Multiple sequence alignment - TraesCS2B01G471200

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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 TraesCS2B01G471200 chr2B 100.000 2549 0 0 1 2549 667900353 667897805 0 4708
1 TraesCS2B01G471200 chr2B 95.409 2004 79 11 554 2549 692955884 692957882 0 3179
2 TraesCS2B01G471200 chr7B 95.643 1997 78 8 561 2549 720989198 720987203 0 3197
3 TraesCS2B01G471200 chr1B 95.689 1995 75 7 565 2549 581717564 581715571 0 3197
4 TraesCS2B01G471200 chr1B 95.668 1985 81 4 569 2549 520844119 520842136 0 3184
5 TraesCS2B01G471200 chr1B 95.624 1988 77 9 569 2549 671392210 671394194 0 3181
6 TraesCS2B01G471200 chr1B 95.341 1996 86 7 559 2549 561526120 561528113 0 3164
7 TraesCS2B01G471200 chr4A 95.498 1999 79 10 558 2549 705529261 705527267 0 3182
8 TraesCS2B01G471200 chr3B 95.569 1986 83 5 569 2549 46395680 46393695 0 3175
9 TraesCS2B01G471200 chr3B 95.434 1993 82 6 565 2549 108092315 108090324 0 3168
10 TraesCS2B01G471200 chr3B 97.711 568 11 1 1 568 658745904 658746469 0 976
11 TraesCS2B01G471200 chr6B 97.887 568 12 0 1 568 193036094 193036661 0 983
12 TraesCS2B01G471200 chr5B 97.887 568 10 1 1 568 464942451 464941886 0 981
13 TraesCS2B01G471200 chr5B 97.711 568 13 0 1 568 283840486 283841053 0 977
14 TraesCS2B01G471200 chr5B 97.707 567 13 0 1 567 598709464 598710030 0 976
15 TraesCS2B01G471200 chrUn 97.715 569 12 1 1 568 64534575 64534007 0 977
16 TraesCS2B01G471200 chr4B 97.711 568 13 0 1 568 146926753 146927320 0 977
17 TraesCS2B01G471200 chr2D 97.711 568 13 0 1 568 528018232 528017665 0 977
18 TraesCS2B01G471200 chr4D 97.711 568 12 1 1 568 44937625 44937059 0 976


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 TraesCS2B01G471200 chr2B 667897805 667900353 2548 True 4708 4708 100.000 1 2549 1 chr2B.!!$R1 2548
1 TraesCS2B01G471200 chr2B 692955884 692957882 1998 False 3179 3179 95.409 554 2549 1 chr2B.!!$F1 1995
2 TraesCS2B01G471200 chr7B 720987203 720989198 1995 True 3197 3197 95.643 561 2549 1 chr7B.!!$R1 1988
3 TraesCS2B01G471200 chr1B 581715571 581717564 1993 True 3197 3197 95.689 565 2549 1 chr1B.!!$R2 1984
4 TraesCS2B01G471200 chr1B 520842136 520844119 1983 True 3184 3184 95.668 569 2549 1 chr1B.!!$R1 1980
5 TraesCS2B01G471200 chr1B 671392210 671394194 1984 False 3181 3181 95.624 569 2549 1 chr1B.!!$F2 1980
6 TraesCS2B01G471200 chr1B 561526120 561528113 1993 False 3164 3164 95.341 559 2549 1 chr1B.!!$F1 1990
7 TraesCS2B01G471200 chr4A 705527267 705529261 1994 True 3182 3182 95.498 558 2549 1 chr4A.!!$R1 1991
8 TraesCS2B01G471200 chr3B 46393695 46395680 1985 True 3175 3175 95.569 569 2549 1 chr3B.!!$R1 1980
9 TraesCS2B01G471200 chr3B 108090324 108092315 1991 True 3168 3168 95.434 565 2549 1 chr3B.!!$R2 1984
10 TraesCS2B01G471200 chr3B 658745904 658746469 565 False 976 976 97.711 1 568 1 chr3B.!!$F1 567
11 TraesCS2B01G471200 chr6B 193036094 193036661 567 False 983 983 97.887 1 568 1 chr6B.!!$F1 567
12 TraesCS2B01G471200 chr5B 464941886 464942451 565 True 981 981 97.887 1 568 1 chr5B.!!$R1 567
13 TraesCS2B01G471200 chr5B 283840486 283841053 567 False 977 977 97.711 1 568 1 chr5B.!!$F1 567
14 TraesCS2B01G471200 chr5B 598709464 598710030 566 False 976 976 97.707 1 567 1 chr5B.!!$F2 566
15 TraesCS2B01G471200 chrUn 64534007 64534575 568 True 977 977 97.715 1 568 1 chrUn.!!$R1 567
16 TraesCS2B01G471200 chr4B 146926753 146927320 567 False 977 977 97.711 1 568 1 chr4B.!!$F1 567
17 TraesCS2B01G471200 chr2D 528017665 528018232 567 True 977 977 97.711 1 568 1 chr2D.!!$R1 567
18 TraesCS2B01G471200 chr4D 44937059 44937625 566 True 976 976 97.711 1 568 1 chr4D.!!$R1 567

