Multiple sequence alignment - TraesCS1A01G337000

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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 TraesCS1A01G337000 chr1A 100.000 2414 0 0 1 2414 525145014 525142601 0.000000e+00 4458.0
1 TraesCS1A01G337000 chr1A 96.169 1279 47 2 1 1278 523379464 523378187 0.000000e+00 2089.0
2 TraesCS1A01G337000 chr1A 98.652 816 9 1 1599 2414 522974832 522975645 0.000000e+00 1445.0
3 TraesCS1A01G337000 chr1A 93.046 834 41 8 1578 2409 504399081 504399899 0.000000e+00 1203.0
4 TraesCS1A01G337000 chr1A 90.951 862 40 7 1 824 272609157 272610018 0.000000e+00 1125.0
5 TraesCS1A01G337000 chr1A 94.810 578 29 1 1003 1579 504398307 504398884 0.000000e+00 900.0
6 TraesCS1A01G337000 chr1A 98.209 335 6 0 1273 1607 523369591 523369257 9.620000e-164 586.0
7 TraesCS1A01G337000 chr1A 86.164 318 18 10 130 436 481644845 481645147 1.080000e-83 320.0
8 TraesCS1A01G337000 chr1A 85.220 318 21 10 130 436 34350424 34350726 1.080000e-78 303.0
9 TraesCS1A01G337000 chr1A 92.982 57 4 0 1804 1860 539593323 539593267 1.540000e-12 84.2
10 TraesCS1A01G337000 chr7A 92.755 842 48 8 1578 2414 655417632 655416799 0.000000e+00 1205.0
11 TraesCS1A01G337000 chr7A 94.464 578 31 1 1003 1579 655418406 655417829 0.000000e+00 889.0
12 TraesCS1A01G337000 chr7A 85.849 318 19 10 130 436 158274204 158273902 5.010000e-82 315.0
13 TraesCS1A01G337000 chr7A 80.702 171 27 4 1690 1860 21874627 21874791 7.010000e-26 128.0
14 TraesCS1A01G337000 chr7A 93.750 80 5 0 1691 1770 21855531 21855610 1.170000e-23 121.0
15 TraesCS1A01G337000 chr7A 97.143 35 0 1 850 883 10913191 10913225 9.320000e-05 58.4
16 TraesCS1A01G337000 chr3A 92.148 866 29 7 1 828 646308811 646309675 0.000000e+00 1186.0
17 TraesCS1A01G337000 chr3A 86.478 318 17 10 130 436 611173187 611172885 2.310000e-85 326.0
18 TraesCS1A01G337000 chr3A 84.806 283 30 8 1308 1579 505216112 505216392 3.060000e-69 272.0
19 TraesCS1A01G337000 chr3A 86.667 60 6 2 848 906 103589010 103589068 5.570000e-07 65.8
20 TraesCS1A01G337000 chr3D 95.100 653 24 7 1770 2414 43582782 43582130 0.000000e+00 1022.0
21 TraesCS1A01G337000 chr3D 95.147 577 25 1 1003 1579 43583807 43583234 0.000000e+00 907.0
22 TraesCS1A01G337000 chr3D 91.165 249 19 2 1878 2126 422642950 422642705 3.850000e-88 335.0
23 TraesCS1A01G337000 chr3D 96.923 195 4 1 1578 1770 43583034 43582840 2.310000e-85 326.0
24 TraesCS1A01G337000 chr3D 85.512 283 28 8 1308 1579 381985036 381985316 1.410000e-72 283.0
25 TraesCS1A01G337000 chr3D 96.000 75 3 0 875 949 43583882 43583808 3.260000e-24 122.0
26 TraesCS1A01G337000 chr4A 93.800 629 28 6 1789 2414 312732030 312731410 0.000000e+00 935.0
27 TraesCS1A01G337000 chr4A 94.746 552 27 2 1029 1579 312733045 312732495 0.000000e+00 857.0
28 TraesCS1A01G337000 chr4A 87.313 402 40 5 460 850 722870413 722870814 1.320000e-122 449.0
29 TraesCS1A01G337000 chr4A 90.000 290 18 5 163 441 722869968 722870257 4.900000e-97 364.0
30 TraesCS1A01G337000 chr4A 96.373 193 7 0 1578 1770 312732298 312732106 3.870000e-83 318.0
31 TraesCS1A01G337000 chr4A 88.393 112 12 1 850 961 304840008 304839898 1.510000e-27 134.0
32 TraesCS1A01G337000 chr4A 92.593 81 6 0 1690 1770 102386717 102386637 1.520000e-22 117.0
