Multiple sequence alignment - TraesCS1A01G132200

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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 TraesCS1A01G132200 chr1A 100.000 3671 0 0 1 3671 179534050 179530380 0.000000e+00 6780.0
1 TraesCS1A01G132200 chr5A 86.410 2178 243 20 975 3129 328954568 328956715 0.000000e+00 2333.0
2 TraesCS1A01G132200 chr5A 89.981 539 54 0 3133 3671 328956755 328957293 0.000000e+00 697.0
3 TraesCS1A01G132200 chr3B 85.853 2163 242 22 987 3129 439340180 439338062 0.000000e+00 2241.0
4 TraesCS1A01G132200 chr3B 88.868 539 59 1 3133 3671 439338022 439337485 0.000000e+00 662.0
5 TraesCS1A01G132200 chr4B 86.045 2114 231 24 1036 3129 94512247 94510178 0.000000e+00 2211.0
6 TraesCS1A01G132200 chr4B 95.962 941 34 4 1 940 299746650 299747587 0.000000e+00 1524.0
7 TraesCS1A01G132200 chr6B 96.068 941 32 4 1 940 719430873 719431809 0.000000e+00 1528.0
8 TraesCS1A01G132200 chr4D 89.101 945 96 6 1 943 205901290 205900351 0.000000e+00 1168.0
9 TraesCS1A01G132200 chr5D 85.807 923 128 3 1 921 191263292 191264213 0.000000e+00 976.0
10 TraesCS1A01G132200 chr5D 85.590 923 130 3 1 921 196350780 196349859 0.000000e+00 965.0
11 TraesCS1A01G132200 chr2A 85.699 923 129 3 1 921 475805031 475805952 0.000000e+00 970.0
12 TraesCS1A01G132200 chr2A 100.000 29 0 0 3382 3410 632502545 632502573 2.000000e-03 54.7
13 TraesCS1A01G132200 chr2B 93.466 551 36 0 3121 3671 313443246 313442696 0.000000e+00 819.0
14 TraesCS1A01G132200 chr6A 83.354 799 121 12 134 926 390583193 390583985 0.000000e+00 728.0
15 TraesCS1A01G132200 chr3D 81.352 858 142 14 976 1824 434021874 434021026 0.000000e+00 682.0
16 TraesCS1A01G132200 chr3D 81.074 745 121 13 1950 2676 434020927 434020185 8.840000e-161 577.0
17 TraesCS1A01G132200 chr3D 84.743 544 75 7 3132 3671 433872574 433872035 4.170000e-149 538.0
18 TraesCS1A01G132200 chr7D 98.046 307 5 1 3365 3671 206611168 206611473 1.940000e-147 532.0
19 TraesCS1A01G132200 chr7A 95.139 288 13 1 651 937 25355794 25356081 1.550000e-123 453.0


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 TraesCS1A01G132200 chr1A 179530380 179534050 3670 True 6780.0 6780 100.0000 1 3671 1 chr1A.!!$R1 3670
1 TraesCS1A01G132200 chr5A 328954568 328957293 2725 False 1515.0 2333 88.1955 975 3671 2 chr5A.!!$F1 2696
2 TraesCS1A01G132200 chr3B 439337485 439340180 2695 True 1451.5 2241 87.3605 987 3671 2 chr3B.!!$R1 2684
3 TraesCS1A01G132200 chr4B 94510178 94512247 2069 True 2211.0 2211 86.0450 1036 3129 1 chr4B.!!$R1 2093
4 TraesCS1A01G132200 chr4B 299746650 299747587 937 False 1524.0 1524 95.9620 1 940 1 chr4B.!!$F1 939
5 TraesCS1A01G132200 chr6B 719430873 719431809 936 False 1528.0 1528 96.0680 1 940 1 chr6B.!!$F1 939
6 TraesCS1A01G132200 chr4D 205900351 205901290 939 True 1168.0 1168 89.1010 1 943 1 chr4D.!!$R1 942
