Multiple sequence alignment - TraesCS7A01G297100

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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 TraesCS7A01G297100 chr7A 100.000 2354 0 0 1 2354 398576568 398574215 0.000000e+00 4348
1 TraesCS7A01G297100 chr1D 97.320 1455 37 2 901 2354 160657233 160655780 0.000000e+00 2470
2 TraesCS7A01G297100 chr1D 82.230 906 116 22 11 894 184710241 184709359 0.000000e+00 739
3 TraesCS7A01G297100 chr1D 83.631 672 93 10 244 900 218877256 218877925 1.200000e-172 616
4 TraesCS7A01G297100 chr1D 83.686 662 89 12 259 904 218881176 218881834 7.190000e-170 606
5 TraesCS7A01G297100 chr1D 86.400 500 51 8 415 900 167377228 167377724 4.450000e-147 531
6 TraesCS7A01G297100 chrUn 97.320 1455 36 3 901 2354 143237572 143236120 0.000000e+00 2468
7 TraesCS7A01G297100 chrUn 96.980 1457 41 3 899 2354 15264653 15263199 0.000000e+00 2444
8 TraesCS7A01G297100 chr6A 97.113 1455 39 3 901 2354 265558983 265560435 0.000000e+00 2451
9 TraesCS7A01G297100 chr6A 85.672 335 33 5 572 894 112314046 112314377 2.900000e-89 339
10 TraesCS7A01G297100 chr3A 96.920 1461 42 3 896 2354 315557111 315555652 0.000000e+00 2446
11 TraesCS7A01G297100 chr3A 85.236 657 77 17 259 900 343588251 343588902 0.000000e+00 658
12 TraesCS7A01G297100 chr3A 86.573 499 50 8 415 900 738697077 738696583 3.440000e-148 534
13 TraesCS7A01G297100 chr6D 96.976 1455 41 3 901 2354 207988031 207989483 0.000000e+00 2440
14 TraesCS7A01G297100 chr1A 96.907 1455 43 2 901 2354 186455611 186457064 0.000000e+00 2436
15 TraesCS7A01G297100 chr4A 96.907 1455 42 2 901 2354 314450378 314448926 0.000000e+00 2435
16 TraesCS7A01G297100 chr4A 84.670 698 81 16 216 894 415770755 415771445 0.000000e+00 673
17 TraesCS7A01G297100 chr4A 83.838 693 92 13 216 891 415766708 415767397 1.970000e-180 641
18 TraesCS7A01G297100 chr4A 84.660 515 62 8 400 900 409266056 409265545 4.520000e-137 497
19 TraesCS7A01G297100 chr2A 96.838 1455 44 2 901 2354 325463327 325461874 0.000000e+00 2431
20 TraesCS7A01G297100 chr4D 83.959 879 108 23 48 900 320416621 320415750 0.000000e+00 811
21 TraesCS7A01G297100 chr4D 86.974 499 52 8 413 900 261995680 261996176 1.230000e-152 549
22 TraesCS7A01G297100 chr7D 84.266 661 79 19 259 900 393878187 393877533 2.570000e-174 621
23 TraesCS7A01G297100 chr7D 86.804 485 44 10 432 900 118365717 118366197 7.450000e-145 523
24 TraesCS7A01G297100 chr2D 80.788 838 115 29 74 894 232107679 232108487 4.300000e-172 614
