Multiple sequence alignment - TraesCS1D01G121500

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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 TraesCS1D01G121500 chr1D 100.000 3161 0 0 1 3161 121307926 121311086 0.000000e+00 5838.0
1 TraesCS1D01G121500 chr1D 83.777 826 82 27 1 787 482501626 482502438 0.000000e+00 736.0
2 TraesCS1D01G121500 chr1A 94.286 2380 99 13 794 3152 133126006 133128369 0.000000e+00 3607.0
3 TraesCS1D01G121500 chr1B 93.992 2014 86 8 1170 3161 184741849 184743849 0.000000e+00 3016.0
4 TraesCS1D01G121500 chr1B 91.089 101 8 1 805 905 184741578 184741677 5.500000e-28 135.0
5 TraesCS1D01G121500 chr7A 87.361 807 67 18 1 793 39272740 39273525 0.000000e+00 893.0
6 TraesCS1D01G121500 chr6D 100.000 28 0 0 866 893 455092677 455092704 6.000000e-03 52.8
7 TraesCS1D01G121500 chr6D 100.000 28 0 0 866 893 455093636 455093663 6.000000e-03 52.8


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 TraesCS1D01G121500 chr1D 121307926 121311086 3160 False 5838.0 5838 100.0000 1 3161 1 chr1D.!!$F1 3160
1 TraesCS1D01G121500 chr1D 482501626 482502438 812 False 736.0 736 83.7770 1 787 1 chr1D.!!$F2 786
2 TraesCS1D01G121500 chr1A 133126006 133128369 2363 False 3607.0 3607 94.2860 794 3152 1 chr1A.!!$F1 2358
3 TraesCS1D01G121500 chr1B 184741578 184743849 2271 False 1575.5 3016 92.5405 805 3161 2 chr1B.!!$F1 2356
4 TraesCS1D01G121500 chr7A 39272740 39273525 785 False 893.0 893 87.3610 1 793 1 chr7A.!!$F1 792

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
305 317 0.044855 AGACAGAGGCCAATAGGGGT 59.955 55.0 5.01 0.0 37.04 4.95 F
891 979 0.466007 TGATGCATCGGGTTGGATGG 60.466 55.0 21.34 0.0 43.19 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 1998 1.129624 TCGTGCAAATTGTATGCGACC 59.870 47.619 0.0 0.0 46.76 4.79 R
2872 2993 0.458669 CTGATGCTCCACCCAAATGC 59.541 55.000 0.0 0.0 0.00 3.56 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
51 52 7.626664 GCCGTCTATAGATTGTATCTCATCGTT 60.627 40.741 5.57 0.00 40.76 3.85
220 223 2.266055 CAACTCCAGAGGCCGACC 59.734 66.667 0.00 0.00 0.00 4.79
305 317 0.044855 AGACAGAGGCCAATAGGGGT 59.955 55.000 5.01 0.00 37.04 4.95
354 366 1.202879 ACCACACGGTTCATCACCAAT 60.203 47.619 0.00 0.00 46.31 3.16
402 414 1.225426 GCTGGCCACATGGATCTGA 59.775 57.895 0.00 0.00 37.39 3.27
446 464 3.431725 CTTGGGCCGTTTCGCTCC 61.432 66.667 0.00 0.00 0.00 4.70
