Multiple sequence alignment - TraesCS3D01G521300

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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 TraesCS3D01G521300 chr3D 100.000 2667 0 0 1 2667 603150839 603153505 0.000000e+00 4926.0
1 TraesCS3D01G521300 chr3D 97.395 2111 46 6 1 2107 603115268 603117373 0.000000e+00 3585.0
2 TraesCS3D01G521300 chr3D 100.000 31 0 0 2109 2139 55089729 55089759 1.030000e-04 58.4
3 TraesCS3D01G521300 chr3A 94.689 1996 94 9 117 2107 732913007 732911019 0.000000e+00 3088.0
4 TraesCS3D01G521300 chr3A 92.405 79 5 1 2023 2100 705251218 705251296 7.800000e-21 111.0
5 TraesCS3D01G521300 chr3B 93.540 1997 98 13 117 2107 810622975 810621004 0.000000e+00 2944.0
6 TraesCS3D01G521300 chr3B 94.235 503 24 4 1607 2107 810598106 810597607 0.000000e+00 763.0
7 TraesCS3D01G521300 chr3B 93.029 416 25 4 1138 1552 810598518 810598106 2.940000e-169 604.0
8 TraesCS3D01G521300 chr3B 92.399 421 30 2 722 1142 810602627 810602209 1.370000e-167 599.0
9 TraesCS3D01G521300 chr3B 80.678 295 48 8 2125 2416 77313401 77313113 1.240000e-53 220.0
10 TraesCS3D01G521300 chr6B 95.179 560 14 2 2107 2666 269692811 269692265 0.000000e+00 872.0
11 TraesCS3D01G521300 chr4B 92.771 83 5 1 2023 2105 605566474 605566393 4.660000e-23 119.0
12 TraesCS3D01G521300 chr7D 78.804 184 32 6 2105 2285 461648269 461648448 1.680000e-22 117.0
13 TraesCS3D01G521300 chr7D 91.667 84 6 1 2023 2106 565531846 565531764 6.030000e-22 115.0
14 TraesCS3D01G521300 chr7D 76.667 180 39 3 2107 2285 461648041 461648218 2.190000e-16 97.1
15 TraesCS3D01G521300 chr7D 100.000 31 0 0 2109 2139 497580123 497580093 1.030000e-04 58.4
16 TraesCS3D01G521300 chr7A 92.754 69 4 1 2024 2092 6061766 6061833 6.080000e-17 99.0
17 TraesCS3D01G521300 chr7A 88.462 78 8 1 2023 2100 6857029 6857105 2.830000e-15 93.5
18 TraesCS3D01G521300 chr5D 92.500 40 3 0 2109 2148 22580957 22580996 1.030000e-04 58.4
19 TraesCS3D01G521300 chr4D 96.970 33 1 0 2106 2138 324002678 324002710 3.710000e-04 56.5


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 TraesCS3D01G521300 chr3D 603150839 603153505 2666 False 4926.000000 4926 100.000 1 2667 1 chr3D.!!$F3 2666
1 TraesCS3D01G521300 chr3D 603115268 603117373 2105 False 3585.000000 3585 97.395 1 2107 1 chr3D.!!$F2 2106
2 TraesCS3D01G521300 chr3A 732911019 732913007 1988 True 3088.000000 3088 94.689 117 2107 1 chr3A.!!$R1 1990
3 TraesCS3D01G521300 chr3B 810621004 810622975 1971 True 2944.000000 2944 93.540 117 2107 1 chr3B.!!$R2 1990
4 TraesCS3D01G521300 chr3B 810597607 810602627 5020 True 655.333333 763 93.221 722 2107 3 chr3B.!!$R3 1385
5 TraesCS3D01G521300 chr6B 269692265 269692811 546 True 872.000000 872 95.179 2107 2666 1 chr6B.!!$R1 559

