Multiple sequence alignment - TraesCS7A01G133600

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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 TraesCS7A01G133600 chr7A 100.000 2708 0 0 1 2708 85692839 85695546 0.000000e+00 5001.0
1 TraesCS7A01G133600 chr7A 90.960 708 63 1 2001 2708 18945904 18946610 0.000000e+00 952.0
2 TraesCS7A01G133600 chr7B 89.160 1882 116 39 1 1855 33955393 33957213 0.000000e+00 2265.0
3 TraesCS7A01G133600 chr7B 91.006 1401 73 19 14 1397 34140006 34141370 0.000000e+00 1840.0
4 TraesCS7A01G133600 chr7B 88.304 1445 107 25 439 1834 34048126 34049557 0.000000e+00 1676.0
5 TraesCS7A01G133600 chr7B 83.333 1092 122 31 677 1721 23318264 23317186 0.000000e+00 953.0
6 TraesCS7A01G133600 chr7B 82.662 1067 137 30 674 1716 665522797 665523839 0.000000e+00 902.0
7 TraesCS7A01G133600 chr7B 81.296 1080 144 35 674 1712 23325916 23324854 0.000000e+00 822.0
8 TraesCS7A01G133600 chr7B 82.113 956 111 28 792 1714 665534602 665535530 0.000000e+00 763.0
9 TraesCS7A01G133600 chr7B 91.943 422 23 7 17 434 34047545 34047959 5.030000e-162 580.0
10 TraesCS7A01G133600 chr7B 79.564 597 57 31 736 1289 665525603 665526177 1.530000e-97 366.0
11 TraesCS7A01G133600 chr7B 93.023 43 1 2 1855 1897 34146937 34146977 8.100000e-06 62.1
12 TraesCS7A01G133600 chr7B 97.059 34 1 0 1913 1946 722319471 722319504 1.050000e-04 58.4
13 TraesCS7A01G133600 chr7D 90.520 1635 88 22 1 1612 84405878 84407468 0.000000e+00 2098.0
14 TraesCS7A01G133600 chr7D 85.287 836 92 16 896 1712 590647666 590648489 0.000000e+00 833.0
15 TraesCS7A01G133600 chr7D 92.797 236 7 5 1608 1834 84408025 84408259 1.550000e-87 333.0
16 TraesCS7A01G133600 chr7D 79.112 383 64 13 121 500 560598776 560598407 1.610000e-62 250.0
17 TraesCS7A01G133600 chr7D 82.479 234 26 12 674 906 590647427 590647646 9.900000e-45 191.0
18 TraesCS7A01G133600 chr7D 95.349 43 0 2 1855 1897 84408216 84408256 1.740000e-07 67.6
19 TraesCS7A01G133600 chr7D 87.719 57 3 4 1903 1956 547332736 547332681 2.250000e-06 63.9
20 TraesCS7A01G133600 chr7D 97.059 34 1 0 1913 1946 36491523 36491556 1.050000e-04 58.4
21 TraesCS7A01G133600 chr4D 91.292 712 52 8 1997 2708 73323975 73323274 0.000000e+00 963.0
22 TraesCS7A01G133600 chr2D 90.295 711 61 6 1998 2708 334084749 334084047 0.000000e+00 924.0
23 TraesCS7A01G133600 chr2D 89.776 714 61 6 2001 2708 334079753 334079046 0.000000e+00 904.0
24 TraesCS7A01G133600 chr2D 100.000 34 0 0 1913 1946 195421402 195421369 2.250000e-06 63.9
25 TraesCS7A01G133600 chr2D 91.111 45 3 1 1903 1946 454962854 454962898 2.910000e-05 60.2
26 TraesCS7A01G133600 chr6D 90.042 713 65 4 2001 2708 438815988 438816699 0.000000e+00 918.0
27 TraesCS7A01G133600 chr6D 89.510 715 63 6 2001 2708 336525056 336525765 0.000000e+00 894.0
28 TraesCS7A01G133600 chr6D 82.450 547 92 4 1155 1699 457630175 457630719 2.440000e-130 475.0
