Multiple sequence alignment - TraesCS6A01G100200

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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 TraesCS6A01G100200 chr6A 100.000 3660 0 0 1 3660 67497143 67500802 0.000000e+00 6759
1 TraesCS6A01G100200 chr6A 98.030 1421 26 2 1523 2941 158978404 158976984 0.000000e+00 2468
2 TraesCS6A01G100200 chr6A 93.729 590 32 5 1 588 158980216 158979630 0.000000e+00 880
3 TraesCS6A01G100200 chr2A 97.678 1421 31 2 1523 2941 685099256 685097836 0.000000e+00 2440
4 TraesCS6A01G100200 chr2A 97.257 1422 35 4 1523 2941 284804974 284806394 0.000000e+00 2407
5 TraesCS6A01G100200 chr2A 96.143 726 26 2 2935 3660 685097806 685097083 0.000000e+00 1184
6 TraesCS6A01G100200 chr2A 96.011 727 26 3 2935 3660 80126120 80126844 0.000000e+00 1179
7 TraesCS6A01G100200 chr2A 95.868 726 28 2 2935 3660 572963413 572962690 0.000000e+00 1173
8 TraesCS6A01G100200 chr2A 93.898 590 32 4 1 588 572966668 572966081 0.000000e+00 887
9 TraesCS6A01G100200 chr2A 93.997 583 32 3 1 581 284803162 284803743 0.000000e+00 880
10 TraesCS6A01G100200 chr2A 94.118 578 30 4 13 588 685101057 685100482 0.000000e+00 876
11 TraesCS6A01G100200 chr5A 97.539 1422 32 3 1523 2941 465659177 465660598 0.000000e+00 2429
12 TraesCS6A01G100200 chr5A 97.396 1421 35 2 1523 2941 34938303 34936883 0.000000e+00 2418
13 TraesCS6A01G100200 chr5A 96.429 728 22 3 2935 3660 465660626 465661351 0.000000e+00 1197
14 TraesCS6A01G100200 chr5A 96.281 726 25 2 2935 3660 541983407 541984130 0.000000e+00 1190
15 TraesCS6A01G100200 chr5A 96.154 728 24 4 2935 3660 528078059 528078784 0.000000e+00 1186
16 TraesCS6A01G100200 chr5A 96.143 726 26 2 2935 3660 34936852 34936129 0.000000e+00 1184
17 TraesCS6A01G100200 chr5A 95.868 726 28 2 2935 3660 142245270 142244547 0.000000e+00 1173
18 TraesCS6A01G100200 chr5A 93.390 590 36 3 1 588 465657364 465657952 0.000000e+00 870
19 TraesCS6A01G100200 chr5A 93.220 590 35 5 1 588 541980148 541980734 0.000000e+00 863
20 TraesCS6A01G100200 chr1A 97.467 1421 31 4 1523 2941 70940704 70939287 0.000000e+00 2420
21 TraesCS6A01G100200 chr1A 96.011 727 26 3 2935 3660 70939258 70938534 0.000000e+00 1179
22 TraesCS6A01G100200 chr3A 97.393 1419 33 4 1526 2941 662005341 662003924 0.000000e+00 2412
23 TraesCS6A01G100200 chr3A 97.324 1420 37 1 1523 2941 554832502 554833921 0.000000e+00 2410
24 TraesCS6A01G100200 chr3A 94.078 591 31 4 1 588 662007157 662006568 0.000000e+00 894
