Multiple sequence alignment - TraesCS2D01G423900

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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 TraesCS2D01G423900 chr2D 100.000 4021 0 0 1 4021 536996550 536992530 0.000000e+00 7426.0
1 TraesCS2D01G423900 chr2B 95.373 2550 74 25 790 3306 639027977 639025439 0.000000e+00 4015.0
2 TraesCS2D01G423900 chr2B 86.213 573 27 24 790 1331 639037231 639036680 1.250000e-159 573.0
3 TraesCS2D01G423900 chr2B 88.727 275 9 6 3371 3635 639025415 639025153 2.330000e-82 316.0
4 TraesCS2D01G423900 chr2B 86.264 182 13 4 3739 3910 639025016 639024837 1.910000e-43 187.0
5 TraesCS2D01G423900 chr2A 96.197 2130 53 12 1092 3201 679547662 679545541 0.000000e+00 3459.0
6 TraesCS2D01G423900 chr2A 94.904 785 37 3 1 783 202056112 202055329 0.000000e+00 1225.0
7 TraesCS2D01G423900 chr2A 90.572 297 16 8 789 1076 679548277 679547984 2.270000e-102 383.0
8 TraesCS2D01G423900 chr2A 86.935 199 17 4 3692 3889 679544105 679543915 8.750000e-52 215.0
9 TraesCS2D01G423900 chr2A 86.822 129 14 1 3261 3389 679545536 679545411 1.510000e-29 141.0
10 TraesCS2D01G423900 chr5D 97.229 794 12 7 1 788 77883000 77882211 0.000000e+00 1336.0
11 TraesCS2D01G423900 chr5D 75.373 536 109 17 2066 2589 454204481 454205005 1.870000e-58 237.0
12 TraesCS2D01G423900 chr1D 96.843 792 20 3 1 788 443113053 443113843 0.000000e+00 1319.0
13 TraesCS2D01G423900 chr1D 95.614 798 24 5 1 788 114311056 114311852 0.000000e+00 1269.0
14 TraesCS2D01G423900 chr4D 96.352 795 22 5 1 789 503689800 503690593 0.000000e+00 1301.0
15 TraesCS2D01G423900 chr7D 94.856 797 27 7 1 790 102563191 102563980 0.000000e+00 1232.0
16 TraesCS2D01G423900 chr7D 94.507 801 30 6 1 791 452961659 452960863 0.000000e+00 1223.0
17 TraesCS2D01G423900 chr1A 94.677 789 38 4 1 788 42472362 42473147 0.000000e+00 1221.0
18 TraesCS2D01G423900 chr6A 94.318 792 38 4 1 788 608727453 608726665 0.000000e+00 1206.0
19 TraesCS2D01G423900 chr5A 75.940 532 113 12 2066 2589 573602309 573602833 3.990000e-65 259.0
20 TraesCS2D01G423900 chr7B 90.476 42 3 1 3198 3238 654137472 654137513 2.000000e-03 54.7


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 TraesCS2D01G423900 chr2D 536992530 536996550 4020 True 7426.0 7426 100.000000 1 4021 1 chr2D.!!$R1 4020
1 TraesCS2D01G423900 chr2B 639024837 639027977 3140 True 1506.0 4015 90.121333 790 3910 3 chr2B.!!$R2 3120
2 TraesCS2D01G423900 chr2B 639036680 639037231 551 True 573.0 573 86.213000 790 1331 1 chr2B.!!$R1 541
