Multiple sequence alignment - TraesCS2A01G435600

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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 TraesCS2A01G435600 chr2A 100.000 1919 0 0 479 2397 687889477 687891395 0.000000e+00 3544
1 TraesCS2A01G435600 chr2A 94.981 1554 70 6 848 2397 485199712 485201261 0.000000e+00 2431
2 TraesCS2A01G435600 chr2A 94.703 1548 75 5 855 2397 485220280 485221825 0.000000e+00 2398
3 TraesCS2A01G435600 chr2A 91.781 511 31 6 891 1394 724520798 724520292 0.000000e+00 701
4 TraesCS2A01G435600 chr2A 90.428 397 19 7 1392 1770 724520239 724519844 2.750000e-139 505
5 TraesCS2A01G435600 chr2A 95.222 293 14 0 596 888 92185248 92185540 4.670000e-127 464
6 TraesCS2A01G435600 chr2A 94.631 298 16 0 591 888 5155484 5155781 1.680000e-126 462
7 TraesCS2A01G435600 chr2A 95.000 280 13 1 1898 2176 724518957 724518678 2.830000e-119 438
8 TraesCS2A01G435600 chr2A 100.000 122 0 0 1 122 687888999 687889120 2.400000e-55 226
9 TraesCS2A01G435600 chr2A 92.908 141 9 1 1763 1902 724519176 724519036 1.120000e-48 204
10 TraesCS2A01G435600 chr2A 85.207 169 11 4 2230 2397 724518675 724518520 6.860000e-36 161
11 TraesCS2A01G435600 chr2B 96.030 1738 65 3 660 2397 263832143 263833876 0.000000e+00 2824
12 TraesCS2A01G435600 chr2B 95.182 1515 65 1 883 2397 772923892 772922386 0.000000e+00 2386
13 TraesCS2A01G435600 chr2B 92.857 476 30 3 919 1394 714782686 714782215 0.000000e+00 688
14 TraesCS2A01G435600 chr2B 93.296 358 24 0 479 836 772924251 772923894 1.630000e-146 529
15 TraesCS2A01G435600 chr2B 98.361 122 2 0 1 122 263831593 263831714 5.190000e-52 215
16 TraesCS2A01G435600 chr6B 95.586 1518 67 0 880 2397 95969838 95971355 0.000000e+00 2433
17 TraesCS2A01G435600 chr6B 92.416 356 20 2 479 827 95969475 95969830 3.560000e-138 501
18 TraesCS2A01G435600 chr2D 90.110 637 43 7 1766 2397 590151578 590150957 0.000000e+00 809
19 TraesCS2A01G435600 chr2D 97.098 379 10 1 1392 1770 590152635 590152258 2.600000e-179 638
20 TraesCS2A01G435600 chr2D 91.353 451 28 7 944 1394 590153127 590152688 7.330000e-170 606
21 TraesCS2A01G435600 chr6A 96.271 295 11 0 594 888 17431431 17431137 3.580000e-133 484
22 TraesCS2A01G435600 chr6A 97.581 124 1 2 1 122 576188214 576188337 6.710000e-51 211
23 TraesCS2A01G435600 chr1A 94.983 299 13 2 590 888 66228507 66228803 3.610000e-128 468
24 TraesCS2A01G435600 chr1A 98.361 122 1 1 1 122 536836864 536836744 1.870000e-51 213
25 TraesCS2A01G435600 chr1A 98.333 120 2 0 1 120 66228228 66228347 6.710000e-51 211
26 TraesCS2A01G435600 chr1A 95.714 70 3 0 479 548 23085685 23085754 1.950000e-21 113
27 TraesCS2A01G435600 chr1A 95.714 70 3 0 479 548 566574578 566574647 1.950000e-21 113
28 TraesCS2A01G435600 chr3A 94.915 295 15 0 594 888 207114975 207114681 1.680000e-126 462
29 TraesCS2A01G435600 chr3A 98.347 121 2 0 1 121 701655589 701655469 1.870000e-51 213
30 TraesCS2A01G435600 chr5A 94.295 298 15 1 591 888 573419202 573419497 2.810000e-124 455
31 TraesCS2A01G435600 chr5A 93.960 298 18 0 591 888 1871774 1872071 3.630000e-123 451
32 TraesCS2A01G435600 chr5A 98.361 122 2 0 1 122 573418922 573419043 5.190000e-52 215
33 TraesCS2A01G435600 chr5A 98.361 122 2 0 1 122 702266354 702266475 5.190000e-52 215
34 TraesCS2A01G435600 chr5B 93.694 222 14 0 479 700 676287024 676286803 1.370000e-87 333
35 TraesCS2A01G435600 chr7A 99.167 120 1 0 1 120 29867565 29867684 1.440000e-52 217
36 TraesCS2A01G435600 chr1B 98.361 122 2 0 1 122 585353619 585353740 5.190000e-52 215


