Multiple sequence alignment - TraesCS4A01G368100

Loading Multiple Alignment...

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 TraesCS4A01G368100 chr4A 100.000 2399 0 0 1 2399 640999229 641001627 0.000000e+00 4431.0
1 TraesCS4A01G368100 chr4A 80.581 860 102 36 557 1402 640916089 640916897 9.490000e-169 603.0
2 TraesCS4A01G368100 chr4A 79.739 153 15 13 476 619 640941885 640942030 1.960000e-16 97.1
3 TraesCS4A01G368100 chr4A 94.000 50 3 0 251 300 640903722 640903771 2.560000e-10 76.8
4 TraesCS4A01G368100 chr5D 86.713 1731 123 52 34 1708 531413065 531411386 0.000000e+00 1823.0
5 TraesCS4A01G368100 chr5D 83.566 858 78 33 566 1405 531445516 531444704 0.000000e+00 745.0
6 TraesCS4A01G368100 chr5D 92.490 506 37 1 1738 2243 329429336 329428832 0.000000e+00 723.0
7 TraesCS4A01G368100 chr5D 85.876 708 57 27 34 721 531419078 531418394 0.000000e+00 713.0
8 TraesCS4A01G368100 chr5D 81.777 889 99 33 565 1443 531463045 531462210 0.000000e+00 686.0
9 TraesCS4A01G368100 chr5D 95.531 179 8 0 2221 2399 496734697 496734875 1.090000e-73 287.0
10 TraesCS4A01G368100 chr5D 96.970 33 1 0 1 33 370736557 370736525 3.330000e-04 56.5
11 TraesCS4A01G368100 chr5D 96.970 33 1 0 1 33 532654470 532654438 3.330000e-04 56.5
12 TraesCS4A01G368100 chr5B 86.169 1352 80 47 430 1741 670695219 670693935 0.000000e+00 1362.0
13 TraesCS4A01G368100 chr5B 84.436 816 80 27 566 1368 670717196 670716415 0.000000e+00 760.0
14 TraesCS4A01G368100 chr5B 88.757 169 8 4 34 202 670710403 670710246 1.880000e-46 196.0
15 TraesCS4A01G368100 chr5B 83.471 121 13 6 563 678 670802056 670801938 3.260000e-19 106.0
16 TraesCS4A01G368100 chr2A 97.882 661 14 0 1739 2399 433711168 433711828 0.000000e+00 1144.0
17 TraesCS4A01G368100 chr7A 95.008 661 32 1 1739 2399 38946626 38947285 0.000000e+00 1037.0
18 TraesCS4A01G368100 chr3D 92.643 666 45 4 1735 2398 1305483 1304820 0.000000e+00 955.0
19 TraesCS4A01G368100 chr6D 92.157 663 49 3 1738 2398 469369978 469369317 0.000000e+00 933.0
20 TraesCS4A01G368100 chr6D 85.714 658 84 6 1742 2398 356194729 356194081 0.000000e+00 686.0
21 TraesCS4A01G368100 chr1D 92.145 662 49 3 1739 2398 75855283 75854623 0.000000e+00 931.0
22 TraesCS4A01G368100 chr1D 91.403 663 54 3 1738 2398 50045376 50046037 0.000000e+00 905.0
23 TraesCS4A01G368100 chr1D 81.022 137 24 2 1046 1180 425921397 425921533 9.070000e-20 108.0
24 TraesCS4A01G368100 chr1D 96.970 33 1 0 1 33 359714652 359714684 3.330000e-04 56.5
25 TraesCS4A01G368100 chr1A 91.248 537 46 1 1743 2279 560439265 560438730 0.000000e+00 730.0
