Multiple sequence alignment - TraesCS4B01G290600

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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 TraesCS4B01G290600 chr4B 100.000 2646 0 0 1 2646 575619047 575616402 0 4887
1 TraesCS4B01G290600 chr4B 90.120 668 40 14 1984 2646 237927630 237928276 0 845
2 TraesCS4B01G290600 chr4B 89.970 668 41 15 1984 2646 282379071 282378425 0 839
3 TraesCS4B01G290600 chr4B 88.348 678 52 14 1984 2646 607715078 607714413 0 789
4 TraesCS4B01G290600 chr4B 86.804 682 62 16 1984 2646 667312056 667312728 0 736
5 TraesCS4B01G290600 chr7A 95.063 1985 91 6 1 1985 641404630 641402653 0 3116
6 TraesCS4B01G290600 chr4D 94.867 1987 95 2 1 1987 379508953 379506974 0 3097
7 TraesCS4B01G290600 chr1A 94.207 1985 109 4 1 1985 520786913 520788891 0 3024
8 TraesCS4B01G290600 chr3B 93.860 1987 115 6 1 1984 62531776 62529794 0 2987
9 TraesCS4B01G290600 chr3B 92.279 1062 79 3 925 1984 605446113 605445053 0 1504
10 TraesCS4B01G290600 chr3B 92.264 1060 74 7 925 1982 612314088 612315141 0 1496
11 TraesCS4B01G290600 chr3B 91.168 668 33 14 1984 2646 279069899 279070545 0 883
12 TraesCS4B01G290600 chr3B 90.318 661 48 6 1994 2646 171907087 171906435 0 852
13 TraesCS4B01G290600 chr3B 86.880 625 73 8 1 622 629796854 629797472 0 691
14 TraesCS4B01G290600 chr3A 94.333 1941 101 6 1 1939 170229715 170227782 0 2966
15 TraesCS4B01G290600 chr5B 92.897 1985 121 9 1 1984 395331108 395333073 0 2867
16 TraesCS4B01G290600 chr2A 95.276 1143 51 3 1 1142 123740677 123739537 0 1808
17 TraesCS4B01G290600 chr1D 93.421 1064 70 0 925 1988 467476026 467474963 0 1578
18 TraesCS4B01G290600 chr2B 95.107 654 26 1 1993 2646 662986157 662986804 0 1026
19 TraesCS4B01G290600 chr2B 88.772 668 44 18 1984 2646 562824789 562824148 0 789
20 TraesCS4B01G290600 chr7B 90.361 664 46 6 1993 2646 177272366 177271711 0 856
21 TraesCS4B01G290600 chr7B 90.361 664 46 6 1993 2646 177279972 177279317 0 856
22 TraesCS4B01G290600 chr7B 88.772 668 42 17 1984 2646 583885145 583885784 0 787
23 TraesCS4B01G290600 chr1B 89.521 668 44 15 1984 2646 618656924 618657570 0 822
24 TraesCS4B01G290600 chr6B 86.931 681 60 19 1984 2646 25325368 25326037 0 737
25 TraesCS4B01G290600 chr2D 87.241 627 67 11 1 622 344565324 344565942 0 702


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 TraesCS4B01G290600 chr4B 575616402 575619047 2645 True 4887 4887 100.000 1 2646 1 chr4B.!!$R2 2645
1 TraesCS4B01G290600 chr4B 237927630 237928276 646 False 845 845 90.120 1984 2646 1 chr4B.!!$F1 662
2 TraesCS4B01G290600 chr4B 282378425 282379071 646 True 839 839 89.970 1984 2646 1 chr4B.!!$R1 662
3 TraesCS4B01G290600 chr4B 607714413 607715078 665 True 789 789 88.348 1984 2646 1 chr4B.!!$R3 662
4 TraesCS4B01G290600 chr4B 667312056 667312728 672 False 736 736 86.804 1984 2646 1 chr4B.!!$F2 662
