Multiple sequence alignment - TraesCS2A01G277400

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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 TraesCS2A01G277400 chr2A 100.000 2366 0 0 1 2366 459067329 459069694 0.000000e+00 4370.0
1 TraesCS2A01G277400 chr2A 88.307 1642 161 21 1 1633 761624539 761622920 0.000000e+00 1940.0
2 TraesCS2A01G277400 chr2A 92.105 532 18 1 1859 2366 52225703 52225172 0.000000e+00 728.0
3 TraesCS2A01G277400 chr2A 91.871 529 22 8 1859 2366 52201610 52201082 0.000000e+00 719.0
4 TraesCS2A01G277400 chr2A 96.685 181 6 0 1859 2039 475996352 475996532 3.820000e-78 302.0
5 TraesCS2A01G277400 chr2A 90.055 181 18 0 1859 2039 17419082 17419262 3.930000e-58 235.0
6 TraesCS2A01G277400 chr2A 93.750 80 2 2 1633 1711 761622891 761622814 1.490000e-22 117.0
7 TraesCS2A01G277400 chr3A 88.075 1652 172 17 1 1633 272551576 272553221 0.000000e+00 1936.0
8 TraesCS2A01G277400 chr3A 90.611 458 17 11 1935 2366 87957238 87957695 3.390000e-163 584.0
9 TraesCS2A01G277400 chr3A 91.749 303 9 7 1339 1633 589382599 589382893 7.870000e-110 407.0
10 TraesCS2A01G277400 chr3A 88.387 155 18 0 1704 1858 641867388 641867234 1.120000e-43 187.0
11 TraesCS2A01G277400 chr3A 93.671 79 2 2 1633 1710 589382922 589382998 5.340000e-22 115.0
12 TraesCS2A01G277400 chr3A 90.476 84 4 3 1633 1714 272553250 272553331 8.940000e-20 108.0
13 TraesCS2A01G277400 chr1A 88.063 1642 167 21 1 1633 32285517 32283896 0.000000e+00 1919.0
14 TraesCS2A01G277400 chr1A 90.977 532 23 9 1859 2366 569488687 569488157 0.000000e+00 693.0
15 TraesCS2A01G277400 chrUn 88.526 1377 139 13 272 1633 302503683 302505055 0.000000e+00 1650.0
16 TraesCS2A01G277400 chrUn 88.526 1377 139 13 272 1633 302521789 302523161 0.000000e+00 1650.0
17 TraesCS2A01G277400 chrUn 88.526 1377 139 13 272 1633 325318088 325316716 0.000000e+00 1650.0
18 TraesCS2A01G277400 chrUn 91.941 273 19 2 1 270 82328760 82328488 1.720000e-101 379.0
19 TraesCS2A01G277400 chrUn 91.941 273 19 2 1 270 234384941 234385213 1.720000e-101 379.0
20 TraesCS2A01G277400 chrUn 92.405 79 3 2 1633 1710 302505084 302505160 2.490000e-20 110.0
21 TraesCS2A01G277400 chrUn 92.405 79 3 2 1633 1710 302523190 302523266 2.490000e-20 110.0
22 TraesCS2A01G277400 chrUn 92.405 79 3 2 1633 1710 325316687 325316611 2.490000e-20 110.0
23 TraesCS2A01G277400 chr5A 92.325 899 61 6 1 892 313458711 313457814 0.000000e+00 1271.0
24 TraesCS2A01G277400 chr5A 91.541 532 21 1 1859 2366 100647842 100648373 0.000000e+00 712.0
25 TraesCS2A01G277400 chr5A 90.807 533 25 2 1858 2366 6920906 6920374 0.000000e+00 691.0
26 TraesCS2A01G277400 chr5A 90.226 532 28 6 1859 2366 14989795 14989264 0.000000e+00 673.0
27 TraesCS2A01G277400 chr1B 85.161 775 106 8 2 770 117272750 117271979 0.000000e+00 785.0