25 TraesCS6A01G100200 chr3A 93.559 590 35 3 1 588 554830685 554831273 0.000000e+00 876
26 TraesCS6A01G100200 chr7A 97.328 1422 33 5 1523 2941 245430993 245429574 0.000000e+00 2410
27 TraesCS6A01G100200 chr6D 83.520 2148 243 73 1523 3612 229643556 229641462 0.000000e+00 1903
28 TraesCS6A01G100200 chr6D 82.033 2154 260 79 1523 3612 197908006 197910096 0.000000e+00 1716
29 TraesCS6A01G100200 chr6D 82.879 1945 229 66 1725 3612 179216989 179215092 0.000000e+00 1652
30 TraesCS6A01G100200 chr6D 88.414 889 61 20 1523 2385 186931414 186930542 0.000000e+00 1033
31 TraesCS6A01G100200 chr6D 89.143 175 18 1 1523 1697 179217222 179217049 2.210000e-52 217
32 TraesCS6A01G100200 chr1D 89.434 1448 108 25 1523 2941 238011575 238013006 0.000000e+00 1784
33 TraesCS6A01G100200 chr6B 94.966 894 42 2 628 1520 85667176 85668067 0.000000e+00 1399
34 TraesCS6A01G100200 chr4B 94.295 894 47 3 628 1520 434984187 434985077 0.000000e+00 1365
35 TraesCS6A01G100200 chr4B 94.365 834 47 0 625 1458 173392796 173391963 0.000000e+00 1280
36 TraesCS6A01G100200 chr7B 93.960 894 50 3 628 1520 300045891 300046781 0.000000e+00 1349
37 TraesCS6A01G100200 chr7B 81.196 803 113 25 732 1523 292478473 292479248 2.420000e-171 612
38 TraesCS6A01G100200 chr5B 93.757 897 54 2 625 1520 358456087 358455192 0.000000e+00 1345
39 TraesCS6A01G100200 chr5B 92.099 886 69 1 635 1520 358460076 358459192 0.000000e+00 1247
40 TraesCS6A01G100200 chr3B 93.799 887 52 3 635 1520 151818177 151817293 0.000000e+00 1330
41 TraesCS6A01G100200 chr3B 93.371 890 54 5 635 1520 545968200 545967312 0.000000e+00 1312
42 TraesCS6A01G100200 chr1B 94.365 834 47 0 625 1458 413056570 413057403 0.000000e+00 1280
43 TraesCS6A01G100200 chr1B 93.301 612 34 5 1 608 84522428 84521820 0.000000e+00 896


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 TraesCS6A01G100200 chr6A 67497143 67500802 3659 False 6759.000000 6759 100.000000 1 3660 1 chr6A.!!$F1 3659
1 TraesCS6A01G100200 chr6A 158976984 158980216 3232 True 1674.000000 2468 95.879500 1 2941 2 chr6A.!!$R1 2940
2 TraesCS6A01G100200 chr2A 284803162 284806394 3232 False 1643.500000 2407 95.627000 1 2941 2 chr2A.!!$F2 2940
3 TraesCS6A01G100200 chr2A 685097083 685101057 3974 True 1500.000000 2440 95.979667 13 3660 3 chr2A.!!$R2 3647
4 TraesCS6A01G100200 chr2A 80126120 80126844 724 False 1179.000000 1179 96.011000 2935 3660 1 chr2A.!!$F1 725
5 TraesCS6A01G100200 chr2A 572962690 572966668 3978 True 1030.000000 1173 94.883000 1 3660 2 chr2A.!!$R1 3659
