Multiple sequence alignment - TraesCS2D01G277500

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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 TraesCS2D01G277500 chr2D 100.000 3291 0 0 1 3291 347800580 347797290 0.000000e+00 6078.0
1 TraesCS2D01G277500 chr2D 87.153 576 59 8 1 562 184850204 184849630 9.960000e-180 640.0
2 TraesCS2D01G277500 chr5D 97.868 2345 47 2 922 3264 465027104 465024761 0.000000e+00 4050.0
3 TraesCS2D01G277500 chr5D 98.272 926 16 0 1 926 465029136 465028211 0.000000e+00 1622.0
4 TraesCS2D01G277500 chr5A 85.269 1059 111 22 356 1376 13528967 13527916 0.000000e+00 1050.0
5 TraesCS2D01G277500 chr5A 92.462 650 46 2 1366 2012 13509031 13508382 0.000000e+00 926.0
6 TraesCS2D01G277500 chr5A 87.204 633 47 14 2088 2704 13508382 13507768 0.000000e+00 689.0
7 TraesCS2D01G277500 chr4D 98.195 554 10 0 1 554 15420667 15420114 0.000000e+00 968.0
8 TraesCS2D01G277500 chr4D 97.714 175 4 0 3091 3265 15417991 15417817 5.340000e-78 302.0
9 TraesCS2D01G277500 chr1D 87.370 578 55 10 1 562 421844363 421844938 0.000000e+00 647.0
10 TraesCS2D01G277500 chr1D 90.189 265 21 1 570 834 421844982 421845241 1.130000e-89 340.0
11 TraesCS2D01G277500 chr1D 79.505 444 77 11 760 1195 356923807 356924244 1.480000e-78 303.0
12 TraesCS2D01G277500 chr2B 86.979 576 57 13 1 562 573723530 573722959 1.670000e-177 632.0
13 TraesCS2D01G277500 chr7D 85.590 576 67 10 1 562 542256052 542255479 1.020000e-164 590.0
14 TraesCS2D01G277500 chr7D 77.823 974 160 36 1 953 608362496 608361558 4.800000e-153 551.0
15 TraesCS2D01G277500 chr7D 85.448 268 30 4 935 1195 608360951 608360686 1.510000e-68 270.0
16 TraesCS2D01G277500 chr4A 92.537 268 16 1 569 836 662748592 662748329 6.660000e-102 381.0
17 TraesCS2D01G277500 chr4A 83.688 141 23 0 890 1030 40219719 40219579 2.060000e-27 134.0
18 TraesCS2D01G277500 chr3D 81.778 450 75 5 750 1194 18929553 18930000 1.440000e-98 370.0
19 TraesCS2D01G277500 chr6B 81.882 425 66 11 633 1054 233028784 233028368 6.760000e-92 348.0
20 TraesCS2D01G277500 chr7A 80.637 408 65 12 797 1195 79121881 79121479 1.480000e-78 303.0
21 TraesCS2D01G277500 chr3B 86.716 271 36 0 760 1030 59851449 59851719 5.340000e-78 302.0
22 TraesCS2D01G277500 chr4B 84.946 279 41 1 760 1037 63891490 63891768 6.950000e-72 281.0
23 TraesCS2D01G277500 chr1A 75.460 652 112 31 1392 2012 1199385 1198751 1.160000e-69 274.0
24 TraesCS2D01G277500 chr6D 78.370 319 56 9 68 384 362257467 362257160 9.320000e-46 195.0
25 TraesCS2D01G277500 chr3A 77.736 265 42 7 1730 1978 747740006 747739743 2.650000e-31 147.0
26 TraesCS2D01G277500 chr2A 86.364 88 10 2 1821 1907 677042390 677042476 9.720000e-16 95.3
27 TraesCS2D01G277500 chr5B 84.810 79 12 0 1829 1907 206060400 206060478 2.720000e-11 80.5


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 TraesCS2D01G277500 chr2D 347797290 347800580 3290 True 6078.0 6078 100.0000 1 3291 1 chr2D.!!$R2 3290
1 TraesCS2D01G277500 chr2D 184849630 184850204 574 True 640.0 640 87.1530 1 562 1 chr2D.!!$R1 561
2 TraesCS2D01G277500 chr5D 465024761 465029136 4375 True 2836.0 4050 98.0700 1 3264 2 chr5D.!!$R1 3263
