Multiple sequence alignment - TraesCS4D01G223200

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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 TraesCS4D01G223200 chr4D 100.000 2287 0 0 1 2287 380246192 380248478 0.000000e+00 4224
1 TraesCS4D01G223200 chr4D 92.398 1710 113 10 1 1707 504270336 504272031 0.000000e+00 2422
2 TraesCS4D01G223200 chr4D 92.065 1714 114 17 1 1706 466289366 466291065 0.000000e+00 2392
3 TraesCS4D01G223200 chr7D 92.619 1707 117 7 1 1704 98406303 98404603 0.000000e+00 2446
4 TraesCS4D01G223200 chr1D 91.998 1712 116 12 1 1709 421086757 421085064 0.000000e+00 2383
5 TraesCS4D01G223200 chr2A 91.735 1706 133 6 1 1704 165347573 165345874 0.000000e+00 2362
6 TraesCS4D01G223200 chr4A 91.137 1715 135 11 1 1708 619180421 619182125 0.000000e+00 2309
7 TraesCS4D01G223200 chr4A 83.209 536 46 13 1787 2287 83760588 83760062 3.460000e-123 451
8 TraesCS4D01G223200 chr3A 91.159 1708 120 13 2 1706 113367065 113365386 0.000000e+00 2289
9 TraesCS4D01G223200 chr6A 90.415 1711 153 9 2 1708 479912663 479910960 0.000000e+00 2241
10 TraesCS4D01G223200 chr7A 90.423 1702 138 17 9 1705 680904168 680902487 0.000000e+00 2217
11 TraesCS4D01G223200 chr4B 84.615 273 31 9 2016 2287 467270869 467271131 6.270000e-66 261


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 TraesCS4D01G223200 chr4D 380246192 380248478 2286 False 4224 4224 100.000 1 2287 1 chr4D.!!$F1 2286
1 TraesCS4D01G223200 chr4D 504270336 504272031 1695 False 2422 2422 92.398 1 1707 1 chr4D.!!$F3 1706
2 TraesCS4D01G223200 chr4D 466289366 466291065 1699 False 2392 2392 92.065 1 1706 1 chr4D.!!$F2 1705
3 TraesCS4D01G223200 chr7D 98404603 98406303 1700 True 2446 2446 92.619 1 1704 1 chr7D.!!$R1 1703
4 TraesCS4D01G223200 chr1D 421085064 421086757 1693 True 2383 2383 91.998 1 1709 1 chr1D.!!$R1 1708
5 TraesCS4D01G223200 chr2A 165345874 165347573 1699 True 2362 2362 91.735 1 1704 1 chr2A.!!$R1 1703
6 TraesCS4D01G223200 chr4A 619180421 619182125 1704 False 2309 2309 91.137 1 1708 1 chr4A.!!$F1 1707
7 TraesCS4D01G223200 chr4A 83760062 83760588 526 True 451 451 83.209 1787 2287 1 chr4A.!!$R1 500
8 TraesCS4D01G223200 chr3A 113365386 113367065 1679 True 2289 2289 91.159 2 1706 1 chr3A.!!$R1 1704
9 TraesCS4D01G223200 chr6A 479910960 479912663 1703 True 2241 2241 90.415 2 1708 1 chr6A.!!$R1 1706
10 TraesCS4D01G223200 chr7A 680902487 680904168 1681 True 2217 2217 90.423 9 1705 1 chr7A.!!$R1 1696

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
776 778 0.182061 GGAGAGCAATCAGATGGGCA 59.818 55.0 9.38 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2011 0.110056 GCCATGCTTGTCGTCAACTG 60.11 55.0 0.0 0.0 0.0 3.16 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
53 54 1.260033 CATCTTCTTCTTCATCGCCGC 59.740 52.381 0.00 0.00 0.00 6.53
85 86 1.955663 TCGTTGTCGTCGTCCTCGA 60.956 57.895 0.00 0.00 38.59 4.04
110 111 0.614697 TCGAGGTTGATCTGCCAGGA 60.615 55.000 8.45 3.14 0.00 3.86
112 113 1.743996 GAGGTTGATCTGCCAGGAAC 58.256 55.000 8.45 0.00 0.00 3.62
118 119 3.665675 ATCTGCCAGGAACGACGGC 62.666 63.158 0.00 0.00 46.43 5.68
