Multiple sequence alignment - TraesCS5D01G454800

Loading Multiple Alignment...

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 TraesCS5D01G454800 chr5D 100.000 3743 0 0 1 3743 501775471 501771729 0.000000e+00 6913.0
1 TraesCS5D01G454800 chr5B 95.070 3205 71 33 542 3692 625524620 625521449 0.000000e+00 4963.0
2 TraesCS5D01G454800 chr5B 94.200 1569 58 18 1467 3023 630286945 630285398 0.000000e+00 2362.0
3 TraesCS5D01G454800 chr5B 93.098 681 37 7 2291 2968 629277378 629278051 0.000000e+00 989.0
4 TraesCS5D01G454800 chr5B 93.098 681 37 7 2291 2968 629359948 629360621 0.000000e+00 989.0
5 TraesCS5D01G454800 chr5B 88.567 656 34 16 123 740 628610280 628609628 0.000000e+00 758.0
6 TraesCS5D01G454800 chr5B 88.397 655 35 16 123 739 625039207 625038556 0.000000e+00 750.0
7 TraesCS5D01G454800 chr5B 84.075 427 31 14 803 1203 628606397 628605982 9.810000e-101 377.0
8 TraesCS5D01G454800 chr5B 83.641 379 30 12 803 1156 625035671 625035300 1.000000e-85 327.0
9 TraesCS5D01G454800 chr5B 94.536 183 5 2 1022 1203 625032891 625032713 1.020000e-70 278.0
10 TraesCS5D01G454800 chr5B 78.959 461 54 21 1559 1996 629276758 629277198 1.320000e-69 274.0
11 TraesCS5D01G454800 chr5B 78.959 461 54 21 1559 1996 629359328 629359768 1.320000e-69 274.0
12 TraesCS5D01G454800 chr5B 93.793 145 9 0 2011 2155 629277183 629277327 6.290000e-53 219.0
13 TraesCS5D01G454800 chr5B 93.793 145 9 0 2011 2155 629359753 629359897 6.290000e-53 219.0
14 TraesCS5D01G454800 chr5B 81.017 295 36 7 1706 1996 625014553 625014275 2.260000e-52 217.0
15 TraesCS5D01G454800 chr5B 81.017 295 36 7 1706 1996 628587389 628587111 2.260000e-52 217.0
16 TraesCS5D01G454800 chr5B 95.833 120 3 2 3625 3743 625521464 625521346 3.820000e-45 193.0
17 TraesCS5D01G454800 chr5B 93.600 125 7 1 2011 2135 625014290 625014167 6.380000e-43 185.0
18 TraesCS5D01G454800 chr5B 93.600 125 7 1 2011 2135 628587126 628587003 6.380000e-43 185.0
19 TraesCS5D01G454800 chr5A 86.462 1625 89 45 525 2037 629709188 629710793 0.000000e+00 1661.0
20 TraesCS5D01G454800 chr5A 96.319 978 24 5 2034 3009 629712234 629713201 0.000000e+00 1596.0
21 TraesCS5D01G454800 chr5A 81.250 176 30 3 3247 3420 578829705 578829879 5.040000e-29 139.0
22 TraesCS5D01G454800 chr7A 88.494 817 39 25 1000 1774 676591906 676591103 0.000000e+00 937.0
23 TraesCS5D01G454800 chr7A 88.525 61 5 1 2233 2293 8523387 8523445 5.190000e-09 73.1
24 TraesCS5D01G454800 chr3A 88.171 820 40 26 997 1774 580560914 580561718 0.000000e+00 924.0
25 TraesCS5D01G454800 chr3A 79.787 94 10 2 2233 2319 552797567 552797658 4.040000e-05 60.2
26 TraesCS5D01G454800 chr1B 94.737 57 3 0 3365 3421 614105355 614105411 5.150000e-14 89.8
27 TraesCS5D01G454800 chr3D 92.982 57 1 3 2233 2289 614199314 614199261 3.100000e-11 80.5
28 TraesCS5D01G454800 chr7B 92.593 54 2 1 2236 2289 539786206 539786257 4.010000e-10 76.8
29 TraesCS5D01G454800 chr7B 87.879 66 5 3 2245 2309 159527330 159527393 1.440000e-09 75.0
30 TraesCS5D01G454800 chr3B 90.909 55 4 1 2236 2290 86108405 86108352 5.190000e-09 73.1
31 TraesCS5D01G454800 chr2B 80.435 92 9 2 2233 2317 584130166 584130255 1.120000e-05 62.1
32 TraesCS5D01G454800 chr4D 100.000 28 0 0 3695 3722 394398617 394398644 7.000000e-03 52.8


