Origin IGS: gcccccgaaatgttacatctcaaaccgttttttctcgaactctctatctcgaatgggcgcaaaaacattacgttcgaaagagggaaatcactcctccgttcaatcgcattgagagctaaaaaagaagagtcgggaagcaaaagctgcaactcgactcttctcggttcttctgtcttttcttcgtttacgaaaaagggaagtatttattggcttaagatgtggaaccgc .........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 gcggttccacatcttaagccaataaatacttccctttttcgtaaacgaagaaaagacagaagaaccgagaagagtcgagttgcagcttttgcttcccgactcttcttttttagctctcaatgcgattgaacggaggagtgatttccctctttcgaacgtaatgtttttgcgcccattcgagatagagagttcgagaaaaaacggtttgagatgtaacatttcgggggc Mask Tandem Repeat Region ================================================ gcccccgaaatgttacatctcaaaccgttttttctcgaactctctatctcgaatgggcgcaaaaacattacgttcgaaagagggaaatcactcctccgttcaatcgcattgagagctaaaaaagaagagtcgggaagcaaaagctgcaactcgactcttctcggttcttctgtcttttcttcgtttacgaaaaagggaagtatttattggcttaagatgtggaaccgc Find is-nt database================================================ Query_seq: PG0419:PG0421|PG0419:PG0421:hypothetical protein:hypothetical protein:<-<-:460698..460925 228 gcccccgaaatgttacatctcaaaccgttttttctcgaactctctatctcgaatgggcgcaaaaacattacgttcgaaagagggaaatcactcctccgttcaatcgcattgagagctaaaaaagaagagtcgggaagcaaaagctgcaactcgactcttctcggttcttctgtcttttcttcgtttacgaaaaagggaagtatttattggcttaagatgtggaaccgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0419:PG0421|PG0419:PG0421:hypothetical protein:hypothetical protein:<-<-:460698..460925 228 gcccccgaaatgttacatctcaaaccgttttttctcgaactctctatctcgaatgggcgcaaaaacattacgttcgaaagagggaaatcactcctccgttcaatcgcattgagagctaaaaaagaagagtcgggaagcaaaagctgcaactcgactcttctcggttcttctgtcttttcttcgtttacgaaaaagggaagtatttattggcttaagatgtggaaccgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0419:PG0421|PG0419:PG0421:hypothetical protein:hypothetical protein:<-<-:460698..460925 228 gcccccgaaatgttacatctcaaaccgttttttctcgaactctctatctcgaatgggcgcaaaaacattacgttcgaaagagggaaatcactcctccgttcaatcgcattgagagctaaaaaagaagagtcgggaagcaaaagctgcaactcgactcttctcggttcttctgtcttttcttcgtttacgaaaaagggaagtatttattggcttaagatgtggaaccgc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcccccgaaatgttacatctcaaaccgttttttctcgaactctctatctcgaatgggcgcaaaaacattacgttcgaaagagggaaatcactcctccgttcaatcgcattgagagctaaaaaagaagagtcgggaagcaaaagctgcaactcgactcttctcggttcttctgtcttttcttcgtttacgaaaaagggaagtatttattggcttaagatgtggaaccgc Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 17 End: 109 ................ M S N R F F S N S L S R M G A K T L R S K E G N H S S V Q S H ....................................................................................................................... Protein_Len: 60 Strand: + Start: 10 End: 228 ......... M L H L K P F F L E L S I S N G R K N I T F E R G K S L L R S I A L R A K K E E S G S K S C N S T L L G S S V F S S F T Protein_Len: 35 Strand: - Start: 103 End: 207 ...................................................................................................... D C Q S S F F F L R S A F A A V R S K E T R R D K R R K R F L S T N M ..................... Protein_Len: 60 Strand: - Start: 3 End: 203 .. G N K R S S E I E F P R L F M V N S L P F D S R R E I A N L A L F S S D P L L L Q L E V R R P E E T K E E N V F F P L M ......................... gcccccgaaatgttacatctcaaaccgttttttctcgaactctctatctcgaatgggcgcaaaaacattacgttcgaaagagggaaatcactcctccgttcaatcgcattgagagctaaaaaagaagagtcgggaagcaaaagctgcaactcgactcttctcggttcttctgtcttttcttcgtttacgaaaaagggaagtatttattggcttaagatgtggaaccgc 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================================================ gcccccgaaatgttacatctcaaaccgttttttctcgaactctctatctcgaatgggcgcaaaaacattacgttcgaaagagggaaatcactcctccgttcaatcgcattgagagctaaaaaagaagagtcgggaagcaaaagctgcaactcgactcttctcggttcttctgtcttttcttcgtttacgaaaaagggaagtatttattggcttaagatgtggaaccgc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 77 HP_score: -11.6 Tail_Score: -2.70665 Start: 124 End: 160 Full_Region: TTGAGAGCTAAAAAA GAAGAGTCGGGAAGCA AAAGC TGCAACTCGACTCTTC TCGGTTCTTCTGTCT ...........................................................................................................................GAAGAGTCGGGAAGCAAAAGCTGCAACTCGACTCTTC.................................................................... TransTerm Strand: - Conf: 93 HP_score: -10.1 Tail_Score: -5.1287 Start: 124 End: 160 Full_Region: agacagaagaaccga gaagagtcgagttgcag ctt ttgcttcccgactcttc ttttttagctctcaa ...........................................................................................................................gaagagtcgagttgcagcttttgcttcccgactcttc.................................................................... Find igs database================================================ Query_seq: PG0419:PG0421|PG0419:PG0421:hypothetical protein:hypothetical protein:<-<-:460698..460925 228 gcccccgaaatgttacatctcaaaccgttttttctcgaactctctatctcgaatgggcgcaaaaacattacgttcgaaagagggaaatcactcctccgttcaatcgcattgagagctaaaaaagaagagtcgggaagcaaaagctgcaactcgactcttctcggttcttctgtcttttcttcgtttacgaaaaagggaagtatttattggcttaagatgtggaaccgc Intra-Species Hit: Count: 1 Min: 1 Max: 228 Len: 228 Subject: NC_002950_PG0419_PG0421|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[460698,460925]|228 HSP 1 e-value: 1.0E-126 bit: 452.0 Len: 228 Query Start:1 Query End:228 Subject Strand: POSITIVE Subject Start: 1 Subject End: 228 gcccccgaaatgttacatctcaaaccgttttttctcgaactctctatctcgaatgggcgcaaaaacattacgttcgaaagagggaaatcactcctccgttcaatcgcattgagagctaaaaaagaagagtcgggaagcaaaagctgcaactcgactcttctcggttcttctgtcttttcttcgtttacgaaaaagggaagtatttattggcttaagatgtggaaccgc gcccccgaaatgttacatctcaaaccgttttttctcgaactctctatctcgaatgggcgcaaaaacattacgttcgaaagagggaaatcactcctccgttcaatcgcattgagagctaaaaaagaagagtcgggaagcaaaagctgcaactcgactcttctcggttcttctgtcttttcttcgtttacgaaaaagggaagtatttattggcttaagatgtggaaccgc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCCCCGAAAUGUUACAUCUCAAACCGUUUUUUCUCGAACUCUCUAUCUCGAAUGGGCGCAAAAACAUUACGUUCGAAAGAGGGAAAUCACUCCUCCGUUCAAUCGCAUUGAGAGCUAAAAAAGAAGAGUCGGGAAGCAAAAGCUGCAACUCGACUCUUCUCGGUUCUUCUGUCUUUUCUUCGUUUACGAAAAAGGGAAGUAUUUAUUGGCUUAAGAUGUGGAACCGC ............((((((((..(((((............(((((.....(((.((((((..............((....)).(((......)))..)))))).)))....))))).......((((((((((((..(((.....)))..)))))))))))))))))......((((((.((((....)))).))))))................))))))))...... (-61.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCGGUUCCACAUCUUAAGCCAAUAAAUACUUCCCUUUUUCGUAAACGAAGAAAAGACAGAAGAACCGAGAAGAGUCGAGUUGCAGCUUUUGCUUCCCGACUCUUCUUUUUUAGCUCUCAAUGCGAUUGAACGGAGGAGUGAUUUCCCUCUUUCGAACGUAAUGUUUUUGCGCCCAUUCGAGAUAGAGAGUUCGAGAAAAAACGGUUUGAGAUGUAACAUUUCGGGGGC ...(((((((((((((((((........((((..(((((((....)))))))......))))....(((((((((((.(..((((...))))..).)))))))))))(((((((((((.((.(((.((..((((((((.(....).))))))))..(((((.....)))))..)).)))..)).))))))).))))......)))))))))))).........))))) (-71.