Multiple sequence alignment - TraesCS2B01G084700

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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 TraesCS2B01G084700 chr2B 100.000 2264 0 0 1 2264 47387783 47385520 0.000000e+00 4181.0
1 TraesCS2B01G084700 chr2B 91.684 1948 122 24 1 1918 29754565 29752628 0.000000e+00 2663.0
2 TraesCS2B01G084700 chr2B 90.090 333 33 0 1928 2260 649655584 649655252 1.240000e-117 433.0
3 TraesCS2B01G084700 chr2B 96.154 78 3 0 2187 2264 42195797 42195874 6.560000e-26 128.0
4 TraesCS2B01G084700 chr2B 85.542 83 8 2 1756 1834 153866795 153866877 1.440000e-12 84.2
5 TraesCS2B01G084700 chr2B 84.706 85 6 4 1756 1834 45597680 45597763 6.700000e-11 78.7
6 TraesCS2B01G084700 chr2B 95.556 45 2 0 1759 1803 47386088 47386044 3.120000e-09 73.1
7 TraesCS2B01G084700 chr7B 92.014 1941 116 24 1 1911 27326578 27328509 0.000000e+00 2689.0
8 TraesCS2B01G084700 chr6A 93.403 1819 111 5 1 1812 74992229 74990413 0.000000e+00 2686.0
9 TraesCS2B01G084700 chr5B 91.889 1948 119 24 1 1918 428831261 428833199 0.000000e+00 2686.0
10 TraesCS2B01G084700 chr5B 91.838 1948 120 24 1 1918 428825810 428827748 0.000000e+00 2680.0
11 TraesCS2B01G084700 chr5B 93.341 1757 109 4 1 1750 454660900 454662655 0.000000e+00 2590.0
12 TraesCS2B01G084700 chr5B 85.183 1559 167 38 660 2168 578836897 578835353 0.000000e+00 1541.0
13 TraesCS2B01G084700 chr5B 85.802 486 49 14 1430 1909 491717805 491717334 4.340000e-137 497.0
14 TraesCS2B01G084700 chr5B 92.582 337 24 1 1928 2264 35440154 35440489 1.220000e-132 483.0
15 TraesCS2B01G084700 chr6B 92.341 1867 122 12 1 1856 687514435 687512579 0.000000e+00 2636.0
16 TraesCS2B01G084700 chr6B 91.278 1949 127 25 1 1918 650646701 650644765 0.000000e+00 2617.0
17 TraesCS2B01G084700 chr6B 93.622 1756 105 3 1 1750 661051609 661053363 0.000000e+00 2615.0
18 TraesCS2B01G084700 chr6B 91.696 855 69 2 1330 2183 425597321 425598174 0.000000e+00 1184.0
19 TraesCS2B01G084700 chr6B 92.239 335 26 0 1926 2260 425598130 425598464 2.030000e-130 475.0
20 TraesCS2B01G084700 chr6B 89.922 258 25 1 1926 2183 425598060 425598316 4.660000e-87 331.0
21 TraesCS2B01G084700 chr6B 94.872 78 4 0 2187 2264 694765745 694765822 3.050000e-24 122.0
22 TraesCS2B01G084700 chr6B 95.946 74 1 1 2187 2260 661054028 661054099 3.950000e-23 119.0
23 TraesCS2B01G084700 chr6B 86.747 83 7 2 1756 1834 661053306 661053388 3.100000e-14 89.8
