Multiple sequence alignment - TraesCS5D01G249800

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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 TraesCS5D01G249800 chr5D 100.000 4757 0 0 1 4757 356200918 356205674 0.000000e+00 8785
1 TraesCS5D01G249800 chr5D 85.874 269 25 9 3506 3773 235908693 235908437 1.690000e-69 274
2 TraesCS5D01G249800 chr5A 96.681 4790 108 21 1 4755 457899913 457904686 0.000000e+00 7917
3 TraesCS5D01G249800 chr5B 97.847 3112 47 8 1 3103 421181784 421184884 0.000000e+00 5358
4 TraesCS5D01G249800 chr5B 92.519 1671 92 18 3104 4757 421184995 421186649 0.000000e+00 2362
5 TraesCS5D01G249800 chr6D 79.795 876 96 39 3597 4458 38239378 38238570 3.210000e-156 562
6 TraesCS5D01G249800 chr6B 79.475 877 97 40 3597 4458 89142823 89142015 3.240000e-151 545
7 TraesCS5D01G249800 chr2A 84.015 269 33 10 3506 3773 377595797 377595538 2.840000e-62 250
8 TraesCS5D01G249800 chr3A 83.643 269 33 8 3506 3773 377488280 377488022 4.760000e-60 243
9 TraesCS5D01G249800 chr1A 83.643 269 29 10 3506 3773 254958173 254957919 6.150000e-59 239
10 TraesCS5D01G249800 chr4B 86.857 175 12 7 3506 3679 422773121 422772957 8.130000e-43 185
11 TraesCS5D01G249800 chr4B 85.083 181 14 8 3500 3679 440443215 440443383 6.330000e-39 172
12 TraesCS5D01G249800 chr1B 86.857 175 12 7 3506 3679 499391988 499391824 8.130000e-43 185
13 TraesCS5D01G249800 chr4A 85.714 70 10 0 2588 2657 660080547 660080616 1.840000e-09 75


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 TraesCS5D01G249800 chr5D 356200918 356205674 4756 False 8785 8785 100.000 1 4757 1 chr5D.!!$F1 4756
1 TraesCS5D01G249800 chr5A 457899913 457904686 4773 False 7917 7917 96.681 1 4755 1 chr5A.!!$F1 4754
2 TraesCS5D01G249800 chr5B 421181784 421186649 4865 False 3860 5358 95.183 1 4757 2 chr5B.!!$F1 4756
3 TraesCS5D01G249800 chr6D 38238570 38239378 808 True 562 562 79.795 3597 4458 1 chr6D.!!$R1 861
4 TraesCS5D01G249800 chr6B 89142015 89142823 808 True 545 545 79.475 3597 4458 1 chr6B.!!$R1 861

