Multiple sequence alignment - TraesCS4A01G337600

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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 TraesCS4A01G337600 chr4A 100.000 2264 0 0 1 2264 619685152 619687415 0 4181
1 TraesCS4A01G337600 chr4A 93.966 2287 97 14 1 2264 708970204 708972472 0 3421
2 TraesCS4A01G337600 chr4A 96.559 1337 45 1 929 2264 619636759 619638095 0 2213
3 TraesCS4A01G337600 chr7B 94.571 2284 99 11 1 2264 712690280 712692558 0 3507
4 TraesCS4A01G337600 chr7B 92.085 1554 110 8 718 2261 77501883 77503433 0 2176
5 TraesCS4A01G337600 chr7B 93.951 1306 67 1 718 2011 154497322 154498627 0 1964
6 TraesCS4A01G337600 chr5B 94.282 2291 101 7 1 2264 470487370 470489657 0 3478
7 TraesCS4A01G337600 chr1B 94.092 2285 101 7 1 2264 660603850 660606121 0 3441
8 TraesCS4A01G337600 chr6D 94.308 1546 76 4 718 2261 365492209 365493744 0 2357
9 TraesCS4A01G337600 chr1D 93.070 1544 74 4 718 2259 482464954 482466466 0 2228
10 TraesCS4A01G337600 chr6B 95.525 1296 56 2 970 2264 631477687 631478981 0 2071
11 TraesCS4A01G337600 chr6B 89.955 1573 130 15 718 2264 94808694 94807124 0 2004
12 TraesCS4A01G337600 chr6B 96.339 956 31 4 1 953 631453261 631454215 0 1568
13 TraesCS4A01G337600 chrUn 95.389 1171 51 3 1096 2264 247963146 247961977 0 1860
14 TraesCS4A01G337600 chrUn 95.389 1171 51 3 1096 2264 331975238 331976407 0 1860
15 TraesCS4A01G337600 chrUn 95.541 897 38 2 1 895 247964029 247963133 0 1434
16 TraesCS4A01G337600 chrUn 95.541 897 38 2 1 895 331974355 331975251 0 1434
17 TraesCS4A01G337600 chr4B 95.318 897 39 3 1 895 578267222 578268117 0 1421
18 TraesCS4A01G337600 chr4B 95.206 897 40 3 1 895 578282677 578283572 0 1415


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 TraesCS4A01G337600 chr4A 619685152 619687415 2263 False 4181 4181 100.000 1 2264 1 chr4A.!!$F2 2263
1 TraesCS4A01G337600 chr4A 708970204 708972472 2268 False 3421 3421 93.966 1 2264 1 chr4A.!!$F3 2263
2 TraesCS4A01G337600 chr4A 619636759 619638095 1336 False 2213 2213 96.559 929 2264 1 chr4A.!!$F1 1335
3 TraesCS4A01G337600 chr7B 712690280 712692558 2278 False 3507 3507 94.571 1 2264 1 chr7B.!!$F3 2263
4 TraesCS4A01G337600 chr7B 77501883 77503433 1550 False 2176 2176 92.085 718 2261 1 chr7B.!!$F1 1543
5 TraesCS4A01G337600 chr7B 154497322 154498627 1305 False 1964 1964 93.951 718 2011 1 chr7B.!!$F2 1293
6 TraesCS4A01G337600 chr5B 470487370 470489657 2287 False 3478 3478 94.282 1 2264 1 chr5B.!!$F1 2263
7 TraesCS4A01G337600 chr1B 660603850 660606121 2271 False 3441 3441 94.092 1 2264 1 chr1B.!!$F1 2263
8 TraesCS4A01G337600 chr6D 365492209 365493744 1535 False 2357 2357 94.308 718 2261 1 chr6D.!!$F1 1543
9 TraesCS4A01G337600 chr1D 482464954 482466466 1512 False 2228 2228 93.070 718 2259 1 chr1D.!!$F1 1541
10 TraesCS4A01G337600 chr6B 631477687 631478981 1294 False 2071 2071 95.525 970 2264 1 chr6B.!!$F2 1294
11 TraesCS4A01G337600 chr6B 94807124 94808694 1570 True 2004 2004 89.955 718 2264 1 chr6B.!!$R1 1546
12 TraesCS4A01G337600 chr6B 631453261 631454215 954 False 1568 1568 96.339 1 953 1 chr6B.!!$F1 952
13 TraesCS4A01G337600 chrUn 247961977 247964029 2052 True 1647 1860 95.465 1 2264 2 chrUn.!!$R1 2263
14 TraesCS4A01G337600 chrUn 331974355 331976407 2052 False 1647 1860 95.465 1 2264 2 chrUn.!!$F1 2263
15 TraesCS4A01G337600 chr4B 578267222 578268117 895 False 1421 1421 95.318 1 895 1 chr4B.!!$F1 894
16 TraesCS4A01G337600 chr4B 578282677 578283572 895 False 1415 1415 95.206 1 895 1 chr4B.!!$F2 894

