Multiple sequence alignment - TraesCS2D01G182200

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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 TraesCS2D01G182200 chr2D 100.000 2687 0 0 1 2687 126946605 126949291 0.000000e+00 4963
1 TraesCS2D01G182200 chr2D 75.615 894 154 42 955 1819 126958540 126959398 4.200000e-103 385
2 TraesCS2D01G182200 chr2D 76.957 677 131 19 50 722 126958614 126959269 1.970000e-96 363
3 TraesCS2D01G182200 chr2A 95.067 2696 90 19 1 2687 133473072 133475733 0.000000e+00 4202
4 TraesCS2D01G182200 chr2A 76.320 663 115 33 1028 1671 133484893 133485532 1.550000e-82 316
5 TraesCS2D01G182200 chr2A 76.131 641 125 19 50 685 133484907 133485524 7.220000e-81 311
6 TraesCS2D01G182200 chr2B 96.181 1990 48 13 1 1984 180539874 180541841 0.000000e+00 3229
7 TraesCS2D01G182200 chr2B 92.764 691 19 3 2011 2687 180541836 180542509 0.000000e+00 970
8 TraesCS2D01G182200 chr2B 76.618 680 126 23 50 722 180546256 180546909 7.120000e-91 344


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 TraesCS2D01G182200 chr2D 126946605 126949291 2686 False 4963.000000 4963 100.0000 1 2687 1 chr2D.!!$F1 2686
1 TraesCS2D01G182200 chr2D 126958540 126959398 858 False 374.000000 385 76.2860 50 1819 2 chr2D.!!$F2 1769
2 TraesCS2D01G182200 chr2A 133473072 133475733 2661 False 4202.000000 4202 95.0670 1 2687 1 chr2A.!!$F1 2686
3 TraesCS2D01G182200 chr2A 133484893 133485532 639 False 313.500000 316 76.2255 50 1671 2 chr2A.!!$F2 1621
4 TraesCS2D01G182200 chr2B 180539874 180546909 7035 False 1514.333333 3229 88.5210 1 2687 3 chr2B.!!$F1 2686

