Multiple sequence alignment - TraesCS5A01G110100

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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 TraesCS5A01G110100 chr5A 100.000 5410 0 0 1 5410 207660148 207654739 0.000000e+00 9991.0
1 TraesCS5A01G110100 chr5A 80.620 645 80 23 4762 5395 139688446 139687836 1.780000e-124 457.0
2 TraesCS5A01G110100 chr5D 98.051 4566 75 8 1 4560 158170862 158166305 0.000000e+00 7926.0
3 TraesCS5A01G110100 chr5D 90.947 486 39 3 4559 5043 158166221 158165740 0.000000e+00 649.0
4 TraesCS5A01G110100 chr5B 98.830 2223 23 2 942 3161 159711444 159713666 0.000000e+00 3958.0
5 TraesCS5A01G110100 chr5B 92.791 2275 82 32 3154 5409 159715160 159717371 0.000000e+00 3217.0
6 TraesCS5A01G110100 chr5B 75.227 662 107 30 4762 5409 33615198 33614580 1.490000e-65 261.0
7 TraesCS5A01G110100 chr5B 76.980 404 62 24 4927 5323 604845281 604844902 9.190000e-48 202.0
8 TraesCS5A01G110100 chr3A 80.689 668 103 13 4762 5409 27036452 27035791 3.760000e-136 496.0
9 TraesCS5A01G110100 chr3A 80.183 656 101 13 4762 5408 25538550 25537915 1.060000e-126 464.0
10 TraesCS5A01G110100 chr6B 79.968 629 85 25 4762 5364 206021509 206022122 5.010000e-115 425.0
11 TraesCS5A01G110100 chr6B 80.493 487 72 9 4762 5235 135704317 135703841 8.620000e-93 351.0
12 TraesCS5A01G110100 chr6B 76.947 321 52 18 5082 5390 92615495 92615805 4.340000e-36 163.0
13 TraesCS5A01G110100 chr6D 78.636 660 94 23 4762 5409 419442610 419441986 1.410000e-105 394.0
14 TraesCS5A01G110100 chr6A 80.297 472 70 18 4856 5316 541422163 541422622 8.680000e-88 335.0
15 TraesCS5A01G110100 chr6A 78.378 444 60 20 4779 5203 593347796 593348222 6.950000e-64 255.0
16 TraesCS5A01G110100 chr7A 78.873 497 75 18 4934 5409 232070028 232070515 5.260000e-80 309.0
17 TraesCS5A01G110100 chr2B 76.453 654 91 34 4762 5392 444548510 444547897 4.100000e-76 296.0
18 TraesCS5A01G110100 chr2B 81.597 288 35 4 4929 5203 1303527 1303809 7.050000e-54 222.0
19 TraesCS5A01G110100 chr3B 78.571 462 60 24 4952 5404 445251621 445252052 8.930000e-68 268.0
20 TraesCS5A01G110100 chr7B 75.038 665 117 34 4762 5409 484740132 484740764 4.160000e-66 263.0
21 TraesCS5A01G110100 chr7B 82.258 124 17 4 5290 5408 566050992 566050869 9.590000e-18 102.0
22 TraesCS5A01G110100 chr3D 78.667 450 54 17 4762 5197 343710718 343710297 1.490000e-65 261.0
23 TraesCS5A01G110100 chr2A 74.281 661 130 22 4762 5409 676991349 676991982 5.410000e-60 243.0
