Origin IGS: ctgcttgatgctttcttttgacacccccaaaaatagccaattcgatccataccgaggtcgtaagatattcacacccattggatgcacattccggtctcgagtgcaacgtgaccgattgggttttatagccggatacggcagtgtaggggtgcagaagttctgttcgactttttaggttccggaattttctcgttttacagtcagcaaaacgtggttcgagaaaatttttgttttggcgtggaaaaaataatttatcgaaccaaaacgaaaaaaattacgcgcgagttttcccgttttcaggaacggcaatttcatcatttttggttccaaaatcgggaggcactcctatcgaatcaccttaaaagagcctcgatattgcccatgaagtgtaaagaatccttggcagataaatattcagttggattaaactccatgtgaaagcagatttaattctctgtatttttttgttggtttttatctaaagtttatgtgtacatttgtttttcaaaacttcaaaaatcaattcgt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acgaattgatttttgaagttttgaaaaacaaatgtacacataaactttagataaaaaccaacaaaaaaatacagagaattaaatctgctttcacatggagtttaatccaactgaatatttatctgccaaggattctttacacttcatgggcaatatcgaggctcttttaaggtgattcgataggagtgcctcccgattttggaaccaaaaatgatgaaattgccgttcctgaaaacgggaaaactcgcgcgtaatttttttcgttttggttcgataaattattttttccacgccaaaacaaaaattttctcgaaccacgttttgctgactgtaaaacgagaaaattccggaacctaaaaagtcgaacagaacttctgcacccctacactgccgtatccggctataaaacccaatcggtcacgttgcactcgagaccggaatgtgcatccaatgggtgtgaatatcttacgacctcggtatggatcgaattggctatttttgggggtgtcaaaagaaagcatcaagcag Mask Tandem Repeat Region ================================================ ctgcttgatgctttcttttgacacccccaaaaatagccaattcgatccataccgaggtcgtaagatattcacacccattggatgcacattccggtctcgagtgcaacgtgaccgattgggttttatagccggatacggcagtgtaggggtgcagaagttctgttcgactttttaggttccggaattttctcgttttacagtcagcaaaacgtggttcgagaaaatttttgttttggcgtggaaaaaataatttatcgaaccaaaacgaaaaaaattacgcgcgagttttcccgttttcaggaacggcaatttcatcatttttggttccaaaatcgggaggcactcctatcgaatcaccttaaaagagcctcgatattgcccatgaagtgtaaagaatccttggcagataaatattcagttggattaaactccatgtgaaagcagatttaattctctgtatttttttgttggtttttatctaaagtttatgtgtacatttgtttttcaaaacttcaaaaatcaattcgt Find is-nt database================================================ Query_seq: PG1589:PG1591|PG1589:PG1591:dihydropteroate synthase:hypothetical protein:<-->:1667529..1668056 528 ctgcttgatgctttcttttgacacccccaaaaatagccaattcgatccataccgaggtcgtaagatattcacacccattggatgcacattccggtctcgagtgcaacgtgaccgattgggttttatagccggatacggcagtgtaggggtgcagaagttctgttcgactttttaggttccggaattttctcgttttacagtcagcaaaacgtggttcgagaaaatttttgttttggcgtggaaaaaataatttatcgaaccaaaacgaaaaaaattacgcgcgagttttcccgttttcaggaacggcaatttcatcatttttggttccaaaatcgggaggcactcctatcgaatcaccttaaaagagcctcgatattgcccatgaagtgtaaagaatccttggcagataaatattcagttggattaaactccatgtgaaagcagatttaattctctgtatttttttgttggtttttatctaaagtttatgtgtacatttgtttttcaaaacttcaaaaatcaattcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1589:PG1591|PG1589:PG1591:dihydropteroate synthase:hypothetical protein:<-->:1667529..1668056 528 ctgcttgatgctttcttttgacacccccaaaaatagccaattcgatccataccgaggtcgtaagatattcacacccattggatgcacattccggtctcgagtgcaacgtgaccgattgggttttatagccggatacggcagtgtaggggtgcagaagttctgttcgactttttaggttccggaattttctcgttttacagtcagcaaaacgtggttcgagaaaatttttgttttggcgtggaaaaaataatttatcgaaccaaaacgaaaaaaattacgcgcgagttttcccgttttcaggaacggcaatttcatcatttttggttccaaaatcgggaggcactcctatcgaatcaccttaaaagagcctcgatattgcccatgaagtgtaaagaatccttggcagataaatattcagttggattaaactccatgtgaaagcagatttaattctctgtatttttttgttggtttttatctaaagtttatgtgtacatttgtttttcaaaacttcaaaaatcaattcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1589:PG1591|PG1589:PG1591:dihydropteroate synthase:hypothetical protein:<-->:1667529..1668056 528 