Multiple sequence alignment - TraesCS3D01G157600

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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 TraesCS3D01G157600 chr3D 100.000 3366 0 0 1 3366 125773211 125776576 0.000000e+00 6216.0
1 TraesCS3D01G157600 chr3D 100.000 569 0 0 3743 4311 125776953 125777521 0.000000e+00 1051.0
2 TraesCS3D01G157600 chr3B 93.847 3283 146 28 125 3366 179670607 179673874 0.000000e+00 4892.0
3 TraesCS3D01G157600 chr3B 93.728 574 24 5 3743 4311 179673963 179674529 0.000000e+00 850.0
4 TraesCS3D01G157600 chr3B 89.908 109 8 2 1 108 179670521 179670627 2.090000e-28 137.0
5 TraesCS3D01G157600 chr3A 93.761 2292 104 18 125 2394 134599827 134602101 0.000000e+00 3404.0
6 TraesCS3D01G157600 chr3A 92.357 942 55 5 2432 3366 134602091 134603022 0.000000e+00 1325.0
7 TraesCS3D01G157600 chr3A 92.989 542 24 8 3743 4278 134603025 134603558 0.000000e+00 778.0
8 TraesCS3D01G157600 chr3A 100.000 34 0 0 4278 4311 134603601 134603634 3.600000e-06 63.9


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 TraesCS3D01G157600 chr3D 125773211 125777521 4310 False 3633.500000 6216 100.000000 1 4311 2 chr3D.!!$F1 4310
1 TraesCS3D01G157600 chr3B 179670521 179674529 4008 False 1959.666667 4892 92.494333 1 4311 3 chr3B.!!$F1 4310
2 TraesCS3D01G157600 chr3A 134599827 134603634 3807 False 1392.725000 3404 94.776750 125 4311 4 chr3A.!!$F1 4186

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
614 632 0.109873 CTGGTCAGGTGACGTACGAC 60.110 60.0 24.41 17.22 45.65 4.34 F
2575 2621 0.178918 GCCTAGGGAGATGCTAGGGT 60.179 60.0 11.72 0.00 40.28 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2598 2644 0.329596 GGAACCACCTGAGAAGCCAT 59.670 55.0 0.0 0.0 35.41 4.40 R
4116 4259 0.519175 GCGCGCACATTTACTCACAG 60.519 55.0 29.1 0.0 0.00 3.66 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
47 48 5.660460 CAAATAAGTTGGGATAAAGCACCC 58.340 41.667 0.00 0.00 45.74 4.61
87 89 9.939802 AAATTACTAGGTGTTTTAATCTCTCGT 57.060 29.630 0.00 0.00 0.00 4.18
90 92 6.549952 ACTAGGTGTTTTAATCTCTCGTACG 58.450 40.000 9.53 9.53 0.00 3.67
91 93 5.382618 AGGTGTTTTAATCTCTCGTACGT 57.617 39.130 16.05 0.00 0.00 3.57
92 94 5.397326 AGGTGTTTTAATCTCTCGTACGTC 58.603 41.667 16.05 0.00 0.00 4.34
93 95 5.182760 AGGTGTTTTAATCTCTCGTACGTCT 59.817 40.000 16.05 0.00 0.00 4.18
94 96 6.372659 AGGTGTTTTAATCTCTCGTACGTCTA 59.627 38.462 16.05 1.01 0.00 2.59
95 97 6.467364 GGTGTTTTAATCTCTCGTACGTCTAC 59.533 42.308 16.05 1.70 0.00 2.59
96 98 7.017645 GTGTTTTAATCTCTCGTACGTCTACA 58.982 38.462 16.05 4.05 0.00 2.74