24 TraesCS2B01G084700 chr6B 93.750 48 3 0 1756 1803 425597684 425597731 3.120000e-09 73.1
25 TraesCS2B01G084700 chr7D 82.230 816 93 26 1257 2023 21073387 21072575 0.000000e+00 656.0
26 TraesCS2B01G084700 chr7D 91.098 337 30 0 1926 2262 16797485 16797149 7.370000e-125 457.0
27 TraesCS2B01G084700 chr1D 94.395 339 19 0 1926 2264 490890712 490891050 2.580000e-144 521.0
28 TraesCS2B01G084700 chr7A 92.035 339 27 0 1926 2264 595030033 595029695 5.660000e-131 477.0
29 TraesCS2B01G084700 chr3B 83.740 492 56 8 1692 2183 40991833 40991366 5.740000e-121 444.0
30 TraesCS2B01G084700 chr3B 96.104 77 3 0 2187 2263 803582546 803582470 2.360000e-25 126.0
31 TraesCS2B01G084700 chr3B 95.556 45 2 0 1759 1803 40991892 40991848 3.120000e-09 73.1


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 TraesCS2B01G084700 chr2B 47385520 47387783 2263 True 2127.050000 4181 97.77800 1 2264 2 chr2B.!!$R3 2263
1 TraesCS2B01G084700 chr2B 29752628 29754565 1937 True 2663.000000 2663 91.68400 1 1918 1 chr2B.!!$R1 1917
2 TraesCS2B01G084700 chr7B 27326578 27328509 1931 False 2689.000000 2689 92.01400 1 1911 1 chr7B.!!$F1 1910
3 TraesCS2B01G084700 chr6A 74990413 74992229 1816 True 2686.000000 2686 93.40300 1 1812 1 chr6A.!!$R1 1811
4 TraesCS2B01G084700 chr5B 428825810 428833199 7389 False 2683.000000 2686 91.86350 1 1918 2 chr5B.!!$F3 1917
5 TraesCS2B01G084700 chr5B 454660900 454662655 1755 False 2590.000000 2590 93.34100 1 1750 1 chr5B.!!$F2 1749
6 TraesCS2B01G084700 chr5B 578835353 578836897 1544 True 1541.000000 1541 85.18300 660 2168 1 chr5B.!!$R2 1508
7 TraesCS2B01G084700 chr6B 687512579 687514435 1856 True 2636.000000 2636 92.34100 1 1856 1 chr6B.!!$R2 1855
8 TraesCS2B01G084700 chr6B 650644765 650646701 1936 True 2617.000000 2617 91.27800 1 1918 1 chr6B.!!$R1 1917
9 TraesCS2B01G084700 chr6B 661051609 661054099 2490 False 941.266667 2615 92.10500 1 2260 3 chr6B.!!$F3 2259
10 TraesCS2B01G084700 chr6B 425597321 425598464 1143 False 515.775000 1184 91.90175 1330 2260 4 chr6B.!!$F2 930
11 TraesCS2B01G084700 chr7D 21072575 21073387 812 True 656.000000 656 82.23000 1257 2023 1 chr7D.!!$R2 766
12 TraesCS2B01G084700 chr3B 40991366 40991892 526 True 258.550000 444 89.64800 1692 2183 2 chr3B.!!$R2 491

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
