Multiple sequence alignment - TraesCS2B01G417100

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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 TraesCS2B01G417100 chr2B 100.000 4266 0 0 1 4266 596652900 596648635 0.000000e+00 7878.0
1 TraesCS2B01G417100 chr2B 100.000 61 0 0 3429 3489 596649430 596649370 3.490000e-21 113.0
2 TraesCS2B01G417100 chr2B 100.000 61 0 0 3471 3531 596649472 596649412 3.490000e-21 113.0
3 TraesCS2B01G417100 chr2D 93.586 3539 124 27 1 3489 507828534 507825049 0.000000e+00 5182.0
4 TraesCS2B01G417100 chr2D 95.931 811 17 10 3471 4266 507825109 507824300 0.000000e+00 1301.0
5 TraesCS2B01G417100 chr2A 96.576 2015 58 2 1078 3081 652332197 652330183 0.000000e+00 3328.0
6 TraesCS2B01G417100 chr2A 86.761 1065 50 25 1 1046 652333261 652332269 0.000000e+00 1101.0
7 TraesCS2B01G417100 chr2A 91.919 693 22 17 3578 4266 652329283 652328621 0.000000e+00 939.0
8 TraesCS2B01G417100 chr2A 86.992 369 24 2 3077 3421 652329872 652329504 1.110000e-105 394.0
9 TraesCS2B01G417100 chr6D 82.198 646 109 6 1156 1798 338933006 338933648 6.230000e-153 551.0
10 TraesCS2B01G417100 chr6D 81.114 413 64 11 1940 2345 338933801 338934206 6.880000e-83 318.0
11 TraesCS2B01G417100 chr6B 82.198 646 109 6 1156 1798 481397778 481397136 6.230000e-153 551.0
12 TraesCS2B01G417100 chr6B 81.818 583 96 10 2430 3006 481396588 481396010 8.300000e-132 481.0
13 TraesCS2B01G417100 chr6B 82.238 411 63 10 1940 2345 481396987 481396582 3.160000e-91 346.0
14 TraesCS2B01G417100 chr6A 82.198 646 109 6 1156 1798 479635715 479636357 6.230000e-153 551.0
15 TraesCS2B01G417100 chr6A 82.302 582 94 7 2431 3006 479636907 479637485 2.960000e-136 496.0
16 TraesCS2B01G417100 chr6A 81.022 411 68 9 1940 2345 479636508 479636913 6.880000e-83 318.0
17 TraesCS2B01G417100 chr4D 79.354 557 101 12 1179 1728 500851801 500851252 3.110000e-101 379.0
18 TraesCS2B01G417100 chr4D 73.514 589 126 23 2435 3005 500850557 500849981 3.370000e-46 196.0
19 TraesCS2B01G417100 chr1B 78.238 579 114 9 2435 3007 350398094 350397522 1.130000e-95 361.0
20 TraesCS2B01G417100 chr1A 77.665 591 122 7 2422 3007 338589550 338588965 6.790000e-93 351.0
21 TraesCS2B01G417100 chr4B 78.191 564 111 10 1171 1728 644828289 644827732 2.440000e-92 350.0
22 TraesCS2B01G417100 chr4B 74.194 589 122 23 2435 3005 644827051 644826475 7.180000e-53 219.0
23 TraesCS2B01G417100 chr1D 77.665 591 120 9 2423 3007 261735491 261736075 2.440000e-92 350.0
24 TraesCS2B01G417100 chr5A 74.106 587 126 20 2435 3005 683232307 683231731 7.180000e-53 219.0
25 TraesCS2B01G417100 chr7A 81.102 127 15 8 1949 2068 10985262 10985138 4.540000e-15 93.5
26 TraesCS2B01G417100 chr7D 92.308 52 4 0 2017 2068 11611740 11611689 1.650000e-09 75.0
