Multiple sequence alignment - TraesCS3A01G109500

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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 TraesCS3A01G109500 chr3A 100.000 4089 0 0 1 4089 75544607 75548695 0.000000e+00 7552
1 TraesCS3A01G109500 chr3A 99.054 846 3 3 1 843 457933764 457934607 0.000000e+00 1513
2 TraesCS3A01G109500 chr3D 93.764 1748 58 23 1798 3538 64762683 64764386 0.000000e+00 2577
3 TraesCS3A01G109500 chr3D 96.134 957 24 4 840 1792 64761669 64762616 0.000000e+00 1550
4 TraesCS3A01G109500 chr3D 93.593 437 26 2 3614 4049 64764888 64765323 0.000000e+00 651
5 TraesCS3A01G109500 chr3B 92.016 1766 63 36 1798 3539 107959591 107961302 0.000000e+00 2409
6 TraesCS3A01G109500 chr3B 98.932 843 4 3 1 840 572844697 572843857 0.000000e+00 1502
7 TraesCS3A01G109500 chr3B 93.688 903 30 10 840 1736 107958576 107959457 0.000000e+00 1327
8 TraesCS3A01G109500 chr3B 84.270 445 21 10 3548 3988 107961286 107961685 4.960000e-104 388
9 TraesCS3A01G109500 chr4A 98.932 843 6 2 1 840 604852243 604851401 0.000000e+00 1504
10 TraesCS3A01G109500 chr4A 98.932 843 4 3 1 840 607377018 607376178 0.000000e+00 1502
11 TraesCS3A01G109500 chr7B 98.932 843 4 3 1 840 412900053 412900893 0.000000e+00 1502
12 TraesCS3A01G109500 chr7A 98.932 843 4 3 1 840 332824118 332823278 0.000000e+00 1502
13 TraesCS3A01G109500 chr5B 98.817 845 5 3 1 842 705520466 705519624 0.000000e+00 1500
14 TraesCS3A01G109500 chrUn 98.814 843 7 2 1 840 380178921 380179763 0.000000e+00 1498
15 TraesCS3A01G109500 chr1B 97.592 872 13 6 1 869 348477523 348478389 0.000000e+00 1487


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 TraesCS3A01G109500 chr3A 75544607 75548695 4088 False 7552.000000 7552 100.000000 1 4089 1 chr3A.!!$F1 4088
1 TraesCS3A01G109500 chr3A 457933764 457934607 843 False 1513.000000 1513 99.054000 1 843 1 chr3A.!!$F2 842
2 TraesCS3A01G109500 chr3D 64761669 64765323 3654 False 1592.666667 2577 94.497000 840 4049 3 chr3D.!!$F1 3209
3 TraesCS3A01G109500 chr3B 572843857 572844697 840 True 1502.000000 1502 98.932000 1 840 1 chr3B.!!$R1 839
4 TraesCS3A01G109500 chr3B 107958576 107961685 3109 False 1374.666667 2409 89.991333 840 3988 3 chr3B.!!$F1 3148
5 TraesCS3A01G109500 chr4A 604851401 604852243 842 True 1504.000000 1504 98.932000 1 840 1 chr4A.!!$R1 839
6 TraesCS3A01G109500 chr4A 607376178 607377018 840 True 1502.000000 1502 98.932000 1 840 1 chr4A.!!$R2 839
7 TraesCS3A01G109500 chr7B 412900053 412900893 840 False 1502.000000 1502 98.932000 1 840 1 chr7B.!!$F1 839
8 TraesCS3A01G109500 chr7A 332823278 332824118 840 True 1502.000000 1502 98.932000 1 840 1 chr7A.!!$R1 839
9 TraesCS3A01G109500 chr5B 705519624 705520466 842 True 1500.000000 1500 98.817000 1 842 1 chr5B.!!$R1 841
10 TraesCS3A01G109500 chrUn 380178921 380179763 842 False 1498.000000 1498 98.814000 1 840 1 chrUn.!!$F1 839
