Multiple sequence alignment - TraesCS5B01G247000

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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 TraesCS5B01G247000 chr5B 100.000 2531 0 0 1 2531 429036682 429039212 0.000000e+00 4674.0
1 TraesCS5B01G247000 chr5B 95.056 1618 26 7 967 2531 413608403 413610019 0.000000e+00 2495.0
2 TraesCS5B01G247000 chr5B 93.185 1614 46 25 967 2531 432877690 432879288 0.000000e+00 2313.0
3 TraesCS5B01G247000 chr5B 90.652 813 50 12 1 808 580699648 580700439 0.000000e+00 1057.0
4 TraesCS5B01G247000 chr5B 91.813 171 10 2 799 966 580700611 580700780 4.210000e-58 235.0
5 TraesCS5B01G247000 chr3B 96.113 1595 26 5 972 2531 201559802 201558209 0.000000e+00 2569.0
6 TraesCS5B01G247000 chr3B 90.406 813 55 12 1 808 582471811 582472605 0.000000e+00 1048.0
7 TraesCS5B01G247000 chr3B 86.957 184 10 4 799 969 582472777 582472959 7.140000e-46 195.0
8 TraesCS5B01G247000 chr4D 94.034 1609 44 16 972 2531 245649653 245651258 0.000000e+00 2392.0
9 TraesCS5B01G247000 chr4D 91.481 810 44 12 1 806 416137248 416136460 0.000000e+00 1090.0
10 TraesCS5B01G247000 chr4D 90.370 810 47 13 1 806 448392002 448392784 0.000000e+00 1035.0
11 TraesCS5B01G247000 chr4D 91.813 171 9 3 799 966 416136246 416136078 1.510000e-57 233.0
12 TraesCS5B01G247000 chr4D 85.333 150 7 4 835 970 448393151 448393299 9.440000e-30 141.0
13 TraesCS5B01G247000 chr4A 93.680 1598 63 8 967 2531 310763374 310764966 0.000000e+00 2357.0
14 TraesCS5B01G247000 chr3A 94.441 1529 30 14 972 2447 672877462 672875936 0.000000e+00 2302.0
15 TraesCS5B01G247000 chr1A 93.062 1571 54 28 1010 2531 371922144 371923708 0.000000e+00 2246.0
16 TraesCS5B01G247000 chr1A 90.909 44 4 0 924 967 267442512 267442555 2.720000e-05 60.2
17 TraesCS5B01G247000 chr2D 96.883 1155 16 2 972 2107 630271258 630272411 0.000000e+00 1916.0
18 TraesCS5B01G247000 chr2D 96.727 1161 16 4 967 2107 33934777 33935935 0.000000e+00 1914.0
19 TraesCS5B01G247000 chr2D 90.741 702 43 8 110 806 81482399 81483083 0.000000e+00 917.0
20 TraesCS5B01G247000 chr2D 98.383 433 5 2 2101 2531 33935980 33936412 0.000000e+00 760.0
21 TraesCS5B01G247000 chr2D 98.605 430 4 2 2104 2531 630272457 630272886 0.000000e+00 760.0
22 TraesCS5B01G247000 chr2D 93.182 220 11 3 1 217 81480893 81481111 1.130000e-83 320.0
23 TraesCS5B01G247000 chr2D 85.965 171 10 3 799 966 81483293 81483452 1.200000e-38 171.0
24 TraesCS5B01G247000 chrUn 96.727 1161 16 4 967 2107 371049414 371050572 0.000000e+00 1914.0
25 TraesCS5B01G247000 chrUn 98.383 433 5 2 2101 2531 371050617 371051049 0.000000e+00 760.0
26 TraesCS5B01G247000 chrUn 92.722 371 4 12 1770 2119 451362693 451362325 4.830000e-142 514.0
27 TraesCS5B01G247000 chr1B 97.666 1071 24 1 967 2037 633727898 633726829 0.000000e+00 1838.0
