Multiple sequence alignment - TraesCS7A01G243200

Loading Multiple Alignment...

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 TraesCS7A01G243200 chr7A 100.000 2414 0 0 1 2414 218264396 218266809 0.000000e+00 4458
1 TraesCS7A01G243200 chr7D 94.313 2110 84 12 73 2176 205952903 205954982 0.000000e+00 3199
2 TraesCS7A01G243200 chr7D 87.417 151 18 1 2264 2413 205956282 205956432 3.190000e-39 172
3 TraesCS7A01G243200 chr7D 100.000 89 0 0 1 89 205951030 205951118 5.340000e-37 165
4 TraesCS7A01G243200 chr7B 93.568 2161 89 13 1 2139 196277813 196275681 0.000000e+00 3175


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 TraesCS7A01G243200 chr7A 218264396 218266809 2413 False 4458.000000 4458 100.000 1 2414 1 chr7A.!!$F1 2413
1 TraesCS7A01G243200 chr7D 205951030 205956432 5402 False 1178.666667 3199 93.910 1 2413 3 chr7D.!!$F1 2412
2 TraesCS7A01G243200 chr7B 196275681 196277813 2132 True 3175.000000 3175 93.568 1 2139 1 chr7B.!!$R1 2138

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
955 2760 0.766131 ACACAATAACACGGGGTGGA 59.234 50.0 0.0 0.0 37.94 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2369 5407 0.106894 GCCCAGTATAGCACCTGGAC 59.893 60.0 0.0 0.0 39.19 4.02 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
133 1935 7.180079 GGTCAAGATACAACATAATTGTGTCG 58.820 38.462 8.40 0.00 42.76 4.35
240 2042 5.066375 TGTGTTGATGGTGAACTCTGAAAAG 59.934 40.000 0.00 0.00 0.00 2.27
429 2234 7.556635 TGAGTTTCTCGTAATCTTCCTAGATGA 59.443 37.037 0.00 0.00 35.87 2.92
448 2253 3.909732 TGACAATGGATATCCCCCAAAC 58.090 45.455 19.34 7.07 37.22 2.93
475 2280 2.619074 GGGATTCCAACCTCCAACAGAG 60.619 54.545 4.80 0.00 42.83 3.35
479 2284 2.338809 TCCAACCTCCAACAGAGTCAT 58.661 47.619 0.00 0.00 41.47 3.06
490 2295 3.325293 ACAGAGTCATACAACAGCAGG 57.675 47.619 0.00 0.00 0.00 4.85
551 2356 6.345096 TCTTATATGCACTGCTAGCACATA 57.655 37.500 21.88 21.88 45.95 2.29
552 2357 6.159293 TCTTATATGCACTGCTAGCACATAC 58.841 40.000 22.01 10.73 45.95 2.39
553 2358 2.696989 ATGCACTGCTAGCACATACA 57.303 45.000 14.93 10.23 45.95 2.29
554 2359 2.470983 TGCACTGCTAGCACATACAA 57.529 45.000 14.93 0.00 37.02 2.41
555 2360 2.989909 TGCACTGCTAGCACATACAAT 58.010 42.857 14.93 0.00 37.02 2.71
556 2361 2.679336 TGCACTGCTAGCACATACAATG 59.321 45.455 14.93 3.88 37.02 2.82
557 2362 2.938451 GCACTGCTAGCACATACAATGA 59.062 45.455 14.93 0.00 0.00 2.57
558 2363 3.562973 GCACTGCTAGCACATACAATGAT 59.437 43.478 14.93 0.00 0.00 2.45
559 2364 4.751600 GCACTGCTAGCACATACAATGATA 59.248 41.667 14.93 0.00 0.00 2.15
601 2406 7.104974 AGTCTAGGCTACTATAATCCCTCAA 57.895 40.000 0.00 0.00 0.00 3.02
602 2407 6.949463 AGTCTAGGCTACTATAATCCCTCAAC 59.051 42.308 0.00 0.00 0.00 3.18
603 2408 6.153170 GTCTAGGCTACTATAATCCCTCAACC 59.847 46.154 0.00 0.00 0.00 3.77
