Multiple sequence alignment - TraesCS4A01G412900

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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 TraesCS4A01G412900 chr4A 100.000 2426 0 0 1 2426 684470199 684472624 0.000000e+00 4481.0
1 TraesCS4A01G412900 chr4A 90.896 703 39 14 852 1540 684449412 684448721 0.000000e+00 920.0
2 TraesCS4A01G412900 chr4A 95.580 181 7 1 664 843 684449825 684449645 3.050000e-74 289.0
3 TraesCS4A01G412900 chr4A 97.778 135 2 1 2293 2426 626134271 626134405 5.220000e-57 231.0
4 TraesCS4A01G412900 chr4D 90.060 1660 124 18 664 2303 477558693 477560331 0.000000e+00 2113.0
5 TraesCS4A01G412900 chr4D 92.136 852 50 9 654 1500 477543860 477543021 0.000000e+00 1186.0
6 TraesCS4A01G412900 chr4B 90.562 890 66 10 664 1540 603148128 603149012 0.000000e+00 1162.0
7 TraesCS4A01G412900 chr4B 91.507 836 59 9 668 1500 603037719 603038545 0.000000e+00 1140.0
8 TraesCS4A01G412900 chr4B 91.289 838 64 3 664 1500 602893894 602893065 0.000000e+00 1134.0
9 TraesCS4A01G412900 chr4B 91.211 842 61 7 664 1500 602873976 602873143 0.000000e+00 1133.0
10 TraesCS4A01G412900 chr4B 89.263 624 51 7 858 1476 603026251 603025639 0.000000e+00 767.0
11 TraesCS4A01G412900 chr4B 82.853 764 97 11 1546 2303 603162629 603163364 0.000000e+00 654.0
12 TraesCS4A01G412900 chr4B 91.030 301 20 4 654 948 603145300 603145001 1.350000e-107 399.0
13 TraesCS4A01G412900 chr4B 94.258 209 11 1 654 861 603028916 603028708 3.890000e-83 318.0
14 TraesCS4A01G412900 chr4B 92.208 77 6 0 1464 1540 603144486 603144410 2.550000e-20 110.0
15 TraesCS4A01G412900 chr5D 93.598 656 37 3 1 651 221003332 221003987 0.000000e+00 974.0
16 TraesCS4A01G412900 chr5D 76.955 243 53 3 2025 2266 75261467 75261227 4.210000e-28 135.0
17 TraesCS4A01G412900 chr5D 75.419 179 24 6 1855 2026 6370060 6370225 4.330000e-08 69.4
18 TraesCS4A01G412900 chr7A 93.009 658 38 7 1 650 370678086 370677429 0.000000e+00 953.0
19 TraesCS4A01G412900 chr7A 100.000 28 0 0 1706 1733 597566847 597566874 4.000000e-03 52.8
20 TraesCS4A01G412900 chr1D 92.846 657 39 5 1 650 556147 556802 0.000000e+00 946.0
21 TraesCS4A01G412900 chr3D 92.727 660 34 9 1 650 85274402 85273747 0.000000e+00 941.0
22 TraesCS4A01G412900 chr3D 80.827 266 49 2 2038 2303 515802967 515802704 8.790000e-50 207.0
23 TraesCS4A01G412900 chr3A 92.802 653 39 5 1 650 607113690 607113043 0.000000e+00 939.0
24 TraesCS4A01G412900 chr3A 92.214 655 46 5 1 650 577236195 577236849 0.000000e+00 922.0
25 TraesCS4A01G412900 chr3A 96.403 139 4 1 2289 2426 118697420 118697558 6.750000e-56 228.0
26 TraesCS4A01G412900 chr6A 92.758 649 42 5 1 644 537047457 537046809 0.000000e+00 933.0
