Multiple sequence alignment - TraesCS1A01G073700

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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 TraesCS1A01G073700 chr1A 100.000 3320 0 0 1 3320 57405820 57402501 0.000 6131.0
1 TraesCS1A01G073700 chr1A 90.720 1541 129 8 15 1547 57640159 57638625 0.000 2041.0
2 TraesCS1A01G073700 chr1D 97.310 3308 78 6 17 3320 58628629 58625329 0.000 5605.0
3 TraesCS1A01G073700 chr1D 89.572 2359 226 14 17 2362 58764136 58761785 0.000 2976.0
4 TraesCS1A01G073700 chr1D 94.162 1062 32 10 2286 3320 58438868 58439926 0.000 1591.0
5 TraesCS1A01G073700 chr1D 82.824 1473 241 12 832 2298 38559351 38557885 0.000 1308.0
6 TraesCS1A01G073700 chr1D 82.738 1483 238 16 832 2305 38367077 38365604 0.000 1304.0
7 TraesCS1A01G073700 chr1D 82.203 1489 253 9 832 2317 49425366 49423887 0.000 1271.0
8 TraesCS1A01G073700 chr1D 80.772 1633 286 21 832 2446 50023566 50025188 0.000 1251.0
9 TraesCS1A01G073700 chr1D 83.100 787 128 5 52 834 37964720 37963935 0.000 712.0
10 TraesCS1A01G073700 chr1D 83.205 780 120 11 62 834 36624534 36623759 0.000 704.0
11 TraesCS1A01G073700 chr1D 82.503 783 127 8 62 839 49426241 49425464 0.000 678.0
12 TraesCS1A01G073700 chr1D 82.071 792 126 14 62 842 38259614 38258828 0.000 662.0
13 TraesCS1A01G073700 chr1D 96.774 31 1 0 1 31 58628676 58628646 0.006 52.8
14 TraesCS1A01G073700 chr1B 88.818 2343 245 11 31 2362 94233210 94230874 0.000 2859.0
15 TraesCS1A01G073700 chr1B 80.432 2683 457 48 74 2738 94327151 94324519 0.000 1984.0
16 TraesCS1A01G073700 chr6A 82.892 1473 240 11 832 2298 547816112 547817578 0.000 1314.0
17 TraesCS1A01G073700 chr6B 82.456 1482 247 12 840 2316 601866823 601868296 0.000 1284.0


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 TraesCS1A01G073700 chr1A 57402501 57405820 3319 True 6131.0 6131 100.000 1 3320 1 chr1A.!!$R1 3319
1 TraesCS1A01G073700 chr1A 57638625 57640159 1534 True 2041.0 2041 90.720 15 1547 1 chr1A.!!$R2 1532
2 TraesCS1A01G073700 chr1D 58761785 58764136 2351 True 2976.0 2976 89.572 17 2362 1 chr1D.!!$R6 2345
3 TraesCS1A01G073700 chr1D 58625329 58628676 3347 True 2828.9 5605 97.042 1 3320 2 chr1D.!!$R8 3319
4 TraesCS1A01G073700 chr1D 58438868 58439926 1058 False 1591.0 1591 94.162 2286 3320 1 chr1D.!!$F2 1034
5 TraesCS1A01G073700 chr1D 38557885 38559351 1466 True 1308.0 1308 82.824 832 2298 1 chr1D.!!$R5 1466
6 TraesCS1A01G073700 chr1D 38365604 38367077 1473 True 1304.0 1304 82.738 832 2305 1 chr1D.!!$R4 1473
7 TraesCS1A01G073700 chr1D 50023566 50025188 1622 False 1251.0 1251 80.772 832 2446 1 chr1D.!!$F1 1614
8 TraesCS1A01G073700 chr1D 49423887 49426241 2354 True 974.5 1271 82.353 62 2317 2 chr1D.!!$R7 2255
9 TraesCS1A01G073700 chr1D 37963935 37964720 785 True 712.0 712 83.100 52 834 1 chr1D.!!$R2 782
10 TraesCS1A01G073700 chr1D 36623759 36624534 775 True 704.0 704 83.205 62 834 1 chr1D.!!$R1 772
11 TraesCS1A01G073700 chr1D 38258828 38259614 786 True 662.0 662 82.071 62 842 1 chr1D.!!$R3 780
12 TraesCS1A01G073700 chr1B 94230874 94233210 2336 True 2859.0 2859 88.818 31 2362 1 chr1B.!!$R1 2331
13 TraesCS1A01G073700 chr1B 94324519 94327151 2632 True 1984.0 1984 80.432 74 2738 1 chr1B.!!$R2 2664
14 TraesCS1A01G073700 chr6A 547816112 547817578 1466 False 1314.0 1314 82.892 832 2298 1 chr6A.!!$F1 1466
15 TraesCS1A01G073700 chr6B 601866823 601868296 1473 False 1284.0 1284 82.456 840 2316 1 chr6B.!!$F1 1476

