Multiple sequence alignment - TraesCS2A01G367900

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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 TraesCS2A01G367900 chr2A 100.000 2549 0 0 1 2549 611725721 611723173 0.000000e+00 4708
1 TraesCS2A01G367900 chr2A 96.097 1973 73 3 578 2549 233255253 233257222 0.000000e+00 3214
2 TraesCS2A01G367900 chr2A 94.013 1971 108 7 579 2546 674415068 674413105 0.000000e+00 2977
3 TraesCS2A01G367900 chr6A 96.510 1977 61 7 576 2549 57901151 57903122 0.000000e+00 3262
4 TraesCS2A01G367900 chr6A 96.304 1975 65 7 580 2549 203520917 203518946 0.000000e+00 3236
5 TraesCS2A01G367900 chr7A 95.762 1982 63 6 586 2549 689996369 689994391 0.000000e+00 3175
6 TraesCS2A01G367900 chr3A 95.665 1984 65 6 583 2549 735555338 735557317 0.000000e+00 3168
7 TraesCS2A01G367900 chr3A 95.617 1985 65 6 583 2549 617401019 617402999 0.000000e+00 3164
8 TraesCS2A01G367900 chr2D 94.761 1966 95 7 586 2549 498471644 498469685 0.000000e+00 3053
9 TraesCS2A01G367900 chr2D 93.702 1969 85 13 586 2549 547242743 547240809 0.000000e+00 2913
10 TraesCS2A01G367900 chr2D 95.028 362 14 3 581 942 16065482 16065839 1.320000e-157 566
11 TraesCS2A01G367900 chr1A 93.098 594 19 6 1 585 552149923 552150503 0.000000e+00 850
12 TraesCS2A01G367900 chr5D 92.833 586 23 13 1 585 388058251 388057684 0.000000e+00 832
13 TraesCS2A01G367900 chr6D 90.820 610 28 5 1 585 30484342 30484948 0.000000e+00 791
14 TraesCS2A01G367900 chr1D 91.587 523 38 4 64 585 416141679 416142196 0.000000e+00 717
15 TraesCS2A01G367900 chr1B 93.388 363 21 2 581 942 645321431 645321791 3.730000e-148 534
16 TraesCS2A01G367900 chr5A 93.036 359 21 3 586 944 689409578 689409224 2.910000e-144 521


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 TraesCS2A01G367900 chr2A 611723173 611725721 2548 True 4708 4708 100.000 1 2549 1 chr2A.!!$R1 2548
1 TraesCS2A01G367900 chr2A 233255253 233257222 1969 False 3214 3214 96.097 578 2549 1 chr2A.!!$F1 1971
2 TraesCS2A01G367900 chr2A 674413105 674415068 1963 True 2977 2977 94.013 579 2546 1 chr2A.!!$R2 1967
3 TraesCS2A01G367900 chr6A 57901151 57903122 1971 False 3262 3262 96.510 576 2549 1 chr6A.!!$F1 1973
4 TraesCS2A01G367900 chr6A 203518946 203520917 1971 True 3236 3236 96.304 580 2549 1 chr6A.!!$R1 1969
5 TraesCS2A01G367900 chr7A 689994391 689996369 1978 True 3175 3175 95.762 586 2549 1 chr7A.!!$R1 1963
6 TraesCS2A01G367900 chr3A 735555338 735557317 1979 False 3168 3168 95.665 583 2549 1 chr3A.!!$F2 1966
7 TraesCS2A01G367900 chr3A 617401019 617402999 1980 False 3164 3164 95.617 583 2549 1 chr3A.!!$F1 1966
8 TraesCS2A01G367900 chr2D 498469685 498471644 1959 True 3053 3053 94.761 586 2549 1 chr2D.!!$R1 1963
9 TraesCS2A01G367900 chr2D 547240809 547242743 1934 True 2913 2913 93.702 586 2549 1 chr2D.!!$R2 1963
10 TraesCS2A01G367900 chr1A 552149923 552150503 580 False 850 850 93.098 1 585 1 chr1A.!!$F1 584
11 TraesCS2A01G367900 chr5D 388057684 388058251 567 True 832 832 92.833 1 585 1 chr5D.!!$R1 584
12 TraesCS2A01G367900 chr6D 30484342 30484948 606 False 791 791 90.820 1 585 1 chr6D.!!$F1 584
13 TraesCS2A01G367900 chr1D 416141679 416142196 517 False 717 717 91.587 64 585 1 chr1D.!!$F1 521

