Multiple sequence alignment - TraesCS6B01G182400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)



BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G182400 chr6B 100.000 4254 0 0 1 4254 204329849 204334102 0.000000e+00 7856.0
1 TraesCS6B01G182400 chr6B 81.779 697 84 24 1302 1992 88718767 88719426 1.040000e-150 544.0
2 TraesCS6B01G182400 chr6A 93.701 3572 165 18 724 4254 143373977 143377529 0.000000e+00 5295.0
3 TraesCS6B01G182400 chr6A 75.877 713 99 37 2030 2704 608337046 608337723 3.220000e-76 296.0
4 TraesCS6B01G182400 chr6A 93.878 49 3 0 4104 4152 520869964 520869916 1.640000e-09 75.0
5 TraesCS6B01G182400 chr6D 94.936 2350 96 9 1910 4254 115018925 115021256 0.000000e+00 3659.0
6 TraesCS6B01G182400 chr6D 92.791 1193 60 13 716 1885 115017740 115018929 0.000000e+00 1703.0
7 TraesCS6B01G182400 chr6D 78.144 334 46 13 2036 2367 86739905 86739597 2.020000e-43 187.0
8 TraesCS6B01G182400 chr5B 93.194 720 43 5 1 716 648667244 648667961 0.000000e+00 1053.0
9 TraesCS6B01G182400 chr5B 90.529 718 62 5 2 715 33895910 33896625 0.000000e+00 944.0
10 TraesCS6B01G182400 chr5B 84.375 64 8 2 4084 4146 123760713 123760775 1.280000e-05 62.1
11 TraesCS6B01G182400 chr1B 91.771 717 52 6 3 715 575837787 575837074 0.000000e+00 990.0
12 TraesCS6B01G182400 chr1B 78.834 326 56 6 2250 2573 633192328 633192014 1.550000e-49 207.0
13 TraesCS6B01G182400 chr3B 91.389 720 57 4 1 715 704907168 704907887 0.000000e+00 981.0
14 TraesCS6B01G182400 chr3B 89.291 719 70 6 1 715 744229361 744228646 0.000000e+00 894.0
15 TraesCS6B01G182400 chr3B 76.641 518 93 19 2243 2753 735245353 735245849 1.170000e-65 261.0
16 TraesCS6B01G182400 chr3B 87.755 147 17 1 566 711 661661797 661661651 2.030000e-38 171.0
17 TraesCS6B01G182400 chr7B 90.694 720 62 4 1 715 449621005 449621724 0.000000e+00 953.0
18 TraesCS6B01G182400 chr7B 90.251 718 64 5 1 712 14161270 14161987 0.000000e+00 933.0
19 TraesCS6B01G182400 chr7B 77.629 523 88 17 2243 2757 113921597 113922098 1.500000e-74 291.0
20 TraesCS6B01G182400 chrUn 92.308 598 42 3 1 594 84379209 84378612 0.000000e+00 846.0
21 TraesCS6B01G182400 chr2B 88.889 684 71 4 36 715 747792865 747792183 0.000000e+00 837.0
22 TraesCS6B01G182400 chr1A 81.229 602 73 14 1400 1991 462129890 462129319 2.330000e-122 449.0
23 TraesCS6B01G182400 chr1A 77.652 443 67 16 2355 2783 548490025 548490449 1.530000e-59 241.0