6 TraesCS6A01G100200 chr5A 34936129 34938303 2174 True 1801.000000 2418 96.769500 1523 3660 2 chr5A.!!$R2 2137
7 TraesCS6A01G100200 chr5A 465657364 465661351 3987 False 1498.666667 2429 95.786000 1 3660 3 chr5A.!!$F2 3659
8 TraesCS6A01G100200 chr5A 528078059 528078784 725 False 1186.000000 1186 96.154000 2935 3660 1 chr5A.!!$F1 725
9 TraesCS6A01G100200 chr5A 142244547 142245270 723 True 1173.000000 1173 95.868000 2935 3660 1 chr5A.!!$R1 725
10 TraesCS6A01G100200 chr5A 541980148 541984130 3982 False 1026.500000 1190 94.750500 1 3660 2 chr5A.!!$F3 3659
11 TraesCS6A01G100200 chr1A 70938534 70940704 2170 True 1799.500000 2420 96.739000 1523 3660 2 chr1A.!!$R1 2137
12 TraesCS6A01G100200 chr3A 662003924 662007157 3233 True 1653.000000 2412 95.735500 1 2941 2 chr3A.!!$R1 2940
13 TraesCS6A01G100200 chr3A 554830685 554833921 3236 False 1643.000000 2410 95.441500 1 2941 2 chr3A.!!$F1 2940
14 TraesCS6A01G100200 chr7A 245429574 245430993 1419 True 2410.000000 2410 97.328000 1523 2941 1 chr7A.!!$R1 1418
15 TraesCS6A01G100200 chr6D 229641462 229643556 2094 True 1903.000000 1903 83.520000 1523 3612 1 chr6D.!!$R2 2089
16 TraesCS6A01G100200 chr6D 197908006 197910096 2090 False 1716.000000 1716 82.033000 1523 3612 1 chr6D.!!$F1 2089
17 TraesCS6A01G100200 chr6D 186930542 186931414 872 True 1033.000000 1033 88.414000 1523 2385 1 chr6D.!!$R1 862
18 TraesCS6A01G100200 chr6D 179215092 179217222 2130 True 934.500000 1652 86.011000 1523 3612 2 chr6D.!!$R3 2089
19 TraesCS6A01G100200 chr1D 238011575 238013006 1431 False 1784.000000 1784 89.434000 1523 2941 1 chr1D.!!$F1 1418
20 TraesCS6A01G100200 chr6B 85667176 85668067 891 False 1399.000000 1399 94.966000 628 1520 1 chr6B.!!$F1 892
21 TraesCS6A01G100200 chr4B 434984187 434985077 890 False 1365.000000 1365 94.295000 628 1520 1 chr4B.!!$F1 892
22 TraesCS6A01G100200 chr4B 173391963 173392796 833 True 1280.000000 1280 94.365000 625 1458 1 chr4B.!!$R1 833
23 TraesCS6A01G100200 chr7B 300045891 300046781 890 False 1349.000000 1349 93.960000 628 1520 1 chr7B.!!$F2 892
24 TraesCS6A01G100200 chr7B 292478473 292479248 775 False 612.000000 612 81.196000 732 1523 1 chr7B.!!$F1 791
25 TraesCS6A01G100200 chr5B 358455192 358460076 4884 True 1296.000000 1345 92.928000 625 1520 2 chr5B.!!$R1 895
26 TraesCS6A01G100200 chr3B 151817293 151818177 884 True 1330.000000 1330 93.799000 635 1520 1 chr3B.!!$R1 885
