Multiple sequence alignment - TraesCS1A01G140000

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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 TraesCS1A01G140000 chr1A 100.000 2288 0 0 1 2288 238074954 238077241 0 4226
1 TraesCS1A01G140000 chr1A 91.341 1409 117 3 7 1411 327011926 327010519 0 1921
2 TraesCS1A01G140000 chr1A 90.277 1409 131 4 7 1411 387995193 387996599 0 1838
3 TraesCS1A01G140000 chr1A 91.516 884 75 0 1405 2288 524601829 524602712 0 1218
4 TraesCS1A01G140000 chr3A 91.779 1411 106 4 10 1411 418765665 418764256 0 1954
5 TraesCS1A01G140000 chr3A 91.506 883 74 1 1407 2288 113864000 113863118 0 1214
6 TraesCS1A01G140000 chr4D 91.643 1412 109 5 7 1411 493971117 493969708 0 1945
7 TraesCS1A01G140000 chr4D 91.489 1410 113 5 7 1411 116524565 116523158 0 1932
8 TraesCS1A01G140000 chr4D 90.800 1413 117 6 9 1411 48683934 48682525 0 1877
9 TraesCS1A01G140000 chr4D 90.645 1411 121 5 10 1411 421048641 421047233 0 1864
10 TraesCS1A01G140000 chr4A 90.864 1412 118 5 9 1411 327748380 327746971 0 1882
11 TraesCS1A01G140000 chr3B 90.523 1414 119 6 7 1411 700809799 700811206 0 1855
12 TraesCS1A01G140000 chr3B 92.647 884 63 2 1407 2288 451816421 451817304 0 1271
13 TraesCS1A01G140000 chr5A 92.639 883 65 0 1406 2288 331379708 331378826 0 1271
14 TraesCS1A01G140000 chrUn 92.195 884 67 1 1407 2288 27611216 27612099 0 1249
15 TraesCS1A01G140000 chr4B 92.186 883 68 1 1406 2288 602042860 602041979 0 1247
16 TraesCS1A01G140000 chr6D 91.383 882 76 0 1407 2288 39780233 39781114 0 1208
17 TraesCS1A01G140000 chr7B 91.270 882 76 1 1407 2288 484626091 484626971 0 1201
18 TraesCS1A01G140000 chr7A 91.270 882 76 1 1407 2288 251996270 251995390 0 1201


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 TraesCS1A01G140000 chr1A 238074954 238077241 2287 False 4226 4226 100.000 1 2288 1 chr1A.!!$F1 2287
1 TraesCS1A01G140000 chr1A 327010519 327011926 1407 True 1921 1921 91.341 7 1411 1 chr1A.!!$R1 1404
2 TraesCS1A01G140000 chr1A 387995193 387996599 1406 False 1838 1838 90.277 7 1411 1 chr1A.!!$F2 1404
3 TraesCS1A01G140000 chr1A 524601829 524602712 883 False 1218 1218 91.516 1405 2288 1 chr1A.!!$F3 883
4 TraesCS1A01G140000 chr3A 418764256 418765665 1409 True 1954 1954 91.779 10 1411 1 chr3A.!!$R2 1401
5 TraesCS1A01G140000 chr3A 113863118 113864000 882 True 1214 1214 91.506 1407 2288 1 chr3A.!!$R1 881
6 TraesCS1A01G140000 chr4D 493969708 493971117 1409 True 1945 1945 91.643 7 1411 1 chr4D.!!$R4 1404
7 TraesCS1A01G140000 chr4D 116523158 116524565 1407 True 1932 1932 91.489 7 1411 1 chr4D.!!$R2 1404
8 TraesCS1A01G140000 chr4D 48682525 48683934 1409 True 1877 1877 90.800 9 1411 1 chr4D.!!$R1 1402
9 TraesCS1A01G140000 chr4D 421047233 421048641 1408 True 1864 1864 90.645 10 1411 1 chr4D.!!$R3 1401
10 TraesCS1A01G140000 chr4A 327746971 327748380 1409 True 1882 1882 90.864 9 1411 1 chr4A.!!$R1 1402
