Multiple sequence alignment - TraesCS2B01G395800

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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 TraesCS2B01G395800 chr2B 100.000 2531 0 0 1 2531 561260403 561257873 0 4674
1 TraesCS2B01G395800 chr2D 93.489 1797 92 7 1 1787 478697767 478699548 0 2647
2 TraesCS2B01G395800 chr2A 92.806 1126 57 8 657 1766 621516331 621515214 0 1609
3 TraesCS2B01G395800 chr2A 88.404 664 45 7 1 660 621516990 621516355 0 771
4 TraesCS2B01G395800 chr5B 91.598 726 56 4 1808 2531 400552866 400552144 0 998
5 TraesCS2B01G395800 chr5B 90.833 720 61 4 1813 2531 492104259 492104974 0 959
6 TraesCS2B01G395800 chr7B 91.643 718 57 3 1813 2529 428923810 428923095 0 990
7 TraesCS2B01G395800 chr7B 90.746 724 63 3 1811 2531 591524006 591524728 0 963
8 TraesCS2B01G395800 chr3D 91.334 727 56 7 1808 2531 228165253 228165975 0 987
9 TraesCS2B01G395800 chr5D 91.209 728 58 6 1808 2530 106691411 106690685 0 985
10 TraesCS2B01G395800 chr7D 91.071 728 58 7 1808 2531 581024096 581023372 0 977
11 TraesCS2B01G395800 chr7D 90.707 721 63 4 1813 2531 100991635 100992353 0 957
12 TraesCS2B01G395800 chr1D 90.859 722 58 6 1814 2531 318099988 318099271 0 961


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 TraesCS2B01G395800 chr2B 561257873 561260403 2530 True 4674 4674 100.000 1 2531 1 chr2B.!!$R1 2530
1 TraesCS2B01G395800 chr2D 478697767 478699548 1781 False 2647 2647 93.489 1 1787 1 chr2D.!!$F1 1786
2 TraesCS2B01G395800 chr2A 621515214 621516990 1776 True 1190 1609 90.605 1 1766 2 chr2A.!!$R1 1765
3 TraesCS2B01G395800 chr5B 400552144 400552866 722 True 998 998 91.598 1808 2531 1 chr5B.!!$R1 723
4 TraesCS2B01G395800 chr5B 492104259 492104974 715 False 959 959 90.833 1813 2531 1 chr5B.!!$F1 718
5 TraesCS2B01G395800 chr7B 428923095 428923810 715 True 990 990 91.643 1813 2529 1 chr7B.!!$R1 716
6 TraesCS2B01G395800 chr7B 591524006 591524728 722 False 963 963 90.746 1811 2531 1 chr7B.!!$F1 720
7 TraesCS2B01G395800 chr3D 228165253 228165975 722 False 987 987 91.334 1808 2531 1 chr3D.!!$F1 723
8 TraesCS2B01G395800 chr5D 106690685 106691411 726 True 985 985 91.209 1808 2530 1 chr5D.!!$R1 722
9 TraesCS2B01G395800 chr7D 581023372 581024096 724 True 977 977 91.071 1808 2531 1 chr7D.!!$R1 723
10 TraesCS2B01G395800 chr7D 100991635 100992353 718 False 957 957 90.707 1813 2531 1 chr7D.!!$F1 718
11 TraesCS2B01G395800 chr1D 318099271 318099988 717 True 961 961 90.859 1814 2531 1 chr1D.!!$R1 717

