Multiple sequence alignment - TraesCS5D01G040900

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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 TraesCS5D01G040900 chr5D 100.000 4214 0 0 1 4214 41540067 41544280 0.000000e+00 7782
1 TraesCS5D01G040900 chr5D 95.798 119 5 0 3126 3244 41600446 41600564 4.300000e-45 193
2 TraesCS5D01G040900 chr5A 94.041 3759 148 36 481 4212 29886505 29890214 0.000000e+00 5631
3 TraesCS5D01G040900 chr5A 92.289 402 27 4 1 398 29885802 29886203 6.110000e-158 568
4 TraesCS5D01G040900 chr5B 95.801 2596 94 5 911 3492 36072685 36075279 0.000000e+00 4176
5 TraesCS5D01G040900 chr5B 88.900 973 79 22 1 950 36071812 36072778 0.000000e+00 1171
6 TraesCS5D01G040900 chr5B 85.890 489 36 10 344 830 38699531 38699988 1.360000e-134 490
7 TraesCS5D01G040900 chr5B 84.104 346 40 10 1 339 38685349 38685686 1.890000e-83 320
8 TraesCS5D01G040900 chr7D 88.473 668 65 10 1393 2055 404391015 404390355 0.000000e+00 797
9 TraesCS5D01G040900 chr7D 89.048 210 20 2 1076 1282 404391220 404391011 1.500000e-64 257
10 TraesCS5D01G040900 chr7D 91.304 184 12 1 2096 2279 404390350 404390171 9.050000e-62 248
11 TraesCS5D01G040900 chrUn 90.402 448 37 4 1835 2280 38373542 38373985 6.070000e-163 584


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 TraesCS5D01G040900 chr5D 41540067 41544280 4213 False 7782.0 7782 100.000000 1 4214 1 chr5D.!!$F1 4213
1 TraesCS5D01G040900 chr5A 29885802 29890214 4412 False 3099.5 5631 93.165000 1 4212 2 chr5A.!!$F1 4211
2 TraesCS5D01G040900 chr5B 36071812 36075279 3467 False 2673.5 4176 92.350500 1 3492 2 chr5B.!!$F3 3491
3 TraesCS5D01G040900 chr7D 404390171 404391220 1049 True 434.0 797 89.608333 1076 2279 3 chr7D.!!$R1 1203

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
455 463 0.320247 GCGGGACTGCTGATAGATGG 60.320 60.000 0.00 0.0 0.00 3.51 F
1487 1752 2.125753 GTCCACCGCTCTGCTCAG 60.126 66.667 0.00 0.0 0.00 3.35 F
2212 2479 0.682209 GCATGTGCAGAATGGGGAGT 60.682 55.000 10.51 0.0 41.59 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 1941 0.108992 CCGCACTAAGAACTGCCGTA 60.109 55.000 0.0 0.0 0.0 4.02 R
2352 2619 1.067974 CCCAAACCAAACCCGAACTTC 59.932 52.381 0.0 0.0 0.0 3.01 R
3762 4038 0.235665 CGTGAACAGTGTGACCATGC 59.764 55.000 0.0 0.0 0.0 4.06 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