27 TraesCS6A01G100200 chr3B 545967312 545968200 888 True 1312.000000 1312 93.371000 635 1520 1 chr3B.!!$R2 885
28 TraesCS6A01G100200 chr1B 413056570 413057403 833 False 1280.000000 1280 94.365000 625 1458 1 chr1B.!!$F1 833
29 TraesCS6A01G100200 chr1B 84521820 84522428 608 True 896.000000 896 93.301000 1 608 1 chr1B.!!$R1 607

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
941 1413 0.247185 ACCATTGCCGCTTCCATTTG 59.753 50.000 0.00 0.00 0.0 2.32 F
2326 6909 2.202987 CGGATGCTGCAGGAGTCC 60.203 66.667 17.12 18.75 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2408 6991 3.818787 GCCTGCAACATCGGCCAG 61.819 66.667 2.24 0.0 37.86 4.85 R
3197 7824 4.574828 TCAACTGTACCAGAACTTTTCAGC 59.425 41.667 0.00 0.0 35.18 4.26 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
105 106 0.393808 GCTATCTGGGCCGGAAAACA 60.394 55.000 21.02 4.19 0.00 2.83
182 184 2.002018 AACCAGAGGGCGGGACAAAA 62.002 55.000 0.00 0.00 37.90 2.44
608 700 2.997986 GTCCACACCATAACGAACGATT 59.002 45.455 0.14 0.00 0.00 3.34
610 702 4.626604 GTCCACACCATAACGAACGATTTA 59.373 41.667 0.14 0.00 0.00 1.40
611 703 4.865925 TCCACACCATAACGAACGATTTAG 59.134 41.667 0.14 0.00 0.00 1.85
612 704 4.493545 CCACACCATAACGAACGATTTAGC 60.494 45.833 0.14 0.00 0.00 3.09
613 705 4.092237 CACACCATAACGAACGATTTAGCA 59.908 41.667 0.14 0.00 0.00 3.49
615 707 4.565166 CACCATAACGAACGATTTAGCAGA 59.435 41.667 0.14 0.00 0.00 4.26
616 708 5.234329 CACCATAACGAACGATTTAGCAGAT 59.766 40.000 0.14 0.00 0.00 2.90
617 709 5.815740 ACCATAACGAACGATTTAGCAGATT 59.184 36.000 0.14 0.00 0.00 2.40
618 710 6.315393 ACCATAACGAACGATTTAGCAGATTT 59.685 34.615 0.14 0.00 0.00 2.17
656 1121 1.477553 ATGCCATCATCACAACCACC 58.522 50.000 0.00 0.00 0.00 4.61
723 1188 4.457834 AGACTAATCAGTGCACCAGTAC 57.542 45.455 14.63 4.43 34.21 2.73
747 1212 5.838531 AAACATTTGACTTGGACGGTTAA 57.161 34.783 0.00 0.00 0.00 2.01
906 1378 2.507058 CCCATTGTCTTCCATCTCTCCA 59.493 50.000 0.00 0.00 0.00 3.86
941 1413 0.247185 ACCATTGCCGCTTCCATTTG 59.753 50.000 0.00 0.00 0.00 2.32
1378 5854 3.504906 CCTACTCATTTGCCCTGCATATG 59.495 47.826 11.66 11.66 44.89 1.78
1379 5855 2.313317 ACTCATTTGCCCTGCATATGG 58.687 47.619 15.99 10.87 44.12 2.74
1380 5856 2.313317 CTCATTTGCCCTGCATATGGT 58.687 47.619 15.99 0.00 44.12 3.55
1381 5857 2.696707 CTCATTTGCCCTGCATATGGTT 59.303 45.455 15.99 0.00 44.12 3.67
1382 5858 3.106054 TCATTTGCCCTGCATATGGTTT 58.894 40.909 15.99 0.00 44.12 3.27
1383 5859 4.285020 TCATTTGCCCTGCATATGGTTTA 58.715 39.130 15.99 0.00 44.12 2.01
