Multiple sequence alignment - TraesCS5D01G058100

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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 TraesCS5D01G058100 chr5D 100.000 2552 0 0 1 2552 54920566 54918015 0.000000e+00 4713.0
1 TraesCS5D01G058100 chr5D 87.828 838 76 14 29 847 546467289 546468119 0.000000e+00 959.0
2 TraesCS5D01G058100 chr5D 81.443 1164 184 21 1008 2161 42809084 42807943 0.000000e+00 924.0
3 TraesCS5D01G058100 chr5D 81.250 1184 184 22 972 2135 43135019 43136184 0.000000e+00 922.0
4 TraesCS5D01G058100 chr5D 82.208 1096 170 13 1008 2095 43092093 43093171 0.000000e+00 920.0
5 TraesCS5D01G058100 chr5D 93.127 291 18 2 2263 2552 460237297 460237008 2.860000e-115 425.0
6 TraesCS5D01G058100 chr5D 100.000 89 0 0 3016 3104 54917551 54917463 6.890000e-37 165.0
7 TraesCS5D01G058100 chr5A 92.231 1403 81 12 840 2242 43270460 43269086 0.000000e+00 1962.0
8 TraesCS5D01G058100 chr5A 92.492 1292 72 12 882 2160 42735907 42734628 0.000000e+00 1825.0
9 TraesCS5D01G058100 chr5A 82.188 1106 158 15 1008 2095 32992593 32993677 0.000000e+00 915.0
10 TraesCS5D01G058100 chr5A 80.052 1158 186 27 975 2125 32998966 33000085 0.000000e+00 817.0
11 TraesCS5D01G058100 chr5A 93.638 503 32 0 1659 2161 43268364 43267862 0.000000e+00 752.0
12 TraesCS5D01G058100 chr5A 91.582 297 23 2 2243 2539 566231617 566231911 2.880000e-110 409.0
13 TraesCS5D01G058100 chr5B 91.348 1410 103 11 840 2237 57498869 57497467 0.000000e+00 1910.0
14 TraesCS5D01G058100 chr5B 81.985 1038 163 18 1013 2043 40458478 40459498 0.000000e+00 859.0
15 TraesCS5D01G058100 chr5B 80.874 1098 181 20 1008 2095 40556871 40557949 0.000000e+00 837.0
16 TraesCS5D01G058100 chr5B 79.058 1189 198 32 972 2135 40775532 40776694 0.000000e+00 769.0
17 TraesCS5D01G058100 chr5B 92.308 65 5 0 3016 3080 498296064 498296128 3.300000e-15 93.5
18 TraesCS5D01G058100 chr7A 92.075 858 44 8 1 835 676343979 676344835 0.000000e+00 1186.0
19 TraesCS5D01G058100 chr7A 86.369 829 81 15 1 809 186406760 186407576 0.000000e+00 876.0
20 TraesCS5D01G058100 chr7A 84.652 834 91 19 1 809 36992734 36993555 0.000000e+00 797.0
21 TraesCS5D01G058100 chr7A 83.781 857 101 26 1 829 734607699 734606853 0.000000e+00 778.0
22 TraesCS5D01G058100 chr7A 82.981 852 117 15 1 833 650591431 650592273 0.000000e+00 745.0
23 TraesCS5D01G058100 chr1A 92.169 779 39 5 79 835 566333267 566334045 0.000000e+00 1081.0
24 TraesCS5D01G058100 chr1A 97.590 83 2 0 1 83 566320404 566320486 3.230000e-30 143.0
25 TraesCS5D01G058100 chr2B 87.395 833 75 16 1 810 644419336 644418511 0.000000e+00 929.0
26 TraesCS5D01G058100 chr7D 83.875 862 108 17 1 841 80751664 80750813 0.000000e+00 793.0
