Multiple sequence alignment - TraesCS1B01G397200

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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 TraesCS1B01G397200 chr1B 100.000 2529 0 0 1 2529 628810454 628812982 0.000000e+00 4671
1 TraesCS1B01G397200 chr1B 92.461 1963 129 8 1 1961 629091201 629093146 0.000000e+00 2787
2 TraesCS1B01G397200 chr1B 95.658 1497 60 3 640 2135 628975167 628976659 0.000000e+00 2399
3 TraesCS1B01G397200 chr1B 94.548 1504 66 11 640 2135 628856096 628857591 0.000000e+00 2309
4 TraesCS1B01G397200 chr1B 92.448 1536 87 12 1 1512 629052938 629054468 0.000000e+00 2167
5 TraesCS1B01G397200 chr1B 92.318 1523 101 11 1 1512 628993595 628995112 0.000000e+00 2150
6 TraesCS1B01G397200 chr1B 91.520 1533 105 11 1 1512 628917249 628918777 0.000000e+00 2087
7 TraesCS1B01G397200 chr1B 96.306 785 28 1 640 1423 628898949 628899733 0.000000e+00 1288
8 TraesCS1B01G397200 chr1B 95.899 756 29 2 1381 2135 628899732 628900486 0.000000e+00 1223
9 TraesCS1B01G397200 chr1B 88.501 887 86 9 36 920 628996754 628997626 0.000000e+00 1059
10 TraesCS1B01G397200 chr1B 88.162 887 89 9 36 920 628920432 628921304 0.000000e+00 1042
11 TraesCS1B01G397200 chr1B 87.599 887 94 9 36 920 629056117 629056989 0.000000e+00 1014
12 TraesCS1B01G397200 chr1B 98.087 366 7 0 2164 2529 628857590 628857955 2.740000e-179 638
13 TraesCS1B01G397200 chr1B 98.087 366 7 0 2164 2529 628900485 628900850 2.740000e-179 638
14 TraesCS1B01G397200 chr1B 98.087 366 7 0 2164 2529 628976658 628977023 2.740000e-179 638
15 TraesCS1B01G397200 chr1B 83.871 155 21 2 1565 1715 628804972 628805126 7.290000e-31 145
16 TraesCS1B01G397200 chr1D 87.581 2158 146 47 1 2131 458272052 458274114 0.000000e+00 2388
17 TraesCS1B01G397200 chr1D 91.283 803 48 10 716 1515 458229790 458230573 0.000000e+00 1075
18 TraesCS1B01G397200 chr1D 95.128 431 17 4 1818 2247 458239155 458239582 0.000000e+00 676
19 TraesCS1B01G397200 chr1D 83.394 554 72 13 1700 2247 458201098 458201637 1.750000e-136 496
20 TraesCS1B01G397200 chr1D 79.752 726 88 32 1556 2247 458234339 458235039 2.940000e-129 472
21 TraesCS1B01G397200 chr1D 93.031 287 17 3 2243 2529 458253923 458254206 1.400000e-112 416
22 TraesCS1B01G397200 chr1D 88.502 287 13 5 2243 2529 458277179 458277445 1.880000e-86 329
23 TraesCS1B01G397200 chr1A 86.800 1803 160 45 467 2247 550654884 550656630 0.000000e+00 1940
24 TraesCS1B01G397200 chr1A 90.433 1432 83 14 1 1423 550792330 550793716 0.000000e+00 1836
25 TraesCS1B01G397200 chr1A 85.607 1591 161 39 669 2247 550695218 550696752 0.000000e+00 1607
26 TraesCS1B01G397200 chr1A 90.921 760 45 6 1490 2247 550824969 550825706 0.000000e+00 1000
27 TraesCS1B01G397200 chr1A 91.252 743 42 8 1507 2247 550669683 550670404 0.000000e+00 990
28 TraesCS1B01G397200 chr1A 93.080 289 18 2 2243 2529 550657497 550657785 3.010000e-114 422
29 TraesCS1B01G397200 chr1A 88.502 287 24 4 2243 2529 550671259 550671536 3.120000e-89 339
30 TraesCS1B01G397200 chr1A 89.811 265 22 4 2269 2529 550696974 550697237 4.030000e-88 335
31 TraesCS1B01G397200 chr1A 94.416 197 7 4 2243 2439 550826577 550826769 1.470000e-77 300


