Multiple sequence alignment - TraesCS2B01G261600

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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 TraesCS2B01G261600 chr2B 100.000 2433 0 0 1 2433 336571777 336574209 0 4494
1 TraesCS2B01G261600 chr2B 91.069 2452 177 24 1 2433 395994187 395996615 0 3277
2 TraesCS2B01G261600 chr2B 90.872 2443 169 30 2 2433 721096775 721094376 0 3227
3 TraesCS2B01G261600 chr3B 91.496 2446 171 21 1 2433 502065539 502063118 0 3330
4 TraesCS2B01G261600 chr1B 91.173 2447 161 21 1 2433 246844730 246842325 0 3271
5 TraesCS2B01G261600 chr7D 92.386 2167 143 16 1 2156 424431240 424429085 0 3068
6 TraesCS2B01G261600 chr7D 89.843 1979 142 33 1 1951 574344817 574342870 0 2486
7 TraesCS2B01G261600 chr3D 91.712 2220 136 29 1 2196 609658002 609660197 0 3037
8 TraesCS2B01G261600 chr3D 89.898 1970 139 32 1 1951 272546626 272548554 0 2481
9 TraesCS2B01G261600 chr5B 91.821 1834 132 12 610 2433 435355969 435357794 0 2540
10 TraesCS2B01G261600 chr5B 90.784 1888 138 18 554 2433 74815837 74817696 0 2490
11 TraesCS2B01G261600 chr5B 90.678 1888 140 18 554 2433 74793741 74795600 0 2479
12 TraesCS2B01G261600 chr5B 92.683 861 53 9 1580 2433 612347463 612346606 0 1232
13 TraesCS2B01G261600 chr5D 90.952 1890 139 23 1 1877 129952208 129950338 0 2514
14 TraesCS2B01G261600 chr5D 92.849 1706 104 18 1 1694 217939316 217937617 0 2459
15 TraesCS2B01G261600 chr7B 91.801 1549 104 12 893 2433 555201884 555203417 0 2135
16 TraesCS2B01G261600 chr6B 93.074 823 50 5 1613 2433 450671248 450672065 0 1197


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 TraesCS2B01G261600 chr2B 336571777 336574209 2432 False 4494 4494 100.000 1 2433 1 chr2B.!!$F1 2432
1 TraesCS2B01G261600 chr2B 395994187 395996615 2428 False 3277 3277 91.069 1 2433 1 chr2B.!!$F2 2432
2 TraesCS2B01G261600 chr2B 721094376 721096775 2399 True 3227 3227 90.872 2 2433 1 chr2B.!!$R1 2431
3 TraesCS2B01G261600 chr3B 502063118 502065539 2421 True 3330 3330 91.496 1 2433 1 chr3B.!!$R1 2432
4 TraesCS2B01G261600 chr1B 246842325 246844730 2405 True 3271 3271 91.173 1 2433 1 chr1B.!!$R1 2432
5 TraesCS2B01G261600 chr7D 424429085 424431240 2155 True 3068 3068 92.386 1 2156 1 chr7D.!!$R1 2155
6 TraesCS2B01G261600 chr7D 574342870 574344817 1947 True 2486 2486 89.843 1 1951 1 chr7D.!!$R2 1950
7 TraesCS2B01G261600 chr3D 609658002 609660197 2195 False 3037 3037 91.712 1 2196 1 chr3D.!!$F2 2195
8 TraesCS2B01G261600 chr3D 272546626 272548554 1928 False 2481 2481 89.898 1 1951 1 chr3D.!!$F1 1950
9 TraesCS2B01G261600 chr5B 435355969 435357794 1825 False 2540 2540 91.821 610 2433 1 chr5B.!!$F3 1823
10 TraesCS2B01G261600 chr5B 74815837 74817696 1859 False 2490 2490 90.784 554 2433 1 chr5B.!!$F2 1879
