Origin IGS: tgaaggtgatattccgaattatgagagttttttgctgtggtcgccctatggggcattgtagaatttgctgcattctacaaaagtgtttcctgatgatgtagtattaggatcaggcaatctgaatgaaaaaaagccggaat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attccggctttttttcattcagattgcctgatcctaatactacatcatcaggaaacacttttgtagaatgcagcaaattctacaatgccccatagggcgaccacagcaaaaaactctcataattcggaatatcaccttca Mask Tandem Repeat Region ================================================ tgaaggtgatattccgaattatgagagttttttgctgtggtcgccctatggggcattgtagaatttgctgcattctacaaaagtgtttcctgatgatgtagtattaggatcaggcaatctgaatgaaaaaaagccggaat Find is-nt database================================================ Query_seq: PG1427:PG1428|PG1427:PG1428:thiol protease/hemagglutinin PrtT precursor, putative:riboflavin synthase subunit beta:<-<-:1514487..1514626 140 tgaaggtgatattccgaattatgagagttttttgctgtggtcgccctatggggcattgtagaatttgctgcattctacaaaagtgtttcctgatgatgtagtattaggatcaggcaatctgaatgaaaaaaagccggaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1427:PG1428|PG1427:PG1428:thiol protease/hemagglutinin PrtT precursor, putative:riboflavin synthase subunit beta:<-<-:1514487..1514626 140 tgaaggtgatattccgaattatgagagttttttgctgtggtcgccctatggggcattgtagaatttgctgcattctacaaaagtgtttcctgatgatgtagtattaggatcaggcaatctgaatgaaaaaaagccggaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1427:PG1428|PG1427:PG1428:thiol protease/hemagglutinin PrtT precursor, putative:riboflavin synthase subunit beta:<-<-:1514487..1514626 140 tgaaggtgatattccgaattatgagagttttttgctgtggtcgccctatggggcattgtagaatttgctgcattctacaaaagtgtttcctgatgatgtagtattaggatcaggcaatctgaatgaaaaaaagccggaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgaaggtgatattccgaattatgagagttttttgctgtggtcgccctatggggcattgtagaatttgctgcattctacaaaagtgtttcctgatgatgtagtattaggatcaggcaatctgaatgaaaaaaagccggaat Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 6 End: 98 ..... M I F R I M R V F C C G R P M G H C R I C C I L Q K C F L M M .......................................... Protein_Len: 32 Strand: - Start: 2 End: 97 . F T I N R I I L T K Q Q P R G I P C Q L I Q Q M R C F H K R I M ........................................... tgaaggtgatattccgaattatgagagttttttgctgtggtcgccctatggggcattgtagaatttgctgcattctacaaaagtgtttcctgatgatgtagtattaggatcaggcaatctgaatgaaaaaaagccggaat 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================================================ tgaaggtgatattccgaattatgagagttttttgctgtggtcgccctatggggcattgtagaatttgctgcattctacaaaagtgtttcctgatgatgtagtattaggatcaggcaatctgaatgaaaaaaagccggaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1427:PG1428|PG1427:PG1428:thiol protease/hemagglutinin PrtT precursor, putative:riboflavin synthase subunit beta:<-<-:1514487..1514626 140 tgaaggtgatattccgaattatgagagttttttgctgtggtcgccctatggggcattgtagaatttgctgcattctacaaaagtgtttcctgatgatgtagtattaggatcaggcaatctgaatgaaaaaaagccggaat Intra-Species Hit: Count: 1 Min: 1 Max: 125 Len: 125 Subject: NC_002950_PG1427_PG1428|thiol protease/hemagglutinin PrtT precursor, putative:riboflavin synthase subunit beta|NEGATIVE:NEGATIVE|[1514487,1514626]|140 HSP 1 e-value: 4.0E-65 bit: 248.0 Len: 125 Query Start:1 Query End:125 Subject Strand: POSITIVE Subject Start: 1 Subject End: 125 tgaaggtgatattccgaattatgagagttttttgctgtggtcgccctatggggcattgtagaatttgctgcattctacaaaagtgtttcctgatgatgtagtattaggatcaggcaatctgaatg............... tgaaggtgatattccgaattatgagagttttttgctgtggtcgccctatggggcattgtagaatttgctgcattctacaaaagtgtttcctgatgatgtagtattaggatcaggcaatctgaatg............... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAAGGUGAUAUUCCGAAUUAUGAGAGUUUUUUGCUGUGGUCGCCCUAUGGGGCAUUGUAGAAUUUGCUGCAUUCUACAAAAGUGUUUCCUGAUGAUGUAGUAUUAGGAUCAGGCAAUCUGAAUG ....((.......))...........((((.(((((......((((....)))).(((((((((.......))))))))).......((((((((......))))))))...)))))...)))). (-29.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUUCAGAUUGCCUGAUCCUAAUACUACAUCAUCAGGAAACACUUUUGUAGAAUGCAGCAAAUUCUACAAUGCCCCAUAGGGCGACCACAGCAAAAAACUCUCAUAAUUCGGAAUAUCACCUUCA .