Multiple sequence alignment - TraesCS4A01G141300

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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 TraesCS4A01G141300 chr4A 100.000 2549 0 0 1 2549 219340681 219338133 0 4708
1 TraesCS4A01G141300 chr3A 95.290 2569 96 11 2 2549 672879243 672876679 0 4050
2 TraesCS4A01G141300 chr3B 95.216 2571 98 11 2 2549 201561586 201559018 0 4043
3 TraesCS4A01G141300 chr1B 94.942 2570 105 11 2 2549 633729676 633727110 0 4002
4 TraesCS4A01G141300 chr5D 94.438 2571 117 15 2 2549 432293531 432290964 0 3932
5 TraesCS4A01G141300 chr5B 93.855 2571 119 17 2 2549 432875913 432878467 0 3836
6 TraesCS4A01G141300 chr5B 93.942 1172 50 9 1399 2549 413608022 413609193 0 1751
7 TraesCS4A01G141300 chr2D 95.637 2269 80 12 298 2549 33933300 33935566 0 3624
8 TraesCS4A01G141300 chr2D 95.161 1984 69 15 2 1966 272802475 272800500 0 3107
9 TraesCS4A01G141300 chr2D 95.838 1802 63 7 760 2549 630270241 630272042 0 2902
10 TraesCS4A01G141300 chr7A 92.053 2567 171 25 2 2549 352678257 352675705 0 3579
11 TraesCS4A01G141300 chr4D 93.655 1576 81 8 992 2549 245648863 245650437 0 2338
12 TraesCS4A01G141300 chrUn 95.969 918 33 2 1636 2549 371049286 371050203 0 1487


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 TraesCS4A01G141300 chr4A 219338133 219340681 2548 True 4708 4708 100.000 1 2549 1 chr4A.!!$R1 2548
1 TraesCS4A01G141300 chr3A 672876679 672879243 2564 True 4050 4050 95.290 2 2549 1 chr3A.!!$R1 2547
2 TraesCS4A01G141300 chr3B 201559018 201561586 2568 True 4043 4043 95.216 2 2549 1 chr3B.!!$R1 2547
3 TraesCS4A01G141300 chr1B 633727110 633729676 2566 True 4002 4002 94.942 2 2549 1 chr1B.!!$R1 2547
4 TraesCS4A01G141300 chr5D 432290964 432293531 2567 True 3932 3932 94.438 2 2549 1 chr5D.!!$R1 2547
5 TraesCS4A01G141300 chr5B 432875913 432878467 2554 False 3836 3836 93.855 2 2549 1 chr5B.!!$F2 2547
6 TraesCS4A01G141300 chr5B 413608022 413609193 1171 False 1751 1751 93.942 1399 2549 1 chr5B.!!$F1 1150
7 TraesCS4A01G141300 chr2D 33933300 33935566 2266 False 3624 3624 95.637 298 2549 1 chr2D.!!$F1 2251
8 TraesCS4A01G141300 chr2D 272800500 272802475 1975 True 3107 3107 95.161 2 1966 1 chr2D.!!$R1 1964
9 TraesCS4A01G141300 chr2D 630270241 630272042 1801 False 2902 2902 95.838 760 2549 1 chr2D.!!$F2 1789
10 TraesCS4A01G141300 chr7A 352675705 352678257 2552 True 3579 3579 92.053 2 2549 1 chr7A.!!$R1 2547
11 TraesCS4A01G141300 chr4D 245648863 245650437 1574 False 2338 2338 93.655 992 2549 1 chr4D.!!$F1 1557
12 TraesCS4A01G141300 chrUn 371049286 371050203 917 False 1487 1487 95.969 1636 2549 1 chrUn.!!$F1 913

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