11 TraesCS1A01G140000 chr3B 700809799 700811206 1407 False 1855 1855 90.523 7 1411 1 chr3B.!!$F2 1404
12 TraesCS1A01G140000 chr3B 451816421 451817304 883 False 1271 1271 92.647 1407 2288 1 chr3B.!!$F1 881
13 TraesCS1A01G140000 chr5A 331378826 331379708 882 True 1271 1271 92.639 1406 2288 1 chr5A.!!$R1 882
14 TraesCS1A01G140000 chrUn 27611216 27612099 883 False 1249 1249 92.195 1407 2288 1 chrUn.!!$F1 881
15 TraesCS1A01G140000 chr4B 602041979 602042860 881 True 1247 1247 92.186 1406 2288 1 chr4B.!!$R1 882
16 TraesCS1A01G140000 chr6D 39780233 39781114 881 False 1208 1208 91.383 1407 2288 1 chr6D.!!$F1 881
17 TraesCS1A01G140000 chr7B 484626091 484626971 880 False 1201 1201 91.270 1407 2288 1 chr7B.!!$F1 881
18 TraesCS1A01G140000 chr7A 251995390 251996270 880 True 1201 1201 91.270 1407 2288 1 chr7A.!!$R1 881

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
962 978 0.17899 GGTGGCCCAACTCACTTCTT 60.179 55.0 0.0 0.0 34.57 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 1940 0.463833 TGATCGCCTAGAGTGCTCGA 60.464 55.0 0.0 0.0 34.09 4.04 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
33 34 2.281761 CGCTGGGTTGAGTGGCTT 60.282 61.111 0.00 0.00 0.00 4.35
63 64 0.530288 TCTTGTCCATCATCGTGCGA 59.470 50.000 0.00 0.00 0.00 5.10
172 173 1.481363 CCGGTTCTTCCTCCTCCTTAC 59.519 57.143 0.00 0.00 0.00 2.34
182 183 1.686110 CCTCCTTACGCTCCCCACT 60.686 63.158 0.00 0.00 0.00 4.00
319 320 1.134098 CGACCTAATTCATGGCCCAGT 60.134 52.381 0.00 0.00 0.00 4.00
383 386 5.036117 ACCAGTGTATTCAACTCTTGTGT 57.964 39.130 0.00 0.00 29.28 3.72
424 430 7.495901 CACTACATCAGATTCCTTCTACACAT 58.504 38.462 0.00 0.00 31.77 3.21
523 529 2.225792 GCCCTCCAGCCAATACTCT 58.774 57.895 0.00 0.00 0.00 3.24
544 556 3.680786 GGAAGGGGTTGGCGTTGC 61.681 66.667 0.00 0.00 0.00 4.17
552 564 3.286751 TTGGCGTTGCAGCTGGAC 61.287 61.111 17.12 6.79 37.29 4.02
574 586 2.632028 CTCATGGTGATGTAGAGGAGGG 59.368 54.545 0.00 0.00 0.00 4.30
576 588 2.940514 TGGTGATGTAGAGGAGGGAA 57.059 50.000 0.00 0.00 0.00 3.97
588 600 4.027437 AGAGGAGGGAAGTTGATAGTGAC 58.973 47.826 0.00 0.00 0.00 3.67
706 722 5.597182 ACATGCTCTTCAATAAGCCATGAAT 59.403 36.000 17.56 3.01 40.65 2.57
709 725 5.653330 TGCTCTTCAATAAGCCATGAATTCA 59.347 36.000 11.26 11.26 37.73 2.57
731 747 1.271001 TGTTGTGCCTGACTCCATGAG 60.271 52.381 0.00 0.00 35.52 2.90
825 841 0.243636 CGGTTCTTCCAATGCCCAAC 59.756 55.000 0.00 0.00 35.57 3.77
839 855 4.671549 CAACGTGGTGCTGCTGCG 62.672 66.667 11.21 2.87 43.34 5.18
856 872 1.738099 CGCACCACCGAGGAAGAAG 60.738 63.158 0.00 0.00 41.22 2.85
861 877 0.320421 CCACCGAGGAAGAAGCGAAA 60.320 55.000 0.00 0.00 41.22 3.46
869 885 1.663161 GGAAGAAGCGAAAACGCCAAG 60.663 52.381 10.85 0.00 35.12 3.61
898 914 2.755876 ACGAGCGCATGGAGGAGA 60.756 61.111 11.47 0.00 0.00 3.71
962 978 0.178990 GGTGGCCCAACTCACTTCTT 60.179 55.000 0.00 0.00 34.57 2.52
