Multiple sequence alignment - TraesCS3D01G263500

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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 TraesCS3D01G263500 chr3D 100.000 2417 0 0 1 2417 365527651 365525235 0.000000e+00 4464.0
1 TraesCS3D01G263500 chr3B 92.065 2445 124 29 1 2417 476037697 476035295 0.000000e+00 3376.0
2 TraesCS3D01G263500 chr3B 100.000 29 0 0 1779 1807 8035386 8035358 1.000000e-03 54.7
3 TraesCS3D01G263500 chr3A 88.315 1027 42 32 663 1683 487444032 487443078 0.000000e+00 1160.0
4 TraesCS3D01G263500 chr3A 97.293 665 17 1 1 665 487444751 487444088 0.000000e+00 1127.0
5 TraesCS3D01G263500 chr3A 87.266 267 24 9 2156 2417 487442248 487441987 1.820000e-76 296.0
6 TraesCS3D01G263500 chr6D 80.769 156 17 11 1747 1893 229413525 229413374 2.540000e-20 110.0
7 TraesCS3D01G263500 chr6D 89.157 83 9 0 1534 1616 230778597 230778679 1.180000e-18 104.0
8 TraesCS3D01G263500 chr6D 87.500 88 11 0 1532 1619 58245461 58245374 4.250000e-18 102.0
9 TraesCS3D01G263500 chr4B 89.535 86 9 0 1531 1616 270831668 270831753 2.540000e-20 110.0
10 TraesCS3D01G263500 chr1A 89.535 86 9 0 1537 1622 292767987 292767902 2.540000e-20 110.0
11 TraesCS3D01G263500 chr1A 87.952 83 10 0 1531 1613 148958977 148958895 5.500000e-17 99.0
12 TraesCS3D01G263500 chr6A 87.500 88 10 1 1532 1619 73562077 73561991 1.530000e-17 100.0
13 TraesCS3D01G263500 chr4A 87.209 86 11 0 1531 1616 340508470 340508555 5.500000e-17 99.0


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 TraesCS3D01G263500 chr3D 365525235 365527651 2416 True 4464 4464 100.000 1 2417 1 chr3D.!!$R1 2416
1 TraesCS3D01G263500 chr3B 476035295 476037697 2402 True 3376 3376 92.065 1 2417 1 chr3B.!!$R2 2416
2 TraesCS3D01G263500 chr3A 487441987 487444751 2764 True 861 1160 90.958 1 2417 3 chr3A.!!$R1 2416

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
849 911 0.103937 GCAGAGGAGTTGGAGGATCG 59.896 60.0 0.0 0.0 34.37 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2008 2595 0.397941 CCGGGCATGACTATGGATGT 59.602 55.0 0.0 0.0 34.79 3.06 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
215 216 1.451747 GCGACCTCGACCTAGACCT 60.452 63.158 0.00 0.00 43.02 3.85
227 228 1.583495 CTAGACCTGTGGTGCGACGA 61.583 60.000 0.00 0.00 35.25 4.20
255 256 1.997874 CCCCCTCTCCCTTGACCTG 60.998 68.421 0.00 0.00 0.00 4.00
372 373 4.456253 GGCGAGCGAGAACGACGA 62.456 66.667 0.00 0.00 42.66 4.20
426 427 4.686437 CTGGTGGGGGTGGGGGTA 62.686 72.222 0.00 0.00 0.00 3.69
703 764 2.239201 GCTCAAAACCAAACGCGATAC 58.761 47.619 15.93 0.00 0.00 2.24
728 789 3.833304 GCCCATACAGAAGGCAGC 58.167 61.111 0.00 0.00 46.34 5.25
729 790 1.077501 GCCCATACAGAAGGCAGCA 60.078 57.895 0.00 0.00 46.34 4.41