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
230 232 0.034337 TTCTAGCTTCGGTTTGCGGT 59.966 50.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1805 1853 0.519961 GTTAATGCCCACACGGTGTC 59.48 55.0 11.54 0.86 0.0 3.67 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
28 29 4.188462 CCTTGAACTAATACACCGCATCA 58.812 43.478 0.00 0.00 0.00 3.07
61 62 2.618241 TCTTTGCGTGTTGATTCAAGCT 59.382 40.909 0.00 0.00 41.76 3.74
144 145 4.539870 CTCTCGTCCGTTACAAACTTACA 58.460 43.478 0.00 0.00 0.00 2.41
147 148 4.681744 TCGTCCGTTACAAACTTACAACT 58.318 39.130 0.00 0.00 0.00 3.16
148 149 4.739716 TCGTCCGTTACAAACTTACAACTC 59.260 41.667 0.00 0.00 0.00 3.01
149 150 4.374309 CGTCCGTTACAAACTTACAACTCG 60.374 45.833 0.00 0.00 0.00 4.18
151 152 3.453928 CGTTACAAACTTACAACTCGCG 58.546 45.455 0.00 0.00 0.00 5.87
152 153 3.061006 CGTTACAAACTTACAACTCGCGT 60.061 43.478 5.77 0.00 0.00 6.01
153 154 4.198584 GTTACAAACTTACAACTCGCGTG 58.801 43.478 5.77 6.24 0.00 5.34
154 155 2.273557 ACAAACTTACAACTCGCGTGT 58.726 42.857 8.21 8.21 0.00 4.49
155 156 2.674357 ACAAACTTACAACTCGCGTGTT 59.326 40.909 19.92 19.92 0.00 3.32
230 232 0.034337 TTCTAGCTTCGGTTTGCGGT 59.966 50.000 0.00 0.00 0.00 5.68
233 235 0.249953 TAGCTTCGGTTTGCGGTGAA 60.250 50.000 0.00 0.00 0.00 3.18
277 279 2.396157 CGCTGAAGAGCTGCATGCA 61.396 57.895 21.29 21.29 43.77 3.96
278 280 1.880894 GCTGAAGAGCTGCATGCAA 59.119 52.632 22.88 3.60 45.94 4.08
285 287 5.539979 TGAAGAGCTGCATGCAAAATTTTA 58.460 33.333 22.88 8.23 45.94 1.52
291 293 5.084055 GCTGCATGCAAAATTTTAGCTTTC 58.916 37.500 22.88 11.98 42.31 2.62
318 323 1.757699 GATCGAGCTAGAACCCTGGTT 59.242 52.381 0.00 0.07 41.54 3.67
559 564 0.038166 TGATGGCCAAGACAACTCCC 59.962 55.000 10.96 0.00 0.00 4.30
651 656 7.888021 TCATTTTTCCCTTCTAGAAACAGCATA 59.112 33.333 6.63 0.00 33.11 3.14
757 791 2.751166 ATTTGAGCGTGTCTAGCACT 57.249 45.000 13.14 0.00 45.57 4.40
810 849 1.174712 TTGTGCTTGCTTCTCAGGCC 61.175 55.000 0.00 0.00 46.08 5.19
864 903 1.064003 AGCCCACTGTGACACCAATA 58.936 50.000 9.86 0.00 0.00 1.90
875 914 6.493115 ACTGTGACACCAATAATTTTCATCCA 59.507 34.615 2.45 0.00 0.00 3.41
882 930 9.396022 ACACCAATAATTTTCATCCACTACTAG 57.604 33.333 0.00 0.00 0.00 2.57
884 932 8.557450 ACCAATAATTTTCATCCACTACTAGGT 58.443 33.333 0.00 0.00 0.00 3.08
928 976 1.983224 CAAGGACGGTCCAGGTCAT 59.017 57.895 27.87 4.19 39.61 3.06
1071 1119 3.764466 CGCAGCCTCCTCGTCCTT 61.764 66.667 0.00 0.00 0.00 3.36
1124 1172 4.373116 GCGCCGACTCCTCCACAA 62.373 66.667 0.00 0.00 0.00 3.33
