Multiple sequence alignment - TraesCS1B01G106600

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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 TraesCS1B01G106600 chr1B 100.000 2828 0 0 1 2828 118176478 118173651 0.000000e+00 5223.0
1 TraesCS1B01G106600 chr1B 98.313 2845 31 3 1 2828 118089627 118092471 0.000000e+00 4972.0
2 TraesCS1B01G106600 chr1B 92.321 599 46 0 121 719 550753990 550753392 0.000000e+00 852.0
3 TraesCS1B01G106600 chr1B 94.656 131 7 0 2698 2828 389089376 389089246 1.330000e-48 204.0
4 TraesCS1B01G106600 chr1B 93.939 132 8 0 2697 2828 319161371 319161502 1.720000e-47 200.0
5 TraesCS1B01G106600 chr1B 95.349 43 2 0 1869 1911 118091426 118091468 5.060000e-08 69.4
6 TraesCS1B01G106600 chr1B 95.349 43 2 0 1784 1826 118091511 118091553 5.060000e-08 69.4
7 TraesCS1B01G106600 chr1B 95.349 43 2 0 1784 1826 118174610 118174568 5.060000e-08 69.4
8 TraesCS1B01G106600 chr1B 95.349 43 2 0 1869 1911 118174695 118174653 5.060000e-08 69.4
9 TraesCS1B01G106600 chr1D 94.208 846 33 8 1033 1874 74294723 74293890 0.000000e+00 1277.0
10 TraesCS1B01G106600 chr4B 93.410 607 37 3 120 724 180942821 180943426 0.000000e+00 896.0
11 TraesCS1B01G106600 chr4B 86.724 693 87 5 1918 2607 18477305 18477995 0.000000e+00 765.0
12 TraesCS1B01G106600 chr4B 94.656 131 7 0 2698 2828 517364354 517364224 1.330000e-48 204.0
13 TraesCS1B01G106600 chr4B 94.656 131 7 0 2698 2828 653974039 653973909 1.330000e-48 204.0
14 TraesCS1B01G106600 chr6B 93.478 598 37 2 122 718 692012175 692012771 0.000000e+00 887.0
15 TraesCS1B01G106600 chr2B 89.811 687 64 6 1924 2607 800318182 800317499 0.000000e+00 876.0
16 TraesCS1B01G106600 chr2B 100.000 31 0 0 2667 2697 503939108 503939078 1.090000e-04 58.4
17 TraesCS1B01G106600 chr3B 89.374 687 67 6 1924 2607 821196562 821195879 0.000000e+00 859.0
18 TraesCS1B01G106600 chr7D 89.229 687 69 5 1924 2607 365281831 365281147 0.000000e+00 854.0
19 TraesCS1B01G106600 chr7D 87.734 693 81 4 1918 2607 30927015 30927706 0.000000e+00 806.0
20 TraesCS1B01G106600 chr5B 92.346 601 44 2 120 719 489389571 489388972 0.000000e+00 854.0
21 TraesCS1B01G106600 chr3D 91.680 613 47 4 120 729 563634655 563635266 0.000000e+00 846.0
22 TraesCS1B01G106600 chr7B 92.000 600 47 1 120 719 481279461 481278863 0.000000e+00 841.0
23 TraesCS1B01G106600 chr5D 92.000 600 46 2 121 718 13738304 13737705 0.000000e+00 841.0
24 TraesCS1B01G106600 chr5D 100.000 30 0 0 2668 2697 125996009 125995980 3.940000e-04 56.5
25 TraesCS1B01G106600 chr6D 91.860 602 48 1 120 720 469591251 469591852 0.000000e+00 839.0
26 TraesCS1B01G106600 chr4A 88.372 688 73 7 1924 2607 455855013 455854329 0.000000e+00 821.0
27 TraesCS1B01G106600 chr4A 93.284 134 9 0 2695 2828 22873206 22873339 6.180000e-47 198.0
28 TraesCS1B01G106600 chr4D 87.901 686 79 4 1924 2607 118242215 118241532 0.000000e+00 804.0
29 TraesCS1B01G106600 chr4D 100.000 30 0 0 2668 2697 245467099 245467070 3.940000e-04 56.5
30 TraesCS1B01G106600 chr4D 100.000 30 0 0 2668 2697 282093062 282093091 3.940000e-04 56.5
31 TraesCS1B01G106600 chr1A 93.123 538 37 0 1179 1716 74320474 74321011 0.000000e+00 789.0
32 TraesCS1B01G106600 chr1A 93.491 169 9 1 1708 1874 74326518 74326686 1.680000e-62 250.0
33 TraesCS1B01G106600 chr1A 97.561 82 1 1 1033 1113 74320390 74320471 3.800000e-29 139.0
34 TraesCS1B01G106600 chr1A 94.872 39 1 1 950 988 74320268 74320305 3.040000e-05 60.2
35 TraesCS1B01G106600 chr1A 100.000 30 0 0 2668 2697 391682051 391682080 3.940000e-04 56.5
36 TraesCS1B01G106600 chr1A 100.000 30 0 0 2668 2697 391706338 391706367 3.940000e-04 56.5
37 TraesCS1B01G106600 chr1A 100.000 30 0 0 2668 2697 391767154 391767183 3.940000e-04 56.5
38 TraesCS1B01G106600 chr5A 86.706 677 84 6 1918 2591 108912805 108913478 0.000000e+00 747.0
39 TraesCS1B01G106600 chr2A 95.420 131 6 0 2698 2828 177873709 177873579 2.850000e-50 209.0
40 TraesCS1B01G106600 chr2A 95.420 131 6 0 2698 2828 177984893 177984763 2.850000e-50 209.0
41 TraesCS1B01G106600 chrUn 94.656 131 7 0 2698 2828 13788715 13788585 1.330000e-48 204.0
42 TraesCS1B01G106600 chr2D 100.000 30 0 0 2668 2697 7272773 7272802 3.940000e-04 56.5


