Multiple sequence alignment - TraesCS1D01G295000

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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 TraesCS1D01G295000 chr1D 100.000 3079 0 0 1 3079 393955177 393952099 0.000000e+00 5686
1 TraesCS1D01G295000 chr1D 87.391 230 14 9 1173 1398 460187154 460186936 1.830000e-62 250
2 TraesCS1D01G295000 chr5D 99.313 1601 10 1 1480 3079 375000455 375002055 0.000000e+00 2894
3 TraesCS1D01G295000 chr5D 97.027 1480 26 6 1 1479 374998884 375000346 0.000000e+00 2473
4 TraesCS1D01G295000 chr5D 95.910 1198 38 4 1891 3079 397465441 397466636 0.000000e+00 1930
5 TraesCS1D01G295000 chr5D 94.979 1215 30 5 1894 3079 397474329 397473117 0.000000e+00 1877
6 TraesCS1D01G295000 chr5D 96.999 833 16 4 2254 3079 184452258 184453088 0.000000e+00 1391
7 TraesCS1D01G295000 chr5D 87.204 930 91 24 1 912 405996162 405997081 0.000000e+00 1033
8 TraesCS1D01G295000 chr5D 91.322 484 32 5 917 1398 397475114 397474639 0.000000e+00 652
9 TraesCS1D01G295000 chr5D 91.004 478 31 7 923 1398 397464667 397465134 4.330000e-178 634
10 TraesCS1D01G295000 chr6B 95.703 1187 50 1 1894 3079 666362091 666360905 0.000000e+00 1908
11 TraesCS1D01G295000 chr6B 91.661 1355 93 11 1 1346 296978991 296977648 0.000000e+00 1858
12 TraesCS1D01G295000 chr6B 87.230 1433 118 25 1 1398 666363802 666362400 0.000000e+00 1572
13 TraesCS1D01G295000 chr6B 94.842 349 18 0 1554 1902 296977649 296977301 2.090000e-151 545
14 TraesCS1D01G295000 chr7B 92.411 1344 85 12 8 1346 634851877 634853208 0.000000e+00 1901
15 TraesCS1D01G295000 chr7B 90.621 789 54 15 1 777 2886786 2887566 0.000000e+00 1029
16 TraesCS1D01G295000 chr7B 88.050 477 40 10 1954 2425 19955803 19955339 1.610000e-152 549
17 TraesCS1D01G295000 chr7B 94.842 349 14 2 1554 1902 634853207 634853551 2.700000e-150 542
18 TraesCS1D01G295000 chr7B 86.842 228 17 8 1173 1398 19956351 19956135 3.070000e-60 243
19 TraesCS1D01G295000 chr7B 79.646 226 25 11 1915 2140 633832192 633832396 3.200000e-30 143
20 TraesCS1D01G295000 chr2A 91.778 1350 96 9 1 1346 664863306 664864644 0.000000e+00 1864
21 TraesCS1D01G295000 chr2A 95.889 827 32 2 2254 3079 478454829 478455654 0.000000e+00 1338
22 TraesCS1D01G295000 chr2A 91.409 745 55 9 1 740 761131546 761132286 0.000000e+00 1013
23 TraesCS1D01G295000 chr2A 94.861 467 20 2 2254 2719 33473642 33473179 0.000000e+00 726
24 TraesCS1D01G295000 chr2A 94.556 349 19 0 1554 1902 664864643 664864991 9.710000e-150 540
25 TraesCS1D01G295000 chr2B 96.521 1121 36 2 1960 3079 574051068 574052186 0.000000e+00 1851
26 TraesCS1D01G295000 chr2B 91.512 1343 95 13 1 1337 177027990 177029319 0.000000e+00 1831
27 TraesCS1D01G295000 chr2B 96.562 349 12 0 1554 1902 177029327 177029675 2.060000e-161 579
28 TraesCS1D01G295000 chr3B 90.970 1351 91 12 1 1346 33632166 33633490 0.000000e+00 1790
29 TraesCS1D01G295000 chr3B 96.275 349 13 0 1554 1902 33633489 33633837 9.580000e-160 573
30 TraesCS1D01G295000 chr3B 97.048 271 6 1 1554 1822 777718297 777718027 3.620000e-124 455
31 TraesCS1D01G295000 chr3A 88.881 1430 105 24 1 1393 720604006 720602594 0.000000e+00 1711
