Multiple sequence alignment - TraesCS2D01G282600

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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 TraesCS2D01G282600 chr2D 100.000 2309 0 0 1 2309 355482239 355484547 0.000000e+00 4265.0
1 TraesCS2D01G282600 chr2D 95.538 762 34 0 1548 2309 320206197 320205436 0.000000e+00 1219.0
2 TraesCS2D01G282600 chr2D 94.882 762 38 1 1548 2309 192843344 192842584 0.000000e+00 1190.0
3 TraesCS2D01G282600 chr2D 90.323 465 35 5 1083 1547 193993453 193993907 3.280000e-168 601.0
4 TraesCS2D01G282600 chr5A 96.574 1547 52 1 1 1547 315535476 315537021 0.000000e+00 2562.0
5 TraesCS2D01G282600 chr3B 95.995 1548 59 3 1 1547 782022538 782024083 0.000000e+00 2512.0
6 TraesCS2D01G282600 chr2A 95.364 1553 66 5 1 1550 755357970 755356421 0.000000e+00 2464.0
7 TraesCS2D01G282600 chr2A 97.592 1246 28 2 303 1547 377108675 377109919 0.000000e+00 2134.0
8 TraesCS2D01G282600 chr7D 89.090 1549 157 8 3 1547 23563084 23564624 0.000000e+00 1914.0
9 TraesCS2D01G282600 chr7D 88.853 1552 161 8 3 1550 400291674 400290131 0.000000e+00 1897.0
10 TraesCS2D01G282600 chr7D 88.832 1549 161 8 3 1547 135769095 135770635 0.000000e+00 1892.0
11 TraesCS2D01G282600 chr7D 88.702 1549 163 8 3 1547 14171009 14169469 0.000000e+00 1881.0
12 TraesCS2D01G282600 chr7D 94.488 762 42 0 1548 2309 212496705 212495944 0.000000e+00 1175.0
13 TraesCS2D01G282600 chr6B 88.330 1551 166 11 3 1547 96339365 96340906 0.000000e+00 1847.0
14 TraesCS2D01G282600 chr6B 90.164 61 6 0 1486 1546 143431274 143431214 1.900000e-11 80.5
15 TraesCS2D01G282600 chr3D 94.619 762 41 0 1548 2309 86881042 86881803 0.000000e+00 1181.0
16 TraesCS2D01G282600 chr3D 94.488 762 42 0 1548 2309 469117602 469118363 0.000000e+00 1175.0
17 TraesCS2D01G282600 chr3D 94.226 762 44 0 1548 2309 88313855 88314616 0.000000e+00 1164.0
18 TraesCS2D01G282600 chr3D 94.226 762 44 0 1548 2309 97291840 97291079 0.000000e+00 1164.0
19 TraesCS2D01G282600 chr6D 94.488 762 42 0 1548 2309 438496052 438495291 0.000000e+00 1175.0
20 TraesCS2D01G282600 chr1D 94.598 759 40 1 1551 2309 135822683 135821926 0.000000e+00 1173.0
21 TraesCS2D01G282600 chr5D 92.094 468 27 5 1083 1549 450667817 450667359 0.000000e+00 651.0
22 TraesCS2D01G282600 chr4D 91.649 467 28 6 1083 1548 483639168 483638712 9.000000e-179 636.0


