Origin IGS: attggatcttgtggccgaacagtggatgactatatatttgatggtattcattgttttggatgttgatagatgaaaaaattaaacccattatagaaagacaaaggccggagacaaaagcaaatttccttgtctccggccttccgattagattcccgtccctgctcgaatacaggaggaatacggatcagaa .........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 ttctgatccgtattcctcctgtattcgagcagggacgggaatctaatcggaaggccggagacaaggaaatttgcttttgtctccggcctttgtctttctataatgggtttaattttttcatctatcaacatccaaaacaatgaataccatcaaatatatagtcatccactgttcggccacaagatccaat Mask Tandem Repeat Region ================================================ attggatcttgtggccgaacagtggatgactatatatttgatggtattcattgttttggatgttgatagatgaaaaaattaaacccattatagaaagacaaaggccggagacaaaagcaaatttccttgtctccggccttccgattagattcccgtccctgctcgaatacaggaggaatacggatcagaa Find is-nt database================================================ Query_seq: PG2038:PG2040|PG2038:PG2040:N-acetylmuramoyl-L-alanine amidase, putative:DNA-binding protein, histone-like family:<-<-:2138298..2138487 190 attggatcttgtggccgaacagtggatgactatatatttgatggtattcattgttttggatgttgatagatgaaaaaattaaacccattatagaaagacaaaggccggagacaaaagcaaatttccttgtctccggccttccgattagattcccgtccctgctcgaatacaggaggaatacggatcagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2038:PG2040|PG2038:PG2040:N-acetylmuramoyl-L-alanine amidase, putative:DNA-binding protein, histone-like family:<-<-:2138298..2138487 190 attggatcttgtggccgaacagtggatgactatatatttgatggtattcattgttttggatgttgatagatgaaaaaattaaacccattatagaaagacaaaggccggagacaaaagcaaatttccttgtctccggccttccgattagattcccgtccctgctcgaatacaggaggaatacggatcagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2038:PG2040|PG2038:PG2040:N-acetylmuramoyl-L-alanine amidase, putative:DNA-binding protein, histone-like family:<-<-:2138298..2138487 190 attggatcttgtggccgaacagtggatgactatatatttgatggtattcattgttttggatgttgatagatgaaaaaattaaacccattatagaaagacaaaggccggagacaaaagcaaatttccttgtctccggccttccgattagattcccgtccctgctcgaatacaggaggaatacggatcagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 attggatcttgtggccgaacagtggatgactatatatttgatggtattcattgttttggatgttgatagatgaaaaaattaaacccattatagaaagacaaaggccggagacaaaagcaaatttccttgtctccggccttccgattagattcccgtccctgctcgaatacaggaggaatacggatcagaa Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 51 End: 188 .................................................. M F W M L I D E K I K P I I E R Q R P E T K A N F L V S G L P I R F P S L L E Y R R N T D Q .. Protein_Len: 46 Strand: - Start: 51 End: 188 .................................................. Q K P H Q Y I F F N F G N Y F S L P R L C F C I E K D G A K R N S E R G Q E F V P P I R I M .. Protein_Len: 57 Strand: - Start: 2 End: 172 . Q I K H G F L P H S Y I Q H Y E N N Q I N I S S F I L G M I S L C L G S V F A F K R T E P R G I L N G D R S S Y M .................. attggatcttgtggccgaacagtggatgactatatatttgatggtattcattgttttggatgttgatagatgaaaaaattaaacccattatagaaagacaaaggccggagacaaaagcaaatttccttgtctccggccttccgattagattcccgtccctgctcgaatacaggaggaatacggatcagaa Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 62 End: 91 .............................................................GTTGATAGATGAAAAAATTAAACCCATTAT................