSITIVE 293 162 127 68 25 NC_002950:PG1430|3end_TPR_domain_protein_1515114..1515264_NEGATIVE 291 119 71 104 55 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 291 216 174 109 71 NC_002950:PG0166|3end_peptidyl-tRNA_hydrolase_187813..187963_NEGATIVE 287 127 81 56 12 NC_002950:PG1241|3end_GTP-binding_protein_LepA_1317480..1317630_POSITIVE 286 134 100 82 52 NC_002950:PG2092|3end_hypothetical_protein_2191651..2191801_NEGATIVE 284 149 101 99 44 NC_002950:PG0070|3end_UDP-N-acetylglucosamine_acyltransferase_83940..84090_NEGATIVE 280 160 112 127 75 NC_002950:PG2062|3end_histidyl-tRNA_synthetase_2160415..2160565_POSITIVE 280 126 87 103 56 NC_002950:PG0569|3end_hypothetical_protein_624697..624847_NEGATIVE 279 133 91 86 42 NC_002950:PG1619|3end_biotin_synthesis_protein_BioC,_putative_1699415..1699565_POSITIVE 275 112 77 46 5 NC_002950:PG1306|3end_metallo-beta-lactamase_family_protein_1386543..1386693_NEGATIVE 275 120 71 54 8 NC_002950:PG1250|3end_hypothetical_protein_1327184..1327334_NEGATIVE 273 169 122 126 64 NC_002950:PG1431|3end_DNA-binding_response_regulator,_LuxR_family_1515986..1516136_NEGATIVE 272 116 74 89 43 NC_002950:PG0785|3end_tonB_protein,_putative_836900..837050_NEGATIVE