Origin IGS: gacttctacgagatccgatcggatctttcattactccctcacggggctgtaccgaaggaactatccgggtacagccccgtgttcttttccggatattatcgactaaccaattcccctccaatatcatcagatagccgcacg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cgtgcggctatctgatgatattggaggggaattggttagtcgataatatccggaaaagaacacggggctgtacccggatagttccttcggtacagccccgtgagggagtaatgaaagatccgatcggatctcgtagaagtc Mask Tandem Repeat Region ================================================ gacttctacgagatccgatcggatctttcattactccctcacggggctgtaccgaaggaactatccgggtacagccccgtgttcttttccggatattatcgactaaccaattcccctccaatatcatcagatagccgcacg Find is-nt database================================================ Query_seq: PG2124:PG2125|PG2124:PG2125:glyceraldehyde 3-phosphate dehydrogenase, type I:transcriptional regulator, AraC family:-><-:2231325..2231465 141 gacttctacgagatccgatcggatctttcattactccctcacggggctgtaccgaaggaactatccgggtacagccccgtgttcttttccggatattatcgactaaccaattcccctccaatatcatcagatagccgcacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2124:PG2125|PG2124:PG2125:glyceraldehyde 3-phosphate dehydrogenase, type I:transcriptional regulator, AraC family:-><-:2231325..2231465 141 gacttctacgagatccgatcggatctttcattactccctcacggggctgtaccgaaggaactatccgggtacagccccgtgttcttttccggatattatcgactaaccaattcccctccaatatcatcagatagccgcacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2124:PG2125|PG2124:PG2125:glyceraldehyde 3-phosphate dehydrogenase, type I:transcriptional regulator, AraC family:-><-:2231325..2231465 141 gacttctacgagatccgatcggatctttcattactccctcacggggctgtaccgaaggaactatccgggtacagccccgtgttcttttccggatattatcgactaaccaattcccctccaatatcatcagatagccgcacg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacttctacgagatccgatcggatctttcattactccctcacggggctgtaccgaaggaactatccgggtacagccccgtgttcttttccggatattatcgactaaccaattcccctccaatatcatcagatagccgcacg Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 18 End: 131 ................. M G S F I T P S R G C T E G T I R V Q P R V L F R I L S T N Q F P S N I I R .......... Protein_Len: 43 Strand: + Start: 13 End: 141 ............ M R S D L S L L P H G A V P K E L S G Y S P V F F S G Y Y R L T N S P P I S S D S R T Protein_Len: 43 Strand: - Start: 2 End: 130 . S R R S G I P D K M V G E R P Q V S P V I R T C G R T R K R I N D V L W N G E L I M M ........... gacttctacgagatccgatcggatctttcattactccctcacggggctgtaccgaaggaactatccgggtacagccccgtgttcttttccggatattatcgactaaccaattcccctccaatatcatcagatagccgcacg 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================================================ gacttctacgagatccgatcggatctttcattactccctcacggggctgtaccgaaggaactatccgggtacagccccgtgttcttttccggatattatcgactaaccaattcccctccaatatcatcagatagccgcacg Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -15.3 Tail_Score: -4.18908 Start: 40 End: 81 Full_Region: CTTTCATTACTCCCT CACGGGGCTGTACCGAA GGAACTA TCCGGGTACAGCCCCGTG TTCTTTTCCGGATAT .......................................CACGGGGCTGTACCGAAGGAACTATCCGGGTACAGCCCCGTG............................................................ Find igs database================================================ Query_seq: PG2124:PG2125|PG2124:PG2125:glyceraldehyde 3-phosphate dehydrogenase, type I:transcriptional regulator, AraC family:-><-:2231325..2231465 141 gacttctacgagatccgatcggatctttcattactccctcacggggctgtaccgaaggaactatccgggtacagccccgtgttcttttccggatattatcgactaaccaattcccctccaatatcatcagatagccgcacg Intra-Species Hit: Count: 1 Min: 1 Max: 141 Len: 141 Subject: NC_002950_PG2124_PG2125|glyceraldehyde 3-phosphate dehydrogenase, type I:transcriptional regulator, AraC family|POSITIVE:NEGATIVE|[2231325,2231465]|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 gacttctacgagatccgatcggatctttcattactccctcacggggctgtaccgaaggaactatccgggtacagccccgtgttcttttccggatattatcgactaaccaattcccctccaatatcatcagatagccgcacg gacttctacgagatccgatcggatctttcattactccctcacggggctgtaccgaaggaactatccgggtacagccccgtgttcttttccggatattatcgactaaccaattcccctccaatatcatcagatagccgcacg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACUUCUACGAGAUCCGAUCGGAUCUUUCAUUACUCCCUCACGGGGCUGUACCGAAGGAACUAUCCGGGUACAGCCCCGUGUUCUUUUCCGGAUAUUAUCGACUAACCAAUUCCCCUCCAAUAUCAUCAGAUAGCCGCACG .........(((((((....)))))))............((((((((((((((...(((....))).))))))))))))))........(((....