Multiple sequence alignment - TraesCS3D01G402600

Loading Multiple Alignment...

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 TraesCS3D01G402600 chr3D 100.000 2669 0 0 1 2669 516879728 516877060 0.000000e+00 4929.0
1 TraesCS3D01G402600 chr3B 91.774 2711 130 50 1 2669 680424197 680426856 0.000000e+00 3685.0
2 TraesCS3D01G402600 chr3A 91.700 2711 124 50 1 2669 652026753 652024102 0.000000e+00 3666.0
3 TraesCS3D01G402600 chr4D 85.345 116 17 0 142 257 74370435 74370320 1.300000e-23 121.0
4 TraesCS3D01G402600 chr4B 85.345 116 17 0 142 257 106855604 106855489 1.300000e-23 121.0
5 TraesCS3D01G402600 chr4A 87.500 104 13 0 142 245 513292616 513292719 1.300000e-23 121.0
6 TraesCS3D01G402600 chr6D 95.122 41 1 1 2515 2554 132775281 132775241 2.220000e-06 63.9


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 TraesCS3D01G402600 chr3D 516877060 516879728 2668 True 4929 4929 100.000 1 2669 1 chr3D.!!$R1 2668
1 TraesCS3D01G402600 chr3B 680424197 680426856 2659 False 3685 3685 91.774 1 2669 1 chr3B.!!$F1 2668
2 TraesCS3D01G402600 chr3A 652024102 652026753 2651 True 3666 3666 91.700 1 2669 1 chr3A.!!$R1 2668

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
952 979 0.319405 AACCCCGTAACCTTCTCGTG 59.681 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2251 2318 0.172803 ACACGTTACTCATCGGCTCC 59.827 55.0 0.0 0.0 0.0 4.7 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
77 79 7.575414 TCTGTTAAACTTGATAAAACTGCCA 57.425 32.000 0.00 0.00 0.00 4.92
125 127 9.352784 GACAATGCTCACAGATATTATAGACTC 57.647 37.037 0.00 0.00 0.00 3.36
128 130 7.459795 TGCTCACAGATATTATAGACTCCTG 57.540 40.000 0.00 0.00 0.00 3.86
202 204 3.003689 CAGAGATGTGTGGTTTTGTGACC 59.996 47.826 0.00 0.00 40.23 4.02
331 340 6.768381 ACTTCTAACTTTCTGGCATTATAGGC 59.232 38.462 0.00 0.00 0.00 3.93
385 394 2.747446 ACATGGTGATGAAAACGGCTAC 59.253 45.455 0.00 0.00 33.36 3.58
442 451 3.609703 CTCCCTCTGAGGTCACCG 58.390 66.667 21.70 6.76 37.45 4.94
745 767 6.642733 ATGGGGAAAGAATCTGAAGAACTA 57.357 37.500 0.00 0.00 0.00 2.24
800 823 2.159393 TGCGCACTATTTTCTCATTGGC 60.159 45.455 5.66 0.00 0.00 4.52
816 839 1.154225 GGCGGTGATGTTCTTTGCG 60.154 57.895 0.00 0.00 0.00 4.85
952 979 0.319405 AACCCCGTAACCTTCTCGTG 59.681 55.000 0.00 0.00 0.00 4.35
