Multiple sequence alignment - TraesCS1A01G370500

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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 TraesCS1A01G370500 chr1A 100.000 2303 0 0 1 2303 547876266 547873964 0.000000e+00 4253
1 TraesCS1A01G370500 chr1A 96.797 1998 56 6 312 2303 84283152 84285147 0.000000e+00 3328
2 TraesCS1A01G370500 chr1A 95.870 1235 36 4 1071 2303 587713494 587712273 0.000000e+00 1984
3 TraesCS1A01G370500 chr1A 94.093 237 14 0 1 237 498215438 498215674 6.050000e-96 361
4 TraesCS1A01G370500 chr1A 89.540 239 21 4 1 236 84282979 84283216 1.340000e-77 300
5 TraesCS1A01G370500 chr1A 82.520 246 24 11 2072 2303 588894575 588894335 5.020000e-47 198
6 TraesCS1A01G370500 chr7A 96.095 2305 86 4 1 2303 646805474 646803172 0.000000e+00 3755
7 TraesCS1A01G370500 chr7A 97.108 1660 45 3 647 2303 516847442 516845783 0.000000e+00 2796
8 TraesCS1A01G370500 chr6A 96.037 2069 73 5 237 2303 608732391 608730330 0.000000e+00 3358
9 TraesCS1A01G370500 chr6A 95.848 1927 72 5 1 1925 585133760 585131840 0.000000e+00 3109
10 TraesCS1A01G370500 chr4A 96.040 2020 74 6 289 2303 589095347 589097365 0.000000e+00 3282
11 TraesCS1A01G370500 chr5A 96.502 1658 50 5 234 1889 99540417 99542068 0.000000e+00 2734
12 TraesCS1A01G370500 chr5A 95.281 551 24 2 1754 2303 404496207 404495658 0.000000e+00 872
13 TraesCS1A01G370500 chr4D 93.193 1660 104 7 1 1654 85739104 85740760 0.000000e+00 2431
14 TraesCS1A01G370500 chr2D 92.952 1660 108 7 1 1654 166115295 166116951 0.000000e+00 2409
15 TraesCS1A01G370500 chr2D 87.681 276 30 2 1 274 516817059 516817332 3.690000e-83 318
16 TraesCS1A01G370500 chr2D 83.012 259 40 3 1 257 627339515 627339771 4.950000e-57 231
17 TraesCS1A01G370500 chr5D 91.475 1654 98 16 687 2303 193611367 193609720 0.000000e+00 2233
18 TraesCS1A01G370500 chr6D 91.012 1680 98 16 661 2303 8979106 8977443 0.000000e+00 2217
19 TraesCS1A01G370500 chr5B 91.450 655 52 4 1651 2303 62934494 62935146 0.000000e+00 896


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 TraesCS1A01G370500 chr1A 547873964 547876266 2302 True 4253 4253 100.0000 1 2303 1 chr1A.!!$R1 2302
1 TraesCS1A01G370500 chr1A 587712273 587713494 1221 True 1984 1984 95.8700 1071 2303 1 chr1A.!!$R2 1232
2 TraesCS1A01G370500 chr1A 84282979 84285147 2168 False 1814 3328 93.1685 1 2303 2 chr1A.!!$F2 2302
3 TraesCS1A01G370500 chr7A 646803172 646805474 2302 True 3755 3755 96.0950 1 2303 1 chr7A.!!$R2 2302
4 TraesCS1A01G370500 chr7A 516845783 516847442 1659 True 2796 2796 97.1080 647 2303 1 chr7A.!!$R1 1656
5 TraesCS1A01G370500 chr6A 608730330 608732391 2061 True 3358 3358 96.0370 237 2303 1 chr6A.!!$R2 2066
6 TraesCS1A01G370500 chr6A 585131840 585133760 1920 True 3109 3109 95.8480 1 1925 1 chr6A.!!$R1 1924
7 TraesCS1A01G370500 chr4A 589095347 589097365 2018 False 3282 3282 96.0400 289 2303 1 chr4A.!!$F1 2014
8 TraesCS1A01G370500 chr5A 99540417 99542068 1651 False 2734 2734 96.5020 234 1889 1 chr5A.!!$F1 1655
9 TraesCS1A01G370500 chr5A 404495658 404496207 549 True 872 872 95.2810 1754 2303 1 chr5A.!!$R1 549
10 TraesCS1A01G370500 chr4D 85739104 85740760 1656 False 2431 2431 93.1930 1 1654 1 chr4D.!!$F1 1653
11 TraesCS1A01G370500 chr2D 166115295 166116951 1656 False 2409 2409 92.9520 1 1654 1 chr2D.!!$F1 1653
12 TraesCS1A01G370500 chr5D 193609720 193611367 1647 True 2233 2233 91.4750 687 2303 1 chr5D.!!$R1 1616
13 TraesCS1A01G370500 chr6D 8977443 8979106 1663 True 2217 2217 91.0120 661 2303 1 chr6D.!!$R1 1642
14 TraesCS1A01G370500 chr5B 62934494 62935146 652 False 896 896 91.4500 1651 2303 1 chr5B.!!$F1 652

