Multiple sequence alignment - TraesCS5A01G017500

Loading Multiple Alignment...

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 TraesCS5A01G017500 chr5A 100.000 3681 0 0 1 3681 13418357 13414677 0.000000e+00 6798.0
1 TraesCS5A01G017500 chr5A 88.129 994 92 10 229 1205 688510611 688511595 0.000000e+00 1158.0
2 TraesCS5A01G017500 chr5A 84.104 843 98 19 2715 3525 688513487 688514325 0.000000e+00 782.0
3 TraesCS5A01G017500 chr5A 91.209 91 7 1 1878 1968 688512347 688512436 4.990000e-24 122.0
4 TraesCS5A01G017500 chr3B 99.321 3681 23 2 1 3681 769886651 769882973 0.000000e+00 6658.0
5 TraesCS5A01G017500 chr3B 86.017 801 84 8 422 1205 74183785 74184574 0.000000e+00 833.0
6 TraesCS5A01G017500 chr3B 84.801 704 79 17 1283 1968 74184809 74185502 0.000000e+00 682.0
7 TraesCS5A01G017500 chr3B 85.238 630 67 5 1 616 74183169 74183786 3.120000e-175 625.0
8 TraesCS5A01G017500 chr3B 85.872 545 64 8 2916 3449 74199118 74199660 5.330000e-158 568.0
9 TraesCS5A01G017500 chr3B 84.706 255 23 11 2166 2415 74186317 74186560 1.320000e-59 241.0
10 TraesCS5A01G017500 chr3B 84.211 95 15 0 3568 3662 74199720 74199814 3.910000e-15 93.5
11 TraesCS5A01G017500 chr7A 99.601 3011 12 0 1 3011 483815130 483812120 0.000000e+00 5494.0
12 TraesCS5A01G017500 chr7A 99.291 705 4 1 2977 3681 483812123 483811420 0.000000e+00 1273.0
13 TraesCS5A01G017500 chr7A 89.489 352 34 2 1436 1785 309672329 309672679 3.370000e-120 442.0
14 TraesCS5A01G017500 chr7A 84.293 382 36 10 2212 2588 309672677 309673039 5.850000e-93 351.0
15 TraesCS5A01G017500 chr7A 90.574 244 19 2 1205 1444 309666171 309666414 1.650000e-83 320.0
16 TraesCS5A01G017500 chr7A 88.587 184 19 2 1 182 309582643 309582826 4.780000e-54 222.0
17 TraesCS5A01G017500 chrUn 98.783 2712 28 3 1 2708 82493161 82495871 0.000000e+00 4820.0
18 TraesCS5A01G017500 chrUn 98.198 888 16 0 2794 3681 377700027 377699140 0.000000e+00 1552.0
19 TraesCS5A01G017500 chr1D 93.966 895 46 6 2794 3681 276748771 276747878 0.000000e+00 1347.0
20 TraesCS5A01G017500 chr1D 88.171 820 74 7 2591 3403 111967555 111966752 0.000000e+00 955.0
21 TraesCS5A01G017500 chr1D 95.122 82 4 0 1973 2054 111968359 111968278 2.980000e-26 130.0
22 TraesCS5A01G017500 chr1D 100.000 28 0 0 3611 3638 408539352 408539325 7.000000e-03 52.8
23 TraesCS5A01G017500 chr7B 88.262 869 89 8 2591 3448 707756439 707755573 0.000000e+00 1027.0
24 TraesCS5A01G017500 chr7B 82.803 1099 145 23 2591 3666 279851604 279852681 0.000000e+00 942.0
25 TraesCS5A01G017500 chr7B 86.392 801 80 9 422 1205 707759809 707759021 0.000000e+00 848.0
26 TraesCS5A01G017500 chr7B 86.124 627 67 4 4 616 707760428 707759808 0.000000e+00 658.0
27 TraesCS5A01G017500 chr7B 82.692 104 18 0 3568 3671 707755517 707755414 3.910000e-15 93.5
28 TraesCS5A01G017500 chr4B 87.271 872 97 8 2591 3449 111991544 111992414 0.000000e+00 983.0
29 TraesCS5A01G017500 chr4B 86.517 801 80 8 422 1205 111987972 111988761 0.000000e+00 856.0
30 TraesCS5A01G017500 chr4B 86.032 630 71 3 1 616 111987347 111987973 0.000000e+00 660.0
31 TraesCS5A01G017500 chr6A 88.720 789 69 11 1283 2054 171412046 171412831 0.000000e+00 946.0
32 TraesCS5A01G017500 chr6A 84.836 488 56 13 3187 3670 171413694 171414167 3.330000e-130 475.0
33 TraesCS5A01G017500 chr2B 86.567 871 95 11 2591 3449 53574996 53575856 0.000000e+00 941.0
34 TraesCS5A01G017500 chr2B 86.142 801 83 8 422 1205 53571326 53572115 0.000000e+00 839.0
35 TraesCS5A01G017500 chr2B 85.556 630 65 5 1 616 53570710 53571327 1.440000e-178 636.0
36 TraesCS5A01G017500 chr2B 79.446 433 70 10 1205 1628 108993078 108992656 4.650000e-74 289.0
37 TraesCS5A01G017500 chr2B 83.529 255 27 9 2166 2415 53573861 53574105 1.330000e-54 224.0
38 TraesCS5A01G017500 chr2B 84.375 96 14 1 3568 3662 53575916 53576011 3.910000e-15 93.5
39 TraesCS5A01G017500 chr3A 87.683 820 72 10 2591 3403 410123916 410124713 0.000000e+00 928.0
40 TraesCS5A01G017500 chr3A 86.464 724 66 9 1 701 410121201 410121915 0.000000e+00 765.0
41 TraesCS5A01G017500 chr3A 95.294 85 4 0 1970 2054 410122460 410122544 6.410000e-28 135.0
42 TraesCS5A01G017500 chr1B 87.838 740 78 7 470 1205 213332612 213333343 0.000000e+00 857.0
43 TraesCS5A01G017500 chr1B 78.899 436 69 11 1205 1628 562211617 562211193 1.300000e-69 274.0
44 TraesCS5A01G017500 chr4A 89.577 355 35 2 4 358 623994158 623993806 2.020000e-122 449.0
45 TraesCS5A01G017500 chr4A 79.215 433 71 10 1205 1628 743701929 743701507 2.160000e-72 283.0
46 TraesCS5A01G017500 chr5B 87.719 114 6 2 2166 2279 516091325 516091220 3.860000e-25 126.0
47 TraesCS5A01G017500 chr4D 88.288 111 5 3 2170 2280 24333952 24333850 3.860000e-25 126.0
48 TraesCS5A01G017500 chr5D 87.500 112 6 2 2166 2277 426294270 426294167 4.990000e-24 122.0
49 TraesCS5A01G017500 chr6D 89.773 88 9 0 1967 2054 455904126 455904213 3.000000e-21 113.0
50 TraesCS5A01G017500 chr6B 89.773 88 9 0 1967 2054 693274107 693274194 3.000000e-21 113.0


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 TraesCS5A01G017500 chr5A 13414677 13418357 3680 True 6798.000000 6798 100.000000 1 3681 1 chr5A.!!$R1 3680
1 TraesCS5A01G017500 chr5A 688510611 688514325 3714 False 687.333333 1158 87.814000 229 3525 3 chr5A.!!$F1 3296
2 TraesCS5A01G017500 chr3B 769882973 769886651 3678 True 6658.000000 6658 99.321000 1 3681 1 chr3B.!!$R1 3680
3 TraesCS5A01G017500 chr3B 74183169 74186560 3391 False 595.250000 833 85.190500 1 2415 4 chr3B.!!$F1 2414
4 TraesCS5A01G017500 chr3B 74199118 74199814 696 False 330.750000 568 85.041500 2916 3662 2 chr3B.!!$F2 746
5 TraesCS5A01G017500 chr7A 483811420 483815130 3710 True 3383.500000 5494 99.446000 1 3681 2 chr7A.!!$R1 3680
6 TraesCS5A01G017500 chr7A 309672329 309673039 710 False 396.500000 442 86.891000 1436 2588 2 chr7A.!!$F3 1152
7 TraesCS5A01G017500 chrUn 82493161 82495871 2710 False 4820.000000 4820 98.783000 1 2708 1 chrUn.!!$F1 2707
8 TraesCS5A01G017500 chrUn 377699140 377700027 887 True 1552.000000 1552 98.198000 2794 3681 1 chrUn.!!$R1 887
9 TraesCS5A01G017500 chr1D 276747878 276748771 893 True 1347.000000 1347 93.966000 2794 3681 1 chr1D.!!$R1 887
10 TraesCS5A01G017500 chr1D 111966752 111968359 1607 True 542.500000 955 91.646500 1973 3403 2 chr1D.!!$R3 1430
11 TraesCS5A01G017500 chr7B 279851604 279852681 1077 False 942.000000 942 82.803000 2591 3666 1 chr7B.!!$F1 1075
12 TraesCS5A01G017500 chr7B 707755414 707760428 5014 True 656.625000 1027 85.867500 4 3671 4 chr7B.!!$R1 3667
13 TraesCS5A01G017500 chr4B 111987347 111992414 5067 False 833.000000 983 86.606667 1 3449 3 chr4B.!!$F1 3448
14 TraesCS5A01G017500 chr6A 171412046 171414167 2121 False 710.500000 946 86.778000 1283 3670 2 chr6A.!!$F1 2387
15 TraesCS5A01G017500 chr2B 53570710 53576011 5301 False 546.700000 941 85.233800 1 3662 5 chr2B.!!$F1 3661
16 TraesCS5A01G017500 chr3A 410121201 410124713 3512 False 609.333333 928 89.813667 1 3403 3 chr3A.!!$F1 3402
17 TraesCS5A01G017500 chr1B 213332612 213333343 731 False 857.000000 857 87.838000 470 1205 1 chr1B.!!$F1 735

