Multiple sequence alignment - TraesCS1D01G169100

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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 TraesCS1D01G169100 chr1D 100.000 2588 0 0 1 2588 241476803 241474216 0 4780
1 TraesCS1D01G169100 chr1D 97.358 2612 44 5 1 2588 479819184 479816574 0 4418
2 TraesCS1D01G169100 chr1D 97.283 2613 45 6 1 2588 442318545 442321156 0 4409
3 TraesCS1D01G169100 chr1D 96.249 1706 32 6 900 2588 415406239 415407929 0 2767
4 TraesCS1D01G169100 chr6D 97.246 2614 46 6 1 2588 57832710 57835323 0 4405
5 TraesCS1D01G169100 chr6D 97.093 2614 48 7 1 2588 448503446 448500835 0 4381
6 TraesCS1D01G169100 chr6D 97.178 2020 36 8 586 2588 464130027 464132042 0 3395
7 TraesCS1D01G169100 chr2D 96.672 2614 48 10 1 2588 499310741 499313341 0 4309
8 TraesCS1D01G169100 chr2D 96.134 1707 33 7 900 2588 606639536 606641227 0 2756
9 TraesCS1D01G169100 chr3D 96.440 2612 49 7 1 2588 550468091 550465500 0 4268
10 TraesCS1D01G169100 chr5D 95.596 2634 68 15 1 2588 430991309 430988678 0 4178
11 TraesCS1D01G169100 chr5D 94.666 1706 38 15 900 2588 288074919 288073250 0 2597
12 TraesCS1D01G169100 chr4D 95.518 2633 70 10 1 2588 374041297 374043926 0 4165
13 TraesCS1D01G169100 chr4D 95.767 2197 52 8 430 2588 374748960 374746767 0 3504
14 TraesCS1D01G169100 chrUn 95.952 2273 41 7 1 2250 29129207 29131451 0 3640
15 TraesCS1D01G169100 chrUn 95.877 2207 46 5 1 2162 26236175 26233969 0 3530
16 TraesCS1D01G169100 chr7D 96.602 1913 35 4 1 1890 530362583 530364488 0 3145
17 TraesCS1D01G169100 chr7D 95.799 1452 30 3 900 2335 151286650 151285214 0 2314


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 TraesCS1D01G169100 chr1D 241474216 241476803 2587 True 4780 4780 100.000 1 2588 1 chr1D.!!$R1 2587
1 TraesCS1D01G169100 chr1D 479816574 479819184 2610 True 4418 4418 97.358 1 2588 1 chr1D.!!$R2 2587
2 TraesCS1D01G169100 chr1D 442318545 442321156 2611 False 4409 4409 97.283 1 2588 1 chr1D.!!$F2 2587
3 TraesCS1D01G169100 chr1D 415406239 415407929 1690 False 2767 2767 96.249 900 2588 1 chr1D.!!$F1 1688
4 TraesCS1D01G169100 chr6D 57832710 57835323 2613 False 4405 4405 97.246 1 2588 1 chr6D.!!$F1 2587
5 TraesCS1D01G169100 chr6D 448500835 448503446 2611 True 4381 4381 97.093 1 2588 1 chr6D.!!$R1 2587
6 TraesCS1D01G169100 chr6D 464130027 464132042 2015 False 3395 3395 97.178 586 2588 1 chr6D.!!$F2 2002
7 TraesCS1D01G169100 chr2D 499310741 499313341 2600 False 4309 4309 96.672 1 2588 1 chr2D.!!$F1 2587
8 TraesCS1D01G169100 chr2D 606639536 606641227 1691 False 2756 2756 96.134 900 2588 1 chr2D.!!$F2 1688
9 TraesCS1D01G169100 chr3D 550465500 550468091 2591 True 4268 4268 96.440 1 2588 1 chr3D.!!$R1 2587
10 TraesCS1D01G169100 chr5D 430988678 430991309 2631 True 4178 4178 95.596 1 2588 1 chr5D.!!$R2 2587
11 TraesCS1D01G169100 chr5D 288073250 288074919 1669 True 2597 2597 94.666 900 2588 1 chr5D.!!$R1 1688
12 TraesCS1D01G169100 chr4D 374041297 374043926 2629 False 4165 4165 95.518 1 2588 1 chr4D.!!$F1 2587
13 TraesCS1D01G169100 chr4D 374746767 374748960 2193 True 3504 3504 95.767 430 2588 1 chr4D.!!$R1 2158
14 TraesCS1D01G169100 chrUn 29129207 29131451 2244 False 3640 3640 95.952 1 2250 1 chrUn.!!$F1 2249
15 TraesCS1D01G169100 chrUn 26233969 26236175 2206 True 3530 3530 95.877 1 2162 1 chrUn.!!$R1 2161
16 TraesCS1D01G169100 chr7D 530362583 530364488 1905 False 3145 3145 96.602 1 1890 1 chr7D.!!$F1 1889
17 TraesCS1D01G169100 chr7D 151285214 151286650 1436 True 2314 2314 95.799 900 2335 1 chr7D.!!$R1 1435

