Multiple sequence alignment - TraesCS4D01G206400

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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 TraesCS4D01G206400 chr4D 100.000 2267 0 0 1 2267 354051959 354049693 0.000000e+00 4187
1 TraesCS4D01G206400 chr4B 94.155 1728 65 17 1 1710 437837401 437835692 0.000000e+00 2599
2 TraesCS4D01G206400 chr4A 94.178 1374 60 9 64 1428 110875941 110877303 0.000000e+00 2076
3 TraesCS4D01G206400 chr4A 94.527 402 19 2 1869 2267 110878988 110879389 3.200000e-173 617
4 TraesCS4D01G206400 chr4A 90.239 461 27 13 1419 1870 110878321 110878772 9.020000e-164 586
5 TraesCS4D01G206400 chr5D 89.444 180 19 0 2088 2267 58277227 58277406 6.300000e-56 228
6 TraesCS4D01G206400 chr5D 88.889 180 20 0 2088 2267 98733592 98733413 2.930000e-54 222
7 TraesCS4D01G206400 chr1D 88.889 180 19 1 2088 2267 6543570 6543748 1.050000e-53 220
8 TraesCS4D01G206400 chr1D 88.333 180 21 0 2088 2267 27881886 27881707 1.360000e-52 217
9 TraesCS4D01G206400 chr1D 88.333 180 21 0 2088 2267 254636571 254636750 1.360000e-52 217
10 TraesCS4D01G206400 chr7D 88.333 180 21 0 2088 2267 31061845 31062024 1.360000e-52 217
11 TraesCS4D01G206400 chr5A 88.398 181 20 1 2088 2267 482391232 482391052 1.360000e-52 217
12 TraesCS4D01G206400 chr2D 88.333 180 21 0 2088 2267 295166406 295166585 1.360000e-52 217


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 TraesCS4D01G206400 chr4D 354049693 354051959 2266 True 4187 4187 100.000000 1 2267 1 chr4D.!!$R1 2266
1 TraesCS4D01G206400 chr4B 437835692 437837401 1709 True 2599 2599 94.155000 1 1710 1 chr4B.!!$R1 1709
2 TraesCS4D01G206400 chr4A 110875941 110879389 3448 False 1093 2076 92.981333 64 2267 3 chr4A.!!$F1 2203

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
656 662 0.03759 ATGGCTCGGTGTTTGCCTTA 59.962 50.0 0.0 0.0 46.23 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 2842 0.171231 GCAAGCCTTCCGGTCATTTC 59.829 55.0 0.0 0.0 0.0 2.17 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
37 38 7.360101 GGCGATTTATTATTTGCTATCGACAGT 60.360 37.037 0.00 0.0 41.75 3.55
59 64 9.404848 ACAGTAGCATTACTAGTCATTACAGTA 57.595 33.333 0.00 0.0 38.05 2.74
60 65 9.885934 CAGTAGCATTACTAGTCATTACAGTAG 57.114 37.037 0.00 0.0 38.05 2.57
61 66 9.848710 AGTAGCATTACTAGTCATTACAGTAGA 57.151 33.333 0.00 0.0 38.35 2.59
62 67 9.881529 GTAGCATTACTAGTCATTACAGTAGAC 57.118 37.037 0.00 0.0 0.00 2.59
161 166 1.460699 GACCTTCTGCCCCCAGTTT 59.539 57.895 0.00 0.0 40.09 2.66
