Multiple sequence alignment - TraesCS6A01G301700

Loading Multiple Alignment...

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 TraesCS6A01G301700 chr6A 100.000 5307 0 0 1 5307 535148684 535143378 0.000000e+00 9801
1 TraesCS6A01G301700 chr6A 87.097 558 39 17 817 1345 74244596 74244043 7.600000e-168 601
2 TraesCS6A01G301700 chr6A 87.207 555 38 17 817 1342 498536821 498537371 7.600000e-168 601
3 TraesCS6A01G301700 chr6A 82.799 686 93 16 4629 5307 74242956 74242289 1.650000e-164 590
4 TraesCS6A01G301700 chr6A 82.774 685 93 16 4629 5306 498538461 498539127 5.920000e-164 588
5 TraesCS6A01G301700 chr4B 96.495 2739 71 13 2589 5307 662393126 662395859 0.000000e+00 4503
6 TraesCS6A01G301700 chr4B 97.236 977 26 1 1543 2518 662391994 662392970 0.000000e+00 1653
7 TraesCS6A01G301700 chr4D 94.698 2810 130 14 2512 5306 489788440 489785635 0.000000e+00 4346
8 TraesCS6A01G301700 chr4D 95.605 2207 91 4 313 2517 489790740 489788538 0.000000e+00 3533
9 TraesCS6A01G301700 chr4D 99.048 315 3 0 1 315 489792466 489792152 2.770000e-157 566
10 TraesCS6A01G301700 chr7A 95.489 2527 105 6 1 2521 112936664 112934141 0.000000e+00 4026
11 TraesCS6A01G301700 chr7A 99.085 2077 19 0 2270 4346 26782597 26780521 0.000000e+00 3731
12 TraesCS6A01G301700 chr7A 94.907 1767 77 8 2588 4345 112933989 112932227 0.000000e+00 2752
13 TraesCS6A01G301700 chr7A 96.828 725 22 1 4582 5306 26780525 26779802 0.000000e+00 1210
14 TraesCS6A01G301700 chr7A 83.140 688 94 17 4629 5307 112931335 112930661 4.540000e-170 608
15 TraesCS6A01G301700 chr7A 91.623 382 31 1 1082 1462 14180969 14180588 1.310000e-145 527
16 TraesCS6A01G301700 chr3B 93.203 2501 144 11 1 2477 493202431 493204929 0.000000e+00 3653
17 TraesCS6A01G301700 chr3B 94.204 1294 69 5 2588 3879 493204967 493206256 0.000000e+00 1969
18 TraesCS6A01G301700 chr3B 92.821 780 40 3 3878 4657 493271514 493272277 0.000000e+00 1116
19 TraesCS6A01G301700 chrUn 95.637 2246 67 14 2589 4813 77277372 77275137 0.000000e+00 3576
20 TraesCS6A01G301700 chrUn 97.339 977 25 1 1543 2518 77278504 77277528 0.000000e+00 1659
21 TraesCS6A01G301700 chr1B 95.706 2189 90 3 295 2480 639562416 639564603 0.000000e+00 3518
22 TraesCS6A01G301700 chr1B 93.408 1790 93 8 2613 4400 639564697 639566463 0.000000e+00 2628
23 TraesCS6A01G301700 chr3D 95.577 1967 85 2 121 2085 535432550 535434516 0.000000e+00 3149
24 TraesCS6A01G301700 chr3D 94.526 1425 62 11 2512 3923 535443712 535445133 0.000000e+00 2185
25 TraesCS6A01G301700 chr3D 93.565 1321 71 9 3998 5306 535445135 535446453 0.000000e+00 1956
26 TraesCS6A01G301700 chr3D 94.977 438 22 0 2081 2518 535443178 535443615 0.000000e+00 688
27 TraesCS6A01G301700 chr7B 92.308 1209 74 5 1280 2477 57838374 57839574 0.000000e+00 1700
28 TraesCS6A01G301700 chr7B 93.974 1062 61 2 2588 3648 57839612 57840671 0.000000e+00 1604
29 TraesCS6A01G301700 chr7B 95.412 959 44 0 5 963 57837375 57838333 0.000000e+00 1528
30 TraesCS6A01G301700 chr7B 95.305 639 27 2 3708 4346 57840686 57841321 0.000000e+00 1011
31 TraesCS6A01G301700 chr6B 98.753 802 8 1 4506 5307 91167647 91166848 0.000000e+00 1424
32 TraesCS6A01G301700 chr6B 87.207 555 38 17 817 1342 13855158 13855708 7.600000e-168 601
33 TraesCS6A01G301700 chr4A 89.967 897 79 9 3476 4368 661670267 661671156 0.000000e+00 1147