29 TraesCS7A01G133600 chr6D 89.362 47 4 1 1901 1946 387882170 387882124 1.050000e-04 58.4
30 TraesCS7A01G133600 chr5A 90.071 705 62 2 2004 2708 34869218 34868522 0.000000e+00 907.0
31 TraesCS7A01G133600 chr2A 89.496 714 64 7 2001 2708 507716239 507715531 0.000000e+00 893.0
32 TraesCS7A01G133600 chr3D 89.356 714 65 5 2001 2708 1662285 1661577 0.000000e+00 887.0
33 TraesCS7A01G133600 chr6A 82.505 543 91 4 1159 1699 604537637 604538177 8.770000e-130 473.0
34 TraesCS7A01G133600 chr3A 91.489 47 3 1 1901 1946 31804462 31804416 2.250000e-06 63.9
35 TraesCS7A01G133600 chr1D 90.476 42 3 1 1916 1956 477507018 477507059 1.000000e-03 54.7
36 TraesCS7A01G133600 chr3B 87.234 47 5 1 1901 1946 412873145 412873099 5.000000e-03 52.8


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 TraesCS7A01G133600 chr7A 85692839 85695546 2707 False 5001.000000 5001 100.000000 1 2708 1 chr7A.!!$F2 2707
1 TraesCS7A01G133600 chr7A 18945904 18946610 706 False 952.000000 952 90.960000 2001 2708 1 chr7A.!!$F1 707
2 TraesCS7A01G133600 chr7B 33955393 33957213 1820 False 2265.000000 2265 89.160000 1 1855 1 chr7B.!!$F1 1854
3 TraesCS7A01G133600 chr7B 34140006 34141370 1364 False 1840.000000 1840 91.006000 14 1397 1 chr7B.!!$F2 1383
4 TraesCS7A01G133600 chr7B 34047545 34049557 2012 False 1128.000000 1676 90.123500 17 1834 2 chr7B.!!$F6 1817
5 TraesCS7A01G133600 chr7B 23317186 23318264 1078 True 953.000000 953 83.333000 677 1721 1 chr7B.!!$R1 1044
6 TraesCS7A01G133600 chr7B 23324854 23325916 1062 True 822.000000 822 81.296000 674 1712 1 chr7B.!!$R2 1038
7 TraesCS7A01G133600 chr7B 665534602 665535530 928 False 763.000000 763 82.113000 792 1714 1 chr7B.!!$F4 922
8 TraesCS7A01G133600 chr7B 665522797 665526177 3380 False 634.000000 902 81.113000 674 1716 2 chr7B.!!$F7 1042
9 TraesCS7A01G133600 chr7D 84405878 84408259 2381 False 832.866667 2098 92.888667 1 1897 3 chr7D.!!$F2 1896
10 TraesCS7A01G133600 chr7D 590647427 590648489 1062 False 512.000000 833 83.883000 674 1712 2 chr7D.!!$F3 1038
11 TraesCS7A01G133600 chr4D 73323274 73323975 701 True 963.000000 963 91.292000 1997 2708 1 chr4D.!!$R1 711
12 TraesCS7A01G133600 chr2D 334084047 334084749 702 True 924.000000 924 90.295000 1998 2708 1 chr2D.!!$R3 710
13 TraesCS7A01G133600 chr2D 334079046 334079753 707 True 904.000000 904 89.776000 2001 2708 1 chr2D.!!$R2 707
14 TraesCS7A01G133600 chr6D 438815988 438816699 711 False 918.000000 918 90.042000 2001 2708 1 chr6D.!!$F2 707
15 TraesCS7A01G133600 chr6D 336525056 336525765 709 False 894.000000 894 89.510000 2001 2708 1 chr6D.!!$F1 707
16 TraesCS7A01G133600 chr6D 457630175 457630719 544 False 475.000000 475 82.450000 1155 1699 1 chr6D.!!$F3 544
17 TraesCS7A01G133600 chr5A 34868522 34869218 696 True 907.000000 907 90.071000 2004 2708 1 chr5A.!!$R1 704
18 TraesCS7A01G133600 chr2A 507715531 507716239 708 True 893.000000 893 89.496000 2001 2708 1 chr2A.!!$R1 707
