Multiple sequence alignment - TraesCS3D01G078800

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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 TraesCS3D01G078800 chr3D 100.000 2397 0 0 1 2397 39313802 39316198 0.000000e+00 4427
1 TraesCS3D01G078800 chr3D 85.730 918 75 19 47 920 101022222 101021317 0.000000e+00 918
2 TraesCS3D01G078800 chr2D 91.871 898 55 9 9 904 47710945 47711826 0.000000e+00 1238
3 TraesCS3D01G078800 chr2A 89.342 957 54 17 6 920 456481062 456480112 0.000000e+00 1158
4 TraesCS3D01G078800 chr7D 91.667 816 47 10 6 804 25182240 25183051 0.000000e+00 1110
5 TraesCS3D01G078800 chr3B 87.694 967 65 24 6 922 802839384 802838422 0.000000e+00 1077
6 TraesCS3D01G078800 chr3B 87.500 968 68 20 6 922 803341644 803342609 0.000000e+00 1068
7 TraesCS3D01G078800 chr3B 86.837 942 71 23 6 922 803369667 803370580 0.000000e+00 1003
8 TraesCS3D01G078800 chr3B 92.240 567 24 11 1475 2031 62292991 62293547 0.000000e+00 785
9 TraesCS3D01G078800 chr3B 92.966 526 30 2 921 1446 62292477 62292995 0.000000e+00 760
10 TraesCS3D01G078800 chr3B 84.201 538 64 12 387 920 727782859 727782339 9.890000e-139 503
11 TraesCS3D01G078800 chr3A 88.204 746 51 20 916 1654 50720132 50720847 0.000000e+00 856
12 TraesCS3D01G078800 chr3A 83.215 703 55 27 1682 2373 50720843 50721493 9.550000e-164 586
13 TraesCS3D01G078800 chr6D 91.362 602 41 8 6 600 275920909 275920312 0.000000e+00 813
14 TraesCS3D01G078800 chr6D 84.875 562 53 17 365 920 275920592 275920057 2.710000e-149 538
15 TraesCS3D01G078800 chr4A 82.594 609 82 16 9 600 626331419 626332020 1.270000e-142 516
16 TraesCS3D01G078800 chr7B 93.919 148 9 0 771 918 334326391 334326538 8.620000e-55 224


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 TraesCS3D01G078800 chr3D 39313802 39316198 2396 False 4427.0 4427 100.0000 1 2397 1 chr3D.!!$F1 2396
1 TraesCS3D01G078800 chr3D 101021317 101022222 905 True 918.0 918 85.7300 47 920 1 chr3D.!!$R1 873
2 TraesCS3D01G078800 chr2D 47710945 47711826 881 False 1238.0 1238 91.8710 9 904 1 chr2D.!!$F1 895
3 TraesCS3D01G078800 chr2A 456480112 456481062 950 True 1158.0 1158 89.3420 6 920 1 chr2A.!!$R1 914
4 TraesCS3D01G078800 chr7D 25182240 25183051 811 False 1110.0 1110 91.6670 6 804 1 chr7D.!!$F1 798
5 TraesCS3D01G078800 chr3B 802838422 802839384 962 True 1077.0 1077 87.6940 6 922 1 chr3B.!!$R2 916
6 TraesCS3D01G078800 chr3B 803341644 803342609 965 False 1068.0 1068 87.5000 6 922 1 chr3B.!!$F1 916
7 TraesCS3D01G078800 chr3B 803369667 803370580 913 False 1003.0 1003 86.8370 6 922 1 chr3B.!!$F2 916
8 TraesCS3D01G078800 chr3B 62292477 62293547 1070 False 772.5 785 92.6030 921 2031 2 chr3B.!!$F3 1110
