Multiple sequence alignment - TraesCS6A01G199500

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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 TraesCS6A01G199500 chr6A 100.000 2435 0 0 1 2435 315562298 315564732 0 4497
1 TraesCS6A01G199500 chr1A 94.625 2437 126 5 1 2435 404256804 404254371 0 3770
2 TraesCS6A01G199500 chr1A 94.641 2426 127 3 10 2435 518494094 518491672 0 3757
3 TraesCS6A01G199500 chr4A 94.609 2430 121 6 10 2435 270135582 270133159 0 3753
4 TraesCS6A01G199500 chr7A 94.596 2424 125 4 10 2433 503387811 503385394 0 3746
5 TraesCS6A01G199500 chr7A 94.477 2426 131 2 10 2435 643156142 643158564 0 3735
6 TraesCS6A01G199500 chr3A 94.518 2426 127 5 10 2435 69767238 69764819 0 3738
7 TraesCS6A01G199500 chr3A 94.477 2426 132 2 10 2435 278604096 278606519 0 3736
8 TraesCS6A01G199500 chr5A 94.511 2423 130 3 10 2432 26319687 26322106 0 3735
9 TraesCS6A01G199500 chr5A 94.479 2427 129 5 10 2435 457709606 457712028 0 3735


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 TraesCS6A01G199500 chr6A 315562298 315564732 2434 False 4497 4497 100.000 1 2435 1 chr6A.!!$F1 2434
1 TraesCS6A01G199500 chr1A 404254371 404256804 2433 True 3770 3770 94.625 1 2435 1 chr1A.!!$R1 2434
2 TraesCS6A01G199500 chr1A 518491672 518494094 2422 True 3757 3757 94.641 10 2435 1 chr1A.!!$R2 2425
3 TraesCS6A01G199500 chr4A 270133159 270135582 2423 True 3753 3753 94.609 10 2435 1 chr4A.!!$R1 2425
4 TraesCS6A01G199500 chr7A 503385394 503387811 2417 True 3746 3746 94.596 10 2433 1 chr7A.!!$R1 2423
5 TraesCS6A01G199500 chr7A 643156142 643158564 2422 False 3735 3735 94.477 10 2435 1 chr7A.!!$F1 2425
6 TraesCS6A01G199500 chr3A 69764819 69767238 2419 True 3738 3738 94.518 10 2435 1 chr3A.!!$R1 2425
7 TraesCS6A01G199500 chr3A 278604096 278606519 2423 False 3736 3736 94.477 10 2435 1 chr3A.!!$F1 2425
8 TraesCS6A01G199500 chr5A 26319687 26322106 2419 False 3735 3735 94.511 10 2432 1 chr5A.!!$F1 2422
9 TraesCS6A01G199500 chr5A 457709606 457712028 2422 False 3735 3735 94.479 10 2435 1 chr5A.!!$F2 2425