24 TraesCS6B01G182400 chr7A 78.447 515 85 15 2250 2757 579013494 579012999 3.190000e-81 313.0
25 TraesCS6B01G182400 chr7A 86.567 134 17 1 2358 2490 643649383 643649250 3.430000e-31 147.0
26 TraesCS6B01G182400 chr5A 78.161 522 87 17 2243 2757 622374653 622375154 1.490000e-79 307.0
27 TraesCS6B01G182400 chr5A 84.375 64 8 2 4084 4146 118670754 118670816 1.280000e-05 62.1
28 TraesCS6B01G182400 chr2A 78.330 443 64 14 2355 2783 174456420 174456844 1.520000e-64 257.0
29 TraesCS6B01G182400 chr3A 80.272 294 44 8 2250 2541 40814594 40814313 4.310000e-50 209.0
30 TraesCS6B01G182400 chr5D 94.937 79 2 2 2335 2412 478728674 478728751 5.780000e-24 122.0
31 TraesCS6B01G182400 chr5D 84.375 64 8 2 4084 4146 113391529 113391591 1.280000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G182400 chr6B 204329849 204334102 4253 False 7856 7856 100.0000 1 4254 1 chr6B.!!$F2 4253
1 TraesCS6B01G182400 chr6B 88718767 88719426 659 False 544 544 81.7790 1302 1992 1 chr6B.!!$F1 690
2 TraesCS6B01G182400 chr6A 143373977 143377529 3552 False 5295 5295 93.7010 724 4254 1 chr6A.!!$F1 3530
3 TraesCS6B01G182400 chr6A 608337046 608337723 677 False 296 296 75.8770 2030 2704 1 chr6A.!!$F2 674
4 TraesCS6B01G182400 chr6D 115017740 115021256 3516 False 2681 3659 93.8635 716 4254 2 chr6D.!!$F1 3538
5 TraesCS6B01G182400 chr5B 648667244 648667961 717 False 1053 1053 93.1940 1 716 1 chr5B.!!$F3 715
6 TraesCS6B01G182400 chr5B 33895910 33896625 715 False 944 944 90.5290 2 715 1 chr5B.!!$F1 713
7 TraesCS6B01G182400 chr1B 575837074 575837787 713 True 990 990 91.7710 3 715 1 chr1B.!!$R1 712
8 TraesCS6B01G182400 chr3B 704907168 704907887 719 False 981 981 91.3890 1 715 1 chr3B.!!$F1 714
9 TraesCS6B01G182400 chr3B 744228646 744229361 715 True 894 894 89.2910 1 715 1 chr3B.!!$R2 714
10 TraesCS6B01G182400 chr7B 449621005 449621724 719 False 953 953 90.6940 1 715 1 chr7B.!!$F3 714
11 TraesCS6B01G182400 chr7B 14161270 14161987 717 False 933 933 90.2510 1 712 1 chr7B.!!$F1 711
12 TraesCS6B01G182400 chr7B 113921597 113922098 501 False 291 291 77.6290 2243 2757 1 chr7B.!!$F2 514
13 TraesCS6B01G182400 chrUn 84378612 84379209 597 True 846 846 92.3080 1 594 1 chrUn.!!$R1 593
14 TraesCS6B01G182400 chr2B 747792183 747792865 682 True 837 837 88.8890 36 715 1 chr2B.!!$R1 679
15 TraesCS6B01G182400 chr1A 462129319 462129890 571 True 449 449 81.2290 1400 1991 1 chr1A.!!$R1 591
