Multiple sequence alignment - TraesCS5A01G522600

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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 TraesCS5A01G522600 chr5A 100.000 4084 0 0 1 4084 683629973 683634056 0.000000e+00 7542.0
1 TraesCS5A01G522600 chr5A 99.291 4093 19 3 1 4084 681900553 681896462 0.000000e+00 7389.0
2 TraesCS5A01G522600 chr5A 79.692 1167 151 55 1481 2627 684647752 684648852 0.000000e+00 763.0
3 TraesCS5A01G522600 chr5A 87.048 664 71 10 3428 4077 602793190 602792528 0.000000e+00 736.0
4 TraesCS5A01G522600 chr5A 89.339 469 46 2 993 1461 684646744 684647208 1.640000e-163 586.0
5 TraesCS5A01G522600 chr5A 94.118 374 21 1 2128 2501 12880104 12880476 5.920000e-158 568.0
6 TraesCS5A01G522600 chr5A 93.357 286 18 1 2216 2501 52524242 52524526 4.880000e-114 422.0
7 TraesCS5A01G522600 chr5A 93.793 145 9 0 2357 2501 296677921 296678065 6.870000e-53 219.0
8 TraesCS5A01G522600 chr5A 94.697 132 7 0 2370 2501 591608041 591608172 5.350000e-49 206.0
9 TraesCS5A01G522600 chr5A 93.333 60 2 2 2979 3036 684649161 684649220 2.020000e-13 87.9
10 TraesCS5A01G522600 chr4D 89.991 3247 179 67 165 3318 500719636 500716443 0.000000e+00 4061.0
11 TraesCS5A01G522600 chr4D 90.213 470 43 1 992 1461 502013340 502013806 9.710000e-171 610.0
12 TraesCS5A01G522600 chr4D 79.072 927 115 51 1720 2623 502014283 502015153 7.660000e-157 564.0
13 TraesCS5A01G522600 chr4D 82.741 197 29 3 1472 1663 502013854 502014050 1.950000e-38 171.0
14 TraesCS5A01G522600 chr4B 90.290 1102 50 27 776 1855 644682008 644680942 0.000000e+00 1389.0
15 TraesCS5A01G522600 chr4B 91.709 989 68 11 1922 2904 644680909 644679929 0.000000e+00 1360.0
16 TraesCS5A01G522600 chr4B 91.048 458 41 0 992 1449 646112703 646113160 1.610000e-173 619.0
17 TraesCS5A01G522600 chr4B 79.344 915 116 45 1713 2604 646113978 646114842 3.540000e-160 575.0
18 TraesCS5A01G522600 chr4B 86.560 439 23 14 2902 3318 644679816 644679392 6.230000e-123 451.0
19 TraesCS5A01G522600 chr4B 83.150 273 38 8 1929 2200 644289524 644289789 4.080000e-60 243.0
20 TraesCS5A01G522600 chr4B 87.143 140 18 0 1524 1663 646113676 646113815 4.230000e-35 159.0
21 TraesCS5A01G522600 chr2D 80.239 1756 216 82 999 2720 483632975 483631317 0.000000e+00 1199.0
22 TraesCS5A01G522600 chr2D 87.048 664 70 9 3428 4077 241221900 241221239 0.000000e+00 736.0
23 TraesCS5A01G522600 chr2D 80.427 843 115 32 999 1822 527491687 527492498 7.560000e-167 597.0
24 TraesCS5A01G522600 chr2A 79.529 1656 226 76 999 2616 627513548 627511968 0.000000e+00 1075.0
25 TraesCS5A01G522600 chr2A 87.160 662 68 9 3428 4077 452786074 452786730 0.000000e+00 736.0
26 TraesCS5A01G522600 chr2A 81.807 841 107 31 999 1822 672368282 672369093 0.000000e+00 664.0
27 TraesCS5A01G522600 chr2A 79.619 682 90 28 1953 2616 672369090 672369740 1.040000e-120 444.0
28 TraesCS5A01G522600 chr1A 88.705 664 57 10 3428 4077 393013903 393013244 0.000000e+00 795.0
29 TraesCS5A01G522600 chr7B 88.333 660 66 6 3428 4077 432494878 432494220 0.000000e+00 782.0
30 TraesCS5A01G522600 chr7B 87.632 663 68 10 3428 4077 449033663 449033002 0.000000e+00 758.0
31 TraesCS5A01G522600 chr7B 78.947 152 27 4 6 155 468422130 468422278 9.340000e-17 99.0
32 TraesCS5A01G522600 chr5B 88.351 661 59 11 3430 4077 374450362 374449707 0.000000e+00 778.0
33 TraesCS5A01G522600 chr4A 87.292 661 68 9 3428 4077 194759092 194759747 0.000000e+00 741.0
34 TraesCS5A01G522600 chr2B 83.158 855 93 36 999 1834 568469092 568468270 0.000000e+00 734.0
35 TraesCS5A01G522600 chr2B 81.667 840 107 32 999 1822 624768161 624768969 0.000000e+00 654.0
36 TraesCS5A01G522600 chr7D 94.444 198 10 1 2361 2557 134508080 134508277 1.840000e-78 303.0
37 TraesCS5A01G522600 chr7A 87.013 154 17 3 3 155 26687669 26687820 1.950000e-38 171.0
38 TraesCS5A01G522600 chr3D 82.353 153 19 7 6 155 442751346 442751493 4.290000e-25 126.0
39 TraesCS5A01G522600 chr3D 81.579 152 24 4 6 155 352929871 352929722 5.540000e-24 122.0
40 TraesCS5A01G522600 chr3D 81.457 151 25 3 6 155 411870165 411870017 1.990000e-23 121.0
41 TraesCS5A01G522600 chr6B 80.519 154 22 7 6 155 668715956 668715807 1.200000e-20 111.0
42 TraesCS5A01G522600 chr5D 82.500 80 14 0 77 156 21669944 21669865 2.040000e-08 71.3