579 585 0.033504 GGTCGAGGAAGCACAAGTGA 59.966 55.0 4.04 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1533 7005 0.17915 CCTCTCTTCTTGACGAGCCG 60.179 60.0 0.0 0.0 0.0 5.52 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
163 169 1.730064 GCGAAGGCGAGAAACATACAA 59.270 47.619 0.00 0.00 40.82 2.41
164 170 2.351726 GCGAAGGCGAGAAACATACAAT 59.648 45.455 0.00 0.00 40.82 2.71
291 297 4.910913 TGAGTACCATGGCCCTCATATTAA 59.089 41.667 23.38 6.32 34.12 1.40
446 452 0.767998 TATCAACTGTGGGGTGTGCA 59.232 50.000 0.00 0.00 33.62 4.57
455 461 2.985847 GGGTGTGCAGTGAAGGGC 60.986 66.667 0.00 0.00 0.00 5.19
467 473 0.684535 TGAAGGGCGACACAATGAGA 59.315 50.000 0.00 0.00 0.00 3.27
481 487 4.216902 CACAATGAGAGGACATGCAAGAAA 59.783 41.667 0.00 0.00 0.00 2.52
493 499 5.683681 ACATGCAAGAAAAGGAAAACCAAT 58.316 33.333 0.00 0.00 0.00 3.16
499 505 7.281999 TGCAAGAAAAGGAAAACCAATAAAAGG 59.718 33.333 0.00 0.00 0.00 3.11
579 585 0.033504 GGTCGAGGAAGCACAAGTGA 59.966 55.000 4.04 0.00 0.00 3.41
590 596 1.586422 CACAAGTGACAGAGGTGGTG 58.414 55.000 0.00 0.00 0.00 4.17
600 606 2.367648 AGGTGGTGGTGGTGGTCA 60.368 61.111 0.00 0.00 0.00 4.02
728 6125 1.072331 CAAGTGCTAGAGGTGGTGGTT 59.928 52.381 0.00 0.00 0.00 3.67
1177 6647 1.202758 ACCGCAAGAAGTCATGGACAA 60.203 47.619 0.00 0.00 43.02 3.18
1196 6666 5.297527 GGACAAAAGGTAGAAGGTTTTTCGA 59.702 40.000 0.00 0.00 0.00 3.71
1339 6810 4.448210 TGATTTTTATGTAGTCGCCTCCC 58.552 43.478 0.00 0.00 0.00 4.30
1414 6885 6.069440 TCCAAGAGGACCAACATCAAGATTAT 60.069 38.462 0.00 0.00 39.61 1.28
1426 6897 6.119536 ACATCAAGATTATTTACGGAGGCAA 58.880 36.000 0.00 0.00 0.00 4.52
1521 6993 0.247460 CGTGATCAAGAGAGGGCACA 59.753 55.000 2.01 0.00 0.00 4.57
1533 7005 0.538287 AGGGCACACAAAGAGAAGGC 60.538 55.000 0.00 0.00 0.00 4.35
1618 7090 1.880027 GCACGTGACAAGAAGGGAAAT 59.120 47.619 22.23 0.00 0.00 2.17
1677 7151 1.202568 GGCATCGATGATGGACTGTCA 60.203 52.381 29.20 0.00 40.10 3.58
1767 7285 3.123804 AGACATCACGTGTGAACTTGTC 58.876 45.455 19.94 19.94 42.75 3.18
1768 7286 2.210116 ACATCACGTGTGAACTTGTCC 58.790 47.619 16.51 0.00 43.58 4.02
1797 7378 2.736721 CCTTGTGTGGTCATGAACTACG 59.263 50.000 12.94 0.34 41.99 3.51
1808 7389 5.445939 GGTCATGAACTACGTATGTGCAAAG 60.446 44.000 2.64 6.39 0.00 2.77
1862 7501 8.600449 TGTTCATATTTTTGGTTGATTTCCAC 57.400 30.769 0.00 0.00 34.45 4.02
1864 7503 9.271828 GTTCATATTTTTGGTTGATTTCCACTT 57.728 29.630 0.00 0.00 34.45 3.16
1935 7596 1.407656 AACTCTGGTCCAGACGCCAA 61.408 55.000 18.15 0.00 35.39 4.52
