Multiple sequence alignment - TraesCS5D01G362500

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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 TraesCS5D01G362500 chr5D 100.000 2786 0 0 1 2786 441098169 441100954 0.000000e+00 5145.0
1 TraesCS5D01G362500 chr5B 90.743 2895 123 50 1 2786 536655662 536658520 0.000000e+00 3727.0
2 TraesCS5D01G362500 chr5A 89.099 2009 80 48 791 2746 557314532 557316454 0.000000e+00 2368.0
3 TraesCS5D01G362500 chr5A 83.721 258 14 12 405 649 557313957 557314199 4.670000e-53 219.0
4 TraesCS5D01G362500 chr6B 79.456 331 57 8 1222 1542 717968691 717968362 1.000000e-54 224.0
5 TraesCS5D01G362500 chr6D 79.228 337 53 11 1222 1542 472897338 472897003 4.670000e-53 219.0
6 TraesCS5D01G362500 chr6A 79.154 331 55 9 1222 1542 616916961 616917287 1.680000e-52 217.0
7 TraesCS5D01G362500 chr2A 91.011 89 2 3 2201 2289 315960229 315960311 6.310000e-22 115.0
8 TraesCS5D01G362500 chr7A 89.130 92 4 2 2201 2292 474142951 474142866 2.930000e-20 110.0
9 TraesCS5D01G362500 chr4B 89.888 89 3 2 2201 2289 235738965 235739047 2.930000e-20 110.0
10 TraesCS5D01G362500 chr4B 87.640 89 5 2 2201 2289 225958579 225958661 6.350000e-17 99.0
11 TraesCS5D01G362500 chr7B 86.517 89 6 2 2201 2289 604278578 604278660 2.950000e-15 93.5


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 TraesCS5D01G362500 chr5D 441098169 441100954 2785 False 5145.0 5145 100.000 1 2786 1 chr5D.!!$F1 2785
1 TraesCS5D01G362500 chr5B 536655662 536658520 2858 False 3727.0 3727 90.743 1 2786 1 chr5B.!!$F1 2785
2 TraesCS5D01G362500 chr5A 557313957 557316454 2497 False 1293.5 2368 86.410 405 2746 2 chr5A.!!$F1 2341

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
812 1035 0.842467 CAACTCCAACCTCCCCCTCT 60.842 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2074 2379 0.102844 TGAACACCTTGCTTGCTTGC 59.897 50.0 0.0 0.0 0.0 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
32 33 3.744238 ACCTTTTAAACGCTTGCCAAT 57.256 38.095 0.00 0.00 0.00 3.16
38 39 1.627864 AAACGCTTGCCAATAACCCT 58.372 45.000 0.00 0.00 0.00 4.34
64 65 5.586339 TCTTGACGAGTCAGATGAATGATC 58.414 41.667 6.03 0.00 41.13 2.92
76 77 9.770097 GTCAGATGAATGATCTTATCAACCTTA 57.230 33.333 0.00 0.00 43.50 2.69
86 87 9.661563 TGATCTTATCAACCTTAACGTTTACAT 57.338 29.630 5.91 0.00 36.11 2.29