19 TraesCS7A01G133600 chr3D 1661577 1662285 708 True 887.000000 887 89.356000 2001 2708 1 chr3D.!!$R1 707
20 TraesCS7A01G133600 chr6A 604537637 604538177 540 False 473.000000 473 82.505000 1159 1699 1 chr6A.!!$F1 540

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
719 916 0.039437 AAGAAGACATCGTCGCACGT 60.039 50.0 8.22 0.0 43.14 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2643 5190 0.184451 CATAGGAGCCCTGGTGCAAT 59.816 55.0 9.36 0.0 34.61 3.56 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
250 254 6.764877 TGTAGACGTTGACAAGAATTTCTC 57.235 37.500 0.00 0.00 0.00 2.87
255 259 8.023050 AGACGTTGACAAGAATTTCTCTAATG 57.977 34.615 0.00 0.00 32.46 1.90
279 287 6.870965 TGTTGCACAAAGTTTACAAAGTTGAT 59.129 30.769 0.00 0.00 32.20 2.57
399 413 3.845781 TCTTGTGCTTCCAAGTCTTCT 57.154 42.857 9.94 0.00 42.01 2.85
400 414 4.156455 TCTTGTGCTTCCAAGTCTTCTT 57.844 40.909 9.94 0.00 42.01 2.52
401 415 4.130118 TCTTGTGCTTCCAAGTCTTCTTC 58.870 43.478 9.94 0.00 42.01 2.87
488 665 8.748380 ATATGTATGCGTTCATATGATATCCG 57.252 34.615 15.04 8.03 37.49 4.18
530 714 6.754209 AGAGTCACAGTATTGATTTCTAAGCG 59.246 38.462 0.00 0.00 0.00 4.68
593 780 4.316025 TTTAGAGCAATAAAGGCAGGGT 57.684 40.909 0.00 0.00 0.00 4.34
719 916 0.039437 AAGAAGACATCGTCGCACGT 60.039 50.000 8.22 0.00 43.14 4.49
726 923 1.443872 ATCGTCGCACGTTCAGGAC 60.444 57.895 8.22 0.00 43.14 3.85
727 924 2.814183 ATCGTCGCACGTTCAGGACC 62.814 60.000 8.22 0.00 43.14 4.46
728 925 2.028484 GTCGCACGTTCAGGACCA 59.972 61.111 0.00 0.00 0.00 4.02
729 926 2.028484 TCGCACGTTCAGGACCAC 59.972 61.111 0.00 0.00 0.00 4.16
731 928 2.028484 GCACGTTCAGGACCACGA 59.972 61.111 9.61 0.00 39.76 4.35
732 929 2.308039 GCACGTTCAGGACCACGAC 61.308 63.158 9.61 0.00 39.76 4.34
733 930 2.014554 CACGTTCAGGACCACGACG 61.015 63.158 9.61 10.21 39.76 5.12
734 931 2.333938 CGTTCAGGACCACGACGT 59.666 61.111 0.00 0.00 38.76 4.34
817 1038 6.587608 GGGATGCAAACTTAAGACAATTCAAG 59.412 38.462 10.09 0.00 0.00 3.02
906 1162 1.724623 CCACACCACGTAGACAAATCG 59.275 52.381 0.00 0.00 0.00 3.34
1344 1649 1.889829 CTCTTCTCCTTCACCGACAGT 59.110 52.381 0.00 0.00 0.00 3.55
1551 1856 1.303091 GCGACGTGGGGCTACAAAAT 61.303 55.000 0.00 0.00 0.00 1.82
1671 2537 0.035056 CAAAGAGGAAGGGCATCGGT 60.035 55.000 0.00 0.00 31.26 4.69
1829 2778 8.804688 TTGTGTATTGTTTAGTTTGTTATGCC 57.195 30.769 0.00 0.00 0.00 4.40
1830 2779 7.941919 TGTGTATTGTTTAGTTTGTTATGCCA 58.058 30.769 0.00 0.00 0.00 4.92
1831 2780 8.580720 TGTGTATTGTTTAGTTTGTTATGCCAT 58.419 29.630 0.00 0.00 0.00 4.40
1832 2781 8.859156 GTGTATTGTTTAGTTTGTTATGCCATG 58.141 33.333 0.00 0.00 0.00 3.66
1833 2782 8.031864 TGTATTGTTTAGTTTGTTATGCCATGG 58.968 33.333 7.63 7.63 0.00 3.66
1834 2783 4.815269 TGTTTAGTTTGTTATGCCATGGC 58.185 39.130 30.54 30.54 42.35 4.40
1835 2784 4.180817 GTTTAGTTTGTTATGCCATGGCC 58.819 43.478 33.44 18.47 41.09 5.36
