Multiple sequence alignment - TraesCS6B01G269800

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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 TraesCS6B01G269800 chr6B 100.000 2648 0 0 1 2648 485547481 485550128 0.000000e+00 4891
1 TraesCS6B01G269800 chr6B 81.899 1696 300 7 1 1693 599413228 599411537 0.000000e+00 1424
2 TraesCS6B01G269800 chr6B 94.015 802 45 2 1849 2648 150776272 150777072 0.000000e+00 1212
3 TraesCS6B01G269800 chr6B 93.035 804 48 5 1845 2648 80960679 80959884 0.000000e+00 1168
4 TraesCS6B01G269800 chr6B 91.646 802 59 6 1849 2648 129266791 129267586 0.000000e+00 1103
5 TraesCS6B01G269800 chr6B 91.272 802 59 10 1849 2648 478887408 478886616 0.000000e+00 1083
6 TraesCS6B01G269800 chr3B 94.544 1613 87 1 81 1692 275009431 275007819 0.000000e+00 2490
7 TraesCS6B01G269800 chr3B 92.612 1692 125 0 1 1692 778911073 778912764 0.000000e+00 2433
8 TraesCS6B01G269800 chr3B 92.158 1696 132 1 1 1696 778993283 778994977 0.000000e+00 2394
9 TraesCS6B01G269800 chr3B 91.925 805 59 5 1846 2648 809332551 809331751 0.000000e+00 1122
10 TraesCS6B01G269800 chr2B 92.359 1662 122 2 1 1661 756620873 756619216 0.000000e+00 2361
11 TraesCS6B01G269800 chr2B 90.414 1690 160 2 1 1689 126425461 126423773 0.000000e+00 2222
12 TraesCS6B01G269800 chr2B 88.675 1713 189 4 1 1712 783645725 783644017 0.000000e+00 2084
13 TraesCS6B01G269800 chr2B 93.524 803 47 3 1847 2648 796286618 796285820 0.000000e+00 1190
14 TraesCS6B01G269800 chr4A 84.525 1693 254 8 1 1690 152768685 152770372 0.000000e+00 1668
15 TraesCS6B01G269800 chr4D 83.570 1692 269 9 1 1689 47251015 47249330 0.000000e+00 1576
16 TraesCS6B01G269800 chr7B 93.375 800 47 3 1849 2648 369876913 369876120 0.000000e+00 1179
17 TraesCS6B01G269800 chr7B 91.532 803 58 6 1847 2648 275464540 275463747 0.000000e+00 1098
18 TraesCS6B01G269800 chr3A 91.656 803 61 5 1849 2648 663279667 663280466 0.000000e+00 1107
19 TraesCS6B01G269800 chr6D 96.104 154 6 0 1695 1848 335057887 335057734 4.380000e-63 252
20 TraesCS6B01G269800 chr6A 96.324 136 5 0 1714 1849 474326566 474326431 9.540000e-55 224
21 TraesCS6B01G269800 chr6A 91.772 158 9 2 1695 1849 474326938 474326782 1.600000e-52 217


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 TraesCS6B01G269800 chr6B 485547481 485550128 2647 False 4891.0 4891 100.000 1 2648 1 chr6B.!!$F3 2647
1 TraesCS6B01G269800 chr6B 599411537 599413228 1691 True 1424.0 1424 81.899 1 1693 1 chr6B.!!$R3 1692
2 TraesCS6B01G269800 chr6B 150776272 150777072 800 False 1212.0 1212 94.015 1849 2648 1 chr6B.!!$F2 799
3 TraesCS6B01G269800 chr6B 80959884 80960679 795 True 1168.0 1168 93.035 1845 2648 1 chr6B.!!$R1 803