11 TraesCS3A01G109500 chr1B 348477523 348478389 866 False 1487.000000 1487 97.592000 1 869 1 chr1B.!!$F1 868

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
678 682 0.108615 GCGTGGTAGCTCAGACATGT 60.109 55.0 0.00 0.0 0.0 3.21 F
1598 1606 0.179145 CTGGACGTCATCACCGGTAC 60.179 60.0 18.91 0.0 0.0 3.34 F
2768 2883 0.512952 CGCACTTAACTGACACTGGC 59.487 55.0 0.00 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 2040 1.146263 GCCGGGTGGAGTAATGGAG 59.854 63.158 2.18 0.0 37.49 3.86 R
3005 3120 0.320374 TTCATCTCCACGAAGCGGTT 59.680 50.000 0.00 0.0 0.00 4.44 R
4058 4639 1.899814 AGGGTACGAAGAATGAGCACA 59.100 47.619 0.00 0.0 0.00 4.57 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
393 397 1.336755 GTGTGGAATGTGTGTCCCAAC 59.663 52.381 0.00 0.00 33.89 3.77
465 469 5.240403 GGAAGATATTGCCCTGAATTCTCAC 59.760 44.000 7.05 0.00 0.00 3.51
678 682 0.108615 GCGTGGTAGCTCAGACATGT 60.109 55.000 0.00 0.00 0.00 3.21
963 971 2.289506 ACCCAGCAGATCATCATCATCG 60.290 50.000 0.00 0.00 0.00 3.84
973 981 3.129871 TCATCATCATCGCATTAACGCA 58.870 40.909 0.00 0.00 0.00 5.24
976 984 0.944386 ATCATCGCATTAACGCACCC 59.056 50.000 0.00 0.00 0.00 4.61
993 1001 0.872021 CCCAGCTAGCTAAACGCGAG 60.872 60.000 18.86 0.00 45.59 5.03
1275 1283 1.527370 GTGGCCCTACACCATCTCC 59.473 63.158 0.00 0.00 39.95 3.71
1284 1292 3.470888 ACCATCTCCTTCCGCGGG 61.471 66.667 27.83 10.29 0.00 6.13
1497 1505 1.321074 GGACGGACTACCTCCACCTG 61.321 65.000 0.00 0.00 39.39 4.00
1595 1603 2.509336 GCTGGACGTCATCACCGG 60.509 66.667 18.91 0.00 0.00 5.28
1596 1604 2.970639 CTGGACGTCATCACCGGT 59.029 61.111 18.91 0.00 0.00 5.28
1597 1605 1.940883 GCTGGACGTCATCACCGGTA 61.941 60.000 18.91 0.00 33.13 4.02
1598 1606 0.179145 CTGGACGTCATCACCGGTAC 60.179 60.000 18.91 0.00 0.00 3.34
1749 1790 1.743394 TCGCAACTCGCTCATCTTCTA 59.257 47.619 0.00 0.00 39.08 2.10
1750 1791 1.849219 CGCAACTCGCTCATCTTCTAC 59.151 52.381 0.00 0.00 39.08 2.59
1751 1792 1.849219 GCAACTCGCTCATCTTCTACG 59.151 52.381 0.00 0.00 37.77 3.51
1771 1813 2.472232 TACGCACACGGCAGTCTCAG 62.472 60.000 0.00 0.00 46.04 3.35
1936 2039 8.387813 ACATTTCCCCTCTGTGTTAAATTACTA 58.612 33.333 0.00 0.00 0.00 1.82
1937 2040 8.674607 CATTTCCCCTCTGTGTTAAATTACTAC 58.325 37.037 0.00 0.00 0.00 2.73
1938 2041 7.563724 TTCCCCTCTGTGTTAAATTACTACT 57.436 36.000 0.00 0.00 0.00 2.57
1948 2051 9.880157 TGTGTTAAATTACTACTCCATTACTCC 57.120 33.333 0.00 0.00 0.00 3.85
2042 2154 2.091112 CGTGCTCCAAGTCGCTCAG 61.091 63.158 0.00 0.00 0.00 3.35
2370 2482 3.039588 GCCACCACCGTGTACGTG 61.040 66.667 0.00 0.00 38.41 4.49
2395 2507 2.486322 GCGACGCTCAACTACGACG 61.486 63.158 13.73 0.00 46.91 5.12
2698 2813 2.340337 ACAAATCCAAGTACGTACGCC 58.660 47.619 19.49 6.28 0.00 5.68
2764 2879 2.470821 ACTCACGCACTTAACTGACAC 58.529 47.619 0.00 0.00 0.00 3.67
2765 2880 2.100916 ACTCACGCACTTAACTGACACT 59.899 45.455 0.00 0.00 0.00 3.55
2766 2881 2.469826 TCACGCACTTAACTGACACTG 58.530 47.619 0.00 0.00 0.00 3.66
