Multiple sequence alignment - TraesCS2A01G031900

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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 TraesCS2A01G031900 chr2A 100.000 3488 0 0 1 3488 14684464 14680977 0.000000e+00 6442
1 TraesCS2A01G031900 chr2A 94.508 965 48 5 1 964 15971487 15970527 0.000000e+00 1483
2 TraesCS2A01G031900 chr2A 90.989 1021 79 10 965 1974 14721079 14720061 0.000000e+00 1363
3 TraesCS2A01G031900 chr2A 91.498 988 77 6 965 1947 14730408 14729423 0.000000e+00 1352
4 TraesCS2A01G031900 chr2A 90.775 1019 73 17 965 1974 14740533 14739527 0.000000e+00 1341
5 TraesCS2A01G031900 chr2A 91.122 980 79 8 965 1937 14711813 14710835 0.000000e+00 1321
6 TraesCS2A01G031900 chr2A 89.912 1021 93 9 965 1977 14703572 14702554 0.000000e+00 1306
7 TraesCS2A01G031900 chr2A 99.694 653 2 0 312 964 14690092 14689440 0.000000e+00 1195
8 TraesCS2A01G031900 chr2A 87.473 942 89 17 2007 2922 14720067 14719129 0.000000e+00 1059
9 TraesCS2A01G031900 chr2A 88.462 754 73 7 2004 2746 14739536 14738786 0.000000e+00 898
10 TraesCS2A01G031900 chr2A 89.201 713 53 14 2786 3482 14707438 14706734 0.000000e+00 869
11 TraesCS2A01G031900 chr2A 86.763 763 72 18 1996 2754 14710816 14710079 0.000000e+00 822
12 TraesCS2A01G031900 chr2A 86.957 736 70 14 2013 2746 14729403 14728692 0.000000e+00 804
13 TraesCS2A01G031900 chr2A 86.631 748 70 17 2005 2746 14702562 14701839 0.000000e+00 800
14 TraesCS2A01G031900 chr2A 89.219 538 42 9 2786 3311 14726648 14726115 0.000000e+00 658
15 TraesCS2A01G031900 chr2A 89.140 442 37 8 2829 3266 14694954 14694520 1.100000e-149 540
16 TraesCS2A01G031900 chr2A 84.553 369 33 10 3118 3482 14726119 14725771 9.270000e-91 344
17 TraesCS2A01G031900 chr2A 93.617 188 9 3 3297 3482 14694521 14694335 9.540000e-71 278
18 TraesCS2A01G031900 chr2D 97.053 2545 52 5 965 3488 12626603 12624061 0.000000e+00 4263
19 TraesCS2A01G031900 chr2D 91.139 1027 76 12 965 1983 12632405 12631386 0.000000e+00 1378
20 TraesCS2A01G031900 chr2D 90.385 572 40 13 2921 3488 12630512 12629952 0.000000e+00 737
21 TraesCS2A01G031900 chr2D 88.327 514 45 8 1985 2490 12631410 12630904 1.390000e-168 603
22 TraesCS2A01G031900 chr2D 86.441 295 22 5 2507 2801 12630790 12630514 1.220000e-79 307
23 TraesCS2A01G031900 chr2D 82.229 332 59 0 2011 2342 37297264 37297595 1.580000e-73 287
24 TraesCS2A01G031900 chr2B 92.284 985 68 7 965 1942 20146605 20147588 0.000000e+00 1391
25 TraesCS2A01G031900 chr2B 85.281 890 74 22 2007 2864 20147605 20148469 0.000000e+00 865
26 TraesCS2A01G031900 chr2B 80.928 582 70 21 2907 3486 20148462 20149004 4.160000e-114 422
27 TraesCS2A01G031900 chr6B 87.835 970 76 27 4 964 710975617 710974681 0.000000e+00 1099
28 TraesCS2A01G031900 chr6B 85.333 975 120 19 1 964 446001939 446002901 0.000000e+00 987
29 TraesCS2A01G031900 chr6B 86.254 662 75 13 312 964 445996356 445997010 0.000000e+00 704
30 TraesCS2A01G031900 chr5B 87.642 971 83 22 1 964 125738914 125739854 0.000000e+00 1094
31 TraesCS2A01G031900 chr5B 87.359 973 82 25 1 964 694855552 694856492 0.000000e+00 1077
32 TraesCS2A01G031900 chr5B 86.653 974 87 27 1 964 695139446 695140386 0.000000e+00 1038