27 TraesCS2B01G417100 chr4A 88.462 52 6 0 2017 2068 726326244 726326295 3.560000e-06 63.9


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 TraesCS2B01G417100 chr2B 596648635 596652900 4265 True 2701.333333 7878 100.000000 1 4266 3 chr2B.!!$R1 4265
1 TraesCS2B01G417100 chr2D 507824300 507828534 4234 True 3241.500000 5182 94.758500 1 4266 2 chr2D.!!$R1 4265
2 TraesCS2B01G417100 chr2A 652328621 652333261 4640 True 1440.500000 3328 90.562000 1 4266 4 chr2A.!!$R1 4265
3 TraesCS2B01G417100 chr6D 338933006 338934206 1200 False 434.500000 551 81.656000 1156 2345 2 chr6D.!!$F1 1189
4 TraesCS2B01G417100 chr6B 481396010 481397778 1768 True 459.333333 551 82.084667 1156 3006 3 chr6B.!!$R1 1850
5 TraesCS2B01G417100 chr6A 479635715 479637485 1770 False 455.000000 551 81.840667 1156 3006 3 chr6A.!!$F1 1850
6 TraesCS2B01G417100 chr4D 500849981 500851801 1820 True 287.500000 379 76.434000 1179 3005 2 chr4D.!!$R1 1826
7 TraesCS2B01G417100 chr1B 350397522 350398094 572 True 361.000000 361 78.238000 2435 3007 1 chr1B.!!$R1 572
8 TraesCS2B01G417100 chr1A 338588965 338589550 585 True 351.000000 351 77.665000 2422 3007 1 chr1A.!!$R1 585
9 TraesCS2B01G417100 chr4B 644826475 644828289 1814 True 284.500000 350 76.192500 1171 3005 2 chr4B.!!$R1 1834
10 TraesCS2B01G417100 chr1D 261735491 261736075 584 False 350.000000 350 77.665000 2423 3007 1 chr1D.!!$F1 584
11 TraesCS2B01G417100 chr5A 683231731 683232307 576 True 219.000000 219 74.106000 2435 3005 1 chr5A.!!$R1 570

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
733 736 0.394192 TGAGCTCACTGGTTGTCTGG 59.606 55.0 13.74 0.0 0.00 3.86 F
1161 1233 0.028770 CCGTGAAACAAAAGCAGCGA 59.971 50.0 0.00 0.0 35.74 4.93 F
1697 1769 0.396435 TTGGCGGCTCCATATTCGAT 59.604 50.0 11.43 0.0 46.04 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2399 2500 0.815615 GCGGGGATCACAGATGTTCC 60.816 60.000 0.0 0.0 42.09 3.62 R
3013 3150 2.696187 TGTACCCCAAAGGAGCAAAAAC 59.304 45.455 0.0 0.0 39.89 2.43 R
3275 3730 0.813184 AATGTGCCTGCCAATCTTCG 59.187 50.000 0.0 0.0 0.00 3.79 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
80 81 3.731652 CTGAGGAGGCTGATCAGTAAG 57.268 52.381 23.38 2.56 36.52 2.34
110 111 8.637196 TTTCTACTCTCTGAAGAATGTACAGA 57.363 34.615 0.33 0.00 38.16 3.41
214 216 9.528018 AACTTCAATAAACTGTGTAAATGTTGG 57.472 29.630 0.00 0.00 0.00 3.77
246 248 3.058501 CGTCCATGTAAGAAAAAGGCGTT 60.059 43.478 0.00 0.00 0.00 4.84
255 257 2.685897 AGAAAAAGGCGTTGTAGTGCAA 59.314 40.909 0.00 0.00 34.16 4.08
349 352 6.641169 TGCATTTAGTGTGTGTTGGAAATA 57.359 33.333 0.00 0.00 0.00 1.40
381 384 1.089920 GATTTCTGGCGCACACTGAT 58.910 50.000 10.83 0.00 0.00 2.90
