Origin IGS: cccgacctgagcagcaaggaagaacgggaaagccaaaccgaaaaaagcagatatcgtaattgttgccggagatatgaatggcgacaaggcagccaagagataacaggacgtaatccccagattgataattaccgaaacagaatggagcaatgttccaattctgccccttgctttcttcttctttttttcactcatctcttgcagacgac .........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 gtcgtctgcaagagatgagtgaaaaaaagaagaagaaagcaaggggcagaattggaacattgctccattctgtttcggtaattatcaatctggggattacgtcctgttatctcttggctgccttgtcgccattcatatctccggcaacaattacgatatctgcttttttcggtttggctttcccgttcttccttgctgctcaggtcggg Mask Tandem Repeat Region ================================================ cccgacctgagcagcaaggaagaacgggaaagccaaaccgaaaaaagcagatatcgtaattgttgccggagatatgaatggcgacaaggcagccaagagataacaggacgtaatccccagattgataattaccgaaacagaatggagcaatgttccaattctgccccttgctttcttcttctttttttcactcatctcttgcagacgac Find is-nt database================================================ Query_seq: PG1402:PG1403|PG1402:PG1403:AP endonuclease domain protein:rhomboid family protein:<-<-:1486054..1486262 209 cccgacctgagcagcaaggaagaacgggaaagccaaaccgaaaaaagcagatatcgtaattgttgccggagatatgaatggcgacaaggcagccaagagataacaggacgtaatccccagattgataattaccgaaacagaatggagcaatgttccaattctgccccttgctttcttcttctttttttcactcatctcttgcagacgac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1402:PG1403|PG1402:PG1403:AP endonuclease domain protein:rhomboid family protein:<-<-:1486054..1486262 209 cccgacctgagcagcaaggaagaacgggaaagccaaaccgaaaaaagcagatatcgtaattgttgccggagatatgaatggcgacaaggcagccaagagataacaggacgtaatccccagattgataattaccgaaacagaatggagcaatgttccaattctgccccttgctttcttcttctttttttcactcatctcttgcagacgac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1402:PG1403|PG1402:PG1403:AP endonuclease domain protein:rhomboid family protein:<-<-:1486054..1486262 209 cccgacctgagcagcaaggaagaacgggaaagccaaaccgaaaaaagcagatatcgtaattgttgccggagatatgaatggcgacaaggcagccaagagataacaggacgtaatccccagattgataattaccgaaacagaatggagcaatgttccaattctgccccttgctttcttcttctttttttcactcatctcttgcagacgac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cccgacctgagcagcaaggaagaacgggaaagccaaaccgaaaaaagcagatatcgtaattgttgccggagatatgaatggcgacaaggcagccaagagataacaggacgtaatccccagattgataattaccgaaacagaatggagcaatgttccaattctgccccttgctttcttcttctttttttcactcatctcttgcagacgac Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 7 End: 207 ...... M S S K E E R E S Q T E K S R Y R N C C R R Y E W R Q G S Q E I T G R N P Q I D N Y R N R M E Q C S N S A P C F L L L F .. Protein_Len: 32 Strand: + Start: 113 End: 208 ................................................................................................................ M P R L I I T E T E W S N V P I L P L A F F F F F S L I S C R R . Protein_Len: 40 Strand: - Start: 3 End: 122 .. S R L L L S S R S L W V S F L L Y R L Q Q R L Y S H R C P L W S I V P R L G W M ....................................................................................... Protein_Len: 50 Strand: - Start: 2 End: 151 . R G S C C P L V P F G F R F F C I D Y N N G S I H I A V L C G L S L L V Y D G S Q Y N G F C F P A M .......................................................... Protein_Len: 60 Strand: - Start: 1 End: 204 P F A L G F F A S I T I T A P S I F P S L A A L L Y C S T I G L N I I V S V S H L L T G I R