Multiple sequence alignment - TraesCS5A01G015700

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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 TraesCS5A01G015700 chr5A 100.000 2273 0 0 1 2273 11114754 11117026 0.000000e+00 4198.0
1 TraesCS5A01G015700 chr5A 90.248 1087 77 15 386 1468 42251745 42250684 0.000000e+00 1393.0
2 TraesCS5A01G015700 chr5A 90.649 663 51 7 813 1469 435255728 435256385 0.000000e+00 870.0
3 TraesCS5A01G015700 chr5A 91.354 347 24 3 386 728 435255386 435255730 9.510000e-129 470.0
4 TraesCS5A01G015700 chr5A 85.088 228 29 2 1242 1469 589355159 589354937 6.320000e-56 228.0
5 TraesCS5A01G015700 chr5A 80.751 213 32 9 1488 1696 585400831 585401038 8.410000e-35 158.0
6 TraesCS5A01G015700 chr5A 84.848 66 7 2 174 239 11266910 11266972 1.880000e-06 63.9
7 TraesCS5A01G015700 chr1A 89.478 1093 82 16 386 1465 64548367 64547295 0.000000e+00 1351.0
8 TraesCS5A01G015700 chr6A 89.406 1095 77 15 386 1471 610213043 610214107 0.000000e+00 1343.0
9 TraesCS5A01G015700 chr6A 88.327 1088 89 11 387 1466 526573872 526572815 0.000000e+00 1271.0
10 TraesCS5A01G015700 chr6A 79.294 652 57 39 385 1015 17387874 17387280 3.540000e-103 385.0
11 TraesCS5A01G015700 chr6A 88.462 156 15 3 382 535 68631774 68631620 3.860000e-43 185.0
12 TraesCS5A01G015700 chr7A 87.978 1098 94 19 381 1468 696676945 696678014 0.000000e+00 1262.0
13 TraesCS5A01G015700 chr7A 82.474 97 15 2 1928 2023 669509143 669509238 1.450000e-12 84.2
14 TraesCS5A01G015700 chr5B 90.098 818 64 10 1469 2273 13461246 13462059 0.000000e+00 1046.0
15 TraesCS5A01G015700 chr5B 95.039 383 18 1 4 385 13460871 13461253 3.230000e-168 601.0
16 TraesCS5A01G015700 chr6B 91.991 462 29 8 1014 1468 235427239 235426779 1.900000e-180 641.0
17 TraesCS5A01G015700 chr3B 92.019 426 31 3 1043 1468 687069071 687069493 1.500000e-166 595.0
18 TraesCS5A01G015700 chr3B 80.093 648 64 38 385 1015 687067961 687068560 2.700000e-114 422.0
19 TraesCS5A01G015700 chr2D 89.530 468 36 9 1010 1468 291873323 291872860 4.210000e-162 580.0
20 TraesCS5A01G015700 chr2D 77.021 235 44 8 1469 1698 544207404 544207175 2.370000e-25 126.0
21 TraesCS5A01G015700 chr2D 78.750 160 26 8 1910 2064 497321988 497322144 1.440000e-17 100.0
22 TraesCS5A01G015700 chr2D 93.333 45 1 2 2023 2066 9779305 9779262 5.240000e-07 65.8
23 TraesCS5A01G015700 chr3D 86.334 461 59 4 1010 1468 573603999 573603541 1.210000e-137 499.0
24 TraesCS5A01G015700 chr2B 86.623 456 51 8 1020 1470 249668305 249668755 1.570000e-136 496.0
25 TraesCS5A01G015700 chr2A 82.171 645 45 35 385 1015 39971348 39970760 7.300000e-135 490.0
26 TraesCS5A01G015700 chr1D 83.043 230 36 3 1469 1697 487543480 487543253 2.960000e-49 206.0
