Multiple sequence alignment - TraesCS2D01G089700

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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 TraesCS2D01G089700 chr2D 100.000 2297 0 0 1 2297 39589461 39591757 0 4242
1 TraesCS2D01G089700 chr2D 96.875 2304 65 5 1 2297 644701523 644703826 0 3849
2 TraesCS2D01G089700 chrUn 97.004 2303 62 5 1 2297 261514803 261512502 0 3864
3 TraesCS2D01G089700 chrUn 96.874 2303 63 5 1 2297 45099055 45101354 0 3845
4 TraesCS2D01G089700 chr5B 96.874 2303 63 5 1 2297 130613164 130615463 0 3845
5 TraesCS2D01G089700 chr5B 96.658 2304 70 5 1 2297 130570496 130568193 0 3821
6 TraesCS2D01G089700 chr5B 96.613 2303 69 5 1 2297 130608140 130610439 0 3812
7 TraesCS2D01G089700 chr3A 96.743 2303 67 5 1 2297 66032051 66029751 0 3831
8 TraesCS2D01G089700 chr7B 96.439 2303 74 5 1 2297 743035438 743033138 0 3792
9 TraesCS2D01G089700 chr2B 96.353 2303 75 6 1 2297 112867376 112869675 0 3779


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 TraesCS2D01G089700 chr2D 39589461 39591757 2296 False 4242.0 4242 100.0000 1 2297 1 chr2D.!!$F1 2296
1 TraesCS2D01G089700 chr2D 644701523 644703826 2303 False 3849.0 3849 96.8750 1 2297 1 chr2D.!!$F2 2296
2 TraesCS2D01G089700 chrUn 261512502 261514803 2301 True 3864.0 3864 97.0040 1 2297 1 chrUn.!!$R1 2296
3 TraesCS2D01G089700 chrUn 45099055 45101354 2299 False 3845.0 3845 96.8740 1 2297 1 chrUn.!!$F1 2296
4 TraesCS2D01G089700 chr5B 130608140 130615463 7323 False 3828.5 3845 96.7435 1 2297 2 chr5B.!!$F1 2296
5 TraesCS2D01G089700 chr5B 130568193 130570496 2303 True 3821.0 3821 96.6580 1 2297 1 chr5B.!!$R1 2296
6 TraesCS2D01G089700 chr3A 66029751 66032051 2300 True 3831.0 3831 96.7430 1 2297 1 chr3A.!!$R1 2296
7 TraesCS2D01G089700 chr7B 743033138 743035438 2300 True 3792.0 3792 96.4390 1 2297 1 chr7B.!!$R1 2296
8 TraesCS2D01G089700 chr2B 112867376 112869675 2299 False 3779.0 3779 96.3530 1 2297 1 chr2B.!!$F1 2296


