Multiple sequence alignment - TraesCS5D01G258000

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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 TraesCS5D01G258000 chr5D 100.000 2582 0 0 1 2582 364672016 364669435 0.000000e+00 4769
1 TraesCS5D01G258000 chr5A 93.816 2636 76 30 1 2582 465998101 465995499 0.000000e+00 3884
2 TraesCS5D01G258000 chr5B 95.059 1943 48 18 1 1905 430681320 430679388 0.000000e+00 3013
3 TraesCS5D01G258000 chr5B 92.396 697 30 9 1899 2582 430674729 430674043 0.000000e+00 972
4 TraesCS5D01G258000 chr7D 85.317 252 37 0 1262 1513 136253355 136253104 7.090000e-66 261
5 TraesCS5D01G258000 chr7B 84.959 246 37 0 1265 1510 99130798 99130553 1.530000e-62 250
6 TraesCS5D01G258000 chr7A 84.524 252 33 6 1262 1510 135901495 135901247 7.140000e-61 244


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 TraesCS5D01G258000 chr5D 364669435 364672016 2581 True 4769 4769 100.000 1 2582 1 chr5D.!!$R1 2581
1 TraesCS5D01G258000 chr5A 465995499 465998101 2602 True 3884 3884 93.816 1 2582 1 chr5A.!!$R1 2581
2 TraesCS5D01G258000 chr5B 430679388 430681320 1932 True 3013 3013 95.059 1 1905 1 chr5B.!!$R2 1904
3 TraesCS5D01G258000 chr5B 430674043 430674729 686 True 972 972 92.396 1899 2582 1 chr5B.!!$R1 683

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
207 224 1.337260 CGCTAATCTAATGGCCGAGCT 60.337 52.381 0.0 0.0 0.0 4.09 F
1523 1573 0.317603 CAGCAAGCACAACAGAGCAC 60.318 55.000 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 1599 1.008538 CAGCGGCAGTGGTGTTTTC 60.009 57.895 1.45 0.0 32.82 2.29 R
2324 2388 0.169009 CTTGCTACTGAAAAGGCGGC 59.831 55.000 0.00 0.0 0.00 6.53 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
207 224 1.337260 CGCTAATCTAATGGCCGAGCT 60.337 52.381 0.00 0.00 0.00 4.09
208 225 2.072298 GCTAATCTAATGGCCGAGCTG 58.928 52.381 0.00 0.00 0.00 4.24
209 226 2.289072 GCTAATCTAATGGCCGAGCTGA 60.289 50.000 0.00 0.00 0.00 4.26
210 227 3.618507 GCTAATCTAATGGCCGAGCTGAT 60.619 47.826 0.00 0.00 0.00 2.90
211 228 2.758736 ATCTAATGGCCGAGCTGATC 57.241 50.000 0.00 0.00 0.00 2.92
213 230 2.876581 TCTAATGGCCGAGCTGATCTA 58.123 47.619 0.00 0.00 0.00 1.98
283 302 1.831106 CCACAGTGGCTACATGTCCTA 59.169 52.381 6.67 0.00 0.00 2.94
284 303 2.236146 CCACAGTGGCTACATGTCCTAA 59.764 50.000 6.67 0.00 0.00 2.69
287 306 2.874701 CAGTGGCTACATGTCCTAATGC 59.125 50.000 0.00 0.00 0.00 3.56
303 322 2.124277 ATGCCCATCATCATCCATCG 57.876 50.000 0.00 0.00 0.00 3.84
309 328 1.732809 CATCATCATCCATCGAGCAGC 59.267 52.381 0.00 0.00 0.00 5.25