1125 1173 2.432628 CGCCGACTCCTCCACAAC 60.433 66.667 0.00 0.00 0.00 3.32
1260 1308 3.782443 CCTAGCCCCGCGTTCCTT 61.782 66.667 4.92 0.00 0.00 3.36
1332 1380 0.035458 CCGTCTCTTCCTGCTTTGGT 59.965 55.000 0.00 0.00 0.00 3.67
1415 1463 1.202746 GGAAGATGAGGCTGATGGGTC 60.203 57.143 0.00 0.00 0.00 4.46
1469 1517 0.909610 AGGGCGGAGGAGTTCATCAA 60.910 55.000 0.00 0.00 0.00 2.57
1509 1557 2.282180 GCGCAGAACTTTCCCCCA 60.282 61.111 0.30 0.00 0.00 4.96
1551 1599 3.260483 GCGACGCTGAGGCATGAG 61.260 66.667 13.73 0.00 38.60 2.90
1619 1667 2.027003 AGAGGAGAGGAGTACGTTCG 57.973 55.000 0.00 0.00 0.00 3.95
1725 1773 3.028850 ACTACGTACACATGTGGGCTAT 58.971 45.455 28.64 10.75 34.19 2.97
1728 1776 1.810031 CGTACACATGTGGGCTATGGG 60.810 57.143 28.64 1.54 35.10 4.00
1737 1785 3.513517 TGTGGGCTATGGGTATACCTAC 58.486 50.000 21.25 6.54 41.11 3.18
1742 1790 3.447944 GGCTATGGGTATACCTACTGAGC 59.552 52.174 21.25 21.33 41.11 4.26
1744 1792 4.527038 GCTATGGGTATACCTACTGAGCAA 59.473 45.833 23.19 5.75 41.11 3.91
1787 1835 5.178797 TGCCTTTCGAAATTTGGTTTCAAA 58.821 33.333 11.70 0.00 45.24 2.69
1788 1836 5.643777 TGCCTTTCGAAATTTGGTTTCAAAA 59.356 32.000 11.70 0.00 45.24 2.44
1789 1837 6.183360 TGCCTTTCGAAATTTGGTTTCAAAAG 60.183 34.615 11.70 6.87 44.67 2.27
1790 1838 6.183360 GCCTTTCGAAATTTGGTTTCAAAAGT 60.183 34.615 11.70 0.00 44.06 2.66
1791 1839 7.010645 GCCTTTCGAAATTTGGTTTCAAAAGTA 59.989 33.333 11.70 0.00 44.06 2.24
1792 1840 8.539674 CCTTTCGAAATTTGGTTTCAAAAGTAG 58.460 33.333 11.70 0.00 44.06 2.57
1793 1841 8.989653 TTTCGAAATTTGGTTTCAAAAGTAGT 57.010 26.923 6.47 0.00 45.24 2.73
1805 1853 9.931210 GGTTTCAAAAGTAGTAATTATCATCGG 57.069 33.333 0.00 0.00 0.00 4.18
1808 1856 9.878667 TTCAAAAGTAGTAATTATCATCGGACA 57.121 29.630 0.00 0.00 0.00 4.02
1809 1857 9.309516 TCAAAAGTAGTAATTATCATCGGACAC 57.690 33.333 0.00 0.00 0.00 3.67
1824 1873 0.519961 GACACCGTGTGGGCATTAAC 59.480 55.000 9.42 0.00 40.62 2.01
1865 1914 4.590918 TGTGTGGTGTCTAAGAAAACCAA 58.409 39.130 4.21 0.00 44.02 3.67
1873 1923 5.010933 TGTCTAAGAAAACCAACCACACAA 58.989 37.500 0.00 0.00 0.00 3.33
1897 1948 2.492484 ACGTGTGGGCAAAACAAGTAAA 59.508 40.909 4.50 0.00 38.27 2.01
1899 1950 3.927142 CGTGTGGGCAAAACAAGTAAAAA 59.073 39.130 0.00 0.00 0.00 1.94
1990 2043 4.078516 GCCCGTACGTCAGGCCTT 62.079 66.667 19.62 0.00 41.00 4.35
2014 2067 3.467226 CATGGTCCCGTACGCCCT 61.467 66.667 10.49 0.00 0.00 5.19
2088 2141 4.497340 CCATGTTCGTTTAACTGCAGTTGT 60.497 41.667 36.50 18.51 38.90 3.32
