Origin IGS: gtatttcgatgctatcggttaggacggtacatggcaatcgaatctccataacttacaagggtgaaatccgtattacgaattatgaacggacgctctgttgcgatcggagccgatatggtggaatacacggcacaaccggagtctatgtaatccgtatcacaaaagattttttacagtctcagaagtttggtgtcaccgctattggatttttatgccgaaatatttggctatatgcaattttatggttactttgcgcagcaaaggaaagcaagtagagtgttttcctgaattttataaacaaaaaaaataaaagact .........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 agtcttttattttttttgtttataaaattcaggaaaacactctacttgctttcctttgctgcgcaaagtaaccataaaattgcatatagccaaatatttcggcataaaaatccaatagcggtgacaccaaacttctgagactgtaaaaaatcttttgtgatacggattacatagactccggttgtgccgtgtattccaccatatcggctccgatcgcaacagagcgtccgttcataattcgtaatacggatttcacccttgtaagttatggagattcgattgccatgtaccgtcctaaccgatagcatcgaaatac Mask Tandem Repeat Region ================================================ gtatttcgatgctatcggttaggacggtacatggcaatcgaatctccataacttacaagggtgaaatccgtattacgaattatgaacggacgctctgttgcgatcggagccgatatggtggaatacacggcacaaccggagtctatgtaatccgtatcacaaaagattttttacagtctcagaagtttggtgtcaccgctattggatttttatgccgaaatatttggctatatgcaattttatggttactttgcgcagcaaaggaaagcaagtagagtgttttcctgaattttataaacaaaaaaaataaaagact Find is-nt database================================================ Query_seq: PG1490:PG1491|PG1490:PG1491:TraG family protein:hypothetical protein:->->:1565565..1565880 316 gtatttcgatgctatcggttaggacggtacatggcaatcgaatctccataacttacaagggtgaaatccgtattacgaattatgaacggacgctctgttgcgatcggagccgatatggtggaatacacggcacaaccggagtctatgtaatccgtatcacaaaagattttttacagtctcagaagtttggtgtcaccgctattggatttttatgccgaaatatttggctatatgcaattttatggttactttgcgcagcaaaggaaagcaagtagagtgttttcctgaattttataaacaaaaaaaataaaagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1490:PG1491|PG1490:PG1491:TraG family protein:hypothetical protein:->->:1565565..1565880 316 gtatttcgatgctatcggttaggacggtacatggcaatcgaatctccataacttacaagggtgaaatccgtattacgaattatgaacggacgctctgttgcgatcggagccgatatggtggaatacacggcacaaccggagtctatgtaatccgtatcacaaaagattttttacagtctcagaagtttggtgtcaccgctattggatttttatgccgaaatatttggctatatgcaattttatggttactttgcgcagcaaaggaaagcaagtagagtgttttcctgaattttataaacaaaaaaaataaaagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1490:PG1491|PG1490:PG1491:TraG family protein:hypothetical protein:->->:1565565..1565880 316 gtatttcgatgctatcggttaggacggtacatggcaatcgaatctccataacttacaagggtgaaatccgtattacgaattatgaacggacgctctgttgcgatcggagccgatatggtggaatacacggcacaaccggagtctatgtaatccgtatcacaaaagattttttacagtctcagaagtttggtgtcaccgctattggatttttatgccgaaatatttggctatatgcaattttatggttactttgcgcagcaaaggaaagcaagtagagtgttttcctgaattttataaacaaaaaaaataaaagact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtatttcgatgctatcggttaggacggtacatggcaatcgaatctccataacttacaagggtgaaatccgtattacgaattatgaacggacgctctgttgcgatcggagccgatatggtggaatacacggcacaaccggagtctatgtaatccgtatcacaaaagattttttacagtctcagaagtttggtgtcaccgctattggatttttatgccgaaatatttggctatatgcaattttatggttactttgcgcagcaaaggaaagcaagtagagtgttttcctgaattttataaacaaaaaaaataaaagact Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 3 End: 272 .. M S M L S V R T V H G N R I S I T Y K G E I R I T N Y E R T L C C D R S R Y G G I H G T T G V Y V I R I T K D F L Q S Q ............................................ Protein_Len: 40 Strand: + Start: 166 End: 285 ..................................................................................................................................................................... M F Y S L R S L V S P L L D F Y A E I F G Y M Q F Y G Y F A Q Q R K A S R V F S ............................... Protein_Len: 60 Strand: + Start: 95 End: 307 .............................................................................................. M L R S E P I W W N T R H N R S L C N P Y H K R F F T V S E V W C H R Y W I F M P K Y L A I C N F M V T L R S K G K Q V ......... Protein_Len: 40 Strand: - Start: 182 End: 301 ..................................................................................................................................................................................... F N P T V A I P N K H R F I Q S Y A I K H N S Q A A F S L L Y L T K R F K I F M ............... Protein_Len: 51 Strand: - Start: 15 End: 167 .............. R N P R Y M A I S D G Y S V L T F D T N R I I F P R E T A I P A S I T S Y V A C G S D I Y D T D C F M ..................................................................................................................................................... gtatttcgatgctatcggttaggacggtacatggcaatcgaatctccataacttacaagggtgaaatccgtattacgaattatgaacggacgctctgttgcgatcggagccgatatggtggaatacacggcacaaccggagtctatgtaatccgtatcacaaaagattttttacagtctcagaagtttggtgtcaccgctattggatttttatgccgaaatatttggctatatgcaattttatggttactttgcgcagcaaaggaaagcaagtagagtgttttcctgaattttataaacaaaaaaaataaaagact Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 9 End: 38 ........ATTGCCATGTACCGTCCTAACCGATAGCAT...................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtatttcgatgctatcggttaggacggtacatggcaatcgaatctccataacttacaagggtgaaatccgtattacgaattatgaacggacgctctgttgcgatcggagccgatatggtggaatacacggcacaaccggagtctatgtaatccgtatcacaaaagattttttacagtctcagaagtttggtgtcaccgctattggatttttatgccgaaatatttggctatatgcaattttatggttactttgcgcagcaaaggaaagcaagtagagtgttttcctgaattttataaacaaaaaaaataaaagact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 46 HP_score: -4.2 Tail_Score: -2.80077 Start: 263 End: 285 Full_Region: ACTTTGCGCAGCAAA GGAAAGCA AGTAGAG TGTTTTCC TGAATTTTATAAACA ......................................................................................................................................................................................................................................................................GGAAAGCAAGTAGAGTGTTTTCC............................... Find igs database================================================ Query_seq: PG1490:PG1491|PG1490:PG1491:TraG family protein:hypothetical protein:->->:1565565..1565880 316 gtatttcgatgctatcggttaggacggtacatggcaatcgaatctccataacttacaagggtgaaatccgtattacgaattatgaacggacgctctgttgcgatcggagccgatatggtggaatacacggcacaaccggagtctatgtaatccgtatcacaaaagattttttacagtctcagaagtttggtgtcaccgctattggatttttatgccgaaatatttggctatatgcaattttatggttactttgcgcagcaaaggaaagcaagtagagtgttttcctgaattttataaacaaaaaaaataaaagact