Origin IGS: aatactatgctcagaattaaatggttgagtttcttttattttaggtctgcaaatatagtgctttttctcttagttactttactccgacatttttaagtttgcatgacggat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atccgtcatgcaaacttaaaaatgtcggagtaaagtaactaagagaaaaagcactatatttgcagacctaaaataaaagaaactcaaccatttaattctgagcatagtatt Mask Tandem Repeat Region ================================================ aatactatgctcagaattaaatggttgagtttcttttattttaggtctgcaaatatagtgctttttctcttagttactttactccgacatttttaagtttgcatgacggat Find is-nt database================================================ Query_seq: PG1258:PG1259|PG1258:PG1259:DNA-binding protein HU:anaerobic ribonucleoside-triphosphate reductase activating protein:<-<-:1334953..1335063 111 aatactatgctcagaattaaatggttgagtttcttttattttaggtctgcaaatatagtgctttttctcttagttactttactccgacatttttaagtttgcatgacggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1258:PG1259|PG1258:PG1259:DNA-binding protein HU:anaerobic ribonucleoside-triphosphate reductase activating protein:<-<-:1334953..1335063 111 aatactatgctcagaattaaatggttgagtttcttttattttaggtctgcaaatatagtgctttttctcttagttactttactccgacatttttaagtttgcatgacggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1258:PG1259|PG1258:PG1259:DNA-binding protein HU:anaerobic ribonucleoside-triphosphate reductase activating protein:<-<-:1334953..1335063 111 aatactatgctcagaattaaatggttgagtttcttttattttaggtctgcaaatatagtgctttttctcttagttactttactccgacatttttaagtttgcatgacggat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatactatgctcagaattaaatggttgagtttcttttattttaggtctgcaaatatagtgctttttctcttagttactttactccgacatttttaagtttgcatgacggat Predict ORF larger than 30AA ================================================ aatactatgctcagaattaaatggttgagtttcttttattttaggtctgcaaatatagtgctttttctcttagttactttactccgacatttttaagtttgcatgacggat 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================================================ aatactatgctcagaattaaatggttgagtttcttttattttaggtctgcaaatatagtgctttttctcttagttactttactccgacatttttaagtttgcatgacggat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1258:PG1259|PG1258:PG1259:DNA-binding protein HU:anaerobic ribonucleoside-triphosphate reductase activating protein:<-<-:1334953..1335063 111 aatactatgctcagaattaaatggttgagtttcttttattttaggtctgcaaatatagtgctttttctcttagttactttactccgacatttttaagtttgcatgacggat Intra-Species Hit: Count: 1 Min: 1 Max: 111 Len: 111 Subject: NC_002950_PG1258_PG1259|DNA-binding protein HU:anaerobic ribonucleoside-triphosphate reductase activating protein|NEGATIVE:NEGATIVE|[1334953,1335063]|111 HSP 1 e-value: 7.0E-57 bit: 220.0 Len: 111 Query Start:1 Query End:111 Subject Strand: POSITIVE Subject Start: 1 Subject End: 111 aatactatgctcagaattaaatggttgagtttcttttattttaggtctgcaaatatagtgctttttctcttagttactttactccgacatttttaagtttgcatgacggat aatactatgctcagaattaaatggttgagtttcttttattttaggtctgcaaatatagtgctttttctcttagttactttactccgacatttttaagtttgcatgacggat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUACUAUGCUCAGAAUUAAAUGGUUGAGUUUCUUUUAUUUUAGGUCUGCAAAUAUAGUGCUUUUUCUCUUAGUUACUUUACUCCGACAUUUUUAAGUUUGCAUGACGGAU ..(((((((..((((...((((((..(.....)..))))))....))))....)))))))......................((((.(((.(........).))).)))). (-14.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCCGUCAUGCAAACUUAAAAAUGUCGGAGUAAAGUAACUAAGAGAAAAAGCACUAUAUUUGCAGACCUAAAAUAAAAGAAACUCAACCAUUUAAUUCUGAGCAUAGUAUU .((((.(((............))).))))........((((.........(((.......)))...................((((............))))..))))... (-12.