Multiple sequence alignment - TraesCS6A01G187300

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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 TraesCS6A01G187300 chr6A 100.000 3842 0 0 1 3842 223550796 223554637 0.000000e+00 7095.0
1 TraesCS6A01G187300 chr6D 94.859 2237 78 15 3 2221 163329163 163331380 0.000000e+00 3459.0
2 TraesCS6A01G187300 chr6D 95.012 1644 49 12 2214 3842 163332542 163334167 0.000000e+00 2551.0
3 TraesCS6A01G187300 chr6B 93.319 2350 115 22 559 2899 298827348 298825032 0.000000e+00 3432.0
4 TraesCS6A01G187300 chr6B 92.708 576 20 4 3 566 298828883 298828318 0.000000e+00 811.0
5 TraesCS6A01G187300 chr6B 100.000 38 0 0 3591 3628 93576942 93576905 1.910000e-08 71.3
6 TraesCS6A01G187300 chr6B 93.333 45 0 3 3595 3639 20322122 20322081 3.200000e-06 63.9
7 TraesCS6A01G187300 chr6B 90.000 50 2 3 3597 3643 676297544 676297593 1.150000e-05 62.1
8 TraesCS6A01G187300 chr7A 85.246 244 34 2 2637 2879 106926321 106926079 2.290000e-62 250.0
9 TraesCS6A01G187300 chr7A 89.796 49 3 2 3454 3502 567378788 567378742 1.150000e-05 62.1
10 TraesCS6A01G187300 chr4B 91.228 57 4 1 3454 3509 497553561 497553617 4.120000e-10 76.8
11 TraesCS6A01G187300 chr4B 100.000 34 0 0 3589 3622 615160735 615160768 3.200000e-06 63.9
12 TraesCS6A01G187300 chr4A 91.228 57 4 1 3454 3509 59483636 59483692 4.120000e-10 76.8
13 TraesCS6A01G187300 chrUn 97.368 38 1 0 3591 3628 19198768 19198805 8.910000e-07 65.8
14 TraesCS6A01G187300 chr7B 91.667 48 2 2 3454 3501 461473690 461473735 8.910000e-07 65.8
15 TraesCS6A01G187300 chr7D 91.489 47 3 1 3454 3500 445118558 445118603 3.200000e-06 63.9
16 TraesCS6A01G187300 chr3B 93.182 44 2 1 3589 3632 237334286 237334328 3.200000e-06 63.9
17 TraesCS6A01G187300 chr3D 97.222 36 0 1 3597 3632 372629455 372629489 4.150000e-05 60.2
18 TraesCS6A01G187300 chr1D 83.333 66 6 3 3456 3521 332898 332838 5.360000e-04 56.5
19 TraesCS6A01G187300 chr4D 100.000 29 0 0 3591 3619 305978309 305978337 2.000000e-03 54.7


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 TraesCS6A01G187300 chr6A 223550796 223554637 3841 False 7095.0 7095 100.0000 1 3842 1 chr6A.!!$F1 3841
1 TraesCS6A01G187300 chr6D 163329163 163334167 5004 False 3005.0 3459 94.9355 3 3842 2 chr6D.!!$F1 3839
