Multiple sequence alignment - TraesCS2D01G327300

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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 TraesCS2D01G327300 chr2D 100.000 2351 0 0 1 2351 420561510 420563860 0.000000e+00 4342.0
1 TraesCS2D01G327300 chr2D 94.437 1546 58 16 824 2351 16242357 16240822 0.000000e+00 2353.0
2 TraesCS2D01G327300 chr2D 92.649 1442 64 20 917 2351 537454520 537455926 0.000000e+00 2037.0
3 TraesCS2D01G327300 chr2D 94.321 810 39 6 1 807 20064621 20065426 0.000000e+00 1234.0
4 TraesCS2D01G327300 chr7B 90.328 2378 169 40 1 2351 651070562 651072905 0.000000e+00 3061.0
5 TraesCS2D01G327300 chr7B 95.281 1441 52 8 917 2351 742265914 742267344 0.000000e+00 2270.0
6 TraesCS2D01G327300 chr7B 95.509 1002 32 6 1354 2351 744244299 744245291 0.000000e+00 1589.0
7 TraesCS2D01G327300 chr7B 90.110 455 41 4 1 453 742264936 742265388 2.600000e-164 588.0
8 TraesCS2D01G327300 chr7B 90.741 54 2 3 654 704 34848534 34848587 4.190000e-08 69.4
9 TraesCS2D01G327300 chr7B 90.196 51 0 3 654 704 47338154 47338109 7.020000e-06 62.1
10 TraesCS2D01G327300 chr7D 95.489 1596 53 9 765 2351 438690040 438691625 0.000000e+00 2531.0
11 TraesCS2D01G327300 chr2B 94.394 1552 54 15 824 2351 619941914 619943456 0.000000e+00 2353.0
12 TraesCS2D01G327300 chr2B 94.097 1423 60 10 937 2351 45564337 45562931 0.000000e+00 2141.0
13 TraesCS2D01G327300 chr6B 94.125 1549 60 16 824 2351 78311188 78309650 0.000000e+00 2327.0
14 TraesCS2D01G327300 chr6B 95.448 1428 50 8 930 2351 219562340 219563758 0.000000e+00 2263.0
15 TraesCS2D01G327300 chr6B 93.467 1546 65 17 827 2351 261460927 261462457 0.000000e+00 2263.0
16 TraesCS2D01G327300 chr6B 89.011 455 46 4 1 453 261454593 261455045 5.670000e-156 560.0
17 TraesCS2D01G327300 chr2A 95.284 1442 53 7 916 2351 759092078 759093510 0.000000e+00 2272.0
18 TraesCS2D01G327300 chr2A 82.374 278 22 20 891 1146 703335226 703335498 1.410000e-52 217.0
19 TraesCS2D01G327300 chr2A 94.828 58 2 1 854 911 364516547 364516491 3.220000e-14 89.8
20 TraesCS2D01G327300 chr2A 100.000 35 0 0 826 860 364531118 364531084 5.420000e-07 65.8
21 TraesCS2D01G327300 chr4B 94.668 1444 55 12 917 2351 451906090 451904660 0.000000e+00 2220.0
22 TraesCS2D01G327300 chr4B 94.598 1444 58 11 915 2351 622316363 622314933 0.000000e+00 2217.0
23 TraesCS2D01G327300 chr4B 89.868 454 41 5 1 452 622317371 622316921 1.570000e-161 579.0
24 TraesCS2D01G327300 chr4B 94.340 53 1 2 654 704 134354297 134354349 1.940000e-11 80.5
25 TraesCS2D01G327300 chr7A 92.581 1550 76 14 824 2351 635855539 635854007 0.000000e+00 2189.0
