Multiple sequence alignment - TraesCS2A01G327900

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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 TraesCS2A01G327900 chr2A 100.000 3286 0 0 1 3286 559619803 559623088 0.000000e+00 6069.0
1 TraesCS2A01G327900 chr2A 91.806 720 46 9 3 712 678607701 678608417 0.000000e+00 990.0
2 TraesCS2A01G327900 chr2A 89.861 503 41 5 2 496 610054498 610053998 3.580000e-179 638.0
3 TraesCS2A01G327900 chr2A 87.552 241 19 6 491 720 610051906 610051666 5.400000e-68 268.0
4 TraesCS2A01G327900 chr2D 94.223 2354 78 17 714 3042 427958728 427956408 0.000000e+00 3541.0
5 TraesCS2A01G327900 chr2D 91.724 725 50 6 1 715 535477112 535477836 0.000000e+00 998.0
6 TraesCS2A01G327900 chr2D 86.010 579 38 16 154 713 13362377 13361823 6.110000e-162 580.0
7 TraesCS2A01G327900 chr2D 97.183 213 6 0 3069 3281 427956407 427956195 8.670000e-96 361.0
8 TraesCS2A01G327900 chr2B 93.801 1484 53 10 805 2280 504829239 504827787 0.000000e+00 2194.0
9 TraesCS2A01G327900 chr2B 94.234 1370 47 13 883 2222 512342285 512343652 0.000000e+00 2063.0
10 TraesCS2A01G327900 chr2B 86.831 1139 109 23 2165 3283 512343710 512344827 0.000000e+00 1234.0
11 TraesCS2A01G327900 chr2B 83.824 884 111 14 2406 3282 504787336 504786478 0.000000e+00 811.0
12 TraesCS2A01G327900 chr2B 97.333 75 2 0 714 788 504977906 504977832 9.570000e-26 128.0
13 TraesCS2A01G327900 chr2B 80.240 167 20 7 715 880 512342095 512342249 2.680000e-21 113.0
14 TraesCS2A01G327900 chr2B 94.828 58 2 1 2165 2222 512343653 512343709 4.520000e-14 89.8
15 TraesCS2A01G327900 chr7B 92.582 728 35 11 2 711 648279927 648280653 0.000000e+00 1027.0
16 TraesCS2A01G327900 chr7B 78.211 615 55 30 1309 1907 614282862 614282311 1.470000e-83 320.0
17 TraesCS2A01G327900 chr7B 84.959 246 23 6 1949 2191 614282312 614282078 1.520000e-58 237.0
18 TraesCS2A01G327900 chr7B 96.774 31 1 0 2656 2686 458862179 458862149 6.000000e-03 52.8
19 TraesCS2A01G327900 chr4B 91.929 731 39 10 1 713 437094373 437093645 0.000000e+00 1005.0
20 TraesCS2A01G327900 chr6B 90.574 732 45 12 2 715 720235948 720236673 0.000000e+00 948.0
21 TraesCS2A01G327900 chr1B 89.011 728 59 10 1 712 679725586 679726308 0.000000e+00 881.0
22 TraesCS2A01G327900 chr4D 90.417 647 42 8 2 630 485768510 485769154 0.000000e+00 833.0
23 TraesCS2A01G327900 chr3D 93.612 454 26 3 2 454 519323476 519323927 0.000000e+00 675.0
24 TraesCS2A01G327900 chr3D 88.973 263 18 3 463 714 519326047 519326309 6.840000e-82 315.0
25 TraesCS2A01G327900 chr7D 89.030 474 34 9 1367 1825 564577658 564578128 3.680000e-159 571.0
26 TraesCS2A01G327900 chr7D 87.258 361 28 5 1823 2176 563684408 563684757 2.380000e-106 396.0