26 TraesCS4A01G368100 chrUn 90.850 153 14 0 2245 2397 477905164 477905012 3.130000e-49 206.0
27 TraesCS4A01G368100 chrUn 96.970 33 1 0 1 33 283046356 283046324 3.330000e-04 56.5
28 TraesCS4A01G368100 chrUn 96.970 33 1 0 1 33 287221707 287221675 3.330000e-04 56.5
29 TraesCS4A01G368100 chrUn 96.970 33 1 0 1 33 364763775 364763743 3.330000e-04 56.5
30 TraesCS4A01G368100 chr3B 100.000 33 0 0 1 33 42176243 42176275 7.160000e-06 62.1
31 TraesCS4A01G368100 chr3B 100.000 33 0 0 1 33 568294878 568294846 7.160000e-06 62.1
32 TraesCS4A01G368100 chr4D 96.970 33 1 0 1 33 306427359 306427327 3.330000e-04 56.5


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 TraesCS4A01G368100 chr4A 640999229 641001627 2398 False 4431 4431 100.000 1 2399 1 chr4A.!!$F4 2398
1 TraesCS4A01G368100 chr4A 640916089 640916897 808 False 603 603 80.581 557 1402 1 chr4A.!!$F2 845
2 TraesCS4A01G368100 chr5D 531411386 531413065 1679 True 1823 1823 86.713 34 1708 1 chr5D.!!$R3 1674
3 TraesCS4A01G368100 chr5D 531444704 531445516 812 True 745 745 83.566 566 1405 1 chr5D.!!$R5 839
4 TraesCS4A01G368100 chr5D 329428832 329429336 504 True 723 723 92.490 1738 2243 1 chr5D.!!$R1 505
5 TraesCS4A01G368100 chr5D 531418394 531419078 684 True 713 713 85.876 34 721 1 chr5D.!!$R4 687
6 TraesCS4A01G368100 chr5D 531462210 531463045 835 True 686 686 81.777 565 1443 1 chr5D.!!$R6 878
7 TraesCS4A01G368100 chr5B 670693935 670695219 1284 True 1362 1362 86.169 430 1741 1 chr5B.!!$R1 1311
8 TraesCS4A01G368100 chr5B 670716415 670717196 781 True 760 760 84.436 566 1368 1 chr5B.!!$R3 802
9 TraesCS4A01G368100 chr2A 433711168 433711828 660 False 1144 1144 97.882 1739 2399 1 chr2A.!!$F1 660
10 TraesCS4A01G368100 chr7A 38946626 38947285 659 False 1037 1037 95.008 1739 2399 1 chr7A.!!$F1 660
11 TraesCS4A01G368100 chr3D 1304820 1305483 663 True 955 955 92.643 1735 2398 1 chr3D.!!$R1 663
12 TraesCS4A01G368100 chr6D 469369317 469369978 661 True 933 933 92.157 1738 2398 1 chr6D.!!$R2 660
13 TraesCS4A01G368100 chr6D 356194081 356194729 648 True 686 686 85.714 1742 2398 1 chr6D.!!$R1 656
14 TraesCS4A01G368100 chr1D 75854623 75855283 660 True 931 931 92.145 1739 2398 1 chr1D.!!$R1 659
15 TraesCS4A01G368100 chr1D 50045376 50046037 661 False 905 905 91.403 1738 2398 1 chr1D.!!$F1 660
16 TraesCS4A01G368100 chr1A 560438730 560439265 535 True 730 730 91.248 1743 2279 1 chr1A.!!$R1 536

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
505 535 0.037697 TAGACACCACACACGGATGC 60.038 55.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 1844 0.801251 AAATGAGCAGAGACGCAAGC 59.199 50.0 0.0 0.0 45.62 4.01 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
