Multiple sequence alignment - TraesCS3D01G518500

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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 TraesCS3D01G518500 chr3D 100.000 3038 0 0 1 3038 601479598 601482635 0.000000e+00 5611
1 TraesCS3D01G518500 chr3D 96.484 256 7 2 2481 2734 601496779 601497034 3.620000e-114 422
2 TraesCS3D01G518500 chr3D 98.095 105 2 0 2732 2836 601497080 601497184 1.860000e-42 183
3 TraesCS3D01G518500 chr2B 95.978 2039 38 7 1 2030 228913516 228911513 0.000000e+00 3271
4 TraesCS3D01G518500 chr2B 95.080 813 38 1 2228 3038 228840711 228839899 0.000000e+00 1279
5 TraesCS3D01G518500 chr2B 94.293 368 9 3 2481 2836 228761962 228761595 1.230000e-153 553
6 TraesCS3D01G518500 chr2B 92.920 113 7 1 2128 2240 228910780 228910669 2.420000e-36 163
7 TraesCS3D01G518500 chr1D 78.067 1076 194 26 957 2022 383723358 383722315 2.550000e-180 641
8 TraesCS3D01G518500 chr1A 77.829 1087 190 31 956 2029 483648906 483647858 2.570000e-175 625


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 TraesCS3D01G518500 chr3D 601479598 601482635 3037 False 5611 5611 100.000 1 3038 1 chr3D.!!$F1 3037
1 TraesCS3D01G518500 chr2B 228910669 228913516 2847 True 1717 3271 94.449 1 2240 2 chr2B.!!$R3 2239
2 TraesCS3D01G518500 chr2B 228839899 228840711 812 True 1279 1279 95.080 2228 3038 1 chr2B.!!$R2 810
3 TraesCS3D01G518500 chr1D 383722315 383723358 1043 True 641 641 78.067 957 2022 1 chr1D.!!$R1 1065
4 TraesCS3D01G518500 chr1A 483647858 483648906 1048 True 625 625 77.829 956 2029 1 chr1A.!!$R1 1073

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
535 540 1.057636 AGAACAACGCATACACGACG 58.942 50.0 0.0 0.0 36.70 5.12 F
1167 1173 0.033504 TTCTCCTGCACACCGAAGAC 59.966 55.0 0.0 0.0 0.00 3.01 F
2030 2052 0.034380 TCACTACCCAGTCCCTCTCG 60.034 60.0 0.0 0.0 30.46 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1601 1615 0.234884 GGCAACGTCGAAGGTTTCAG 59.765 55.0 0.0 0.0 0.00 3.02 R
2035 2057 0.464373 GCCGGCATTTCTCCAGATCA 60.464 55.0 24.8 0.0 0.00 2.92 R
2836 3495 5.688807 AGCTAACATGCTCTGATACCATTT 58.311 37.5 0.0 0.0 39.34 2.32 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
106 107 9.213799 CTTTGATTTTCTTCTGCTTAGTACTCT 57.786 33.333 0.00 0.00 0.00 3.24
285 290 8.045176 AGTTGAACATATTCTTAAGAAGCACC 57.955 34.615 21.75 10.04 37.48 5.01
