Multiple sequence alignment - TraesCS7A01G104500

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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 TraesCS7A01G104500 chr7A 100.000 2317 0 0 1 2317 63574192 63576508 0.000000e+00 4279.0
1 TraesCS7A01G104500 chr7A 96.327 1470 47 5 852 2317 180639864 180638398 0.000000e+00 2409.0
2 TraesCS7A01G104500 chr7A 93.004 1601 41 18 746 2317 42989693 42988135 0.000000e+00 2270.0
3 TraesCS7A01G104500 chr7A 96.166 313 12 0 356 668 180640309 180639997 1.590000e-141 512.0
4 TraesCS7A01G104500 chr7A 86.164 318 28 5 671 988 161732905 161733206 1.720000e-86 329.0
5 TraesCS7A01G104500 chr5A 91.707 1664 76 21 675 2317 592641348 592642970 0.000000e+00 2252.0
6 TraesCS7A01G104500 chr5A 94.643 168 9 0 501 668 592641135 592641302 6.350000e-66 261.0
7 TraesCS7A01G104500 chr5A 83.962 106 6 7 361 466 592641040 592641134 8.820000e-15 91.6
8 TraesCS7A01G104500 chr5B 91.286 1664 83 21 675 2317 75684535 75682913 0.000000e+00 2213.0
9 TraesCS7A01G104500 chr5B 94.643 168 9 0 501 668 75684748 75684581 6.350000e-66 261.0
10 TraesCS7A01G104500 chr5B 83.962 106 6 7 361 466 75684843 75684749 8.820000e-15 91.6
11 TraesCS7A01G104500 chr3B 91.046 1664 87 21 675 2317 110277519 110275897 0.000000e+00 2191.0
12 TraesCS7A01G104500 chr3B 92.899 859 44 10 1464 2317 281743895 281743049 0.000000e+00 1232.0
13 TraesCS7A01G104500 chr3B 94.643 168 9 0 501 668 110277732 110277565 6.350000e-66 261.0
14 TraesCS7A01G104500 chr7D 94.524 1333 58 9 990 2317 32371233 32372555 0.000000e+00 2043.0
15 TraesCS7A01G104500 chr7D 83.176 529 54 20 990 1483 160630067 160630595 3.510000e-123 451.0
16 TraesCS7A01G104500 chr7D 90.938 320 11 5 671 990 32370889 32371190 4.610000e-112 414.0
17 TraesCS7A01G104500 chr7D 94.492 236 13 0 356 591 32349295 32349530 4.700000e-97 364.0
18 TraesCS7A01G104500 chr7D 86.164 318 28 3 671 988 160629721 160630022 1.720000e-86 329.0
19 TraesCS7A01G104500 chr7D 89.535 258 26 1 107 364 32348852 32349108 2.220000e-85 326.0
20 TraesCS7A01G104500 chr7D 94.366 71 4 0 593 663 32370779 32370849 2.430000e-20 110.0
21 TraesCS7A01G104500 chr1B 93.154 1081 63 8 990 2066 41747649 41748722 0.000000e+00 1576.0
22 TraesCS7A01G104500 chr1B 92.332 313 22 1 356 668 41746955 41747265 5.870000e-121 444.0
23 TraesCS7A01G104500 chr1B 89.720 321 14 6 671 991 136919622 136919923 2.160000e-105 392.0
24 TraesCS7A01G104500 chr1B 88.679 318 16 8 674 991 41747310 41747607 1.010000e-98 370.0
25 TraesCS7A01G104500 chr1B 88.519 270 23 5 98 365 41746504 41746767 1.030000e-83 320.0
26 TraesCS7A01G104500 chr1B 90.830 229 19 1 356 584 136918957 136919183 2.890000e-79 305.0
27 TraesCS7A01G104500 chr1B 91.398 93 6 1 578 668 136919488 136919580 2.420000e-25 126.0
28 TraesCS7A01G104500 chr2B 92.144 1082 61 11 990 2066 547410957 547412019 0.000000e+00 1506.0
29 TraesCS7A01G104500 chr2B 89.097 321 16 6 671 991 547410614 547410915 4.670000e-102 381.0
30 TraesCS7A01G104500 chr2B 90.037 271 26 1 396 666 547410301 547410570 1.320000e-92 350.0
31 TraesCS7A01G104500 chr2B 85.161 155 19 3 2166 2317 549452 549299 3.080000e-34 156.0
32 TraesCS7A01G104500 chr4B 85.404 507 61 12 990 1485 423402825 423402321 4.410000e-142 514.0
33 TraesCS7A01G104500 chr3A 85.323 511 56 11 993 1485 745811844 745811335 5.710000e-141 510.0
34 TraesCS7A01G104500 chr6A 84.843 508 61 8 993 1485 412853465 412852959 4.450000e-137 497.0
35 TraesCS7A01G104500 chr6A 84.810 158 20 3 2163 2317 584756685 584756841 3.080000e-34 156.0
36 TraesCS7A01G104500 chr7B 82.543 527 59 13 990 1483 121884812 121885338 1.270000e-117 433.0
37 TraesCS7A01G104500 chr7B 85.358 321 31 3 671 991 121884466 121884770 3.720000e-83 318.0
38 TraesCS7A01G104500 chr7B 80.636 346 47 9 356 682 121884094 121884438 1.370000e-62 250.0
39 TraesCS7A01G104500 chr6B 84.783 414 35 15 1816 2203 197245561 197245150 7.760000e-105 390.0
40 TraesCS7A01G104500 chr6B 89.723 253 24 2 993 1244 197246836 197246585 2.870000e-84 322.0
41 TraesCS7A01G104500 chr2D 84.177 158 21 3 2163 2317 148872945 148873101 1.430000e-32 150.0


