Origin IGS: agcaatcttggacgaggagaccgaaggcgtttgagcgcatcggaggcttttcggtctcttcccttggatagtgatgaagcaacgctatcgggagctatgccggcaagga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tccttgccggcatagctcccgatagcgttgcttcatcactatccaagggaagagaccgaaaagcctccgatgcgctcaaacgccttcggtctcctcgtccaagattgct Mask Tandem Repeat Region ================================================ agcaatcttggacgaggagaccgaaggcgtttgagcgcatcggaggcttttcggtctcttcccttggatagtgatgaagcaacgctatcgggagctatgccggcaagga Find is-nt database================================================ Query_seq: PG0881:PG0882|PG0881:PG0882:recombinase A:hypothetical protein:->->:944226..944334 109 agcaatcttggacgaggagaccgaaggcgtttgagcgcatcggaggcttttcggtctcttcccttggatagtgatgaagcaacgctatcgggagctatgccggcaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0881:PG0882|PG0881:PG0882:recombinase A:hypothetical protein:->->:944226..944334 109 agcaatcttggacgaggagaccgaaggcgtttgagcgcatcggaggcttttcggtctcttcccttggatagtgatgaagcaacgctatcgggagctatgccggcaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0881:PG0882|PG0881:PG0882:recombinase A:hypothetical protein:->->:944226..944334 109 agcaatcttggacgaggagaccgaaggcgtttgagcgcatcggaggcttttcggtctcttcccttggatagtgatgaagcaacgctatcgggagctatgccggcaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agcaatcttggacgaggagaccgaaggcgtttgagcgcatcggaggcttttcggtctcttcccttggatagtgatgaagcaacgctatcgggagctatgccggcaagga Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: - Start: 3 End: 98 .. L R P R P S R L R K L A D S A K R D R G K S L S S A V S D P A M ........... agcaatcttggacgaggagaccgaaggcgtttgagcgcatcggaggcttttcggtctcttcccttggatagtgatgaagcaacgctatcgggagctatgccggcaagga 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================================================ agcaatcttggacgaggagaccgaaggcgtttgagcgcatcggaggcttttcggtctcttcccttggatagtgatgaagcaacgctatcgggagctatgccggcaagga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0881:PG0882|PG0881:PG0882:recombinase A:hypothetical protein:->->:944226..944334 109 agcaatcttggacgaggagaccgaaggcgtttgagcgcatcggaggcttttcggtctcttcccttggatagtgatgaagcaacgctatcgggagctatgccggcaagga Intra-Species Hit: Count: 1 Min: 1 Max: 109 Len: 109 Subject: NC_002950_PG0881_PG0882|recombinase A:hypothetical protein|POSITIVE:POSITIVE|[944226,944334]|109 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 109 Query Start:1 Query End:109 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 agcaatcttggacgaggagaccgaaggcgtttgagcgcatcggaggcttttcggtctcttcccttggatagtgatgaagcaacgctatcgggagctatgccggcaagga agcaatcttggacgaggagaccgaaggcgtttgagcgcatcggaggcttttcggtctcttcccttggatagtgatgaagcaacgctatcgggagctatgccggcaagga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCAAUCUUGGACGAGGAGACCGAAGGCGUUUGAGCGCAUCGGAGGCUUUUCGGUCUCUUCCCUUGGAUAGUGAUGAAGCAACGCUAUCGGGAGCUAUGCCGGCAAGGA .....(((((...(((((((((((((((.(((((.....))))).)).)))))))))))))...((((((((..((((((...))).)))...))))).))).))))). (-42.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUUGCCGGCAUAGCUCCCGAUAGCGUUGCUUCAUCACUAUCCAAGGGAAGAGACCGAAAAGCCUCCGAUGCGCUCAAACGCCUUCGGUCUCCUCGUCCAAGAUUGCU ..((((..(((.....(((((((((.(.((...)).).)))))...)))).(((((((((..((....((.....))....)).)))))))))...)))))))...... (-28.