Multiple sequence alignment - TraesCS5D01G432800

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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 TraesCS5D01G432800 chr5D 100.000 3983 0 0 1 3983 488852584 488856566 0.000000e+00 7356.0
1 TraesCS5D01G432800 chr5A 93.443 2379 97 27 1579 3914 609863896 609866258 0.000000e+00 3474.0
2 TraesCS5D01G432800 chr5A 94.118 374 7 4 690 1058 609862574 609862937 4.500000e-154 555.0
3 TraesCS5D01G432800 chr5A 89.160 369 16 5 1156 1513 609863391 609863746 4.730000e-119 438.0
4 TraesCS5D01G432800 chr5A 89.437 284 20 7 304 578 609862245 609862527 2.280000e-92 350.0
5 TraesCS5D01G432800 chr5A 82.410 307 42 7 170 474 332327321 332327617 1.420000e-64 257.0
6 TraesCS5D01G432800 chr5A 100.000 63 0 0 3920 3982 609866294 609866356 2.510000e-22 117.0
7 TraesCS5D01G432800 chr5B 87.959 1279 58 23 2729 3983 602244468 602245674 0.000000e+00 1421.0
8 TraesCS5D01G432800 chr5B 94.466 777 42 1 1579 2354 602242779 602243555 0.000000e+00 1195.0
9 TraesCS5D01G432800 chr5B 87.089 790 51 18 170 944 602240963 602241716 0.000000e+00 846.0
10 TraesCS5D01G432800 chr5B 91.031 446 22 5 1077 1513 602242192 602242628 1.590000e-163 586.0
11 TraesCS5D01G432800 chr5B 90.690 290 22 4 2430 2716 602243745 602244032 8.080000e-102 381.0
12 TraesCS5D01G432800 chr5B 97.037 135 4 0 38 172 602240750 602240884 1.110000e-55 228.0
13 TraesCS5D01G432800 chr5B 96.341 82 3 0 2339 2420 602243572 602243653 6.940000e-28 135.0
14 TraesCS5D01G432800 chr5B 98.611 72 1 0 1507 1578 602242667 602242738 1.160000e-25 128.0
15 TraesCS5D01G432800 chr3D 84.783 92 12 2 32 123 456542385 456542474 1.520000e-14 91.6
16 TraesCS5D01G432800 chr6B 87.671 73 8 1 61 132 703682016 703681944 2.550000e-12 84.2
17 TraesCS5D01G432800 chr2D 90.741 54 3 1 50 101 557265661 557265714 1.990000e-08 71.3
18 TraesCS5D01G432800 chr2A 87.037 54 5 1 50 101 697298399 697298452 4.300000e-05 60.2
19 TraesCS5D01G432800 chr1B 79.787 94 10 7 3 94 420560229 420560143 4.300000e-05 60.2


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 TraesCS5D01G432800 chr5D 488852584 488856566 3982 False 7356.0 7356 100.0000 1 3983 1 chr5D.!!$F1 3982
1 TraesCS5D01G432800 chr5A 609862245 609866356 4111 False 986.8 3474 93.2316 304 3982 5 chr5A.!!$F2 3678
2 TraesCS5D01G432800 chr5B 602240750 602245674 4924 False 615.0 1421 92.9030 38 3983 8 chr5B.!!$F1 3945


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
296 378 0.882474 GGGAGTCCGGATATCTGTCG 59.118 60.0 7.81 2.09 0.00 4.35 F
644 736 0.890683 CTGAGCCCACCAAAATGACC 59.109 55.0 0.00 0.00 0.00 4.02 F
1663 2540 0.242017 GTGTTGGCACTTCATCTGGC 59.758 55.0 0.00 0.00 42.13 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1246 2021 0.307760 CCGAAGCACAATTATCGGCC 59.692 55.000 0.00 0.0 46.97 6.13 R