25 TraesCS7A01G297100 chr7B 87.371 483 45 6 432 900 461951527 461951047 7.400000e-150 540
26 TraesCS7A01G297100 chr3D 85.078 516 59 12 400 900 243372890 243372378 5.800000e-141 510


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 TraesCS7A01G297100 chr7A 398574215 398576568 2353 True 4348 4348 100.0000 1 2354 1 chr7A.!!$R1 2353
1 TraesCS7A01G297100 chr1D 160655780 160657233 1453 True 2470 2470 97.3200 901 2354 1 chr1D.!!$R1 1453
2 TraesCS7A01G297100 chr1D 184709359 184710241 882 True 739 739 82.2300 11 894 1 chr1D.!!$R2 883
3 TraesCS7A01G297100 chr1D 218877256 218881834 4578 False 611 616 83.6585 244 904 2 chr1D.!!$F2 660
4 TraesCS7A01G297100 chrUn 143236120 143237572 1452 True 2468 2468 97.3200 901 2354 1 chrUn.!!$R2 1453
5 TraesCS7A01G297100 chrUn 15263199 15264653 1454 True 2444 2444 96.9800 899 2354 1 chrUn.!!$R1 1455
6 TraesCS7A01G297100 chr6A 265558983 265560435 1452 False 2451 2451 97.1130 901 2354 1 chr6A.!!$F2 1453
7 TraesCS7A01G297100 chr3A 315555652 315557111 1459 True 2446 2446 96.9200 896 2354 1 chr3A.!!$R1 1458
8 TraesCS7A01G297100 chr3A 343588251 343588902 651 False 658 658 85.2360 259 900 1 chr3A.!!$F1 641
9 TraesCS7A01G297100 chr6D 207988031 207989483 1452 False 2440 2440 96.9760 901 2354 1 chr6D.!!$F1 1453
10 TraesCS7A01G297100 chr1A 186455611 186457064 1453 False 2436 2436 96.9070 901 2354 1 chr1A.!!$F1 1453
11 TraesCS7A01G297100 chr4A 314448926 314450378 1452 True 2435 2435 96.9070 901 2354 1 chr4A.!!$R1 1453
12 TraesCS7A01G297100 chr4A 415766708 415771445 4737 False 657 673 84.2540 216 894 2 chr4A.!!$F1 678
13 TraesCS7A01G297100 chr4A 409265545 409266056 511 True 497 497 84.6600 400 900 1 chr4A.!!$R2 500
14 TraesCS7A01G297100 chr2A 325461874 325463327 1453 True 2431 2431 96.8380 901 2354 1 chr2A.!!$R1 1453
15 TraesCS7A01G297100 chr4D 320415750 320416621 871 True 811 811 83.9590 48 900 1 chr4D.!!$R1 852
16 TraesCS7A01G297100 chr7D 393877533 393878187 654 True 621 621 84.2660 259 900 1 chr7D.!!$R1 641
17 TraesCS7A01G297100 chr2D 232107679 232108487 808 False 614 614 80.7880 74 894 1 chr2D.!!$F1 820
18 TraesCS7A01G297100 chr3D 243372378 243372890 512 True 510 510 85.0780 400 900 1 chr3D.!!$R1 500

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
77 79 0.391793 CTCGCCCTTCTTCTCCAACC 60.392 60.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2027 6285 0.242825 CCGTGTCAACCGAAGCTCTA 59.757 55.0 0.0 0.0 0.0 2.43 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
