Multiple sequence alignment - TraesCS2D01G341300

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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 TraesCS2D01G341300 chr2D 100.000 2324 0 0 1 2324 436019534 436017211 0.000000e+00 4292.0
1 TraesCS2D01G341300 chr2D 96.405 612 17 4 1716 2324 500686642 500687251 0.000000e+00 1003.0
2 TraesCS2D01G341300 chr2D 96.020 603 23 1 1723 2324 27252143 27252745 0.000000e+00 979.0
3 TraesCS2D01G341300 chr2D 96.007 601 23 1 1725 2324 368790236 368789636 0.000000e+00 976.0
4 TraesCS2D01G341300 chr2D 96.000 600 22 2 1726 2324 648276925 648276327 0.000000e+00 974.0
5 TraesCS2D01G341300 chr2D 86.784 681 89 1 1 680 531196681 531197361 0.000000e+00 758.0
6 TraesCS2D01G341300 chr2B 92.919 1031 37 15 684 1696 515012226 515013238 0.000000e+00 1467.0
7 TraesCS2D01G341300 chr2B 84.604 682 104 1 1 681 25452067 25452748 0.000000e+00 676.0
8 TraesCS2D01G341300 chr2B 96.875 32 1 0 1694 1725 717694765 717694796 1.000000e-03 54.7
9 TraesCS2D01G341300 chr2A 91.642 1005 37 11 684 1674 550203011 550202040 0.000000e+00 1347.0
10 TraesCS2D01G341300 chr2A 86.364 682 91 2 1 681 675575852 675576532 0.000000e+00 743.0
11 TraesCS2D01G341300 chr1D 97.512 603 13 2 1723 2324 43028202 43028803 0.000000e+00 1029.0
12 TraesCS2D01G341300 chr7D 97.000 600 17 1 1726 2324 160017315 160016716 0.000000e+00 1007.0
13 TraesCS2D01G341300 chr3D 97.000 600 15 2 1726 2324 355420823 355421420 0.000000e+00 1005.0
14 TraesCS2D01G341300 chr3D 96.013 602 22 2 1725 2324 578244590 578243989 0.000000e+00 977.0
15 TraesCS2D01G341300 chr3D 85.000 80 6 5 770 844 591673747 591673669 2.480000e-10 76.8
16 TraesCS2D01G341300 chr4D 96.173 601 20 3 1725 2324 415909625 415910223 0.000000e+00 979.0
17 TraesCS2D01G341300 chrUn 89.181 684 73 1 1 683 143851393 143850710 0.000000e+00 852.0
18 TraesCS2D01G341300 chr1B 89.019 683 72 2 2 683 583848753 583849433 0.000000e+00 843.0
19 TraesCS2D01G341300 chr7B 87.537 682 83 2 1 681 619618852 619618172 0.000000e+00 787.0
20 TraesCS2D01G341300 chr1A 82.963 675 114 1 6 679 117871787 117872461 1.970000e-170 608.0
21 TraesCS2D01G341300 chr5A 81.991 683 118 5 1 680 589883744 589884424 2.000000e-160 575.0
22 TraesCS2D01G341300 chr5A 82.261 637 110 3 49 682 590051452 590052088 4.370000e-152 547.0
23 TraesCS2D01G341300 chr4A 93.035 201 14 0 1 201 581864942 581864742 6.280000e-76 294.0
24 TraesCS2D01G341300 chr3A 82.857 105 5 10 770 868 722357152 722357249 5.320000e-12 82.4
25 TraesCS2D01G341300 chr3B 85.185 81 4 6 770 844 793001544 793001622 2.480000e-10 76.8