27 TraesCS5A01G015700 chr1D 79.487 234 44 4 1471 1701 446291070 446290838 1.810000e-36 163.0
28 TraesCS5A01G015700 chr1B 86.275 102 13 1 1480 1580 678062768 678062869 2.390000e-20 110.0
29 TraesCS5A01G015700 chr7D 79.861 144 28 1 1922 2064 160536058 160535915 1.110000e-18 104.0
30 TraesCS5A01G015700 chr5D 76.301 173 34 6 1529 1699 421999384 421999551 4.020000e-13 86.1
31 TraesCS5A01G015700 chr5D 90.476 42 3 1 1774 1815 533209652 533209692 1.000000e-03 54.7
32 TraesCS5A01G015700 chr4A 86.441 59 8 0 1640 1698 625316926 625316868 5.240000e-07 65.8
33 TraesCS5A01G015700 chrUn 85.000 60 8 1 1640 1699 67391830 67391772 2.440000e-05 60.2


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 TraesCS5A01G015700 chr5A 11114754 11117026 2272 False 4198.0 4198 100.0000 1 2273 1 chr5A.!!$F1 2272
1 TraesCS5A01G015700 chr5A 42250684 42251745 1061 True 1393.0 1393 90.2480 386 1468 1 chr5A.!!$R1 1082
2 TraesCS5A01G015700 chr5A 435255386 435256385 999 False 670.0 870 91.0015 386 1469 2 chr5A.!!$F4 1083
3 TraesCS5A01G015700 chr1A 64547295 64548367 1072 True 1351.0 1351 89.4780 386 1465 1 chr1A.!!$R1 1079
4 TraesCS5A01G015700 chr6A 610213043 610214107 1064 False 1343.0 1343 89.4060 386 1471 1 chr6A.!!$F1 1085
5 TraesCS5A01G015700 chr6A 526572815 526573872 1057 True 1271.0 1271 88.3270 387 1466 1 chr6A.!!$R3 1079
6 TraesCS5A01G015700 chr6A 17387280 17387874 594 True 385.0 385 79.2940 385 1015 1 chr6A.!!$R1 630
7 TraesCS5A01G015700 chr7A 696676945 696678014 1069 False 1262.0 1262 87.9780 381 1468 1 chr7A.!!$F2 1087
8 TraesCS5A01G015700 chr5B 13460871 13462059 1188 False 823.5 1046 92.5685 4 2273 2 chr5B.!!$F1 2269
9 TraesCS5A01G015700 chr3B 687067961 687069493 1532 False 508.5 595 86.0560 385 1468 2 chr3B.!!$F1 1083
10 TraesCS5A01G015700 chr2A 39970760 39971348 588 True 490.0 490 82.1710 385 1015 1 chr2A.!!$R1 630

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
378 380 0.102663 GCTAGACCGGTTAGTGCTCC 59.897 60.0 9.42 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 2484 0.519961 GCGCATTTTAAGGGTCACGT 59.48 50.0 0.3 0.0 0.0 4.49 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
36 37 2.496470 GGAACCAAGTGACTATCGACCT 59.504 50.000 0.00 0.00 0.00 3.85
70 71 3.482436 ACCGATTGTGCTCCAAAAAGTA 58.518 40.909 0.00 0.00 36.44 2.24
74 75 4.142902 CGATTGTGCTCCAAAAAGTATCGT 60.143 41.667 0.00 0.00 36.44 3.73
76 77 2.225491 TGTGCTCCAAAAAGTATCGTGC 59.775 45.455 0.00 0.00 0.00 5.34
141 143 3.978460 GCTCTACTTAGCCTGCTCC 57.022 57.895 0.00 0.00 36.45 4.70
177 179 2.104281 GAGCGGTAATATTGGGTCCAGT 59.896 50.000 0.00 0.00 0.00 4.00
