Multiple sequence alignment - TraesCS2A01G345200

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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 TraesCS2A01G345200 chr2A 100.000 3449 0 0 1 3449 583255357 583251909 0.000000e+00 6370
1 TraesCS2A01G345200 chr2A 96.664 2368 48 13 347 2703 583098081 583095734 0.000000e+00 3906
2 TraesCS2A01G345200 chr2A 96.622 2368 50 12 347 2703 583105668 583103320 0.000000e+00 3903
3 TraesCS2A01G345200 chr2A 93.994 2331 83 17 385 2703 583266727 583264442 0.000000e+00 3476
4 TraesCS2A01G345200 chr2A 95.580 1561 39 12 905 2454 582839797 582841338 0.000000e+00 2473
5 TraesCS2A01G345200 chr2A 96.801 1313 37 3 1395 2703 583111360 583110049 0.000000e+00 2187
6 TraesCS2A01G345200 chr2A 96.232 345 13 0 2 346 583098523 583098179 1.800000e-157 566
7 TraesCS2A01G345200 chr2A 96.232 345 13 0 2 346 583106111 583105767 1.800000e-157 566
8 TraesCS2A01G345200 chr2D 96.604 2326 66 8 385 2703 439680976 439683295 0.000000e+00 3845
9 TraesCS2A01G345200 chr2D 96.002 2326 74 9 385 2703 439936319 439934006 0.000000e+00 3762
10 TraesCS2A01G345200 chr2D 96.035 1715 44 9 995 2703 439693799 439695495 0.000000e+00 2769
11 TraesCS2A01G345200 chr2D 89.573 585 28 15 2699 3252 69246732 69247314 0.000000e+00 712
12 TraesCS2A01G345200 chr2D 87.127 536 24 9 2699 3210 584832706 584833220 1.800000e-157 566
13 TraesCS2A01G345200 chr2B 94.750 1543 44 12 382 1911 517750899 517752417 0.000000e+00 2366
14 TraesCS2A01G345200 chr2B 98.141 807 15 0 1897 2703 517753893 517754699 0.000000e+00 1408
15 TraesCS2A01G345200 chr2B 97.899 714 14 1 1991 2703 517746505 517747218 0.000000e+00 1234
16 TraesCS2A01G345200 chr2B 96.034 580 16 1 347 919 517758182 517758761 0.000000e+00 937
17 TraesCS2A01G345200 chr2B 93.792 451 27 1 461 911 517746064 517746513 0.000000e+00 676
18 TraesCS2A01G345200 chr2B 97.971 345 7 0 2 346 517750204 517750548 1.770000e-167 599
19 TraesCS2A01G345200 chr2B 97.971 345 4 1 2 346 517757742 517758083 2.290000e-166 595
20 TraesCS2A01G345200 chrUn 98.023 1062 18 1 1628 2686 444720735 444719674 0.000000e+00 1842
21 TraesCS2A01G345200 chrUn 99.101 556 5 0 347 902 376841621 376842176 0.000000e+00 1000
22 TraesCS2A01G345200 chrUn 89.971 698 35 12 2699 3363 76782767 76782072 0.000000e+00 869
23 TraesCS2A01G345200 chrUn 89.957 697 34 19 2699 3363 27090581 27089889 0.000000e+00 867
24 TraesCS2A01G345200 chrUn 97.391 345 9 0 2 346 376841177 376841521 3.830000e-164 588
25 TraesCS2A01G345200 chrUn 95.203 271 12 1 3179 3449 76756013 76756282 8.850000e-116 427
26 TraesCS2A01G345200 chrUn 95.522 268 11 1 3182 3449 76782069 76781803 8.850000e-116 427
27 TraesCS2A01G345200 chr3A 98.404 752 11 1 2699 3449 725704590 725703839 0.000000e+00 1321
28 TraesCS2A01G345200 chr6A 97.207 752 20 1 2699 3449 307680147 307679396 0.000000e+00 1271
29 TraesCS2A01G345200 chr1A 98.466 717 9 2 2699 3414 219373887 219374602 0.000000e+00 1262
30 TraesCS2A01G345200 chr1B 93.218 752 38 5 2699 3449 163725228 163725967 0.000000e+00 1094
31 TraesCS2A01G345200 chr4B 89.894 752 36 8 2699 3449 49938471 49939183 0.000000e+00 931
32 TraesCS2A01G345200 chr5A 89.685 698 37 12 2699 3363 333446724 333447419 0.000000e+00 857
33 TraesCS2A01G345200 chr6B 94.601 426 15 6 2699 3117 637398972 637399396 0.000000e+00 652
34 TraesCS2A01G345200 chr6D 89.412 340 29 4 3110 3449 386104557 386104889 4.120000e-114 422
35 TraesCS2A01G345200 chr7B 89.937 318 30 2 3132 3449 56445386 56445071 3.200000e-110 409


