Multiple sequence alignment - TraesCS2A01G258600

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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 TraesCS2A01G258600 chr2A 100.000 2696 0 0 1 2696 406661765 406664460 0.000000e+00 4979.0
1 TraesCS2A01G258600 chr2A 87.654 162 17 3 2343 2502 300683178 300683018 4.580000e-43 185.0
2 TraesCS2A01G258600 chr2B 92.576 2492 117 29 247 2696 391950039 391947574 0.000000e+00 3515.0
3 TraesCS2A01G258600 chr2B 91.558 154 11 1 94 245 391950309 391950156 7.560000e-51 211.0
4 TraesCS2A01G258600 chr2D 92.610 2287 96 27 449 2696 323747996 323745744 0.000000e+00 3219.0
5 TraesCS2A01G258600 chr1B 88.889 108 9 3 2397 2502 308118320 308118426 2.180000e-26 130.0
6 TraesCS2A01G258600 chr3A 73.408 267 56 11 2245 2502 180919646 180919386 4.780000e-13 86.1
7 TraesCS2A01G258600 chr3D 100.000 37 0 0 2466 2502 545836651 545836615 4.820000e-08 69.4
8 TraesCS2A01G258600 chr5B 100.000 35 0 0 2466 2500 52936207 52936241 6.230000e-07 65.8
9 TraesCS2A01G258600 chr5A 95.238 42 1 1 2466 2506 430483422 430483381 6.230000e-07 65.8
10 TraesCS2A01G258600 chr6D 86.207 58 6 2 2445 2501 2473242 2473298 8.060000e-06 62.1


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 TraesCS2A01G258600 chr2A 406661765 406664460 2695 False 4979 4979 100.000 1 2696 1 chr2A.!!$F1 2695
1 TraesCS2A01G258600 chr2B 391947574 391950309 2735 True 1863 3515 92.067 94 2696 2 chr2B.!!$R1 2602
2 TraesCS2A01G258600 chr2D 323745744 323747996 2252 True 3219 3219 92.610 449 2696 1 chr2D.!!$R1 2247

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
38 39 0.178068 AAGGTGTGCGATATTCGGCT 59.822 50.0 0.0 0.0 40.84 5.52 F
533 651 1.183549 CGTCAAGTAGGTAGGGTGCT 58.816 55.0 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 1834 0.399091 ATCGGCCAGATCCCTCTCAA 60.399 55.0 2.24 0.00 33.45 3.02 R
2294 2452 0.644331 CTCGCTCTTGCATGAGAACG 59.356 55.0 28.50 22.59 39.64 3.95 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 5.473039 GAATACGGTACACAACTACAAGGT 58.527 41.667 0.00 0.00 0.00 3.50
24 25 3.102052 ACGGTACACAACTACAAGGTG 57.898 47.619 0.00 0.00 39.30 4.00
30 31 2.543777 ACAACTACAAGGTGTGCGAT 57.456 45.000 0.00 0.00 45.96 4.58
31 32 3.671008 ACAACTACAAGGTGTGCGATA 57.329 42.857 0.00 0.00 45.96 2.92
32 33 4.202245 ACAACTACAAGGTGTGCGATAT 57.798 40.909 0.00 0.00 45.96 1.63
33 34 4.575885 ACAACTACAAGGTGTGCGATATT 58.424 39.130 0.00 0.00 45.96 1.28
34 35 4.630069 ACAACTACAAGGTGTGCGATATTC 59.370 41.667 0.00 0.00 45.96 1.75
35 36 3.444916 ACTACAAGGTGTGCGATATTCG 58.555 45.455 0.00 0.00 43.89 3.34