ctgcttgatgctttcttttgacacccccaaaaatagccaattcgatccataccgaggtcgtaagatattcacacccattggatgcacattccggtctcgagtgcaacgtgaccgattgggttttatagccggatacggcagtgtaggggtgcagaagttctgttcgactttttaggttccggaattttctcgttttacagtcagcaaaacgtggttcgagaaaatttttgttttggcgtggaaaaaataatttatcgaaccaaaacgaaaaaaattacgcgcgagttttcccgttttcaggaacggcaatttcatcatttttggttccaaaatcgggaggcactcctatcgaatcaccttaaaagagcctcgatattgcccatgaagtgtaaagaatccttggcagataaatattcagttggattaaactccatgtgaaagcagatttaattctctgtatttttttgttggtttttatctaaagtttatgtgtacatttgtttttcaaaacttcaaaaatcaattcgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctgcttgatgctttcttttgacacccccaaaaatagccaattcgatccataccgaggtcgtaagatattcacacccattggatgcacattccggtctcgagtgcaacgtgaccgattgggttttatagccggatacggcagtgtaggggtgcagaagttctgttcgactttttaggttccggaattttctcgttttacagtcagcaaaacgtggttcgagaaaatttttgttttggcgtggaaaaaataatttatcgaaccaaaacgaaaaaaattacgcgcgagttttcccgttttcaggaacggcaatttcatcatttttggttccaaaatcgggaggcactcctatcgaatcaccttaaaagagcctcgatattgcccatgaagtgtaaagaatccttggcagataaatattcagttggattaaactccatgtgaaagcagatttaattctctgtatttttttgttggtttttatctaaagtttatgtgtacatttgtttttcaaaacttcaaaaatcaattcgt Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 18 End: 125 ................. M T P P K I A N S I H T E V V R Y S H P L D A H S G L E C N V T D W V L ................................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 56 Strand: + Start: 5 End: 172 .... M M L S F D T P K N S Q F D P Y R G R K I F T P I G C T F R S R V Q R D R L G F I A G Y G S V G V Q K F C S T F .................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 44 Strand: + Start: 228 End: 359 ................................................................................................................................................................................................................................... M F W R G K N N L S N Q N E K N Y A R V F P F S G T A I S S F L V P K S G G T P I E S P ......................................................................................................................................................................... Protein_Len: 43 Strand: + Start: 254 End: 382 ............................................................................................................................................................................................................................................................. M E P K R K K L R A S F P V F R N G N F I I F G S K I G R H S Y R I T L K E P R Y C P .................................................................................................................................................. Protein_Len: 60 Strand: + Start: 115 End: 435 .................................................................................................................. M G F Y S R I R Q C R G A E V L F D F L G S G I F S F Y S Q Q N V V R E N F C F G V E K I I Y R T K T K K I T R E F S R ............................................................................................. Protein_Len: 39 Strand: - Start: 362 End: 478 ......................................................................................................................................................................................................................................................................................................................................................................... F L R S I A W S T Y L I R P L Y I N L Q I L S W T F A S K I R Q I K K N T K M .................................................. Protein_Len: 30 Strand: - Start: 357 End: 446 .................................................................................................................................................................................................................................................................................................................................................................... R