Multiple sequence alignment - TraesCS4A01G254500

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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 TraesCS4A01G254500 chr4A 100.000 2445 0 0 1 2445 566611346 566608902 0.000000e+00 4516.0
1 TraesCS4A01G254500 chr4A 99.253 2410 18 0 1 2410 566590644 566588235 0.000000e+00 4351.0
2 TraesCS4A01G254500 chr4A 95.298 638 30 0 1 638 101106754 101106117 0.000000e+00 1013.0
3 TraesCS4A01G254500 chr4A 95.298 638 26 3 1 635 465373702 465373066 0.000000e+00 1009.0
4 TraesCS4A01G254500 chr4A 95.276 635 30 0 1 635 604131221 604130587 0.000000e+00 1007.0
5 TraesCS4A01G254500 chr4A 92.952 681 46 1 1 679 476644615 476645295 0.000000e+00 990.0
6 TraesCS4A01G254500 chr4A 100.000 42 0 0 2404 2445 218883288 218883329 7.250000e-11 78.7
7 TraesCS4A01G254500 chr4A 100.000 42 0 0 2404 2445 566629214 566629173 7.250000e-11 78.7
8 TraesCS4A01G254500 chr3A 95.701 1791 75 2 621 2410 128659595 128657806 0.000000e+00 2880.0
9 TraesCS4A01G254500 chr3A 95.570 632 28 0 1 632 87633058 87633689 0.000000e+00 1013.0
10 TraesCS4A01G254500 chr3A 100.000 42 0 0 2404 2445 141658773 141658732 7.250000e-11 78.7
11 TraesCS4A01G254500 chr3A 100.000 42 0 0 2404 2445 348709294 348709335 7.250000e-11 78.7
12 TraesCS4A01G254500 chr3A 100.000 42 0 0 2404 2445 590108816 590108857 7.250000e-11 78.7
13 TraesCS4A01G254500 chr2A 95.087 1791 70 3 621 2410 276858469 276860242 0.000000e+00 2804.0
14 TraesCS4A01G254500 chr5A 94.305 1791 76 10 621 2410 136567991 136569756 0.000000e+00 2719.0
15 TraesCS4A01G254500 chr5A 96.006 626 25 0 1 626 569902904 569903529 0.000000e+00 1018.0
16 TraesCS4A01G254500 chr5A 100.000 42 0 0 2404 2445 293103593 293103634 7.250000e-11 78.7
17 TraesCS4A01G254500 chr3B 92.045 1785 136 5 632 2410 367032886 367031102 0.000000e+00 2505.0
18 TraesCS4A01G254500 chr3B 91.755 1783 140 7 632 2410 379653319 379655098 0.000000e+00 2471.0
19 TraesCS4A01G254500 chr3B 91.089 101 9 0 621 721 375068398 375068298 1.180000e-28 137.0
20 TraesCS4A01G254500 chr6B 92.068 1765 132 8 650 2410 129700708 129702468 0.000000e+00 2477.0
21 TraesCS4A01G254500 chr5B 90.444 1800 137 12 622 2410 328273371 328275146 0.000000e+00 2338.0
22 TraesCS4A01G254500 chr6D 90.903 1528 108 8 888 2410 17043132 17041631 0.000000e+00 2023.0
23 TraesCS4A01G254500 chr1A 95.276 635 30 0 1 635 27066494 27065860 0.000000e+00 1007.0
24 TraesCS4A01G254500 chr1A 95.141 638 31 0 1 638 127800040 127799403 0.000000e+00 1007.0
25 TraesCS4A01G254500 chr7A 100.000 42 0 0 2404 2445 298090712 298090753 7.250000e-11 78.7
26 TraesCS4A01G254500 chr7A 100.000 42 0 0 2404 2445 300592955 300592914 7.250000e-11 78.7
27 TraesCS4A01G254500 chr6A 100.000 42 0 0 2404 2445 395376485 395376444 7.250000e-11 78.7


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 TraesCS4A01G254500 chr4A 566608902 566611346 2444 True 4516 4516 100.000 1 2445 1 chr4A.!!$R4 2444
1 TraesCS4A01G254500 chr4A 566588235 566590644 2409 True 4351 4351 99.253 1 2410 1 chr4A.!!$R3 2409
2 TraesCS4A01G254500 chr4A 101106117 101106754 637 True 1013 1013 95.298 1 638 1 chr4A.!!$R1 637
3 TraesCS4A01G254500 chr4A 465373066 465373702 636 True 1009 1009 95.298 1 635 1 chr4A.!!$R2 634
4 TraesCS4A01G254500 chr4A 604130587 604131221 634 True 1007 1007 95.276 1 635 1 chr4A.!!$R6 634
5 TraesCS4A01G254500 chr4A 476644615 476645295 680 False 990 990 92.952 1 679 1 chr4A.!!$F2 678
6 TraesCS4A01G254500 chr3A 128657806 128659595 1789 True 2880 2880 95.701 621 2410 1 chr3A.!!$R1 1789
7 TraesCS4A01G254500 chr3A 87633058 87633689 631 False 1013 1013 95.570 1 632 1 chr3A.!!$F1 631
8 TraesCS4A01G254500 chr2A 276858469 276860242 1773 False 2804 2804 95.087 621 2410 1 chr2A.!!$F1 1789
9 TraesCS4A01G254500 chr5A 136567991 136569756 1765 False 2719 2719 94.305 621 2410 1 chr5A.!!$F1 1789
10 TraesCS4A01G254500 chr5A 569902904 569903529 625 False 1018 1018 96.006 1 626 1 chr5A.!!$F3 625
11 TraesCS4A01G254500 chr3B 367031102 367032886 1784 True 2505 2505 92.045 632 2410 1 chr3B.!!$R1 1778
12 TraesCS4A01G254500 chr3B 379653319 379655098 1779 False 2471 2471 91.755 632 2410 1 chr3B.!!$F1 1778
13 TraesCS4A01G254500 chr6B 129700708 129702468 1760 False 2477 2477 92.068 650 2410 1 chr6B.!!$F1 1760
14 TraesCS4A01G254500 chr5B 328273371 328275146 1775 False 2338 2338 90.444 622 2410 1 chr5B.!!$F1 1788
15 TraesCS4A01G254500 chr6D 17041631 17043132 1501 True 2023 2023 90.903 888 2410 1 chr6D.!!$R1 1522
16 TraesCS4A01G254500 chr1A 27065860 27066494 634 True 1007 1007 95.276 1 635 1 chr1A.!!$R1 634
17 TraesCS4A01G254500 chr1A 127799403 127800040 637 True 1007 1007 95.141 1 638 1 chr1A.!!$R2 637

