Primer Verrucosispora gap
From CSBLwiki
Contents |
Primer Naming Format
Scf&SolCtg primer format
Gap primer format
- >[scaffold #]_[Front Contig #]_[Back Contig #]_[primer postion from Gap(Ns)(bp)]_[Forward/Reverse]
ex) >scaffold00001_1_2_1105_F, >scaffold00001_1_2_529_R CONTIG 1 CONTIG 2 ------> 5' 3' --------CTCAGGTCAGGCAGGCGTGATGATCTCTTC----------------NNNNNNNNN---------------------------------------- GTTAGAGGAGAGTGCGGCTGGGCTCCAATCAT 3' 5' <-------
1105bp 529bp
List of primer
primers of scaffold & sole contigs
scf1
>scaffold00001_223_H TTGCGTGGGTTGAAGCAGAGCAAAGCAGTT >scaffold00001_2007_T ATGACCGCCAGGTGACTCTGCAACCCACTC
scf2
scf3
>scaffold00003_1985_H CCGATCTCGTCATGTCCAGCCTGGATGAGT >scaffold00003_1004_T CCAAGTCCGACGGCTCGAAGTTCGGCAAGA
scf4
>scaffold00004_151_H GTTGATCTGCTGAGCGTGATTCGGATAGTT >scaffold00004_548_T CAACATCACCTCGCCGAAGACCGTCTATCT
ctg205
- 23s, 5s
>23s5s_H TGGTGTGGTGTTGTTTGATATGTTGATAGG >23s5s_T ACGTCTCAGCCTACATGTGCCACGGATTTG
ctg231
- 16s
>16s_H CGTGTTACTCACCCGTTCGCCGCTCGAGTA >16s_T TGGCGATTGGGACGAAGTCGTAACAAGGTA
- By Using Primer3
- "Can't find proper primer" means Primer3 couldn't found primer which satisfies several conditions (length, GC contents, Tm, complementarity between primers and complementarity between chromosome and 3' of primer).
primer intergenic
>scaffold00001_2_3_751_F CAGAACTGGAGAACGTCCATGCTCGAGAAC >scaffold00001_2_3_1360_R TCGATCACCAGCTCACGGAAGTCCTCGTTG >scaffold00001_3_4_586_F GTCAGTGCCGATCAGGATGTTGTCCAC >scaffold00001_3_4_183_R ATCAACTGCCAGAACTCGTCGGTCCTCATG >scaffold00001_4_5_568_F TACGTCGAGGAACTGGGCGACTTCAAGACC >scaffold00001_4_5_838_R CATGTCGTCGATCTGCACGTTGACCAG >scaffold00001_9_10_1135_F AGACCGGATTGAGTGCTTCCTCTGCTGGTG >scaffold00001_9_10_1408_R CGACCAATTTCCGACGAGGTGACATTC >scaffold00001_11_12_354_F AAGGTCAGGATGGCGGTGAACACCTTGGTC >scaffold00001_11_12_345_R ATGTTGTCGCTGACCTTCGCGATACGGGAG >scaffold00001_12_13_1313_F TTTCAGGCTTTGAGGATCGAGGTAAACAGG >scaffold00001_12_13_315_R TCGCATCTTCTCAGCCAGTTCCGAG >scaffold00001_15_16_126613_F Can't find proper primer >scaffold00001_15_16_569_R CTTCTACCACGACACACACACCGATCC >scaffold00001_17_18_225_F GATCGTGACGAACGTGAAGGTCCAC >scaffold00001_17_18_408_R CAGATCCGGTACAGCTCCTTGTATTCCAG >scaffold00001_18_19_320_F CAGATAGATGGTGAAGTCAGGACGACGG >scaffold00001_18_19_177_R ATGAACTTTCCACCGATGCCGGTCGTCTTC >scaffold00001_21_22_243_F