Multiple sequence alignment - TraesCS3D01G065900

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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 TraesCS3D01G065900 chr3D 100.000 2930 0 0 1 2930 29251423 29248494 0.000000e+00 5411.0
1 TraesCS3D01G065900 chr3D 94.961 1409 36 8 1 1403 29228900 29227521 0.000000e+00 2176.0
2 TraesCS3D01G065900 chr3D 86.246 349 31 9 2521 2860 29217727 29217387 2.150000e-96 363.0
3 TraesCS3D01G065900 chr3D 97.101 207 6 0 438 644 29241963 29241757 1.670000e-92 350.0
4 TraesCS3D01G065900 chr3D 84.182 373 41 11 1759 2125 29227513 29227153 2.160000e-91 346.0
5 TraesCS3D01G065900 chr3D 96.517 201 7 0 444 644 29267217 29267017 1.680000e-87 333.0
6 TraesCS3D01G065900 chr3D 100.000 47 0 0 1054 1100 29275225 29275179 1.450000e-13 87.9
7 TraesCS3D01G065900 chr3A 93.702 1302 56 10 875 2159 38436247 38434955 0.000000e+00 1927.0
8 TraesCS3D01G065900 chr3A 91.994 1399 71 21 761 2142 38474667 38473293 0.000000e+00 1925.0
9 TraesCS3D01G065900 chr3A 85.019 1295 134 27 990 2246 38538312 38537040 0.000000e+00 1262.0
10 TraesCS3D01G065900 chr3A 82.382 823 86 26 1942 2722 38434207 38433402 0.000000e+00 662.0
11 TraesCS3D01G065900 chr3A 81.023 880 91 38 1942 2781 38472454 38471611 5.330000e-177 630.0
12 TraesCS3D01G065900 chr3A 100.000 37 0 0 820 856 38436281 38436245 5.240000e-08 69.4
13 TraesCS3D01G065900 chr3B 91.733 1379 79 15 761 2126 49780593 49779237 0.000000e+00 1882.0
14 TraesCS3D01G065900 chr3B 86.643 1138 100 19 1041 2158 49858754 49857649 0.000000e+00 1212.0
15 TraesCS3D01G065900 chr3B 90.370 810 38 14 2157 2930 49857566 49856761 0.000000e+00 1027.0
16 TraesCS3D01G065900 chr3B 89.275 690 40 15 2263 2930 49778916 49778239 0.000000e+00 833.0
17 TraesCS3D01G065900 chr3B 79.269 1013 109 53 1942 2912 49775124 49774171 5.370000e-172 614.0
18 TraesCS3D01G065900 chr3B 88.182 110 13 0 643 752 49847369 49847260 6.590000e-27 132.0
19 TraesCS3D01G065900 chr4A 96.589 645 21 1 1 645 531369813 531369170 0.000000e+00 1068.0
20 TraesCS3D01G065900 chr4A 96.226 212 7 1 433 644 531383214 531383004 2.160000e-91 346.0
21 TraesCS3D01G065900 chr5A 95.814 645 23 3 1 645 602046474 602045834 0.000000e+00 1038.0
22 TraesCS3D01G065900 chr5A 96.209 211 6 2 435 644 602094760 602094551 7.770000e-91 344.0
23 TraesCS3D01G065900 chr5D 99.459 555 3 0 1319 1873 412359324 412358770 0.000000e+00 1009.0
24 TraesCS3D01G065900 chr5D 88.415 656 60 12 1 647 432451187 432450539 0.000000e+00 776.0
25 TraesCS3D01G065900 chr5D 86.207 58 8 0 2696 2753 532804591 532804534 2.440000e-06 63.9
26 TraesCS3D01G065900 chr7A 93.093 666 24 12 1 646 735123084 735123747 0.000000e+00 955.0
27 TraesCS3D01G065900 chr5B 93.161 658 25 11 1 640 523399701 523400356 0.000000e+00 948.0
28 TraesCS3D01G065900 chr1D 91.284 654 45 7 1 644 11003160 11002509 0.000000e+00 881.0
29 TraesCS3D01G065900 chr1D 91.131 654 45 6 1 644 11117249 11116599 0.000000e+00 874.0
30 TraesCS3D01G065900 chr1D 90.826 654 48 7 1 644 11034028 11033377 0.000000e+00 865.0


