Multiple sequence alignment - TraesCS2D01G301800

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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 TraesCS2D01G301800 chr2D 100.000 3558 0 0 1 3558 385166634 385163077 0.000000e+00 6571
1 TraesCS2D01G301800 chr2B 92.921 2133 96 28 1 2100 456024309 456022199 0.000000e+00 3051
2 TraesCS2D01G301800 chr2B 97.459 787 15 2 2096 2881 456022120 456021338 0.000000e+00 1338
3 TraesCS2D01G301800 chr2B 98.430 637 10 0 2922 3558 456021146 456020510 0.000000e+00 1122
4 TraesCS2D01G301800 chr2A 90.363 1982 117 27 1613 3558 520303727 520301784 0.000000e+00 2534
5 TraesCS2D01G301800 chr2A 92.707 905 33 10 555 1432 520307625 520306727 0.000000e+00 1275
6 TraesCS2D01G301800 chr2A 94.798 519 18 1 1 519 520308420 520307911 0.000000e+00 800
7 TraesCS2D01G301800 chr2A 92.958 71 2 1 1485 1555 520306726 520306659 2.260000e-17 100


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 TraesCS2D01G301800 chr2D 385163077 385166634 3557 True 6571.00 6571 100.0000 1 3558 1 chr2D.!!$R1 3557
1 TraesCS2D01G301800 chr2B 456020510 456024309 3799 True 1837.00 3051 96.2700 1 3558 3 chr2B.!!$R1 3557
2 TraesCS2D01G301800 chr2A 520301784 520308420 6636 True 1177.25 2534 92.7065 1 3558 4 chr2A.!!$R1 3557

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
981 1254 1.087771 GGTGGTATTCCCGCGAACTG 61.088 60.0 8.23 0.0 45.28 3.16 F
2001 5183 0.032678 ACTGCCAGACTGTGAGTTCG 59.967 55.0 0.00 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2275 5555 1.280133 AGCACAGGTACATCACTGCAT 59.720 47.619 0.00 0.0 38.25 3.96 R
3366 6811 1.072648 ACCGCCTGCCAAAGTACTTAA 59.927 47.619 8.92 0.0 0.00 1.85 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
54 55 2.101770 CGGGAGTCGTAGAACGCC 59.898 66.667 0.00 0.00 42.21 5.68
168 169 1.202879 CCTTTGGCCACAAGGTACTCA 60.203 52.381 26.30 1.06 38.49 3.41
656 913 2.482490 CCAGGATAATTTGCTTGCAGCC 60.482 50.000 5.82 0.00 41.51 4.85
741 998 2.359975 GTTTGGGGAGAGGTGCGG 60.360 66.667 0.00 0.00 0.00 5.69
753 1010 2.735857 GTGCGGGTACACGTGGAC 60.736 66.667 23.21 23.21 35.98 4.02
936 1205 7.442364 TCATGGAAAAGAATGGAATATCTCGTC 59.558 37.037 0.00 0.00 0.00 4.20
981 1254 1.087771 GGTGGTATTCCCGCGAACTG 61.088 60.000 8.23 0.00 45.28 3.16
1009 1282 1.890174 GGAAAGGAAATGGCGTGGG 59.110 57.895 0.00 0.00 0.00 4.61
1010 1283 1.604147 GGAAAGGAAATGGCGTGGGG 61.604 60.000 0.00 0.00 0.00 4.96
1108 1381 2.481276 CCGTCCAACATAATGAGCTCGA 60.481 50.000 9.64 0.00 0.00 4.04
1157 1430 2.036862 GTCTCGTAAGTTTCCACCCACT 59.963 50.000 0.00 0.00 39.48 4.00
