Multiple sequence alignment - TraesCS1D01G036700

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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 TraesCS1D01G036700 chr1D 100.000 3371 0 0 1 3371 17170613 17167243 0.000000e+00 6226
1 TraesCS1D01G036700 chr1B 94.879 3398 119 24 4 3371 24934596 24931224 0.000000e+00 5260
2 TraesCS1D01G036700 chr1A 93.011 3162 142 44 245 3371 18463021 18459904 0.000000e+00 4542
3 TraesCS1D01G036700 chr3B 93.004 243 14 3 1499 1738 828111441 828111683 5.350000e-93 351
4 TraesCS1D01G036700 chr3B 86.498 237 28 4 1505 1738 823129941 823129706 1.200000e-64 257
5 TraesCS1D01G036700 chr3D 92.181 243 16 3 1499 1738 610544041 610544283 1.160000e-89 340
6 TraesCS1D01G036700 chr3D 87.295 244 26 5 1505 1744 613806091 613805849 1.190000e-69 274
7 TraesCS1D01G036700 chr3D 86.842 228 30 0 1499 1726 610697282 610697055 4.320000e-64 255
8 TraesCS1D01G036700 chr3A 91.358 243 18 3 1499 1738 744879511 744879753 2.510000e-86 329
9 TraesCS1D01G036700 chr3A 86.420 243 30 3 1505 1744 750298755 750298513 2.580000e-66 263


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 TraesCS1D01G036700 chr1D 17167243 17170613 3370 True 6226 6226 100.000 1 3371 1 chr1D.!!$R1 3370
1 TraesCS1D01G036700 chr1B 24931224 24934596 3372 True 5260 5260 94.879 4 3371 1 chr1B.!!$R1 3367
2 TraesCS1D01G036700 chr1A 18459904 18463021 3117 True 4542 4542 93.011 245 3371 1 chr1A.!!$R1 3126

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
35 36 0.250338 ACGTTTTCTCCCACTGAGCC 60.250 55.000 0.0 0.0 41.18 4.70 F
969 980 1.815408 GCACAAGGCTCACTTTCTCCA 60.815 52.381 0.0 0.0 37.29 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1603 1.227823 CTTGGTGTTGGCGGAGTCA 60.228 57.895 0.00 0.0 45.3 3.41 R
2884 2945 0.395586 TGGTATGGCATTGCAGGGTC 60.396 55.000 4.78 0.0 0.0 4.46 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
35 36 0.250338 ACGTTTTCTCCCACTGAGCC 60.250 55.000 0.00 0.00 41.18 4.70
42 43 1.980784 CTCCCACTGAGCCCTGATGG 61.981 65.000 0.00 0.00 33.47 3.51
58 59 3.035363 TGATGGGGAAATACGAGCACTA 58.965 45.455 0.00 0.00 0.00 2.74
60 61 2.463752 TGGGGAAATACGAGCACTAGT 58.536 47.619 0.00 0.00 0.00 2.57
62 63 2.167900 GGGGAAATACGAGCACTAGTGT 59.832 50.000 23.44 10.82 0.00 3.55
80 81 6.665680 ACTAGTGTCATGTCTAGGATTTGAGT 59.334 38.462 18.52 3.90 38.24 3.41
93 94 3.562176 GGATTTGAGTCCTGATGGGTTGT 60.562 47.826 0.00 0.00 35.32 3.32
118 119 3.676093 CTCCACAAGGAACCTAACCTTC 58.324 50.000 0.00 0.00 45.19 3.46
268 269 7.931015 ATATGGTATCTCAACCTAGAAACCA 57.069 36.000 0.00 0.00 40.44 3.67
443 450 6.705381 CACCATGGCTTTTTAAAATCAAGTCA 59.295 34.615 13.04 7.63 36.61 3.41
