Multiple sequence alignment - TraesCS3D01G128100

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 TraesCS3D01G128100 chr3D 100.000 2397 0 0 1 2397 86081408 86079012 0.000000e+00 4427
1 TraesCS3D01G128100 chr7D 96.710 2401 73 6 1 2397 180439621 180442019 0.000000e+00 3991
2 TraesCS3D01G128100 chr3A 96.501 2401 79 5 1 2397 703853573 703851174 0.000000e+00 3964
3 TraesCS3D01G128100 chr3A 96.226 1113 40 2 655 1766 171150785 171151896 0.000000e+00 1821
4 TraesCS3D01G128100 chr6D 96.168 2401 83 6 1 2397 150886680 150884285 0.000000e+00 3916
5 TraesCS3D01G128100 chr2B 94.730 2296 111 10 104 2393 696855918 696858209 0.000000e+00 3561
6 TraesCS3D01G128100 chr2B 90.991 111 9 1 1878 1988 452383627 452383518 5.340000e-32 148
7 TraesCS3D01G128100 chr4A 93.378 2401 137 7 1 2397 644923846 644921464 0.000000e+00 3533
8 TraesCS3D01G128100 chr3B 92.125 2400 147 13 2 2397 702151889 702149528 0.000000e+00 3347
9 TraesCS3D01G128100 chr7B 94.354 1895 103 4 1 1892 30075427 30073534 0.000000e+00 2904
10 TraesCS3D01G128100 chr5A 93.758 1618 67 10 148 1762 241459561 241457975 0.000000e+00 2398
11 TraesCS3D01G128100 chr5A 93.878 833 47 3 1 831 667547777 667548607 0.000000e+00 1253
12 TraesCS3D01G128100 chr2A 93.572 1618 66 7 148 1762 111272867 111271285 0.000000e+00 2377
13 TraesCS3D01G128100 chr2A 94.859 389 19 1 2010 2397 545065869 545066257 7.330000e-170 606
14 TraesCS3D01G128100 chr1A 91.797 512 34 6 2 509 548669992 548670499 0.000000e+00 706
15 TraesCS3D01G128100 chr4B 96.124 387 14 1 2012 2397 145028664 145029050 4.350000e-177 630
16 TraesCS3D01G128100 chr4B 95.103 388 19 0 2010 2397 20175992 20176379 1.580000e-171 612
17 TraesCS3D01G128100 chr5D 84.211 399 18 13 1597 1972 483324111 483324487 1.760000e-91 346
18 TraesCS3D01G128100 chr7A 93.396 106 6 1 1880 1985 5194573 5194677 3.190000e-34 156


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 TraesCS3D01G128100 chr3D 86079012 86081408 2396 True 4427 4427 100.000 1 2397 1 chr3D.!!$R1 2396
1 TraesCS3D01G128100 chr7D 180439621 180442019 2398 False 3991 3991 96.710 1 2397 1 chr7D.!!$F1 2396
2 TraesCS3D01G128100 chr3A 703851174 703853573 2399 True 3964 3964 96.501 1 2397 1 chr3A.!!$R1 2396
3 TraesCS3D01G128100 chr3A 171150785 171151896 1111 False 1821 1821 96.226 655 1766 1 chr3A.!!$F1 1111
4 TraesCS3D01G128100 chr6D 150884285 150886680 2395 True 3916 3916 96.168 1 2397 1 chr6D.!!$R1 2396
5 TraesCS3D01G128100 chr2B 696855918 696858209 2291 False 3561 3561 94.730 104 2393 1 chr2B.!!$F1 2289
6 TraesCS3D01G128100 chr4A 644921464 644923846 2382 True 3533 3533 93.378 1 2397 1 chr4A.!!$R1 2396
7 TraesCS3D01G128100 chr3B 702149528 702151889 2361 True 3347 3347 92.125 2 2397 1 chr3B.!!$R1 2395
8 TraesCS3D01G128100 chr7B 30073534 30075427 1893 True 2904 2904 94.354 1 1892 1 chr7B.!!$R1 1891
9 TraesCS3D01G128100 chr5A 241457975 241459561 1586 True 2398 2398 93.758 148 1762 1 chr5A.!!$R1 1614
10 TraesCS3D01G128100 chr5A 667547777 667548607 830 False 1253 1253 93.878 1 831 1 chr5A.!!$F1 830
11 TraesCS3D01G128100 chr2A 111271285 111272867 1582 True 2377 2377 93.572 148 1762 1 chr2A.!!$R1 1614
12 TraesCS3D01G128100 chr1A 548669992 548670499 507 False 706 706 91.797 2 509 1 chr1A.!!$F1 507