36 37 1.651987 ACAAGGTGTGCGATATTCGG 58.348 50.000 0.00 0.00 40.84 4.30
37 38 0.304705 CAAGGTGTGCGATATTCGGC 59.695 55.000 0.00 0.00 40.84 5.54
38 39 0.178068 AAGGTGTGCGATATTCGGCT 59.822 50.000 0.00 0.00 40.84 5.52
39 40 0.178068 AGGTGTGCGATATTCGGCTT 59.822 50.000 0.00 0.00 40.84 4.35
40 41 1.411246 AGGTGTGCGATATTCGGCTTA 59.589 47.619 0.00 0.00 40.84 3.09
41 42 2.159014 AGGTGTGCGATATTCGGCTTAA 60.159 45.455 0.00 0.00 40.84 1.85
42 43 2.221055 GGTGTGCGATATTCGGCTTAAG 59.779 50.000 0.00 0.00 40.84 1.85
43 44 1.864711 TGTGCGATATTCGGCTTAAGC 59.135 47.619 19.53 19.53 40.84 3.09
44 45 2.135933 GTGCGATATTCGGCTTAAGCT 58.864 47.619 25.88 9.66 40.84 3.74
45 46 2.544267 GTGCGATATTCGGCTTAAGCTT 59.456 45.455 25.88 3.48 40.84 3.74
46 47 2.543848 TGCGATATTCGGCTTAAGCTTG 59.456 45.455 25.88 18.48 40.84 4.01
47 48 2.544267 GCGATATTCGGCTTAAGCTTGT 59.456 45.455 25.88 12.63 40.84 3.16
48 49 3.002348 GCGATATTCGGCTTAAGCTTGTT 59.998 43.478 25.88 12.00 40.84 2.83
49 50 4.518217 CGATATTCGGCTTAAGCTTGTTG 58.482 43.478 25.88 11.58 41.70 3.33
50 51 4.034048 CGATATTCGGCTTAAGCTTGTTGT 59.966 41.667 25.88 9.59 41.70 3.32
51 52 3.831715 ATTCGGCTTAAGCTTGTTGTC 57.168 42.857 25.88 7.43 41.70 3.18
52 53 2.543777 TCGGCTTAAGCTTGTTGTCT 57.456 45.000 25.88 0.00 41.70 3.41
53 54 2.846193 TCGGCTTAAGCTTGTTGTCTT 58.154 42.857 25.88 0.00 41.70 3.01
54 55 3.211045 TCGGCTTAAGCTTGTTGTCTTT 58.789 40.909 25.88 0.00 41.70 2.52
55 56 3.003275 TCGGCTTAAGCTTGTTGTCTTTG 59.997 43.478 25.88 3.48 41.70 2.77
56 57 3.243068 CGGCTTAAGCTTGTTGTCTTTGT 60.243 43.478 25.88 0.00 41.70 2.83
57 58 4.682787 GGCTTAAGCTTGTTGTCTTTGTT 58.317 39.130 25.88 0.00 41.70 2.83
58 59 4.504097 GGCTTAAGCTTGTTGTCTTTGTTG 59.496 41.667 25.88 0.00 41.70 3.33
59 60 5.339990 GCTTAAGCTTGTTGTCTTTGTTGA 58.660 37.500 20.38 0.00 38.21 3.18
60 61 5.230097 GCTTAAGCTTGTTGTCTTTGTTGAC 59.770 40.000 20.38 0.00 38.21 3.18
61 62 4.782019 AAGCTTGTTGTCTTTGTTGACA 57.218 36.364 0.00 0.00 44.17 3.58
62 63 4.361451 AGCTTGTTGTCTTTGTTGACAG 57.639 40.909 0.00 0.00 46.02 3.51
63 64 3.758554 AGCTTGTTGTCTTTGTTGACAGT 59.241 39.130 0.00 0.00 46.02 3.55
64 65 4.098416 GCTTGTTGTCTTTGTTGACAGTC 58.902 43.478 0.00 0.00 46.02 3.51
65 66 4.379394 GCTTGTTGTCTTTGTTGACAGTCA 60.379 41.667 0.00 0.00 46.02 3.41
66 67 4.678509 TGTTGTCTTTGTTGACAGTCAC 57.321 40.909 1.52 0.00 46.02 3.67
67 68 4.323417 TGTTGTCTTTGTTGACAGTCACT 58.677 39.130 1.52 0.00 46.02 3.41
68 69 4.154015 TGTTGTCTTTGTTGACAGTCACTG 59.846 41.667 2.22 2.22 46.02 3.66
69 70 3.270027 TGTCTTTGTTGACAGTCACTGG 58.730 45.455 10.28 0.00 41.43 4.00