16 TraesCS6B01G182400 chr5A 622374653 622375154 501 False 307 307 78.1610 2243 2757 1 chr5A.!!$F2 514


AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
750 758 0.533755 ACACTGTGTGAAGAGCTGCC 60.534 55.0 13.50 0.00 36.96 4.85 F
1519 1539 0.108804 GAATCACGGCGTCCAAGAGA 60.109 55.0 10.85 3.23 0.00 3.10 F
1521 1541 0.179100 ATCACGGCGTCCAAGAGATG 60.179 55.0 10.85 0.00 34.31 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 1924 0.251787 GGGGGAGGTTTTGCATGACT 60.252 55.0 0.00 0.00 0.00 3.41 R
2607 2723 1.078759 CACAGCGACGAGGAACATCC 61.079 60.0 0.00 0.00 36.58 3.51 R
3360 3487 1.352083 ACCCGGAGTATATGCATGCT 58.648 50.0 20.33 7.07 0.00 3.79 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 6.040054 TGCTATTCGATAGTTGGCTGTAGTTA 59.960 38.462 0.00 0.00 35.29 2.24
112 113 7.636259 TTTGAACTATGTGTTTGCTATTTGC 57.364 32.000 0.00 0.00 39.30 3.68
144 145 6.435428 CGTTTGCTATGTGGAACTAAGTTTT 58.565 36.000 0.00 0.00 38.04 2.43
217 218 6.222389 TGCCCAAGTTTAATTGTTTGAGATG 58.778 36.000 0.00 0.00 0.00 2.90
289 290 9.143631 AGTTTGAGATCTGTTGTTTTTGAAAAG 57.856 29.630 0.00 0.00 0.00 2.27
292 294 9.703892 TTGAGATCTGTTGTTTTTGAAAAGAAA 57.296 25.926 0.00 0.00 33.70 2.52
338 343 1.382146 CCTACCGCCAAGGACCCTA 60.382 63.158 0.00 0.00 45.00 3.53
464 470 3.000819 CACACCCTACCGCCAGGA 61.001 66.667 0.00 0.00 41.02 3.86
488 494 2.091720 TCTGGCGGTAGGGTTATACAGA 60.092 50.000 0.00 0.00 0.00 3.41
489 495 2.897969 CTGGCGGTAGGGTTATACAGAT 59.102 50.000 0.00 0.00 0.00 2.90
518 524 2.132089 TTTCCCTGGCGGTAAGGTGG 62.132 60.000 0.00 0.00 32.45 4.61
721 729 7.806014 TCAAAACACGAAATTTAGCCATCTAAC 59.194 33.333 0.00 0.00 34.71 2.34
729 737 8.122952 CGAAATTTAGCCATCTAACGAAAGAAT 58.877 33.333 0.00 0.00 34.71 2.40
734 742 4.631813 AGCCATCTAACGAAAGAATCACAC 59.368 41.667 0.00 0.00 0.00 3.82
735 743 4.631813 GCCATCTAACGAAAGAATCACACT 59.368 41.667 0.00 0.00 0.00 3.55
750 758 0.533755 ACACTGTGTGAAGAGCTGCC 60.534 55.000 13.50 0.00 36.96 4.85
783 791 3.187227 GTCAGCGAGAGATTCTTTGCAAA 59.813 43.478 12.14 12.14 32.69 3.68
904 914 7.559170 ACGTACTAATCCCTACTACAAGAACAT 59.441 37.037 0.00 0.00 0.00 2.71
938 948 0.606604 ACAGTAATCACGTCCGCCTT 59.393 50.000 0.00 0.00 0.00 4.35
955 965 1.584380 CTTTCGTCCTCGTCCCGACT 61.584 60.000 0.00 0.00 38.33 4.18
964 974 2.863346 CGTCCCGACTGACCCAACA 61.863 63.158 0.00 0.00 31.35 3.33
965 975 1.448497 GTCCCGACTGACCCAACAA 59.552 57.895 0.00 0.00 0.00 2.83