388 391 3.119884 TCTGGCGCACACTGATAAATTTG 60.120 43.478 10.83 0.00 0.00 2.32
456 459 4.785453 CTGAGCTCCCAACGCCCC 62.785 72.222 12.15 0.00 0.00 5.80
461 464 4.101448 CTCCCAACGCCCCCTGAG 62.101 72.222 0.00 0.00 0.00 3.35
464 467 4.785453 CCAACGCCCCCTGAGCTC 62.785 72.222 6.82 6.82 0.00 4.09
465 468 4.785453 CAACGCCCCCTGAGCTCC 62.785 72.222 12.15 0.00 0.00 4.70
469 472 4.432741 GCCCCCTGAGCTCCCAAC 62.433 72.222 12.15 0.00 0.00 3.77
470 473 4.101448 CCCCCTGAGCTCCCAACG 62.101 72.222 12.15 0.00 0.00 4.10
471 474 4.785453 CCCCTGAGCTCCCAACGC 62.785 72.222 12.15 0.00 0.00 4.84
472 475 4.785453 CCCTGAGCTCCCAACGCC 62.785 72.222 12.15 0.00 0.00 5.68
473 476 4.785453 CCTGAGCTCCCAACGCCC 62.785 72.222 12.15 0.00 0.00 6.13
544 547 0.945813 TGGGGCGTGTTAAAGAAACG 59.054 50.000 0.00 0.00 41.30 3.60
578 581 2.885644 TTTCGAGCGCGCCAGATC 60.886 61.111 30.33 18.08 37.46 2.75
729 732 1.277557 GGAGATGAGCTCACTGGTTGT 59.722 52.381 20.97 0.05 45.81 3.32
730 733 2.615869 GAGATGAGCTCACTGGTTGTC 58.384 52.381 20.97 10.93 43.38 3.18
731 734 2.233431 GAGATGAGCTCACTGGTTGTCT 59.767 50.000 20.97 15.94 43.38 3.41
732 735 2.028294 AGATGAGCTCACTGGTTGTCTG 60.028 50.000 20.97 0.00 0.00 3.51
733 736 0.394192 TGAGCTCACTGGTTGTCTGG 59.606 55.000 13.74 0.00 0.00 3.86
734 737 0.394565 GAGCTCACTGGTTGTCTGGT 59.605 55.000 9.40 0.00 0.00 4.00
735 738 0.839946 AGCTCACTGGTTGTCTGGTT 59.160 50.000 0.00 0.00 0.00 3.67
736 739 0.947244 GCTCACTGGTTGTCTGGTTG 59.053 55.000 0.00 0.00 0.00 3.77
744 747 1.070786 TTGTCTGGTTGCTCCGGTC 59.929 57.895 0.00 0.00 42.90 4.79
794 797 3.503363 GCTCATGGCGTGCTCACC 61.503 66.667 0.65 0.00 0.00 4.02
819 822 3.067011 TGCTGTACCCTAGCACACT 57.933 52.632 2.41 0.00 45.52 3.55
820 823 0.608130 TGCTGTACCCTAGCACACTG 59.392 55.000 2.41 0.00 45.52 3.66
821 824 0.741221 GCTGTACCCTAGCACACTGC 60.741 60.000 0.00 0.00 45.46 4.40
830 833 2.935955 GCACACTGCACACGTACC 59.064 61.111 0.00 0.00 44.26 3.34
831 834 2.938823 GCACACTGCACACGTACCG 61.939 63.158 0.00 0.00 44.26 4.02
832 835 1.590525 CACACTGCACACGTACCGT 60.591 57.895 0.00 0.00 42.36 4.83
849 852 2.438254 TGGGATGTGGTCGCATGC 60.438 61.111 7.91 7.91 43.96 4.06
979 987 2.022129 CAGTCCAACCTCGTCACGC 61.022 63.158 0.00 0.00 0.00 5.34
983 991 2.254350 CAACCTCGTCACGCTCGA 59.746 61.111 0.00 0.00 35.96 4.04
994 1014 1.442184 ACGCTCGACTTGCACGTAG 60.442 57.895 0.00 0.00 34.79 3.51
1111 1179 1.411246 GTCCATCATGCATTGTGCCAT 59.589 47.619 0.00 0.00 44.23 4.40
1142 1210 0.099968 ATTGATGAGCGTGTGCATGC 59.900 50.000 11.82 11.82 46.23 4.06
1161 1233 0.028770 CCGTGAAACAAAAGCAGCGA 59.971 50.000 0.00 0.00 35.74 4.93
1166 1238 1.873591 GAAACAAAAGCAGCGAGAGGA 59.126 47.619 0.00 0.00 0.00 3.71