7 TraesCS1A01G132200 chr5D 191263292 191264213 921 False 976.0 976 85.8070 1 921 1 chr5D.!!$F1 920
8 TraesCS1A01G132200 chr5D 196349859 196350780 921 True 965.0 965 85.5900 1 921 1 chr5D.!!$R1 920
9 TraesCS1A01G132200 chr2A 475805031 475805952 921 False 970.0 970 85.6990 1 921 1 chr2A.!!$F1 920
10 TraesCS1A01G132200 chr2B 313442696 313443246 550 True 819.0 819 93.4660 3121 3671 1 chr2B.!!$R1 550
11 TraesCS1A01G132200 chr6A 390583193 390583985 792 False 728.0 728 83.3540 134 926 1 chr6A.!!$F1 792
12 TraesCS1A01G132200 chr3D 434020185 434021874 1689 True 629.5 682 81.2130 976 2676 2 chr3D.!!$R2 1700
13 TraesCS1A01G132200 chr3D 433872035 433872574 539 True 538.0 538 84.7430 3132 3671 1 chr3D.!!$R1 539

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
826 834 0.115944 TCCACCCATTTTGGCCATGA 59.884 50.0 6.09 0.0 35.79 3.07 F
1589 1612 0.099968 CGACGATCCTTGCCTTCGTA 59.900 55.0 0.00 0.0 45.30 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 1956 0.034198 TTTTGGATCCACTCGTCGCA 59.966 50.0 15.91 0.0 0.00 5.1 R
2961 3015 0.179179 GCATCTTCAACTGCCTTCGC 60.179 55.0 0.00 0.0 32.15 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
61 62 1.339055 TGCATTTCTTCCTCCCTCACG 60.339 52.381 0.00 0.00 0.00 4.35
92 93 3.237268 TGGCCAACATAGTGTCCTTTT 57.763 42.857 0.61 0.00 0.00 2.27
266 268 7.758609 TGATAAGTCAACATCATCCCCATATT 58.241 34.615 0.00 0.00 0.00 1.28
344 346 2.503765 TCAGGAGAATTCATACCGGCAA 59.496 45.455 8.44 0.00 0.00 4.52
656 662 4.574674 TGGCACTTTGTTATGAGGATCT 57.425 40.909 0.00 0.00 34.92 2.75
679 685 5.617252 TCAACCGAAACCACTCTTTTCTAT 58.383 37.500 0.00 0.00 31.82 1.98
758 765 5.592282 TGTTGAACAGTGAAATTAGCTCCAA 59.408 36.000 0.00 0.00 0.00 3.53
826 834 0.115944 TCCACCCATTTTGGCCATGA 59.884 50.000 6.09 0.00 35.79 3.07
840 848 2.424812 GGCCATGATACCTTCCCACATT 60.425 50.000 0.00 0.00 0.00 2.71
940 948 7.915397 CCTGCAAGCGTTCATTATAGTTAAATT 59.085 33.333 0.00 0.00 0.00 1.82
973 981 7.455331 TGCATCTATCATATAATCTTTCGCG 57.545 36.000 0.00 0.00 0.00 5.87
974 982 7.257722 TGCATCTATCATATAATCTTTCGCGA 58.742 34.615 3.71 3.71 0.00 5.87
975 983 7.759433 TGCATCTATCATATAATCTTTCGCGAA 59.241 33.333 19.38 19.38 0.00 4.70
976 984 8.595533 GCATCTATCATATAATCTTTCGCGAAA 58.404 33.333 30.47 30.47 0.00 3.46
994 1002 0.323451 AAAAAGGATGTCGCTCCCCC 60.323 55.000 0.00 0.00 35.79 5.40
1076 1098 3.241530 ACTCCTTCACCAGCCGCA 61.242 61.111 0.00 0.00 0.00 5.69
1137 1160 2.626780 GCCAAGGTTTGCTCGGGAC 61.627 63.158 0.00 0.00 0.00 4.46
1161 1184 0.539669 TCGTGCTCTCTCTGTTCCCA 60.540 55.000 0.00 0.00 0.00 4.37
1170 1193 3.114616 CTGTTCCCACAGCTCGCG 61.115 66.667 0.00 0.00 44.16 5.87
1190 1213 1.596477 GATCCACGCCAGATCCAGC 60.596 63.158 0.00 0.00 35.16 4.85
1194 1217 3.842923 ACGCCAGATCCAGCCTCG 61.843 66.667 0.00 0.00 0.00 4.63
1242 1265 0.107654 CTTCTTTCGGCCGGGATTCT 60.108 55.000 27.83 0.00 0.00 2.40
