Multiple sequence alignment - TraesCS1A01G220800

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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 TraesCS1A01G220800 chr1A 100.000 3812 0 0 1 3812 389826449 389822638 0.000000e+00 7040.0
1 TraesCS1A01G220800 chr3A 97.847 2462 33 6 626 3083 128560199 128562644 0.000000e+00 4235.0
2 TraesCS1A01G220800 chr3A 91.184 760 16 8 3072 3812 128562692 128563419 0.000000e+00 985.0
3 TraesCS1A01G220800 chr3A 94.401 643 23 3 1 633 128558225 128558864 0.000000e+00 976.0
4 TraesCS1A01G220800 chr3A 93.313 643 30 3 1 633 128548968 128548329 0.000000e+00 937.0
5 TraesCS1A01G220800 chr1D 91.433 1856 90 22 187 1994 309979414 309977580 0.000000e+00 2483.0
6 TraesCS1A01G220800 chr1D 89.122 1287 50 35 2139 3369 309977462 309976210 0.000000e+00 1519.0
7 TraesCS1A01G220800 chr1D 80.779 385 23 22 3413 3757 309974891 309974518 1.760000e-63 254.0
8 TraesCS1A01G220800 chr1B 91.904 1087 41 23 2022 3083 419982050 419983114 0.000000e+00 1476.0
9 TraesCS1A01G220800 chr1B 88.335 1123 89 19 204 1301 419978305 419979410 0.000000e+00 1310.0
10 TraesCS1A01G220800 chr1B 86.611 717 36 18 3083 3757 419983165 419983863 0.000000e+00 737.0
11 TraesCS1A01G220800 chr1B 85.230 413 45 8 1429 1827 419979446 419979856 9.860000e-111 411.0
12 TraesCS1A01G220800 chr1B 89.447 199 20 1 1825 2023 419981794 419981991 2.270000e-62 250.0
13 TraesCS1A01G220800 chr5B 83.938 386 26 23 2444 2816 461609950 461610312 1.700000e-88 337.0
14 TraesCS1A01G220800 chr5B 88.742 151 10 7 2670 2816 461703023 461703170 1.090000e-40 178.0
15 TraesCS1A01G220800 chr5D 91.946 149 8 2 2589 2733 384741941 384742089 4.990000e-49 206.0
16 TraesCS1A01G220800 chr5D 91.667 48 4 0 2769 2816 384742152 384742199 2.460000e-07 67.6


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 TraesCS1A01G220800 chr1A 389822638 389826449 3811 True 7040.000000 7040 100.000000 1 3812 1 chr1A.!!$R1 3811
1 TraesCS1A01G220800 chr3A 128558225 128563419 5194 False 2065.333333 4235 94.477333 1 3812 3 chr3A.!!$F1 3811
2 TraesCS1A01G220800 chr3A 128548329 128548968 639 True 937.000000 937 93.313000 1 633 1 chr3A.!!$R1 632
3 TraesCS1A01G220800 chr1D 309974518 309979414 4896 True 1418.666667 2483 87.111333 187 3757 3 chr1D.!!$R1 3570
4 TraesCS1A01G220800 chr1B 419978305 419983863 5558 False 836.800000 1476 88.305400 204 3757 5 chr1B.!!$F1 3553

