Multiple sequence alignment - TraesCS5D01G234500

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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 TraesCS5D01G234500 chr5D 100.000 2312 0 0 1 2312 341951650 341949339 0 4270
1 TraesCS5D01G234500 chr4B 95.039 2318 104 8 1 2312 661662764 661665076 0 3633
2 TraesCS5D01G234500 chr2A 94.991 2316 107 7 1 2312 469185431 469187741 0 3626
3 TraesCS5D01G234500 chr3A 94.862 2316 110 7 1 2312 235218878 235221188 0 3609
4 TraesCS5D01G234500 chr6A 94.816 2315 112 6 1 2312 609192865 609190556 0 3603
5 TraesCS5D01G234500 chr6A 94.687 2315 113 6 1 2312 615678188 615680495 0 3585
6 TraesCS5D01G234500 chr7A 94.775 2316 112 7 1 2312 287010917 287013227 0 3598
7 TraesCS5D01G234500 chr3B 94.775 2316 112 7 1 2312 770209689 770211999 0 3598
8 TraesCS5D01G234500 chr5B 94.732 2316 111 9 1 2312 508768286 508770594 0 3591
9 TraesCS5D01G234500 chr4D 94.557 2315 119 5 1 2312 465555174 465552864 0 3570


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 TraesCS5D01G234500 chr5D 341949339 341951650 2311 True 4270 4270 100.000 1 2312 1 chr5D.!!$R1 2311
1 TraesCS5D01G234500 chr4B 661662764 661665076 2312 False 3633 3633 95.039 1 2312 1 chr4B.!!$F1 2311
2 TraesCS5D01G234500 chr2A 469185431 469187741 2310 False 3626 3626 94.991 1 2312 1 chr2A.!!$F1 2311
3 TraesCS5D01G234500 chr3A 235218878 235221188 2310 False 3609 3609 94.862 1 2312 1 chr3A.!!$F1 2311
4 TraesCS5D01G234500 chr6A 609190556 609192865 2309 True 3603 3603 94.816 1 2312 1 chr6A.!!$R1 2311
5 TraesCS5D01G234500 chr6A 615678188 615680495 2307 False 3585 3585 94.687 1 2312 1 chr6A.!!$F1 2311
6 TraesCS5D01G234500 chr7A 287010917 287013227 2310 False 3598 3598 94.775 1 2312 1 chr7A.!!$F1 2311
7 TraesCS5D01G234500 chr3B 770209689 770211999 2310 False 3598 3598 94.775 1 2312 1 chr3B.!!$F1 2311
8 TraesCS5D01G234500 chr5B 508768286 508770594 2308 False 3591 3591 94.732 1 2312 1 chr5B.!!$F1 2311
9 TraesCS5D01G234500 chr4D 465552864 465555174 2310 True 3570 3570 94.557 1 2312 1 chr4D.!!$R1 2311

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
362 365 0.037232 CTTTCAGACCCGGACAGACC 60.037 60.0 0.73 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 1951 0.313043 CCTGGTTCTGCTTGCACAAG 59.687 55.0 6.01 6.01 41.24 3.16 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
35 36 1.229625 TGGTGAGGAGGAGGTGCAT 60.230 57.895 0.00 0.00 0.00 3.96
48 49 4.393155 TGCATCTTCGTGCCGCCT 62.393 61.111 0.00 0.00 44.43 5.52
63 64 4.796495 CCTAGGGGGTGGCGTTGC 62.796 72.222 0.00 0.00 0.00 4.17
75 76 0.317020 GGCGTTGCTGTTGTCTGTTC 60.317 55.000 0.00 0.00 0.00 3.18