34 TraesCS6A01G301700 chr5B 82.920 685 96 13 4629 5306 596891518 596890848 9.840000e-167 597
35 TraesCS6A01G301700 chr7D 87.097 434 47 5 1082 1506 14872979 14872546 2.870000e-132 483
36 TraesCS6A01G301700 chr3A 85.128 195 24 5 4365 4558 22934682 22934492 1.510000e-45 195


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 TraesCS6A01G301700 chr6A 535143378 535148684 5306 True 9801.000000 9801 100.000000 1 5307 1 chr6A.!!$R1 5306
1 TraesCS6A01G301700 chr6A 74242289 74244596 2307 True 595.500000 601 84.948000 817 5307 2 chr6A.!!$R2 4490
2 TraesCS6A01G301700 chr6A 498536821 498539127 2306 False 594.500000 601 84.990500 817 5306 2 chr6A.!!$F1 4489
3 TraesCS6A01G301700 chr4B 662391994 662395859 3865 False 3078.000000 4503 96.865500 1543 5307 2 chr4B.!!$F1 3764
4 TraesCS6A01G301700 chr4D 489785635 489792466 6831 True 2815.000000 4346 96.450333 1 5306 3 chr4D.!!$R1 5305
5 TraesCS6A01G301700 chr7A 26779802 26782597 2795 True 2470.500000 3731 97.956500 2270 5306 2 chr7A.!!$R2 3036
6 TraesCS6A01G301700 chr7A 112930661 112936664 6003 True 2462.000000 4026 91.178667 1 5307 3 chr7A.!!$R3 5306
7 TraesCS6A01G301700 chr3B 493202431 493206256 3825 False 2811.000000 3653 93.703500 1 3879 2 chr3B.!!$F2 3878
8 TraesCS6A01G301700 chr3B 493271514 493272277 763 False 1116.000000 1116 92.821000 3878 4657 1 chr3B.!!$F1 779
9 TraesCS6A01G301700 chrUn 77275137 77278504 3367 True 2617.500000 3576 96.488000 1543 4813 2 chrUn.!!$R1 3270
10 TraesCS6A01G301700 chr1B 639562416 639566463 4047 False 3073.000000 3518 94.557000 295 4400 2 chr1B.!!$F1 4105
11 TraesCS6A01G301700 chr3D 535432550 535434516 1966 False 3149.000000 3149 95.577000 121 2085 1 chr3D.!!$F1 1964
12 TraesCS6A01G301700 chr3D 535443178 535446453 3275 False 1609.666667 2185 94.356000 2081 5306 3 chr3D.!!$F2 3225
13 TraesCS6A01G301700 chr7B 57837375 57841321 3946 False 1460.750000 1700 94.249750 5 4346 4 chr7B.!!$F1 4341
14 TraesCS6A01G301700 chr6B 91166848 91167647 799 True 1424.000000 1424 98.753000 4506 5307 1 chr6B.!!$R1 801
15 TraesCS6A01G301700 chr6B 13855158 13855708 550 False 601.000000 601 87.207000 817 1342 1 chr6B.!!$F1 525
16 TraesCS6A01G301700 chr4A 661670267 661671156 889 False 1147.000000 1147 89.967000 3476 4368 1 chr4A.!!$F1 892
17 TraesCS6A01G301700 chr5B 596890848 596891518 670 True 597.000000 597 82.920000 4629 5306 1 chr5B.!!$R1 677

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
806 2221 2.671070 CCTGATGCTGGGGTTCGT 59.329 61.111 0.00 0.0 0.00 3.85 F
1521 2968 4.437682 AGTGGTGAGGAAACTGAATCAA 57.562 40.909 0.00 0.0 44.43 2.57 F
3461 5082 1.005867 CTTGCGCCTGTGCCAAAAT 60.006 52.632 4.18 0.0 30.65 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 3478 4.750952 TGTGACAACTTGTTCGTTGAAA 57.249 36.364 10.29 0.0 45.4 2.69 R
3493 5115 4.220602 AGTGGTGTTTGAAATATTCCTGGC 59.779 41.667 0.00 0.0 0.0 4.85 R
5117 7509 3.380142 CATGTTTAAAACGCCAGCAAGT 58.620 40.909 0.00 0.0 0.0 3.16 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
268 269 3.097614 TCTCTGAACTAGCAGTAACCCC 58.902 50.000 0.00 0.00 37.20 4.95
453 1868 8.499162 GTGGAGATATTGCATTGACTATGTTAC 58.501 37.037 0.00 0.00 36.57 2.50
551 1966 3.921677 TCGGATGGTGAGAAAGTACAAC 58.078 45.455 0.00 0.00 0.00 3.32
728 2143 5.006165 CCGAATCACTGAAATAGTTGAGCTC 59.994 44.000 6.82 6.82 37.60 4.09