1263 1286 2.669133 CCCCGAAGATCCACCTGCA 61.669 63.158 0.00 0.00 0.00 4.41
1314 1337 1.583477 GAAGGTCTGCTTTGCTGCC 59.417 57.895 0.00 0.00 0.00 4.85
1398 1421 3.993234 GCATCGTCATCTGCGCGG 61.993 66.667 10.86 10.86 0.00 6.46
1443 1466 2.920912 ACGCCCGTTCCTTCCAGA 60.921 61.111 0.00 0.00 0.00 3.86
1470 1493 2.998667 CCGCGTGCTTCTTCGATC 59.001 61.111 4.92 0.00 0.00 3.69
1472 1495 1.867812 CGCGTGCTTCTTCGATCGA 60.868 57.895 15.15 15.15 0.00 3.59
1497 1520 2.530151 AGTGGGGAAGCCAGCTCA 60.530 61.111 0.00 0.00 0.00 4.26
1560 1583 2.989824 CTGTCTCCCGACCACCGT 60.990 66.667 0.00 0.00 39.47 4.83
1580 1603 1.595357 GTTCACCCCGACGATCCTT 59.405 57.895 0.00 0.00 0.00 3.36
1589 1612 0.099968 CGACGATCCTTGCCTTCGTA 59.900 55.000 0.00 0.00 45.30 3.43
1631 1654 2.273370 TTCGTCAAGCTCCATCGTAC 57.727 50.000 0.00 0.00 0.00 3.67
1638 1661 0.680280 AGCTCCATCGTACGACCTGT 60.680 55.000 22.14 0.77 0.00 4.00
1757 1780 4.680237 CAAGACGCCGCCTCCACA 62.680 66.667 0.00 0.00 0.00 4.17
1758 1781 3.936203 AAGACGCCGCCTCCACAA 61.936 61.111 0.00 0.00 0.00 3.33
1772 1795 0.393077 CCACAACAAGACCGTCTCCT 59.607 55.000 0.35 0.00 0.00 3.69
1914 1940 0.108615 CTCACCCTGGACGTGCTAAG 60.109 60.000 8.99 0.00 0.00 2.18
1915 1941 1.741770 CACCCTGGACGTGCTAAGC 60.742 63.158 8.99 0.00 0.00 3.09
1917 1943 1.003839 CCCTGGACGTGCTAAGCAA 60.004 57.895 8.99 0.00 41.47 3.91
1918 1944 1.021390 CCCTGGACGTGCTAAGCAAG 61.021 60.000 8.99 0.00 41.47 4.01
1920 1946 1.639298 CTGGACGTGCTAAGCAAGGC 61.639 60.000 8.99 0.00 44.90 4.35
1921 1947 3.178539 GACGTGCTAAGCAAGGCC 58.821 61.111 0.00 0.00 40.03 5.19
1922 1948 1.671054 GACGTGCTAAGCAAGGCCA 60.671 57.895 5.01 0.00 40.03 5.36
1923 1949 1.228124 ACGTGCTAAGCAAGGCCAA 60.228 52.632 5.01 0.00 41.94 4.52
1924 1950 1.237285 ACGTGCTAAGCAAGGCCAAG 61.237 55.000 5.01 0.00 41.94 3.61
1925 1951 0.955428 CGTGCTAAGCAAGGCCAAGA 60.955 55.000 5.01 0.00 41.47 3.02
1926 1952 0.523519 GTGCTAAGCAAGGCCAAGAC 59.476 55.000 5.01 0.00 41.47 3.01
1927 1953 0.401738 TGCTAAGCAAGGCCAAGACT 59.598 50.000 5.01 0.00 34.76 3.24
1928 1954 1.090728 GCTAAGCAAGGCCAAGACTC 58.909 55.000 5.01 0.00 0.00 3.36
1929 1955 1.363744 CTAAGCAAGGCCAAGACTCG 58.636 55.000 5.01 0.00 0.00 4.18
1930 1956 0.685097 TAAGCAAGGCCAAGACTCGT 59.315 50.000 5.01 0.00 0.00 4.18
1931 1957 0.886490 AAGCAAGGCCAAGACTCGTG 60.886 55.000 5.01 0.00 0.00 4.35
1932 1958 2.970974 GCAAGGCCAAGACTCGTGC 61.971 63.158 5.01 0.00 0.00 5.34
1933 1959 2.357517 AAGGCCAAGACTCGTGCG 60.358 61.111 5.01 0.00 0.00 5.34
1934 1960 2.867855 AAGGCCAAGACTCGTGCGA 61.868 57.895 5.01 0.00 0.00 5.10
1935 1961 3.112709 GGCCAAGACTCGTGCGAC 61.113 66.667 0.00 0.00 0.00 5.19
1945 1983 2.579787 CGTGCGACGAGTGGATCC 60.580 66.667 4.20 4.20 46.05 3.36
1946 1984 2.571757 GTGCGACGAGTGGATCCA 59.428 61.111 11.44 11.44 0.00 3.41
1956 1994 2.160417 CGAGTGGATCCAAAAAGACAGC 59.840 50.000 18.20 0.00 0.00 4.40
