Multiple sequence alignment - TraesCS1A01G074000

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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 TraesCS1A01G074000 chr1A 100.000 2948 0 0 1 2948 57641207 57638260 0.000000e+00 5445
1 TraesCS1A01G074000 chr1A 90.720 1541 129 8 1049 2583 57405806 57404274 0.000000e+00 2041
2 TraesCS1A01G074000 chr1A 82.073 1534 258 13 1059 2584 37512185 37510661 0.000000e+00 1293
3 TraesCS1A01G074000 chr1A 91.068 918 69 11 1 913 199940333 199939424 0.000000e+00 1229
4 TraesCS1A01G074000 chr1A 82.465 787 127 9 1097 1874 36188248 36187464 0.000000e+00 678
5 TraesCS1A01G074000 chr1A 83.840 724 100 13 1856 2573 36614129 36614841 0.000000e+00 673
6 TraesCS1A01G074000 chr1D 92.124 1676 118 10 916 2584 58764276 58762608 0.000000e+00 2351
7 TraesCS1A01G074000 chr1D 91.611 1645 114 10 959 2584 58628733 58627094 0.000000e+00 2252
8 TraesCS1A01G074000 chr1D 82.150 1535 240 25 1062 2583 58869887 58868374 0.000000e+00 1286
9 TraesCS1A01G074000 chr1D 82.270 846 136 9 1036 1871 50059264 50060105 0.000000e+00 719
10 TraesCS1A01G074000 chr1D 83.571 700 107 8 1889 2584 38367056 38366361 0.000000e+00 649
11 TraesCS1A01G074000 chr1D 83.357 697 113 3 1887 2582 36623637 36622943 2.480000e-180 641
12 TraesCS1A01G074000 chr1D 81.715 793 123 20 1088 1866 37964719 37963935 2.480000e-180 641
13 TraesCS1A01G074000 chr1D 83.051 708 112 6 1864 2569 37424787 37425488 1.150000e-178 636
14 TraesCS1A01G074000 chr1D 95.902 366 15 0 2583 2948 58761571 58761206 7.030000e-166 593
15 TraesCS1A01G074000 chr1B 92.101 1671 125 3 914 2584 94233360 94231697 0.000000e+00 2348
16 TraesCS1A01G074000 chr1B 82.333 1449 238 15 1062 2503 94327198 94325761 0.000000e+00 1242
17 TraesCS1A01G074000 chr1B 84.187 683 104 3 1904 2584 58115637 58114957 0.000000e+00 660
18 TraesCS1A01G074000 chr1B 93.817 372 17 1 2583 2948 94230702 94230331 3.320000e-154 555
19 TraesCS1A01G074000 chr2A 94.317 915 51 1 1 914 474686300 474687214 0.000000e+00 1400
20 TraesCS1A01G074000 chr2A 93.021 917 56 6 1 913 350187277 350186365 0.000000e+00 1332
21 TraesCS1A01G074000 chr2A 91.913 915 56 10 1 913 350179717 350178819 0.000000e+00 1264
22 TraesCS1A01G074000 chr2A 90.481 914 83 4 1 911 324739763 324740675 0.000000e+00 1203
23 TraesCS1A01G074000 chr2A 89.989 929 81 11 1 925 728223342 728222422 0.000000e+00 1190
24 TraesCS1A01G074000 chr2A 89.794 921 84 9 1 918 322057211 322058124 0.000000e+00 1171
25 TraesCS1A01G074000 chr6A 90.721 916 72 12 1 911 290137213 290136306 0.000000e+00 1208
26 TraesCS1A01G074000 chr3A 89.559 929 81 15 1 923 310419883 310420801 0.000000e+00 1164


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 TraesCS1A01G074000 chr1A 57638260 57641207 2947 True 5445.0 5445 100.000 1 2948 1 chr1A.!!$R4 2947