46 47 6.048509 GGGGTGCTATTTTCCATTTATGTTG 58.951 40.000 0.00 0.00 0.00 3.33
67 68 2.227968 GATTGACACGCACGGTCTGC 62.228 60.000 11.19 0.00 43.21 4.26
73 74 4.662961 CGCACGGTCTGCTGGACA 62.663 66.667 11.29 0.00 46.16 4.02
105 106 1.009389 GTTCACGCGCTAGCTTCAGT 61.009 55.000 13.93 4.36 42.32 3.41
214 217 1.070601 AGAAAAGGCACACCAAATGGC 59.929 47.619 0.00 0.00 42.75 4.40
231 235 3.072468 CTCACCGGTCCCGCCTTA 61.072 66.667 2.59 0.00 38.24 2.69
247 254 4.557205 CGCCTTAATCCCAGTAGTACATC 58.443 47.826 2.52 0.00 0.00 3.06
249 256 4.557205 CCTTAATCCCAGTAGTACATCGC 58.443 47.826 2.52 0.00 0.00 4.58
250 257 4.038763 CCTTAATCCCAGTAGTACATCGCA 59.961 45.833 2.52 0.00 0.00 5.10
253 260 2.172679 TCCCAGTAGTACATCGCAACA 58.827 47.619 2.52 0.00 0.00 3.33
254 261 2.764010 TCCCAGTAGTACATCGCAACAT 59.236 45.455 2.52 0.00 0.00 2.71
255 262 2.866156 CCCAGTAGTACATCGCAACATG 59.134 50.000 2.52 0.00 0.00 3.21
256 263 2.285220 CCAGTAGTACATCGCAACATGC 59.715 50.000 2.52 0.00 40.69 4.06
257 264 2.929398 CAGTAGTACATCGCAACATGCA 59.071 45.455 2.52 0.00 45.36 3.96
258 265 3.370672 CAGTAGTACATCGCAACATGCAA 59.629 43.478 2.52 0.00 45.36 4.08
260 267 5.234116 CAGTAGTACATCGCAACATGCAATA 59.766 40.000 2.52 0.00 45.36 1.90
261 268 4.801147 AGTACATCGCAACATGCAATAG 57.199 40.909 2.99 0.00 45.36 1.73
271 290 5.120519 CGCAACATGCAATAGTTTTTGGAAT 59.879 36.000 2.99 0.00 45.36 3.01
286 305 3.438216 TGGAATGGAAATCTGCACTGA 57.562 42.857 0.00 0.00 0.00 3.41
335 354 7.717568 TGCTCTGGTAGTACTCAAATTAGATC 58.282 38.462 0.00 0.00 0.00 2.75
348 367 6.003326 TCAAATTAGATCAGTGCCAAAGTGA 58.997 36.000 0.00 0.00 42.49 3.41
354 373 2.722094 TCAGTGCCAAAGTGAAAGTGT 58.278 42.857 0.00 0.00 35.20 3.55
356 375 2.684881 CAGTGCCAAAGTGAAAGTGTCT 59.315 45.455 0.00 0.00 0.00 3.41
357 376 2.684881 AGTGCCAAAGTGAAAGTGTCTG 59.315 45.455 0.00 0.00 0.00 3.51
373 392 2.028203 TGTCTGTCGATCCTCAAATGCA 60.028 45.455 0.00 0.00 0.00 3.96
374 393 2.349886 GTCTGTCGATCCTCAAATGCAC 59.650 50.000 0.00 0.00 0.00 4.57
413 441 2.101700 GAAGCATTCCTTCGCCTGG 58.898 57.895 0.00 0.00 40.49 4.45
414 442 0.678048 GAAGCATTCCTTCGCCTGGT 60.678 55.000 0.00 0.00 40.49 4.00
415 443 0.962356 AAGCATTCCTTCGCCTGGTG 60.962 55.000 0.00 0.00 0.00 4.17
425 453 2.398554 CGCCTGGTGAAATGGTCGG 61.399 63.158 0.00 0.00 0.00 4.79
436 464 3.766591 TGAAATGGTCGGGTTTATGCAAT 59.233 39.130 0.00 0.00 0.00 3.56
443 471 3.376859 GTCGGGTTTATGCAATGTCATCA 59.623 43.478 0.00 0.00 0.00 3.07
488 516 7.981789 ACATGTATTACACTGACTTCCATGTAG 59.018 37.037 0.00 0.00 38.74 2.74
501 531 1.428448 CATGTAGACACCACACACGG 58.572 55.000 0.00 0.00 0.00 4.94
