Multiple sequence alignment - TraesCS5B01G549900

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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 TraesCS5B01G549900 chr5B 100.000 3159 0 0 1 3159 701464822 701467980 0.000000e+00 5834.0
1 TraesCS5B01G549900 chr1B 98.040 3164 55 4 3 3159 23815840 23819003 0.000000e+00 5493.0
2 TraesCS5B01G549900 chr1B 95.650 2299 73 4 1 2295 48529647 48531922 0.000000e+00 3666.0
3 TraesCS5B01G549900 chr1B 94.565 736 26 7 2437 3159 666991387 666990653 0.000000e+00 1125.0
4 TraesCS5B01G549900 chr1B 95.098 102 3 1 2296 2395 388032449 388032550 3.260000e-35 159.0
5 TraesCS5B01G549900 chr1B 95.000 100 5 0 2296 2395 48532430 48532529 1.170000e-34 158.0
6 TraesCS5B01G549900 chr7A 98.487 2247 30 3 1 2244 206573454 206575699 0.000000e+00 3958.0
7 TraesCS5B01G549900 chr7A 97.230 722 14 4 2437 3153 206576216 206576936 0.000000e+00 1218.0
8 TraesCS5B01G549900 chr2B 96.399 2277 64 6 1 2274 142887184 142889445 0.000000e+00 3735.0
9 TraesCS5B01G549900 chr2B 93.197 735 34 6 2437 3159 573751799 573752529 0.000000e+00 1066.0
10 TraesCS5B01G549900 chr2B 91.506 259 12 1 1 259 634208851 634209099 6.480000e-92 348.0
11 TraesCS5B01G549900 chr5A 96.346 1642 50 8 1 1634 670476772 670475133 0.000000e+00 2691.0
12 TraesCS5B01G549900 chr5A 95.630 1602 65 4 1 1598 696328870 696327270 0.000000e+00 2566.0
13 TraesCS5B01G549900 chr5A 95.588 680 27 2 1595 2274 670475032 670474356 0.000000e+00 1086.0
14 TraesCS5B01G549900 chr3B 96.545 1621 46 4 1 1612 607523084 607521465 0.000000e+00 2675.0
15 TraesCS5B01G549900 chr3B 97.820 688 15 0 1608 2295 607501966 607501279 0.000000e+00 1188.0
16 TraesCS5B01G549900 chr3B 94.505 728 32 5 2437 3159 487852967 487852243 0.000000e+00 1116.0
17 TraesCS5B01G549900 chr3B 98.540 137 2 0 1 137 581344665 581344529 3.150000e-60 243.0
18 TraesCS5B01G549900 chr3B 96.970 99 3 0 2297 2395 607500771 607500673 1.950000e-37 167.0
19 TraesCS5B01G549900 chr3B 100.000 39 0 0 2393 2431 487853550 487853512 4.370000e-09 73.1
20 TraesCS5B01G549900 chr1A 95.128 1642 69 10 1 1634 449450045 449451683 0.000000e+00 2579.0
21 TraesCS5B01G549900 chr1A 95.147 680 30 2 1595 2274 449451784 449452460 0.000000e+00 1070.0
22 TraesCS5B01G549900 chr1A 93.061 735 35 9 2437 3159 387225355 387224625 0.000000e+00 1061.0
23 TraesCS5B01G549900 chr1A 100.000 39 0 0 2393 2431 387225935 387225897 4.370000e-09 73.1
24 TraesCS5B01G549900 chr2D 95.587 1609 65 5 1 1603 197523408 197521800 0.000000e+00 2573.0
25 TraesCS5B01G549900 chr2D 95.595 681 25 3 1595 2274 197521669 197520993 0.000000e+00 1086.0
26 TraesCS5B01G549900 chr3A 93.905 1608 89 8 1 1603 218192078 218190475 0.000000e+00 2418.0