1066 1083 1.211703 TCAAGCTGAGGAACAACACCA 59.788 47.619 0.00 0.00 0.00 4.17
1190 1207 1.338200 GGTGACGTTCAAGCTCCTGAT 60.338 52.381 0.00 0.00 0.00 2.90
1321 1338 6.766944 CACCTCCTTCTTAAGTACTATCGAGA 59.233 42.308 1.63 0.00 0.00 4.04
1346 1363 9.450807 GACTGCTTTATATTTTATGCGTTGAAT 57.549 29.630 0.00 0.00 0.00 2.57
1494 1520 3.656559 AGTGGGTACAACGTTACATCAC 58.343 45.455 0.00 9.23 0.00 3.06
1496 1522 3.998341 GTGGGTACAACGTTACATCACAT 59.002 43.478 0.00 0.00 0.00 3.21
1724 1750 3.952535 AGTCAACTTCAATGTGTTTCGC 58.047 40.909 0.00 0.00 0.00 4.70
1737 1763 1.302913 TTTCGCTCGGGCATGGAAA 60.303 52.632 8.62 6.39 38.60 3.13
1767 1793 2.304470 TGCAGAAAGGTATGTAGCACCA 59.696 45.455 0.00 0.00 38.62 4.17
1791 1817 4.141287 TGTTGTCACACCAAAGAATAGGG 58.859 43.478 0.00 0.00 0.00 3.53
1830 1856 3.782992 ACCCAATTCCTGAAGCAAAGAT 58.217 40.909 0.00 0.00 0.00 2.40
1914 1940 5.636543 ACTACGCGAAATAGTAGCTTGTTTT 59.363 36.000 15.93 0.00 42.87 2.43
1935 1961 1.202302 CGAGCACTCTAGGCGATCAAA 60.202 52.381 0.00 0.00 36.08 2.69
2025 2052 0.452184 CAGTGTACGCCGAGATGACT 59.548 55.000 1.98 0.00 0.00 3.41
2049 2076 2.305927 AGAGGGATTTGGTCGAATGTGT 59.694 45.455 0.00 0.00 0.00 3.72
2063 2090 4.338400 TCGAATGTGTAGACCATAGGACAG 59.662 45.833 0.00 0.00 0.00 3.51
2116 2143 2.039480 ACAGCAGACCAATGAGTGTCAT 59.961 45.455 0.00 0.00 39.09 3.06
2157 2184 6.767902 ACTGACATACTCTGTTGACAACAAAT 59.232 34.615 20.91 11.95 41.61 2.32
2216 2243 4.130118 CCACCAACAATGCTCCTATACTC 58.870 47.826 0.00 0.00 0.00 2.59
2271 2298 3.482156 ACAGCAGTGATCTTGTCAGTT 57.518 42.857 0.00 0.00 38.45 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.270986 GGCAAGCCACTCAACCCAG 61.271 63.158 6.14 0.00 35.81 4.45
19 20 2.203480 GGCAAGCCACTCAACCCA 60.203 61.111 6.14 0.00 35.81 4.51
24 25 0.694771 AGATGAAGGCAAGCCACTCA 59.305 50.000 14.40 15.01 38.92 3.41
33 34 3.009363 TGATGGACAAGAAGATGAAGGCA 59.991 43.478 0.00 0.00 0.00 4.75
144 145 1.480954 GAGGAAGAACCGGTGCAGATA 59.519 52.381 16.99 0.00 44.74 1.98
172 173 1.300465 CGATCATCAGTGGGGAGCG 60.300 63.158 7.90 7.90 34.03 5.03
182 183 1.153647 GTGTCACCGGCGATCATCA 60.154 57.895 9.30 0.00 0.00 3.07
305 306 3.104519 TCATTCACTGGGCCATGAATT 57.895 42.857 27.23 16.97 41.69 2.17
319 320 2.696989 ATGGCAGTCGACATCATTCA 57.303 45.000 19.50 7.35 35.13 2.57
366 368 4.994852 GCCACTACACAAGAGTTGAATACA 59.005 41.667 0.00 0.00 0.00 2.29
369 371 3.412386 GGCCACTACACAAGAGTTGAAT 58.588 45.455 0.00 0.00 0.00 2.57
383 386 0.618680 AGTGCTCATGAGGGCCACTA 60.619 55.000 24.50 0.00 0.00 2.74
424 430 0.250684 TCGAACTTTGGCTCCATGCA 60.251 50.000 0.00 0.00 45.15 3.96
462 468 1.593209 TGACCGCACCAAGTTCGAC 60.593 57.895 0.00 0.00 0.00 4.20
484 490 0.765135 TTCTTCCTCGGGTGGTTGGA 60.765 55.000 0.00 0.00 0.00 3.53
487 493 2.067197 CCTTCTTCCTCGGGTGGTT 58.933 57.895 0.00 0.00 0.00 3.67
