Multiple sequence alignment - TraesCS2D01G473900

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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 TraesCS2D01G473900 chr2D 100.000 2781 0 0 1 2781 577326507 577329287 0.000000e+00 5136
1 TraesCS2D01G473900 chr2D 89.759 166 16 1 16 180 387193856 387193691 7.800000e-51 211
2 TraesCS2D01G473900 chr2D 89.506 162 16 1 16 176 50240045 50239884 1.310000e-48 204
3 TraesCS2D01G473900 chr2D 88.554 166 18 1 15 179 571079120 571078955 1.690000e-47 200
4 TraesCS2D01G473900 chr2A 94.638 2816 109 24 2 2781 715404681 715407490 0.000000e+00 4325
5 TraesCS2D01G473900 chr2A 78.723 423 73 14 1409 1824 715632887 715632475 1.640000e-67 267
6 TraesCS2D01G473900 chr2A 89.506 162 16 1 16 176 342647399 342647560 1.310000e-48 204
7 TraesCS2D01G473900 chr2B 94.219 1851 73 8 25 1843 694265490 694267338 0.000000e+00 2795
8 TraesCS2D01G473900 chr2B 91.636 550 35 4 2233 2781 694267961 694268500 0.000000e+00 750
9 TraesCS2D01G473900 chr2B 91.954 261 21 0 1976 2236 694267608 694267868 1.570000e-97 366
10 TraesCS2D01G473900 chr2B 78.422 431 75 15 1401 1824 694541988 694541569 5.910000e-67 265
11 TraesCS2D01G473900 chr2B 97.794 136 2 1 1842 1977 694267312 694267446 1.670000e-57 233
12 TraesCS2D01G473900 chr7D 90.741 162 14 1 16 176 500775618 500775457 6.030000e-52 215
13 TraesCS2D01G473900 chr3D 90.123 162 15 1 16 176 87926000 87926161 2.810000e-50 209
14 TraesCS2D01G473900 chr4D 87.791 172 18 2 6 176 334164383 334164552 6.080000e-47 198


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 TraesCS2D01G473900 chr2D 577326507 577329287 2780 False 5136 5136 100.00000 1 2781 1 chr2D.!!$F1 2780
1 TraesCS2D01G473900 chr2A 715404681 715407490 2809 False 4325 4325 94.63800 2 2781 1 chr2A.!!$F2 2779
2 TraesCS2D01G473900 chr2B 694265490 694268500 3010 False 1036 2795 93.90075 25 2781 4 chr2B.!!$F1 2756

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
946 982 0.250727 ATCCAGAACACAACACCCGG 60.251 55.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2413 2719 3.433615 GCTTGCCTGTACAGTTCTACTTG 59.566 47.826 21.18 4.76 0.0 3.16 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
23 24 6.636454 TCAGTAATTCAATGGTACTCCCTT 57.364 37.500 0.00 0.00 0.00 3.95
28 29 3.713826 TCAATGGTACTCCCTTGGTTC 57.286 47.619 0.00 0.00 39.00 3.62
40 41 6.602278 ACTCCCTTGGTTCCTAAATATAAGC 58.398 40.000 0.00 0.00 0.00 3.09
81 83 3.255725 CGGACTACATACGGAGCAAAAA 58.744 45.455 0.00 0.00 0.00 1.94
166 169 7.678194 TCTAAAAAGACTTGCATTTTGAACG 57.322 32.000 5.44 0.00 30.78 3.95
167 170 7.254852 TCTAAAAAGACTTGCATTTTGAACGT 58.745 30.769 5.44 0.00 30.78 3.99
168 171 8.399425 TCTAAAAAGACTTGCATTTTGAACGTA 58.601 29.630 5.44 0.00 30.78 3.57