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
659 661 0.476338 TTTTGCCCCTAGTCAGTGCA 59.524 50.0 0.0 0.0 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2295 2316 2.02072 TGTGCAAACATTCACGGTCTT 58.979 42.857 0.0 0.0 36.06 3.01 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
78 79 2.422832 TGCATTGCACGCATGAGATTTA 59.577 40.909 7.38 0.00 33.55 1.40
399 400 8.004801 TGGAGTCTTCTAGATTATACATGTGGA 58.995 37.037 9.11 0.00 0.00 4.02
654 656 1.271379 GCTCAGTTTTGCCCCTAGTCA 60.271 52.381 0.00 0.00 0.00 3.41
659 661 0.476338 TTTTGCCCCTAGTCAGTGCA 59.524 50.000 0.00 0.00 0.00 4.57
735 737 0.546747 CCTTACAGGTGGGACCAGGA 60.547 60.000 0.00 0.00 41.95 3.86
955 959 1.520666 GGCGGTTGGAAGCTAGCTA 59.479 57.895 19.70 0.00 0.00 3.32
966 970 2.872388 GCTAGCTATGGAGGGCGCA 61.872 63.158 10.83 0.00 0.00 6.09
967 971 1.978473 CTAGCTATGGAGGGCGCAT 59.022 57.895 10.83 0.00 0.00 4.73
1060 1064 4.760047 GGGCGCGTGTGGAGATGT 62.760 66.667 8.43 0.00 0.00 3.06
1071 1075 3.190744 GTGTGGAGATGTCTGTCTTCGTA 59.809 47.826 0.00 0.00 0.00 3.43
1083 1087 1.068055 GTCTTCGTATGTCCGTGGTGT 60.068 52.381 0.00 0.00 0.00 4.16
1100 1104 1.080093 GTCGGGCGAGTGTTGATCA 60.080 57.895 0.00 0.00 0.00 2.92
1117 1121 3.390967 TGATCAGAGGGTTTCTCACACAA 59.609 43.478 0.00 0.00 44.81 3.33
1143 1147 3.518590 GAACCACAATCGTCCGTTCTAT 58.481 45.455 0.00 0.00 32.36 1.98
1198 1202 1.802069 TGCATCATTTTCGTGGTCGA 58.198 45.000 0.00 0.00 44.66 4.20
1199 1203 2.355197 TGCATCATTTTCGTGGTCGAT 58.645 42.857 0.00 0.00 45.65 3.59
1230 1234 2.742053 CAATCGGTTGATCTGTTCCGTT 59.258 45.455 0.90 7.05 42.95 4.44
1264 1268 3.565307 ACATGCTTCTTTCTTTGGGTCA 58.435 40.909 0.00 0.00 0.00 4.02
1266 1270 4.038402 ACATGCTTCTTTCTTTGGGTCAAG 59.962 41.667 0.00 0.00 0.00 3.02
1316 1320 2.674852 TGCAAGAAGAGCATGACGAATC 59.325 45.455 0.00 0.00 37.02 2.52
2005 2017 0.531200 GGACTCGAACCCAAGATCGT 59.469 55.000 0.00 0.00 39.91 3.73
2221 2239 0.464452 GCTGGTAACCGCTAGGACAT 59.536 55.000 0.00 0.00 41.02 3.06