1938 7599 2.847234 TGGTCCAGACGCCAAGGT 60.847 61.111 0.00 0.00 0.00 3.50
1975 7636 5.050490 GTCGCTATCCAGAGAGCATTTTTA 58.950 41.667 14.11 0.00 45.29 1.52
1977 7638 4.212214 CGCTATCCAGAGAGCATTTTTACC 59.788 45.833 14.11 0.00 45.29 2.85
1978 7639 4.212214 GCTATCCAGAGAGCATTTTTACCG 59.788 45.833 9.33 0.00 44.47 4.02
2059 7862 6.161381 AGAGCATTTTTCCAGTTTGCTAATG 58.839 36.000 0.00 0.00 43.29 1.90
2066 8091 2.553602 TCCAGTTTGCTAATGTGCACAG 59.446 45.455 25.84 12.89 43.20 3.66
2176 8201 1.335132 GCGTCTGGGTCCCTATCCAA 61.335 60.000 10.00 0.00 34.67 3.53
2184 8209 2.025321 GGGTCCCTATCCAAAGAGCAAA 60.025 50.000 0.00 0.00 0.00 3.68
2256 8308 1.394532 TCTCCACCTCTACCCCTCTT 58.605 55.000 0.00 0.00 0.00 2.85
2260 8312 3.898741 CTCCACCTCTACCCCTCTTATTC 59.101 52.174 0.00 0.00 0.00 1.75
2261 8313 2.973406 CCACCTCTACCCCTCTTATTCC 59.027 54.545 0.00 0.00 0.00 3.01
2262 8314 3.632645 CCACCTCTACCCCTCTTATTCCA 60.633 52.174 0.00 0.00 0.00 3.53
2263 8315 4.235372 CACCTCTACCCCTCTTATTCCAT 58.765 47.826 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 169 3.807071 GCACGGTTTTTCCATCACAAAAT 59.193 39.130 0.00 0.00 35.57 1.82
164 170 3.190874 GCACGGTTTTTCCATCACAAAA 58.809 40.909 0.00 0.00 35.57 2.44
291 297 1.274712 CTTCAGAAGAGGGTCTGGCT 58.725 55.000 3.82 0.00 44.40 4.75
446 452 0.396435 TCATTGTGTCGCCCTTCACT 59.604 50.000 0.00 0.00 35.82 3.41
455 461 1.662629 GCATGTCCTCTCATTGTGTCG 59.337 52.381 0.00 0.00 0.00 4.35
467 473 4.202253 GGTTTTCCTTTTCTTGCATGTCCT 60.202 41.667 0.00 0.00 36.94 3.85
481 487 9.173021 CTTGTTTTCCTTTTATTGGTTTTCCTT 57.827 29.630 0.00 0.00 41.38 3.36
493 499 4.577283 CCTCCACGACTTGTTTTCCTTTTA 59.423 41.667 0.00 0.00 0.00 1.52
499 505 1.602377 CCACCTCCACGACTTGTTTTC 59.398 52.381 0.00 0.00 0.00 2.29
537 543 1.052124 ACCACCGTCACCTCTTCCAA 61.052 55.000 0.00 0.00 0.00 3.53
579 585 2.452064 CCACCACCACCACCTCTGT 61.452 63.158 0.00 0.00 0.00 3.41
590 596 1.123928 CTCCCTCTATGACCACCACC 58.876 60.000 0.00 0.00 0.00 4.61
600 606 1.577736 AGCACTTGTGCTCCCTCTAT 58.422 50.000 20.95 0.00 42.12 1.98
624 630 7.067421 TGTACTCCCTCTATAAACAGTAGCAT 58.933 38.462 0.00 0.00 0.00 3.79
630 636 6.043411 GCACTTGTACTCCCTCTATAAACAG 58.957 44.000 0.00 0.00 0.00 3.16
728 6125 1.070601 TCTAGCACTTGTGCTTGCTCA 59.929 47.619 29.37 13.06 46.31 4.26
1177 6647 5.434408 ACACTCGAAAAACCTTCTACCTTT 58.566 37.500 0.00 0.00 0.00 3.11
1196 6666 2.305635 TCATGTGCATAGTTGGGACACT 59.694 45.455 0.00 0.00 39.44 3.55
