Multiple sequence alignment - TraesCS1A01G211400

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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 TraesCS1A01G211400 chr1A 100.000 3298 0 0 1 3298 374207766 374211063 0.000000e+00 6091.0
1 TraesCS1A01G211400 chr1A 96.544 3299 103 6 1 3295 449450053 449453344 0.000000e+00 5450.0
2 TraesCS1A01G211400 chr5A 97.183 3301 84 5 1 3298 670476764 670473470 0.000000e+00 5572.0
3 TraesCS1A01G211400 chr5A 95.725 3298 128 7 3 3298 696328860 696325574 0.000000e+00 5297.0
4 TraesCS1A01G211400 chr2D 95.613 3305 128 11 1 3298 197523400 197520106 0.000000e+00 5284.0
5 TraesCS1A01G211400 chr3A 95.154 3302 123 13 1 3298 1716800 1713532 0.000000e+00 5177.0
6 TraesCS1A01G211400 chr3A 90.423 1608 124 14 1676 3258 218169215 218167613 0.000000e+00 2089.0
7 TraesCS1A01G211400 chr3A 93.651 63 4 0 1619 1681 218173134 218173072 9.740000e-16 95.3
8 TraesCS1A01G211400 chr3D 92.961 2486 151 10 738 3206 303482138 303479660 0.000000e+00 3600.0
9 TraesCS1A01G211400 chr5D 93.662 1988 100 11 393 2376 51806380 51804415 0.000000e+00 2950.0
10 TraesCS1A01G211400 chr5D 89.145 912 74 11 2371 3258 51750724 51749814 0.000000e+00 1112.0
11 TraesCS1A01G211400 chr7A 95.750 1600 58 5 1 1598 206573462 206575053 0.000000e+00 2569.0
12 TraesCS1A01G211400 chr7A 94.153 1009 50 2 1 1007 491891125 491892126 0.000000e+00 1528.0
13 TraesCS1A01G211400 chr2B 95.785 1566 61 4 1736 3298 142888768 142890331 0.000000e+00 2521.0
14 TraesCS1A01G211400 chr2B 89.886 1582 102 22 1723 3255 634220834 634222406 0.000000e+00 1982.0
15 TraesCS1A01G211400 chr1B 95.125 1600 72 5 1 1598 23815846 23817441 0.000000e+00 2518.0
16 TraesCS1A01G211400 chr3B 94.938 1600 77 4 1 1598 607523076 607521479 0.000000e+00 2503.0


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 TraesCS1A01G211400 chr1A 374207766 374211063 3297 False 6091.00 6091 100.000 1 3298 1 chr1A.!!$F1 3297
1 TraesCS1A01G211400 chr1A 449450053 449453344 3291 False 5450.00 5450 96.544 1 3295 1 chr1A.!!$F2 3294
2 TraesCS1A01G211400 chr5A 670473470 670476764 3294 True 5572.00 5572 97.183 1 3298 1 chr5A.!!$R1 3297
3 TraesCS1A01G211400 chr5A 696325574 696328860 3286 True 5297.00 5297 95.725 3 3298 1 chr5A.!!$R2 3295
4 TraesCS1A01G211400 chr2D 197520106 197523400 3294 True 5284.00 5284 95.613 1 3298 1 chr2D.!!$R1 3297
5 TraesCS1A01G211400 chr3A 1713532 1716800 3268 True 5177.00 5177 95.154 1 3298 1 chr3A.!!$R1 3297
6 TraesCS1A01G211400 chr3A 218167613 218173134 5521 True 1092.15 2089 92.037 1619 3258 2 chr3A.!!$R2 1639
7 TraesCS1A01G211400 chr3D 303479660 303482138 2478 True 3600.00 3600 92.961 738 3206 1 chr3D.!!$R1 2468
8 TraesCS1A01G211400 chr5D 51804415 51806380 1965 True 2950.00 2950 93.662 393 2376 1 chr5D.!!$R2 1983
