Multiple sequence alignment - TraesCS4D01G261300

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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 TraesCS4D01G261300 chr4D 100.000 3187 0 0 1 3187 432429578 432426392 0 5886
1 TraesCS4D01G261300 chr4A 89.510 2326 102 60 946 3187 33646125 33643858 0 2813
2 TraesCS4D01G261300 chr4A 92.492 959 29 21 1 924 33647065 33646115 0 1332
3 TraesCS4D01G261300 chr4B 93.363 1793 62 23 1431 3187 530207278 530205507 0 2599
4 TraesCS4D01G261300 chr4B 98.052 924 14 2 1 924 530208666 530207747 0 1604
5 TraesCS4D01G261300 chr4B 98.241 398 7 0 948 1345 530207755 530207358 0 697


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 TraesCS4D01G261300 chr4D 432426392 432429578 3186 True 5886.000000 5886 100.000 1 3187 1 chr4D.!!$R1 3186
1 TraesCS4D01G261300 chr4A 33643858 33647065 3207 True 2072.500000 2813 91.001 1 3187 2 chr4A.!!$R1 3186
2 TraesCS4D01G261300 chr4B 530205507 530208666 3159 True 1633.333333 2599 96.552 1 3187 3 chr4B.!!$R1 3186

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
29 30 1.144913 GGCCTATTTACTGCATGGGGA 59.855 52.381 0.0 0.0 0.0 4.81 F
919 954 1.277842 ACTCAGTTCCACACACACACA 59.722 47.619 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1860 1953 2.266055 CTCCAGGTTCACGCCCTC 59.734 66.667 0.0 0.0 0.00 4.30 R
2423 2544 0.179029 GGGGCAACAGTGTGTGTACT 60.179 55.000 0.0 0.0 39.03 2.73 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
29 30 1.144913 GGCCTATTTACTGCATGGGGA 59.855 52.381 0.00 0.00 0.00 4.81
53 54 2.980233 GTGGTGAGGCCTGTGTGC 60.980 66.667 12.00 0.00 38.35 4.57
242 248 4.618920 ACGAGAGGTTTTAAGACATGGT 57.381 40.909 0.00 0.00 0.00 3.55
290 298 2.224548 GCCTTGTGGGTTTCACTCTAGT 60.225 50.000 0.00 0.00 46.20 2.57
440 458 2.335316 AGTAGTTCCAACCAACGCAA 57.665 45.000 0.00 0.00 0.00 4.85
463 483 1.839424 GGTTTCTCCATTGGACAGGG 58.161 55.000 0.00 0.00 35.97 4.45
808 838 3.775316 ACGATCCCTTCTTTAGTGTCCAT 59.225 43.478 0.00 0.00 0.00 3.41
851 881 4.362932 TCAATCGTGCTGTAGAAGAGAG 57.637 45.455 0.00 0.00 0.00 3.20
852 882 2.857152 CAATCGTGCTGTAGAAGAGAGC 59.143 50.000 0.00 0.00 44.81 4.09
915 950 2.034179 CGAGTACTCAGTTCCACACACA 59.966 50.000 22.37 0.00 0.00 3.72
916 951 3.381949 GAGTACTCAGTTCCACACACAC 58.618 50.000 18.20 0.00 0.00 3.82
917 952 2.764010 AGTACTCAGTTCCACACACACA 59.236 45.455 0.00 0.00 0.00 3.72
918 953 2.024176 ACTCAGTTCCACACACACAC 57.976 50.000 0.00 0.00 0.00 3.82
919 954 1.277842 ACTCAGTTCCACACACACACA 59.722 47.619 0.00 0.00 0.00 3.72
920 955 2.092968 ACTCAGTTCCACACACACACAT 60.093 45.455 0.00 0.00 0.00 3.21
921 956 3.133901 ACTCAGTTCCACACACACACATA 59.866 43.478 0.00 0.00 0.00 2.29
922 957 4.202357 ACTCAGTTCCACACACACACATAT 60.202 41.667 0.00 0.00 0.00 1.78