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
670 715 1.144913 TGCTCAGTTTTGCCCCTAGTT 59.855 47.619 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 2272 0.103937 AAACACCACAAACCCATGCG 59.896 50.0 0.0 0.0 0.0 4.73 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
61 62 5.104569 TGTGGTATGATTCCTCTTGTATGCA 60.105 40.000 0.00 0.00 0.00 3.96
126 134 3.706183 TGGTTTGATATTGTGCCCATGA 58.294 40.909 0.00 0.00 0.00 3.07
153 161 6.455360 TGCAACTGAGAGAAAACAATCTTT 57.545 33.333 0.00 0.00 0.00 2.52
398 431 4.254492 GGTAGCCTTCTTACAAACCTCAG 58.746 47.826 0.00 0.00 0.00 3.35
546 591 7.168637 GCGAACTCGGTCACAAAGAAATATATA 59.831 37.037 0.69 0.00 40.23 0.86
547 592 9.027129 CGAACTCGGTCACAAAGAAATATATAA 57.973 33.333 0.00 0.00 35.37 0.98
609 654 5.423931 GGGTTAATTATCCTTTTGCCCTCAA 59.576 40.000 11.51 0.00 0.00 3.02
670 715 1.144913 TGCTCAGTTTTGCCCCTAGTT 59.855 47.619 0.00 0.00 0.00 2.24
779 824 5.123820 CAGAGACGGCCAATTTTATTCAGAA 59.876 40.000 2.24 0.00 0.00 3.02
780 825 5.888161 AGAGACGGCCAATTTTATTCAGAAT 59.112 36.000 2.24 0.20 0.00 2.40
784 829 7.122055 AGACGGCCAATTTTATTCAGAATGTTA 59.878 33.333 2.24 0.00 37.40 2.41
881 956 2.049156 CGACAGAGAGCACGGCAA 60.049 61.111 0.00 0.00 0.00 4.52
903 982 1.450491 CCACGGCGAGAGAGAGAGA 60.450 63.158 16.62 0.00 0.00 3.10
904 983 1.436195 CCACGGCGAGAGAGAGAGAG 61.436 65.000 16.62 0.00 0.00 3.20
1075 1154 3.341823 GACATGCCTGTCTTCATCTGTT 58.658 45.455 14.17 0.00 46.84 3.16
1117 1196 1.124780 TCGGAGGGTTTCTCACACAA 58.875 50.000 0.00 0.00 44.19 3.33
1144 1223 3.389925 ACCAAAATCGTCCGTTCTACA 57.610 42.857 0.00 0.00 0.00 2.74
1150 1229 0.455464 TCGTCCGTTCTACATGTGCG 60.455 55.000 9.11 7.69 0.00 5.34
1190 1269 3.165875 TCGGGGAAATTGCACCATTTTA 58.834 40.909 5.29 0.00 0.00 1.52
1209 1288 1.938585 AGTGGTCGGGATCTTTGAGA 58.061 50.000 0.00 0.00 0.00 3.27
1218 1297 4.226394 TCGGGATCTTTGAGAAATGGGTTA 59.774 41.667 0.00 0.00 0.00 2.85
1303 1382 5.766670 ACTCTGATGAATGAACTGCAAGAAA 59.233 36.000 0.00 0.00 37.43 2.52
1313 1392 4.098349 TGAACTGCAAGAAAAGCATGAAGT 59.902 37.500 0.00 0.00 41.82 3.01
1366 1445 2.342279 CACCACGAGCTCCGGAAA 59.658 61.111 20.88 0.00 43.93 3.13
1511 1590 5.061179 GGCATTTGTAGGTATGGTAATCGT 58.939 41.667 0.00 0.00 0.00 3.73
1949 2034 3.426787 TCCGGAGCCAAACAATTAAGA 57.573 42.857 0.00 0.00 0.00 2.10
2145 2234 4.914177 AAATGAAGGGTGGAAAATGCAT 57.086 36.364 0.00 0.00 0.00 3.96
2183 2272 1.295746 GGACTCGAACCCAAGACCC 59.704 63.158 0.00 0.00 0.00 4.46
2226 2315 2.493030 GCGCTGGTAACCGCTAGA 59.507 61.111 0.00 0.00 46.14 2.43
2234 2323 4.250464 CTGGTAACCGCTAGAACAAATGA 58.750 43.478 0.00 0.00 0.00 2.57
2281 2370 7.943447 GGAAGGAAGGTATACATAGTGAGACTA 59.057 40.741 5.01 0.00 34.82 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 4.558095 GCAACAAAGAATCACAGCACTCAT 60.558 41.667 0.00 0.00 0.00 2.90
69 70 1.606668 GTCGGGCAACAAAGAATCACA 59.393 47.619 0.00 0.00 39.74 3.58
