Origin IGS: aaattgcttgccctcggtcgatgccggtcgtcgcttaggcggcaagaacgagcaaaagagtcccttagacctgttctttgggactttttttttattttagcggccacaaataatcttttccggcgggatatggtctttaaaaagggccggtgcccgtccattatgcaacaaattcgatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatcgaatttgttgcataatggacgggcaccggccctttttaaagaccatatcccgccggaaaagattatttgtggccgctaaaataaaaaaaaagtcccaaagaacaggtctaagggactcttttgctcgttcttgccgcctaagcgacgaccggcatcgaccgagggcaagcaattt Mask Tandem Repeat Region ================================================ aaattgcttgccctcggtcgatgccggtcgtcgcttaggcggcaagaacgagcaaaagagtcccttagacctgttctttgggactttttttttattttagcggccacaaataatcttttccggcgggatatggtctttaaaaagggccggtgcccgtccattatgcaacaaattcgatt Find is-nt database================================================ Query_seq: PG2140:PG2141|PG2140:PG2141:ribosomal protein L32:3-oxoacyl-(acyl carrier protein) synthase:->->:2246460..2246638 179 aaattgcttgccctcggtcgatgccggtcgtcgcttaggcggcaagaacgagcaaaagagtcccttagacctgttctttgggactttttttttattttagcggccacaaataatcttttccggcgggatatggtctttaaaaagggccggtgcccgtccattatgcaacaaattcgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2140:PG2141|PG2140:PG2141:ribosomal protein L32:3-oxoacyl-(acyl carrier protein) synthase:->->:2246460..2246638 179 aaattgcttgccctcggtcgatgccggtcgtcgcttaggcggcaagaacgagcaaaagagtcccttagacctgttctttgggactttttttttattttagcggccacaaataatcttttccggcgggatatggtctttaaaaagggccggtgcccgtccattatgcaacaaattcgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2140:PG2141|PG2140:PG2141:ribosomal protein L32:3-oxoacyl-(acyl carrier protein) synthase:->->:2246460..2246638 179 aaattgcttgccctcggtcgatgccggtcgtcgcttaggcggcaagaacgagcaaaagagtcccttagacctgttctttgggactttttttttattttagcggccacaaataatcttttccggcgggatatggtctttaaaaagggccggtgcccgtccattatgcaacaaattcgatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaattgcttgccctcggtcgatgccggtcgtcgcttaggcggcaagaacgagcaaaagagtcccttagacctgttctttgggactttttttttattttagcggccacaaataatcttttccggcgggatatggtctttaaaaagggccggtgcccgtccattatgcaacaaattcgatt Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 8 End: 97 ....... M P S V D A G R R L G G K N E Q K S P L D L F F G T F F L F .................................................................................. Protein_Len: 58 Strand: + Start: 4 End: 177 ... M L A L G R C R S S L R R Q E R A K E S L R P V L W D F F F I L A A T N N L F R R D M V F K K G R C P S I M Q Q I R .. Protein_Len: 57 Strand: - Start: 3 End: 173 .. N S A R P R H R D D S L R C S R A F S D R L G T R Q S K K K I K A A V F L R K R R S I T K L F P R H G D M I C C M ...... aaattgcttgccctcggtcgatgccggtcgtcgcttaggcggcaagaacgagcaaaagagtcccttagacctgttctttgggactttttttttattttagcggccacaaataatcttttccggcgggatatggtctttaaaaagggccggtgcccgtccattatgcaacaaattcgatt 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================================================ aaattgcttgccctcggtcgatgccggtcgtcgcttaggcggcaagaacgagcaaaagagtcccttagacctgttctttgggactttttttttattttagcggccacaaataatcttttccggcgggatatggtctttaaaaagggccggtgcccgtccattatgcaacaaattcgatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -4.2 Tail_Score: -6.55664 Start: 60 End: 