1702 2579 1.006102 AGAGGCCTCAACAACGTCG 60.006 57.895 33.90 0.0 0.00 5.12 R
3591 5039 0.317020 AAACAACGCGCTTCAGCTTC 60.317 50.000 5.73 0.0 39.32 3.86 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
23 24 5.747951 AAAACCCGAAAACACGTATACAA 57.252 34.783 3.32 0.00 0.00 2.41
24 25 4.996062 AACCCGAAAACACGTATACAAG 57.004 40.909 3.32 0.00 0.00 3.16
25 26 4.255833 ACCCGAAAACACGTATACAAGA 57.744 40.909 3.32 0.00 0.00 3.02
26 27 4.824289 ACCCGAAAACACGTATACAAGAT 58.176 39.130 3.32 0.00 0.00 2.40
27 28 5.964758 ACCCGAAAACACGTATACAAGATA 58.035 37.500 3.32 0.00 0.00 1.98
28 29 6.038356 ACCCGAAAACACGTATACAAGATAG 58.962 40.000 3.32 0.00 0.00 2.08
29 30 6.127647 ACCCGAAAACACGTATACAAGATAGA 60.128 38.462 3.32 0.00 0.00 1.98
30 31 6.753279 CCCGAAAACACGTATACAAGATAGAA 59.247 38.462 3.32 0.00 0.00 2.10
31 32 7.276218 CCCGAAAACACGTATACAAGATAGAAA 59.724 37.037 3.32 0.00 0.00 2.52
32 33 8.649841 CCGAAAACACGTATACAAGATAGAAAA 58.350 33.333 3.32 0.00 0.00 2.29
176 258 3.702555 GTGACACGTGGCGCTGTC 61.703 66.667 27.45 17.80 37.90 3.51
206 288 1.173043 TTGTCATCAAATGCGGTCCC 58.827 50.000 0.00 0.00 0.00 4.46
243 325 3.582743 GTCCGGACGTCTGTTTTCT 57.417 52.632 20.85 0.00 0.00 2.52
252 334 1.656429 CGTCTGTTTTCTCGCAAACCG 60.656 52.381 0.00 0.00 36.03 4.44
271 353 1.264288 CGGAGACAAACAAAGTGGAGC 59.736 52.381 0.00 0.00 0.00 4.70
296 378 0.882474 GGGAGTCCGGATATCTGTCG 59.118 60.000 7.81 2.09 0.00 4.35
617 709 2.181521 GTTTGTGGGTCGGCGTTGA 61.182 57.895 6.85 0.00 0.00 3.18
627 719 3.365265 GGCGTTGAAGGTGCCCTG 61.365 66.667 0.00 0.00 43.06 4.45
644 736 0.890683 CTGAGCCCACCAAAATGACC 59.109 55.000 0.00 0.00 0.00 4.02
686 778 4.512944 CCTGAATGATTCGGACCACAATAG 59.487 45.833 15.33 0.00 38.34 1.73
687 779 3.876914 TGAATGATTCGGACCACAATAGC 59.123 43.478 0.18 0.00 0.00 2.97
688 780 3.558931 ATGATTCGGACCACAATAGCA 57.441 42.857 0.00 0.00 0.00 3.49
689 781 2.905075 TGATTCGGACCACAATAGCAG 58.095 47.619 0.00 0.00 0.00 4.24
703 795 1.204146 TAGCAGCCCGAGGAGAAAAT 58.796 50.000 0.00 0.00 0.00 1.82
1089 1529 1.991264 CTGATGATGGATCGATCGTGC 59.009 52.381 18.81 10.56 33.17 5.34
1226 2001 2.744202 CAGGAACATCTTTCGGGAAGTG 59.256 50.000 0.00 0.00 36.70 3.16
1227 2002 2.637872 AGGAACATCTTTCGGGAAGTGA 59.362 45.455 0.00 0.00 36.70 3.41
1246 2021 2.609002 TGATGCGAATTCAGGAACGATG 59.391 45.455 6.22 0.00 0.00 3.84
1247 2022 1.368641 TGCGAATTCAGGAACGATGG 58.631 50.000 6.22 0.00 0.00 3.51
1264 2039 1.013596 TGGCCGATAATTGTGCTTCG 58.986 50.000 0.00 0.00 0.00 3.79
1306 2081 3.260740 GAAGTTGAGATGGCTCTGAGTG 58.739 50.000 6.53 0.00 41.84 3.51
1379 2161 3.560636 TTAGCTCCTGTGCTTATTCCC 57.439 47.619 0.00 0.00 43.74 3.97
