Multiple sequence alignment - TraesCS6D01G208300

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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 TraesCS6D01G208300 chr6D 100.000 3581 0 0 1 3581 293812522 293808942 0.000000e+00 6613
1 TraesCS6D01G208300 chr6A 95.527 3376 118 15 221 3581 426952708 426956065 0.000000e+00 5367
2 TraesCS6D01G208300 chr6A 85.176 398 49 4 3191 3581 476832279 476832673 2.000000e-107 399
3 TraesCS6D01G208300 chr6B 96.841 2216 58 3 983 3197 458506894 458504690 0.000000e+00 3694
4 TraesCS6D01G208300 chr6B 93.139 481 30 3 1 479 458508467 458507988 0.000000e+00 702
5 TraesCS6D01G208300 chr6B 90.204 490 37 6 475 960 458507736 458507254 2.350000e-176 628
6 TraesCS6D01G208300 chr3A 86.835 395 42 4 3194 3581 51281723 51282114 1.970000e-117 433
7 TraesCS6D01G208300 chr5B 85.678 391 47 3 3198 3581 418523502 418523114 1.550000e-108 403
8 TraesCS6D01G208300 chr3B 85.974 385 45 6 3198 3581 747209294 747208918 1.550000e-108 403
9 TraesCS6D01G208300 chr3B 85.455 385 47 6 3198 3581 747152169 747151793 3.350000e-105 392
10 TraesCS6D01G208300 chr1B 85.316 395 49 3 3194 3581 226455998 226455606 2.000000e-107 399
11 TraesCS6D01G208300 chr2D 85.101 396 49 5 3195 3581 293662206 293662600 2.590000e-106 396
12 TraesCS6D01G208300 chr2D 85.128 390 49 4 3198 3581 403074034 403073648 1.210000e-104 390


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 TraesCS6D01G208300 chr6D 293808942 293812522 3580 True 6613.000000 6613 100.000000 1 3581 1 chr6D.!!$R1 3580
1 TraesCS6D01G208300 chr6A 426952708 426956065 3357 False 5367.000000 5367 95.527000 221 3581 1 chr6A.!!$F1 3360
2 TraesCS6D01G208300 chr6B 458504690 458508467 3777 True 1674.666667 3694 93.394667 1 3197 3 chr6B.!!$R1 3196

