Multiple sequence alignment - TraesCS3A01G332800

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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 TraesCS3A01G332800 chr3A 100.000 3405 0 0 1 3405 577245166 577248570 0 6288
1 TraesCS3A01G332800 chr3D 97.870 2770 53 4 635 3403 41716728 41719492 0 4783
2 TraesCS3A01G332800 chr3D 98.758 644 7 1 1 644 41716063 41716705 0 1144
3 TraesCS3A01G332800 chr7A 97.292 2770 70 4 635 3403 620743873 620746638 0 4695
4 TraesCS3A01G332800 chr7A 97.185 2771 73 4 635 3403 727630584 727627817 0 4680
5 TraesCS3A01G332800 chr7A 94.448 2774 135 14 638 3405 5511319 5508559 0 4252
6 TraesCS3A01G332800 chr7A 98.758 644 7 1 1 644 620743208 620743850 0 1144
7 TraesCS3A01G332800 chr7A 98.137 644 11 1 1 644 91406902 91407544 0 1122
8 TraesCS3A01G332800 chr7A 97.205 644 17 1 1 644 112119888 112119246 0 1088
9 TraesCS3A01G332800 chr2B 97.256 2770 73 2 635 3403 776589479 776592246 0 4691
10 TraesCS3A01G332800 chr4D 97.220 2770 70 5 635 3403 40415646 40412883 0 4682
11 TraesCS3A01G332800 chr7B 97.005 2771 72 4 635 3403 523629187 523631948 0 4647
12 TraesCS3A01G332800 chr4A 96.570 2770 89 5 635 3403 716468978 716471742 0 4584
13 TraesCS3A01G332800 chr4A 98.095 630 12 0 1 630 90404559 90403930 0 1098
14 TraesCS3A01G332800 chr4A 97.205 644 17 1 1 644 716468313 716468955 0 1088
15 TraesCS3A01G332800 chr4B 96.499 2771 90 6 635 3403 545204275 545207040 0 4573
16 TraesCS3A01G332800 chr2A 97.364 645 14 3 1 644 27480242 27480884 0 1094
17 TraesCS3A01G332800 chr2A 97.360 644 16 1 1 644 57802667 57803309 0 1094
18 TraesCS3A01G332800 chr3B 97.205 644 17 1 1 644 16084583 16085225 0 1088


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 TraesCS3A01G332800 chr3A 577245166 577248570 3404 False 6288.0 6288 100.0000 1 3405 1 chr3A.!!$F1 3404
1 TraesCS3A01G332800 chr3D 41716063 41719492 3429 False 2963.5 4783 98.3140 1 3403 2 chr3D.!!$F1 3402
2 TraesCS3A01G332800 chr7A 727627817 727630584 2767 True 4680.0 4680 97.1850 635 3403 1 chr7A.!!$R3 2768
3 TraesCS3A01G332800 chr7A 5508559 5511319 2760 True 4252.0 4252 94.4480 638 3405 1 chr7A.!!$R1 2767
4 TraesCS3A01G332800 chr7A 620743208 620746638 3430 False 2919.5 4695 98.0250 1 3403 2 chr7A.!!$F2 3402
5 TraesCS3A01G332800 chr7A 91406902 91407544 642 False 1122.0 1122 98.1370 1 644 1 chr7A.!!$F1 643
6 TraesCS3A01G332800 chr7A 112119246 112119888 642 True 1088.0 1088 97.2050 1 644 1 chr7A.!!$R2 643
7 TraesCS3A01G332800 chr2B 776589479 776592246 2767 False 4691.0 4691 97.2560 635 3403 1 chr2B.!!$F1 2768
8 TraesCS3A01G332800 chr4D 40412883 40415646 2763 True 4682.0 4682 97.2200 635 3403 1 chr4D.!!$R1 2768
