Multiple sequence alignment - TraesCS3A01G479000

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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 TraesCS3A01G479000 chr3A 100.000 3758 0 0 1 3758 710837449 710841206 0.000000e+00 6940
1 TraesCS3A01G479000 chr3A 83.806 2785 391 33 1 2748 711057155 711059916 0.000000e+00 2590
2 TraesCS3A01G479000 chr3A 83.248 2340 341 29 477 2779 710937207 710939532 0.000000e+00 2102
3 TraesCS3A01G479000 chr3A 88.247 485 53 1 1 485 710936040 710936520 9.050000e-161 577
4 TraesCS3A01G479000 chr3A 89.573 211 21 1 3476 3686 710952407 710952616 2.230000e-67 267
5 TraesCS3A01G479000 chr3D 95.613 3260 121 5 1 3244 574782424 574779171 0.000000e+00 5208
6 TraesCS3A01G479000 chr3D 89.121 1820 179 8 792 2593 575479921 575481739 0.000000e+00 2246
7 TraesCS3A01G479000 chr3D 83.351 1874 280 18 743 2589 575527340 575529208 0.000000e+00 1703
8 TraesCS3A01G479000 chr3D 81.894 2027 326 28 769 2763 575546577 575548594 0.000000e+00 1672
9 TraesCS3A01G479000 chr3D 81.250 2032 346 23 743 2746 574770175 574768151 0.000000e+00 1609
10 TraesCS3A01G479000 chr3D 81.250 2032 346 23 743 2746 575488002 575490026 0.000000e+00 1609
11 TraesCS3A01G479000 chr3D 90.394 812 56 15 2950 3755 575481724 575482519 0.000000e+00 1048
12 TraesCS3A01G479000 chr3D 93.548 589 32 3 3136 3723 574779083 574778500 0.000000e+00 872
13 TraesCS3A01G479000 chr3D 78.764 777 128 25 1 768 575479101 575479849 1.570000e-133 486
14 TraesCS3A01G479000 chr3D 88.060 67 2 5 3132 3193 575529973 575530038 1.450000e-09 75
15 TraesCS3A01G479000 chr3B 92.715 2471 139 17 678 3131 765549080 765551526 0.000000e+00 3528
16 TraesCS3A01G479000 chr3B 83.362 2302 340 22 477 2748 765669983 765672271 0.000000e+00 2089
17 TraesCS3A01G479000 chr3B 82.965 2307 340 36 477 2749 765623269 765625556 0.000000e+00 2034
18 TraesCS3A01G479000 chr3B 82.129 2020 302 33 477 2467 765658031 765660020 0.000000e+00 1676
19 TraesCS3A01G479000 chr3B 81.237 1940 307 34 842 2738 765854958 765856883 0.000000e+00 1513
20 TraesCS3A01G479000 chr3B 94.822 676 30 2 1 676 765548354 765549024 0.000000e+00 1050
21 TraesCS3A01G479000 chr3B 90.432 648 38 11 3128 3758 765551559 765552199 0.000000e+00 832
22 TraesCS3A01G479000 chr3B 80.715 1063 172 27 1613 2651 765676761 765677814 0.000000e+00 797
23 TraesCS3A01G479000 chr3B 90.947 486 39 2 1 486 765668644 765669124 0.000000e+00 649
24 TraesCS3A01G479000 chr3B 90.397 479 41 4 1 479 765622394 765622867 3.190000e-175 625
