Multiple sequence alignment - TraesCS5A01G311400

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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 TraesCS5A01G311400 chr5A 100.000 3534 0 0 1 3534 523078483 523082016 0.000000e+00 6527.0
1 TraesCS5A01G311400 chr5A 89.507 1115 60 25 261 1340 456680001 456678909 0.000000e+00 1358.0
2 TraesCS5A01G311400 chr5A 94.751 743 37 2 2791 3532 523088863 523089604 0.000000e+00 1155.0
3 TraesCS5A01G311400 chr5A 91.117 743 60 5 2791 3532 211331062 211330325 0.000000e+00 1002.0
4 TraesCS5A01G311400 chr5A 91.117 743 58 7 2791 3532 211373433 211372698 0.000000e+00 1000.0
5 TraesCS5A01G311400 chr5A 96.642 268 9 0 1 268 523088604 523088871 2.500000e-121 446.0
6 TraesCS5A01G311400 chr5A 92.734 289 19 2 2503 2791 440977471 440977757 1.960000e-112 416.0
7 TraesCS5A01G311400 chr5A 93.657 268 17 0 1 268 211373692 211373425 5.500000e-108 401.0
8 TraesCS5A01G311400 chr5A 89.925 268 27 0 1 268 211331321 211331054 2.610000e-91 346.0
9 TraesCS5A01G311400 chr5A 89.179 268 28 1 1 267 425111073 425111340 2.030000e-87 333.0
10 TraesCS5A01G311400 chr6B 98.736 2532 23 7 269 2791 16263725 16266256 0.000000e+00 4490.0
11 TraesCS5A01G311400 chr4A 98.154 1463 22 4 1336 2795 650658891 650660351 0.000000e+00 2547.0
12 TraesCS5A01G311400 chr4A 97.041 1453 38 4 1336 2786 19535360 19536809 0.000000e+00 2440.0
13 TraesCS5A01G311400 chr4A 93.165 1112 35 13 269 1340 650656842 650657952 0.000000e+00 1594.0
14 TraesCS5A01G311400 chr4A 95.714 560 23 1 781 1340 19533864 19534422 0.000000e+00 900.0
15 TraesCS5A01G311400 chr4A 88.246 536 26 14 269 773 19533358 19533887 1.080000e-169 606.0
16 TraesCS5A01G311400 chr1D 98.080 1458 24 3 1336 2791 27682898 27681443 0.000000e+00 2534.0
17 TraesCS5A01G311400 chr1D 96.429 784 23 3 557 1340 27684613 27683835 0.000000e+00 1288.0
18 TraesCS5A01G311400 chr1D 86.214 943 78 29 269 1191 467932718 467931808 0.000000e+00 974.0
19 TraesCS5A01G311400 chr1A 97.599 1458 30 4 1336 2791 537445872 537447326 0.000000e+00 2494.0
20 TraesCS5A01G311400 chr1A 92.040 603 46 2 2931 3532 235003261 235002660 0.000000e+00 846.0
21 TraesCS5A01G311400 chr3A 97.531 1458 31 4 1336 2791 57561779 57563233 0.000000e+00 2488.0
22 TraesCS5A01G311400 chr3A 93.172 1113 35 11 268 1340 57559729 57560840 0.000000e+00 1596.0
23 TraesCS5A01G311400 chr3A 94.261 575 26 3 747 1321 714380590 714381157 0.000000e+00 872.0
24 TraesCS5A01G311400 chr3A 90.543 497 41 6 2928 3423 239576051 239576542 0.000000e+00 652.0
