Multiple sequence alignment - TraesCS7B01G013000

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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 TraesCS7B01G013000 chr7B 100.000 2504 0 0 1 2504 8995132 8992629 0.000000e+00 4625.0
1 TraesCS7B01G013000 chr7B 92.678 997 28 14 1 955 16522157 16521164 0.000000e+00 1395.0
2 TraesCS7B01G013000 chr7B 90.080 998 37 16 1 957 658147061 658148037 0.000000e+00 1238.0
3 TraesCS7B01G013000 chr7B 86.994 692 43 21 313 959 688129791 688129102 0.000000e+00 736.0
4 TraesCS7B01G013000 chr7A 93.806 1550 74 10 961 2497 73730448 73731988 0.000000e+00 2311.0
5 TraesCS7B01G013000 chr7A 90.741 54 4 1 2412 2464 73732611 73732664 1.240000e-08 71.3
6 TraesCS7B01G013000 chr7D 91.208 1399 74 20 959 2342 66980062 66978698 0.000000e+00 1857.0
7 TraesCS7B01G013000 chr7D 93.651 63 4 0 2321 2383 66978692 66978630 7.370000e-16 95.3
8 TraesCS7B01G013000 chr1B 92.462 995 30 11 1 955 630515351 630514362 0.000000e+00 1380.0
9 TraesCS7B01G013000 chr1B 91.683 998 34 16 1 956 539878516 539877526 0.000000e+00 1338.0
10 TraesCS7B01G013000 chr1B 87.662 1005 49 23 1 956 183921551 183920573 0.000000e+00 1099.0
11 TraesCS7B01G013000 chr1B 83.968 630 59 32 360 956 509109390 509110010 1.300000e-157 566.0
12 TraesCS7B01G013000 chr2B 92.129 991 33 12 1 949 58871569 58872556 0.000000e+00 1356.0
13 TraesCS7B01G013000 chr2B 91.556 983 45 17 3 955 601434557 601433583 0.000000e+00 1321.0
14 TraesCS7B01G013000 chr2B 90.728 1003 40 14 1 955 718013 719010 0.000000e+00 1288.0
15 TraesCS7B01G013000 chr2B 95.289 658 16 6 1 645 49408046 49408701 0.000000e+00 1029.0
16 TraesCS7B01G013000 chr2B 89.557 316 26 6 1095 1408 65418031 65418341 6.490000e-106 394.0
17 TraesCS7B01G013000 chr2B 88.889 333 18 10 640 956 49408867 49409196 2.330000e-105 392.0
18 TraesCS7B01G013000 chr3B 92.127 978 41 12 3 955 29348548 29349514 0.000000e+00 1347.0
19 TraesCS7B01G013000 chr3B 91.491 999 34 18 1 955 427341307 427342298 0.000000e+00 1327.0
20 TraesCS7B01G013000 chr3B 87.140 972 77 32 30 969 96436303 96437258 0.000000e+00 1059.0
21 TraesCS7B01G013000 chr3B 90.265 565 22 9 427 962 159461100 159460540 0.000000e+00 708.0
22 TraesCS7B01G013000 chr2A 91.802 988 37 19 1 949 524140492 524141474 0.000000e+00 1336.0
23 TraesCS7B01G013000 chr6B 91.558 995 41 10 1 955 370148442 370147451 0.000000e+00 1332.0
24 TraesCS7B01G013000 chr4B 91.474 997 42 13 1 955 608387926 608386931 0.000000e+00 1330.0
25 TraesCS7B01G013000 chr4B 86.192 927 64 31 87 956 2340208 2339289 0.000000e+00 944.0
26 TraesCS7B01G013000 chr4A 91.539 981 44 21 1 955 744270259 744271226 0.000000e+00 1315.0
