Multiple sequence alignment - TraesCS2D01G303900

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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 TraesCS2D01G303900 chr2D 100.000 2882 0 0 1 2882 388482997 388480116 0.000000e+00 5323.0
1 TraesCS2D01G303900 chr2B 93.061 2205 94 29 95 2278 460552548 460550382 0.000000e+00 3169.0
2 TraesCS2D01G303900 chr2B 91.333 450 10 4 2434 2882 460550004 460549583 3.200000e-164 588.0
3 TraesCS2D01G303900 chr2B 98.000 50 1 0 2354 2403 460550054 460550005 1.420000e-13 87.9
4 TraesCS2D01G303900 chr2A 94.959 1706 41 20 658 2331 524953647 524951955 0.000000e+00 2632.0
5 TraesCS2D01G303900 chr2A 93.032 531 21 4 2354 2882 524951968 524951452 0.000000e+00 761.0
6 TraesCS2D01G303900 chr2A 96.328 463 13 3 97 558 524954256 524953797 0.000000e+00 758.0
7 TraesCS2D01G303900 chr3D 80.142 141 25 1 1068 1205 305622296 305622436 5.080000e-18 102.0
8 TraesCS2D01G303900 chr3A 80.142 141 25 1 1068 1205 423671786 423671926 5.080000e-18 102.0
9 TraesCS2D01G303900 chr3B 79.433 141 26 1 1068 1205 416135829 416135689 2.360000e-16 97.1
10 TraesCS2D01G303900 chr6B 78.378 148 19 6 1069 1205 539195669 539195524 1.840000e-12 84.2
11 TraesCS2D01G303900 chr6A 78.378 148 19 6 1069 1205 499955051 499955196 1.840000e-12 84.2
12 TraesCS2D01G303900 chr1D 97.500 40 1 0 1162 1201 74929951 74929912 5.150000e-08 69.4
13 TraesCS2D01G303900 chr1A 97.500 40 1 0 1162 1201 75256107 75256068 5.150000e-08 69.4


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 TraesCS2D01G303900 chr2D 388480116 388482997 2881 True 5323.000000 5323 100.000000 1 2882 1 chr2D.!!$R1 2881
1 TraesCS2D01G303900 chr2B 460549583 460552548 2965 True 1281.633333 3169 94.131333 95 2882 3 chr2B.!!$R1 2787
2 TraesCS2D01G303900 chr2A 524951452 524954256 2804 True 1383.666667 2632 94.773000 97 2882 3 chr2A.!!$R1 2785

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
50 51 0.235665 ATCAACGCGTGTGAGCAAAG 59.764 50.0 14.98 0.0 36.85 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 2078 0.820891 ACCTGCTTGCTCACAACTGG 60.821 55.0 0.0 0.0 34.8 4.0 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
24 25 5.957842 AGGTTTCGTGCAAAATAGAATCA 57.042 34.783 0.00 0.00 0.00 2.57
25 26 6.325919 AGGTTTCGTGCAAAATAGAATCAA 57.674 33.333 0.00 0.00 0.00 2.57
26 27 6.149633 AGGTTTCGTGCAAAATAGAATCAAC 58.850 36.000 0.00 0.00 0.00 3.18
27 28 5.918011 GGTTTCGTGCAAAATAGAATCAACA 59.082 36.000 0.00 0.00 0.00 3.33
28 29 6.586082 GGTTTCGTGCAAAATAGAATCAACAT 59.414 34.615 0.00 0.00 0.00 2.71
29 30 7.410728 GGTTTCGTGCAAAATAGAATCAACATG 60.411 37.037 0.00 0.00 0.00 3.21