405 410 4.703645 TGTCAGTGAAATACTCTCTCCG 57.296 45.455 0.00 0.00 37.60 4.63
470 475 6.054941 GCCAAATTTTCTTATATTGTGGGGG 58.945 40.000 0.00 0.00 0.00 5.40
535 540 1.057636 AGAACAACGCATACACGACG 58.942 50.000 0.00 0.00 36.70 5.12
856 861 6.377996 TGGATTAGAGTGATTGACCAAAATGG 59.622 38.462 0.00 0.00 45.02 3.16
1157 1163 1.304962 TCCCGCTACTTCTCCTGCA 60.305 57.895 0.00 0.00 0.00 4.41
1167 1173 0.033504 TTCTCCTGCACACCGAAGAC 59.966 55.000 0.00 0.00 0.00 3.01
1268 1274 2.415608 CCTTCCTCTACGCCTCGCA 61.416 63.158 0.00 0.00 0.00 5.10
1269 1275 1.736586 CTTCCTCTACGCCTCGCAT 59.263 57.895 0.00 0.00 0.00 4.73
1272 1278 0.823769 TCCTCTACGCCTCGCATCAT 60.824 55.000 0.00 0.00 0.00 2.45
1280 1286 1.072678 CCTCGCATCATGGCTGGAT 59.927 57.895 0.00 0.00 0.00 3.41
1332 1338 1.001641 GCTGCATCCCTTCACCAGT 60.002 57.895 0.00 0.00 0.00 4.00
1602 1616 4.338539 GTGACGACCGTGGACGCT 62.339 66.667 10.55 0.00 36.83 5.07
1869 1891 1.608336 TTCGTGGACCACCTCCGAT 60.608 57.895 19.11 0.00 43.03 4.18
1878 1900 1.296392 CACCTCCGATGGTTCTGCA 59.704 57.895 0.00 0.00 38.45 4.41
1886 1908 1.153086 ATGGTTCTGCATCGAGGCC 60.153 57.895 20.64 3.31 0.00 5.19
2030 2052 0.034380 TCACTACCCAGTCCCTCTCG 60.034 60.000 0.00 0.00 30.46 4.04
2031 2053 1.380112 ACTACCCAGTCCCTCTCGC 60.380 63.158 0.00 0.00 0.00 5.03
2032 2054 1.076632 CTACCCAGTCCCTCTCGCT 60.077 63.158 0.00 0.00 0.00 4.93
2033 2055 1.076923 TACCCAGTCCCTCTCGCTC 60.077 63.158 0.00 0.00 0.00 5.03
2034 2056 2.888464 TACCCAGTCCCTCTCGCTCG 62.888 65.000 0.00 0.00 0.00 5.03
2035 2057 2.752238 CCAGTCCCTCTCGCTCGT 60.752 66.667 0.00 0.00 0.00 4.18
2036 2058 2.487428 CAGTCCCTCTCGCTCGTG 59.513 66.667 0.00 0.00 0.00 4.35
2037 2059 2.041115 CAGTCCCTCTCGCTCGTGA 61.041 63.158 0.00 0.00 0.00 4.35
2038 2060 1.077357 AGTCCCTCTCGCTCGTGAT 60.077 57.895 0.00 0.00 0.00 3.06
2039 2061 1.098712 AGTCCCTCTCGCTCGTGATC 61.099 60.000 0.00 0.00 0.00 2.92
2040 2062 1.098712 GTCCCTCTCGCTCGTGATCT 61.099 60.000 0.00 0.00 0.00 2.75
2041 2063 1.098129 TCCCTCTCGCTCGTGATCTG 61.098 60.000 0.00 0.00 0.00 2.90
2042 2064 1.358402 CCTCTCGCTCGTGATCTGG 59.642 63.158 0.00 0.00 0.00 3.86
2043 2065 1.098129 CCTCTCGCTCGTGATCTGGA 61.098 60.000 0.00 0.00 0.00 3.86
2044 2066 0.307453 CTCTCGCTCGTGATCTGGAG 59.693 60.000 8.65 8.65 0.00 3.86
2045 2067 0.107654 TCTCGCTCGTGATCTGGAGA 60.108 55.000 15.09 6.02 31.90 3.71
