Multiple sequence alignment - TraesCS2D01G282100

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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 TraesCS2D01G282100 chr2D 100.000 2315 0 0 1 2315 354969674 354967360 0.000000e+00 4276.0
1 TraesCS2D01G282100 chr2D 98.826 852 10 0 1 852 36399482 36398631 0.000000e+00 1519.0
2 TraesCS2D01G282100 chr3D 98.357 852 14 0 1 852 384648055 384648906 0.000000e+00 1496.0
3 TraesCS2D01G282100 chr2A 97.281 846 21 2 1472 2315 474796337 474795492 0.000000e+00 1434.0
4 TraesCS2D01G282100 chr2A 92.549 510 30 4 969 1474 474796999 474796494 0.000000e+00 725.0
5 TraesCS2D01G282100 chr2A 96.386 83 3 0 862 944 474797074 474796992 1.120000e-28 137.0
6 TraesCS2D01G282100 chrUn 98.489 662 9 1 15 676 470870112 470870772 0.000000e+00 1166.0
7 TraesCS2D01G282100 chr2B 92.035 791 39 11 1490 2270 422509293 422508517 0.000000e+00 1090.0
8 TraesCS2D01G282100 chr2B 90.461 304 9 7 1174 1474 422509796 422509510 1.300000e-102 383.0
9 TraesCS2D01G282100 chr2B 95.364 151 7 0 970 1120 422509946 422509796 8.270000e-60 241.0
10 TraesCS2D01G282100 chr2B 97.872 47 1 0 2269 2315 422508423 422508377 5.300000e-12 82.4
11 TraesCS2D01G282100 chr7D 99.020 306 3 0 1 306 30380372 30380067 1.210000e-152 549.0
12 TraesCS2D01G282100 chr7D 98.693 306 4 0 1 306 30372770 30372465 5.630000e-151 544.0
13 TraesCS2D01G282100 chr7D 98.571 140 2 0 167 306 30375492 30375353 4.940000e-62 248.0
14 TraesCS2D01G282100 chr7D 79.861 144 27 2 505 647 123434838 123434980 1.130000e-18 104.0
15 TraesCS2D01G282100 chr1D 98.397 312 5 0 1 312 463489043 463489354 1.210000e-152 549.0
16 TraesCS2D01G282100 chr4D 97.714 175 4 0 678 852 507939107 507938933 3.740000e-78 302.0
17 TraesCS2D01G282100 chr4D 97.714 175 4 0 678 852 507939208 507939382 3.740000e-78 302.0
18 TraesCS2D01G282100 chr1B 71.894 644 165 12 177 812 528394199 528393564 3.060000e-39 172.0
19 TraesCS2D01G282100 chr7B 78.049 205 36 9 482 681 382625031 382624831 1.120000e-23 121.0
20 TraesCS2D01G282100 chr7A 73.333 330 74 13 487 809 125269544 125269866 2.430000e-20 110.0
21 TraesCS2D01G282100 chr7A 77.037 135 25 5 600 731 5480854 5480723 3.190000e-09 73.1
22 TraesCS2D01G282100 chr6B 77.049 183 38 4 498 678 680169132 680169312 4.070000e-18 102.0


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 TraesCS2D01G282100 chr2D 354967360 354969674 2314 True 4276.000000 4276 100.000000 1 2315 1 chr2D.!!$R2 2314
1 TraesCS2D01G282100 chr2D 36398631 36399482 851 True 1519.000000 1519 98.826000 1 852 1 chr2D.!!$R1 851
2 TraesCS2D01G282100 chr3D 384648055 384648906 851 False 1496.000000 1496 98.357000 1 852 1 chr3D.!!$F1 851
3 TraesCS2D01G282100 chr2A 474795492 474797074 1582 True 765.333333 1434 95.405333 862 2315 3 chr2A.!!$R1 1453