30 31 6.252967 TCGTGCAAAATAGAATCAACATGT 57.747 33.333 0.00 0.00 0.00 3.21
31 32 7.371126 TCGTGCAAAATAGAATCAACATGTA 57.629 32.000 0.00 0.00 0.00 2.29
32 33 7.984391 TCGTGCAAAATAGAATCAACATGTAT 58.016 30.769 0.00 0.00 0.00 2.29
33 34 8.122330 TCGTGCAAAATAGAATCAACATGTATC 58.878 33.333 0.00 0.00 0.00 2.24
34 35 7.909641 CGTGCAAAATAGAATCAACATGTATCA 59.090 33.333 0.00 0.00 0.00 2.15
35 36 9.571810 GTGCAAAATAGAATCAACATGTATCAA 57.428 29.630 0.00 0.00 0.00 2.57
36 37 9.571810 TGCAAAATAGAATCAACATGTATCAAC 57.428 29.630 0.00 0.00 0.00 3.18
37 38 8.736742 GCAAAATAGAATCAACATGTATCAACG 58.263 33.333 0.00 0.00 0.00 4.10
38 39 8.736742 CAAAATAGAATCAACATGTATCAACGC 58.263 33.333 0.00 0.00 0.00 4.84
39 40 4.520743 AGAATCAACATGTATCAACGCG 57.479 40.909 3.53 3.53 0.00 6.01
40 41 3.932710 AGAATCAACATGTATCAACGCGT 59.067 39.130 5.58 5.58 0.00 6.01
41 42 3.656651 ATCAACATGTATCAACGCGTG 57.343 42.857 14.98 7.52 0.00 5.34
42 43 2.409012 TCAACATGTATCAACGCGTGT 58.591 42.857 14.98 4.69 0.00 4.49
43 44 2.156697 TCAACATGTATCAACGCGTGTG 59.843 45.455 14.98 13.75 0.00 3.82
44 45 2.073117 ACATGTATCAACGCGTGTGA 57.927 45.000 14.98 18.81 0.00 3.58
45 46 1.992667 ACATGTATCAACGCGTGTGAG 59.007 47.619 14.98 8.95 0.00 3.51
46 47 0.999406 ATGTATCAACGCGTGTGAGC 59.001 50.000 14.98 14.99 0.00 4.26
47 48 0.319125 TGTATCAACGCGTGTGAGCA 60.319 50.000 14.98 17.10 36.85 4.26
48 49 0.787787 GTATCAACGCGTGTGAGCAA 59.212 50.000 14.98 6.22 36.85 3.91
49 50 1.193650 GTATCAACGCGTGTGAGCAAA 59.806 47.619 14.98 3.90 36.85 3.68
50 51 0.235665 ATCAACGCGTGTGAGCAAAG 59.764 50.000 14.98 0.00 36.85 2.77
51 52 1.087202 TCAACGCGTGTGAGCAAAGT 61.087 50.000 14.98 0.00 36.85 2.66
52 53 0.925267 CAACGCGTGTGAGCAAAGTG 60.925 55.000 14.98 0.00 36.85 3.16
53 54 1.366111 AACGCGTGTGAGCAAAGTGT 61.366 50.000 14.98 0.00 36.85 3.55
54 55 0.528901 ACGCGTGTGAGCAAAGTGTA 60.529 50.000 12.93 0.00 36.85 2.90
55 56 0.579630 CGCGTGTGAGCAAAGTGTAA 59.420 50.000 0.00 0.00 36.85 2.41
56 57 1.004398 CGCGTGTGAGCAAAGTGTAAA 60.004 47.619 0.00 0.00 36.85 2.01
57 58 2.372350 GCGTGTGAGCAAAGTGTAAAC 58.628 47.619 0.00 0.00 37.05 2.01
58 59 2.223157 GCGTGTGAGCAAAGTGTAAACA 60.223 45.455 0.00 0.00 37.05 2.83
59 60 3.548014 GCGTGTGAGCAAAGTGTAAACAT 60.548 43.478 0.00 0.00 37.05 2.71
60 61 3.968096 CGTGTGAGCAAAGTGTAAACATG 59.032 43.478 0.00 0.00 0.00 3.21
61 62 3.730715 GTGTGAGCAAAGTGTAAACATGC 59.269 43.478 5.86 5.86 37.28 4.06
62 63 3.379688 TGTGAGCAAAGTGTAAACATGCA 59.620 39.130 14.18 0.00 39.42 3.96
63 64 4.142293 TGTGAGCAAAGTGTAAACATGCAA 60.142 37.500 14.18 2.20 39.42 4.08
64 65 4.207019 GTGAGCAAAGTGTAAACATGCAAC 59.793 41.667 14.18 9.17 39.42 4.17