33 TraesCS1A01G337000 chr5B 93.643 582 33 3 1836 2414 275020178 275019598 0.000000e+00 867.0
34 TraesCS1A01G337000 chr5B 86.051 552 58 10 1027 1577 275021148 275020615 2.080000e-160 575.0
35 TraesCS1A01G337000 chr5B 94.709 189 9 1 1578 1765 275020416 275020228 2.350000e-75 292.0
36 TraesCS1A01G337000 chr6A 92.162 421 27 1 436 850 18544046 18543626 7.430000e-165 590.0
37 TraesCS1A01G337000 chr6A 92.162 421 27 1 436 850 18547012 18546592 7.430000e-165 590.0
38 TraesCS1A01G337000 chr6A 92.162 421 27 1 436 850 18549999 18549579 7.430000e-165 590.0
39 TraesCS1A01G337000 chr6A 92.162 421 27 1 436 850 18552964 18552544 7.430000e-165 590.0
40 TraesCS1A01G337000 chr6A 96.875 32 0 1 846 877 555434957 555434987 4.000000e-03 52.8
41 TraesCS1A01G337000 chr5A 91.193 352 21 4 507 850 558302899 558303248 1.010000e-128 470.0
42 TraesCS1A01G337000 chr5A 83.732 209 22 4 2076 2280 324969828 324970028 1.140000e-43 187.0
43 TraesCS1A01G337000 chr5A 100.000 30 0 0 850 879 610209617 610209646 3.350000e-04 56.5
44 TraesCS1A01G337000 chr3B 84.452 283 31 8 1308 1579 497704523 497704803 1.420000e-67 267.0
45 TraesCS1A01G337000 chr3B 92.982 57 4 0 1804 1860 104696024 104695968 1.540000e-12 84.2
46 TraesCS1A01G337000 chr3B 97.059 34 0 1 846 879 582027806 582027774 3.350000e-04 56.5
47 TraesCS1A01G337000 chr6D 84.689 209 20 5 2076 2280 461000989 461000789 5.260000e-47 198.0
48 TraesCS1A01G337000 chr6D 84.286 210 20 6 2076 2280 435547103 435546902 2.450000e-45 193.0
49 TraesCS1A01G337000 chr7D 94.737 114 6 0 328 441 412227472 412227585 6.860000e-41 178.0
50 TraesCS1A01G337000 chr2B 88.333 60 7 0 1801 1860 144064157 144064098 3.330000e-09 73.1
51 TraesCS1A01G337000 chrUn 84.211 57 9 0 850 906 12458720 12458664 3.350000e-04 56.5


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 TraesCS1A01G337000 chr1A 525142601 525145014 2413 True 4458.000000 4458 100.000000 1 2414 1 chr1A.!!$R3 2413
1 TraesCS1A01G337000 chr1A 523378187 523379464 1277 True 2089.000000 2089 96.169000 1 1278 1 chr1A.!!$R2 1277
2 TraesCS1A01G337000 chr1A 522974832 522975645 813 False 1445.000000 1445 98.652000 1599 2414 1 chr1A.!!$F4 815
3 TraesCS1A01G337000 chr1A 272609157 272610018 861 False 1125.000000 1125 90.951000 1 824 1 chr1A.!!$F2 823
4 TraesCS1A01G337000 chr1A 504398307 504399899 1592 False 1051.500000 1203 93.928000 1003 2409 2 chr1A.!!$F5 1406
5 TraesCS1A01G337000 chr7A 655416799 655418406 1607 True 1047.000000 1205 93.609500 1003 2414 2 chr7A.!!$R2 1411
6 TraesCS1A01G337000 chr3A 646308811 646309675 864 False 1186.000000 1186 92.148000 1 828 1 chr3A.!!$F3 827
7 TraesCS1A01G337000 chr3D 43582130 43583882 1752 True 594.250000 1022 95.792500 875 2414 4 chr3D.!!$R2 1539
8 TraesCS1A01G337000 chr4A 312731410 312733045 1635 True 703.333333 935 94.973000 1029 2414 3 chr4A.!!$R3 1385
9 TraesCS1A01G337000 chr4A 722869968 722870814 846 False 406.500000 449 88.656500 163 850 2 chr4A.!!$F1 687
10 TraesCS1A01G337000 chr5B 275019598 275021148 1550 True 578.000000 867 91.467667 1027 2414 3 chr5B.!!$R1 1387
11 TraesCS1A01G337000 chr6A 18543626 18552964 9338 True 590.000000 590 92.162000 436 850 4 chr6A.!!$R1 414

