Multiple sequence alignment - TraesCS2B01G425800

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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 TraesCS2B01G425800 chr2B 100.000 3824 0 0 1 3824 612063815 612067638 0.000000e+00 7062.0
1 TraesCS2B01G425800 chr2B 98.875 2134 23 1 1 2133 612009896 612012029 0.000000e+00 3807.0
2 TraesCS2B01G425800 chr2B 80.507 631 111 4 2178 2799 611312245 611311618 1.240000e-129 473.0
3 TraesCS2B01G425800 chr2B 86.792 159 21 0 1964 2122 611312525 611312367 1.090000e-40 178.0
4 TraesCS2B01G425800 chr2B 89.474 133 13 1 895 1027 611313872 611313741 2.360000e-37 167.0
5 TraesCS2B01G425800 chr2B 100.000 36 0 0 3713 3748 611066439 611066404 2.470000e-07 67.6
6 TraesCS2B01G425800 chr2D 97.881 2076 24 4 1757 3824 520040152 520042215 0.000000e+00 3572.0
7 TraesCS2B01G425800 chr2D 96.314 1275 28 11 507 1768 520037875 520039143 0.000000e+00 2076.0
8 TraesCS2B01G425800 chr2D 96.724 519 9 2 1 511 520036129 520036647 0.000000e+00 857.0
9 TraesCS2B01G425800 chr2D 81.090 624 110 6 2178 2799 519900600 519899983 3.430000e-135 492.0
10 TraesCS2B01G425800 chr2D 95.263 190 9 0 526 715 39517602 39517791 6.210000e-78 302.0
11 TraesCS2B01G425800 chr2D 94.030 134 6 2 894 1027 519902751 519902620 6.480000e-48 202.0
12 TraesCS2B01G425800 chr2D 87.209 172 22 0 1964 2135 519340202 519340031 3.010000e-46 196.0
13 TraesCS2B01G425800 chr2D 82.609 184 28 3 1941 2122 519901062 519900881 3.950000e-35 159.0
14 TraesCS2B01G425800 chr2D 83.582 134 7 5 894 1027 519341502 519341384 1.120000e-20 111.0
15 TraesCS2B01G425800 chr2D 100.000 53 0 0 760 812 520038179 520038127 8.740000e-17 99.0
16 TraesCS2B01G425800 chr2A 81.570 586 101 6 2204 2787 661669757 661669177 9.610000e-131 477.0
17 TraesCS2B01G425800 chrUn 94.737 190 10 0 526 715 206789410 206789599 2.890000e-76 296.0
18 TraesCS2B01G425800 chr7D 94.737 190 10 0 526 715 203490762 203490951 2.890000e-76 296.0
19 TraesCS2B01G425800 chr7D 94.737 190 10 0 526 715 381910739 381910928 2.890000e-76 296.0
20 TraesCS2B01G425800 chr7A 94.737 190 10 0 526 715 120850401 120850212 2.890000e-76 296.0
21 TraesCS2B01G425800 chr6D 94.737 190 10 0 526 715 124508286 124508475 2.890000e-76 296.0
22 TraesCS2B01G425800 chr4D 94.737 190 10 0 526 715 123326235 123326424 2.890000e-76 296.0
23 TraesCS2B01G425800 chr4D 100.000 28 0 0 2216 2243 480850439 480850412 7.000000e-03 52.8


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 TraesCS2B01G425800 chr2B 612063815 612067638 3823 False 7062.000000 7062 100.000000 1 3824 1 chr2B.!!$F2 3823
1 TraesCS2B01G425800 chr2B 612009896 612012029 2133 False 3807.000000 3807 98.875000 1 2133 1 chr2B.!!$F1 2132
2 TraesCS2B01G425800 chr2B 611311618 611313872 2254 True 272.666667 473 85.591000 895 2799 3 chr2B.!!$R2 1904
3 TraesCS2B01G425800 chr2D 520036129 520042215 6086 False 2168.333333 3572 96.973000 1 3824 3 chr2D.!!$F2 3823
4 TraesCS2B01G425800 chr2D 519899983 519902751 2768 True 284.333333 492 85.909667 894 2799 3 chr2D.!!$R3 1905
5 TraesCS2B01G425800 chr2A 661669177 661669757 580 True 477.000000 477 81.570000 2204 2787 1 chr2A.!!$R1 583

