Multiple sequence alignment - TraesCS5B01G006100

Loading Multiple Alignment...

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 TraesCS5B01G006100 chr5B 100.000 2667 0 0 1 2667 7305699 7303033 0.000000e+00 4926
1 TraesCS5B01G006100 chr5B 95.358 2693 99 10 1 2667 7384287 7381595 0.000000e+00 4257
2 TraesCS5B01G006100 chr5B 91.657 2685 152 23 2 2667 7185958 7183327 0.000000e+00 3651
3 TraesCS5B01G006100 chr5B 91.626 2687 149 23 1 2667 7150220 7147590 0.000000e+00 3646
4 TraesCS5B01G006100 chr5B 92.480 2141 128 14 530 2667 7163305 7161195 0.000000e+00 3031
5 TraesCS5B01G006100 chr5B 90.509 727 39 7 1 711 7448904 7448192 0.000000e+00 933
6 TraesCS5B01G006100 chr5D 88.035 2641 269 26 1 2599 7121022 7118387 0.000000e+00 3083
7 TraesCS5B01G006100 chr5D 88.153 2566 253 31 79 2599 7126237 7123678 0.000000e+00 3007
8 TraesCS5B01G006100 chr5D 87.519 2636 276 30 1 2593 3868805 3871430 0.000000e+00 2996
9 TraesCS5B01G006100 chr5D 87.184 2653 283 29 1 2601 3874377 3877024 0.000000e+00 2963
10 TraesCS5B01G006100 chr5D 87.795 1819 180 23 1 1788 7131598 7129791 0.000000e+00 2091
11 TraesCS5B01G006100 chr5D 86.746 1177 126 11 1 1150 3879715 3880888 0.000000e+00 1282
12 TraesCS5B01G006100 chr4A 87.263 2481 262 30 1 2444 18738388 18735925 0.000000e+00 2782
13 TraesCS5B01G006100 chr4A 88.931 2105 209 16 510 2599 18743499 18741404 0.000000e+00 2575
14 TraesCS5B01G006100 chr5A 86.990 2475 274 29 7 2444 4791880 4789417 0.000000e+00 2743
15 TraesCS5B01G006100 chr5A 86.873 1036 98 20 1 1002 4874754 4875785 0.000000e+00 1125
16 TraesCS5B01G006100 chrUn 82.671 554 63 18 1 526 400903052 400902504 6.730000e-126 460


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 TraesCS5B01G006100 chr5B 7303033 7305699 2666 True 4926.000000 4926 100.000000 1 2667 1 chr5B.!!$R4 2666
1 TraesCS5B01G006100 chr5B 7381595 7384287 2692 True 4257.000000 4257 95.358000 1 2667 1 chr5B.!!$R5 2666
2 TraesCS5B01G006100 chr5B 7183327 7185958 2631 True 3651.000000 3651 91.657000 2 2667 1 chr5B.!!$R3 2665
3 TraesCS5B01G006100 chr5B 7147590 7150220 2630 True 3646.000000 3646 91.626000 1 2667 1 chr5B.!!$R1 2666
4 TraesCS5B01G006100 chr5B 7161195 7163305 2110 True 3031.000000 3031 92.480000 530 2667 1 chr5B.!!$R2 2137
5 TraesCS5B01G006100 chr5B 7448192 7448904 712 True 933.000000 933 90.509000 1 711 1 chr5B.!!$R6 710
6 TraesCS5B01G006100 chr5D 7118387 7131598 13211 True 2727.000000 3083 87.994333 1 2599 3 chr5D.!!$R1 2598
7 TraesCS5B01G006100 chr5D 3868805 3880888 12083 False 2413.666667 2996 87.149667 1 2601 3 chr5D.!!$F1 2600
8 TraesCS5B01G006100 chr4A 18735925 18743499 7574 True 2678.500000 2782 88.097000 1 2599 2 chr4A.!!$R1 2598
9 TraesCS5B01G006100 chr5A 4789417 4791880 2463 True 2743.000000 2743 86.990000 7 2444 1 chr5A.!!$R1 2437
10 TraesCS5B01G006100 chr5A 4874754 4875785 1031 False 1125.000000 1125 86.873000 1 1002 1 chr5A.!!$F1 1001
11 TraesCS5B01G006100 chrUn 400902504 400903052 548 True 460.000000 460 82.671000 1 526 1 chrUn.!!$R1 525