11 TraesCS2B01G261600 chr5B 74793741 74795600 1859 False 2479 2479 90.678 554 2433 1 chr5B.!!$F1 1879
12 TraesCS2B01G261600 chr5B 612346606 612347463 857 True 1232 1232 92.683 1580 2433 1 chr5B.!!$R1 853
13 TraesCS2B01G261600 chr5D 129950338 129952208 1870 True 2514 2514 90.952 1 1877 1 chr5D.!!$R1 1876
14 TraesCS2B01G261600 chr5D 217937617 217939316 1699 True 2459 2459 92.849 1 1694 1 chr5D.!!$R2 1693
15 TraesCS2B01G261600 chr7B 555201884 555203417 1533 False 2135 2135 91.801 893 2433 1 chr7B.!!$F1 1540
16 TraesCS2B01G261600 chr6B 450671248 450672065 817 False 1197 1197 93.074 1613 2433 1 chr6B.!!$F1 820

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
639 675 0.313987 GTCAAAGCCTTGGAAACCCG 59.686 55.0 0.0 0.0 33.01 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1896 1975 0.240945 GCCAGCGTGTGCACTATTTT 59.759 50.0 19.41 0.0 46.23 1.82 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
64 71 3.421844 ACCTACTCCAAATGAGCCAAAC 58.578 45.455 0.00 0.00 45.61 2.93
214 227 7.754924 ACACGTTTAGCATATGAAAATGGAAAG 59.245 33.333 19.29 12.28 0.00 2.62
357 374 3.982475 ACGTGATAGCTCATATGTGTGG 58.018 45.455 1.90 0.00 32.98 4.17
501 528 1.898902 ACCTCGATCGTGCTAGCTAT 58.101 50.000 17.23 6.88 0.00 2.97
593 627 7.801783 ACGAAAGACGAAGGTTTCATATTTTTC 59.198 33.333 0.00 0.00 45.77 2.29
594 628 7.006210 CGAAAGACGAAGGTTTCATATTTTTCG 59.994 37.037 0.00 3.24 45.77 3.46
595 629 7.429636 AAGACGAAGGTTTCATATTTTTCGA 57.570 32.000 10.84 0.00 39.60 3.71
596 630 7.611213 AGACGAAGGTTTCATATTTTTCGAT 57.389 32.000 10.84 0.00 39.60 3.59
639 675 0.313987 GTCAAAGCCTTGGAAACCCG 59.686 55.000 0.00 0.00 33.01 5.28
700 738 2.897326 TGCCTAACACTAGCTCTGAACA 59.103 45.455 0.00 0.00 0.00 3.18
709 747 5.047943 ACACTAGCTCTGAACATTAGTCGTT 60.048 40.000 0.00 0.00 0.00 3.85
720 758 5.769484 ACATTAGTCGTTCGATCATACCT 57.231 39.130 0.00 0.00 0.00 3.08
721 759 5.520632 ACATTAGTCGTTCGATCATACCTG 58.479 41.667 0.00 0.00 0.00 4.00
723 761 5.823209 TTAGTCGTTCGATCATACCTGAA 57.177 39.130 0.00 0.00 34.37 3.02
732 770 3.609853 GATCATACCTGAACACCAAGCA 58.390 45.455 0.00 0.00 34.37 3.91
776 815 1.208165 AAGGAATTCCGAGGGCAGGT 61.208 55.000 18.82 0.00 42.08 4.00
790 829 3.946201 AGGTTGCGTGCAGGCTCT 61.946 61.111 29.43 20.67 0.00 4.09
906 945 0.729116 TTCTGCTGCTTATTCTGCGC 59.271 50.000 0.00 0.00 34.22 6.09
942 981 3.933955 CACTCCTCATCTGCTTCTTCTTG 59.066 47.826 0.00 0.00 0.00 3.02
944 983 4.041444 ACTCCTCATCTGCTTCTTCTTGTT 59.959 41.667 0.00 0.00 0.00 2.83
996 1035 1.380785 TTCTCCGGCGACTATGGGT 60.381 57.895 9.30 0.00 0.00 4.51
1018 1057 3.447229 TGATATGTCGAGCTCCACTTCAA 59.553 43.478 12.86 0.00 0.00 2.69
1045 1084 0.981277 CCCCTCGTGGACCCAGTATT 60.981 60.000 4.76 0.00 35.39 1.89