25 TraesCS5A01G311400 chr3A 89.388 490 47 5 2935 3423 239583886 239584371 2.330000e-171 612.0
26 TraesCS5A01G311400 chr3A 84.837 521 35 17 269 754 714379896 714380407 5.300000e-133 484.0
27 TraesCS5A01G311400 chr3A 89.809 157 15 1 2 158 204264218 204264063 2.150000e-47 200.0
28 TraesCS5A01G311400 chr3A 91.034 145 13 0 4 148 204254723 204254579 2.780000e-46 196.0
29 TraesCS5A01G311400 chr2B 97.051 1458 36 3 1336 2791 39938397 39939849 0.000000e+00 2447.0
30 TraesCS5A01G311400 chr2B 88.276 580 25 11 269 816 39937779 39938347 0.000000e+00 654.0
31 TraesCS5A01G311400 chr7D 92.339 992 68 7 1336 2323 566129982 566128995 0.000000e+00 1404.0
32 TraesCS5A01G311400 chr4D 84.198 1215 187 4 1336 2546 301347493 301346280 0.000000e+00 1175.0
33 TraesCS5A01G311400 chr3B 85.303 1007 105 24 269 1261 766065113 766066090 0.000000e+00 1000.0
34 TraesCS5A01G311400 chr3B 96.796 593 19 0 748 1340 750995513 750994921 0.000000e+00 990.0
35 TraesCS5A01G311400 chr3B 85.632 522 21 24 269 754 750996335 750995832 1.890000e-137 499.0
36 TraesCS5A01G311400 chr3B 100.000 30 0 0 1250 1279 766094368 766094397 4.930000e-04 56.5
37 TraesCS5A01G311400 chr6A 90.836 742 51 13 2791 3522 585874684 585873950 0.000000e+00 977.0
38 TraesCS5A01G311400 chr6A 95.539 269 11 1 1 268 585874944 585874676 2.520000e-116 429.0
39 TraesCS5A01G311400 chr6A 88.433 268 9 2 1 268 585866991 585866746 1.590000e-78 303.0
40 TraesCS5A01G311400 chr7A 85.053 950 83 29 269 1183 68225399 68224474 0.000000e+00 913.0
41 TraesCS5A01G311400 chr7A 90.965 653 55 2 2881 3532 381589857 381589208 0.000000e+00 876.0
42 TraesCS5A01G311400 chr7A 90.673 654 45 10 2881 3532 381597383 381596744 0.000000e+00 856.0
43 TraesCS5A01G311400 chr7A 95.979 373 15 0 2422 2794 68224476 68224104 1.080000e-169 606.0
44 TraesCS5A01G311400 chr6D 80.330 788 89 39 268 1004 457553181 457552409 1.440000e-148 536.0
45 TraesCS5A01G311400 chr2A 89.811 265 27 0 4 268 457434733 457434469 1.210000e-89 340.0
46 TraesCS5A01G311400 chr2A 89.080 174 18 1 3359 3532 323636150 323635978 7.680000e-52 215.0
47 TraesCS5A01G311400 chr2A 91.667 120 10 0 3415 3534 152989072 152988953 2.180000e-37 167.0
48 TraesCS5A01G311400 chr2A 83.234 167 19 7 3358 3523 305728762 305728920 1.020000e-30 145.0
49 TraesCS5A01G311400 chr1B 80.669 269 26 17 269 516 15515408 15515671 6.020000e-43 185.0


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 TraesCS5A01G311400 chr5A 523078483 523082016 3533 False 6527.000000 6527 100.0000 1 3534 1 chr5A.!!$F3 3533
