Multiple sequence alignment - TraesCS5B01G527100

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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 TraesCS5B01G527100 chr5B 100.000 3466 0 0 1 3466 686431143 686434608 0.000000e+00 6401
1 TraesCS5B01G527100 chr5B 85.893 1517 188 14 1094 2605 686201105 686202600 0.000000e+00 1592
2 TraesCS5B01G527100 chr5B 88.074 914 89 12 1693 2605 686342920 686343814 0.000000e+00 1066
3 TraesCS5B01G527100 chr5B 93.124 669 39 3 1027 1695 686333911 686334572 0.000000e+00 974
4 TraesCS5B01G527100 chr5B 98.485 132 2 0 902 1033 686333743 686333874 2.080000e-57 233
5 TraesCS5B01G527100 chr5B 87.302 126 9 2 2781 2900 686202886 686203010 1.680000e-28 137
6 TraesCS5B01G527100 chr5B 93.827 81 3 1 831 909 602839828 602839748 1.690000e-23 121
7 TraesCS5B01G527100 chr5D 92.822 2466 133 25 1027 3463 544231401 544233851 0.000000e+00 3533
8 TraesCS5B01G527100 chr5D 86.406 1508 180 13 1094 2591 544148965 544150457 0.000000e+00 1626
9 TraesCS5B01G527100 chr5D 78.824 1327 250 16 1095 2416 544481609 544482909 0.000000e+00 865
10 TraesCS5B01G527100 chr5D 77.601 1317 272 14 1095 2410 544459877 544461171 0.000000e+00 776
11 TraesCS5B01G527100 chr5D 83.051 295 50 0 1093 1387 543803615 543803909 5.700000e-68 268
12 TraesCS5B01G527100 chr5D 81.356 295 55 0 1093 1387 543771938 543772232 1.240000e-59 241
13 TraesCS5B01G527100 chr5D 88.095 126 8 2 2781 2900 544150749 544150873 3.610000e-30 143
14 TraesCS5B01G527100 chr5D 86.458 96 13 0 1842 1937 450204396 450204301 4.730000e-19 106
15 TraesCS5B01G527100 chr4A 92.345 2469 146 28 1027 3466 625077687 625075233 0.000000e+00 3472
16 TraesCS5B01G527100 chr4A 85.573 1518 199 9 1094 2605 625166245 625164742 0.000000e+00 1572
17 TraesCS5B01G527100 chr4A 98.113 424 8 0 394 817 693426478 693426901 0.000000e+00 739
18 TraesCS5B01G527100 chr4A 78.736 1044 206 10 1095 2127 624992940 624991902 0.000000e+00 684
19 TraesCS5B01G527100 chr4A 73.995 423 98 7 1819 2233 625372439 625372021 9.960000e-36 161
20 TraesCS5B01G527100 chr7B 93.795 838 18 12 1 816 693387055 693386230 0.000000e+00 1229
21 TraesCS5B01G527100 chr7B 95.413 654 19 7 174 816 698923264 698922611 0.000000e+00 1031
22 TraesCS5B01G527100 chr7B 78.082 292 52 6 3152 3442 20964239 20963959 1.280000e-39 174
23 TraesCS5B01G527100 chr7B 94.872 78 2 1 831 906 557179530 557179453 1.690000e-23 121
24 TraesCS5B01G527100 chr7B 94.872 78 2 1 831 906 652967521 652967444 1.690000e-23 121
25 TraesCS5B01G527100 chr2B 88.782 829 40 19 1 816 788663257 788662469 0.000000e+00 966
26 TraesCS5B01G527100 chr2B 98.357 426 4 1 394 816 617149551 617149976 0.000000e+00 745