78 79 1.332028 CGTTGCTGTTGTCTGTTCGTC 60.332 52.381 0.00 0.00 0.00 4.20
122 123 4.686091 CACACGCATCGAAGGTATAATCAT 59.314 41.667 0.00 0.00 0.00 2.45
172 174 0.740149 TGCTGGCATTTTAGCGGATG 59.260 50.000 0.00 0.00 42.74 3.51
190 192 3.118665 GGATGGTTAGTGTAGCCGGTAAA 60.119 47.826 1.90 0.00 0.00 2.01
192 194 4.556592 TGGTTAGTGTAGCCGGTAAAAT 57.443 40.909 1.90 0.00 0.00 1.82
198 201 7.094848 GGTTAGTGTAGCCGGTAAAATTTTGTA 60.095 37.037 13.76 0.00 0.00 2.41
223 226 6.095440 ACATTGCAATTAATTAGAAGGTCGCT 59.905 34.615 9.83 0.00 0.00 4.93
230 233 9.692749 CAATTAATTAGAAGGTCGCTATGTCTA 57.307 33.333 0.00 0.00 0.00 2.59
245 248 6.128282 CGCTATGTCTAACAGGTGAAAATGTT 60.128 38.462 0.00 0.00 42.15 2.71
251 254 8.908903 TGTCTAACAGGTGAAAATGTTTGTATT 58.091 29.630 0.00 0.00 40.09 1.89
362 365 0.037232 CTTTCAGACCCGGACAGACC 60.037 60.000 0.73 0.00 0.00 3.85
379 382 4.954202 ACAGACCGGACATTAGATAGTTGA 59.046 41.667 9.46 0.00 0.00 3.18
380 383 5.421056 ACAGACCGGACATTAGATAGTTGAA 59.579 40.000 9.46 0.00 0.00 2.69
381 384 6.070995 ACAGACCGGACATTAGATAGTTGAAA 60.071 38.462 9.46 0.00 0.00 2.69
413 416 2.290071 TGACTACTAGTTTTGGGCTGGC 60.290 50.000 0.00 0.00 0.00 4.85
480 484 4.518970 TCCTGTAAAAATGTCAAGTGGAGC 59.481 41.667 0.00 0.00 0.00 4.70
511 515 1.419387 AGATAGGAGCCAGCATTGGTC 59.581 52.381 0.00 0.00 46.80 4.02
513 517 1.971505 TAGGAGCCAGCATTGGTCGG 61.972 60.000 0.00 0.00 46.80 4.79
536 540 2.607187 CTGTTAAGTCGTTGCCGAGAT 58.393 47.619 0.00 0.00 45.26 2.75
561 565 5.046304 CGAAGAATCCACCCATATGTCCTAT 60.046 44.000 1.24 0.00 0.00 2.57
590 594 1.757699 GTGGCGAAGGAGGAGAATACT 59.242 52.381 0.00 0.00 0.00 2.12
665 669 5.308825 GAGATTCATTTATCCGGGTCACAT 58.691 41.667 0.00 0.00 0.00 3.21
741 745 6.597672 GGACAATGTTTGTGGTCATGATACTA 59.402 38.462 0.00 0.00 45.52 1.82
781 785 6.704493 TCGATAATATTAGTTGGTTCTGGTGC 59.296 38.462 1.02 0.00 0.00 5.01
957 961 0.392863 TGTGAACGATGGCCATGAGG 60.393 55.000 26.56 14.63 38.23 3.86
997 1001 1.490910 GAACCAAGTCCAGATAGGGGG 59.509 57.143 0.00 0.00 38.24 5.40
1068 1072 5.338463 GGCTATGTCTACTCAGAGGGTTTTT 60.338 44.000 1.53 0.00 0.00 1.94
1077 1081 2.105821 TCAGAGGGTTTTTCGGACACAT 59.894 45.455 0.00 0.00 0.00 3.21
1086 1090 7.067008 AGGGTTTTTCGGACACATATATCAAAG 59.933 37.037 0.00 0.00 0.00 2.77
1105 1109 5.184864 TCAAAGCCAACAAACTATACCATGG 59.815 40.000 11.19 11.19 0.00 3.66
1259 1263 0.512518 TCAACTCTCATTGCGCAACG 59.487 50.000 27.64 19.21 0.00 4.10
1309 1313 7.472334 AAAGATATGGAAGCAAAACACATCT 57.528 32.000 0.00 0.00 0.00 2.90
1327 1331 1.813178 TCTAGACAGCAGTGAAGGTCG 59.187 52.381 0.00 0.00 35.49 4.79
1410 1415 1.145803 GGTTTGGGACGTTCTTCGAG 58.854 55.000 0.00 0.00 42.86 4.04