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
134 135 0.106268 TTGGGTGCAAAAGCTCCTGA 60.106 50.0 8.27 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 1944 0.035534 TGCAGCGCCTTTATTCTGGA 60.036 50.0 2.29 0.0 0.0 3.86 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
103 104 0.179089 CTTAGGCGCTGCAGACTGAT 60.179 55.000 20.43 0.66 0.00 2.90
134 135 0.106268 TTGGGTGCAAAAGCTCCTGA 60.106 50.000 8.27 0.00 0.00 3.86
159 160 2.232452 GCTTCTGTTGCTCTCTGGACTA 59.768 50.000 0.00 0.00 0.00 2.59
167 168 2.243478 TGCTCTCTGGACTAGGATGTCT 59.757 50.000 0.00 0.00 37.16 3.41
198 199 2.801631 CCTAAGGGAGAGGCGCCAG 61.802 68.421 31.54 14.45 33.58 4.85
205 206 3.240134 GAGAGGCGCCAGACACCAA 62.240 63.158 31.54 0.00 0.00 3.67
300 301 4.015764 AGCTTTTGCACCCAAAAATTTGT 58.984 34.783 5.27 0.00 46.84 2.83
306 307 8.561738 TTTTGCACCCAAAAATTTGTTAAGTA 57.438 26.923 5.27 0.00 45.24 2.24
477 480 1.964344 GCTCTCTGGACTGGGATGTCT 60.964 57.143 0.00 0.00 37.16 3.41
490 493 1.405821 GGATGTCTAGTAGTGCAGCGT 59.594 52.381 0.00 0.00 0.00 5.07
520 524 3.653009 CGCTGCACTGTGGTGTGG 61.653 66.667 10.21 0.00 44.65 4.17
625 632 1.228737 CCCCCACACAAACCCGAAT 60.229 57.895 0.00 0.00 0.00 3.34
867 875 5.056480 AGTTTCTTTGCTAATTTGGGTTGC 58.944 37.500 0.00 0.00 0.00 4.17
1352 1360 4.945543 TCCTCTATGCAAGTACTTCACGTA 59.054 41.667 4.77 6.09 0.00 3.57
1511 1520 2.363147 GAGGAGGAGAGGGCACGT 60.363 66.667 0.00 0.00 0.00 4.49
1585 1594 1.893919 GAGGCGCAAGAGGAGGACTT 61.894 60.000 10.83 0.00 43.02 3.01
1734 1769 9.194271 CATTTGTCATTTGTAATGAATGTGTCA 57.806 29.630 3.83 0.00 41.67 3.58
1825 1866 6.224584 TGTTCAAATTGTTGTGATGATGCAT 58.775 32.000 0.00 0.00 36.07 3.96
1876 1917 5.997129 TGAAATGAATGTGCTGTCAACTCTA 59.003 36.000 0.00 0.00 0.00 2.43
1900 1941 1.313772 TGCAGTAAACAACCGTGCAT 58.686 45.000 0.00 0.00 35.13 3.96
1903 1944 1.529438 CAGTAAACAACCGTGCATCGT 59.471 47.619 0.00 0.00 37.94 3.73
1910 1951 0.036388 AACCGTGCATCGTCCAGAAT 60.036 50.000 0.00 0.00 37.94 2.40
1937 1978 3.629548 TGCACTGTTCTATGCAGCA 57.370 47.368 0.00 0.00 46.63 4.41
2070 2112 2.050350 CAGCCATGGCCAGTGAAGG 61.050 63.158 33.14 9.06 43.17 3.46
2084 2126 0.764369 TGAAGGAGCGCCTATGGGAT 60.764 55.000 10.31 0.00 46.28 3.85
2095 2137 2.759641 CTATGGGATGGGCGCTGCAT 62.760 60.000 7.64 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 6.515272 TTTTGCACCCAAAAATTTGCTAAA 57.485 29.167 0.29 0.00 45.24 1.85
