Origin IGS: tgtatcactcctaaaagaaaaatcctacagacagataatcggtctgcaaaccacaggggggcttccttcttatcttaccggcatactttttctcgtaaatttttcatcggcctcagatgaatgtcttacgcaaaccgcagaaagaaacgtttttatctgacaccaatgattctgatgatcacagtttgcaagagagctgtttcctaaggaattagtttgccgatatgttttatttggtacctttgcgctggcaaaagatgcacctatgcatccaatgactgcagaacaagaaaaattactaataactaaccacttaaacattgttttctcag .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctgagaaaacaatgtttaagtggttagttattagtaatttttcttgttctgcagtcattggatgcataggtgcatcttttgccagcgcaaaggtaccaaataaaacatatcggcaaactaattccttaggaaacagctctcttgcaaactgtgatcatcagaatcattggtgtcagataaaaacgtttctttctgcggtttgcgtaagacattcatctgaggccgatgaaaaatttacgagaaaaagtatgccggtaagataagaaggaagcccccctgtggtttgcagaccgattatctgtctgtaggatttttcttttaggagtgataca Mask Tandem Repeat Region ================================================ tgtatcactcctaaaagaaaaatcctacagacagataatcggtctgcaaaccacaggggggcttccttcttatcttaccggcatactttttctcgtaaatttttcatcggcctcagatgaatgtcttacgcaaaccgcagaaagaaacgtttttatctgacaccaatgattctgatgatcacagtttgcaagagagctgtttcctaaggaattagtttgccgatatgttttatttggtacctttgcgctggcaaaagatgcacctatgcatccaatgactgcagaacaagaaaaattactaataactaaccacttaaacattgttttctcag Find is-nt database================================================ Query_seq: PG1277:PG1278|PG1277:PG1278:UDP-glucose-6 dehydrogenase, putative:phosphoserine aminotransferase:->->:1355160..1355491 332 tgtatcactcctaaaagaaaaatcctacagacagataatcggtctgcaaaccacaggggggcttccttcttatcttaccggcatactttttctcgtaaatttttcatcggcctcagatgaatgtcttacgcaaaccgcagaaagaaacgtttttatctgacaccaatgattctgatgatcacagtttgcaagagagctgtttcctaaggaattagtttgccgatatgttttatttggtacctttgcgctggcaaaagatgcacctatgcatccaatgactgcagaacaagaaaaattactaataactaaccacttaaacattgttttctcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1277:PG1278|PG1277:PG1278:UDP-glucose-6 dehydrogenase, putative:phosphoserine aminotransferase:->->:1355160..1355491 332 tgtatcactcctaaaagaaaaatcctacagacagataatcggtctgcaaaccacaggggggcttccttcttatcttaccggcatactttttctcgtaaatttttcatcggcctcagatgaatgtcttacgcaaaccgcagaaagaaacgtttttatctgacaccaatgattctgatgatcacagtttgcaagagagctgtttcctaaggaattagtttgccgatatgttttatttggtacctttgcgctggcaaaagatgcacctatgcatccaatgactgcagaacaagaaaaattactaataactaaccacttaaacattgttttctcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1277:PG1278|PG1277:PG1278:UDP-glucose-6 dehydrogenase, putative:phosphoserine aminotransferase:->->:1355160..1355491 332 tgtatcactcctaaaagaaaaatcctacagacagataatcggtctgcaaaccacaggggggcttccttcttatcttaccggcatactttttctcgtaaatttttcatcggcctcagatgaatgtcttacgcaaaccgcagaaagaaacgtttttatctgacaccaatgattctgatgatcacagtttgcaagagagctgtttcctaaggaattagtttgccgatatgttttatttggtacctttgcgctggcaaaagatgcacctatgcatccaatgactgcagaacaagaaaaattactaataactaaccacttaaacattgttttctcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtatcactcctaaaagaaaaatcctacagacagataatcggtctgcaaaccacaggggggcttccttcttatcttaccggcatactttttctcgtaaatttttcatcggcctcagatgaatgtcttacgcaaaccgcagaaagaaacgtttttatctgacaccaatgattctgatgatcacagtttgcaagagagctgtttcctaaggaattagtttgccgatatgttttatttggtacctttgcgctggcaaaagatgcacctatgcatccaatgactgcagaacaagaaaaattactaataactaaccacttaaacattgttttctcag Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 4 End: 117 ... M T P K R K I L Q T D N R S A N H R G A S F L S Y R H T F S R K F F I G L R ....................................................................................................................................................................................................................... Protein_Len: 41 Strand: + Start: 35 End: 157 .................................. M I G L Q T T G G L P S Y L T G I L F L V N F S S A S D E C L T Q T A E R N V F I ............................................................................................................................................................................... Protein_Len: 38 Strand: + Start: 99 End: 212 .................................................................................................. M F H R P Q M N V L R K P Q K E T F L S D T N D S D D H S L Q E S C F L R N ........................................................................................................................ Protein_Len: 32 Strand: + Start: 211 End: 306 .................................................................................................................................................................................................................. M S L P I C F I W Y L C A G K R C T Y A S N D C R T R K I T N N .......................... Protein_Len: 45 Strand: + Start: 197 End: 331 .................................................................................................................................................................................................... M F P K E L V C R Y V L F G T F A L A K D A P M H P M T A E Q E K L L I T N H L N I V F S . Protein_Len: 60 Strand: - Start: 73 End: 321 ........................................................................ L F T K I Q C W H N Q H D C N A L S S N G L S N T Q R Y T K N P V K A S A F S A G I C G I V A S C S F N S I V L W K F M ........... tgtatcactcctaaaagaaaaatcctacagacagataatcggtctgcaaaccacaggggggcttccttcttatcttaccggcatactttttctcgtaaatttttcatcggcctcagatgaatgtcttacgcaaaccgcagaaagaaacgtttttatctgacaccaatgattctgatgatcacagtttgcaagagagctgtttcctaaggaattagtttgccgatatgttttatttggtacctttgcgctggcaaaagatgcacctatgcatccaatgactgcagaacaagaaaaattactaataactaaccacttaaacattgttttctcag 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================================================ tgtatcactcctaaaagaaaaatcctacagacagataatcggtctgcaaaccacaggggggcttccttcttatcttaccggcatactttttctcgtaaatttttcatcggcctcagatgaatgtcttacgcaaaccgcagaaagaaacgtttttatctgacaccaatgattctgatgatcacagtttgcaagagagctgtttcctaaggaattagtttgccgatatgttttatttggtacctttgcgctggcaaaagatgcacctatgcatccaatgactgcagaacaagaaaaattactaataactaaccacttaaacattgttttctcag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -7.6 Tail_Score: -4.07568 Start: 257 End: 272 Full_Region: gttctgcagtcattg gatgca tagg tgcatc ttttgccagcgcaaa ................................................................................................................................................................................................................................................................gatgcataggtgcatc............................................................ Find igs database================================================ Query_seq: PG1277:PG1278|PG1277:PG1278:UDP-glucose-6 dehydrogenase, putative:phosphoserine aminotransferase:->->:1355160..1355491 332 tgtatcactcctaaaagaaaaatcctacagacagataatcggtctgcaaaccacaggggggcttccttcttatcttaccggcatactttttctcgtaaatttttcatcggcctcagatgaatgtcttacgcaaaccgcagaaagaaacgtttttatctgacaccaatgattctgatgatcacagtttgcaagagagctgtttcctaaggaattagtttgccgatatgttttatttggtacctttgcgctggcaaaagatgcacctatgcatccaatgactgcagaacaagaaaaattactaataactaaccacttaaacattgttttctcag Intra-Species Hit: Count: 1 Min: 1 Max: 332 Len: 332 Subject: NC_002950_PG1277_PG1278|UDP-glucose-6 dehydrogenase, putative:phosphoserine aminotransferase|POSITIVE:POSITIVE|[1355160,1355491]|332 HSP 1 e-value: 0.0 bit: 658.0 Len: 332 Query Start:1 Query End:332 Subject Strand: POSITIVE Subject Start: 1 Subject End: 332 tgtatcactcctaaaagaaaaatcctacagacagataatcggtctgcaaaccacaggggggcttccttcttatcttaccggcatactttttctcgtaaatttttcatcggcctcagatgaatgtcttacgcaaaccgcagaaagaaacgtttttatctgacaccaatgattctgatgatcacagtttgcaagagagctgtttcctaaggaattagtttgccgatatgttttatttggtacctttgcgctggcaaaagatgcacctatgcatccaatgactgcagaacaagaaaaattactaataactaaccacttaaacattgttttctcag tgtatcactcctaaaagaaaaatcctacagacagataatcggtctgcaaaccacaggggggcttccttcttatcttaccggcatactttttctcgtaaatttttcatcggcctcagatgaatgtcttacgcaaaccgcagaaagaaacgtttttatctgacaccaatgattctgatgatcacagtttgcaagagagctgtttcctaaggaattagtttgccgatatgttttatttggtacctttgcgctggcaaaagatgcacctatgcatccaatgactgcagaacaagaaaaattactaataactaaccacttaaacattgttttctcag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUAUCACUCCUAAAAGAAAAAUCCUACAGACAGAUAAUCGGUCUGCAAACCACAGGGGGGCUUCCUUCUUAUCUUACCGGCAUACUUUUUCUCGUAAAUUUUUCAUCGGCCUCAGAUGAAUGUCUUACGCAAACCGCAGAAAGAAACGUUUUUAUCUGACACCAAUGAUUCUGAUGAUCACAGUUUGCAAGAGAGCUGUUUCCUAAGGAAUUAGUUUGCCGAUAUGUUUUAUUUGGUACCUUUGCGCUGGCAAAAGAUGCACCUAUGCAUCCAAUGACUGCAGAACAAGAAAAAUUACUAAUAACUAACCACUUAAACAUUGUUUUCUCAG .((((((.......((((.........(((((.(.....).)))))........((((((....))))))..))))..(((((.(((..(((((((.......((((.((..(((((((((..((((.(((.....)).).))))......)))))))))..)).)))).....)))...(((((((......))))))).......))))..))).)))))............)))))).(((((....))))).((((((....))))))......(((.(((((((...............................)))))))..))) (-70.38) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGAGAAAACAAUGUUUAAGUGGUUAGUUAUUAGUAAUUUUUCUUGUUCUGCAGUCAUUGGAUGCAUAGGUGCAUCUUUUGCCAGCGCAAAGGUACCAAAUAAAACAUAUCGGCAAACUAAUUCCUUAGGAAACAGCUCUCUUGCAAACUGUGAUCAUCAGAAUCAUUGGUGUCAGAUAAAAACGUUUCUUUCUGCGGUUUGCGUAAGACAUUCAUCUGAGGCCGAUGAAAAAUUUACGAGAAAAAGUAUGCCGGUAAGAUAAGAAGGAAGCCCCCCUGUGGUUUGCAGACCGAUUAUCUGUCUGUAGGAUUUUUCUUUUAGGAGUGAUACA ..(((((((............((((............(((((((((((.((((.((....))))))..(((((....(((((....))))).)))))..........((((((((.(((.........(....)...((((.......(((.......)))..((((((((.((((((.....(((........)))...(((....).))...)))))).)))))))).........))))...))).)))))))).)))))))))))))))..((((..(...(((((.......))))))..))))..))))))).............. (-81.