189 191 2.649312 TGGGTCCAGTTTCTCCATGAAT 59.351 45.455 0.00 0.00 34.24 2.57
198 200 8.306038 TCCAGTTTCTCCATGAATTTTGTAATG 58.694 33.333 0.00 0.00 34.24 1.90
270 272 9.896645 TTGAAGATAATCAGATGCTTAAAGACT 57.103 29.630 0.00 0.00 0.00 3.24
307 309 9.997482 TCGTTTTTAAATGGATCTATAAAGTGC 57.003 29.630 0.00 0.00 0.00 4.40
308 310 9.781834 CGTTTTTAAATGGATCTATAAAGTGCA 57.218 29.630 0.00 0.00 0.00 4.57
315 317 8.839310 AATGGATCTATAAAGTGCACATAGTC 57.161 34.615 21.04 15.02 0.00 2.59
316 318 7.360113 TGGATCTATAAAGTGCACATAGTCA 57.640 36.000 21.04 13.35 0.00 3.41
317 319 7.436933 TGGATCTATAAAGTGCACATAGTCAG 58.563 38.462 21.04 8.67 0.00 3.51
318 320 6.367422 GGATCTATAAAGTGCACATAGTCAGC 59.633 42.308 21.04 5.52 0.00 4.26
319 321 6.220726 TCTATAAAGTGCACATAGTCAGCA 57.779 37.500 21.04 0.00 35.63 4.41
320 322 6.639563 TCTATAAAGTGCACATAGTCAGCAA 58.360 36.000 21.04 0.00 40.35 3.91
321 323 3.904136 AAAGTGCACATAGTCAGCAAC 57.096 42.857 21.04 0.00 40.35 4.17
322 324 1.813513 AGTGCACATAGTCAGCAACC 58.186 50.000 21.04 0.00 40.35 3.77
323 325 1.349026 AGTGCACATAGTCAGCAACCT 59.651 47.619 21.04 0.00 40.35 3.50
324 326 2.567169 AGTGCACATAGTCAGCAACCTA 59.433 45.455 21.04 0.00 40.35 3.08
325 327 2.673368 GTGCACATAGTCAGCAACCTAC 59.327 50.000 13.17 0.00 40.35 3.18
326 328 2.280628 GCACATAGTCAGCAACCTACC 58.719 52.381 0.00 0.00 0.00 3.18
327 329 2.906354 CACATAGTCAGCAACCTACCC 58.094 52.381 0.00 0.00 0.00 3.69
328 330 2.236146 CACATAGTCAGCAACCTACCCA 59.764 50.000 0.00 0.00 0.00 4.51
329 331 2.501723 ACATAGTCAGCAACCTACCCAG 59.498 50.000 0.00 0.00 0.00 4.45
332 334 1.151899 TCAGCAACCTACCCAGGGT 60.152 57.895 17.82 17.82 45.62 4.34
338 340 3.965660 CCTACCCAGGGTGCGTAT 58.034 61.111 23.01 0.00 38.41 3.06
339 341 1.445942 CCTACCCAGGGTGCGTATG 59.554 63.158 23.01 4.20 38.41 2.39
340 342 1.227556 CTACCCAGGGTGCGTATGC 60.228 63.158 23.01 0.00 36.19 3.14
362 364 3.449227 CACGCTCAGGGTCCGCTA 61.449 66.667 0.00 0.00 0.00 4.26
363 365 3.141488 ACGCTCAGGGTCCGCTAG 61.141 66.667 0.00 0.00 0.00 3.42
364 366 2.829003 CGCTCAGGGTCCGCTAGA 60.829 66.667 0.00 0.00 0.00 2.43
365 367 2.809010 GCTCAGGGTCCGCTAGAC 59.191 66.667 0.00 0.00 45.51 2.59
375 377 1.226888 CCGCTAGACCGGTTAGTGC 60.227 63.158 21.86 17.07 43.24 4.40
376 378 1.664321 CCGCTAGACCGGTTAGTGCT 61.664 60.000 21.86 12.87 43.24 4.40
377 379 0.248539 CGCTAGACCGGTTAGTGCTC 60.249 60.000 9.42 0.00 0.00 4.26
378 380 0.102663 GCTAGACCGGTTAGTGCTCC 59.897 60.000 9.42 0.00 0.00 4.70
379 381 1.765230 CTAGACCGGTTAGTGCTCCT 58.235 55.000 9.42 0.00 0.00 3.69
383 385 2.660064 CCGGTTAGTGCTCCTGGCT 61.660 63.158 0.00 0.00 42.39 4.75
443 445 4.278170 CCGCATAGAGCCCATAATTTTGAA 59.722 41.667 0.00 0.00 41.38 2.69