1 TraesCS5A01G311400 chr5A 456678909 456680001 1092 True 1358.000000 1358 89.5070 261 1340 1 chr5A.!!$R1 1079
2 TraesCS5A01G311400 chr5A 523088604 523089604 1000 False 800.500000 1155 95.6965 1 3532 2 chr5A.!!$F4 3531
3 TraesCS5A01G311400 chr5A 211372698 211373692 994 True 700.500000 1000 92.3870 1 3532 2 chr5A.!!$R3 3531
4 TraesCS5A01G311400 chr5A 211330325 211331321 996 True 674.000000 1002 90.5210 1 3532 2 chr5A.!!$R2 3531
5 TraesCS5A01G311400 chr6B 16263725 16266256 2531 False 4490.000000 4490 98.7360 269 2791 1 chr6B.!!$F1 2522
6 TraesCS5A01G311400 chr4A 650656842 650660351 3509 False 2070.500000 2547 95.6595 269 2795 2 chr4A.!!$F2 2526
7 TraesCS5A01G311400 chr4A 19533358 19536809 3451 False 1315.333333 2440 93.6670 269 2786 3 chr4A.!!$F1 2517
8 TraesCS5A01G311400 chr1D 27681443 27684613 3170 True 1911.000000 2534 97.2545 557 2791 2 chr1D.!!$R2 2234
9 TraesCS5A01G311400 chr1D 467931808 467932718 910 True 974.000000 974 86.2140 269 1191 1 chr1D.!!$R1 922
10 TraesCS5A01G311400 chr1A 537445872 537447326 1454 False 2494.000000 2494 97.5990 1336 2791 1 chr1A.!!$F1 1455
11 TraesCS5A01G311400 chr1A 235002660 235003261 601 True 846.000000 846 92.0400 2931 3532 1 chr1A.!!$R1 601
12 TraesCS5A01G311400 chr3A 57559729 57563233 3504 False 2042.000000 2488 95.3515 268 2791 2 chr3A.!!$F3 2523
13 TraesCS5A01G311400 chr3A 714379896 714381157 1261 False 678.000000 872 89.5490 269 1321 2 chr3A.!!$F4 1052
14 TraesCS5A01G311400 chr2B 39937779 39939849 2070 False 1550.500000 2447 92.6635 269 2791 2 chr2B.!!$F1 2522
15 TraesCS5A01G311400 chr7D 566128995 566129982 987 True 1404.000000 1404 92.3390 1336 2323 1 chr7D.!!$R1 987
16 TraesCS5A01G311400 chr4D 301346280 301347493 1213 True 1175.000000 1175 84.1980 1336 2546 1 chr4D.!!$R1 1210
17 TraesCS5A01G311400 chr3B 766065113 766066090 977 False 1000.000000 1000 85.3030 269 1261 1 chr3B.!!$F1 992
18 TraesCS5A01G311400 chr3B 750994921 750996335 1414 True 744.500000 990 91.2140 269 1340 2 chr3B.!!$R1 1071
19 TraesCS5A01G311400 chr6A 585873950 585874944 994 True 703.000000 977 93.1875 1 3522 2 chr6A.!!$R2 3521
20 TraesCS5A01G311400 chr7A 381589208 381589857 649 True 876.000000 876 90.9650 2881 3532 1 chr7A.!!$R1 651
21 TraesCS5A01G311400 chr7A 381596744 381597383 639 True 856.000000 856 90.6730 2881 3532 1 chr7A.!!$R2 651
22 TraesCS5A01G311400 chr7A 68224104 68225399 1295 True 759.500000 913 90.5160 269 2794 2 chr7A.!!$R3 2525
23 TraesCS5A01G311400 chr6D 457552409 457553181 772 True 536.000000 536 80.3300 268 1004 1 chr6D.!!$R1 736