2090 2143 3.242155 TGTTCGTTTAACTGCAGTTGTCG 60.242 43.478 36.50 32.09 38.90 4.35
2238 2292 3.417101 TGGTTTACTACAGTTGCCATGG 58.583 45.455 7.63 7.63 0.00 3.66
2252 2307 7.990314 ACAGTTGCCATGGTTTAAAAACTTTAT 59.010 29.630 14.67 0.83 38.89 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.030638 GTTGTTTGCTGATGCGGTGT 59.969 50.000 0.00 0.00 43.34 4.16
20 21 0.961019 ATGTTGTTTGCTGATGCGGT 59.039 45.000 0.00 0.00 43.34 5.68
61 62 1.302192 GGGCACGTTGGCTAGTCAA 60.302 57.895 5.45 5.45 43.20 3.18
153 154 2.930826 TTCTGGAGGAGTTGTGGAAC 57.069 50.000 0.00 0.00 37.35 3.62
154 155 4.349636 TGTAATTCTGGAGGAGTTGTGGAA 59.650 41.667 0.00 0.00 0.00 3.53
155 156 3.907474 TGTAATTCTGGAGGAGTTGTGGA 59.093 43.478 0.00 0.00 0.00 4.02
211 213 0.034337 ACCGCAAACCGAAGCTAGAA 59.966 50.000 0.00 0.00 40.02 2.10
230 232 1.821666 GCCTACCCTTGCTTGGTTTCA 60.822 52.381 0.00 0.00 37.31 2.69
233 235 1.303317 CGCCTACCCTTGCTTGGTT 60.303 57.895 0.00 0.00 37.31 3.67
243 245 4.968197 CGAGCTTATCGCCTACCC 57.032 61.111 0.00 0.00 45.98 3.69
264 266 4.390909 GCTAAAATTTTGCATGCAGCTCTT 59.609 37.500 21.50 13.63 45.94 2.85
265 267 3.930848 GCTAAAATTTTGCATGCAGCTCT 59.069 39.130 21.50 4.54 45.94 4.09
271 273 5.510323 GCATGAAAGCTAAAATTTTGCATGC 59.490 36.000 22.35 22.35 45.84 4.06
277 279 6.470235 CGATCTCGCATGAAAGCTAAAATTTT 59.530 34.615 8.75 8.75 0.00 1.82
278 280 5.967674 CGATCTCGCATGAAAGCTAAAATTT 59.032 36.000 0.00 0.00 0.00 1.82
285 287 1.850377 CTCGATCTCGCATGAAAGCT 58.150 50.000 0.00 0.00 39.60 3.74
291 293 2.315011 GTTCTAGCTCGATCTCGCATG 58.685 52.381 0.00 0.00 39.60 4.06
412 417 1.377072 CCATGCATGTCCCACACGA 60.377 57.895 24.58 0.00 0.00 4.35
413 418 2.409055 CCCATGCATGTCCCACACG 61.409 63.158 24.58 7.10 0.00 4.49
463 468 2.978489 GTCAGTAGACGTCAAACCTTCG 59.022 50.000 19.50 4.99 34.60 3.79
726 760 4.155826 ACACGCTCAAATTAGCTGCATTTA 59.844 37.500 1.02 0.00 40.49 1.40
810 849 5.337250 GGGGCAAGAAAGGTTAATTTAGTGG 60.337 44.000 0.00 0.00 0.00 4.00
864 903 7.862675 AGCTAACCTAGTAGTGGATGAAAATT 58.137 34.615 0.00 0.00 0.00 1.82
928 976 7.928167 CAGTCTACATGTAGCATGAGGAATTTA 59.072 37.037 25.31 3.29 33.32 1.40
999 1047 2.545952 CCGGAATCGATCTTCGTCCATT 60.546 50.000 12.41 0.00 41.35 3.16
1071 1119 1.185618 ACTTGAGGTAGTCTGCGGCA 61.186 55.000 1.29 1.29 0.00 5.69
1150 1198 1.255667 TTGCCGTGGTAGGAGGAGAC 61.256 60.000 0.00 0.00 0.00 3.36
1260 1308 2.922503 TGGAGTCTCTTGGCCGCA 60.923 61.111 0.00 0.00 0.00 5.69
1272 1320 1.668294 CTTCAGCCGTGACTGGAGT 59.332 57.895 0.00 0.00 38.33 3.85
