Multiple sequence alignment - TraesCS1A01G421300

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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 TraesCS1A01G421300 chr1A 100.000 3373 0 0 1 3373 577613557 577610185 0.000000e+00 6229
1 TraesCS1A01G421300 chr1A 95.806 1049 22 5 2347 3373 532160951 532161999 0.000000e+00 1674
2 TraesCS1A01G421300 chr1A 92.213 244 12 6 3110 3350 529314100 529314339 4.170000e-89 339
3 TraesCS1A01G421300 chr7A 97.324 3401 63 8 1 3373 21044144 21040744 0.000000e+00 5751
4 TraesCS1A01G421300 chr7A 97.022 3391 63 9 1 3373 688928646 688932016 0.000000e+00 5668
5 TraesCS1A01G421300 chr7A 95.217 230 11 0 3130 3359 595582365 595582594 6.880000e-97 364
6 TraesCS1A01G421300 chr7A 95.217 230 11 0 3130 3359 595670120 595670349 6.880000e-97 364
7 TraesCS1A01G421300 chr7A 94.783 230 12 0 3130 3359 595750807 595751036 3.200000e-95 359
8 TraesCS1A01G421300 chr7A 91.538 260 20 2 3110 3367 712323433 712323692 1.150000e-94 357
9 TraesCS1A01G421300 chr5A 97.226 3389 69 10 1 3373 663200067 663203446 0.000000e+00 5714
10 TraesCS1A01G421300 chr5A 96.894 3252 74 7 4 3229 100350420 100347170 0.000000e+00 5421
11 TraesCS1A01G421300 chr5A 95.833 216 9 0 3152 3367 388937757 388937972 1.930000e-92 350
12 TraesCS1A01G421300 chr3A 97.197 3389 74 9 1 3373 714222432 714225815 0.000000e+00 5712
13 TraesCS1A01G421300 chr6A 96.813 3389 77 12 1 3373 562226314 562222941 0.000000e+00 5631
14 TraesCS1A01G421300 chr3B 96.694 3388 87 13 3 3373 778356451 778353072 0.000000e+00 5613
15 TraesCS1A01G421300 chr3B 95.058 344 17 0 1 344 62349507 62349850 2.960000e-150 542
16 TraesCS1A01G421300 chrUn 96.991 2825 67 10 564 3373 308012124 308009303 0.000000e+00 4730
17 TraesCS1A01G421300 chrUn 96.991 2825 67 10 564 3373 308106821 308109642 0.000000e+00 4730
18 TraesCS1A01G421300 chrUn 96.991 2825 67 10 564 3373 323644452 323647273 0.000000e+00 4730
19 TraesCS1A01G421300 chr2B 95.058 344 17 0 1 344 681388378 681388721 2.960000e-150 542
20 TraesCS1A01G421300 chr7B 94.094 254 12 3 3122 3373 627288634 627288382 1.900000e-102 383
21 TraesCS1A01G421300 chr2A 92.692 260 17 2 3110 3367 728997341 728997600 1.140000e-99 374
22 TraesCS1A01G421300 chr2A 92.278 259 18 2 3111 3367 734861289 734861547 1.910000e-97 366


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 TraesCS1A01G421300 chr1A 577610185 577613557 3372 True 6229 6229 100.000 1 3373 1 chr1A.!!$R1 3372
1 TraesCS1A01G421300 chr1A 532160951 532161999 1048 False 1674 1674 95.806 2347 3373 1 chr1A.!!$F2 1026
2 TraesCS1A01G421300 chr7A 21040744 21044144 3400 True 5751 5751 97.324 1 3373 1 chr7A.!!$R1 3372
3 TraesCS1A01G421300 chr7A 688928646 688932016 3370 False 5668 5668 97.022 1 3373 1 chr7A.!!$F4 3372
4 TraesCS1A01G421300 chr5A 663200067 663203446 3379 False 5714 5714 97.226 1 3373 1 chr5A.!!$F2 3372
5 TraesCS1A01G421300 chr5A 100347170 100350420 3250 True 5421 5421 96.894 4 3229 1 chr5A.!!$R1 3225
6 TraesCS1A01G421300 chr3A 714222432 714225815 3383 False 5712 5712 97.197 1 3373 1 chr3A.!!$F1 3372
7 TraesCS1A01G421300 chr6A 562222941 562226314 3373 True 5631 5631 96.813 1 3373 1 chr6A.!!$R1 3372
8 TraesCS1A01G421300 chr3B 778353072 778356451 3379 True 5613 5613 96.694 3 3373 1 chr3B.!!$R1 3370
9 TraesCS1A01G421300 chrUn 308009303 308012124 2821 True 4730 4730 96.991 564 3373 1 chrUn.!!$R1 2809
10 TraesCS1A01G421300 chrUn 308106821 308109642 2821 False 4730 4730 96.991 564 3373 1 chrUn.!!$F1 2809
11 TraesCS1A01G421300 chrUn 323644452 323647273 2821 False 4730 4730 96.991 564 3373 1 chrUn.!!$F2 2809