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 TraesCS2A01G345200 chr2A 583251909 583255357 3448 True 6370.000000 6370 100.000000 1 3449 1 chr2A.!!$R1 3448
1 TraesCS2A01G345200 chr2A 583264442 583266727 2285 True 3476.000000 3476 93.994000 385 2703 1 chr2A.!!$R2 2318
2 TraesCS2A01G345200 chr2A 582839797 582841338 1541 False 2473.000000 2473 95.580000 905 2454 1 chr2A.!!$F1 1549
3 TraesCS2A01G345200 chr2A 583095734 583098523 2789 True 2236.000000 3906 96.448000 2 2703 2 chr2A.!!$R3 2701
4 TraesCS2A01G345200 chr2A 583103320 583111360 8040 True 2218.666667 3903 96.551667 2 2703 3 chr2A.!!$R4 2701
5 TraesCS2A01G345200 chr2D 439680976 439683295 2319 False 3845.000000 3845 96.604000 385 2703 1 chr2D.!!$F2 2318
6 TraesCS2A01G345200 chr2D 439934006 439936319 2313 True 3762.000000 3762 96.002000 385 2703 1 chr2D.!!$R1 2318
7 TraesCS2A01G345200 chr2D 439693799 439695495 1696 False 2769.000000 2769 96.035000 995 2703 1 chr2D.!!$F3 1708
8 TraesCS2A01G345200 chr2D 69246732 69247314 582 False 712.000000 712 89.573000 2699 3252 1 chr2D.!!$F1 553
9 TraesCS2A01G345200 chr2D 584832706 584833220 514 False 566.000000 566 87.127000 2699 3210 1 chr2D.!!$F4 511
10 TraesCS2A01G345200 chr2B 517746064 517758761 12697 False 1116.428571 2366 96.651143 2 2703 7 chr2B.!!$F1 2701
11 TraesCS2A01G345200 chrUn 444719674 444720735 1061 True 1842.000000 1842 98.023000 1628 2686 1 chrUn.!!$R2 1058
12 TraesCS2A01G345200 chrUn 27089889 27090581 692 True 867.000000 867 89.957000 2699 3363 1 chrUn.!!$R1 664
13 TraesCS2A01G345200 chrUn 376841177 376842176 999 False 794.000000 1000 98.246000 2 902 2 chrUn.!!$F2 900
14 TraesCS2A01G345200 chrUn 76781803 76782767 964 True 648.000000 869 92.746500 2699 3449 2 chrUn.!!$R3 750
15 TraesCS2A01G345200 chr3A 725703839 725704590 751 True 1321.000000 1321 98.404000 2699 3449 1 chr3A.!!$R1 750
16 TraesCS2A01G345200 chr6A 307679396 307680147 751 True 1271.000000 1271 97.207000 2699 3449 1 chr6A.!!$R1 750
17 TraesCS2A01G345200 chr1A 219373887 219374602 715 False 1262.000000 1262 98.466000 2699 3414 1 chr1A.!!$F1 715
18 TraesCS2A01G345200 chr1B 163725228 163725967 739 False 1094.000000 1094 93.218000 2699 3449 1 chr1B.!!$F1 750
19 TraesCS2A01G345200 chr4B 49938471 49939183 712 False 931.000000 931 89.894000 2699 3449 1 chr4B.!!$F1 750
20 TraesCS2A01G345200 chr5A 333446724 333447419 695 False 857.000000 857 89.685000 2699 3363 1 chr5A.!!$F1 664