1962 2000 3.181506 GGATCCAAAAAGACAGCGACATC 60.182 47.826 6.95 0.00 0.00 3.06
2013 2051 0.467804 GTCTGGAGCTCCCAATCCTC 59.532 60.000 29.95 9.47 46.07 3.71
2022 2060 3.833645 CCAATCCTCGACGCCCGA 61.834 66.667 0.00 0.66 46.35 5.14
2033 2071 1.153353 GACGCCCGAAGAATCAACAA 58.847 50.000 0.00 0.00 0.00 2.83
2064 2102 0.108585 AACACCTTCGTGATGGCACT 59.891 50.000 0.00 0.00 43.14 4.40
2079 2117 1.296392 CACTGTCATCCCGGCTTCA 59.704 57.895 0.00 0.00 0.00 3.02
2116 2154 2.528743 CGCCCATCTGACATGACGC 61.529 63.158 0.00 0.00 0.00 5.19
2122 2160 0.179089 ATCTGACATGACGCTGAGGC 60.179 55.000 0.00 0.00 0.00 4.70
2232 2270 3.511595 ATCATTGTGCTGCGGCCG 61.512 61.111 24.05 24.05 37.74 6.13
2272 2310 2.279517 GCGGAAGATCGTCGCCAT 60.280 61.111 15.80 0.00 43.17 4.40
2304 2342 1.552337 ACCGCTCACAGAGACATCATT 59.448 47.619 0.00 0.00 0.00 2.57
2328 2366 2.651361 CGTCCTTCACCGACTGCT 59.349 61.111 0.00 0.00 0.00 4.24
2428 2475 2.736995 GTCTGCTACGGCGTGCAA 60.737 61.111 27.60 19.18 42.25 4.08
2431 2478 4.610714 TGCTACGGCGTGCAACCA 62.611 61.111 26.46 13.17 42.25 3.67
2481 2534 3.073735 CAGTCGGCTCCTGGCTCT 61.074 66.667 0.00 0.00 41.46 4.09
2482 2535 3.073735 AGTCGGCTCCTGGCTCTG 61.074 66.667 0.00 0.00 41.46 3.35
2487 2540 2.587247 GGCTCCTGGCTCTGTCACA 61.587 63.158 0.00 0.00 41.46 3.58
2512 2565 1.643868 GCACCAACATGCCGATTCGA 61.644 55.000 7.83 0.00 39.86 3.71
2521 2574 1.734137 GCCGATTCGACTGGCTCTA 59.266 57.895 7.83 0.00 45.40 2.43
2612 2666 1.605058 ATGTCCACGCGCCTAGAAGT 61.605 55.000 5.73 0.00 0.00 3.01
2615 2669 2.571757 CACGCGCCTAGAAGTCCA 59.428 61.111 5.73 0.00 0.00 4.02
2616 2670 1.517257 CACGCGCCTAGAAGTCCAG 60.517 63.158 5.73 0.00 0.00 3.86
2620 2674 1.142748 CGCCTAGAAGTCCAGCAGG 59.857 63.158 0.00 0.00 0.00 4.85
2696 2750 1.077625 AAGCTCCTCTCCACCTCGT 59.922 57.895 0.00 0.00 0.00 4.18
2698 2752 1.379309 GCTCCTCTCCACCTCGTCT 60.379 63.158 0.00 0.00 0.00 4.18
2702 2756 1.979155 CTCTCCACCTCGTCTGCCA 60.979 63.158 0.00 0.00 0.00 4.92
2744 2798 2.035442 GGGCGTCTCAGGCTTCAAC 61.035 63.158 0.00 0.00 36.85 3.18
2784 2838 1.583054 GCTACGTGCCAATAAGAGGG 58.417 55.000 0.00 0.00 35.15 4.30
2867 2921 1.220206 CCAGCAGCTCACCGAAGAT 59.780 57.895 0.00 0.00 0.00 2.40
2876 2930 0.617935 TCACCGAAGATGCCATTGGA 59.382 50.000 6.95 0.00 0.00 3.53
2882 2936 3.428045 CCGAAGATGCCATTGGAAAGTTC 60.428 47.826 6.95 2.72 0.00 3.01
2937 2991 1.003233 GTTTCTGCCCTTCGAGCCT 60.003 57.895 0.00 0.00 0.00 4.58
2939 2993 0.606401 TTTCTGCCCTTCGAGCCTTG 60.606 55.000 0.00 0.00 0.00 3.61
2958 3012 4.499696 CCTTGTTCAACCTTGATTGTGACC 60.500 45.833 0.00 0.00 37.00 4.02
2961 3015 2.862541 TCAACCTTGATTGTGACCTGG 58.137 47.619 0.00 0.00 31.01 4.45
2963 3017 0.606401 ACCTTGATTGTGACCTGGCG 60.606 55.000 0.00 0.00 0.00 5.69
2990 3044 1.815003 GTTGAAGATGCCCTTGTGGAG 59.185 52.381 0.00 0.00 34.68 3.86
3029 3083 2.665185 GAGCTGCAAACGACGGGT 60.665 61.111 1.02 0.00 0.00 5.28