27 TraesCS2A01G327900 chr7D 74.373 359 77 9 2644 2988 191870533 191870176 4.420000e-29 139.0
28 TraesCS2A01G327900 chr6A 79.680 625 95 18 1204 1801 358573553 358572934 3.920000e-114 422.0
29 TraesCS2A01G327900 chr6D 77.745 683 124 18 1472 2135 263044214 263043541 8.550000e-106 394.0
30 TraesCS2A01G327900 chr1A 87.398 246 16 4 463 693 508127732 508127977 5.400000e-68 268.0
31 TraesCS2A01G327900 chr1D 82.031 128 23 0 2513 2640 61968961 61968834 3.470000e-20 110.0
32 TraesCS2A01G327900 chr4A 81.890 127 15 7 2515 2637 522261947 522261825 2.090000e-17 100.0
33 TraesCS2A01G327900 chr3A 95.455 44 2 0 2640 2683 66910928 66910971 1.640000e-08 71.3
34 TraesCS2A01G327900 chr3B 100.000 29 0 0 3140 3168 527300329 527300301 2.000000e-03 54.7


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 TraesCS2A01G327900 chr2A 559619803 559623088 3285 False 6069.00 6069 100.00000 1 3286 1 chr2A.!!$F1 3285
1 TraesCS2A01G327900 chr2A 678607701 678608417 716 False 990.00 990 91.80600 3 712 1 chr2A.!!$F2 709
2 TraesCS2A01G327900 chr2A 610051666 610054498 2832 True 453.00 638 88.70650 2 720 2 chr2A.!!$R1 718
3 TraesCS2A01G327900 chr2D 427956195 427958728 2533 True 1951.00 3541 95.70300 714 3281 2 chr2D.!!$R2 2567
4 TraesCS2A01G327900 chr2D 535477112 535477836 724 False 998.00 998 91.72400 1 715 1 chr2D.!!$F1 714
5 TraesCS2A01G327900 chr2D 13361823 13362377 554 True 580.00 580 86.01000 154 713 1 chr2D.!!$R1 559
6 TraesCS2A01G327900 chr2B 504827787 504829239 1452 True 2194.00 2194 93.80100 805 2280 1 chr2B.!!$R2 1475
7 TraesCS2A01G327900 chr2B 512342095 512344827 2732 False 874.95 2063 89.03325 715 3283 4 chr2B.!!$F1 2568
8 TraesCS2A01G327900 chr2B 504786478 504787336 858 True 811.00 811 83.82400 2406 3282 1 chr2B.!!$R1 876
9 TraesCS2A01G327900 chr7B 648279927 648280653 726 False 1027.00 1027 92.58200 2 711 1 chr7B.!!$F1 709
10 TraesCS2A01G327900 chr7B 614282078 614282862 784 True 278.50 320 81.58500 1309 2191 2 chr7B.!!$R2 882
11 TraesCS2A01G327900 chr4B 437093645 437094373 728 True 1005.00 1005 91.92900 1 713 1 chr4B.!!$R1 712
12 TraesCS2A01G327900 chr6B 720235948 720236673 725 False 948.00 948 90.57400 2 715 1 chr6B.!!$F1 713
13 TraesCS2A01G327900 chr1B 679725586 679726308 722 False 881.00 881 89.01100 1 712 1 chr1B.!!$F1 711
14 TraesCS2A01G327900 chr4D 485768510 485769154 644 False 833.00 833 90.41700 2 630 1 chr4D.!!$F1 628
15 TraesCS2A01G327900 chr3D 519323476 519326309 2833 False 495.00 675 91.29250 2 714 2 chr3D.!!$F1 712
16 TraesCS2A01G327900 chr6A 358572934 358573553 619 True 422.00 422 79.68000 1204 1801 1 chr6A.!!$R1 597
17 TraesCS2A01G327900 chr6D 263043541 263044214 673 True 394.00 394 77.74500 1472 2135 1 chr6D.!!$R1 663