25 TraesCS3A01G479000 chr3B 92.476 412 30 1 1 412 765657178 765657588 4.180000e-164 588
26 TraesCS3A01G479000 chr3B 81.221 639 105 11 1 631 765854133 765854764 5.600000e-138 501
27 TraesCS3A01G479000 chr3B 80.000 490 57 21 3165 3647 765678113 765678568 1.300000e-84 324
28 TraesCS3A01G479000 chr3B 79.133 369 35 23 3335 3686 765857613 765857956 2.270000e-52 217
29 TraesCS3A01G479000 chr3B 81.100 291 36 9 3154 3435 765599796 765600076 8.180000e-52 215
30 TraesCS3A01G479000 chr3B 87.742 155 19 0 3493 3647 765601599 765601753 8.290000e-42 182


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 TraesCS3A01G479000 chr3A 710837449 710841206 3757 False 6940.000000 6940 100.000000 1 3758 1 chr3A.!!$F1 3757
1 TraesCS3A01G479000 chr3A 711057155 711059916 2761 False 2590.000000 2590 83.806000 1 2748 1 chr3A.!!$F3 2747
2 TraesCS3A01G479000 chr3A 710936040 710939532 3492 False 1339.500000 2102 85.747500 1 2779 2 chr3A.!!$F4 2778
3 TraesCS3A01G479000 chr3D 574778500 574782424 3924 True 3040.000000 5208 94.580500 1 3723 2 chr3D.!!$R2 3722
4 TraesCS3A01G479000 chr3D 575546577 575548594 2017 False 1672.000000 1672 81.894000 769 2763 1 chr3D.!!$F2 1994
5 TraesCS3A01G479000 chr3D 574768151 574770175 2024 True 1609.000000 1609 81.250000 743 2746 1 chr3D.!!$R1 2003
6 TraesCS3A01G479000 chr3D 575488002 575490026 2024 False 1609.000000 1609 81.250000 743 2746 1 chr3D.!!$F1 2003
7 TraesCS3A01G479000 chr3D 575479101 575482519 3418 False 1260.000000 2246 86.093000 1 3755 3 chr3D.!!$F3 3754
8 TraesCS3A01G479000 chr3D 575527340 575530038 2698 False 889.000000 1703 85.705500 743 3193 2 chr3D.!!$F4 2450
9 TraesCS3A01G479000 chr3B 765548354 765552199 3845 False 1803.333333 3528 92.656333 1 3758 3 chr3B.!!$F1 3757
10 TraesCS3A01G479000 chr3B 765668644 765672271 3627 False 1369.000000 2089 87.154500 1 2748 2 chr3B.!!$F5 2747
11 TraesCS3A01G479000 chr3B 765622394 765625556 3162 False 1329.500000 2034 86.681000 1 2749 2 chr3B.!!$F3 2748
12 TraesCS3A01G479000 chr3B 765657178 765660020 2842 False 1132.000000 1676 87.302500 1 2467 2 chr3B.!!$F4 2466
13 TraesCS3A01G479000 chr3B 765854133 765857956 3823 False 743.666667 1513 80.530333 1 3686 3 chr3B.!!$F7 3685
14 TraesCS3A01G479000 chr3B 765676761 765678568 1807 False 560.500000 797 80.357500 1613 3647 2 chr3B.!!$F6 2034

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
954 2327 1.647346 TTACGACAACCCGCATCATC 58.353 50.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2928 4569 0.389948 CTCTCGCCGCCTAAAACTGT 60.39 55.0 0.0 0.0 0.0 3.55 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