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 TraesCS5D01G454800 chr5D 501771729 501775471 3742 True 6913.000000 6913 100.000000 1 3743 1 chr5D.!!$R1 3742
1 TraesCS5D01G454800 chr5B 625521346 625524620 3274 True 2578.000000 4963 95.451500 542 3743 2 chr5B.!!$R4 3201
2 TraesCS5D01G454800 chr5B 630285398 630286945 1547 True 2362.000000 2362 94.200000 1467 3023 1 chr5B.!!$R1 1556
3 TraesCS5D01G454800 chr5B 628605982 628610280 4298 True 567.500000 758 86.321000 123 1203 2 chr5B.!!$R6 1080
4 TraesCS5D01G454800 chr5B 629276758 629278051 1293 False 494.000000 989 88.616667 1559 2968 3 chr5B.!!$F1 1409
5 TraesCS5D01G454800 chr5B 629359328 629360621 1293 False 494.000000 989 88.616667 1559 2968 3 chr5B.!!$F2 1409
6 TraesCS5D01G454800 chr5B 625032713 625039207 6494 True 451.666667 750 88.858000 123 1203 3 chr5B.!!$R3 1080
7 TraesCS5D01G454800 chr5A 629709188 629713201 4013 False 1628.500000 1661 91.390500 525 3009 2 chr5A.!!$F2 2484
8 TraesCS5D01G454800 chr7A 676591103 676591906 803 True 937.000000 937 88.494000 1000 1774 1 chr7A.!!$R1 774
9 TraesCS5D01G454800 chr3A 580560914 580561718 804 False 924.000000 924 88.171000 997 1774 1 chr3A.!!$F2 777

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
59 60 0.034380 TCTGTACCGGGGAGAGTGAG 60.034 60.0 6.32 0.0 0.0 3.51 F
67 68 0.036858 GGGGAGAGTGAGTGTGAAGC 60.037 60.0 0.00 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1232 7081 1.756561 TCGATCACCATCTGCCGGA 60.757 57.895 5.05 0.0 0.0 5.14 R
3523 10921 5.221441 GGGAAAAGTCAACAGCTACCAATTT 60.221 40.000 0.00 0.0 0.0 1.82 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
22 23 5.344743 TGGAGATTTCACAGAGGATACAC 57.655 43.478 0.00 0.00 41.41 2.90
23 24 4.142160 TGGAGATTTCACAGAGGATACACG 60.142 45.833 0.00 0.00 41.41 4.49
24 25 3.786635 AGATTTCACAGAGGATACACGC 58.213 45.455 0.00 0.00 41.41 5.34
25 26 3.449018 AGATTTCACAGAGGATACACGCT 59.551 43.478 0.00 0.00 41.41 5.07
26 27 2.941453 TTCACAGAGGATACACGCTC 57.059 50.000 0.00 0.00 41.41 5.03
27 28 2.130272 TCACAGAGGATACACGCTCT 57.870 50.000 0.00 0.00 41.41 4.09
28 29 1.745653 TCACAGAGGATACACGCTCTG 59.254 52.381 12.24 12.24 43.20 3.35
29 30 1.107114 ACAGAGGATACACGCTCTGG 58.893 55.000 16.52 3.26 42.56 3.86
30 31 0.249238 CAGAGGATACACGCTCTGGC 60.249 60.000 0.00 0.00 38.76 4.85
31 32 0.684479 AGAGGATACACGCTCTGGCA 60.684 55.000 0.00 0.00 37.40 4.92
32 33 0.390860 GAGGATACACGCTCTGGCAT 59.609 55.000 0.00 0.00 37.40 4.40
33 34 0.390860 AGGATACACGCTCTGGCATC 59.609 55.000 0.00 0.00 37.40 3.91
34 35 0.390860 GGATACACGCTCTGGCATCT 59.609 55.000 0.00 0.00 38.60 2.90
35 36 1.495878 GATACACGCTCTGGCATCTG 58.504 55.000 0.00 0.00 38.60 2.90
36 37 0.105593 ATACACGCTCTGGCATCTGG 59.894 55.000 0.00 0.00 38.60 3.86
37 38 1.960040 TACACGCTCTGGCATCTGGG 61.960 60.000 0.00 0.00 38.60 4.45
38 39 3.005539 ACGCTCTGGCATCTGGGT 61.006 61.111 0.00 0.00 38.60 4.51
39 40 2.270205 CGCTCTGGCATCTGGGTT 59.730 61.111 0.00 0.00 38.60 4.11
40 41 1.377725 CGCTCTGGCATCTGGGTTT 60.378 57.895 0.00 0.00 38.60 3.27
41 42 1.372087 CGCTCTGGCATCTGGGTTTC 61.372 60.000 0.00 0.00 38.60 2.78
42 43 0.034670 GCTCTGGCATCTGGGTTTCT 60.035 55.000 0.00 0.00 38.54 2.52