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
267 269 0.802494 CTGCACCCCACGTGAATAAC 59.198 55.0 19.30 3.94 46.20 1.89 F
1486 2093 0.260816 TGGGTACTCGAGGTATGGCT 59.739 55.0 18.41 0.00 32.56 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 2499 0.744414 ATCAAACATCCACCTCGCCG 60.744 55.0 0.00 0.0 0.00 6.46 R
3329 3944 1.241315 CCACCGGAAAACGCCATTCT 61.241 55.0 9.46 0.0 42.52 2.40 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
71 72 6.074729 CGCATATGCTTTTGTTAACATGGATG 60.075 38.462 24.56 7.69 39.32 3.51
83 84 1.027357 CATGGATGGCTTGCTACACC 58.973 55.000 0.00 0.00 0.00 4.16
119 120 5.321927 ACGGAATGGAAGGTTTTCTACATT 58.678 37.500 0.00 0.00 36.52 2.71
145 146 5.213675 CCACGTAGCAGATTTAGTAGTAGC 58.786 45.833 0.00 0.00 0.00 3.58
150 151 3.964031 AGCAGATTTAGTAGTAGCTGGCT 59.036 43.478 0.00 0.00 0.00 4.75
151 152 4.038642 AGCAGATTTAGTAGTAGCTGGCTC 59.961 45.833 0.00 0.00 0.00 4.70
154 155 2.431954 TTAGTAGTAGCTGGCTCGGT 57.568 50.000 0.00 0.00 0.00 4.69
267 269 0.802494 CTGCACCCCACGTGAATAAC 59.198 55.000 19.30 3.94 46.20 1.89
346 348 6.211584 ACGGTTATCAACTAGATGATGCCTAT 59.788 38.462 22.05 12.86 40.21 2.57
356 358 1.995376 TGATGCCTATCAGACGCCTA 58.005 50.000 0.00 0.00 38.37 3.93
628 890 5.181690 TGAGCATTTTCTAAAAACGCACT 57.818 34.783 6.07 0.00 34.61 4.40
629 891 5.587289 TGAGCATTTTCTAAAAACGCACTT 58.413 33.333 6.07 0.00 34.61 3.16
630 892 6.730175 TGAGCATTTTCTAAAAACGCACTTA 58.270 32.000 6.07 0.00 34.61 2.24
631 893 7.197017 TGAGCATTTTCTAAAAACGCACTTAA 58.803 30.769 6.07 0.00 34.61 1.85
632 894 7.166804 TGAGCATTTTCTAAAAACGCACTTAAC 59.833 33.333 6.07 0.00 34.61 2.01
633 895 6.975772 AGCATTTTCTAAAAACGCACTTAACA 59.024 30.769 6.07 0.00 34.61 2.41
634 896 7.651704 AGCATTTTCTAAAAACGCACTTAACAT 59.348 29.630 6.07 0.00 34.61 2.71
635 897 8.272866 GCATTTTCTAAAAACGCACTTAACATT 58.727 29.630 0.00 0.00 33.27 2.71
768 1038 4.460263 AGCTCCATACAAAACAACAGTCA 58.540 39.130 0.00 0.00 0.00 3.41
788 1058 5.861787 AGTCAGTTTTGTTTGGAGAAAAACG 59.138 36.000 0.00 0.00 44.59 3.60
823 1093 8.669394 AAAACTAAAGAGACAGAAAAACGTTG 57.331 30.769 0.00 0.00 0.00 4.10
889 1159 1.743623 CGCCTGTTTGACGCCCATA 60.744 57.895 0.00 0.00 0.00 2.74
916 1186 2.306341 TACAGGAGGTCTCGTCGTAG 57.694 55.000 0.00 0.00 0.00 3.51
960 1230 3.373748 TGTAAAACTCACACACAGCACAG 59.626 43.478 0.00 0.00 0.00 3.66
964 1234 1.217585 CTCACACACAGCACAGACCG 61.218 60.000 0.00 0.00 0.00 4.79
965 1235 1.227234 CACACACAGCACAGACCGA 60.227 57.895 0.00 0.00 0.00 4.69
1486 2093 0.260816 TGGGTACTCGAGGTATGGCT 59.739 55.000 18.41 0.00 32.56 4.75
1723 2330 1.290134 GATGGTGGAAGAGGGGTTCT 58.710 55.000 0.00 0.00 37.93 3.01
1750 2357 0.465460 TGGGACCACAGTTGCTTGTC 60.465 55.000 0.00 0.00 0.00 3.18
1791 2398 2.094675 CTTGGGATGCTGAAAATCGGT 58.905 47.619 0.00 0.00 0.00 4.69
1892 2499 0.603065 AAATGCGGGACTTTGAAGGC 59.397 50.000 0.00 0.00 0.00 4.35
2031 2638 1.279271 AGGGACTCAGGAATTGAACCG 59.721 52.381 0.00 0.00 34.81 4.44
2160 2767 3.252701 CAGAGATTGAGCATTATGGGTGC 59.747 47.826 0.00 0.00 42.81 5.01
2573 3180 1.188863 GCCTCAATGGAAATGTGCCT 58.811 50.000 0.00 0.00 38.35 4.75
2668 3275 5.193099 AGCCTAAATAGAAGAAAAGCCCA 57.807 39.130 0.00 0.00 0.00 5.36
2850 3457 2.766263 TCCATGCCAGAGGTAGTACTTG 59.234 50.000 0.00 0.00 0.00 3.16
2907 3515 3.244345 TGCGTTACTATTTCATAGCGCAC 59.756 43.478 11.47 0.00 42.55 5.34
3022 3630 6.489127 TTGGTGTCGGTTTAATAATCAGTG 57.511 37.500 0.00 0.00 0.00 3.66
3090 3698 3.627577 TCTTTTGTCTTCACTGCTGTTCC 59.372 43.478 0.00 0.00 0.00 3.62
3191 3799 2.094675 TGGTGGAAGGTAGCGTACTAC 58.905 52.381 0.00 0.00 46.85 2.73
3225 3833 4.616953 TGAAAATGGAGCGAAAACTTTCC 58.383 39.130 0.00 0.00 33.68 3.13
3355 3970 1.519408 CGTTTTCCGGTGGAACAGAT 58.481 50.000 0.00 0.00 41.87 2.90
3371 3986 5.710099 GGAACAGATGTGGAAATGGAACTTA 59.290 40.000 0.00 0.00 0.00 2.24