28 TraesCS2A01G277400 chr7A 91.806 537 19 7 1855 2366 180345499 180346035 0.000000e+00 725.0
29 TraesCS2A01G277400 chr6A 91.165 532 23 6 1859 2366 92026896 92027427 0.000000e+00 701.0
30 TraesCS2A01G277400 chr6A 91.165 532 23 6 1859 2366 92041298 92041829 0.000000e+00 701.0
31 TraesCS2A01G277400 chr4A 90.414 532 26 7 1859 2366 624594384 624594914 0.000000e+00 676.0
32 TraesCS2A01G277400 chr2D 86.559 558 34 11 1848 2366 181314949 181315504 5.670000e-161 577.0
33 TraesCS2A01G277400 chr2D 87.097 62 4 3 1653 1712 468951214 468951155 1.520000e-07 67.6
34 TraesCS2A01G277400 chr2D 84.127 63 8 2 1653 1714 617220234 617220295 2.540000e-05 60.2
35 TraesCS2A01G277400 chr1D 85.949 548 38 11 1857 2365 487098582 487098035 1.240000e-152 549.0
36 TraesCS2A01G277400 chr1D 86.318 497 28 10 1855 2311 75913536 75913040 2.710000e-139 505.0
37 TraesCS2A01G277400 chr1D 88.693 283 27 4 2 280 462184746 462184465 8.100000e-90 340.0
38 TraesCS2A01G277400 chr6D 95.364 151 7 0 1708 1858 457724516 457724366 8.450000e-60 241.0
39 TraesCS2A01G277400 chr3B 81.690 213 32 6 1893 2100 627621092 627620882 1.120000e-38 171.0
40 TraesCS2A01G277400 chr3B 86.755 151 19 1 1708 1858 664122817 664122668 1.450000e-37 167.0
41 TraesCS2A01G277400 chr5B 87.719 57 4 3 1656 1711 54123668 54123614 1.960000e-06 63.9


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 TraesCS2A01G277400 chr2A 459067329 459069694 2365 False 4370.0 4370 100.0000 1 2366 1 chr2A.!!$F2 2365
1 TraesCS2A01G277400 chr2A 761622814 761624539 1725 True 1028.5 1940 91.0285 1 1711 2 chr2A.!!$R3 1710
2 TraesCS2A01G277400 chr2A 52225172 52225703 531 True 728.0 728 92.1050 1859 2366 1 chr2A.!!$R2 507
3 TraesCS2A01G277400 chr2A 52201082 52201610 528 True 719.0 719 91.8710 1859 2366 1 chr2A.!!$R1 507
4 TraesCS2A01G277400 chr3A 272551576 272553331 1755 False 1022.0 1936 89.2755 1 1714 2 chr3A.!!$F2 1713
5 TraesCS2A01G277400 chr1A 32283896 32285517 1621 True 1919.0 1919 88.0630 1 1633 1 chr1A.!!$R1 1632
6 TraesCS2A01G277400 chr1A 569488157 569488687 530 True 693.0 693 90.9770 1859 2366 1 chr1A.!!$R2 507
7 TraesCS2A01G277400 chrUn 302503683 302505160 1477 False 880.0 1650 90.4655 272 1710 2 chrUn.!!$F2 1438
8 TraesCS2A01G277400 chrUn 302521789 302523266 1477 False 880.0 1650 90.4655 272 1710 2 chrUn.!!$F3 1438
9 TraesCS2A01G277400 chrUn 325316611 325318088 1477 True 880.0 1650 90.4655 272 1710 2 chrUn.!!$R2 1438
10 TraesCS2A01G277400 chr5A 313457814 313458711 897 True 1271.0 1271 92.3250 1 892 1 chr5A.!!$R3 891
11 TraesCS2A01G277400 chr5A 100647842 100648373 531 False 712.0 712 91.5410 1859 2366 1 chr5A.!!$F1 507
12 TraesCS2A01G277400 chr5A 6920374 6920906 532 True 691.0 691 90.8070 1858 2366 1 chr5A.!!$R1 508