535 549 2.125106 CGTTGGAGCTGGGCCTAC 60.125 66.667 4.53 0.00 0.00 3.18
536 550 2.954684 CGTTGGAGCTGGGCCTACA 61.955 63.158 4.53 0.00 31.83 2.74
592 622 4.063689 GCTACTACAGGCTACAGATCGTA 58.936 47.826 1.84 0.00 0.00 3.43
625 656 6.492087 TGGAAAAACAGATCGTCCCTAAAAAT 59.508 34.615 0.00 0.00 0.00 1.82
680 712 6.861065 AGAAAAACGAGATCTTTGTGCTAA 57.139 33.333 0.00 0.00 0.00 3.09
808 848 1.392710 ATCCACGGATCGTCTGGTCC 61.393 60.000 0.00 0.00 38.32 4.46
856 896 2.037772 CCCGACTTCCTCTCCCATATTG 59.962 54.545 0.00 0.00 0.00 1.90
861 901 5.486526 GACTTCCTCTCCCATATTGCATAG 58.513 45.833 0.00 0.00 0.00 2.23
864 904 4.492646 TCCTCTCCCATATTGCATAGTCA 58.507 43.478 0.00 0.00 0.00 3.41
868 911 4.349048 TCTCCCATATTGCATAGTCAGCTT 59.651 41.667 0.00 0.00 0.00 3.74
873 916 5.506815 CCATATTGCATAGTCAGCTTGTTGG 60.507 44.000 0.00 0.00 0.00 3.77
1000 1051 3.410631 TTTGCAGGGATCGTTACTTCA 57.589 42.857 0.00 0.00 0.00 3.02
1016 1067 6.531594 CGTTACTTCATGTCTTCATTAGAGCA 59.468 38.462 0.00 0.00 32.23 4.26
1072 1605 8.960591 CATATAAAGTTCTGTTGACCATTCCTT 58.039 33.333 0.00 0.00 0.00 3.36
1110 1643 9.275398 TCGGCAGAAATAAGTTTTTCTAAGTTA 57.725 29.630 10.65 0.00 42.58 2.24
1154 1687 8.737168 ATGCATACTACTATGACACAACAAAT 57.263 30.769 0.00 0.00 32.66 2.32
1180 1713 2.166829 ACGATTTGGCCACAATAGCAA 58.833 42.857 3.88 0.00 36.29 3.91
1193 1726 5.330295 CACAATAGCAATTGAGAGTGAAGC 58.670 41.667 10.34 0.00 44.50 3.86
1486 2023 4.101448 CTGGCTAGCTGGCGGGTT 62.101 66.667 16.50 0.00 45.14 4.11
1494 2031 3.673484 CTGGCGGGTTGCTTGGTG 61.673 66.667 0.00 0.00 45.43 4.17
1535 2072 2.935481 CCTGGGGCCTGGTCAGAA 60.935 66.667 0.84 0.00 0.00 3.02
1565 2102 1.636148 ACTTGTAGGTAGGGCGACAA 58.364 50.000 0.00 0.00 0.00 3.18
1583 2120 3.420893 ACAATTTTCGCCAGGAAGATGA 58.579 40.909 0.00 0.00 35.70 2.92
1584 2121 3.826157 ACAATTTTCGCCAGGAAGATGAA 59.174 39.130 0.00 0.00 35.70 2.57
1588 2125 6.773976 ATTTTCGCCAGGAAGATGAATTTA 57.226 33.333 0.00 0.00 35.70 1.40
1589 2126 5.818136 TTTCGCCAGGAAGATGAATTTAG 57.182 39.130 0.00 0.00 35.70 1.85
1675 2212 3.591196 TTTTGATGCAAAATCCGGAGG 57.409 42.857 11.34 0.02 43.20 4.30
1681 2218 8.076351 TTTGATGCAAAATCCGGAGGTAATCC 62.076 42.308 11.34 0.00 38.65 3.01
1737 2274 4.601406 AGGACCAAGCCCATAATTAACA 57.399 40.909 0.00 0.00 0.00 2.41
1762 2299 4.955811 TTTCACTCTTGAGCTACCAGAA 57.044 40.909 0.00 0.00 31.71 3.02
1770 2307 5.240891 TCTTGAGCTACCAGAAAACAGATG 58.759 41.667 0.00 0.00 0.00 2.90
1783 2320 4.307032 AAACAGATGGCTTCATACCACT 57.693 40.909 3.03 0.00 40.82 4.00
1800 2337 2.372172 CCACTTCCTACCACCAAGTCTT 59.628 50.000 0.00 0.00 0.00 3.01
1825 2362 2.054453 GGAGCAAGGCATCCCCAAC 61.054 63.158 0.00 0.00 35.39 3.77