966 976 0.883370 GTCCCGACTGACCCAACAAC 60.883 60.000 0.00 0.00 0.00 3.32
1089 1099 4.185413 GTCAAGAAGGCGATCGCA 57.815 55.556 38.00 16.00 44.11 5.10
1248 1258 2.361230 TGCTCGCCGGAGAAGAGA 60.361 61.111 9.83 0.00 43.27 3.10
1263 1273 2.035940 AGAGCCGTCCTCCTCGTT 59.964 61.111 0.00 0.00 41.74 3.85
1375 1385 1.259142 TGGGTTCTTCGGCGTGGATA 61.259 55.000 6.85 0.00 0.00 2.59
1419 1429 2.741211 GACGTGCCGGTTTCCTCC 60.741 66.667 1.90 0.00 0.00 4.30
1487 1501 3.699955 CTTCGCTGCCGACCGATCA 62.700 63.158 0.00 0.00 44.30 2.92
1499 1513 1.956170 CCGATCACGTGGGCTATGC 60.956 63.158 17.00 0.00 37.88 3.14
1519 1539 0.108804 GAATCACGGCGTCCAAGAGA 60.109 55.000 10.85 3.23 0.00 3.10
1520 1540 0.537188 AATCACGGCGTCCAAGAGAT 59.463 50.000 10.85 5.95 0.00 2.75
1521 1541 0.179100 ATCACGGCGTCCAAGAGATG 60.179 55.000 10.85 0.00 34.31 2.90
1596 1619 0.627451 ATGGCAGCAATGGAGAAGGA 59.373 50.000 0.00 0.00 0.00 3.36
1603 1626 4.267536 CAGCAATGGAGAAGGAGAATCAA 58.732 43.478 0.00 0.00 36.25 2.57
1880 1923 3.197333 GTCCCCTACCAGAAGAAAGGTAC 59.803 52.174 0.00 0.00 39.31 3.34
1881 1924 3.178865 CCCCTACCAGAAGAAAGGTACA 58.821 50.000 0.00 0.00 39.31 2.90
1882 1925 3.197983 CCCCTACCAGAAGAAAGGTACAG 59.802 52.174 0.00 0.00 39.31 2.74
1883 1926 3.838903 CCCTACCAGAAGAAAGGTACAGT 59.161 47.826 0.00 0.00 39.31 3.55
1884 1927 4.081586 CCCTACCAGAAGAAAGGTACAGTC 60.082 50.000 0.00 0.00 39.31 3.51
1885 1928 4.527038 CCTACCAGAAGAAAGGTACAGTCA 59.473 45.833 0.00 0.00 39.31 3.41
1886 1929 5.187967 CCTACCAGAAGAAAGGTACAGTCAT 59.812 44.000 0.00 0.00 39.31 3.06
1887 1930 4.899502 ACCAGAAGAAAGGTACAGTCATG 58.100 43.478 0.00 0.00 36.07 3.07
1888 1931 3.686726 CCAGAAGAAAGGTACAGTCATGC 59.313 47.826 0.00 0.00 0.00 4.06
1889 1932 4.318332 CAGAAGAAAGGTACAGTCATGCA 58.682 43.478 0.00 0.00 0.00 3.96
1890 1933 4.756642 CAGAAGAAAGGTACAGTCATGCAA 59.243 41.667 0.00 0.00 0.00 4.08
1891 1934 5.239306 CAGAAGAAAGGTACAGTCATGCAAA 59.761 40.000 0.00 0.00 0.00 3.68
1892 1935 5.827797 AGAAGAAAGGTACAGTCATGCAAAA 59.172 36.000 0.00 0.00 0.00 2.44
1893 1936 5.438761 AGAAAGGTACAGTCATGCAAAAC 57.561 39.130 0.00 0.00 0.00 2.43
1894 1937 4.278419 AGAAAGGTACAGTCATGCAAAACC 59.722 41.667 0.00 0.00 0.00 3.27
1895 1938 3.508845 AGGTACAGTCATGCAAAACCT 57.491 42.857 0.00 0.00 0.00 3.50
1896 1939 3.412386 AGGTACAGTCATGCAAAACCTC 58.588 45.455 0.00 0.00 0.00 3.85
