Origin IGS: cttgtttcgtttgagtttattcttgttctacttgcttataaaaacggaaaagcggccaaaaagttcattccctttccggtcgctttctcaaaaaatactgctatcggctactgccgacgccatatcagtctgtgttt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaacacagactgatatggcgtcggcagtagccgatagcagtattttttgagaaagcgaccggaaagggaatgaactttttggccgcttttccgtttttataagcaagtagaacaagaataaactcaaacgaaacaag Mask Tandem Repeat Region ================================================ cttgtttcgtttgagtttattcttgttctacttgcttataaaaacggaaaagcggccaaaaagttcattccctttccggtcgctttctcaaaaaatactgctatcggctactgccgacgccatatcagtctgtgttt Find is-nt database================================================ Query_seq: PG0275:PG0276|PG0275:PG0276:thioredoxin family protein:hypothetical protein:<-<-:307555..307691 137 cttgtttcgtttgagtttattcttgttctacttgcttataaaaacggaaaagcggccaaaaagttcattccctttccggtcgctttctcaaaaaatactgctatcggctactgccgacgccatatcagtctgtgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0275:PG0276|PG0275:PG0276:thioredoxin family protein:hypothetical protein:<-<-:307555..307691 137 cttgtttcgtttgagtttattcttgttctacttgcttataaaaacggaaaagcggccaaaaagttcattccctttccggtcgctttctcaaaaaatactgctatcggctactgccgacgccatatcagtctgtgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0275:PG0276|PG0275:PG0276:thioredoxin family protein:hypothetical protein:<-<-:307555..307691 137 cttgtttcgtttgagtttattcttgttctacttgcttataaaaacggaaaagcggccaaaaagttcattccctttccggtcgctttctcaaaaaatactgctatcggctactgccgacgccatatcagtctgtgttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttgtttcgtttgagtttattcttgttctacttgcttataaaaacggaaaagcggccaaaaagttcattccctttccggtcgctttctcaaaaaatactgctatcggctactgccgacgccatatcagtctgtgttt Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 19 End: 135 .................. M L V L L A Y K N G K A A K K F I P F P V A F S K N T A I G Y C R R H I S L C .. Protein_Len: 45 Strand: + Start: 2 End: 136 . M F R L S L F L F Y L L I K T E K R P K S S F P F R S L S Q K I L L S A T A D A I S V C V . cttgtttcgtttgagtttattcttgttctacttgcttataaaaacggaaaagcggccaaaaagttcattccctttccggtcgctttctcaaaaaatactgctatcggctactgccgacgccatatcagtctgtgttt 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================================================ cttgtttcgtttgagtttattcttgttctacttgcttataaaaacggaaaagcggccaaaaagttcattccctttccggtcgctttctcaaaaaatactgctatcggctactgccgacgccatatcagtctgtgttt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 67 HP_score: -3.3 Tail_Score: -4.83169 Start: 45 End: 90 Full_Region: gatagcagtattttt tgagaaagcgaccggaaag ggaatgaa ctttttggccgcttttccg tttttataagcaagt ............................................tgagaaagcgaccggaaagggaatgaactttttggccgcttttccg............................................... TransTerm Strand: - Conf: 53 HP_score: -4.6 Tail_Score: -3.49419 Start: 46 End: 89 Full_Region: atagcagtatttttt gagaaagcgaccggaaag ggaatgaa ctttttggccgcttttcc gtttttataagcaag .............................................gagaaagcgaccggaaagggaatgaactttttggccgcttttcc................................................ TransTerm Strand: - Conf: 66 HP_score: -4.4 Tail_Score: -4.5115 Start: 52 End: 83 Full_Region: gtattttttgagaaa gcgaccggaaag ggaatgaa ctttttggccgc ttttccgtttttata ...................................................gcgaccggaaagggaatgaactttttggccgc...................................................... Find igs database================================================ Query_seq: PG0275:PG0276|PG0275:PG0276:thioredoxin family protein:hypothetical protein:<-<-:307555..307691 137 cttgtttcgtttgagtttattcttgttctacttgcttataaaaacggaaaagcggccaaaaagttcattccctttccggtcgctttctcaaaaaatactgctatcggctactgccgacgccatatcagtctgtgttt Intra-Species Hit: Count: 1 Min: 1 Max: 137 Len: 137 Subject: NC_002950_PG0275_PG0276|thioredoxin family protein:hypothetical protein|NEGATIVE:NEGATIVE|[307555,307691]|137 HSP 1 e-value: 3.0E-72 bit: 272.0 Len: 137 Query Start:1 Query End:137 Subject Strand: POSITIVE Subject Start: 1 Subject End: 137 cttgtttcgtttgagtttattcttgttctacttgcttataaaaacggaaaagcggccaaaaagttcattccctttccggtcgctttctcaaaaaatactgctatcggctactgccgacgccatatcagtctgtgttt cttgtttcgtttgagtttattcttgttctacttgcttataaaaacggaaaagcggccaaaaagttcattccctttccggtcgctttctcaaaaaatactgctatcggctactgccgacgccatatcagtctgtgttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGUUUCGUUUGAGUUUAUUCUUGUUCUACUUGCUUAUAAAAACGGAAAAGCGGCCAAAAAGUUCAUUCCCUUUCCGGUCGCUUUCUCAAAAAAUACUGCUAUCGGCUACUGCCGACGCCAUAUCAGUCUGUGUUU ............................