Multiple sequence alignment - TraesCS5A01G260200

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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 TraesCS5A01G260200 chr5A 100.000 2360 0 0 1 2360 474317684 474315325 0.000000e+00 4359.0
1 TraesCS5A01G260200 chr5A 98.578 1617 19 3 1 1615 474052260 474050646 0.000000e+00 2856.0
2 TraesCS5A01G260200 chr5A 98.603 1575 20 2 1 1574 474185737 474184164 0.000000e+00 2785.0
3 TraesCS5A01G260200 chr5A 99.015 711 7 0 1650 2360 474050381 474049671 0.000000e+00 1275.0
4 TraesCS5A01G260200 chr5A 99.015 711 7 0 1650 2360 474183842 474183132 0.000000e+00 1275.0
5 TraesCS5A01G260200 chr5A 97.326 187 4 1 1678 1863 364976820 364977006 1.360000e-82 316.0
6 TraesCS5A01G260200 chr5A 96.045 177 2 2 63 239 474379326 474379155 1.380000e-72 283.0
7 TraesCS5A01G260200 chr5D 95.543 920 33 4 684 1598 371270463 371271379 0.000000e+00 1465.0
8 TraesCS5A01G260200 chr5D 92.906 437 21 3 236 662 371269942 371270378 5.540000e-176 627.0
9 TraesCS5A01G260200 chr5D 95.413 109 5 0 1422 1530 371020405 371020297 8.670000e-40 174.0
10 TraesCS5A01G260200 chr5D 93.750 80 3 2 1 79 448259395 448259317 4.120000e-23 119.0
11 TraesCS5A01G260200 chrUn 94.934 533 22 4 1069 1598 272192250 272191720 0.000000e+00 830.0
12 TraesCS5A01G260200 chrUn 94.934 533 22 4 1069 1598 281137410 281136880 0.000000e+00 830.0
13 TraesCS5A01G260200 chrUn 92.874 435 19 6 239 662 272195357 272194924 2.580000e-174 621.0
14 TraesCS5A01G260200 chrUn 94.045 403 21 1 684 1083 272194839 272194437 2.010000e-170 608.0
15 TraesCS5A01G260200 chrUn 94.045 403 21 1 684 1083 281139999 281139597 2.010000e-170 608.0
16 TraesCS5A01G260200 chrUn 92.640 394 17 6 280 662 281140476 281140084 7.370000e-155 556.0
17 TraesCS5A01G260200 chr7A 96.078 510 17 2 1854 2360 111953243 111952734 0.000000e+00 828.0
18 TraesCS5A01G260200 chr7A 97.326 187 3 2 1678 1863 195395447 195395632 1.360000e-82 316.0
19 TraesCS5A01G260200 chr2D 95.155 516 21 3 1848 2360 437666591 437667105 0.000000e+00 811.0
20 TraesCS5A01G260200 chr2D 94.915 177 6 2 63 239 11799708 11799535 8.310000e-70 274.0
21 TraesCS5A01G260200 chr3D 94.971 517 22 3 1847 2360 501418388 501418903 0.000000e+00 808.0
22 TraesCS5A01G260200 chr3D 95.294 510 20 3 1854 2360 58425821 58425313 0.000000e+00 806.0
23 TraesCS5A01G260200 chr3D 95.161 124 3 2 116 239 512978092 512978212 2.390000e-45 193.0
24 TraesCS5A01G260200 chr3D 97.561 41 1 0 63 103 512978055 512978095 1.170000e-08 71.3
25 TraesCS5A01G260200 chr3A 95.098 510 20 4 1854 2360 609937499 609938006 0.000000e+00 798.0
26 TraesCS5A01G260200 chr3A 94.912 511 21 4 1854 2360 44269027 44269536 0.000000e+00 795.0
27 TraesCS5A01G260200 chr3A 93.782 193 8 4 1672 1863 54877559 54877748 1.070000e-73 287.0
28 TraesCS5A01G260200 chr3A 90.957 188 17 0 1677 1864 731029833 731029646 1.080000e-63 254.0
29 TraesCS5A01G260200 chr1D 94.706 510 23 3 1854 2360 363511556 363512064 0.000000e+00 789.0
30 TraesCS5A01G260200 chr1D 98.551 69 1 0 1 69 65410766 65410698 3.190000e-24 122.0
31 TraesCS5A01G260200 chr5B 94.929 493 24 1 1105 1597 440539684 440540175 0.000000e+00 771.0
32 TraesCS5A01G260200 chr5B 94.200 431 20 3 236 662 440516410 440516839 0.000000e+00 652.0