2767 2882 1.526887 CACGCACTTAACTGACACTGG 59.473 52.381 0.00 0.00 0.00 4.00
2768 2883 0.512952 CGCACTTAACTGACACTGGC 59.487 55.000 0.00 0.00 0.00 4.85
2769 2884 1.873903 CGCACTTAACTGACACTGGCT 60.874 52.381 0.00 0.00 0.00 4.75
3005 3120 3.936203 ACTTCGGCGGCAAGTGGA 61.936 61.111 20.26 3.10 32.65 4.02
3007 3122 2.966309 CTTCGGCGGCAAGTGGAAC 61.966 63.158 10.53 0.00 0.00 3.62
3079 3194 1.815003 GGCCAAGACATCTTCAACCTG 59.185 52.381 0.00 0.00 33.11 4.00
3080 3195 1.815003 GCCAAGACATCTTCAACCTGG 59.185 52.381 0.00 0.00 33.11 4.45
3101 3216 6.061022 TGGTCCTTTGAGTAGATGCAATTA 57.939 37.500 0.00 0.00 0.00 1.40
3102 3217 5.880332 TGGTCCTTTGAGTAGATGCAATTAC 59.120 40.000 0.00 0.00 0.00 1.89
3103 3218 6.116126 GGTCCTTTGAGTAGATGCAATTACT 58.884 40.000 11.90 11.90 33.00 2.24
3104 3219 7.093068 TGGTCCTTTGAGTAGATGCAATTACTA 60.093 37.037 12.01 2.32 30.58 1.82
3105 3220 7.224949 GGTCCTTTGAGTAGATGCAATTACTAC 59.775 40.741 12.01 12.28 37.38 2.73
3131 3246 9.924650 CTAGTTGTTACTACTTGTGGATTAACT 57.075 33.333 4.66 0.00 35.78 2.24
3132 3247 8.828688 AGTTGTTACTACTTGTGGATTAACTC 57.171 34.615 0.00 0.00 31.21 3.01
3252 3367 4.100035 TCGAGCTTGAATCTCCACATGTAT 59.900 41.667 0.00 0.00 0.00 2.29
3260 3375 5.362717 TGAATCTCCACATGTATCCGTTACT 59.637 40.000 0.00 0.00 0.00 2.24
3263 3378 6.778834 TCTCCACATGTATCCGTTACTAAA 57.221 37.500 0.00 0.00 0.00 1.85
3267 3382 7.149973 TCCACATGTATCCGTTACTAAATAGC 58.850 38.462 0.00 0.00 0.00 2.97
3294 3409 6.604735 AGTACTGTAAGCAAAAGTGTGAAG 57.395 37.500 0.00 0.00 37.60 3.02
3306 3421 0.868406 GTGTGAAGAAAGCTCCACCG 59.132 55.000 0.00 0.00 0.00 4.94
3322 3437 1.876799 CACCGATGTACACTTTGCCAA 59.123 47.619 0.00 0.00 0.00 4.52
3337 3452 8.344098 ACACTTTGCCAAATAAATGTTTCATTG 58.656 29.630 0.00 0.00 0.00 2.82
3344 3460 7.412237 GCCAAATAAATGTTTCATTGAGCTCAC 60.412 37.037 18.03 4.16 0.00 3.51
3400 3516 9.965824 TCCTTTATTTGTTTGAGCTCTTTTAAG 57.034 29.630 16.19 6.15 0.00 1.85
3404 3520 9.950680 TTATTTGTTTGAGCTCTTTTAAGACTG 57.049 29.630 16.19 0.00 0.00 3.51
3405 3521 5.424121 TGTTTGAGCTCTTTTAAGACTGC 57.576 39.130 16.19 0.00 0.00 4.40
3406 3522 5.126067 TGTTTGAGCTCTTTTAAGACTGCT 58.874 37.500 16.19 6.08 38.71 4.24
3408 3524 3.931578 TGAGCTCTTTTAAGACTGCTCC 58.068 45.455 21.36 10.82 45.47 4.70
3409 3525 3.324846 TGAGCTCTTTTAAGACTGCTCCA 59.675 43.478 21.36 12.42 45.47 3.86
3410 3526 4.202357 TGAGCTCTTTTAAGACTGCTCCAA 60.202 41.667 21.36 9.08 45.47 3.53
3411 3527 4.916183 AGCTCTTTTAAGACTGCTCCAAT 58.084 39.130 1.61 0.00 32.94 3.16
3415 3537 7.613411 AGCTCTTTTAAGACTGCTCCAATTTAT 59.387 33.333 1.61 0.00 32.94 1.40
3439 3566 5.027385 TCCTAGGGGGTAAGAGTGTTTAA 57.973 43.478 9.46 0.00 36.25 1.52
3451 3578 8.198109 GGTAAGAGTGTTTAATCTGAGCTATCA 58.802 37.037 0.00 0.00 30.50 2.15
3466 3593 4.970711 AGCTATCAATGACTGATCAAGGG 58.029 43.478 0.00 0.00 44.05 3.95
3467 3594 4.411540 AGCTATCAATGACTGATCAAGGGT 59.588 41.667 0.00 0.00 44.05 4.34