2 TraesCS6A01G187300 chr6B 298825032 298828883 3851 True 2121.5 3432 93.0135 3 2899 2 chr6B.!!$R3 2896

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
626 1619 0.264657 AAGCAGGGAAACTTGGGGTT 59.735 50.000 0.00 0.0 38.01 4.11 F
1314 2311 2.106511 TCAGGTGGCTGCTCTTTTTACT 59.893 45.455 0.00 0.0 0.00 2.24 F
2170 3170 0.036010 TAGCTGCTTCAGGTTCAGGC 60.036 55.000 7.79 0.0 42.44 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 2659 0.252479 AGCATCTGCAGGAGACAAGG 59.748 55.000 15.13 0.0 45.16 3.61 R
2371 4540 1.208293 GGCAGGGAAGGTCTTACTGAG 59.792 57.143 14.85 0.0 32.62 3.35 R
3479 5662 0.553333 AAGGAGGCTTAATCCCTGGC 59.447 55.000 0.00 0.0 37.57 4.85 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
74 75 6.068010 TGACTACAATGGTTGGTCATCTTTT 58.932 36.000 5.08 0.00 35.31 2.27
75 76 6.016360 TGACTACAATGGTTGGTCATCTTTTG 60.016 38.462 5.08 0.00 35.31 2.44
76 77 4.605640 ACAATGGTTGGTCATCTTTTGG 57.394 40.909 0.00 0.00 34.12 3.28
303 307 3.529533 CAAGGCCATGAACAAAACAACA 58.470 40.909 5.01 0.00 0.00 3.33
397 402 2.225467 GATTACCCCAGCATCTTCAGC 58.775 52.381 0.00 0.00 0.00 4.26
479 491 1.110442 TTTGGCACTTTGTGACCTGG 58.890 50.000 0.76 0.00 41.60 4.45
551 567 2.484417 GCAGGATGATCGATGGTTCAGT 60.484 50.000 0.54 0.00 39.69 3.41
626 1619 0.264657 AAGCAGGGAAACTTGGGGTT 59.735 50.000 0.00 0.00 38.01 4.11
667 1660 2.364632 CATCGGTGGTTTCTTGGCATA 58.635 47.619 0.00 0.00 0.00 3.14
727 1720 6.092748 CCAATCGGTGGTTTTCTGAATTTAG 58.907 40.000 0.00 0.00 43.20 1.85
776 1769 7.785033 TGATGTAGTGTCATATGTCAACAGAT 58.215 34.615 4.15 0.38 0.00 2.90
836 1830 2.623416 CACTTCCCTGAAACCTCCAAAC 59.377 50.000 0.00 0.00 0.00 2.93
974 1971 6.365518 ACGAGCTTGTTAAGTTCTAGCTTTAC 59.634 38.462 0.00 0.00 42.04 2.01
1312 2309 2.371841 TCTCAGGTGGCTGCTCTTTTTA 59.628 45.455 0.00 0.00 0.00 1.52
1313 2310 2.485814 CTCAGGTGGCTGCTCTTTTTAC 59.514 50.000 0.00 0.00 0.00 2.01
1314 2311 2.106511 TCAGGTGGCTGCTCTTTTTACT 59.893 45.455 0.00 0.00 0.00 2.24
1315 2312 2.485814 CAGGTGGCTGCTCTTTTTACTC 59.514 50.000 0.00 0.00 0.00 2.59
1322 2321 3.003480 CTGCTCTTTTTACTCCCTTCCG 58.997 50.000 0.00 0.00 0.00 4.30
1356 2355 6.367374 TCTTCACCTCAAATGTACCATACA 57.633 37.500 0.00 0.00 43.80 2.29
1357 2356 6.170506 TCTTCACCTCAAATGTACCATACAC 58.829 40.000 0.00 0.00 42.23 2.90
1365 2364 5.177881 TCAAATGTACCATACACAACGTCAC 59.822 40.000 0.00 0.00 42.23 3.67