153 154 1.674651 CACTGGCATCTGCACTGCT 60.675 57.895 14.37 0.00 44.36 4.24
178 179 0.716591 TTCCTCCTCCTTAGGCTCCA 59.283 55.000 0.00 0.00 43.31 3.86
287 288 3.748568 CACCACTTCTTCCTCTGTTTAGC 59.251 47.826 0.00 0.00 0.00 3.09
292 293 2.156917 TCTTCCTCTGTTTAGCGTCGA 58.843 47.619 0.00 0.00 0.00 4.20
402 403 1.279496 TACTGGCCTTCATGAGCACT 58.721 50.000 3.32 0.00 0.00 4.40
476 478 2.028476 CCATGGTGTTCTCGACTTGGTA 60.028 50.000 2.57 0.00 0.00 3.25
617 619 1.205055 GAAGAGAGGGGGTGGGTAAG 58.795 60.000 0.00 0.00 0.00 2.34
702 704 4.212636 TGCCGTTTTAACTACAAGCTCTTC 59.787 41.667 0.00 0.00 0.00 2.87
718 720 5.259632 AGCTCTTCAATTAGCCATGAACTT 58.740 37.500 0.00 0.00 39.64 2.66
724 726 4.523943 TCAATTAGCCATGAACTTTGTGCT 59.476 37.500 0.00 0.00 0.00 4.40
725 727 3.921119 TTAGCCATGAACTTTGTGCTG 57.079 42.857 0.00 0.00 0.00 4.41
729 731 1.401530 CATGAACTTTGTGCTGTGCG 58.598 50.000 0.00 0.00 0.00 5.34
741 743 0.950555 GCTGTGCGTGACTCCATGAA 60.951 55.000 0.00 0.00 0.00 2.57
760 762 2.306341 ATTGTGTGCAGATCGAGGAG 57.694 50.000 0.00 0.00 0.00 3.69
762 764 0.813821 TGTGTGCAGATCGAGGAGAG 59.186 55.000 0.00 0.00 0.00 3.20
763 765 0.527385 GTGTGCAGATCGAGGAGAGC 60.527 60.000 0.00 0.00 35.01 4.09
764 766 0.967380 TGTGCAGATCGAGGAGAGCA 60.967 55.000 0.00 0.00 37.82 4.26
766 768 1.117994 TGCAGATCGAGGAGAGCAAT 58.882 50.000 0.00 0.00 37.82 3.56
767 769 1.068281 TGCAGATCGAGGAGAGCAATC 59.932 52.381 0.00 0.00 37.82 2.67
768 770 1.068281 GCAGATCGAGGAGAGCAATCA 59.932 52.381 0.00 0.00 37.82 2.57
770 772 2.622470 CAGATCGAGGAGAGCAATCAGA 59.378 50.000 0.00 0.00 37.82 3.27
772 774 3.256383 AGATCGAGGAGAGCAATCAGATG 59.744 47.826 0.00 0.00 37.82 2.90
773 775 1.685517 TCGAGGAGAGCAATCAGATGG 59.314 52.381 0.00 0.00 0.00 3.51
774 776 1.270199 CGAGGAGAGCAATCAGATGGG 60.270 57.143 0.00 0.00 0.00 4.00
775 777 0.473326 AGGAGAGCAATCAGATGGGC 59.527 55.000 0.00 0.00 0.00 5.36
776 778 0.182061 GGAGAGCAATCAGATGGGCA 59.818 55.000 9.38 0.00 0.00 5.36
778 780 0.463295 AGAGCAATCAGATGGGCACG 60.463 55.000 9.38 0.00 0.00 5.34
779 781 1.442526 GAGCAATCAGATGGGCACGG 61.443 60.000 9.38 0.00 0.00 4.94
780 782 1.451927 GCAATCAGATGGGCACGGA 60.452 57.895 3.05 0.00 0.00 4.69
781 783 1.442526 GCAATCAGATGGGCACGGAG 61.443 60.000 3.05 0.00 0.00 4.63
789 791 2.063015 ATGGGCACGGAGGTTGACAA 62.063 55.000 0.00 0.00 0.00 3.18
831 833 1.671054 CAATGCCCGACGAGGTTGT 60.671 57.895 0.00 0.00 38.74 3.32
1014 1019 2.772924 CCCATGCCCCTGGACTTT 59.227 61.111 0.00 0.00 38.69 2.66
1032 1037 0.249531 TTACCAAGCACTTCGTCGCA 60.250 50.000 0.00 0.00 0.00 5.10
1193 1201 0.605589 CGTTCAAGCTCCTCACTCCT 59.394 55.000 0.00 0.00 0.00 3.69
1317 1325 3.381908 CACCTCTTTCCAGCGTACTATCT 59.618 47.826 0.00 0.00 0.00 1.98
1332 1340 8.361139 AGCGTACTATCTGAATTATGCTAGTTT 58.639 33.333 7.93 0.00 35.49 2.66
1358 1366 8.862325 ATGGTTTATGAGTTGAACTGTTATGA 57.138 30.769 0.90 0.00 0.00 2.15
1359 1367 8.684386 TGGTTTATGAGTTGAACTGTTATGAA 57.316 30.769 0.90 0.00 0.00 2.57
1360 1368 8.783093 TGGTTTATGAGTTGAACTGTTATGAAG 58.217 33.333 0.90 0.00 0.00 3.02
1367 1375 5.296780 AGTTGAACTGTTATGAAGTGTGGTG 59.703 40.000 0.00 0.00 0.00 4.17
1378 1386 5.351948 TGAAGTGTGGTGCTGCTTATATA 57.648 39.130 0.00 0.00 0.00 0.86
