Origin IGS: ttccacagggtaaatagcctcaaacgatataatcagggctgtgtcggaggttttctcctttgacactgctctgattattttattttttactgatttccggataagtaacctccttattttgtggttattccgactttcagacttatttttgcaatatacaaggatggaagatattgatagagaagcactttcccctcgattcttcgccggatctcataataatagttctacggcctttcttcctcgttgtacggatttgagcaaatagacattctctgaacacttat .........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 ataagtgttcagagaatgtctatttgctcaaatccgtacaacgaggaagaaaggccgtagaactattattatgagatccggcgaagaatcgaggggaaagtgcttctctatcaatatcttccatccttgtatattgcaaaaataagtctgaaagtcggaataaccacaaaataaggaggttacttatccggaaatcagtaaaaaataaaataatcagagcagtgtcaaaggagaaaacctccgacacagccctgattatatcgtttgaggctatttaccctgtggaa Mask Tandem Repeat Region ================================================ ttccacagggtaaatagcctcaaacgatataatcagggctgtgtcggaggttttctcctttgacactgctctgattattttattttttactgatttccggataagtaacctccttattttgtggttattccgactttcagacttatttttgcaatatacaaggatggaagatattgatagagaagcactttcccctcgattcttcgccggatctcataataatagttctacggcctttcttcctcgttgtacggatttgagcaaatagacattctctgaacacttat Find is-nt database================================================ Query_seq: PG0395:PG0396|PG0395:PG0396:DNA-directed RNA polymerase beta' subunit:transcriptional regulator, Crp/Fnr family:->->:433366..433652 287 ttccacagggtaaatagcctcaaacgatataatcagggctgtgtcggaggttttctcctttgacactgctctgattattttattttttactgatttccggataagtaacctccttattttgtggttattccgactttcagacttatttttgcaatatacaaggatggaagatattgatagagaagcactttcccctcgattcttcgccggatctcataataatagttctacggcctttcttcctcgttgtacggatttgagcaaatagacattctctgaacacttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0395:PG0396|PG0395:PG0396:DNA-directed RNA polymerase beta' subunit:transcriptional regulator, Crp/Fnr family:->->:433366..433652 287 ttccacagggtaaatagcctcaaacgatataatcagggctgtgtcggaggttttctcctttgacactgctctgattattttattttttactgatttccggataagtaacctccttattttgtggttattccgactttcagacttatttttgcaatatacaaggatggaagatattgatagagaagcactttcccctcgattcttcgccggatctcataataatagttctacggcctttcttcctcgttgtacggatttgagcaaatagacattctctgaacacttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0395:PG0396|PG0395:PG0396:DNA-directed RNA polymerase beta' subunit:transcriptional regulator, Crp/Fnr family:->->:433366..433652 287 ttccacagggtaaatagcctcaaacgatataatcagggctgtgtcggaggttttctcctttgacactgctctgattattttattttttactgatttccggataagtaacctccttattttgtggttattccgactttcagacttatttttgcaatatacaaggatggaagatattgatagagaagcactttcccctcgattcttcgccggatctcataataatagttctacggcctttcttcctcgttgtacggatttgagcaaatagacattctctgaacacttat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttccacagggtaaatagcctcaaacgatataatcagggctgtgtcggaggttttctcctttgacactgctctgattattttattttttactgatttccggataagtaacctccttattttgtggttattccgactttcagacttatttttgcaatatacaaggatggaagatattgatagagaagcactttcccctcgattcttcgccggatctcataataatagttctacggcctttcttcctcgttgtacggatttgagcaaatagacattctctgaacacttat Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 156 End: 257 ........................................................................................................................................................... M Q G W K I L I E K H F P L D S S P D L I I I V L R P F F L V V R I .............................. Protein_Len: 60 Strand: + Start: 14 End: 265 ............. M A S N D I I R A V S E V F S F D T A L I I L F F T D F R I S N L L I L W L F R L S D L F L Q Y T R M E D I D R E A L S ...................... Protein_Len: 46 Strand: - Start: 146 End: 283 ................................................................................................................................................. K Q L I C P H F I N I S F C K G R S E E G S R M I I T R R G K K R T T R I Q A F L C E R F M .... Protein_Len: 32 Strand: - Start: 117 End: 212 .................................................................................................................... K T T I G V K L S I K A I Y L S P L Y Q Y L L V K G E I R R R M ........................................................................... Protein_Len: 58 Strand: - Start: 1 End: 174 E V P Y I A E F S I I L A T D S T K E K S V A R I I K N K V S K R I L L R R I K H N N R S E S K N K C Y V L I S S M ................................................................................................................. ttccacagggtaaatagcctcaaacgatataatcagggctgtgtcggaggttttctcctttgacactgctctgattattttattttttactgatttccggataagtaacctccttattttgtggttattccgactttcagacttatttttgcaatatacaaggatggaagatattgatagagaagcactttcccctcgattcttcgccggatctcataataatagttctacggcctttcttcctcgttgtacggatttgagcaaatagacattctctgaacacttat 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================================================ ttccacagggtaaatagcctcaaacgatataatcagggctgtgtcggaggttttctcctttgacactgctctgattattttattttttactgatttccggataagtaacctccttattttgtggttattccgactttcagacttatttttgcaatatacaaggatggaagatattgatagagaagcactttcccctcgattcttcgccggatctcataataatagttctacggcctttcttcctcgttgtacggatttgagcaaatagacattctctgaacacttat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -16.5 Tail_Score: -5.45813 Start: 30 End: 77 Full_Region: TAGCCTCAAACGATA TAATCAGGGCTGTGTCGGAGG TTTTCT CCTTTGACACTGCTCTGATTA TTTTATTTTTTACTG .............................TAATCAGGGCTGTGTCGGAGGTTTTCTCCTTTGACACTGCTCTGATTA.................................................................................................................................................................................................................. TransTerm Strand: - Conf: 72 HP_score: -9.9 Tail_Score: -3.01001 Start: 30 End: 77 Full_Region: cagtaaaaaataaaa taatcagagcagtgtcaaagg agaaaa cctccgacacagccctgatta tatcgtttgaggcta .............................taatcagagcagtgtcaaaggagaaaacctccgacacagccctgatta.................................................................................................................................................................................................................. TransTerm Strand: - Conf: 68 HP_score: -7.2 Tail_Score: -3.6471 Start: 33 End: 74 Full_Region: taaaaaataaaataa tcagagcagtgtcaaagg agaaaa cctccgacacagccctga ttatatcgtttgagg ................................tcagagcagtgtcaaaggagaaaacctccgacacagccctga..................