Intra-Species Hit: Count: 1 Min: 1 Max: 299 Len: 299 Subject: NC_002950_PG1490_PG1491|TraG family protein:hypothetical protein|POSITIVE:POSITIVE|[1565565,1565880]|316 HSP 1 e-value: 1.0E-168 bit: 593.0 Len: 299 Query Start:1 Query End:299 Subject Strand: POSITIVE Subject Start: 1 Subject End: 299 gtatttcgatgctatcggttaggacggtacatggcaatcgaatctccataacttacaagggtgaaatccgtattacgaattatgaacggacgctctgttgcgatcggagccgatatggtggaatacacggcacaaccggagtctatgtaatccgtatcacaaaagattttttacagtctcagaagtttggtgtcaccgctattggatttttatgccgaaatatttggctatatgcaattttatggttactttgcgcagcaaaggaaagcaagtagagtgttttcctgaattttataaac................. gtatttcgatgctatcggttaggacggtacatggcaatcgaatctccataacttacaagggtgaaatccgtattacgaattatgaacggacgctctgttgcgatcggagccgatatggtggaatacacggcacaaccggagtctatgtaatccgtatcacaaaagattttttacagtctcagaagtttggtgtcaccgctattggatttttatgccgaaatatttggctatatgcaattttatggttactttgcgcagcaaaggaaagcaagtagagtgttttcctgaattttataaac................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUAUUUCGAUGCUAUCGGUUAGGACGGUACAUGGCAAUCGAAUCUCCAUAACUUACAAGGGUGAAAUCCGUAUUACGAAUUAUGAACGGACGCUCUGUUGCGAUCGGAGCCGAUAUGGUGGAAUACACGGCACAACCGGAGUCUAUGUAAUCCGUAUCACAAAAGAUUUUUUACAGUCUCAGAAGUUUGGUGUCACCGCUAUUGGAUUUUUAUGCCGAAAUAUUUGGCUAUAUGCAAUUUUAUGGUUACUUUGCGCAGCAAAGGAAAGCAAGUAGAGUGUUUUCCUGAAUUUUAUAAAC ....(((((((((((((.......))))....))).))))))...............((((((...(((((..............)))))))))))((((((...((((((((((((((.(((((..(((((......(((....(((((.....(((......)))...)))))..))).((((((..(((.......)))..))))))..)))))...))))).))))))).........))))).))...))))))..(((((((((.......)))))))))............. (-73.54) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUAUAAAAUUCAGGAAAACACUCUACUUGCUUUCCUUUGCUGCGCAAAGUAACCAUAAAAUUGCAUAUAGCCAAAUAUUUCGGCAUAAAAAUCCAAUAGCGGUGACACCAAACUUCUGAGACUGUAAAAAAUCUUUUGUGAUACGGAUUACAUAGACUCCGGUUGUGCCGUGUAUUCCACCAUAUCGGCUCCGAUCGCAACAGAGCGUCCGUUCAUAAUUCGUAAUACGGAUUUCACCCUUGUAAGUUAUGGAGAUUCGAUUGCCAUGUACCGUCCUAACCGAUAGCAUCGAAAUAC .............((((((.((.......)).))))))(..((((.....((((........)))).....(((.........)))..............))))..)..((((((((..(((..((....((((((...(((.(((((((((.........((((((.((((.((((......))))))))..)))))).....((((....)))).))))))))).)))))))))))..)))..))))).)))...((((((.((..(((.(.((....)).)))))))))))).... (-59.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 443 138 92 229 175 NC_002950:PG1913|5end_30S_ribosomal_protein_S11_2012926..2013156_NEGATIVE 416 140 91 70 28 NC_002950:PG1486|5end_conjugative_transposon_protein_TraA_1561166..1561396_NEGATIVE 380 139 91 221 160 NC_002950:PG1927|5end_50S_ribosomal_protein_L24_2019557..2019787_NEGATIVE 366 135 92 175 136 NC_002950:PG1300|5end_hypothetical_protein_1379069..1379299_NEGATIVE 360 110 67 209 147 NC_002950:PG2082|5end_POT_family_protein_2183384..2183614_NEGATIVE 356 128 81 225 170 NC_002950:PG1594|5end_ComEC/Rec2-related_protein_1673587..1673817_NEGATIVE 354 129 88 73 20 NC_002950:PG1706|5end_hypothetical_protein_1794211..1794441_NEGATIVE 352 49 5 166 122 