Multiple sequence alignment - TraesCS4A01G261400

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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 TraesCS4A01G261400 chr4A 100.000 3469 0 0 1 3469 573674733 573671265 0.000000e+00 6407
1 TraesCS4A01G261400 chr4A 97.679 1939 40 2 1531 3469 608863238 608865171 0.000000e+00 3326
2 TraesCS4A01G261400 chr4A 95.642 826 33 1 1 826 608862421 608863243 0.000000e+00 1323
3 TraesCS4A01G261400 chr4A 94.862 253 13 0 1 253 608862372 608862624 2.510000e-106 396
4 TraesCS4A01G261400 chr4A 79.121 455 67 20 250 684 85528529 85528975 4.380000e-74 289
5 TraesCS4A01G261400 chr3A 96.833 3473 92 6 1 3469 714634790 714631332 0.000000e+00 5788
6 TraesCS4A01G261400 chr3A 96.443 253 9 0 1 253 714634888 714634636 5.350000e-113 418
7 TraesCS4A01G261400 chr4D 96.089 3426 103 6 44 3469 477879863 477883257 0.000000e+00 5555
8 TraesCS4A01G261400 chr4D 96.475 2979 77 2 516 3469 433382863 433385838 0.000000e+00 4894
9 TraesCS4A01G261400 chr4D 91.156 294 25 1 44 337 433382558 433382850 6.980000e-107 398
10 TraesCS4A01G261400 chr5D 96.836 2813 81 4 659 3469 375446732 375443926 0.000000e+00 4695
11 TraesCS4A01G261400 chr5D 92.571 2948 132 28 579 3469 449917551 449914634 0.000000e+00 4150
12 TraesCS4A01G261400 chr5D 89.873 316 20 1 269 584 449926574 449926271 2.510000e-106 396
13 TraesCS4A01G261400 chr4B 93.434 2924 170 8 44 2954 14627915 14630829 0.000000e+00 4316
14 TraesCS4A01G261400 chr5A 94.552 1597 80 3 1876 3469 396676974 396678566 0.000000e+00 2460
15 TraesCS4A01G261400 chr5A 88.655 1375 122 15 25 1397 396616545 396617887 0.000000e+00 1644
16 TraesCS4A01G261400 chr5A 80.998 421 32 12 1506 1879 396667827 396668246 1.220000e-74 291
17 TraesCS4A01G261400 chr5A 90.678 118 10 1 1399 1516 396631418 396631534 4.640000e-34 156
18 TraesCS4A01G261400 chr3D 93.907 1510 62 15 1961 3469 149761355 149759875 0.000000e+00 2252
19 TraesCS4A01G261400 chr3D 89.809 157 16 0 1381 1537 149761506 149761350 5.870000e-48 202
20 TraesCS4A01G261400 chr2B 94.701 1321 55 5 2149 3469 685367142 685368447 0.000000e+00 2037
21 TraesCS4A01G261400 chr2B 95.394 1129 50 2 1025 2153 685356952 685358078 0.000000e+00 1796
22 TraesCS4A01G261400 chr2B 93.849 943 54 2 90 1032 685285211 685286149 0.000000e+00 1417
23 TraesCS4A01G261400 chr1D 93.878 49 3 0 1709 1757 392707066 392707114 1.340000e-09 75


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 TraesCS4A01G261400 chr4A 573671265 573674733 3468 True 6407.000000 6407 100.0000 1 3469 1 chr4A.!!$R1 3468
1 TraesCS4A01G261400 chr4A 608862372 608865171 2799 False 1681.666667 3326 96.0610 1 3469 3 chr4A.!!$F2 3468
2 TraesCS4A01G261400 chr3A 714631332 714634888 3556 True 3103.000000 5788 96.6380 1 3469 2 chr3A.!!$R1 3468
3 TraesCS4A01G261400 chr4D 477879863 477883257 3394 False 5555.000000 5555 96.0890 44 3469 1 chr4D.!!$F1 3425
4 TraesCS4A01G261400 chr4D 433382558 433385838 3280 False 2646.000000 4894 93.8155 44 3469 2 chr4D.!!$F2 3425
5 TraesCS4A01G261400 chr5D 375443926 375446732 2806 True 4695.000000 4695 96.8360 659 3469 1 chr5D.!!$R1 2810
6 TraesCS4A01G261400 chr5D 449914634 449917551 2917 True 4150.000000 4150 92.5710 579 3469 1 chr5D.!!$R2 2890
7 TraesCS4A01G261400 chr4B 14627915 14630829 2914 False 4316.000000 4316 93.4340 44 2954 1 chr4B.!!$F1 2910
8 TraesCS4A01G261400 chr5A 396676974 396678566 1592 False 2460.000000 2460 94.5520 1876 3469 1 chr5A.!!$F4 1593
9 TraesCS4A01G261400 chr5A 396616545 396617887 1342 False 1644.000000 1644 88.6550 25 1397 1 chr5A.!!$F1 1372
10 TraesCS4A01G261400 chr3D 149759875 149761506 1631 True 1227.000000 2252 91.8580 1381 3469 2 chr3D.!!$R1 2088
11 TraesCS4A01G261400 chr2B 685367142 685368447 1305 False 2037.000000 2037 94.7010 2149 3469 1 chr2B.!!$F3 1320
12 TraesCS4A01G261400 chr2B 685356952 685358078 1126 False 1796.000000 1796 95.3940 1025 2153 1 chr2B.!!$F2 1128
13 TraesCS4A01G261400 chr2B 685285211 685286149 938 False 1417.000000 1417 93.8490 90 1032 1 chr2B.!!$F1 942