65 66 4.142293 TGAGCAAAGTGTAAACATGCAACA 60.142 37.500 14.18 11.04 39.42 3.33
66 67 4.947645 AGCAAAGTGTAAACATGCAACAT 58.052 34.783 14.18 0.00 39.42 2.71
67 68 4.746115 AGCAAAGTGTAAACATGCAACATG 59.254 37.500 14.18 6.03 39.42 3.21
68 69 4.507388 GCAAAGTGTAAACATGCAACATGT 59.493 37.500 7.38 7.38 37.00 3.21
69 70 5.556758 GCAAAGTGTAAACATGCAACATGTG 60.557 40.000 13.55 0.00 37.00 3.21
70 71 5.512753 AAGTGTAAACATGCAACATGTGA 57.487 34.783 13.55 3.18 31.80 3.58
71 72 5.112220 AGTGTAAACATGCAACATGTGAG 57.888 39.130 13.55 0.00 31.80 3.51
72 73 3.670055 GTGTAAACATGCAACATGTGAGC 59.330 43.478 13.55 14.72 31.80 4.26
73 74 2.054687 AAACATGCAACATGTGAGCG 57.945 45.000 13.55 7.63 31.80 5.03
74 75 0.953727 AACATGCAACATGTGAGCGT 59.046 45.000 13.55 13.78 31.80 5.07
75 76 0.953727 ACATGCAACATGTGAGCGTT 59.046 45.000 12.18 4.74 0.00 4.84
76 77 2.150390 ACATGCAACATGTGAGCGTTA 58.850 42.857 12.18 1.10 0.00 3.18
77 78 2.749076 ACATGCAACATGTGAGCGTTAT 59.251 40.909 12.18 4.99 0.00 1.89
78 79 3.191162 ACATGCAACATGTGAGCGTTATT 59.809 39.130 12.18 1.93 0.00 1.40
79 80 4.394610 ACATGCAACATGTGAGCGTTATTA 59.605 37.500 12.18 0.00 0.00 0.98
80 81 5.066375 ACATGCAACATGTGAGCGTTATTAT 59.934 36.000 12.18 1.95 0.00 1.28
81 82 5.559427 TGCAACATGTGAGCGTTATTATT 57.441 34.783 16.05 0.00 0.00 1.40
82 83 5.948588 TGCAACATGTGAGCGTTATTATTT 58.051 33.333 16.05 0.00 0.00 1.40
83 84 5.799435 TGCAACATGTGAGCGTTATTATTTG 59.201 36.000 16.05 0.49 0.00 2.32
84 85 5.229887 GCAACATGTGAGCGTTATTATTTGG 59.770 40.000 0.00 0.00 0.00 3.28
85 86 5.499139 ACATGTGAGCGTTATTATTTGGG 57.501 39.130 0.00 0.00 0.00 4.12
86 87 4.947388 ACATGTGAGCGTTATTATTTGGGT 59.053 37.500 0.00 0.00 0.00 4.51
87 88 6.116806 ACATGTGAGCGTTATTATTTGGGTA 58.883 36.000 0.00 0.00 0.00 3.69
88 89 6.600032 ACATGTGAGCGTTATTATTTGGGTAA 59.400 34.615 0.00 0.00 0.00 2.85
89 90 7.121463 ACATGTGAGCGTTATTATTTGGGTAAA 59.879 33.333 0.00 0.00 0.00 2.01
90 91 7.450124 TGTGAGCGTTATTATTTGGGTAAAA 57.550 32.000 0.00 0.00 0.00 1.52
91 92 7.883217 TGTGAGCGTTATTATTTGGGTAAAAA 58.117 30.769 0.00 0.00 0.00 1.94
184 185 9.877137 CGTGTAATTAAATCAGCTGCAAATATA 57.123 29.630 9.47 0.00 0.00 0.86
199 201 8.697067 GCTGCAAATATAATGATCAATTGACAC 58.303 33.333 11.07 8.78 0.00 3.67
206 208 5.814764 AATGATCAATTGACACAGAGAGC 57.185 39.130 11.07 0.00 0.00 4.09
207 209 4.276058 TGATCAATTGACACAGAGAGCA 57.724 40.909 11.07 0.00 0.00 4.26
210 212 3.807553 TCAATTGACACAGAGAGCAACA 58.192 40.909 3.38 0.00 0.00 3.33
230 232 2.939103 CAAAGATTGGAGCTAGAACCCG 59.061 50.000 0.00 0.00 0.00 5.28
231 233 1.123928 AGATTGGAGCTAGAACCCGG 58.876 55.000 0.00 0.00 0.00 5.73
350 352 2.721859 CGTCCGATCGCATCAGGA 59.278 61.111 10.32 0.00 32.36 3.86