1370 2369 2.223876 ACCATACACAACGTCACGAGTT 60.224 45.455 2.91 0.00 0.00 3.01
1389 2388 6.367695 ACGAGTTTCGACAACAATATGAATGA 59.632 34.615 5.38 0.00 43.74 2.57
1395 2394 9.905171 TTTCGACAACAATATGAATGAATGAAA 57.095 25.926 0.00 0.00 0.00 2.69
1396 2395 8.894409 TCGACAACAATATGAATGAATGAAAC 57.106 30.769 0.00 0.00 0.00 2.78
1397 2396 8.729756 TCGACAACAATATGAATGAATGAAACT 58.270 29.630 0.00 0.00 0.00 2.66
1398 2397 9.345517 CGACAACAATATGAATGAATGAAACTT 57.654 29.630 0.00 0.00 0.00 2.66
1412 2411 8.301730 TGAATGAAACTTTTTGCAGATTGATC 57.698 30.769 0.00 0.00 0.00 2.92
1706 2705 5.105997 ACAGCATGGATTCAAAGCTTTACTC 60.106 40.000 12.25 8.62 43.62 2.59
1769 2768 8.391106 GTGTATGTTCTAGATCAATTCACCAAC 58.609 37.037 7.56 0.00 0.00 3.77
2026 3026 6.170506 TCCATGCAACGTTCTACTCTTTATT 58.829 36.000 0.00 0.00 0.00 1.40
2027 3027 6.653320 TCCATGCAACGTTCTACTCTTTATTT 59.347 34.615 0.00 0.00 0.00 1.40
2028 3028 6.742718 CCATGCAACGTTCTACTCTTTATTTG 59.257 38.462 0.00 0.00 0.00 2.32
2029 3029 6.854496 TGCAACGTTCTACTCTTTATTTGT 57.146 33.333 0.00 0.00 0.00 2.83
2030 3030 7.949903 TGCAACGTTCTACTCTTTATTTGTA 57.050 32.000 0.00 0.00 0.00 2.41
2170 3170 0.036010 TAGCTGCTTCAGGTTCAGGC 60.036 55.000 7.79 0.00 42.44 4.85
2217 3217 4.559862 ATCTCAAGACGAAGAACCCATT 57.440 40.909 0.00 0.00 0.00 3.16
2325 4494 4.533919 ATGATACTCCTGCTAGACATGC 57.466 45.455 0.00 0.00 0.00 4.06
2330 4499 0.107508 TCCTGCTAGACATGCTTGGC 60.108 55.000 4.44 0.08 0.00 4.52
2342 4511 1.963172 TGCTTGGCTATGCTCATCAG 58.037 50.000 9.34 0.00 0.00 2.90
2362 4531 4.003648 CAGTAACCTGGCTACCTTTCTTG 58.996 47.826 3.69 0.00 34.90 3.02
2364 4533 1.742308 ACCTGGCTACCTTTCTTGGA 58.258 50.000 0.00 0.00 0.00 3.53
2371 4540 5.007682 TGGCTACCTTTCTTGGATTGTAAC 58.992 41.667 0.00 0.00 0.00 2.50
2373 4542 5.354513 GGCTACCTTTCTTGGATTGTAACTC 59.645 44.000 0.00 0.00 0.00 3.01
2381 4550 8.603242 TTTCTTGGATTGTAACTCAGTAAGAC 57.397 34.615 0.00 0.00 0.00 3.01
2632 4803 9.057089 TCTTTTTCAACAGTCTAGGATCTTTTC 57.943 33.333 0.00 0.00 0.00 2.29
2849 5021 3.947868 ACATGACCTTCTGATGTTCAGG 58.052 45.455 0.00 2.14 44.39 3.86
2884 5056 2.978278 AGCTTAGGGATGATCCAGAAGG 59.022 50.000 19.92 5.94 38.64 3.46
2995 5167 5.008331 CAGGTTACAGAGGATAGCGGTATA 58.992 45.833 7.19 0.00 0.00 1.47
2996 5168 5.475909 CAGGTTACAGAGGATAGCGGTATAA 59.524 44.000 7.19 0.00 0.00 0.98
