Multiple sequence alignment - TraesCS7A01G300100

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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 TraesCS7A01G300100 chr7A 100.000 2538 0 0 1 2538 415464099 415461562 0.000000e+00 4687
1 TraesCS7A01G300100 chr7A 98.593 1421 19 1 83 1502 415923415 415921995 0.000000e+00 2512
2 TraesCS7A01G300100 chr7A 99.176 364 3 0 2124 2487 415922003 415921640 0.000000e+00 656
3 TraesCS7A01G300100 chr7A 100.000 85 0 0 1 85 415923528 415923444 9.400000e-35 158
4 TraesCS7A01G300100 chr7A 98.824 85 1 0 1 85 622989662 622989578 4.370000e-33 152
5 TraesCS7A01G300100 chr7A 98.824 85 1 0 1 85 683261282 683261366 4.370000e-33 152
6 TraesCS7A01G300100 chr1A 97.307 2191 33 5 372 2538 47378733 47376545 0.000000e+00 3696
7 TraesCS7A01G300100 chr1A 90.051 1578 118 10 370 1917 17306510 17304942 0.000000e+00 2008
8 TraesCS7A01G300100 chr1A 96.194 289 11 0 83 371 55107562 55107850 8.220000e-130 473
9 TraesCS7A01G300100 chr1A 96.194 289 11 0 83 371 566180183 566180471 8.220000e-130 473
10 TraesCS7A01G300100 chr1A 98.824 85 1 0 1 85 414659840 414659756 4.370000e-33 152
11 TraesCS7A01G300100 chr1A 98.824 85 1 0 1 85 552896957 552897041 4.370000e-33 152
12 TraesCS7A01G300100 chr6A 96.950 1836 33 3 725 2538 589252444 589250610 0.000000e+00 3059
13 TraesCS7A01G300100 chr6A 96.540 289 10 0 83 371 596068866 596068578 1.770000e-131 479
14 TraesCS7A01G300100 chr6A 98.824 85 1 0 1 85 251904347 251904431 4.370000e-33 152
15 TraesCS7A01G300100 chr6A 98.824 85 1 0 1 85 346449871 346449955 4.370000e-33 152
16 TraesCS7A01G300100 chr3A 91.418 2214 128 17 372 2538 723838464 723840662 0.000000e+00 2979
17 TraesCS7A01G300100 chr3A 83.441 622 72 16 371 971 746942391 746943002 1.330000e-152 549
18 TraesCS7A01G300100 chr3A 96.540 289 10 0 83 371 123234818 123234530 1.770000e-131 479
19 TraesCS7A01G300100 chr3A 98.824 85 1 0 1 85 304227 304143 4.370000e-33 152
20 TraesCS7A01G300100 chr3A 98.824 85 1 0 1 85 251612930 251613014 4.370000e-33 152
21 TraesCS7A01G300100 chr4B 87.329 513 56 7 371 875 41007214 41007725 1.690000e-161 579
22 TraesCS7A01G300100 chr5A 96.540 289 10 0 83 371 426912408 426912120 1.770000e-131 479
23 TraesCS7A01G300100 chr5A 96.540 289 10 0 83 371 601584131 601584419 1.770000e-131 479
24 TraesCS7A01G300100 chr6D 96.194 289 11 0 83 371 278710584 278710296 8.220000e-130 473
25 TraesCS7A01G300100 chr6D 96.194 289 11 0 83 371 282785617 282785329 8.220000e-130 473
26 TraesCS7A01G300100 chr3B 84.615 429 48 8 1697 2111 703832090 703831666 6.530000e-111 411
27 TraesCS7A01G300100 chr3B 84.382 429 49 8 1697 2111 73184000 73183576 3.040000e-109 405
28 TraesCS7A01G300100 chr2A 86.035 401 34 10 1697 2079 541819046 541818650 6.530000e-111 411
29 TraesCS7A01G300100 chr2A 82.759 290 40 6 1239 1525 541819817 541819535 1.510000e-62 250
30 TraesCS7A01G300100 chr6B 80.536 560 63 16 1547 2066 643521460 643520907 3.060000e-104 388
31 TraesCS7A01G300100 chr6B 84.615 130 19 1 372 500 565747960 565748089 7.370000e-26 128
32 TraesCS7A01G300100 chr5D 80.545 257 38 10 1291 1540 426053921 426053670 1.200000e-43 187
33 TraesCS7A01G300100 chr4D 84.733 131 17 3 372 500 143450635 143450764 7.370000e-26 128
34 TraesCS7A01G300100 chr4A 84.615 130 19 1 372 500 520442758 520442629 7.370000e-26 128


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 TraesCS7A01G300100 chr7A 415461562 415464099 2537 True 4687.000000 4687 100.000000 1 2538 1 chr7A.!!$R1 2537
1 TraesCS7A01G300100 chr7A 415921640 415923528 1888 True 1108.666667 2512 99.256333 1 2487 3 chr7A.!!$R3 2486
2 TraesCS7A01G300100 chr1A 47376545 47378733 2188 True 3696.000000 3696 97.307000 372 2538 1 chr1A.!!$R2 2166
3 TraesCS7A01G300100 chr1A 17304942 17306510 1568 True 2008.000000 2008 90.051000 370 1917 1 chr1A.!!$R1 1547
4 TraesCS7A01G300100 chr6A 589250610 589252444 1834 True 3059.000000 3059 96.950000 725 2538 1 chr6A.!!$R1 1813
5 TraesCS7A01G300100 chr3A 723838464 723840662 2198 False 2979.000000 2979 91.418000 372 2538 1 chr3A.!!$F2 2166
6 TraesCS7A01G300100 chr3A 746942391 746943002 611 False 549.000000 549 83.441000 371 971 1 chr3A.!!$F3 600
7 TraesCS7A01G300100 chr4B 41007214 41007725 511 False 579.000000 579 87.329000 371 875 1 chr4B.!!$F1 504
8 TraesCS7A01G300100 chr2A 541818650 541819817 1167 True 330.500000 411 84.397000 1239 2079 2 chr2A.!!$R1 840
9 TraesCS7A01G300100 chr6B 643520907 643521460 553 True 388.000000 388 80.536000 1547 2066 1 chr6B.!!$R1 519