502 532 1.000394 CATGTAGACACCACACACGGA 60.000 52.381 0.00 0.00 0.00 4.69
503 533 1.334160 TGTAGACACCACACACGGAT 58.666 50.000 0.00 0.00 0.00 4.18
504 534 1.000394 TGTAGACACCACACACGGATG 60.000 52.381 0.00 0.00 0.00 3.51
505 535 0.037697 TAGACACCACACACGGATGC 60.038 55.000 0.00 0.00 0.00 3.91
506 536 2.281484 ACACCACACACGGATGCC 60.281 61.111 0.00 0.00 0.00 4.40
539 570 1.620819 TCTCCTCAAGCACCAGAGAAC 59.379 52.381 0.00 0.00 33.74 3.01
543 574 2.951642 CCTCAAGCACCAGAGAACAAAA 59.048 45.455 0.00 0.00 33.74 2.44
551 594 7.440523 AGCACCAGAGAACAAAAATACTAAG 57.559 36.000 0.00 0.00 0.00 2.18
619 662 5.843673 TTTCCAATCAAGCACAAAGTGTA 57.156 34.783 0.00 0.00 35.75 2.90
624 671 6.883756 TCCAATCAAGCACAAAGTGTATGATA 59.116 34.615 15.15 3.77 38.75 2.15
632 680 6.593770 AGCACAAAGTGTATGATATTGTCGAA 59.406 34.615 0.00 0.00 35.75 3.71
693 752 3.434299 ACGTCCAAGGTTAGCATAAAACG 59.566 43.478 0.00 0.00 0.00 3.60
820 897 1.549493 GCCGCTCCCTCCCTATAAGTA 60.549 57.143 0.00 0.00 0.00 2.24
885 962 1.153086 TACCGCTACTCGTCCTCCC 60.153 63.158 0.00 0.00 36.19 4.30
888 965 1.828660 CGCTACTCGTCCTCCCCAT 60.829 63.158 0.00 0.00 0.00 4.00
905 982 0.651610 CATCGCACGCGCTTAATCAC 60.652 55.000 5.73 0.00 39.59 3.06
927 1005 3.339141 CTTCTTCTACCACCTTCTTGCC 58.661 50.000 0.00 0.00 0.00 4.52
945 1029 1.679898 CTCCACCACCAAGAGACCC 59.320 63.158 0.00 0.00 0.00 4.46
952 1036 1.920835 ACCAAGAGACCCAGAGCCC 60.921 63.158 0.00 0.00 0.00 5.19
973 1062 4.798344 CAGAGCCAGCCAGCCAGG 62.798 72.222 0.00 0.00 41.84 4.45
985 1075 1.849823 AGCCAGGAGCCAAGAACCT 60.850 57.895 0.00 0.00 45.47 3.50
990 1080 1.377856 GGAGCCAAGAACCTGCCTC 60.378 63.158 0.00 0.00 0.00 4.70
1013 1103 2.570181 GCCCATGTCTGTGCAAGC 59.430 61.111 0.00 0.00 0.00 4.01
1122 1218 2.571757 CGACGGCAGCTGTTCCTA 59.428 61.111 16.64 0.00 0.00 2.94
1125 1221 2.209064 GACGGCAGCTGTTCCTACGA 62.209 60.000 16.64 0.00 0.00 3.43
1402 1509 0.176680 CGTCTGCTTCTGGTAGCCAT 59.823 55.000 0.00 0.00 40.49 4.40
1403 1510 1.409064 CGTCTGCTTCTGGTAGCCATA 59.591 52.381 0.00 0.00 40.49 2.74
1484 1609 3.192422 TGAAACAATTAGCCGGTGAATGG 59.808 43.478 1.90 3.19 0.00 3.16
1489 1614 0.179094 TTAGCCGGTGAATGGTAGCG 60.179 55.000 1.90 0.00 38.63 4.26
1533 1658 2.804090 GGAGTGTTCGTCGTCGCC 60.804 66.667 0.00 0.00 36.96 5.54
1538 1663 3.470567 GTTCGTCGTCGCCTGCTG 61.471 66.667 0.00 0.00 36.96 4.41
1558 1683 1.721926 GTGCTCGCTGTTTGACTAGAC 59.278 52.381 0.00 0.00 0.00 2.59
1559 1684 1.613925 TGCTCGCTGTTTGACTAGACT 59.386 47.619 0.00 0.00 0.00 3.24
1560 1685 2.817844 TGCTCGCTGTTTGACTAGACTA 59.182 45.455 0.00 0.00 0.00 2.59