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
232 234 0.449388 GCCAGTCGATTGCTTGAAGG 59.551 55.0 1.73 0.00 0.00 3.46 F
890 1545 2.549754 CACAGAACACAGTGGATGGTTC 59.450 50.0 5.31 9.74 38.42 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1378 4873 4.299155 ACGGTGTTTATGATGATAGAGCG 58.701 43.478 0.00 0.0 0.0 5.03 R
2838 6343 0.178998 TCCTCGCGCTACCTCCTTAT 60.179 55.000 5.56 0.0 0.0 1.73 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
110 111 2.202878 GCGGACGGCAGAAGCATA 60.203 61.111 0.00 0.00 44.61 3.14
232 234 0.449388 GCCAGTCGATTGCTTGAAGG 59.551 55.000 1.73 0.00 0.00 3.46
644 759 4.451150 CCGCGAGCAGGTTAGCCA 62.451 66.667 8.23 0.00 37.19 4.75
809 1448 3.379452 CCTGAACAGAACCTAGATCCCT 58.621 50.000 3.19 0.00 0.00 4.20
890 1545 2.549754 CACAGAACACAGTGGATGGTTC 59.450 50.000 5.31 9.74 38.42 3.62
912 1567 7.392393 GGTTCCTAATTTAGTAGGCAAGTTTCA 59.608 37.037 2.88 0.00 40.58 2.69
1378 4873 8.166422 TCTATTTCTCAAGTCTTCCAAAAACC 57.834 34.615 0.00 0.00 0.00 3.27
2379 5879 3.243636 GGGCATGCATTTTCCAGTATGAG 60.244 47.826 21.36 0.00 39.69 2.90
2791 6296 1.795170 TTTTCAAGCTCCGCCACTGC 61.795 55.000 0.00 0.00 0.00 4.40
2794 6299 2.749044 AAGCTCCGCCACTGCATG 60.749 61.111 0.00 0.00 37.32 4.06
2810 6315 0.727970 CATGCAGTGCAAGAGAGAGC 59.272 55.000 23.90 0.00 43.62 4.09
2811 6316 0.740164 ATGCAGTGCAAGAGAGAGCG 60.740 55.000 23.90 0.00 43.62 5.03
2812 6317 1.080230 GCAGTGCAAGAGAGAGCGA 60.080 57.895 11.09 0.00 0.00 4.93
2813 6318 1.077645 GCAGTGCAAGAGAGAGCGAG 61.078 60.000 11.09 0.00 0.00 5.03
2814 6319 0.525311 CAGTGCAAGAGAGAGCGAGA 59.475 55.000 0.00 0.00 0.00 4.04
2815 6320 0.810648 AGTGCAAGAGAGAGCGAGAG 59.189 55.000 0.00 0.00 0.00 3.20
2816 6321 0.808125 GTGCAAGAGAGAGCGAGAGA 59.192 55.000 0.00 0.00 0.00 3.10
2817 6322 1.405105 GTGCAAGAGAGAGCGAGAGAT 59.595 52.381 0.00 0.00 0.00 2.75
2818 6323 1.404748 TGCAAGAGAGAGCGAGAGATG 59.595 52.381 0.00 0.00 0.00 2.90
2819 6324 1.675483 GCAAGAGAGAGCGAGAGATGA 59.325 52.381 0.00 0.00 0.00 2.92
2820 6325 2.287188 GCAAGAGAGAGCGAGAGATGAG 60.287 54.545 0.00 0.00 0.00 2.90
2821 6326 3.205338 CAAGAGAGAGCGAGAGATGAGA 58.795 50.000 0.00 0.00 0.00 3.27
2822 6327 2.838736 AGAGAGAGCGAGAGATGAGAC 58.161 52.381 0.00 0.00 0.00 3.36
2823 6328 2.170397 AGAGAGAGCGAGAGATGAGACA 59.830 50.000 0.00 0.00 0.00 3.41
2824 6329 2.545526 GAGAGAGCGAGAGATGAGACAG 59.454 54.545 0.00 0.00 0.00 3.51
2825 6330 1.603802 GAGAGCGAGAGATGAGACAGG 59.396 57.143 0.00 0.00 0.00 4.00
2826 6331 0.667993 GAGCGAGAGATGAGACAGGG 59.332 60.000 0.00 0.00 0.00 4.45