4 TraesCS2D01G282100 chrUn 470870112 470870772 660 False 1166.000000 1166 98.489000 15 676 1 chrUn.!!$F1 661
5 TraesCS2D01G282100 chr2B 422508377 422509946 1569 True 449.100000 1090 93.933000 970 2315 4 chr2B.!!$R1 1345
6 TraesCS2D01G282100 chr7D 30372465 30375492 3027 True 396.000000 544 98.632000 1 306 2 chr7D.!!$R2 305

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
937 3660 1.037493 ACACACCGCACAAGTAGAGA 58.963 50.0 0.0 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 4803 1.136891 CCTGATGTGTGGAGCGACATA 59.863 52.381 0.0 0.0 32.85 2.29 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 2752 3.281332 TGGCAGCCCCAAATACTTC 57.719 52.632 9.64 0.0 41.82 3.01
287 3010 4.627801 TGCAACAACCCGCGCCTA 62.628 61.111 0.00 0.0 0.00 3.93
583 3306 1.452145 TTGCTTTTGTGGAGCCGACC 61.452 55.000 0.00 0.0 39.38 4.79
614 3337 4.000325 CCCGAACATACATGAAGTTGTCA 59.000 43.478 0.00 0.0 41.67 3.58
632 3355 8.114331 AGTTGTCATGAATGCATCTCTTTTTA 57.886 30.769 0.00 0.0 30.68 1.52
741 3464 3.821033 GGCATAAATGAGGCTTATCGGTT 59.179 43.478 0.00 0.0 34.44 4.44
749 3472 4.448210 TGAGGCTTATCGGTTTGTAATCC 58.552 43.478 0.00 0.0 0.00 3.01
852 3575 6.149973 CAGATTGTTGAAACAGAGAATGGCTA 59.850 38.462 0.00 0.0 40.50 3.93
853 3576 6.716628 AGATTGTTGAAACAGAGAATGGCTAA 59.283 34.615 0.00 0.0 40.50 3.09
854 3577 5.689383 TGTTGAAACAGAGAATGGCTAAC 57.311 39.130 0.00 0.0 34.30 2.34
855 3578 5.129634 TGTTGAAACAGAGAATGGCTAACA 58.870 37.500 0.00 0.0 34.30 2.41
856 3579 5.769662 TGTTGAAACAGAGAATGGCTAACAT 59.230 36.000 0.00 0.0 36.47 2.71
857 3580 6.265196 TGTTGAAACAGAGAATGGCTAACATT 59.735 34.615 0.00 0.0 42.12 2.71
858 3581 7.201902 TGTTGAAACAGAGAATGGCTAACATTT 60.202 33.333 0.00 0.0 40.83 2.32
934 3657 1.710013 CCTACACACCGCACAAGTAG 58.290 55.000 0.00 0.0 33.67 2.57
936 3659 2.596452 CTACACACCGCACAAGTAGAG 58.404 52.381 0.00 0.0 35.38 2.43
937 3660 1.037493 ACACACCGCACAAGTAGAGA 58.963 50.000 0.00 0.0 0.00 3.10
938 3661 1.411246 ACACACCGCACAAGTAGAGAA 59.589 47.619 0.00 0.0 0.00 2.87
939 3662 2.061773 CACACCGCACAAGTAGAGAAG 58.938 52.381 0.00 0.0 0.00 2.85
940 3663 1.961394 ACACCGCACAAGTAGAGAAGA 59.039 47.619 0.00 0.0 0.00 2.87
941 3664 2.364324 ACACCGCACAAGTAGAGAAGAA 59.636 45.455 0.00 0.0 0.00 2.52
942 3665 3.181469 ACACCGCACAAGTAGAGAAGAAA 60.181 43.478 0.00 0.0 0.00 2.52
943 3666 3.184581 CACCGCACAAGTAGAGAAGAAAC 59.815 47.826 0.00 0.0 0.00 2.78
944 3667 2.408704 CCGCACAAGTAGAGAAGAAACG 59.591 50.000 0.00 0.0 0.00 3.60
945 3668 2.408704 CGCACAAGTAGAGAAGAAACGG 59.591 50.000 0.00 0.0 0.00 4.44
946 3669 2.737252 GCACAAGTAGAGAAGAAACGGG 59.263 50.000 0.00 0.0 0.00 5.28
947 3670 3.326747 CACAAGTAGAGAAGAAACGGGG 58.673 50.000 0.00 0.0 0.00 5.73
948 3671 2.289506 ACAAGTAGAGAAGAAACGGGGC 60.290 50.000 0.00 0.0 0.00 5.80
