Multiple sequence alignment - TraesCS6A01G092700

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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 TraesCS6A01G092700 chr6A 100.000 2411 0 0 1 2411 60607599 60605189 0.000000e+00 4453.0
1 TraesCS6A01G092700 chr6A 89.946 557 50 1 1861 2411 195277353 195276797 0.000000e+00 713.0
2 TraesCS6A01G092700 chr6A 87.664 608 58 6 1810 2411 435782835 435782239 0.000000e+00 691.0
3 TraesCS6A01G092700 chr6A 86.700 609 63 9 1810 2411 319172554 319173151 0.000000e+00 660.0
4 TraesCS6A01G092700 chr6A 88.474 321 31 1 2097 2411 593366364 593366044 1.350000e-102 383.0
5 TraesCS6A01G092700 chr6A 83.333 402 51 8 1067 1466 195277762 195277375 8.200000e-95 357.0
6 TraesCS6A01G092700 chr1A 96.613 1624 45 2 794 2411 494701577 494699958 0.000000e+00 2686.0
7 TraesCS6A01G092700 chr1A 99.374 799 5 0 1 799 355537409 355536611 0.000000e+00 1448.0
8 TraesCS6A01G092700 chr1A 92.092 999 75 2 794 1788 152714508 152713510 0.000000e+00 1404.0
9 TraesCS6A01G092700 chr1A 88.723 603 45 10 1810 2406 117808917 117809502 0.000000e+00 715.0
10 TraesCS6A01G092700 chr1A 92.203 295 17 1 2123 2411 152705606 152705312 1.720000e-111 412.0
11 TraesCS6A01G092700 chr3A 97.921 1058 22 0 794 1851 340259317 340260374 0.000000e+00 1832.0
12 TraesCS6A01G092700 chr3A 97.910 957 19 1 895 1851 17494227 17493272 0.000000e+00 1655.0
13 TraesCS6A01G092700 chr3A 98.006 953 19 0 899 1851 599892295 599891343 0.000000e+00 1655.0
14 TraesCS6A01G092700 chr3B 95.477 995 41 1 794 1788 499928185 499927195 0.000000e+00 1585.0
15 TraesCS6A01G092700 chr3B 99.622 794 3 0 1 794 489526421 489527214 0.000000e+00 1450.0
16 TraesCS6A01G092700 chr3B 95.000 640 26 1 1778 2411 499927096 499926457 0.000000e+00 1000.0
17 TraesCS6A01G092700 chr3B 89.803 608 50 4 1811 2411 815429762 815430364 0.000000e+00 769.0
18 TraesCS6A01G092700 chr3B 83.642 593 97 0 794 1386 815401339 815401931 2.090000e-155 558.0
19 TraesCS6A01G092700 chr6B 100.000 793 0 0 1 793 233650022 233650814 0.000000e+00 1465.0
20 TraesCS6A01G092700 chr6B 90.580 552 43 5 1861 2411 274389355 274389898 0.000000e+00 723.0
21 TraesCS6A01G092700 chr6B 82.709 694 80 16 794 1460 274388647 274389327 4.470000e-162 580.0
22 TraesCS6A01G092700 chr5A 100.000 793 0 0 1 793 441694056 441694848 0.000000e+00 1465.0
23 TraesCS6A01G092700 chr5A 99.748 793 2 0 1 793 280291412 280292204 0.000000e+00 1454.0
24 TraesCS6A01G092700 chr5A 99.005 804 8 0 1 804 695315408 695316211 0.000000e+00 1441.0
25 TraesCS6A01G092700 chr5A 97.611 628 15 0 794 1421 536905059 536905686 0.000000e+00 1077.0
26 TraesCS6A01G092700 chr5B 99.623 795 3 0 1 795 549117730 549118524 0.000000e+00 1452.0
27 TraesCS6A01G092700 chr5B 99.497 796 4 0 1 796 180231864 180231069 0.000000e+00 1448.0
28 TraesCS6A01G092700 chr1B 99.373 798 5 0 1 798 225464913 225464116 0.000000e+00 1447.0
29 TraesCS6A01G092700 chr4D 89.552 603 47 7 1810 2406 55490962 55491554 0.000000e+00 750.0
30 TraesCS6A01G092700 chr4D 100.000 28 0 0 1786 1813 480473798 480473771 4.000000e-03 52.8
31 TraesCS6A01G092700 chr4A 88.614 606 53 7 1810 2409 541425882 541425287 0.000000e+00 723.0
32 TraesCS6A01G092700 chr7A 88.226 603 52 10 1810 2406 100252625 100253214 0.000000e+00 702.0
33 TraesCS6A01G092700 chr6D 88.510 557 45 4 1861 2411 149886069 149886612 0.000000e+00 656.0
34 TraesCS6A01G092700 chr4B 100.000 28 0 0 1786 1813 298154958 298154931 4.000000e-03 52.8
35 TraesCS6A01G092700 chr3D 100.000 28 0 0 1786 1813 147502600 147502573 4.000000e-03 52.8
36 TraesCS6A01G092700 chr1D 100.000 28 0 0 1786 1813 390073526 390073553 4.000000e-03 52.8


