Multiple sequence alignment - TraesCS2A01G135100

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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 TraesCS2A01G135100 chr2A 100.000 2989 0 0 1 2989 81488244 81485256 0.000000e+00 5520.0
1 TraesCS2A01G135100 chr2A 96.976 893 15 5 2099 2989 81526806 81525924 0.000000e+00 1489.0
2 TraesCS2A01G135100 chr2A 82.620 374 58 6 2397 2765 739497794 739498165 1.030000e-84 324.0
3 TraesCS2A01G135100 chr1A 97.713 2099 44 4 1 2099 566222186 566220092 0.000000e+00 3607.0
4 TraesCS2A01G135100 chr3A 97.189 2099 57 2 1 2099 101862375 101860279 0.000000e+00 3548.0
5 TraesCS2A01G135100 chr3A 87.982 441 50 3 2393 2831 495506784 495506345 4.420000e-143 518.0
6 TraesCS2A01G135100 chr5B 86.230 1329 166 10 772 2099 620954164 620955476 0.000000e+00 1424.0
7 TraesCS2A01G135100 chr2B 87.115 520 28 5 2474 2989 132579434 132578950 1.210000e-153 553.0
8 TraesCS2A01G135100 chr2B 90.028 361 20 7 2099 2457 132579890 132579544 1.260000e-123 453.0
9 TraesCS2A01G135100 chr2B 82.620 374 56 7 2401 2770 741257608 741257976 3.720000e-84 322.0
10 TraesCS2A01G135100 chr3D 89.048 420 43 3 2410 2826 373840085 373839666 4.420000e-143 518.0
11 TraesCS2A01G135100 chr7A 82.921 445 64 9 2393 2833 733830510 733830074 1.000000e-104 390.0
12 TraesCS2A01G135100 chr4A 90.625 288 25 2 2544 2831 680457525 680457810 6.050000e-102 381.0
13 TraesCS2A01G135100 chr4A 83.740 369 42 9 2398 2750 719148996 719149362 1.720000e-87 333.0
14 TraesCS2A01G135100 chr1B 85.556 270 34 3 1766 2032 28046658 28046391 8.160000e-71 278.0
15 TraesCS2A01G135100 chr1B 93.182 44 3 0 1731 1774 28048019 28047976 6.920000e-07 65.8
16 TraesCS2A01G135100 chr1D 85.606 264 33 3 1662 1921 465594685 465594423 3.800000e-69 272.0
17 TraesCS2A01G135100 chr1D 88.235 153 15 3 1726 1877 18945383 18945233 2.370000e-41 180.0
18 TraesCS2A01G135100 chr7D 87.963 108 10 2 2393 2497 124034081 124033974 1.120000e-24 124.0
19 TraesCS2A01G135100 chr6A 93.182 44 2 1 2056 2099 18832362 18832404 2.490000e-06 63.9


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 TraesCS2A01G135100 chr2A 81485256 81488244 2988 True 5520 5520 100.0000 1 2989 1 chr2A.!!$R1 2988
1 TraesCS2A01G135100 chr2A 81525924 81526806 882 True 1489 1489 96.9760 2099 2989 1 chr2A.!!$R2 890
2 TraesCS2A01G135100 chr1A 566220092 566222186 2094 True 3607 3607 97.7130 1 2099 1 chr1A.!!$R1 2098
3 TraesCS2A01G135100 chr3A 101860279 101862375 2096 True 3548 3548 97.1890 1 2099 1 chr3A.!!$R1 2098
4 TraesCS2A01G135100 chr5B 620954164 620955476 1312 False 1424 1424 86.2300 772 2099 1 chr5B.!!$F1 1327
5 TraesCS2A01G135100 chr2B 132578950 132579890 940 True 503 553 88.5715 2099 2989 2 chr2B.!!$R1 890