G R A K K K K K E S M E Q M ..... cccgacctgagcagcaaggaagaacgggaaagccaaaccgaaaaaagcagatatcgtaattgttgccggagatatgaatggcgacaaggcagccaagagataacaggacgtaatccccagattgataattaccgaaacagaatggagcaatgttccaattctgccccttgctttcttcttctttttttcactcatctcttgcagacgac 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================================================ cccgacctgagcagcaaggaagaacgggaaagccaaaccgaaaaaagcagatatcgtaattgttgccggagatatgaatggcgacaaggcagccaagagataacaggacgtaatccccagattgataattaccgaaacagaatggagcaatgttccaattctgccccttgctttcttcttctttttttcactcatctcttgcagacgac Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1402:PG1403|PG1402:PG1403:AP endonuclease domain protein:rhomboid family protein:<-<-:1486054..1486262 209 cccgacctgagcagcaaggaagaacgggaaagccaaaccgaaaaaagcagatatcgtaattgttgccggagatatgaatggcgacaaggcagccaagagataacaggacgtaatccccagattgataattaccgaaacagaatggagcaatgttccaattctgccccttgctttcttcttctttttttcactcatctcttgcagacgac Intra-Species Hit: Count: 1 Min: 1 Max: 209 Len: 209 Subject: NC_002950_PG1402_PG1403|AP endonuclease domain protein:rhomboid family protein|NEGATIVE:NEGATIVE|[1486054,1486262]|209 HSP 1 e-value: 1.0E-102 bit: 373.0 Len: 209 Query Start:1 Query End:209 Subject Strand: POSITIVE Subject Start: 1 Subject End: 209 cccgacctgagcagcaaggaagaacgggaaagccaaaccgaaaaaagcagatatcgtaattgttgccggagatatgaatggcgacaaggcagccaagagataacaggacgtaatccccagattgataattaccgaaacagaatggagcaatgttccaattctgccccttgctttcttcttcnnnnnnncactcatctcttgcagacgac cccgacctgagcagcaaggaagaacgggaaagccaaaccgaaaaaagcagatatcgtaattgttgccggagatatgaatggcgacaaggcagccaagagataacaggacgtaatccccagattgataattaccgaaacagaatggagcaatgttccaattctgccccttgctttcttcttctttttttcactcatctcttgcagacgac Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCGACCUGAGCAGCAAGGAAGAACGGGAAAGCCAAACCGAAAAAAGCAGAUAUCGUAAUUGUUGCCGGAGAUAUGAAUGGCGACAAGGCAGCCAAGAGAUAACAGGACGUAAUCCCCAGAUUGAUAAUUACCGAAACAGAAUGGAGCAAUGUUCCAAUUCUGCCCCUUGCUUUCUUCUUCUUUUUUUCACUCAUCUCUUGCAGACGAC ...((..((((..(.(((((((((..(((((((..................((((....(((((((((..........)))))))))((...))....))))..(((...(((((....))))).............(((((((((((...))))).))))))..))).)))))))..))))))))).).))))..))........... (-48.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUCGUCUGCAAGAGAUGAGUGAAAAAAAGAAGAAGAAAGCAAGGGGCAGAAUUGGAACAUUGCUCCAUUCUGUUUCGGUAAUUAUCAAUCUGGGGAUUACGUCCUGUUAUCUCUUGGCUGCCUUGUCGCCAUUCAUAUCUCCGGCAACAAUUACGAUAUCUGCUUUUUUCGGUUUGGCUUUCCCGUUCUUCCUUGCUGCUCAGGUCGGG .(((.(((((((.((.(((.((((..(((..((((((((((.(..(((((((.(((.......))))))))))..).((((((......((((((((.................((((.((...)).)))).....))))))))....))))))......))))))))))..)))...))))...))).)))))))......)).))). (-55.75) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1019 50 1 141 92 NC_002950:PG1402|5end_AP_endonuclease_domain_protein_1485963..1486193_NEGATIVE 359 109 66 229 186 NC_002950:PG1947|5end_TPR_domain_protein_2032932..2033162_POSITIVE 343 110 61 181 136 NC_002950:PG1196|5end_hypothetical_protein_1275127..1275357_POSITIVE 342 99 64 164 118 NC_002950:PG0606|5end_hypothetical_protein_662558..662788_NEGATIVE 336 110 62 59 1 NC_002950:PG1966|5end_hypothetical_protein_2056924..2057154_NEGATIVE 334 110 64 67 20 