27 TraesCS7B01G013000 chr5B 90.824 959 43 14 38 956 545588286 545587333 0.000000e+00 1242.0
28 TraesCS7B01G013000 chr5A 89.562 776 43 13 214 956 707654878 707655648 0.000000e+00 950.0


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 TraesCS7B01G013000 chr7B 8992629 8995132 2503 True 4625.00 4625 100.0000 1 2504 1 chr7B.!!$R1 2503
1 TraesCS7B01G013000 chr7B 16521164 16522157 993 True 1395.00 1395 92.6780 1 955 1 chr7B.!!$R2 954
2 TraesCS7B01G013000 chr7B 658147061 658148037 976 False 1238.00 1238 90.0800 1 957 1 chr7B.!!$F1 956
3 TraesCS7B01G013000 chr7B 688129102 688129791 689 True 736.00 736 86.9940 313 959 1 chr7B.!!$R3 646
4 TraesCS7B01G013000 chr7A 73730448 73732664 2216 False 1191.15 2311 92.2735 961 2497 2 chr7A.!!$F1 1536
5 TraesCS7B01G013000 chr7D 66978630 66980062 1432 True 976.15 1857 92.4295 959 2383 2 chr7D.!!$R1 1424
6 TraesCS7B01G013000 chr1B 630514362 630515351 989 True 1380.00 1380 92.4620 1 955 1 chr1B.!!$R3 954
7 TraesCS7B01G013000 chr1B 539877526 539878516 990 True 1338.00 1338 91.6830 1 956 1 chr1B.!!$R2 955
8 TraesCS7B01G013000 chr1B 183920573 183921551 978 True 1099.00 1099 87.6620 1 956 1 chr1B.!!$R1 955
9 TraesCS7B01G013000 chr1B 509109390 509110010 620 False 566.00 566 83.9680 360 956 1 chr1B.!!$F1 596
10 TraesCS7B01G013000 chr2B 58871569 58872556 987 False 1356.00 1356 92.1290 1 949 1 chr2B.!!$F2 948
11 TraesCS7B01G013000 chr2B 601433583 601434557 974 True 1321.00 1321 91.5560 3 955 1 chr2B.!!$R1 952
12 TraesCS7B01G013000 chr2B 718013 719010 997 False 1288.00 1288 90.7280 1 955 1 chr2B.!!$F1 954
13 TraesCS7B01G013000 chr2B 49408046 49409196 1150 False 710.50 1029 92.0890 1 956 2 chr2B.!!$F4 955
14 TraesCS7B01G013000 chr3B 29348548 29349514 966 False 1347.00 1347 92.1270 3 955 1 chr3B.!!$F1 952
15 TraesCS7B01G013000 chr3B 427341307 427342298 991 False 1327.00 1327 91.4910 1 955 1 chr3B.!!$F3 954
16 TraesCS7B01G013000 chr3B 96436303 96437258 955 False 1059.00 1059 87.1400 30 969 1 chr3B.!!$F2 939
17 TraesCS7B01G013000 chr3B 159460540 159461100 560 True 708.00 708 90.2650 427 962 1 chr3B.!!$R1 535
18 TraesCS7B01G013000 chr2A 524140492 524141474 982 False 1336.00 1336 91.8020 1 949 1 chr2A.!!$F1 948
19 TraesCS7B01G013000 chr6B 370147451 370148442 991 True 1332.00 1332 91.5580 1 955 1 chr6B.!!$R1 954
20 TraesCS7B01G013000 chr4B 608386931 608387926 995 True 1330.00 1330 91.4740 1 955 1 chr4B.!!$R2 954
21 TraesCS7B01G013000 chr4B 2339289 2340208 919 True 944.00 944 86.1920 87 956 1 chr4B.!!$R1 869
22 TraesCS7B01G013000 chr4A 744270259 744271226 967 False 1315.00 1315 91.5390 1 955 1 chr4A.!!$F1 954
23 TraesCS7B01G013000 chr5B 545587333 545588286 953 True 1242.00 1242 90.8240 38 956 1 chr5B.!!$R1 918
