Multiple sequence alignment - TraesCS2D01G241900

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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 TraesCS2D01G241900 chr2D 100.000 2411 0 0 1 2411 265065542 265067952 0 4453
1 TraesCS2D01G241900 chr3D 96.982 1657 32 10 1 1640 239006008 239007663 0 2767
2 TraesCS2D01G241900 chr5D 96.982 1657 31 11 1 1640 189874349 189876003 0 2765
3 TraesCS2D01G241900 chr5D 96.800 1656 37 8 1 1640 185040504 185038849 0 2750
4 TraesCS2D01G241900 chr1D 96.866 1659 30 10 1 1640 160656053 160654398 0 2756
5 TraesCS2D01G241900 chr1D 96.628 771 26 0 1641 2411 253415699 253414929 0 1280
6 TraesCS2D01G241900 chr1D 96.498 771 27 0 1641 2411 213128504 213129274 0 1275
7 TraesCS2D01G241900 chr1D 96.239 771 29 0 1641 2411 213146922 213147692 0 1264
8 TraesCS2D01G241900 chr1D 96.239 771 29 0 1641 2411 253407250 253406480 0 1264
9 TraesCS2D01G241900 chr6A 96.082 1659 42 12 1 1640 248617002 248618656 0 2682
10 TraesCS2D01G241900 chr4B 95.957 1657 50 9 1 1640 336603217 336604873 0 2673
11 TraesCS2D01G241900 chr4B 95.471 1656 47 8 1 1640 317640552 317642195 0 2617
12 TraesCS2D01G241900 chrUn 95.791 1663 47 11 1 1640 15263472 15261810 0 2662
13 TraesCS2D01G241900 chrUn 95.673 1664 48 11 1 1640 15269714 15268051 0 2652
14 TraesCS2D01G241900 chrUn 96.626 1215 21 7 445 1640 282054235 282053022 0 1999
15 TraesCS2D01G241900 chrUn 96.626 1215 21 7 445 1640 285057187 285058400 0 1999
16 TraesCS2D01G241900 chrUn 96.061 457 4 4 1198 1640 106462683 106463139 0 732
17 TraesCS2D01G241900 chr3A 95.833 1656 50 10 4 1640 315555922 315554267 0 2658
18 TraesCS2D01G241900 chr7A 95.788 1662 42 13 1 1640 398574488 398572833 0 2656
19 TraesCS2D01G241900 chr6D 96.507 1546 38 8 1 1530 207989210 207990755 0 2542
20 TraesCS2D01G241900 chr6D 97.406 771 20 0 1641 2411 77431816 77431046 0 1314
21 TraesCS2D01G241900 chr6D 97.017 771 23 0 1641 2411 121715981 121716751 0 1297
22 TraesCS2D01G241900 chr6D 96.641 774 25 1 1638 2411 121735040 121735812 0 1284
23 TraesCS2D01G241900 chr6D 96.498 771 20 5 1645 2411 103713324 103714091 0 1267
24 TraesCS2D01G241900 chr6D 96.239 771 28 1 1641 2411 147329289 147328520 0 1262


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 TraesCS2D01G241900 chr2D 265065542 265067952 2410 False 4453 4453 100.000 1 2411 1 chr2D.!!$F1 2410
1 TraesCS2D01G241900 chr3D 239006008 239007663 1655 False 2767 2767 96.982 1 1640 1 chr3D.!!$F1 1639
2 TraesCS2D01G241900 chr5D 189874349 189876003 1654 False 2765 2765 96.982 1 1640 1 chr5D.!!$F1 1639
3 TraesCS2D01G241900 chr5D 185038849 185040504 1655 True 2750 2750 96.800 1 1640 1 chr5D.!!$R1 1639
4 TraesCS2D01G241900 chr1D 160654398 160656053 1655 True 2756 2756 96.866 1 1640 1 chr1D.!!$R1 1639
