Origin IGS: ataaagaatttcaatttctgacaacgaaggctgcggctgccgatatgggtggttgcagcctttgatgtttttgcttgaattaacttcggtaggggagcaagagggcaaccgcatcaaatctttagtagctttttgagatagtctatat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atatagactatctcaaaaagctactaaagatttgatgcggttgccctcttgctcccctaccgaagttaattcaagcaaaaacatcaaaggctgcaaccacccatatcggcagccgcagccttcgttgtcagaaattgaaattctttat Mask Tandem Repeat Region ================================================ ataaagaatttcaatttctgacaacgaaggctgcggctgccgatatgggtggttgcagcctttgatgtttttgcttgaattaacttcggtaggggagcaagagggcaaccgcatcaaatctttagtagctttttgagatagtctatat Find is-nt database================================================ Query_seq: PG1786:PG1787|PG1786:PG1787:hypothetical protein:hypothetical protein:-><-:1875383..1875530 148 ataaagaatttcaatttctgacaacgaaggctgcggctgccgatatgggtggttgcagcctttgatgtttttgcttgaattaacttcggtaggggagcaagagggcaaccgcatcaaatctttagtagctttttgagatagtctatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1786:PG1787|PG1786:PG1787:hypothetical protein:hypothetical protein:-><-:1875383..1875530 148 ataaagaatttcaatttctgacaacgaaggctgcggctgccgatatgggtggttgcagcctttgatgtttttgcttgaattaacttcggtaggggagcaagagggcaaccgcatcaaatctttagtagctttttgagatagtctatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1786:PG1787|PG1786:PG1787:hypothetical protein:hypothetical protein:-><-:1875383..1875530 148 ataaagaatttcaatttctgacaacgaaggctgcggctgccgatatgggtggttgcagcctttgatgtttttgcttgaattaacttcggtaggggagcaagagggcaaccgcatcaaatctttagtagctttttgagatagtctatat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataaagaatttcaatttctgacaacgaaggctgcggctgccgatatgggtggttgcagcctttgatgtttttgcttgaattaacttcggtaggggagcaagagggcaaccgcatcaaatctttagtagctttttgagatagtctatat Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 8 End: 133 ....... M S I S D N E G C G C R Y G W L Q P L M F L L E L T S V G E Q E G N R I K S L V A F ............... Protein_Len: 39 Strand: - Start: 1 End: 117 Y L I E I E S L S P Q P Q R Y P H N C G K I N K S S N V E T P S C S P L R M M ............................... ataaagaatttcaatttctgacaacgaaggctgcggctgccgatatgggtggttgcagcctttgatgtttttgcttgaattaacttcggtaggggagcaagagggcaaccgcatcaaatctttagtagctttttgagatagtctatat 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================================================ ataaagaatttcaatttctgacaacgaaggctgcggctgccgatatgggtggttgcagcctttgatgtttttgcttgaattaacttcggtaggggagcaagagggcaaccgcatcaaatctttagtagctttttgagatagtctatat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -12.6 Tail_Score: -4.90013 Start: 22 End: 67 Full_Region: AATTTCAATTTCTGA CAACGAAGGCTGCGGCTGCC GATATG GGTGGTTGCAGCCTTTGATG TTTTTGCTTGAATTA .....................CAACGAAGGCTGCGGCTGCCGATATGGGTGGTTGCAGCCTTTGATG................................................................................. TransTerm Strand: + Conf: 86 HP_score: -12.9 Tail_Score: -3.02518 Start: 25 End: 64 Full_Region: TTCAATTTCTGACAA CGAAGGCTGCGGCTGCC GATATG GGTGGTTGCAGCCTTTG ATGTTTTTGCTTGAA ........................CGAAGGCTGCGGCTGCCGATATGGGTGGTTGCAGCCTTTG.................................................................................... Find igs database================================================ Query_seq: PG1786:PG1787|PG1786:PG1787:hypothetical protein:hypothetical protein:-><-:1875383..1875530 148 ataaagaatttcaatttctgacaacgaaggctgcggctgccgatatgggtggttgcagcctttgatgtttttgcttgaattaacttcggtaggggagcaagagggcaaccgcatcaaatctttagtagctttttgagatagtctatat Intra-Species Hit: Count: 1 Min: 1 Max: 148 Len: 148 Subject: NC_002950_PG1786_PG1787|hypothetical protein:hypothetical protein|POSITIVE:NEGATIVE|[1875383,1875530]|148 HSP 1 e-value: 8.0E-79 bit: 293.0 Len: 148 Query Start:1 Query End:148 Subject Strand: POSITIVE Subject Start: 1 Subject End: 148 ataaagaatttcaatttctgacaacgaaggctgcggctgccgatatgggtggttgcagcctttgatgtttttgcttgaattaacttcggtaggggagcaagagggcaaccgcatcaaatctttagtagctttttgagatagtctatat ataaagaatttcaatttctgacaacgaaggctgcggctgccgatatgggtggttgcagcctttgatgtttttgcttgaattaacttcggtaggggagcaagagggcaaccgcatcaaatctttagtagctttttgagatagtctatat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAAGAAUUUCAAUUUCUGACAACGAAGGCUGCGGCUGCCGAUAUGGGUGGUUGCAGCCUUUGAUGUUUUUGCUUGAAUUAACUUCGGUAGGGGAGCAAGAGGGCAACCGCAUCAAAUCUUUAGUAGCUUUUUGAGAUAGUCUAUAU ....