Multiple sequence alignment - TraesCS2D01G262500

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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 TraesCS2D01G262500 chr2D 100.000 2620 0 0 1 2620 318716625 318714006 0.000000e+00 4839
1 TraesCS2D01G262500 chr2B 91.671 2005 144 8 1 1984 387154147 387152145 0.000000e+00 2756
2 TraesCS2D01G262500 chr2A 96.387 1190 42 1 685 1873 412370769 412371958 0.000000e+00 1958
3 TraesCS2D01G262500 chr2A 91.029 680 59 2 3 682 412368393 412369070 0.000000e+00 917
4 TraesCS2D01G262500 chr2A 86.667 105 3 4 1880 1984 412374716 412374809 3.570000e-19 106
5 TraesCS2D01G262500 chr1A 86.657 667 50 23 1987 2620 449559978 449560638 0.000000e+00 702
6 TraesCS2D01G262500 chr5D 89.928 417 18 4 1987 2383 502666663 502666251 1.390000e-142 516
7 TraesCS2D01G262500 chr5D 94.142 239 10 3 2385 2620 502666209 502665972 6.890000e-96 361
8 TraesCS2D01G262500 chr1B 86.585 410 31 14 1987 2372 124009850 124009441 5.180000e-117 431
9 TraesCS2D01G262500 chr5A 86.967 399 30 16 1991 2367 477447297 477446899 1.860000e-116 429
10 TraesCS2D01G262500 chr5A 86.722 241 28 4 2383 2620 477446848 477446609 5.560000e-67 265
11 TraesCS2D01G262500 chr6A 88.378 370 19 5 1989 2337 17383507 17383873 8.670000e-115 424
12 TraesCS2D01G262500 chr6A 93.671 237 15 0 2384 2620 17384114 17384350 3.210000e-94 355
13 TraesCS2D01G262500 chr6A 87.847 288 30 5 2084 2366 8445042 8444755 1.500000e-87 333
14 TraesCS2D01G262500 chr3A 88.194 288 29 3 2084 2366 674504345 674504632 3.230000e-89 339
15 TraesCS2D01G262500 chr3A 87.847 288 30 5 2084 2366 594584981 594584694 1.500000e-87 333
16 TraesCS2D01G262500 chr3A 75.949 237 45 11 2391 2620 694499905 694500136 7.670000e-21 111
17 TraesCS2D01G262500 chr4A 87.589 282 30 5 2084 2360 616622531 616622812 3.250000e-84 322
18 TraesCS2D01G262500 chr7A 88.608 237 23 3 2387 2620 584375293 584375058 4.270000e-73 285
19 TraesCS2D01G262500 chr7A 79.918 244 40 6 2384 2620 34506281 34506040 1.250000e-38 171
20 TraesCS2D01G262500 chr4B 85.833 240 23 7 2384 2620 15131067 15131298 7.240000e-61 244


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 TraesCS2D01G262500 chr2D 318714006 318716625 2619 True 4839.000000 4839 100.0000 1 2620 1 chr2D.!!$R1 2619
1 TraesCS2D01G262500 chr2B 387152145 387154147 2002 True 2756.000000 2756 91.6710 1 1984 1 chr2B.!!$R1 1983
2 TraesCS2D01G262500 chr2A 412368393 412374809 6416 False 993.666667 1958 91.3610 3 1984 3 chr2A.!!$F1 1981
3 TraesCS2D01G262500 chr1A 449559978 449560638 660 False 702.000000 702 86.6570 1987 2620 1 chr1A.!!$F1 633