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
58 59 0.539051 CAATCCTCTCCGTGCTCCTT 59.461 55.000 0.00 0.0 0.00 3.36 F
878 2256 1.053835 TGGGACTGCCACTGTGAAGA 61.054 55.000 9.86 0.0 35.15 2.87 F
1816 3228 2.633967 TGGCAGTGCATTGAAGGAATTT 59.366 40.909 18.61 0.0 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 3190 4.516698 ACTGCCAAGTGTCTTTACAATGAG 59.483 41.667 0.0 0.0 37.36 2.90 R
2282 5694 0.603707 CACGCCAAAGAAGCTCCTCA 60.604 55.000 0.0 0.0 0.00 3.86 R
3227 6736 0.445436 CATGAGTGAGCGAGGCAAAC 59.555 55.000 0.0 0.0 0.00 2.93 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
24 25 4.008933 GTCTCCACCTGCACCGCT 62.009 66.667 0.00 0.00 0.00 5.52
32 33 3.399181 CTGCACCGCTTCCCCCTA 61.399 66.667 0.00 0.00 0.00 3.53
58 59 0.539051 CAATCCTCTCCGTGCTCCTT 59.461 55.000 0.00 0.00 0.00 3.36
96 97 2.853077 AGCCCCTAGGTAAGCAAAGATT 59.147 45.455 15.70 0.00 34.57 2.40
168 169 1.553248 TCCACTAATGTGTTCTCCCCG 59.447 52.381 0.00 0.00 42.34 5.73
338 348 7.445707 GGGGTCATGGATCTTCTAATTTTCTAC 59.554 40.741 0.00 0.00 0.00 2.59
361 371 1.545136 TGGTTTGCATGCAGTGTATGG 59.455 47.619 21.50 5.08 0.00 2.74
370 381 4.999311 GCATGCAGTGTATGGAAGATATCA 59.001 41.667 20.87 0.00 30.55 2.15
707 2084 4.122776 GCCACATTACATCCTGAGTAGTG 58.877 47.826 0.00 0.00 35.89 2.74
878 2256 1.053835 TGGGACTGCCACTGTGAAGA 61.054 55.000 9.86 0.00 35.15 2.87
1674 3083 6.798427 TCTATTGCAACTCTACCTGATTCT 57.202 37.500 0.00 0.00 0.00 2.40
1778 3190 8.261492 ACAATTCAGTCACTTTCATCTACATC 57.739 34.615 0.00 0.00 0.00 3.06
1816 3228 2.633967 TGGCAGTGCATTGAAGGAATTT 59.366 40.909 18.61 0.00 0.00 1.82
2282 5694 1.002087 GATTCAGGTGTTGAGGTCGGT 59.998 52.381 0.00 0.00 37.07 4.69
2817 6237 0.031994 GTTGGCTTGGTTGAATGCGT 59.968 50.000 0.00 0.00 0.00 5.24
3077 6554 4.742201 GCGCAACGGCTGAGGAGA 62.742 66.667 0.30 0.00 38.10 3.71
3078 6555 2.811317 CGCAACGGCTGAGGAGAC 60.811 66.667 0.00 0.00 38.10 3.36
3227 6736 3.819337 CTGTATCCATCATGAAGGCCTTG 59.181 47.826 26.25 10.14 0.00 3.61
3255 6764 0.445436 GCTCACTCATGAAACAGGCG 59.555 55.000 0.00 0.00 33.30 5.52
3553 8377 0.179073 ATACCTCTCACGCATGTGGC 60.179 55.000 11.65 0.00 46.42 5.01
3664 8508 4.162690 GGCGACCGATTCCCTGCT 62.163 66.667 0.00 0.00 0.00 4.24
3665 8509 2.586357 GCGACCGATTCCCTGCTC 60.586 66.667 0.00 0.00 0.00 4.26
3666 8510 2.892640 CGACCGATTCCCTGCTCA 59.107 61.111 0.00 0.00 0.00 4.26
3667 8511 1.227089 CGACCGATTCCCTGCTCAG 60.227 63.158 0.00 0.00 0.00 3.35
3668 8512 1.901085 GACCGATTCCCTGCTCAGT 59.099 57.895 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.345112 GGATTGAGAGGGTAGGGGGAA 60.345 57.143 0.00 0.00 0.00 3.97
28 29 2.604139 GAGAGGATTGAGAGGGTAGGG 58.396 57.143 0.00 0.00 0.00 3.53
32 33 0.336737 ACGGAGAGGATTGAGAGGGT 59.663 55.000 0.00 0.00 0.00 4.34
58 59 0.618968 GCTGGGGGAAGAAGAGGAGA 60.619 60.000 0.00 0.00 0.00 3.71
338 348 0.386476 ACACTGCATGCAAACCACAG 59.614 50.000 22.88 10.56 0.00 3.66
393 404 7.342799 AGGCATGACCATTACAATAATCACTTT 59.657 33.333 0.00 0.00 43.14 2.66
599 623 2.334838 CTTAGCAGTTAAACGACGCCT 58.665 47.619 0.00 0.00 0.00 5.52
707 2084 2.295909 TGCAACAATTACTTGGGTGAGC 59.704 45.455 0.00 0.00 36.64 4.26
774 2152 6.778069 CAGATCTTAAGTGGGGATACTAGTGA 59.222 42.308 5.39 0.00 0.00 3.41
878 2256 8.583296 AGAGCTCAAAATTCTTCAGCTAATTTT 58.417 29.630 17.77 10.51 42.88 1.82
1278 2656 7.442364 TCATAAGCATTACCAAGCTATCTTGTC 59.558 37.037 5.64 0.00 39.32 3.18
1484 2879 7.361286 GGGATGTGTCTCAAGTAAGTGAATTTC 60.361 40.741 0.00 0.00 0.00 2.17
1663 3072 6.700520 GGTAATCCGTAAACAGAATCAGGTAG 59.299 42.308 0.00 0.00 0.00 3.18
1778 3190 4.516698 ACTGCCAAGTGTCTTTACAATGAG 59.483 41.667 0.00 0.00 37.36 2.90
1816 3228 9.787435 AGGTGATTACAACAAGTTATACAAAGA 57.213 29.630 0.00 0.00 35.97 2.52
2282 5694 0.603707 CACGCCAAAGAAGCTCCTCA 60.604 55.000 0.00 0.00 0.00 3.86
2817 6237 1.606668 GGACATCCGCAAAAGTCACAA 59.393 47.619 0.00 0.00 32.79 3.33
3062 6539 2.811317 CGTCTCCTCAGCCGTTGC 60.811 66.667 0.00 0.00 37.95 4.17
3063 6540 2.811317 GCGTCTCCTCAGCCGTTG 60.811 66.667 0.00 0.00 0.00 4.10
3064 6541 4.421479 CGCGTCTCCTCAGCCGTT 62.421 66.667 0.00 0.00 0.00 4.44
3111 6615 4.412796 TCACCAAAGGAGCAGATAGATG 57.587 45.455 0.00 0.00 0.00 2.90
3227 6736 0.445436 CATGAGTGAGCGAGGCAAAC 59.555 55.000 0.00 0.00 0.00 2.93
3255 6764 0.527565 AATGATGGTGTTTGCCTCGC 59.472 50.000 0.00 0.00 0.00 5.03
3322 6831 2.747436 TGTATGATCAGCATCAGTCGC 58.253 47.619 0.09 0.00 42.53 5.19
3369 6878 0.591659 GGAGTTTGAAGGAACGGCAC 59.408 55.000 0.00 0.00 34.74 5.01
3381 6984 7.695618 GTGTACGTATCAACTAGTAGGAGTTTG 59.304 40.741 0.00 0.00 37.57 2.93
3553 8377 0.871163 CCGCCAAAACAAGTGTGCTG 60.871 55.000 0.00 0.00 0.00 4.41
3667 8511 4.846779 AACAAGAGTCTGAGACTGAGAC 57.153 45.455 21.45 13.62 43.53 3.36
3668 8512 6.717084 TGATTAACAAGAGTCTGAGACTGAGA 59.283 38.462 21.45 0.00 43.53 3.27


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

AutoCloner maintained by Alex Coulton.