Multiple sequence alignment - TraesCS2D01G247200

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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 TraesCS2D01G247200 chr2D 100.000 1302 0 0 1 1302 291638570 291639871 0 2405
1 TraesCS2D01G247200 chr2D 97.625 1305 28 3 1 1302 644703237 644701933 0 2235
2 TraesCS2D01G247200 chr2D 100.000 1066 0 0 1548 2613 291640117 291641182 0 1969
3 TraesCS2D01G247200 chr2D 96.998 1066 31 1 1548 2613 635069142 635070206 0 1790
4 TraesCS2D01G247200 chr5B 97.701 1305 27 3 1 1302 130614874 130613570 0 2241
5 TraesCS2D01G247200 chr5B 97.471 1305 30 3 1 1302 130609850 130608546 0 2224
6 TraesCS2D01G247200 chr5B 97.165 1305 34 3 1 1302 130568782 130570086 0 2202
7 TraesCS2D01G247200 chr5B 96.904 1066 31 2 1548 2613 130608536 130607473 0 1784
8 TraesCS2D01G247200 chr5B 96.904 1066 32 1 1548 2613 130613560 130612496 0 1784
9 TraesCS2D01G247200 chr5B 96.717 1066 34 1 1548 2613 130570100 130571164 0 1773
10 TraesCS2D01G247200 chrUn 97.548 1305 29 3 1 1302 45100765 45099461 0 2230
11 TraesCS2D01G247200 chrUn 97.548 1305 29 3 1 1302 261513091 261514395 0 2230
12 TraesCS2D01G247200 chrUn 96.717 1066 33 2 1548 2613 45099451 45098388 0 1773
13 TraesCS2D01G247200 chrUn 96.717 1066 33 2 1548 2613 186162441 186161378 0 1773
14 TraesCS2D01G247200 chrUn 96.623 1066 34 2 1548 2613 261514407 261515470 0 1768
15 TraesCS2D01G247200 chr7D 97.318 1305 32 3 1 1302 626650238 626648934 0 2213
16 TraesCS2D01G247200 chr7B 97.241 1305 33 3 1 1302 743033727 743035031 0 2207
17 TraesCS2D01G247200 chr7B 96.629 1068 33 2 1548 2613 743035042 743036108 0 1770
18 TraesCS2D01G247200 chr3A 97.241 1305 33 3 1 1302 66030340 66031644 0 2207
19 TraesCS2D01G247200 chr1D 96.813 1067 30 3 1548 2613 493803111 493802048 0 1779


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 TraesCS2D01G247200 chr2D 291638570 291641182 2612 False 2187.00 2405 100.0000 1 2613 2 chr2D.!!$F2 2612
1 TraesCS2D01G247200 chr2D 644701933 644703237 1304 True 2235.00 2235 97.6250 1 1302 1 chr2D.!!$R1 1301
2 TraesCS2D01G247200 chr2D 635069142 635070206 1064 False 1790.00 1790 96.9980 1548 2613 1 chr2D.!!$F1 1065
3 TraesCS2D01G247200 chr5B 130607473 130614874 7401 True 2008.25 2241 97.2450 1 2613 4 chr5B.!!$R1 2612
4 TraesCS2D01G247200 chr5B 130568782 130571164 2382 False 1987.50 2202 96.9410 1 2613 2 chr5B.!!$F1 2612
5 TraesCS2D01G247200 chrUn 45098388 45100765 2377 True 2001.50 2230 97.1325 1 2613 2 chrUn.!!$R2 2612
6 TraesCS2D01G247200 chrUn 261513091 261515470 2379 False 1999.00 2230 97.0855 1 2613 2 chrUn.!!$F1 2612
7 TraesCS2D01G247200 chrUn 186161378 186162441 1063 True 1773.00 1773 96.7170 1548 2613 1 chrUn.!!$R1 1065
8 TraesCS2D01G247200 chr7D 626648934 626650238 1304 True 2213.00 2213 97.3180 1 1302 1 chr7D.!!$R1 1301
9 TraesCS2D01G247200 chr7B 743033727 743036108 2381 False 1988.50 2207 96.9350 1 2613 2 chr7B.!!$F1 2612
10 TraesCS2D01G247200 chr3A 66030340 66031644 1304 False 2207.00 2207 97.2410 1 1302 1 chr3A.!!$F1 1301
11 TraesCS2D01G247200 chr1D 493802048 493803111 1063 True 1779.00 1779 96.8130 1548 2613 1 chr1D.!!$R1 1065

