Multiple sequence alignment - TraesCS3A01G212800

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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 TraesCS3A01G212800 chr3A 100.000 2937 0 0 1 2937 384194407 384197343 0.000000e+00 5424
1 TraesCS3A01G212800 chr3D 96.721 2013 53 11 930 2936 291225798 291227803 0.000000e+00 3339
2 TraesCS3A01G212800 chr3D 92.252 413 20 6 1 407 291224375 291224781 2.540000e-160 575
3 TraesCS3A01G212800 chr3D 87.767 515 13 13 457 928 291225151 291225658 9.200000e-155 556
4 TraesCS3A01G212800 chr3B 96.650 1642 46 7 930 2566 384311369 384313006 0.000000e+00 2719
5 TraesCS3A01G212800 chr3B 87.873 973 52 28 1 928 384310266 384311217 0.000000e+00 1083
6 TraesCS3A01G212800 chr3B 94.832 387 20 0 2550 2936 384314301 384314687 3.240000e-169 604


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 TraesCS3A01G212800 chr3A 384194407 384197343 2936 False 5424.000000 5424 100.000000 1 2937 1 chr3A.!!$F1 2936
1 TraesCS3A01G212800 chr3D 291224375 291227803 3428 False 1490.000000 3339 92.246667 1 2936 3 chr3D.!!$F1 2935
2 TraesCS3A01G212800 chr3B 384310266 384314687 4421 False 1468.666667 2719 93.118333 1 2936 3 chr3B.!!$F1 2935

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
63 64 0.197661 AGAGAAAGGGGGTTGGGGTA 59.802 55.000 0.00 0.0 0.00 3.69 F
440 453 0.669619 TTCCGCGTTTCTTTTTCCCC 59.330 50.000 4.92 0.0 0.00 4.81 F
1194 1730 1.909302 ACCAAATCACCCAGATCGTCT 59.091 47.619 0.00 0.0 35.39 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1279 1815 1.069978 GGGTGTGGGGTTGTTTTCATG 59.930 52.381 0.00 0.0 0.0 3.07 R
1892 2431 1.271871 ACGATTGTCAAAGGATGGGCA 60.272 47.619 0.00 0.0 0.0 5.36 R
2776 4629 0.035439 ATCATGGTGTGGTTCCGGAC 60.035 55.000 1.83 0.0 0.0 4.79 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
26 27 2.958355 CAGAGGAGAGAGCCCTAGAAAG 59.042 54.545 0.00 0.00 33.36 2.62
49 50 7.496346 AGAGAAAGTAGAGAGAGAGAGAGAA 57.504 40.000 0.00 0.00 0.00 2.87
52 53 7.112779 AGAAAGTAGAGAGAGAGAGAGAAAGG 58.887 42.308 0.00 0.00 0.00 3.11
53 54 5.373812 AGTAGAGAGAGAGAGAGAAAGGG 57.626 47.826 0.00 0.00 0.00 3.95
54 55 3.669939 AGAGAGAGAGAGAGAAAGGGG 57.330 52.381 0.00 0.00 0.00 4.79
56 57 2.007636 AGAGAGAGAGAGAAAGGGGGT 58.992 52.381 0.00 0.00 0.00 4.95
57 58 2.385417 AGAGAGAGAGAGAAAGGGGGTT 59.615 50.000 0.00 0.00 0.00 4.11
61 62 0.846870 AGAGAGAAAGGGGGTTGGGG 60.847 60.000 0.00 0.00 0.00 4.96
63 64 0.197661 AGAGAAAGGGGGTTGGGGTA 59.802 55.000 0.00 0.00 0.00 3.69
116 121 7.898014 AAAGTTCTCACATAAACCTTTCCTT 57.102 32.000 0.00 0.00 0.00 3.36
254 267 1.007359 GAGAGGAGACCAAGGTAGGGT 59.993 57.143 0.00 0.00 42.61 4.34
316 329 2.116533 GCGTTGGGGATTTACCGGG 61.117 63.158 6.32 0.00 40.11 5.73
357 370 2.991190 GGAACAGATTAGAACGCGTTCA 59.009 45.455 42.89 29.36 41.84 3.18