692 723 2.439338 TGGTGGTGGTGTGTGTGC 60.439 61.111 0.00 0.00 0.00 4.57
949 993 1.487976 CCATCTGCTTTCTGGCTCCTA 59.512 52.381 0.00 0.00 0.00 2.94
950 994 2.092753 CCATCTGCTTTCTGGCTCCTAA 60.093 50.000 0.00 0.00 0.00 2.69
951 995 3.434739 CCATCTGCTTTCTGGCTCCTAAT 60.435 47.826 0.00 0.00 0.00 1.73
952 996 4.202398 CCATCTGCTTTCTGGCTCCTAATA 60.202 45.833 0.00 0.00 0.00 0.98
1080 1124 1.298667 GCCGTTCCACACCCACTAT 59.701 57.895 0.00 0.00 0.00 2.12
1149 1193 0.978146 ACTTCTCACCGGCAGCCTAT 60.978 55.000 10.54 0.00 0.00 2.57
1523 1573 0.317603 CAGCAAGCACAACAGAGCAC 60.318 55.000 0.00 0.00 0.00 4.40
1527 1577 1.134753 CAAGCACAACAGAGCACCAAA 59.865 47.619 0.00 0.00 0.00 3.28
1546 1599 1.756408 ATCCTCAGAGCCATGCGAGG 61.756 60.000 0.00 0.00 45.40 4.63
1815 1871 0.782384 GTGTTACTGACGAGTTGCCG 59.218 55.000 0.00 0.00 33.21 5.69
2096 2158 2.287909 GGTGACTGTGTGTCTGAGAGTC 60.288 54.545 0.00 0.00 45.54 3.36
2110 2172 2.554462 TGAGAGTCGAGACAAACCAGAG 59.446 50.000 5.99 0.00 0.00 3.35
2177 2239 9.985730 ATGAAATTGCTTAGATCTGAAACAAAA 57.014 25.926 5.18 0.00 0.00 2.44
2184 2246 8.076178 TGCTTAGATCTGAAACAAAAGCTAAAC 58.924 33.333 19.61 0.00 38.84 2.01
2235 2299 6.312918 TCTCACGCAAATAAGGAACTGATAAC 59.687 38.462 0.00 0.00 40.86 1.89
2275 2339 3.265221 TCCAGTGAGCTCATGGAAGATTT 59.735 43.478 29.94 6.97 40.13 2.17
2317 2381 9.301153 GGGTATAAAACAGTTTTGCATCATTAG 57.699 33.333 19.77 0.00 34.19 1.73
2319 2383 7.832503 ATAAAACAGTTTTGCATCATTAGGC 57.167 32.000 19.77 0.00 34.19 3.93
2320 2384 3.492421 ACAGTTTTGCATCATTAGGCG 57.508 42.857 0.00 0.00 34.35 5.52
2321 2385 2.187707 CAGTTTTGCATCATTAGGCGC 58.812 47.619 0.00 0.00 34.35 6.53
2322 2386 1.134946 AGTTTTGCATCATTAGGCGCC 59.865 47.619 21.89 21.89 34.35 6.53
2323 2387 0.459489 TTTTGCATCATTAGGCGCCC 59.541 50.000 26.15 5.30 34.35 6.13
2324 2388 1.723608 TTTGCATCATTAGGCGCCCG 61.724 55.000 26.15 9.88 34.35 6.13
2325 2389 4.030452 GCATCATTAGGCGCCCGC 62.030 66.667 26.15 10.88 41.06 6.13
2375 2439 9.476202 AAGATACAAAATCCTAAACAAAAGTGC 57.524 29.630 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
207 224 3.634448 GAGCCAGTGAAGTAGCTAGATCA 59.366 47.826 0.00 0.00 35.23 2.92
208 225 3.888930 AGAGCCAGTGAAGTAGCTAGATC 59.111 47.826 0.00 0.00 35.23 2.75
209 226 3.888930 GAGAGCCAGTGAAGTAGCTAGAT 59.111 47.826 0.00 0.00 35.23 1.98
210 227 3.053991 AGAGAGCCAGTGAAGTAGCTAGA 60.054 47.826 0.00 0.00 35.23 2.43
211 228 3.287222 AGAGAGCCAGTGAAGTAGCTAG 58.713 50.000 0.00 0.00 35.23 3.42