1849 2386 8.928270 ACAATCGACGAATAGTTTAATTCTCT 57.072 30.769 0.00 0.00 34.34 3.10
1893 2430 7.545362 AATTGTCTAGTCTGATTGTATGCAC 57.455 36.000 0.00 0.00 0.00 4.57
1894 2431 5.011090 TGTCTAGTCTGATTGTATGCACC 57.989 43.478 0.00 0.00 0.00 5.01
1903 2440 5.293324 TCTGATTGTATGCACCGATTGTTAC 59.707 40.000 0.00 0.00 0.00 2.50
1904 2441 4.938226 TGATTGTATGCACCGATTGTTACA 59.062 37.500 0.00 0.00 0.00 2.41
1905 2442 4.671880 TTGTATGCACCGATTGTTACAC 57.328 40.909 0.00 0.00 30.34 2.90
1913 2450 4.491924 GCACCGATTGTTACACGTATTCAG 60.492 45.833 0.00 0.00 0.00 3.02
1915 2452 4.860907 ACCGATTGTTACACGTATTCAGAC 59.139 41.667 0.00 0.00 0.00 3.51
1949 2486 9.935682 AAAATAGTGTGCTATGATCAAATAACG 57.064 29.630 0.00 0.00 37.92 3.18
1963 2500 8.240682 TGATCAAATAACGTGACCCTTAAAATG 58.759 33.333 0.00 0.00 0.00 2.32
1965 2502 2.981400 AACGTGACCCTTAAAATGCG 57.019 45.000 0.00 0.00 0.00 4.73
1972 2509 5.220700 CGTGACCCTTAAAATGCGCTATTAA 60.221 40.000 9.73 10.40 0.00 1.40
1973 2510 6.512741 CGTGACCCTTAAAATGCGCTATTAAT 60.513 38.462 9.73 0.00 0.00 1.40
1985 2522 9.988350 AAATGCGCTATTAATGTGCTATATTAC 57.012 29.630 9.73 0.00 41.05 1.89
1987 2524 6.120812 GCGCTATTAATGTGCTATATTACGC 58.879 40.000 0.00 0.00 37.87 4.42
2013 2550 5.515797 AGCGTGCTATTAGTGAGACATTA 57.484 39.130 0.00 0.00 0.00 1.90
2044 2581 7.043391 TCGATTATTTACGAAGACATTGCTCAG 60.043 37.037 0.00 0.00 35.62 3.35
2047 2584 5.591643 TTTACGAAGACATTGCTCAGAAC 57.408 39.130 0.00 0.00 0.00 3.01
2048 2585 3.111853 ACGAAGACATTGCTCAGAACA 57.888 42.857 0.00 0.00 0.00 3.18
2049 2586 2.802816 ACGAAGACATTGCTCAGAACAC 59.197 45.455 0.00 0.00 0.00 3.32
2059 2597 1.855360 GCTCAGAACACTATAGCGCAC 59.145 52.381 11.47 0.00 0.00 5.34
2143 2682 6.459066 ACATCATGAATTACCGATAGACCAG 58.541 40.000 0.00 0.00 39.76 4.00
2165 2704 6.071728 CCAGCAAAATTATGACTTGAACTCCT 60.072 38.462 0.00 0.00 0.00 3.69
2170 2709 0.329596 ATGACTTGAACTCCTGCCCC 59.670 55.000 0.00 0.00 0.00 5.80
2178 2717 2.203209 CTCCTGCCCCGCATAACC 60.203 66.667 0.00 0.00 38.13 2.85
2258 2808 1.953686 TGCCACTACCTTTTTCAGTGC 59.046 47.619 0.00 0.00 38.67 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.288961 AAATAACACGCGAGGTCGAT 57.711 45.000 15.93 5.24 43.02 3.59
30 31 2.518949 GTAAATAACACGCGAGGTCGA 58.481 47.619 15.93 2.89 43.02 4.20
36 37 3.061028 CACAATCGGTAAATAACACGCGA 59.939 43.478 15.93 0.00 0.00 5.87
70 71 1.878953 AAAGTGAAGAACCGCACGAT 58.121 45.000 0.00 0.00 39.88 3.73
74 75 1.098869 TGCAAAAGTGAAGAACCGCA 58.901 45.000 0.00 0.00 0.00 5.69
76 77 2.973224 CGAATGCAAAAGTGAAGAACCG 59.027 45.455 0.00 0.00 0.00 4.44
123 125 1.408969 AGGAGCAGGCTAAGTAGAGC 58.591 55.000 0.00 0.00 42.05 4.09