13 TraesCS2A01G277400 chr5A 14989264 14989795 531 True 673.0 673 90.2260 1859 2366 1 chr5A.!!$R2 507
14 TraesCS2A01G277400 chr1B 117271979 117272750 771 True 785.0 785 85.1610 2 770 1 chr1B.!!$R1 768
15 TraesCS2A01G277400 chr7A 180345499 180346035 536 False 725.0 725 91.8060 1855 2366 1 chr7A.!!$F1 511
16 TraesCS2A01G277400 chr6A 92026896 92027427 531 False 701.0 701 91.1650 1859 2366 1 chr6A.!!$F1 507
17 TraesCS2A01G277400 chr6A 92041298 92041829 531 False 701.0 701 91.1650 1859 2366 1 chr6A.!!$F2 507
18 TraesCS2A01G277400 chr4A 624594384 624594914 530 False 676.0 676 90.4140 1859 2366 1 chr4A.!!$F1 507
19 TraesCS2A01G277400 chr2D 181314949 181315504 555 False 577.0 577 86.5590 1848 2366 1 chr2D.!!$F1 518
20 TraesCS2A01G277400 chr1D 487098035 487098582 547 True 549.0 549 85.9490 1857 2365 1 chr1D.!!$R3 508

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
80 81 0.259938 GAGGCCTGGATTGGGAATGT 59.74 55.0 12.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 1448 0.174617 TAGCGATGCACACGGAATGA 59.825 50.0 15.09 0.0 0.0 2.57 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
59 60 4.094442 GGACGAACGATTCCTAAAATGCTT 59.906 41.667 0.14 0.00 0.00 3.91
80 81 0.259938 GAGGCCTGGATTGGGAATGT 59.740 55.000 12.00 0.00 0.00 2.71
288 292 4.167307 AGATCGAAAAATAAAGGGGGCCTA 59.833 41.667 0.84 0.00 31.13 3.93
291 295 3.372241 CGAAAAATAAAGGGGGCCTAGGA 60.372 47.826 14.75 0.00 31.13 2.94
417 422 1.757682 AAAAAGACACGGTTGCCTCA 58.242 45.000 0.00 0.00 0.00 3.86
453 459 6.544327 TTGGTGATTCCCCTATATGGAAAT 57.456 37.500 7.69 0.00 44.64 2.17
559 566 2.954318 CTGTGGATAATGAGCCCCTTTG 59.046 50.000 0.00 0.00 0.00 2.77
568 575 1.017387 GAGCCCCTTTGCGTGATAAG 58.983 55.000 0.00 0.00 36.02 1.73
612 619 5.300969 TGCAACTATCAAGAAATCACAGC 57.699 39.130 0.00 0.00 0.00 4.40
728 735 3.117888 GGACTCCTGGCCTCAATCAAATA 60.118 47.826 3.32 0.00 0.00 1.40
787 794 7.785033 AGAAGAAATTCACAACCAAATCTGTT 58.215 30.769 0.00 0.00 0.00 3.16
832 841 0.678950 GGGGTGTGACAACAAATGGG 59.321 55.000 1.89 0.00 38.27 4.00
893 903 4.038402 CCTCTGGCAACTTTTTCAAGATGT 59.962 41.667 0.00 0.00 35.66 3.06
996 1006 6.005583 TCTCAACATCTTTTCTTCACATGC 57.994 37.500 0.00 0.00 0.00 4.06
1000 1010 4.922206 ACATCTTTTCTTCACATGCCCTA 58.078 39.130 0.00 0.00 0.00 3.53
1021 1031 0.755686 GGCTAGGGTGATGTGGAGAG 59.244 60.000 0.00 0.00 0.00 3.20
1173 1183 5.008619 TGTGGAACTGTCGTAACAAAGTA 57.991 39.130 0.00 0.00 38.04 2.24
1183 1193 6.950545 TGTCGTAACAAAGTAACATTTGAGG 58.049 36.000 6.22 0.00 41.71 3.86
1213 1223 3.771577 TGAGGTCTCCTTTTGAGGTTC 57.228 47.619 0.00 0.00 41.76 3.62
1237 1247 2.795329 ACTCAGCTTGTGGGTATTTGG 58.205 47.619 0.00 0.00 38.52 3.28
1265 1275 1.487976 GGCAGGACTGATGAATGGAGA 59.512 52.381 3.00 0.00 0.00 3.71
