Multiple sequence alignment - TraesCS1B01G458800

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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 TraesCS1B01G458800 chr1B 100.000 3999 0 0 1 3999 672571647 672567649 0.000000e+00 7385
1 TraesCS1B01G458800 chrUn 98.752 4008 28 7 1 3999 206781112 206785106 0.000000e+00 7105
2 TraesCS1B01G458800 chr7A 98.502 4006 39 7 1 3999 60261768 60265759 0.000000e+00 7046
3 TraesCS1B01G458800 chr7A 97.953 4006 63 12 1 3999 120858684 120854691 0.000000e+00 6926
4 TraesCS1B01G458800 chr3B 97.907 4013 64 7 1 3999 483383157 483387163 0.000000e+00 6927
5 TraesCS1B01G458800 chr3B 97.707 4012 76 7 1 3999 669798076 669794068 0.000000e+00 6885
6 TraesCS1B01G458800 chr3B 89.604 202 16 3 792 992 628316435 628316632 6.630000e-63 252
7 TraesCS1B01G458800 chr6B 97.082 4010 102 11 1 3999 297455569 297459574 0.000000e+00 6743
8 TraesCS1B01G458800 chr6B 98.705 3243 37 5 1 3241 394456093 394459332 0.000000e+00 5751
9 TraesCS1B01G458800 chr2B 98.378 3144 41 6 865 3999 391093547 391090405 0.000000e+00 5515
10 TraesCS1B01G458800 chr2B 97.419 1395 27 8 1 1392 357444645 357443257 0.000000e+00 2368
11 TraesCS1B01G458800 chr2B 97.202 1394 31 5 1 1392 357568778 357570165 0.000000e+00 2351
12 TraesCS1B01G458800 chr2B 96.838 854 23 1 1 850 310044045 310043192 0.000000e+00 1424
13 TraesCS1B01G458800 chr2B 98.468 718 8 3 84 801 391182634 391183348 0.000000e+00 1262
14 TraesCS1B01G458800 chr5A 97.904 3101 48 8 913 3999 238849203 238846106 0.000000e+00 5350


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 TraesCS1B01G458800 chr1B 672567649 672571647 3998 True 7385 7385 100.000 1 3999 1 chr1B.!!$R1 3998
1 TraesCS1B01G458800 chrUn 206781112 206785106 3994 False 7105 7105 98.752 1 3999 1 chrUn.!!$F1 3998
2 TraesCS1B01G458800 chr7A 60261768 60265759 3991 False 7046 7046 98.502 1 3999 1 chr7A.!!$F1 3998
3 TraesCS1B01G458800 chr7A 120854691 120858684 3993 True 6926 6926 97.953 1 3999 1 chr7A.!!$R1 3998
4 TraesCS1B01G458800 chr3B 483383157 483387163 4006 False 6927 6927 97.907 1 3999 1 chr3B.!!$F1 3998
5 TraesCS1B01G458800 chr3B 669794068 669798076 4008 True 6885 6885 97.707 1 3999 1 chr3B.!!$R1 3998
6 TraesCS1B01G458800 chr6B 297455569 297459574 4005 False 6743 6743 97.082 1 3999 1 chr6B.!!$F1 3998
7 TraesCS1B01G458800 chr6B 394456093 394459332 3239 False 5751 5751 98.705 1 3241 1 chr6B.!!$F2 3240
8 TraesCS1B01G458800 chr2B 391090405 391093547 3142 True 5515 5515 98.378 865 3999 1 chr2B.!!$R3 3134
9 TraesCS1B01G458800 chr2B 357443257 357444645 1388 True 2368 2368 97.419 1 1392 1 chr2B.!!$R2 1391
10 TraesCS1B01G458800 chr2B 357568778 357570165 1387 False 2351 2351 97.202 1 1392 1 chr2B.!!$F1 1391
11 TraesCS1B01G458800 chr2B 310043192 310044045 853 True 1424 1424 96.838 1 850 1 chr2B.!!$R1 849
12 TraesCS1B01G458800 chr2B 391182634 391183348 714 False 1262 1262 98.468 84 801 1 chr2B.!!$F2 717
13 TraesCS1B01G458800 chr5A 238846106 238849203 3097 True 5350 5350 97.904 913 3999 1 chr5A.!!$R1 3086