1897 1940 2.488153 GGTACAGTCATGCAAAACCTCC 59.512 50.000 0.00 0.00 0.00 4.30
1898 1941 1.620822 ACAGTCATGCAAAACCTCCC 58.379 50.000 0.00 0.00 0.00 4.30
1899 1942 0.890683 CAGTCATGCAAAACCTCCCC 59.109 55.000 0.00 0.00 0.00 4.81
1900 1943 0.251787 AGTCATGCAAAACCTCCCCC 60.252 55.000 0.00 0.00 0.00 5.40
1946 2025 6.582636 TGAATTATACCCTGTCATGTCAGTC 58.417 40.000 17.01 7.38 34.02 3.51
1958 2037 3.194329 TCATGTCAGTCGCTCTTCTTCAT 59.806 43.478 0.00 0.00 0.00 2.57
1959 2038 2.951726 TGTCAGTCGCTCTTCTTCATG 58.048 47.619 0.00 0.00 0.00 3.07
2241 2322 3.674682 CGCTTCTCTCCGAATTCAACTCT 60.675 47.826 6.22 0.00 0.00 3.24
2303 2384 6.481313 AGGACGAAGATGTGATATGAAATGTG 59.519 38.462 0.00 0.00 0.00 3.21
2541 2655 0.182061 AGCTCATCCGAGGGTACGTA 59.818 55.000 0.00 0.00 39.88 3.57
2547 2661 5.381174 TCATCCGAGGGTACGTATATTTG 57.619 43.478 0.00 0.00 0.00 2.32
2573 2689 3.467226 TGCTCGATCGGTTCCCCC 61.467 66.667 16.41 0.00 0.00 5.40
2607 2723 1.673760 CGCAGGTGTTTGATTTGACG 58.326 50.000 0.00 0.00 0.00 4.35
2651 2773 2.233566 AGGCTGGCAAGGATGTGGA 61.234 57.895 3.38 0.00 0.00 4.02
3088 3211 2.052690 CGAGGAGGAAGGGAAGCGA 61.053 63.158 0.00 0.00 0.00 4.93
3257 3380 3.340034 CAAAACAATCCACCGTAGCCTA 58.660 45.455 0.00 0.00 0.00 3.93
3290 3414 3.119096 GAAGGGAAGTGCGCCGTC 61.119 66.667 4.18 3.98 0.00 4.79
3352 3479 6.455647 TCACAGTTAACTGACATGGTCTTAG 58.544 40.000 36.14 10.38 46.59 2.18
3353 3480 5.120830 CACAGTTAACTGACATGGTCTTAGC 59.879 44.000 36.14 0.00 46.59 3.09
3354 3481 5.221641 ACAGTTAACTGACATGGTCTTAGCA 60.222 40.000 36.14 0.00 46.59 3.49
3355 3482 5.877012 CAGTTAACTGACATGGTCTTAGCAT 59.123 40.000 28.17 0.00 46.59 3.79
3357 3484 4.558226 AACTGACATGGTCTTAGCATCA 57.442 40.909 0.00 0.00 33.46 3.07
3358 3485 4.767578 ACTGACATGGTCTTAGCATCAT 57.232 40.909 0.00 0.00 33.46 2.45
3359 3486 5.876651 ACTGACATGGTCTTAGCATCATA 57.123 39.130 0.00 0.00 33.46 2.15
3360 3487 6.239217 ACTGACATGGTCTTAGCATCATAA 57.761 37.500 0.00 0.00 33.46 1.90
3361 3488 6.286758 ACTGACATGGTCTTAGCATCATAAG 58.713 40.000 0.00 0.00 33.46 1.73
3362 3489 5.059161 TGACATGGTCTTAGCATCATAAGC 58.941 41.667 0.00 0.00 33.46 3.09
3363 3490 5.039920 ACATGGTCTTAGCATCATAAGCA 57.960 39.130 0.00 0.00 33.46 3.91
3364 3491 5.628130 ACATGGTCTTAGCATCATAAGCAT 58.372 37.500 0.00 0.00 33.46 3.79
3365 3492 5.472478 ACATGGTCTTAGCATCATAAGCATG 59.528 40.000 9.93 9.93 38.21 4.06
3375 3502 6.057627 GCATCATAAGCATGCATATACTCC 57.942 41.667 21.98 4.08 45.19 3.85