24 TraesCS5A01G110100 chr2A 71.219 681 125 49 4777 5407 714322085 714322744 7.410000e-19 106.0
25 TraesCS5A01G110100 chr2A 81.250 112 19 2 4762 4871 707177195 707177084 7.460000e-14 89.8
26 TraesCS5A01G110100 chr4A 84.530 181 24 2 5024 5204 447318385 447318561 5.570000e-40 176.0
27 TraesCS5A01G110100 chr1B 74.009 227 49 8 5194 5410 364908122 364908348 3.470000e-12 84.2


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 TraesCS5A01G110100 chr5A 207654739 207660148 5409 True 9991.0 9991 100.0000 1 5410 1 chr5A.!!$R2 5409
1 TraesCS5A01G110100 chr5A 139687836 139688446 610 True 457.0 457 80.6200 4762 5395 1 chr5A.!!$R1 633
2 TraesCS5A01G110100 chr5D 158165740 158170862 5122 True 4287.5 7926 94.4990 1 5043 2 chr5D.!!$R1 5042
3 TraesCS5A01G110100 chr5B 159711444 159717371 5927 False 3587.5 3958 95.8105 942 5409 2 chr5B.!!$F1 4467
4 TraesCS5A01G110100 chr5B 33614580 33615198 618 True 261.0 261 75.2270 4762 5409 1 chr5B.!!$R1 647
5 TraesCS5A01G110100 chr3A 27035791 27036452 661 True 496.0 496 80.6890 4762 5409 1 chr3A.!!$R2 647
6 TraesCS5A01G110100 chr3A 25537915 25538550 635 True 464.0 464 80.1830 4762 5408 1 chr3A.!!$R1 646
7 TraesCS5A01G110100 chr6B 206021509 206022122 613 False 425.0 425 79.9680 4762 5364 1 chr6B.!!$F2 602
8 TraesCS5A01G110100 chr6D 419441986 419442610 624 True 394.0 394 78.6360 4762 5409 1 chr6D.!!$R1 647
9 TraesCS5A01G110100 chr2B 444547897 444548510 613 True 296.0 296 76.4530 4762 5392 1 chr2B.!!$R1 630
10 TraesCS5A01G110100 chr7B 484740132 484740764 632 False 263.0 263 75.0380 4762 5409 1 chr7B.!!$F1 647
11 TraesCS5A01G110100 chr2A 676991349 676991982 633 False 243.0 243 74.2810 4762 5409 1 chr2A.!!$F1 647

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
745 749 0.107831 ACTTCTAGTGGTTTGCGGCA 59.892 50.000 0.00 0.0 0.00 5.69 F
757 761 2.437200 TTGCGGCATTTCCTTTTGAG 57.563 45.000 2.28 0.0 0.00 3.02 F
920 925 2.859404 TCTCCTCTCCATCCAAGGACTA 59.141 50.000 0.00 0.0 35.38 2.59 F
2149 2155 3.084786 GCAGAGCCTGTATCTGGTTTTT 58.915 45.455 5.22 0.0 43.61 1.94 F
3001 3009 3.366985 GGTGCAATACCTGGCTTACAAAC 60.367 47.826 0.00 0.0 46.51 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2628 2634 4.692625 ACTGATGTTGTTTCTGGATCTTCG 59.307 41.667 0.00 0.00 0.00 3.79 R
2952 2960 9.703892 ATACAAAAGATTCTTATGAGAGGATCG 57.296 33.333 0.00 0.00 42.67 3.69 R