3 TraesCS2D01G423900 chr2A 202055329 202056112 783 True 1225.0 1225 94.904000 1 783 1 chr2A.!!$R1 782
4 TraesCS2D01G423900 chr2A 679543915 679548277 4362 True 1049.5 3459 90.131500 789 3889 4 chr2A.!!$R2 3100
5 TraesCS2D01G423900 chr5D 77882211 77883000 789 True 1336.0 1336 97.229000 1 788 1 chr5D.!!$R1 787
6 TraesCS2D01G423900 chr5D 454204481 454205005 524 False 237.0 237 75.373000 2066 2589 1 chr5D.!!$F1 523
7 TraesCS2D01G423900 chr1D 443113053 443113843 790 False 1319.0 1319 96.843000 1 788 1 chr1D.!!$F2 787
8 TraesCS2D01G423900 chr1D 114311056 114311852 796 False 1269.0 1269 95.614000 1 788 1 chr1D.!!$F1 787
9 TraesCS2D01G423900 chr4D 503689800 503690593 793 False 1301.0 1301 96.352000 1 789 1 chr4D.!!$F1 788
10 TraesCS2D01G423900 chr7D 102563191 102563980 789 False 1232.0 1232 94.856000 1 790 1 chr7D.!!$F1 789
11 TraesCS2D01G423900 chr7D 452960863 452961659 796 True 1223.0 1223 94.507000 1 791 1 chr7D.!!$R1 790
12 TraesCS2D01G423900 chr1A 42472362 42473147 785 False 1221.0 1221 94.677000 1 788 1 chr1A.!!$F1 787
13 TraesCS2D01G423900 chr6A 608726665 608727453 788 True 1206.0 1206 94.318000 1 788 1 chr6A.!!$R1 787
14 TraesCS2D01G423900 chr5A 573602309 573602833 524 False 259.0 259 75.940000 2066 2589 1 chr5A.!!$F1 523

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
595 615 0.392327 TTAGGCGCTGCAATGCTGTA 60.392 50.000 7.64 0.0 0.0 2.74 F
1197 1554 1.685224 CCAGCCTTTCCCAGCAGTA 59.315 57.895 0.00 0.0 0.0 2.74 F
1712 2069 1.449601 CGCCGGGAACATACTGCTT 60.450 57.895 2.18 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1586 1943 0.610509 AGCAGAAGGACGAGAGCAGA 60.611 55.000 0.00 0.0 0.0 4.26 R
2369 2726 1.065109 CGGGATCATGTGCGTACGA 59.935 57.895 21.65 0.0 0.0 3.43 R
3699 5123 0.041576 GCACCGGACGAAAAGAACAC 60.042 55.000 9.46 0.0 0.0 3.32 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
412 429 4.713792 AACTTCAGATTTGAGAGGGTGT 57.286 40.909 0.00 0.00 34.15 4.16
595 615 0.392327 TTAGGCGCTGCAATGCTGTA 60.392 50.000 7.64 0.00 0.00 2.74
930 957 3.427161 ACTACGTACGTATTTGGCTCC 57.573 47.619 26.98 0.00 0.00 4.70
1195 1552 2.220786 ATCCCAGCCTTTCCCAGCAG 62.221 60.000 0.00 0.00 0.00 4.24
1197 1554 1.685224 CCAGCCTTTCCCAGCAGTA 59.315 57.895 0.00 0.00 0.00 2.74
1400 1757 3.274586 CGATCGTCCGAGGCCGTA 61.275 66.667 7.03 0.00 0.00 4.02
1712 2069 1.449601 CGCCGGGAACATACTGCTT 60.450 57.895 2.18 0.00 0.00 3.91
2369 2726 1.139734 CTACACCACGCAGATCGCT 59.860 57.895 7.71 0.00 43.23 4.93