27 TraesCS5D01G058100 chr7D 83.100 858 111 20 1 835 507199483 507200329 0.000000e+00 750.0
28 TraesCS5D01G058100 chr7D 93.684 285 17 1 2269 2552 62792532 62792248 2.860000e-115 425.0
29 TraesCS5D01G058100 chr7D 89.157 83 9 0 3022 3104 154601968 154601886 1.520000e-18 104.0
30 TraesCS5D01G058100 chr7B 81.893 856 127 16 1 835 88960432 88959584 0.000000e+00 697.0
31 TraesCS5D01G058100 chr7B 92.135 89 7 0 3016 3104 44240301 44240389 3.250000e-25 126.0
32 TraesCS5D01G058100 chr4D 93.559 295 17 2 2259 2552 481899513 481899806 3.670000e-119 438.0
33 TraesCS5D01G058100 chr4D 92.808 292 20 1 2259 2549 505166126 505166417 3.700000e-114 422.0
34 TraesCS5D01G058100 chr1D 93.220 295 19 1 2259 2552 40470573 40470279 1.710000e-117 433.0
35 TraesCS5D01G058100 chr1D 92.466 292 21 1 2259 2549 407495295 407495586 1.720000e-112 416.0
36 TraesCS5D01G058100 chr1D 89.062 64 7 0 2160 2223 464860447 464860510 2.570000e-11 80.5
37 TraesCS5D01G058100 chr3A 91.558 308 23 2 2243 2549 7331812 7332117 3.700000e-114 422.0
38 TraesCS5D01G058100 chr3A 88.506 87 10 0 3018 3104 729512931 729513017 4.230000e-19 106.0
39 TraesCS5D01G058100 chr3A 90.541 74 7 0 3025 3098 670663897 670663824 7.080000e-17 99.0
40 TraesCS5D01G058100 chr3A 87.500 80 10 0 3025 3104 36910810 36910731 3.300000e-15 93.5
41 TraesCS5D01G058100 chr2D 92.466 292 21 1 2259 2549 25854909 25855200 1.720000e-112 416.0
42 TraesCS5D01G058100 chr2D 93.151 73 5 0 3028 3100 33846072 33846144 1.180000e-19 108.0
43 TraesCS5D01G058100 chr3D 90.909 88 8 0 3016 3103 588762490 588762577 5.440000e-23 119.0
44 TraesCS5D01G058100 chr2A 87.640 89 11 0 3016 3104 736200299 736200211 1.520000e-18 104.0


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 TraesCS5D01G058100 chr5D 54917463 54920566 3103 True 2439 4713 100.0000 1 3104 2 chr5D.!!$R3 3103
1 TraesCS5D01G058100 chr5D 546467289 546468119 830 False 959 959 87.8280 29 847 1 chr5D.!!$F3 818
2 TraesCS5D01G058100 chr5D 42807943 42809084 1141 True 924 924 81.4430 1008 2161 1 chr5D.!!$R1 1153
3 TraesCS5D01G058100 chr5D 43135019 43136184 1165 False 922 922 81.2500 972 2135 1 chr5D.!!$F2 1163
4 TraesCS5D01G058100 chr5D 43092093 43093171 1078 False 920 920 82.2080 1008 2095 1 chr5D.!!$F1 1087
5 TraesCS5D01G058100 chr5A 42734628 42735907 1279 True 1825 1825 92.4920 882 2160 1 chr5A.!!$R1 1278
6 TraesCS5D01G058100 chr5A 43267862 43270460 2598 True 1357 1962 92.9345 840 2242 2 chr5A.!!$R2 1402
7 TraesCS5D01G058100 chr5A 32992593 32993677 1084 False 915 915 82.1880 1008 2095 1 chr5A.!!$F1 1087
8 TraesCS5D01G058100 chr5A 32998966 33000085 1119 False 817 817 80.0520 975 2125 1 chr5A.!!$F2 1150
9 TraesCS5D01G058100 chr5B 57497467 57498869 1402 True 1910 1910 91.3480 840 2237 1 chr5B.!!$R1 1397
