Multiple sequence alignment - TraesCS2A01G267800

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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 TraesCS2A01G267800 chr2A 100.000 2526 0 0 1 2526 429467805 429465280 0.000000e+00 4665.0
1 TraesCS2A01G267800 chr2A 92.907 1424 100 1 1104 2526 429413446 429412023 0.000000e+00 2069.0
2 TraesCS2A01G267800 chr2A 88.922 993 93 14 1 977 429459688 429458697 0.000000e+00 1208.0
3 TraesCS2A01G267800 chr2A 87.333 150 19 0 1357 1506 279065110 279065259 3.340000e-39 172.0
4 TraesCS2A01G267800 chr1A 89.362 1974 196 14 557 2526 79998093 80000056 0.000000e+00 2470.0
5 TraesCS2A01G267800 chr1A 89.311 1974 198 13 557 2526 79985778 79987742 0.000000e+00 2464.0
6 TraesCS2A01G267800 chr1A 88.055 1733 175 24 810 2525 177432989 177431272 0.000000e+00 2025.0
7 TraesCS2A01G267800 chr1A 88.739 1412 148 10 817 2225 177425145 177423742 0.000000e+00 1716.0
8 TraesCS2A01G267800 chr1A 88.608 553 45 10 1 537 177433810 177433260 0.000000e+00 656.0
9 TraesCS2A01G267800 chr1A 88.468 555 43 9 1 537 177425954 177425403 0.000000e+00 651.0
10 TraesCS2A01G267800 chr1A 86.630 546 52 14 1 537 204319543 204319010 3.620000e-163 584.0
11 TraesCS2A01G267800 chr1A 85.745 463 46 9 95 537 204304216 204303754 2.940000e-129 472.0
12 TraesCS2A01G267800 chr3A 85.889 1063 121 25 1479 2526 441363541 441364589 0.000000e+00 1105.0
13 TraesCS2A01G267800 chr3A 85.891 404 43 10 849 1243 324034906 324035304 3.890000e-113 418.0
14 TraesCS2A01G267800 chr3A 89.922 129 13 0 1235 1363 332132081 332132209 1.550000e-37 167.0
15 TraesCS2A01G267800 chr3A 86.395 147 18 2 1233 1378 307280668 307280813 2.600000e-35 159.0
16 TraesCS2A01G267800 chr3A 90.083 121 12 0 669 789 409575448 409575568 9.350000e-35 158.0
17 TraesCS2A01G267800 chr3A 89.167 120 13 0 669 788 364870104 364869985 1.570000e-32 150.0
18 TraesCS2A01G267800 chr3A 87.805 123 11 4 530 649 409567309 409567430 9.420000e-30 141.0
19 TraesCS2A01G267800 chr3A 87.379 103 11 2 542 643 364870198 364870097 1.590000e-22 117.0
20 TraesCS2A01G267800 chr3A 80.240 167 21 7 694 851 354320449 354320612 5.710000e-22 115.0
21 TraesCS2A01G267800 chr3A 80.000 155 25 3 691 839 362623984 362624138 2.660000e-20 110.0
22 TraesCS2A01G267800 chr3A 86.275 102 13 1 530 630 409575342 409575443 2.660000e-20 110.0
23 TraesCS2A01G267800 chr3A 84.906 106 14 2 539 643 364895459 364895355 3.440000e-19 106.0
24 TraesCS2A01G267800 chr4A 87.146 988 107 19 1545 2526 207187050 207188023 0.000000e+00 1103.0
25 TraesCS2A01G267800 chr4A 86.130 1031 122 21 1501 2526 277564960 277565974 0.000000e+00 1092.0
26 TraesCS2A01G267800 chr4A 89.316 234 18 6 1 230 429013709 429013479 1.140000e-73 287.0
27 TraesCS2A01G267800 chr4A 92.800 125 9 0 665 789 346741027 346740903 5.550000e-42 182.0