28 TraesCS5B01G247000 chr5D 92.506 814 43 12 1 808 139131802 139131001 0.000000e+00 1149.0
29 TraesCS5B01G247000 chr5D 90.199 704 44 10 110 806 30721343 30720658 0.000000e+00 894.0
30 TraesCS5B01G247000 chr5D 93.304 224 7 7 1 217 30723255 30723033 8.730000e-85 324.0
31 TraesCS5B01G247000 chr5D 89.941 169 10 3 799 967 139130796 139130635 7.090000e-51 211.0
32 TraesCS5B01G247000 chr5D 87.978 183 8 3 799 968 30720445 30720264 1.190000e-48 204.0
33 TraesCS5B01G247000 chr7D 92.515 815 40 14 1 808 566239820 566240620 0.000000e+00 1147.0
34 TraesCS5B01G247000 chr7D 94.709 567 10 10 1560 2107 231585231 231585796 0.000000e+00 863.0
35 TraesCS5B01G247000 chr7D 85.955 178 17 6 799 970 566240824 566240999 1.550000e-42 183.0
36 TraesCS5B01G247000 chr5A 98.174 438 5 3 2097 2531 482027244 482026807 0.000000e+00 761.0
37 TraesCS5B01G247000 chr5A 97.297 74 2 0 2034 2107 482027334 482027261 2.640000e-25 126.0
38 TraesCS5B01G247000 chr4B 93.687 396 6 9 1731 2107 1 396 2.180000e-160 575.0
39 TraesCS5B01G247000 chr2B 78.000 100 15 6 510 606 716593138 716593233 3.520000e-04 56.5


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 TraesCS5B01G247000 chr5B 429036682 429039212 2530 False 4674.000000 4674 100.000000 1 2531 1 chr5B.!!$F2 2530
1 TraesCS5B01G247000 chr5B 413608403 413610019 1616 False 2495.000000 2495 95.056000 967 2531 1 chr5B.!!$F1 1564
2 TraesCS5B01G247000 chr5B 432877690 432879288 1598 False 2313.000000 2313 93.185000 967 2531 1 chr5B.!!$F3 1564
3 TraesCS5B01G247000 chr5B 580699648 580700780 1132 False 646.000000 1057 91.232500 1 966 2 chr5B.!!$F4 965
4 TraesCS5B01G247000 chr3B 201558209 201559802 1593 True 2569.000000 2569 96.113000 972 2531 1 chr3B.!!$R1 1559
5 TraesCS5B01G247000 chr3B 582471811 582472959 1148 False 621.500000 1048 88.681500 1 969 2 chr3B.!!$F1 968
6 TraesCS5B01G247000 chr4D 245649653 245651258 1605 False 2392.000000 2392 94.034000 972 2531 1 chr4D.!!$F1 1559
7 TraesCS5B01G247000 chr4D 416136078 416137248 1170 True 661.500000 1090 91.647000 1 966 2 chr4D.!!$R1 965
8 TraesCS5B01G247000 chr4D 448392002 448393299 1297 False 588.000000 1035 87.851500 1 970 2 chr4D.!!$F2 969
9 TraesCS5B01G247000 chr4A 310763374 310764966 1592 False 2357.000000 2357 93.680000 967 2531 1 chr4A.!!$F1 1564
10 TraesCS5B01G247000 chr3A 672875936 672877462 1526 True 2302.000000 2302 94.441000 972 2447 1 chr3A.!!$R1 1475
11 TraesCS5B01G247000 chr1A 371922144 371923708 1564 False 2246.000000 2246 93.062000 1010 2531 1 chr1A.!!$F2 1521
12 TraesCS5B01G247000 chr2D 630271258 630272886 1628 False 1338.000000 1916 97.744000 972 2531 2 chr2D.!!$F3 1559
13 TraesCS5B01G247000 chr2D 33934777 33936412 1635 False 1337.000000 1914 97.555000 967 2531 2 chr2D.!!$F1 1564
14 TraesCS5B01G247000 chr2D 81480893 81483452 2559 False 469.333333 917 89.962667 1 966 3 chr2D.!!$F2 965
