Multiple sequence alignment - TraesCS3B01G420400

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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 TraesCS3B01G420400 chr3B 100.000 2580 0 0 1 2580 657348219 657345640 0.000000e+00 4765
1 TraesCS3B01G420400 chr3A 88.505 1592 104 38 146 1711 637289497 637291035 0.000000e+00 1853
2 TraesCS3B01G420400 chr3D 89.937 1431 102 20 325 1735 497374093 497372685 0.000000e+00 1807
3 TraesCS3B01G420400 chr3D 89.198 324 31 4 11 331 497376501 497376179 4.000000e-108 401
4 TraesCS3B01G420400 chr4A 98.137 805 14 1 1777 2580 742251240 742250436 0.000000e+00 1402
5 TraesCS3B01G420400 chr4B 97.888 805 16 1 1777 2580 662026130 662025326 0.000000e+00 1391
6 TraesCS3B01G420400 chr2B 97.519 806 18 2 1777 2580 25664072 25664877 0.000000e+00 1376
7 TraesCS3B01G420400 chr2B 97.516 805 17 3 1777 2580 23320890 23320088 0.000000e+00 1373
8 TraesCS3B01G420400 chr2B 95.782 806 31 3 1777 2580 93633125 93633929 0.000000e+00 1297
9 TraesCS3B01G420400 chr1A 95.539 807 34 2 1776 2580 534238510 534237704 0.000000e+00 1290
10 TraesCS3B01G420400 chr7B 95.533 806 34 2 1777 2580 96900910 96900105 0.000000e+00 1288
11 TraesCS3B01G420400 chr5B 94.913 806 39 2 1777 2580 492095809 492095004 0.000000e+00 1260
12 TraesCS3B01G420400 chr5A 94.907 805 40 1 1777 2580 708587674 708586870 0.000000e+00 1258


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 TraesCS3B01G420400 chr3B 657345640 657348219 2579 True 4765 4765 100.0000 1 2580 1 chr3B.!!$R1 2579
1 TraesCS3B01G420400 chr3A 637289497 637291035 1538 False 1853 1853 88.5050 146 1711 1 chr3A.!!$F1 1565
2 TraesCS3B01G420400 chr3D 497372685 497376501 3816 True 1104 1807 89.5675 11 1735 2 chr3D.!!$R1 1724
3 TraesCS3B01G420400 chr4A 742250436 742251240 804 True 1402 1402 98.1370 1777 2580 1 chr4A.!!$R1 803
4 TraesCS3B01G420400 chr4B 662025326 662026130 804 True 1391 1391 97.8880 1777 2580 1 chr4B.!!$R1 803
5 TraesCS3B01G420400 chr2B 25664072 25664877 805 False 1376 1376 97.5190 1777 2580 1 chr2B.!!$F1 803
6 TraesCS3B01G420400 chr2B 23320088 23320890 802 True 1373 1373 97.5160 1777 2580 1 chr2B.!!$R1 803
7 TraesCS3B01G420400 chr2B 93633125 93633929 804 False 1297 1297 95.7820 1777 2580 1 chr2B.!!$F2 803
8 TraesCS3B01G420400 chr1A 534237704 534238510 806 True 1290 1290 95.5390 1776 2580 1 chr1A.!!$R1 804
9 TraesCS3B01G420400 chr7B 96900105 96900910 805 True 1288 1288 95.5330 1777 2580 1 chr7B.!!$R1 803
10 TraesCS3B01G420400 chr5B 492095004 492095809 805 True 1260 1260 94.9130 1777 2580 1 chr5B.!!$R1 803
11 TraesCS3B01G420400 chr5A 708586870 708587674 804 True 1258 1258 94.9070 1777 2580 1 chr5A.!!$R1 803

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
767 2880 0.03601 ATCTCCGCCAACTGAAGGTG 60.036 55.0 0.0 0.0 36.41 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2366 4504 0.389948 AACGACGATGCCTCCAGAAC 60.39 55.0 0.0 0.0 0.0 3.01 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
