Multiple sequence alignment - TraesCS3A01G273100

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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 TraesCS3A01G273100 chr3A 100.000 3164 0 0 1 3164 502266766 502269929 0.000000e+00 5843
1 TraesCS3A01G273100 chr3A 91.186 624 43 8 201 819 135527476 135528092 0.000000e+00 837
2 TraesCS3A01G273100 chr3A 86.893 206 24 1 1312 1514 38291378 38291173 8.830000e-56 228
3 TraesCS3A01G273100 chr3D 96.000 2100 80 3 945 3044 378142713 378144808 0.000000e+00 3410
4 TraesCS3A01G273100 chr3D 93.243 222 13 2 2944 3164 378144810 378145030 3.040000e-85 326
5 TraesCS3A01G273100 chr3B 93.869 2153 100 12 875 2998 492751837 492753986 0.000000e+00 3216
6 TraesCS3A01G273100 chr3B 90.469 661 57 5 175 832 54991195 54991852 0.000000e+00 867
7 TraesCS3A01G273100 chr3B 92.486 173 11 2 2991 3162 492754588 492754759 2.440000e-61 246
8 TraesCS3A01G273100 chr2A 98.558 832 10 2 2 832 71075697 71074867 0.000000e+00 1469
9 TraesCS3A01G273100 chr2A 96.690 846 24 4 2 845 778138290 778137447 0.000000e+00 1404
10 TraesCS3A01G273100 chr6A 97.865 843 16 2 2 842 75948759 75949601 0.000000e+00 1456
11 TraesCS3A01G273100 chr4A 98.079 833 12 4 2 832 4009031 4009861 0.000000e+00 1447
12 TraesCS3A01G273100 chr4A 96.759 833 23 4 2 832 174148421 174147591 0.000000e+00 1386
13 TraesCS3A01G273100 chr5A 97.959 833 14 3 2 832 77754681 77753850 0.000000e+00 1441
14 TraesCS3A01G273100 chr7A 95.444 834 20 4 2 832 714679267 714678449 0.000000e+00 1314
15 TraesCS3A01G273100 chr7A 97.963 589 10 2 2 589 679006877 679007464 0.000000e+00 1020
16 TraesCS3A01G273100 chr2B 90.576 764 57 8 4 765 318311161 318311911 0.000000e+00 998
17 TraesCS3A01G273100 chr2B 90.499 621 44 8 201 820 683764859 683765465 0.000000e+00 806


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 TraesCS3A01G273100 chr3A 502266766 502269929 3163 False 5843 5843 100.0000 1 3164 1 chr3A.!!$F2 3163
1 TraesCS3A01G273100 chr3A 135527476 135528092 616 False 837 837 91.1860 201 819 1 chr3A.!!$F1 618
2 TraesCS3A01G273100 chr3D 378142713 378145030 2317 False 1868 3410 94.6215 945 3164 2 chr3D.!!$F1 2219
3 TraesCS3A01G273100 chr3B 492751837 492754759 2922 False 1731 3216 93.1775 875 3162 2 chr3B.!!$F2 2287
4 TraesCS3A01G273100 chr3B 54991195 54991852 657 False 867 867 90.4690 175 832 1 chr3B.!!$F1 657
5 TraesCS3A01G273100 chr2A 71074867 71075697 830 True 1469 1469 98.5580 2 832 1 chr2A.!!$R1 830