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
357 358 0.38852 CTCGTGTCATGCTCAACGGA 60.389 55.0 8.66 0.96 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 2016 1.267574 GGAGTGATCAGACAGGGGCA 61.268 60.0 0.0 0.0 0.0 5.36 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
207 208 3.908103 ACTCCAAAAGGCTTCCACTAGTA 59.092 43.478 0.00 0.00 0.00 1.82
357 358 0.388520 CTCGTGTCATGCTCAACGGA 60.389 55.000 8.66 0.96 0.00 4.69
390 391 1.143684 CCATTCTACCATCACCAGGGG 59.856 57.143 0.00 0.00 0.00 4.79
403 404 3.185203 AGGGGTTGAGGCAAGGCA 61.185 61.111 0.00 0.00 0.00 4.75
432 433 3.591527 TCTCCCCCATGTTGTTCATACTT 59.408 43.478 0.00 0.00 34.67 2.24
466 467 2.604914 CTGCAGCGTATGTTCTCGAAAT 59.395 45.455 0.00 0.00 0.00 2.17
470 471 3.804325 CAGCGTATGTTCTCGAAATCCAT 59.196 43.478 0.00 0.00 0.00 3.41
537 538 0.905357 GGACCAGCCTATATGCCGAT 59.095 55.000 0.00 0.00 0.00 4.18
679 680 1.649321 AAGATGCACAGACCCTGAGA 58.351 50.000 0.45 0.00 35.18 3.27
728 729 2.570302 GTGCTGAAGGAAACCTACCCTA 59.430 50.000 0.00 0.00 31.13 3.53
1400 1401 9.683069 CAAATCTTACAGTTCATAAAGCTTTGT 57.317 29.630 22.02 12.64 33.57 2.83
1498 1499 6.176183 ACACTGCTAAATCTGCTTATGAAGT 58.824 36.000 0.00 0.00 0.00 3.01
1616 1617 6.929625 TCAAAACAGAAATTGGACAACAGAA 58.070 32.000 0.00 0.00 0.00 3.02
1673 1674 4.020617 CCCCTCTGCGACCAAGCA 62.021 66.667 0.00 0.00 45.96 3.91
1965 1967 3.432326 GGTTAAAGATGATGTCGGCCTCT 60.432 47.826 0.00 0.00 0.00 3.69
2014 2016 2.492025 TGTAATCCTTGGGGCTGATCT 58.508 47.619 0.00 0.00 0.00 2.75
2254 2256 5.065218 CCTAATGTGTCTGAATGTTGTAGCC 59.935 44.000 0.00 0.00 0.00 3.93
2284 2286 3.504863 TCTTGTTTTAGTACTAGCGGCG 58.495 45.455 0.51 0.51 0.00 6.46
2292 2294 0.179145 GTACTAGCGGCGAAGAAGCA 60.179 55.000 12.98 0.00 39.27 3.91
2741 2844 6.156748 AGTTTAAACCCCAAAACTGTCATC 57.843 37.500 14.72 0.00 42.72 2.92
2855 2958 4.574828 GGGTGCATATTCAGTCGTGTTAAT 59.425 41.667 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
207 208 7.716560 GCTTTGGCAATATCCAATTTTAGGAAT 59.283 33.333 0.00 0.00 44.78 3.01
357 358 0.695803 AGAATGGATCTCCGGGGCTT 60.696 55.000 0.00 0.00 39.43 4.35
390 391 0.244721 GTGGATTGCCTTGCCTCAAC 59.755 55.000 0.00 0.00 34.31 3.18
403 404 1.285962 CAACATGGGGGAGAGTGGATT 59.714 52.381 0.00 0.00 0.00 3.01
466 467 9.753674 GGGTGATAAAATTCCAATATCTATGGA 57.246 33.333 0.00 0.00 45.09 3.41
537 538 0.323302 TTATGAACAGGGCAGCGTCA 59.677 50.000 0.00 0.00 0.00 4.35
679 680 4.744795 ACTCCATTAGAATCTCTGCGTT 57.255 40.909 0.00 0.00 0.00 4.84
728 729 3.800826 GGCAAACCCAGGTATCGAT 57.199 52.632 2.16 2.16 0.00 3.59
1258 1259 4.450053 AGAGCTCTGGTGCAATATCTTTC 58.550 43.478 17.42 0.00 34.99 2.62
1400 1401 6.822667 AGTTGTATTGTCTGCATCAATTCA 57.177 33.333 17.94 16.31 36.92 2.57
1478 1479 7.686438 TTGAACTTCATAAGCAGATTTAGCA 57.314 32.000 0.00 0.00 0.00 3.49
1498 1499 2.430332 GGGATTCGGCCAATGAATTGAA 59.570 45.455 2.24 0.00 40.14 2.69
1632 1633 4.467795 GCAGATAGGATTATGAGGCCACTA 59.532 45.833 5.01 0.00 0.00 2.74
1673 1674 1.666872 GTGTAGCGCAGTTTCCGGT 60.667 57.895 11.47 0.00 39.88 5.28
1724 1725 6.398918 GTGAATACTTCTAGCAGAGAACCAA 58.601 40.000 0.00 0.00 39.36 3.67
2014 2016 1.267574 GGAGTGATCAGACAGGGGCA 61.268 60.000 0.00 0.00 0.00 5.36
2254 2256 5.552178 AGTACTAAAACAAGAGGCCAAGAG 58.448 41.667 5.01 0.00 0.00 2.85
2284 2286 2.099062 CGTGCGCCATGCTTCTTC 59.901 61.111 4.18 0.00 46.63 2.87
2479 2577 0.536724 TGCTACAGCGTCCATCACAT 59.463 50.000 0.00 0.00 45.83 3.21
2492 2590 6.712179 TGAATCCAAATGCATAATGCTACA 57.288 33.333 0.00 0.00 45.31 2.74
2516 2618 7.464273 TGTTGATCAAATAGGCCATATGAGAT 58.536 34.615 10.35 7.31 0.00 2.75
2715 2818 5.360429 TGACAGTTTTGGGGTTTAAACTACC 59.640 40.000 17.50 18.56 41.34 3.18
2741 2844 7.165154 CCACCAATTACTATTCATTTTTACGCG 59.835 37.037 3.53 3.53 0.00 6.01
2855 2958 7.279615 CCCACACCAACTTGATAGTAATATCA 58.720 38.462 8.76 8.76 34.91 2.15


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

AutoCloner maintained by Alex Coulton.