590 592 1.466851 ATCTCGCCGCCTCATCATCA 61.467 55.000 0.00 0.00 0.00 3.07
615 687 3.377485 ACAAAGCAGCATAGCAGATCAAG 59.623 43.478 0.00 0.00 36.85 3.02
618 690 3.666274 AGCAGCATAGCAGATCAAGATC 58.334 45.455 1.81 1.81 38.09 2.75
635 707 8.918202 ATCAAGATCAGTTTTACTGTTGGTAA 57.082 30.769 6.71 0.00 46.03 2.85
747 846 3.234353 TCTGTGAGCATAGTATGAGGGG 58.766 50.000 14.52 0.00 0.00 4.79
900 1008 3.984508 CGATACGCCTTCCTTCTTCTA 57.015 47.619 0.00 0.00 0.00 2.10
946 1058 3.311110 GTGGGTGGGTGAGCGAGA 61.311 66.667 0.00 0.00 0.00 4.04
1916 2037 5.469421 GCTAGCTAATGAGTACCGAGTTCTA 59.531 44.000 7.70 0.00 0.00 2.10
1917 2038 6.017275 GCTAGCTAATGAGTACCGAGTTCTAA 60.017 42.308 7.70 0.00 0.00 2.10
1957 2078 9.787532 TTTAGATTTAATTAATGCACTGTCAGC 57.212 29.630 0.00 0.00 0.00 4.26
1988 2109 1.263217 CAAGCAGGTGGTGTAAACGAC 59.737 52.381 0.00 0.00 0.00 4.34
2100 2221 2.434185 CTAGGCGCCGCTGTTTGA 60.434 61.111 23.20 0.00 0.00 2.69
2143 2264 7.779073 TGTCTTGCTTTAATCCTAGTACTACC 58.221 38.462 0.00 0.00 0.00 3.18
2192 2322 3.549471 GCAGTGAGTGACTAATCATCGTG 59.451 47.826 0.00 0.00 37.14 4.35
2196 2326 2.101582 GAGTGACTAATCATCGTGCCCT 59.898 50.000 0.00 0.00 37.14 5.19
2197 2327 2.159043 AGTGACTAATCATCGTGCCCTG 60.159 50.000 0.00 0.00 37.14 4.45
2198 2328 1.831106 TGACTAATCATCGTGCCCTGT 59.169 47.619 0.00 0.00 0.00 4.00
2199 2329 2.159099 TGACTAATCATCGTGCCCTGTC 60.159 50.000 0.00 0.00 0.00 3.51
2200 2330 1.831106 ACTAATCATCGTGCCCTGTCA 59.169 47.619 0.00 0.00 0.00 3.58
2201 2331 2.236146 ACTAATCATCGTGCCCTGTCAA 59.764 45.455 0.00 0.00 0.00 3.18
2202 2332 1.742761 AATCATCGTGCCCTGTCAAG 58.257 50.000 0.00 0.00 0.00 3.02
2250 2381 0.463295 CCCTGGCAGTAGAGTGCATG 60.463 60.000 14.43 3.34 45.93 4.06
2328 2748 0.249531 TCGCACTCGTGTGGCTTTAA 60.250 50.000 18.41 0.00 43.97 1.52
2329 2749 0.163788 CGCACTCGTGTGGCTTTAAG 59.836 55.000 18.41 0.00 43.97 1.85
2330 2750 0.110192 GCACTCGTGTGGCTTTAAGC 60.110 55.000 18.41 8.66 43.97 3.09
2331 2751 1.512926 CACTCGTGTGGCTTTAAGCT 58.487 50.000 16.89 0.00 41.99 3.74
2332 2752 1.461127 CACTCGTGTGGCTTTAAGCTC 59.539 52.381 16.89 10.64 41.99 4.09
2333 2753 1.344763 ACTCGTGTGGCTTTAAGCTCT 59.655 47.619 16.89 0.00 41.99 4.09
2334 2754 2.224305 ACTCGTGTGGCTTTAAGCTCTT 60.224 45.455 16.89 0.00 41.99 2.85
2335 2755 2.808543 CTCGTGTGGCTTTAAGCTCTTT 59.191 45.455 16.89 0.00 41.99 2.52
2336 2756 3.211045 TCGTGTGGCTTTAAGCTCTTTT 58.789 40.909 16.89 0.00 41.99 2.27
2337 2757 3.630312 TCGTGTGGCTTTAAGCTCTTTTT 59.370 39.130 16.89 0.00 41.99 1.94
2360 2780 3.902881 TTTTTGAATGTTGGTGTGGCT 57.097 38.095 0.00 0.00 0.00 4.75
2361 2781 3.902881 TTTTGAATGTTGGTGTGGCTT 57.097 38.095 0.00 0.00 0.00 4.35