3 TraesCS2D01G277500 chr5A 13527916 13528967 1051 True 1050.0 1050 85.2690 356 1376 1 chr5A.!!$R1 1020
4 TraesCS2D01G277500 chr5A 13507768 13509031 1263 True 807.5 926 89.8330 1366 2704 2 chr5A.!!$R2 1338
5 TraesCS2D01G277500 chr4D 15417817 15420667 2850 True 635.0 968 97.9545 1 3265 2 chr4D.!!$R1 3264
6 TraesCS2D01G277500 chr1D 421844363 421845241 878 False 493.5 647 88.7795 1 834 2 chr1D.!!$F2 833
7 TraesCS2D01G277500 chr2B 573722959 573723530 571 True 632.0 632 86.9790 1 562 1 chr2B.!!$R1 561
8 TraesCS2D01G277500 chr7D 542255479 542256052 573 True 590.0 590 85.5900 1 562 1 chr7D.!!$R1 561
9 TraesCS2D01G277500 chr7D 608360686 608362496 1810 True 410.5 551 81.6355 1 1195 2 chr7D.!!$R2 1194
10 TraesCS2D01G277500 chr1A 1198751 1199385 634 True 274.0 274 75.4600 1392 2012 1 chr1A.!!$R1 620

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
100 102 0.603569 ACAGGTTCGAATCTGCTCGT 59.396 50.000 33.09 14.95 40.85 4.18 F
296 307 2.042831 GGCGGCTTCAAGTGCAGAT 61.043 57.895 0.00 0.00 0.00 2.90 F
1331 2828 2.003548 GAAGGCTCCTGGGGTGGAT 61.004 63.158 0.00 0.00 35.30 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1331 2828 0.693622 TCAACCCCAATACCTTCGCA 59.306 50.000 0.00 0.0 0.0 5.10 R
2019 3683 1.231221 TGGTACGCGCAAAATTCACT 58.769 45.000 5.73 0.0 0.0 3.41 R
2998 5033 1.765314 AGCTCCTTTATGACATCCGCT 59.235 47.619 0.00 0.0 0.0 5.52 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
22 23 1.532794 TGCGGCAAAAGGGGATTGT 60.533 52.632 0.00 0.00 0.00 2.71
38 39 2.665185 GTGCGGTCCAGCGAGTTT 60.665 61.111 1.59 0.00 40.67 2.66
100 102 0.603569 ACAGGTTCGAATCTGCTCGT 59.396 50.000 33.09 14.95 40.85 4.18
296 307 2.042831 GGCGGCTTCAAGTGCAGAT 61.043 57.895 0.00 0.00 0.00 2.90
1163 2471 5.049405 AGTTGAAAATACTCGTTCTTGCCAG 60.049 40.000 0.00 0.00 0.00 4.85
1331 2828 2.003548 GAAGGCTCCTGGGGTGGAT 61.004 63.158 0.00 0.00 35.30 3.41
1377 2880 8.056407 AGAAAATTCTTTAGTGATTAGGCACC 57.944 34.615 0.00 0.00 35.14 5.01
1561 3094 7.246027 ACTGAATTTAATAGGTTGGGTTTCCT 58.754 34.615 0.00 0.00 37.80 3.36
1577 3110 6.216662 TGGGTTTCCTTGGTAGAGATTATTCA 59.783 38.462 0.00 0.00 0.00 2.57
1946 3607 5.908499 GGCTAAACGTTAATCGAACAAAACA 59.092 36.000 0.00 0.00 42.86 2.83
2019 3683 2.634453 TCTGGAGTTTGCATCTGACTCA 59.366 45.455 16.69 6.97 41.15 3.41
2033 3697 1.069973 TGACTCAGTGAATTTTGCGCG 60.070 47.619 0.00 0.00 0.00 6.86
2073 3737 2.355197 TCATTGTGCCTGATTACACGG 58.645 47.619 0.00 0.00 39.71 4.94
2151 3815 3.440522 GGTTTTAGGAGCACATCAGAACC 59.559 47.826 0.00 0.00 0.00 3.62
2306 4324 3.205338 CACTGAACACATCCACAACAGA 58.795 45.455 0.00 0.00 0.00 3.41
2334 4352 6.528321 TGTTAGGAGGCATCAGAATTAGATG 58.472 40.000 13.41 13.41 44.38 2.90
2432 4450 1.062658 TCATCATCCTCAGGGAGCTCA 60.063 52.381 17.19 0.00 45.86 4.26
2458 4476 6.485984 GCTGAAGATGGAGATAATGTTGACAT 59.514 38.462 0.00 0.00 38.41 3.06
2460 4478 7.799081 TGAAGATGGAGATAATGTTGACATCT 58.201 34.615 0.00 0.00 43.68 2.90
2611 4632 2.553028 GCAGTGAATTGTCTTCCCAGGA 60.553 50.000 0.00 0.00 0.00 3.86
2820 4853 2.497273 ACCCATGAATAACCTGCTTTGC 59.503 45.455 0.00 0.00 0.00 3.68