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 TraesCS3D01G065900 chr3D 29248494 29251423 2929 True 5411.000000 5411 100.0000 1 2930 1 chr3D.!!$R3 2929
1 TraesCS3D01G065900 chr3D 29227153 29228900 1747 True 1261.000000 2176 89.5715 1 2125 2 chr3D.!!$R6 2124
2 TraesCS3D01G065900 chr3A 38471611 38474667 3056 True 1277.500000 1925 86.5085 761 2781 2 chr3A.!!$R3 2020
3 TraesCS3D01G065900 chr3A 38537040 38538312 1272 True 1262.000000 1262 85.0190 990 2246 1 chr3A.!!$R1 1256
4 TraesCS3D01G065900 chr3A 38433402 38436281 2879 True 886.133333 1927 92.0280 820 2722 3 chr3A.!!$R2 1902
5 TraesCS3D01G065900 chr3B 49856761 49858754 1993 True 1119.500000 1212 88.5065 1041 2930 2 chr3B.!!$R3 1889
6 TraesCS3D01G065900 chr3B 49774171 49780593 6422 True 1109.666667 1882 86.7590 761 2930 3 chr3B.!!$R2 2169
7 TraesCS3D01G065900 chr4A 531369170 531369813 643 True 1068.000000 1068 96.5890 1 645 1 chr4A.!!$R1 644
8 TraesCS3D01G065900 chr5A 602045834 602046474 640 True 1038.000000 1038 95.8140 1 645 1 chr5A.!!$R1 644
9 TraesCS3D01G065900 chr5D 412358770 412359324 554 True 1009.000000 1009 99.4590 1319 1873 1 chr5D.!!$R1 554
10 TraesCS3D01G065900 chr5D 432450539 432451187 648 True 776.000000 776 88.4150 1 647 1 chr5D.!!$R2 646
11 TraesCS3D01G065900 chr7A 735123084 735123747 663 False 955.000000 955 93.0930 1 646 1 chr7A.!!$F1 645
12 TraesCS3D01G065900 chr5B 523399701 523400356 655 False 948.000000 948 93.1610 1 640 1 chr5B.!!$F1 639
13 TraesCS3D01G065900 chr1D 11002509 11003160 651 True 881.000000 881 91.2840 1 644 1 chr1D.!!$R1 643
14 TraesCS3D01G065900 chr1D 11116599 11117249 650 True 874.000000 874 91.1310 1 644 1 chr1D.!!$R3 643
15 TraesCS3D01G065900 chr1D 11033377 11034028 651 True 865.000000 865 90.8260 1 644 1 chr1D.!!$R2 643