2046 2068 0.735471 CTCGCTCGTGATCTGGAGAA 59.265 55.000 15.09 4.28 31.90 2.87
2047 2069 1.133216 CTCGCTCGTGATCTGGAGAAA 59.867 52.381 15.09 4.00 31.90 2.52
2048 2070 1.751351 TCGCTCGTGATCTGGAGAAAT 59.249 47.619 15.09 0.00 31.90 2.17
2049 2071 1.857217 CGCTCGTGATCTGGAGAAATG 59.143 52.381 15.09 1.50 31.90 2.32
2050 2072 1.596727 GCTCGTGATCTGGAGAAATGC 59.403 52.381 15.09 0.16 31.90 3.56
2051 2073 2.208431 CTCGTGATCTGGAGAAATGCC 58.792 52.381 7.56 0.00 31.90 4.40
2052 2074 0.933097 CGTGATCTGGAGAAATGCCG 59.067 55.000 0.00 0.00 0.00 5.69
2053 2075 1.303309 GTGATCTGGAGAAATGCCGG 58.697 55.000 0.00 0.00 0.00 6.13
2054 2076 0.464373 TGATCTGGAGAAATGCCGGC 60.464 55.000 22.73 22.73 0.00 6.13
2055 2077 1.502163 GATCTGGAGAAATGCCGGCG 61.502 60.000 23.90 0.00 0.00 6.46
2056 2078 3.880846 CTGGAGAAATGCCGGCGC 61.881 66.667 23.90 11.21 0.00 6.53
2065 2087 4.752879 TGCCGGCGCAGTAGGTTC 62.753 66.667 23.90 0.00 41.12 3.62
2066 2088 4.452733 GCCGGCGCAGTAGGTTCT 62.453 66.667 12.58 0.00 34.03 3.01
2067 2089 2.509336 CCGGCGCAGTAGGTTCTG 60.509 66.667 10.83 0.00 38.35 3.02
2068 2090 2.509336 CGGCGCAGTAGGTTCTGG 60.509 66.667 10.83 0.00 36.12 3.86
2069 2091 2.820037 GGCGCAGTAGGTTCTGGC 60.820 66.667 10.83 0.00 36.12 4.85
2070 2092 2.047274 GCGCAGTAGGTTCTGGCA 60.047 61.111 0.30 0.00 36.12 4.92
2071 2093 1.671054 GCGCAGTAGGTTCTGGCAA 60.671 57.895 0.30 0.00 36.12 4.52
2072 2094 1.026718 GCGCAGTAGGTTCTGGCAAT 61.027 55.000 0.30 0.00 36.12 3.56
2073 2095 0.729116 CGCAGTAGGTTCTGGCAATG 59.271 55.000 0.00 0.00 36.12 2.82
2074 2096 1.098050 GCAGTAGGTTCTGGCAATGG 58.902 55.000 0.00 0.00 36.12 3.16
2075 2097 1.098050 CAGTAGGTTCTGGCAATGGC 58.902 55.000 0.00 0.00 40.13 4.40
2085 2107 4.118584 GCAATGGCCCTCCTGTTT 57.881 55.556 0.00 0.00 0.00 2.83
2086 2108 2.365410 GCAATGGCCCTCCTGTTTT 58.635 52.632 0.00 0.00 0.00 2.43
2087 2109 0.686789 GCAATGGCCCTCCTGTTTTT 59.313 50.000 0.00 0.00 0.00 1.94
2115 2375 2.959707 GAGACCCCTCGATCTGTGTTAT 59.040 50.000 0.00 0.00 0.00 1.89
2143 2800 7.404671 TGTAGTATCTCAACTCATGCACTAA 57.595 36.000 0.00 0.00 0.00 2.24
2155 2812 1.961793 TGCACTAACTCAACACCACC 58.038 50.000 0.00 0.00 0.00 4.61
2197 2854 7.231722 CACAAGCTAGACCCTAGAACTATACAT 59.768 40.741 5.27 0.00 0.00 2.29
2205 2862 5.241064 ACCCTAGAACTATACATACAGCACG 59.759 44.000 0.00 0.00 0.00 5.34