23 24 3.383185 GGTCTCTCCCTCAATACTGTCAG 59.617 52.174 0.00 0.00 0.00 3.51
26 27 6.065374 GTCTCTCCCTCAATACTGTCAGATA 58.935 44.000 6.91 0.00 0.00 1.98
47 49 6.617371 AGATAGTGTCAATCCCTGATTAACCT 59.383 38.462 0.00 0.00 36.14 3.50
52 54 3.134458 CAATCCCTGATTAACCTCGCTC 58.866 50.000 0.00 0.00 30.44 5.03
55 57 1.473434 CCCTGATTAACCTCGCTCACC 60.473 57.143 0.00 0.00 0.00 4.02
58 60 1.621317 TGATTAACCTCGCTCACCACA 59.379 47.619 0.00 0.00 0.00 4.17
60 62 1.873698 TTAACCTCGCTCACCACAAC 58.126 50.000 0.00 0.00 0.00 3.32
61 63 0.753867 TAACCTCGCTCACCACAACA 59.246 50.000 0.00 0.00 0.00 3.33
65 68 0.514255 CTCGCTCACCACAACACATG 59.486 55.000 0.00 0.00 0.00 3.21
102 105 6.794374 TGATCCAAATCATCAAATACCAACG 58.206 36.000 0.00 0.00 36.98 4.10
103 106 6.376864 TGATCCAAATCATCAAATACCAACGT 59.623 34.615 0.00 0.00 36.98 3.99
107 110 8.577296 TCCAAATCATCAAATACCAACGTAAAA 58.423 29.630 0.00 0.00 0.00 1.52
131 134 0.179076 CATCGCATGTGAGGGTGCTA 60.179 55.000 15.24 0.00 39.16 3.49
132 135 0.179073 ATCGCATGTGAGGGTGCTAC 60.179 55.000 15.24 0.00 39.16 3.58
134 137 1.086067 CGCATGTGAGGGTGCTACTG 61.086 60.000 0.00 0.00 39.16 2.74
138 141 1.121407 TGTGAGGGTGCTACTGCTGT 61.121 55.000 0.66 0.66 40.48 4.40
144 147 2.496470 AGGGTGCTACTGCTGTTACTAC 59.504 50.000 0.09 0.00 40.48 2.73
241 251 0.845768 CAAAGCCACGCAAAACTTCG 59.154 50.000 0.00 0.00 0.00 3.79
243 253 1.724582 AAGCCACGCAAAACTTCGCT 61.725 50.000 0.00 0.00 0.00 4.93
275 285 2.671963 GCTTTTTCCCCGCGTCCT 60.672 61.111 4.92 0.00 0.00 3.85
306 316 1.282157 CCCCTTGGCTATACCTATGCC 59.718 57.143 0.00 0.00 46.26 4.40
328 2433 5.334957 GCCATAGCACTCTGATGAATCATTG 60.335 44.000 0.00 0.00 39.53 2.82
332 2437 3.377485 GCACTCTGATGAATCATTGCACT 59.623 43.478 10.85 0.00 37.13 4.40
378 2483 4.488136 TGGGCTGCAGCATACGGG 62.488 66.667 37.63 0.24 44.36 5.28
441 2546 4.193865 CCGGGATTATTTTTCGTGGTACT 58.806 43.478 0.00 0.00 0.00 2.73
442 2547 5.358922 CCGGGATTATTTTTCGTGGTACTA 58.641 41.667 0.00 0.00 0.00 1.82
443 2548 5.234972 CCGGGATTATTTTTCGTGGTACTAC 59.765 44.000 0.00 0.00 0.00 2.73
445 2550 6.237915 CGGGATTATTTTTCGTGGTACTACAC 60.238 42.308 10.21 1.28 37.99 2.90
455 2560 5.012239 TCGTGGTACTACACTACCAATCTT 58.988 41.667 10.21 0.00 46.32 2.40
469 2574 5.424121 ACCAATCTTGCGCATTTCTATAC 57.576 39.130 12.75 0.00 0.00 1.47
470 2575 4.881273 ACCAATCTTGCGCATTTCTATACA 59.119 37.500 12.75 0.00 0.00 2.29
563 2673 2.676121 CCTCCCGCCACATTTGCA 60.676 61.111 0.00 0.00 0.00 4.08
564 2674 2.274645 CCTCCCGCCACATTTGCAA 61.275 57.895 0.00 0.00 0.00 4.08
565 2675 1.606885 CCTCCCGCCACATTTGCAAT 61.607 55.000 0.00 0.00 0.00 3.56
566 2676 0.247185 CTCCCGCCACATTTGCAATT 59.753 50.000 0.00 0.00 0.00 2.32
567 2677 0.037512 TCCCGCCACATTTGCAATTG 60.038 50.000 17.53 17.53 0.00 2.32
568 2678 1.637478 CCCGCCACATTTGCAATTGC 61.637 55.000 23.69 23.69 42.50 3.56
573 2683 0.791422 CACATTTGCAATTGCCACCG 59.209 50.000 26.94 15.32 41.18 4.94
604 2714 1.552337 AGCTGAGATCTCGCTTTTGGA 59.448 47.619 26.10 5.79 36.57 3.53
605 2715 2.170187 AGCTGAGATCTCGCTTTTGGAT 59.830 45.455 26.10 10.88 36.57 3.41
606 2716 2.287373 GCTGAGATCTCGCTTTTGGATG 59.713 50.000 23.48 5.86 0.00 3.51
607 2717 2.871022 CTGAGATCTCGCTTTTGGATGG 59.129 50.000 17.76 0.00 0.00 3.51
608 2718 2.237143 TGAGATCTCGCTTTTGGATGGT 59.763 45.455 17.76 0.00 0.00 3.55
610 2720 3.274288 AGATCTCGCTTTTGGATGGTTC 58.726 45.455 0.00 0.00 0.00 3.62
611 2721 2.559698 TCTCGCTTTTGGATGGTTCA 57.440 45.000 0.00 0.00 0.00 3.18
621 2732 1.380302 GATGGTTCAGTGGGTGGCT 59.620 57.895 0.00 0.00 0.00 4.75
661 2772 0.689080 AGCCAGGCTAGCTCTGCTTA 60.689 55.000 14.18 0.00 40.44 3.09
666 2777 1.480137 AGGCTAGCTCTGCTTACTGTG 59.520 52.381 15.72 0.00 40.44 3.66
685 2796 1.554583 GGGTTCTTTCCTCCGCTCCT 61.555 60.000 0.00 0.00 0.00 3.69
695 2806 2.232298 CTCCGCTCCTGTCCTGGAAC 62.232 65.000 0.00 0.00 35.43 3.62
734 2846 2.022195 CCTTCATCAACCCATCAGCAG 58.978 52.381 0.00 0.00 0.00 4.24
735 2847 2.356432 CCTTCATCAACCCATCAGCAGA 60.356 50.000 0.00 0.00 0.00 4.26
748 2861 2.300433 TCAGCAGAAGCAAAGCAAGAA 58.700 42.857 0.00 0.00 45.49 2.52
753 2866 3.672781 GCAGAAGCAAAGCAAGAATCTCC 60.673 47.826 0.00 0.00 41.58 3.71
754 2867 2.746362 AGAAGCAAAGCAAGAATCTCCG 59.254 45.455 0.00 0.00 0.00 4.63
767 2880 0.036010 ATCTCCGCCAACTGAAGGTG 60.036 55.000 0.00 0.00 36.41 4.00
778 2891 5.710984 CCAACTGAAGGTGTGTAGTAGTAG 58.289 45.833 0.00 0.00 0.00 2.57
779 2892 5.243283 CCAACTGAAGGTGTGTAGTAGTAGT 59.757 44.000 0.00 0.00 0.00 2.73
780 2893 6.380190 CAACTGAAGGTGTGTAGTAGTAGTC 58.620 44.000 0.00 0.00 0.00 2.59
837 2953 3.152341 ACTTCTGGGTGCTTTTCATCTG 58.848 45.455 0.00 0.00 0.00 2.90
903 3019 6.334202 AGTGCTGCTACTATAGTTGAACTTC 58.666 40.000 17.09 5.25 0.00 3.01
978 3100 0.947244 GACTGTTGTGGCTGTGAAGG 59.053 55.000 0.00 0.00 0.00 3.46
981 3103 0.836606 TGTTGTGGCTGTGAAGGAGA 59.163 50.000 0.00 0.00 0.00 3.71
991 3113 1.132849 TGTGAAGGAGACCCAAGGAGA 60.133 52.381 0.00 0.00 33.88 3.71
996 3118 1.201429 GGAGACCCAAGGAGAAGGCA 61.201 60.000 0.00 0.00 0.00 4.75
1146 3268 2.107141 GACGCCATCTCCTTCGGG 59.893 66.667 0.00 0.00 0.00 5.14
1200 3322 1.139654 CTCCTCATGGCCATCTTCGAA 59.860 52.381 17.61 0.00 0.00 3.71
1310 3432 2.203015 CCCGCCCATGGTAAGACG 60.203 66.667 11.73 6.21 0.00 4.18
1322 3444 4.171878 TGGTAAGACGATCCTGATCTCT 57.828 45.455 5.66 4.91 35.72 3.10
1338 3460 0.523966 CTCTCTCCGTGACCACTCAC 59.476 60.000 0.00 0.00 43.17 3.51
1340 3462 1.152631 TCTCCGTGACCACTCACCA 60.153 57.895 0.00 0.00 43.64 4.17
1343 3465 1.300931 CCGTGACCACTCACCACTG 60.301 63.158 0.00 0.00 43.64 3.66
1346 3468 1.766059 TGACCACTCACCACTGGCT 60.766 57.895 0.00 0.00 0.00 4.75
1351 3473 0.604780 CACTCACCACTGGCTCCTTG 60.605 60.000 0.00 0.00 0.00 3.61
1380 3502 2.945984 CAATGCGTCGTGGTTGCT 59.054 55.556 0.00 0.00 0.00 3.91
1381 3503 1.282570 CAATGCGTCGTGGTTGCTT 59.717 52.632 0.00 0.00 0.00 3.91
1382 3504 0.998226 CAATGCGTCGTGGTTGCTTG 60.998 55.000 0.00 0.00 0.00 4.01
1383 3505 1.163420 AATGCGTCGTGGTTGCTTGA 61.163 50.000 0.00 0.00 0.00 3.02
1384 3506 0.955428 ATGCGTCGTGGTTGCTTGAT 60.955 50.000 0.00 0.00 0.00 2.57
1385 3507 1.154413 GCGTCGTGGTTGCTTGATG 60.154 57.895 0.00 0.00 0.00 3.07
1386 3508 1.565156 GCGTCGTGGTTGCTTGATGA 61.565 55.000 0.00 0.00 0.00 2.92
1387 3509 0.439985 CGTCGTGGTTGCTTGATGAG 59.560 55.000 0.00 0.00 0.00 2.90
1391 3513 3.932710 GTCGTGGTTGCTTGATGAGATAA 59.067 43.478 0.00 0.00 0.00 1.75
1397 3519 5.046376 TGGTTGCTTGATGAGATAACTGAGA 60.046 40.000 0.00 0.00 0.00 3.27
1398 3520 6.054295 GGTTGCTTGATGAGATAACTGAGAT 58.946 40.000 0.00 0.00 0.00 2.75
1403 3525 7.924947 TGCTTGATGAGATAACTGAGATGTTAG 59.075 37.037 0.00 0.00 36.10 2.34
1410 3532 8.637099 TGAGATAACTGAGATGTTAGAATCTGG 58.363 37.037 8.24 0.00 37.03 3.86
1412 3534 4.052159 ACTGAGATGTTAGAATCTGGCG 57.948 45.455 0.00 0.00 37.03 5.69
1433 3556 0.531974 GTTTCAGGTGCAGACGGTGA 60.532 55.000 0.00 0.00 0.00 4.02
1602 3725 3.307242 CCATCTCACTCGGTCGAAAATTC 59.693 47.826 0.00 0.00 0.00 2.17
1609 3732 2.477375 CTCGGTCGAAAATTCCGTTCAA 59.523 45.455 10.72 0.00 43.94 2.69
1637 3768 1.207329 ACAGCGGGAGATTGTAAGGAC 59.793 52.381 0.00 0.00 0.00 3.85
1686 3818 0.098200 GGTGCCGTTCTTTTATCCGC 59.902 55.000 0.00 0.00 0.00 5.54
1700 3832 0.447801 ATCCGCACGAATTTGCAGAC 59.552 50.000 3.20 0.00 43.15 3.51
1704 3836 1.201855 CGCACGAATTTGCAGACTCTC 60.202 52.381 3.20 0.00 43.15 3.20
1712 3844 2.260844 TTGCAGACTCTCCTTGTTGG 57.739 50.000 0.00 0.00 37.10 3.77
1722 3854 6.611642 AGACTCTCCTTGTTGGTGCTATATTA 59.388 38.462 0.00 0.00 37.07 0.98
1727 3859 6.125719 TCCTTGTTGGTGCTATATTATGCAA 58.874 36.000 0.00 0.00 41.10 4.08
1729 3861 6.039717 CCTTGTTGGTGCTATATTATGCAAGT 59.960 38.462 0.00 0.00 41.10 3.16
1730 3862 7.228507 CCTTGTTGGTGCTATATTATGCAAGTA 59.771 37.037 0.00 0.00 41.10 2.24
1734 3866 9.965824 GTTGGTGCTATATTATGCAAGTATTTT 57.034 29.630 0.00 0.00 41.10 1.82
1735 3867 9.964303 TTGGTGCTATATTATGCAAGTATTTTG 57.036 29.630 0.00 0.00 41.10 2.44
1736 3868 8.575589 TGGTGCTATATTATGCAAGTATTTTGG 58.424 33.333 0.00 0.00 41.10 3.28
1737 3869 7.542130 GGTGCTATATTATGCAAGTATTTTGGC 59.458 37.037 0.00 0.00 41.10 4.52
1738 3870 8.081633 GTGCTATATTATGCAAGTATTTTGGCA 58.918 33.333 0.00 0.00 41.10 4.92
1740 3872 9.294030 GCTATATTATGCAAGTATTTTGGCATC 57.706 33.333 0.74 0.00 45.09 3.91
1741 3873 9.793252 CTATATTATGCAAGTATTTTGGCATCC 57.207 33.333 0.74 0.00 45.09 3.51
1742 3874 5.929058 TTATGCAAGTATTTTGGCATCCA 57.071 34.783 0.74 0.00 45.09 3.41
1743 3875 4.822685 ATGCAAGTATTTTGGCATCCAA 57.177 36.364 0.00 0.00 42.96 3.53
1744 3876 3.924144 TGCAAGTATTTTGGCATCCAAC 58.076 40.909 0.00 0.00 43.82 3.77
1745 3877 3.261580 GCAAGTATTTTGGCATCCAACC 58.738 45.455 0.00 0.00 43.82 3.77
1746 3878 3.055891 GCAAGTATTTTGGCATCCAACCT 60.056 43.478 0.00 0.00 43.82 3.50
1747 3879 4.159506 GCAAGTATTTTGGCATCCAACCTA 59.840 41.667 0.00 0.00 43.82 3.08
1748 3880 5.679638 GCAAGTATTTTGGCATCCAACCTAG 60.680 44.000 0.00 0.00 43.82 3.02
1749 3881 5.450818 AGTATTTTGGCATCCAACCTAGA 57.549 39.130 0.00 0.00 43.82 2.43
1750 3882 5.826643 AGTATTTTGGCATCCAACCTAGAA 58.173 37.500 0.00 0.00 43.82 2.10
1751 3883 6.252995 AGTATTTTGGCATCCAACCTAGAAA 58.747 36.000 0.00 0.00 43.82 2.52
1752 3884 4.864704 TTTTGGCATCCAACCTAGAAAC 57.135 40.909 0.00 0.00 43.82 2.78
1753 3885 2.107950 TGGCATCCAACCTAGAAACG 57.892 50.000 0.00 0.00 0.00 3.60
1754 3886 1.626321 TGGCATCCAACCTAGAAACGA 59.374 47.619 0.00 0.00 0.00 3.85
1755 3887 2.039216 TGGCATCCAACCTAGAAACGAA 59.961 45.455 0.00 0.00 0.00 3.85
1756 3888 3.078837 GGCATCCAACCTAGAAACGAAA 58.921 45.455 0.00 0.00 0.00 3.46
1757 3889 3.504520 GGCATCCAACCTAGAAACGAAAA 59.495 43.478 0.00 0.00 0.00 2.29
1758 3890 4.022676 GGCATCCAACCTAGAAACGAAAAA 60.023 41.667 0.00 0.00 0.00 1.94
1759 3891 5.336451 GGCATCCAACCTAGAAACGAAAAAT 60.336 40.000 0.00 0.00 0.00 1.82
1760 3892 5.800438 GCATCCAACCTAGAAACGAAAAATC 59.200 40.000 0.00 0.00 0.00 2.17
1761 3893 6.349363 GCATCCAACCTAGAAACGAAAAATCT 60.349 38.462 0.00 0.00 0.00 2.40
1762 3894 6.796705 TCCAACCTAGAAACGAAAAATCTC 57.203 37.500 0.00 0.00 0.00 2.75
1763 3895 5.704053 TCCAACCTAGAAACGAAAAATCTCC 59.296 40.000 0.00 0.00 0.00 3.71
1764 3896 5.106277 CCAACCTAGAAACGAAAAATCTCCC 60.106 44.000 0.00 0.00 0.00 4.30
1765 3897 4.586884 ACCTAGAAACGAAAAATCTCCCC 58.413 43.478 0.00 0.00 0.00 4.81
1766 3898 4.042435 ACCTAGAAACGAAAAATCTCCCCA 59.958 41.667 0.00 0.00 0.00 4.96
1767 3899 5.193679 CCTAGAAACGAAAAATCTCCCCAT 58.806 41.667 0.00 0.00 0.00 4.00
1768 3900 5.652452 CCTAGAAACGAAAAATCTCCCCATT 59.348 40.000 0.00 0.00 0.00 3.16
1769 3901 6.152831 CCTAGAAACGAAAAATCTCCCCATTT 59.847 38.462 0.00 0.00 0.00 2.32
1770 3902 6.419484 AGAAACGAAAAATCTCCCCATTTT 57.581 33.333 0.00 0.00 37.53 1.82
1771 3903 6.826668 AGAAACGAAAAATCTCCCCATTTTT 58.173 32.000 4.04 4.04 44.86 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.011821 TGACAGTATTGAGGGAGAGACCT 59.988 47.826 0.00 0.00 45.57 3.85
1 2 3.366396 TGACAGTATTGAGGGAGAGACC 58.634 50.000 0.00 0.00 38.08 3.85
2 3 4.274147 TCTGACAGTATTGAGGGAGAGAC 58.726 47.826 1.59 0.00 0.00 3.36
3 4 4.592997 TCTGACAGTATTGAGGGAGAGA 57.407 45.455 1.59 0.00 0.00 3.10
4 5 6.016360 CACTATCTGACAGTATTGAGGGAGAG 60.016 46.154 1.59 0.00 0.00 3.20
5 6 5.830457 CACTATCTGACAGTATTGAGGGAGA 59.170 44.000 1.59 0.00 0.00 3.71
6 7 5.596361 ACACTATCTGACAGTATTGAGGGAG 59.404 44.000 1.59 0.00 0.00 4.30
7 8 5.519808 ACACTATCTGACAGTATTGAGGGA 58.480 41.667 1.59 0.00 0.00 4.20
8 9 5.360999 TGACACTATCTGACAGTATTGAGGG 59.639 44.000 1.59 0.00 0.00 4.30
9 10 6.456795 TGACACTATCTGACAGTATTGAGG 57.543 41.667 1.59 0.00 0.00 3.86
23 24 6.831976 AGGTTAATCAGGGATTGACACTATC 58.168 40.000 13.56 0.00 39.33 2.08
26 27 4.383118 CGAGGTTAATCAGGGATTGACACT 60.383 45.833 13.56 9.17 39.33 3.55
47 49 1.506309 GCATGTGTTGTGGTGAGCGA 61.506 55.000 0.00 0.00 0.00 4.93
52 54 1.601162 GCTTCAGCATGTGTTGTGGTG 60.601 52.381 0.00 0.00 44.22 4.17
55 57 0.038892 GGGCTTCAGCATGTGTTGTG 60.039 55.000 0.30 0.00 44.36 3.33
58 60 1.153524 TGGGGCTTCAGCATGTGTT 59.846 52.632 0.30 0.00 44.36 3.32
60 62 1.303888 AGTGGGGCTTCAGCATGTG 60.304 57.895 0.30 0.00 44.36 3.21
61 63 1.303888 CAGTGGGGCTTCAGCATGT 60.304 57.895 0.30 0.00 44.36 3.21
65 68 1.452833 GGATCAGTGGGGCTTCAGC 60.453 63.158 0.00 0.00 41.14 4.26
102 105 2.093625 TCACATGCGATGCGAGTTTTAC 59.906 45.455 0.00 0.00 0.00 2.01
103 106 2.342179 TCACATGCGATGCGAGTTTTA 58.658 42.857 0.00 0.00 0.00 1.52
107 110 1.520120 CCTCACATGCGATGCGAGT 60.520 57.895 10.95 0.00 37.67 4.18
131 134 6.102897 ACAGAGATTTGTAGTAACAGCAGT 57.897 37.500 0.00 0.00 36.83 4.40
132 135 6.251589 CGTACAGAGATTTGTAGTAACAGCAG 59.748 42.308 0.00 0.00 36.83 4.24
134 137 6.320171 TCGTACAGAGATTTGTAGTAACAGC 58.680 40.000 0.00 0.00 36.83 4.40
138 141 6.127563 TGGCATCGTACAGAGATTTGTAGTAA 60.128 38.462 0.00 0.00 34.41 2.24
144 147 3.525537 AGTGGCATCGTACAGAGATTTG 58.474 45.455 0.00 0.00 0.00 2.32
196 199 3.135348 CAGAGATCAGGGACCAATTAGCA 59.865 47.826 0.00 0.00 0.00 3.49
203 213 1.267574 GGTGCAGAGATCAGGGACCA 61.268 60.000 14.24 0.00 42.00 4.02
241 251 3.431725 CGGGGCGTGGAAAGAAGC 61.432 66.667 0.00 0.00 0.00 3.86
243 253 2.969300 AAAGCGGGGCGTGGAAAGAA 62.969 55.000 0.00 0.00 0.00 2.52
275 285 0.391228 GCCAAGGGGAAAGCGAAAAA 59.609 50.000 0.00 0.00 35.59 1.94
306 316 5.238650 TGCAATGATTCATCAGAGTGCTATG 59.761 40.000 16.92 3.53 40.63 2.23
307 317 5.238868 GTGCAATGATTCATCAGAGTGCTAT 59.761 40.000 16.92 0.00 40.63 2.97
308 318 4.573607 GTGCAATGATTCATCAGAGTGCTA 59.426 41.667 16.92 5.56 40.63 3.49
319 332 1.068402 CGTTGGCAGTGCAATGATTCA 60.068 47.619 20.00 9.62 0.00 2.57
378 2483 1.227205 CTCCCATGCACTCTCGAGC 60.227 63.158 7.81 0.00 0.00 5.03
441 2546 2.753055 TGCGCAAGATTGGTAGTGTA 57.247 45.000 8.16 0.00 43.02 2.90
442 2547 2.113860 ATGCGCAAGATTGGTAGTGT 57.886 45.000 17.11 0.00 43.02 3.55
443 2548 3.127548 AGAAATGCGCAAGATTGGTAGTG 59.872 43.478 17.11 0.00 43.02 2.74
445 2550 5.679734 ATAGAAATGCGCAAGATTGGTAG 57.320 39.130 17.11 0.00 43.02 3.18
455 2560 3.126073 CAGCTCTGTATAGAAATGCGCA 58.874 45.455 14.96 14.96 31.21 6.09
563 2673 2.828549 GATCCGGCGGTGGCAATT 60.829 61.111 27.32 3.04 42.47 2.32
564 2674 3.797353 AGATCCGGCGGTGGCAAT 61.797 61.111 27.32 11.75 42.47 3.56
565 2675 4.776322 CAGATCCGGCGGTGGCAA 62.776 66.667 27.32 6.22 42.47 4.52
573 2683 2.380433 ATCTCAGCTGCAGATCCGGC 62.380 60.000 20.43 0.47 37.37 6.13
583 2693 1.664659 CCAAAAGCGAGATCTCAGCTG 59.335 52.381 29.69 21.73 38.63 4.24
604 2714 0.251341 GAAGCCACCCACTGAACCAT 60.251 55.000 0.00 0.00 0.00 3.55
605 2715 1.150536 GAAGCCACCCACTGAACCA 59.849 57.895 0.00 0.00 0.00 3.67
606 2716 1.603739 GGAAGCCACCCACTGAACC 60.604 63.158 0.00 0.00 0.00 3.62
607 2717 4.081050 GGAAGCCACCCACTGAAC 57.919 61.111 0.00 0.00 0.00 3.18
621 2732 2.910319 TGCAGCCTCTACTTAAAGGGAA 59.090 45.455 0.00 0.00 32.98 3.97
661 2772 0.396811 CGGAGGAAAGAACCCACAGT 59.603 55.000 0.00 0.00 0.00 3.55
666 2777 1.078356 GGAGCGGAGGAAAGAACCC 60.078 63.158 0.00 0.00 0.00 4.11
685 2796 1.228245 GCTGCCAAGTTCCAGGACA 60.228 57.895 0.00 0.00 0.00 4.02
695 2806 2.281970 TCAGTGCTGGCTGCCAAG 60.282 61.111 23.51 16.91 42.00 3.61
723 2835 1.542492 CTTTGCTTCTGCTGATGGGT 58.458 50.000 8.29 0.00 40.48 4.51
734 2846 2.730402 GCGGAGATTCTTGCTTTGCTTC 60.730 50.000 5.00 0.00 0.00 3.86
735 2847 1.200948 GCGGAGATTCTTGCTTTGCTT 59.799 47.619 5.00 0.00 0.00 3.91
748 2861 0.036010 CACCTTCAGTTGGCGGAGAT 60.036 55.000 0.00 0.00 0.00 2.75
753 2866 1.148310 CTACACACCTTCAGTTGGCG 58.852 55.000 0.00 0.00 0.00 5.69
754 2867 2.256117 ACTACACACCTTCAGTTGGC 57.744 50.000 0.00 0.00 0.00 4.52
767 2880 6.305160 GCAAAAGAGAACGACTACTACTACAC 59.695 42.308 0.00 0.00 0.00 2.90
778 2891 0.944386 TGCAGGCAAAAGAGAACGAC 59.056 50.000 0.00 0.00 0.00 4.34
779 2892 1.674359 TTGCAGGCAAAAGAGAACGA 58.326 45.000 3.86 0.00 32.44 3.85
780 2893 2.287788 ACATTGCAGGCAAAAGAGAACG 60.288 45.455 11.10 0.00 39.55 3.95
837 2953 3.612860 ACTACGAGTGATCAATTGAACGC 59.387 43.478 17.08 18.53 0.00 4.84
966 3084 1.003233 GGGTCTCCTTCACAGCCAC 60.003 63.158 0.00 0.00 0.00 5.01
978 3100 0.251634 CTGCCTTCTCCTTGGGTCTC 59.748 60.000 0.00 0.00 0.00 3.36
981 3103 2.759795 GCTGCCTTCTCCTTGGGT 59.240 61.111 0.00 0.00 0.00 4.51
991 3113 2.124819 CTCGCTCATGGCTGCCTT 60.125 61.111 21.03 11.16 39.13 4.35
996 3118 2.186384 GCAGACTCGCTCATGGCT 59.814 61.111 0.00 0.00 39.13 4.75
1104 3226 2.636412 CGTGCCGAAGTCCCTCAGA 61.636 63.158 0.00 0.00 0.00 3.27
1200 3322 2.204136 TGGGGCCTGATGAGGTGT 60.204 61.111 0.84 0.00 42.15 4.16
1292 3414 2.192175 GTCTTACCATGGGCGGGG 59.808 66.667 18.09 1.45 0.00 5.73
1310 3432 2.552315 GTCACGGAGAGAGATCAGGATC 59.448 54.545 0.95 0.95 38.09 3.36
1338 3460 1.202806 TCAAGTTCAAGGAGCCAGTGG 60.203 52.381 4.20 4.20 0.00 4.00
1340 3462 1.490490 TGTCAAGTTCAAGGAGCCAGT 59.510 47.619 0.00 0.00 0.00 4.00
1343 3465 0.868406 CGTGTCAAGTTCAAGGAGCC 59.132 55.000 0.00 0.00 0.00 4.70
1346 3468 2.031258 TTGCGTGTCAAGTTCAAGGA 57.969 45.000 0.00 0.00 0.00 3.36
1371 3493 3.935203 AGTTATCTCATCAAGCAACCACG 59.065 43.478 0.00 0.00 0.00 4.94
1372 3494 4.937620 TCAGTTATCTCATCAAGCAACCAC 59.062 41.667 0.00 0.00 0.00 4.16
1373 3495 5.046376 TCTCAGTTATCTCATCAAGCAACCA 60.046 40.000 0.00 0.00 0.00 3.67
1374 3496 5.423015 TCTCAGTTATCTCATCAAGCAACC 58.577 41.667 0.00 0.00 0.00 3.77
1376 3498 6.647229 ACATCTCAGTTATCTCATCAAGCAA 58.353 36.000 0.00 0.00 0.00 3.91
1378 3500 8.140628 TCTAACATCTCAGTTATCTCATCAAGC 58.859 37.037 0.00 0.00 33.82 4.01
1384 3506 8.637099 CCAGATTCTAACATCTCAGTTATCTCA 58.363 37.037 0.00 0.00 33.82 3.27
1385 3507 7.598493 GCCAGATTCTAACATCTCAGTTATCTC 59.402 40.741 0.00 0.00 33.82 2.75
1386 3508 7.441017 GCCAGATTCTAACATCTCAGTTATCT 58.559 38.462 0.00 0.00 33.82 1.98
1387 3509 6.364706 CGCCAGATTCTAACATCTCAGTTATC 59.635 42.308 0.00 0.00 33.82 1.75
1391 3513 3.449018 ACGCCAGATTCTAACATCTCAGT 59.551 43.478 0.00 0.00 30.50 3.41
1397 3519 4.323417 TGAAACACGCCAGATTCTAACAT 58.677 39.130 0.00 0.00 0.00 2.71
1398 3520 3.734463 TGAAACACGCCAGATTCTAACA 58.266 40.909 0.00 0.00 0.00 2.41
1403 3525 1.197721 CACCTGAAACACGCCAGATTC 59.802 52.381 0.00 0.00 32.37 2.52
1410 3532 1.279840 GTCTGCACCTGAAACACGC 59.720 57.895 0.00 0.00 0.00 5.34
1412 3534 0.814010 ACCGTCTGCACCTGAAACAC 60.814 55.000 0.00 0.00 0.00 3.32
1474 3597 2.749865 CGCGAGGTACGTCGGGTAA 61.750 63.158 33.59 0.00 45.15 2.85
1568 3691 1.222936 GAGATGGTCAGGGTGGCAG 59.777 63.158 0.00 0.00 0.00 4.85
1602 3725 2.977169 CCGCTGTACAAAAATTGAACGG 59.023 45.455 0.00 0.00 0.00 4.44
1609 3732 4.079253 ACAATCTCCCGCTGTACAAAAAT 58.921 39.130 0.00 0.00 0.00 1.82
1637 3768 5.175491 CGAACCAGGATTTTTGTTCACATTG 59.825 40.000 0.00 0.00 37.53 2.82
1686 3818 2.693069 AGGAGAGTCTGCAAATTCGTG 58.307 47.619 14.66 0.00 0.00 4.35
1700 3832 6.148480 GCATAATATAGCACCAACAAGGAGAG 59.852 42.308 0.00 0.00 41.22 3.20
1704 3836 6.039717 ACTTGCATAATATAGCACCAACAAGG 59.960 38.462 0.00 0.00 41.05 3.61
1712 3844 8.081633 TGCCAAAATACTTGCATAATATAGCAC 58.918 33.333 0.00 0.00 41.05 4.40
1722 3854 4.506758 GTTGGATGCCAAAATACTTGCAT 58.493 39.130 0.00 0.00 45.73 3.96
1727 3859 5.450818 TCTAGGTTGGATGCCAAAATACT 57.549 39.130 0.00 0.83 45.73 2.12
1729 3861 5.124776 CGTTTCTAGGTTGGATGCCAAAATA 59.875 40.000 0.00 0.00 45.73 1.40
1730 3862 4.082245 CGTTTCTAGGTTGGATGCCAAAAT 60.082 41.667 0.00 0.00 45.73 1.82
1734 3866 1.626321 TCGTTTCTAGGTTGGATGCCA 59.374 47.619 0.00 0.00 0.00 4.92
1735 3867 2.396590 TCGTTTCTAGGTTGGATGCC 57.603 50.000 0.00 0.00 0.00 4.40
1736 3868 4.759516 TTTTCGTTTCTAGGTTGGATGC 57.240 40.909 0.00 0.00 0.00 3.91
1737 3869 7.145932 AGATTTTTCGTTTCTAGGTTGGATG 57.854 36.000 0.00 0.00 0.00 3.51
1738 3870 6.374613 GGAGATTTTTCGTTTCTAGGTTGGAT 59.625 38.462 0.00 0.00 0.00 3.41
1739 3871 5.704053 GGAGATTTTTCGTTTCTAGGTTGGA 59.296 40.000 0.00 0.00 0.00 3.53
1740 3872 5.106277 GGGAGATTTTTCGTTTCTAGGTTGG 60.106 44.000 0.00 0.00 0.00 3.77
1741 3873 5.106277 GGGGAGATTTTTCGTTTCTAGGTTG 60.106 44.000 0.00 0.00 0.00 3.77
1742 3874 5.008331 GGGGAGATTTTTCGTTTCTAGGTT 58.992 41.667 0.00 0.00 0.00 3.50
1743 3875 4.042435 TGGGGAGATTTTTCGTTTCTAGGT 59.958 41.667 0.00 0.00 0.00 3.08
1744 3876 4.585879 TGGGGAGATTTTTCGTTTCTAGG 58.414 43.478 0.00 0.00 0.00 3.02
1745 3877 6.759497 AATGGGGAGATTTTTCGTTTCTAG 57.241 37.500 0.00 0.00 0.00 2.43
1746 3878 7.533289 AAAATGGGGAGATTTTTCGTTTCTA 57.467 32.000 0.00 0.00 32.70 2.10
1747 3879 6.419484 AAAATGGGGAGATTTTTCGTTTCT 57.581 33.333 0.00 0.00 32.70 2.52
1768 3900 1.901464 GCGAGGGGTGCCTCAAAAA 60.901 57.895 0.00 0.00 36.70 1.94
1769 3901 2.282180 GCGAGGGGTGCCTCAAAA 60.282 61.111 0.00 0.00 36.70 2.44
1770 3902 4.697756 CGCGAGGGGTGCCTCAAA 62.698 66.667 0.00 0.00 36.70 2.69
2366 4504 0.389948 AACGACGATGCCTCCAGAAC 60.390 55.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.