Multiple sequence alignment - TraesCS1A01G209200

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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 TraesCS1A01G209200 chr1A 100.000 4421 0 0 1 4421 371315911 371320331 0.000000e+00 8165
1 TraesCS1A01G209200 chr1A 92.321 599 37 4 754 1350 562292723 562292132 0.000000e+00 843
2 TraesCS1A01G209200 chr5B 94.135 1381 72 6 1347 2721 472026411 472025034 0.000000e+00 2093
3 TraesCS1A01G209200 chr5B 94.649 598 31 1 754 1350 631209546 631210143 0.000000e+00 926
4 TraesCS1A01G209200 chr5B 85.714 595 56 6 1 570 472027206 472026616 6.330000e-168 601
5 TraesCS1A01G209200 chr5B 88.925 307 30 2 2266 2569 328278775 328278470 4.170000e-100 375
6 TraesCS1A01G209200 chr5B 88.710 186 19 1 572 755 472026579 472026394 4.450000e-55 226
7 TraesCS1A01G209200 chr2B 93.917 1381 75 6 1347 2721 222940147 222941524 0.000000e+00 2076
8 TraesCS1A01G209200 chr2B 92.453 636 37 5 3788 4421 707739610 707740236 0.000000e+00 898
9 TraesCS1A01G209200 chr2B 91.853 626 47 3 3007 3632 707737966 707738587 0.000000e+00 870
10 TraesCS1A01G209200 chr2B 91.536 638 41 8 3788 4421 407885658 407886286 0.000000e+00 867
11 TraesCS1A01G209200 chr2B 91.379 638 42 7 3788 4421 371367353 371366725 0.000000e+00 861
12 TraesCS1A01G209200 chr2B 85.428 549 53 9 47 570 222939397 222939943 3.010000e-151 545
13 TraesCS1A01G209200 chr2B 94.767 172 7 2 3632 3803 371367543 371367374 2.620000e-67 267
14 TraesCS1A01G209200 chr2B 93.820 178 9 2 3626 3803 407885462 407885637 2.620000e-67 267
15 TraesCS1A01G209200 chr2B 94.771 153 7 1 572 724 222939980 222940131 2.060000e-58 237
16 TraesCS1A01G209200 chr2B 82.486 177 21 6 1 175 376460744 376460576 3.560000e-31 147
17 TraesCS1A01G209200 chr7B 93.845 1381 79 4 1347 2721 478619336 478617956 0.000000e+00 2074
18 TraesCS1A01G209200 chr7B 85.333 600 79 8 754 1350 496648404 496648997 2.920000e-171 612
19 TraesCS1A01G209200 chr7B 87.292 480 60 1 92 570 478620021 478619542 8.360000e-152 547
20 TraesCS1A01G209200 chr7B 94.798 173 6 3 3632 3803 43124791 43124621 2.620000e-67 267
21 TraesCS1A01G209200 chr7B 88.770 187 18 2 572 755 478619505 478619319 4.450000e-55 226
22 TraesCS1A01G209200 chr4B 93.551 1380 81 6 1347 2719 115709337 115707959 0.000000e+00 2049
23 TraesCS1A01G209200 chr4B 87.772 597 63 4 754 1350 51452078 51452664 0.000000e+00 689
24 TraesCS1A01G209200 chr4B 83.878 490 55 11 105 570 115710031 115709542 3.140000e-121 446
25 TraesCS1A01G209200 chr4B 93.464 153 10 0 572 724 115709505 115709353 1.240000e-55 228
26 TraesCS1A01G209200 chr4B 83.750 160 17 5 20 177 434965326 434965478 4.610000e-30 143
27 TraesCS1A01G209200 chr4B 82.530 166 20 4 9 172 444498535 444498377 2.140000e-28 137
28 TraesCS1A01G209200 chr6B 93.560 1382 66 11 1347 2721 140954832 140956197 0.000000e+00 2037
29 TraesCS1A01G209200 chr6B 91.223 638 43 7 3788 4421 308976223 308976851 0.000000e+00 856
30 TraesCS1A01G209200 chr6B 90.909 638 45 7 3788 4421 570078675 570079303 0.000000e+00 845
31 TraesCS1A01G209200 chr6B 91.069 627 47 4 3007 3632 308974588 308975206 0.000000e+00 839
32 TraesCS1A01G209200 chr6B 95.930 172 5 2 3632 3803 361273066 361272897 1.210000e-70 278
