Multiple sequence alignment - TraesCS4A01G196200

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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 TraesCS4A01G196200 chr4A 100.000 2303 0 0 1 2303 478227425 478229727 0 4253
1 TraesCS4A01G196200 chr4A 95.328 2333 77 5 1 2303 731637056 731634726 0 3675
2 TraesCS4A01G196200 chr5D 96.635 2318 61 5 1 2303 552028752 552026437 0 3832
3 TraesCS4A01G196200 chr5D 94.957 2340 73 7 1 2303 78602640 78600309 0 3626
4 TraesCS4A01G196200 chr5D 96.581 1755 36 2 1 1733 555413829 555415581 0 2887
5 TraesCS4A01G196200 chr7D 96.177 2328 62 5 1 2303 531067433 531065108 0 3781
6 TraesCS4A01G196200 chr2D 95.981 2339 56 7 1 2303 617341038 617343374 0 3764
7 TraesCS4A01G196200 chr1D 95.983 2340 55 5 1 2303 316243676 316241339 0 3764
8 TraesCS4A01G196200 chr3D 95.853 2339 59 5 1 2303 334427 336763 0 3747
9 TraesCS4A01G196200 chr3D 95.468 2339 63 5 1 2303 468955311 468957642 0 3692
10 TraesCS4A01G196200 chr3D 95.926 1031 26 4 1285 2303 610059709 610058683 0 1657
11 TraesCS4A01G196200 chr6D 95.846 2335 63 4 1 2303 420171510 420173842 0 3744
12 TraesCS4A01G196200 chr4D 95.812 2340 59 5 1 2303 491381783 491384120 0 3742
13 TraesCS4A01G196200 chr1A 94.363 2324 91 17 1 2303 25270712 25268408 0 3530
14 TraesCS4A01G196200 chr1A 94.231 2340 84 17 1 2303 77263658 77265983 0 3526
15 TraesCS4A01G196200 chr5A 93.937 2342 96 11 1 2303 666200222 666197888 0 3496
16 TraesCS4A01G196200 chr5A 93.819 2346 89 16 1 2303 540624877 540622545 0 3478
17 TraesCS4A01G196200 chr6A 93.889 2340 92 23 1 2303 587986532 587984207 0 3482
18 TraesCS4A01G196200 chr3A 93.838 2337 79 20 1 2303 693613334 693611029 0 3458


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 TraesCS4A01G196200 chr4A 478227425 478229727 2302 False 4253 4253 100.000 1 2303 1 chr4A.!!$F1 2302
1 TraesCS4A01G196200 chr4A 731634726 731637056 2330 True 3675 3675 95.328 1 2303 1 chr4A.!!$R1 2302
2 TraesCS4A01G196200 chr5D 552026437 552028752 2315 True 3832 3832 96.635 1 2303 1 chr5D.!!$R2 2302
3 TraesCS4A01G196200 chr5D 78600309 78602640 2331 True 3626 3626 94.957 1 2303 1 chr5D.!!$R1 2302
4 TraesCS4A01G196200 chr5D 555413829 555415581 1752 False 2887 2887 96.581 1 1733 1 chr5D.!!$F1 1732
5 TraesCS4A01G196200 chr7D 531065108 531067433 2325 True 3781 3781 96.177 1 2303 1 chr7D.!!$R1 2302
6 TraesCS4A01G196200 chr2D 617341038 617343374 2336 False 3764 3764 95.981 1 2303 1 chr2D.!!$F1 2302
7 TraesCS4A01G196200 chr1D 316241339 316243676 2337 True 3764 3764 95.983 1 2303 1 chr1D.!!$R1 2302
8 TraesCS4A01G196200 chr3D 334427 336763 2336 False 3747 3747 95.853 1 2303 1 chr3D.!!$F1 2302
9 TraesCS4A01G196200 chr3D 468955311 468957642 2331 False 3692 3692 95.468 1 2303 1 chr3D.!!$F2 2302
10 TraesCS4A01G196200 chr3D 610058683 610059709 1026 True 1657 1657 95.926 1285 2303 1 chr3D.!!$R1 1018
11 TraesCS4A01G196200 chr6D 420171510 420173842 2332 False 3744 3744 95.846 1 2303 1 chr6D.!!$F1 2302
12 TraesCS4A01G196200 chr4D 491381783 491384120 2337 False 3742 3742 95.812 1 2303 1 chr4D.!!$F1 2302
13 TraesCS4A01G196200 chr1A 25268408 25270712 2304 True 3530 3530 94.363 1 2303 1 chr1A.!!$R1 2302
14 TraesCS4A01G196200 chr1A 77263658 77265983 2325 False 3526 3526 94.231 1 2303 1 chr1A.!!$F1 2302
15 TraesCS4A01G196200 chr5A 666197888 666200222 2334 True 3496 3496 93.937 1 2303 1 chr5A.!!$R2 2302
16 TraesCS4A01G196200 chr5A 540622545 540624877 2332 True 3478 3478 93.819 1 2303 1 chr5A.!!$R1 2302
17 TraesCS4A01G196200 chr6A 587984207 587986532 2325 True 3482 3482 93.889 1 2303 1 chr6A.!!$R1 2302
18 TraesCS4A01G196200 chr3A 693611029 693613334 2305 True 3458 3458 93.838 1 2303 1 chr3A.!!$R1 2302