33 TraesCS5A01G260200 chr5B 93.968 431 21 3 236 662 440536078 440536507 0.000000e+00 647.0
34 TraesCS5A01G260200 chr5B 94.500 400 19 1 684 1080 440536592 440536991 4.310000e-172 614.0
35 TraesCS5A01G260200 chr5B 95.017 301 13 1 684 984 440516924 440517222 2.750000e-129 472.0
36 TraesCS5A01G260200 chr5B 84.091 88 11 3 820 905 324572089 324572175 5.410000e-12 82.4
37 TraesCS5A01G260200 chr6A 98.396 187 1 2 1678 1863 52151602 52151787 6.290000e-86 327.0
38 TraesCS5A01G260200 chr6A 90.909 88 5 3 1 86 575974287 575974373 5.330000e-22 115.0
39 TraesCS5A01G260200 chr4A 97.753 178 1 2 63 240 552889195 552889369 1.060000e-78 303.0
40 TraesCS5A01G260200 chr1B 97.753 178 0 2 63 240 228763920 228764093 1.060000e-78 303.0
41 TraesCS5A01G260200 chr1B 90.811 185 15 2 1678 1862 179681049 179680867 1.810000e-61 246.0
42 TraesCS5A01G260200 chr4D 95.266 169 7 1 1676 1843 54796716 54796548 1.390000e-67 267.0
43 TraesCS5A01G260200 chr4D 96.000 75 2 1 1 75 163814084 163814011 1.150000e-23 121.0
44 TraesCS5A01G260200 chr2A 98.571 70 1 0 1 70 83173295 83173226 8.860000e-25 124.0
45 TraesCS5A01G260200 chr1A 97.260 73 2 0 1 73 174947237 174947165 8.860000e-25 124.0
46 TraesCS5A01G260200 chr2B 97.222 72 2 0 1 72 452988767 452988838 3.190000e-24 122.0
47 TraesCS5A01G260200 chr2B 85.246 61 6 3 182 239 257926024 257926084 2.530000e-05 60.2
48 TraesCS5A01G260200 chr4B 75.974 154 32 5 807 958 552662528 552662378 9.050000e-10 75.0
49 TraesCS5A01G260200 chr6D 97.222 36 1 0 206 241 38806264 38806229 7.040000e-06 62.1


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 TraesCS5A01G260200 chr5A 474315325 474317684 2359 True 4359.000000 4359 100.000000 1 2360 1 chr5A.!!$R1 2359
1 TraesCS5A01G260200 chr5A 474049671 474052260 2589 True 2065.500000 2856 98.796500 1 2360 2 chr5A.!!$R3 2359
2 TraesCS5A01G260200 chr5A 474183132 474185737 2605 True 2030.000000 2785 98.809000 1 2360 2 chr5A.!!$R4 2359
3 TraesCS5A01G260200 chr5D 371269942 371271379 1437 False 1046.000000 1465 94.224500 236 1598 2 chr5D.!!$F1 1362
4 TraesCS5A01G260200 chrUn 272191720 272195357 3637 True 686.333333 830 93.951000 239 1598 3 chrUn.!!$R1 1359
5 TraesCS5A01G260200 chrUn 281136880 281140476 3596 True 664.666667 830 93.873000 280 1598 3 chrUn.!!$R2 1318
6 TraesCS5A01G260200 chr7A 111952734 111953243 509 True 828.000000 828 96.078000 1854 2360 1 chr7A.!!$R1 506
7 TraesCS5A01G260200 chr2D 437666591 437667105 514 False 811.000000 811 95.155000 1848 2360 1 chr2D.!!$F1 512
8 TraesCS5A01G260200 chr3D 501418388 501418903 515 False 808.000000 808 94.971000 1847 2360 1 chr3D.!!$F1 513
9 TraesCS5A01G260200 chr3D 58425313 58425821 508 True 806.000000 806 95.294000 1854 2360 1 chr3D.!!$R1 506
10 TraesCS5A01G260200 chr3A 609937499 609938006 507 False 798.000000 798 95.098000 1854 2360 1 chr3A.!!$F3 506
11 TraesCS5A01G260200 chr3A 44269027 44269536 509 False 795.000000 795 94.912000 1854 2360 1 chr3A.!!$F1 506
12 TraesCS5A01G260200 chr1D 363511556 363512064 508 False 789.000000 789 94.706000 1854 2360 1 chr1D.!!$F1 506
13 TraesCS5A01G260200 chr5B 440536078 440540175 4097 False 677.333333 771 94.465667 236 1597 3 chr5B.!!$F3 1361
14 TraesCS5A01G260200 chr5B 440516410 440517222 812 False 562.000000 652 94.608500 236 984 2 chr5B.!!$F2 748