33 TraesCS2A01G031900 chr5B 82.243 963 138 21 976 1914 533035293 533034340 0.000000e+00 800
34 TraesCS2A01G031900 chr5B 80.702 969 162 23 958 1912 533018678 533017721 0.000000e+00 730
35 TraesCS2A01G031900 chr5B 80.621 934 160 18 964 1888 533494088 533493167 0.000000e+00 702
36 TraesCS2A01G031900 chr5B 81.829 809 124 21 1114 1914 533508983 533508190 0.000000e+00 658
37 TraesCS2A01G031900 chr5B 81.026 780 124 15 1114 1890 533451072 533450314 1.790000e-167 599
38 TraesCS2A01G031900 chr5B 79.219 794 141 20 1109 1888 531817220 531818003 6.630000e-147 531
39 TraesCS2A01G031900 chr5B 80.745 483 78 12 2001 2474 533034294 533033818 2.560000e-96 363
40 TraesCS2A01G031900 chr5B 83.642 324 50 2 2019 2342 533088020 533087700 5.660000e-78 302
41 TraesCS2A01G031900 chr5B 81.525 341 54 6 2003 2340 533514221 533513887 4.440000e-69 272
42 TraesCS2A01G031900 chr3B 87.241 964 94 16 4 965 380385083 380384147 0.000000e+00 1072
43 TraesCS2A01G031900 chr3B 87.113 970 92 15 1 964 652245914 652246856 0.000000e+00 1068
44 TraesCS2A01G031900 chr3B 84.715 1001 101 26 4 964 27421709 27420721 0.000000e+00 953
45 TraesCS2A01G031900 chr3B 88.264 622 54 15 353 964 27427774 27427162 0.000000e+00 726
46 TraesCS2A01G031900 chr1A 84.270 979 114 27 1 964 409079892 409080845 0.000000e+00 918
47 TraesCS2A01G031900 chr4A 91.212 660 38 8 312 964 660722592 660721946 0.000000e+00 880
48 TraesCS2A01G031900 chr5D 82.827 955 137 19 976 1914 438438663 438437720 0.000000e+00 830
49 TraesCS2A01G031900 chr5D 80.704 938 153 23 964 1888 438589498 438588576 0.000000e+00 704
50 TraesCS2A01G031900 chr5D 79.769 954 156 23 976 1914 438545012 438544081 0.000000e+00 658
51 TraesCS2A01G031900 chr5D 81.706 809 126 20 1114 1914 438604903 438604109 0.000000e+00 654
52 TraesCS2A01G031900 chr5D 81.306 781 128 15 1116 1889 438722065 438721296 4.950000e-173 617
53 TraesCS2A01G031900 chr5D 77.568 954 166 37 967 1888 437867291 437868228 1.840000e-147 532
54 TraesCS2A01G031900 chr5D 77.948 653 111 16 1116 1761 438658181 438657555 9.140000e-101 377
55 TraesCS2A01G031900 chr5D 80.538 483 79 13 2001 2474 438437674 438437198 1.190000e-94 357
56 TraesCS2A01G031900 chr5D 84.084 333 50 1 2004 2336 438454080 438453751 5.620000e-83 318
57 TraesCS2A01G031900 chr5D 82.059 340 58 1 2003 2342 438721226 438720890 1.580000e-73 287
58 TraesCS2A01G031900 chr5D 81.763 329 51 7 2020 2342 438060467 438060792 2.060000e-67 267
59 TraesCS2A01G031900 chr5D 81.818 308 53 3 2026 2331 438442242 438441936 4.470000e-64 255
60 TraesCS2A01G031900 chr5D 79.714 350 65 5 1993 2340 438624123 438623778 7.480000e-62 248
61 TraesCS2A01G031900 chr5D 80.435 322 57 5 2020 2340 438604041 438603725 1.250000e-59 241
62 TraesCS2A01G031900 chr5A 80.086 929 156 23 976 1888 554201157 554200242 0.000000e+00 664
63 TraesCS2A01G031900 chr5A 91.529 484 32 8 483 964 544297801 544298277 0.000000e+00 658
64 TraesCS2A01G031900 chr5A 83.378 373 56 5 2001 2371 553490547 553490179 1.200000e-89 340
65 TraesCS2A01G031900 chr5A 84.071 339 51 1 2004 2342 553537876 553537541 1.210000e-84 324