27 TraesCS4A01G412900 chr6A 96.403 139 4 1 2289 2426 288353776 288353914 6.750000e-56 228.0
28 TraesCS4A01G412900 chr2A 92.436 661 37 10 1 651 89150367 89149710 0.000000e+00 931.0
29 TraesCS4A01G412900 chr2A 96.429 140 4 1 2288 2426 752530004 752530143 1.880000e-56 230.0
30 TraesCS4A01G412900 chr1A 92.226 656 41 6 1 652 384323258 384323907 0.000000e+00 920.0
31 TraesCS4A01G412900 chr1B 83.293 820 100 22 668 1473 401992690 401991894 0.000000e+00 721.0
32 TraesCS4A01G412900 chr7D 100.000 128 0 0 2299 2426 31975283 31975410 1.120000e-58 237.0
33 TraesCS4A01G412900 chr7D 97.778 135 3 0 2292 2426 21349203 21349337 1.450000e-57 233.0
34 TraesCS4A01G412900 chr6B 94.000 150 7 2 2278 2426 456278383 456278531 2.430000e-55 226.0
35 TraesCS4A01G412900 chr5A 94.483 145 6 2 2284 2426 31542174 31542030 3.140000e-54 222.0
36 TraesCS4A01G412900 chr2B 94.444 144 6 1 2283 2426 771237882 771237741 1.130000e-53 220.0
37 TraesCS4A01G412900 chr3B 78.889 180 26 9 1857 2026 721918815 721918638 7.090000e-21 111.0
38 TraesCS4A01G412900 chr2D 79.851 134 11 5 1895 2026 617110237 617110356 1.550000e-12 84.2


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 TraesCS4A01G412900 chr4A 684470199 684472624 2425 False 4481.0 4481 100.0000 1 2426 1 chr4A.!!$F2 2425
1 TraesCS4A01G412900 chr4A 684448721 684449825 1104 True 604.5 920 93.2380 664 1540 2 chr4A.!!$R1 876
2 TraesCS4A01G412900 chr4D 477558693 477560331 1638 False 2113.0 2113 90.0600 664 2303 1 chr4D.!!$F1 1639
3 TraesCS4A01G412900 chr4D 477543021 477543860 839 True 1186.0 1186 92.1360 654 1500 1 chr4D.!!$R1 846
4 TraesCS4A01G412900 chr4B 603148128 603149012 884 False 1162.0 1162 90.5620 664 1540 1 chr4B.!!$F2 876
5 TraesCS4A01G412900 chr4B 603037719 603038545 826 False 1140.0 1140 91.5070 668 1500 1 chr4B.!!$F1 832
6 TraesCS4A01G412900 chr4B 602893065 602893894 829 True 1134.0 1134 91.2890 664 1500 1 chr4B.!!$R2 836
7 TraesCS4A01G412900 chr4B 602873143 602873976 833 True 1133.0 1133 91.2110 664 1500 1 chr4B.!!$R1 836
8 TraesCS4A01G412900 chr4B 603162629 603163364 735 False 654.0 654 82.8530 1546 2303 1 chr4B.!!$F3 757
9 TraesCS4A01G412900 chr4B 603025639 603028916 3277 True 542.5 767 91.7605 654 1476 2 chr4B.!!$R3 822
10 TraesCS4A01G412900 chr4B 603144410 603145300 890 True 254.5 399 91.6190 654 1540 2 chr4B.!!$R4 886
11 TraesCS4A01G412900 chr5D 221003332 221003987 655 False 974.0 974 93.5980 1 651 1 chr5D.!!$F2 650
12 TraesCS4A01G412900 chr7A 370677429 370678086 657 True 953.0 953 93.0090 1 650 1 chr7A.!!$R1 649
13 TraesCS4A01G412900 chr1D 556147 556802 655 False 946.0 946 92.8460 1 650 1 chr1D.!!$F1 649