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
990 7035 1.968493 GGATAGTCCTATGCCGTTCCA 59.032 52.381 0.00 0.0 32.53 3.53 F
1026 7071 1.231221 CGATCGGAACAAACCACCAA 58.769 50.000 7.38 0.0 0.00 3.67 F
1198 7243 1.553248 TCGTTTCCTCCATTGATCGGT 59.447 47.619 0.00 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2144 9687 0.250338 GGAGGGCACTCGAACTTGTT 60.250 55.000 10.51 0.00 44.93 2.83 R
2296 9839 2.350772 CCGCCTCATCACAAGTTGAAAC 60.351 50.000 10.54 0.00 37.92 2.78 R
2927 10471 3.861689 GCAGCAAGAAAGCATTATGGTTC 59.138 43.478 10.16 4.64 37.04 3.62 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
58 5770 3.291584 TGGCTCACATCGACTCTAGATT 58.708 45.455 0.00 0.00 0.00 2.40
699 6728 2.745698 CTGCTCACCAGGAGTGCA 59.254 61.111 12.38 12.38 46.81 4.57
830 6859 4.070552 GGCAGACGGCGGAGAAGT 62.071 66.667 13.24 0.00 46.16 3.01
990 7035 1.968493 GGATAGTCCTATGCCGTTCCA 59.032 52.381 0.00 0.00 32.53 3.53
991 7036 2.567615 GGATAGTCCTATGCCGTTCCAT 59.432 50.000 0.00 0.00 32.53 3.41
992 7037 3.767673 GGATAGTCCTATGCCGTTCCATA 59.232 47.826 0.00 0.00 32.53 2.74
993 7038 4.406003 GGATAGTCCTATGCCGTTCCATAT 59.594 45.833 0.00 0.00 32.53 1.78
1026 7071 1.231221 CGATCGGAACAAACCACCAA 58.769 50.000 7.38 0.00 0.00 3.67
1028 7073 2.033550 CGATCGGAACAAACCACCAAAA 59.966 45.455 7.38 0.00 0.00 2.44
1140 7185 3.033764 GCGTCGCCGTTGTCTGAA 61.034 61.111 5.75 0.00 36.15 3.02
1190 7235 2.584608 CGGCCTCGTTTCCTCCAT 59.415 61.111 0.00 0.00 0.00 3.41
1198 7243 1.553248 TCGTTTCCTCCATTGATCGGT 59.447 47.619 0.00 0.00 0.00 4.69
1389 7437 1.971149 TCCCCTGGATTGTCATGTCT 58.029 50.000 0.00 0.00 0.00 3.41
1491 7539 3.724494 GCCTCGGCTGATAGTTGC 58.276 61.111 0.00 0.00 38.26 4.17
1520 7568 2.202797 CCGCACGGATGTCAGGAG 60.203 66.667 2.01 0.00 37.50 3.69
1582 7630 2.345244 CTGTGCCGCTTCCAGAGT 59.655 61.111 0.00 0.00 0.00 3.24
2119 9662 3.127203 CCACTGGTACTTAGTCGAGTCAG 59.873 52.174 0.00 0.00 31.39 3.51
2144 9687 8.333235 AGGTGGAAAACTATTAATGGTGATACA 58.667 33.333 5.10 2.04 0.00 2.29
2222 9765 1.973281 CGGATGCCTGCAAAGGTGT 60.973 57.895 0.00 0.00 0.00 4.16
2766 10309 0.235665 CGCACGAGCTCACATTTTGT 59.764 50.000 15.40 0.00 39.10 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 5770 2.904434 GTTTCTGGTTCCTCCTGGTAGA 59.096 50.000 0.00 0.00 36.08 2.59
247 5959 9.921637 AATTTTGAGCGTATTTAGGAATTCAAA 57.078 25.926 7.93 0.48 33.11 2.69
443 6472 2.692368 GGGATGACCTGGCCTGGA 60.692 66.667 33.43 14.02 35.85 3.86
699 6728 2.064581 CCTCCCCGATCCTTCCGTT 61.065 63.158 0.00 0.00 0.00 4.44
830 6859 4.124351 CGAGCACCGCGAACCCTA 62.124 66.667 8.23 0.00 0.00 3.53
1026 7071 1.373812 GTGCCCCGTAGTCCTGTTT 59.626 57.895 0.00 0.00 0.00 2.83
1028 7073 3.001406 GGTGCCCCGTAGTCCTGT 61.001 66.667 0.00 0.00 0.00 4.00
1067 7112 2.934887 CAGCTCTCTGGATCTCTCTGA 58.065 52.381 0.00 0.00 36.68 3.27
1140 7185 0.175073 GTAGCACGTCCTCGGGAATT 59.825 55.000 0.00 0.00 43.98 2.17
1190 7235 2.264480 CGAGGCCACACCGATCAA 59.736 61.111 5.01 0.00 46.52 2.57
1389 7437 0.037326 GTGTGAGGAACGAGCCATCA 60.037 55.000 0.00 0.00 0.00 3.07
1491 7539 3.827898 GTGCGGTCGAGGAGGAGG 61.828 72.222 0.00 0.00 0.00 4.30
1520 7568 3.719173 AGAAGTAGCTATGCGTCTTCC 57.281 47.619 14.29 1.93 40.63 3.46
1575 7623 0.750249 TCACAGCGTCAAACTCTGGA 59.250 50.000 2.55 0.00 35.38 3.86
1582 7630 2.032634 GGCCGATCACAGCGTCAAA 61.033 57.895 0.00 0.00 0.00 2.69
2119 9662 8.514330 TGTATCACCATTAATAGTTTTCCACC 57.486 34.615 0.00 0.00 0.00 4.61
2144 9687 0.250338 GGAGGGCACTCGAACTTGTT 60.250 55.000 10.51 0.00 44.93 2.83
2296 9839 2.350772 CCGCCTCATCACAAGTTGAAAC 60.351 50.000 10.54 0.00 37.92 2.78
2620 10163 6.492429 TCTTACGACATTGCATAGTATACCCT 59.508 38.462 0.00 0.00 0.00 4.34
2626 10169 6.592220 TGCTTTTCTTACGACATTGCATAGTA 59.408 34.615 0.00 0.00 0.00 1.82
2766 10309 6.132791 TCACGGTTTATGTTTTGCAACTAA 57.867 33.333 0.00 0.00 33.58 2.24
2874 10417 4.519213 ACTTATGCAATTACCAACGCCTA 58.481 39.130 0.00 0.00 0.00 3.93
2887 10430 6.528537 AGCATCATGGTTAAACTTATGCAA 57.471 33.333 20.05 0.00 40.45 4.08
2927 10471 3.861689 GCAGCAAGAAAGCATTATGGTTC 59.138 43.478 10.16 4.64 37.04 3.62


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

AutoCloner maintained by Alex Coulton.