28 TraesCS2A01G267800 chr4A 94.393 107 6 0 382 488 117817050 117816944 5.590000e-37 165.0
29 TraesCS2A01G267800 chr4A 91.765 85 6 1 382 465 290808057 290808141 1.590000e-22 117.0
30 TraesCS2A01G267800 chr6A 85.308 1055 136 18 1478 2526 389255878 389254837 0.000000e+00 1072.0
31 TraesCS2A01G267800 chr6A 87.413 143 14 3 1233 1372 240645989 240645848 7.230000e-36 161.0
32 TraesCS2A01G267800 chr6A 89.916 119 12 0 671 789 323413663 323413545 1.210000e-33 154.0
33 TraesCS2A01G267800 chr6A 100.000 29 0 0 509 537 125596798 125596826 1.000000e-03 54.7
34 TraesCS2A01G267800 chr7A 91.743 327 26 1 1233 1558 370142400 370142074 1.070000e-123 453.0
35 TraesCS2A01G267800 chr7A 89.270 233 20 4 1 230 347595780 347595550 1.140000e-73 287.0
36 TraesCS2A01G267800 chr7A 93.333 60 3 1 384 443 444382732 444382790 1.240000e-13 87.9
37 TraesCS2A01G267800 chr7A 88.710 62 6 1 382 443 444378359 444378419 9.690000e-10 75.0
38 TraesCS2A01G267800 chr4D 89.247 372 26 8 876 1241 95163961 95163598 1.070000e-123 453.0
39 TraesCS2A01G267800 chr4D 87.435 382 33 9 869 1243 369625459 369625086 2.320000e-115 425.0
40 TraesCS2A01G267800 chr5D 87.696 382 32 9 869 1243 273834068 273833695 4.990000e-117 431.0
41 TraesCS2A01G267800 chr2D 87.402 381 34 8 869 1243 424197490 424197118 2.320000e-115 425.0
42 TraesCS2A01G267800 chr6B 83.793 290 32 12 6 291 366192334 366192612 6.930000e-66 261.0
43 TraesCS2A01G267800 chr6B 80.757 317 43 15 6 317 271185200 271185503 5.430000e-57 231.0
44 TraesCS2A01G267800 chr6B 80.757 317 41 17 6 317 504380629 504380328 1.950000e-56 230.0
45 TraesCS2A01G267800 chr6B 80.818 318 39 19 6 317 504397436 504397135 1.950000e-56 230.0
46 TraesCS2A01G267800 chr7B 82.019 317 39 15 6 317 16362175 16362478 1.160000e-63 254.0
47 TraesCS2A01G267800 chr7B 100.000 32 0 0 569 600 273689284 273689315 2.710000e-05 60.2
48 TraesCS2A01G267800 chr7B 96.875 32 1 0 569 600 299928595 299928564 1.000000e-03 54.7
49 TraesCS2A01G267800 chr2B 89.542 153 14 2 1357 1508 632547873 632547722 2.560000e-45 193.0
50 TraesCS2A01G267800 chr3B 87.417 151 16 3 1357 1506 149320993 149321141 1.200000e-38 171.0
51 TraesCS2A01G267800 chr5A 90.179 112 11 0 676 787 293910670 293910559 2.020000e-31 147.0
52 TraesCS2A01G267800 chr5A 89.423 104 11 0 669 772 647145672 647145569 5.670000e-27 132.0
53 TraesCS2A01G267800 chr5A 89.423 104 11 0 669 772 647153415 647153312 5.670000e-27 132.0
54 TraesCS2A01G267800 chr4B 91.304 46 2 2 417 461 413147946 413147990 7.550000e-06 62.1


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 TraesCS2A01G267800 chr2A 429465280 429467805 2525 True 4665.0 4665 100.0000 1 2526 1 chr2A.!!$R3 2525
1 TraesCS2A01G267800 chr2A 429412023 429413446 1423 True 2069.0 2069 92.9070 1104 2526 1 chr2A.!!$R1 1422
2 TraesCS2A01G267800 chr2A 429458697 429459688 991 True 1208.0 1208 88.9220 1 977 1 chr2A.!!$R2 976