24 TraesCS7B01G013000 chr5A 707654878 707655648 770 False 950.00 950 89.5620 214 956 1 chr5A.!!$F1 742

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
957 1287 0.468648 GTCCAATAGGAGTTCCCCGG 59.531 60.0 0.0 0.0 46.92 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 2375 0.03759 AATTCCAGCTACAACCGCCA 59.962 50.0 0.0 0.0 0.0 5.69 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
321 353 5.413499 GGTGAACATTTTTCAGCTGCATAT 58.587 37.500 9.47 0.00 41.98 1.78
780 1096 9.891828 AAAACGAAAAATGAAAAAGAAAAAGCT 57.108 22.222 0.00 0.00 0.00 3.74
957 1287 0.468648 GTCCAATAGGAGTTCCCCGG 59.531 60.000 0.00 0.00 46.92 5.73
980 1310 2.906389 TCCTGGGCGAGCATATCTTTAT 59.094 45.455 0.00 0.00 0.00 1.40
981 1311 3.327757 TCCTGGGCGAGCATATCTTTATT 59.672 43.478 0.00 0.00 0.00 1.40
1013 1343 1.518572 GGTGTATGCACGAGACCGG 60.519 63.158 7.89 0.00 46.13 5.28
1017 1347 2.651105 TATGCACGAGACCGGCCAA 61.651 57.895 0.00 0.00 40.78 4.52
1020 1350 2.171725 GCACGAGACCGGCCAATAC 61.172 63.158 0.00 0.00 40.78 1.89
1257 1593 1.878656 CGTTCTCCAGTTCCGCCTCT 61.879 60.000 0.00 0.00 0.00 3.69
1372 1708 3.723235 GATGCTGGCGCGAGGAAGA 62.723 63.158 18.68 0.00 39.65 2.87
1532 1868 0.681243 GCCAGCTGGGAGGGTAAAAG 60.681 60.000 33.46 4.31 40.01 2.27
1559 1895 4.734917 CTCTCGGATTCGTTCTAAGTTGT 58.265 43.478 0.00 0.00 37.69 3.32
1560 1896 5.675575 GCTCTCGGATTCGTTCTAAGTTGTA 60.676 44.000 0.00 0.00 37.69 2.41
1624 1966 2.363359 CTGCTGGGGGAATAAATCTTGC 59.637 50.000 0.00 0.00 0.00 4.01
1647 1989 8.437360 TGCTGTTATACTGAACATAATTCTGG 57.563 34.615 0.00 0.00 38.60 3.86
1664 2006 5.871396 TTCTGGAGTTTCAGAGTACTGTT 57.129 39.130 0.00 0.00 43.64 3.16
1711 2057 9.980780 GCTTTCTAAGTTCTCTGTATGAATTTC 57.019 33.333 0.00 0.00 0.00 2.17
1767 2116 3.808984 CCCCCTTAAGCTCCATGAC 57.191 57.895 0.00 0.00 0.00 3.06
1856 2205 3.700038 CGAGTGATTCCTTGGTACCTACT 59.300 47.826 14.36 4.68 0.00 2.57
1923 2272 3.305403 GCTTCCTTCCTAAAACTTGGTGC 60.305 47.826 0.00 0.00 0.00 5.01
1936 2285 1.834263 CTTGGTGCCTCCTTAGCTAGT 59.166 52.381 0.00 0.00 37.07 2.57
1943 2292 5.163290 GGTGCCTCCTTAGCTAGTATTTCTT 60.163 44.000 0.00 0.00 0.00 2.52
2005 2356 0.607489 CAGGCTGGACAGGAAGTTGG 60.607 60.000 6.61 0.00 0.00 3.77
2024 2375 0.185175 GAACTTGGGTTGGGGTGACT 59.815 55.000 0.00 0.00 35.58 3.41
2284 2661 6.998673 AGATAACAGCAGTAACCTGAAACTTT 59.001 34.615 0.00 0.00 41.50 2.66
2289 2666 6.428159 ACAGCAGTAACCTGAAACTTTAGATG 59.572 38.462 0.00 0.00 41.50 2.90
2318 2695 6.458888 GCAGTAACCTTGAGCCATCTTATTTC 60.459 42.308 0.00 0.00 0.00 2.17
2390 2767 8.486210 AGAATGGTATTGAAGTTACATCTAGCA 58.514 33.333 0.00 0.00 0.00 3.49