1 TraesCS1A01G074000 chr1A 57404274 57405806 1532 True 2041.0 2041 90.720 1049 2583 1 chr1A.!!$R3 1534
2 TraesCS1A01G074000 chr1A 37510661 37512185 1524 True 1293.0 1293 82.073 1059 2584 1 chr1A.!!$R2 1525
3 TraesCS1A01G074000 chr1A 199939424 199940333 909 True 1229.0 1229 91.068 1 913 1 chr1A.!!$R5 912
4 TraesCS1A01G074000 chr1A 36187464 36188248 784 True 678.0 678 82.465 1097 1874 1 chr1A.!!$R1 777
5 TraesCS1A01G074000 chr1A 36614129 36614841 712 False 673.0 673 83.840 1856 2573 1 chr1A.!!$F1 717
6 TraesCS1A01G074000 chr1D 58627094 58628733 1639 True 2252.0 2252 91.611 959 2584 1 chr1D.!!$R4 1625
7 TraesCS1A01G074000 chr1D 58761206 58764276 3070 True 1472.0 2351 94.013 916 2948 2 chr1D.!!$R6 2032
8 TraesCS1A01G074000 chr1D 58868374 58869887 1513 True 1286.0 1286 82.150 1062 2583 1 chr1D.!!$R5 1521
9 TraesCS1A01G074000 chr1D 50059264 50060105 841 False 719.0 719 82.270 1036 1871 1 chr1D.!!$F2 835
10 TraesCS1A01G074000 chr1D 38366361 38367056 695 True 649.0 649 83.571 1889 2584 1 chr1D.!!$R3 695
11 TraesCS1A01G074000 chr1D 36622943 36623637 694 True 641.0 641 83.357 1887 2582 1 chr1D.!!$R1 695
12 TraesCS1A01G074000 chr1D 37963935 37964719 784 True 641.0 641 81.715 1088 1866 1 chr1D.!!$R2 778
13 TraesCS1A01G074000 chr1D 37424787 37425488 701 False 636.0 636 83.051 1864 2569 1 chr1D.!!$F1 705
14 TraesCS1A01G074000 chr1B 94230331 94233360 3029 True 1451.5 2348 92.959 914 2948 2 chr1B.!!$R3 2034
15 TraesCS1A01G074000 chr1B 94325761 94327198 1437 True 1242.0 1242 82.333 1062 2503 1 chr1B.!!$R2 1441
16 TraesCS1A01G074000 chr1B 58114957 58115637 680 True 660.0 660 84.187 1904 2584 1 chr1B.!!$R1 680
17 TraesCS1A01G074000 chr2A 474686300 474687214 914 False 1400.0 1400 94.317 1 914 1 chr2A.!!$F3 913
18 TraesCS1A01G074000 chr2A 350186365 350187277 912 True 1332.0 1332 93.021 1 913 1 chr2A.!!$R2 912
19 TraesCS1A01G074000 chr2A 350178819 350179717 898 True 1264.0 1264 91.913 1 913 1 chr2A.!!$R1 912
20 TraesCS1A01G074000 chr2A 324739763 324740675 912 False 1203.0 1203 90.481 1 911 1 chr2A.!!$F2 910
21 TraesCS1A01G074000 chr2A 728222422 728223342 920 True 1190.0 1190 89.989 1 925 1 chr2A.!!$R3 924
22 TraesCS1A01G074000 chr2A 322057211 322058124 913 False 1171.0 1171 89.794 1 918 1 chr2A.!!$F1 917
23 TraesCS1A01G074000 chr6A 290136306 290137213 907 True 1208.0 1208 90.721 1 911 1 chr6A.!!$R1 910
24 TraesCS1A01G074000 chr3A 310419883 310420801 918 False 1164.0 1164 89.559 1 923 1 chr3A.!!$F1 922

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
266 267 0.250770 GAAAGCCCAGAACTTCCGGT 60.251 55.0 0.00 0.0 0.00 5.28 F
1268 1342 0.822811 GCTGCTCTCAGAGATGGACA 59.177 55.0 5.62 0.0 42.95 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1821 0.319813 GGCACAATCCCTTGTTGCAC 60.32 55.0 0.0 0.0 43.05 4.57 R