97 99 7.006920 GTGTTTTAATCTCTCGTACGTCTACAC 59.993 40.741 16.05 11.36 0.00 2.90
98 100 6.726258 TTTAATCTCTCGTACGTCTACACA 57.274 37.500 16.05 0.00 0.00 3.72
99 101 6.726258 TTAATCTCTCGTACGTCTACACAA 57.274 37.500 16.05 1.14 0.00 3.33
100 102 5.618056 AATCTCTCGTACGTCTACACAAA 57.382 39.130 16.05 0.00 0.00 2.83
101 103 4.658713 TCTCTCGTACGTCTACACAAAG 57.341 45.455 16.05 1.68 0.00 2.77
102 104 4.060900 TCTCTCGTACGTCTACACAAAGT 58.939 43.478 16.05 0.00 0.00 2.66
103 105 4.512944 TCTCTCGTACGTCTACACAAAGTT 59.487 41.667 16.05 0.00 0.00 2.66
104 106 5.008019 TCTCTCGTACGTCTACACAAAGTTT 59.992 40.000 16.05 0.00 0.00 2.66
105 107 5.581605 TCTCGTACGTCTACACAAAGTTTT 58.418 37.500 16.05 0.00 0.00 2.43
106 108 6.035843 TCTCGTACGTCTACACAAAGTTTTT 58.964 36.000 16.05 0.00 0.00 1.94
152 154 1.269522 CAAAGTTGTTTGCACGCGC 59.730 52.632 5.73 0.00 36.86 6.86
221 223 4.668289 GAAAACCACAAGTACCAACACAG 58.332 43.478 0.00 0.00 0.00 3.66
379 387 3.412408 GTGCCTTCTCCCTCCCCC 61.412 72.222 0.00 0.00 0.00 5.40
401 409 1.141185 TCGATCCTCCTCTCCTAGCA 58.859 55.000 0.00 0.00 0.00 3.49
547 559 0.176680 CAGACCCCAGATCTCCAACG 59.823 60.000 0.00 0.00 0.00 4.10
588 600 0.583438 CCCAAGCGATGCATCTAACG 59.417 55.000 23.73 12.74 0.00 3.18
600 618 0.824759 ATCTAACGCAGACCCTGGTC 59.175 55.000 8.31 8.31 44.86 4.02
613 631 1.239296 CCTGGTCAGGTGACGTACGA 61.239 60.000 24.41 0.00 45.65 3.43
614 632 0.109873 CTGGTCAGGTGACGTACGAC 60.110 60.000 24.41 17.22 45.65 4.34
615 633 0.535780 TGGTCAGGTGACGTACGACT 60.536 55.000 24.41 11.19 45.65 4.18
618 636 0.887836 TCAGGTGACGTACGACTGCT 60.888 55.000 24.41 0.00 0.00 4.24
619 637 0.800631 CAGGTGACGTACGACTGCTA 59.199 55.000 24.41 0.00 0.00 3.49
903 921 3.384789 TGAGAAATAGAGCTACGCCACAT 59.615 43.478 0.00 0.00 0.00 3.21
910 928 4.442375 AGAGCTACGCCACATATATGTC 57.558 45.455 15.60 5.04 39.39 3.06
942 965 3.004944 GCTTAACCTCTTCCTCGATCGAT 59.995 47.826 19.78 0.00 0.00 3.59
1038 1067 1.433534 CTGAAGGAAAGAGGTCGCAC 58.566 55.000 0.00 0.00 0.00 5.34
1269 1298 2.417787 GCATCTCCCCAAACAATTCTGC 60.418 50.000 0.00 0.00 0.00 4.26
1293 1322 1.456331 CCCACTCATGCCATTCCCC 60.456 63.158 0.00 0.00 0.00 4.81
1641 1670 4.798574 CAGGTTATGCTGGAAAACAAGTC 58.201 43.478 0.00 0.00 0.00 3.01
1719 1748 6.095440 ACCACAATGCAATAACTTCTATGGTC 59.905 38.462 0.00 0.00 29.67 4.02
1725 1754 4.025979 GCAATAACTTCTATGGTCGTTCGG 60.026 45.833 0.00 0.00 0.00 4.30
1750 1779 6.255950 GGCACGGTGAGTCTAATTTATTTTC 58.744 40.000 13.29 0.00 0.00 2.29
1773 1802 7.545362 TCTCTTTGGAATTGATCGAAGATTC 57.455 36.000 9.15 9.15 45.12 2.52
1774 1803 7.334090 TCTCTTTGGAATTGATCGAAGATTCT 58.666 34.615 14.44 0.00 45.12 2.40