169 172 7.449934 AAAAAGACTTGCATTTTGAACGTAG 57.550 32.000 0.00 0.00 0.00 3.51
170 173 4.147219 AGACTTGCATTTTGAACGTAGC 57.853 40.909 0.00 0.00 0.00 3.58
396 401 4.817464 ACATGTGCATGCACTTTTGATTTT 59.183 33.333 41.43 21.61 46.30 1.82
489 496 2.235016 TCCATTCCAAGGGAAAACGTG 58.765 47.619 1.25 0.00 45.41 4.49
599 606 4.754114 CAGAAAACTGGATAGCTATCAGCC 59.246 45.833 30.03 17.32 43.77 4.85
695 702 1.174712 TTCCAACTGCTTCTGCTGCC 61.175 55.000 0.00 0.00 41.07 4.85
783 818 3.000322 CGATCAAGAGACCATTACAACGC 60.000 47.826 0.00 0.00 0.00 4.84
825 860 2.409241 TTTAAAACGGGCGCCAGTGC 62.409 55.000 32.85 11.99 0.00 4.40
917 953 2.355837 GTCAGCACGAGCCGAACA 60.356 61.111 0.00 0.00 43.56 3.18
946 982 0.250727 ATCCAGAACACAACACCCGG 60.251 55.000 0.00 0.00 0.00 5.73
968 1005 2.035530 AGAAGCTTATCACTGCTGCC 57.964 50.000 0.00 0.00 39.71 4.85
1023 1061 1.195448 GAGAACACAACATCGCCACAG 59.805 52.381 0.00 0.00 0.00 3.66
1045 1083 4.189188 CTTGCATCAGCCAGCCGC 62.189 66.667 0.00 0.00 41.13 6.53
1193 1234 2.102925 CCTCTGGCTTCTCTTCCTCATC 59.897 54.545 0.00 0.00 0.00 2.92
1212 1253 2.278245 TCTGATTCCTTGGGTGATGGT 58.722 47.619 0.00 0.00 0.00 3.55
1257 1298 2.366916 GTCGGACCTCATGGATGAAGAT 59.633 50.000 0.00 0.00 36.18 2.40
1260 1301 3.737850 GGACCTCATGGATGAAGATGAC 58.262 50.000 0.00 0.00 36.18 3.06
1435 1477 7.406031 TGATTTTTGTTGTACAGGTAACCAA 57.594 32.000 0.00 0.00 37.17 3.67
1511 1553 1.078497 CGCCCAGCTGGTATGTTCA 60.078 57.895 30.63 0.00 36.04 3.18
1522 1564 4.397417 GCTGGTATGTTCAAGAAGCAATCT 59.603 41.667 0.00 0.00 41.32 2.40
1565 1607 5.227908 TCCTTCAGACGTTGTTTAGATGTC 58.772 41.667 0.00 0.00 34.09 3.06
1634 1676 1.867233 CCAAGTATTTCCTCGATGCGG 59.133 52.381 0.00 0.00 0.00 5.69
1671 1713 2.281484 TGGTGCGGTTCCAGAAGC 60.281 61.111 0.00 0.00 35.61 3.86
2082 2291 8.018520 TGTATGTGTACCGAAACATTTCAAATC 58.981 33.333 5.28 0.00 38.05 2.17
2089 2298 6.208644 ACCGAAACATTTCAAATCTCAAGTG 58.791 36.000 5.28 0.00 37.01 3.16
2093 2302 5.972107 ACATTTCAAATCTCAAGTGGAGG 57.028 39.130 0.00 0.00 44.19 4.30
2425 2731 5.979288 CCAGTAGGTACAAGTAGAACTGT 57.021 43.478 0.00 0.00 32.84 3.55
2474 2780 7.871853 TGACACAAAGGCTAATCTTTCTTTAC 58.128 34.615 0.00 0.00 35.04 2.01
2737 3047 3.461085 AGCATCCAGTGGACCTTCAATAT 59.539 43.478 15.86 0.00 32.98 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.636454 AAGGGAGTACCATTGAATTACTGA 57.364 37.500 0.00 0.00 43.89 3.41
23 24 8.774183 TCTAAACAGGCTTATATTTAGGAACCA 58.226 33.333 13.31 0.00 35.99 3.67
40 41 4.401519 TCCGTACTGGAATCTCTAAACAGG 59.598 45.833 4.28 0.00 46.38 4.00
81 83 9.026121 ACATACTTTACAGTGTAGATTCACTCT 57.974 33.333 2.68 0.00 45.37 3.24
150 152 2.902484 CGCTACGTTCAAAATGCAAGTC 59.098 45.455 0.00 0.00 0.00 3.01