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 TraesCS1B01G106600 chr1B 118173651 118176478 2827 True 1787.266667 5223 96.899333 1 2828 3 chr1B.!!$R3 2827
1 TraesCS1B01G106600 chr1B 118089627 118092471 2844 False 1703.600000 4972 96.337000 1 2828 3 chr1B.!!$F2 2827
2 TraesCS1B01G106600 chr1B 550753392 550753990 598 True 852.000000 852 92.321000 121 719 1 chr1B.!!$R2 598
3 TraesCS1B01G106600 chr1D 74293890 74294723 833 True 1277.000000 1277 94.208000 1033 1874 1 chr1D.!!$R1 841
4 TraesCS1B01G106600 chr4B 180942821 180943426 605 False 896.000000 896 93.410000 120 724 1 chr4B.!!$F2 604
5 TraesCS1B01G106600 chr4B 18477305 18477995 690 False 765.000000 765 86.724000 1918 2607 1 chr4B.!!$F1 689
6 TraesCS1B01G106600 chr6B 692012175 692012771 596 False 887.000000 887 93.478000 122 718 1 chr6B.!!$F1 596
7 TraesCS1B01G106600 chr2B 800317499 800318182 683 True 876.000000 876 89.811000 1924 2607 1 chr2B.!!$R2 683
8 TraesCS1B01G106600 chr3B 821195879 821196562 683 True 859.000000 859 89.374000 1924 2607 1 chr3B.!!$R1 683
9 TraesCS1B01G106600 chr7D 365281147 365281831 684 True 854.000000 854 89.229000 1924 2607 1 chr7D.!!$R1 683
10 TraesCS1B01G106600 chr7D 30927015 30927706 691 False 806.000000 806 87.734000 1918 2607 1 chr7D.!!$F1 689
11 TraesCS1B01G106600 chr5B 489388972 489389571 599 True 854.000000 854 92.346000 120 719 1 chr5B.!!$R1 599
12 TraesCS1B01G106600 chr3D 563634655 563635266 611 False 846.000000 846 91.680000 120 729 1 chr3D.!!$F1 609
13 TraesCS1B01G106600 chr7B 481278863 481279461 598 True 841.000000 841 92.000000 120 719 1 chr7B.!!$R1 599
14 TraesCS1B01G106600 chr5D 13737705 13738304 599 True 841.000000 841 92.000000 121 718 1 chr5D.!!$R1 597
15 TraesCS1B01G106600 chr6D 469591251 469591852 601 False 839.000000 839 91.860000 120 720 1 chr6D.!!$F1 600
16 TraesCS1B01G106600 chr4A 455854329 455855013 684 True 821.000000 821 88.372000 1924 2607 1 chr4A.!!$R1 683
17 TraesCS1B01G106600 chr4D 118241532 118242215 683 True 804.000000 804 87.901000 1924 2607 1 chr4D.!!$R1 683
18 TraesCS1B01G106600 chr1A 74320268 74321011 743 False 329.400000 789 95.185333 950 1716 3 chr1A.!!$F5 766
19 TraesCS1B01G106600 chr5A 108912805 108913478 673 False 747.000000 747 86.706000 1918 2591 1 chr5A.!!$F1 673