9 TraesCS1A01G211400 chr5D 51749814 51750724 910 True 1112.00 1112 89.145 2371 3258 1 chr5D.!!$R1 887
10 TraesCS1A01G211400 chr7A 206573462 206575053 1591 False 2569.00 2569 95.750 1 1598 1 chr7A.!!$F1 1597
11 TraesCS1A01G211400 chr7A 491891125 491892126 1001 False 1528.00 1528 94.153 1 1007 1 chr7A.!!$F2 1006
12 TraesCS1A01G211400 chr2B 142888768 142890331 1563 False 2521.00 2521 95.785 1736 3298 1 chr2B.!!$F1 1562
13 TraesCS1A01G211400 chr2B 634220834 634222406 1572 False 1982.00 1982 89.886 1723 3255 1 chr2B.!!$F2 1532
14 TraesCS1A01G211400 chr1B 23815846 23817441 1595 False 2518.00 2518 95.125 1 1598 1 chr1B.!!$F1 1597
15 TraesCS1A01G211400 chr3B 607521479 607523076 1597 True 2503.00 2503 94.938 1 1598 1 chr3B.!!$R1 1597

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
376 382 0.918983 TGGGAAGGGTCTGCATAAGG 59.081 55.0 0.0 0.0 0.00 2.69 F
1244 1257 0.522180 GACTCTCGGAAACAGAGCGA 59.478 55.0 0.0 0.0 38.42 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 5556 0.251742 TGCCACCCATTCCAGAAAGG 60.252 55.0 0.0 0.0 39.47 3.11 R
2665 6579 0.730494 GAACGCAATCACAAGGCTGC 60.730 55.0 0.0 0.0 0.00 5.25 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
111 112 4.657814 ATTTCCAGGTGAACCACTACAT 57.342 40.909 1.62 0.00 38.89 2.29
243 245 3.117926 TGGAACACATATCCCCATCACTG 60.118 47.826 0.00 0.00 36.04 3.66
258 260 5.181009 CCATCACTGTTGCTGAAGATAAGA 58.819 41.667 0.00 0.00 0.00 2.10
262 264 3.274288 CTGTTGCTGAAGATAAGACCCC 58.726 50.000 0.00 0.00 0.00 4.95
263 265 2.026262 TGTTGCTGAAGATAAGACCCCC 60.026 50.000 0.00 0.00 0.00 5.40
373 379 1.279025 GGGTGGGAAGGGTCTGCATA 61.279 60.000 0.00 0.00 0.00 3.14
376 382 0.918983 TGGGAAGGGTCTGCATAAGG 59.081 55.000 0.00 0.00 0.00 2.69
496 502 2.107366 TGCACCATATCGAGGAGTTCA 58.893 47.619 0.00 0.00 0.00 3.18
653 662 4.026052 CCCTATCTTGAAAGTGGGCAATT 58.974 43.478 0.00 0.00 0.00 2.32
696 705 2.513666 GATTCCGGCGGCATGTGA 60.514 61.111 23.83 0.00 0.00 3.58
992 1004 5.261216 AGTACCCCATTGTTGGTTCAATAG 58.739 41.667 0.97 0.00 41.91 1.73
1007 1019 4.486125 TCAATAGTGTAGCAATGGCAGA 57.514 40.909 0.00 0.00 44.61 4.26
1154 1167 9.657419 AAATACATTCAATCAGAAATTTCCACC 57.343 29.630 14.61 0.00 40.22 4.61
1174 1187 3.640967 ACCAGCTAATTTCACCAAGCAAA 59.359 39.130 0.00 0.00 37.44 3.68
1244 1257 0.522180 GACTCTCGGAAACAGAGCGA 59.478 55.000 0.00 0.00 38.42 4.93
1514 1527 2.608506 CCTGTATCACGTGTTTCCGTCA 60.609 50.000 16.51 5.92 39.45 4.35
1580 1593 8.915057 ATAGTATTTGGGAGATTGTTGAGATG 57.085 34.615 0.00 0.00 0.00 2.90
1639 1652 6.855403 GCTTGAGTGCTCTTTTTCTTTCTAAG 59.145 38.462 0.68 0.00 0.00 2.18
1670 1683 3.063997 CGATGAAGGACCAAGTTATGTGC 59.936 47.826 0.00 0.00 0.00 4.57
