Multiple sequence alignment - TraesCS2B01G253000

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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 TraesCS2B01G253000 chr2B 100.000 2921 0 0 1 2921 272995442 272992522 0 5395
1 TraesCS2B01G253000 chr2B 93.752 2945 131 18 8 2911 268753511 268756443 0 4370
2 TraesCS2B01G253000 chr2B 94.236 1891 104 3 1 1891 606226536 606224651 0 2883
3 TraesCS2B01G253000 chr2B 93.781 1817 102 9 75 1887 570605841 570604032 0 2719
4 TraesCS2B01G253000 chr2B 85.467 1039 101 32 1923 2921 337501837 337502865 0 1037
5 TraesCS2B01G253000 chr6D 90.327 2657 182 46 71 2662 246671074 246673720 0 3413
6 TraesCS2B01G253000 chr6D 88.136 1003 80 25 1950 2921 238803753 238804747 0 1157
7 TraesCS2B01G253000 chr5B 93.902 1886 104 8 1 1882 337439068 337437190 0 2835
8 TraesCS2B01G253000 chr4D 93.963 1822 100 10 71 1888 226171217 226173032 0 2747
9 TraesCS2B01G253000 chr7B 93.959 1821 92 10 73 1886 595538789 595540598 0 2737
10 TraesCS2B01G253000 chr7B 92.165 1889 132 12 1 1882 654664604 654666483 0 2654
11 TraesCS2B01G253000 chr4B 93.805 1824 99 10 69 1886 349261051 349262866 0 2730
12 TraesCS2B01G253000 chr4B 85.930 1059 97 35 1890 2917 503289725 503288688 0 1083
13 TraesCS2B01G253000 chr3D 94.073 1063 30 6 1890 2921 197125914 197124854 0 1583
14 TraesCS2B01G253000 chr3D 86.654 1064 87 20 1895 2919 226749076 226748029 0 1127
15 TraesCS2B01G253000 chr3D 86.217 1052 101 32 1890 2911 251244162 251245199 0 1099
16 TraesCS2B01G253000 chr7A 89.133 1003 75 22 1950 2921 582573118 582574117 0 1218
17 TraesCS2B01G253000 chr7A 88.190 1050 85 29 1896 2914 396203139 396202098 0 1216
18 TraesCS2B01G253000 chr7A 85.618 1043 112 28 1892 2911 522958800 522959827 0 1061
19 TraesCS2B01G253000 chr7A 87.281 857 65 11 1892 2711 400450248 400449399 0 939
20 TraesCS2B01G253000 chr7A 89.438 587 50 8 1892 2470 400445923 400445341 0 730
21 TraesCS2B01G253000 chr6A 87.240 1058 97 26 1892 2921 337479771 337480818 0 1171
22 TraesCS2B01G253000 chr2A 87.353 1020 87 32 1928 2918 343444892 343443886 0 1131
23 TraesCS2B01G253000 chr1D 85.354 1072 105 30 1892 2920 288163735 288164797 0 1062
24 TraesCS2B01G253000 chr2D 85.136 1063 106 29 1890 2917 380724412 380723367 0 1040


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 TraesCS2B01G253000 chr2B 272992522 272995442 2920 True 5395.0 5395 100.0000 1 2921 1 chr2B.!!$R1 2920
1 TraesCS2B01G253000 chr2B 268753511 268756443 2932 False 4370.0 4370 93.7520 8 2911 1 chr2B.!!$F1 2903
2 TraesCS2B01G253000 chr2B 606224651 606226536 1885 True 2883.0 2883 94.2360 1 1891 1 chr2B.!!$R3 1890
3 TraesCS2B01G253000 chr2B 570604032 570605841 1809 True 2719.0 2719 93.7810 75 1887 1 chr2B.!!$R2 1812