4 TraesCS6B01G269800 chr6B 129266791 129267586 795 False 1103.0 1103 91.646 1849 2648 1 chr6B.!!$F1 799
5 TraesCS6B01G269800 chr6B 478886616 478887408 792 True 1083.0 1083 91.272 1849 2648 1 chr6B.!!$R2 799
6 TraesCS6B01G269800 chr3B 275007819 275009431 1612 True 2490.0 2490 94.544 81 1692 1 chr3B.!!$R1 1611
7 TraesCS6B01G269800 chr3B 778911073 778912764 1691 False 2433.0 2433 92.612 1 1692 1 chr3B.!!$F1 1691
8 TraesCS6B01G269800 chr3B 778993283 778994977 1694 False 2394.0 2394 92.158 1 1696 1 chr3B.!!$F2 1695
9 TraesCS6B01G269800 chr3B 809331751 809332551 800 True 1122.0 1122 91.925 1846 2648 1 chr3B.!!$R2 802
10 TraesCS6B01G269800 chr2B 756619216 756620873 1657 True 2361.0 2361 92.359 1 1661 1 chr2B.!!$R2 1660
11 TraesCS6B01G269800 chr2B 126423773 126425461 1688 True 2222.0 2222 90.414 1 1689 1 chr2B.!!$R1 1688
12 TraesCS6B01G269800 chr2B 783644017 783645725 1708 True 2084.0 2084 88.675 1 1712 1 chr2B.!!$R3 1711
13 TraesCS6B01G269800 chr2B 796285820 796286618 798 True 1190.0 1190 93.524 1847 2648 1 chr2B.!!$R4 801
14 TraesCS6B01G269800 chr4A 152768685 152770372 1687 False 1668.0 1668 84.525 1 1690 1 chr4A.!!$F1 1689
15 TraesCS6B01G269800 chr4D 47249330 47251015 1685 True 1576.0 1576 83.570 1 1689 1 chr4D.!!$R1 1688
16 TraesCS6B01G269800 chr7B 369876120 369876913 793 True 1179.0 1179 93.375 1849 2648 1 chr7B.!!$R2 799
17 TraesCS6B01G269800 chr7B 275463747 275464540 793 True 1098.0 1098 91.532 1847 2648 1 chr7B.!!$R1 801
18 TraesCS6B01G269800 chr3A 663279667 663280466 799 False 1107.0 1107 91.656 1849 2648 1 chr3A.!!$F1 799
19 TraesCS6B01G269800 chr6A 474326431 474326938 507 True 220.5 224 94.048 1695 1849 2 chr6A.!!$R1 154

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
849 855 0.035152 ATGCGATCTTTGGGTGCTCA 60.035 50.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 2200 0.328258 TGGAGTTGGCCTAAAGCTCC 59.672 55.0 15.26 15.26 44.31 4.7 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
45 46 1.264020 GACGGGGAAAACCAACGTAAC 59.736 52.381 0.00 0.00 42.91 2.50
102 103 2.280079 GAAAGAGGGGGCATGGGG 59.720 66.667 0.00 0.00 0.00 4.96
160 161 2.029918 GCTAAACAGGTTTGGAGGCTTG 60.030 50.000 11.76 0.00 33.57 4.01
373 379 2.205022 CTGGATTCCCAACAGCTCAA 57.795 50.000 0.00 0.00 42.98 3.02
440 446 5.671493 AGTTAATGAACTTATCGACCCAGG 58.329 41.667 0.00 0.00 43.70 4.45
460 466 1.146566 GCTCTGGGGAATGGGATGAAT 59.853 52.381 0.00 0.00 0.00 2.57
512 518 2.033550 ACGCTGATCGGATCTTACAGAC 59.966 50.000 18.16 4.75 43.86 3.51
567 573 1.273048 GCATGGCATTTGACAAGGTCA 59.727 47.619 0.00 0.00 41.09 4.02
630 636 4.243270 AGGACTCGTATGTAAGCAACAAC 58.757 43.478 0.00 0.00 42.70 3.32
