Multiple sequence alignment - TraesCS1A01G105100

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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 TraesCS1A01G105100 chr1A 100.000 2201 0 0 1 2201 100417788 100419988 0 4065
1 TraesCS1A01G105100 chr1B 94.133 1551 62 12 24 1566 136926744 136928273 0 2333
2 TraesCS1A01G105100 chr1D 94.133 1551 54 15 4 1541 83914602 83916128 0 2326
3 TraesCS1A01G105100 chr3D 90.402 646 49 9 1566 2201 554949229 554948587 0 837
4 TraesCS1A01G105100 chr3D 89.465 636 58 6 1568 2198 164544948 164544317 0 795
5 TraesCS1A01G105100 chr3A 89.937 636 60 3 1570 2201 696371419 696372054 0 817
6 TraesCS1A01G105100 chr4B 90.338 621 56 4 1583 2201 551075137 551074519 0 811
7 TraesCS1A01G105100 chr2D 89.474 627 62 2 1571 2196 304662723 304663346 0 789
8 TraesCS1A01G105100 chr2A 88.640 625 64 4 1573 2195 82052452 82053071 0 754
9 TraesCS1A01G105100 chr5B 87.790 647 63 7 1570 2200 21530311 21530957 0 743
10 TraesCS1A01G105100 chr2B 89.130 598 51 13 1611 2198 798752401 798752994 0 732
11 TraesCS1A01G105100 chr6B 90.128 547 48 6 1570 2113 69240607 69240064 0 706


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 TraesCS1A01G105100 chr1A 100417788 100419988 2200 False 4065 4065 100.000 1 2201 1 chr1A.!!$F1 2200
1 TraesCS1A01G105100 chr1B 136926744 136928273 1529 False 2333 2333 94.133 24 1566 1 chr1B.!!$F1 1542
2 TraesCS1A01G105100 chr1D 83914602 83916128 1526 False 2326 2326 94.133 4 1541 1 chr1D.!!$F1 1537
3 TraesCS1A01G105100 chr3D 554948587 554949229 642 True 837 837 90.402 1566 2201 1 chr3D.!!$R2 635
4 TraesCS1A01G105100 chr3D 164544317 164544948 631 True 795 795 89.465 1568 2198 1 chr3D.!!$R1 630
5 TraesCS1A01G105100 chr3A 696371419 696372054 635 False 817 817 89.937 1570 2201 1 chr3A.!!$F1 631
6 TraesCS1A01G105100 chr4B 551074519 551075137 618 True 811 811 90.338 1583 2201 1 chr4B.!!$R1 618
7 TraesCS1A01G105100 chr2D 304662723 304663346 623 False 789 789 89.474 1571 2196 1 chr2D.!!$F1 625
8 TraesCS1A01G105100 chr2A 82052452 82053071 619 False 754 754 88.640 1573 2195 1 chr2A.!!$F1 622
9 TraesCS1A01G105100 chr5B 21530311 21530957 646 False 743 743 87.790 1570 2200 1 chr5B.!!$F1 630
10 TraesCS1A01G105100 chr2B 798752401 798752994 593 False 732 732 89.130 1611 2198 1 chr2B.!!$F1 587
11 TraesCS1A01G105100 chr6B 69240064 69240607 543 True 706 706 90.128 1570 2113 1 chr6B.!!$R1 543