556 595 1.131303 AGGGATCCAACGGTTGACCA 61.131 55.000 21.88 6.07 35.14 4.02
558 597 1.305930 GGATCCAACGGTTGACCAGC 61.306 60.000 21.88 8.07 35.14 4.85
561 600 1.525995 CCAACGGTTGACCAGCAGT 60.526 57.895 21.88 0.00 35.14 4.40
610 650 4.635223 GGAATGGATCTCGTGATGATCAA 58.365 43.478 4.41 0.00 41.35 2.57
625 665 3.595173 TGATCAACCGTACAATCACCTG 58.405 45.455 0.00 0.00 0.00 4.00
627 667 1.972075 TCAACCGTACAATCACCTGGA 59.028 47.619 0.00 0.00 0.00 3.86
646 716 1.277557 GAGGAGAAGCAGCAAGGAGAA 59.722 52.381 0.00 0.00 0.00 2.87
739 826 3.394635 GAGGCCGGCGAATGGGTTA 62.395 63.158 22.54 0.00 0.00 2.85
754 841 2.822255 TTATTGCGGTGGAGGCGC 60.822 61.111 0.00 0.00 0.00 6.53
891 979 0.466007 TGATGCATCGGGTTGGATGG 60.466 55.000 21.34 0.00 43.19 3.51
911 999 6.603599 GGATGGCCAACTCTCTTAAAACTATT 59.396 38.462 10.96 0.00 0.00 1.73
925 1013 4.419522 AAACTATTCGTGGACATGTTGC 57.580 40.909 0.00 0.00 0.00 4.17
931 1019 3.454941 GTGGACATGTTGCACGAAC 57.545 52.632 0.00 0.00 36.75 3.95
961 1051 3.187842 GTGTTCGTTTTGATGTAGGACCC 59.812 47.826 0.00 0.00 0.00 4.46
968 1058 5.878116 CGTTTTGATGTAGGACCCTGATAAA 59.122 40.000 0.00 0.00 0.00 1.40
976 1066 3.924922 AGGACCCTGATAAATACCGAGT 58.075 45.455 0.00 0.00 0.00 4.18
993 1083 2.971915 CGAGTGTCAAGTACGAGAACAC 59.028 50.000 12.83 12.83 0.00 3.32
1016 1106 4.390603 CGACAACTCCGAACATTTTGGATA 59.609 41.667 0.00 0.00 42.31 2.59
1026 1116 7.040340 TCCGAACATTTTGGATAGCAAGTTTAA 60.040 33.333 0.00 0.00 38.32 1.52
1030 1120 9.995003 AACATTTTGGATAGCAAGTTTAATGAA 57.005 25.926 0.00 0.00 0.00 2.57
1042 1132 3.938963 AGTTTAATGAACGCGATGGTGAT 59.061 39.130 15.93 0.00 43.20 3.06
1161 1252 3.659786 TGTCATCGAAAAACCGAGTGAT 58.340 40.909 0.00 0.00 42.21 3.06
1198 1295 8.413229 GCACTTGTAATTTGGGTTGATGTATAT 58.587 33.333 0.00 0.00 0.00 0.86
1213 1310 5.469760 TGATGTATATTGTTGAAGATGCCCG 59.530 40.000 0.00 0.00 0.00 6.13
1214 1311 4.133820 TGTATATTGTTGAAGATGCCCGG 58.866 43.478 0.00 0.00 0.00 5.73
1217 1314 2.214376 TTGTTGAAGATGCCCGGAAT 57.786 45.000 0.73 0.00 0.00 3.01
1362 1466 2.915659 ACGAACGCCAGACCTCCA 60.916 61.111 0.00 0.00 0.00 3.86
1479 1583 2.501610 GAAGCGCGGGAGGAGATT 59.498 61.111 8.83 0.00 0.00 2.40
1816 1930 7.791029 TCTGATTGGGAAATAAAATTAAGGCC 58.209 34.615 0.00 0.00 0.00 5.19
1867 1981 1.667236 TGGAGCTAATTGTCCATGCG 58.333 50.000 2.68 0.00 37.96 4.73
1887 2001 3.062504 GCGGATGCAAATTGAAATTGGTC 59.937 43.478 0.00 0.00 42.15 4.02