1410 2202 3.040147 ACAGGTGTGTAGATGGTTTCG 57.960 47.619 0.00 0.00 34.05 3.46
1555 2392 8.145767 AGCAATTTCTTCATTTCATTCAGTCAA 58.854 29.630 0.00 0.00 0.00 3.18
1663 2540 0.242017 GTGTTGGCACTTCATCTGGC 59.758 55.000 0.00 0.00 42.13 4.85
1678 2555 2.681421 GGCCCAGCCCCTTTCAAG 60.681 66.667 0.00 0.00 44.06 3.02
1702 2579 1.143620 CTCTGGAGGCAGCACTAGC 59.856 63.158 0.00 0.00 42.56 3.42
1911 2789 5.889853 TGCTCTTTCTGGCTTGAATGATAAT 59.110 36.000 8.76 0.00 32.32 1.28
1932 2810 9.763465 GATAATTTTTCAATCAAAATGCAGGTG 57.237 29.630 0.00 0.00 36.63 4.00
1970 2848 7.397192 ACCTATAATTCATATGGTGGATTTGGC 59.603 37.037 2.13 0.00 37.26 4.52
2040 2918 0.529119 GTATGGAGGTGGTTACGGCG 60.529 60.000 4.80 4.80 0.00 6.46
2051 2929 2.328856 TTACGGCGGTTCGTACGGA 61.329 57.895 16.52 2.84 43.99 4.69
2060 2938 2.050350 TTCGTACGGAGGCTCTGGG 61.050 63.158 26.25 15.11 0.00 4.45
2121 2999 0.843309 ATACGGTGGAATGGGCATGA 59.157 50.000 0.00 0.00 0.00 3.07
2122 3000 0.180171 TACGGTGGAATGGGCATGAG 59.820 55.000 0.00 0.00 0.00 2.90
2142 3020 3.108376 AGTCCTTACAATCAGGGTCCTC 58.892 50.000 0.00 0.00 31.50 3.71
2147 3025 2.698855 ACAATCAGGGTCCTCATTCG 57.301 50.000 0.00 0.00 0.00 3.34
2153 3031 0.322546 AGGGTCCTCATTCGTTTGGC 60.323 55.000 0.00 0.00 0.00 4.52
2485 3478 3.492102 ATCTATGGCGTGGCTATTGTT 57.508 42.857 0.00 0.00 31.02 2.83
2575 3572 3.941573 TGGGGACAACGTTCTATTTACC 58.058 45.455 0.00 0.00 37.44 2.85
2579 3576 4.564199 GGGACAACGTTCTATTTACCCTGT 60.564 45.833 0.00 0.00 32.93 4.00
2622 3619 3.700538 TGGGATTGTGAATTTCTCTGGG 58.299 45.455 0.00 0.00 0.00 4.45
2649 3646 3.282021 TGCATTCCTTATCAGCCAGAAC 58.718 45.455 0.00 0.00 0.00 3.01
2716 3713 1.808411 TGACGAGTGCCTTTCCATTC 58.192 50.000 0.00 0.00 0.00 2.67
2724 3727 3.826157 AGTGCCTTTCCATTCGATTCAAA 59.174 39.130 0.00 0.00 0.00 2.69
3131 4553 4.624604 GCGAGGAAACCAAGTAATCCCTAA 60.625 45.833 0.00 0.00 32.15 2.69
3276 4698 1.931635 TACCCAAAATGCCTTGTCCC 58.068 50.000 0.00 0.00 0.00 4.46
3282 4704 1.534729 AAATGCCTTGTCCCGAGAAC 58.465 50.000 0.00 0.00 0.00 3.01
3292 4714 0.761323 TCCCGAGAACTGGTCCACAA 60.761 55.000 0.00 0.00 0.00 3.33
3371 4793 1.134367 GCACAGGAGTATACTGACGCA 59.866 52.381 10.90 0.00 39.24 5.24
3387 4809 1.447140 GCACCTCGTGATAACGGCA 60.447 57.895 1.94 0.00 35.23 5.69
3418 4840 6.734104 ATTATCTGCTCTCACAGTTGTTTC 57.266 37.500 0.00 0.00 38.84 2.78
3460 4882 7.394923 TGATCATGATTAATCAGCAATATGCCA 59.605 33.333 21.97 12.37 46.52 4.92
3511 4934 0.793250 GTTCTTCGGCTCTTGCAGAC 59.207 55.000 0.00 0.00 42.66 3.51
3532 4955 2.159476 CGGTAGTGCTGCTACTCGTAAA 60.159 50.000 15.15 0.00 46.99 2.01
3573 5021 2.210116 GCGAAACTGGTCTGAAGTTGA 58.790 47.619 0.00 0.00 37.90 3.18
3574 5022 2.032808 GCGAAACTGGTCTGAAGTTGAC 60.033 50.000 0.00 0.00 37.90 3.18
