Multiple sequence alignment - TraesCS2A01G516700

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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 TraesCS2A01G516700 chr2A 100.000 4302 0 0 1 4302 740120015 740115714 0.000000e+00 7945.0
1 TraesCS2A01G516700 chr2A 99.093 4302 39 0 1 4302 740144203 740139902 0.000000e+00 7729.0
2 TraesCS2A01G516700 chr2A 98.121 2820 41 7 1 2819 740080171 740077363 0.000000e+00 4903.0
3 TraesCS2A01G516700 chr2A 100.000 57 0 0 3696 3752 740140451 740140395 5.880000e-19 106.0
4 TraesCS2A01G516700 chr2A 98.246 57 1 0 3696 3752 740116263 740116207 2.740000e-17 100.0
5 TraesCS2A01G516700 chr2A 98.246 57 1 0 3753 3809 740116320 740116264 2.740000e-17 100.0
6 TraesCS2A01G516700 chr2A 98.246 57 1 0 3753 3809 740140508 740140452 2.740000e-17 100.0
7 TraesCS2A01G516700 chr2D 90.154 2397 172 31 646 3017 608578913 608576556 0.000000e+00 3061.0
8 TraesCS2A01G516700 chr2D 90.034 2037 174 17 813 2838 608559738 608557720 0.000000e+00 2610.0
9 TraesCS2A01G516700 chr2D 85.714 238 16 1 3128 3347 608576344 608576107 7.190000e-58 235.0
10 TraesCS2A01G516700 chr2B 90.280 2356 176 30 655 3003 742173242 742170933 0.000000e+00 3033.0
11 TraesCS2A01G516700 chr2B 90.842 1900 160 8 813 2701 742110633 742108737 0.000000e+00 2532.0
12 TraesCS2A01G516700 chr2B 88.696 345 34 3 313 653 742174647 742174304 2.390000e-112 416.0
13 TraesCS2A01G516700 chr2B 90.123 324 27 3 1 321 742174995 742174674 2.390000e-112 416.0
14 TraesCS2A01G516700 chr2B 90.968 155 9 1 3128 3282 742170761 742170612 2.030000e-48 204.0
15 TraesCS2A01G516700 chr2B 100.000 38 0 0 4265 4302 364488573 364488610 2.150000e-08 71.3
16 TraesCS2A01G516700 chr2B 97.500 40 0 1 4263 4302 534922746 534922784 2.780000e-07 67.6
17 TraesCS2A01G516700 chr7B 86.505 2023 234 28 824 2838 525598810 525596819 0.000000e+00 2187.0
18 TraesCS2A01G516700 chr7B 86.179 123 7 6 3105 3221 525596644 525596526 1.620000e-24 124.0
19 TraesCS2A01G516700 chr7A 89.290 1690 176 5 1152 2838 563246828 563245141 0.000000e+00 2113.0
20 TraesCS2A01G516700 chr7A 79.705 271 50 4 45 313 571739963 571740230 1.580000e-44 191.0
21 TraesCS2A01G516700 chr7A 87.402 127 16 0 3450 3576 156951143 156951269 3.470000e-31 147.0
22 TraesCS2A01G516700 chr7D 88.975 1687 173 8 1152 2838 497320731 497319058 0.000000e+00 2073.0
23 TraesCS2A01G516700 chr7D 84.932 146 20 2 3448 3591 117761376 117761521 3.470000e-31 147.0
24 TraesCS2A01G516700 chr7D 86.022 93 9 1 3120 3208 497345659 497345567 3.540000e-16 97.1
25 TraesCS2A01G516700 chr7D 84.211 95 13 2 29 121 13337302 13337396 1.650000e-14 91.6
26 TraesCS2A01G516700 chr4D 94.231 104 4 2 3349 3451 195626643 195626541 1.600000e-34 158.0
27 TraesCS2A01G516700 chr4D 78.488 172 29 7 50 216 439781829 439781661 5.880000e-19 106.0
28 TraesCS2A01G516700 chr6D 86.861 137 18 0 3449 3585 119147793 119147657 2.070000e-33 154.0
29 TraesCS2A01G516700 chr6D 87.218 133 15 2 3450 3581 332501511 332501380 2.680000e-32 150.0
30 TraesCS2A01G516700 chr3B 87.500 136 13 3 3443 3576 513905461 513905594 2.070000e-33 154.0
31 TraesCS2A01G516700 chr3B 94.872 78 4 0 3021 3098 155674564 155674487 5.840000e-24 122.0
32 TraesCS2A01G516700 chr3B 94.872 78 4 0 3021 3098 441933704 441933627 5.840000e-24 122.0
33 TraesCS2A01G516700 chr3B 96.000 75 3 0 3021 3095 556332509 556332583 5.840000e-24 122.0
34 TraesCS2A01G516700 chr3B 94.872 78 4 0 3021 3098 565962857 565962780 5.840000e-24 122.0
35 TraesCS2A01G516700 chr5A 87.402 127 16 0 3450 3576 353920970 353920844 3.470000e-31 147.0
36 TraesCS2A01G516700 chr5A 75.517 290 62 8 29 314 472707866 472707582 2.700000e-27 134.0
37 TraesCS2A01G516700 chr4A 87.402 127 16 0 3450 3576 197356316 197356442 3.470000e-31 147.0
38 TraesCS2A01G516700 chr4A 100.000 38 0 0 4265 4302 408548740 408548703 2.150000e-08 71.3
39 TraesCS2A01G516700 chr4A 97.368 38 1 0 4265 4302 378103874 378103837 9.990000e-07 65.8
40 TraesCS2A01G516700 chr1B 76.868 281 52 8 824 1094 50900365 50900642 3.470000e-31 147.0
41 TraesCS2A01G516700 chr1B 76.512 281 50 11 824 1094 50950267 50950541 5.800000e-29 139.0
42 TraesCS2A01G516700 chr1B 94.872 78 4 0 3021 3098 586455744 586455667 5.840000e-24 122.0
43 TraesCS2A01G516700 chr6B 86.567 134 14 3 3449 3580 16271681 16271550 1.250000e-30 145.0
44 TraesCS2A01G516700 chr6B 96.154 78 3 0 3021 3098 580932262 580932185 1.260000e-25 128.0
45 TraesCS2A01G516700 chr6B 96.000 75 3 0 3021 3095 86528211 86528285 5.840000e-24 122.0
46 TraesCS2A01G516700 chr6B 100.000 38 0 0 4265 4302 183466590 183466553 2.150000e-08 71.3
47 TraesCS2A01G516700 chr5B 94.872 78 4 0 3021 3098 314435400 314435323 5.840000e-24 122.0
48 TraesCS2A01G516700 chr1D 86.408 103 11 3 45 145 309578493 309578594 4.550000e-20 110.0
49 TraesCS2A01G516700 chr3A 77.778 180 36 3 53 231 510693642 510693818 1.640000e-19 108.0
50 TraesCS2A01G516700 chr3A 100.000 37 0 0 4266 4302 354871129 354871165 7.720000e-08 69.4
51 TraesCS2A01G516700 chr3A 97.368 38 1 0 4265 4302 354145932 354145895 9.990000e-07 65.8
52 TraesCS2A01G516700 chr5D 84.259 108 14 3 37 142 421209933 421209827 7.610000e-18 102.0
53 TraesCS2A01G516700 chr6A 95.122 41 2 0 4262 4302 457485538 457485578 9.990000e-07 65.8