84 Full_Region: AGAACGAGCAAAAGA GTCCCTTAGA CCTGT TCTTTGGGAC TTTTTTTTTATTTTA ...........................................................GTCCCTTAGACCTGTTCTTTGGGAC............................................................................................... TransTerm Strand: - Conf: 55 HP_score: -4.2 Tail_Score: -3.78529 Start: 60 End: 84 Full_Region: taaaataaaaaaaaa gtcccaaaga acagg tctaagggac tcttttgctcgttct ...........................................................gtcccaaagaacaggtctaagggac............................................................................................... Find igs database================================================ Query_seq: PG2140:PG2141|PG2140:PG2141:ribosomal protein L32:3-oxoacyl-(acyl carrier protein) synthase:->->:2246460..2246638 179 aaattgcttgccctcggtcgatgccggtcgtcgcttaggcggcaagaacgagcaaaagagtcccttagacctgttctttgggactttttttttattttagcggccacaaataatcttttccggcgggatatggtctttaaaaagggccggtgcccgtccattatgcaacaaattcgatt Intra-Species Hit: Count: 1 Min: 1 Max: 179 Len: 179 Subject: NC_002950_PG2140_PG2141|ribosomal protein L32:3-oxoacyl-(acyl carrier protein) synthase|POSITIVE:POSITIVE|[2246460,2246638]|179 HSP 1 e-value: 4.0E-81 bit: 301.0 Len: 179 Query Start:1 Query End:179 Subject Strand: POSITIVE Subject Start: 1 Subject End: 179 aaattgcttgccctcggtcgatgccggtcgtcgcttaggcggcaagaacgagcaaaagagtcccttagacctgttctttgggacnnnnnnnnnattttagcggccacaaataatcttttccggcgggatatggtctttaaaaagggccggtgcccgtccattatgcaacaaattcgatt aaattgcttgccctcggtcgatgccggtcgtcgcttaggcggcaagaacgagcaaaagagtcccttagacctgttctttgggactttttttttattttagcggccacaaataatcttttccggcgggatatggtctttaaaaagggccggtgcccgtccattatgcaacaaattcgatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUGCUUGCCCUCGGUCGAUGCCGGUCGUCGCUUAGGCGGCAAGAACGAGCAAAAGAGUCCCUUAGACCUGUUCUUUGGGACUUUUUUUUUAUUUUAGCGGCCACAAAUAAUCUUUUCCGGCGGGAUAUGGUCUUUAAAAAGGGCCGGUGCCCGUCCAUUAUGCAACAAAUUCGAUU ...((((..((...((..((....))..))..))...(((.((.((((..((.(((((((((((..(((.....)))..)))))))))))))..)))).)).)))................((((((...(((((((.....)))))))...))))))......))))........... (-60.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUCGAAUUUGUUGCAUAAUGGACGGGCACCGGCCCUUUUUAAAGACCAUAUCCCGCCGGAAAAGAUUAUUUGUGGCCGCUAAAAUAAAAAAAAAGUCCCAAAGAACAGGUCUAAGGGACUCUUUUGCUCGUUCUUGCCGCCUAAGCGACGACCGGCAUCGACCGAGGGCAAGCAAUUU ..........(((((.....((((((((..(((((.....((((.......(((....)))........)))).)))))..........((((.((((((..(((.....)))..)))))).)))))))))))).....((((...((.(((......)))..)).))))..))))).. (-46.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 427 50 4 208 143 NC_002950:PG2199|5end_ABC_transporter,_ATP-binding_protein,_putative_2306723..2306953_NEGATIVE 420 47 8 155 115 NC_002950:PG2116|5end_hypothetical_protein_2224635..2224865_POSITIVE 413 158 111 47 6 NC_002950:PG1289|5end_GDP-fucose_synthetase_1367041..1367271_POSITIVE 407 47 7 63 19 NC_002950:PG1621|5end_hypothetical_protein_1701431..1701661_NEGATIVE 406 47 8 126 91 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 404 54 11 142 79 NC_002950:PG0326|5end_hypothetical_protein_360974..361204_NEGATIVE 403 49 5 218 163 