2362 2782 3.902881 TTTGAATGTTGGTGTGGCTTT 57.097 38.095 0.00 0.00 0.00 3.51
2363 2783 3.451141 TTGAATGTTGGTGTGGCTTTC 57.549 42.857 0.00 0.00 0.00 2.62
2413 2833 2.588314 GCTCTCCAGCCAGCATCG 60.588 66.667 0.00 0.00 40.14 3.84
2414 2834 2.588314 CTCTCCAGCCAGCATCGC 60.588 66.667 0.00 0.00 0.00 4.58
2415 2835 4.166888 TCTCCAGCCAGCATCGCC 62.167 66.667 0.00 0.00 0.00 5.54
2564 2985 2.887568 CGGCTTGGCGCTCTACTG 60.888 66.667 7.64 0.00 39.13 2.74
2565 2986 3.198489 GGCTTGGCGCTCTACTGC 61.198 66.667 7.64 3.59 39.13 4.40
2566 2987 2.125350 GCTTGGCGCTCTACTGCT 60.125 61.111 7.64 0.00 35.14 4.24
2642 3065 0.535335 GTCTCATCGGCTTGGGTGTA 59.465 55.000 0.00 0.00 0.00 2.90
2755 3178 2.272146 GGGATTTGGCCTCTCGCA 59.728 61.111 3.32 0.00 40.31 5.10
2758 3181 1.078143 GATTTGGCCTCTCGCACCT 60.078 57.895 3.32 0.00 40.31 4.00
2789 3212 3.490526 TGTTGTCGCCTAAAACTTCGTAC 59.509 43.478 0.00 0.00 0.00 3.67
2835 3258 0.393820 CCAGCAATGCCCTGTGTTTT 59.606 50.000 0.00 0.00 0.00 2.43
2840 3263 1.411977 CAATGCCCTGTGTTTTGGTGA 59.588 47.619 0.00 0.00 0.00 4.02
2850 3273 2.104170 TGTTTTGGTGACAGGAAACCC 58.896 47.619 5.62 0.00 44.54 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.441890 TGATTCTATTTTGCACGAAACCTAA 57.558 32.000 0.00 0.00 0.00 2.69
1 2 7.041030 TGTTGATTCTATTTTGCACGAAACCTA 60.041 33.333 0.00 0.00 0.00 3.08
2 3 5.957842 TGATTCTATTTTGCACGAAACCT 57.042 34.783 0.00 0.00 0.00 3.50
3 4 5.918011 TGTTGATTCTATTTTGCACGAAACC 59.082 36.000 0.00 0.00 0.00 3.27
4 5 6.984740 TGTTGATTCTATTTTGCACGAAAC 57.015 33.333 0.00 0.00 0.00 2.78
5 6 7.144661 ACATGTTGATTCTATTTTGCACGAAA 58.855 30.769 0.00 0.00 0.00 3.46
6 7 6.676950 ACATGTTGATTCTATTTTGCACGAA 58.323 32.000 0.00 0.00 0.00 3.85
7 8 6.252967 ACATGTTGATTCTATTTTGCACGA 57.747 33.333 0.00 0.00 0.00 4.35
8 9 7.909641 TGATACATGTTGATTCTATTTTGCACG 59.090 33.333 2.30 0.00 0.00 5.34
9 10 9.571810 TTGATACATGTTGATTCTATTTTGCAC 57.428 29.630 2.30 0.00 0.00 4.57
10 11 9.571810 GTTGATACATGTTGATTCTATTTTGCA 57.428 29.630 2.30 0.00 0.00 4.08
11 12 8.736742 CGTTGATACATGTTGATTCTATTTTGC 58.263 33.333 2.30 0.00 0.00 3.68
12 13 8.736742 GCGTTGATACATGTTGATTCTATTTTG 58.263 33.333 2.30 0.00 0.00 2.44
13 14 7.639850 CGCGTTGATACATGTTGATTCTATTTT 59.360 33.333 2.30 0.00 0.00 1.82
14 15 7.125755 CGCGTTGATACATGTTGATTCTATTT 58.874 34.615 2.30 0.00 0.00 1.40
15 16 6.257849 ACGCGTTGATACATGTTGATTCTATT 59.742 34.615 5.58 0.00 0.00 1.73
16 17 5.753438 ACGCGTTGATACATGTTGATTCTAT 59.247 36.000 5.58 0.00 0.00 1.98
17 18 5.005299 CACGCGTTGATACATGTTGATTCTA 59.995 40.000 10.22 0.00 0.00 2.10
18 19 3.932710 ACGCGTTGATACATGTTGATTCT 59.067 39.130 5.58 0.00 0.00 2.40
