Multiple sequence alignment - TraesCS5D01G171200

Loading Multiple Alignment...

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 TraesCS5D01G171200 chr5D 100.000 2414 0 0 1 2414 268480176 268477763 0 4458
1 TraesCS5D01G171200 chr5A 96.365 2421 79 8 1 2414 355847737 355845319 0 3975
2 TraesCS5D01G171200 chr5B 96.003 2427 74 14 1 2414 303914254 303911838 0 3923


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 TraesCS5D01G171200 chr5D 268477763 268480176 2413 True 4458 4458 100.000 1 2414 1 chr5D.!!$R1 2413
1 TraesCS5D01G171200 chr5A 355845319 355847737 2418 True 3975 3975 96.365 1 2414 1 chr5A.!!$R1 2413
2 TraesCS5D01G171200 chr5B 303911838 303914254 2416 True 3923 3923 96.003 1 2414 1 chr5B.!!$R1 2413

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
729 733 0.978907 TCTTGCCTGACTGCATCTCA 59.021 50.0 0.0 0.0 41.7 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2091 0.033601 CAATCCCACGAAATCCCCCA 60.034 55.0 0.0 0.0 0.0 4.96 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
193 194 5.689383 TCTTGAAGGTGCAGAACATTTAC 57.311 39.130 0.00 0.00 31.65 2.01
275 276 7.105588 ACATAAGAGTGCTCATATTGTTGTCA 58.894 34.615 1.82 0.00 0.00 3.58
408 409 9.136323 GGAAGTCAACCTGGAAAATGATTATAT 57.864 33.333 0.00 0.00 0.00 0.86
431 432 1.000163 GTCACAACTTCGGCAGAGAGA 60.000 52.381 3.82 0.00 0.00 3.10
729 733 0.978907 TCTTGCCTGACTGCATCTCA 59.021 50.000 0.00 0.00 41.70 3.27
744 748 6.439692 ACTGCATCTCATGTATCATATCCTCA 59.560 38.462 0.00 0.00 0.00 3.86
782 786 3.765381 TCATGTGGTCATCAAATGTGGT 58.235 40.909 0.00 0.00 40.97 4.16
792 796 5.123027 GTCATCAAATGTGGTCTTTCTCCTC 59.877 44.000 0.00 0.00 0.00 3.71
793 797 4.705110 TCAAATGTGGTCTTTCTCCTCA 57.295 40.909 0.00 0.00 33.88 3.86
795 799 5.634118 TCAAATGTGGTCTTTCTCCTCAAT 58.366 37.500 0.00 0.00 33.25 2.57
839 843 4.690748 TGAATCACCAAGACTTTCATCGAC 59.309 41.667 0.00 0.00 0.00 4.20
858 862 3.350833 GACCTCATCATCAAAACCAGCT 58.649 45.455 0.00 0.00 0.00 4.24
900 904 6.859420 TCTTCATCTTCGTCATCAAACAAA 57.141 33.333 0.00 0.00 0.00 2.83
987 991 5.644636 CACTGATTCCCAAATCCCAAATTTG 59.355 40.000 11.40 11.40 40.57 2.32
1212 1216 0.527817 GTGTGAATACCTCCTCCGCG 60.528 60.000 0.00 0.00 0.00 6.46
1302 1306 3.650942 TCCAACACAGGGTATTCTTCACT 59.349 43.478 0.00 0.00 0.00 3.41
1625 1629 1.128692 CGTGCCGTCTGGAAAGAAATC 59.871 52.381 0.00 0.00 37.49 2.17
1636 1640 4.261801 TGGAAAGAAATCCGGAGACATTC 58.738 43.478 11.34 11.70 42.76 2.67
1749 1758 3.604629 ACGGAGTGGTCGATGGAG 58.395 61.111 0.00 0.00 42.51 3.86
1826 1835 3.771160 GTGGAGCCGGATCGTGGT 61.771 66.667 14.60 0.00 0.00 4.16
1907 1916 1.115326 TCGTGGATCAGGATGGCGAT 61.115 55.000 0.00 0.00 36.16 4.58
2066 2077 2.881352 CTTCGCGTCCGAGGCTTC 60.881 66.667 5.77 0.00 45.35 3.86