730 791 0.680921 GCCCATACAGAAGGCAGCAA 60.681 55.000 0.00 0.00 46.34 3.91
731 792 1.098050 CCCATACAGAAGGCAGCAAC 58.902 55.000 0.00 0.00 0.00 4.17
732 793 1.614051 CCCATACAGAAGGCAGCAACA 60.614 52.381 0.00 0.00 0.00 3.33
734 795 2.557924 CCATACAGAAGGCAGCAACAAA 59.442 45.455 0.00 0.00 0.00 2.83
735 796 3.005684 CCATACAGAAGGCAGCAACAAAA 59.994 43.478 0.00 0.00 0.00 2.44
736 797 4.501229 CCATACAGAAGGCAGCAACAAAAA 60.501 41.667 0.00 0.00 0.00 1.94
737 798 2.892374 ACAGAAGGCAGCAACAAAAAC 58.108 42.857 0.00 0.00 0.00 2.43
738 799 2.204237 CAGAAGGCAGCAACAAAAACC 58.796 47.619 0.00 0.00 0.00 3.27
739 800 1.830477 AGAAGGCAGCAACAAAAACCA 59.170 42.857 0.00 0.00 0.00 3.67
740 801 1.933181 GAAGGCAGCAACAAAAACCAC 59.067 47.619 0.00 0.00 0.00 4.16
742 803 0.813610 GGCAGCAACAAAAACCACCC 60.814 55.000 0.00 0.00 0.00 4.61
746 807 3.342719 CAGCAACAAAAACCACCCTTTT 58.657 40.909 0.00 0.00 0.00 2.27
747 808 3.126686 CAGCAACAAAAACCACCCTTTTG 59.873 43.478 6.51 6.51 45.26 2.44
748 809 2.159448 GCAACAAAAACCACCCTTTTGC 60.159 45.455 7.71 0.00 44.17 3.68
749 810 3.342719 CAACAAAAACCACCCTTTTGCT 58.657 40.909 7.71 0.00 44.17 3.91
750 811 3.712016 ACAAAAACCACCCTTTTGCTT 57.288 38.095 7.71 0.00 44.17 3.91
751 812 4.027674 ACAAAAACCACCCTTTTGCTTT 57.972 36.364 7.71 0.00 44.17 3.51
752 813 4.402829 ACAAAAACCACCCTTTTGCTTTT 58.597 34.783 7.71 0.00 44.17 2.27
753 814 4.217334 ACAAAAACCACCCTTTTGCTTTTG 59.783 37.500 7.71 0.00 44.17 2.44
754 815 2.708216 AACCACCCTTTTGCTTTTGG 57.292 45.000 0.00 0.00 0.00 3.28
820 882 0.733223 GTCTCCGAGTCGAACAAGGC 60.733 60.000 15.64 3.64 0.00 4.35
840 902 1.274712 CAGGGAGAAGCAGAGGAGTT 58.725 55.000 0.00 0.00 0.00 3.01
844 906 1.206849 GGAGAAGCAGAGGAGTTGGAG 59.793 57.143 0.00 0.00 0.00 3.86
845 907 1.206849 GAGAAGCAGAGGAGTTGGAGG 59.793 57.143 0.00 0.00 0.00 4.30
846 908 1.203237 AGAAGCAGAGGAGTTGGAGGA 60.203 52.381 0.00 0.00 0.00 3.71
847 909 1.836802 GAAGCAGAGGAGTTGGAGGAT 59.163 52.381 0.00 0.00 0.00 3.24
848 910 1.494960 AGCAGAGGAGTTGGAGGATC 58.505 55.000 0.00 0.00 0.00 3.36
849 911 0.103937 GCAGAGGAGTTGGAGGATCG 59.896 60.000 0.00 0.00 34.37 3.69
850 912 0.749649 CAGAGGAGTTGGAGGATCGG 59.250 60.000 0.00 0.00 34.37 4.18
851 913 0.397816 AGAGGAGTTGGAGGATCGGG 60.398 60.000 0.00 0.00 34.37 5.14
852 914 0.397254 GAGGAGTTGGAGGATCGGGA 60.397 60.000 0.00 0.00 34.37 5.14
853 915 0.688087 AGGAGTTGGAGGATCGGGAC 60.688 60.000 0.00 0.00 34.37 4.46
854 916 0.976073 GGAGTTGGAGGATCGGGACA 60.976 60.000 0.00 0.00 34.37 4.02
855 917 0.175989 GAGTTGGAGGATCGGGACAC 59.824 60.000 0.00 0.00 34.37 3.67
856 918 1.221021 GTTGGAGGATCGGGACACC 59.779 63.158 0.00 0.00 34.37 4.16
901 964 2.901042 GGTAGCCACCTCCCTTCG 59.099 66.667 0.00 0.00 42.11 3.79
902 965 1.988406 GGTAGCCACCTCCCTTCGT 60.988 63.158 0.00 0.00 42.11 3.85