43 44 1.747709 CTCTGGCATCTGGGTTTCTG 58.252 55.000 0.00 0.00 0.00 3.02
44 45 1.004044 CTCTGGCATCTGGGTTTCTGT 59.996 52.381 0.00 0.00 0.00 3.41
45 46 2.237143 CTCTGGCATCTGGGTTTCTGTA 59.763 50.000 0.00 0.00 0.00 2.74
46 47 2.027192 TCTGGCATCTGGGTTTCTGTAC 60.027 50.000 0.00 0.00 0.00 2.90
47 48 1.004277 TGGCATCTGGGTTTCTGTACC 59.996 52.381 0.00 0.00 37.47 3.34
48 49 1.369625 GCATCTGGGTTTCTGTACCG 58.630 55.000 0.00 0.00 39.18 4.02
49 50 2.012051 GCATCTGGGTTTCTGTACCGG 61.012 57.143 0.00 0.00 39.18 5.28
50 51 0.909623 ATCTGGGTTTCTGTACCGGG 59.090 55.000 6.32 0.00 39.18 5.73
51 52 1.196104 TCTGGGTTTCTGTACCGGGG 61.196 60.000 6.32 0.00 39.18 5.73
52 53 1.152074 TGGGTTTCTGTACCGGGGA 60.152 57.895 6.32 0.00 39.18 4.81
53 54 1.196104 TGGGTTTCTGTACCGGGGAG 61.196 60.000 6.32 0.00 39.18 4.30
54 55 0.906282 GGGTTTCTGTACCGGGGAGA 60.906 60.000 6.32 0.00 39.18 3.71
55 56 0.535797 GGTTTCTGTACCGGGGAGAG 59.464 60.000 6.32 0.00 0.00 3.20
56 57 1.264295 GTTTCTGTACCGGGGAGAGT 58.736 55.000 6.32 0.00 0.00 3.24
57 58 1.067071 GTTTCTGTACCGGGGAGAGTG 60.067 57.143 6.32 0.00 0.00 3.51
58 59 0.406750 TTCTGTACCGGGGAGAGTGA 59.593 55.000 6.32 0.00 0.00 3.41
59 60 0.034380 TCTGTACCGGGGAGAGTGAG 60.034 60.000 6.32 0.00 0.00 3.51
60 61 0.323542 CTGTACCGGGGAGAGTGAGT 60.324 60.000 6.32 0.00 0.00 3.41
61 62 0.611062 TGTACCGGGGAGAGTGAGTG 60.611 60.000 6.32 0.00 0.00 3.51
62 63 0.611340 GTACCGGGGAGAGTGAGTGT 60.611 60.000 6.32 0.00 0.00 3.55
63 64 0.611062 TACCGGGGAGAGTGAGTGTG 60.611 60.000 6.32 0.00 0.00 3.82
64 65 1.606601 CCGGGGAGAGTGAGTGTGA 60.607 63.158 0.00 0.00 0.00 3.58
65 66 1.185618 CCGGGGAGAGTGAGTGTGAA 61.186 60.000 0.00 0.00 0.00 3.18
66 67 0.244994 CGGGGAGAGTGAGTGTGAAG 59.755 60.000 0.00 0.00 0.00 3.02
67 68 0.036858 GGGGAGAGTGAGTGTGAAGC 60.037 60.000 0.00 0.00 0.00 3.86
68 69 0.036858 GGGAGAGTGAGTGTGAAGCC 60.037 60.000 0.00 0.00 0.00 4.35
69 70 0.681733 GGAGAGTGAGTGTGAAGCCA 59.318 55.000 0.00 0.00 0.00 4.75
70 71 1.277557 GGAGAGTGAGTGTGAAGCCAT 59.722 52.381 0.00 0.00 0.00 4.40
71 72 2.289945 GGAGAGTGAGTGTGAAGCCATT 60.290 50.000 0.00 0.00 0.00 3.16
72 73 3.406764 GAGAGTGAGTGTGAAGCCATTT 58.593 45.455 0.00 0.00 0.00 2.32
73 74 3.817647 GAGAGTGAGTGTGAAGCCATTTT 59.182 43.478 0.00 0.00 0.00 1.82
74 75 4.973168 AGAGTGAGTGTGAAGCCATTTTA 58.027 39.130 0.00 0.00 0.00 1.52
75 76 4.999950 AGAGTGAGTGTGAAGCCATTTTAG 59.000 41.667 0.00 0.00 0.00 1.85
76 77 4.973168 AGTGAGTGTGAAGCCATTTTAGA 58.027 39.130 0.00 0.00 0.00 2.10
77 78 5.376625 AGTGAGTGTGAAGCCATTTTAGAA 58.623 37.500 0.00 0.00 0.00 2.10
78 79 5.827797 AGTGAGTGTGAAGCCATTTTAGAAA 59.172 36.000 0.00 0.00 0.00 2.52
79 80 5.915196 GTGAGTGTGAAGCCATTTTAGAAAC 59.085 40.000 0.00 0.00 0.00 2.78
80 81 5.108385 AGTGTGAAGCCATTTTAGAAACG 57.892 39.130 0.00 0.00 0.00 3.60
81 82 4.023193 AGTGTGAAGCCATTTTAGAAACGG 60.023 41.667 0.00 0.00 0.00 4.44
82 83 3.254657 TGTGAAGCCATTTTAGAAACGGG 59.745 43.478 0.00 0.00 0.00 5.28
83 84 3.504520 GTGAAGCCATTTTAGAAACGGGA 59.495 43.478 0.00 0.00 0.00 5.14
84 85 3.756434 TGAAGCCATTTTAGAAACGGGAG 59.244 43.478 0.00 0.00 0.00 4.30
85 86 3.713826 AGCCATTTTAGAAACGGGAGA 57.286 42.857 0.00 0.00 0.00 3.71
86 87 3.610911 AGCCATTTTAGAAACGGGAGAG 58.389 45.455 0.00 0.00 0.00 3.20