3468 3595 5.604231 AGCTATCAATGACTGATCAAGGGTA 59.396 40.000 0.00 0.00 44.05 3.69
3485 3612 5.256806 AGGGTAGTTTTGGCTAAATGAGT 57.743 39.130 0.00 0.00 0.00 3.41
3486 3613 6.382919 AGGGTAGTTTTGGCTAAATGAGTA 57.617 37.500 0.00 0.00 0.00 2.59
3487 3614 6.178324 AGGGTAGTTTTGGCTAAATGAGTAC 58.822 40.000 0.00 0.27 0.00 2.73
3488 3615 5.064325 GGGTAGTTTTGGCTAAATGAGTACG 59.936 44.000 0.00 0.00 0.00 3.67
3489 3616 5.640783 GGTAGTTTTGGCTAAATGAGTACGT 59.359 40.000 0.00 0.00 0.00 3.57
3538 3666 6.211384 AGCATCCACTTAAGGCAAGTTATTTT 59.789 34.615 7.53 0.00 45.54 1.82
3539 3667 6.873605 GCATCCACTTAAGGCAAGTTATTTTT 59.126 34.615 7.53 0.00 45.54 1.94
3568 3696 8.842358 AGGTTTAAGTCGAGTTATTTTGATGA 57.158 30.769 13.32 0.00 0.00 2.92
3646 4225 7.429374 GGAGATCTTCCATATATGATGGTGA 57.571 40.000 14.54 4.50 46.01 4.02
3735 4314 0.321919 TGTGCAGCCTCCAAAGCTAG 60.322 55.000 0.00 0.00 38.95 3.42
3737 4316 0.914644 TGCAGCCTCCAAAGCTAGAT 59.085 50.000 0.00 0.00 38.95 1.98
3798 4378 5.245751 GTCTCATATGACATCCATCCAGACT 59.754 44.000 0.00 0.00 35.05 3.24
3800 4380 6.435591 TCTCATATGACATCCATCCAGACTAC 59.564 42.308 0.00 0.00 36.71 2.73
3843 4423 7.508134 CATCTCATGTTCGAACACATCATATC 58.492 38.462 31.87 0.36 42.51 1.63
3848 4428 4.329801 TGTTCGAACACATCATATCTGTGC 59.670 41.667 26.53 0.00 46.27 4.57
3853 4433 5.276726 CGAACACATCATATCTGTGCTGAAG 60.277 44.000 12.71 1.00 46.27 3.02
3929 4510 7.018826 CACTACTCAAAGTCAAACACGAAAAA 58.981 34.615 0.00 0.00 0.00 1.94
3988 4569 7.041721 TGTGTCCTATTCATAGCAAACTAGTG 58.958 38.462 0.00 0.00 0.00 2.74
3999 4580 9.296400 TCATAGCAAACTAGTGTTTTTGAAAAC 57.704 29.630 11.41 11.41 43.13 2.43
4006 4587 9.705290 AAACTAGTGTTTTTGAAAACTCACAAT 57.295 25.926 19.58 11.40 46.37 2.71
4039 4620 4.095036 TGTTTTGCTAATGACGTGTGAACA 59.905 37.500 0.00 0.00 0.00 3.18
4049 4630 3.498777 TGACGTGTGAACAACTTTGAACA 59.501 39.130 0.00 0.00 0.00 3.18
4050 4631 3.817238 ACGTGTGAACAACTTTGAACAC 58.183 40.909 12.93 12.93 37.28 3.32
4051 4632 3.251245 ACGTGTGAACAACTTTGAACACA 59.749 39.130 18.41 17.19 41.21 3.72
4052 4633 4.083003 ACGTGTGAACAACTTTGAACACAT 60.083 37.500 19.68 8.58 43.10 3.21
4053 4634 5.122554 ACGTGTGAACAACTTTGAACACATA 59.877 36.000 19.68 5.14 43.10 2.29
4054 4635 5.451023 CGTGTGAACAACTTTGAACACATAC 59.549 40.000 19.68 12.17 43.10 2.39
4055 4636 6.551736 GTGTGAACAACTTTGAACACATACT 58.448 36.000 19.68 0.00 43.10 2.12
4056 4637 6.687105 GTGTGAACAACTTTGAACACATACTC 59.313 38.462 19.68 10.03 43.10 2.59
4057 4638 6.597672 TGTGAACAACTTTGAACACATACTCT 59.402 34.615 15.85 0.00 39.97 3.24
4058 4639 7.120579 TGTGAACAACTTTGAACACATACTCTT 59.879 33.333 15.85 0.00 39.97 2.85
4059 4640 7.429340 GTGAACAACTTTGAACACATACTCTTG 59.571 37.037 13.75 0.00 37.53 3.02
4060 4641 7.120579 TGAACAACTTTGAACACATACTCTTGT 59.879 33.333 0.00 0.00 0.00 3.16
4066 4647 5.308014 TTGAACACATACTCTTGTGCTCAT 58.692 37.500 10.42 0.00 46.38 2.90
4067 4648 5.764686 TTGAACACATACTCTTGTGCTCATT 59.235 36.000 10.42 0.00 46.38 2.57