155 156 5.288472 CCAACAAGCAGTTCACTTTACAAAC 59.712 40.000 0.00 0.00 38.74 2.93
164 165 2.550606 TCACTTTACAAACGACCCATGC 59.449 45.455 0.00 0.00 0.00 4.06
209 210 4.150980 CGTTCACACGCCTAGTTAATTTGA 59.849 41.667 0.00 0.00 40.18 2.69
213 214 5.178623 TCACACGCCTAGTTAATTTGAACTG 59.821 40.000 4.21 0.00 39.96 3.16
228 229 8.635765 AATTTGAACTGAGCTAATGTTCCTTA 57.364 30.769 17.61 8.03 39.24 2.69
246 247 2.825861 TACCCGAGACAACAAACCTC 57.174 50.000 0.00 0.00 0.00 3.85
250 251 2.135933 CCGAGACAACAAACCTCTGAC 58.864 52.381 0.00 0.00 0.00 3.51
338 357 1.076332 GTTGGACCGATGAAGGAACG 58.924 55.000 0.00 0.00 34.73 3.95
355 374 2.370281 ACGTAAGCATCACTGGTCAG 57.630 50.000 0.00 0.00 45.62 3.51
385 404 2.760650 ACAGTCTCACGAATAGCATCCA 59.239 45.455 0.00 0.00 0.00 3.41
389 408 3.932710 GTCTCACGAATAGCATCCACAAA 59.067 43.478 0.00 0.00 0.00 2.83
413 432 7.259290 AGAAGAATTTCGCAAAGTACAAGAA 57.741 32.000 0.00 0.00 38.38 2.52
414 433 7.703328 AGAAGAATTTCGCAAAGTACAAGAAA 58.297 30.769 0.00 0.06 38.38 2.52
444 464 8.124586 TGCAAAACATAAACAACACATAACTG 57.875 30.769 0.00 0.00 0.00 3.16
493 513 3.483411 CCAAAGCAAAGCGAAAAACACAC 60.483 43.478 0.00 0.00 0.00 3.82
494 514 1.921243 AGCAAAGCGAAAAACACACC 58.079 45.000 0.00 0.00 0.00 4.16
660 692 3.276091 CCAAGACACGCAACCGCA 61.276 61.111 0.00 0.00 38.40 5.69
661 693 2.052237 CAAGACACGCAACCGCAC 60.052 61.111 0.00 0.00 38.40 5.34
738 770 4.413760 CTCGACCTCCTTTATATACCCCA 58.586 47.826 0.00 0.00 0.00 4.96
745 777 3.212631 TCCTTTATATACCCCAGGACCCA 59.787 47.826 0.00 0.00 0.00 4.51
747 779 4.227527 CCTTTATATACCCCAGGACCCATC 59.772 50.000 0.00 0.00 0.00 3.51
789 1012 3.576550 GTCTCTCTGTCCTGTCCTTTCTT 59.423 47.826 0.00 0.00 0.00 2.52
795 1018 3.045634 TGTCCTGTCCTTTCTTCTCCAA 58.954 45.455 0.00 0.00 0.00 3.53
812 1035 0.842467 CAACTCCAACCTCCCCCTCT 60.842 60.000 0.00 0.00 0.00 3.69
963 1190 1.187567 AAGCAGTGGGTGATTTGGGC 61.188 55.000 0.00 0.00 27.05 5.36
988 1215 2.767960 GGTTAGGGTTTCGGATCTGGTA 59.232 50.000 0.62 0.00 0.00 3.25
1833 2121 0.810031 CACCGTGCCCTGTACATAGC 60.810 60.000 9.69 9.69 0.00 2.97
1834 2122 1.227556 CCGTGCCCTGTACATAGCC 60.228 63.158 13.09 5.60 0.00 3.93
1854 2142 2.038975 CCGTCCCTTCCTCCTCCA 59.961 66.667 0.00 0.00 0.00 3.86
1855 2143 1.612442 CCGTCCCTTCCTCCTCCAA 60.612 63.158 0.00 0.00 0.00 3.53
1857 2145 1.192146 CGTCCCTTCCTCCTCCAACA 61.192 60.000 0.00 0.00 0.00 3.33