1561 1686 3.119814 TGCTCGCTGTTTGACTAGACTAG 60.120 47.826 8.00 8.00 0.00 2.57
1562 1687 3.127203 GCTCGCTGTTTGACTAGACTAGA 59.873 47.826 16.55 0.00 0.00 2.43
1563 1688 4.729458 GCTCGCTGTTTGACTAGACTAGAG 60.729 50.000 16.55 3.15 0.00 2.43
1564 1689 4.576879 TCGCTGTTTGACTAGACTAGAGA 58.423 43.478 16.55 0.00 0.00 3.10
1569 1694 6.542370 GCTGTTTGACTAGACTAGAGAGAGAT 59.458 42.308 16.55 0.00 0.00 2.75
1577 1702 5.246981 AGACTAGAGAGAGATGGAGGATG 57.753 47.826 0.00 0.00 0.00 3.51
1691 1817 8.191446 TGAGTTAACTGTGTATCTATCTGAAGC 58.809 37.037 14.14 0.00 0.00 3.86
1709 1835 1.419387 AGCCTTCTCTGTTCTTGCTGT 59.581 47.619 0.00 0.00 0.00 4.40
1714 1840 1.486310 TCTCTGTTCTTGCTGTGGTGT 59.514 47.619 0.00 0.00 0.00 4.16
1718 1844 1.476085 TGTTCTTGCTGTGGTGTTTGG 59.524 47.619 0.00 0.00 0.00 3.28
1719 1845 0.459489 TTCTTGCTGTGGTGTTTGGC 59.541 50.000 0.00 0.00 0.00 4.52
1721 1847 0.461135 CTTGCTGTGGTGTTTGGCTT 59.539 50.000 0.00 0.00 0.00 4.35
1722 1848 0.175302 TTGCTGTGGTGTTTGGCTTG 59.825 50.000 0.00 0.00 0.00 4.01
1723 1849 1.592400 GCTGTGGTGTTTGGCTTGC 60.592 57.895 0.00 0.00 0.00 4.01
1725 1851 2.003658 CTGTGGTGTTTGGCTTGCGT 62.004 55.000 0.00 0.00 0.00 5.24
1733 1859 1.230635 TTTGGCTTGCGTCTCTGCTC 61.231 55.000 0.00 0.00 35.36 4.26
1942 2070 2.414481 GCAATTGCAACAAACACACACA 59.586 40.909 25.36 0.00 41.59 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.916934 AGGTACCCTAACTTGCATCCAA 59.083 45.455 8.74 0.00 28.47 3.53
1 2 2.238646 CAGGTACCCTAACTTGCATCCA 59.761 50.000 8.74 0.00 29.64 3.41
2 3 2.421529 CCAGGTACCCTAACTTGCATCC 60.422 54.545 8.74 0.00 29.64 3.51
3 4 2.421529 CCCAGGTACCCTAACTTGCATC 60.422 54.545 8.74 0.00 29.64 3.91
4 5 1.564348 CCCAGGTACCCTAACTTGCAT 59.436 52.381 8.74 0.00 29.64 3.96
5 6 0.988832 CCCAGGTACCCTAACTTGCA 59.011 55.000 8.74 0.00 29.64 4.08
6 7 0.255033 CCCCAGGTACCCTAACTTGC 59.745 60.000 8.74 0.00 29.64 4.01
7 8 1.280998 CACCCCAGGTACCCTAACTTG 59.719 57.143 8.74 0.00 32.11 3.16
8 9 1.665137 CACCCCAGGTACCCTAACTT 58.335 55.000 8.74 0.00 32.11 2.66
9 10 0.912968 GCACCCCAGGTACCCTAACT 60.913 60.000 8.74 0.00 32.11 2.24
10 11 0.912968 AGCACCCCAGGTACCCTAAC 60.913 60.000 8.74 0.00 32.11 2.34
11 12 0.717801 TAGCACCCCAGGTACCCTAA 59.282 55.000 8.74 0.00 32.11 2.69
12 13 0.946522 ATAGCACCCCAGGTACCCTA 59.053 55.000 8.74 1.02 32.11 3.53
13 14 0.045778 AATAGCACCCCAGGTACCCT 59.954 55.000 8.74 0.00 32.11 4.34
14 15 0.924090 AAATAGCACCCCAGGTACCC 59.076 55.000 8.74 0.00 32.11 3.69
15 16 2.651455 GAAAATAGCACCCCAGGTACC 58.349 52.381 2.73 2.73 32.11 3.34
16 17 2.025699 TGGAAAATAGCACCCCAGGTAC 60.026 50.000 0.00 0.00 32.11 3.34