14 TraesCS4A01G412900 chr3D 85273747 85274402 655 True 941.0 941 92.7270 1 650 1 chr3D.!!$R1 649
15 TraesCS4A01G412900 chr3A 607113043 607113690 647 True 939.0 939 92.8020 1 650 1 chr3A.!!$R1 649
16 TraesCS4A01G412900 chr3A 577236195 577236849 654 False 922.0 922 92.2140 1 650 1 chr3A.!!$F2 649
17 TraesCS4A01G412900 chr6A 537046809 537047457 648 True 933.0 933 92.7580 1 644 1 chr6A.!!$R1 643
18 TraesCS4A01G412900 chr2A 89149710 89150367 657 True 931.0 931 92.4360 1 651 1 chr2A.!!$R1 650
19 TraesCS4A01G412900 chr1A 384323258 384323907 649 False 920.0 920 92.2260 1 652 1 chr1A.!!$F1 651
20 TraesCS4A01G412900 chr1B 401991894 401992690 796 True 721.0 721 83.2930 668 1473 1 chr1B.!!$R1 805

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
973 3703 0.325203 ACCCAAACCCAAAGCACTGT 60.325 50.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2218 5012 0.257328 TTCCTTGTGTGGCACTTCCA 59.743 50.0 19.83 9.94 44.18 3.53 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
50 51 0.615331 GGGTGCTGGACTTGATCTCA 59.385 55.000 0.00 0.00 0.00 3.27
239 241 1.439644 GTCGAGGAGTGAGGCCATC 59.560 63.158 5.01 0.00 0.00 3.51
368 372 7.333528 AGTTGTGGTGGCAAATATAATACAG 57.666 36.000 0.00 0.00 0.00 2.74
370 374 6.935741 TGTGGTGGCAAATATAATACAGAC 57.064 37.500 0.00 0.00 0.00 3.51
371 375 6.658849 TGTGGTGGCAAATATAATACAGACT 58.341 36.000 0.00 0.00 0.00 3.24
416 420 2.666022 CGTGTGCGTGTGAAATAGATGA 59.334 45.455 0.00 0.00 0.00 2.92
512 527 3.194620 AGAGGAAGGGAGAGAGAGTGTA 58.805 50.000 0.00 0.00 0.00 2.90
516 531 4.479056 AGGAAGGGAGAGAGAGTGTATGTA 59.521 45.833 0.00 0.00 0.00 2.29
652 672 3.363280 CGCACGGGTGTTCTTTTAGTTAC 60.363 47.826 0.25 0.00 0.00 2.50
820 851 1.219124 GCAGTCTCCAAGCCGATCA 59.781 57.895 0.00 0.00 0.00 2.92
868 3587 3.393800 GCACACATGCCTAATCGACTAT 58.606 45.455 0.00 0.00 46.97 2.12
950 3680 2.764572 TCTCTCAAGCTCTCATGCATCA 59.235 45.455 0.00 0.00 34.99 3.07
961 3691 3.005684 TCTCATGCATCACAAACCCAAAC 59.994 43.478 0.00 0.00 0.00 2.93
962 3692 2.036992 TCATGCATCACAAACCCAAACC 59.963 45.455 0.00 0.00 0.00 3.27
963 3693 0.755686 TGCATCACAAACCCAAACCC 59.244 50.000 0.00 0.00 0.00 4.11
964 3694 0.755686 GCATCACAAACCCAAACCCA 59.244 50.000 0.00 0.00 0.00 4.51
965 3695 1.139853 GCATCACAAACCCAAACCCAA 59.860 47.619 0.00 0.00 0.00 4.12
966 3696 2.420687 GCATCACAAACCCAAACCCAAA 60.421 45.455 0.00 0.00 0.00 3.28
972 3702 0.829990 AACCCAAACCCAAAGCACTG 59.170 50.000 0.00 0.00 0.00 3.66
973 3703 0.325203 ACCCAAACCCAAAGCACTGT 60.325 50.000 0.00 0.00 0.00 3.55
981 3718 2.237392 ACCCAAAGCACTGTCTATCCTC 59.763 50.000 0.00 0.00 0.00 3.71
1027 3769 0.108472 CAGAGCTGCCATCTTCGTCA 60.108 55.000 0.00 0.00 0.00 4.35
1054 3796 3.997400 CTCCTCCTCTCCGCCGTCA 62.997 68.421 0.00 0.00 0.00 4.35