2772 3896 0.839946 CTTGCTGGCACCCCTAGTAT 59.16 55.0 0.0 0.0 0.00 2.12 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
17 18 2.257371 TCAAGAGTCCGTTCGGCG 59.743 61.111 0.00 0.00 40.95 6.46
49 50 2.540101 GCGGCATCTACTTCACATACAC 59.460 50.000 0.00 0.00 0.00 2.90
121 122 5.535029 TGGTATACTACTTGACCCTCCATT 58.465 41.667 2.25 0.00 0.00 3.16
255 256 2.306847 GACAAGTTTCTGGAAAGCCCA 58.693 47.619 0.00 0.00 44.25 5.36
266 267 0.250770 GAAAGCCCAGAACTTCCGGT 60.251 55.000 0.00 0.00 0.00 5.28
494 495 0.974383 CACTTACCCCTTCGTGGACT 59.026 55.000 0.00 0.00 38.35 3.85
538 539 2.701423 CTCCTCCTTTCTAGGGTTAGCC 59.299 54.545 0.00 0.00 42.26 3.93
620 621 3.077556 ACTGCGGCCTCTTCGGAT 61.078 61.111 0.00 0.00 33.16 4.18
649 650 2.414250 TTGGATTCAAGCCCCCTTTT 57.586 45.000 0.00 0.00 0.00 2.27
683 686 0.905357 CCCGTGGATTCAAGACCTCT 59.095 55.000 0.00 0.00 0.00 3.69
773 779 1.892209 TCGAGGATCTAGCGCATGTA 58.108 50.000 11.47 0.00 0.00 2.29
785 791 6.924111 TCTAGCGCATGTATGATCATTCTTA 58.076 36.000 14.65 0.00 0.00 2.10
789 795 6.652062 AGCGCATGTATGATCATTCTTATTGA 59.348 34.615 14.65 0.00 0.00 2.57
846 899 2.572290 CTCGTTTCCCTCCTTGTGTTT 58.428 47.619 0.00 0.00 0.00 2.83
906 959 2.653366 TCGGGCTATAGGATTCCTACCT 59.347 50.000 14.72 2.96 39.10 3.08
907 960 3.854389 TCGGGCTATAGGATTCCTACCTA 59.146 47.826 14.72 3.99 39.10 3.08
908 961 3.952967 CGGGCTATAGGATTCCTACCTAC 59.047 52.174 14.72 6.24 41.87 3.18
909 962 4.569228 CGGGCTATAGGATTCCTACCTACA 60.569 50.000 14.72 0.00 41.87 2.74
910 963 5.530243 GGGCTATAGGATTCCTACCTACAT 58.470 45.833 14.72 1.80 41.87 2.29
911 964 5.599242 GGGCTATAGGATTCCTACCTACATC 59.401 48.000 14.72 2.08 41.87 3.06
912 965 6.195700 GGCTATAGGATTCCTACCTACATCA 58.804 44.000 14.72 0.00 41.87 3.07
930 983 1.086696 CACATTTGGTACAGCGGAGG 58.913 55.000 0.00 0.00 42.39 4.30
949 1002 3.691744 CTCCTCTCAGTCGCGCACC 62.692 68.421 8.75 0.00 0.00 5.01
1016 1070 2.800541 CCATGGCTCGCCTCTGCTA 61.801 63.158 9.65 0.00 36.94 3.49
1268 1342 0.822811 GCTGCTCTCAGAGATGGACA 59.177 55.000 5.62 0.00 42.95 4.02
1323 1397 3.435186 GAAGAAGCAGGGCCGTGC 61.435 66.667 37.16 37.16 44.35 5.34
1368 1442 3.198635 CCTACAACATCCTCATGGACAGT 59.801 47.826 0.00 0.00 46.51 3.55
1385 1459 2.594013 TTGCTGTCGTGCATGCCA 60.594 55.556 16.68 4.59 42.96 4.92
1457 1531 1.439228 CAGACCAGATCGTCGCCAT 59.561 57.895 0.00 0.00 37.85 4.40
1687 1764 2.867647 GCATATAGCACAGTCATCCGCA 60.868 50.000 0.00 0.00 44.79 5.69
1701 1778 2.386661 TCCGCAGCTTCTTTAAGGAG 57.613 50.000 0.00 0.00 32.98 3.69
1713 1790 6.744622 GCTTCTTTAAGGAGGGTGAAGTAAGT 60.745 42.308 2.08 0.00 34.96 2.24
1879 1959 7.724305 GGTGTTCGACCAAATATGTATACAT 57.276 36.000 21.57 21.57 45.34 2.29
1880 1960 7.572759 GGTGTTCGACCAAATATGTATACATG 58.427 38.462 25.48 12.11 45.34 3.21
1919 1999 2.800250 ACTCCCTTTGCAAGAATGGAG 58.200 47.619 23.21 23.21 43.20 3.86
2070 2150 9.630098 TCTCTTTAATTCAATGAAAGACAATGC 57.370 29.630 5.87 0.00 34.95 3.56