5 TraesCS4B01G290600 chr7A 641402653 641404630 1977 True 3116 3116 95.063 1 1985 1 chr7A.!!$R1 1984
6 TraesCS4B01G290600 chr4D 379506974 379508953 1979 True 3097 3097 94.867 1 1987 1 chr4D.!!$R1 1986
7 TraesCS4B01G290600 chr1A 520786913 520788891 1978 False 3024 3024 94.207 1 1985 1 chr1A.!!$F1 1984
8 TraesCS4B01G290600 chr3B 62529794 62531776 1982 True 2987 2987 93.860 1 1984 1 chr3B.!!$R1 1983
9 TraesCS4B01G290600 chr3B 605445053 605446113 1060 True 1504 1504 92.279 925 1984 1 chr3B.!!$R3 1059
10 TraesCS4B01G290600 chr3B 612314088 612315141 1053 False 1496 1496 92.264 925 1982 1 chr3B.!!$F2 1057
11 TraesCS4B01G290600 chr3B 279069899 279070545 646 False 883 883 91.168 1984 2646 1 chr3B.!!$F1 662
12 TraesCS4B01G290600 chr3B 171906435 171907087 652 True 852 852 90.318 1994 2646 1 chr3B.!!$R2 652
13 TraesCS4B01G290600 chr3B 629796854 629797472 618 False 691 691 86.880 1 622 1 chr3B.!!$F3 621
14 TraesCS4B01G290600 chr3A 170227782 170229715 1933 True 2966 2966 94.333 1 1939 1 chr3A.!!$R1 1938
15 TraesCS4B01G290600 chr5B 395331108 395333073 1965 False 2867 2867 92.897 1 1984 1 chr5B.!!$F1 1983
16 TraesCS4B01G290600 chr2A 123739537 123740677 1140 True 1808 1808 95.276 1 1142 1 chr2A.!!$R1 1141
17 TraesCS4B01G290600 chr1D 467474963 467476026 1063 True 1578 1578 93.421 925 1988 1 chr1D.!!$R1 1063
18 TraesCS4B01G290600 chr2B 662986157 662986804 647 False 1026 1026 95.107 1993 2646 1 chr2B.!!$F1 653
19 TraesCS4B01G290600 chr2B 562824148 562824789 641 True 789 789 88.772 1984 2646 1 chr2B.!!$R1 662
20 TraesCS4B01G290600 chr7B 177271711 177272366 655 True 856 856 90.361 1993 2646 1 chr7B.!!$R1 653
21 TraesCS4B01G290600 chr7B 177279317 177279972 655 True 856 856 90.361 1993 2646 1 chr7B.!!$R2 653
22 TraesCS4B01G290600 chr7B 583885145 583885784 639 False 787 787 88.772 1984 2646 1 chr7B.!!$F1 662
23 TraesCS4B01G290600 chr1B 618656924 618657570 646 False 822 822 89.521 1984 2646 1 chr1B.!!$F1 662
24 TraesCS4B01G290600 chr6B 25325368 25326037 669 False 737 737 86.931 1984 2646 1 chr6B.!!$F1 662
25 TraesCS4B01G290600 chr2D 344565324 344565942 618 False 702 702 87.241 1 622 1 chr2D.!!$F1 621

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
985 992 1.376683 TCGGGCCCAACGATTTCTG 60.377 57.895 24.92 0.23 35.12 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2489 2562 0.808847 GGAATCCGTTACTCGTGGGC 60.809 60.0 0.0 0.0 37.94 5.36 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
67 68 4.464008 AGAATCAGGTTCTTGAGTTTGCA 58.536 39.130 0.00 0.00 44.80 4.08
85 86 1.406341 GCATGCTTAACCGTGTCCCTA 60.406 52.381 11.37 0.00 0.00 3.53
379 380 5.659440 TTTGCTCAAAGAAAGGTTGTCTT 57.341 34.783 0.00 0.00 36.90 3.01
421 422 6.569179 TTAAGAAATAGGCTGACACCAAAC 57.431 37.500 0.00 0.00 0.00 2.93
432 433 4.564821 GCTGACACCAAACCAGTAATCCTA 60.565 45.833 0.00 0.00 0.00 2.94
673 678 4.167307 ACCCTTCTTTAGAACCCAACAAGA 59.833 41.667 0.00 0.00 0.00 3.02