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 381 83 41 43 8 NC_002950:PG0574|5end_hypothetical_protein_629018..629248_POSITIVE 377 90 41 202 153 NC_002950:PG0030|5end_cytidine_deaminase_35846..36076_POSITIVE 363 83 56 211 182 NC_002950:PG0226|5end_transglutaminase-related_protein_262531..262761_NEGATIVE 337 96 51 101 48 NC_002950:PG1347|5end_hypothetical_protein_1428116..1428346_POSITIVE 336 80 31 80 12 NC_002950:PG1247|5end_3-dehydroquinate_synthase_1324444..1324674_POSITIVE 335 263 232 191 154 NC_002950:PG1727|5end_yitL_protein_1816709..1816939_POSITIVE 319 86 43 81 29 NC_002950:PG0605|5end_hypothetical_protein_662406..662636_NEGATIVE 316 279 241 73 37 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 314 80 32 196 159 NC_002950:PG0264|5end_glycosyl_transferase,_group_2_family_protein_296975..297205_POSITIVE 312 89 41 212 156 NC_002950:PG1930|5end_50S_ribosomal_protein_L29_2020409..2020639_NEGATIVE 311 273 233 224 171 NC_002950:PG0623|5end_triosephosphate_isomerase_677261..677491_POSITIVE 310 270 221 94 42 NC_002950:PG1970|5end_hypothetical_protein_2059783..2060013_NEGATIVE 309 200 161 209 170 NC_002950:PG0802|5end_alpha_keto_acid_dehydrogenase_complex,_E3_component,_lipoamide_dehydrogenase_859722..859952_NEGATIVE 308 116 73 174 134 NC_002950:PG0058|5end_nicotinic_acid_mononucleotide_adenyltransferase_70919..71149_POSITIVE 305 260 219 65 27 NC_002950:PG1068|5end_hypothetical_protein_1134636..1134866_POSITIVE 305 82 41 215 160 NC_002950:PG0172|5end_exonuclease_193493..193723_POSITIVE 305 90 41 141 86 NC_002950:PG0124|5end_hypothetical_protein_146234..146464_NEGATIVE 305 280 234 67 27 NC_002950:PG0123|5end_hypothetical_protein_144987..145217_POSITIVE 303 97 53 205 151 NC_002950:PG1814|5end_DNA_primase_1910627..1910857_NEGATIVE 303 286 241 156 105 NC_002950:PG0750|5end_glycosyl_transferase,_group_2_family_protein_796692..796922_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 381 83 41 43 8 NC_002950:PG0573|3end_S-adenosyl-methyltransferase_MraW_629098..629248_POSITIVE 363 83 56 149 120 NC_002950:PG0227|3end_DNA_repair_protein_RadA_262593..262743_NEGATIVE 327 199 154 135 94 NC_002950:PG1030|3end_hypothetical_protein_1092820..1092970_POSITIVE 325 96 51 43 6 NC_002950:PG1382|3end_hypothetical_protein_1462550..1462700_POSITIVE 321 64 22 150 93 NC_002950:PG2091|3end_dihydroneopterin_aldolase_2191610..2191760_POSITIVE 320 96 55 70 20 NC_002950:PG0172|3end_exonuclease_194355..194505_POSITIVE 317 100 54 119 73 NC_002950:PG1722|3end_hypothetical_protein_1812633..1812783_NEGATIVE 311 138 107 106 71 NC_002950:PG2082|3end_POT_family_protein_2181843..2181993_NEGATIVE 309 80 32 43 1 NC_002950:PG1285|3end_glucosamine-6-phosphate_deaminase_1364941..1365091_POSITIVE 307 254 212 44 1 NC_002950:PG0053|3end_hypothetical_protein_64967..65117_NEGATIVE 305 90 41 137 82 NC_002950:PG0125|3end_hypothetical_protein_146238..146388_NEGATIVE 294 70 24 133 68 NC_002950:PG0191|3end_outer_membrane_protein,_putative_229613..229763_POSITIVE 293 76 31 71 23 NC_002950:PG0721|3end_NLP/P60_family_protein_774535..774685_POSITIVE 292 82 43 145 100 NC_002950:PG1815|3end_3-deoxy-manno-octulosonate_cytidylyltransferase_1910669..1910819_NEGATIVE 291 80 39 68 34 NC_002950:PG1774|3end_transcription-repair_coupling_factor_1861179..1861329_NEGATIVE 291 150 108 88 46 NC_002950:PG0523|3end_inositol-5-monophosphate_dehydrogenase_566898..567048_NEGATIVE 290 83 49 143 102 NC_002950:PG2064|3end_hypothetical_protein_2161034..2161184_POSITIVE 289 280 231 71 10 NC_002950:PG0997|3end_transcriptional_regulator,_putative_1057012..1057162_POSITIVE 286 93 51 101 62 NC_002950:PG0954|3end_TPR_domain_protein_1015005..1015155_POSITIVE 285 90 46 86 36 NC_002950:PG1967|3end_TPR_domain_protein_2058135..2058285_POSITIVE