1122 3867 2.359354 CCGCCCATTGTCGTTCCA 60.359 61.111 0.00 0.00 0.00 3.53
1199 3947 0.320771 CTAAAGCTGAGGGTGTGCGT 60.321 55.000 0.00 0.00 0.00 5.24
1234 3982 2.922503 TGCTCGGCCTCAAGGTCA 60.923 61.111 0.00 0.00 40.62 4.02
1297 4045 3.289062 TCGACCTTGACGCCGTCA 61.289 61.111 17.22 17.22 41.09 4.35
1333 4081 2.525629 TCAGGGCCAACGTCCTCA 60.526 61.111 6.18 0.00 0.00 3.86
1517 4302 4.900684 TCGTGTCCACATTTGAATCCTTA 58.099 39.130 0.00 0.00 0.00 2.69
1523 4308 6.317642 TGTCCACATTTGAATCCTTATAACCG 59.682 38.462 0.00 0.00 0.00 4.44
1599 4384 5.765182 CACATGGAACCTGAGTAATAATCCC 59.235 44.000 0.00 0.00 0.00 3.85
1638 4425 0.924090 CGATGCACGGTAGCTCTTTC 59.076 55.000 0.00 0.00 38.46 2.62
1673 4460 8.792538 CCGTAGTAAGTAAAATCACTAAGAACG 58.207 37.037 0.00 0.00 0.00 3.95
1711 4498 0.248702 AACGAACGCGCCATTTGTTT 60.249 45.000 15.62 0.00 42.48 2.83
1734 4521 3.926821 TTTTTGTCTATTTGGGTCGGC 57.073 42.857 0.00 0.00 0.00 5.54
1735 4522 2.570415 TTTGTCTATTTGGGTCGGCA 57.430 45.000 0.00 0.00 0.00 5.69
1736 4523 2.799126 TTGTCTATTTGGGTCGGCAT 57.201 45.000 0.00 0.00 0.00 4.40
1740 4527 0.307760 CTATTTGGGTCGGCATTCGC 59.692 55.000 0.00 0.00 39.05 4.70
1797 4584 2.435938 CGCCCAACGCATACACCT 60.436 61.111 0.00 0.00 37.30 4.00
1800 4587 0.944386 GCCCAACGCATACACCTATG 59.056 55.000 0.00 0.00 37.47 2.23
1848 4642 0.037882 CCGCGGTCATAGATCATGCT 60.038 55.000 19.50 0.00 34.35 3.79
1851 4645 3.515630 CGCGGTCATAGATCATGCTAAT 58.484 45.455 0.00 0.00 34.35 1.73
1853 4647 4.498241 GCGGTCATAGATCATGCTAATGA 58.502 43.478 0.00 0.00 46.71 2.57
1864 4658 2.732844 TGCTAATGACCATGCCATCA 57.267 45.000 0.00 0.00 0.00 3.07
1866 4660 2.092267 TGCTAATGACCATGCCATCACT 60.092 45.455 0.00 0.00 0.00 3.41
1879 4673 2.680221 GCCATCACTCAGAGTTCATGCT 60.680 50.000 0.00 0.00 0.00 3.79
1881 4675 3.369157 CCATCACTCAGAGTTCATGCTGA 60.369 47.826 0.00 0.00 38.72 4.26
1884 4678 1.615883 ACTCAGAGTTCATGCTGACGT 59.384 47.619 0.00 0.00 36.31 4.34
1889 4683 2.232208 AGAGTTCATGCTGACGTCATGA 59.768 45.455 20.40 17.12 45.91 3.07
1907 4701 1.779025 GACAGCCATACATGCCAGCG 61.779 60.000 0.00 0.00 0.00 5.18
1974 4768 0.823356 AACACACATCCCAGCACACC 60.823 55.000 0.00 0.00 0.00 4.16
1980 4774 1.688197 ACATCCCAGCACACCAAAAAG 59.312 47.619 0.00 0.00 0.00 2.27
2047 4841 2.286121 ATTTCCTCTGGCCCCCGA 60.286 61.111 0.00 0.00 0.00 5.14
2068 4862 2.207988 AGGATGATCCACCCATCACAA 58.792 47.619 14.90 0.00 41.52 3.33
2146 4940 1.672854 CTACGGTGAGCATTCCCCGA 61.673 60.000 3.93 0.00 43.01 5.14
2179 4973 2.508526 GCTTGCGGATAGGGATGAAAT 58.491 47.619 0.00 0.00 0.00 2.17
2200 4994 1.895707 GGGAATCAGAGGCATGGCG 60.896 63.158 14.30 0.00 0.00 5.69
