Multiple sequence alignment - TraesCS5D01G012000

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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 TraesCS5D01G012000 chr5D 100.000 4081 0 0 1 4081 6454614 6458694 0.000000e+00 7537
1 TraesCS5D01G012000 chr5D 89.371 1176 101 18 2068 3225 5424520 5425689 0.000000e+00 1458
2 TraesCS5D01G012000 chr5D 86.022 558 67 6 979 1528 5423585 5424139 4.540000e-164 588
3 TraesCS5D01G012000 chr5A 96.751 4094 106 7 1 4068 3198043 3193951 0.000000e+00 6798


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 TraesCS5D01G012000 chr5D 6454614 6458694 4080 False 7537 7537 100.0000 1 4081 1 chr5D.!!$F1 4080
1 TraesCS5D01G012000 chr5D 5423585 5425689 2104 False 1023 1458 87.6965 979 3225 2 chr5D.!!$F2 2246
2 TraesCS5D01G012000 chr5A 3193951 3198043 4092 True 6798 6798 96.7510 1 4068 1 chr5A.!!$R1 4067

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
432 433 1.070134 TGGAGGCGTATTCAGGTATGC 59.930 52.381 0.00 0.00 36.17 3.14 F
1869 1927 1.529438 GCGCCGTTAATAGCATGCTAA 59.471 47.619 30.06 14.28 31.73 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1925 1983 1.062525 GCGCAGGCCTCAAAATACG 59.937 57.895 0.0 0.0 0.00 3.06 R
3861 3985 0.099436 GTTGATGGCTTCGCATCCAC 59.901 55.000 0.0 0.0 34.81 4.02 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
171 172 7.517734 GCGTTCAAACTTTCACTATCAGTACAA 60.518 37.037 0.00 0.00 0.00 2.41
432 433 1.070134 TGGAGGCGTATTCAGGTATGC 59.930 52.381 0.00 0.00 36.17 3.14
517 518 8.410141 GCACTAGAACAGAACTATCAAGTCTAT 58.590 37.037 0.00 0.00 33.75 1.98
596 597 4.070630 AGCCTTGTCATATCTCAAGAGC 57.929 45.455 14.40 14.51 42.22 4.09
611 612 5.129485 TCTCAAGAGCTTATCGAGGGAAATT 59.871 40.000 0.00 0.00 0.00 1.82
670 671 3.145212 GGCAACAACCCGATCAAATAC 57.855 47.619 0.00 0.00 0.00 1.89
672 673 3.427503 GGCAACAACCCGATCAAATACAG 60.428 47.826 0.00 0.00 0.00 2.74
816 834 9.257651 GTTTCGTCATAAGTATAAGCCTACATT 57.742 33.333 0.00 0.00 0.00 2.71
869 887 4.835927 CCGCTGGGTGAGATGTAC 57.164 61.111 0.00 0.00 0.00 2.90
1143 1167 1.602668 CCTGTGGTGAATGGTTTTGCG 60.603 52.381 0.00 0.00 0.00 4.85
1461 1485 3.131933 AGTTGAGGAGACATCTTGATCCG 59.868 47.826 0.00 0.00 33.89 4.18
1509 1535 6.504398 CACGCTATCTTCTGTAACCTTCATA 58.496 40.000 0.00 0.00 0.00 2.15
1700 1758 9.884814 ATAACTACTAGAGAAGTTACCATGGAT 57.115 33.333 21.47 5.32 40.10 3.41
1701 1759 8.611051 AACTACTAGAGAAGTTACCATGGATT 57.389 34.615 21.47 7.36 39.80 3.01
1702 1760 8.012957 ACTACTAGAGAAGTTACCATGGATTG 57.987 38.462 21.47 0.00 39.80 2.67
