Multiple sequence alignment - TraesCS1A01G141300

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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 TraesCS1A01G141300 chr1A 100.000 4275 0 0 1 4275 239106291 239102017 0 7895
1 TraesCS1A01G141300 chr1B 93.425 4350 154 56 1 4275 267971976 267967684 0 6327
2 TraesCS1A01G141300 chr1D 93.964 3479 138 23 1 3450 193364252 193360817 0 5195
3 TraesCS1A01G141300 chr1D 96.774 775 21 4 3503 4275 193360819 193360047 0 1290


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 TraesCS1A01G141300 chr1A 239102017 239106291 4274 True 7895.0 7895 100.000 1 4275 1 chr1A.!!$R1 4274
1 TraesCS1A01G141300 chr1B 267967684 267971976 4292 True 6327.0 6327 93.425 1 4275 1 chr1B.!!$R1 4274
2 TraesCS1A01G141300 chr1D 193360047 193364252 4205 True 3242.5 5195 95.369 1 4275 2 chr1D.!!$R1 4274

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
819 853 0.250727 TTGCCTCTTCTGAAACCCCG 60.251 55.0 0.0 0.0 0.0 5.73 F
1667 1738 0.105709 AACTTTCTTGGGGTGGTGGG 60.106 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2260 0.033796 CCCATCAGGTGCTGGACAAT 60.034 55.000 0.77 0.0 33.33 2.71 R
3415 3519 1.226773 CATTAGGCTTGCCGCTTGC 60.227 57.895 5.95 0.0 39.13 4.01 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
38 39 7.504924 AAACGACTAAATGGAGAAAATCACA 57.495 32.000 0.00 0.00 0.00 3.58
84 85 5.182760 ACAAATGTTGCTTTCTGAGAGATCC 59.817 40.000 0.00 0.00 0.00 3.36
86 87 2.562738 TGTTGCTTTCTGAGAGATCCGA 59.437 45.455 0.00 0.00 0.00 4.55
135 137 2.453521 ACGCTCCACTGGTGATTACTA 58.546 47.619 1.93 0.00 0.00 1.82
140 142 5.220662 CGCTCCACTGGTGATTACTATTTTG 60.221 44.000 1.93 0.00 0.00 2.44
145 147 7.037873 TCCACTGGTGATTACTATTTTGGTAGT 60.038 37.037 1.93 0.00 38.42 2.73
146 148 7.280205 CCACTGGTGATTACTATTTTGGTAGTC 59.720 40.741 1.93 0.00 36.39 2.59
205 207 1.210478 CTACCCCACAACCCTGATGAG 59.790 57.143 0.00 0.00 0.00 2.90
253 258 1.686110 ATTTCCCTCTCCTCGCCGT 60.686 57.895 0.00 0.00 0.00 5.68
254 259 1.961180 ATTTCCCTCTCCTCGCCGTG 61.961 60.000 0.00 0.00 0.00 4.94
281 286 1.600636 AACACCTGCACCCATCACG 60.601 57.895 0.00 0.00 0.00 4.35
315 341 2.348888 TTTCTCTCGCGTCCCCTCC 61.349 63.158 5.77 0.00 0.00 4.30
316 342 4.816984 TCTCTCGCGTCCCCTCCC 62.817 72.222 5.77 0.00 0.00 4.30
345 371 1.080974 CTCCCAAAGCAAGCAAGCG 60.081 57.895 0.00 0.00 40.15 4.68
346 372 1.518056 CTCCCAAAGCAAGCAAGCGA 61.518 55.000 0.00 0.00 40.15 4.93
347 373 1.080974 CCCAAAGCAAGCAAGCGAG 60.081 57.895 0.00 0.00 40.15 5.03
348 374 1.731969 CCAAAGCAAGCAAGCGAGC 60.732 57.895 4.06 4.06 40.15 5.03