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 TraesCS2D01G341300 chr2D 436017211 436019534 2323 True 4292 4292 100.000 1 2324 1 chr2D.!!$R2 2323
1 TraesCS2D01G341300 chr2D 500686642 500687251 609 False 1003 1003 96.405 1716 2324 1 chr2D.!!$F2 608
2 TraesCS2D01G341300 chr2D 27252143 27252745 602 False 979 979 96.020 1723 2324 1 chr2D.!!$F1 601
3 TraesCS2D01G341300 chr2D 368789636 368790236 600 True 976 976 96.007 1725 2324 1 chr2D.!!$R1 599
4 TraesCS2D01G341300 chr2D 648276327 648276925 598 True 974 974 96.000 1726 2324 1 chr2D.!!$R3 598
5 TraesCS2D01G341300 chr2D 531196681 531197361 680 False 758 758 86.784 1 680 1 chr2D.!!$F3 679
6 TraesCS2D01G341300 chr2B 515012226 515013238 1012 False 1467 1467 92.919 684 1696 1 chr2B.!!$F2 1012
7 TraesCS2D01G341300 chr2B 25452067 25452748 681 False 676 676 84.604 1 681 1 chr2B.!!$F1 680
8 TraesCS2D01G341300 chr2A 550202040 550203011 971 True 1347 1347 91.642 684 1674 1 chr2A.!!$R1 990
9 TraesCS2D01G341300 chr2A 675575852 675576532 680 False 743 743 86.364 1 681 1 chr2A.!!$F1 680
10 TraesCS2D01G341300 chr1D 43028202 43028803 601 False 1029 1029 97.512 1723 2324 1 chr1D.!!$F1 601
11 TraesCS2D01G341300 chr7D 160016716 160017315 599 True 1007 1007 97.000 1726 2324 1 chr7D.!!$R1 598
12 TraesCS2D01G341300 chr3D 355420823 355421420 597 False 1005 1005 97.000 1726 2324 1 chr3D.!!$F1 598
13 TraesCS2D01G341300 chr3D 578243989 578244590 601 True 977 977 96.013 1725 2324 1 chr3D.!!$R1 599
14 TraesCS2D01G341300 chr4D 415909625 415910223 598 False 979 979 96.173 1725 2324 1 chr4D.!!$F1 599
15 TraesCS2D01G341300 chrUn 143850710 143851393 683 True 852 852 89.181 1 683 1 chrUn.!!$R1 682
16 TraesCS2D01G341300 chr1B 583848753 583849433 680 False 843 843 89.019 2 683 1 chr1B.!!$F1 681
17 TraesCS2D01G341300 chr7B 619618172 619618852 680 True 787 787 87.537 1 681 1 chr7B.!!$R1 680
18 TraesCS2D01G341300 chr1A 117871787 117872461 674 False 608 608 82.963 6 679 1 chr1A.!!$F1 673
19 TraesCS2D01G341300 chr5A 589883744 589884424 680 False 575 575 81.991 1 680 1 chr5A.!!$F1 679
20 TraesCS2D01G341300 chr5A 590051452 590052088 636 False 547 547 82.261 49 682 1 chr5A.!!$F2 633

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
193 196 0.193069 AGATGGATCCCTCCTCCTGG 59.807 60.0 9.90 0.0 42.59 4.45 F
843 865 0.243095 GAAGGAGCAAGTCGTACGGT 59.757 55.0 16.52 0.0 0.00 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1027 1058 0.556380 AGGAGGAGGAGGAAGAGGGA 60.556 60.0 0.0 0.0 0.00 4.20 R
2199 2241 0.238289 GTGGCGTTGTCTCCAATGTG 59.762 55.0 0.0 0.0 39.36 3.21 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
32 33 0.600557 TATGGGCACTTTGGTTTGCG 59.399 50.000 0.00 0.00 39.81 4.85