15 TraesCS5B01G247000 chrUn 371049414 371051049 1635 False 1337.000000 1914 97.555000 967 2531 2 chrUn.!!$F1 1564
16 TraesCS5B01G247000 chr1B 633726829 633727898 1069 True 1838.000000 1838 97.666000 967 2037 1 chr1B.!!$R1 1070
17 TraesCS5B01G247000 chr5D 139130635 139131802 1167 True 680.000000 1149 91.223500 1 967 2 chr5D.!!$R2 966
18 TraesCS5B01G247000 chr5D 30720264 30723255 2991 True 474.000000 894 90.493667 1 968 3 chr5D.!!$R1 967
19 TraesCS5B01G247000 chr7D 231585231 231585796 565 False 863.000000 863 94.709000 1560 2107 1 chr7D.!!$F1 547
20 TraesCS5B01G247000 chr7D 566239820 566240999 1179 False 665.000000 1147 89.235000 1 970 2 chr7D.!!$F2 969
21 TraesCS5B01G247000 chr5A 482026807 482027334 527 True 443.500000 761 97.735500 2034 2531 2 chr5A.!!$R1 497

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
811 4207 1.00358 CACATAGTCACAACCCAGCCT 59.996 52.381 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 5791 7.316393 TCCTATTACGATGGATGGAAGAAAT 57.684 36.0 0.0 0.0 0.0 2.17 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
107 108 1.562475 ACAACTAGGGGTGTGTGTGTT 59.438 47.619 0.00 0.00 0.00 3.32
161 1966 1.805943 TGTCAACCATCGACATGCAAG 59.194 47.619 0.00 0.00 38.45 4.01
177 1982 2.937149 TGCAAGTACAAGCGTTGTTACA 59.063 40.909 8.33 0.00 42.22 2.41
206 3411 4.429212 ACGCGCGCATAGTGACCA 62.429 61.111 32.58 0.00 0.00 4.02
270 3475 3.698539 TCTCATCTCGAGCTCAAATGACT 59.301 43.478 15.40 0.00 41.98 3.41
294 3499 9.182214 ACTCTGCATGAACAGTAAAATCATAAT 57.818 29.630 0.00 0.00 38.84 1.28
362 3567 5.431420 TTTCTGAGTGCTCGCAAATTTTA 57.569 34.783 0.00 0.00 0.00 1.52
376 3581 9.507280 CTCGCAAATTTTAATATCACATCTGTT 57.493 29.630 0.00 0.00 0.00 3.16
384 3589 5.824904 AATATCACATCTGTTGAAGTGGC 57.175 39.130 0.00 0.00 40.90 5.01
439 3648 8.730970 AAATGCCATTTTCAAAATCATTTTCG 57.269 26.923 13.19 0.00 31.14 3.46
442 3651 6.927936 TGCCATTTTCAAAATCATTTTCGAGA 59.072 30.769 0.00 0.00 0.00 4.04
444 3653 7.116805 GCCATTTTCAAAATCATTTTCGAGAGT 59.883 33.333 0.00 0.00 0.00 3.24
450 3659 9.748708 TTCAAAATCATTTTCGAGAGTTGATTT 57.251 25.926 16.55 16.55 44.57 2.17
635 3850 4.674101 CGAAGGACACTTTTGCTGTTTGAA 60.674 41.667 0.00 0.00 36.97 2.69
639 3854 4.869861 GGACACTTTTGCTGTTTGAACAAT 59.130 37.500 0.00 0.00 38.66 2.71
647 3862 7.518731 TTTGCTGTTTGAACAATTACTTGTC 57.481 32.000 0.00 0.00 44.83 3.18
686 3901 9.368674 CTTAGCATCAGATATGTAGATTTCCTG 57.631 37.037 0.00 0.00 0.00 3.86
768 3983 9.858247 TCGTTTTATGAAATTATATTCACTCGC 57.142 29.630 0.00 0.00 41.78 5.03
811 4207 1.003580 CACATAGTCACAACCCAGCCT 59.996 52.381 0.00 0.00 0.00 4.58
846 4242 2.119801 ACAAAGCATAGACAGCCCAG 57.880 50.000 0.00 0.00 0.00 4.45
859 4255 3.036429 GCCCAGAAGGATGTCGCCT 62.036 63.158 0.00 0.00 40.93 5.52
