Multiple sequence alignment - TraesCS6B01G052500

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 TraesCS6B01G052500 chr6B 100.000 2448 0 0 1 2448 31792336 31794783 0.000000e+00 4521.0
1 TraesCS6B01G052500 chr6B 95.979 1517 51 7 777 2286 32024270 32025783 0.000000e+00 2455.0
2 TraesCS6B01G052500 chr6B 94.307 808 44 1 777 1582 32171942 32172749 0.000000e+00 1236.0
3 TraesCS6B01G052500 chr6B 92.131 521 41 0 948 1468 32075907 32076427 0.000000e+00 736.0
4 TraesCS6B01G052500 chr6B 91.555 521 44 0 948 1468 31844251 31844771 0.000000e+00 719.0
5 TraesCS6B01G052500 chr6B 97.391 115 3 0 1468 1582 32087057 32087171 1.920000e-46 196.0
6 TraesCS6B01G052500 chr6B 95.652 115 5 0 1468 1582 31869197 31869311 4.160000e-43 185.0
7 TraesCS6B01G052500 chr1D 95.727 866 37 0 1583 2448 291257727 291256862 0.000000e+00 1395.0
8 TraesCS6B01G052500 chr1D 95.276 868 39 2 1581 2448 112685003 112684138 0.000000e+00 1375.0
9 TraesCS6B01G052500 chr6D 95.718 864 36 1 1585 2448 132563827 132562965 0.000000e+00 1389.0
10 TraesCS6B01G052500 chr6D 93.424 806 47 1 777 1582 17892279 17893078 0.000000e+00 1190.0
11 TraesCS6B01G052500 chr6D 83.394 277 32 10 509 778 379489308 379489039 6.760000e-61 244.0
12 TraesCS6B01G052500 chr3D 95.718 864 35 2 1585 2447 447927402 447928264 0.000000e+00 1389.0
13 TraesCS6B01G052500 chr7D 95.486 864 39 0 1585 2448 259422372 259421509 0.000000e+00 1380.0
14 TraesCS6B01G052500 chr7D 95.392 868 37 3 1583 2448 483983120 483982254 0.000000e+00 1378.0
15 TraesCS6B01G052500 chr7D 85.448 268 31 8 508 772 50422669 50422931 3.100000e-69 272.0
16 TraesCS6B01G052500 chr5D 95.486 864 38 1 1585 2448 142370472 142371334 0.000000e+00 1378.0
17 TraesCS6B01G052500 chr3B 95.486 864 37 1 1585 2448 536347053 536346192 0.000000e+00 1378.0
18 TraesCS6B01G052500 chr3B 93.068 779 11 6 1 778 406537943 406538679 0.000000e+00 1099.0
19 TraesCS6B01G052500 chr6A 93.812 808 43 2 777 1582 18624913 18625715 0.000000e+00 1208.0
20 TraesCS6B01G052500 chr6A 96.639 238 8 0 1 238 250826080 250825843 1.760000e-106 396.0
21 TraesCS6B01G052500 chr6A 83.058 242 21 12 280 521 250825847 250825626 4.130000e-48 202.0
22 TraesCS6B01G052500 chr7B 93.598 781 20 4 1 779 732527079 732526327 0.000000e+00 1138.0
23 TraesCS6B01G052500 chr7B 92.381 735 26 4 1 734 286048202 286048907 0.000000e+00 1020.0
24 TraesCS6B01G052500 chr7B 81.172 239 28 12 538 772 502661697 502661922 2.500000e-40 176.0
25 TraesCS6B01G052500 chr7B 81.172 239 28 12 538 772 502666138 502666363 2.500000e-40 176.0
26 TraesCS6B01G052500 chr7B 85.185 81 9 1 245 325 651389084 651389007 2.020000e-11 80.5
27 TraesCS6B01G052500 chr2B 92.949 780 24 5 1 778 729180741 729181491 0.000000e+00 1107.0
28 TraesCS6B01G052500 chr1B 76.835 436 79 14 908 1325 623851682 623852113 2.450000e-55 226.0
29 TraesCS6B01G052500 chr1B 82.143 252 28 11 530 778 52568596 52568833 1.480000e-47 200.0
30 TraesCS6B01G052500 chr4A 89.032 155 16 1 627 780 647411799 647411645 8.930000e-45 191.0
31 TraesCS6B01G052500 chr4D 91.339 127 10 1 1 126 234402925 234403051 3.240000e-39 172.0