1523 1595 2.361610 GACGTCGGGTGGGACCTA 60.362 66.667 0.00 0.00 38.64 3.08
1525 1597 3.834799 CGTCGGGTGGGACCTAGC 61.835 72.222 0.00 0.00 38.64 3.42
1679 1751 0.991920 ACATCGATGGGACCAAGGTT 59.008 50.000 28.09 1.12 0.00 3.50
1697 1769 0.396435 TTGGCGGCTCCATATTCGAT 59.604 50.000 11.43 0.00 46.04 3.59
2399 2500 1.811965 TGCCAAATGATCAGTGGAACG 59.188 47.619 25.42 0.86 45.86 3.95
2601 2726 2.262915 CTCGAGCTGCGGAACCTT 59.737 61.111 0.00 0.00 41.33 3.50
2650 2775 1.080025 AACTACTTCTCGCACCCGC 60.080 57.895 0.00 0.00 0.00 6.13
3046 3183 3.816398 TGGGGTACATGTCATTTTGGA 57.184 42.857 0.00 0.00 0.00 3.53
3090 3542 4.263331 CCACTTTTTAGCCAAGGTCCTAGA 60.263 45.833 0.00 0.00 0.00 2.43
3244 3699 4.335647 AGGGTGCGTGCTGAAGGG 62.336 66.667 0.00 0.00 0.00 3.95
3272 3727 4.040584 GGAGGAGAAAACTGTAGTCCACTT 59.959 45.833 0.00 0.00 0.00 3.16
3275 3730 4.750598 GGAGAAAACTGTAGTCCACTTGAC 59.249 45.833 0.00 0.00 44.82 3.18
3298 3753 3.022557 AGATTGGCAGGCACATTATGT 57.977 42.857 0.00 0.00 0.00 2.29
3356 3832 1.396996 GCGCGTCATTATTGGAAGTGT 59.603 47.619 8.43 0.00 0.00 3.55
3363 3839 5.049749 CGTCATTATTGGAAGTGTGTGTTCA 60.050 40.000 0.00 0.00 0.00 3.18
3371 3847 4.034626 TGGAAGTGTGTGTTCATTTGTACG 59.965 41.667 0.00 0.00 0.00 3.67
3380 3856 6.795114 GTGTGTTCATTTGTACGGTTATCAAG 59.205 38.462 0.00 0.00 0.00 3.02
3400 3876 3.782046 AGACGAAATCTGTATTGTCCGG 58.218 45.455 0.00 0.00 35.81 5.14
3476 4043 7.881775 ACTGACTTACTTTTGGTCAAATCTT 57.118 32.000 0.00 0.00 39.11 2.40
3480 4047 8.188139 TGACTTACTTTTGGTCAAATCTTGTTC 58.812 33.333 0.00 0.00 37.10 3.18
3481 4048 8.062065 ACTTACTTTTGGTCAAATCTTGTTCA 57.938 30.769 0.00 0.00 0.00 3.18
3482 4049 8.190784 ACTTACTTTTGGTCAAATCTTGTTCAG 58.809 33.333 0.00 0.00 0.00 3.02
3483 4050 6.773976 ACTTTTGGTCAAATCTTGTTCAGA 57.226 33.333 0.00 0.00 35.33 3.27
3484 4051 7.169158 ACTTTTGGTCAAATCTTGTTCAGAA 57.831 32.000 0.00 0.00 34.16 3.02
3485 4052 7.610865 ACTTTTGGTCAAATCTTGTTCAGAAA 58.389 30.769 0.00 0.00 34.16 2.52
3487 4054 5.168526 TGGTCAAATCTTGTTCAGAAACG 57.831 39.130 0.00 0.00 38.28 3.60
3488 4055 4.638421 TGGTCAAATCTTGTTCAGAAACGT 59.362 37.500 0.00 0.00 38.28 3.99
3489 4056 5.124776 TGGTCAAATCTTGTTCAGAAACGTT 59.875 36.000 0.00 0.00 38.28 3.99
3490 4057 6.033966 GGTCAAATCTTGTTCAGAAACGTTT 58.966 36.000 14.57 14.57 38.28 3.60
3491 4058 6.020678 GGTCAAATCTTGTTCAGAAACGTTTG 60.021 38.462 20.10 5.88 38.28 2.93
3492 4059 5.514914 TCAAATCTTGTTCAGAAACGTTTGC 59.485 36.000 20.10 10.09 38.28 3.68
3493 4060 4.900635 ATCTTGTTCAGAAACGTTTGCT 57.099 36.364 20.10 12.24 38.28 3.91
3494 4061 6.371809 AATCTTGTTCAGAAACGTTTGCTA 57.628 33.333 20.10 0.00 38.28 3.49
3495 4062 5.151632 TCTTGTTCAGAAACGTTTGCTAC 57.848 39.130 20.10 11.09 38.28 3.58