70 71 3.270877 GTCTTTGTTGACAGTCACTGGT 58.729 45.455 10.28 0.00 35.51 4.00
71 72 4.081365 TGTCTTTGTTGACAGTCACTGGTA 60.081 41.667 10.28 0.00 41.43 3.25
72 73 5.057149 GTCTTTGTTGACAGTCACTGGTAT 58.943 41.667 10.28 0.00 35.51 2.73
73 74 5.527582 GTCTTTGTTGACAGTCACTGGTATT 59.472 40.000 10.28 0.00 35.51 1.89
74 75 6.038271 GTCTTTGTTGACAGTCACTGGTATTT 59.962 38.462 10.28 0.00 35.51 1.40
75 76 6.601613 TCTTTGTTGACAGTCACTGGTATTTT 59.398 34.615 10.28 0.00 35.51 1.82
76 77 6.371809 TTGTTGACAGTCACTGGTATTTTC 57.628 37.500 10.28 0.00 35.51 2.29
77 78 4.819630 TGTTGACAGTCACTGGTATTTTCC 59.180 41.667 10.28 0.00 35.51 3.13
78 79 4.015872 TGACAGTCACTGGTATTTTCCC 57.984 45.455 10.28 0.00 35.51 3.97
79 80 3.000727 GACAGTCACTGGTATTTTCCCG 58.999 50.000 10.28 0.00 35.51 5.14
80 81 1.737793 CAGTCACTGGTATTTTCCCGC 59.262 52.381 0.00 0.00 0.00 6.13
81 82 1.349688 AGTCACTGGTATTTTCCCGCA 59.650 47.619 0.00 0.00 0.00 5.69
82 83 2.156098 GTCACTGGTATTTTCCCGCAA 58.844 47.619 0.00 0.00 0.00 4.85
83 84 2.554893 GTCACTGGTATTTTCCCGCAAA 59.445 45.455 0.00 0.00 0.00 3.68
84 85 3.004944 GTCACTGGTATTTTCCCGCAAAA 59.995 43.478 0.00 0.00 38.38 2.44
85 86 3.637229 TCACTGGTATTTTCCCGCAAAAA 59.363 39.130 0.00 0.00 37.52 1.94
111 112 9.574516 AAAAAGACAGTCACTGGTATAAGATTT 57.425 29.630 10.28 0.00 35.51 2.17
138 139 2.239654 CAGTGGCTATGGGAGAAAAGGA 59.760 50.000 0.00 0.00 0.00 3.36
155 158 9.387123 GAGAAAAGGAAATTATAAAGCTATGCG 57.613 33.333 0.00 0.00 0.00 4.73
174 177 8.818057 GCTATGCGAAATACCCTATATTTGTAG 58.182 37.037 0.00 0.00 0.00 2.74
194 197 8.657074 TTGTAGTATATATTGCTCGCTTGTTT 57.343 30.769 0.00 0.00 0.00 2.83
200 203 9.072294 GTATATATTGCTCGCTTGTTTGTTTTT 57.928 29.630 0.00 0.00 0.00 1.94
214 217 9.956797 CTTGTTTGTTTTTGTCATAAACTTCAG 57.043 29.630 16.59 5.61 36.64 3.02
216 219 7.064016 TGTTTGTTTTTGTCATAAACTTCAGCC 59.936 33.333 16.59 3.91 36.64 4.85
266 384 8.915871 AACAGATTTATGTTTGAATCAATCCG 57.084 30.769 0.00 0.00 40.47 4.18
326 444 8.166422 ACTACAAAATGCAGTAAAGTTAAGCT 57.834 30.769 0.00 0.00 0.00 3.74
391 509 7.687941 ATTGTGTAAATTCAGGTGACTAAGG 57.312 36.000 0.00 0.00 40.21 2.69
392 510 5.001232 TGTGTAAATTCAGGTGACTAAGGC 58.999 41.667 0.00 0.00 40.21 4.35
413 531 5.362717 AGGCATAAAACTATTTTAGGTGGGC 59.637 40.000 7.35 5.81 38.68 5.36
432 550 3.308530 GGCAACCGAAAATGAAGAACAG 58.691 45.455 0.00 0.00 0.00 3.16
463 581 2.880268 CAGATGTGTGAGAGGTTGCAAA 59.120 45.455 0.00 0.00 0.00 3.68
533 651 1.183549 CGTCAAGTAGGTAGGGTGCT 58.816 55.000 0.00 0.00 0.00 4.40