3054 3062 1.661463 AAGGAGACCATGCAGGAGAA 58.339 50.000 0.00 0.00 41.22 2.87 R
3810 5319 0.886490 GTGTTCCTGCAGGGTGACAG 60.886 60.000 32.23 5.15 34.70 3.51 R
4968 6611 0.678395 TAACCGTGGTAGTTTGGCGA 59.322 50.000 0.00 0.00 0.00 5.54 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
196 197 7.663905 TGTTACTAACAAGTAATGCCATCAGTT 59.336 33.333 0.00 0.00 38.72 3.16
316 319 3.386726 GGGGTTTGGGTTTATGGCTTATC 59.613 47.826 0.00 0.00 0.00 1.75
334 337 5.751028 GCTTATCTGTTCGCTTCAGTTAGAT 59.249 40.000 0.00 0.00 34.86 1.98
426 429 9.388672 ACTGAGCCATAATAAATAGGGTTAGTA 57.611 33.333 5.33 0.00 43.68 1.82
496 499 8.320396 TGTATAGCTAGTAGTCTAATTGTCCG 57.680 38.462 0.00 0.00 0.00 4.79
497 500 7.935755 TGTATAGCTAGTAGTCTAATTGTCCGT 59.064 37.037 0.00 0.00 0.00 4.69
498 501 5.754543 AGCTAGTAGTCTAATTGTCCGTC 57.245 43.478 0.00 0.00 0.00 4.79
499 502 5.438833 AGCTAGTAGTCTAATTGTCCGTCT 58.561 41.667 0.00 0.00 0.00 4.18
508 511 8.307921 AGTCTAATTGTCCGTCTTCTTTTTAC 57.692 34.615 0.00 0.00 0.00 2.01
745 749 0.107831 ACTTCTAGTGGTTTGCGGCA 59.892 50.000 0.00 0.00 0.00 5.69
757 761 2.437200 TTGCGGCATTTCCTTTTGAG 57.563 45.000 2.28 0.00 0.00 3.02
920 925 2.859404 TCTCCTCTCCATCCAAGGACTA 59.141 50.000 0.00 0.00 35.38 2.59
1246 1252 7.587037 ATTTTCAAGGATTCAGTTTCTGTCA 57.413 32.000 0.00 0.00 32.61 3.58
1368 1374 7.601705 AAAAGTGGGAAAGATCATCTGAAAA 57.398 32.000 0.00 0.00 0.00 2.29
1372 1378 6.827762 AGTGGGAAAGATCATCTGAAAATCTC 59.172 38.462 0.00 0.00 0.00 2.75
1861 1867 6.127366 ACAAGGTGAACAACTGATTTGATTGT 60.127 34.615 0.00 0.00 38.73 2.71
2149 2155 3.084786 GCAGAGCCTGTATCTGGTTTTT 58.915 45.455 5.22 0.00 43.61 1.94
2628 2634 6.095021 ACCGAGGTATTTCTTATTTTGCCTTC 59.905 38.462 0.00 0.00 0.00 3.46
2679 2685 7.038799 ACCTTTCAGATTTTTATGCTGGTTGAT 60.039 33.333 0.00 0.00 0.00 2.57
2952 2960 5.350091 GCTCTTCAGAGTGATGTAAGTTTCC 59.650 44.000 5.72 0.00 43.85 3.13
3001 3009 3.366985 GGTGCAATACCTGGCTTACAAAC 60.367 47.826 0.00 0.00 46.51 2.93
3005 3013 4.703093 GCAATACCTGGCTTACAAACCTTA 59.297 41.667 0.00 0.00 0.00 2.69
3169 4678 6.156256 TGAATAGCTATCAGTGGTAAGTGGTT 59.844 38.462 6.72 0.00 0.00 3.67
3171 4680 7.857404 ATAGCTATCAGTGGTAAGTGGTTAT 57.143 36.000 0.00 0.00 0.00 1.89
3238 4747 7.147724 TGCATCTACCTGTAGTACTTTGCTTAT 60.148 37.037 0.00 0.00 34.84 1.73
3569 5078 7.035612 GGAAATGAAAATCATGTAACCAGTCC 58.964 38.462 0.00 0.00 37.15 3.85
3632 5141 6.127253 CCAGATTATTGCTTGAGTTCCCAATT 60.127 38.462 0.00 0.00 0.00 2.32