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
839 1038 0.108774 TGCGTGGTGGTTCATGGTAA 59.891 50.0 0.00 0.0 0.00 2.85 F
1027 1226 0.253160 TGGAGAGGGTTGGCATAGGT 60.253 55.0 0.00 0.0 0.00 3.08 F
1967 2261 0.625849 CATTCCCCACTAGCAAGGGT 59.374 55.0 12.92 0.0 43.89 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 2261 1.554160 CCAAATAGCATGGCAACCCAA 59.446 47.619 0.00 0.00 46.14 4.12 R
1992 2286 4.373116 ATCTTGGTCACCGCGCGT 62.373 61.111 29.95 14.24 0.00 6.01 R
3109 3441 1.674962 GAATGTCATTGCTGAGCTCCC 59.325 52.381 12.15 2.65 30.18 4.30 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
74 75 5.535029 ACCTATTATGTGGTCTGAACCCTA 58.465 41.667 0.00 0.00 45.83 3.53
88 89 3.826157 TGAACCCTATTTGGCACTTTCTG 59.174 43.478 0.00 0.00 0.00 3.02
89 90 3.806949 ACCCTATTTGGCACTTTCTGA 57.193 42.857 0.00 0.00 0.00 3.27
157 256 6.877611 TCTAAATTTGTCTGAACCTGTTCC 57.122 37.500 7.51 0.00 38.77 3.62
177 325 2.033299 CCGTGCTCTGAAACATGTTTGT 59.967 45.455 27.85 5.40 37.82 2.83
200 348 8.099364 TGTCTATTTCTGAATTTGTCTGAACC 57.901 34.615 0.00 0.00 42.11 3.62
214 362 3.005897 GTCTGAACCTGTTCTGTGCTCTA 59.994 47.826 11.03 0.00 40.14 2.43
404 603 0.471617 AGCCAAAGAGATGGATCCCG 59.528 55.000 9.90 0.00 43.54 5.14
449 648 1.205460 GGAGGAGTTGGGTAGGGCAA 61.205 60.000 0.00 0.00 0.00 4.52
504 703 3.964221 GACATGAGCGACGGCGACA 62.964 63.158 18.90 15.08 46.35 4.35
788 987 5.580691 TCTGAATGTATGCGAAGTTAACTGG 59.419 40.000 9.34 5.74 0.00 4.00
839 1038 0.108774 TGCGTGGTGGTTCATGGTAA 59.891 50.000 0.00 0.00 0.00 2.85
1027 1226 0.253160 TGGAGAGGGTTGGCATAGGT 60.253 55.000 0.00 0.00 0.00 3.08
1050 1249 3.849951 CGGGAGCTATGTGCCGGT 61.850 66.667 1.90 0.00 46.90 5.28
1528 1727 4.075963 TGCTGCAATGTAGATGATGCTA 57.924 40.909 0.00 0.00 39.49 3.49
1638 1857 7.415989 GCATGGTTGATCTATGTGAATGAAACT 60.416 37.037 0.00 0.00 37.35 2.66
1660 1919 5.717178 ACTTGCTCTGAACTACCTCTGAATA 59.283 40.000 0.00 0.00 0.00 1.75
1690 1949 2.038952 TGTGCACTGCCTCTAAATCTGT 59.961 45.455 19.41 0.00 0.00 3.41
1967 2261 0.625849 CATTCCCCACTAGCAAGGGT 59.374 55.000 12.92 0.00 43.89 4.34
1992 2286 2.121291 TGCCATGCTATTTGGTTCGA 57.879 45.000 0.00 0.00 36.57 3.71
2015 2309 2.550978 CGCGGTGACCAAGATCTATTT 58.449 47.619 1.11 0.00 0.00 1.40
2182 2476 2.426024 TCGACACTCTACTATGGGCAAC 59.574 50.000 0.00 0.00 0.00 4.17
2574 2871 3.978855 TGTTCACAAGTTCAGTATCGTCG 59.021 43.478 0.00 0.00 0.00 5.12