3379 3994 5.300792 TGTGGAAATGGAACTTACTGTTTCC 59.699 40.000 11.62 11.62 39.30 3.13
3458 4078 2.851235 CCAAACAACACACAATGACACG 59.149 45.455 0.00 0.00 0.00 4.49
3490 4110 3.963129 TCGATCATTTAGGCCCAACTTT 58.037 40.909 0.00 0.00 0.00 2.66
3523 4143 7.226325 ACACACGTACTCAACTAGATCCTATAC 59.774 40.741 0.00 0.00 0.00 1.47
3548 4168 6.976349 CGCAATTGTCCAGTACTACTACAATA 59.024 38.462 20.95 4.92 36.76 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 3.577848 AGCAAGCCATCCATGTTAACAAA 59.422 39.130 13.23 1.73 0.00 2.83
71 72 1.235724 AGAAAACGGTGTAGCAAGCC 58.764 50.000 0.00 0.00 0.00 4.35
83 84 4.602995 TCCATTCCGTTCAAAAGAAAACG 58.397 39.130 0.93 0.93 45.83 3.60
119 120 4.703575 ACTACTAAATCTGCTACGTGGTCA 59.296 41.667 0.00 0.00 0.00 4.02
145 146 1.406065 ATCTCCATGGACCGAGCCAG 61.406 60.000 11.44 0.00 42.15 4.85
150 151 0.465705 GAAGCATCTCCATGGACCGA 59.534 55.000 11.44 8.40 0.00 4.69
151 152 0.178767 TGAAGCATCTCCATGGACCG 59.821 55.000 11.44 1.85 0.00 4.79
154 155 1.213678 CCCTTGAAGCATCTCCATGGA 59.786 52.381 15.27 15.27 0.00 3.41
248 250 0.802494 GTTATTCACGTGGGGTGCAG 59.198 55.000 17.00 0.00 46.56 4.41
267 269 2.635229 CGGGAATCAGACCGCTCAGG 62.635 65.000 0.00 0.00 43.96 3.86
346 348 3.306917 TGAACGAAAATAGGCGTCTGA 57.693 42.857 0.00 0.00 40.23 3.27
462 465 9.826574 AGTTCAGTGTGTACTAAAGAACAAATA 57.173 29.630 15.64 0.00 38.67 1.40
609 871 7.155858 TGTTAAGTGCGTTTTTAGAAAATGC 57.844 32.000 18.52 18.52 41.27 3.56
624 886 7.486551 TCACGGCATATTAAAAATGTTAAGTGC 59.513 33.333 7.25 7.25 32.97 4.40
768 1038 5.047590 AGTCCGTTTTTCTCCAAACAAAACT 60.048 36.000 0.00 0.00 37.97 2.66
808 1078 0.028902 GCGCCAACGTTTTTCTGTCT 59.971 50.000 0.00 0.00 42.83 3.41
848 1118 0.608640 CTACGCCTGAAAGTCTGGGT 59.391 55.000 3.69 3.06 36.17 4.51
889 1159 0.033011 AGACCTCCTGTATGACGCCT 60.033 55.000 0.00 0.00 0.00 5.52
916 1186 1.079503 GACAGGAGATGTGTTTCGCC 58.920 55.000 0.00 0.00 44.17 5.54
927 1197 4.404394 TGTGAGTTTTACACAGACAGGAGA 59.596 41.667 0.00 0.00 42.20 3.71
1035 1642 1.800713 GGAGAGAACGCCGACGAAC 60.801 63.158 0.00 0.00 43.93 3.95
1384 1991 1.689273 GATCGACCTAACCAGCTGGAT 59.311 52.381 39.19 29.77 38.94 3.41
1671 2278 1.528129 CCAGAGCCTCCAGAAACAAC 58.472 55.000 0.00 0.00 0.00 3.32
1723 2330 3.253061 TGTGGTCCCATTCGGCCA 61.253 61.111 2.24 0.00 36.00 5.36
1791 2398 3.135712 ACGCATAACCATGGATCACCTTA 59.864 43.478 21.47 5.67 37.04 2.69
1892 2499 0.744414 ATCAAACATCCACCTCGCCG 60.744 55.000 0.00 0.00 0.00 6.46
2017 2624 2.092968 CCTCATCCGGTTCAATTCCTGA 60.093 50.000 0.00 0.00 0.00 3.86
2031 2638 3.963129 TCCCACAAATGTAACCTCATCC 58.037 45.455 0.00 0.00 0.00 3.51
2402 3009 1.405526 GCATCAGCTTCCGTACCTTCA 60.406 52.381 0.00 0.00 37.91 3.02
2573 3180 8.725405 TGTTGCGTCTATAAGAAATTAATCCA 57.275 30.769 0.00 0.00 0.00 3.41
3040 3648 1.359848 CTACACGTGGGACTGAATGC 58.640 55.000 21.57 0.00 0.00 3.56
3090 3698 5.516696 ACACAGAACATCGATCTAATCAACG 59.483 40.000 0.00 0.00 0.00 4.10
3191 3799 5.066593 GCTCCATTTTCATCCCTAACTAGG 58.933 45.833 0.00 0.00 43.25 3.02
3329 3944 1.241315 CCACCGGAAAACGCCATTCT 61.241 55.000 9.46 0.00 42.52 2.40
3355 3970 5.300792 GGAAACAGTAAGTTCCATTTCCACA 59.699 40.000 8.35 0.00 42.98 4.17
3371 3986 4.553330 AGTCCATATTCACGGAAACAGT 57.447 40.909 0.00 0.00 31.67 3.55
3379 3994 6.898041 TGAAAACAGAAAGTCCATATTCACG 58.102 36.000 0.00 0.00 0.00 4.35
3458 4078 5.163874 GCCTAAATGATCGATTCTGCTCATC 60.164 44.000 0.00 0.00 0.00 2.92
3490 4110 8.496707 TCTAGTTGAGTACGTGTGTGATATTA 57.503 34.615 0.00 0.00 0.00 0.98
3523 4143 4.740268 TGTAGTAGTACTGGACAATTGCG 58.260 43.478 13.29 0.00 0.00 4.85
3548 4168 9.784531 ATGATTATGTTAGCAACTTAGCATAGT 57.215 29.630 0.00 0.00 36.85 2.12


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

AutoCloner maintained by Alex Coulton.