3398 3525 6.156602 TCCGGGTAGAAAGTTCCATTACATAA 59.843 38.462 0.00 0.00 0.00 1.90
3470 3600 3.495001 GGACTCTGAAAAACTCAAGTCCG 59.505 47.826 14.59 0.00 43.97 4.79
3530 3664 0.824759 GTACGCAGACAGGGAGGAAT 59.175 55.000 0.00 0.00 0.00 3.01
3538 3672 0.682209 ACAGGGAGGAATGTGCATGC 60.682 55.000 11.82 11.82 0.00 4.06
3539 3673 0.681887 CAGGGAGGAATGTGCATGCA 60.682 55.000 18.46 18.46 0.00 3.96
3540 3674 0.260816 AGGGAGGAATGTGCATGCAT 59.739 50.000 25.64 8.04 0.00 3.96
3541 3675 1.496001 AGGGAGGAATGTGCATGCATA 59.504 47.619 25.64 22.69 0.00 3.14
3863 3997 2.032528 TCCGCCAGCTTCACCTTG 59.967 61.111 0.00 0.00 0.00 3.61
3872 4006 1.371183 CTTCACCTTGACCCGCAGA 59.629 57.895 0.00 0.00 0.00 4.26
4037 4171 5.949735 TGAACTCAACTGAACCTTGAAAAC 58.050 37.500 0.00 0.00 0.00 2.43
4062 4196 0.523546 CTAGTCAGTACGCACGCCAG 60.524 60.000 0.00 0.00 0.00 4.85
4063 4197 1.929806 TAGTCAGTACGCACGCCAGG 61.930 60.000 0.00 0.00 0.00 4.45
4209 4343 4.645535 CAGTGAATGAAGAACAGAAGGGA 58.354 43.478 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 8.621286 CATAGTTTCACAACCACTAGACTTTTT 58.379 33.333 0.00 0.00 32.70 1.94
309 311 1.002502 GCGGTAGGGTCTTGCCTTT 60.003 57.895 0.00 0.00 37.43 3.11
338 343 1.104630 GGCTGTCTAACTCTACCGCT 58.895 55.000 0.00 0.00 0.00 5.52
346 351 0.613853 TGGCGGTAGGCTGTCTAACT 60.614 55.000 2.49 0.00 44.18 2.24
415 421 4.766375 TCGAGGCAAAACCCTTCTATAAG 58.234 43.478 0.00 0.00 40.58 1.73
464 470 1.875488 ATAACCCTACCGCCAGAAGT 58.125 50.000 0.00 0.00 0.00 3.01
488 494 3.569873 CAGGGAAACTGGCGGTAAT 57.430 52.632 0.00 0.00 43.70 1.89
692 700 4.339814 TGGCTAAATTTCGTGTTTTGACCT 59.660 37.500 0.00 0.00 0.00 3.85
734 742 1.233285 GGTGGCAGCTCTTCACACAG 61.233 60.000 9.90 0.00 33.91 3.66
735 743 1.227943 GGTGGCAGCTCTTCACACA 60.228 57.895 9.90 0.00 33.91 3.72
744 752 1.251251 GACAAGAAATGGTGGCAGCT 58.749 50.000 18.53 0.00 0.00 4.24
750 758 2.414481 CTCTCGCTGACAAGAAATGGTG 59.586 50.000 0.00 0.00 0.00 4.17
783 791 2.290577 GGAAACATGGAAGAGCTCAGGT 60.291 50.000 17.77 0.00 0.00 4.00
904 914 6.639686 GTGATTACTGTCTCGTTCTGTTTACA 59.360 38.462 0.00 0.00 0.00 2.41
955 965 2.904866 GCTGCCGTTGTTGGGTCA 60.905 61.111 0.00 0.00 0.00 4.02
964 974 2.482296 GATTGCTTGCTGCTGCCGTT 62.482 55.000 13.47 0.00 43.37 4.44
965 975 2.986306 GATTGCTTGCTGCTGCCGT 61.986 57.895 13.47 4.59 43.37 5.68
