Multiple sequence alignment - TraesCS5D01G300100

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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 TraesCS5D01G300100 chr5D 100.000 3548 0 0 1 3548 397427448 397423901 0.000000e+00 6553.0
1 TraesCS5D01G300100 chr5A 90.599 2319 118 44 56 2286 502788976 502786670 0.000000e+00 2983.0
2 TraesCS5D01G300100 chr5A 95.592 431 12 4 2780 3209 502786285 502785861 0.000000e+00 684.0
3 TraesCS5D01G300100 chr5A 94.444 342 15 4 2340 2680 502786664 502786326 1.130000e-144 523.0
4 TraesCS5D01G300100 chr5A 84.419 353 30 12 3206 3548 502785605 502785268 1.230000e-84 324.0
5 TraesCS5D01G300100 chr5B 94.278 1468 42 13 856 2302 477611750 477610304 0.000000e+00 2207.0
6 TraesCS5D01G300100 chr5B 96.166 913 19 7 2318 3229 477610328 477609431 0.000000e+00 1478.0
7 TraesCS5D01G300100 chr5B 95.561 383 14 2 121 501 477612999 477612618 8.420000e-171 610.0
8 TraesCS5D01G300100 chr5B 88.854 323 21 9 511 820 477612578 477612258 2.000000e-102 383.0
9 TraesCS5D01G300100 chr5B 87.805 82 9 1 3468 3548 681766126 681766045 1.050000e-15 95.3
10 TraesCS5D01G300100 chr7D 77.737 274 36 22 1562 1824 245484799 245484540 1.030000e-30 145.0
11 TraesCS5D01G300100 chr7D 93.976 83 5 0 1380 1462 245484949 245484867 3.720000e-25 126.0
12 TraesCS5D01G300100 chr7B 77.580 281 36 22 1562 1830 221914528 221914263 1.030000e-30 145.0
13 TraesCS5D01G300100 chr7B 92.771 83 6 0 1380 1462 221914680 221914598 1.730000e-23 121.0
14 TraesCS5D01G300100 chr7B 82.727 110 16 2 1920 2029 221914131 221914025 1.050000e-15 95.3
15 TraesCS5D01G300100 chr7B 87.952 83 7 3 3468 3548 491127174 491127093 1.050000e-15 95.3
16 TraesCS5D01G300100 chr7A 77.289 273 39 20 1562 1824 261880431 261880172 4.780000e-29 139.0
17 TraesCS5D01G300100 chr7A 93.976 83 5 0 1380 1462 261880583 261880501 3.720000e-25 126.0
18 TraesCS5D01G300100 chr2A 92.771 83 4 2 3468 3548 20001285 20001367 6.220000e-23 119.0
19 TraesCS5D01G300100 chr1D 88.095 84 7 3 3467 3548 188537156 188537238 2.920000e-16 97.1
20 TraesCS5D01G300100 chr3B 87.805 82 9 1 3468 3548 763294747 763294666 1.050000e-15 95.3
21 TraesCS5D01G300100 chr3B 86.585 82 11 0 3467 3548 758067622 758067703 1.360000e-14 91.6
22 TraesCS5D01G300100 chr3A 87.654 81 8 2 3468 3547 1766475 1766554 3.770000e-15 93.5
23 TraesCS5D01G300100 chr4B 87.059 85 6 4 3467 3548 495118315 495118233 1.360000e-14 91.6
24 TraesCS5D01G300100 chr3D 86.747 83 10 1 3467 3548 114693408 114693326 1.360000e-14 91.6


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 TraesCS5D01G300100 chr5D 397423901 397427448 3547 True 6553.0 6553 100.00000 1 3548 1 chr5D.!!$R1 3547
1 TraesCS5D01G300100 chr5A 502785268 502788976 3708 True 1128.5 2983 91.26350 56 3548 4 chr5A.!!$R1 3492
2 TraesCS5D01G300100 chr5B 477609431 477612999 3568 True 1169.5 2207 93.71475 121 3229 4 chr5B.!!$R2 3108

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
833 882 0.393537 CATGCAACTCTCCCACCTCC 60.394 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2814 3387 1.043022 CCCTGGCCAGCATTATTTCC 58.957 55.0 28.39 0.0 0.0 3.13 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
