Multiple sequence alignment - TraesCS2D01G210600

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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 TraesCS2D01G210600 chr2D 100.000 2280 0 0 1 2280 166867545 166865266 0.000000e+00 4211.0
1 TraesCS2D01G210600 chr2B 95.631 2289 67 8 1 2280 230967198 230969462 0.000000e+00 3642.0
2 TraesCS2D01G210600 chr2B 77.162 1191 244 25 119 1296 698957375 698956200 0.000000e+00 667.0
3 TraesCS2D01G210600 chr2A 91.593 2272 147 19 38 2280 183512249 183514505 0.000000e+00 3097.0
4 TraesCS2D01G210600 chr2A 100.000 33 0 0 1 33 183408317 183408349 6.800000e-06 62.1
5 TraesCS2D01G210600 chr5D 77.881 1189 243 16 117 1296 565330792 565329615 0.000000e+00 721.0
6 TraesCS2D01G210600 chr1B 76.535 1189 260 16 117 1297 282309672 282310849 1.150000e-177 632.0
7 TraesCS2D01G210600 chr4B 80.297 538 97 7 773 1307 665225346 665224815 4.560000e-107 398.0
8 TraesCS2D01G210600 chr4A 76.727 666 148 5 633 1296 562294590 562295250 4.630000e-97 364.0


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 TraesCS2D01G210600 chr2D 166865266 166867545 2279 True 4211 4211 100.000 1 2280 1 chr2D.!!$R1 2279
1 TraesCS2D01G210600 chr2B 230967198 230969462 2264 False 3642 3642 95.631 1 2280 1 chr2B.!!$F1 2279
2 TraesCS2D01G210600 chr2B 698956200 698957375 1175 True 667 667 77.162 119 1296 1 chr2B.!!$R1 1177
3 TraesCS2D01G210600 chr2A 183512249 183514505 2256 False 3097 3097 91.593 38 2280 1 chr2A.!!$F2 2242
4 TraesCS2D01G210600 chr5D 565329615 565330792 1177 True 721 721 77.881 117 1296 1 chr5D.!!$R1 1179
5 TraesCS2D01G210600 chr1B 282309672 282310849 1177 False 632 632 76.535 117 1297 1 chr1B.!!$F1 1180
6 TraesCS2D01G210600 chr4B 665224815 665225346 531 True 398 398 80.297 773 1307 1 chr4B.!!$R1 534
7 TraesCS2D01G210600 chr4A 562294590 562295250 660 False 364 364 76.727 633 1296 1 chr4A.!!$F1 663