1384 5860 4.900652 TCATTTGCCCTGCATATGGTTTAT 59.099 37.500 15.99 0.00 44.12 1.40
1385 5861 4.935352 TTTGCCCTGCATATGGTTTATC 57.065 40.909 4.56 0.00 38.76 1.75
1386 5862 3.882102 TGCCCTGCATATGGTTTATCT 57.118 42.857 4.56 0.00 31.71 1.98
1387 5863 3.489355 TGCCCTGCATATGGTTTATCTG 58.511 45.455 4.56 0.00 31.71 2.90
1388 5864 3.117550 TGCCCTGCATATGGTTTATCTGT 60.118 43.478 4.56 0.00 31.71 3.41
1389 5865 3.891366 GCCCTGCATATGGTTTATCTGTT 59.109 43.478 4.56 0.00 0.00 3.16
1390 5866 4.342092 GCCCTGCATATGGTTTATCTGTTT 59.658 41.667 4.56 0.00 0.00 2.83
1391 5867 5.163416 GCCCTGCATATGGTTTATCTGTTTT 60.163 40.000 4.56 0.00 0.00 2.43
1392 5868 6.040391 GCCCTGCATATGGTTTATCTGTTTTA 59.960 38.462 4.56 0.00 0.00 1.52
1393 5869 7.255942 GCCCTGCATATGGTTTATCTGTTTTAT 60.256 37.037 4.56 0.00 0.00 1.40
1394 5870 8.641541 CCCTGCATATGGTTTATCTGTTTTATT 58.358 33.333 4.56 0.00 0.00 1.40
1436 5912 9.665719 AAATTTAATCACACTTGTTTTCCAACT 57.334 25.926 0.00 0.00 33.58 3.16
1438 5914 9.965824 ATTTAATCACACTTGTTTTCCAACTAG 57.034 29.630 0.00 0.00 40.45 2.57
1439 5915 8.740123 TTAATCACACTTGTTTTCCAACTAGA 57.260 30.769 0.00 0.00 37.81 2.43
1440 5916 7.823745 AATCACACTTGTTTTCCAACTAGAT 57.176 32.000 0.00 0.00 37.81 1.98
1441 5917 6.618287 TCACACTTGTTTTCCAACTAGATG 57.382 37.500 0.00 0.00 37.81 2.90
1442 5918 6.119536 TCACACTTGTTTTCCAACTAGATGT 58.880 36.000 0.00 2.76 37.81 3.06
1443 5919 7.276658 TCACACTTGTTTTCCAACTAGATGTA 58.723 34.615 0.00 0.00 37.81 2.29
1444 5920 7.225931 TCACACTTGTTTTCCAACTAGATGTAC 59.774 37.037 0.00 0.00 37.81 2.90
1445 5921 7.226720 CACACTTGTTTTCCAACTAGATGTACT 59.773 37.037 0.00 0.00 37.81 2.73
1446 5922 8.426489 ACACTTGTTTTCCAACTAGATGTACTA 58.574 33.333 0.00 0.00 37.81 1.82
1459 5935 5.801531 AGATGTACTAGTGTGGTTTGTGA 57.198 39.130 5.39 0.00 0.00 3.58
1460 5936 6.169557 AGATGTACTAGTGTGGTTTGTGAA 57.830 37.500 5.39 0.00 0.00 3.18
1461 5937 6.588204 AGATGTACTAGTGTGGTTTGTGAAA 58.412 36.000 5.39 0.00 0.00 2.69
1462 5938 7.051623 AGATGTACTAGTGTGGTTTGTGAAAA 58.948 34.615 5.39 0.00 0.00 2.29
1463 5939 6.671614 TGTACTAGTGTGGTTTGTGAAAAG 57.328 37.500 5.39 0.00 0.00 2.27
1464 5940 6.174760 TGTACTAGTGTGGTTTGTGAAAAGT 58.825 36.000 5.39 0.00 0.00 2.66
1465 5941 5.560966 ACTAGTGTGGTTTGTGAAAAGTG 57.439 39.130 0.00 0.00 0.00 3.16
1466 5942 3.866883 AGTGTGGTTTGTGAAAAGTGG 57.133 42.857 0.00 0.00 0.00 4.00
1467 5943 3.426615 AGTGTGGTTTGTGAAAAGTGGA 58.573 40.909 0.00 0.00 0.00 4.02