27 TraesCS5B01G527100 chr2B 98.345 423 4 1 397 816 752930820 752930398 0.000000e+00 739
28 TraesCS5B01G527100 chr2B 97.887 426 6 1 394 816 369806876 369807301 0.000000e+00 734
29 TraesCS5B01G527100 chr2B 94.195 379 11 2 1 371 794225118 794225493 5.020000e-158 568
30 TraesCS5B01G527100 chr2B 89.514 391 18 5 1 374 123280457 123280073 1.130000e-129 473
31 TraesCS5B01G527100 chr2B 96.053 76 3 0 831 906 24249302 24249377 1.310000e-24 124
32 TraesCS5B01G527100 chr2B 85.593 118 15 2 1840 1956 390364316 390364200 4.700000e-24 122
33 TraesCS5B01G527100 chr4B 99.050 421 4 0 397 817 640825968 640825548 0.000000e+00 756
34 TraesCS5B01G527100 chr4B 97.907 430 6 1 390 816 28266075 28265646 0.000000e+00 741
35 TraesCS5B01G527100 chr4B 97.333 75 2 0 831 905 5837672 5837598 1.010000e-25 128
36 TraesCS5B01G527100 chr6B 98.122 426 5 1 394 816 704691064 704691489 0.000000e+00 739
37 TraesCS5B01G527100 chr6B 97.892 427 6 1 394 817 566153580 566154006 0.000000e+00 736
38 TraesCS5B01G527100 chr6B 89.460 389 20 4 1 374 98596036 98595654 4.050000e-129 472
39 TraesCS5B01G527100 chr6B 98.592 71 1 0 831 901 502744764 502744834 3.630000e-25 126
40 TraesCS5B01G527100 chr6B 96.104 77 1 1 831 905 591189104 591189028 1.310000e-24 124
41 TraesCS5B01G527100 chr6A 89.031 392 16 7 1 371 584520595 584520980 8.760000e-126 460
42 TraesCS5B01G527100 chr1A 88.608 395 18 11 1 374 557161854 557161466 4.080000e-124 455
43 TraesCS5B01G527100 chr7A 88.041 393 22 9 1 374 515741331 515740945 3.170000e-120 442
44 TraesCS5B01G527100 chr3A 86.632 389 26 10 1 374 143020963 143020586 1.160000e-109 407
45 TraesCS5B01G527100 chr1B 97.368 76 2 0 831 906 633529082 633529007 2.810000e-26 130
46 TraesCS5B01G527100 chr3B 96.000 75 3 0 831 905 607293621 607293547 4.700000e-24 122
47 TraesCS5B01G527100 chr5A 72.902 417 81 18 1826 2224 569544330 569543928 7.860000e-22 115


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 TraesCS5B01G527100 chr5B 686431143 686434608 3465 False 6401.0 6401 100.0000 1 3466 1 chr5B.!!$F2 3465
1 TraesCS5B01G527100 chr5B 686342920 686343814 894 False 1066.0 1066 88.0740 1693 2605 1 chr5B.!!$F1 912
2 TraesCS5B01G527100 chr5B 686201105 686203010 1905 False 864.5 1592 86.5975 1094 2900 2 chr5B.!!$F3 1806
3 TraesCS5B01G527100 chr5B 686333743 686334572 829 False 603.5 974 95.8045 902 1695 2 chr5B.!!$F4 793
4 TraesCS5B01G527100 chr5D 544231401 544233851 2450 False 3533.0 3533 92.8220 1027 3463 1 chr5D.!!$F3 2436
5 TraesCS5B01G527100 chr5D 544148965 544150873 1908 False 884.5 1626 87.2505 1094 2900 2 chr5D.!!$F6 1806
