Multiple sequence alignment - TraesCS2A01G235100

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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 TraesCS2A01G235100 chr2A 100.000 4410 0 0 1 4410 290318351 290322760 0 8144
1 TraesCS2A01G235100 chr5A 97.589 3028 67 1 1389 4410 631068560 631065533 0 5182
2 TraesCS2A01G235100 chr5A 96.598 3028 69 9 1389 4410 213048192 213051191 0 4990
3 TraesCS2A01G235100 chr5A 97.059 1394 39 2 1 1392 213046757 213048150 0 2346
4 TraesCS2A01G235100 chr6A 97.557 3029 67 2 1389 4410 307921214 307918186 0 5177
5 TraesCS2A01G235100 chr6A 96.908 1423 38 1 2994 4410 595797244 595798666 0 2379
6 TraesCS2A01G235100 chr6A 96.838 1423 36 2 2994 4410 592958089 592956670 0 2370
7 TraesCS2A01G235100 chr6A 96.915 1394 40 3 1 1392 307922648 307921256 0 2333
8 TraesCS2A01G235100 chr6A 94.811 1060 47 6 9 1062 592961294 592960237 0 1646
9 TraesCS2A01G235100 chr7A 97.358 3028 74 1 1389 4410 395514958 395517985 0 5144
10 TraesCS2A01G235100 chr7A 96.485 1394 47 2 1 1392 395513523 395514916 0 2302
11 TraesCS2A01G235100 chr1A 97.325 3028 74 2 1389 4410 236392446 236395472 0 5136
12 TraesCS2A01G235100 chr3B 96.995 3028 85 1 1389 4410 817687778 817690805 0 5083
13 TraesCS2A01G235100 chr3B 96.764 3028 92 1 1389 4410 817710933 817713960 0 5044
14 TraesCS2A01G235100 chr3B 97.079 2636 67 4 1389 4015 745861 748495 0 4433
15 TraesCS2A01G235100 chr3B 96.818 2451 73 3 1963 4410 784350889 784348441 0 4089
16 TraesCS2A01G235100 chr3B 96.201 1395 49 4 1 1392 817686343 817687736 0 2279
17 TraesCS2A01G235100 chr7B 96.334 3028 105 1 1389 4410 695574744 695571717 0 4972
18 TraesCS2A01G235100 chr7B 95.839 1394 54 4 1 1392 681953023 681954414 0 2250
19 TraesCS2A01G235100 chr7B 95.556 1395 58 4 1 1392 695576179 695574786 0 2230
20 TraesCS2A01G235100 chr6B 95.627 1395 56 5 1 1392 83866044 83867436 0 2233
21 TraesCS2A01G235100 chrUn 95.265 1394 59 3 1 1392 87506301 87504913 0 2202
22 TraesCS2A01G235100 chrUn 95.197 1395 54 6 1 1392 87516123 87514739 0 2193


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 TraesCS2A01G235100 chr2A 290318351 290322760 4409 False 8144 8144 100.0000 1 4410 1 chr2A.!!$F1 4409
1 TraesCS2A01G235100 chr5A 631065533 631068560 3027 True 5182 5182 97.5890 1389 4410 1 chr5A.!!$R1 3021
2 TraesCS2A01G235100 chr5A 213046757 213051191 4434 False 3668 4990 96.8285 1 4410 2 chr5A.!!$F1 4409
3 TraesCS2A01G235100 chr6A 307918186 307922648 4462 True 3755 5177 97.2360 1 4410 2 chr6A.!!$R1 4409
4 TraesCS2A01G235100 chr6A 595797244 595798666 1422 False 2379 2379 96.9080 2994 4410 1 chr6A.!!$F1 1416
5 TraesCS2A01G235100 chr6A 592956670 592961294 4624 True 2008 2370 95.8245 9 4410 2 chr6A.!!$R2 4401
6 TraesCS2A01G235100 chr7A 395513523 395517985 4462 False 3723 5144 96.9215 1 4410 2 chr7A.!!$F1 4409
7 TraesCS2A01G235100 chr1A 236392446 236395472 3026 False 5136 5136 97.3250 1389 4410 1 chr1A.!!$F1 3021
8 TraesCS2A01G235100 chr3B 817710933 817713960 3027 False 5044 5044 96.7640 1389 4410 1 chr3B.!!$F2 3021
9 TraesCS2A01G235100 chr3B 745861 748495 2634 False 4433 4433 97.0790 1389 4015 1 chr3B.!!$F1 2626
10 TraesCS2A01G235100 chr3B 784348441 784350889 2448 True 4089 4089 96.8180 1963 4410 1 chr3B.!!$R1 2447
11 TraesCS2A01G235100 chr3B 817686343 817690805 4462 False 3681 5083 96.5980 1 4410 2 chr3B.!!$F3 4409
12 TraesCS2A01G235100 chr7B 695571717 695576179 4462 True 3601 4972 95.9450 1 4410 2 chr7B.!!$R1 4409
13 TraesCS2A01G235100 chr7B 681953023 681954414 1391 False 2250 2250 95.8390 1 1392 1 chr7B.!!$F1 1391
14 TraesCS2A01G235100 chr6B 83866044 83867436 1392 False 2233 2233 95.6270 1 1392 1 chr6B.!!$F1 1391
15 TraesCS2A01G235100 chrUn 87504913 87506301 1388 True 2202 2202 95.2650 1 1392 1 chrUn.!!$R1 1391
16 TraesCS2A01G235100 chrUn 87514739 87516123 1384 True 2193 2193 95.1970 1 1392 1 chrUn.!!$R2 1391

