Multiple sequence alignment - TraesCS3B01G348500

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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 TraesCS3B01G348500 chr3B 100.000 2264 0 0 1 2264 558278372 558276109 0.000000e+00 4181
1 TraesCS3B01G348500 chr3B 94.830 2205 76 9 1 2169 604266042 604263840 0.000000e+00 3406
2 TraesCS3B01G348500 chr3B 90.380 894 44 7 1413 2264 760824947 760825840 0.000000e+00 1136
3 TraesCS3B01G348500 chr4B 94.893 2291 71 13 1 2264 551060038 551062309 0.000000e+00 3541
4 TraesCS3B01G348500 chr6B 95.402 2175 81 8 1 2169 679251632 679253793 0.000000e+00 3445
5 TraesCS3B01G348500 chr6B 95.421 2140 71 6 1 2114 181111563 181109425 0.000000e+00 3384
6 TraesCS3B01G348500 chr5B 95.841 2140 61 2 1 2114 506965544 506967681 0.000000e+00 3434
7 TraesCS3B01G348500 chr5B 94.857 350 18 0 1765 2114 709185000 709184651 4.250000e-152 547
8 TraesCS3B01G348500 chr2B 95.201 2167 85 8 1 2161 68145332 68147485 0.000000e+00 3408
9 TraesCS3B01G348500 chr2B 94.528 2193 87 6 1 2161 549352846 549355037 0.000000e+00 3354
10 TraesCS3B01G348500 chr2B 95.726 2059 58 5 1 2031 454449226 454451282 0.000000e+00 3288
11 TraesCS3B01G348500 chr2B 95.580 2059 61 5 1 2031 454473359 454475415 0.000000e+00 3271
12 TraesCS3B01G348500 chr1B 96.034 2017 54 5 1 1991 571422403 571420387 0.000000e+00 3258
13 TraesCS3B01G348500 chr6A 92.711 2291 103 16 1 2263 23004684 23006938 0.000000e+00 3247
14 TraesCS3B01G348500 chrUn 92.261 827 36 11 1465 2264 86408365 86409190 0.000000e+00 1147
15 TraesCS3B01G348500 chr2A 88.901 883 66 13 1410 2264 770003764 770002886 0.000000e+00 1059
16 TraesCS3B01G348500 chr5D 85.088 114 16 1 2151 2263 348343834 348343947 5.110000e-22 115


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 TraesCS3B01G348500 chr3B 558276109 558278372 2263 True 4181 4181 100.000 1 2264 1 chr3B.!!$R1 2263
1 TraesCS3B01G348500 chr3B 604263840 604266042 2202 True 3406 3406 94.830 1 2169 1 chr3B.!!$R2 2168
2 TraesCS3B01G348500 chr3B 760824947 760825840 893 False 1136 1136 90.380 1413 2264 1 chr3B.!!$F1 851
3 TraesCS3B01G348500 chr4B 551060038 551062309 2271 False 3541 3541 94.893 1 2264 1 chr4B.!!$F1 2263
4 TraesCS3B01G348500 chr6B 679251632 679253793 2161 False 3445 3445 95.402 1 2169 1 chr6B.!!$F1 2168
5 TraesCS3B01G348500 chr6B 181109425 181111563 2138 True 3384 3384 95.421 1 2114 1 chr6B.!!$R1 2113
6 TraesCS3B01G348500 chr5B 506965544 506967681 2137 False 3434 3434 95.841 1 2114 1 chr5B.!!$F1 2113
7 TraesCS3B01G348500 chr2B 68145332 68147485 2153 False 3408 3408 95.201 1 2161 1 chr2B.!!$F1 2160
8 TraesCS3B01G348500 chr2B 549352846 549355037 2191 False 3354 3354 94.528 1 2161 1 chr2B.!!$F4 2160
9 TraesCS3B01G348500 chr2B 454449226 454451282 2056 False 3288 3288 95.726 1 2031 1 chr2B.!!$F2 2030
10 TraesCS3B01G348500 chr2B 454473359 454475415 2056 False 3271 3271 95.580 1 2031 1 chr2B.!!$F3 2030
11 TraesCS3B01G348500 chr1B 571420387 571422403 2016 True 3258 3258 96.034 1 1991 1 chr1B.!!$R1 1990
12 TraesCS3B01G348500 chr6A 23004684 23006938 2254 False 3247 3247 92.711 1 2263 1 chr6A.!!$F1 2262
13 TraesCS3B01G348500 chrUn 86408365 86409190 825 False 1147 1147 92.261 1465 2264 1 chrUn.!!$F1 799
14 TraesCS3B01G348500 chr2A 770002886 770003764 878 True 1059 1059 88.901 1410 2264 1 chr2A.!!$R1 854