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
281 282 0.326927 TTTGGCTTTAGACGAGGGGG 59.673 55.0 0.0 0.0 0.0 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 1458 0.585357 TCTACGAACTAGGATCGCGC 59.415 55.0 17.05 0.0 43.88 6.86 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
121 122 9.309516 CGATAGGAGCTTGTTATACAAACTTTA 57.690 33.333 0.00 0.00 34.94 1.85
162 163 6.559810 CGACCATATTAAACATTCCTTTGCA 58.440 36.000 0.00 0.00 0.00 4.08
242 243 4.893608 TGCTAAATCGGCATATTGAGCTA 58.106 39.130 16.50 5.11 41.97 3.32
253 254 5.063186 GGCATATTGAGCTATCGTGAATCAG 59.937 44.000 0.00 0.00 0.00 2.90
281 282 0.326927 TTTGGCTTTAGACGAGGGGG 59.673 55.000 0.00 0.00 0.00 5.40
309 310 3.184541 CCGGTACTTTAGTGGATCAACG 58.815 50.000 0.00 0.00 0.00 4.10
310 311 3.184541 CGGTACTTTAGTGGATCAACGG 58.815 50.000 0.00 0.00 0.00 4.44
439 440 6.170506 TCGCCACATAAGAGAAATTAACACT 58.829 36.000 0.00 0.00 0.00 3.55
622 623 4.801330 TTCTGAAAAGGACAGAGCGATA 57.199 40.909 0.00 0.00 43.67 2.92
669 670 1.863454 GATGTCTCGCAATCGCTTGAT 59.137 47.619 2.58 0.00 34.04 2.57
810 812 7.256799 CCCCCAGATGTTTCTCATATCAAGATA 60.257 40.741 0.00 0.00 36.83 1.98
1054 1058 4.046938 TGGAATTCTCGCTACACTGATC 57.953 45.455 5.23 0.00 0.00 2.92
1055 1059 3.046390 GGAATTCTCGCTACACTGATCG 58.954 50.000 5.23 0.00 0.00 3.69
1056 1060 2.783828 ATTCTCGCTACACTGATCGG 57.216 50.000 0.00 0.00 0.00 4.18
1057 1061 0.738975 TTCTCGCTACACTGATCGGG 59.261 55.000 6.47 0.00 0.00 5.14
1155 1160 5.845103 TGTACTAAGATCAACAAACGGTCA 58.155 37.500 0.00 0.00 0.00 4.02
1175 1180 6.051717 GGTCATGCACATCTCTGTACTAATT 58.948 40.000 0.00 0.00 33.14 1.40
1201 1206 3.300852 TGTACGCTTAATGTGACCGAA 57.699 42.857 0.00 0.00 0.00 4.30
1203 1208 4.056740 TGTACGCTTAATGTGACCGAAAA 58.943 39.130 0.00 0.00 0.00 2.29
1251 1265 0.835941 ATCAGTAGCTTCCTGGCTGG 59.164 55.000 3.65 3.65 43.01 4.85
1254 1268 0.325671 AGTAGCTTCCTGGCTGGCTA 60.326 55.000 5.39 9.73 43.01 3.93
1300 1315 3.399440 AGCTCTGTGAAGTTCCTTGAG 57.601 47.619 0.00 6.15 0.00 3.02
1380 1397 3.353557 ACAGTAGCATCTCCGTGAGTTA 58.646 45.455 0.00 0.00 0.00 2.24
1438 1458 1.096967 TAGCATTGCTGGGCATGTCG 61.097 55.000 21.31 0.00 40.10 4.35
1597 1628 3.190849 CATCCACAGTCCGCGCTG 61.191 66.667 5.56 11.54 41.92 5.18
1989 2023 4.202243 GCCATAAACTCTCTCATCTCTGCT 60.202 45.833 0.00 0.00 0.00 4.24
2001 2035 1.518133 CTCTGCTTCCTTCTCCGCG 60.518 63.158 0.00 0.00 0.00 6.46
2039 2073 1.300963 GGCAGCTCATCAGGGACAA 59.699 57.895 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 163 1.513087 ATCTTTGCCCCCTCCTTGCT 61.513 55.000 0.00 0.00 0.00 3.91
242 243 3.238108 ACGCTCTTTCTGATTCACGAT 57.762 42.857 0.00 0.00 0.00 3.73
281 282 7.043565 TGATCCACTAAAGTACCGGTAATTTC 58.956 38.462 35.55 22.99 35.38 2.17
310 311 5.710513 TCCAAATAGCATTCCACATATGC 57.289 39.130 1.58 0.00 46.78 3.14
439 440 3.689161 CCATGGCGAGACAAATCTTACAA 59.311 43.478 0.00 0.00 34.34 2.41
622 623 1.305219 CCCACATCACCGCGACAATT 61.305 55.000 8.23 0.00 0.00 2.32
669 670 3.114606 TCTATCCTTTCCAGGTCATGCA 58.885 45.455 0.00 0.00 41.69 3.96
810 812 3.120321 TGAACTGCACCGTCTGTATTT 57.880 42.857 0.00 0.00 0.00 1.40
1155 1160 7.739825 ACCATAATTAGTACAGAGATGTGCAT 58.260 34.615 0.00 0.00 0.00 3.96
1175 1180 4.871557 GGTCACATTAAGCGTACAACCATA 59.128 41.667 0.00 0.00 0.00 2.74
1201 1206 7.133483 AGATAGGGATAGTGTCTAACCAGTTT 58.867 38.462 5.67 0.00 0.00 2.66
1203 1208 6.282568 AGATAGGGATAGTGTCTAACCAGT 57.717 41.667 5.67 0.00 0.00 4.00
1251 1265 1.955762 GAATGCATTCGCCGAATAGC 58.044 50.000 22.90 17.30 37.32 2.97
1389 1406 5.585047 ACGAAAAATGTTAGGAGATGCTACC 59.415 40.000 0.00 0.00 0.00 3.18
1401 1421 6.709145 ATGCTACACGTACGAAAAATGTTA 57.291 33.333 24.41 6.07 0.00 2.41
1438 1458 0.585357 TCTACGAACTAGGATCGCGC 59.415 55.000 17.05 0.00 43.88 6.86
1745 1776 6.964807 TTACTAGTTATGGTATGCGGAGAA 57.035 37.500 0.00 0.00 0.00 2.87
1989 2023 2.283676 AGGGACGCGGAGAAGGAA 60.284 61.111 12.47 0.00 0.00 3.36
2001 2035 1.219393 CTTGAGCGGGAAGAGGGAC 59.781 63.158 0.00 0.00 0.00 4.46
2039 2073 2.030562 CGTGGAGCCGGTTGAACT 59.969 61.111 1.90 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.