Origin IGS: tgtcagaaatgcctaaaaaacatttaggttccttttaggacaatccatagtaaaggtttttgcgtttttgttcatatcttcgttttagaatcttgccttttgaaaaagaataacatcagctattaatagt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 actattaatagctgatgttattctttttcaaaaggcaagattctaaaacgaagatatgaacaaaaacgcaaaaacctttactatggattgtcctaaaaggaacctaaatgttttttaggcatttctgaca Mask Tandem Repeat Region ================================================ tgtcagaaatgcctaaaaaacatttaggttccttttaggacaatccatagtaaaggtttttgcgtttttgttcatatcttcgttttagaatcttgccttttgaaaaagaataacatcagctattaatagt Find is-nt database================================================ Query_seq: PG0055:PG0056|PG0055:PG0056:hypothetical protein:hypothetical protein:->->:68012..68141 130 tgtcagaaatgcctaaaaaacatttaggttccttttaggacaatccatagtaaaggtttttgcgtttttgttcatatcttcgttttagaatcttgccttttgaaaaagaataacatcagctattaatagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0055:PG0056|PG0055:PG0056:hypothetical protein:hypothetical protein:->->:68012..68141 130 tgtcagaaatgcctaaaaaacatttaggttccttttaggacaatccatagtaaaggtttttgcgtttttgttcatatcttcgttttagaatcttgccttttgaaaaagaataacatcagctattaatagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0055:PG0056|PG0055:PG0056:hypothetical protein:hypothetical protein:->->:68012..68141 130 tgtcagaaatgcctaaaaaacatttaggttccttttaggacaatccatagtaaaggtttttgcgtttttgttcatatcttcgttttagaatcttgccttttgaaaaagaataacatcagctattaatagt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtcagaaatgcctaaaaaacatttaggttccttttaggacaatccatagtaaaggtttttgcgtttttgttcatatcttcgttttagaatcttgccttttgaaaaagaataacatcagctattaatagt Predict ORF larger than 30AA ================================================ tgtcagaaatgcctaaaaaacatttaggttccttttaggacaatccatagtaaaggtttttgcgtttttgttcatatcttcgttttagaatcttgccttttgaaaaagaataacatcagctattaatagt 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================================================ tgtcagaaatgcctaaaaaacatttaggttccttttaggacaatccatagtaaaggtttttgcgtttttgttcatatcttcgttttagaatcttgccttttgaaaaagaataacatcagctattaatagt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0055:PG0056|PG0055:PG0056:hypothetical protein:hypothetical protein:->->:68012..68141 130 tgtcagaaatgcctaaaaaacatttaggttccttttaggacaatccatagtaaaggtttttgcgtttttgttcatatcttcgttttagaatcttgccttttgaaaaagaataacatcagctattaatagt Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: NC_002950_PG0055_PG0056|hypothetical protein:hypothetical protein|POSITIVE:POSITIVE|[68012,68141]|130 HSP 1 e-value: 4.0E-68 bit: 258.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 tgtcagaaatgcctaaaaaacatttaggttccttttaggacaatccatagtaaaggtttttgcgtttttgttcatatcttcgttttagaatcttgccttttgaaaaagaataacatcagctattaatagt tgtcagaaatgcctaaaaaacatttaggttccttttaggacaatccatagtaaaggtttttgcgtttttgttcatatcttcgttttagaatcttgccttttgaaaaagaataacatcagctattaatagt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCAGAAAUGCCUAAAAAACAUUUAGGUUCCUUUUAGGACAAUCCAUAGUAAAGGUUUUUGCGUUUUUGUUCAUAUCUUCGUUUUAGAAUCUUGCCUUUUGAAAAAGAAUAACAUCAGCUAUUAAUAGU ((((..(((.(((((((.....)))))))....)))..))))....(((((.((((((((.(((................)))...))))))))...((((....)))).........)))))....... (-20.09) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUAUUAAUAGCUGAUGUUAUUCUUUUUCAAAAGGCAAGAUUCUAAAACGAAGAUAUGAACAAAAACGCAAAAACCUUUACUAUGGAUUGUCCUAAAAGGAACCUAAAUGUUUUUUAGGCAUUUCUGACA ......((((((....)))))).............................(((.(((................(((((.....((.....))..)))))..((((((.....))))))))).))).... (-15.