1288 1298 4.819761 GCGAGACCATGGAGCGCA 62.820 66.667 30.56 0.00 46.19 6.09
1332 1342 0.660595 CGTCGACCCTGATGCGTATC 60.661 60.000 10.58 6.54 0.00 2.24
1373 1383 3.063180 GCAAGACAAGGATGATTCAGACG 59.937 47.826 0.00 0.00 0.00 4.18
1376 1386 3.511540 AGACAAGGATGATTCAGACGTGA 59.488 43.478 0.00 0.00 0.00 4.35
1377 1412 3.854666 ACAAGGATGATTCAGACGTGAG 58.145 45.455 0.00 0.00 32.98 3.51
1382 1417 3.452474 GATGATTCAGACGTGAGGGAAG 58.548 50.000 0.00 0.00 32.98 3.46
1390 1425 0.251386 ACGTGAGGGAAGCAGAGAGA 60.251 55.000 0.00 0.00 0.00 3.10
1396 1431 0.908198 GGGAAGCAGAGAGACATGGT 59.092 55.000 0.00 0.00 0.00 3.55
1398 1433 2.501723 GGGAAGCAGAGAGACATGGTTA 59.498 50.000 0.00 0.00 37.27 2.85
1399 1434 3.135530 GGGAAGCAGAGAGACATGGTTAT 59.864 47.826 0.00 0.00 37.27 1.89
1400 1435 4.345257 GGGAAGCAGAGAGACATGGTTATA 59.655 45.833 0.00 0.00 37.27 0.98
1402 1437 5.931146 GGAAGCAGAGAGACATGGTTATATG 59.069 44.000 0.00 0.00 37.27 1.78
1403 1438 4.892433 AGCAGAGAGACATGGTTATATGC 58.108 43.478 0.00 1.19 0.00 3.14
1404 1439 4.346127 AGCAGAGAGACATGGTTATATGCA 59.654 41.667 13.07 0.00 32.53 3.96
1405 1440 4.689812 GCAGAGAGACATGGTTATATGCAG 59.310 45.833 7.72 0.00 0.00 4.41
1406 1441 5.741383 GCAGAGAGACATGGTTATATGCAGT 60.741 44.000 7.72 0.00 0.00 4.40
1407 1442 6.517362 GCAGAGAGACATGGTTATATGCAGTA 60.517 42.308 7.72 0.00 0.00 2.74
1409 1444 8.093307 CAGAGAGACATGGTTATATGCAGTATT 58.907 37.037 0.00 0.00 0.00 1.89
1410 1445 8.654997 AGAGAGACATGGTTATATGCAGTATTT 58.345 33.333 0.00 0.00 0.00 1.40
1411 1446 8.613060 AGAGACATGGTTATATGCAGTATTTG 57.387 34.615 0.00 0.00 0.00 2.32
1412 1447 7.663081 AGAGACATGGTTATATGCAGTATTTGG 59.337 37.037 0.00 0.00 0.00 3.28
1413 1448 7.290061 AGACATGGTTATATGCAGTATTTGGT 58.710 34.615 0.00 0.00 0.00 3.67
1414 1449 7.445402 AGACATGGTTATATGCAGTATTTGGTC 59.555 37.037 0.00 0.00 0.00 4.02
1415 1450 7.059788 ACATGGTTATATGCAGTATTTGGTCA 58.940 34.615 0.00 0.00 0.00 4.02
1416 1451 7.725397 ACATGGTTATATGCAGTATTTGGTCAT 59.275 33.333 0.00 0.00 0.00 3.06
1420 1455 5.947228 ATATGCAGTATTTGGTCATTCCG 57.053 39.130 0.00 0.00 39.52 4.30
1435 1470 0.735978 TTCCGTGTGCATCGCTAGTG 60.736 55.000 8.40 0.00 0.00 2.74
1439 1474 2.193447 CGTGTGCATCGCTAGTGTTAT 58.807 47.619 2.66 0.00 0.00 1.89
1450 1485 6.505044 TCGCTAGTGTTATCTTTGTGTCTA 57.495 37.500 2.66 0.00 0.00 2.59
1452 1487 7.544622 TCGCTAGTGTTATCTTTGTGTCTATT 58.455 34.615 2.66 0.00 0.00 1.73
1530 1565 3.067461 GTGGCTAGTGTGATCCTAGACTG 59.933 52.174 10.57 0.00 40.57 3.51
1568 1603 1.798813 GTGATGTTGGTTCTGACGGTC 59.201 52.381 0.00 0.00 0.00 4.79
1640 1704 1.686587 GGGTTTCCCAGTGTTTCCTTG 59.313 52.381 0.00 0.00 44.65 3.61
1689 1754 7.309560 CCGTTATGAAAGTAATGAAAAGGGGTT 60.310 37.037 0.00 0.00 0.00 4.11
1690 1755 8.732531 CGTTATGAAAGTAATGAAAAGGGGTTA 58.267 33.333 0.00 0.00 0.00 2.85