10 TraesCS5D01G058100 chr5B 40458478 40459498 1020 False 859 859 81.9850 1013 2043 1 chr5B.!!$F1 1030
11 TraesCS5D01G058100 chr5B 40556871 40557949 1078 False 837 837 80.8740 1008 2095 1 chr5B.!!$F2 1087
12 TraesCS5D01G058100 chr5B 40775532 40776694 1162 False 769 769 79.0580 972 2135 1 chr5B.!!$F3 1163
13 TraesCS5D01G058100 chr7A 676343979 676344835 856 False 1186 1186 92.0750 1 835 1 chr7A.!!$F4 834
14 TraesCS5D01G058100 chr7A 186406760 186407576 816 False 876 876 86.3690 1 809 1 chr7A.!!$F2 808
15 TraesCS5D01G058100 chr7A 36992734 36993555 821 False 797 797 84.6520 1 809 1 chr7A.!!$F1 808
16 TraesCS5D01G058100 chr7A 734606853 734607699 846 True 778 778 83.7810 1 829 1 chr7A.!!$R1 828
17 TraesCS5D01G058100 chr7A 650591431 650592273 842 False 745 745 82.9810 1 833 1 chr7A.!!$F3 832
18 TraesCS5D01G058100 chr1A 566333267 566334045 778 False 1081 1081 92.1690 79 835 1 chr1A.!!$F2 756
19 TraesCS5D01G058100 chr2B 644418511 644419336 825 True 929 929 87.3950 1 810 1 chr2B.!!$R1 809
20 TraesCS5D01G058100 chr7D 80750813 80751664 851 True 793 793 83.8750 1 841 1 chr7D.!!$R2 840
21 TraesCS5D01G058100 chr7D 507199483 507200329 846 False 750 750 83.1000 1 835 1 chr7D.!!$F1 834
22 TraesCS5D01G058100 chr7B 88959584 88960432 848 True 697 697 81.8930 1 835 1 chr7B.!!$R1 834

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
965 1046 0.318762 GCAGTCGTCTTCCACTCCTT 59.681 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2338 2466 0.038526 GGGCTACACCGACGGATATG 60.039 60.0 23.38 11.4 40.62 1.78 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
21 22 1.066143 ACTTCGCCGGAGATGTTGATT 60.066 47.619 18.96 0.00 0.00 2.57
115 116 1.681538 GTGGTCGCTCTCTCATCCTA 58.318 55.000 0.00 0.00 0.00 2.94
127 128 2.625314 TCTCATCCTATGAAGCCGAGTG 59.375 50.000 0.00 0.00 39.11 3.51
129 130 0.394565 ATCCTATGAAGCCGAGTGCC 59.605 55.000 0.00 0.00 42.71 5.01
263 279 3.490348 ACCCTGTTTTCCATGACAGAAG 58.510 45.455 12.56 7.11 44.65 2.85
274 290 2.259266 TGACAGAAGCAAGCACATCA 57.741 45.000 0.00 0.00 0.00 3.07
397 413 1.827399 GCCTCGGGTGAAGTTCCAGA 61.827 60.000 0.00 0.00 0.00 3.86
477 496 5.049129 GTCAGTTAATCAGCTGCAGAAGTTT 60.049 40.000 20.43 11.98 33.31 2.66
480 501 3.911661 AATCAGCTGCAGAAGTTTGTC 57.088 42.857 20.43 0.00 0.00 3.18
511 538 5.687780 TCGACAGATATAGGTGTAGGTTCA 58.312 41.667 0.00 0.00 0.00 3.18
835 902 1.791103 GCTCGAGCGCTAGGTCTGAT 61.791 60.000 23.61 0.00 42.35 2.90
852 919 1.672363 TGATAGCAAAATGGCAGAGCG 59.328 47.619 0.00 0.00 35.83 5.03
856 923 2.359850 AAAATGGCAGAGCGCGGA 60.360 55.556 8.83 0.00 43.84 5.54
857 924 2.690778 AAAATGGCAGAGCGCGGAC 61.691 57.895 8.83 0.00 43.84 4.79
859 926 4.827087 ATGGCAGAGCGCGGACAG 62.827 66.667 8.83 1.61 43.84 3.51