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
934 947 0.912486 CGAGGGTTTTCTCCTCCCAT 59.088 55.0 4.74 0.0 46.01 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 2336 1.007238 AGGAACCAGAGCAGCTACCTA 59.993 52.381 0.0 0.0 0.0 3.08 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
24 25 2.435437 TGCACTCATTAGCCATCTAGCA 59.565 45.455 0.00 0.00 34.23 3.49
119 120 1.364269 TATTGACCCCACCTCGGTTT 58.636 50.000 0.00 0.00 32.27 3.27
138 139 4.107029 TTGGACCTCCGACACGAT 57.893 55.556 0.00 0.00 39.43 3.73
141 142 1.226603 GGACCTCCGACACGATTCG 60.227 63.158 4.14 4.14 38.80 3.34
159 160 2.194056 CTTCCCTCGGCATGCCAT 59.806 61.111 34.93 0.00 35.37 4.40
783 788 2.351276 GCACGGGGAGGTGTGAAT 59.649 61.111 0.00 0.00 40.08 2.57
934 947 0.912486 CGAGGGTTTTCTCCTCCCAT 59.088 55.000 4.74 0.00 46.01 4.00
1429 1526 4.759183 ACCTAGATTCGTTAGATCCGGTAC 59.241 45.833 0.00 0.00 0.00 3.34
1430 1527 4.758674 CCTAGATTCGTTAGATCCGGTACA 59.241 45.833 0.00 0.00 0.00 2.90
1524 1622 2.816411 AGATCTACCAACCACTCCGAA 58.184 47.619 0.00 0.00 0.00 4.30
1958 2056 8.697507 TCATGTGTGTACTATCTCTATGATGT 57.302 34.615 0.00 0.00 36.65 3.06
1959 2057 9.136323 TCATGTGTGTACTATCTCTATGATGTT 57.864 33.333 0.00 0.00 36.65 2.71
2061 2160 3.795688 ATGCCTTCTGGACTCAAAAGA 57.204 42.857 0.00 0.00 34.57 2.52
2084 2183 5.343249 ACAACTTGATTTCAGCTGTTTGAC 58.657 37.500 14.67 3.90 0.00 3.18
2184 2284 4.201920 GCTAGGTTGCATTAGTTTAGGCAC 60.202 45.833 0.00 0.00 35.74 5.01
2236 2336 9.646522 AAAATATTCTGCTATTTATGTGGGACT 57.353 29.630 0.00 0.00 32.39 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.435437 TGCTAGATGGCTAATGAGTGCA 59.565 45.455 0.00 0.00 0.00 4.57
24 25 2.202236 CTAGGTGTGCATGGCTGGGT 62.202 60.000 0.00 0.00 0.00 4.51
119 120 1.183030 ATCGTGTCGGAGGTCCAACA 61.183 55.000 0.00 0.00 35.14 3.33
138 139 2.125147 CATGCCGAGGGAAGCGAA 60.125 61.111 0.00 0.00 0.00 4.70
141 142 4.802051 TGGCATGCCGAGGGAAGC 62.802 66.667 30.87 5.02 39.42 3.86
159 160 1.070242 CGCGTGTTGCTTTGACATACA 60.070 47.619 0.00 0.00 43.27 2.29
180 181 2.276201 TCGGTGTGCAATATGTGTAGC 58.724 47.619 0.00 0.00 0.00 3.58
327 328 0.253894 TCTGGACCCATGTCATGCAG 59.746 55.000 7.35 9.15 43.65 4.41
434 435 2.665165 ACACATGGTTTCCAAGCTTCA 58.335 42.857 0.00 0.00 36.95 3.02
627 631 0.323360 TTGTAGAAGGCATGGTGGGC 60.323 55.000 0.00 0.00 0.00 5.36
666 670 1.425066 TCCTTCCAAAGACATGTGGCT 59.575 47.619 1.15 0.00 34.68 4.75
674 678 6.403049 TCCTTTTGTTTTTCCTTCCAAAGAC 58.597 36.000 0.00 0.00 0.00 3.01
783 788 2.165437 GTCAAAAGGAGTTGTTGCCACA 59.835 45.455 0.00 0.00 0.00 4.17
934 947 2.031012 CAGGCGAGTTGTGAGGCA 59.969 61.111 0.00 0.00 0.00 4.75
1047 1094 0.107263 TGGATGCTTCTTGCGCCATA 60.107 50.000 4.18 0.00 46.63 2.74
1147 1194 1.690219 GGAGCCTGGATGTGGTCGAT 61.690 60.000 0.00 0.00 0.00 3.59
1208 1255 0.900421 CAGATGAGTCACCTGCTCCA 59.100 55.000 0.28 0.00 32.31 3.86
1429 1526 0.740737 GTGGATCCGCCCTTGAAATG 59.259 55.000 14.81 0.00 34.97 2.32
1430 1527 0.331278 TGTGGATCCGCCCTTGAAAT 59.669 50.000 22.48 0.00 34.97 2.17
1524 1622 1.153289 GATGCACGAGAGCCATGGT 60.153 57.895 14.67 0.00 0.00 3.55
2061 2160 5.105797 TGTCAAACAGCTGAAATCAAGTTGT 60.106 36.000 23.35 0.00 0.00 3.32
2084 2183 6.690528 GCAAACCAAAACCACAACAATATTTG 59.309 34.615 0.00 0.00 0.00 2.32
2127 2227 3.641436 GGACCCAGAATTTCAAAGTTGGT 59.359 43.478 0.00 0.00 0.00 3.67
2236 2336 1.007238 AGGAACCAGAGCAGCTACCTA 59.993 52.381 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.