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ attggatcttgtggccgaacagtggatgactatatatttgatggtattcattgttttggatgttgatagatgaaaaaattaaacccattatagaaagacaaaggccggagacaaaagcaaatttccttgtctccggccttccgattagattcccgtccctgctcgaatacaggaggaatacggatcagaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 46 HP_score: -3.1 Tail_Score: -3.18274 Start: 98 End: 144 Full_Region: ACCCATTATAGAAAG ACAAAGGCCGGAGACAA AAGCAAATTTCC TTGTCTCCGGCCTTCCGA TTAGATTCCCGTCCC .................................................................................................ACAAAGGCCGGAGACAAAAGCAAATTTCCTTGTCTCCGGCCTTCCGA.............................................. TransTerm Strand: - Conf: 100 HP_score: -13.4 Tail_Score: -4.43283 Start: 103 End: 138 Full_Region: ggaatctaatcggaa ggccggagacaaggaa att tgcttttgtctccggcc tttgtctttctataa ......................................................................................................ggccggagacaaggaaatttgcttttgtctccggcc.................................................... Find igs database================================================ Query_seq: PG2038:PG2040|PG2038:PG2040:N-acetylmuramoyl-L-alanine amidase, putative:DNA-binding protein, histone-like family:<-<-:2138298..2138487 190 attggatcttgtggccgaacagtggatgactatatatttgatggtattcattgttttggatgttgatagatgaaaaaattaaacccattatagaaagacaaaggccggagacaaaagcaaatttccttgtctccggccttccgattagattcccgtccctgctcgaatacaggaggaatacggatcagaa Intra-Species Hit: Count: 1 Min: 1 Max: 190 Len: 190 Subject: NC_002950_PG2038_PG2040|N-acetylmuramoyl-L-alanine amidase, putative:DNA-binding protein, histone-like family|NEGATIVE:NEGATIVE|[2138298,2138487]|190 HSP 1 e-value: 1.0E-104 bit: 377.0 Len: 190 Query Start:1 Query End:190 Subject Strand: POSITIVE Subject Start: 1 Subject End: 190 attggatcttgtggccgaacagtggatgactatatatttgatggtattcattgttttggatgttgatagatgaaaaaattaaacccattatagaaagacaaaggccggagacaaaagcaaatttccttgtctccggccttccgattagattcccgtccctgctcgaatacaggaggaatacggatcagaa attggatcttgtggccgaacagtggatgactatatatttgatggtattcattgttttggatgttgatagatgaaaaaattaaacccattatagaaagacaaaggccggagacaaaagcaaatttccttgtctccggccttccgattagattcccgtccctgctcgaatacaggaggaatacggatcagaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGGAUCUUGUGGCCGAACAGUGGAUGACUAUAUAUUUGAUGGUAUUCAUUGUUUUGGAUGUUGAUAGAUGAAAAAAUUAAACCCAUUAUAGAAAGACAAAGGCCGGAGACAAAAGCAAAUUUCCUUGUCUCCGGCCUUCCGAUUAGAUUCCCGUCCCUGCUCGAAUACAGGAGGAAUACGGAUCAGAA ......(((.((((((((((((((((((.((((.......))))))))))))).))))).........(((......)))....))))...)))......((((((((((((((............))))))))))))))..((((..(((((....((((........)))).)))))...)))).... (-56.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUGAUCCGUAUUCCUCCUGUAUUCGAGCAGGGACGGGAAUCUAAUCGGAAGGCCGGAGACAAGGAAAUUUGCUUUUGUCUCCGGCCUUUGUCUUUCUAUAAUGGGUUUAAUUUUUUCAUCUAUCAACAUCCAAAACAAUGAAUACCAUCAAAUAUAUAGUCAUCCACUGUUCGGCCACAAGAUCCAAU .((((((..(.(((((((((((......)))))...)))))))..)))))).((((((((((((((........))))))))))))))...............(((((((..............................(((......))).....(((((.....))))).........))))))).. (-50.