902 969 1.425412 CCACGTGAAGGTAAACGAGG 58.575 55.000 19.30 0.00 42.57 4.63
906 973 2.257034 CGTGAAGGTAAACGAGGCTAC 58.743 52.381 0.00 0.00 42.32 3.58
907 974 2.094854 CGTGAAGGTAAACGAGGCTACT 60.095 50.000 0.00 0.00 42.32 2.57
908 975 3.127548 CGTGAAGGTAAACGAGGCTACTA 59.872 47.826 0.00 0.00 42.32 1.82
912 979 3.424703 AGGTAAACGAGGCTACTACACA 58.575 45.455 0.00 0.00 0.00 3.72
920 987 2.490903 GAGGCTACTACACAAGTTCCGA 59.509 50.000 0.00 0.00 39.80 4.55
938 1019 7.141363 AGTTCCGATTTTTCTTTCTGAATGTG 58.859 34.615 3.59 0.00 34.24 3.21
952 1033 1.728971 GAATGTGAACAGAGGCAGTCG 59.271 52.381 0.00 0.00 0.00 4.18
963 1044 1.079750 GGCAGTCGTCTTCCACTCC 60.080 63.158 0.00 0.00 0.00 3.85
965 1046 0.318762 GCAGTCGTCTTCCACTCCTT 59.681 55.000 0.00 0.00 0.00 3.36
994 1075 2.859273 CTACCTCAGCCCAACGCCAG 62.859 65.000 0.00 0.00 38.78 4.85
995 1076 4.020617 CCTCAGCCCAACGCCAGA 62.021 66.667 0.00 0.00 38.78 3.86
996 1077 2.032528 CTCAGCCCAACGCCAGAA 59.967 61.111 0.00 0.00 38.78 3.02
997 1078 1.377725 CTCAGCCCAACGCCAGAAT 60.378 57.895 0.00 0.00 38.78 2.40
1003 1084 1.802508 GCCCAACGCCAGAATTAATGC 60.803 52.381 0.00 0.00 0.00 3.56
1182 1263 5.106317 CGTCAAGTATTACCCAAACAGCAAT 60.106 40.000 0.00 0.00 0.00 3.56
1262 1373 2.452600 AAGGCCAAAGTCACCTTCAA 57.547 45.000 5.01 0.00 39.65 2.69
1299 1410 2.846206 TGGAGAACCAGTGCCTTCATAT 59.154 45.455 0.00 0.00 41.77 1.78
1448 1565 0.036388 GTGGCCGTGAAGAAGATCCA 60.036 55.000 0.00 0.00 0.00 3.41
1451 1568 2.503765 TGGCCGTGAAGAAGATCCATAA 59.496 45.455 0.00 0.00 0.00 1.90
1580 1697 1.335132 GGTGGCCAGGTATTCGAGGA 61.335 60.000 5.11 0.00 0.00 3.71
1789 1906 3.517602 ACGCACGAAGATATAGCAACAA 58.482 40.909 0.00 0.00 0.00 2.83
2016 2135 7.724061 AGTGATGGTTACCAACATCTAAAAAGT 59.276 33.333 17.06 0.00 42.96 2.66
2078 2197 2.541288 CTGTTGAGCTGACAGCAGG 58.459 57.895 28.43 8.28 45.56 4.85
2137 2261 3.863424 GTGTGTGGGTACTAATGATCGTG 59.137 47.826 0.00 0.00 0.00 4.35
2242 2370 8.333186 ACGACAAATAAATATTTAGAACGGAGC 58.667 33.333 13.15 0.00 34.36 4.70
2243 2371 8.332464 CGACAAATAAATATTTAGAACGGAGCA 58.668 33.333 13.15 0.00 34.36 4.26
2244 2372 9.434559 GACAAATAAATATTTAGAACGGAGCAC 57.565 33.333 13.15 0.00 34.36 4.40
2245 2373 9.174166 ACAAATAAATATTTAGAACGGAGCACT 57.826 29.630 13.15 0.00 34.36 4.40
2248 2376 8.828688 ATAAATATTTAGAACGGAGCACTACC 57.171 34.615 13.15 0.00 0.00 3.18
2254 2382 4.732106 CGGAGCACTACCGGAATC 57.268 61.111 9.46 0.00 45.65 2.52
2255 2383 1.299165 CGGAGCACTACCGGAATCG 60.299 63.158 9.46 0.00 45.65 3.34
2256 2384 1.591863 GGAGCACTACCGGAATCGC 60.592 63.158 9.46 5.39 34.56 4.58
2257 2385 1.141019 GAGCACTACCGGAATCGCA 59.859 57.895 9.46 0.00 34.56 5.10