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
355 359 0.040067 GAGTTAACGACCGGACGTGT 60.04 55.0 31.17 21.86 45.83 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 6921 0.340208 TTTGGGGGAAAACTGGTGGT 59.66 50.0 0.0 0.0 0.0 4.16 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
51 52 3.756434 GGCTTGGATTACTTAGTGTTGCA 59.244 43.478 0.00 0.00 0.00 4.08
93 94 0.398318 GGGATGCGGAGGAGCTATTT 59.602 55.000 0.00 0.00 32.33 1.40
95 96 2.576615 GGATGCGGAGGAGCTATTTTT 58.423 47.619 0.00 0.00 32.33 1.94
121 122 0.600255 CTCCCTAACCTAATGCGGCG 60.600 60.000 0.51 0.51 0.00 6.46
188 189 2.513666 CGCAAGGCCGGCTAATCA 60.514 61.111 28.56 0.00 0.00 2.57
238 239 2.027192 GGTTCAGGAAGGCACATGAGTA 60.027 50.000 0.00 0.00 32.42 2.59
239 240 3.559171 GGTTCAGGAAGGCACATGAGTAA 60.559 47.826 0.00 0.00 32.42 2.24
297 298 1.398390 GTAGGTACTTGTGCATGCAGC 59.602 52.381 23.41 16.34 41.75 5.25
307 311 2.749044 CATGCAGCTGAGGCGGTT 60.749 61.111 20.43 0.00 44.37 4.44
355 359 0.040067 GAGTTAACGACCGGACGTGT 60.040 55.000 31.17 21.86 45.83 4.49
377 381 1.584724 CAACCTAGGGATCACCAGGT 58.415 55.000 9.57 9.57 46.30 4.00
406 5434 2.508716 TCGCTCTATAGGGATATCGGGT 59.491 50.000 2.98 0.00 39.58 5.28
587 5617 4.642429 GGTAGATGATAATGCGAAAGGGT 58.358 43.478 0.00 0.00 0.00 4.34
675 5705 5.476983 AGGGGACATGATCAATAGAACCTA 58.523 41.667 0.00 0.00 0.00 3.08
677 5707 5.308237 GGGGACATGATCAATAGAACCTAGT 59.692 44.000 0.00 0.00 0.00 2.57
700 5730 2.621672 ATCCGGGCTGGGATAGTGGT 62.622 60.000 13.58 0.00 44.97 4.16
721 5751 3.054655 GTGCCCATTCCTAACCAGTTCTA 60.055 47.826 0.00 0.00 0.00 2.10
733 5764 3.816994 ACCAGTTCTAAAAGGTTCGCTT 58.183 40.909 0.00 0.00 0.00 4.68
887 5918 3.295304 TTGCTTCTGCTCGCCGCTA 62.295 57.895 0.00 0.00 40.48 4.26
921 5952 9.166222 TCTCCTAACTATTGCCCATTTATTCTA 57.834 33.333 0.00 0.00 0.00 2.10
1009 6041 4.390264 TGGTACCATTTCGATGTGTTTCA 58.610 39.130 11.60 0.00 0.00 2.69
1169 6201 3.950087 TTATGTGATCGCAGCATCAAC 57.050 42.857 15.24 0.00 34.50 3.18
1176 6208 3.441222 TGATCGCAGCATCAACAAGAAAT 59.559 39.130 5.37 0.00 29.41 2.17
1196 6228 8.198807 AGAAATTCTGAATTTTCCATGGAAGT 57.801 30.769 25.69 16.45 40.97 3.01
1198 6230 7.543359 AATTCTGAATTTTCCATGGAAGTCA 57.457 32.000 25.69 25.10 35.38 3.41
1199 6231 6.975196 TTCTGAATTTTCCATGGAAGTCAA 57.025 33.333 25.69 18.27 35.38 3.18
1382 6414 0.102120 GGCTGTGTCTCGATCTCCTG 59.898 60.000 0.00 0.00 0.00 3.86
1383 6415 0.814457 GCTGTGTCTCGATCTCCTGT 59.186 55.000 0.00 0.00 0.00 4.00
1387 6419 0.960861 TGTCTCGATCTCCTGTGCGT 60.961 55.000 0.00 0.00 0.00 5.24
1402 6434 5.105513 TCCTGTGCGTGAAAGATAAGATACA 60.106 40.000 0.00 0.00 0.00 2.29
1412 6444 4.726035 AGATAAGATACAGGAGACGGGA 57.274 45.455 0.00 0.00 0.00 5.14
1454 6486 2.844348 ACCCTTGGTCTAATTCCACGAT 59.156 45.455 0.00 0.00 34.45 3.73
1476 6508 2.723719 GAGTCGGCGTGGCGTAAAC 61.724 63.158 15.55 6.85 0.00 2.01
1512 6544 2.981859 TAGAGCAAAATCCCCGTCTC 57.018 50.000 0.00 0.00 0.00 3.36
1555 6587 2.503382 GCAACGAAAAAGGGGCCCA 61.503 57.895 27.72 0.00 0.00 5.36
1557 6589 0.249699 CAACGAAAAAGGGGCCCAAC 60.250 55.000 27.72 7.11 0.00 3.77
1619 6651 1.399714 TCCAGTGTCACACGTTCTCT 58.600 50.000 1.22 0.00 39.64 3.10
1791 6823 2.482142 CCAGAAAGACTCGGTCATAGGC 60.482 54.545 6.78 0.00 34.60 3.93
1889 6921 5.523438 AAAGAATTAACACGCCAAAAGGA 57.477 34.783 0.00 0.00 0.00 3.36
1897 6929 1.528309 CGCCAAAAGGACCACCAGT 60.528 57.895 0.00 0.00 38.94 4.00
2050 7082 9.561069 AAAGAAATGTGAGAATGTAGTTACAGT 57.439 29.630 0.00 0.00 39.92 3.55
2057 7089 9.772973 TGTGAGAATGTAGTTACAGTTGTAAAT 57.227 29.630 9.53 9.53 41.58 1.40