2455 2535 1.074889 TGCAAGGAAGGAAGGGTTACC 59.925 52.381 0.00 0.00 0.00 2.85
2458 2538 1.569653 AGGAAGGAAGGGTTACCGAG 58.430 55.000 0.00 0.00 43.47 4.63
2578 2658 6.493802 AGATGGATAAAGCATTCGGAGTACTA 59.506 38.462 0.00 0.00 0.00 1.82
2617 3741 9.638239 TTTGAGTATTTCAAGGAAAATATGTGC 57.362 29.630 0.00 0.00 46.01 4.57
2686 3810 4.394729 AGAAAATCTTGGTGAAAGCGGTA 58.605 39.130 0.00 0.00 36.92 4.02
2772 3896 7.112452 TCAGCTTAGCACTATGATAGAAACA 57.888 36.000 7.07 0.00 0.00 2.83
2865 3989 1.620323 GAAAGTGGATGCCTTGGCTTT 59.380 47.619 13.18 3.81 0.00 3.51
2904 4028 6.233905 TCAACATTACCATGCTAGCTAGAA 57.766 37.500 25.15 15.37 33.05 2.10
2912 4036 4.410228 ACCATGCTAGCTAGAAAAGGATGA 59.590 41.667 25.15 0.00 40.37 2.92
2914 4038 5.363101 CATGCTAGCTAGAAAAGGATGACA 58.637 41.667 25.15 8.73 40.37 3.58
2945 4069 1.745653 GCAACAGAGTTTCCTATGGGC 59.254 52.381 0.00 0.00 34.14 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.103911 GTGTCACTCGCCGAACGG 61.104 66.667 9.00 9.00 43.89 4.44
10 11 2.354305 ACGTGTCACTCGCCGAAC 60.354 61.111 0.00 0.00 0.00 3.95
17 18 2.730672 GATGCCGCACGTGTCACTC 61.731 63.158 18.38 4.61 0.00 3.51
31 32 5.643777 ACCTTTGTGTATGTGAAGTAGATGC 59.356 40.000 0.00 0.00 0.00 3.91
61 62 2.059541 GTGAGCACGTGTAAAGGAGAC 58.940 52.381 18.38 0.00 0.00 3.36
121 122 2.871633 CGACAATACCTATGCATGCACA 59.128 45.455 25.37 11.52 0.00 4.57
255 256 2.048127 GCAGCGACCGGAAGTTCT 60.048 61.111 9.46 0.00 0.00 3.01
494 495 8.780003 GGAGGTGGAGGAGTATATATAGTCTAA 58.220 40.741 21.59 7.40 34.04 2.10
538 539 8.358895 TCTATCTCTCAAATGAGCTATCACAAG 58.641 37.037 5.53 0.00 41.80 3.16
620 621 4.956075 GGGCTTGAATCCAAAAGGATCTTA 59.044 41.667 0.00 0.00 0.00 2.10
628 629 2.414250 AAGGGGGCTTGAATCCAAAA 57.586 45.000 0.00 0.00 0.00 2.44
773 779 7.709947 ACACGCAAATCAATAAGAATGATCAT 58.290 30.769 1.18 1.18 0.00 2.45
785 791 4.036734 ACACAAGAGAACACGCAAATCAAT 59.963 37.500 0.00 0.00 0.00 2.57
789 795 3.243068 GGAACACAAGAGAACACGCAAAT 60.243 43.478 0.00 0.00 0.00 2.32
794 800 1.202651 AGGGGAACACAAGAGAACACG 60.203 52.381 0.00 0.00 0.00 4.49
846 899 3.001838 CGAATCCCGCGATGAATACAAAA 59.998 43.478 8.23 0.00 0.00 2.44
849 902 1.778334 CGAATCCCGCGATGAATACA 58.222 50.000 8.23 0.00 0.00 2.29
872 925 2.171635 GCCCGAGCTTTCACGAAAT 58.828 52.632 0.00 0.00 35.50 2.17
897 950 6.327386 ACCAAATGTGATGTAGGTAGGAAT 57.673 37.500 0.00 0.00 0.00 3.01
906 959 3.055747 TCCGCTGTACCAAATGTGATGTA 60.056 43.478 0.00 0.00 0.00 2.29
907 960 2.083774 CCGCTGTACCAAATGTGATGT 58.916 47.619 0.00 0.00 0.00 3.06
908 961 2.352651 CTCCGCTGTACCAAATGTGATG 59.647 50.000 0.00 0.00 0.00 3.07
909 962 2.632377 CTCCGCTGTACCAAATGTGAT 58.368 47.619 0.00 0.00 0.00 3.06
910 963 1.338674 CCTCCGCTGTACCAAATGTGA 60.339 52.381 0.00 0.00 0.00 3.58
911 964 1.086696 CCTCCGCTGTACCAAATGTG 58.913 55.000 0.00 0.00 0.00 3.21