3496 4063 4.873827 TCTTGTTCAGAAACGTTTGCTACT 59.126 37.500 20.10 6.18 38.28 2.57
3497 4064 4.530094 TGTTCAGAAACGTTTGCTACTG 57.470 40.909 20.10 18.23 38.28 2.74
3498 4065 4.185394 TGTTCAGAAACGTTTGCTACTGA 58.815 39.130 20.10 20.17 38.28 3.41
3499 4066 4.033587 TGTTCAGAAACGTTTGCTACTGAC 59.966 41.667 22.57 18.39 38.28 3.51
3500 4067 4.054780 TCAGAAACGTTTGCTACTGACT 57.945 40.909 20.10 3.40 31.02 3.41
3501 4068 4.439057 TCAGAAACGTTTGCTACTGACTT 58.561 39.130 20.10 0.00 31.02 3.01
3502 4069 5.593968 TCAGAAACGTTTGCTACTGACTTA 58.406 37.500 20.10 0.76 31.02 2.24
3503 4070 5.461078 TCAGAAACGTTTGCTACTGACTTAC 59.539 40.000 20.10 0.00 31.02 2.34
3504 4071 5.462398 CAGAAACGTTTGCTACTGACTTACT 59.538 40.000 20.10 1.06 0.00 2.24
3505 4072 6.018994 CAGAAACGTTTGCTACTGACTTACTT 60.019 38.462 20.10 0.00 0.00 2.24
3506 4073 6.537660 AGAAACGTTTGCTACTGACTTACTTT 59.462 34.615 20.10 0.00 0.00 2.66
3507 4074 6.673154 AACGTTTGCTACTGACTTACTTTT 57.327 33.333 0.00 0.00 0.00 2.27
3508 4075 6.044512 ACGTTTGCTACTGACTTACTTTTG 57.955 37.500 0.00 0.00 0.00 2.44
3509 4076 5.007332 ACGTTTGCTACTGACTTACTTTTGG 59.993 40.000 0.00 0.00 0.00 3.28
3510 4077 5.007332 CGTTTGCTACTGACTTACTTTTGGT 59.993 40.000 0.00 0.00 0.00 3.67
3511 4078 6.427974 GTTTGCTACTGACTTACTTTTGGTC 58.572 40.000 0.00 0.00 0.00 4.02
3512 4079 5.284861 TGCTACTGACTTACTTTTGGTCA 57.715 39.130 0.00 0.00 38.16 4.02
3513 4080 5.676552 TGCTACTGACTTACTTTTGGTCAA 58.323 37.500 0.00 0.00 39.11 3.18
3514 4081 6.116806 TGCTACTGACTTACTTTTGGTCAAA 58.883 36.000 0.00 0.00 39.11 2.69
3515 4082 6.770785 TGCTACTGACTTACTTTTGGTCAAAT 59.229 34.615 0.00 0.00 39.11 2.32
3516 4083 7.041372 TGCTACTGACTTACTTTTGGTCAAATC 60.041 37.037 0.00 0.00 39.11 2.17
3517 4084 7.173390 GCTACTGACTTACTTTTGGTCAAATCT 59.827 37.037 0.00 0.00 39.11 2.40
3518 4085 7.881775 ACTGACTTACTTTTGGTCAAATCTT 57.118 32.000 0.00 0.00 39.11 2.40
3553 4120 5.362430 GTCATCTACTCACCCATCTCTTCTT 59.638 44.000 0.00 0.00 0.00 2.52
3851 4448 8.490311 AGGAAGAAGAAGAAGAAGAAGAAGAAA 58.510 33.333 0.00 0.00 0.00 2.52
3853 4450 8.675705 AAGAAGAAGAAGAAGAAGAAGAAAGG 57.324 34.615 0.00 0.00 0.00 3.11
3855 4452 8.490311 AGAAGAAGAAGAAGAAGAAGAAAGGAA 58.510 33.333 0.00 0.00 0.00 3.36
3857 4454 6.710295 AGAAGAAGAAGAAGAAGAAAGGAAGC 59.290 38.462 0.00 0.00 0.00 3.86
3859 4456 4.608948 AGAAGAAGAAGAAAGGAAGCGA 57.391 40.909 0.00 0.00 0.00 4.93
3906 4503 8.749354 TCAGTAGTGAGATGTCTAATTAAGCAA 58.251 33.333 0.00 0.00 0.00 3.91
4027 4624 2.755103 GCTTAAGGTTCAGGGATTGTGG 59.245 50.000 4.29 0.00 0.00 4.17
4029 4626 1.158007 AAGGTTCAGGGATTGTGGGT 58.842 50.000 0.00 0.00 0.00 4.51
4069 4666 1.082690 GCCTTCAGCTACACTGCTTC 58.917 55.000 0.00 0.00 46.76 3.86
4079 4680 1.447489 CACTGCTTCCAGCCTCTCG 60.447 63.158 0.00 0.00 43.02 4.04