977 1004 3.625853 TCAAACCCAACAATCTCACACA 58.374 40.909 0.00 0.00 0.00 3.72
978 1005 3.380004 TCAAACCCAACAATCTCACACAC 59.620 43.478 0.00 0.00 0.00 3.82
983 1010 0.889186 AACAATCTCACACACCCGCC 60.889 55.000 0.00 0.00 0.00 6.13
997 1024 3.777925 CGCCTGCACACGCACTAC 61.778 66.667 0.00 0.00 45.36 2.73
1013 1040 1.340405 ACTACCAATGGCTGAGCAAGG 60.340 52.381 6.82 4.42 0.00 3.61
1048 1075 0.596083 GGTGCTCATCGATCAGACCG 60.596 60.000 0.00 0.00 0.00 4.79
1461 1488 3.716006 CTGTTCCACACCGCGCTG 61.716 66.667 5.56 0.00 0.00 5.18
1639 1666 2.187163 GCTACCCGTTCCTGCTCC 59.813 66.667 0.00 0.00 0.00 4.70
1687 1736 1.336755 GAACATTTTGGCGACCTGTGT 59.663 47.619 0.00 0.00 0.00 3.72
1706 1755 1.550976 GTAGTGGACCTGAACCCTGAG 59.449 57.143 0.00 0.00 0.00 3.35
1722 1771 3.091694 AGGTCGAGGCCTCTCTGA 58.908 61.111 29.73 17.30 37.86 3.27
1723 1772 1.379309 AGGTCGAGGCCTCTCTGAC 60.379 63.158 29.73 26.33 39.96 3.51
1724 1773 1.379309 GGTCGAGGCCTCTCTGACT 60.379 63.158 29.73 0.00 40.24 3.41
1725 1774 1.381165 GGTCGAGGCCTCTCTGACTC 61.381 65.000 29.73 17.87 40.24 3.36
1726 1775 0.393808 GTCGAGGCCTCTCTGACTCT 60.394 60.000 29.73 0.00 38.85 3.24
1727 1776 0.393673 TCGAGGCCTCTCTGACTCTG 60.394 60.000 29.73 11.42 37.86 3.35
1728 1777 0.679640 CGAGGCCTCTCTGACTCTGT 60.680 60.000 29.73 0.00 37.86 3.41
1740 1789 2.017782 TGACTCTGTCTGTATCGGAGC 58.982 52.381 0.00 0.00 40.71 4.70
1748 1797 0.313987 CTGTATCGGAGCCGCATGTA 59.686 55.000 3.59 0.00 39.59 2.29
1752 1801 2.032860 ATCGGAGCCGCATGTAAGCT 62.033 55.000 3.59 6.04 40.24 3.74
1779 1828 9.752961 TTGCATATATGATTTGATTTGTTGGAG 57.247 29.630 17.10 0.00 0.00 3.86
1814 1863 4.454161 TGAAAGGTGTTACACGATTGATGG 59.546 41.667 9.52 0.00 34.83 3.51
1837 1886 3.596214 TCTCTTGTGGAATTAACCGAGC 58.404 45.455 0.00 0.00 0.00 5.03
1880 1934 6.923508 ACGTATGTACATACATCATTGTCCTG 59.076 38.462 34.07 20.52 45.11 3.86
1883 1937 5.744171 TGTACATACATCATTGTCCTGCTT 58.256 37.500 0.00 0.00 37.28 3.91
1884 1938 6.179756 TGTACATACATCATTGTCCTGCTTT 58.820 36.000 0.00 0.00 37.28 3.51
1930 1984 1.008995 GCGAGAGATGAGACGAGGC 60.009 63.158 0.00 0.00 0.00 4.70
1934 1988 1.067250 GAGATGAGACGAGGCAGCC 59.933 63.158 1.84 1.84 0.00 4.85
1978 2032 3.838271 GCGTCCGGATCAGGCTCA 61.838 66.667 7.81 0.00 0.00 4.26