1290 1563 4.779733 ATCCGCCAGAGGGTCGGT 62.780 66.667 13.49 2.89 46.91 4.69
1421 1709 4.404098 CACCGGCGGTAAGGGCTT 62.404 66.667 33.65 2.71 32.11 4.35
1461 1749 3.297472 GTTTTAAGCTTCAGTTCGTGGC 58.703 45.455 0.00 0.00 0.00 5.01
1462 1750 2.543777 TTAAGCTTCAGTTCGTGGCT 57.456 45.000 0.00 0.00 34.52 4.75
1463 1751 2.080286 TAAGCTTCAGTTCGTGGCTC 57.920 50.000 0.00 0.00 32.46 4.70
1468 1756 2.765250 TTCAGTTCGTGGCTCGCTCC 62.765 60.000 3.73 0.00 39.67 4.70
1470 1758 2.507324 GTTCGTGGCTCGCTCCTC 60.507 66.667 3.73 0.00 39.67 3.71
1474 1762 2.435059 GTGGCTCGCTCCTCAACC 60.435 66.667 0.00 0.00 0.00 3.77
1533 1821 6.036083 CCATGTCTTCGTTTCTCGTATGATTT 59.964 38.462 0.00 0.00 40.80 2.17
1565 1856 5.638234 GTCCTTAGTGCAGGTAGTTTGTTAG 59.362 44.000 0.00 0.00 35.15 2.34
1570 1861 5.539048 AGTGCAGGTAGTTTGTTAGTACAG 58.461 41.667 0.00 0.00 34.83 2.74
1583 1874 9.141400 GTTTGTTAGTACAGGATAGAAGACTTG 57.859 37.037 0.00 0.00 35.28 3.16
1586 1877 8.904834 TGTTAGTACAGGATAGAAGACTTGATC 58.095 37.037 0.00 0.00 0.00 2.92
1587 1878 8.904834 GTTAGTACAGGATAGAAGACTTGATCA 58.095 37.037 0.00 0.00 0.00 2.92
1588 1879 9.647918 TTAGTACAGGATAGAAGACTTGATCAT 57.352 33.333 0.00 0.00 0.00 2.45
1590 1881 9.821240 AGTACAGGATAGAAGACTTGATCATAT 57.179 33.333 0.00 0.00 0.00 1.78
1695 4857 7.865706 ATTCAACTTTATGTTCGAATAGGCT 57.134 32.000 0.00 0.00 36.63 4.58
1697 4859 7.303634 TCAACTTTATGTTCGAATAGGCTTC 57.696 36.000 0.00 0.00 36.63 3.86
1698 4860 7.103641 TCAACTTTATGTTCGAATAGGCTTCT 58.896 34.615 0.00 0.00 36.63 2.85
1699 4861 7.277981 TCAACTTTATGTTCGAATAGGCTTCTC 59.722 37.037 0.00 0.00 36.63 2.87
1700 4862 6.640518 ACTTTATGTTCGAATAGGCTTCTCA 58.359 36.000 0.00 0.00 0.00 3.27
1701 4863 7.275920 ACTTTATGTTCGAATAGGCTTCTCAT 58.724 34.615 0.00 0.00 0.00 2.90
1734 4899 3.817084 CACTGTTTGAGGATTGAAGCTCA 59.183 43.478 0.00 0.00 0.00 4.26
1769 4938 4.973168 TCTCAGTGCTTAGATTGGTTGTT 58.027 39.130 0.00 0.00 0.00 2.83
1770 4939 4.756642 TCTCAGTGCTTAGATTGGTTGTTG 59.243 41.667 0.00 0.00 0.00 3.33
1780 4949 3.960102 AGATTGGTTGTTGGTGTGTCAAT 59.040 39.130 0.00 0.00 0.00 2.57
1781 4950 3.516981 TTGGTTGTTGGTGTGTCAATG 57.483 42.857 0.00 0.00 0.00 2.82
1790 4959 1.002468 GGTGTGTCAATGTGTGTGAGC 60.002 52.381 0.00 0.00 0.00 4.26
1827 4997 9.053840 TGTGCTACTAGTGTCTAATGTACTATC 57.946 37.037 5.39 0.00 0.00 2.08
1828 4998 8.222433 GTGCTACTAGTGTCTAATGTACTATCG 58.778 40.741 5.39 0.00 0.00 2.92
1876 5046 5.902613 TCTTAGATTGCTTGTTCCATTGG 57.097 39.130 0.00 0.00 0.00 3.16