604 2409 5.094569 AGGCTACTATAATCCCTCAACCT 57.905 43.478 0.00 0.00 0.00 3.50
605 2410 5.088026 AGGCTACTATAATCCCTCAACCTC 58.912 45.833 0.00 0.00 0.00 3.85
606 2411 4.838986 GGCTACTATAATCCCTCAACCTCA 59.161 45.833 0.00 0.00 0.00 3.86
607 2412 5.307196 GGCTACTATAATCCCTCAACCTCAA 59.693 44.000 0.00 0.00 0.00 3.02
616 2421 1.250328 CTCAACCTCAATTGGCAGCA 58.750 50.000 5.42 0.00 0.00 4.41
624 2429 3.259064 CTCAATTGGCAGCAAGAAATGG 58.741 45.455 5.42 0.00 0.00 3.16
714 2519 4.832266 ACCCAACAGCAAATAATCAACTCA 59.168 37.500 0.00 0.00 0.00 3.41
853 2658 6.071560 GCCCAAAGTTTTATTACAGCCTAGTT 60.072 38.462 0.00 0.00 0.00 2.24
955 2760 0.766131 ACACAATAACACGGGGTGGA 59.234 50.000 0.00 0.00 37.94 4.02
1189 2994 0.460987 GATCGAAGGGACACCAGCTG 60.461 60.000 6.78 6.78 40.13 4.24
1224 3029 1.003233 GGTCTGCCCACTGAACTCC 60.003 63.158 0.00 0.00 0.00 3.85
1240 3045 0.736053 CTCCGACTTCTCTTCCGAGG 59.264 60.000 0.00 0.00 37.86 4.63
1291 3096 0.603065 CATCGGTGGAGTGTCTGTGA 59.397 55.000 0.00 0.00 0.00 3.58
1302 3107 5.059833 GGAGTGTCTGTGAGAAGTCAAAAT 58.940 41.667 0.00 0.00 33.27 1.82
1433 3245 0.107508 ACAGATGAGGGGTTGATGCG 60.108 55.000 0.00 0.00 0.00 4.73
1565 3377 3.527507 TCCAGTTCTGTAGAGGACACT 57.472 47.619 0.42 0.00 33.31 3.55
1581 3393 0.516877 CACTGGCACCATGTAACACG 59.483 55.000 0.00 0.00 0.00 4.49
1635 3454 4.054780 TGAGGTTTACGAGGATATGCAC 57.945 45.455 0.00 0.00 0.00 4.57
1641 3460 2.082140 ACGAGGATATGCACTACCCA 57.918 50.000 0.00 0.00 0.00 4.51
1652 3471 7.014615 GGATATGCACTACCCAAAATTCAGAAT 59.985 37.037 0.00 0.00 0.00 2.40
1658 3477 9.435688 GCACTACCCAAAATTCAGAATTATTTT 57.564 29.630 8.88 0.00 35.05 1.82
1680 3499 4.469657 TCTTTCTTAGCAGGAAAAGGCAA 58.530 39.130 0.00 0.00 33.17 4.52
1706 3525 8.712285 ATTCATTCTAAAATTGCATCCTTGTG 57.288 30.769 0.00 0.00 0.00 3.33
1713 3532 8.677300 TCTAAAATTGCATCCTTGTGATAGTTC 58.323 33.333 0.00 0.00 30.56 3.01
1715 3534 7.414222 AAATTGCATCCTTGTGATAGTTCAT 57.586 32.000 0.00 0.00 33.56 2.57
1717 3536 4.122046 TGCATCCTTGTGATAGTTCATCG 58.878 43.478 0.00 0.00 36.33 3.84
1734 3553 0.109039 TCGAATGATGACGCCAACGA 60.109 50.000 0.00 0.00 43.93 3.85
1768 3587 4.620982 TGTATCATGCGTAGGATTGACAG 58.379 43.478 5.87 0.00 35.32 3.51
1814 3639 3.552478 GCCGTAGCTATAGGGTGAAGAAC 60.552 52.174 16.76 0.00 38.87 3.01
1902 3728 8.738645 ATTTTACTCGGATTTTCAAGCTATCT 57.261 30.769 0.00 0.00 0.00 1.98
1914 3740 0.972983 AGCTATCTGTGGGCACGAGT 60.973 55.000 0.00 0.00 0.00 4.18
1918 3744 0.615331 ATCTGTGGGCACGAGTGAAT 59.385 50.000 7.50 0.00 0.00 2.57
1949 3775 5.401750 AGATAGGATACCTTCATCTGCAGT 58.598 41.667 14.67 0.00 30.36 4.40
1956 3782 1.078918 TTCATCTGCAGTCTGGCGG 60.079 57.895 14.67 0.00 41.61 6.13
1986 3812 0.107017 AGTGAATGCTTCCATCCCGG 60.107 55.000 0.00 0.00 0.00 5.73
2174 5174 4.814294 CGGCGAGGGGAGGTTTCG 62.814 72.222 0.00 0.00 37.40 3.46