2244 2358 6.303839 TCTGTAGTAATGCTTGGGAAAACTT 58.696 36.000 0.00 0.00 0.00 2.66
2271 2385 6.802348 CAGCTTTTGATGACATCTTTTCTGAG 59.198 38.462 16.25 6.20 38.24 3.35
2564 2683 8.475639 CATTCATTCCTTTCTTTCCAGATTGAT 58.524 33.333 0.00 0.00 0.00 2.57
2584 2704 3.118454 CCAACGAGCGCCACGATT 61.118 61.111 26.37 15.56 34.70 3.34
2840 2961 1.676014 GGTTATCCGCAGTTCAGCACT 60.676 52.381 0.00 0.00 35.35 4.40
2866 2987 0.807496 GCCAAGCTAGCCAAGTGAAG 59.193 55.000 12.13 0.00 0.00 3.02
2930 3051 4.192429 GCAAAAGGTGGCTTGATACAAT 57.808 40.909 0.00 0.00 0.00 2.71
3012 3133 2.825836 CAATGAGTCCGGCTGGCC 60.826 66.667 6.73 0.00 34.14 5.36
3098 3219 3.518705 AGTCAGATCAGCCTTGAAGTGAT 59.481 43.478 0.00 0.00 36.78 3.06
3146 3267 5.007626 GCATCTTTAATTGTGATCCTACGCA 59.992 40.000 0.00 0.00 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 1.490490 ACTCTGGCCAGTTTGTCTTCA 59.510 47.619 31.58 8.74 0.00 3.02
277 289 1.007118 TGGCCTCTGTCTGACCTATGA 59.993 52.381 3.32 0.00 0.00 2.15
285 297 0.471617 CCCCTATTGGCCTCTGTCTG 59.528 60.000 3.32 0.00 0.00 3.51
305 317 1.223487 GGCTTAGCGTTGGATGGGA 59.777 57.895 0.00 0.00 0.00 4.37
402 414 1.178276 CTGTCTCTAGCCCGTCTGTT 58.822 55.000 0.00 0.00 0.00 3.16
460 478 3.019003 AATCTGACGGGTCTGGCCG 62.019 63.158 0.00 0.00 38.44 6.13
461 479 1.450312 CAATCTGACGGGTCTGGCC 60.450 63.158 0.00 0.00 0.00 5.36
462 480 1.450312 CCAATCTGACGGGTCTGGC 60.450 63.158 5.97 0.00 0.00 4.85
546 569 0.830444 TCCTACTGCTGGTCAACCGT 60.830 55.000 0.00 0.00 39.43 4.83
556 595 2.358267 GCTACGTGTATGTCCTACTGCT 59.642 50.000 0.00 0.00 0.00 4.24
558 597 2.686405 TGGCTACGTGTATGTCCTACTG 59.314 50.000 0.00 0.00 0.00 2.74
561 600 3.131577 CCTTTGGCTACGTGTATGTCCTA 59.868 47.826 0.00 0.00 0.00 2.94
592 632 2.223805 CGGTTGATCATCACGAGATCCA 60.224 50.000 0.00 0.00 40.87 3.41
610 650 0.902531 CCTCCAGGTGATTGTACGGT 59.097 55.000 0.00 0.00 0.00 4.83
625 665 0.107752 CTCCTTGCTGCTTCTCCTCC 60.108 60.000 0.00 0.00 0.00 4.30
627 667 1.356124 TTCTCCTTGCTGCTTCTCCT 58.644 50.000 0.00 0.00 0.00 3.69
646 716 3.541713 GGCGGCGGGATCTCTCTT 61.542 66.667 9.78 0.00 0.00 2.85
690 760 3.770040 CGCCGGTCATCACCTCCA 61.770 66.667 1.90 0.00 41.17 3.86
716 786 3.541713 ATTCGCCGGCCTCTCCTC 61.542 66.667 23.46 0.00 0.00 3.71
717 787 3.854669 CATTCGCCGGCCTCTCCT 61.855 66.667 23.46 0.00 0.00 3.69
718 788 4.918201 CCATTCGCCGGCCTCTCC 62.918 72.222 23.46 0.00 0.00 3.71