2080 2091 1.073897 GCTTCCTTGGTGAGCTGGT 59.926 57.895 0.00 0.00 33.72 4.00
2094 2106 1.378514 CTGGTGGGGGATTTCGTGG 60.379 63.158 0.00 0.00 0.00 4.94
2139 2152 4.670621 GGCGTTTTATGTTTCGATATGCTG 59.329 41.667 0.00 0.00 0.00 4.41
2167 2180 1.225376 ACGAGTGGCGCGAAATTTCA 61.225 50.000 12.10 0.00 46.04 2.69
2175 2188 1.977188 CGCGAAATTTCAGGGGTTTC 58.023 50.000 17.99 0.00 0.00 2.78
2249 2262 1.355066 GACTCCTCGCGGAAAGCTTG 61.355 60.000 6.13 0.00 45.59 4.01
2252 2265 2.328099 CCTCGCGGAAAGCTTGCTT 61.328 57.895 6.13 1.55 45.59 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
408 409 2.560981 TCTCTGCCGAAGTTGTGACATA 59.439 45.455 0.00 0.00 0.00 2.29
631 635 0.961753 GCAACTTCTGGAAGGTTGGG 59.038 55.000 13.86 0.00 42.53 4.12
744 748 6.100859 ACCACATGAATGGAGATAGTGAAGAT 59.899 38.462 9.25 0.00 43.02 2.40
782 786 3.329386 CACAAGCGATTGAGGAGAAAGA 58.671 45.455 21.96 0.00 0.00 2.52
792 796 2.034558 ACCTTTCAACCACAAGCGATTG 59.965 45.455 12.67 12.67 0.00 2.67
793 797 2.034558 CACCTTTCAACCACAAGCGATT 59.965 45.455 0.00 0.00 0.00 3.34
795 799 1.021202 CACCTTTCAACCACAAGCGA 58.979 50.000 0.00 0.00 0.00 4.93
839 843 3.349927 TCAGCTGGTTTTGATGATGAGG 58.650 45.455 15.13 0.00 0.00 3.86
858 862 3.225104 AGAAGAAAAGCCAAGCACATCA 58.775 40.909 0.00 0.00 0.00 3.07
1121 1125 0.902531 GAGGTACCTGGCAACTGCTA 59.097 55.000 22.10 0.00 41.70 3.49
1272 1276 1.004918 CCTGTGTTGGAGTCCCGAC 60.005 63.158 6.74 6.28 45.41 4.79
1302 1306 0.037697 CATTCGGTTCCGACCACTCA 60.038 55.000 13.66 0.00 46.91 3.41
1625 1629 2.542618 CGAGATCTGTGAATGTCTCCGG 60.543 54.545 0.00 0.00 34.93 5.14
1636 1640 5.657470 TTGTTTTCACTTCGAGATCTGTG 57.343 39.130 0.00 1.77 0.00 3.66
1662 1666 6.150318 CGCGGTGTCTTATCTGAGTATTTAT 58.850 40.000 0.00 0.00 0.00 1.40
1663 1667 5.516996 CGCGGTGTCTTATCTGAGTATTTA 58.483 41.667 0.00 0.00 0.00 1.40
1664 1668 4.360563 CGCGGTGTCTTATCTGAGTATTT 58.639 43.478 0.00 0.00 0.00 1.40
1666 1670 2.287668 GCGCGGTGTCTTATCTGAGTAT 60.288 50.000 8.83 0.00 0.00 2.12
1797 1806 2.432628 CTCCACAAGGACGGCGTC 60.433 66.667 30.72 30.72 39.61 5.19
2033 2042 0.593773 GAAGCATCTCTCTCGCGGTC 60.594 60.000 6.13 0.00 0.00 4.79
2066 2077 2.034687 CCCACCAGCTCACCAAGG 59.965 66.667 0.00 0.00 0.00 3.61
2080 2091 0.033601 CAATCCCACGAAATCCCCCA 60.034 55.000 0.00 0.00 0.00 4.96
2094 2106 2.492773 CCCGCATCTTGGCCAATCC 61.493 63.158 20.85 6.68 0.00 3.01
2139 2152 2.437895 GCCACTCGTTTAGCCCCC 60.438 66.667 0.00 0.00 0.00 5.40
2249 2262 4.966787 TGGCCCACGGTGGAAAGC 62.967 66.667 28.36 21.40 40.96 3.51
2252 2265 4.939368 CGTTGGCCCACGGTGGAA 62.939 66.667 28.36 12.04 40.96 3.53
2373 2389 2.049888 TGGTCAGAACATTGCACACA 57.950 45.000 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.