1836 2785 0.817013 AGTTTGTTATGCCATGGCCG 59.183 50.000 33.44 0.00 41.09 6.13
1837 2786 0.814457 GTTTGTTATGCCATGGCCGA 59.186 50.000 33.44 18.71 41.09 5.54
1838 2787 1.408702 GTTTGTTATGCCATGGCCGAT 59.591 47.619 33.44 22.91 41.09 4.18
1839 2788 1.031235 TTGTTATGCCATGGCCGATG 58.969 50.000 33.44 3.07 41.09 3.84
1846 2795 4.585070 CATGGCCGATGGAACCAT 57.415 55.556 6.00 6.00 45.08 3.55
1847 2796 2.334307 CATGGCCGATGGAACCATC 58.666 57.895 20.17 20.17 42.31 3.51
1860 2809 4.616181 GGAACCATCCGTGTATTTTGAG 57.384 45.455 0.00 0.00 35.59 3.02
1861 2810 4.258543 GGAACCATCCGTGTATTTTGAGA 58.741 43.478 0.00 0.00 35.59 3.27
1862 2811 4.698304 GGAACCATCCGTGTATTTTGAGAA 59.302 41.667 0.00 0.00 35.59 2.87
1863 2812 5.182380 GGAACCATCCGTGTATTTTGAGAAA 59.818 40.000 0.00 0.00 35.59 2.52
1864 2813 6.127730 GGAACCATCCGTGTATTTTGAGAAAT 60.128 38.462 0.00 0.00 36.35 2.17
1865 2814 7.066525 GGAACCATCCGTGTATTTTGAGAAATA 59.933 37.037 0.00 0.00 35.10 1.40
1866 2815 8.519799 AACCATCCGTGTATTTTGAGAAATAT 57.480 30.769 0.00 0.00 39.29 1.28
1867 2816 9.621629 AACCATCCGTGTATTTTGAGAAATATA 57.378 29.630 0.00 0.00 39.29 0.86
1897 2853 6.920758 TGTATTGTTTAGTTTGTTCATGCCAC 59.079 34.615 0.00 0.00 0.00 5.01
1900 2856 2.264005 TAGTTTGTTCATGCCACGGT 57.736 45.000 0.00 0.00 0.00 4.83
1901 2857 0.951558 AGTTTGTTCATGCCACGGTC 59.048 50.000 0.00 0.00 0.00 4.79
1904 2860 2.063015 TTGTTCATGCCACGGTCCCT 62.063 55.000 0.00 0.00 0.00 4.20
1905 2861 1.745489 GTTCATGCCACGGTCCCTC 60.745 63.158 0.00 0.00 0.00 4.30
1906 2862 2.220586 TTCATGCCACGGTCCCTCA 61.221 57.895 0.00 0.00 0.00 3.86
1908 2864 0.689412 TCATGCCACGGTCCCTCATA 60.689 55.000 0.00 0.00 0.00 2.15
1909 2865 0.532862 CATGCCACGGTCCCTCATAC 60.533 60.000 0.00 0.00 0.00 2.39
1910 2866 0.691078 ATGCCACGGTCCCTCATACT 60.691 55.000 0.00 0.00 0.00 2.12
1911 2867 1.144057 GCCACGGTCCCTCATACTG 59.856 63.158 0.00 0.00 0.00 2.74
1913 2869 1.144057 CACGGTCCCTCATACTGGC 59.856 63.158 0.00 0.00 0.00 4.85
1914 2870 1.001760 ACGGTCCCTCATACTGGCT 59.998 57.895 0.00 0.00 0.00 4.75
1917 2873 1.204146 GGTCCCTCATACTGGCTCAA 58.796 55.000 0.00 0.00 0.00 3.02
1921 2877 4.042187 GGTCCCTCATACTGGCTCAAATAT 59.958 45.833 0.00 0.00 0.00 1.28
1922 2878 4.999950 GTCCCTCATACTGGCTCAAATATG 59.000 45.833 0.00 0.00 0.00 1.78
1923 2879 4.907269 TCCCTCATACTGGCTCAAATATGA 59.093 41.667 0.00 0.00 33.93 2.15
1935 2891 4.220693 TCAAATATGAGGCGGATATGGG 57.779 45.455 0.00 0.00 0.00 4.00
1937 2893 0.839946 ATATGAGGCGGATATGGGGC 59.160 55.000 0.00 0.00 0.00 5.80
1938 2894 1.613317 TATGAGGCGGATATGGGGCG 61.613 60.000 0.00 0.00 0.00 6.13
1962 2918 3.402681 CTGACCGGCACCCCTCAT 61.403 66.667 0.00 0.00 0.00 2.90
1963 2919 3.687321 CTGACCGGCACCCCTCATG 62.687 68.421 0.00 0.00 0.00 3.07
1968 2924 3.006677 GGCACCCCTCATGGCTAA 58.993 61.111 0.00 0.00 39.45 3.09
1969 2925 1.453928 GGCACCCCTCATGGCTAAC 60.454 63.158 0.00 0.00 39.45 2.34