1426 1431 8.420945 CGTTCTTCGAGTCATATGATAATGTTC 58.579 37.037 9.02 0.00 42.86 3.18
1446 1451 5.129980 TGTTCTCCGTCTCCTAGATGTACTA 59.870 44.000 0.00 0.00 29.27 1.82
1516 1521 4.286032 TGCTGAGTATACCAGGTTTCAAGT 59.714 41.667 17.67 0.00 32.51 3.16
1565 1570 3.119388 GCTATGTGCATTGAAGCTTTCCA 60.119 43.478 0.00 0.00 42.31 3.53
1679 1686 3.940209 TCAAATCATTCCACTTGCCAC 57.060 42.857 0.00 0.00 0.00 5.01
1681 1688 2.198827 AATCATTCCACTTGCCACGA 57.801 45.000 0.00 0.00 0.00 4.35
1835 1842 4.833390 ACACTAAGGAATCCAACAGTAGC 58.167 43.478 0.61 0.00 0.00 3.58
1944 1951 6.254804 AGCGGTTGATGAACTTGTTTAAAAAC 59.745 34.615 0.00 0.00 34.59 2.43
1977 1985 3.262405 AGAACCAGGAGCGTAATACCAAA 59.738 43.478 0.00 0.00 0.00 3.28
2019 2027 8.423906 TGATGAGTTTACTAAGAAGAAGGTCT 57.576 34.615 0.00 0.00 0.00 3.85
2102 2110 2.297701 GAGCCAGTTGGTCTTTGTGAA 58.702 47.619 0.00 0.00 38.47 3.18
2131 2139 6.240002 CCAGCAATTGACCCTCCTAATACTAT 60.240 42.308 10.34 0.00 0.00 2.12
2242 2250 2.304180 GAGCTAGGTATGGCCACATGAT 59.696 50.000 8.16 0.00 40.61 2.45
2246 2254 3.126001 AGGTATGGCCACATGATAACG 57.874 47.619 8.16 0.00 40.61 3.18
2258 2266 4.154015 CACATGATAACGAACCTTGCAGAA 59.846 41.667 0.00 0.00 0.00 3.02
2259 2267 4.943705 ACATGATAACGAACCTTGCAGAAT 59.056 37.500 0.00 0.00 0.00 2.40
2290 2298 5.659079 ACTTTGTACTCAGAGGGAATAGAGG 59.341 44.000 1.53 0.00 31.18 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 4.028490 CAGCAACGCCACCCCCTA 62.028 66.667 0.00 0.00 0.00 3.53
63 64 2.550978 ACTTGGACGAACAGACAACAG 58.449 47.619 0.00 0.00 0.00 3.16
75 76 0.388649 CCTCACGGAGAACTTGGACG 60.389 60.000 2.84 0.00 0.00 4.79
78 79 0.320771 CCACCTCACGGAGAACTTGG 60.321 60.000 2.84 0.00 0.00 3.61
106 107 4.923871 GTGACGCATGATTATACCTTCGAT 59.076 41.667 0.00 0.00 0.00 3.59
172 174 5.885230 AAATTTTACCGGCTACACTAACC 57.115 39.130 0.00 0.00 0.00 2.85
198 201 6.095440 AGCGACCTTCTAATTAATTGCAATGT 59.905 34.615 13.82 6.06 0.00 2.71
220 223 5.351465 ACATTTTCACCTGTTAGACATAGCG 59.649 40.000 0.00 0.00 0.00 4.26
223 226 8.458573 ACAAACATTTTCACCTGTTAGACATA 57.541 30.769 0.00 0.00 34.61 2.29
251 254 8.354426 GGCCAAAGTAAACAGTCAAATTTACTA 58.646 33.333 0.00 0.00 46.15 1.82
272 275 0.693622 TCGAACATTACCAGGGCCAA 59.306 50.000 6.18 0.00 0.00 4.52
362 365 6.961554 GTGCTTTTTCAACTATCTAATGTCCG 59.038 38.462 0.00 0.00 0.00 4.79
373 376 4.947388 AGTCAACCAGTGCTTTTTCAACTA 59.053 37.500 0.00 0.00 0.00 2.24
379 382 5.681639 ACTAGTAGTCAACCAGTGCTTTTT 58.318 37.500 0.00 0.00 28.04 1.94
380 383 5.291905 ACTAGTAGTCAACCAGTGCTTTT 57.708 39.130 0.00 0.00 28.04 2.27
381 384 4.957684 ACTAGTAGTCAACCAGTGCTTT 57.042 40.909 0.00 0.00 28.04 3.51