656 664 1.376812 CTACTTGGGCGGGTGGAAC 60.377 63.158 0.0 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2149 2201 3.716431 AGTCCAAAGAATTCCATGCCAT 58.284 40.909 0.65 0.0 0.0 4.4 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
161 163 5.365021 AAGGATGAGATCAATTCGGAAGT 57.635 39.130 0.00 0.00 0.00 3.01
164 166 2.632377 TGAGATCAATTCGGAAGTGCC 58.368 47.619 12.96 7.60 0.00 5.01
286 292 7.712204 ACAAAACAGTCCTTTCCTTTTTCTA 57.288 32.000 0.00 0.00 0.00 2.10
291 297 7.511959 ACAGTCCTTTCCTTTTTCTAATCAC 57.488 36.000 0.00 0.00 0.00 3.06
339 345 6.561737 TTCATGTACGGTTTTGAAATAGCA 57.438 33.333 0.00 0.00 0.00 3.49
358 364 4.770795 AGCAGTGGGAACTATGATGTTAC 58.229 43.478 0.00 0.00 0.00 2.50
451 458 3.214328 GGATGGAATATTTGGCGTCAGT 58.786 45.455 0.00 0.00 0.00 3.41
520 528 7.396055 TGAAAGATTACCCTTTGATTTACCAGG 59.604 37.037 0.00 0.00 36.58 4.45
547 555 6.406737 GCGGAGGAAGAATTAGTAGTAGGTTT 60.407 42.308 0.00 0.00 0.00 3.27
554 562 8.543862 AAGAATTAGTAGTAGGTTTCCAAACG 57.456 34.615 0.00 0.00 39.77 3.60
562 570 8.761689 AGTAGTAGGTTTCCAAACGGAATATTA 58.238 33.333 0.00 0.00 42.22 0.98
656 664 1.376812 CTACTTGGGCGGGTGGAAC 60.377 63.158 0.00 0.00 0.00 3.62
733 744 7.227116 CAGTTGGAATTTTGGAAATGACAATGT 59.773 33.333 0.00 0.00 0.00 2.71
734 745 8.428063 AGTTGGAATTTTGGAAATGACAATGTA 58.572 29.630 0.00 0.00 0.00 2.29
824 836 4.056740 CGAGGATGAGAATGGATCAGTTG 58.943 47.826 0.00 0.00 0.00 3.16
981 993 9.003658 TCTCAAACAAGAGAAAGAAACATATCC 57.996 33.333 0.00 0.00 41.45 2.59
1029 1041 3.658705 TGTTCCCTATGGTAACTGGGTTT 59.341 43.478 0.00 0.00 41.11 3.27
1055 1067 7.809546 TGAGTTATGGTCAACAAACAATACA 57.190 32.000 0.00 0.00 0.00 2.29
1064 1076 7.090173 GGTCAACAAACAATACATGCTACAAT 58.910 34.615 0.00 0.00 0.00 2.71
1134 1146 6.655078 TTACCTATAACGATTCACTACCCC 57.345 41.667 0.00 0.00 0.00 4.95
1228 1240 6.462073 GTGAAGTATGTGTTCACGTATGTT 57.538 37.500 7.91 5.64 43.17 2.71
1235 1247 4.417506 TGTGTTCACGTATGTTCGATAGG 58.582 43.478 0.00 0.00 34.70 2.57
1269 1281 5.243730 TGTGGATTGGAGATTTGAAAAGGAC 59.756 40.000 0.00 0.00 0.00 3.85
1358 1370 4.100344 TGTTGAGTACTGTCCAACAAGCTA 59.900 41.667 20.40 3.51 44.66 3.32
1431 1443 9.384682 GAATTGAATTACAACCAAATTGCTTTG 57.615 29.630 0.00 4.61 42.62 2.77
1841 1878 5.072741 TGAGATTCTTATGCTATTTGGGGC 58.927 41.667 0.00 0.00 0.00 5.80
1980 2022 3.000727 ACTTTGTAGCTATCGCACAACC 58.999 45.455 0.00 0.00 37.10 3.77
1999 2041 5.044846 ACAACCTCTTATTTATGTGGGAGCT 60.045 40.000 0.00 0.00 0.00 4.09
2035 2087 8.192068 TGATCATATTCGTTGTAATGTTCGTT 57.808 30.769 0.00 0.00 0.00 3.85
2099 2151 2.224523 GGACATGGGTTCACTTCACTCA 60.225 50.000 0.00 0.00 0.00 3.41
2149 2201 9.467796 CTAATGACTACTATCCCAGATACATCA 57.532 37.037 0.00 0.00 0.00 3.07
