Multiple sequence alignment - TraesCS1B01G320600

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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 TraesCS1B01G320600 chr1B 100.000 3314 0 0 1 3314 544951356 544954669 0.000000e+00 6120
1 TraesCS1B01G320600 chr1B 94.640 3321 138 21 1 3296 544808034 544811339 0.000000e+00 5110
2 TraesCS1B01G320600 chr1B 84.885 2170 274 32 427 2578 544787402 544789535 0.000000e+00 2141
3 TraesCS1B01G320600 chr1B 92.667 150 10 1 280 429 544786428 544786576 7.200000e-52 215
4 TraesCS1B01G320600 chr1D 93.361 3329 184 19 1 3314 405067200 405070506 0.000000e+00 4889
5 TraesCS1B01G320600 chr1D 87.236 1990 225 15 520 2498 404987782 404989753 0.000000e+00 2241
6 TraesCS1B01G320600 chr1D 90.631 523 49 0 1 523 404980828 404981350 0.000000e+00 695
7 TraesCS1B01G320600 chr1D 85.443 158 22 1 2124 2281 405063013 405063169 2.650000e-36 163
8 TraesCS1B01G320600 chr1A 92.710 3251 207 14 89 3314 500376263 500379508 0.000000e+00 4663
9 TraesCS1B01G320600 chr1A 94.794 2939 140 7 1 2929 500365052 500367987 0.000000e+00 4567
10 TraesCS1B01G320600 chr1A 87.374 2582 302 18 1 2566 500353070 500355643 0.000000e+00 2940
11 TraesCS1B01G320600 chr1A 84.334 383 37 12 2930 3296 500368070 500368445 1.460000e-93 353
12 TraesCS1B01G320600 chr1A 87.402 127 16 0 2155 2281 500359889 500360015 2.660000e-31 147
13 TraesCS1B01G320600 chrUn 100.000 414 0 0 1494 1907 477401061 477401474 0.000000e+00 765


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 TraesCS1B01G320600 chr1B 544951356 544954669 3313 False 6120 6120 100.000 1 3314 1 chr1B.!!$F2 3313
1 TraesCS1B01G320600 chr1B 544808034 544811339 3305 False 5110 5110 94.640 1 3296 1 chr1B.!!$F1 3295
2 TraesCS1B01G320600 chr1B 544786428 544789535 3107 False 1178 2141 88.776 280 2578 2 chr1B.!!$F3 2298
3 TraesCS1B01G320600 chr1D 405067200 405070506 3306 False 4889 4889 93.361 1 3314 1 chr1D.!!$F4 3313
4 TraesCS1B01G320600 chr1D 404987782 404989753 1971 False 2241 2241 87.236 520 2498 1 chr1D.!!$F2 1978
5 TraesCS1B01G320600 chr1D 404980828 404981350 522 False 695 695 90.631 1 523 1 chr1D.!!$F1 522
6 TraesCS1B01G320600 chr1A 500376263 500379508 3245 False 4663 4663 92.710 89 3314 1 chr1A.!!$F3 3225
7 TraesCS1B01G320600 chr1A 500353070 500355643 2573 False 2940 2940 87.374 1 2566 1 chr1A.!!$F1 2565
8 TraesCS1B01G320600 chr1A 500365052 500368445 3393 False 2460 4567 89.564 1 3296 2 chr1A.!!$F4 3295

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
709 1538 0.892755 ACCGGCGAGACATTACTGAA 59.107 50.0 9.3 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2501 3353 1.463444 GCTTGCGGTTAGGTGTTACAG 59.537 52.381 0.0 0.0 0.0 2.74 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
244 246 4.728882 GCCATACTGAAGAGATGTTTTGCG 60.729 45.833 0.00 0.00 0.00 4.85
255 257 1.142778 TGTTTTGCGTTTTGCTCGGC 61.143 50.000 0.00 0.00 46.63 5.54
286 288 9.903682 CACAAAGATTATGTGTTTGAGAAAGAT 57.096 29.630 8.78 0.00 42.10 2.40
331 333 3.430453 CCTTGGGTTTATTCAGCCTCAA 58.570 45.455 0.00 0.00 35.15 3.02