3030 3084 2.665185 AGCTGCAAACGACGGGTC 60.665 61.111 1.02 0.00 0.00 4.46
3039 3093 3.812019 CGACGGGTCAGGAGGTCG 61.812 72.222 0.00 0.00 44.92 4.79
3078 3132 2.799126 TGGACTGTGTTTGTTCCAGT 57.201 45.000 0.00 0.00 41.90 4.00
3088 3142 4.150098 GTGTTTGTTCCAGTCGATGTACTC 59.850 45.833 0.00 0.00 0.00 2.59
3096 3150 3.193691 CCAGTCGATGTACTCTGTTCCTT 59.806 47.826 0.00 0.00 0.00 3.36
3113 3167 8.475639 TCTGTTCCTTATGTTAGATACAACCTC 58.524 37.037 0.00 0.00 40.89 3.85
3115 3169 8.475639 TGTTCCTTATGTTAGATACAACCTCTC 58.524 37.037 0.00 0.00 40.89 3.20
3129 3219 1.276421 ACCTCTCGATGGTTCTGGTTG 59.724 52.381 4.62 0.00 33.34 3.77
3185 3275 4.142071 TGGCTGTTGTTTGATGTTGCTAAA 60.142 37.500 0.00 0.00 0.00 1.85
3195 3285 3.066064 TGATGTTGCTAAACGTGTTGCTT 59.934 39.130 13.30 0.00 39.30 3.91
3224 3314 5.054477 GGTGTTGTTGTACTCTGCTTCTTA 58.946 41.667 0.00 0.00 0.00 2.10
3332 3422 2.636830 CGAGGCTTGAATTGTCCTGAT 58.363 47.619 0.00 0.00 0.00 2.90
3342 3432 1.170442 TTGTCCTGATCGTCGTGCTA 58.830 50.000 0.00 0.00 0.00 3.49
3440 3530 4.441079 CCTTTCATTGCTGCATTTCTAGGG 60.441 45.833 1.84 0.00 0.00 3.53
3452 3542 6.091555 TGCATTTCTAGGGGGATATAGACTT 58.908 40.000 0.00 0.00 0.00 3.01
3526 3616 6.131972 TCTCTGGGATGAGAATTTTGTCTT 57.868 37.500 0.00 0.00 39.80 3.01
3531 3621 5.832595 TGGGATGAGAATTTTGTCTTTGTCA 59.167 36.000 0.00 0.00 30.84 3.58
3569 3659 1.328279 CCTTTTTCCTTTCGGCCACT 58.672 50.000 2.24 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 0.827368 TGTTGGCCAACTTGGTTTCC 59.173 50.000 40.40 18.25 40.46 3.13
266 268 6.464892 CCAGAATATGAGTTGGGCAGAGATAA 60.465 42.308 0.00 0.00 0.00 1.75
344 346 7.633789 AGTTATACTGATGATGTTTTGAGGGT 58.366 34.615 0.00 0.00 0.00 4.34
656 662 3.881220 AGAAAAGAGTGGTTTCGGTTGA 58.119 40.909 0.00 0.00 39.48 3.18
826 834 5.103940 AGAGTATGCAAATGTGGGAAGGTAT 60.104 40.000 0.00 0.00 0.00 2.73
840 848 6.430616 TGTGTCAATGATGAAAGAGTATGCAA 59.569 34.615 0.00 0.00 37.30 4.08
871 879 0.663153 GGAATAATGGTCGCACTGGC 59.337 55.000 0.00 0.00 0.00 4.85
947 955 8.382875 CGCGAAAGATTATATGATAGATGCAAA 58.617 33.333 0.00 0.00 0.00 3.68
948 956 7.759433 TCGCGAAAGATTATATGATAGATGCAA 59.241 33.333 6.20 0.00 0.00 4.08
949 957 7.257722 TCGCGAAAGATTATATGATAGATGCA 58.742 34.615 6.20 0.00 0.00 3.96
950 958 7.685532 TCGCGAAAGATTATATGATAGATGC 57.314 36.000 6.20 0.00 0.00 3.91
975 983 0.323451 GGGGGAGCGACATCCTTTTT 60.323 55.000 0.00 0.00 39.50 1.94
976 984 1.303282 GGGGGAGCGACATCCTTTT 59.697 57.895 0.00 0.00 39.50 2.27
977 985 2.998949 GGGGGAGCGACATCCTTT 59.001 61.111 0.00 0.00 39.50 3.11
1053 1075 4.329545 TGGTGAAGGAGTGGCGCC 62.330 66.667 22.73 22.73 0.00 6.53
1054 1076 2.743928 CTGGTGAAGGAGTGGCGC 60.744 66.667 0.00 0.00 0.00 6.53
1055 1077 2.743928 GCTGGTGAAGGAGTGGCG 60.744 66.667 0.00 0.00 0.00 5.69
1056 1078 2.360475 GGCTGGTGAAGGAGTGGC 60.360 66.667 0.00 0.00 0.00 5.01