NC_002950:PG0002|5end_hexapeptide_transferase_family_protein_1295..1525_POSITIVE 349 118 91 39 11 NC_002950:PG1690|5end_Sua5/YciO/YrdC/YwlC_family_protein_1775773..1776003_NEGATIVE 348 129 87 217 168 NC_002950:PG2072|5end_UvrD/REP_helicase_domain_protein_2167369..2167599_POSITIVE 347 143 102 47 7 NC_002950:PG2150|5end_LysM_domain_protein_2259172..2259402_NEGATIVE 347 139 92 180 123 NC_002950:PG1250|5end_hypothetical_protein_1327846..1328076_NEGATIVE 346 130 81 226 174 NC_002950:PG2112|5end_hypothetical_protein_2221471..2221701_POSITIVE 341 140 98 178 142 NC_002950:PG1465|5end_hypothetical_protein_1541982..1542212_POSITIVE 340 131 91 168 120 NC_002950:PG1692|5end_ABC_transporter,_ATP-binding_protein_1777173..1777403_NEGATIVE 338 110 69 178 141 NC_002950:PG1729|5end_thiol_peroxidase_1818881..1819111_NEGATIVE 336 121 81 68 17 NC_002950:PG1305|5end_glycine_dehydrogenase_1386538..1386768_NEGATIVE 335 130 87 229 173 NC_002950:PG2223|5end_glycosyl_transferase,_group_2_family_protein_2337713..2337943_POSITIVE 335 57 15 152 99 NC_002950:PG1271|5end_acetylornithine_aminotransferase,_putative_1351443..1351673_NEGATIVE 334 120 71 228 169 NC_002950:PG1374|5end_immunoreactive_47_kDa_antigen_PG97_1456540..1456770_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 366 135 92 138 99 NC_002950:PG1301|3end_hypothetical_protein_1379106..1379256_NEGATIVE 355 130 83 127 73 NC_002950:PG1758|3end_ribosomal_protein_S15_1845534..1845684_POSITIVE 351 130 87 60 9 NC_002950:PG1943|3end_hypothetical_protein_2028974..2029124_NEGATIVE 349 118 91 32 4 NC_002950:PG1691|3end_hypothetical_protein_1775780..1775930_NEGATIVE 344 46 1 92 49 NC_002950:PG1145|3end_long-chain-fatty-acid--CoA_ligase,_putative_1228482..1228632_NEGATIVE 340 131 92 59 6 NC_002950:PG1707|3end_hypothetical_protein_1794232..1794382_NEGATIVE 339 112 74 151 103 NC_002950:PG1977|3end_hypothetical_protein_2064687..2064837_NEGATIVE 338 110 69 132 95 NC_002950:PG1730|3end_O-methyltransferase_family_protein_1818927..1819077_NEGATIVE 336 121 81 63 12 NC_002950:PG1306|3end_metallo-beta-lactamase_family_protein_1386543..1386693_NEGATIVE 332 129 92 146 116 NC_002950:PG1484|3end_hypothetical_protein_1559275..1559425_NEGATIVE 328 130 87 89 42 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 328 123 81 78 28 NC_002950:PG1459|3end_hypothetical_protein_1539632..1539782_NEGATIVE 328 129 81 103 40 NC_002950:PG0534|3end_hypothetical_protein_585805..585955_POSITIVE 326 135 92 48 1 NC_002950:PG0413|3end_hypothetical_protein_451437..451587_NEGATIVE 325 130 82 76 30 NC_002950:PG1885|3end_polyphosphate_kinase_1981065..1981215_NEGATIVE 324 129 87 76 22 NC_002950:PG0246|3end_hypothetical_protein_281050..281200_NEGATIVE 323 139 92 77 11 NC_002950:PG1371|3end_phosphorylase_family_protein_1452352..1452502_NEGATIVE 323 109 76 74 37 NC_002950:PG0733|3end_riboflavin_synthase_subunit_alpha_783856..784006_POSITIVE 322 47 5 151 109 NC_002950:PG0001|3end_chromosomal_replication_initiation_protein_1362..1512_POSITIVE 321 138 96 60 21 NC_002950:PG2123|3end_hypothetical_protein_2230243..2230393_POSITIVE