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 940 140 91 231 182 NC_002950:PG2038|5end_N-acetylmuramoyl-L-alanine_amidase,_putative_2138207..2138437_NEGATIVE 418 165 126 196 144 NC_002950:PG1057|5end_hypothetical_protein_1123419..1123649_POSITIVE 384 140 92 119 69 NC_002950:PG1029|5end_hypothetical_protein_1091080..1091310_POSITIVE 374 189 141 45 2 NC_002950:PG2063|5end_hypothetical_protein_2160596..2160826_NEGATIVE 372 180 135 69 9 NC_002950:PG1249|5end_1-acyl-sn-glycerol-3-phosphate_acetyltransferase,_putative_1327161..1327391_NEGATIVE 367 175 131 163 118 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 364 176 132 189 130 NC_002950:PG0200|5end_hypothetical_protein_238351..238581_NEGATIVE 361 136 92 87 38 NC_002950:PG0140|5end_hypothetical_protein_163858..164088_NEGATIVE 360 170 121 130 71 NC_002950:PG0563|5end_hypothetical_protein_621438..621668_NEGATIVE 354 182 153 189 157 NC_002950:PG2201|5end_peptide_deformylase_2309412..2309642_NEGATIVE 346 189 150 65 14 NC_002950:PG0509|5end_hypothetical_protein_549588..549818_NEGATIVE 342 140 93 173 124 NC_002950:PG0327|5end_hypothetical_protein_362061..362291_NEGATIVE 339 144 102 192 146 NC_002950:PG0163|5end_diphosphate--fructose-6-phosphate_1-phosphotransferase_186885..187115_NEGATIVE 335 167 125 211 158 NC_002950:PG1478|5end_conjugative_transposon_protein_TraK_1554116..1554346_NEGATIVE 334 166 121 165 122 NC_002950:PG0657|5end_Maf-like_protein_707782..708012_NEGATIVE 330 177 131 46 4 NC_002950:PG1754|5end_hypothetical_protein_1839679..1839909_POSITIVE 328 179 133 95 40 NC_002950:PG1270|5end_hypothetical_protein_1350207..1350437_NEGATIVE 326 176 131 176 133 NC_002950:PG0159|5end_endopeptidase_PepO_183164..183394_NEGATIVE 323 183 144 189 149 NC_002950:PG1466|5end_hypothetical_protein_1542623..1542853_POSITIVE 323 167 122 44 1 NC_002950:PG0790|5end_GTP-binding_protein_Obg_842583..842813_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 405 165 125 112 68 NC_002950:PG1881|3end_hypothetical_protein_1978046..1978196_POSITIVE 384 140 92 55 5 NC_002950:PG1028|3end_TPR_domain_protein_1091096..1091246_POSITIVE 361 136 92 67 18 NC_002950:PG0141|3end_spoOJ_protein_163878..164028_NEGATIVE 354 182 153 84 52 NC_002950:PG2202|3end_Holliday_junction_resolvase-like_protein_2309517..2309667_NEGATIVE 346 165 121 146 93 NC_002950:PG0564|3end_hypothetical_protein_621416..621566_NEGATIVE 345 165 124 86 36 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 342 140 93 79 30 NC_002950:PG0328|3end_imidazolonepropionase_362155..362305_NEGATIVE 337 178 131 145 101 NC_002950:PG1625|3end_hypothetical_protein_1708718..1708868_POSITIVE 334 166 121 149 106 NC_002950:PG0658|3end_phosphatase,_YrbI_family_707798..707948_NEGATIVE 332 180 135 65 14 NC_002950:PG1118|3end_clpB_protein_1192083..1192233_NEGATIVE 328 179 133 88 33 NC_002950:PG1271|3end_acetylornithine_aminotransferase,_putative_1350214..1350364_NEGATIVE 327 167 121 70 23 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 324 189 141 95 46 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE 317 148 102 70 21 NC_002950:PG1433|3end_hydrolase_1519126..1519276_POSITIVE 317 176 133 146 101 NC_002950:PG0222|3end_DNA-binding_protein,_histone-like_family_255913..256063_NEGATIVE 317 156 114 136 93 NC_002950:PG0160|3end_hypothetical_protein_183183..183333_NEGATIVE 316 178 131 70 31 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 316 189 154 48 5 NC_002950:PG0510|3end_hypothetical_protein_549605..549755_NEGATIVE 315 165 123 139 95 NC_002950:PG0745|3end_lactoylglutathione_lyase,_putative_791982..792132_NEGATIVE 309 176 133 124 78 NC_002950:PG0157|3end_regulatory_protein_RecX_180271..180421_POSITIVE