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
175 176 0.526211 CCCCTTTTTCGTTGCCTAGC 59.474 55.0 0.0 0.0 0.0 3.42 F
299 300 0.651124 ACCCATACCATAGGACCCCA 59.349 55.0 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1567 1571 0.543749 GCTGCAACCTAGGGATCACT 59.456 55.0 14.81 1.44 0.00 3.41 R
1621 1625 0.737219 CGTCGGTCGGTCCTAGAAAT 59.263 55.0 0.00 0.00 35.71 2.17 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
109 110 0.539986 AGAACGTGTGACACTGGGTT 59.460 50.000 14.42 10.40 31.34 4.11
153 154 5.408356 GTCGCTCCTTTAGTTGAAGTATCA 58.592 41.667 0.00 0.00 0.00 2.15
175 176 0.526211 CCCCTTTTTCGTTGCCTAGC 59.474 55.000 0.00 0.00 0.00 3.42
239 240 2.432444 CCCCAATCTTCACTTTACGCA 58.568 47.619 0.00 0.00 0.00 5.24
299 300 0.651124 ACCCATACCATAGGACCCCA 59.349 55.000 0.00 0.00 0.00 4.96
321 322 5.047943 CCATCTCCCGTATCTTATCTTTCGT 60.048 44.000 0.00 0.00 0.00 3.85
342 343 1.400846 GCGTAGGAGATCGAGACACAA 59.599 52.381 0.00 0.00 0.00 3.33
351 352 2.297698 TCGAGACACAACCTTAGGGA 57.702 50.000 2.32 0.00 36.25 4.20
369 370 2.716424 GGGATATGGGGAAAGTGGATCA 59.284 50.000 0.00 0.00 0.00 2.92
451 452 2.806608 TTGATCGGTAGTATTCCGGC 57.193 50.000 0.00 0.00 46.82 6.13
516 517 3.761218 TCAAATATTTTGAGCCGGCTTCA 59.239 39.130 33.34 25.57 0.00 3.02
541 542 9.801873 CAGTGGAAAATTCAGACTTTCTTTTTA 57.198 29.630 4.78 0.00 33.06 1.52
561 562 7.504922 TTTTAATGCTGCGATCACATAAAAC 57.495 32.000 0.00 0.00 0.00 2.43
938 941 2.230508 TCTTCGGATTGCGTGAACTAGT 59.769 45.455 0.00 0.00 0.00 2.57
976 979 2.766828 GGTTAGTACCTCCAGCATGAGT 59.233 50.000 0.00 0.00 41.53 3.41
990 994 4.070716 AGCATGAGTGACCTTTTCAGAAG 58.929 43.478 0.00 0.00 33.71 2.85
1022 1026 3.479203 CGCCACTATCCCAGCCCA 61.479 66.667 0.00 0.00 0.00 5.36
1140 1144 3.935203 CGCCCTTTCGCATTATCATCTAT 59.065 43.478 0.00 0.00 0.00 1.98
1141 1145 4.201753 CGCCCTTTCGCATTATCATCTATG 60.202 45.833 0.00 0.00 0.00 2.23
1142 1146 4.937620 GCCCTTTCGCATTATCATCTATGA 59.062 41.667 0.00 0.00 41.70 2.15
1615 1619 2.611292 GTCGTTAACTCCTCGCTAGCTA 59.389 50.000 13.93 0.00 0.00 3.32
1618 1622 2.950975 GTTAACTCCTCGCTAGCTACCT 59.049 50.000 13.93 0.00 0.00 3.08
1621 1625 0.179015 CTCCTCGCTAGCTACCTCCA 60.179 60.000 13.93 0.00 0.00 3.86
1642 1646 4.233635 CTAGGACCGACCGACGCG 62.234 72.222 3.53 3.53 44.74 6.01
1749 1753 1.743252 GAGTTCCCTTGCTCCTGCG 60.743 63.158 0.00 0.00 43.34 5.18
1845 1849 1.968493 CCGCATTAGGTTAGGGAGCTA 59.032 52.381 0.00 0.00 37.30 3.32
1986 1990 9.817809 GTACTAAATACAACTCCATGAATGAGA 57.182 33.333 4.68 0.00 33.54 3.27
2111 2115 2.416836 CCGTCTTCCAAATCGCAGAGTA 60.417 50.000 0.00 0.00 43.63 2.59
2113 2117 3.865745 CGTCTTCCAAATCGCAGAGTAAT 59.134 43.478 0.00 0.00 43.63 1.89
2181 2185 2.948889 TTCCCTTCTCAGATCCTCCA 57.051 50.000 0.00 0.00 0.00 3.86
2343 2347 1.762370 TCCATTTCCAGATAGCGAGCA 59.238 47.619 0.00 0.00 0.00 4.26
2361 2365 3.826236 GCAATCGCTCAGCAATGATAT 57.174 42.857 0.00 0.00 34.30 1.63
2364 2368 2.800881 TCGCTCAGCAATGATATCGT 57.199 45.000 0.00 0.00 0.00 3.73
2371 2375 1.002430 AGCAATGATATCGTGCCGGAT 59.998 47.619 21.43 6.31 0.00 4.18
