Origin IGS: ctctcttgtcttctgccaaaaggtcgggtctgtcaaaacgtctagacctttcgcgaaaaacgtctagacgtttgcttcgatacgtctagacgtttcagtcaaaacgtctagacgtttttgtcggaacgtctagacgttttttcgggtacgtccgtccgttccgttcgcaagggcttgtcgtaccccctcggaggctctgtccgttccgcccc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggggcggaacggacagagcctccgagggggtacgacaagcccttgcgaacggaacggacggacgtacccgaaaaaacgtctagacgttccgacaaaaacgtctagacgttttgactgaaacgtctagacgtatcgaagcaaacgtctagacgtttttcgcgaaaggtctagacgttttgacagacccgaccttttggcagaagacaagagag Mask Tandem Repeat Region ================================================ ctctcttgtcttctgccaaaaggtcgggtctgtcaaaacgtctagacctttcgcgaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngtacgtccgtccgttccgttcgcaagggcttgtcgtaccccctcggaggctctgtccgttccgcccc Find is-nt database================================================ Query_seq: PG0144:PG0145|PG0144:PG0145:hypothetical protein:hypothetical protein:<-->:167759..167970 212 ctctcttgtcttctgccaaaaggtcgggtctgtcaaaacgtctagacctttcgcgaaaaacgtctagacgtttgcttcgatacgtctagacgtttcagtcaaaacgtctagacgtttttgtcggaacgtctagacgttttttcgggtacgtccgtccgttccgttcgcaagggcttgtcgtaccccctcggaggctctgtccgttccgcccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0144:PG0145|PG0144:PG0145:hypothetical protein:hypothetical protein:<-->:167759..167970 212 ctctcttgtcttctgccaaaaggtcgggtctgtcaaaacgtctagacctttcgcgaaaaacgtctagacgtttgcttcgatacgtctagacgtttcagtcaaaacgtctagacgtttttgtcggaacgtctagacgttttttcgggtacgtccgtccgttccgttcgcaagggcttgtcgtaccccctcggaggctctgtccgttccgcccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0144:PG0145|PG0144:PG0145:hypothetical protein:hypothetical protein:<-->:167759..167970 212 ctctcttgtcttctgccaaaaggtcgggtctgtcaaaacgtctagacctttcgcgaaaaacgtctagacgtttgcttcgatacgtctagacgtttcagtcaaaacgtctagacgtttttgtcggaacgtctagacgttttttcgggtacgtccgtccgttccgttcgcaagggcttgtcgtaccccctcggaggctctgtccgttccgcccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctctcttgtcttctgccaaaaggtcgggtctgtcaaaacgtctagacctttcgcgaaaaacgtctagacgtttgcttcgatacgtctagacgtttcagtcaaaacgtctagacgtttttgtcggaacgtctagacgttttttcgggtacgtccgtccgttccgttcgcaagggcttgtcgtaccccctcggaggctctgtccgttccgcccc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 118 End: 210 ..................................................................................................................... M S E R L D V F S G T S V R S V R K G L S Y P L G G S V R S A .. ctctcttgtcttctgccaaaaggtcgggtctgtcaaaacgtctagacctttcgcgaaaaacgtctagacgtttgcttcgatacgtctagacgtttcagtcaaaacgtctagacgtttttgtcggaacgtctagacgttttttcgggtacgtccgtccgttccgttcgcaagggcttgtcgtaccccctcggaggctctgtccgttccgcccc 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================================================ ctctcttgtcttctgccaaaaggtcgggtctgtcaaaacgtctagacctttcgcgaaaaacgtctagacgtttgcttcgatacgtctagacgtttcagtcaaaacgtctagacgtttttgtcggaacgtctagacgttttttcgggtacgtccgtccgttccgttcgcaagggcttgtcgtaccccctcggaggctctgtccgttccgcccc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 82 HP_score: -10.3 Tail_Score: -3.93556 Start: 39 End: 70 Full_Region: TCGGGTCTGTCAAAA CGTCTAGACCTTT CGCGAA AAACGTCTAGACG TTTGCTTCGATACGT ......................................CGTCTAGACCTTTCGCGAAAAACGTCTAGACG.............................................................................................................................................. TransTerm Strand: - Conf: 86 HP_score: -11.0 Tail_Score: -4.07568 Start: 39 End: 70 Full_Region: acgtatcgaagcaaa cgtctagacgtttt tcgc gaaaggtctagacg ttttgacagacccga ......................................cgtctagacgtttttcgcgaaaggtctagacg.............................................................................................................................................. TransTerm Strand: + Conf: 86 HP_score: -13.2 Tail_Score: -3.64822 Start: 61 End: 92 Full_Region: ACCTTTCGCGAAAAA CGTCTAGACGTTTG CTT CGATACGTCTAGACG TTTCAGTCAAAACGT ............................................................CGTCTAGACGTTTGCTTCGATACGTCTAGACG........................................................................................................................ TransTerm Strand: - Conf: 100 HP_score: -11.7 Tail_Score: -4.56775 Start: 61 End: 92 Full_Region: acgttttgactgaaa cgtctagacgtat cgaagc aaacgtctagacg tttttcgcgaaaggt ............................................................cgtctagacgtatcgaagcaaacgtctagacg........................................................................................................................ TransTerm Strand: + Conf: 100 HP_score: -17.7 Tail_Score: -5.05782 Start: 83 End: 136 Full_Region: ACGTTTGCTTCGATA CGTCTAGACGTTTCAGTCAAAACGT CTAG ACGTTTTTGTCGGAACGTCTAGACG TTTTTTCGGGTACGT ..................................................................................CGTCTAGACGTTTCAGTCAAAACGTCTAGACGTTTTTGTCGGAACGTCTAGACG............................................................................ TransTerm Strand: - Conf: 100 HP_score: -13.2 Tail_Score: -4.18197 Start: 105 End: 136 Full_Region: acgtacccgaaaaaa cgtctagacgtt ccgacaaa aacgtctagacg ttttgactgaaacgt ........................................................................................................cgtctagacgttccgacaaaaacgtctagacg............................................................................ Find igs database================================================ Query_seq: PG0144:PG0145|PG0144:PG0145:hypothetical protein:hypothetical protein:<-->:167759..167970 212 ctctcttgtcttctgccaaaaggtcgggtctgtcaaaacgtctagacctttcgcgaaaaacgtctagacgtttgcttcgatacgtctagacgtttcagtcaaaacgtctagacgtttttgtcggaacgtctagacgttttttcgggtacgtccgtccgttccgttcgcaagggcttgtcgtaccccctcggaggctctgtccgttccgcccc Intra-Species Hit: Count: 2 Min: 1 Max: 212 Len: 212 Subject: NC_002950_PG0144_PG0145|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[167759,167970]|212 HSP 1 e-value: 1.0E-117 bit: 420.0 Len: 212 Query Start:1 Query End:212 Subject Strand: POSITIVE Subject Start: 1 Subject End: 212 ctctcttgtcttctgccaaaaggtcgggtctgtcaaaacgtctagacctttcgcgaaaaacgtctagacgtttgcttcgatacgtctagacgtttcagtcaaaacgtctagacgtttttgtcggaacgtctagacgttttttcgggtacgtccgtccgttccgttcgcaagggcttgtcgtaccccctcggaggctctgtccgttccgcccc ctctcttgtcttctgccaaaaggtcgggtctgtcaaaacgtctagacctttcgcgaaaaacgtctagacgtttgcttcgatacgtctagacgtttcagtcaaaacgtctagacgtttttgtcggaacgtctagacgttttttcgggtacgtccgtccgttccgttcgcaagggcttgtcgtaccccctcggaggctctgtccgttccgcccc Subject: NC_002950_PG0330_PG0332|DNA-binding protein, histone-like family:transcription termination factor Rho|NEGATIVE:POSITIVE|[365084,365758]|675 HSP 1 e-value: 2.0E-12 bit: 73.8 Len: 85 Query Start:56 Query End:140 Subject Strand: NEGATIVE Subject Start: 96 Subject End: 180 .......................................................aaaaacgtctagacgtttgcttcgatacgtctagacgtttcagtcaaaacgtctagacgtttttgtcggaacgtctagacgtttt........................................................................ .......................................................aaaaacgtctagacgttttgcccgaaacgtctagaccttttgctcgaaacgtctagacgttttattcggaacgtctagacgtttt........................................................................ HSP 2 e-value: 8.0E-12 bit: 71.9 Len: 108 Query Start:35 Query End:142 Subject Strand: NEGATIVE Subject Start: 72 Subject End: 179 ..................................aaaacgtctagacctttcgcgaaaaacgtctagacgtttgcttcgatacgtctagacgtttcagtcaaaacgtctagacgtttttgtcggaacgtctagacgtttttt...................................................................... ..................................aaaacgtctagacgttttgcccgaaacgtctagaccttttgctcgaaacgtctagacgttttattcggaacgtctagacgttttcctccgaacgtccagacgtttttt...................................................................... HSP 3 e-value: 1.0E-7 bit: 58.0 Len: 85 Query Start:35 Query End:119 Subject Strand: POSITIVE Subject Start: 96 Subject End: 180 ..................................aaaacgtctagacctttcgcgaaaaacgtctagacgtttgcttcgatacgtctagacgtttcagtcaaaacgtctagacgttttt............................................................................................. ..................................aaaacgtctagacgttccgaataaaacgtctagacgtttcgagcaaaaggtctagacgtttcgggcaaaacgtctagacgttttt............................................................................................. HSP 4 e-value: 2.0E-6 bit: 54.0 Len: 63 Query Start:82 Query End:144 Subject Strand: POSITIVE Subject Start: 121 Subject End: 183 .................................................................................acgtctagacgtttcagtcaaaacgtctagacgtttttgtcggaacgtctagacgttttttcg.................................................................... .................................................................................acgtctagacgtttcgagcaaaaggtctagacgtttcgggcaaaacgtctagacgttttttcg.................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUCUUGUCUUCUGCCAAAAGGUCGGGUCUGUCAAAACGUCUAGACCUUUCGCGAAAAACGUCUAGACGUUUGCUUCGAUACGUCUAGACGUUUCAGUCAAAACGUCUAGACGUUUUUGUCGGAACGUCUAGACGUUUUUUCGGGUACGUCCGUCCGUUCCGUUCGCAAGGGCUUGUCGUACCCCCUCGGAGGCUCUGUCCGUUCCGCCCC ..............((.....((.(((((((...(((((((((((((.(((((..((((((((((((((((((.....((.((((....)))).)).....))))))))))))))))))..))))).)))))))))))))...(((((((.(.((((.............))))..).)))))))......)))).))).)).....))... (-84.42) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGGCGGAACGGACAGAGCCUCCGAGGGGGUACGACAAGCCCUUGCGAACGGAACGGACGGACGUACCCGAAAAAACGUCUAGACGUUCCGACAAAAACGUCUAGACGUUUUGACUGAAACGUCUAGACGUAUCGAAGCAAACGUCUAGACGUUUUUCGCGAAAGGUCUAGACGUUUUGACAGACCCGACCUUUUGGCAGAAGACAAGAGAG (((.((.((.((...(.(((((....))))).)......)).)).))..(((((((...((((((..........))))))...)))))))...(((((((((((((.(((((...(((((((((((((((..........)))))))))))))))...))))).)))))))))))))......)))...((((((........)))))).. (-88.