9 TraesCS3D01G078800 chr3B 727782339 727782859 520 True 503.0 503 84.2010 387 920 1 chr3B.!!$R1 533
10 TraesCS3D01G078800 chr3A 50720132 50721493 1361 False 721.0 856 85.7095 916 2373 2 chr3A.!!$F1 1457
11 TraesCS3D01G078800 chr6D 275920057 275920909 852 True 675.5 813 88.1185 6 920 2 chr6D.!!$R1 914
12 TraesCS3D01G078800 chr4A 626331419 626332020 601 False 516.0 516 82.5940 9 600 1 chr4A.!!$F1 591

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
746 927 0.971386 ACCGGTCTACCATGAAACGT 59.029 50.0 0.0 0.0 35.14 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 2025 0.532862 AGGTGTGGCGAAGTGACAAG 60.533 55.0 0.0 0.0 0.0 3.16 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
39 40 2.358737 GCCTTATGCGCCCGCTAT 60.359 61.111 14.13 8.22 42.51 2.97
127 136 4.737765 CCTCTGTTTTTCAAATCGCGAAAA 59.262 37.500 15.24 6.19 39.84 2.29
194 205 3.023119 CAATAAGCTGCATAACCACCCA 58.977 45.455 1.02 0.00 0.00 4.51
222 234 2.289195 CCCAACTGGACGTGCTACTTTA 60.289 50.000 8.99 0.00 37.39 1.85
352 413 7.971004 ACTTTTTCTGAAATTCGTGAACTTC 57.029 32.000 3.31 0.00 0.00 3.01
568 744 8.791355 TTAGGTGAACTTTTTCTAAATTTCGC 57.209 30.769 0.00 0.00 40.15 4.70
633 811 8.746052 TCATGAACCTTATATCAAAATCGGTT 57.254 30.769 0.00 0.00 36.10 4.44
746 927 0.971386 ACCGGTCTACCATGAAACGT 59.029 50.000 0.00 0.00 35.14 3.99
804 985 1.664151 GAAACAAACGAGCGGGATAGG 59.336 52.381 0.00 0.00 0.00 2.57
972 1154 1.075601 ACTTCCCAAATCCAGAGCCA 58.924 50.000 0.00 0.00 0.00 4.75
976 1158 1.693640 CCAAATCCAGAGCCACCCT 59.306 57.895 0.00 0.00 0.00 4.34
1043 1225 3.234630 TTTCTGCCGACCGGGACAG 62.235 63.158 6.32 7.70 39.71 3.51
1178 1361 0.031817 CTTGCCCATTCCCCTCCATT 60.032 55.000 0.00 0.00 0.00 3.16
1179 1362 1.217689 CTTGCCCATTCCCCTCCATTA 59.782 52.381 0.00 0.00 0.00 1.90
1180 1363 1.544764 TGCCCATTCCCCTCCATTAT 58.455 50.000 0.00 0.00 0.00 1.28
1217 1400 1.008875 TTCGCAGCGTCACAGCTTAG 61.009 55.000 15.93 0.00 46.80 2.18
1229 1412 0.108138 CAGCTTAGTCTGTTCCCCCG 60.108 60.000 0.00 0.00 0.00 5.73
1419 1602 5.735285 TCTAATCTAGATGCTGGTGGATG 57.265 43.478 5.86 0.00 0.00 3.51
1420 1603 3.784511 AATCTAGATGCTGGTGGATGG 57.215 47.619 5.86 0.00 0.00 3.51
1421 1604 0.761187 TCTAGATGCTGGTGGATGGC 59.239 55.000 0.00 0.00 0.00 4.40
1422 1605 0.250640 CTAGATGCTGGTGGATGGCC 60.251 60.000 0.00 0.00 0.00 5.36
1441 1624 2.771089 CCGGCCGTAGTATCAGTAGTA 58.229 52.381 26.12 0.00 0.00 1.82
1442 1625 2.740981 CCGGCCGTAGTATCAGTAGTAG 59.259 54.545 26.12 0.00 0.00 2.57
1443 1626 3.397482 CGGCCGTAGTATCAGTAGTAGT 58.603 50.000 19.50 0.00 0.00 2.73
1444 1627 4.560128 CGGCCGTAGTATCAGTAGTAGTA 58.440 47.826 19.50 0.00 0.00 1.82
1445 1628 4.624882 CGGCCGTAGTATCAGTAGTAGTAG 59.375 50.000 19.50 0.00 0.00 2.57
1446 1629 4.934602 GGCCGTAGTATCAGTAGTAGTAGG 59.065 50.000 0.00 0.00 0.00 3.18
