Multiple sequence alignment - TraesCS2A01G200800

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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 TraesCS2A01G200800 chr2A 100.000 2321 0 0 1 2321 173782777 173785097 0.000000e+00 4287.0
1 TraesCS2A01G200800 chr2A 93.846 65 3 1 2194 2258 73540726 73540663 1.900000e-16 97.1
2 TraesCS2A01G200800 chr2A 90.164 61 3 3 2196 2256 639061715 639061658 2.470000e-10 76.8
3 TraesCS2A01G200800 chr2D 96.138 1424 45 4 902 2318 174239733 174241153 0.000000e+00 2316.0
4 TraesCS2A01G200800 chr2D 98.400 125 2 0 893 1017 174239621 174239745 1.080000e-53 220.0
5 TraesCS2A01G200800 chr2D 91.803 61 2 3 2196 2256 494650861 494650918 5.320000e-12 82.4
6 TraesCS2A01G200800 chr2B 96.117 1133 41 2 938 2068 222093433 222094564 0.000000e+00 1845.0
7 TraesCS2A01G200800 chr2B 95.940 1133 43 2 938 2068 222088810 222089941 0.000000e+00 1834.0
8 TraesCS2A01G200800 chr2B 93.200 250 10 3 2076 2318 222094687 222094936 6.100000e-96 361.0
9 TraesCS2A01G200800 chr2B 93.694 222 5 4 2076 2290 222090064 222090283 8.000000e-85 324.0
10 TraesCS2A01G200800 chr2B 96.226 53 2 0 895 947 222088726 222088778 1.140000e-13 87.9
11 TraesCS2A01G200800 chr2B 97.059 34 1 0 1823 1856 793461939 793461906 8.960000e-05 58.4
12 TraesCS2A01G200800 chr6A 91.454 901 68 8 3 896 262050339 262049441 0.000000e+00 1229.0
13 TraesCS2A01G200800 chr5A 90.576 902 76 8 3 898 534360864 534359966 0.000000e+00 1186.0
14 TraesCS2A01G200800 chr1A 90.576 902 74 8 3 896 101105658 101106556 0.000000e+00 1184.0
15 TraesCS2A01G200800 chr3A 90.122 901 78 9 3 896 550298235 550299131 0.000000e+00 1160.0
16 TraesCS2A01G200800 chr6B 89.659 909 77 16 3 899 117763142 117764045 0.000000e+00 1142.0
17 TraesCS2A01G200800 chr4B 89.724 905 76 16 3 896 65949524 65950422 0.000000e+00 1140.0
18 TraesCS2A01G200800 chr4B 91.304 69 3 1 2193 2258 35022476 35022544 8.830000e-15 91.6
19 TraesCS2A01G200800 chr4B 88.571 70 2 1 2196 2259 553018490 553018421 1.910000e-11 80.5
20 TraesCS2A01G200800 chr3B 89.712 904 78 14 3 896 744905171 744906069 0.000000e+00 1140.0
21 TraesCS2A01G200800 chr7B 89.503 905 80 10 3 896 735000886 735001786 0.000000e+00 1131.0
22 TraesCS2A01G200800 chr5B 89.427 908 79 16 3 898 664252532 664253434 0.000000e+00 1129.0
23 TraesCS2A01G200800 chr5B 97.059 34 1 0 1823 1856 24283028 24282995 8.960000e-05 58.4
24 TraesCS2A01G200800 chr7D 91.045 67 3 1 2191 2257 111055315 111055252 1.140000e-13 87.9
25 TraesCS2A01G200800 chrUn 97.059 34 1 0 1823 1856 50555800 50555767 8.960000e-05 58.4
26 TraesCS2A01G200800 chrUn 97.059 34 1 0 1823 1856 401384211 401384178 8.960000e-05 58.4
27 TraesCS2A01G200800 chrUn 97.059 34 1 0 1823 1856 436530158 436530125 8.960000e-05 58.4
28 TraesCS2A01G200800 chr4A 97.059 34 1 0 1823 1856 704303532 704303499 8.960000e-05 58.4


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 TraesCS2A01G200800 chr2A 173782777 173785097 2320 False 4287.00 4287 100.0000 1 2321 1 chr2A.!!$F1 2320