366 392 2.110213 AGCGAGCGACCAACCAAA 59.890 55.556 0.00 0.00 0.00 3.28
430 456 6.321945 TGACCTACTAACTACGCAATCCAATA 59.678 38.462 0.00 0.00 0.00 1.90
431 457 7.014905 TGACCTACTAACTACGCAATCCAATAT 59.985 37.037 0.00 0.00 0.00 1.28
647 680 2.183478 TGGCTTGAAAGATCTTGCGA 57.817 45.000 9.17 5.90 0.00 5.10
679 712 0.536724 TGATCGTCTCCATGGGTGTG 59.463 55.000 13.02 0.00 0.00 3.82
736 769 3.074412 CCTTGTTTAGATTGGTGCGTCT 58.926 45.455 0.00 0.00 0.00 4.18
745 779 3.505680 AGATTGGTGCGTCTTTTGCATTA 59.494 39.130 0.00 0.00 45.34 1.90
819 853 0.250727 TTGCCTCTTCTGAAACCCCG 60.251 55.000 0.00 0.00 0.00 5.73
857 915 1.270893 ACGCCTTCAAGGTTTCTCTCC 60.271 52.381 5.03 0.00 37.80 3.71
877 935 1.555533 CCTCCCTCCTTCTGGTTGTAC 59.444 57.143 0.00 0.00 34.23 2.90
878 936 2.541466 CTCCCTCCTTCTGGTTGTACT 58.459 52.381 0.00 0.00 34.23 2.73
880 938 3.702045 CTCCCTCCTTCTGGTTGTACTAG 59.298 52.174 0.00 0.00 34.23 2.57
884 942 5.897824 CCCTCCTTCTGGTTGTACTAGAATA 59.102 44.000 6.16 0.00 43.27 1.75
885 943 6.383147 CCCTCCTTCTGGTTGTACTAGAATAA 59.617 42.308 6.16 0.00 43.27 1.40
886 944 7.071321 CCCTCCTTCTGGTTGTACTAGAATAAT 59.929 40.741 6.16 0.00 43.27 1.28
887 945 7.928706 CCTCCTTCTGGTTGTACTAGAATAATG 59.071 40.741 6.16 0.00 43.27 1.90
888 946 7.792032 TCCTTCTGGTTGTACTAGAATAATGG 58.208 38.462 6.16 4.89 43.27 3.16
922 985 3.077359 CACCTGGTCTTCTTCACAATCC 58.923 50.000 0.00 0.00 0.00 3.01
1167 1238 3.295304 CTCCACGGACCATGACGCA 62.295 63.158 0.00 0.00 0.00 5.24
1209 1280 3.384014 CTCGCTCACCGTCTCGTCC 62.384 68.421 0.00 0.00 38.35 4.79
1230 1301 1.133407 GAGATCAGCGTCGAGTCCTTT 59.867 52.381 0.00 0.00 0.00 3.11
1470 1541 4.153117 CAGGTGACATTCTCTTCTTTTCCG 59.847 45.833 0.00 0.00 0.00 4.30
1499 1570 0.111253 CTTCCAGCTCCACCCAACTT 59.889 55.000 0.00 0.00 0.00 2.66
1556 1627 1.070134 GATCCGATCATCCACCCGAAA 59.930 52.381 3.33 0.00 0.00 3.46
1565 1636 0.478942 TCCACCCGAAAAACCATCCA 59.521 50.000 0.00 0.00 0.00 3.41
1603 1674 5.195185 TGATGCAGATGATAACACCAATGT 58.805 37.500 0.00 0.00 42.46 2.71
1667 1738 0.105709 AACTTTCTTGGGGTGGTGGG 60.106 55.000 0.00 0.00 0.00 4.61
1888 1959 6.092670 CGAAGATTCTGAATTCAAGGTAAGCA 59.907 38.462 9.88 0.00 0.00 3.91
1930 2001 6.976349 GCAACTCATTCAAATGCTATGATTGA 59.024 34.615 0.00 9.52 35.79 2.57
1931 2002 7.652105 GCAACTCATTCAAATGCTATGATTGAT 59.348 33.333 10.02 0.00 36.89 2.57
1932 2003 9.529325 CAACTCATTCAAATGCTATGATTGATT 57.471 29.630 10.02 4.93 36.89 2.57
1933 2004 9.529325 AACTCATTCAAATGCTATGATTGATTG 57.471 29.630 10.02 0.00 36.89 2.67
1934 2005 8.141909 ACTCATTCAAATGCTATGATTGATTGG 58.858 33.333 10.02 0.00 36.89 3.16