65 70 9.981114 CACAAAATTATACTCAAGGTTTCCTTT 57.019 29.630 0.00 0.00 41.69 3.11
73 78 8.990163 ATACTCAAGGTTTCCTTTCAAAACTA 57.010 30.769 0.00 0.00 41.69 2.24
151 158 5.303078 AGGCACATGTCTAGTCTTAATCGAT 59.697 40.000 0.00 0.00 0.00 3.59
172 179 7.156000 TCGATAGTTTGACCAACATAACAGAA 58.844 34.615 0.00 0.00 37.93 3.02
201 208 8.905103 ATGTATGTTAAATCGGTTTTGCTAAC 57.095 30.769 0.00 0.00 0.00 2.34
203 210 9.217278 TGTATGTTAAATCGGTTTTGCTAACTA 57.783 29.630 0.00 0.00 0.00 2.24
274 281 2.478335 GAAGGTGGGGATGGCGTGAA 62.478 60.000 0.00 0.00 0.00 3.18
359 366 1.568612 CGATGTGAGCGGCAACAAGT 61.569 55.000 11.73 0.00 0.00 3.16
401 409 4.454504 GGCGAGAAAGAAACTTAATGTGGA 59.545 41.667 0.00 0.00 0.00 4.02
405 413 4.767409 AGAAAGAAACTTAATGTGGAGGGC 59.233 41.667 0.00 0.00 0.00 5.19
417 425 4.741239 GAGGGCCAGGGAGGGTGA 62.741 72.222 6.18 0.00 38.09 4.02
418 426 4.748798 AGGGCCAGGGAGGGTGAG 62.749 72.222 6.18 0.00 38.09 3.51
438 446 3.200593 GGGCTGCTCATCAGTGCG 61.201 66.667 0.00 0.00 44.66 5.34
439 447 3.200593 GGCTGCTCATCAGTGCGG 61.201 66.667 0.00 0.00 44.66 5.69
449 457 2.267006 CAGTGCGGGACTGCTGAT 59.733 61.111 16.75 0.00 45.72 2.90
451 459 0.529337 CAGTGCGGGACTGCTGATAG 60.529 60.000 16.75 0.00 45.72 2.08
452 460 0.684479 AGTGCGGGACTGCTGATAGA 60.684 55.000 0.00 0.00 31.75 1.98
455 463 0.320247 GCGGGACTGCTGATAGATGG 60.320 60.000 0.00 0.00 0.00 3.51
464 472 3.311110 GATAGATGGCCGGGGCGA 61.311 66.667 16.47 1.63 43.06 5.54
465 473 2.607750 ATAGATGGCCGGGGCGAT 60.608 61.111 16.47 6.93 42.09 4.58
595 821 2.229302 GCTACGCGAGGAAGAAGGATAT 59.771 50.000 15.93 0.00 0.00 1.63
823 1062 9.026074 CGTTTGCACCTCTTTTATTTCTTTTTA 57.974 29.630 0.00 0.00 0.00 1.52
1454 1719 2.901042 CAAGGTCCCCTCGGCTAC 59.099 66.667 0.00 0.00 30.89 3.58
1487 1752 2.125753 GTCCACCGCTCTGCTCAG 60.126 66.667 0.00 0.00 0.00 3.35
1674 1941 4.402155 TCACAGAAAAATGAGTTTGTGGCT 59.598 37.500 3.00 0.00 36.38 4.75
1764 2031 0.856982 TGAAGGATGGGTTGGTGGTT 59.143 50.000 0.00 0.00 0.00 3.67
1980 2247 3.065371 CACCAACTGAGTTCACTTTGGTC 59.935 47.826 15.65 0.00 41.62 4.02
2066 2333 1.692411 GTGAAGCTTGGGTTTGAGGT 58.308 50.000 2.10 0.00 0.00 3.85
2115 2382 1.675483 GACATGTATGCCAAATGCGGA 59.325 47.619 0.00 0.00 45.60 5.54