1681 5556 8.936864 GGACCAAGTTATGTGCATATATACTTC 58.063 37.037 18.77 12.72 0.00 3.01
2093 5975 4.942761 ACAATCTGCAAAACTGGTTGAT 57.057 36.364 3.16 0.00 39.91 2.57
2301 6185 8.231007 AGGAGGAGATTTCTGAGATGTAGATAA 58.769 37.037 0.00 0.00 0.00 1.75
2645 6559 7.012704 CCTGTTCATCTGAAGACTTTTTCAAGA 59.987 37.037 0.00 0.00 36.69 3.02
2665 6579 5.545063 AGAAAACAAATTGGGTTACTGGG 57.455 39.130 0.00 0.00 0.00 4.45
2698 6612 9.602568 TGTGATTGCGTTCCTAAACTATATTTA 57.397 29.630 0.00 0.00 32.95 1.40
2937 6876 5.419542 CATCTTGTTCGAAAGTATCCCTGA 58.580 41.667 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 200 7.728532 TCCATCTATAGCACCAATGTAGTTCTA 59.271 37.037 0.00 0.00 0.00 2.10
205 207 5.126067 GTGTTCCATCTATAGCACCAATGT 58.874 41.667 0.00 0.00 0.00 2.71
243 245 2.644676 GGGGGTCTTATCTTCAGCAAC 58.355 52.381 0.00 0.00 0.00 4.17
271 277 7.186594 AGAGGGTTCCTTTCCTATTCCTAAATT 59.813 37.037 0.00 0.00 31.76 1.82
373 379 3.073650 AGAATGAAGAACTCCTGCACCTT 59.926 43.478 0.00 0.00 31.94 3.50
376 382 2.161211 GCAGAATGAAGAACTCCTGCAC 59.839 50.000 0.00 0.00 44.40 4.57
653 662 7.727578 TGATTTGTGACTCTATTGGGTAGTA 57.272 36.000 0.00 0.00 0.00 1.82
696 705 9.664332 GAGCTCTAATGATGTTATGGAATACAT 57.336 33.333 6.43 0.00 43.68 2.29
1244 1257 1.416401 GTGTATCATCCCATCCCGTGT 59.584 52.381 0.00 0.00 0.00 4.49
1514 1527 7.732222 TGAAAAGGATTTAATATGCAGGGTT 57.268 32.000 0.00 0.00 37.28 4.11
1603 1616 1.457346 CACTCAAGCAGGGTCCAATC 58.543 55.000 0.00 0.00 0.00 2.67
1606 1619 2.116983 GAGCACTCAAGCAGGGTCCA 62.117 60.000 0.00 0.00 36.85 4.02
1639 1652 3.921677 TGGTCCTTCATCGTACAACTTC 58.078 45.455 0.00 0.00 0.00 3.01
1681 5556 0.251742 TGCCACCCATTCCAGAAAGG 60.252 55.000 0.00 0.00 39.47 3.11
1732 5608 4.627467 AGCATGTTCTCGTAGAAACATCAC 59.373 41.667 0.00 0.00 42.05 3.06
1950 5829 3.510388 TGTAGCTTCAGGTTCATCTCG 57.490 47.619 0.00 0.00 0.00 4.04
2093 5975 3.822735 CTGGCTTTGATTCCTTCAACTCA 59.177 43.478 0.00 0.00 43.99 3.41
2194 6078 4.636249 TGGGCATTTAAAAAGTCGCAATT 58.364 34.783 0.00 0.00 0.00 2.32
2201 6085 6.696411 TCGATTCATTGGGCATTTAAAAAGT 58.304 32.000 0.00 0.00 0.00 2.66
2376 6264 2.609459 CGCTTATACAAAGCTCCAGTGG 59.391 50.000 1.40 1.40 40.94 4.00
2377 6265 3.062639 CACGCTTATACAAAGCTCCAGTG 59.937 47.826 8.00 5.03 40.94 3.66
2397 6285 7.763172 ATCATCGATTAACAGAGAGAAACAC 57.237 36.000 0.00 0.00 0.00 3.32
2429 6317 9.921637 AAAAGAATGAAGTGTGTTTTGTCTTTA 57.078 25.926 0.00 0.00 33.01 1.85
2497 6385 5.479027 ACACAGAAACTACCAAACAAAAGGT 59.521 36.000 0.00 0.00 41.89 3.50
2631 6545 8.729756 CCCAATTTGTTTTCTTGAAAAAGTCTT 58.270 29.630 9.71 1.31 0.00 3.01
2645 6559 3.456277 TGCCCAGTAACCCAATTTGTTTT 59.544 39.130 0.00 0.00 0.00 2.43
2665 6579 0.730494 GAACGCAATCACAAGGCTGC 60.730 55.000 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.