2109 7141 1.906824 GGGGCGTCCTATCCGATGA 60.907 63.158 5.77 0.00 0.00 2.92
2257 7289 7.543868 GCTATATCATGACTGCTAGAACGAAAT 59.456 37.037 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 1.140134 AGGTTAGGGAGCTGGGCAAA 61.140 55.000 0.00 0.00 34.08 3.68
95 96 0.252974 TTAGGTTAGGGAGCTGGGCA 60.253 55.000 0.00 0.00 37.30 5.36
121 122 2.253403 CTAAGGTTCCCTGCGGTCCC 62.253 65.000 0.00 0.00 32.13 4.46
188 189 1.153289 CCTTGCTCCTGCTGCGTAT 60.153 57.895 0.00 0.00 40.48 3.06
238 239 4.808895 TCGCACATTCATAATAGCGTTCTT 59.191 37.500 14.26 0.00 41.97 2.52
239 240 4.209288 GTCGCACATTCATAATAGCGTTCT 59.791 41.667 14.26 0.00 41.97 3.01
285 286 2.632544 GCCTCAGCTGCATGCACAA 61.633 57.895 18.46 1.20 45.94 3.33
297 298 0.970937 TCTAGGACCAACCGCCTCAG 60.971 60.000 0.00 0.00 44.74 3.35
307 311 1.223487 GCCGCCATTTCTAGGACCA 59.777 57.895 0.00 0.00 0.00 4.02
355 359 1.281867 CTGGTGATCCCTAGGTTGCAA 59.718 52.381 8.29 0.00 0.00 4.08
675 5705 3.411517 CCCAGCCCGGATCCAACT 61.412 66.667 13.41 2.16 36.56 3.16
677 5707 1.074090 TATCCCAGCCCGGATCCAA 60.074 57.895 13.41 0.00 41.92 3.53
700 5730 1.992557 AGAACTGGTTAGGAATGGGCA 59.007 47.619 0.00 0.00 0.00 5.36
733 5764 3.990369 AGTGGTTAGTACCTCCAGCATA 58.010 45.455 2.19 0.00 45.27 3.14
887 5918 2.074729 ATAGTTAGGAGAGGTGCGCT 57.925 50.000 9.73 0.00 0.00 5.92
986 6018 4.822350 TGAAACACATCGAAATGGTACCAA 59.178 37.500 20.76 1.33 37.19 3.67
1017 6049 5.829924 AGAAGCATCAAACCTCTCTTTTTCA 59.170 36.000 0.00 0.00 0.00 2.69
1137 6169 7.253420 GCTGCGATCACATAAAAACATAAACTG 60.253 37.037 0.00 0.00 0.00 3.16
1169 6201 8.836268 TTCCATGGAAAATTCAGAATTTCTTG 57.164 30.769 25.13 15.08 40.05 3.02
1176 6208 6.550854 AGTTGACTTCCATGGAAAATTCAGAA 59.449 34.615 26.87 12.85 33.34 3.02
1190 6222 9.300681 AGATCAAATATTTTGAGTTGACTTCCA 57.699 29.630 8.47 0.00 36.35 3.53
1198 6230 9.023962 TGCACCTAAGATCAAATATTTTGAGTT 57.976 29.630 8.47 7.05 0.00 3.01
1199 6231 8.579850 TGCACCTAAGATCAAATATTTTGAGT 57.420 30.769 8.47 0.00 0.00 3.41
1382 6414 5.348986 TCCTGTATCTTATCTTTCACGCAC 58.651 41.667 0.00 0.00 0.00 5.34
1383 6415 5.359860 TCTCCTGTATCTTATCTTTCACGCA 59.640 40.000 0.00 0.00 0.00 5.24
1387 6419 5.302059 CCCGTCTCCTGTATCTTATCTTTCA 59.698 44.000 0.00 0.00 0.00 2.69
1402 6434 0.861155 ACCATAGGATCCCGTCTCCT 59.139 55.000 8.55 3.52 45.22 3.69
1412 6444 4.127918 TCGAAGACCCATACCATAGGAT 57.872 45.455 0.00 0.00 0.00 3.24
1555 6587 3.808174 GTCGCTCCTTTAGTTGAAGTGTT 59.192 43.478 0.00 0.00 0.00 3.32
1557 6589 2.737252 GGTCGCTCCTTTAGTTGAAGTG 59.263 50.000 0.00 0.00 0.00 3.16
1600 6632 1.399714 AGAGAACGTGTGACACTGGA 58.600 50.000 14.42 0.00 31.34 3.86
1619 6651 0.635009 ACTGGATCCCTTCGGACCTA 59.365 55.000 9.90 0.00 42.48 3.08
1791 6823 0.801067 GCGCGTAGGTGGTCTAAGTG 60.801 60.000 8.43 0.00 39.71 3.16
1864 6896 4.555348 TTTGGCGTGTTAATTCTTTCGT 57.445 36.364 0.00 0.00 0.00 3.85
1889 6921 0.340208 TTTGGGGGAAAACTGGTGGT 59.660 50.000 0.00 0.00 0.00 4.16
1911 6943 1.482593 CAGTAAGCAACGGATCTCCCT 59.517 52.381 0.00 0.00 0.00 4.20
2057 7089 7.837863 ACCAAGAGAACGAGATATTGACTTTA 58.162 34.615 0.00 0.00 0.00 1.85
2109 7141 2.158986 CGACAGAGGCTCCTCATTCATT 60.159 50.000 17.40 0.00 44.99 2.57
2176 7208 2.565391 TCTTGGCTTGAATCACCGACTA 59.435 45.455 0.00 0.00 0.00 2.59
2183 7215 1.159285 CGCACTCTTGGCTTGAATCA 58.841 50.000 0.00 0.00 0.00 2.57
2257 7289 4.644234 TGGTACGAAAATACTCATCGGGTA 59.356 41.667 0.00 0.00 40.71 3.69



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

AutoCloner maintained by Alex Coulton.