1726 1791 2.549064 AAAGCAAAACTCCCAATGGC 57.451 45.000 0.00 0.00 0.00 4.40
1727 1792 0.686789 AAGCAAAACTCCCAATGGCC 59.313 50.000 0.00 0.00 0.00 5.36
1728 1793 1.079888 GCAAAACTCCCAATGGCCG 60.080 57.895 0.00 0.00 0.00 6.13
1729 1794 1.531739 GCAAAACTCCCAATGGCCGA 61.532 55.000 0.00 0.00 0.00 5.54
1730 1795 0.965439 CAAAACTCCCAATGGCCGAA 59.035 50.000 0.00 0.00 0.00 4.30
1731 1796 0.966179 AAAACTCCCAATGGCCGAAC 59.034 50.000 0.00 0.00 0.00 3.95
1732 1797 0.178975 AAACTCCCAATGGCCGAACA 60.179 50.000 0.00 0.00 0.00 3.18
1733 1798 0.609131 AACTCCCAATGGCCGAACAG 60.609 55.000 0.00 0.00 0.00 3.16
1734 1799 1.750399 CTCCCAATGGCCGAACAGG 60.750 63.158 0.00 0.00 44.97 4.00
1784 1849 4.424711 GGATTCTGCGGGGCCACA 62.425 66.667 5.46 1.30 0.00 4.17
1785 1850 3.134127 GATTCTGCGGGGCCACAC 61.134 66.667 5.46 0.00 0.00 3.82
1795 1860 3.948719 GGCCACACGGACCTTCCA 61.949 66.667 0.00 0.00 35.91 3.53
1796 1861 2.668550 GCCACACGGACCTTCCAC 60.669 66.667 0.00 0.00 35.91 4.02
1797 1862 2.825982 CCACACGGACCTTCCACA 59.174 61.111 0.00 0.00 35.91 4.17
1798 1863 1.147376 CCACACGGACCTTCCACAA 59.853 57.895 0.00 0.00 35.91 3.33
1799 1864 1.164041 CCACACGGACCTTCCACAAC 61.164 60.000 0.00 0.00 35.91 3.32
1800 1865 1.227438 ACACGGACCTTCCACAACG 60.227 57.895 0.00 0.00 35.91 4.10
1801 1866 1.227438 CACGGACCTTCCACAACGT 60.227 57.895 0.00 0.00 35.91 3.99
1802 1867 1.068585 ACGGACCTTCCACAACGTC 59.931 57.895 0.00 0.00 35.91 4.34
1803 1868 1.666872 CGGACCTTCCACAACGTCC 60.667 63.158 0.00 0.00 41.20 4.79
1804 1869 1.666872 GGACCTTCCACAACGTCCG 60.667 63.158 0.00 0.00 35.78 4.79
1805 1870 2.280592 ACCTTCCACAACGTCCGC 60.281 61.111 0.00 0.00 0.00 5.54
1806 1871 2.030562 CCTTCCACAACGTCCGCT 59.969 61.111 0.00 0.00 0.00 5.52
1807 1872 2.317609 CCTTCCACAACGTCCGCTG 61.318 63.158 0.00 0.00 0.00 5.18
1808 1873 2.954753 CTTCCACAACGTCCGCTGC 61.955 63.158 0.00 0.00 0.00 5.25
1809 1874 3.741830 TTCCACAACGTCCGCTGCA 62.742 57.895 0.00 0.00 0.00 4.41
1810 1875 3.716006 CCACAACGTCCGCTGCAG 61.716 66.667 10.11 10.11 0.00 4.41
1811 1876 4.374702 CACAACGTCCGCTGCAGC 62.375 66.667 29.12 29.12 37.78 5.25
1812 1877 4.609018 ACAACGTCCGCTGCAGCT 62.609 61.111 34.22 14.50 39.32 4.24
1813 1878 3.782244 CAACGTCCGCTGCAGCTC 61.782 66.667 34.22 22.48 39.32 4.09
1814 1879 4.299547 AACGTCCGCTGCAGCTCA 62.300 61.111 34.22 18.95 39.32 4.26
1815 1880 4.731612 ACGTCCGCTGCAGCTCAG 62.732 66.667 34.22 23.77 45.62 3.35
1841 1906 2.892425 CTGCCGCCGGAATCACTC 60.892 66.667 7.68 0.00 0.00 3.51
1842 1907 4.467084 TGCCGCCGGAATCACTCC 62.467 66.667 7.68 0.00 41.40 3.85
1844 1909 4.891727 CCGCCGGAATCACTCCCG 62.892 72.222 5.05 0.00 41.87 5.14
1848 1913 3.294750 CGGAATCACTCCCGGTCA 58.705 61.111 0.00 0.00 41.87 4.02
