Multiple sequence alignment - TraesCS5A01G546400

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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 TraesCS5A01G546400 chr5A 100.000 3111 0 0 1 3111 700611577 700614687 0.000000e+00 5746.0
1 TraesCS5A01G546400 chr4A 98.183 2367 39 4 597 2960 640937240 640934875 0.000000e+00 4130.0
2 TraesCS5A01G546400 chr4A 100.000 134 0 0 2978 3111 640934650 640934517 6.660000e-62 248.0
3 TraesCS5A01G546400 chr4A 96.748 123 4 0 500 622 640937376 640937254 4.070000e-49 206.0
4 TraesCS5A01G546400 chr2A 97.051 2374 60 3 597 2960 688774893 688777266 0.000000e+00 3988.0
5 TraesCS5A01G546400 chr2A 93.853 2359 91 26 597 2923 84021774 84024110 0.000000e+00 3504.0
6 TraesCS5A01G546400 chr2A 98.812 505 4 2 1 503 44233744 44234248 0.000000e+00 898.0
7 TraesCS5A01G546400 chr2A 97.701 522 7 5 1 521 200947367 200946850 0.000000e+00 893.0
8 TraesCS5A01G546400 chr2A 98.507 134 2 0 2978 3111 84024547 84024680 1.440000e-58 237.0
9 TraesCS5A01G546400 chr2A 97.761 134 3 0 2978 3111 688777539 688777672 6.710000e-57 231.0
10 TraesCS5A01G546400 chr2A 95.833 120 5 0 500 619 84021638 84021757 8.800000e-46 195.0
11 TraesCS5A01G546400 chr2A 95.000 120 6 0 500 619 688774757 688774876 4.100000e-44 189.0
12 TraesCS5A01G546400 chr6D 94.599 2370 95 13 597 2960 472511279 472513621 0.000000e+00 3637.0
13 TraesCS5A01G546400 chr6D 92.710 2483 121 24 500 2960 156246672 156249116 0.000000e+00 3528.0
14 TraesCS5A01G546400 chr6D 94.918 1594 58 9 597 2187 29978463 29976890 0.000000e+00 2473.0
15 TraesCS5A01G546400 chr6D 97.015 134 2 2 2978 3111 306315368 306315237 1.120000e-54 224.0
16 TraesCS5A01G546400 chr3D 94.312 2391 97 20 585 2960 359622800 359625166 0.000000e+00 3626.0
17 TraesCS5A01G546400 chr3D 93.952 2381 103 17 597 2960 85226448 85228804 0.000000e+00 3561.0
18 TraesCS5A01G546400 chr7D 94.430 2370 99 17 597 2960 245402111 245399769 0.000000e+00 3615.0
19 TraesCS5A01G546400 chr7D 91.250 2320 121 37 498 2773 36177282 36175001 0.000000e+00 3085.0
20 TraesCS5A01G546400 chr7D 94.743 1598 65 12 1371 2960 608523830 608522244 0.000000e+00 2468.0
21 TraesCS5A01G546400 chr1D 94.283 2379 98 16 597 2960 475527982 475525627 0.000000e+00 3605.0
22 TraesCS5A01G546400 chr1D 94.264 2371 99 20 597 2960 12354789 12357129 0.000000e+00 3591.0
23 TraesCS5A01G546400 chr1D 94.051 2370 106 17 597 2960 6491581 6489241 0.000000e+00 3563.0
24 TraesCS5A01G546400 chr1D 91.660 2386 136 23 597 2960 110903939 110901595 0.000000e+00 3245.0
25 TraesCS5A01G546400 chr1D 97.015 134 2 2 2978 3111 475525311 475525180 1.120000e-54 224.0
26 TraesCS5A01G546400 chr2D 93.789 2399 99 18 597 2960 634824261 634821878 0.000000e+00 3559.0