NC_002950:PG0325|5end_hypothetical_protein_359714..359944_NEGATIVE 393 59 12 224 169 NC_002950:PG1743|5end_2-dehydro-3-deoxyphosphooctonate_aldolase_1828348..1828578_NEGATIVE 393 60 11 206 142 NC_002950:PG0899|5end_cytochrome_d_ubiquinol_oxidase,_subunit_II_964660..964890_NEGATIVE 392 43 3 222 178 NC_002950:PG1259|5end_anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_1335465..1335695_NEGATIVE 386 44 5 50 2 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 384 49 4 170 122 NC_002950:PG1132|5end_valyl-tRNA_synthetase_1210912..1211142_POSITIVE 382 44 9 39 1 NC_002950:PG1479|5end_conjugative_transposon_protein_TraJ_1555234..1555464_NEGATIVE 378 44 6 218 170 NC_002950:PG2189|5end_aspartate_kinase_2297151..2297381_NEGATIVE 378 44 6 187 143 NC_002950:PG1588|5end_hypothetical_protein_1666532..1666762_NEGATIVE 376 53 13 169 126 NC_002950:PG0423|5end_hypothetical_protein_462251..462481_POSITIVE 375 50 5 65 13 NC_002950:PG1483|5end_conjugative_transposon_protein_TraE_1559085..1559315_NEGATIVE 372 43 6 60 6 NC_002950:PG0660|5end_nitroreductase_family_protein_709695..709925_NEGATIVE 370 50 9 102 58 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 370 60 15 122 72 NC_002950:PG0018|5end_hypothetical_protein_19648..19878_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 413 158 111 54 13 NC_002950:PG1288|3end_GDP-mannose_4,6-dehydratase_1367128..1367278_POSITIVE 407 47 7 76 32 NC_002950:PG1622|3end_DNA_topoisomerase_IV_subunit_A_1701418..1701568_NEGATIVE 406 47 8 145 110 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 395 159 114 151 105 NC_002950:PG0052|3end_sensor_histidine_kinase_64686..64836_POSITIVE 392 56 11 148 96 NC_002950:PG1743|3end_2-dehydro-3-deoxyphosphooctonate_aldolase_1827530..1827680_NEGATIVE 392 67 23 93 34 NC_002950:PG1723|3end_ribosomal_protein_S20_1813403..1813553_POSITIVE 391 47 7 71 15 NC_002950:PG1330|3end_large_conductance_mechanosensitive_channel_protein_1410165..1410315_POSITIVE 378 44 6 126 82 NC_002950:PG1589|3end_dihydropteroate_synthase_1666593..1666743_NEGATIVE 372 53 11 148 94 NC_002950:PG2091|3end_dihydroneopterin_aldolase_2191610..2191760_POSITIVE 372 43 6 63 9 NC_002950:PG0661|3end_hypothetical_protein_709692..709842_NEGATIVE 371 69 33 45 1 NC_002950:PG0775|3end_acyl-CoA_dehydrogenase_family_protein_827432..827582_NEGATIVE 370 60 15 118 68 NC_002950:PG0017|3end_sensor_histidine_kinase_19724..19874_POSITIVE 363 54 12 75 27 NC_002950:PG0380|3end_excinuclease_ABC_subunit_B_411218..411368_POSITIVE 363 167 122 61 18 NC_002950:PG0321|3end_arginine/ornithine_transport_system_ATPase_355759..355909_POSITIVE 362 48 1 108 69 NC_002950:PG0199|3end_TatD_family_protein_237424..237574_NEGATIVE 361 43 3 88 41 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 358 46 4 84 40 NC_002950:PG2140|3end_ribosomal_protein_L32_2246399..2246549_POSITIVE 354 40 6 64 33 NC_002950:PG1739|3end_hypothetical_protein_1825128..1825278_NEGATIVE 350 165 121 121 71 NC_002950:PG1218|3end_hypothetical_protein_1296475..1296625_POSITIVE 349 45 6 48 1 NC_002950:PG0413|3end_hypothetical_protein_451437..451587_NEGATIVE