33 TraesCS1A01G209200 chr6B 91.457 199 14 1 44 239 140947314 140947512 2.030000e-68 270
34 TraesCS1A01G209200 chr6B 93.820 178 8 3 3626 3803 570078480 570078654 9.430000e-67 265
35 TraesCS1A01G209200 chr6B 93.258 178 10 2 3626 3803 308976027 308976202 1.220000e-65 261
36 TraesCS1A01G209200 chr6B 92.258 155 12 0 570 724 140954662 140954816 2.070000e-53 220
37 TraesCS1A01G209200 chr6B 83.884 242 27 3 2683 2924 293587612 293587841 2.070000e-53 220
38 TraesCS1A01G209200 chrUn 93.761 1122 64 4 1605 2721 116803744 116802624 0.000000e+00 1679
39 TraesCS1A01G209200 chrUn 84.538 595 67 10 1 570 116804765 116804171 2.310000e-157 566
40 TraesCS1A01G209200 chr1B 94.303 983 50 4 1744 2721 278152290 278153271 0.000000e+00 1500
41 TraesCS1A01G209200 chr1B 93.049 633 35 3 3788 4420 519434570 519433947 0.000000e+00 917
42 TraesCS1A01G209200 chr3B 93.553 636 30 5 3788 4421 446527270 446527896 0.000000e+00 937
43 TraesCS1A01G209200 chr3B 93.322 584 39 0 3049 3632 522282125 522281542 0.000000e+00 863
44 TraesCS1A01G209200 chr3B 87.914 513 49 8 2266 2768 522246408 522245899 3.810000e-165 592
45 TraesCS1A01G209200 chr3B 85.321 327 47 1 1934 2259 434509613 434509939 1.970000e-88 337
46 TraesCS1A01G209200 chr3B 87.692 260 32 0 1991 2250 383355666 383355407 2.000000e-78 303
47 TraesCS1A01G209200 chr3B 94.253 174 8 2 3630 3803 446527078 446527249 9.430000e-67 265
48 TraesCS1A01G209200 chr3B 79.897 194 30 4 1 192 151832024 151831838 2.770000e-27 134
49 TraesCS1A01G209200 chr3A 92.982 627 41 3 3007 3632 87730092 87730716 0.000000e+00 911
50 TraesCS1A01G209200 chr3A 92.453 636 36 9 3788 4421 87731752 87732377 0.000000e+00 898
51 TraesCS1A01G209200 chr3A 92.453 636 35 8 3788 4421 476147871 476147247 0.000000e+00 896
52 TraesCS1A01G209200 chr3A 91.759 631 49 3 3004 3632 476157134 476156505 0.000000e+00 874
53 TraesCS1A01G209200 chr3A 91.547 627 49 3 3007 3632 679990336 679990959 0.000000e+00 861
54 TraesCS1A01G209200 chr3A 87.173 421 38 12 1355 1765 217011965 217012379 8.660000e-127 464
55 TraesCS1A01G209200 chr3A 86.682 428 39 15 1348 1765 216936493 216936912 4.030000e-125 459
56 TraesCS1A01G209200 chr3A 92.697 178 11 2 3626 3803 87731556 87731731 5.670000e-64 255
57 TraesCS1A01G209200 chr2A 93.802 597 36 1 754 1350 770167172 770166577 0.000000e+00 896
58 TraesCS1A01G209200 chr2A 91.820 599 43 2 753 1350 477613944 477613351 0.000000e+00 830
59 TraesCS1A01G209200 chr2A 80.928 194 27 6 1 192 488386288 488386103 1.280000e-30 145
60 TraesCS1A01G209200 chr6A 92.151 637 37 9 3788 4421 370481494 370482120 0.000000e+00 887
61 TraesCS1A01G209200 chr6A 91.707 627 47 5 3007 3632 29436178 29436800 0.000000e+00 865
62 TraesCS1A01G209200 chr6A 89.202 639 31 12 3788 4421 347378769 347378164 0.000000e+00 763
63 TraesCS1A01G209200 chr5A 91.879 628 47 4 3007 3632 564441686 564441061 0.000000e+00 874
64 TraesCS1A01G209200 chr5A 91.261 595 45 2 754 1348 408131773 408131186 0.000000e+00 804
65 TraesCS1A01G209200 chr7A 91.325 634 41 8 3788 4419 587285047 587284426 0.000000e+00 854
66 TraesCS1A01G209200 chr7A 91.200 625 51 4 3009 3632 587286694 587286073 0.000000e+00 846
