Origin IGS: ctttcgtttgtttttttgttaagttatacttattagacgaagtgacgaaagccatgagcttccactacttctattctctgttttcttttttagtttgtctttatgccgaagacgaagaaaaagtttattcatcttttttaccggcaccgactccgcaaatataggaaataattcaaatggacgcttcgcactcctctcaatattgtttcacaaaccatatttatgtgtcagattatccatgtttgattagttttacaccggaattgacttgcatatagaaagccaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttggctttctatatgcaagtcaattccggtgtaaaactaatcaaacatggataatctgacacataaatatggtttgtgaaacaatattgagaggagtgcgaagcgtccatttgaattatttcctatatttgcggagtcggtgccggtaaaaaagatgaataaactttttcttcgtcttcggcataaagacaaactaaaaaagaaaacagagaatagaagtagtggaagctcatggctttcgtcacttcgtctaataagtataacttaacaaaaaaacaaacgaaag Mask Tandem Repeat Region ================================================ ctttcgtttgtttttttgttaagttatacttattagacgaagtgacgaaagccatgagcttccactacttctattctctgttttcttttttagtttgtctttatgccgaagacgaagaaaaagtttattcatcttttttaccggcaccgactccgcaaatataggaaataattcaaatggacgcttcgcactcctctcaatattgtttcacaaaccatatttatgtgtcagattatccatgtttgattagttttacaccggaattgacttgcatatagaaagccaa Find is-nt database================================================ Query_seq: PG1795:PG1797|PG1795:PG1797:hypothetical protein:DNA-binding response regulator/sensor histidine kinase:<-->:1889867..1890152 286 ctttcgtttgtttttttgttaagttatacttattagacgaagtgacgaaagccatgagcttccactacttctattctctgttttcttttttagtttgtctttatgccgaagacgaagaaaaagtttattcatcttttttaccggcaccgactccgcaaatataggaaataattcaaatggacgcttcgcactcctctcaatattgtttcacaaaccatatttatgtgtcagattatccatgtttgattagttttacaccggaattgacttgcatatagaaagccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1795:PG1797|PG1795:PG1797:hypothetical protein:DNA-binding response regulator/sensor histidine kinase:<-->:1889867..1890152 286 ctttcgtttgtttttttgttaagttatacttattagacgaagtgacgaaagccatgagcttccactacttctattctctgttttcttttttagtttgtctttatgccgaagacgaagaaaaagtttattcatcttttttaccggcaccgactccgcaaatataggaaataattcaaatggacgcttcgcactcctctcaatattgtttcacaaaccatatttatgtgtcagattatccatgtttgattagttttacaccggaattgacttgcatatagaaagccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1795:PG1797|PG1795:PG1797:hypothetical protein:DNA-binding response regulator/sensor histidine kinase:<-->:1889867..1890152 286 ctttcgtttgtttttttgttaagttatacttattagacgaagtgacgaaagccatgagcttccactacttctattctctgttttcttttttagtttgtctttatgccgaagacgaagaaaaagtttattcatcttttttaccggcaccgactccgcaaatataggaaataattcaaatggacgcttcgcactcctctcaatattgtttcacaaaccatatttatgtgtcagattatccatgtttgattagttttacaccggaattgacttgcatatagaaagccaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctttcgtttgtttttttgttaagttatacttattagacgaagtgacgaaagccatgagcttccactacttctattctctgttttcttttttagtttgtctttatgccgaagacgaagaaaaagtttattcatcttttttaccggcaccgactccgcaaatataggaaataattcaaatggacgcttcgcactcctctcaatattgtttcacaaaccatatttatgtgtcagattatccatgtttgattagttttacaccggaattgacttgcatatagaaagccaa Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 42 End: 161 ......................................... M T K A M S F H Y F Y S L F S F L V C L Y A E D E E K V Y S S F L P A P T P Q I ............................................................................................................................. Protein_Len: 60 Strand: + Start: 26 End: 247 ......................... M L I R R S D E S H E L P L L L F S V F F F S L S L C R R R R K S L F I F F T G T D S A N I G N N S N G R F A L L S I L ....................................... Protein_Len: 36 Strand: + Start: 168 End: 275 ....................................................................................................................................................................... M I Q M D A S H S S Q Y C F T N H I Y V S D Y P C L I S F T P E L T C I ........... Protein_Len: 60 Strand: - Start: 22 End: 201 ..................... T I S I L R L S S L W S S G S S R N E T K K K L K D K H R L R L F L K N M K K V P V S E A F I P F L E F P R K A S R E M ..................................................................................... ctttcgtttgtttttttgttaagttatacttattagacgaagtgacgaaagccatgagcttccactacttctattctctgttttcttttttagtttgtctttatgccgaagacgaagaaaaagtttattcatcttttttaccggcaccgactccgcaaatataggaaataattcaaatggacgcttcgcactcctctcaatattgtttcacaaaccatatttatgtgtcagattatccatgtttgattagttttacaccggaattgacttgcatatagaaagccaa 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================================================ ctttcgtttgtttttttgttaagttatacttattagacgaagtgacgaaagccatgagcttccactacttctattctctgttttcttttttagtttgtctttatgccgaagacgaagaaaaagtttattcatcttttttaccggcaccgactccgcaaatataggaaataattcaaatggacgcttcgcactcctctcaatattgtttcacaaaccatatttatgtgtcagattatccatgtttgattagttttacaccggaattgacttgcatatagaaagccaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1795:PG1797|PG1795:PG1797:hypothetical protein:DNA-binding response regulator/sensor histidine kinase:<-->:1889867..1890152 286 ctttcgtttgtttttttgttaagttatacttattagacgaagtgacgaaagccatgagcttccactacttctattctctgttttcttttttagtttgtctttatgccgaagacgaagaaaaagtttattcatcttttttaccggcaccgactccgcaaatataggaaataattcaaatggacgcttcgcactcctctcaatattgtttcacaaaccatatttatgtgtcagattatccatgtttgattagttttacaccggaattgacttgcatatagaaagccaa Intra-Species Hit: Count: 1 Min: 18 Max: 286 Len: 269 Subject: NC_002950_PG1795_PG1797|hypothetical protein:DNA-binding response regulator/sensor histidine kinase|NEGATIVE:POSITIVE|[1889867,1890152]|286 HSP 1 e-value: 1.0E-150 bit: 533.0 Len: 269 Query Start:18 Query End:286 Subject Strand: POSITIVE Subject Start: 18 Subject End: 286 .................gttaagttatacttattagacgaagtgacgaaagccatgagcttccactacttctattctctgttttcttttttagtttgtctttatgccgaagacgaagaaaaagtttattcatcttttttaccggcaccgactccgcaaatataggaaataattcaaatggacgcttcgcactcctctcaatattgtttcacaaaccatatttatgtgtcagattatccatgtttgattagttttacaccggaattgacttgcatatagaaagccaa .................gttaagttatacttattagacgaagtgacgaaagccatgagcttccactacttctattctctgttttcttttttagtttgtctttatgccgaagacgaagaaaaagtttattcatcttttttaccggcaccgactccgcaaatataggaaataattcaaatggacgcttcgcactcctctcaatattgtttcacaaaccatatttatgtgtcagattatccatgtttgattagttttacaccggaattgacttgcatatagaaagccaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUAAGUUAUACUUAUUAGACGAAGUGACGAAAGCCAUGAGCUUCCACUACUUCUAUUCUCUGUUUUCUUUUUUAGUUUGUCUUUAUGCCGAAGACGAAGAAAAAGUUUAUUCAUCUUUUUUACCGGCACCGACUCCGCAAAUAUAGGAAAUAAUUCAAAUGGACGCUUCGCACUCCUCUCAAUAUUGUUUCACAAACCAUAUUUAUGUGUCAGAUUAUCCAUGUUUGAUUAGUUUUACACCGGAAUUGACUUGCAUAUAGAAAGCCAA ..((((.....))))......((((((..(.((((.....)))).)..))))))........(((((((......((..(((....(((((..((.(((((..((.....))..))))).))..))))).....((((.........((((((((......(((.((...))..))).......))))))))...............((((.((((((..((....))..)))))).))))))))...)))..))....)))))))... (-49.02) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGGCUUUCUAUAUGCAAGUCAAUUCCGGUGUAAAACUAAUCAAACAUGGAUAAUCUGACACAUAAAUAUGGUUUGUGAAACAAUAUUGAGAGGAGUGCGAAGCGUCCAUUUGAAUUAUUUCCUAUAUUUGCGGAGUCGGUGCCGGUAAAAAAGAUGAAUAAACUUUUUCUUCGUCUUCGGCAUAAAGACAAACUAAAAAAGAAAACAGAGAAUAGAAGUAGUGGAAGCUCAUGGCUUUCGUCACUUCGUCUAAUAAGUAUAACUUAAC (((((((.(.....).))))))).((((((((.......(((.......)))......)))).(((((((((.....((((.(((.(..((.(((.(((...)))))).))..)))).)))))))))))))))))(((.(((((((......(((((((.((.....)).))))))))))))))...)))...................(((...(((((..(((((((.....)))))))..))))).)))..