2588 2885 7.709947 TCAGTATCGTCGGTTATGTTTATCTT 58.290 34.615 0.00 0.00 0.00 2.40
3109 3441 1.586154 GCACCCATGACCAACCTTCG 61.586 60.000 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 9.594478 AAACAAATAAAGAAAGTACCAAACAGG 57.406 29.630 0.00 0.00 45.67 4.00
47 48 6.177610 GGTTCAGACCACATAATAGGTTCAA 58.822 40.000 0.00 0.00 45.77 2.69
74 75 6.822676 TCAAACAAATTCAGAAAGTGCCAAAT 59.177 30.769 0.00 0.00 0.00 2.32
88 89 5.005682 GCACAGAACAGGTTCAAACAAATTC 59.994 40.000 14.06 0.00 41.84 2.17
89 90 4.869861 GCACAGAACAGGTTCAAACAAATT 59.130 37.500 14.06 0.00 41.84 1.82
157 256 3.002656 AGACAAACATGTTTCAGAGCACG 59.997 43.478 20.85 9.77 0.00 5.34
177 325 7.939039 ACAGGTTCAGACAAATTCAGAAATAGA 59.061 33.333 0.00 0.00 31.98 1.98
200 348 5.679734 ACATGTTTTAGAGCACAGAACAG 57.320 39.130 0.00 0.00 34.17 3.16
214 362 8.907222 AATTCAGAAATAGCCAAACATGTTTT 57.093 26.923 21.10 9.94 0.00 2.43
404 603 0.038166 TCAACAACCTCTCCATGGCC 59.962 55.000 6.96 0.00 0.00 5.36
449 648 3.117888 TCTTCTCTTGCAACCCTTCTTGT 60.118 43.478 0.00 0.00 0.00 3.16
802 1001 3.228749 CGCACAAACAATTACAGAGCAG 58.771 45.455 0.00 0.00 0.00 4.24
839 1038 7.071196 TGTGGATGCTTCTAGACCTACATTAAT 59.929 37.037 0.00 0.00 0.00 1.40
994 1193 1.819208 CTCCAAATGCCATCGCCGA 60.819 57.895 0.00 0.00 0.00 5.54
1050 1249 0.251033 ACTGCAGCTTCTTGGCATCA 60.251 50.000 15.27 0.00 36.87 3.07
1397 1596 1.148048 GAGCATGCTTCCTCCTCCC 59.852 63.158 23.61 1.03 0.00 4.30
1460 1659 0.039437 ACGCTCTGAACGACGAACAT 60.039 50.000 7.54 0.00 0.00 2.71
1528 1727 4.026744 ACAGGTAGATCATACACTGCAGT 58.973 43.478 15.25 15.25 0.00 4.40
1638 1857 6.381133 TCATATTCAGAGGTAGTTCAGAGCAA 59.619 38.462 0.00 0.00 0.00 3.91
1660 1919 4.275810 AGAGGCAGTGCACAATAATTCAT 58.724 39.130 21.04 0.00 0.00 2.57
1967 2261 1.554160 CCAAATAGCATGGCAACCCAA 59.446 47.619 0.00 0.00 46.14 4.12
1992 2286 4.373116 ATCTTGGTCACCGCGCGT 62.373 61.111 29.95 14.24 0.00 6.01
2015 2309 5.470437 CGTAGCTATCTTCATGTAGTCCAGA 59.530 44.000 0.00 0.00 0.00 3.86
2182 2476 4.655921 AGGACTCTGCCTCTCTCG 57.344 61.111 0.00 0.00 30.76 4.04
2588 2885 5.639757 GCACATACATGCACATCAAGTTTA 58.360 37.500 0.00 0.00 45.39 2.01
3109 3441 1.674962 GAATGTCATTGCTGAGCTCCC 59.325 52.381 12.15 2.65 30.18 4.30


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

AutoCloner maintained by Alex Coulton.