1933 2227 2.486592 TCACAATCAGCATCAGCAGTTG 59.513 45.455 0.00 0.00 45.49 3.16
1956 2250 6.115446 TGAATTAGCATCCTAGAACCAGTTG 58.885 40.000 0.00 0.00 0.00 3.16
2029 2331 3.205056 TGTCATTAGCCAGATCCCCATTT 59.795 43.478 0.00 0.00 0.00 2.32
2031 2333 2.638480 TTAGCCAGATCCCCATTTCG 57.362 50.000 0.00 0.00 0.00 3.46
2040 2345 0.679640 TCCCCATTTCGTGTCCATGC 60.680 55.000 0.00 0.00 0.00 4.06
2074 2379 4.321230 GCATTAGGAGTCAACCAAACCAAG 60.321 45.833 0.00 0.00 0.00 3.61
2086 2392 1.595794 CAAACCAAGCAAGCAAGCAAG 59.404 47.619 3.19 0.00 36.85 4.01
2104 2410 5.423015 AGCAAGGTGTTCATGTAGATGTAG 58.577 41.667 0.00 0.00 0.00 2.74
2105 2411 4.034510 GCAAGGTGTTCATGTAGATGTAGC 59.965 45.833 0.00 0.00 0.00 3.58
2106 2412 4.046938 AGGTGTTCATGTAGATGTAGCG 57.953 45.455 0.00 0.00 0.00 4.26
2108 2414 3.430374 GGTGTTCATGTAGATGTAGCGGT 60.430 47.826 0.00 0.00 0.00 5.68
2109 2415 4.181578 GTGTTCATGTAGATGTAGCGGTT 58.818 43.478 0.00 0.00 0.00 4.44
2110 2416 5.345702 GTGTTCATGTAGATGTAGCGGTTA 58.654 41.667 0.00 0.00 0.00 2.85
2111 2417 5.808540 GTGTTCATGTAGATGTAGCGGTTAA 59.191 40.000 0.00 0.00 0.00 2.01
2113 2419 6.700081 TGTTCATGTAGATGTAGCGGTTAATC 59.300 38.462 0.00 0.00 0.00 1.75
2114 2420 5.458015 TCATGTAGATGTAGCGGTTAATCG 58.542 41.667 3.08 3.08 0.00 3.34
2115 2421 4.233123 TGTAGATGTAGCGGTTAATCGG 57.767 45.455 10.66 0.00 0.00 4.18
2258 2575 5.833406 TGTGATTCTGAACATGTTGTTGT 57.167 34.783 17.58 0.00 41.28 3.32
2282 2601 4.463539 TCCATTATTGCACTGCATTCTGTT 59.536 37.500 4.10 0.00 38.76 3.16
2293 2612 3.489355 TGCATTCTGTTCCATTCTGTGT 58.511 40.909 0.00 0.00 0.00 3.72
2296 2615 2.936919 TCTGTTCCATTCTGTGTGCT 57.063 45.000 0.00 0.00 0.00 4.40
2297 2616 2.771089 TCTGTTCCATTCTGTGTGCTC 58.229 47.619 0.00 0.00 0.00 4.26
2300 2619 0.321564 TTCCATTCTGTGTGCTCCCG 60.322 55.000 0.00 0.00 0.00 5.14
2398 2721 6.263168 GCCGTGGGAGTTTTATACTACTACTA 59.737 42.308 0.92 0.00 44.74 1.82
2448 2771 3.771568 TTTTGCTGTGCTGGCGTGC 62.772 57.895 0.00 0.00 0.00 5.34
2670 3028 3.637273 GGAGGCGAGTGGTTGGGT 61.637 66.667 0.00 0.00 0.00 4.51
2720 3078 3.056179 TGTGACGACAGAATCTTGGCATA 60.056 43.478 0.00 0.00 0.00 3.14
2758 3116 2.844362 CGGGCCATCCAGGAGCTA 60.844 66.667 4.39 0.00 41.22 3.32
2761 3119 0.480252 GGGCCATCCAGGAGCTATTT 59.520 55.000 4.39 0.00 41.22 1.40