6 TraesCS5B01G527100 chr5D 544481609 544482909 1300 False 865.0 865 78.8240 1095 2416 1 chr5D.!!$F5 1321
7 TraesCS5B01G527100 chr5D 544459877 544461171 1294 False 776.0 776 77.6010 1095 2410 1 chr5D.!!$F4 1315
8 TraesCS5B01G527100 chr4A 625075233 625077687 2454 True 3472.0 3472 92.3450 1027 3466 1 chr4A.!!$R2 2439
9 TraesCS5B01G527100 chr4A 625164742 625166245 1503 True 1572.0 1572 85.5730 1094 2605 1 chr4A.!!$R3 1511
10 TraesCS5B01G527100 chr4A 624991902 624992940 1038 True 684.0 684 78.7360 1095 2127 1 chr4A.!!$R1 1032
11 TraesCS5B01G527100 chr7B 693386230 693387055 825 True 1229.0 1229 93.7950 1 816 1 chr7B.!!$R4 815
12 TraesCS5B01G527100 chr7B 698922611 698923264 653 True 1031.0 1031 95.4130 174 816 1 chr7B.!!$R5 642
13 TraesCS5B01G527100 chr2B 788662469 788663257 788 True 966.0 966 88.7820 1 816 1 chr2B.!!$R4 815

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
834 876 0.038343 GCTGGAGCGGCATTTCAAAA 60.038 50.0 1.45 0.00 35.55 2.44 F
2262 2365 0.036164 ATAAAGTGACGGGCTGCACA 59.964 50.0 18.56 6.67 37.48 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2316 2419 0.033504 ATACCGTATTGCTGCTCCCG 59.966 55.0 0.0 0.0 0.0 5.14 R
3305 3575 0.324943 CGACCCACACCCAATCTCTT 59.675 55.0 0.0 0.0 0.0 2.85 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
372 403 2.087462 AAAAAGCTTGCAGGGCGTCC 62.087 55.000 0.00 0.00 34.52 4.79
380 411 4.735132 CAGGGCGTCCGCGAAGAA 62.735 66.667 8.23 0.00 43.06 2.52
381 412 4.436998 AGGGCGTCCGCGAAGAAG 62.437 66.667 8.23 0.00 43.06 2.85
382 413 4.430765 GGGCGTCCGCGAAGAAGA 62.431 66.667 8.23 0.00 43.06 2.87
383 414 2.431942 GGCGTCCGCGAAGAAGAA 60.432 61.111 8.23 0.00 43.06 2.52
384 415 2.727684 GGCGTCCGCGAAGAAGAAC 61.728 63.158 8.23 0.00 43.06 3.01
385 416 2.019951 GCGTCCGCGAAGAAGAACA 61.020 57.895 8.23 0.00 41.33 3.18
386 417 1.554042 GCGTCCGCGAAGAAGAACAA 61.554 55.000 8.23 0.00 41.33 2.83
387 418 0.435008 CGTCCGCGAAGAAGAACAAG 59.565 55.000 8.23 0.00 41.33 3.16
388 419 0.790814 GTCCGCGAAGAAGAACAAGG 59.209 55.000 8.23 0.00 0.00 3.61
389 420 0.949105 TCCGCGAAGAAGAACAAGGC 60.949 55.000 8.23 0.00 0.00 4.35
390 421 0.951040 CCGCGAAGAAGAACAAGGCT 60.951 55.000 8.23 0.00 0.00 4.58
392 423 0.799393 GCGAAGAAGAACAAGGCTCC 59.201 55.000 0.00 0.00 0.00 4.70
393 424 1.071605 CGAAGAAGAACAAGGCTCCG 58.928 55.000 0.00 0.00 0.00 4.63
394 425 1.443802 GAAGAAGAACAAGGCTCCGG 58.556 55.000 0.00 0.00 0.00 5.14
395 426 0.606673 AAGAAGAACAAGGCTCCGGC 60.607 55.000 0.00 0.00 37.82 6.13
537 576 3.188100 CGTGATGCGGTGCGTGAT 61.188 61.111 0.00 0.00 36.85 3.06
540 579 1.375268 TGATGCGGTGCGTGATGAA 60.375 52.632 0.00 0.00 0.00 2.57