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
311 11069 1.078497 CCATAGTCGGGCAAGTGCA 60.078 57.895 5.52 0.00 44.36 4.57 F
1421 12214 1.740025 GATAACTTGTGCTGGCCAGAC 59.260 52.381 37.21 27.91 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 12435 0.829333 AATTGTGCAAGCAACCCACA 59.171 45.0 0.00 0.0 37.67 4.17 R
2401 13262 0.611618 ATTGGACTGCATGGCGGAAA 60.612 50.0 3.71 0.0 38.46 3.13 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 5139 8.885494 TCAGAAAAATGAACGAAATTCCAAAT 57.115 26.923 0.00 0.00 36.36 2.32
311 11069 1.078497 CCATAGTCGGGCAAGTGCA 60.078 57.895 5.52 0.00 44.36 4.57
789 11569 6.100424 CCATTCTAAGAGGTCAATTCTACCCT 59.900 42.308 3.34 0.00 37.77 4.34
903 11684 8.166726 AGAAGGAACCATGAATCTTTAGAAGTT 58.833 33.333 0.00 0.00 0.00 2.66
939 11720 5.447818 GGAAATTCAGACAAGCCATAACTCG 60.448 44.000 0.00 0.00 0.00 4.18
940 11721 3.678056 TTCAGACAAGCCATAACTCGT 57.322 42.857 0.00 0.00 0.00 4.18
1082 11873 7.306781 AGAGTACCACCTATTAATAGCCTCTT 58.693 38.462 15.86 2.93 0.00 2.85
1164 11955 7.455641 TTCTTTTCTTCTTGTGGTGTGTTTA 57.544 32.000 0.00 0.00 0.00 2.01
1421 12214 1.740025 GATAACTTGTGCTGGCCAGAC 59.260 52.381 37.21 27.91 0.00 3.51
1663 12475 5.677319 TTTTGTGGTTGGATTTGTTACCA 57.323 34.783 0.00 0.00 38.29 3.25
1767 12581 4.636206 GGACATCAGGACAAAATGTACTCC 59.364 45.833 0.00 0.00 36.70 3.85
1788 12614 3.452264 CCACTCTCTCTCTCTCTCTCTCA 59.548 52.174 0.00 0.00 0.00 3.27
2020 12873 8.570068 TTGGTTTTAACACTACTTCTTTCACT 57.430 30.769 0.00 0.00 0.00 3.41
2053 12906 8.522830 CCTTAAAGCAAATTGAGTTGGATAAGA 58.477 33.333 0.00 0.00 0.00 2.10
2060 12913 7.469181 GCAAATTGAGTTGGATAAGATAGGGTG 60.469 40.741 0.00 0.00 0.00 4.61
2139 12992 2.607635 TCGACTCTTTCAACAACTGCAC 59.392 45.455 0.00 0.00 0.00 4.57
2363 13221 5.906113 TTCTTAGATCAGAGGTCACAGAC 57.094 43.478 0.00 0.00 0.00 3.51
2364 13222 4.923415 TCTTAGATCAGAGGTCACAGACA 58.077 43.478 0.00 0.00 33.68 3.41
2391 13252 3.518998 GCTCGGCCAGCTAGACGA 61.519 66.667 10.38 10.38 45.83 4.20
2401 13262 2.093973 CCAGCTAGACGAACACCTTCAT 60.094 50.000 0.00 0.00 0.00 2.57
2529 13390 5.735922 GCAACAACAAGGAAAGCACATTCTA 60.736 40.000 0.00 0.00 0.00 2.10
2624 13485 1.748493 TGAAGAAAACACACTGCCCAC 59.252 47.619 0.00 0.00 0.00 4.61
2652 13513 3.998913 TTGATCATGTAGCAACCCTCA 57.001 42.857 0.00 0.00 0.00 3.86
2656 13517 1.630369 TCATGTAGCAACCCTCAGCTT 59.370 47.619 0.00 0.00 42.05 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 10885 1.986575 GCGCTGAGCCAATCCACTTC 61.987 60.000 0.00 0.00 40.81 3.01
261 11004 5.418209 CGTTAATTCTCGGGACTCCCTATAT 59.582 44.000 12.62 0.00 42.67 0.86
789 11569 4.920640 TTGACCGCTTATTGTTTCCAAA 57.079 36.364 0.00 0.00 33.44 3.28
1082 11873 5.607477 ACTTTGTCATCGTCACTAAGGAAA 58.393 37.500 8.95 0.00 32.75 3.13
1164 11955 2.664402 ATGTGCCTCCAAGACAAGTT 57.336 45.000 0.00 0.00 0.00 2.66
1391 12184 6.349280 GCCAGCACAAGTTATCTATTTGACAA 60.349 38.462 0.00 0.00 0.00 3.18
1623 12435 0.829333 AATTGTGCAAGCAACCCACA 59.171 45.000 0.00 0.00 37.67 4.17
1697 12509 8.875168 ACACCTAGGAGGAGATAATCAAAATAG 58.125 37.037 17.98 0.00 37.67 1.73
1708 12520 4.505918 CGATCAGTACACCTAGGAGGAGAT 60.506 50.000 17.98 4.19 37.67 2.75
1767 12581 4.081476 TGTGAGAGAGAGAGAGAGAGAGTG 60.081 50.000 0.00 0.00 0.00 3.51
2020 12873 6.872920 ACTCAATTTGCTTTAAGGTTTGTGA 58.127 32.000 0.00 0.00 0.00 3.58
2053 12906 4.699925 ACACACACTAAACACACCCTAT 57.300 40.909 0.00 0.00 0.00 2.57
2060 12913 6.755141 TCACTTCTTCTACACACACTAAACAC 59.245 38.462 0.00 0.00 0.00 3.32
2271 13129 6.128956 CGCTGCTTAGCAAATCTAGACTTATC 60.129 42.308 8.68 0.00 38.41 1.75
2299 13157 0.899253 CCATGGTGCATGTGGGTTGA 60.899 55.000 2.57 0.00 39.94 3.18
2363 13221 3.782244 GCCGAGCAGACGCACTTG 61.782 66.667 0.00 0.00 42.27 3.16
2388 13249 0.872388 GCGGAAATGAAGGTGTTCGT 59.128 50.000 0.00 0.00 35.17 3.85
2391 13252 1.545582 CATGGCGGAAATGAAGGTGTT 59.454 47.619 0.00 0.00 0.00 3.32
2401 13262 0.611618 ATTGGACTGCATGGCGGAAA 60.612 50.000 3.71 0.00 38.46 3.13
2529 13390 9.612620 CTTTTCTACTTGAATTTTAAGATGCGT 57.387 29.630 7.82 0.00 34.24 5.24
2549 13410 6.903534 TCTCTCTACATTGGGTATCCTTTTCT 59.096 38.462 0.00 0.00 0.00 2.52
2624 13485 5.271625 GTTGCTACATGATCAATTGCTGAG 58.728 41.667 0.00 0.00 37.52 3.35


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

AutoCloner maintained by Alex Coulton.