Origin IGS: aaaaacaggacaacgaactgtgaaagccgatcggggcgttcggcttgtcctcactttgctctgattccttagtgagcagacaaagaatatggacaaagccgatgcatccgcaacgaccgactctgtttcagggttgctatttcagaatacaagaccgaaattattactttttataactaaaaaccaaa .........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 tttggtttttagttataaaaagtaataatttcggtcttgtattctgaaatagcaaccctgaaacagagtcggtcgttgcggatgcatcggctttgtccatattctttgtctgctcactaaggaatcagagcaaagtgaggacaagccgaacgccccgatcggctttcacagttcgttgtcctgttttt Mask Tandem Repeat Region ================================================ aaaaacaggacaacgaactgtgaaagccgatcggggcgttcggcttgtcctcactttgctctgattccttagtgagcagacaaagaatatggacaaagccgatgcatccgcaacgaccgactctgtttcagggttgctatttcagaatacaagaccgaaattattactttttataactaaaaaccaaa Find is-nt database================================================ Query_seq: PG0547:PG0548|PG0547:PG0548:hypothetical protein:pyruvate ferredoxin/flavodoxin oxidoreductase family protein:->->:602050..602237 188 aaaaacaggacaacgaactgtgaaagccgatcggggcgttcggcttgtcctcactttgctctgattccttagtgagcagacaaagaatatggacaaagccgatgcatccgcaacgaccgactctgtttcagggttgctatttcagaatacaagaccgaaattattactttttataactaaaaaccaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0547:PG0548|PG0547:PG0548:hypothetical protein:pyruvate ferredoxin/flavodoxin oxidoreductase family protein:->->:602050..602237 188 aaaaacaggacaacgaactgtgaaagccgatcggggcgttcggcttgtcctcactttgctctgattccttagtgagcagacaaagaatatggacaaagccgatgcatccgcaacgaccgactctgtttcagggttgctatttcagaatacaagaccgaaattattactttttataactaaaaaccaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0547:PG0548|PG0547:PG0548:hypothetical protein:pyruvate ferredoxin/flavodoxin oxidoreductase family protein:->->:602050..602237 188 aaaaacaggacaacgaactgtgaaagccgatcggggcgttcggcttgtcctcactttgctctgattccttagtgagcagacaaagaatatggacaaagccgatgcatccgcaacgaccgactctgtttcagggttgctatttcagaatacaagaccgaaattattactttttataactaaaaaccaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaacaggacaacgaactgtgaaagccgatcggggcgttcggcttgtcctcactttgctctgattccttagtgagcagacaaagaatatggacaaagccgatgcatccgcaacgaccgactctgtttcagggttgctatttcagaatacaagaccgaaattattactttttataactaaaaaccaaa Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 30 End: 173 ............................. M G A F G L S S L C S D S L V S R Q R I W T K P M H P Q R P T L F Q G C Y F R I Q D R N Y Y F L ............... Protein_Len: 33 Strand: + Start: 89 End: 187 ........................................................................................ M D K A D A S A T T D S V S G L L F Q N T R P K L L L F I T K N Q . Protein_Len: 31 Strand: - Start: 72 End: 164 ....................................................................... H A S L S Y P C L R H M R L S R S Q K L T A I E S Y L V S I M ........................ Protein_Len: 34 Strand: - Start: 2 End: 103 . F C S L S S H F G I P A N P K D E S Q E S E K T L L C L I H V F G M ..................................................................................... Protein_Len: 32 Strand: - Start: 1 End: 96 F V P C R V T F A S R P T R S T R V K S Q N R L S C V F F I S M ............................................................................................ aaaaacaggacaacgaactgtgaaagccgatcggggcgttcggcttgtcctcactttgctctgattccttagtgagcagacaaagaatatggacaaagccgatgcatccgcaacgaccgactctgtttcagggttgctatttcagaatacaagaccgaaattattactttttataactaaaaaccaaa 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================================================ aaaaacaggacaacgaactgtgaaagccgatcggggcgttcggcttgtcctcactttgctctgattccttagtgagcagacaaagaatatggacaaagccgatgcatccgcaacgaccgactctgtttcagggttgctatttcagaatacaagaccgaaattattactttttataactaaaaaccaaa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 79 HP_score: -10.2 Tail_Score: -3.62478 Start: 26 End: 44 Full_Region: gcaaagtgaggacaa gccgaacg ccc cgatcggc tttcacagttcgttg .........................gccgaacgccccgatcggc................................................................................................................................................ Find igs database================================================ Query_seq: PG0547:PG0548|PG0547:PG0548:hypothetical protein:pyruvate ferredoxin/flavodoxin oxidoreductase family protein:->->:602050..602237 188 aaaaacaggacaacgaactgtgaaagccgatcggggcgttcggcttgtcctcactttgctctgattccttagtgagcagacaaagaatatggacaaagccgatgcatccgcaacgaccgactctgtttcagggttgctatttcagaatacaagaccgaaattattactttttataactaaaaaccaaa Intra-Species Hit: Count: 1 Min: 1 Max: 188 Len: 188 Subject: NC_002950_PG0547_PG0548|hypothetical protein:pyruvate ferredoxin/flavodoxin oxidoreductase family protein|POSITIVE:POSITIVE|[602050,602237]|188 HSP 1 e-value: 1.0E-102 bit: 373.0 Len: 188 Query Start:1 Query End:188 Subject Strand: POSITIVE Subject Start: 1 Subject End: 188 aaaaacaggacaacgaactgtgaaagccgatcggggcgttcggcttgtcctcactttgctctgattccttagtgagcagacaaagaatatggacaaagccgatgcatccgcaacgaccgactctgtttcagggttgctatttcagaatacaagaccgaaattattactttttataactaaaaaccaaa aaaaacaggacaacgaactgtgaaagccgatcggggcgttcggcttgtcctcactttgctctgattccttagtgagcagacaaagaatatggacaaagccgatgcatccgcaacgaccgactctgtttcagggttgctatttcagaatacaagaccgaaattattactttttataactaaaaaccaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAACAGGACAACGAACUGUGAAAGCCGAUCGGGGCGUUCGGCUUGUCCUCACUUUGCUCUGAUUCCUUAGUGAGCAGACAAAGAAUAUGGACAAAGCCGAUGCAUCCGCAACGACCGACUCUGUUUCAGGGUUGCUAUUUCAGAAUACAAGACCGAAAUUAUUACUUUUUAUAACUAAAAACCAAA .......((.........(.(((((..((..((((((((.((((((((((...(((((.((((.(((......)))))))))))).....)))).)))))))))).))))...))..((((((((...))))))))...))))).)..........((((........))))...........))... (-47.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGGUUUUUAGUUAUAAAAAGUAAUAAUUUCGGUCUUGUAUUCUGAAAUAGCAACCCUGAAACAGAGUCGGUCGUUGCGGAUGCAUCGGCUUUGUCCAUAUUCUUUGUCUGCUCACUAAGGAAUCAGAGCAAAGUGAGGACAAGCCGAACGCCCCGAUCGGCUUUCACAGUUCGUUGUCCUGUUUUU .(((.((((((....)))))).)))..(((((((.........))))))).(((((.(((....(((((((((((..(((......(((((((.((((.....(((((((((.((......))..)))).)))))...))))))))))).)))..)))))))))))..)))...)))))......... (-54.