2387 7414 1.900486 CGGATGAAGTACCTATCCCCC 59.100 57.143 12.48 3.32 37.64 5.40
2467 7496 3.599730 TTGTTTGTGTTCATGTTGGCA 57.400 38.095 0.00 0.00 0.00 4.92
2525 7554 2.032071 GGGTTCCCCAGTGACACG 59.968 66.667 0.00 0.00 44.65 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 2.207229 GGCAACGAAAAAGGGGCCT 61.207 57.895 0.84 0.00 38.37 5.19
276 277 2.372172 GGGTCCTATGGTATGGGTCTTG 59.628 54.545 0.00 0.00 31.94 3.02
299 300 5.565045 GCACGAAAGATAAGATACGGGAGAT 60.565 44.000 0.00 0.00 0.00 2.75
321 322 1.015109 GTGTCTCGATCTCCTACGCA 58.985 55.000 0.00 0.00 0.00 5.24
342 343 3.722101 CACTTTCCCCATATCCCTAAGGT 59.278 47.826 0.00 0.00 0.00 3.50
351 352 4.590222 GCAATTGATCCACTTTCCCCATAT 59.410 41.667 10.34 0.00 0.00 1.78
369 370 6.412214 ACGTAGTTGTAATTCTAGGGCAATT 58.588 36.000 0.00 0.00 37.78 2.32
451 452 3.058501 GGAATATTATTGTTCGGGTGCGG 60.059 47.826 0.00 0.00 0.00 5.69
541 542 3.443329 TGGTTTTATGTGATCGCAGCATT 59.557 39.130 15.24 0.02 0.00 3.56
697 698 6.404293 GCTGGTACCATTTCGATGTGTTTTAT 60.404 38.462 16.75 0.00 0.00 1.40
698 699 5.106475 GCTGGTACCATTTCGATGTGTTTTA 60.106 40.000 16.75 0.00 0.00 1.52
835 837 7.664552 TTCCTTCGGTATCTAATAACCTTGA 57.335 36.000 0.00 0.00 33.34 3.02
938 941 1.933021 ACCACTTAGTGATCGGTCCA 58.067 50.000 14.66 0.00 35.23 4.02
976 979 4.410883 TCCTAACCACTTCTGAAAAGGTCA 59.589 41.667 12.21 0.10 34.17 4.02
990 994 2.119029 GGCGCCCATTCCTAACCAC 61.119 63.158 18.11 0.00 0.00 4.16
1140 1144 0.690762 CGGGAGGAAAGAAAGGGTCA 59.309 55.000 0.00 0.00 0.00 4.02
1141 1145 0.691332 ACGGGAGGAAAGAAAGGGTC 59.309 55.000 0.00 0.00 0.00 4.46
1142 1146 0.691332 GACGGGAGGAAAGAAAGGGT 59.309 55.000 0.00 0.00 0.00 4.34
1567 1571 0.543749 GCTGCAACCTAGGGATCACT 59.456 55.000 14.81 1.44 0.00 3.41
1615 1619 2.108970 GTCGGTCCTAGAAATGGAGGT 58.891 52.381 0.00 0.00 33.78 3.85
1618 1622 1.108776 CGGTCGGTCCTAGAAATGGA 58.891 55.000 0.00 0.00 0.00 3.41
1621 1625 0.737219 CGTCGGTCGGTCCTAGAAAT 59.263 55.000 0.00 0.00 35.71 2.17
1680 1684 3.717707 ACGCTATTATGAATGTGCGACT 58.282 40.909 20.13 4.59 43.02 4.18
1749 1753 3.034343 GCCGCCTAATCGTACGCC 61.034 66.667 11.24 0.00 0.00 5.68
1845 1849 1.178276 CGGAGGAGCTATTATCGCCT 58.822 55.000 0.00 0.00 36.43 5.52
1893 1897 3.756434 GGCTTGGATTACTTAGTGTTGCA 59.244 43.478 0.00 0.00 0.00 4.08
2078 2082 4.093472 TGGAAGACGGAGGAAATGAAAA 57.907 40.909 0.00 0.00 0.00 2.29
2111 2115 9.309224 AGTAATAACACCTAGGCTTTTGAAATT 57.691 29.630 9.30 7.58 0.00 1.82
2113 2117 7.940137 TCAGTAATAACACCTAGGCTTTTGAAA 59.060 33.333 9.30 0.00 0.00 2.69
2181 2185 6.160814 AGTGAGTAGGATAAGGAGGAGTAGTT 59.839 42.308 0.00 0.00 0.00 2.24
2343 2347 3.431233 CACGATATCATTGCTGAGCGATT 59.569 43.478 3.98 0.00 34.12 3.34
2364 2368 1.968493 GGATAGGTACTTCATCCGGCA 59.032 52.381 0.00 0.00 41.75 5.69
2371 2375 0.105349 CCCGGGGGATAGGTACTTCA 60.105 60.000 14.71 0.00 37.39 3.02
2448 7477 3.599730 TTGCCAACATGAACACAAACA 57.400 38.095 0.00 0.00 0.00 2.83
2467 7496 3.379372 CGGCCTCATTCACATCTGAAATT 59.621 43.478 0.00 0.00 39.90 1.82
2525 7554 2.671963 GGAAGGGGCGTGGTTGAC 60.672 66.667 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.