Multiple sequence alignment - TraesCS2D01G047700

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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 TraesCS2D01G047700 chr2D 100.000 2222 0 0 1 2222 17496609 17498830 0.000000e+00 4104.0
1 TraesCS2D01G047700 chr2D 83.787 808 113 11 372 1165 17464763 17465566 0.000000e+00 750.0
2 TraesCS2D01G047700 chr2A 95.806 2146 31 8 26 2146 18909108 18911219 0.000000e+00 3410.0
3 TraesCS2D01G047700 chr2A 97.882 850 6 3 26 872 18899128 18899968 0.000000e+00 1459.0
4 TraesCS2D01G047700 chr2A 81.503 1011 153 22 355 1347 18881124 18882118 0.000000e+00 800.0
5 TraesCS2D01G047700 chr2A 78.901 910 159 22 443 1343 18858779 18859664 8.840000e-164 586.0
6 TraesCS2D01G047700 chr2A 98.621 145 2 0 2078 2222 18911221 18911365 7.870000e-65 257.0
7 TraesCS2D01G047700 chr2B 88.164 1825 154 28 436 2222 29722027 29720227 0.000000e+00 2117.0
8 TraesCS2D01G047700 chr2B 80.132 906 147 21 445 1343 29743786 29742907 0.000000e+00 645.0
9 TraesCS2D01G047700 chr2B 83.716 479 70 6 702 1177 29731382 29730909 1.570000e-121 446.0
10 TraesCS2D01G047700 chr2B 90.909 99 5 1 613 707 29732156 29732058 1.790000e-26 130.0
11 TraesCS2D01G047700 chr3A 76.355 203 28 12 223 420 577631898 577631711 8.450000e-15 91.6
12 TraesCS2D01G047700 chr7D 100.000 30 0 0 80 109 379328941 379328970 3.080000e-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 TraesCS2D01G047700 chr2D 17496609 17498830 2221 False 4104.0 4104 100.0000 1 2222 1 chr2D.!!$F2 2221
1 TraesCS2D01G047700 chr2D 17464763 17465566 803 False 750.0 750 83.7870 372 1165 1 chr2D.!!$F1 793
2 TraesCS2D01G047700 chr2A 18909108 18911365 2257 False 1833.5 3410 97.2135 26 2222 2 chr2A.!!$F4 2196
3 TraesCS2D01G047700 chr2A 18899128 18899968 840 False 1459.0 1459 97.8820 26 872 1 chr2A.!!$F3 846
4 TraesCS2D01G047700 chr2A 18881124 18882118 994 False 800.0 800 81.5030 355 1347 1 chr2A.!!$F2 992
5 TraesCS2D01G047700 chr2A 18858779 18859664 885 False 586.0 586 78.9010 443 1343 1 chr2A.!!$F1 900
6 TraesCS2D01G047700 chr2B 29720227 29722027 1800 True 2117.0 2117 88.1640 436 2222 1 chr2B.!!$R1 1786
7 TraesCS2D01G047700 chr2B 29742907 29743786 879 True 645.0 645 80.1320 445 1343 1 chr2B.!!$R2 898
8 TraesCS2D01G047700 chr2B 29730909 29732156 1247 True 288.0 446 87.3125 613 1177 2 chr2B.!!$R3 564