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
777 787 3.046374 AGTATGGTATCCAGGTTCACCC 58.954 50.000 0.0 0.0 36.75 4.61 F
1555 1569 1.978580 CCTATACCCCGAAATGCTCCT 59.021 52.381 0.0 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2299 2322 0.744874 CGGAAAGGGATGCTAGTCGA 59.255 55.0 0.00 0.00 0.0 4.20 R
3133 3157 0.248539 GCTCGTGTAGTAAGGCCTCG 60.249 60.0 5.23 2.95 0.0 4.63 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
189 190 6.295067 CCCCTTAAACTAACCACTTGAATTGG 60.295 42.308 0.00 0.00 40.32 3.16
777 787 3.046374 AGTATGGTATCCAGGTTCACCC 58.954 50.000 0.00 0.00 36.75 4.61
1224 1238 4.019174 AGCAAACTAATCCAATCCCACAG 58.981 43.478 0.00 0.00 0.00 3.66
1370 1384 6.376978 CAGCCATTACTATCAAAGCTATTGC 58.623 40.000 0.00 0.00 40.05 3.56
1422 1436 2.811431 CGAGGGTGATTTAAGTGCAACA 59.189 45.455 0.00 0.00 41.43 3.33
1555 1569 1.978580 CCTATACCCCGAAATGCTCCT 59.021 52.381 0.00 0.00 0.00 3.69
2131 2147 3.365220 CGAGGTCTCATGAACGAGTTTTC 59.635 47.826 0.00 0.00 34.49 2.29
2236 2259 2.666098 GCCTTCGACTTGGCCCCTA 61.666 63.158 0.00 0.00 43.11 3.53
3069 3093 1.892819 CTCCAGGAAGGCTTCGCTCA 61.893 60.000 20.26 4.52 37.29 4.26
3154 3178 1.477295 GAGGCCTTACTACACGAGCTT 59.523 52.381 6.77 0.00 0.00 3.74
3215 3239 3.672511 CGCTTCATCATCTTGCTTGCTTT 60.673 43.478 0.00 0.00 0.00 3.51
3485 3509 7.599621 TGCATTTTCTTACTTGATTGACATTGG 59.400 33.333 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 190 4.083271 GCACTCAACCTAACAAATCCTGAC 60.083 45.833 0.00 0.00 0.00 3.51
559 565 5.047943 AGTTCGTGGGGATATAAGAAGATCG 60.048 44.000 0.00 0.00 0.00 3.69
945 958 6.456501 CGAAAAGAGAAAGGAAAGGAGACTA 58.543 40.000 0.00 0.00 42.68 2.59
1224 1238 6.642950 CGATAGTAGTTCCATGAACAATCCTC 59.357 42.308 9.42 0.93 44.11 3.71
1370 1384 2.545526 GCACTCCGATACCATTGATGTG 59.454 50.000 0.00 0.00 0.00 3.21
1422 1436 0.876399 GCGAACCACCGGTACATTTT 59.124 50.000 6.87 0.00 33.12 1.82
1712 1726 2.490902 CCAGCCCTTAGGTCCAAAGTTT 60.491 50.000 0.00 0.00 34.57 2.66
1802 1816 1.807814 ACAGGTTGTCCTCTCTTGGT 58.192 50.000 0.00 0.00 43.07 3.67
2131 2147 3.846360 AGACCGGAAAGTATGTCGAAAG 58.154 45.455 9.46 0.00 33.04 2.62
2236 2259 2.703007 GTGATTCCTCACCTATCCTGCT 59.297 50.000 0.00 0.00 45.06 4.24
2299 2322 0.744874 CGGAAAGGGATGCTAGTCGA 59.255 55.000 0.00 0.00 0.00 4.20
3133 3157 0.248539 GCTCGTGTAGTAAGGCCTCG 60.249 60.000 5.23 2.95 0.00 4.63
3154 3178 1.067364 TCGTTCCGTGCTTGACTTACA 59.933 47.619 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.