Multiple sequence alignment - TraesCS5D01G083800

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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 TraesCS5D01G083800 chr5D 100.000 2201 0 0 1 2201 87533291 87535491 0 4065
1 TraesCS5D01G083800 chr5D 97.011 2208 51 13 1 2201 503250592 503248393 0 3698
2 TraesCS5D01G083800 chr5D 96.922 2209 52 13 1 2201 503259455 503261655 0 3688
3 TraesCS5D01G083800 chr2A 97.418 2208 43 12 1 2201 726901133 726903333 0 3749
4 TraesCS5D01G083800 chr3B 97.283 2208 46 12 1 2201 201569465 201571665 0 3733
5 TraesCS5D01G083800 chr7B 97.101 2208 49 11 1 2201 662732235 662730036 0 3709
6 TraesCS5D01G083800 chr7B 96.875 2208 54 11 1 2201 663094104 663096303 0 3681
7 TraesCS5D01G083800 chr2D 96.875 2208 51 15 1 2201 272806928 272809124 0 3679
8 TraesCS5D01G083800 chr7A 96.738 2207 59 10 1 2201 258305492 258307691 0 3664


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 TraesCS5D01G083800 chr5D 87533291 87535491 2200 False 4065 4065 100.000 1 2201 1 chr5D.!!$F1 2200
1 TraesCS5D01G083800 chr5D 503248393 503250592 2199 True 3698 3698 97.011 1 2201 1 chr5D.!!$R1 2200
2 TraesCS5D01G083800 chr5D 503259455 503261655 2200 False 3688 3688 96.922 1 2201 1 chr5D.!!$F2 2200
3 TraesCS5D01G083800 chr2A 726901133 726903333 2200 False 3749 3749 97.418 1 2201 1 chr2A.!!$F1 2200
4 TraesCS5D01G083800 chr3B 201569465 201571665 2200 False 3733 3733 97.283 1 2201 1 chr3B.!!$F1 2200
5 TraesCS5D01G083800 chr7B 662730036 662732235 2199 True 3709 3709 97.101 1 2201 1 chr7B.!!$R1 2200
6 TraesCS5D01G083800 chr7B 663094104 663096303 2199 False 3681 3681 96.875 1 2201 1 chr7B.!!$F1 2200
7 TraesCS5D01G083800 chr2D 272806928 272809124 2196 False 3679 3679 96.875 1 2201 1 chr2D.!!$F1 2200
8 TraesCS5D01G083800 chr7A 258305492 258307691 2199 False 3664 3664 96.738 1 2201 1 chr7A.!!$F1 2200