((((.((...((((((..............))))))........(((((((((.......))))))))).((((....)))).........................)).)))).......... (-23.64) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 954 80 31 171 122 NC_002950:PG1427|5end_thiol_protease/hemagglutinin_PrtT_precursor,_putative_1514396..1514626_NEGATIVE 345 70 33 35 2 NC_002950:PG1179|5end_hypothetical_protein_1261132..1261362_NEGATIVE 341 58 15 229 187 NC_002950:PG1565|5end_3-deoxy-D-manno-octulosonic-acid_transferase,_putative_1645859..1646089_NEGATIVE 340 69 22 59 6 NC_002950:PG0411|5end_hemagglutinin,_putative_446501..446731_POSITIVE 331 70 25 63 23 NC_002950:PG1043|5end_ferrous_iron_transport_protein_B_1112852..1113082_NEGATIVE 330 58 22 44 4 NC_002950:PG0401|5end_hypothetical_protein_439306..439536_NEGATIVE 317 70 23 164 122 NC_002950:PG1214|5end_hypothetical_protein_1293032..1293262_POSITIVE 313 59 14 184 144 NC_002950:PG1612|5end_methylmalonyl-CoA_decarboxylase,_alpha_subunit_1693065..1693295_NEGATIVE 312 69 23 103 54 NC_002950:PG1718|5end_hypothetical_protein_1806807..1807037_NEGATIVE 311 59 15 140 94 NC_002950:PG1556|5end_hypothetical_protein_1636595..1636825_POSITIVE 310 46 1 191 142 NC_002950:PG1482|5end_conjugative_transposon_protein_TraF_1558779..1559009_NEGATIVE 305 55 13 62 27 NC_002950:PG0615|5end_GTP-binding_protein_TypA_667033..667263_POSITIVE 305 70 26 193 142 NC_002950:PG0141|5end_spoOJ_protein_164747..164977_NEGATIVE 302 68 32 201 158 NC_002950:PG1020|5end_hypothetical_protein_1080568..1080798_POSITIVE 301 59 12 85 40 NC_002950:PG1462|5end_hypothetical_protein_1540860..1541090_POSITIVE 300 59 14 97 42 NC_002950:PG0560|5end_hypothetical_protein_617423..617653_POSITIVE 298 109 67 69 27 NC_002950:PG2144|5end_hypothetical_protein_2249911..2250141_POSITIVE 295 62 28 228 175 NC_002950:PG2154|5end_hypothetical_protein_2260945..2261175_NEGATIVE 295 68 27 78 36 NC_002950:PG1241|5end_GTP-binding_protein_LepA_1315613..1315843_POSITIVE 295 62 26 75 30 NC_002950:PG0791|5end_adenylate_kinase_843177..843407_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 69 22 59 6 NC_002950:PG0410|3end_hypothetical_protein_446581..446731_POSITIVE 318 58 14 136 88 NC_002950:PG1961|3end_hypothetical_protein_2048886..2049036_NEGATIVE 313 59 14 85 45 NC_002950:PG1613|3end_glyoxalase_family_protein_1693164..1693314_NEGATIVE 311 59 15 134 88 NC_002950:PG1555|3end_hypothetical_protein_1636669..1636819_POSITIVE 310 70 33 51 19 NC_002950:PG1760|3end_ABC_transporter,_ATP-binding_protein_1847216..1847366_POSITIVE 307 71 32 104 52 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 305 69 22 87 33 NC_002950:PG0196|3end_peptidase,_M16_family_235808..235958_POSITIVE 303 72 36 44 1 NC_002950:PG0086|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_100545..100695_NEGATIVE 301 59 12 72 27 NC_002950:PG1461|3end_hypothetical_protein_1540927..1541077_POSITIVE 296 71 32 104 58 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 295 62 26 74 29 NC_002950:PG0792|3end_hypoxanthine_phosphoribosyltransferase_843178..843328_NEGATIVE 295 76 34 140 100 NC_002950:PG0076|3end_N-acetylmuramoyl-L-alanine_amidase,_family_4_90392..90542_NEGATIVE 292 76 34 70 19 NC_002950:PG1739|3end_hypothetical_protein_1825128..1825278_NEGATIVE 292 47 6 143 100 NC_002950:PG0625|3end_GTP_cyclohydrolase_I_679249..679399_POSITIVE 292 54 11 77 23 NC_002950:PG0606|3end_hypothetical_protein_662451..662601_NEGATIVE 291 54 25 146 117 NC_002950:PG2125|3end_transcriptional_regulator,_AraC_family_2231376..2231526_NEGATIVE 290 71 31 143 109 NC_002950:PG1932|3end_ribosomal_protein_S3_2020870..2021020_NEGATIVE 289 70 28 128 86 NC_002950:PG0744|3end_RNA_methyltransferase,_TrmH_family_791133..791283_NEGATIVE 288 78 31 134 90 NC_002950:PG0514|3end_translocase_552929..553079_NEGATIVE 286 47 3 57 16 NC_002950:PG2010|3end_phosphomannomutase,_putative_2100952..2101102_POSITIVE