2827 6332 0.257328 AGCGAGAGATGAGACAGGGA 59.743 55.000 0.00 0.00 0.00 4.20
2828 6333 1.107114 GCGAGAGATGAGACAGGGAA 58.893 55.000 0.00 0.00 0.00 3.97
2829 6334 1.478510 GCGAGAGATGAGACAGGGAAA 59.521 52.381 0.00 0.00 0.00 3.13
2830 6335 2.481104 GCGAGAGATGAGACAGGGAAAG 60.481 54.545 0.00 0.00 0.00 2.62
2831 6336 3.020274 CGAGAGATGAGACAGGGAAAGA 58.980 50.000 0.00 0.00 0.00 2.52
2832 6337 3.445450 CGAGAGATGAGACAGGGAAAGAA 59.555 47.826 0.00 0.00 0.00 2.52
2833 6338 4.439974 CGAGAGATGAGACAGGGAAAGAAG 60.440 50.000 0.00 0.00 0.00 2.85
2834 6339 4.682563 AGAGATGAGACAGGGAAAGAAGA 58.317 43.478 0.00 0.00 0.00 2.87
2835 6340 4.711355 AGAGATGAGACAGGGAAAGAAGAG 59.289 45.833 0.00 0.00 0.00 2.85
2836 6341 4.682563 AGATGAGACAGGGAAAGAAGAGA 58.317 43.478 0.00 0.00 0.00 3.10
2837 6342 5.090139 AGATGAGACAGGGAAAGAAGAGAA 58.910 41.667 0.00 0.00 0.00 2.87
2838 6343 5.545723 AGATGAGACAGGGAAAGAAGAGAAA 59.454 40.000 0.00 0.00 0.00 2.52
2839 6344 5.832539 TGAGACAGGGAAAGAAGAGAAAT 57.167 39.130 0.00 0.00 0.00 2.17
2840 6345 6.935240 TGAGACAGGGAAAGAAGAGAAATA 57.065 37.500 0.00 0.00 0.00 1.40
2841 6346 7.316393 TGAGACAGGGAAAGAAGAGAAATAA 57.684 36.000 0.00 0.00 0.00 1.40
2842 6347 7.390027 TGAGACAGGGAAAGAAGAGAAATAAG 58.610 38.462 0.00 0.00 0.00 1.73
2843 6348 6.716284 AGACAGGGAAAGAAGAGAAATAAGG 58.284 40.000 0.00 0.00 0.00 2.69
2844 6349 6.502158 AGACAGGGAAAGAAGAGAAATAAGGA 59.498 38.462 0.00 0.00 0.00 3.36
2845 6350 6.716284 ACAGGGAAAGAAGAGAAATAAGGAG 58.284 40.000 0.00 0.00 0.00 3.69
2846 6351 6.118852 CAGGGAAAGAAGAGAAATAAGGAGG 58.881 44.000 0.00 0.00 0.00 4.30
2847 6352 5.793237 AGGGAAAGAAGAGAAATAAGGAGGT 59.207 40.000 0.00 0.00 0.00 3.85
2848 6353 6.966461 AGGGAAAGAAGAGAAATAAGGAGGTA 59.034 38.462 0.00 0.00 0.00 3.08
2849 6354 7.126573 AGGGAAAGAAGAGAAATAAGGAGGTAG 59.873 40.741 0.00 0.00 0.00 3.18
2850 6355 6.764085 GGAAAGAAGAGAAATAAGGAGGTAGC 59.236 42.308 0.00 0.00 0.00 3.58
2851 6356 5.523438 AGAAGAGAAATAAGGAGGTAGCG 57.477 43.478 0.00 0.00 0.00 4.26
2852 6357 3.737032 AGAGAAATAAGGAGGTAGCGC 57.263 47.619 0.00 0.00 0.00 5.92
2853 6358 2.034812 AGAGAAATAAGGAGGTAGCGCG 59.965 50.000 0.00 0.00 0.00 6.86
2854 6359 2.029623 AGAAATAAGGAGGTAGCGCGA 58.970 47.619 12.10 0.00 0.00 5.87
2855 6360 2.034812 AGAAATAAGGAGGTAGCGCGAG 59.965 50.000 12.10 0.00 0.00 5.03
2856 6361 0.674534 AATAAGGAGGTAGCGCGAGG 59.325 55.000 12.10 0.00 0.00 4.63
2857 6362 0.178998 ATAAGGAGGTAGCGCGAGGA 60.179 55.000 12.10 0.00 0.00 3.71
2858 6363 0.818445 TAAGGAGGTAGCGCGAGGAG 60.818 60.000 12.10 0.00 0.00 3.69