87 88 3.263425 AGCCATTTTAGAAACGGGAGAGA 59.737 43.478 0.00 0.00 0.00 3.10
88 89 4.007659 GCCATTTTAGAAACGGGAGAGAA 58.992 43.478 0.00 0.00 0.00 2.87
89 90 4.095036 GCCATTTTAGAAACGGGAGAGAAG 59.905 45.833 0.00 0.00 0.00 2.85
90 91 5.246307 CCATTTTAGAAACGGGAGAGAAGT 58.754 41.667 0.00 0.00 0.00 3.01
91 92 5.705905 CCATTTTAGAAACGGGAGAGAAGTT 59.294 40.000 0.00 0.00 0.00 2.66
92 93 6.206829 CCATTTTAGAAACGGGAGAGAAGTTT 59.793 38.462 0.00 0.00 40.32 2.66
93 94 6.613755 TTTTAGAAACGGGAGAGAAGTTTG 57.386 37.500 0.00 0.00 38.09 2.93
94 95 3.127425 AGAAACGGGAGAGAAGTTTGG 57.873 47.619 0.00 0.00 38.09 3.28
95 96 2.438392 AGAAACGGGAGAGAAGTTTGGT 59.562 45.455 0.00 0.00 38.09 3.67
96 97 2.545537 AACGGGAGAGAAGTTTGGTC 57.454 50.000 0.00 0.00 0.00 4.02
97 98 1.420430 ACGGGAGAGAAGTTTGGTCA 58.580 50.000 0.00 0.00 0.00 4.02
98 99 1.070289 ACGGGAGAGAAGTTTGGTCAC 59.930 52.381 0.00 0.00 0.00 3.67
99 100 1.797025 GGGAGAGAAGTTTGGTCACG 58.203 55.000 0.00 0.00 0.00 4.35
100 101 1.608283 GGGAGAGAAGTTTGGTCACGG 60.608 57.143 0.00 0.00 0.00 4.94
101 102 1.149148 GAGAGAAGTTTGGTCACGGC 58.851 55.000 0.00 0.00 0.00 5.68
102 103 0.468226 AGAGAAGTTTGGTCACGGCA 59.532 50.000 0.00 0.00 0.00 5.69
103 104 0.586802 GAGAAGTTTGGTCACGGCAC 59.413 55.000 0.00 0.00 0.00 5.01
116 117 3.181367 GGCACGGAGATGTTGCTG 58.819 61.111 0.00 0.00 0.00 4.41
117 118 2.401766 GGCACGGAGATGTTGCTGG 61.402 63.158 0.00 0.00 0.00 4.85
118 119 3.044059 GCACGGAGATGTTGCTGGC 62.044 63.158 0.00 0.00 0.00 4.85
119 120 1.672030 CACGGAGATGTTGCTGGCA 60.672 57.895 0.00 0.00 0.00 4.92
120 121 1.073025 ACGGAGATGTTGCTGGCAA 59.927 52.632 3.72 3.72 0.00 4.52
163 164 3.418047 ACCTCCTTTTGGGTTTATGTCG 58.582 45.455 0.00 0.00 40.87 4.35
250 251 1.086696 CCCATGTAGCTCAACCAACG 58.913 55.000 0.00 0.00 0.00 4.10
298 299 0.468226 TCGACAGAAAACACCAGCCT 59.532 50.000 0.00 0.00 0.00 4.58
333 334 2.418628 ACGTCAACTCAACCAACACAAG 59.581 45.455 0.00 0.00 0.00 3.16
357 358 2.435938 TGCCGATCGGAACCTTGC 60.436 61.111 37.64 19.80 37.50 4.01
366 367 1.407258 TCGGAACCTTGCAAACCTTTG 59.593 47.619 0.00 0.00 41.03 2.77
414 415 1.946745 CTAGCCTAGCCAGCTTCAAC 58.053 55.000 0.00 0.00 41.83 3.18
453 455 4.803426 CTGTCTCTGCCCCGTCGC 62.803 72.222 0.00 0.00 0.00 5.19
475 477 5.337554 GCGTTGAGGGTAAATAAATGAACC 58.662 41.667 0.00 0.00 0.00 3.62
599 639 1.136500 TGCATTGCATTGTGTGTGTGT 59.864 42.857 7.38 0.00 31.71 3.72
600 640 1.523515 GCATTGCATTGTGTGTGTGTG 59.476 47.619 10.11 0.00 0.00 3.82
601 641 2.811855 CATTGCATTGTGTGTGTGTGT 58.188 42.857 0.30 0.00 0.00 3.72
602 642 2.274920 TTGCATTGTGTGTGTGTGTG 57.725 45.000 0.00 0.00 0.00 3.82
603 643 1.172175 TGCATTGTGTGTGTGTGTGT 58.828 45.000 0.00 0.00 0.00 3.72
604 644 1.135460 TGCATTGTGTGTGTGTGTGTG 60.135 47.619 0.00 0.00 0.00 3.82
605 645 1.135431 GCATTGTGTGTGTGTGTGTGT 60.135 47.619 0.00 0.00 0.00 3.72
606 646 2.517935 CATTGTGTGTGTGTGTGTGTG 58.482 47.619 0.00 0.00 0.00 3.82
607 647 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
608 648 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
609 649 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
610 650 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
611 651 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