30 31 7.814264 ATAAGAAATAGTTGATTCCCAGCTG 57.186 36.000 6.78 6.78 36.94 4.24
31 32 5.441718 AGAAATAGTTGATTCCCAGCTGA 57.558 39.130 17.39 0.00 36.94 4.26
32 33 5.189180 AGAAATAGTTGATTCCCAGCTGAC 58.811 41.667 17.39 2.95 36.94 3.51
33 34 4.851639 AATAGTTGATTCCCAGCTGACT 57.148 40.909 17.39 11.23 36.94 3.41
34 35 2.486472 AGTTGATTCCCAGCTGACTG 57.514 50.000 17.39 3.18 44.05 3.51
42 43 5.033589 ATTCCCAGCTGACTGAGAATTAG 57.966 43.478 17.39 0.00 45.93 1.73
43 44 4.685575 ATTCCCAGCTGACTGAGAATTAGC 60.686 45.833 17.39 0.00 45.93 3.09
44 45 7.923973 ATTCCCAGCTGACTGAGAATTAGCG 62.924 48.000 17.39 0.00 45.93 4.26
46 47 3.876274 AGCTGACTGAGAATTAGCGAA 57.124 42.857 0.00 0.00 39.27 4.70
47 48 4.193826 AGCTGACTGAGAATTAGCGAAA 57.806 40.909 0.00 0.00 39.27 3.46
48 49 3.929610 AGCTGACTGAGAATTAGCGAAAC 59.070 43.478 0.00 0.00 39.27 2.78
49 50 3.929610 GCTGACTGAGAATTAGCGAAACT 59.070 43.478 0.00 0.00 0.00 2.66
50 51 4.201666 GCTGACTGAGAATTAGCGAAACTG 60.202 45.833 0.00 0.00 0.00 3.16
51 52 4.883083 TGACTGAGAATTAGCGAAACTGT 58.117 39.130 0.00 0.00 0.00 3.55
52 53 6.020971 TGACTGAGAATTAGCGAAACTGTA 57.979 37.500 0.00 0.00 0.00 2.74
53 54 6.631016 TGACTGAGAATTAGCGAAACTGTAT 58.369 36.000 0.00 0.00 0.00 2.29
54 55 7.768240 TGACTGAGAATTAGCGAAACTGTATA 58.232 34.615 0.00 0.00 0.00 1.47
80 81 7.775561 ACTTAATCCTATTTCATCCAGACAACC 59.224 37.037 0.00 0.00 0.00 3.77
81 82 4.503714 TCCTATTTCATCCAGACAACCC 57.496 45.455 0.00 0.00 0.00 4.11
100 101 2.426842 CCCCCTCCTTCTGATCAAAC 57.573 55.000 0.00 0.00 0.00 2.93
101 102 1.918957 CCCCCTCCTTCTGATCAAACT 59.081 52.381 0.00 0.00 0.00 2.66
104 105 3.519510 CCCCTCCTTCTGATCAAACTACA 59.480 47.826 0.00 0.00 0.00 2.74
119 120 6.843752 TCAAACTACAATTCCCAGGAAAGTA 58.156 36.000 2.65 8.67 37.69 2.24
247 249 4.270808 TCTTTTGACTACCGTCCGAAAAAC 59.729 41.667 0.00 0.00 39.47 2.43
295 299 6.873997 TGTAGTTAATACTCACTGTCATGGG 58.126 40.000 0.00 0.00 35.78 4.00
349 353 2.866156 GCAGCGACTTTATATGCACAGA 59.134 45.455 0.00 0.00 36.88 3.41
356 360 5.576774 CGACTTTATATGCACAGAACAGTGA 59.423 40.000 0.00 0.00 42.05 3.41
357 361 6.237675 CGACTTTATATGCACAGAACAGTGAG 60.238 42.308 0.00 0.00 42.05 3.51
426 430 8.471609 GTCTCAGAAGGTAGCTAGATTTAAAGT 58.528 37.037 0.00 0.00 0.00 2.66
431 435 9.036980 AGAAGGTAGCTAGATTTAAAGTCAGAA 57.963 33.333 0.00 0.00 0.00 3.02
443 447 6.867662 TTAAAGTCAGAAGCTTTTCTCTGG 57.132 37.500 12.16 0.00 37.37 3.86
501 507 9.498307 GCTAATGCACGTACTTAAACAAATTAT 57.502 29.630 0.00 0.00 39.41 1.28
504 510 9.769093 AATGCACGTACTTAAACAAATTATCTC 57.231 29.630 0.00 0.00 0.00 2.75
505 511 8.542497 TGCACGTACTTAAACAAATTATCTCT 57.458 30.769 0.00 0.00 0.00 3.10
506 512 8.995220 TGCACGTACTTAAACAAATTATCTCTT 58.005 29.630 0.00 0.00 0.00 2.85
525 561 7.554959 TCTCTTTACAGAGGGAGTAATTTGT 57.445 36.000 6.07 0.00 46.17 2.83
526 562 8.660295 TCTCTTTACAGAGGGAGTAATTTGTA 57.340 34.615 6.07 0.00 46.17 2.41
536 572 5.656859 AGGGAGTAATTTGTAGGGAAAATGC 59.343 40.000 0.00 0.00 0.00 3.56
671 707 3.260632 CCCACCCCACAAAAATTTCCTAG 59.739 47.826 0.00 0.00 0.00 3.02