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
448 457 5.931146 TGAAAACAGTTGTCAAAACAGCAAT 59.069 32.000 3.41 0.0 38.93 3.56 F
2347 6114 5.719173 AGTCTGAAGATGAAGTGTTAGCTC 58.281 41.667 0.00 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2491 6267 1.567649 ACAATGATCAGGCCATGACCT 59.432 47.619 5.01 0.0 41.91 3.85 R
3662 7441 0.811616 GCCCACTTCACTAGCATCCG 60.812 60.000 0.00 0.0 0.00 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
438 447 8.600449 AAACAAGATTTTGAAAACAGTTGTCA 57.400 26.923 1.56 1.56 37.73 3.58
448 457 5.931146 TGAAAACAGTTGTCAAAACAGCAAT 59.069 32.000 3.41 0.00 38.93 3.56
2347 6114 5.719173 AGTCTGAAGATGAAGTGTTAGCTC 58.281 41.667 0.00 0.00 0.00 4.09
2491 6267 1.557371 TGGGCATCCGAGTTGTTGATA 59.443 47.619 0.00 0.00 35.24 2.15
2945 6722 5.520288 CCTACCTGTTGTACTTGATTCATCG 59.480 44.000 0.00 0.00 0.00 3.84
2946 6723 3.684788 ACCTGTTGTACTTGATTCATCGC 59.315 43.478 0.00 0.00 0.00 4.58
3111 6888 3.327757 TGTAGCATCCTCCAGAACTTTGT 59.672 43.478 0.00 0.00 0.00 2.83
3206 6983 6.432162 TCGTGTACTTGTAGTCTGGAACTTAT 59.568 38.462 0.00 0.00 39.55 1.73
3211 6988 1.852895 GTAGTCTGGAACTTATGCGCG 59.147 52.381 0.00 0.00 39.55 6.86
3339 7118 1.452108 GGCGTCTGGAAGGGATTGG 60.452 63.158 0.00 0.00 0.00 3.16
3376 7155 5.391873 GGGTGACAGAAGTGGATCAACCA 62.392 52.174 2.27 0.00 46.44 3.67
3512 7291 1.329906 GCGATGTTGAAGCTGATCAGG 59.670 52.381 23.89 6.34 0.00 3.86
3597 7376 7.828717 TGTTGAACCATGACTGTTATACATCAT 59.171 33.333 0.00 0.00 31.39 2.45
3662 7441 2.146073 AACACGCTGCCTGCAAATCC 62.146 55.000 0.00 0.00 43.06 3.01
3669 7448 2.123428 GCCTGCAAATCCGGATGCT 61.123 57.895 26.04 11.87 42.97 3.79
3766 7545 7.297614 ACAACAAATATAATGGCTACCAGGAT 58.702 34.615 0.00 0.00 36.75 3.24
3805 7589 3.667497 TTCACCAGTTGCTAGAGACTG 57.333 47.619 15.31 15.31 42.21 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
438 447 5.402270 GCGAATTGTAGTTGATTGCTGTTTT 59.598 36.000 0.00 0.00 0.00 2.43
2491 6267 1.567649 ACAATGATCAGGCCATGACCT 59.432 47.619 5.01 0.00 41.91 3.85
2945 6722 1.017177 TACCACATCGGAGCAAACGC 61.017 55.000 0.00 0.00 38.63 4.84
2946 6723 1.651987 ATACCACATCGGAGCAAACG 58.348 50.000 0.00 0.00 38.63 3.60
3137 6914 8.912988 TCAAATAGAAGAAGAAACACAACCAAT 58.087 29.630 0.00 0.00 0.00 3.16
3138 6915 8.287439 TCAAATAGAAGAAGAAACACAACCAA 57.713 30.769 0.00 0.00 0.00 3.67
3139 6916 7.873719 TCAAATAGAAGAAGAAACACAACCA 57.126 32.000 0.00 0.00 0.00 3.67
3140 6917 8.787852 AGATCAAATAGAAGAAGAAACACAACC 58.212 33.333 0.00 0.00 0.00 3.77
3141 6918 9.604626 CAGATCAAATAGAAGAAGAAACACAAC 57.395 33.333 0.00 0.00 0.00 3.32
3142 6919 9.559732 TCAGATCAAATAGAAGAAGAAACACAA 57.440 29.630 0.00 0.00 0.00 3.33
3143 6920 9.730705 ATCAGATCAAATAGAAGAAGAAACACA 57.269 29.630 0.00 0.00 0.00 3.72
3144 6921 9.985318 CATCAGATCAAATAGAAGAAGAAACAC 57.015 33.333 0.00 0.00 0.00 3.32
3145 6922 9.730705 ACATCAGATCAAATAGAAGAAGAAACA 57.269 29.630 0.00 0.00 0.00 2.83
3211 6988 1.984990 CTTTGTGTTGTGTGTGTGTGC 59.015 47.619 0.00 0.00 0.00 4.57
3376 7155 1.886655 GCAAAATCCACCGAGGGACTT 60.887 52.381 0.00 0.00 41.55 3.01
3378 7157 1.313091 GGCAAAATCCACCGAGGGAC 61.313 60.000 0.00 0.00 40.44 4.46
3469 7248 4.774200 CCCTTCCTTTCCTCATCAAACAAT 59.226 41.667 0.00 0.00 0.00 2.71
3597 7376 5.888724 ACTTCTATCACTAGCAGCTACTTGA 59.111 40.000 10.29 10.29 0.00 3.02
3662 7441 0.811616 GCCCACTTCACTAGCATCCG 60.812 60.000 0.00 0.00 0.00 4.18
3669 7448 2.540383 AGATGTCTGCCCACTTCACTA 58.460 47.619 2.17 0.00 0.00 2.74
3766 7545 7.957002 TGGTGAAAATATTTACTTGCCTTCAA 58.043 30.769 0.01 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.