949 3672 1.640917 AGTAGAGAAGAAACGGGGCA 58.359 50.000 0.00 0.0 0.00 5.36
950 3673 1.975680 AGTAGAGAAGAAACGGGGCAA 59.024 47.619 0.00 0.0 0.00 4.52
951 3674 2.370849 AGTAGAGAAGAAACGGGGCAAA 59.629 45.455 0.00 0.0 0.00 3.68
952 3675 2.358322 AGAGAAGAAACGGGGCAAAA 57.642 45.000 0.00 0.0 0.00 2.44
953 3676 2.230660 AGAGAAGAAACGGGGCAAAAG 58.769 47.619 0.00 0.0 0.00 2.27
954 3677 2.158667 AGAGAAGAAACGGGGCAAAAGA 60.159 45.455 0.00 0.0 0.00 2.52
955 3678 2.820197 GAGAAGAAACGGGGCAAAAGAT 59.180 45.455 0.00 0.0 0.00 2.40
956 3679 2.820197 AGAAGAAACGGGGCAAAAGATC 59.180 45.455 0.00 0.0 0.00 2.75
957 3680 1.545841 AGAAACGGGGCAAAAGATCC 58.454 50.000 0.00 0.0 0.00 3.36
958 3681 1.203001 AGAAACGGGGCAAAAGATCCA 60.203 47.619 0.00 0.0 0.00 3.41
959 3682 1.616374 GAAACGGGGCAAAAGATCCAA 59.384 47.619 0.00 0.0 0.00 3.53
960 3683 1.937191 AACGGGGCAAAAGATCCAAT 58.063 45.000 0.00 0.0 0.00 3.16
961 3684 1.937191 ACGGGGCAAAAGATCCAATT 58.063 45.000 0.00 0.0 0.00 2.32
962 3685 2.256306 ACGGGGCAAAAGATCCAATTT 58.744 42.857 0.00 0.0 0.00 1.82
963 3686 2.233676 ACGGGGCAAAAGATCCAATTTC 59.766 45.455 0.00 0.0 0.00 2.17
964 3687 2.497273 CGGGGCAAAAGATCCAATTTCT 59.503 45.455 0.00 0.0 0.00 2.52
965 3688 3.429410 CGGGGCAAAAGATCCAATTTCTC 60.429 47.826 0.00 0.0 0.00 2.87
966 3689 3.429410 GGGGCAAAAGATCCAATTTCTCG 60.429 47.826 0.00 0.0 0.00 4.04
967 3690 3.429410 GGGCAAAAGATCCAATTTCTCGG 60.429 47.826 0.00 0.0 0.00 4.63
1381 4107 3.633525 TCTTGTTTTGCTTGAGTGATGCT 59.366 39.130 0.00 0.0 0.00 3.79
1384 4110 3.047796 GTTTTGCTTGAGTGATGCTGTG 58.952 45.455 0.00 0.0 0.00 3.66
1403 4129 3.040099 GTGCGTGTGTTGTGTAAAATCC 58.960 45.455 0.00 0.0 0.00 3.01
1600 4540 5.008613 TGCCTTCTACAAAACATCAACAGAC 59.991 40.000 0.00 0.0 0.00 3.51
1843 4785 2.035783 GGCAGTTGGAACTCCCCC 59.964 66.667 0.00 0.0 37.08 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 2752 1.689233 TCGGACCTCCTTCCCCATG 60.689 63.158 0.00 0.00 31.03 3.66
287 3010 1.134580 CAGATCCTCGACATTGCCACT 60.135 52.381 0.00 0.00 0.00 4.00
583 3306 1.077787 TATGTTCGGGGCCTTGCTG 60.078 57.895 0.84 0.00 0.00 4.41
614 3337 7.709613 GCCTTCATTAAAAAGAGATGCATTCAT 59.290 33.333 0.00 0.00 35.17 2.57
632 3355 1.081242 CGCGCAAAGTGCCTTCATT 60.081 52.632 8.75 0.00 41.12 2.57
724 3447 6.039382 GGATTACAAACCGATAAGCCTCATTT 59.961 38.462 0.00 0.00 34.62 2.32
741 3464 2.885266 CGGAGGAGATCTCGGATTACAA 59.115 50.000 16.46 0.00 43.12 2.41
749 3472 4.335584 GGCGCGGAGGAGATCTCG 62.336 72.222 16.46 6.90 43.34 4.04
859 3582 9.095700 AGTAGTTTCTGAATCCTTCTTTCTAGT 57.904 33.333 0.00 0.00 0.00 2.57
894 3617 2.743938 CTCGAGGTATTCCGTTCATGG 58.256 52.381 3.91 0.00 39.05 3.66
934 3657 2.227194 TCTTTTGCCCCGTTTCTTCTC 58.773 47.619 0.00 0.00 0.00 2.87
936 3659 2.094700 GGATCTTTTGCCCCGTTTCTTC 60.095 50.000 0.00 0.00 0.00 2.87