71 74 2.293122 CGAACACATTTTTCAGAGCCCA 59.707 45.455 0.00 0.00 0.00 5.36
135 138 3.065510 TGACGAATGCAAACCGAAGAAAA 59.934 39.130 11.72 0.00 0.00 2.29
136 139 4.035278 ACGAATGCAAACCGAAGAAAAA 57.965 36.364 11.72 0.00 0.00 1.94
140 143 5.627367 CGAATGCAAACCGAAGAAAAATACA 59.373 36.000 0.00 0.00 0.00 2.29
141 144 6.307800 CGAATGCAAACCGAAGAAAAATACAT 59.692 34.615 0.00 0.00 0.00 2.29
148 151 5.556915 ACCGAAGAAAAATACATCTGGACA 58.443 37.500 0.00 0.00 0.00 4.02
170 173 0.968901 CAATGGTGGCTCCTGCACAT 60.969 55.000 7.19 0.00 41.91 3.21
173 176 2.821366 GTGGCTCCTGCACATCCG 60.821 66.667 0.00 0.00 41.91 4.18
193 196 0.193069 AGATGGATCCCTCCTCCTGG 59.807 60.000 9.90 0.00 42.59 4.45
309 313 1.026718 GGGTGCTTCGGTCATCAAGG 61.027 60.000 0.00 0.00 0.00 3.61
311 315 1.523758 GTGCTTCGGTCATCAAGGTT 58.476 50.000 0.00 0.00 0.00 3.50
402 406 2.899339 GCCTTGCTCGCATCCTCC 60.899 66.667 0.00 0.00 0.00 4.30
418 422 4.803426 CCTCGCGAGTGACAGCCC 62.803 72.222 32.41 0.00 0.00 5.19
423 427 2.997315 CGAGTGACAGCCCAGGGA 60.997 66.667 10.89 0.00 0.00 4.20
431 435 1.139853 GACAGCCCAGGGATAGTGAAG 59.860 57.143 10.89 0.00 0.00 3.02
470 474 4.082523 GGAGCCTACGCCAGCACA 62.083 66.667 0.00 0.00 35.48 4.57
482 486 0.393537 CCAGCACAACCAGGGAGATC 60.394 60.000 0.00 0.00 0.00 2.75
615 622 2.445682 TGTGTGGCTTTTACACCCTT 57.554 45.000 5.89 0.00 45.95 3.95
654 662 6.573664 TCCCATGAACTTGTTTGAGTAATG 57.426 37.500 0.00 0.00 0.00 1.90
753 761 6.712114 AGACTAGAGAGATTATAGGAGGCA 57.288 41.667 0.00 0.00 0.00 4.75
780 795 5.912892 TCACTCGTTATCTTATCCATGCAA 58.087 37.500 0.00 0.00 0.00 4.08
781 796 5.753438 TCACTCGTTATCTTATCCATGCAAC 59.247 40.000 0.00 0.00 0.00 4.17
788 803 2.613595 TCTTATCCATGCAACATCGTGC 59.386 45.455 0.00 0.00 45.15 5.34
816 831 4.384647 GCAGAGGAATAGGTCATGGAGTTT 60.385 45.833 0.00 0.00 0.00 2.66
843 865 0.243095 GAAGGAGCAAGTCGTACGGT 59.757 55.000 16.52 0.00 0.00 4.83
853 875 2.429571 CGTACGGTCGGTGTGTGG 60.430 66.667 7.57 0.00 0.00 4.17
854 876 2.730094 GTACGGTCGGTGTGTGGT 59.270 61.111 0.00 0.00 0.00 4.16
898 923 7.363793 GGGTACTTCAATTTATCAAGGCATTGT 60.364 37.037 11.36 1.36 37.68 2.71
913 938 1.113788 ATTGTGCTTGTGTGCCTTGT 58.886 45.000 0.00 0.00 0.00 3.16
941 972 5.227908 GTGAAACAACCGAGAGAGATACAA 58.772 41.667 0.00 0.00 36.32 2.41
951 982 5.530915 CCGAGAGAGATACAAGTGAGAGAAT 59.469 44.000 0.00 0.00 0.00 2.40
955 986 6.039717 AGAGAGATACAAGTGAGAGAATCAGC 59.960 42.308 0.00 0.00 39.07 4.26
956 987 5.893255 AGAGATACAAGTGAGAGAATCAGCT 59.107 40.000 0.00 0.00 39.07 4.24
957 988 6.039717 AGAGATACAAGTGAGAGAATCAGCTC 59.960 42.308 0.00 0.00 39.07 4.09