27 TraesCS5A01G546400 chr2D 92.857 126 3 5 500 619 74953303 74953428 8.870000e-41 178.0
28 TraesCS5A01G546400 chr4D 92.735 2519 95 40 500 2960 428530040 428532528 0.000000e+00 3557.0
29 TraesCS5A01G546400 chr4D 97.015 134 2 2 2978 3111 502870288 502870419 1.120000e-54 224.0
30 TraesCS5A01G546400 chr5D 93.927 2371 103 15 597 2960 244414011 244411675 0.000000e+00 3542.0
31 TraesCS5A01G546400 chr6A 95.893 1607 57 7 1360 2960 608466207 608464604 0.000000e+00 2593.0
32 TraesCS5A01G546400 chr6A 95.769 1607 59 7 1360 2960 608439921 608438318 0.000000e+00 2582.0
33 TraesCS5A01G546400 chr6A 95.227 1236 50 6 1730 2960 584382527 584381296 0.000000e+00 1947.0
34 TraesCS5A01G546400 chr6A 90.694 1268 69 16 498 1738 584389710 584388465 0.000000e+00 1642.0
35 TraesCS5A01G546400 chr6A 99.205 503 4 0 1 503 522488741 522488239 0.000000e+00 907.0
36 TraesCS5A01G546400 chr6A 99.254 134 0 1 2978 3111 608437904 608437772 1.110000e-59 241.0
37 TraesCS5A01G546400 chr6A 99.254 134 0 1 2978 3111 608464190 608464058 1.110000e-59 241.0
38 TraesCS5A01G546400 chr6A 100.000 31 0 0 2629 2659 584381569 584381539 1.210000e-04 58.4
39 TraesCS5A01G546400 chr3B 97.331 1461 37 2 1467 2927 766033480 766034938 0.000000e+00 2481.0
40 TraesCS5A01G546400 chr3B 98.333 120 2 0 500 619 766032727 766032846 8.740000e-51 211.0
41 TraesCS5A01G546400 chrUn 99.399 499 3 0 1 499 17762758 17763256 0.000000e+00 905.0
42 TraesCS5A01G546400 chr7B 99.399 499 3 0 1 499 717370797 717371295 0.000000e+00 905.0
43 TraesCS5A01G546400 chr7B 99.202 501 4 0 1 501 32204176 32204676 0.000000e+00 904.0
44 TraesCS5A01G546400 chr7A 99.202 501 4 0 1 501 647234039 647234539 0.000000e+00 904.0
45 TraesCS5A01G546400 chr3A 99.004 502 5 0 1 502 700181355 700180854 0.000000e+00 900.0
46 TraesCS5A01G546400 chr3A 99.254 134 1 0 2978 3111 244331650 244331783 3.100000e-60 243.0
47 TraesCS5A01G546400 chr3A 95.122 123 4 1 497 619 244307765 244307885 3.170000e-45 193.0
48 TraesCS5A01G546400 chr5B 99.002 501 5 0 1 501 357818316 357818816 0.000000e+00 898.0


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 TraesCS5A01G546400 chr5A 700611577 700614687 3110 False 5746.000000 5746 100.000000 1 3111 1 chr5A.!!$F1 3110
1 TraesCS5A01G546400 chr4A 640934517 640937376 2859 True 1528.000000 4130 98.310333 500 3111 3 chr4A.!!$R1 2611
2 TraesCS5A01G546400 chr2A 688774757 688777672 2915 False 1469.333333 3988 96.604000 500 3111 3 chr2A.!!$F3 2611
3 TraesCS5A01G546400 chr2A 84021638 84024680 3042 False 1312.000000 3504 96.064333 500 3111 3 chr2A.!!$F2 2611
4 TraesCS5A01G546400 chr2A 44233744 44234248 504 False 898.000000 898 98.812000 1 503 1 chr2A.!!$F1 502
5 TraesCS5A01G546400 chr2A 200946850 200947367 517 True 893.000000 893 97.701000 1 521 1 chr2A.!!$R1 520