903 966 0.685458 GGTAGCCACCTCCCTTCGTA 60.685 60.000 0.00 0.00 42.11 3.43
904 967 0.745468 GTAGCCACCTCCCTTCGTAG 59.255 60.000 0.00 0.00 0.00 3.51
905 968 0.333993 TAGCCACCTCCCTTCGTAGT 59.666 55.000 0.00 0.00 0.00 2.73
906 969 0.544595 AGCCACCTCCCTTCGTAGTT 60.545 55.000 0.00 0.00 0.00 2.24
907 970 0.108281 GCCACCTCCCTTCGTAGTTC 60.108 60.000 0.00 0.00 0.00 3.01
924 987 4.305989 AGTTCGTACACAGGACGTAAAA 57.694 40.909 1.34 0.00 41.11 1.52
925 988 4.874970 AGTTCGTACACAGGACGTAAAAT 58.125 39.130 1.34 0.00 41.11 1.82
927 990 6.446318 AGTTCGTACACAGGACGTAAAATAA 58.554 36.000 1.34 0.00 41.11 1.40
928 991 6.363357 AGTTCGTACACAGGACGTAAAATAAC 59.637 38.462 1.34 0.00 41.11 1.89
1458 1544 4.838986 AGCAAGAGGAAGAGTTTAGGTACA 59.161 41.667 0.00 0.00 0.00 2.90
1465 1551 5.041940 GGAAGAGTTTAGGTACATGCTACG 58.958 45.833 0.00 0.00 0.00 3.51
1500 1586 7.277981 CAGACATGGTATACTTTGAGGTGTTAC 59.722 40.741 2.25 0.00 0.00 2.50
1623 1711 1.333619 CGAACAAAGGGTGGACTTGTG 59.666 52.381 0.00 0.00 0.00 3.33
1683 1771 6.591935 TCTCGCTTTTGGAATGGATTACTAT 58.408 36.000 0.00 0.00 0.00 2.12
1695 2280 9.825109 GGAATGGATTACTATTAAGGAGATAGC 57.175 37.037 0.00 0.00 31.67 2.97
1718 2303 3.393089 TGCCACCGCAAAATGTTAAAT 57.607 38.095 0.00 0.00 43.74 1.40
1725 2310 7.063544 GCCACCGCAAAATGTTAAATTTATGTA 59.936 33.333 0.00 0.00 34.03 2.29
1759 2344 5.066593 TGTGTGTGAATTGTGCTATGGTTA 58.933 37.500 0.00 0.00 0.00 2.85
1775 2360 7.172532 TGCTATGGTTAGATTTGTAATTAGCGG 59.827 37.037 0.00 0.00 0.00 5.52
1813 2398 1.067425 TCGAACATGTGTAACCCGAGG 60.067 52.381 0.00 0.00 34.36 4.63
1829 2414 3.511934 CCCGAGGCTAATATAAGAGCACT 59.488 47.826 10.45 5.99 40.64 4.40
1867 2453 5.127356 AGTGACTAGGCATAAGTTGTAGACC 59.873 44.000 0.00 0.00 0.00 3.85
1889 2476 1.276421 AGACAAATCACCAGAGGACGG 59.724 52.381 0.00 0.00 0.00 4.79
1960 2547 2.887568 GCAGTCTGACGGCATCGG 60.888 66.667 24.59 0.00 39.14 4.18
1976 2563 1.887707 CGGCAGGTTTATCCTCGGC 60.888 63.158 0.00 0.00 46.24 5.54
2030 2617 0.473694 TCCATAGTCATGCCCGGGAT 60.474 55.000 29.31 12.55 0.00 3.85
2035 2622 1.302832 GTCATGCCCGGGATGGATC 60.303 63.158 29.31 5.43 42.00 3.36
2057 2644 6.295039 TCCACGTTAACAAATTTCACTCTC 57.705 37.500 6.39 0.00 0.00 3.20
2087 2674 5.468746 TGTACTTGTGTTATTGCTTGTCCTC 59.531 40.000 0.00 0.00 0.00 3.71
2090 2677 3.937814 TGTGTTATTGCTTGTCCTCGAT 58.062 40.909 0.00 0.00 0.00 3.59
2110 2697 4.129737 ATCGACGTGCACCCTCGG 62.130 66.667 24.03 9.00 32.62 4.63
2112 2699 4.129737 CGACGTGCACCCTCGGAT 62.130 66.667 19.25 0.00 32.62 4.18
2301 2892 6.432162 AGTTTCACTTGCAGACATCATGTTAT 59.568 34.615 0.00 0.00 0.00 1.89
2331 2922 7.931407 ACCTAGAAATTTTAGGCAAAACTTTGG 59.069 33.333 18.59 6.94 41.16 3.28