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 TraesCS6A01G092700 chr6A 60605189 60607599 2410 True 4453.0 4453 100.0000 1 2411 1 chr6A.!!$R1 2410
1 TraesCS6A01G092700 chr6A 435782239 435782835 596 True 691.0 691 87.6640 1810 2411 1 chr6A.!!$R2 601
2 TraesCS6A01G092700 chr6A 319172554 319173151 597 False 660.0 660 86.7000 1810 2411 1 chr6A.!!$F1 601
3 TraesCS6A01G092700 chr6A 195276797 195277762 965 True 535.0 713 86.6395 1067 2411 2 chr6A.!!$R4 1344
4 TraesCS6A01G092700 chr1A 494699958 494701577 1619 True 2686.0 2686 96.6130 794 2411 1 chr1A.!!$R4 1617
5 TraesCS6A01G092700 chr1A 355536611 355537409 798 True 1448.0 1448 99.3740 1 799 1 chr1A.!!$R3 798
6 TraesCS6A01G092700 chr1A 152713510 152714508 998 True 1404.0 1404 92.0920 794 1788 1 chr1A.!!$R2 994
7 TraesCS6A01G092700 chr1A 117808917 117809502 585 False 715.0 715 88.7230 1810 2406 1 chr1A.!!$F1 596
8 TraesCS6A01G092700 chr3A 340259317 340260374 1057 False 1832.0 1832 97.9210 794 1851 1 chr3A.!!$F1 1057
9 TraesCS6A01G092700 chr3A 17493272 17494227 955 True 1655.0 1655 97.9100 895 1851 1 chr3A.!!$R1 956
10 TraesCS6A01G092700 chr3A 599891343 599892295 952 True 1655.0 1655 98.0060 899 1851 1 chr3A.!!$R2 952
11 TraesCS6A01G092700 chr3B 489526421 489527214 793 False 1450.0 1450 99.6220 1 794 1 chr3B.!!$F1 793
12 TraesCS6A01G092700 chr3B 499926457 499928185 1728 True 1292.5 1585 95.2385 794 2411 2 chr3B.!!$R1 1617
13 TraesCS6A01G092700 chr3B 815429762 815430364 602 False 769.0 769 89.8030 1811 2411 1 chr3B.!!$F3 600
14 TraesCS6A01G092700 chr3B 815401339 815401931 592 False 558.0 558 83.6420 794 1386 1 chr3B.!!$F2 592
15 TraesCS6A01G092700 chr6B 233650022 233650814 792 False 1465.0 1465 100.0000 1 793 1 chr6B.!!$F1 792
16 TraesCS6A01G092700 chr6B 274388647 274389898 1251 False 651.5 723 86.6445 794 2411 2 chr6B.!!$F2 1617
17 TraesCS6A01G092700 chr5A 441694056 441694848 792 False 1465.0 1465 100.0000 1 793 1 chr5A.!!$F2 792
18 TraesCS6A01G092700 chr5A 280291412 280292204 792 False 1454.0 1454 99.7480 1 793 1 chr5A.!!$F1 792
19 TraesCS6A01G092700 chr5A 695315408 695316211 803 False 1441.0 1441 99.0050 1 804 1 chr5A.!!$F4 803
20 TraesCS6A01G092700 chr5A 536905059 536905686 627 False 1077.0 1077 97.6110 794 1421 1 chr5A.!!$F3 627
21 TraesCS6A01G092700 chr5B 549117730 549118524 794 False 1452.0 1452 99.6230 1 795 1 chr5B.!!$F1 794
22 TraesCS6A01G092700 chr5B 180231069 180231864 795 True 1448.0 1448 99.4970 1 796 1 chr5B.!!$R1 795
23 TraesCS6A01G092700 chr1B 225464116 225464913 797 True 1447.0 1447 99.3730 1 798 1 chr1B.!!$R1 797
24 TraesCS6A01G092700 chr4D 55490962 55491554 592 False 750.0 750 89.5520 1810 2406 1 chr4D.!!$F1 596
25 TraesCS6A01G092700 chr4A 541425287 541425882 595 True 723.0 723 88.6140 1810 2409 1 chr4A.!!$R1 599
26 TraesCS6A01G092700 chr7A 100252625 100253214 589 False 702.0 702 88.2260 1810 2406 1 chr7A.!!$F1 596
27 TraesCS6A01G092700 chr6D 149886069 149886612 543 False 656.0 656 88.5100 1861 2411 1 chr6D.!!$F1 550