3575 5023 3.194861 CGAAACTGGTCTGAAGTTGACA 58.805 45.455 0.00 0.00 37.90 3.58
3576 5024 3.809832 CGAAACTGGTCTGAAGTTGACAT 59.190 43.478 0.00 0.00 37.90 3.06
3577 5025 4.319046 CGAAACTGGTCTGAAGTTGACATG 60.319 45.833 0.00 0.00 37.90 3.21
3578 5026 2.498167 ACTGGTCTGAAGTTGACATGC 58.502 47.619 0.00 0.00 36.26 4.06
3579 5027 1.462283 CTGGTCTGAAGTTGACATGCG 59.538 52.381 0.00 0.00 36.26 4.73
3580 5028 0.166814 GGTCTGAAGTTGACATGCGC 59.833 55.000 0.00 0.00 36.26 6.09
3581 5029 0.166814 GTCTGAAGTTGACATGCGCC 59.833 55.000 4.18 0.00 34.80 6.53
3582 5030 0.955428 TCTGAAGTTGACATGCGCCC 60.955 55.000 4.18 0.00 0.00 6.13
3583 5031 0.957395 CTGAAGTTGACATGCGCCCT 60.957 55.000 4.18 0.00 0.00 5.19
3584 5032 1.236616 TGAAGTTGACATGCGCCCTG 61.237 55.000 4.18 5.05 0.00 4.45
3585 5033 0.955428 GAAGTTGACATGCGCCCTGA 60.955 55.000 4.18 0.00 0.00 3.86
3586 5034 0.957395 AAGTTGACATGCGCCCTGAG 60.957 55.000 4.18 0.00 0.00 3.35
3587 5035 2.747460 TTGACATGCGCCCTGAGC 60.747 61.111 4.18 1.64 38.52 4.26
3588 5036 3.258228 TTGACATGCGCCCTGAGCT 62.258 57.895 4.18 0.00 40.39 4.09
3589 5037 2.894387 GACATGCGCCCTGAGCTC 60.894 66.667 6.82 6.82 40.39 4.09
3590 5038 3.382803 GACATGCGCCCTGAGCTCT 62.383 63.158 16.19 0.00 40.39 4.09
3591 5039 2.895865 CATGCGCCCTGAGCTCTG 60.896 66.667 16.19 14.67 40.39 3.35
3592 5040 3.079478 ATGCGCCCTGAGCTCTGA 61.079 61.111 21.10 1.91 40.39 3.27
3593 5041 2.663075 ATGCGCCCTGAGCTCTGAA 61.663 57.895 21.10 0.00 40.39 3.02
3594 5042 2.511145 GCGCCCTGAGCTCTGAAG 60.511 66.667 21.10 12.95 40.39 3.02
3625 5073 3.689649 CGTTGTTTCTTATCCTCCTTGGG 59.310 47.826 0.00 0.00 36.20 4.12
3626 5074 4.663334 GTTGTTTCTTATCCTCCTTGGGT 58.337 43.478 0.00 0.00 36.20 4.51
3627 5075 5.570034 CGTTGTTTCTTATCCTCCTTGGGTA 60.570 44.000 0.00 0.00 36.20 3.69
3628 5076 5.431179 TGTTTCTTATCCTCCTTGGGTAC 57.569 43.478 0.00 0.00 36.20 3.34
3629 5077 5.098663 TGTTTCTTATCCTCCTTGGGTACT 58.901 41.667 0.00 0.00 36.20 2.73
3630 5078 5.045869 TGTTTCTTATCCTCCTTGGGTACTG 60.046 44.000 0.00 0.00 36.20 2.74
3631 5079 3.039011 TCTTATCCTCCTTGGGTACTGC 58.961 50.000 0.00 0.00 36.20 4.40
3632 5080 2.561209 TATCCTCCTTGGGTACTGCA 57.439 50.000 0.00 0.00 36.20 4.41
3633 5081 1.668826 ATCCTCCTTGGGTACTGCAA 58.331 50.000 0.00 0.00 36.20 4.08
3634 5082 0.984230 TCCTCCTTGGGTACTGCAAG 59.016 55.000 0.00 0.00 36.69 4.01
3635 5083 0.035056 CCTCCTTGGGTACTGCAAGG 60.035 60.000 0.00 0.00 45.20 3.61
3636 5084 0.035056 CTCCTTGGGTACTGCAAGGG 60.035 60.000 2.15 0.00 44.38 3.95
3649 5097 1.298014 CAAGGGTGCCTGACTCTCC 59.702 63.158 0.00 0.00 32.34 3.71
3711 5165 7.307989 CCTTTTGAAAACTGTATGACACGAGAT 60.308 37.037 0.00 0.00 0.00 2.75
3720 5174 5.399013 TGTATGACACGAGATACTGTTGTG 58.601 41.667 0.00 0.00 36.64 3.33