400 402 2.569404 ACTAAGCAGGTCCTTCTTCCAG 59.431 50.000 7.09 3.53 0.00 3.86
414 416 0.961019 TTCCAGCATCACAAAGGTGC 59.039 50.000 0.00 0.00 44.87 5.01
492 1321 2.095461 TCTCAGACTGGATGACCTTCG 58.905 52.381 1.81 0.00 37.04 3.79
685 1514 6.540438 TTAAGGTACCTCCATGTACTTGAG 57.460 41.667 16.64 5.31 40.72 3.02
709 1538 0.892755 ACCGGCGAGACATTACTGAA 59.107 50.000 9.30 0.00 0.00 3.02
820 1649 4.934602 AGACTCTTCAGCTTGCAAATACTC 59.065 41.667 0.00 0.00 0.00 2.59
903 1732 3.827008 TCGATGGCTAGAAGCAAGAAT 57.173 42.857 0.00 0.00 44.75 2.40
1492 2329 5.568620 AAGGTGGACTTCTGTACAAGATT 57.431 39.130 0.00 0.00 39.00 2.40
2058 2896 7.971201 AGATCCTCAATTGCAGTAATCTGATA 58.029 34.615 0.00 0.00 43.76 2.15
2176 3014 5.123979 GGGTCATTGAAAGAACTGTACATCC 59.876 44.000 0.00 0.00 0.00 3.51
2186 3024 4.018960 AGAACTGTACATCCAAGAATGCCT 60.019 41.667 0.00 0.00 0.00 4.75
2268 3106 6.108687 TGTACCAATCATTGAGATCAGTGAC 58.891 40.000 9.84 0.00 43.69 3.67
2320 3158 6.040955 ACGAAGAAGATTATCATGAGTGCCTA 59.959 38.462 0.09 0.00 0.00 3.93
2348 3186 5.163622 GCAGTGCTACACAAATGGTATGAAT 60.164 40.000 8.18 0.00 36.74 2.57
2534 3387 3.085533 ACCGCAAGCAATAACCATACAA 58.914 40.909 0.00 0.00 0.00 2.41
2537 3390 5.358442 ACCGCAAGCAATAACCATACAATAA 59.642 36.000 0.00 0.00 0.00 1.40
2583 3436 4.093556 GCAACACTGTATAGTCAAGCCTTC 59.906 45.833 0.00 0.00 34.07 3.46
2593 3446 3.160269 AGTCAAGCCTTCCATTCAAAGG 58.840 45.455 0.00 0.00 45.12 3.11
2604 3457 6.424812 CCTTCCATTCAAAGGAAAATGAACAC 59.575 38.462 0.00 0.00 45.15 3.32
2659 3512 8.579850 TTGCCAATTTGAGACTGAGTAATAAT 57.420 30.769 0.00 0.00 0.00 1.28
2727 3581 9.029368 TCATGTATCCTAGAATCATCTAAGTGG 57.971 37.037 0.00 0.00 37.70 4.00
2764 3618 1.670811 GTTTCATATCCACAGGTGCGG 59.329 52.381 0.00 0.00 0.00 5.69
2803 3660 3.388024 TGGTCAAGTCATATAGCTGTCCC 59.612 47.826 0.00 0.00 0.00 4.46
2840 3697 5.700402 ACCTAAACCTTCAGCTGTGATAT 57.300 39.130 14.67 0.00 30.85 1.63
2843 3700 6.115446 CCTAAACCTTCAGCTGTGATATGAA 58.885 40.000 14.67 0.00 30.85 2.57
2844 3701 6.259608 CCTAAACCTTCAGCTGTGATATGAAG 59.740 42.308 14.67 8.07 46.11 3.02
2904 3761 6.604795 AGCAAGCTTATCTGGTCAACATTTAT 59.395 34.615 0.00 0.00 0.00 1.40
3056 4007 3.316029 TGTTGCATATGCCTGTCTAATGC 59.684 43.478 24.54 0.00 42.52 3.56
3082 4033 5.362263 ACAGAATGCAGTTCAAAGCAAAAT 58.638 33.333 10.26 0.00 44.88 1.82
3083 4034 5.235616 ACAGAATGCAGTTCAAAGCAAAATG 59.764 36.000 10.26 0.00 44.88 2.32
3087 4038 6.774354 ATGCAGTTCAAAGCAAAATGTAAG 57.226 33.333 0.00 0.00 44.88 2.34
3195 4154 5.865085 TCAAGAGCACCTTACACTTTATGT 58.135 37.500 0.00 0.00 46.06 2.29
3221 4180 5.453057 CCACCTCCATCAGAAGACTAATCTG 60.453 48.000 0.00 0.00 44.53 2.90
3224 4183 3.389329 TCCATCAGAAGACTAATCTGGCC 59.611 47.826 0.00 0.00 43.58 5.36
3239 4198 1.080569 GGCCCATGTGCAAAACTCG 60.081 57.895 1.71 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
244 246 0.383949 TGTGAAAGGCCGAGCAAAAC 59.616 50.000 0.00 0.00 0.00 2.43
255 257 8.352201 TCTCAAACACATAATCTTTGTGAAAGG 58.648 33.333 10.51 0.00 45.83 3.11
331 333 2.763448 CTCTTCCATTCTTCTCCTCCGT 59.237 50.000 0.00 0.00 0.00 4.69