967 998 2.890945 GAGAATCAGCTCTCCTCCTACC 59.109 54.545 0.00 0.00 36.60 3.18
1071 1102 2.499732 GCTTTTCTTGCGTCGCCG 60.500 61.111 15.88 6.00 37.07 6.46
1703 1741 7.784470 ACTCCCTCCAATCTATATTGTAGAC 57.216 40.000 0.74 0.00 40.84 2.59
1704 1742 7.306013 ACTCCCTCCAATCTATATTGTAGACA 58.694 38.462 0.74 0.00 40.84 3.41
1705 1743 7.453126 ACTCCCTCCAATCTATATTGTAGACAG 59.547 40.741 0.74 0.00 40.84 3.51
1706 1744 7.535738 TCCCTCCAATCTATATTGTAGACAGA 58.464 38.462 0.74 0.00 40.84 3.41
1707 1745 8.180165 TCCCTCCAATCTATATTGTAGACAGAT 58.820 37.037 0.74 0.00 40.84 2.90
1708 1746 8.256605 CCCTCCAATCTATATTGTAGACAGATG 58.743 40.741 0.74 0.00 40.84 2.90
1709 1747 9.029368 CCTCCAATCTATATTGTAGACAGATGA 57.971 37.037 0.74 0.00 40.84 2.92
1720 1758 6.588348 TGTAGACAGATGATTTGCAATACG 57.412 37.500 0.00 0.00 0.00 3.06
1721 1759 6.337356 TGTAGACAGATGATTTGCAATACGA 58.663 36.000 0.00 0.00 0.00 3.43
1805 1844 4.212425 CGTAAGCACCAACATTACAAGACA 59.788 41.667 0.00 0.00 31.25 3.41
1813 1852 5.531287 ACCAACATTACAAGACAGAAAGGAC 59.469 40.000 0.00 0.00 0.00 3.85
1938 1977 1.227350 CGGCTCCATCGCTGATCAA 60.227 57.895 0.00 0.00 38.57 2.57
2199 2241 1.566298 AACCTCCCTGCTCCACCATC 61.566 60.000 0.00 0.00 0.00 3.51
2202 2244 1.538629 TCCCTGCTCCACCATCACA 60.539 57.895 0.00 0.00 0.00 3.58
2204 2246 0.033796 CCCTGCTCCACCATCACATT 60.034 55.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.300009 GCTCTGAAAAATGTGTTCGTGG 58.700 45.455 0.00 0.00 0.00 4.94
50 51 2.293122 TGGGCTCTGAAAAATGTGTTCG 59.707 45.455 0.00 0.00 0.00 3.95
71 74 6.437477 TCAAGATGAAGTGGTATGTAGACAGT 59.563 38.462 0.00 0.00 0.00 3.55
103 106 1.815421 CATTCGTCAAGCTCCCGGG 60.815 63.158 16.85 16.85 0.00 5.73
135 138 4.706476 CACCATTGGTTGTCCAGATGTATT 59.294 41.667 5.34 0.00 45.22 1.89
136 139 4.272489 CACCATTGGTTGTCCAGATGTAT 58.728 43.478 5.34 0.00 45.22 2.29
140 143 1.892329 GCCACCATTGGTTGTCCAGAT 60.892 52.381 5.34 0.00 45.98 2.90
141 144 0.539438 GCCACCATTGGTTGTCCAGA 60.539 55.000 5.34 0.00 45.98 3.86
148 151 1.607467 GCAGGAGCCACCATTGGTT 60.607 57.895 5.34 0.00 45.98 3.67
173 176 1.643310 CAGGAGGAGGGATCCATCTC 58.357 60.000 24.69 19.56 39.47 2.75
193 196 3.288092 ACCCGGATTTTAGCAATTCCTC 58.712 45.455 0.73 0.00 32.29 3.71
302 306 3.623060 CCGTTACTCCATGAACCTTGATG 59.377 47.826 0.00 0.00 0.00 3.07
309 313 2.470821 CGGATCCGTTACTCCATGAAC 58.529 52.381 26.35 0.00 34.35 3.18
311 315 1.037493 CCGGATCCGTTACTCCATGA 58.963 55.000 31.22 0.00 37.81 3.07
402 406 3.978723 CTGGGCTGTCACTCGCGAG 62.979 68.421 33.45 33.45 0.00 5.03
418 422 4.406972 TCTTGATGTCCTTCACTATCCCTG 59.593 45.833 0.00 0.00 0.00 4.45
423 427 6.094603 GTGCAATTCTTGATGTCCTTCACTAT 59.905 38.462 0.00 0.00 0.00 2.12
