Multiple sequence alignment - TraesCS6A01G043400

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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 TraesCS6A01G043400 chr6A 100.000 4005 0 0 1 4005 22698206 22694202 0.000000e+00 7396.0
1 TraesCS6A01G043400 chr6A 88.057 988 86 10 1793 2750 22804441 22803456 0.000000e+00 1142.0
2 TraesCS6A01G043400 chr6A 86.631 187 16 3 2927 3110 23332045 23331865 8.780000e-47 198.0
3 TraesCS6A01G043400 chr6A 81.600 250 28 6 1256 1487 22805364 22805115 1.470000e-44 191.0
4 TraesCS6A01G043400 chr6A 77.833 203 30 8 2757 2950 22803392 22803196 1.180000e-20 111.0
5 TraesCS6A01G043400 chr6A 83.495 103 12 2 3736 3834 23332373 23332272 1.530000e-14 91.6
6 TraesCS6A01G043400 chr6A 78.723 141 20 7 3452 3591 23331496 23331365 7.130000e-13 86.1
7 TraesCS6A01G043400 chr6A 87.273 55 5 2 3688 3740 23428738 23428792 1.200000e-05 62.1
8 TraesCS6A01G043400 chr6A 100.000 29 0 0 3712 3740 23259556 23259528 2.000000e-03 54.7
9 TraesCS6A01G043400 chr6B 90.402 3032 178 35 932 3871 39199946 39196936 0.000000e+00 3882.0
10 TraesCS6A01G043400 chr6B 86.842 1026 91 17 1764 2747 39339895 39338872 0.000000e+00 1107.0
11 TraesCS6A01G043400 chr6B 88.430 847 78 10 1 828 39200826 39199981 0.000000e+00 1003.0
12 TraesCS6A01G043400 chr6B 83.777 376 56 4 1062 1433 336900624 336900250 6.370000e-93 351.0
13 TraesCS6A01G043400 chr6B 81.236 453 67 9 137 576 39212695 39212248 2.290000e-92 350.0
14 TraesCS6A01G043400 chr6B 98.261 115 2 0 3891 4005 39196606 39196492 6.790000e-48 202.0
15 TraesCS6A01G043400 chr6B 89.333 150 14 1 1256 1405 39340501 39340354 1.900000e-43 187.0
16 TraesCS6A01G043400 chr6B 87.500 96 8 3 1571 1664 39340030 39339937 1.520000e-19 108.0
17 TraesCS6A01G043400 chr6B 95.833 48 2 0 1495 1542 336892489 336892442 1.190000e-10 78.7
18 TraesCS6A01G043400 chr6B 100.000 39 0 0 3862 3900 39196658 39196620 5.550000e-09 73.1
19 TraesCS6A01G043400 chr6B 84.722 72 9 2 2900 2970 39197823 39197753 2.000000e-08 71.3
20 TraesCS6A01G043400 chr6B 85.965 57 2 5 3690 3740 40592715 40592771 5.590000e-04 56.5
21 TraesCS6A01G043400 chr6D 92.335 2544 78 27 1539 3991 24231635 24229118 0.000000e+00 3509.0
22 TraesCS6A01G043400 chr6D 88.107 1051 79 15 480 1492 24232800 24231758 0.000000e+00 1206.0
23 TraesCS6A01G043400 chr6D 87.610 1025 84 19 1766 2750 24262722 24261701 0.000000e+00 1149.0
24 TraesCS6A01G043400 chr6D 83.553 304 31 5 1 286 24233100 24232798 2.370000e-67 267.0
25 TraesCS6A01G043400 chr6D 88.205 195 14 3 2907 3098 24892876 24893064 1.450000e-54 224.0
26 TraesCS6A01G043400 chr3D 88.616 571 65 0 1793 2363 459468762 459468192 0.000000e+00 695.0
27 TraesCS6A01G043400 chr3D 79.327 416 47 20 2572 2975 459467950 459467562 5.140000e-64 255.0
28 TraesCS6A01G043400 chr3D 85.792 183 18 5 2982 3161 459467653 459467476 1.900000e-43 187.0