19 20 4.021822 CACGCGTTGATACATGTTGATTC 58.978 43.478 10.22 0.00 0.00 2.52
20 21 3.435327 ACACGCGTTGATACATGTTGATT 59.565 39.130 10.22 0.00 0.00 2.57
21 22 3.000041 ACACGCGTTGATACATGTTGAT 59.000 40.909 10.22 0.00 0.00 2.57
22 23 2.156697 CACACGCGTTGATACATGTTGA 59.843 45.455 10.22 0.00 0.00 3.18
23 24 2.156697 TCACACGCGTTGATACATGTTG 59.843 45.455 10.22 0.00 0.00 3.33
24 25 2.409012 TCACACGCGTTGATACATGTT 58.591 42.857 10.22 0.00 0.00 2.71
25 26 1.992667 CTCACACGCGTTGATACATGT 59.007 47.619 10.22 2.69 0.00 3.21
26 27 1.267038 GCTCACACGCGTTGATACATG 60.267 52.381 10.22 6.18 0.00 3.21
27 28 0.999406 GCTCACACGCGTTGATACAT 59.001 50.000 10.22 0.00 0.00 2.29
28 29 0.319125 TGCTCACACGCGTTGATACA 60.319 50.000 10.22 14.42 0.00 2.29
29 30 0.787787 TTGCTCACACGCGTTGATAC 59.212 50.000 10.22 12.19 0.00 2.24
30 31 1.459209 CTTTGCTCACACGCGTTGATA 59.541 47.619 10.22 6.71 0.00 2.15
31 32 0.235665 CTTTGCTCACACGCGTTGAT 59.764 50.000 10.22 0.00 0.00 2.57
32 33 1.087202 ACTTTGCTCACACGCGTTGA 61.087 50.000 10.22 15.89 0.00 3.18
33 34 0.925267 CACTTTGCTCACACGCGTTG 60.925 55.000 10.22 12.12 0.00 4.10
34 35 1.351707 CACTTTGCTCACACGCGTT 59.648 52.632 10.22 0.00 0.00 4.84
35 36 0.528901 TACACTTTGCTCACACGCGT 60.529 50.000 5.58 5.58 0.00 6.01
36 37 0.579630 TTACACTTTGCTCACACGCG 59.420 50.000 3.53 3.53 0.00 6.01
37 38 2.223157 TGTTTACACTTTGCTCACACGC 60.223 45.455 0.00 0.00 0.00 5.34
38 39 3.666883 TGTTTACACTTTGCTCACACG 57.333 42.857 0.00 0.00 0.00 4.49
39 40 3.730715 GCATGTTTACACTTTGCTCACAC 59.269 43.478 0.00 0.00 32.84 3.82
40 41 3.379688 TGCATGTTTACACTTTGCTCACA 59.620 39.130 8.03 0.00 35.17 3.58
41 42 3.963665 TGCATGTTTACACTTTGCTCAC 58.036 40.909 8.03 0.00 35.17 3.51
42 43 4.142293 TGTTGCATGTTTACACTTTGCTCA 60.142 37.500 8.03 5.46 35.17 4.26
43 44 4.358851 TGTTGCATGTTTACACTTTGCTC 58.641 39.130 8.03 3.57 35.17 4.26
44 45 4.383850 TGTTGCATGTTTACACTTTGCT 57.616 36.364 8.03 0.00 35.17 3.91
45 46 4.507388 ACATGTTGCATGTTTACACTTTGC 59.493 37.500 8.75 1.09 34.88 3.68
46 47 5.747675 TCACATGTTGCATGTTTACACTTTG 59.252 36.000 11.54 0.00 0.00 2.77
47 48 5.900425 TCACATGTTGCATGTTTACACTTT 58.100 33.333 11.54 0.00 0.00 2.66
48 49 5.512753 TCACATGTTGCATGTTTACACTT 57.487 34.783 11.54 0.00 0.00 3.16
49 50 4.557296 GCTCACATGTTGCATGTTTACACT 60.557 41.667 11.54 0.00 0.00 3.55
50 51 3.670055 GCTCACATGTTGCATGTTTACAC 59.330 43.478 11.54 0.00 0.00 2.90
51 52 3.608941 CGCTCACATGTTGCATGTTTACA 60.609 43.478 17.43 0.00 0.00 2.41
52 53 2.910482 CGCTCACATGTTGCATGTTTAC 59.090 45.455 17.43 4.20 0.00 2.01
53 54 2.551887 ACGCTCACATGTTGCATGTTTA 59.448 40.909 17.43 3.64 0.00 2.01
54 55 1.337703 ACGCTCACATGTTGCATGTTT 59.662 42.857 17.43 0.00 0.00 2.83