1969 2045 8.618702 AGATCATAGAAGCATGACCTATTTTG 57.381 34.615 0.00 0.00 37.74 2.44
2011 2087 4.468868 CCAGTCCTGATATCATCTGCCATA 59.531 45.833 18.83 0.00 0.00 2.74
2172 2260 3.181469 GGTATGTAACGAGCCCATCTTCA 60.181 47.826 0.00 0.00 0.00 3.02
2186 2274 2.189594 TCTTCATTGTCCAGCACCTG 57.810 50.000 0.00 0.00 0.00 4.00
2187 2275 1.699083 TCTTCATTGTCCAGCACCTGA 59.301 47.619 0.00 0.00 32.44 3.86
2188 2276 2.306805 TCTTCATTGTCCAGCACCTGAT 59.693 45.455 0.00 0.00 32.44 2.90
2189 2277 2.118313 TCATTGTCCAGCACCTGATG 57.882 50.000 0.00 0.00 32.44 3.07
2261 2349 3.580458 AGCATACTGTGACTTTCAGAGGT 59.420 43.478 5.43 0.00 41.56 3.85
2391 2481 6.073327 CCAGGAGTGGTTAAAAGAAAACTC 57.927 41.667 0.00 0.00 39.30 3.01
2529 2623 1.648116 TAGGCACTTCCGGGTTAGTT 58.352 50.000 0.00 0.00 41.75 2.24
2542 2636 4.501071 CGGGTTAGTTAACATGCTAGTGT 58.499 43.478 8.61 0.00 37.92 3.55
2563 2657 2.617658 AGGAAGACCGGTTAGGAAAGT 58.382 47.619 9.42 0.00 45.00 2.66
2593 2687 3.323403 CCCTGCTGGTTGGTTAAAATCAA 59.677 43.478 9.00 0.00 0.00 2.57
2624 2721 3.696051 TCTGGCTGATTTCCAATTGTAGC 59.304 43.478 4.43 4.47 32.41 3.58
2864 2967 4.704103 AGCTCCTCACAGGCCGGA 62.704 66.667 10.86 2.50 34.61 5.14
2884 2987 2.283529 GCCTCTGGACCGGAACAGA 61.284 63.158 24.13 24.13 41.13 3.41
2950 3053 3.202906 CTCCGACACCAAGAAGTTTGAA 58.797 45.455 0.00 0.00 0.00 2.69
2987 3090 0.246635 GCTCGAAGGGAACTACAGCA 59.753 55.000 0.00 0.00 42.68 4.41
3415 3519 9.793252 CATGATAACTAAAAACAGGAGATTTGG 57.207 33.333 0.00 0.00 0.00 3.28
3416 3520 7.826690 TGATAACTAAAAACAGGAGATTTGGC 58.173 34.615 0.00 0.00 0.00 4.52
3417 3521 7.450014 TGATAACTAAAAACAGGAGATTTGGCA 59.550 33.333 0.00 0.00 0.00 4.92
3418 3522 6.478512 AACTAAAAACAGGAGATTTGGCAA 57.521 33.333 0.00 0.00 0.00 4.52
3419 3523 6.089249 ACTAAAAACAGGAGATTTGGCAAG 57.911 37.500 0.00 0.00 0.00 4.01
3420 3524 3.391506 AAAACAGGAGATTTGGCAAGC 57.608 42.857 0.00 0.00 0.00 4.01
3496 3600 4.885426 CACAGGCAGTGTCCACTT 57.115 55.556 1.31 0.00 43.40 3.16
3552 3656 5.829924 AGAGCTGGAAAATCAAAACTGAAGA 59.170 36.000 0.00 0.00 0.00 2.87
3625 3729 6.509837 CGCATTTTTGCTGACTGAATTTTGAA 60.510 34.615 0.00 0.00 0.00 2.69
3970 4077 4.387256 GCTAACTGCTCTTTGTGTACTCTG 59.613 45.833 0.00 0.00 38.95 3.35
4084 4191 1.754234 ATGCTCCGGATGTTTGGCC 60.754 57.895 3.57 0.00 0.00 5.36
4090 4197 1.140852 TCCGGATGTTTGGCCTGATAG 59.859 52.381 0.00 0.00 0.00 2.08
4270 4377 6.942532 TGATCCTAGCAATTGGTACATTTC 57.057 37.500 13.22 8.64 39.30 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 2.562738 TCGGATCTCTCAGAAAGCAACA 59.437 45.455 0.00 0.00 0.00 3.33