324 329 2.997315 CCGTCTCCCTCTGGTGCA 60.997 66.667 0.00 0.0 0.00 4.57
392 397 1.872234 GCGCGCAGAACAGACGATA 60.872 57.895 29.10 0.0 0.00 2.92
397 402 1.649171 CGCAGAACAGACGATACACAC 59.351 52.381 0.00 0.0 0.00 3.82
406 411 3.987220 CAGACGATACACACACATGTCAA 59.013 43.478 0.00 0.0 36.72 3.18
467 473 2.916269 TGGTGATGGGGATTACTTGTGA 59.084 45.455 0.00 0.0 0.00 3.58
538 544 1.597027 CCGACTTGGGCACGTCTTT 60.597 57.895 0.00 0.0 0.00 2.52
607 613 4.452733 GGCTCGTCCCTTCCGTGG 62.453 72.222 0.00 0.0 0.00 4.94
656 662 0.037590 ATGGCTCGGTGTTTGCCTTA 59.962 50.000 0.00 0.0 46.23 2.69
660 666 0.521735 CTCGGTGTTTGCCTTAAGCC 59.478 55.000 0.00 0.0 42.71 4.35
663 669 0.039527 GGTGTTTGCCTTAAGCCGTG 60.040 55.000 0.00 0.0 42.71 4.94
664 670 0.666374 GTGTTTGCCTTAAGCCGTGT 59.334 50.000 0.00 0.0 42.71 4.49
910 917 1.067565 CACTGACACGTAGCCACAGAT 60.068 52.381 0.00 0.0 33.53 2.90
940 947 0.608035 TTTAAGAAGCCGGGTGCCAG 60.608 55.000 7.07 0.0 42.71 4.85
950 957 1.153549 GGGTGCCAGCTCTAAGACG 60.154 63.158 0.00 0.0 0.00 4.18
971 978 1.106944 AACGCCAAAGTCCAACCCAG 61.107 55.000 0.00 0.0 0.00 4.45
972 979 1.228124 CGCCAAAGTCCAACCCAGA 60.228 57.895 0.00 0.0 0.00 3.86
973 980 1.515521 CGCCAAAGTCCAACCCAGAC 61.516 60.000 0.00 0.0 34.31 3.51
974 981 1.179174 GCCAAAGTCCAACCCAGACC 61.179 60.000 0.00 0.0 34.67 3.85
975 982 0.539669 CCAAAGTCCAACCCAGACCC 60.540 60.000 0.00 0.0 34.67 4.46
976 983 0.184933 CAAAGTCCAACCCAGACCCA 59.815 55.000 0.00 0.0 34.67 4.51
1122 1132 1.811679 GCCAAGGACAGAGCTACGC 60.812 63.158 0.00 0.0 0.00 4.42
1183 1193 2.035940 AGAAGGTCGAGGACGCCT 59.964 61.111 0.00 0.0 43.60 5.52
1377 1392 4.902448 AGGAGTGGAATAAGATACCCAGAC 59.098 45.833 0.00 0.0 0.00 3.51
1395 1410 7.726216 ACCCAGACCAGAATAAAAAGAAAAAG 58.274 34.615 0.00 0.0 0.00 2.27
1423 2465 1.056660 TCCAAGGCGACTCTCCTTTT 58.943 50.000 0.00 0.0 41.73 2.27
1436 2478 5.849140 ACTCTCCTTTTATCTTCCTCCTCT 58.151 41.667 0.00 0.0 0.00 3.69
1458 2504 5.966935 TCTTAAGTCATCTTCCCCATCTTCT 59.033 40.000 1.63 0.0 35.36 2.85
1459 2505 6.445139 TCTTAAGTCATCTTCCCCATCTTCTT 59.555 38.462 1.63 0.0 35.36 2.52
1460 2506 5.527026 AAGTCATCTTCCCCATCTTCTTT 57.473 39.130 0.00 0.0 0.00 2.52
1473 2519 1.028905 CTTCTTTTCCAACCGTGGCA 58.971 50.000 0.00 0.0 45.54 4.92
1505 2551 0.539051 CGAGGACTTGATGAGCCCTT 59.461 55.000 0.00 0.0 0.00 3.95
1668 2725 1.093496 CATCCCGTTAAACCTCGCCC 61.093 60.000 0.00 0.0 0.00 6.13
1710 2767 1.153978 CGCTTAACGTCGTGGGCTA 60.154 57.895 0.00 0.0 36.87 3.93
1718 2775 1.227380 GTCGTGGGCTATGCTCTGG 60.227 63.158 0.00 0.0 0.00 3.86