338 339 4.053983 AGTATGCACGCAATCATAGTGAG 58.946 43.478 0.00 0.00 38.06 3.51
360 361 5.206587 AGGAATGGGAAGAAAATCATCTGG 58.793 41.667 0.00 0.00 0.00 3.86
503 1707 7.263100 TGCATCTTGATACCATATTGTTGAC 57.737 36.000 0.00 0.00 0.00 3.18
509 1713 9.952030 TCTTGATACCATATTGTTGACTTACAA 57.048 29.630 0.00 0.00 41.81 2.41
683 1985 7.938140 AGTTGCACATAAGTTATGGTATGTT 57.062 32.000 23.49 2.27 38.57 2.71
885 2258 5.660864 TGACATATGGGATACAGAAGTGTGA 59.339 40.000 7.80 0.00 37.52 3.58
954 2327 1.647346 TTACGACAACCCGCATCATC 58.353 50.000 0.00 0.00 0.00 2.92
1954 3349 0.671781 AAGACGTCTGATGTGCCTGC 60.672 55.000 20.85 0.00 0.00 4.85
2000 3395 3.641906 CCGTCTGGGATAAGTAATCTGGT 59.358 47.826 0.00 0.00 38.47 4.00
2029 3428 5.939764 AGAAGTGCTAGGTACAATGATGA 57.060 39.130 0.00 0.00 0.00 2.92
2232 3646 0.622665 AAGATTGGGTGCCTCCTCTG 59.377 55.000 0.00 0.00 36.25 3.35
2286 3706 1.064758 AGTTGGTTCAAGACACTGCCA 60.065 47.619 0.00 0.00 0.00 4.92
2299 3719 2.956333 ACACTGCCATCATGGATCAATG 59.044 45.455 8.30 3.40 40.96 2.82
2617 4127 4.681025 GTGAAAACATCGATTTGTGCATGT 59.319 37.500 0.00 0.00 0.00 3.21
2928 4569 8.215050 TGTTTAATTCCTCTCCACTTCTTTGTA 58.785 33.333 0.00 0.00 0.00 2.41
2935 4576 5.823045 CCTCTCCACTTCTTTGTACAGTTTT 59.177 40.000 0.00 0.00 0.00 2.43
2943 4584 1.149987 TTGTACAGTTTTAGGCGGCG 58.850 50.000 0.51 0.51 0.00 6.46
2967 4627 2.000447 GTGCTAGGTCGATTCACCAAC 59.000 52.381 0.00 0.00 39.16 3.77
2972 4632 3.771577 AGGTCGATTCACCAACTCTTT 57.228 42.857 0.00 0.00 39.16 2.52
3055 4742 2.950781 AGCTAGGTCGATTGATCTGGA 58.049 47.619 10.69 0.00 35.96 3.86
3107 4808 6.702329 ACTACTTCTACTTATGCAGCAAAGT 58.298 36.000 20.00 20.00 39.25 2.66
3189 5165 5.048083 TGTTTCTATTGGATGAAACCTGTGC 60.048 40.000 13.63 0.00 46.58 4.57
3233 5210 5.781210 TTTGACTGAACCATTTGTATGCA 57.219 34.783 0.00 0.00 0.00 3.96
3289 5274 2.738147 CAGTATATGCTACGCGCCC 58.262 57.895 5.73 0.00 38.05 6.13
3407 5456 5.292765 AGATCACATATAAAGTGCTCCACG 58.707 41.667 0.00 0.00 39.64 4.94
3461 5511 5.857471 AGTACAAATACGTGCCCTGTATA 57.143 39.130 0.00 0.00 36.33 1.47
3487 5537 3.007635 CCCTTTTCGTAGTTGGATGGAC 58.992 50.000 0.00 0.00 0.00 4.02
3523 5573 3.053693 TCTGTAACATTTAGCTGGGCCAT 60.054 43.478 6.72 0.00 0.00 4.40
3525 5575 3.446873 TGTAACATTTAGCTGGGCCATTG 59.553 43.478 6.72 0.00 0.00 2.82
3679 5751 0.103390 TCCGTCTTCGTTCTGCAACA 59.897 50.000 0.00 0.00 35.01 3.33
3686 5758 3.742882 TCTTCGTTCTGCAACAAGATGAG 59.257 43.478 0.00 0.00 30.85 2.90
