Multiple sequence alignment - TraesCS1A01G011000

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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 TraesCS1A01G011000 chr1A 100.000 2473 0 0 1 2473 6554457 6556929 0.000000e+00 4567
1 TraesCS1A01G011000 chr1A 98.949 2474 24 2 1 2473 6540882 6543354 0.000000e+00 4423
2 TraesCS1A01G011000 chr2A 95.342 1975 84 5 4 1971 203391144 203389171 0.000000e+00 3131
3 TraesCS1A01G011000 chr2A 94.079 1841 102 5 1 1839 34831009 34832844 0.000000e+00 2789
4 TraesCS1A01G011000 chr2A 97.228 505 12 2 1970 2473 618997359 618996856 0.000000e+00 854
5 TraesCS1A01G011000 chr2A 94.667 225 11 1 1745 1968 602051654 602051878 5.060000e-92 348
6 TraesCS1A01G011000 chr1D 95.718 1845 71 4 1 1839 28017874 28019716 0.000000e+00 2963
7 TraesCS1A01G011000 chr7A 94.574 1843 95 3 1 1839 7721970 7723811 0.000000e+00 2844
8 TraesCS1A01G011000 chr7A 91.429 210 17 1 1763 1971 537770628 537770419 1.120000e-73 287
9 TraesCS1A01G011000 chr7A 90.909 209 18 1 1764 1971 168463668 168463876 1.870000e-71 279
10 TraesCS1A01G011000 chr7A 90.909 209 18 1 1764 1971 370679770 370679978 1.870000e-71 279
11 TraesCS1A01G011000 chr7A 90.909 209 17 2 1764 1971 552376753 552376546 1.870000e-71 279
12 TraesCS1A01G011000 chr5A 94.348 1840 94 5 4 1839 311293655 311291822 0.000000e+00 2813
13 TraesCS1A01G011000 chr5A 94.255 1845 92 8 4 1839 48344922 48343083 0.000000e+00 2808
14 TraesCS1A01G011000 chr4A 94.239 1840 102 4 1 1839 522257289 522259125 0.000000e+00 2808
15 TraesCS1A01G011000 chr6A 94.118 1836 105 3 4 1839 94342172 94344004 0.000000e+00 2789
16 TraesCS1A01G011000 chrUn 98.603 716 8 1 1758 2473 410966375 410965662 0.000000e+00 1266
17 TraesCS1A01G011000 chrUn 98.807 503 5 1 1971 2473 469416387 469416888 0.000000e+00 894
18 TraesCS1A01G011000 chr3D 94.083 507 26 4 1968 2473 268137472 268137975 0.000000e+00 767
19 TraesCS1A01G011000 chr7D 93.861 505 27 3 1970 2473 552319693 552319192 0.000000e+00 758
20 TraesCS1A01G011000 chr7D 93.638 503 30 2 1972 2473 419798962 419799463 0.000000e+00 750
21 TraesCS1A01G011000 chr5B 91.897 506 36 4 1971 2473 589566635 589566132 0.000000e+00 702
22 TraesCS1A01G011000 chr3B 91.683 505 41 1 1970 2473 668080638 668080134 0.000000e+00 699
23 TraesCS1A01G011000 chr3A 90.909 209 18 1 1764 1971 479180116 479180324 1.870000e-71 279


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 TraesCS1A01G011000 chr1A 6554457 6556929 2472 False 4567 4567 100.000 1 2473 1 chr1A.!!$F2 2472
1 TraesCS1A01G011000 chr1A 6540882 6543354 2472 False 4423 4423 98.949 1 2473 1 chr1A.!!$F1 2472
2 TraesCS1A01G011000 chr2A 203389171 203391144 1973 True 3131 3131 95.342 4 1971 1 chr2A.!!$R1 1967
3 TraesCS1A01G011000 chr2A 34831009 34832844 1835 False 2789 2789 94.079 1 1839 1 chr2A.!!$F1 1838
4 TraesCS1A01G011000 chr2A 618996856 618997359 503 True 854 854 97.228 1970 2473 1 chr2A.!!$R2 503
5 TraesCS1A01G011000 chr1D 28017874 28019716 1842 False 2963 2963 95.718 1 1839 1 chr1D.!!$F1 1838
6 TraesCS1A01G011000 chr7A 7721970 7723811 1841 False 2844 2844 94.574 1 1839 1 chr7A.!!$F1 1838
7 TraesCS1A01G011000 chr5A 311291822 311293655 1833 True 2813 2813 94.348 4 1839 1 chr5A.!!$R2 1835
8 TraesCS1A01G011000 chr5A 48343083 48344922 1839 True 2808 2808 94.255 4 1839 1 chr5A.!!$R1 1835
9 TraesCS1A01G011000 chr4A 522257289 522259125 1836 False 2808 2808 94.239 1 1839 1 chr4A.!!$F1 1838
10 TraesCS1A01G011000 chr6A 94342172 94344004 1832 False 2789 2789 94.118 4 1839 1 chr6A.!!$F1 1835
11 TraesCS1A01G011000 chrUn 410965662 410966375 713 True 1266 1266 98.603 1758 2473 1 chrUn.!!$R1 715
12 TraesCS1A01G011000 chrUn 469416387 469416888 501 False 894 894 98.807 1971 2473 1 chrUn.!!$F1 502
13 TraesCS1A01G011000 chr3D 268137472 268137975 503 False 767 767 94.083 1968 2473 1 chr3D.!!$F1 505
14 TraesCS1A01G011000 chr7D 552319192 552319693 501 True 758 758 93.861 1970 2473 1 chr7D.!!$R1 503
15 TraesCS1A01G011000 chr7D 419798962 419799463 501 False 750 750 93.638 1972 2473 1 chr7D.!!$F1 501
16 TraesCS1A01G011000 chr5B 589566132 589566635 503 True 702 702 91.897 1971 2473 1 chr5B.!!$R1 502
17 TraesCS1A01G011000 chr3B 668080134 668080638 504 True 699 699 91.683 1970 2473 1 chr3B.!!$R1 503