6 TraesCS5A01G546400 chr6D 472511279 472513621 2342 False 3637.000000 3637 94.599000 597 2960 1 chr6D.!!$F2 2363
7 TraesCS5A01G546400 chr6D 156246672 156249116 2444 False 3528.000000 3528 92.710000 500 2960 1 chr6D.!!$F1 2460
8 TraesCS5A01G546400 chr6D 29976890 29978463 1573 True 2473.000000 2473 94.918000 597 2187 1 chr6D.!!$R1 1590
9 TraesCS5A01G546400 chr3D 359622800 359625166 2366 False 3626.000000 3626 94.312000 585 2960 1 chr3D.!!$F2 2375
10 TraesCS5A01G546400 chr3D 85226448 85228804 2356 False 3561.000000 3561 93.952000 597 2960 1 chr3D.!!$F1 2363
11 TraesCS5A01G546400 chr7D 245399769 245402111 2342 True 3615.000000 3615 94.430000 597 2960 1 chr7D.!!$R2 2363
12 TraesCS5A01G546400 chr7D 36175001 36177282 2281 True 3085.000000 3085 91.250000 498 2773 1 chr7D.!!$R1 2275
13 TraesCS5A01G546400 chr7D 608522244 608523830 1586 True 2468.000000 2468 94.743000 1371 2960 1 chr7D.!!$R3 1589
14 TraesCS5A01G546400 chr1D 12354789 12357129 2340 False 3591.000000 3591 94.264000 597 2960 1 chr1D.!!$F1 2363
15 TraesCS5A01G546400 chr1D 6489241 6491581 2340 True 3563.000000 3563 94.051000 597 2960 1 chr1D.!!$R1 2363
16 TraesCS5A01G546400 chr1D 110901595 110903939 2344 True 3245.000000 3245 91.660000 597 2960 1 chr1D.!!$R2 2363
17 TraesCS5A01G546400 chr1D 475525180 475527982 2802 True 1914.500000 3605 95.649000 597 3111 2 chr1D.!!$R3 2514
18 TraesCS5A01G546400 chr2D 634821878 634824261 2383 True 3559.000000 3559 93.789000 597 2960 1 chr2D.!!$R1 2363
19 TraesCS5A01G546400 chr4D 428530040 428532528 2488 False 3557.000000 3557 92.735000 500 2960 1 chr4D.!!$F1 2460
20 TraesCS5A01G546400 chr5D 244411675 244414011 2336 True 3542.000000 3542 93.927000 597 2960 1 chr5D.!!$R1 2363
21 TraesCS5A01G546400 chr6A 584388465 584389710 1245 True 1642.000000 1642 90.694000 498 1738 1 chr6A.!!$R2 1240
22 TraesCS5A01G546400 chr6A 608464058 608466207 2149 True 1417.000000 2593 97.573500 1360 3111 2 chr6A.!!$R5 1751
23 TraesCS5A01G546400 chr6A 608437772 608439921 2149 True 1411.500000 2582 97.511500 1360 3111 2 chr6A.!!$R4 1751
24 TraesCS5A01G546400 chr6A 584381296 584382527 1231 True 1002.700000 1947 97.613500 1730 2960 2 chr6A.!!$R3 1230
25 TraesCS5A01G546400 chr6A 522488239 522488741 502 True 907.000000 907 99.205000 1 503 1 chr6A.!!$R1 502
26 TraesCS5A01G546400 chr3B 766032727 766034938 2211 False 1346.000000 2481 97.832000 500 2927 2 chr3B.!!$F1 2427
27 TraesCS5A01G546400 chr7B 32204176 32204676 500 False 904.000000 904 99.202000 1 501 1 chr7B.!!$F1 500
28 TraesCS5A01G546400 chr7A 647234039 647234539 500 False 904.000000 904 99.202000 1 501 1 chr7A.!!$F1 500
29 TraesCS5A01G546400 chr3A 700180854 700181355 501 True 900.000000 900 99.004000 1 502 1 chr3A.!!$R1 501