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 TraesCS2A01G435600 chr2A 687888999 687891395 2396 False 1885.000000 3544 100.000000 1 2397 2 chr2A.!!$F5 2396
1 TraesCS2A01G435600 chr2A 485199712 485201261 1549 False 2431.000000 2431 94.981000 848 2397 1 chr2A.!!$F3 1549
2 TraesCS2A01G435600 chr2A 485220280 485221825 1545 False 2398.000000 2398 94.703000 855 2397 1 chr2A.!!$F4 1542
3 TraesCS2A01G435600 chr2A 724518520 724520798 2278 True 401.800000 701 91.064800 891 2397 5 chr2A.!!$R1 1506
4 TraesCS2A01G435600 chr2B 263831593 263833876 2283 False 1519.500000 2824 97.195500 1 2397 2 chr2B.!!$F1 2396
5 TraesCS2A01G435600 chr2B 772922386 772924251 1865 True 1457.500000 2386 94.239000 479 2397 2 chr2B.!!$R2 1918
6 TraesCS2A01G435600 chr6B 95969475 95971355 1880 False 1467.000000 2433 94.001000 479 2397 2 chr6B.!!$F1 1918
7 TraesCS2A01G435600 chr2D 590150957 590153127 2170 True 684.333333 809 92.853667 944 2397 3 chr2D.!!$R1 1453
8 TraesCS2A01G435600 chr1A 66228228 66228803 575 False 339.500000 468 96.658000 1 888 2 chr1A.!!$F3 887
9 TraesCS2A01G435600 chr5A 573418922 573419497 575 False 335.000000 455 96.328000 1 888 2 chr5A.!!$F3 887