912 965 0.676782 GCCTCCGCTGTACCAAATGT 60.677 55.000 0.00 0.00 0.00 2.71
930 983 4.121669 TGCGCGACTGAGAGGAGC 62.122 66.667 12.10 0.00 0.00 4.70
949 1002 2.716017 GGAGTGGGAGTGGCGAGAG 61.716 68.421 0.00 0.00 0.00 3.20
994 1047 3.474570 GAGGCGAGCCATGGGACT 61.475 66.667 15.13 3.80 38.92 3.85
1203 1274 2.218603 GCAAGGAAGTCGTTGAAGGAA 58.781 47.619 15.89 0.00 42.45 3.36
1207 1278 1.503818 GCGGCAAGGAAGTCGTTGAA 61.504 55.000 15.89 0.00 42.45 2.69
1236 1307 4.828925 GCAGCGGAGGACAGAGCC 62.829 72.222 0.00 0.00 0.00 4.70
1241 1312 2.283173 TGAGAGCAGCGGAGGACA 60.283 61.111 0.00 0.00 0.00 4.02
1285 1359 0.670546 CGGCAGACACGGTTGAAGAT 60.671 55.000 0.00 0.00 0.00 2.40
1323 1397 4.602259 ACTGTGGGTGGCGTCACG 62.602 66.667 14.98 1.88 44.50 4.35
1327 1401 4.626081 GCAGACTGTGGGTGGCGT 62.626 66.667 3.99 0.00 0.00 5.68
1385 1459 2.687566 CAGGGCCTAGGTTCGGGT 60.688 66.667 5.28 0.00 0.00 5.28
1457 1531 0.687354 GAGGCACTTGAGGAGGTTGA 59.313 55.000 0.00 0.00 41.55 3.18
1493 1567 1.681166 GCATGTTGACAGCCTCATCCT 60.681 52.381 0.00 0.00 0.00 3.24
1685 1762 2.087646 CACCCTCCTTAAAGAAGCTGC 58.912 52.381 0.00 0.00 0.00 5.25
1687 1764 3.653352 ACTTCACCCTCCTTAAAGAAGCT 59.347 43.478 0.00 0.00 36.77 3.74
1701 1778 2.683362 GCATGCCTTACTTACTTCACCC 59.317 50.000 6.36 0.00 0.00 4.61
1741 1821 0.319813 GGCACAATCCCTTGTTGCAC 60.320 55.000 0.00 0.00 43.05 4.57
1746 1826 3.091545 CACATTAGGCACAATCCCTTGT 58.908 45.455 0.00 0.00 46.54 3.16
1879 1959 4.847198 AGTACATGAATGAGTTCCATGCA 58.153 39.130 0.00 0.00 44.63 3.96
1880 1960 4.274459 GGAGTACATGAATGAGTTCCATGC 59.726 45.833 0.00 0.00 35.24 4.06
1919 1999 1.242076 TCTGCAGCTTCTTTGCTTCC 58.758 50.000 9.47 0.00 41.98 3.46
2070 2150 4.970662 ACATTGCAGTTGGCTACAATAG 57.029 40.909 1.24 0.00 45.15 1.73
2455 2535 1.399572 CGAAGATATCGTGTGCCTCG 58.600 55.000 0.00 0.00 46.52 4.63
2578 2658 8.621532 TGAAATACTCAAAAGTGTTAGCATCT 57.378 30.769 0.00 0.00 35.98 2.90
2602 3720 9.512435 CTTATTCTCTTGCACATATTTTCCTTG 57.488 33.333 0.00 0.00 0.00 3.61
2686 3810 2.267174 AGTCAGACATTGCTTGTGCT 57.733 45.000 2.66 0.00 39.18 4.40
2689 3813 3.815401 GGTGTAAGTCAGACATTGCTTGT 59.185 43.478 2.66 0.00 42.79 3.16
2772 3896 0.839946 CTTGCTGGCACCCCTAGTAT 59.160 55.000 0.00 0.00 0.00 2.12
2777 3901 4.357279 GCTCTTGCTGGCACCCCT 62.357 66.667 0.00 0.00 36.03 4.79
2801 3925 5.923684 CGCCAACTAAGCCAAAGAATTTAAA 59.076 36.000 0.00 0.00 35.03 1.52
2865 3989 2.700371 TGTTGAAGAGCTGGAGAGACAA 59.300 45.455 0.00 0.00 0.00 3.18
2904 4028 3.679389 CCTGCAGTAACTGTCATCCTTT 58.321 45.455 13.81 0.00 33.43 3.11
2912 4036 1.140852 TCTGTTGCCTGCAGTAACTGT 59.859 47.619 23.36 0.00 41.29 3.55
2914 4038 1.417890 ACTCTGTTGCCTGCAGTAACT 59.582 47.619 23.36 8.08 41.29 2.24


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

AutoCloner maintained by Alex Coulton.