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
264 267 0.417841 ATGCCGGATACTCCCCCTAT 59.582 55.0 5.05 0.0 31.13 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 2092 0.396811 GCGCTCATTATACCTGGGGT 59.603 55.0 0.0 0.0 40.16 4.95 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
61 63 3.371063 GCGGTCAGGACGGAGACA 61.371 66.667 10.70 0.00 36.50 3.41
264 267 0.417841 ATGCCGGATACTCCCCCTAT 59.582 55.000 5.05 0.00 31.13 2.57
352 355 2.954868 GCCGTACTCCGTGATGCG 60.955 66.667 0.00 0.00 40.95 4.73
459 462 4.652421 GGACCAGTATGTAAGGGATGTACA 59.348 45.833 0.00 0.00 35.98 2.90
548 551 7.062322 TGGTTTAAGGATCATCTATTGTGCAT 58.938 34.615 0.00 0.00 0.00 3.96
569 572 6.818644 TGCATGTTCTTACAGAGAAGAATACC 59.181 38.462 2.21 0.00 44.92 2.73
793 796 2.031314 TAAAGGCTGGCGAACGCA 59.969 55.556 20.16 6.38 44.11 5.24
926 929 1.801512 GGCTTTGACGCGGCATTTC 60.802 57.895 19.26 7.48 0.00 2.17
990 996 3.958798 AGAAGCCGGCTAACAGAGTTATA 59.041 43.478 33.07 0.00 0.00 0.98
1140 1146 2.060980 ATCCGTCTCCCTGCCAGAC 61.061 63.158 0.00 0.00 37.51 3.51
1228 1234 4.329545 GCCGTCAAGGTGCCAGGA 62.330 66.667 0.00 0.00 43.70 3.86
1279 1285 0.944386 CAAGACTGACCCAAACCACG 59.056 55.000 0.00 0.00 0.00 4.94
1285 1291 4.130554 ACCCAAACCACGTGGCCA 62.131 61.111 34.26 0.00 39.32 5.36
1295 1301 4.003788 CGTGGCCAAGGTCGGACT 62.004 66.667 7.24 0.00 33.86 3.85
1357 1363 3.951563 ATGGGCAAGTAGAATTAGCCA 57.048 42.857 0.00 0.00 46.96 4.75
1400 1406 4.625800 GCTAGACAGCCTGTTGGG 57.374 61.111 0.00 0.00 42.37 4.12
1756 1762 0.248743 TACGATAGGAAACGCAGGCG 60.249 55.000 12.71 12.71 43.40 5.52
1791 1797 7.016072 TGGGGGCACATATGGAAAATAAATAAG 59.984 37.037 7.80 0.00 0.00 1.73
1901 1907 2.688507 CAGTAACAATCGCAGAGGTGT 58.311 47.619 0.00 0.00 43.63 4.16
1914 1920 0.623723 GAGGTGTTCCCCTTATGCCA 59.376 55.000 0.00 0.00 34.03 4.92
2066 2072 3.003480 GCATGAAGCCCGGATAGATAAC 58.997 50.000 0.73 0.00 37.23 1.89
2177 2184 7.459795 AGGCCTTGAGAAAGAATAAAAGAAG 57.540 36.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.202698 GGCCTCGGTGCTTCTTATGAT 60.203 52.381 0.00 0.00 0.00 2.45
8 9 2.577059 CGGCCTCGGTGCTTCTTA 59.423 61.111 0.00 0.00 0.00 2.10
32 34 0.039165 CTGACCGCCTTCCTTTTTGC 60.039 55.000 0.00 0.00 0.00 3.68
61 63 2.758327 TCATACCTCTGCGCCGGT 60.758 61.111 15.89 15.89 37.31 5.28
150 153 1.560860 GGACATATTCTGGCGAGCGC 61.561 60.000 6.27 6.27 41.06 5.92
264 267 4.783055 GGATAGTCTATCCGCATCCTCTA 58.217 47.826 20.77 0.00 44.75 2.43
352 355 0.035630 ATGCCTCTGGTGAGAAGCAC 60.036 55.000 0.00 0.00 46.98 4.40
459 462 8.150945 ACATATAATCGTCAGATTTGCTTACCT 58.849 33.333 0.00 0.00 44.11 3.08
525 528 7.934457 ACATGCACAATAGATGATCCTTAAAC 58.066 34.615 0.00 0.00 0.00 2.01
548 551 6.928348 TGGGTATTCTTCTCTGTAAGAACA 57.072 37.500 9.13 0.00 46.34 3.18
569 572 1.833630 TCCAGCTCCTATGACAGTTGG 59.166 52.381 0.00 0.00 41.24 3.77
618 621 2.893424 AGGTTCCTTCAATGTGGCAAT 58.107 42.857 0.00 0.00 0.00 3.56
624 627 5.538813 GGGACTTTTTAGGTTCCTTCAATGT 59.461 40.000 0.00 0.00 29.96 2.71
680 683 0.813610 GCCGCATGCTACATGGTACA 60.814 55.000 17.13 0.00 39.45 2.90
688 691 3.937918 TATAGCCACGCCGCATGCTAC 62.938 57.143 17.13 6.43 38.97 3.58
926 929 2.223377 GGTTCGTTCAAGCACTTACTGG 59.777 50.000 0.00 0.00 32.27 4.00
956 959 2.665603 GCTTCTCCGCTGTCCCTT 59.334 61.111 0.00 0.00 0.00 3.95
957 960 3.394836 GGCTTCTCCGCTGTCCCT 61.395 66.667 0.00 0.00 0.00 4.20
1100 1106 0.397535 CCACAAGGCCTGGGCAATAT 60.398 55.000 23.25 2.51 44.11 1.28
1140 1146 2.796651 GCAAGCTCTCCAATGCCG 59.203 61.111 0.00 0.00 32.73 5.69
1192 1198 2.419297 GGCAGGCCGATATCTTCCATAG 60.419 54.545 0.00 4.03 0.00 2.23
1228 1234 2.284112 CACCATGGCCCAGGCTTT 60.284 61.111 13.04 0.00 41.60 3.51
1279 1285 1.966451 CAAGTCCGACCTTGGCCAC 60.966 63.158 3.88 0.00 38.51 5.01
1285 1291 3.157680 CCCCACAAGTCCGACCTT 58.842 61.111 0.00 0.00 0.00 3.50
1400 1406 8.697292 ACTGACTAAATTCCTCTTCTATACCAC 58.303 37.037 0.00 0.00 0.00 4.16
1451 1457 3.372206 CGGCTAGAAGGCATTATACATGC 59.628 47.826 0.00 9.90 41.44 4.06
1756 1762 1.560505 ATGTGCCCCCAGATGTTTTC 58.439 50.000 0.00 0.00 0.00 2.29
1791 1797 4.669197 CGGTCGGTGAACAAAAGATGATTC 60.669 45.833 0.00 0.00 0.00 2.52
1901 1907 0.400213 CGGCTATGGCATAAGGGGAA 59.600 55.000 8.79 0.00 40.87 3.97
2086 2092 0.396811 GCGCTCATTATACCTGGGGT 59.603 55.000 0.00 0.00 40.16 4.95
2227 2238 1.003759 CCGGACTCTATGTTCGTCTCG 60.004 57.143 0.00 0.00 45.78 4.04


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

AutoCloner maintained by Alex Coulton.