830 872 2.796651 CTGCTGGAGCGGCATTTC 59.203 61.111 1.45 0.00 45.18 2.17
831 873 2.033911 TGCTGGAGCGGCATTTCA 59.966 55.556 1.45 0.00 41.16 2.69
832 874 1.588824 CTGCTGGAGCGGCATTTCAA 61.589 55.000 1.45 0.00 45.18 2.69
833 875 1.177895 TGCTGGAGCGGCATTTCAAA 61.178 50.000 1.45 0.00 41.16 2.69
834 876 0.038343 GCTGGAGCGGCATTTCAAAA 60.038 50.000 1.45 0.00 35.55 2.44
835 877 1.701704 CTGGAGCGGCATTTCAAAAC 58.298 50.000 1.45 0.00 0.00 2.43
836 878 0.316841 TGGAGCGGCATTTCAAAACC 59.683 50.000 1.45 0.00 0.00 3.27
837 879 0.316841 GGAGCGGCATTTCAAAACCA 59.683 50.000 1.45 0.00 0.00 3.67
838 880 1.669795 GGAGCGGCATTTCAAAACCAG 60.670 52.381 1.45 0.00 0.00 4.00
839 881 0.319813 AGCGGCATTTCAAAACCAGC 60.320 50.000 1.45 0.00 0.00 4.85
840 882 1.291184 GCGGCATTTCAAAACCAGCC 61.291 55.000 0.00 0.00 38.73 4.85
841 883 2.826277 GGCATTTCAAAACCAGCCG 58.174 52.632 0.00 0.00 31.88 5.52
842 884 1.291184 GGCATTTCAAAACCAGCCGC 61.291 55.000 0.00 0.00 31.88 6.53
843 885 0.599728 GCATTTCAAAACCAGCCGCA 60.600 50.000 0.00 0.00 0.00 5.69
844 886 1.421382 CATTTCAAAACCAGCCGCAG 58.579 50.000 0.00 0.00 0.00 5.18
845 887 0.319813 ATTTCAAAACCAGCCGCAGC 60.320 50.000 0.00 0.00 40.32 5.25
846 888 2.676016 TTTCAAAACCAGCCGCAGCG 62.676 55.000 8.18 8.18 46.67 5.18
861 903 4.084888 GCGCGCGCTAACAGGTTT 62.085 61.111 44.38 0.00 38.26 3.27
862 904 2.554272 CGCGCGCTAACAGGTTTT 59.446 55.556 30.48 0.00 0.00 2.43
863 905 1.082366 CGCGCGCTAACAGGTTTTT 60.082 52.632 30.48 0.00 0.00 1.94
891 933 4.811761 GCTTTAGCGCGGCCGTTG 62.812 66.667 28.70 20.73 36.67 4.10
892 934 4.160635 CTTTAGCGCGGCCGTTGG 62.161 66.667 28.70 17.42 36.67 3.77
893 935 4.683721 TTTAGCGCGGCCGTTGGA 62.684 61.111 28.70 7.49 36.67 3.53
900 942 2.892425 CGGCCGTTGGAGATGCTC 60.892 66.667 19.50 0.00 0.00 4.26
982 1024 1.073177 AACACGTACGCATGCTTACC 58.927 50.000 23.95 10.17 0.00 2.85
1037 1122 0.605319 CGCCCAGCAGGTTTCTTACA 60.605 55.000 0.00 0.00 38.26 2.41
1057 1142 1.743958 AGAGTAGCTGCGTTCGTGTAT 59.256 47.619 0.00 0.00 0.00 2.29
1058 1143 2.941064 AGAGTAGCTGCGTTCGTGTATA 59.059 45.455 0.00 0.00 0.00 1.47
1059 1144 3.034562 GAGTAGCTGCGTTCGTGTATAC 58.965 50.000 0.00 0.00 0.00 1.47
1060 1145 2.421073 AGTAGCTGCGTTCGTGTATACA 59.579 45.455 0.08 0.08 0.00 2.29
1061 1146 2.579207 AGCTGCGTTCGTGTATACAT 57.421 45.000 9.18 0.00 0.00 2.29
1062 1147 3.703286 AGCTGCGTTCGTGTATACATA 57.297 42.857 9.18 0.00 0.00 2.29
1063 1148 3.629058 AGCTGCGTTCGTGTATACATAG 58.371 45.455 9.18 6.89 0.00 2.23
1064 1149 2.153247 GCTGCGTTCGTGTATACATAGC 59.847 50.000 9.18 10.62 0.00 2.97
1135 1223 1.014044 GCTCGTCTTCATGGCGTTCA 61.014 55.000 0.00 0.00 45.15 3.18