1 TraesCS2A01G200800 chr2D 174239621 174241153 1532 False 1268.00 2316 97.2690 893 2318 2 chr2D.!!$F2 1425
2 TraesCS2A01G200800 chr2B 222088726 222094936 6210 False 890.38 1845 95.0354 895 2318 5 chr2B.!!$F1 1423
3 TraesCS2A01G200800 chr6A 262049441 262050339 898 True 1229.00 1229 91.4540 3 896 1 chr6A.!!$R1 893
4 TraesCS2A01G200800 chr5A 534359966 534360864 898 True 1186.00 1186 90.5760 3 898 1 chr5A.!!$R1 895
5 TraesCS2A01G200800 chr1A 101105658 101106556 898 False 1184.00 1184 90.5760 3 896 1 chr1A.!!$F1 893
6 TraesCS2A01G200800 chr3A 550298235 550299131 896 False 1160.00 1160 90.1220 3 896 1 chr3A.!!$F1 893
7 TraesCS2A01G200800 chr6B 117763142 117764045 903 False 1142.00 1142 89.6590 3 899 1 chr6B.!!$F1 896
8 TraesCS2A01G200800 chr4B 65949524 65950422 898 False 1140.00 1140 89.7240 3 896 1 chr4B.!!$F2 893
9 TraesCS2A01G200800 chr3B 744905171 744906069 898 False 1140.00 1140 89.7120 3 896 1 chr3B.!!$F1 893
10 TraesCS2A01G200800 chr7B 735000886 735001786 900 False 1131.00 1131 89.5030 3 896 1 chr7B.!!$F1 893
11 TraesCS2A01G200800 chr5B 664252532 664253434 902 False 1129.00 1129 89.4270 3 898 1 chr5B.!!$F1 895

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
453 466 0.814457 AGAGTGTGAGATCACCGAGC 59.186 55.0 10.34 0.0 45.88 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1325 6022 1.139853 TGACATTGGTTTTGGGTTGCC 59.86 47.619 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
74 75 4.003788 CCGTTGGTGGCCTCGAGT 62.004 66.667 12.31 0.00 0.00 4.18
104 105 3.276846 CGGCGGCGGAAATAAGGG 61.277 66.667 25.36 0.00 0.00 3.95
444 457 1.299562 GACGGCGAGAGAGTGTGAGA 61.300 60.000 16.62 0.00 0.00 3.27
453 466 0.814457 AGAGTGTGAGATCACCGAGC 59.186 55.000 10.34 0.00 45.88 5.03
454 467 0.814457 GAGTGTGAGATCACCGAGCT 59.186 55.000 10.34 0.00 45.88 4.09
477 490 1.816835 CTGGGGCGCGTCTTATATAGA 59.183 52.381 11.94 0.00 0.00 1.98
645 670 4.609995 GGGAAACGAGGCGATGAA 57.390 55.556 0.00 0.00 0.00 2.57
666 691 2.971452 GACGAAGGGCCGAGAAGT 59.029 61.111 0.00 0.00 0.00 3.01
707 732 3.972276 GCCCGTGGCTTTTTCGCA 61.972 61.111 7.58 0.00 46.69 5.10
785 814 3.284449 GCCGGCACTGTTTTCGGT 61.284 61.111 24.80 0.00 43.87 4.69
789 818 1.841663 CGGCACTGTTTTCGGTCCAG 61.842 60.000 0.00 0.00 37.30 3.86
812 841 1.161843 GGCGAAAATCGGGTTTCTGA 58.838 50.000 1.64 0.00 40.84 3.27
840 869 1.270625 ACTGGACTGATTTTTCGGCGA 60.271 47.619 4.99 4.99 0.00 5.54
872 904 2.150397 AACGTCTGGAAAGGTCTTCG 57.850 50.000 0.00 0.00 0.00 3.79
947 5644 1.270550 GCAGACCACCAACAAATCCAG 59.729 52.381 0.00 0.00 0.00 3.86
1012 5709 0.179065 CGATTCCATGAGCAGGAGCA 60.179 55.000 0.00 0.00 45.49 4.26
1325 6022 1.273606 CGAGGCCCATACATGACCTAG 59.726 57.143 0.00 1.93 35.27 3.02
1339 6036 0.558712 ACCTAGGCAACCCAAAACCA 59.441 50.000 9.30 0.00 37.17 3.67
1344 6041 1.416030 AGGCAACCCAAAACCAATGTC 59.584 47.619 0.00 0.00 37.17 3.06
