Origin IGS: gttttttgagcaattagtgatgaataacaacctcctcgcagcttatcaaaagcttattgtggaggtatatccactttcgtaaatataacaatctcagaatatatatttgttctggtttttcatcgaggaaaaaagtgcatatgctcattacgcctcaagcaggatacgagcctgaaatgctccgattgtggtctgtgttttgtgaaaagcaggcgcgagatttttttcgttttggtttcactttttttcttttcccacgccaaaagcaaaaagttcacgtgccacacttttgggtgtcataaacccgaaaatttaggcgtgtgaacccaatcggatagggatgatacatcctatggctgaatcggaagtgaatatggtgcaaaaaaagagggacagtgcacgaatttggcactgtccctcgaaaagagatgattaagattccttctctatcgggttatttagcctcgaaagaaggaaatttaa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaaatttccttctttcgaggctaaataacccgatagagaaggaatcttaatcatctcttttcgagggacagtgccaaattcgtgcactgtccctctttttttgcaccatattcacttccgattcagccataggatgtatcatccctatccgattgggttcacacgcctaaattttcgggtttatgacacccaaaagtgtggcacgtgaactttttgcttttggcgtgggaaaagaaaaaaagtgaaaccaaaacgaaaaaaatctcgcgcctgcttttcacaaaacacagaccacaatcggagcatttcaggctcgtatcctgcttgaggcgtaatgagcatatgcacttttttcctcgatgaaaaaccagaacaaatatatattctgagattgttatatttacgaaagtggatatacctccacaataagcttttgataagctgcgaggaggttgttattcatcactaattgctcaaaaaac Mask Tandem Repeat Region ================================================ gttttttgagcaattagtgatgaataacaacctcctcgcagcttatcaaaagcttattgtggaggtatatccactttcgtaaatataacaatctcagaatatatatttgttctggtttttcatcgaggaaaaaagtgcatatgctcattacgcctcaagcaggatacgagcctgaaatgctccgattgtggtctgtgttttgtgaaaagcaggcgcgagatttttttcgttttggtttcactttttttcttttcccacgccaaaagcaaaaagttcacgtgccacacttttgggtgtcataaacccgaaaatttaggcgtgtgaacccaatcggatagggatgatacatcctatggctgaatcggaagtgaatatggtgcaaaaaaagagggacagtgcacgaatttggcactgtccctcgaaaagagatgattaagattccttctctatcgggttatttagcctcgaaagaaggaaatttaa Find is-nt database================================================ Query_seq: PG0686:PG0687|PG0686:PG0687:hypothetical protein:succinate-semialdehyde dehydrogenase:<-<-:742775..743257 483 gttttttgagcaattagtgatgaataacaacctcctcgcagcttatcaaaagcttattgtggaggtatatccactttcgtaaatataacaatctcagaatatatatttgttctggtttttcatcgaggaaaaaagtgcatatgctcattacgcctcaagcaggatacgagcctgaaatgctccgattgtggtctgtgttttgtgaaaagcaggcgcgagatttttttcgttttggtttcactttttttcttttcccacgccaaaagcaaaaagttcacgtgccacacttttgggtgtcataaacccgaaaatttaggcgtgtgaacccaatcggatagggatgatacatcctatggctgaatcggaagtgaatatggtgcaaaaaaagagggacagtgcacgaatttggcactgtccctcgaaaagagatgattaagattccttctctatcgggttatttagcctcgaaagaaggaaatttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0686:PG0687|PG0686:PG0687:hypothetical protein:succinate-semialdehyde dehydrogenase:<-<-:742775..743257 483 gttttttgagcaattagtgatgaataacaacctcctcgcagcttatcaaaagcttattgtggaggtatatccactttcgtaaatataacaatctcagaatatatatttgttctggtttttcatcgaggaaaaaagtgcatatgctcattacgcctcaagcaggatacgagcctgaaatgctccgattgtggtctgtgttttgtgaaaagcaggcgcgagatttttttcgttttggtttcactttttttcttttcccacgccaaaagcaaaaagttcacgtgccacacttttgggtgtcataaacccgaaaatttaggcgtgtgaacccaatcggatagggatgatacatcctatggctgaatcggaagtgaatatggtgcaaaaaaagagggacagtgcacgaatttggcactgtccctcgaaaagagatgattaagattccttctctatcgggttatttagcctcgaaagaaggaaatttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0686:PG0687|PG0686:PG0687:hypothetical protein:succinate-semialdehyde dehydrogenase:<-<-:742775..743257 483 gttttttgagcaattagtgatgaataacaacctcctcgcagcttatcaaaagcttattgtggaggtatatccactttcgtaaatataacaatctcagaatatatatttgttctggtttttcatcgaggaaaaaagtgcatatgctcattacgcctcaagcaggatacgagcctgaaatgctccgattgtggtctgtgttttgtgaaaagcaggcgcgagatttttttcgttttggtttcactttttttcttttcccacgccaaaagcaaaaagttcacgtgccacacttttgggtgtcataaacccgaaaatttaggcgtgtgaacccaatcggatagggatgatacatcctatggctgaatcggaagtgaatatggtgcaaaaaaagagggacagtgcacgaatttggcactgtccctcgaaaagagatgattaagattccttctctatcgggttatttagcctcgaaagaaggaaatttaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttttttgagcaattagtgatgaataacaacctcctcgcagcttatcaaaagcttattgtggaggtatatccactttcgtaaatataacaatctcagaatatatatttgttctggtttttcatcgaggaaaaaagtgcatatgctcattacgcctcaagcaggatacgagcctgaaatgctccgattgtggtctgtgttttgtgaaaagcaggcgcgagatttttttcgttttggtttcactttttttcttttcccacgccaaaagcaaaaagttcacgtgccacacttttgggtgtcataaacccgaaaatttaggcgtgtgaacccaatcggatagggatgatacatcctatggctgaatcggaagtgaatatggtgcaaaaaaagagggacagtgcacgaatttggcactgtccctcgaaaagagatgattaagattccttctctatcgggttatttagcctcgaaagaaggaaatttaa Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 