Multiple sequence alignment - TraesCS5A01G128800

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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 TraesCS5A01G128800 chr5A 100.000 3635 0 0 1 3635 288261595 288265229 0 6713
1 TraesCS5A01G128800 chr5A 96.342 3636 113 16 9 3635 606695985 606692361 0 5960
2 TraesCS5A01G128800 chr7A 97.218 3630 84 7 9 3635 192632919 192629304 0 6128
3 TraesCS5A01G128800 chr7A 96.068 3637 125 15 8 3635 38744679 38741052 0 5908
4 TraesCS5A01G128800 chr7A 95.933 3639 106 23 7 3635 643634464 643630858 0 5862
5 TraesCS5A01G128800 chr2A 95.587 3535 125 14 6 3533 778420235 778416725 0 5635
6 TraesCS5A01G128800 chr2A 94.777 1168 45 13 9 1172 677891712 677892867 0 1805
7 TraesCS5A01G128800 chr1B 94.200 3638 170 22 7 3635 629315300 629311695 0 5511
8 TraesCS5A01G128800 chr4B 93.223 3615 188 27 7 3605 563815866 563812293 0 5265
9 TraesCS5A01G128800 chr2B 93.110 3614 192 29 7 3605 42200306 42196735 0 5241
10 TraesCS5A01G128800 chr7B 94.539 2948 134 12 700 3635 720228619 720231551 0 4527
11 TraesCS5A01G128800 chr4A 89.353 958 81 19 10 959 664923365 664924309 0 1184
12 TraesCS5A01G128800 chr3B 88.554 961 83 22 6 955 173097035 173096091 0 1140


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 TraesCS5A01G128800 chr5A 288261595 288265229 3634 False 6713 6713 100.000 1 3635 1 chr5A.!!$F1 3634
1 TraesCS5A01G128800 chr5A 606692361 606695985 3624 True 5960 5960 96.342 9 3635 1 chr5A.!!$R1 3626
2 TraesCS5A01G128800 chr7A 192629304 192632919 3615 True 6128 6128 97.218 9 3635 1 chr7A.!!$R2 3626
3 TraesCS5A01G128800 chr7A 38741052 38744679 3627 True 5908 5908 96.068 8 3635 1 chr7A.!!$R1 3627
4 TraesCS5A01G128800 chr7A 643630858 643634464 3606 True 5862 5862 95.933 7 3635 1 chr7A.!!$R3 3628
5 TraesCS5A01G128800 chr2A 778416725 778420235 3510 True 5635 5635 95.587 6 3533 1 chr2A.!!$R1 3527
6 TraesCS5A01G128800 chr2A 677891712 677892867 1155 False 1805 1805 94.777 9 1172 1 chr2A.!!$F1 1163
7 TraesCS5A01G128800 chr1B 629311695 629315300 3605 True 5511 5511 94.200 7 3635 1 chr1B.!!$R1 3628
8 TraesCS5A01G128800 chr4B 563812293 563815866 3573 True 5265 5265 93.223 7 3605 1 chr4B.!!$R1 3598
9 TraesCS5A01G128800 chr2B 42196735 42200306 3571 True 5241 5241 93.110 7 3605 1 chr2B.!!$R1 3598
10 TraesCS5A01G128800 chr7B 720228619 720231551 2932 False 4527 4527 94.539 700 3635 1 chr7B.!!$F1 2935
11 TraesCS5A01G128800 chr4A 664923365 664924309 944 False 1184 1184 89.353 10 959 1 chr4A.!!$F1 949
