Origin IGS: tgcctcgaatgaggaggaacaaatgcatcctttctcctaatccttctcgtctgtagtcggccaaggatagtttctattgctgtcggtaaaaaaatgaagattcttcaaaacatactgtaataatggaatttactttactaccatttatacgtggttaggctgttttccccttcgtaatgactcttgatagaacagtaatggctaagaaagggagattttatttcgaatttcctaaccgtccaaattttcccggacagcaatagatagtttcacagccatgaaactaaagtttcgtagtagtgaaactaaagtttctcgactgtgaaaataaagtttcttaaccgtgaaacttc .........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 gaagtttcacggttaagaaactttattttcacagtcgagaaactttagtttcactactacgaaactttagtttcatggctgtgaaactatctattgctgtccgggaaaatttggacggttaggaaattcgaaataaaatctccctttcttagccattactgttctatcaagagtcattacgaaggggaaaacagcctaaccacgtataaatggtagtaaagtaaattccattattacagtatgttttgaagaatcttcatttttttaccgacagcaatagaaactatccttggccgactacagacgagaaggattaggagaaaggatgcatttgttcctcctcattcgaggca Mask Tandem Repeat Region ================================================ tgcctcgaatgaggaggaacaaatgcatcctttctcctaatccttctcgtctgtagtcggccaaggatagtttctattgctgtcggtaaaaaaatgaagattcttcaaaacatactgtaataatggaatttactttactaccatttatacgtggttaggctgttttccccttcgtaatgactcttgatagaacagtaatggctaagaaagggagattttatttcgaatttcctaaccgtccaaattttcccggacagcaatagatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncttc Find is-nt database================================================ Query_seq: PG1769:PG1770|PG1769:PG1770:hypothetical protein:hypothetical protein:->->:1857071..1857423 353 tgcctcgaatgaggaggaacaaatgcatcctttctcctaatccttctcgtctgtagtcggccaaggatagtttctattgctgtcggtaaaaaaatgaagattcttcaaaacatactgtaataatggaatttactttactaccatttatacgtggttaggctgttttccccttcgtaatgactcttgatagaacagtaatggctaagaaagggagattttatttcgaatttcctaaccgtccaaattttcccggacagcaatagatagtttcacagccatgaaactaaagtttcgtagtagtgaaactaaagtttctcgactgtgaaaataaagtttcttaaccgtgaaacttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1769:PG1770|PG1769:PG1770:hypothetical protein:hypothetical protein:->->:1857071..1857423 353 tgcctcgaatgaggaggaacaaatgcatcctttctcctaatccttctcgtctgtagtcggccaaggatagtttctattgctgtcggtaaaaaaatgaagattcttcaaaacatactgtaataatggaatttactttactaccatttatacgtggttaggctgttttccccttcgtaatgactcttgatagaacagtaatggctaagaaagggagattttatttcgaatttcctaaccgtccaaattttcccggacagcaatagatagtttcacagccatgaaactaaagtttcgtagtagtgaaactaaagtttctcgactgtgaaaataaagtttcttaaccgtgaaacttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1769:PG1770|PG1769:PG1770:hypothetical protein:hypothetical protein:->->:1857071..1857423 353 tgcctcgaatgaggaggaacaaatgcatcctttctcctaatccttctcgtctgtagtcggccaaggatagtttctattgctgtcggtaaaaaaatgaagattcttcaaaacatactgtaataatggaatttactttactaccatttatacgtggttaggctgttttccccttcgtaatgactcttgatagaacagtaatggctaagaaagggagattttatttcgaatttcctaaccgtccaaattttcccggacagcaatagatagtttcacagccatgaaactaaagtttcgtagtagtgaaactaaagtttctcgactgtgaaaataaagtttcttaaccgtgaaacttc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcctcgaatgaggaggaacaaatgcatcctttctcctaatccttctcgtctgtagtcggccaaggatagtttctattgctgtcggtaaaaaaatgaagattcttcaaaacatactgtaataatggaatttactttactaccatttatacgtggttaggctgttttccccttcgtaatgactcttgatagaacagtaatggctaagaaagggagattttatttcgaatttcctaaccgtccaaattttcccggacagcaatagatagtttcacagccatgaaactaaagtttcgtagtagtgaaactaaagtttctcgactgtgaaaataaagtttcttaaccgtgaaacttc Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 141 End: 260 ............................................................................................................................................ W K Y T T L S N E G E Y H S K I S C Y H S L F P S K I E F K R V T