17 18 2.280103 TGGAAAATAGCACCCCAGGTA 58.720 47.619 0.00 0.00 32.11 3.08
18 19 1.080638 TGGAAAATAGCACCCCAGGT 58.919 50.000 0.00 0.00 35.62 4.00
19 20 2.459555 ATGGAAAATAGCACCCCAGG 57.540 50.000 0.00 0.00 0.00 4.45
20 21 5.363580 ACATAAATGGAAAATAGCACCCCAG 59.636 40.000 0.00 0.00 0.00 4.45
21 22 5.276440 ACATAAATGGAAAATAGCACCCCA 58.724 37.500 0.00 0.00 0.00 4.96
22 23 5.869649 ACATAAATGGAAAATAGCACCCC 57.130 39.130 0.00 0.00 0.00 4.95
23 24 6.048509 CCAACATAAATGGAAAATAGCACCC 58.951 40.000 0.00 0.00 40.56 4.61
24 25 6.048509 CCCAACATAAATGGAAAATAGCACC 58.951 40.000 0.00 0.00 40.56 5.01
25 26 6.872920 TCCCAACATAAATGGAAAATAGCAC 58.127 36.000 0.00 0.00 40.56 4.40
26 27 7.673641 ATCCCAACATAAATGGAAAATAGCA 57.326 32.000 0.00 0.00 40.56 3.49
27 28 8.203485 TCAATCCCAACATAAATGGAAAATAGC 58.797 33.333 0.00 0.00 40.56 2.97
28 29 9.533253 GTCAATCCCAACATAAATGGAAAATAG 57.467 33.333 0.00 0.00 40.56 1.73
29 30 9.040259 TGTCAATCCCAACATAAATGGAAAATA 57.960 29.630 0.00 0.00 40.56 1.40
30 31 7.823799 GTGTCAATCCCAACATAAATGGAAAAT 59.176 33.333 0.00 0.00 40.56 1.82
31 32 7.158021 GTGTCAATCCCAACATAAATGGAAAA 58.842 34.615 0.00 0.00 40.56 2.29
32 33 6.571344 CGTGTCAATCCCAACATAAATGGAAA 60.571 38.462 0.00 0.00 40.56 3.13
46 47 2.358247 ACCGTGCGTGTCAATCCC 60.358 61.111 0.00 0.00 0.00 3.85
67 68 0.167470 CGCATGCTGAAACTGTCCAG 59.833 55.000 17.13 5.97 0.00 3.86
73 74 0.235665 CGTGAACGCATGCTGAAACT 59.764 50.000 17.13 0.00 0.00 2.66
74 75 2.699910 CGTGAACGCATGCTGAAAC 58.300 52.632 17.13 8.13 0.00 2.78
105 106 2.483877 CGCCTCTGTGCATGTTTAAAGA 59.516 45.455 0.00 0.00 0.00 2.52
149 152 3.890527 CCAGGCAGGCTTTAGACAT 57.109 52.632 0.00 0.00 0.00 3.06
174 177 1.001974 TCCTCTTGTGACCGTTGGATG 59.998 52.381 0.00 0.00 0.00 3.51
214 217 1.968050 ATTAAGGCGGGACCGGTGAG 61.968 60.000 14.63 3.56 46.52 3.51
231 235 3.196901 TGTTGCGATGTACTACTGGGATT 59.803 43.478 0.00 0.00 0.00 3.01
249 256 6.649973 TCCATTCCAAAAACTATTGCATGTTG 59.350 34.615 0.00 0.00 0.00 3.33
250 257 6.767456 TCCATTCCAAAAACTATTGCATGTT 58.233 32.000 0.00 0.00 0.00 2.71
253 260 8.323567 AGATTTCCATTCCAAAAACTATTGCAT 58.676 29.630 0.00 0.00 0.00 3.96
254 261 7.603404 CAGATTTCCATTCCAAAAACTATTGCA 59.397 33.333 0.00 0.00 0.00 4.08
255 262 7.413328 GCAGATTTCCATTCCAAAAACTATTGC 60.413 37.037 0.00 0.00 0.00 3.56
256 263 7.603404 TGCAGATTTCCATTCCAAAAACTATTG 59.397 33.333 0.00 0.00 0.00 1.90
257 264 7.603784 GTGCAGATTTCCATTCCAAAAACTATT 59.396 33.333 0.00 0.00 0.00 1.73
258 265 7.038799 AGTGCAGATTTCCATTCCAAAAACTAT 60.039 33.333 0.00 0.00 0.00 2.12
260 267 5.070847 AGTGCAGATTTCCATTCCAAAAACT 59.929 36.000 0.00 0.00 0.00 2.66