L L A E I N G M F H L S D K A S L Y E T P N F E M H F C M .................................................................................. Protein_Len: 53 Strand: - Start: 175 End: 333 .............................................................................................................................................................................. T G S N E R K V T L L V H N S F I K T K A H F F Y N I S G F R F F N R A L K G T K L F P L K M M K P E L M ................................................................................................................................................................................................... Protein_Len: 51 Strand: - Start: 2 End: 154 . A Q H K R K V G G F I A L E I W V S T T L Y E C G N S A C E P R S H L T V S Q T K Y G S V A T Y P H M ...................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 47 Strand: - Start: 1 End: 141 Q K I S E K S V G L F L W N S G Y R P R L I N V G M P H V N R D R T C R S R N P K I A P Y P M ................................................................................................................................................................................................................................................................................................................................................................................................... ctgcttgatgctttcttttgacacccccaaaaatagccaattcgatccataccgaggtcgtaagatattcacacccattggatgcacattccggtctcgagtgcaacgtgaccgattgggttttatagccggatacggcagtgtaggggtgcagaagttctgttcgactttttaggttccggaattttctcgttttacagtcagcaaaacgtggttcgagaaaatttttgttttggcgtggaaaaaataatttatcgaaccaaaacgaaaaaaattacgcgcgagttttcccgttttcaggaacggcaatttcatcatttttggttccaaaatcgggaggcactcctatcgaatcaccttaaaagagcctcgatattgcccatgaagtgtaaagaatccttggcagataaatattcagttggattaaactccatgtgaaagcagatttaattctctgtatttttttgttggtttttatctaaagtttatgtgtacatttgtttttcaaaacttcaaaaatcaattcgt 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================================================ ctgcttgatgctttcttttgacacccccaaaaatagccaattcgatccataccgaggtcgtaagatattcacacccattggatgcacattccggtctcgagtgcaacgtgaccgattgggttttatagccggatacggcagtgtaggggtgcagaagttctgttcgactttttaggttccggaattttctcgttttacagtcagcaaaacgtggttcgagaaaatttttgttttggcgtggaaaaaataatttatcgaaccaaaacgaaaaaaattacgcgcgagttttcccgttttcaggaacggcaatttcatcatttttggttccaaaatcgggaggcactcctatcgaatcaccttaaaagagcctcgatattgcccatgaagtgtaaagaatccttggcagataaatattcagttggattaaactccatgtgaaagcagatttaattctctgtatttttttgttggtttttatctaaagtttatgtgtacatttgtttttcaaaacttcaaaaatcaattcgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1589:PG1591|PG1589:PG1591:dihydropteroate synthase:hypothetical protein:<-->:1667529..1668056 528 ctgcttgatgctttcttttgacacccccaaaaatagccaattcgatccataccgaggtcgtaagatattcacacccattggatgcacattccggtctcgagtgcaacgtgaccgattgggttttatagccggatacggcagtgtaggggtgcagaagttctgttcgactttttaggttccggaattttctcgttttacagtcagcaaaacgtggttcgagaaaatttttgttttggcgtggaaaaaataatttatcgaaccaaaacgaaaaaaattacgcgcgagttttcccgttttcaggaacggcaatttcatcatttttggttccaaaatcgggaggcactcctatcgaatcaccttaaaagagcctcgatattgcccatgaagtgtaaagaatccttggcagataaatattcagttggattaaactccatgtgaaagcagatttaattctctgtatttttttgttggtttttatctaaagtttatgtgtacatttgtttttcaaaacttcaaaaatcaattcgt Intra-Species Hit: Count: 1 Min: 1 Max: 528 Len: 528 Subject: NC_002950_PG1589_PG1591|dihydropteroate synthase:hypothetical protein|NEGATIVE:POSITIVE|[1667529,1668056]|528 HSP 1 e-value: 0.0 bit: 963.0 Len: 528 Query