27 TraesCS5B01G549900 chr3A 95.588 680 22 4 1595 2274 1715090 1714419 0.000000e+00 1083.0
28 TraesCS5B01G549900 chr5D 95.062 729 29 5 2437 3159 498378946 498379673 0.000000e+00 1140.0
29 TraesCS5B01G549900 chr4A 93.188 734 37 7 2437 3159 706560986 706560255 0.000000e+00 1066.0
30 TraesCS5B01G549900 chr4A 92.424 726 26 14 2437 3156 324709708 324709006 0.000000e+00 1009.0
31 TraesCS5B01G549900 chr4A 90.909 726 36 16 2437 3156 551275275 551275976 0.000000e+00 948.0
32 TraesCS5B01G549900 chr4A 94.872 39 2 0 2393 2431 324710292 324710254 9.460000e-06 62.1
33 TraesCS5B01G549900 chr2A 94.000 100 6 0 2296 2395 729535047 729534948 5.460000e-33 152.0


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 TraesCS5B01G549900 chr5B 701464822 701467980 3158 False 5834.00 5834 100.0000 1 3159 1 chr5B.!!$F1 3158
1 TraesCS5B01G549900 chr1B 23815840 23819003 3163 False 5493.00 5493 98.0400 3 3159 1 chr1B.!!$F1 3156
2 TraesCS5B01G549900 chr1B 48529647 48532529 2882 False 1912.00 3666 95.3250 1 2395 2 chr1B.!!$F3 2394
3 TraesCS5B01G549900 chr1B 666990653 666991387 734 True 1125.00 1125 94.5650 2437 3159 1 chr1B.!!$R1 722
4 TraesCS5B01G549900 chr7A 206573454 206576936 3482 False 2588.00 3958 97.8585 1 3153 2 chr7A.!!$F1 3152
5 TraesCS5B01G549900 chr2B 142887184 142889445 2261 False 3735.00 3735 96.3990 1 2274 1 chr2B.!!$F1 2273
6 TraesCS5B01G549900 chr2B 573751799 573752529 730 False 1066.00 1066 93.1970 2437 3159 1 chr2B.!!$F2 722
7 TraesCS5B01G549900 chr5A 696327270 696328870 1600 True 2566.00 2566 95.6300 1 1598 1 chr5A.!!$R1 1597
8 TraesCS5B01G549900 chr5A 670474356 670476772 2416 True 1888.50 2691 95.9670 1 2274 2 chr5A.!!$R2 2273
9 TraesCS5B01G549900 chr3B 607521465 607523084 1619 True 2675.00 2675 96.5450 1 1612 1 chr3B.!!$R2 1611
10 TraesCS5B01G549900 chr3B 607500673 607501966 1293 True 677.50 1188 97.3950 1608 2395 2 chr3B.!!$R4 787
11 TraesCS5B01G549900 chr3B 487852243 487853550 1307 True 594.55 1116 97.2525 2393 3159 2 chr3B.!!$R3 766
12 TraesCS5B01G549900 chr1A 449450045 449452460 2415 False 1824.50 2579 95.1375 1 2274 2 chr1A.!!$F1 2273
13 TraesCS5B01G549900 chr1A 387224625 387225935 1310 True 567.05 1061 96.5305 2393 3159 2 chr1A.!!$R1 766
14 TraesCS5B01G549900 chr2D 197520993 197523408 2415 True 1829.50 2573 95.5910 1 2274 2 chr2D.!!$R1 2273
15 TraesCS5B01G549900 chr3A 218190475 218192078 1603 True 2418.00 2418 93.9050 1 1603 1 chr3A.!!$R2 1602
16 TraesCS5B01G549900 chr3A 1714419 1715090 671 True 1083.00 1083 95.5880 1595 2274 1 chr3A.!!$R1 679
17 TraesCS5B01G549900 chr5D 498378946 498379673 727 False 1140.00 1140 95.0620 2437 3159 1 chr5D.!!$F1 722