1775 1804 7.493971 TCTCTTTGGAATTGATCGAAGATTCTC 59.506 37.037 14.44 8.38 45.12 2.87
1848 1878 8.353423 AGCACACCACTTTAGAAATTAATGAT 57.647 30.769 0.00 0.00 0.00 2.45
1924 1957 8.085296 TGTTATTTGTCAATTACGCATTCCTTT 58.915 29.630 0.00 0.00 0.00 3.11
1931 1964 9.114952 TGTCAATTACGCATTCCTTTCATTATA 57.885 29.630 0.00 0.00 0.00 0.98
2133 2167 7.043854 CCACATAATTGACATGATTTTTCTCGC 60.044 37.037 0.00 0.00 0.00 5.03
2377 2418 0.707024 TATTTGTGTGGGGCCCATGA 59.293 50.000 31.48 16.39 35.28 3.07
2427 2473 8.482128 TCTTTACAAAACAAAAATGAGGGTCAT 58.518 29.630 0.00 0.00 39.09 3.06
2575 2621 0.178918 GCCTAGGGAGATGCTAGGGT 60.179 60.000 11.72 0.00 40.28 4.34
2598 2644 4.042809 TGCTCCACTTTTGGGATCTCTTTA 59.957 41.667 0.00 0.00 44.11 1.85
2918 2964 0.310543 TGCGGTGTTTTCATGAGCAC 59.689 50.000 14.74 14.74 33.87 4.40
2999 3045 7.450323 ACAGGTTACAAAAGCAATGTACCTTAT 59.550 33.333 0.00 0.00 34.98 1.73
3046 3099 8.341903 CACTATCCAATATTGTTACAATCGCAA 58.658 33.333 14.29 0.00 0.00 4.85
3079 3132 6.924111 AGCATATTCAACCTGTTAAACCTTG 58.076 36.000 0.00 0.00 0.00 3.61
3084 3137 5.699097 TCAACCTGTTAAACCTTGTATGC 57.301 39.130 0.00 0.00 0.00 3.14
3085 3138 5.133941 TCAACCTGTTAAACCTTGTATGCA 58.866 37.500 0.00 0.00 0.00 3.96
3172 3225 4.307032 AAATGGTCTCTATGCTGTTGGT 57.693 40.909 0.00 0.00 0.00 3.67
3182 3235 0.756294 TGCTGTTGGTTTCTCGAGGA 59.244 50.000 13.56 0.00 0.00 3.71
3223 3276 2.322355 AGGATGCAACCAAGATCTCG 57.678 50.000 16.21 0.00 0.00 4.04
3267 3320 4.143030 GCGTGATATGTGTATGGAAGATGC 60.143 45.833 0.00 0.00 0.00 3.91
3279 3332 4.008074 TGGAAGATGCGAGAGAAACTTT 57.992 40.909 0.00 0.00 0.00 2.66
3293 3346 7.275779 CGAGAGAAACTTTATCCAATCGAAGAA 59.724 37.037 0.00 0.00 43.58 2.52
3312 3365 6.761242 CGAAGAACACCATGTCCTATTTGATA 59.239 38.462 0.00 0.00 0.00 2.15
3341 3394 6.754702 ATTTTGCGTACTAGTCAGTCTAGA 57.245 37.500 0.00 0.00 46.53 2.43
4109 4252 9.868277 TCTTTAAATGATCATTTGCCGTATTTT 57.132 25.926 33.94 14.34 40.83 1.82
4254 4400 7.090173 CCATTTATGTTCAGGTAACCAGTTTG 58.910 38.462 0.00 0.00 37.27 2.93
4255 4401 7.255801 CCATTTATGTTCAGGTAACCAGTTTGT 60.256 37.037 0.00 0.00 37.27 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 8.177663 CGTACGAGAGATTAAAACACCTAGTAA 58.822 37.037 10.44 0.00 0.00 2.24
65 66 7.334421 ACGTACGAGAGATTAAAACACCTAGTA 59.666 37.037 24.41 0.00 0.00 1.82
67 68 6.549952 ACGTACGAGAGATTAAAACACCTAG 58.450 40.000 24.41 0.00 0.00 3.02
78 80 5.180868 ACTTTGTGTAGACGTACGAGAGATT 59.819 40.000 24.41 0.00 30.95 2.40
116 118 7.118101 ACAACTTTGTGTAGACGTAGTTTTCAA 59.882 33.333 6.78 0.00 40.30 2.69