1445 1539 2.214181 GAGCTCTTCGGCCTCGTCAA 62.214 60.000 6.43 0.00 37.69 3.18
1542 1636 2.949447 ACCTTGTTGGATTTGTCTGCT 58.051 42.857 0.00 0.00 39.71 4.24
1743 1840 1.503542 CGACATGCCACTTCTTGCC 59.496 57.895 0.00 0.00 0.00 4.52
2184 2287 6.764085 CCCTCGTATGTGGAAACAACAATATA 59.236 38.462 4.55 0.00 46.06 0.86
2214 2317 2.909662 TGACCACCATGTTGTATCTGGA 59.090 45.455 0.00 0.00 34.08 3.86
2262 2365 0.036164 ATAAAGTGACGGGCTGCACA 59.964 50.000 18.56 6.67 37.48 4.57
2316 2419 2.011947 GGGAGCAACAATACCGTAACC 58.988 52.381 0.00 0.00 0.00 2.85
2385 2488 1.163554 ACAGAGTCGTAACCGGAGAC 58.836 55.000 9.46 12.09 35.30 3.36
2394 2497 4.036027 GTCGTAACCGGAGACTAATGATCA 59.964 45.833 9.46 0.00 33.95 2.92
2426 2534 8.539544 TGGACTGATTTCATCTACAAGTATGAA 58.460 33.333 0.00 0.00 39.66 2.57
2479 2587 7.201565 CGTGAAGAGAAGAATAAATGGTTCTCC 60.202 40.741 7.20 0.00 44.01 3.71
2503 2611 5.632034 AGTCTGAACTGAAAACCTAGGTT 57.368 39.130 21.96 21.96 35.46 3.50
2513 2627 6.215636 ACTGAAAACCTAGGTTGATGGATACT 59.784 38.462 27.75 5.89 38.47 2.12
2545 2659 0.322546 AAGTTTGGGGACGCTCCATC 60.323 55.000 0.00 0.00 38.64 3.51
2548 2662 0.111446 TTTGGGGACGCTCCATCAAA 59.889 50.000 14.38 14.38 38.64 2.69
2690 2869 7.837202 ATATCCAATGAACTCGTCGTTTTTA 57.163 32.000 0.00 0.00 35.56 1.52
2900 3136 4.219919 TCATATACAGATGGGTTGGACGA 58.780 43.478 0.00 0.00 0.00 4.20
2901 3137 4.280929 TCATATACAGATGGGTTGGACGAG 59.719 45.833 0.00 0.00 0.00 4.18
2902 3138 1.191535 TACAGATGGGTTGGACGAGG 58.808 55.000 0.00 0.00 0.00 4.63
2903 3139 1.450312 CAGATGGGTTGGACGAGGC 60.450 63.158 0.00 0.00 0.00 4.70
2904 3140 1.918293 AGATGGGTTGGACGAGGCA 60.918 57.895 0.00 0.00 0.00 4.75
2905 3141 1.450312 GATGGGTTGGACGAGGCAG 60.450 63.158 0.00 0.00 0.00 4.85
3004 3266 4.730966 TCCCCTCTATCTCATGTAGTCAC 58.269 47.826 0.00 0.00 0.00 3.67
3100 3370 3.119316 CCTCGTGCTTTCTCTCTGTGTAT 60.119 47.826 0.00 0.00 0.00 2.29
3101 3371 4.096532 CCTCGTGCTTTCTCTCTGTGTATA 59.903 45.833 0.00 0.00 0.00 1.47
3129 3399 2.760634 ATGCACGTATGTCCTTGACA 57.239 45.000 0.00 0.00 46.90 3.58
3144 3414 0.108472 TGACAGGCTGCAGAGAATCG 60.108 55.000 20.43 0.99 42.67 3.34
3232 3502 2.300597 GATTTGCCCCGCGAACGTAC 62.301 60.000 8.23 0.00 34.53 3.67
3258 3528 5.708697 TGGCATCAGGCTATCAATAATTCAG 59.291 40.000 0.00 0.00 44.01 3.02
3267 3537 6.197276 GCTATCAATAATTCAGCACACACTG 58.803 40.000 0.00 0.00 39.12 3.66
3305 3575 1.354031 TGGCTCCCTGCACAGATAAAA 59.646 47.619 0.00 0.00 45.15 1.52
3315 3585 5.163581 CCTGCACAGATAAAAAGAGATTGGG 60.164 44.000 0.00 0.00 0.00 4.12
3339 3609 1.008538 GTCGGCCACAACAAGCTTG 60.009 57.895 24.84 24.84 0.00 4.01