6 TraesCS3A01G273100 chr2A 778137447 778138290 843 True 1404 1404 96.6900 2 845 1 chr2A.!!$R2 843
7 TraesCS3A01G273100 chr6A 75948759 75949601 842 False 1456 1456 97.8650 2 842 1 chr6A.!!$F1 840
8 TraesCS3A01G273100 chr4A 4009031 4009861 830 False 1447 1447 98.0790 2 832 1 chr4A.!!$F1 830
9 TraesCS3A01G273100 chr4A 174147591 174148421 830 True 1386 1386 96.7590 2 832 1 chr4A.!!$R1 830
10 TraesCS3A01G273100 chr5A 77753850 77754681 831 True 1441 1441 97.9590 2 832 1 chr5A.!!$R1 830
11 TraesCS3A01G273100 chr7A 714678449 714679267 818 True 1314 1314 95.4440 2 832 1 chr7A.!!$R1 830
12 TraesCS3A01G273100 chr7A 679006877 679007464 587 False 1020 1020 97.9630 2 589 1 chr7A.!!$F1 587
13 TraesCS3A01G273100 chr2B 318311161 318311911 750 False 998 998 90.5760 4 765 1 chr2B.!!$F1 761
14 TraesCS3A01G273100 chr2B 683764859 683765465 606 False 806 806 90.4990 201 820 1 chr2B.!!$F2 619

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
832 866 0.73084 GCGTCCAATAGGGTTTTCCG 59.269 55.0 0.0 0.0 41.82 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2661 2701 0.24912 TGCACGCACTAGCCAGTAAT 59.751 50.0 0.0 0.0 37.52 1.89 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
425 432 3.829886 TTATGGAAACTCGCAGCAAAG 57.170 42.857 0.00 0.00 0.00 2.77
832 866 0.730840 GCGTCCAATAGGGTTTTCCG 59.269 55.000 0.00 0.00 41.82 4.30
834 868 1.735571 CGTCCAATAGGGTTTTCCGTG 59.264 52.381 0.00 0.00 41.82 4.94
852 886 4.402528 CCGCCCCACGTTCATCCA 62.403 66.667 0.00 0.00 41.42 3.41
853 887 2.819595 CGCCCCACGTTCATCCAG 60.820 66.667 0.00 0.00 36.87 3.86
854 888 2.438434 GCCCCACGTTCATCCAGG 60.438 66.667 0.00 0.00 0.00 4.45
855 889 2.272146 CCCCACGTTCATCCAGGG 59.728 66.667 0.00 0.00 39.29 4.45
856 890 2.602676 CCCCACGTTCATCCAGGGT 61.603 63.158 4.36 0.00 37.84 4.34
857 891 1.377202 CCCACGTTCATCCAGGGTG 60.377 63.158 0.00 0.00 34.75 4.61
858 892 1.377202 CCACGTTCATCCAGGGTGG 60.377 63.158 0.00 0.00 41.81 4.61
859 893 1.377202 CACGTTCATCCAGGGTGGG 60.377 63.158 0.00 0.00 38.32 4.61
860 894 2.438434 CGTTCATCCAGGGTGGGC 60.438 66.667 0.00 0.00 38.32 5.36
861 895 2.043953 GTTCATCCAGGGTGGGCC 60.044 66.667 0.00 0.00 38.32 5.80
862 896 3.727258 TTCATCCAGGGTGGGCCG 61.727 66.667 0.00 0.00 38.32 6.13
909 944 1.079612 GCCCATTTGTTGCCTCTGC 60.080 57.895 0.00 0.00 38.26 4.26
912 947 1.213537 CATTTGTTGCCTCTGCCGG 59.786 57.895 0.00 0.00 36.33 6.13