639 645 2.290071 TGTAAGCAACAACCCTAGCTCC 60.290 50.000 0.00 0.00 36.07 4.70
640 646 1.068121 AAGCAACAACCCTAGCTCCT 58.932 50.000 0.00 0.00 36.07 3.69
644 650 2.619074 GCAACAACCCTAGCTCCTTCAT 60.619 50.000 0.00 0.00 0.00 2.57
663 669 4.575885 TCATAAGTGCTTCTGGTAACCAC 58.424 43.478 0.00 0.00 0.00 4.16
729 735 3.513515 TGAAAATTTTCTTATGGCGGGCT 59.486 39.130 26.73 0.00 38.02 5.19
769 775 2.837591 TGCTTTGGAGTACTGGCTGATA 59.162 45.455 0.00 0.00 0.00 2.15
843 849 1.314534 TGGCACATGCGATCTTTGGG 61.315 55.000 0.00 0.00 43.26 4.12
849 855 0.035152 ATGCGATCTTTGGGTGCTCA 60.035 50.000 0.00 0.00 0.00 4.26
939 945 0.038159 CGGGAGCGGAGATATTGGAC 60.038 60.000 0.00 0.00 0.00 4.02
955 961 4.350368 TTGGACTTTCTGCTGTGTGATA 57.650 40.909 0.00 0.00 0.00 2.15
1015 1021 0.904649 AGAGATGATTGCGGTGACCA 59.095 50.000 1.11 0.00 0.00 4.02
1105 1111 0.526211 ACAAGCGATACGAGCTGTCA 59.474 50.000 0.00 0.00 45.31 3.58
1153 1159 2.056906 AAAGGCAGTCGCTCCAAGGT 62.057 55.000 0.00 0.00 38.60 3.50
1245 1251 4.574674 TTATTCTGGATCTTGTGGTGCT 57.425 40.909 0.00 0.00 0.00 4.40
1273 1279 2.416547 CGAGATGGTGCTGGTTACTTTG 59.583 50.000 0.00 0.00 0.00 2.77
1288 1294 3.758973 TTTGTTGCGGCCTCCACGA 62.759 57.895 0.00 0.00 0.00 4.35
1305 1311 1.202582 ACGACGAAGCTAGAGCATGTT 59.797 47.619 0.00 0.00 45.16 2.71
1364 1370 1.518903 GGCTTGAAGCTTGCTCGGTT 61.519 55.000 17.59 0.00 41.99 4.44
1383 1389 4.039973 CGGTTAGTGGGAGCTAATTCCATA 59.960 45.833 0.00 0.00 39.09 2.74
1432 1439 4.202336 TGGTGGATGCAATGACAAACAATT 60.202 37.500 0.00 0.00 0.00 2.32
1464 1471 2.263895 TGGTGGCTAGTCCCATACTT 57.736 50.000 0.87 0.00 39.80 2.24
1710 1717 3.601685 AAACAAACAGGCCGGCGG 61.602 61.111 24.35 24.35 0.00 6.13
1758 2118 3.427863 GCGTTTACCACTGTAGTCTTGTC 59.572 47.826 0.00 0.00 0.00 3.18
1769 2129 0.898320 AGTCTTGTCCACTCCCGATG 59.102 55.000 0.00 0.00 0.00 3.84
1822 2182 2.821366 CCTGTGCATGACCGAGGC 60.821 66.667 0.00 0.00 0.00 4.70
1840 2200 1.014564 GCCGAGTTCTTGGGAAGACG 61.015 60.000 8.04 0.00 37.23 4.18
1862 2222 0.251165 GCTTTAGGCCAACTCCACCA 60.251 55.000 5.01 0.00 34.27 4.17
1865 2225 1.412453 TTAGGCCAACTCCACCACGT 61.412 55.000 5.01 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.206132 CGTCACCCCACTAGTAATGCA 59.794 52.381 0.00 0.00 0.00 3.96
17 18 2.079911 TTTTCCCCGTCACCCCACT 61.080 57.895 0.00 0.00 0.00 4.00
45 46 0.244450 ACCAAGCGAACCAATGCATG 59.756 50.000 0.00 0.00 0.00 4.06
102 103 4.946784 AAAGCTATGGACATCACGAAAC 57.053 40.909 0.00 0.00 0.00 2.78
160 161 2.816087 ACAATGAGTCATGGTGCTCAAC 59.184 45.455 12.58 0.00 43.79 3.18
373 379 2.302733 GGGGCATCACAATTTTCCTTGT 59.697 45.455 0.00 0.00 39.91 3.16
440 446 0.552848 TTCATCCCATTCCCCAGAGC 59.447 55.000 0.00 0.00 0.00 4.09