2153 2205 4.833478 ACTATCCCAGATACATCATGGC 57.167 45.455 0.00 0.00 32.46 4.40
2176 2228 5.393461 GCATGGAATTCTTTGGACTACAAGG 60.393 44.000 5.23 0.00 40.82 3.61
2316 2368 3.931907 AGGTGCAATTACTATGGCTCA 57.068 42.857 0.00 0.00 31.51 4.26
2462 2514 9.698309 TTTTCTCTTTTGTTGTGTAATTGTTCA 57.302 25.926 0.00 0.00 0.00 3.18
2514 2566 6.834969 TCTTGCCCTCATATTGAAATGAATCA 59.165 34.615 0.00 0.00 35.51 2.57
2517 2569 6.041182 TGCCCTCATATTGAAATGAATCAAGG 59.959 38.462 0.00 0.00 42.21 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 163 4.870426 CGTCTGCTAGAATAAGAAAAGGCA 59.130 41.667 0.00 0.00 0.00 4.75
164 166 7.778470 ATTCCGTCTGCTAGAATAAGAAAAG 57.222 36.000 0.00 0.00 0.00 2.27
286 292 4.437239 CTTCATACGGCTTCTCTGTGATT 58.563 43.478 0.00 0.00 35.51 2.57
291 297 2.593346 AGCTTCATACGGCTTCTCTG 57.407 50.000 0.00 0.00 34.96 3.35
358 364 9.347934 GAACTGTTAGATAATCATAGTCGATGG 57.652 37.037 0.00 0.00 36.08 3.51
391 397 5.874810 TGACTGTGCTTCAACTATATCAACC 59.125 40.000 0.00 0.00 0.00 3.77
520 528 4.922471 ACTACTAATTCTTCCTCCGCTC 57.078 45.455 0.00 0.00 0.00 5.03
547 555 6.159299 TGATACCGTAATATTCCGTTTGGA 57.841 37.500 0.00 0.00 44.61 3.53
853 865 4.821532 AAGAGATTGCCCAGGGAAATAT 57.178 40.909 12.45 9.21 0.00 1.28
1029 1041 9.508642 TGTATTGTTTGTTGACCATAACTCATA 57.491 29.630 0.00 0.00 0.00 2.15
1055 1067 7.338710 ACTTTGACCTATGTACATTGTAGCAT 58.661 34.615 14.77 13.01 0.00 3.79
1134 1146 7.641411 CGCTCTGGTGTAATTGATTTTTCATAG 59.359 37.037 0.00 0.00 0.00 2.23
1228 1240 3.833650 TCCACAACAGGTAAACCTATCGA 59.166 43.478 0.25 0.00 46.65 3.59
1235 1247 4.394729 TCTCCAATCCACAACAGGTAAAC 58.605 43.478 0.00 0.00 0.00 2.01
1419 1431 3.369546 AACCGACTCAAAGCAATTTGG 57.630 42.857 0.00 0.00 32.99 3.28
1431 1443 3.821421 ATGGAGATTGGTAACCGACTC 57.179 47.619 0.00 0.00 0.00 3.36
1603 1629 9.308318 TCCAATAAGCAGTAGTTTTTGTTTTTC 57.692 29.630 0.00 0.00 0.00 2.29
1608 1636 9.476202 GAATTTCCAATAAGCAGTAGTTTTTGT 57.524 29.630 0.00 0.00 0.00 2.83
1609 1637 9.696917 AGAATTTCCAATAAGCAGTAGTTTTTG 57.303 29.630 0.00 0.00 0.00 2.44
1841 1878 5.189934 AGACCCCCTAGTAGAAGAACAAATG 59.810 44.000 0.00 0.00 0.00 2.32
2035 2087 6.560003 TCTTTAGACCATTCTGAGCCATTA 57.440 37.500 0.00 0.00 32.75 1.90
2081 2133 4.279169 ACAAATGAGTGAAGTGAACCCATG 59.721 41.667 0.00 0.00 0.00 3.66
2114 2166 8.822805 TGGGATAGTAGTCATTAGTGAAAAACT 58.177 33.333 0.00 0.00 43.40 2.66
2115 2167 9.099454 CTGGGATAGTAGTCATTAGTGAAAAAC 57.901 37.037 0.00 0.00 35.80 2.43
2149 2201 3.716431 AGTCCAAAGAATTCCATGCCAT 58.284 40.909 0.65 0.00 0.00 4.40
2153 2205 5.711976 ACCTTGTAGTCCAAAGAATTCCATG 59.288 40.000 0.65 1.42 31.20 3.66
2176 2228 6.002082 ACCCTGTTCTACTATTTGGTTTGAC 58.998 40.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.