1468 5944 4.023291 AGTGTGGTTTGTGAAAAGTGGAT 58.977 39.130 0.00 0.00 0.00 3.41
1469 5945 4.111916 GTGTGGTTTGTGAAAAGTGGATG 58.888 43.478 0.00 0.00 0.00 3.51
1470 5946 3.123050 GTGGTTTGTGAAAAGTGGATGC 58.877 45.455 0.00 0.00 0.00 3.91
1471 5947 2.762887 TGGTTTGTGAAAAGTGGATGCA 59.237 40.909 0.00 0.00 0.00 3.96
1472 5948 3.123050 GGTTTGTGAAAAGTGGATGCAC 58.877 45.455 9.70 9.70 0.00 4.57
1473 5949 3.181476 GGTTTGTGAAAAGTGGATGCACT 60.181 43.478 14.93 14.93 36.92 4.40
1474 5950 4.037446 GGTTTGTGAAAAGTGGATGCACTA 59.963 41.667 21.06 1.41 34.56 2.74
1475 5951 4.829064 TTGTGAAAAGTGGATGCACTAC 57.171 40.909 21.06 14.89 34.56 2.73
1476 5952 4.085357 TGTGAAAAGTGGATGCACTACT 57.915 40.909 21.06 10.47 42.02 2.57
1477 5953 3.814842 TGTGAAAAGTGGATGCACTACTG 59.185 43.478 21.06 0.00 40.15 2.74
1478 5954 2.813754 TGAAAAGTGGATGCACTACTGC 59.186 45.455 21.06 10.08 40.15 4.40
1490 5966 4.756084 GCACTACTGCATTTTCTCAAGT 57.244 40.909 0.00 0.00 43.62 3.16
1491 5967 5.862924 GCACTACTGCATTTTCTCAAGTA 57.137 39.130 0.00 0.00 43.62 2.24
1492 5968 5.862811 GCACTACTGCATTTTCTCAAGTAG 58.137 41.667 6.61 6.61 43.62 2.57
1493 5969 5.639506 GCACTACTGCATTTTCTCAAGTAGA 59.360 40.000 13.51 0.00 43.62 2.59
1494 5970 6.314896 GCACTACTGCATTTTCTCAAGTAGAT 59.685 38.462 13.51 0.00 43.62 1.98
1495 5971 7.492669 GCACTACTGCATTTTCTCAAGTAGATA 59.507 37.037 13.51 0.00 43.62 1.98
1496 5972 9.539825 CACTACTGCATTTTCTCAAGTAGATAT 57.460 33.333 13.51 0.00 33.05 1.63
1843 6378 7.379750 GTGAAGTGGTATAGGTCCATATCTTC 58.620 42.308 0.00 0.00 36.75 2.87
1872 6407 8.063630 GCACATGTTTCTCAAACTAATTTTTGG 58.936 33.333 0.00 0.00 41.90 3.28
1963 6519 9.651913 AAAGAAAACTAAACTTGAATCAAGCAA 57.348 25.926 21.69 7.49 44.43 3.91
2326 6909 2.202987 CGGATGCTGCAGGAGTCC 60.203 66.667 17.12 18.75 0.00 3.85
2408 6991 2.167900 ACCAGCAAATACTACGACTCCC 59.832 50.000 0.00 0.00 0.00 4.30
2539 7125 4.871513 TCATCACGTATGCAGGAATAGAC 58.128 43.478 0.00 0.00 35.38 2.59
2800 7388 3.699038 TCAGGGTTTGAACAAGTTTCCTG 59.301 43.478 14.67 14.67 41.17 3.86
3073 7700 7.615790 ACGAACACTAAAAAGACTAAGTTTCG 58.384 34.615 0.00 0.00 37.84 3.46
3126 7753 9.686683 AGCATCATGGTAAAAAGTAGTTAGAAT 57.313 29.630 0.00 0.00 0.00 2.40
3197 7824 3.074687 TCCTAGTCACTAGCATCCTAGGG 59.925 52.174 9.46 0.00 44.83 3.53
3289 7916 5.009610 AGCTTCAGTTCGCATTCCTTAAAAA 59.990 36.000 0.00 0.00 0.00 1.94
3295 7922 4.497473 TCGCATTCCTTAAAAACAGTGG 57.503 40.909 0.00 0.00 0.00 4.00