3341 3611 2.848858 CGGCCACAACAAGCTTGCT 61.849 57.895 26.27 11.98 0.00 3.91
3353 3623 4.384056 ACAAGCTTGCTTGATATAGCGAT 58.616 39.130 33.32 11.66 44.18 4.58
3365 3636 4.452114 TGATATAGCGATGTTGACAATGCC 59.548 41.667 7.16 0.00 32.59 4.40
3366 3637 1.006086 TAGCGATGTTGACAATGCCG 58.994 50.000 7.16 0.00 32.59 5.69
3373 3644 2.020720 TGTTGACAATGCCGACACTTT 58.979 42.857 0.00 0.00 0.00 2.66
3379 3650 1.136252 CAATGCCGACACTTTCACTCG 60.136 52.381 0.00 0.00 0.00 4.18
3394 3665 2.002586 CACTCGCATCAAATTCCTCGT 58.997 47.619 0.00 0.00 0.00 4.18
3404 3675 1.148157 AATTCCTCGTGCTCGCATCG 61.148 55.000 2.69 1.50 36.96 3.84
3425 3696 3.642705 GATGAAGGGTTGTGAAGCAAAC 58.357 45.455 0.00 0.00 43.83 2.93
3451 3722 0.470341 GAGGTAGGGTGCAGAATCCC 59.530 60.000 1.76 1.76 43.71 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
339 360 0.611896 CTTTTTCCCCCTCGCCATGT 60.612 55.000 0.00 0.00 0.00 3.21
372 403 0.440371 GAGCCTTGTTCTTCTTCGCG 59.560 55.000 0.00 0.00 0.00 5.87
373 404 0.799393 GGAGCCTTGTTCTTCTTCGC 59.201 55.000 0.00 0.00 0.00 4.70
374 405 1.071605 CGGAGCCTTGTTCTTCTTCG 58.928 55.000 0.00 0.00 0.00 3.79
376 407 0.606673 GCCGGAGCCTTGTTCTTCTT 60.607 55.000 5.05 0.00 0.00 2.52
379 410 1.302832 CTGCCGGAGCCTTGTTCTT 60.303 57.895 5.05 0.00 38.69 2.52
380 411 2.348998 CTGCCGGAGCCTTGTTCT 59.651 61.111 5.05 0.00 38.69 3.01
381 412 2.747855 CCTGCCGGAGCCTTGTTC 60.748 66.667 5.05 0.00 38.69 3.18
384 415 4.809496 ATGCCTGCCGGAGCCTTG 62.809 66.667 5.05 0.00 38.69 3.61
385 416 4.809496 CATGCCTGCCGGAGCCTT 62.809 66.667 5.05 0.00 38.69 4.35
537 576 4.074799 TGAACCTTCCTCCCTATCTTCA 57.925 45.455 0.00 0.00 0.00 3.02
540 579 4.567987 AGATGAACCTTCCTCCCTATCT 57.432 45.455 0.00 0.00 0.00 1.98
816 858 1.669795 GGTTTTGAAATGCCGCTCCAG 60.670 52.381 0.00 0.00 0.00 3.86
817 859 0.316841 GGTTTTGAAATGCCGCTCCA 59.683 50.000 0.00 0.00 0.00 3.86
818 860 0.316841 TGGTTTTGAAATGCCGCTCC 59.683 50.000 0.00 0.00 0.00 4.70
819 861 1.701704 CTGGTTTTGAAATGCCGCTC 58.298 50.000 0.00 0.00 0.00 5.03
820 862 0.319813 GCTGGTTTTGAAATGCCGCT 60.320 50.000 0.00 0.00 0.00 5.52
821 863 1.291184 GGCTGGTTTTGAAATGCCGC 61.291 55.000 0.00 0.00 0.00 6.53
822 864 2.826277 GGCTGGTTTTGAAATGCCG 58.174 52.632 0.00 0.00 0.00 5.69
823 865 1.291184 GCGGCTGGTTTTGAAATGCC 61.291 55.000 0.00 0.00 37.24 4.40
824 866 0.599728 TGCGGCTGGTTTTGAAATGC 60.600 50.000 0.00 0.00 0.00 3.56
825 867 1.421382 CTGCGGCTGGTTTTGAAATG 58.579 50.000 0.00 0.00 0.00 2.32
826 868 0.319813 GCTGCGGCTGGTTTTGAAAT 60.320 50.000 11.21 0.00 35.22 2.17
827 869 1.067250 GCTGCGGCTGGTTTTGAAA 59.933 52.632 11.21 0.00 35.22 2.69