2184 5184 3.609422 GAGGTTTCGCGCGTTCGTG 62.609 63.158 30.98 0.00 46.68 4.35
2206 5206 4.742201 GCGAGCAGGGCAAGACGA 62.742 66.667 0.00 0.00 0.00 4.20
2236 5236 2.811317 GCCGAACAGGTGCTCTCG 60.811 66.667 0.00 0.00 43.70 4.04
2238 5238 2.049156 CGAACAGGTGCTCTCGCA 60.049 61.111 0.00 0.00 45.60 5.10
2296 5333 1.376466 CCCATCCTAATCGGGCCTG 59.624 63.158 4.71 4.71 31.89 4.85
2332 5370 2.478894 GTCATGGCACGATTATTACCGG 59.521 50.000 0.00 0.00 0.00 5.28
2341 5379 0.249573 ATTATTACCGGGCCGTGTCG 60.250 55.000 26.32 12.04 0.00 4.35
2367 5405 2.233566 TGTCTTCCAGCCCAGGCAT 61.234 57.895 12.03 0.00 44.88 4.40
2370 5408 3.267233 TTCCAGCCCAGGCATGGT 61.267 61.111 17.55 0.00 46.10 3.55
2374 5412 3.736224 AGCCCAGGCATGGTCCAG 61.736 66.667 17.55 1.39 46.10 3.86
2383 5421 1.543429 GGCATGGTCCAGGTGCTATAC 60.543 57.143 15.45 0.00 38.83 1.47
2384 5422 1.417890 GCATGGTCCAGGTGCTATACT 59.582 52.381 9.79 0.00 36.02 2.12
2385 5423 2.808202 GCATGGTCCAGGTGCTATACTG 60.808 54.545 9.79 0.00 36.02 2.74
2394 5432 0.870307 GTGCTATACTGGGCGACACG 60.870 60.000 0.00 0.00 0.00 4.49
2395 5433 1.299926 GCTATACTGGGCGACACGG 60.300 63.158 0.00 0.00 0.00 4.94
2413 5451 0.246086 GGCGGCATGTCCAAAATCAA 59.754 50.000 3.07 0.00 34.01 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
240 2042 4.580580 ACTATAGCAAAAGCTGGCATAACC 59.419 41.667 0.00 0.00 39.84 2.85
429 2234 4.557899 ATGTTTGGGGGATATCCATTGT 57.442 40.909 23.27 0.00 37.91 2.71
464 2269 4.248859 CTGTTGTATGACTCTGTTGGAGG 58.751 47.826 0.00 0.00 45.83 4.30
475 2280 3.003480 GGAAGTCCTGCTGTTGTATGAC 58.997 50.000 0.00 0.00 0.00 3.06
479 2284 3.788227 AATGGAAGTCCTGCTGTTGTA 57.212 42.857 0.00 0.00 36.82 2.41
490 2295 6.477688 TCAACGGATATTACGAAATGGAAGTC 59.522 38.462 7.62 0.00 34.93 3.01
554 2359 9.988815 GACTATGTCTGGACTTTATTGTATCAT 57.011 33.333 2.38 0.00 0.00 2.45
555 2360 9.201989 AGACTATGTCTGGACTTTATTGTATCA 57.798 33.333 0.00 0.00 41.76 2.15
558 2363 9.132923 CCTAGACTATGTCTGGACTTTATTGTA 57.867 37.037 11.71 0.00 42.49 2.41
559 2364 7.418025 GCCTAGACTATGTCTGGACTTTATTGT 60.418 40.741 11.71 0.00 42.49 2.71
601 2406 1.999648 TTCTTGCTGCCAATTGAGGT 58.000 45.000 7.12 0.00 0.00 3.85
602 2407 3.259064 CATTTCTTGCTGCCAATTGAGG 58.741 45.455 7.12 0.00 0.00 3.86
603 2408 3.259064 CCATTTCTTGCTGCCAATTGAG 58.741 45.455 7.12 0.00 0.00 3.02
604 2409 2.633967 ACCATTTCTTGCTGCCAATTGA 59.366 40.909 7.12 0.00 0.00 2.57
605 2410 3.048337 ACCATTTCTTGCTGCCAATTG 57.952 42.857 0.00 0.00 0.00 2.32
606 2411 4.888326 TTACCATTTCTTGCTGCCAATT 57.112 36.364 0.00 0.00 0.00 2.32
607 2412 4.888326 TTTACCATTTCTTGCTGCCAAT 57.112 36.364 0.00 0.00 0.00 3.16
714 2519 2.604686 TGCCGAGAGAAGCCTGGT 60.605 61.111 0.00 0.00 0.00 4.00
757 2562 6.066032 TCCTTAGTTTGGAACTTTTGGTAGG 58.934 40.000 0.00 0.00 42.81 3.18
955 2760 9.107177 GTGAGATGAGATAGTGAATCAATTTGT 57.893 33.333 0.00 0.00 37.03 2.83