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 TraesCS5A01G522600 chr5A 683629973 683634056 4083 False 7542.000000 7542 100.000000 1 4084 1 chr5A.!!$F5 4083
1 TraesCS5A01G522600 chr5A 681896462 681900553 4091 True 7389.000000 7389 99.291000 1 4084 1 chr5A.!!$R2 4083
2 TraesCS5A01G522600 chr5A 602792528 602793190 662 True 736.000000 736 87.048000 3428 4077 1 chr5A.!!$R1 649
3 TraesCS5A01G522600 chr5A 684646744 684649220 2476 False 478.966667 763 87.454667 993 3036 3 chr5A.!!$F6 2043
4 TraesCS5A01G522600 chr4D 500716443 500719636 3193 True 4061.000000 4061 89.991000 165 3318 1 chr4D.!!$R1 3153
5 TraesCS5A01G522600 chr4D 502013340 502015153 1813 False 448.333333 610 84.008667 992 2623 3 chr4D.!!$F1 1631
6 TraesCS5A01G522600 chr4B 644679392 644682008 2616 True 1066.666667 1389 89.519667 776 3318 3 chr4B.!!$R1 2542
7 TraesCS5A01G522600 chr4B 646112703 646114842 2139 False 451.000000 619 85.845000 992 2604 3 chr4B.!!$F2 1612
8 TraesCS5A01G522600 chr2D 483631317 483632975 1658 True 1199.000000 1199 80.239000 999 2720 1 chr2D.!!$R2 1721
9 TraesCS5A01G522600 chr2D 241221239 241221900 661 True 736.000000 736 87.048000 3428 4077 1 chr2D.!!$R1 649
10 TraesCS5A01G522600 chr2D 527491687 527492498 811 False 597.000000 597 80.427000 999 1822 1 chr2D.!!$F1 823
11 TraesCS5A01G522600 chr2A 627511968 627513548 1580 True 1075.000000 1075 79.529000 999 2616 1 chr2A.!!$R1 1617
12 TraesCS5A01G522600 chr2A 452786074 452786730 656 False 736.000000 736 87.160000 3428 4077 1 chr2A.!!$F1 649
13 TraesCS5A01G522600 chr2A 672368282 672369740 1458 False 554.000000 664 80.713000 999 2616 2 chr2A.!!$F2 1617
14 TraesCS5A01G522600 chr1A 393013244 393013903 659 True 795.000000 795 88.705000 3428 4077 1 chr1A.!!$R1 649
15 TraesCS5A01G522600 chr7B 432494220 432494878 658 True 782.000000 782 88.333000 3428 4077 1 chr7B.!!$R1 649
16 TraesCS5A01G522600 chr7B 449033002 449033663 661 True 758.000000 758 87.632000 3428 4077 1 chr7B.!!$R2 649
17 TraesCS5A01G522600 chr5B 374449707 374450362 655 True 778.000000 778 88.351000 3430 4077 1 chr5B.!!$R1 647
18 TraesCS5A01G522600 chr4A 194759092 194759747 655 False 741.000000 741 87.292000 3428 4077 1 chr4A.!!$F1 649
19 TraesCS5A01G522600 chr2B 568468270 568469092 822 True 734.000000 734 83.158000 999 1834 1 chr2B.!!$R1 835
20 TraesCS5A01G522600 chr2B 624768161 624768969 808 False 654.000000 654 81.667000 999 1822 1 chr2B.!!$F1 823