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 815 90 41 181 132 NC_002950:PG1258|5end_DNA-binding_protein_HU_1334862..1335092_NEGATIVE 293 87 46 171 133 NC_002950:PG0531|5end_NAD(+)_synthetase_581139..581369_NEGATIVE 282 67 21 62 17 NC_002950:PG0317|5end_peptidase,_M49_family_352431..352661_NEGATIVE 280 69 22 161 115 NC_002950:PG1824|5end_phosphopyruvate_hydratase_1919430..1919660_NEGATIVE 275 70 21 175 119 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 271 90 41 209 157 NC_002950:PG0558|5end_purine_nucleoside_phosphorylase_616331..616561_NEGATIVE 256 74 31 196 154 NC_002950:PG1467|5end_methlytransferase,_UbiE/COQ5_family_1543210..1543440_POSITIVE 240 108 68 171 125 NC_002950:PG1546|5end_hypothetical_protein_1624087..1624317_POSITIVE 240 68 21 109 50 NC_002950:PG0955|5end_hypothetical_protein_1014832..1015062_POSITIVE 238 87 42 103 54 NC_002950:PG0209|5end_formate/nitrite_transporter_243231..243461_POSITIVE 236 98 52 169 121 NC_002950:PG1923|5end_50S_ribosomal_protein_L6_2017941..2018171_NEGATIVE 231 87 55 49 17 NC_002950:PG1235|5end_epimerase/reductase,_putative_1311256..1311486_NEGATIVE 230 71 38 151 118 NC_002950:PG1126|5end_uracil_permease_1202933..1203163_NEGATIVE 229 87 43 60 16 NC_002950:PG1150|5end_hypothetical_protein_1232906..1233136_POSITIVE 227 68 22 72 19 NC_002950:PG0737|5end_hypothetical_protein_786188..786418_POSITIVE 227 63 27 203 169 NC_002950:PG0545|5end_hypothetical_protein_598043..598273_POSITIVE 226 50 6 183 133 NC_002950:PG0485|5end_preprotein_translocase,_YajC_subunit_525324..525554_NEGATIVE 225 70 22 81 30 NC_002950:PG1121|5end_asparaginyl-tRNA_synthetase_1197555..1197785_NEGATIVE 225 60 13 183 136 NC_002950:PG0048|5end_conserved_hypothetical_protein_TIGR00092_60557..60787_NEGATIVE 223 108 61 169 115 NC_002950:PG1831|5end_ATP-dependent_DNA_helicase_RecQ_1925422..1925652_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 87 46 61 23 NC_002950:PG0532|3end_hypothetical_protein_581249..581399_NEGATIVE 280 69 22 81 35 NC_002950:PG1825|3end_hypothetical_protein_1919510..1919660_NEGATIVE 236 98 52 150 102 NC_002950:PG1924|3end_ribosomal_protein_S8_2017960..2018110_NEGATIVE 227 68 22 97 44 NC_002950:PG0736|3end_ribonuclease_HII_786293..786443_POSITIVE 227 89 43 41 3 NC_002950:PG0557|3end_hypothetical_protein_615007..615157_POSITIVE 226 50 6 100 50 NC_002950:PG0486|3end_methylated-DNA--protein-cysteine_S-methyltransferase_525407..525557_NEGATIVE 217 106 61 143 102 NC_002950:PG1805|3end_V-type_ATP_synthase_subunit_D_1900283..1900433_POSITIVE 217 48 3 51 3 NC_002950:PG0488|3end_Holliday_junction_DNA_helicase_RuvB_529280..529430_POSITIVE 216 88 59 73 41 NC_002950:PG2121|3end_L-asparaginase_2228545..2228695_NEGATIVE 215 69 21 123 87 NC_002950:PG1381|3end_ABC_transporter,_permease_protein_1461451..1461601_POSITIVE 208 91 58 48 20 NC_002950:PG1355|3end_acyltransferase,_putative_1434762..1434912_NEGATIVE 207 109 72 33 1 NC_002950:PG1937|3end_50S_ribosomal_protein_L4_2023507..2023657_NEGATIVE 207 88 43 120 82 NC_002950:PG1891|3end_hypothetical_protein_1988445..1988595_POSITIVE 204 110 62 143 81 NC_002950:PG0348|3end_ATP-dependent_DNA_helicase_RecG_384521..384671_POSITIVE 202 51 11 76 33 NC_002950:PG1612|3end_methylmalonyl-CoA_decarboxylase,_alpha_subunit_1691512..1691662_NEGATIVE 202 87 43 125 67 NC_002950:PG0615|3end_GTP-binding_protein_TypA_668912..669062_POSITIVE 202 86 42 57 8 NC_002950:PG0544|3end_type_I_restriction-modification_system,_M_subunit,_putative_598078..598228_POSITIVE 200 86 41 51 9 NC_002950:PG1676|3end_phosphoenolpyruvate_carboxykinase_1760489..1760639_NEGATIVE 200 70 24 145 90 NC_002950:PG0709|3end_peptidyl-prolyl_cis-trans_isomerase_FkpA,_FKBP-type_764656..764806_NEGATIVE 200 109 76 128 88 NC_002950:PG0278|3end_hypothetical_protein_310477..310627_POSITIVE