476 483 8.703604 TGAAATCCATCTAAAAACTAGTCGAG 57.296 34.615 0.00 0.00 0.00 4.04
505 512 2.038557 GGCTCATATTCCTCGGGCTTTA 59.961 50.000 0.00 0.00 0.00 1.85
509 516 5.510861 GCTCATATTCCTCGGGCTTTACTTA 60.511 44.000 0.00 0.00 0.00 2.24
512 519 3.604875 TTCCTCGGGCTTTACTTACAG 57.395 47.619 0.00 0.00 0.00 2.74
565 572 4.431524 TCCTCCCCGGCCCTCAAT 62.432 66.667 0.00 0.00 0.00 2.57
852 863 2.428890 CAAACACCACAACCTTTAGCCA 59.571 45.455 0.00 0.00 0.00 4.75
969 980 1.815408 GCACAAGGCTCACTTTCTCCA 60.815 52.381 0.00 0.00 37.29 3.86
1121 1140 7.978975 ACTTTTGCACAAGCTCAAATAAAGTTA 59.021 29.630 12.50 0.00 42.74 2.24
1186 1205 6.586344 TGCAAAGAAGAGAATGATACTAGGG 58.414 40.000 0.00 0.00 0.00 3.53
1380 1405 2.118404 CGCAAGTTGTGGTGGTGGT 61.118 57.895 8.61 0.00 0.00 4.16
1623 1651 4.223953 ACTTCAACAACTACTCCCTCTCA 58.776 43.478 0.00 0.00 0.00 3.27
1834 1862 3.777925 CTTCCGCTTGCACGACCG 61.778 66.667 0.00 0.00 34.06 4.79
1980 2008 4.115199 GGCATGGGGAAGCCGTCT 62.115 66.667 0.00 0.00 41.70 4.18
1986 2014 3.703127 GGGAAGCCGTCTCCCGTT 61.703 66.667 0.00 0.00 33.55 4.44
2055 2083 4.106925 GGGCTGGAGCAGTGGAGG 62.107 72.222 0.20 0.00 44.36 4.30
2437 2465 1.204146 GGTAGCATGGACTTGGAGGA 58.796 55.000 0.00 0.00 0.00 3.71
2646 2675 8.240267 TCTACTTCTTCTTATTTAGGGCTCTC 57.760 38.462 0.00 0.00 0.00 3.20
2650 2679 8.044309 ACTTCTTCTTATTTAGGGCTCTCTTTC 58.956 37.037 0.00 0.00 0.00 2.62
2651 2680 7.741554 TCTTCTTATTTAGGGCTCTCTTTCT 57.258 36.000 0.00 0.00 0.00 2.52
2652 2681 7.787028 TCTTCTTATTTAGGGCTCTCTTTCTC 58.213 38.462 0.00 0.00 0.00 2.87
2840 2886 8.620416 TGAAGAAATTCAATGATGGTATTACCG 58.380 33.333 8.32 0.00 42.58 4.02
2845 2891 4.133820 TCAATGATGGTATTACCGCCAAG 58.866 43.478 8.32 6.21 42.58 3.61
2853 2899 3.942748 GGTATTACCGCCAAGATTGTGAA 59.057 43.478 0.00 0.00 0.00 3.18
2858 2919 3.009723 ACCGCCAAGATTGTGAATACTG 58.990 45.455 0.00 0.00 0.00 2.74
2881 2942 5.514279 GCATTCTACATGGACTAAATGCAC 58.486 41.667 17.26 0.00 45.07 4.57
2884 2945 4.180817 TCTACATGGACTAAATGCACACG 58.819 43.478 0.00 0.00 0.00 4.49
2888 2949 1.084289 GGACTAAATGCACACGACCC 58.916 55.000 0.00 0.00 0.00 4.46
2891 2952 0.447801 CTAAATGCACACGACCCTGC 59.552 55.000 0.00 0.00 0.00 4.85
2893 2954 1.106351 AAATGCACACGACCCTGCAA 61.106 50.000 0.00 0.00 46.18 4.08
2894 2955 0.895100 AATGCACACGACCCTGCAAT 60.895 50.000 0.00 0.00 46.18 3.56
2895 2956 1.588824 ATGCACACGACCCTGCAATG 61.589 55.000 0.00 0.00 46.18 2.82
2896 2957 2.562912 CACACGACCCTGCAATGC 59.437 61.111 0.00 0.00 0.00 3.56
2897 2958 2.672996 ACACGACCCTGCAATGCC 60.673 61.111 1.53 0.00 0.00 4.40
2898 2959 2.672651 CACGACCCTGCAATGCCA 60.673 61.111 1.53 0.00 0.00 4.92