2536 2563 3.117131 ACCCCCTCTTTTGAATGACAACT 60.117 43.478 0.00 0.00 38.29 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 9.730420 GTCGTATTTATTCATAATTTGGTTGCT 57.270 29.630 0.00 0.00 0.00 3.91
102 103 5.824429 TCAAAGCTTGCATGCTATAATGTC 58.176 37.500 25.56 0.00 43.24 3.06
399 400 7.630005 ATCATCTAGATTCCACCAGATTTCT 57.370 36.000 1.33 0.00 31.20 2.52
561 563 9.321532 GGCAAAAGGATAATTAACCCCTATATT 57.678 33.333 8.09 0.00 0.00 1.28
654 656 1.299926 GAACGAGTCGGTGTGCACT 60.300 57.895 19.41 0.00 0.00 4.40
735 737 1.187567 AAAATTGGCCGCCTCTGCTT 61.188 50.000 11.61 0.00 34.43 3.91
943 947 1.722034 CCCTCCATAGCTAGCTTCCA 58.278 55.000 24.88 5.13 0.00 3.53
966 970 1.956629 AACGGGATCTCAACGCCGAT 61.957 55.000 12.02 0.00 0.00 4.18
967 971 2.552585 GAACGGGATCTCAACGCCGA 62.553 60.000 12.02 0.00 0.00 5.54
1060 1064 1.471287 CCACGGACATACGAAGACAGA 59.529 52.381 0.00 0.00 37.61 3.41
1083 1087 1.215382 CTGATCAACACTCGCCCGA 59.785 57.895 0.00 0.00 0.00 5.14
1092 1096 3.390967 TGTGAGAAACCCTCTGATCAACA 59.609 43.478 0.00 0.00 42.44 3.33
1100 1104 1.760613 TCGTTGTGTGAGAAACCCTCT 59.239 47.619 0.00 0.00 42.44 3.69
1117 1121 0.037605 GGACGATTGTGGTTCCTCGT 60.038 55.000 4.07 4.07 46.09 4.18
1143 1147 1.672030 CCCATTCTCGCTGCACACA 60.672 57.895 0.00 0.00 0.00 3.72
1198 1202 6.204301 CAGATCAACCGATTGCTCAAAGATAT 59.796 38.462 0.00 0.00 34.09 1.63
1199 1203 5.525012 CAGATCAACCGATTGCTCAAAGATA 59.475 40.000 0.00 0.00 34.09 1.98
1230 1234 1.913778 AGCATGTCACCTGCATGAAA 58.086 45.000 7.87 0.00 44.60 2.69
1359 1363 0.755686 CCTCCATCTCTTCTTCCGGG 59.244 60.000 0.00 0.00 0.00 5.73
1581 1585 9.329913 CAACATTTAAACTAGGTGAATTTCTCG 57.670 33.333 0.00 0.00 0.00 4.04
1585 1589 8.919145 TGACCAACATTTAAACTAGGTGAATTT 58.081 29.630 7.84 0.00 0.00 1.82
2005 2017 2.379972 CCTAAACACCACAAACCCACA 58.620 47.619 0.00 0.00 0.00 4.17
2221 2239 4.299586 TCCATGTCAAACTCTTGCCATA 57.700 40.909 0.00 0.00 29.52 2.74
2294 2315 2.223456 TGTGCAAACATTCACGGTCTTG 60.223 45.455 0.00 0.00 36.06 3.02
2295 2316 2.020720 TGTGCAAACATTCACGGTCTT 58.979 42.857 0.00 0.00 36.06 3.01


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

AutoCloner maintained by Alex Coulton.