1849 1914 1.823295 CGGAATCACTCCCGGTCAT 59.177 57.895 0.00 0.00 41.87 3.06
1850 1915 0.530650 CGGAATCACTCCCGGTCATG 60.531 60.000 0.00 0.00 41.87 3.07
1851 1916 0.179045 GGAATCACTCCCGGTCATGG 60.179 60.000 0.00 0.00 38.44 3.66
2006 2071 5.779922 TGGTATCAGATTAGGTTACGATGC 58.220 41.667 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 1.009997 ATTCCCAATCCAGGCCTCAA 58.990 50.000 0.00 0.00 0.00 3.02
136 139 9.646427 GGAAGAAGAAACATAGCCATATAGTAG 57.354 37.037 0.00 0.00 0.00 2.57
217 221 2.620242 GTACCGTTTTCGCCCTTCATA 58.380 47.619 0.00 0.00 42.58 2.15
246 250 2.846206 TCTGCATATTCTGGACCACCTT 59.154 45.455 0.00 0.00 37.04 3.50
288 292 6.899393 TGTTTATGCAAATCTTTCACTCCT 57.101 33.333 0.00 0.00 0.00 3.69
291 295 9.328845 ACATTTTGTTTATGCAAATCTTTCACT 57.671 25.926 0.00 0.00 38.05 3.41
417 422 6.014584 GGGGAATCACCAAATTTACTTTCACT 60.015 38.462 0.00 0.00 41.20 3.41
471 477 4.829872 TTCTCCCCGCAAAGTAATTCTA 57.170 40.909 0.00 0.00 0.00 2.10
485 491 7.285629 CCTGAATTAAGGATTACTTTTCTCCCC 59.714 40.741 2.04 0.00 40.02 4.81
497 503 5.086621 ACCAAGTTGCCTGAATTAAGGATT 58.913 37.500 13.69 0.00 40.02 3.01
527 533 3.644966 TTATCCACAGGATCAACCCAC 57.355 47.619 1.05 0.00 42.11 4.61
559 566 8.583810 TGTATAACATAGGAAACTTATCACGC 57.416 34.615 0.00 0.00 43.67 5.34
612 619 7.986085 TCAACTCCTTTTCTAAAATCTGAGG 57.014 36.000 11.17 0.00 0.00 3.86
728 735 2.624029 CCCAGGTAACCTCATTTGGCAT 60.624 50.000 0.00 0.00 37.17 4.40
832 841 2.108952 AGGGAATCTTGGATGCCCATAC 59.891 50.000 21.85 0.00 43.12 2.39
917 927 1.000896 CCCGCCCATTTCCTTCTGT 60.001 57.895 0.00 0.00 0.00 3.41
1000 1010 1.135094 CTCCACATCACCCTAGCCAT 58.865 55.000 0.00 0.00 0.00 4.40
1008 1018 1.021390 CAACGGCTCTCCACATCACC 61.021 60.000 0.00 0.00 0.00 4.02
1011 1021 1.450312 CCCAACGGCTCTCCACATC 60.450 63.158 0.00 0.00 0.00 3.06
1021 1031 2.978010 CAGGACACACCCAACGGC 60.978 66.667 0.00 0.00 40.05 5.68
1080 1090 2.375174 AGGAAGGAACATGTAGCACCAA 59.625 45.455 0.00 0.00 0.00 3.67
1089 1099 1.565759 TCCCCATCAGGAAGGAACATG 59.434 52.381 0.00 0.00 38.24 3.21
1173 1183 3.896888 TCATCTGTTTGGCCTCAAATGTT 59.103 39.130 3.32 0.00 43.73 2.71
1183 1193 1.280421 AGGAGACCTCATCTGTTTGGC 59.720 52.381 0.00 0.00 38.00 4.52
1213 1223 3.895232 ATACCCACAAGCTGAGTACAG 57.105 47.619 0.00 0.00 45.91 2.74
1237 1247 2.435805 TCATCAGTCCTGCCCAGTAATC 59.564 50.000 0.00 0.00 0.00 1.75
1265 1275 0.316522 CTCCATGGTCTCGCGATCAT 59.683 55.000 10.36 11.47 41.64 2.45
1276 1286 4.479993 GGCTCTGCGCTCCATGGT 62.480 66.667 12.58 0.00 39.13 3.55
1288 1298 2.165998 GGTCTTCAGCATTTTGGCTCT 58.834 47.619 0.00 0.00 43.68 4.09
1347 1357 4.851843 TGAATCATCCTTGTCTTGCATCT 58.148 39.130 0.00 0.00 0.00 2.90
1354 1364 3.511540 TCACGTCTGAATCATCCTTGTCT 59.488 43.478 0.00 0.00 0.00 3.41