1075 1114 0.531532 CATGGAGCGATGTCCTGACC 60.532 60.000 0.00 0.00 37.52 4.02
1198 1240 7.716998 GGCAGGTTAGATCTCATGATTTTTCTA 59.283 37.037 0.00 0.00 32.19 2.10
1415 1462 0.770499 TCTGACAGTTGGGGATGCAA 59.230 50.000 1.59 0.00 0.00 4.08
1567 1623 1.893137 TGCTGGTCATCACTCGTTAGT 59.107 47.619 0.00 0.00 35.91 2.24
1607 1663 4.469586 TGTCATGTGCTCTAGGATTTGGTA 59.530 41.667 0.00 0.00 0.00 3.25
1610 1666 6.543831 GTCATGTGCTCTAGGATTTGGTAAAT 59.456 38.462 0.00 0.00 0.00 1.40
1613 1669 7.156876 TGTGCTCTAGGATTTGGTAAATTTG 57.843 36.000 0.00 0.00 0.00 2.32
1615 1671 7.029563 GTGCTCTAGGATTTGGTAAATTTGTG 58.970 38.462 0.00 0.00 0.00 3.33
1633 1690 3.977427 TGTGGATCATGTGCTATACGAC 58.023 45.455 0.00 0.00 0.00 4.34
1733 1801 6.587206 TGCTTAATTTGTGGATCATGTCAA 57.413 33.333 0.00 0.00 0.00 3.18
1833 1912 6.481976 CCCAAATTGAAACCCTTGAAACTAAC 59.518 38.462 0.00 0.00 0.00 2.34
1838 1917 6.503560 TGAAACCCTTGAAACTAACCTCTA 57.496 37.500 0.00 0.00 0.00 2.43
1848 1927 0.464452 CTAACCTCTAGTTGGGCCGG 59.536 60.000 0.00 0.00 39.67 6.13
1886 1965 4.038642 TGTCAAAGGCCCACAAAGATAAAC 59.961 41.667 0.00 0.00 0.00 2.01
1890 1969 1.132453 GGCCCACAAAGATAAACGAGC 59.868 52.381 0.00 0.00 0.00 5.03
1895 1974 4.451900 CCACAAAGATAAACGAGCCCTAT 58.548 43.478 0.00 0.00 0.00 2.57
1896 1975 5.454187 CCCACAAAGATAAACGAGCCCTATA 60.454 44.000 0.00 0.00 0.00 1.31
1987 2069 5.696270 GCCAAACAAAAATACTTCCTCCTTG 59.304 40.000 0.00 0.00 0.00 3.61
2215 2300 8.087982 AGTAGTGCATATGGTAAATCGATTTG 57.912 34.615 29.20 14.98 0.00 2.32
2371 2462 5.449297 TCATGATATCCACCTGAAACCAA 57.551 39.130 0.00 0.00 0.00 3.67
2372 2463 5.825532 TCATGATATCCACCTGAAACCAAA 58.174 37.500 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 181 8.922058 TGCTAAACGTGTTTTTAATGGTTTTA 57.078 26.923 2.97 0.00 34.23 1.52
197 210 9.316730 TGAATTTAGCTTTCCATTTTCATATGC 57.683 29.630 0.00 0.00 0.00 3.14
240 253 7.486802 AAAATCACCAAAGCTTGATTTCAAG 57.513 32.000 19.41 14.57 46.81 3.02
292 307 3.310435 GGAGAGAGGTAGGGTTCCCTTTA 60.310 52.174 16.05 0.00 37.64 1.85
475 502 2.550978 AGCACGATCGAGGTTAAATGG 58.449 47.619 24.34 0.00 0.00 3.16
481 508 1.676746 TAGCTAGCACGATCGAGGTT 58.323 50.000 24.34 13.58 0.00 3.50
602 638 7.814587 GGCTTTGACTGAGCATAACTAATTTTT 59.185 33.333 0.00 0.00 41.89 1.94
603 639 7.177392 AGGCTTTGACTGAGCATAACTAATTTT 59.823 33.333 0.00 0.00 41.89 1.82
639 675 0.673985 GGGTTTTGAGCTGGTCAACC 59.326 55.000 20.72 19.25 45.23 3.77
700 738 6.183360 TGTTCAGGTATGATCGAACGACTAAT 60.183 38.462 0.00 0.00 40.47 1.73
709 747 3.678806 GCTTGGTGTTCAGGTATGATCGA 60.679 47.826 0.00 0.00 34.73 3.59
720 758 0.395586 AGGCTGTTGCTTGGTGTTCA 60.396 50.000 0.00 0.00 39.59 3.18
721 759 0.312102 GAGGCTGTTGCTTGGTGTTC 59.688 55.000 0.00 0.00 39.59 3.18