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
19 21 0.324183 CAGCTCTCTCACTCTCCCCA 60.324 60.0 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 1992 1.679311 CAGAGCTGCCACCTACCAA 59.321 57.895 0.0 0.0 0.0 3.67 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
19 21 0.324183 CAGCTCTCTCACTCTCCCCA 60.324 60.000 0.00 0.00 0.00 4.96
75 77 1.000163 TGTTTCTTCTTCTCGCGCTCT 60.000 47.619 5.56 0.00 0.00 4.09
158 160 2.029020 AGTACATGAGCGAGTTCAGCAA 60.029 45.455 0.00 0.00 37.01 3.91
306 336 9.987272 TGTGAGTTGTTCTTGATATAGATATGG 57.013 33.333 0.00 0.00 0.00 2.74
457 488 3.378512 ACACTGGCAGGAGATTCATAGA 58.621 45.455 20.34 0.00 0.00 1.98
549 580 5.485662 AACAGACTGTTTAGTTGCTGTTC 57.514 39.130 15.23 0.00 43.16 3.18
554 586 6.701841 CAGACTGTTTAGTTGCTGTTCTTCTA 59.298 38.462 0.00 0.00 37.25 2.10
557 589 8.276252 ACTGTTTAGTTGCTGTTCTTCTAAAA 57.724 30.769 0.00 0.00 34.10 1.52
596 628 9.952030 TGAAAACATTGGTATGTCTGAATACTA 57.048 29.630 0.00 2.83 44.14 1.82
723 770 8.020861 TGATTTGTTATTCTGAATTTGCTTGC 57.979 30.769 8.38 0.00 0.00 4.01
943 990 2.938956 GGCCAATCAGTATAGCCAGT 57.061 50.000 0.00 0.00 43.32 4.00
1228 1275 6.305272 AGAAGAAGCTGGAGAATGTCATTA 57.695 37.500 0.00 0.00 0.00 1.90
1267 1314 1.273327 GTCATGGGTGCAAGGAAAAGG 59.727 52.381 0.00 0.00 0.00 3.11
1467 1541 1.407437 CCCTGATCTGTACTGCCCAAC 60.407 57.143 0.00 0.00 0.00 3.77
1548 1622 8.087982 AGTCTGATGTAGTTTATTTGTGTGTG 57.912 34.615 0.00 0.00 0.00 3.82
1549 1623 7.715249 AGTCTGATGTAGTTTATTTGTGTGTGT 59.285 33.333 0.00 0.00 0.00 3.72
1753 1842 2.486982 CTGAGATTGCAAACACCCTGAG 59.513 50.000 1.71 0.00 0.00 3.35
1871 1978 3.222354 GACCTGACCGTCGCACCTT 62.222 63.158 0.00 0.00 0.00 3.50
1948 2055 1.133041 TGACGATGATGGGAGGAGGAT 60.133 52.381 0.00 0.00 0.00 3.24
1995 2102 0.749049 CGATGATCTGCAGGTCCTCA 59.251 55.000 25.82 17.99 0.00 3.86
2033 2140 3.560636 AGTTGGAGTTGTAGCTTGTGT 57.439 42.857 0.00 0.00 0.00 3.72
2111 2218 0.685458 GCCTCCTTCATTGCCCACAT 60.685 55.000 0.00 0.00 0.00 3.21