AAGGACGGACGTGGACATCGATCAGCAATC >scaffold00001_21_22_1379_R AGGACTCCTGTACGTCGATCACGACGAGTG >scaffold00001_23_24_410_F ACTGACCACGGTGCAGCTCTACTTCAC >scaffold00001_23_24_1184_R AGCGTGTAGTCGGCGGTATACACCTTC >scaffold00001_25_26_203_F GTCGAGGGGATCAACACAAGTGGAATCAAG >scaffold00001_25_26_184_R GTACCGTCGACAAGCAACTCCTGATCGTC >scaffold00001_27_28_280_F TGACGTGAGGGGACTACGGATGTAC >scaffold00001_27_28_260_R ACTTCGACAGGTAGGCCTTGCAGAG >scaffold00001_31_32_566_F AAACGAGCCGTACAACGGGCAACTG >scaffold00001_31_32_169_R ATCTTCCTGACCTCGTCGGTGTGGTACTTC >scaffold00001_34_35_1071_F CAGTACGTCATCTTCGACCGGACCATTTG >scaffold00001_34_35_2096_R AGTCGTCGTCGTCGAACATCGTGAC >scaffold00001_35_36_685_F GTCGTTCAGGTTCAGGTAGAACTCGGTGAC >scaffold00001_35_36_0_R Can't find proper primer >scaffold00001_36_37_1073_F GATCGGTTTGCCGCGGTCGTTGTATTCGAC >scaffold00001_36_37_740_R ATACGGCTTCGTCGAGAACCTGACC >scaffold00001_38_39_612_F AACATGTCGTTGAGCGCGGCCAGTTTG >scaffold00001_38_39_672_R CTCTTCGACGAGATCATCCAGGTGCTG >scaffold00001_41_42_205_F ACCGAAGCAGTCGAAGACGGTACAC >scaffold00001_41_42_339_R GTCTTCTTCTGGCCCCGCAACGAGATCATG >scaffold00001_42_43_389_F TAAAATCTGTGATCTGGGCTAACCTTGGGG >scaffold00001_42_43_223_R GTGATCGGTGTGTTCGTGGCTGACCAGTAC >scaffold00001_45_46_401_F GGATCAGCTCCGGATAGTTGAAGTCGTC >scaffold00001_45_46_423_R ACAACGAGGACTTCGACAACGGCTTCAAGG >scaffold00001_47_48_1970_F GACGACTACCTGCGTAAACCCTTCGACCTG >scaffold00001_47_48_1044_R CACCAATCTGCTTGTGGGTCTGGTGCTGAC >scaffold00001_48_49_1639_F GATGTTCATCGACCTGGAGAACGTGC >scaffold00001_48_49_244_R CATCTCTCCCGTCAGCTCATCGTTCGAAG >scaffold00001_49_50_1297_F CAGGGTTTCCTGAGCCACCTTGAAC >scaffold00001_49_50_822_R CTGTTCTCCCAGGACCCGATCTTCAACTC >scaffold00001_50_51_227_F CGTGCCATGTTCTGAACGAGAACGATC >scaffold00001_50_51_860_R GTGACCAGCGAGTGAATCTTGTCGCGTTG >scaffold00001_55_56_239_F CACCTGACCTCTGACAATGAACGCCGAAAG >scaffold00001_55_56_206_R GATTGGCTTCTATACAAACTAAGGTGGCGC >scaffold00001_57_58_1204_F TCATGCTGTCCGTATCCATTTAGGACCTTC >scaffold00001_57_58_939_R TTCTACCGTGCCTACTTCGAGACCGAC >scaffold00001_61_62_285_F TCAGGTTGAGATCGACCATCGCGAG >scaffold00001_61_62_944_R TTGCACCATCAGCTCAGCATCGTCTTCGAC >scaffold00001_62_63_898_F CTGATGATCAAGGTGTTGCGGCTGTC >scaffold00001_62_63_367_R GTTGTAGCCGCCGAAGTCGTTCATGCTGAC >scaffold00001_67_68_5122_F Can't find proper primer >scaffold00001_67_68_0_R Can't find proper primer >scaffold00001_71_72_349_F