413 416 3.193691 ACTGACGGAACATACTTCAGGAG 59.806 47.826 1.76 0.00 0.00 3.69
480 484 2.100584 GGCTCCTATCTATCGGCATCAG 59.899 54.545 0.00 0.00 0.00 2.90
511 515 1.908066 GCAACGACTTAACAGGGCCG 61.908 60.000 0.00 0.00 0.00 6.13
513 517 1.873863 GGCAACGACTTAACAGGGC 59.126 57.895 0.00 0.00 0.00 5.19
536 540 3.071023 GGACATATGGGTGGATTCTTCGA 59.929 47.826 7.80 0.00 0.00 3.71
561 565 2.192861 CCTTCGCCACTGGTTGCAA 61.193 57.895 0.00 0.00 0.00 4.08
590 594 1.440618 ACCCCACATGGAGTTGTACA 58.559 50.000 0.00 0.00 37.39 2.90
769 773 0.111061 ATCAGCAGCACCAGAACCAA 59.889 50.000 0.00 0.00 0.00 3.67
781 785 0.841961 TTCCTCATCCCCATCAGCAG 59.158 55.000 0.00 0.00 0.00 4.24
957 961 5.105997 GGTTCAGATTATATTGCCATGGAGC 60.106 44.000 18.40 0.45 0.00 4.70
1068 1072 4.681074 TGGCTTTGATATATGTGTCCGA 57.319 40.909 0.00 0.00 0.00 4.55
1077 1081 9.860650 ATGGTATAGTTTGTTGGCTTTGATATA 57.139 29.630 0.00 0.00 0.00 0.86
1086 1090 4.096382 CACTCCATGGTATAGTTTGTTGGC 59.904 45.833 12.58 0.00 0.00 4.52
1105 1109 3.181500 GGACAACCTGTTTCAACACACTC 60.181 47.826 0.00 0.00 34.70 3.51
1259 1263 6.825944 TCTCCACTATCTCAGTATACATGC 57.174 41.667 5.50 0.00 34.98 4.06
1309 1313 0.888619 CCGACCTTCACTGCTGTCTA 59.111 55.000 0.00 0.00 0.00 2.59
1353 1357 1.034292 GCTTAGCCCTCCAAGCCTTG 61.034 60.000 0.00 0.00 41.04 3.61
1381 1386 1.617322 GTCCCAAACCTTTCCTCCAC 58.383 55.000 0.00 0.00 0.00 4.02
1410 1415 6.809196 GGAGACGGAGAACATTATCATATGAC 59.191 42.308 7.78 0.00 0.00 3.06
1426 1431 5.470777 CCTTTAGTACATCTAGGAGACGGAG 59.529 48.000 0.00 0.00 0.00 4.63
1446 1451 1.283321 GTGCCAGGATTCCTCTCCTTT 59.717 52.381 0.98 0.00 43.33 3.11
1516 1521 8.433421 AAAGAGAAGAATACTCGTTTCAACAA 57.567 30.769 0.00 0.00 39.12 2.83
1565 1570 1.632409 ACATCACAGGAGGACAATGCT 59.368 47.619 0.00 0.00 0.00 3.79
1679 1686 1.001974 TCTCACCCTCCACAAATGTCG 59.998 52.381 0.00 0.00 0.00 4.35
1681 1688 2.443255 AGTTCTCACCCTCCACAAATGT 59.557 45.455 0.00 0.00 0.00 2.71
1944 1951 0.313043 CCTGGTTCTGCTTGCACAAG 59.687 55.000 6.01 6.01 41.24 3.16
2019 2027 2.673775 TCCATTTTCTTCCTGGCACA 57.326 45.000 0.00 0.00 0.00 4.57
2131 2139 0.475632 TGCCCTCCCCTTCTTTCTCA 60.476 55.000 0.00 0.00 0.00 3.27
2242 2250 7.604927 AGTTATACAATTCTGCAAGGTTCGTTA 59.395 33.333 0.00 0.00 0.00 3.18
2246 2254 8.082242 ACAAAGTTATACAATTCTGCAAGGTTC 58.918 33.333 0.00 0.00 0.00 3.62
2258 2266 8.375493 TCCCTCTGAGTACAAAGTTATACAAT 57.625 34.615 3.66 0.00 0.00 2.71
2259 2267 7.786046 TCCCTCTGAGTACAAAGTTATACAA 57.214 36.000 3.66 0.00 0.00 2.41
2290 2298 3.012518 ACAATAGCTGTGAGTGGCAATC 58.987 45.455 8.21 8.21 36.69 2.67


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

AutoCloner maintained by Alex Coulton.