2372 2729 3.749064 ACCACGCAGATCGCTCGT 61.749 61.111 7.71 6.15 43.23 4.18
2581 2938 3.020627 CTACTACGTCGCCGGGAG 58.979 66.667 2.18 0.00 38.78 4.30
2648 3005 2.202756 GTCCTGTCGTCCATCGGC 60.203 66.667 0.00 0.00 45.13 5.54
3048 3411 3.578716 TGAGAGTGGTTTCTAGTTGGAGG 59.421 47.826 0.00 0.00 0.00 4.30
3088 3462 3.678548 CGGTCTGTGAACTTTTAGGCTAC 59.321 47.826 0.00 0.00 0.00 3.58
3205 3580 7.139287 TCCATAGCTAGTACAGTACTCTCTT 57.861 40.000 16.91 4.65 40.14 2.85
3207 3582 6.146510 CCATAGCTAGTACAGTACTCTCTTCG 59.853 46.154 16.91 9.10 40.14 3.79
3220 3596 7.062371 CAGTACTCTCTTCGTCCAAAATAAGTG 59.938 40.741 0.00 0.00 0.00 3.16
3222 3598 6.289064 ACTCTCTTCGTCCAAAATAAGTGTT 58.711 36.000 0.00 0.00 0.00 3.32
3245 3621 8.798402 TGTTATTGATTTAGTACAACTTTGGGG 58.202 33.333 0.00 0.00 0.00 4.96
3248 3624 5.318630 TGATTTAGTACAACTTTGGGGGAC 58.681 41.667 0.00 0.00 0.00 4.46
3249 3625 4.792513 TTTAGTACAACTTTGGGGGACA 57.207 40.909 0.00 0.00 0.00 4.02
3254 3630 1.850345 ACAACTTTGGGGGACAGAGAA 59.150 47.619 0.00 0.00 35.02 2.87
3255 3631 2.447047 ACAACTTTGGGGGACAGAGAAT 59.553 45.455 0.00 0.00 35.02 2.40
3292 3668 8.327832 CTTGTTTTCTGTACAAGCTAAAACAG 57.672 34.615 23.11 15.09 45.45 3.16
3331 3707 1.511850 TGCACCTGTGTGATCTTTCG 58.488 50.000 0.00 0.00 45.76 3.46
3334 3710 2.754472 CACCTGTGTGATCTTTCGTCA 58.246 47.619 0.00 0.00 45.76 4.35
3337 3713 3.748048 ACCTGTGTGATCTTTCGTCATTG 59.252 43.478 0.00 0.00 0.00 2.82
3338 3714 3.748048 CCTGTGTGATCTTTCGTCATTGT 59.252 43.478 0.00 0.00 0.00 2.71
3339 3715 4.214119 CCTGTGTGATCTTTCGTCATTGTT 59.786 41.667 0.00 0.00 0.00 2.83
3340 3716 5.408299 CCTGTGTGATCTTTCGTCATTGTTA 59.592 40.000 0.00 0.00 0.00 2.41
3341 3717 6.073276 CCTGTGTGATCTTTCGTCATTGTTAA 60.073 38.462 0.00 0.00 0.00 2.01
3343 3719 6.073276 TGTGTGATCTTTCGTCATTGTTAAGG 60.073 38.462 0.00 0.00 0.00 2.69
3344 3720 5.995282 TGTGATCTTTCGTCATTGTTAAGGT 59.005 36.000 0.00 0.00 0.00 3.50
3345 3721 6.485313 TGTGATCTTTCGTCATTGTTAAGGTT 59.515 34.615 0.00 0.00 0.00 3.50
3444 4806 4.095483 AGAGTGAAATCATGCCTTTTAGCG 59.905 41.667 0.00 0.00 34.65 4.26
3515 4878 2.098280 ACTATGTCAGCGCACTCACTAG 59.902 50.000 11.47 5.79 0.00 2.57
3519 4882 1.469308 GTCAGCGCACTCACTAGTAGT 59.531 52.381 11.47 0.00 33.48 2.73
3522 4885 4.510711 GTCAGCGCACTCACTAGTAGTATA 59.489 45.833 11.47 0.00 33.48 1.47
3523 4886 5.179742 GTCAGCGCACTCACTAGTAGTATAT 59.820 44.000 11.47 0.00 33.48 0.86