32 TraesCS1D01G295000 chr3A 96.907 388 12 0 2692 3079 117787218 117786831 0.000000e+00 651
33 TraesCS1D01G295000 chr1A 95.296 829 35 3 2254 3079 205552522 205553349 0.000000e+00 1312
34 TraesCS1D01G295000 chr1A 87.764 237 17 5 1173 1399 551739782 551739548 1.820000e-67 267
35 TraesCS1D01G295000 chr7A 96.741 675 18 1 2409 3079 692228755 692229429 0.000000e+00 1122
36 TraesCS1D01G295000 chr7A 90.189 795 61 16 1 782 579787392 579788182 0.000000e+00 1020
37 TraesCS1D01G295000 chr7A 85.990 414 24 22 1480 1871 3910649 3910248 2.210000e-111 412
38 TraesCS1D01G295000 chr2D 87.460 941 87 17 1 913 614127564 614128501 0.000000e+00 1055
39 TraesCS1D01G295000 chr2D 89.222 334 17 8 2125 2440 488994170 488993838 1.720000e-107 399
40 TraesCS1D01G295000 chr2D 86.640 247 20 7 1905 2140 488994431 488994187 8.470000e-66 261
41 TraesCS1D01G295000 chr4A 90.705 624 48 4 777 1398 444375284 444375899 0.000000e+00 822
42 TraesCS1D01G295000 chr4A 82.968 411 37 20 1480 1871 739521837 739522233 1.060000e-89 340
43 TraesCS1D01G295000 chr7D 83.417 398 24 24 1499 1871 4075758 4075378 6.360000e-87 331
44 TraesCS1D01G295000 chr5B 80.088 226 24 9 1915 2140 676859099 676858895 6.880000e-32 148


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 TraesCS1D01G295000 chr1D 393952099 393955177 3078 True 5686.0 5686 100.0000 1 3079 1 chr1D.!!$R1 3078
1 TraesCS1D01G295000 chr5D 374998884 375002055 3171 False 2683.5 2894 98.1700 1 3079 2 chr5D.!!$F3 3078
2 TraesCS1D01G295000 chr5D 184452258 184453088 830 False 1391.0 1391 96.9990 2254 3079 1 chr5D.!!$F1 825
3 TraesCS1D01G295000 chr5D 397464667 397466636 1969 False 1282.0 1930 93.4570 923 3079 2 chr5D.!!$F4 2156
4 TraesCS1D01G295000 chr5D 397473117 397475114 1997 True 1264.5 1877 93.1505 917 3079 2 chr5D.!!$R1 2162
5 TraesCS1D01G295000 chr5D 405996162 405997081 919 False 1033.0 1033 87.2040 1 912 1 chr5D.!!$F2 911
6 TraesCS1D01G295000 chr6B 666360905 666363802 2897 True 1740.0 1908 91.4665 1 3079 2 chr6B.!!$R2 3078
7 TraesCS1D01G295000 chr6B 296977301 296978991 1690 True 1201.5 1858 93.2515 1 1902 2 chr6B.!!$R1 1901
8 TraesCS1D01G295000 chr7B 634851877 634853551 1674 False 1221.5 1901 93.6265 8 1902 2 chr7B.!!$F3 1894
9 TraesCS1D01G295000 chr7B 2886786 2887566 780 False 1029.0 1029 90.6210 1 777 1 chr7B.!!$F1 776
10 TraesCS1D01G295000 chr7B 19955339 19956351 1012 True 396.0 549 87.4460 1173 2425 2 chr7B.!!$R1 1252
11 TraesCS1D01G295000 chr2A 478454829 478455654 825 False 1338.0 1338 95.8890 2254 3079 1 chr2A.!!$F1 825
12 TraesCS1D01G295000 chr2A 664863306 664864991 1685 False 1202.0 1864 93.1670 1 1902 2 chr2A.!!$F3 1901
13 TraesCS1D01G295000 chr2A 761131546 761132286 740 False 1013.0 1013 91.4090 1 740 1 chr2A.!!$F2 739
14 TraesCS1D01G295000 chr2B 574051068 574052186 1118 False 1851.0 1851 96.5210 1960 3079 1 chr2B.!!$F1 1119
15 TraesCS1D01G295000 chr2B 177027990 177029675 1685 False 1205.0 1831 94.0370 1 1902 2 chr2B.!!$F2 1901
16 TraesCS1D01G295000 chr3B 33632166 33633837 1671 False 1181.5 1790 93.6225 1 1902 2 chr3B.!!$F1 1901