9 TraesCS3A01G332800 chr7B 523629187 523631948 2761 False 4647.0 4647 97.0050 635 3403 1 chr7B.!!$F1 2768
10 TraesCS3A01G332800 chr4A 716468313 716471742 3429 False 2836.0 4584 96.8875 1 3403 2 chr4A.!!$F1 3402
11 TraesCS3A01G332800 chr4A 90403930 90404559 629 True 1098.0 1098 98.0950 1 630 1 chr4A.!!$R1 629
12 TraesCS3A01G332800 chr4B 545204275 545207040 2765 False 4573.0 4573 96.4990 635 3403 1 chr4B.!!$F1 2768
13 TraesCS3A01G332800 chr2A 27480242 27480884 642 False 1094.0 1094 97.3640 1 644 1 chr2A.!!$F1 643
14 TraesCS3A01G332800 chr2A 57802667 57803309 642 False 1094.0 1094 97.3600 1 644 1 chr2A.!!$F2 643
15 TraesCS3A01G332800 chr3B 16084583 16085225 642 False 1088.0 1088 97.2050 1 644 1 chr3B.!!$F1 643

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
21 22 0.819582 GGTTCCATGCCTTCACCATG 59.18 55.000 0.00 0.00 39.74 3.66 F
1675 1744 2.430332 ACGGTGATAAATGGGCCATTTG 59.57 45.455 41.15 29.45 42.91 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 2084 0.165944 CATCGCGAAACAAGGACACC 59.834 55.0 15.24 0.0 0.0 4.16 R
2552 2625 2.173569 GTCCCATCAATTGCTCCTAGGT 59.826 50.0 9.08 0.0 0.0 3.08 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
21 22 0.819582 GGTTCCATGCCTTCACCATG 59.180 55.000 0.00 0.00 39.74 3.66
189 190 8.980481 ACCTGGTAATCTGTTAATCTAAATGG 57.020 34.615 0.00 0.00 0.00 3.16
525 527 6.881570 TGTGATGTCATCTGATGTTGATAGT 58.118 36.000 16.66 0.00 0.00 2.12
796 864 7.939588 AGAAGGAAAACACAGATAAAGCTAAGT 59.060 33.333 0.00 0.00 0.00 2.24
1118 1186 9.827411 GGTAAGTTTGTTCAAGTAGAATTCATC 57.173 33.333 8.44 0.00 38.76 2.92
1349 1417 5.305585 ACGGAAGTTGAAGTACATGACATT 58.694 37.500 0.00 0.00 46.40 2.71
1570 1639 6.451064 AGCACAACAAACTAAAGCTTACTT 57.549 33.333 0.00 0.00 37.90 2.24
1584 1653 9.827411 CTAAAGCTTACTTGGTTAAATCTTGTC 57.173 33.333 0.00 0.00 35.85 3.18
1665 1734 5.437060 AGGCATTTACAGACGGTGATAAAT 58.563 37.500 0.00 0.00 0.00 1.40
1675 1744 2.430332 ACGGTGATAAATGGGCCATTTG 59.570 45.455 41.15 29.45 42.91 2.32
1922 1992 8.956446 TTATCCAGAGATGATATGGTCAACTA 57.044 34.615 0.00 0.00 39.75 2.24
2014 2084 8.788813 CAAGTGCTTATTAATAACTTTTCTGCG 58.211 33.333 3.71 0.00 0.00 5.18
2087 2157 7.983484 CCCGTAACACTTCTATATTAACTGGTT 59.017 37.037 0.00 0.00 0.00 3.67
2188 2259 0.821301 TGTTGCGGGATGCTTTGTGA 60.821 50.000 0.00 0.00 46.63 3.58
2191 2262 0.250684 TGCGGGATGCTTTGTGAGAA 60.251 50.000 0.00 0.00 46.63 2.87
2250 2321 4.151867 GGACGAACAACTACTCATGTTTCC 59.848 45.833 0.00 0.00 39.73 3.13
2262 2333 5.713025 ACTCATGTTTCCACATACAATTGC 58.287 37.500 5.05 0.00 42.14 3.56
2280 2351 6.183360 ACAATTGCTCACAATGTTAGAAACCA 60.183 34.615 5.05 0.00 45.90 3.67
2387 2458 5.509272 CGTGATGTTTGCATAACAGATTCAC 59.491 40.000 21.51 21.51 36.46 3.18