(((..(((.(((.....(..(((((((((..((((........))))..)))))))))..)..........((..(((((....))))).))..))).)))..)))... (-30.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAACACAGACUGAUAUGGCGUCGGCAGUAGCCGAUAGCAGUAUUUUUUGAGAAAGCGACCGGAAAGGGAAUGAACUUUUUGGCCGCUUUUCCGUUUUUAUAAGCAAGUAGAACAAGAAUAAACUCAAACGAAACAAG ...........(((((.((((((((....)))))).)).))))).((((((.(((((.((((((((........)))))))).)))))(((...((((((......))))))...)))....))))))......... (-35.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1007 120 71 211 162 NC_002950:PG0275|5end_thioredoxin_family_protein_307464..307694_NEGATIVE 409 120 75 45 2 NC_002950:PG0441|5end_hypothetical_protein_478734..478964_POSITIVE 400 120 71 101 44 NC_002950:PG1198|5end_hypothetical_protein_1276650..1276880_POSITIVE 379 120 71 230 179 NC_002950:PG1478|5end_conjugative_transposon_protein_TraK_1554116..1554346_NEGATIVE 347 117 76 225 184 NC_002950:PG0952|5end_4-hydroxy-3-methylbut-2-en-1-yl_diphosphate_synthase_1010922..1011152_POSITIVE 344 120 79 114 72 NC_002950:PG0065|5end_efflux_transporter,_RND_family,_MFP_subunit_81187..81417_NEGATIVE 335 115 72 197 150 NC_002950:PG1163|5end_cobyrinic_acid_a,c-diamide_synthase_1243381..1243611_NEGATIVE 332 120 72 69 17 NC_002950:PG0376|5end_30S_ribosomal_protein_S9_406399..406629_POSITIVE 328 119 73 176 119 NC_002950:PG1042|5end_glycogen_synthase,_putative_1110638..1110868_NEGATIVE 328 119 72 221 161 NC_002950:PG0149|5end_hypothetical_protein_172203..172433_NEGATIVE 326 119 71 214 155 NC_002950:PG1953|5end_YitT_family_protein_2043574..2043804_POSITIVE 325 117 71 77 22 NC_002950:PG0076|5end_N-acetylmuramoyl-L-alanine_amidase,_family_4_91333..91563_NEGATIVE 319 120 76 154 108 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 318 120 71 206 161 NC_002950:PG0185|5end_ragA_protein_218329..218559_POSITIVE 317 119 77 106 61 NC_002950:PG0769|5end_fibronectin_type_III_domain_protein_824177..824407_NEGATIVE 312 86 45 214 162 NC_002950:PG1828|5end_lipoprotein,_putative_1921136..1921366_NEGATIVE 309 120 75 207 160 NC_002950:PG1381|5end_ABC_transporter,_permease_protein_1460622..1460852_POSITIVE 308 90 44 166 106 NC_002950:PG2202|5end_Holliday_junction_resolvase-like_protein_2309933..2310163_NEGATIVE 308 130 98 184 160 NC_002950:PG0399|5end_lipoprotein,_putative_436237..436467_NEGATIVE 307 130 87 58 16 NC_002950:PG0034|5end_thioredoxin_42549..42779_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 368 89 45 56 7 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 347 89 41 56 17 NC_002950:PG1473|3end_conjugative_transposon_protein_TraQ_1549761..1549911_NEGATIVE 347 117 76 51 10 NC_002950:PG0951|3end_phosphoribosylaminoimidazole_carboxylase,_PurE_protein_1010828..1010978_POSITIVE 332 120 72 59 7 NC_002950:PG0375|3end_50S_ribosomal_protein_L13_406469..406619_POSITIVE 330 49 1 101 49 NC_002950:PG1685|3end_hypothetical_protein_1772216..1772366_NEGATIVE 328 119 73 139 82 NC_002950:PG1043|3end_ferrous_iron_transport_protein_B_1110675..1110825_NEGATIVE 328 119 71 121 60 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 326 120 78 41 1 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 323 87 45 65 16 NC_002950:PG0062|3end_TPR_domain_protein_75810..75960_POSITIVE 317 119 77 124 79 NC_002950:PG0770|3end_hypothetical_protein_824159..824309_NEGATIVE 310 116 71 149 111 NC_002950:PG1943|3end_hypothetical_protein_2028974..2029124_NEGATIVE 303 120 76 139 98 NC_002950:PG0603|3end_cytidylate_kinase_660345..660495_POSITIVE 302 120 71 68 22 NC_002950:PG1863|3end_hypothetical_protein_1960364..1960514_NEGATIVE 290 88 44 103 40 NC_002950:PG0786|3end_hypothetical_protein_837570..837720_NEGATIVE 286 120 71 117 57 NC_002950:PG1370|3end_lysyl-tRNA_synthetase_1450493..1450643_NEGATIVE 286 118 76 112 84 NC_002950:PG0555|3end_DNA-binding_protein,_histone-like_family_611716..611866_NEGATIVE 285 84 44 76 40 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 285 120 71 118 63 NC_002950:PG0237|3end_uracil-DNA_glycosylase_275526..275676_POSITIVE 282 129 95 142 115 NC_002950:PG1259|3end_anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_1334974..1335124_NEGATIVE 281 120 71 150 99 NC_002950:PG0377|3end_30S_ribosomal_protein_S2_407845..407995_POSITIVE