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
77 78 0.389948 CTGGCGTTGTGAGGTAGACC 60.39 60.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1946 2016 5.33574 GCTAAGAACCTTCTTTTACCCAAGC 60.336 44.0 5.63 3.74 44.7 4.01 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
77 78 0.389948 CTGGCGTTGTGAGGTAGACC 60.390 60.000 0.00 0.00 0.00 3.85
161 163 3.216985 TTGGGGGCGGCATTCTTGA 62.217 57.895 12.47 0.00 0.00 3.02
173 175 2.417933 GCATTCTTGAAGATGCACTCGT 59.582 45.455 18.24 0.00 39.61 4.18
285 287 1.499056 CTTGGCGTCAGATGTGTGC 59.501 57.895 0.00 2.11 0.00 4.57
312 314 4.498520 CGCGCAGGAGGTCGACAT 62.499 66.667 18.91 11.04 0.00 3.06
517 520 7.726291 CCTCAGGTCTTAGATATTAGGTCTGAA 59.274 40.741 0.00 0.00 0.00 3.02
542 545 6.530120 TGTGATGTGTGTTTGGTATTAGACT 58.470 36.000 0.00 0.00 0.00 3.24
597 600 3.183775 GGTGTAGCGACAGTTGTTACTTG 59.816 47.826 14.18 0.00 35.82 3.16
815 834 2.090524 GGGACACGCGTCGTTTAGG 61.091 63.158 9.86 0.00 43.61 2.69
900 919 3.761218 ACAGGTGTCTCTGTGACTATGAG 59.239 47.826 10.76 0.00 45.27 2.90
1946 2016 3.706594 TGGAATAGCAGAGGACTAGTTGG 59.293 47.826 0.00 0.00 0.00 3.77
2277 2349 8.211629 ACCCGAATTTATAGCAGATTTTCTAGT 58.788 33.333 0.00 0.00 0.00 2.57
2620 2694 1.227383 CGGGATGGAAGGGGGAAAG 59.773 63.158 0.00 0.00 0.00 2.62
2635 2709 1.279558 GGAAAGTGGAACCTCTCCTCC 59.720 57.143 0.00 0.00 45.64 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 1.938577 CCATCCACATCTCGCTTCTTG 59.061 52.381 0.00 0.00 0.00 3.02
173 175 4.020617 CCGCTGGTCCCTCAAGCA 62.021 66.667 0.34 0.00 0.00 3.91
285 287 3.190849 CCTGCGCGTGTCCATCAG 61.191 66.667 8.43 4.15 0.00 2.90
312 314 1.287815 CCACCACGACGCTAGACAA 59.712 57.895 0.00 0.00 0.00 3.18
517 520 7.168219 AGTCTAATACCAAACACACATCACAT 58.832 34.615 0.00 0.00 0.00 3.21
597 600 8.903820 ACAATAATAAGACTAAAGCCACCATTC 58.096 33.333 0.00 0.00 0.00 2.67
720 723 3.059120 CGTTCTTTCTTCCCCTTCGTTTC 60.059 47.826 0.00 0.00 0.00 2.78
815 834 1.338200 ACCGACTGATCCAACAGCTTC 60.338 52.381 0.00 0.00 41.06 3.86
900 919 2.433436 AGATTTTTAGGTGACCACGGC 58.567 47.619 3.63 0.00 0.00 5.68
1946 2016 5.335740 GCTAAGAACCTTCTTTTACCCAAGC 60.336 44.000 5.63 3.74 44.70 4.01
2277 2349 1.271934 CACAAATCCGCACCAAATCCA 59.728 47.619 0.00 0.00 0.00 3.41
2424 2497 3.059884 TGTGAGTTCAATCTCTCGCAAC 58.940 45.455 6.05 0.00 44.52 4.17
2701 2776 2.348998 GACCTGGCCCACTCACAG 59.651 66.667 0.00 0.00 0.00 3.66
2760 2835 2.821969 GGGAATCATACCCATGCATGTC 59.178 50.000 24.58 12.70 46.05 3.06


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

AutoCloner maintained by Alex Coulton.