140 142 9.290483 CAAAGTTCAAAAGAAGAAAAGACTACC 57.710 33.333 0.00 0.00 0.00 3.18
205 207 2.808543 ACAATCGCAGGAACAAGAACTC 59.191 45.455 0.00 0.00 0.00 3.01
253 258 2.295909 GGTGCAGGTGTTGAAATAAGCA 59.704 45.455 0.00 0.00 0.00 3.91
254 259 2.352715 GGGTGCAGGTGTTGAAATAAGC 60.353 50.000 0.00 0.00 0.00 3.09
281 286 2.742589 GAGAAACGTGAGGGTTTGGATC 59.257 50.000 0.00 0.00 40.05 3.36
316 342 2.527951 CTTTGGGAGCTGGGACGAGG 62.528 65.000 0.00 0.00 0.00 4.63
317 343 1.078848 CTTTGGGAGCTGGGACGAG 60.079 63.158 0.00 0.00 0.00 4.18
318 344 3.068881 CTTTGGGAGCTGGGACGA 58.931 61.111 0.00 0.00 0.00 4.20
345 371 3.482783 GTTGGTCGCTCGCTGCTC 61.483 66.667 0.00 0.00 40.11 4.26
348 374 2.250939 TTTGGTTGGTCGCTCGCTG 61.251 57.895 0.00 0.00 0.00 5.18
353 379 1.676006 CTTTCTGTTTGGTTGGTCGCT 59.324 47.619 0.00 0.00 0.00 4.93
366 392 1.001406 CTTCGGGCTGTCTCTTTCTGT 59.999 52.381 0.00 0.00 0.00 3.41
391 417 3.219198 GTCAATGGATGGCCGGCC 61.219 66.667 39.40 39.40 36.79 6.13
430 456 1.887797 TCAGGGTACGGGATTTGGAT 58.112 50.000 0.00 0.00 0.00 3.41
431 457 1.279846 GTTCAGGGTACGGGATTTGGA 59.720 52.381 0.00 0.00 0.00 3.53
647 680 2.499289 AGACGATCAGCCAGACAGAAAT 59.501 45.455 0.00 0.00 0.00 2.17
679 712 1.600916 GCCACCAGGACCAGAACAC 60.601 63.158 0.00 0.00 36.89 3.32
736 769 9.806203 CTGGATCAATCAATTACTAATGCAAAA 57.194 29.630 0.00 0.00 0.00 2.44
819 853 5.817988 AGGCGTCAAAAGAAGAAAACTAAC 58.182 37.500 0.00 0.00 0.00 2.34
857 915 1.555533 GTACAACCAGAAGGAGGGAGG 59.444 57.143 0.00 0.00 38.69 4.30
877 935 3.812053 AGAAAGCAGCGCCATTATTCTAG 59.188 43.478 2.29 0.00 0.00 2.43
878 936 3.561310 CAGAAAGCAGCGCCATTATTCTA 59.439 43.478 2.29 0.00 0.00 2.10
880 938 2.724349 CAGAAAGCAGCGCCATTATTC 58.276 47.619 2.29 2.93 0.00 1.75
884 942 2.570181 GCAGAAAGCAGCGCCATT 59.430 55.556 2.29 0.00 44.79 3.16
922 985 0.173481 TCTCGGATCTTGGAAGCACG 59.827 55.000 0.00 0.00 0.00 5.34
993 1064 5.622914 GCAATAACATGACAGCATCAAAGGT 60.623 40.000 0.00 0.00 41.93 3.50
1080 1151 1.078848 CTCCTTGTCCCGCTCCTTG 60.079 63.158 0.00 0.00 0.00 3.61
1209 1280 1.010574 GGACTCGACGCTGATCTCG 60.011 63.158 6.44 6.44 0.00 4.04
1499 1570 4.080919 AGCTCTGACACCATGTTTATGCTA 60.081 41.667 0.00 0.00 32.79 3.49
1548 1619 4.644685 AGATTATGGATGGTTTTTCGGGTG 59.355 41.667 0.00 0.00 0.00 4.61
1565 1636 4.079970 CTGCATCAAGCCATCCAGATTAT 58.920 43.478 0.00 0.00 44.83 1.28
1603 1674 3.244735 TGTCCCTGGATGACGAATCAAAA 60.245 43.478 0.00 0.00 38.69 2.44
1667 1738 1.826385 CTTCACCAGGTTGGGATGAC 58.174 55.000 0.00 0.00 43.37 3.06
1888 1959 1.669115 GCCGCATGCCTATGACGAT 60.669 57.895 13.15 0.00 36.56 3.73