923 958 5.011635 ACTCAGTTCCACACACACACATATA 59.988 40.000 0.00 0.00 0.00 0.86
924 959 6.048732 TCAGTTCCACACACACACATATAT 57.951 37.500 0.00 0.00 0.00 0.86
925 960 7.093509 ACTCAGTTCCACACACACACATATATA 60.094 37.037 0.00 0.00 0.00 0.86
926 961 7.791029 TCAGTTCCACACACACACATATATAT 58.209 34.615 0.00 0.00 0.00 0.86
927 962 8.919145 TCAGTTCCACACACACACATATATATA 58.081 33.333 0.00 0.00 0.00 0.86
928 963 9.710900 CAGTTCCACACACACACATATATATAT 57.289 33.333 0.00 0.00 0.00 0.86
1062 1097 1.956869 TGAGAGCCAAGAGGATGGAA 58.043 50.000 0.00 0.00 43.54 3.53
1306 1341 1.608717 CCAAGTGAGTCCCTCCCTCG 61.609 65.000 0.00 0.00 0.00 4.63
1339 1378 9.967346 TCATCAGTAGCTAATTATTCTGTGTAC 57.033 33.333 0.00 0.00 0.00 2.90
1340 1379 9.973450 CATCAGTAGCTAATTATTCTGTGTACT 57.027 33.333 0.00 0.00 0.00 2.73
1452 1534 5.629020 TCAACTAAAACAAAATCGAGCATGC 59.371 36.000 10.51 10.51 0.00 4.06
1474 1556 3.770424 GGCGCCGACACGTGTTAC 61.770 66.667 24.26 13.97 34.88 2.50
1496 1582 3.842732 AGCCGGTAAAGTTAATTGTGC 57.157 42.857 1.90 0.00 0.00 4.57
1649 1736 2.285977 CCTACTATTTTGTGACGCCCC 58.714 52.381 0.00 0.00 0.00 5.80
1667 1754 1.473434 CCCCGAGGCATCTTTGTACTC 60.473 57.143 0.00 0.00 0.00 2.59
1668 1755 1.482593 CCCGAGGCATCTTTGTACTCT 59.517 52.381 0.00 0.00 31.15 3.24
1669 1756 2.093447 CCCGAGGCATCTTTGTACTCTT 60.093 50.000 0.00 0.00 31.15 2.85
1670 1757 3.600388 CCGAGGCATCTTTGTACTCTTT 58.400 45.455 0.00 0.00 31.15 2.52
1688 1775 3.573538 TCTTTGTAGTACCACGTTGCCTA 59.426 43.478 0.00 0.00 0.00 3.93
1689 1776 3.581024 TTGTAGTACCACGTTGCCTAG 57.419 47.619 0.00 0.00 0.00 3.02
1690 1777 2.794103 TGTAGTACCACGTTGCCTAGA 58.206 47.619 0.00 0.00 0.00 2.43
1691 1778 3.156293 TGTAGTACCACGTTGCCTAGAA 58.844 45.455 0.00 0.00 0.00 2.10
1692 1779 3.192001 TGTAGTACCACGTTGCCTAGAAG 59.808 47.826 0.00 0.00 0.00 2.85
1693 1780 2.245582 AGTACCACGTTGCCTAGAAGT 58.754 47.619 0.00 0.00 0.00 3.01
1710 1797 8.026607 GCCTAGAAGTAGAAGATGCAAGTATAG 58.973 40.741 0.00 0.00 0.00 1.31
1799 1892 4.924305 ATGTGATGTTGTTTTGCAGTCT 57.076 36.364 0.00 0.00 0.00 3.24
1802 1895 3.066621 GTGATGTTGTTTTGCAGTCTGGA 59.933 43.478 1.14 0.00 0.00 3.86
1860 1953 2.356667 GGAACAGGCCCAAGGAGG 59.643 66.667 0.00 0.00 37.03 4.30
2222 2321 5.046087 GGCTGTAGAAAGGAAACCCTAGTAA 60.046 44.000 0.00 0.00 32.65 2.24
2296 2411 4.916983 TGCATGTATGTTAATCAAGGGC 57.083 40.909 0.00 0.00 0.00 5.19
2535 2658 4.446413 GTGGACGGCCGGTGGTAG 62.446 72.222 31.76 0.00 36.79 3.18
2553 2676 2.526888 AGTGGTGCTGCTAGGTACTA 57.473 50.000 0.00 0.00 41.75 1.82
2649 2776 1.946475 GCCACACCTACTCGGACTCC 61.946 65.000 0.00 0.00 36.31 3.85
2690 2817 1.067295 TGCACACTCCATTCCCTTCT 58.933 50.000 0.00 0.00 0.00 2.85