4068 4649 6.073058 TTGAACACATACTCTTGTGCTCATTC 60.073 38.462 10.42 5.50 46.38 2.67
4069 4650 8.170894 TTGAACACATACTCTTGTGCTCATTCT 61.171 37.037 10.42 0.00 46.38 2.40
4071 4652 6.104439 CACATACTCTTGTGCTCATTCTTC 57.896 41.667 0.00 0.00 40.45 2.87
4072 4653 4.867047 ACATACTCTTGTGCTCATTCTTCG 59.133 41.667 0.00 0.00 0.00 3.79
4073 4654 3.393089 ACTCTTGTGCTCATTCTTCGT 57.607 42.857 0.00 0.00 0.00 3.85
4074 4655 4.521130 ACTCTTGTGCTCATTCTTCGTA 57.479 40.909 0.00 0.00 0.00 3.43
4075 4656 4.238514 ACTCTTGTGCTCATTCTTCGTAC 58.761 43.478 0.00 0.00 0.00 3.67
4076 4657 3.585862 TCTTGTGCTCATTCTTCGTACC 58.414 45.455 0.00 0.00 0.00 3.34
4077 4658 2.380084 TGTGCTCATTCTTCGTACCC 57.620 50.000 0.00 0.00 0.00 3.69
4078 4659 1.899814 TGTGCTCATTCTTCGTACCCT 59.100 47.619 0.00 0.00 0.00 4.34
4079 4660 2.094182 TGTGCTCATTCTTCGTACCCTC 60.094 50.000 0.00 0.00 0.00 4.30
4080 4661 2.094182 GTGCTCATTCTTCGTACCCTCA 60.094 50.000 0.00 0.00 0.00 3.86
4081 4662 2.094182 TGCTCATTCTTCGTACCCTCAC 60.094 50.000 0.00 0.00 0.00 3.51
4082 4663 2.094182 GCTCATTCTTCGTACCCTCACA 60.094 50.000 0.00 0.00 0.00 3.58
4083 4664 3.430929 GCTCATTCTTCGTACCCTCACAT 60.431 47.826 0.00 0.00 0.00 3.21
4084 4665 4.202121 GCTCATTCTTCGTACCCTCACATA 60.202 45.833 0.00 0.00 0.00 2.29
4085 4666 5.515797 TCATTCTTCGTACCCTCACATAG 57.484 43.478 0.00 0.00 0.00 2.23
4086 4667 4.954202 TCATTCTTCGTACCCTCACATAGT 59.046 41.667 0.00 0.00 0.00 2.12
4087 4668 4.978083 TTCTTCGTACCCTCACATAGTC 57.022 45.455 0.00 0.00 0.00 2.59
4088 4669 4.232188 TCTTCGTACCCTCACATAGTCT 57.768 45.455 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
393 397 8.504005 ACAATCTTTTTATACCTTCTGTCAACG 58.496 33.333 0.00 0.00 0.00 4.10
678 682 4.988540 CGTCATTGTCTTTCTTCCACACTA 59.011 41.667 0.00 0.00 0.00 2.74
799 805 4.915704 CGTTGCCACGGATTAACAAATAT 58.084 39.130 1.68 0.00 43.16 1.28
800 806 4.343811 CGTTGCCACGGATTAACAAATA 57.656 40.909 1.68 0.00 43.16 1.40
973 981 1.153628 CGCGTTTAGCTAGCTGGGT 60.154 57.895 27.68 7.07 45.59 4.51
976 984 1.483424 GCCTCGCGTTTAGCTAGCTG 61.483 60.000 27.68 11.48 45.59 4.24
1473 1481 1.375098 GGAGGTAGTCCGTCCACGAG 61.375 65.000 0.00 0.00 43.02 4.18
1739 1780 3.099362 GTGTGCGTACGTAGAAGATGAG 58.901 50.000 17.90 0.00 0.00 2.90
1749 1790 4.274700 ACTGCCGTGTGCGTACGT 62.275 61.111 17.90 0.00 45.60 3.57
1750 1791 3.467119 GACTGCCGTGTGCGTACG 61.467 66.667 11.84 11.84 45.60 3.67
1751 1792 2.049433 AGACTGCCGTGTGCGTAC 60.049 61.111 0.00 0.00 45.60 3.67
1796 1838 3.238108 CTGGTCAGCTGTGGTAACTAG 57.762 52.381 14.67 7.52 37.61 2.57
1898 2001 2.607038 GGGGAAATGTCAAAGTCAACGC 60.607 50.000 0.00 0.00 0.00 4.84
1936 2039 1.623542 GCCGGGTGGAGTAATGGAGT 61.624 60.000 2.18 0.00 37.49 3.85
1937 2040 1.146263 GCCGGGTGGAGTAATGGAG 59.854 63.158 2.18 0.00 37.49 3.86
1938 2041 2.372074 GGCCGGGTGGAGTAATGGA 61.372 63.158 2.18 0.00 37.49 3.41
2285 2397 3.249837 AAGAACCCGCCCGAGTTCC 62.250 63.158 10.73 0.00 42.73 3.62