2034 2088 7.177832 TGAATTTTCTCCTGCATCAATCAAT 57.822 32.000 0.00 0.00 0.00 2.57
2035 2089 7.262772 TGAATTTTCTCCTGCATCAATCAATC 58.737 34.615 0.00 0.00 0.00 2.67
2048 2102 1.941325 ATCAATCCGGCTCGAAAGTC 58.059 50.000 0.00 0.00 0.00 3.01
2056 2110 1.798223 CGGCTCGAAAGTCATTCACAA 59.202 47.619 0.00 0.00 37.96 3.33
2058 2112 3.067106 GGCTCGAAAGTCATTCACAAGA 58.933 45.455 0.00 0.00 37.96 3.02
2059 2113 3.124297 GGCTCGAAAGTCATTCACAAGAG 59.876 47.826 0.00 0.00 37.96 2.85
2060 2114 3.990469 GCTCGAAAGTCATTCACAAGAGA 59.010 43.478 0.00 0.00 37.96 3.10
2061 2115 4.091220 GCTCGAAAGTCATTCACAAGAGAG 59.909 45.833 0.00 0.00 37.96 3.20
2062 2116 5.453567 TCGAAAGTCATTCACAAGAGAGA 57.546 39.130 0.00 0.00 37.96 3.10
2063 2117 5.842907 TCGAAAGTCATTCACAAGAGAGAA 58.157 37.500 0.00 0.00 37.96 2.87
2064 2118 5.692204 TCGAAAGTCATTCACAAGAGAGAAC 59.308 40.000 0.00 0.00 37.96 3.01
2065 2119 5.463392 CGAAAGTCATTCACAAGAGAGAACA 59.537 40.000 0.00 0.00 37.96 3.18
2066 2120 6.563010 CGAAAGTCATTCACAAGAGAGAACAC 60.563 42.308 0.00 0.00 37.96 3.32
2067 2121 5.543507 AGTCATTCACAAGAGAGAACACT 57.456 39.130 0.00 0.00 0.00 3.55
2068 2122 5.537188 AGTCATTCACAAGAGAGAACACTC 58.463 41.667 0.00 0.00 37.19 3.51
2069 2123 4.384247 GTCATTCACAAGAGAGAACACTCG 59.616 45.833 0.00 0.00 41.25 4.18
2070 2124 4.038042 TCATTCACAAGAGAGAACACTCGT 59.962 41.667 0.00 0.00 41.25 4.18
2071 2125 3.627732 TCACAAGAGAGAACACTCGTC 57.372 47.619 0.00 0.00 41.25 4.20
2072 2126 3.215151 TCACAAGAGAGAACACTCGTCT 58.785 45.455 0.00 0.00 41.25 4.18
2073 2127 3.003793 TCACAAGAGAGAACACTCGTCTG 59.996 47.826 0.00 0.00 41.25 3.51
2074 2128 2.952978 ACAAGAGAGAACACTCGTCTGT 59.047 45.455 0.00 0.00 41.25 3.41
2075 2129 3.003897 ACAAGAGAGAACACTCGTCTGTC 59.996 47.826 0.00 0.00 41.25 3.51
2076 2130 2.852449 AGAGAGAACACTCGTCTGTCA 58.148 47.619 2.01 0.00 41.25 3.58
2077 2131 3.417101 AGAGAGAACACTCGTCTGTCAT 58.583 45.455 2.01 0.00 41.25 3.06
2078 2132 3.190327 AGAGAGAACACTCGTCTGTCATG 59.810 47.826 2.01 0.00 41.25 3.07
2079 2133 2.230025 AGAGAACACTCGTCTGTCATGG 59.770 50.000 0.00 0.00 35.98 3.66
2080 2134 1.964223 AGAACACTCGTCTGTCATGGT 59.036 47.619 0.00 0.00 0.00 3.55
2081 2135 2.365617 AGAACACTCGTCTGTCATGGTT 59.634 45.455 0.00 0.00 0.00 3.67
2082 2136 2.910688 ACACTCGTCTGTCATGGTTT 57.089 45.000 0.00 0.00 0.00 3.27