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
948 953 1.492764 TCTGTACCCCGGGAAGATTC 58.507 55.0 26.32 6.59 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 2033 0.179103 GCTTCCTCAGAGCTCAGAGC 60.179 60.0 26.24 15.25 42.84 4.09 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
21 22 1.965754 AATCGCAGCAGGAGGAGGAC 61.966 60.000 0.00 0.00 0.00 3.85
690 691 2.122813 CCCAGCCCTCCGATACCT 60.123 66.667 0.00 0.00 0.00 3.08
709 710 3.067180 ACCTTCGTTCGACTACAAGTGAA 59.933 43.478 0.00 0.00 0.00 3.18
745 748 6.531948 CGTTCTTCTCTCCGATCTGTATTTTT 59.468 38.462 0.00 0.00 0.00 1.94
753 756 7.109501 TCTCCGATCTGTATTTTTGGATTCAA 58.890 34.615 0.00 0.00 0.00 2.69
770 773 8.059798 TGGATTCAATTTCAGATCTTTTCTCC 57.940 34.615 0.00 0.00 29.93 3.71
771 774 7.892241 TGGATTCAATTTCAGATCTTTTCTCCT 59.108 33.333 0.00 0.00 29.93 3.69
772 775 8.189460 GGATTCAATTTCAGATCTTTTCTCCTG 58.811 37.037 0.00 0.00 29.93 3.86
773 776 6.506500 TCAATTTCAGATCTTTTCTCCTGC 57.493 37.500 0.00 0.00 29.93 4.85
774 777 6.243900 TCAATTTCAGATCTTTTCTCCTGCT 58.756 36.000 0.00 0.00 29.93 4.24
775 778 6.150641 TCAATTTCAGATCTTTTCTCCTGCTG 59.849 38.462 0.00 0.00 29.93 4.41
776 779 4.630644 TTCAGATCTTTTCTCCTGCTGT 57.369 40.909 0.00 0.00 29.93 4.40
777 780 4.630644 TCAGATCTTTTCTCCTGCTGTT 57.369 40.909 0.00 0.00 29.93 3.16
778 781 4.978099 TCAGATCTTTTCTCCTGCTGTTT 58.022 39.130 0.00 0.00 29.93 2.83
779 782 5.380043 TCAGATCTTTTCTCCTGCTGTTTT 58.620 37.500 0.00 0.00 29.93 2.43
780 783 5.829924 TCAGATCTTTTCTCCTGCTGTTTTT 59.170 36.000 0.00 0.00 29.93 1.94
781 784 6.998074 TCAGATCTTTTCTCCTGCTGTTTTTA 59.002 34.615 0.00 0.00 29.93 1.52
791 794 5.060506 TCCTGCTGTTTTTAAGTTCGATCA 58.939 37.500 0.00 0.00 0.00 2.92
799 802 7.992008 TGTTTTTAAGTTCGATCAGGTTTCTT 58.008 30.769 0.00 0.00 0.00 2.52
800 803 8.126700 TGTTTTTAAGTTCGATCAGGTTTCTTC 58.873 33.333 0.00 0.00 0.00 2.87
831 834 7.229506 GCTTATTTATTACTTGGTGATGAGGCT 59.770 37.037 0.00 0.00 0.00 4.58
839 842 4.819761 TGATGAGGCTGTCCGCGC 62.820 66.667 0.00 0.00 40.44 6.86
889 892 9.660180 CAAGAAGCCTTATTACCTCCTTATATC 57.340 37.037 0.00 0.00 0.00 1.63
890 893 8.974292 AGAAGCCTTATTACCTCCTTATATCA 57.026 34.615 0.00 0.00 0.00 2.15
891 894 9.041354 AGAAGCCTTATTACCTCCTTATATCAG 57.959 37.037 0.00 0.00 0.00 2.90
893 896 8.368962 AGCCTTATTACCTCCTTATATCAGAC 57.631 38.462 0.00 0.00 0.00 3.51
926 931 9.904647 GATCGTGTTATATATACTCTCGTTCTC 57.095 37.037 13.34 8.69 0.00 2.87
927 932 7.947090 TCGTGTTATATATACTCTCGTTCTCG 58.053 38.462 13.34 0.00 38.55 4.04
928 933 7.596621 TCGTGTTATATATACTCTCGTTCTCGT 59.403 37.037 13.34 0.00 38.33 4.18
929 934 8.219769 CGTGTTATATATACTCTCGTTCTCGTT 58.780 37.037 0.00 0.00 38.33 3.85
930 935 9.527566 GTGTTATATATACTCTCGTTCTCGTTC 57.472 37.037 0.00 0.00 38.33 3.95
931 936 9.486497 TGTTATATATACTCTCGTTCTCGTTCT 57.514 33.333 0.00 0.00 38.33 3.01
932 937 9.743937 GTTATATATACTCTCGTTCTCGTTCTG 57.256 37.037 0.00 0.00 38.33 3.02
933 938 7.966246 ATATATACTCTCGTTCTCGTTCTGT 57.034 36.000 0.00 0.00 38.33 3.41
948 953 1.492764 TCTGTACCCCGGGAAGATTC 58.507 55.000 26.32 6.59 0.00 2.52
990 999 3.644884 ATCTTCAGATAGGGTTACGCG 57.355 47.619 3.53 3.53 32.01 6.01
1120 1129 4.039973 TCGGTGGTTCTGTCTATCACTTTT 59.960 41.667 0.00 0.00 0.00 2.27
1152 1161 0.255890 ATAACTCGCCCAATGGTGCT 59.744 50.000 10.23 0.00 42.19 4.40
1263 1273 1.293498 CTGCACCTCAGCCTACGTT 59.707 57.895 0.00 0.00 35.78 3.99
1371 1381 4.988598 CGCTCGGCACTTGTGGGT 62.989 66.667 2.81 0.00 0.00 4.51
1422 1432 1.978617 CCTCATGGCCAACCGCTTT 60.979 57.895 10.96 0.00 39.70 3.51
1686 1714 7.072177 GATACCATCGTTTGATTTCAAGTGA 57.928 36.000 0.00 0.00 37.15 3.41
1990 2033 3.853671 GCTGCTGTGGTTTTATTTCATCG 59.146 43.478 0.00 0.00 0.00 3.84
2001 2044 4.662468 TTATTTCATCGCTCTGAGCTCT 57.338 40.909 25.59 11.05 39.60 4.09
2160 2203 3.394606 AGATAATTAACGGACCCATGCCT 59.605 43.478 0.00 0.00 0.00 4.75