1409 1417 7.721286 ATGCTAGTTCATGCTCTGTTTATAC 57.279 36.000 0.00 0.00 0.00 1.47
1470 1478 3.306472 AACCTCACCAACTAGCCAAAA 57.694 42.857 0.00 0.00 0.00 2.44
1478 1486 4.583073 CACCAACTAGCCAAAAAGGTTACT 59.417 41.667 0.00 0.00 40.61 2.24
1484 1492 5.761726 ACTAGCCAAAAAGGTTACTACACAC 59.238 40.000 0.00 0.00 40.61 3.82
1490 1498 0.606604 AGGTTACTACACACCAGGCG 59.393 55.000 0.00 0.00 35.25 5.52
1498 1506 0.322456 ACACACCAGGCGTTGCATAT 60.322 50.000 0.00 0.00 0.00 1.78
1526 1534 1.974543 CCATGCCTTGGGTTTGTCC 59.025 57.895 0.00 0.00 42.33 4.02
1566 1577 2.366469 CACCAGGTAGTGTGGCTCT 58.634 57.895 0.00 0.00 38.83 4.09
1585 1597 3.145551 CCCATGCAGGCAAGAGGC 61.146 66.667 0.00 0.00 43.74 4.70
1610 1638 1.372872 GGCGACCAAACAACATGCC 60.373 57.895 0.00 0.00 0.00 4.40
1611 1639 1.729131 GCGACCAAACAACATGCCG 60.729 57.895 0.00 0.00 0.00 5.69
1617 1645 1.815613 CCAAACAACATGCCGATGGTA 59.184 47.619 0.00 0.00 33.39 3.25
1649 1677 2.620242 GCATTTGCATAACCAGGTTGG 58.380 47.619 15.82 8.20 41.68 3.77
1652 1680 1.626686 TTGCATAACCAGGTTGGGTG 58.373 50.000 15.82 11.68 38.40 4.61
1666 1694 1.303561 GGGTGGAGAAGTGCATGCA 60.304 57.895 18.46 18.46 0.00 3.96
1680 1708 1.085893 CATGCAATGCGGACACTGTA 58.914 50.000 0.00 0.00 37.62 2.74
1683 1711 1.709760 CAATGCGGACACTGTAGCG 59.290 57.895 5.08 0.00 0.00 4.26
1709 1737 2.414957 GCAACCAAACACGCCCTATAAC 60.415 50.000 0.00 0.00 0.00 1.89
1710 1738 3.078837 CAACCAAACACGCCCTATAACT 58.921 45.455 0.00 0.00 0.00 2.24
1711 1739 2.981898 ACCAAACACGCCCTATAACTC 58.018 47.619 0.00 0.00 0.00 3.01
1712 1740 2.303600 ACCAAACACGCCCTATAACTCA 59.696 45.455 0.00 0.00 0.00 3.41
1713 1741 2.676342 CCAAACACGCCCTATAACTCAC 59.324 50.000 0.00 0.00 0.00 3.51
1714 1742 2.288961 AACACGCCCTATAACTCACG 57.711 50.000 0.00 0.00 0.00 4.35
1715 1743 1.466856 ACACGCCCTATAACTCACGA 58.533 50.000 0.00 0.00 0.00 4.35
1716 1744 1.133790 ACACGCCCTATAACTCACGAC 59.866 52.381 0.00 0.00 0.00 4.34
1717 1745 0.743097 ACGCCCTATAACTCACGACC 59.257 55.000 0.00 0.00 0.00 4.79
1718 1746 0.742505 CGCCCTATAACTCACGACCA 59.257 55.000 0.00 0.00 0.00 4.02
1719 1747 1.135527 CGCCCTATAACTCACGACCAA 59.864 52.381 0.00 0.00 0.00 3.67
1720 1748 2.798499 CGCCCTATAACTCACGACCAAG 60.798 54.545 0.00 0.00 0.00 3.61
1721 1749 2.483188 GCCCTATAACTCACGACCAAGG 60.483 54.545 0.00 0.00 0.00 3.61
1722 1750 3.028850 CCCTATAACTCACGACCAAGGA 58.971 50.000 0.00 0.00 0.00 3.36
1723 1751 3.449737 CCCTATAACTCACGACCAAGGAA 59.550 47.826 0.00 0.00 0.00 3.36
1724 1752 4.441634 CCCTATAACTCACGACCAAGGAAG 60.442 50.000 0.00 0.00 0.00 3.46
1725 1753 4.401519 CCTATAACTCACGACCAAGGAAGA 59.598 45.833 0.00 0.00 0.00 2.87
1726 1754 4.884668 ATAACTCACGACCAAGGAAGAA 57.115 40.909 0.00 0.00 0.00 2.52
1727 1755 2.528041 ACTCACGACCAAGGAAGAAC 57.472 50.000 0.00 0.00 0.00 3.01
1728 1756 1.269621 ACTCACGACCAAGGAAGAACG 60.270 52.381 0.00 0.00 0.00 3.95
1729 1757 0.748450 TCACGACCAAGGAAGAACGT 59.252 50.000 0.00 0.00 34.40 3.99
1730 1758 1.137513 CACGACCAAGGAAGAACGTC 58.862 55.000 0.00 0.00 31.82 4.34
1731 1759 2.431539 CGACCAAGGAAGAACGTCG 58.568 57.895 0.00 0.00 40.15 5.12
