Multiple sequence alignment - TraesCS3D01G058700

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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 TraesCS3D01G058700 chr3D 100.000 7210 0 0 1 7210 25400165 25392956 0.000000e+00 13315.0
1 TraesCS3D01G058700 chr3D 88.225 2191 238 15 2987 5159 40009642 40007454 0.000000e+00 2599.0
2 TraesCS3D01G058700 chr3D 86.016 615 66 12 1470 2081 40011405 40010808 6.100000e-180 641.0
3 TraesCS3D01G058700 chr3D 97.778 90 2 0 5632 5721 25394488 25394399 9.680000e-34 156.0
4 TraesCS3D01G058700 chr3D 97.778 90 2 0 5678 5767 25394534 25394445 9.680000e-34 156.0
5 TraesCS3D01G058700 chr3D 81.343 134 15 7 2476 2602 40010188 40010058 4.600000e-17 100.0
6 TraesCS3D01G058700 chr3D 95.455 44 2 0 5632 5675 25394442 25394399 3.610000e-08 71.3
7 TraesCS3D01G058700 chr3D 95.455 44 2 0 5724 5767 25394534 25394491 3.610000e-08 71.3
8 TraesCS3D01G058700 chr7D 98.865 7226 32 13 1 7210 37798918 37806109 0.000000e+00 12844.0
9 TraesCS3D01G058700 chr7D 79.911 448 54 22 2365 2784 65506643 65506204 5.470000e-76 296.0
10 TraesCS3D01G058700 chr7D 86.154 195 26 1 5122 5315 37833977 37834171 7.330000e-50 209.0
11 TraesCS3D01G058700 chr7D 97.778 90 2 0 5678 5767 37804534 37804623 9.680000e-34 156.0
12 TraesCS3D01G058700 chr7D 97.778 90 2 0 5632 5721 37804580 37804669 9.680000e-34 156.0
13 TraesCS3D01G058700 chr7D 95.455 44 2 0 5724 5767 37804534 37804577 3.610000e-08 71.3
14 TraesCS3D01G058700 chr7D 95.455 44 2 0 5632 5675 37804626 37804669 3.610000e-08 71.3
15 TraesCS3D01G058700 chr7A 95.283 4282 138 30 1426 5675 37112254 37116503 0.000000e+00 6730.0
16 TraesCS3D01G058700 chr7A 87.128 940 66 24 1 899 37110358 37111283 0.000000e+00 1014.0
17 TraesCS3D01G058700 chr7A 94.151 530 26 4 890 1414 37111682 37112211 0.000000e+00 802.0
18 TraesCS3D01G058700 chr7A 92.518 548 38 3 5724 6271 37116460 37117004 0.000000e+00 782.0
19 TraesCS3D01G058700 chr7A 84.783 782 49 25 6492 7210 37117140 37117914 0.000000e+00 721.0
20 TraesCS3D01G058700 chr7A 81.403 613 65 24 5096 5672 37121687 37122286 8.530000e-124 455.0
21 TraesCS3D01G058700 chr7A 92.453 53 4 0 6281 6333 41021480 41021428 7.760000e-10 76.8
22 TraesCS3D01G058700 chr7A 95.455 44 2 0 5678 5721 37116460 37116503 3.610000e-08 71.3
23 TraesCS3D01G058700 chr4A 95.254 3203 99 25 2496 5675 687181457 687178285 0.000000e+00 5024.0
24 TraesCS3D01G058700 chr4A 94.660 1030 44 6 1425 2449 687182476 687181453 0.000000e+00 1587.0
25 TraesCS3D01G058700 chr4A 90.106 1132 63 27 53 1153 687184088 687182975 0.000000e+00 1424.0
26 TraesCS3D01G058700 chr4A 93.671 553 32 3 5724 6275 687178328 687177778 0.000000e+00 824.0