2226 2883 7.018826 GCACGCATATTTTTAAGTGTCTGTAA 58.981 34.615 0.00 0.00 32.74 2.41
2295 2952 1.270305 ACACAGTCCCAACGAGACATG 60.270 52.381 0.00 0.00 36.68 3.21
2366 3023 2.282816 TGCCAACCCCAACCATCG 60.283 61.111 0.00 0.00 0.00 3.84
2370 3027 2.046285 CAACCCCAACCATCGAGCC 61.046 63.158 0.00 0.00 0.00 4.70
2466 3123 6.149973 TCACATAAGAATTTCCAAGAGTGCAG 59.850 38.462 0.00 0.00 0.00 4.41
2542 3199 5.966636 GGCAAAACCAACTTTTCTAAGTG 57.033 39.130 0.00 0.00 43.74 3.16
2549 3206 3.253432 CCAACTTTTCTAAGTGCCCTGAC 59.747 47.826 0.00 0.00 43.74 3.51
2564 3221 1.850289 TGACTGGGGGCAAAGGCTA 60.850 57.895 0.00 0.00 40.87 3.93
2568 3225 1.228737 TGGGGGCAAAGGCTACAAC 60.229 57.895 0.00 0.00 40.87 3.32
2575 3232 2.494059 GCAAAGGCTACAACTGACAGA 58.506 47.619 10.08 0.00 36.96 3.41
2661 3320 7.016661 AGGTGATAAGAAAAGAGAGAGAACCAA 59.983 37.037 0.00 0.00 0.00 3.67
2683 3342 2.958578 CTTGAACACCCCACGGCTGT 62.959 60.000 0.00 0.00 0.00 4.40
2709 3368 3.730761 GCAAGCACAGGAGCCACG 61.731 66.667 0.00 0.00 34.23 4.94
2742 3401 2.503356 CCTGCACCTTCCTATGAAGTCT 59.497 50.000 6.96 0.00 45.45 3.24
2760 3419 6.723515 TGAAGTCTTAGATGCTATATCCAGCT 59.276 38.462 0.00 0.07 42.30 4.24
2803 3462 3.286353 TGTTTGATCTTGTGTGGCTCAA 58.714 40.909 0.00 0.00 0.00 3.02
2808 3467 4.401022 TGATCTTGTGTGGCTCAATTCTT 58.599 39.130 0.00 0.00 0.00 2.52
2836 3495 8.390143 AGCTAGATGATCCTGAGTATCTCTAAA 58.610 37.037 0.00 0.00 34.92 1.85
2854 3513 7.568349 TCTCTAAAAATGGTATCAGAGCATGT 58.432 34.615 0.00 0.00 45.65 3.21
2855 3514 8.049117 TCTCTAAAAATGGTATCAGAGCATGTT 58.951 33.333 0.00 0.00 45.65 2.71
2939 3598 8.605325 ACTAAAGATCAAGTTTAGCCCTACTA 57.395 34.615 11.09 0.00 39.96 1.82
2949 3608 8.429641 CAAGTTTAGCCCTACTATTATGAGGAA 58.570 37.037 0.00 0.00 31.45 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
285 290 8.607441 TCCATTTCATCAGGTAAAATATCTCG 57.393 34.615 0.00 0.00 0.00 4.04
470 475 0.538746 TCAAAACTTTCCCCCTCCGC 60.539 55.000 0.00 0.00 0.00 5.54
502 507 3.058016 CGTTGTTCTGTGATTTGCCTGAT 60.058 43.478 0.00 0.00 0.00 2.90
571 576 1.149148 GGAAAGTTCGGTGTGAGAGC 58.851 55.000 0.00 0.00 0.00 4.09
657 662 1.855295 TACAACCATACTCCCGCTCA 58.145 50.000 0.00 0.00 0.00 4.26
856 861 0.928229 AGTTCAAGTTCGACGCACAC 59.072 50.000 0.00 0.00 0.00 3.82
945 950 5.190357 AGGAATGGAAGAGAGCAAAGAAT 57.810 39.130 0.00 0.00 0.00 2.40