2083 2137 2.483876 ACACTCGTCTGTCATGGTTTG 58.516 47.619 0.00 0.00 0.00 2.93
2084 2138 2.158957 ACACTCGTCTGTCATGGTTTGT 60.159 45.455 0.00 0.00 0.00 2.83
2116 2183 4.081198 GTGAGAGTTCAGGTGGAGATTGAT 60.081 45.833 0.00 0.00 32.98 2.57
2212 2279 0.823356 GCCTTGGACAGAACCTGCAA 60.823 55.000 0.00 0.00 34.37 4.08
2226 2293 1.202087 CCTGCAAACGAAACGAACACA 60.202 47.619 0.00 0.00 0.00 3.72
2231 2298 1.348276 AACGAAACGAACACACGACA 58.652 45.000 0.00 0.00 37.03 4.35
2232 2299 0.918619 ACGAAACGAACACACGACAG 59.081 50.000 0.00 0.00 37.03 3.51
2233 2300 1.193644 CGAAACGAACACACGACAGA 58.806 50.000 0.00 0.00 37.03 3.41
2234 2301 1.072348 CGAAACGAACACACGACAGAC 60.072 52.381 0.00 0.00 37.03 3.51
2276 2343 2.177977 CGATGAGTAACGTGTGAGAGC 58.822 52.381 0.00 0.00 0.00 4.09
2300 2367 2.420827 CGAGAGCCTGAGAGAGACCTTA 60.421 54.545 0.00 0.00 0.00 2.69
2444 2516 2.111043 CACCGCACCCAAGTCAGT 59.889 61.111 0.00 0.00 0.00 3.41
2446 2518 1.525995 ACCGCACCCAAGTCAGTTG 60.526 57.895 0.00 0.00 35.71 3.16
2447 2519 1.525995 CCGCACCCAAGTCAGTTGT 60.526 57.895 0.00 0.00 33.87 3.32
2448 2520 1.101049 CCGCACCCAAGTCAGTTGTT 61.101 55.000 0.00 0.00 33.87 2.83
2449 2521 1.588674 CGCACCCAAGTCAGTTGTTA 58.411 50.000 0.00 0.00 33.87 2.41
2450 2522 1.944024 CGCACCCAAGTCAGTTGTTAA 59.056 47.619 0.00 0.00 33.87 2.01
2451 2523 2.032030 CGCACCCAAGTCAGTTGTTAAG 60.032 50.000 0.00 0.00 33.87 1.85
2452 2524 2.949644 GCACCCAAGTCAGTTGTTAAGT 59.050 45.455 0.00 0.00 33.87 2.24
2471 2543 2.159310 AGTAGCAGAGCAGACGACATTC 60.159 50.000 0.00 0.00 0.00 2.67
2484 2556 2.262572 GACATTCATGGCGGTGAAAC 57.737 50.000 8.84 2.13 41.09 2.78
2488 2560 0.953471 TTCATGGCGGTGAAACGGAG 60.953 55.000 3.05 0.00 39.89 4.63
2490 2562 1.079127 ATGGCGGTGAAACGGAGAG 60.079 57.895 0.00 0.00 39.89 3.20
2492 2564 2.654877 GCGGTGAAACGGAGAGGA 59.345 61.111 0.00 0.00 39.89 3.71
2494 2566 1.289800 GCGGTGAAACGGAGAGGAAC 61.290 60.000 0.00 0.00 39.89 3.62
2495 2567 1.007336 CGGTGAAACGGAGAGGAACG 61.007 60.000 0.00 0.00 39.89 3.95
2496 2568 0.669625 GGTGAAACGGAGAGGAACGG 60.670 60.000 0.00 0.00 38.12 4.44
2497 2569 1.005394 TGAAACGGAGAGGAACGGC 60.005 57.895 0.00 0.00 0.00 5.68
2498 2570 2.048503 AAACGGAGAGGAACGGCG 60.049 61.111 4.80 4.80 0.00 6.46
2499 2571 2.482296 GAAACGGAGAGGAACGGCGA 62.482 60.000 16.62 0.00 0.00 5.54