189 191 4.517075 TCCAACGCACTCATCATTACAAAA 59.483 37.500 0.00 0.00 0.00 2.44
198 200 2.205074 CACCTATCCAACGCACTCATC 58.795 52.381 0.00 0.00 0.00 2.92
281 283 9.997482 GCACTTTATAGATCCATTTAAAAACGA 57.003 29.630 0.00 0.00 0.00 3.85
282 284 9.781834 TGCACTTTATAGATCCATTTAAAAACG 57.218 29.630 0.00 0.00 0.00 3.60
289 291 9.277783 GACTATGTGCACTTTATAGATCCATTT 57.722 33.333 22.69 5.08 0.00 2.32
290 292 8.432013 TGACTATGTGCACTTTATAGATCCATT 58.568 33.333 22.69 5.64 0.00 3.16
291 293 7.966812 TGACTATGTGCACTTTATAGATCCAT 58.033 34.615 22.69 6.50 0.00 3.41
292 294 7.360113 TGACTATGTGCACTTTATAGATCCA 57.640 36.000 22.69 15.68 0.00 3.41
293 295 6.367422 GCTGACTATGTGCACTTTATAGATCC 59.633 42.308 22.69 14.03 0.00 3.36
294 296 6.925718 TGCTGACTATGTGCACTTTATAGATC 59.074 38.462 22.69 17.13 0.00 2.75
295 297 6.820335 TGCTGACTATGTGCACTTTATAGAT 58.180 36.000 22.69 8.76 0.00 1.98
296 298 6.220726 TGCTGACTATGTGCACTTTATAGA 57.779 37.500 22.69 1.86 0.00 1.98
297 299 6.238211 GGTTGCTGACTATGTGCACTTTATAG 60.238 42.308 19.41 17.94 36.37 1.31
298 300 5.584649 GGTTGCTGACTATGTGCACTTTATA 59.415 40.000 19.41 6.79 36.37 0.98
299 301 4.396166 GGTTGCTGACTATGTGCACTTTAT 59.604 41.667 19.41 5.86 36.37 1.40
300 302 3.751175 GGTTGCTGACTATGTGCACTTTA 59.249 43.478 19.41 8.99 36.37 1.85
301 303 2.554032 GGTTGCTGACTATGTGCACTTT 59.446 45.455 19.41 8.24 36.37 2.66
302 304 2.154462 GGTTGCTGACTATGTGCACTT 58.846 47.619 19.41 14.68 36.37 3.16
303 305 1.349026 AGGTTGCTGACTATGTGCACT 59.651 47.619 19.41 6.22 36.37 4.40
304 306 1.813513 AGGTTGCTGACTATGTGCAC 58.186 50.000 10.75 10.75 36.37 4.57
305 307 2.354704 GGTAGGTTGCTGACTATGTGCA 60.355 50.000 0.00 0.00 34.69 4.57
306 308 2.280628 GGTAGGTTGCTGACTATGTGC 58.719 52.381 0.00 0.00 0.00 4.57
307 309 2.236146 TGGGTAGGTTGCTGACTATGTG 59.764 50.000 0.00 0.00 0.00 3.21
308 310 2.501723 CTGGGTAGGTTGCTGACTATGT 59.498 50.000 0.00 0.00 0.00 2.29
309 311 2.158900 CCTGGGTAGGTTGCTGACTATG 60.159 54.545 0.00 0.00 39.39 2.23
310 312 2.119495 CCTGGGTAGGTTGCTGACTAT 58.881 52.381 0.00 0.00 39.39 2.12
311 313 1.568504 CCTGGGTAGGTTGCTGACTA 58.431 55.000 0.00 0.00 39.39 2.59
312 314 1.201429 CCCTGGGTAGGTTGCTGACT 61.201 60.000 3.97 0.00 42.96 3.41
313 315 1.299976 CCCTGGGTAGGTTGCTGAC 59.700 63.158 3.97 0.00 42.96 3.51
314 316 1.151899 ACCCTGGGTAGGTTGCTGA 60.152 57.895 18.99 0.00 42.96 4.26
315 317 1.002134 CACCCTGGGTAGGTTGCTG 60.002 63.158 20.09 0.00 42.96 4.41
316 318 3.495729 CACCCTGGGTAGGTTGCT 58.504 61.111 20.09 0.00 42.96 3.91
318 320 1.546589 TACGCACCCTGGGTAGGTTG 61.547 60.000 20.09 7.01 41.98 3.77
319 321 0.619543 ATACGCACCCTGGGTAGGTT 60.620 55.000 20.09 5.88 46.53 3.50
320 322 1.002533 ATACGCACCCTGGGTAGGT 59.997 57.895 20.09 20.42 46.53 3.08
