Multiple sequence alignment - TraesCS3D01G405100

Loading Multiple Alignment...

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 TraesCS3D01G405100 chr3D 100.000 2553 0 0 1 2553 519644222 519641670 0.000000e+00 4715.0
1 TraesCS3D01G405100 chr3D 88.219 2572 275 16 1 2549 519597221 519599787 0.000000e+00 3046.0
2 TraesCS3D01G405100 chr3D 86.699 1030 107 18 1218 2226 519620583 519621603 0.000000e+00 1116.0
3 TraesCS3D01G405100 chr3A 94.343 2563 130 14 1 2553 654584655 654582098 0.000000e+00 3916.0
4 TraesCS3D01G405100 chr3A 87.398 2571 294 18 1 2547 654518508 654521072 0.000000e+00 2926.0
5 TraesCS3D01G405100 chr3A 86.584 2087 252 16 10 2073 654499664 654501745 0.000000e+00 2278.0
6 TraesCS3D01G405100 chr3A 88.789 446 49 1 2105 2549 654501746 654502191 1.730000e-151 545.0
7 TraesCS3D01G405100 chr3A 83.544 553 57 19 1700 2226 654562134 654562678 1.060000e-133 486.0
8 TraesCS3D01G405100 chr6A 88.340 2573 268 19 2 2549 35563484 35560919 0.000000e+00 3061.0
9 TraesCS3D01G405100 chrUn 87.631 2571 290 16 2 2549 101062802 101065367 0.000000e+00 2961.0
10 TraesCS3D01G405100 chr3B 86.892 2571 297 21 4 2549 684136699 684134144 0.000000e+00 2844.0
11 TraesCS3D01G405100 chr7D 72.279 1966 467 64 22 1945 612711783 612713712 8.040000e-150 540.0
12 TraesCS3D01G405100 chr7B 72.536 1613 385 45 363 1944 702196549 702194964 2.970000e-129 472.0
13 TraesCS3D01G405100 chr7B 78.873 142 30 0 985 1126 702469840 702469981 2.090000e-16 97.1


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 TraesCS3D01G405100 chr3D 519641670 519644222 2552 True 4715.0 4715 100.0000 1 2553 1 chr3D.!!$R1 2552
1 TraesCS3D01G405100 chr3D 519597221 519599787 2566 False 3046.0 3046 88.2190 1 2549 1 chr3D.!!$F1 2548
2 TraesCS3D01G405100 chr3D 519620583 519621603 1020 False 1116.0 1116 86.6990 1218 2226 1 chr3D.!!$F2 1008
3 TraesCS3D01G405100 chr3A 654582098 654584655 2557 True 3916.0 3916 94.3430 1 2553 1 chr3A.!!$R1 2552
4 TraesCS3D01G405100 chr3A 654518508 654521072 2564 False 2926.0 2926 87.3980 1 2547 1 chr3A.!!$F1 2546
5 TraesCS3D01G405100 chr3A 654499664 654502191 2527 False 1411.5 2278 87.6865 10 2549 2 chr3A.!!$F3 2539
6 TraesCS3D01G405100 chr3A 654562134 654562678 544 False 486.0 486 83.5440 1700 2226 1 chr3A.!!$F2 526
7 TraesCS3D01G405100 chr6A 35560919 35563484 2565 True 3061.0 3061 88.3400 2 2549 1 chr6A.!!$R1 2547
8 TraesCS3D01G405100 chrUn 101062802 101065367 2565 False 2961.0 2961 87.6310 2 2549 1 chrUn.!!$F1 2547
9 TraesCS3D01G405100 chr3B 684134144 684136699 2555 True 2844.0 2844 86.8920 4 2549 1 chr3B.!!$R1 2545
10 TraesCS3D01G405100 chr7D 612711783 612713712 1929 False 540.0 540 72.2790 22 1945 1 chr7D.!!$F1 1923
11 TraesCS3D01G405100 chr7B 702194964 702196549 1585 True 472.0 472 72.5360 363 1944 1 chr7B.!!$R1 1581