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 TraesCS2D01G282600 chr2D 355482239 355484547 2308 False 4265 4265 100.000 1 2309 1 chr2D.!!$F2 2308
1 TraesCS2D01G282600 chr2D 320205436 320206197 761 True 1219 1219 95.538 1548 2309 1 chr2D.!!$R2 761
2 TraesCS2D01G282600 chr2D 192842584 192843344 760 True 1190 1190 94.882 1548 2309 1 chr2D.!!$R1 761
3 TraesCS2D01G282600 chr5A 315535476 315537021 1545 False 2562 2562 96.574 1 1547 1 chr5A.!!$F1 1546
4 TraesCS2D01G282600 chr3B 782022538 782024083 1545 False 2512 2512 95.995 1 1547 1 chr3B.!!$F1 1546
5 TraesCS2D01G282600 chr2A 755356421 755357970 1549 True 2464 2464 95.364 1 1550 1 chr2A.!!$R1 1549
6 TraesCS2D01G282600 chr2A 377108675 377109919 1244 False 2134 2134 97.592 303 1547 1 chr2A.!!$F1 1244
7 TraesCS2D01G282600 chr7D 23563084 23564624 1540 False 1914 1914 89.090 3 1547 1 chr7D.!!$F1 1544
8 TraesCS2D01G282600 chr7D 400290131 400291674 1543 True 1897 1897 88.853 3 1550 1 chr7D.!!$R3 1547
9 TraesCS2D01G282600 chr7D 135769095 135770635 1540 False 1892 1892 88.832 3 1547 1 chr7D.!!$F2 1544
10 TraesCS2D01G282600 chr7D 14169469 14171009 1540 True 1881 1881 88.702 3 1547 1 chr7D.!!$R1 1544
11 TraesCS2D01G282600 chr7D 212495944 212496705 761 True 1175 1175 94.488 1548 2309 1 chr7D.!!$R2 761
12 TraesCS2D01G282600 chr6B 96339365 96340906 1541 False 1847 1847 88.330 3 1547 1 chr6B.!!$F1 1544
13 TraesCS2D01G282600 chr3D 86881042 86881803 761 False 1181 1181 94.619 1548 2309 1 chr3D.!!$F1 761
14 TraesCS2D01G282600 chr3D 469117602 469118363 761 False 1175 1175 94.488 1548 2309 1 chr3D.!!$F3 761
15 TraesCS2D01G282600 chr3D 88313855 88314616 761 False 1164 1164 94.226 1548 2309 1 chr3D.!!$F2 761
16 TraesCS2D01G282600 chr3D 97291079 97291840 761 True 1164 1164 94.226 1548 2309 1 chr3D.!!$R1 761
17 TraesCS2D01G282600 chr6D 438495291 438496052 761 True 1175 1175 94.488 1548 2309 1 chr6D.!!$R1 761
18 TraesCS2D01G282600 chr1D 135821926 135822683 757 True 1173 1173 94.598 1551 2309 1 chr1D.!!$R1 758