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 TraesCS6B01G052500 chr6B 31792336 31794783 2447 False 4521 4521 100.000 1 2448 1 chr6B.!!$F1 2447
1 TraesCS6B01G052500 chr6B 32024270 32025783 1513 False 2455 2455 95.979 777 2286 1 chr6B.!!$F4 1509
2 TraesCS6B01G052500 chr6B 32171942 32172749 807 False 1236 1236 94.307 777 1582 1 chr6B.!!$F7 805
3 TraesCS6B01G052500 chr6B 32075907 32076427 520 False 736 736 92.131 948 1468 1 chr6B.!!$F5 520
4 TraesCS6B01G052500 chr6B 31844251 31844771 520 False 719 719 91.555 948 1468 1 chr6B.!!$F2 520
5 TraesCS6B01G052500 chr1D 291256862 291257727 865 True 1395 1395 95.727 1583 2448 1 chr1D.!!$R2 865
6 TraesCS6B01G052500 chr1D 112684138 112685003 865 True 1375 1375 95.276 1581 2448 1 chr1D.!!$R1 867
7 TraesCS6B01G052500 chr6D 132562965 132563827 862 True 1389 1389 95.718 1585 2448 1 chr6D.!!$R1 863
8 TraesCS6B01G052500 chr6D 17892279 17893078 799 False 1190 1190 93.424 777 1582 1 chr6D.!!$F1 805
9 TraesCS6B01G052500 chr3D 447927402 447928264 862 False 1389 1389 95.718 1585 2447 1 chr3D.!!$F1 862
10 TraesCS6B01G052500 chr7D 259421509 259422372 863 True 1380 1380 95.486 1585 2448 1 chr7D.!!$R1 863
11 TraesCS6B01G052500 chr7D 483982254 483983120 866 True 1378 1378 95.392 1583 2448 1 chr7D.!!$R2 865
12 TraesCS6B01G052500 chr5D 142370472 142371334 862 False 1378 1378 95.486 1585 2448 1 chr5D.!!$F1 863
13 TraesCS6B01G052500 chr3B 536346192 536347053 861 True 1378 1378 95.486 1585 2448 1 chr3B.!!$R1 863
14 TraesCS6B01G052500 chr3B 406537943 406538679 736 False 1099 1099 93.068 1 778 1 chr3B.!!$F1 777
15 TraesCS6B01G052500 chr6A 18624913 18625715 802 False 1208 1208 93.812 777 1582 1 chr6A.!!$F1 805
16 TraesCS6B01G052500 chr7B 732526327 732527079 752 True 1138 1138 93.598 1 779 1 chr7B.!!$R2 778
17 TraesCS6B01G052500 chr7B 286048202 286048907 705 False 1020 1020 92.381 1 734 1 chr7B.!!$F1 733
18 TraesCS6B01G052500 chr2B 729180741 729181491 750 False 1107 1107 92.949 1 778 1 chr2B.!!$F1 777