12 TraesCS5A01G128800 chr3B 173096091 173097035 944 True 1140 1140 88.554 6 955 1 chr3B.!!$R1 949

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
49 50 2.301870 TCTTTAGGTGACGCCAACATCT 59.698 45.455 7.99 0.0 40.61 2.90 F
1441 1471 0.601841 CGGACAAGCTGTTACCGGTT 60.602 55.000 15.04 0.0 39.92 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 1601 0.544357 ACCCTGAGGACACGGATTGA 60.544 55.0 0.0 0.0 36.73 2.57 R
3117 3153 0.322648 CACTGGACTGAGCACCATGA 59.677 55.0 0.0 0.0 35.54 3.07 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
49 50 2.301870 TCTTTAGGTGACGCCAACATCT 59.698 45.455 7.99 0.00 40.61 2.90
323 343 3.321950 CCCCTTGATCTACTCCATCCTT 58.678 50.000 0.00 0.00 0.00 3.36
375 396 2.439507 GCATCCTTGAGGTATTCTCCCA 59.560 50.000 0.00 0.00 41.76 4.37
511 532 7.373617 TGATAGATGATTTGGTAGGCAGTAA 57.626 36.000 0.00 0.00 0.00 2.24
536 557 6.353404 TGATGTGTAGTTGAACATGTAGGA 57.647 37.500 0.00 0.00 37.15 2.94
537 558 6.398095 TGATGTGTAGTTGAACATGTAGGAG 58.602 40.000 0.00 0.00 37.15 3.69
549 570 7.174413 TGAACATGTAGGAGAAATCAATTCCA 58.826 34.615 0.00 0.00 38.94 3.53
1441 1471 0.601841 CGGACAAGCTGTTACCGGTT 60.602 55.000 15.04 0.00 39.92 4.44
1571 1601 4.395231 GCTAAAAGCGGTTAGAGGAAACAT 59.605 41.667 0.00 0.00 33.62 2.71
1679 1709 0.400213 TCAGATGCAACCGGGAACTT 59.600 50.000 6.32 0.00 0.00 2.66
1763 1793 3.745975 GCCGCACTAGCATATTTGTATCA 59.254 43.478 0.00 0.00 42.27 2.15
1928 1958 0.689412 TGTGGATGTGGGAGCGGATA 60.689 55.000 0.00 0.00 0.00 2.59
1961 1991 1.705186 CCCGATATCAAGGACCCCAAT 59.295 52.381 3.12 0.00 0.00 3.16
2014 2044 4.276183 GCTGCATGATGATGATCCATATCC 59.724 45.833 0.00 0.00 0.00 2.59
2229 2261 5.645056 TGGTTGCCTTATATGGAAGATCA 57.355 39.130 8.82 0.00 0.00 2.92
2311 2343 4.036027 CCAATGATATGCTTCTTCGCAGTT 59.964 41.667 0.00 0.00 44.10 3.16
2355 2387 2.552315 TGGCGAGACAATTTGGAAGAAC 59.448 45.455 0.78 0.00 0.00 3.01
2611 2643 6.438741 AGAGAATAGACCTCACAATCAGTCAA 59.561 38.462 0.00 0.00 33.25 3.18
2634 2666 8.531146 TCAACATATCAGAAGTATCAAGTGTGA 58.469 33.333 0.00 0.00 38.41 3.58
2710 2742 1.341531 CGGAGTTGGTGTCTGAAGACT 59.658 52.381 11.55 0.00 44.99 3.24
2747 2779 4.224370 AGGTTATCATACCTTCAACACGGT 59.776 41.667 0.00 0.00 46.39 4.83
2832 2868 8.837389 GTCTGTTTGACCTATTCTAACAAACTT 58.163 33.333 17.45 0.00 45.50 2.66
2833 2869 8.836413 TCTGTTTGACCTATTCTAACAAACTTG 58.164 33.333 17.45 12.17 45.50 3.16
2834 2870 7.422399 TGTTTGACCTATTCTAACAAACTTGC 58.578 34.615 17.45 0.00 43.99 4.01
