Multiple sequence alignment - TraesCS2D01G240700

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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 TraesCS2D01G240700 chr2D 100.000 3485 0 0 1 3485 259243890 259240406 0.000000e+00 6436
1 TraesCS2D01G240700 chr7D 95.877 3493 135 5 1 3485 291611953 291615444 0.000000e+00 5644
2 TraesCS2D01G240700 chr3D 95.652 3496 135 12 1 3485 323154460 323157949 0.000000e+00 5598
3 TraesCS2D01G240700 chr7A 95.563 3493 142 10 2 3485 458658712 458655224 0.000000e+00 5579
4 TraesCS2D01G240700 chr7A 94.081 3497 187 13 1 3485 265358190 265361678 0.000000e+00 5293
5 TraesCS2D01G240700 chr5D 95.219 3493 151 12 3 3485 190781136 190777650 0.000000e+00 5511
6 TraesCS2D01G240700 chr1D 95.114 3500 141 19 3 3485 371719920 371723406 0.000000e+00 5489
7 TraesCS2D01G240700 chr2A 94.934 3494 150 12 1 3485 160670695 160667220 0.000000e+00 5446
8 TraesCS2D01G240700 chr1B 92.647 3373 229 13 57 3414 425399448 425402816 0.000000e+00 4837
9 TraesCS2D01G240700 chr7B 92.673 3371 223 15 57 3414 365271355 365267996 0.000000e+00 4835
10 TraesCS2D01G240700 chr3B 90.720 3502 268 37 4 3484 247151033 247154498 0.000000e+00 4614
11 TraesCS2D01G240700 chr3B 87.602 492 32 18 2998 3485 162274654 162274188 8.510000e-151 544
12 TraesCS2D01G240700 chr3B 77.727 220 35 10 4 222 247150884 247151090 4.720000e-24 122


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 TraesCS2D01G240700 chr2D 259240406 259243890 3484 True 6436 6436 100.0000 1 3485 1 chr2D.!!$R1 3484
1 TraesCS2D01G240700 chr7D 291611953 291615444 3491 False 5644 5644 95.8770 1 3485 1 chr7D.!!$F1 3484
2 TraesCS2D01G240700 chr3D 323154460 323157949 3489 False 5598 5598 95.6520 1 3485 1 chr3D.!!$F1 3484
3 TraesCS2D01G240700 chr7A 458655224 458658712 3488 True 5579 5579 95.5630 2 3485 1 chr7A.!!$R1 3483
4 TraesCS2D01G240700 chr7A 265358190 265361678 3488 False 5293 5293 94.0810 1 3485 1 chr7A.!!$F1 3484
5 TraesCS2D01G240700 chr5D 190777650 190781136 3486 True 5511 5511 95.2190 3 3485 1 chr5D.!!$R1 3482
6 TraesCS2D01G240700 chr1D 371719920 371723406 3486 False 5489 5489 95.1140 3 3485 1 chr1D.!!$F1 3482
7 TraesCS2D01G240700 chr2A 160667220 160670695 3475 True 5446 5446 94.9340 1 3485 1 chr2A.!!$R1 3484
8 TraesCS2D01G240700 chr1B 425399448 425402816 3368 False 4837 4837 92.6470 57 3414 1 chr1B.!!$F1 3357
9 TraesCS2D01G240700 chr7B 365267996 365271355 3359 True 4835 4835 92.6730 57 3414 1 chr7B.!!$R1 3357
10 TraesCS2D01G240700 chr3B 247150884 247154498 3614 False 2368 4614 84.2235 4 3484 2 chr3B.!!$F1 3480