126 134 6.489361 AGATTGTTTTCTCTCAGTTGCAATCT 59.511 34.615 0.59 9.72 43.36 2.40
153 161 7.446931 TGAACTTATTGAGCTTGGTACATGAAA 59.553 33.333 0.00 0.00 39.30 2.69
303 335 2.362760 TCCATTGCAGCGCCCAAT 60.363 55.556 15.69 15.69 33.41 3.16
510 544 1.349627 CGAGTTCGCATGCATCCAC 59.650 57.895 19.57 7.92 0.00 4.02
546 591 9.736414 CAGGGAAGTTTCTATCATGATCATATT 57.264 33.333 12.53 1.30 0.00 1.28
547 592 7.828223 GCAGGGAAGTTTCTATCATGATCATAT 59.172 37.037 12.53 5.52 0.00 1.78
548 593 7.164122 GCAGGGAAGTTTCTATCATGATCATA 58.836 38.462 12.53 0.00 0.00 2.15
549 594 6.002704 GCAGGGAAGTTTCTATCATGATCAT 58.997 40.000 12.53 1.18 0.00 2.45
550 595 5.371526 GCAGGGAAGTTTCTATCATGATCA 58.628 41.667 12.53 0.00 0.00 2.92
551 596 4.759183 GGCAGGGAAGTTTCTATCATGATC 59.241 45.833 12.53 0.00 0.00 2.92
552 597 4.166725 TGGCAGGGAAGTTTCTATCATGAT 59.833 41.667 13.81 13.81 0.00 2.45
553 598 3.523157 TGGCAGGGAAGTTTCTATCATGA 59.477 43.478 0.00 0.00 0.00 3.07
554 599 3.889815 TGGCAGGGAAGTTTCTATCATG 58.110 45.455 0.00 0.00 0.00 3.07
555 600 4.591321 TTGGCAGGGAAGTTTCTATCAT 57.409 40.909 0.00 0.00 0.00 2.45
556 601 4.380843 TTTGGCAGGGAAGTTTCTATCA 57.619 40.909 0.00 0.00 0.00 2.15
609 654 5.278463 GCAAAACTGAGTACATGAACACCAT 60.278 40.000 0.00 0.00 35.44 3.55
779 824 1.866237 CAAGCCACGCGTGTAACAT 59.134 52.632 34.81 16.06 35.74 2.71
780 825 3.325072 CAAGCCACGCGTGTAACA 58.675 55.556 34.81 0.00 35.74 2.41
881 956 1.378646 TCTCTCTCGCCGTGGTCAT 60.379 57.895 0.00 0.00 0.00 3.06
1117 1196 1.804601 GGACGATTTTGGTTCCTCGT 58.195 50.000 4.07 4.07 46.09 4.18
1144 1223 2.514592 CCCATTCTCGCCGCACAT 60.515 61.111 0.00 0.00 0.00 3.21
1150 1229 2.495084 GATTCTTACCCCATTCTCGCC 58.505 52.381 0.00 0.00 0.00 5.54
1190 1269 1.938585 TCTCAAAGATCCCGACCACT 58.061 50.000 0.00 0.00 0.00 4.00
1209 1288 6.098982 TGAACACCAAACAGATTAACCCATTT 59.901 34.615 0.00 0.00 0.00 2.32
1218 1297 3.006110 CCTGCATGAACACCAAACAGATT 59.994 43.478 0.00 0.00 35.16 2.40
1303 1382 1.133025 GCGCAACCATACTTCATGCTT 59.867 47.619 0.30 0.00 34.93 3.91
1366 1445 0.107459 GCTTCGCCCTCCATCTCTTT 60.107 55.000 0.00 0.00 0.00 2.52
1696 1778 7.227910 AGCTGCATTTCATTGATCAAAAGTTTT 59.772 29.630 13.09 0.00 0.00 2.43
1889 1974 6.222389 TCCACAAAAAGTTTCAGCATTATGG 58.778 36.000 0.00 0.00 0.00 2.74
1979 2064 9.921637 ATTTAAATCACGGTGTATTTGAATTGT 57.078 25.926 19.56 8.03 31.17 2.71
2183 2272 0.103937 AAACACCACAAACCCATGCG 59.896 50.000 0.00 0.00 0.00 4.73
2226 2315 6.275335 CCATGTCAAAGTCTTGTCATTTGTT 58.725 36.000 0.00 0.00 38.66 2.83
2234 2323 3.244911 CCCTACCCATGTCAAAGTCTTGT 60.245 47.826 0.00 0.00 33.94 3.16
2366 2459 3.680777 TTTTCAACCTTCCAACCCTCT 57.319 42.857 0.00 0.00 0.00 3.69
2515 2637 1.925972 GAGGGGGTGAGAAGCCCTT 60.926 63.158 12.46 5.11 45.39 3.95


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

AutoCloner maintained by Alex Coulton.