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
689 4917 3.46814 GACCACCGGTAGCTCCCC 61.468 72.222 6.87 0.0 35.25 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2625 7128 0.184451 GGCAGATGTGACATCCCCAT 59.816 55.0 21.05 0.45 0.0 4.0 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
562 4790 9.351570 GTAAAAAGTACTACACTATCCTGACAC 57.648 37.037 0.00 0.00 36.04 3.67
673 4901 5.245531 GTCAGTACATCATTGGTGGAAAGA 58.754 41.667 1.31 0.00 0.00 2.52
689 4917 3.468140 GACCACCGGTAGCTCCCC 61.468 72.222 6.87 0.00 35.25 4.81
1159 5435 4.752879 GGGCTGCTTCCGCGTGTA 62.753 66.667 4.92 0.00 39.65 2.90
1405 5681 1.449601 CCAGGTCGGACCAAATCGG 60.450 63.158 27.87 15.58 41.95 4.18
1834 6150 3.610040 TCAGCTCTAAATTCTTGGCGA 57.390 42.857 0.00 0.00 0.00 5.54
1882 6204 2.219325 CTGAGTGAGCACCCCGTCTC 62.219 65.000 0.00 0.00 0.00 3.36
2074 6396 4.670992 GCGTTCAACTACGATGACTACAGA 60.671 45.833 0.00 0.00 43.99 3.41
2154 6485 2.201490 TAGCTATCTGGCGGGGCT 59.799 61.111 12.29 12.29 37.29 5.19
2163 6506 2.035155 GGCGGGGCTTGTTTAGGT 59.965 61.111 0.00 0.00 0.00 3.08
2170 6513 2.074576 GGGCTTGTTTAGGTTCGAGAC 58.925 52.381 0.00 0.00 0.00 3.36
2262 6722 6.130298 TGTGAATTGTCGTTGTTTTCATCT 57.870 33.333 0.00 0.00 0.00 2.90
2504 7005 3.066760 AGTGTTGTGCTTACCTTTTCAGC 59.933 43.478 0.00 0.00 0.00 4.26
2507 7008 0.109735 GTGCTTACCTTTTCAGCGGC 60.110 55.000 0.00 0.00 36.24 6.53
2529 7030 4.462133 CTCATCCATCCTCAAATTGCTCT 58.538 43.478 0.00 0.00 0.00 4.09
2641 7144 7.392766 TCTATTAAATGGGGATGTCACATCT 57.607 36.000 17.46 0.00 0.00 2.90
2902 7406 1.181098 GGCAGAGTGGCACCAAACAT 61.181 55.000 15.27 0.00 43.14 2.71
2965 7469 3.426159 CGTTTTGAAATGTCTATGGCGCT 60.426 43.478 7.64 0.00 0.00 5.92
2982 7486 3.630312 GGCGCTAATTTTTAGGTGGATGA 59.370 43.478 7.64 0.00 0.00 2.92
3053 7563 2.685106 TGGAGCACCCACCAAAAATA 57.315 45.000 0.00 0.00 40.82 1.40
3054 7564 2.243810 TGGAGCACCCACCAAAAATAC 58.756 47.619 0.00 0.00 40.82 1.89
3158 7669 5.700832 CAGGCCGATATAATGACTTTGCTAA 59.299 40.000 0.00 0.00 0.00 3.09
3220 7731 2.779506 GGTGGTAGAACAAGGTTCTGG 58.220 52.381 19.03 0.00 0.00 3.86
3285 7796 6.899393 CACATGTGTGGGGCTAATATTATT 57.101 37.500 18.03 0.00 42.10 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 139 8.429641 TCAGGTTTCTGAAGTAAGTGAAATACT 58.570 33.333 0.00 0.00 46.08 2.12
197 201 5.122239 TGAACTTGTTATTTCAGAGATGCGG 59.878 40.000 0.00 0.00 0.00 5.69
457 461 9.974980 GTTTAAAATTTTAGATGACCAACCTGA 57.025 29.630 10.40 0.00 0.00 3.86
689 4917 3.488489 CAAAGTCATTTTTACCGGAGCG 58.512 45.455 9.46 0.00 0.00 5.03
1054 5330 2.134287 ACCGGGATCTCCACCATCG 61.134 63.158 6.32 0.00 37.91 3.84
1189 5465 4.161295 CGGCGGCCTTCATCTCCA 62.161 66.667 18.34 0.00 0.00 3.86