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
177 178 0.703056 CCTCCCCTCCTCCTCTCCTA 60.703 65.000 0.00 0.0 0.0 2.94 F
435 443 1.072965 CTTCTGCAGGTCCCTTTCAGT 59.927 52.381 15.13 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1121 1150 2.356695 TGGAAATTCATCAGCTCATGCG 59.643 45.455 0.0 0.0 45.42 4.73 R
2075 2200 4.148838 AGTTGGTTTAGTTGCAGCCAATA 58.851 39.130 0.0 0.0 40.69 1.90 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
91 92 4.271816 CCGCGCGCTGACTAGGAT 62.272 66.667 30.48 0.00 0.00 3.24
177 178 0.703056 CCTCCCCTCCTCCTCTCCTA 60.703 65.000 0.00 0.00 0.00 2.94
268 276 2.430921 CGAAAGCAGCGACGACCT 60.431 61.111 0.00 0.00 0.00 3.85
305 313 3.053842 ACATGCATTCTTCCTCCACAGAT 60.054 43.478 0.00 0.00 0.00 2.90
435 443 1.072965 CTTCTGCAGGTCCCTTTCAGT 59.927 52.381 15.13 0.00 0.00 3.41
686 697 5.435686 TGGTTCATAGTGGCATTAGAGTT 57.564 39.130 0.00 0.00 0.00 3.01
694 705 5.824904 AGTGGCATTAGAGTTGCTTATTG 57.175 39.130 0.00 0.00 40.03 1.90
858 871 9.507329 TGGTCTGATGCTAAATTTAGATATTCC 57.493 33.333 26.00 17.38 32.47 3.01
1019 1048 4.004982 GCAATGGTTGAAGATGCCAAAAT 58.995 39.130 0.00 0.00 35.74 1.82
1121 1150 2.977914 TGACAAGCTAGTCCAAGATGC 58.022 47.619 0.00 0.00 37.73 3.91
1137 1166 1.535896 GATGCGCATGAGCTGATGAAT 59.464 47.619 30.76 6.73 39.10 2.57
1465 1494 4.020662 CCCAAGAGAAGCTAGAGTTGAAGT 60.021 45.833 0.00 0.00 0.00 3.01
1572 1601 0.551131 AGTTCAGGGGGATTCAGGCT 60.551 55.000 0.00 0.00 0.00 4.58
1754 1783 7.950512 TGCTATTCATCCTTTTGTGAGAAAAA 58.049 30.769 0.00 0.00 0.00 1.94
1785 1814 5.796424 ATGCATTTGAAGTTGAACTCCTT 57.204 34.783 0.00 0.00 0.00 3.36
1814 1843 9.454859 TGTATTGTGAACAATGGTTATGTATGA 57.545 29.630 17.00 0.00 45.34 2.15
2040 2165 7.716799 TGATCCATTACAACTTGGCTTAAAT 57.283 32.000 0.00 0.00 32.80 1.40
2075 2200 7.466746 AAACCAGACAGTACATTGCATTTAT 57.533 32.000 0.00 0.00 0.00 1.40
2124 2249 6.884295 ACTAACTTAATATCTTGCCTGCAACA 59.116 34.615 0.00 0.00 0.00 3.33
2236 2361 4.454678 AGTTTGCAGAGACAGAAACATGA 58.545 39.130 0.00 0.00 31.92 3.07
2276 2401 3.071457 TCTTCACTTGGAGTCAGCATTGA 59.929 43.478 0.00 0.00 0.00 2.57
2319 2444 2.666317 ACAGTTGCACCTTTAAGCCTT 58.334 42.857 0.00 0.00 0.00 4.35
2372 2498 2.204748 CCAGAATGTGGGCAATGGG 58.795 57.895 0.00 0.00 43.63 4.00
2521 2653 0.251634 TCACCATAGCATCCACGCAA 59.748 50.000 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 178 1.372623 GCGACGGAGGAAACGAGTT 60.373 57.895 0.00 0.00 34.93 3.01
268 276 1.399714 CATGTACGGGAGGCTAGACA 58.600 55.000 0.00 0.00 0.00 3.41
305 313 1.884579 GTACTGACCTCGTTGAGACCA 59.115 52.381 0.00 0.00 0.00 4.02
435 443 5.104360 CCCCTTGTAATCTGGATCTTCAAGA 60.104 44.000 16.04 0.00 34.62 3.02
694 705 6.261826 AGCAAAATATACTCATGCTTGACCTC 59.738 38.462 0.00 0.00 44.43 3.85
774 787 6.836527 AGCTGACTGACTAGGTTAGTTATCAT 59.163 38.462 0.00 0.00 39.59 2.45
858 871 4.510038 AGATAACTGCAGTTGCCAAAAG 57.490 40.909 36.50 1.23 41.18 2.27
1019 1048 4.574674 AGATTGTCATTCACCCTAGCAA 57.425 40.909 0.00 0.00 0.00 3.91
1121 1150 2.356695 TGGAAATTCATCAGCTCATGCG 59.643 45.455 0.00 0.00 45.42 4.73
1137 1166 3.010138 CCACCACCTTATCTTCCTGGAAA 59.990 47.826 10.86 2.43 0.00 3.13
1417 1446 5.221722 TGAGCTTCTCCTGACACTTTGTTAT 60.222 40.000 0.00 0.00 0.00 1.89
1572 1601 7.724490 TCATCTTCTTCACTTCTCCAAGATA 57.276 36.000 0.00 0.00 31.00 1.98
1754 1783 7.692460 TCAACTTCAAATGCATAGTTCATCT 57.308 32.000 9.19 0.00 0.00 2.90
2040 2165 5.546621 ACTGTCTGGTTTAGTTGCTCTAA 57.453 39.130 0.00 0.00 36.91 2.10
2075 2200 4.148838 AGTTGGTTTAGTTGCAGCCAATA 58.851 39.130 0.00 0.00 40.69 1.90
2124 2249 6.909550 TTCACTATATTTGTGCTTGGGTTT 57.090 33.333 4.31 0.00 35.58 3.27
2319 2444 5.137551 TGGGATCTACGTGATGAAGTATGA 58.862 41.667 0.00 0.00 35.14 2.15
2521 2653 4.323054 ACCCTGGTAGGAGGTACTATAGT 58.677 47.826 10.87 10.87 41.55 2.12


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

AutoCloner maintained by Alex Coulton.