1306 1354 4.443266 GGAAGAGACGGCAGCGCT 62.443 66.667 2.64 2.64 0.00 5.92
1362 1410 4.988716 TCCTCCTGTGTCGCCGGT 62.989 66.667 1.90 0.00 0.00 5.28
1372 1420 0.608130 TCAACCACATCGTCCTCCTG 59.392 55.000 0.00 0.00 0.00 3.86
1415 1463 2.887568 CAAGCTCGTAGCAGGCCG 60.888 66.667 0.00 0.00 45.56 6.13
1469 1517 4.020396 CCCTGAGCTGCTCATAGAACATAT 60.020 45.833 30.50 0.00 39.92 1.78
1509 1557 4.030452 GGCGAGCGCTGCAAAACT 62.030 61.111 18.48 0.00 41.60 2.66
1545 1593 2.101082 TCTCAGCTCTCATGTCTCATGC 59.899 50.000 5.03 0.00 0.00 4.06
1546 1594 3.633065 TCTCTCAGCTCTCATGTCTCATG 59.367 47.826 3.65 3.65 0.00 3.07
1547 1595 3.900971 TCTCTCAGCTCTCATGTCTCAT 58.099 45.455 0.00 0.00 0.00 2.90
1548 1596 3.362870 TCTCTCAGCTCTCATGTCTCA 57.637 47.619 0.00 0.00 0.00 3.27
1549 1597 3.058708 CGATCTCTCAGCTCTCATGTCTC 60.059 52.174 0.00 0.00 0.00 3.36
1550 1598 2.880268 CGATCTCTCAGCTCTCATGTCT 59.120 50.000 0.00 0.00 0.00 3.41
1551 1599 2.877786 TCGATCTCTCAGCTCTCATGTC 59.122 50.000 0.00 0.00 0.00 3.06
1619 1667 4.425520 CTGTCCTTCCTCATCGAAAGTAC 58.574 47.826 0.00 0.00 0.00 2.73
1725 1773 5.765576 TTTTTGCTCAGTAGGTATACCCA 57.234 39.130 18.65 1.25 36.42 4.51
1737 1785 7.697710 TCGCATCTAACATTTATTTTTGCTCAG 59.302 33.333 0.00 0.00 0.00 3.35
1742 1790 7.436080 AGGCATCGCATCTAACATTTATTTTTG 59.564 33.333 0.00 0.00 0.00 2.44
1744 1792 7.042797 AGGCATCGCATCTAACATTTATTTT 57.957 32.000 0.00 0.00 0.00 1.82
1804 1852 0.606944 TTAATGCCCACACGGTGTCC 60.607 55.000 11.54 3.61 0.00 4.02
1805 1853 0.519961 GTTAATGCCCACACGGTGTC 59.480 55.000 11.54 0.86 0.00 3.67
1806 1854 1.231958 CGTTAATGCCCACACGGTGT 61.232 55.000 8.21 8.21 0.00 4.16
1807 1855 1.499949 CGTTAATGCCCACACGGTG 59.500 57.895 6.58 6.58 0.00 4.94
1808 1856 1.673009 CCGTTAATGCCCACACGGT 60.673 57.895 1.36 0.00 45.85 4.83
1809 1857 3.183259 CCGTTAATGCCCACACGG 58.817 61.111 0.00 0.00 45.75 4.94
1824 1873 4.619227 AACGTGTGGCCAGACCCG 62.619 66.667 26.07 18.29 37.83 5.28
1959 2012 2.748647 GGGCGTGTGGGCGTTATT 60.749 61.111 0.00 0.00 43.46 1.40
2221 2275 7.584122 TTTTAAACCATGGCAACTGTAGTAA 57.416 32.000 13.04 0.00 37.61 2.24
2238 2292 7.709182 AGGTGGCAACTCATAAAGTTTTTAAAC 59.291 33.333 0.00 0.00 46.26 2.01
2252 2307 2.969950 AGTGTTAGTAGGTGGCAACTCA 59.030 45.455 9.14 0.00 37.61 3.41
2446 2503 8.589338 AGTAGATGGCAACTCCTAAATATACTG 58.411 37.037 0.00 0.00 27.91 2.74
2447 2504 8.728596 AGTAGATGGCAACTCCTAAATATACT 57.271 34.615 0.00 0.00 35.26 2.12


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

AutoCloner maintained by Alex Coulton.