30 TraesCS5A01G546400 chr5B 357818316 357818816 500 False 898.000000 898 99.002000 1 501 1 chr5B.!!$F1 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
615 660 0.099259 CTCGCTCTGCTCTCACTCTG 59.901 60.0 0.0 0.0 0.0 3.35 F
1620 1761 1.027357 CCCTGGCATCCAATTCTTCG 58.973 55.0 0.0 0.0 30.8 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 2161 1.202794 TCACCACATGCTCAAGCTTGA 60.203 47.619 26.87 26.87 45.61 3.02 R
2498 2660 2.874245 TGGAGGGAGGAGGGTGGA 60.874 66.667 0.00 0.00 0.00 4.02 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
249 251 4.961585 ACTCACCTTAAACCCTCTCCTAT 58.038 43.478 0.00 0.0 0.00 2.57
376 379 2.439883 GGCTCCGAGACGTAGGGT 60.440 66.667 0.00 0.0 0.00 4.34
599 603 0.107312 TAAGTCGTCTCCCTCCCTCG 60.107 60.000 0.00 0.0 0.00 4.63
615 660 0.099259 CTCGCTCTGCTCTCACTCTG 59.901 60.000 0.00 0.0 0.00 3.35
1097 1151 1.406539 GCACCACATGAGGCCAATTAG 59.593 52.381 9.34 0.0 0.00 1.73
1229 1302 6.811253 TTTACAAGGATGACCACACAATAC 57.189 37.500 0.00 0.0 38.94 1.89
1543 1684 9.448438 TTGAGTGCACTTAGTGATGTATATTTT 57.552 29.630 22.65 0.0 35.23 1.82
1569 1710 1.068055 CCAAATGCAGACTGAAGGTGC 60.068 52.381 6.65 0.0 37.73 5.01
1620 1761 1.027357 CCCTGGCATCCAATTCTTCG 58.973 55.000 0.00 0.0 30.80 3.79
1635 1776 3.071874 TCTTCGGAATTGCTTGTCCAT 57.928 42.857 0.00 0.0 33.10 3.41
1762 1903 3.466836 TGAGTACACAAAGCTTGTCCAG 58.533 45.455 0.00 0.0 43.23 3.86
2019 2161 8.317776 AGAGATTTGCTTAAGATAGAGAAGGT 57.682 34.615 6.67 0.0 0.00 3.50
2498 2660 5.545723 ACTGCTCATAAATAGCCTACTCCAT 59.454 40.000 0.00 0.0 39.30 3.41
2858 3031 5.174398 GCCGTTTCTTCGATCGTTATGATTA 59.826 40.000 15.94 0.0 37.47 1.75
2938 3122 5.689383 TCCATTTCTGTACAACTCTTTGC 57.311 39.130 0.00 0.0 36.00 3.68
2960 3144 7.185318 TGCATGAAAGAATATTTGGATGGTT 57.815 32.000 0.00 0.0 0.00 3.67
2961 3145 7.622713 TGCATGAAAGAATATTTGGATGGTTT 58.377 30.769 0.00 0.0 0.00 3.27
2962 3146 7.549842 TGCATGAAAGAATATTTGGATGGTTTG 59.450 33.333 0.00 0.0 0.00 2.93
2963 3147 7.011669 GCATGAAAGAATATTTGGATGGTTTGG 59.988 37.037 0.00 0.0 0.00 3.28
2964 3148 7.789202 TGAAAGAATATTTGGATGGTTTGGA 57.211 32.000 0.00 0.0 0.00 3.53
2965 3149 7.839907 TGAAAGAATATTTGGATGGTTTGGAG 58.160 34.615 0.00 0.0 0.00 3.86
2966 3150 5.859205 AGAATATTTGGATGGTTTGGAGC 57.141 39.130 0.00 0.0 0.00 4.70
2967 3151 5.522641 AGAATATTTGGATGGTTTGGAGCT 58.477 37.500 0.00 0.0 0.00 4.09
2968 3152 6.672593 AGAATATTTGGATGGTTTGGAGCTA 58.327 36.000 0.00 0.0 0.00 3.32
2969 3153 7.300658 AGAATATTTGGATGGTTTGGAGCTAT 58.699 34.615 0.00 0.0 0.00 2.97
2970 3154 6.906157 ATATTTGGATGGTTTGGAGCTATG 57.094 37.500 0.00 0.0 0.00 2.23
2971 3155 3.737559 TTGGATGGTTTGGAGCTATGT 57.262 42.857 0.00 0.0 0.00 2.29
2972 3156 3.281727 TGGATGGTTTGGAGCTATGTC 57.718 47.619 0.00 0.0 0.00 3.06