321 323 1.445942 CATACGCACCCTGGGTAGG 59.554 63.158 20.09 15.54 46.53 3.18
322 324 1.227556 GCATACGCACCCTGGGTAG 60.228 63.158 20.09 17.76 46.53 3.18
324 326 4.467084 CGCATACGCACCCTGGGT 62.467 66.667 14.05 14.05 45.76 4.51
326 328 4.467084 ACCGCATACGCACCCTGG 62.467 66.667 0.00 0.00 38.40 4.45
327 329 3.195002 CACCGCATACGCACCCTG 61.195 66.667 0.00 0.00 38.40 4.45
345 347 3.417275 CTAGCGGACCCTGAGCGTG 62.417 68.421 0.00 0.00 35.78 5.34
346 348 3.141488 CTAGCGGACCCTGAGCGT 61.141 66.667 0.00 0.00 35.78 5.07
347 349 2.829003 TCTAGCGGACCCTGAGCG 60.829 66.667 0.00 0.00 35.78 5.03
348 350 2.809010 GTCTAGCGGACCCTGAGC 59.191 66.667 2.17 0.00 38.93 4.26
355 357 0.100146 CACTAACCGGTCTAGCGGAC 59.900 60.000 25.85 4.63 43.79 4.79
356 358 1.660560 GCACTAACCGGTCTAGCGGA 61.661 60.000 25.85 4.79 0.00 5.54
357 359 1.226888 GCACTAACCGGTCTAGCGG 60.227 63.158 18.37 18.37 0.00 5.52
358 360 0.248539 GAGCACTAACCGGTCTAGCG 60.249 60.000 8.04 7.45 0.00 4.26
359 361 0.102663 GGAGCACTAACCGGTCTAGC 59.897 60.000 8.04 10.52 0.00 3.42
360 362 1.405821 CAGGAGCACTAACCGGTCTAG 59.594 57.143 8.04 14.34 0.00 2.43
361 363 1.471119 CAGGAGCACTAACCGGTCTA 58.529 55.000 8.04 1.62 0.00 2.59
362 364 1.258445 CCAGGAGCACTAACCGGTCT 61.258 60.000 8.04 0.00 0.00 3.85
363 365 1.218316 CCAGGAGCACTAACCGGTC 59.782 63.158 8.04 0.00 0.00 4.79
364 366 2.955881 GCCAGGAGCACTAACCGGT 61.956 63.158 0.00 0.00 42.97 5.28
365 367 2.125106 GCCAGGAGCACTAACCGG 60.125 66.667 0.00 0.00 42.97 5.28
443 445 5.402630 CCTACATATAAAATTTGGGGCCCT 58.597 41.667 25.93 4.22 0.00 5.19
535 549 3.003394 TGGCCTCAAGACATAACCATG 57.997 47.619 3.32 0.00 38.21 3.66
536 550 3.745480 CGATGGCCTCAAGACATAACCAT 60.745 47.826 3.32 0.00 39.08 3.55
592 622 6.371825 GGACGATCTGTTTTTCCATCTTACTT 59.628 38.462 0.00 0.00 0.00 2.24
625 656 7.704271 ACAATCTGTTTCTATCTTACGATCGA 58.296 34.615 24.34 2.23 0.00 3.59
638 669 7.562454 TTTTCTTTACGGACAATCTGTTTCT 57.438 32.000 0.00 0.00 37.20 2.52
648 679 5.535333 AGATCTCGTTTTTCTTTACGGACA 58.465 37.500 0.00 0.00 38.26 4.02
808 848 4.918201 GCCCGATGAGGCGAAGGG 62.918 72.222 0.00 0.00 44.57 3.95
856 896 2.286294 CGATCCAACAAGCTGACTATGC 59.714 50.000 0.00 0.00 0.00 3.14
861 901 0.716108 CGACGATCCAACAAGCTGAC 59.284 55.000 0.00 0.00 0.00 3.51
864 904 0.537188 ATCCGACGATCCAACAAGCT 59.463 50.000 0.00 0.00 0.00 3.74
868 911 2.484558 TCGATCCGACGATCCAACA 58.515 52.632 0.00 0.00 41.77 3.33
932 982 4.701651 TGAGTAGGAACCGAAGTTAATCGA 59.298 41.667 0.05 0.00 45.48 3.59
977 1028 4.764823 TGAAGTAACGATCCCTGCAAAAAT 59.235 37.500 0.00 0.00 0.00 1.82
1000 1051 4.815308 GTCATGCTGCTCTAATGAAGACAT 59.185 41.667 0.00 0.00 38.50 3.06