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
296 297 0.673333 TGCTCGCATTTGATGACCGT 60.673 50.0 0.0 0.0 0.0 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 1608 0.179056 AGTCATACGGGGCCATTTCG 60.179 55.0 4.39 5.2 0.0 3.46 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
202 203 2.225217 ACAAGGGACGGTAGGTCTTACT 60.225 50.000 0.00 0.00 45.35 2.24
296 297 0.673333 TGCTCGCATTTGATGACCGT 60.673 50.000 0.00 0.00 0.00 4.83
312 313 3.204505 CGTAGCACGGGTGAGAAAA 57.795 52.632 2.38 0.00 38.08 2.29
622 625 1.364721 TGACACAGGACACAACGTTG 58.635 50.000 26.20 26.20 0.00 4.10
674 677 2.816689 CACTAGTCAAACACGTGGACA 58.183 47.619 21.57 7.70 34.04 4.02
1050 1054 1.676916 CCGTGTGCTCACCATGAAGAT 60.677 52.381 13.00 0.00 41.09 2.40
1226 1230 0.934496 TATGCTTACAATCGTGCGCC 59.066 50.000 4.18 0.00 0.00 6.53
1308 1312 4.615588 TGTGTGTCATCACTAACATCCA 57.384 40.909 6.97 0.00 44.14 3.41
1442 1446 5.281727 GCTGTTCGAAGAAAGGTTTCAAAT 58.718 37.500 0.00 0.00 45.90 2.32
1501 1505 2.048127 GGAAGCAACGCGAGGAGT 60.048 61.111 15.93 0.00 0.00 3.85
1604 1608 3.050275 GGCACGTGACAGGAAGGC 61.050 66.667 22.23 0.00 0.00 4.35
1631 1635 2.104281 GGCCCCGTATGACTCAGTAAAT 59.896 50.000 0.00 0.00 0.00 1.40
1661 1665 2.097036 TCGGTGGACTCGTCATGTAAT 58.903 47.619 0.00 0.00 0.00 1.89
1801 1942 8.706322 AGTTTGTTAGTGTATTCTGGGATTTT 57.294 30.769 0.00 0.00 0.00 1.82
1845 1986 0.250467 TGTGCTGGGAAGAGAAGTGC 60.250 55.000 0.00 0.00 0.00 4.40
1846 1987 0.250467 GTGCTGGGAAGAGAAGTGCA 60.250 55.000 0.00 0.00 0.00 4.57
1869 2010 6.980978 GCAATATAACAGAACAGAGTGCTCTA 59.019 38.462 0.93 0.00 37.98 2.43
1875 2016 5.858381 ACAGAACAGAGTGCTCTATTTTCA 58.142 37.500 10.79 0.00 37.98 2.69
2080 2344 1.685180 GGTAGGGTGGGCAAATCTTCC 60.685 57.143 0.00 0.00 0.00 3.46
2161 2440 2.751688 GGTCAACCCTACCGCCAA 59.248 61.111 0.00 0.00 0.00 4.52
2204 2483 1.005450 GAAGATTTGCCCACCCTACCA 59.995 52.381 0.00 0.00 0.00 3.25
2208 2487 1.656092 TTTGCCCACCCTACCACCAA 61.656 55.000 0.00 0.00 0.00 3.67
2254 2533 1.271840 ATACCGCCATGTCCTGTGGT 61.272 55.000 9.45 9.45 39.01 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 203 1.045407 ACCTCGTAAGCAACTCCACA 58.955 50.000 0.00 0.00 37.18 4.17
296 297 3.410631 TCATTTTTCTCACCCGTGCTA 57.589 42.857 0.00 0.00 0.00 3.49
622 625 2.151202 TCTTCGTTTCTTGCATGTCCC 58.849 47.619 0.00 0.00 0.00 4.46
674 677 0.980231 CCCTCCAAGGCTACTGCTCT 60.980 60.000 0.00 0.00 39.59 4.09
812 815 2.963782 GTCCTAGAACCACCGGATACAT 59.036 50.000 9.46 0.00 0.00 2.29
1226 1230 2.431057 AGGTCATAGGCGTTAGTTGGAG 59.569 50.000 0.00 0.00 0.00 3.86
1308 1312 3.815401 GAGGCGGTGACTGCATATAAAAT 59.185 43.478 19.20 0.00 0.00 1.82
1442 1446 0.614979 ACGCTCTTCCTCCAAGCCTA 60.615 55.000 0.00 0.00 32.31 3.93
1526 1530 1.456705 GCCCTCTCCTCCTCACGAT 60.457 63.158 0.00 0.00 0.00 3.73
1604 1608 0.179056 AGTCATACGGGGCCATTTCG 60.179 55.000 4.39 5.20 0.00 3.46
1661 1665 0.323269 TTTGGCATGGCTTCATCCGA 60.323 50.000 21.08 0.00 0.00 4.55
1845 1986 9.539825 AATAGAGCACTCTGTTCTGTTATATTG 57.460 33.333 10.46 0.00 37.30 1.90
1869 2010 5.731591 CGGTAGGGTTCTAACTCTGAAAAT 58.268 41.667 5.47 0.00 40.68 1.82
1875 2016 1.272872 TGGCGGTAGGGTTCTAACTCT 60.273 52.381 0.16 0.16 43.51 3.24
1942 2200 0.558712 AAACTTTGCCACCCCTACCA 59.441 50.000 0.00 0.00 0.00 3.25
2080 2344 1.082756 GCTGGCGTTTCTTGTCACG 60.083 57.895 0.00 0.00 39.49 4.35
2204 2483 0.988832 TTACCGCCAGATTCCTTGGT 59.011 50.000 0.00 0.00 0.00 3.67
2208 2487 0.831307 GACCTTACCGCCAGATTCCT 59.169 55.000 0.00 0.00 0.00 3.36
2235 2514 1.271840 ACCACAGGACATGGCGGTAT 61.272 55.000 0.00 0.00 41.31 2.73


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

AutoCloner maintained by Alex Coulton.