3296 7923 3.886505 TCGCATTCCTTAAAAACAGTGGT 59.113 39.130 0.00 0.00 0.00 4.16
3503 8154 7.826252 ACAGAAGACATACTAGCATCAAACAAT 59.174 33.333 0.00 0.00 0.00 2.71
3552 8207 6.711277 AGTACTAGCACAATTGGAATCTCAA 58.289 36.000 10.83 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.148279 CGCTAGTCGAGGGGGCTT 61.148 66.667 0.98 0.00 41.67 4.35
656 1121 0.670546 AATCCCACTTGCACGTCTCG 60.671 55.000 0.00 0.00 0.00 4.04
723 1188 4.040445 ACCGTCCAAGTCAAATGTTTTG 57.960 40.909 0.00 0.00 0.00 2.44
747 1212 1.384191 GGTGGTGGCCTGGAAGAAT 59.616 57.895 3.32 0.00 34.07 2.40
884 1356 2.158696 GGAGAGATGGAAGACAATGGGG 60.159 54.545 0.00 0.00 0.00 4.96
906 1378 0.908910 TGGTGCTATGTGGGAACGAT 59.091 50.000 0.00 0.00 0.00 3.73
941 1413 1.360192 GGAGGTTTGTGTGCAGTGC 59.640 57.895 8.58 8.58 0.00 4.40
1045 1517 0.180406 ACGAGGTTGCTCCACTTGTT 59.820 50.000 0.00 0.00 39.02 2.83
1051 1523 1.532604 ATGTCGACGAGGTTGCTCCA 61.533 55.000 11.62 0.00 39.02 3.86
1348 5824 2.289002 GGCAAATGAGTAGGATTGCTCG 59.711 50.000 8.94 0.00 45.60 5.03
1410 5886 9.665719 AGTTGGAAAACAAGTGTGATTAAATTT 57.334 25.926 0.00 0.00 41.13 1.82
1412 5888 9.965824 CTAGTTGGAAAACAAGTGTGATTAAAT 57.034 29.630 0.00 0.00 42.57 1.40
1413 5889 9.179909 TCTAGTTGGAAAACAAGTGTGATTAAA 57.820 29.630 0.00 0.00 42.57 1.52
1414 5890 8.740123 TCTAGTTGGAAAACAAGTGTGATTAA 57.260 30.769 0.00 0.00 42.57 1.40
1415 5891 8.783093 CATCTAGTTGGAAAACAAGTGTGATTA 58.217 33.333 0.00 0.00 42.57 1.75
1416 5892 7.285401 ACATCTAGTTGGAAAACAAGTGTGATT 59.715 33.333 5.80 0.00 42.57 2.57
1417 5893 6.772716 ACATCTAGTTGGAAAACAAGTGTGAT 59.227 34.615 5.80 0.00 42.57 3.06
1418 5894 6.119536 ACATCTAGTTGGAAAACAAGTGTGA 58.880 36.000 5.80 0.00 42.57 3.58
1419 5895 6.377327 ACATCTAGTTGGAAAACAAGTGTG 57.623 37.500 5.80 0.00 42.57 3.82
1420 5896 7.280356 AGTACATCTAGTTGGAAAACAAGTGT 58.720 34.615 5.80 0.00 42.57 3.55
1421 5897 7.730364 AGTACATCTAGTTGGAAAACAAGTG 57.270 36.000 5.80 0.00 42.57 3.16
1436 5912 6.904463 TCACAAACCACACTAGTACATCTA 57.096 37.500 0.00 0.00 0.00 1.98
1437 5913 5.801531 TCACAAACCACACTAGTACATCT 57.198 39.130 0.00 0.00 0.00 2.90
1438 5914 6.854496 TTTCACAAACCACACTAGTACATC 57.146 37.500 0.00 0.00 0.00 3.06
1439 5915 6.826741 ACTTTTCACAAACCACACTAGTACAT 59.173 34.615 0.00 0.00 0.00 2.29
1440 5916 6.092944 CACTTTTCACAAACCACACTAGTACA 59.907 38.462 0.00 0.00 0.00 2.90
1441 5917 6.457799 CCACTTTTCACAAACCACACTAGTAC 60.458 42.308 0.00 0.00 0.00 2.73
1442 5918 5.587043 CCACTTTTCACAAACCACACTAGTA 59.413 40.000 0.00 0.00 0.00 1.82