2737 2865 0.613260 ATTAAGCCGCACTGACTCCA 59.387 50.000 0.00 0.00 0.00 3.86
2751 2879 2.034685 TGACTCCAACTCAGAGTGAACG 59.965 50.000 3.05 0.00 44.55 3.95
2753 2881 2.294791 ACTCCAACTCAGAGTGAACGAG 59.705 50.000 3.05 8.99 42.94 4.18
2762 2890 2.673368 CAGAGTGAACGAGCAATAACCC 59.327 50.000 0.00 0.00 0.00 4.11
2787 2932 1.935799 AGCTCTGAGCAAGAAGAGGA 58.064 50.000 29.49 0.00 45.56 3.71
2788 2933 2.255406 AGCTCTGAGCAAGAAGAGGAA 58.745 47.619 29.49 0.00 45.56 3.36
2918 3089 4.182433 TGCACTTCCCCACGCACA 62.182 61.111 0.00 0.00 0.00 4.57
2936 3107 0.914551 CACAAGGCGTCGAATCTACG 59.085 55.000 2.80 2.80 43.12 3.51
3015 3194 1.075536 ACTTGGCCCTAGGTTGGAAAG 59.924 52.381 8.29 6.69 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 3.971702 GGCCTCACCACCCAAGCT 61.972 66.667 0.00 0.00 38.86 3.74
53 54 5.559608 CGCTGATGCATAATAAAGACACAGG 60.560 44.000 0.00 0.00 39.64 4.00
119 120 1.139498 TCATGGCTTTCTCCACCCCA 61.139 55.000 0.00 0.00 39.25 4.96
217 221 6.435277 ACCATGTCTTAAAACCTCTCGTACTA 59.565 38.462 0.00 0.00 0.00 1.82
290 298 0.612744 TGAGTTCATGGCGATGGACA 59.387 50.000 20.81 8.05 40.27 4.02
440 458 1.144093 TGTCCAATGGAGAAACCGGTT 59.856 47.619 15.86 15.86 42.61 4.44
463 483 2.731217 GTGATGTTGGTTGTGCAACTC 58.269 47.619 13.78 5.03 40.94 3.01
808 838 3.731728 GTCATGCAGGGGAGGGCA 61.732 66.667 0.00 0.00 45.23 5.36
851 881 1.065564 AGGAGAATTGAGTGAGCTGGC 60.066 52.381 0.00 0.00 0.00 4.85
852 882 2.235650 TGAGGAGAATTGAGTGAGCTGG 59.764 50.000 0.00 0.00 0.00 4.85
945 980 8.802640 AGACACCACCACTCCCTATATATATAT 58.197 37.037 10.10 10.10 0.00 0.86
946 981 8.059461 CAGACACCACCACTCCCTATATATATA 58.941 40.741 2.49 2.49 0.00 0.86
1025 1060 2.880890 CTCAACTCCTGGTGAAACTTGG 59.119 50.000 2.23 0.00 36.74 3.61
1306 1341 3.438297 TTAGCTACTGATGAAGACGGC 57.562 47.619 0.00 0.00 0.00 5.68
1382 1421 5.670792 TGTACCCAAGGTAGAACATACAG 57.329 43.478 0.00 0.00 39.02 2.74
1474 1556 4.393680 TGCACAATTAACTTTACCGGCTAG 59.606 41.667 0.00 0.00 0.00 3.42
1496 1582 3.240401 CGCGCCATAAATAGCTTTTGTTG 59.760 43.478 0.00 0.00 0.00 3.33
1550 1636 3.630168 CCACCAATAACCATGTCCATGA 58.370 45.455 8.82 0.00 41.20 3.07
1649 1736 2.969628 AGAGTACAAAGATGCCTCGG 57.030 50.000 0.00 0.00 34.61 4.63
1667 1754 2.762745 AGGCAACGTGGTACTACAAAG 58.237 47.619 10.21 0.00 46.39 2.77
1668 1755 2.914695 AGGCAACGTGGTACTACAAA 57.085 45.000 10.21 0.00 46.39 2.83
1669 1756 3.156293 TCTAGGCAACGTGGTACTACAA 58.844 45.455 10.21 0.00 46.39 2.41
1670 1757 2.794103 TCTAGGCAACGTGGTACTACA 58.206 47.619 10.21 0.00 46.39 2.74
1681 1768 4.759782 TGCATCTTCTACTTCTAGGCAAC 58.240 43.478 0.00 0.00 0.00 4.17
1688 1775 8.511321 CGATCTATACTTGCATCTTCTACTTCT 58.489 37.037 0.00 0.00 0.00 2.85
1689 1776 8.508062 TCGATCTATACTTGCATCTTCTACTTC 58.492 37.037 0.00 0.00 0.00 3.01
