Multiple sequence alignment - TraesCS4D01G134800

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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 TraesCS4D01G134800 chr4D 100.000 2711 0 0 1 2711 121473053 121475763 0.000000e+00 5007.0
1 TraesCS4D01G134800 chr4A 94.447 2035 96 7 1 2026 449401043 449399017 0.000000e+00 3116.0
2 TraesCS4D01G134800 chr4A 91.581 487 36 5 2229 2711 449398199 449397714 0.000000e+00 667.0
3 TraesCS4D01G134800 chr4A 95.322 171 5 1 2072 2239 449399012 449398842 4.450000e-68 268.0
4 TraesCS4D01G134800 chr4B 94.796 1768 61 7 266 2033 184300417 184302153 0.000000e+00 2726.0
5 TraesCS4D01G134800 chr4B 89.072 485 40 8 2229 2711 184302979 184303452 8.360000e-165 590.0
6 TraesCS4D01G134800 chr4B 90.688 247 21 2 1 245 184299611 184299857 7.240000e-86 327.0
7 TraesCS4D01G134800 chr4B 93.567 171 8 1 2072 2239 184302151 184302321 4.480000e-63 252.0
8 TraesCS4D01G134800 chr3D 96.875 32 1 0 89 120 595676010 595675979 1.000000e-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 TraesCS4D01G134800 chr4D 121473053 121475763 2710 False 5007.000000 5007 100.000000 1 2711 1 chr4D.!!$F1 2710
1 TraesCS4D01G134800 chr4A 449397714 449401043 3329 True 1350.333333 3116 93.783333 1 2711 3 chr4A.!!$R1 2710
2 TraesCS4D01G134800 chr4B 184299611 184303452 3841 False 973.750000 2726 92.030750 1 2711 4 chr4B.!!$F1 2710

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
797 1339 0.954452 GCAAACAACAGTAGCCAGCT 59.046 50.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2301 3524 0.385473 CGGCGGTTTGTCATGTTCAC 60.385 55.0 0.0 0.0 0.0 3.18 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 73 1.004758 AGGCCTTATGGGAGAGCCA 59.995 57.895 0.00 0.00 46.35 4.75
79 81 2.206576 ATGGGAGAGCCAGTCAAAAC 57.793 50.000 0.00 0.00 35.15 2.43
81 83 1.214175 TGGGAGAGCCAGTCAAAACAA 59.786 47.619 0.00 0.00 35.15 2.83
87 89 3.821033 AGAGCCAGTCAAAACAATACCAC 59.179 43.478 0.00 0.00 0.00 4.16
94 96 3.187842 GTCAAAACAATACCACCTCCGAC 59.812 47.826 0.00 0.00 0.00 4.79
100 102 2.011122 ATACCACCTCCGACCCATAG 57.989 55.000 0.00 0.00 0.00 2.23
121 123 2.844122 AAGTGTCGCAGTTTTGAACC 57.156 45.000 0.00 0.00 0.00 3.62
154 156 6.561945 TCAAAACAACGACACTTATTTTGC 57.438 33.333 0.00 0.00 37.10 3.68
158 160 4.463209 ACAACGACACTTATTTTGCATCG 58.537 39.130 0.00 0.00 0.00 3.84
164 166 3.119495 ACACTTATTTTGCATCGAAGGGC 60.119 43.478 0.00 0.00 0.00 5.19
455 997 6.986817 GGAGTTTATGATCTTCTCATTCGGAA 59.013 38.462 0.00 0.00 42.07 4.30
597 1139 8.037758 CAGTGACCAGTTAAGATCAAGTATTCT 58.962 37.037 0.00 0.00 0.00 2.40
797 1339 0.954452 GCAAACAACAGTAGCCAGCT 59.046 50.000 0.00 0.00 0.00 4.24
821 1363 7.622256 GCTTAAACTGCACACTATCTTGTACTG 60.622 40.741 0.00 0.00 0.00 2.74
822 1364 4.193826 ACTGCACACTATCTTGTACTGG 57.806 45.455 0.00 0.00 0.00 4.00
823 1365 2.932614 CTGCACACTATCTTGTACTGGC 59.067 50.000 0.00 0.00 0.00 4.85