2899 2960 2.048023 CACGACCCTGCAATGCCAT 61.048 57.895 1.53 0.00 0.00 4.40
2900 2961 0.747644 CACGACCCTGCAATGCCATA 60.748 55.000 1.53 0.00 0.00 2.74
2974 3035 2.356382 CGACAGGTGCAACTAACCAAAA 59.644 45.455 2.54 0.00 40.40 2.44
3016 3083 6.951971 ACTGATATGCCACTCTTCTAACTTT 58.048 36.000 0.00 0.00 0.00 2.66
3088 3155 9.347240 AGAAAGAGAAAATCAAAGTGAAGATGA 57.653 29.630 0.00 0.00 0.00 2.92
3148 3219 1.980232 TTGCCTGCATGCCTCCAAG 60.980 57.895 16.68 5.00 0.00 3.61
3189 3260 5.963140 GATGGATCGATATATGTGCAGTG 57.037 43.478 0.00 0.00 0.00 3.66
3195 3266 4.546570 TCGATATATGTGCAGTGTAGTGC 58.453 43.478 4.77 4.77 44.27 4.40
3265 3336 0.522626 CTGCAATGTTGATCACGGCA 59.477 50.000 0.00 0.29 37.08 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.140852 TGCTCGTATTTCCCCATCAGG 59.859 52.381 0.00 0.00 0.00 3.86
42 43 3.119245 TGACACTAGTGCTCGTATTTCCC 60.119 47.826 22.90 0.00 0.00 3.97
44 45 5.103000 ACATGACACTAGTGCTCGTATTTC 58.897 41.667 22.90 10.45 0.00 2.17
58 59 5.105146 GGACTCAAATCCTAGACATGACACT 60.105 44.000 0.00 0.00 35.68 3.55
60 61 5.344743 GGACTCAAATCCTAGACATGACA 57.655 43.478 0.00 0.00 35.68 3.58
80 81 1.354368 GGAGGAAACAACCCATCAGGA 59.646 52.381 0.00 0.00 39.89 3.86
118 119 2.355132 ACGCGAACTGATAGTACCTCAG 59.645 50.000 15.93 17.31 44.60 3.35
164 165 5.590530 TCAATTTGCGGCATAGGTTATTT 57.409 34.783 2.28 0.00 0.00 1.40
178 179 6.768029 TTTGAACAAGCACTATCAATTTGC 57.232 33.333 0.00 0.00 36.45 3.68
242 243 8.210946 TGGTTTCTAGGTTGAGATACCATATTG 58.789 37.037 10.52 0.00 46.41 1.90
469 476 3.574445 GCCGCTCGAGCTCGACTA 61.574 66.667 33.84 15.22 44.22 2.59
476 483 1.011451 GGAATATGAGCCGCTCGAGC 61.011 60.000 27.64 27.64 32.35 5.03
505 512 1.486726 GCAGACATAGGGGCTGTAAGT 59.513 52.381 0.00 0.00 35.30 2.24
509 516 1.200760 TGTGCAGACATAGGGGCTGT 61.201 55.000 0.00 0.00 32.39 4.40
512 519 1.544724 TTTTGTGCAGACATAGGGGC 58.455 50.000 0.00 0.00 30.13 5.80
565 572 3.815809 CTTTTCTTCCCTGTGGTGTACA 58.184 45.455 0.00 0.00 37.78 2.90
852 863 2.951642 CCTTCAATTCTGGTGTGTGTGT 59.048 45.455 0.00 0.00 0.00 3.72
905 916 3.884895 TGTCTTCTCCTTTGCTTTGTGA 58.115 40.909 0.00 0.00 0.00 3.58
969 980 1.564348 GGGTGGGTGGTGATGTTATCT 59.436 52.381 0.00 0.00 0.00 1.98
1121 1140 3.244249 CCGAACAACTTTCTCCTCCTCTT 60.244 47.826 0.00 0.00 0.00 2.85
1158 1177 7.789273 AGTATCATTCTCTTCTTTGCATCAG 57.211 36.000 0.00 0.00 0.00 2.90
1170 1189 4.415596 CCAGAGCCCTAGTATCATTCTCT 58.584 47.826 0.00 0.00 0.00 3.10
1186 1205 7.502120 TTGAATCAGAATATTTAGCCAGAGC 57.498 36.000 0.00 0.00 40.32 4.09
1575 1603 1.227823 CTTGGTGTTGGCGGAGTCA 60.228 57.895 0.00 0.00 45.30 3.41
1785 1813 3.998672 GTCGACCCACCCGAAGCA 61.999 66.667 3.51 0.00 37.81 3.91