543 661 2.174854 AGGTAGGGTGCTCAACTTTTGT 59.825 45.455 0.00 0.00 0.00 2.83
683 822 3.490526 GCATTTTCTTTTCTGCGAGCAAA 59.509 39.130 0.00 0.00 0.00 3.68
1021 1160 2.649129 GCAATGGTGGTGAAGGCCC 61.649 63.158 0.00 0.00 0.00 5.80
1170 1309 2.043852 TCTCCGGGAGACAGCCTC 60.044 66.667 22.70 0.00 41.22 4.70
1255 1397 2.014128 CCGACCTGACAAACTTGTTGT 58.986 47.619 0.00 0.00 42.43 3.32
1260 1402 2.099098 CCTGACAAACTTGTTGTGGTCC 59.901 50.000 0.00 0.00 42.43 4.46
1706 1848 1.478288 GGCCATTTGAGAGGGATCTGG 60.478 57.143 0.00 0.00 0.00 3.86
1742 1884 2.029918 CCAAGGCTTAGTTTTGGAGTGC 60.030 50.000 0.00 0.00 43.15 4.40
1744 1886 2.784347 AGGCTTAGTTTTGGAGTGCTC 58.216 47.619 0.00 0.00 0.00 4.26
1757 1899 4.569943 TGGAGTGCTCAAGTCTTAATCAC 58.430 43.478 1.41 0.00 0.00 3.06
1843 1985 3.274288 CTGCATGTTCCTTCCTTCCTAC 58.726 50.000 0.00 0.00 0.00 3.18
1844 1986 2.912956 TGCATGTTCCTTCCTTCCTACT 59.087 45.455 0.00 0.00 0.00 2.57
1845 1987 4.101114 TGCATGTTCCTTCCTTCCTACTA 58.899 43.478 0.00 0.00 0.00 1.82
1846 1988 4.162320 TGCATGTTCCTTCCTTCCTACTAG 59.838 45.833 0.00 0.00 0.00 2.57
1955 2097 5.943706 AGTATCGTCTGTCTGCGTTATAT 57.056 39.130 0.00 0.00 0.00 0.86
1956 2098 8.538409 TTAGTATCGTCTGTCTGCGTTATATA 57.462 34.615 0.00 0.00 0.00 0.86
1957 2099 7.612668 AGTATCGTCTGTCTGCGTTATATAT 57.387 36.000 0.00 0.00 0.00 0.86
1958 2100 7.686519 AGTATCGTCTGTCTGCGTTATATATC 58.313 38.462 0.00 0.00 0.00 1.63
1959 2101 6.745159 ATCGTCTGTCTGCGTTATATATCT 57.255 37.500 0.00 0.00 0.00 1.98
1961 2103 6.371389 TCGTCTGTCTGCGTTATATATCTTG 58.629 40.000 0.00 0.00 0.00 3.02
1963 2105 7.172019 TCGTCTGTCTGCGTTATATATCTTGTA 59.828 37.037 0.00 0.00 0.00 2.41
2020 2162 0.465460 TCAGTGTCCTGTTGGTTGGC 60.465 55.000 0.00 0.00 39.82 4.52
2022 2164 0.258774 AGTGTCCTGTTGGTTGGCTT 59.741 50.000 0.00 0.00 34.23 4.35
2023 2165 0.668535 GTGTCCTGTTGGTTGGCTTC 59.331 55.000 0.00 0.00 34.23 3.86
2085 2227 3.825328 ACAACAGAAACCAGAGCAGAAT 58.175 40.909 0.00 0.00 0.00 2.40
2134 2278 1.530419 AACCGGCAGGAACATTGCA 60.530 52.632 10.86 0.00 43.28 4.08
2160 2304 4.072839 TCGTTAAGTGAGAAGCAGAGAGA 58.927 43.478 0.00 0.00 0.00 3.10
2161 2305 4.155099 TCGTTAAGTGAGAAGCAGAGAGAG 59.845 45.833 0.00 0.00 0.00 3.20
2162 2306 4.155099 CGTTAAGTGAGAAGCAGAGAGAGA 59.845 45.833 0.00 0.00 0.00 3.10
2225 2369 2.885894 CACACCTAAACCCCGCTAAAAA 59.114 45.455 0.00 0.00 0.00 1.94
2258 2416 2.479560 GCGGGCTATGACATTTTTGACC 60.480 50.000 0.00 0.00 0.00 4.02
2266 2424 6.867816 GCTATGACATTTTTGACCATGTGAAA 59.132 34.615 0.00 0.00 0.00 2.69
2407 2567 5.425630 GTGACTTACACCCAACCTTATAGG 58.574 45.833 0.00 0.00 43.05 2.57