213 230 2.230130 AGAGAGCCAGTGAAGTAGCT 57.770 50.000 0.00 0.00 38.56 3.32
283 302 2.040679 TCGATGGATGATGATGGGCATT 59.959 45.455 0.00 0.00 37.34 3.56
284 303 1.631898 TCGATGGATGATGATGGGCAT 59.368 47.619 0.00 0.00 40.77 4.40
287 306 1.002773 TGCTCGATGGATGATGATGGG 59.997 52.381 0.00 0.00 0.00 4.00
303 322 2.267324 GGGACAGGACAGCTGCTC 59.733 66.667 15.27 10.56 0.00 4.26
309 328 1.372683 CACCACAGGGACAGGACAG 59.627 63.158 0.00 0.00 38.05 3.51
452 473 0.887933 CACGCCAAACCCTGCTTTAT 59.112 50.000 0.00 0.00 0.00 1.40
949 993 1.488393 GTGGAGAGAGCTGGGCTTATT 59.512 52.381 0.00 0.00 39.88 1.40
950 994 1.127343 GTGGAGAGAGCTGGGCTTAT 58.873 55.000 0.00 0.00 39.88 1.73
951 995 0.041833 AGTGGAGAGAGCTGGGCTTA 59.958 55.000 0.00 0.00 39.88 3.09
952 996 1.229464 AGTGGAGAGAGCTGGGCTT 60.229 57.895 0.00 0.00 39.88 4.35
1005 1049 3.586843 GCCATGGTGGTAATGGTGA 57.413 52.632 14.67 0.00 45.46 4.02
1080 1124 3.014538 ATCATGCCGGGGTGGTGA 61.015 61.111 2.18 0.00 41.21 4.02
1149 1193 3.413327 GATAGGCTCGTCCTCATACTCA 58.587 50.000 0.00 0.00 43.20 3.41
1523 1573 1.030457 GCATGGCTCTGAGGATTTGG 58.970 55.000 6.83 0.00 0.00 3.28
1527 1577 1.747145 CTCGCATGGCTCTGAGGAT 59.253 57.895 6.83 0.00 0.00 3.24
1546 1599 1.008538 CAGCGGCAGTGGTGTTTTC 60.009 57.895 1.45 0.00 32.82 2.29
1815 1871 6.072728 TGTTGCACTATAATTTGTCCACTGAC 60.073 38.462 0.00 0.00 42.12 3.51
1937 1993 6.779117 CACATCATTATCAGTGGAAAGTGAC 58.221 40.000 0.00 0.00 0.00 3.67
1938 1994 6.990341 CACATCATTATCAGTGGAAAGTGA 57.010 37.500 0.00 0.00 0.00 3.41
2096 2158 1.151668 CAAGGCTCTGGTTTGTCTCG 58.848 55.000 0.00 0.00 0.00 4.04
2110 2172 2.292292 TCCGCTGAAGTTAAAACAAGGC 59.708 45.455 0.00 0.00 0.00 4.35
2162 2224 7.390718 GGGAGTTTAGCTTTTGTTTCAGATCTA 59.609 37.037 0.00 0.00 0.00 1.98
2164 2226 6.382608 GGGAGTTTAGCTTTTGTTTCAGATC 58.617 40.000 0.00 0.00 0.00 2.75
2235 2299 3.340034 TGGATTTGGTACGTAAGCCTTG 58.660 45.455 12.31 0.00 45.62 3.61
2321 2385 2.046700 TACTGAAAAGGCGGCGGG 60.047 61.111 9.78 0.00 0.00 6.13
2322 2386 2.750888 GCTACTGAAAAGGCGGCGG 61.751 63.158 9.78 0.00 0.00 6.13
2323 2387 1.573829 TTGCTACTGAAAAGGCGGCG 61.574 55.000 0.51 0.51 0.00 6.46
2324 2388 0.169009 CTTGCTACTGAAAAGGCGGC 59.831 55.000 0.00 0.00 0.00 6.53
2325 2389 1.464997 GACTTGCTACTGAAAAGGCGG 59.535 52.381 0.00 0.00 0.00 6.13
2330 2394 5.196341 TCTTCGAGACTTGCTACTGAAAA 57.804 39.130 0.00 0.00 0.00 2.29
2407 2472 6.909550 AAATCTTGGCACCTACATACAAAA 57.090 33.333 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.