612 652 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
624 664 2.169561 TGTGTGTGTGTGTGTGTATCCT 59.830 45.455 0.00 0.00 0.00 3.24
642 683 4.346734 TCCTAGCTTACTTGTAACGACG 57.653 45.455 0.00 0.00 0.00 5.12
644 685 3.127548 CCTAGCTTACTTGTAACGACGGA 59.872 47.826 0.00 0.00 0.00 4.69
655 721 5.138125 TGTAACGACGGACCTTTAATTCT 57.862 39.130 0.00 0.00 0.00 2.40
658 724 4.532314 ACGACGGACCTTTAATTCTTCT 57.468 40.909 0.00 0.00 0.00 2.85
730 806 6.088719 TGACGCATCAAAAGTTTCAAAAAC 57.911 33.333 0.00 0.00 0.00 2.43
791 4019 0.539669 TGGCGCCTCTAGCTATGCTA 60.540 55.000 29.70 0.00 40.44 3.49
832 4089 2.383527 CGGCGAGTCACAAGGAAGC 61.384 63.158 0.00 0.00 0.00 3.86
855 4125 3.832237 CTGGACAGCACGCACCCTT 62.832 63.158 0.00 0.00 0.00 3.95
866 4136 4.410400 CACCCTTCCCTCCACCGC 62.410 72.222 0.00 0.00 0.00 5.68
923 4194 1.531578 GTTGCTTCGGTTCAGAGTTCC 59.468 52.381 0.00 0.00 0.00 3.62
933 4219 3.471680 GTTCAGAGTTCCTTCAGCAGTT 58.528 45.455 0.00 0.00 0.00 3.16
934 4220 3.117491 TCAGAGTTCCTTCAGCAGTTG 57.883 47.619 0.00 0.00 0.00 3.16
946 4232 3.902112 CAGTTGCCCCACCCCACT 61.902 66.667 0.00 0.00 0.00 4.00
1020 4322 2.182030 GGCTCCTTCCTGTCGTCG 59.818 66.667 0.00 0.00 0.00 5.12
1232 7081 1.712977 GCTAATCTGCTGCGCTTGCT 61.713 55.000 22.08 8.52 40.12 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.142160 CGTGTATCCTCTGTGAAATCTCCA 60.142 45.833 0.00 0.00 0.00 3.86
1 2 4.363999 CGTGTATCCTCTGTGAAATCTCC 58.636 47.826 0.00 0.00 0.00 3.71
2 3 3.799420 GCGTGTATCCTCTGTGAAATCTC 59.201 47.826 0.00 0.00 0.00 2.75
3 4 3.449018 AGCGTGTATCCTCTGTGAAATCT 59.551 43.478 0.00 0.00 0.00 2.40
4 5 3.786635 AGCGTGTATCCTCTGTGAAATC 58.213 45.455 0.00 0.00 0.00 2.17
5 6 3.449018 AGAGCGTGTATCCTCTGTGAAAT 59.551 43.478 0.00 0.00 37.07 2.17
6 7 2.826128 AGAGCGTGTATCCTCTGTGAAA 59.174 45.455 0.00 0.00 37.07 2.69
7 8 2.164422 CAGAGCGTGTATCCTCTGTGAA 59.836 50.000 8.98 0.00 46.23 3.18
8 9 1.745653 CAGAGCGTGTATCCTCTGTGA 59.254 52.381 8.98 0.00 46.23 3.58
9 10 2.200792 CAGAGCGTGTATCCTCTGTG 57.799 55.000 8.98 0.00 46.23 3.66
12 13 0.684479 TGCCAGAGCGTGTATCCTCT 60.684 55.000 0.00 0.00 44.31 3.69
13 14 0.390860 ATGCCAGAGCGTGTATCCTC 59.609 55.000 0.00 0.00 44.31 3.71
14 15 0.390860 GATGCCAGAGCGTGTATCCT 59.609 55.000 0.00 0.00 44.31 3.24
15 16 0.390860 AGATGCCAGAGCGTGTATCC 59.609 55.000 0.00 0.00 44.31 2.59
16 17 1.495878 CAGATGCCAGAGCGTGTATC 58.504 55.000 0.00 0.00 44.31 2.24
17 18 0.105593 CCAGATGCCAGAGCGTGTAT 59.894 55.000 0.00 0.00 44.31 2.29
18 19 1.517361 CCAGATGCCAGAGCGTGTA 59.483 57.895 0.00 0.00 44.31 2.90
19 20 2.267006 CCAGATGCCAGAGCGTGT 59.733 61.111 0.00 0.00 44.31 4.49
20 21 2.513204 CCCAGATGCCAGAGCGTG 60.513 66.667 0.00 0.00 44.31 5.34
21 22 2.129555 AAACCCAGATGCCAGAGCGT 62.130 55.000 0.00 0.00 44.31 5.07
22 23 1.372087 GAAACCCAGATGCCAGAGCG 61.372 60.000 0.00 0.00 44.31 5.03
23 24 0.034670 AGAAACCCAGATGCCAGAGC 60.035 55.000 0.00 0.00 40.48 4.09
24 25 1.004044 ACAGAAACCCAGATGCCAGAG 59.996 52.381 0.00 0.00 0.00 3.35
25 26 1.067295 ACAGAAACCCAGATGCCAGA 58.933 50.000 0.00 0.00 0.00 3.86
26 27 2.359900 GTACAGAAACCCAGATGCCAG 58.640 52.381 0.00 0.00 0.00 4.85
27 28 1.004277 GGTACAGAAACCCAGATGCCA 59.996 52.381 0.00 0.00 33.02 4.92