672 708 3.901222 CCACCCCACAAAAATTTCCTAGT 59.099 43.478 0.00 0.00 0.00 2.57
718 766 6.248433 TGGGCATCTCCTCCATTATTAATTC 58.752 40.000 0.00 0.00 34.39 2.17
820 869 6.604396 AGTGATGATTTGGTCTTATCATGCAA 59.396 34.615 0.00 0.00 40.58 4.08
826 875 4.142609 TGGTCTTATCATGCAACTCTCC 57.857 45.455 0.00 0.00 0.00 3.71
828 877 3.118261 GGTCTTATCATGCAACTCTCCCA 60.118 47.826 0.00 0.00 0.00 4.37
830 879 3.118261 TCTTATCATGCAACTCTCCCACC 60.118 47.826 0.00 0.00 0.00 4.61
831 880 1.293062 ATCATGCAACTCTCCCACCT 58.707 50.000 0.00 0.00 0.00 4.00
832 881 0.615331 TCATGCAACTCTCCCACCTC 59.385 55.000 0.00 0.00 0.00 3.85
833 882 0.393537 CATGCAACTCTCCCACCTCC 60.394 60.000 0.00 0.00 0.00 4.30
834 883 0.548682 ATGCAACTCTCCCACCTCCT 60.549 55.000 0.00 0.00 0.00 3.69
1023 1546 0.543749 CAGGATTCTCACACCTCCCC 59.456 60.000 0.00 0.00 31.06 4.81
1045 1568 0.320247 GCAGATGGAGTATGGCCTCG 60.320 60.000 3.32 0.00 31.98 4.63
1222 1757 2.759355 CCCACTCCAAGGTACTCCATA 58.241 52.381 0.00 0.00 38.49 2.74
1288 1833 7.350744 TCATTATTGCTGTTGCTTATGGATT 57.649 32.000 0.00 0.00 40.48 3.01
1289 1834 7.784037 TCATTATTGCTGTTGCTTATGGATTT 58.216 30.769 0.00 0.00 40.48 2.17
1291 1836 8.545420 CATTATTGCTGTTGCTTATGGATTTTC 58.455 33.333 0.00 0.00 40.48 2.29
1292 1837 4.454728 TGCTGTTGCTTATGGATTTTCC 57.545 40.909 0.00 0.00 40.48 3.13
1492 2037 7.816995 TGCTCTTCTTCACTATCTTTTCTCTTC 59.183 37.037 0.00 0.00 0.00 2.87
1678 2224 5.163447 TGACCACTCCTAATTAGAATCACCG 60.163 44.000 14.28 0.00 0.00 4.94
1760 2311 5.097742 TGATTTGTGTATAGGTCACTGGG 57.902 43.478 0.00 0.00 36.83 4.45
1889 2442 1.280421 ACTCAAGCCTTGGAGATGTCC 59.720 52.381 4.30 0.83 44.24 4.02
1891 2444 1.556911 TCAAGCCTTGGAGATGTCCTC 59.443 52.381 10.72 0.00 44.30 3.71
2018 2575 1.002659 TGACCAATCACAAGTACGGGG 59.997 52.381 0.00 0.00 0.00 5.73
2019 2576 1.276989 GACCAATCACAAGTACGGGGA 59.723 52.381 0.00 0.00 0.00 4.81
2275 2846 2.604382 GCACCCAGGTTTGGCCAT 60.604 61.111 6.09 0.00 43.58 4.40
2276 2847 2.216331 GCACCCAGGTTTGGCCATT 61.216 57.895 6.09 0.00 43.58 3.16
2277 2848 1.767654 GCACCCAGGTTTGGCCATTT 61.768 55.000 6.09 0.00 43.58 2.32
2278 2849 0.321346 CACCCAGGTTTGGCCATTTC 59.679 55.000 6.09 0.00 43.58 2.17
2279 2850 0.190815 ACCCAGGTTTGGCCATTTCT 59.809 50.000 6.09 0.59 43.58 2.52
2280 2851 0.897621 CCCAGGTTTGGCCATTTCTC 59.102 55.000 6.09 0.00 43.58 2.87
2281 2852 1.550869 CCCAGGTTTGGCCATTTCTCT 60.551 52.381 6.09 0.00 43.58 3.10
2282 2853 1.821136 CCAGGTTTGGCCATTTCTCTC 59.179 52.381 6.09 0.00 37.73 3.20
2283 2854 2.556114 CCAGGTTTGGCCATTTCTCTCT 60.556 50.000 6.09 0.00 37.73 3.10
2284 2855 2.751806 CAGGTTTGGCCATTTCTCTCTC 59.248 50.000 6.09 0.00 40.61 3.20
2285 2856 2.646798 AGGTTTGGCCATTTCTCTCTCT 59.353 45.455 6.09 0.00 40.61 3.10
2286 2857 3.013219 GGTTTGGCCATTTCTCTCTCTC 58.987 50.000 6.09 0.00 37.17 3.20
2287 2858 3.308046 GGTTTGGCCATTTCTCTCTCTCT 60.308 47.826 6.09 0.00 37.17 3.10
2288 2859 3.902881 TTGGCCATTTCTCTCTCTCTC 57.097 47.619 6.09 0.00 0.00 3.20
2289 2860 3.113191 TGGCCATTTCTCTCTCTCTCT 57.887 47.619 0.00 0.00 0.00 3.10
2290 2861 3.030291 TGGCCATTTCTCTCTCTCTCTC 58.970 50.000 0.00 0.00 0.00 3.20