2973 3157 2.092429 TGGATGGTTTGGAGCTATGTCC 60.092 50.000 0.00 0.0 37.10 4.02
2974 3158 2.576615 GATGGTTTGGAGCTATGTCCC 58.423 52.381 0.00 0.0 35.49 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
574 578 1.757699 GAGGGAGACGACTTAAGGCAT 59.242 52.381 9.49 0.00 0.00 4.40
599 603 0.179129 GAGCAGAGTGAGAGCAGAGC 60.179 60.000 0.00 0.00 0.00 4.09
615 660 1.824230 TCAAAGAGCAGAGAGGAGAGC 59.176 52.381 0.00 0.00 0.00 4.09
673 719 3.602104 CATTCCAGGAAGGCATGGT 57.398 52.632 8.20 0.00 45.89 3.55
692 738 2.136196 CTCTGAGCTCGTATCCCCGC 62.136 65.000 9.64 0.00 0.00 6.13
1097 1151 1.327303 TCCTTCAAATGCCACACACC 58.673 50.000 0.00 0.00 0.00 4.16
1229 1302 7.015226 TCAGAACAACAACTTGTCAACATAG 57.985 36.000 0.00 0.00 39.88 2.23
1413 1552 7.747690 TCAAACTATAACTGAAACCCAACCTA 58.252 34.615 0.00 0.00 0.00 3.08
1543 1684 5.774690 ACCTTCAGTCTGCATTTGGAAAATA 59.225 36.000 0.00 0.00 0.00 1.40
1545 1686 3.960102 ACCTTCAGTCTGCATTTGGAAAA 59.040 39.130 0.00 0.00 0.00 2.29
1569 1710 4.307432 CCACTCAGTAACACCACAGTTAG 58.693 47.826 0.00 0.00 34.85 2.34
1620 1761 3.973657 CATAGCATGGACAAGCAATTCC 58.026 45.455 2.24 0.00 0.00 3.01
2019 2161 1.202794 TCACCACATGCTCAAGCTTGA 60.203 47.619 26.87 26.87 45.61 3.02
2255 2401 4.337555 AGCATTAAAGGTTCTAGCAGCATG 59.662 41.667 0.00 0.00 40.87 4.06
2498 2660 2.874245 TGGAGGGAGGAGGGTGGA 60.874 66.667 0.00 0.00 0.00 4.02
2938 3122 8.259411 TCCAAACCATCCAAATATTCTTTCATG 58.741 33.333 0.00 0.00 0.00 3.07
2960 3144 4.591321 ATTTGAAGGGACATAGCTCCAA 57.409 40.909 0.00 0.00 30.97 3.53
2961 3145 4.473196 TGTATTTGAAGGGACATAGCTCCA 59.527 41.667 0.00 0.00 30.97 3.86
2962 3146 5.036117 TGTATTTGAAGGGACATAGCTCC 57.964 43.478 0.00 0.00 0.00 4.70
2963 3147 6.876257 CCTATGTATTTGAAGGGACATAGCTC 59.124 42.308 13.10 0.00 45.42 4.09
2964 3148 6.330250 ACCTATGTATTTGAAGGGACATAGCT 59.670 38.462 13.10 0.00 45.42 3.32
2965 3149 6.534634 ACCTATGTATTTGAAGGGACATAGC 58.465 40.000 13.10 0.00 45.42 2.97
2966 3150 8.980481 AAACCTATGTATTTGAAGGGACATAG 57.020 34.615 12.02 12.02 45.94 2.23
2967 3151 8.553153 TGAAACCTATGTATTTGAAGGGACATA 58.447 33.333 0.00 0.00 34.46 2.29
2968 3152 7.410174 TGAAACCTATGTATTTGAAGGGACAT 58.590 34.615 0.00 0.00 36.52 3.06
2969 3153 6.785076 TGAAACCTATGTATTTGAAGGGACA 58.215 36.000 0.00 0.00 33.16 4.02
2970 3154 6.183360 GCTGAAACCTATGTATTTGAAGGGAC 60.183 42.308 0.00 0.00 33.16 4.46
2971 3155 5.885912 GCTGAAACCTATGTATTTGAAGGGA 59.114 40.000 0.00 0.00 33.16 4.20
2972 3156 5.652014 TGCTGAAACCTATGTATTTGAAGGG 59.348 40.000 0.00 0.00 33.16 3.95
2973 3157 6.757897 TGCTGAAACCTATGTATTTGAAGG 57.242 37.500 0.00 0.00 35.14 3.46
2974 3158 6.749118 GCTTGCTGAAACCTATGTATTTGAAG 59.251 38.462 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.