((((((((((.....((((.(((((((((((((..((......))..))))))))))))).))))(((((((...(..((....))..).))))))).((....))......................)))))))..))).... (-49.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAUAGACUAUCUCAAAAAGCUACUAAAGAUUUGAUGCGGUUGCCCUCUUGCUCCCCUACCGAAGUUAAUUCAAGCAAAAACAUCAAAGGCUGCAACCACCCAUAUCGGCAGCCGCAGCCUUCGUUGUCAGAAAUUGAAAUUCUUUAU ..(((((..((.((((....((((....((.....((((((((((...(((((.....((....)).......)))))..........((.((....)).)).....))))))))))....))...)).))...)))).))..))))) (-28.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 388 130 88 192 152 NC_002950:PG0742|5end_antigen_PgaA_790637..790867_NEGATIVE 373 69 29 46 11 NC_002950:PG0010|5end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpC_8775..9005_POSITIVE 360 74 37 210 168 NC_002950:PG0658|5end_phosphatase,_YrbI_family_708319..708549_NEGATIVE 358 74 32 109 64 NC_002950:PG0758|5end_peptidyl-dipeptidase_Dcp_808554..808784_NEGATIVE 356 59 18 222 176 NC_002950:PG1927|5end_50S_ribosomal_protein_L24_2019557..2019787_NEGATIVE 356 70 25 59 6 NC_002950:PG0886|5end_hypothetical_protein_948842..949072_POSITIVE 355 68 23 214 167 NC_002950:PG0603|5end_cytidylate_kinase_659570..659800_POSITIVE 354 66 23 213 154 NC_002950:PG0215|5end_hypothetical_protein_251460..251690_POSITIVE 352 65 22 63 1 NC_002950:PG2187|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_2294643..2294873_NEGATIVE 352 70 21 84 33 NC_002950:PG1634|5end_hypothetical_protein_1715148..1715378_NEGATIVE 351 76 32 109 49 NC_002950:PG0052|5end_sensor_histidine_kinase_63419..63649_POSITIVE 349 140 95 221 172 NC_002950:PG1461|5end_hypothetical_protein_1540326..1540556_POSITIVE 348 59 17 55 6 NC_002950:PG2041|5end_hypothetical_protein_2139966..2140196_NEGATIVE 348 118 81 179 139 NC_002950:PG0188|5end_lipoprotein,_putative_223934..224164_POSITIVE 347 60 11 146 88 NC_002950:PG1862|5end_hypothetical_protein_1960363..1960593_NEGATIVE 347 64 28 212 174 NC_002950:PG0221|5end_hypothetical_protein_255834..256064_NEGATIVE 346 59 14 202 155 NC_002950:PG0430|5end_ferrodoxin_oxidoreductase_beta_subunit_467986..468216_POSITIVE 345 116 72 196 145 NC_002950:PG2064|5end_hypothetical_protein_2160550..2160780_POSITIVE 345 74 32 208 165 NC_002950:PG1723|5end_ribosomal_protein_S20_1813069..1813299_POSITIVE 345 67 25 205 150 NC_002950:PG0684|5end_ABC_transporter,_permease_protein,_putative_737648..737878_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 654 140 102 117 79 NC_002950:PG1061|3end_ISPg6,_transposase_1128730..1128880_NEGATIVE 555 68 21 70 23 NC_002950:PG1786|3end_hypothetical_protein_1875322..1875472_POSITIVE 433 68 29 75 26 NC_002950:PG1593|3end_shikimate_kinase_1672143..1672293_POSITIVE 381 59 12 54 2 NC_002950:PG2188|3end_diaminopimelate_decarboxylase_2294633..2294783_NEGATIVE 378 70 24 127 71 NC_002950:PG2089|3end_hypothetical_protein_2189904..2190054_POSITIVE 376 67 29 136 103 NC_002950:PG1677|3end_phosphoglycerate_kinase_1763678..1763828_POSITIVE 363 68 26 67 16 NC_002950:PG1290|3end_branched-chain_amino_acid_aminotransferase_1369352..1369502_POSITIVE 362 66 28 61 11 NC_002950:PG2010|3end_phosphomannomutase,_putative_2100952..2101102_POSITIVE 356 70 25 62 9 NC_002950:PG0885|3end_phospho-2-dehydro-3-deoxyheptonate_aldolase/chorismate_mutase_948925..949075_POSITIVE 355 76 32 140 96 NC_002950:PG0291|3end_hypothetical_protein_326622..326772_POSITIVE 348 63 24 62 17 NC_002950:PG0775|3end_acyl-CoA_dehydrogenase_family_protein_827432..827582_NEGATIVE 348 63 24 88 42 NC_002950:PG0725|3end_hydrolase,_haloacid_dehalogenase-like_family_777966..778116_POSITIVE 347 60 11 145 87 NC_002950:PG1863|3end_hypothetical_protein_1960364..1960514_NEGATIVE 347 64 28 133 95 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 346 55 15 53 4 NC_002950:PG1706|3end_hypothetical_protein_1793849..1793999_NEGATIVE 345 60 14 133 86 NC_002950:PG0045|3end_heat_shock_protein_90_56193..56343_POSITIVE 344 60 17 53 17 NC_002950:PG1864|3end_leucine-rich_protein_1960509..1960659_NEGATIVE 343 66 25 54 14 NC_002950:PG0327|3end_hypothetical_protein_360907..361057_NEGATIVE 339 59 15 56 4 NC_002950:PG0535|3end_hypothetical_protein_585956..586106_NEGATIVE 339 67 28 140 95 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE