Origin IGS: actacagtgttctgtactcaaaaacgtttaggacactattgggtgtacaccggtttgctctttgaggtattattgcttcgtgggggtatatttcccaaaagcaatcctttcttcttatctgttcaaaaccatgagactgactcagccatccatgaggtgctctaagttcaaagctaagtgtcgaacgcccttgagggtagttctgtgtacaaagatcgataaccgatatcgaa .........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 ttcgatatcggttatcgatctttgtacacagaactaccctcaagggcgttcgacacttagctttgaacttagagcacctcatggatggctgagtcagtctcatggttttgaacagataagaagaaaggattgcttttgggaaatatacccccacgaagcaataatacctcaaagagcaaaccggtgtacacccaatagtgtcctaaacgtttttgagtacagaacactgtagt Mask Tandem Repeat Region ================================================ actacagtgttctgtactcaaaaacgtttaggacactattgggtgtacaccggtttgctctttgaggtattattgcttcgtgggggtatatttcccaaaagcaatcctttcttcttatctgttcaaaaccatgagactgactcagccatccatgaggtgctctaagttcaaagctaagtgtcgaacgcccttgagggtagttctgtgtacaaagatcgataaccgatatcgaa Find is-nt database================================================ Query_seq: PG1038:PG1039|PG1038:PG1039:ATP-dependent DNA helicase UvrD/PcrA/Rep Family:integral membrane protein:-><-:1105182..1105414 233 actacagtgttctgtactcaaaaacgtttaggacactattgggtgtacaccggtttgctctttgaggtattattgcttcgtgggggtatatttcccaaaagcaatcctttcttcttatctgttcaaaaccatgagactgactcagccatccatgaggtgctctaagttcaaagctaagtgtcgaacgcccttgagggtagttctgtgtacaaagatcgataaccgatatcgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1038:PG1039|PG1038:PG1039:ATP-dependent DNA helicase UvrD/PcrA/Rep Family:integral membrane protein:-><-:1105182..1105414 233 actacagtgttctgtactcaaaaacgtttaggacactattgggtgtacaccggtttgctctttgaggtattattgcttcgtgggggtatatttcccaaaagcaatcctttcttcttatctgttcaaaaccatgagactgactcagccatccatgaggtgctctaagttcaaagctaagtgtcgaacgcccttgagggtagttctgtgtacaaagatcgataaccgatatcgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1038:PG1039|PG1038:PG1039:ATP-dependent DNA helicase UvrD/PcrA/Rep Family:integral membrane protein:-><-:1105182..1105414 233 actacagtgttctgtactcaaaaacgtttaggacactattgggtgtacaccggtttgctctttgaggtattattgcttcgtgggggtatatttcccaaaagcaatcctttcttcttatctgttcaaaaccatgagactgactcagccatccatgaggtgctctaagttcaaagctaagtgtcgaacgcccttgagggtagttctgtgtacaaagatcgataaccgatatcgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actacagtgttctgtactcaaaaacgtttaggacactattgggtgtacaccggtttgctctttgaggtattattgcttcgtgggggtatatttcccaaaagcaatcctttcttcttatctgttcaaaaccatgagactgactcagccatccatgaggtgctctaagttcaaagctaagtgtcgaacgcccttgagggtagttctgtgtacaaagatcgataaccgatatcgaa Predict ORF larger than 30AA ================================================ Protein_Len: 52 Strand: + Start: 7 End: 162 ...... M F C T Q K R L G H Y W V Y T G L L F E V L L L R G G I F P K S N P F F L S V Q N H E T D S A I H E V L ....................................................................... Protein_Len: 60 Strand: + Start: 38 End: 232 ..................................... M G C T P V C S L R Y Y C F V G V Y F P K A I L S S Y L F K T M R L T Q P S M R C S K F K A K C R T P L R V V L C T K I . Protein_Len: 60 Strand: - Start: 5 End: 229 .... R N A R Q P I I A E H P Y I E W F C D K R R I Q E F G H S Q S L W G H P A R L E F S L T S R G Q P Y N Q T C L D I V S M .... actacagtgttctgtactcaaaaacgtttaggacactattgggtgtacaccggtttgctctttgaggtattattgcttcgtgggggtatatttcccaaaagcaatcctttcttcttatctgttcaaaaccatgagactgactcagccatccatgaggtgctctaagttcaaagctaagtgtcgaacgcccttgagggtagttctgtgtacaaagatcgataaccgatatcgaa 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================================================ actacagtgttctgtactcaaaaacgtttaggacactattgggtgtacaccggtttgctctttgaggtattattgcttcgtgggggtatatttcccaaaagcaatcctttcttcttatctgttcaaaaccatgagactgactcagccatccatgaggtgctctaagttcaaagctaagtgtcgaacgcccttgagggtagttctgtgtacaaagatcgataaccgatatcgaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1038:PG1039|PG1038:PG1039:ATP-dependent DNA helicase UvrD/PcrA/Rep Family:integral membrane protein:-><-:1105182..1105414 233 actacagtgttctgtactcaaaaacgtttaggacactattgggtgtacaccggtttgctctttgaggtattattgcttcgtgggggtatatttcccaaaagcaatcctttcttcttatctgttcaaaaccatgagactgactcagccatccatgaggtgctctaagttcaaagctaagtgtcgaacgcccttgagggtagttctgtgtacaaagatcgataaccgatatcgaa Intra-Species Hit: Count: 1 Min: 1 Max: 233 Len: 233 Subject: NC_002950_PG1038_PG1039|ATP-dependent DNA helicase UvrD/PcrA/Rep Family:integral membrane protein|POSITIVE:NEGATIVE|[1105182,1105414]|233 HSP 1 e-value: 1.0E-129 bit: 462.0 Len: 233 Query Start:1 Query End:233 Subject Strand: POSITIVE Subject Start: 1 Subject End: 233 actacagtgttctgtactcaaaaacgtttaggacactattgggtgtacaccggtttgctctttgaggtattattgcttcgtgggggtatatttcccaaaagcaatcctttcttcttatctgttcaaaaccatgagactgactcagccatccatgaggtgctctaagttcaaagctaagtgtcgaacgcccttgagggtagttctgtgtacaaagatcgataaccgatatcgaa actacagtgttctgtactcaaaaacgtttaggacactattgggtgtacaccggtttgctctttgaggtattattgcttcgtgggggtatatttcccaaaagcaatcctttcttcttatctgttcaaaaccatgagactgactcagccatccatgaggtgctctaagttcaaagctaagtgtcgaacgcccttgagggtagttctgtgtacaaagatcgataaccgatatcgaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUACAGUGUUCUGUACUCAAAAACGUUUAGGACACUAUUGGGUGUACACCGGUUUGCUCUUUGAGGUAUUAUUGCUUCGUGGGGGUAUAUUUCCCAAAAGCAAUCCUUUCUUCUUAUCUGUUCAAAACCAUGAGACUGACUCAGCCAUCCAUGAGGUGCUCUAAGUUCAAAGCUAAGUGUCGAACGCCCUUGAGGGUAGUUCUGUGUACAAAGAUCGAUAACCGAUAUCGAA .(((.(((((((((.((........)).)))))))))..))).(((((((.(..((((.(((..(((....(((((((..((((((.....)))))).)))))))...............((((........(((.(...((((........))))..))))..(((.....))).......))))..)))..)))))))..).)))))))....((((((.....)))))). (-64.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCGAUAUCGGUUAUCGAUCUUUGUACACAGAACUACCCUCAAGGGCGUUCGACACUUAGCUUUGAACUUAGAGCACCUCAUGGAUGGCUGAGUCAGUCUCAUGGUUUUGAACAGAUAAGAAGAAAGGAUUGCUUUUGGGAAAUAUACCCCCACGAAGCAAUAAUACCUCAAAGAGCAAACCGGUGUACACCCAAUAGUGUCCUAAACGUUUUUGAGUACAGAACACUGUAGU .((((((.....))))))..((((....))))......((((((((((((.((((((..(((((....(((((((....(((((..(((((...)))))))))))))))))..............(((((((((((((((.........)))).))))))))....)))...))))).....(((....)))....))))))...))))))))))))(((((....))))).. (-60.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 417 94 51 177 131 NC_002950:PG1392|5end_rod_shape-determining_protein_RodA,_putative_1474416..1474646_NEGATIVE 347 109 74 213 177 NC_002950:PG0153|5end_aspartyl-tRNA_synthetase_177430..177660_NEGATIVE 345 88 43 157 115 NC_002950:PG0522|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_566901..567131_NEGATIVE 338 87 41 194 140 NC_002950:PG1943|5end_hypothetical_protein_2030260..2030490_NEGATIVE 334 190 143 106 39 NC_002950:PG1251|5end_hypothetical_protein_1327779..1328009_POSITIVE 