2478 2638 4.649218 TCATGTCTACATAGCCAGCAACTA 59.351 41.667 0.00 0.00 34.26 2.24
2530 2690 5.012148 ACAGAAGTATTACTGAGGTGTTGCT 59.988 40.000 0.00 0.00 37.54 3.91
2541 2701 3.594775 TGTTGCTGCAACGGCCAG 61.595 61.111 32.71 0.00 46.13 4.85
2607 2767 6.688385 CCTCAATGTTGTGATTAATTAGCACG 59.312 38.462 12.85 0.00 35.37 5.34
2636 2796 3.515059 GGGAAATCTACCCTTGCCC 57.485 57.895 0.00 0.00 43.65 5.36
2651 2811 1.293179 GCCCAAACCTTCATGTGGC 59.707 57.895 7.28 0.00 0.00 5.01
2658 2818 0.896940 ACCTTCATGTGGCTGCCTTG 60.897 55.000 21.03 14.38 0.00 3.61
2677 2837 2.094659 CGCAACCGACGCATCTCTT 61.095 57.895 0.00 0.00 36.29 2.85
2683 2845 2.093106 ACCGACGCATCTCTTTCTAGT 58.907 47.619 0.00 0.00 0.00 2.57
2686 2848 3.064958 CCGACGCATCTCTTTCTAGTGTA 59.935 47.826 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.346822 CACCTTGTAGTTGTGTACCGTATTC 59.653 44.000 0.00 0.00 0.00 1.75
1 2 5.221501 ACACCTTGTAGTTGTGTACCGTATT 60.222 40.000 0.00 0.00 41.18 1.89
2 3 4.281688 ACACCTTGTAGTTGTGTACCGTAT 59.718 41.667 0.00 0.00 41.18 3.06
3 4 3.636300 ACACCTTGTAGTTGTGTACCGTA 59.364 43.478 0.00 0.00 41.18 4.02
4 5 2.431782 ACACCTTGTAGTTGTGTACCGT 59.568 45.455 0.00 0.00 41.18 4.83
5 6 2.798283 CACACCTTGTAGTTGTGTACCG 59.202 50.000 0.00 0.00 41.04 4.02
6 7 2.546789 GCACACCTTGTAGTTGTGTACC 59.453 50.000 6.30 0.00 41.04 3.34
7 8 2.220133 CGCACACCTTGTAGTTGTGTAC 59.780 50.000 6.30 0.00 41.04 2.90
8 9 2.101082 TCGCACACCTTGTAGTTGTGTA 59.899 45.455 6.30 0.00 41.04 2.90
9 10 1.134640 TCGCACACCTTGTAGTTGTGT 60.135 47.619 6.30 0.00 43.62 3.72
10 11 1.577468 TCGCACACCTTGTAGTTGTG 58.423 50.000 0.60 0.60 36.11 3.33
11 12 2.543777 ATCGCACACCTTGTAGTTGT 57.456 45.000 0.00 0.00 0.00 3.32
12 13 4.259810 CGAATATCGCACACCTTGTAGTTG 60.260 45.833 0.00 0.00 31.14 3.16
13 14 3.863424 CGAATATCGCACACCTTGTAGTT 59.137 43.478 0.00 0.00 31.14 2.24
14 15 3.444916 CGAATATCGCACACCTTGTAGT 58.555 45.455 0.00 0.00 31.14 2.73
15 16 2.794910 CCGAATATCGCACACCTTGTAG 59.205 50.000 0.00 0.00 38.82 2.74
16 17 2.816689 CCGAATATCGCACACCTTGTA 58.183 47.619 0.00 0.00 38.82 2.41
17 18 1.651987 CCGAATATCGCACACCTTGT 58.348 50.000 0.00 0.00 38.82 3.16
18 19 0.304705 GCCGAATATCGCACACCTTG 59.695 55.000 0.00 0.00 38.82 3.61
19 20 0.178068 AGCCGAATATCGCACACCTT 59.822 50.000 0.00 0.00 38.82 3.50
20 21 0.178068 AAGCCGAATATCGCACACCT 59.822 50.000 0.00 0.00 38.82 4.00
21 22 1.860676 TAAGCCGAATATCGCACACC 58.139 50.000 0.00 0.00 38.82 4.16
22 23 2.348591 GCTTAAGCCGAATATCGCACAC 60.349 50.000 17.00 0.00 38.82 3.82
23 24 1.864711 GCTTAAGCCGAATATCGCACA 59.135 47.619 17.00 0.00 38.82 4.57