1817 1875 4.026475 CGTACTTCGTACTCGGTAACCTAG 60.026 50.000 3.07 0.00 36.93 3.02
1834 1892 5.102953 ACCTAGCAGCATCACTGATTAAA 57.897 39.130 0.00 0.00 44.43 1.52
1864 1922 4.713824 TCTATAGCGCCGTTAATAGCAT 57.286 40.909 2.29 0.00 0.00 3.79
1869 1927 1.529438 GCGCCGTTAATAGCATGCTAA 59.471 47.619 30.06 14.28 31.73 3.09
1919 1977 2.018542 TTAGTGTACAATGCCTCGCC 57.981 50.000 5.98 0.00 0.00 5.54
1925 1983 1.264288 GTACAATGCCTCGCCAATAGC 59.736 52.381 0.00 0.00 38.52 2.97
1938 1996 2.287608 GCCAATAGCGTATTTTGAGGCC 60.288 50.000 0.00 0.00 31.11 5.19
2093 2198 5.056894 TCTTTTGTCCGTAGAGCTACTTC 57.943 43.478 6.14 0.00 34.04 3.01
2168 2273 2.225019 GCTCATGTTGATATCAAGCCGG 59.775 50.000 18.47 8.80 36.39 6.13
2655 2760 9.679661 TTCATAATTGTATCAAAGAGGCACTTA 57.320 29.630 0.00 0.00 41.55 2.24
2658 2763 3.873910 TGTATCAAAGAGGCACTTAGGC 58.126 45.455 0.00 0.00 41.55 3.93
3160 3275 5.878116 TGGGTGCATCACTTATTACTTGTAC 59.122 40.000 0.00 0.00 34.40 2.90
3162 3277 6.258068 GGGTGCATCACTTATTACTTGTACTC 59.742 42.308 0.00 0.00 34.40 2.59
3224 3342 7.311549 CCCTTGGATGAGCTATATATGGTCTTT 60.312 40.741 12.44 4.36 33.59 2.52
3228 3346 8.097038 TGGATGAGCTATATATGGTCTTTTCAC 58.903 37.037 12.44 0.00 33.59 3.18
3260 3378 6.870971 TCACTAGTAAACATTTGGTTGGTC 57.129 37.500 0.00 0.00 40.35 4.02
3274 3392 3.650942 TGGTTGGTCTCCATTAACTCAGT 59.349 43.478 0.00 0.00 31.53 3.41
3303 3421 3.181423 ACCCATTAGCTGGTCTTTTTCCA 60.181 43.478 0.00 0.00 44.30 3.53
3370 3488 9.988815 ATTAATAGAAGTACATGCAGTAGGAAG 57.011 33.333 0.00 0.00 32.19 3.46
3374 3492 4.473477 AGTACATGCAGTAGGAAGTTCC 57.527 45.455 14.54 14.54 36.58 3.62
3434 3553 3.947612 AGGATGGACTTGCAGATTGAT 57.052 42.857 0.00 0.00 0.00 2.57
3486 3605 2.045926 AGCGATGTTGGGAGCCAC 60.046 61.111 0.00 0.00 30.78 5.01
3508 3627 2.002586 GTCACAATGAGATGGTGGTCG 58.997 52.381 0.00 0.00 33.45 4.79
3517 3636 1.006832 GATGGTGGTCGTCGGAAATG 58.993 55.000 0.00 0.00 0.00 2.32
3526 3645 0.921347 CGTCGGAAATGACCTTAGCG 59.079 55.000 0.00 0.00 35.40 4.26
3533 3652 3.487544 GGAAATGACCTTAGCGTTGCATC 60.488 47.826 0.00 0.00 0.00 3.91
3539 3658 3.412386 ACCTTAGCGTTGCATCTTTTCT 58.588 40.909 0.00 0.00 0.00 2.52
3564 3683 1.831106 TCCTCATAGCACAACCATCGT 59.169 47.619 0.00 0.00 0.00 3.73
3591 3710 3.444805 GCAGAGGCGAGGTCGAGT 61.445 66.667 2.94 0.00 43.02 4.18
3592 3711 2.995872 GCAGAGGCGAGGTCGAGTT 61.996 63.158 2.94 0.00 43.02 3.01
3607 3726 2.684374 TCGAGTTGGAAATCATGCCATG 59.316 45.455 0.00 0.00 33.46 3.66
3643 3763 2.167861 GCTTCGACGATGGGAGCAC 61.168 63.158 13.06 0.00 0.00 4.40