784 791 3.034635 TCTTTTTGCCTGCCCTTGTTTA 58.965 40.909 0.00 0.00 0.00 2.01
842 849 5.001232 TGAGTGCTTACTTATGGTTTGTCC 58.999 41.667 0.00 0.00 0.00 4.02
886 893 6.367422 CAGTCTTCATACTTTCAGACACCTTC 59.633 42.308 0.00 0.00 38.53 3.46
985 992 1.376683 TCGGGCCCAACGATTTCTG 60.377 57.895 24.92 0.23 35.12 3.02
1016 1023 8.906867 TGGAACCTTGATGATTTATCTCATTTC 58.093 33.333 0.00 0.00 36.01 2.17
1020 1027 8.400947 ACCTTGATGATTTATCTCATTTCAACG 58.599 33.333 0.00 0.00 36.01 4.10
1082 1089 2.224548 ACCTCCTATGCCCGCTTAATTC 60.225 50.000 0.00 0.00 0.00 2.17
1263 1270 3.973516 TGTTGCCTCGAGTCGCGT 61.974 61.111 12.31 0.00 41.80 6.01
1273 1280 2.989824 AGTCGCGTGGCCACTACT 60.990 61.111 32.28 26.76 0.00 2.57
1277 1284 2.701780 CGCGTGGCCACTACTCTCT 61.702 63.158 32.28 0.00 0.00 3.10
1434 1442 2.734673 GGTTCTTCTGCAGCTCGCG 61.735 63.158 9.47 0.00 46.97 5.87
1490 1498 2.763448 CCAAGAAGTCCTTCTCGGAGAT 59.237 50.000 8.81 0.00 44.53 2.75
1499 1507 2.366916 CCTTCTCGGAGATGTAAGCCAT 59.633 50.000 8.81 0.00 33.89 4.40
1518 1526 1.216178 GGCGCATGTTTCTGCCATT 59.784 52.632 10.83 0.00 46.76 3.16
1564 1572 9.418045 CGTGGATTTAGGTGTTGAAAAATTATT 57.582 29.630 0.00 0.00 0.00 1.40
1597 1605 4.141711 TGCAGGATTAAGGACATGTACCTC 60.142 45.833 3.84 0.00 36.67 3.85
1608 1616 4.442706 GACATGTACCTCCACTACAATGG 58.557 47.826 0.00 0.00 41.57 3.16
1649 1657 5.860941 TTGTGGCTTCCAAACTTGAAATA 57.139 34.783 0.00 0.00 34.18 1.40
1658 1666 8.825745 GCTTCCAAACTTGAAATATTTGTTTGA 58.174 29.630 27.61 17.91 45.75 2.69
1807 1817 9.200817 AGCCTTCCATGCTTTATATTTTCTTTA 57.799 29.630 0.00 0.00 34.87 1.85
2109 2132 4.398044 CGACACCACATAAAGGGCTTAAAT 59.602 41.667 0.00 0.00 0.00 1.40
2112 2135 7.165460 ACACCACATAAAGGGCTTAAATAAC 57.835 36.000 0.00 0.00 0.00 1.89
2115 2138 7.759433 CACCACATAAAGGGCTTAAATAACAAG 59.241 37.037 0.00 0.00 0.00 3.16
2116 2139 6.756542 CCACATAAAGGGCTTAAATAACAAGC 59.243 38.462 0.00 0.00 46.18 4.01
2144 2183 2.107750 CGGGCATCTGAGCGACAT 59.892 61.111 0.00 0.00 34.64 3.06
2470 2543 6.873997 TCGAATAGGTTTAATCTCTGCAGAA 58.126 36.000 18.85 9.34 30.24 3.02
2488 2561 4.566987 CAGAAGGTGTACTCTTTACCCAC 58.433 47.826 0.00 0.00 35.03 4.61
2489 2562 3.257624 AGAAGGTGTACTCTTTACCCACG 59.742 47.826 0.00 0.00 35.03 4.94
2490 2563 1.274447 AGGTGTACTCTTTACCCACGC 59.726 52.381 0.00 0.00 35.03 5.34
2491 2564 1.673923 GGTGTACTCTTTACCCACGCC 60.674 57.143 0.00 0.00 33.08 5.68
2492 2565 0.609662 TGTACTCTTTACCCACGCCC 59.390 55.000 0.00 0.00 0.00 6.13
2493 2566 0.609662 GTACTCTTTACCCACGCCCA 59.390 55.000 0.00 0.00 0.00 5.36
2574 2647 2.930950 ACACACCTAACTTGCACACAT 58.069 42.857 0.00 0.00 0.00 3.21
2616 2689 1.298859 GAATCACCCACGACACCTGC 61.299 60.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 2.745152 GCATAGGGACACGGTTAAGCAT 60.745 50.000 5.38 0.00 0.00 3.79
85 86 1.547372 GAGGTTGGTGAGCAATTGCAT 59.453 47.619 30.89 16.58 45.16 3.96