3813 5293 0.935196 GTTCGTTCACTGCGTCCTTT 59.065 50.000 0.00 0.00 0.00 3.11
3815 5295 2.512485 TCGTTCACTGCGTCCTTTAA 57.488 45.000 0.00 0.00 0.00 1.52
3816 5296 2.400399 TCGTTCACTGCGTCCTTTAAG 58.600 47.619 0.00 0.00 0.00 1.85
3817 5297 2.132762 CGTTCACTGCGTCCTTTAAGT 58.867 47.619 0.00 0.00 0.00 2.24
3818 5298 2.096909 CGTTCACTGCGTCCTTTAAGTG 60.097 50.000 0.00 0.00 41.11 3.16
3820 5300 3.462483 TCACTGCGTCCTTTAAGTGAA 57.538 42.857 2.03 0.00 44.45 3.18
3821 5301 3.128349 TCACTGCGTCCTTTAAGTGAAC 58.872 45.455 2.03 0.00 44.45 3.18
3822 5302 2.869801 CACTGCGTCCTTTAAGTGAACA 59.130 45.455 0.00 0.00 42.09 3.18
3823 5303 2.870411 ACTGCGTCCTTTAAGTGAACAC 59.130 45.455 0.00 0.00 0.00 3.32
3835 5321 1.549170 AGTGAACACGGTCCCTGTATC 59.451 52.381 0.00 0.00 36.20 2.24
3839 5325 2.822707 ACACGGTCCCTGTATCTACT 57.177 50.000 0.00 0.00 0.00 2.57
3843 5329 1.955080 CGGTCCCTGTATCTACTCCAC 59.045 57.143 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.703607 TCTTGTATACGTGTTTTCGGGTTTTA 59.296 34.615 0.00 0.00 34.94 1.52
1 2 5.526846 TCTTGTATACGTGTTTTCGGGTTTT 59.473 36.000 0.00 0.00 34.94 2.43
2 3 5.055812 TCTTGTATACGTGTTTTCGGGTTT 58.944 37.500 0.00 0.00 34.94 3.27
3 4 4.630111 TCTTGTATACGTGTTTTCGGGTT 58.370 39.130 0.00 0.00 34.94 4.11
4 5 4.255833 TCTTGTATACGTGTTTTCGGGT 57.744 40.909 0.00 0.00 34.94 5.28
5 6 6.267817 TCTATCTTGTATACGTGTTTTCGGG 58.732 40.000 0.00 0.00 34.94 5.14
6 7 7.745022 TTCTATCTTGTATACGTGTTTTCGG 57.255 36.000 0.00 0.00 34.94 4.30
30 31 6.761242 GGGCGCTTTCATAGGATTTTATTTTT 59.239 34.615 7.64 0.00 0.00 1.94
31 32 6.127196 TGGGCGCTTTCATAGGATTTTATTTT 60.127 34.615 7.64 0.00 0.00 1.82
32 33 5.362430 TGGGCGCTTTCATAGGATTTTATTT 59.638 36.000 7.64 0.00 0.00 1.40
33 34 4.892934 TGGGCGCTTTCATAGGATTTTATT 59.107 37.500 7.64 0.00 0.00 1.40
34 35 4.469657 TGGGCGCTTTCATAGGATTTTAT 58.530 39.130 7.64 0.00 0.00 1.40
35 36 3.882888 CTGGGCGCTTTCATAGGATTTTA 59.117 43.478 7.64 0.00 0.00 1.52
36 37 2.689983 CTGGGCGCTTTCATAGGATTTT 59.310 45.455 7.64 0.00 0.00 1.82
201 283 3.810896 GCGAACCAATGCGGGACC 61.811 66.667 0.00 0.00 40.22 4.46
206 288 1.275657 GTATCGGCGAACCAATGCG 59.724 57.895 15.93 0.00 34.57 4.73
211 293 2.491152 GGACGTATCGGCGAACCA 59.509 61.111 15.93 0.00 34.63 3.67
230 312 2.599142 GGTTTGCGAGAAAACAGACGTC 60.599 50.000 7.70 7.70 41.00 4.34
233 315 1.333791 CCGGTTTGCGAGAAAACAGAC 60.334 52.381 8.75 0.00 41.00 3.51
243 325 0.462225 TGTTTGTCTCCGGTTTGCGA 60.462 50.000 0.00 0.00 0.00 5.10
252 334 2.576615 AGCTCCACTTTGTTTGTCTCC 58.423 47.619 0.00 0.00 0.00 3.71
287 369 1.434188 TGGATTGGCCCGACAGATAT 58.566 50.000 0.00 0.00 34.97 1.63
288 370 1.208706 TTGGATTGGCCCGACAGATA 58.791 50.000 0.00 0.00 34.97 1.98
296 378 0.324275 TACTGGCTTTGGATTGGCCC 60.324 55.000 0.00 0.00 44.71 5.80