2370 2482 2.102357 TTGAGCGTCGCCTCGATC 59.898 61.111 14.86 4.95 44.74 3.69
2493 2605 2.995574 ACCCGGTCCAGGAACTCG 60.996 66.667 2.07 2.10 34.60 4.18
2698 2813 1.585297 TGCATGCATGTACGATGGAG 58.415 50.000 26.79 0.00 0.00 3.86
2731 2846 3.675225 GTGCGTGAGTATATACCATGCAG 59.325 47.826 30.78 14.43 43.36 4.41
2732 2847 3.320826 AGTGCGTGAGTATATACCATGCA 59.679 43.478 28.65 28.65 42.01 3.96
2733 2848 3.914312 AGTGCGTGAGTATATACCATGC 58.086 45.455 25.87 25.87 38.60 4.06
2734 2849 7.114953 CAGTTAAGTGCGTGAGTATATACCATG 59.885 40.741 9.32 12.51 0.00 3.66
2735 2850 7.013942 TCAGTTAAGTGCGTGAGTATATACCAT 59.986 37.037 9.32 0.00 0.00 3.55
2736 2851 6.319405 TCAGTTAAGTGCGTGAGTATATACCA 59.681 38.462 9.32 4.81 0.00 3.25
2737 2852 6.636044 GTCAGTTAAGTGCGTGAGTATATACC 59.364 42.308 9.32 2.29 0.00 2.73
2738 2853 7.165483 GTGTCAGTTAAGTGCGTGAGTATATAC 59.835 40.741 4.60 4.60 0.00 1.47
2739 2854 7.066645 AGTGTCAGTTAAGTGCGTGAGTATATA 59.933 37.037 5.35 0.00 0.00 0.86
2740 2855 6.034591 GTGTCAGTTAAGTGCGTGAGTATAT 58.965 40.000 5.35 0.00 0.00 0.86
2741 2856 5.182570 AGTGTCAGTTAAGTGCGTGAGTATA 59.817 40.000 5.35 0.00 0.00 1.47
2742 2857 4.022242 AGTGTCAGTTAAGTGCGTGAGTAT 60.022 41.667 5.35 0.00 0.00 2.12
2743 2858 3.317149 AGTGTCAGTTAAGTGCGTGAGTA 59.683 43.478 5.35 0.00 0.00 2.59
2744 2859 2.100916 AGTGTCAGTTAAGTGCGTGAGT 59.899 45.455 5.35 0.00 0.00 3.41
2745 2860 2.472861 CAGTGTCAGTTAAGTGCGTGAG 59.527 50.000 5.35 0.00 0.00 3.51
2764 2879 4.504916 CGACCGAGCCAGAGCCAG 62.505 72.222 0.00 0.00 41.25 4.85
2766 2881 4.500116 GACGACCGAGCCAGAGCC 62.500 72.222 0.00 0.00 41.25 4.70
2767 2882 4.838486 CGACGACCGAGCCAGAGC 62.838 72.222 0.00 0.00 41.76 4.09
2768 2883 2.473664 AAACGACGACCGAGCCAGAG 62.474 60.000 0.00 0.00 41.76 3.35
2769 2884 2.467946 GAAACGACGACCGAGCCAGA 62.468 60.000 0.00 0.00 41.76 3.86
2870 2985 2.811317 CAGCCGCTTCAGGTCGTC 60.811 66.667 0.00 0.00 0.00 4.20
2986 3101 2.972505 CACTTGCCGCCGAAGTGT 60.973 61.111 13.08 0.00 43.55 3.55
3005 3120 0.320374 TTCATCTCCACGAAGCGGTT 59.680 50.000 0.00 0.00 0.00 4.44
3007 3122 0.807667 CCTTCATCTCCACGAAGCGG 60.808 60.000 0.00 0.00 37.83 5.52
3079 3194 6.116126 AGTAATTGCATCTACTCAAAGGACC 58.884 40.000 3.05 0.00 0.00 4.46
3080 3195 7.982354 AGTAGTAATTGCATCTACTCAAAGGAC 59.018 37.037 10.60 4.49 39.77 3.85
3101 3216 8.647256 ATCCACAAGTAGTAACAACTAGTAGT 57.353 34.615 0.00 0.00 0.00 2.73
3104 3219 9.702494 GTTAATCCACAAGTAGTAACAACTAGT 57.298 33.333 0.00 0.00 0.00 2.57
3105 3220 9.924650 AGTTAATCCACAAGTAGTAACAACTAG 57.075 33.333 0.00 0.00 0.00 2.57
3131 3246 2.362717 TGATGTGTTACTGTCCACACGA 59.637 45.455 13.37 6.58 45.37 4.35
3132 3247 2.731451 CTGATGTGTTACTGTCCACACG 59.269 50.000 13.37 4.53 45.37 4.49
3168 3283 6.676237 TGCTATTGCATGAGTAAAATCGAA 57.324 33.333 0.00 0.00 45.31 3.71
3207 3322 5.798934 CGACAGAGCATATTATTACCGTACC 59.201 44.000 0.00 0.00 0.00 3.34
3237 3352 5.844004 AGTAACGGATACATGTGGAGATTC 58.156 41.667 9.11 0.00 36.94 2.52