998 2803 3.057969 AGCAGCACTGTAAGCACATTA 57.942 42.857 0.00 0.00 37.60 1.90
1160 2965 2.974698 CTTCGATCGCCCCCATGC 60.975 66.667 11.09 0.00 0.00 4.06
1161 2966 2.281070 CCTTCGATCGCCCCCATG 60.281 66.667 11.09 0.00 0.00 3.66
1189 2994 1.750206 GACCTTCGGAGAGTACCTTCC 59.250 57.143 0.00 3.66 38.43 3.46
1240 3045 2.414559 CGTTGATGATTGGTGAGTTGCC 60.415 50.000 0.00 0.00 0.00 4.52
1291 3096 2.778299 TGCGGCACTATTTTGACTTCT 58.222 42.857 0.00 0.00 0.00 2.85
1302 3107 1.476891 CTAACTCTCCTTGCGGCACTA 59.523 52.381 0.05 0.00 0.00 2.74
1366 3171 7.344134 TCACTGGAATCATCATCTGAATCTTT 58.656 34.615 0.00 0.00 37.44 2.52
1367 3172 6.896883 TCACTGGAATCATCATCTGAATCTT 58.103 36.000 0.00 0.00 37.44 2.40
1433 3245 2.711009 TGTACCATGATGAATCCCCTCC 59.289 50.000 0.00 0.00 0.00 4.30
1478 3290 0.390860 CGCCATAGTCCTTCAGAGGG 59.609 60.000 0.00 0.00 43.72 4.30
1565 3377 4.388229 CCGTGTTACATGGTGCCA 57.612 55.556 15.05 0.00 35.92 4.92
1581 3393 9.289303 CAATTACATAATTCTTGTGCTGTTACC 57.711 33.333 4.62 0.00 33.88 2.85
1652 3471 8.088365 GCCTTTTCCTGCTAAGAAAGAAAATAA 58.912 33.333 0.00 0.00 36.25 1.40
1658 3477 4.098914 TGCCTTTTCCTGCTAAGAAAGA 57.901 40.909 0.00 0.00 34.84 2.52
1680 3499 9.158233 CACAAGGATGCAATTTTAGAATGAATT 57.842 29.630 0.00 0.00 0.00 2.17
1713 3532 3.614673 TCGTTGGCGTCATCATTCGATG 61.615 50.000 0.00 0.00 42.60 3.84
1715 3534 0.109039 TCGTTGGCGTCATCATTCGA 60.109 50.000 0.00 0.00 39.49 3.71
1717 3536 1.359848 ACTCGTTGGCGTCATCATTC 58.640 50.000 0.00 0.00 39.49 2.67
1734 3553 4.635765 ACGCATGATACAGTTTGCATAACT 59.364 37.500 0.00 8.03 34.80 2.24
1768 3587 2.076863 CAGACGGGGTCATTTCTTCAC 58.923 52.381 0.00 0.00 34.60 3.18
1814 3639 9.494479 CTACACAATATTGCTTTATCAAGTGTG 57.506 33.333 15.48 4.74 39.91 3.82
1902 3728 1.686355 AAAATTCACTCGTGCCCACA 58.314 45.000 0.00 0.00 0.00 4.17
1956 3782 1.060937 CATTCACTTACGCGCCAGC 59.939 57.895 5.73 0.00 40.74 4.85
1986 3812 2.100631 CCACCACTGAACGCCGATC 61.101 63.158 0.00 0.00 0.00 3.69
2088 3914 4.263572 CTCCGGCACCCACAACCA 62.264 66.667 0.00 0.00 0.00 3.67
2310 5347 2.154963 CGGTAATAATCGTGCCATGACG 59.845 50.000 0.00 0.00 40.83 4.35
2320 5357 0.249573 ACACGGCCCGGTAATAATCG 60.250 55.000 8.57 0.00 0.00 3.34
2341 5379 3.248029 CTGGAAGACACAGCACGC 58.752 61.111 0.00 0.00 34.07 5.34
2367 5405 1.496060 CCAGTATAGCACCTGGACCA 58.504 55.000 0.00 0.00 39.19 4.02
2369 5407 0.106894 GCCCAGTATAGCACCTGGAC 59.893 60.000 0.00 0.00 39.19 4.02
2370 5408 1.399744 CGCCCAGTATAGCACCTGGA 61.400 60.000 0.00 0.00 39.19 3.86
2374 5412 0.529992 GTGTCGCCCAGTATAGCACC 60.530 60.000 0.00 0.00 0.00 5.01
2394 5432 0.246086 TTGATTTTGGACATGCCGCC 59.754 50.000 0.00 0.00 40.66 6.13
2395 5433 3.810579 TTGATTTTGGACATGCCGC 57.189 47.368 0.00 0.00 40.66 6.53


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

AutoCloner maintained by Alex Coulton.