161 164 6.642131 ACAAAAAGTAATACTCGCTACGTTCA 59.358 34.615 0.00 0.00 0.00 3.18
165 168 6.557351 CGCTACAAAAAGTAATACTCGCTACG 60.557 42.308 0.00 0.00 30.92 3.51
166 169 6.252228 ACGCTACAAAAAGTAATACTCGCTAC 59.748 38.462 0.00 0.00 30.92 3.58
167 170 6.324819 ACGCTACAAAAAGTAATACTCGCTA 58.675 36.000 0.00 0.00 30.92 4.26
168 171 5.166398 ACGCTACAAAAAGTAATACTCGCT 58.834 37.500 0.00 0.00 30.92 4.93
169 172 5.446031 ACGCTACAAAAAGTAATACTCGC 57.554 39.130 0.00 0.00 30.92 5.03
170 173 7.496704 TGTACGCTACAAAAAGTAATACTCG 57.503 36.000 0.00 0.00 35.38 4.18
489 496 5.625150 AGTATTATCTCTCCATTTGTGCCC 58.375 41.667 0.00 0.00 0.00 5.36
599 606 3.758023 TCTTGCCAATCACAATGTGGTAG 59.242 43.478 13.95 2.91 34.71 3.18
783 818 6.475596 AAATTGGCAATGGAGGAATCTTAG 57.524 37.500 14.47 0.00 0.00 2.18
914 950 2.821969 GTTCTGGATGGAATGCTGTGTT 59.178 45.455 0.00 0.00 34.76 3.32
917 953 2.224843 TGTGTTCTGGATGGAATGCTGT 60.225 45.455 0.00 0.00 34.76 4.40
946 982 2.543430 GCAGCAGTGATAAGCTTCTAGC 59.457 50.000 0.00 0.00 39.50 3.42
968 1005 2.265904 TGCAAGCAGAAGCAGGCTG 61.266 57.895 10.94 10.94 45.49 4.85
1023 1061 0.450983 GCTGGCTGATGCAAGAAGAC 59.549 55.000 0.00 0.00 42.81 3.01
1104 1145 1.948834 CTGTTGTCTGTTGATGCCACA 59.051 47.619 0.00 0.00 0.00 4.17
1193 1234 2.814805 ACCATCACCCAAGGAATCAG 57.185 50.000 0.00 0.00 0.00 2.90
1212 1253 1.530013 GGAAGGAGTCGGTGTCGGAA 61.530 60.000 0.00 0.00 36.95 4.30
1257 1298 2.100418 CTGCAGAGAATCATCCTCGTCA 59.900 50.000 8.42 0.00 37.82 4.35
1260 1301 1.685517 TCCTGCAGAGAATCATCCTCG 59.314 52.381 17.39 0.00 37.82 4.63
1342 1384 8.264347 TGTTCATCAAGTTATCTATGCCTAACA 58.736 33.333 0.00 0.00 31.64 2.41
1348 1390 6.259608 ACTGCTGTTCATCAAGTTATCTATGC 59.740 38.462 0.00 0.00 0.00 3.14
1357 1399 7.928307 AAATATGTACTGCTGTTCATCAAGT 57.072 32.000 17.01 0.78 36.04 3.16
1511 1553 8.707449 AGAAAGAGATGATAGAGATTGCTTCTT 58.293 33.333 0.00 0.00 33.74 2.52
1522 1564 7.782168 TGAAGGAAGCTAGAAAGAGATGATAGA 59.218 37.037 0.00 0.00 0.00 1.98
1634 1676 3.741476 CGCCTGCTGCCTTGAACC 61.741 66.667 0.00 0.00 36.24 3.62
1671 1713 2.554142 TGCTATTTCCACTGCTGATCG 58.446 47.619 0.00 0.00 0.00 3.69
1679 1721 3.003480 GCTTCTCGTTGCTATTTCCACT 58.997 45.455 0.00 0.00 0.00 4.00
2093 2302 4.391830 TGATGAATCGCACTGAGGTTTTAC 59.608 41.667 0.00 0.00 0.00 2.01
2413 2719 3.433615 GCTTGCCTGTACAGTTCTACTTG 59.566 47.826 21.18 4.76 0.00 3.16
2474 2780 4.634883 TGGTACTTTCTAGTGAGTAGCGAG 59.365 45.833 21.18 0.00 45.23 5.03
2529 2835 7.363031 ACTTATAGAAAGTCAGAGATACCCCA 58.637 38.462 0.00 0.00 0.00 4.96
2561 2867 5.842907 AGAACTTGTTTTGATTTGGTAGGC 58.157 37.500 0.00 0.00 0.00 3.93
2737 3047 6.461092 CGAGGAATGTGCTTATAGGTGTCTAA 60.461 42.308 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.