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
882 1583 1.808411 TTCAGGTTCGATCCAAGCAC 58.192 50.0 14.83 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 2806 2.734673 GAACTCCAAGCGAGCGCAG 61.735 63.158 17.68 3.93 43.01 5.18 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
253 257 5.104941 CCTCCTTCGACATGGCCATATATAA 60.105 44.000 20.30 10.00 0.00 0.98
343 347 9.830975 TTATGTTGACTTTATGCATCTTAGCTA 57.169 29.630 0.19 0.00 34.99 3.32
344 348 7.539712 TGTTGACTTTATGCATCTTAGCTAC 57.460 36.000 0.19 0.00 34.99 3.58
345 349 6.255670 TGTTGACTTTATGCATCTTAGCTACG 59.744 38.462 0.19 0.00 34.99 3.51
346 350 4.745125 TGACTTTATGCATCTTAGCTACGC 59.255 41.667 0.19 0.00 34.99 4.42
347 351 4.693283 ACTTTATGCATCTTAGCTACGCA 58.307 39.130 0.19 8.32 36.95 5.24
348 352 4.747108 ACTTTATGCATCTTAGCTACGCAG 59.253 41.667 0.19 0.00 35.79 5.18
350 354 5.447624 TTATGCATCTTAGCTACGCAGTA 57.552 39.130 0.19 0.00 45.11 2.74
376 380 3.869272 GCCTGGCGTTGCTCATCG 61.869 66.667 1.35 0.00 0.00 3.84
880 1581 2.478539 GCATTTCAGGTTCGATCCAAGC 60.479 50.000 14.83 5.46 0.00 4.01
882 1583 1.808411 TTCAGGTTCGATCCAAGCAC 58.192 50.000 14.83 0.00 0.00 4.40
892 1593 5.339008 TCGATCCAAGCACATAACTAGTT 57.661 39.130 13.68 13.68 0.00 2.24
895 1596 7.145985 TCGATCCAAGCACATAACTAGTTATC 58.854 38.462 22.60 13.30 33.79 1.75
1291 1996 4.457834 ACGAGGAATCAAGAAGTACTGG 57.542 45.455 0.00 0.00 0.00 4.00
1348 2056 3.502595 GGTCTACAAGAAAAAGGCAGTCC 59.497 47.826 0.00 0.00 0.00 3.85
1477 2190 9.483916 TTTATGTATACCTTCGGATTGTATGTG 57.516 33.333 0.00 0.00 0.00 3.21
1942 2679 0.259938 ACCAATGCTCTCATTCCCCC 59.740 55.000 0.00 0.00 40.74 5.40
1988 2726 2.568956 CCAAGACAACCTCTCATCCTCA 59.431 50.000 0.00 0.00 0.00 3.86
2085 2825 3.491652 GCGCTCGCTTGGAGTTCC 61.492 66.667 0.00 0.00 45.03 3.62
2160 2970 3.318275 AGAGACGTACGGCATCACAATAT 59.682 43.478 25.52 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.987992 CGGGAGTAAATAGCATAAAACTACCA 59.012 38.462 9.60 0.00 37.75 3.25
1 2 6.426025 CCGGGAGTAAATAGCATAAAACTACC 59.574 42.308 0.00 0.00 35.05 3.18
2 3 6.073385 GCCGGGAGTAAATAGCATAAAACTAC 60.073 42.308 2.18 0.00 0.00 2.73
3 4 5.993441 GCCGGGAGTAAATAGCATAAAACTA 59.007 40.000 2.18 0.00 0.00 2.24
4 5 4.820173 GCCGGGAGTAAATAGCATAAAACT 59.180 41.667 2.18 0.00 0.00 2.66
5 6 4.820173 AGCCGGGAGTAAATAGCATAAAAC 59.180 41.667 2.18 0.00 0.00 2.43
6 7 4.819630 CAGCCGGGAGTAAATAGCATAAAA 59.180 41.667 2.18 0.00 0.00 1.52
7 8 4.385825 CAGCCGGGAGTAAATAGCATAAA 58.614 43.478 2.18 0.00 0.00 1.40
8 9 3.244422 CCAGCCGGGAGTAAATAGCATAA 60.244 47.826 2.18 0.00 40.01 1.90
9 10 2.301870 CCAGCCGGGAGTAAATAGCATA 59.698 50.000 2.18 0.00 40.01 3.14
10 11 1.072331 CCAGCCGGGAGTAAATAGCAT 59.928 52.381 2.18 0.00 40.01 3.79
11 12 0.468226 CCAGCCGGGAGTAAATAGCA 59.532 55.000 2.18 0.00 40.01 3.49
12 13 0.756903 TCCAGCCGGGAGTAAATAGC 59.243 55.000 2.18 0.00 42.15 2.97
21 22 0.105401 TGGTATATGTCCAGCCGGGA 60.105 55.000 2.18 0.00 45.89 5.14
22 23 0.762418 TTGGTATATGTCCAGCCGGG 59.238 55.000 2.18 0.00 36.28 5.73
23 24 2.631160 TTTGGTATATGTCCAGCCGG 57.369 50.000 0.00 0.00 36.28 6.13
24 25 4.253685 CCTATTTGGTATATGTCCAGCCG 58.746 47.826 2.56 0.00 36.28 5.52
59 60 2.270986 GCAAGCACTCCCACCCTTG 61.271 63.158 0.00 0.00 38.12 3.61
253 257 6.516860 GCAGTAAAGTCATATAGGACCGACAT 60.517 42.308 13.67 0.00 38.59 3.06
300 304 1.031235 TAACCGGTCTGACACAACGA 58.969 50.000 8.04 0.00 0.00 3.85
343 347 2.432628 GCCTCTGCGTTACTGCGT 60.433 61.111 0.00 0.00 37.81 5.24
344 348 3.188786 GGCCTCTGCGTTACTGCG 61.189 66.667 0.00 0.00 38.85 5.18
345 349 2.103042 CAGGCCTCTGCGTTACTGC 61.103 63.158 0.00 0.00 38.85 4.40
346 350 1.448540 CCAGGCCTCTGCGTTACTG 60.449 63.158 0.00 0.00 39.61 2.74
347 351 2.982130 CCAGGCCTCTGCGTTACT 59.018 61.111 0.00 0.00 39.61 2.24
348 352 2.820037 GCCAGGCCTCTGCGTTAC 60.820 66.667 0.00 0.00 39.61 2.50
349 353 4.451150 CGCCAGGCCTCTGCGTTA 62.451 66.667 29.36 0.00 39.61 3.18
880 1581 8.246430 TCTAAGGGTGGATAACTAGTTATGTG 57.754 38.462 28.61 10.34 36.02 3.21
882 1583 9.930693 GATTCTAAGGGTGGATAACTAGTTATG 57.069 37.037 28.61 13.31 36.02 1.90
892 1593 2.531463 AGGGGGATTCTAAGGGTGGATA 59.469 50.000 0.00 0.00 0.00 2.59
895 1596 1.608425 AAGGGGGATTCTAAGGGTGG 58.392 55.000 0.00 0.00 0.00 4.61
960 1661 2.270352 ATCTGCGTGGGAAAGAAACA 57.730 45.000 0.00 0.00 0.00 2.83
1061 1766 4.084888 CCAACTTTCGCGCCGGAC 62.085 66.667 5.05 0.00 0.00 4.79
1071 1776 1.611673 CCGTCATCTCCTGCCAACTTT 60.612 52.381 0.00 0.00 0.00 2.66
1105 1810 1.726791 CTCCGTCTTCGTCACCATTTG 59.273 52.381 0.00 0.00 35.01 2.32
1816 2532 5.291178 TGTCAGATTTTGGAAATGCACTTG 58.709 37.500 0.00 0.00 0.00 3.16
2066 2806 2.734673 GAACTCCAAGCGAGCGCAG 61.735 63.158 17.68 3.93 43.01 5.18


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

AutoCloner maintained by Alex Coulton.