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 TraesCS2A01G516700 chr2A 740139902 740144203 4301 True 2645.00 7729 99.113000 1 4302 3 chr2A.!!$R3 4301
1 TraesCS2A01G516700 chr2A 740077363 740080171 2808 True 4903.00 4903 98.121000 1 2819 1 chr2A.!!$R1 2818
2 TraesCS2A01G516700 chr2A 740115714 740120015 4301 True 2715.00 7945 98.830667 1 4302 3 chr2A.!!$R2 4301
3 TraesCS2A01G516700 chr2D 608557720 608559738 2018 True 2610.00 2610 90.034000 813 2838 1 chr2D.!!$R1 2025
4 TraesCS2A01G516700 chr2D 608576107 608578913 2806 True 1648.00 3061 87.934000 646 3347 2 chr2D.!!$R2 2701
5 TraesCS2A01G516700 chr2B 742108737 742110633 1896 True 2532.00 2532 90.842000 813 2701 1 chr2B.!!$R1 1888
6 TraesCS2A01G516700 chr2B 742170612 742174995 4383 True 1017.25 3033 90.016750 1 3282 4 chr2B.!!$R2 3281
7 TraesCS2A01G516700 chr7B 525596526 525598810 2284 True 1155.50 2187 86.342000 824 3221 2 chr7B.!!$R1 2397
8 TraesCS2A01G516700 chr7A 563245141 563246828 1687 True 2113.00 2113 89.290000 1152 2838 1 chr7A.!!$R1 1686
9 TraesCS2A01G516700 chr7D 497319058 497320731 1673 True 2073.00 2073 88.975000 1152 2838 1 chr7D.!!$R1 1686

