Origin IGS: tgtgtatatatttattggtttcttacaaaagtagggcttttcatacaaccgacaagctaccaccggaagactataccaagacagaccacaacaggatttggctccaccccgaacaaccggcggaggaatcccccgagagaactctttcaccgatacattcgccctttcgggctacatacgaaggcaacagaaaaggaaaaaacgg .........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 ccgttttttccttttctgttgccttcgtatgtagcccgaaagggcgaatgtatcggtgaaagagttctctcgggggattcctccgccggttgttcggggtggagccaaatcctgttgtggtctgtcttggtatagtcttccggtggtagcttgtcggttgtatgaaaagccctacttttgtaagaaaccaataaatatatacaca Mask Tandem Repeat Region ================================================ tgtgtatatatttattggtttcttacaaaagtagggcttttcatacaaccgacaagctaccaccggaagactataccaagacagaccacaacaggatttggctccaccccgaacaaccggcggaggaatcccccgagagaactctttcaccgatacattcgccctttcgggctacatacgaaggcaacagaaaaggaaaaaacgg Find is-nt database================================================ Query_seq: PG1853:PG1854|PG1853:PG1854:DNA polymerase III, beta subunit:5-formyltetrahydrofolate cyclo-ligase family protein:<-<-:1953210..1953414 205 tgtgtatatatttattggtttcttacaaaagtagggcttttcatacaaccgacaagctaccaccggaagactataccaagacagaccacaacaggatttggctccaccccgaacaaccggcggaggaatcccccgagagaactctttcaccgatacattcgccctttcgggctacatacgaaggcaacagaaaaggaaaaaacgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1853:PG1854|PG1853:PG1854:DNA polymerase III, beta subunit:5-formyltetrahydrofolate cyclo-ligase family protein:<-<-:1953210..1953414 205 tgtgtatatatttattggtttcttacaaaagtagggcttttcatacaaccgacaagctaccaccggaagactataccaagacagaccacaacaggatttggctccaccccgaacaaccggcggaggaatcccccgagagaactctttcaccgatacattcgccctttcgggctacatacgaaggcaacagaaaaggaaaaaacgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1853:PG1854|PG1853:PG1854:DNA polymerase III, beta subunit:5-formyltetrahydrofolate cyclo-ligase family protein:<-<-:1953210..1953414 205 tgtgtatatatttattggtttcttacaaaagtagggcttttcatacaaccgacaagctaccaccggaagactataccaagacagaccacaacaggatttggctccaccccgaacaaccggcggaggaatcccccgagagaactctttcaccgatacattcgccctttcgggctacatacgaaggcaacagaaaaggaaaaaacgg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtgtatatatttattggtttcttacaaaagtagggcttttcatacaaccgacaagctaccaccggaagactataccaagacagaccacaacaggatttggctccaccccgaacaaccggcggaggaatcccccgagagaactctttcaccgatacattcgccctttcgggctacatacgaaggcaacagaaaaggaaaaaacgg Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 6 End: 203 ..... M Y L L V S Y K S R A F H T T D K L P P E D Y T K T D H N R I W L H P E Q P A E E S P E R T L S P I H S P F R A T Y E G .. Protein_Len: 60 Strand: + Start: 10 End: 204 ......... M Y W F L T K V G L F I Q P T S Y H R K T I P R Q T T T G F G S T P N N R R R N P P R E L F H R Y I R P F G L H T K A T . Protein_Len: 36 Strand: + Start: 98 End: 205 ................................................................................................. M A P P R T T G G G I P R E N S F T D T F A L S G Y I R R Q Q K R K K R Protein_Len: 39 Strand: - Start: 74 End: 190 ......................................................................... V L V S W L L I Q S W G S C G A S S D G S L V R E G I C E G K R A V Y S P L M ............... Protein_Len: 50 Strand: - Start: 1 End: 150 T Y I N I P K K C F Y P K E Y L R C A V V P L S