117 119 6.591062 ACAACTTTGTGTAGACGTAGTTTTCA 59.409 34.615 6.78 0.00 40.30 2.69
118 120 6.997222 ACAACTTTGTGTAGACGTAGTTTTC 58.003 36.000 6.78 0.00 40.30 2.29
119 121 6.973229 ACAACTTTGTGTAGACGTAGTTTT 57.027 33.333 6.78 0.25 40.30 2.43
120 122 6.973229 AACAACTTTGTGTAGACGTAGTTT 57.027 33.333 6.78 0.00 40.84 2.66
121 123 6.673796 GCAAACAACTTTGTGTAGACGTAGTT 60.674 38.462 0.00 4.39 40.84 2.24
122 124 5.220529 GCAAACAACTTTGTGTAGACGTAGT 60.221 40.000 0.00 0.00 43.14 2.73
123 125 5.195379 GCAAACAACTTTGTGTAGACGTAG 58.805 41.667 0.00 0.00 41.31 3.51
135 137 2.220887 CGCGCGTGCAAACAACTTT 61.221 52.632 24.19 0.00 42.97 2.66
152 154 1.498865 GGAACCTGTGTCTGTGTGCG 61.499 60.000 0.00 0.00 0.00 5.34
160 162 1.896220 TCTGCAATGGAACCTGTGTC 58.104 50.000 0.00 0.00 0.00 3.67
195 197 0.594602 GGTACTTGTGGTTTTCGCCC 59.405 55.000 0.00 0.00 0.00 6.13
202 204 2.650322 CCTGTGTTGGTACTTGTGGTT 58.350 47.619 0.00 0.00 0.00 3.67
236 238 4.704103 TGCCAGCCTCGACTCCCT 62.704 66.667 0.00 0.00 0.00 4.20
239 241 4.803426 CCGTGCCAGCCTCGACTC 62.803 72.222 6.02 0.00 0.00 3.36
379 387 2.627945 CTAGGAGAGGAGGATCGATCG 58.372 57.143 18.81 9.36 34.37 3.69
514 526 3.781407 TGGGGTCTGGTTTTCGGATAATA 59.219 43.478 0.00 0.00 32.64 0.98
515 527 2.578940 TGGGGTCTGGTTTTCGGATAAT 59.421 45.455 0.00 0.00 32.64 1.28
600 618 0.800631 TAGCAGTCGTACGTCACCTG 59.199 55.000 16.05 16.47 0.00 4.00
609 627 1.082300 GCGCGCTATAGCAGTCGTA 60.082 57.895 26.67 0.00 42.21 3.43
610 628 2.353607 GCGCGCTATAGCAGTCGT 60.354 61.111 26.67 0.00 42.21 4.34
611 629 2.353492 TGCGCGCTATAGCAGTCG 60.353 61.111 33.29 21.73 42.21 4.18
825 843 3.611674 GGAGGAGGAGGCTAGCGC 61.612 72.222 9.00 0.00 0.00 5.92
910 928 8.024285 CGAGGAAGAGGTTAAGCTATATAAGTG 58.976 40.741 7.26 0.00 0.00 3.16
920 941 2.358267 TCGATCGAGGAAGAGGTTAAGC 59.642 50.000 15.15 0.00 0.00 3.09
942 965 4.711846 AGACACTATTGCTATCCACTGTGA 59.288 41.667 9.86 0.00 0.00 3.58
1038 1067 4.347096 TTGCAGTACAACGGGTCG 57.653 55.556 0.00 0.00 31.73 4.79
1269 1298 2.202987 GGCATGAGTGGGAGCTCG 60.203 66.667 7.83 0.00 38.28 5.03
1293 1322 0.879090 GGTACGTGGGGAAGCTTTTG 59.121 55.000 0.00 0.00 0.00 2.44
1472 1501 1.090625 TGTTTTGCCGCTGTACGTGT 61.091 50.000 0.00 0.00 41.42 4.49
1477 1506 2.803451 CAAAGTTGTTTTGCCGCTGTA 58.197 42.857 0.00 0.00 39.71 2.74
1623 1652 5.452078 CAAGGACTTGTTTTCCAGCATAA 57.548 39.130 3.93 0.00 35.33 1.90
1641 1670 2.357034 CCACACCCGACGACAAGG 60.357 66.667 0.00 0.00 0.00 3.61
1725 1754 2.109425 AAATTAGACTCACCGTGCCC 57.891 50.000 0.00 0.00 0.00 5.36
1750 1779 7.279536 TGAGAATCTTCGATCAATTCCAAAGAG 59.720 37.037 9.88 0.00 34.92 2.85