3723 5795 7.421087 ACTCTTCTAACTTTATACAGGGGAC 57.579 40.000 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
338 339 4.958581 ACCAGATGATTTTCTTCCCATTCC 59.041 41.667 0.00 0.00 0.00 3.01
503 1707 6.704512 ACGCCAAAAGCATAAAATTGTAAG 57.295 33.333 0.00 0.00 44.04 2.34
509 1713 7.548780 ACATCATTTACGCCAAAAGCATAAAAT 59.451 29.630 0.00 0.00 41.95 1.82
683 1985 6.627087 ATTCTGAGACCTAGATTTCCACAA 57.373 37.500 0.00 0.00 0.00 3.33
885 2258 5.863935 GGAGAAAGCGCACTTGATTAATTTT 59.136 36.000 11.47 0.00 35.85 1.82
1019 2392 8.846943 TTTATAGAAGAGCATTCTTGACACAA 57.153 30.769 9.20 0.00 43.63 3.33
1054 2427 3.652869 TCTTGAGGACACCCTTTCTCATT 59.347 43.478 0.00 0.00 44.53 2.57
1421 2797 5.472137 TCATTGAAGTAGTTGTTACCAAGCC 59.528 40.000 0.00 0.00 32.37 4.35
1566 2948 2.327568 GTGCCATCCAAAATTGTGACG 58.672 47.619 0.00 0.00 0.00 4.35
1954 3349 6.348295 GGCAGCTTCATATGATAGTCAACATG 60.348 42.308 6.17 0.00 0.00 3.21
2029 3428 3.256631 GCATTGAGGTCCTTGTCAAACAT 59.743 43.478 0.00 0.00 36.31 2.71
2232 3646 1.739067 AAGCCAATCTACGGAGTTGC 58.261 50.000 0.00 0.00 37.78 4.17
2286 3706 3.190744 GCGATGAAGCATTGATCCATGAT 59.809 43.478 10.85 0.99 35.13 2.45
2299 3719 2.200899 GAGGAGAGAAAGCGATGAAGC 58.799 52.381 0.00 0.00 37.41 3.86
2617 4127 2.538141 CCAAGGAAGGGAGGTGGCA 61.538 63.158 0.00 0.00 0.00 4.92
2718 4241 1.151587 ATGGTTGGGGTGGTCCTCT 60.152 57.895 0.00 0.00 34.72 3.69
2928 4569 0.389948 CTCTCGCCGCCTAAAACTGT 60.390 55.000 0.00 0.00 0.00 3.55
2935 4576 2.124445 TAGCACTCTCGCCGCCTA 60.124 61.111 0.00 0.00 0.00 3.93
2943 4584 2.223618 GGTGAATCGACCTAGCACTCTC 60.224 54.545 0.00 0.00 32.69 3.20
2967 4627 5.236047 GCATAATACCTGCTGAGTGAAAGAG 59.764 44.000 0.00 0.00 36.68 2.85
3100 4801 9.448438 TCACATATGTAATCTTGTAACTTTGCT 57.552 29.630 8.32 0.00 0.00 3.91
3189 5165 9.243637 TCAAATGTTCCGAACAGAAAATAAAAG 57.756 29.630 18.46 1.64 45.95 2.27
3233 5210 0.606130 TGTGGATCGTGCAAGCACAT 60.606 50.000 23.23 15.53 46.47 3.21
3281 5266 0.459585 GAACTTCAGATGGGCGCGTA 60.460 55.000 8.43 0.00 0.00 4.42
3289 5274 4.674623 GCAGATTTGCTGGAACTTCAGATG 60.675 45.833 0.00 0.00 46.95 2.90
3407 5456 5.567138 AGTGGATTGCTTGCTAATGTAAC 57.433 39.130 0.00 0.00 0.00 2.50
3449 5499 0.884704 GGGCACATATACAGGGCACG 60.885 60.000 3.90 0.00 0.00 5.34
3461 5511 2.159382 CCAACTACGAAAAGGGCACAT 58.841 47.619 0.00 0.00 0.00 3.21
3679 5751 2.749621 GTCGGTTGATTTGCCTCATCTT 59.250 45.455 0.00 0.00 0.00 2.40
3686 5758 2.427506 AGAAGAGTCGGTTGATTTGCC 58.572 47.619 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.