Origin IGS: tgttctgtaatttattattcgggcctacacagtgaaacccgatgattattcacttctatattctctaaccgaaaaatatccccttttgttcacccctcggagcaatcttgccacgccttccatattcctgcctgttccggccgaatattcaccggcgagagaacatagcactttatacttaaaagtcttacccctttataccataaagcctccatacttgataatatgaagatcccttgggagtctcgatggagatcccttaggagtctcgatagggatcccttaggggtctcgatagggatcccttaggagtctcgatggggatcccttaggagtctcgatggggatcccttaggggtctcagcaaaggcagccctctactgtcatttcggaggaaaaacaaagcatcctgcattatcgtgggaggaatgagtacttttgcagggaatcatattatttgcttgagccggtcaagattaggaatccggtctttccgattatgaaaaagaaa .........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 tttctttttcataatcggaaagaccggattcctaatcttgaccggctcaagcaaataatatgattccctgcaaaagtactcattcctcccacgataatgcaggatgctttgtttttcctccgaaatgacagtagagggctgcctttgctgagacccctaagggatccccatcgagactcctaagggatccccatcgagactcctaagggatccctatcgagacccctaagggatccctatcgagactcctaagggatctccatcgagactcccaagggatcttcatattatcaagtatggaggctttatggtataaaggggtaagacttttaagtataaagtgctatgttctctcgccggtgaatattcggccggaacaggcaggaatatggaaggcgtggcaagattgctccgaggggtgaacaaaaggggatatttttcggttagagaatatagaagtgaataatcatcgggtttcactgtgtaggcccgaataataaattacagaaca Mask Tandem Repeat Region ================================================ tgttctgtaatttattattcgggcctacacagtgaaacccgatgattattcacttctatattctctaaccgaaaaatatccccttttgttcacccctcggagcaatcttgccacgccttccatattcctgcctgttccggccgaatattcaccggcgagagaacatagcactttatacttaaaagtcttacccctttataccataaagcctccatacttgataatatgaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnagcaaaggcagccctctactgtcatttcggaggaaaaacaaagcatcctgcattatcgtgggaggaatgagtacttttgcagggaatcatattatttgcttgagccggtcaagattaggaatccggtctttccgattatgaaaaagaaa Find is-nt database================================================ Query_seq: PG1286:PG1288|PG1286:PG1288:ferritin:GDP-mannose 4,6-dehydratase:<-->:1365592..1366102 511 tgttctgtaatttattattcgggcctacacagtgaaacccgatgattattcacttctatattctctaaccgaaaaatatccccttttgttcacccctcggagcaatcttgccacgccttccatattcctgcctgttccggccgaatattcaccggcgagagaacatagcactttatacttaaaagtcttacccctttataccataaagcctccatacttgataatatgaagatcccttgggagtctcgatggagatcccttaggagtctcgatagggatcccttaggggtctcgatagggatcccttaggagtctcgatggggatcccttaggagtctcgatggggatcccttaggggtctcagcaaaggcagccctctactgtcatttcggaggaaaaacaaagcatcctgcattatcgtgggaggaatgagtacttttgcagggaatcatattatttgcttgagccggtcaagattaggaatccggtctttccgattatgaaaaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1286:PG1288|PG1286:PG1288:ferritin:GDP-mannose 4,6-dehydratase:<-->:1365592..1366102 511 tgttctgtaatttattattcgggcctacacagtgaaacccgatgattattcacttctatattctctaaccgaaaaatatccccttttgttcacccctcggagcaatcttgccacgccttccatattcctgcctgttccggccgaatattcaccggcgagagaacatagcactttatacttaaaagtcttacccctttataccataaagcctccatacttgataatatgaagatcccttgggagtctcgatggagatcccttaggagtctcgatagggatcccttaggggtctcgatagggatcccttaggagtctcgatggggatcccttaggagtctcgatggggatcccttaggggtctcagcaaaggcagccctctactgtcatttcggaggaaaaacaaagcatcctgcattatcgtgggaggaatgagtacttttgcagggaatcatattatttgcttgagccggtcaagattaggaatccggtctttccgattatgaaaaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1286:PG1288|PG1286:PG1288:ferritin:GDP-mannose 4,6-dehydratase:<-->:1365592..1366102 511 