W I K G S L M ............................................................................................. Protein_Len: 30 Strand: - Start: 40 End: 129 ....................................... D K E D T T P W P Y N R N S D T F F H L N K L V Y Q L L P M ................................................................................................................................................................................................................................ Protein_Len: 33 Strand: - Start: 3 End: 101 .. R S H P P V F A D K R R I R R T Q L R G L I T E I A T P L F I F M ............................................................................................................................................................................................................................................................ tgcctcgaatgaggaggaacaaatgcatcctttctcctaatccttctcgtctgtagtcggccaaggatagtttctattgctgtcggtaaaaaaatgaagattcttcaaaacatactgtaataatggaatttactttactaccatttatacgtggttaggctgttttccccttcgtaatgactcttgatagaacagtaatggctaagaaagggagattttatttcgaatttcctaaccgtccaaattttcccggacagcaatagatagtttcacagccatgaaactaaagtttcgtagtagtgaaactaaagtttctcgactgtgaaaataaagtttcttaaccgtgaaacttc 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================================================ tgcctcgaatgaggaggaacaaatgcatcctttctcctaatccttctcgtctgtagtcggccaaggatagtttctattgctgtcggtaaaaaaatgaagattcttcaaaacatactgtaataatggaatttactttactaccatttatacgtggttaggctgttttccccttcgtaatgactcttgatagaacagtaatggctaagaaagggagattttatttcgaatttcctaaccgtccaaattttcccggacagcaatagatagtttcacagccatgaaactaaagtttcgtagtagtgaaactaaagtttctcgactgtgaaaataaagtttcttaaccgtgaaacttc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 85 HP_score: -6.3 Tail_Score: -5.40072 Start: 95 End: 107 Full_Region: tattacagtatgttt tgaag aat cttca tttttttaccgacag ..............................................................................................tgaagaatcttca...................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 70 HP_score: -9.0 Tail_Score: -3.16071 Start: 265 End: 308 Full_Region: acagtcgagaaactt tagtttcactactacgaaac ttta gtttcatggctgtgaaacta tctattgctgtccgg ........................................................................................................................................................................................................................................................................tagtttcactactacgaaactttagtttcatggctgtgaaacta............................................. Find igs database================================================ Query_seq: PG1769:PG1770|PG1769:PG1770:hypothetical protein:hypothetical protein:->->:1857071..1857423 353 tgcctcgaatgaggaggaacaaatgcatcctttctcctaatccttctcgtctgtagtcggccaaggatagtttctattgctgtcggtaaaaaaatgaagattcttcaaaacatactgtaataatggaatttactttactaccatttatacgtggttaggctgttttccccttcgtaatgactcttgatagaacagtaatggctaagaaagggagattttatttcgaatttcctaaccgtccaaattttcccggacagcaatagatagtttcacagccatgaaactaaagtttcgtagtagtgaaactaaagtttctcgactgtgaaaataaagtttcttaaccgtgaaacttc Intra-Species Hit: Count: 2 Min: 1 Max: 353 Len: 353 Subject: NC_002950_PG1769_PG1770|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[1857071,1857423]|353 HSP 1 e-value: 0.0 bit: 658.0 Len: 353 Query Start:1 Query End:353 Subject Strand: POSITIVE Subject Start: 1 Subject End: 353 