2762 3120 1.133356 GGGCCATCCAGGAGCTATTTT 60.133 52.381 4.39 0.00 41.22 1.82
2763 3121 2.234143 GGCCATCCAGGAGCTATTTTC 58.766 52.381 0.00 0.00 41.22 2.29
2764 3122 2.234143 GCCATCCAGGAGCTATTTTCC 58.766 52.381 0.00 0.00 41.22 3.13
2765 3123 2.158549 GCCATCCAGGAGCTATTTTCCT 60.159 50.000 0.00 0.00 45.92 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.449632 TGGCAAGCGTTTAAAAGGTTTC 58.550 40.909 14.56 10.66 0.00 2.78
32 33 4.342951 TCTGACTCGTCAAGAAAAGGGTTA 59.657 41.667 1.02 0.00 39.39 2.85
38 39 6.223120 TCATTCATCTGACTCGTCAAGAAAA 58.777 36.000 1.02 2.35 39.39 2.29
64 65 9.755064 CTGAATGTAAACGTTAAGGTTGATAAG 57.245 33.333 13.87 3.51 0.00 1.73
76 77 7.696453 GCATATTTGCTACTGAATGTAAACGTT 59.304 33.333 0.00 0.00 45.77 3.99
100 101 8.540507 AAACTCTCCTATGAAGATAGTTAGCA 57.459 34.615 0.00 0.00 30.98 3.49
112 113 3.096852 TGGCTTCGAAACTCTCCTATGA 58.903 45.455 0.00 0.00 0.00 2.15
155 156 3.803082 CCTTGCACGCATGGGTCG 61.803 66.667 13.22 9.83 37.53 4.79
164 165 0.788391 GTTCGTCTTACCCTTGCACG 59.212 55.000 0.00 0.00 0.00 5.34
187 188 5.600908 TCAAATTAACTAGGCGTGTGAAC 57.399 39.130 0.00 0.00 0.00 3.18
200 201 8.515414 AGGAACATTAGCTCAGTTCAAATTAAC 58.485 33.333 20.53 7.55 42.50 2.01
209 210 4.623171 CGGGTAAGGAACATTAGCTCAGTT 60.623 45.833 0.00 0.00 34.37 3.16
213 214 3.383825 TCTCGGGTAAGGAACATTAGCTC 59.616 47.826 0.00 0.02 34.37 4.09
228 229 1.129058 AGAGGTTTGTTGTCTCGGGT 58.871 50.000 0.00 0.00 33.16 5.28
246 247 2.704572 GAACCAGGTGAATGAGGTCAG 58.295 52.381 0.00 0.00 32.05 3.51
250 251 1.361668 CGCGAACCAGGTGAATGAGG 61.362 60.000 0.00 0.00 0.00 3.86
327 346 4.033358 CAGTGATGCTTACGTTCCTTCATC 59.967 45.833 0.00 1.29 0.00 2.92
328 347 3.935203 CAGTGATGCTTACGTTCCTTCAT 59.065 43.478 0.00 0.00 0.00 2.57
338 357 1.002366 CGCTGACCAGTGATGCTTAC 58.998 55.000 4.67 0.00 41.24 2.34
355 374 2.793933 TCGTGAGACTGTATTTAGCGC 58.206 47.619 0.00 0.00 33.31 5.92
385 404 6.791303 TGTACTTTGCGAAATTCTTCTTTGT 58.209 32.000 0.00 0.00 0.00 2.83
389 408 6.861065 TCTTGTACTTTGCGAAATTCTTCT 57.139 33.333 0.00 0.00 0.00 2.85
413 432 8.261492 TGTGTTGTTTATGTTTTGCATCTTTT 57.739 26.923 0.00 0.00 38.94 2.27
414 433 7.840342 TGTGTTGTTTATGTTTTGCATCTTT 57.160 28.000 0.00 0.00 38.94 2.52
444 464 9.444534 GTTGTCATCTTTTCTTCTTCTTCTTTC 57.555 33.333 0.00 0.00 0.00 2.62
592 624 1.340697 CGCATCCATCCATCCATCCAT 60.341 52.381 0.00 0.00 0.00 3.41