1447 1630 5.512232 GGCCGTAGTATCAGTAGTAGTAGGT 60.512 48.000 0.00 0.00 0.00 3.08
1448 1631 5.637387 GCCGTAGTATCAGTAGTAGTAGGTC 59.363 48.000 0.00 0.00 0.00 3.85
1449 1632 6.518200 GCCGTAGTATCAGTAGTAGTAGGTCT 60.518 46.154 0.00 0.00 0.00 3.85
1450 1633 7.441017 CCGTAGTATCAGTAGTAGTAGGTCTT 58.559 42.308 0.00 0.00 0.00 3.01
1451 1634 7.384660 CCGTAGTATCAGTAGTAGTAGGTCTTG 59.615 44.444 0.00 0.00 0.00 3.02
1452 1635 7.925483 CGTAGTATCAGTAGTAGTAGGTCTTGT 59.075 40.741 0.00 0.00 0.00 3.16
1453 1636 9.612066 GTAGTATCAGTAGTAGTAGGTCTTGTT 57.388 37.037 0.00 0.00 0.00 2.83
1454 1637 8.508883 AGTATCAGTAGTAGTAGGTCTTGTTG 57.491 38.462 0.00 0.00 0.00 3.33
1455 1638 8.108364 AGTATCAGTAGTAGTAGGTCTTGTTGT 58.892 37.037 0.00 0.00 0.00 3.32
1456 1639 6.814506 TCAGTAGTAGTAGGTCTTGTTGTC 57.185 41.667 0.00 0.00 0.00 3.18
1457 1640 6.301486 TCAGTAGTAGTAGGTCTTGTTGTCA 58.699 40.000 0.00 0.00 0.00 3.58
1458 1641 6.206243 TCAGTAGTAGTAGGTCTTGTTGTCAC 59.794 42.308 0.00 0.00 0.00 3.67
1459 1642 4.500603 AGTAGTAGGTCTTGTTGTCACG 57.499 45.455 0.00 0.00 0.00 4.35
1460 1643 2.814280 AGTAGGTCTTGTTGTCACGG 57.186 50.000 0.00 0.00 0.00 4.94
1461 1644 1.145803 GTAGGTCTTGTTGTCACGGC 58.854 55.000 0.00 0.00 0.00 5.68
1462 1645 0.319211 TAGGTCTTGTTGTCACGGCG 60.319 55.000 4.80 4.80 0.00 6.46
1463 1646 2.248431 GTCTTGTTGTCACGGCGC 59.752 61.111 6.90 0.00 0.00 6.53
1464 1647 2.970324 TCTTGTTGTCACGGCGCC 60.970 61.111 19.07 19.07 0.00 6.53
1465 1648 4.025401 CTTGTTGTCACGGCGCCC 62.025 66.667 23.46 7.25 0.00 6.13
1466 1649 4.555709 TTGTTGTCACGGCGCCCT 62.556 61.111 23.46 6.45 0.00 5.19
1467 1650 4.980805 TGTTGTCACGGCGCCCTC 62.981 66.667 23.46 9.35 0.00 4.30
1468 1651 4.681978 GTTGTCACGGCGCCCTCT 62.682 66.667 23.46 0.00 0.00 3.69
1469 1652 3.936203 TTGTCACGGCGCCCTCTT 61.936 61.111 23.46 0.00 0.00 2.85
1470 1653 3.469863 TTGTCACGGCGCCCTCTTT 62.470 57.895 23.46 0.00 0.00 2.52
1471 1654 2.102109 TTGTCACGGCGCCCTCTTTA 62.102 55.000 23.46 0.00 0.00 1.85
1472 1655 1.375013 GTCACGGCGCCCTCTTTAA 60.375 57.895 23.46 0.00 0.00 1.52
1473 1656 0.952010 GTCACGGCGCCCTCTTTAAA 60.952 55.000 23.46 0.00 0.00 1.52
1504 1687 0.968405 AGTAGTCCCGCCGTGTTAAA 59.032 50.000 0.00 0.00 0.00 1.52
1548 1752 1.745653 GGGCTTTGATTAGTGCAGTCC 59.254 52.381 0.00 0.00 0.00 3.85
1649 1853 2.344535 GCTGTGCCACCATTTGTCT 58.655 52.632 0.00 0.00 0.00 3.41
1650 1854 0.038892 GCTGTGCCACCATTTGTCTG 60.039 55.000 0.00 0.00 0.00 3.51
1651 1855 0.599558 CTGTGCCACCATTTGTCTGG 59.400 55.000 0.00 0.00 42.35 3.86
1653 1857 0.598065 GTGCCACCATTTGTCTGGTC 59.402 55.000 0.00 0.00 46.79 4.02
1654 1858 0.478072 TGCCACCATTTGTCTGGTCT 59.522 50.000 0.00 0.00 46.79 3.85