24 End: 299 ....................... M T T S S Q L I K S L L W R Y I H F R K Y N N L R I Y I C S G F S S R K K V H M L I T P Q A G Y E P E M L R L W S V F C ........................................................................................................................................................................................ Protein_Len: 60 Strand: + Start: 67 End: 321 .................................................................. M S T F V N I T I S E Y I F V L V F H R G K K C I C S L R L K Q D T S L K C S D C G L C F V K S R R E I F F V L V S L F .................................................................................................................................................................. Protein_Len: 33 Strand: + Start: 335 End: 433 .............................................................................................................................................................................................................................................................................................................................................. M G M I H P M A E S E V N M V Q K K R D S A R I W H C P S K R D D .................................................. Protein_Len: 37 Strand: + Start: 372 End: 482 ................................................................................................................................................................................................................................................................................................................................................................................... M W C K K R G T V H E F G T V P R K E M I K I P S L S G Y L A S K E G N L . Protein_Len: 30 Strand: - Start: 316 End: 405 ........................................................................................................................................................................................................................................................................................................................... A H S G L R I P I I C G I A S D S T F I T C F F L S L A R M .............................................................................. Protein_Len: 54 Strand: - Start: 278 End: 439 ..................................................................................................................................................................................................................................................................................... T G C K Q T D Y V R F N L R T F G I P Y P H Y M R H S F R F H I H H L F L P V T C S N P V T G R F S I I L M ............................................ Protein_Len: 55 Strand: - Start: 123 End: 287 .......................................................................................................................... R P F F H M H E N R R L C S V L R F H E S Q P R H K T F L L R S I K K T K T E S K K K E W A L L L F N V H W M .................................................................................................................................................................................................... Protein_Len: 44 Strand: - Start: 17 End: 148 ................ H H I V V E E C S I L L K N H L Y I W K R L Y L L R L I Y I Q E P K E D L F F T C I S M ............................................................................................................................................................................................................................................................................................................................................... gttttttgagcaattagtgatgaataacaacctcctcgcagcttatcaaaagcttattgtggaggtatatccactttcgtaaatataacaatctcagaatatatatttgttctggtttttcatcgaggaaaaaagtgcatatgctcattacgcctcaagcaggatacgagcctgaaatgctccgattgtggtctgtgttttgtgaaaagcaggcgcgagatttttttcgttttggtttcactttttttcttttcccacgccaaaagcaaaaagttcacgtgccacacttttgggtgtcataaacccgaaaatttaggcgtgtgaacccaatcggatagggatgatacatcctatggctgaatcggaagtgaatatggtgcaaaaaaagagggacagtgcacgaatttggcactgtccctcgaaaagagatgattaagattccttctctatcgggttatttagcctcgaaagaaggaaatttaa 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================================================ gttttttgagcaattagtgatgaataacaacctcctcgcagcttatcaaaagcttattgtggaggtatatccactttcgtaaatataacaatctcagaatatatatttgttctggtttttcatcgaggaaaaaagtgcatatgctcattacgcctcaagcaggatacgagcctgaaatgctccgattgtggtctgtgttttgtgaaaagcaggcgcgagatttttttcgttttggtttcactttttttcttttcccacgccaaaagcaaaaagttcacgtgccacacttttgggtgtcataaacccgaaaatttaggcgtgtgaacccaatcggatagggatgatacatcctatggctgaatcggaagtgaatatggtgcaaaaaaagagggacagtgcacgaatttggcactgtccctcgaaaagagatgattaagattccttctctatcgggttatttagcctcgaaagaaggaaatttaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 46 HP_score: -2.9 Tail_Score: -3.43042 Start: 95 End: 114 Full_Region: TAAATATAACAATCT CAGAATA TATATT TGTTCTG GTTTTTCATCGAGGA ..............................................................................................CAGAATATATATTTGTTCTG................................................................................................................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 74 HP_score: -3.9 Tail_Score: -5.0925 Start: 273 End: 326 Full_Region: tccctatccgattgg gttcacacgcctaaattttcgggttt atg acacccaaaagtgtggcacgtgaac tttttgcttttggcg ................................................................................................................................................................................................................................................................................gttcacacgcctaaattttcgggtttatgacacccaaaagtgtggcacgtgaac............................................................................................................................................................. TransTerm Strand: - Conf: 100 HP_score: -15.0 Tail_Score: -5.41143 Start: 388 End: 420 Full_Region: taatcatctcttttc gagggacagtgc caaattcgt gcactgtccctc tttttttgcaccata ...................................................................................................................................................................................................................................................................................................................................................................................................gagggacagtgccaaattcgtgcactgtccctc............................................................... Find igs database================================================ Query_seq: PG0686:PG0687|PG0686:PG0687:hypothetical protein:succinate-semialdehyde dehydrogenase:<-<-:742775..743257 483 gttttttgagcaattagtgatgaataacaacctcctcgcagcttatcaaaagcttattgtggaggtatatccactttcgtaaatataacaatctcagaatatatatttgttctggtttttcatcgaggaaaaaagtgcatatgctcattacgcctcaagcaggatacgagcctgaaatgctccgattgtggtctgtgttttgtgaaaagcaggcgcgagatttttttcgttttggtttcactttttttcttttcccacgccaaaagcaaaaagttcacgtgccacacttttgggtgtcataaacccgaaaatttaggcgtgtgaacccaatcggatagggatgatacatcctatggctgaatcggaagtgaatatggtgcaaaaaaagagggacagtgcacgaatttggcactgtccctcgaaaagagatgattaagattccttctctatcgggttatttagcctcgaaagaaggaaatttaa Intra-Species Hit: Count: 1 Min: 1 Max: 483 Len: 483 Subject: NC_002950_PG0686_PG0687|hypothetical protein:succinate-semialdehyde dehydrogenase|NEGATIVE:NEGATIVE|[742775,743257]|483 HSP 1 e-value: 1.0E-121 bit: 436.0 Len: 220 Query Start:1 Query End:220 Subject Strand: POSITIVE Subject Start: 1 Subject End: 220 