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
903 1038 1.35572 CAACCCCTTCTCCAGTGGAAT 59.644 52.381 14.17 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1800 2700 3.003689 AGGTCAAGTTCAGTGCAAAATCG 59.996 43.478 0.0 0.0 0.0 3.34 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
527 528 3.933722 CCTCAGATCCGCCGCCAT 61.934 66.667 0.00 0.00 0.00 4.40
528 529 2.356793 CTCAGATCCGCCGCCATC 60.357 66.667 0.00 0.00 0.00 3.51
529 530 3.873026 CTCAGATCCGCCGCCATCC 62.873 68.421 0.00 0.00 0.00 3.51
530 531 4.240103 CAGATCCGCCGCCATCCA 62.240 66.667 0.00 0.00 0.00 3.41
531 532 4.241555 AGATCCGCCGCCATCCAC 62.242 66.667 0.00 0.00 0.00 4.02
559 560 4.033776 CCTCCATGCACACCCCGT 62.034 66.667 0.00 0.00 0.00 5.28
560 561 2.436646 CTCCATGCACACCCCGTC 60.437 66.667 0.00 0.00 0.00 4.79
561 562 3.976701 CTCCATGCACACCCCGTCC 62.977 68.421 0.00 0.00 0.00 4.79
562 563 4.343323 CCATGCACACCCCGTCCA 62.343 66.667 0.00 0.00 0.00 4.02
563 564 3.055719 CATGCACACCCCGTCCAC 61.056 66.667 0.00 0.00 0.00 4.02
564 565 4.697756 ATGCACACCCCGTCCACG 62.698 66.667 0.00 0.00 39.44 4.94
574 575 3.449227 CGTCCACGCCAGCCTCTA 61.449 66.667 0.00 0.00 0.00 2.43
575 576 2.184579 GTCCACGCCAGCCTCTAC 59.815 66.667 0.00 0.00 0.00 2.59
576 577 3.449227 TCCACGCCAGCCTCTACG 61.449 66.667 0.00 0.00 0.00 3.51
586 587 3.849951 CCTCTACGCGCACCCCAT 61.850 66.667 5.73 0.00 0.00 4.00
587 588 2.279517 CTCTACGCGCACCCCATC 60.280 66.667 5.73 0.00 0.00 3.51
588 589 3.792053 CTCTACGCGCACCCCATCC 62.792 68.421 5.73 0.00 0.00 3.51
589 590 3.849951 CTACGCGCACCCCATCCT 61.850 66.667 5.73 0.00 0.00 3.24
684 810 1.794714 ACCCTAACGCTCAGATCCAT 58.205 50.000 0.00 0.00 0.00 3.41
729 855 2.284699 CCCCGTCTCCCTCACCTT 60.285 66.667 0.00 0.00 0.00 3.50
771 902 2.449322 CCCCTCCCCTCCCTCATG 60.449 72.222 0.00 0.00 0.00 3.07
903 1038 1.355720 CAACCCCTTCTCCAGTGGAAT 59.644 52.381 14.17 0.00 0.00 3.01
904 1039 1.760405 ACCCCTTCTCCAGTGGAATT 58.240 50.000 14.17 0.00 0.00 2.17
1121 1263 2.965716 GATGACCCCATTCTGGCCGG 62.966 65.000 4.71 4.71 35.79 6.13
1179 1321 0.965866 TCATCAACCTCGAGCTCGGT 60.966 55.000 33.98 22.62 40.29 4.69
1226 1368 0.031585 CTGGACAACACCTCGTTCGA 59.968 55.000 0.00 0.00 34.86 3.71
1280 1422 5.604650 ACATTTTTGTCCAAATCCCTTACCA 59.395 36.000 0.00 0.00 0.00 3.25
1318 1460 4.703897 TCTCAATTCGTGTTCCTCTTGTT 58.296 39.130 0.00 0.00 0.00 2.83
1336 1478 3.127589 TGTTGTTGTGGTGAGTGATACG 58.872 45.455 0.00 0.00 0.00 3.06
1414 1611 9.965902 AGGAAGTGATAGTCAGATTTATTTGTT 57.034 29.630 0.00 0.00 0.00 2.83
1661 1868 7.490657 TTAACCTGAATTCTTAGTAGGCTCA 57.509 36.000 7.05 0.00 31.69 4.26
1800 2700 9.723447 GCTGGAGCTTATTCTAATTTTTAGTTC 57.277 33.333 0.00 0.00 38.21 3.01
1849 2749 5.804639 TGGTATTGACTAGCTGAATGTGTT 58.195 37.500 0.00 0.00 0.00 3.32
2228 3216 2.365617 AGTATGAGGATTGTAGTGCCGG 59.634 50.000 0.00 0.00 0.00 6.13
2381 3370 7.573096 GCTTCAGCTGCATAAGTGTAAAACTAA 60.573 37.037 9.47 0.00 36.64 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
542 543 3.976701 GACGGGGTGTGCATGGAGG 62.977 68.421 0.00 0.0 0.00 4.30
543 544 2.436646 GACGGGGTGTGCATGGAG 60.437 66.667 0.00 0.0 0.00 3.86
544 545 4.028490 GGACGGGGTGTGCATGGA 62.028 66.667 0.00 0.0 39.04 3.41
545 546 4.343323 TGGACGGGGTGTGCATGG 62.343 66.667 0.00 0.0 44.74 3.66
557 558 3.449227 TAGAGGCTGGCGTGGACG 61.449 66.667 0.00 0.0 43.27 4.79
558 559 2.184579 GTAGAGGCTGGCGTGGAC 59.815 66.667 0.00 0.0 0.00 4.02
559 560 3.449227 CGTAGAGGCTGGCGTGGA 61.449 66.667 0.00 0.0 0.00 4.02
569 570 3.792053 GATGGGGTGCGCGTAGAGG 62.792 68.421 8.43 0.0 0.00 3.69
570 571 2.279517 GATGGGGTGCGCGTAGAG 60.280 66.667 8.43 0.0 0.00 2.43
571 572 3.845259 GGATGGGGTGCGCGTAGA 61.845 66.667 8.43 0.0 0.00 2.59
572 573 3.792053 GAGGATGGGGTGCGCGTAG 62.792 68.421 8.43 0.0 0.00 3.51
573 574 3.845259 GAGGATGGGGTGCGCGTA 61.845 66.667 8.43 0.0 0.00 4.42
684 810 3.311110 GCGGCGATGGGAGGGATA 61.311 66.667 12.98 0.0 0.00 2.59
903 1038 4.838152 GCGCTCGGGGAGATGCAA 62.838 66.667 0.00 0.0 34.38 4.08
1020 1162 2.122954 ACCTCCTCCTCGGGCTTT 59.877 61.111 0.00 0.0 0.00 3.51
1149 1291 0.602638 GGTTGATGAGCGTGTCCACA 60.603 55.000 0.00 0.0 0.00 4.17
1179 1321 2.731571 GGTCACCCTCATGGCGCTA 61.732 63.158 7.64 0.0 37.83 4.26
1198 1340 1.512926 GTGTTGTCCAGCTTGACGAT 58.487 50.000 10.88 0.0 38.11 3.73
1226 1368 5.104485 GGGTTCGAAGAGGGCCATATTATAT 60.104 44.000 6.18 0.0 38.43 0.86
1280 1422 3.558931 TGAGATGTGGGATAAACGCAT 57.441 42.857 0.00 0.0 43.03 4.73
1318 1460 1.964933 TCCGTATCACTCACCACAACA 59.035 47.619 0.00 0.0 0.00 3.33
1336 1478 1.225376 TGTTCAACACCGCGACATCC 61.225 55.000 8.23 0.0 0.00 3.51
1414 1611 6.016024 CAGAATTCATCCTTCCACAGTTTCAA 60.016 38.462 8.44 0.0 0.00 2.69
1611 1811 0.326264 ACATCTTGTGACCCTCAGCC 59.674 55.000 0.00 0.0 0.00 4.85
1661 1868 5.946942 TCAGCTAGGATTCTCAACATCTT 57.053 39.130 0.00 0.0 0.00 2.40
1800 2700 3.003689 AGGTCAAGTTCAGTGCAAAATCG 59.996 43.478 0.00 0.0 0.00 3.34
2197 3183 8.272889 ACTACAATCCTCATACTACACAGTAGA 58.727 37.037 10.87 0.0 40.57 2.59
2311 3300 4.558178 TGTCGGCTCGTAATTTTCTACAA 58.442 39.130 0.00 0.0 0.00 2.41


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

AutoCloner maintained by Alex Coulton.