Multiple sequence alignment - TraesCS2D01G123400

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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 TraesCS2D01G123400 chr2D 100.000 2616 0 0 1 2616 72370614 72373229 0.000000e+00 4831
1 TraesCS2D01G123400 chr2D 97.992 2241 15 5 404 2616 72651472 72653710 0.000000e+00 3862
2 TraesCS2D01G123400 chr2D 97.508 602 9 2 399 994 72627817 72628418 0.000000e+00 1024
3 TraesCS2D01G123400 chr2D 99.162 358 3 0 1 358 72651115 72651472 0.000000e+00 645
4 TraesCS2D01G123400 chr2D 97.759 357 8 0 1 357 72627459 72627815 1.330000e-172 616
5 TraesCS2D01G123400 chr2A 97.658 1580 26 4 437 2006 71112250 71113828 0.000000e+00 2702
6 TraesCS2D01G123400 chr2A 93.691 634 15 3 2006 2616 71114239 71114870 0.000000e+00 926
7 TraesCS2D01G123400 chr2A 88.690 725 68 9 1359 2076 71078583 71079300 0.000000e+00 872
8 TraesCS2D01G123400 chr2A 91.211 512 29 3 2121 2616 71210867 71211378 0.000000e+00 682
9 TraesCS2D01G123400 chr2A 91.016 512 30 3 2121 2616 71158107 71158618 0.000000e+00 676
10 TraesCS2D01G123400 chr2A 90.820 512 31 3 2121 2616 71312424 71312935 0.000000e+00 671
11 TraesCS2D01G123400 chr2A 91.387 476 35 2 704 1173 71073592 71074067 0.000000e+00 647
12 TraesCS2D01G123400 chr2A 94.836 213 11 0 6 218 71111032 71111244 1.500000e-87 333
13 TraesCS2D01G123400 chr2A 95.862 145 6 0 453 597 71073466 71073610 4.350000e-58 235
14 TraesCS2D01G123400 chr2A 93.333 105 5 2 254 358 71072698 71072800 1.250000e-33 154
15 TraesCS2D01G123400 chr2A 84.571 175 5 6 1199 1361 71074543 71074707 1.250000e-33 154
16 TraesCS2D01G123400 chr2A 95.506 89 4 0 254 342 71111785 71111873 2.710000e-30 143
17 TraesCS2D01G123400 chr2B 95.719 1565 49 9 419 1969 109082333 109083893 0.000000e+00 2503
18 TraesCS2D01G123400 chr2B 97.014 1306 28 3 414 1712 109161586 109162887 0.000000e+00 2185
19 TraesCS2D01G123400 chr2B 96.735 1317 31 5 404 1712 109789149 109790461 0.000000e+00 2183
20 TraesCS2D01G123400 chr2B 91.462 937 34 7 1703 2616 109180351 109181264 0.000000e+00 1245
21 TraesCS2D01G123400 chr2B 93.358 813 28 4 1827 2616 109868846 109869655 0.000000e+00 1179
22 TraesCS2D01G123400 chr2B 91.004 667 26 5 1982 2616 109084098 109084762 0.000000e+00 869
23 TraesCS2D01G123400 chr2B 88.956 661 64 8 1260 1918 109357666 109358319 0.000000e+00 808
24 TraesCS2D01G123400 chr2B 89.514 391 35 4 408 793 109356818 109357207 8.410000e-135 490
25 TraesCS2D01G123400 chr2B 93.243 222 11 1 1 218 109075772 109075993 9.030000e-85 324
26 TraesCS2D01G123400 chr2B 94.483 145 8 0 984 1128 109357463 109357607 9.420000e-55 224
27 TraesCS2D01G123400 chr2B 99.038 104 1 0 254 357 109161482 109161585 1.240000e-43 187
28 TraesCS2D01G123400 chr2B 97.087 103 3 0 254 356 109076570 109076672 9.620000e-40 174
29 TraesCS2D01G123400 chr2B 97.590 83 2 0 254 336 109789050 109789132 2.710000e-30 143
30 TraesCS2D01G123400 chrUn 90.820 512 31 3 2121 2616 289659233 289659744 0.000000e+00 671
31 TraesCS2D01G123400 chr6B 80.301 863 126 33 787 1619 176969891 176969043 1.720000e-171 612
32 TraesCS2D01G123400 chr6D 84.016 488 65 10 777 1258 95787880 95788360 8.530000e-125 457
33 TraesCS2D01G123400 chr1D 92.411 224 13 2 3 225 315546257 315546477 1.510000e-82 316
34 TraesCS2D01G123400 chr7A 92.202 218 17 0 1 218 421732622 421732839 2.530000e-80 309
35 TraesCS2D01G123400 chr5A 89.778 225 19 2 3 226 703411994 703411773 4.260000e-73 285
36 TraesCS2D01G123400 chr1A 90.367 218 20 1 1 218 78545883 78546099 4.260000e-73 285
37 TraesCS2D01G123400 chr3B 89.333 225 21 1 1 225 592853166 592852945 1.980000e-71 279