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
650 652 1.457346 ATTCTCTTTTCCTGGCAGCG 58.543 50.0 9.56 2.56 0.0 5.18 F
1435 1445 1.102978 GGGTGCTGTCTTGTTGTTGT 58.897 50.0 0.00 0.00 0.0 3.32 F
2168 2178 0.095935 CTTTCGACATCAAGCGGCTG 59.904 55.0 1.81 0.00 0.0 4.85 F
3190 3323 0.408700 AACTACGGGGGACACTCTCT 59.591 55.0 0.00 0.00 0.0 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 1920 1.815003 CACCTGAGCTGTGGGAAAATC 59.185 52.381 0.0 0.0 0.0 2.17 R
3172 3305 0.408700 AAGAGAGTGTCCCCCGTAGT 59.591 55.000 0.0 0.0 0.0 2.73 R
3292 3425 1.089920 CACTACAAGCAGGCACCATC 58.910 55.000 0.0 0.0 0.0 3.51 R
4335 4507 1.545841 CTTTGAAAGGCTACCCACCC 58.454 55.000 0.0 0.0 0.0 4.61 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
314 316 5.898174 ACGTGGATGAGAATACGTAATCAA 58.102 37.500 12.96 1.39 46.50 2.57
341 343 2.616842 CAACAACCGTCCAGCTAAAAGT 59.383 45.455 0.00 0.00 0.00 2.66
470 472 4.584325 GCATGCCTAAGACATCCCATTTAA 59.416 41.667 6.36 0.00 0.00 1.52
594 596 1.467920 AGCTCCATGCAAGTTTAGGC 58.532 50.000 0.00 0.00 45.94 3.93
650 652 1.457346 ATTCTCTTTTCCTGGCAGCG 58.543 50.000 9.56 2.56 0.00 5.18
878 883 7.781219 TGTTATAGACCTACACTACCTGCATTA 59.219 37.037 0.00 0.00 0.00 1.90
953 958 1.886542 GGACTCAAAATTGCCGTCCTT 59.113 47.619 18.84 0.00 41.30 3.36
991 996 2.054799 TGCAACCTACCCTTGAAGAGT 58.945 47.619 0.00 0.00 0.00 3.24
1283 1288 7.821595 TCAGATGAAATAAGCTTGCAATTTG 57.178 32.000 9.86 2.03 0.00 2.32
1284 1289 6.814644 TCAGATGAAATAAGCTTGCAATTTGG 59.185 34.615 9.86 0.00 0.00 3.28
1433 1443 3.290948 TTAGGGTGCTGTCTTGTTGTT 57.709 42.857 0.00 0.00 0.00 2.83
1434 1444 1.392589 AGGGTGCTGTCTTGTTGTTG 58.607 50.000 0.00 0.00 0.00 3.33
1435 1445 1.102978 GGGTGCTGTCTTGTTGTTGT 58.897 50.000 0.00 0.00 0.00 3.32
1910 1920 2.965671 ATATGAACCATGCTCCCAGG 57.034 50.000 0.00 0.00 0.00 4.45
1938 1948 2.353704 CCACAGCTCAGGTGAACGATAA 60.354 50.000 11.79 0.00 38.54 1.75
1966 1976 9.883142 TTATGGTTTTTGACTTCTTGTTGATTT 57.117 25.926 0.00 0.00 0.00 2.17
2168 2178 0.095935 CTTTCGACATCAAGCGGCTG 59.904 55.000 1.81 0.00 0.00 4.85
2296 2308 9.706691 TTGTATTGGATGCTAGTTATAGTAAGC 57.293 33.333 0.00 0.00 35.51 3.09
2497 2509 6.419484 TCATGTGACAGGTTAAGAAGAAGA 57.581 37.500 0.00 0.00 0.00 2.87
2498 2510 6.826668 TCATGTGACAGGTTAAGAAGAAGAA 58.173 36.000 0.00 0.00 0.00 2.52
2499 2511 6.931281 TCATGTGACAGGTTAAGAAGAAGAAG 59.069 38.462 0.00 0.00 0.00 2.85
2718 2739 4.320714 GCATGTGCTTGATTTGACTGAAGA 60.321 41.667 0.00 0.00 38.21 2.87
3172 3305 8.274322 ACCATTTCTACATGACAGGATGATAAA 58.726 33.333 0.00 0.00 39.69 1.40
3190 3323 0.408700 AACTACGGGGGACACTCTCT 59.591 55.000 0.00 0.00 0.00 3.10
3292 3425 1.067354 GCAAATTTGGAGACTGGCCAG 60.067 52.381 31.60 31.60 36.64 4.85
3315 3448 0.868406 GTGCCTGCTTGTAGTGACAC 59.132 55.000 0.00 0.00 34.48 3.67
3473 3616 2.671914 GCAAATTCGCCAAGCAAGATCA 60.672 45.455 0.00 0.00 0.00 2.92
3489 3632 4.286297 AGATCACCAAAATGAAGTCCGA 57.714 40.909 0.00 0.00 30.82 4.55
3523 3666 4.637534 GTCAATGCTCTGCCAGAGATTTTA 59.362 41.667 25.62 6.41 45.07 1.52
3549 3692 3.118992 TCTCTGCATGACATACACCAGTC 60.119 47.826 0.00 0.00 34.74 3.51
3564 3707 6.121776 ACACCAGTCACCAATTAGTTGATA 57.878 37.500 0.00 0.00 37.53 2.15
3642 3785 7.151308 ACTGACTGCTATAGCTTGATAATGTC 58.849 38.462 24.61 17.12 42.66 3.06
3818 3965 2.338500 GAATAAAGAGATAGCCGCCGG 58.662 52.381 0.00 0.00 0.00 6.13
3870 4018 2.026507 CGCTTCGCTTTGTACGTAGAAG 59.973 50.000 13.01 13.01 38.37 2.85
3949 4112 4.274950 TGAAGAAGAACGCTTTACCCTTTG 59.725 41.667 0.00 0.00 33.61 2.77