66 TraesCS2A01G031900 chrUn 81.992 783 132 8 1114 1890 63291670 63290891 0.000000e+00 656
67 TraesCS2A01G031900 chrUn 83.262 466 75 3 1427 1890 299954523 299954059 3.220000e-115 425
68 TraesCS2A01G031900 chrUn 80.337 356 65 3 2001 2355 63290847 63290496 7.420000e-67 265
69 TraesCS2A01G031900 chrUn 80.337 356 65 3 2001 2355 299954015 299953664 7.420000e-67 265
70 TraesCS2A01G031900 chrUn 80.541 185 36 0 2175 2359 63340445 63340261 3.630000e-30 143
71 TraesCS2A01G031900 chr7D 77.825 947 174 31 965 1886 101732788 101733723 1.410000e-153 553
72 TraesCS2A01G031900 chr7A 77.683 941 171 27 965 1888 105512550 105513468 3.960000e-149 538
73 TraesCS2A01G031900 chr7B 77.399 938 177 24 965 1888 59072721 59073637 3.080000e-145 525
74 TraesCS2A01G031900 chr7B 77.191 947 172 32 965 1886 59066467 59067394 2.400000e-141 512
75 TraesCS2A01G031900 chr4B 76.613 248 56 2 1402 1648 659483067 659482821 6.070000e-28 135
76 TraesCS2A01G031900 chr4B 75.806 248 58 2 1402 1648 659498601 659498355 1.310000e-24 124


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 TraesCS2A01G031900 chr2A 14680977 14684464 3487 True 6442.000000 6442 100.000000 1 3488 1 chr2A.!!$R1 3487
1 TraesCS2A01G031900 chr2A 15970527 15971487 960 True 1483.000000 1483 94.508000 1 964 1 chr2A.!!$R3 963
2 TraesCS2A01G031900 chr2A 14719129 14721079 1950 True 1211.000000 1363 89.231000 965 2922 2 chr2A.!!$R6 1957
3 TraesCS2A01G031900 chr2A 14689440 14690092 652 True 1195.000000 1195 99.694000 312 964 1 chr2A.!!$R2 652
4 TraesCS2A01G031900 chr2A 14738786 14740533 1747 True 1119.500000 1341 89.618500 965 2746 2 chr2A.!!$R8 1781
5 TraesCS2A01G031900 chr2A 14701839 14711813 9974 True 1023.600000 1321 88.725800 965 3482 5 chr2A.!!$R5 2517
6 TraesCS2A01G031900 chr2A 14725771 14730408 4637 True 789.500000 1352 88.056750 965 3482 4 chr2A.!!$R7 2517
7 TraesCS2A01G031900 chr2A 14694335 14694954 619 True 409.000000 540 91.378500 2829 3482 2 chr2A.!!$R4 653
8 TraesCS2A01G031900 chr2D 12624061 12632405 8344 True 1457.600000 4263 90.669000 965 3488 5 chr2D.!!$R1 2523
9 TraesCS2A01G031900 chr2B 20146605 20149004 2399 False 892.666667 1391 86.164333 965 3486 3 chr2B.!!$F1 2521
10 TraesCS2A01G031900 chr6B 710974681 710975617 936 True 1099.000000 1099 87.835000 4 964 1 chr6B.!!$R1 960
11 TraesCS2A01G031900 chr6B 446001939 446002901 962 False 987.000000 987 85.333000 1 964 1 chr6B.!!$F2 963
12 TraesCS2A01G031900 chr6B 445996356 445997010 654 False 704.000000 704 86.254000 312 964 1 chr6B.!!$F1 652
13 TraesCS2A01G031900 chr5B 125738914 125739854 940 False 1094.000000 1094 87.642000 1 964 1 chr5B.!!$F1 963
14 TraesCS2A01G031900 chr5B 694855552 694856492 940 False 1077.000000 1077 87.359000 1 964 1 chr5B.!!$F3 963
15 TraesCS2A01G031900 chr5B 695139446 695140386 940 False 1038.000000 1038 86.653000 1 964 1 chr5B.!!$F4 963
16 TraesCS2A01G031900 chr5B 533017721 533018678 957 True 730.000000 730 80.702000 958 1912 1 chr5B.!!$R1 954
17 TraesCS2A01G031900 chr5B 533493167 533494088 921 True 702.000000 702 80.621000 964 1888 1 chr5B.!!$R4 924