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
634 652 0.976641 AAGAGATTCTGTGGCCACGA 59.023 50.0 30.07 25.24 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 5083 0.110869 CCCGTTTCCCCCACTTTACA 59.889 55.0 0.0 0.0 0.0 2.41 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
247 248 4.080687 GGCATTCGACTAGTACCCTCTAT 58.919 47.826 0.00 0.00 0.00 1.98
352 360 4.537751 TCCCAGGACACTATAGTCTTCAG 58.462 47.826 1.26 0.00 38.57 3.02
634 652 0.976641 AAGAGATTCTGTGGCCACGA 59.023 50.000 30.07 25.24 0.00 4.35
1067 1151 4.511082 CCCTAACAACATTTGGCAGTTTTG 59.489 41.667 0.00 0.00 34.12 2.44
1621 4403 2.697431 TTTGAATTTTCACGCGAGGG 57.303 45.000 15.93 1.17 36.83 4.30
1622 4404 0.878416 TTGAATTTTCACGCGAGGGG 59.122 50.000 15.93 0.00 36.83 4.79
1623 4405 0.958382 TGAATTTTCACGCGAGGGGG 60.958 55.000 15.93 0.00 33.12 5.40
1646 4428 3.916184 GGAGTTTCCCCCACCTGA 58.084 61.111 0.00 0.00 0.00 3.86
1647 4429 2.160646 GGAGTTTCCCCCACCTGAA 58.839 57.895 0.00 0.00 0.00 3.02
1648 4430 0.704664 GGAGTTTCCCCCACCTGAAT 59.295 55.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
247 248 3.198200 ACCAACAGCCCATACACGTATAA 59.802 43.478 0.00 0.00 0.00 0.98
324 325 5.375956 AGACTATAGTGTCCTGGGATTCCTA 59.624 44.000 10.90 0.00 37.66 2.94
352 360 3.786818 GCGCATGTAAATTCTCTGCAGAC 60.787 47.826 13.74 2.01 33.13 3.51
806 887 3.383698 TCCACTTAAAACCACAACCCA 57.616 42.857 0.00 0.00 0.00 4.51
1152 3931 1.421382 CAAAGGTTGCTTGATTGCGG 58.579 50.000 0.00 0.00 35.36 5.69
1630 4412 3.953542 ATATTCAGGTGGGGGAAACTC 57.046 47.619 0.00 0.00 0.00 3.01
1631 4413 5.073691 CAGATATATTCAGGTGGGGGAAACT 59.926 44.000 0.00 0.00 0.00 2.66
1632 4414 5.163088 ACAGATATATTCAGGTGGGGGAAAC 60.163 44.000 0.00 0.00 0.00 2.78
1633 4415 4.981647 ACAGATATATTCAGGTGGGGGAAA 59.018 41.667 0.00 0.00 0.00 3.13
1634 4416 4.577096 ACAGATATATTCAGGTGGGGGAA 58.423 43.478 0.00 0.00 0.00 3.97
1635 4417 4.228237 ACAGATATATTCAGGTGGGGGA 57.772 45.455 0.00 0.00 0.00 4.81
1636 4418 4.263506 GGAACAGATATATTCAGGTGGGGG 60.264 50.000 0.00 0.00 0.00 5.40
1637 4419 4.563580 CGGAACAGATATATTCAGGTGGGG 60.564 50.000 0.00 0.00 0.00 4.96
1638 4420 4.569943 CGGAACAGATATATTCAGGTGGG 58.430 47.826 0.00 0.00 0.00 4.61
1639 4421 3.997021 GCGGAACAGATATATTCAGGTGG 59.003 47.826 0.00 0.00 0.00 4.61
1640 4422 4.631131 TGCGGAACAGATATATTCAGGTG 58.369 43.478 0.00 0.00 0.00 4.00
1641 4423 4.955811 TGCGGAACAGATATATTCAGGT 57.044 40.909 0.00 0.00 0.00 4.00
1642 4424 5.300752 AGTTGCGGAACAGATATATTCAGG 58.699 41.667 22.29 0.00 34.17 3.86
1643 4425 5.406780 GGAGTTGCGGAACAGATATATTCAG 59.593 44.000 22.29 0.00 34.17 3.02
1644 4426 5.297547 GGAGTTGCGGAACAGATATATTCA 58.702 41.667 22.29 0.00 34.17 2.57
1645 4427 4.386049 CGGAGTTGCGGAACAGATATATTC 59.614 45.833 22.29 7.64 34.17 1.75
1646 4428 4.307432 CGGAGTTGCGGAACAGATATATT 58.693 43.478 22.29 0.00 34.17 1.28
1647 4429 3.861131 GCGGAGTTGCGGAACAGATATAT 60.861 47.826 22.29 0.00 34.17 0.86
1648 4430 2.545113 GCGGAGTTGCGGAACAGATATA 60.545 50.000 22.29 0.00 34.17 0.86
1778 4805 2.264813 CCAAAGCCAGCAAAATCATCG 58.735 47.619 0.00 0.00 0.00 3.84
2054 5083 0.110869 CCCGTTTCCCCCACTTTACA 59.889 55.000 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.