tgcctcgaatgaggaggaacaaatgcatcctttctcctaatccttctcgtctgtagtcggccaaggatagtttctattgctgtcggtnnnnnnntgaagattcttcaaaacatactgtaataatggaatttactttactaccatttatacgtggttaggctgttttccccttcgtaatgactcttgatagaacagtaatggctaagaaagggagattttatttcgaatttcctaaccgtccaaattttcccggacagcaatagatagtttcacagccatgaaactaaagtttcgtagtagtgaaactaaagtttctcgactgtgaaaataaagtttcttaaccgtgaaacttc tgcctcgaatgaggaggaacaaatgcatcctttctcctaatccttctcgtctgtagtcggccaaggatagtttctattgctgtcggtaaaaaaatgaagattcttcaaaacatactgtaataatggaatttactttactaccatttatacgtggttaggctgttttccccttcgtaatgactcttgatagaacagtaatggctaagaaagggagattttatttcgaatttcctaaccgtccaaattttcccggacagcaatagatagtttcacagccatgaaactaaagtttcgtagtagtgaaactaaagtttctcgactgtgaaaataaagtttcttaaccgtgaaacttc Subject: NC_002950_PG0293_PG0294|secretion activator protein, putative:glycosyl transferase, group 2 family protein|NEGATIVE:NEGATIVE|[328762,329360]|599 HSP 1 e-value: 4.0E-55 bit: 216.0 Len: 165 Query Start:95 Query End:259 Subject Strand: POSITIVE Subject Start: 220 Subject End: 384 ..............................................................................................tgaagattcttcaaaacatactgtaataatggaatttactttactaccatttatacgtggttaggctgttttccccttcgtaatgactcttgatagaacagtaatggctaagaaagggagattttatttcgaatttcctaaccgtccaaattttcccggacagca.............................................................................................. ..............................................................................................tgaagattcttcaaaacatactgtaataatggagtttgctttactgccatttatatgtggttaggctgttttccccttcgtaatgacactttatagaacagtaatggcaaagaagggaagattttatctcgaatttcctgactgcccaaattttaccggacagca.............................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCCUCGAAUGAGGAGGAACAAAUGCAUCCUUUCUCCUAAUCCUUCUCGUCUGUAGUCGGCCAAGGAUAGUUUCUAUUGCUGUCGGUAAAAAAAUGAAGAUUCUUCAAAACAUACUGUAAUAAUGGAAUUUACUUUACUACCAUUUAUACGUGGUUAGGCUGUUUUCCCCUUCGUAAUGACUCUUGAUAGAACAGUAAUGGCUAAGAAAGGGAGAUUUUAUUUCGAAUUUCCUAACCGUCCAAAUUUUCCCGGACAGCAAUAGAUAGUUUCACAGCCAUGAAACUAAAGUUUCGUAGUAGUGAAACUAAAGUUUCUCGACUGUGAAAAUAAAGUUUCUUAACCGUGAAACUUC ......((.(((((((((......................)))))))))))..(((((((............((((((((((((.(..((((..(((((...))))).........(((..(((((..............)))))..)))..(((((((..((((((((.(((........(((....))).((....)).....))).))))...........))))..))))))).......))))..).))))))))))))(((((((((.((.(((((((....))))))).)).))))))))).......)))))))........(((((((........))))))). (-91.79) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGUUUCACGGUUAAGAAACUUUAUUUUCACAGUCGAGAAACUUUAGUUUCACUACUACGAAACUUUAGUUUCAUGGCUGUGAAACUAUCUAUUGCUGUCCGGGAAAAUUUGGACGGUUAGGAAAUUCGAAAUAAAAUCUCCCUUUCUUAGCCAUUACUGUUCUAUCAAGAGUCAUUACGAAGGGGAAAACAGCCUAACCACGUAUAAAUGGUAGUAAAGUAAAUUCCAUUAUUACAGUAUGUUUUGAAGAAUCUUCAUUUUUUUACCGACAGCAAUAGAAACUAUCCUUGGCCGACUACAGACGAGAAGGAUUAGGAGAAAGGAUGCAUUUGUUCCUCCUCAUUCGAGGCA ...(((((.((((((((.........(((((((((((.((((((..((((((........))))))..)))))).)))))))))))...((((((((((((.(((((((..((((.((((......(((((((((.....((((((((.(((..(((..((......))..)))..))).))))))))...............(((..(((((.(((.......))))))))..)))....))))))))).))))))))..))))).)))))))))))))).......))))))))..............((((.(((((.((.((.....)).)).))))).))))))))). (-106.