2506 2578 2.125673 AGGAACGGCGATCGGTTG 60.126 61.111 16.62 0.00 39.92 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 7.164230 AGTTTAACAGAACCATTTGTTGACA 57.836 32.000 0.00 0.00 37.98 3.58
51 53 7.918562 TGGCAGTTTTATCAAGTTTAACAGAAC 59.081 33.333 0.00 0.00 0.00 3.01
71 73 5.621193 ACTCTATACAACAAAACTGGCAGT 58.379 37.500 15.88 15.88 0.00 4.40
77 79 9.826574 TTGTCACTAACTCTATACAACAAAACT 57.173 29.630 0.00 0.00 0.00 2.66
85 87 7.093945 TGTGAGCATTGTCACTAACTCTATACA 60.094 37.037 15.53 0.00 46.06 2.29
125 127 3.118629 TCCTGCAAGCAAGTACTATCAGG 60.119 47.826 0.00 7.16 39.11 3.86
128 130 3.868077 CAGTCCTGCAAGCAAGTACTATC 59.132 47.826 0.00 0.00 0.00 2.08
202 204 5.259632 AGAAGAAATGTCCCAGAAAGGATG 58.740 41.667 0.00 0.00 41.22 3.51
331 340 2.856039 TAGGCAGAGTCGGTGGGAGG 62.856 65.000 0.00 0.00 0.00 4.30
385 394 3.442996 AGGAATTCCTTCAGACGCG 57.557 52.632 21.89 3.53 46.09 6.01
442 451 4.440663 GGTCAAAATTATTCTGCTGCCCTC 60.441 45.833 0.00 0.00 0.00 4.30
637 647 9.672673 TTCCTCAAAAACAAAAATACATGGAAA 57.327 25.926 0.00 0.00 0.00 3.13
638 648 9.103861 GTTCCTCAAAAACAAAAATACATGGAA 57.896 29.630 0.00 0.00 0.00 3.53
639 649 7.713073 GGTTCCTCAAAAACAAAAATACATGGA 59.287 33.333 0.00 0.00 0.00 3.41
640 650 7.307101 CGGTTCCTCAAAAACAAAAATACATGG 60.307 37.037 0.00 0.00 0.00 3.66
652 662 3.842732 CCATACCGGTTCCTCAAAAAC 57.157 47.619 15.04 0.00 0.00 2.43
714 736 7.557875 TCAGATTCTTTCCCCATTTTCAAAT 57.442 32.000 0.00 0.00 0.00 2.32
724 746 7.761038 TTTTAGTTCTTCAGATTCTTTCCCC 57.239 36.000 0.00 0.00 0.00 4.81
800 823 0.586319 ACACGCAAAGAACATCACCG 59.414 50.000 0.00 0.00 0.00 4.94
816 839 1.202177 CGGAGCATTGCCATTACACAC 60.202 52.381 4.70 0.00 0.00 3.82
952 979 4.278170 TGTGAGATTGTTGGGTTTGATGAC 59.722 41.667 0.00 0.00 0.00 3.06
995 1022 0.991146 TCCTTGCTCAGCCATTGGTA 59.009 50.000 4.26 0.00 0.00 3.25
997 1024 1.035932 CCTCCTTGCTCAGCCATTGG 61.036 60.000 0.00 0.00 0.00 3.16
1013 1040 4.081420 TGAGCACCTTGTATTCTTCTCCTC 60.081 45.833 0.00 0.00 0.00 3.71
1095 1122 1.512310 GAAGCTCGAGGTGTCGTCG 60.512 63.158 19.39 5.66 46.85 5.12
1639 1666 2.482374 GTACACGAGGTCGGTCCG 59.518 66.667 4.39 4.39 44.95 4.79
1687 1736 1.552486 CCTCAGGGTTCAGGTCCACTA 60.552 57.143 0.00 0.00 0.00 2.74