27 TraesCS3D01G058700 chr4A 86.979 768 41 15 6492 7209 687177529 687176771 0.000000e+00 809.0
28 TraesCS3D01G058700 chr4A 87.678 211 19 1 1212 1415 687182727 687182517 9.350000e-59 239.0
29 TraesCS3D01G058700 chr4A 89.474 57 4 2 6286 6341 595568202 595568147 3.610000e-08 71.3
30 TraesCS3D01G058700 chr4A 95.455 44 2 0 5678 5721 687178328 687178285 3.610000e-08 71.3
31 TraesCS3D01G058700 chr4A 92.500 40 3 0 6119 6158 687174260 687174221 2.810000e-04 58.4
32 TraesCS3D01G058700 chr3B 88.157 2187 238 16 2992 5160 63410624 63408441 0.000000e+00 2584.0
33 TraesCS3D01G058700 chr3B 82.731 747 88 23 1482 2224 63412194 63411485 1.710000e-175 627.0
34 TraesCS3D01G058700 chr3B 77.561 205 33 8 2404 2602 63411240 63411043 2.130000e-20 111.0
35 TraesCS3D01G058700 chr3A 86.990 2306 269 20 2987 5263 51472175 51469872 0.000000e+00 2567.0
36 TraesCS3D01G058700 chr3A 86.144 599 68 7 1485 2081 51473751 51473166 3.670000e-177 632.0
37 TraesCS3D01G058700 chr1B 91.667 60 4 1 6270 6328 457378679 457378620 1.670000e-11 82.4
38 TraesCS3D01G058700 chr2D 95.833 48 2 0 6281 6328 436503532 436503485 2.160000e-10 78.7
39 TraesCS3D01G058700 chr2D 92.453 53 4 0 6281 6333 643235863 643235915 7.760000e-10 76.8
40 TraesCS3D01G058700 chr7B 92.453 53 4 0 6281 6333 595454810 595454862 7.760000e-10 76.8
41 TraesCS3D01G058700 chr6D 95.745 47 2 0 6281 6327 140086894 140086940 7.760000e-10 76.8
42 TraesCS3D01G058700 chr4D 89.474 57 5 1 6281 6336 379147233 379147289 3.610000e-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 TraesCS3D01G058700 chr3D 25392956 25400165 7209 True 13315.000000 13315 100.000000 1 7210 1 chr3D.!!$R1 7209
1 TraesCS3D01G058700 chr3D 40007454 40011405 3951 True 1113.333333 2599 85.194667 1470 5159 3 chr3D.!!$R3 3689
2 TraesCS3D01G058700 chr7D 37798918 37806109 7191 False 2659.720000 12844 97.066200 1 7210 5 chr7D.!!$F2 7209
3 TraesCS3D01G058700 chr7A 37110358 37122286 11928 False 1510.757143 6730 90.103000 1 7210 7 chr7A.!!$F1 7209
4 TraesCS3D01G058700 chr4A 687174221 687184088 9867 True 1254.587500 5024 92.037875 53 7209 8 chr4A.!!$R2 7156
5 TraesCS3D01G058700 chr3B 63408441 63412194 3753 True 1107.333333 2584 82.816333 1482 5160 3 chr3B.!!$R1 3678
6 TraesCS3D01G058700 chr3A 51469872 51473751 3879 True 1599.500000 2567 86.567000 1485 5263 2 chr3A.!!$R1 3778

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
801 844 3.565670 GGCCTAGAAATTTCCCTTGGGAA 60.566 47.826 16.54 16.54 0.00 3.97 F
2021 2723 3.368948 GCACAGGGTGACAAAAGGAAAAA 60.369 43.478 0.00 0.00 35.23 1.94 F
2114 2817 8.722480 TCTTTCACATTATACTCAATGGTCTG 57.278 34.615 1.36 0.00 39.71 3.51 F