961 996 1.200948 GTGCTCAGATTTTCAGCCCAC 59.799 52.381 0.00 0.00 31.68 4.61
993 1028 4.069232 CCTCGAAGCTGCGGGTGA 62.069 66.667 14.32 0.00 0.00 4.02
995 1030 3.288308 CTCGAAGCTGCGGGTGACT 62.288 63.158 15.70 0.00 0.00 3.41
997 1032 2.343758 GAAGCTGCGGGTGACTGA 59.656 61.111 0.00 0.00 39.98 3.41
1084 1119 3.834799 CCCCGTCACCGCTCTACC 61.835 72.222 0.00 0.00 0.00 3.18
1105 1140 1.530771 GCCAGCCAGATCCAGATGT 59.469 57.895 0.00 0.00 0.00 3.06
1247 1282 4.322801 CGTTCTCCTCTACTCCAAAACCAT 60.323 45.833 0.00 0.00 0.00 3.55
1270 1305 3.192922 CGTCCCAAATCGTCGGCC 61.193 66.667 0.00 0.00 0.00 6.13
1942 1977 4.021981 GGTTGTCTGAAAGGATTTGGAAGG 60.022 45.833 0.00 0.00 39.27 3.46
1959 1994 3.181443 GGAAGGTTTTCAGTGAGGAAGGA 60.181 47.826 0.00 0.00 34.90 3.36
1963 1998 7.997643 GAAGGTTTTCAGTGAGGAAGGATTCG 61.998 46.154 0.00 0.00 38.45 3.34
2062 2097 0.105142 GGAGGTATCCCAGTGGGCTA 60.105 60.000 24.75 16.12 43.94 3.93
2073 2108 0.698238 AGTGGGCTAAGCACATCCAA 59.302 50.000 0.00 0.00 46.32 3.53
2210 2248 3.057019 TGTTCGTTGCTGTCTGTCATAC 58.943 45.455 0.00 0.00 0.00 2.39
2248 2286 6.808321 AGGATGAAATGGTGCTAGTAGTTA 57.192 37.500 0.00 0.00 0.00 2.24
2366 2404 3.906720 ACTACGGAACATACAGGCATT 57.093 42.857 0.00 0.00 0.00 3.56
2557 2597 4.640789 TTTTTGCGTTCTTAAGAGCCAA 57.359 36.364 13.05 13.98 0.00 4.52
2606 2646 2.542020 TGAACCATCGCACTCTGAAA 57.458 45.000 0.00 0.00 0.00 2.69
2626 2666 9.950680 TCTGAAACTGAATCATTGTTTTAGTTC 57.049 29.630 14.42 10.33 38.01 3.01
2675 2715 3.869065 TGGTACAATTACTGGCTAGTGC 58.131 45.455 13.76 0.00 34.76 4.40
2680 2720 0.249120 ATTACTGGCTAGTGCGTGCA 59.751 50.000 13.76 0.00 40.82 4.57
2738 2778 7.589395 AGCTCGATATCTTTATGTGAGTACAG 58.411 38.462 0.34 0.00 40.79 2.74
2778 2818 5.304686 TCACACTTGATGTTTACCCTCTT 57.695 39.130 0.00 0.00 40.64 2.85
2780 2820 7.016153 TCACACTTGATGTTTACCCTCTTAT 57.984 36.000 0.00 0.00 40.64 1.73
2826 2889 1.808411 AGTACACTTGCATTGGGTCG 58.192 50.000 0.00 0.00 0.00 4.79
2866 2929 6.912203 TCATTCATTTTGCTGCAAATATGG 57.088 33.333 28.76 20.10 33.19 2.74
2868 2931 3.533547 TCATTTTGCTGCAAATATGGCC 58.466 40.909 28.76 0.00 33.19 5.36
2953 3016 8.052748 GGATATGGCCCAAGTGTCAATAATATA 58.947 37.037 0.00 0.00 0.00 0.86
3021 3694 6.282930 GCATGTTGAAACTTATGGGCAATAT 58.717 36.000 0.00 0.00 0.00 1.28
3022 3695 6.762661 GCATGTTGAAACTTATGGGCAATATT 59.237 34.615 0.00 0.00 0.00 1.28
3044 3717 4.463050 TTTTGGGGTACAATGACCTCTT 57.537 40.909 0.00 0.00 41.04 2.85