3670 3790 1.903404 CCACCTGGAAGCACAACCC 60.903 63.158 0.00 0.00 37.39 4.11
3718 3838 2.167900 GCACCCGAAGAATAGGTACTGT 59.832 50.000 0.00 0.00 41.52 3.55
3729 3849 2.570386 AGGTACTGTATGGCCTCCTT 57.430 50.000 3.32 0.00 37.18 3.36
3751 3871 1.416401 TCCCCACAGAAGACACAACTC 59.584 52.381 0.00 0.00 0.00 3.01
3752 3872 1.140852 CCCCACAGAAGACACAACTCA 59.859 52.381 0.00 0.00 0.00 3.41
3753 3873 2.224621 CCCCACAGAAGACACAACTCAT 60.225 50.000 0.00 0.00 0.00 2.90
3754 3874 2.810274 CCCACAGAAGACACAACTCATG 59.190 50.000 0.00 0.00 0.00 3.07
3804 3928 3.770040 CACGGGAGGCGATGACCA 61.770 66.667 0.00 0.00 0.00 4.02
3836 3960 9.831737 CAGAGTCAAATGAATAACTTAAACCTG 57.168 33.333 0.00 0.00 0.00 4.00
3861 3985 1.144936 GCGAAGGGTCTCCAGATGG 59.855 63.158 0.00 0.00 34.83 3.51
3901 4025 0.034186 GGGTGATGAGCCATGGTCAA 60.034 55.000 14.67 0.00 43.29 3.18
3931 4055 2.401766 CGACTGCCATGAAGGGTGC 61.402 63.158 0.00 0.00 38.09 5.01
3933 4057 2.036098 CTGCCATGAAGGGTGCCA 59.964 61.111 0.00 0.00 38.09 4.92
3934 4058 2.036098 TGCCATGAAGGGTGCCAG 59.964 61.111 0.00 0.00 38.09 4.85
3940 4064 0.846427 ATGAAGGGTGCCAGGAAGGA 60.846 55.000 0.00 0.00 41.22 3.36
3950 4074 1.676967 CAGGAAGGAGGCAAGCACC 60.677 63.158 0.00 0.00 0.00 5.01
3979 4103 4.102524 GTCATCCACACCCATACATAGGAA 59.897 45.833 0.00 0.00 0.00 3.36
3987 4111 3.657239 ACCCATACATAGGAATCATGGCA 59.343 43.478 0.00 0.00 35.78 4.92
4018 4142 4.101585 CAGAGTTGGGGAGCAGTAATGATA 59.898 45.833 0.00 0.00 0.00 2.15
4025 4149 7.149202 TGGGGAGCAGTAATGATACTTTTAT 57.851 36.000 0.00 0.00 40.44 1.40
4069 4193 5.043189 GCACCTATTGTGGTTGTTTAGTC 57.957 43.478 0.00 0.00 45.55 2.59
4070 4194 4.082949 GCACCTATTGTGGTTGTTTAGTCC 60.083 45.833 0.00 0.00 45.55 3.85
4071 4195 5.067273 CACCTATTGTGGTTGTTTAGTCCA 58.933 41.667 0.00 0.00 41.52 4.02
4072 4196 5.533154 CACCTATTGTGGTTGTTTAGTCCAA 59.467 40.000 0.00 0.00 41.52 3.53
4073 4197 6.208599 CACCTATTGTGGTTGTTTAGTCCAAT 59.791 38.462 0.00 0.00 41.52 3.16
4074 4198 6.208599 ACCTATTGTGGTTGTTTAGTCCAATG 59.791 38.462 0.00 0.00 36.89 2.82
4075 4199 4.314740 TTGTGGTTGTTTAGTCCAATGC 57.685 40.909 0.00 0.00 32.82 3.56
4076 4200 3.291584 TGTGGTTGTTTAGTCCAATGCA 58.708 40.909 0.00 0.00 32.82 3.96
4077 4201 3.894427 TGTGGTTGTTTAGTCCAATGCAT 59.106 39.130 0.00 0.00 32.82 3.96
4078 4202 4.236935 GTGGTTGTTTAGTCCAATGCATG 58.763 43.478 0.00 0.00 32.82 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.210873 ACTCTCTTGATATTCCCGTGTTAATC 58.789 38.462 0.00 0.00 0.00 1.75
171 172 4.478206 AGTCAATGCTAGCAGTACATGT 57.522 40.909 23.89 2.69 0.00 3.21