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
3209 4559 4.422073 TTGGTCCTATCTAACTGCCATG 57.578 45.455 0.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4070 5443 1.623973 CGTTCGGTTTTCCTCCGCTC 61.624 60.0 0.0 0.0 46.49 5.03 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
3209 4559 4.422073 TTGGTCCTATCTAACTGCCATG 57.578 45.455 0.00 0.0 0.00 3.66
3345 4718 2.978156 TGCAAAGGAAAGGACCATCT 57.022 45.000 0.00 0.0 0.00 2.90
3624 4997 2.534298 CCTGTGTGCTCATTCTCTACG 58.466 52.381 0.00 0.0 0.00 3.51
3639 5012 4.995124 TCTCTACGTTATTCAGACCTTGC 58.005 43.478 0.00 0.0 0.00 4.01
3672 5045 4.594970 TCTCTTCTGTAACCTCTCTCTGG 58.405 47.826 0.00 0.0 0.00 3.86
3687 5060 5.188434 TCTCTCTGGTAAGCCAATGAAATG 58.812 41.667 0.00 0.0 45.51 2.32
3778 5151 5.596845 TGGGTCTTTCAAAAAGAAAATCCG 58.403 37.500 3.82 0.0 45.11 4.18
3855 5228 2.760092 TCCCAGAGGCAATATTTTGTGC 59.240 45.455 0.00 0.0 40.14 4.57
3903 5276 2.353208 GGCGCCACAAAATAAACCATGA 60.353 45.455 24.80 0.0 0.00 3.07
3925 5298 7.681939 TGATCCACTAAAAAGCTACGAAAAT 57.318 32.000 0.00 0.0 0.00 1.82
3932 5305 8.500773 CACTAAAAAGCTACGAAAATAACTGGA 58.499 33.333 0.00 0.0 0.00 3.86
4007 5380 6.493458 TCGTCAATATCCATGGATCTAGACAA 59.507 38.462 31.50 21.9 36.17 3.18
4011 5384 8.663167 TCAATATCCATGGATCTAGACAACATT 58.337 33.333 30.61 17.4 36.17 2.71
4029 5402 2.281276 GTTTCGCCCGTTCCCAGT 60.281 61.111 0.00 0.0 0.00 4.00
4049 5422 4.750098 CAGTTTATCAACCACAACTCGTCT 59.250 41.667 0.00 0.0 32.70 4.18
4132 5505 6.606234 TGTACGTGCTCTTAAAATTGTGAA 57.394 33.333 4.97 0.0 0.00 3.18
4188 5561 2.774234 ACTAGAGTAGGGCGGTACTACA 59.226 50.000 0.00 0.0 42.47 2.74
4235 5608 0.601558 TCAGTACTCGCAACCAGTCC 59.398 55.000 0.00 0.0 0.00 3.85
4291 5664 3.472652 TGGTTAATAATGTAGCCGGCTG 58.527 45.455 38.98 0.0 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3090 4272 3.370104 CAACATACCCATTTTGCCCCTA 58.630 45.455 0.00 0.00 0.00 3.53
3209 4559 6.921857 CCATTAATTCAGACAGATGGAATTGC 59.078 38.462 8.61 0.00 40.41 3.56
3345 4718 4.789075 GCAGGCCGCGAGAACGTA 62.789 66.667 8.23 0.00 41.98 3.57
3560 4933 6.015940 GCAAAAATATTACTCCCTCCATCTGG 60.016 42.308 0.00 0.00 0.00 3.86
3565 4938 5.200483 CCAGCAAAAATATTACTCCCTCCA 58.800 41.667 0.00 0.00 0.00 3.86
3646 5019 7.279615 CAGAGAGAGGTTACAGAAGAGAGATA 58.720 42.308 0.00 0.00 0.00 1.98
3656 5029 3.131400 GGCTTACCAGAGAGAGGTTACAG 59.869 52.174 0.00 0.00 40.54 2.74
3672 5045 2.094078 TGCTGGCATTTCATTGGCTTAC 60.094 45.455 0.00 0.00 42.34 2.34
3778 5151 2.806244 AGCCACGTTCATACTCAAACAC 59.194 45.455 0.00 0.00 0.00 3.32
3903 5276 9.227777 AGTTATTTTCGTAGCTTTTTAGTGGAT 57.772 29.630 0.00 0.00 0.00 3.41
3984 5357 7.445121 TGTTGTCTAGATCCATGGATATTGAC 58.555 38.462 36.45 36.45 43.48 3.18
4007 5380 1.520600 GGGAACGGGCGAAACAATGT 61.521 55.000 0.00 0.00 0.00 2.71
4011 5384 2.281208 CTGGGAACGGGCGAAACA 60.281 61.111 0.00 0.00 0.00 2.83
4029 5402 3.496884 GCAGACGAGTTGTGGTTGATAAA 59.503 43.478 0.00 0.00 0.00 1.40
4070 5443 1.623973 CGTTCGGTTTTCCTCCGCTC 61.624 60.000 0.00 0.00 46.49 5.03
4132 5505 2.300723 TGCCTGCTTTGCTTTCATTGAT 59.699 40.909 0.00 0.00 0.00 2.57
4188 5561 6.239217 TCCATTCAGCATACAGTCATTACT 57.761 37.500 0.00 0.00 35.91 2.24


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

AutoCloner maintained by Alex Coulton.