2291 2862 3.299503 GGCCATTTCTCTCTCTCTCTCT 58.700 50.000 0.00 0.00 0.00 3.10
2292 2863 3.319122 GGCCATTTCTCTCTCTCTCTCTC 59.681 52.174 0.00 0.00 0.00 3.20
2293 2864 4.210331 GCCATTTCTCTCTCTCTCTCTCT 58.790 47.826 0.00 0.00 0.00 3.10
2294 2865 4.276926 GCCATTTCTCTCTCTCTCTCTCTC 59.723 50.000 0.00 0.00 0.00 3.20
2295 2866 5.688807 CCATTTCTCTCTCTCTCTCTCTCT 58.311 45.833 0.00 0.00 0.00 3.10
2296 2867 5.762218 CCATTTCTCTCTCTCTCTCTCTCTC 59.238 48.000 0.00 0.00 0.00 3.20
2297 2868 6.409005 CCATTTCTCTCTCTCTCTCTCTCTCT 60.409 46.154 0.00 0.00 0.00 3.10
2298 2869 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
2299 2870 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2300 2871 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2301 2872 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2302 2873 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2303 2874 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2304 2875 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2305 2876 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2306 2877 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2307 2878 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2308 2879 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2309 2880 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2310 2881 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2311 2882 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2312 2883 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2313 2884 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2316 2887 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2392 2963 5.048782 TCCAAAGCACTGTTCAATGTACATC 60.049 40.000 9.23 0.00 0.00 3.06
2588 3160 5.717078 TGACAACGTCTAGGTAAAGTGAT 57.283 39.130 0.00 0.00 33.15 3.06
2637 3209 2.435805 AGTAGGCATCATACCACTGTGG 59.564 50.000 24.80 24.80 45.02 4.17
2761 3334 8.943085 ACCCAGATGATTAGTTCTAATCTGATT 58.057 33.333 23.93 8.14 44.53 2.57
2813 3386 2.354704 CGTTTGTGATTAGCAGGGGAGA 60.355 50.000 0.00 0.00 0.00 3.71
2814 3387 3.274288 GTTTGTGATTAGCAGGGGAGAG 58.726 50.000 0.00 0.00 0.00 3.20
2840 3413 4.052518 GCTGGCCAGGGTGGTGAT 62.053 66.667 33.46 0.00 40.46 3.06
3123 3696 2.796593 GCCATTTCTGCTGTGACAAAAC 59.203 45.455 0.00 0.00 0.00 2.43
3275 4110 0.896923 TACGCGGAAATACCCAGTGT 59.103 50.000 12.47 0.00 34.64 3.55
3276 4111 0.672401 ACGCGGAAATACCCAGTGTG 60.672 55.000 12.47 0.00 34.64 3.82
3308 4143 4.888326 CAATGGACCTGGATTGGAAAAA 57.112 40.909 0.00 0.00 0.00 1.94
3309 4144 4.568956 CAATGGACCTGGATTGGAAAAAC 58.431 43.478 0.00 0.00 0.00 2.43
3310 4145 3.611025 TGGACCTGGATTGGAAAAACT 57.389 42.857 0.00 0.00 0.00 2.66
3311 4146 4.733077 TGGACCTGGATTGGAAAAACTA 57.267 40.909 0.00 0.00 0.00 2.24
3312 4147 5.068215 TGGACCTGGATTGGAAAAACTAA 57.932 39.130 0.00 0.00 0.00 2.24
3318 4153 8.721133 ACCTGGATTGGAAAAACTAATTTAGT 57.279 30.769 0.00 3.16 41.73 2.24
3414 4249 3.251817 CGCGAGGAAATAGCTTCGA 57.748 52.632 0.00 0.00 39.40 3.71
3415 4250 0.847035 CGCGAGGAAATAGCTTCGAC 59.153 55.000 0.00 0.00 39.40 4.20
3416 4251 1.209998 GCGAGGAAATAGCTTCGACC 58.790 55.000 7.39 0.04 39.40 4.79