1016 1067 2.028748 GCATTGGGAAAACAGTCATGCT 60.029 45.455 0.00 0.00 0.00 3.79
1052 1585 5.067805 GTCAAAGGAATGGTCAACAGAACTT 59.932 40.000 0.00 0.00 0.00 2.66
1072 1605 4.471761 TGCCGATGCAACTGTCAA 57.528 50.000 0.00 0.00 46.66 3.18
1110 1643 9.442047 GTATGCATATAGGACTTCAATAGCTTT 57.558 33.333 10.16 0.00 0.00 3.51
1154 1687 2.552599 TGTGGCCAAATCGTTGAGTA 57.447 45.000 7.24 0.00 36.83 2.59
1180 1713 2.300152 TCTCCAACGCTTCACTCTCAAT 59.700 45.455 0.00 0.00 0.00 2.57
1193 1726 4.504461 CCTCGTAATCAATCTTCTCCAACG 59.496 45.833 0.00 0.00 0.00 4.10
1478 2015 4.196778 TCACCAAGCAACCCGCCA 62.197 61.111 0.00 0.00 44.04 5.69
1494 2031 3.077359 CACCAAGAAATCTGGTGGTCTC 58.923 50.000 13.13 0.00 46.71 3.36
1502 2039 1.542915 CCAGGCACACCAAGAAATCTG 59.457 52.381 0.00 0.00 39.06 2.90
1526 2063 4.321718 AGTTGATGATGTGTTCTGACCAG 58.678 43.478 0.00 0.00 0.00 4.00
1535 2072 5.338381 CCCTACCTACAAGTTGATGATGTGT 60.338 44.000 10.54 0.00 0.00 3.72
1565 2102 5.665916 AAATTCATCTTCCTGGCGAAAAT 57.334 34.783 0.00 0.00 0.00 1.82
1617 2154 8.488668 TCCATCTTCATCACATTATTCAGAAGA 58.511 33.333 0.00 0.00 42.60 2.87
1710 2247 0.849094 ATGGGCTTGGTCCTTGGGTA 60.849 55.000 0.00 0.00 0.00 3.69
1762 2299 4.307032 AGTGGTATGAAGCCATCTGTTT 57.693 40.909 0.00 0.00 38.40 2.83
1770 2307 2.504175 TGGTAGGAAGTGGTATGAAGCC 59.496 50.000 0.00 0.00 0.00 4.35
1783 2320 7.238096 TCCTTATAAAAGACTTGGTGGTAGGAA 59.762 37.037 0.00 0.00 34.37 3.36
1800 2337 3.436470 GGGGATGCCTTGCTCCTTATAAA 60.436 47.826 2.19 0.00 0.00 1.40
1868 2405 7.066284 GGTGCATACAATCAGACTAGACAATTT 59.934 37.037 0.00 0.00 0.00 1.82
1877 2414 3.827008 ATCGGTGCATACAATCAGACT 57.173 42.857 0.00 0.00 0.00 3.24
1893 2430 4.266976 GGTCTGAATACGTGTAACAATCGG 59.733 45.833 0.00 0.00 35.74 4.18
1894 2431 4.860352 TGGTCTGAATACGTGTAACAATCG 59.140 41.667 0.00 0.00 35.74 3.34
1941 2478 5.285134 CGCATTTTAAGGGTCACGTTATTTG 59.715 40.000 0.00 0.00 0.00 2.32
1947 2484 0.519961 GCGCATTTTAAGGGTCACGT 59.480 50.000 0.30 0.00 0.00 4.49
1949 2486 4.632538 AATAGCGCATTTTAAGGGTCAC 57.367 40.909 11.47 0.00 0.00 3.67
1963 2500 6.019801 AGCGTAATATAGCACATTAATAGCGC 60.020 38.462 0.00 0.00 33.42 5.92
1987 2524 6.242508 TGTCTCACTAATAGCACGCTATAG 57.757 41.667 11.80 11.33 38.20 1.31
2027 2564 3.987868 GTGTTCTGAGCAATGTCTTCGTA 59.012 43.478 0.00 0.00 0.00 3.43
2093 2632 6.780198 TTTATGCCCCTACCTATCAAATCT 57.220 37.500 0.00 0.00 0.00 2.40
2094 2633 8.957466 GTATTTTATGCCCCTACCTATCAAATC 58.043 37.037 0.00 0.00 0.00 2.17
2143 2682 5.574443 GCAGGAGTTCAAGTCATAATTTTGC 59.426 40.000 0.00 0.00 0.00 3.68
2196 2746 4.335082 TTTTCTTTATCGTCGGTGCATG 57.665 40.909 0.00 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.