2999 5171 7.338957 AGGTTACAGAGGATAGCGGTATAATAC 59.661 40.741 7.19 0.00 0.00 1.89
3001 5173 9.388506 GTTACAGAGGATAGCGGTATAATACTA 57.611 37.037 7.19 0.00 0.00 1.82
3004 5176 7.502895 ACAGAGGATAGCGGTATAATACTATGG 59.497 40.741 7.19 1.00 0.00 2.74
3149 5329 7.700656 GTGAGTTAAGTTCAGAGCTAGAATCTC 59.299 40.741 4.58 8.12 0.00 2.75
3212 5392 4.326826 ACTTGTCCATCACCATACTGTTG 58.673 43.478 0.00 0.00 0.00 3.33
3217 5397 7.610580 TGTCCATCACCATACTGTTGATATA 57.389 36.000 0.00 0.00 0.00 0.86
3270 5450 8.408043 ACAAATCAAATTTACTGAGACATCCA 57.592 30.769 0.00 0.00 0.00 3.41
3300 5480 1.406539 CTGGTATTCTGCCCAACATGC 59.593 52.381 0.00 0.00 0.00 4.06
3304 5484 0.244450 ATTCTGCCCAACATGCAACG 59.756 50.000 0.00 0.00 38.46 4.10
3336 5516 3.769844 ACCCTAACTGTCACATGACCTAG 59.230 47.826 9.48 3.99 44.15 3.02
3395 5575 3.672295 GAAGCAGGGCCGTCCTCAG 62.672 68.421 0.00 0.00 46.12 3.35
3400 5580 0.035056 CAGGGCCGTCCTCAGAAATT 60.035 55.000 0.00 0.00 46.12 1.82
3401 5581 0.035056 AGGGCCGTCCTCAGAAATTG 60.035 55.000 0.00 0.00 44.06 2.32
3491 5674 0.548031 TGCAGAGGCCAGGGATTAAG 59.452 55.000 5.01 0.00 40.13 1.85
3508 5691 2.375014 AAGCCTCCTTTTCGGGAAAA 57.625 45.000 6.44 6.44 37.90 2.29
3682 5865 1.679139 CGGCATCCTTCTGGCATTTA 58.321 50.000 0.00 0.00 41.51 1.40
3752 5935 3.967987 AGAGGAAATAATACCAGGCGAGT 59.032 43.478 0.00 0.00 0.00 4.18
3782 5967 6.248433 GGATATCCATGAAAGAATAGGGCAA 58.752 40.000 17.34 0.00 35.64 4.52
3824 6009 2.768527 TCTAAGAGCAACTCCATCAGGG 59.231 50.000 0.00 0.00 34.83 4.45
3827 6012 2.440980 GCAACTCCATCAGGGCCC 60.441 66.667 16.46 16.46 36.21 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 104 9.845305 GATTCTACGTACATACTGCAAATAAAC 57.155 33.333 0.00 0.00 0.00 2.01
107 110 5.585820 TGGATTCTACGTACATACTGCAA 57.414 39.130 0.00 0.00 0.00 4.08
115 118 4.682787 CTGATGCTTGGATTCTACGTACA 58.317 43.478 0.00 0.00 0.00 2.90
195 198 9.367444 GGTGTATCGGATTATTACATAGGAAAG 57.633 37.037 0.00 0.00 0.00 2.62
303 307 4.062293 TGTGTGCTATAAAACAACTCGCT 58.938 39.130 0.00 0.00 0.00 4.93
397 402 4.669318 ACGACTGGTTACGTATTCATGAG 58.331 43.478 0.00 0.00 40.92 2.90
479 491 7.096477 GCAGTGATGGATTATTTCGCAATTTAC 60.096 37.037 0.00 0.00 0.00 2.01
538 554 7.921786 TTTTAATCTGAACTGAACCATCGAT 57.078 32.000 0.00 0.00 0.00 3.59
626 1619 1.478654 GGTTGGAAGCCTGGAACTTGA 60.479 52.381 0.00 0.00 0.00 3.02