4 TraesCS2D01G262500 chr5D 502665972 502666663 691 True 438.500000 516 92.0350 1987 2620 2 chr5D.!!$R1 633
5 TraesCS2D01G262500 chr5A 477446609 477447297 688 True 347.000000 429 86.8445 1991 2620 2 chr5A.!!$R1 629
6 TraesCS2D01G262500 chr6A 17383507 17384350 843 False 389.500000 424 91.0245 1989 2620 2 chr6A.!!$F1 631

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
845 2543 0.179004 TTCCACAAGACACGGCCAAT 60.179 50.0 2.24 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 6453 2.936498 CCTGTGTCAAATATCACGGTCC 59.064 50.0 0.0 0.0 38.73 4.46 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
28 29 0.472352 TTACCTCCCAGGAACACGGT 60.472 55.000 0.00 1.43 37.67 4.83
30 31 2.347490 CTCCCAGGAACACGGTGG 59.653 66.667 13.48 0.00 0.00 4.61
57 58 8.615211 TGAATTGGTCGATCTGATCTAATTTTG 58.385 33.333 15.16 0.00 0.00 2.44
85 86 7.885297 TCTTGAAGACAAACAATTTGATAGGG 58.115 34.615 8.24 0.00 43.26 3.53
104 105 2.777692 GGGGGATGTAGAGATGGTTTCA 59.222 50.000 0.00 0.00 0.00 2.69
111 112 5.400066 TGTAGAGATGGTTTCATTGACGA 57.600 39.130 0.00 0.00 32.98 4.20
131 132 0.541392 TTGCGTGCTGATCAGGGTAT 59.459 50.000 23.89 0.00 0.00 2.73
135 136 2.905075 CGTGCTGATCAGGGTATTTCA 58.095 47.619 23.89 8.70 0.00 2.69
208 209 1.210478 ACAAAGCGATCCCTAGCACAT 59.790 47.619 0.00 0.00 35.48 3.21
246 247 1.864711 TGAAACGCAGCAAGAGTACAC 59.135 47.619 0.00 0.00 0.00 2.90
301 302 1.305201 ACAGCCTACAAACAACCACG 58.695 50.000 0.00 0.00 0.00 4.94
341 342 0.689745 ACTAGCTCCCCGCATAACCA 60.690 55.000 0.00 0.00 42.61 3.67
344 345 1.148273 GCTCCCCGCATAACCATCA 59.852 57.895 0.00 0.00 38.92 3.07
403 404 2.101770 GCATCAGGCAGCTTTCGC 59.898 61.111 0.00 0.00 43.97 4.70
435 436 1.403647 CGAGCACATTCTAACCACCGA 60.404 52.381 0.00 0.00 0.00 4.69
456 457 2.177531 GCTGCACTGACATTGGCG 59.822 61.111 0.00 0.00 0.00 5.69
481 482 0.739112 GAGCTTGAACAGAGCCCTCG 60.739 60.000 0.00 0.00 41.03 4.63
494 495 2.710902 CCCTCGTGCTCCGATCACA 61.711 63.158 3.44 0.00 46.23 3.58
518 519 2.416893 GTCAAGGAGGCGATTCTTGAAC 59.583 50.000 11.70 4.83 45.40 3.18
541 542 2.368548 TCTTGCTAAGTTGTCCAGAGCA 59.631 45.455 0.00 0.00 41.23 4.26
571 572 2.455674 TGTCCTCACCATTCTGAACG 57.544 50.000 0.00 0.00 0.00 3.95
675 676 4.589908 AGGGTTCTTGAATAGACGCAATT 58.410 39.130 0.00 0.00 30.90 2.32
845 2543 0.179004 TTCCACAAGACACGGCCAAT 60.179 50.000 2.24 0.00 0.00 3.16
860 2558 3.130164 CGGCCAATGAATCATTACACCAA 59.870 43.478 8.29 0.00 32.35 3.67
914 2612 5.241064 CCTCATCATTCTGGTGATCATTTCC 59.759 44.000 0.00 0.00 36.82 3.13
945 2643 3.380004 ACAAGAACAAACGAGAATTGGCA 59.620 39.130 0.00 0.00 32.02 4.92
996 2694 8.090214 ACAACAACAATTAGCAATAGAGCAATT 58.910 29.630 0.00 0.00 36.85 2.32