3524 4887 5.763698 TCAGCGCACTCACTAGTAGTATATT 59.236 40.000 11.47 0.00 33.48 1.28
3542 4905 8.627208 AGTATATTACAGATTGGCAGGAAATG 57.373 34.615 0.00 0.00 0.00 2.32
3660 5084 5.738909 TCTGAAATGATTCCTCTTCACTCC 58.261 41.667 0.00 0.00 34.49 3.85
3669 5093 4.008074 TCCTCTTCACTCCATGTTGTTC 57.992 45.455 0.00 0.00 0.00 3.18
3670 5094 3.390967 TCCTCTTCACTCCATGTTGTTCA 59.609 43.478 0.00 0.00 0.00 3.18
3676 5100 5.169992 TCACTCCATGTTGTTCATCATCT 57.830 39.130 0.00 0.00 34.09 2.90
3679 5103 5.646793 CACTCCATGTTGTTCATCATCTTCT 59.353 40.000 0.00 0.00 34.09 2.85
3680 5104 5.646793 ACTCCATGTTGTTCATCATCTTCTG 59.353 40.000 0.00 0.00 34.09 3.02
3681 5105 5.807909 TCCATGTTGTTCATCATCTTCTGA 58.192 37.500 0.00 0.00 38.53 3.27
3695 5119 5.732633 CATCTTCTGATGTGTTCCTCTTCT 58.267 41.667 0.00 0.00 43.68 2.85
3696 5120 5.144692 TCTTCTGATGTGTTCCTCTTCTG 57.855 43.478 0.00 0.00 0.00 3.02
3697 5121 3.969287 TCTGATGTGTTCCTCTTCTGG 57.031 47.619 0.00 0.00 0.00 3.86
3698 5122 3.242867 TCTGATGTGTTCCTCTTCTGGT 58.757 45.455 0.00 0.00 0.00 4.00
3699 5123 3.007290 TCTGATGTGTTCCTCTTCTGGTG 59.993 47.826 0.00 0.00 0.00 4.17
3722 5146 2.529780 TCTTTTCGTCCGGTGCTAAA 57.470 45.000 0.00 0.00 0.00 1.85
3931 5366 5.753721 AGGTATCCTCAAATAGATGGAGC 57.246 43.478 0.00 0.00 30.50 4.70
3932 5367 5.158141 AGGTATCCTCAAATAGATGGAGCA 58.842 41.667 0.00 0.00 30.50 4.26
3933 5368 5.789575 AGGTATCCTCAAATAGATGGAGCAT 59.210 40.000 0.00 0.00 30.50 3.79
3934 5369 6.070309 AGGTATCCTCAAATAGATGGAGCATC 60.070 42.308 0.00 0.00 40.80 3.91
3935 5370 5.837770 ATCCTCAAATAGATGGAGCATCA 57.162 39.130 0.00 0.00 42.72 3.07
3936 5371 5.224821 TCCTCAAATAGATGGAGCATCAG 57.775 43.478 0.00 0.00 42.72 2.90
3937 5372 3.752222 CCTCAAATAGATGGAGCATCAGC 59.248 47.826 0.00 0.00 42.72 4.26
3951 5386 4.536364 GCATCAGCTATTCGTTTTAGCA 57.464 40.909 13.59 0.00 43.63 3.49
3952 5387 5.100751 GCATCAGCTATTCGTTTTAGCAT 57.899 39.130 13.59 1.19 43.63 3.79
3953 5388 5.514279 GCATCAGCTATTCGTTTTAGCATT 58.486 37.500 13.59 0.12 43.63 3.56
3954 5389 5.973565 GCATCAGCTATTCGTTTTAGCATTT 59.026 36.000 13.59 0.00 43.63 2.32
3955 5390 7.132213 GCATCAGCTATTCGTTTTAGCATTTA 58.868 34.615 13.59 1.14 43.63 1.40
3956 5391 7.112148 GCATCAGCTATTCGTTTTAGCATTTAC 59.888 37.037 13.59 0.00 43.63 2.01
3957 5392 7.603963 TCAGCTATTCGTTTTAGCATTTACA 57.396 32.000 13.59 0.00 43.63 2.41
3958 5393 8.208718 TCAGCTATTCGTTTTAGCATTTACAT 57.791 30.769 13.59 0.00 43.63 2.29
3959 5394 9.320352 TCAGCTATTCGTTTTAGCATTTACATA 57.680 29.630 13.59 0.00 43.63 2.29
3960 5395 9.370126 CAGCTATTCGTTTTAGCATTTACATAC 57.630 33.333 13.59 0.00 43.63 2.39
3961 5396 8.557029 AGCTATTCGTTTTAGCATTTACATACC 58.443 33.333 13.59 0.00 43.63 2.73
3962 5397 7.801783 GCTATTCGTTTTAGCATTTACATACCC 59.198 37.037 8.46 0.00 41.38 3.69
3963 5398 7.875327 ATTCGTTTTAGCATTTACATACCCT 57.125 32.000 0.00 0.00 0.00 4.34
3964 5399 7.690952 TTCGTTTTAGCATTTACATACCCTT 57.309 32.000 0.00 0.00 0.00 3.95
3965 5400 7.690952 TCGTTTTAGCATTTACATACCCTTT 57.309 32.000 0.00 0.00 0.00 3.11
3966 5401 8.113173 TCGTTTTAGCATTTACATACCCTTTT 57.887 30.769 0.00 0.00 0.00 2.27
3967 5402 8.578151 TCGTTTTAGCATTTACATACCCTTTTT 58.422 29.630 0.00 0.00 0.00 1.94
3992 5427 7.943079 TGTGCATAAATTAGATATGGGATGG 57.057 36.000 0.00 0.00 32.54 3.51
3993 5428 7.469343 TGTGCATAAATTAGATATGGGATGGT 58.531 34.615 0.00 0.00 32.54 3.55
3994 5429 7.949565 TGTGCATAAATTAGATATGGGATGGTT 59.050 33.333 0.00 0.00 32.54 3.67
3995 5430 8.462016 GTGCATAAATTAGATATGGGATGGTTC 58.538 37.037 0.00 0.00 32.54 3.62
3996 5431 8.169393 TGCATAAATTAGATATGGGATGGTTCA 58.831 33.333 0.00 0.00 32.54 3.18
3997 5432 8.680903 GCATAAATTAGATATGGGATGGTTCAG 58.319 37.037 0.00 0.00 32.54 3.02
3998 5433 9.745018 CATAAATTAGATATGGGATGGTTCAGT 57.255 33.333 0.00 0.00 0.00 3.41
4001 5436 8.742125 AATTAGATATGGGATGGTTCAGTAGA 57.258 34.615 0.00 0.00 0.00 2.59
4002 5437 7.782897 TTAGATATGGGATGGTTCAGTAGAG 57.217 40.000 0.00 0.00 0.00 2.43
4003 5438 5.721225 AGATATGGGATGGTTCAGTAGAGT 58.279 41.667 0.00 0.00 0.00 3.24
4004 5439 6.864421 AGATATGGGATGGTTCAGTAGAGTA 58.136 40.000 0.00 0.00 0.00 2.59
4005 5440 7.483018 AGATATGGGATGGTTCAGTAGAGTAT 58.517 38.462 0.00 0.00 0.00 2.12
4006 5441 5.815233 ATGGGATGGTTCAGTAGAGTATG 57.185 43.478 0.00 0.00 0.00 2.39
4007 5442 3.388024 TGGGATGGTTCAGTAGAGTATGC 59.612 47.826 0.00 0.00 0.00 3.14
4008 5443 3.643792 GGGATGGTTCAGTAGAGTATGCT 59.356 47.826 0.00 0.00 0.00 3.79
4009 5444 4.833380 GGGATGGTTCAGTAGAGTATGCTA 59.167 45.833 0.00 0.00 0.00 3.49
4010 5445 5.279056 GGGATGGTTCAGTAGAGTATGCTAC 60.279 48.000 0.00 0.00 40.78 3.58
4019 5454 2.734893 AGTATGCTACTCCCTCCGC 58.265 57.895 0.00 0.00 32.47 5.54
4020 5455 0.186386 AGTATGCTACTCCCTCCGCT 59.814 55.000 0.00 0.00 32.47 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
480 500 2.993853 CCCCTCCCAGCAGTTCTC 59.006 66.667 0.00 0.00 0.00 2.87
588 608 2.192979 CGGCCCCACATACAGCAT 59.807 61.111 0.00 0.00 0.00 3.79
632 652 1.378911 TTAGGCGTCGCACCTCCTA 60.379 57.895 20.50 7.78 38.81 2.94