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
652 660 8.941995 AGATACATCTAGGCTATTCTGTTACA 57.058 34.615 0.0 0.0 34.85 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2405 2431 1.714414 CAGCAAGCATCGTCTCAGC 59.286 57.895 0.0 0.0 0.0 4.26 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
652 660 8.941995 AGATACATCTAGGCTATTCTGTTACA 57.058 34.615 0.0 0.0 34.85 2.41
1552 1567 8.620533 ACTTCTTTTCAATTCTCTTTTTGACG 57.379 30.769 0.0 0.0 31.87 4.35
2405 2431 4.032900 GGTAGAGCACACACGATAAACATG 59.967 45.833 0.0 0.0 0.00 3.21
2410 2436 3.725895 GCACACACGATAAACATGCTGAG 60.726 47.826 0.0 0.0 0.00 3.35
2411 2437 3.679502 CACACACGATAAACATGCTGAGA 59.320 43.478 0.0 0.0 0.00 3.27
2412 2438 3.679980 ACACACGATAAACATGCTGAGAC 59.320 43.478 0.0 0.0 0.00 3.36
2413 2439 2.923655 ACACGATAAACATGCTGAGACG 59.076 45.455 0.0 0.0 0.00 4.18
2414 2440 3.179048 CACGATAAACATGCTGAGACGA 58.821 45.455 0.0 0.0 0.00 4.20
2415 2441 3.798878 CACGATAAACATGCTGAGACGAT 59.201 43.478 0.0 0.0 0.00 3.73
2416 2442 3.798878 ACGATAAACATGCTGAGACGATG 59.201 43.478 0.0 0.0 0.00 3.84
2417 2443 3.362401 CGATAAACATGCTGAGACGATGC 60.362 47.826 0.0 0.0 0.00 3.91
2418 2444 2.105006 AAACATGCTGAGACGATGCT 57.895 45.000 0.0 0.0 0.00 3.79
2419 2445 2.105006 AACATGCTGAGACGATGCTT 57.895 45.000 0.0 0.0 0.00 3.91
2420 2446 1.366679 ACATGCTGAGACGATGCTTG 58.633 50.000 0.0 0.0 37.70 4.01
2421 2447 0.027716 CATGCTGAGACGATGCTTGC 59.972 55.000 0.0 0.0 0.00 4.01
2422 2448 0.107800 ATGCTGAGACGATGCTTGCT 60.108 50.000 0.0 0.0 0.00 3.91
2423 2449 1.017701 TGCTGAGACGATGCTTGCTG 61.018 55.000 0.0 0.0 0.00 4.41
2424 2450 1.714414 CTGAGACGATGCTTGCTGC 59.286 57.895 0.0 0.0 43.25 5.25
2425 2451 0.740164 CTGAGACGATGCTTGCTGCT 60.740 55.000 0.0 0.0 43.37 4.24
2426 2452 0.321034 TGAGACGATGCTTGCTGCTT 60.321 50.000 0.0 0.0 43.37 3.91
2427 2453 0.096628 GAGACGATGCTTGCTGCTTG 59.903 55.000 0.0 0.0 43.37 4.01
2428 2454 0.604780 AGACGATGCTTGCTGCTTGT 60.605 50.000 0.0 0.0 43.37 3.16
2429 2455 0.179205 GACGATGCTTGCTGCTTGTC 60.179 55.000 0.0 0.0 43.37 3.18
2430 2456 1.136147 CGATGCTTGCTGCTTGTCC 59.864 57.895 0.0 0.0 43.37 4.02
2431 2457 1.509923 GATGCTTGCTGCTTGTCCC 59.490 57.895 0.0 0.0 43.37 4.46
2432 2458 1.941999 GATGCTTGCTGCTTGTCCCC 61.942 60.000 0.0 0.0 43.37 4.81
2433 2459 3.376918 GCTTGCTGCTTGTCCCCC 61.377 66.667 0.0 0.0 38.95 5.40
2434 2460 3.058160 CTTGCTGCTTGTCCCCCG 61.058 66.667 0.0 0.0 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1037 1051 4.873810 ACTGTTGCAGGCACGCCA 62.874 61.111 11.35 0.0 38.92 5.69
1552 1567 8.973378 GTAGTAACTCACATAATCTCATCAAGC 58.027 37.037 0.00 0.0 0.00 4.01
2405 2431 1.714414 CAGCAAGCATCGTCTCAGC 59.286 57.895 0.00 0.0 0.00 4.26
2416 2442 3.376918 GGGGGACAAGCAGCAAGC 61.377 66.667 0.00 0.0 46.19 4.01
2417 2443 3.058160 CGGGGGACAAGCAGCAAG 61.058 66.667 0.00 0.0 0.00 4.01


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

AutoCloner maintained by Alex Coulton.