28 29 1.751437 GGTACAGAAACCCAGATGCC 58.249 55.000 0.00 0.00 33.02 4.40
29 30 1.369625 CGGTACAGAAACCCAGATGC 58.630 55.000 0.00 0.00 36.03 3.91
30 31 1.406887 CCCGGTACAGAAACCCAGATG 60.407 57.143 0.00 0.00 36.03 2.90
31 32 0.909623 CCCGGTACAGAAACCCAGAT 59.090 55.000 0.00 0.00 36.03 2.90
32 33 1.196104 CCCCGGTACAGAAACCCAGA 61.196 60.000 0.00 0.00 36.03 3.86
33 34 1.196104 TCCCCGGTACAGAAACCCAG 61.196 60.000 0.00 0.00 36.03 4.45
34 35 1.152074 TCCCCGGTACAGAAACCCA 60.152 57.895 0.00 0.00 36.03 4.51
35 36 0.906282 TCTCCCCGGTACAGAAACCC 60.906 60.000 0.00 0.00 36.03 4.11
36 37 0.535797 CTCTCCCCGGTACAGAAACC 59.464 60.000 0.00 0.00 36.08 3.27
37 38 1.067071 CACTCTCCCCGGTACAGAAAC 60.067 57.143 0.00 0.00 0.00 2.78
38 39 1.203087 TCACTCTCCCCGGTACAGAAA 60.203 52.381 0.00 0.00 0.00 2.52
39 40 0.406750 TCACTCTCCCCGGTACAGAA 59.593 55.000 0.00 0.00 0.00 3.02
40 41 0.034380 CTCACTCTCCCCGGTACAGA 60.034 60.000 0.00 0.00 0.00 3.41
41 42 0.323542 ACTCACTCTCCCCGGTACAG 60.324 60.000 0.00 0.00 0.00 2.74
42 43 0.611062 CACTCACTCTCCCCGGTACA 60.611 60.000 0.00 0.00 0.00 2.90
43 44 0.611340 ACACTCACTCTCCCCGGTAC 60.611 60.000 0.00 0.00 0.00 3.34
44 45 0.611062 CACACTCACTCTCCCCGGTA 60.611 60.000 0.00 0.00 0.00 4.02
45 46 1.908793 CACACTCACTCTCCCCGGT 60.909 63.158 0.00 0.00 0.00 5.28
46 47 1.185618 TTCACACTCACTCTCCCCGG 61.186 60.000 0.00 0.00 0.00 5.73
47 48 0.244994 CTTCACACTCACTCTCCCCG 59.755 60.000 0.00 0.00 0.00 5.73
48 49 0.036858 GCTTCACACTCACTCTCCCC 60.037 60.000 0.00 0.00 0.00 4.81
49 50 0.036858 GGCTTCACACTCACTCTCCC 60.037 60.000 0.00 0.00 0.00 4.30
50 51 0.681733 TGGCTTCACACTCACTCTCC 59.318 55.000 0.00 0.00 0.00 3.71
51 52 2.758736 ATGGCTTCACACTCACTCTC 57.241 50.000 0.00 0.00 0.00 3.20
52 53 3.498774 AAATGGCTTCACACTCACTCT 57.501 42.857 0.00 0.00 0.00 3.24
53 54 4.997395 TCTAAAATGGCTTCACACTCACTC 59.003 41.667 0.00 0.00 0.00 3.51
54 55 4.973168 TCTAAAATGGCTTCACACTCACT 58.027 39.130 0.00 0.00 0.00 3.41
55 56 5.689383 TTCTAAAATGGCTTCACACTCAC 57.311 39.130 0.00 0.00 0.00 3.51
56 57 5.277779 CGTTTCTAAAATGGCTTCACACTCA 60.278 40.000 0.00 0.00 0.00 3.41
57 58 5.147162 CGTTTCTAAAATGGCTTCACACTC 58.853 41.667 0.00 0.00 0.00 3.51
58 59 4.023193 CCGTTTCTAAAATGGCTTCACACT 60.023 41.667 0.00 0.00 0.00 3.55
59 60 4.226761 CCGTTTCTAAAATGGCTTCACAC 58.773 43.478 0.00 0.00 0.00 3.82
60 61 3.254657 CCCGTTTCTAAAATGGCTTCACA 59.745 43.478 5.33 0.00 0.00 3.58
61 62 3.504520 TCCCGTTTCTAAAATGGCTTCAC 59.495 43.478 5.33 0.00 0.00 3.18
62 63 3.756434 CTCCCGTTTCTAAAATGGCTTCA 59.244 43.478 5.33 0.00 0.00 3.02
63 64 4.007659 TCTCCCGTTTCTAAAATGGCTTC 58.992 43.478 5.33 0.00 0.00 3.86
64 65 4.010349 CTCTCCCGTTTCTAAAATGGCTT 58.990 43.478 5.33 0.00 0.00 4.35
65 66 3.263425 TCTCTCCCGTTTCTAAAATGGCT 59.737 43.478 5.33 0.00 0.00 4.75
66 67 3.606687 TCTCTCCCGTTTCTAAAATGGC 58.393 45.455 5.33 0.00 0.00 4.40
67 68 5.246307 ACTTCTCTCCCGTTTCTAAAATGG 58.754 41.667 4.06 4.06 0.00 3.16
68 69 6.803154 AACTTCTCTCCCGTTTCTAAAATG 57.197 37.500 0.00 0.00 0.00 2.32
69 70 6.206829 CCAAACTTCTCTCCCGTTTCTAAAAT 59.793 38.462 0.00 0.00 0.00 1.82
70 71 5.529800 CCAAACTTCTCTCCCGTTTCTAAAA 59.470 40.000 0.00 0.00 0.00 1.52
71 72 5.061179 CCAAACTTCTCTCCCGTTTCTAAA 58.939 41.667 0.00 0.00 0.00 1.85