Y W S L G C C S K A G G R V V P P P I G R S F E K M ....................................................... tgtgtatatatttattggtttcttacaaaagtagggcttttcatacaaccgacaagctaccaccggaagactataccaagacagaccacaacaggatttggctccaccccgaacaaccggcggaggaatcccccgagagaactctttcaccgatacattcgccctttcgggctacatacgaaggcaacagaaaaggaaaaaacgg 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================================================ tgtgtatatatttattggtttcttacaaaagtagggcttttcatacaaccgacaagctaccaccggaagactataccaagacagaccacaacaggatttggctccaccccgaacaaccggcggaggaatcccccgagagaactctttcaccgatacattcgccctttcgggctacatacgaaggcaacagaaaaggaaaaaacgg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1853:PG1854|PG1853:PG1854:DNA polymerase III, beta subunit:5-formyltetrahydrofolate cyclo-ligase family protein:<-<-:1953210..1953414 205 tgtgtatatatttattggtttcttacaaaagtagggcttttcatacaaccgacaagctaccaccggaagactataccaagacagaccacaacaggatttggctccaccccgaacaaccggcggaggaatcccccgagagaactctttcaccgatacattcgccctttcgggctacatacgaaggcaacagaaaaggaaaaaacgg Intra-Species Hit: Count: 1 Min: 1 Max: 205 Len: 205 Subject: NC_002950_PG1853_PG1854|DNA polymerase III, beta subunit:5-formyltetrahydrofolate cyclo-ligase family protein|NEGATIVE:NEGATIVE|[1953210,1953414]|205 HSP 1 e-value: 1.0E-112 bit: 406.0 Len: 205 Query Start:1 Query End:205 Subject Strand: POSITIVE Subject Start: 1 Subject End: 205 tgtgtatatatttattggtttcttacaaaagtagggcttttcatacaaccgacaagctaccaccggaagactataccaagacagaccacaacaggatttggctccaccccgaacaaccggcggaggaatcccccgagagaactctttcaccgatacattcgccctttcgggctacatacgaaggcaacagaaaaggaaaaaacgg tgtgtatatatttattggtttcttacaaaagtagggcttttcatacaaccgacaagctaccaccggaagactataccaagacagaccacaacaggatttggctccaccccgaacaaccggcggaggaatcccccgagagaactctttcaccgatacattcgccctttcgggctacatacgaaggcaacagaaaaggaaaaaacgg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUGUAUAUAUUUAUUGGUUUCUUACAAAAGUAGGGCUUUUCAUACAACCGACAAGCUACCACCGGAAGACUAUACCAAGACAGACCACAACAGGAUUUGGCUCCACCCCGAACAACCGGCGGAGGAAUCCCCCGAGAGAACUCUUUCACCGAUACAUUCGCCCUUUCGGGCUACAUACGAAGGCAACAGAAAAGGAAAAAACGG ((.(((((..(((..((((..(((((....)))))((((.((........)).)))).))))...)))...)))))))...((((((......)).))))..(((..((((((.....((((((.(.(((....(((((....)))))...))).).))))))..))))))...........(....)......)))........ (-44.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGUUUUUUCCUUUUCUGUUGCCUUCGUAUGUAGCCCGAAAGGGCGAAUGUAUCGGUGAAAGAGUUCUCUCGGGGGAUUCCUCCGCCGGUUGUUCGGGGUGGAGCCAAAUCCUGUUGUGGUCUGUCUUGGUAUAGUCUUCCGGUGGUAGCUUGUCGGUUGUAUGAAAAGCCCUACUUUUGUAAGAAACCAAUAAAUAUAUACACA .................((((((.(((......((((....))))...((((((((.((.(((.(.(...((((((.((((.((.((((....)))))).))))))....))))..).).))).))))))))))......))).)))))).....((((.((..(((........)))..))...))))................ (-57.