1045 1051 1.807226 CGTGCGAGGTGATCCTGTA 59.193 57.895 0.00 0.00 45.24 2.74
1244 1250 1.285373 AGGCGTAGAGGAAGGAGAAGA 59.715 52.381 0.00 0.00 0.00 2.87
1332 1338 3.138798 GGTAGGCTCTCGGACGCA 61.139 66.667 0.00 0.00 0.00 5.24
1519 1533 1.171308 GTGATGCTGCTGACATGGTT 58.829 50.000 0.00 0.00 0.00 3.67
1579 1593 2.355837 CACGGTCGTCACCCTGTG 60.356 66.667 0.00 0.00 40.01 3.66
1583 1597 4.712425 CGTCCACGGTCGTCACCC 62.712 72.222 0.00 0.00 40.01 4.61
1601 1615 0.234884 GGCAACGTCGAAGGTTTCAG 59.765 55.000 0.00 0.00 0.00 3.02
1602 1616 2.313267 GGCAACGTCGAAGGTTTCA 58.687 52.632 0.00 0.00 0.00 2.69
1869 1891 2.123248 TTGGCCTCGATGCAGAACCA 62.123 55.000 14.77 0.00 0.00 3.67
1878 1900 3.782443 GACCCCGTTGGCCTCGAT 61.782 66.667 19.23 7.09 37.83 3.59
1886 1908 4.259131 ACCCCGTTGACCCCGTTG 62.259 66.667 0.00 0.00 0.00 4.10
1917 1939 0.750546 TACGAGCTGGCCACGTAGAT 60.751 55.000 19.75 1.40 40.61 1.98
2030 2052 1.596727 GCATTTCTCCAGATCACGAGC 59.403 52.381 0.00 0.00 0.00 5.03
2031 2053 2.208431 GGCATTTCTCCAGATCACGAG 58.792 52.381 0.00 0.00 0.00 4.18
2032 2054 1.471501 CGGCATTTCTCCAGATCACGA 60.472 52.381 0.00 0.00 0.00 4.35
2033 2055 0.933097 CGGCATTTCTCCAGATCACG 59.067 55.000 0.00 0.00 0.00 4.35
2034 2056 1.303309 CCGGCATTTCTCCAGATCAC 58.697 55.000 0.00 0.00 0.00 3.06
2035 2057 0.464373 GCCGGCATTTCTCCAGATCA 60.464 55.000 24.80 0.00 0.00 2.92
2036 2058 1.502163 CGCCGGCATTTCTCCAGATC 61.502 60.000 28.98 0.00 0.00 2.75
2037 2059 1.524621 CGCCGGCATTTCTCCAGAT 60.525 57.895 28.98 0.00 0.00 2.90
2038 2060 2.125147 CGCCGGCATTTCTCCAGA 60.125 61.111 28.98 0.00 0.00 3.86
2039 2061 3.880846 GCGCCGGCATTTCTCCAG 61.881 66.667 28.98 7.61 39.62 3.86
2040 2062 4.713735 TGCGCCGGCATTTCTCCA 62.714 61.111 28.98 8.07 46.21 3.86
2049 2071 4.452733 AGAACCTACTGCGCCGGC 62.453 66.667 19.07 19.07 40.52 6.13
2050 2072 2.509336 CAGAACCTACTGCGCCGG 60.509 66.667 4.18 0.00 0.00 6.13
2051 2073 2.509336 CCAGAACCTACTGCGCCG 60.509 66.667 4.18 0.00 36.67 6.46
2052 2074 2.820037 GCCAGAACCTACTGCGCC 60.820 66.667 4.18 0.00 36.67 6.53
2053 2075 1.026718 ATTGCCAGAACCTACTGCGC 61.027 55.000 0.00 0.00 36.67 6.09
2054 2076 0.729116 CATTGCCAGAACCTACTGCG 59.271 55.000 0.00 0.00 36.67 5.18
2055 2077 1.098050 CCATTGCCAGAACCTACTGC 58.902 55.000 0.00 0.00 36.67 4.40
2056 2078 1.098050 GCCATTGCCAGAACCTACTG 58.902 55.000 0.00 0.00 37.61 2.74