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
648 654 0.106217 CCTCTCTCCTCTCCCTCACC 60.106 65.0 0.0 0.0 0.0 4.02 F
842 853 0.678684 CCGCCACCCCTAAATTCGTT 60.679 55.0 0.0 0.0 0.0 3.85 F
1870 2151 0.178891 AAGGAGCAGAAGGAGGGACA 60.179 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 2132 0.178891 TGTCCCTCCTTCTGCTCCTT 60.179 55.000 0.00 0.0 0.00 3.36 R
1990 2271 1.377202 GAGCAATTGGTCCGAGCCA 60.377 57.895 24.03 0.0 36.62 4.75 R
3492 4335 2.223044 GCACAGACTAAATAAGCCACGC 60.223 50.000 0.00 0.0 0.00 5.34 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
253 255 5.913137 AAAGAACTCATTTTGGACACACA 57.087 34.783 0.00 0.00 0.00 3.72
525 530 0.318529 CTCTCATGCGGATCGTGGAG 60.319 60.000 0.00 0.00 32.54 3.86
546 552 0.467474 ATCACCGTCGGATGCTCCTA 60.467 55.000 20.51 0.00 33.30 2.94
621 627 1.002274 ACCCTTCTCTCCCTCGCAT 59.998 57.895 0.00 0.00 0.00 4.73
648 654 0.106217 CCTCTCTCCTCTCCCTCACC 60.106 65.000 0.00 0.00 0.00 4.02
756 767 1.303806 TCGACGACCCTCACCATCA 60.304 57.895 0.00 0.00 0.00 3.07
842 853 0.678684 CCGCCACCCCTAAATTCGTT 60.679 55.000 0.00 0.00 0.00 3.85
1373 1585 5.273208 AGACCAGGAAGATTGTAGCTTCTA 58.727 41.667 0.00 0.00 41.11 2.10
1377 1589 3.712218 AGGAAGATTGTAGCTTCTACCCC 59.288 47.826 0.00 0.00 41.11 4.95
1472 1753 6.707608 GTGTCCTGTGATTAGATGCAATATGA 59.292 38.462 0.00 0.00 0.00 2.15
1758 2039 6.404844 GCAGTTAGTCTGTATCTGTCTTAGCA 60.405 42.308 0.00 0.00 45.23 3.49
1851 2132 1.538629 TGCAGGTCACCCATCCTCA 60.539 57.895 0.00 0.00 30.91 3.86
1870 2151 0.178891 AAGGAGCAGAAGGAGGGACA 60.179 55.000 0.00 0.00 0.00 4.02
1904 2185 4.093291 AAGGGCCTGCTCTGCTCG 62.093 66.667 6.92 0.00 33.29 5.03
1990 2271 0.255318 CATGCCTCCTTTGCTCTCCT 59.745 55.000 0.00 0.00 0.00 3.69
2004 2285 0.909610 TCTCCTGGCTCGGACCAATT 60.910 55.000 0.00 0.00 39.86 2.32
2253 2536 7.062839 GGCATTCGTTTGTATTTGCAAATTAGA 59.937 33.333 28.45 15.58 40.01 2.10
2256 2539 9.691362 ATTCGTTTGTATTTGCAAATTAGAAGT 57.309 25.926 28.45 7.20 40.01 3.01
2351 2634 5.596361 TGGAGATAGTTTAGCAGAGGAAGAG 59.404 44.000 0.00 0.00 0.00 2.85
2570 2853 6.121776 ACAACCTGATCAATGTACAACCTA 57.878 37.500 0.00 0.00 0.00 3.08
2815 3098 7.495934 ACAGTATCAGGCAGTAACACATTAATC 59.504 37.037 0.00 0.00 0.00 1.75
3279 4094 5.190677 GGGCTAAACTTGTATTTGCTCCTA 58.809 41.667 0.00 0.00 0.00 2.94
3344 4159 3.099905 CTCCTTGTACCAGATGAGTCCA 58.900 50.000 0.00 0.00 0.00 4.02
3425 4268 3.006967 GCTTTGACTACAACCTCCTCTCA 59.993 47.826 0.00 0.00 35.63 3.27
3426 4269 4.503296 GCTTTGACTACAACCTCCTCTCAA 60.503 45.833 0.00 0.00 35.63 3.02