24 25 2.135933 AGCTTAAGCCGAATATCGCAC 58.864 47.619 23.71 0.00 43.38 5.34
25 26 2.526304 AGCTTAAGCCGAATATCGCA 57.474 45.000 23.71 0.00 43.38 5.10
26 27 2.544267 ACAAGCTTAAGCCGAATATCGC 59.456 45.455 23.71 0.00 43.38 4.58
27 28 4.034048 ACAACAAGCTTAAGCCGAATATCG 59.966 41.667 23.71 7.82 43.38 2.92
28 29 5.294552 AGACAACAAGCTTAAGCCGAATATC 59.705 40.000 23.71 14.54 43.38 1.63
29 30 5.186198 AGACAACAAGCTTAAGCCGAATAT 58.814 37.500 23.71 6.20 43.38 1.28
30 31 4.575885 AGACAACAAGCTTAAGCCGAATA 58.424 39.130 23.71 0.00 43.38 1.75
31 32 3.412386 AGACAACAAGCTTAAGCCGAAT 58.588 40.909 23.71 2.13 43.38 3.34
32 33 2.846193 AGACAACAAGCTTAAGCCGAA 58.154 42.857 23.71 0.00 43.38 4.30
33 34 2.543777 AGACAACAAGCTTAAGCCGA 57.456 45.000 23.71 0.00 43.38 5.54
34 35 3.243068 ACAAAGACAACAAGCTTAAGCCG 60.243 43.478 23.71 17.25 43.38 5.52
35 36 4.307443 ACAAAGACAACAAGCTTAAGCC 57.693 40.909 23.71 6.68 43.38 4.35
36 37 5.230097 GTCAACAAAGACAACAAGCTTAAGC 59.770 40.000 20.09 20.09 38.40 3.09
37 38 6.321717 TGTCAACAAAGACAACAAGCTTAAG 58.678 36.000 0.00 0.00 44.92 1.85
38 39 6.072175 ACTGTCAACAAAGACAACAAGCTTAA 60.072 34.615 0.00 0.00 46.90 1.85
39 40 5.414454 ACTGTCAACAAAGACAACAAGCTTA 59.586 36.000 0.00 0.00 46.90 3.09
40 41 4.218417 ACTGTCAACAAAGACAACAAGCTT 59.782 37.500 0.00 0.00 46.90 3.74
41 42 3.758554 ACTGTCAACAAAGACAACAAGCT 59.241 39.130 0.00 0.00 46.90 3.74
42 43 4.096732 ACTGTCAACAAAGACAACAAGC 57.903 40.909 0.00 0.00 46.90 4.01
43 44 5.088739 GTGACTGTCAACAAAGACAACAAG 58.911 41.667 12.81 0.00 46.90 3.16
44 45 4.759693 AGTGACTGTCAACAAAGACAACAA 59.240 37.500 12.81 0.00 46.90 2.83
45 46 4.154015 CAGTGACTGTCAACAAAGACAACA 59.846 41.667 12.81 0.00 46.90 3.33
46 47 4.437390 CCAGTGACTGTCAACAAAGACAAC 60.437 45.833 12.81 0.00 46.90 3.32
47 48 3.689161 CCAGTGACTGTCAACAAAGACAA 59.311 43.478 12.81 0.00 46.90 3.18
48 49 3.270027 CCAGTGACTGTCAACAAAGACA 58.730 45.455 12.81 0.00 45.64 3.41
49 50 3.270877 ACCAGTGACTGTCAACAAAGAC 58.729 45.455 12.81 0.00 38.99 3.01
50 51 3.627395 ACCAGTGACTGTCAACAAAGA 57.373 42.857 12.81 0.00 0.00 2.52
51 52 6.377327 AAATACCAGTGACTGTCAACAAAG 57.623 37.500 12.81 2.86 0.00 2.77
52 53 6.183360 GGAAAATACCAGTGACTGTCAACAAA 60.183 38.462 12.81 0.00 0.00 2.83
53 54 5.298276 GGAAAATACCAGTGACTGTCAACAA 59.702 40.000 12.81 0.00 0.00 2.83
54 55 4.819630 GGAAAATACCAGTGACTGTCAACA 59.180 41.667 12.81 0.00 0.00 3.33
55 56 4.215613 GGGAAAATACCAGTGACTGTCAAC 59.784 45.833 12.81 7.12 0.00 3.18
56 57 4.394729 GGGAAAATACCAGTGACTGTCAA 58.605 43.478 12.81 0.00 0.00 3.18