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
867 868 0.043334 TCTTCCTCCTCTCCCCCAAG 59.957 60.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2385 2534 3.0649 AGAGAAACATCCAGGCACTTC 57.935 47.619 0.0 0.0 34.6 3.01 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
867 868 0.043334 TCTTCCTCCTCTCCCCCAAG 59.957 60.000 0.00 0.00 0.00 3.61
946 947 2.034104 TTGCTGGTGATGCAGAGATC 57.966 50.000 0.00 0.00 41.71 2.75
978 979 2.038033 GGTCCATATAAGCTGCCGGTAA 59.962 50.000 1.90 0.00 0.00 2.85
1029 1057 2.904131 GGAGGAGAAGAAGCCGGG 59.096 66.667 2.18 0.00 0.00 5.73
1603 1632 4.365514 TGAAAAGTAGTTGGCTGGATGA 57.634 40.909 0.00 0.00 0.00 2.92
1859 2001 0.395311 CCCAGAGTCCAGCATTGCAT 60.395 55.000 11.91 0.00 0.00 3.96
1931 2073 3.249091 CCTGCGTGATGCTCTCATATAC 58.751 50.000 0.00 0.00 46.63 1.47
1941 2083 3.095016 GCTCTCATATACTTCGCGATCG 58.905 50.000 10.88 11.69 0.00 3.69
2158 2300 5.636903 ATTGTTAGACACCAGCCTATCAT 57.363 39.130 0.00 0.00 0.00 2.45
2385 2534 4.616835 GCTGGTAGCACCTTTTGAATCAAG 60.617 45.833 0.00 0.00 41.89 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
867 868 1.906333 GGATCGGGAGGGAGAGAGC 60.906 68.421 0.00 0.00 0.00 4.09
946 947 0.538057 ATATGGACCGGCTGCCATTG 60.538 55.000 23.91 8.87 42.03 2.82
978 979 0.895100 ATGCGGTTTGATGCACACCT 60.895 50.000 0.00 0.00 45.07 4.00
1029 1057 1.318158 CCTTGACTTGCTGGCCATCC 61.318 60.000 5.51 0.18 0.00 3.51
1603 1632 5.439721 TGATATGCAGCCACACTTAGATTT 58.560 37.500 0.00 0.00 0.00 2.17
1844 1986 4.191544 TGTACTTATGCAATGCTGGACTC 58.808 43.478 6.82 0.00 0.00 3.36
1859 2001 3.133141 TGTGGTGCAATGCTGTACTTA 57.867 42.857 6.82 0.00 38.18 2.24
1941 2083 8.184848 GGAAATCTTCCTAATGTTTTAGACTGC 58.815 37.037 0.00 0.00 46.57 4.40
2158 2300 9.653287 CCTATTTTCTTCACTACAGTCAATGTA 57.347 33.333 0.00 0.00 43.66 2.29
2252 2395 5.236263 GGTTTTCTTAATGTTGTTGCCCAAG 59.764 40.000 0.00 0.00 32.51 3.61
2385 2534 3.064900 AGAGAAACATCCAGGCACTTC 57.935 47.619 0.00 0.00 34.60 3.01


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

AutoCloner maintained by Alex Coulton.