1655 1859 0.883833 GCCACCATTTGTCTGGTCTG 59.116 55.000 0.00 0.00 46.79 3.51
1656 1860 1.538047 CCACCATTTGTCTGGTCTGG 58.462 55.000 0.00 0.00 46.79 3.86
1657 1861 1.202927 CCACCATTTGTCTGGTCTGGT 60.203 52.381 0.00 0.00 46.79 4.00
1658 1862 2.154462 CACCATTTGTCTGGTCTGGTC 58.846 52.381 0.00 0.00 46.79 4.02
1659 1863 2.057922 ACCATTTGTCTGGTCTGGTCT 58.942 47.619 0.00 0.00 46.79 3.85
1660 1864 2.224621 ACCATTTGTCTGGTCTGGTCTG 60.225 50.000 0.00 0.00 46.79 3.51
1661 1865 2.430465 CATTTGTCTGGTCTGGTCTGG 58.570 52.381 0.00 0.00 0.00 3.86
1662 1866 1.507140 TTTGTCTGGTCTGGTCTGGT 58.493 50.000 0.00 0.00 0.00 4.00
1663 1867 1.048601 TTGTCTGGTCTGGTCTGGTC 58.951 55.000 0.00 0.00 0.00 4.02
1664 1868 0.105709 TGTCTGGTCTGGTCTGGTCA 60.106 55.000 0.00 0.00 0.00 4.02
1665 1869 0.605589 GTCTGGTCTGGTCTGGTCAG 59.394 60.000 0.00 0.00 0.00 3.51
1666 1870 1.188219 TCTGGTCTGGTCTGGTCAGC 61.188 60.000 0.00 0.00 32.63 4.26
1667 1871 1.459348 TGGTCTGGTCTGGTCAGCA 60.459 57.895 0.00 0.00 32.63 4.41
1668 1872 1.004440 GGTCTGGTCTGGTCAGCAC 60.004 63.158 0.00 0.00 32.63 4.40
1669 1873 1.373497 GTCTGGTCTGGTCAGCACG 60.373 63.158 0.00 0.00 32.63 5.34
1670 1874 2.740055 CTGGTCTGGTCAGCACGC 60.740 66.667 0.00 0.00 0.00 5.34
1671 1875 3.231889 CTGGTCTGGTCAGCACGCT 62.232 63.158 0.00 0.00 0.00 5.07
1672 1876 2.031163 GGTCTGGTCAGCACGCTT 59.969 61.111 0.00 0.00 0.00 4.68
1673 1877 2.320587 GGTCTGGTCAGCACGCTTG 61.321 63.158 0.00 0.00 0.00 4.01
1701 1935 9.881773 AAATTATGGTCCACTATGTAATCCATT 57.118 29.630 0.00 0.00 36.01 3.16
1787 2025 5.484173 TCCAAATATCAAATGAGCACGAC 57.516 39.130 0.00 0.00 0.00 4.34
1821 2059 4.780815 CCACACCTGCCTCTATTATTGAA 58.219 43.478 0.00 0.00 0.00 2.69
1905 2144 1.821136 CTCCCATGCTCCAAACTTTCC 59.179 52.381 0.00 0.00 0.00 3.13
1919 2158 8.413899 TCCAAACTTTCCAAAAACTAATTTCG 57.586 30.769 0.00 0.00 0.00 3.46
1921 2160 8.874816 CCAAACTTTCCAAAAACTAATTTCGAA 58.125 29.630 0.00 0.00 0.00 3.71
1967 2208 2.562298 TGGGAATGTTCAAAGGACATGC 59.438 45.455 0.00 0.00 37.76 4.06
2103 2346 7.573968 AAGTGTTCAAGCTCTTCAAAAGTAT 57.426 32.000 0.00 0.00 0.00 2.12
2110 2353 4.504858 AGCTCTTCAAAAGTATACCCACG 58.495 43.478 0.00 0.00 0.00 4.94
2111 2354 4.020485 AGCTCTTCAAAAGTATACCCACGT 60.020 41.667 0.00 0.00 0.00 4.49
2167 2410 8.663771 AAAAGTGTTCACGTAACTTAACAAAG 57.336 30.769 5.78 0.00 38.99 2.77
2169 2412 7.781548 AGTGTTCACGTAACTTAACAAAGAT 57.218 32.000 0.00 0.00 38.99 2.40
2232 2476 7.558161 TGATCACATGTCTCCAAATATGTTC 57.442 36.000 0.00 0.00 31.84 3.18
2240 2484 6.561614 TGTCTCCAAATATGTTCGAGACTAC 58.438 40.000 22.10 7.64 46.22 2.73
2279 2523 6.676237 ACCATTCAAAAACATGTTTGTTCC 57.324 33.333 23.93 0.00 45.30 3.62
2284 2528 9.570488 CATTCAAAAACATGTTTGTTCCATTTT 57.430 25.926 23.93 9.39 45.30 1.82