1059 1081 3.241530 TGCGGCTGGTGAAGGAGT 61.242 61.111 0.00 0.00 0.00 3.85
1066 1088 4.767255 GGAGAGGTGCGGCTGGTG 62.767 72.222 0.00 0.00 0.00 4.17
1076 1098 4.021925 GCGTTGCAGGGGAGAGGT 62.022 66.667 0.00 0.00 0.00 3.85
1137 1160 3.137459 AGAGAGAGCACGAGGCCG 61.137 66.667 0.00 0.00 46.50 6.13
1161 1184 4.148825 GTGGATCCCGCGAGCTGT 62.149 66.667 8.23 0.00 0.00 4.40
1200 1223 1.151810 TGAAGAGGGAGGGTGCCTT 60.152 57.895 0.00 0.00 38.79 4.35
1205 1228 1.306568 GAGCCTGAAGAGGGAGGGT 60.307 63.158 0.00 0.00 42.87 4.34
1242 1265 1.717032 CAGGTGGATCTTCGGGGATA 58.283 55.000 0.00 0.00 0.00 2.59
1263 1286 0.533755 AAGCAACGAGAGCAGCAACT 60.534 50.000 0.00 0.00 36.75 3.16
1314 1337 0.096628 GATGCAGCAGAACTTCAGCG 59.903 55.000 0.00 0.00 33.83 5.18
1341 1364 3.691342 CCACGGACGAGCCCAAGA 61.691 66.667 0.00 0.00 0.00 3.02
1389 1412 3.121030 GCACTGAACCGCGCAGAT 61.121 61.111 17.39 0.00 36.86 2.90
1435 1458 1.817099 GCGATGCAGGTCTGGAAGG 60.817 63.158 0.00 0.00 33.77 3.46
1472 1495 3.322466 CTTCCCCACTGGACGGCT 61.322 66.667 0.00 0.00 45.11 5.52
1488 1511 2.365370 CCCTCCTCTGAGCTGGCT 60.365 66.667 0.00 0.00 37.29 4.75
1497 1520 0.695347 CAAGCTTCCAACCCTCCTCT 59.305 55.000 0.00 0.00 0.00 3.69
1560 1583 2.703798 GGATCGTCGGGGTGAACGA 61.704 63.158 0.00 0.00 38.13 3.85
1562 1585 0.739813 CAAGGATCGTCGGGGTGAAC 60.740 60.000 0.00 0.00 0.00 3.18
1564 1587 3.014085 GCAAGGATCGTCGGGGTGA 62.014 63.158 0.00 0.00 0.00 4.02
1580 1603 0.619255 TGGAGGGGAATACGAAGGCA 60.619 55.000 0.00 0.00 0.00 4.75
1589 1612 0.846427 TCTGCTGGTTGGAGGGGAAT 60.846 55.000 0.00 0.00 34.66 3.01
1631 1654 2.887568 GGCAGCGATGACAGGTCG 60.888 66.667 4.02 0.00 41.77 4.79
1737 1760 4.143333 GGAGGCGGCGTCTTGCTA 62.143 66.667 17.96 0.00 45.43 3.49
1744 1767 4.555709 TTGTTGTGGAGGCGGCGT 62.556 61.111 9.37 0.00 0.00 5.68
1757 1780 1.371558 GGCAGGAGACGGTCTTGTT 59.628 57.895 12.67 0.00 34.68 2.83
1758 1781 1.837051 TGGCAGGAGACGGTCTTGT 60.837 57.895 12.67 0.00 34.68 3.16
1790 1816 4.925861 GCAGAGGCGAGGGATGGC 62.926 72.222 0.00 0.00 0.00 4.40
1824 1850 0.721718 GAGTCCTTTCGGCAACATCG 59.278 55.000 0.00 0.00 0.00 3.84
1829 1855 1.846124 AGGGGAGTCCTTTCGGCAA 60.846 57.895 9.58 0.00 45.47 4.52
1875 1901 3.777925 CTTGAGCGTTGGCGGACG 61.778 66.667 8.61 8.61 46.35 4.79
1898 1924 1.764571 TTGCTTAGCACGTCCAGGGT 61.765 55.000 6.34 0.00 38.71 4.34
1914 1940 2.970974 GCACGAGTCTTGGCCTTGC 61.971 63.158 3.32 0.00 0.00 4.01
1915 1941 2.671177 CGCACGAGTCTTGGCCTTG 61.671 63.158 3.32 0.00 0.00 3.61
1917 1943 3.303135 TCGCACGAGTCTTGGCCT 61.303 61.111 3.32 0.00 0.00 5.19
1918 1944 3.112709 GTCGCACGAGTCTTGGCC 61.113 66.667 0.00 0.00 0.00 5.36
1920 1946 2.254350 TCGTCGCACGAGTCTTGG 59.746 61.111 7.20 0.00 46.73 3.61
1928 1954 2.579787 GGATCCACTCGTCGCACG 60.580 66.667 6.95 2.79 44.19 5.34
1929 1955 0.669318 TTTGGATCCACTCGTCGCAC 60.669 55.000 15.91 0.00 0.00 5.34