1732 1760 1.615107 CGACCAAGGAAGAACGTCGC 61.615 60.000 0.00 0.00 39.72 5.19
1733 1761 1.615107 GACCAAGGAAGAACGTCGCG 61.615 60.000 0.00 0.00 0.00 5.87
1734 1762 1.663702 CCAAGGAAGAACGTCGCGT 60.664 57.895 5.77 0.00 43.97 6.01
1745 1773 2.915738 ACGTCGCGTTTCTTCTAGAT 57.084 45.000 5.77 0.00 36.35 1.98
1746 1774 2.516923 ACGTCGCGTTTCTTCTAGATG 58.483 47.619 5.77 0.00 36.35 2.90
1747 1775 2.095364 ACGTCGCGTTTCTTCTAGATGT 60.095 45.455 5.77 0.00 36.35 3.06
1748 1776 3.125829 ACGTCGCGTTTCTTCTAGATGTA 59.874 43.478 5.77 0.00 36.35 2.29
1749 1777 3.477802 CGTCGCGTTTCTTCTAGATGTAC 59.522 47.826 5.77 5.03 0.00 2.90
1750 1778 4.660105 GTCGCGTTTCTTCTAGATGTACT 58.340 43.478 5.77 0.00 0.00 2.73
1751 1779 5.501413 CGTCGCGTTTCTTCTAGATGTACTA 60.501 44.000 5.77 0.00 0.00 1.82
1752 1780 5.676310 GTCGCGTTTCTTCTAGATGTACTAC 59.324 44.000 5.77 0.00 0.00 2.73
1753 1781 5.583854 TCGCGTTTCTTCTAGATGTACTACT 59.416 40.000 5.77 0.00 0.00 2.57
1754 1782 5.902981 CGCGTTTCTTCTAGATGTACTACTC 59.097 44.000 0.00 0.00 0.00 2.59
1755 1783 6.200808 GCGTTTCTTCTAGATGTACTACTCC 58.799 44.000 5.60 0.00 0.00 3.85
1756 1784 6.183360 GCGTTTCTTCTAGATGTACTACTCCA 60.183 42.308 5.60 0.00 0.00 3.86
1757 1785 7.468906 GCGTTTCTTCTAGATGTACTACTCCAT 60.469 40.741 5.60 0.00 0.00 3.41
1758 1786 8.407064 CGTTTCTTCTAGATGTACTACTCCATT 58.593 37.037 5.60 0.00 0.00 3.16
1807 1835 7.202016 TGCCTTGTATAGCTGCAAAATATAC 57.798 36.000 1.02 6.17 34.42 1.47
1886 1919 3.821421 AATTGACATCGAGTAGACCCC 57.179 47.619 0.00 0.00 0.00 4.95
1889 1922 1.210234 TGACATCGAGTAGACCCCGTA 59.790 52.381 0.00 0.00 0.00 4.02
1894 1927 2.726821 TCGAGTAGACCCCGTAATTGT 58.273 47.619 0.00 0.00 0.00 2.71
1898 1931 2.167900 AGTAGACCCCGTAATTGTGAGC 59.832 50.000 0.00 0.00 0.00 4.26
1925 1958 9.496873 CCAAATATGACCCGTATACAAATTAGA 57.503 33.333 3.32 0.00 0.00 2.10
1951 1996 1.408822 CCCTCATTGTTGACTAGCCCC 60.409 57.143 0.00 0.00 0.00 5.80
1953 1998 2.420687 CCTCATTGTTGACTAGCCCCTC 60.421 54.545 0.00 0.00 0.00 4.30
1954 1999 2.503356 CTCATTGTTGACTAGCCCCTCT 59.497 50.000 0.00 0.00 0.00 3.69
1955 2000 2.237143 TCATTGTTGACTAGCCCCTCTG 59.763 50.000 0.00 0.00 0.00 3.35
1956 2001 0.984230 TTGTTGACTAGCCCCTCTGG 59.016 55.000 0.00 0.00 37.09 3.86
1966 2011 1.908483 CCCCTCTGGCTCAGGTAAC 59.092 63.158 2.86 0.00 31.51 2.50
1983 2028 3.363970 GGTAACAGTTGACGACAAGCATG 60.364 47.826 0.00 3.53 36.64 4.06
1988 2033 1.737236 GTTGACGACAAGCATGGCATA 59.263 47.619 0.00 0.00 36.64 3.14
1989 2034 1.368641 TGACGACAAGCATGGCATAC 58.631 50.000 0.00 0.00 32.33 2.39
1997 2042 0.816825 AGCATGGCATACCTCAAGCG 60.817 55.000 0.00 0.00 36.63 4.68
2000 2045 0.816825 ATGGCATACCTCAAGCGCAG 60.817 55.000 11.47 0.72 36.63 5.18
2014 2059 2.809181 CGCAGCGTCAGTCTTTACA 58.191 52.632 6.65 0.00 0.00 2.41
2037 2082 5.392995 AGCTGACATCAGATGGTAGAGTAT 58.607 41.667 15.13 0.00 46.59 2.12
2047 2092 6.156949 TCAGATGGTAGAGTATCCAGCTTTTT 59.843 38.462 0.00 0.00 46.35 1.94
2077 2129 3.391049 GCCTCTGACTACGTTTGAAACT 58.609 45.455 6.49 0.00 0.00 2.66
2082 2134 6.700520 CCTCTGACTACGTTTGAAACTAACTT 59.299 38.462 6.49 0.00 0.00 2.66
2083 2135 7.096147 CCTCTGACTACGTTTGAAACTAACTTC 60.096 40.741 6.49 0.00 0.00 3.01