55 56 0.953727 ACGCTCACATGTTGCATGTT 59.046 45.000 17.43 0.00 0.00 2.71
56 57 0.953727 AACGCTCACATGTTGCATGT 59.046 45.000 17.43 8.75 0.00 3.21
57 58 2.898181 TAACGCTCACATGTTGCATG 57.102 45.000 17.43 7.48 0.00 4.06
58 59 5.756195 ATAATAACGCTCACATGTTGCAT 57.244 34.783 17.43 9.91 0.00 3.96
59 60 5.559427 AATAATAACGCTCACATGTTGCA 57.441 34.783 17.43 0.00 0.00 4.08
60 61 5.229887 CCAAATAATAACGCTCACATGTTGC 59.770 40.000 0.00 2.76 0.00 4.17
61 62 5.743398 CCCAAATAATAACGCTCACATGTTG 59.257 40.000 0.00 0.00 0.00 3.33
62 63 5.417580 ACCCAAATAATAACGCTCACATGTT 59.582 36.000 0.00 0.00 0.00 2.71
63 64 4.947388 ACCCAAATAATAACGCTCACATGT 59.053 37.500 0.00 0.00 0.00 3.21
64 65 5.499139 ACCCAAATAATAACGCTCACATG 57.501 39.130 0.00 0.00 0.00 3.21
65 66 7.633193 TTTACCCAAATAATAACGCTCACAT 57.367 32.000 0.00 0.00 0.00 3.21
66 67 7.450124 TTTTACCCAAATAATAACGCTCACA 57.550 32.000 0.00 0.00 0.00 3.58
89 90 3.881220 TCTCCAACTTCGGTGTCTTTTT 58.119 40.909 0.00 0.00 0.00 1.94
90 91 3.553828 TCTCCAACTTCGGTGTCTTTT 57.446 42.857 0.00 0.00 0.00 2.27
91 92 3.553828 TTCTCCAACTTCGGTGTCTTT 57.446 42.857 0.00 0.00 0.00 2.52
92 93 3.553828 TTTCTCCAACTTCGGTGTCTT 57.446 42.857 0.00 0.00 0.00 3.01
93 94 3.557264 GGATTTCTCCAACTTCGGTGTCT 60.557 47.826 0.00 0.00 41.64 3.41
184 185 5.250982 TGCTCTCTGTGTCAATTGATCATT 58.749 37.500 12.12 0.00 0.00 2.57
185 186 4.840271 TGCTCTCTGTGTCAATTGATCAT 58.160 39.130 12.12 0.00 0.00 2.45
199 201 3.119919 GCTCCAATCTTTGTTGCTCTCTG 60.120 47.826 0.00 0.00 0.00 3.35
204 206 4.292186 TCTAGCTCCAATCTTTGTTGCT 57.708 40.909 0.00 0.00 39.44 3.91
205 207 4.379918 GGTTCTAGCTCCAATCTTTGTTGC 60.380 45.833 0.00 0.00 0.00 4.17
206 208 4.156739 GGGTTCTAGCTCCAATCTTTGTTG 59.843 45.833 0.00 0.00 0.00 3.33
207 209 4.336280 GGGTTCTAGCTCCAATCTTTGTT 58.664 43.478 0.00 0.00 0.00 2.83
210 212 2.092914 CCGGGTTCTAGCTCCAATCTTT 60.093 50.000 0.00 0.00 0.00 2.52
590 592 2.507484 TCTGCTATGCTGCTTTGTGTT 58.493 42.857 0.00 0.00 0.00 3.32
747 846 4.199575 CGTTAATTAATGCGACGACTTTGC 59.800 41.667 0.00 0.00 35.90 3.68
781 880 3.895025 CCCATCAGGTGTGAAGCG 58.105 61.111 0.00 0.00 35.88 4.68
900 1008 4.172772 CACTCTCGCTCGCTCGCT 62.173 66.667 0.00 0.00 0.00 4.93
946 1058 4.363990 CCACCACTCACGCGCTCT 62.364 66.667 5.73 0.00 0.00 4.09
1763 1878 3.726517 CTCCAACGCCAACGCCAG 61.727 66.667 0.00 0.00 45.53 4.85
1803 1924 2.662857 TCCGTGTCGTCGTCGTCT 60.663 61.111 1.33 0.00 38.33 4.18
1957 2078 0.820891 ACCTGCTTGCTCACAACTGG 60.821 55.000 0.00 0.00 34.80 4.00
2100 2221 7.449704 AGCAAGACAAGAAAGATAATGAACCTT 59.550 33.333 0.00 0.00 0.00 3.50
2192 2322 2.191128 ATCTTGACACTTGACAGGGC 57.809 50.000 0.00 0.00 0.00 5.19