tgttctgtaatttattattcgggcctacacagtgaaacccgatgattattcacttctatattctctaaccgaaaaatatccccttttgttcacccctcggagcaatcttgccacgccttccatattcctgcctgttccggccgaatattcaccggcgagagaacatagcactttatacttaaaagtcttacccctttataccataaagcctccatacttgataatatgaagatcccttgggagtctcgatggagatcccttaggagtctcgatagggatcccttaggggtctcgatagggatcccttaggagtctcgatggggatcccttaggagtctcgatggggatcccttaggggtctcagcaaaggcagccctctactgtcatttcggaggaaaaacaaagcatcctgcattatcgtgggaggaatgagtacttttgcagggaatcatattatttgcttgagccggtcaagattaggaatccggtctttccgattatgaaaaagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgttctgtaatttattattcgggcctacacagtgaaacccgatgattattcacttctatattctctaaccgaaaaatatccccttttgttcacccctcggagcaatcttgccacgccttccatattcctgcctgttccggccgaatattcaccggcgagagaacatagcactttatacttaaaagtcttacccctttataccataaagcctccatacttgataatatgaagatcccttgggagtctcgatggagatcccttaggagtctcgatagggatcccttaggggtctcgatagggatcccttaggagtctcgatggggatcccttaggagtctcgatggggatcccttaggggtctcagcaaaggcagccctctactgtcatttcggaggaaaaacaaagcatcctgcattatcgtgggaggaatgagtacttttgcagggaatcatattatttgcttgagccggtcaagattaggaatccggtctttccgattatgaaaaagaaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 58 End: 165 ......................................................... M F S N R K I S P F V H P S E Q S C H A F H I P A C S G R I F T G E R T .......................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 34 Strand: + Start: 78 End: 179 ............................................................................. M P F C S P L G A I L P R L P Y S C L F R P N I H R R E N I A L Y T ............................................................................................................................................................................................................................................................................................................................................ Protein_Len: 60 Strand: + Start: 14 End: 226 ............. M I R A Y T V K P D D Y S L L Y S L T E K Y P L L F T P R S N L A T P S I F L P V P A E Y S P A R E H S T L Y L K V L P ............................................................................................................................................................................................................................................................................................. Protein_Len: 44 Strand: + Start: 175 End: 306 .............................................................................................................................................................................. M L K S L T P L Y H K A S I L D N M K I P W E S R W R S L R S L D R D P L G V S I G I P ............................................................................................................................................................................................................. Protein_Len: 40 Strand: + Start: 381 End: 500 ............................................................................................................................................................................................................................................................................................................................................................................................ M S F R R K N K A S C I I V G G M S T F A G N H I I C L S R S R L G I R S F R L ........... Protein_Len: 42 Strand: + Start: 386 End: 511 ................................................................................................................................................................................................................................................................................................................................................................................................. M S E E K Q S I L H Y R G R N E Y F C R E S Y Y L L E P V K I R N P V F P I M K K K Protein_Len: 33 Strand: - Start: 332 End: 430 ........................................................................................................................................................................................................................................................................................................................................... S D R H P D R L P R L L P L G R S D N R L F F L A D Q M I T P P M ................................................................................. Protein_Len: 60 Strand: - Start: 93 End: 302 ............................................................................................ I G A Q E P R I N V P S L V Y C K I S L L R V G K Y W L A E M S S L I F I G Q S D R H L D R L L R S L S G K P T E I P M ................................................................................................................................................................................................................. Protein_Len: 41 Strand: - Start: 49 End: 171 ................................................ E S R Y E R V S F Y G R K N V G R L L R A V G E M N R G T G A S Y E G A L S C L M .................................................................................................................................................................................................................................................................................................................................................... tgttctgtaatttattattcgggcctacacagtgaaacccgatgattattcacttctatattctctaaccgaaaaatatccccttttgttcacccctcggagcaatcttgccacgccttccatattcctgcctgttccggccgaatattcaccggcgagagaacatagcactttatacttaaaagtcttacccctttataccataaagcctccatacttgataatatgaagatcccttgggagtctcgatggagatcccttaggagtctcgatagggatcccttaggggtctcgatagggatcccttaggagtctcgatggggatcccttaggagtctcgatggggatcccttaggggtctcagcaaaggcagccctctactgtcatttcggaggaaaaacaaagcatcctgcattatcgtgggaggaatgagtacttttgcagggaatcatattatttgcttgagccggtcaagattaggaatccggtctttccgattatgaaaaagaaa 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================================================ tgttctgtaatttattattcgggcctacacagtgaaacccgatgattattcacttctatattctctaaccgaaaaatatccccttttgttcacccctcggagcaatcttgccacgccttccatattcctgcctgttccggccgaatattcaccggcgagagaacatagcactttatacttaaaagtcttacccctttataccataaagcctccatacttgataatatgaagatcccttgggagtctcgatggagatcccttaggagtctcgatagggatcccttaggggtctcgatagggatcccttaggagtctcgatggggatcccttaggagtctcgatggggatcccttaggggtctcagcaaaggcagccctctactgtcatttcggaggaaaaacaaagcatcctgcattatcgtgggaggaatgagtacttttgcagggaatcatattatttgcttgagccggtcaagattaggaatccggtctttccgattatgaaaaagaaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 73 HP_score: -11.3 Tail_Score: -2.53581 Start: 244 End: 301 Full_Region: AAGATCCCTTGGGAG TCTCGATGGAGATCCCTTAGGAGTCTC GATA GGGATCCCTTAGGGGTCTCGATAGGGA TCCCTTAGGAGTCTC ...................................................................................................................................................................................................................................................TCTCGATGGAGATCCCTTAGGAGTCTCGATAGGGATCCCTTAGGGGTCTCGATAGGGA.................................................................................................................................................................................................................. Find igs database================================================ Query_seq: PG1286:PG1288|PG1286:PG1288:ferritin:GDP-mannose 4,6-dehydratase:<-->:1365592..1366102 511 tgttctgtaatttattattcgggcctacacagtgaaacccgatgattattcacttctatattctctaaccgaaaaatatccccttttgttcacccctcggagcaatcttgccacgccttccatattcctgcctgttccggccgaatattcaccggcgagagaacatagcactttatacttaaaagtcttacccctttataccataaagcctccatacttgataatatgaagatcccttgggagtctcgatggagatcccttaggagtctcgatagggatcccttaggggtctcgatagggatcccttaggagtctcgatggggatcccttaggagtctcgatggggatcccttaggggtctcagcaaaggcagccctctactgtcatttcggaggaaaaacaaagcatcctgcattatcgtgggaggaatgagtacttttgcagggaatcatattatttgcttgagccggtcaagattaggaatccggtctttccgattatgaaaaagaaa