57 58 3.556213 CGGGAAAATACCAGTGACTGTCA 60.556 47.826 12.15 6.36 0.00 3.58
58 59 3.000727 CGGGAAAATACCAGTGACTGTC 58.999 50.000 12.15 0.00 0.00 3.51
59 60 2.874457 GCGGGAAAATACCAGTGACTGT 60.874 50.000 12.15 2.56 0.00 3.55
60 61 1.737793 GCGGGAAAATACCAGTGACTG 59.262 52.381 5.42 5.42 0.00 3.51
61 62 1.349688 TGCGGGAAAATACCAGTGACT 59.650 47.619 0.00 0.00 0.00 3.41
62 63 1.816074 TGCGGGAAAATACCAGTGAC 58.184 50.000 0.00 0.00 0.00 3.67
63 64 2.570415 TTGCGGGAAAATACCAGTGA 57.430 45.000 0.00 0.00 0.00 3.41
64 65 3.651803 TTTTGCGGGAAAATACCAGTG 57.348 42.857 3.11 0.00 0.00 3.66
85 86 9.574516 AAATCTTATACCAGTGACTGTCTTTTT 57.425 29.630 12.15 0.00 0.00 1.94
86 87 9.574516 AAAATCTTATACCAGTGACTGTCTTTT 57.425 29.630 12.15 3.20 0.00 2.27
87 88 9.574516 AAAAATCTTATACCAGTGACTGTCTTT 57.425 29.630 12.15 0.00 0.00 2.52
105 106 7.582719 TCCCATAGCCACTGTATAAAAATCTT 58.417 34.615 0.00 0.00 0.00 2.40
106 107 7.072454 TCTCCCATAGCCACTGTATAAAAATCT 59.928 37.037 0.00 0.00 0.00 2.40
111 112 6.569127 TTTCTCCCATAGCCACTGTATAAA 57.431 37.500 0.00 0.00 0.00 1.40
116 117 2.025887 CCTTTTCTCCCATAGCCACTGT 60.026 50.000 0.00 0.00 0.00 3.55
138 139 9.297037 AGGGTATTTCGCATAGCTTTATAATTT 57.703 29.630 0.00 0.00 0.00 1.82
174 177 8.614994 AAAACAAACAAGCGAGCAATATATAC 57.385 30.769 0.00 0.00 0.00 1.47
194 197 6.039616 GTGGCTGAAGTTTATGACAAAAACA 58.960 36.000 2.00 0.00 38.92 2.83
200 203 4.518970 GGAAAGTGGCTGAAGTTTATGACA 59.481 41.667 0.00 0.00 0.00 3.58
214 217 4.949856 TCTCCAAATGATTAGGAAAGTGGC 59.050 41.667 0.00 0.00 0.00 5.01
245 248 9.781834 TTGTACGGATTGATTCAAACATAAATC 57.218 29.630 2.68 0.00 33.42 2.17
305 423 7.928908 TTCAGCTTAACTTTACTGCATTTTG 57.071 32.000 0.00 0.00 0.00 2.44
391 509 6.215495 TGCCCACCTAAAATAGTTTTATGC 57.785 37.500 0.00 0.00 34.84 3.14
392 510 7.039270 GGTTGCCCACCTAAAATAGTTTTATG 58.961 38.462 0.00 0.00 43.29 1.90
413 531 5.821204 ACTTCTGTTCTTCATTTTCGGTTG 58.179 37.500 0.00 0.00 0.00 3.77
432 550 7.324178 ACCTCTCACACATCTGTAATTACTTC 58.676 38.462 16.33 0.00 0.00 3.01
533 651 1.305201 GCGGGAGTGACAAAAGTTGA 58.695 50.000 0.00 0.00 0.00 3.18
683 822 0.601558 CATTGCTGCAGCTTCCTTGT 59.398 50.000 36.61 13.53 42.66 3.16
705 844 6.942532 TCAACAACTCTCCATTATTATGCC 57.057 37.500 0.00 0.00 0.00 4.40
1170 1309 3.118542 GGGTGAGCTTAAATACGTACCG 58.881 50.000 0.00 0.00 0.00 4.02
1190 1329 0.537828 GAGCTAGGTCGAGTAGGGGG 60.538 65.000 6.12 0.00 0.00 5.40
1255 1397 2.897271 AATACTGCAACCATGGACCA 57.103 45.000 21.47 10.92 0.00 4.02
1260 1402 5.545658 AGTACGAAAATACTGCAACCATG 57.454 39.130 0.00 0.00 34.02 3.66