5 TraesCS2D01G241900 chr1D 253414929 253415699 770 True 1280 1280 96.628 1641 2411 1 chr1D.!!$R3 770
6 TraesCS2D01G241900 chr1D 213128504 213129274 770 False 1275 1275 96.498 1641 2411 1 chr1D.!!$F1 770
7 TraesCS2D01G241900 chr1D 213146922 213147692 770 False 1264 1264 96.239 1641 2411 1 chr1D.!!$F2 770
8 TraesCS2D01G241900 chr1D 253406480 253407250 770 True 1264 1264 96.239 1641 2411 1 chr1D.!!$R2 770
9 TraesCS2D01G241900 chr6A 248617002 248618656 1654 False 2682 2682 96.082 1 1640 1 chr6A.!!$F1 1639
10 TraesCS2D01G241900 chr4B 336603217 336604873 1656 False 2673 2673 95.957 1 1640 1 chr4B.!!$F2 1639
11 TraesCS2D01G241900 chr4B 317640552 317642195 1643 False 2617 2617 95.471 1 1640 1 chr4B.!!$F1 1639
12 TraesCS2D01G241900 chrUn 15261810 15263472 1662 True 2662 2662 95.791 1 1640 1 chrUn.!!$R1 1639
13 TraesCS2D01G241900 chrUn 15268051 15269714 1663 True 2652 2652 95.673 1 1640 1 chrUn.!!$R2 1639
14 TraesCS2D01G241900 chrUn 282053022 282054235 1213 True 1999 1999 96.626 445 1640 1 chrUn.!!$R3 1195
15 TraesCS2D01G241900 chrUn 285057187 285058400 1213 False 1999 1999 96.626 445 1640 1 chrUn.!!$F2 1195
16 TraesCS2D01G241900 chr3A 315554267 315555922 1655 True 2658 2658 95.833 4 1640 1 chr3A.!!$R1 1636
17 TraesCS2D01G241900 chr7A 398572833 398574488 1655 True 2656 2656 95.788 1 1640 1 chr7A.!!$R1 1639
18 TraesCS2D01G241900 chr6D 207989210 207990755 1545 False 2542 2542 96.507 1 1530 1 chr6D.!!$F4 1529
19 TraesCS2D01G241900 chr6D 77431046 77431816 770 True 1314 1314 97.406 1641 2411 1 chr6D.!!$R1 770
20 TraesCS2D01G241900 chr6D 121715981 121716751 770 False 1297 1297 97.017 1641 2411 1 chr6D.!!$F2 770
21 TraesCS2D01G241900 chr6D 121735040 121735812 772 False 1284 1284 96.641 1638 2411 1 chr6D.!!$F3 773
22 TraesCS2D01G241900 chr6D 103713324 103714091 767 False 1267 1267 96.498 1645 2411 1 chr6D.!!$F1 766
23 TraesCS2D01G241900 chr6D 147328520 147329289 769 True 1262 1262 96.239 1641 2411 1 chr6D.!!$R2 770

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
270 276 1.934849 GCATTTCGAAAAGCCCACACC 60.935 52.381 23.78 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 2241 0.895559 GGTTCCCCAAGTGCCTCAAG 60.896 60.0 0.0 0.0 0.0 3.02 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
73 78 3.023832 GCCCTTTGCAGCCTTTAATCTA 58.976 45.455 0.00 0.0 40.77 1.98
129 134 8.352942 CCACTAGATCTTTGTTTTTAGTTGCTT 58.647 33.333 0.00 0.0 0.00 3.91
188 194 5.437289 TTTTCGTGCACAGATTTCAGATT 57.563 34.783 18.64 0.0 0.00 2.40
256 262 6.597614 TGTTTTGAGTGTTTTTGTGCATTTC 58.402 32.000 0.00 0.0 0.00 2.17
270 276 1.934849 GCATTTCGAAAAGCCCACACC 60.935 52.381 23.78 0.0 0.00 4.16