1079 1130 7.327975 ACCGAAAACCTGAAAAAGAAAATCTT 58.672 30.769 0.00 0.00 38.59 2.40
1080 1131 6.873997 ACCGAAAACCTGAAAAAGAAAATCT 58.126 32.000 0.00 0.00 0.00 2.40
1096 1453 7.237920 TCTCAACTAACAAACTACCGAAAAC 57.762 36.000 0.00 0.00 0.00 2.43
1195 1552 2.007608 GGATTGGAACTTGGACGCTAC 58.992 52.381 0.00 0.00 0.00 3.58
1197 1554 0.322546 GGGATTGGAACTTGGACGCT 60.323 55.000 0.00 0.00 0.00 5.07
1266 1623 3.391382 GCTCCACCGCCAGTACCT 61.391 66.667 0.00 0.00 0.00 3.08
1586 1943 0.610509 AGCAGAAGGACGAGAGCAGA 60.611 55.000 0.00 0.00 0.00 4.26
1826 2183 2.609427 TGGGATCGAGCAGATTGAAG 57.391 50.000 1.84 0.00 40.26 3.02
2369 2726 1.065109 CGGGATCATGTGCGTACGA 59.935 57.895 21.65 0.00 0.00 3.43
2372 2729 2.038814 ATGGCGGGATCATGTGCGTA 62.039 55.000 0.00 0.00 0.00 4.42
3048 3411 3.206150 ACCGACATGGCAATATGACTTC 58.794 45.455 0.00 0.00 43.94 3.01
3088 3462 1.468520 CGAGTAACCAGCCACCAAATG 59.531 52.381 0.00 0.00 0.00 2.32
3220 3596 8.248253 CCCCCAAAGTTGTACTAAATCAATAAC 58.752 37.037 0.00 0.00 0.00 1.89
3222 3598 7.612633 GTCCCCCAAAGTTGTACTAAATCAATA 59.387 37.037 0.00 0.00 0.00 1.90
3233 3609 2.696775 TCTCTGTCCCCCAAAGTTGTA 58.303 47.619 0.00 0.00 0.00 2.41
3268 3644 7.822658 ACTGTTTTAGCTTGTACAGAAAACAA 58.177 30.769 24.55 16.07 44.75 2.83
3292 3668 8.773645 AGGTGCAAAGCTTAATTGAATAAAAAC 58.226 29.630 0.00 0.00 0.00 2.43
3357 3733 9.377383 ACGACGTTCATTTTCTTAAATTTACTG 57.623 29.630 0.00 0.00 31.63 2.74
3385 3761 4.084537 ACGACGTCACAGCTGAAAAATAAG 60.085 41.667 23.35 7.68 0.00 1.73
3459 4821 4.517453 ACTGCTTTATGAAACACGGCTTTA 59.483 37.500 0.00 0.00 0.00 1.85
3515 4878 9.726438 ATTTCCTGCCAATCTGTAATATACTAC 57.274 33.333 0.00 0.00 0.00 2.73
3519 4882 7.452880 GCATTTCCTGCCAATCTGTAATATA 57.547 36.000 0.00 0.00 45.66 0.86
3522 4885 4.660789 GCATTTCCTGCCAATCTGTAAT 57.339 40.909 0.00 0.00 45.66 1.89
3623 4986 7.856145 ATCATTTCAGAGTGAGTTATGGAAC 57.144 36.000 0.00 0.00 35.64 3.62
3676 5100 3.648067 ACCAGAAGAGGAACACATCAGAA 59.352 43.478 0.00 0.00 0.00 3.02
3679 5103 2.705658 ACACCAGAAGAGGAACACATCA 59.294 45.455 0.00 0.00 0.00 3.07
3680 5104 3.070018 CACACCAGAAGAGGAACACATC 58.930 50.000 0.00 0.00 0.00 3.06
3681 5105 2.439507 ACACACCAGAAGAGGAACACAT 59.560 45.455 0.00 0.00 0.00 3.21
3683 5107 2.622064 ACACACCAGAAGAGGAACAC 57.378 50.000 0.00 0.00 0.00 3.32
3684 5108 2.771943 AGAACACACCAGAAGAGGAACA 59.228 45.455 0.00 0.00 0.00 3.18
3685 5109 3.477210 AGAACACACCAGAAGAGGAAC 57.523 47.619 0.00 0.00 0.00 3.62