2344 2935 5.500131 GCAAAACTTTGGTCGTGTTCATTTC 60.500 40.000 4.45 0.00 38.57 2.17
2361 2952 9.912634 TGTTCATTTCCAGAGTATCAATTTTTC 57.087 29.630 0.00 0.00 37.82 2.29
2409 3000 5.787953 TTCCATGATGAAAGTTTGCAAGA 57.212 34.783 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 4.327885 CCGTCATAGCTCGAAGGC 57.672 61.111 5.33 0.00 0.00 4.35
215 216 4.961511 GCAGGTCGTCGCACCACA 62.962 66.667 13.85 0.00 39.16 4.17
721 782 1.406751 GGTGGTTTTTGTTGCTGCCTT 60.407 47.619 0.00 0.00 0.00 4.35
722 783 0.177836 GGTGGTTTTTGTTGCTGCCT 59.822 50.000 0.00 0.00 0.00 4.75
726 787 3.342719 CAAAAGGGTGGTTTTTGTTGCT 58.657 40.909 3.06 0.00 39.49 3.91
728 789 3.342719 AGCAAAAGGGTGGTTTTTGTTG 58.657 40.909 10.88 0.00 43.80 3.33
729 790 3.712016 AGCAAAAGGGTGGTTTTTGTT 57.288 38.095 10.88 3.82 43.80 2.83
730 791 3.712016 AAGCAAAAGGGTGGTTTTTGT 57.288 38.095 10.88 0.00 43.80 2.83
735 796 2.192263 TCCAAAAGCAAAAGGGTGGTT 58.808 42.857 0.00 0.00 40.84 3.67
736 797 1.872773 TCCAAAAGCAAAAGGGTGGT 58.127 45.000 0.00 0.00 0.00 4.16
737 798 2.998316 TTCCAAAAGCAAAAGGGTGG 57.002 45.000 0.00 0.00 0.00 4.61
738 799 3.871006 GTCTTTCCAAAAGCAAAAGGGTG 59.129 43.478 0.00 0.00 32.20 4.61
739 800 3.774766 AGTCTTTCCAAAAGCAAAAGGGT 59.225 39.130 0.00 0.00 32.20 4.34
740 801 4.141959 TGAGTCTTTCCAAAAGCAAAAGGG 60.142 41.667 0.00 0.00 32.20 3.95
742 803 6.456047 GCTTTGAGTCTTTCCAAAAGCAAAAG 60.456 38.462 14.97 3.44 32.63 2.27
746 807 3.181476 GGCTTTGAGTCTTTCCAAAAGCA 60.181 43.478 19.22 0.00 32.63 3.91
747 808 3.384668 GGCTTTGAGTCTTTCCAAAAGC 58.615 45.455 12.59 12.59 32.63 3.51
748 809 3.384467 TGGGCTTTGAGTCTTTCCAAAAG 59.616 43.478 0.00 0.00 32.63 2.27
749 810 3.370104 TGGGCTTTGAGTCTTTCCAAAA 58.630 40.909 0.00 0.00 32.63 2.44
750 811 2.958355 CTGGGCTTTGAGTCTTTCCAAA 59.042 45.455 0.00 0.00 0.00 3.28
751 812 2.586425 CTGGGCTTTGAGTCTTTCCAA 58.414 47.619 0.00 0.00 0.00 3.53
752 813 1.819305 GCTGGGCTTTGAGTCTTTCCA 60.819 52.381 0.00 0.00 0.00 3.53
753 814 0.884514 GCTGGGCTTTGAGTCTTTCC 59.115 55.000 0.00 0.00 0.00 3.13
754 815 1.809547 GAGCTGGGCTTTGAGTCTTTC 59.190 52.381 0.00 0.00 39.88 2.62
820 882 0.617249 ACTCCTCTGCTTCTCCCTGG 60.617 60.000 0.00 0.00 0.00 4.45
860 922 1.324740 TTATCCCTGGTCCGGTCACG 61.325 60.000 0.00 0.00 40.55 4.35
861 923 0.906775 TTTATCCCTGGTCCGGTCAC 59.093 55.000 0.00 0.00 0.00 3.67
862 924 1.766496 GATTTATCCCTGGTCCGGTCA 59.234 52.381 0.00 0.09 0.00 4.02
863 925 1.766496 TGATTTATCCCTGGTCCGGTC 59.234 52.381 0.00 0.00 0.00 4.79
900 963 1.195448 ACGTCCTGTGTACGAACTACG 59.805 52.381 2.27 7.92 42.90 3.51
901 964 2.977405 ACGTCCTGTGTACGAACTAC 57.023 50.000 2.27 0.00 42.90 2.73
902 965 5.431420 TTTTACGTCCTGTGTACGAACTA 57.569 39.130 0.00 0.00 42.90 2.24
903 966 3.988379 TTTACGTCCTGTGTACGAACT 57.012 42.857 0.00 0.00 42.90 3.01