937 3660 1.893137 GGATCTTTTGCCCCGTTTCTT 59.107 47.619 0.00 0.00 0.00 2.52
938 3661 1.203001 TGGATCTTTTGCCCCGTTTCT 60.203 47.619 0.00 0.00 0.00 2.52
939 3662 1.253100 TGGATCTTTTGCCCCGTTTC 58.747 50.000 0.00 0.00 0.00 2.78
940 3663 1.710816 TTGGATCTTTTGCCCCGTTT 58.289 45.000 0.00 0.00 0.00 3.60
941 3664 1.937191 ATTGGATCTTTTGCCCCGTT 58.063 45.000 0.00 0.00 0.00 4.44
942 3665 1.937191 AATTGGATCTTTTGCCCCGT 58.063 45.000 0.00 0.00 0.00 5.28
943 3666 2.497273 AGAAATTGGATCTTTTGCCCCG 59.503 45.455 0.00 0.00 0.00 5.73
944 3667 3.429410 CGAGAAATTGGATCTTTTGCCCC 60.429 47.826 0.00 0.00 0.00 5.80
945 3668 3.429410 CCGAGAAATTGGATCTTTTGCCC 60.429 47.826 0.00 0.00 0.00 5.36
946 3669 3.429410 CCCGAGAAATTGGATCTTTTGCC 60.429 47.826 0.00 0.00 0.00 4.52
947 3670 3.443681 TCCCGAGAAATTGGATCTTTTGC 59.556 43.478 0.00 0.00 0.00 3.68
948 3671 5.415701 TCTTCCCGAGAAATTGGATCTTTTG 59.584 40.000 0.00 0.00 0.00 2.44
949 3672 5.570320 TCTTCCCGAGAAATTGGATCTTTT 58.430 37.500 0.00 0.00 0.00 2.27
950 3673 5.179452 TCTTCCCGAGAAATTGGATCTTT 57.821 39.130 0.00 0.00 0.00 2.52
951 3674 4.844349 TCTTCCCGAGAAATTGGATCTT 57.156 40.909 0.00 0.00 0.00 2.40
952 3675 4.844349 TTCTTCCCGAGAAATTGGATCT 57.156 40.909 0.00 0.00 41.34 2.75
961 3684 3.991773 CGTTGTATGTTTCTTCCCGAGAA 59.008 43.478 0.00 0.00 42.56 2.87
962 3685 3.256383 TCGTTGTATGTTTCTTCCCGAGA 59.744 43.478 0.00 0.00 0.00 4.04
963 3686 3.367025 GTCGTTGTATGTTTCTTCCCGAG 59.633 47.826 0.00 0.00 0.00 4.63
964 3687 3.243805 TGTCGTTGTATGTTTCTTCCCGA 60.244 43.478 0.00 0.00 0.00 5.14
965 3688 3.061322 TGTCGTTGTATGTTTCTTCCCG 58.939 45.455 0.00 0.00 0.00 5.14
966 3689 3.187842 GGTGTCGTTGTATGTTTCTTCCC 59.812 47.826 0.00 0.00 0.00 3.97
967 3690 4.062991 AGGTGTCGTTGTATGTTTCTTCC 58.937 43.478 0.00 0.00 0.00 3.46
1166 3889 1.845627 CTGCACAGTGATCACCCCCT 61.846 60.000 22.21 0.34 0.00 4.79
1224 3947 3.665675 AATGTCAGCGTCGCCTCCC 62.666 63.158 14.86 0.00 0.00 4.30
1348 4074 4.936891 AGCAAAACAAGATCGAAAAGCTT 58.063 34.783 0.00 0.00 0.00 3.74
1381 4107 3.487711 GGATTTTACACAACACACGCACA 60.488 43.478 0.00 0.00 0.00 4.57
1384 4110 2.657184 GGGATTTTACACAACACACGC 58.343 47.619 0.00 0.00 0.00 5.34
1403 4129 3.961477 TGTTCAACTCAAACATCACGG 57.039 42.857 0.00 0.00 31.90 4.94
1600 4540 6.082338 GCATGTTCTTCATTTCATATAGGCG 58.918 40.000 0.00 0.00 34.09 5.52
1816 4758 2.751436 CAACTGCCGGTCCATGGG 60.751 66.667 13.02 0.00 0.00 4.00
1860 4802 2.418609 CCTGATGTGTGGAGCGACATAA 60.419 50.000 0.00 0.00 32.85 1.90
1861 4803 1.136891 CCTGATGTGTGGAGCGACATA 59.863 52.381 0.00 0.00 32.85 2.29
1863 4805 1.293179 CCTGATGTGTGGAGCGACA 59.707 57.895 0.00 0.00 0.00 4.35
1864 4806 2.103042 GCCTGATGTGTGGAGCGAC 61.103 63.158 0.00 0.00 0.00 5.19
2098 5043 4.857871 TTCTTGCATAACACAGTATCGC 57.142 40.909 0.00 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.