3686 5110 4.503714 AAAGAACACACCAGAAGAGGAA 57.496 40.909 0.00 0.00 0.00 3.36
3687 5111 4.451900 GAAAAGAACACACCAGAAGAGGA 58.548 43.478 0.00 0.00 0.00 3.71
3688 5112 3.248602 CGAAAAGAACACACCAGAAGAGG 59.751 47.826 0.00 0.00 0.00 3.69
3689 5113 3.871594 ACGAAAAGAACACACCAGAAGAG 59.128 43.478 0.00 0.00 0.00 2.85
3691 5115 3.002348 GGACGAAAAGAACACACCAGAAG 59.998 47.826 0.00 0.00 0.00 2.85
3692 5116 2.940410 GGACGAAAAGAACACACCAGAA 59.060 45.455 0.00 0.00 0.00 3.02
3693 5117 2.557317 GGACGAAAAGAACACACCAGA 58.443 47.619 0.00 0.00 0.00 3.86
3694 5118 1.260561 CGGACGAAAAGAACACACCAG 59.739 52.381 0.00 0.00 0.00 4.00
3695 5119 1.292061 CGGACGAAAAGAACACACCA 58.708 50.000 0.00 0.00 0.00 4.17
3696 5120 0.584876 CCGGACGAAAAGAACACACC 59.415 55.000 0.00 0.00 0.00 4.16
3697 5121 1.004292 CACCGGACGAAAAGAACACAC 60.004 52.381 9.46 0.00 0.00 3.82
3698 5122 1.292061 CACCGGACGAAAAGAACACA 58.708 50.000 9.46 0.00 0.00 3.72
3699 5123 0.041576 GCACCGGACGAAAAGAACAC 60.042 55.000 9.46 0.00 0.00 3.32
3860 5295 6.748969 TCTAATCTCCTCCTTTAGTGGGTAA 58.251 40.000 0.00 0.00 0.00 2.85
3861 5296 6.351317 TCTAATCTCCTCCTTTAGTGGGTA 57.649 41.667 0.00 0.00 0.00 3.69
3862 5297 5.222278 TCTAATCTCCTCCTTTAGTGGGT 57.778 43.478 0.00 0.00 0.00 4.51
3870 5305 9.787334 AGAATCATGATATCTAATCTCCTCCTT 57.213 33.333 9.04 0.00 0.00 3.36
3906 5341 7.459125 TGCTCCATCTATTTGAGGATACCTATT 59.541 37.037 0.00 0.00 31.76 1.73
3908 5343 6.322931 TGCTCCATCTATTTGAGGATACCTA 58.677 40.000 0.00 0.00 31.76 3.08
3909 5344 5.158141 TGCTCCATCTATTTGAGGATACCT 58.842 41.667 0.00 0.00 36.03 3.08
3910 5345 5.489792 TGCTCCATCTATTTGAGGATACC 57.510 43.478 0.00 0.00 37.17 2.73
3911 5346 6.705302 TGATGCTCCATCTATTTGAGGATAC 58.295 40.000 6.74 0.00 41.06 2.24
3912 5347 6.575847 GCTGATGCTCCATCTATTTGAGGATA 60.576 42.308 6.74 0.00 41.06 2.59
3913 5348 5.803795 GCTGATGCTCCATCTATTTGAGGAT 60.804 44.000 6.74 0.00 41.06 3.24
3914 5349 4.504514 GCTGATGCTCCATCTATTTGAGGA 60.505 45.833 6.74 0.00 41.06 3.71
3915 5350 3.752222 GCTGATGCTCCATCTATTTGAGG 59.248 47.826 6.74 0.00 41.06 3.86
3930 5365 4.536364 TGCTAAAACGAATAGCTGATGC 57.464 40.909 15.82 0.00 44.79 3.91
3931 5366 8.122330 TGTAAATGCTAAAACGAATAGCTGATG 58.878 33.333 15.82 0.00 44.79 3.07
3932 5367 8.208718 TGTAAATGCTAAAACGAATAGCTGAT 57.791 30.769 15.82 4.23 44.79 2.90
3933 5368 7.603963 TGTAAATGCTAAAACGAATAGCTGA 57.396 32.000 15.82 2.52 44.79 4.26
3934 5369 9.370126 GTATGTAAATGCTAAAACGAATAGCTG 57.630 33.333 15.82 0.00 44.79 4.24