2196 2326 4.154015 CGGCATTAATCTTGACACTTGACA 59.846 41.667 0.00 0.00 0.00 3.58
2197 2327 4.651994 CGGCATTAATCTTGACACTTGAC 58.348 43.478 0.00 0.00 0.00 3.18
2198 2328 3.126858 GCGGCATTAATCTTGACACTTGA 59.873 43.478 0.00 0.00 0.00 3.02
2199 2329 3.119884 TGCGGCATTAATCTTGACACTTG 60.120 43.478 0.00 0.00 0.00 3.16
2200 2330 3.081061 TGCGGCATTAATCTTGACACTT 58.919 40.909 0.00 0.00 0.00 3.16
2201 2331 2.710377 TGCGGCATTAATCTTGACACT 58.290 42.857 0.00 0.00 0.00 3.55
2202 2332 3.698029 ATGCGGCATTAATCTTGACAC 57.302 42.857 10.23 0.00 0.00 3.67
2250 2381 1.607801 GCTTCCAGGCACAAATCCCC 61.608 60.000 0.00 0.00 0.00 4.81
2340 2760 3.902881 AGCCACACCAACATTCAAAAA 57.097 38.095 0.00 0.00 0.00 1.94
2341 2761 3.902881 AAGCCACACCAACATTCAAAA 57.097 38.095 0.00 0.00 0.00 2.44
2342 2762 3.736433 CGAAAGCCACACCAACATTCAAA 60.736 43.478 0.00 0.00 0.00 2.69
2343 2763 2.223688 CGAAAGCCACACCAACATTCAA 60.224 45.455 0.00 0.00 0.00 2.69
2344 2764 1.336440 CGAAAGCCACACCAACATTCA 59.664 47.619 0.00 0.00 0.00 2.57
2345 2765 1.335872 CCGAAAGCCACACCAACATTC 60.336 52.381 0.00 0.00 0.00 2.67
2346 2766 0.673437 CCGAAAGCCACACCAACATT 59.327 50.000 0.00 0.00 0.00 2.71
2347 2767 1.805428 GCCGAAAGCCACACCAACAT 61.805 55.000 0.00 0.00 34.35 2.71
2348 2768 2.485795 GCCGAAAGCCACACCAACA 61.486 57.895 0.00 0.00 34.35 3.33
2349 2769 2.193536 AGCCGAAAGCCACACCAAC 61.194 57.895 0.00 0.00 45.47 3.77
2350 2770 2.192861 CAGCCGAAAGCCACACCAA 61.193 57.895 0.00 0.00 45.47 3.67
2351 2771 2.594303 CAGCCGAAAGCCACACCA 60.594 61.111 0.00 0.00 45.47 4.17
2352 2772 3.365265 CCAGCCGAAAGCCACACC 61.365 66.667 0.00 0.00 45.47 4.16
2353 2773 2.281484 TCCAGCCGAAAGCCACAC 60.281 61.111 0.00 0.00 45.47 3.82
2354 2774 2.032528 CTCCAGCCGAAAGCCACA 59.967 61.111 0.00 0.00 45.47 4.17
2355 2775 2.032681 ACTCCAGCCGAAAGCCAC 59.967 61.111 0.00 0.00 45.47 5.01
2356 2776 2.032528 CACTCCAGCCGAAAGCCA 59.967 61.111 0.00 0.00 45.47 4.75
2357 2777 3.435186 GCACTCCAGCCGAAAGCC 61.435 66.667 0.00 0.00 45.47 4.35
2358 2778 3.435186 GGCACTCCAGCCGAAAGC 61.435 66.667 0.00 0.00 46.12 3.51
2564 2985 4.695231 CCACGCAACAGCAGCAGC 62.695 66.667 0.00 0.00 42.56 5.25
2565 2986 4.034258 CCCACGCAACAGCAGCAG 62.034 66.667 0.00 0.00 0.00 4.24
2642 3065 2.408271 AATCGCCATCATCACACACT 57.592 45.000 0.00 0.00 0.00 3.55
2758 3181 0.745128 AGGCGACAACAAAACCACGA 60.745 50.000 0.00 0.00 0.00 4.35
2835 3258 2.112297 GCGGGTTTCCTGTCACCA 59.888 61.111 0.00 0.00 34.36 4.17
2840 3263 3.966543 CAGGGGCGGGTTTCCTGT 61.967 66.667 0.00 0.00 42.17 4.00


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

AutoCloner maintained by Alex Coulton.