18 TraesCS2A01G031900 chr5B 533508190 533508983 793 True 658.000000 658 81.829000 1114 1914 1 chr5B.!!$R5 800
19 TraesCS2A01G031900 chr5B 533450314 533451072 758 True 599.000000 599 81.026000 1114 1890 1 chr5B.!!$R3 776
20 TraesCS2A01G031900 chr5B 533033818 533035293 1475 True 581.500000 800 81.494000 976 2474 2 chr5B.!!$R7 1498
21 TraesCS2A01G031900 chr5B 531817220 531818003 783 False 531.000000 531 79.219000 1109 1888 1 chr5B.!!$F2 779
22 TraesCS2A01G031900 chr3B 380384147 380385083 936 True 1072.000000 1072 87.241000 4 965 1 chr3B.!!$R3 961
23 TraesCS2A01G031900 chr3B 652245914 652246856 942 False 1068.000000 1068 87.113000 1 964 1 chr3B.!!$F1 963
24 TraesCS2A01G031900 chr3B 27420721 27421709 988 True 953.000000 953 84.715000 4 964 1 chr3B.!!$R1 960
25 TraesCS2A01G031900 chr3B 27427162 27427774 612 True 726.000000 726 88.264000 353 964 1 chr3B.!!$R2 611
26 TraesCS2A01G031900 chr1A 409079892 409080845 953 False 918.000000 918 84.270000 1 964 1 chr1A.!!$F1 963
27 TraesCS2A01G031900 chr4A 660721946 660722592 646 True 880.000000 880 91.212000 312 964 1 chr4A.!!$R1 652
28 TraesCS2A01G031900 chr5D 438588576 438589498 922 True 704.000000 704 80.704000 964 1888 1 chr5D.!!$R3 924
29 TraesCS2A01G031900 chr5D 438544081 438545012 931 True 658.000000 658 79.769000 976 1914 1 chr5D.!!$R2 938
30 TraesCS2A01G031900 chr5D 437867291 437868228 937 False 532.000000 532 77.568000 967 1888 1 chr5D.!!$F1 921
31 TraesCS2A01G031900 chr5D 438437198 438442242 5044 True 480.666667 830 81.727667 976 2474 3 chr5D.!!$R6 1498
32 TraesCS2A01G031900 chr5D 438720890 438722065 1175 True 452.000000 617 81.682500 1116 2342 2 chr5D.!!$R8 1226
33 TraesCS2A01G031900 chr5D 438603725 438604903 1178 True 447.500000 654 81.070500 1114 2340 2 chr5D.!!$R7 1226
34 TraesCS2A01G031900 chr5D 438657555 438658181 626 True 377.000000 377 77.948000 1116 1761 1 chr5D.!!$R5 645
35 TraesCS2A01G031900 chr5A 554200242 554201157 915 True 664.000000 664 80.086000 976 1888 1 chr5A.!!$R3 912
36 TraesCS2A01G031900 chrUn 63290496 63291670 1174 True 460.500000 656 81.164500 1114 2355 2 chrUn.!!$R2 1241
37 TraesCS2A01G031900 chrUn 299953664 299954523 859 True 345.000000 425 81.799500 1427 2355 2 chrUn.!!$R3 928
38 TraesCS2A01G031900 chr7D 101732788 101733723 935 False 553.000000 553 77.825000 965 1886 1 chr7D.!!$F1 921
39 TraesCS2A01G031900 chr7A 105512550 105513468 918 False 538.000000 538 77.683000 965 1888 1 chr7A.!!$F1 923
40 TraesCS2A01G031900 chr7B 59072721 59073637 916 False 525.000000 525 77.399000 965 1888 1 chr7B.!!$F2 923
41 TraesCS2A01G031900 chr7B 59066467 59067394 927 False 512.000000 512 77.191000 965 1886 1 chr7B.!!$F1 921

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
230 242 3.057806 ACAAAAATTCTTAACCCGGAGCG 60.058 43.478 0.73 0.0 0.0 5.03 F
971 1046 3.275143 ACAAATCCACGACACAACTCAA 58.725 40.909 0.00 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1336 3981 3.548770 AGGATATGATGGTGTGTTGCTG 58.451 45.455 0.00 0.0 0.0 4.41 R
2554 11129 2.346803 CCACCTAATCACTTGTGTCCG 58.653 52.381 0.46 0.0 0.0 4.79 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