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 TraesCS2D01G123400 chr2D 72370614 72373229 2615 False 4831.000000 4831 100.000000 1 2616 1 chr2D.!!$F1 2615
1 TraesCS2D01G123400 chr2D 72651115 72653710 2595 False 2253.500000 3862 98.577000 1 2616 2 chr2D.!!$F3 2615
2 TraesCS2D01G123400 chr2D 72627459 72628418 959 False 820.000000 1024 97.633500 1 994 2 chr2D.!!$F2 993
3 TraesCS2D01G123400 chr2A 71111032 71114870 3838 False 1026.000000 2702 95.422750 6 2616 4 chr2A.!!$F5 2610
4 TraesCS2D01G123400 chr2A 71210867 71211378 511 False 682.000000 682 91.211000 2121 2616 1 chr2A.!!$F2 495
5 TraesCS2D01G123400 chr2A 71158107 71158618 511 False 676.000000 676 91.016000 2121 2616 1 chr2A.!!$F1 495
6 TraesCS2D01G123400 chr2A 71312424 71312935 511 False 671.000000 671 90.820000 2121 2616 1 chr2A.!!$F3 495
7 TraesCS2D01G123400 chr2A 71072698 71079300 6602 False 412.400000 872 90.768600 254 2076 5 chr2A.!!$F4 1822
8 TraesCS2D01G123400 chr2B 109082333 109084762 2429 False 1686.000000 2503 93.361500 419 2616 2 chr2B.!!$F4 2197
9 TraesCS2D01G123400 chr2B 109180351 109181264 913 False 1245.000000 1245 91.462000 1703 2616 1 chr2B.!!$F1 913
10 TraesCS2D01G123400 chr2B 109161482 109162887 1405 False 1186.000000 2185 98.026000 254 1712 2 chr2B.!!$F5 1458
11 TraesCS2D01G123400 chr2B 109868846 109869655 809 False 1179.000000 1179 93.358000 1827 2616 1 chr2B.!!$F2 789
12 TraesCS2D01G123400 chr2B 109789050 109790461 1411 False 1163.000000 2183 97.162500 254 1712 2 chr2B.!!$F7 1458
13 TraesCS2D01G123400 chr2B 109356818 109358319 1501 False 507.333333 808 90.984333 408 1918 3 chr2B.!!$F6 1510
14 TraesCS2D01G123400 chr2B 109075772 109076672 900 False 249.000000 324 95.165000 1 356 2 chr2B.!!$F3 355
15 TraesCS2D01G123400 chrUn 289659233 289659744 511 False 671.000000 671 90.820000 2121 2616 1 chrUn.!!$F1 495
16 TraesCS2D01G123400 chr6B 176969043 176969891 848 True 612.000000 612 80.301000 787 1619 1 chr6B.!!$R1 832