1889 5071 8.610035 GCTTGTTCCATTGGTAAATACTAGTAC 58.390 37.037 4.31 0.00 0.00 2.73
1930 5112 4.983538 TCATTGTGTTATTTTGCTGCACTG 59.016 37.500 0.00 0.00 0.00 3.66
1946 5128 5.484173 TGCACTGCTACACATTATAAAGC 57.516 39.130 1.98 0.05 0.00 3.51
1965 5147 1.787155 GCCATAGCGTCATAACTCACG 59.213 52.381 0.00 0.00 39.09 4.35
1986 5168 2.398498 CGCTCACTATCATGGTACTGC 58.602 52.381 0.00 0.00 0.00 4.40
2001 5183 0.032678 ACTGCCAGACTGTGAGTTCG 59.967 55.000 0.00 0.00 0.00 3.95
2003 5185 1.269723 CTGCCAGACTGTGAGTTCGTA 59.730 52.381 0.93 0.00 0.00 3.43
2031 5213 3.060602 GCACTAATGCGTAGATCCTTCC 58.939 50.000 1.48 0.00 43.33 3.46
2036 5218 6.316390 CACTAATGCGTAGATCCTTCCTTTTT 59.684 38.462 1.48 0.00 33.61 1.94
2041 5223 5.873164 TGCGTAGATCCTTCCTTTTTAGAAC 59.127 40.000 0.00 0.00 0.00 3.01
2045 5227 9.032420 CGTAGATCCTTCCTTTTTAGAACATAC 57.968 37.037 0.00 0.00 0.00 2.39
2051 5233 9.063615 TCCTTCCTTTTTAGAACATACAAGAAC 57.936 33.333 0.00 0.00 0.00 3.01
2177 5457 7.510549 TCATCTGTTTTTAGTTCTTTGGGAG 57.489 36.000 0.00 0.00 0.00 4.30
2190 5470 2.163818 TTGGGAGTTTAGTCTGCACG 57.836 50.000 0.00 0.00 0.00 5.34
2191 5471 1.045407 TGGGAGTTTAGTCTGCACGT 58.955 50.000 0.00 0.00 0.00 4.49
2192 5472 2.241160 TGGGAGTTTAGTCTGCACGTA 58.759 47.619 0.00 0.00 0.00 3.57
2210 5490 7.295930 TGCACGTATAGAGAAGATATGTAACG 58.704 38.462 0.00 0.00 29.73 3.18
2275 5555 5.389520 TGTTCCTGGAACCAAAATGTCATA 58.610 37.500 31.00 9.88 41.35 2.15
2549 5829 4.179298 GGCCATTGAGAATTCTTTCTTGC 58.821 43.478 9.87 10.04 42.34 4.01
2807 6088 9.791820 TCATGATTGTTATCATTGATGTCAAAC 57.208 29.630 9.46 12.06 46.88 2.93
2808 6089 9.027129 CATGATTGTTATCATTGATGTCAAACC 57.973 33.333 9.46 10.17 46.88 3.27
2838 6119 5.932883 GGTCGAATATTTAAGGCCCTTAGAG 59.067 44.000 2.94 0.00 0.00 2.43
2861 6142 9.829507 AGAGATATCTTGTTAAATGAGGTCAAG 57.170 33.333 6.70 0.00 37.44 3.02
2908 6351 1.805254 GTGCCTCACATCATGCACC 59.195 57.895 2.19 0.00 46.33 5.01
2910 6353 2.475466 GCCTCACATCATGCACCGG 61.475 63.158 0.00 0.00 0.00 5.28
2911 6354 1.820906 CCTCACATCATGCACCGGG 60.821 63.158 6.32 0.00 0.00 5.73
2912 6355 2.438254 TCACATCATGCACCGGGC 60.438 61.111 6.32 7.25 45.13 6.13
2913 6356 2.438975 CACATCATGCACCGGGCT 60.439 61.111 6.32 0.00 45.15 5.19
2914 6357 2.438975 ACATCATGCACCGGGCTG 60.439 61.111 6.32 7.15 45.15 4.85
2915 6358 3.896133 CATCATGCACCGGGCTGC 61.896 66.667 6.32 8.50 45.15 5.25
2960 6403 9.660180 TTTGCACCCCTTATGTATTAAAATTTC 57.340 29.630 0.00 0.00 0.00 2.17
3099 6543 2.499289 TGCAATTGTTGTTTCTGTGGGT 59.501 40.909 7.40 0.00 0.00 4.51
3243 6688 6.404074 CCTTGGTTATCATGCAGAACTTCTTC 60.404 42.308 0.00 0.00 0.00 2.87