22 23 4.695560 CTCCTTCGCCGGAGTTTT 57.304 55.556 5.05 0.00 44.49 2.43
24 25 1.004200 TCCTTCGCCGGAGTTTTCC 60.004 57.895 5.05 0.00 40.33 3.13
29 30 0.680618 TCGCCGGAGTTTTCCTGTAA 59.319 50.000 5.05 0.00 41.67 2.41
77 79 0.391793 CTCGCCCTTCTTCTCCAACC 60.392 60.000 0.00 0.00 0.00 3.77
121 123 2.202797 CGGTGAGCACATCTCCCG 60.203 66.667 2.75 0.00 43.74 5.14
125 127 1.305297 TGAGCACATCTCCCGACCT 60.305 57.895 0.00 0.00 41.18 3.85
153 155 1.020333 TGTTTTAACCGCCCGGATCG 61.020 55.000 14.44 5.99 38.96 3.69
159 161 4.770874 CCGCCCGGATCGGTTGTT 62.771 66.667 21.98 0.00 46.80 2.83
160 162 3.496131 CGCCCGGATCGGTTGTTG 61.496 66.667 0.73 0.00 46.80 3.33
212 223 2.436115 GTCCACCAGTTAGCCGCC 60.436 66.667 0.00 0.00 0.00 6.13
226 4059 3.215568 CGCCACAGCAAACACCCA 61.216 61.111 0.00 0.00 39.83 4.51
251 4084 1.413767 CTATCACAGTGCGCCACGTC 61.414 60.000 4.18 0.00 39.64 4.34
270 4105 7.590279 CCACGTCTCAGGTATTTTGTTTTAAT 58.410 34.615 0.00 0.00 0.00 1.40
292 4129 6.916360 ATTAGAAAAGGGCAGATTTGTTCA 57.084 33.333 0.00 0.00 0.00 3.18
356 4193 3.296322 TGATGAAACCAACGCCAAATC 57.704 42.857 0.00 0.00 0.00 2.17
369 4206 3.956199 ACGCCAAATCCTTCATCATGATT 59.044 39.130 5.16 0.00 0.00 2.57
370 4207 5.132502 ACGCCAAATCCTTCATCATGATTA 58.867 37.500 5.16 0.00 0.00 1.75
374 4211 6.041296 GCCAAATCCTTCATCATGATTACCTT 59.959 38.462 5.16 0.00 0.00 3.50
381 4218 8.501904 TCCTTCATCATGATTACCTTTATCCAA 58.498 33.333 5.16 0.00 0.00 3.53
454 4291 8.178313 AGAATTTGAATTTAACCTTTCGGAGT 57.822 30.769 0.00 0.00 0.00 3.85
456 4293 6.945938 TTTGAATTTAACCTTTCGGAGTCA 57.054 33.333 0.00 0.00 0.00 3.41
457 4294 6.554334 TTGAATTTAACCTTTCGGAGTCAG 57.446 37.500 0.00 0.00 0.00 3.51
478 4315 5.347635 TCAGTATCTTTCAAACCGTTGATCG 59.652 40.000 0.00 0.00 43.29 3.69
507 4345 6.833342 AGTTGATTCTTTTTGCATTGTGAC 57.167 33.333 0.00 0.00 0.00 3.67
584 4431 4.525912 ATTGAATTCCTTGCTGTTGACC 57.474 40.909 2.27 0.00 0.00 4.02
607 4458 9.378551 GACCTTATTGTGATTGTTATGTGAGTA 57.621 33.333 0.00 0.00 0.00 2.59
612 4463 6.435430 TGTGATTGTTATGTGAGTAATGGC 57.565 37.500 0.00 0.00 0.00 4.40
638 4490 1.949465 ATCGGTGCCTTCGTTAATCC 58.051 50.000 0.00 0.00 0.00 3.01
647 4499 7.576287 CGGTGCCTTCGTTAATCCTATAGATTA 60.576 40.741 0.00 1.48 43.65 1.75
684 4537 4.863131 GCGGATCGGAATTAATCGTTAGAT 59.137 41.667 4.16 0.00 39.12 1.98
701 4554 7.088905 TCGTTAGATTACTTCAACAGAGTTCC 58.911 38.462 0.00 0.00 0.00 3.62