18 TraesCS5B01G549900 chr4A 706560255 706560986 731 True 1066.00 1066 93.1880 2437 3159 1 chr4A.!!$R1 722
19 TraesCS5B01G549900 chr4A 551275275 551275976 701 False 948.00 948 90.9090 2437 3156 1 chr4A.!!$F1 719
20 TraesCS5B01G549900 chr4A 324709006 324710292 1286 True 535.55 1009 93.6480 2393 3156 2 chr4A.!!$R2 763

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
539 577 0.038159 AGGCGGCGCTCATCTAATAC 60.038 55.0 32.30 10.68 0.0 1.89 F
542 580 0.732880 CGGCGCTCATCTAATACGGG 60.733 60.0 7.64 0.00 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 2315 1.955778 CAGCCACACAGTTTCCAATCA 59.044 47.619 0.0 0.0 0.00 2.57 R
2431 3269 4.976116 ACGTTTTTCAAATCAAGCTGTAGC 59.024 37.500 0.0 0.0 42.49 3.58 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
117 118 5.755849 CCTTATTTCCAGGTGAACCACTAT 58.244 41.667 1.62 0.00 38.89 2.12
160 162 5.587289 TGGAATTTTTGAAACTTCTCCACG 58.413 37.500 6.54 0.00 30.87 4.94
266 268 5.180868 CCATCACTATTGCTGAAGATAAGGC 59.819 44.000 0.00 0.00 0.00 4.35
523 561 3.636153 ACCTGAGTGAATTTAGGAGGC 57.364 47.619 0.00 0.00 34.42 4.70
524 562 2.093447 ACCTGAGTGAATTTAGGAGGCG 60.093 50.000 0.00 0.00 34.42 5.52
525 563 2.555199 CTGAGTGAATTTAGGAGGCGG 58.445 52.381 0.00 0.00 0.00 6.13
526 564 1.300481 GAGTGAATTTAGGAGGCGGC 58.700 55.000 0.00 0.00 0.00 6.53
527 565 0.462047 AGTGAATTTAGGAGGCGGCG 60.462 55.000 0.51 0.51 0.00 6.46
528 566 1.817941 TGAATTTAGGAGGCGGCGC 60.818 57.895 26.17 26.17 0.00 6.53
529 567 1.523938 GAATTTAGGAGGCGGCGCT 60.524 57.895 32.30 17.73 0.00 5.92
530 568 1.499688 GAATTTAGGAGGCGGCGCTC 61.500 60.000 32.30 24.43 0.00 5.03
531 569 2.252072 AATTTAGGAGGCGGCGCTCA 62.252 55.000 32.30 11.09 0.00 4.26
532 570 2.044806 ATTTAGGAGGCGGCGCTCAT 62.045 55.000 32.30 24.35 0.00 2.90
533 571 2.644555 TTTAGGAGGCGGCGCTCATC 62.645 60.000 32.30 24.56 0.00 2.92
535 573 2.692273 TAGGAGGCGGCGCTCATCTA 62.692 60.000 32.30 22.41 0.00 1.98
536 574 2.417516 GAGGCGGCGCTCATCTAA 59.582 61.111 32.30 0.00 0.00 2.10
537 575 1.005630 GAGGCGGCGCTCATCTAAT 60.006 57.895 32.30 7.43 0.00 1.73
538 576 0.243907 GAGGCGGCGCTCATCTAATA 59.756 55.000 32.30 0.00 0.00 0.98
539 577 0.038159 AGGCGGCGCTCATCTAATAC 60.038 55.000 32.30 10.68 0.00 1.89
540 578 1.344942 GGCGGCGCTCATCTAATACG 61.345 60.000 32.30 0.00 0.00 3.06
541 579 1.344942 GCGGCGCTCATCTAATACGG 61.345 60.000 26.86 0.00 0.00 4.02
542 580 0.732880 CGGCGCTCATCTAATACGGG 60.733 60.000 7.64 0.00 0.00 5.28
674 712 4.920640 ATCACTACCCAATAGAGTCACG 57.079 45.455 0.00 0.00 34.65 4.35
876 914 3.917988 AGATCAGATCGCGATGCAAATA 58.082 40.909 29.09 5.98 0.00 1.40
905 943 6.755141 GCTGATTATAACAACTAGTCGGACAA 59.245 38.462 11.27 0.00 0.00 3.18