2084 2136 6.698766 TCTGACTACGTTTGAAACTAACTTCC 59.301 38.462 6.49 0.00 0.00 3.46
2097 2149 7.983484 TGAAACTAACTTCCGTAATCTATTCCC 59.017 37.037 0.00 0.00 0.00 3.97
2107 2159 6.206634 TCCGTAATCTATTCCCAAATGCAATC 59.793 38.462 0.00 0.00 0.00 2.67
2113 2176 2.488204 TCCCAAATGCAATCGTCTCA 57.512 45.000 0.00 0.00 0.00 3.27
2117 2180 2.749076 CCAAATGCAATCGTCTCAAGGA 59.251 45.455 0.00 0.00 0.00 3.36
2121 2184 4.691860 ATGCAATCGTCTCAAGGAAAAG 57.308 40.909 0.00 0.00 0.00 2.27
2126 2189 5.977129 GCAATCGTCTCAAGGAAAAGAAAAA 59.023 36.000 0.00 0.00 0.00 1.94
2234 2297 1.180456 TGCACATCACCCAAAGGCAG 61.180 55.000 0.00 0.00 36.11 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.581309 TGAAGAAGAAGATGAAGGCCAT 57.419 40.909 5.01 0.00 38.43 4.40
85 86 0.811915 CAGATCAACCTCGACTCCGT 59.188 55.000 0.00 0.00 37.05 4.69
98 99 1.215382 CGTCGTTCCTGGCAGATCA 59.785 57.895 17.94 0.00 0.00 2.92
135 136 1.241990 AAGCAGTGCAGATGCCAGTG 61.242 55.000 19.20 5.27 44.97 3.66
136 137 0.959372 GAAGCAGTGCAGATGCCAGT 60.959 55.000 19.20 6.19 44.97 4.00
144 145 2.075338 GAGGAAGAAGAAGCAGTGCAG 58.925 52.381 19.20 0.00 0.00 4.41
292 293 1.330655 ATGAATCAGGCCGTCTCCGT 61.331 55.000 0.00 0.00 0.00 4.69
402 403 3.940852 ACATGCAGAACGAATCTAATGCA 59.059 39.130 0.00 0.00 38.50 3.96
490 492 1.545706 GGCCTTCTTCCTCGAGTGGT 61.546 60.000 12.31 0.00 0.00 4.16
495 497 4.035843 GAGGGCCTTCTTCCTCGA 57.964 61.111 7.89 0.00 39.95 4.04
617 619 2.185310 CTCACCCTGCCCACCACTAC 62.185 65.000 0.00 0.00 0.00 2.73
702 704 4.624024 CAGCACAAAGTTCATGGCTAATTG 59.376 41.667 0.00 0.00 0.00 2.32
718 720 1.887242 GGAGTCACGCACAGCACAA 60.887 57.895 0.00 0.00 0.00 3.33
724 726 1.805943 CAATTCATGGAGTCACGCACA 59.194 47.619 0.00 0.00 0.00 4.57
725 727 1.806542 ACAATTCATGGAGTCACGCAC 59.193 47.619 0.00 0.00 0.00 5.34
729 731 2.553602 TGCACACAATTCATGGAGTCAC 59.446 45.455 0.00 0.00 0.00 3.67
741 743 1.827344 TCTCCTCGATCTGCACACAAT 59.173 47.619 0.00 0.00 0.00 2.71
760 762 1.442526 CCGTGCCCATCTGATTGCTC 61.443 60.000 9.54 5.94 0.00 4.26
762 764 1.442526 CTCCGTGCCCATCTGATTGC 61.443 60.000 2.73 2.73 0.00 3.56
763 765 0.816825 CCTCCGTGCCCATCTGATTG 60.817 60.000 0.00 0.00 0.00 2.67
764 766 1.274703 ACCTCCGTGCCCATCTGATT 61.275 55.000 0.00 0.00 0.00 2.57
766 768 1.918293 AACCTCCGTGCCCATCTGA 60.918 57.895 0.00 0.00 0.00 3.27
767 769 1.746615 CAACCTCCGTGCCCATCTG 60.747 63.158 0.00 0.00 0.00 2.90
768 770 1.918293 TCAACCTCCGTGCCCATCT 60.918 57.895 0.00 0.00 0.00 2.90
770 772 2.063015 TTGTCAACCTCCGTGCCCAT 62.063 55.000 0.00 0.00 0.00 4.00
772 774 2.112297 TTGTCAACCTCCGTGCCC 59.888 61.111 0.00 0.00 0.00 5.36
773 775 1.098712 TTGTTGTCAACCTCCGTGCC 61.099 55.000 13.13 0.00 0.00 5.01
774 776 0.307760 CTTGTTGTCAACCTCCGTGC 59.692 55.000 13.13 0.00 0.00 5.34
775 777 0.944386 CCTTGTTGTCAACCTCCGTG 59.056 55.000 13.13 0.00 0.00 4.94
776 778 0.179029 CCCTTGTTGTCAACCTCCGT 60.179 55.000 13.13 0.00 0.00 4.69
778 780 0.467290 TGCCCTTGTTGTCAACCTCC 60.467 55.000 13.13 0.00 0.00 4.30
779 781 1.338020 CTTGCCCTTGTTGTCAACCTC 59.662 52.381 13.13 0.00 0.00 3.85
780 782 1.402787 CTTGCCCTTGTTGTCAACCT 58.597 50.000 13.13 0.00 0.00 3.50
