Multiple sequence alignment - TraesCS2A01G471200

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 TraesCS2A01G471200 chr2A 100.000 2531 0 0 1 2531 713460642 713463172 0.000000e+00 4674
1 TraesCS2A01G471200 chr2A 89.398 349 37 0 1191 1539 713453496 713453844 8.310000e-120 440
2 TraesCS2A01G471200 chr2A 96.400 250 9 0 513 762 713456251 713456500 1.810000e-111 412
3 TraesCS2A01G471200 chrUn 98.690 992 10 2 1540 2531 78910471 78911459 0.000000e+00 1757
4 TraesCS2A01G471200 chrUn 98.589 992 9 4 1540 2531 183987821 183988807 0.000000e+00 1749
5 TraesCS2A01G471200 chrUn 97.996 998 15 4 1536 2531 76847862 76846868 0.000000e+00 1727
6 TraesCS2A01G471200 chr1A 98.390 994 12 3 1540 2531 559830350 559829359 0.000000e+00 1744
7 TraesCS2A01G471200 chr6A 98.390 994 11 2 1540 2531 73487925 73486935 0.000000e+00 1742
8 TraesCS2A01G471200 chr3B 98.389 993 10 4 1539 2531 132973685 132972699 0.000000e+00 1740
9 TraesCS2A01G471200 chr1B 98.196 998 10 5 1537 2531 461822365 461821373 0.000000e+00 1736
10 TraesCS2A01G471200 chr7A 98.195 997 10 4 1539 2531 712525073 712526065 0.000000e+00 1735
11 TraesCS2A01G471200 chr5B 97.782 992 18 2 1540 2531 508061186 508060199 0.000000e+00 1707
12 TraesCS2A01G471200 chr5B 96.063 762 29 1 1 762 598157902 598157142 0.000000e+00 1240
13 TraesCS2A01G471200 chr5B 94.444 252 11 3 513 762 598162396 598162146 3.950000e-103 385
14 TraesCS2A01G471200 chr1D 96.199 763 25 4 1 762 477492466 477491707 0.000000e+00 1245
15 TraesCS2A01G471200 chr1D 93.574 249 12 2 514 762 477496941 477496697 3.980000e-98 368
16 TraesCS2A01G471200 chr2D 93.822 777 48 0 763 1539 575216654 575217430 0.000000e+00 1170
17 TraesCS2A01G471200 chr2D 90.458 765 61 11 1 762 518076070 518075315 0.000000e+00 998
18 TraesCS2A01G471200 chr2B 93.872 767 47 0 773 1539 691189642 691190408 0.000000e+00 1157
19 TraesCS2A01G471200 chr2B 91.560 782 60 3 763 1538 691413588 691414369 0.000000e+00 1074
20 TraesCS2A01G471200 chr2B 85.990 778 104 3 763 1539 691402370 691403143 0.000000e+00 828
21 TraesCS2A01G471200 chr2B 85.641 780 103 7 763 1539 691187264 691188037 0.000000e+00 811
22 TraesCS2A01G471200 chr7B 91.711 760 59 4 1 758 481850578 481851335 0.000000e+00 1051
23 TraesCS2A01G471200 chr7D 93.713 684 43 0 1 684 578713493 578714176 0.000000e+00 1026
24 TraesCS2A01G471200 chr7D 93.284 134 8 1 629 762 578714171 578714303 1.990000e-46 196
25 TraesCS2A01G471200 chr7D 93.233 133 8 1 630 762 578709171 578709302 7.140000e-46 195
26 TraesCS2A01G471200 chr4D 88.296 769 71 15 1 762 506745375 506746131 0.000000e+00 904
27 TraesCS2A01G471200 chr5D 88.105 765 80 10 1 762 130303735 130304491 0.000000e+00 898
28 TraesCS2A01G471200 chr6B 86.405 765 78 16 1 763 593716917 593716177 0.000000e+00 813
29 TraesCS2A01G471200 chr3A 81.142 753 103 30 11 750 748424778 748425504 3.650000e-158 568