134 135 1.869767 CAGAGAGCAACAGAAGCGTTT 59.130 47.619 0.00 0.00 37.01 3.60
159 160 1.404391 CGTTGTACGGCTAGACATCCT 59.596 52.381 0.00 0.00 38.08 3.24
174 175 2.287829 CCTCTCCCTTAGGCGTTGT 58.712 57.895 0.00 0.00 0.00 3.32
198 199 1.299089 GGCGTTGCACTTTGGTGTC 60.299 57.895 0.00 0.00 44.65 3.67
205 206 2.032681 GGGAGAGGCGTTGCACTT 59.967 61.111 0.00 0.00 0.00 3.16
300 301 3.536956 AGGCGCTGCATACTTACTTAA 57.463 42.857 7.64 0.00 0.00 1.85
306 307 0.179045 CCCTTAGGCGCTGCATACTT 60.179 55.000 7.64 0.00 0.00 2.24
427 429 3.628032 GCTTCTAGTATGTTTTCTGCCCC 59.372 47.826 0.00 0.00 0.00 5.80
444 446 2.289569 CCAGAGAGCAACAGAAGCTTCT 60.290 50.000 23.49 23.49 43.58 2.85
477 480 2.426024 CCCTTTAGACGCTGCACTACTA 59.574 50.000 0.00 0.00 0.00 1.82
490 493 1.261938 TGCAGCGCCTACCCTTTAGA 61.262 55.000 2.29 0.00 0.00 2.10
520 524 3.551407 CCTAAGGGAGAGGCGCCC 61.551 72.222 26.15 15.34 44.04 6.13
625 632 1.305633 CAGAGGGGAGGCACTGAGA 60.306 63.158 0.00 0.00 41.55 3.27
867 875 6.014156 ACCCTAGCATACTATGAAAGCCTAAG 60.014 42.308 0.00 0.00 0.00 2.18
1292 1300 9.848172 GCATACAAAATTTTTGTTAGTGTTGAG 57.152 29.630 27.27 11.45 34.11 3.02
1352 1360 5.660417 TCTTCTGGCACTTCAAGATCTATCT 59.340 40.000 0.00 0.00 39.22 1.98
1527 1536 0.906756 CTTGCCCTCTCCTCCTCACA 60.907 60.000 0.00 0.00 0.00 3.58
1585 1594 2.429930 CCTTCTTGTCACGGGCCA 59.570 61.111 4.39 0.00 0.00 5.36
1734 1769 6.876789 TCAAACATTACTACGACATGGTTCAT 59.123 34.615 0.00 0.00 0.00 2.57
1825 1866 9.051679 CCGGAACATCATAATACTTACAATGAA 57.948 33.333 0.00 0.00 32.47 2.57
1876 1917 3.553917 GCACGGTTGTTTACTGCAAAAAT 59.446 39.130 0.00 0.00 36.53 1.82
1900 1941 0.535335 AGCGCCTTTATTCTGGACGA 59.465 50.000 2.29 0.00 0.00 4.20
1903 1944 0.035534 TGCAGCGCCTTTATTCTGGA 60.036 50.000 2.29 0.00 0.00 3.86
1910 1951 0.250295 AGAACAGTGCAGCGCCTTTA 60.250 50.000 2.29 0.00 0.00 1.85
2070 2112 2.348998 CCCATCCCATAGGCGCTC 59.651 66.667 7.64 0.00 0.00 5.03
2084 2126 3.057548 CTCACAATGCAGCGCCCA 61.058 61.111 2.29 1.25 0.00 5.36
2095 2137 2.786539 CTAGGCGCTGCACCTCACAA 62.787 60.000 13.32 0.00 38.81 3.33
2218 2294 7.374272 TGTCTTTGTTCAGTTGAATTGTTCAA 58.626 30.769 1.24 1.24 46.68 2.69


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

AutoCloner maintained by Alex Coulton.