3424 4259 2.017559 ATAGCTTCGACCGGCTCCAC 62.018 60.000 0.00 0.00 39.65 4.02
3433 4268 0.605589 ACCGGCTCCACTGCTAAAAC 60.606 55.000 0.00 0.00 0.00 2.43
3444 4282 8.608317 GCTCCACTGCTAAAACAAAAATAAAAA 58.392 29.630 0.00 0.00 0.00 1.94
3515 4353 4.761975 TCGTGAAGATACCAATTACACCC 58.238 43.478 0.00 0.00 0.00 4.61
3516 4354 4.223255 TCGTGAAGATACCAATTACACCCA 59.777 41.667 0.00 0.00 0.00 4.51
3517 4355 4.938832 CGTGAAGATACCAATTACACCCAA 59.061 41.667 0.00 0.00 0.00 4.12
3519 4357 6.238374 CGTGAAGATACCAATTACACCCAATC 60.238 42.308 0.00 0.00 0.00 2.67
3532 4370 1.076024 ACCCAATCTCTGCACCAACAT 59.924 47.619 0.00 0.00 0.00 2.71
3537 4375 1.456296 TCTCTGCACCAACATGATGC 58.544 50.000 0.00 4.38 37.42 3.91
3539 4377 0.966875 TCTGCACCAACATGATGCCC 60.967 55.000 0.00 0.00 35.54 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.342308 CAGCTGGGAATCAACTATTTCTTATTA 57.658 33.333 5.57 0.00 0.00 0.98
5 6 8.055181 TCAGCTGGGAATCAACTATTTCTTATT 58.945 33.333 15.13 0.00 0.00 1.40
6 7 7.500559 GTCAGCTGGGAATCAACTATTTCTTAT 59.499 37.037 15.13 0.00 0.00 1.73
7 8 6.823689 GTCAGCTGGGAATCAACTATTTCTTA 59.176 38.462 15.13 0.00 0.00 2.10
8 9 5.649831 GTCAGCTGGGAATCAACTATTTCTT 59.350 40.000 15.13 0.00 0.00 2.52
9 10 5.045286 AGTCAGCTGGGAATCAACTATTTCT 60.045 40.000 15.13 0.00 0.00 2.52
10 11 5.065731 CAGTCAGCTGGGAATCAACTATTTC 59.934 44.000 15.13 0.00 39.01 2.17
11 12 4.946157 CAGTCAGCTGGGAATCAACTATTT 59.054 41.667 15.13 0.00 39.01 1.40
12 13 4.225942 TCAGTCAGCTGGGAATCAACTATT 59.774 41.667 15.13 0.00 42.78 1.73
13 14 3.776969 TCAGTCAGCTGGGAATCAACTAT 59.223 43.478 15.13 0.00 42.78 2.12
14 15 3.173151 TCAGTCAGCTGGGAATCAACTA 58.827 45.455 15.13 0.00 42.78 2.24
15 16 1.980765 TCAGTCAGCTGGGAATCAACT 59.019 47.619 15.13 4.92 42.78 3.16
16 17 2.354259 CTCAGTCAGCTGGGAATCAAC 58.646 52.381 15.13 2.28 45.98 3.18
17 18 2.775911 CTCAGTCAGCTGGGAATCAA 57.224 50.000 15.13 0.00 45.98 2.57
23 24 2.559440 GCTAATTCTCAGTCAGCTGGG 58.441 52.381 15.13 4.18 44.48 4.45
24 25 2.159184 TCGCTAATTCTCAGTCAGCTGG 60.159 50.000 15.13 0.00 42.78 4.85
25 26 3.156511 TCGCTAATTCTCAGTCAGCTG 57.843 47.619 7.63 7.63 43.87 4.24
26 27 3.876274 TTCGCTAATTCTCAGTCAGCT 57.124 42.857 0.00 0.00 0.00 4.24
27 28 3.929610 AGTTTCGCTAATTCTCAGTCAGC 59.070 43.478 0.00 0.00 0.00 4.26
28 29 4.926238 ACAGTTTCGCTAATTCTCAGTCAG 59.074 41.667 0.00 0.00 0.00 3.51
29 30 4.883083 ACAGTTTCGCTAATTCTCAGTCA 58.117 39.130 0.00 0.00 0.00 3.41
30 31 7.916450 AGTATACAGTTTCGCTAATTCTCAGTC 59.084 37.037 5.50 0.00 0.00 3.51
31 32 7.773149 AGTATACAGTTTCGCTAATTCTCAGT 58.227 34.615 5.50 0.00 0.00 3.41
32 33 8.635877 AAGTATACAGTTTCGCTAATTCTCAG 57.364 34.615 5.50 0.00 0.00 3.35
53 54 9.832445 GTTGTCTGGATGAAATAGGATTAAGTA 57.168 33.333 0.00 0.00 0.00 2.24
54 55 7.775561 GGTTGTCTGGATGAAATAGGATTAAGT 59.224 37.037 0.00 0.00 0.00 2.24
81 82 1.918957 AGTTTGATCAGAAGGAGGGGG 59.081 52.381 0.00 0.00 0.00 5.40
90 91 5.250543 TCCTGGGAATTGTAGTTTGATCAGA 59.749 40.000 0.00 0.00 0.00 3.27
91 92 5.500234 TCCTGGGAATTGTAGTTTGATCAG 58.500 41.667 0.00 0.00 0.00 2.90
93 94 6.434340 ACTTTCCTGGGAATTGTAGTTTGATC 59.566 38.462 2.69 0.00 33.79 2.92