3 TraesCS2A01G267800 chr1A 79998093 80000056 1963 False 2470.0 2470 89.3620 557 2526 1 chr1A.!!$F2 1969
4 TraesCS2A01G267800 chr1A 79985778 79987742 1964 False 2464.0 2464 89.3110 557 2526 1 chr1A.!!$F1 1969
5 TraesCS2A01G267800 chr1A 177431272 177433810 2538 True 1340.5 2025 88.3315 1 2525 2 chr1A.!!$R4 2524
6 TraesCS2A01G267800 chr1A 177423742 177425954 2212 True 1183.5 1716 88.6035 1 2225 2 chr1A.!!$R3 2224
7 TraesCS2A01G267800 chr1A 204319010 204319543 533 True 584.0 584 86.6300 1 537 1 chr1A.!!$R2 536
8 TraesCS2A01G267800 chr3A 441363541 441364589 1048 False 1105.0 1105 85.8890 1479 2526 1 chr3A.!!$F7 1047
9 TraesCS2A01G267800 chr4A 207187050 207188023 973 False 1103.0 1103 87.1460 1545 2526 1 chr4A.!!$F1 981
10 TraesCS2A01G267800 chr4A 277564960 277565974 1014 False 1092.0 1092 86.1300 1501 2526 1 chr4A.!!$F2 1025
11 TraesCS2A01G267800 chr6A 389254837 389255878 1041 True 1072.0 1072 85.3080 1478 2526 1 chr6A.!!$R3 1048

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
560 591 0.252012 CTCTCCACCTCCACTCCAGT 60.252 60.0 0.0 0.0 0.0 4.00 F
891 1039 0.321671 CAACTCCTTCTCCCTCGCAA 59.678 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1485 1635 1.153978 TCGTACACGTTCGGGATGC 60.154 57.895 0.34 0.0 40.8 3.91 R
1760 1923 1.470805 GGCGGTGCAAAAGAAAGTGTT 60.471 47.619 0.00 0.0 0.0 3.32 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
59 60 9.136323 ACTTCAAAAATCAAGTCCTAGTTCAAT 57.864 29.630 0.00 0.00 0.00 2.57
198 200 1.379776 ACCCCTAACCCCTTCCTTTC 58.620 55.000 0.00 0.00 0.00 2.62
219 221 7.888546 CCTTTCCTTCTCCTTTCCTTTGTTATA 59.111 37.037 0.00 0.00 0.00 0.98
256 259 3.878103 GGTTAGCGAGTAGTGAGAGATCA 59.122 47.826 0.00 0.00 0.00 2.92
269 272 3.520721 TGAGAGATCAATGAGAAGGCCAA 59.479 43.478 5.01 0.00 0.00 4.52
326 338 2.427245 CCCACCTCTCTACTGGGCG 61.427 68.421 0.00 0.00 38.42 6.13
360 376 2.478872 AGCCACTCTAATCCTAGCCA 57.521 50.000 0.00 0.00 0.00 4.75
379 395 4.864334 CACCCAGCGCCCATCTCC 62.864 72.222 2.29 0.00 0.00 3.71
398 428 2.685380 CCCTCGTTCCCTCTGCCT 60.685 66.667 0.00 0.00 0.00 4.75
498 529 2.113139 CCCACGCCCTCACAACTT 59.887 61.111 0.00 0.00 0.00 2.66
537 568 3.798954 CTCGATCTTGAGCGCCCCC 62.799 68.421 2.29 0.00 0.00 5.40
555 586 2.681778 CGCCTCTCCACCTCCACT 60.682 66.667 0.00 0.00 0.00 4.00
560 591 0.252012 CTCTCCACCTCCACTCCAGT 60.252 60.000 0.00 0.00 0.00 4.00
740 772 3.379445 GTCGACCTCCTCGGCCAA 61.379 66.667 3.51 0.00 41.45 4.52
741 773 3.379445 TCGACCTCCTCGGCCAAC 61.379 66.667 2.24 0.00 43.16 3.77
782 822 2.927864 CGCCCTCCTCCTCTCCTA 59.072 66.667 0.00 0.00 0.00 2.94
840 986 0.994247 ACCACCATCTTGCTCCATCA 59.006 50.000 0.00 0.00 0.00 3.07
842 988 1.064906 CCACCATCTTGCTCCATCACT 60.065 52.381 0.00 0.00 0.00 3.41
851 997 1.965754 GCTCCATCACTCGCTTCCCT 61.966 60.000 0.00 0.00 0.00 4.20
890 1038 1.544825 CCAACTCCTTCTCCCTCGCA 61.545 60.000 0.00 0.00 0.00 5.10