2212 2479 0.682209 GCATGTGCAGAATGGGGAGT 60.682 55.000 10.51 0.00 41.59 3.85
2283 2550 8.289939 TCATTCCGACTAACTTGACTATAACT 57.710 34.615 0.00 0.00 0.00 2.24
2343 2610 0.963962 CAGGGAAGCAATTGCACACT 59.036 50.000 30.89 25.45 45.16 3.55
2346 2613 1.068055 GGGAAGCAATTGCACACTCAG 60.068 52.381 30.89 0.00 45.16 3.35
2352 2619 2.159421 GCAATTGCACACTCAGATCCTG 60.159 50.000 25.36 0.00 41.59 3.86
2435 2702 0.521735 GGAAACCTTGACGATGGCAC 59.478 55.000 0.00 0.00 0.00 5.01
2716 2983 5.221106 GCTTGCATGGTTGATATTCTTAGCA 60.221 40.000 1.34 0.00 0.00 3.49
2835 3102 2.319136 TACGGGATTTTGATGTCGGG 57.681 50.000 0.00 0.00 0.00 5.14
2862 3129 2.380365 AGGTGAGCAGCTGATGGAA 58.620 52.632 20.43 0.00 37.82 3.53
3141 3408 7.260603 GTCCAACATCTAAATTTTCATGGGAG 58.739 38.462 0.00 0.00 0.00 4.30
3247 3514 5.810587 TGACAAGAACAGTGAGTACTTCAAC 59.189 40.000 0.00 0.00 37.61 3.18
3307 3574 4.281688 AGCTATGCTGTGAAATTTTGTGGT 59.718 37.500 0.00 0.00 37.57 4.16
3366 3641 5.823209 TCACTGTTTCTATGCATCATTGG 57.177 39.130 0.19 0.00 0.00 3.16
3373 3648 5.756195 TTCTATGCATCATTGGTAAGTGC 57.244 39.130 0.19 0.00 36.39 4.40
3519 3794 5.221126 GCTAGCTTGATATTGTTTTCCCAGG 60.221 44.000 7.70 0.00 0.00 4.45
3521 3796 5.332743 AGCTTGATATTGTTTTCCCAGGAA 58.667 37.500 0.00 0.00 0.00 3.36
3547 3822 1.873698 TTTTGGCTCTACACCACGTC 58.126 50.000 0.00 0.00 36.76 4.34
3631 3907 5.235616 TCACTCTTAAGCAAACCAAGTAACG 59.764 40.000 0.00 0.00 0.00 3.18
3745 4021 2.681848 GCACTCATCATCTCCCAAACAG 59.318 50.000 0.00 0.00 0.00 3.16
3782 4059 0.867746 CATGGTCACACTGTTCACGG 59.132 55.000 0.00 0.00 0.00 4.94
3801 4078 5.186215 TCACGGAAGGTTTGTGATATACTCA 59.814 40.000 0.00 0.00 37.69 3.41
3802 4079 5.520288 CACGGAAGGTTTGTGATATACTCAG 59.480 44.000 0.00 0.00 35.66 3.35
3842 4128 6.478512 ACAAATTTCTCAAGGCCTTGTTTA 57.521 33.333 37.97 24.23 41.16 2.01
3856 4142 5.704053 GGCCTTGTTTAGCACTAGAGTTTTA 59.296 40.000 0.00 0.00 30.28 1.52
3858 4144 6.128254 GCCTTGTTTAGCACTAGAGTTTTAGG 60.128 42.308 0.00 0.00 30.28 2.69
3859 4145 7.159372 CCTTGTTTAGCACTAGAGTTTTAGGA 58.841 38.462 0.00 0.00 30.28 2.94
3860 4146 7.332182 CCTTGTTTAGCACTAGAGTTTTAGGAG 59.668 40.741 0.00 0.00 30.28 3.69
3861 4147 7.534723 TGTTTAGCACTAGAGTTTTAGGAGA 57.465 36.000 0.00 0.00 0.00 3.71
3862 4148 7.603651 TGTTTAGCACTAGAGTTTTAGGAGAG 58.396 38.462 0.00 0.00 0.00 3.20