95 96 5.701224 ACTTTCCTGGGAATTGTAGTTTGA 58.299 37.500 2.69 0.00 33.79 2.69
96 97 6.715264 AGTACTTTCCTGGGAATTGTAGTTTG 59.285 38.462 8.98 0.00 33.79 2.93
97 98 6.849151 AGTACTTTCCTGGGAATTGTAGTTT 58.151 36.000 8.98 0.00 33.79 2.66
98 99 6.449830 AGTACTTTCCTGGGAATTGTAGTT 57.550 37.500 8.98 3.60 33.79 2.24
99 100 7.624077 AGATAGTACTTTCCTGGGAATTGTAGT 59.376 37.037 0.00 18.15 34.61 2.73
100 101 7.928706 CAGATAGTACTTTCCTGGGAATTGTAG 59.071 40.741 0.00 0.67 33.79 2.74
101 102 7.635089 GCAGATAGTACTTTCCTGGGAATTGTA 60.635 40.741 0.00 7.14 33.79 2.41
104 105 5.191722 TGCAGATAGTACTTTCCTGGGAATT 59.808 40.000 0.00 0.00 33.79 2.17
192 194 4.299978 GTGAGAATACTACCGCTTCCATC 58.700 47.826 0.00 0.00 0.00 3.51
247 249 2.522836 ACTCAAGTGCTGTGACAGAG 57.477 50.000 18.18 6.25 32.44 3.35
349 353 5.940470 CCTAAAAGATAACCTGCTCACTGTT 59.060 40.000 0.00 0.00 0.00 3.16
356 360 4.226168 AGTGCTCCTAAAAGATAACCTGCT 59.774 41.667 0.00 0.00 0.00 4.24
357 361 4.518249 AGTGCTCCTAAAAGATAACCTGC 58.482 43.478 0.00 0.00 0.00 4.85
426 430 2.705658 TGTCCCAGAGAAAAGCTTCTGA 59.294 45.455 13.60 0.00 42.19 3.27
431 435 2.039613 CCTCTTGTCCCAGAGAAAAGCT 59.960 50.000 0.00 0.00 42.81 3.74
443 447 6.716934 TTGACTACTGATATCCTCTTGTCC 57.283 41.667 0.00 0.00 0.00 4.02
501 507 7.554959 ACAAATTACTCCCTCTGTAAAGAGA 57.445 36.000 11.85 0.00 38.13 3.10
502 508 7.982354 CCTACAAATTACTCCCTCTGTAAAGAG 59.018 40.741 2.55 2.55 34.20 2.85
503 509 7.093024 CCCTACAAATTACTCCCTCTGTAAAGA 60.093 40.741 0.00 0.00 34.20 2.52
504 510 7.048512 CCCTACAAATTACTCCCTCTGTAAAG 58.951 42.308 0.00 0.00 34.20 1.85
505 511 6.731919 TCCCTACAAATTACTCCCTCTGTAAA 59.268 38.462 0.00 0.00 34.20 2.01
506 512 6.266080 TCCCTACAAATTACTCCCTCTGTAA 58.734 40.000 0.00 0.00 34.87 2.41
513 549 5.449999 CGCATTTTCCCTACAAATTACTCCC 60.450 44.000 0.00 0.00 0.00 4.30
522 558 2.026636 AGGCTACGCATTTTCCCTACAA 60.027 45.455 0.00 0.00 0.00 2.41
525 561 1.557832 ACAGGCTACGCATTTTCCCTA 59.442 47.619 0.00 0.00 0.00 3.53
526 562 0.328258 ACAGGCTACGCATTTTCCCT 59.672 50.000 0.00 0.00 0.00 4.20
536 572 2.481449 CCTACTTTGGCTACAGGCTACG 60.481 54.545 4.30 0.00 41.69 3.51
541 577 5.476945 ACATTTTTCCTACTTTGGCTACAGG 59.523 40.000 0.00 0.00 0.00 4.00
672 708 9.890629 GCCCATCATATATGAGTTTAGTTGATA 57.109 33.333 19.73 0.00 40.64 2.15
718 766 3.981071 TGTCTCTTGTTGTAGGATGGG 57.019 47.619 0.00 0.00 0.00 4.00
820 869 0.853586 AGAGGAGGAGGTGGGAGAGT 60.854 60.000 0.00 0.00 0.00 3.24
826 875 0.926293 AGAGAGAGAGGAGGAGGTGG 59.074 60.000 0.00 0.00 0.00 4.61
828 877 2.132686 GGTAGAGAGAGAGGAGGAGGT 58.867 57.143 0.00 0.00 0.00 3.85
830 879 4.453480 AATGGTAGAGAGAGAGGAGGAG 57.547 50.000 0.00 0.00 0.00 3.69
831 880 6.012333 GGTATAATGGTAGAGAGAGAGGAGGA 60.012 46.154 0.00 0.00 0.00 3.71
832 881 6.184789 GGTATAATGGTAGAGAGAGAGGAGG 58.815 48.000 0.00 0.00 0.00 4.30
833 882 6.184789 GGGTATAATGGTAGAGAGAGAGGAG 58.815 48.000 0.00 0.00 0.00 3.69
834 883 5.015391 GGGGTATAATGGTAGAGAGAGAGGA 59.985 48.000 0.00 0.00 0.00 3.71
998 1521 2.042162 AGGTGTGAGAATCCTGCCATTT 59.958 45.455 0.00 0.00 0.00 2.32