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1126 140 91 231 182 NC_002950:PG1853|5end_DNA_polymerase_III,_beta_subunit_1953119..1953349_NEGATIVE 393 149 101 193 152 NC_002950:PG0356|5end_hypothetical_protein_390611..390841_POSITIVE 392 139 91 213 159 NC_002950:PG1979|5end_hypothetical_protein_2067272..2067502_POSITIVE 390 140 94 68 20 NC_002950:PG0491|5end_hypothetical_protein_532184..532414_POSITIVE 388 139 94 136 79 NC_002950:PG1675|5end_hypothetical_protein_1760182..1760412_POSITIVE 386 160 116 51 2 NC_002950:PG1840|5end_hypothetical_protein_1937102..1937332_POSITIVE 385 138 91 180 132 NC_002950:PG0809|5end_hypothetical_protein_872014..872244_NEGATIVE 375 149 102 80 7 NC_002950:PG0493|5end_hypothetical_protein_534900..535130_NEGATIVE 371 138 94 54 3 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 369 132 93 220 184 NC_002950:PG0883|5end_hypothetical_protein_945121..945351_POSITIVE 364 180 133 210 162 NC_002950:PG0170|5end_methionyl-tRNA_synthetase_189652..189882_POSITIVE 363 147 103 198 151 NC_002950:PG1478|5end_conjugative_transposon_protein_TraK_1554116..1554346_NEGATIVE 362 137 92 117 53 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 360 134 91 106 53 NC_002950:PG1273|5end_hypothetical_protein_1351837..1352067_NEGATIVE 354 135 92 137 92 NC_002950:PG2087|5end_hypothetical_protein_2186990..2187220_POSITIVE 350 138 92 201 129 NC_002950:PG1676|5end_phosphoenolpyruvate_carboxykinase_1762096..1762326_NEGATIVE 344 140 96 214 179 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 343 126 86 175 123 NC_002950:PG0734|5end_nitroreductase_family_protein_783773..784003_POSITIVE 338 140 92 81 20 NC_002950:PG0485|5end_preprotein_translocase,_YajC_subunit_525324..525554_NEGATIVE 338 184 141 126 60 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 390 140 94 52 4 NC_002950:PG0490|3end_hypothetical_protein_532248..532398_POSITIVE 376 140 97 97 32 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 369 153 113 137 88 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 354 135 92 137 92 NC_002950:PG2086|3end_hypothetical_protein_2187070..2187220_POSITIVE 339 77 33 97 43 NC_002950:PG1030|3end_hypothetical_protein_1092820..1092970_POSITIVE 338 184 141 121 55 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 336 139 91 53 3 NC_002950:PG0082|3end_hypothetical_protein_97026..97176_POSITIVE 334 140 92 147 77 NC_002950:PG0026|3end_hypothetical_protein_32685..32835_POSITIVE 332 170 126 119 75 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 330 180 133 103 42 NC_002950:PG1814|3end_DNA_primase_1908606..1908756_NEGATIVE 330 140 93 50 1 NC_002950:PG0770|3end_hypothetical_protein_824159..824309_NEGATIVE 329 138 94 68 11 NC_002950:PG1522|3end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1599100..1599250_NEGATIVE 329 140 91 83 28 NC_002950:PG1416|3end_enoyl-(acyl-carrier-protein)_reductase_II_1501078..1501228_POSITIVE 328 170 121 66 21 NC_002950:PG1112|3end_hypothetical_protein_1185571..1185721_POSITIVE 328 189 143 72 18 NC_002950:PG0119|3end_glycosyl_transferase,_WecB/TagA/CpsF_family_143078..143228_POSITIVE 325 136 91 56 10 NC_002950:PG0715|3end_transporter_768676..768826_NEGATIVE 325 139 92 143 92 NC_002950:PG0541|3end_hypothetical_protein_595136..595286_POSITIVE 322 154 119 97 61 NC_002950:PG1887|3end_rhodanese-like_domain_protein_1985679..1985829_POSITIVE 322 180 133 133 85 NC_002950:PG0210|3end_precorrin-6x_reductase/cobalamin_biosynthetic_protein_CbiD_244161..244311_NEGATIVE 319 70 27 143 104 NC_002950:PG1544|3end_hypothetical_protein_1623442..1623592_POSITIVE