4 TraesCS2B01G253000 chr2B 337501837 337502865 1028 False 1037.0 1037 85.4670 1923 2921 1 chr2B.!!$F2 998
5 TraesCS2B01G253000 chr6D 246671074 246673720 2646 False 3413.0 3413 90.3270 71 2662 1 chr6D.!!$F2 2591
6 TraesCS2B01G253000 chr6D 238803753 238804747 994 False 1157.0 1157 88.1360 1950 2921 1 chr6D.!!$F1 971
7 TraesCS2B01G253000 chr5B 337437190 337439068 1878 True 2835.0 2835 93.9020 1 1882 1 chr5B.!!$R1 1881
8 TraesCS2B01G253000 chr4D 226171217 226173032 1815 False 2747.0 2747 93.9630 71 1888 1 chr4D.!!$F1 1817
9 TraesCS2B01G253000 chr7B 595538789 595540598 1809 False 2737.0 2737 93.9590 73 1886 1 chr7B.!!$F1 1813
10 TraesCS2B01G253000 chr7B 654664604 654666483 1879 False 2654.0 2654 92.1650 1 1882 1 chr7B.!!$F2 1881
11 TraesCS2B01G253000 chr4B 349261051 349262866 1815 False 2730.0 2730 93.8050 69 1886 1 chr4B.!!$F1 1817
12 TraesCS2B01G253000 chr4B 503288688 503289725 1037 True 1083.0 1083 85.9300 1890 2917 1 chr4B.!!$R1 1027
13 TraesCS2B01G253000 chr3D 197124854 197125914 1060 True 1583.0 1583 94.0730 1890 2921 1 chr3D.!!$R1 1031
14 TraesCS2B01G253000 chr3D 226748029 226749076 1047 True 1127.0 1127 86.6540 1895 2919 1 chr3D.!!$R2 1024
15 TraesCS2B01G253000 chr3D 251244162 251245199 1037 False 1099.0 1099 86.2170 1890 2911 1 chr3D.!!$F1 1021
16 TraesCS2B01G253000 chr7A 582573118 582574117 999 False 1218.0 1218 89.1330 1950 2921 1 chr7A.!!$F2 971
17 TraesCS2B01G253000 chr7A 396202098 396203139 1041 True 1216.0 1216 88.1900 1896 2914 1 chr7A.!!$R1 1018
18 TraesCS2B01G253000 chr7A 522958800 522959827 1027 False 1061.0 1061 85.6180 1892 2911 1 chr7A.!!$F1 1019
19 TraesCS2B01G253000 chr7A 400445341 400450248 4907 True 834.5 939 88.3595 1892 2711 2 chr7A.!!$R2 819
20 TraesCS2B01G253000 chr6A 337479771 337480818 1047 False 1171.0 1171 87.2400 1892 2921 1 chr6A.!!$F1 1029
21 TraesCS2B01G253000 chr2A 343443886 343444892 1006 True 1131.0 1131 87.3530 1928 2918 1 chr2A.!!$R1 990
22 TraesCS2B01G253000 chr1D 288163735 288164797 1062 False 1062.0 1062 85.3540 1892 2920 1 chr1D.!!$F1 1028
23 TraesCS2B01G253000 chr2D 380723367 380724412 1045 True 1040.0 1040 85.1360 1890 2917 1 chr2D.!!$R1 1027

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
643 665 0.671781 GCACTTGCTCCGAGTCATGT 60.672 55.0 0.0 2.19 38.21 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2461 2573 1.831106 ACATGCCACCGATAGTCAGAA 59.169 47.619 0.0 0.0 0.0 3.02 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
213 221 7.417911 GGGCGTAAAAACCCTACTATACTTACT 60.418 40.741 0.00 0.00 43.36 2.24
214 222 7.981789 GGCGTAAAAACCCTACTATACTTACTT 59.018 37.037 0.00 0.00 0.00 2.24
476 498 1.337167 CGGAGATATGGCGATGCTTCA 60.337 52.381 0.08 0.00 0.00 3.02