667 1660 2.818751 TGGAACACAAGTTTCCCTGT 57.181 45.000 0.00 0.00 38.30 4.00
748 1741 7.386059 TGTTGACATATGACACTACATCAGTT 58.614 34.615 10.38 0.00 34.26 3.16
793 1786 2.305927 TCCCTGAAACTTCCATCCAGAC 59.694 50.000 0.00 0.00 0.00 3.51
794 1787 2.305927 GTCCCTGAAACTTCCATCCAGA 59.694 50.000 0.00 0.00 0.00 3.86
913 1907 2.225467 GGATGCACAGAAATAGGAGGC 58.775 52.381 0.00 0.00 0.00 4.70
921 1915 4.933505 TGAACAAATGGATGCACAGAAA 57.066 36.364 0.00 0.00 0.00 2.52
974 1971 9.706691 TTTCTCTGGTACTTATTCTACAACAAG 57.293 33.333 0.00 0.00 0.00 3.16
1237 2234 3.181458 GGTACGGCTCAATCTTCCCAATA 60.181 47.826 0.00 0.00 0.00 1.90
1356 2355 1.194495 GTCGAAACTCGTGACGTTGT 58.806 50.000 4.40 2.58 41.35 3.32
1357 2356 1.193644 TGTCGAAACTCGTGACGTTG 58.806 50.000 4.40 1.89 41.35 4.10
1365 2364 6.761117 TCATTCATATTGTTGTCGAAACTCG 58.239 36.000 10.41 0.00 42.10 4.18
1370 2369 9.340695 GTTTCATTCATTCATATTGTTGTCGAA 57.659 29.630 0.00 0.00 0.00 3.71
1389 2388 7.147312 TCGATCAATCTGCAAAAAGTTTCATT 58.853 30.769 0.00 0.00 0.00 2.57
1395 2394 5.947228 TCTTCGATCAATCTGCAAAAAGT 57.053 34.783 0.00 0.00 0.00 2.66
1396 2395 5.229469 GCATCTTCGATCAATCTGCAAAAAG 59.771 40.000 0.00 0.00 0.00 2.27
1397 2396 5.097529 GCATCTTCGATCAATCTGCAAAAA 58.902 37.500 0.00 0.00 0.00 1.94
1398 2397 4.156373 TGCATCTTCGATCAATCTGCAAAA 59.844 37.500 4.94 0.00 35.42 2.44
1412 2411 2.548875 CCTTTCTCCTCTGCATCTTCG 58.451 52.381 0.00 0.00 0.00 3.79
1574 2573 1.134521 TCTACGCCAAGGAATCGCATT 60.135 47.619 0.00 0.00 0.00 3.56
1582 2581 1.927487 TACCACTTCTACGCCAAGGA 58.073 50.000 0.00 0.00 0.00 3.36
1660 2659 0.252479 AGCATCTGCAGGAGACAAGG 59.748 55.000 15.13 0.00 45.16 3.61
1706 2705 6.392625 TTCTTCATCTGTTCTACCCTATCG 57.607 41.667 0.00 0.00 0.00 2.92
1769 2768 2.492773 GGCATCGGGATTTGCAGGG 61.493 63.158 0.00 0.00 40.66 4.45
2065 3065 3.460648 GCATTAGTGCCGAGGTTCT 57.539 52.632 0.00 0.00 45.76 3.01
2217 3217 9.347934 CTGGTTCAACGCATATTAATTTTACAA 57.652 29.630 0.00 0.00 0.00 2.41
2310 4479 1.950828 CCAAGCATGTCTAGCAGGAG 58.049 55.000 0.00 0.00 33.07 3.69
2315 4484 1.534595 GCATAGCCAAGCATGTCTAGC 59.465 52.381 0.00 0.00 0.00 3.42
2325 4494 3.812053 GGTTACTGATGAGCATAGCCAAG 59.188 47.826 0.00 0.00 0.00 3.61
2342 4511 3.008704 TCCAAGAAAGGTAGCCAGGTTAC 59.991 47.826 4.86 4.86 0.00 2.50