Start:1 Query End:528 Subject Strand: POSITIVE Subject Start: 1 Subject End: 528 ctgcttgatgctttcttttgacacccccaaaaatagccaattcgatccataccgaggtcgtaagatattcacacccattggatgcacattccggtctcgagtgcaacgtgaccgattgggttttatagccggatacggcagtgtaggggtgcagaagttctgttcgactttttaggttccggaattttctcgttttacagtcagcaaaacgtggttcgagaaaatttttgttttggcgtggaaaaaataatttatcgaaccaaaacgnnnnnnnttacgcgcgagttttcccgttttcaggaacggcaatttcatcatttttggttccaaaatcgggaggcactcctatcgaatcaccttaaaagagcctcgatattgcccatgaagtgtaaagaatccttggcagataaatattcagttggattaaactccatgtgaaagcagatttaattctctgtannnnnnngttggtttttatctaaagtttatgtgtacatttgtttttcaaaacttcaaaaatcaattcgt ctgcttgatgctttcttttgacacccccaaaaatagccaattcgatccataccgaggtcgtaagatattcacacccattggatgcacattccggtctcgagtgcaacgtgaccgattgggttttatagccggatacggcagtgtaggggtgcagaagttctgttcgactttttaggttccggaattttctcgttttacagtcagcaaaacgtggttcgagaaaatttttgttttggcgtggaaaaaataatttatcgaaccaaaacgaaaaaaattacgcgcgagttttcccgttttcaggaacggcaatttcatcatttttggttccaaaatcgggaggcactcctatcgaatcaccttaaaagagcctcgatattgcccatgaagtgtaaagaatccttggcagataaatattcagttggattaaactccatgtgaaagcagatttaattctctgtatttttttgttggtttttatctaaagtttatgtgtacatttgtttttcaaaacttcaaaaatcaattcgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGCUUGAUGCUUUCUUUUGACACCCCCAAAAAUAGCCAAUUCGAUCCAUACCGAGGUCGUAAGAUAUUCACACCCAUUGGAUGCACAUUCCGGUCUCGAGUGCAACGUGACCGAUUGGGUUUUAUAGCCGGAUACGGCAGUGUAGGGGUGCAGAAGUUCUGUUCGACUUUUUAGGUUCCGGAAUUUUCUCGUUUUACAGUCAGCAAAACGUGGUUCGAGAAAAUUUUUGUUUUGGCGUGGAAAAAAUAAUUUAUCGAACCAAAACGAAAAAAAUUACGCGCGAGUUUUCCCGUUUUCAGGAACGGCAAUUUCAUCAUUUUUGGUUCCAAAAUCGGGAGGCACUCCUAUCGAAUCACCUUAAAAGAGCCUCGAUAUUGCCCAUGAAGUGUAAAGAAUCCUUGGCAGAUAAAUAUUCAGUUGGAUUAAACUCCAUGUGAAAGCAGAUUUAAUUCUCUGUAUUUUUUUGUUGGUUUUUAUCUAAAGUUUAUGUGUACAUUUGUUUUUCAAAACUUCAAAAAUCAAUUCGU ..((((..((((..((((((.((((((.........((((((((........))).(((....)))..........))))).(((((....(((((.((.......)).))))).............((((....)))).)))))))))))))))))..((((..(((.....(((((....)))))....)))..))))..))))....(((((((((.....((((((((((((..(((.(((.....))).)))..))))))))))))...........(((((((((((.(((..(((((.(.((.........)).).))))).))).))))))).))))...))))))))).......))))..(((.((((....((((((...((((((...(((((.((((((......((((((.(((((.((...(((.(((((........))))).)))...))..)))))..)))))).)))))).))).))...))))))....)))))).....))))))). (-133.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGAAUUGAUUUUUGAAGUUUUGAAAAACAAAUGUACACAUAAACUUUAGAUAAAAACCAACAAAAAAAUACAGAGAAUUAAAUCUGCUUUCACAUGGAGUUUAAUCCAACUGAAUAUUUAUCUGCCAAGGAUUCUUUACACUUCAUGGGCAAUAUCGAGGCUCUUUUAAGGUGAUUCGAUAGGAGUGCCUCCCGAUUUUGGAACCAAAAAUGAUGAAAUUGCCGUUCCUGAAAACGGGAAAACUCGCGCGUAAUUUUUUUCGUUUUGGUUCGAUAAAUUAUUUUUUCCACGCCAAAACAAAAAUUUUCUCGAACCACGUUUUGCUGACUGUAAAACGAGAAAAUUCCGGAACCUAAAAAGUCGAACAGAACUUCUGCACCCCUACACUGCCGUAUCCGGCUAUAAAACCCAAUCGGUCACGUUGCACUCGAGACCGGAAUGUGCAUCCAAUGGGUGUGAAUAUCUUACGACCUCGGUAUGGAUCGAAUUGGCUAUUUUUGGGGGUGUCAAAAGAAAGCAUCAAGCAG .....(((((....(((((((((........(((....)))..((((((((((((................((((........))))..((((..((((......))))..))))..)))))))....(((.((((............(((......(((((.((((((.((....))..)))))).)))))..((((((.(((((((((.(((.((((((((((((((((....)))))......))).))))))))..)))))))))))).).)))))...........)))........(((((((((.......(((((((.....))))))))))))))))..)))))))..)))))....))))))))).(((((((((....((((....))))........((((((((((.(((...((.((((..((..((((((((((...))))))..))))....))..)))))))))))))).))))).......)))))))))