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
395 405 0.179062 GATCAGAAGCAGCCGTCCAT 60.179 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 2031 0.178958 ACTCAGGAAGGTGAGACGGT 60.179 55.0 7.85 0.0 46.02 4.83 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
32 36 4.702247 TCAGTTCAACACGTAAACGATG 57.298 40.909 9.86 6.54 43.02 3.84
115 120 1.159713 CGCGGATGGCAATGAAGCTA 61.160 55.000 0.00 0.00 43.84 3.32
187 192 1.724623 CGTGGATCATTTTCACGTCGT 59.275 47.619 11.76 0.00 46.04 4.34
188 193 2.222508 CGTGGATCATTTTCACGTCGTC 60.223 50.000 11.76 0.00 46.04 4.20
189 194 2.734606 GTGGATCATTTTCACGTCGTCA 59.265 45.455 0.00 0.00 0.00 4.35
190 195 2.734606 TGGATCATTTTCACGTCGTCAC 59.265 45.455 0.00 0.00 0.00 3.67
191 196 2.734606 GGATCATTTTCACGTCGTCACA 59.265 45.455 0.00 0.00 0.00 3.58
192 197 3.185594 GGATCATTTTCACGTCGTCACAA 59.814 43.478 0.00 0.00 0.00 3.33
193 198 4.142902 GGATCATTTTCACGTCGTCACAAT 60.143 41.667 0.00 0.00 0.00 2.71
222 227 3.326006 TCACAAGCAGTTTCTCTGAGGAT 59.674 43.478 4.59 0.00 46.27 3.24
246 251 2.036556 AGAAAATCGCAACGCACTTG 57.963 45.000 0.00 0.00 0.00 3.16
247 252 1.601903 AGAAAATCGCAACGCACTTGA 59.398 42.857 0.00 0.00 30.42 3.02
251 257 2.806288 ATCGCAACGCACTTGAATAC 57.194 45.000 0.00 0.00 30.42 1.89
284 290 1.084370 CGAGTCGGTCCAATGCTTCC 61.084 60.000 4.10 0.00 0.00 3.46
395 405 0.179062 GATCAGAAGCAGCCGTCCAT 60.179 55.000 0.00 0.00 0.00 3.41
834 844 2.283604 TGGTAGCTGAGGTGCCGA 60.284 61.111 13.88 1.00 38.59 5.54
876 886 4.057428 GCGACGAGGTCCTGCACT 62.057 66.667 0.00 0.00 0.00 4.40
1106 1116 0.391661 ACGCGCATCTTGGAGAACAT 60.392 50.000 5.73 0.00 0.00 2.71
1203 1213 1.811266 CAGGAGCCCGTTGTGATCG 60.811 63.158 0.00 0.00 0.00 3.69
1207 1217 3.554692 GCCCGTTGTGATCGCTCG 61.555 66.667 7.94 11.74 0.00 5.03
1287 1302 4.141321 TGGAGGAGCAAGCTATGATGATTT 60.141 41.667 0.00 0.00 0.00 2.17
1357 1372 0.752054 AGTGACGGTTTGGGTCGTAA 59.248 50.000 0.00 0.00 39.88 3.18
1513 1529 4.633175 TCATGTCGGTAGCTTAACAACAA 58.367 39.130 0.00 0.00 0.00 2.83
1518 1534 4.931002 GTCGGTAGCTTAACAACAATGGTA 59.069 41.667 0.00 0.00 0.00 3.25
1559 1575 3.959495 AAGGAACACCATCATGGCTAT 57.041 42.857 2.52 0.00 42.67 2.97
1560 1576 3.959495 AGGAACACCATCATGGCTATT 57.041 42.857 2.52 0.00 42.67 1.73
1566 1582 7.345392 AGGAACACCATCATGGCTATTTTATTT 59.655 33.333 2.52 0.00 42.67 1.40