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
959 1135 0.664761 CTCCACTGCACACAAACCAG 59.335 55.0 0.0 0.0 0.00 4.00 F
1261 1438 0.107643 TGTGGATTTCACCAGCGACA 59.892 50.0 0.0 0.0 45.48 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2248 2436 1.312371 ATTACGCCGCCTGCAACATT 61.312 50.0 0.00 0.00 41.33 2.71 R
2725 2914 2.603135 GATGCGTGGCAGCCATCAAC 62.603 60.0 19.75 13.62 43.65 3.18 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
803 979 1.152756 GGTTGCCACAAGGGACTGT 60.153 57.895 0.00 0.00 40.86 3.55
917 1093 1.683938 CCATCTCTGCCTCATTGCCAA 60.684 52.381 0.00 0.00 0.00 4.52
959 1135 0.664761 CTCCACTGCACACAAACCAG 59.335 55.000 0.00 0.00 0.00 4.00
1005 1182 4.161295 CGGAGGAAGGCGATGGCA 62.161 66.667 1.01 0.00 42.47 4.92
1056 1233 2.125912 CCGTCGGACAAGAGCAGG 60.126 66.667 4.91 0.00 0.00 4.85
1150 1327 1.933247 CAAAGAGACGCTGGAGATCC 58.067 55.000 0.00 0.00 0.00 3.36
1248 1425 3.801698 CTTCATCGGAGTTGATGTGGAT 58.198 45.455 3.90 0.00 44.82 3.41
1261 1438 0.107643 TGTGGATTTCACCAGCGACA 59.892 50.000 0.00 0.00 45.48 4.35
1592 1769 8.621532 TTAATTTCTGAACTTGATGTGCTAGT 57.378 30.769 3.54 0.00 33.94 2.57
1615 1792 7.960262 AGTATAGATTCTGATCTTGATGCACA 58.040 34.615 0.00 0.00 42.55 4.57
1758 1935 5.276461 TGTATCAAGCACTGGTATAGGTG 57.724 43.478 0.00 0.00 36.62 4.00
2086 2273 1.600636 CCCAAGCGCCTCAAAGACA 60.601 57.895 2.29 0.00 0.00 3.41
2119 2306 6.206634 GGAGGAGAAATTGTACACATTTGTCA 59.793 38.462 24.67 3.56 37.15 3.58
2149 2336 1.296715 GGAGGTGACAAGCGGATGT 59.703 57.895 0.00 0.00 35.90 3.06
2190 2377 4.482990 AGATCAACCCCAACAACTTCATT 58.517 39.130 0.00 0.00 0.00 2.57
2208 2395 2.503375 GACATGCAGCGCAAGTGC 60.503 61.111 11.47 12.23 40.58 4.40
2248 2436 2.154567 ATACTACGACTCCTTGGCCA 57.845 50.000 0.00 0.00 0.00 5.36
2428 2616 2.616842 GACAACATCGTGAAAGGTTGGT 59.383 45.455 0.00 0.00 43.61 3.67
2490 2678 0.824109 ACTTCGCGGGATGAAGATGA 59.176 50.000 20.11 0.00 44.42 2.92
2691 2880 5.294306 TGCTAGCTTCCTATTTTGTTCATCG 59.706 40.000 17.23 0.00 0.00 3.84
2725 2914 7.321745 AGTTGAAGTAGGTTGAAGTTGAAAG 57.678 36.000 0.00 0.00 0.00 2.62
2743 2932 2.361483 TTGATGGCTGCCACGCAT 60.361 55.556 25.99 8.09 38.13 4.73
3006 3201 2.908688 TTACTGAGTGCTGCAACAGA 57.091 45.000 30.47 18.16 32.44 3.41
3206 3402 7.946655 TGAAATGTCAGTACAACTTAGTCTG 57.053 36.000 0.00 0.00 39.58 3.51
3415 3617 7.701539 AAATGATCAAAGTACCAGCACAATA 57.298 32.000 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
917 1093 0.033366 GAAGCGGCAATGGTGGTTTT 59.967 50.000 1.45 0.00 0.00 2.43
959 1135 1.065782 GGGCTTGGGAGAGAGAGTTTC 60.066 57.143 0.00 0.00 0.00 2.78
1005 1182 2.920912 TTGGCGGACGGTTCCTCT 60.921 61.111 0.00 0.00 40.23 3.69
1150 1327 2.031012 TGGTTCGCTGGTGCAGAG 59.969 61.111 0.00 0.00 39.64 3.35
1248 1425 1.606668 GGTTCATTGTCGCTGGTGAAA 59.393 47.619 0.00 0.00 32.93 2.69
1719 1896 7.916977 GCTTGATACATCTTTGTGCATCAATTA 59.083 33.333 0.00 0.00 38.87 1.40
1839 2021 3.256631 GTGCTTCACCAAATGATTCACCT 59.743 43.478 0.00 0.00 37.11 4.00
1846 2028 3.819368 TCTTCAGTGCTTCACCAAATGA 58.181 40.909 0.00 0.00 34.49 2.57
2119 2306 4.098914 TGTCACCTCCAATGCTAAAACT 57.901 40.909 0.00 0.00 0.00 2.66
2149 2336 4.229304 TCTCCAAACCAGACTTGTTCAA 57.771 40.909 0.00 0.00 0.00 2.69
2190 2377 2.948323 CACTTGCGCTGCATGTCA 59.052 55.556 9.73 0.00 43.35 3.58
2208 2395 4.589216 TTTGCTGGTCTTTGGATCTTTG 57.411 40.909 0.00 0.00 0.00 2.77
2248 2436 1.312371 ATTACGCCGCCTGCAACATT 61.312 50.000 0.00 0.00 41.33 2.71
2420 2608 7.093771 CCTGCTCTTTTGAAATATACCAACCTT 60.094 37.037 0.00 0.00 0.00 3.50
2490 2678 4.539870 CAACACGAATGCAGACTTTCATT 58.460 39.130 0.00 0.60 35.79 2.57
2691 2880 8.099364 TCAACCTACTTCAACTTCAAATGATC 57.901 34.615 0.00 0.00 0.00 2.92
2725 2914 2.603135 GATGCGTGGCAGCCATCAAC 62.603 60.000 19.75 13.62 43.65 3.18
2743 2932 6.691754 TTTTTGTTTCTGCATGACTAGTGA 57.308 33.333 0.00 0.00 0.00 3.41
2914 3109 6.432162 TCGGCTGAAACTTAGTCTTCTTAGTA 59.568 38.462 0.00 0.00 33.25 1.82
2996 3191 3.189285 TCTTTGCTTTTTCTGTTGCAGC 58.811 40.909 0.00 0.00 36.75 5.25
3006 3201 6.560711 ACGTACTGATTGTTCTTTGCTTTTT 58.439 32.000 0.00 0.00 0.00 1.94
3206 3402 7.667557 TGGTATGATCATAGTACTTGCCTTAC 58.332 38.462 15.83 2.03 0.00 2.34
3284 3481 6.403636 CCTTGGTCGAACTGATATCTTTTTGG 60.404 42.308 0.33 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.