2859 6364 3.597728 GGAGGTAGCGCGAGGAGG 61.598 72.222 12.10 0.00 0.00 4.30
2860 6365 3.597728 GAGGTAGCGCGAGGAGGG 61.598 72.222 12.10 0.00 0.00 4.30
2874 6379 1.076923 GAGGGAGTCCGGTCTAGCA 60.077 63.158 0.00 0.00 38.33 3.49
3036 6541 3.083349 CCTGGGCCGTCAGATCCA 61.083 66.667 10.34 0.00 36.93 3.41
3049 6554 1.592669 GATCCACGATCTGGCGGTG 60.593 63.158 6.38 0.00 40.39 4.94
3086 6591 1.303317 GCGGTTGGTGGAGTGGATT 60.303 57.895 0.00 0.00 0.00 3.01
3091 6596 2.558359 GGTTGGTGGAGTGGATTTGAAG 59.442 50.000 0.00 0.00 0.00 3.02
3250 6756 2.183679 GGCTATCTCATCCCTCCGATT 58.816 52.381 0.00 0.00 0.00 3.34
3256 6762 4.607293 TCTCATCCCTCCGATTGTAATG 57.393 45.455 0.00 0.00 0.00 1.90
3275 6781 9.573166 TTGTAATGGAATGATCTCGGATAAATT 57.427 29.630 0.00 0.00 0.00 1.82
3387 6893 4.961511 ACAGCTTTCGGACGCGCA 62.962 61.111 5.73 0.00 0.00 6.09
3478 6993 1.199615 GTCTGAGAGAAGGGGGAAGG 58.800 60.000 0.00 0.00 0.00 3.46
3508 7024 0.672401 GGCACGATTTCCGAAGACCA 60.672 55.000 0.00 0.00 41.76 4.02
3528 7044 3.615496 CCAAAAACGTCCGACGATAAGAT 59.385 43.478 27.03 0.47 46.05 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 3.507924 CAAATGCCAGCGCCGCTA 61.508 61.111 13.03 0.00 36.40 4.26
246 248 1.219124 GCATGCTCGAACAGGAGGA 59.781 57.895 11.37 0.00 38.80 3.71
809 1448 9.612066 GAAATATTCAGCCAATTGGGAATTTTA 57.388 29.630 24.98 13.66 40.01 1.52
890 1545 9.788960 GAAATGAAACTTGCCTACTAAATTAGG 57.211 33.333 4.92 0.00 41.65 2.69
912 1567 4.624604 GCCCAATTGCTCAATTCTGGAAAT 60.625 41.667 17.76 0.00 38.84 2.17
1378 4873 4.299155 ACGGTGTTTATGATGATAGAGCG 58.701 43.478 0.00 0.00 0.00 5.03
2358 5858 3.243636 CCTCATACTGGAAAATGCATGCC 60.244 47.826 16.68 3.02 0.00 4.40
2361 5861 5.698104 TGATCCTCATACTGGAAAATGCAT 58.302 37.500 0.00 0.00 37.13 3.96
2379 5879 3.612423 GCGCAACCTTGTTTTAATGATCC 59.388 43.478 0.30 0.00 0.00 3.36
2791 6296 0.727970 GCTCTCTCTTGCACTGCATG 59.272 55.000 4.10 7.57 38.76 4.06
2794 6299 1.077645 CTCGCTCTCTCTTGCACTGC 61.078 60.000 0.00 0.00 0.00 4.40
2795 6300 0.525311 TCTCGCTCTCTCTTGCACTG 59.475 55.000 0.00 0.00 0.00 3.66
2796 6301 0.810648 CTCTCGCTCTCTCTTGCACT 59.189 55.000 0.00 0.00 0.00 4.40
2797 6302 0.808125 TCTCTCGCTCTCTCTTGCAC 59.192 55.000 0.00 0.00 0.00 4.57
2798 6303 1.404748 CATCTCTCGCTCTCTCTTGCA 59.595 52.381 0.00 0.00 0.00 4.08
2799 6304 1.675483 TCATCTCTCGCTCTCTCTTGC 59.325 52.381 0.00 0.00 0.00 4.01
2800 6305 3.002656 GTCTCATCTCTCGCTCTCTCTTG 59.997 52.174 0.00 0.00 0.00 3.02
2801 6306 3.206150 GTCTCATCTCTCGCTCTCTCTT 58.794 50.000 0.00 0.00 0.00 2.85
2802 6307 2.170397 TGTCTCATCTCTCGCTCTCTCT 59.830 50.000 0.00 0.00 0.00 3.10