331 220 177 106 65 NC_002950:PG2027|5end_hypothetical_protein_2125494..2125724_POSITIVE 330 128 81 152 109 NC_002950:PG0707|5end_TonB-dependent_receptor,_putative_763632..763862_NEGATIVE 322 190 143 107 39 NC_002950:PG1363|5end_hypothetical_protein_1443804..1444034_POSITIVE 321 154 115 96 54 NC_002950:PG1899|5end_TonB-dependent_receptor,_putative_1999724..1999954_NEGATIVE 320 89 42 231 176 NC_002950:PG0219|5end_hypothetical_protein_255558..255788_NEGATIVE 320 218 172 80 30 NC_002950:PG0146|5end_hypothetical_protein_169115..169345_NEGATIVE 319 90 47 231 186 NC_002950:PG0047|5end_cell_division_protein_FtsH,_putative_59250..59480_NEGATIVE 315 175 132 126 84 NC_002950:PG1752|5end_hypothetical_protein_1838394..1838624_POSITIVE 315 200 151 225 178 NC_002950:PG0854|5end_hypothetical_protein_914870..915100_POSITIVE 314 69 25 196 150 NC_002950:PG1589|5end_dihydropteroate_synthase_1667438..1667668_NEGATIVE 314 90 41 228 161 NC_002950:PG0978|5end_shikimate_5-dehydrogenase_1040033..1040263_POSITIVE 310 218 186 209 174 NC_002950:PG1020|5end_hypothetical_protein_1080568..1080798_POSITIVE 310 226 192 159 118 NC_002950:PG1017|5end_pyruvate_phosphate_dikinase_1076138..1076368_POSITIVE 308 67 25 153 93 NC_002950:PG0062|5end_TPR_domain_protein_73688..73918_POSITIVE 306 174 134 94 57 NC_002950:PG0811|5end_Holliday_junction_DNA_helicase_motor_protein_873209..873439_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 388 87 41 129 75 NC_002950:PG0132|3end_hypothetical_protein_153054..153204_POSITIVE 374 86 41 55 14 NC_002950:PG2124|3end_glyceraldehyde_3-phosphate_dehydrogenase,_type_I_2231264..2231414_POSITIVE 358 189 142 140 91 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 331 220 177 77 36 NC_002950:PG2026|3end_phosphoglycerate_mutase_family_protein_2125545..2125695_POSITIVE 327 87 41 143 100 NC_002950:PG0025|3end_fumarylacetoacetate_hydrolase_family_protein_29196..29346_POSITIVE 326 220 177 135 96 NC_002950:PG2126|3end_conserved_hypothetical_protein_TIGR00044_2232438..2232588_NEGATIVE 324 90 42 61 1 NC_002950:PG0133|3end_hypothetical_protein_154259..154409_NEGATIVE 323 88 41 71 12 NC_002950:PG0790|3end_GTP-binding_protein_Obg_841399..841549_NEGATIVE 320 218 172 67 17 NC_002950:PG0147|3end_hypothetical_protein_169128..169278_NEGATIVE 318 85 42 142 100 NC_002950:PG0328|3end_imidazolonepropionase_362155..362305_NEGATIVE 315 175 132 142 100 NC_002950:PG1751|3end_aminotransferase,_class_V_1838490..1838640_POSITIVE 311 217 178 151 102 NC_002950:PG0409|3end_hypothetical_protein_442350..442500_POSITIVE 310 218 186 37 2 NC_002950:PG1019|3end_lipoprotein,_putative_1080476..1080626_POSITIVE 308 67 25 148 88 NC_002950:PG0061|3end_yngK_protein_73763..73913_POSITIVE 304 87 41 66 8 NC_002950:PG1213|3end_ribonuclease_H_1293163..1293313_POSITIVE 292 160 111 54 12 NC_002950:PG0881|3end_recombinase_A_944165..944315_POSITIVE 290 80 31 75 15 NC_002950:PG0563|3end_hypothetical_protein_620935..621085_NEGATIVE 289 88 41 71 22 NC_002950:PG1342|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_1423681..1423831_POSITIVE 289 68 24 149 107 NC_002950:PG0221|3end_hypothetical_protein_255613..255763_NEGATIVE 288 86 41 70 15 NC_002950:PG0909|3end_hypothetical_protein_971738..971888_NEGATIVE