904 967 6.363357 AGTTATTTTACGTCCTGTGTACGAAC 59.637 38.462 0.00 0.00 42.90 3.95
905 968 6.446318 AGTTATTTTACGTCCTGTGTACGAA 58.554 36.000 0.00 0.00 42.90 3.85
906 969 6.012658 AGTTATTTTACGTCCTGTGTACGA 57.987 37.500 0.00 0.00 42.90 3.43
907 970 6.695292 AAGTTATTTTACGTCCTGTGTACG 57.305 37.500 0.00 0.00 45.64 3.67
924 987 6.572314 GCCACCAGCAAGATAACAAAAGTTAT 60.572 38.462 0.84 0.84 42.97 1.89
925 988 5.278758 GCCACCAGCAAGATAACAAAAGTTA 60.279 40.000 0.00 0.00 42.97 2.24
927 990 3.005791 GCCACCAGCAAGATAACAAAAGT 59.994 43.478 0.00 0.00 42.97 2.66
928 991 3.578688 GCCACCAGCAAGATAACAAAAG 58.421 45.455 0.00 0.00 42.97 2.27
1458 1544 1.100510 TCTGAAGCCGTACGTAGCAT 58.899 50.000 15.21 4.11 0.00 3.79
1465 1551 2.953466 TACCATGTCTGAAGCCGTAC 57.047 50.000 0.00 0.00 0.00 3.67
1623 1711 6.381481 TGATTCACATAATCACATTGAGCC 57.619 37.500 0.00 0.00 32.21 4.70
1683 1771 3.744214 CGGTGGCAATGCTATCTCCTTAA 60.744 47.826 4.82 0.00 0.00 1.85
1725 2310 9.304731 GCACAATTCACACACATAATATTTGAT 57.695 29.630 0.00 0.00 0.00 2.57
1759 2344 6.766467 CCTAACCTTCCGCTAATTACAAATCT 59.234 38.462 0.00 0.00 0.00 2.40
1775 2360 3.986277 TCGACTCAAACACCTAACCTTC 58.014 45.455 0.00 0.00 0.00 3.46
1813 2398 2.996621 CCCGCAGTGCTCTTATATTAGC 59.003 50.000 14.33 0.90 39.25 3.09
1829 2414 1.134037 AGTCACTTTTGGTTACCCGCA 60.134 47.619 0.00 0.00 0.00 5.69
1840 2425 7.603024 GTCTACAACTTATGCCTAGTCACTTTT 59.397 37.037 0.00 0.00 0.00 2.27
1841 2426 7.097834 GTCTACAACTTATGCCTAGTCACTTT 58.902 38.462 0.00 0.00 0.00 2.66
1867 2453 2.738846 CGTCCTCTGGTGATTTGTCTTG 59.261 50.000 0.00 0.00 0.00 3.02
1944 2531 2.887568 GCCGATGCCGTCAGACTG 60.888 66.667 0.00 0.00 0.00 3.51
2008 2595 0.397941 CCGGGCATGACTATGGATGT 59.602 55.000 0.00 0.00 34.79 3.06
2030 2617 5.533154 AGTGAAATTTGTTAACGTGGATCCA 59.467 36.000 11.44 11.44 0.00 3.41
2035 2622 5.137403 CGAGAGTGAAATTTGTTAACGTGG 58.863 41.667 0.00 0.00 0.00 4.94
2057 2644 3.906008 GCAATAACACAAGTACAAGCACG 59.094 43.478 0.00 0.00 0.00 5.34
2090 2677 2.994995 AGGGTGCACGTCGATCCA 60.995 61.111 11.45 0.00 0.00 3.41
2097 2684 0.539986 AATAATCCGAGGGTGCACGT 59.460 50.000 11.45 0.00 0.00 4.49
2182 2771 9.862149 AAAAACCATATATTCTCCGAAACCTAT 57.138 29.630 0.00 0.00 0.00 2.57
2217 2808 5.647230 TCGGTTAACCATATATCCTCCAGA 58.353 41.667 24.14 5.76 35.14 3.86
2285 2876 5.744171 AGGTACAATAACATGATGTCTGCA 58.256 37.500 0.00 0.00 0.00 4.41
2301 2892 9.138596 AGTTTTGCCTAAAATTTCTAGGTACAA 57.861 29.630 19.14 14.37 38.59 2.41
2331 2922 5.168569 TGATACTCTGGAAATGAACACGAC 58.831 41.667 0.00 0.00 0.00 4.34
2344 2935 6.587608 GTGGCAAAGAAAAATTGATACTCTGG 59.412 38.462 0.00 0.00 0.00 3.86
2361 2952 2.956987 CTGGAAGGCGTGGCAAAG 59.043 61.111 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.