2293 2537 9.183368 ACATGTTTGTTCCATTTTAAAAATGGT 57.817 25.926 19.84 0.00 45.65 3.55
2296 2540 9.014297 TGTTTGTTCCATTTTAAAAATGGTTGT 57.986 25.926 19.84 0.00 45.65 3.32
2297 2541 9.283420 GTTTGTTCCATTTTAAAAATGGTTGTG 57.717 29.630 19.84 8.20 45.65 3.33
2314 2559 6.294473 TGGTTGTGGCATTGAAAACAATATT 58.706 32.000 0.00 0.00 35.20 1.28
2340 2586 7.986320 TCACATGTTTCAAAAGAATGTTTGGAT 59.014 29.630 0.00 0.00 38.72 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.574828 GGCGTCAAATAGGATTTAGCAAGA 59.425 41.667 0.00 0.00 0.00 3.02
3 4 4.523083 AGGCGTCAAATAGGATTTAGCAA 58.477 39.130 0.00 0.00 0.00 3.91
4 5 4.150897 AGGCGTCAAATAGGATTTAGCA 57.849 40.909 0.00 0.00 0.00 3.49
39 40 1.470285 GCCCGATTGCGAGTTGTACTA 60.470 52.381 0.00 0.00 40.82 1.82
127 136 6.597672 TCGAATCAAAGCACTACCATATGTTT 59.402 34.615 1.24 0.00 0.00 2.83
130 139 6.422223 GTTCGAATCAAAGCACTACCATATG 58.578 40.000 0.00 0.00 0.00 1.78
133 144 3.689649 GGTTCGAATCAAAGCACTACCAT 59.310 43.478 2.82 0.00 0.00 3.55
194 205 3.580319 GTCCAGTTGGGGGTGGCT 61.580 66.667 0.00 0.00 37.22 4.75
222 234 7.034685 ACAAAGTAAAAGGCGTAGAAACATT 57.965 32.000 0.00 0.00 0.00 2.71
262 301 7.220875 CGAAAGAGAAAACCAGAAAAAGGAAAG 59.779 37.037 0.00 0.00 0.00 2.62
352 413 8.282592 TGACAAAAGTTGATCGATGTTAAGAAG 58.717 33.333 0.54 0.00 0.00 2.85
568 744 8.227119 AGTTCAACAAAATTTGGAAAAAGTTCG 58.773 29.630 10.71 0.00 34.28 3.95
972 1154 1.306654 TGGAATCGCTGGGTAGGGT 60.307 57.895 0.00 0.00 38.02 4.34
976 1158 1.683025 TCGGTGGAATCGCTGGGTA 60.683 57.895 0.00 0.00 0.00 3.69
1052 1234 3.461773 AGTCCGTGCAGGGGATCG 61.462 66.667 24.54 5.33 41.52 3.69
1080 1262 1.039233 GGGAGGCAATGGTGGTGATG 61.039 60.000 0.00 0.00 0.00 3.07
1082 1264 2.763215 GGGAGGCAATGGTGGTGA 59.237 61.111 0.00 0.00 0.00 4.02
1113 1295 1.232216 GTAGATCTGGGTCCCGGGA 59.768 63.158 22.63 22.63 0.00 5.14
1122 1304 3.190874 GCGGAGTTTCTTGTAGATCTGG 58.809 50.000 5.18 0.00 0.00 3.86
1178 1361 4.499188 CGAAATGCAGGAGGACGACTAATA 60.499 45.833 0.00 0.00 0.00 0.98
1179 1362 3.738281 CGAAATGCAGGAGGACGACTAAT 60.738 47.826 0.00 0.00 0.00 1.73
1180 1363 2.416836 CGAAATGCAGGAGGACGACTAA 60.417 50.000 0.00 0.00 0.00 2.24
1217 1400 2.322830 GCGAAACGGGGGAACAGAC 61.323 63.158 0.00 0.00 0.00 3.51
1229 1412 0.040067 CCAAGAACAGCCTGCGAAAC 60.040 55.000 0.00 0.00 0.00 2.78
1319 1502 0.687354 AGGTTGACGAGCAGATTGGT 59.313 50.000 0.00 0.00 0.00 3.67
1419 1602 1.174712 TACTGATACTACGGCCGGCC 61.175 60.000 36.69 36.69 0.00 6.13
1420 1603 0.240411 CTACTGATACTACGGCCGGC 59.760 60.000 31.76 21.18 0.00 6.13
1421 1604 1.602311 ACTACTGATACTACGGCCGG 58.398 55.000 31.76 15.62 0.00 6.13
1422 1605 3.397482 ACTACTACTGATACTACGGCCG 58.603 50.000 26.86 26.86 0.00 6.13
