Multiple sequence alignment - TraesCS5B01G520800

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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 TraesCS5B01G520800 chr5B 100.000 2732 0 0 1 2732 682932565 682929834 0 5046
1 TraesCS5B01G520800 chr5B 97.306 891 24 0 1 891 682924118 682923228 0 1513
2 TraesCS5B01G520800 chr2B 97.504 1963 49 0 770 2732 103274203 103276165 0 3354
3 TraesCS5B01G520800 chr2B 96.485 1963 68 1 770 2732 564596215 564594254 0 3241
4 TraesCS5B01G520800 chr2B 97.044 778 22 1 1 777 564597014 564596237 0 1308
5 TraesCS5B01G520800 chr2B 96.799 781 23 2 1 779 564588443 564587663 0 1303
6 TraesCS5B01G520800 chr2B 96.791 779 25 0 1 779 714923595 714924373 0 1301
7 TraesCS5B01G520800 chr3B 97.045 1963 58 0 770 2732 667130834 667128872 0 3304
8 TraesCS5B01G520800 chr3B 96.081 1965 73 3 770 2732 358721846 358719884 0 3199
9 TraesCS5B01G520800 chr3B 96.077 1963 74 3 770 2732 37011364 37013323 0 3195
10 TraesCS5B01G520800 chr7B 96.996 1964 56 2 770 2732 570947874 570949835 0 3297
11 TraesCS5B01G520800 chr4B 96.226 1961 70 3 770 2730 333792400 333794356 0 3208
12 TraesCS5B01G520800 chr1B 95.825 1964 78 4 770 2732 237175327 237177287 0 3169
13 TraesCS5B01G520800 chr1B 95.825 1964 79 3 770 2732 555559390 555561351 0 3169
14 TraesCS5B01G520800 chr7D 83.399 2789 375 62 1 2732 226909082 226906325 0 2505
15 TraesCS5B01G520800 chr3D 83.291 2759 380 61 1 2710 151484574 151487300 0 2466
16 TraesCS5B01G520800 chr5A 87.060 1507 173 15 1 1495 503080898 503082394 0 1683
17 TraesCS5B01G520800 chr5A 91.769 899 62 10 1 891 412337565 412338459 0 1240
18 TraesCS5B01G520800 chr2A 83.784 1369 195 23 1 1353 418880553 418879196 0 1273


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 TraesCS5B01G520800 chr5B 682929834 682932565 2731 True 5046.0 5046 100.0000 1 2732 1 chr5B.!!$R2 2731
1 TraesCS5B01G520800 chr5B 682923228 682924118 890 True 1513.0 1513 97.3060 1 891 1 chr5B.!!$R1 890
2 TraesCS5B01G520800 chr2B 103274203 103276165 1962 False 3354.0 3354 97.5040 770 2732 1 chr2B.!!$F1 1962
3 TraesCS5B01G520800 chr2B 564594254 564597014 2760 True 2274.5 3241 96.7645 1 2732 2 chr2B.!!$R2 2731
4 TraesCS5B01G520800 chr2B 564587663 564588443 780 True 1303.0 1303 96.7990 1 779 1 chr2B.!!$R1 778
5 TraesCS5B01G520800 chr2B 714923595 714924373 778 False 1301.0 1301 96.7910 1 779 1 chr2B.!!$F2 778
6 TraesCS5B01G520800 chr3B 667128872 667130834 1962 True 3304.0 3304 97.0450 770 2732 1 chr3B.!!$R2 1962
7 TraesCS5B01G520800 chr3B 358719884 358721846 1962 True 3199.0 3199 96.0810 770 2732 1 chr3B.!!$R1 1962
8 TraesCS5B01G520800 chr3B 37011364 37013323 1959 False 3195.0 3195 96.0770 770 2732 1 chr3B.!!$F1 1962
9 TraesCS5B01G520800 chr7B 570947874 570949835 1961 False 3297.0 3297 96.9960 770 2732 1 chr7B.!!$F1 1962
10 TraesCS5B01G520800 chr4B 333792400 333794356 1956 False 3208.0 3208 96.2260 770 2730 1 chr4B.!!$F1 1960
11 TraesCS5B01G520800 chr1B 237175327 237177287 1960 False 3169.0 3169 95.8250 770 2732 1 chr1B.!!$F1 1962
12 TraesCS5B01G520800 chr1B 555559390 555561351 1961 False 3169.0 3169 95.8250 770 2732 1 chr1B.!!$F2 1962
13 TraesCS5B01G520800 chr7D 226906325 226909082 2757 True 2505.0 2505 83.3990 1 2732 1 chr7D.!!$R1 2731
14 TraesCS5B01G520800 chr3D 151484574 151487300 2726 False 2466.0 2466 83.2910 1 2710 1 chr3D.!!$F1 2709
15 TraesCS5B01G520800 chr5A 503080898 503082394 1496 False 1683.0 1683 87.0600 1 1495 1 chr5A.!!$F2 1494
16 TraesCS5B01G520800 chr5A 412337565 412338459 894 False 1240.0 1240 91.7690 1 891 1 chr5A.!!$F1 890
17 TraesCS5B01G520800 chr2A 418879196 418880553 1357 True 1273.0 1273 83.7840 1 1353 1 chr2A.!!$R1 1352

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
233 239 0.320374 TGCGAGAAATCAACGGAGGT 59.680 50.0 0.0 0.0 0.00 3.85 F
614 639 1.532604 ATGTGCTGACCCGTTCTCGA 61.533 55.0 0.0 0.0 39.71 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1106 1170 1.079681 GTGGCATTGTACGTCCCGA 60.080 57.895 0.00 0.0 0.00 5.14 R
2610 2717 1.540797 GCTTATGCTGAGCTCCTGAGG 60.541 57.143 12.15 0.0 37.18 3.86 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
41 43 3.585862 TCATGCTAGAAACTTCCGTGTC 58.414 45.455 0.00 0.0 0.00 3.67
150 154 1.832998 GGTTTGGTATGGTCTACCCGA 59.167 52.381 0.00 0.0 36.79 5.14
233 239 0.320374 TGCGAGAAATCAACGGAGGT 59.680 50.000 0.00 0.0 0.00 3.85
587 612 9.764363 TTCATTCTACTGTGTTATATTGCTAGG 57.236 33.333 0.00 0.0 0.00 3.02
614 639 1.532604 ATGTGCTGACCCGTTCTCGA 61.533 55.000 0.00 0.0 39.71 4.04
984 1046 9.520204 CTACTCATTTCTGATTTCTCTTCTCTC 57.480 37.037 0.00 0.0 0.00 3.20
991 1053 7.493499 TCTGATTTCTCTTCTCTCTTTCCAT 57.507 36.000 0.00 0.0 0.00 3.41
1285 1349 2.166664 GGACGCATTGGAGAAGTCTACT 59.833 50.000 0.00 0.0 32.86 2.57
1550 1614 2.225963 CACTACTGGAGAAGAACGACGT 59.774 50.000 0.00 0.0 0.00 4.34
1691 1767 8.154856 TGATGATGATTATGAAGATGAAGCTGA 58.845 33.333 0.00 0.0 0.00 4.26
1952 2056 1.404035 GTGACACCGGTTTTGCTTTCT 59.596 47.619 2.97 0.0 0.00 2.52
2160 2267 3.069158 CGTATCGGAAGGGAGTTAACCAT 59.931 47.826 0.88 0.0 0.00 3.55
2302 2409 1.519408 TTCAGCAGGCTTTTCGTACC 58.481 50.000 0.00 0.0 0.00 3.34
2327 2434 0.613260 TGTTTCCGCTGGAGCTATGT 59.387 50.000 0.00 0.0 39.32 2.29
2340 2447 4.651045 TGGAGCTATGTAGATGAAGAAGCA 59.349 41.667 0.00 0.0 0.00 3.91
2568 2675 0.326264 ATCGAAGGGAAGCAACAGCT 59.674 50.000 0.00 0.0 41.23 4.24
2610 2717 5.011840 GGAAGTATGGTCAGGGGAAGTATAC 59.988 48.000 0.00 0.0 0.00 1.47
2634 2741 0.467384 GGAGCTCAGCATAAGCCTCA 59.533 55.000 17.19 0.0 43.56 3.86
2642 2749 3.519510 TCAGCATAAGCCTCACTTAACCT 59.480 43.478 0.00 0.0 43.99 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 64 8.129840 CACGTAACTTACTCAACTATGCTAGAT 58.870 37.037 0.00 0.0 0.00 1.98
233 239 1.639722 TTCCCCACAAGACTCGATCA 58.360 50.000 0.00 0.0 0.00 2.92
408 424 4.675063 ACATTGAGAAGGTAACCCCAAT 57.325 40.909 0.00 0.0 34.66 3.16
587 612 2.146342 CGGGTCAGCACATGGAATATC 58.854 52.381 0.00 0.0 0.00 1.63
984 1046 3.316308 CCGGCATCCTAAAGAATGGAAAG 59.684 47.826 0.00 0.0 35.81 2.62
991 1053 3.038280 TCATCTCCGGCATCCTAAAGAA 58.962 45.455 0.00 0.0 0.00 2.52
1106 1170 1.079681 GTGGCATTGTACGTCCCGA 60.080 57.895 0.00 0.0 0.00 5.14
1285 1349 5.964477 AGATGGTGTCCTTGAGTTCCTTATA 59.036 40.000 0.00 0.0 0.00 0.98
1550 1614 7.123697 TGAATACTCCGATCTTCTTAACCAAGA 59.876 37.037 0.00 0.0 39.06 3.02
1691 1767 4.137543 GGAAGATTCCATAATGTCGGCTT 58.862 43.478 6.74 0.0 46.76 4.35
1760 1840 5.527214 CGCAAAAGTGATCTATTACATGGGA 59.473 40.000 0.00 0.0 0.00 4.37
2302 2409 3.814268 CCAGCGGAAACATGGGCG 61.814 66.667 0.00 0.0 34.07 6.13
2327 2434 4.697352 GCAAAACTCCTGCTTCTTCATCTA 59.303 41.667 0.00 0.0 36.84 1.98
2340 2447 4.023193 CCTGACGTAAATTGCAAAACTCCT 60.023 41.667 1.71 0.0 0.00 3.69
2568 2675 2.735151 TCCTCTTACGGCTCTCAATCA 58.265 47.619 0.00 0.0 0.00 2.57
2610 2717 1.540797 GCTTATGCTGAGCTCCTGAGG 60.541 57.143 12.15 0.0 37.18 3.86
2634 2741 2.692041 CCTCCCGTATTCGAGGTTAAGT 59.308 50.000 0.00 0.0 39.71 2.24
2642 2749 0.974010 ACAAGCCCTCCCGTATTCGA 60.974 55.000 0.00 0.0 39.71 3.71


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

AutoCloner maintained by Alex Coulton.