3366 6811 8.275040 AGTTTAGATTAGGTGCAGGAATATTGT 58.725 33.333 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 160 2.711922 CCTCGCCGCTGAGTACCTT 61.712 63.158 10.10 0.00 34.04 3.50
183 184 2.729479 CGAGGTGCTCATGGAGGCT 61.729 63.158 0.00 0.00 0.00 4.58
256 257 4.203618 GAAGCACTTCTACCGGCC 57.796 61.111 0.00 0.00 36.69 6.13
423 424 1.703438 CTCTGTCGCCTTGCATCTGC 61.703 60.000 0.00 0.00 42.50 4.26
433 434 1.954146 TTGCGTGTTCTCTGTCGCC 60.954 57.895 5.98 0.00 46.57 5.54
527 528 2.663188 GATCGATGGTCCGGCAGC 60.663 66.667 0.54 0.00 0.00 5.25
528 529 2.355126 CGATCGATGGTCCGGCAG 60.355 66.667 10.26 0.00 0.00 4.85
656 913 1.961180 ATTTCTCCTCTCCACCCGCG 61.961 60.000 0.00 0.00 0.00 6.46
936 1205 2.853731 ACTAGTGCTCGAATTCTCGG 57.146 50.000 3.52 0.00 45.49 4.63
951 1220 5.539048 CGGGAATACCACCAGAAATACTAG 58.461 45.833 0.00 0.00 40.22 2.57
981 1254 3.912745 TTCCTTTCCGGGCGCCTTC 62.913 63.158 28.56 9.89 0.00 3.46
987 1260 2.892640 GCCATTTCCTTTCCGGGC 59.107 61.111 0.00 0.00 0.00 6.13
1092 1365 3.000322 GTCCGTTCGAGCTCATTATGTTG 60.000 47.826 15.40 0.00 0.00 3.33
1096 1369 1.269102 CGGTCCGTTCGAGCTCATTAT 60.269 52.381 15.40 0.00 36.81 1.28
1157 1430 1.915614 GAGTCGTGGCGGAGAACGTA 61.916 60.000 0.00 0.00 46.52 3.57
1290 1563 2.123428 GGAGGAGCCGTAGCCGTAA 61.123 63.158 0.00 0.00 41.25 3.18
1420 1708 3.309582 GGATCACCCAGCGAGGAA 58.690 61.111 1.68 0.00 41.22 3.36
1468 1756 2.678336 GGAAATGGAACTAGCGGTTGAG 59.322 50.000 2.41 0.00 38.41 3.02
1470 1758 1.396996 CGGAAATGGAACTAGCGGTTG 59.603 52.381 0.00 0.00 38.41 3.77
1474 1762 2.739913 TGAAACGGAAATGGAACTAGCG 59.260 45.455 0.00 0.00 0.00 4.26
1533 1821 7.124052 ACTACCTGCACTAAGGACTAATAAGA 58.876 38.462 0.00 0.00 40.02 2.10
1583 1874 8.204836 AGTGGCCCGAACTTAATATATATGATC 58.795 37.037 0.00 0.00 0.00 2.92
1586 1877 7.414098 GCAAGTGGCCCGAACTTAATATATATG 60.414 40.741 6.63 0.00 35.70 1.78
1587 1878 6.598064 GCAAGTGGCCCGAACTTAATATATAT 59.402 38.462 6.63 0.00 35.70 0.86
1588 1879 5.935789 GCAAGTGGCCCGAACTTAATATATA 59.064 40.000 6.63 0.00 35.70 0.86
1589 1880 4.760204 GCAAGTGGCCCGAACTTAATATAT 59.240 41.667 6.63 0.00 35.70 0.86
1590 1881 4.131596 GCAAGTGGCCCGAACTTAATATA 58.868 43.478 6.63 0.00 35.70 0.86
1592 1883 2.026636 AGCAAGTGGCCCGAACTTAATA 60.027 45.455 6.63 0.00 46.50 0.98
1695 4857 7.714813 TCAAACAGTGACATACTTCAATGAGAA 59.285 33.333 7.50 0.00 42.86 2.87
1697 4859 7.360691 CCTCAAACAGTGACATACTTCAATGAG 60.361 40.741 7.50 0.00 42.86 2.90
1698 4860 6.427853 CCTCAAACAGTGACATACTTCAATGA 59.572 38.462 7.50 0.00 42.86 2.57