1443 5919 4.398044 CCACTTTTCACAAACCACACTAGT 59.602 41.667 0.00 0.00 0.00 2.57
1444 5920 4.638421 TCCACTTTTCACAAACCACACTAG 59.362 41.667 0.00 0.00 0.00 2.57
1445 5921 4.590918 TCCACTTTTCACAAACCACACTA 58.409 39.130 0.00 0.00 0.00 2.74
1446 5922 3.426615 TCCACTTTTCACAAACCACACT 58.573 40.909 0.00 0.00 0.00 3.55
1447 5923 3.859411 TCCACTTTTCACAAACCACAC 57.141 42.857 0.00 0.00 0.00 3.82
1448 5924 3.430098 GCATCCACTTTTCACAAACCACA 60.430 43.478 0.00 0.00 0.00 4.17
1449 5925 3.123050 GCATCCACTTTTCACAAACCAC 58.877 45.455 0.00 0.00 0.00 4.16
1450 5926 2.762887 TGCATCCACTTTTCACAAACCA 59.237 40.909 0.00 0.00 0.00 3.67
1451 5927 3.123050 GTGCATCCACTTTTCACAAACC 58.877 45.455 0.00 0.00 38.93 3.27
1469 5945 6.314896 ATCTACTTGAGAAAATGCAGTAGTGC 59.685 38.462 15.93 15.93 43.61 4.40
1470 5946 7.840342 ATCTACTTGAGAAAATGCAGTAGTG 57.160 36.000 0.00 0.00 37.85 2.74
1503 5979 9.744468 GAACAGTACTGGTTCAAAAATACATTT 57.256 29.630 26.12 5.93 43.16 2.32
1515 5991 5.934625 ACAGATGAATGAACAGTACTGGTTC 59.065 40.000 26.12 23.32 43.78 3.62
1516 5992 5.869579 ACAGATGAATGAACAGTACTGGTT 58.130 37.500 26.12 17.08 34.19 3.67
1517 5993 5.489792 ACAGATGAATGAACAGTACTGGT 57.510 39.130 26.12 21.30 34.19 4.00
1518 5994 5.702670 ACAACAGATGAATGAACAGTACTGG 59.297 40.000 26.12 9.07 34.19 4.00
1519 5995 6.791887 ACAACAGATGAATGAACAGTACTG 57.208 37.500 21.44 21.44 0.00 2.74
1520 5996 6.874134 GGTACAACAGATGAATGAACAGTACT 59.126 38.462 0.00 0.00 0.00 2.73
1521 5997 6.649141 TGGTACAACAGATGAATGAACAGTAC 59.351 38.462 0.00 0.00 31.92 2.73
1843 6378 7.878477 AATTAGTTTGAGAAACATGTGCATG 57.122 32.000 10.31 10.31 43.79 4.06
1963 6519 5.946942 ACCAGAGTCAATGATAGATGTGT 57.053 39.130 0.00 0.00 0.00 3.72
2004 6571 4.935352 TTGCTTTACCAAATGCTTCACT 57.065 36.364 0.00 0.00 36.85 3.41
2408 6991 3.818787 GCCTGCAACATCGGCCAG 61.819 66.667 2.24 0.00 37.86 4.85
2800 7388 5.577164 AGCAAACGATGTACTTGATAGACAC 59.423 40.000 0.00 0.00 0.00 3.67
3073 7700 0.321653 ACTGAATGTTGTCCTCGGCC 60.322 55.000 0.00 0.00 0.00 6.13
3126 7753 9.706691 CTTTTCCTGATGTAGTACTTAGTGAAA 57.293 33.333 0.00 0.00 0.00 2.69
3140 7767 5.351458 GTGTTTCTTTGCTTTTCCTGATGT 58.649 37.500 0.00 0.00 0.00 3.06
3197 7824 4.574828 TCAACTGTACCAGAACTTTTCAGC 59.425 41.667 0.00 0.00 35.18 4.26
3449 8077 9.139174 GTGTTTCTTGTGATTTTTCTCTTTTGA 57.861 29.630 0.00 0.00 0.00 2.69
3552 8207 8.876790 GCACTTACCGAATAAACTTAGTTGTAT 58.123 33.333 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.