Intra-Species Hit: Count: 1 Min: 1 Max: 511 Len: 511 Subject: NC_002950_PG1286_PG1288|ferritin:GDP-mannose 4,6-dehydratase|NEGATIVE:POSITIVE|[1365592,1366102]|511 HSP 1 e-value: 0.0 bit: 1013.0 Len: 511 Query Start:1 Query End:511 Subject Strand: POSITIVE Subject Start: 1 Subject End: 511 tgttctgtaatttattattcgggcctacacagtgaaacccgatgattattcacttctatattctctaaccgaaaaatatccccttttgttcacccctcggagcaatcttgccacgccttccatattcctgcctgttccggccgaatattcaccggcgagagaacatagcactttatacttaaaagtcttacccctttataccataaagcctccatacttgataatatgaagatcccttgggagtctcgatggagatcccttaggagtctcgatagggatcccttaggggtctcgatagggatcccttaggagtctcgatggggatcccttaggagtctcgatggggatcccttaggggtctcagcaaaggcagccctctactgtcatttcggaggaaaaacaaagcatcctgcattatcgtgggaggaatgagtacttttgcagggaatcatattatttgcttgagccggtcaagattaggaatccggtctttccgattatgaaaaagaaa tgttctgtaatttattattcgggcctacacagtgaaacccgatgattattcacttctatattctctaaccgaaaaatatccccttttgttcacccctcggagcaatcttgccacgccttccatattcctgcctgttccggccgaatattcaccggcgagagaacatagcactttatacttaaaagtcttacccctttataccataaagcctccatacttgataatatgaagatcccttgggagtctcgatggagatcccttaggagtctcgatagggatcccttaggggtctcgatagggatcccttaggagtctcgatggggatcccttaggagtctcgatggggatcccttaggggtctcagcaaaggcagccctctactgtcatttcggaggaaaaacaaagcatcctgcattatcgtgggaggaatgagtacttttgcagggaatcatattatttgcttgagccggtcaagattaggaatccggtctttccgattatgaaaaagaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUCUGUAAUUUAUUAUUCGGGCCUACACAGUGAAACCCGAUGAUUAUUCACUUCUAUAUUCUCUAACCGAAAAAUAUCCCCUUUUGUUCACCCCUCGGAGCAAUCUUGCCACGCCUUCCAUAUUCCUGCCUGUUCCGGCCGAAUAUUCACCGGCGAGAGAACAUAGCACUUUAUACUUAAAAGUCUUACCCCUUUAUACCAUAAAGCCUCCAUACUUGAUAAUAUGAAGAUCCCUUGGGAGUCUCGAUGGAGAUCCCUUAGGAGUCUCGAUAGGGAUCCCUUAGGGGUCUCGAUAGGGAUCCCUUAGGAGUCUCGAUGGGGAUCCCUUAGGAGUCUCGAUGGGGAUCCCUUAGGGGUCUCAGCAAAGGCAGCCCUCUACUGUCAUUUCGGAGGAAAAACAAAGCAUCCUGCAUUAUCGUGGGAGGAAUGAGUACUUUUGCAGGGAAUCAUAUUAUUUGCUUGAGCCGGUCAAGAUUAGGAAUCCGGUCUUUCCGAUUAUGAAAAAGAAA ..((((....(((((...(((((....((.((..((.....((((((........((((.((((((..(((..............((((((........))))))................((((((..(((......))).))))))....)))..)))))).)))).........(((((((((((((..((((....((((....(((((.............(((.(((((((.(((..((((.((.((((..(((.(((..((((.((.((((..(((.(((((((((....))))))))).)))..)))).)).))))..))).)))..)))).)).))))..))).)))))))))).....(((((.......))))).....))))).........((.....))......))))))))..)))).))))))).))..))))))....))..)))).(((((((........))..)))))...)))))..)))))..)))). (-162.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCUUUUUCAUAAUCGGAAAGACCGGAUUCCUAAUCUUGACCGGCUCAAGCAAAUAAUAUGAUUCCCUGCAAAAGUACUCAUUCCUCCCACGAUAAUGCAGGAUGCUUUGUUUUUCCUCCGAAAUGACAGUAGAGGGCUGCCUUUGCUGAGACCCCUAAGGGAUCCCCAUCGAGACUCCUAAGGGAUCCCCAUCGAGACUCCUAAGGGAUCCCUAUCGAGACCCCUAAGGGAUCCCUAUCGAGACUCCUAAGGGAUCUCCAUCGAGACUCCCAAGGGAUCUUCAUAUUAUCAAGUAUGGAGGCUUUAUGGUAUAAAGGGGUAAGACUUUUAAGUAUAAAGUGCUAUGUUCUCUCGCCGGUGAAUAUUCGGCCGGAACAGGCAGGAAUAUGGAAGGCGUGGCAAGAUUGCUCCGAGGGGUGAACAAAAGGGGAUAUUUUUCGGUUAGAGAAUAUAGAAGUGAAUAAUCAUCGGGUUUCACUGUGUAGGCCCGAAUAAUAAAUUACAGAACA ((((((((((.((((((((((((((((..((........)))))).))..............(((((((......((..(((((((((...((((..(((...(((((((.(..(((((((.......(((((((((....)))))))))..((((((..((((((((....(((.(((....((((((((....(((.(((...((((((((((....((....)).))))))))))...))).)))....))))))))....))).)))....)))))))).(((((((.((((......)))).)))))))..)))))).(((((((.......))))).))..(((((...(((((.......))))).))))).)).)))))...).))))))).)))..))))....)))))))))))...)))))))..)))))))))))))))...)))))..........