891 1039 0.321671 CAACTCCTTCTCCCTCGCAA 59.678 55.000 0.00 0.00 0.00 4.85
958 1107 1.748122 GCAGGACCTCCTCGTCGTA 60.748 63.158 0.00 0.00 46.65 3.43
977 1126 2.752358 CTCTGCCTCCACCAGCAA 59.248 61.111 0.00 0.00 38.82 3.91
984 1133 0.909610 CCTCCACCAGCAACCTCCTA 60.910 60.000 0.00 0.00 0.00 2.94
1129 1279 1.667830 CGCGCCAAGTTCCTCTTCA 60.668 57.895 0.00 0.00 33.63 3.02
1249 1399 2.660802 CGCCAAGTACCCCTTCGT 59.339 61.111 0.00 0.00 0.00 3.85
1300 1450 1.004595 GTTCCGATAAGACCGGCAAC 58.995 55.000 0.00 0.00 46.10 4.17
1366 1516 1.182667 GCATTTCACCAAGTACCCCC 58.817 55.000 0.00 0.00 0.00 5.40
1406 1556 5.195185 TCTATGATCCGTGTACCACTACAA 58.805 41.667 0.00 0.00 34.53 2.41
1421 1571 4.059511 CACTACAACCGGTGTGTATTTCA 58.940 43.478 21.83 8.66 41.89 2.69
1432 1582 4.330074 GGTGTGTATTTCATCAAGTCCGAG 59.670 45.833 0.00 0.00 0.00 4.63
1462 1612 2.110901 ACGACTACACGATGACTCCT 57.889 50.000 0.00 0.00 37.03 3.69
1485 1635 4.552166 AGAACATGGAAACGTCAAGTTG 57.448 40.909 0.00 0.00 43.37 3.16
1539 1690 0.886563 CCGTGAACGTCTACTTCCCT 59.113 55.000 1.75 0.00 37.74 4.20
1695 1858 1.198094 TTCCTCCTCGGTTGCCATGA 61.198 55.000 0.00 0.00 0.00 3.07
1696 1859 0.982852 TCCTCCTCGGTTGCCATGAT 60.983 55.000 0.00 0.00 0.00 2.45
1707 1870 1.883084 GCCATGATGTCGACCCGTC 60.883 63.158 14.12 9.26 0.00 4.79
1779 1942 1.921243 AACACTTTCTTTTGCACCGC 58.079 45.000 0.00 0.00 0.00 5.68
1837 2002 0.385473 GCACCATTTCCGTTGTCGTG 60.385 55.000 0.00 0.00 35.01 4.35
1959 2125 3.609373 CCGCATCATGACAACAACATTTC 59.391 43.478 0.00 0.00 0.00 2.17
2015 2183 1.909986 TGTCATGTGGGGATTTACCGA 59.090 47.619 0.00 0.00 40.11 4.69
2036 2204 5.407084 CCGAAATGGTTATTTGTTGTTTCCC 59.593 40.000 0.00 0.00 36.66 3.97
2046 2214 1.141254 TGTTGTTTCCCGCCTCACTTA 59.859 47.619 0.00 0.00 0.00 2.24
2155 2327 8.131731 GGGAGAGAACTAAATAATTGAATGTGC 58.868 37.037 0.00 0.00 0.00 4.57
2329 2502 2.755655 TGTTTGCTTCTTTCCGGTTTGA 59.244 40.909 0.00 0.00 0.00 2.69
2355 2530 3.058293 TCTCGTTAGCTTCGGTTTCGTTA 60.058 43.478 10.26 0.00 37.69 3.18
2405 2580 3.433615 GTCCGTTTGTCTTCTTCATGGAG 59.566 47.826 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 5.779241 AATGGGATTGAACTAGGACTTGA 57.221 39.130 0.00 0.00 0.00 3.02
109 110 3.945285 GGTCCGAGAAAATAGAAATGGCA 59.055 43.478 0.00 0.00 0.00 4.92
198 200 8.055790 AGGAATATAACAAAGGAAAGGAGAAGG 58.944 37.037 0.00 0.00 0.00 3.46
240 243 6.370433 TTCTCATTGATCTCTCACTACTCG 57.630 41.667 0.00 0.00 0.00 4.18
311 323 2.042843 CCCGCCCAGTAGAGAGGT 60.043 66.667 0.00 0.00 0.00 3.85
352 368 2.954684 CGCTGGGTGTTGGCTAGGA 61.955 63.158 0.00 0.00 0.00 2.94
360 376 3.628646 GAGATGGGCGCTGGGTGTT 62.629 63.158 7.64 0.00 0.00 3.32
379 395 3.787001 GCAGAGGGAACGAGGGGG 61.787 72.222 0.00 0.00 0.00 5.40
490 521 1.883638 GCTGCAGGGATGAAGTTGTGA 60.884 52.381 17.12 0.00 0.00 3.58
