Multiple sequence alignment - TraesCS3B01G477300

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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 TraesCS3B01G477300 chr3B 100.000 3060 0 0 1 3060 725706334 725709393 0 5651
1 TraesCS3B01G477300 chr3A 94.114 3075 129 17 1 3060 685118816 685121853 0 4628
2 TraesCS3B01G477300 chr3D 92.629 2564 121 29 545 3060 548246698 548249241 0 3626
3 TraesCS3B01G477300 chr3D 94.843 543 28 0 1 543 548246107 548246649 0 848


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 TraesCS3B01G477300 chr3B 725706334 725709393 3059 False 5651 5651 100.000 1 3060 1 chr3B.!!$F1 3059
1 TraesCS3B01G477300 chr3A 685118816 685121853 3037 False 4628 4628 94.114 1 3060 1 chr3A.!!$F1 3059
2 TraesCS3B01G477300 chr3D 548246107 548249241 3134 False 2237 3626 93.736 1 3060 2 chr3D.!!$F1 3059

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
975 1049 1.229529 GGGTGTGGAGAAGAGGGGA 60.23 63.158 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2286 2384 0.037232 GAGAGTAGCGCCAAACTGGT 60.037 55.0 11.88 0.31 40.46 4.0 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
64 65 1.477700 TGCTTCATACTTGCATTGGCC 59.522 47.619 0.00 0.00 40.13 5.36
293 294 2.505819 ACCGAGGAGCTGGTTATGAAAT 59.494 45.455 0.00 0.00 33.81 2.17
294 295 3.054361 ACCGAGGAGCTGGTTATGAAATT 60.054 43.478 0.00 0.00 33.81 1.82
346 347 6.473758 ACCAGGTAATCTTCTTGTAAACTCC 58.526 40.000 0.00 0.00 0.00 3.85
377 378 4.724399 TGTTGGCATTCTAAGGTTTCTGA 58.276 39.130 0.00 0.00 0.00 3.27
381 382 6.916360 TGGCATTCTAAGGTTTCTGAATTT 57.084 33.333 0.00 0.00 0.00 1.82
411 412 1.998315 GTGCTGACATGCTGACACTAG 59.002 52.381 0.00 0.00 0.00 2.57
434 436 4.322725 GGTCTTTTCATTTTAAGGGGGCAG 60.323 45.833 0.00 0.00 0.00 4.85
723 780 5.359860 GGTATTTTCCTTCCCCTTATGTGTG 59.640 44.000 0.00 0.00 0.00 3.82
733 790 6.134535 TCCCCTTATGTGTGAACATAAAGT 57.865 37.500 11.31 0.00 40.67 2.66
734 791 6.548321 TCCCCTTATGTGTGAACATAAAGTT 58.452 36.000 11.31 0.00 44.93 2.66
828 885 4.757149 AGTTTCTGTGAGTTGATTACTGGC 59.243 41.667 0.00 0.00 37.17 4.85
975 1049 1.229529 GGGTGTGGAGAAGAGGGGA 60.230 63.158 0.00 0.00 0.00 4.81
984 1058 2.530151 AAGAGGGGAGGCACAGCA 60.530 61.111 0.00 0.00 0.00 4.41
1053 1136 3.368571 GCCACTGCTGCTTGTCCC 61.369 66.667 0.00 0.00 33.53 4.46
1289 1378 1.672363 TCTTGTTCTTGCTGCTGTGTG 59.328 47.619 0.00 0.00 0.00 3.82
1290 1379 1.402968 CTTGTTCTTGCTGCTGTGTGT 59.597 47.619 0.00 0.00 0.00 3.72
1298 1387 1.016627 GCTGCTGTGTGTTGTCTGAA 58.983 50.000 0.00 0.00 0.00 3.02
1457 1546 4.866682 ATGCGTTTCTCTAGCTAAAAGC 57.133 40.909 15.46 15.46 42.84 3.51
1471 1560 0.524862 AAAAGCTGCGCTGATTCTGG 59.475 50.000 18.14 0.00 39.62 3.86