1706 1755 1.379309 AGTCAGAGAGGCCTCGACC 60.379 63.158 26.95 19.08 44.08 4.79
1721 1770 1.335496 GGCTCCGATACAGACAGAGTC 59.665 57.143 0.00 0.00 0.00 3.36
1722 1771 1.394618 GGCTCCGATACAGACAGAGT 58.605 55.000 0.00 0.00 0.00 3.24
1723 1772 0.309302 CGGCTCCGATACAGACAGAG 59.691 60.000 1.35 0.00 42.83 3.35
1724 1773 1.725557 GCGGCTCCGATACAGACAGA 61.726 60.000 13.11 0.00 42.83 3.41
1725 1774 1.299468 GCGGCTCCGATACAGACAG 60.299 63.158 13.11 0.00 42.83 3.51
1726 1775 1.391933 ATGCGGCTCCGATACAGACA 61.392 55.000 13.11 0.00 42.83 3.41
1727 1776 0.941463 CATGCGGCTCCGATACAGAC 60.941 60.000 13.11 0.00 42.83 3.51
1728 1777 1.363807 CATGCGGCTCCGATACAGA 59.636 57.895 13.11 0.00 42.83 3.41
1740 1789 3.631145 ATATGCAAAGCTTACATGCGG 57.369 42.857 19.91 0.00 42.91 5.69
1748 1797 9.826574 ACAAATCAAATCATATATGCAAAGCTT 57.173 25.926 7.92 0.00 0.00 3.74
1779 1828 7.589954 GTGTAACACCTTTCAAACATACACATC 59.410 37.037 0.00 0.00 40.76 3.06
1814 1863 4.142881 GCTCGGTTAATTCCACAAGAGAAC 60.143 45.833 12.62 0.00 0.00 3.01
1837 1886 6.929049 ACATACGTATACATTTGACATCTGGG 59.071 38.462 7.96 0.00 0.00 4.45
1867 1921 5.804639 TGTACTAAAGCAGGACAATGATGT 58.195 37.500 0.00 0.00 45.62 3.06
1883 1937 5.235616 CACTCCGTTTTCAGCTTTGTACTAA 59.764 40.000 0.00 0.00 0.00 2.24
1884 1938 4.748102 CACTCCGTTTTCAGCTTTGTACTA 59.252 41.667 0.00 0.00 0.00 1.82
1902 1956 2.025155 TCATCTCTCGCCTTACACTCC 58.975 52.381 0.00 0.00 0.00 3.85
1978 2032 1.071385 CTGAAGCAGATATCGGGCCTT 59.929 52.381 15.87 7.01 32.44 4.35
1990 2044 0.603707 TCTGGAAACCGCTGAAGCAG 60.604 55.000 2.79 0.00 42.21 4.24
2034 2088 0.606096 TGAATGACTTTCGAGCCGGA 59.394 50.000 5.05 0.00 37.13 5.14
2035 2089 0.721718 GTGAATGACTTTCGAGCCGG 59.278 55.000 0.00 0.00 37.13 6.13
2048 2102 4.302455 ACGAGTGTTCTCTCTTGTGAATG 58.698 43.478 0.00 0.00 38.45 2.67
2056 2110 2.852449 TGACAGACGAGTGTTCTCTCT 58.148 47.619 0.00 0.00 38.45 3.10
2058 2112 2.230025 CCATGACAGACGAGTGTTCTCT 59.770 50.000 0.00 0.00 38.45 3.10
2059 2113 2.029828 ACCATGACAGACGAGTGTTCTC 60.030 50.000 0.00 0.00 37.35 2.87
2060 2114 1.964223 ACCATGACAGACGAGTGTTCT 59.036 47.619 0.00 0.00 0.00 3.01
2061 2115 2.440539 ACCATGACAGACGAGTGTTC 57.559 50.000 0.00 0.00 0.00 3.18
2062 2116 2.872245 CAAACCATGACAGACGAGTGTT 59.128 45.455 0.00 0.00 0.00 3.32