gttttttgagcaattagtgatgaataacaacctcctcgcagcttatcaaaagcttattgtggaggtatatccactttcgtaaatataacaatctcagaatatatatttgttctggtttttcatcgaggaaaaaagtgcatatgctcattacgcctcaagcaggatacgagcctgaaatgctccgattgtggtctgtgttttgtgaaaagcaggcgcgaga....................................................................................................................................................................................................................................................................... gttttttgagcaattagtgatgaataacaacctcctcgcagcttatcaaaagcttattgtggaggtatatccactttcgtaaatataacaatctcagaatatatatttgttctggtttttcatcgaggaaaaaagtgcatatgctcattacgcctcaagcaggatacgagcctgaaatgctccgattgtggtctgtgttttgtgaaaagcaggcgcgaga....................................................................................................................................................................................................................................................................... HSP 2 e-value: 1.0E-114 bit: 412.0 Len: 229 Query Start:255 Query End:483 Subject Strand: POSITIVE Subject Start: 255 Subject End: 483 ..............................................................................................................................................................................................................................................................ccacgccaaaagcaaaaagttcacgtgccacacttttgggtgtcataaacccgaaaatttaggcgtgtgaacccaatcggatagggatgatacatcctatggctgaatcggaagtgaatatggtgcnnnnnnngagggacagtgcacgaatttggcactgtccctcgaaaagagatgattaagattccttctctatcgggttatttagcctcgaaagaaggaaatttaa ..............................................................................................................................................................................................................................................................ccacgccaaaagcaaaaagttcacgtgccacacttttgggtgtcataaacccgaaaatttaggcgtgtgaacccaatcggatagggatgatacatcctatggctgaatcggaagtgaatatggtgcaaaaaaagagggacagtgcacgaatttggcactgtccctcgaaaagagatgattaagattccttctctatcgggttatttagcctcgaaagaaggaaatttaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUUUGAGCAAUUAGUGAUGAAUAACAACCUCCUCGCAGCUUAUCAAAAGCUUAUUGUGGAGGUAUAUCCACUUUCGUAAAUAUAACAAUCUCAGAAUAUAUAUUUGUUCUGGUUUUUCAUCGAGGAAAAAAGUGCAUAUGCUCAUUACGCCUCAAGCAGGAUACGAGCCUGAAAUGCUCCGAUUGUGGUCUGUGUUUUGUGAAAAGCAGGCGCGAGAUUUUUUUCGUUUUGGUUUCACUUUUUUUCUUUUCCCACGCCAAAAGCAAAAAGUUCACGUGCCACACUUUUGGGUGUCAUAAACCCGAAAAUUUAGGCGUGUGAACCCAAUCGGAUAGGGAUGAUACAUCCUAUGGCUGAAUCGGAAGUGAAUAUGGUGCAAAAAAAGAGGGACAGUGCACGAAUUUGGCACUGUCCCUCGAAAAGAGAUGAUUAAGAUUCCUUCUCUAUCGGGUUAUUUAGCCUCGAAAGAAGGAAAUUUAA (((((((..(((.................((((((.((.(((((.....)))))...)).))))))((((.((((((((..............((((((((......))))))))...(((...(((((((((((((.....(((.....((((((..((((((((((..((...(((......)))..))..)))))))))).....).)))))(((((....)))))....)))..))))))))))))).......((((..........(((((((((((....((((((((.......)))))))).....)))))))))))...........((((((...)))))).)))).))).)))))))).))))..))).......((((((((((((.((....))))))))))))))...)))))))..(((((.((((((((...(((((((....)))).))).)))))))).))))) (-153.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAAUUUCCUUCUUUCGAGGCUAAAUAACCCGAUAGAGAAGGAAUCUUAAUCAUCUCUUUUCGAGGGACAGUGCCAAAUUCGUGCACUGUCCCUCUUUUUUUGCACCAUAUUCACUUCCGAUUCAGCCAUAGGAUGUAUCAUCCCUAUCCGAUUGGGUUCACACGCCUAAAUUUUCGGGUUUAUGACACCCAAAAGUGUGGCACGUGAACUUUUUGCUUUUGGCGUGGGAAAAGAAAAAAAGUGAAACCAAAACGAAAAAAAUCUCGCGCCUGCUUUUCACAAAACACAGACCACAAUCGGAGCAUUUCAGGCUCGUAUCCUGCUUGAGGCGUAAUGAGCAUAUGCACUUUUUUCCUCGAUGAAAAACCAGAACAAAUAUAUAUUCUGAGAUUGUUAUAUUUACGAAAGUGGAUAUACCUCCACAAUAAGCUUUUGAUAAGCUGCGAGGAGGUUGUUAUUCAUCACUAAUUGCUCAAAAAAC ((((..((((((((((((.((........)))))..)))))))))..))))............(((((((((((((......).)))))))))))).(((((((................(((.(((((...(((((...)))))...((((((((((((.....(((...(((((.((((.......)))).)))))..)))..(((((......((....(((((((((............((....))............))))))))).))..)))))........)))).))))))))........)))).).)))..((..((((......(.((....)).)