2433 2810 1.372128 GTTTGCCTTGAGCTTGCCG 60.372 57.895 0.00 0.00 44.23 5.69
2465 2842 9.109393 TCAGATAGGACACATTTATTTAAGTGC 57.891 33.333 0.00 0.00 35.47 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
765 1069 6.696411 TCTTGAACCAGCTTTTTCTTTTTCA 58.304 32.000 5.80 0.00 0.00 2.69
780 1096 3.583086 CCTCCTAGAAGGTTCTTGAACCA 59.417 47.826 27.80 11.36 45.23 3.67
957 1287 0.394565 AGATATGCTCGCCCAGGAAC 59.605 55.000 0.00 0.00 0.00 3.62
967 1297 3.192212 GGCCCAGCAATAAAGATATGCTC 59.808 47.826 0.00 0.00 33.09 4.26
980 1310 3.884774 ACCAGTTCGGCCCAGCAA 61.885 61.111 0.00 0.00 39.03 3.91
981 1311 4.641645 CACCAGTTCGGCCCAGCA 62.642 66.667 0.00 0.00 39.03 4.41
1188 1524 2.441164 GAGAGGCGGGAGAGAGCA 60.441 66.667 0.00 0.00 34.54 4.26
1316 1652 4.821589 CCTCCTTCACGGCGCTCC 62.822 72.222 6.90 0.00 0.00 4.70
1372 1708 3.756783 CTCCTCCTCCTCCCCCGT 61.757 72.222 0.00 0.00 0.00 5.28
1517 1853 1.177401 CAAGCTTTTACCCTCCCAGC 58.823 55.000 0.00 0.00 0.00 4.85
1532 1868 0.647925 GAACGAATCCGAGAGCAAGC 59.352 55.000 0.00 0.00 39.50 4.01
1559 1895 7.814356 TGCCATGCCATATCCTTATGATTATA 58.186 34.615 0.00 0.00 37.94 0.98
1560 1896 6.675565 TGCCATGCCATATCCTTATGATTAT 58.324 36.000 0.00 0.00 37.94 1.28
1624 1966 9.823647 ACTCCAGAATTATGTTCAGTATAACAG 57.176 33.333 0.00 0.00 42.33 3.16
1640 1982 6.426646 ACAGTACTCTGAAACTCCAGAATT 57.573 37.500 0.00 0.00 42.05 2.17
1664 2006 6.924913 AGCTTAGATACATGCTAAGATGGA 57.075 37.500 17.73 0.00 44.75 3.41
1711 2057 5.204833 CAAACAATCAGTTACCACTCAACG 58.795 41.667 0.00 0.00 40.26 4.10
1856 2205 1.677576 CACCCGCTACGTATAACCTCA 59.322 52.381 0.00 0.00 0.00 3.86
1865 2214 0.748005 ACCGTATACACCCGCTACGT 60.748 55.000 3.32 0.00 37.20 3.57
1923 2272 9.482627 CATAACAAGAAATACTAGCTAAGGAGG 57.517 37.037 0.00 0.00 0.00 4.30
2005 2356 0.185175 AGTCACCCCAACCCAAGTTC 59.815 55.000 0.00 0.00 32.45 3.01
2024 2375 0.037590 AATTCCAGCTACAACCGCCA 59.962 50.000 0.00 0.00 0.00 5.69
2210 2561 4.807304 TGAAGTTTCAGGTTACTGTCGTTC 59.193 41.667 0.00 0.00 45.14 3.95
2284 2661 4.382040 GCTCAAGGTTACTGCTGTCATCTA 60.382 45.833 0.00 0.00 0.00 1.98
2289 2666 1.270839 TGGCTCAAGGTTACTGCTGTC 60.271 52.381 0.00 0.00 0.00 3.51
2318 2695 0.625849 ATGGCCCAAGGTAGTTCTGG 59.374 55.000 0.00 0.00 0.00 3.86
2356 2733 6.240549 ACTTCAATACCATTCTACTGGAGG 57.759 41.667 0.00 0.00 39.73 4.30
2360 2737 9.823647 AGATGTAACTTCAATACCATTCTACTG 57.176 33.333 0.00 0.00 0.00 2.74
2396 2773 8.207545 AGGCAAACAGAACAAAATATTTTACCA 58.792 29.630 12.98 0.00 0.00 3.25
2411 2788 1.067516 GCAAGCTCAAGGCAAACAGAA 59.932 47.619 0.00 0.00 44.79 3.02


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

AutoCloner maintained by Alex Coulton.