AACCCACGCATCCCACTCAACGAGCTGAAC >scaffold00001_71_72_0_R Can't find proper primer >scaffold00001_73_74_2968_F Can't find proper primer >scaffold00001_73_74_0_R Can't find proper primer >scaffold00001_75_76_788_F GTCGACGTTTCATCACGTCACTGGGTG >scaffold00001_75_76_0_R Can't find proper primer >scaffold00001_76_77_1854_F GTGATCAAGGTGATCGAAGCCCTGC >scaffold00001_76_77_535_R ATCTACAACCACCTGGGCGGCAAGGAGAAC >scaffold00001_80_81_426_F CACTGCCCAAACCGATCTATCCGACGTTC >scaffold00001_80_81_202_R GATCCAAGCTGTCTTAACGAGGAGTTGCC >scaffold00001_87_88_204_F GAAGTGATCACGCGATCCACGGGATTCCAC >scaffold00001_87_88_267_R AGCTTCCAGACCCTGGTCAACAGTC >scaffold00001_88_89_1973_F AGTAGCCGATGACCCCGTTGAGTTG >scaffold00001_88_89_463_R CAGGTGTTCAACCTCGCCCAGACCTTCTAC >scaffold00003_3_4_218_F ACAAGCTCATTGCCTACTAGATCGACTTCG >scaffold00003_3_4_1054_R GCATCGTCCAACGGTAGCCTTCTTTC >scaffold00003_7_8_365_F ATCCGACGAGTACGACATCCACCTG >scaffold00003_7_8_601_R CAGACCAACTACGCCACAAGCAAGG >scaffold00003_8_9_472_F CTGTTCCAGACCTTCCTCACCGTGCTTGAC >scaffold00003_8_9_218_R CTTATGCCCTGACAGAAGGTGCAAGATCAG >scaffold00003_10_11_1436_F TGGTCCTGCCGTACTTCCTGATCACCACTG >scaffold00003_10_11_232_R GATGGGACAGACTTCGTACACCGGTTG >scaffold00003_11_12_266_F CTGTATTGATGATCCACTCGCTGCCGCTC >scaffold00003_11_12_1184_R TACAGTGATCGGCCGTTGTTGGAGTGTGTG >scaffold00003_17_18_314_F TCTGAACGAGACGGAATGGGAGATCCTCAC >scaffold00003_17_18_222_R GACATCACCATCCAGGCAGAGAACATGCTG >scaffold00003_19_20_655_F GAAGGAACGGCAACTTTCGGTCACGGTAC >scaffold00003_19_20_485_R CAAGGAGACCGTCTACAAGATCTGGCATC >scaffold00003_23_24_235_F CCCAGGGAATATAACGATGGTTCAGGTCAG >scaffold00003_23_24_1163_R GAACTGCTGGTTCATCGAATGGTCGTTGAC >scaffold00003_24_25_268_F CTCGAAGTCCCGGTCAAGAAGATCCTCAC >scaffold00003_24_25_666_R TATCGTTCGCGTCGATGGCCGACAACATTG >scaffold00003_26_27_1270_F GAAATCAAGATCCTGAACCAGTCCCGGAAG >scaffold00003_26_27_244_R CCCGATTCCTTGTCCTGGAACAGATAGAAG >scaffold00003_27_28_833_F GTACTCGCCGACTTTCCCGTTCTCATC >scaffold00003_27_28_474_R GTACACCTCGTGCTCGGGACACAAATGGTC >scaffold00003_28_29_210_F GTACACGTGCCGTTCCCGTTTCTGGTGAAC >scaffold00003_28_29_173_R ACGGCGTCACGAACAACACCTACTG >scaffold00003_30_31_256_F TTCCGGGGATGAGTAGCCGACCAATTGTCC >scaffold00003_30_31_1239_R GATCACCGGTTGGTAGACCAGATCCAG >scaffold00003_31_32_351_F CACAAATTGAACTTGAGCTGGGATGTCAGG >scaffold00003_31_32_565_R CAGGATGACAGTGTGAGTCAGCCATGGAC >scaffold00003_35_36_707_F AAGTTGAAGGAAATGGGCGAGTTCGTGAAG >scaffold00003_35_36_243_R CAGGTTGAACATCTCCTGGACCAGCGAAC >scaffold00003_42_43_317_F GTTCCTGTCCTCGTGCAGCACAATTCGATC >scaffold00003_42_43_298_R ACCGGGGATCATCGTGGTCTTGTAC >scaffold00003_43_44_737_F ATCGTTCGCAGCGGCATCGATTCAC >scaffold00003_43_44_992_R TGAAGCTGACCAAGCTGGTGGTCTC >scaffold00003_45_46_422_F GTGATGCCCTCGGATCCCAGTTCTTCGTAC >scaffold00003_45_46_399_R AACTCGGTCAAGCTCGAGTTCCTGGTG >scaffold00003_47_48_427_F CATCACGGCGAACAACAACCAGACCTAC >scaffold00003_47_48_271_R GAACAACGGCATGAGGTCCTTGAACATGAC >scaffold00003_48_49_532_F GAAGGGTCAACAGTGAGATCGCCTGGTTC >scaffold00003_48_49_741_R TGTAGCTGCCCTTCTCCTCCTGTTC >scaffold00003_49_50_208_F GTGGTGTGCATCGTGCAGATCCCGTTCTAC >scaffold00003_49_50_975_R AACCCGGAGCCGAAGAGTTCGAGAAAC >scaffold00003_50_51_1445_F TGGCGTACCTGGAGAAGGTGGTTTC >scaffold00003_50_51_439_R CAATGGCACCCTCACATATGGCAGATAATTG >scaffold00004_8_9_447_F GAACCTGCTGTTCATGGTCGGTCTG >scaffold00004_8_9_234_R ACAGTGGTCTCCGTCTACAGTCCAC >scaffold00004_12_13_750_F TCGATGGACATGCTCTCCTCCGAGATCGTC >scaffold00004_12_13_895_R TATGCGAGCGTCCGAAAAAGATCGACCAGC >scaffold00004_13_14_550_F GAGCACATCAAGATCACTGACAATGGGATC >scaffold00004_13_14_243_R AACACTCCGAAATCCGCTGGCTCTC >scaffold00004_14_15_556_F CTGGTGGGACTCGTTGAGCATCCAATG >scaffold00004_14_15_220_R CCGAGGGAAAGAACCGGACATTGTG >scaffold00004_15_16_1515_F CTTCACCGGCCTGTTCTTCGTCATCAC >scaffold00004_15_16_167_R CAGTACCTGTGGCGTCACACGCGATAAGAG >scaffold00004_16_17_236_F GGTTCGACACCAGGATTTCGAGGTCAC >scaffold00004_16_17_467_R GATCTGGTTCCACATCTGTCCCTGGTG >scaffold00004_18_19_226_F GTGTGATCGACACGGTTACGTCGAAG >scaffold00004_18_19_492_R TTAACAGGGGGCCCTTCCTTCAACACGGTC >scaffold00004_20_21_2075_F AACTCAAGTAGACCTACCGCAAGCAGGTCGGACG >scaffold00004_20_21_521_R TGAAGATCACCCAGGATCTCAAGGAGTACG >scaffold00004_21_22_386_F GAAGACTTCGCCACCGAATACCTCAGC >scaffold00004_21_22_182_R TTCGACGTACACACCACCCTCGCCGTAATC >scaffold00004_23_24_720_F TCCACCGGAACATGGGTGATACTCGAC >scaffold00004_23_24_552_R GTTGCCTTTGCACAGGTAGATCCCG >scaffold00004_24_25_667_F CAAGCCATGTCGAAGCAGCACTACTC >scaffold00004_24_25_322_R AAGCACCTGCTGTTCACAAGCGAACTGATC >scaffold00004_25_26_542_F GCAGATCGACGAGTACCTGGAGTTCTAC >scaffold00004_25_26_247_R AGGAGTCCGACCATGAAGATCAGGAAGATC >scaffold00004_29_30_278_F CATTTGTGACACCTGTCCAGCAGTACG >scaffold00004_29_30_264_R TCTGGTGAGCCGACAGGTATTCCTC