313 395 4.583489 TCCGGACAGAAAGAGGATATGTAC 59.417 45.833 0.00 0.00 0.00 2.90
366 456 0.889186 GCAACCTTCCGCCAAAGAGA 60.889 55.000 0.00 0.00 0.00 3.10
579 671 1.161563 GGACACGGACCGCTCAAAAA 61.162 55.000 15.39 0.00 0.00 1.94
580 672 1.595929 GGACACGGACCGCTCAAAA 60.596 57.895 15.39 0.00 0.00 2.44
581 673 2.029964 GGACACGGACCGCTCAAA 59.970 61.111 15.39 0.00 0.00 2.69
582 674 4.351938 CGGACACGGACCGCTCAA 62.352 66.667 15.39 0.00 43.74 3.02
588 680 2.248835 CCACAAACGGACACGGACC 61.249 63.158 0.00 0.00 46.48 4.46
589 681 2.248835 CCCACAAACGGACACGGAC 61.249 63.158 0.00 0.00 46.48 4.79
590 682 2.109387 CCCACAAACGGACACGGA 59.891 61.111 0.00 0.00 46.48 4.69
627 719 0.251787 AGGGTCATTTTGGTGGGCTC 60.252 55.000 0.00 0.00 0.00 4.70
644 736 0.322546 GCCAGTCAAGGGGTACAAGG 60.323 60.000 0.00 0.00 0.00 3.61
686 778 1.997928 GCATTTTCTCCTCGGGCTGC 61.998 60.000 0.00 0.00 0.00 5.25
687 779 1.379642 GGCATTTTCTCCTCGGGCTG 61.380 60.000 0.00 0.00 0.00 4.85
688 780 1.077429 GGCATTTTCTCCTCGGGCT 60.077 57.895 0.00 0.00 0.00 5.19
689 781 1.077429 AGGCATTTTCTCCTCGGGC 60.077 57.895 0.00 0.00 0.00 6.13
703 795 0.793861 GACGTTTTACATGCGAGGCA 59.206 50.000 0.00 0.00 44.86 4.75
953 1050 1.815840 GCTAGTTCTGCGGCCCTTC 60.816 63.158 0.00 0.00 0.00 3.46
993 1090 4.120331 GAACCTGCCATGGCGTGC 62.120 66.667 30.87 18.77 45.51 5.34
994 1091 3.803082 CGAACCTGCCATGGCGTG 61.803 66.667 30.87 25.21 45.51 5.34
1060 1177 7.358765 CGATCGATCCATCATCAGAAAAGTAAC 60.359 40.741 19.51 0.00 0.00 2.50
1089 1529 1.080569 GCACCAAAATCGCACCCAG 60.081 57.895 0.00 0.00 0.00 4.45
1212 1987 1.207089 TCGCATCACTTCCCGAAAGAT 59.793 47.619 4.76 0.00 38.44 2.40
1226 2001 2.032549 CCATCGTTCCTGAATTCGCATC 60.033 50.000 0.04 0.00 0.00 3.91
1227 2002 1.942657 CCATCGTTCCTGAATTCGCAT 59.057 47.619 0.04 0.00 0.00 4.73
1246 2021 0.307760 CCGAAGCACAATTATCGGCC 59.692 55.000 0.00 0.00 46.97 6.13
1247 2022 3.825812 CCGAAGCACAATTATCGGC 57.174 52.632 0.00 0.00 46.97 5.54
1264 2039 3.267551 TCAACCCCAAACTATACCTTCCC 59.732 47.826 0.00 0.00 0.00 3.97
1306 2081 9.325198 TGACATATAATACCTCACATGACAAAC 57.675 33.333 0.00 0.00 0.00 2.93
1398 2182 2.415512 GTGCAGGAACGAAACCATCTAC 59.584 50.000 0.00 0.00 0.00 2.59
1410 2202 2.798976 TGCAAGAAATGTGCAGGAAC 57.201 45.000 0.00 0.00 46.76 3.62
1453 2245 2.042259 CAGCCAGCCATGAAAGCGA 61.042 57.895 0.00 0.00 34.64 4.93
1504 2296 7.500992 TCTAACTATGAGGAACCATGCTTTAG 58.499 38.462 0.00 0.00 0.00 1.85
1555 2392 3.199508 AGCAATCTGAGCTGGTACATTCT 59.800 43.478 0.00 0.00 41.61 2.40
1663 2540 2.681421 GGCTTGAAAGGGGCTGGG 60.681 66.667 0.00 0.00 0.00 4.45
1684 2561 1.143620 GCTAGTGCTGCCTCCAGAG 59.856 63.158 0.00 0.00 41.77 3.35
1702 2579 1.006102 AGAGGCCTCAACAACGTCG 60.006 57.895 33.90 0.00 0.00 5.12