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 TraesCS2A01G471200 chr2A 713460642 713463172 2530 False 4674 4674 100.0000 1 2531 1 chr2A.!!$F1 2530
1 TraesCS2A01G471200 chr2A 713453496 713456500 3004 False 426 440 92.8990 513 1539 2 chr2A.!!$F2 1026
2 TraesCS2A01G471200 chrUn 78910471 78911459 988 False 1757 1757 98.6900 1540 2531 1 chrUn.!!$F1 991
3 TraesCS2A01G471200 chrUn 183987821 183988807 986 False 1749 1749 98.5890 1540 2531 1 chrUn.!!$F2 991
4 TraesCS2A01G471200 chrUn 76846868 76847862 994 True 1727 1727 97.9960 1536 2531 1 chrUn.!!$R1 995
5 TraesCS2A01G471200 chr1A 559829359 559830350 991 True 1744 1744 98.3900 1540 2531 1 chr1A.!!$R1 991
6 TraesCS2A01G471200 chr6A 73486935 73487925 990 True 1742 1742 98.3900 1540 2531 1 chr6A.!!$R1 991
7 TraesCS2A01G471200 chr3B 132972699 132973685 986 True 1740 1740 98.3890 1539 2531 1 chr3B.!!$R1 992
8 TraesCS2A01G471200 chr1B 461821373 461822365 992 True 1736 1736 98.1960 1537 2531 1 chr1B.!!$R1 994
9 TraesCS2A01G471200 chr7A 712525073 712526065 992 False 1735 1735 98.1950 1539 2531 1 chr7A.!!$F1 992
10 TraesCS2A01G471200 chr5B 508060199 508061186 987 True 1707 1707 97.7820 1540 2531 1 chr5B.!!$R1 991
11 TraesCS2A01G471200 chr5B 598157142 598157902 760 True 1240 1240 96.0630 1 762 1 chr5B.!!$R2 761
12 TraesCS2A01G471200 chr1D 477491707 477492466 759 True 1245 1245 96.1990 1 762 1 chr1D.!!$R1 761
13 TraesCS2A01G471200 chr2D 575216654 575217430 776 False 1170 1170 93.8220 763 1539 1 chr2D.!!$F1 776
14 TraesCS2A01G471200 chr2D 518075315 518076070 755 True 998 998 90.4580 1 762 1 chr2D.!!$R1 761
15 TraesCS2A01G471200 chr2B 691413588 691414369 781 False 1074 1074 91.5600 763 1538 1 chr2B.!!$F2 775
16 TraesCS2A01G471200 chr2B 691187264 691190408 3144 False 984 1157 89.7565 763 1539 2 chr2B.!!$F3 776
17 TraesCS2A01G471200 chr2B 691402370 691403143 773 False 828 828 85.9900 763 1539 1 chr2B.!!$F1 776
18 TraesCS2A01G471200 chr7B 481850578 481851335 757 False 1051 1051 91.7110 1 758 1 chr7B.!!$F1 757
19 TraesCS2A01G471200 chr7D 578713493 578714303 810 False 611 1026 93.4985 1 762 2 chr7D.!!$F2 761
20 TraesCS2A01G471200 chr4D 506745375 506746131 756 False 904 904 88.2960 1 762 1 chr4D.!!$F1 761
21 TraesCS2A01G471200 chr5D 130303735 130304491 756 False 898 898 88.1050 1 762 1 chr5D.!!$F1 761
22 TraesCS2A01G471200 chr6B 593716177 593716917 740 True 813 813 86.4050 1 763 1 chr6B.!!$R1 762
23 TraesCS2A01G471200 chr3A 748424778 748425504 726 False 568 568 81.1420 11 750 1 chr3A.!!$F1 739