1595 1685 0.322975 ACACTCACTCATGGTGCCTC 59.677 55.000 8.87 0.00 44.98 4.70
1629 1720 6.653320 TGGAAACAGTATACATGTCCTTGAAC 59.347 38.462 0.00 0.00 35.01 3.18
1647 1738 6.183360 CCTTGAACCTTTCTCATTAGCATCAG 60.183 42.308 0.00 0.00 0.00 2.90
1651 1742 4.225942 ACCTTTCTCATTAGCATCAGTGGA 59.774 41.667 0.00 0.00 0.00 4.02
1868 1963 1.069204 GGGCAGCTATCTTCATCGTCA 59.931 52.381 0.00 0.00 0.00 4.35
2074 2169 3.356290 ACCATAGGTGCCATTCAGAAAC 58.644 45.455 0.00 0.00 32.98 2.78
2076 2171 3.270027 CATAGGTGCCATTCAGAAACGA 58.730 45.455 0.00 0.00 0.00 3.85
2162 2257 4.100373 AGCACTCTCTAAGGAAATCAGGT 58.900 43.478 0.00 0.00 0.00 4.00
2194 2289 5.242615 AGCTCCAAGAAAAGGATCTTCAAAC 59.757 40.000 0.00 0.00 37.56 2.93
2201 2296 6.877236 AGAAAAGGATCTTCAAACAAAGCAA 58.123 32.000 0.00 0.00 0.00 3.91
2232 2327 2.039818 ATGCAGAGCAGATTGTCAGG 57.960 50.000 0.00 0.00 43.65 3.86
2302 2400 1.346722 AGTTACCAGTTTGGCGCTACT 59.653 47.619 7.64 5.92 42.67 2.57
2309 2407 0.802607 GTTTGGCGCTACTCTCTCGG 60.803 60.000 7.64 0.00 0.00 4.63
2454 2554 0.309922 CACTTGAGTTGCACAGCTGG 59.690 55.000 19.93 8.27 0.00 4.85
2538 2638 9.549078 CTAATCTATAACCCTGAAAGAGGAAAC 57.451 37.037 0.00 0.00 46.33 2.78
2573 2673 7.223387 GCCTTTGAAATGCTATAACTTTCCATG 59.777 37.037 0.00 0.00 0.00 3.66
2665 2765 1.494960 GTCCTCCTGATCTCCTGCTT 58.505 55.000 0.00 0.00 0.00 3.91
2684 2784 1.682740 TGCGTATCCGGTGTATCTCA 58.317 50.000 0.00 0.00 33.68 3.27
2809 2909 5.604231 TGGTCATTCTCCTATCTGCTATTGT 59.396 40.000 0.00 0.00 0.00 2.71
3038 3138 4.398044 ACAAGGAACACACCAAAACTGTAG 59.602 41.667 0.00 0.00 0.00 2.74
3047 3147 5.050091 CACACCAAAACTGTAGACATCACTC 60.050 44.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 8.196802 TGATTGTAAGAACCTTTCATATGACG 57.803 34.615 4.48 0.00 0.00 4.35
293 294 8.677148 AATTGAGTTTACTAGCTTTGTCTGAA 57.323 30.769 0.00 0.00 0.00 3.02
294 295 8.559536 CAAATTGAGTTTACTAGCTTTGTCTGA 58.440 33.333 0.00 0.00 0.00 3.27
369 370 6.442112 CACTTCTTGGAGAAATTCAGAAACC 58.558 40.000 0.00 0.00 33.19 3.27
377 378 4.464008 TGTCAGCACTTCTTGGAGAAATT 58.536 39.130 0.00 0.00 33.19 1.82
381 382 2.873245 GCATGTCAGCACTTCTTGGAGA 60.873 50.000 0.00 0.00 0.00 3.71
411 412 3.580895 TGCCCCCTTAAAATGAAAAGACC 59.419 43.478 0.00 0.00 0.00 3.85
414 415 3.582647 ACCTGCCCCCTTAAAATGAAAAG 59.417 43.478 0.00 0.00 0.00 2.27
416 417 3.268034 ACCTGCCCCCTTAAAATGAAA 57.732 42.857 0.00 0.00 0.00 2.69
470 472 1.309499 CGCGTCTCTCCTCAACCTCT 61.309 60.000 0.00 0.00 0.00 3.69
473 475 2.182030 CCGCGTCTCTCCTCAACC 59.818 66.667 4.92 0.00 0.00 3.77
584 633 3.507233 TCCTTGAACATCTCCACATTTGC 59.493 43.478 0.00 0.00 0.00 3.68
787 844 3.222173 ACTGTTACATGGCTGGACAAA 57.778 42.857 0.00 0.00 0.00 2.83
828 885 7.764443 TCCTTTTCCTTGATATCTGTAAACTCG 59.236 37.037 3.98 0.00 0.00 4.18
