Multiple sequence alignment - TraesCS1A01G045500

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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 TraesCS1A01G045500 chr1A 100.000 2333 0 0 1 2333 27055812 27053480 0.000000e+00 4309.0
1 TraesCS1A01G045500 chr1B 95.811 1695 64 5 1 1694 41368057 41366369 0.000000e+00 2730.0
2 TraesCS1A01G045500 chr1B 79.732 1120 147 50 439 1511 41414240 41413154 0.000000e+00 737.0
3 TraesCS1A01G045500 chr1B 94.883 469 18 4 1691 2158 41366289 41365826 0.000000e+00 728.0
4 TraesCS1A01G045500 chr1B 91.623 191 15 1 2143 2333 41365882 41365693 1.780000e-66 263.0
5 TraesCS1A01G045500 chr1D 95.737 1337 44 6 1 1333 25773240 25771913 0.000000e+00 2141.0
6 TraesCS1A01G045500 chr1D 94.313 422 22 2 1739 2158 25771450 25771029 0.000000e+00 645.0
7 TraesCS1A01G045500 chr1D 95.479 376 14 2 1366 1741 25771915 25771543 4.290000e-167 597.0
8 TraesCS1A01G045500 chr1D 80.539 668 85 28 688 1333 25766960 25766316 2.710000e-129 472.0
9 TraesCS1A01G045500 chr1D 77.705 610 69 39 998 1569 25784504 25783924 6.260000e-81 311.0
10 TraesCS1A01G045500 chr1D 93.750 192 11 1 2143 2333 25771086 25770895 1.050000e-73 287.0
11 TraesCS1A01G045500 chr5D 89.773 88 8 1 2245 2331 315162045 315162132 6.810000e-21 111.0
12 TraesCS1A01G045500 chr7D 83.621 116 19 0 2216 2331 167246674 167246559 2.450000e-20 110.0
13 TraesCS1A01G045500 chr7D 85.507 69 9 1 2264 2331 427211606 427211538 1.160000e-08 71.3


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 TraesCS1A01G045500 chr1A 27053480 27055812 2332 True 4309.000000 4309 100.000000 1 2333 1 chr1A.!!$R1 2332
1 TraesCS1A01G045500 chr1B 41365693 41368057 2364 True 1240.333333 2730 94.105667 1 2333 3 chr1B.!!$R2 2332
2 TraesCS1A01G045500 chr1B 41413154 41414240 1086 True 737.000000 737 79.732000 439 1511 1 chr1B.!!$R1 1072
3 TraesCS1A01G045500 chr1D 25766316 25773240 6924 True 828.400000 2141 91.963600 1 2333 5 chr1D.!!$R2 2332
4 TraesCS1A01G045500 chr1D 25783924 25784504 580 True 311.000000 311 77.705000 998 1569 1 chr1D.!!$R1 571

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
447 451 1.180029 GCGTGTAGTTCTGGACCCTA 58.82 55.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 2395 0.101579 AAAGGAAACAACCGCGTTGG 59.898 50.0 20.19 1.36 46.5 3.77 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
199 203 1.540707 GGCGTGACCTATACTAGAGGC 59.459 57.143 0.00 0.00 37.63 4.70
276 280 1.951602 GGGAAGGTAACAAAACGCACT 59.048 47.619 0.00 0.00 41.41 4.40
382 386 4.019174 CCCCAGCAAAACTATGATCTGTT 58.981 43.478 0.00 0.00 0.00 3.16
386 390 6.259608 CCCAGCAAAACTATGATCTGTTCTAG 59.740 42.308 0.00 0.00 0.00 2.43
447 451 1.180029 GCGTGTAGTTCTGGACCCTA 58.820 55.000 0.00 0.00 0.00 3.53
497 503 5.384063 TTGGCATATTGTAAACTGGTGTG 57.616 39.130 0.00 0.00 0.00 3.82