1567 1583 7.986889 GGAACACCATCATGGCTATTTTATTTT 59.013 33.333 2.52 0.00 42.67 1.82
1638 1654 6.202188 ACAGTACAACGAACACCAGAAATAAG 59.798 38.462 0.00 0.00 0.00 1.73
1661 1677 5.983720 AGAATTACATCCAGATCCGTAAACG 59.016 40.000 0.00 0.00 39.44 3.60
1672 1688 0.168788 CCGTAAACGACCTAGCGACA 59.831 55.000 3.65 0.00 43.02 4.35
1725 1750 2.202610 CGTCATCGCCGAAGCTGA 60.203 61.111 0.00 0.00 36.60 4.26
1789 1814 1.694169 CCCCATAGGACCAGCACCT 60.694 63.158 0.00 0.00 41.05 4.00
1834 1859 7.762615 TGATGAAAAATAACGTAGATCGGAAGT 59.237 33.333 0.00 0.00 44.69 3.01
1857 1882 4.247267 TCTAAACCGAAGACACACGAAT 57.753 40.909 0.00 0.00 0.00 3.34
1870 1895 4.114073 ACACACGAATGTAGACGAACAAA 58.886 39.130 0.00 0.00 36.72 2.83
1871 1896 4.567558 ACACACGAATGTAGACGAACAAAA 59.432 37.500 0.00 0.00 36.72 2.44
1908 1933 5.643421 AATCCACCAAAGATAGATCTGCT 57.357 39.130 5.18 0.00 37.19 4.24
1925 1950 0.946221 GCTGAAGACACACCTCCACG 60.946 60.000 0.00 0.00 0.00 4.94
1946 1971 1.544093 CGCCCACCAATGATGCTAGAT 60.544 52.381 0.00 0.00 0.00 1.98
1970 1996 2.068213 GCCTAAACGGGGGCTAGGA 61.068 63.158 0.00 0.00 44.48 2.94
2004 2031 2.586245 CATCTTCAGGAGCCGCCA 59.414 61.111 0.00 0.00 40.02 5.69
2047 2078 6.195600 AGGACACAAACCCTAACAAGATTA 57.804 37.500 0.00 0.00 0.00 1.75
2184 2223 6.040054 GGCACAAACCCTAACTTTCTTTCTTA 59.960 38.462 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.034048 ACGTGTTGAACTGATGAAGTCAAC 59.966 41.667 8.14 8.14 41.86 3.18
11 12 4.114073 ACATCGTTTACGTGTTGAACTGA 58.886 39.130 0.00 1.56 40.80 3.41
32 36 3.891786 CAGTGATGCTGCGAATGAC 57.108 52.632 0.00 0.00 38.52 3.06
57 61 2.691526 TCGTTCGAGGTACATAGCCAAT 59.308 45.455 0.00 0.00 0.00 3.16
58 62 2.093890 TCGTTCGAGGTACATAGCCAA 58.906 47.619 0.00 0.00 0.00 4.52
60 64 1.945394 TCTCGTTCGAGGTACATAGCC 59.055 52.381 19.65 0.00 33.41 3.93
95 100 2.025156 CTTCATTGCCATCCGCGC 59.975 61.111 0.00 0.00 42.08 6.86
96 101 1.159713 TAGCTTCATTGCCATCCGCG 61.160 55.000 0.00 0.00 42.08 6.46
97 102 1.002033 CTTAGCTTCATTGCCATCCGC 60.002 52.381 0.00 0.00 38.31 5.54
98 103 2.292267 ACTTAGCTTCATTGCCATCCG 58.708 47.619 0.00 0.00 0.00 4.18
115 120 9.831682 TCTAGGGGTTTTCCAATAAATAAACTT 57.168 29.630 0.00 0.00 42.91 2.66
185 190 3.846023 GCTTGTGAGTTGTGATTGTGACG 60.846 47.826 0.00 0.00 0.00 4.35
187 192 3.277715 TGCTTGTGAGTTGTGATTGTGA 58.722 40.909 0.00 0.00 0.00 3.58
188 193 3.065786 ACTGCTTGTGAGTTGTGATTGTG 59.934 43.478 0.00 0.00 0.00 3.33