498 529 3.092511 GGAGGGCTGCAGGGATGA 61.093 66.667 17.12 0.00 0.00 2.92
537 568 3.775654 GTGGAGGTGGAGAGGCGG 61.776 72.222 0.00 0.00 0.00 6.13
645 677 4.973055 CGGTTCGTTGACGGGGCA 62.973 66.667 3.48 0.00 40.29 5.36
840 986 1.270893 GGAGAAACAAGGGAAGCGAGT 60.271 52.381 0.00 0.00 0.00 4.18
842 988 1.056660 AGGAGAAACAAGGGAAGCGA 58.943 50.000 0.00 0.00 0.00 4.93
851 997 1.533625 CGCATGGGAAGGAGAAACAA 58.466 50.000 3.11 0.00 0.00 2.83
890 1038 2.912624 GCAGCAGCAAGGCTTCGTT 61.913 57.895 0.00 0.00 42.71 3.85
891 1039 3.360340 GCAGCAGCAAGGCTTCGT 61.360 61.111 0.00 0.00 42.71 3.85
958 1107 3.715097 GCTGGTGGAGGCAGAGCT 61.715 66.667 0.00 0.00 0.00 4.09
977 1126 1.007721 AGATGACAGGCAGTAGGAGGT 59.992 52.381 0.00 0.00 0.00 3.85
984 1133 0.545171 CCATGGAGATGACAGGCAGT 59.455 55.000 5.56 0.00 0.00 4.40
1017 1166 0.752009 AGAGCGACCGATAGCTTGGA 60.752 55.000 6.36 0.00 44.69 3.53
1049 1198 1.464997 GTCTCCTCGGTTCAAACATGC 59.535 52.381 0.00 0.00 0.00 4.06
1052 1201 0.032952 CGGTCTCCTCGGTTCAAACA 59.967 55.000 0.00 0.00 0.00 2.83
1129 1279 4.035324 CGGTCATCATGTAGACGTACTTCT 59.965 45.833 7.11 7.11 35.63 2.85
1249 1399 2.685106 AGAGATCCTCCTTGGCGATA 57.315 50.000 0.00 0.00 35.26 2.92
1296 1446 1.066136 GGAAGTAGTCGTTCGGTTGC 58.934 55.000 0.00 0.00 0.00 4.17
1300 1450 0.518636 TCGTGGAAGTAGTCGTTCGG 59.481 55.000 0.00 0.00 0.00 4.30
1366 1516 2.515926 AGATGTTCGGGTCATCGATG 57.484 50.000 19.61 19.61 44.20 3.84
1406 1556 4.000988 GACTTGATGAAATACACACCGGT 58.999 43.478 0.00 0.00 0.00 5.28
1421 1571 2.156917 TGTGTCGTACTCGGACTTGAT 58.843 47.619 0.00 0.00 37.69 2.57
1432 1582 2.398451 CGTGTAGTCGTTTGTGTCGTAC 59.602 50.000 0.00 0.00 0.00 3.67
1462 1612 5.504994 GCAACTTGACGTTTCCATGTTCTTA 60.505 40.000 0.00 0.00 32.27 2.10
1485 1635 1.153978 TCGTACACGTTCGGGATGC 60.154 57.895 0.34 0.00 40.80 3.91
1760 1923 1.470805 GGCGGTGCAAAAGAAAGTGTT 60.471 47.619 0.00 0.00 0.00 3.32
1779 1942 6.389906 GGTTCTGGTAACTCAATTGAAATGG 58.610 40.000 9.88 0.06 37.61 3.16
1837 2002 1.682344 GGAAAGGGGTGCCATGGAC 60.682 63.158 18.40 10.81 0.00 4.02
1915 2081 5.870978 CGGATGACATATGCAAGTGATATGA 59.129 40.000 10.48 0.00 37.27 2.15
1959 2125 8.450385 AAGCAAACAACAAATTCAAACATTTG 57.550 26.923 4.90 4.90 45.86 2.32
2015 2183 4.752604 GCGGGAAACAACAAATAACCATTT 59.247 37.500 0.00 0.00 34.60 2.32
2036 2204 3.575965 AGGCAATTTTTAAGTGAGGCG 57.424 42.857 0.00 0.00 0.00 5.52
2117 2288 4.091549 AGTTCTCTCCCGTTTATGTACCA 58.908 43.478 0.00 0.00 0.00 3.25
2155 2327 5.281693 TGAGTTGCATATTGACGAAACAG 57.718 39.130 0.00 0.00 0.00 3.16
2329 2502 3.870633 AACCGAAGCTAACGAGAGAAT 57.129 42.857 13.51 0.00 0.00 2.40
2355 2530 1.546961 ACGAATCCTCTCAACTCCGT 58.453 50.000 0.00 0.00 0.00 4.69
2405 2580 2.492484 TCCTGCTAGGAAGAAGAACGAC 59.508 50.000 2.78 0.00 42.51 4.34


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

AutoCloner maintained by Alex Coulton.