29 TraesCS6A01G043400 chr3D 94.872 39 2 0 2497 2535 459468001 459467963 1.200000e-05 62.1
30 TraesCS6A01G043400 chr3D 91.304 46 3 1 3696 3740 598715360 598715315 1.200000e-05 62.1
31 TraesCS6A01G043400 chr3D 94.444 36 1 1 2642 2676 459468070 459468035 2.000000e-03 54.7
32 TraesCS6A01G043400 chr3B 88.636 572 63 2 1793 2363 607385473 607384903 0.000000e+00 695.0
33 TraesCS6A01G043400 chr3B 80.288 416 41 17 2572 2975 607384661 607384275 3.940000e-70 276.0
34 TraesCS6A01G043400 chr3B 79.387 359 48 17 2977 3320 607384371 607384024 3.110000e-56 230.0
35 TraesCS6A01G043400 chr3B 85.976 164 14 5 1258 1412 530702718 530702555 2.480000e-37 167.0
36 TraesCS6A01G043400 chr3B 94.872 39 2 0 2497 2535 607384712 607384674 1.200000e-05 62.1
37 TraesCS6A01G043400 chr3A 88.112 572 67 1 1793 2363 601555434 601556005 0.000000e+00 678.0
38 TraesCS6A01G043400 chr3A 79.327 416 45 17 2572 2975 601556247 601556633 1.850000e-63 254.0
39 TraesCS6A01G043400 chr3A 79.552 357 45 16 2977 3317 601556537 601556881 3.110000e-56 230.0
40 TraesCS6A01G043400 chr3A 89.796 98 10 0 2362 2459 601556031 601556128 4.200000e-25 126.0
41 TraesCS6A01G043400 chr3A 94.872 39 2 0 2497 2535 601556196 601556234 1.200000e-05 62.1
42 TraesCS6A01G043400 chr3A 94.444 36 1 1 2642 2676 601556127 601556162 2.000000e-03 54.7
43 TraesCS6A01G043400 chr5B 83.429 694 92 12 1794 2466 166167978 166167287 1.220000e-174 623.0
44 TraesCS6A01G043400 chr5B 83.285 694 93 12 1794 2466 165776643 165775952 5.690000e-173 617.0
45 TraesCS6A01G043400 chr5B 85.714 161 14 5 1258 1409 205585252 205585412 1.150000e-35 161.0
46 TraesCS6A01G043400 chr4A 90.753 292 27 0 1077 1368 696691183 696691474 1.350000e-104 390.0
47 TraesCS6A01G043400 chr4A 90.690 290 27 0 1079 1368 696667135 696667424 1.750000e-103 387.0
48 TraesCS6A01G043400 chr4A 89.726 292 30 0 1077 1368 696647196 696647487 1.360000e-99 374.0
49 TraesCS6A01G043400 chr4A 90.741 162 14 1 1539 1700 696668200 696668360 8.720000e-52 215.0
50 TraesCS6A01G043400 chr4A 90.741 162 14 1 1539 1700 696692250 696692410 8.720000e-52 215.0
51 TraesCS6A01G043400 chr4A 89.222 167 17 1 1539 1705 696648262 696648427 1.460000e-49 207.0
52 TraesCS6A01G043400 chr4A 94.444 36 1 1 1713 1747 623967084 623967119 2.000000e-03 54.7
53 TraesCS6A01G043400 chr2B 80.156 257 28 9 1256 1491 693801753 693802007 1.910000e-38 171.0
54 TraesCS6A01G043400 chr2B 88.889 54 3 2 3688 3740 681409052 681409103 3.340000e-06 63.9
55 TraesCS6A01G043400 chr2A 77.778 342 32 20 1258 1561 425814005 425813670 1.910000e-38 171.0
56 TraesCS6A01G043400 chr1B 91.667 96 6 2 1614 1708 179580982 179580888 9.030000e-27 132.0
57 TraesCS6A01G043400 chr4D 91.667 72 6 0 2942 3013 381837081 381837152 2.550000e-17 100.0
58 TraesCS6A01G043400 chr4D 92.157 51 1 2 1715 1765 281208858 281208905 7.180000e-08 69.4