1734 2791 4.858680 GGAGGCCGGGCTGTTAGC 62.859 72.222 38.01 20.4 41.46 3.09
1794 2852 8.082242 ACTATTTTCAGAAAAAGAAATGACCGG 58.918 33.333 12.38 0.0 37.76 5.28
1796 2854 6.458232 TTTCAGAAAAAGAAATGACCGGAA 57.542 33.333 9.46 0.0 30.56 4.30
1797 2855 5.689383 TCAGAAAAAGAAATGACCGGAAG 57.311 39.130 9.46 0.0 0.00 3.46
1798 2856 6.460953 TTTCAGAAAAAGAAATGACCGGAAGG 60.461 38.462 9.46 0.0 42.71 3.46
1799 2857 9.759756 TTTCAGAAAAAGAAATGACCGGAAGGC 62.760 40.741 9.46 0.0 41.64 4.35
1852 2910 6.627395 TCAACATCGGACTGTAAAATGTTT 57.373 33.333 9.92 0.0 38.21 2.83
1907 3183 9.793252 GATCATAATTATGCCATTTGTATCCAC 57.207 33.333 18.89 0.0 33.76 4.02
1994 3272 9.349145 ACGCCAAAAACAGATTAATTAACATAC 57.651 29.630 0.00 0.0 0.00 2.39
2110 3388 5.690865 TCCCTCCATTTCAAAATATAGCGT 58.309 37.500 0.00 0.0 0.00 5.07
2113 3391 6.430451 CCTCCATTTCAAAATATAGCGTGTC 58.570 40.000 0.00 0.0 0.00 3.67
2114 3392 6.371809 TCCATTTCAAAATATAGCGTGTCC 57.628 37.500 0.00 0.0 0.00 4.02
2115 3393 6.119536 TCCATTTCAAAATATAGCGTGTCCT 58.880 36.000 0.00 0.0 0.00 3.85
2123 3401 2.005971 ATAGCGTGTCCTCGGTTTTC 57.994 50.000 0.00 0.0 41.64 2.29
2139 3417 4.973663 CGGTTTTCGTGCTTTAACTTTGAT 59.026 37.500 0.00 0.0 0.00 2.57
2203 3481 7.745620 AAGTTCTACCAATGAATTCGTCTTT 57.254 32.000 0.00 0.0 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.952064 GTCGATAGCAAATAATAAATCGCCG 59.048 40.000 0.00 0.0 36.92 6.46
37 38 9.623000 TGTCTACTGTAATGACTAGTAATGCTA 57.377 33.333 0.00 0.0 0.00 3.49
59 64 1.067283 CATCCTTGCTCGTGTCTGTCT 60.067 52.381 0.00 0.0 0.00 3.41
60 65 1.354040 CATCCTTGCTCGTGTCTGTC 58.646 55.000 0.00 0.0 0.00 3.51
61 66 0.671781 GCATCCTTGCTCGTGTCTGT 60.672 55.000 0.00 0.0 45.77 3.41
62 67 2.084844 GCATCCTTGCTCGTGTCTG 58.915 57.895 0.00 0.0 45.77 3.51
302 307 3.062466 CAGAGGGAGACGGACGCA 61.062 66.667 0.00 0.0 0.00 5.24
392 397 1.311859 CCAGCTTGACATGTGTGTGT 58.688 50.000 1.15 0.0 39.09 3.72
397 402 2.693762 CGGGCCAGCTTGACATGTG 61.694 63.158 1.15 0.0 0.00 3.21
607 613 0.819582 TTAGCAGTAGCACCCGTACC 59.180 55.000 0.00 0.0 45.49 3.34
663 669 0.603975 AGAGCCAAGGAAGACGCAAC 60.604 55.000 0.00 0.0 0.00 4.17
664 670 0.320771 GAGAGCCAAGGAAGACGCAA 60.321 55.000 0.00 0.0 0.00 4.85
910 917 3.366679 CGGCTTCTTAAACTAGGACGTGA 60.367 47.826 0.00 0.0 0.00 4.35
940 947 0.389426 TTGGCGTTCCGTCTTAGAGC 60.389 55.000 0.00 0.0 34.14 4.09
944 951 1.606224 GGACTTTGGCGTTCCGTCTTA 60.606 52.381 0.00 0.0 34.14 2.10
950 957 1.658114 GGTTGGACTTTGGCGTTCC 59.342 57.895 0.00 0.0 0.00 3.62