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
64 65 0.394192 CTCTGATGCGGATTGGGCTA 59.606 55.0 0.00 0.0 0.0 3.93 F
879 2486 0.665835 CGCTTAGAGCTCTGTCGGAT 59.334 55.0 26.78 0.0 39.6 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1090 2698 0.178990 AGCTCGGCCTTGAAAACCTT 60.179 50.000 0.0 0.0 0.00 3.50 R
1750 5327 3.556306 CCCCACGGGTATGCCGAT 61.556 66.667 0.0 0.0 38.25 4.18 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
64 65 0.394192 CTCTGATGCGGATTGGGCTA 59.606 55.000 0.00 0.00 0.00 3.93
132 133 6.247676 TCATGGACCAAATCTGATTTCTTGA 58.752 36.000 12.50 11.60 0.00 3.02
363 364 9.778993 CACATCGAGATAGATTTTCATTTTGTT 57.221 29.630 0.00 0.00 0.00 2.83
506 507 8.533657 TCTCAACCTAGTTCGGTTTTGATTATA 58.466 33.333 0.00 0.00 44.65 0.98
629 631 8.536340 TTTAACTCCTTATCTCTTCTCCCTAC 57.464 38.462 0.00 0.00 0.00 3.18
729 782 2.880629 ATACCTGCGGCTCTCCCTGT 62.881 60.000 0.00 0.00 0.00 4.00
750 803 3.764237 TTTGGAGAGTAGGAACGCTTT 57.236 42.857 0.00 0.00 35.71 3.51
879 2486 0.665835 CGCTTAGAGCTCTGTCGGAT 59.334 55.000 26.78 0.00 39.60 4.18
909 2517 2.277084 GGCCGTTTCACGATAAGATGT 58.723 47.619 0.00 0.00 46.05 3.06
993 2601 2.683212 AGCCTGCGAGAGAGCCTT 60.683 61.111 0.00 0.00 36.02 4.35
1090 2698 0.179070 TGTGTTGGCTGCACGTTCTA 60.179 50.000 0.50 0.00 39.53 2.10
1168 2776 3.770040 TGGACGACATGGAGCCCG 61.770 66.667 0.00 0.00 0.00 6.13
1182 2790 3.068881 CCCGAGGTCTTTGAGGCA 58.931 61.111 0.00 0.00 0.00 4.75
1206 2819 3.909430 TCTTCACTTCATGTACACGGAC 58.091 45.455 0.00 0.00 0.00 4.79
1332 2945 2.776536 AGACAAGCTCTATGAGGGCATT 59.223 45.455 0.40 0.00 35.94 3.56
1344 2957 0.904649 AGGGCATTGATGTCGAGACA 59.095 50.000 8.48 8.48 46.44 3.41
1444 3057 0.961019 ACGGGACAAACTACGTGCTA 59.039 50.000 0.00 0.00 38.24 3.49
1473 3086 5.473039 GCAACTAATGGATTCAAGCAACTT 58.527 37.500 0.00 0.00 0.00 2.66
1521 3134 3.051341 AGGATATACTGAAGGGGGTGTCA 60.051 47.826 0.00 0.00 0.00 3.58
1718 5180 2.479730 GCCGTCGGCCTATCTACATATG 60.480 54.545 26.23 0.00 44.06 1.78
1750 5327 1.080093 CGTCAGCTTACGAAGGCCA 60.080 57.895 15.24 0.00 45.68 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 0.173481 CGACGATCATCCACACACCT 59.827 55.000 0.00 0.00 0.00 4.00
132 133 2.431782 AGTGGCTTGTTTCTTTGCACAT 59.568 40.909 0.00 0.00 0.00 3.21
363 364 5.680619 TCTTTGTTGGCAACTCTTTCTCTA 58.319 37.500 28.71 4.58 33.82 2.43
506 507 5.697067 TGTTACAATGTTTAACACTCCCCT 58.303 37.500 0.00 0.00 35.07 4.79
629 631 1.372683 CCCAGAGATACATGCGGGG 59.627 63.158 0.00 0.00 0.00 5.73
729 782 3.764237 AAGCGTTCCTACTCTCCAAAA 57.236 42.857 0.00 0.00 0.00 2.44
750 803 3.270027 CTGGCCGTCTTGTGAAATATGA 58.730 45.455 0.00 0.00 0.00 2.15
909 2517 5.013079 AGTTTCATGTATGACCTGGAGAACA 59.987 40.000 0.00 0.00 36.36 3.18
1090 2698 0.178990 AGCTCGGCCTTGAAAACCTT 60.179 50.000 0.00 0.00 0.00 3.50
1168 2776 2.849294 AGAAGTGCCTCAAAGACCTC 57.151 50.000 0.00 0.00 0.00 3.85
1182 2790 4.038763 TCCGTGTACATGAAGTGAAGAAGT 59.961 41.667 16.87 0.00 0.00 3.01
1206 2819 1.066136 CATCGTCATCTGGCATAGCG 58.934 55.000 0.00 0.00 0.00 4.26
1332 2945 2.135139 GTTGCAACTGTCTCGACATCA 58.865 47.619 22.36 0.00 41.01 3.07
1390 3003 4.773323 ACTGAATGCAAGCTTCCTTAAC 57.227 40.909 0.00 0.00 0.00 2.01
1444 3057 5.221382 GCTTGAATCCATTAGTTGCCATGAT 60.221 40.000 0.00 0.00 0.00 2.45
1473 3086 3.323691 TGAGCAAAGGACAACTAGCTACA 59.676 43.478 0.00 0.00 39.79 2.74
1521 3134 2.238144 AGTGCTCACATTCTAGGTGCAT 59.762 45.455 2.63 0.00 36.22 3.96
1660 4388 1.437986 GCCGTCGGCTTATCTCTGT 59.562 57.895 28.98 0.00 46.69 3.41
1750 5327 3.556306 CCCCACGGGTATGCCGAT 61.556 66.667 0.00 0.00 38.25 4.18


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

AutoCloner maintained by Alex Coulton.