1373 1383 1.261480 TGTCTCTCTGCTTCCCTCAC 58.739 55.000 0.00 0.00 0.00 3.51
1376 1386 1.202330 CCATGTCTCTCTGCTTCCCT 58.798 55.000 0.00 0.00 0.00 4.20
1377 1412 0.908198 ACCATGTCTCTCTGCTTCCC 59.092 55.000 0.00 0.00 0.00 3.97
1382 1417 4.635223 TGCATATAACCATGTCTCTCTGC 58.365 43.478 0.00 0.00 0.00 4.26
1390 1425 7.059788 TGACCAAATACTGCATATAACCATGT 58.940 34.615 0.00 0.00 0.00 3.21
1396 1431 6.995686 ACGGAATGACCAAATACTGCATATAA 59.004 34.615 0.00 0.00 38.90 0.98
1398 1433 5.239306 CACGGAATGACCAAATACTGCATAT 59.761 40.000 0.00 0.00 38.90 1.78
1399 1434 4.574421 CACGGAATGACCAAATACTGCATA 59.426 41.667 0.00 0.00 38.90 3.14
1400 1435 3.378112 CACGGAATGACCAAATACTGCAT 59.622 43.478 0.00 0.00 38.90 3.96
1402 1437 2.747446 ACACGGAATGACCAAATACTGC 59.253 45.455 0.00 0.00 38.90 4.40
1403 1438 3.426159 GCACACGGAATGACCAAATACTG 60.426 47.826 0.00 0.00 38.90 2.74
1404 1439 2.747446 GCACACGGAATGACCAAATACT 59.253 45.455 0.00 0.00 38.90 2.12
1405 1440 2.486203 TGCACACGGAATGACCAAATAC 59.514 45.455 0.00 0.00 38.90 1.89
1406 1441 2.784347 TGCACACGGAATGACCAAATA 58.216 42.857 0.00 0.00 38.90 1.40
1407 1442 1.614996 TGCACACGGAATGACCAAAT 58.385 45.000 0.00 0.00 38.90 2.32
1409 1444 1.164411 GATGCACACGGAATGACCAA 58.836 50.000 0.00 0.00 38.90 3.67
1410 1445 1.018752 CGATGCACACGGAATGACCA 61.019 55.000 7.16 0.00 38.90 4.02
1411 1446 1.715585 CGATGCACACGGAATGACC 59.284 57.895 7.16 0.00 0.00 4.02
1412 1447 1.060937 GCGATGCACACGGAATGAC 59.939 57.895 15.09 0.00 0.00 3.06
1413 1448 0.174617 TAGCGATGCACACGGAATGA 59.825 50.000 15.09 0.00 0.00 2.57
1414 1449 0.578683 CTAGCGATGCACACGGAATG 59.421 55.000 15.09 0.00 0.00 2.67
1415 1450 0.175760 ACTAGCGATGCACACGGAAT 59.824 50.000 15.09 0.00 0.00 3.01
1416 1451 0.735978 CACTAGCGATGCACACGGAA 60.736 55.000 15.09 0.00 0.00 4.30
1420 1455 3.448686 AGATAACACTAGCGATGCACAC 58.551 45.455 0.00 0.00 0.00 3.82
1439 1474 8.445275 TGAAGTTTAGCAAATAGACACAAAGA 57.555 30.769 0.00 0.00 0.00 2.52
1450 1485 6.096846 ACAAAGGACACTGAAGTTTAGCAAAT 59.903 34.615 0.00 0.00 0.00 2.32
1452 1487 4.947388 ACAAAGGACACTGAAGTTTAGCAA 59.053 37.500 0.00 0.00 0.00 3.91
1493 1528 1.294780 CCACAGGAGGCTCAGACAC 59.705 63.158 17.69 0.00 0.00 3.67
1514 1549 3.176924 ACCACAGTCTAGGATCACACT 57.823 47.619 0.00 0.00 0.00 3.55
1530 1565 0.539518 ACCAACCCAAAAGCAACCAC 59.460 50.000 0.00 0.00 0.00 4.16
1711 1776 0.965439 TTCGGCCATTGGGAGTTTTG 59.035 50.000 2.24 0.00 35.59 2.44
1712 1777 0.966179 GTTCGGCCATTGGGAGTTTT 59.034 50.000 2.24 0.00 35.59 2.43
1715 1780 1.002134 CTGTTCGGCCATTGGGAGT 60.002 57.895 2.24 0.00 35.59 3.85
1716 1781 1.750399 CCTGTTCGGCCATTGGGAG 60.750 63.158 2.24 0.00 35.59 4.30
1717 1782 2.354729 CCTGTTCGGCCATTGGGA 59.645 61.111 2.24 0.00 35.59 4.37
1767 1832 4.424711 TGTGGCCCCGCAGAATCC 62.425 66.667 0.00 0.00 32.23 3.01