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
22 23 0.395311 ATCCTCTTCGTCGGCCACTA 60.395 55.0 2.24 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 2013 0.890996 CGCCTGAGCAAAAAGGGAGT 60.891 55.0 0.0 0.0 39.83 3.85 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
22 23 0.395311 ATCCTCTTCGTCGGCCACTA 60.395 55.000 2.24 0.00 0.00 2.74
24 25 1.226323 CTCTTCGTCGGCCACTACG 60.226 63.158 14.35 14.35 40.40 3.51
127 128 1.812507 AACGTAAGATTCCGGCGCC 60.813 57.895 19.07 19.07 43.62 6.53
131 132 3.394635 TAAGATTCCGGCGCCCCAC 62.395 63.158 23.46 8.25 0.00 4.61
279 280 6.397272 TGCAATTTTCTGAAGCCGATTTAAT 58.603 32.000 0.00 0.00 0.00 1.40
363 366 2.014128 CGCCAGGGTAAAGGTGTTATG 58.986 52.381 0.00 0.00 0.00 1.90
368 371 5.566032 GCCAGGGTAAAGGTGTTATGTTTTC 60.566 44.000 0.00 0.00 0.00 2.29
588 593 1.980052 CCGCCCTACAAGAACCTCA 59.020 57.895 0.00 0.00 0.00 3.86
630 636 1.228245 GGCAAGACCACCTGCTTCA 60.228 57.895 0.00 0.00 38.86 3.02
1014 1020 2.420547 GGTGTTGATGCAGGCAGATCTA 60.421 50.000 0.00 0.00 0.00 1.98
1087 1093 1.296392 TGGGTCACCATGAAGCGAG 59.704 57.895 0.00 0.00 43.37 5.03
1118 1126 2.474112 CCCTACCCTTACAGCTGGTTA 58.526 52.381 19.93 0.00 33.55 2.85
1155 1163 5.263599 TGTAGATTTGATGGGTTCAGCAAT 58.736 37.500 0.00 0.00 46.75 3.56
1157 1165 6.889177 TGTAGATTTGATGGGTTCAGCAATTA 59.111 34.615 0.00 0.00 46.75 1.40
1205 1214 0.388520 CGTCGATGAAGTGTCAGGCA 60.389 55.000 0.00 0.00 37.14 4.75
1221 1230 3.152341 CAGGCAAGGTTGAAGAAGATGT 58.848 45.455 0.00 0.00 0.00 3.06
1341 1350 0.304705 GGTTCGGCATTATGTCTGCG 59.695 55.000 0.00 0.00 40.59 5.18
1464 1473 2.010145 TTCCTTCGTGTATCTGCTGC 57.990 50.000 0.00 0.00 0.00 5.25
1478 1487 2.291465 TCTGCTGCATGAACTGAAACAC 59.709 45.455 1.31 0.00 0.00 3.32
1658 1678 8.239998 GGTCTTTTCTGATAATGGAAGAACTTG 58.760 37.037 0.00 0.00 30.32 3.16
1755 1775 2.348666 GGAGTACATGCTTGTAACAGCG 59.651 50.000 13.52 0.00 43.37 5.18
1993 2013 1.065410 TTGCCCTCAACCTTCTCCCA 61.065 55.000 0.00 0.00 0.00 4.37
2026 2046 4.722700 GGCGGTGGTGCACATCCT 62.723 66.667 20.43 0.00 35.86 3.24
2083 2103 2.608268 GAAGAAGGACTACAAGGACGC 58.392 52.381 0.00 0.00 0.00 5.19
2126 2146 2.094659 CGCCGTCGACATGAAGCTT 61.095 57.895 17.16 0.00 38.10 3.74
2293 2314 4.528987 TGTGTCTTGCCTGGTAGTATACAA 59.471 41.667 5.50 0.00 45.43 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 2.046314 CCCGAGCCCAACGAACAT 60.046 61.111 0.00 0.00 0.00 2.71