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
920 993 0.537188 GATGGTGTGTCGAGGTGGAT 59.463 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 2614 5.335661 CCCGCTGAATATAAACCTTATTGCC 60.336 44.0 0.0 0.0 0.0 4.52 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
85 86 1.905894 TGTCGTTCCATCCATCCAAGA 59.094 47.619 0.00 0.0 0.00 3.02
172 204 4.530946 TCCGTAGAACATCCCTCTTTTTCT 59.469 41.667 0.00 0.0 0.00 2.52
179 211 5.511386 ACATCCCTCTTTTTCTGATGACT 57.489 39.130 4.93 0.0 37.01 3.41
331 363 0.544357 AGGTTCTGGTGATCCCGTCA 60.544 55.000 0.00 0.0 33.59 4.35
682 718 4.376146 GAAAAGTTTGCACCAAATAGCCA 58.624 39.130 0.00 0.0 35.74 4.75
903 976 1.605058 CTCCCTTCGACACCACCGAT 61.605 60.000 0.00 0.0 35.84 4.18
916 989 1.906824 ACCGATGGTGTGTCGAGGT 60.907 57.895 0.00 0.0 41.40 3.85
917 990 1.446099 CCGATGGTGTGTCGAGGTG 60.446 63.158 0.00 0.0 41.40 4.00
918 991 1.446099 CGATGGTGTGTCGAGGTGG 60.446 63.158 0.00 0.0 41.40 4.61
919 992 1.873270 CGATGGTGTGTCGAGGTGGA 61.873 60.000 0.00 0.0 41.40 4.02
920 993 0.537188 GATGGTGTGTCGAGGTGGAT 59.463 55.000 0.00 0.0 0.00 3.41
921 994 0.537188 ATGGTGTGTCGAGGTGGATC 59.463 55.000 0.00 0.0 0.00 3.36
922 995 1.218316 GGTGTGTCGAGGTGGATCC 59.782 63.158 4.20 4.2 0.00 3.36
923 996 1.153823 GTGTGTCGAGGTGGATCCG 60.154 63.158 7.39 0.0 41.99 4.18
1093 1182 2.417516 GCGCTCCTATTCTCCGCA 59.582 61.111 0.00 0.0 43.67 5.69
1356 1447 6.704050 CCCAACTTATTGTTTGGTCGATTTTT 59.296 34.615 0.00 0.0 36.88 1.94
1957 2386 4.192317 CAACCTGAATGTACTAGAAGGGC 58.808 47.826 0.00 0.0 0.00 5.19
2162 2591 4.272489 TGGAAGTCTGAAAATATGCTGGG 58.728 43.478 0.00 0.0 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 0.881796 TCAGCGTCTCGACATGAAGT 59.118 50.000 0.00 0.00 0.00 3.01
172 204 6.320418 CCAAATCATCATGAAGGAAGTCATCA 59.680 38.462 0.00 0.00 36.04 3.07
179 211 3.710724 TGCCCAAATCATCATGAAGGAA 58.289 40.909 0.00 0.00 0.00 3.36
248 280 4.665009 TGGGCAAAGGACATAGGAGATATT 59.335 41.667 0.00 0.00 0.00 1.28
331 363 1.352083 ACACCACATGCTGGAGTACT 58.648 50.000 17.76 0.00 41.72 2.73
682 718 0.255033 GAAGACCTATTTGGGGCGGT 59.745 55.000 0.00 0.00 39.91 5.68
903 976 1.541310 GGATCCACCTCGACACACCA 61.541 60.000 6.95 0.00 35.41 4.17
916 989 2.411701 GCGACATCGACGGATCCA 59.588 61.111 13.41 0.00 43.02 3.41
917 990 2.354773 GGCGACATCGACGGATCC 60.355 66.667 5.26 0.00 43.02 3.36
1356 1447 1.340017 GCTGTCCATGGTAGCAGGAAA 60.340 52.381 27.50 5.73 37.40 3.13
1525 1616 4.885907 CCCTACGTATTCTACTCACTTCCA 59.114 45.833 0.00 0.00 0.00 3.53
1639 1803 9.990360 TTAGTGGCGAAAATCAGATTATATGTA 57.010 29.630 0.00 0.00 0.00 2.29
1695 1859 8.019669 CACTTGTGTTCCTCTCAAATAAATCAG 58.980 37.037 0.00 0.00 0.00 2.90
1957 2386 6.974622 GCTGGTTATAGTTTCATGAATGTTGG 59.025 38.462 9.40 0.00 0.00 3.77
2185 2614 5.335661 CCCGCTGAATATAAACCTTATTGCC 60.336 44.000 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.