1699 4861 6.427853 TCCTCAAACAGTGACATACTTCAATG 59.572 38.462 0.00 0.00 45.11 2.82
1700 4862 6.533730 TCCTCAAACAGTGACATACTTCAAT 58.466 36.000 0.00 0.00 37.60 2.57
1701 4863 5.924356 TCCTCAAACAGTGACATACTTCAA 58.076 37.500 0.00 0.00 37.60 2.69
1710 4875 3.817647 AGCTTCAATCCTCAAACAGTGAC 59.182 43.478 0.00 0.00 31.13 3.67
1734 4899 2.693069 CACTGAGAACGCTTCATTCCT 58.307 47.619 0.00 0.00 0.00 3.36
1769 4938 2.287769 CTCACACACATTGACACACCA 58.712 47.619 0.00 0.00 0.00 4.17
1770 4939 1.002468 GCTCACACACATTGACACACC 60.002 52.381 0.00 0.00 0.00 4.16
1790 4959 4.914504 CACTAGTAGCACATCAGCGATTAG 59.085 45.833 0.00 0.00 40.15 1.73
1799 4968 7.932335 AGTACATTAGACACTAGTAGCACATC 58.068 38.462 0.00 0.00 0.00 3.06
1827 4997 1.949525 CATGGGGCTGTATTTTCCTCG 59.050 52.381 0.00 0.00 0.00 4.63
1828 4998 3.018423 ACATGGGGCTGTATTTTCCTC 57.982 47.619 0.00 0.00 0.00 3.71
1889 5071 3.876198 GGCCAGGCGTACAATGCG 61.876 66.667 5.00 0.00 0.00 4.73
1930 5112 5.408604 ACGCTATGGCTTTATAATGTGTAGC 59.591 40.000 0.00 14.56 36.09 3.58
1965 5147 2.398498 CAGTACCATGATAGTGAGCGC 58.602 52.381 0.00 0.00 0.00 5.92
1986 5168 3.309388 CTTGTACGAACTCACAGTCTGG 58.691 50.000 4.53 0.00 0.00 3.86
1995 5177 1.784525 AGTGCAGCTTGTACGAACTC 58.215 50.000 0.00 0.00 38.05 3.01
2051 5233 8.948631 TCACAGAGATTAACTAAGCTAATTGG 57.051 34.615 0.00 0.00 31.17 3.16
2174 5454 5.296283 TCTCTATACGTGCAGACTAAACTCC 59.704 44.000 0.00 0.00 0.00 3.85
2177 5457 6.783162 TCTTCTCTATACGTGCAGACTAAAC 58.217 40.000 0.00 0.00 0.00 2.01
2192 5472 8.921353 ACACTACCGTTACATATCTTCTCTAT 57.079 34.615 0.00 0.00 0.00 1.98
2210 5490 6.567891 GCTGTACAAATGGAAAGAACACTACC 60.568 42.308 0.00 0.00 0.00 3.18
2275 5555 1.280133 AGCACAGGTACATCACTGCAT 59.720 47.619 0.00 0.00 38.25 3.96
2807 6088 4.036380 GCCTTAAATATTCGACCCTGTTGG 59.964 45.833 0.00 0.00 41.37 3.77
2808 6089 4.036380 GGCCTTAAATATTCGACCCTGTTG 59.964 45.833 0.00 0.00 0.00 3.33
2873 6154 9.378551 TGTGAGGCACATAAAGTAAAGTATAAG 57.621 33.333 0.00 0.00 39.62 1.73
2960 6403 4.433615 TCTAGCTCTGAAAAATAGCACGG 58.566 43.478 0.00 0.00 38.75 4.94
3099 6543 6.463049 GGGACAATTAGCTCAGTATTAGCAGA 60.463 42.308 0.00 0.00 42.62 4.26
3139 6583 6.758254 AGCACAAGGTTTAATAAAACATGCT 58.242 32.000 16.36 16.36 45.68 3.79
3193 6637 9.465985 GGTTTAGCTTGTTGAGTCTAGATATAC 57.534 37.037 0.00 0.00 0.00 1.47
3243 6688 5.998363 CCTAGGCAAGCTAAAGGGTAATAAG 59.002 44.000 0.00 0.00 0.00 1.73
3366 6811 1.072648 ACCGCCTGCCAAAGTACTTAA 59.927 47.619 8.92 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.