432 433 8.722394 GTGGAGAGGAAACAAATTAACTTCTAG 58.278 37.037 0.00 0.00 0.00 2.43
517 518 5.171476 CGAAGAAGACAAGGCTTTAGATGA 58.829 41.667 0.00 0.00 0.00 2.92
596 597 4.699925 TGGGGTAATTTCCCTCGATAAG 57.300 45.455 18.68 0.00 46.27 1.73
624 625 8.517878 CGAGAGGAAATACCCGATAATTAGTTA 58.482 37.037 0.00 0.00 40.05 2.24
646 647 1.079405 GATCGGGTTGTTGCCGAGA 60.079 57.895 0.00 0.00 39.31 4.04
670 671 4.099266 TGTTTCCATTTCCTTGTTGGTCTG 59.901 41.667 0.00 0.00 37.07 3.51
672 673 4.340950 TCTGTTTCCATTTCCTTGTTGGTC 59.659 41.667 0.00 0.00 37.07 4.02
711 713 5.122554 TGTGTGTGTGTGTAGTTTAAACAGG 59.877 40.000 20.06 0.00 0.00 4.00
788 806 7.919091 TGTAGGCTTATACTTATGACGAAACTG 59.081 37.037 0.00 0.00 0.00 3.16
790 808 8.813643 ATGTAGGCTTATACTTATGACGAAAC 57.186 34.615 0.00 0.00 0.00 2.78
845 863 0.400213 TCTCACCCAGCGGTCAAATT 59.600 50.000 0.00 0.00 42.04 1.82
851 869 0.902984 TGTACATCTCACCCAGCGGT 60.903 55.000 0.00 0.00 46.31 5.68
869 887 0.743688 AGTAGCTCAGTCTCCGCATG 59.256 55.000 0.00 0.00 0.00 4.06
1461 1485 1.205893 ACCTCGACCTCTTGAAGCATC 59.794 52.381 0.00 0.00 0.00 3.91
1509 1535 8.757982 ATGATGTATTAAAGCTTCTGAATGGT 57.242 30.769 0.00 0.00 0.00 3.55
1800 1858 2.283298 CTGCTAGGTTACCGAGTACGA 58.717 52.381 12.84 0.00 42.66 3.43
1817 1875 5.397534 CGCTATTTTTAATCAGTGATGCTGC 59.602 40.000 6.34 0.00 44.66 5.25
1864 1922 2.099141 ATTCTCAGCACGCTTTAGCA 57.901 45.000 2.29 0.00 42.21 3.49
1903 1961 1.094785 ATTGGCGAGGCATTGTACAC 58.905 50.000 0.00 0.00 0.00 2.90
1919 1977 3.548818 GCAGGCCTCAAAATACGCTATTG 60.549 47.826 0.00 0.00 0.00 1.90
1925 1983 1.062525 GCGCAGGCCTCAAAATACG 59.937 57.895 0.00 0.00 0.00 3.06
2168 2273 5.400703 CGAACCTCTTTTCCTAGTAGACAC 58.599 45.833 0.00 0.00 0.00 3.67
2655 2760 0.755327 GTTGTTGGTGGGTTCAGCCT 60.755 55.000 0.00 0.00 40.42 4.58
2658 2763 2.430332 ACATTGTTGTTGGTGGGTTCAG 59.570 45.455 0.00 0.00 29.55 3.02
2856 2961 2.514803 AGAAAACTTGCCGCCAACTAT 58.485 42.857 0.00 0.00 0.00 2.12
3236 3354 7.231467 AGACCAACCAAATGTTTACTAGTGAT 58.769 34.615 5.39 0.00 34.00 3.06
3237 3355 6.597562 AGACCAACCAAATGTTTACTAGTGA 58.402 36.000 5.39 0.00 34.00 3.41
3260 3378 4.878397 GGTGAATCCACTGAGTTAATGGAG 59.122 45.833 1.53 0.00 45.53 3.86
3274 3392 2.734755 CCAGCTAATGGGTGAATCCA 57.265 50.000 0.00 0.00 46.36 3.41
3351 3469 4.870991 GGAACTTCCTACTGCATGTACTTC 59.129 45.833 0.00 0.00 32.53 3.01
3401 3520 0.469331 CCATCCTAGAGGCGTGGGTA 60.469 60.000 10.44 0.00 37.18 3.69
3408 3527 0.833287 TGCAAGTCCATCCTAGAGGC 59.167 55.000 0.00 0.00 34.44 4.70