719 789 4.918201 CCCATTCGCCGGCCTCTC 62.918 72.222 23.46 0.00 0.00 3.20
721 791 2.676163 ATAACCCATTCGCCGGCCTC 62.676 60.000 23.46 0.00 0.00 4.70
722 792 2.279037 AATAACCCATTCGCCGGCCT 62.279 55.000 23.46 2.24 0.00 5.19
723 793 1.826487 AATAACCCATTCGCCGGCC 60.826 57.895 23.46 2.84 0.00 6.13
724 794 1.358759 CAATAACCCATTCGCCGGC 59.641 57.895 19.07 19.07 0.00 6.13
725 795 1.358759 GCAATAACCCATTCGCCGG 59.641 57.895 0.00 0.00 0.00 6.13
726 796 1.010125 CGCAATAACCCATTCGCCG 60.010 57.895 0.00 0.00 0.00 6.46
727 797 1.358759 CCGCAATAACCCATTCGCC 59.641 57.895 0.00 0.00 0.00 5.54
728 798 0.248458 CACCGCAATAACCCATTCGC 60.248 55.000 0.00 0.00 0.00 4.70
729 799 0.380378 CCACCGCAATAACCCATTCG 59.620 55.000 0.00 0.00 0.00 3.34
732 802 0.106719 CCTCCACCGCAATAACCCAT 60.107 55.000 0.00 0.00 0.00 4.00
803 890 9.238368 CAAAAGTTAAGGGTCTTTATCCATGTA 57.762 33.333 0.00 0.00 34.14 2.29
859 947 6.183360 ACCCGATGCATCAAATAAAATTGGAT 60.183 34.615 25.70 0.00 0.00 3.41
891 979 6.402226 CCACGAATAGTTTTAAGAGAGTTGGC 60.402 42.308 0.00 0.00 0.00 4.52
896 984 7.545965 ACATGTCCACGAATAGTTTTAAGAGAG 59.454 37.037 0.00 0.00 0.00 3.20
929 1017 2.570442 AAACGAACACGGCAAATGTT 57.430 40.000 0.00 0.00 42.95 2.71
931 1019 2.455032 TCAAAACGAACACGGCAAATG 58.545 42.857 0.00 0.00 0.00 2.32
941 1031 3.435671 CAGGGTCCTACATCAAAACGAAC 59.564 47.826 0.00 0.00 0.00 3.95
944 1034 3.328382 TCAGGGTCCTACATCAAAACG 57.672 47.619 0.00 0.00 0.00 3.60
961 1051 6.414109 CGTACTTGACACTCGGTATTTATCAG 59.586 42.308 0.00 0.00 0.00 2.90
968 1058 3.603532 TCTCGTACTTGACACTCGGTAT 58.396 45.455 0.00 0.00 0.00 2.73
976 1066 2.355444 TGTCGTGTTCTCGTACTTGACA 59.645 45.455 0.00 0.00 33.58 3.58
993 1083 2.546368 TCCAAAATGTTCGGAGTTGTCG 59.454 45.455 0.00 0.00 0.00 4.35
1016 1106 3.426159 CCATCGCGTTCATTAAACTTGCT 60.426 43.478 5.77 0.00 35.59 3.91
1026 1116 2.210116 GGTTATCACCATCGCGTTCAT 58.790 47.619 5.77 0.00 43.61 2.57
1067 1157 8.525071 CGTCAAAAATAAACTAAAGCACGAAAA 58.475 29.630 0.00 0.00 0.00 2.29
1101 1192 8.561738 AATAGCAAATTTGGTAGGGTATATCG 57.438 34.615 28.16 0.00 43.44 2.92
1108 1199 5.587043 TCACGTAATAGCAAATTTGGTAGGG 59.413 40.000 28.16 18.69 43.44 3.53
1161 1252 5.950758 AATTACAAGTGCCACAATTCGTA 57.049 34.783 0.00 0.00 0.00 3.43
1198 1295 2.214376 ATTCCGGGCATCTTCAACAA 57.786 45.000 0.00 0.00 0.00 2.83
1213 1310 1.413077 CTCCTTCCCTGTCGGTATTCC 59.587 57.143 0.00 0.00 0.00 3.01