2232 5026 0.546122 AACTCTGGAAGTGCCACACA 59.454 50.000 0.00 0.00 43.33 3.72
2242 5036 1.109323 GTGCCACACAAGGAAAGGCT 61.109 55.000 0.00 0.00 45.42 4.58
2303 5097 2.912025 CGTGCTGGCCTGGGTTTT 60.912 61.111 12.06 0.00 0.00 2.43
2304 5098 2.736531 GTGCTGGCCTGGGTTTTG 59.263 61.111 12.06 0.00 0.00 2.44
2305 5099 1.832167 GTGCTGGCCTGGGTTTTGA 60.832 57.895 12.06 0.00 0.00 2.69
2306 5100 1.075674 TGCTGGCCTGGGTTTTGAA 60.076 52.632 12.06 0.00 0.00 2.69
2307 5101 1.114722 TGCTGGCCTGGGTTTTGAAG 61.115 55.000 12.06 0.00 0.00 3.02
2308 5102 1.820010 GCTGGCCTGGGTTTTGAAGG 61.820 60.000 12.06 0.00 0.00 3.46
2309 5103 0.178964 CTGGCCTGGGTTTTGAAGGA 60.179 55.000 3.32 0.00 0.00 3.36
2310 5104 0.263172 TGGCCTGGGTTTTGAAGGAA 59.737 50.000 3.32 0.00 0.00 3.36
2311 5105 1.343478 TGGCCTGGGTTTTGAAGGAAA 60.343 47.619 3.32 0.00 0.00 3.13
2312 5106 1.977854 GGCCTGGGTTTTGAAGGAAAT 59.022 47.619 0.00 0.00 0.00 2.17
2313 5107 3.169908 GGCCTGGGTTTTGAAGGAAATA 58.830 45.455 0.00 0.00 0.00 1.40
2314 5108 3.774766 GGCCTGGGTTTTGAAGGAAATAT 59.225 43.478 0.00 0.00 0.00 1.28
2315 5109 4.383010 GGCCTGGGTTTTGAAGGAAATATG 60.383 45.833 0.00 0.00 0.00 1.78
2316 5110 4.758688 CCTGGGTTTTGAAGGAAATATGC 58.241 43.478 0.00 0.00 0.00 3.14
2317 5111 4.383010 CCTGGGTTTTGAAGGAAATATGCC 60.383 45.833 0.00 0.00 0.00 4.40
2318 5112 3.517500 TGGGTTTTGAAGGAAATATGCCC 59.482 43.478 0.00 0.00 0.00 5.36
2319 5113 3.774766 GGGTTTTGAAGGAAATATGCCCT 59.225 43.478 0.00 0.00 0.00 5.19
2320 5114 4.959839 GGGTTTTGAAGGAAATATGCCCTA 59.040 41.667 0.00 0.00 31.36 3.53
2321 5115 5.069119 GGGTTTTGAAGGAAATATGCCCTAG 59.931 44.000 0.00 0.00 31.36 3.02
2322 5116 5.891551 GGTTTTGAAGGAAATATGCCCTAGA 59.108 40.000 0.00 0.00 31.36 2.43
2323 5117 6.039829 GGTTTTGAAGGAAATATGCCCTAGAG 59.960 42.308 0.00 0.00 31.36 2.43
2324 5118 4.982241 TGAAGGAAATATGCCCTAGAGG 57.018 45.455 0.00 0.00 39.47 3.69
2400 5194 9.851686 ATTCATGCTAGAATTGTATTAACTGGA 57.148 29.630 0.00 0.00 34.70 3.86
2401 5195 9.679661 TTCATGCTAGAATTGTATTAACTGGAA 57.320 29.630 0.00 0.00 0.00 3.53
2402 5196 9.679661 TCATGCTAGAATTGTATTAACTGGAAA 57.320 29.630 0.00 0.00 0.00 3.13
2403 5197 9.722056 CATGCTAGAATTGTATTAACTGGAAAC 57.278 33.333 0.00 0.00 0.00 2.78
2404 5198 8.856153 TGCTAGAATTGTATTAACTGGAAACA 57.144 30.769 0.00 0.00 39.59 2.83
2405 5199 9.461312 TGCTAGAATTGTATTAACTGGAAACAT 57.539 29.630 0.00 0.00 41.51 2.71
2418 5212 7.994425 AACTGGAAACATAATACATGTGTGA 57.006 32.000 9.11 0.00 41.51 3.58
2419 5213 7.994425 ACTGGAAACATAATACATGTGTGAA 57.006 32.000 9.11 0.00 41.51 3.18
2420 5214 8.579850 ACTGGAAACATAATACATGTGTGAAT 57.420 30.769 9.11 0.00 41.51 2.57
2421 5215 9.679661 ACTGGAAACATAATACATGTGTGAATA 57.320 29.630 9.11 0.00 41.51 1.75