3863 4149 7.450634 TGTTTAGCACTAGAGTTTTAGGAGAGA 59.549 37.037 0.00 0.00 0.00 3.10
3864 4150 5.907866 AGCACTAGAGTTTTAGGAGAGAC 57.092 43.478 0.00 0.00 0.00 3.36
3865 4151 5.576128 AGCACTAGAGTTTTAGGAGAGACT 58.424 41.667 0.00 0.00 0.00 3.24
3879 4165 4.577283 AGGAGAGACTGAGAGTATTTACGC 59.423 45.833 0.00 0.00 0.00 4.42
3929 4215 2.951229 AGAACCTCAATGGACCGTTT 57.049 45.000 0.00 0.00 39.71 3.60
3945 4231 1.605202 CGTTTGGTGGGCCATTTTCAG 60.605 52.381 10.70 0.00 45.56 3.02
3996 4282 1.345112 CCCTACCCCTCCCTGTGTAAT 60.345 57.143 0.00 0.00 0.00 1.89
4004 4290 3.552273 CCCTCCCTGTGTAATTCGATACG 60.552 52.174 0.00 0.00 0.00 3.06
4009 4295 3.050619 CTGTGTAATTCGATACGCTCCC 58.949 50.000 10.24 0.00 37.23 4.30
4017 4303 1.459730 GATACGCTCCCCTCCCCTT 60.460 63.158 0.00 0.00 0.00 3.95
4033 4319 6.070538 CCCTCCCCTTGTGTATCTTCTATATG 60.071 46.154 0.00 0.00 0.00 1.78
4073 4359 5.298026 GCCACTCTTTTTCTTCTGTCTCTTT 59.702 40.000 0.00 0.00 0.00 2.52
4077 4363 8.619546 CACTCTTTTTCTTCTGTCTCTTTTGAT 58.380 33.333 0.00 0.00 0.00 2.57
4129 4418 1.676014 GGCTGATGTGACCGTAAAGCT 60.676 52.381 0.00 0.00 0.00 3.74
4212 4501 6.488344 TGCACACCATCTATTCAGTTTGTAAA 59.512 34.615 0.00 0.00 0.00 2.01
4213 4502 7.013750 TGCACACCATCTATTCAGTTTGTAAAA 59.986 33.333 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 62 5.505159 CCGAGTGGTAGTTTTGAAAGGAAAC 60.505 44.000 0.00 0.00 37.28 2.78
65 70 0.035739 GCCCCGAGTGGTAGTTTTGA 59.964 55.000 0.00 0.00 0.00 2.69
66 71 1.296056 CGCCCCGAGTGGTAGTTTTG 61.296 60.000 0.00 0.00 0.00 2.44
73 78 1.078708 CATTAACGCCCCGAGTGGT 60.079 57.895 0.00 0.00 0.00 4.16
274 281 0.319900 ATGCTCGTCGCTGTTGTTCT 60.320 50.000 0.00 0.00 40.11 3.01
359 366 0.388520 CTCCACATGAGACGTCGCAA 60.389 55.000 25.63 8.21 44.42 4.85
401 409 4.748798 CTCACCCTCCCTGGCCCT 62.749 72.222 0.00 0.00 0.00 5.19
435 443 0.390492 CATCTATCAGCAGTCCCGCA 59.610 55.000 0.00 0.00 0.00 5.69
438 446 0.036022 GGCCATCTATCAGCAGTCCC 59.964 60.000 0.00 0.00 0.00 4.46
439 447 0.320247 CGGCCATCTATCAGCAGTCC 60.320 60.000 2.24 0.00 0.00 3.85
445 453 2.348998 GCCCCGGCCATCTATCAG 59.651 66.667 2.24 0.00 34.56 2.90
449 457 3.625897 CATCGCCCCGGCCATCTA 61.626 66.667 2.24 0.00 37.98 1.98
464 472 2.034066 CACCCTCGTGTTGGCCAT 59.966 61.111 6.09 0.00 35.10 4.40