17 TraesCS1D01G295000 chr3A 720602594 720604006 1412 True 1711.0 1711 88.8810 1 1393 1 chr3A.!!$R2 1392
18 TraesCS1D01G295000 chr1A 205552522 205553349 827 False 1312.0 1312 95.2960 2254 3079 1 chr1A.!!$F1 825
19 TraesCS1D01G295000 chr7A 692228755 692229429 674 False 1122.0 1122 96.7410 2409 3079 1 chr7A.!!$F2 670
20 TraesCS1D01G295000 chr7A 579787392 579788182 790 False 1020.0 1020 90.1890 1 782 1 chr7A.!!$F1 781
21 TraesCS1D01G295000 chr2D 614127564 614128501 937 False 1055.0 1055 87.4600 1 913 1 chr2D.!!$F1 912
22 TraesCS1D01G295000 chr2D 488993838 488994431 593 True 330.0 399 87.9310 1905 2440 2 chr2D.!!$R1 535
23 TraesCS1D01G295000 chr4A 444375284 444375899 615 False 822.0 822 90.7050 777 1398 1 chr4A.!!$F1 621

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
815 912 3.314331 CCTGCTCCTCGTGGTGGT 61.314 66.667 2.99 0.00 34.23 4.16 F
1466 1588 0.751277 ATTCATTTCGATGCCGGCCA 60.751 50.000 26.77 12.96 36.24 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 2394 1.966451 CCGTCCAGGAACCACAAGC 60.966 63.158 0.0 0.0 45.0 4.01 R
2603 3085 9.962783 AAGATGAACCGTATATAACAGACTAAC 57.037 33.333 0.0 0.0 0.0 2.34 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
27 28 3.791973 TGACACAATGCGAAGGTTTTT 57.208 38.095 0.00 0.00 0.00 1.94
222 235 4.768968 AGGCAGCTACAGTTCAAATTTGAT 59.231 37.500 21.10 9.25 37.00 2.57
360 374 7.527568 AAATGATTTGGTCCAATTTTGCAAT 57.472 28.000 4.80 0.00 0.00 3.56
600 621 9.844257 AAACCATAAATTTTCTGAACCAATCAA 57.156 25.926 0.00 0.00 37.67 2.57
815 912 3.314331 CCTGCTCCTCGTGGTGGT 61.314 66.667 2.99 0.00 34.23 4.16
1261 1383 3.810812 GTCGACCTCTCCGACGAT 58.189 61.111 3.51 0.00 45.23 3.73
1466 1588 0.751277 ATTCATTTCGATGCCGGCCA 60.751 50.000 26.77 12.96 36.24 5.36
1475 1597 3.301222 ATGCCGGCCACCTCCAAAT 62.301 57.895 26.77 3.74 0.00 2.32
1585 1815 4.034742 GTCAACGTCACCACAAACTACAAT 59.965 41.667 0.00 0.00 0.00 2.71
1674 1904 1.487976 CCCCACACTGCTCTCATATGT 59.512 52.381 1.90 0.00 0.00 2.29
1980 2394 7.921786 TCTATTTGTATTCAGTTTGGTCAGG 57.078 36.000 0.00 0.00 0.00 3.86
2096 2520 8.000709 TGCATCTTATCTTATCTGTGGGAAAAT 58.999 33.333 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
181 194 5.354234 GCTGCCTTGTAGTTTGCTCTTTATA 59.646 40.000 0.00 0.00 0.00 0.98
600 621 1.306141 TGATCCGTGGGAAGAGCCT 60.306 57.895 0.00 0.00 34.34 4.58
1174 1296 4.504916 CTGTCGAGGCTGCTCGGG 62.505 72.222 17.09 7.93 45.82 5.14
1175 1297 4.504916 CCTGTCGAGGCTGCTCGG 62.505 72.222 17.09 5.81 45.82 4.63
1177 1299 3.071206 TCCCTGTCGAGGCTGCTC 61.071 66.667 0.00 0.00 38.17 4.26
1234 1356 2.282958 AGGTCGACCTTGGCGAGA 60.283 61.111 31.69 0.00 46.55 4.04
1466 1588 2.888414 CAACCGGTTAACATTTGGAGGT 59.112 45.455 21.79 2.27 0.00 3.85
1475 1597 2.110901 ACACACACAACCGGTTAACA 57.889 45.000 21.79 0.00 0.00 2.41
1674 1904 4.100035 CCATGACTGTAATGACTCAGCCTA 59.900 45.833 6.71 0.00 35.37 3.93
1980 2394 1.966451 CCGTCCAGGAACCACAAGC 60.966 63.158 0.00 0.00 45.00 4.01
2096 2520 3.530535 TCCTGCAATTCGATTCGATCAA 58.469 40.909 9.96 0.00 35.23 2.57
2603 3085 9.962783 AAGATGAACCGTATATAACAGACTAAC 57.037 33.333 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.