781 783 0.249447 GCTTGCCCTTGTTGTCAACC 60.249 55.000 13.13 0.00 0.00 3.77
846 848 1.103803 CATCTTCGGGTCTTCCTCGA 58.896 55.000 0.00 0.00 35.68 4.04
981 986 0.112995 TGGGGATGCACTCAAGCTTT 59.887 50.000 0.00 0.00 34.99 3.51
1032 1037 1.006102 CTTGAACTCCGTCGGCACT 60.006 57.895 6.34 0.00 0.00 4.40
1115 1120 2.204291 TGGCCCAACCCTGATCCT 60.204 61.111 0.00 0.00 37.83 3.24
1305 1313 7.309177 ACTAGCATAATTCAGATAGTACGCTG 58.691 38.462 6.28 6.99 35.41 5.18
1332 1340 9.952030 TCATAACAGTTCAACTCATAAACCATA 57.048 29.630 0.00 0.00 0.00 2.74
1343 1351 5.296780 CACCACACTTCATAACAGTTCAACT 59.703 40.000 0.00 0.00 0.00 3.16
1357 1365 5.991606 TCATATATAAGCAGCACCACACTTC 59.008 40.000 0.00 0.00 0.00 3.01
1358 1366 5.928976 TCATATATAAGCAGCACCACACTT 58.071 37.500 0.00 0.00 0.00 3.16
1359 1367 5.551305 TCATATATAAGCAGCACCACACT 57.449 39.130 0.00 0.00 0.00 3.55
1360 1368 6.808008 ATTCATATATAAGCAGCACCACAC 57.192 37.500 0.00 0.00 0.00 3.82
1378 1386 6.996879 ACAGAGCATGAACTAGCATAATTCAT 59.003 34.615 0.00 0.84 42.43 2.57
1409 1417 4.692155 TCACACATCATAAGCACAACAGAG 59.308 41.667 0.00 0.00 0.00 3.35
1470 1478 1.001633 CGCCTGGTGTGTAGTAACCTT 59.998 52.381 0.00 0.00 37.36 3.50
1478 1486 0.321996 TATGCAACGCCTGGTGTGTA 59.678 50.000 14.59 8.20 36.45 2.90
1484 1492 1.674359 TGGTTATATGCAACGCCTGG 58.326 50.000 0.00 0.00 0.00 4.45
1490 1498 4.566360 GCATGGTGTTTGGTTATATGCAAC 59.434 41.667 0.00 0.00 39.25 4.17
1498 1506 1.967066 CCAAGGCATGGTGTTTGGTTA 59.033 47.619 0.00 0.00 44.85 2.85
1525 1533 0.527565 GGTTGCCTGCATGTTAGTGG 59.472 55.000 0.00 0.00 0.00 4.00
1526 1534 1.246649 TGGTTGCCTGCATGTTAGTG 58.753 50.000 0.00 0.00 0.00 2.74
1585 1597 1.804396 TTGTTTGGTCGCCTGCATGG 61.804 55.000 0.00 0.00 39.35 3.66
1595 1623 1.402720 CCATCGGCATGTTGTTTGGTC 60.403 52.381 0.00 0.00 0.00 4.02
1610 1638 2.942376 TGCAGCCTTAAATGTACCATCG 59.058 45.455 0.00 0.00 0.00 3.84
1611 1639 5.520376 AATGCAGCCTTAAATGTACCATC 57.480 39.130 0.00 0.00 0.00 3.51
1649 1677 1.135199 CATTGCATGCACTTCTCCACC 60.135 52.381 22.58 0.00 0.00 4.61
1666 1694 2.100631 GCGCTACAGTGTCCGCATT 61.101 57.895 26.62 0.00 45.21 3.56
1673 1701 3.800685 TTGCCGTGCGCTACAGTGT 62.801 57.895 9.73 0.00 38.78 3.55
1680 1708 4.264638 GTTTGGTTGCCGTGCGCT 62.265 61.111 9.73 0.00 38.78 5.92
1683 1711 2.653766 CGTGTTTGGTTGCCGTGC 60.654 61.111 0.00 0.00 0.00 5.34
1709 1737 1.269621 ACGTTCTTCCTTGGTCGTGAG 60.270 52.381 0.00 0.00 0.00 3.51
1710 1738 0.748450 ACGTTCTTCCTTGGTCGTGA 59.252 50.000 0.00 0.00 0.00 4.35
1711 1739 1.137513 GACGTTCTTCCTTGGTCGTG 58.862 55.000 0.00 0.00 0.00 4.35
1712 1740 0.318445 CGACGTTCTTCCTTGGTCGT 60.318 55.000 3.93 0.00 43.81 4.34
1713 1741 2.431539 CGACGTTCTTCCTTGGTCG 58.568 57.895 0.00 0.00 43.43 4.79
1714 1742 1.615107 CGCGACGTTCTTCCTTGGTC 61.615 60.000 0.00 0.00 0.00 4.02
1715 1743 1.663702 CGCGACGTTCTTCCTTGGT 60.664 57.895 0.00 0.00 0.00 3.67
1716 1744 1.663702 ACGCGACGTTCTTCCTTGG 60.664 57.895 15.93 0.00 36.35 3.61
1717 1745 3.932289 ACGCGACGTTCTTCCTTG 58.068 55.556 15.93 0.00 36.35 3.61
1726 1754 2.095364 ACATCTAGAAGAAACGCGACGT 60.095 45.455 15.93 1.50 43.97 4.34
1727 1755 2.516923 ACATCTAGAAGAAACGCGACG 58.483 47.619 15.93 0.00 0.00 5.12