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
365 913 0.038983 CCGTATCCGACACACACACA 60.039 55.0 0.0 0.0 35.63 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2056 8566 0.392863 CGGTGCTGGGAATGTCATGA 60.393 55.0 0.0 0.0 0.0 3.07 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
169 174 2.521126 TCAAGTCTGGTGTACGGATCA 58.479 47.619 0.00 0.0 36.72 2.92
357 905 0.104120 CTGATTGCCCGTATCCGACA 59.896 55.000 0.00 0.0 35.63 4.35
358 906 0.179094 TGATTGCCCGTATCCGACAC 60.179 55.000 0.00 0.0 35.63 3.67
359 907 0.179094 GATTGCCCGTATCCGACACA 60.179 55.000 0.00 0.0 35.63 3.72
360 908 0.461339 ATTGCCCGTATCCGACACAC 60.461 55.000 0.00 0.0 35.63 3.82
361 909 1.817911 TTGCCCGTATCCGACACACA 61.818 55.000 0.00 0.0 35.63 3.72
362 910 1.808390 GCCCGTATCCGACACACAC 60.808 63.158 0.00 0.0 35.63 3.82
363 911 1.587568 CCCGTATCCGACACACACA 59.412 57.895 0.00 0.0 35.63 3.72
364 912 0.734942 CCCGTATCCGACACACACAC 60.735 60.000 0.00 0.0 35.63 3.82
365 913 0.038983 CCGTATCCGACACACACACA 60.039 55.000 0.00 0.0 35.63 3.72
366 914 1.057636 CGTATCCGACACACACACAC 58.942 55.000 0.00 0.0 35.63 3.82
367 915 1.600912 CGTATCCGACACACACACACA 60.601 52.381 0.00 0.0 35.63 3.72
368 916 1.790623 GTATCCGACACACACACACAC 59.209 52.381 0.00 0.0 0.00 3.82
369 917 0.176910 ATCCGACACACACACACACA 59.823 50.000 0.00 0.0 0.00 3.72
370 918 0.738063 TCCGACACACACACACACAC 60.738 55.000 0.00 0.0 0.00 3.82
371 919 1.016653 CCGACACACACACACACACA 61.017 55.000 0.00 0.0 0.00 3.72
372 920 0.094558 CGACACACACACACACACAC 59.905 55.000 0.00 0.0 0.00 3.82
373 921 1.152510 GACACACACACACACACACA 58.847 50.000 0.00 0.0 0.00 3.72
374 922 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.0 0.00 3.82
375 923 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72
376 924 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.0 0.00 3.82
377 925 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72
378 926 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.0 0.00 3.82
379 927 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72
380 928 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.0 0.00 3.82
381 929 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72
382 930 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.0 0.00 3.82
383 931 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72
384 932 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.0 0.00 3.82
385 933 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72
386 934 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.0 0.00 3.82
387 935 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72
388 936 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.0 0.00 3.82
389 937 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72
390 938 1.468127 CACACACACACACACACACAT 59.532 47.619 0.00 0.0 0.00 3.21
391 939 2.675348 CACACACACACACACACACATA 59.325 45.455 0.00 0.0 0.00 2.29
392 940 3.312146 CACACACACACACACACACATAT 59.688 43.478 0.00 0.0 0.00 1.78
393 941 4.509600 CACACACACACACACACACATATA 59.490 41.667 0.00 0.0 0.00 0.86
394 942 5.179182 CACACACACACACACACACATATAT 59.821 40.000 0.00 0.0 0.00 0.86
395 943 6.367422 CACACACACACACACACACATATATA 59.633 38.462 0.00 0.0 0.00 0.86
396 944 7.064490 CACACACACACACACACACATATATAT 59.936 37.037 0.00 0.0 0.00 0.86
397 945 8.254508 ACACACACACACACACACATATATATA 58.745 33.333 0.00 0.0 0.00 0.86
2056 8566 8.035394 ACTGATTAGTGTGTTTCATTCGTATCT 58.965 33.333 0.00 0.0 35.34 1.98
2057 8567 8.407457 TGATTAGTGTGTTTCATTCGTATCTC 57.593 34.615 0.00 0.0 0.00 2.75
2097 8607 7.545965 CACCGAAATCTGAATAGTTAGACAACT 59.454 37.037 0.00 0.0 46.77 3.16
2123 8655 1.094785 ACCTTCATCGCCGGAATTTG 58.905 50.000 5.05 0.0 0.00 2.32
2525 9064 8.980832 ATATCTGGTAGAAATATCAGGGAGTT 57.019 34.615 0.00 0.0 0.00 3.01
2526 9065 6.732896 TCTGGTAGAAATATCAGGGAGTTC 57.267 41.667 0.00 0.0 0.00 3.01
2545 9093 6.093909 GGAGTTCTAAGTGTGTAGTCTAGGAC 59.906 46.154 0.00 0.0 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
357 905 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.0 0.00 0.00 3.72
358 906 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.0 0.00 0.00 3.82
359 907 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.0 0.00 0.00 3.72
360 908 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.0 0.00 0.00 3.82
361 909 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.0 0.00 0.00 3.72
362 910 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.0 0.00 0.00 3.82
363 911 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.0 0.00 0.00 3.72
364 912 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.0 0.00 0.00 3.82
365 913 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.0 0.00 0.00 3.72
366 914 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.0 0.00 0.00 3.82
367 915 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.0 0.00 0.00 3.72
368 916 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.0 0.00 0.00 3.82
369 917 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.0 0.00 0.00 3.72
370 918 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.0 0.00 0.00 3.82
371 919 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.0 0.00 0.00 3.72
372 920 5.861222 ATATATGTGTGTGTGTGTGTGTG 57.139 39.130 0.0 0.00 0.00 3.82
1896 7789 2.686405 GAGCAACAGCAATGGATCATCA 59.314 45.455 0.0 0.00 0.00 3.07
2056 8566 0.392863 CGGTGCTGGGAATGTCATGA 60.393 55.000 0.0 0.00 0.00 3.07
2057 8567 0.392863 TCGGTGCTGGGAATGTCATG 60.393 55.000 0.0 0.00 0.00 3.07
2097 8607 2.431419 TCCGGCGATGAAGGTTTACATA 59.569 45.455 9.3 0.00 0.00 2.29
2123 8655 2.245096 GTGCAAATTCTGATGTCGTGC 58.755 47.619 0.0 0.00 0.00 5.34
2525 9064 5.509832 TGGTCCTAGACTACACACTTAGA 57.490 43.478 0.0 0.00 32.47 2.10
2526 9065 5.652891 ACATGGTCCTAGACTACACACTTAG 59.347 44.000 0.0 0.00 32.47 2.18
2545 9093 5.359194 AACTATGTTCCTCCTGTACATGG 57.641 43.478 0.0 0.14 36.97 3.66


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

AutoCloner maintained by Alex Coulton.