2835 2871 7.067615 TGTTTGACCTATTCTAACAAACTTGCA 59.932 33.333 17.45 0.00 43.99 4.08
2849 2885 4.787260 AACTTGCATGCATCATGTTGTA 57.213 36.364 23.37 1.46 43.10 2.41
2982 3018 3.204158 TCTGAGAGGACTCTTAGGAGCAT 59.796 47.826 17.70 0.00 41.85 3.79
3117 3153 1.042229 TGGCAGCAATGCTTTCTTGT 58.958 45.000 4.36 0.00 36.40 3.16
3571 3616 0.603707 GCCTACACTTGCAGCACTCA 60.604 55.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 4.680237 CGCAACCCAGACGCCAGA 62.680 66.667 0.00 0.00 0.00 3.86
169 179 0.474854 TCCACTTACCAGGGCCAGAA 60.475 55.000 6.18 0.00 0.00 3.02
250 269 3.427309 GAGAAGCCCTCTGTTCGTC 57.573 57.895 0.00 0.00 38.86 4.20
323 343 5.824624 GCCTCAGATCCACAAATTTAGATGA 59.175 40.000 0.00 0.00 0.00 2.92
511 532 7.394016 TCCTACATGTTCAACTACACATCATT 58.606 34.615 2.30 0.00 30.90 2.57
536 557 9.104965 CATATGCACAAAATGGAATTGATTTCT 57.895 29.630 0.00 0.00 36.10 2.52
537 558 8.885722 ACATATGCACAAAATGGAATTGATTTC 58.114 29.630 1.58 0.00 36.10 2.17
549 570 6.606796 TCCTATGGACAACATATGCACAAAAT 59.393 34.615 1.58 0.00 41.07 1.82
1441 1471 1.876799 CCAATTAACGGCACTGACACA 59.123 47.619 0.00 0.00 0.00 3.72
1571 1601 0.544357 ACCCTGAGGACACGGATTGA 60.544 55.000 0.00 0.00 36.73 2.57
1623 1653 3.931907 AGCACATACCAAAGATAGGCA 57.068 42.857 0.00 0.00 0.00 4.75
1679 1709 1.229951 AGGAACATCCAGAGGGCCA 60.230 57.895 6.18 0.00 39.61 5.36
1763 1793 6.662755 TGGTTGCAAATATCTCTTACCTGAT 58.337 36.000 0.00 0.00 0.00 2.90
1961 1991 2.357056 CCCCGTGGGTTTGCCATA 59.643 61.111 3.83 0.00 38.25 2.74
2229 2261 8.373220 TGCACATCTCATTAAGATCATAGTCAT 58.627 33.333 0.00 0.00 43.13 3.06
2311 2343 1.270094 CGGTCTACAAAGTGCCACTCA 60.270 52.381 0.00 0.00 0.00 3.41
2355 2387 5.500234 TCTCCTCAATTGGAATACCTTGTG 58.500 41.667 5.42 0.00 35.43 3.33
2456 2488 2.164219 CACGGGACAAAGCATTAGCAAT 59.836 45.455 0.00 0.00 45.49 3.56
2710 2742 1.919240 TAACCTTCTGCAGTCTCCGA 58.081 50.000 14.67 0.00 0.00 4.55
2832 2868 5.585820 AAGAATACAACATGATGCATGCA 57.414 34.783 25.04 25.04 44.80 3.96
2833 2869 6.037726 TGAAAGAATACAACATGATGCATGC 58.962 36.000 11.82 11.82 44.80 4.06
2834 2870 8.468720 TTTGAAAGAATACAACATGATGCATG 57.531 30.769 2.46 5.90 46.18 4.06
2982 3018 6.514012 AATATATTGGTCACACCTCCATCA 57.486 37.500 0.00 0.00 39.58 3.07
3117 3153 0.322648 CACTGGACTGAGCACCATGA 59.677 55.000 0.00 0.00 35.54 3.07
3454 3496 5.841267 TGCATTCCTATTGGGATAAGCTA 57.159 39.130 0.00 0.00 44.66 3.32
3571 3616 3.774216 CACTTCCTCCTTCCTCTCTTCAT 59.226 47.826 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.