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 505 120 71 145 91 NC_002950:PG0722|5end_hypothetical_protein_774891..775121_NEGATIVE 411 260 211 182 134 NC_002950:PG0572|5end_hypothetical_protein_627571..627801_NEGATIVE 350 67 28 76 29 NC_002950:PG1252|5end_hypothetical_protein_1329584..1329814_NEGATIVE 349 85 43 150 102 NC_002950:PG0098|5end_hypothetical_protein_115843..116073_NEGATIVE 345 88 44 82 44 NC_002950:PG1214|5end_hypothetical_protein_1293032..1293262_POSITIVE 338 90 41 102 52 NC_002950:PG2202|5end_Holliday_junction_resolvase-like_protein_2309933..2310163_NEGATIVE 328 86 41 208 157 NC_002950:PG0069|5end_hypothetical_protein_83935..84165_NEGATIVE 327 70 22 78 36 NC_002950:PG1356|5end_hypothetical_protein_1435849..1436079_NEGATIVE 321 70 25 140 93 NC_002950:PG1510|5end_hypothetical_protein_1587536..1587766_NEGATIVE 317 86 43 175 129 NC_002950:PG1306|5end_metallo-beta-lactamase_family_protein_1387187..1387417_NEGATIVE 315 87 42 173 135 NC_002950:PG0715|5end_transporter_769596..769826_NEGATIVE 315 60 11 226 169 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 312 67 24 72 23 NC_002950:PG0464|5end_adenylosuccinate_synthetase_508874..509104_NEGATIVE 311 86 46 78 45 NC_002950:PG1660|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1744268..1744498_NEGATIVE 309 79 34 219 175 NC_002950:PG0803|5end_glucosamine-6-phosphate_deaminase_860518..860748_NEGATIVE 307 88 49 65 26 NC_002950:PG0500|5end_queuine_tRNA-ribosyltransferase_539197..539427_POSITIVE 306 87 41 85 21 NC_002950:PG1155|5end_ADP-heptose--LPS_heptosyltransferase,_putative_1235861..1236091_POSITIVE 302 63 23 194 141 NC_002950:PG2126|5end_conserved_hypothetical_protein_TIGR00044_2233112..2233342_NEGATIVE 302 86 42 198 148 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 299 86 41 48 2 NC_002950:PG2102|5end_immunoreactive_61_kDa_antigen_PG91_2213046..2213276_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 538 265 223 81 36 NC_002950:PG1697|3end_type_II_restriction_endonuclease,_putative_1785074..1785224_POSITIVE 421 307 266 48 7 NC_002950:PG2079|3end_hypothetical_protein_2178890..2179040_NEGATIVE 350 67 28 63 16 NC_002950:PG1253|3end_DNA_ligase,_NAD-dependent_1329597..1329747_NEGATIVE 345 88 44 133 95 NC_002950:PG1213|3end_ribonuclease_H_1293163..1293313_POSITIVE 338 62 23 135 88 NC_002950:PG2076|3end_hypothetical_protein_2177073..2177223_POSITIVE 331 68 23 146 98 NC_002950:PG0520|3end_chaperonin_GroEL_563618..563768_NEGATIVE 331 67 23 104 64 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 330 90 45 64 13 NC_002950:PG1268|3end_hypothetical_protein_1347549..1347699_POSITIVE 325 86 43 130 84 NC_002950:PG0610|3end_hypothetical_protein_663604..663754_NEGATIVE 311 60 11 76 16 NC_002950:PG0172|3end_exonuclease_194355..194505_POSITIVE 304 99 69 34 3 NC_002950:PG0373|3end_hypothetical_protein_405453..405603_POSITIVE 297 89 41 143 105 NC_002950:PG0816|3end_hypothetical_protein_876386..876536_NEGATIVE 294 86 41 59 12 NC_002950:PG1495|3end_DNA_topoisomerase_III_1573416..1573566_POSITIVE 294 86 48 119 70 NC_002950:PG1389|3end_DNA-binding_protein,_histone-like_family_1470870..1471020_NEGATIVE 294 60 16 118 72 NC_002950:PG0400|3end_hypothetical_protein_436245..436395_NEGATIVE 293 49 2 97 47 NC_002950:PG0786|3end_hypothetical_protein_837570..837720_NEGATIVE 291 60 11 89 25 NC_002950:PG0249|3end_oxaloacetate_decarboxylase,_putative_281939..282089_NEGATIVE 290 68 25 146 101 NC_002950:PG2107|3end_thiamine_biosynthesis_protein_ThiH_2215546..2215696_NEGATIVE 290 87 45 141 108 NC_002950:PG1560|3end_dTDP-glucose_4,6-dehydratase_1639067..1639217_NEGATIVE 290 88 43 124 74 NC_002950:PG0789|3end_hypothetical_protein_840702..840852_NEGATIVE