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
834 849 6.480524 TGCTGCAATGTAGTAGTACAAAAG 57.519 37.500 14.26 10.15 42.54 2.27 F
2265 3462 4.630894 TTTAGCAGGTTTCATATTGGCG 57.369 40.909 0.00 0.00 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2265 3462 6.651225 GCCTGTAAATAGGATGGTGAAGATAC 59.349 42.308 0.00 0.0 40.42 2.24 R
3497 4934 1.949525 GAATGGCGCATAGGTCATTGT 59.050 47.619 10.83 0.0 30.97 2.71 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
126 127 7.031226 TGCTATCAATCTGCTTTTAATGTCC 57.969 36.000 0.00 0.00 0.00 4.02
127 128 6.830324 TGCTATCAATCTGCTTTTAATGTCCT 59.170 34.615 0.00 0.00 0.00 3.85
138 139 7.822658 TGCTTTTAATGTCCTAATTGTGGTAC 58.177 34.615 0.00 0.00 0.00 3.34
834 849 6.480524 TGCTGCAATGTAGTAGTACAAAAG 57.519 37.500 14.26 10.15 42.54 2.27
2265 3462 4.630894 TTTAGCAGGTTTCATATTGGCG 57.369 40.909 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 127 7.945033 AATTGCACAAAAGTACCACAATTAG 57.055 32.000 0.00 0.0 35.22 1.73
127 128 9.250624 GTTAATTGCACAAAAGTACCACAATTA 57.749 29.630 0.00 0.0 37.42 1.40
138 139 8.183830 TCACAGAAAAGTTAATTGCACAAAAG 57.816 30.769 0.00 0.0 0.00 2.27
745 752 2.761208 ACTCTATCCTTCCAACGACCAG 59.239 50.000 0.00 0.0 0.00 4.00
834 849 0.522076 CGGCTCTGCTTTTCATTCGC 60.522 55.000 0.00 0.0 0.00 4.70
2265 3462 6.651225 GCCTGTAAATAGGATGGTGAAGATAC 59.349 42.308 0.00 0.0 40.42 2.24
3496 4933 2.057137 ATGGCGCATAGGTCATTGTT 57.943 45.000 10.83 0.0 0.00 2.83
3497 4934 1.949525 GAATGGCGCATAGGTCATTGT 59.050 47.619 10.83 0.0 30.97 2.71


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

AutoCloner maintained by Alex Coulton.