966 976 2.202570 GATTGCTTGCTGCTGCCG 60.203 61.111 13.47 5.42 43.37 5.69
1248 1258 2.600769 ACAACGAGGAGGACGGCT 60.601 61.111 0.00 0.00 34.93 5.52
1487 1501 0.810031 GTGATTCGCATAGCCCACGT 60.810 55.000 0.00 0.00 0.00 4.49
1499 1513 1.413767 CTCTTGGACGCCGTGATTCG 61.414 60.000 0.00 0.00 39.52 3.34
1519 1539 4.851843 TCTTCTTGATCAGCATTCACCAT 58.148 39.130 0.00 0.00 0.00 3.55
1520 1540 4.290711 TCTTCTTGATCAGCATTCACCA 57.709 40.909 0.00 0.00 0.00 4.17
1521 1541 4.036498 CCATCTTCTTGATCAGCATTCACC 59.964 45.833 0.00 0.00 32.05 4.02
1596 1619 1.843206 GCCTCCTCCTCCTTTGATTCT 59.157 52.381 0.00 0.00 0.00 2.40
1603 1626 4.406763 AGGCGCCTCCTCCTCCTT 62.407 66.667 27.08 0.00 43.20 3.36
1621 1644 1.135139 CTCCACTACCACCTCATGACG 59.865 57.143 0.00 0.00 0.00 4.35
1880 1923 0.890683 GGGGAGGTTTTGCATGACTG 59.109 55.000 0.00 0.00 0.00 3.51
1881 1924 0.251787 GGGGGAGGTTTTGCATGACT 60.252 55.000 0.00 0.00 0.00 3.41
1882 1925 2.276869 GGGGGAGGTTTTGCATGAC 58.723 57.895 0.00 0.00 0.00 3.06
1883 1926 4.863415 GGGGGAGGTTTTGCATGA 57.137 55.556 0.00 0.00 0.00 3.07
1898 1941 3.379452 AGTTCAGACTTCAGATAGGGGG 58.621 50.000 0.00 0.00 29.87 5.40
1946 2025 4.560136 TCTAGTAGCATGAAGAAGAGCG 57.440 45.455 0.00 0.00 0.00 5.03
1958 2037 6.782082 ATGATTCACTCTGTTCTAGTAGCA 57.218 37.500 0.00 0.00 0.00 3.49
1959 2038 7.261325 TGAATGATTCACTCTGTTCTAGTAGC 58.739 38.462 3.29 0.00 34.08 3.58
2241 2322 9.661187 GAACTTCTGACGATTATACGAGAATTA 57.339 33.333 0.00 0.00 37.03 1.40
2303 2384 2.361737 GCTCCCCTGCCTGGAAAC 60.362 66.667 0.00 0.00 38.35 2.78
2541 2655 3.462982 TCGAGCACGCCATAACAAATAT 58.537 40.909 0.00 0.00 39.58 1.28
2547 2661 1.548973 CCGATCGAGCACGCCATAAC 61.549 60.000 18.66 0.00 39.58 1.89
2573 2689 4.147322 GCGGCGTCACCATTGTCG 62.147 66.667 9.37 0.00 39.03 4.35
2604 2720 1.872679 GCGACGAGGAACATCCGTC 60.873 63.158 0.00 0.00 46.27 4.79
2605 2721 2.181021 GCGACGAGGAACATCCGT 59.819 61.111 0.00 0.00 42.75 4.69
2606 2722 1.874019 CAGCGACGAGGAACATCCG 60.874 63.158 0.00 0.00 42.75 4.18
2607 2723 1.078759 CACAGCGACGAGGAACATCC 61.079 60.000 0.00 0.00 36.58 3.51
3257 3380 2.965147 CCCTTCCCGCCATTTCATTTAT 59.035 45.455 0.00 0.00 0.00 1.40
3285 3409 5.502544 GCTTCATTTACAGATTACAGACGGC 60.503 44.000 0.00 0.00 0.00 5.68
3290 3414 8.391106 GTGGTAAGCTTCATTTACAGATTACAG 58.609 37.037 0.00 0.00 41.60 2.74
3352 3479 5.277202 CGGAGTATATGCATGCTTATGATGC 60.277 44.000 27.64 20.76 45.45 3.91