1895 2772 9.373603 TGATTGAAAAATTATCATTCAAGCCAG 57.626 29.630 14.05 0.00 44.53 4.85
1911 2789 6.205076 CCATCACCTGCATTTTGATTGAAAAA 59.795 34.615 2.84 0.00 37.10 1.94
1932 2810 5.865085 TGAATTATAGGTACTGGCACCATC 58.135 41.667 0.00 0.00 41.52 3.51
1970 2848 1.269936 CCACCGTTACTATAAGCCCCG 60.270 57.143 0.00 0.00 0.00 5.73
2040 2918 1.139095 CAGAGCCTCCGTACGAACC 59.861 63.158 18.76 1.89 0.00 3.62
2051 2929 1.135094 CACCATACATCCCAGAGCCT 58.865 55.000 0.00 0.00 0.00 4.58
2060 2938 9.733556 TTATTATACATTGACCCACCATACATC 57.266 33.333 0.00 0.00 0.00 3.06
2111 2989 3.737559 TTGTAAGGACTCATGCCCATT 57.262 42.857 0.00 0.00 0.00 3.16
2121 2999 3.108376 GAGGACCCTGATTGTAAGGACT 58.892 50.000 0.00 0.00 36.91 3.85
2122 3000 2.838202 TGAGGACCCTGATTGTAAGGAC 59.162 50.000 0.00 0.00 36.91 3.85
2142 3020 1.937546 GCTGGAGGGCCAAACGAATG 61.938 60.000 6.18 0.00 45.41 2.67
2147 3025 2.991540 GGTGCTGGAGGGCCAAAC 60.992 66.667 6.18 0.00 45.41 2.93
2247 3125 8.129496 TGCTCAACGGTATGGATTATAGATTA 57.871 34.615 0.00 0.00 0.00 1.75
2251 3129 6.398095 TCATGCTCAACGGTATGGATTATAG 58.602 40.000 0.00 0.00 31.77 1.31
2264 3142 3.168963 CAAAGCTGAATCATGCTCAACG 58.831 45.455 7.45 0.00 38.75 4.10
2485 3478 3.791973 AAGGAACAAATTGTGCGTTGA 57.208 38.095 10.87 0.00 33.15 3.18
2534 3529 9.476202 GTCCCCATTTAAAGCATATAAAATGAC 57.524 33.333 7.92 0.00 40.24 3.06
2564 3561 7.159372 TCAGTGAGAAACAGGGTAAATAGAAC 58.841 38.462 0.00 0.00 0.00 3.01
2575 3572 3.405831 TCTGCAATCAGTGAGAAACAGG 58.594 45.455 12.58 0.00 41.10 4.00
2622 3619 2.286654 GCTGATAAGGAATGCAACTCGC 60.287 50.000 0.00 0.00 42.89 5.03
2631 3628 4.225942 TGAGTGTTCTGGCTGATAAGGAAT 59.774 41.667 0.00 0.00 0.00 3.01
2649 3646 1.830279 ACATGTGGAATGCCTGAGTG 58.170 50.000 0.00 0.00 34.31 3.51
2716 3713 7.301054 AGAACTTAAGAAGCATGTTTGAATCG 58.699 34.615 10.09 0.00 0.00 3.34
2724 3727 7.992754 ATTCAGAAGAACTTAAGAAGCATGT 57.007 32.000 10.09 0.00 36.39 3.21
3131 4553 3.852286 TCACGGTAAATACAACGAGCAT 58.148 40.909 0.00 0.00 0.00 3.79
3276 4698 6.036083 CAGTAATATTTGTGGACCAGTTCTCG 59.964 42.308 0.00 0.00 0.00 4.04
3282 4704 7.312899 GGAAAACAGTAATATTTGTGGACCAG 58.687 38.462 0.00 0.00 0.00 4.00
3387 4809 7.743749 ACTGTGAGAGCAGATAATAATTCCAT 58.256 34.615 0.00 0.00 39.62 3.41
3433 4855 8.414003 GGCATATTGCTGATTAATCATGATCAT 58.586 33.333 18.26 1.18 44.28 2.45
3457 4879 1.273327 CAACTGTTCCAAAGGGATGGC 59.727 52.381 0.00 0.00 44.48 4.40
3460 4882 2.242043 CAGCAACTGTTCCAAAGGGAT 58.758 47.619 0.00 0.00 44.48 3.85
3532 4955 2.007049 GCACCACGCAGCTAGTAACAT 61.007 52.381 0.00 0.00 41.79 2.71
3578 5026 2.511145 GCTTCAGAGCTCAGGGCG 60.511 66.667 17.77 1.07 45.65 6.13
3587 5035 1.287730 AACGCGCTTCAGCTTCAGAG 61.288 55.000 5.73 0.00 39.32 3.35