2258 2386 1.146358 GAGCACTACCGGAATCGCAC 61.146 60.000 9.46 0.00 34.56 5.34
2261 2389 1.684734 ACTACCGGAATCGCACCCT 60.685 57.895 9.46 0.00 34.56 4.34
2263 2391 2.644555 CTACCGGAATCGCACCCTGG 62.645 65.000 9.46 0.00 34.56 4.45
2268 2396 4.778143 AATCGCACCCTGGCCGTC 62.778 66.667 0.00 0.00 0.00 4.79
2294 2422 4.812476 CCTGATTGGCCGTCGCGA 62.812 66.667 3.71 3.71 35.02 5.87
2295 2423 3.554692 CTGATTGGCCGTCGCGAC 61.555 66.667 28.96 28.96 35.02 5.19
2297 2425 3.554692 GATTGGCCGTCGCGACAG 61.555 66.667 35.71 27.45 35.02 3.51
2347 2475 1.148310 CCATCGGCAACATATCCGTC 58.852 55.000 0.47 0.00 45.44 4.79
2348 2476 0.784178 CATCGGCAACATATCCGTCG 59.216 55.000 0.47 0.00 45.44 5.12
2351 2479 1.487452 CGGCAACATATCCGTCGGTG 61.487 60.000 11.88 4.91 40.72 4.94
2353 2481 1.202440 GGCAACATATCCGTCGGTGTA 60.202 52.381 11.88 6.39 0.00 2.90
2354 2482 2.124903 GCAACATATCCGTCGGTGTAG 58.875 52.381 11.88 3.22 0.00 2.74
2355 2483 2.124903 CAACATATCCGTCGGTGTAGC 58.875 52.381 11.88 0.00 0.00 3.58
2356 2484 0.672342 ACATATCCGTCGGTGTAGCC 59.328 55.000 11.88 0.00 0.00 3.93
2357 2485 0.038526 CATATCCGTCGGTGTAGCCC 60.039 60.000 11.88 0.00 0.00 5.19
2381 2509 3.719214 CCGTCGGCATAGAAAGGC 58.281 61.111 0.00 0.00 0.00 4.35
2386 2514 3.719214 GGCATAGAAAGGCCGTCG 58.281 61.111 0.00 0.00 43.74 5.12
2387 2515 1.887707 GGCATAGAAAGGCCGTCGG 60.888 63.158 6.99 6.99 43.74 4.79
2405 2533 1.597461 GCATAGGCCCTATCCCGAC 59.403 63.158 0.00 0.00 0.00 4.79
2406 2534 1.890894 CATAGGCCCTATCCCGACG 59.109 63.158 0.00 0.00 0.00 5.12
2411 3297 3.126528 CCCTATCCCGACGGTGTC 58.873 66.667 13.94 0.00 0.00 3.67
2412 3298 2.496291 CCCTATCCCGACGGTGTCC 61.496 68.421 13.94 0.00 0.00 4.02
2429 3315 0.589708 TCCGTACATCTATGCCGACG 59.410 55.000 0.00 5.36 33.90 5.12
2430 3316 0.386858 CCGTACATCTATGCCGACGG 60.387 60.000 10.29 10.29 41.85 4.79
2489 3375 4.454948 TCAAGTGCTGACCAACGG 57.545 55.556 0.00 0.00 0.00 4.44
2495 3381 4.187056 GCTGACCAACGGCTACTC 57.813 61.111 0.00 0.00 46.39 2.59
2496 3382 1.805945 GCTGACCAACGGCTACTCG 60.806 63.158 0.00 0.00 46.39 4.18
2497 3383 1.805945 CTGACCAACGGCTACTCGC 60.806 63.158 0.00 0.00 38.13 5.03
2514 3400 3.323000 CCACGTGGCGCATCTATG 58.677 61.111 24.02 0.00 0.00 2.23
2543 3429 4.272100 GCCGTCGGCTTAGTTTGA 57.728 55.556 28.98 0.00 46.69 2.69
2544 3430 2.535588 GCCGTCGGCTTAGTTTGAA 58.464 52.632 28.98 0.00 46.69 2.69
2545 3431 0.869730 GCCGTCGGCTTAGTTTGAAA 59.130 50.000 28.98 0.00 46.69 2.69
2546 3432 1.399343 GCCGTCGGCTTAGTTTGAAAC 60.399 52.381 28.98 0.00 46.69 2.78
2547 3433 2.140717 CCGTCGGCTTAGTTTGAAACT 58.859 47.619 15.57 15.57 45.40 2.66
2548 3434 3.319755 CCGTCGGCTTAGTTTGAAACTA 58.680 45.455 13.39 13.39 42.81 2.24
2549 3435 3.930848 CCGTCGGCTTAGTTTGAAACTAT 59.069 43.478 17.54 0.00 43.09 2.12