876 4272 2.239400 GCCTAGCCCAGAAAAACAACT 58.761 47.619 0.00 0.00 0.00 3.16
879 4275 3.253432 CCTAGCCCAGAAAAACAACTCAC 59.747 47.826 0.00 0.00 0.00 3.51
886 4282 2.098870 GAAAAACAACTCACACGACGC 58.901 47.619 0.00 0.00 0.00 5.19
920 4319 2.262915 GAGGGACACGTCAGCTGG 59.737 66.667 15.13 0.36 0.00 4.85
970 4379 3.134458 GAGTTCTAGGCGATCCCAAATG 58.866 50.000 3.45 0.00 35.39 2.32
1379 5179 6.055588 CGTGGTATGGAATTCTTTGGACTAT 58.944 40.000 5.23 0.00 0.00 2.12
1767 5575 8.524870 AATGATGTTTGAGCATGTACTTTTTC 57.475 30.769 0.00 0.00 28.65 2.29
1849 5657 7.654116 GGTTAGAGCTCTAATATGTCTTGAACC 59.346 40.741 32.99 24.30 40.20 3.62
2331 6305 3.687212 TCTTCACGCTTTCTCACAAACAA 59.313 39.130 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 1.691976 CACACACCCCTAGTTGTGAGA 59.308 52.381 18.38 0.00 38.60 3.27
107 108 3.057876 ACGCTTGACAAAAAGACACACAA 60.058 39.130 0.00 0.00 0.00 3.33
161 1966 4.985044 AGTCATGTAACAACGCTTGTAC 57.015 40.909 4.24 0.00 44.59 2.90
177 1982 1.762222 GCGCGCGTGGATTTAGTCAT 61.762 55.000 32.35 0.00 0.00 3.06
206 3411 1.064166 CCCCTTCATGCTCCTCATTGT 60.064 52.381 0.00 0.00 31.79 2.71
362 3567 4.333649 CGCCACTTCAACAGATGTGATATT 59.666 41.667 11.61 0.00 38.83 1.28
431 3640 8.925161 AAAACAAAATCAACTCTCGAAAATGA 57.075 26.923 0.00 0.00 0.00 2.57
459 3672 7.669427 AGAAATAACATTCATGGAAGTTGCAA 58.331 30.769 4.84 0.00 0.00 4.08
582 3797 2.352960 GCTCAAATGAGATCGGGTGAAC 59.647 50.000 14.43 0.00 44.74 3.18
612 3827 3.108144 CAAACAGCAAAAGTGTCCTTCG 58.892 45.455 0.00 0.00 0.00 3.79
627 3842 5.816919 ACGGACAAGTAATTGTTCAAACAG 58.183 37.500 14.33 3.26 40.50 3.16
635 3850 8.626526 AGATAAAACAAACGGACAAGTAATTGT 58.373 29.630 8.54 8.54 37.97 2.71
639 3854 8.284693 GCTAAGATAAAACAAACGGACAAGTAA 58.715 33.333 0.00 0.00 0.00 2.24
647 3862 7.072177 TCTGATGCTAAGATAAAACAAACGG 57.928 36.000 0.00 0.00 0.00 4.44
727 3942 8.689251 TCATAAAACGAAACACACAAATTGAA 57.311 26.923 0.00 0.00 0.00 2.69
728 3943 8.689251 TTCATAAAACGAAACACACAAATTGA 57.311 26.923 0.00 0.00 0.00 2.57
768 3983 1.332375 GAGAGTACTAGAGCGCACCTG 59.668 57.143 11.47 1.12 0.00 4.00
846 4242 1.069935 GGGCTAGGCGACATCCTTC 59.930 63.158 10.58 0.00 37.66 3.46
859 4255 3.630312 GTGTGAGTTGTTTTTCTGGGCTA 59.370 43.478 0.00 0.00 0.00 3.93
876 4272 4.700365 CTCGCCAGCGTCGTGTGA 62.700 66.667 12.32 0.00 40.74 3.58
909 4308 1.735920 GTCTCAGCCAGCTGACGTG 60.736 63.158 18.14 9.37 46.80 4.49
910 4309 2.653702 GTCTCAGCCAGCTGACGT 59.346 61.111 18.14 0.00 46.80 4.34
1444 5244 4.957759 ACGGAAGATAAAAATCGGTTGG 57.042 40.909 0.00 0.00 0.00 3.77
1767 5575 8.883731 ACCAATCGAAAATAAATAGACACTCAG 58.116 33.333 0.00 0.00 0.00 3.35
1983 5791 7.316393 TCCTATTACGATGGATGGAAGAAAT 57.684 36.000 0.00 0.00 0.00 2.17
2380 6360 8.638873 TGAGTTATATGTATTGTAGACACCAGG 58.361 37.037 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.