521 527 1.559065 CGCCAACCCCTTCCCTTAGA 61.559 60.000 0.00 0.00 0.00 2.10
523 529 1.428718 AACGCCAACCCCTTCCCTTA 61.429 55.000 0.00 0.00 0.00 2.69
552 564 2.632028 CCTCCTCTACATCACCATGAGG 59.368 54.545 0.00 0.00 44.00 3.86
560 572 4.061131 TCAACTTCCCTCCTCTACATCA 57.939 45.455 0.00 0.00 0.00 3.07
565 577 5.202004 GTCACTATCAACTTCCCTCCTCTA 58.798 45.833 0.00 0.00 0.00 2.43
574 586 6.329496 CCTCTCTTCTGTCACTATCAACTTC 58.671 44.000 0.00 0.00 0.00 3.01
576 588 4.709397 CCCTCTCTTCTGTCACTATCAACT 59.291 45.833 0.00 0.00 0.00 3.16
588 600 0.042731 TACCCACCCCCTCTCTTCTG 59.957 60.000 0.00 0.00 0.00 3.02
706 722 1.475034 GGAGTCAGGCACAACACTGAA 60.475 52.381 0.00 0.00 44.53 3.02
709 725 0.767375 ATGGAGTCAGGCACAACACT 59.233 50.000 0.00 0.00 0.00 3.55
731 747 1.067565 TCTCCTCGATCTGCACACAAC 60.068 52.381 0.00 0.00 0.00 3.32
812 828 1.152652 ACCACGTTGGGCATTGGAA 60.153 52.632 8.57 0.00 43.37 3.53
839 855 2.035442 GCTTCTTCCTCGGTGGTGC 61.035 63.158 0.00 0.00 37.07 5.01
980 996 0.322816 GGGGATGCACTCAAGCTTCA 60.323 55.000 0.00 0.00 39.62 3.02
1066 1083 3.007920 CACCCTCCAGGAGCAGCT 61.008 66.667 11.57 0.00 39.89 4.24
1190 1207 3.478780 CCTTGAGGGTGTCGGGAA 58.521 61.111 0.00 0.00 0.00 3.97
1321 1338 9.801873 AATTCAACGCATAAAATATAAAGCAGT 57.198 25.926 0.00 0.00 0.00 4.40
1352 1369 5.957842 ACCACACATCATAACGATTGTTT 57.042 34.783 3.03 0.00 39.54 2.83
1356 1373 7.497595 ACATAGTACCACACATCATAACGATT 58.502 34.615 0.00 0.00 29.21 3.34
1509 1535 4.079096 AGGGTGTTAGACTGTATAGCTCCT 60.079 45.833 14.17 10.07 0.00 3.69
1513 1539 3.321396 GGGAGGGTGTTAGACTGTATAGC 59.679 52.174 0.00 0.00 0.00 2.97
1724 1750 2.406616 CCGGTTTTCCATGCCCGAG 61.407 63.158 0.00 0.00 43.01 4.63
1737 1763 1.995376 ACCTTTCTGCAAATCCGGTT 58.005 45.000 0.00 0.00 0.00 4.44
1767 1793 5.243730 CCCTATTCTTTGGTGTGACAACATT 59.756 40.000 3.26 0.00 38.92 2.71
1791 1817 3.709653 TGGGTATACCTCAATCACAGTCC 59.290 47.826 21.25 0.76 41.11 3.85
1830 1856 7.545265 GCAACTGCAAAAATTATCTGGATACAA 59.455 33.333 0.00 0.00 44.35 2.41
1847 1873 4.537374 GCTGTGGCTAATGCAACTGCAA 62.537 50.000 18.11 0.00 43.37 4.08
1914 1940 0.463833 TGATCGCCTAGAGTGCTCGA 60.464 55.000 0.00 0.00 34.09 4.04
1924 1950 4.811969 TTGGTTCTACTTTGATCGCCTA 57.188 40.909 0.00 0.00 0.00 3.93
1935 1961 4.150897 TGCTGTGTTCTTTGGTTCTACT 57.849 40.909 0.00 0.00 0.00 2.57
2009 2036 0.678684 TGGAGTCATCTCGGCGTACA 60.679 55.000 6.85 0.00 41.26 2.90
2049 2076 2.430248 TCACGCTGTCCTATGGTCTA 57.570 50.000 0.00 0.00 0.00 2.59
2063 2090 3.909137 CGCTATATTCGCTTCACGC 57.091 52.632 0.00 0.00 43.23 5.34
2116 2143 3.024547 GTCAGTATCTACAGGCACCTCA 58.975 50.000 0.00 0.00 0.00 3.86
2157 2184 4.142249 ACGATCACACGACCAGATATTTCA 60.142 41.667 0.00 0.00 37.03 2.69
2216 2243 0.997932 GACTTCTGCTGATGCGACAG 59.002 55.000 6.42 5.73 43.34 3.51


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

AutoCloner maintained by Alex Coulton.