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 TraesCS1B01G397200 chr1B 628810454 628812982 2528 False 4671.000000 4671 100.0000 1 2529 1 chr1B.!!$F2 2528
1 TraesCS1B01G397200 chr1B 629091201 629093146 1945 False 2787.000000 2787 92.4610 1 1961 1 chr1B.!!$F3 1960
2 TraesCS1B01G397200 chr1B 628993595 628997626 4031 False 1604.500000 2150 90.4095 1 1512 2 chr1B.!!$F8 1511
3 TraesCS1B01G397200 chr1B 629052938 629056989 4051 False 1590.500000 2167 90.0235 1 1512 2 chr1B.!!$F9 1511
4 TraesCS1B01G397200 chr1B 628917249 628921304 4055 False 1564.500000 2087 89.8410 1 1512 2 chr1B.!!$F6 1511
5 TraesCS1B01G397200 chr1B 628975167 628977023 1856 False 1518.500000 2399 96.8725 640 2529 2 chr1B.!!$F7 1889
6 TraesCS1B01G397200 chr1B 628856096 628857955 1859 False 1473.500000 2309 96.3175 640 2529 2 chr1B.!!$F4 1889
7 TraesCS1B01G397200 chr1B 628898949 628900850 1901 False 1049.666667 1288 96.7640 640 2529 3 chr1B.!!$F5 1889
8 TraesCS1B01G397200 chr1D 458272052 458277445 5393 False 1358.500000 2388 88.0415 1 2529 2 chr1D.!!$F5 2528
9 TraesCS1B01G397200 chr1D 458229790 458235039 5249 False 773.500000 1075 85.5175 716 2247 2 chr1D.!!$F4 1531
10 TraesCS1B01G397200 chr1D 458201098 458201637 539 False 496.000000 496 83.3940 1700 2247 1 chr1D.!!$F1 547
11 TraesCS1B01G397200 chr1A 550792330 550793716 1386 False 1836.000000 1836 90.4330 1 1423 1 chr1A.!!$F1 1422
12 TraesCS1B01G397200 chr1A 550654884 550657785 2901 False 1181.000000 1940 89.9400 467 2529 2 chr1A.!!$F2 2062
13 TraesCS1B01G397200 chr1A 550695218 550697237 2019 False 971.000000 1607 87.7090 669 2529 2 chr1A.!!$F4 1860
14 TraesCS1B01G397200 chr1A 550669683 550671536 1853 False 664.500000 990 89.8770 1507 2529 2 chr1A.!!$F3 1022
15 TraesCS1B01G397200 chr1A 550824969 550826769 1800 False 650.000000 1000 92.6685 1490 2439 2 chr1A.!!$F5 949