3935 5370 8.557029 GGTATGTAAATGCTAAAACGAATAGCT 58.443 33.333 15.82 0.00 44.79 3.32
3936 5371 7.801783 GGGTATGTAAATGCTAAAACGAATAGC 59.198 37.037 10.48 10.48 44.77 2.97
3937 5372 9.052759 AGGGTATGTAAATGCTAAAACGAATAG 57.947 33.333 0.00 0.00 0.00 1.73
3938 5373 8.967664 AGGGTATGTAAATGCTAAAACGAATA 57.032 30.769 0.00 0.00 0.00 1.75
3939 5374 7.875327 AGGGTATGTAAATGCTAAAACGAAT 57.125 32.000 0.00 0.00 0.00 3.34
3940 5375 7.690952 AAGGGTATGTAAATGCTAAAACGAA 57.309 32.000 0.00 0.00 0.00 3.85
3941 5376 7.690952 AAAGGGTATGTAAATGCTAAAACGA 57.309 32.000 0.00 0.00 0.00 3.85
3942 5377 8.751302 AAAAAGGGTATGTAAATGCTAAAACG 57.249 30.769 0.00 0.00 0.00 3.60
3966 5401 8.805175 CCATCCCATATCTAATTTATGCACAAA 58.195 33.333 0.00 0.00 0.00 2.83
3967 5402 7.949565 ACCATCCCATATCTAATTTATGCACAA 59.050 33.333 0.00 0.00 0.00 3.33
3968 5403 7.469343 ACCATCCCATATCTAATTTATGCACA 58.531 34.615 0.00 0.00 0.00 4.57
3969 5404 7.944729 ACCATCCCATATCTAATTTATGCAC 57.055 36.000 0.00 0.00 0.00 4.57
3970 5405 8.169393 TGAACCATCCCATATCTAATTTATGCA 58.831 33.333 0.00 0.00 0.00 3.96
3971 5406 8.579850 TGAACCATCCCATATCTAATTTATGC 57.420 34.615 0.00 0.00 0.00 3.14
3972 5407 9.745018 ACTGAACCATCCCATATCTAATTTATG 57.255 33.333 0.00 0.00 0.00 1.90
3975 5410 9.170890 TCTACTGAACCATCCCATATCTAATTT 57.829 33.333 0.00 0.00 0.00 1.82
3976 5411 8.742125 TCTACTGAACCATCCCATATCTAATT 57.258 34.615 0.00 0.00 0.00 1.40
3977 5412 7.958583 ACTCTACTGAACCATCCCATATCTAAT 59.041 37.037 0.00 0.00 0.00 1.73
3978 5413 7.306013 ACTCTACTGAACCATCCCATATCTAA 58.694 38.462 0.00 0.00 0.00 2.10
3979 5414 6.864421 ACTCTACTGAACCATCCCATATCTA 58.136 40.000 0.00 0.00 0.00 1.98
3980 5415 5.721225 ACTCTACTGAACCATCCCATATCT 58.279 41.667 0.00 0.00 0.00 1.98
3981 5416 7.551585 CATACTCTACTGAACCATCCCATATC 58.448 42.308 0.00 0.00 0.00 1.63
3982 5417 6.070538 GCATACTCTACTGAACCATCCCATAT 60.071 42.308 0.00 0.00 0.00 1.78
3983 5418 5.246203 GCATACTCTACTGAACCATCCCATA 59.754 44.000 0.00 0.00 0.00 2.74
3984 5419 4.040952 GCATACTCTACTGAACCATCCCAT 59.959 45.833 0.00 0.00 0.00 4.00
3985 5420 3.388024 GCATACTCTACTGAACCATCCCA 59.612 47.826 0.00 0.00 0.00 4.37
3986 5421 3.643792 AGCATACTCTACTGAACCATCCC 59.356 47.826 0.00 0.00 0.00 3.85
3987 5422 4.946478 AGCATACTCTACTGAACCATCC 57.054 45.455 0.00 0.00 0.00 3.51
4002 5437 2.734893 AGCGGAGGGAGTAGCATAC 58.265 57.895 0.00 0.00 43.47 2.39


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

AutoCloner maintained by Alex Coulton.