1971 2927 1.904771 CACCCCTCATGGCTAACGA 59.095 57.895 0.00 0.00 0.00 3.85
1974 2930 1.564348 ACCCCTCATGGCTAACGAATT 59.436 47.619 0.00 0.00 0.00 2.17
1976 2932 2.358898 CCCCTCATGGCTAACGAATTTG 59.641 50.000 0.00 0.00 0.00 2.32
1977 2933 3.278574 CCCTCATGGCTAACGAATTTGA 58.721 45.455 0.00 0.00 0.00 2.69
1979 2935 4.191544 CCTCATGGCTAACGAATTTGAGA 58.808 43.478 0.00 0.00 32.77 3.27
1980 2936 4.818546 CCTCATGGCTAACGAATTTGAGAT 59.181 41.667 0.00 0.00 32.77 2.75
1981 2937 5.277683 CCTCATGGCTAACGAATTTGAGATG 60.278 44.000 0.00 0.00 32.77 2.90
1982 2938 5.427378 TCATGGCTAACGAATTTGAGATGA 58.573 37.500 0.00 0.00 0.00 2.92
1984 2940 5.991328 TGGCTAACGAATTTGAGATGATC 57.009 39.130 0.00 0.00 0.00 2.92
1985 2941 5.674525 TGGCTAACGAATTTGAGATGATCT 58.325 37.500 0.00 0.00 0.00 2.75
1986 2942 6.816136 TGGCTAACGAATTTGAGATGATCTA 58.184 36.000 0.00 0.00 0.00 1.98
1987 2943 6.925718 TGGCTAACGAATTTGAGATGATCTAG 59.074 38.462 0.00 0.00 0.00 2.43
1988 2944 6.128688 GGCTAACGAATTTGAGATGATCTAGC 60.129 42.308 0.00 0.00 0.00 3.42
1989 2945 6.422100 GCTAACGAATTTGAGATGATCTAGCA 59.578 38.462 0.00 0.00 0.00 3.49
1991 2947 6.595772 ACGAATTTGAGATGATCTAGCAAC 57.404 37.500 0.00 0.00 0.00 4.17
1992 2948 6.108687 ACGAATTTGAGATGATCTAGCAACA 58.891 36.000 0.00 0.00 0.00 3.33
1993 2949 6.257411 ACGAATTTGAGATGATCTAGCAACAG 59.743 38.462 0.00 0.00 0.00 3.16
1994 2950 6.374565 AATTTGAGATGATCTAGCAACAGC 57.625 37.500 0.00 0.00 0.00 4.40
1996 2952 4.684484 TGAGATGATCTAGCAACAGCAT 57.316 40.909 0.00 0.00 0.00 3.79
1997 2953 4.629092 TGAGATGATCTAGCAACAGCATC 58.371 43.478 0.00 0.00 34.02 3.91
1998 2954 3.651206 AGATGATCTAGCAACAGCATCG 58.349 45.455 0.00 0.00 37.71 3.84
1999 2955 1.575244 TGATCTAGCAACAGCATCGC 58.425 50.000 0.00 0.00 0.00 4.58
2076 3032 2.386100 GGCATGTCCATCCTCCCCA 61.386 63.158 0.00 0.00 34.01 4.96
2193 3154 4.033776 CGGGTCACCCATGGCACT 62.034 66.667 15.17 0.00 45.83 4.40
2213 3177 3.551407 GGTGCTCTCCCCCGATCC 61.551 72.222 0.00 0.00 0.00 3.36
2221 3185 4.969196 CCCCCGATCCGCGTCATG 62.969 72.222 4.92 0.00 38.67 3.07
2222 3186 4.969196 CCCCGATCCGCGTCATGG 62.969 72.222 4.92 1.03 38.67 3.66
2322 3299 1.215647 GAAGATCTGGTGGCGACGT 59.784 57.895 0.00 0.00 0.00 4.34
2325 3302 2.994995 ATCTGGTGGCGACGTCCA 60.995 61.111 10.58 0.00 35.99 4.02
2506 3484 1.342496 GGATCTGCATCACCGATCTCA 59.658 52.381 11.39 0.00 35.18 3.27
2514 3492 3.876914 GCATCACCGATCTCATGGTTTTA 59.123 43.478 0.00 0.00 35.96 1.52
2635 5182 4.626081 GTGGTGGCGCACTCAGGT 62.626 66.667 10.83 0.00 34.40 4.00
2648 5195 0.035152 CTCAGGTAGTGGCCATTGCA 60.035 55.000 17.77 0.00 40.13 4.08
2686 5233 0.172352 CACTGTTGTTGCGGTTGGTT 59.828 50.000 0.00 0.00 0.00 3.67
2694 5241 0.250945 TTGCGGTTGGTTGCCAGATA 60.251 50.000 0.00 0.00 33.81 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.899661 TTTAGAATATGCCACAACTATTGTACT 57.100 29.630 0.00 0.00 43.23 2.73