2688 2761 9.889128 TCATTTGACATGACATTCTCTTATGTA 57.111 29.630 0.00 0.00 38.80 2.29
2723 2796 1.407437 GGGTTCTGCATCGGATCAAGT 60.407 52.381 0.00 0.00 0.00 3.16
2889 2962 3.495001 GGCTACGCAAATACTCCAAGATC 59.505 47.826 0.00 0.00 0.00 2.75
3017 3090 3.059461 GCGGAATGTTGTTGAACGAACTA 60.059 43.478 10.38 1.39 35.37 2.24
3063 3137 7.808279 TTCCAATTCTAAGTAGGAAAGGAGA 57.192 36.000 0.00 0.00 35.57 3.71
3104 3178 8.902806 ACAGAACTCAAGTGAAAATTGTTATGA 58.097 29.630 10.25 0.00 43.42 2.15
3231 3305 1.069049 ACAAGTTCATGGGCAAGCAAC 59.931 47.619 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
443 445 9.521841 AGCTCTTACTGCACACTATATATTCTA 57.478 33.333 0.00 0.00 0.00 2.10
525 527 0.535335 CTCGCTTGCCCCAAGTACTA 59.465 55.000 0.00 0.00 42.77 1.82
1349 1417 6.183360 GGGAAGCATTGATTTCATCAGAATCA 60.183 38.462 0.00 0.00 40.94 2.57
1529 1598 3.968724 GTGCTACTGTTTTCTTTGCTTCG 59.031 43.478 0.00 0.00 0.00 3.79
1570 1639 6.245408 AGTATTGCCAGACAAGATTTAACCA 58.755 36.000 0.00 0.00 42.87 3.67
1655 1724 2.802774 GCAAATGGCCCATTTATCACCG 60.803 50.000 20.89 9.18 41.40 4.94
1665 1734 1.483004 CATCTCAATGCAAATGGCCCA 59.517 47.619 0.00 0.00 43.89 5.36
1675 1744 3.493877 CGTCTCTTCATCCATCTCAATGC 59.506 47.826 0.00 0.00 0.00 3.56
1896 1966 8.267620 AGTTGACCATATCATCTCTGGATAAA 57.732 34.615 0.00 0.00 37.11 1.40
2006 2076 1.757682 AACAAGGACACCGCAGAAAA 58.242 45.000 0.00 0.00 0.00 2.29
2014 2084 0.165944 CATCGCGAAACAAGGACACC 59.834 55.000 15.24 0.00 0.00 4.16
2045 2115 5.221803 TGTTACGGGGTGTTCTAAATAACCA 60.222 40.000 0.00 0.00 34.18 3.67
2053 2123 3.233507 AGAAGTGTTACGGGGTGTTCTA 58.766 45.455 0.00 0.00 0.00 2.10
2087 2157 9.627395 CTCTAAAAACTCTATCGTTTTCTGAGA 57.373 33.333 16.91 12.30 43.97 3.27
2191 2262 9.379791 CGATTTGTATCCTTAAGTAACTTCCTT 57.620 33.333 0.97 0.00 0.00 3.36
2250 2321 7.529158 TCTAACATTGTGAGCAATTGTATGTG 58.471 34.615 7.40 0.81 42.91 3.21
2262 2333 6.558771 TGACATGGTTTCTAACATTGTGAG 57.441 37.500 0.00 0.00 31.04 3.51
2280 2351 7.492077 TGCTGATATCTATCTTGGATGACAT 57.508 36.000 3.98 0.00 33.88 3.06
2552 2625 2.173569 GTCCCATCAATTGCTCCTAGGT 59.826 50.000 9.08 0.00 0.00 3.08
2688 2761 3.095163 CCCTCCCATCCAGCAGCT 61.095 66.667 0.00 0.00 0.00 4.24
2723 2796 3.327757 AGTCACAGCCCATCTTAGAACAA 59.672 43.478 0.00 0.00 0.00 2.83
2889 2962 3.210857 CCACGATACGGGGCAATAG 57.789 57.895 0.00 0.00 45.77 1.73
3017 3090 5.767816 AAACGAGCTTTTAGAACACCAAT 57.232 34.783 0.00 0.00 0.00 3.16
3063 3137 9.401058 CTTGAGTTCTGTATGGATAAGGAATTT 57.599 33.333 0.00 0.00 0.00 1.82
3104 3178 5.301551 TGAAGTTGTGGATAATGCAACAAGT 59.698 36.000 8.93 0.91 43.31 3.16
3231 3305 4.809958 CACCAGCAACTCTATCATCTTCTG 59.190 45.833 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.