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
89 90 2.045926 GACCACCTCGCTGGCAAT 60.046 61.111 0.0 0.0 40.22 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 2288 1.299976 GAGATTTGGGTGGGCTCGT 59.7 57.895 0.0 0.0 0.0 4.18 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
60 61 2.479198 CGCGTCGCTACAGAGACA 59.521 61.111 16.36 0.00 43.61 3.41
89 90 2.045926 GACCACCTCGCTGGCAAT 60.046 61.111 0.00 0.00 40.22 3.56
285 287 3.019003 GCGGGCTAGGAGCTTGTCA 62.019 63.158 0.00 0.00 41.99 3.58
1300 1320 9.772973 GGTTGTTATCAAGGAAAGGTAAAAATT 57.227 29.630 0.00 0.00 33.97 1.82
1613 1633 8.764287 CCAATAAAAGGAATCGATTAATTTGCC 58.236 33.333 11.38 6.91 0.00 4.52
1615 1635 9.750125 AATAAAAGGAATCGATTAATTTGCCTC 57.250 29.630 11.38 0.00 0.00 4.70
1626 1646 8.912988 TCGATTAATTTGCCTCATTTAAGGAAT 58.087 29.630 0.00 0.00 38.87 3.01
1675 1695 9.981114 TTTCCTGAAATTCTCTTATTTGTTTCC 57.019 29.630 0.00 0.00 0.00 3.13
1676 1696 8.940397 TCCTGAAATTCTCTTATTTGTTTCCT 57.060 30.769 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 2.513738 CACCCTTATCCATTCCCCTTCA 59.486 50.000 0.00 0.00 0.00 3.02
285 287 2.508586 GAAGGCGTTCGGAGCTCCTT 62.509 60.000 29.73 14.81 39.63 3.36
953 961 4.528674 CGCATAGCAGCAGGAAGT 57.471 55.556 0.00 0.00 0.00 3.01
1674 1694 9.855021 CCACTTATTGGTTTAATTTGTCTTAGG 57.145 33.333 0.00 0.00 41.10 2.69
1679 1699 9.921637 TGATTCCACTTATTGGTTTAATTTGTC 57.078 29.630 0.00 0.00 46.97 3.18
1688 1708 9.439500 CAAATCAATTGATTCCACTTATTGGTT 57.561 29.630 29.08 10.05 43.41 3.67
1689 1709 7.550196 GCAAATCAATTGATTCCACTTATTGGT 59.450 33.333 29.08 10.23 43.41 3.67
1690 1710 7.549842 TGCAAATCAATTGATTCCACTTATTGG 59.450 33.333 29.08 8.13 43.41 3.16
1691 1711 8.481974 TGCAAATCAATTGATTCCACTTATTG 57.518 30.769 29.08 21.74 43.41 1.90
1695 1715 9.675464 AATTATGCAAATCAATTGATTCCACTT 57.325 25.926 29.08 20.64 43.41 3.16
1696 1716 9.675464 AAATTATGCAAATCAATTGATTCCACT 57.325 25.926 29.08 18.15 43.41 4.00
1707 1727 9.859427 CTGACTTCCTTAAATTATGCAAATCAA 57.141 29.630 0.00 0.00 0.00 2.57
1708 1728 9.241919 TCTGACTTCCTTAAATTATGCAAATCA 57.758 29.630 0.00 0.00 0.00 2.57
1751 1977 9.710900 GAAACAAATAACAGATTTCCAGGAAAT 57.289 29.630 25.18 25.18 43.77 2.17
2045 2279 1.668151 GTGGGCTCGTCACCAGAAC 60.668 63.158 0.00 0.00 37.45 3.01
2046 2280 2.741092 GTGGGCTCGTCACCAGAA 59.259 61.111 0.00 0.00 37.45 3.02
2054 2288 1.299976 GAGATTTGGGTGGGCTCGT 59.700 57.895 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.