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
561 563 0.395311 CGCAGGACCTCCCTACAGTA 60.395 60.0 0.0 0.0 45.6 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1553 1561 0.383949 GGCGTGCAAAGGTTTTCTCA 59.616 50.0 0.0 0.0 0.0 3.27 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 4.961440 TGACCCTTAGGAGTAGGTAACT 57.039 45.455 0.00 0.00 44.36 2.24
57 58 7.259882 TCGTTCGCTATCCTTGTTTCTATTTA 58.740 34.615 0.00 0.00 0.00 1.40
87 88 8.522830 TGCATTCTATCTCATCGTATCACATTA 58.477 33.333 0.00 0.00 0.00 1.90
149 150 6.932947 ACCTAAGTTCAATAGCTTTACGTCT 58.067 36.000 0.00 0.00 0.00 4.18
301 303 2.285969 AGGCCCAGCTGTCTCCAT 60.286 61.111 13.81 0.00 0.00 3.41
463 465 7.550712 ACCTTTGCATTTTAGATTTGGATCTC 58.449 34.615 0.00 0.00 41.68 2.75
559 561 3.211288 CGCAGGACCTCCCTACAG 58.789 66.667 0.00 0.00 45.60 2.74
560 562 1.682684 CGCAGGACCTCCCTACAGT 60.683 63.158 0.00 0.00 45.60 3.55
561 563 0.395311 CGCAGGACCTCCCTACAGTA 60.395 60.000 0.00 0.00 45.60 2.74
562 564 1.754555 CGCAGGACCTCCCTACAGTAT 60.755 57.143 0.00 0.00 45.60 2.12
623 627 1.079336 GTGTGGTTCCTCTACGCCC 60.079 63.158 0.00 0.00 33.00 6.13
769 773 1.558756 CAAGAGATGGAAGGGCAGAGT 59.441 52.381 0.00 0.00 0.00 3.24
770 774 1.963985 AGAGATGGAAGGGCAGAGTT 58.036 50.000 0.00 0.00 0.00 3.01
875 881 4.377022 CGTGTAGGAACAAGGTTCAAATCG 60.377 45.833 10.86 5.41 37.36 3.34
876 882 4.514066 GTGTAGGAACAAGGTTCAAATCGT 59.486 41.667 10.86 0.00 37.36 3.73
877 883 5.008316 GTGTAGGAACAAGGTTCAAATCGTT 59.992 40.000 10.86 0.00 37.36 3.85
878 884 4.830826 AGGAACAAGGTTCAAATCGTTC 57.169 40.909 10.86 0.00 33.62 3.95
939 945 5.001232 GCACTTCCACTTGACACCTATTTA 58.999 41.667 0.00 0.00 0.00 1.40
1056 1062 1.403814 CGGATGCTCTAGGGAAGTCA 58.596 55.000 0.00 0.00 0.00 3.41
1069 1075 2.175202 GGAAGTCAGAGGAGAGAGCAA 58.825 52.381 0.00 0.00 0.00 3.91
1194 1200 1.305046 GTCCTTCCCGGTCCTCTCA 60.305 63.158 0.00 0.00 0.00 3.27
1210 1216 4.232122 TCCTCTCATACTAGGGAAAGGTCA 59.768 45.833 0.00 0.00 33.40 4.02
1233 1239 1.065491 TCAATGCTCTAACGCCCACAT 60.065 47.619 0.00 0.00 0.00 3.21
1337 1343 0.766674 ACCTACAACTCCAGGTGGCA 60.767 55.000 0.00 0.00 43.64 4.92
1395 1401 1.134670 GTGGACTCTTGGGGAAGATCG 60.135 57.143 0.00 0.00 0.00 3.69
1437 1443 1.270971 TTTATACGTTGAGCGACGGC 58.729 50.000 14.13 0.00 46.77 5.68
1478 1485 2.093658 GGATCACTAAGGCCGACTTTCA 60.094 50.000 0.00 0.00 40.64 2.69
1530 1538 1.003580 CTCCCTTCTGCCTTTGCACTA 59.996 52.381 0.00 0.00 44.23 2.74
1544 1552 2.540383 TGCACTAGAGGACCAATGTCT 58.460 47.619 0.00 0.00 41.47 3.41
1553 1561 0.326264 GACCAATGTCTGTCTGGCCT 59.674 55.000 3.32 0.00 38.53 5.19
1597 1605 2.040679 GTTACCTTTTGGGAGGCCTACA 59.959 50.000 19.26 11.77 46.08 2.74
1619 1627 4.960469 CACCCCATAGAAACTGTCTACCTA 59.040 45.833 0.00 0.00 41.75 3.08
1655 1664 2.908073 GCGGGTCTGCACAAGGTTG 61.908 63.158 0.00 0.00 34.15 3.77
1896 1906 2.809601 CTTTCGTGCGGGTCGGAG 60.810 66.667 0.00 0.00 0.00 4.63
1916 1926 4.510571 GAGCTTACCCGACAAGGAATTTA 58.489 43.478 0.00 0.00 45.00 1.40