67 TraesCS1A01G209200 chr2D 91.333 600 42 4 754 1350 303501395 303500803 0.000000e+00 811
68 TraesCS1A01G209200 chr2D 87.648 421 36 14 1355 1765 161651795 161651381 4.000000e-130 475
69 TraesCS1A01G209200 chr4D 90.297 639 24 14 3788 4421 255552770 255553375 0.000000e+00 802
70 TraesCS1A01G209200 chr4D 85.464 571 65 13 2443 3006 448360124 448359565 2.960000e-161 579
71 TraesCS1A01G209200 chr4D 93.258 178 10 2 3626 3803 255552574 255552749 1.220000e-65 261
72 TraesCS1A01G209200 chr3D 90.847 590 46 4 754 1342 227670788 227670206 0.000000e+00 784
73 TraesCS1A01G209200 chr3D 84.393 346 50 2 14 356 236112470 236112814 1.970000e-88 337
74 TraesCS1A01G209200 chr6D 89.671 639 28 12 3788 4421 225586819 225586214 0.000000e+00 780
75 TraesCS1A01G209200 chr6D 87.173 421 38 14 1355 1765 197263410 197263824 8.660000e-127 464
76 TraesCS1A01G209200 chr6D 86.041 437 46 13 1356 1782 338138541 338138110 5.210000e-124 455


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 TraesCS1A01G209200 chr1A 371315911 371320331 4420 False 8165.000000 8165 100.000000 1 4421 1 chr1A.!!$F1 4420
1 TraesCS1A01G209200 chr1A 562292132 562292723 591 True 843.000000 843 92.321000 754 1350 1 chr1A.!!$R1 596
2 TraesCS1A01G209200 chr5B 472025034 472027206 2172 True 973.333333 2093 89.519667 1 2721 3 chr5B.!!$R2 2720
3 TraesCS1A01G209200 chr5B 631209546 631210143 597 False 926.000000 926 94.649000 754 1350 1 chr5B.!!$F1 596
4 TraesCS1A01G209200 chr2B 222939397 222941524 2127 False 952.666667 2076 91.372000 47 2721 3 chr2B.!!$F1 2674
5 TraesCS1A01G209200 chr2B 707737966 707740236 2270 False 884.000000 898 92.153000 3007 4421 2 chr2B.!!$F3 1414
6 TraesCS1A01G209200 chr2B 407885462 407886286 824 False 567.000000 867 92.678000 3626 4421 2 chr2B.!!$F2 795
7 TraesCS1A01G209200 chr2B 371366725 371367543 818 True 564.000000 861 93.073000 3632 4421 2 chr2B.!!$R2 789
8 TraesCS1A01G209200 chr7B 478617956 478620021 2065 True 949.000000 2074 89.969000 92 2721 3 chr7B.!!$R2 2629
9 TraesCS1A01G209200 chr7B 496648404 496648997 593 False 612.000000 612 85.333000 754 1350 1 chr7B.!!$F1 596
10 TraesCS1A01G209200 chr4B 115707959 115710031 2072 True 907.666667 2049 90.297667 105 2719 3 chr4B.!!$R2 2614
11 TraesCS1A01G209200 chr4B 51452078 51452664 586 False 689.000000 689 87.772000 754 1350 1 chr4B.!!$F1 596
12 TraesCS1A01G209200 chr6B 140954662 140956197 1535 False 1128.500000 2037 92.909000 570 2721 2 chr6B.!!$F3 2151
13 TraesCS1A01G209200 chr6B 308974588 308976851 2263 False 652.000000 856 91.850000 3007 4421 3 chr6B.!!$F4 1414
14 TraesCS1A01G209200 chr6B 570078480 570079303 823 False 555.000000 845 92.364500 3626 4421 2 chr6B.!!$F5 795
15 TraesCS1A01G209200 chrUn 116802624 116804765 2141 True 1122.500000 1679 89.149500 1 2721 2 chrUn.!!$R1 2720
16 TraesCS1A01G209200 chr1B 278152290 278153271 981 False 1500.000000 1500 94.303000 1744 2721 1 chr1B.!!$F1 977
17 TraesCS1A01G209200 chr1B 519433947 519434570 623 True 917.000000 917 93.049000 3788 4420 1 chr1B.!!$R1 632
18 TraesCS1A01G209200 chr3B 522281542 522282125 583 True 863.000000 863 93.322000 3049 3632 1 chr3B.!!$R4 583