72 73 4.102054 ACCAAACTTCTCTCCCGTTTCTAA 59.898 41.667 0.00 0.00 0.00 2.10
73 74 3.644738 ACCAAACTTCTCTCCCGTTTCTA 59.355 43.478 0.00 0.00 0.00 2.10
74 75 2.438392 ACCAAACTTCTCTCCCGTTTCT 59.562 45.455 0.00 0.00 0.00 2.52
75 76 2.806818 GACCAAACTTCTCTCCCGTTTC 59.193 50.000 0.00 0.00 0.00 2.78
76 77 2.171870 TGACCAAACTTCTCTCCCGTTT 59.828 45.455 0.00 0.00 0.00 3.60
77 78 1.766496 TGACCAAACTTCTCTCCCGTT 59.234 47.619 0.00 0.00 0.00 4.44
78 79 1.070289 GTGACCAAACTTCTCTCCCGT 59.930 52.381 0.00 0.00 0.00 5.28
79 80 1.797025 GTGACCAAACTTCTCTCCCG 58.203 55.000 0.00 0.00 0.00 5.14
80 81 1.608283 CCGTGACCAAACTTCTCTCCC 60.608 57.143 0.00 0.00 0.00 4.30
81 82 1.797025 CCGTGACCAAACTTCTCTCC 58.203 55.000 0.00 0.00 0.00 3.71
82 83 1.149148 GCCGTGACCAAACTTCTCTC 58.851 55.000 0.00 0.00 0.00 3.20
83 84 0.468226 TGCCGTGACCAAACTTCTCT 59.532 50.000 0.00 0.00 0.00 3.10
84 85 0.586802 GTGCCGTGACCAAACTTCTC 59.413 55.000 0.00 0.00 0.00 2.87
85 86 1.157870 CGTGCCGTGACCAAACTTCT 61.158 55.000 0.00 0.00 0.00 2.85
86 87 1.278637 CGTGCCGTGACCAAACTTC 59.721 57.895 0.00 0.00 0.00 3.01
87 88 2.184167 CCGTGCCGTGACCAAACTT 61.184 57.895 0.00 0.00 0.00 2.66
88 89 2.590575 CCGTGCCGTGACCAAACT 60.591 61.111 0.00 0.00 0.00 2.66
89 90 2.589442 TCCGTGCCGTGACCAAAC 60.589 61.111 0.00 0.00 0.00 2.93
90 91 2.107041 ATCTCCGTGCCGTGACCAAA 62.107 55.000 0.00 0.00 0.00 3.28
91 92 2.579657 ATCTCCGTGCCGTGACCAA 61.580 57.895 0.00 0.00 0.00 3.67
92 93 2.994995 ATCTCCGTGCCGTGACCA 60.995 61.111 0.00 0.00 0.00 4.02
93 94 2.509336 CATCTCCGTGCCGTGACC 60.509 66.667 0.00 0.00 0.00 4.02
94 95 1.374252 AACATCTCCGTGCCGTGAC 60.374 57.895 0.00 0.00 0.00 3.67
95 96 1.374125 CAACATCTCCGTGCCGTGA 60.374 57.895 0.00 0.00 0.00 4.35
96 97 3.027170 GCAACATCTCCGTGCCGTG 62.027 63.158 0.00 0.00 0.00 4.94
97 98 2.742372 GCAACATCTCCGTGCCGT 60.742 61.111 0.00 0.00 0.00 5.68
98 99 2.434884 AGCAACATCTCCGTGCCG 60.435 61.111 0.00 0.00 0.00 5.69
99 100 2.401766 CCAGCAACATCTCCGTGCC 61.402 63.158 0.00 0.00 0.00 5.01
100 101 3.044059 GCCAGCAACATCTCCGTGC 62.044 63.158 0.00 0.00 0.00 5.34
101 102 1.236616 TTGCCAGCAACATCTCCGTG 61.237 55.000 0.00 0.00 0.00 4.94
102 103 1.073025 TTGCCAGCAACATCTCCGT 59.927 52.632 0.00 0.00 0.00 4.69
103 104 3.985877 TTGCCAGCAACATCTCCG 58.014 55.556 0.00 0.00 0.00 4.63
111 112 1.686052 CCCTACAAAAGTTGCCAGCAA 59.314 47.619 0.00 0.00 0.00 3.91
112 113 1.327303 CCCTACAAAAGTTGCCAGCA 58.673 50.000 0.00 0.00 0.00 4.41
113 114 0.603065 CCCCTACAAAAGTTGCCAGC 59.397 55.000 0.00 0.00 0.00 4.85
114 115 1.613437 CACCCCTACAAAAGTTGCCAG 59.387 52.381 0.00 0.00 0.00 4.85
115 116 1.698506 CACCCCTACAAAAGTTGCCA 58.301 50.000 0.00 0.00 0.00 4.92
116 117 0.317160 GCACCCCTACAAAAGTTGCC 59.683 55.000 0.00 0.00 0.00 4.52
117 118 1.328279 AGCACCCCTACAAAAGTTGC 58.672 50.000 0.00 0.00 0.00 4.17
118 119 3.636764 AGAAAGCACCCCTACAAAAGTTG 59.363 43.478 0.00 0.00 0.00 3.16
119 120 3.910989 AGAAAGCACCCCTACAAAAGTT 58.089 40.909 0.00 0.00 0.00 2.66
120 121 3.595190 AGAAAGCACCCCTACAAAAGT 57.405 42.857 0.00 0.00 0.00 2.66
121 122 4.217767 GGTTAGAAAGCACCCCTACAAAAG 59.782 45.833 0.00 0.00 0.00 2.27
163 164 3.665675 AAGTGCACCGATCCCGCTC 62.666 63.158 14.63 0.00 0.00 5.03