828 870 2.727544 GCTGCGGCTGGTTTTGAA 59.272 55.556 11.21 0.00 35.22 2.69
829 871 3.659092 CGCTGCGGCTGGTTTTGA 61.659 61.111 17.03 0.00 36.09 2.69
844 886 3.588891 AAAACCTGTTAGCGCGCGC 62.589 57.895 45.10 45.10 42.33 6.86
845 887 1.082366 AAAAACCTGTTAGCGCGCG 60.082 52.632 28.44 28.44 0.00 6.86
846 888 4.935630 AAAAACCTGTTAGCGCGC 57.064 50.000 26.66 26.66 0.00 6.86
874 916 4.811761 CAACGGCCGCGCTAAAGC 62.812 66.667 28.58 2.59 37.78 3.51
875 917 4.160635 CCAACGGCCGCGCTAAAG 62.161 66.667 28.58 7.06 0.00 1.85
876 918 4.683721 TCCAACGGCCGCGCTAAA 62.684 61.111 28.58 2.77 0.00 1.85
883 925 2.892425 GAGCATCTCCAACGGCCG 60.892 66.667 26.86 26.86 0.00 6.13
894 936 1.520342 GCCCACGACTGAGAGCATC 60.520 63.158 0.00 0.00 0.00 3.91
895 937 2.581354 GCCCACGACTGAGAGCAT 59.419 61.111 0.00 0.00 0.00 3.79
896 938 3.695606 GGCCCACGACTGAGAGCA 61.696 66.667 0.00 0.00 0.00 4.26
897 939 3.386237 AGGCCCACGACTGAGAGC 61.386 66.667 0.00 0.00 0.00 4.09
898 940 2.575993 CAGGCCCACGACTGAGAG 59.424 66.667 0.00 0.00 36.86 3.20
899 941 2.997315 CCAGGCCCACGACTGAGA 60.997 66.667 0.00 0.00 36.86 3.27
900 942 3.314331 ACCAGGCCCACGACTGAG 61.314 66.667 0.00 0.00 36.86 3.35
1037 1122 1.162698 TACACGAACGCAGCTACTCT 58.837 50.000 0.00 0.00 0.00 3.24
1057 1142 5.995282 GTGGTGGTTTGCTATATGCTATGTA 59.005 40.000 0.00 0.00 43.37 2.29
1058 1143 4.821805 GTGGTGGTTTGCTATATGCTATGT 59.178 41.667 0.00 0.00 43.37 2.29
1059 1144 5.049198 CAGTGGTGGTTTGCTATATGCTATG 60.049 44.000 0.00 0.00 43.37 2.23
1060 1145 5.065914 CAGTGGTGGTTTGCTATATGCTAT 58.934 41.667 0.00 0.00 43.37 2.97
1061 1146 4.163268 TCAGTGGTGGTTTGCTATATGCTA 59.837 41.667 0.00 0.00 43.37 3.49
1062 1147 3.054434 TCAGTGGTGGTTTGCTATATGCT 60.054 43.478 0.00 0.00 43.37 3.79
1063 1148 3.278574 TCAGTGGTGGTTTGCTATATGC 58.721 45.455 0.00 0.00 43.25 3.14
1064 1149 5.009010 GGATTCAGTGGTGGTTTGCTATATG 59.991 44.000 0.00 0.00 0.00 1.78
1073 1158 3.624777 GATGATGGATTCAGTGGTGGTT 58.375 45.455 0.00 0.00 37.89 3.67
1347 1441 2.123683 CCCGCTAGAGAGCCTCCA 60.124 66.667 0.00 0.00 46.86 3.86
1352 1446 3.972276 CGAGGCCCGCTAGAGAGC 61.972 72.222 0.00 0.00 46.00 4.09
1542 1636 3.777910 GGGCCGGAGAAGCGGTTA 61.778 66.667 5.05 0.00 0.00 2.85
1614 1711 1.204146 AGAAGCCGGAGAAGCCATTA 58.796 50.000 5.05 0.00 35.94 1.90
1743 1840 3.065371 AGTTTGTGGAAAAGTCAAGCGAG 59.935 43.478 0.00 0.00 0.00 5.03
1780 1877 2.913060 GGCGAGGCTAGTCGGGAT 60.913 66.667 5.07 0.00 40.44 3.85
1968 2071 5.457992 ATGAAAACCATACCCGATGAACGG 61.458 45.833 0.00 0.00 46.71 4.44
2214 2317 7.996098 ACTGTTAGTTACAATATGGTTGCTT 57.004 32.000 0.00 0.00 36.02 3.91
2262 2365 5.765510 TGGTTGCTCCCAGATACATTATTT 58.234 37.500 0.00 0.00 34.77 1.40