420 433 1.066587 CCTCTCCGATCCTTCGTGC 59.933 63.158 0.00 0.00 43.97 5.34
431 444 1.154654 CTTCGTGCTTCCGCGTTTC 60.155 57.895 4.92 0.00 44.80 2.78
440 453 0.669619 TTCCGCGTTTCTTTTTCCCC 59.330 50.000 4.92 0.00 0.00 4.81
446 459 2.801699 GCGTTTCTTTTTCCCCCACTTG 60.802 50.000 0.00 0.00 0.00 3.16
503 843 2.498481 TCCGCTCCTTTTTCGAGGATAA 59.502 45.455 0.00 0.00 44.56 1.75
504 844 3.055675 TCCGCTCCTTTTTCGAGGATAAA 60.056 43.478 0.00 0.00 44.56 1.40
505 845 3.877508 CCGCTCCTTTTTCGAGGATAAAT 59.122 43.478 0.00 0.00 44.56 1.40
506 846 4.024809 CCGCTCCTTTTTCGAGGATAAATC 60.025 45.833 0.00 0.00 44.56 2.17
783 1158 4.705023 GCTTTAATCCAAGCCAAGGAACTA 59.295 41.667 0.00 0.00 43.03 2.24
791 1166 4.339247 CCAAGCCAAGGAACTACAATATGG 59.661 45.833 0.00 0.00 38.49 2.74
814 1189 4.178956 ACCCTTTTAGTTTGGCTCTTGA 57.821 40.909 0.00 0.00 0.00 3.02
876 1251 4.058124 TCGTGGAGTGATTCTTCTGTTTG 58.942 43.478 0.00 0.00 0.00 2.93
877 1252 3.364366 CGTGGAGTGATTCTTCTGTTTGC 60.364 47.826 0.00 0.00 0.00 3.68
878 1253 3.817647 GTGGAGTGATTCTTCTGTTTGCT 59.182 43.478 0.00 0.00 0.00 3.91
949 1485 8.888579 TTCTTCTATTAGATTAGAAAAGGCCG 57.111 34.615 0.00 0.00 37.66 6.13
950 1486 8.246430 TCTTCTATTAGATTAGAAAAGGCCGA 57.754 34.615 0.00 0.00 37.66 5.54
951 1487 8.701895 TCTTCTATTAGATTAGAAAAGGCCGAA 58.298 33.333 0.00 0.00 37.66 4.30
952 1488 8.658499 TTCTATTAGATTAGAAAAGGCCGAAC 57.342 34.615 0.00 0.00 35.73 3.95
953 1489 8.019656 TCTATTAGATTAGAAAAGGCCGAACT 57.980 34.615 0.00 0.00 0.00 3.01
955 1491 6.737254 TTAGATTAGAAAAGGCCGAACTTG 57.263 37.500 0.00 0.00 0.00 3.16
956 1492 4.652822 AGATTAGAAAAGGCCGAACTTGT 58.347 39.130 0.00 0.00 0.00 3.16
957 1493 5.801380 AGATTAGAAAAGGCCGAACTTGTA 58.199 37.500 0.00 0.00 0.00 2.41
966 1502 4.394729 AGGCCGAACTTGTAAAATCAAGA 58.605 39.130 12.38 0.00 45.11 3.02
1072 1608 2.831565 AGATGGGCTTCTTCAGAGTCT 58.168 47.619 0.00 0.00 0.00 3.24
1140 1676 4.681978 GTCCGCAGCCCAACGTCT 62.682 66.667 0.00 0.00 0.00 4.18
1194 1730 1.909302 ACCAAATCACCCAGATCGTCT 59.091 47.619 0.00 0.00 35.39 4.18
1279 1815 3.518634 GACTGGTGGATTCTCTCAGTC 57.481 52.381 13.53 13.53 44.58 3.51
1690 2229 9.869667 ACATCTATATCTACCAGTAAGTGTTCT 57.130 33.333 0.00 0.00 0.00 3.01
1764 2303 6.105333 AGATCTACTGCTGTTCTGATTGTTC 58.895 40.000 0.09 0.00 0.00 3.18
1765 2304 4.237724 TCTACTGCTGTTCTGATTGTTCG 58.762 43.478 0.09 0.00 0.00 3.95
1771 2310 6.017109 ACTGCTGTTCTGATTGTTCGTTAATT 60.017 34.615 0.00 0.00 0.00 1.40
1772 2311 7.172532 ACTGCTGTTCTGATTGTTCGTTAATTA 59.827 33.333 0.00 0.00 0.00 1.40
1892 2431 0.042431 AGGTCACTCTGATCCCAGCT 59.958 55.000 0.00 0.00 40.20 4.24
1937 2476 4.616835 GCATTTTCCAACTGATCCAGTGAC 60.617 45.833 0.00 0.00 44.62 3.67
2038 2578 3.916761 TCATGCTGATCAAGTTTTTGCC 58.083 40.909 0.00 0.00 34.21 4.52
2151 2692 2.611473 CCTGAACGATGACTGTGCTTCT 60.611 50.000 0.00 0.00 0.00 2.85