1834 1862 4.717313 GGGAGCCGGGTTGGACAC 62.717 72.222 8.00 0.00 42.00 3.67
2193 2221 3.700970 TCGTCTTCATGGCCGCCA 61.701 61.111 16.17 16.17 38.19 5.69
2244 2272 2.432510 CGGGTAGCCTTCTCTCTTTGAT 59.567 50.000 9.73 0.00 0.00 2.57
2437 2465 6.185114 AGCCTTTTCTATATCTCACAGCAT 57.815 37.500 0.00 0.00 0.00 3.79
2646 2675 2.658325 CCGAATGCGCAAAAAGAGAAAG 59.342 45.455 17.11 0.00 35.83 2.62
2650 2679 0.456653 CCCCGAATGCGCAAAAAGAG 60.457 55.000 17.11 1.44 35.83 2.85
2651 2680 1.175983 ACCCCGAATGCGCAAAAAGA 61.176 50.000 17.11 0.00 35.83 2.52
2652 2681 1.008361 CACCCCGAATGCGCAAAAAG 61.008 55.000 17.11 6.35 35.83 2.27
2735 2775 5.755375 AGAAATGCGAGAATTGTACATCGAT 59.245 36.000 18.21 7.81 37.35 3.59
2784 2830 5.163683 GGATTCACACTCTTGGATCACATTG 60.164 44.000 0.00 0.00 0.00 2.82
2837 2883 3.009723 CAGTATTCACAATCTTGGCGGT 58.990 45.455 0.00 0.00 0.00 5.68
2840 2886 4.644103 ATGCAGTATTCACAATCTTGGC 57.356 40.909 0.00 0.00 0.00 4.52
2845 2891 7.227314 TCCATGTAGAATGCAGTATTCACAATC 59.773 37.037 13.15 0.79 46.20 2.67
2853 2899 7.173907 GCATTTAGTCCATGTAGAATGCAGTAT 59.826 37.037 17.28 0.00 45.14 2.12
2858 2919 5.066375 TGTGCATTTAGTCCATGTAGAATGC 59.934 40.000 16.18 16.18 45.68 3.56
2881 2942 0.747644 TATGGCATTGCAGGGTCGTG 60.748 55.000 4.78 0.00 0.00 4.35
2884 2945 0.395586 TGGTATGGCATTGCAGGGTC 60.396 55.000 4.78 0.00 0.00 4.46
2888 2949 0.747852 TGCATGGTATGGCATTGCAG 59.252 50.000 18.00 2.13 34.58 4.41
2894 2955 7.015974 TCCATAAATAAAATGCATGGTATGGCA 59.984 33.333 17.41 0.00 45.23 4.92
2895 2956 7.385267 TCCATAAATAAAATGCATGGTATGGC 58.615 34.615 17.41 0.00 37.64 4.40
2896 2957 8.805175 TCTCCATAAATAAAATGCATGGTATGG 58.195 33.333 0.00 11.19 38.62 2.74
2912 2973 9.404848 CCATGCTCATATGTATTCTCCATAAAT 57.595 33.333 1.90 0.00 0.00 1.40
2913 2974 8.385491 ACCATGCTCATATGTATTCTCCATAAA 58.615 33.333 1.90 0.00 0.00 1.40
2916 2977 6.013119 TGACCATGCTCATATGTATTCTCCAT 60.013 38.462 1.90 0.00 0.00 3.41
2935 2996 5.586243 CCTGTCGATTCAAGTTAATGACCAT 59.414 40.000 0.00 0.00 0.00 3.55
3016 3083 7.290014 TGGCTCCTACTATGATTTTGAGTGATA 59.710 37.037 0.00 0.00 0.00 2.15
3123 3194 0.738412 GGCATGCAGGCAACATGAAC 60.738 55.000 26.25 0.39 46.33 3.18
3125 3196 1.304630 AGGCATGCAGGCAACATGA 60.305 52.632 26.25 0.00 46.33 3.07
3148 3219 4.282068 CATCGCTGGTATTGCATGTTAAC 58.718 43.478 0.00 0.00 0.00 2.01
3189 3260 5.920273 GCTTAGAGAGATTGAGATGCACTAC 59.080 44.000 0.00 0.00 0.00 2.73
3195 3266 6.158598 GCCTTAGCTTAGAGAGATTGAGATG 58.841 44.000 0.16 0.00 35.50 2.90
3198 3269 5.509501 CCTGCCTTAGCTTAGAGAGATTGAG 60.510 48.000 0.16 0.00 40.80 3.02
3265 3336 3.084786 GACTAGTCCCTTTTTGCATGCT 58.915 45.455 20.33 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.