2422 5216 9.935682 CTGGAAACATAATACATGTGTGAATAC 57.064 33.333 9.11 0.00 41.51 1.89
2423 5217 9.454859 TGGAAACATAATACATGTGTGAATACA 57.545 29.630 9.11 1.84 33.40 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.084370 GCTACTTCGTCTGCGCCAAT 61.084 55.000 4.18 0.00 38.14 3.16
328 332 4.451900 CACAACTTATATTTCCCCGAGCT 58.548 43.478 0.00 0.00 0.00 4.09
368 372 7.009631 CGCTAGTGCATAACAATATGGATAGTC 59.990 40.741 0.00 0.00 41.20 2.59
370 374 6.237942 GCGCTAGTGCATAACAATATGGATAG 60.238 42.308 23.15 2.11 41.20 2.08
371 375 5.580691 GCGCTAGTGCATAACAATATGGATA 59.419 40.000 23.15 0.00 41.20 2.59
416 420 7.324388 TCTTATTGGGTACGGGATCATAATT 57.676 36.000 0.00 0.00 0.00 1.40
474 487 3.076785 TCCTCTTCCTCACTTTCTCTCCT 59.923 47.826 0.00 0.00 0.00 3.69
482 497 2.112691 TCTCCCTTCCTCTTCCTCACTT 59.887 50.000 0.00 0.00 0.00 3.16
652 672 9.184523 TCATCCATGTTAACCATAGTTTTAAGG 57.815 33.333 2.48 0.00 37.42 2.69
666 686 4.160065 CCCTTGCATGTTCATCCATGTTAA 59.840 41.667 0.00 0.00 43.33 2.01
820 851 0.675208 TACGTGGCCATGTGCGATTT 60.675 50.000 35.93 13.49 42.61 2.17
861 1120 2.037902 TGGAACTGTTTGGCATAGTCGA 59.962 45.455 0.00 0.00 0.00 4.20
868 3587 0.187117 TGGGATGGAACTGTTTGGCA 59.813 50.000 0.00 0.00 0.00 4.92
904 3631 4.259356 GTTGTATTTATAGCCGGGGGATC 58.741 47.826 2.18 0.00 0.00 3.36
950 3680 1.065782 GTGCTTTGGGTTTGGGTTTGT 60.066 47.619 0.00 0.00 0.00 2.83
961 3691 2.420687 GGAGGATAGACAGTGCTTTGGG 60.421 54.545 0.00 0.00 0.00 4.12
962 3692 2.503356 AGGAGGATAGACAGTGCTTTGG 59.497 50.000 0.00 0.00 0.00 3.28
963 3693 3.196469 TGAGGAGGATAGACAGTGCTTTG 59.804 47.826 0.00 0.00 0.00 2.77
964 3694 3.445008 TGAGGAGGATAGACAGTGCTTT 58.555 45.455 0.00 0.00 0.00 3.51
965 3695 3.107402 TGAGGAGGATAGACAGTGCTT 57.893 47.619 0.00 0.00 0.00 3.91
966 3696 2.836636 TGAGGAGGATAGACAGTGCT 57.163 50.000 0.00 0.00 0.00 4.40
972 3702 2.480416 CGTGTGCTTGAGGAGGATAGAC 60.480 54.545 0.00 0.00 0.00 2.59
973 3703 1.751351 CGTGTGCTTGAGGAGGATAGA 59.249 52.381 0.00 0.00 0.00 1.98
1027 3769 2.236959 GAGAGGAGGAGGCTCAGGGT 62.237 65.000 17.69 0.00 0.00 4.34
1333 4081 2.573869 CACGTCGAGGTGGATGCT 59.426 61.111 26.51 0.00 34.27 3.79
1517 4302 8.367156 TGTTACAAAAAGAGTAGTACCGGTTAT 58.633 33.333 15.04 4.05 0.00 1.89
1599 4384 2.541346 CGAAGCCTGCCATATATATGCG 59.459 50.000 16.08 10.88 32.40 4.73
1638 4425 9.537192 TGATTTTACTTACTACGGACAATATGG 57.463 33.333 0.00 0.00 0.00 2.74
1673 4460 2.775032 TTAGTGGGCGCGTTGGAGTC 62.775 60.000 8.43 0.00 0.00 3.36
1687 4474 0.165079 AATGGCGCGTTCGTTTAGTG 59.835 50.000 8.43 0.00 38.14 2.74
1722 4509 2.399856 GCGAATGCCGACCCAAATA 58.600 52.632 0.00 0.00 41.76 1.40
1723 4510 3.196648 GCGAATGCCGACCCAAAT 58.803 55.556 0.00 0.00 41.76 2.32