4102 4703 2.665185 GTGTGGCACCGGTGAGTC 60.665 66.667 38.30 24.37 0.00 3.36
4247 4852 0.178973 AAAAGGGAAGAACACGGGGG 60.179 55.000 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 7.234577 ACATTCTTCAGAGAGTAGAAAAGGTCT 59.765 37.037 0.00 0.00 37.22 3.85
80 81 7.382898 ACATTCTTCAGAGAGTAGAAAAGGTC 58.617 38.462 0.00 0.00 37.22 3.85
188 190 9.528018 CCAACATTTACACAGTTTATTGAAGTT 57.472 29.630 0.00 0.00 0.00 2.66
189 191 8.691797 ACCAACATTTACACAGTTTATTGAAGT 58.308 29.630 0.00 0.00 0.00 3.01
214 216 1.790755 TACATGGACGTGCAACAGAC 58.209 50.000 15.51 0.00 35.74 3.51
349 352 4.276678 CGCCAGAAATCATATCCATGTTGT 59.723 41.667 0.00 0.00 33.57 3.32
352 355 2.816087 GCGCCAGAAATCATATCCATGT 59.184 45.455 0.00 0.00 33.57 3.21
388 391 6.590677 GGAGTACAGAAATACCTTGTCACTTC 59.409 42.308 0.00 0.00 0.00 3.01
456 459 4.785453 GGGCGTTGGGAGCTCAGG 62.785 72.222 17.19 1.77 34.67 3.86
729 732 2.504274 AACGACCGGAGCAACCAGA 61.504 57.895 9.46 0.00 38.90 3.86
730 733 2.030562 AACGACCGGAGCAACCAG 59.969 61.111 9.46 0.00 38.90 4.00
731 734 2.280524 CAACGACCGGAGCAACCA 60.281 61.111 9.46 0.00 38.90 3.67
732 735 2.027625 CTCAACGACCGGAGCAACC 61.028 63.158 9.46 0.00 0.00 3.77
733 736 1.282930 GACTCAACGACCGGAGCAAC 61.283 60.000 9.46 0.00 34.48 4.17
734 737 1.006571 GACTCAACGACCGGAGCAA 60.007 57.895 9.46 0.00 34.48 3.91
735 738 2.649034 GACTCAACGACCGGAGCA 59.351 61.111 9.46 0.00 34.48 4.26
736 739 2.126031 GGACTCAACGACCGGAGC 60.126 66.667 9.46 0.00 34.48 4.70
744 747 2.334838 CGGTAGGAAAAGGACTCAACG 58.665 52.381 0.00 0.00 0.00 4.10
826 829 1.153706 CGACCACATCCCACGGTAC 60.154 63.158 0.00 0.00 31.63 3.34
827 830 3.009192 GCGACCACATCCCACGGTA 62.009 63.158 0.00 0.00 31.63 4.02
828 831 4.388499 GCGACCACATCCCACGGT 62.388 66.667 0.00 0.00 35.12 4.83
829 832 3.680620 ATGCGACCACATCCCACGG 62.681 63.158 0.00 0.00 0.00 4.94
830 833 2.125147 ATGCGACCACATCCCACG 60.125 61.111 0.00 0.00 0.00 4.94
831 834 2.764314 GCATGCGACCACATCCCAC 61.764 63.158 0.00 0.00 0.00 4.61
832 835 2.438254 GCATGCGACCACATCCCA 60.438 61.111 0.00 0.00 0.00 4.37
833 836 3.576356 CGCATGCGACCACATCCC 61.576 66.667 35.82 0.00 42.83 3.85
834 837 2.819595 ACGCATGCGACCACATCC 60.820 61.111 43.72 0.00 42.83 3.51
835 838 2.400798 CACGCATGCGACCACATC 59.599 61.111 43.72 0.00 42.83 3.06
836 839 3.803082 GCACGCATGCGACCACAT 61.803 61.111 43.72 20.03 43.33 3.21
849 852 1.542272 GCATGCACACTTGTTGCACG 61.542 55.000 14.21 0.00 41.61 5.34
956 964 0.109039 GACGAGGTTGGACTGAGAGC 60.109 60.000 0.00 0.00 0.00 4.09
983 991 1.014044 CATGGCGACTACGTGCAAGT 61.014 55.000 10.83 10.83 41.98 3.16
1111 1179 4.754618 ACGCTCATCAATCAGTAACACAAA 59.245 37.500 0.00 0.00 0.00 2.83