((((.............................)))).))).... (-44.45) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUGCGGCUAUCUGAUGAUAUUGGAGGGGAAUUGGUUAGUCGAUAAUAUCCGGAAAAGAACACGGGGCUGUACCCGGAUAGUUCCUUCGGUACAGCCCCGUGAGGGAGUAAUGAAAGAUCCGAUCGGAUCUCGUAGAAGUC .....((((.(((.((((.(((.((..(((.((.((((.((.........(......)..((((((((((((((.(((....)))...))))))))))))))...)).)))).))...)))..)).))).))))))))))) (-52.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 442 78 43 174 136 NC_002950:PG0480|5end_precorrin-2_C20-methyltransferase,_putative_521319..521549_NEGATIVE 421 78 34 191 141 NC_002950:PG0095|5end_DNA_mismatch_repair_protein_114763..114993_NEGATIVE 411 84 41 220 169 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 411 78 34 198 151 NC_002950:PG1719|5end_ABC_transporter,_ATP-binding_protein,_MsbA_family_1806749..1806979_POSITIVE 398 90 42 207 147 NC_002950:PG2028|5end_ebsC_protein_2126027..2126257_POSITIVE 377 57 13 61 14 NC_002950:PG2060|5end_thymidylate_synthase_2157573..2157803_POSITIVE 374 74 34 45 5 NC_002950:PG0425|5end_esterase,_putative_463989..464219_NEGATIVE 367 77 34 198 151 NC_002950:PG1163|5end_cobyrinic_acid_a,c-diamide_synthase_1243381..1243611_NEGATIVE 365 79 34 227 171 NC_002950:PG0335|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_370706..370936_NEGATIVE 364 130 85 49 7 NC_002950:PG1332|5end_NAD(P)_transhydrogenase,_beta_subunit_1412042..1412272_POSITIVE 363 79 32 216 172 NC_002950:PG1392|5end_rod_shape-determining_protein_RodA,_putative_1474416..1474646_NEGATIVE 362 90 41 210 163 NC_002950:PG1481|5end_conjugative_transposon_protein_TraG_1558447..1558677_NEGATIVE 361 90 42 207 154 NC_002950:PG1180|5end_hypothetical_protein_1263615..1263845_NEGATIVE 358 79 32 56 19 NC_002950:PG1572|5end_hypothetical_protein_1651252..1651482_NEGATIVE 355 47 1 128 81 NC_002950:PG1125|5end_hypothetical_protein_1201727..1201957_NEGATIVE 352 87 42 98 41 NC_002950:PG0021|5end_TIM-barrel_protein,_putative,_NifR3_family_25123..25353_NEGATIVE 350 68 21 179 116 NC_002950:PG1098|5end_hypothetical_protein_1167009..1167239_NEGATIVE 349 68 36 183 151 NC_002950:PG0237|5end_uracil-DNA_glycosylase_274778..275008_POSITIVE 346 81 42 147 100 NC_002950:PG1691|5end_hypothetical_protein_1776484..1776714_NEGATIVE 346 59 15 192 147 NC_002950:PG1116|5end_methylenetetrahydrofolate_dehydrogenase/methenyltetrahydrofolate_cyclohydrolase_1188931..1189161_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 573 80 40 50 10 NC_002950:PG2124|3end_glyceraldehyde_3-phosphate_dehydrogenase,_type_I_2231264..2231414_POSITIVE 486 89 43 59 14 NC_002950:PG1754|3end_hypothetical_protein_1842284..1842434_POSITIVE 453 77 36 57 7 NC_002950:PG0349|3end_hydrolase,_haloacid_dehalogenase-like_family_385291..385441_POSITIVE 442 78 43 61 23 NC_002950:PG0481|3end_2-amino-3-ketobutyrate_coenzyme_A_ligase_521432..521582_NEGATIVE 440 87 43 92 50 NC_002950:PG0725|3end_hydrolase,_haloacid_dehalogenase-like_family_777966..778116_POSITIVE 411 84 41 73 22 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 403 89 43 71 26 NC_002950:PG0726|3end_lipoprotein,_putative_778003..778153_NEGATIVE 399 85 43 66 30 NC_002950:PG1055|3end_thiol_protease_1121202..1121352_NEGATIVE 397 79 42 66 33 NC_002950:PG1729|3end_thiol_peroxidase_1818342..1818492_NEGATIVE 396 80 34 40 1 NC_002950:PG1458|3end_hypothetical_protein_1539682..1539832_POSITIVE 386 77 39 67 28 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 384 80 43 76 26 NC_002950:PG0350|3end_internalin-related_protein_385356..385506_NEGATIVE 374 88 43 67 20 NC_002950:PG2170|3end_sugar_transporter_2276685..2276835_NEGATIVE 374 77 36 50 5 NC_002950:PG1038|3end_ATP-dependent_DNA_helicase_UvrD/PcrA/Rep_Family_1105121..1105271_POSITIVE 371 60 11 134 66 NC_002950:PG1846|3end_hypothetical_protein_1946254..1946404_POSITIVE 362 79 35 60 9 NC_002950:PG1186|3end_hypothetical_protein_1267703..1267853_NEGATIVE 361 88 43 43 7 NC_002950:PG1297|3end_ribosomal_protein_S1_1377710..1377860_POSITIVE 355 47 1 109 62 NC_002950:PG1126|3end_uracil_permease_1201746..1201896_NEGATIVE 352 87 42 101 44 NC_002950:PG0022|3end_sulfate_permease_family_protein_25120..25270_NEGATIVE 349 78 37 41 1 NC_002950:PG1950|3end_hypothetical_protein_2040840..2040990_POSITIVE