261 268 5.178067 CAGTGCAGATTTCCATTCCAAAAAC 59.822 40.000 0.00 0.00 0.00 2.43
271 290 2.636647 TGTGTCAGTGCAGATTTCCA 57.363 45.000 0.00 0.00 0.00 3.53
317 336 7.265673 TGGCACTGATCTAATTTGAGTACTAC 58.734 38.462 0.00 0.00 0.00 2.73
322 341 6.006449 ACTTTGGCACTGATCTAATTTGAGT 58.994 36.000 0.00 0.00 0.00 3.41
323 342 6.149973 TCACTTTGGCACTGATCTAATTTGAG 59.850 38.462 0.00 0.00 0.00 3.02
324 343 6.003326 TCACTTTGGCACTGATCTAATTTGA 58.997 36.000 0.00 0.00 0.00 2.69
325 344 6.258230 TCACTTTGGCACTGATCTAATTTG 57.742 37.500 0.00 0.00 0.00 2.32
326 345 6.899393 TTCACTTTGGCACTGATCTAATTT 57.101 33.333 0.00 0.00 0.00 1.82
335 354 2.684881 AGACACTTTCACTTTGGCACTG 59.315 45.455 0.00 0.00 0.00 3.66
348 367 4.336889 TTTGAGGATCGACAGACACTTT 57.663 40.909 0.00 0.00 38.61 2.66
354 373 2.234661 AGTGCATTTGAGGATCGACAGA 59.765 45.455 0.00 0.00 38.61 3.41
356 375 2.289631 ACAGTGCATTTGAGGATCGACA 60.290 45.455 8.02 0.00 38.61 4.35
357 376 2.094894 CACAGTGCATTTGAGGATCGAC 59.905 50.000 8.02 0.00 38.61 4.20
374 393 7.819753 GCTTCAGAGCAAAATTTATGGCACAG 61.820 42.308 10.75 3.66 46.35 3.66
406 434 1.375396 CGACCATTTCACCAGGCGA 60.375 57.895 0.00 0.00 0.00 5.54
407 435 2.398554 CCGACCATTTCACCAGGCG 61.399 63.158 0.00 0.00 0.00 5.52
409 437 0.251165 AACCCGACCATTTCACCAGG 60.251 55.000 0.00 0.00 0.00 4.45
410 438 1.616159 AAACCCGACCATTTCACCAG 58.384 50.000 0.00 0.00 0.00 4.00
411 439 2.953284 TAAACCCGACCATTTCACCA 57.047 45.000 0.00 0.00 0.00 4.17
412 440 2.159296 GCATAAACCCGACCATTTCACC 60.159 50.000 0.00 0.00 0.00 4.02
413 441 2.490115 TGCATAAACCCGACCATTTCAC 59.510 45.455 0.00 0.00 0.00 3.18
414 442 2.796557 TGCATAAACCCGACCATTTCA 58.203 42.857 0.00 0.00 0.00 2.69
415 443 3.859411 TTGCATAAACCCGACCATTTC 57.141 42.857 0.00 0.00 0.00 2.17
425 453 5.124457 ACAGTCTGATGACATTGCATAAACC 59.876 40.000 6.91 0.00 45.20 3.27
436 464 4.999311 CAGAAATTGGACAGTCTGATGACA 59.001 41.667 6.91 0.00 45.20 3.58
469 497 5.279306 GGTGTCTACATGGAAGTCAGTGTAA 60.279 44.000 0.00 0.00 0.00 2.41
488 516 2.325082 GGCATCCGTGTGTGGTGTC 61.325 63.158 0.00 0.00 0.00 3.67
501 531 2.935201 GAGAGTTGTCATGTCTGGCATC 59.065 50.000 0.00 0.00 36.73 3.91
502 532 2.355513 GGAGAGTTGTCATGTCTGGCAT 60.356 50.000 0.00 0.00 36.73 4.40
503 533 1.002430 GGAGAGTTGTCATGTCTGGCA 59.998 52.381 0.00 0.00 34.48 4.92
504 534 1.277557 AGGAGAGTTGTCATGTCTGGC 59.722 52.381 0.00 0.00 0.00 4.85
505 535 2.564504 TGAGGAGAGTTGTCATGTCTGG 59.435 50.000 0.00 0.00 0.00 3.86
506 536 3.949842 TGAGGAGAGTTGTCATGTCTG 57.050 47.619 0.00 0.00 0.00 3.51
551 594 7.171630 TCCTTCTAGTCTCTACCACAATTTC 57.828 40.000 0.00 0.00 0.00 2.17
