Primer Verrucosispora gap
From CSBLwiki
Contents |
Primer Naming 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'
<-------
Positions: 1105bp 529bp
List of primer
- 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).
primers(intergenic)
- 72 gaps, 72 pairs (144 primers)
>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 GTTCCCGGTTGCGATCGGTGAGGAT >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 CCCGACCGAACGGCACGCACACAA
>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 GACCGTTGCGACCAGATATTCGGCGATT >scaffold00001_67_68_0_R AACCGCTGACCGCGTTCGTGCTGTTCT
>scaffold00001_71_72_349_F AACCCACGCATCCCACTCAACGAGCTGAAC >scaffold00001_71_72_0_R TCGTTGTCCACCACGCCGACGAACA
>scaffold00001_73_74_2968_F TACGCGGCAGTCGGACGGGTGTGTT >scaffold00001_73_74_0_R GCTCACCGTGCCGGTGAGGACCAA
>scaffold00001_75_76_788_F GTCGACGTTTCATCACGTCACTGGGTG >scaffold00001_75_76_0_R GTGCGCCAAGACCTGCGCGAACAGT
>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
</pre>
primers(intragenic)
- 43 gaps, 43 pairs (86 primers)
>scf1_10_11_191_R ATTCCTCGCGCAGTTGACCCAGTTC >scf1_10_11_533_F TTCGCCACCACCGGTCTAGGATGAGAGATC >scf1_13_14_1221_R AGTCGTCGAAGCGCAGAAGGTACATGTAGG >scf1_13_14_961_F GTCATCGGACAGCCGATTCTTCGACGACTG >scf1_14_15_1407_F CTTGTTTCGATAGCATTACCGCCCAGTAAC >scf1_14_15_533_R GTACTCGTCGAAGGTGGACACGTTCACTC >scf1_16_17_1785_F CTCGAAGACGTCAACAACCACACCAATCTG >scf1_16_17_478_R CTCGTAACTCTCCATCGGTTCTCCAGTAAC >scf1_22_23_238_F GTTTCACTCATCGGTGTACCCTCCCGATC >scf1_22_23_244_R GAAGTTCGTCATCGAGAACGTCTCCGTGC >scf1_24_25_444_F ATTCGACGGGCAGGACGTCAACAAG >scf1_24_25_458_R TAGGTGTGCTCCAGGTAGGTGAGGAAC >scf1_26_27_369_F ATGAGCGAGCAGGTCTTCCTCCTAC >scf1_26_27_706_R GAACACGCCGTAGTTGTTCAGCGTGAAG >scf1_29_30_1643_F CCGATCCAGGCGAAGATCAGATTGGTC >scf1_29_30_767_R ATCGACATAGCGCTCCAACAGATCGGTGAC >scf1_32_33_169_R TTGTCAATGTAGCGTTGACGGGTGCCTGAC >scf1_32_33_266_F AACATTGACAGGGTGGCACGCAGTTCG >scf1_33_34_365_R GTTCCCTGCTGCTGAACTGGTTCTTCAC >scf1_33_34_795_F GTCGACGACGAGAATCCGGTTCATG >scf1_37_38_498_F TTCGACGAACTGTGGCAACGCTTCTCC >scf1_37_38_562_R AGGACGTCATGCACGGTCAACACAC >scf1_40_41_522_F GACTACAAGCCGGAGAACGTGCTCATCTC >scf1_40_41_660_R GTGCAGAAGGGATAGAGGGTGACGTAC >scf1_43_44_440_F CTCGGAGGAAAACGGTGAACAGTCAGCAAC >scf1_43_44_563_R TGAACGCCTCCACCCAGCATTTGATCACAG >scf1_44_45_485_R GTGTTGCGATCGGATTCGTAGCTGAC >scf1_44_45_93801_F ACACTGCTGCCGCCACGGTTGACTGT >scf1_46_47_370_F GTAAACTCCTGATCTCAGCCGCTCTCGTG >scf1_46_47_845_R CTCGTCGTCTCTGGTGTAGAAGTCGTCCTG >scf1_53_54_414_F TTCTGGAAGACCATCTGCAGACCGATCTCG >scf1_53_54_823_R TACGCGAAGGGACGTTAGAGATGGCAC >scf1_54_55_1250_F CTGGAACCGGATGATGTTGGAGTCCTC >scf1_54_55_175_R TACCGAGGAACTGATCGACCTCTCC >scf1_56_57_184_R CAAACCGGTGGTCGGGCTGATCATGTATTC >scf1_56_57_412_F GTACTCACGATGGTCCTTCTCCTCGTTG >scf1_59_60_1979_F GTGACCAGCCAGGTCTGTTCGAATCTCAC >scf1_59_60_625_R GAGATCATGTACGCCGACTTCAGCTTCGTG >scf1_63_64_1286_R CGATAGGTGAGACTCGATGCATGGTTAGTG >scf1_63_64_711_F ACGTAGTTCCCGACCGTAGAGCAGTTC >scf1_66_67_346_R ACTGTTCCTGCTGTACTCCTCGGTG >scf1_66_67_428_F CTTCGTCACTGGCTGTGTCAAGGTCAAC >scf1_6_7_870_R CGATCTCCACGTTTGACAGGATGCTCTG >scf1_6_7_939_F ATCAGCGGTTACGTCTGGTGGTGAC >scf1_7_8_545_R ATCAGTTTGATCGGCGAGACGTGCGAGACC >scf1_7_8_818_F GAACTGGAGTTGATGGAGCAGCGCGAAAC >scf3_12_13_2070_F CTCCAGCAGGGTTTCATCGATTCGGTAG >scf3_12_13_324_R CTGGACCAGTTCACCCTCCAGATCATG >scf3_18_19_471_R GTATACCGCAACATCGGCGAAATGAAGTC >scf3_18_19_746_F GTTGCTTCGAATCTGGTGACGGGAG >scf3_20_21_200_R GAAGATCGGCAGCTCCATCGTCTCATC >scf3_20_21_294_F ATCAGCCCCGAGCAATTGACCGACCTGAAC >scf3_21_22_1034_F GAAGTAACCGGTGGTGTTTTCGGCCAG >scf3_21_22_354_R ATCTCGCCGGTTACAAGCAGATCCTC >scf3_22_23_1299_F TTCAGATGGTTAAGGACAGCTTCATGAGCG >scf3_22_23_368_R ACGTGATCGGTGGGAACTTCGACTC >scf3_25_26_360_F GAAAGGCTGACCATCTACCCGGAGTAC >scf3_25_26_636_R TGATCCACGTGTCCGTACATCATCGTG >scf3_33_34_1969_F GTCCTCAAGCATCGCAAGCGCAAGGAAAAG >scf3_33_34_485_R CTCCAACTGCTCGGAGAGGAACTTGTAAC >scf3_34_35_222_R ATCTCCGCAGTCATATCGGTACGGG >scf3_34_35_491_F GAACGAGACCAGGAGACATAGTGGCGAGTC >scf3_36_37_355_F CTGCTCTTCCTCGGCATGCTCATGTTC >scf3_36_37_430_R ATAGCCCGCCCACTGCATGACAAAC >scf3_38_39_613_R GTACGAGCAGTTCACCAGTTGCGTG >scf3_38_39_791_F AACTGTCGACGAAGAACCGCGTCATGAGAG >scf3_39_40_333_R CTGATCCGTCATGGCGCACATTCCACGATG >scf3_39_40_351_F CACTTGTCTTCTCCTCCGGATACCTGG >scf3_44_45_1117_F CTCTGTGAGTACGTGGAACAGGCGATG >scf3_44_45_224_R AAGATCACCACGGCGTCGACACAGCTCAAC >scf3_6_7_245_R GCATGCTGTTGTTGATGCTGTCCTTCAG >scf3_6_7_918_F ATGCTCAGTCCGGGAGTACAGCTCGGTAAC >scf3_9_10_212_R TTTCCGTTGAGCCGCCACTCGTACTTGTAG >scf3_9_10_376_F CATGCACAAGCAGGACCTCATCGAG >scf4_19_20_273_F GTCTCCTTGGTCGAGGTGCTGTTCTGAGTC >scf4_19_20_878_R GACGAGCAACTGGACTCGCTGAACAAG >scf4_26_27_255_F GATCGTTCGACTACCCACAATCCGCAGATC >scf4_26_27_671_R GGTAGAGCAGCCATTCCAGTTCCTGTG >scf4_27_28_485_R GAAAACGGGGTGTTCCAGCTTCATCGCTTC >scf4_27_28_577_F CTGTTCACCGAGGAGGGCGAGTTCTTCTTC >scf4_28_29_1409_F AACCGACACACCTGCAGTTGCCGTACCAAC >scf4_28_29_207_R TACTCCGGGATAAGCAAGGCTGAGCTG >scf4_30_31_444_F ACCTTCTTGCTCTTACGGCCCACCTTG >scf4_30_31_739_R GAGTACGTCAAGTTCATTTTCGCCACCAC >scf3_1_2_276_F GACGTGTACATCTCGAACATCTCGCGG >scf3_1_2_387_R AAAACGGGCGTTCACCGCATGGTAC