2550 3436 4.201685 CCGTCGGCTTAGTTTGAAACTATG 60.202 45.833 17.54 19.16 43.09 2.23
3064 3950 2.843077 GCCGTCGGCTTAGTTTTAAAC 58.157 47.619 28.98 0.00 46.69 2.01
3065 3951 2.481568 GCCGTCGGCTTAGTTTTAAACT 59.518 45.455 28.98 14.99 46.69 2.66
3066 3952 3.679502 GCCGTCGGCTTAGTTTTAAACTA 59.320 43.478 28.98 12.92 46.69 2.24
3067 3953 4.434725 GCCGTCGGCTTAGTTTTAAACTAC 60.435 45.833 28.98 6.94 46.69 2.73
3068 3954 4.201523 CCGTCGGCTTAGTTTTAAACTACG 60.202 45.833 16.10 16.46 43.30 3.51
3074 3960 5.827568 CTTAGTTTTAAACTACGCCGACA 57.172 39.130 16.10 0.85 43.30 4.35
3075 3961 5.827568 TTAGTTTTAAACTACGCCGACAG 57.172 39.130 16.10 0.00 43.30 3.51
3076 3962 2.477754 AGTTTTAAACTACGCCGACAGC 59.522 45.455 8.76 0.00 40.69 4.40
3077 3963 2.443887 TTTAAACTACGCCGACAGCT 57.556 45.000 0.00 0.00 40.39 4.24
3078 3964 3.574284 TTTAAACTACGCCGACAGCTA 57.426 42.857 0.00 0.00 40.39 3.32
3079 3965 2.838386 TAAACTACGCCGACAGCTAG 57.162 50.000 0.00 0.00 40.39 3.42
3080 3966 0.172803 AAACTACGCCGACAGCTAGG 59.827 55.000 0.00 0.00 40.39 3.02
3087 3973 4.554363 CGACAGCTAGGCCGTCGG 62.554 72.222 18.87 6.99 46.59 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.824109 CCGGATGTGCTCTTCCTGTA 59.176 55.000 16.09 0.00 36.23 2.74
263 279 1.510623 CGCGTCTTGATGTGCTTGC 60.511 57.895 0.00 0.00 0.00 4.01
274 290 2.673368 GGATGAAGTGAAATCGCGTCTT 59.327 45.455 5.77 0.00 36.18 3.01
397 413 2.046507 CAGCTTCTCCCGCAGCTT 60.047 61.111 0.00 0.00 44.28 3.74
445 461 4.269603 CAGCTGATTAACTGACAATCTCCG 59.730 45.833 8.42 0.00 35.90 4.63
477 496 6.377429 ACCTATATCTGTCGAAACTGAAGACA 59.623 38.462 0.00 0.00 41.90 3.41
480 501 6.565234 ACACCTATATCTGTCGAAACTGAAG 58.435 40.000 0.00 0.00 36.98 3.02
511 538 3.215151 TCTGACGAAACTGACAGAGACT 58.785 45.455 10.08 0.00 36.10 3.24
779 827 0.237235 GAAGATGTTTTGTGCCGCGA 59.763 50.000 8.23 0.00 0.00 5.87
835 902 1.802636 GCGCTCTGCCATTTTGCTA 59.197 52.632 0.00 0.00 37.76 3.49
852 919 4.166011 GTTGCATCGCCTGTCCGC 62.166 66.667 0.00 0.00 0.00 5.54
856 923 1.130373 CGTTAATGTTGCATCGCCTGT 59.870 47.619 0.00 0.00 0.00 4.00
857 924 1.396648 TCGTTAATGTTGCATCGCCTG 59.603 47.619 0.00 0.00 0.00 4.85
859 926 1.810197 GTCGTTAATGTTGCATCGCC 58.190 50.000 0.00 0.00 0.00 5.54
902 969 5.857822 AAAATCGGAACTTGTGTAGTAGC 57.142 39.130 0.00 0.00 35.54 3.58
906 973 7.587757 CAGAAAGAAAAATCGGAACTTGTGTAG 59.412 37.037 0.00 0.00 0.00 2.74
907 974 7.281324 TCAGAAAGAAAAATCGGAACTTGTGTA 59.719 33.333 0.00 0.00 0.00 2.90
908 975 6.094881 TCAGAAAGAAAAATCGGAACTTGTGT 59.905 34.615 0.00 0.00 0.00 3.72
912 979 7.649306 CACATTCAGAAAGAAAAATCGGAACTT 59.351 33.333 0.00 0.00 40.22 2.66
920 987 8.139989 CCTCTGTTCACATTCAGAAAGAAAAAT 58.860 33.333 0.00 0.00 40.22 1.82