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 276 79 31 97 43 NC_002950:PG0838|5end_integrase_895477..895707_POSITIVE 260 99 54 189 147 NC_002950:PG0929|5end_hypothetical_protein_987149..987379_NEGATIVE 259 99 56 114 74 NC_002950:PG1951|5end_glutaminyl-tRNA_synthetase_2041142..2041372_POSITIVE 256 103 61 128 91 NC_002950:PG1533|5end_Toprim_domain_protein_1613761..1613991_NEGATIVE 248 63 21 193 149 NC_002950:PG0312|5end_hypothetical_protein_347048..347278_NEGATIVE 244 97 55 116 70 NC_002950:PG1393|5end_penicillin-binding_protein_2,_putative_1476271..1476501_NEGATIVE 241 96 61 74 29 NC_002950:PG1205|5end_DNA-binding_protein,_histone-like_family_1283953..1284183_POSITIVE 241 99 54 210 163 NC_002950:PG0498|5end_S-ribosylhomocysteinase_537968..538198_POSITIVE 238 84 44 50 6 NC_002950:PG1030|5end_hypothetical_protein_1091400..1091630_POSITIVE 236 120 71 202 142 NC_002950:PG0450|5end_hypothetical_protein_490812..491042_POSITIVE 232 89 43 211 168 NC_002950:PG1301|5end_hypothetical_protein_1379921..1380151_NEGATIVE 231 99 53 227 169 NC_002950:PG2016|5end_CRISPR-associated_helicase_Cas3_2108370..2108600_NEGATIVE 225 97 55 183 141 NC_002950:PG1769|5end_hypothetical_protein_1856607..1856837_POSITIVE 225 86 42 94 50 NC_002950:PG0627|5end_RNA-binding_protein_681435..681665_NEGATIVE 224 102 61 184 146 NC_002950:PG2131|5end_60_kDa_protein_2236174..2236404_POSITIVE 223 96 53 115 69 NC_002950:PG1998|5end_polyprenyl_synthetase_2088029..2088259_NEGATIVE 222 129 90 63 20 NC_002950:PG1426|5end_hypothetical_protein_1511310..1511540_NEGATIVE 220 84 41 231 189 NC_002950:PG1942|5end_30S_ribosomal_protein_S12_2028350..2028580_NEGATIVE 220 79 31 95 45 NC_002950:PG0785|5end_tonB_protein,_putative_837592..837822_NEGATIVE 217 96 59 201 164 NC_002950:PG1948|5end_lipoprotein,_putative_2036439..2036669_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 103 61 131 94 NC_002950:PG1534|3end_hypothetical_protein_1613758..1613908_NEGATIVE 254 88 41 110 51 NC_002950:PG0428|3end_hypothetical_protein_465753..465903_NEGATIVE 251 82 43 115 73 NC_002950:PG0963|3end_hypothetical_protein_1024087..1024237_NEGATIVE 247 102 64 90 51 NC_002950:PG0922|3end_hypothetical_protein_981228..981378_NEGATIVE 244 97 55 123 77 NC_002950:PG1394|3end_hypothetical_protein_1476264..1476414_NEGATIVE 232 94 52 91 51 NC_002950:PG2106|3end_hypothetical_protein_2215457..2215607_POSITIVE 231 95 54 88 40 NC_002950:PG0076|3end_N-acetylmuramoyl-L-alanine_amidase,_family_4_90392..90542_NEGATIVE 223 84 46 76 32 NC_002950:PG1015|3end_hypothetical_protein_1075877..1076027_NEGATIVE 222 97 54 118 77 NC_002950:PG0711|3end_hypothetical_protein_766281..766431_POSITIVE 220 79 31 117 67 NC_002950:PG0786|3end_hypothetical_protein_837570..837720_NEGATIVE 219 98 54 149 115 NC_002950:PG1494|3end_hypothetical_protein_1571234..1571384_POSITIVE 219 46 1 56 7 NC_002950:PG1332|3end_NAD(P)_transhydrogenase,_beta_subunit_1414110..1414260_POSITIVE 219 103 61 149 98 NC_002950:PG1145|3end_long-chain-fatty-acid--CoA_ligase,_putative_1228482..1228632_NEGATIVE 218 110 63 66 14 NC_002950:PG0130|3end_phosphoglyceromutase_151922..152072_NEGATIVE 215 82 45 142 100 NC_002950:PG0956|3end_peptidase,_M23/M37_family,_putative_1017172..1017322_POSITIVE 214 98 55 109 55 NC_002950:PG2069|3end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_2165609..2165759_POSITIVE 214 70 27 139 102 NC_002950:PG1802|3end_hypothetical_protein_1896558..1896708_POSITIVE 212 85 43 148 109 NC_002950:PG1860|3end_hypothetical_protein_1958574..1958724_NEGATIVE 212 64 27 42 11 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 211 107 63 68 12 NC_002950:PG0717|3end_lipoprotein,_putative_769991..770141_NEGATIVE