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
687 726 1.471964 GCTCTATCGAGTGTTCGCTG 58.528 55.0 0.0 0.0 46.28 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2260 7869 0.31904 CATAGGGATGGCGTCAGTCG 60.319 60.0 9.27 0.0 43.12 4.18 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
373 376 4.586841 TGGCTTTACAAAAGCACTACCAAT 59.413 37.500 21.96 0.00 44.71 3.16
441 444 7.998964 AGTTATGATTATGGGAGGGTGTTTAAG 59.001 37.037 0.00 0.00 0.00 1.85
455 458 5.163519 GGGTGTTTAAGCGTATAGGTACAGA 60.164 44.000 0.00 0.00 0.00 3.41
458 461 7.198390 GTGTTTAAGCGTATAGGTACAGATGA 58.802 38.462 0.00 0.00 0.00 2.92
606 645 2.483014 TATATAACATGCGGGTGCCC 57.517 50.000 0.00 0.00 41.78 5.36
653 692 5.443301 CGATACAATTTCACACTGTCGTCAG 60.443 44.000 8.17 8.17 46.18 3.51
687 726 1.471964 GCTCTATCGAGTGTTCGCTG 58.528 55.000 0.00 0.00 46.28 5.18
909 969 3.093172 GGGCCCCTTCTCCCTCTG 61.093 72.222 12.23 0.00 39.46 3.35
1035 1095 1.135046 CTGGATCATCGTCGATGCAC 58.865 55.000 26.86 21.28 38.63 4.57
1923 2037 2.154567 TCACCGGCCAGAAGTATACT 57.845 50.000 0.00 0.00 0.00 2.12
1940 2057 6.607019 AGTATACTCTCTAGAAGACCCAAGG 58.393 44.000 0.00 0.00 0.00 3.61
2260 7869 6.276847 ACTCGATCATGATTAAGTCTTGGTC 58.723 40.000 10.14 0.00 38.25 4.02
2319 7928 4.706962 TCTCCTTCTTCGATGATCTTGACA 59.293 41.667 1.37 0.00 0.00 3.58
2380 7991 1.058404 GTGCTCGTCGGTTGTAGTTC 58.942 55.000 0.00 0.00 0.00 3.01
2397 8026 1.957877 GTTCAACGGGATTTGGGTTGA 59.042 47.619 2.02 2.02 45.83 3.18
2409 8038 3.518634 TTGGGTTGAACTTTGTGCTTC 57.481 42.857 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 139 2.009774 CTTGAGCATGGACTTAACCCG 58.990 52.381 0.00 0.00 0.00 5.28
441 444 5.037015 CAGACTCATCTGTACCTATACGC 57.963 47.826 0.00 0.00 46.39 4.42
455 458 1.446792 CGAACCAGCGCAGACTCAT 60.447 57.895 11.47 0.00 0.00 2.90
458 461 3.165160 AACCGAACCAGCGCAGACT 62.165 57.895 11.47 0.00 0.00 3.24
606 645 0.930310 CGTCTCAATGCCCATACACG 59.070 55.000 0.00 0.00 0.00 4.49
653 692 5.690409 TCGATAGAGCCAACGATAATTGTTC 59.310 40.000 0.00 0.00 42.67 3.18
687 726 4.495184 GCATGCGCCCCGTTATATTAATAC 60.495 45.833 4.18 0.00 0.00 1.89
909 969 2.994417 TGGATTTGTTGGCCGGGC 60.994 61.111 23.42 23.42 0.00 6.13
1923 2037 3.090037 CGTTCCTTGGGTCTTCTAGAGA 58.910 50.000 0.00 0.00 0.00 3.10
1940 2057 3.002246 TGCAGACATTGTTTCAGTCGTTC 59.998 43.478 0.00 0.00 37.36 3.95
2196 7796 5.966636 TTCGGATGTTGATAATTCTCACG 57.033 39.130 0.00 0.00 0.00 4.35
2260 7869 0.319040 CATAGGGATGGCGTCAGTCG 60.319 60.000 9.27 0.00 43.12 4.18
2319 7928 1.615392 GAGCCAAGGCAAAGACAACAT 59.385 47.619 14.40 0.00 44.88 2.71
2380 7991 1.960689 AGTTCAACCCAAATCCCGTTG 59.039 47.619 0.00 0.00 38.56 4.10
2397 8026 4.696455 CAAGGAATTGGAAGCACAAAGTT 58.304 39.130 0.00 0.00 33.48 2.66
2668 8344 7.147976 ACTTTTAGAAGTGTTCATGCCATTTC 58.852 34.615 0.00 10.47 44.27 2.17


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

AutoCloner maintained by Alex Coulton.