1142 1210 0.028770 TCGCTGCTTTTGTTTCACGG 59.971 50.000 0.00 0.00 0.00 4.94
1602 1674 2.679092 CATGAGCCCCCTCTGCAA 59.321 61.111 0.00 0.00 38.93 4.08
1972 2066 1.377725 CTTGTGCATCCGCCCTCTT 60.378 57.895 0.00 0.00 37.32 2.85
2376 2477 1.820519 TCCACTGATCATTTGGCAAGC 59.179 47.619 15.75 0.00 0.00 4.01
2399 2500 0.815615 GCGGGGATCACAGATGTTCC 60.816 60.000 0.00 0.00 42.09 3.62
2535 2660 3.008517 TCCAGGATGAAGCCGCCA 61.009 61.111 0.00 0.00 39.69 5.69
2601 2726 2.929903 CGGGTTGTCGTCCGGGTTA 61.930 63.158 0.00 0.00 42.32 2.85
2931 3068 2.885861 GTGGAGCCGTCGATGACT 59.114 61.111 6.11 0.00 0.00 3.41
3013 3150 2.696187 TGTACCCCAAAGGAGCAAAAAC 59.304 45.455 0.00 0.00 39.89 2.43
3046 3183 6.562608 AGTGGTATACATTTAGGGATGGTCAT 59.437 38.462 5.01 0.00 0.00 3.06
3067 3204 2.876581 AGGACCTTGGCTAAAAAGTGG 58.123 47.619 0.00 0.00 0.00 4.00
3090 3542 5.071370 CGAATCAGTACCCACTATAGGAGT 58.929 45.833 4.43 1.00 39.82 3.85
3244 3699 6.164876 GGACTACAGTTTTCTCCTCCTTAAC 58.835 44.000 0.00 0.00 0.00 2.01
3272 3727 0.955428 GTGCCTGCCAATCTTCGTCA 60.955 55.000 0.00 0.00 0.00 4.35
3275 3730 0.813184 AATGTGCCTGCCAATCTTCG 59.187 50.000 0.00 0.00 0.00 3.79
3298 3753 7.971183 TGTTCACATACTGCAGTTACAAATA 57.029 32.000 27.06 4.97 0.00 1.40
3356 3832 6.706716 TCTTGATAACCGTACAAATGAACACA 59.293 34.615 0.00 0.00 0.00 3.72
3363 3839 7.548075 AGATTTCGTCTTGATAACCGTACAAAT 59.452 33.333 0.00 0.00 31.47 2.32
3371 3847 8.197988 ACAATACAGATTTCGTCTTGATAACC 57.802 34.615 0.00 0.00 34.00 2.85
3380 3856 3.777478 TCCGGACAATACAGATTTCGTC 58.223 45.455 0.00 0.00 0.00 4.20
3437 4004 4.054780 AGTCAGTAGCAAACGTTTCTGA 57.945 40.909 20.21 20.21 0.00 3.27
3476 4043 4.033587 GTCAGTAGCAAACGTTTCTGAACA 59.966 41.667 23.73 7.25 35.44 3.18
3480 4047 4.795970 AAGTCAGTAGCAAACGTTTCTG 57.204 40.909 11.37 14.93 0.00 3.02
3481 4048 5.598769 AGTAAGTCAGTAGCAAACGTTTCT 58.401 37.500 11.37 13.36 0.00 2.52
3482 4049 5.902051 AGTAAGTCAGTAGCAAACGTTTC 57.098 39.130 11.37 6.47 0.00 2.78
3483 4050 6.673154 AAAGTAAGTCAGTAGCAAACGTTT 57.327 33.333 7.96 7.96 0.00 3.60
3484 4051 6.457799 CCAAAAGTAAGTCAGTAGCAAACGTT 60.458 38.462 0.00 0.00 0.00 3.99
3485 4052 5.007332 CCAAAAGTAAGTCAGTAGCAAACGT 59.993 40.000 0.00 0.00 0.00 3.99
3487 4054 6.037830 TGACCAAAAGTAAGTCAGTAGCAAAC 59.962 38.462 0.00 0.00 35.67 2.93
3488 4055 6.116806 TGACCAAAAGTAAGTCAGTAGCAAA 58.883 36.000 0.00 0.00 35.67 3.68
3489 4056 5.676552 TGACCAAAAGTAAGTCAGTAGCAA 58.323 37.500 0.00 0.00 35.67 3.91
3490 4057 5.284861 TGACCAAAAGTAAGTCAGTAGCA 57.715 39.130 0.00 0.00 35.67 3.49
3491 4058 6.613755 TTTGACCAAAAGTAAGTCAGTAGC 57.386 37.500 0.00 0.00 41.27 3.58
3492 4059 8.608844 AGATTTGACCAAAAGTAAGTCAGTAG 57.391 34.615 0.00 0.00 41.27 2.57