3252 3367 7.923888 CAGTACTACTGCTATTTAGTAACGGA 58.076 38.462 3.21 0.00 39.62 4.69
3294 3409 2.000447 GTGTACATCGGTGGAGCTTTC 59.000 52.381 0.00 0.00 0.00 2.62
3306 3421 8.532977 AACATTTATTTGGCAAAGTGTACATC 57.467 30.769 18.61 0.00 0.00 3.06
3322 3437 7.144722 TCGTGAGCTCAATGAAACATTTATT 57.855 32.000 20.19 0.00 0.00 1.40
3344 3460 1.649664 CCAAAGTCATCCTCTGCTCG 58.350 55.000 0.00 0.00 0.00 5.03
3352 3468 2.821969 ACAAGACATGCCAAAGTCATCC 59.178 45.455 0.00 0.00 37.23 3.51
3355 3471 2.622942 GGAACAAGACATGCCAAAGTCA 59.377 45.455 0.00 0.00 37.23 3.41
3399 3515 5.306678 CCTAGGAGATAAATTGGAGCAGTCT 59.693 44.000 1.05 0.00 0.00 3.24
3400 3516 5.512232 CCCTAGGAGATAAATTGGAGCAGTC 60.512 48.000 11.48 0.00 0.00 3.51
3402 3518 4.263243 CCCCTAGGAGATAAATTGGAGCAG 60.263 50.000 11.48 0.00 33.47 4.24
3403 3519 3.652869 CCCCTAGGAGATAAATTGGAGCA 59.347 47.826 11.48 0.00 33.47 4.26
3404 3520 3.009584 CCCCCTAGGAGATAAATTGGAGC 59.990 52.174 11.48 0.00 38.24 4.70
3405 3521 4.243643 ACCCCCTAGGAGATAAATTGGAG 58.756 47.826 11.48 0.00 39.89 3.86
3406 3522 4.311208 ACCCCCTAGGAGATAAATTGGA 57.689 45.455 11.48 0.00 39.89 3.53
3408 3524 6.559157 ACTCTTACCCCCTAGGAGATAAATTG 59.441 42.308 11.48 0.00 39.89 2.32
3409 3525 6.559157 CACTCTTACCCCCTAGGAGATAAATT 59.441 42.308 11.48 0.00 39.89 1.82
3410 3526 6.085416 CACTCTTACCCCCTAGGAGATAAAT 58.915 44.000 11.48 0.00 39.89 1.40
3411 3527 5.042827 ACACTCTTACCCCCTAGGAGATAAA 60.043 44.000 11.48 0.00 39.89 1.40
3415 3537 2.295143 ACACTCTTACCCCCTAGGAGA 58.705 52.381 11.48 3.43 39.89 3.71
3439 3566 6.667558 TGATCAGTCATTGATAGCTCAGAT 57.332 37.500 0.00 0.00 46.51 2.90
3451 3578 5.711976 CCAAAACTACCCTTGATCAGTCATT 59.288 40.000 0.00 0.00 33.56 2.57
3466 3593 6.716898 ACGTACTCATTTAGCCAAAACTAC 57.283 37.500 0.00 0.00 0.00 2.73
3467 3594 7.707893 GGATACGTACTCATTTAGCCAAAACTA 59.292 37.037 0.00 0.00 0.00 2.24
3468 3595 6.537660 GGATACGTACTCATTTAGCCAAAACT 59.462 38.462 0.00 0.00 0.00 2.66
3485 3612 3.945981 TGCAGTGAAAGTGGATACGTA 57.054 42.857 0.00 0.00 37.87 3.57
3486 3613 2.831685 TGCAGTGAAAGTGGATACGT 57.168 45.000 0.00 0.00 37.87 3.57
3487 3614 4.481930 TTTTGCAGTGAAAGTGGATACG 57.518 40.909 0.00 0.00 37.49 3.06
3542 3670 9.932207 TCATCAAAATAACTCGACTTAAACCTA 57.068 29.630 0.00 0.00 0.00 3.08
3543 3671 8.842358 TCATCAAAATAACTCGACTTAAACCT 57.158 30.769 0.00 0.00 0.00 3.50
3544 3672 7.692705 GCTCATCAAAATAACTCGACTTAAACC 59.307 37.037 0.00 0.00 0.00 3.27
3545 3673 8.443937 AGCTCATCAAAATAACTCGACTTAAAC 58.556 33.333 0.00 0.00 0.00 2.01
3546 3674 8.547967 AGCTCATCAAAATAACTCGACTTAAA 57.452 30.769 0.00 0.00 0.00 1.52
3547 3675 9.647797 TTAGCTCATCAAAATAACTCGACTTAA 57.352 29.630 0.00 0.00 0.00 1.85
3548 3676 9.647797 TTTAGCTCATCAAAATAACTCGACTTA 57.352 29.630 0.00 0.00 0.00 2.24
3549 3677 8.547967 TTTAGCTCATCAAAATAACTCGACTT 57.452 30.769 0.00 0.00 0.00 3.01
3550 3678 8.547967 TTTTAGCTCATCAAAATAACTCGACT 57.452 30.769 0.00 0.00 0.00 4.18