703 4556 7.148787 CGTTAGATTACTTCAACAGAGTTCCAC 60.149 40.741 0.00 0.00 0.00 4.02
743 4598 8.985315 TTGATTTTGCTCATCCTATATTCTGT 57.015 30.769 0.00 0.00 0.00 3.41
762 4618 6.641169 TCTGTTATGCATGTGTGGTTTTAA 57.359 33.333 10.16 0.00 0.00 1.52
763 4619 7.225784 TCTGTTATGCATGTGTGGTTTTAAT 57.774 32.000 10.16 0.00 0.00 1.40
764 4620 7.089538 TCTGTTATGCATGTGTGGTTTTAATG 58.910 34.615 10.16 0.00 0.00 1.90
765 4621 5.636965 TGTTATGCATGTGTGGTTTTAATGC 59.363 36.000 10.16 0.00 43.08 3.56
766 4622 4.540359 ATGCATGTGTGGTTTTAATGCT 57.460 36.364 0.00 0.00 43.17 3.79
814 4687 8.594687 GTTATCATGTTTTGGTATTGATTGTGC 58.405 33.333 0.00 0.00 0.00 4.57
820 4693 8.341892 TGTTTTGGTATTGATTGTGCTATGTA 57.658 30.769 0.00 0.00 0.00 2.29
880 4753 3.258123 TGTCGAGTGATCCATGAAAGTGA 59.742 43.478 0.00 0.00 0.00 3.41
886 4759 6.550938 AGTGATCCATGAAAGTGATGAGTA 57.449 37.500 0.00 0.00 0.00 2.59
943 4816 8.424918 GTTCACCTCATTTATCATCTTCTCCTA 58.575 37.037 0.00 0.00 0.00 2.94
1200 5073 6.263168 CCCATACAACAAGTTTGAAGAGAACT 59.737 38.462 0.00 0.00 38.92 3.01
1371 5244 2.493030 GCATCCAGCATGTGTGGC 59.507 61.111 10.55 0.00 44.79 5.01
1471 5344 1.538047 TGAGAGTTCCAATGCAAGCC 58.462 50.000 0.00 0.00 0.00 4.35
1511 5384 1.021390 CGCGAGGCTCCATGAGTTTT 61.021 55.000 9.32 0.00 31.39 2.43
2027 6285 4.714632 CAACCCCGTATCATCTTGGTATT 58.285 43.478 0.00 0.00 0.00 1.89
2100 6358 6.831353 TGTTCTTGTTCATCCTAAAAGTCCAA 59.169 34.615 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.003718 AGGAAAACTCCGGCGAAGG 60.004 57.895 9.30 0.00 34.28 3.46
9 10 0.680618 TACAGGAAAACTCCGGCGAA 59.319 50.000 9.30 0.00 34.28 4.70
59 60 1.677552 GGTTGGAGAAGAAGGGCGA 59.322 57.895 0.00 0.00 0.00 5.54
60 61 1.377333 GGGTTGGAGAAGAAGGGCG 60.377 63.158 0.00 0.00 0.00 6.13
100 102 1.142748 GAGATGTGCTCACCGGAGG 59.857 63.158 9.46 0.00 44.51 4.30
121 123 3.688185 GGTTAAAACAAGATCGGGAGGTC 59.312 47.826 0.00 0.00 41.38 3.85
125 127 2.078392 GCGGTTAAAACAAGATCGGGA 58.922 47.619 0.00 0.00 0.00 5.14
153 155 3.976306 CCGGTTCGAATAAAACAACAACC 59.024 43.478 0.00 0.00 0.00 3.77
157 159 4.789629 GCATACCGGTTCGAATAAAACAAC 59.210 41.667 15.04 0.00 0.00 3.32
159 161 4.001652 TGCATACCGGTTCGAATAAAACA 58.998 39.130 15.04 0.00 0.00 2.83
160 162 4.093850 AGTGCATACCGGTTCGAATAAAAC 59.906 41.667 15.04 0.00 0.00 2.43
200 211 3.127533 GCTGTGGCGGCTAACTGG 61.128 66.667 11.43 0.00 32.24 4.00
212 223 0.038892 GCTGATGGGTGTTTGCTGTG 60.039 55.000 0.00 0.00 0.00 3.66