2203 2744 1.009675 GTGCGTGTGTTTGCCTGAG 60.010 57.895 0.00 0.00 0.00 3.35
2206 2747 2.908073 CGTGTGTTTGCCTGAGCCC 61.908 63.158 0.00 0.00 38.69 5.19
2476 3017 3.911989 GATGCTGCCATCAGTTTCG 57.088 52.632 0.00 0.00 45.75 3.46
2479 3021 3.056313 GCTGCCATCAGTTTCGGGC 62.056 63.158 0.00 0.00 46.58 6.13
2590 4443 3.131396 GTGTCTAATACTGCGAATGGGG 58.869 50.000 0.00 0.00 0.00 4.96
2709 4562 1.070776 GTTCCGCGTGTTTGAGAGTTC 60.071 52.381 4.92 0.00 0.00 3.01
2776 4629 2.093973 ACAAAGCTCGTCCCTGATACAG 60.094 50.000 0.00 0.00 0.00 2.74
2792 4645 1.374947 CAGTCCGGAACCACACCAT 59.625 57.895 5.23 0.00 0.00 3.55
2819 4672 9.155975 GATAAATACGATTTACATCCTGCTCAT 57.844 33.333 0.00 0.00 0.00 2.90
2872 4725 4.068599 TCAAATCACGCCTGACATGTAAA 58.931 39.130 0.00 0.00 0.00 2.01
2925 4778 2.482374 GATGCCAGCGACAACAGC 59.518 61.111 0.00 0.00 0.00 4.40
2936 4789 0.178990 GACAACAGCCCCCACTCTTT 60.179 55.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.709886 ACTTTCTCTTTCTAGGGCTCTCTC 59.290 45.833 0.00 0.00 0.00 3.20
26 27 7.281100 CCTTTCTCTCTCTCTCTCTACTTTCTC 59.719 44.444 0.00 0.00 0.00 2.87
49 50 1.774735 TACCCTACCCCAACCCCCTT 61.775 60.000 0.00 0.00 0.00 3.95
52 53 1.695239 CCTACCCTACCCCAACCCC 60.695 68.421 0.00 0.00 0.00 4.95
53 54 1.695239 CCCTACCCTACCCCAACCC 60.695 68.421 0.00 0.00 0.00 4.11
54 55 0.984961 GACCCTACCCTACCCCAACC 60.985 65.000 0.00 0.00 0.00 3.77
56 57 1.397413 GGACCCTACCCTACCCCAA 59.603 63.158 0.00 0.00 0.00 4.12
57 58 1.462575 TTGGACCCTACCCTACCCCA 61.463 60.000 0.00 0.00 0.00 4.96
61 62 2.263545 AGTTGTTGGACCCTACCCTAC 58.736 52.381 0.00 0.00 0.00 3.18
63 64 2.158050 AGTAGTTGTTGGACCCTACCCT 60.158 50.000 2.30 0.00 32.12 4.34
116 121 1.615814 CGGAGAGGGGAGAGAAGGA 59.384 63.158 0.00 0.00 0.00 3.36
179 187 1.720694 GGAGGAAGAGCGGAGTCGAG 61.721 65.000 0.00 0.00 39.00 4.04
332 345 1.287425 CGTTCTAATCTGTTCCGCCC 58.713 55.000 0.00 0.00 0.00 6.13
335 348 1.625616 ACGCGTTCTAATCTGTTCCG 58.374 50.000 5.58 0.00 0.00 4.30
357 370 0.466124 GCAGATTAGAAGCCCCTCGT 59.534 55.000 0.00 0.00 0.00 4.18
367 380 2.489255 CCGAGGACCTAGGCAGATTAGA 60.489 54.545 9.30 0.00 0.00 2.10
420 433 1.335597 GGGGAAAAAGAAACGCGGAAG 60.336 52.381 12.47 0.00 0.00 3.46
470 810 0.179026 GGAGCGGAGATTAAACCCCC 60.179 60.000 0.00 0.00 0.00 5.40
503 843 5.738909 ACCACGAGAAGAGATTGATTGATT 58.261 37.500 0.00 0.00 0.00 2.57
504 844 5.350504 ACCACGAGAAGAGATTGATTGAT 57.649 39.130 0.00 0.00 0.00 2.57
505 845 4.808414 ACCACGAGAAGAGATTGATTGA 57.192 40.909 0.00 0.00 0.00 2.57
506 846 5.869753 AAACCACGAGAAGAGATTGATTG 57.130 39.130 0.00 0.00 0.00 2.67
598 941 3.175240 CGGCTGCGTCGTGAAGAG 61.175 66.667 0.00 0.00 0.00 2.85
783 1158 6.295632 GCCAAACTAAAAGGGTTCCATATTGT 60.296 38.462 0.00 0.00 0.00 2.71