1690 1777 8.397575 TCGATCTATACTTGCATCTTCTACTT 57.602 34.615 0.00 0.00 0.00 2.24
1691 1778 7.987750 TCGATCTATACTTGCATCTTCTACT 57.012 36.000 0.00 0.00 0.00 2.57
1692 1779 9.929722 CTATCGATCTATACTTGCATCTTCTAC 57.070 37.037 0.00 0.00 0.00 2.59
1693 1780 9.114952 CCTATCGATCTATACTTGCATCTTCTA 57.885 37.037 0.00 0.00 0.00 2.10
1710 1797 5.419155 TCCATGTTGGATACTCCTATCGATC 59.581 44.000 0.00 0.00 42.67 3.69
1781 1874 3.286353 TCCAGACTGCAAAACAACATCA 58.714 40.909 0.00 0.00 0.00 3.07
1782 1875 3.988379 TCCAGACTGCAAAACAACATC 57.012 42.857 0.00 0.00 0.00 3.06
1786 1879 4.402155 ACATCTTTCCAGACTGCAAAACAA 59.598 37.500 0.00 0.00 0.00 2.83
1799 1892 6.214615 TCCTGTTCAGGTAATACATCTTTCCA 59.785 38.462 17.00 0.00 0.00 3.53
1802 1895 7.824779 GTCTTCCTGTTCAGGTAATACATCTTT 59.175 37.037 17.00 0.00 0.00 2.52
1860 1953 2.266055 CTCCAGGTTCACGCCCTC 59.734 66.667 0.00 0.00 0.00 4.30
2222 2321 5.187967 CCTGGTTTTGATCTGGTCTACTAGT 59.812 44.000 0.00 0.00 0.00 2.57
2296 2411 7.819900 AGTACAAGATTTACTTACTTGCTCCAG 59.180 37.037 0.00 0.00 42.93 3.86
2421 2542 2.140717 GGGCAACAGTGTGTGTACTAC 58.859 52.381 0.00 0.00 39.03 2.73
2422 2543 1.071071 GGGGCAACAGTGTGTGTACTA 59.929 52.381 0.00 0.00 39.03 1.82
2423 2544 0.179029 GGGGCAACAGTGTGTGTACT 60.179 55.000 0.00 0.00 39.03 2.73
2493 2616 6.660949 CCCTCTTCTTTAATGGACAAGACAAT 59.339 38.462 0.00 0.00 0.00 2.71
2534 2657 2.100989 GTAGTACCTAGCAGCACCACT 58.899 52.381 0.00 0.00 0.00 4.00
2535 2658 1.822990 TGTAGTACCTAGCAGCACCAC 59.177 52.381 0.00 0.00 0.00 4.16
2536 2659 2.100197 CTGTAGTACCTAGCAGCACCA 58.900 52.381 0.00 0.00 0.00 4.17
2649 2776 1.394618 CGAAGGAGGAGGGAGTAGTG 58.605 60.000 0.00 0.00 0.00 2.74
2690 2817 2.983192 TGTTTTGGGGATAGGAGACACA 59.017 45.455 0.00 0.00 0.00 3.72
2737 2865 2.890808 TTGCTCGTTCACTCTGAGTT 57.109 45.000 7.77 0.00 32.32 3.01
2751 2879 3.257127 AGAGCTATCTCGGGTTATTGCTC 59.743 47.826 10.95 10.95 45.41 4.26
2753 2881 3.005897 TCAGAGCTATCTCGGGTTATTGC 59.994 47.826 0.00 0.00 44.02 3.56
2762 2890 3.314913 TCTTCTTGCTCAGAGCTATCTCG 59.685 47.826 23.15 4.38 42.97 4.04
2787 2932 1.657804 CACAACCTAGGACCCCTCTT 58.342 55.000 17.98 0.00 34.61 2.85
2788 2933 0.910088 GCACAACCTAGGACCCCTCT 60.910 60.000 17.98 0.00 34.61 3.69
2834 2979 1.934589 TGCATGTATAGGTGTCGTGC 58.065 50.000 0.00 0.00 42.29 5.34
2918 3089 0.524862 ACGTAGATTCGACGCCTTGT 59.475 50.000 17.54 0.00 44.14 3.16
2936 3107 1.738830 GCAATGGCCACATGCACAC 60.739 57.895 30.70 9.43 43.89 3.82
2957 3136 2.989639 CCACGCCTGATTCCTGGA 59.010 61.111 0.00 0.00 33.65 3.86
3015 3194 0.807496 GACCAAGGAACAGAGCATGC 59.193 55.000 10.51 10.51 0.00 4.06


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

AutoCloner maintained by Alex Coulton.