......))))((((((.((((((((..........))))).......(((((((((....)))))))))(((((.(....(((((.....)))))..).)))))..))).)))))).......)).))))))). (-142.55) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 928 80 31 171 122 NC_002950:PG0686|5end_hypothetical_protein_742684..742914_NEGATIVE 557 220 174 48 2 NC_002950:PG1980|5end_hypothetical_protein_2067930..2068160_NEGATIVE 526 260 213 86 37 NC_002950:PG1617|5end_hypothetical_protein_1697755..1697985_NEGATIVE 489 293 252 87 46 NC_002950:PG0313|5end_hypothetical_protein_347366..347596_POSITIVE 463 260 212 110 62 NC_002950:PG0007|5end_hypothetical_protein_6913..7143_NEGATIVE 461 230 181 58 9 NC_002950:PG0174|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_197628..197858_NEGATIVE 426 180 135 186 134 NC_002950:PG1058|5end_OmpA_family_protein_1124034..1124264_POSITIVE 404 197 154 63 21 NC_002950:PG1847|5end_endoribonuclease_L-PSP,_putative_1946607..1946837_NEGATIVE 401 237 192 136 92 NC_002950:PG2063|5end_hypothetical_protein_2160596..2160826_NEGATIVE 399 235 193 41 1 NC_002950:PG1799|5end_hypothetical_protein_1894499..1894729_POSITIVE 384 188 141 201 153 NC_002950:PG2202|5end_Holliday_junction_resolvase-like_protein_2309933..2310163_NEGATIVE 379 200 152 83 23 NC_002950:PG1049|5end_hypothetical_protein_1116387..1116617_POSITIVE 378 198 152 70 24 NC_002950:PG0676|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_727275..727505_NEGATIVE 360 340 291 130 77 NC_002950:PG0340|5end_hypothetical_protein_376066..376296_POSITIVE 354 300 255 91 46 NC_002950:PG2064|5end_hypothetical_protein_2160550..2160780_POSITIVE 354 187 143 66 16 NC_002950:PG1691|5end_hypothetical_protein_1776484..1776714_NEGATIVE 353 420 376 118 73 NC_002950:PG1130|5end_TPR_domain_protein_1208053..1208283_POSITIVE 352 198 151 63 5 NC_002950:PG0728|5end_hypothetical_protein_779807..780037_NEGATIVE 349 198 151 187 131 NC_002950:PG2134|5end_lipoprotein,_putative_2239927..2240157_POSITIVE 343 240 195 154 113 NC_002950:PG1635|5end_hypothetical_protein_1715861..1716091_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 432 188 142 63 13 NC_002950:PG0547|3end_hypothetical_protein_601989..602139_POSITIVE 402 173 135 149 112 NC_002950:PG1057|3end_hypothetical_protein_1124092..1124242_POSITIVE 390 419 376 62 14 NC_002950:PG0034|3end_thioredoxin_42235..42385_NEGATIVE 376 204 161 48 1 NC_002950:PG1848|3end_RNA_methyltransferase,_TrmH_family_1946633..1946783_NEGATIVE 369 345 301 52 8 NC_002950:PG0354|3end_hypothetical_protein_389131..389281_NEGATIVE 365 217 182 59 24 NC_002950:PG1174|3end_thioesterase_family_protein_1253210..1253360_NEGATIVE 358 198 151 85 36 NC_002950:PG0155|3end_riboflavin_biosynthesis_protein_RibD_177861..178011_NEGATIVE 343 240 195 140 99 NC_002950:PG1636|3end_FtsK/SpoIIIE_family_protein_1715875..1716025_NEGATIVE 343 220 171 79 30 NC_002950:PG1256|3end_ribonuclease,_Rne/Rng_family_1332748..1332898_NEGATIVE 339 197 151 60 11 NC_002950:PG1929|3end_ribosomal_protein_S17_2019947..2020097_NEGATIVE 339 180 133 132 73 NC_002950:PG1467|3end_methlytransferase,_UbiE/COQ5_family_1543901..1544051_POSITIVE 333 339 293 55 11 NC_002950:PG0705|3end_glutamate_racemase_760433..760583_POSITIVE 330 229 183 145 92 NC_002950:PG1486|3end_conjugative_transposon_protein_TraA_1560357..1560507_NEGATIVE 330 377 331 144 94 NC_002950:PG1345|3end_glycosyl_transferase,_group_1_family_protein_1426791..1426941_POSITIVE 329 355 315 123 76 NC_002950:PG1021|3end_hypothetical_protein_1083395..1083545_NEGATIVE 325 420 376 65 17 NC_002950:PG2117|3end_30S_ribosomal_protein_S16_2225235..2225385_NEGATIVE 325 357 315 83 33 NC_002950:PG0223|3end_exonuclease_257119..257269_NEGATIVE 322 199 152 111 73 NC_002950:PG1855|3end_carboxyl-terminal_protease_1953842..1953992_NEGATIVE 321 198 151 89 40 NC_002950:PG1593|3end_shikimate_kinase_1672143..1672293_POSITIVE 320 196 152 95 51 NC_002950:PG1641|3end_phosphotyrosine_protein_phosphatase_1721260..1721410_NEGATIVE