1316 6787 5.063880 GGGAGGCGACTACATAAAAATCAT 58.936 41.667 0.98 0.00 46.31 2.45
1317 6788 4.448210 GGGAGGCGACTACATAAAAATCA 58.552 43.478 0.98 0.00 46.31 2.57
1319 6790 3.434596 GGGGGAGGCGACTACATAAAAAT 60.435 47.826 0.98 0.00 46.31 1.82
1426 6897 3.444805 GACTCCTCGAGCAGGCGT 61.445 66.667 8.54 0.00 43.49 5.68
1433 6904 0.734253 CGTGCAAAGGACTCCTCGAG 60.734 60.000 5.13 5.13 30.89 4.04
1507 6979 1.768275 TCTTTGTGTGCCCTCTCTTGA 59.232 47.619 0.00 0.00 0.00 3.02
1521 6993 1.374758 CGAGCCGCCTTCTCTTTGT 60.375 57.895 0.00 0.00 0.00 2.83
1533 7005 0.179150 CCTCTCTTCTTGACGAGCCG 60.179 60.000 0.00 0.00 0.00 5.52
1618 7090 1.879575 ACTGAGCAGTATAGGGCCAA 58.120 50.000 6.18 0.00 40.43 4.52
1625 7097 7.418337 TTCCATTTGTCTACTGAGCAGTATA 57.582 36.000 10.49 1.62 42.44 1.47
1626 7098 5.939764 TCCATTTGTCTACTGAGCAGTAT 57.060 39.130 10.49 0.00 42.44 2.12
1631 7103 3.127721 GCCTTTCCATTTGTCTACTGAGC 59.872 47.826 0.00 0.00 0.00 4.26
1753 7271 1.135527 TCGAAGGACAAGTTCACACGT 59.864 47.619 0.00 0.00 0.00 4.49
1754 7272 1.787155 CTCGAAGGACAAGTTCACACG 59.213 52.381 0.00 0.00 0.00 4.49
1767 7285 0.393077 ACCACACAAGGTCTCGAAGG 59.607 55.000 0.00 0.00 37.28 3.46
1768 7286 3.989104 ACCACACAAGGTCTCGAAG 57.011 52.632 0.00 0.00 37.28 3.79
1862 7501 7.116061 ACTTGTTGCACACACTTTTAAAAAG 57.884 32.000 1.66 0.00 33.98 2.27
1864 7503 6.564873 GCAACTTGTTGCACACACTTTTAAAA 60.565 34.615 27.19 0.00 46.60 1.52
1924 7585 3.319198 GGGACCTTGGCGTCTGGA 61.319 66.667 6.64 0.00 33.07 3.86
1975 7636 1.335496 GTGTGCACATTACCAAACGGT 59.665 47.619 24.69 0.00 40.86 4.83
1977 7638 1.335506 GGGTGTGCACATTACCAAACG 60.336 52.381 24.69 0.00 36.19 3.60
1978 7639 1.683917 TGGGTGTGCACATTACCAAAC 59.316 47.619 27.88 13.15 36.19 2.93
1984 7645 0.953471 GCGTCTGGGTGTGCACATTA 60.953 55.000 24.69 11.37 0.00 1.90
1988 7791 4.927782 TGGCGTCTGGGTGTGCAC 62.928 66.667 10.75 10.75 0.00 4.57
2026 7829 4.785301 TGGAAAAATGCTCTCTGGATAGG 58.215 43.478 0.00 0.00 0.00 2.57
2059 7862 2.209064 CTTGGCATCTGGCTGTGCAC 62.209 60.000 10.75 10.75 43.00 4.57
2066 8091 2.440980 GGGACCTTGGCATCTGGC 60.441 66.667 0.00 0.00 43.74 4.85
2097 8122 4.847198 TGCAAAAATGCTCTCTGGATAGA 58.153 39.130 2.22 0.00 35.49 1.98
2176 8201 6.173339 TCTTATCCACTCGAAATTTGCTCTT 58.827 36.000 0.00 0.00 0.00 2.85
2184 8209 6.543831 CCCAAAGAATCTTATCCACTCGAAAT 59.456 38.462 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.