3633 5142 7.068593 CCAGATTATTGCTTGAGTTCCCAATTA 59.931 37.037 0.00 0.00 0.00 1.40
3810 5319 1.134371 GGAAGTACATCTGCCTGTCCC 60.134 57.143 0.00 0.00 38.84 4.46
4473 5982 1.338105 CGGATTTCAGAGGTGTCAGCA 60.338 52.381 4.59 0.00 0.00 4.41
4488 5997 2.029288 AGCACCACATTCGTCTGCG 61.029 57.895 0.00 0.00 32.99 5.18
4788 6383 1.418342 CGCAGGTACCCATTTCGTCG 61.418 60.000 8.74 0.00 0.00 5.12
4946 6589 1.362717 CACGTGTCCTCTCGGTGTT 59.637 57.895 7.58 0.00 35.30 3.32
4950 6593 1.901948 TGTCCTCTCGGTGTTCGCT 60.902 57.895 0.00 0.00 39.05 4.93
5008 6652 7.004691 GGTTAGCTTTATTAATGATGACCCCT 58.995 38.462 9.18 0.00 28.42 4.79
5269 6948 4.478371 CCATCAGCCGAGGCAGCA 62.478 66.667 17.18 0.00 44.88 4.41
5275 6954 4.819761 GCCGAGGCAGCACATCGA 62.820 66.667 14.24 0.00 41.49 3.59
5277 6956 2.125952 CGAGGCAGCACATCGACA 60.126 61.111 7.91 0.00 38.72 4.35
5286 6965 2.103373 AGCACATCGACATCCTAGTGT 58.897 47.619 0.00 0.00 34.39 3.55
5288 6967 3.316588 AGCACATCGACATCCTAGTGTAG 59.683 47.826 0.00 0.00 31.16 2.74
5346 7030 1.347097 CTCGACATGACACTGCCACG 61.347 60.000 0.00 0.00 0.00 4.94
5353 7037 1.227263 GACACTGCCACGTGACTGT 60.227 57.895 19.30 13.37 38.27 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 8.814448 TCTTCTATTAATATTGGAAGGGAGGT 57.186 34.615 16.81 0.00 35.49 3.85
180 181 4.202441 CCTAGCAACTGATGGCATTACTT 58.798 43.478 0.00 0.00 0.00 2.24
196 197 8.617809 GGTTAATATTGAATTTTCGACCTAGCA 58.382 33.333 0.00 0.00 0.00 3.49
426 429 7.708998 TGCTGGAAAAAGAACTTACGTAAATT 58.291 30.769 9.68 5.48 0.00 1.82
433 436 7.084486 CACCTATTGCTGGAAAAAGAACTTAC 58.916 38.462 0.00 0.00 0.00 2.34
496 499 8.617809 TGTTCCACATAACAGTAAAAAGAAGAC 58.382 33.333 0.00 0.00 34.50 3.01
497 500 8.740123 TGTTCCACATAACAGTAAAAAGAAGA 57.260 30.769 0.00 0.00 34.50 2.87
498 501 9.965824 AATGTTCCACATAACAGTAAAAAGAAG 57.034 29.630 0.00 0.00 42.33 2.85
499 502 9.743057 CAATGTTCCACATAACAGTAAAAAGAA 57.257 29.630 0.00 0.00 42.33 2.52
508 511 5.964958 AAGGTCAATGTTCCACATAACAG 57.035 39.130 0.00 0.00 42.33 3.16
622 625 7.665559 AGTTATCAGCTATGTTCTGTTCCAAAA 59.334 33.333 0.00 0.00 33.48 2.44
816 821 6.310149 AGATTTCACAGAAATGAAGTTCCCT 58.690 36.000 9.49 0.00 39.68 4.20
817 822 6.432472 AGAGATTTCACAGAAATGAAGTTCCC 59.568 38.462 9.49 0.00 39.68 3.97
833 838 7.398618 AGACCAGAACAGAAGATAGAGATTTCA 59.601 37.037 0.00 0.00 0.00 2.69
920 925 2.206322 TGGTGCCTACTCCCCATTAT 57.794 50.000 0.00 0.00 0.00 1.28