379 380 1.619654 AAGCACAAAGTAGCATGGCA 58.380 45.000 0.00 0.00 0.00 4.92
421 422 5.606348 AAGCAGAAGTCTAGGATTACTGG 57.394 43.478 0.00 0.00 0.00 4.00
432 433 1.322442 GGCCAACAAAGCAGAAGTCT 58.678 50.000 0.00 0.00 0.00 3.24
542 547 2.535166 CACGCATTCAAAAATATGGCCG 59.465 45.455 0.00 0.00 0.00 6.13
686 692 9.449719 AACGAATCACTAACCAAGATCTTTAAT 57.550 29.630 4.86 0.00 0.00 1.40
702 708 1.468520 CGGCCATTGAAACGAATCACT 59.531 47.619 2.24 0.00 0.00 3.41
979 986 6.012113 TCATCAAGGTTCCAATGACAGAAAT 58.988 36.000 0.72 0.00 0.00 2.17
985 992 8.230472 AGATAAATCATCAAGGTTCCAATGAC 57.770 34.615 4.55 0.00 35.96 3.06
1016 1023 4.730949 TCAGAGGGGTTAGATTACGTTG 57.269 45.455 0.00 0.00 0.00 4.10
1020 1027 7.610305 TGACAAAAATCAGAGGGGTTAGATTAC 59.390 37.037 0.00 0.00 31.01 1.89
1060 1067 2.091098 TTAAGCGGGCATAGGAGGTA 57.909 50.000 0.00 0.00 0.00 3.08
1107 1114 4.255510 ACCCAGCCATAAAATCAGATGT 57.744 40.909 0.00 0.00 0.00 3.06
1248 1255 4.717629 CCACGCGACTCGAGGCAA 62.718 66.667 20.47 0.00 41.72 4.52
1263 1270 2.052690 GGCGAGAGAGTAGTGGCCA 61.053 63.158 0.00 0.00 40.24 5.36
1273 1280 3.452786 CTCCGCCTTGGCGAGAGA 61.453 66.667 32.16 20.28 37.80 3.10
1297 1304 2.750637 GAGGGCGTCGAGAGTGGA 60.751 66.667 0.00 0.00 0.00 4.02
1434 1442 1.327303 TGGACACAACAATCCTTGCC 58.673 50.000 0.00 0.00 35.86 4.52
1458 1466 5.184892 AGGACTTCTTGGCATTCTTATGT 57.815 39.130 0.00 0.00 34.12 2.29
1490 1498 0.964860 AACATGCGCCATGGCTTACA 60.965 50.000 33.07 26.72 45.16 2.41
1564 1572 0.918258 TAATCCTGCATCCACAGCCA 59.082 50.000 0.00 0.00 36.29 4.75
1597 1605 2.105477 CCCAGATCTCCCATTGTAGTGG 59.895 54.545 0.00 0.00 39.05 4.00
1608 1616 0.545646 AAGAAGCAGCCCAGATCTCC 59.454 55.000 0.00 0.00 0.00 3.71
2028 2047 5.845391 TTTATAAGCCCTTTATGTGGTGC 57.155 39.130 0.00 0.00 33.96 5.01
2109 2132 1.155889 CGACTGTGGCATGCTTGTTA 58.844 50.000 18.92 0.00 0.00 2.41
2112 2135 2.693762 CCCGACTGTGGCATGCTTG 61.694 63.158 18.92 7.84 0.00 4.01
2132 2171 4.375272 CCTTTATGTGATGTCGCTCAGAT 58.625 43.478 0.00 0.00 34.00 2.90
2180 2231 2.596338 TCAGACGCCCGACTGTGA 60.596 61.111 16.85 0.28 38.61 3.58
2233 2292 8.877195 GGTTTTACCTCCTGGATATTCACTATA 58.123 37.037 0.00 0.00 34.73 1.31
2470 2543 1.274447 GCGTGGGTAAAGAGTACACCT 59.726 52.381 0.00 0.00 32.66 4.00
2488 2561 1.143969 GAATCCGTTACTCGTGGGCG 61.144 60.000 0.00 0.00 37.94 6.13
2489 2562 0.808847 GGAATCCGTTACTCGTGGGC 60.809 60.000 0.00 0.00 37.94 5.36
2490 2563 0.822164 AGGAATCCGTTACTCGTGGG 59.178 55.000 0.00 0.00 37.94 4.61
2491 2564 2.667473 AAGGAATCCGTTACTCGTGG 57.333 50.000 0.00 0.00 37.94 4.94
2492 2565 4.741342 ACTAAAGGAATCCGTTACTCGTG 58.259 43.478 3.56 0.00 37.94 4.35
2493 2566 4.142293 GGACTAAAGGAATCCGTTACTCGT 60.142 45.833 3.56 1.41 37.94 4.18
2574 2647 4.309933 CAGACACATGTGAGTTAAGCTGA 58.690 43.478 31.94 0.00 0.00 4.26
2616 2689 2.558359 CCCCACTTAGAGTTTTGCTTGG 59.442 50.000 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.