1441 1624 1.270147 GCCGTGACAACAAGACCTACT 60.270 52.381 0.00 0.00 0.00 2.57
1442 1625 1.145803 GCCGTGACAACAAGACCTAC 58.854 55.000 0.00 0.00 0.00 3.18
1443 1626 0.319211 CGCCGTGACAACAAGACCTA 60.319 55.000 0.00 0.00 0.00 3.08
1444 1627 1.594293 CGCCGTGACAACAAGACCT 60.594 57.895 0.00 0.00 0.00 3.85
1445 1628 2.935955 CGCCGTGACAACAAGACC 59.064 61.111 0.00 0.00 0.00 3.85
1446 1629 2.248431 GCGCCGTGACAACAAGAC 59.752 61.111 0.00 0.00 0.00 3.01
1447 1630 2.970324 GGCGCCGTGACAACAAGA 60.970 61.111 12.58 0.00 0.00 3.02
1448 1631 4.025401 GGGCGCCGTGACAACAAG 62.025 66.667 22.54 0.00 0.00 3.16
1449 1632 4.555709 AGGGCGCCGTGACAACAA 62.556 61.111 22.97 0.00 0.00 2.83
1450 1633 4.980805 GAGGGCGCCGTGACAACA 62.981 66.667 28.98 0.00 0.00 3.33
1451 1634 4.681978 AGAGGGCGCCGTGACAAC 62.682 66.667 28.98 11.77 0.00 3.32
1452 1635 2.102109 TAAAGAGGGCGCCGTGACAA 62.102 55.000 28.98 6.55 0.00 3.18
1453 1636 2.102109 TTAAAGAGGGCGCCGTGACA 62.102 55.000 28.98 5.77 0.00 3.58
1454 1637 0.952010 TTTAAAGAGGGCGCCGTGAC 60.952 55.000 28.98 13.41 0.00 3.67
1455 1638 0.250381 TTTTAAAGAGGGCGCCGTGA 60.250 50.000 28.98 5.92 0.00 4.35
1456 1639 0.808755 ATTTTAAAGAGGGCGCCGTG 59.191 50.000 28.98 0.00 0.00 4.94
1457 1640 1.541379 AATTTTAAAGAGGGCGCCGT 58.459 45.000 23.89 23.89 0.00 5.68
1458 1641 2.540973 GCTAATTTTAAAGAGGGCGCCG 60.541 50.000 22.54 1.58 0.00 6.46
1459 1642 2.540973 CGCTAATTTTAAAGAGGGCGCC 60.541 50.000 21.18 21.18 35.34 6.53
1460 1643 2.096980 ACGCTAATTTTAAAGAGGGCGC 59.903 45.455 19.57 0.00 44.17 6.53
1461 1644 3.486875 CCACGCTAATTTTAAAGAGGGCG 60.487 47.826 18.67 18.67 45.49 6.13
1462 1645 3.442625 ACCACGCTAATTTTAAAGAGGGC 59.557 43.478 9.43 4.08 0.00 5.19
1463 1646 5.878669 ACTACCACGCTAATTTTAAAGAGGG 59.121 40.000 8.46 8.46 0.00 4.30
1464 1647 6.980051 ACTACCACGCTAATTTTAAAGAGG 57.020 37.500 0.00 0.00 0.00 3.69
1465 1648 8.699283 ACTACTACCACGCTAATTTTAAAGAG 57.301 34.615 0.00 0.00 0.00 2.85
1466 1649 7.761249 GGACTACTACCACGCTAATTTTAAAGA 59.239 37.037 0.00 0.00 0.00 2.52
1467 1650 7.010830 GGGACTACTACCACGCTAATTTTAAAG 59.989 40.741 0.00 0.00 0.00 1.85
1468 1651 6.818142 GGGACTACTACCACGCTAATTTTAAA 59.182 38.462 0.00 0.00 0.00 1.52
1469 1652 6.340522 GGGACTACTACCACGCTAATTTTAA 58.659 40.000 0.00 0.00 0.00 1.52
1470 1653 5.450412 CGGGACTACTACCACGCTAATTTTA 60.450 44.000 0.00 0.00 0.00 1.52
1471 1654 4.678840 CGGGACTACTACCACGCTAATTTT 60.679 45.833 0.00 0.00 0.00 1.82
1472 1655 3.181483 CGGGACTACTACCACGCTAATTT 60.181 47.826 0.00 0.00 0.00 1.82
1473 1656 2.360165 CGGGACTACTACCACGCTAATT 59.640 50.000 0.00 0.00 0.00 1.40
1548 1752 3.369147 CGCACTAATTTGACACAGAGAGG 59.631 47.826 0.00 0.00 0.00 3.69
1601 1805 0.762418 AACACTCCATCGTCAACCCA 59.238 50.000 0.00 0.00 0.00 4.51