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 476 50 4 77 15 NC_002950:PG1966|5end_hypothetical_protein_2056924..2057154_NEGATIVE 431 78 31 66 19 NC_002950:PG1454|5end_integrase_1538106..1538336_NEGATIVE 431 78 31 66 19 NC_002950:PG0819|5end_integrase_877326..877556_POSITIVE 420 74 33 231 175 NC_002950:PG0961|5end_hypothetical_protein_1022272..1022502_NEGATIVE 412 70 26 190 129 NC_002950:PG1617|5end_hypothetical_protein_1697755..1697985_NEGATIVE 393 64 21 177 135 NC_002950:PG1269|5end_delta-1-pyrroline-5-carboxylate_dehydrogenase_1349201..1349431_NEGATIVE 393 65 27 191 149 NC_002950:PG0659|5end_hypothetical_protein_709148..709378_NEGATIVE 386 79 32 52 4 NC_002950:PG0851|5end_hypothetical_protein_912732..912962_NEGATIVE 374 50 5 216 165 NC_002950:PG1042|5end_glycogen_synthase,_putative_1110638..1110868_NEGATIVE 365 59 12 213 162 NC_002950:PG1847|5end_endoribonuclease_L-PSP,_putative_1946607..1946837_NEGATIVE 365 138 91 207 158 NC_002950:PG1499|5end_hypothetical_protein_1575524..1575754_POSITIVE 364 50 6 184 132 NC_002950:PG0829|5end_hypothetical_protein_886746..886976_NEGATIVE 360 63 26 168 135 NC_002950:PG0327|5end_hypothetical_protein_362061..362291_NEGATIVE 356 49 7 183 139 NC_002950:PG1242|5end_replicative_DNA_helicase_1317435..1317665_POSITIVE 355 61 26 192 150 NC_002950:PG1633|5end_galactokinase_1713385..1713615_POSITIVE 351 49 12 167 124 NC_002950:PG2031|5end_hypothetical_protein_2130339..2130569_POSITIVE 351 70 25 108 61 NC_002950:PG0844|5end_hypothetical_protein_905289..905519_POSITIVE 350 137 91 104 41 NC_002950:PG0326|5end_hypothetical_protein_360974..361204_NEGATIVE 349 80 31 51 2 NC_002950:PG0143|5end_hydrolase,_carbon-nitrogen_family_166625..166855_NEGATIVE 347 139 97 216 163 NC_002950:PG1134|5end_thioredoxin_reductase_1214350..1214580_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 408 137 97 49 15 NC_002950:PG0317|3end_peptidase,_M49_family_349771..349921_NEGATIVE 393 64 21 100 58 NC_002950:PG1270|3end_hypothetical_protein_1349278..1349428_NEGATIVE 387 67 25 135 86 NC_002950:PG1473|3end_conjugative_transposon_protein_TraQ_1549761..1549911_NEGATIVE 387 69 25 136 88 NC_002950:PG1218|3end_hypothetical_protein_1296475..1296625_POSITIVE 365 49 6 150 103 NC_002950:PG1402|3end_AP_endonuclease_domain_protein_1485031..1485181_NEGATIVE 360 63 26 74 41 NC_002950:PG0328|3end_imidazolonepropionase_362155..362305_NEGATIVE 356 49 7 148 104 NC_002950:PG1241|3end_GTP-binding_protein_LepA_1317480..1317630_POSITIVE 355 61 26 142 100 NC_002950:PG1632|3end_aldose_1-epimerase_1713415..1713565_POSITIVE 354 59 14 102 59 NC_002950:PG1104|3end_hypothetical_protein_1175782..1175932_POSITIVE 348 79 31 113 62 NC_002950:PG1942|3end_30S_ribosomal_protein_S12_2027946..2028096_NEGATIVE 343 51 18 41 4 NC_002950:PG1739|3end_hypothetical_protein_1825128..1825278_NEGATIVE 343 76 33 123 83 NC_002950:PG0843|3end_hypothetical_protein_904871..905021_NEGATIVE 343 80 43 102 59 NC_002950:PG0669|3end_heme-binding_protein_FetB_720714..720864_POSITIVE 341 69 25 122 61 NC_002950:PG0132|3end_hypothetical_protein_153054..153204_POSITIVE 339 60 13 70 16 NC_002950:PG0555|3end_DNA-binding_protein,_histone-like_family_611716..611866_NEGATIVE 339 69 27 55 6 NC_002950:PG0332|3end_transcription_termination_factor_Rho_367675..367825_POSITIVE 338 59 13 146 100 NC_002950:PG0962|3end_prolyl-tRNA_synthetase_1022327..1022477_NEGATIVE 336 50 5 75 32 NC_002950:PG1613|3end_glyoxalase_family_protein_1693164..1693314_NEGATIVE 335 49 2 145 76 NC_002950:PG1375|3end_hypothetical_protein_1456743..1456893_POSITIVE 334 77 33 65 12 NC_002950:PG0790|3end_GTP-binding_protein_Obg_841399..841549_NEGATIVE