1376 6073 9.787532 GTACATTCATATGCTGTTTTGTTGTAT 57.212 29.630 13.71 0.00 35.03 2.29
1382 6079 9.571810 TCATATGCTGTTTTGTTGTATGATTTC 57.428 29.630 0.00 0.00 0.00 2.17
1595 6292 9.543783 AATAGATTCGTTTATCTCCTTGTAACC 57.456 33.333 0.00 0.00 36.34 2.85
1655 6352 9.682465 TTCATCTCTCTCATTTTTCTGATTCAT 57.318 29.630 0.00 0.00 0.00 2.57
1743 6440 4.970662 TTCTGCTGAAATCTTACATGGC 57.029 40.909 3.21 0.00 0.00 4.40
1787 6484 6.861065 ACTGTGTTACTATGAAACCTTGTG 57.139 37.500 0.00 0.00 0.00 3.33
1999 6698 3.531538 GGAAAGAGGCAATATGACGACA 58.468 45.455 0.00 0.00 0.00 4.35
2001 6700 2.231215 AGAGGCAATATGACGACAGC 57.769 50.000 0.00 0.00 0.00 4.40
2004 6703 0.305922 GGCAATATGACGACAGCAGC 59.694 55.000 0.00 0.00 0.00 5.25
2073 6772 9.911788 ACTTAACTCTGATCCAATGTATGATTT 57.088 29.630 0.00 0.00 0.00 2.17
2101 6915 4.513000 GCTAAAGCTTTCAGATCGTCAG 57.487 45.455 16.57 5.21 38.21 3.51
2168 6987 1.277557 TGAAAAGAGAGCTCTGAGGGC 59.722 52.381 23.91 6.06 40.36 5.19
2177 6998 1.488393 AGCTCTGAGGGCCATAAGTTC 59.512 52.381 6.18 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
373 374 0.323633 CAGTTCATCACCCATGGCCA 60.324 55.000 8.56 8.56 32.64 5.36
614 639 0.462225 TTTCCCGCGGCGAATCAATA 60.462 50.000 25.92 6.61 0.00 1.90
645 670 2.048503 CTCGGCCCTTCGTCGTTT 60.049 61.111 0.00 0.00 0.00 3.60
666 691 4.700365 CGTCAGCGACACGGCTCA 62.700 66.667 8.91 0.00 42.53 4.26
695 720 1.066858 TGTTTTGGTGCGAAAAAGCCA 60.067 42.857 0.00 0.00 36.02 4.75
707 732 2.190841 CCGGGCGAACTGTTTTGGT 61.191 57.895 0.00 0.00 0.00 3.67
774 803 1.228154 GGCCTGGACCGAAAACAGT 60.228 57.895 0.00 0.00 0.00 3.55
785 814 2.437716 GATTTTCGCCGGCCTGGA 60.438 61.111 23.46 10.06 42.00 3.86
806 835 2.048222 CAGTCGCGCCCTCAGAAA 60.048 61.111 0.00 0.00 0.00 2.52
825 854 1.908066 GCCGTCGCCGAAAAATCAGT 61.908 55.000 0.00 0.00 35.63 3.41
827 856 2.864589 GCCGTCGCCGAAAAATCA 59.135 55.556 0.00 0.00 35.63 2.57
1325 6022 1.139853 TGACATTGGTTTTGGGTTGCC 59.860 47.619 0.00 0.00 0.00 4.52
1339 6036 5.412594 GCATATGAATGTACCGGATGACATT 59.587 40.000 24.28 24.28 46.40 2.71
1344 6041 4.318332 ACAGCATATGAATGTACCGGATG 58.682 43.478 9.46 0.00 35.38 3.51
1376 6073 8.298854 CAACATCAGTGAATTTACAGGAAATCA 58.701 33.333 0.00 0.00 36.71 2.57
1382 6079 5.939883 TCTCCAACATCAGTGAATTTACAGG 59.060 40.000 0.00 0.00 0.00 4.00
1655 6352 4.183865 CAACACTAGCTATAACTGCTGCA 58.816 43.478 0.88 0.88 41.32 4.41
1743 6440 2.918712 ATGTGGAAGCCCGAAGATAG 57.081 50.000 0.00 0.00 34.29 2.08
1787 6484 3.092334 ACTTGGACAAAATTTCACCGC 57.908 42.857 0.00 0.00 0.00 5.68
1999 6698 6.770746 AAAAGAATCTATCAATGTGCTGCT 57.229 33.333 0.00 0.00 0.00 4.24
2101 6915 6.263344 GTGTGTTCTTTCTTTTAGGGACAAC 58.737 40.000 0.00 0.00 0.00 3.32
2160 6979 2.501723 GAGTGAACTTATGGCCCTCAGA 59.498 50.000 0.00 0.00 0.00 3.27
2168 6987 3.012518 CAAGGCTGGAGTGAACTTATGG 58.987 50.000 0.00 0.00 0.00 2.74
2177 6998 3.432326 GGGTAGTTATCAAGGCTGGAGTG 60.432 52.174 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.