26 TraesCS2D01G327300 chr7A 89.767 430 19 14 768 1175 251824432 251824858 5.750000e-146 527.0
27 TraesCS2D01G327300 chr7A 80.665 331 43 14 854 1171 273499642 273499964 1.090000e-58 237.0
28 TraesCS2D01G327300 chr3D 95.551 1371 51 5 982 2351 606922317 606920956 0.000000e+00 2185.0
29 TraesCS2D01G327300 chrUn 87.839 921 84 21 1 913 108425323 108426223 0.000000e+00 1055.0
30 TraesCS2D01G327300 chr1B 92.704 699 46 4 1 698 653523676 653522982 0.000000e+00 1003.0
31 TraesCS2D01G327300 chr6D 91.748 412 28 5 1 410 30418538 30418131 3.390000e-158 568.0
32 TraesCS2D01G327300 chr4A 91.525 413 30 5 1 410 522161510 522161920 4.390000e-157 564.0
33 TraesCS2D01G327300 chr3A 81.176 425 33 26 634 1030 711334090 711333685 4.910000e-77 298.0


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 TraesCS2D01G327300 chr2D 420561510 420563860 2350 False 4342 4342 100.0000 1 2351 1 chr2D.!!$F2 2350
1 TraesCS2D01G327300 chr2D 16240822 16242357 1535 True 2353 2353 94.4370 824 2351 1 chr2D.!!$R1 1527
2 TraesCS2D01G327300 chr2D 537454520 537455926 1406 False 2037 2037 92.6490 917 2351 1 chr2D.!!$F3 1434
3 TraesCS2D01G327300 chr2D 20064621 20065426 805 False 1234 1234 94.3210 1 807 1 chr2D.!!$F1 806
4 TraesCS2D01G327300 chr7B 651070562 651072905 2343 False 3061 3061 90.3280 1 2351 1 chr7B.!!$F2 2350
5 TraesCS2D01G327300 chr7B 744244299 744245291 992 False 1589 1589 95.5090 1354 2351 1 chr7B.!!$F3 997
6 TraesCS2D01G327300 chr7B 742264936 742267344 2408 False 1429 2270 92.6955 1 2351 2 chr7B.!!$F4 2350
7 TraesCS2D01G327300 chr7D 438690040 438691625 1585 False 2531 2531 95.4890 765 2351 1 chr7D.!!$F1 1586
8 TraesCS2D01G327300 chr2B 619941914 619943456 1542 False 2353 2353 94.3940 824 2351 1 chr2B.!!$F1 1527
9 TraesCS2D01G327300 chr2B 45562931 45564337 1406 True 2141 2141 94.0970 937 2351 1 chr2B.!!$R1 1414
10 TraesCS2D01G327300 chr6B 78309650 78311188 1538 True 2327 2327 94.1250 824 2351 1 chr6B.!!$R1 1527
11 TraesCS2D01G327300 chr6B 219562340 219563758 1418 False 2263 2263 95.4480 930 2351 1 chr6B.!!$F1 1421
12 TraesCS2D01G327300 chr6B 261460927 261462457 1530 False 2263 2263 93.4670 827 2351 1 chr6B.!!$F3 1524
13 TraesCS2D01G327300 chr2A 759092078 759093510 1432 False 2272 2272 95.2840 916 2351 1 chr2A.!!$F2 1435
14 TraesCS2D01G327300 chr4B 451904660 451906090 1430 True 2220 2220 94.6680 917 2351 1 chr4B.!!$R1 1434
15 TraesCS2D01G327300 chr4B 622314933 622317371 2438 True 1398 2217 92.2330 1 2351 2 chr4B.!!$R2 2350
16 TraesCS2D01G327300 chr7A 635854007 635855539 1532 True 2189 2189 92.5810 824 2351 1 chr7A.!!$R1 1527