5088 6247 3.244215 TGTGAAGCCCTTCTGTAGACAAG 60.244 47.826 9.23 0.00 40.14 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2114 2817 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82 R
5088 6247 3.863142 ACTGCAGATGAAGATTTTGCC 57.137 42.857 23.35 0.00 33.98 4.52 R
5417 6593 3.426191 CAGATTGTGCAATTGACAAACGG 59.574 43.478 20.00 15.97 36.90 4.44 R
6438 7710 2.344950 CTTGCTCCAGACACTGATGAC 58.655 52.381 0.00 0.00 32.44 3.06 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
501 528 8.380743 TGCTCACAAAATAAGATTGCAAAATT 57.619 26.923 1.71 3.83 0.00 1.82
677 704 9.967245 GTTTGGTTTAAAAGAAAAGATCAACAC 57.033 29.630 0.00 0.00 0.00 3.32
801 844 3.565670 GGCCTAGAAATTTCCCTTGGGAA 60.566 47.826 16.54 16.54 0.00 3.97
956 1413 6.696441 AGACTCGAGAGTAAATTACGGAAT 57.304 37.500 21.68 0.00 42.66 3.01
1472 2170 9.143155 ACTTTCCAGTACCAGAATGTAATTTTT 57.857 29.630 10.52 0.00 36.07 1.94
1830 2528 8.277713 GCAAGTAGACGTTTTTGTCATTAGTAA 58.722 33.333 0.00 0.00 41.41 2.24
2021 2723 3.368948 GCACAGGGTGACAAAAGGAAAAA 60.369 43.478 0.00 0.00 35.23 1.94
2114 2817 8.722480 TCTTTCACATTATACTCAATGGTCTG 57.278 34.615 1.36 0.00 39.71 3.51
5088 6247 3.244215 TGTGAAGCCCTTCTGTAGACAAG 60.244 47.826 9.23 0.00 40.14 3.16
5417 6593 0.685458 AGAGGGGGAACATTGCATGC 60.685 55.000 11.82 11.82 0.00 4.06
6438 7710 1.079127 AAGACTGCACCGATTCCCG 60.079 57.895 0.00 0.00 38.18 5.14
6696 7995 8.988060 TGATTTCCTCCACTGAGTAATAACATA 58.012 33.333 0.00 0.00 36.86 2.29
6956 8255 8.853077 TTATTAAGCCCAATGACATCTCTATG 57.147 34.615 0.00 0.00 39.17 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 103 9.178758 GGATTGTTAGTCTCAAAATGGTCTATT 57.821 33.333 0.00 0.00 0.00 1.73
677 704 6.531594 TCGATGAGAAACAACTTGCTATACTG 59.468 38.462 0.00 0.00 0.00 2.74
956 1413 1.470051 TATACGCTCAGTGGCAGACA 58.530 50.000 0.00 0.00 0.00 3.41
1472 2170 8.562892 CACTGCATTTTAGAAGAAGAAGAAGAA 58.437 33.333 0.00 0.00 0.00 2.52
1473 2171 7.716998 ACACTGCATTTTAGAAGAAGAAGAAGA 59.283 33.333 0.00 0.00 0.00 2.87
1474 2172 7.869800 ACACTGCATTTTAGAAGAAGAAGAAG 58.130 34.615 0.00 0.00 0.00 2.85
1830 2528 2.136026 AGACAAACCTGTTCTCCCCTT 58.864 47.619 0.00 0.00 35.30 3.95
2021 2723 2.110578 ACTTGTTTTTGGAAGCTGGCT 58.889 42.857 0.00 0.00 0.00 4.75
2114 2817 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5088 6247 3.863142 ACTGCAGATGAAGATTTTGCC 57.137 42.857 23.35 0.00 33.98 4.52
5417 6593 3.426191 CAGATTGTGCAATTGACAAACGG 59.574 43.478 20.00 15.97 36.90 4.44
5834 7037 5.410746 GCTACAGAACTTTAAGTTACACCCC 59.589 44.000 10.57 0.00 38.80 4.95
6438 7710 2.344950 CTTGCTCCAGACACTGATGAC 58.655 52.381 0.00 0.00 32.44 3.06
6956 8255 3.134458 GCATTAGAGGTGCCATGTACTC 58.866 50.000 0.00 0.00 36.61 2.59


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

AutoCloner maintained by Alex Coulton.