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
27 28 0.388520 GTTTTCAATGGGTGGCGAGC 60.389 55.0 0.00 0.0 0.00 5.03 F
182 185 1.016627 GCATAGCAATCTTGGTGCGA 58.983 50.0 4.94 0.0 46.86 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1372 1455 0.315568 AGAAGAAGAAGACGCTGCGT 59.684 50.000 29.37 29.37 45.1 5.24 R
1681 1964 3.665745 AAATTGCTGAAATGCCGTTCT 57.334 38.095 0.00 0.00 0.0 3.01 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
27 28 0.388520 GTTTTCAATGGGTGGCGAGC 60.389 55.000 0.00 0.00 0.00 5.03
31 32 3.706373 AATGGGTGGCGAGCGAGT 61.706 61.111 0.00 0.00 0.00 4.18
32 33 3.665675 AATGGGTGGCGAGCGAGTC 62.666 63.158 0.00 0.00 0.00 3.36
47 48 2.543641 CGAGTCTCTGTATGCATGCAA 58.456 47.619 26.68 11.45 0.00 4.08
49 50 2.274437 AGTCTCTGTATGCATGCAACG 58.726 47.619 26.68 17.63 0.00 4.10
72 73 8.918961 ACGATCTGTTCTTCTCTACTTTTATG 57.081 34.615 0.00 0.00 0.00 1.90
177 180 2.617308 CAGGTCAGCATAGCAATCTTGG 59.383 50.000 0.00 0.00 0.00 3.61
182 185 1.016627 GCATAGCAATCTTGGTGCGA 58.983 50.000 4.94 0.00 46.86 5.10
199 202 1.291877 CGAAGACGAAGGGCAACAGG 61.292 60.000 0.00 0.00 42.66 4.00
257 260 5.063438 TGCTTTCTATGTCGATTGCTACAAC 59.937 40.000 0.00 0.00 0.00 3.32
260 263 7.515371 GCTTTCTATGTCGATTGCTACAACTAC 60.515 40.741 0.00 0.00 0.00 2.73
581 587 3.119137 GGCCAAATTAAAGTGAGGCGATT 60.119 43.478 0.00 0.00 42.89 3.34
605 611 2.281970 CCTGAGCACCAGCAAGCA 60.282 61.111 0.00 0.00 45.49 3.91
695 718 2.217750 CACGAACACTTGTGGATGGAA 58.782 47.619 5.72 0.00 32.47 3.53
1357 1436 2.982130 GACTCGTCCATGCCCACT 59.018 61.111 0.00 0.00 0.00 4.00
1477 1641 1.499502 GCTGGAGAGTTTGAAGCGC 59.500 57.895 0.00 0.00 0.00 5.92
1516 1681 1.335496 GTTCCTCTAGCTCAGCTACCG 59.665 57.143 0.83 0.00 40.44 4.02
1527 1692 2.355132 CTCAGCTACCGGTGTACTAGTG 59.645 54.545 19.93 7.37 39.58 2.74
1681 1964 0.036164 AGCCGTCACTTGCCACAATA 59.964 50.000 0.00 0.00 0.00 1.90
1685 1968 2.159627 CCGTCACTTGCCACAATAGAAC 59.840 50.000 0.00 0.00 0.00 3.01
1739 5687 1.402968 GAATACACTCTCGCACCGGTA 59.597 52.381 6.87 0.00 0.00 4.02
1808 5764 4.866508 AGTGTTAGTGTGTAGCTAAGCA 57.133 40.909 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.214387 TGCATGCATACAGAGACTCG 57.786 50.000 18.46 0.00 0.00 4.18
31 32 2.671130 TCGTTGCATGCATACAGAGA 57.329 45.000 23.37 11.60 0.00 3.10
32 33 3.059800 CAGATCGTTGCATGCATACAGAG 60.060 47.826 23.37 9.45 0.00 3.35
47 48 8.740906 TCATAAAAGTAGAGAAGAACAGATCGT 58.259 33.333 0.00 0.00 0.00 3.73
72 73 5.234543 GCCCATGATAGTAGTTTTTCGTCTC 59.765 44.000 0.00 0.00 0.00 3.36
177 180 1.959226 TTGCCCTTCGTCTTCGCAC 60.959 57.895 0.00 0.00 36.96 5.34
182 185 0.535102 CACCTGTTGCCCTTCGTCTT 60.535 55.000 0.00 0.00 0.00 3.01
257 260 6.467723 AGCATTTTCAACTTCTGTACGTAG 57.532 37.500 0.00 0.00 0.00 3.51
260 263 5.408604 ACCTAGCATTTTCAACTTCTGTACG 59.591 40.000 0.00 0.00 0.00 3.67
581 587 1.371183 CTGGTGCTCAGGTTCGGAA 59.629 57.895 0.00 0.00 39.76 4.30
605 611 3.560882 CCCAAGAGAAGAAGCACTGGATT 60.561 47.826 0.00 0.00 0.00 3.01
695 718 8.011844 ACTCAAAAGTAATTTTTCTTGAGGCT 57.988 30.769 15.59 0.00 36.29 4.58
704 727 8.764287 GCAGTTGCATACTCAAAAGTAATTTTT 58.236 29.630 0.00 0.00 41.25 1.94
1372 1455 0.315568 AGAAGAAGAAGACGCTGCGT 59.684 50.000 29.37 29.37 45.10 5.24
1535 1700 5.393866 ACACTGGGTATTTTCCAACTCAAT 58.606 37.500 0.00 0.00 33.36 2.57
1587 1753 7.217200 TCAGACTTTCAACACTAAGCAACTAT 58.783 34.615 0.00 0.00 0.00 2.12
1681 1964 3.665745 AAATTGCTGAAATGCCGTTCT 57.334 38.095 0.00 0.00 0.00 3.01
1685 1968 5.120519 ACAAACATAAATTGCTGAAATGCCG 59.879 36.000 0.00 0.00 0.00 5.69
1808 5764 5.767665 TCCCAATATGCGTGCATATAAAACT 59.232 36.000 23.49 8.55 45.66 2.66


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

AutoCloner maintained by Alex Coulton.