975 1049 2.284112 CCCCCAAATGCTGTGCCT 60.284 61.111 0.00 0.00 0.00 4.75
984 1058 3.205056 TGCTCATTATCTCACCCCCAAAT 59.795 43.478 0.00 0.00 0.00 2.32
1021 1104 2.183555 GGCTGCTGCAGAAATGGC 59.816 61.111 32.30 16.63 41.91 4.40
1256 1345 5.063438 GCAAGAACAAGAAAACCAAGGAAAC 59.937 40.000 0.00 0.00 0.00 2.78
1289 1378 4.761739 TGTCATCCCAATTCTTCAGACAAC 59.238 41.667 0.00 0.00 32.46 3.32
1290 1379 4.761739 GTGTCATCCCAATTCTTCAGACAA 59.238 41.667 0.00 0.00 36.63 3.18
1298 1387 2.915604 ACTCCAGTGTCATCCCAATTCT 59.084 45.455 0.00 0.00 0.00 2.40
1435 1524 5.968387 GCTTTTAGCTAGAGAAACGCATA 57.032 39.130 9.64 0.00 38.45 3.14
1457 1546 0.671472 TCACACCAGAATCAGCGCAG 60.671 55.000 11.47 0.00 0.00 5.18
1460 1549 1.395954 CACATCACACCAGAATCAGCG 59.604 52.381 0.00 0.00 0.00 5.18
1595 1685 7.712639 ACATGTATACTGTTTCCAGATAGCAAG 59.287 37.037 0.00 0.00 41.50 4.01
1629 1720 4.774124 TCCACTGATGCTAATGAGAAAGG 58.226 43.478 0.00 0.00 0.00 3.11
1647 1738 2.157738 AGTGCTGCAAGAGATTTCCAC 58.842 47.619 2.77 0.00 34.07 4.02
1651 1742 3.940221 GAGATGAGTGCTGCAAGAGATTT 59.060 43.478 2.77 0.00 34.07 2.17
1755 1846 6.835174 ACAGATGATGCATGTAAATAGGAGT 58.165 36.000 2.46 0.00 0.00 3.85
1868 1963 2.467838 CATCTCGATGACGCAGAACAT 58.532 47.619 0.59 0.00 41.20 2.71
2074 2169 0.249447 TCTAGCCAATGCGACCATCG 60.249 55.000 0.00 0.00 44.33 3.84
2076 2171 2.158769 TGAATCTAGCCAATGCGACCAT 60.159 45.455 0.00 0.00 44.33 3.55
2162 2257 4.165950 TCCTTTTCTTGGAGCTATGCCATA 59.834 41.667 0.00 0.00 34.90 2.74
2223 2318 6.109359 AGTAGCATAGTGTTTCCTGACAATC 58.891 40.000 0.00 0.00 0.00 2.67
2232 2327 6.677781 TTGCCATTAGTAGCATAGTGTTTC 57.322 37.500 0.00 0.00 39.11 2.78
2286 2384 0.037232 GAGAGTAGCGCCAAACTGGT 60.037 55.000 11.88 0.31 40.46 4.00
2302 2400 4.931661 AGACTTTTGTAACACCGAGAGA 57.068 40.909 0.00 0.00 0.00 3.10
2470 2570 6.266131 TGCCCCATTAGTTTCTTCTCATAT 57.734 37.500 0.00 0.00 0.00 1.78
2538 2638 3.950395 AGCATTTCAAAGGCTAAGCTAGG 59.050 43.478 7.70 0.00 35.82 3.02
2640 2740 1.028905 GAGATCAGGAGGACGACAGG 58.971 60.000 0.00 0.00 0.00 4.00
2684 2784 1.606531 GATGAGCCTGGTGGAAGCT 59.393 57.895 0.00 0.00 40.24 3.74
2713 2813 1.006571 GTGAACCCGACAAGCGAGA 60.007 57.895 0.00 0.00 44.57 4.04
2816 2916 9.305925 GTTCAAAACTTTCAAGAATCAAGTGAT 57.694 29.630 0.00 0.00 36.07 3.06
2837 2937 4.409901 TCCATCTCTGATATGCAGGTTCAA 59.590 41.667 0.00 0.00 44.98 2.69
2838 2938 3.969312 TCCATCTCTGATATGCAGGTTCA 59.031 43.478 0.00 0.00 44.98 3.18
2927 3027 8.591072 ACTGATTCCTGATGATTGTTCAATTTT 58.409 29.630 0.00 0.00 34.96 1.82
2928 3028 8.130671 ACTGATTCCTGATGATTGTTCAATTT 57.869 30.769 0.00 0.00 34.96 1.82


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

AutoCloner maintained by Alex Coulton.