1768 1833 3.134127 GTGTGGCCCCGCAGAATC 61.134 66.667 0.00 0.00 37.10 2.52
1776 1841 4.717313 GAAGGTCCGTGTGGCCCC 62.717 72.222 0.00 0.00 33.40 5.80
1777 1842 4.717313 GGAAGGTCCGTGTGGCCC 62.717 72.222 0.00 0.00 33.40 5.80
1778 1843 3.948719 TGGAAGGTCCGTGTGGCC 61.949 66.667 0.00 0.00 40.17 5.36
1779 1844 2.668550 GTGGAAGGTCCGTGTGGC 60.669 66.667 0.00 0.00 40.17 5.01
1780 1845 1.147376 TTGTGGAAGGTCCGTGTGG 59.853 57.895 0.00 0.00 40.17 4.17
1781 1846 1.495584 CGTTGTGGAAGGTCCGTGTG 61.496 60.000 0.00 0.00 40.17 3.82
1782 1847 1.227438 CGTTGTGGAAGGTCCGTGT 60.227 57.895 0.00 0.00 40.17 4.49
1783 1848 1.219522 GACGTTGTGGAAGGTCCGTG 61.220 60.000 0.00 0.00 40.17 4.94
1784 1849 1.068585 GACGTTGTGGAAGGTCCGT 59.931 57.895 0.00 0.00 40.17 4.69
1785 1850 3.946907 GACGTTGTGGAAGGTCCG 58.053 61.111 0.00 0.00 40.17 4.79
1787 1852 2.315386 GCGGACGTTGTGGAAGGTC 61.315 63.158 0.00 0.00 43.37 3.85
1788 1853 2.280592 GCGGACGTTGTGGAAGGT 60.281 61.111 0.00 0.00 32.85 3.50
1789 1854 2.030562 AGCGGACGTTGTGGAAGG 59.969 61.111 0.00 0.00 0.00 3.46
1790 1855 2.954753 GCAGCGGACGTTGTGGAAG 61.955 63.158 10.10 0.00 0.00 3.46
1791 1856 2.970324 GCAGCGGACGTTGTGGAA 60.970 61.111 10.10 0.00 0.00 3.53
1792 1857 4.228567 TGCAGCGGACGTTGTGGA 62.229 61.111 10.10 0.00 0.00 4.02
1793 1858 3.716006 CTGCAGCGGACGTTGTGG 61.716 66.667 0.00 0.54 0.00 4.17
1794 1859 4.374702 GCTGCAGCGGACGTTGTG 62.375 66.667 25.23 5.20 0.00 3.33
1824 1889 2.892425 GAGTGATTCCGGCGGCAG 60.892 66.667 23.83 0.00 0.00 4.85
1825 1890 4.467084 GGAGTGATTCCGGCGGCA 62.467 66.667 23.83 12.24 35.91 5.69
1832 1897 0.179045 CCATGACCGGGAGTGATTCC 60.179 60.000 6.32 0.00 46.00 3.01
1833 1898 3.386543 CCATGACCGGGAGTGATTC 57.613 57.895 6.32 0.00 0.00 2.52
1844 1909 3.961838 TAACACCGCGCCCATGACC 62.962 63.158 0.00 0.00 0.00 4.02
1845 1910 2.435234 TAACACCGCGCCCATGAC 60.435 61.111 0.00 0.00 0.00 3.06
1846 1911 2.125310 CTAACACCGCGCCCATGA 60.125 61.111 0.00 0.00 0.00 3.07
1847 1912 2.125310 TCTAACACCGCGCCCATG 60.125 61.111 0.00 0.00 0.00 3.66
1848 1913 1.324740 TAGTCTAACACCGCGCCCAT 61.325 55.000 0.00 0.00 0.00 4.00
1849 1914 1.324740 ATAGTCTAACACCGCGCCCA 61.325 55.000 0.00 0.00 0.00 5.36
1850 1915 0.670162 TATAGTCTAACACCGCGCCC 59.330 55.000 0.00 0.00 0.00 6.13
1851 1916 2.719426 ATATAGTCTAACACCGCGCC 57.281 50.000 0.00 0.00 0.00 6.53
1852 1917 5.872635 TGTATATATAGTCTAACACCGCGC 58.127 41.667 0.00 0.00 0.00 6.86
1853 1918 8.824781 ACTATGTATATATAGTCTAACACCGCG 58.175 37.037 14.52 0.00 39.10 6.46
2006 2071 4.335647 AGGTGGTGCAGCGGAAGG 62.336 66.667 11.91 0.00 36.92 3.46
2229 2348 1.071471 CCATAGGATGGCACGGGAC 59.929 63.158 0.00 0.00 44.70 4.46


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

AutoCloner maintained by Alex Coulton.