280 286 3.056458 CCCACACCGTGTGCTCTA 58.944 61.111 23.81 0.0 46.51 2.43
410 416 8.514594 GGTTGACTTCATCTATTGTGATTTTCA 58.485 33.333 0.00 0.0 0.00 2.69
532 579 5.643379 AGAAAGAAAGTGTGTGCAAGAAA 57.357 34.783 0.00 0.0 0.00 2.52
695 742 7.576861 TGTACCTCACGTATATCTCATTCAA 57.423 36.000 0.00 0.0 0.00 2.69
914 961 2.989840 CTGCTCTCACTTGGAAGTTACG 59.010 50.000 0.00 0.0 37.08 3.18
1026 1073 4.143094 GCAGGTGAAGAAAACGAGTATGAC 60.143 45.833 0.00 0.0 0.00 3.06
1742 1806 4.411256 ACCGGAGTTCTTAAGTTGAACA 57.589 40.909 9.46 0.0 44.30 3.18
1743 1807 4.124970 ACCGGAGTTCTTAAGTTGAACAC 58.875 43.478 9.46 0.0 44.30 3.32
1748 1812 6.049790 GGAGTTCTTAAGTTGAACACTCTGT 58.950 40.000 1.63 0.0 44.30 3.41
1869 1933 5.006941 GCTACTACGAGTCTCTAGGTTTCAG 59.993 48.000 0.00 0.0 0.00 3.02
1981 2045 8.112822 TGGTTAGGATCTGAATTAAATTGTGGA 58.887 33.333 0.00 0.0 0.00 4.02
1990 2054 8.093927 TCTGAATTAAATTGTGGATTTTGGGAC 58.906 33.333 0.00 0.0 38.80 4.46
2062 2129 7.117379 GGAGTTACTTCTACGTTTGCTTATTGT 59.883 37.037 0.00 0.0 0.00 2.71
2064 2131 8.280497 AGTTACTTCTACGTTTGCTTATTGTTG 58.720 33.333 0.00 0.0 0.00 3.33
2087 2154 2.666069 GCTATGCTCGTAGACGTGGATC 60.666 54.545 13.19 0.0 41.55 3.36
2174 2241 3.763897 ACTTTAATTCACATCTGGGTGGC 59.236 43.478 0.00 0.0 39.27 5.01
2396 2463 4.030913 CAGATGTAGGGGAAAGTAGGTGA 58.969 47.826 0.00 0.0 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 194 2.601240 TGATTTGGTGGAGGATGCAA 57.399 45.000 0.00 0.00 39.09 4.08
256 262 2.184167 ACACGGTGTGGGCTTTTCG 61.184 57.895 13.92 0.00 37.94 3.46
270 276 3.170791 AGGATGAATGTAGAGCACACG 57.829 47.619 0.00 0.00 40.86 4.49
280 286 7.718753 GGAATCAGATCTAACAAGGATGAATGT 59.281 37.037 0.00 0.00 0.00 2.71
410 416 2.158325 ACACACACTTTGGGGGAATCAT 60.158 45.455 0.00 0.00 29.81 2.45
491 538 5.712152 TTCTTTGGGCAGATCTCTTTTTC 57.288 39.130 0.00 0.00 0.00 2.29
532 579 5.358160 CAGTCCCAAGTTTTCTCTCTTTTGT 59.642 40.000 0.00 0.00 0.00 2.83
695 742 8.796475 ACACAAGATTCTAATGCATTTAGTTGT 58.204 29.630 18.75 14.75 38.76 3.32
914 961 1.798813 CACTTACCAACCGAAGCTCAC 59.201 52.381 0.00 0.00 0.00 3.51
1026 1073 2.094675 AGATGCCCATTTCCTTCAACG 58.905 47.619 0.00 0.00 0.00 4.10
1253 1300 3.244215 ACTTGCATCTTCTCGGTTCTGAA 60.244 43.478 0.00 0.00 0.00 3.02
1869 1933 1.030457 CTTGCCTTGCTGATGATCCC 58.970 55.000 0.00 0.00 0.00 3.85
1981 2045 4.715297 ACTACCTCATCTACGTCCCAAAAT 59.285 41.667 0.00 0.00 0.00 1.82
2062 2129 1.471287 ACGTCTACGAGCATAGCACAA 59.529 47.619 9.86 0.00 43.02 3.33
2064 2131 1.467875 CACGTCTACGAGCATAGCAC 58.532 55.000 9.86 0.00 43.02 4.40
2087 2154 3.505680 TCATGGAAATTCACTCAAACCCG 59.494 43.478 0.00 0.00 0.00 5.28
2174 2241 0.895559 GGTTCCCCAAGTGCCTCAAG 60.896 60.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.