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PG0395:PG0396|PG0395:PG0396:DNA-directed RNA polymerase beta' subunit:transcriptional regulator, Crp/Fnr family:->->:433366..433652 287 ttccacagggtaaatagcctcaaacgatataatcagggctgtgtcggaggttttctcctttgacactgctctgattattttattttttactgatttccggataagtaacctccttattttgtggttattccgactttcagacttatttttgcaatatacaaggatggaagatattgatagagaagcactttcccctcgattcttcgccggatctcataataatagttctacggcctttcttcctcgttgtacggatttgagcaaatagacattctctgaacacttat Intra-Species Hit: Count: 1 Min: 1 Max: 287 Len: 287 Subject: NC_002950_PG0395_PG0396|DNA-directed RNA polymerase beta' subunit:transcriptional regulator, Crp/Fnr family|POSITIVE:POSITIVE|[433366,433652]|287 HSP 1 e-value: 1.0E-161 bit: 569.0 Len: 287 Query Start:1 Query End:287 Subject Strand: POSITIVE Subject Start: 1 Subject End: 287 ttccacagggtaaatagcctcaaacgatataatcagggctgtgtcggaggttttctcctttgacactgctctgattattttattttttactgatttccggataagtaacctccttattttgtggttattccgactttcagacttatttttgcaatatacaaggatggaagatattgatagagaagcactttcccctcgattcttcgccggatctcataataatagttctacggcctttcttcctcgttgtacggatttgagcaaatagacattctctgaacacttat ttccacagggtaaatagcctcaaacgatataatcagggctgtgtcggaggttttctcctttgacactgctctgattattttattttttactgatttccggataagtaacctccttattttgtggttattccgactttcagacttatttttgcaatatacaaggatggaagatattgatagagaagcactttcccctcgattcttcgccggatctcataataatagttctacggcctttcttcctcgttgtacggatttgagcaaatagacattctctgaacacttat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCACAGGGUAAAUAGCCUCAAACGAUAUAAUCAGGGCUGUGUCGGAGGUUUUCUCCUUUGACACUGCUCUGAUUAUUUUAUUUUUUACUGAUUUCCGGAUAAGUAACCUCCUUAUUUUGUGGUUAUUCCGACUUUCAGACUUAUUUUUGCAAUAUACAAGGAUGGAAGAUAUUGAUAGAGAAGCACUUUCCCCUCGAUUCUUCGCCGGAUCUCAUAAUAAUAGUUCUACGGCCUUUCUUCCUCGUUGUACGGAUUUGAGCAAAUAGACAUUCUCUGAACACUUAU .....(((((....((..((((((.((.(((((((((((.((((((((((......)))))))))).))))))))))).))........((((....((((...((((((.(........).))))))))))....))))................(((((.((.((((((.(((((..((((.....))))...))))).....((((.....................))))...)))))))).)))))....))))))....))......)))))......... (-77.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAGUGUUCAGAGAAUGUCUAUUUGCUCAAAUCCGUACAACGAGGAAGAAAGGCCGUAGAACUAUUAUUAUGAGAUCCGGCGAAGAAUCGAGGGGAAAGUGCUUCUCUAUCAAUAUCUUCCAUCCUUGUAUAUUGCAAAAAUAAGUCUGAAAGUCGGAAUAACCACAAAAUAAGGAGGUUACUUAUCCGGAAAUCAGUAAAAAAUAAAAUAAUCAGAGCAGUGUCAAAGGAGAAAACCUCCGACACAGCCCUGAUUAUAUCGUUUGAGGCUAUUUACCCUGUGGAA .......((((.((...((..((...(((((((..((((((.((((((((...((((..((.((.........)).))))))........((((((......))))))........)))))).)).))))))...............((((...(((((.(((((.(........).)))))....)))))...))))...........((((((((.((.(((((...((((.....))))))))).)).))))))))...)))))))...))..)).)).)))). (-72.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 412 73 35 216 175 NC_002950:PG1739|5end_hypothetical_protein_1825709..1825939_NEGATIVE 365 276 233 221 180 NC_002950:PG2214|5end_hypothetical_protein_2326575..2326805_NEGATIVE 359 71 35 155 115 NC_002950:PG1759|5end_adhesion_protein,_putative_1845570..1845800_POSITIVE 346 58 16 207 156 NC_002950:PG0635|5end_ribosomal_protein_L11_methyltransferase_687773..688003_NEGATIVE 327 278 231 216 161 NC_002950:PG0242|5end_conserved_hypothetical_protein_TIGR00096_278960..279190_NEGATIVE 323 56 16 69 25 NC_002950:PG1546|5end_hypothetical_protein_1624087..1624317_POSITIVE 322 262 227 63 19 NC_002950:PG1596|5end_isoleucyl-tRNA_synthetase,_putative_1674543..1674773_POSITIVE 