2239 2282 2.110967 CAAGGCCGCATGTCCTCTG 61.111 63.158 0.00 0.00 0.00 3.35
2308 2351 3.183775 CGTAGGTTTGTGGAAGACTTTCG 59.816 47.826 0.00 0.00 33.98 3.46
2383 2440 0.941542 TTCTTCTGGCCAACGAAACG 59.058 50.000 7.01 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
716 717 0.173708 ATCGGAGAGAAGAACGCACC 59.826 55.000 0.00 0.00 43.63 5.01
718 719 1.133216 CAGATCGGAGAGAAGAACGCA 59.867 52.381 0.00 0.00 43.63 5.24
719 720 1.133407 ACAGATCGGAGAGAAGAACGC 59.867 52.381 0.00 0.00 43.63 4.84
720 721 4.822036 ATACAGATCGGAGAGAAGAACG 57.178 45.455 0.00 0.00 43.63 3.95
724 727 6.341316 TCCAAAAATACAGATCGGAGAGAAG 58.659 40.000 0.00 0.00 43.63 2.85
745 748 7.892241 AGGAGAAAAGATCTGAAATTGAATCCA 59.108 33.333 0.00 0.00 38.96 3.41
753 756 5.568392 ACAGCAGGAGAAAAGATCTGAAAT 58.432 37.500 0.00 0.00 38.96 2.17
762 765 6.414987 CGAACTTAAAAACAGCAGGAGAAAAG 59.585 38.462 0.00 0.00 0.00 2.27
770 773 5.049405 ACCTGATCGAACTTAAAAACAGCAG 60.049 40.000 0.00 0.00 0.00 4.24
771 774 4.819630 ACCTGATCGAACTTAAAAACAGCA 59.180 37.500 0.00 0.00 0.00 4.41
772 775 5.358298 ACCTGATCGAACTTAAAAACAGC 57.642 39.130 0.00 0.00 0.00 4.40
773 776 7.639945 AGAAACCTGATCGAACTTAAAAACAG 58.360 34.615 0.00 0.00 0.00 3.16
774 777 7.562454 AGAAACCTGATCGAACTTAAAAACA 57.438 32.000 0.00 0.00 0.00 2.83
775 778 7.590322 GGAAGAAACCTGATCGAACTTAAAAAC 59.410 37.037 0.00 0.00 0.00 2.43
776 779 7.501225 AGGAAGAAACCTGATCGAACTTAAAAA 59.499 33.333 0.00 0.00 39.01 1.94
777 780 6.996282 AGGAAGAAACCTGATCGAACTTAAAA 59.004 34.615 0.00 0.00 39.01 1.52
778 781 6.531021 AGGAAGAAACCTGATCGAACTTAAA 58.469 36.000 0.00 0.00 39.01 1.52
779 782 6.110411 AGGAAGAAACCTGATCGAACTTAA 57.890 37.500 0.00 0.00 39.01 1.85
780 783 5.740290 AGGAAGAAACCTGATCGAACTTA 57.260 39.130 0.00 0.00 39.01 2.24
781 784 4.625607 AGGAAGAAACCTGATCGAACTT 57.374 40.909 0.00 0.00 39.01 2.66
831 834 2.707849 GGACTCCTAAGCGCGGACA 61.708 63.158 8.83 0.00 0.00 4.02
839 842 3.442625 TGTACACGACATGGACTCCTAAG 59.557 47.826 0.00 0.00 43.47 2.18
926 931 1.217244 CTTCCCGGGGTACAGAACG 59.783 63.158 23.50 0.00 0.00 3.95
927 932 1.201424 ATCTTCCCGGGGTACAGAAC 58.799 55.000 23.50 0.00 0.00 3.01
928 933 1.835531 GAATCTTCCCGGGGTACAGAA 59.164 52.381 23.50 5.08 0.00 3.02
929 934 1.007963 AGAATCTTCCCGGGGTACAGA 59.992 52.381 23.50 17.11 0.00 3.41
930 935 1.497161 AGAATCTTCCCGGGGTACAG 58.503 55.000 23.50 12.01 0.00 2.74
931 936 2.023695 ACTAGAATCTTCCCGGGGTACA 60.024 50.000 23.50 0.00 0.00 2.90
932 937 2.675583 ACTAGAATCTTCCCGGGGTAC 58.324 52.381 23.50 6.78 0.00 3.34
933 938 3.303049 GAACTAGAATCTTCCCGGGGTA 58.697 50.000 23.50 8.50 0.00 3.69
948 953 1.390123 CGATGCGTTGTGGTGAACTAG 59.610 52.381 0.00 0.00 0.00 2.57
990 999 2.826725 AGGAGCCGACATAGTATTAGCC 59.173 50.000 0.00 0.00 0.00 3.93
1120 1129 2.939640 GCGAGTTATGAAGGCCCTTGAA 60.940 50.000 0.00 0.00 0.00 2.69
1152 1161 1.436195 GCATGCCGCCAGTAATTCGA 61.436 55.000 6.36 0.00 32.94 3.71
1202 1212 2.281761 ACACAGCAAAGCTCCCGG 60.282 61.111 0.00 0.00 36.40 5.73
1677 1705 2.357637 CGCACCTTCCTTTCACTTGAAA 59.642 45.455 4.39 4.39 41.29 2.69
1679 1707 1.593196 CGCACCTTCCTTTCACTTGA 58.407 50.000 0.00 0.00 0.00 3.02
1686 1714 0.744281 CAAACACCGCACCTTCCTTT 59.256 50.000 0.00 0.00 0.00 3.11
1990 2033 0.179103 GCTTCCTCAGAGCTCAGAGC 60.179 60.000 26.24 15.25 42.84 4.09
2001 2044 7.775053 ATAATTAACCACAAAAGCTTCCTCA 57.225 32.000 0.00 0.00 0.00 3.86
2160 2203 6.293571 CGCTGCATCATCAAAAATATGGTCTA 60.294 38.462 0.00 0.00 0.00 2.59
2239 2282 9.331282 AGATCACATAAAGCTATTTTACAGTCC 57.669 33.333 0.00 0.00 34.22 3.85
2308 2351 7.448748 AACTCACCACTAATAAACCAACATC 57.551 36.000 0.00 0.00 0.00 3.06
2383 2440 8.764287 ACTTGCAAATGCTTTATTTTGAGTTAC 58.236 29.630 0.00 0.00 42.66 2.50


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

AutoCloner maintained by Alex Coulton.