1848 1878 9.013229 ACAGTGATTGCATAGAAAAGAATTACA 57.987 29.630 0.00 0.00 0.00 2.41
1897 1930 7.250569 AGGAATGCGTAATTGACAAATAACAG 58.749 34.615 0.00 0.00 0.00 3.16
2094 2128 4.900635 ATTATGTGGTGATTTTCCTCGC 57.099 40.909 0.00 0.00 0.00 5.03
2259 2293 7.750014 GTGGCCACATTAAATTAAAAAGCATTG 59.250 33.333 31.23 0.00 0.00 2.82
2264 2298 6.310224 CCTCGTGGCCACATTAAATTAAAAAG 59.690 38.462 34.16 13.43 0.00 2.27
2299 2339 1.818674 GTGTGAAAATGGCCGGAGATT 59.181 47.619 5.05 0.00 0.00 2.40
2333 2374 7.272978 AGGAGTATGCGACTTGTATTGTTATT 58.727 34.615 0.00 0.00 39.06 1.40
2341 2382 6.040247 CACAAATAGGAGTATGCGACTTGTA 58.960 40.000 0.00 0.00 39.06 2.41
2343 2384 4.870426 ACACAAATAGGAGTATGCGACTTG 59.130 41.667 0.00 0.00 39.06 3.16
2352 2393 1.562475 GGCCCCACACAAATAGGAGTA 59.438 52.381 0.00 0.00 0.00 2.59
2394 2440 7.604164 TCATTTTTGTTTTGTAAAGAGCCAACA 59.396 29.630 0.00 0.00 0.00 3.33
2399 2445 6.761242 ACCCTCATTTTTGTTTTGTAAAGAGC 59.239 34.615 0.00 0.00 0.00 4.09
2598 2644 0.329596 GGAACCACCTGAGAAGCCAT 59.670 55.000 0.00 0.00 35.41 4.40
2634 2680 2.222027 GCCATCATAAGGAGAAACCGG 58.778 52.381 0.00 0.00 44.74 5.28
2894 2940 0.950836 CATGAAAACACCGCACTCCA 59.049 50.000 0.00 0.00 0.00 3.86
2918 2964 1.730064 CCGTCAATAAACTCCACACCG 59.270 52.381 0.00 0.00 0.00 4.94
3046 3099 5.711976 ACAGGTTGAATATGCTTTACTTGCT 59.288 36.000 0.00 0.00 0.00 3.91
3103 3156 2.644299 TGGGAAGCCATCTTTCTCTGAA 59.356 45.455 0.00 0.00 31.48 3.02
3106 3159 2.915604 TCTTGGGAAGCCATCTTTCTCT 59.084 45.455 0.00 0.00 31.48 3.10
3172 3225 4.560919 GCTAAAAGTCCACTCCTCGAGAAA 60.561 45.833 15.71 0.04 33.32 2.52
3182 3235 3.975168 ATACACCGCTAAAAGTCCACT 57.025 42.857 0.00 0.00 0.00 4.00
3223 3276 4.498009 CGCCATTGTTGAACAATATCCTCC 60.498 45.833 21.71 7.26 46.22 4.30
3267 3320 6.752351 TCTTCGATTGGATAAAGTTTCTCTCG 59.248 38.462 0.00 0.00 0.00 4.04
3279 3332 5.097742 ACATGGTGTTCTTCGATTGGATA 57.902 39.130 0.00 0.00 0.00 2.59
3312 3365 9.216117 AGACTGACTAGTACGCAAAATAATTTT 57.784 29.630 0.00 0.00 37.25 1.82
3322 3375 4.468765 ACTCTAGACTGACTAGTACGCA 57.531 45.455 12.61 0.00 46.15 5.24
3341 3394 1.504912 ACTGATCTGGCATGCCTACT 58.495 50.000 35.53 20.22 36.94 2.57
4109 4252 5.270083 CGCACATTTACTCACAGTCAAAAA 58.730 37.500 0.00 0.00 0.00 1.94
4110 4253 4.788201 GCGCACATTTACTCACAGTCAAAA 60.788 41.667 0.30 0.00 0.00 2.44
4111 4254 3.303725 GCGCACATTTACTCACAGTCAAA 60.304 43.478 0.30 0.00 0.00 2.69
4116 4259 0.519175 GCGCGCACATTTACTCACAG 60.519 55.000 29.10 0.00 0.00 3.66
4118 4261 1.495509 TGCGCGCACATTTACTCAC 59.504 52.632 33.09 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.