431 435 1.133025 CCGGTGCAATTCTTGATGTCC 59.867 52.381 0.00 0.00 0.00 4.02
470 474 1.003233 GTTTCCACGATCTCCCTGGTT 59.997 52.381 0.00 0.00 0.00 3.67
482 486 6.055231 TCAAAACTAGTTGATGTTTCCACG 57.945 37.500 9.34 0.00 35.63 4.94
605 612 6.126409 ACAAGAGATGTTTGAAGGGTGTAAA 58.874 36.000 0.00 0.00 40.06 2.01
615 622 6.312141 TCATGGGATACAAGAGATGTTTGA 57.688 37.500 0.00 0.00 43.63 2.69
753 761 6.870965 GCATGGATAAGATAACGAGTGATCTT 59.129 38.462 17.29 17.29 43.28 2.40
788 803 3.032609 CCTATTCCTCTGCGCGCG 61.033 66.667 28.44 28.44 0.00 6.86
816 831 2.297701 GACTTGCTCCTTCAACCAACA 58.702 47.619 0.00 0.00 0.00 3.33
843 865 5.353938 GCTCTTAATTATACCACACACCGA 58.646 41.667 0.00 0.00 0.00 4.69
853 875 2.344025 CCGCCCGGCTCTTAATTATAC 58.656 52.381 8.05 0.00 0.00 1.47
854 876 1.276989 CCCGCCCGGCTCTTAATTATA 59.723 52.381 8.05 0.00 0.00 0.98
877 901 6.103997 AGCACAATGCCTTGATAAATTGAAG 58.896 36.000 8.84 0.00 46.52 3.02
898 923 1.021202 GTACACAAGGCACACAAGCA 58.979 50.000 0.00 0.00 35.83 3.91
913 938 2.358582 TCTCTCGGTTGTTTCACGTACA 59.641 45.455 0.00 0.00 0.00 2.90
951 982 0.704664 TGTGGTAGGAGGAGAGCTGA 59.295 55.000 0.00 0.00 0.00 4.26
955 986 5.450688 CGATTAAGTTGTGGTAGGAGGAGAG 60.451 48.000 0.00 0.00 0.00 3.20
956 987 4.401519 CGATTAAGTTGTGGTAGGAGGAGA 59.598 45.833 0.00 0.00 0.00 3.71
957 988 4.401519 TCGATTAAGTTGTGGTAGGAGGAG 59.598 45.833 0.00 0.00 0.00 3.69
958 989 4.346730 TCGATTAAGTTGTGGTAGGAGGA 58.653 43.478 0.00 0.00 0.00 3.71
959 990 4.730949 TCGATTAAGTTGTGGTAGGAGG 57.269 45.455 0.00 0.00 0.00 4.30
967 998 5.460419 GGAGCACTAGATCGATTAAGTTGTG 59.540 44.000 10.04 9.52 0.00 3.33
1027 1058 0.556380 AGGAGGAGGAGGAAGAGGGA 60.556 60.000 0.00 0.00 0.00 4.20
1696 1734 6.816140 TCGTATTGCAAATCATCTGTCTACAA 59.184 34.615 1.71 0.00 0.00 2.41
1697 1735 6.337356 TCGTATTGCAAATCATCTGTCTACA 58.663 36.000 1.71 0.00 0.00 2.74
1698 1736 6.828502 TCGTATTGCAAATCATCTGTCTAC 57.171 37.500 1.71 0.00 0.00 2.59
1699 1737 9.710900 AATATCGTATTGCAAATCATCTGTCTA 57.289 29.630 1.71 0.00 0.00 2.59
1700 1738 8.613060 AATATCGTATTGCAAATCATCTGTCT 57.387 30.769 1.71 0.00 0.00 3.41
1701 1739 9.669353 AAAATATCGTATTGCAAATCATCTGTC 57.331 29.630 1.71 0.00 0.00 3.51
1938 1977 0.963962 TTCGAGGTCCGTAAAGCTGT 59.036 50.000 0.00 0.00 39.75 4.40
2029 2069 2.359531 GGGTGTCAGATCTAGAGTTCGG 59.640 54.545 0.00 0.00 0.00 4.30
2199 2241 0.238289 GTGGCGTTGTCTCCAATGTG 59.762 55.000 0.00 0.00 39.36 3.21
2202 2244 1.237285 GCTGTGGCGTTGTCTCCAAT 61.237 55.000 0.00 0.00 33.57 3.16
2204 2246 2.280797 GCTGTGGCGTTGTCTCCA 60.281 61.111 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.