1288 1833 9.883142 AATTATTTTTCAGTCACAAACAGGAAA 57.117 25.926 0.00 0.00 33.96 3.13
1289 1834 9.883142 AAATTATTTTTCAGTCACAAACAGGAA 57.117 25.926 0.00 0.00 0.00 3.36
1678 2224 5.043248 ACAACAAGTTATTTCAAGTGCAGC 58.957 37.500 0.00 0.00 0.00 5.25
1760 2311 4.521146 TCTCATCCAAAATGAGAGCCTTC 58.479 43.478 12.49 0.00 46.66 3.46
2014 2567 2.766313 TCGAGCATATTGATTTCCCCG 58.234 47.619 0.00 0.00 0.00 5.73
2275 2846 5.960811 AGAGAGAGAGAGAGAGAGAGAGAAA 59.039 44.000 0.00 0.00 0.00 2.52
2276 2847 5.523588 AGAGAGAGAGAGAGAGAGAGAGAA 58.476 45.833 0.00 0.00 0.00 2.87
2277 2848 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2278 2849 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2279 2850 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2280 2851 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2281 2852 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2282 2853 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2283 2854 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2284 2855 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2285 2856 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2286 2857 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2287 2858 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2288 2859 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2289 2860 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2290 2861 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2291 2862 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2292 2863 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2293 2864 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2294 2865 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2295 2866 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2296 2867 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2297 2868 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2298 2869 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2299 2870 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2300 2871 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2301 2872 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2302 2873 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2303 2874 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2304 2875 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2305 2876 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2306 2877 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2307 2878 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2308 2879 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2309 2880 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2310 2881 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2311 2882 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2312 2883 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2313 2884 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2316 2887 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2392 2963 2.513204 CTCATCAGCACGGCAGGG 60.513 66.667 0.00 0.00 0.00 4.45