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
90 91 1.371558 GGGACTTCTCGTGTGCCTT 59.628 57.895 0.00 0.0 41.75 4.35 F
1015 1024 1.409064 TGCTCATGGCTCGTACTAAGG 59.591 52.381 7.54 0.0 42.39 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 1746 1.279496 CCAGAGACATTCCCACAGGA 58.721 55.000 0.00 0.00 41.88 3.86 R
2402 2413 2.741517 TGCAAACATCGGATGTACTGTG 59.258 45.455 22.91 17.94 44.07 3.66 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
90 91 1.371558 GGGACTTCTCGTGTGCCTT 59.628 57.895 0.00 0.00 41.75 4.35
344 347 4.933505 TGACCATTGCTTGTTCAATCAA 57.066 36.364 4.68 4.68 34.68 2.57
594 600 7.615365 TGATCATGGTAGCCTTGTTTTCTTTAT 59.385 33.333 0.00 0.00 31.64 1.40
1015 1024 1.409064 TGCTCATGGCTCGTACTAAGG 59.591 52.381 7.54 0.00 42.39 2.69
1090 1099 5.772672 ACCAAGGTTTGTGACTGCAATATTA 59.227 36.000 0.00 0.00 0.00 0.98
1170 1179 3.228188 TGAACCTCAACCTTCATTGCT 57.772 42.857 0.00 0.00 0.00 3.91
1217 1226 8.972127 ACTGATGTATATGGACTATCATGGTAC 58.028 37.037 0.00 0.00 0.00 3.34
1267 1276 1.747325 GCTTTTTGACAGGCTGCCCA 61.747 55.000 16.57 10.34 0.00 5.36
1676 1685 2.759114 CCCTTCAGGAGGCTGCAA 59.241 61.111 9.23 0.00 44.85 4.08
1737 1746 1.344438 GGGCTTAAGGTGCTTGCTTTT 59.656 47.619 4.29 0.00 0.00 2.27
1807 1816 7.277760 GCTGTTTTTAGTGATTGTTTGGAACTT 59.722 33.333 0.00 0.00 0.00 2.66
2304 2315 1.350684 TGCCAAACAGAGCCTGTGATA 59.649 47.619 8.37 0.00 44.62 2.15
2362 2373 4.324563 CCCACTTGATGATCTTAACCACCT 60.325 45.833 0.00 0.00 0.00 4.00
2374 2385 6.328782 TCTTAACCACCTAGATCTCTGAGA 57.671 41.667 10.23 10.23 0.00 3.27
2377 2388 5.718801 AACCACCTAGATCTCTGAGACTA 57.281 43.478 10.00 11.92 0.00 2.59
2415 2426 3.445805 TGTTATCAGCACAGTACATCCGA 59.554 43.478 0.00 0.00 0.00 4.55
2474 2485 3.689161 TGTCGTTGGATATTGCTGGAAAG 59.311 43.478 0.00 0.00 0.00 2.62
2686 2733 6.381498 TGTTGTTATTCACCCTATCCTTGA 57.619 37.500 0.00 0.00 0.00 3.02
2993 3040 5.527214 TCATGCGACCCACTTATCAAAATAG 59.473 40.000 0.00 0.00 0.00 1.73
3359 3420 5.523916 CGTCTTCGACCATTCCATAAGAAAT 59.476 40.000 0.00 0.00 37.34 2.17
3362 3423 6.884295 TCTTCGACCATTCCATAAGAAATGTT 59.116 34.615 0.00 0.00 38.21 2.71
3369 3430 9.420118 ACCATTCCATAAGAAATGTTGCTAATA 57.580 29.630 0.00 0.00 38.21 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
344 347 7.449704 AGAAGCCAAGAACACTGAAGAATTTAT 59.550 33.333 0.00 0.00 0.00 1.40
763 771 1.486726 ACAGCTATACACCCCTTCAGC 59.513 52.381 0.00 0.00 0.00 4.26
1015 1024 1.813786 AGTGGACTTACGAGCAGTCTC 59.186 52.381 11.39 6.98 40.60 3.36
1170 1179 7.699878 TCAGTAGGATATCTGGTCATAAGCTA 58.300 38.462 2.05 0.00 33.13 3.32
1217 1226 7.765307 AGAGCACATGGTCAAATTAACAATAG 58.235 34.615 13.20 0.00 44.42 1.73
1267 1276 2.026822 CCAGTTGTGGGAGCAGACTTAT 60.027 50.000 0.00 0.00 40.67 1.73
1586 1595 8.630054 ACATGATGGTGCTTTTAGTTTACTTA 57.370 30.769 0.00 0.00 0.00 2.24
1737 1746 1.279496 CCAGAGACATTCCCACAGGA 58.721 55.000 0.00 0.00 41.88 3.86
2402 2413 2.741517 TGCAAACATCGGATGTACTGTG 59.258 45.455 22.91 17.94 44.07 3.66
2474 2485 7.066284 ACCAAGAAATTGATGTGACATAGCTAC 59.934 37.037 0.00 0.00 0.00 3.58
2686 2733 4.402155 TCTGCCAACAAGAAAACAGAACAT 59.598 37.500 0.00 0.00 31.60 2.71
2993 3040 7.339953 GTCAGAAATTTCAAATGTGCTCAAAC 58.660 34.615 19.99 0.39 0.00 2.93


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

AutoCloner maintained by Alex Coulton.