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 TraesCS7A01G104500 chr7A 63574192 63576508 2316 False 4279.000000 4279 100.000000 1 2317 1 chr7A.!!$F1 2316
1 TraesCS7A01G104500 chr7A 42988135 42989693 1558 True 2270.000000 2270 93.004000 746 2317 1 chr7A.!!$R1 1571
2 TraesCS7A01G104500 chr7A 180638398 180640309 1911 True 1460.500000 2409 96.246500 356 2317 2 chr7A.!!$R2 1961
3 TraesCS7A01G104500 chr5A 592641040 592642970 1930 False 868.200000 2252 90.104000 361 2317 3 chr5A.!!$F1 1956
4 TraesCS7A01G104500 chr5B 75682913 75684843 1930 True 855.200000 2213 89.963667 361 2317 3 chr5B.!!$R1 1956
5 TraesCS7A01G104500 chr3B 281743049 281743895 846 True 1232.000000 1232 92.899000 1464 2317 1 chr3B.!!$R1 853
6 TraesCS7A01G104500 chr3B 110275897 110277732 1835 True 1226.000000 2191 92.844500 501 2317 2 chr3B.!!$R2 1816
7 TraesCS7A01G104500 chr7D 32370779 32372555 1776 False 855.666667 2043 93.276000 593 2317 3 chr7D.!!$F2 1724
8 TraesCS7A01G104500 chr7D 160629721 160630595 874 False 390.000000 451 84.670000 671 1483 2 chr7D.!!$F3 812
9 TraesCS7A01G104500 chr7D 32348852 32349530 678 False 345.000000 364 92.013500 107 591 2 chr7D.!!$F1 484
10 TraesCS7A01G104500 chr1B 41746504 41748722 2218 False 677.500000 1576 90.671000 98 2066 4 chr1B.!!$F1 1968
11 TraesCS7A01G104500 chr1B 136918957 136919923 966 False 274.333333 392 90.649333 356 991 3 chr1B.!!$F2 635
12 TraesCS7A01G104500 chr2B 547410301 547412019 1718 False 745.666667 1506 90.426000 396 2066 3 chr2B.!!$F1 1670
13 TraesCS7A01G104500 chr4B 423402321 423402825 504 True 514.000000 514 85.404000 990 1485 1 chr4B.!!$R1 495
14 TraesCS7A01G104500 chr3A 745811335 745811844 509 True 510.000000 510 85.323000 993 1485 1 chr3A.!!$R1 492
15 TraesCS7A01G104500 chr6A 412852959 412853465 506 True 497.000000 497 84.843000 993 1485 1 chr6A.!!$R1 492
16 TraesCS7A01G104500 chr7B 121884094 121885338 1244 False 333.666667 433 82.845667 356 1483 3 chr7B.!!$F1 1127
17 TraesCS7A01G104500 chr6B 197245150 197246836 1686 True 356.000000 390 87.253000 993 2203 2 chr6B.!!$R1 1210


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
100 101 0.178912 ACCGTACCCCACTCCTTTCT 60.179 55.0 0.0 0.0 0.0 2.52 F
596 1130 0.239082 GCCCTTACCGTGTTTTTCCG 59.761 55.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 2304 2.437281 ACACATCCAATCTAGCTCCCAG 59.563 50.000 0.00 0.0 0.0 4.45 R
2227 3439 2.301870 AGAGAAATAGTGGGTTGCGACA 59.698 45.455 6.39 0.0 0.0 4.35 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)



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AutoCloner maintained by Alex Coulton.