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
985 9478 2.45149 TGTCTCTCGATCTGCTTTCCT 58.549 47.619 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 10660 4.394729 CAAGTCAACCAAAACCCTAGCTA 58.605 43.478 0.0 0.0 0.0 3.32 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
447 5965 7.231317 GGATAAATGTCAAAGATATGCTCCCAA 59.769 37.037 0.00 0.00 0.00 4.12
582 9066 7.393234 CCTTCTGTTTATACATGACCTTTTGGA 59.607 37.037 0.00 0.00 36.99 3.53
583 9067 8.698973 TTCTGTTTATACATGACCTTTTGGAA 57.301 30.769 0.00 0.00 36.99 3.53
625 9109 3.550639 GCACAATGCACTTGTTCTTGCTA 60.551 43.478 10.56 0.00 45.98 3.49
817 9310 3.692593 GCACCGCCTAAATTCCTTTTAGA 59.307 43.478 6.67 0.00 46.59 2.10
972 9465 2.676463 GCTGGGAGAACACATGTCTCTC 60.676 54.545 19.75 19.75 34.48 3.20
985 9478 2.451490 TGTCTCTCGATCTGCTTTCCT 58.549 47.619 0.00 0.00 0.00 3.36
1150 9644 2.284921 CTCTCCTGGGTCCCTGCA 60.285 66.667 10.00 0.00 0.00 4.41
1412 9907 0.106619 GGCTTCGTCCTCCTCCTCTA 60.107 60.000 0.00 0.00 0.00 2.43
1440 9935 3.658398 CCTTGCTCAGGTCCAACAT 57.342 52.632 0.00 0.00 37.99 2.71
1547 10042 2.163509 CTCTGAACTCGGAGGAAGTGA 58.836 52.381 10.23 0.63 43.83 3.41
1571 10066 2.552093 TGGGTTGGGGAAGTTTTTCA 57.448 45.000 0.00 0.00 34.90 2.69
1573 10068 2.502130 TGGGTTGGGGAAGTTTTTCAAC 59.498 45.455 0.00 0.00 37.54 3.18
1670 10369 5.601729 TGATGATTAGATGTGCCTTCTCTCT 59.398 40.000 0.00 0.00 0.00 3.10
2127 10933 0.961753 CTTGTCTTGGGTGAAAGGCC 59.038 55.000 0.00 0.00 30.43 5.19
2165 10971 7.319052 TCAGATACTAAAAGGTAACCCACAA 57.681 36.000 0.00 0.00 37.17 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
424 457 7.572523 CTTGGGAGCATATCTTTGACATTTA 57.427 36.000 0.00 0.00 0.00 1.40
582 9066 9.453572 TTGTGCTATCATTAGAGTTGATCTTTT 57.546 29.630 0.00 0.00 39.64 2.27
583 9067 9.624373 ATTGTGCTATCATTAGAGTTGATCTTT 57.376 29.630 0.00 0.00 39.64 2.52
683 9173 2.742589 GTTTAGAAAGCTCTTCCACCCG 59.257 50.000 0.00 0.00 32.70 5.28
833 9326 5.132480 TGGTTTTAACTAGTAGTTGGGGTGT 59.868 40.000 23.14 0.01 39.11 4.16
835 9328 5.910355 TGGTTTTAACTAGTAGTTGGGGT 57.090 39.130 23.14 1.44 39.11 4.95
885 9378 1.134818 TGTGATGACGTGGCTATCACC 60.135 52.381 20.10 9.67 46.23 4.02
887 9380 1.471501 GCTGTGATGACGTGGCTATCA 60.472 52.381 0.00 0.00 0.00 2.15
972 9465 2.675348 GTGAGGAAAGGAAAGCAGATCG 59.325 50.000 0.00 0.00 0.00 3.69
985 9478 2.151202 GGACATTGCTTCGTGAGGAAA 58.849 47.619 0.57 0.00 39.28 3.13
1062 9556 2.258591 GAGCCGTGCTCGTTCTCA 59.741 61.111 17.20 0.00 45.85 3.27
1170 9664 2.182030 GGACGAGAAGACGCAGGG 59.818 66.667 0.00 0.00 36.70 4.45
1412 9907 2.665185 GAGCAAGGTGGCGACGTT 60.665 61.111 0.58 0.58 39.27 3.99
1440 9935 2.447572 TGGGGCGATGGATAGGCA 60.448 61.111 0.00 0.00 34.32 4.75
1547 10042 4.871871 AAAACTTCCCCAACCCAATTTT 57.128 36.364 0.00 0.00 0.00 1.82
1571 10066 3.112263 TGGTCTTCCCATAATCGAGGTT 58.888 45.455 0.00 0.00 38.72 3.50
1573 10068 3.467803 GTTGGTCTTCCCATAATCGAGG 58.532 50.000 0.00 0.00 44.74 4.63
1670 10369 2.946785 ACCCCCAAACAATGTACGAAA 58.053 42.857 0.00 0.00 0.00 3.46
1856 10660 4.394729 CAAGTCAACCAAAACCCTAGCTA 58.605 43.478 0.00 0.00 0.00 3.32
2127 10933 5.464965 AGTATCTGAATTAACAAACGCCG 57.535 39.130 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.