723 761 1.893808 CGAGGCTGTTGCTTGGTGT 60.894 57.895 0.00 0.00 39.59 4.16
732 770 1.194781 AGACCACATCCGAGGCTGTT 61.195 55.000 0.00 0.00 0.00 3.16
790 829 0.809636 CCATGTGATCTAACGGCGCA 60.810 55.000 10.83 0.00 0.00 6.09
799 838 1.826024 GGAGCCGTCCATGTGATCT 59.174 57.895 0.00 0.00 43.31 2.75
853 892 0.179067 AACCAACAAGTCTCGCGGAA 60.179 50.000 6.13 0.00 0.00 4.30
906 945 1.216710 GAGTGGCTCCTCTCGTTGG 59.783 63.158 2.66 0.00 0.00 3.77
928 967 2.079925 GCCGAACAAGAAGAAGCAGAT 58.920 47.619 0.00 0.00 0.00 2.90
942 981 2.100603 CTCCTCTCGTCGCCGAAC 59.899 66.667 0.00 0.00 43.69 3.95
996 1035 3.023832 TGAAGTGGAGCTCGACATATCA 58.976 45.455 27.72 23.42 0.00 2.15
1045 1084 1.685224 GCTCCATGGGAAGTGGACA 59.315 57.895 13.02 0.00 40.72 4.02
1166 1205 2.293184 TGAGATCTAACCTGCCCCTCTT 60.293 50.000 0.00 0.00 0.00 2.85
1232 1278 4.778213 TGAACCCTAAATCCCAGATCTG 57.222 45.455 16.24 16.24 0.00 2.90
1282 1328 5.015515 TCATCCAGCCATTCAAAATGTGTA 58.984 37.500 0.00 0.00 0.00 2.90
1415 1462 6.658555 TCTTCTTTATTCCCCCTTCAGATT 57.341 37.500 0.00 0.00 0.00 2.40
1567 1623 6.371271 CACATGACACCACACTAATAACATCA 59.629 38.462 0.00 0.00 0.00 3.07
1607 1663 6.542005 TCGTATAGCACATGATCCACAAATTT 59.458 34.615 0.00 0.00 0.00 1.82
1610 1666 4.808895 GTCGTATAGCACATGATCCACAAA 59.191 41.667 0.00 0.00 0.00 2.83
1613 1669 4.244425 AGTCGTATAGCACATGATCCAC 57.756 45.455 0.00 0.00 0.00 4.02
1615 1671 3.430218 GCAAGTCGTATAGCACATGATCC 59.570 47.826 0.00 0.00 0.00 3.36
1633 1690 6.183360 GCACATGATCCACAAATTTAAGCAAG 60.183 38.462 0.00 0.00 0.00 4.01
1799 1878 3.580895 GGTTTCAATTTGGGCCCTAGAAA 59.419 43.478 25.70 20.53 0.00 2.52
1833 1912 3.083997 AGCCGGCCCAACTAGAGG 61.084 66.667 26.15 0.00 0.00 3.69
1838 1917 2.361610 CAATGAGCCGGCCCAACT 60.362 61.111 26.15 6.43 0.00 3.16
1886 1965 4.211374 GTGTGCACTATTTTATAGGGCTCG 59.789 45.833 19.41 0.00 43.96 5.03
1890 1969 4.024893 CAGCGTGTGCACTATTTTATAGGG 60.025 45.833 19.41 0.00 46.23 3.53
1895 1974 1.466950 GCCAGCGTGTGCACTATTTTA 59.533 47.619 19.41 0.00 46.23 1.52
1896 1975 0.240945 GCCAGCGTGTGCACTATTTT 59.759 50.000 19.41 0.00 46.23 1.82
1987 2069 4.181578 ACGTGCATGTCCTATAAACTGAC 58.818 43.478 5.51 0.00 0.00 3.51
2143 2227 0.815734 ACGTGGTTCTAGGTCATCGG 59.184 55.000 0.00 0.00 0.00 4.18
2215 2300 1.000274 GACATGGGCAAGTCCAACAAC 60.000 52.381 0.00 0.00 40.62 3.32
2296 2381 4.535526 AAATCAAGGGACCCAAAAATCG 57.464 40.909 14.60 0.00 0.00 3.34
2361 2452 9.639601 GGACTTTATTTTAGATTTGGTTTCAGG 57.360 33.333 0.00 0.00 0.00 3.86
2371 2462 5.124936 GTGCCACCGGACTTTATTTTAGATT 59.875 40.000 9.46 0.00 0.00 2.40
2372 2463 4.638865 GTGCCACCGGACTTTATTTTAGAT 59.361 41.667 9.46 0.00 0.00 1.98
2404 2495 4.715792 ACATGCTCTCTAGATGGATATGGG 59.284 45.833 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.