938 1019 1.670380 GGAAGACGACTGCCTCTGTTC 60.670 57.143 4.45 0.00 38.77 3.18
952 1033 3.990959 AGATTGGAAGGAGTGGAAGAC 57.009 47.619 0.00 0.00 0.00 3.01
990 1071 1.597937 CGCTTCGGCATTAATTCTGGC 60.598 52.381 4.85 4.85 41.88 4.85
994 1075 2.005188 CGACGCTTCGGCATTAATTC 57.995 50.000 4.41 0.00 41.89 2.17
1182 1263 4.041567 ACAGATATGTGACCTGGTTTGTCA 59.958 41.667 6.90 0.00 40.28 3.58
1299 1410 2.809307 TTCCGGGGCGACTTTGACA 61.809 57.895 0.00 0.00 0.00 3.58
1448 1565 5.643348 TGATTTGCATGTGTCTCTTCGTTAT 59.357 36.000 0.00 0.00 0.00 1.89
1451 1568 3.402110 TGATTTGCATGTGTCTCTTCGT 58.598 40.909 0.00 0.00 0.00 3.85
1580 1697 1.109920 AGCGAGCACGGACCTATGAT 61.110 55.000 5.52 0.00 40.15 2.45
1773 1890 3.248602 GGCCAGTTGTTGCTATATCTTCG 59.751 47.826 0.00 0.00 0.00 3.79
1789 1906 1.137086 CGCTACAAGTAGATGGCCAGT 59.863 52.381 13.05 3.89 35.21 4.00
2016 2135 1.134699 CGCAGAAGAGATGGGCAACTA 60.135 52.381 0.00 0.00 0.00 2.24
2078 2197 7.885399 ACTAAATGTCCCTGATAATATCCTTGC 59.115 37.037 0.00 0.00 0.00 4.01
2242 2370 1.520787 GGGTGCGATTCCGGTAGTG 60.521 63.158 0.00 0.00 36.06 2.74
2243 2371 1.684734 AGGGTGCGATTCCGGTAGT 60.685 57.895 0.00 0.00 36.06 2.73
2244 2372 1.227263 CAGGGTGCGATTCCGGTAG 60.227 63.158 0.00 0.00 36.06 3.18
2245 2373 2.727392 CCAGGGTGCGATTCCGGTA 61.727 63.158 0.00 0.00 36.06 4.02
2246 2374 4.096003 CCAGGGTGCGATTCCGGT 62.096 66.667 0.00 0.00 36.06 5.28
2250 2378 4.778143 ACGGCCAGGGTGCGATTC 62.778 66.667 2.24 0.00 0.00 2.52
2251 2379 4.778143 GACGGCCAGGGTGCGATT 62.778 66.667 2.24 0.00 0.00 3.34
2277 2405 4.812476 TCGCGACGGCCAATCAGG 62.812 66.667 3.71 0.00 41.84 3.86
2278 2406 3.554692 GTCGCGACGGCCAATCAG 61.555 66.667 25.19 0.00 35.02 2.90
2286 2414 3.900892 ATAGGCCTGTCGCGACGG 61.901 66.667 35.64 35.64 38.94 4.79
2287 2415 2.655364 CATAGGCCTGTCGCGACG 60.655 66.667 31.88 25.06 38.94 5.12
2333 2461 0.461339 ACACCGACGGATATGTTGCC 60.461 55.000 23.38 0.00 0.00 4.52
2335 2463 2.124903 GCTACACCGACGGATATGTTG 58.875 52.381 23.38 16.01 0.00 3.33
2336 2464 1.068127 GGCTACACCGACGGATATGTT 59.932 52.381 23.38 2.45 0.00 2.71
2338 2466 0.038526 GGGCTACACCGACGGATATG 60.039 60.000 23.38 11.40 40.62 1.78
2340 2468 3.846180 GGGCTACACCGACGGATA 58.154 61.111 23.38 11.46 40.62 2.59
2364 2492 1.887707 GGCCTTTCTATGCCGACGG 60.888 63.158 10.29 10.29 38.00 4.79
2365 2493 3.719214 GGCCTTTCTATGCCGACG 58.281 61.111 0.00 0.00 38.00 5.12
2369 2497 1.887707 CCGACGGCCTTTCTATGCC 60.888 63.158 0.00 0.00 44.41 4.40
2370 2498 2.534903 GCCGACGGCCTTTCTATGC 61.535 63.158 28.74 0.00 44.06 3.14
2371 2499 3.719214 GCCGACGGCCTTTCTATG 58.281 61.111 28.74 0.00 44.06 2.23
2387 2515 1.597461 GTCGGGATAGGGCCTATGC 59.403 63.158 30.77 30.77 34.69 3.14
2388 2516 1.605058 CCGTCGGGATAGGGCCTATG 61.605 65.000 30.27 16.05 34.06 2.23