1728 1756 4.660105 AGTACATCTAGAAGAAACGCGAC 58.340 43.478 15.93 3.56 0.00 5.19
1729 1757 4.959596 AGTACATCTAGAAGAAACGCGA 57.040 40.909 15.93 0.00 0.00 5.87
1730 1758 5.808403 AGTAGTACATCTAGAAGAAACGCG 58.192 41.667 3.53 3.53 0.00 6.01
1731 1759 6.183360 TGGAGTAGTACATCTAGAAGAAACGC 60.183 42.308 1.17 0.00 0.00 4.84
1732 1760 7.317842 TGGAGTAGTACATCTAGAAGAAACG 57.682 40.000 1.17 0.00 0.00 3.60
1760 1788 9.855021 GGCAACAAATGTTAATCAAGTATAAGT 57.145 29.630 0.00 0.00 36.32 2.24
1763 1791 9.853555 CAAGGCAACAAATGTTAATCAAGTATA 57.146 29.630 0.00 0.00 36.32 1.47
1764 1792 8.367156 ACAAGGCAACAAATGTTAATCAAGTAT 58.633 29.630 0.00 0.00 36.32 2.12
1765 1793 7.721402 ACAAGGCAACAAATGTTAATCAAGTA 58.279 30.769 0.00 0.00 36.32 2.24
1766 1794 6.581712 ACAAGGCAACAAATGTTAATCAAGT 58.418 32.000 0.00 0.00 36.32 3.16
1767 1795 8.761575 ATACAAGGCAACAAATGTTAATCAAG 57.238 30.769 0.00 0.00 36.32 3.02
1768 1796 9.853555 CTATACAAGGCAACAAATGTTAATCAA 57.146 29.630 0.00 0.00 36.32 2.57
1769 1797 7.973388 GCTATACAAGGCAACAAATGTTAATCA 59.027 33.333 0.00 0.00 36.32 2.57
1770 1798 8.190784 AGCTATACAAGGCAACAAATGTTAATC 58.809 33.333 0.00 0.00 36.32 1.75
1771 1799 7.975616 CAGCTATACAAGGCAACAAATGTTAAT 59.024 33.333 0.00 0.00 36.32 1.40
1772 1800 7.312154 CAGCTATACAAGGCAACAAATGTTAA 58.688 34.615 0.00 0.00 36.32 2.01
1773 1801 6.624861 GCAGCTATACAAGGCAACAAATGTTA 60.625 38.462 0.00 0.00 36.32 2.41
1774 1802 5.713025 CAGCTATACAAGGCAACAAATGTT 58.287 37.500 0.00 0.00 39.12 2.71
1775 1803 4.380867 GCAGCTATACAAGGCAACAAATGT 60.381 41.667 0.00 0.00 41.41 2.71
1776 1804 4.107622 GCAGCTATACAAGGCAACAAATG 58.892 43.478 0.00 0.00 41.41 2.32
1777 1805 3.763360 TGCAGCTATACAAGGCAACAAAT 59.237 39.130 0.00 0.00 41.41 2.32
1778 1806 3.153130 TGCAGCTATACAAGGCAACAAA 58.847 40.909 0.00 0.00 41.41 2.83
1779 1807 2.789213 TGCAGCTATACAAGGCAACAA 58.211 42.857 0.00 0.00 41.41 2.83
1780 1808 2.488204 TGCAGCTATACAAGGCAACA 57.512 45.000 0.00 0.00 41.41 3.33
1781 1809 3.848272 TTTGCAGCTATACAAGGCAAC 57.152 42.857 5.00 0.00 43.38 4.17
1782 1810 6.713762 ATATTTTGCAGCTATACAAGGCAA 57.286 33.333 1.58 1.58 42.15 4.52
1783 1811 6.998074 AGTATATTTTGCAGCTATACAAGGCA 59.002 34.615 17.52 0.00 32.97 4.75
1784 1812 7.440523 AGTATATTTTGCAGCTATACAAGGC 57.559 36.000 17.52 0.00 32.97 4.35
1837 1867 6.697892 CGTCAGGATCACTAAAGAAATACTCC 59.302 42.308 0.00 0.00 0.00 3.85
1841 1871 5.128827 AGGCGTCAGGATCACTAAAGAAATA 59.871 40.000 0.00 0.00 0.00 1.40
1886 1919 5.505654 GGTCATATTTGGGCTCACAATTACG 60.506 44.000 0.00 0.00 0.00 3.18
1889 1922 3.706086 GGGTCATATTTGGGCTCACAATT 59.294 43.478 0.00 0.00 0.00 2.32
1894 1927 0.916086 ACGGGTCATATTTGGGCTCA 59.084 50.000 0.00 0.00 0.00 4.26
1898 1931 7.519032 AATTTGTATACGGGTCATATTTGGG 57.481 36.000 0.00 0.00 0.00 4.12
1925 1958 4.706962 GCTAGTCAACAATGAGGGGAAAAT 59.293 41.667 0.00 0.00 35.88 1.82
1951 1996 2.300152 TCAACTGTTACCTGAGCCAGAG 59.700 50.000 4.00 0.00 32.44 3.35
1953 1998 2.417719 GTCAACTGTTACCTGAGCCAG 58.582 52.381 0.00 0.00 0.00 4.85
1954 1999 1.270094 CGTCAACTGTTACCTGAGCCA 60.270 52.381 0.00 0.00 0.00 4.75
1955 2000 1.000506 TCGTCAACTGTTACCTGAGCC 59.999 52.381 0.00 0.00 0.00 4.70