3086 3759 3.364465 CGTTTGTGATTACAATGCCGTCA 60.364 43.478 3.63 0.00 45.56 4.35
3097 3770 1.174712 ATGCCGTCAGTTTTGCAGCT 61.175 50.000 0.00 0.00 37.12 4.24
3152 3826 3.825328 AGAGTGCTTTTGGTCACAATCT 58.175 40.909 0.00 0.00 36.29 2.40
3153 3827 4.210331 AGAGTGCTTTTGGTCACAATCTT 58.790 39.130 0.00 0.00 34.08 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 91 5.689383 AAGTGTTCGCTGTTTCATACAAT 57.311 34.783 0.00 0.00 36.02 2.71
842 876 3.077907 CCCACCCTGGATGAACGT 58.922 61.111 0.00 0.00 40.96 3.99
843 877 2.438434 GCCCACCCTGGATGAACG 60.438 66.667 0.00 0.00 40.96 3.95
844 878 2.043953 GGCCCACCCTGGATGAAC 60.044 66.667 0.00 0.00 40.96 3.18
845 879 3.727258 CGGCCCACCCTGGATGAA 61.727 66.667 0.00 0.00 40.96 2.57
867 901 4.139234 GTACCCGGACACCGCTCC 62.139 72.222 0.73 0.00 46.86 4.70
868 902 4.487412 CGTACCCGGACACCGCTC 62.487 72.222 0.73 0.00 46.86 5.03
869 903 3.918253 TACGTACCCGGACACCGCT 62.918 63.158 0.73 0.00 46.86 5.52
870 904 3.401243 CTACGTACCCGGACACCGC 62.401 68.421 0.73 0.00 46.86 5.68
872 906 0.453390 CTTCTACGTACCCGGACACC 59.547 60.000 0.73 0.00 38.78 4.16
873 907 0.179153 GCTTCTACGTACCCGGACAC 60.179 60.000 0.73 0.00 38.78 3.67
874 908 1.315257 GGCTTCTACGTACCCGGACA 61.315 60.000 0.73 0.00 38.78 4.02
875 909 1.435105 GGCTTCTACGTACCCGGAC 59.565 63.158 0.73 0.00 38.78 4.79
876 910 1.754234 GGGCTTCTACGTACCCGGA 60.754 63.158 0.73 0.00 38.78 5.14
877 911 1.397390 ATGGGCTTCTACGTACCCGG 61.397 60.000 12.85 0.00 46.02 5.73
878 912 0.462789 AATGGGCTTCTACGTACCCG 59.537 55.000 12.85 0.00 46.02 5.28
879 913 2.285977 CAAATGGGCTTCTACGTACCC 58.714 52.381 11.22 11.22 43.14 3.69
912 947 1.160137 GGCCGAATATGGACTGCATC 58.840 55.000 0.00 0.00 32.64 3.91
920 955 0.464373 AGTGTGCAGGCCGAATATGG 60.464 55.000 0.00 0.00 0.00 2.74
943 978 0.813821 GGTGGGCTGAAAATCTGAGC 59.186 55.000 0.00 0.00 0.00 4.26
961 996 1.216710 GAGGAGAACGGCTGAGTGG 59.783 63.158 0.00 0.00 0.00 4.00
993 1028 2.223947 GGTTTCGGTTGCCATTTTCAGT 60.224 45.455 0.00 0.00 0.00 3.41
995 1030 1.069358 GGGTTTCGGTTGCCATTTTCA 59.931 47.619 0.00 0.00 0.00 2.69
997 1032 0.032815 CGGGTTTCGGTTGCCATTTT 59.967 50.000 0.00 0.00 34.75 1.82
1081 1116 3.161450 GATCTGGCTGGCCGGGTA 61.161 66.667 15.02 2.67 42.60 3.69
1084 1119 4.559063 CTGGATCTGGCTGGCCGG 62.559 72.222 7.41 7.41 43.69 6.13
1227 1262 3.775316 GGATGGTTTTGGAGTAGAGGAGA 59.225 47.826 0.00 0.00 0.00 3.71