2208 2315 1.404851 GCCTTCTTCCTCACCTCTTCG 60.405 57.143 0.00 0.00 0.00 3.79
2265 2372 5.101648 TCATGGCAATCTTCATGTAGTCA 57.898 39.130 0.00 0.00 40.94 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 21 1.077005 AGAGAGGAGTGGAGTGAGCTT 59.923 52.381 0.00 0.00 0.00 3.74
158 160 4.292186 ACAAAGTACTCCATCTGCATGT 57.708 40.909 0.00 0.00 0.00 3.21
306 336 6.091986 TCAGGAGTTTGATGCAAAAACAAAAC 59.908 34.615 22.91 13.10 39.49 2.43
320 351 4.832823 TCTATCACAGTGTCAGGAGTTTGA 59.167 41.667 0.00 0.00 0.00 2.69
407 438 1.761784 TCAAATGCCACAAACTTGCCT 59.238 42.857 0.00 0.00 0.00 4.75
457 488 4.384208 GGTCCATTACCTCAGTAGCACATT 60.384 45.833 0.00 0.00 45.75 2.71
557 589 8.250143 ACCAATGTTTTCAGACTTAAGGAAAT 57.750 30.769 7.53 0.00 31.30 2.17
596 628 6.852420 TCCAGTGCTCTTTACTACAAGTAT 57.148 37.500 0.00 0.00 29.64 2.12
825 872 5.089434 TGCTCATGATACATATCCCAGAGT 58.911 41.667 0.00 0.00 31.87 3.24
943 990 2.108075 ACTTGGACACATCATCCACCAA 59.892 45.455 0.00 0.00 46.09 3.67
994 1041 2.689471 GGCTTGTGCAATCCATGTCATA 59.311 45.455 0.00 0.00 41.91 2.15
1228 1275 2.303311 GACCAACCTTAAGGAGCTCAGT 59.697 50.000 28.52 14.76 38.94 3.41
1267 1314 7.259290 TCACAACTTTCTTTATCTTGTCCAC 57.741 36.000 0.00 0.00 0.00 4.02
1467 1541 6.164876 CCAGTTCTCAGCATCAGGATAATAG 58.835 44.000 0.00 0.00 0.00 1.73
1548 1622 7.331934 TCTCAGCAAGAACTTATGATACAACAC 59.668 37.037 0.00 0.00 0.00 3.32
1549 1623 7.386059 TCTCAGCAAGAACTTATGATACAACA 58.614 34.615 0.00 0.00 0.00 3.33
1753 1842 7.715265 TGTTAGATTCAGTTCTGTCAGTTTC 57.285 36.000 0.00 0.00 0.00 2.78
1871 1978 4.278170 CACCTACCAATCAAGTCAAGCAAA 59.722 41.667 0.00 0.00 0.00 3.68
1885 1992 1.679311 CAGAGCTGCCACCTACCAA 59.321 57.895 0.00 0.00 0.00 3.67
1995 2102 2.029623 ACTACTATGGGCAACGACGAT 58.970 47.619 0.00 0.00 37.60 3.73
2033 2140 2.338809 CCCACTGCTATATCCCTCCAA 58.661 52.381 0.00 0.00 0.00 3.53
2111 2218 1.065564 TCATGCCCATCGACATGTTGA 60.066 47.619 18.14 18.14 43.34 3.18


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

AutoCloner maintained by Alex Coulton.