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 976 70 21 161 112 NC_002950:PG0144|5end_hypothetical_protein_167668..167898_NEGATIVE 500 148 101 231 187 NC_002950:PG0330|5end_DNA-binding_protein,_histone-like_family_364993..365223_NEGATIVE 429 199 151 215 146 NC_002950:PG1495|5end_DNA_topoisomerase_III_1571243..1571473_POSITIVE 427 210 161 231 186 NC_002950:PG1392|5end_rod_shape-determining_protein_RodA,_putative_1474416..1474646_NEGATIVE 427 197 152 178 126 NC_002950:PG0444|5end_oligopeptide_transporter,_OPT_family_483256..483486_POSITIVE 412 186 141 67 10 NC_002950:PG0021|5end_TIM-barrel_protein,_putative,_NifR3_family_25123..25353_NEGATIVE 409 210 161 84 22 NC_002950:PG0930|5end_hypothetical_protein_987542..987772_NEGATIVE 407 200 151 146 99 NC_002950:PG0657|5end_Maf-like_protein_707782..708012_NEGATIVE 405 210 161 205 144 NC_002950:PG0053|5end_hypothetical_protein_65086..65316_NEGATIVE 404 210 161 209 163 NC_002950:PG1952|5end_DedA_family_protein_2042870..2043100_POSITIVE 401 198 151 197 133 NC_002950:PG2061|5end_dihydrofolate_reductase_2158422..2158652_POSITIVE 398 210 171 58 2 NC_002950:PG1693|5end_HesA/MoeB/ThiF_family_protein_1777919..1778149_NEGATIVE 395 184 143 217 174 NC_002950:PG2155|5end_lipoprotein,_putative_2261862..2262092_NEGATIVE 394 190 141 56 14 NC_002950:PG1758|5end_ribosomal_protein_S15_1845185..1845415_POSITIVE 393 209 162 230 171 NC_002950:PG0961|5end_hypothetical_protein_1022272..1022502_NEGATIVE 392 206 161 117 51 NC_002950:PG2052|5end_dihydrodipicolinate_synthase_2149636..2149866_POSITIVE 392 209 161 119 54 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 391 199 151 210 151 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 389 192 151 183 134 NC_002950:PG1248|5end_hypothetical_protein_1326532..1326762_NEGATIVE 388 208 162 195 146 NC_002950:PG1621|5end_hypothetical_protein_1701431..1701661_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 482 210 162 51 3 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 429 199 151 126 57 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 422 180 135 56 3 NC_002950:PG1484|3end_hypothetical_protein_1559275..1559425_NEGATIVE 416 200 152 146 98 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 414 210 167 61 1 NC_002950:PG1694|3end_hypothetical_protein_1777916..1778066_NEGATIVE 412 186 141 70 13 NC_002950:PG0022|3end_sulfate_permease_family_protein_25120..25270_NEGATIVE 411 200 151 94 36 NC_002950:PG0915|3end_hypothetical_protein_977057..977207_POSITIVE 407 200 151 130 83 NC_002950:PG0658|3end_phosphatase,_YrbI_family_707798..707948_NEGATIVE 401 198 151 151 87 NC_002950:PG2060|3end_thymidylate_synthase_2158456..2158606_POSITIVE 397 209 161 65 19 NC_002950:PG0334|3end_glycosyl_transferase,_group_2_family_protein_368792..368942_NEGATIVE 392 209 161 138 73 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 389 193 152 137 98 NC_002950:PG2040|3end_DNA-binding_protein,_histone-like_family_2138398..2138548_NEGATIVE 386 210 161 120 74 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 385 209 164 68 9 NC_002950:PG1649|3end_hypothetical_protein_1730030..1730180_NEGATIVE 383 200 154 151 96 NC_002950:PG0747|3end_sigma-54_dependent_DNA-binding_response_regulator_793900..794050_NEGATIVE 382 208 169 143 95 NC_002950:PG2086|3end_hypothetical_protein_2187070..2187220_POSITIVE 382 210 161 141 65 NC_002950:PG1218|3end_hypothetical_protein_1296475..1296625_POSITIVE 382 210 161 75 15 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 381 210 161 62 20 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 379 210 162 151 95 NC_002950:PG1560|3end_dTDP-glucose_4,6-dehydratase_1639067..1639217_NEGATIVE