3715 4558 3.132467 TCTGCACTCTCAGGATCATCTTG 59.868 47.826 0.00 0.00 34.91 3.02
4036 4882 4.451557 CGCGTAACTTCTTTACTTGGTTG 58.548 43.478 0.00 0.00 38.40 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
525 530 2.594541 GAGCATCCGACGGTGATTC 58.405 57.895 14.79 9.08 0.00 2.52
546 552 4.778143 GTGCGGGCCGTTGGATCT 62.778 66.667 28.82 0.00 0.00 2.75
621 627 1.682684 GAGGAGAGAGGGGCGTCAA 60.683 63.158 0.00 0.00 0.00 3.18
648 654 2.289320 GGTGGATTCAGATCAGATCGGG 60.289 54.545 10.32 4.99 33.77 5.14
842 853 1.227102 CCGGATTTGGCAGATCCCA 59.773 57.895 26.26 0.00 39.97 4.37
1373 1585 1.787058 AGAAGGCACTAAAAAGGGGGT 59.213 47.619 0.00 0.00 38.49 4.95
1377 1589 2.412847 CGCGAAGAAGGCACTAAAAAGG 60.413 50.000 0.00 0.00 38.49 3.11
1472 1753 7.361542 GCTGAAATCACTGAGTTGAACATACAT 60.362 37.037 0.00 0.00 0.00 2.29
1758 2039 6.640518 TGTAACAGTCTTCTCTTGTGTCTTT 58.359 36.000 0.00 0.00 0.00 2.52
1851 2132 0.178891 TGTCCCTCCTTCTGCTCCTT 60.179 55.000 0.00 0.00 0.00 3.36
1870 2151 2.575279 CCCTTGATGGCCAGCTAGATAT 59.425 50.000 30.14 1.94 0.00 1.63
1904 2185 2.028020 ACCGATGGTCAAGGAAGAAGAC 60.028 50.000 3.51 0.00 0.00 3.01
1981 2262 2.283894 TCCGAGCCAGGAGAGCAA 60.284 61.111 0.00 0.00 34.92 3.91
1990 2271 1.377202 GAGCAATTGGTCCGAGCCA 60.377 57.895 24.03 0.00 36.62 4.75
2253 2536 3.629398 GGCACATATTCTGCAAGCTACTT 59.371 43.478 4.83 0.00 36.27 2.24
2256 2539 2.212652 CGGCACATATTCTGCAAGCTA 58.787 47.619 4.83 0.00 36.27 3.32
2499 2782 4.702131 CCTAGTGCAAGAAGGCATTTACTT 59.298 41.667 0.00 0.00 46.92 2.24
2815 3098 6.539649 TTTGATTTCAAGTAACCGAGACTG 57.460 37.500 0.00 0.00 37.15 3.51
2902 3187 3.763897 ACAAGCAAGTGTTCTCAGGTTTT 59.236 39.130 0.00 0.00 0.00 2.43
3279 4094 4.401202 TCATGATCATCAAAATGCAGCAGT 59.599 37.500 4.86 0.00 32.58 4.40
3344 4159 2.963854 CGCTGCCGCTTCATCGAT 60.964 61.111 0.00 0.00 0.00 3.59
3407 4250 3.574396 CACTTGAGAGGAGGTTGTAGTCA 59.426 47.826 0.00 0.00 0.00 3.41
3425 4268 3.335484 AGAGGTAGGAGAAGGACTCACTT 59.665 47.826 0.00 0.00 46.54 3.16
3426 4269 2.923629 AGAGGTAGGAGAAGGACTCACT 59.076 50.000 0.00 0.00 46.54 3.41
3492 4335 2.223044 GCACAGACTAAATAAGCCACGC 60.223 50.000 0.00 0.00 0.00 5.34
3601 4444 6.446318 CAAACAACCTTAGCAGAATAAGCAA 58.554 36.000 0.00 0.00 32.42 3.91
3715 4558 5.580297 ACACCAAAAATTGATTGTGTGTCAC 59.420 36.000 16.74 0.00 37.49 3.67
3981 4827 5.604758 TGCTACAGATCAGCTATCAACTT 57.395 39.130 5.26 0.00 39.83 2.66


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

AutoCloner maintained by Alex Coulton.