NC_002950:PG2187|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_2294643..2294873_NEGATIVE 328 99 60 142 88 NC_002950:PG0518|5end_abortive_infection_protein_family_562939..563169_NEGATIVE 321 177 139 67 20 NC_002950:PG1913|5end_30S_ribosomal_protein_S11_2012926..2013156_NEGATIVE 321 90 47 226 178 NC_002950:PG0893|5end_hydroxylamine_reductase_955853..956083_NEGATIVE 317 48 2 219 178 NC_002950:PG1876|5end_hypothetical_protein_1971460..1971690_NEGATIVE 316 49 3 165 122 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 313 35 7 90 52 NC_002950:PG0272|5end_CBS_domain_protein_304399..304629_POSITIVE 309 77 33 75 25 NC_002950:PG0754|5end_DNA_topoisomerase_I_800943..801173_POSITIVE 305 107 65 68 25 NC_002950:PG0115|5end_hexapeptide_transferase_family_protein_138038..138268_POSITIVE 304 186 141 148 102 NC_002950:PG2185|5end_transporter,_putative_2293249..2293479_NEGATIVE 304 110 66 165 118 NC_002950:PG1481|5end_conjugative_transposon_protein_TraG_1558447..1558677_NEGATIVE 303 107 62 47 7 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 302 40 2 77 21 NC_002950:PG1855|5end_carboxyl-terminal_protease_1955476..1955706_NEGATIVE 297 110 61 139 78 NC_002950:PG1884|5end_alpha-L-fucosidase_precursor,_putative_1980992..1981222_NEGATIVE 297 48 1 72 18 NC_002950:PG0018|5end_hypothetical_protein_19648..19878_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 110 64 77 30 NC_002950:PG2188|3end_diaminopimelate_decarboxylase_2294633..2294783_NEGATIVE 321 177 139 55 8 NC_002950:PG1914|3end_30S_ribosomal_protein_S13_2012938..2013088_NEGATIVE 320 99 61 147 99 NC_002950:PG0308|3end_electron_transport_complex,_RnfABCDGE_type,_A_subunit_343827..343977_POSITIVE 307 179 133 77 24 NC_002950:PG0507|3end_hypothetical_protein_548190..548340_POSITIVE 305 89 48 130 80 NC_002950:PG0917|3end_GtrA_family_protein_977702..977852_NEGATIVE 304 186 141 113 67 NC_002950:PG2186|3end_transcriptional_regulator,_putative_2293284..2293434_NEGATIVE 302 40 2 69 13 NC_002950:PG1856|3end_cytidine/deoxycytidylate_deaminase_family_protein_1955484..1955634_NEGATIVE 302 50 1 49 8 NC_002950:PG0770|3end_hypothetical_protein_824159..824309_NEGATIVE 301 47 9 146 107 NC_002950:PG1359|3end_hypothetical_protein_1437644..1437794_NEGATIVE 300 177 131 59 14 NC_002950:PG1195|3end_8-amino-7-oxononanoate_synthase_1275207..1275357_POSITIVE 298 69 21 69 14 NC_002950:PG2105|3end_lipoprotein,_putative_2214579..2214729_POSITIVE 297 110 61 66 5 NC_002950:PG1885|3end_polyphosphate_kinase_1981065..1981215_NEGATIVE 297 48 1 68 14 NC_002950:PG0017|3end_sensor_histidine_kinase_19724..19874_POSITIVE 296 109 63 48 6 NC_002950:PG2210|3end_excinuclease_ABC,_A_subunit_2320952..2321102_NEGATIVE 296 97 56 151 111 NC_002950:PG1807|3end_v-type_ATPase,_subunit_K_1902625..1902775_POSITIVE 296 120 81 67 18 NC_002950:PG0954|3end_TPR_domain_protein_1015005..1015155_POSITIVE 294 180 131 51 5 NC_002950:PG2037|3end_hypothetical_protein_2137591..2137741_NEGATIVE 293 40 1 45 2 NC_002950:PG1978|3end_hypothetical_protein_2066723..2066873_NEGATIVE 293 49 1 100 48 NC_002950:PG0324|3end_histidine_ammonia-lyase_357589..357739_NEGATIVE 291 189 142 110 70 NC_002950:PG0400|3end_hypothetical_protein_436245..436395_NEGATIVE