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 941 140 91 231 182 NC_002950:PG0419|5end_hypothetical_protein_460607..460837_NEGATIVE 367 159 112 119 57 NC_002950:PG1029|5end_hypothetical_protein_1091080..1091310_POSITIVE 364 65 25 61 19 NC_002950:PG1249|5end_1-acyl-sn-glycerol-3-phosphate_acetyltransferase,_putative_1327161..1327391_NEGATIVE 347 187 141 90 29 NC_002950:PG1195|5end_8-amino-7-oxononanoate_synthase_1273979..1274209_POSITIVE 346 138 93 54 19 NC_002950:PG1418|5end_DNA_polymerase_III,_gamma_and_tau_subunits_1503064..1503294_POSITIVE 343 177 131 165 120 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 343 188 141 186 145 NC_002950:PG0335|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_370706..370936_NEGATIVE 334 168 121 106 49 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 332 189 143 82 28 NC_002950:PG0930|5end_hypothetical_protein_987542..987772_NEGATIVE 332 170 121 197 134 NC_002950:PG0677|5end_saccharopine_dehydrogenase_727653..727883_POSITIVE 327 187 142 216 161 NC_002950:PG1524|5end_2-succinyl-6-hydroxy-2,_4-cyclohexadiene-1-carboxylic_acid_synthase/2-oxoglutarate_decarboxylase_1602746..1602976_NEGATIVE 322 170 121 167 112 NC_002950:PG1079|5end_enoyl-CoA_hydratase/isomerase_family_protein_1146549..1146779_POSITIVE 320 118 71 214 166 NC_002950:PG0264|5end_glycosyl_transferase,_group_2_family_protein_296975..297205_POSITIVE 319 179 133 218 147 NC_002950:PG1621|5end_hypothetical_protein_1701431..1701661_NEGATIVE 318 100 57 194 155 NC_002950:PG0108|5end_UDP-N-acetyl-D-mannosaminuronic_acid_dehydrogenase_130101..130331_POSITIVE 317 173 131 35 2 NC_002950:PG1457|5end_hypothetical_protein_1538650..1538880_POSITIVE 315 163 121 211 164 NC_002950:PG2156|5end_conserved_hypothetical_protein_TIGR00046_2262645..2262875_NEGATIVE 315 136 91 69 23 NC_002950:PG2032|5end_primosomal_protein_N'_2133381..2133611_NEGATIVE 313 117 71 107 61 NC_002950:PG2052|5end_dihydrodipicolinate_synthase_2149636..2149866_POSITIVE 313 48 3 214 170 NC_002950:PG1003|5end_hypothetical_protein_1059232..1059462_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 358 169 122 55 4 NC_002950:PG1028|3end_TPR_domain_protein_1091096..1091246_POSITIVE 355 168 125 58 7 NC_002950:PG1997|3end_hypothetical_protein_2087072..2087222_POSITIVE 342 65 27 38 5 NC_002950:PG1250|3end_hypothetical_protein_1327184..1327334_NEGATIVE 339 168 127 110 62 NC_002950:PG0173|3end_transcriptional_regulator,_putative_194388..194538_NEGATIVE 334 168 121 92 35 NC_002950:PG2099|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2206649..2206799_NEGATIVE 324 180 131 57 14 NC_002950:PG1473|3end_conjugative_transposon_protein_TraQ_1549761..1549911_NEGATIVE 322 170 121 63 8 NC_002950:PG1078|3end_electron_transfer_flavoprotein,_alpha_subunit_1146525..1146675_POSITIVE 314 139 91 128 84 NC_002950:PG0424|3end_hypothetical_protein_463213..463363_POSITIVE 313 48 3 139 95 NC_002950:PG1002|3end_hypothetical_protein_1059237..1059387_POSITIVE 311 182 141 120 50 NC_002950:PG0047|3end_cell_division_protein_FtsH,_putative_57229..57379_NEGATIVE 308 180 131 63 10 NC_002950:PG2205|3end_2-dehydropantoate_2-reductase_2317145..2317295_POSITIVE 305 170 124 77 30 NC_002950:PG0881|3end_recombinase_A_944165..944315_POSITIVE 299 50 3 117 59 NC_002950:PG0310|3end_nitroreductase_family_protein_345020..345170_NEGATIVE 295 164 124 84 35 NC_002950:PG2044|3end_hypothetical_protein_2144165..2144315_POSITIVE 295 188 141 94 37 NC_002950:PG1483|3end_conjugative_transposon_protein_TraE_1558783..1558933_NEGATIVE 293 199 151 113 68 NC_002950:PG1253|3end_DNA_ligase,_NAD-dependent_1329597..1329747_NEGATIVE 293 170 121 52 4 NC_002950:PG0712|3end_hypothetical_protein_766784..766934_NEGATIVE 292 210 162 140 86 NC_002950:PG2110|3end_thiamine_biosynthesis_protein_ThiC_2219449..2219599_NEGATIVE 291 139 96 41 6 NC_002950:PG1271|3end_acetylornithine_aminotransferase,_putative_1350214..1350364_NEGATIVE 291 197 152 110 64 NC_002950:PG0404|3end_hypothetical_protein_439768..439918_NEGATIVE