((((.....)))).. (-60.82) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 897 70 21 178 129 NC_002950:PG1795|5end_hypothetical_protein_1889776..1890006_NEGATIVE 325 89 42 192 150 NC_002950:PG1104|5end_hypothetical_protein_1174935..1175165_POSITIVE 316 76 34 130 87 NC_002950:PG0596|5end_ribosomal_protein_S18_653365..653595_POSITIVE 309 138 93 225 175 NC_002950:PG0226|5end_transglutaminase-related_protein_262531..262761_NEGATIVE 299 194 154 188 145 NC_002950:PG2164|5end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2270125..2270355_NEGATIVE 292 74 37 71 29 NC_002950:PG1913|5end_30S_ribosomal_protein_S11_2012926..2013156_NEGATIVE 287 147 104 60 9 NC_002950:PG2106|5end_hypothetical_protein_2214694..2214924_POSITIVE 286 138 91 157 116 NC_002950:PG1836|5end_nucleoside_permease_NupG_1928543..1928773_POSITIVE 278 116 77 211 177 NC_002950:PG0163|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_186885..187115_NEGATIVE 277 180 131 106 43 NC_002950:PG0738|5end_cytidine/deoxycytidylate_deaminase_family_protein_786463..786693_POSITIVE 276 139 102 156 115 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 274 63 21 212 163 NC_002950:PG0638|5end_tetraacyldisaccharide_4'-kinase_691183..691413_NEGATIVE 274 89 41 202 155 NC_002950:PG0580|5end_N-acetylglucosaminyl_transferase_637097..637327_POSITIVE 271 258 219 191 147 NC_002950:PG2041|5end_hypothetical_protein_2139966..2140196_NEGATIVE 271 169 123 205 161 NC_002950:PG0525|5end_CTP_synthetase_568999..569229_POSITIVE 270 130 81 160 108 NC_002950:PG0710|5end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_766034..766264_NEGATIVE 266 63 21 224 187 NC_002950:PG0888|5end_hypothetical_protein_949910..950140_POSITIVE 263 164 125 208 174 NC_002950:PG1271|5end_acetylornithine_aminotransferase,_putative_1351443..1351673_NEGATIVE 261 175 135 59 6 NC_002950:PG1220|5end_erythronate-4-phosphate_dehydrogenase_1296986..1297216_POSITIVE 260 149 112 227 186 NC_002950:PG0203|5end_hypothetical_protein_240211..240441_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 316 76 34 126 83 NC_002950:PG0595|3end_30S_ribosomal_protein_S6_653441..653591_POSITIVE 312 70 25 71 23 NC_002950:PG0068|3end_hypothetical_protein_82079..82229_POSITIVE 292 74 37 59 17 NC_002950:PG1914|3end_30S_ribosomal_protein_S13_2012938..2013088_NEGATIVE 286 138 91 54 13 NC_002950:PG1835|3end_lipoprotein,_putative_1928520..1928670_POSITIVE 277 180 131 109 46 NC_002950:PG0737|3end_hypothetical_protein_786546..786696_POSITIVE 276 139 102 126 85 NC_002950:PG0170|3end_methionyl-tRNA_synthetase_191774..191924_POSITIVE 271 258 219 58 14 NC_002950:PG2042|3end_thioredoxin_family_protein_2140099..2140249_NEGATIVE 271 169 123 89 45 NC_002950:PG0524|3end_hypothetical_protein_568963..569113_POSITIVE 271 130 81 150 97 NC_002950:PG0227|3end_DNA_repair_protein_RadA_262593..262743_NEGATIVE 265 92 52 140 89 NC_002950:PG0386|3end_site-specific_recombinase,_phage_integrase_family/ribosomal_subunit_interface_protein_420329..420479_POSITIVE 261 175 135 55 2 NC_002950:PG1219|3end_hypothetical_protein_1297062..1297212_POSITIVE 260 70 21 130 87 NC_002950:PG1222|3end_hypothetical_protein_1299075..1299225_NEGATIVE 252 72 34 75 26 NC_002950:PG1474|3end_conjugative_transposon_protein_TraO_1550238..1550388_NEGATIVE 250 70 21 51 7 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 249 80 40 130 76 NC_002950:PG0952|3end_4-hydroxy-3-methylbut-2-en-1-yl_diphosphate_synthase_1012747..1012897_POSITIVE 245 58 11 142 86 NC_002950:PG0926|3end_hypothetical_protein_984407..984557_NEGATIVE 244 167 122 34 3 NC_002950:PG2136|3end_hypothetical_protein_2245104..2245254_POSITIVE 243 90 41 81 21 NC_002950:PG2142|3end_GTP-binding_protein_Era_2248564..2248714_POSITIVE 243 66 21 54 10 NC_002950:PG1723|3end_ribosomal_protein_S20_1813403..1813553_POSITIVE 243 89 51 145 110 NC_002950:PG1357|3end_hypothetical_protein_1436327..1436477_NEGATIVE