3551 3679 9.774742 ATTTTTAGCTCATCAAAATAACTCGAC 57.225 29.630 0.00 0.00 30.09 4.20
3552 3680 9.773328 CATTTTTAGCTCATCAAAATAACTCGA 57.227 29.630 0.00 0.00 30.60 4.04
3553 3681 9.013490 CCATTTTTAGCTCATCAAAATAACTCG 57.987 33.333 0.00 0.00 30.60 4.18
3622 4201 7.429374 TCACCATCATATATGGAAGATCTCC 57.571 40.000 12.78 0.00 45.64 3.71
3645 4224 5.457140 TGAAATAAAGTGCGATGGTGTTTC 58.543 37.500 0.00 0.00 0.00 2.78
3646 4225 5.446143 TGAAATAAAGTGCGATGGTGTTT 57.554 34.783 0.00 0.00 0.00 2.83
3735 4314 9.123709 CAAACACGATATCTTAGCTTCTCTATC 57.876 37.037 0.00 0.00 0.00 2.08
3737 4316 8.221965 TCAAACACGATATCTTAGCTTCTCTA 57.778 34.615 0.00 0.00 0.00 2.43
3800 4380 3.865745 AGATGCTTTTGAGTACGAATCCG 59.134 43.478 0.00 0.00 42.50 4.18
3813 4393 4.275689 TGTGTTCGAACATGAGATGCTTTT 59.724 37.500 31.81 0.00 41.59 2.27
3843 4423 3.120889 CGTCATGTACAACTTCAGCACAG 60.121 47.826 0.00 0.00 0.00 3.66
3848 4428 4.559251 GCTAGACGTCATGTACAACTTCAG 59.441 45.833 19.50 0.56 0.00 3.02
3853 4433 2.592897 CGTGCTAGACGTCATGTACAAC 59.407 50.000 19.50 5.59 43.50 3.32
3959 4540 6.540189 AGTTTGCTATGAATAGGACACATCAC 59.460 38.462 9.78 0.00 34.92 3.06
4006 4587 9.469807 ACGTCATTAGCAAAACATTCATAAAAA 57.530 25.926 0.00 0.00 0.00 1.94
4022 4603 4.468095 AAGTTGTTCACACGTCATTAGC 57.532 40.909 0.00 0.00 0.00 3.09
4031 4612 6.551736 AGTATGTGTTCAAAGTTGTTCACAC 58.448 36.000 18.22 15.52 41.29 3.82
4049 4630 4.867047 CGAAGAATGAGCACAAGAGTATGT 59.133 41.667 0.00 0.00 0.00 2.29
4050 4631 4.867047 ACGAAGAATGAGCACAAGAGTATG 59.133 41.667 0.00 0.00 0.00 2.39
4051 4632 5.078411 ACGAAGAATGAGCACAAGAGTAT 57.922 39.130 0.00 0.00 0.00 2.12
4052 4633 4.521130 ACGAAGAATGAGCACAAGAGTA 57.479 40.909 0.00 0.00 0.00 2.59
4053 4634 3.393089 ACGAAGAATGAGCACAAGAGT 57.607 42.857 0.00 0.00 0.00 3.24
4054 4635 3.614616 GGTACGAAGAATGAGCACAAGAG 59.385 47.826 0.00 0.00 0.00 2.85
4055 4636 3.585862 GGTACGAAGAATGAGCACAAGA 58.414 45.455 0.00 0.00 0.00 3.02
4056 4637 2.673368 GGGTACGAAGAATGAGCACAAG 59.327 50.000 0.00 0.00 0.00 3.16
4057 4638 2.301870 AGGGTACGAAGAATGAGCACAA 59.698 45.455 0.00 0.00 0.00 3.33
4058 4639 1.899814 AGGGTACGAAGAATGAGCACA 59.100 47.619 0.00 0.00 0.00 4.57
4059 4640 2.094182 TGAGGGTACGAAGAATGAGCAC 60.094 50.000 0.00 0.00 0.00 4.40
4060 4641 2.094182 GTGAGGGTACGAAGAATGAGCA 60.094 50.000 0.00 0.00 0.00 4.26
4061 4642 2.094182 TGTGAGGGTACGAAGAATGAGC 60.094 50.000 0.00 0.00 0.00 4.26
4062 4643 3.868757 TGTGAGGGTACGAAGAATGAG 57.131 47.619 0.00 0.00 0.00 2.90
4063 4644 4.954202 ACTATGTGAGGGTACGAAGAATGA 59.046 41.667 0.00 0.00 0.00 2.57
4064 4645 5.067936 AGACTATGTGAGGGTACGAAGAATG 59.932 44.000 0.00 0.00 0.00 2.67
4065 4646 5.202004 AGACTATGTGAGGGTACGAAGAAT 58.798 41.667 0.00 0.00 0.00 2.40
4066 4647 4.597004 AGACTATGTGAGGGTACGAAGAA 58.403 43.478 0.00 0.00 0.00 2.52
4067 4648 4.232188 AGACTATGTGAGGGTACGAAGA 57.768 45.455 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.