17 TraesCS2D01G327300 chr3D 606920956 606922317 1361 True 2185 2185 95.5510 982 2351 1 chr3D.!!$R1 1369
18 TraesCS2D01G327300 chrUn 108425323 108426223 900 False 1055 1055 87.8390 1 913 1 chrUn.!!$F1 912
19 TraesCS2D01G327300 chr1B 653522982 653523676 694 True 1003 1003 92.7040 1 698 1 chr1B.!!$R1 697

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
466 528 0.099082 AGTCGGCGAGATCGAAACTC 59.901 55.0 11.2 11.37 43.02 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2132 2334 1.139853 GCCGTCCTCTCTCCAATCATT 59.86 52.381 0.0 0.0 0.0 2.57 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
52 53 3.645884 TCGCTTAGACTTGGTGTTGTAC 58.354 45.455 0.00 0.00 0.00 2.90
116 117 6.790461 TGTACCCTTGGCCTCTTATATATGAA 59.210 38.462 3.32 0.00 0.00 2.57
245 247 1.153628 GAGCGCCCGTAGTCATTGT 60.154 57.895 2.29 0.00 0.00 2.71
294 296 3.744426 CCTCGTTAACAAATCTCGGTGTT 59.256 43.478 6.39 0.00 40.88 3.32
303 305 2.479566 ATCTCGGTGTTGTCATTGCT 57.520 45.000 0.00 0.00 0.00 3.91
304 306 1.795768 TCTCGGTGTTGTCATTGCTC 58.204 50.000 0.00 0.00 0.00 4.26
305 307 1.069978 TCTCGGTGTTGTCATTGCTCA 59.930 47.619 0.00 0.00 0.00 4.26
322 324 2.229543 GCTCATGTGATTGCTTGTTCCA 59.770 45.455 0.00 0.00 0.00 3.53
466 528 0.099082 AGTCGGCGAGATCGAAACTC 59.901 55.000 11.20 11.37 43.02 3.01
624 694 1.735360 TGCTTGTGCAGGTTTCAGC 59.265 52.632 0.00 0.00 45.31 4.26
637 707 2.159198 GGTTTCAGCGGTTATCTCGGTA 60.159 50.000 0.00 0.00 36.55 4.02
923 1089 2.488545 ACGTGAAGACCAGCTAGTAGTG 59.511 50.000 0.00 0.00 0.00 2.74
1011 1183 4.207891 ACAAAGAACTATGACGCCATCT 57.792 40.909 0.00 0.00 34.31 2.90
1043 1215 1.760613 TGAGGTGGAGAAGTTCAACGT 59.239 47.619 5.50 2.28 29.68 3.99
1113 1290 0.112995 AACAGGGATGCTTGAAGGCA 59.887 50.000 2.61 0.00 46.63 4.75
1368 1564 7.776745 AGGGGTAAGATCTTGTGGAGTATATA 58.223 38.462 18.47 0.00 0.00 0.86
1400 1596 2.708051 TCAAGTCGTGACGGATCTAGT 58.292 47.619 4.70 0.00 36.20 2.57
1685 1884 3.605634 ACAGTGTCACAAGTGTAAGCAA 58.394 40.909 5.62 0.00 31.86 3.91
1731 1930 1.142688 AGAACTCAATGGTGGGGCCT 61.143 55.000 0.84 0.00 38.35 5.19
1834 2036 2.228822 GTGAAGCGTGGATGTTGGATTT 59.771 45.455 0.00 0.00 0.00 2.17
1889 2091 3.635373 AGTGGTTCTCTTCGTACAAGTCA 59.365 43.478 0.00 0.00 0.00 3.41
1890 2092 4.281182 AGTGGTTCTCTTCGTACAAGTCAT 59.719 41.667 0.00 0.00 0.00 3.06
1891 2093 5.475909 AGTGGTTCTCTTCGTACAAGTCATA 59.524 40.000 0.00 0.00 0.00 2.15
1892 2094 5.572126 GTGGTTCTCTTCGTACAAGTCATAC 59.428 44.000 0.00 0.00 0.00 2.39
1893 2095 5.242171 TGGTTCTCTTCGTACAAGTCATACA 59.758 40.000 0.00 0.00 0.00 2.29
1894 2096 6.154445 GGTTCTCTTCGTACAAGTCATACAA 58.846 40.000 0.00 0.00 0.00 2.41