1292 2990 7.905126 TGCATACAACTTAGTTACATGAATCG 58.095 34.615 17.08 0.00 0.00 3.34
1304 3002 8.997621 AGTTACATGAATCGTAATGTACTTGT 57.002 30.769 0.00 0.00 38.62 3.16
1370 3068 0.326618 AGGACGACAAGATGGGGGAT 60.327 55.000 0.00 0.00 0.00 3.85
1373 3071 1.224315 CGACAAGATGGGGGATGCA 59.776 57.895 0.00 0.00 0.00 3.96
1896 6363 6.650427 ATACCAAGTCTTCTTTTCCCAAAC 57.350 37.500 0.00 0.00 0.00 2.93
1979 6446 8.604035 CATATGTGTGTATGTAGGTTGTCTTTC 58.396 37.037 0.00 0.00 0.00 2.62
1984 6451 6.018588 TGTGTATGTAGGTTGTCTTTCGTTTG 60.019 38.462 0.00 0.00 0.00 2.93
1985 6452 6.018507 GTGTATGTAGGTTGTCTTTCGTTTGT 60.019 38.462 0.00 0.00 0.00 2.83
1986 6453 4.868450 TGTAGGTTGTCTTTCGTTTGTG 57.132 40.909 0.00 0.00 0.00 3.33
1987 6454 3.623960 TGTAGGTTGTCTTTCGTTTGTGG 59.376 43.478 0.00 0.00 0.00 4.17
2006 6473 3.370978 GTGGACCGTGATATTTGACACAG 59.629 47.826 0.00 0.00 36.91 3.66
2031 6498 3.058914 GTGCCATATAGCTAAAACTGCCG 60.059 47.826 0.00 0.00 0.00 5.69
2100 6587 7.872138 TGAATCCTCCTCCTTTAATTACATGT 58.128 34.615 2.69 2.69 0.00 3.21
2108 6595 7.498900 TCCTCCTTTAATTACATGTATGCACTG 59.501 37.037 6.36 0.00 0.00 3.66
2462 7149 2.364002 TGTGACTCAAACTGTCGATCCA 59.636 45.455 0.00 0.00 37.26 3.41
2471 7158 4.789012 AACTGTCGATCCAATGCAAAAT 57.211 36.364 0.00 0.00 0.00 1.82
2472 7159 4.361451 ACTGTCGATCCAATGCAAAATC 57.639 40.909 0.00 0.00 0.00 2.17
2483 7171 5.469421 TCCAATGCAAAATCCATTTTCACAC 59.531 36.000 0.00 0.00 37.86 3.82
2501 7189 6.793492 TCACACAAAATATTCATCACGACA 57.207 33.333 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.452264 AGATCAGATCGACCAATTCACCA 59.548 43.478 4.67 0.0 0.00 4.17
30 31 7.721286 AATTAGATCAGATCGACCAATTCAC 57.279 36.000 4.67 0.0 0.00 3.18
85 86 5.529060 GTCAATGAAACCATCTCTACATCCC 59.471 44.000 0.00 0.0 0.00 3.85
111 112 0.541392 TACCCTGATCAGCACGCAAT 59.459 50.000 17.76 0.0 0.00 3.56
131 132 3.420893 CTGGAATGTACAAGGGCTGAAA 58.579 45.455 0.00 0.0 0.00 2.69
135 136 0.698238 TGCTGGAATGTACAAGGGCT 59.302 50.000 0.00 0.0 0.00 5.19
246 247 7.436673 CCTTTAGCTACTCTATTAGTGCAAGTG 59.563 40.741 0.00 0.0 39.39 3.16
312 313 1.455217 GGAGCTAGTCCCCGTGCTA 60.455 63.158 0.00 0.0 39.88 3.49
341 342 6.735678 TGTTATGTTAATGCGTTCACTGAT 57.264 33.333 0.00 0.0 0.00 2.90
344 345 6.307031 TGTTGTTATGTTAATGCGTTCACT 57.693 33.333 0.00 0.0 0.00 3.41
420 421 1.403780 GCTCGTCGGTGGTTAGAATGT 60.404 52.381 0.00 0.0 0.00 2.71
435 436 0.952497 CCAATGTCAGTGCAGCTCGT 60.952 55.000 0.00 0.0 0.00 4.18
456 457 1.332178 CTCTGTTCAAGCTCGACGAC 58.668 55.000 0.00 0.0 0.00 4.34
518 519 3.434984 GCTCTGGACAACTTAGCAAGAAG 59.565 47.826 3.37 0.0 33.38 2.85