...........))))).... (-137.31) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1055 140 91 231 182 NC_002950:PG1589|5end_dihydropteroate_synthase_1667438..1667668_NEGATIVE 400 140 92 224 181 NC_002950:PG0810|5end_hypothetical_protein_872567..872797_NEGATIVE 389 160 112 188 138 NC_002950:PG1754|5end_hypothetical_protein_1839679..1839909_POSITIVE 386 105 83 231 209 NC_002950:PG1656|5end_methylmalonyl-CoA_mutase,_small_subunit_1737459..1737689_POSITIVE 379 167 125 91 42 NC_002950:PG1671|5end_hypothetical_protein_1757658..1757888_NEGATIVE 379 167 125 91 42 NC_002950:PG0101|5end_hypothetical_protein_119198..119428_POSITIVE 377 109 63 55 1 NC_002950:PG0811|5end_Holliday_junction_DNA_helicase_motor_protein_873209..873439_NEGATIVE 372 139 91 216 175 NC_002950:PG1993|5end_excinuclease_ABC,_C_subunit_2083321..2083551_POSITIVE 372 153 112 194 147 NC_002950:PG1250|5end_hypothetical_protein_1327846..1328076_NEGATIVE 372 159 111 76 22 NC_002950:PG1241|5end_GTP-binding_protein_LepA_1315613..1315843_POSITIVE 370 127 83 213 170 NC_002950:PG0754|5end_DNA_topoisomerase_I_800943..801173_POSITIVE 367 155 113 53 2 NC_002950:PG1947|5end_TPR_domain_protein_2032932..2033162_POSITIVE 362 153 112 141 99 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 361 160 116 62 1 NC_002950:PG1599|5end_hypothetical_protein_1679087..1679317_POSITIVE 358 139 92 133 91 NC_002950:PG0031|5end_hypothetical_protein_37579..37809_NEGATIVE 356 270 225 98 52 NC_002950:PG1980|5end_hypothetical_protein_2067930..2068160_NEGATIVE 356 242 206 163 126 NC_002950:PG0081|5end_hypothetical_protein_93805..94035_POSITIVE 354 139 92 139 97 NC_002950:PG0229|5end_hypothetical_protein_264872..265102_POSITIVE 354 289 251 139 97 NC_002950:PG0007|5end_hypothetical_protein_6913..7143_NEGATIVE 352 167 126 221 179 NC_002950:PG1815|5end_3-deoxy-manno-octulosonate_cytidylyltransferase_1911433..1911663_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 467 130 83 114 54 NC_002950:PG1655|3end_hypothetical_protein_1737384..1737534_POSITIVE 369 151 113 99 54 NC_002950:PG2041|3end_hypothetical_protein_2139235..2139385_NEGATIVE 367 155 113 60 9 NC_002950:PG1946|3end_ABC_3_transporter_family_protein_2033019..2033169_POSITIVE 364 159 114 113 71 NC_002950:PG1638|3end_thioredoxin_family_protein_1718664..1718814_NEGATIVE 362 153 112 128 86 NC_002950:PG1862|3end_hypothetical_protein_1960070..1960220_NEGATIVE 361 160 116 65 4 NC_002950:PG1598|3end_lipoprotein_signal_peptidase,_putative_1679170..1679320_POSITIVE 361 139 91 105 45 NC_002950:PG0987|3end_hypothetical_protein_1048858..1049008_POSITIVE 358 139 92 85 43 NC_002950:PG0032|3end_beta-mannosidase,_putative_37627..37777_NEGATIVE 348 160 113 99 42 NC_002950:PG0534|3end_hypothetical_protein_585805..585955_POSITIVE 344 168 126 114 68 NC_002950:PG2008|3end_TonB-dependent_receptor,_putative_2097824..2097974_POSITIVE 341 150 102 67 23 NC_002950:PG1302|3end_hypothetical_protein_1379939..1380089_NEGATIVE 339 138 91 131 80 NC_002950:PG0068|3end_hypothetical_protein_82079..82229_POSITIVE 338 214 174 131 95 NC_002950:PG1949|3end_malate_dehydrogenase_2038184..2038334_NEGATIVE 337 139 92 111 60 NC_002950:PG2092|3end_hypothetical_protein_2191651..2191801_NEGATIVE 335 160 111 130 76 NC_002950:PG1789|3end_peptidyl-dipeptidase_Dcp_1877417..1877567_NEGATIVE 335 159 113 65 24 NC_002950:PG0672|3end_iron_compound_ABC_transporter,_ATP-binding_protein_723840..723990_POSITIVE 333 150 104 129 72 NC_002950:PG2085|3end_tryptophanyl-tRNA_synthetase_2186595..2186745_POSITIVE 333 140 94 77 28 NC_002950:PG1761|3end_acetyltransferase,_GNAT_family_1847739..1847889_POSITIVE 330 248 206 53 6 NC_002950:PG0732|3end_hypothetical_protein_783018..783168_POSITIVE 329 148 107 132 77 NC_002950:PG0729|3end_D-alanylalanine_synthetase_779826..779976_NEGATIVE