460 466 8.421002 GGGCCAAAAATTATCTTTGATAAGCTA 58.579 33.333 4.39 0.00 36.12 3.32
512 518 0.040204 ATCTTCCTGGTGCAAAGGGG 59.960 55.000 15.05 9.50 35.35 4.79
567 573 2.076863 GAGCGTACACTGAAAATGCCT 58.923 47.619 0.00 0.00 0.00 4.75
630 636 2.703007 AGCACTTATGAAGGAGCTAGGG 59.297 50.000 6.64 0.00 40.60 3.53
639 645 5.122396 GTGGTTACCAGAAGCACTTATGAAG 59.878 44.000 3.45 0.00 43.18 3.02
640 646 5.001232 GTGGTTACCAGAAGCACTTATGAA 58.999 41.667 3.45 0.00 43.18 2.57
644 650 3.412237 GGTGGTTACCAGAAGCACTTA 57.588 47.619 3.45 0.00 46.71 2.24
663 669 3.010138 TCCATAGTTTCCTCCAAACAGGG 59.990 47.826 0.40 0.00 46.20 4.45
729 735 2.934887 CATGGGATGGCATTGTGTAGA 58.065 47.619 0.00 0.00 0.00 2.59
769 775 4.285020 TGAGAAGATGTAGAGATGTGCCT 58.715 43.478 0.00 0.00 0.00 4.75
843 849 2.435059 GTCCGGGCTCTTGAGCAC 60.435 66.667 21.97 18.37 36.33 4.40
849 855 2.427245 CCAGATCGTCCGGGCTCTT 61.427 63.158 3.66 0.00 0.00 2.85
955 961 6.487331 TCATAATAACTCCGTTGGTTTGTTGT 59.513 34.615 0.00 0.00 0.00 3.32
1015 1021 2.158534 TCTGCCACCAAATGTACCAAGT 60.159 45.455 0.00 0.00 0.00 3.16
1153 1159 5.007034 TGAAGGTCGCTTCCAAATATTCAA 58.993 37.500 0.00 0.00 32.70 2.69
1245 1251 1.138859 CCAGCACCATCTCGGATAACA 59.861 52.381 0.00 0.00 38.63 2.41
1288 1294 3.056536 TCAGAAACATGCTCTAGCTTCGT 60.057 43.478 3.26 0.00 42.66 3.85
1305 1311 1.000394 TCCGCTGATTCAACGTCAGAA 60.000 47.619 8.49 5.71 44.57 3.02
1364 1370 4.523173 CGACTATGGAATTAGCTCCCACTA 59.477 45.833 0.00 0.00 34.22 2.74
1432 1439 5.155161 ACTAGCCACCATAGAATGTCCATA 58.845 41.667 0.00 0.00 0.00 2.74
1464 1471 2.267426 CATATTTGCCGACAGTCGTCA 58.733 47.619 21.34 12.75 42.74 4.35
1602 1609 9.921637 TCCGCAAGTAAATTCAAAATAAAATCT 57.078 25.926 0.00 0.00 0.00 2.40
1692 1699 2.354539 CGCCGGCCTGTTTGTTTG 60.355 61.111 23.46 0.00 0.00 2.93
1736 2096 3.387397 ACAAGACTACAGTGGTAAACGC 58.613 45.455 0.00 0.00 0.00 4.84
1758 2118 4.899239 GAGCGGCATCGGGAGTGG 62.899 72.222 1.45 0.00 36.79 4.00
1769 2129 1.154413 CATGACACGTTTGAGCGGC 60.154 57.895 0.00 0.00 35.98 6.53
1822 2182 0.389948 CCGTCTTCCCAAGAACTCGG 60.390 60.000 0.91 0.91 39.67 4.63
1840 2200 0.328258 TGGAGTTGGCCTAAAGCTCC 59.672 55.000 15.26 15.26 44.31 4.70
1862 2222 2.109593 GTCCGTTTGGGGTCACGT 59.890 61.111 0.00 0.00 34.47 4.49
1865 2225 2.135581 AGACGTCCGTTTGGGGTCA 61.136 57.895 13.01 0.00 39.86 4.02
1973 2333 1.512156 GACACGATTTGGGTTGCGGT 61.512 55.000 0.00 0.00 0.00 5.68
1979 2339 2.349755 CCCGGACACGATTTGGGT 59.650 61.111 0.73 0.00 44.60 4.51
2165 2532 2.125832 CGCGCGGGAGGAGTTTTA 60.126 61.111 24.84 0.00 0.00 1.52
2464 2831 4.988598 CGGCCGTGTTCCAGCAGT 62.989 66.667 19.50 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.