1930 2001 9.282569 GCTTCTATGATCTTATCTTTCACCAAT 57.717 33.333 0.00 0.00 0.00 3.16
1931 2002 8.267183 TGCTTCTATGATCTTATCTTTCACCAA 58.733 33.333 0.00 0.00 0.00 3.67
1932 2003 7.795047 TGCTTCTATGATCTTATCTTTCACCA 58.205 34.615 0.00 0.00 0.00 4.17
1933 2004 8.719648 CATGCTTCTATGATCTTATCTTTCACC 58.280 37.037 0.00 0.00 0.00 4.02
1934 2005 9.486497 TCATGCTTCTATGATCTTATCTTTCAC 57.514 33.333 0.00 0.00 32.39 3.18
1969 2045 2.039879 TGGGTAAAAGGCAAGAGACTCC 59.960 50.000 0.00 0.00 27.72 3.85
2172 2260 0.033796 CCCATCAGGTGCTGGACAAT 60.034 55.000 0.77 0.00 33.33 2.71
2186 2274 3.181451 TGAGAATAGTGCCATCACCCATC 60.181 47.826 0.00 0.00 44.16 3.51
2187 2275 2.779430 TGAGAATAGTGCCATCACCCAT 59.221 45.455 0.00 0.00 44.16 4.00
2188 2276 2.195727 TGAGAATAGTGCCATCACCCA 58.804 47.619 0.00 0.00 44.16 4.51
2189 2277 3.281727 TTGAGAATAGTGCCATCACCC 57.718 47.619 0.00 0.00 44.16 4.61
2190 2278 4.276926 GGAATTGAGAATAGTGCCATCACC 59.723 45.833 0.00 0.00 44.16 4.02
2191 2279 4.883585 TGGAATTGAGAATAGTGCCATCAC 59.116 41.667 0.00 0.00 43.44 3.06
2192 2280 5.114764 TGGAATTGAGAATAGTGCCATCA 57.885 39.130 0.00 0.00 0.00 3.07
2388 2478 3.067011 TCCATTCACGTGGAGGAGT 57.933 52.632 17.00 0.00 43.20 3.85
2430 2523 5.404466 TTCACAGGCCAATAATCTTTTGG 57.596 39.130 5.01 0.00 45.30 3.28
2431 2524 9.090692 CTTATTTCACAGGCCAATAATCTTTTG 57.909 33.333 5.01 0.00 0.00 2.44
2529 2623 4.097437 CGGTCTTCCTACACTAGCATGTTA 59.903 45.833 0.00 0.00 33.85 2.41
2542 2636 3.766051 GACTTTCCTAACCGGTCTTCCTA 59.234 47.826 8.04 0.00 0.00 2.94
2593 2687 5.385198 TGGAAATCAGCCAGAAAAGTTAGT 58.615 37.500 0.00 0.00 0.00 2.24
2644 2741 7.115378 CAGAGGCTACTTTTACTTGCAAATTTG 59.885 37.037 14.03 14.03 0.00 2.32
2651 2748 5.452777 CAAACAGAGGCTACTTTTACTTGC 58.547 41.667 0.00 0.00 0.00 4.01
2864 2967 3.003763 GTTCCGGTCCAGAGGCCT 61.004 66.667 3.86 3.86 0.00 5.19
2884 2987 1.752833 GTTCTGTTCACCCCTCGGT 59.247 57.895 0.00 0.00 46.31 4.69
2950 3053 3.748668 CGAGCCTTGGATCCATTATGGTT 60.749 47.826 17.06 13.20 39.03 3.67
2987 3090 2.947652 CAATCCTGACTGCCGATTTCAT 59.052 45.455 0.00 0.00 0.00 2.57
3414 3518 2.418083 ATTAGGCTTGCCGCTTGCC 61.418 57.895 16.10 16.10 46.42 4.52
3415 3519 1.226773 CATTAGGCTTGCCGCTTGC 60.227 57.895 5.95 0.00 39.13 4.01
3416 3520 1.226773 GCATTAGGCTTGCCGCTTG 60.227 57.895 5.95 6.25 40.25 4.01
3417 3521 3.200522 GCATTAGGCTTGCCGCTT 58.799 55.556 5.95 0.00 40.25 4.68
3900 4005 3.903714 CCTTTTTCCCCACATTTTCTCCT 59.096 43.478 0.00 0.00 0.00 3.69
4233 4340 1.632409 AGGATCATGTGCCAGAACTGT 59.368 47.619 8.84 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.