2063 2117 2.158957 ACAAACCATGACAGACGAGTGT 60.159 45.455 0.00 0.00 0.00 3.55
2064 2118 2.483876 ACAAACCATGACAGACGAGTG 58.516 47.619 0.00 0.00 0.00 3.51
2065 2119 2.910688 ACAAACCATGACAGACGAGT 57.089 45.000 0.00 0.00 0.00 4.18
2066 2120 5.666969 TTTAACAAACCATGACAGACGAG 57.333 39.130 0.00 0.00 0.00 4.18
2067 2121 6.261158 TGAATTTAACAAACCATGACAGACGA 59.739 34.615 0.00 0.00 0.00 4.20
2068 2122 6.434596 TGAATTTAACAAACCATGACAGACG 58.565 36.000 0.00 0.00 0.00 4.18
2069 2123 7.379529 CACTGAATTTAACAAACCATGACAGAC 59.620 37.037 0.00 0.00 0.00 3.51
2070 2124 7.284261 TCACTGAATTTAACAAACCATGACAGA 59.716 33.333 0.00 0.00 0.00 3.41
2071 2125 7.424803 TCACTGAATTTAACAAACCATGACAG 58.575 34.615 0.00 0.00 0.00 3.51
2072 2126 7.284261 TCTCACTGAATTTAACAAACCATGACA 59.716 33.333 0.00 0.00 0.00 3.58
2073 2127 7.648142 TCTCACTGAATTTAACAAACCATGAC 58.352 34.615 0.00 0.00 0.00 3.06
2074 2128 7.502226 ACTCTCACTGAATTTAACAAACCATGA 59.498 33.333 0.00 0.00 0.00 3.07
2075 2129 7.651808 ACTCTCACTGAATTTAACAAACCATG 58.348 34.615 0.00 0.00 0.00 3.66
2076 2130 7.823745 ACTCTCACTGAATTTAACAAACCAT 57.176 32.000 0.00 0.00 0.00 3.55
2077 2131 7.338196 TGAACTCTCACTGAATTTAACAAACCA 59.662 33.333 0.00 0.00 0.00 3.67
2078 2132 7.703328 TGAACTCTCACTGAATTTAACAAACC 58.297 34.615 0.00 0.00 0.00 3.27
2079 2133 7.857885 CCTGAACTCTCACTGAATTTAACAAAC 59.142 37.037 0.00 0.00 0.00 2.93
2080 2134 7.556275 ACCTGAACTCTCACTGAATTTAACAAA 59.444 33.333 0.00 0.00 0.00 2.83
2081 2135 7.012327 CACCTGAACTCTCACTGAATTTAACAA 59.988 37.037 0.00 0.00 0.00 2.83
2082 2136 6.483307 CACCTGAACTCTCACTGAATTTAACA 59.517 38.462 0.00 0.00 0.00 2.41
2083 2137 6.073003 CCACCTGAACTCTCACTGAATTTAAC 60.073 42.308 0.00 0.00 0.00 2.01
2084 2138 5.997746 CCACCTGAACTCTCACTGAATTTAA 59.002 40.000 0.00 0.00 0.00 1.52
2116 2183 0.958382 GGAATGCGGCAACTGGTACA 60.958 55.000 6.82 0.00 0.00 2.90
2212 2279 1.322338 CTGTCGTGTGTTCGTTTCGTT 59.678 47.619 0.00 0.00 0.00 3.85
2226 2293 3.050619 GTTTCTCATCGTTGTCTGTCGT 58.949 45.455 0.00 0.00 0.00 4.34
2231 2298 2.061773 CGCTGTTTCTCATCGTTGTCT 58.938 47.619 0.00 0.00 32.06 3.41
2232 2299 1.126846 CCGCTGTTTCTCATCGTTGTC 59.873 52.381 0.00 0.00 34.42 3.18
2233 2300 1.148310 CCGCTGTTTCTCATCGTTGT 58.852 50.000 0.00 0.00 34.42 3.32
2234 2301 1.391485 CTCCGCTGTTTCTCATCGTTG 59.609 52.381 0.00 0.00 34.42 4.10