1956 2001 2.059541 GTCGTCAACTGTTACCTGAGC 58.940 52.381 0.00 0.00 0.00 4.26
1966 2011 0.110056 GCCATGCTTGTCGTCAACTG 60.110 55.000 0.00 0.00 0.00 3.16
1983 2028 2.828128 GCTGCGCTTGAGGTATGCC 61.828 63.158 9.73 0.00 0.00 4.40
1988 2033 4.299547 TGACGCTGCGCTTGAGGT 62.300 61.111 23.51 0.00 0.00 3.85
1989 2034 3.485431 CTGACGCTGCGCTTGAGG 61.485 66.667 23.51 2.90 0.00 3.86
1997 2042 0.440371 GCTGTAAAGACTGACGCTGC 59.560 55.000 0.00 0.00 0.00 5.25
2000 2045 2.065993 TCAGCTGTAAAGACTGACGC 57.934 50.000 14.67 0.00 35.58 5.19
2003 2048 4.524328 TCTGATGTCAGCTGTAAAGACTGA 59.476 41.667 14.67 8.34 43.46 3.41
2004 2049 4.814147 TCTGATGTCAGCTGTAAAGACTG 58.186 43.478 14.67 6.33 43.46 3.51
2009 2054 4.558226 ACCATCTGATGTCAGCTGTAAA 57.442 40.909 14.67 0.58 43.46 2.01
2010 2055 4.956075 TCTACCATCTGATGTCAGCTGTAA 59.044 41.667 14.67 3.38 43.46 2.41
2011 2056 4.536765 TCTACCATCTGATGTCAGCTGTA 58.463 43.478 14.67 4.66 43.46 2.74
2012 2057 3.369175 TCTACCATCTGATGTCAGCTGT 58.631 45.455 14.67 8.23 43.46 4.40
2013 2058 3.384146 ACTCTACCATCTGATGTCAGCTG 59.616 47.826 15.95 7.63 43.46 4.24
2014 2059 3.641046 ACTCTACCATCTGATGTCAGCT 58.359 45.455 15.95 0.00 43.46 4.24
2022 2067 4.461450 AGCTGGATACTCTACCATCTGA 57.539 45.455 0.00 0.00 32.48 3.27
2052 2097 2.103432 TCAAACGTAGTCAGAGGCCAAA 59.897 45.455 5.01 0.00 45.00 3.28
2055 2100 2.450609 TTCAAACGTAGTCAGAGGCC 57.549 50.000 0.00 0.00 45.00 5.19
2056 2101 3.391049 AGTTTCAAACGTAGTCAGAGGC 58.609 45.455 0.00 0.00 45.00 4.70
2058 2103 7.096147 GGAAGTTAGTTTCAAACGTAGTCAGAG 60.096 40.741 0.00 0.00 45.00 3.35
2060 2105 6.345565 CGGAAGTTAGTTTCAAACGTAGTCAG 60.346 42.308 0.00 0.00 45.00 3.51
2062 2107 5.460091 ACGGAAGTTAGTTTCAAACGTAGTC 59.540 40.000 0.00 0.00 42.15 2.59
2063 2108 5.351458 ACGGAAGTTAGTTTCAAACGTAGT 58.649 37.500 0.00 0.00 45.79 2.73
2064 2109 5.895216 ACGGAAGTTAGTTTCAAACGTAG 57.105 39.130 0.00 0.00 46.40 3.51
2065 2110 7.867403 AGATTACGGAAGTTAGTTTCAAACGTA 59.133 33.333 0.00 0.00 46.40 3.57
2066 2111 6.703165 AGATTACGGAAGTTAGTTTCAAACGT 59.297 34.615 0.00 0.00 46.40 3.99
2077 2129 7.227910 GCATTTGGGAATAGATTACGGAAGTTA 59.772 37.037 0.00 0.00 46.40 2.24
2082 2134 5.042463 TGCATTTGGGAATAGATTACGGA 57.958 39.130 0.00 0.00 0.00 4.69
2083 2135 5.766150 TTGCATTTGGGAATAGATTACGG 57.234 39.130 0.00 0.00 0.00 4.02
2084 2136 6.079763 CGATTGCATTTGGGAATAGATTACG 58.920 40.000 0.00 0.00 37.71 3.18
2097 2149 4.424061 TTCCTTGAGACGATTGCATTTG 57.576 40.909 0.00 0.00 0.00 2.32
2132 2195 9.026074 GCTCACTTTACTGTCTTATGAAGTATC 57.974 37.037 0.00 0.00 0.00 2.24
2136 2199 5.582665 GGGCTCACTTTACTGTCTTATGAAG 59.417 44.000 0.00 0.00 0.00 3.02
2139 2202 3.865745 CGGGCTCACTTTACTGTCTTATG 59.134 47.826 0.00 0.00 0.00 1.90
2144 2207 1.544691 TCTCGGGCTCACTTTACTGTC 59.455 52.381 0.00 0.00 0.00 3.51
2147 2210 4.382793 GGTTATTCTCGGGCTCACTTTACT 60.383 45.833 0.00 0.00 0.00 2.24
2214 2277 0.542467 TGCCTTTGGGTGATGTGCAT 60.542 50.000 0.00 0.00 34.45 3.96
2234 2297 2.939022 GAGTTGTGCACTCGTGGC 59.061 61.111 19.41 1.90 42.82 5.01


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

AutoCloner maintained by Alex Coulton.