1930 1956 0.034198 TTTTGGATCCACTCGTCGCA 59.966 50.000 15.91 0.00 0.00 5.10
1931 1957 1.128692 CTTTTTGGATCCACTCGTCGC 59.871 52.381 15.91 0.00 0.00 5.19
1932 1958 2.412089 GTCTTTTTGGATCCACTCGTCG 59.588 50.000 15.91 1.20 0.00 5.12
1933 1959 3.399330 TGTCTTTTTGGATCCACTCGTC 58.601 45.455 15.91 4.59 0.00 4.20
1934 1960 3.403038 CTGTCTTTTTGGATCCACTCGT 58.597 45.455 15.91 0.00 0.00 4.18
1935 1961 2.160417 GCTGTCTTTTTGGATCCACTCG 59.840 50.000 15.91 3.49 0.00 4.18
1938 1976 2.095718 GTCGCTGTCTTTTTGGATCCAC 60.096 50.000 15.91 1.87 0.00 4.02
1942 1980 3.438087 CAGATGTCGCTGTCTTTTTGGAT 59.562 43.478 0.00 0.00 0.00 3.41
1943 1981 2.807967 CAGATGTCGCTGTCTTTTTGGA 59.192 45.455 0.00 0.00 0.00 3.53
1945 1983 3.548587 CACAGATGTCGCTGTCTTTTTG 58.451 45.455 0.00 0.00 45.54 2.44
1946 1984 2.549754 CCACAGATGTCGCTGTCTTTTT 59.450 45.455 0.00 0.00 45.54 1.94
1956 1994 1.354337 CTTGACGGCCACAGATGTCG 61.354 60.000 2.24 0.00 34.11 4.35
1962 2000 1.081892 CATCTTCTTGACGGCCACAG 58.918 55.000 2.24 0.00 0.00 3.66
1970 2008 3.260740 CAGAGCCTGTCATCTTCTTGAC 58.739 50.000 0.00 0.00 45.05 3.18
1988 2026 1.610673 GGGAGCTCCAGACCACAGA 60.611 63.158 33.29 0.00 37.91 3.41
1990 2028 2.204034 TGGGAGCTCCAGACCACA 59.796 61.111 33.29 18.23 41.46 4.17
2013 2051 1.011968 TGTTGATTCTTCGGGCGTCG 61.012 55.000 0.00 0.00 40.90 5.12
2022 2060 4.281435 TGCACACATCCATTGTTGATTCTT 59.719 37.500 0.00 0.00 36.00 2.52
2064 2102 2.989639 CCTGAAGCCGGGATGACA 59.010 61.111 2.18 0.00 41.53 3.58
2104 2142 1.216444 GCCTCAGCGTCATGTCAGA 59.784 57.895 0.00 0.00 0.00 3.27
2122 2160 1.409227 CTAGCTCTTGAGCGTGCACG 61.409 60.000 34.01 34.01 40.27 5.34
2127 2165 2.421751 TAGACCTAGCTCTTGAGCGT 57.578 50.000 15.74 8.79 40.27 5.07
2131 2169 4.411927 GGGATGATAGACCTAGCTCTTGA 58.588 47.826 0.00 0.00 0.00 3.02
2133 2171 3.426615 CGGGATGATAGACCTAGCTCTT 58.573 50.000 0.00 0.00 0.00 2.85
2144 2182 0.874175 TTCGTTGCGCGGGATGATAG 60.874 55.000 8.83 0.00 41.72 2.08
2232 2270 3.590574 ACAGGGGCCTTTGGGGAC 61.591 66.667 0.84 0.00 44.23 4.46
2238 2276 1.531602 GCAGTTCACAGGGGCCTTT 60.532 57.895 0.84 0.00 0.00 3.11
2240 2278 4.335647 CGCAGTTCACAGGGGCCT 62.336 66.667 0.84 0.00 0.00 5.19
2286 2324 2.858941 CTCAATGATGTCTCTGTGAGCG 59.141 50.000 0.00 0.00 31.06 5.03
2287 2325 2.608546 GCTCAATGATGTCTCTGTGAGC 59.391 50.000 7.62 7.62 44.33 4.26
2293 2331 1.206610 ACGCAGCTCAATGATGTCTCT 59.793 47.619 0.00 0.00 34.02 3.10
2304 2342 2.343758 GGTGAAGGACGCAGCTCA 59.656 61.111 0.00 0.00 0.00 4.26
2360 2398 4.389576 GCGACACTTGCAAGCCCG 62.390 66.667 26.27 24.28 0.00 6.13
2428 2475 3.637273 GCTTGGAGTCGGGGTGGT 61.637 66.667 0.00 0.00 0.00 4.16
2435 2482 3.003173 TGAGGGGGCTTGGAGTCG 61.003 66.667 0.00 0.00 0.00 4.18
2457 2504 2.997897 GGAGCCGACTGGTGGAGT 60.998 66.667 0.00 0.00 37.76 3.85
2481 2534 1.077858 TTGGTGCAGCAGTGTGACA 60.078 52.632 19.25 0.00 0.00 3.58