2362 4531 6.107343 GGAAGGTCTTACTGAGTTACAATCC 58.893 44.000 0.00 0.00 0.00 3.01
2364 4533 5.785940 AGGGAAGGTCTTACTGAGTTACAAT 59.214 40.000 0.00 0.00 0.00 2.71
2371 4540 1.208293 GGCAGGGAAGGTCTTACTGAG 59.792 57.143 14.85 0.00 32.62 3.35
2373 4542 1.280457 AGGCAGGGAAGGTCTTACTG 58.720 55.000 9.26 9.26 33.46 2.74
2381 4550 2.053244 ACAGATCATAGGCAGGGAAGG 58.947 52.381 0.00 0.00 0.00 3.46
2632 4803 3.937079 TCACTGTAGCATCTGCAAATGAG 59.063 43.478 3.61 0.00 45.16 2.90
2849 5021 1.929836 CTAAGCTGTCATTGCCTCGAC 59.070 52.381 0.00 0.00 0.00 4.20
2941 5113 8.765219 CATATGGTTTGTACTTATGACACTAGC 58.235 37.037 0.00 0.00 0.00 3.42
2995 5167 6.831664 AGGTGATTCCTCAACCATAGTATT 57.168 37.500 0.00 0.00 44.42 1.89
3044 5223 2.170607 GGCTAGTACAAATGAGGGCTCA 59.829 50.000 0.00 0.00 44.59 4.26
3149 5329 7.979444 AGTAATTAATACCGAATGGACCATG 57.021 36.000 8.02 0.00 39.21 3.66
3300 5480 2.048503 GGGTCACCCTCGTCGTTG 60.049 66.667 5.22 0.00 41.34 4.10
3327 5507 5.858381 ACTATGTAACCATGCTAGGTCATG 58.142 41.667 10.50 3.95 42.25 3.07
3329 5509 5.163343 GGAACTATGTAACCATGCTAGGTCA 60.163 44.000 1.07 0.00 42.25 4.02
3336 5516 5.163652 GGAAGTTGGAACTATGTAACCATGC 60.164 44.000 0.00 0.00 38.57 4.06
3395 5575 3.460868 CGCAGGGCCCCCAATTTC 61.461 66.667 21.43 0.00 38.92 2.17
3478 5661 1.151679 GGAGGCTTAATCCCTGGCC 59.848 63.158 0.00 0.00 44.38 5.36
3479 5662 0.553333 AAGGAGGCTTAATCCCTGGC 59.447 55.000 0.00 0.00 37.57 4.85
3480 5663 3.291584 GAAAAGGAGGCTTAATCCCTGG 58.708 50.000 0.00 0.00 37.57 4.45
3481 5664 2.945668 CGAAAAGGAGGCTTAATCCCTG 59.054 50.000 0.00 0.00 37.57 4.45
3482 5665 2.092375 CCGAAAAGGAGGCTTAATCCCT 60.092 50.000 0.00 0.00 45.00 4.20
3483 5666 2.298610 CCGAAAAGGAGGCTTAATCCC 58.701 52.381 0.00 0.00 45.00 3.85
3491 5674 2.724977 CTTTTTCCCGAAAAGGAGGC 57.275 50.000 6.25 0.00 46.78 4.70
3580 5763 6.842807 AGAGGGAGTAATTATTAAGGGTTCGA 59.157 38.462 0.00 0.00 0.00 3.71
3622 5805 6.742559 AGTTTAGTACTCCCTCTGAAAACA 57.257 37.500 0.00 0.00 28.23 2.83
3682 5865 6.838382 ACTAGGTGGAAGAAACTGTGTAATT 58.162 36.000 0.00 0.00 0.00 1.40
3752 5935 4.929819 TCTTTCATGGATATCCGTCGAA 57.070 40.909 13.91 16.34 39.43 3.71
3798 5983 5.911752 TGATGGAGTTGCTCTTAGAGAATC 58.088 41.667 14.14 1.45 0.00 2.52
3824 6009 2.362503 GGGGCTGTGTTTAGGGGC 60.363 66.667 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.