2057 2079 3.577389 GCCATTGCCAGAACCTACT 57.423 52.632 0.00 0.00 0.00 2.57
2068 2090 0.686789 AAAAACAGGAGGGCCATTGC 59.313 50.000 6.18 0.00 36.29 3.56
2089 2111 2.637872 ACAGATCGAGGGGTCTCAAAAA 59.362 45.455 0.00 0.00 39.95 1.94
2090 2112 2.028112 CACAGATCGAGGGGTCTCAAAA 60.028 50.000 0.00 0.00 39.95 2.44
2091 2113 1.550524 CACAGATCGAGGGGTCTCAAA 59.449 52.381 0.00 0.00 39.95 2.69
2143 2800 2.203153 GTGCGGGTGGTGTTGAGT 60.203 61.111 0.00 0.00 0.00 3.41
2197 2854 6.370442 AGACACTTAAAAATATGCGTGCTGTA 59.630 34.615 0.00 0.00 0.00 2.74
2205 2862 8.669243 AGCTCTTACAGACACTTAAAAATATGC 58.331 33.333 0.00 0.00 0.00 3.14
2226 2883 3.981071 TGTGCCACAACTATTAGCTCT 57.019 42.857 0.00 0.00 0.00 4.09
2312 2969 3.382832 CAGGTTCGAGTCCCGGCT 61.383 66.667 0.00 0.00 39.14 5.52
2317 2974 1.522569 CCATCCCAGGTTCGAGTCC 59.477 63.158 1.17 1.17 0.00 3.85
2323 2980 2.590092 CCGACCCATCCCAGGTTC 59.410 66.667 0.00 0.00 37.88 3.62
2345 3002 2.983592 GGTTGGGGTTGGCAGTCG 60.984 66.667 0.00 0.00 0.00 4.18
2358 3015 3.181367 GCAGTGGCTCGATGGTTG 58.819 61.111 0.00 0.00 36.96 3.77
2370 3027 1.016130 ATTGCCGAGAACGAGCAGTG 61.016 55.000 0.00 0.00 42.68 3.66
2466 3123 3.200483 ACCCAACAACAAGTACTCGTTC 58.800 45.455 0.00 0.00 0.00 3.95
2549 3206 1.076549 TTGTAGCCTTTGCCCCCAG 59.923 57.895 0.00 0.00 38.69 4.45
2564 3221 0.693049 GGGACCCATCTGTCAGTTGT 59.307 55.000 5.33 0.00 36.97 3.32
2661 3320 1.388837 GCCGTGGGGTGTTCAAGTTT 61.389 55.000 0.00 0.00 34.97 2.66
2683 3342 0.609957 CCTGTGCTTGCTGGATTGGA 60.610 55.000 0.00 0.00 0.00 3.53
2742 3401 6.441604 TGGAATCAGCTGGATATAGCATCTAA 59.558 38.462 15.13 0.00 46.07 2.10
2760 3419 8.877864 AACATACCTCAAAATTAGTGGAATCA 57.122 30.769 6.07 0.00 0.00 2.57
2803 3462 5.840149 ACTCAGGATCATCTAGCTCAAGAAT 59.160 40.000 0.00 0.00 0.00 2.40
2808 3467 6.012596 AGAGATACTCAGGATCATCTAGCTCA 60.013 42.308 0.00 0.00 32.06 4.26
2836 3495 5.688807 AGCTAACATGCTCTGATACCATTT 58.311 37.500 0.00 0.00 39.34 2.32
2949 3608 6.656693 CCTCACTTTAATTCATCAGGACTTGT 59.343 38.462 0.00 0.00 0.00 3.16
3003 3662 8.803235 ACCTTACTGAAAAATTTCAATCCCTAC 58.197 33.333 9.63 0.00 45.61 3.18
3005 3664 7.855784 ACCTTACTGAAAAATTTCAATCCCT 57.144 32.000 9.63 0.00 45.61 4.20


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

AutoCloner maintained by Alex Coulton.