555 598 4.463186 GCTTCCTTCTAGTCTCTACCACAA 59.537 45.833 0.00 0.00 0.00 3.33
632 680 6.127814 GGCGGGCTAATTTACTTTACTTTTCT 60.128 38.462 0.00 0.00 0.00 2.52
776 845 3.092511 TGGAGGATGAGGGGCTGC 61.093 66.667 0.00 0.00 0.00 5.25
905 982 3.339141 GCAAGAAGGTGGTAGAAGAAGG 58.661 50.000 0.00 0.00 0.00 3.46
927 1005 1.127567 TGGGTCTCTTGGTGGTGGAG 61.128 60.000 0.00 0.00 0.00 3.86
945 1029 4.527583 GGCTCTGCTCGGGCTCTG 62.528 72.222 9.62 0.00 39.59 3.35
971 1060 2.759795 GGCAGGTTCTTGGCTCCT 59.240 61.111 1.60 0.00 40.23 3.69
990 1080 4.457496 ACAGACATGGGCGCGGAG 62.457 66.667 8.83 0.00 0.00 4.63
1107 1203 1.812686 TTCGTAGGAACAGCTGCCGT 61.813 55.000 15.27 10.24 0.00 5.68
1122 1218 0.896226 GGGAGAAGTGGTAGCTTCGT 59.104 55.000 0.00 0.00 46.82 3.85
1125 1221 1.597461 GCGGGAGAAGTGGTAGCTT 59.403 57.895 0.00 0.00 0.00 3.74
1375 1482 4.415332 GAAGCAGACGGACGCGGA 62.415 66.667 12.47 0.00 0.00 5.54
1402 1509 1.080093 CTGACGCGTTGGCCTTCTA 60.080 57.895 15.53 0.00 35.02 2.10
1403 1510 2.357517 CTGACGCGTTGGCCTTCT 60.358 61.111 15.53 0.00 35.02 2.85
1533 1658 1.082300 CAAACAGCGAGCACAGCAG 60.082 57.895 0.00 0.00 37.01 4.24
1538 1663 1.721926 GTCTAGTCAAACAGCGAGCAC 59.278 52.381 0.00 0.00 0.00 4.40
1558 1683 7.890127 ACTTAATCATCCTCCATCTCTCTCTAG 59.110 40.741 0.00 0.00 0.00 2.43
1559 1684 7.764617 ACTTAATCATCCTCCATCTCTCTCTA 58.235 38.462 0.00 0.00 0.00 2.43
1560 1685 6.623329 ACTTAATCATCCTCCATCTCTCTCT 58.377 40.000 0.00 0.00 0.00 3.10
1561 1686 6.916360 ACTTAATCATCCTCCATCTCTCTC 57.084 41.667 0.00 0.00 0.00 3.20
1562 1687 8.646900 GTTTACTTAATCATCCTCCATCTCTCT 58.353 37.037 0.00 0.00 0.00 3.10
1563 1688 8.424918 TGTTTACTTAATCATCCTCCATCTCTC 58.575 37.037 0.00 0.00 0.00 3.20
1564 1689 8.324191 TGTTTACTTAATCATCCTCCATCTCT 57.676 34.615 0.00 0.00 0.00 3.10
1569 1694 5.631481 GCCCTGTTTACTTAATCATCCTCCA 60.631 44.000 0.00 0.00 0.00 3.86
1577 1702 4.622701 CAGCTGCCCTGTTTACTTAATC 57.377 45.455 0.00 0.00 36.79 1.75
1637 1762 9.273016 TCAGAGTAATTAGACACCAAAAAGAAG 57.727 33.333 0.00 0.00 0.00 2.85
1668 1794 7.493367 AGGCTTCAGATAGATACACAGTTAAC 58.507 38.462 0.00 0.00 0.00 2.01
1691 1817 2.149578 CCACAGCAAGAACAGAGAAGG 58.850 52.381 0.00 0.00 0.00 3.46
1709 1835 1.444119 GAGACGCAAGCCAAACACCA 61.444 55.000 0.00 0.00 45.62 4.17
1714 1840 1.227943 AGCAGAGACGCAAGCCAAA 60.228 52.632 0.00 0.00 45.62 3.28
1718 1844 0.801251 AAATGAGCAGAGACGCAAGC 59.199 50.000 0.00 0.00 45.62 4.01
1777 1903 9.790344 AACTCTATTCTTCTATAATGCATTGCT 57.210 29.630 22.27 11.39 0.00 3.91


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

AutoCloner maintained by Alex Coulton.