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
667 670 1.523938 GGCGGGTCAGCATTAGGTC 60.524 63.158 0.0 0.0 39.27 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2397 2454 0.541998 ACGGGCCGGATCTCATATGA 60.542 55.0 31.78 5.07 0.0 2.15 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
73 74 4.143333 GCAAGCGGCGGAGACCTA 62.143 66.667 9.78 0.00 0.00 3.08
265 266 3.562182 GAGAGAGAGGGGTCTTTAGAGG 58.438 54.545 0.00 0.00 0.00 3.69
376 377 4.592192 CGGCGATGGGATGCGAGT 62.592 66.667 0.00 0.00 0.00 4.18
377 378 2.969238 GGCGATGGGATGCGAGTG 60.969 66.667 0.00 0.00 0.00 3.51
378 379 3.643978 GCGATGGGATGCGAGTGC 61.644 66.667 0.00 0.00 43.20 4.40
500 501 2.370445 ACCTGGAGGCCTCATTCCG 61.370 63.158 33.29 17.31 39.32 4.30
667 670 1.523938 GGCGGGTCAGCATTAGGTC 60.524 63.158 0.00 0.00 39.27 3.85
676 679 2.017049 CAGCATTAGGTCGGAAAAGGG 58.983 52.381 0.00 0.00 0.00 3.95
809 812 2.563620 TCTGCAAACCGTATCACAGGTA 59.436 45.455 0.00 0.00 40.37 3.08
854 859 1.532868 GGATTCTGCCGATATGCACAC 59.467 52.381 0.00 0.00 36.04 3.82
1033 1038 3.064408 CAGCATGGTGTATACAGTTGCTG 59.936 47.826 30.39 30.39 43.02 4.41
1219 1226 5.717078 TGTCATATGTAATAGGTCGTCCC 57.283 43.478 1.90 0.00 31.41 4.46
1243 1250 1.534175 CCCGAGAGCACATACGAAGAC 60.534 57.143 0.00 0.00 0.00 3.01
1312 1319 3.486383 ACTTACCTTGGAATGGTGTGTG 58.514 45.455 0.00 0.00 45.07 3.82
1378 1385 4.728110 TGCTGCCTCAATGCGCCT 62.728 61.111 4.18 0.00 32.42 5.52
1454 1461 3.945921 GCTACCAGGAAAATAAGGGTGTC 59.054 47.826 0.00 0.00 33.14 3.67
1637 1644 2.797087 CGTGTTTGTCACAGTAGGTCGT 60.797 50.000 0.00 0.00 46.44 4.34
1702 1713 7.343057 ACAGAATCAAGATAGTCATACCTGTGA 59.657 37.037 0.00 0.00 0.00 3.58
1718 1729 4.202223 ACCTGTGATGTCGTAGAAGTGTTT 60.202 41.667 0.00 0.00 39.69 2.83
1771 1782 3.617263 GTGTCCACTTCCATGACGATAAC 59.383 47.826 0.00 0.00 0.00 1.89
1854 1865 0.103572 GCCGTTAAGCTATCGGGTCA 59.896 55.000 20.20 0.00 43.77 4.02
1856 1867 1.679680 CCGTTAAGCTATCGGGTCAGA 59.320 52.381 13.87 0.00 40.49 3.27
1865 1876 4.593206 AGCTATCGGGTCAGATTTTGGATA 59.407 41.667 0.00 0.00 32.39 2.59
2315 2372 0.983905 TAGGCCGGCCCATTAACTGA 60.984 55.000 41.72 12.89 36.58 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
265 266 2.825836 CGCCAAGATCCTGTGCCC 60.826 66.667 0.00 0.00 0.00 5.36
359 360 4.592192 ACTCGCATCCCATCGCCG 62.592 66.667 0.00 0.00 0.00 6.46
360 361 2.969238 CACTCGCATCCCATCGCC 60.969 66.667 0.00 0.00 0.00 5.54
361 362 3.643978 GCACTCGCATCCCATCGC 61.644 66.667 0.00 0.00 38.36 4.58
362 363 3.333189 CGCACTCGCATCCCATCG 61.333 66.667 0.00 0.00 38.40 3.84
363 364 1.953138 CTCGCACTCGCATCCCATC 60.953 63.158 0.00 0.00 38.40 3.51
364 365 2.107750 CTCGCACTCGCATCCCAT 59.892 61.111 0.00 0.00 38.40 4.00
365 366 4.147449 CCTCGCACTCGCATCCCA 62.147 66.667 0.00 0.00 38.40 4.37
676 679 2.442126 CCTATTTTGGTACCTCCTCCCC 59.558 54.545 14.36 0.00 37.07 4.81
809 812 7.612065 TTGTATATACAAGCTAGGACCACAT 57.388 36.000 21.73 0.00 40.93 3.21
854 859 7.228706 TCAATGTGATTGATTGATGAGAGGATG 59.771 37.037 0.00 0.00 43.84 3.51
1033 1038 0.958822 AGGCACCCGATGAACAAAAC 59.041 50.000 0.00 0.00 0.00 2.43
1219 1226 1.299468 GTATGTGCTCTCGGGCTCG 60.299 63.158 0.00 0.00 37.82 5.03
1243 1250 4.147322 GCCGTGTTGCGATGTCCG 62.147 66.667 0.00 0.00 44.77 4.79
1312 1319 0.539438 TGGTCACACAATCCCTTGCC 60.539 55.000 0.00 0.00 35.69 4.52
1340 1347 0.808453 AAGCAATGATTGGCATGCGC 60.808 50.000 12.44 0.00 37.28 6.09
1378 1385 4.138290 TCGAATTAAAACAAGGTGCTCCA 58.862 39.130 7.70 0.00 35.89 3.86
1454 1461 9.901172 ACAACTTAAACCTATTTCCTACTATGG 57.099 33.333 0.00 0.00 0.00 2.74
1702 1713 5.538118 TGTCATGAAACACTTCTACGACAT 58.462 37.500 0.00 0.00 33.57 3.06
1771 1782 1.706301 CACTTCTGTGATGCGCGAG 59.294 57.895 12.10 0.00 46.55 5.03
1854 1865 5.286267 ACGGGTTATCGTATCCAAAATCT 57.714 39.130 0.00 0.00 41.98 2.40
1856 1867 9.211485 CTATTAACGGGTTATCGTATCCAAAAT 57.789 33.333 0.00 0.00 43.07 1.82
1865 1876 2.037641 GGGGCTATTAACGGGTTATCGT 59.962 50.000 0.00 0.00 46.08 3.73
2233 2290 2.350498 CCGTTAATGTCGGCGAAATCTT 59.650 45.455 13.86 1.76 41.48 2.40
2397 2454 0.541998 ACGGGCCGGATCTCATATGA 60.542 55.000 31.78 5.07 0.00 2.15


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

AutoCloner maintained by Alex Coulton.