513 519 1.939934 GTGTGTAGCAACAGCTCACAA 59.060 47.619 17.64 6.37 42.40 3.33
607 613 4.440880 GAGTGAGAGAAATCTGATGGTGG 58.559 47.826 0.00 0.00 0.00 4.61
706 714 6.518032 GCAGTGATCATCCTGTAGTGATATGT 60.518 42.308 13.23 0.00 35.33 2.29
953 978 7.087007 ACTGTATCATGTATACTTGCTCATCG 58.913 38.462 12.71 4.04 41.05 3.84
1055 1080 4.295051 GCAAACGGAAAGATGTTTAGCAA 58.705 39.130 0.00 0.00 36.22 3.91
1226 1257 4.112634 GTCCTTGAGCAAAAGAAACAACC 58.887 43.478 0.25 0.00 0.00 3.77
1433 1481 8.730680 TGAAAAGTGCTTGACTAAATTATCCTC 58.269 33.333 0.00 0.00 33.09 3.71
1490 1546 4.054780 TGTGTCTGGAGTTGTAGTGTTC 57.945 45.455 0.00 0.00 0.00 3.18
1589 1661 2.098117 GGAGCTCATGTTGCCATGTTAC 59.902 50.000 17.19 0.00 46.99 2.50
1652 1724 2.234414 GGTACCACCGGAGTTTGTATGA 59.766 50.000 9.46 0.00 0.00 2.15
1655 1727 2.838202 ACCACCGGAGTTTGTATGATCT 59.162 45.455 9.46 0.00 0.00 2.75
1666 1738 1.915489 TGTATGATCTGTGGTGGCCTT 59.085 47.619 3.32 0.00 0.00 4.35
1674 1746 1.600916 GTGGTGGCCTTGGAGTGTC 60.601 63.158 3.32 0.00 0.00 3.67
1789 2039 7.736447 ATAACCTTTTGAGAACTTGAGTCTG 57.264 36.000 0.00 0.00 0.00 3.51
1790 2040 5.104259 ACCTTTTGAGAACTTGAGTCTGT 57.896 39.130 0.00 0.00 0.00 3.41
1829 2081 2.299297 AGAGTGTTTACTGCTTAGGCGT 59.701 45.455 0.00 0.00 42.25 5.68
1863 2115 5.384063 TTGCTTTTATTGCCGATTTCTGA 57.616 34.783 0.00 0.00 0.00 3.27
2037 2290 2.432456 TGTTGAGCAGCGCTACCG 60.432 61.111 10.99 0.00 39.88 4.02
2062 2315 2.570302 GGAGTGGTGCCTTAAGTTCCTA 59.430 50.000 0.97 0.00 0.00 2.94
2103 2356 3.941573 TGTACCCGTGGTTTCTAATTCC 58.058 45.455 0.72 0.00 37.09 3.01
2104 2357 3.327172 TGTACCCGTGGTTTCTAATTCCA 59.673 43.478 0.72 0.00 37.09 3.53
2105 2358 3.512219 ACCCGTGGTTTCTAATTCCAA 57.488 42.857 0.00 0.00 27.29 3.53
2106 2359 3.151554 ACCCGTGGTTTCTAATTCCAAC 58.848 45.455 0.00 0.00 27.29 3.77
2107 2360 2.160813 CCCGTGGTTTCTAATTCCAACG 59.839 50.000 0.00 0.00 32.82 4.10
2108 2361 2.413634 CCGTGGTTTCTAATTCCAACGC 60.414 50.000 0.00 0.00 32.82 4.84
2109 2362 2.723618 CGTGGTTTCTAATTCCAACGCG 60.724 50.000 3.53 3.53 32.82 6.01
2110 2363 1.807742 TGGTTTCTAATTCCAACGCGG 59.192 47.619 12.47 0.00 0.00 6.46
2111 2364 1.808343 GGTTTCTAATTCCAACGCGGT 59.192 47.619 12.47 0.00 35.57 5.68
2112 2365 2.227149 GGTTTCTAATTCCAACGCGGTT 59.773 45.455 12.47 0.00 35.57 4.44
2113 2366 3.231160 GTTTCTAATTCCAACGCGGTTG 58.769 45.455 12.47 12.51 42.49 3.77
2114 2367 2.172851 TCTAATTCCAACGCGGTTGT 57.827 45.000 12.47 0.00 41.41 3.32
2115 2368 2.070783 TCTAATTCCAACGCGGTTGTC 58.929 47.619 12.47 0.00 41.41 3.18
2116 2369 2.073816 CTAATTCCAACGCGGTTGTCT 58.926 47.619 12.47 0.00 41.41 3.41
2117 2370 1.314730 AATTCCAACGCGGTTGTCTT 58.685 45.000 12.47 0.00 41.41 3.01
2118 2371 0.872388 ATTCCAACGCGGTTGTCTTC 59.128 50.000 12.47 0.00 41.41 2.87
2119 2372 0.179067 TTCCAACGCGGTTGTCTTCT 60.179 50.000 12.47 0.00 41.41 2.85