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
120 121 0.251354 ACGCACAAGCATCCTCTCAT 59.749 50.0 0.0 0.0 42.27 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 1737 0.548031 ATATGAGGGTGTGGGCACAG 59.452 55.0 0.0 0.0 46.95 3.66 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
17 18 4.892002 GGGTGTCGTCTGGGTTTT 57.108 55.556 0.00 0.00 0.00 2.43
34 35 5.119694 GGGTTTTCTAGATCCAGATCACAC 58.880 45.833 10.17 0.00 40.22 3.82
101 102 2.979120 TGCATCAGCGTTGCAGCA 60.979 55.556 12.77 12.77 44.73 4.41
120 121 0.251354 ACGCACAAGCATCCTCTCAT 59.749 50.000 0.00 0.00 42.27 2.90
123 124 1.681166 GCACAAGCATCCTCTCATGGT 60.681 52.381 0.00 0.00 41.58 3.55
165 166 1.748591 GCCTCCGCCAGATCATCTTTT 60.749 52.381 0.00 0.00 0.00 2.27
353 357 1.604378 CTTCCCTTCGAGCATGGGT 59.396 57.895 12.45 0.00 40.04 4.51
423 427 3.117926 CACCTCCATCATGTTGGACCATA 60.118 47.826 19.59 1.76 40.90 2.74
605 612 1.330655 ATTCGCCGTCACTCCAGGAT 61.331 55.000 0.00 0.00 0.00 3.24
635 642 1.446272 GCCCTTCTCGACAGAACGG 60.446 63.158 0.00 0.00 37.69 4.44
753 764 2.431057 GCTGGTGGTACTGCTACTACAT 59.569 50.000 2.75 0.00 36.34 2.29
891 903 9.243105 CCTCTCCTTTTCAATTTAGTGGAATAA 57.757 33.333 0.00 0.00 0.00 1.40
1026 1038 5.532779 GGTTGTTGACTTCTCTCTTTTGGAT 59.467 40.000 0.00 0.00 0.00 3.41
1126 1138 3.453717 ACTGCAGAGGCTTAAGATCATCA 59.546 43.478 23.35 4.81 41.91 3.07
1127 1139 4.080695 ACTGCAGAGGCTTAAGATCATCAA 60.081 41.667 23.35 0.00 41.91 2.57
1224 1239 8.004087 ACTTTTTGGTCCTAGGTAAAAGAAAC 57.996 34.615 27.76 13.21 38.51 2.78
1345 1360 5.940470 AGTGGACCATGAGTTTGATTTACTC 59.060 40.000 0.00 0.00 41.86 2.59
1366 1381 6.323266 ACTCAAACTACTACTTGTATCTGCG 58.677 40.000 0.00 0.00 0.00 5.18
1369 1384 2.033049 ACTACTACTTGTATCTGCGCCG 59.967 50.000 4.18 0.00 0.00 6.46
1439 1454 9.329913 CAAGTAACACTAGATGCACAAAAATAC 57.670 33.333 0.00 0.00 0.00 1.89
1492 1507 8.902040 CAAAATGTTTTGTCTATCTTAGCTCC 57.098 34.615 9.48 0.00 41.87 4.70
1502 1519 5.004448 TCTATCTTAGCTCCGGTGAGTATG 58.996 45.833 7.92 0.96 40.95 2.39
1715 1737 3.531538 TGCTCTATTCCCACGACATTTC 58.468 45.455 0.00 0.00 0.00 2.17
1776 1803 6.040166 GCTGAATGGTGGAGTGAATGATAAAT 59.960 38.462 0.00 0.00 0.00 1.40
1820 1850 6.474140 TTCCTTACCTTTGTTTCCCTTTTC 57.526 37.500 0.00 0.00 0.00 2.29
1821 1851 5.520751 TCCTTACCTTTGTTTCCCTTTTCA 58.479 37.500 0.00 0.00 0.00 2.69
1908 1945 4.286032 AGAACTGGGCATCAACTAGTTGTA 59.714 41.667 29.83 19.13 41.16 2.41
2011 2068 2.116238 GGCTAGTCCTGGTTGGTATGA 58.884 52.381 0.00 0.00 37.07 2.15
2053 2110 3.199946 TGAGGCTACCTTACCTGAATTGG 59.800 47.826 0.00 0.00 36.05 3.16
2338 2408 5.102953 TCGACAAGATCATCCTTTCCATT 57.897 39.130 0.00 0.00 0.00 3.16