3588 5036 1.300931 AACGCGCTTCAGCTTCAGA 60.301 52.632 5.73 0.00 39.32 3.27
3589 5037 1.154525 CAACGCGCTTCAGCTTCAG 60.155 57.895 5.73 0.00 39.32 3.02
3590 5038 1.436195 AACAACGCGCTTCAGCTTCA 61.436 50.000 5.73 0.00 39.32 3.02
3591 5039 0.317020 AAACAACGCGCTTCAGCTTC 60.317 50.000 5.73 0.00 39.32 3.86
3592 5040 0.317020 GAAACAACGCGCTTCAGCTT 60.317 50.000 5.73 0.00 39.32 3.74
3593 5041 1.160329 AGAAACAACGCGCTTCAGCT 61.160 50.000 5.73 0.00 39.32 4.24
3594 5042 0.317020 AAGAAACAACGCGCTTCAGC 60.317 50.000 5.73 0.00 37.78 4.26
3595 5043 2.941891 TAAGAAACAACGCGCTTCAG 57.058 45.000 5.73 0.00 0.00 3.02
3596 5044 2.158841 GGATAAGAAACAACGCGCTTCA 59.841 45.455 5.73 0.00 0.00 3.02
3597 5045 2.415512 AGGATAAGAAACAACGCGCTTC 59.584 45.455 5.73 4.24 0.00 3.86
3631 5079 1.197430 AGGAGAGTCAGGCACCCTTG 61.197 60.000 0.00 0.00 0.00 3.61
3632 5080 0.474660 AAGGAGAGTCAGGCACCCTT 60.475 55.000 0.00 0.00 0.00 3.95
3633 5081 0.474660 AAAGGAGAGTCAGGCACCCT 60.475 55.000 0.00 0.00 0.00 4.34
3634 5082 1.276622 TAAAGGAGAGTCAGGCACCC 58.723 55.000 0.00 0.00 0.00 4.61
3635 5083 2.911484 CATAAAGGAGAGTCAGGCACC 58.089 52.381 0.00 0.00 0.00 5.01
3636 5084 2.284190 GCATAAAGGAGAGTCAGGCAC 58.716 52.381 0.00 0.00 0.00 5.01
3665 5113 5.757850 AGGCAAAAGTTCAGAGTACAAAG 57.242 39.130 0.00 0.00 0.00 2.77
3711 5165 2.637382 TCTCATGGCCTTCACAACAGTA 59.363 45.455 3.32 0.00 0.00 2.74
3768 5248 2.425592 CCCACAAGACCTGCGTCA 59.574 61.111 0.00 0.00 41.87 4.35
3769 5249 1.961277 CACCCACAAGACCTGCGTC 60.961 63.158 0.00 0.00 39.50 5.19
3770 5250 1.404479 TACACCCACAAGACCTGCGT 61.404 55.000 0.00 0.00 0.00 5.24
3771 5251 0.036388 ATACACCCACAAGACCTGCG 60.036 55.000 0.00 0.00 0.00 5.18
3813 5293 1.416243 ACAGGGACCGTGTTCACTTA 58.584 50.000 14.09 0.00 0.00 2.24
3815 5295 1.549170 GATACAGGGACCGTGTTCACT 59.451 52.381 23.93 7.90 0.00 3.41
3816 5296 1.549170 AGATACAGGGACCGTGTTCAC 59.451 52.381 23.93 15.06 0.00 3.18
3817 5297 1.933021 AGATACAGGGACCGTGTTCA 58.067 50.000 23.93 8.60 0.00 3.18
3818 5298 3.022406 AGTAGATACAGGGACCGTGTTC 58.978 50.000 23.93 18.96 0.00 3.18
3820 5300 2.652590 GAGTAGATACAGGGACCGTGT 58.347 52.381 22.55 22.55 0.00 4.49
3821 5301 1.955080 GGAGTAGATACAGGGACCGTG 59.045 57.143 12.66 12.66 0.00 4.94
3822 5302 1.567649 TGGAGTAGATACAGGGACCGT 59.432 52.381 0.00 0.00 0.00 4.83
3823 5303 1.955080 GTGGAGTAGATACAGGGACCG 59.045 57.143 0.00 0.00 0.00 4.79
3835 5321 3.119101 ACTGTTTGGCGATAGTGGAGTAG 60.119 47.826 0.00 0.00 39.35 2.57
3839 5325 1.066430 GGACTGTTTGGCGATAGTGGA 60.066 52.381 0.00 0.00 39.35 4.02
3843 5329 1.066143 AGTGGGACTGTTTGGCGATAG 60.066 52.381 0.00 0.00 0.00 2.08
3918 5433 1.132453 GGCAGCCAATCTACGGTTTTC 59.868 52.381 6.55 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.