1692 1834 0.399091 ATCGGCCAGATCCCTCTCAA 60.399 55.000 2.24 0.00 33.45 3.02
1706 1848 1.299541 CTTGGTACACATGGATCGGC 58.700 55.000 0.00 0.00 39.29 5.54
1717 1859 4.141344 ACTCCAAAACTAAGCCTTGGTACA 60.141 41.667 0.00 0.00 40.47 2.90
1742 1884 6.255950 TGTATCGACGTGATTAAGACTTGAG 58.744 40.000 0.00 0.00 38.57 3.02
1744 1886 7.451281 AATGTATCGACGTGATTAAGACTTG 57.549 36.000 0.00 0.00 38.57 3.16
1757 1899 3.242284 ACAAATCCGCAAATGTATCGACG 60.242 43.478 0.00 0.00 0.00 5.12
1843 1985 4.645136 TGAACCCTGATAGCACTGTACTAG 59.355 45.833 0.00 0.00 0.00 2.57
1844 1986 4.606210 TGAACCCTGATAGCACTGTACTA 58.394 43.478 0.00 0.00 0.00 1.82
1845 1987 3.441101 TGAACCCTGATAGCACTGTACT 58.559 45.455 0.00 0.00 0.00 2.73
1846 1988 3.195825 ACTGAACCCTGATAGCACTGTAC 59.804 47.826 0.00 0.00 0.00 2.90
1979 2121 9.857656 ACTGAAGATATATGGATTGTCACAAAT 57.142 29.630 0.00 0.00 0.00 2.32
2020 2162 3.671928 CGTTACTAGTCCAACCAACGAAG 59.328 47.826 17.36 0.00 40.74 3.79
2022 2164 2.622942 ACGTTACTAGTCCAACCAACGA 59.377 45.455 25.22 0.00 40.74 3.85
2023 2165 2.727798 CACGTTACTAGTCCAACCAACG 59.272 50.000 19.57 19.57 43.10 4.10
2134 2278 7.067615 TCTCTCTGCTTCTCACTTAACGAATAT 59.932 37.037 0.00 0.00 0.00 1.28
2186 2330 3.692593 GTGTGTTCCCCTAAAATACGCAT 59.307 43.478 0.00 0.00 32.62 4.73
2225 2369 3.386726 TCATAGCCCGCTATTGTACTTGT 59.613 43.478 6.48 0.00 37.16 3.16
2239 2383 4.160252 ACATGGTCAAAAATGTCATAGCCC 59.840 41.667 0.00 0.00 31.33 5.19
2284 2442 3.884169 TGCATGAGAACGCACTTTTTAC 58.116 40.909 0.00 0.00 31.95 2.01
2285 2443 4.274705 TCTTGCATGAGAACGCACTTTTTA 59.725 37.500 0.00 0.00 38.00 1.52
2286 2444 3.066621 TCTTGCATGAGAACGCACTTTTT 59.933 39.130 0.00 0.00 38.00 1.94
2294 2452 0.644331 CTCGCTCTTGCATGAGAACG 59.356 55.000 28.50 22.59 39.64 3.95
2295 2453 1.658095 GACTCGCTCTTGCATGAGAAC 59.342 52.381 28.50 13.65 39.64 3.01
2296 2454 1.547820 AGACTCGCTCTTGCATGAGAA 59.452 47.619 28.50 16.29 39.64 2.87
2297 2455 1.133982 GAGACTCGCTCTTGCATGAGA 59.866 52.381 28.50 10.62 40.61 3.27
2350 2510 8.589701 TCCACTTTTTCTCTAACCTTTTCTTT 57.410 30.769 0.00 0.00 0.00 2.52
2502 2662 6.926313 ACACCTCAGTAATACTTCTGTTCTC 58.074 40.000 0.00 0.00 33.89 2.87
2530 2690 4.641645 CCAGACCTGGCCGTTGCA 62.642 66.667 2.75 0.00 44.73 4.08
2541 2701 0.961753 CTTTCAAAGTGCCCCAGACC 59.038 55.000 0.00 0.00 0.00 3.85
2545 2705 1.691196 CAGACTTTCAAAGTGCCCCA 58.309 50.000 7.75 0.00 43.03 4.96
2636 2796 0.037975 GGCAGCCACATGAAGGTTTG 60.038 55.000 6.55 5.62 0.00 2.93


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

AutoCloner maintained by Alex Coulton.