2588 3160 9.719355 TTACTGAAACTTAAGTGCAGAATCATA 57.281 29.630 30.37 17.11 35.86 2.15
2761 3334 9.394767 GAGAGAGAGATGAGAGCATATATACAA 57.605 37.037 0.00 0.00 34.11 2.41
2772 3345 3.378112 ACGCAAAGAGAGAGAGATGAGAG 59.622 47.826 0.00 0.00 0.00 3.20
2773 3346 3.351740 ACGCAAAGAGAGAGAGATGAGA 58.648 45.455 0.00 0.00 0.00 3.27
2774 3347 3.781079 ACGCAAAGAGAGAGAGATGAG 57.219 47.619 0.00 0.00 0.00 2.90
2775 3348 4.240888 CAAACGCAAAGAGAGAGAGATGA 58.759 43.478 0.00 0.00 0.00 2.92
2776 3349 3.993081 ACAAACGCAAAGAGAGAGAGATG 59.007 43.478 0.00 0.00 0.00 2.90
2777 3350 3.993081 CACAAACGCAAAGAGAGAGAGAT 59.007 43.478 0.00 0.00 0.00 2.75
2778 3351 3.068165 TCACAAACGCAAAGAGAGAGAGA 59.932 43.478 0.00 0.00 0.00 3.10
2813 3386 1.412074 CCCTGGCCAGCATTATTTCCT 60.412 52.381 28.39 0.00 0.00 3.36
2814 3387 1.043022 CCCTGGCCAGCATTATTTCC 58.957 55.000 28.39 0.00 0.00 3.13
2840 3413 3.181451 ACTCATCTGGTGCTTCAACTCAA 60.181 43.478 0.00 0.00 0.00 3.02
3123 3696 6.098679 TGTTTTTGTCCAAGAGTCAATTGTG 58.901 36.000 5.13 0.00 0.00 3.33
3259 4094 1.084289 GACACACTGGGTATTTCCGC 58.916 55.000 0.00 0.00 37.00 5.54
3275 4110 1.229368 TCCATTGGGACCCGAGACA 60.229 57.895 6.61 0.00 38.64 3.41
3276 4111 3.721868 TCCATTGGGACCCGAGAC 58.278 61.111 6.61 0.00 38.64 3.36
3333 4168 8.052141 TGATTCCAAAAGGTTGAAGGAATTTTT 58.948 29.630 6.47 0.00 46.14 1.94
3343 4178 6.477053 TCATGTTTGATTCCAAAAGGTTGA 57.523 33.333 0.00 0.00 43.18 3.18
3396 4231 0.847035 GTCGAAGCTATTTCCTCGCG 59.153 55.000 0.00 0.00 31.82 5.87
3399 4234 1.854227 CCGGTCGAAGCTATTTCCTC 58.146 55.000 0.00 0.00 31.82 3.71
3400 4235 0.179081 GCCGGTCGAAGCTATTTCCT 60.179 55.000 1.90 0.00 31.82 3.36
3402 4237 1.209998 GAGCCGGTCGAAGCTATTTC 58.790 55.000 1.90 0.00 40.11 2.17
3403 4238 0.179081 GGAGCCGGTCGAAGCTATTT 60.179 55.000 1.90 0.00 40.11 1.40
3404 4239 1.327690 TGGAGCCGGTCGAAGCTATT 61.328 55.000 1.90 0.00 40.11 1.73
3405 4240 1.756950 TGGAGCCGGTCGAAGCTAT 60.757 57.895 1.90 0.00 40.11 2.97
3406 4241 2.361992 TGGAGCCGGTCGAAGCTA 60.362 61.111 1.90 0.00 40.11 3.32
3407 4242 4.070552 GTGGAGCCGGTCGAAGCT 62.071 66.667 1.90 5.61 43.55 3.74
3408 4243 4.070552 AGTGGAGCCGGTCGAAGC 62.071 66.667 1.90 0.00 0.00 3.86
3409 4244 2.125912 CAGTGGAGCCGGTCGAAG 60.126 66.667 1.90 0.00 0.00 3.79
3410 4245 4.373116 GCAGTGGAGCCGGTCGAA 62.373 66.667 1.90 0.00 0.00 3.71
3411 4246 3.931190 TAGCAGTGGAGCCGGTCGA 62.931 63.158 1.90 0.00 34.23 4.20
3412 4247 2.501223 TTTAGCAGTGGAGCCGGTCG 62.501 60.000 1.90 0.00 34.23 4.79
3413 4248 0.321298 TTTTAGCAGTGGAGCCGGTC 60.321 55.000 1.90 0.00 34.23 4.79
3414 4249 0.605589 GTTTTAGCAGTGGAGCCGGT 60.606 55.000 1.90 0.00 34.23 5.28
3415 4250 0.605319 TGTTTTAGCAGTGGAGCCGG 60.605 55.000 0.00 0.00 34.23 6.13
3416 4251 1.234821 TTGTTTTAGCAGTGGAGCCG 58.765 50.000 0.00 0.00 34.23 5.52
3444 4282 7.945033 AATCACGCTTTTTGTATTCACAATT 57.055 28.000 0.00 0.00 44.01 2.32
3495 4333 6.828785 AGATTGGGTGTAATTGGTATCTTCAC 59.171 38.462 0.00 0.00 0.00 3.18
3504 4342 3.129287 GTGCAGAGATTGGGTGTAATTGG 59.871 47.826 0.00 0.00 0.00 3.16
3515 4353 4.028852 CATCATGTTGGTGCAGAGATTG 57.971 45.455 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.