189 194 3.282021 ACTGCTTGTGAGTTGTGATTGT 58.718 40.909 0.00 0.00 0.00 2.71
190 195 3.976793 ACTGCTTGTGAGTTGTGATTG 57.023 42.857 0.00 0.00 0.00 2.67
191 196 4.641989 AGAAACTGCTTGTGAGTTGTGATT 59.358 37.500 0.00 0.00 33.85 2.57
192 197 4.202441 AGAAACTGCTTGTGAGTTGTGAT 58.798 39.130 0.00 0.00 33.85 3.06
193 198 3.609853 AGAAACTGCTTGTGAGTTGTGA 58.390 40.909 0.00 0.00 33.85 3.58
222 227 2.786578 GTGCGTTGCGATTTTCTTTTGA 59.213 40.909 0.00 0.00 0.00 2.69
270 276 1.315257 CCCTTGGAAGCATTGGACCG 61.315 60.000 0.00 0.00 0.00 4.79
275 281 1.945394 CTCGATCCCTTGGAAGCATTG 59.055 52.381 0.00 0.00 34.34 2.82
276 282 1.748591 GCTCGATCCCTTGGAAGCATT 60.749 52.381 1.39 0.00 34.35 3.56
284 290 1.088340 CAGTGCTGCTCGATCCCTTG 61.088 60.000 0.00 0.00 0.00 3.61
855 865 4.778415 CAGGACCTCGTCGCCGTG 62.778 72.222 0.00 0.00 32.65 4.94
1216 1226 1.153823 CTCCCGATCACACACCGAC 60.154 63.158 0.00 0.00 0.00 4.79
1287 1302 6.632672 GCCTCCAAGATCTACTTACCATTGAA 60.633 42.308 0.00 0.00 37.03 2.69
1357 1372 1.688197 CCAGACCAAACATTGCAACCT 59.312 47.619 0.00 0.00 0.00 3.50
1473 1489 0.872388 GAACGGGTCACCACACAATC 59.128 55.000 0.00 0.00 36.13 2.67
1580 1596 8.668353 TGAAGATGAATAGATTGGAAGTTTTCG 58.332 33.333 0.00 0.00 0.00 3.46
1638 1654 5.981315 TCGTTTACGGATCTGGATGTAATTC 59.019 40.000 6.47 0.00 40.29 2.17
1658 1674 1.881973 TGTAGTTGTCGCTAGGTCGTT 59.118 47.619 0.00 0.00 0.00 3.85
1661 1677 2.260481 GCTTGTAGTTGTCGCTAGGTC 58.740 52.381 0.00 0.00 0.00 3.85
1672 1688 2.408050 CTCGCTTCAGTGCTTGTAGTT 58.592 47.619 0.00 0.00 0.00 2.24
1719 1744 2.857592 CAACAAGTTGTGCTCAGCTT 57.142 45.000 9.79 11.49 43.85 3.74
1789 1814 2.664851 CGGCGGTTGCTGTTCTGA 60.665 61.111 0.00 0.00 42.79 3.27
1834 1859 5.375417 TTCGTGTGTCTTCGGTTTAGATA 57.625 39.130 0.00 0.00 0.00 1.98
1857 1882 4.682860 GGATCTCGTTTTTGTTCGTCTACA 59.317 41.667 0.00 0.00 0.00 2.74
1870 1895 2.280628 GGATTTGCTCGGATCTCGTTT 58.719 47.619 0.00 0.00 40.32 3.60
1871 1896 1.207089 TGGATTTGCTCGGATCTCGTT 59.793 47.619 0.00 0.00 40.32 3.85
1908 1933 1.069090 GCGTGGAGGTGTGTCTTCA 59.931 57.895 0.00 0.00 0.00 3.02
1925 1950 1.789078 CTAGCATCATTGGTGGGCGC 61.789 60.000 0.00 0.00 34.79 6.53
1955 1980 1.383525 CCCTCCTAGCCCCCGTTTA 60.384 63.158 0.00 0.00 0.00 2.01
2004 2031 0.178958 ACTCAGGAAGGTGAGACGGT 60.179 55.000 7.85 0.00 46.02 4.83


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

AutoCloner maintained by Alex Coulton.