2363 2433 6.549364 TCCAACTAACTCCATTCAACATGTTT 59.451 34.615 8.77 0.00 0.00 2.83
2411 2482 8.276252 TGTTGCTAGTTAAATCCTTAATGGTC 57.724 34.615 0.00 0.00 37.07 4.02
2434 2506 7.542130 GGTCTTGTGCAATTCAATTACTAAAGG 59.458 37.037 0.00 0.00 0.00 3.11
2453 2525 5.545658 AAGGTAATGTGTCAACTTATGCG 57.454 39.130 0.00 0.00 0.00 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.961741 GCTGGTGTGATCTGGATCTAGA 59.038 50.000 11.59 11.59 38.60 2.43
34 35 1.987807 ATCATCGGGAAGGGTGCTGG 61.988 60.000 0.00 0.00 0.00 4.85
101 102 0.251354 ATGAGAGGATGCTTGTGCGT 59.749 50.000 0.00 0.00 43.34 5.24
353 357 6.692849 ATGATGATGGACTTGCCTAATAGA 57.307 37.500 0.00 0.00 37.63 1.98
472 479 6.411376 CCATTACAGTGTAATAGGGACAACA 58.589 40.000 24.54 0.00 0.00 3.33
596 603 2.304180 CCTCACAACAAGATCCTGGAGT 59.696 50.000 1.52 0.00 0.00 3.85
605 612 1.072331 GAGAAGGGCCTCACAACAAGA 59.928 52.381 6.46 0.00 33.50 3.02
635 642 3.157087 CATGGGGGCTATAATGTTGACC 58.843 50.000 0.00 0.00 0.00 4.02
731 741 2.100989 GTAGTAGCAGTACCACCAGCT 58.899 52.381 0.00 0.00 40.92 4.24
856 868 1.897802 GAAAAGGAGAGGGGACGTACA 59.102 52.381 0.00 0.00 0.00 2.90
1026 1038 6.857437 TGTCCATCTGTTTTGAGATCTAGA 57.143 37.500 0.00 0.00 29.72 2.43
1096 1108 0.901124 AGCCTCTGCAGTGAACTAGG 59.099 55.000 17.19 14.18 41.13 3.02
1224 1239 0.680921 AGGACAATCCGTTGGGCATG 60.681 55.000 0.00 0.00 42.75 4.06
1345 1360 4.267928 GGCGCAGATACAAGTAGTAGTTTG 59.732 45.833 10.83 0.00 35.85 2.93
1366 1381 7.861630 TCACTATAATTTTCTTAAGCATCGGC 58.138 34.615 0.00 0.00 41.61 5.54
1369 1384 9.061435 AGCCTCACTATAATTTTCTTAAGCATC 57.939 33.333 0.00 0.00 0.00 3.91
1439 1454 6.331369 ACCATAGGTTTTGAAGATGTTGTG 57.669 37.500 0.00 0.00 27.29 3.33
1509 1528 5.413833 AGGAGCATGCTAATCATAAATTCCG 59.586 40.000 22.74 0.00 31.62 4.30
1715 1737 0.548031 ATATGAGGGTGTGGGCACAG 59.452 55.000 0.00 0.00 46.95 3.66
1821 1851 8.897752 GCTTGACCATTAGAGAAGATTGTAAAT 58.102 33.333 0.00 0.00 0.00 1.40
2039 2096 2.025887 AGGACAGCCAATTCAGGTAAGG 60.026 50.000 0.00 0.00 36.29 2.69
2053 2110 2.115291 GCCAAATCCCGAGGACAGC 61.115 63.158 0.00 0.00 32.98 4.40
2141 2201 5.063180 TCTCACTGGCAAATAAAATGCAG 57.937 39.130 0.00 0.00 45.60 4.41
2264 2334 5.246883 AGGATGATAATCATGTCGATGGTCA 59.753 40.000 0.00 0.00 37.20 4.02
2338 2408 5.630121 ACATGTTGAATGGAGTTAGTTGGA 58.370 37.500 0.00 0.00 0.00 3.53
2411 2482 9.906660 TTACCTTTAGTAATTGAATTGCACAAG 57.093 29.630 8.64 8.83 35.98 3.16
2434 2506 5.347635 TGACTCGCATAAGTTGACACATTAC 59.652 40.000 0.00 0.00 0.00 1.89
2453 2525 9.615295 GCAGTAACTAGCTATAGTAATTGACTC 57.385 37.037 0.84 0.00 41.54 3.36


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

AutoCloner maintained by Alex Coulton.