3434 3553 0.463620 TGGTGATGCGATGATTCCGA 59.536 50.000 0.00 0.00 0.00 4.55
3486 3605 1.339055 ACCACCATCTCATTGTGACCG 60.339 52.381 0.00 0.00 31.66 4.79
3508 3627 2.005971 ACGCTAAGGTCATTTCCGAC 57.994 50.000 0.00 0.00 35.03 4.79
3517 3636 3.437049 AGAAAAGATGCAACGCTAAGGTC 59.563 43.478 0.00 0.00 0.00 3.85
3526 3645 6.992063 TGAGGAATCTAGAAAAGATGCAAC 57.008 37.500 0.00 0.00 44.56 4.17
3533 3652 7.011857 GGTTGTGCTATGAGGAATCTAGAAAAG 59.988 40.741 0.00 0.00 0.00 2.27
3539 3658 5.509670 CGATGGTTGTGCTATGAGGAATCTA 60.510 44.000 0.00 0.00 0.00 1.98
3564 3683 1.374631 CGCCTCTGCTGCACAACTA 60.375 57.895 0.00 0.00 34.43 2.24
3582 3701 2.352960 GCATGATTTCCAACTCGACCTC 59.647 50.000 0.00 0.00 0.00 3.85
3591 3710 3.171528 TGTTCCATGGCATGATTTCCAA 58.828 40.909 28.43 8.17 35.75 3.53
3592 3711 2.761767 CTGTTCCATGGCATGATTTCCA 59.238 45.455 28.43 14.98 36.70 3.53
3607 3726 2.743928 CCTCTGCACGCCTGTTCC 60.744 66.667 0.00 0.00 0.00 3.62
3643 3763 3.266686 TTCCAGGTGGCATGTCCCG 62.267 63.158 0.00 0.00 34.44 5.14
3718 3838 0.694444 GTGGGGAGAAGGAGGCCATA 60.694 60.000 5.01 0.00 0.00 2.74
3729 3849 1.416401 GTTGTGTCTTCTGTGGGGAGA 59.584 52.381 0.00 0.00 0.00 3.71
3751 3871 9.117183 CATCATCCTTGTATTATATCCACCATG 57.883 37.037 0.00 0.00 0.00 3.66
3752 3872 9.061252 TCATCATCCTTGTATTATATCCACCAT 57.939 33.333 0.00 0.00 0.00 3.55
3753 3873 8.448068 TCATCATCCTTGTATTATATCCACCA 57.552 34.615 0.00 0.00 0.00 4.17
3754 3874 9.334947 CATCATCATCCTTGTATTATATCCACC 57.665 37.037 0.00 0.00 0.00 4.61
3797 3921 7.157347 TCATTTGACTCTGCTATATGGTCATC 58.843 38.462 0.00 0.00 36.90 2.92
3829 3953 2.515996 CTTCGCCCCGAGCAGGTTTA 62.516 60.000 0.00 0.00 44.04 2.01
3861 3985 0.099436 GTTGATGGCTTCGCATCCAC 59.901 55.000 0.00 0.00 34.81 4.02
3870 3994 1.843368 CATCACCCTGTTGATGGCTT 58.157 50.000 5.36 0.00 46.29 4.35
3901 4025 2.027605 CAGTCGACGCACACACCT 59.972 61.111 10.46 0.00 0.00 4.00
3931 4055 1.676967 GTGCTTGCCTCCTTCCTGG 60.677 63.158 0.00 0.00 37.10 4.45
3933 4057 2.156098 TGGTGCTTGCCTCCTTCCT 61.156 57.895 5.78 0.00 0.00 3.36
3934 4058 1.973812 GTGGTGCTTGCCTCCTTCC 60.974 63.158 5.78 0.00 0.00 3.46
3940 4064 2.124320 ACAACGTGGTGCTTGCCT 60.124 55.556 0.00 0.00 0.00 4.75
3950 4074 0.533978 TGGGTGTGGATGACAACGTG 60.534 55.000 0.00 0.00 44.07 4.49
3979 4103 4.232188 ACTCTGAGTTGATTGCCATGAT 57.768 40.909 4.06 0.00 0.00 2.45
4038 4162 2.356022 CCACAATAGGTGCTCATGACCA 60.356 50.000 4.98 0.00 46.50 4.02


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

AutoCloner maintained by Alex Coulton.