1368 1374 8.868522 TCTTAACCAAACAATGATTGAGAGAT 57.131 30.769 12.80 0.00 0.00 2.75
1372 1378 9.311916 TGTTTTCTTAACCAAACAATGATTGAG 57.688 29.630 12.80 1.44 39.40 3.02
2149 2155 5.652014 GGAAAGGTCATGTTCCATGTATTCA 59.348 40.000 7.72 0.00 42.51 2.57
2628 2634 4.692625 ACTGATGTTGTTTCTGGATCTTCG 59.307 41.667 0.00 0.00 0.00 3.79
2952 2960 9.703892 ATACAAAAGATTCTTATGAGAGGATCG 57.296 33.333 0.00 0.00 42.67 3.69
3001 3009 7.277174 ACACCAAAGAAAAGTCTGAATAAGG 57.723 36.000 0.00 0.00 33.05 2.69
3005 3013 5.105392 TGCAACACCAAAGAAAAGTCTGAAT 60.105 36.000 0.00 0.00 33.05 2.57
3054 3062 1.661463 AAGGAGACCATGCAGGAGAA 58.339 50.000 0.00 0.00 41.22 2.87
3169 4678 3.343941 AAACCGGCAGCAACTAAGATA 57.656 42.857 0.00 0.00 0.00 1.98
3171 4680 1.877443 GAAAACCGGCAGCAACTAAGA 59.123 47.619 0.00 0.00 0.00 2.10
3238 4747 5.073428 ACTACAGATCCTGAGATATTCGCA 58.927 41.667 0.45 0.00 35.18 5.10
3569 5078 1.211969 GCAGCACCATTGACAGCAG 59.788 57.895 0.00 0.00 0.00 4.24
3810 5319 0.886490 GTGTTCCTGCAGGGTGACAG 60.886 60.000 32.23 5.15 34.70 3.51
4318 5827 1.219469 TGTCCTCGATATTCCCTCCCA 59.781 52.381 0.00 0.00 0.00 4.37
4682 6277 9.668497 GATGAAACTTTAGGTTCAGGTACTATT 57.332 33.333 14.82 0.00 34.60 1.73
4699 6294 5.891551 AGTGTACCAAACCTTGATGAAACTT 59.108 36.000 0.00 0.00 0.00 2.66
4726 6321 6.699575 AAGCAAGAACGGCTCATAATTTAT 57.300 33.333 0.00 0.00 41.66 1.40
4727 6322 7.011109 GTCTAAGCAAGAACGGCTCATAATTTA 59.989 37.037 0.00 0.00 41.66 1.40
4728 6323 5.880332 TCTAAGCAAGAACGGCTCATAATTT 59.120 36.000 0.00 0.00 41.66 1.82
4968 6611 0.678395 TAACCGTGGTAGTTTGGCGA 59.322 50.000 0.00 0.00 0.00 5.54
4973 6616 8.671028 CATTAATAAAGCTAACCGTGGTAGTTT 58.329 33.333 0.00 0.00 0.00 2.66
5079 6738 0.872021 CGTCTGTAAGCGGATGAGCC 60.872 60.000 0.00 0.00 38.90 4.70
5080 6739 1.483424 GCGTCTGTAAGCGGATGAGC 61.483 60.000 0.30 0.00 38.90 4.26
5269 6948 3.288092 TGCTACACTAGGATGTCGATGT 58.712 45.455 0.00 0.00 33.85 3.06
5275 6954 0.747255 CGCCTGCTACACTAGGATGT 59.253 55.000 0.00 0.00 36.11 3.06
5277 6956 1.683917 CTTCGCCTGCTACACTAGGAT 59.316 52.381 0.00 0.00 36.11 3.24
5286 6965 2.047274 GTGCCACTTCGCCTGCTA 60.047 61.111 0.00 0.00 0.00 3.49
5288 6967 3.730761 CAGTGCCACTTCGCCTGC 61.731 66.667 0.00 0.00 0.00 4.85
5328 7011 1.372872 CGTGGCAGTGTCATGTCGA 60.373 57.895 8.86 0.00 0.00 4.20
5346 7030 0.824109 TCCGGATCCATGACAGTCAC 59.176 55.000 13.41 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.