1604 1808 2.602217 GCACAAACACTCCATCGTCAAC 60.602 50.000 0.00 0.00 0.00 3.18
1606 1810 1.202639 AGCACAAACACTCCATCGTCA 60.203 47.619 0.00 0.00 0.00 4.35
1649 1853 1.459348 TGCTGACCAGACCAGACCA 60.459 57.895 0.47 0.00 33.65 4.02
1650 1854 1.004440 GTGCTGACCAGACCAGACC 60.004 63.158 0.47 0.00 33.65 3.85
1651 1855 1.373497 CGTGCTGACCAGACCAGAC 60.373 63.158 0.47 0.00 33.65 3.51
1652 1856 3.051210 CGTGCTGACCAGACCAGA 58.949 61.111 0.47 0.00 33.65 3.86
1653 1857 2.721971 AAGCGTGCTGACCAGACCAG 62.722 60.000 0.47 0.00 34.88 4.00
1654 1858 2.807107 AAGCGTGCTGACCAGACCA 61.807 57.895 0.47 0.00 0.00 4.02
1655 1859 2.031163 AAGCGTGCTGACCAGACC 59.969 61.111 0.47 0.00 0.00 3.85
1656 1860 3.248029 CAAGCGTGCTGACCAGAC 58.752 61.111 0.47 0.00 0.00 3.51
1666 1870 2.094803 TGGACCATAATTTGCAAGCGTG 60.095 45.455 0.00 0.00 0.00 5.34
1667 1871 2.094752 GTGGACCATAATTTGCAAGCGT 60.095 45.455 0.00 0.00 0.00 5.07
1668 1872 2.164219 AGTGGACCATAATTTGCAAGCG 59.836 45.455 0.00 0.00 0.00 4.68
1669 1873 3.874392 AGTGGACCATAATTTGCAAGC 57.126 42.857 0.00 0.00 0.00 4.01
1670 1874 6.455360 ACATAGTGGACCATAATTTGCAAG 57.545 37.500 0.00 0.00 0.00 4.01
1671 1875 7.946381 TTACATAGTGGACCATAATTTGCAA 57.054 32.000 0.00 0.00 0.00 4.08
1672 1876 7.230510 GGATTACATAGTGGACCATAATTTGCA 59.769 37.037 0.00 0.00 0.00 4.08
1673 1877 7.230510 TGGATTACATAGTGGACCATAATTTGC 59.769 37.037 0.00 0.00 0.00 3.68
1674 1878 8.690203 TGGATTACATAGTGGACCATAATTTG 57.310 34.615 0.00 0.00 0.00 2.32
1675 1879 9.881773 AATGGATTACATAGTGGACCATAATTT 57.118 29.630 0.00 0.00 39.40 1.82
1678 1882 8.100791 GCTAATGGATTACATAGTGGACCATAA 58.899 37.037 0.00 0.00 39.40 1.90
1679 1883 7.236640 TGCTAATGGATTACATAGTGGACCATA 59.763 37.037 0.00 0.00 39.40 2.74
1680 1884 6.044287 TGCTAATGGATTACATAGTGGACCAT 59.956 38.462 0.00 0.00 39.40 3.55
1787 2025 0.532862 AGGTGTGGCGAAGTGACAAG 60.533 55.000 0.00 0.00 0.00 3.16
1889 2128 5.118286 AGTTTTTGGAAAGTTTGGAGCATG 58.882 37.500 0.00 0.00 0.00 4.06
1925 2164 7.171653 TCCCAACAAAAATCAGTTTCCTTTTT 58.828 30.769 0.00 0.00 33.57 1.94
1926 2165 6.716284 TCCCAACAAAAATCAGTTTCCTTTT 58.284 32.000 0.00 0.00 0.00 2.27
1927 2166 6.306643 TCCCAACAAAAATCAGTTTCCTTT 57.693 33.333 0.00 0.00 0.00 3.11
1928 2167 5.948742 TCCCAACAAAAATCAGTTTCCTT 57.051 34.783 0.00 0.00 0.00 3.36
1929 2168 5.948742 TTCCCAACAAAAATCAGTTTCCT 57.051 34.783 0.00 0.00 0.00 3.36
1930 2169 6.054941 ACATTCCCAACAAAAATCAGTTTCC 58.945 36.000 0.00 0.00 0.00 3.13
1931 2170 7.279758 TGAACATTCCCAACAAAAATCAGTTTC 59.720 33.333 0.00 0.00 0.00 2.78
2031 2274 3.518634 TGGTTTTGTCTGCTTTTGTCC 57.481 42.857 0.00 0.00 0.00 4.02
2070 2313 9.507329 TGAAGAGCTTGAACACTTATCTAAATT 57.493 29.630 0.00 0.00 0.00 1.82