1279 1321 6.570672 ATGATACACTTTGCATGATCATCC 57.429 37.500 4.86 0.00 30.11 3.51
1532 1574 5.535783 TCCGTCGACCCTACATATTAAATCA 59.464 40.000 10.58 0.00 0.00 2.57
1832 2157 4.734398 AGAGATGAACCTGAAGCTACAG 57.266 45.455 0.00 0.00 37.61 2.74
1967 2293 2.544267 CTGGTTGACGAGTTGAAGGAAC 59.456 50.000 0.00 0.00 34.40 3.62
1989 2315 6.165700 ACCAAAGCAAGATGACATTTTCTT 57.834 33.333 0.00 0.00 32.48 2.52
2694 4075 9.921637 AAAGCTATCCGATAAAAATGTTCAAAA 57.078 25.926 0.00 0.00 0.00 2.44
3006 4396 8.645814 TTCTCTAGTACTTTGTGTCATTCCTA 57.354 34.615 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 162 9.281371 ACAAAGTTGGTAGGTTTAGAAATCTAC 57.719 33.333 14.50 14.5 46.80 2.59
520 558 0.038159 GTATTAGATGAGCGCCGCCT 60.038 55.000 4.98 0.0 0.00 5.52
521 559 1.344942 CGTATTAGATGAGCGCCGCC 61.345 60.000 4.98 0.0 0.00 6.13
522 560 1.344942 CCGTATTAGATGAGCGCCGC 61.345 60.000 2.29 0.0 0.00 6.53
523 561 0.732880 CCCGTATTAGATGAGCGCCG 60.733 60.000 2.29 0.0 0.00 6.46
524 562 1.014564 GCCCGTATTAGATGAGCGCC 61.015 60.000 2.29 0.0 0.00 6.53
525 563 0.038159 AGCCCGTATTAGATGAGCGC 60.038 55.000 0.00 0.0 0.00 5.92
526 564 3.439293 CATAGCCCGTATTAGATGAGCG 58.561 50.000 0.00 0.0 0.00 5.03
527 565 3.190874 GCATAGCCCGTATTAGATGAGC 58.809 50.000 0.00 0.0 0.00 4.26
528 566 3.786635 GGCATAGCCCGTATTAGATGAG 58.213 50.000 0.00 0.0 44.06 2.90
529 567 3.887621 GGCATAGCCCGTATTAGATGA 57.112 47.619 0.00 0.0 44.06 2.92
541 579 1.192146 TCCCTATGGTCGGCATAGCC 61.192 60.000 0.00 0.0 46.75 3.93
542 580 0.247736 CTCCCTATGGTCGGCATAGC 59.752 60.000 0.00 0.0 32.75 2.97
674 712 1.095228 TGCCGCCGGAATCTTGATTC 61.095 55.000 7.68 13.3 0.00 2.52
876 914 6.223852 CGACTAGTTGTTATAATCAGCCCAT 58.776 40.000 0.00 0.0 0.00 4.00
1279 1321 7.518188 AGTTTATCCCATATTACAGGTTCAGG 58.482 38.462 0.00 0.0 0.00 3.86
1340 1382 2.039818 AGAGCATGAATGGCAGTGAG 57.960 50.000 0.00 0.0 0.00 3.51
1601 1926 7.317842 AGAAACATATCAGCATGTTCTCTTG 57.682 36.000 2.23 0.0 46.00 3.02
1832 2157 5.335191 CCTTTTGTTCAGAGTTGGTAGATGC 60.335 44.000 0.00 0.0 0.00 3.91
1967 2293 6.462073 CAAGAAAATGTCATCTTGCTTTGG 57.538 37.500 2.92 0.0 44.12 3.28
1989 2315 1.955778 CAGCCACACAGTTTCCAATCA 59.044 47.619 0.00 0.0 0.00 2.57
2431 3269 4.976116 ACGTTTTTCAAATCAAGCTGTAGC 59.024 37.500 0.00 0.0 42.49 3.58
2506 3887 9.442047 CTCTGACAATAATCTACTGGAAAACTT 57.558 33.333 0.00 0.0 0.00 2.66
2694 4075 4.956075 ACTCAAACTTCCACCATCAACTTT 59.044 37.500 0.00 0.0 0.00 2.66
2714 4095 8.961294 TTGTTGTCGAAATAGTTACTCTACTC 57.039 34.615 0.00 0.0 0.00 2.59
3119 4520 2.416893 GGAGATCACGTCCAGAAAAAGC 59.583 50.000 0.00 0.0 33.84 3.51


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

AutoCloner maintained by Alex Coulton.