2389 2517 1.305046 CCGTCGGGATAGGGCCTAT 60.305 63.158 25.93 25.93 34.06 2.57
2390 2518 2.116772 CCGTCGGGATAGGGCCTA 59.883 66.667 17.16 17.16 34.06 3.93
2391 2519 4.153330 ACCGTCGGGATAGGGCCT 62.153 66.667 17.28 12.58 36.97 5.19
2392 2520 3.925090 CACCGTCGGGATAGGGCC 61.925 72.222 17.28 0.00 36.97 5.80
2393 2521 3.148031 GACACCGTCGGGATAGGGC 62.148 68.421 17.28 0.00 36.97 5.19
2394 2522 2.496291 GGACACCGTCGGGATAGGG 61.496 68.421 17.28 0.19 36.97 3.53
2396 2524 2.719979 CGGACACCGTCGGGATAG 59.280 66.667 17.28 5.01 42.73 2.08
2406 2534 1.602165 CGGCATAGATGTACGGACACC 60.602 57.143 0.33 0.00 38.76 4.16
2411 3297 0.386858 CCGTCGGCATAGATGTACGG 60.387 60.000 14.44 14.44 40.96 4.02
2412 3298 3.087638 CCGTCGGCATAGATGTACG 57.912 57.895 0.00 0.00 33.53 3.67
2439 3325 1.270971 TAAGCGATAACGTTGCCGAC 58.729 50.000 22.33 15.08 41.98 4.79
2441 3327 2.067459 GTTAAGCGATAACGTTGCCG 57.933 50.000 11.99 14.71 41.98 5.69
2466 3352 3.414700 GTCAGCACTTGACGGCGG 61.415 66.667 13.24 0.00 46.13 6.13
2472 3358 1.891919 GCCGTTGGTCAGCACTTGA 60.892 57.895 0.00 0.00 0.00 3.02
2473 3359 0.602638 TAGCCGTTGGTCAGCACTTG 60.603 55.000 0.00 0.00 0.00 3.16
2474 3360 0.602905 GTAGCCGTTGGTCAGCACTT 60.603 55.000 0.00 0.00 0.00 3.16
2475 3361 1.004918 GTAGCCGTTGGTCAGCACT 60.005 57.895 0.00 0.00 0.00 4.40
2476 3362 1.004918 AGTAGCCGTTGGTCAGCAC 60.005 57.895 0.00 0.00 0.00 4.40
2477 3363 1.292223 GAGTAGCCGTTGGTCAGCA 59.708 57.895 0.00 0.00 0.00 4.41
2478 3364 1.805945 CGAGTAGCCGTTGGTCAGC 60.806 63.158 0.00 0.00 0.00 4.26
2480 3366 2.260434 GCGAGTAGCCGTTGGTCA 59.740 61.111 0.00 0.00 40.81 4.02
2497 3383 2.885676 GCATAGATGCGCCACGTGG 61.886 63.158 30.66 30.66 44.67 4.94
2498 3384 2.628106 GCATAGATGCGCCACGTG 59.372 61.111 9.08 9.08 44.67 4.49
2527 3413 2.140717 AGTTTCAAACTAAGCCGACGG 58.859 47.619 10.29 10.29 40.69 4.79
2528 3414 4.882447 CATAGTTTCAAACTAAGCCGACG 58.118 43.478 14.02 0.00 46.24 5.12
3043 3929 4.661326 AGTTTAAAACTAAGCCGACGGCC 61.661 47.826 34.33 17.13 45.02 6.13
3044 3930 2.481568 AGTTTAAAACTAAGCCGACGGC 59.518 45.455 31.49 31.49 44.55 5.68
3045 3931 4.201523 CGTAGTTTAAAACTAAGCCGACGG 60.202 45.833 10.29 10.29 44.95 4.79
3046 3932 4.863437 CGTAGTTTAAAACTAAGCCGACG 58.137 43.478 0.00 0.29 44.95 5.12
3052 3938 5.667156 GCTGTCGGCGTAGTTTAAAACTAAG 60.667 44.000 6.85 0.00 44.95 2.18
3053 3939 4.150451 GCTGTCGGCGTAGTTTAAAACTAA 59.850 41.667 6.85 0.00 44.95 2.24
3054 3940 3.674753 GCTGTCGGCGTAGTTTAAAACTA 59.325 43.478 6.85 0.00 42.81 2.24
3055 3941 2.477754 GCTGTCGGCGTAGTTTAAAACT 59.522 45.455 6.85 0.00 45.40 2.66
3056 3942 2.831116 GCTGTCGGCGTAGTTTAAAAC 58.169 47.619 6.85 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.