59 TraesCS6A01G043400 chr7D 94.872 39 1 1 1668 1705 109922142 109922180 4.320000e-05 60.2
60 TraesCS6A01G043400 chr7D 90.476 42 3 1 1668 1708 60105568 60105527 2.000000e-03 54.7
61 TraesCS6A01G043400 chr1D 90.476 42 4 0 3699 3740 392570488 392570529 5.590000e-04 56.5
62 TraesCS6A01G043400 chr1A 86.538 52 2 3 3689 3740 492801638 492801592 7.000000e-03 52.8


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 TraesCS6A01G043400 chr6A 22694202 22698206 4004 True 7396.000000 7396 100.000000 1 4005 1 chr6A.!!$R1 4004
1 TraesCS6A01G043400 chr6A 22803196 22805364 2168 True 481.333333 1142 82.496667 1256 2950 3 chr6A.!!$R3 1694
2 TraesCS6A01G043400 chr6B 39196492 39200826 4334 True 1046.280000 3882 92.363000 1 4005 5 chr6B.!!$R4 4004
3 TraesCS6A01G043400 chr6B 39338872 39340501 1629 True 467.333333 1107 87.891667 1256 2747 3 chr6B.!!$R5 1491
4 TraesCS6A01G043400 chr6D 24229118 24233100 3982 True 1660.666667 3509 87.998333 1 3991 3 chr6D.!!$R2 3990
5 TraesCS6A01G043400 chr6D 24261701 24262722 1021 True 1149.000000 1149 87.610000 1766 2750 1 chr6D.!!$R1 984
6 TraesCS6A01G043400 chr3D 459467476 459468762 1286 True 250.760000 695 88.610200 1793 3161 5 chr3D.!!$R2 1368
7 TraesCS6A01G043400 chr3B 607384024 607385473 1449 True 315.775000 695 85.795750 1793 3320 4 chr3B.!!$R2 1527
8 TraesCS6A01G043400 chr3A 601555434 601556881 1447 False 234.133333 678 87.683833 1793 3317 6 chr3A.!!$F1 1524
9 TraesCS6A01G043400 chr5B 166167287 166167978 691 True 623.000000 623 83.429000 1794 2466 1 chr5B.!!$R2 672
10 TraesCS6A01G043400 chr5B 165775952 165776643 691 True 617.000000 617 83.285000 1794 2466 1 chr5B.!!$R1 672
11 TraesCS6A01G043400 chr4A 696691183 696692410 1227 False 302.500000 390 90.747000 1077 1700 2 chr4A.!!$F4 623
12 TraesCS6A01G043400 chr4A 696667135 696668360 1225 False 301.000000 387 90.715500 1079 1700 2 chr4A.!!$F3 621
13 TraesCS6A01G043400 chr4A 696647196 696648427 1231 False 290.500000 374 89.474000 1077 1705 2 chr4A.!!$F2 628


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
246 266 0.035725 CTGGCATGTTCTGGAGCTGA 60.036 55.000 0.00 0.0 0.0 4.26 F
530 550 0.107410 ACAGTGTTCCAACGGCTTGA 60.107 50.000 0.00 0.0 0.0 3.02 F
840 862 0.165944 CGTTGTTTGGGTCGAGCATC 59.834 55.000 17.59 0.0 0.0 3.91 F
1971 3054 1.004758 TCATGGAGGGGAGGAAGGG 59.995 63.158 0.00 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 2881 0.859232 ACTTTCACAGCTACAACGCG 59.141 50.000 3.53 3.53 34.4 6.01 R
2405 3560 0.738389 AGGTTGTTTGACTGTTGGCG 59.262 50.000 0.00 0.00 0.0 5.69 R
2867 4153 8.981659 TGTCTAGGAGAAGAATTTGATATGACA 58.018 33.333 0.00 0.00 0.0 3.58 R
3443 4774 1.270826 TCAGAGAAGAGAGGTGCGTTG 59.729 52.381 0.00 0.00 0.0 4.10 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)



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AutoCloner maintained by Alex Coulton.