3493 4060 8.836413 CAAGATTTGACCAAAAGTAAGTCAGTA 58.164 33.333 0.00 0.00 41.27 2.74
3494 4061 7.339466 ACAAGATTTGACCAAAAGTAAGTCAGT 59.661 33.333 0.00 0.00 41.27 3.41
3495 4062 7.707104 ACAAGATTTGACCAAAAGTAAGTCAG 58.293 34.615 0.00 0.00 41.27 3.51
3496 4063 7.639113 ACAAGATTTGACCAAAAGTAAGTCA 57.361 32.000 0.00 0.00 38.70 3.41
3497 4064 8.188139 TGAACAAGATTTGACCAAAAGTAAGTC 58.812 33.333 0.00 0.00 33.56 3.01
3498 4065 8.062065 TGAACAAGATTTGACCAAAAGTAAGT 57.938 30.769 0.00 0.00 33.56 2.24
3499 4066 8.405531 TCTGAACAAGATTTGACCAAAAGTAAG 58.594 33.333 0.00 0.67 33.56 2.34
3500 4067 8.287439 TCTGAACAAGATTTGACCAAAAGTAA 57.713 30.769 0.00 0.00 33.56 2.24
3501 4068 7.873719 TCTGAACAAGATTTGACCAAAAGTA 57.126 32.000 0.00 0.00 33.56 2.24
3502 4069 6.773976 TCTGAACAAGATTTGACCAAAAGT 57.226 33.333 0.00 0.00 33.56 2.66
3503 4070 7.253750 CGTTTCTGAACAAGATTTGACCAAAAG 60.254 37.037 0.00 0.00 35.44 2.27
3504 4071 6.529829 CGTTTCTGAACAAGATTTGACCAAAA 59.470 34.615 0.00 0.00 35.44 2.44
3505 4072 6.033341 CGTTTCTGAACAAGATTTGACCAAA 58.967 36.000 0.00 0.00 35.44 3.28
3506 4073 5.124776 ACGTTTCTGAACAAGATTTGACCAA 59.875 36.000 0.00 0.00 35.44 3.67
3507 4074 4.638421 ACGTTTCTGAACAAGATTTGACCA 59.362 37.500 0.00 0.00 35.44 4.02
3508 4075 5.169836 ACGTTTCTGAACAAGATTTGACC 57.830 39.130 0.00 0.00 35.44 4.02
3509 4076 5.806286 TGACGTTTCTGAACAAGATTTGAC 58.194 37.500 0.00 0.00 35.44 3.18
3510 4077 6.483307 AGATGACGTTTCTGAACAAGATTTGA 59.517 34.615 0.00 0.00 35.44 2.69
3511 4078 6.662616 AGATGACGTTTCTGAACAAGATTTG 58.337 36.000 0.00 0.00 35.44 2.32
3512 4079 6.867662 AGATGACGTTTCTGAACAAGATTT 57.132 33.333 0.00 0.00 35.44 2.17
3513 4080 7.155328 AGTAGATGACGTTTCTGAACAAGATT 58.845 34.615 11.10 0.00 35.44 2.40
3514 4081 6.692486 AGTAGATGACGTTTCTGAACAAGAT 58.308 36.000 11.10 0.00 35.44 2.40
3515 4082 6.085555 AGTAGATGACGTTTCTGAACAAGA 57.914 37.500 11.10 0.00 35.44 3.02
3516 4083 5.920840 TGAGTAGATGACGTTTCTGAACAAG 59.079 40.000 11.10 0.00 35.44 3.16
3517 4084 5.690409 GTGAGTAGATGACGTTTCTGAACAA 59.310 40.000 11.10 0.00 35.44 2.83
3518 4085 5.220381 GTGAGTAGATGACGTTTCTGAACA 58.780 41.667 11.10 6.33 35.44 3.18
3851 4448 1.412710 TGTTCAGAACAGTCGCTTCCT 59.587 47.619 12.24 0.00 36.25 3.36
3853 4450 4.059008 GATTGTTCAGAACAGTCGCTTC 57.941 45.455 19.67 7.52 43.27 3.86
3906 4503 0.915364 GAGGAGCCCTGAAACTGGAT 59.085 55.000 0.00 0.00 31.76 3.41
4027 4624 0.739813 AAGCTGTCAACGCCGATACC 60.740 55.000 0.00 0.00 0.00 2.73
4029 4626 0.800683 CGAAGCTGTCAACGCCGATA 60.801 55.000 0.00 0.00 0.00 2.92
4102 4703 3.005554 AGAGATCAAAGACCATTGCACG 58.994 45.455 0.00 0.00 0.00 5.34
4247 4852 3.746949 CTGCACCTCCCGGCTGATC 62.747 68.421 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.