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
136 137 1.068748 GTGCTTGTCACAGCCTGAATG 60.069 52.381 0.0 0.0 44.98 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1607 1616 0.672401 GTCAAAACCGGCGGATCTCA 60.672 55.0 35.78 10.41 0.0 3.27 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
79 80 1.604378 CAAGGGGTACAGGGCAGAG 59.396 63.158 0.00 0.00 0.00 3.35
136 137 1.068748 GTGCTTGTCACAGCCTGAATG 60.069 52.381 0.00 0.00 44.98 2.67
140 141 3.120060 GCTTGTCACAGCCTGAATGTTAG 60.120 47.826 0.00 0.00 33.21 2.34
149 150 4.872691 CAGCCTGAATGTTAGTCTTAGTGG 59.127 45.833 0.00 0.00 0.00 4.00
406 408 2.024176 TGACCCCAAGACTAAGAGCA 57.976 50.000 0.00 0.00 0.00 4.26
487 490 5.069318 TCTGGCATGATGTTTTGTTCACTA 58.931 37.500 0.00 0.00 0.00 2.74
523 526 9.283768 TGAGTAAGAAATTGCAGTCTAAATTCA 57.716 29.630 0.00 0.00 0.00 2.57
1331 1336 1.630369 TCTGGAGGTTTGCTAGCATGT 59.370 47.619 20.13 3.11 0.00 3.21
1406 1412 9.305925 GAACAAAGGCAAGAAAAATATATCAGG 57.694 33.333 0.00 0.00 0.00 3.86
1413 1419 9.696917 GGCAAGAAAAATATATCAGGTATTTGG 57.303 33.333 0.00 0.00 33.35 3.28
1556 1565 4.873129 CGGCCCTGATCGTGTCCG 62.873 72.222 0.00 2.67 0.00 4.79
1575 1584 2.628178 CCGCTATCTCCTGTTACCATCA 59.372 50.000 0.00 0.00 0.00 3.07
1607 1616 2.040114 GTTCGGGACCCCCTACCT 59.960 66.667 4.46 0.00 42.67 3.08
1715 1724 5.105635 TCGTCCTTAAAGACAATATCACCGT 60.106 40.000 5.12 0.00 36.52 4.83
1830 1839 4.134563 CCATCGAAAATCCCCTTCGTATT 58.865 43.478 5.04 0.00 44.64 1.89
1836 1845 3.454371 AATCCCCTTCGTATTGACTCG 57.546 47.619 0.00 0.00 0.00 4.18
1863 1872 1.153107 CAAGCAGATGGATCCGGCA 60.153 57.895 16.60 0.00 32.11 5.69
1906 1915 4.529219 TTGATCGCATCGCCGCCT 62.529 61.111 0.00 0.00 0.00 5.52
1928 1937 1.217882 GGAATCGCCACAGATTACGG 58.782 55.000 0.00 0.00 40.58 4.02
2038 2047 4.591072 ACTCTTCCCCTATACTGAAGATGC 59.409 45.833 0.00 0.00 42.46 3.91
2142 2151 1.524621 CGGGCATAGGCAACCAGAG 60.525 63.158 0.15 0.00 43.71 3.35
2164 2173 0.970937 TACTCCGGAGCTTGGACTGG 60.971 60.000 31.56 4.80 0.00 4.00
2277 2286 4.702831 TGAGCATACAACAACAGTCTCAA 58.297 39.130 0.00 0.00 0.00 3.02
2295 2304 2.021457 CAAGAAACGGTCCACCACTTT 58.979 47.619 0.00 0.00 35.14 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 1.238439 TTAGTTGCAAGCACTCTGCC 58.762 50.000 0.00 0.00 46.52 4.85
136 137 7.553044 AGATTTTGCCATACCACTAAGACTAAC 59.447 37.037 0.00 0.00 0.00 2.34
140 141 6.555315 CAAGATTTTGCCATACCACTAAGAC 58.445 40.000 0.00 0.00 0.00 3.01
406 408 4.248058 GCACTAGCCAAAGATTTTGCATT 58.752 39.130 4.45 0.00 31.82 3.56
487 490 8.121305 TGCAATTTCTTACTCACCATGTTTAT 57.879 30.769 0.00 0.00 0.00 1.40
1525 1534 1.378514 GGCCGGCTCAAGGATTTCA 60.379 57.895 28.56 0.00 0.00 2.69
1575 1584 1.604693 CCGAACTGTGCGTCTAAGGTT 60.605 52.381 7.51 0.00 0.00 3.50
1607 1616 0.672401 GTCAAAACCGGCGGATCTCA 60.672 55.000 35.78 10.41 0.00 3.27
1715 1724 2.683933 GGGCCAGTTCTCCTCCGA 60.684 66.667 4.39 0.00 0.00 4.55
1751 1760 2.124901 TCATGGTAAAGCCGCCCG 60.125 61.111 0.00 0.00 41.21 6.13
1830 1839 1.138069 TGCTTGGAGTGTTTCGAGTCA 59.862 47.619 0.00 0.00 0.00 3.41
1836 1845 2.783135 TCCATCTGCTTGGAGTGTTTC 58.217 47.619 0.21 0.00 40.90 2.78
1863 1872 6.238402 GGAGCTCGTTTAAAGACAAAAACTCT 60.238 38.462 7.83 0.00 34.21 3.24
1906 1915 2.639065 GTAATCTGTGGCGATTCCCAA 58.361 47.619 0.00 0.00 36.46 4.12
1928 1937 0.812811 GGGTTTAAGCCCGATCCGAC 60.813 60.000 12.10 0.00 39.17 4.79
2038 2047 2.106332 GGCGACCCGGACATAGTG 59.894 66.667 0.73 0.00 0.00 2.74
2164 2173 3.810386 GTCTGAAGGTTTTCCAGACTCAC 59.190 47.826 12.80 0.00 43.73 3.51
2277 2286 2.021457 CAAAAGTGGTGGACCGTTTCT 58.979 47.619 0.00 0.00 39.43 2.52


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

AutoCloner maintained by Alex Coulton.