1801 6108 3.510388 AGAGCTGAAACGAATCGATGA 57.490 42.857 10.55 0.00 0.00 2.92
1882 6204 2.954753 GCTCCACGCCTGAAACACG 61.955 63.158 0.00 0.00 0.00 4.49
1954 6276 2.048784 ATGGCGATCGAGATGCGG 60.049 61.111 21.57 0.00 41.33 5.69
2128 6450 0.380733 CCAGATAGCTACGTCACGCA 59.619 55.000 0.00 0.00 0.00 5.24
2154 6485 6.576185 AGTTTACAGTCTCGAACCTAAACAA 58.424 36.000 18.22 0.00 35.67 2.83
2163 6506 3.821600 AGCTCAGAGTTTACAGTCTCGAA 59.178 43.478 0.00 0.00 36.03 3.71
2292 6752 4.314740 TTGCAATTCGTACCAGCTTTTT 57.685 36.364 0.00 0.00 0.00 1.94
2293 6753 4.314740 TTTGCAATTCGTACCAGCTTTT 57.685 36.364 0.00 0.00 0.00 2.27
2294 6754 4.202111 ACTTTTGCAATTCGTACCAGCTTT 60.202 37.500 0.00 0.00 0.00 3.51
2295 6755 3.317993 ACTTTTGCAATTCGTACCAGCTT 59.682 39.130 0.00 0.00 0.00 3.74
2296 6756 2.884639 ACTTTTGCAATTCGTACCAGCT 59.115 40.909 0.00 0.00 0.00 4.24
2297 6757 2.979813 CACTTTTGCAATTCGTACCAGC 59.020 45.455 0.00 0.00 0.00 4.85
2298 6758 4.481930 TCACTTTTGCAATTCGTACCAG 57.518 40.909 0.00 0.00 0.00 4.00
2299 6759 4.902443 TTCACTTTTGCAATTCGTACCA 57.098 36.364 0.00 0.00 0.00 3.25
2300 6760 5.746721 AGTTTTCACTTTTGCAATTCGTACC 59.253 36.000 0.00 0.00 0.00 3.34
2301 6761 6.627274 CAGTTTTCACTTTTGCAATTCGTAC 58.373 36.000 0.00 0.00 0.00 3.67
2302 6762 5.231147 GCAGTTTTCACTTTTGCAATTCGTA 59.769 36.000 0.00 0.00 34.99 3.43
2303 6763 4.032786 GCAGTTTTCACTTTTGCAATTCGT 59.967 37.500 0.00 0.00 34.99 3.85
2304 6764 4.032672 TGCAGTTTTCACTTTTGCAATTCG 59.967 37.500 0.00 0.00 41.34 3.34
2504 7005 2.267174 ATTTGAGGATGGATGAGCCG 57.733 50.000 0.00 0.00 40.66 5.52
2507 7008 4.462133 AGAGCAATTTGAGGATGGATGAG 58.538 43.478 0.00 0.00 0.00 2.90
2585 7088 4.826733 ACCACTCATATCAACAAGTTGCAA 59.173 37.500 8.04 0.00 40.24 4.08
2625 7128 0.184451 GGCAGATGTGACATCCCCAT 59.816 55.000 21.05 0.45 0.00 4.00
2627 7130 1.609239 TGGCAGATGTGACATCCCC 59.391 57.895 21.05 20.41 36.47 4.81
2641 7144 4.233632 TGTGTAGATGGATTTGATGGCA 57.766 40.909 0.00 0.00 0.00 4.92
2674 7177 2.923121 AGCGGCTCATAAATGACACAT 58.077 42.857 0.00 0.00 32.50 3.21
2676 7179 4.094294 TGTTTAGCGGCTCATAAATGACAC 59.906 41.667 5.39 0.00 32.50 3.67
2720 7223 3.511540 GCTTGCCTGGAGGTAAATTTCTT 59.488 43.478 0.00 0.00 39.29 2.52
2965 7469 6.491745 TGTGCACTTCATCCACCTAAAAATTA 59.508 34.615 19.41 0.00 0.00 1.40
2982 7486 0.467844 TGGGCAAGACATGTGCACTT 60.468 50.000 19.41 9.21 45.98 3.16
3053 7563 0.251832 ATCCCATCCTCTATCGCCGT 60.252 55.000 0.00 0.00 0.00 5.68
3054 7564 0.174389 CATCCCATCCTCTATCGCCG 59.826 60.000 0.00 0.00 0.00 6.46
3158 7669 3.307762 GGGATGTGAGGTAAGAGCAACTT 60.308 47.826 2.10 2.10 42.04 2.66
3220 7731 0.526662 CCGCCACCTATATCCTCGTC 59.473 60.000 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.