593 625 0.037160 CGCATCCATCCATCCATCCA 59.963 55.000 0.00 0.00 0.00 3.41
594 626 0.037303 ACGCATCCATCCATCCATCC 59.963 55.000 0.00 0.00 0.00 3.51
595 627 1.002888 AGACGCATCCATCCATCCATC 59.997 52.381 0.00 0.00 0.00 3.51
712 744 1.325355 TATAAAGGAGGTCGAGGCGG 58.675 55.000 0.00 0.00 0.00 6.13
716 748 4.413760 TGGGGTATATAAAGGAGGTCGAG 58.586 47.826 0.00 0.00 0.00 4.04
717 749 4.413760 CTGGGGTATATAAAGGAGGTCGA 58.586 47.826 0.00 0.00 0.00 4.20
719 751 4.531339 GTCCTGGGGTATATAAAGGAGGTC 59.469 50.000 0.00 0.00 37.71 3.85
720 752 4.500452 GTCCTGGGGTATATAAAGGAGGT 58.500 47.826 0.00 0.00 37.71 3.85
723 755 3.212631 TGGGTCCTGGGGTATATAAAGGA 59.787 47.826 0.00 0.00 34.65 3.36
789 1012 0.840722 GGGGAGGTTGGAGTTGGAGA 60.841 60.000 0.00 0.00 0.00 3.71
795 1018 1.081277 GAGAGGGGGAGGTTGGAGT 59.919 63.158 0.00 0.00 0.00 3.85
812 1035 0.709992 CAAATTTGGGGAGGGGAGGA 59.290 55.000 10.49 0.00 0.00 3.71
963 1190 1.629181 ATCCGAAACCCTAACCCCGG 61.629 60.000 0.00 0.00 38.41 5.73
1389 1649 1.223487 GCCCTTCATGGAGCCGTAA 59.777 57.895 0.00 0.00 38.35 3.18
1512 1781 3.680786 CGGCTGAGGTCGTGGTCA 61.681 66.667 0.00 0.00 35.65 4.02
1833 2121 3.400054 GGAGGAAGGGACGGTGGG 61.400 72.222 0.00 0.00 0.00 4.61
1834 2122 2.284699 AGGAGGAAGGGACGGTGG 60.285 66.667 0.00 0.00 0.00 4.61
1915 2203 3.842732 TTCAACTGCTGATGCTGATTG 57.157 42.857 0.00 3.88 40.66 2.67
1916 2204 5.450137 GCTAATTCAACTGCTGATGCTGATT 60.450 40.000 0.00 0.92 40.66 2.57
1933 2227 6.116126 ACAACTGGTTCTAGGATGCTAATTC 58.884 40.000 0.00 0.00 0.00 2.17
1956 2250 5.485209 TCAAGGAAGGAAGGAAGAGTAAC 57.515 43.478 0.00 0.00 0.00 2.50
2029 2331 0.170339 CTACGACTGCATGGACACGA 59.830 55.000 13.36 0.19 0.00 4.35
2031 2333 0.389817 TGCTACGACTGCATGGACAC 60.390 55.000 0.00 0.00 35.31 3.67
2040 2345 2.099921 ACTCCTAATGCTGCTACGACTG 59.900 50.000 0.00 0.00 0.00 3.51
2074 2379 0.102844 TGAACACCTTGCTTGCTTGC 59.897 50.000 0.00 0.00 0.00 4.01
2086 2392 3.123804 CCGCTACATCTACATGAACACC 58.876 50.000 0.00 0.00 33.72 4.16
2105 2411 3.623330 GACGCCGCCGATTAACCG 61.623 66.667 0.00 0.00 38.29 4.44
2106 2412 1.433837 ATTGACGCCGCCGATTAACC 61.434 55.000 0.00 0.00 38.29 2.85
2108 2414 1.433053 CCATTGACGCCGCCGATTAA 61.433 55.000 0.00 0.00 38.29 1.40
2109 2415 1.885388 CCATTGACGCCGCCGATTA 60.885 57.895 0.00 0.00 38.29 1.75