1790 4577 2.047061 ACGGGCATGACATAGGTGTAT 58.953 47.619 0.00 0.00 39.09 2.29
1797 4584 8.678593 TTAAAATTATGTACGGGCATGACATA 57.321 30.769 0.00 0.12 35.48 2.29
1800 4587 8.690680 TTTTTAAAATTATGTACGGGCATGAC 57.309 30.769 0.55 0.00 0.00 3.06
1826 4620 1.270826 CATGATCTATGACCGCGGACT 59.729 52.381 35.90 17.88 39.21 3.85
1848 4642 3.455543 TCTGAGTGATGGCATGGTCATTA 59.544 43.478 3.81 0.00 0.00 1.90
1851 4645 1.208776 CTCTGAGTGATGGCATGGTCA 59.791 52.381 3.81 3.74 0.00 4.02
1853 4647 1.283347 ACTCTGAGTGATGGCATGGT 58.717 50.000 10.00 0.00 0.00 3.55
1879 4673 1.548269 TGTATGGCTGTCATGACGTCA 59.452 47.619 22.48 22.48 37.30 4.35
1881 4675 2.554142 CATGTATGGCTGTCATGACGT 58.446 47.619 20.54 6.99 40.64 4.34
1917 4711 1.501169 CAGCGTGAACTGTGTGATGA 58.499 50.000 0.00 0.00 32.78 2.92
1920 4714 1.887242 GCCAGCGTGAACTGTGTGA 60.887 57.895 0.00 0.00 35.83 3.58
1985 4779 2.025887 AGATGGTGTGATTGAACTCCCC 60.026 50.000 0.00 0.00 33.61 4.81
2010 4804 4.758251 CCGCTGGCATGACCACGA 62.758 66.667 20.81 0.00 46.36 4.35
2047 4841 2.207988 TGTGATGGGTGGATCATCCTT 58.792 47.619 4.96 0.00 40.02 3.36
2068 4862 0.615331 ATCGACCTCAATGCCACACT 59.385 50.000 0.00 0.00 0.00 3.55
2113 4907 1.596934 CGTAGGTGAGCATGGTGGT 59.403 57.895 0.00 0.00 0.00 4.16
2146 4940 1.515521 CGCAAGCCTCCCGTTTTCTT 61.516 55.000 0.00 0.00 0.00 2.52
2179 4973 1.699054 CCATGCCTCTGATTCCCGGA 61.699 60.000 0.73 0.00 0.00 5.14
2218 5012 0.257328 TTCCTTGTGTGGCACTTCCA 59.743 50.000 19.83 9.94 44.18 3.53
2303 5097 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
2315 5109 8.637196 AATAACTTTATTATTGCCTCTAGGGC 57.363 34.615 13.60 13.60 44.71 5.19
2374 5168 9.851686 TCCAGTTAATACAATTCTAGCATGAAT 57.148 29.630 0.00 0.00 38.19 2.57
2375 5169 9.679661 TTCCAGTTAATACAATTCTAGCATGAA 57.320 29.630 0.00 0.00 0.00 2.57
2376 5170 9.679661 TTTCCAGTTAATACAATTCTAGCATGA 57.320 29.630 0.00 0.00 0.00 3.07
2377 5171 9.722056 GTTTCCAGTTAATACAATTCTAGCATG 57.278 33.333 0.00 0.00 0.00 4.06
2378 5172 9.461312 TGTTTCCAGTTAATACAATTCTAGCAT 57.539 29.630 0.00 0.00 0.00 3.79
2379 5173 8.856153 TGTTTCCAGTTAATACAATTCTAGCA 57.144 30.769 0.00 0.00 0.00 3.49
2392 5186 9.508642 TCACACATGTATTATGTTTCCAGTTAA 57.491 29.630 0.00 0.00 0.00 2.01
2393 5187 9.508642 TTCACACATGTATTATGTTTCCAGTTA 57.491 29.630 0.00 0.00 0.00 2.24
2394 5188 7.994425 TCACACATGTATTATGTTTCCAGTT 57.006 32.000 0.00 0.00 0.00 3.16
2395 5189 7.994425 TTCACACATGTATTATGTTTCCAGT 57.006 32.000 0.00 0.00 0.00 4.00
2396 5190 9.935682 GTATTCACACATGTATTATGTTTCCAG 57.064 33.333 0.00 0.00 0.00 3.86
2397 5191 9.454859 TGTATTCACACATGTATTATGTTTCCA 57.545 29.630 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.