319 69 25 72 23 NC_002950:PG0758|5end_peptidyl-dipeptidase_Dcp_808554..808784_NEGATIVE 318 77 34 194 153 NC_002950:PG0660|5end_nitroreductase_family_protein_709695..709925_NEGATIVE 318 216 173 80 38 NC_002950:PG0483|5end_kinase,_putative_523844..524074_NEGATIVE 317 57 16 183 143 NC_002950:PG1069|5end_alcohol_dehydrogenase,_zinc-containing,_putative_1135499..1135729_POSITIVE 314 210 165 143 98 NC_002950:PG0582|5end_cell_division_protein_FtsQ,_putative_639600..639830_POSITIVE 312 215 186 148 120 NC_002950:PG0221|5end_hypothetical_protein_255834..256064_NEGATIVE 308 211 177 61 21 NC_002950:PG1212|5end_TPR_domain_protein_1291392..1291622_POSITIVE 307 243 202 68 29 NC_002950:PG1318|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1397768..1397998_NEGATIVE 307 279 232 137 86 NC_002950:PG0769|5end_fibronectin_type_III_domain_protein_824177..824407_NEGATIVE 305 69 24 96 56 NC_002950:PG1423|5end_hypothetical_protein_1509088..1509318_NEGATIVE 305 259 225 230 195 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 305 69 25 229 177 NC_002950:PG0072|5end_UDP-3-O-[3-hydroxymyristoyl]_glucosamine_N-acyltransferase_87147..87377_NEGATIVE 304 262 222 130 90 NC_002950:PG0678|5end_pyrazinamidase/nicotinamidase,_putative_728879..729109_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 542 78 31 62 15 NC_002950:PG0395|3end_DNA-directed_RNA_polymerase_beta'_subunit_433305..433455_POSITIVE 412 73 35 69 28 NC_002950:PG1741|3end_aspartate_ammonia-lyase_1825856..1826006_NEGATIVE 408 80 35 67 17 NC_002950:PG2010|3end_phosphomannomutase,_putative_2100952..2101102_POSITIVE 379 73 34 51 12 NC_002950:PG1754|3end_hypothetical_protein_1842284..1842434_POSITIVE 376 77 35 73 34 NC_002950:PG0506|3end_arginine-specific_cysteine_proteinase_547625..547775_POSITIVE 336 71 37 39 1 NC_002950:PG1758|3end_ribosomal_protein_S15_1845534..1845684_POSITIVE 329 76 36 61 16 NC_002950:PG0652|3end_hypothetical_protein_703899..704049_NEGATIVE 323 73 36 49 14 NC_002950:PG2124|3end_glyceraldehyde_3-phosphate_dehydrogenase,_type_I_2231264..2231414_POSITIVE 323 56 16 57 13 NC_002950:PG1545|3end_superoxide_dismutase,_Fe-Mn_1624155..1624305_POSITIVE 318 216 173 73 31 NC_002950:PG0484|3end_hypothetical_protein_523851..524001_NEGATIVE 317 262 222 133 80 NC_002950:PG1105|3end_RNA_polymerase_sigma-54_factor_1175716..1175866_NEGATIVE 317 57 16 141 101 NC_002950:PG1068|3end_hypothetical_protein_1135537..1135687_POSITIVE 314 210 165 149 104 NC_002950:PG0581|3end_UDP-N-acetylmuramate--L-alanine_ligase_639686..639836_POSITIVE 313 75 33 58 22 NC_002950:PG0334|3end_glycosyl_transferase,_group_2_family_protein_368792..368942_NEGATIVE 312 215 186 69 41 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 309 72 35 58 25 NC_002950:PG0779|3end_hypothetical_protein_832100..832250_NEGATIVE 308 211 177 48 8 NC_002950:PG1211|3end_hexapeptide_transferase_family_protein_1291459..1291609_POSITIVE 306 54 16 47 9 NC_002950:PG2053|3end_dithiobiotin_synthetase_2151267..2151417_POSITIVE 306 75 31 66 16 NC_002950:PG0495|3end_hypothetical_protein_536936..537086_POSITIVE 305 69 24 47 7 NC_002950:PG1424|3end_peptidylarginine_deiminase_1509137..1509287_NEGATIVE