1247 1282 4.460683 CGATTTGGGACGCCGGGA 62.461 66.667 2.18 0.00 0.00 5.14
1270 1305 1.927174 CGTACTGGATTCCTTTGAGCG 59.073 52.381 3.95 0.00 0.00 5.03
1317 1352 3.121019 CCCTCGATCGACTCCACC 58.879 66.667 15.15 0.00 0.00 4.61
1374 1409 1.608154 GGCTACAAAGAGGACCCCC 59.392 63.158 0.00 0.00 0.00 5.40
1410 1445 2.436824 GGCCAGAAGTTCTCCGGC 60.437 66.667 20.88 20.88 35.49 6.13
1540 1575 4.148825 CTCCTTCCCCAGCGACCG 62.149 72.222 0.00 0.00 0.00 4.79
1759 1794 1.962807 CTTGGGCATGTGAAGGAACAA 59.037 47.619 0.00 0.00 32.81 2.83
1942 1977 4.065789 ACGAATCCTTCCTCACTGAAAAC 58.934 43.478 0.00 0.00 0.00 2.43
1959 1994 1.584724 ACCCCCTCTCATCAACGAAT 58.415 50.000 0.00 0.00 0.00 3.34
1963 1998 2.771943 TCATGTACCCCCTCTCATCAAC 59.228 50.000 0.00 0.00 0.00 3.18
1971 2006 1.132500 CCTTCCTCATGTACCCCCTC 58.868 60.000 0.00 0.00 0.00 4.30
1974 2009 1.421646 CCATCCTTCCTCATGTACCCC 59.578 57.143 0.00 0.00 0.00 4.95
2062 2097 0.990374 AGCTCCTCTTGGATGTGCTT 59.010 50.000 0.00 0.00 42.29 3.91
2073 2108 4.444591 CCATAAGCAAGATTCAGCTCCTCT 60.445 45.833 4.41 0.00 40.90 3.69
2196 2232 1.218047 GCCCGTATGACAGACAGCA 59.782 57.895 7.21 0.00 0.00 4.41
2248 2286 3.995199 TCAGTTTCTTCTTCTGCGACAT 58.005 40.909 0.00 0.00 0.00 3.06
2606 2646 6.877611 ACCGAACTAAAACAATGATTCAGT 57.122 33.333 0.00 0.00 0.00 3.41
2626 2666 3.057734 GGCTCCGTTATCTTATCAACCG 58.942 50.000 0.00 0.00 0.00 4.44
2661 2701 0.249120 TGCACGCACTAGCCAGTAAT 59.751 50.000 0.00 0.00 37.52 1.89
2675 2715 6.413818 CCAAGAACTTTTAGTTTTACTGCACG 59.586 38.462 0.00 0.00 38.80 5.34
2680 2720 8.803397 ACTGACCAAGAACTTTTAGTTTTACT 57.197 30.769 0.00 0.00 38.80 2.24
2780 2820 8.710239 TGGAGATAATAGTAAATGTGCTTACCA 58.290 33.333 0.00 0.00 33.06 3.25
2826 2889 2.910688 TGATGAAGGACGGAATAGGC 57.089 50.000 0.00 0.00 0.00 3.93
2866 2929 3.664107 TCGAAGGTTGCATATATCTGGC 58.336 45.455 0.00 0.00 0.00 4.85
2868 2931 7.664082 AGATTTCGAAGGTTGCATATATCTG 57.336 36.000 0.00 0.00 0.00 2.90
3022 3695 4.463050 AGAGGTCATTGTACCCCAAAAA 57.537 40.909 0.00 0.00 40.71 1.94
3044 3717 5.182169 ACGATAAAAACAGAATACCCCCA 57.818 39.130 0.00 0.00 0.00 4.96
3075 3748 0.743688 TGCAAAACTGACGGCATTGT 59.256 45.000 5.06 0.00 0.00 2.71
3086 3759 3.633525 TGATTTCAGTCAGCTGCAAAACT 59.366 39.130 9.47 4.16 42.29 2.66
3097 3770 5.749596 AAAACACACGATGATTTCAGTCA 57.250 34.783 0.00 0.00 27.55 3.41


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

AutoCloner maintained by Alex Coulton.