2251 2318 0.172803 ACACGTTACTCATCGGCTCC 59.827 55.000 0.00 0.00 0.00 4.70
2263 2330 2.126618 CGCCGCTCTCACACGTTA 60.127 61.111 0.00 0.00 0.00 3.18
2285 2352 2.306847 GAGGCTAAGGTCTCTCTCAGG 58.693 57.143 0.00 0.00 40.72 3.86
2286 2353 1.946768 CGAGGCTAAGGTCTCTCTCAG 59.053 57.143 0.00 0.00 41.64 3.35
2289 2356 2.773087 TCTACGAGGCTAAGGTCTCTCT 59.227 50.000 0.00 0.00 41.64 3.10
2300 2367 1.749638 CGTCTGGGTCTACGAGGCT 60.750 63.158 0.00 0.00 41.55 4.58
2425 2492 4.947147 TGACTTGGGTGCGGTGCC 62.947 66.667 0.00 0.00 0.00 5.01
2429 2501 1.101049 AACAACTGACTTGGGTGCGG 61.101 55.000 0.00 0.00 33.66 5.69
2437 2509 4.991687 GCTCTGCTACTTAACAACTGACTT 59.008 41.667 0.00 0.00 0.00 3.01
2444 2516 3.254903 TCGTCTGCTCTGCTACTTAACAA 59.745 43.478 0.00 0.00 0.00 2.83
2446 2518 3.172824 GTCGTCTGCTCTGCTACTTAAC 58.827 50.000 0.00 0.00 0.00 2.01
2447 2519 2.817844 TGTCGTCTGCTCTGCTACTTAA 59.182 45.455 0.00 0.00 0.00 1.85
2448 2520 2.433436 TGTCGTCTGCTCTGCTACTTA 58.567 47.619 0.00 0.00 0.00 2.24
2449 2521 1.248486 TGTCGTCTGCTCTGCTACTT 58.752 50.000 0.00 0.00 0.00 2.24
2450 2522 1.468985 ATGTCGTCTGCTCTGCTACT 58.531 50.000 0.00 0.00 0.00 2.57
2451 2523 2.189342 GAATGTCGTCTGCTCTGCTAC 58.811 52.381 0.00 0.00 0.00 3.58
2452 2524 1.818674 TGAATGTCGTCTGCTCTGCTA 59.181 47.619 0.00 0.00 0.00 3.49
2471 2543 1.361668 CTCTCCGTTTCACCGCCATG 61.362 60.000 0.00 0.00 0.00 3.66
2479 2551 1.005394 GCCGTTCCTCTCCGTTTCA 60.005 57.895 0.00 0.00 0.00 2.69
2484 2556 2.026301 GATCGCCGTTCCTCTCCG 59.974 66.667 0.00 0.00 0.00 4.63
2488 2560 2.165301 CAACCGATCGCCGTTCCTC 61.165 63.158 10.32 0.00 36.31 3.71
2490 2562 2.433664 ACAACCGATCGCCGTTCC 60.434 61.111 10.32 0.00 36.31 3.62
2492 2564 3.419759 GCACAACCGATCGCCGTT 61.420 61.111 10.32 6.77 36.31 4.44
2494 2566 3.853330 CAGCACAACCGATCGCCG 61.853 66.667 10.32 0.00 38.18 6.46
2495 2567 2.434185 TCAGCACAACCGATCGCC 60.434 61.111 10.32 0.00 0.00 5.54
2496 2568 2.778679 GTCAGCACAACCGATCGC 59.221 61.111 10.32 0.00 0.00 4.58
2497 2569 2.444624 CCGTCAGCACAACCGATCG 61.445 63.158 8.51 8.51 0.00 3.69
2498 2570 1.080093 TCCGTCAGCACAACCGATC 60.080 57.895 0.00 0.00 0.00 3.69
2499 2571 1.374252 GTCCGTCAGCACAACCGAT 60.374 57.895 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.