973 980 4.371417 ATGGTGCTGGGCTGTGGG 62.371 66.667 0.00 0.0 0.00 4.61
974 981 2.753043 GATGGTGCTGGGCTGTGG 60.753 66.667 0.00 0.0 0.00 4.17
975 982 1.180456 TTTGATGGTGCTGGGCTGTG 61.180 55.000 0.00 0.0 0.00 3.66
976 983 0.251922 ATTTGATGGTGCTGGGCTGT 60.252 50.000 0.00 0.0 0.00 4.40
1176 1186 3.787001 CCCTTCCCAGAGGCGTCC 61.787 72.222 2.06 0.0 35.37 4.79
1233 1243 4.394712 CCTGTGACGCCCAGGTCC 62.395 72.222 7.30 0.0 43.73 4.46
1371 1386 7.015195 TCCTTTTTCTTTTTATTCTGGTCTGGG 59.985 37.037 0.00 0.0 0.00 4.45
1395 1410 2.356069 GAGTCGCCTTGGAATTCAATCC 59.644 50.000 7.93 0.0 40.10 3.01
1423 2465 7.507616 GGAAGATGACTTAAGAGGAGGAAGATA 59.492 40.741 10.09 0.0 36.39 1.98
1436 2478 6.642733 AAGAAGATGGGGAAGATGACTTAA 57.357 37.500 0.00 0.0 36.39 1.85
1604 2655 1.823976 GAGGGAAGGCTAACTCGGG 59.176 63.158 0.00 0.0 0.00 5.14
1607 2662 1.144276 GGCGAGGGAAGGCTAACTC 59.856 63.158 0.00 0.0 0.00 3.01
1608 2663 1.306226 AGGCGAGGGAAGGCTAACT 60.306 57.895 0.00 0.0 42.96 2.24
1634 2691 0.746923 GGATGGTTAACTGGGCCGAC 60.747 60.000 5.42 0.0 0.00 4.79
1646 2703 1.947212 GCGAGGTTTAACGGGATGGTT 60.947 52.381 0.00 0.0 0.00 3.67
1668 2725 2.027605 ATCTACGCGATGCCCACG 59.972 61.111 15.93 0.0 0.00 4.94
1700 2757 1.227380 CCAGAGCATAGCCCACGAC 60.227 63.158 0.00 0.0 0.00 4.34
1718 2775 2.370647 CTAGCTAACAGCCCGGCCTC 62.371 65.000 5.55 0.0 43.77 4.70
1734 2791 8.649973 ATGAAGAATAAAACGGAGCTAACTAG 57.350 34.615 0.00 0.0 0.00 2.57
1784 2842 0.171231 GCAAGCCTTCCGGTCATTTC 59.829 55.000 0.00 0.0 0.00 2.17
1788 2846 0.546122 ATATGCAAGCCTTCCGGTCA 59.454 50.000 0.00 0.0 0.00 4.02
1789 2847 0.947244 CATATGCAAGCCTTCCGGTC 59.053 55.000 0.00 0.0 0.00 4.79
1790 2848 1.103398 GCATATGCAAGCCTTCCGGT 61.103 55.000 22.84 0.0 41.59 5.28
1907 3183 9.716484 GTAAAAACAAGTTAAACAAGTCAAACG 57.284 29.630 0.00 0.0 0.00 3.60
2042 3320 9.438228 TTTATGCATCATGTTGATCAAAACAAT 57.562 25.926 10.35 0.0 42.98 2.71
2087 3365 5.530915 CACGCTATATTTTGAAATGGAGGGA 59.469 40.000 16.31 0.0 33.05 4.20
2108 3386 1.850640 CACGAAAACCGAGGACACG 59.149 57.895 0.00 0.0 41.76 4.49
2110 3388 0.179067 AAGCACGAAAACCGAGGACA 60.179 50.000 0.00 0.0 41.76 4.02
2113 3391 2.546789 AGTTAAAGCACGAAAACCGAGG 59.453 45.455 0.00 0.0 41.76 4.63
2114 3392 3.872560 AGTTAAAGCACGAAAACCGAG 57.127 42.857 0.00 0.0 41.76 4.63
2115 3393 4.094590 TCAAAGTTAAAGCACGAAAACCGA 59.905 37.500 0.00 0.0 41.76 4.69
2139 3417 7.041235 AGTCGGTTTCGTTGGTTAAATTTATGA 60.041 33.333 0.00 0.0 37.69 2.15


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

AutoCloner maintained by Alex Coulton.