465 473 4.263572 CCACCCTCGTGTTGGCCA 62.264 66.667 0.00 0.00 38.41 5.36
744 979 8.926374 ACTCATGGGCAATTTGATCAATAATAA 58.074 29.630 9.40 0.00 0.00 1.40
746 981 7.369551 ACTCATGGGCAATTTGATCAATAAT 57.630 32.000 9.40 0.00 0.00 1.28
783 1018 2.030185 TGCAAACGGTGTACTCTCTCTC 60.030 50.000 0.00 0.00 0.00 3.20
784 1019 1.961394 TGCAAACGGTGTACTCTCTCT 59.039 47.619 0.00 0.00 0.00 3.10
823 1062 9.643693 CAGCAATAACCTGAAAACAGAATAAAT 57.356 29.630 0.00 0.00 32.03 1.40
1306 1571 2.026822 AGAACATCATGGAGCGGAAGTT 60.027 45.455 0.00 0.00 0.00 2.66
1454 1719 1.219522 GGACACGAACACGTTGGAGG 61.220 60.000 0.00 0.00 38.21 4.30
1674 1941 0.108992 CCGCACTAAGAACTGCCGTA 60.109 55.000 0.00 0.00 0.00 4.02
1764 2031 3.749404 CGAGTTTTCAACCGACACAAAA 58.251 40.909 0.00 0.00 0.00 2.44
2066 2333 1.672737 CGCTCTTCACATACACCTGCA 60.673 52.381 0.00 0.00 0.00 4.41
2115 2382 6.426587 ACCTTCCTTTGCATCAGTAATACAT 58.573 36.000 0.00 0.00 0.00 2.29
2212 2479 2.912956 ACAACCTCAAGGCTTCCTCATA 59.087 45.455 0.00 0.00 39.32 2.15
2343 2610 1.938585 ACCCGAACTTCAGGATCTGA 58.061 50.000 0.00 0.00 38.87 3.27
2346 2613 2.084546 CCAAACCCGAACTTCAGGATC 58.915 52.381 0.00 0.00 0.00 3.36
2352 2619 1.067974 CCCAAACCAAACCCGAACTTC 59.932 52.381 0.00 0.00 0.00 3.01
2435 2702 2.614057 GGCATCCTTCTGAATACAACCG 59.386 50.000 0.00 0.00 0.00 4.44
2835 3102 1.793134 GCTGCTCACCTGCATATGCC 61.793 60.000 24.54 7.99 42.48 4.40
2862 3129 2.866454 AGAGGAGTCCCCAGTACCTAAT 59.134 50.000 5.25 0.00 37.41 1.73
3087 3354 3.394674 TCGTCCTTCATGTGTTTAGCA 57.605 42.857 0.00 0.00 0.00 3.49
3141 3408 4.164221 TCTCCCAATGTATCCAGTTCTTCC 59.836 45.833 0.00 0.00 0.00 3.46
3160 3427 8.680039 AATTGATCTTCTTCATGAGATTCTCC 57.320 34.615 11.12 0.00 33.49 3.71
3247 3514 8.553696 CCATTTTCCAAATTCAAGAAGAAACAG 58.446 33.333 0.00 0.00 40.22 3.16
3373 3648 4.798387 GCTAATGAACGCCAACTAAAATGG 59.202 41.667 0.00 0.00 41.08 3.16
3519 3794 7.061789 CGTGGTGTAGAGCCAAAAATAATTTTC 59.938 37.037 0.00 0.00 36.62 2.29
3521 3796 6.015772 ACGTGGTGTAGAGCCAAAAATAATTT 60.016 34.615 0.00 0.00 37.81 1.82
3547 3822 6.918067 AAAACTCTGGAAAAGGGGATTTAG 57.082 37.500 0.00 0.00 0.00 1.85
3696 3972 1.401761 ACCAAGTTGATGTGCTGCAA 58.598 45.000 2.77 0.00 0.00 4.08
3761 4037 1.597742 GTGAACAGTGTGACCATGCT 58.402 50.000 0.00 0.00 0.00 3.79