806 2221 2.671070 CCTGATGCTGGGGTTCGT 59.329 61.111 0.00 0.00 0.00 3.85
1020 2435 8.945195 AATTGATGGGCATGAAGAATATTAGA 57.055 30.769 0.00 0.00 0.00 2.10
1070 2503 9.986833 ATTGTTTTTGAACTAAATTTCAAGTGC 57.013 25.926 0.00 0.00 44.33 4.40
1080 2523 5.662211 AAATTTCAAGTGCTGTTGATTGC 57.338 34.783 2.66 0.00 36.34 3.56
1521 2968 4.437682 AGTGGTGAGGAAACTGAATCAA 57.562 40.909 0.00 0.00 44.43 2.57
1528 2975 6.207417 GGTGAGGAAACTGAATCAAAAGATGA 59.793 38.462 0.00 0.00 44.43 2.92
1540 2987 6.674694 ATCAAAAGATGAAGAAGATGACGG 57.325 37.500 0.00 0.00 42.54 4.79
1655 3102 4.759693 CAGGAGCAAACACATGGTTAGTTA 59.240 41.667 0.00 0.00 39.29 2.24
1965 3413 4.792068 AGAAAAGTTGTGGGATTCTGTCA 58.208 39.130 0.00 0.00 0.00 3.58
2026 3478 9.657419 ATCTTCAACAAACAAGTCATTTTCTTT 57.343 25.926 0.00 0.00 0.00 2.52
2067 3537 9.116067 TGTCACAACTGTATTTTATAATAGGCC 57.884 33.333 0.00 0.00 0.00 5.19
2792 4394 6.691754 TTCACTTGATACTGCTTTGTTCAA 57.308 33.333 0.00 0.00 0.00 2.69
3457 5078 3.772853 AAGTCTTGCGCCTGTGCCA 62.773 57.895 4.18 0.00 0.00 4.92
3461 5082 1.005867 CTTGCGCCTGTGCCAAAAT 60.006 52.632 4.18 0.00 30.65 1.82
4800 7186 8.230472 AGCTAGATGCAAATTATTAAGCTTGT 57.770 30.769 9.86 0.00 45.94 3.16
5117 7509 5.678583 TGTGGAAAAATGCCTCAAATTGAA 58.321 33.333 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.473162 TGTTTGAGTGAATATGGTTGGACAG 59.527 40.000 0.00 0.00 0.00 3.51
268 269 5.482006 TGTTGTCTACATGAACATGAGAGG 58.518 41.667 19.56 7.81 41.20 3.69
453 1868 7.254590 GGAAATCAATGATTGAACCTAGAGACG 60.255 40.741 12.36 0.00 43.95 4.18
551 1966 5.928839 AGTGCATCCATTTATAGAGTAAGCG 59.071 40.000 0.00 0.00 0.00 4.68
728 2143 4.685628 ACGCTGCCTTTGTTTGAATAATTG 59.314 37.500 0.00 0.00 0.00 2.32
806 2221 6.272324 CCTCAGTTATTCCATATGGGTCCTTA 59.728 42.308 21.78 0.00 38.11 2.69
846 2261 0.749091 TCATTGCCGCTGCTTAGCAT 60.749 50.000 7.58 0.00 38.13 3.79
937 2352 0.322187 AACCACAGCGTACCAATCCC 60.322 55.000 0.00 0.00 0.00 3.85
1020 2435 6.615617 TCAATAGCTCTCACCTAATCCTAGT 58.384 40.000 0.00 0.00 0.00 2.57
1104 2547 9.673454 GTACAATTCAAAACTCGGTTAGAAAAT 57.327 29.630 0.00 0.00 0.00 1.82
1236 2682 7.917505 GCATTCCATTTGAGGTAGATTAACTTG 59.082 37.037 0.00 0.00 0.00 3.16
1521 2968 5.152623 TCACCGTCATCTTCTTCATCTTT 57.847 39.130 0.00 0.00 0.00 2.52
1528 2975 3.244561 ACCATGTTCACCGTCATCTTCTT 60.245 43.478 0.00 0.00 0.00 2.52
1540 2987 5.437289 TTCAGTTTCATCACCATGTTCAC 57.563 39.130 0.00 0.00 0.00 3.18
1965 3413 7.886629 ATGTTAGATTGCATTGACATACCTT 57.113 32.000 0.00 0.00 0.00 3.50
2026 3478 4.750952 TGTGACAACTTGTTCGTTGAAA 57.249 36.364 10.29 0.00 45.40 2.69
2067 3537 9.681692 TTGTATGACTCATCAATGTTGAAAAAG 57.318 29.630 0.00 1.22 41.13 2.27
2262 3732 5.940470 CCATTGAGTACTCACCTTAGCTTTT 59.060 40.000 25.13 0.00 39.66 2.27
2792 4394 6.110033 TGCAAGCATGAATTTTATGAAGCAT 58.890 32.000 5.41 0.00 0.00 3.79
3461 5082 8.330466 TGTTTAGTTGTCTTTGTCTTCTTCAA 57.670 30.769 0.00 0.00 0.00 2.69
3493 5115 4.220602 AGTGGTGTTTGAAATATTCCTGGC 59.779 41.667 0.00 0.00 0.00 4.85
3698 5324 7.752686 GCTTTAGCTTTTCTATCAGTTTTCTGG 59.247 37.037 0.00 0.00 41.98 3.86
4793 7179 9.073475 TGATAAAACCACTATTACAACAAGCTT 57.927 29.630 0.00 0.00 0.00 3.74
5117 7509 3.380142 CATGTTTAAAACGCCAGCAAGT 58.620 40.909 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.