135 138 7.395190 AACTAATGTCAGCAAATTGAGCATA 57.605 32.000 0.00 0.00 0.00 3.14
137 140 8.004087 ACTAATGTCAGCAAATTGAGCATAAT 57.996 30.769 0.00 0.00 0.00 1.28
187 199 7.218314 AGAAGGAGGAATGACAAGGATTTAT 57.782 36.000 0.00 0.00 0.00 1.40
230 242 3.057806 ACAAAAATTCTTAACCCGGAGCG 60.058 43.478 0.73 0.00 0.00 5.03
252 264 5.277825 CGCAACCTGTCAAATTTGTTCTTA 58.722 37.500 17.47 0.00 0.00 2.10
971 1046 3.275143 ACAAATCCACGACACAACTCAA 58.725 40.909 0.00 0.00 0.00 3.02
1198 3843 7.166691 AGGAACAAATGAATTCAGGAATGAG 57.833 36.000 14.54 2.37 0.00 2.90
1336 3981 4.333649 GCTACCCTTTTTGGTACGTATTCC 59.666 45.833 0.00 0.00 39.91 3.01
1462 4131 9.489084 CACGATTTAATATAGTCAAAGGGATCA 57.511 33.333 0.00 0.00 0.00 2.92
1536 4205 4.287067 AGAGACCTGAAAGCTGGAAATGTA 59.713 41.667 0.00 0.00 36.95 2.29
2298 10856 7.911130 ATCAGAGAAGATATTCAGACTTCCA 57.089 36.000 2.42 0.00 40.26 3.53
2825 15241 2.997485 AAGAAAACAGAGCGAATGGC 57.003 45.000 0.00 0.00 44.05 4.40
2935 15367 1.609555 GTTTGTATGGTTGGTGCCGAA 59.390 47.619 0.00 0.00 0.00 4.30
3047 15482 6.260493 GGGACAATTGATCATCTCTTTCTGAG 59.740 42.308 13.59 0.00 43.96 3.35
3345 15956 0.835971 TGAGCTACACAGGAGCCCAA 60.836 55.000 0.00 0.00 41.06 4.12
3348 15959 1.671742 CTACACAGGAGCCCAACGT 59.328 57.895 0.00 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 138 2.025037 TCCAGGTCAATAAGCCAGCATT 60.025 45.455 0.00 0.00 0.00 3.56
137 140 0.991146 TCCAGGTCAATAAGCCAGCA 59.009 50.000 0.00 0.00 0.00 4.41
187 199 0.982852 AACCGGCTCCTGATCATCCA 60.983 55.000 0.00 0.00 0.00 3.41
230 242 6.701400 ACATAAGAACAAATTTGACAGGTTGC 59.299 34.615 24.64 0.00 0.00 4.17
252 264 9.150348 GGTAAACTTATGCTGCAAAATAAACAT 57.850 29.630 6.36 0.00 0.00 2.71
359 372 1.626321 TCAGATAAACCGCCAAGTCCA 59.374 47.619 0.00 0.00 0.00 4.02
537 598 5.075493 ACAACTCTCGGTCTTAACTCCTTA 58.925 41.667 0.00 0.00 0.00 2.69
971 1046 8.137437 CCAATCTTACATGTTTCACAGAAGTTT 58.863 33.333 2.30 0.00 0.00 2.66
1198 3843 5.719173 TGCAGTTTGGCAATTAGAATTACC 58.281 37.500 0.00 0.00 41.65 2.85
1336 3981 3.548770 AGGATATGATGGTGTGTTGCTG 58.451 45.455 0.00 0.00 0.00 4.41
1392 4053 7.757097 TTTTCTCGAGTCATCTGTAAATAGC 57.243 36.000 13.13 0.00 0.00 2.97
1462 4131 4.019231 GTGGAGATAAAGAAGTCCCCTTGT 60.019 45.833 0.00 0.00 0.00 3.16
2298 10856 8.672823 ATTTCGGTAAGAGTAAAACTGTTTCT 57.327 30.769 6.20 0.08 33.48 2.52
2554 11129 2.346803 CCACCTAATCACTTGTGTCCG 58.653 52.381 0.46 0.00 0.00 4.79
2873 15305 9.145865 GGTAGTCTGACTTTCTAGAGAAATTTG 57.854 37.037 16.53 0.00 42.44 2.32
2935 15367 6.942976 TGGTTAGAACACTATTTCTCGGATT 58.057 36.000 0.00 0.00 37.09 3.01
3308 15919 2.039974 ATGTTGCGCCGCTCATTGA 61.040 52.632 11.67 0.00 0.00 2.57
3315 15926 3.195002 TAGCTCATGTTGCGCCGC 61.195 61.111 4.18 0.00 35.28 6.53
3345 15956 1.043022 ACCCTTACTTTCGGTCACGT 58.957 50.000 0.00 0.00 41.85 4.49
3348 15959 0.688487 CCCACCCTTACTTTCGGTCA 59.312 55.000 0.00 0.00 0.00 4.02
3403 16016 3.552132 TTGGTTCAGCTGTGTTAGTCA 57.448 42.857 14.67 1.49 0.00 3.41
3440 16053 6.486657 GCTGGTAGCATATCAATAAAGGTCAA 59.513 38.462 0.00 0.00 41.89 3.18


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

AutoCloner maintained by Alex Coulton.