2316 2419 0.033504 ATACCGTATTGCTGCTCCCG 59.966 55.000 0.00 0.00 0.00 5.14
2426 2534 3.840666 TCTCTTAGATGTGCTTTGGGACT 59.159 43.478 0.00 0.00 34.78 3.85
2479 2587 5.687706 AACCTAGGTTTTCAGTTCAGACTGG 60.688 44.000 21.96 0.00 43.30 4.00
2503 2611 4.962362 TGGAACAAGCTAGAGTATCCATCA 59.038 41.667 0.00 0.00 29.61 3.07
2583 2698 2.723124 ATGGTTGCGGACATTGAAAC 57.277 45.000 0.00 0.00 0.00 2.78
2591 2706 7.900782 AATACATACTAATATGGTTGCGGAC 57.099 36.000 0.00 0.00 42.32 4.79
2770 2953 0.258484 ATCCATCGGCCATGACCAAA 59.742 50.000 14.52 0.00 33.80 3.28
2900 3136 4.437587 GGGGCTCATGCACTGCCT 62.438 66.667 20.89 0.00 45.45 4.75
2902 3138 4.437587 AGGGGGCTCATGCACTGC 62.438 66.667 0.00 0.00 43.40 4.40
2903 3139 2.439701 CAGGGGGCTCATGCACTG 60.440 66.667 0.00 0.00 43.40 3.66
3067 3335 3.522731 CACGAGGAGGGAGGAGCG 61.523 72.222 0.00 0.00 0.00 5.03
3100 3370 4.749598 GGACATACGTGCATTCATGTCATA 59.250 41.667 25.77 0.00 45.84 2.15
3101 3371 3.561310 GGACATACGTGCATTCATGTCAT 59.439 43.478 25.77 3.90 45.84 3.06
3129 3399 1.446907 CAAACGATTCTCTGCAGCCT 58.553 50.000 9.47 0.00 0.00 4.58
3144 3414 3.437049 GCACCAACTGAGATACTCCAAAC 59.563 47.826 0.00 0.00 0.00 2.93
3232 3502 1.888215 ATTGATAGCCTGATGCCACG 58.112 50.000 0.00 0.00 42.71 4.94
3237 3507 6.206048 TGTGCTGAATTATTGATAGCCTGATG 59.794 38.462 0.00 0.00 33.60 3.07
3267 3537 2.755650 CCATAACCCTATGCTCGTCAC 58.244 52.381 0.00 0.00 34.62 3.67
3270 3540 1.344763 GAGCCATAACCCTATGCTCGT 59.655 52.381 0.00 0.00 34.62 4.18
3293 3563 5.183713 CACCCAATCTCTTTTTATCTGTGCA 59.816 40.000 0.00 0.00 0.00 4.57
3305 3575 0.324943 CGACCCACACCCAATCTCTT 59.675 55.000 0.00 0.00 0.00 2.85
3339 3609 5.657470 TTGTCAACATCGCTATATCAAGC 57.343 39.130 0.00 0.00 39.21 4.01
3341 3611 5.049474 GGCATTGTCAACATCGCTATATCAA 60.049 40.000 0.00 0.00 0.00 2.57
3353 3623 1.674359 AAGTGTCGGCATTGTCAACA 58.326 45.000 0.00 0.00 0.00 3.33
3365 3636 1.418373 TGATGCGAGTGAAAGTGTCG 58.582 50.000 0.00 0.00 36.77 4.35
3366 3637 3.878086 TTTGATGCGAGTGAAAGTGTC 57.122 42.857 0.00 0.00 0.00 3.67
3373 3644 2.270923 CGAGGAATTTGATGCGAGTGA 58.729 47.619 0.00 0.00 0.00 3.41
3379 3650 1.267732 CGAGCACGAGGAATTTGATGC 60.268 52.381 0.00 0.00 42.66 3.91
3394 3665 1.227350 CCCTTCATCGATGCGAGCA 60.227 57.895 20.81 0.00 39.91 4.26
3404 3675 3.068024 TGTTTGCTTCACAACCCTTCATC 59.932 43.478 0.00 0.00 38.23 2.92
3425 3696 3.420893 TCTGCACCCTACCTCAAATTTG 58.579 45.455 12.15 12.15 0.00 2.32
3442 3713 2.107141 CGGGACTCGGGATTCTGC 59.893 66.667 0.00 0.00 34.75 4.26


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

AutoCloner maintained by Alex Coulton.