1214 1311 2.385803 TCTCCTTCCCTGTCGGTATTC 58.614 52.381 0.00 0.00 0.00 1.75
1217 1314 1.618888 CCTTCTCCTTCCCTGTCGGTA 60.619 57.143 0.00 0.00 0.00 4.02
1306 1410 3.866582 GGTGGGGCGGAGGAGATG 61.867 72.222 0.00 0.00 0.00 2.90
1479 1583 2.672908 CTGTCCATGGCAGCCTCA 59.327 61.111 19.00 3.60 0.00 3.86
1816 1930 2.095263 CCCACAACAGGAATAAAGTGCG 60.095 50.000 0.00 0.00 0.00 5.34
1867 1981 3.062504 GCGACCAATTTCAATTTGCATCC 59.937 43.478 0.00 0.00 0.00 3.51
1879 1993 4.388469 GTGCAAATTGTATGCGACCAATTT 59.612 37.500 11.83 11.83 46.66 1.82
1880 1994 3.925913 GTGCAAATTGTATGCGACCAATT 59.074 39.130 0.00 2.51 46.76 2.32
1881 1995 3.510719 GTGCAAATTGTATGCGACCAAT 58.489 40.909 0.00 0.00 46.76 3.16
1882 1996 2.666895 CGTGCAAATTGTATGCGACCAA 60.667 45.455 0.00 0.00 46.76 3.67
1883 1997 1.135831 CGTGCAAATTGTATGCGACCA 60.136 47.619 0.00 0.00 46.76 4.02
1884 1998 1.129624 TCGTGCAAATTGTATGCGACC 59.870 47.619 0.00 0.00 46.76 4.79
1887 2001 1.182673 GCTCGTGCAAATTGTATGCG 58.817 50.000 4.26 0.00 46.76 4.73
1900 2014 7.540400 TGAACATAAATACCAATTTTGCTCGTG 59.460 33.333 0.00 0.00 36.67 4.35
1980 2094 5.999205 AATATCACAATTGGCACAGGAAA 57.001 34.783 10.83 0.00 42.39 3.13
2244 2358 4.859304 AAAGATGTCATCAAAAGCTGCA 57.141 36.364 15.20 0.00 0.00 4.41
2328 2442 2.164393 AGGTTTAGTGCCTGGGCTT 58.836 52.632 13.05 4.08 42.51 4.35
2372 2486 5.092554 TGTTTCCCCCTTTGTTTTCTTTC 57.907 39.130 0.00 0.00 0.00 2.62
2496 2615 2.746472 GCTCAGTCACCACTTTGTTCCT 60.746 50.000 0.00 0.00 0.00 3.36
2533 2652 5.243730 TGGAAAGAAAGGAATGAATGTGTCC 59.756 40.000 0.00 0.00 0.00 4.02
2584 2704 1.306141 AGCCAAGTCCCGGAGATCA 60.306 57.895 0.73 0.00 0.00 2.92
2668 2789 1.207089 CAACCGGCTAGTCTCATTCCA 59.793 52.381 0.00 0.00 0.00 3.53
2866 2987 1.405933 GCTCCACCCAAATGCCAATTC 60.406 52.381 0.00 0.00 0.00 2.17
2872 2993 0.458669 CTGATGCTCCACCCAAATGC 59.541 55.000 0.00 0.00 0.00 3.56
2930 3051 2.429971 CCTATGCTCTGCACTTCTCAGA 59.570 50.000 0.00 0.00 43.04 3.27
2983 3104 2.877168 GGACTCATTGACATGGATCTGC 59.123 50.000 0.00 0.00 0.00 4.26
2988 3109 0.107703 GCCGGACTCATTGACATGGA 60.108 55.000 5.05 0.00 0.00 3.41
3012 3133 0.249868 TCAGTTTCAGCTCACCACCG 60.250 55.000 0.00 0.00 0.00 4.94
3019 3140 4.260170 ACAATCTCCATCAGTTTCAGCTC 58.740 43.478 0.00 0.00 0.00 4.09
3098 3219 1.808531 GCACAGGACAAATGGCTGCA 61.809 55.000 0.50 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.