19 TraesCS1A01G209200 chr3B 446527078 446527896 818 False 601.000000 937 93.903000 3630 4421 2 chr3B.!!$F2 791
20 TraesCS1A01G209200 chr3B 522245899 522246408 509 True 592.000000 592 87.914000 2266 2768 1 chr3B.!!$R3 502
21 TraesCS1A01G209200 chr3A 476147247 476147871 624 True 896.000000 896 92.453000 3788 4421 1 chr3A.!!$R1 633
22 TraesCS1A01G209200 chr3A 476156505 476157134 629 True 874.000000 874 91.759000 3004 3632 1 chr3A.!!$R2 628
23 TraesCS1A01G209200 chr3A 679990336 679990959 623 False 861.000000 861 91.547000 3007 3632 1 chr3A.!!$F3 625
24 TraesCS1A01G209200 chr3A 87730092 87732377 2285 False 688.000000 911 92.710667 3007 4421 3 chr3A.!!$F4 1414
25 TraesCS1A01G209200 chr2A 770166577 770167172 595 True 896.000000 896 93.802000 754 1350 1 chr2A.!!$R3 596
26 TraesCS1A01G209200 chr2A 477613351 477613944 593 True 830.000000 830 91.820000 753 1350 1 chr2A.!!$R1 597
27 TraesCS1A01G209200 chr6A 370481494 370482120 626 False 887.000000 887 92.151000 3788 4421 1 chr6A.!!$F2 633
28 TraesCS1A01G209200 chr6A 29436178 29436800 622 False 865.000000 865 91.707000 3007 3632 1 chr6A.!!$F1 625
29 TraesCS1A01G209200 chr6A 347378164 347378769 605 True 763.000000 763 89.202000 3788 4421 1 chr6A.!!$R1 633
30 TraesCS1A01G209200 chr5A 564441061 564441686 625 True 874.000000 874 91.879000 3007 3632 1 chr5A.!!$R2 625
31 TraesCS1A01G209200 chr5A 408131186 408131773 587 True 804.000000 804 91.261000 754 1348 1 chr5A.!!$R1 594
32 TraesCS1A01G209200 chr7A 587284426 587286694 2268 True 850.000000 854 91.262500 3009 4419 2 chr7A.!!$R1 1410
33 TraesCS1A01G209200 chr2D 303500803 303501395 592 True 811.000000 811 91.333000 754 1350 1 chr2D.!!$R2 596
34 TraesCS1A01G209200 chr4D 448359565 448360124 559 True 579.000000 579 85.464000 2443 3006 1 chr4D.!!$R1 563
35 TraesCS1A01G209200 chr4D 255552574 255553375 801 False 531.500000 802 91.777500 3626 4421 2 chr4D.!!$F1 795
36 TraesCS1A01G209200 chr3D 227670206 227670788 582 True 784.000000 784 90.847000 754 1342 1 chr3D.!!$R1 588
37 TraesCS1A01G209200 chr6D 225586214 225586819 605 True 780.000000 780 89.671000 3788 4421 1 chr6D.!!$R1 633


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
704 767 0.103208 AGATAAGCTTGTCCGGCTCG 59.897 55.0 18.49 0.0 39.30 5.03 F
746 809 0.250295 CTTCCCGCAGTTCAAGGACA 60.250 55.0 0.00 0.0 0.00 4.02 F
747 810 0.250295 TTCCCGCAGTTCAAGGACAG 60.250 55.0 0.00 0.0 0.00 3.51 F
1724 1793 0.322456 GGGAGCCACTGTGCATTACA 60.322 55.0 1.29 0.0 37.78 2.41 F
2847 2928 0.110295 CATGTCCCAGTGTCCCACAA 59.890 55.0 0.00 0.0 36.74 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 1768 0.543749 GCACAGTGGCTCCCTTATCT 59.456 55.0 1.84 0.0 0.00 1.98 R
1967 2038 0.999406 AGATGTTCGTCGCATTTCGG 59.001 50.0 0.00 0.0 39.05 4.30 R
2010 2081 2.094894 CGAATTCTCACTGTGTGGATGC 59.905 50.0 7.79 3.4 33.87 3.91 R
2974 3055 0.037139 TGTTCCATTCCCGTGTACCG 60.037 55.0 0.00 0.0 0.00 4.02 R
4375 5355 0.463620 GAGGAGCTTGTAGAGGCAGG 59.536 60.0 0.00 0.0 0.00 4.85 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)



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

AutoCloner maintained by Alex Coulton.