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
1546 2114 1.108776 AGCATCATGACCACAATGGC 58.891 50.0 0.0 0.0 42.67 4.40 F
1723 2294 2.167693 TGCTATTTCCCACGAGGTACTG 59.832 50.0 0.0 0.0 41.55 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2530 4423 2.039084 AGTGAAAGCAAGTAGGAGTGGG 59.961 50.0 0.0 0.0 0.0 4.61 R
3601 6142 5.519927 CAGGAGAAACAAAATTCTTGCGTTT 59.480 36.0 0.0 0.0 39.7 3.60 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
1546 2114 1.108776 AGCATCATGACCACAATGGC 58.891 50.000 0.00 0.0 42.67 4.40
1723 2294 2.167693 TGCTATTTCCCACGAGGTACTG 59.832 50.000 0.00 0.0 41.55 2.74
1801 2373 4.190001 CAAGCAATAGAGCATGAGAGTGT 58.810 43.478 0.00 0.0 35.37 3.55
2530 4423 1.135170 GGTAGACTCGGGTGCAGTTAC 60.135 57.143 0.00 0.0 0.00 2.50
3601 6142 3.630769 AGAACACATATTAGTCGCGAGGA 59.369 43.478 10.24 0.0 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1723 2294 2.224784 ACACGCCGAACACTTTTTATCC 59.775 45.455 0.0 0.0 0.00 2.59
1801 2373 2.680805 GCAGGAATTTGGAGGATCACGA 60.681 50.000 0.0 0.0 36.25 4.35
2530 4423 2.039084 AGTGAAAGCAAGTAGGAGTGGG 59.961 50.000 0.0 0.0 0.00 4.61
3601 6142 5.519927 CAGGAGAAACAAAATTCTTGCGTTT 59.480 36.000 0.0 0.0 39.70 3.60


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

AutoCloner maintained by Alex Coulton.