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
953 959 3.667497 TCTTCTGTCATTGAAGAGCGT 57.333 42.857 2.51 0.0 43.19 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2253 5958 0.318441 CCTGGCAGACACTCTCGAAA 59.682 55.0 17.94 0.0 0.0 3.46 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
502 507 6.015434 GTCACATTCCAATAGTTGTTTTCCCT 60.015 38.462 0.00 0.00 0.00 4.20
667 672 9.880157 AAAACATTATCTTCATAGCAAGCAATT 57.120 25.926 0.00 0.00 0.00 2.32
815 820 5.400066 AGTGTGGCCATGTTTATTTTACC 57.600 39.130 9.72 0.00 0.00 2.85
953 959 3.667497 TCTTCTGTCATTGAAGAGCGT 57.333 42.857 2.51 0.00 43.19 5.07
1026 1032 4.137543 CCCTCATGCTGAATAACCCTAAC 58.862 47.826 0.00 0.00 0.00 2.34
1498 5200 5.513233 ACAGAGAATTTGGGTATGCAGATT 58.487 37.500 0.00 0.00 0.00 2.40
1563 5265 2.612115 AGTGGGGGAGGAGCTTGG 60.612 66.667 0.00 0.00 0.00 3.61
1786 5490 9.884636 ATGTCTATGTGTAAAAACTATGTGCTA 57.115 29.630 0.00 0.00 0.00 3.49
1856 5560 1.135527 CCGTTGATGCTTGAATGCCAT 59.864 47.619 0.00 0.00 0.00 4.40
2102 5807 2.615869 GCACACACACCAAAAACATGT 58.384 42.857 0.00 0.00 0.00 3.21
2143 5848 2.311688 CTAGCCTACCCGCCAACCTG 62.312 65.000 0.00 0.00 0.00 4.00
2195 5900 2.860735 CGCTCGATTCTTTTCCTGTAGG 59.139 50.000 0.00 0.00 0.00 3.18
2253 5958 4.316205 TCGTTTATACATCCGCATCTGT 57.684 40.909 0.00 0.00 0.00 3.41
2257 5962 5.432157 GTTTATACATCCGCATCTGTTTCG 58.568 41.667 0.00 0.00 0.00 3.46
2270 5975 0.750249 TGTTTCGAGAGTGTCTGCCA 59.250 50.000 0.00 0.00 0.00 4.92
2314 6019 4.141959 GGCCCAATAAATCAGCTGCTTTTA 60.142 41.667 19.70 18.82 0.00 1.52
2401 6106 0.998945 CCCCTCTCTCCTCCCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
502 507 0.801872 AGATGCGCGCATTGTAACAA 59.198 45.000 43.17 16.58 36.70 2.83
667 672 1.411977 CAAAACCCATGCCACAAGTCA 59.588 47.619 0.00 0.00 0.00 3.41
815 820 5.176223 GGTTCAATGACAAGCACAAAATCTG 59.824 40.000 0.00 0.00 0.00 2.90
953 959 2.079170 AGATGATCCAGCTTCGAGGA 57.921 50.000 0.00 0.00 38.50 3.71
1026 1032 2.131972 TCACGAACTTTGACCATCACG 58.868 47.619 0.00 0.00 0.00 4.35
1475 5177 4.574674 TCTGCATACCCAAATTCTCTGT 57.425 40.909 0.00 0.00 0.00 3.41
1498 5200 0.840288 TTCCCAGAGCAAGGCCTACA 60.840 55.000 5.16 0.00 0.00 2.74
1563 5265 2.798148 AAAGCCGTCGGTCATGTCCC 62.798 60.000 13.94 0.00 0.00 4.46
1687 5389 5.525378 ACAACACAAAGCAACAAAAGAACAA 59.475 32.000 0.00 0.00 0.00 2.83
1786 5490 4.003648 GTGGTGAATAGCTAGCAAACTGT 58.996 43.478 18.83 0.00 0.00 3.55
2019 5724 5.628193 CGGGTATGTACTCATCGTGTTTATC 59.372 44.000 0.00 0.00 35.70 1.75
2102 5807 7.042051 GCTAGGAGCGTTTATATGTTCAATTGA 60.042 37.037 3.38 3.38 0.00 2.57
2195 5900 2.030958 GCCAGCAGCCAAAATGCAC 61.031 57.895 0.00 0.00 46.31 4.57
2253 5958 0.318441 CCTGGCAGACACTCTCGAAA 59.682 55.000 17.94 0.00 0.00 3.46
2257 5962 1.294780 CCACCTGGCAGACACTCTC 59.705 63.158 17.94 0.00 0.00 3.20
2270 5975 2.683475 GGCTAACATGGCCCACCT 59.317 61.111 0.00 0.00 43.49 4.00
2314 6019 2.685850 GGCATACCTTAGTCACCGTT 57.314 50.000 0.00 0.00 0.00 4.44
2401 6106 3.156288 TCTGAGAGAGGAGGAAAACGA 57.844 47.619 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.