2120 2373 0.179067 TCCAACGCGGTTGTCTTCTT 60.179 50.000 12.47 0.00 41.41 2.52
2121 2374 0.661020 CCAACGCGGTTGTCTTCTTT 59.339 50.000 12.47 0.00 41.41 2.52
2122 2375 1.064952 CCAACGCGGTTGTCTTCTTTT 59.935 47.619 12.47 0.00 41.41 2.27
2123 2376 2.478879 CCAACGCGGTTGTCTTCTTTTT 60.479 45.455 12.47 0.00 41.41 1.94
2232 2486 2.380932 TCCAAGTACTCCCTCTGTACCA 59.619 50.000 0.00 0.00 40.61 3.25
2242 2496 5.044328 ACTCCCTCTGTACCAGTACATTAGA 60.044 44.000 10.89 4.97 44.15 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 115 3.733988 CGTTGTATAGGTCACGAGCATGT 60.734 47.826 0.00 0.00 0.00 3.21
240 244 6.288096 ACCTTCCCCCATATTAATTGCTTA 57.712 37.500 0.00 0.00 0.00 3.09
276 280 4.903049 TGCCTTATCCTCGGAAAAGGTATA 59.097 41.667 0.00 0.00 40.55 1.47
447 451 4.721132 TGTAGGACTTTTCACCGGATTTT 58.279 39.130 9.46 0.00 0.00 1.82
513 519 7.770897 ACTTGTTGACTGTTTCTTATCAGAAGT 59.229 33.333 0.00 0.00 40.28 3.01
607 613 8.861086 TGATGAGGAGTATTTATAGGAGAACAC 58.139 37.037 0.00 0.00 0.00 3.32
706 714 5.970289 ACTATCTCCATTATCACCTCCAGA 58.030 41.667 0.00 0.00 0.00 3.86
800 808 5.418840 CCCCACTGTAATAGAAAGCACAAAT 59.581 40.000 0.00 0.00 0.00 2.32
953 978 8.861101 GCCAATAGTATCATCGTATACAGAAAC 58.139 37.037 3.32 0.00 35.23 2.78
974 999 3.078836 GCCATGCCACCTGCCAAT 61.079 61.111 0.00 0.00 40.16 3.16
1055 1080 6.039493 CCTCTTAAATGCTGCTCTCATTTCAT 59.961 38.462 12.31 0.00 41.59 2.57
1226 1257 2.333014 GTTGTGGTTGTGGTTGTTGTG 58.667 47.619 0.00 0.00 0.00 3.33
1481 1537 3.119065 TGGTCAACACGAAGAACACTACA 60.119 43.478 0.00 0.00 0.00 2.74
1482 1538 3.450578 TGGTCAACACGAAGAACACTAC 58.549 45.455 0.00 0.00 0.00 2.73
1490 1546 1.330521 CCACACTTGGTCAACACGAAG 59.669 52.381 0.00 0.00 42.51 3.79
1589 1661 5.661759 ACTTAAGAGGAACCTACAGTATGGG 59.338 44.000 10.09 0.00 43.62 4.00
1652 1724 1.136329 ACTCCAAGGCCACCACAGAT 61.136 55.000 5.01 0.00 0.00 2.90
1655 1727 2.337879 GACACTCCAAGGCCACCACA 62.338 60.000 5.01 0.00 0.00 4.17
1829 2081 7.700234 CGGCAATAAAAGCAATTGACTTGTATA 59.300 33.333 18.00 11.81 39.73 1.47
1870 2122 5.648092 GGGTACTCATTTTGCTCTGTGTATT 59.352 40.000 0.00 0.00 0.00 1.89
1976 2229 3.445096 AGCAATTTCATAAGTCCTGCCAC 59.555 43.478 0.00 0.00 0.00 5.01
2062 2315 9.774413 GGGTACATATTAATAGCTACTTGTGTT 57.226 33.333 0.00 0.00 0.00 3.32
2085 2338 3.151554 GTTGGAATTAGAAACCACGGGT 58.848 45.455 0.00 0.00 37.65 5.28
2087 2340 2.413634 GCGTTGGAATTAGAAACCACGG 60.414 50.000 0.00 0.00 33.20 4.94
2130 2383 3.121019 CGTTGGTCCCGGCAAAAA 58.879 55.556 0.00 0.00 0.00 1.94
2131 2384 3.597728 GCGTTGGTCCCGGCAAAA 61.598 61.111 0.00 0.00 0.00 2.44
2142 2395 0.101579 AAAGGAAACAACCGCGTTGG 59.898 50.000 20.19 1.36 46.50 3.77
2232 2486 6.407074 GCACCACCTAAGATGTCTAATGTACT 60.407 42.308 0.00 0.00 0.00 2.73
2242 2496 1.743772 GCGATGCACCACCTAAGATGT 60.744 52.381 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.