226 4059 0.531532 GCGCACTGTGATAGGCTGAT 60.532 55.000 12.86 0.00 0.00 2.90
270 4105 6.267471 ACATGAACAAATCTGCCCTTTTCTAA 59.733 34.615 0.00 0.00 0.00 2.10
278 4114 5.055812 TGAAAAACATGAACAAATCTGCCC 58.944 37.500 0.00 0.00 0.00 5.36
356 4193 8.571336 GTTGGATAAAGGTAATCATGATGAAGG 58.429 37.037 9.46 0.00 0.00 3.46
369 4206 5.727279 TGGATAGGTGTGTTGGATAAAGGTA 59.273 40.000 0.00 0.00 0.00 3.08
370 4207 4.538490 TGGATAGGTGTGTTGGATAAAGGT 59.462 41.667 0.00 0.00 0.00 3.50
454 4291 5.347635 CGATCAACGGTTTGAAAGATACTGA 59.652 40.000 0.00 0.00 45.01 3.41
456 4293 5.475719 TCGATCAACGGTTTGAAAGATACT 58.524 37.500 0.00 0.00 45.01 2.12
457 4294 5.773239 TCGATCAACGGTTTGAAAGATAC 57.227 39.130 0.00 0.00 45.01 2.24
563 4408 4.154942 AGGTCAACAGCAAGGAATTCAAT 58.845 39.130 7.93 0.00 0.00 2.57
607 4458 3.832527 AGGCACCGATAAATAAGCCATT 58.167 40.909 0.00 0.00 44.34 3.16
612 4463 6.592798 TTAACGAAGGCACCGATAAATAAG 57.407 37.500 5.59 0.00 0.00 1.73
638 4490 6.326375 GCTTCACACTCCGGATAATCTATAG 58.674 44.000 3.57 0.00 0.00 1.31
647 4499 1.982395 TCCGCTTCACACTCCGGAT 60.982 57.895 3.57 0.00 44.13 4.18
684 4537 3.128349 GCGTGGAACTCTGTTGAAGTAA 58.872 45.455 0.00 0.00 31.75 2.24
743 4598 6.035368 AGCATTAAAACCACACATGCATAA 57.965 33.333 0.00 0.00 42.30 1.90
762 4618 4.163078 GGGATACACATATCAGGCTAGCAT 59.837 45.833 18.24 6.55 39.29 3.79
763 4619 3.515502 GGGATACACATATCAGGCTAGCA 59.484 47.826 18.24 0.00 39.29 3.49
764 4620 3.429547 CGGGATACACATATCAGGCTAGC 60.430 52.174 6.04 6.04 39.29 3.42
765 4621 3.764434 ACGGGATACACATATCAGGCTAG 59.236 47.826 0.00 0.00 39.29 3.42
766 4622 3.509967 CACGGGATACACATATCAGGCTA 59.490 47.826 0.00 0.00 39.29 3.93
814 4687 6.317140 AGCAAGTTGATCACACCATTACATAG 59.683 38.462 7.16 0.00 0.00 2.23
820 4693 4.400251 CCATAGCAAGTTGATCACACCATT 59.600 41.667 7.16 0.00 0.00 3.16
886 4759 7.818997 TGTCCTCATCACTACGACTATAAAT 57.181 36.000 0.00 0.00 0.00 1.40
943 4816 7.058525 TCACTTGATGGCTGAGATTTATCATT 58.941 34.615 0.00 0.00 0.00 2.57
1200 5073 5.930135 AGGCTTTCTTCAGAGTTGAAACTA 58.070 37.500 0.00 0.00 42.48 2.24
1371 5244 7.281774 ACTTCATATGCTCTCCATTTTGTACTG 59.718 37.037 0.00 0.00 35.34 2.74
1511 5384 3.811702 CCAGCTGGTCAAGGGAGA 58.188 61.111 25.53 0.00 0.00 3.71
2027 6285 0.242825 CCGTGTCAACCGAAGCTCTA 59.757 55.000 0.00 0.00 0.00 2.43
2119 6378 4.610333 CAAAGGGCTAGGTAAAGGGATTT 58.390 43.478 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.