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
392 433 0.970937 TTCGACCGCTTCCTCAGGAT 60.971 55.0 0.00 0.00 0.0 3.24 F
985 1140 1.037493 TCACGGGTATGCTAGCGAAT 58.963 50.0 10.77 1.11 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 1878 0.392706 TTCGCAGAAGCAGTTCTCCA 59.607 50.000 0.0 0.0 45.9 3.86 R
2353 2521 3.814625 TGGCACACAATAACTGAACTGA 58.185 40.909 0.0 0.0 0.0 3.41 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
29 64 4.247380 CATGCTCCGCCTCCTCCC 62.247 72.222 0.00 0.00 0.00 4.30
51 87 4.473520 CCTTCACGCCGCTGGGAT 62.474 66.667 0.00 0.00 34.06 3.85
144 182 3.192001 ACCTGTTCGACGAATTGCTACTA 59.808 43.478 14.27 0.00 0.00 1.82
312 353 4.624364 CCGCCCACAGTCTGCACA 62.624 66.667 0.00 0.00 0.00 4.57
392 433 0.970937 TTCGACCGCTTCCTCAGGAT 60.971 55.000 0.00 0.00 0.00 3.24
656 700 4.380839 CGTATAGCACAGTGATTCATGC 57.619 45.455 4.15 3.08 38.39 4.06
690 734 1.538687 GGGAAGCAAGCAAGGCATGT 61.539 55.000 0.00 0.00 29.47 3.21
980 1135 3.381908 ACTCTTCTTCACGGGTATGCTAG 59.618 47.826 0.00 0.00 0.00 3.42
985 1140 1.037493 TCACGGGTATGCTAGCGAAT 58.963 50.000 10.77 1.11 0.00 3.34
1424 1579 5.703130 GCAAAGAAGGAAGAGTTACAGATGT 59.297 40.000 0.00 0.00 0.00 3.06
1665 1820 7.134163 CACTATTCAGCGAAATGATGCATAAA 58.866 34.615 0.00 0.00 32.78 1.40
1723 1878 3.634910 ACTAAATGGGTTGTTTCGTGCTT 59.365 39.130 0.00 0.00 0.00 3.91
1819 1974 8.819643 ATACGCTATAATTCTTGAAGGACTTC 57.180 34.615 5.14 5.14 39.91 3.01
2120 2277 7.022384 CCGGACTCTCGTCTTATTAATGATAC 58.978 42.308 0.00 0.00 40.10 2.24
2250 2407 2.704065 ACGTCTCTTTTCAAGGGAAGGA 59.296 45.455 4.62 0.00 40.33 3.36
2353 2521 1.488393 GGCATAACTCCTCAGAAGGCT 59.512 52.381 0.00 0.00 43.02 4.58
2586 2756 3.582208 TGTTTCCCTTGCAAATTAGGCAT 59.418 39.130 0.00 0.00 41.58 4.40
2591 2761 3.133362 CCCTTGCAAATTAGGCATCACAT 59.867 43.478 0.00 0.00 41.58 3.21
2882 3052 5.184479 CACAATTCCATCCAATGTCTGAAGT 59.816 40.000 0.00 0.00 0.00 3.01
3236 3432 4.286032 TCAGCATAACCTGTACTGGAAACT 59.714 41.667 24.19 11.08 34.47 2.66
3245 3441 4.184629 CTGTACTGGAAACTGTATGCTCC 58.815 47.826 0.00 0.00 44.97 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 69 4.473520 ATCCCAGCGGCGTGAAGG 62.474 66.667 9.37 4.84 0.00 3.46
351 392 3.081409 GCAAGGCCTAGGTCCGGA 61.081 66.667 10.56 0.00 0.00 5.14
377 418 2.370445 CCCATCCTGAGGAAGCGGT 61.370 63.158 4.76 0.00 34.34 5.68
460 501 1.596260 CAGCACGTTGATAGCCTCATG 59.404 52.381 0.00 0.00 32.72 3.07
577 618 0.904865 ACCATCTGGAGCAGGTCGAA 60.905 55.000 2.55 0.00 38.94 3.71
656 700 4.407365 TGCTTCCCCTTCCTTAAAGAAAG 58.593 43.478 0.00 0.00 37.12 2.62
690 734 6.368779 TGCATCATCTCATGGAATAGATCA 57.631 37.500 0.00 0.00 29.93 2.92
922 1077 2.911552 TTAGGTTTAAGGCCCTTGGG 57.088 50.000 6.16 0.32 32.08 4.12
933 1088 7.792374 AGAGTACACGACGATATTAGGTTTA 57.208 36.000 0.00 0.00 0.00 2.01
980 1135 4.628766 TCATATCAGCTAAGCATCATTCGC 59.371 41.667 0.00 0.00 0.00 4.70
985 1140 9.597170 GAGATTAATCATATCAGCTAAGCATCA 57.403 33.333 17.56 0.00 0.00 3.07
1424 1579 3.762288 AGCCAAGTCGAAGATACTGTGTA 59.238 43.478 0.00 0.00 40.67 2.90
1723 1878 0.392706 TTCGCAGAAGCAGTTCTCCA 59.607 50.000 0.00 0.00 45.90 3.86
1819 1974 6.630443 GCTTCATCAGTGCAATTATTTCTACG 59.370 38.462 0.00 0.00 0.00 3.51
2120 2277 8.355169 CACCTTGTTCCAATAATATTCTGATGG 58.645 37.037 0.00 0.00 0.00 3.51
2353 2521 3.814625 TGGCACACAATAACTGAACTGA 58.185 40.909 0.00 0.00 0.00 3.41
3236 3432 3.382227 CAGCAAATCATTGGGAGCATACA 59.618 43.478 0.00 0.00 37.02 2.29
3245 3441 5.389859 TTCCTTGTACAGCAAATCATTGG 57.610 39.130 0.00 0.00 36.53 3.16


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

AutoCloner maintained by Alex Coulton.