(((((((((.....).)))))))).................. (-168.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1101 140 91 231 182 NC_002950:PG1286|5end_ferritin_1365501..1365731_NEGATIVE 408 169 125 95 43 NC_002950:PG0278|5end_hypothetical_protein_310047..310277_POSITIVE 402 160 111 48 5 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 395 340 293 75 30 NC_002950:PG0844|5end_hypothetical_protein_905289..905519_POSITIVE 391 156 112 225 176 NC_002950:PG2209|5end_hypothetical_protein_2320928..2321158_NEGATIVE 388 139 94 128 78 NC_002950:PG0438|5end_hypothetical_protein_476884..477114_POSITIVE 384 170 127 49 6 NC_002950:PG0493|5end_hypothetical_protein_534900..535130_NEGATIVE 381 370 322 170 123 NC_002950:PG1816|5end_NAD(P)H_dehydrogenase,_quinone_family,_putative_1911951..1912181_NEGATIVE 381 160 115 158 98 NC_002950:PG1715|5end_hypothetical_protein_1806056..1806286_NEGATIVE 380 377 332 53 6 NC_002950:PG0500|5end_queuine_tRNA-ribosyltransferase_539197..539427_POSITIVE 375 116 79 181 140 NC_002950:PG1683|5end_hypothetical_protein_1769644..1769874_POSITIVE 373 158 114 219 171 NC_002950:PG0498|5end_S-ribosylhomocysteinase_537968..538198_POSITIVE 372 143 105 112 69 NC_002950:PG0897|5end_alpha-amylase_family_protein_962472..962702_NEGATIVE 372 160 127 180 137 NC_002950:PG0888|5end_hypothetical_protein_949910..950140_POSITIVE 371 121 82 196 148 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 368 158 114 197 145 NC_002950:PG0204|5end_hypothetical_protein_240507..240737_NEGATIVE 366 170 127 49 6 NC_002950:PG0265|5end_hypothetical_protein_298551..298781_NEGATIVE 365 160 112 206 149 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 363 136 94 204 159 NC_002950:PG0559|5end_chlorohydrolase_family_protein_617496..617726_NEGATIVE 360 396 355 195 147 NC_002950:PG1307|5end_glucose-inhibited_division_protein_B_1387849..1388079_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 393 390 341 66 16 NC_002950:PG2194|3end_ISPg4,_transposase_2300962..2301112_NEGATIVE 393 390 341 66 16 NC_002950:PG1673|3end_ISPg4,_transposase_1759625..1759775_POSITIVE 393 390 341 66 16 NC_002950:PG1658|3end_ISPg4,_transposase_1741747..1741897_NEGATIVE 393 390 341 66 16 NC_002950:PG1261|3end_ISPg4,_transposase_1339608..1339758_POSITIVE 393 390 341 66 16 NC_002950:PG0970|3end_ISPg4,_transposase_1030843..1030993_POSITIVE 393 390 341 66 16 NC_002950:PG0487|3end_ISPg4,_transposase_526276..526426_NEGATIVE 393 309 262 71 26 NC_002950:PG0387|3end_elongation_factor_Tu_421910..422060_POSITIVE 393 390 341 66 16 NC_002950:PG0225|3end_ISPg4,_transposase_258485..258635_NEGATIVE 393 390 341 66 16 NC_002950:PG0177|3end_ISPg4,_transposase_200324..200474_POSITIVE 393 390 341 66 16 NC_002950:PG0050|3end_ISPg4,_transposase_62153..62303_POSITIVE 393 390 341 66 16 NC_002950:PG0019|3end_ISPg4_transposase_23277..23427_POSITIVE 372 395 355 107 61 NC_002950:PG1859|3end_glycerate_kinase_family_protein_1957174..1957324_NEGATIVE 367 169 125 135 95 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 367 359 311 69 13 NC_002950:PG1977|3end_hypothetical_protein_2064687..2064837_NEGATIVE 359 165 127 60 15 NC_002950:PG1442|3end_hypothetical_protein_1527602..1527752_NEGATIVE 358 372 331 130 75 NC_002950:PG0740|3end_NLP/P60_family_protein_788485..788635_POSITIVE 357 319 272 91 43 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 354 388 347 147 93 NC_002950:PG1270|3end_hypothetical_protein_1349278..1349428_NEGATIVE 352 349 302 136 88 NC_002950:PG1392|3end_rod_shape-determining_protein_RodA,_putative_1472959..1473109_NEGATIVE 348 147 101 80 16 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE