Multiple sequence alignment - TraesCS2A01G463200

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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 TraesCS2A01G463200 chr2A 100.000 2565 0 0 1 2565 709048138 709050702 0.000000e+00 4737.0
1 TraesCS2A01G463200 chr2D 87.045 1922 83 48 79 1916 569308712 569310551 0.000000e+00 2017.0
2 TraesCS2A01G463200 chr2D 88.336 643 61 9 1928 2565 473093886 473094519 0.000000e+00 760.0
3 TraesCS2A01G463200 chr2D 86.596 664 51 10 1928 2562 52014618 52015272 0.000000e+00 699.0
4 TraesCS2A01G463200 chr2D 89.139 488 42 8 2079 2562 431525015 431525495 4.720000e-167 597.0
5 TraesCS2A01G463200 chr2D 84.031 382 42 15 2188 2565 180090112 180089746 1.460000e-92 350.0
6 TraesCS2A01G463200 chr2D 94.444 162 9 0 1928 2089 431524839 431525000 1.520000e-62 250.0
7 TraesCS2A01G463200 chr2D 98.214 56 1 0 1928 1983 52016173 52016118 5.840000e-17 99.0
8 TraesCS2A01G463200 chr2B 87.478 1134 73 34 795 1906 682138694 682139780 0.000000e+00 1243.0
9 TraesCS2A01G463200 chr2B 87.310 788 33 33 22 787 682137913 682138655 0.000000e+00 839.0
10 TraesCS2A01G463200 chr3A 98.905 639 6 1 1928 2565 651638553 651637915 0.000000e+00 1140.0
11 TraesCS2A01G463200 chr1A 98.724 627 7 1 1940 2565 584705057 584704431 0.000000e+00 1112.0
12 TraesCS2A01G463200 chr6A 84.085 377 50 5 2192 2565 54372808 54372439 3.140000e-94 355.0
13 TraesCS2A01G463200 chr1D 84.127 378 47 7 2190 2565 404241852 404241486 1.130000e-93 353.0
14 TraesCS2A01G463200 chr7A 82.940 381 51 9 2189 2565 393325755 393325385 5.290000e-87 331.0
15 TraesCS2A01G463200 chr7A 88.793 232 15 2 1928 2159 337922989 337922769 9.040000e-70 274.0
16 TraesCS2A01G463200 chr4D 97.059 170 3 2 1928 2096 490980569 490980401 4.180000e-73 285.0
17 TraesCS2A01G463200 chr4D 92.453 106 7 1 2079 2183 490979967 490979862 1.590000e-32 150.0
18 TraesCS2A01G463200 chr4D 96.429 56 2 0 1928 1983 490979403 490979458 2.720000e-15 93.5


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 TraesCS2A01G463200 chr2A 709048138 709050702 2564 False 4737.0 4737 100.0000 1 2565 1 chr2A.!!$F1 2564
1 TraesCS2A01G463200 chr2D 569308712 569310551 1839 False 2017.0 2017 87.0450 79 1916 1 chr2D.!!$F3 1837
2 TraesCS2A01G463200 chr2D 473093886 473094519 633 False 760.0 760 88.3360 1928 2565 1 chr2D.!!$F2 637
3 TraesCS2A01G463200 chr2D 52014618 52015272 654 False 699.0 699 86.5960 1928 2562 1 chr2D.!!$F1 634
4 TraesCS2A01G463200 chr2D 431524839 431525495 656 False 423.5 597 91.7915 1928 2562 2 chr2D.!!$F4 634
5 TraesCS2A01G463200 chr2B 682137913 682139780 1867 False 1041.0 1243 87.3940 22 1906 2 chr2B.!!$F1 1884
6 TraesCS2A01G463200 chr3A 651637915 651638553 638 True 1140.0 1140 98.9050 1928 2565 1 chr3A.!!$R1 637
7 TraesCS2A01G463200 chr1A 584704431 584705057 626 True 1112.0 1112 98.7240 1940 2565 1 chr1A.!!$R1 625
8 TraesCS2A01G463200 chr4D 490979862 490980569 707 True 217.5 285 94.7560 1928 2183 2 chr4D.!!$R1 255

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
37 38 0.03213 GACTGCGTGACTTGACCTCA 59.968 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1568 1667 0.098728 CTAATGAAACCAAGCCGGCG 59.901 55.0 23.2 9.91 39.03 6.46 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
17 18 3.708734 CGCCCGTGTTCGTCCAAC 61.709 66.667 0.00 0.00 35.28 3.77
18 19 3.708734 GCCCGTGTTCGTCCAACG 61.709 66.667 0.00 0.00 44.19 4.10
37 38 0.032130 GACTGCGTGACTTGACCTCA 59.968 55.000 0.00 0.00 0.00 3.86
124 125 2.018542 AATTATGGTCACCGGACACG 57.981 50.000 9.46 0.00 46.17 4.49
220 223 2.408022 CCTACGCGACCGAGGAAG 59.592 66.667 15.93 0.00 35.28 3.46
276 279 1.601759 GGCACGGGATGGATGGATG 60.602 63.158 0.00 0.00 0.00 3.51
277 280 1.601759 GCACGGGATGGATGGATGG 60.602 63.158 0.00 0.00 0.00 3.51
278 281 2.055689 GCACGGGATGGATGGATGGA 62.056 60.000 0.00 0.00 0.00 3.41
279 282 0.694771 CACGGGATGGATGGATGGAT 59.305 55.000 0.00 0.00 0.00 3.41
283 286 1.340795 GGGATGGATGGATGGATCAGC 60.341 57.143 0.00 0.00 0.00 4.26
287 290 0.604780 GGATGGATGGATCAGCGGTG 60.605 60.000 8.67 8.67 0.00 4.94
289 292 1.348008 ATGGATGGATCAGCGGTGGT 61.348 55.000 15.67 7.66 0.00 4.16
319 332 4.756135 CGAGACTAGTCCTAATAGTGGGTC 59.244 50.000 19.38 4.94 33.64 4.46
367 380 3.141767 ACCAAGTAAAGGCTTCCTCAC 57.858 47.619 0.00 0.00 30.89 3.51
368 381 2.441750 ACCAAGTAAAGGCTTCCTCACA 59.558 45.455 0.00 0.00 30.89 3.58
369 382 3.074538 ACCAAGTAAAGGCTTCCTCACAT 59.925 43.478 0.00 0.00 30.89 3.21
370 383 3.441572 CCAAGTAAAGGCTTCCTCACATG 59.558 47.826 0.00 0.00 30.89 3.21
412 438 3.844090 GCCGGCCACCTCTCTCTC 61.844 72.222 18.11 0.00 0.00 3.20
413 439 2.043450 CCGGCCACCTCTCTCTCT 60.043 66.667 2.24 0.00 0.00 3.10
414 440 2.124693 CCGGCCACCTCTCTCTCTC 61.125 68.421 2.24 0.00 0.00 3.20
415 441 1.077068 CGGCCACCTCTCTCTCTCT 60.077 63.158 2.24 0.00 0.00 3.10
416 442 1.101049 CGGCCACCTCTCTCTCTCTC 61.101 65.000 2.24 0.00 0.00 3.20
417 443 0.258774 GGCCACCTCTCTCTCTCTCT 59.741 60.000 0.00 0.00 0.00 3.10
418 444 1.680338 GCCACCTCTCTCTCTCTCTC 58.320 60.000 0.00 0.00 0.00 3.20
419 445 1.212935 GCCACCTCTCTCTCTCTCTCT 59.787 57.143 0.00 0.00 0.00 3.10
420 446 2.746472 GCCACCTCTCTCTCTCTCTCTC 60.746 59.091 0.00 0.00 0.00 3.20
421 447 2.774234 CCACCTCTCTCTCTCTCTCTCT 59.226 54.545 0.00 0.00 0.00 3.10
422 448 3.181461 CCACCTCTCTCTCTCTCTCTCTC 60.181 56.522 0.00 0.00 0.00 3.20
423 449 3.041946 ACCTCTCTCTCTCTCTCTCTCC 58.958 54.545 0.00 0.00 0.00 3.71
424 450 2.370189 CCTCTCTCTCTCTCTCTCTCCC 59.630 59.091 0.00 0.00 0.00 4.30
425 451 2.370189 CTCTCTCTCTCTCTCTCTCCCC 59.630 59.091 0.00 0.00 0.00 4.81
426 452 1.070758 CTCTCTCTCTCTCTCTCCCCG 59.929 61.905 0.00 0.00 0.00 5.73
427 453 0.535102 CTCTCTCTCTCTCTCCCCGC 60.535 65.000 0.00 0.00 0.00 6.13
428 454 1.528309 CTCTCTCTCTCTCCCCGCC 60.528 68.421 0.00 0.00 0.00 6.13
429 455 1.994885 CTCTCTCTCTCTCCCCGCCT 61.995 65.000 0.00 0.00 0.00 5.52
441 467 2.648454 CCGCCTTTGTTTTCCCGG 59.352 61.111 0.00 0.00 0.00 5.73
498 524 0.250467 CACTCACTCCACCACCCAAG 60.250 60.000 0.00 0.00 0.00 3.61
526 552 2.887783 CGAGCCCTACATCACATCTACT 59.112 50.000 0.00 0.00 0.00 2.57
527 553 3.057876 CGAGCCCTACATCACATCTACTC 60.058 52.174 0.00 0.00 0.00 2.59
528 554 4.148838 GAGCCCTACATCACATCTACTCT 58.851 47.826 0.00 0.00 0.00 3.24
529 555 5.317808 GAGCCCTACATCACATCTACTCTA 58.682 45.833 0.00 0.00 0.00 2.43
530 556 5.074115 AGCCCTACATCACATCTACTCTAC 58.926 45.833 0.00 0.00 0.00 2.59
556 582 4.538233 TGCGATGCATGGTGGTAG 57.462 55.556 2.46 0.00 31.71 3.18
557 583 1.601703 TGCGATGCATGGTGGTAGT 59.398 52.632 2.46 0.00 31.71 2.73
558 584 0.744057 TGCGATGCATGGTGGTAGTG 60.744 55.000 2.46 0.00 31.71 2.74
569 595 2.158519 TGGTGGTAGTGAGTGAGTGAGA 60.159 50.000 0.00 0.00 0.00 3.27
573 599 3.328050 TGGTAGTGAGTGAGTGAGAGAGA 59.672 47.826 0.00 0.00 0.00 3.10
686 721 8.643324 GCTCTTATATATACCGGGAATCTTCAT 58.357 37.037 6.32 0.00 0.00 2.57
688 723 8.924303 TCTTATATATACCGGGAATCTTCATGG 58.076 37.037 6.32 0.00 0.00 3.66
689 724 2.568623 ATACCGGGAATCTTCATGGC 57.431 50.000 6.32 0.00 0.00 4.40
690 725 0.472471 TACCGGGAATCTTCATGGCC 59.528 55.000 6.32 0.00 0.00 5.36
691 726 1.281925 ACCGGGAATCTTCATGGCCT 61.282 55.000 6.32 0.00 0.00 5.19
692 727 0.820891 CCGGGAATCTTCATGGCCTG 60.821 60.000 3.32 0.00 0.00 4.85
693 728 0.181114 CGGGAATCTTCATGGCCTGA 59.819 55.000 3.32 2.06 0.00 3.86
694 729 1.813092 CGGGAATCTTCATGGCCTGAG 60.813 57.143 3.32 0.00 34.68 3.35
695 730 1.316651 GGAATCTTCATGGCCTGAGC 58.683 55.000 3.32 0.00 34.68 4.26
714 749 1.884235 CCTCCCACAAGTCACAAGTC 58.116 55.000 0.00 0.00 0.00 3.01
715 750 1.417890 CCTCCCACAAGTCACAAGTCT 59.582 52.381 0.00 0.00 0.00 3.24
718 753 4.058817 CTCCCACAAGTCACAAGTCTTAC 58.941 47.826 0.00 0.00 0.00 2.34
719 754 2.800544 CCCACAAGTCACAAGTCTTACG 59.199 50.000 0.00 0.00 0.00 3.18
720 755 2.221055 CCACAAGTCACAAGTCTTACGC 59.779 50.000 0.00 0.00 0.00 4.42
730 765 0.172352 AGTCTTACGCTGCTCTGCTC 59.828 55.000 0.00 0.00 0.00 4.26
731 766 0.804156 GTCTTACGCTGCTCTGCTCC 60.804 60.000 0.00 0.00 0.00 4.70
732 767 1.875813 CTTACGCTGCTCTGCTCCG 60.876 63.158 0.00 0.00 0.00 4.63
733 768 3.989698 TTACGCTGCTCTGCTCCGC 62.990 63.158 0.00 0.00 0.00 5.54
768 819 4.509970 CACACACACTATCCTTTCGTGAAA 59.490 41.667 0.00 0.00 33.13 2.69
787 838 2.345760 GCTCCCGAGGTACGTTCCA 61.346 63.158 14.14 0.00 40.78 3.53
789 840 0.102481 CTCCCGAGGTACGTTCCATG 59.898 60.000 14.14 4.95 40.78 3.66
790 841 1.143183 CCCGAGGTACGTTCCATGG 59.857 63.158 14.14 4.97 40.78 3.66
792 843 0.459585 CCGAGGTACGTTCCATGGTG 60.460 60.000 12.58 5.74 40.78 4.17
793 844 1.082117 CGAGGTACGTTCCATGGTGC 61.082 60.000 12.58 4.94 37.22 5.01
923 1012 0.321346 ATCTGTCGGTGCATGTGACA 59.679 50.000 15.07 15.07 40.12 3.58
933 1022 4.154015 CGGTGCATGTGACATTTTCTTCTA 59.846 41.667 0.00 0.00 0.00 2.10
934 1023 5.393962 GGTGCATGTGACATTTTCTTCTAC 58.606 41.667 0.00 0.00 0.00 2.59
935 1024 5.182001 GGTGCATGTGACATTTTCTTCTACT 59.818 40.000 0.00 0.00 0.00 2.57
936 1025 6.371548 GGTGCATGTGACATTTTCTTCTACTA 59.628 38.462 0.00 0.00 0.00 1.82
937 1026 7.413438 GGTGCATGTGACATTTTCTTCTACTAG 60.413 40.741 0.00 0.00 0.00 2.57
938 1027 7.118390 GTGCATGTGACATTTTCTTCTACTAGT 59.882 37.037 0.00 0.00 0.00 2.57
939 1028 8.311109 TGCATGTGACATTTTCTTCTACTAGTA 58.689 33.333 1.89 1.89 0.00 1.82
940 1029 8.812329 GCATGTGACATTTTCTTCTACTAGTAG 58.188 37.037 21.87 21.87 34.56 2.57
941 1030 9.862371 CATGTGACATTTTCTTCTACTAGTAGT 57.138 33.333 25.58 8.14 34.84 2.73
960 1049 7.260558 AGTAGTACTTCTTTGGTTGCTTTTC 57.739 36.000 0.00 0.00 0.00 2.29
988 1077 1.175983 TGTCCGGCCATTTGGTGAAC 61.176 55.000 2.24 0.00 37.57 3.18
1022 1117 3.002791 TGATCGTTCTGCATTTCTCCAC 58.997 45.455 0.00 0.00 0.00 4.02
1035 1130 9.881649 CTGCATTTCTCCACATATATATGTACT 57.118 33.333 24.50 3.56 44.57 2.73
1042 1137 8.336987 TCTCCACATATATATGTACTAGCACCT 58.663 37.037 24.50 0.00 44.57 4.00
1047 1142 8.035394 ACATATATATGTACTAGCACCTTGCAC 58.965 37.037 23.90 0.00 44.62 4.57
1061 1156 3.327757 ACCTTGCACCTCATTCAGTCTAA 59.672 43.478 0.00 0.00 0.00 2.10
1062 1157 4.202461 ACCTTGCACCTCATTCAGTCTAAA 60.202 41.667 0.00 0.00 0.00 1.85
1063 1158 4.761739 CCTTGCACCTCATTCAGTCTAAAA 59.238 41.667 0.00 0.00 0.00 1.52
1064 1159 5.416952 CCTTGCACCTCATTCAGTCTAAAAT 59.583 40.000 0.00 0.00 0.00 1.82
1065 1160 6.404074 CCTTGCACCTCATTCAGTCTAAAATC 60.404 42.308 0.00 0.00 0.00 2.17
1066 1161 5.809001 TGCACCTCATTCAGTCTAAAATCT 58.191 37.500 0.00 0.00 0.00 2.40
1067 1162 6.946340 TGCACCTCATTCAGTCTAAAATCTA 58.054 36.000 0.00 0.00 0.00 1.98
1078 1173 7.542890 TCAGTCTAAAATCTAGAGAGCAGTTG 58.457 38.462 0.00 0.00 0.00 3.16
1080 1175 7.487829 CAGTCTAAAATCTAGAGAGCAGTTGAC 59.512 40.741 0.00 0.02 0.00 3.18
1089 1184 2.085320 AGAGCAGTTGACGATCGTAGT 58.915 47.619 22.79 6.64 0.00 2.73
1162 1258 4.560856 GCAGCTCGATCGGCGACT 62.561 66.667 13.76 0.25 45.59 4.18
1168 1264 3.315521 CGATCGGCGACTGAAGCG 61.316 66.667 13.76 0.00 44.57 4.68
1178 1274 2.185350 CTGAAGCGATGGCGTCCT 59.815 61.111 12.62 0.00 45.55 3.85
1179 1275 1.880340 CTGAAGCGATGGCGTCCTC 60.880 63.158 12.62 1.01 45.55 3.71
1352 1448 4.379243 CGGAGGCGCTGGACAACT 62.379 66.667 7.64 0.00 0.00 3.16
1353 1449 2.435059 GGAGGCGCTGGACAACTC 60.435 66.667 7.64 2.84 0.00 3.01
1356 1452 2.045926 GGCGCTGGACAACTCCAT 60.046 61.111 7.64 0.00 46.18 3.41
1411 1510 4.579384 ACCACCAGCACCAACCCG 62.579 66.667 0.00 0.00 0.00 5.28
1590 1696 1.102978 CGGCTTGGTTTCATTAGGGG 58.897 55.000 0.00 0.00 0.00 4.79
1591 1697 1.615919 CGGCTTGGTTTCATTAGGGGT 60.616 52.381 0.00 0.00 0.00 4.95
1594 1700 2.353704 GCTTGGTTTCATTAGGGGTTGC 60.354 50.000 0.00 0.00 0.00 4.17
1634 1740 5.207033 GTCGTGGTTTGCGTTTAGTTAATT 58.793 37.500 0.00 0.00 0.00 1.40
1636 1742 4.143701 CGTGGTTTGCGTTTAGTTAATTGC 60.144 41.667 0.00 0.00 0.00 3.56
1637 1743 3.975670 TGGTTTGCGTTTAGTTAATTGCG 59.024 39.130 0.00 0.00 0.00 4.85
1640 1746 3.881780 TGCGTTTAGTTAATTGCGTGT 57.118 38.095 0.00 0.00 0.00 4.49
1647 1753 7.407558 GCGTTTAGTTAATTGCGTGTTTAGTTC 60.408 37.037 0.00 0.00 0.00 3.01
1648 1754 7.201008 CGTTTAGTTAATTGCGTGTTTAGTTCG 60.201 37.037 0.00 0.00 0.00 3.95
1649 1755 5.910637 AGTTAATTGCGTGTTTAGTTCGA 57.089 34.783 0.00 0.00 0.00 3.71
1701 1809 2.238942 TGTGTGTGTGTGATGGAGAC 57.761 50.000 0.00 0.00 0.00 3.36
1709 1817 1.351017 GTGTGATGGAGACTTGGGGAA 59.649 52.381 0.00 0.00 0.00 3.97
1761 1883 3.488047 GGCATGCATGTTACTGTGATGTC 60.488 47.826 26.79 6.10 0.00 3.06
1797 1921 8.915057 ATGGAGTATTTCACTAGGAATTCATG 57.085 34.615 7.93 0.12 37.72 3.07
1798 1922 7.282585 TGGAGTATTTCACTAGGAATTCATGG 58.717 38.462 7.93 4.68 37.72 3.66
1800 1924 6.904626 AGTATTTCACTAGGAATTCATGGCT 58.095 36.000 7.93 0.00 34.98 4.75
1807 1931 4.884164 ACTAGGAATTCATGGCTACTTTGC 59.116 41.667 7.93 0.00 0.00 3.68
1817 1941 5.945784 TCATGGCTACTTTGCTGTTCTTATT 59.054 36.000 0.00 0.00 0.00 1.40
1818 1942 7.109501 TCATGGCTACTTTGCTGTTCTTATTA 58.890 34.615 0.00 0.00 0.00 0.98
1819 1943 7.775093 TCATGGCTACTTTGCTGTTCTTATTAT 59.225 33.333 0.00 0.00 0.00 1.28
1860 1984 4.486574 GAGTACCTACTCCGCTAATGAC 57.513 50.000 1.49 0.00 45.33 3.06
1887 2011 5.007682 TGGCTAATTGTTGGAGAAACCTAC 58.992 41.667 0.00 0.00 42.97 3.18
1907 2031 1.675714 CGCCAACTGAAGGATGCTACA 60.676 52.381 0.00 0.00 0.00 2.74
1916 2040 2.355010 AGGATGCTACATTCCAAGCC 57.645 50.000 0.00 0.00 37.97 4.35
1917 2041 1.849039 AGGATGCTACATTCCAAGCCT 59.151 47.619 0.00 0.00 37.97 4.58
1918 2042 2.158696 AGGATGCTACATTCCAAGCCTC 60.159 50.000 0.00 0.00 37.97 4.70
1919 2043 2.421952 GGATGCTACATTCCAAGCCTCA 60.422 50.000 0.00 0.00 37.97 3.86
1920 2044 2.877097 TGCTACATTCCAAGCCTCAA 57.123 45.000 0.00 0.00 37.97 3.02
1921 2045 3.370840 TGCTACATTCCAAGCCTCAAT 57.629 42.857 0.00 0.00 37.97 2.57
1922 2046 3.700538 TGCTACATTCCAAGCCTCAATT 58.299 40.909 0.00 0.00 37.97 2.32
1923 2047 4.854173 TGCTACATTCCAAGCCTCAATTA 58.146 39.130 0.00 0.00 37.97 1.40
1924 2048 5.448654 TGCTACATTCCAAGCCTCAATTAT 58.551 37.500 0.00 0.00 37.97 1.28
1925 2049 5.300034 TGCTACATTCCAAGCCTCAATTATG 59.700 40.000 0.00 0.00 37.97 1.90
1926 2050 5.300286 GCTACATTCCAAGCCTCAATTATGT 59.700 40.000 0.00 0.00 32.40 2.29
2169 2746 8.651589 AAAGAAACTATTTCCCCCTAGAAAAG 57.348 34.615 0.00 0.00 39.11 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.708734 GTTGGACGAACACGGGCG 61.709 66.667 0.00 0.00 34.35 6.13
1 2 3.708734 CGTTGGACGAACACGGGC 61.709 66.667 1.13 0.00 46.05 6.13
17 18 1.004277 GAGGTCAAGTCACGCAGTCG 61.004 60.000 0.00 0.00 41.61 4.18
18 19 0.032130 TGAGGTCAAGTCACGCAGTC 59.968 55.000 0.00 0.00 41.61 3.51
20 21 0.315251 TCTGAGGTCAAGTCACGCAG 59.685 55.000 0.00 0.00 0.00 5.18
69 70 0.649475 GCTTCGTCATAGCAGCACTG 59.351 55.000 0.00 0.00 38.51 3.66
76 77 1.063649 TCGTCCGCTTCGTCATAGC 59.936 57.895 0.00 0.00 35.29 2.97
220 223 4.670221 CGGTTACTGTACTCCGTTGTACTC 60.670 50.000 17.10 0.00 42.22 2.59
276 279 1.108776 TACAGTACCACCGCTGATCC 58.891 55.000 0.00 0.00 36.62 3.36
277 280 1.533338 CGTACAGTACCACCGCTGATC 60.533 57.143 5.07 0.00 36.62 2.92
278 281 0.454600 CGTACAGTACCACCGCTGAT 59.545 55.000 5.07 0.00 36.62 2.90
279 282 0.606130 TCGTACAGTACCACCGCTGA 60.606 55.000 5.07 0.00 36.62 4.26
283 286 1.446907 AGTCTCGTACAGTACCACCG 58.553 55.000 5.07 0.00 0.00 4.94
287 290 4.135747 AGGACTAGTCTCGTACAGTACC 57.864 50.000 21.88 1.87 0.00 3.34
289 292 8.140628 CACTATTAGGACTAGTCTCGTACAGTA 58.859 40.741 21.88 4.97 0.00 2.74
319 332 1.075425 CTCTCTGTCGGCTTGCTTCG 61.075 60.000 0.00 0.00 0.00 3.79
408 434 0.535102 GCGGGGAGAGAGAGAGAGAG 60.535 65.000 0.00 0.00 0.00 3.20
409 435 1.529796 GCGGGGAGAGAGAGAGAGA 59.470 63.158 0.00 0.00 0.00 3.10
410 436 1.528309 GGCGGGGAGAGAGAGAGAG 60.528 68.421 0.00 0.00 0.00 3.20
411 437 1.576368 AAGGCGGGGAGAGAGAGAGA 61.576 60.000 0.00 0.00 0.00 3.10
412 438 0.686112 AAAGGCGGGGAGAGAGAGAG 60.686 60.000 0.00 0.00 0.00 3.20
413 439 0.972983 CAAAGGCGGGGAGAGAGAGA 60.973 60.000 0.00 0.00 0.00 3.10
414 440 1.261238 ACAAAGGCGGGGAGAGAGAG 61.261 60.000 0.00 0.00 0.00 3.20
415 441 0.836400 AACAAAGGCGGGGAGAGAGA 60.836 55.000 0.00 0.00 0.00 3.10
416 442 0.036875 AAACAAAGGCGGGGAGAGAG 59.963 55.000 0.00 0.00 0.00 3.20
417 443 0.476771 AAAACAAAGGCGGGGAGAGA 59.523 50.000 0.00 0.00 0.00 3.10
418 444 0.881796 GAAAACAAAGGCGGGGAGAG 59.118 55.000 0.00 0.00 0.00 3.20
419 445 0.538746 GGAAAACAAAGGCGGGGAGA 60.539 55.000 0.00 0.00 0.00 3.71
420 446 1.532604 GGGAAAACAAAGGCGGGGAG 61.533 60.000 0.00 0.00 0.00 4.30
421 447 1.532078 GGGAAAACAAAGGCGGGGA 60.532 57.895 0.00 0.00 0.00 4.81
422 448 2.926420 CGGGAAAACAAAGGCGGGG 61.926 63.158 0.00 0.00 0.00 5.73
423 449 2.648454 CGGGAAAACAAAGGCGGG 59.352 61.111 0.00 0.00 0.00 6.13
424 450 2.648454 CCGGGAAAACAAAGGCGG 59.352 61.111 0.00 0.00 0.00 6.13
425 451 2.648454 CCCGGGAAAACAAAGGCG 59.352 61.111 18.48 0.00 0.00 5.52
426 452 2.579657 CCCCCGGGAAAACAAAGGC 61.580 63.158 26.32 0.00 37.50 4.35
427 453 2.579657 GCCCCCGGGAAAACAAAGG 61.580 63.158 26.32 13.50 37.50 3.11
428 454 1.834822 TGCCCCCGGGAAAACAAAG 60.835 57.895 26.32 1.13 37.50 2.77
429 455 2.134933 GTGCCCCCGGGAAAACAAA 61.135 57.895 26.32 0.00 37.50 2.83
498 524 1.402968 TGATGTAGGGCTCGTCGTTAC 59.597 52.381 0.00 0.00 0.00 2.50
526 552 1.490621 CATCGCATGATGCACGTAGA 58.509 50.000 18.47 6.32 45.36 2.59
552 578 3.938963 CTCTCTCTCACTCACTCACTACC 59.061 52.174 0.00 0.00 0.00 3.18
553 579 4.827692 TCTCTCTCTCACTCACTCACTAC 58.172 47.826 0.00 0.00 0.00 2.73
554 580 5.670485 GATCTCTCTCTCACTCACTCACTA 58.330 45.833 0.00 0.00 0.00 2.74
555 581 4.517285 GATCTCTCTCTCACTCACTCACT 58.483 47.826 0.00 0.00 0.00 3.41
556 582 3.309682 CGATCTCTCTCTCACTCACTCAC 59.690 52.174 0.00 0.00 0.00 3.51
557 583 3.530535 CGATCTCTCTCTCACTCACTCA 58.469 50.000 0.00 0.00 0.00 3.41
558 584 2.872245 CCGATCTCTCTCTCACTCACTC 59.128 54.545 0.00 0.00 0.00 3.51
569 595 5.949354 CCCTATCTAATCAACCGATCTCTCT 59.051 44.000 0.00 0.00 0.00 3.10
573 599 6.078664 AGAACCCTATCTAATCAACCGATCT 58.921 40.000 0.00 0.00 0.00 2.75
688 723 2.045536 CTTGTGGGAGGCTCAGGC 60.046 66.667 17.69 5.70 37.82 4.85
689 724 1.298014 GACTTGTGGGAGGCTCAGG 59.702 63.158 17.69 0.00 0.00 3.86
690 725 0.321122 GTGACTTGTGGGAGGCTCAG 60.321 60.000 17.69 7.05 0.00 3.35
691 726 1.053835 TGTGACTTGTGGGAGGCTCA 61.054 55.000 17.69 0.00 0.00 4.26
692 727 0.108585 TTGTGACTTGTGGGAGGCTC 59.891 55.000 5.78 5.78 0.00 4.70
693 728 0.109342 CTTGTGACTTGTGGGAGGCT 59.891 55.000 0.00 0.00 0.00 4.58
694 729 0.179018 ACTTGTGACTTGTGGGAGGC 60.179 55.000 0.00 0.00 0.00 4.70
695 730 1.417890 AGACTTGTGACTTGTGGGAGG 59.582 52.381 0.00 0.00 0.00 4.30
699 734 2.221055 GCGTAAGACTTGTGACTTGTGG 59.779 50.000 0.00 0.00 43.02 4.17
714 749 1.875813 CGGAGCAGAGCAGCGTAAG 60.876 63.158 0.00 0.00 40.15 2.34
715 750 2.181777 CGGAGCAGAGCAGCGTAA 59.818 61.111 0.00 0.00 40.15 3.18
730 765 4.838486 GTGCGACGGAGAGAGCGG 62.838 72.222 0.00 0.00 0.00 5.52
731 766 4.103103 TGTGCGACGGAGAGAGCG 62.103 66.667 0.00 0.00 0.00 5.03
732 767 2.505118 GTGTGCGACGGAGAGAGC 60.505 66.667 0.00 0.00 0.00 4.09
733 768 1.442857 GTGTGTGCGACGGAGAGAG 60.443 63.158 0.00 0.00 0.00 3.20
734 769 2.190841 TGTGTGTGCGACGGAGAGA 61.191 57.895 0.00 0.00 0.00 3.10
735 770 2.016704 GTGTGTGTGCGACGGAGAG 61.017 63.158 0.00 0.00 0.00 3.20
768 819 2.050934 GGAACGTACCTCGGGAGCT 61.051 63.158 0.00 0.00 44.69 4.09
787 838 4.704833 AGCTCAACGCGGCACCAT 62.705 61.111 12.47 0.00 45.59 3.55
789 840 3.194272 AAAAGCTCAACGCGGCACC 62.194 57.895 12.47 0.00 45.59 5.01
790 841 1.725973 GAAAAGCTCAACGCGGCAC 60.726 57.895 12.47 0.00 45.59 5.01
792 843 2.126850 GGAAAAGCTCAACGCGGC 60.127 61.111 12.47 3.50 45.59 6.53
793 844 0.310854 AAAGGAAAAGCTCAACGCGG 59.689 50.000 12.47 0.00 45.59 6.46
933 1022 6.667558 AGCAACCAAAGAAGTACTACTAGT 57.332 37.500 0.00 0.00 0.00 2.57
934 1023 7.964604 AAAGCAACCAAAGAAGTACTACTAG 57.035 36.000 0.00 0.00 0.00 2.57
935 1024 7.170320 CGAAAAGCAACCAAAGAAGTACTACTA 59.830 37.037 0.00 0.00 0.00 1.82
936 1025 6.018180 CGAAAAGCAACCAAAGAAGTACTACT 60.018 38.462 0.00 0.00 0.00 2.57
937 1026 6.134061 CGAAAAGCAACCAAAGAAGTACTAC 58.866 40.000 0.00 0.00 0.00 2.73
938 1027 6.295039 CGAAAAGCAACCAAAGAAGTACTA 57.705 37.500 0.00 0.00 0.00 1.82
939 1028 5.169836 CGAAAAGCAACCAAAGAAGTACT 57.830 39.130 0.00 0.00 0.00 2.73
960 1049 1.586154 ATGGCCGGACAAAAAGAGCG 61.586 55.000 17.77 0.00 0.00 5.03
988 1077 2.969238 GATCATGCGGCTCGGTGG 60.969 66.667 0.00 0.00 0.00 4.61
998 1087 3.547613 GGAGAAATGCAGAACGATCATGC 60.548 47.826 9.18 9.18 40.40 4.06
1022 1117 7.492669 GGTGCAAGGTGCTAGTACATATATATG 59.507 40.741 19.21 19.21 45.31 1.78
1035 1130 1.350684 TGAATGAGGTGCAAGGTGCTA 59.649 47.619 1.43 0.00 45.31 3.49
1042 1137 6.240894 AGATTTTAGACTGAATGAGGTGCAA 58.759 36.000 0.00 0.00 0.00 4.08
1047 1142 7.867403 GCTCTCTAGATTTTAGACTGAATGAGG 59.133 40.741 0.00 0.00 0.00 3.86
1048 1143 8.412456 TGCTCTCTAGATTTTAGACTGAATGAG 58.588 37.037 0.00 0.00 0.00 2.90
1061 1156 5.587289 GATCGTCAACTGCTCTCTAGATTT 58.413 41.667 0.00 0.00 0.00 2.17
1062 1157 4.260990 CGATCGTCAACTGCTCTCTAGATT 60.261 45.833 7.03 0.00 0.00 2.40
1063 1158 3.249799 CGATCGTCAACTGCTCTCTAGAT 59.750 47.826 7.03 0.00 0.00 1.98
1064 1159 2.609916 CGATCGTCAACTGCTCTCTAGA 59.390 50.000 7.03 0.00 0.00 2.43
1065 1160 2.353269 ACGATCGTCAACTGCTCTCTAG 59.647 50.000 16.60 0.00 0.00 2.43
1066 1161 2.357075 ACGATCGTCAACTGCTCTCTA 58.643 47.619 16.60 0.00 0.00 2.43
1067 1162 1.169577 ACGATCGTCAACTGCTCTCT 58.830 50.000 16.60 0.00 0.00 3.10
1078 1173 4.030306 CAGCAAACTGTTACTACGATCGTC 59.970 45.833 26.48 10.64 39.22 4.20
1080 1175 4.485489 CAGCAAACTGTTACTACGATCG 57.515 45.455 14.88 14.88 39.22 3.69
1125 1221 1.126846 CCGTTGCGAGAATCAACAGTC 59.873 52.381 6.66 0.00 42.78 3.51
1162 1258 2.184322 GAGGACGCCATCGCTTCA 59.816 61.111 0.00 0.00 39.84 3.02
1178 1274 3.219928 GAGCAGATCTCGCCGGGA 61.220 66.667 2.18 0.00 31.20 5.14
1568 1667 0.098728 CTAATGAAACCAAGCCGGCG 59.901 55.000 23.20 9.91 39.03 6.46
1572 1671 2.231716 ACCCCTAATGAAACCAAGCC 57.768 50.000 0.00 0.00 0.00 4.35
1573 1672 2.353704 GCAACCCCTAATGAAACCAAGC 60.354 50.000 0.00 0.00 0.00 4.01
1574 1673 3.165071 AGCAACCCCTAATGAAACCAAG 58.835 45.455 0.00 0.00 0.00 3.61
1575 1674 3.161866 GAGCAACCCCTAATGAAACCAA 58.838 45.455 0.00 0.00 0.00 3.67
1576 1675 2.802719 GAGCAACCCCTAATGAAACCA 58.197 47.619 0.00 0.00 0.00 3.67
1577 1676 1.743394 CGAGCAACCCCTAATGAAACC 59.257 52.381 0.00 0.00 0.00 3.27
1578 1677 2.418976 GACGAGCAACCCCTAATGAAAC 59.581 50.000 0.00 0.00 0.00 2.78
1590 1696 3.181520 ACGCTAATGAATTGACGAGCAAC 60.182 43.478 0.00 0.00 39.78 4.17
1591 1697 3.000041 ACGCTAATGAATTGACGAGCAA 59.000 40.909 0.00 0.00 41.53 3.91
1594 1700 2.852413 ACGACGCTAATGAATTGACGAG 59.148 45.455 0.00 3.81 0.00 4.18
1634 1740 3.580731 TCATCATCGAACTAAACACGCA 58.419 40.909 0.00 0.00 0.00 5.24
1636 1742 6.331170 TCATTCATCATCGAACTAAACACG 57.669 37.500 0.00 0.00 0.00 4.49
1637 1743 9.214953 GAAATCATTCATCATCGAACTAAACAC 57.785 33.333 0.00 0.00 35.54 3.32
1647 1753 5.663795 ACGGAAGAAATCATTCATCATCG 57.336 39.130 0.00 0.00 35.48 3.84
1648 1754 7.256756 AGAACGGAAGAAATCATTCATCATC 57.743 36.000 0.00 0.00 35.48 2.92
1649 1755 7.201767 GGAAGAACGGAAGAAATCATTCATCAT 60.202 37.037 0.00 0.00 35.48 2.45
1701 1809 0.605319 TTACAGCGTGCTTCCCCAAG 60.605 55.000 0.00 0.00 0.00 3.61
1709 1817 4.493545 GCGTTATTTATGTTACAGCGTGCT 60.494 41.667 0.00 0.00 0.00 4.40
1761 1883 7.560368 AGTGAAATACTCCATTCAAGGTCTAG 58.440 38.462 0.00 0.00 37.31 2.43
1797 1921 7.281100 AGTCATAATAAGAACAGCAAAGTAGCC 59.719 37.037 0.00 0.00 34.23 3.93
1798 1922 8.202745 AGTCATAATAAGAACAGCAAAGTAGC 57.797 34.615 0.00 0.00 0.00 3.58
1800 1924 9.502091 ACAAGTCATAATAAGAACAGCAAAGTA 57.498 29.630 0.00 0.00 0.00 2.24
1807 1931 8.023128 CCAAACCACAAGTCATAATAAGAACAG 58.977 37.037 0.00 0.00 0.00 3.16
1817 1941 7.001674 ACTCATAAACCAAACCACAAGTCATA 58.998 34.615 0.00 0.00 0.00 2.15
1818 1942 5.833131 ACTCATAAACCAAACCACAAGTCAT 59.167 36.000 0.00 0.00 0.00 3.06
1819 1943 5.197451 ACTCATAAACCAAACCACAAGTCA 58.803 37.500 0.00 0.00 0.00 3.41
1860 1984 6.378280 AGGTTTCTCCAACAATTAGCCATTAG 59.622 38.462 0.00 0.00 37.07 1.73
1887 2011 1.009829 GTAGCATCCTTCAGTTGGCG 58.990 55.000 0.00 0.00 0.00 5.69
1907 2031 4.870636 TCCACATAATTGAGGCTTGGAAT 58.129 39.130 0.00 0.00 33.94 3.01
1916 2040 2.614057 GAGCCGGTTCCACATAATTGAG 59.386 50.000 7.13 0.00 0.00 3.02
1917 2041 2.639065 GAGCCGGTTCCACATAATTGA 58.361 47.619 7.13 0.00 0.00 2.57
1918 2042 1.676006 GGAGCCGGTTCCACATAATTG 59.324 52.381 30.55 0.00 37.20 2.32
1919 2043 1.564348 AGGAGCCGGTTCCACATAATT 59.436 47.619 35.38 13.33 39.84 1.40
1920 2044 1.141053 GAGGAGCCGGTTCCACATAAT 59.859 52.381 35.38 16.65 39.84 1.28
1921 2045 0.539986 GAGGAGCCGGTTCCACATAA 59.460 55.000 35.38 0.00 39.84 1.90
1922 2046 0.325296 AGAGGAGCCGGTTCCACATA 60.325 55.000 35.38 0.00 39.84 2.29
1923 2047 0.325296 TAGAGGAGCCGGTTCCACAT 60.325 55.000 35.38 23.18 39.84 3.21
1924 2048 1.077805 TAGAGGAGCCGGTTCCACA 59.922 57.895 35.38 18.88 39.84 4.17
1925 2049 1.516423 GTAGAGGAGCCGGTTCCAC 59.484 63.158 35.38 29.76 39.84 4.02
1926 2050 1.684734 GGTAGAGGAGCCGGTTCCA 60.685 63.158 35.38 15.58 39.84 3.53
2353 2931 2.197324 AAGTTTTGCCCGGCTCCA 59.803 55.556 11.61 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.