39 41 3.260632 ACATATACCGCATCTGTATGGCA 59.739 43.478 0.00 0.00 33.38 4.92
40 42 3.861840 ACATATACCGCATCTGTATGGC 58.138 45.455 0.00 0.00 33.38 4.40
207 211 7.436080 GTCTACATTGCCAAATCATTACCATTG 59.564 37.037 0.00 0.00 0.00 2.82
255 259 6.698359 TCAACTTTGTAAACTTTGTGCAAC 57.302 33.333 0.00 0.00 37.35 4.17
328 340 5.520376 AAATGTCCAACCACAAGAAGAAG 57.480 39.130 0.00 0.00 0.00 2.85
329 341 7.286546 TCAATAAATGTCCAACCACAAGAAGAA 59.713 33.333 0.00 0.00 0.00 2.52
330 342 6.775142 TCAATAAATGTCCAACCACAAGAAGA 59.225 34.615 0.00 0.00 0.00 2.87
331 343 6.980593 TCAATAAATGTCCAACCACAAGAAG 58.019 36.000 0.00 0.00 0.00 2.85
399 413 7.707624 ATTTTGATGGAAGTGCAAGATAGAA 57.292 32.000 0.00 0.00 0.00 2.10
400 414 7.613022 AGAATTTTGATGGAAGTGCAAGATAGA 59.387 33.333 0.00 0.00 0.00 1.98
401 415 7.769220 AGAATTTTGATGGAAGTGCAAGATAG 58.231 34.615 0.00 0.00 0.00 2.08
514 691 8.282592 TCATATTGTGCGCTTAGAAATCAATAC 58.717 33.333 9.73 0.00 32.03 1.89
572 757 4.270008 GACCCTGCCTTTATTGCTCTAAA 58.730 43.478 0.00 0.00 0.00 1.85
578 765 1.393603 GAGGACCCTGCCTTTATTGC 58.606 55.000 0.00 0.00 38.73 3.56
593 780 1.741401 CGTCTGGCAAATGCGAGGA 60.741 57.895 15.89 4.03 45.28 3.71
719 916 1.666700 CAAAAACGTCGTGGTCCTGAA 59.333 47.619 0.00 0.00 0.00 3.02
726 923 2.572664 GGCAACAAAAACGTCGTGG 58.427 52.632 0.00 0.00 0.00 4.94
906 1162 3.919973 TTCTACCGTTGGCCGCGTC 62.920 63.158 16.54 0.00 34.38 5.19
1471 1776 0.396974 TGCAAAAAGTCCAGTGGCCT 60.397 50.000 3.51 0.00 0.00 5.19
1476 1781 1.034838 TGGCGTGCAAAAAGTCCAGT 61.035 50.000 0.00 0.00 0.00 4.00
1551 1856 1.901464 GGCGTTGGGGAAGAAGCAA 60.901 57.895 0.00 0.00 0.00 3.91
1584 1889 0.321475 GCAGGTTCTTGAGCAGCTCT 60.321 55.000 23.15 0.00 35.63 4.09
1671 2537 0.963962 GAGGAGTGGTGTCGGTGTAA 59.036 55.000 0.00 0.00 0.00 2.41
1803 2752 9.250624 GGCATAACAAACTAAACAATACACAAA 57.749 29.630 0.00 0.00 0.00 2.83
1804 2753 8.414003 TGGCATAACAAACTAAACAATACACAA 58.586 29.630 0.00 0.00 0.00 3.33
1805 2754 7.941919 TGGCATAACAAACTAAACAATACACA 58.058 30.769 0.00 0.00 0.00 3.72
1806 2755 8.859156 CATGGCATAACAAACTAAACAATACAC 58.141 33.333 0.00 0.00 0.00 2.90
1807 2756 8.031864 CCATGGCATAACAAACTAAACAATACA 58.968 33.333 0.00 0.00 0.00 2.29
1808 2757 7.010091 GCCATGGCATAACAAACTAAACAATAC 59.990 37.037 32.08 0.00 41.49 1.89
1809 2758 7.038659 GCCATGGCATAACAAACTAAACAATA 58.961 34.615 32.08 0.00 41.49 1.90
1810 2759 5.874261 GCCATGGCATAACAAACTAAACAAT 59.126 36.000 32.08 0.00 41.49 2.71
1811 2760 5.233988 GCCATGGCATAACAAACTAAACAA 58.766 37.500 32.08 0.00 41.49 2.83
1812 2761 4.322349 GGCCATGGCATAACAAACTAAACA 60.322 41.667 36.56 0.00 44.11 2.83
1813 2762 4.180817 GGCCATGGCATAACAAACTAAAC 58.819 43.478 36.56 11.42 44.11 2.01
1814 2763 3.119316 CGGCCATGGCATAACAAACTAAA 60.119 43.478 36.56 0.00 44.11 1.85
1815 2764 2.425312 CGGCCATGGCATAACAAACTAA 59.575 45.455 36.56 0.00 44.11 2.24
