Origin IGS: tccgaagaaacagcgatagataaagcgagaggggtgacaaacccgaagcaaagcaggctgttgcagccattatgcttctcgggtttatctctcctctcgtttgcttatacgtctcgtcgcggccgaaaagacgc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gcgtcttttcggccgcgacgagacgtataagcaaacgagaggagagataaacccgagaagcataatggctgcaacagcctgctttgcttcgggtttgtcacccctctcgctttatctatcgctgtttcttcgga Mask Tandem Repeat Region ================================================ tccgaagaaacagcgatagataaagcgagaggggtgacaaacccgaagcaaagcaggctgttgcagccattatgcttctcgggtttatctctcctctcgtttgcttatacgtctcgtcgcggccgaaaagacgc Find is-nt database================================================ Query_seq: PG2205:PG2206|PG2205:PG2206:2-dehydropantoate 2-reductase:ABC transporter, ATP-binding protein:-><-:2317206..2317339 134 tccgaagaaacagcgatagataaagcgagaggggtgacaaacccgaagcaaagcaggctgttgcagccattatgcttctcgggtttatctctcctctcgtttgcttatacgtctcgtcgcggccgaaaagacgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2205:PG2206|PG2205:PG2206:2-dehydropantoate 2-reductase:ABC transporter, ATP-binding protein:-><-:2317206..2317339 134 tccgaagaaacagcgatagataaagcgagaggggtgacaaacccgaagcaaagcaggctgttgcagccattatgcttctcgggtttatctctcctctcgtttgcttatacgtctcgtcgcggccgaaaagacgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2205:PG2206|PG2205:PG2206:2-dehydropantoate 2-reductase:ABC transporter, ATP-binding protein:-><-:2317206..2317339 134 tccgaagaaacagcgatagataaagcgagaggggtgacaaacccgaagcaaagcaggctgttgcagccattatgcttctcgggtttatctctcctctcgtttgcttatacgtctcgtcgcggccgaaaagacgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccgaagaaacagcgatagataaagcgagaggggtgacaaacccgaagcaaagcaggctgttgcagccattatgcttctcgggtttatctctcctctcgtttgcttatacgtctcgtcgcggccgaaaagacgc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 16 End: 132 ............... M D K A R G V T N P K Q S R L L Q P L C F S G L S L L S F A Y T S R R G R K D .. tccgaagaaacagcgatagataaagcgagaggggtgacaaacccgaagcaaagcaggctgttgcagccattatgcttctcgggtttatctctcctctcgtttgcttatacgtctcgtcgcggccgaaaagacgc 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================================================ tccgaagaaacagcgatagataaagcgagaggggtgacaaacccgaagcaaagcaggctgttgcagccattatgcttctcgggtttatctctcctctcgtttgcttatacgtctcgtcgcggccgaaaagacgc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG2205:PG2206|PG2205:PG2206:2-dehydropantoate 2-reductase:ABC transporter, ATP-binding protein:-><-:2317206..2317339 134 tccgaagaaacagcgatagataaagcgagaggggtgacaaacccgaagcaaagcaggctgttgcagccattatgcttctcgggtttatctctcctctcgtttgcttatacgtctcgtcgcggccgaaaagacgc Intra-Species Hit: Count: 1 Min: 1 Max: 134 Len: 134 Subject: NC_002950_PG2205_PG2206|2-dehydropantoate 2-reductase:ABC transporter, ATP-binding protein|POSITIVE:NEGATIVE|[2317206,2317339]|134 HSP 1 e-value: 2.0E-70 bit: 266.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 134 tccgaagaaacagcgatagataaagcgagaggggtgacaaacccgaagcaaagcaggctgttgcagccattatgcttctcgggtttatctctcctctcgtttgcttatacgtctcgtcgcggccgaaaagacgc tccgaagaaacagcgatagataaagcgagaggggtgacaaacccgaagcaaagcaggctgttgcagccattatgcttctcgggtttatctctcctctcgtttgcttatacgtctcgtcgcggccgaaaagacgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCGAAGAAACAGCGAUAGAUAAAGCGAGAGGGGUGACAAACCCGAAGCAAAGCAGGCUGUUGCAGCCAUUAUGCUUCUCGGGUUUAUCUCUCCUCUCGUUUGCUUAUACGUCUCGUCGCGGCCGAAAAGACGC ...........(((((........((((((((((.((.((((((((((((.....(((((...)))))....))))..)))))))).)).)))))))))))))))....(((((..(((....)))..))))). (-53.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGUCUUUUCGGCCGCGACGAGACGUAUAAGCAAACGAGAGGAGAGAUAAACCCGAGAAGCAUAAUGGCUGCAACAGCCUGCUUUGCUUCGGGUUUGUCACCCCUCUCGCUUUAUCUAUCGCUGUUUCUUCGGA (((((((.(((....))).)))))))...(((((((((((((.(.(((((((((((..((((....(((((...))))).....))))))))))))))).).))))))).))).......)))...