2803 6308 2.545526 CTGTCTCATCTCTCGCTCTCTC 59.454 54.545 0.00 0.00 0.00 3.20
2804 6309 2.564771 CTGTCTCATCTCTCGCTCTCT 58.435 52.381 0.00 0.00 0.00 3.10
2805 6310 1.603802 CCTGTCTCATCTCTCGCTCTC 59.396 57.143 0.00 0.00 0.00 3.20
2806 6311 1.679139 CCTGTCTCATCTCTCGCTCT 58.321 55.000 0.00 0.00 0.00 4.09
2807 6312 0.667993 CCCTGTCTCATCTCTCGCTC 59.332 60.000 0.00 0.00 0.00 5.03
2808 6313 0.257328 TCCCTGTCTCATCTCTCGCT 59.743 55.000 0.00 0.00 0.00 4.93
2809 6314 1.107114 TTCCCTGTCTCATCTCTCGC 58.893 55.000 0.00 0.00 0.00 5.03
2810 6315 3.020274 TCTTTCCCTGTCTCATCTCTCG 58.980 50.000 0.00 0.00 0.00 4.04
2811 6316 4.709397 TCTTCTTTCCCTGTCTCATCTCTC 59.291 45.833 0.00 0.00 0.00 3.20
2812 6317 4.682563 TCTTCTTTCCCTGTCTCATCTCT 58.317 43.478 0.00 0.00 0.00 3.10
2813 6318 4.709397 TCTCTTCTTTCCCTGTCTCATCTC 59.291 45.833 0.00 0.00 0.00 2.75
2814 6319 4.682563 TCTCTTCTTTCCCTGTCTCATCT 58.317 43.478 0.00 0.00 0.00 2.90
2815 6320 5.413309 TTCTCTTCTTTCCCTGTCTCATC 57.587 43.478 0.00 0.00 0.00 2.92
2816 6321 5.832539 TTTCTCTTCTTTCCCTGTCTCAT 57.167 39.130 0.00 0.00 0.00 2.90
2817 6322 5.832539 ATTTCTCTTCTTTCCCTGTCTCA 57.167 39.130 0.00 0.00 0.00 3.27
2818 6323 6.821160 CCTTATTTCTCTTCTTTCCCTGTCTC 59.179 42.308 0.00 0.00 0.00 3.36
2819 6324 6.502158 TCCTTATTTCTCTTCTTTCCCTGTCT 59.498 38.462 0.00 0.00 0.00 3.41
2820 6325 6.712276 TCCTTATTTCTCTTCTTTCCCTGTC 58.288 40.000 0.00 0.00 0.00 3.51
2821 6326 6.296720 CCTCCTTATTTCTCTTCTTTCCCTGT 60.297 42.308 0.00 0.00 0.00 4.00
2822 6327 6.118852 CCTCCTTATTTCTCTTCTTTCCCTG 58.881 44.000 0.00 0.00 0.00 4.45
2823 6328 5.793237 ACCTCCTTATTTCTCTTCTTTCCCT 59.207 40.000 0.00 0.00 0.00 4.20
2824 6329 6.068461 ACCTCCTTATTTCTCTTCTTTCCC 57.932 41.667 0.00 0.00 0.00 3.97
2825 6330 6.764085 GCTACCTCCTTATTTCTCTTCTTTCC 59.236 42.308 0.00 0.00 0.00 3.13
2826 6331 6.477360 CGCTACCTCCTTATTTCTCTTCTTTC 59.523 42.308 0.00 0.00 0.00 2.62
2827 6332 6.342111 CGCTACCTCCTTATTTCTCTTCTTT 58.658 40.000 0.00 0.00 0.00 2.52
2828 6333 5.682730 GCGCTACCTCCTTATTTCTCTTCTT 60.683 44.000 0.00 0.00 0.00 2.52
2829 6334 4.202172 GCGCTACCTCCTTATTTCTCTTCT 60.202 45.833 0.00 0.00 0.00 2.85
2830 6335 4.052608 GCGCTACCTCCTTATTTCTCTTC 58.947 47.826 0.00 0.00 0.00 2.87
2831 6336 3.491104 CGCGCTACCTCCTTATTTCTCTT 60.491 47.826 5.56 0.00 0.00 2.85
2832 6337 2.034812 CGCGCTACCTCCTTATTTCTCT 59.965 50.000 5.56 0.00 0.00 3.10
2833 6338 2.034305 TCGCGCTACCTCCTTATTTCTC 59.966 50.000 5.56 0.00 0.00 2.87
2834 6339 2.029623 TCGCGCTACCTCCTTATTTCT 58.970 47.619 5.56 0.00 0.00 2.52