1816 2765 2.020720 CGGCCATGGCATAACAAACTA 58.979 47.619 36.56 0.00 44.11 2.24
1817 2766 0.817013 CGGCCATGGCATAACAAACT 59.183 50.000 36.56 0.00 44.11 2.66
1818 2767 0.814457 TCGGCCATGGCATAACAAAC 59.186 50.000 36.56 16.45 44.11 2.93
1819 2768 1.408340 CATCGGCCATGGCATAACAAA 59.592 47.619 36.56 14.21 44.11 2.83
1820 2769 1.031235 CATCGGCCATGGCATAACAA 58.969 50.000 36.56 15.60 44.11 2.83
1821 2770 0.822944 CCATCGGCCATGGCATAACA 60.823 55.000 36.56 16.03 46.18 2.41
1822 2771 1.959085 CCATCGGCCATGGCATAAC 59.041 57.895 36.56 19.05 46.18 1.89
1823 2772 4.498346 CCATCGGCCATGGCATAA 57.502 55.556 36.56 21.69 46.18 1.90
1829 2778 1.174712 GGATGGTTCCATCGGCCATG 61.175 60.000 20.96 5.85 42.48 3.66
1830 2779 1.151450 GGATGGTTCCATCGGCCAT 59.849 57.895 20.96 0.00 44.82 4.40
1831 2780 2.595095 GGATGGTTCCATCGGCCA 59.405 61.111 20.96 0.00 42.56 5.36
1832 2781 2.591715 CGGATGGTTCCATCGGCC 60.592 66.667 20.96 10.65 42.74 6.13
1833 2782 2.180204 CACGGATGGTTCCATCGGC 61.180 63.158 27.51 14.91 43.20 5.54
1834 2783 0.462375 TACACGGATGGTTCCATCGG 59.538 55.000 26.59 26.59 42.74 4.18
1835 2784 2.526304 ATACACGGATGGTTCCATCG 57.474 50.000 20.96 18.25 42.74 3.84
1836 2785 4.638421 TCAAAATACACGGATGGTTCCATC 59.362 41.667 19.99 19.99 42.74 3.51
1837 2786 4.594970 TCAAAATACACGGATGGTTCCAT 58.405 39.130 3.80 3.80 42.74 3.41
1838 2787 4.006989 CTCAAAATACACGGATGGTTCCA 58.993 43.478 0.00 0.00 42.74 3.53
1839 2788 4.258543 TCTCAAAATACACGGATGGTTCC 58.741 43.478 0.00 0.00 38.81 3.62
1840 2789 5.873179 TTCTCAAAATACACGGATGGTTC 57.127 39.130 0.00 0.00 0.00 3.62
1841 2790 6.834168 ATTTCTCAAAATACACGGATGGTT 57.166 33.333 0.00 0.00 33.27 3.67
1842 2791 9.052759 GTATATTTCTCAAAATACACGGATGGT 57.947 33.333 0.00 0.00 39.52 3.55
1843 2792 9.273016 AGTATATTTCTCAAAATACACGGATGG 57.727 33.333 0.00 0.00 38.96 3.51
1846 2795 9.661563 ACAAGTATATTTCTCAAAATACACGGA 57.338 29.630 0.00 0.00 38.96 4.69
1847 2796 9.702726 CACAAGTATATTTCTCAAAATACACGG 57.297 33.333 0.00 0.00 38.96 4.94
1867 2816 9.515020 CATGAACAAACTAAACAATACACAAGT 57.485 29.630 0.00 0.00 0.00 3.16
1897 2853 1.043116 TGAGCCAGTATGAGGGACCG 61.043 60.000 0.00 0.00 39.69 4.79
1900 2856 4.907269 TCATATTTGAGCCAGTATGAGGGA 59.093 41.667 0.00 0.00 39.69 4.20
1901 2857 5.233083 TCATATTTGAGCCAGTATGAGGG 57.767 43.478 0.00 0.00 39.69 4.30
1904 2860 4.645535 GCCTCATATTTGAGCCAGTATGA 58.354 43.478 7.59 0.00 46.76 2.15
1905 2861 3.434641 CGCCTCATATTTGAGCCAGTATG 59.565 47.826 7.59 0.00 46.76 2.39
1906 2862 3.557898 CCGCCTCATATTTGAGCCAGTAT 60.558 47.826 7.59 0.00 46.76 2.12
1908 2864 1.475751 CCGCCTCATATTTGAGCCAGT 60.476 52.381 7.59 0.00 46.76 4.00
1909 2865 1.202687 TCCGCCTCATATTTGAGCCAG 60.203 52.381 7.59 1.82 46.76 4.85
1910 2866 0.836606 TCCGCCTCATATTTGAGCCA 59.163 50.000 7.59 0.00 46.76 4.75
1911 2867 2.191128 ATCCGCCTCATATTTGAGCC 57.809 50.000 7.59 0.00 46.76 4.70