643 665 0.671781 GCACTTGCTCCGAGTCATGT 60.672 55.000 0.00 2.19 38.21 3.21
701 723 2.295885 AGAAGCTATCAAGTGCATGCC 58.704 47.619 16.68 6.65 0.00 4.40
718 740 1.895798 TGCCGTTCACATTCTCTCTCT 59.104 47.619 0.00 0.00 0.00 3.10
824 846 3.290948 TTTCCCACTACACAAGCAGTT 57.709 42.857 0.00 0.00 0.00 3.16
902 924 4.471025 TGATGCTTGGGAGAGATACAAAGA 59.529 41.667 0.00 0.00 0.00 2.52
934 956 2.641815 AGATGTCCTAATCATGGGCTCC 59.358 50.000 0.00 0.00 0.00 4.70
1242 1264 4.938080 ACGATGATGACACCATTCTAGTC 58.062 43.478 0.00 0.00 32.09 2.59
1251 1273 3.258372 ACACCATTCTAGTCGACACACAT 59.742 43.478 19.50 1.28 0.00 3.21
1787 1813 5.922544 GCATTGTCCCTATCATTTGTATTGC 59.077 40.000 0.00 0.00 0.00 3.56
1788 1814 6.239120 GCATTGTCCCTATCATTTGTATTGCT 60.239 38.462 0.00 0.00 0.00 3.91
1864 1890 3.511540 TGACCAAGTTCGAGATGACATCT 59.488 43.478 17.98 17.98 43.70 2.90
2366 2448 4.434545 AGCATGCTATGTTCTCTGGATT 57.565 40.909 21.21 0.00 0.00 3.01
2650 2821 1.411612 GTTCTCGGGATCGGTGGTATT 59.588 52.381 0.00 0.00 36.95 1.89
2669 2840 5.646360 GGTATTTTCCTTTGGTGAGATCGAA 59.354 40.000 0.00 0.00 0.00 3.71
2721 2893 6.282930 ACAATAAGTGCTTTCAACTGCAATT 58.717 32.000 5.98 5.98 46.66 2.32
2911 3085 7.910683 GCTTTGTAGCACTCTACCATTAATTTC 59.089 37.037 0.00 0.00 46.95 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
213 221 0.179176 CGGCGCCAAAATGATCGAAA 60.179 50.000 28.98 0.00 0.00 3.46
214 222 1.302383 ACGGCGCCAAAATGATCGAA 61.302 50.000 28.98 0.00 0.00 3.71
476 498 2.167693 CTGCTTGGCATCCAAACATCAT 59.832 45.455 2.59 0.00 43.44 2.45
718 740 0.671472 CAAGCACGAGCACCATCTCA 60.671 55.000 7.77 0.00 45.49 3.27
824 846 5.679638 TTGAAGATCTCATCTCGAATTGCGA 60.680 40.000 0.00 0.00 39.84 5.10
934 956 2.429971 TCTGCAGCTCTAACCATCTCTG 59.570 50.000 9.47 0.00 0.00 3.35
1242 1264 2.879826 TGATCTGTAGCATGTGTGTCG 58.120 47.619 0.00 0.00 0.00 4.35
1251 1273 7.890655 ACACTAGTATCCATATGATCTGTAGCA 59.109 37.037 3.65 0.00 34.76 3.49
1669 1694 2.057137 AAATCGCATGGTGCATAGGT 57.943 45.000 2.63 0.00 45.36 3.08
1787 1813 3.508744 AAGCACACTCAACAACCAAAG 57.491 42.857 0.00 0.00 0.00 2.77
1788 1814 3.256879 TGAAAGCACACTCAACAACCAAA 59.743 39.130 0.00 0.00 0.00 3.28
1832 1858 3.365265 CTTGGTCAGCCCGCAACC 61.365 66.667 4.74 4.74 35.15 3.77
1833 1859 2.130073 GAACTTGGTCAGCCCGCAAC 62.130 60.000 0.00 0.00 35.15 4.17
1888 1914 2.802816 CCAACTTCACTCTTCTTCGTGG 59.197 50.000 0.00 0.00 0.00 4.94
2366 2448 4.383010 CCATGTCTAGTTCACATGCTACCA 60.383 45.833 14.61 0.00 46.71 3.25
2461 2573 1.831106 ACATGCCACCGATAGTCAGAA 59.169 47.619 0.00 0.00 0.00 3.02
2721 2893 8.792633 CAGATCACTTATTACCAGGAACAAAAA 58.207 33.333 0.00 0.00 0.00 1.94
2761 2933 6.484308 AGCATGATCCCAAAAACAAAAAGAAG 59.516 34.615 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.