2835 6340 2.395654 CTCGCGCTACCTCCTTATTTC 58.604 52.381 5.56 0.00 0.00 2.17
2836 6341 1.068741 CCTCGCGCTACCTCCTTATTT 59.931 52.381 5.56 0.00 0.00 1.40
2837 6342 0.674534 CCTCGCGCTACCTCCTTATT 59.325 55.000 5.56 0.00 0.00 1.40
2838 6343 0.178998 TCCTCGCGCTACCTCCTTAT 60.179 55.000 5.56 0.00 0.00 1.73
2839 6344 0.818445 CTCCTCGCGCTACCTCCTTA 60.818 60.000 5.56 0.00 0.00 2.69
2840 6345 2.044252 TCCTCGCGCTACCTCCTT 60.044 61.111 5.56 0.00 0.00 3.36
2841 6346 2.517402 CTCCTCGCGCTACCTCCT 60.517 66.667 5.56 0.00 0.00 3.69
2842 6347 3.597728 CCTCCTCGCGCTACCTCC 61.598 72.222 5.56 0.00 0.00 4.30
2843 6348 3.597728 CCCTCCTCGCGCTACCTC 61.598 72.222 5.56 0.00 0.00 3.85
2844 6349 4.124943 TCCCTCCTCGCGCTACCT 62.125 66.667 5.56 0.00 0.00 3.08
2845 6350 3.597728 CTCCCTCCTCGCGCTACC 61.598 72.222 5.56 0.00 0.00 3.18
2846 6351 2.829458 ACTCCCTCCTCGCGCTAC 60.829 66.667 5.56 0.00 0.00 3.58
2847 6352 2.516460 GACTCCCTCCTCGCGCTA 60.516 66.667 5.56 0.00 0.00 4.26
2852 6357 1.980784 TAGACCGGACTCCCTCCTCG 61.981 65.000 9.46 0.00 36.80 4.63
2853 6358 0.179012 CTAGACCGGACTCCCTCCTC 60.179 65.000 9.46 0.00 36.80 3.71
2854 6359 1.924352 CTAGACCGGACTCCCTCCT 59.076 63.158 9.46 0.00 36.80 3.69
2855 6360 1.829096 GCTAGACCGGACTCCCTCC 60.829 68.421 9.46 0.00 35.33 4.30
2856 6361 1.076923 TGCTAGACCGGACTCCCTC 60.077 63.158 9.46 0.00 0.00 4.30
2857 6362 1.076632 CTGCTAGACCGGACTCCCT 60.077 63.158 9.46 0.00 0.00 4.20
2858 6363 2.787567 GCTGCTAGACCGGACTCCC 61.788 68.421 9.46 2.27 0.00 4.30
2859 6364 2.010582 CTGCTGCTAGACCGGACTCC 62.011 65.000 9.46 2.69 0.00 3.85
2860 6365 1.435515 CTGCTGCTAGACCGGACTC 59.564 63.158 9.46 0.00 0.00 3.36
3005 6510 2.935481 CAGGAGGCTCCCCCAACA 60.935 66.667 29.62 0.00 37.19 3.33
3036 6541 1.369091 GATTTGCACCGCCAGATCGT 61.369 55.000 0.00 0.00 0.00 3.73
3049 6554 1.026718 CCACCTCCCACTCGATTTGC 61.027 60.000 0.00 0.00 0.00 3.68
3086 6591 0.250727 CCTTCGGCCCTTGTCTTCAA 60.251 55.000 0.00 0.00 0.00 2.69
3091 6596 0.322546 AATCACCTTCGGCCCTTGTC 60.323 55.000 0.00 0.00 0.00 3.18
3128 6633 1.089123 ACTCCTCCTGTCTCCTCCTT 58.911 55.000 0.00 0.00 0.00 3.36
3250 6756 9.002600 CAATTTATCCGAGATCATTCCATTACA 57.997 33.333 0.00 0.00 0.00 2.41
3256 6762 6.884280 AACCAATTTATCCGAGATCATTCC 57.116 37.500 0.00 0.00 0.00 3.01
3275 6781 1.567175 GTTAATGGGGCTCCCTAACCA 59.433 52.381 11.93 0.00 45.70 3.67
3387 6893 3.518998 CATCGGACCTCCTCGCGT 61.519 66.667 5.77 0.00 0.00 6.01


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

AutoCloner maintained by Alex Coulton.