3762 4038 0.235665 CGTGAACAGTGTGACCATGC 59.764 55.000 0.00 0.00 0.00 4.06
3769 4046 1.663695 AACCTTCCGTGAACAGTGTG 58.336 50.000 0.00 0.00 0.00 3.82
3778 4055 5.416083 TGAGTATATCACAAACCTTCCGTG 58.584 41.667 0.00 0.00 31.12 4.94
3782 4059 6.640518 TCACCTGAGTATATCACAAACCTTC 58.359 40.000 0.00 0.00 33.22 3.46
3801 4078 1.203038 TGTTGGCATTCACCATCACCT 60.203 47.619 0.00 0.00 40.13 4.00
3802 4079 1.255882 TGTTGGCATTCACCATCACC 58.744 50.000 0.00 0.00 40.13 4.02
3842 4128 5.417580 CAGTCTCTCCTAAAACTCTAGTGCT 59.582 44.000 0.00 0.00 0.00 4.40
3856 4142 4.577283 GCGTAAATACTCTCAGTCTCTCCT 59.423 45.833 0.00 0.00 0.00 3.69
3858 4144 4.270566 TCGCGTAAATACTCTCAGTCTCTC 59.729 45.833 5.77 0.00 0.00 3.20
3859 4145 4.190001 TCGCGTAAATACTCTCAGTCTCT 58.810 43.478 5.77 0.00 0.00 3.10
3860 4146 4.533225 TCGCGTAAATACTCTCAGTCTC 57.467 45.455 5.77 0.00 0.00 3.36
3861 4147 5.502153 AATCGCGTAAATACTCTCAGTCT 57.498 39.130 5.77 0.00 0.00 3.24
3862 4148 6.523893 GGATAATCGCGTAAATACTCTCAGTC 59.476 42.308 5.77 0.00 0.00 3.51
3863 4149 6.380190 GGATAATCGCGTAAATACTCTCAGT 58.620 40.000 5.77 0.00 0.00 3.41
3864 4150 5.800941 GGGATAATCGCGTAAATACTCTCAG 59.199 44.000 5.77 0.00 0.00 3.35
3865 4151 5.618418 CGGGATAATCGCGTAAATACTCTCA 60.618 44.000 5.77 0.00 45.92 3.27
3879 4165 1.078426 GGATGGGCCGGGATAATCG 60.078 63.158 2.18 0.00 0.00 3.34
3904 4190 1.553704 GTCCATTGAGGTTCTACGGGT 59.446 52.381 0.00 0.00 39.02 5.28
3907 4193 1.203994 ACGGTCCATTGAGGTTCTACG 59.796 52.381 0.00 0.00 39.02 3.51
3910 4196 2.504367 CAAACGGTCCATTGAGGTTCT 58.496 47.619 0.00 0.00 39.02 3.01
3920 4206 4.589675 GGCCCACCAAACGGTCCA 62.590 66.667 0.00 0.00 33.11 4.02
3938 4224 2.552373 GGGACTGAACCCGTCTGAAAAT 60.552 50.000 0.00 0.00 40.49 1.82
3996 4282 1.831286 GGGAGGGGAGCGTATCGAA 60.831 63.158 0.00 0.00 0.00 3.71
4004 4290 0.988678 ATACACAAGGGGAGGGGAGC 60.989 60.000 0.00 0.00 0.00 4.70
4009 4295 6.498651 ACATATAGAAGATACACAAGGGGAGG 59.501 42.308 0.00 0.00 0.00 4.30
4017 4303 9.929180 GGCATAGAAACATATAGAAGATACACA 57.071 33.333 0.00 0.00 0.00 3.72
4050 4336 6.934048 AAAGAGACAGAAGAAAAAGAGTGG 57.066 37.500 0.00 0.00 0.00 4.00
4073 4359 5.450592 TGTGCAGCATGACTTAAAATCAA 57.549 34.783 0.00 0.00 39.69 2.57
4129 4418 6.921486 TGTCCATCTTTAGTTACAGGTGTA 57.079 37.500 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.