179 180 0.594796 GCAAGTGCCAACGGAACAAG 60.595 55.000 0.00 0.00 32.48 3.16
250 251 4.299796 ATGTGGTGGGGTGGGTGC 62.300 66.667 0.00 0.00 0.00 5.01
306 307 3.026630 TGGTTGAGTTGACGTCTGATC 57.973 47.619 17.92 11.70 0.00 2.92
357 358 1.135689 CGATTCTCCGCCAAAGGTTTG 60.136 52.381 0.00 0.00 37.90 2.93
366 367 0.672401 TTGTCAACCGATTCTCCGCC 60.672 55.000 0.00 0.00 0.00 6.13
414 415 6.372659 ACAGATAATGCCACTACTTGTTCAAG 59.627 38.462 10.50 10.50 0.00 3.02
453 455 5.886992 GGGTTCATTTATTTACCCTCAACG 58.113 41.667 0.00 0.00 45.52 4.10
475 477 9.022884 TCTCATCAAGAATAGATACTGAGATGG 57.977 37.037 0.00 0.00 33.92 3.51
599 639 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
600 640 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
601 641 2.457366 TACACACACACACACACACA 57.543 45.000 0.00 0.00 0.00 3.72
602 642 2.286833 GGATACACACACACACACACAC 59.713 50.000 0.00 0.00 0.00 3.82
603 643 2.169561 AGGATACACACACACACACACA 59.830 45.455 0.00 0.00 41.41 3.72
604 644 2.833794 AGGATACACACACACACACAC 58.166 47.619 0.00 0.00 41.41 3.82
605 645 3.554129 GCTAGGATACACACACACACACA 60.554 47.826 0.00 0.00 41.41 3.72
606 646 2.993899 GCTAGGATACACACACACACAC 59.006 50.000 0.00 0.00 41.41 3.82
607 647 2.897326 AGCTAGGATACACACACACACA 59.103 45.455 0.00 0.00 41.41 3.72
608 648 3.594603 AGCTAGGATACACACACACAC 57.405 47.619 0.00 0.00 41.41 3.82
609 649 4.770531 AGTAAGCTAGGATACACACACACA 59.229 41.667 0.00 0.00 41.41 3.72
610 650 5.326200 AGTAAGCTAGGATACACACACAC 57.674 43.478 0.00 0.00 41.41 3.82
611 651 5.245301 ACAAGTAAGCTAGGATACACACACA 59.755 40.000 0.00 0.00 41.41 3.72
612 652 5.721232 ACAAGTAAGCTAGGATACACACAC 58.279 41.667 0.00 0.00 41.41 3.82
624 664 3.119849 GGTCCGTCGTTACAAGTAAGCTA 60.120 47.826 0.00 0.00 0.00 3.32
655 721 3.500982 GCAACGCAATGCATTCTTAGAA 58.499 40.909 9.53 0.00 45.70 2.10
672 738 2.690778 GCCTCACGGGTGATGCAAC 61.691 63.158 19.69 0.00 46.11 4.17
791 4019 0.967887 TGCCGACTTCTCTGCTAGCT 60.968 55.000 17.23 0.00 0.00 3.32
792 4020 0.527385 CTGCCGACTTCTCTGCTAGC 60.527 60.000 8.10 8.10 0.00 3.42
793 4021 0.814457 ACTGCCGACTTCTCTGCTAG 59.186 55.000 0.00 0.00 0.00 3.42
794 4022 0.528017 CACTGCCGACTTCTCTGCTA 59.472 55.000 0.00 0.00 0.00 3.49
795 4023 1.291588 CACTGCCGACTTCTCTGCT 59.708 57.895 0.00 0.00 0.00 4.24
796 4024 2.386660 GCACTGCCGACTTCTCTGC 61.387 63.158 0.00 0.00 0.00 4.26
797 4025 2.091112 CGCACTGCCGACTTCTCTG 61.091 63.158 0.00 0.00 0.00 3.35
798 4026 2.259818 CGCACTGCCGACTTCTCT 59.740 61.111 0.00 0.00 0.00 3.10
799 4027 2.811317 CCGCACTGCCGACTTCTC 60.811 66.667 0.00 0.00 0.00 2.87
866 4136 1.537202 GGAAGCAATTATAGCTGCGGG 59.463 52.381 0.00 0.00 42.53 6.13
902 4172 1.192534 GAACTCTGAACCGAAGCAACG 59.807 52.381 0.00 0.00 0.00 4.10
923 4194 2.270986 GGTGGGGCAACTGCTGAAG 61.271 63.158 1.06 0.00 41.70 3.02
994 4286 2.250924 CAGGAAGGAGCCCATGTTTTT 58.749 47.619 0.00 0.00 0.00 1.94
995 4287 1.147817 ACAGGAAGGAGCCCATGTTTT 59.852 47.619 0.00 0.00 0.00 2.43
1020 4322 3.658422 GGGGGAGGGGTCCACAAC 61.658 72.222 0.00 0.00 34.04 3.32
1232 7081 1.756561 TCGATCACCATCTGCCGGA 60.757 57.895 5.05 0.00 0.00 5.14
3523 10921 5.221441 GGGAAAAGTCAACAGCTACCAATTT 60.221 40.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.