((....)) (-55.41) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 401 75 31 65 12 NC_002950:PG1335|5end_hypothetical_protein_1416894..1417124_NEGATIVE 397 130 81 77 22 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 373 120 72 196 155 NC_002950:PG0335|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_370706..370936_NEGATIVE 367 122 90 139 101 NC_002950:PG1665|5end_ABC_transporter,_permease_protein,_putative_1747110..1747340_POSITIVE 367 45 1 160 115 NC_002950:PG1419|5end_ISPg5,_transposase_Orf1_1504997..1505227_POSITIVE 365 90 42 101 48 NC_002950:PG0172|5end_exonuclease_193493..193723_POSITIVE 363 69 27 192 148 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 360 120 75 170 135 NC_002950:PG0058|5end_nicotinic_acid_mononucleotide_adenyltransferase_70919..71149_POSITIVE 359 89 43 54 6 NC_002950:PG1391|5end_hypothetical_protein_1471670..1471900_POSITIVE 359 89 42 56 6 NC_002950:PG0898|5end_hypothetical_protein_963350..963580_NEGATIVE 355 125 81 228 165 NC_002950:PG0365|5end_3'-5'_exonuclease_domain_protein_400178..400408_NEGATIVE 353 126 81 175 118 NC_002950:PG1327|5end_aminotransferase,_putative_1406580..1406810_NEGATIVE 352 126 81 200 148 NC_002950:PG2037|5end_hypothetical_protein_2137812..2138042_NEGATIVE 352 49 2 222 171 NC_002950:PG1663|5end_ABC_transporter,_ATP-binding_protein_1745129..1745359_POSITIVE 347 68 22 135 85 NC_002950:PG1029|5end_hypothetical_protein_1091080..1091310_POSITIVE 345 100 53 122 73 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 341 97 55 95 49 NC_002950:PG1549|5end_hypothetical_protein_1627947..1628177_NEGATIVE 335 100 51 112 41 NC_002950:PG1706|5end_hypothetical_protein_1794211..1794441_NEGATIVE 335 79 31 101 38 NC_002950:PG0272|5end_CBS_domain_protein_304399..304629_POSITIVE 335 119 74 60 9 NC_002950:PG0143|5end_hydrolase,_carbon-nitrogen_family_166625..166855_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 510 99 51 65 14 NC_002950:PG2205|3end_2-dehydropantoate_2-reductase_2317145..2317295_POSITIVE 397 130 81 64 9 NC_002950:PG1253|3end_DNA_ligase,_NAD-dependent_1329597..1329747_NEGATIVE 367 122 90 116 78 NC_002950:PG1664|3end_ABC_transporter,_permease_protein,_putative_1747167..1747317_POSITIVE 365 90 42 104 51 NC_002950:PG0171|3end_5'-nucleotidase_family_protein_193576..193726_POSITIVE 355 125 81 151 88 NC_002950:PG0366|3end_hypothetical_protein_400255..400405_NEGATIVE 353 126 81 132 75 NC_002950:PG1328|3end_CoA_ligase_family_protein_1406623..1406773_NEGATIVE 349 123 91 109 76 NC_002950:PG1600|3end_hypothetical_protein_1679959..1680109_NEGATIVE 347 68 22 71 21 NC_002950:PG1028|3end_TPR_domain_protein_1091096..1091246_POSITIVE 345 100 53 108 59 NC_002950:PG2099|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2206649..2206799_NEGATIVE 340 85 43 107 63 NC_002950:PG1761|3end_acetyltransferase,_GNAT_family_1847739..1847889_POSITIVE 335 100 51 91 20 NC_002950:PG1707|3end_hypothetical_protein_1794232..1794382_NEGATIVE 333 130 81 76 12 NC_002950:PG1484|3end_hypothetical_protein_1559275..1559425_NEGATIVE 332 119 73 124 83 NC_002950:PG0615|3end_GTP-binding_protein_TypA_668912..669062_POSITIVE 326 68 22 59 20 NC_002950:PG0775|3end_acyl-CoA_dehydrogenase_family_protein_827432..827582_NEGATIVE 320 60 12 65 8 NC_002950:PG1294|3end_ferrous_iron_transport_protein_B_1374661..1374811_POSITIVE 319 62 25 80 33 NC_002950:PG2097|3end_ribose-phosphate_pyrophosphokinase_2205521..2205671_NEGATIVE 319 69 24 60 6 NC_002950:PG2001|3end_signal_peptidase_I_2089458..2089608_NEGATIVE 317 58 12 148 95 NC_002950:PG0017|3end_sensor_histidine_kinase_19724..19874_POSITIVE 316 68 22 38 4 NC_002950:PG0315|3end_50S_ribosomal_protein_L27_348417..348567_POSITIVE 311 58 14 86 38 NC_002950:PG1585|3end_batD_protein_1664137..1664287_POSITIVE