1914 2870 3.054434 CCCCATATCCGCCTCATATTTGA 60.054 47.826 0.00 0.00 0.00 2.69
1917 2873 1.212935 GCCCCATATCCGCCTCATATT 59.787 52.381 0.00 0.00 0.00 1.28
1921 2877 3.625897 CGCCCCATATCCGCCTCA 61.626 66.667 0.00 0.00 0.00 3.86
1945 2901 3.402681 ATGAGGGGTGCCGGTCAG 61.403 66.667 1.90 0.00 0.00 3.51
1947 2903 4.489771 CCATGAGGGGTGCCGGTC 62.490 72.222 1.90 0.00 0.00 4.79
1955 2911 2.348411 AATTCGTTAGCCATGAGGGG 57.652 50.000 0.00 0.00 37.04 4.79
1956 2912 3.278574 TCAAATTCGTTAGCCATGAGGG 58.721 45.455 0.00 0.00 40.85 4.30
1957 2913 4.191544 TCTCAAATTCGTTAGCCATGAGG 58.808 43.478 0.00 0.00 34.91 3.86
1958 2914 5.525012 TCATCTCAAATTCGTTAGCCATGAG 59.475 40.000 0.00 0.00 35.35 2.90
1959 2915 5.427378 TCATCTCAAATTCGTTAGCCATGA 58.573 37.500 0.00 0.00 0.00 3.07
1960 2916 5.739752 TCATCTCAAATTCGTTAGCCATG 57.260 39.130 0.00 0.00 0.00 3.66
1962 2918 5.674525 AGATCATCTCAAATTCGTTAGCCA 58.325 37.500 0.00 0.00 0.00 4.75
1963 2919 6.128688 GCTAGATCATCTCAAATTCGTTAGCC 60.129 42.308 0.00 0.00 0.00 3.93
1965 2921 7.936950 TGCTAGATCATCTCAAATTCGTTAG 57.063 36.000 0.00 0.00 0.00 2.34
1966 2922 7.763985 TGTTGCTAGATCATCTCAAATTCGTTA 59.236 33.333 0.00 0.00 0.00 3.18
1968 2924 6.108687 TGTTGCTAGATCATCTCAAATTCGT 58.891 36.000 0.00 0.00 0.00 3.85
1969 2925 6.594284 TGTTGCTAGATCATCTCAAATTCG 57.406 37.500 0.00 0.00 0.00 3.34
1971 2927 5.884232 TGCTGTTGCTAGATCATCTCAAATT 59.116 36.000 0.00 0.00 40.48 1.82
1974 2930 4.476628 TGCTGTTGCTAGATCATCTCAA 57.523 40.909 0.00 0.00 40.48 3.02
1976 2932 3.674281 CGATGCTGTTGCTAGATCATCTC 59.326 47.826 7.34 0.00 40.48 2.75
1977 2933 3.651206 CGATGCTGTTGCTAGATCATCT 58.349 45.455 7.34 0.00 40.48 2.90
1979 2935 2.141517 GCGATGCTGTTGCTAGATCAT 58.858 47.619 0.00 0.00 40.48 2.45
1980 2936 1.575244 GCGATGCTGTTGCTAGATCA 58.425 50.000 0.00 0.00 40.48 2.92
1981 2937 0.864455 GGCGATGCTGTTGCTAGATC 59.136 55.000 0.00 0.00 40.48 2.75
1982 2938 0.533755 GGGCGATGCTGTTGCTAGAT 60.534 55.000 0.00 0.00 40.48 1.98
1984 2940 2.182842 GGGGCGATGCTGTTGCTAG 61.183 63.158 0.00 0.00 40.48 3.42
1985 2941 2.124736 GGGGCGATGCTGTTGCTA 60.125 61.111 0.00 0.00 40.48 3.49
2062 3018 1.385915 GGGATGGGGAGGATGGACA 60.386 63.158 0.00 0.00 0.00 4.02
2453 3431 4.947147 AACACCACGCCATGCCGT 62.947 61.111 0.00 0.00 43.11 5.68
2506 3484 4.832266 TGAACCAATCTGCAGTAAAACCAT 59.168 37.500 14.67 0.00 0.00 3.55
2514 3492 3.262660 TCTGATCTGAACCAATCTGCAGT 59.737 43.478 14.67 0.00 0.00 4.40
2584 4254 2.607750 GGCTCTCACCCCACCTCA 60.608 66.667 0.00 0.00 0.00 3.86
2635 5182 1.001020 CCTGGTGCAATGGCCACTA 60.001 57.895 8.16 0.00 40.13 2.74
2643 5190 0.184451 CATAGGAGCCCTGGTGCAAT 59.816 55.000 9.36 0.00 34.61 3.56
2644 5191 1.609239 CATAGGAGCCCTGGTGCAA 59.391 57.895 9.36 0.00 34.61 4.08
2648 5195 0.983378 GTCACCATAGGAGCCCTGGT 60.983 60.000 5.74 5.74 34.61 4.00


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

AutoCloner maintained by Alex Coulton.