1895 2097 6.308282 GGTTCTCTTCGTACAAGTCATACAAG 59.692 42.308 0.00 0.00 0.00 3.16
1896 2098 6.570672 TCTCTTCGTACAAGTCATACAAGT 57.429 37.500 0.00 0.00 0.00 3.16
1897 2099 6.609533 TCTCTTCGTACAAGTCATACAAGTC 58.390 40.000 0.00 0.00 0.00 3.01
2132 2334 4.283337 TCATGGAAGATAAGGTGACCGTA 58.717 43.478 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.421374 AGTCTAAGCGAAACCCAACTAGTAT 59.579 40.000 0.00 0.00 0.00 2.12
31 32 2.902705 ACAACACCAAGTCTAAGCGA 57.097 45.000 0.00 0.00 0.00 4.93
37 38 2.158813 CCCACAGTACAACACCAAGTCT 60.159 50.000 0.00 0.00 0.00 3.24
52 53 4.710375 ACACTACAAGTATCCTACCCACAG 59.290 45.833 0.00 0.00 0.00 3.66
116 117 1.069668 GTTACAACGTGGGGTGTCTCT 59.930 52.381 0.00 0.00 0.00 3.10
120 121 1.148949 GGGTTACAACGTGGGGTGT 59.851 57.895 0.00 0.00 0.00 4.16
245 247 4.517934 CTCGCCTACTCCCCGGGA 62.518 72.222 26.32 5.87 0.00 5.14
294 296 3.086282 AGCAATCACATGAGCAATGACA 58.914 40.909 0.00 0.00 38.72 3.58
466 528 4.374702 GTTGTGCTGCAGGCGTCG 62.375 66.667 17.12 0.00 45.43 5.12
624 694 2.572191 TTGCTGTACCGAGATAACCG 57.428 50.000 0.00 0.00 0.00 4.44
637 707 2.489329 CAAATCCGGTTCTGATTGCTGT 59.511 45.455 0.00 0.00 32.91 4.40
725 810 2.816204 TGCAGCTTTTATTTGCAGCA 57.184 40.000 0.00 0.00 46.45 4.41
923 1089 3.479269 CGAACGGAACCTCTGCGC 61.479 66.667 0.00 0.00 43.80 6.09
957 1124 5.305585 TGAAAAATAACCGAGCAGTCTTCT 58.694 37.500 0.00 0.00 0.00 2.85
1011 1183 2.571653 CTCCACCTCAAACCTGATACCA 59.428 50.000 0.00 0.00 0.00 3.25
1043 1215 4.340617 CCATAACCCAAAGCTTCCAGTTA 58.659 43.478 14.06 14.06 0.00 2.24
1113 1290 0.319405 GCTTGGCTTCCTGCAACAAT 59.681 50.000 0.00 0.00 45.15 2.71
1685 1884 5.664908 ACAGTCCTTTCTCATATGTCTCCAT 59.335 40.000 1.90 0.00 34.97 3.41
1731 1930 3.947196 CCATGAGTTGCCTTATTAGCACA 59.053 43.478 0.00 0.00 40.69 4.57
1889 2091 7.119846 GCTAAACCAAACTCATCAGACTTGTAT 59.880 37.037 0.00 0.00 0.00 2.29
1890 2092 6.426937 GCTAAACCAAACTCATCAGACTTGTA 59.573 38.462 0.00 0.00 0.00 2.41
1891 2093 5.239525 GCTAAACCAAACTCATCAGACTTGT 59.760 40.000 0.00 0.00 0.00 3.16
1892 2094 5.335191 GGCTAAACCAAACTCATCAGACTTG 60.335 44.000 0.00 0.00 38.86 3.16
1893 2095 4.762251 GGCTAAACCAAACTCATCAGACTT 59.238 41.667 0.00 0.00 38.86 3.01
1894 2096 4.042187 AGGCTAAACCAAACTCATCAGACT 59.958 41.667 0.00 0.00 43.14 3.24
1895 2097 4.327680 AGGCTAAACCAAACTCATCAGAC 58.672 43.478 0.00 0.00 43.14 3.51
1896 2098 4.640771 AGGCTAAACCAAACTCATCAGA 57.359 40.909 0.00 0.00 43.14 3.27
1897 2099 5.882557 ACATAGGCTAAACCAAACTCATCAG 59.117 40.000 0.00 0.00 43.14 2.90
2132 2334 1.139853 GCCGTCCTCTCTCCAATCATT 59.860 52.381 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.