791 1166 4.583073 TCAAGAGCCAAACTAAAAGGGTTC 59.417 41.667 0.00 0.00 32.43 3.62
928 1314 8.019656 AGTTCGGCCTTTTCTAATCTAATAGA 57.980 34.615 0.00 0.00 0.00 1.98
940 1476 5.525199 TGATTTTACAAGTTCGGCCTTTTC 58.475 37.500 0.00 0.00 0.00 2.29
944 1480 4.394729 TCTTGATTTTACAAGTTCGGCCT 58.605 39.130 0.00 0.00 44.96 5.19
945 1481 4.759516 TCTTGATTTTACAAGTTCGGCC 57.240 40.909 0.00 0.00 44.96 6.13
946 1482 8.181573 TCAATATCTTGATTTTACAAGTTCGGC 58.818 33.333 0.00 0.00 44.96 5.54
947 1483 9.490663 GTCAATATCTTGATTTTACAAGTTCGG 57.509 33.333 0.00 0.00 43.08 4.30
951 1487 8.739972 GGGTGTCAATATCTTGATTTTACAAGT 58.260 33.333 0.00 0.00 43.08 3.16
952 1488 8.739039 TGGGTGTCAATATCTTGATTTTACAAG 58.261 33.333 0.00 0.00 43.08 3.16
953 1489 8.642935 TGGGTGTCAATATCTTGATTTTACAA 57.357 30.769 0.00 0.00 43.08 2.41
955 1491 9.921637 TTTTGGGTGTCAATATCTTGATTTTAC 57.078 29.630 0.00 0.00 43.08 2.01
957 1493 8.096414 CCTTTTGGGTGTCAATATCTTGATTTT 58.904 33.333 0.00 0.00 38.62 1.82
966 1502 6.172630 GCAATTTCCTTTTGGGTGTCAATAT 58.827 36.000 0.00 0.00 40.87 1.28
1072 1608 4.993584 GCTCAGTTTGACAAGAAGATCAGA 59.006 41.667 0.00 0.00 0.00 3.27
1137 1673 6.744339 TGAACAATTTCAGGTCTAAGGGAGAC 60.744 42.308 0.00 0.00 43.98 3.36
1140 1676 5.163141 TGTGAACAATTTCAGGTCTAAGGGA 60.163 40.000 0.00 0.00 42.60 4.20
1194 1730 3.439540 GCGCCGGCATCAAGGAAA 61.440 61.111 28.98 0.00 39.62 3.13
1279 1815 1.069978 GGGTGTGGGGTTGTTTTCATG 59.930 52.381 0.00 0.00 0.00 3.07
1690 2229 6.216801 ACGATGGTTGCATCTAGTTTACTA 57.783 37.500 0.00 0.00 0.00 1.82
1746 2285 2.838736 ACGAACAATCAGAACAGCAGT 58.161 42.857 0.00 0.00 0.00 4.40
1748 2287 5.940192 ATTAACGAACAATCAGAACAGCA 57.060 34.783 0.00 0.00 0.00 4.41
1772 2311 8.830580 CCTACGATTGAAAGACATGATACAAAT 58.169 33.333 0.00 0.00 0.00 2.32
1892 2431 1.271871 ACGATTGTCAAAGGATGGGCA 60.272 47.619 0.00 0.00 0.00 5.36
1937 2476 1.394917 GTGTTTACTGATGCTCGCTGG 59.605 52.381 0.00 0.00 0.00 4.85
2038 2578 2.413765 CCGCAGCAGACAAAATCTTCAG 60.414 50.000 0.00 0.00 34.41 3.02
2475 3016 1.003262 CAAACAAATGCAGTCGCCCG 61.003 55.000 0.00 0.00 37.32 6.13
2476 3017 0.313672 TCAAACAAATGCAGTCGCCC 59.686 50.000 0.00 0.00 37.32 6.13
2479 3021 3.607422 TCACTCAAACAAATGCAGTCG 57.393 42.857 0.00 0.00 0.00 4.18
2590 4443 1.079503 GCCAATCCGAAGACAGTGAC 58.920 55.000 0.00 0.00 0.00 3.67
2692 4545 1.148310 ATGAACTCTCAAACACGCGG 58.852 50.000 12.47 1.27 34.49 6.46
2776 4629 0.035439 ATCATGGTGTGGTTCCGGAC 60.035 55.000 1.83 0.00 0.00 4.79
2792 4645 8.147704 TGAGCAGGATGTAAATCGTATTTATCA 58.852 33.333 0.00 0.00 39.31 2.15
2819 4672 3.682858 GCACACAAATTAGCTCGGAGTTA 59.317 43.478 6.90 1.78 0.00 2.24
2872 4725 5.009310 GTCCGGGTTTACTTGATGTTCTTTT 59.991 40.000 0.00 0.00 0.00 2.27
2883 4736 1.271656 CTCTCACGTCCGGGTTTACTT 59.728 52.381 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.