4177 4344 2.095567 CACTACTTTCTTGCAATGCGCT 60.096 45.455 9.73 0.00 43.06 5.92
4359 4537 1.313091 GGTAGCCTTTCAAAGCGGGG 61.313 60.000 0.00 0.00 0.00 5.73
4460 4640 5.248640 AGATCTGATCAACGACCAACAATT 58.751 37.500 19.12 0.00 0.00 2.32
4709 4891 0.904649 GGGGGAAAAGGCAAATCTGG 59.095 55.000 0.00 0.00 0.00 3.86
4729 4911 2.061028 GCAAGCATTTCTTCAAACCCG 58.939 47.619 0.00 0.00 31.27 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 140 3.585289 TGTAAGGAAAGGTGATGTAGCCA 59.415 43.478 0.00 0.0 0.00 4.75
314 316 1.167851 CTGGACGGTTGTTGCATCAT 58.832 50.000 0.00 0.0 0.00 2.45
470 472 6.429078 TGTGTACTAGTACGAGTTGATTGACT 59.571 38.462 24.36 0.0 38.85 3.41
594 596 4.036380 GTGTTGGTCCTGTTAGAAAGTTGG 59.964 45.833 0.00 0.0 0.00 3.77
809 814 8.261908 ACGAATAACTTAAACGTGCGATAATAC 58.738 33.333 0.00 0.0 35.91 1.89
878 883 3.485463 TTGGATGAGAACTTTCGTGGT 57.515 42.857 0.00 0.0 0.00 4.16
953 958 4.350368 TGCACAGAATTGTAGTTCTCCA 57.650 40.909 0.00 0.0 36.33 3.86
991 996 3.319031 TCCAGTCTCCATATCTCTGCA 57.681 47.619 0.00 0.0 0.00 4.41
1354 1361 8.377034 TGGCTTATGGAAGTAACTTTACAGTTA 58.623 33.333 0.00 0.0 36.92 2.24
1433 1443 5.248477 ACAATAAAAGAGTAGGGAGCAGACA 59.752 40.000 0.00 0.0 0.00 3.41
1434 1444 5.735766 ACAATAAAAGAGTAGGGAGCAGAC 58.264 41.667 0.00 0.0 0.00 3.51
1435 1445 6.374417 AACAATAAAAGAGTAGGGAGCAGA 57.626 37.500 0.00 0.0 0.00 4.26
1596 1606 2.391926 TTCAGTCCACCAGTCCAGTA 57.608 50.000 0.00 0.0 0.00 2.74
1910 1920 1.815003 CACCTGAGCTGTGGGAAAATC 59.185 52.381 0.00 0.0 0.00 2.17
1966 1976 5.295787 GTGTTACTGGACAAGTTCACAATCA 59.704 40.000 10.97 0.0 40.56 2.57
2296 2308 6.034898 GTGCCATTAAAATGAATTGGTTCTCG 59.965 38.462 4.25 0.0 38.70 4.04
2497 2509 6.576185 ACAAAGCATTCATTGTGTTCTTCTT 58.424 32.000 0.00 0.0 38.29 2.52
2498 2510 6.152932 ACAAAGCATTCATTGTGTTCTTCT 57.847 33.333 0.00 0.0 38.29 2.85
2499 2511 6.833342 AACAAAGCATTCATTGTGTTCTTC 57.167 33.333 0.00 0.0 39.57 2.87
2979 3000 1.769733 CACTTGCCCGTGTGAAAATG 58.230 50.000 0.00 0.0 36.38 2.32
3172 3305 0.408700 AAGAGAGTGTCCCCCGTAGT 59.591 55.000 0.00 0.0 0.00 2.73
3292 3425 1.089920 CACTACAAGCAGGCACCATC 58.910 55.000 0.00 0.0 0.00 3.51
3315 3448 2.419851 GCTTCCTCATTGGTCTCCTCTG 60.420 54.545 0.00 0.0 37.07 3.35
3473 3616 4.559862 AGAGATCGGACTTCATTTTGGT 57.440 40.909 0.00 0.0 0.00 3.67
3489 3632 4.082895 GCAGAGCATTGACACAAAAGAGAT 60.083 41.667 0.00 0.0 0.00 2.75
3523 3666 5.255687 TGGTGTATGTCATGCAGAGAAAAT 58.744 37.500 3.58 0.0 0.00 1.82
3537 3680 5.499004 ACTAATTGGTGACTGGTGTATGT 57.501 39.130 0.00 0.0 0.00 2.29
3549 3692 9.689976 TTCAACAAACATATCAACTAATTGGTG 57.310 29.630 0.00 0.0 35.81 4.17
3818 3965 1.508088 GTACTTGTGCCATGCAGCC 59.492 57.895 0.00 0.0 40.08 4.85
3828 3976 3.611113 CGAAATCGTACCAGGTACTTGTG 59.389 47.826 24.67 11.3 34.29 3.33
3870 4018 6.539103 CCCAAAGCAGAGATAGGTTTAACTAC 59.461 42.308 0.00 0.0 35.19 2.73
3949 4112 5.331876 ACAGCAGTATCTCAAGAAGTACC 57.668 43.478 0.00 0.0 0.00 3.34
4156 4323 2.245096 GCGCATTGCAAGAAAGTAGTG 58.755 47.619 9.69 0.0 45.45 2.74
4187 4354 3.382865 TGCCACTACAGCATTTCACAAAA 59.617 39.130 0.00 0.0 34.69 2.44
4335 4507 1.545841 CTTTGAAAGGCTACCCACCC 58.454 55.000 0.00 0.0 0.00 4.61
4460 4640 4.703575 AGTTATACCTACTTCACACTGCGA 59.296 41.667 0.00 0.0 0.00 5.10
4709 4891 2.061028 CGGGTTTGAAGAAATGCTTGC 58.939 47.619 0.00 0.0 36.83 4.01
4729 4911 3.063588 GGCCGCTAACATGAAAAGTCTAC 59.936 47.826 0.00 0.0 0.00 2.59


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

AutoCloner maintained by Alex Coulton.