2071 2314 9.507329 TTGAAGAGCTTGAACACTTATCTAAAT 57.493 29.630 0.00 0.00 0.00 1.40
2076 2319 7.643579 ACTTTTGAAGAGCTTGAACACTTATC 58.356 34.615 0.00 0.00 0.00 1.75
2078 2321 8.677148 ATACTTTTGAAGAGCTTGAACACTTA 57.323 30.769 0.00 0.00 0.00 2.24
2088 2331 4.020485 ACGTGGGTATACTTTTGAAGAGCT 60.020 41.667 2.25 0.00 0.00 4.09
2138 2381 9.149225 TGTTAAGTTACGTGAACACTTTTCTAA 57.851 29.630 0.00 0.00 40.86 2.10
2139 2382 8.700722 TGTTAAGTTACGTGAACACTTTTCTA 57.299 30.769 0.00 0.00 40.86 2.10
2140 2383 7.599630 TGTTAAGTTACGTGAACACTTTTCT 57.400 32.000 0.00 0.00 40.86 2.52
2141 2384 8.658171 TTTGTTAAGTTACGTGAACACTTTTC 57.342 30.769 0.00 0.00 40.86 2.29
2142 2385 8.505625 TCTTTGTTAAGTTACGTGAACACTTTT 58.494 29.630 0.00 0.00 40.86 2.27
2143 2386 8.031848 TCTTTGTTAAGTTACGTGAACACTTT 57.968 30.769 0.00 0.00 40.86 2.66
2144 2387 7.599630 TCTTTGTTAAGTTACGTGAACACTT 57.400 32.000 0.00 3.97 40.86 3.16
2145 2388 7.781548 ATCTTTGTTAAGTTACGTGAACACT 57.218 32.000 0.00 0.00 40.86 3.55
2146 2389 7.906527 ACAATCTTTGTTAAGTTACGTGAACAC 59.093 33.333 0.00 0.00 42.22 3.32
2147 2390 7.976826 ACAATCTTTGTTAAGTTACGTGAACA 58.023 30.769 0.00 0.00 42.22 3.18
2206 2450 8.529424 AACATATTTGGAGACATGTGATCATT 57.471 30.769 1.15 0.00 42.32 2.57
2207 2451 7.041576 CGAACATATTTGGAGACATGTGATCAT 60.042 37.037 1.15 0.00 42.32 2.45
2208 2452 6.258507 CGAACATATTTGGAGACATGTGATCA 59.741 38.462 1.15 0.00 42.32 2.92
2209 2453 6.479990 TCGAACATATTTGGAGACATGTGATC 59.520 38.462 1.15 0.36 42.32 2.92
2211 2455 5.729510 TCGAACATATTTGGAGACATGTGA 58.270 37.500 1.15 0.00 42.32 3.58
2212 2456 5.812127 TCTCGAACATATTTGGAGACATGTG 59.188 40.000 1.15 0.00 42.32 3.21
2213 2457 5.812642 GTCTCGAACATATTTGGAGACATGT 59.187 40.000 22.61 0.00 42.32 3.21
2214 2458 6.045318 AGTCTCGAACATATTTGGAGACATG 58.955 40.000 25.69 0.00 42.32 3.21
2215 2459 6.227298 AGTCTCGAACATATTTGGAGACAT 57.773 37.500 25.69 16.70 42.32 3.06
2216 2460 5.661056 AGTCTCGAACATATTTGGAGACA 57.339 39.130 25.69 6.41 39.75 3.41
2217 2461 6.797454 AGTAGTCTCGAACATATTTGGAGAC 58.203 40.000 21.38 21.38 38.18 3.36
2218 2462 7.406031 AAGTAGTCTCGAACATATTTGGAGA 57.594 36.000 7.66 7.66 0.00 3.71
2219 2463 9.751542 ATAAAGTAGTCTCGAACATATTTGGAG 57.248 33.333 0.00 0.00 0.00 3.86
2253 2497 8.835439 GGAACAAACATGTTTTTGAATGGTATT 58.165 29.630 21.10 1.02 38.54 1.89
2279 2523 7.646314 TCAATGCCACAACCATTTTTAAAATG 58.354 30.769 19.99 19.99 30.90 2.32
2284 2528 6.599244 TGTTTTCAATGCCACAACCATTTTTA 59.401 30.769 0.00 0.00 30.90 1.52
2290 2534 3.616956 TTGTTTTCAATGCCACAACCA 57.383 38.095 0.00 0.00 34.60 3.67
2314 2559 7.326454 TCCAAACATTCTTTTGAAACATGTGA 58.674 30.769 0.00 0.00 42.31 3.58


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

AutoCloner maintained by Alex Coulton.