2874 4909 0.738762 CACCACAGGAGACGATGCAG 60.739 60.000 0.00 0.00 0.00 4.41
2901 4936 0.768622 TGGGAACGAATTGGAGTGGT 59.231 50.000 0.00 0.00 0.00 4.16
3050 5085 3.458189 GTTAGTCCAGAATCCACGATGG 58.542 50.000 0.00 0.00 39.43 3.51
3055 5090 0.530650 CAGAATCCACGATGGGACGG 60.531 60.000 0.00 0.00 40.44 4.79
3063 5098 0.535780 ACGATGGGACGGCTCGTATA 60.536 55.000 1.71 0.00 43.25 1.47
3265 5497 3.548014 GGGATCACAACAACACTTTCGTG 60.548 47.826 0.00 0.00 46.63 4.35
3277 5509 3.402628 ACTTTCGTGTAGAATGTGCCT 57.597 42.857 0.00 0.00 43.08 4.75
3278 5510 3.740115 ACTTTCGTGTAGAATGTGCCTT 58.260 40.909 0.00 0.00 43.08 4.35
3279 5511 4.134563 ACTTTCGTGTAGAATGTGCCTTT 58.865 39.130 0.00 0.00 43.08 3.11
3280 5512 4.213482 ACTTTCGTGTAGAATGTGCCTTTC 59.787 41.667 0.00 0.00 43.08 2.62
3281 5513 3.394674 TCGTGTAGAATGTGCCTTTCA 57.605 42.857 4.47 0.00 0.00 2.69
3282 5514 3.064207 TCGTGTAGAATGTGCCTTTCAC 58.936 45.455 0.00 0.00 45.82 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.664851 CAAACTCGCTGGACCGCA 60.665 61.111 8.64 0.00 0.00 5.69
100 102 1.969923 CCATGCAAAAGGGAGGTTCAA 59.030 47.619 0.00 0.00 0.00 2.69
296 307 0.948623 CGTCACGACAGATTTGGCCA 60.949 55.000 0.00 0.00 0.00 5.36
1163 2471 3.044059 GAGGGCAGCGCATTCACAC 62.044 63.158 11.47 0.00 0.00 3.82
1206 2514 2.939022 GTCTGCACTTGACACGGC 59.061 61.111 0.00 0.00 34.80 5.68
1331 2828 0.693622 TCAACCCCAATACCTTCGCA 59.306 50.000 0.00 0.00 0.00 5.10
1383 2886 3.903714 AGTTTTGCTTAAATCCAAGGGCT 59.096 39.130 0.00 0.00 0.00 5.19
1561 3094 7.676004 TGACAAGTGTGAATAATCTCTACCAA 58.324 34.615 0.00 0.00 0.00 3.67
1577 3110 8.969260 ATACATCATCATAACATGACAAGTGT 57.031 30.769 0.00 0.00 43.01 3.55
1946 3607 3.603532 CCACACACTATCTCTTGCATGT 58.396 45.455 0.00 0.00 0.00 3.21
2019 3683 1.231221 TGGTACGCGCAAAATTCACT 58.769 45.000 5.73 0.00 0.00 3.41
2033 3697 8.730680 ACAATGAACTATCTCACAAAATGGTAC 58.269 33.333 0.00 0.00 0.00 3.34
2073 3737 6.347644 GCCTACAAAACAGAATTTGGAATTGC 60.348 38.462 4.96 0.00 43.10 3.56
2151 3815 2.245159 TGCTTCACCAGACTGAACTG 57.755 50.000 3.32 0.00 37.61 3.16
2306 4324 2.191400 TCTGATGCCTCCTAACAGCTT 58.809 47.619 0.00 0.00 0.00 3.74
2334 4352 4.340894 TTGCATATCTCTTTTGACGCAC 57.659 40.909 0.00 0.00 0.00 5.34
2432 4450 6.054295 GTCAACATTATCTCCATCTTCAGCT 58.946 40.000 0.00 0.00 0.00 4.24
2458 4476 5.333035 CGAAATCTCGTAGTTTGTTTGCAGA 60.333 40.000 0.00 0.00 40.33 4.26
2460 4478 4.508492 TCGAAATCTCGTAGTTTGTTTGCA 59.492 37.500 0.00 0.00 45.62 4.08
2611 4632 5.307196 AGGTGTAGGTGACTCACTTGTAATT 59.693 40.000 9.08 0.00 43.67 1.40
2874 4909 2.094752 CCAATTCGTTCCCAACCATGTC 60.095 50.000 0.00 0.00 0.00 3.06
2901 4936 3.763360 CCAATCAATTTGAGCTGGTACCA 59.237 43.478 15.39 15.39 37.53 3.25
2998 5033 1.765314 AGCTCCTTTATGACATCCGCT 59.235 47.619 0.00 0.00 0.00 5.52
3050 5085 3.598299 AGATAGACTATACGAGCCGTCC 58.402 50.000 3.45 0.00 41.54 4.79
3055 5090 7.147143 TCAAATGGAGATAGACTATACGAGC 57.853 40.000 0.00 0.00 0.00 5.03
3063 5098 4.502259 GCACGGATCAAATGGAGATAGACT 60.502 45.833 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.