541 542 2.671145 TGAGGACATCACCGAGCTT 58.329 52.632 0.00 0.0 31.12 3.74
675 676 1.626825 GGTTGTGACCTAGGGTGCTAA 59.373 52.381 14.81 0.0 42.99 3.09
845 2543 4.640201 GCTAGCCTTTGGTGTAATGATTCA 59.360 41.667 2.29 0.0 0.00 2.57
914 2612 2.541588 CGTTTGTTCTTGTTGGAGGCAG 60.542 50.000 0.00 0.0 0.00 4.85
945 2643 3.959293 TCTGATCTTGGAATGTGTGCAT 58.041 40.909 0.00 0.0 36.80 3.96
996 2694 2.761195 CGGCTCCGACGTCATCTCA 61.761 63.158 17.16 0.0 42.83 3.27
1054 2752 2.218953 TCACAGTTCACGAGGTTGAC 57.781 50.000 0.00 0.0 0.00 3.18
1292 2990 7.496529 ACATATCCATGCACAAGTACATTAC 57.503 36.000 0.00 0.0 35.39 1.89
1296 2994 5.047188 CGTACATATCCATGCACAAGTACA 58.953 41.667 12.97 0.0 35.39 2.90
1304 3002 1.691434 TCCTGCGTACATATCCATGCA 59.309 47.619 0.00 0.0 35.39 3.96
1370 3068 1.915266 CTCCAGGTCCACCTCTGCA 60.915 63.158 0.00 0.0 46.65 4.41
1373 3071 2.284995 GGCTCCAGGTCCACCTCT 60.285 66.667 0.00 0.0 46.65 3.69
1640 3339 2.184533 ACATGGGTCGGTCATTGAGTA 58.815 47.619 0.00 0.0 0.00 2.59
1641 3340 0.984230 ACATGGGTCGGTCATTGAGT 59.016 50.000 0.00 0.0 0.00 3.41
1728 3439 8.791675 TGCATGACTAAATGTAGAAATTGACAA 58.208 29.630 0.00 0.0 0.00 3.18
1766 3477 5.507149 CCCGAAGAACACATGAAAATTGACA 60.507 40.000 0.00 0.0 0.00 3.58
1844 3563 5.542779 TCTTTGAGTTAGAGAGGCTTCAAC 58.457 41.667 0.00 0.0 0.00 3.18
1845 3564 5.808366 TCTTTGAGTTAGAGAGGCTTCAA 57.192 39.130 0.00 0.0 0.00 2.69
1847 3566 6.459923 TCTTTCTTTGAGTTAGAGAGGCTTC 58.540 40.000 0.00 0.0 0.00 3.86
1849 3568 6.426646 TTCTTTCTTTGAGTTAGAGAGGCT 57.573 37.500 0.00 0.0 0.00 4.58
1896 6363 9.833182 CTCCGCATGCTAGTATATAAGTATATG 57.167 37.037 17.13 0.0 31.69 1.78
1979 6446 3.433957 TCAAATATCACGGTCCACAAACG 59.566 43.478 0.00 0.0 0.00 3.60
1984 6451 3.331150 TGTGTCAAATATCACGGTCCAC 58.669 45.455 0.00 0.0 37.38 4.02
1985 6452 3.595173 CTGTGTCAAATATCACGGTCCA 58.405 45.455 0.00 0.0 37.38 4.02
1986 6453 2.936498 CCTGTGTCAAATATCACGGTCC 59.064 50.000 0.00 0.0 38.73 4.46
1987 6454 3.370978 CACCTGTGTCAAATATCACGGTC 59.629 47.826 0.00 0.0 38.39 4.79
2031 6498 4.336280 ACTAAATGGAAGGAAGAAGGTGC 58.664 43.478 0.00 0.0 0.00 5.01
2089 6576 6.765989 GTCCTCCAGTGCATACATGTAATTAA 59.234 38.462 10.14 0.0 0.00 1.40
2462 7149 6.939132 TTGTGTGAAAATGGATTTTGCATT 57.061 29.167 2.06 0.0 40.20 3.56
2471 7158 9.421806 GTGATGAATATTTTGTGTGAAAATGGA 57.578 29.630 0.00 0.0 32.64 3.41
2472 7159 8.374728 CGTGATGAATATTTTGTGTGAAAATGG 58.625 33.333 0.00 0.0 32.64 3.16
2510 7198 9.100197 AGGAAACATAACATGGGATTTAGTTTT 57.900 29.630 0.00 0.0 33.60 2.43


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

AutoCloner maintained by Alex Coulton.