3353 3480 5.235831 CCGGAGTATATGCATGCTTATGATG 59.764 44.000 27.64 16.02 0.00 3.07
3354 3481 5.363101 CCGGAGTATATGCATGCTTATGAT 58.637 41.667 27.64 18.82 0.00 2.45
3355 3482 4.383010 CCCGGAGTATATGCATGCTTATGA 60.383 45.833 27.64 14.06 0.00 2.15
3357 3484 3.519510 ACCCGGAGTATATGCATGCTTAT 59.480 43.478 24.48 24.48 0.00 1.73
3358 3485 2.903784 ACCCGGAGTATATGCATGCTTA 59.096 45.455 20.33 17.39 0.00 3.09
3359 3486 1.699634 ACCCGGAGTATATGCATGCTT 59.300 47.619 20.33 15.55 0.00 3.91
3360 3487 1.352083 ACCCGGAGTATATGCATGCT 58.648 50.000 20.33 7.07 0.00 3.79
3361 3488 2.496070 TCTACCCGGAGTATATGCATGC 59.504 50.000 11.82 11.82 0.00 4.06
3362 3489 4.801330 TTCTACCCGGAGTATATGCATG 57.199 45.455 10.16 0.00 0.00 4.06
3363 3490 4.838986 ACTTTCTACCCGGAGTATATGCAT 59.161 41.667 0.73 3.79 0.00 3.96
3364 3491 4.220724 ACTTTCTACCCGGAGTATATGCA 58.779 43.478 0.73 0.00 0.00 3.96
3365 3492 4.868314 ACTTTCTACCCGGAGTATATGC 57.132 45.455 0.73 0.00 0.00 3.14
3369 3496 3.716431 TGGAACTTTCTACCCGGAGTAT 58.284 45.455 0.73 0.00 0.00 2.12
3375 3502 7.046033 AGTTATGTAATGGAACTTTCTACCCG 58.954 38.462 0.00 0.00 29.02 5.28
3410 3540 6.030849 CAGTCGGTAATAACTCTCTGTCTTG 58.969 44.000 0.00 0.00 0.00 3.02
3416 3546 3.065095 GCGTCAGTCGGTAATAACTCTCT 59.935 47.826 0.00 0.00 40.26 3.10
3417 3547 3.361414 GCGTCAGTCGGTAATAACTCTC 58.639 50.000 0.00 0.00 40.26 3.20
3470 3600 5.679734 TTGAGCTGATGAAAACTCTTGAC 57.320 39.130 0.00 0.00 0.00 3.18
3530 3664 2.118313 AGTGAAGCTATGCATGCACA 57.882 45.000 25.37 11.52 31.93 4.57
3538 3672 2.357009 GCCATGTCCAAGTGAAGCTATG 59.643 50.000 0.00 0.00 0.00 2.23
3539 3673 2.648059 GCCATGTCCAAGTGAAGCTAT 58.352 47.619 0.00 0.00 0.00 2.97
3540 3674 1.675714 CGCCATGTCCAAGTGAAGCTA 60.676 52.381 0.00 0.00 0.00 3.32
3541 3675 0.957395 CGCCATGTCCAAGTGAAGCT 60.957 55.000 0.00 0.00 0.00 3.74
3863 3997 4.459089 GTGGAGGCTCTGCGGGTC 62.459 72.222 15.23 0.00 0.00 4.46
3872 4006 2.600769 AAGTCGGACGTGGAGGCT 60.601 61.111 0.00 0.00 0.00 4.58
4037 4171 2.284684 CGTGCGTACTGACTAGGAGTAG 59.715 54.545 1.24 2.12 0.00 2.57
4062 4196 0.459759 GACGCAGGTAAGCTACACCC 60.460 60.000 12.66 0.00 36.67 4.61
4063 4197 0.531200 AGACGCAGGTAAGCTACACC 59.469 55.000 9.01 9.01 36.22 4.16
4215 4352 0.804364 GAAACACGAGCCATCATGCA 59.196 50.000 0.00 0.00 0.00 3.96
4220 4357 2.744202 ACATCAAGAAACACGAGCCATC 59.256 45.455 0.00 0.00 0.00 3.51



Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.