2482 2535 1.356624 GTTGGTGCAGCAGTGTGAC 59.643 57.895 19.25 10.25 0.00 3.67
2487 2540 2.567497 GGCATGTTGGTGCAGCAGT 61.567 57.895 19.25 6.69 46.81 4.40
2521 2574 1.670949 ATCGCCATGAGCTCGTCAGT 61.671 55.000 5.16 0.00 39.07 3.41
2540 2593 2.900546 GGAGTCTCTTCTGGAGTGGAAA 59.099 50.000 0.00 0.00 42.40 3.13
2580 2633 2.897326 CGTGGACATAGGGATGTGGATA 59.103 50.000 0.00 0.00 46.64 2.59
2685 2739 1.979155 CTGGCAGACGAGGTGGAGA 60.979 63.158 9.42 0.00 0.00 3.71
2696 2750 3.385384 CTCCTGGTCGCTGGCAGA 61.385 66.667 20.86 0.00 0.00 4.26
2702 2756 2.344203 CGTCTTCCTCCTGGTCGCT 61.344 63.158 0.00 0.00 34.23 4.93
2795 2849 1.712977 GCCTCTCTGCCATCTTTGCG 61.713 60.000 0.00 0.00 0.00 4.85
2816 2870 3.200593 CCCATGCGCTGACAGAGC 61.201 66.667 22.63 22.63 45.20 4.09
2867 2921 1.269517 GCAACGAACTTTCCAATGGCA 60.270 47.619 0.00 0.00 0.00 4.92
2876 2930 2.028130 TGGAACATGGCAACGAACTTT 58.972 42.857 0.00 0.00 42.51 2.66
2882 2936 0.893270 TTCCCTGGAACATGGCAACG 60.893 55.000 0.00 0.00 44.04 4.10
2937 2991 4.097741 CAGGTCACAATCAAGGTTGAACAA 59.902 41.667 0.00 0.00 41.13 2.83
2939 2993 3.004734 CCAGGTCACAATCAAGGTTGAAC 59.995 47.826 0.00 0.00 41.13 3.18
2958 3012 0.603707 TCTTCAACTGCCTTCGCCAG 60.604 55.000 0.00 0.00 0.00 4.85
2961 3015 0.179179 GCATCTTCAACTGCCTTCGC 60.179 55.000 0.00 0.00 32.15 4.70
2990 3044 2.825836 CCGGCTTCTCCACCATGC 60.826 66.667 0.00 0.00 34.01 4.06
3010 3064 3.777925 CCGTCGTTTGCAGCTCCG 61.778 66.667 0.00 0.00 0.00 4.63
3029 3083 4.710167 TCGTCGGCGACCTCCTGA 62.710 66.667 31.86 20.56 42.81 3.86
3030 3084 4.180946 CTCGTCGGCGACCTCCTG 62.181 72.222 31.86 18.61 42.81 3.86
3057 3111 4.431416 ACTGGAACAAACACAGTCCATA 57.569 40.909 0.00 0.00 41.27 2.74
3058 3112 3.297134 ACTGGAACAAACACAGTCCAT 57.703 42.857 0.00 0.00 41.27 3.41
3078 3132 6.525578 AACATAAGGAACAGAGTACATCGA 57.474 37.500 0.00 0.00 0.00 3.59
3088 3142 8.478877 AGAGGTTGTATCTAACATAAGGAACAG 58.521 37.037 0.00 0.00 38.10 3.16
3096 3150 6.776116 ACCATCGAGAGGTTGTATCTAACATA 59.224 38.462 6.52 0.00 38.10 2.29
3113 3167 0.798776 GCACAACCAGAACCATCGAG 59.201 55.000 0.00 0.00 0.00 4.04
3115 3169 1.586154 GGGCACAACCAGAACCATCG 61.586 60.000 0.00 0.00 42.05 3.84
3144 3234 1.062258 CACAACAAACATCGCCATGC 58.938 50.000 0.00 0.00 32.57 4.06
3185 3275 0.532862 CACCAGGAGAAGCAACACGT 60.533 55.000 0.00 0.00 0.00 4.49
3195 3285 3.069586 CAGAGTACAACAACACCAGGAGA 59.930 47.826 0.00 0.00 0.00 3.71
3332 3422 3.411808 GTGAATGGTAGCACGACGA 57.588 52.632 0.00 0.00 0.00 4.20
3342 3432 3.741029 CGATGGTCTCGTGAATGGT 57.259 52.632 0.00 0.00 42.56 3.55
3362 3452 1.913762 AAGGTGGCACGGAGTAGCT 60.914 57.895 12.17 0.00 41.61 3.32
3410 3500 1.337167 GCAGCAATGAAAGGGTCAACC 60.337 52.381 0.00 0.00 40.50 3.77
3440 3530 6.764379 AGCAAAGCTCTTAAGTCTATATCCC 58.236 40.000 1.63 0.00 30.62 3.85


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

AutoCloner maintained by Alex Coulton.