400 402 3.129113 TCACATATGCACCTTTGTGATGC 59.871 43.478 15.05 0.00 45.76 3.91
579 1408 4.273148 AGTGTCCGTGCTCTCTTAAATT 57.727 40.909 0.00 0.00 0.00 1.82
628 1457 4.785376 AGATCACTGGGGATAGAACTTGTT 59.215 41.667 0.00 0.00 0.00 2.83
685 1514 1.392510 GTAATGTCTCGCCGGTTCAAC 59.607 52.381 1.90 0.00 0.00 3.18
709 1538 4.801164 AGCTTCCAATAGAATCTGGCAAT 58.199 39.130 0.00 0.00 29.76 3.56
820 1649 6.607735 AATTGATGGCAGTTTTTCAACTTG 57.392 33.333 2.81 0.00 40.66 3.16
903 1732 1.754803 CTATGCCCGTGACCAACTCTA 59.245 52.381 0.00 0.00 0.00 2.43
944 1773 3.343617 ACCACGAATTCATCCACGAATT 58.656 40.909 6.22 0.00 45.91 2.17
945 1774 2.936498 GACCACGAATTCATCCACGAAT 59.064 45.455 6.22 0.00 37.20 3.34
947 1776 1.404986 GGACCACGAATTCATCCACGA 60.405 52.381 6.22 0.00 0.00 4.35
948 1777 1.006832 GGACCACGAATTCATCCACG 58.993 55.000 6.22 0.00 0.00 4.94
1492 2329 4.202556 TGTGAGGGATGGAAGAAATTCACA 60.203 41.667 0.00 0.32 40.72 3.58
2058 2896 2.752030 TCTAGACCAGCAGGCAAGTAT 58.248 47.619 0.00 0.00 39.06 2.12
2176 3014 4.191544 TCCGATAGAAACAGGCATTCTTG 58.808 43.478 5.70 0.00 38.13 3.02
2186 3024 2.565391 TGGCAACTCTCCGATAGAAACA 59.435 45.455 0.00 0.00 32.46 2.83
2268 3106 5.447279 GCTCTTGTTGGTTATGTTGGTATCG 60.447 44.000 0.00 0.00 0.00 2.92
2320 3158 2.294233 CCATTTGTGTAGCACTGCTGTT 59.706 45.455 14.15 0.00 40.10 3.16
2500 3352 2.868839 GCTTGCGGTTAGGTGTTACAGA 60.869 50.000 0.00 0.00 0.00 3.41
2501 3353 1.463444 GCTTGCGGTTAGGTGTTACAG 59.537 52.381 0.00 0.00 0.00 2.74
2534 3387 7.778470 GCTGATGCTTACACTAGTTTCTTAT 57.222 36.000 0.00 0.00 36.03 1.73
2551 3404 5.449812 ACTATACAGTGTTGCAGCTGATGC 61.450 45.833 20.43 11.57 44.21 3.91
2583 3436 7.733402 AATGTGTTCATTTTCCTTTGAATGG 57.267 32.000 0.00 0.00 40.88 3.16
2617 3470 3.763360 TGGCAATCCCATTAGTTTGACTG 59.237 43.478 0.00 0.00 39.18 3.51
2741 3595 3.063997 CGCACCTGTGGATATGAAACTTC 59.936 47.826 0.00 0.00 0.00 3.01
2764 3618 1.315690 CCATGGTGGATGATCTGTGC 58.684 55.000 2.57 0.00 40.96 4.57
2803 3660 8.716646 AAGGTTTAGGTTTTGTTTTCTGAATG 57.283 30.769 0.00 0.00 0.00 2.67
2840 3697 2.357323 TGCGCATGAACAAACTTCTTCA 59.643 40.909 5.66 0.00 0.00 3.02
2843 3700 1.949525 ACTGCGCATGAACAAACTTCT 59.050 42.857 12.24 0.00 0.00 2.85
2844 3701 2.046313 CACTGCGCATGAACAAACTTC 58.954 47.619 12.24 0.00 0.00 3.01
2917 3774 7.394816 TGGAGTTTGCTAGTTAGAAGCTAATT 58.605 34.615 0.00 0.00 40.73 1.40
3056 4007 3.503363 TGCTTTGAACTGCATTCTGTAGG 59.497 43.478 9.34 0.00 38.25 3.18
3082 4033 7.946381 AGTGAGTACATGATCTTCTCTTACA 57.054 36.000 0.00 0.00 0.00 2.41
3083 4034 8.247562 ACAAGTGAGTACATGATCTTCTCTTAC 58.752 37.037 0.00 0.00 30.44 2.34
3087 4038 7.539436 TGTACAAGTGAGTACATGATCTTCTC 58.461 38.462 0.00 0.46 46.77 2.87
3195 4154 2.907892 AGTCTTCTGATGGAGGTGGAA 58.092 47.619 0.00 0.00 0.00 3.53
3221 4180 1.080569 CGAGTTTTGCACATGGGCC 60.081 57.895 19.33 0.80 0.00 5.80
3224 4183 1.262950 TCGTTCGAGTTTTGCACATGG 59.737 47.619 0.00 0.00 0.00 3.66
3239 4198 4.025145 ACTCATTGAGTTTTCGGTTCGTTC 60.025 41.667 13.61 0.00 40.28 3.95
3277 4236 3.878103 CTCTGCCGAAAGTACTAGCTCTA 59.122 47.826 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.