2188 2199 4.373116 GAGTTGTCTCGCGCCCCA 62.373 66.667 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.587797 AGAAACAAGGATAGCGAACGA 57.412 42.857 0.00 0.00 0.00 3.85
57 58 9.526713 GTGATACGATGAGATAGAATGCAATAT 57.473 33.333 0.00 0.00 0.00 1.28
87 88 8.408043 TTTGTTGAAGTGGAATCATAGAACAT 57.592 30.769 0.00 0.00 0.00 2.71
95 96 6.379703 TCTTTCCTTTTGTTGAAGTGGAATCA 59.620 34.615 0.00 0.00 34.18 2.57
149 150 4.042062 AGGAAAATCATGATCGGGATAGCA 59.958 41.667 9.06 0.00 0.00 3.49
228 230 1.002990 GGTGTCGGGGGTTCGAATT 60.003 57.895 0.00 0.00 41.05 2.17
489 491 7.817418 AAAGCTTAACACCTCTTATTTGACA 57.183 32.000 0.00 0.00 0.00 3.58
555 557 4.703575 ACTCTACTGCGGTGAAATACTGTA 59.296 41.667 8.92 0.00 37.99 2.74
556 558 3.510360 ACTCTACTGCGGTGAAATACTGT 59.490 43.478 8.92 0.00 37.99 3.55
557 559 4.111375 ACTCTACTGCGGTGAAATACTG 57.889 45.455 8.92 0.00 38.77 2.74
558 560 4.803098 AACTCTACTGCGGTGAAATACT 57.197 40.909 8.92 0.00 0.00 2.12
559 561 6.183360 GGTTAAACTCTACTGCGGTGAAATAC 60.183 42.308 8.92 0.00 0.00 1.89
560 562 5.870978 GGTTAAACTCTACTGCGGTGAAATA 59.129 40.000 8.92 0.00 0.00 1.40
561 563 4.694037 GGTTAAACTCTACTGCGGTGAAAT 59.306 41.667 8.92 0.00 0.00 2.17
562 564 4.060205 GGTTAAACTCTACTGCGGTGAAA 58.940 43.478 8.92 0.00 0.00 2.69
623 627 3.118775 TGGTTCGATATTCTGGTGTCCTG 60.119 47.826 0.00 0.00 0.00 3.86
875 881 2.222442 GCATCCTAACGAACGAACGAAC 60.222 50.000 11.97 0.00 37.03 3.95
876 882 1.987770 GCATCCTAACGAACGAACGAA 59.012 47.619 11.97 1.02 37.03 3.85
877 883 1.621107 GCATCCTAACGAACGAACGA 58.379 50.000 11.97 0.00 37.03 3.85
878 884 0.643820 GGCATCCTAACGAACGAACG 59.356 55.000 0.14 0.00 39.31 3.95
939 945 2.737376 GGCGAGACGAGCCGTTTT 60.737 61.111 1.80 0.00 45.58 2.43
1041 1047 1.641192 TCCTCTGACTTCCCTAGAGCA 59.359 52.381 0.00 0.00 37.27 4.26
1056 1062 3.388676 CCAAGATGATTGCTCTCTCCTCT 59.611 47.826 0.00 0.00 0.00 3.69
1069 1075 1.215423 GTAAGCCCACCCCAAGATGAT 59.785 52.381 0.00 0.00 0.00 2.45
1194 1200 6.465035 GCATTGAGATGACCTTTCCCTAGTAT 60.465 42.308 0.00 0.00 35.16 2.12
1210 1216 1.486310 TGGGCGTTAGAGCATTGAGAT 59.514 47.619 0.00 0.00 39.27 2.75
1337 1343 1.813513 CACCTCAATGTCGGCTCTTT 58.186 50.000 0.00 0.00 0.00 2.52
1395 1401 4.224762 AGTTACTCTAGGGATAACAGGCC 58.775 47.826 13.90 0.00 32.33 5.19
1437 1443 4.760047 CGGTGCCGAGTGGAAGGG 62.760 72.222 4.35 0.00 42.83 3.95
1478 1485 1.378646 TCACCCGTCGAGCAGAGAT 60.379 57.895 0.00 0.00 0.00 2.75
1530 1538 1.905215 CCAGACAGACATTGGTCCTCT 59.095 52.381 0.00 0.00 45.48 3.69
1544 1552 1.140312 AGGTTTTCTCAGGCCAGACA 58.860 50.000 5.01 0.00 0.00 3.41
1553 1561 0.383949 GGCGTGCAAAGGTTTTCTCA 59.616 50.000 0.00 0.00 0.00 3.27
1597 1605 4.076175 AGGTAGACAGTTTCTATGGGGT 57.924 45.455 0.00 0.00 39.13 4.95
1619 1627 2.895424 CGGGCCAAGGGACAGTCTT 61.895 63.158 4.39 0.00 27.52 3.01
1896 1906 3.064958 GCTAAATTCCTTGTCGGGTAAGC 59.935 47.826 0.00 0.00 0.00 3.09
1916 1926 5.059134 ACTATAACGGTCCTAAGGTAGCT 57.941 43.478 0.00 0.00 0.00 3.32
2073 2084 2.358984 GCCCGGGCGACTGTTTAA 60.359 61.111 33.60 0.00 33.66 1.52


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

AutoCloner maintained by Alex Coulton.