82 83 0.912486 GTCCCCTTGTACATCCTGCT 59.088 55.000 0.00 0.00 0.00 4.24
127 128 1.026718 GCGTGATCCAGAAAGGTGGG 61.027 60.000 0.00 0.00 38.26 4.61
131 132 1.135575 GCAAAGCGTGATCCAGAAAGG 60.136 52.381 0.00 0.00 39.47 3.11
279 280 6.347321 CGCAACATCAGTGTTTGTAGACATAA 60.347 38.462 2.63 0.00 46.07 1.90
363 366 5.600908 TGTAGTATCAAGCAACCGAAAAC 57.399 39.130 0.00 0.00 0.00 2.43
368 371 4.929808 AGAGTTTGTAGTATCAAGCAACCG 59.070 41.667 0.00 0.00 32.42 4.44
588 593 2.438434 GTTGTGCGCCTGGGCTAT 60.438 61.111 4.18 0.00 39.32 2.97
630 636 2.110627 GCTGAGCATGCCGAGGAT 59.889 61.111 15.66 0.00 0.00 3.24
665 671 2.367512 ATGGCCTGGGGAGTCCTC 60.368 66.667 9.58 5.35 36.20 3.71
812 818 8.062536 ACTGACTTGTCCTATACTAGAAAGGAT 58.937 37.037 13.17 1.37 41.34 3.24
817 823 8.687242 CATTCACTGACTTGTCCTATACTAGAA 58.313 37.037 0.00 0.00 35.26 2.10
1014 1020 1.004044 CTGGTCAGCTTGGTCAGGAAT 59.996 52.381 0.00 0.00 0.00 3.01
1087 1093 1.382833 GGGTAGGGGGTCTCTCACC 60.383 68.421 0.00 0.00 45.97 4.02
1118 1126 3.806949 ATCTACAACCCACACCACATT 57.193 42.857 0.00 0.00 0.00 2.71
1155 1163 6.818142 ACATCGAACAACTCATCACATCATAA 59.182 34.615 0.00 0.00 0.00 1.90
1157 1165 5.064325 CACATCGAACAACTCATCACATCAT 59.936 40.000 0.00 0.00 0.00 2.45
1205 1214 4.608948 ACTCGACATCTTCTTCAACCTT 57.391 40.909 0.00 0.00 0.00 3.50
1221 1230 1.381327 CAGGCTCCCCCTTACTCGA 60.381 63.158 0.00 0.00 43.06 4.04
1268 1277 2.172293 GGAGATGTTCCTCTTGCCATCT 59.828 50.000 0.00 0.00 44.95 2.90
1341 1350 3.259123 AGAATCAAGGCAAAACACATCCC 59.741 43.478 0.00 0.00 0.00 3.85
1464 1473 3.480470 ACTGGAGGTGTTTCAGTTCATG 58.520 45.455 0.00 0.00 38.44 3.07
1658 1678 5.897377 ACCAACAACCAGCAGATTAATAC 57.103 39.130 0.00 0.00 0.00 1.89
1755 1775 8.993121 TCTGAATTCTGAAATGACTAGTTCAAC 58.007 33.333 12.17 0.00 40.01 3.18
1958 1978 1.077265 CAAGGTTCTGCCCCCATGT 59.923 57.895 0.00 0.00 38.26 3.21
1993 2013 0.890996 CGCCTGAGCAAAAAGGGAGT 60.891 55.000 0.00 0.00 39.83 3.85
2026 2046 1.891919 GACACCTTGAACTGGCGCA 60.892 57.895 10.83 0.00 0.00 6.09
2083 2103 1.935327 GACGACCTGGGAGAACCTCG 61.935 65.000 0.00 0.00 41.11 4.63
2126 2146 1.292242 AGCCTCTCAAGGTCATCCCTA 59.708 52.381 0.00 0.00 45.47 3.53


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

AutoCloner maintained by Alex Coulton.