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 457 68 26 214 154 NC_002950:PG1946|5end_ABC_3_transporter_family_protein_2032133..2032363_POSITIVE 404 60 14 82 13 NC_002950:PG1355|5end_acyltransferase,_putative_1435292..1435522_NEGATIVE 396 64 21 202 151 NC_002950:PG0076|5end_N-acetylmuramoyl-L-alanine_amidase,_family_4_91333..91563_NEGATIVE 393 42 1 215 166 NC_002950:PG1932|5end_ribosomal_protein_S3_2021610..2021840_NEGATIVE 392 70 22 201 144 NC_002950:PG0585|5end_YqeY_family_protein_643272..643502_POSITIVE 391 67 21 167 115 NC_002950:PG1593|5end_shikimate_kinase_1671503..1671733_POSITIVE 385 68 22 62 15 NC_002950:PG0634|5end_ThiJ/PfpI_family_protein_686143..686373_POSITIVE 379 57 13 107 67 NC_002950:PG1511|5end_hypothetical_protein_1587609..1587839_POSITIVE 377 67 22 204 156 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 376 69 26 64 23 NC_002950:PG0343|5end_methionine_gamma-lyase_378362..378592_NEGATIVE 374 60 11 167 130 NC_002950:PG1943|5end_hypothetical_protein_2030260..2030490_NEGATIVE 372 100 52 80 29 NC_002950:PG1602|5end_hypothetical_protein_1682144..1682374_NEGATIVE 372 58 11 156 109 NC_002950:PG1079|5end_enoyl-CoA_hydratase/isomerase_family_protein_1146549..1146779_POSITIVE 371 60 15 180 131 NC_002950:PG0598|5end_hypothetical_protein_654477..654707_POSITIVE 370 59 12 210 166 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 368 56 16 180 145 NC_002950:PG1476|5end_conjugative_transposon_protein_TraM_1553219..1553449_NEGATIVE 366 60 15 85 34 NC_002950:PG0648|5end_iron_compound_ABC_transporter,_periplasmic_iron_compound-binding_protein,_putative_701285..701515_NEGATIVE 364 60 12 218 176 NC_002950:PG0215|5end_hypothetical_protein_251460..251690_POSITIVE 361 48 2 71 9 NC_002950:PG1766|5end_phosphoribosylglycinamide_formyltransferase_1853417..1853647_POSITIVE 360 70 22 72 30 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 538 60 14 76 30 NC_002950:PG0881|3end_recombinase_A_944165..944315_POSITIVE 391 67 21 119 67 NC_002950:PG1592|3end_HDIG_domain_protein_1671535..1671685_POSITIVE 372 58 11 52 5 NC_002950:PG1078|3end_electron_transfer_flavoprotein,_alpha_subunit_1146525..1146675_POSITIVE 372 100 52 96 49 NC_002950:PG0933|3end_translation_elongation_factor_G,_putative_992236..992386_POSITIVE 368 55 14 57 17 NC_002950:PG1779|3end_hypothetical_protein_1868498..1868648_POSITIVE 367 48 8 65 19 NC_002950:PG1472|3end_hypothetical_protein_1549760..1549910_POSITIVE 363 55 11 145 100 NC_002950:PG0534|3end_hypothetical_protein_585805..585955_POSITIVE 360 70 22 67 25 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 356 57 11 78 35 NC_002950:PG0328|3end_imidazolonepropionase_362155..362305_NEGATIVE 355 60 11 136 74 NC_002950:PG1218|3end_hypothetical_protein_1296475..1296625_POSITIVE 354 78 34 129 73 NC_002950:PG1846|3end_hypothetical_protein_1946254..1946404_POSITIVE 354 64 21 123 65 NC_002950:PG1404|3end_rhomboid_family_protein_1487071..1487221_NEGATIVE 353 59 11 77 19 NC_002950:PG0459|3end_ISPg5,_transposase_Orf1_501517..501667_NEGATIVE 353 66 21 64 3 NC_002950:PG0046|3end_phosphatidate_cytidylyltransferase_56346..56496_NEGATIVE 352 80 35 56 5 NC_002950:PG0022|3end_sulfate_permease_family_protein_25120..25270_NEGATIVE 351 68 23 47 1 NC_002950:PG0633|3end_hypothetical_protein_686208..686358_POSITIVE 349 67 26 45 9 NC_002950:PG1101|3end_sodium:solute_symporter_family_protein_1169009..1169159_NEGATIVE 349 86 41 91 44 NC_002950:PG0061|3end_yngK_protein_73763..73913_POSITIVE 346 89 41 145 98 NC_002950:PG1559|3end_aminomethyltransferase_1637904..1638054_NEGATIVE 343 70 21 149 98 NC_002950:PG1600|3end_hypothetical_protein_1679959..1680109_NEGATIVE