2110 2416 3.202001 CCATTGACGCCGCCGATT 61.202 61.111 0.00 0.00 38.29 3.34
2164 2470 0.107459 GGCACTGGATCTGGAGGAAC 60.107 60.000 0.00 0.00 0.00 3.62
2165 2471 0.252881 AGGCACTGGATCTGGAGGAA 60.253 55.000 0.00 0.00 37.18 3.36
2166 2472 1.393746 AGGCACTGGATCTGGAGGA 59.606 57.895 0.00 0.00 37.18 3.71
2258 2575 4.463539 ACAGAATGCAGTGCAATAATGGAA 59.536 37.500 23.90 0.00 43.62 3.53
2282 2601 1.296392 CGGGAGCACACAGAATGGA 59.704 57.895 0.00 0.00 43.62 3.41
2293 2612 4.007644 CTGGTGAGCACGGGAGCA 62.008 66.667 0.00 0.00 36.85 4.26
2296 2615 2.981302 CATCTGGTGAGCACGGGA 59.019 61.111 0.00 0.00 0.00 5.14
2297 2616 2.809861 AAGCATCTGGTGAGCACGGG 62.810 60.000 0.00 0.00 0.00 5.28
2300 2619 1.930908 GCCAAGCATCTGGTGAGCAC 61.931 60.000 0.00 0.00 38.86 4.40
2448 2771 4.717927 AAATCGCACGCACGCACG 62.718 61.111 0.00 0.00 39.50 5.34
2449 2772 2.426752 AAAATCGCACGCACGCAC 60.427 55.556 0.00 0.00 0.00 5.34
2450 2773 2.426588 CAAAATCGCACGCACGCA 60.427 55.556 0.00 0.00 0.00 5.24
2451 2774 3.165318 CCAAAATCGCACGCACGC 61.165 61.111 0.00 0.00 0.00 5.34
2452 2775 3.165318 GCCAAAATCGCACGCACG 61.165 61.111 0.00 0.00 0.00 5.34
2453 2776 3.165318 CGCCAAAATCGCACGCAC 61.165 61.111 0.00 0.00 0.00 5.34
2454 2777 3.307505 CTCGCCAAAATCGCACGCA 62.308 57.895 0.00 0.00 0.00 5.24
2455 2778 2.574212 CTCGCCAAAATCGCACGC 60.574 61.111 0.00 0.00 0.00 5.34
2456 2779 1.225745 GTCTCGCCAAAATCGCACG 60.226 57.895 0.00 0.00 0.00 5.34
2457 2780 1.225745 CGTCTCGCCAAAATCGCAC 60.226 57.895 0.00 0.00 0.00 5.34
2458 2781 1.666553 ACGTCTCGCCAAAATCGCA 60.667 52.632 0.00 0.00 0.00 5.10
2459 2782 1.225745 CACGTCTCGCCAAAATCGC 60.226 57.895 0.00 0.00 0.00 4.58
2525 2860 4.059459 GCACTCAACGCACCGTCG 62.059 66.667 0.00 0.00 39.99 5.12
2591 2937 1.599797 CCACCACCCAGTTCGGAAC 60.600 63.158 12.91 12.91 36.56 3.62
2623 2981 1.686741 GGTCATCCTCTTCCTCGGACT 60.687 57.143 0.00 0.00 30.90 3.85
2670 3028 3.682885 CAATGCCACAGCGCCCAA 61.683 61.111 2.29 0.00 44.31 4.12
2720 3078 2.089980 GCAGCATCTTCTCCACACAAT 58.910 47.619 0.00 0.00 0.00 2.71
2756 3114 2.224161 CCAGCCGAGGAGAGGAAAATAG 60.224 54.545 0.00 0.00 0.00 1.73
2758 3116 0.543749 CCAGCCGAGGAGAGGAAAAT 59.456 55.000 0.00 0.00 0.00 1.82
2761 3119 2.770827 TCCAGCCGAGGAGAGGAA 59.229 61.111 0.00 0.00 32.77 3.36


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

AutoCloner maintained by Alex Coulton.