824 1366 2.280628 GCACACTATCTTGTACTGGCC 58.719 52.381 0.00 0.00 0.00 5.36
1279 1821 1.133253 CAAGCTGATGAACCGCACG 59.867 57.895 0.00 0.00 0.00 5.34
1299 1841 1.136984 GGACGACTCTACCAGTGCG 59.863 63.158 0.00 0.00 34.41 5.34
1370 1912 3.849574 TCTTCCCACCTATCAACCATCAA 59.150 43.478 0.00 0.00 0.00 2.57
1397 1939 3.335579 AGAGGAATAACAACAAGGTCGC 58.664 45.455 0.00 0.00 0.00 5.19
1447 1989 2.034685 GCTGCAGATCACCAGTACGATA 59.965 50.000 20.43 0.00 0.00 2.92
1495 2037 1.183549 GAGGAAGAGGAGGCGTGTAA 58.816 55.000 0.00 0.00 0.00 2.41
1536 2078 1.597742 CCTCGCCATATGAACAAGGG 58.402 55.000 3.65 0.00 0.00 3.95
1634 2176 6.547880 GTGGATCAAGGAGAAGTAGATCTGTA 59.452 42.308 5.18 0.00 36.30 2.74
1740 2282 6.034790 TCGAATGCAAAAATTGAAATCGATGG 59.965 34.615 7.05 0.00 35.74 3.51
1805 2347 3.816523 TCCTCGTTAAATTTGCTTCCGTT 59.183 39.130 0.00 0.00 0.00 4.44
1819 2361 3.638484 CTTCCGTTTCCTTTCGCAAAAT 58.362 40.909 0.00 0.00 0.00 1.82
1821 2363 4.832590 TCCGTTTCCTTTCGCAAAATAA 57.167 36.364 0.00 0.00 0.00 1.40
1823 2365 5.589192 TCCGTTTCCTTTCGCAAAATAAAA 58.411 33.333 0.00 0.00 0.00 1.52
1824 2366 6.040878 TCCGTTTCCTTTCGCAAAATAAAAA 58.959 32.000 0.00 0.00 0.00 1.94
1880 2430 7.041440 TGCTTTGTTCATTGTTTCTCTTCGATA 60.041 33.333 0.00 0.00 0.00 2.92
1904 2454 1.028905 CTTCGTTGTTGGCCAAAGGA 58.971 50.000 22.47 14.12 34.07 3.36
2016 2566 5.942872 AGTTGTTTGTTCTGAAGTCTTGTG 58.057 37.500 0.00 0.00 0.00 3.33
2028 2578 6.543465 TCTGAAGTCTTGTGTCATGTTGAATT 59.457 34.615 0.00 0.00 0.00 2.17
2030 2580 6.095300 TGAAGTCTTGTGTCATGTTGAATTGT 59.905 34.615 0.00 0.00 0.00 2.71
2031 2581 7.281999 TGAAGTCTTGTGTCATGTTGAATTGTA 59.718 33.333 0.00 0.00 0.00 2.41
2032 2582 7.566760 AGTCTTGTGTCATGTTGAATTGTAA 57.433 32.000 0.00 0.00 0.00 2.41
2033 2583 8.169977 AGTCTTGTGTCATGTTGAATTGTAAT 57.830 30.769 0.00 0.00 0.00 1.89
2034 2584 8.632679 AGTCTTGTGTCATGTTGAATTGTAATT 58.367 29.630 0.00 0.00 0.00 1.40
2035 2585 9.248291 GTCTTGTGTCATGTTGAATTGTAATTT 57.752 29.630 0.00 0.00 0.00 1.82
2036 2586 9.814899 TCTTGTGTCATGTTGAATTGTAATTTT 57.185 25.926 0.00 0.00 0.00 1.82
2038 2588 9.591792 TTGTGTCATGTTGAATTGTAATTTTCA 57.408 25.926 0.00 0.00 0.00 2.69
2039 2589 9.029243 TGTGTCATGTTGAATTGTAATTTTCAC 57.971 29.630 0.00 0.00 31.87 3.18
2040 2590 8.207252 GTGTCATGTTGAATTGTAATTTTCACG 58.793 33.333 0.00 0.00 31.87 4.35
2041 2591 7.918033 TGTCATGTTGAATTGTAATTTTCACGT 59.082 29.630 0.00 0.00 31.87 4.49
2042 2592 9.388346 GTCATGTTGAATTGTAATTTTCACGTA 57.612 29.630 0.00 0.00 31.87 3.57
2043 2593 9.952188 TCATGTTGAATTGTAATTTTCACGTAA 57.048 25.926 0.00 0.00 31.87 3.18
2119 2669 8.081633 CAGTGGCAGAAAATTTGTAAGTGATTA 58.918 33.333 0.00 0.00 0.00 1.75
2171 2721 7.856398 GTCTTCAAGCTAAACAAAACCTCTAAC 59.144 37.037 0.00 0.00 0.00 2.34
2227 2780 6.150140 ACTTGTACATCATCAAGAAAAGAGGC 59.850 38.462 11.07 0.00 42.22 4.70
2250 3472 4.668289 GGCAACATCGAATTAATCCGTTT 58.332 39.130 0.00 0.00 0.00 3.60
2257 3479 7.808672 ACATCGAATTAATCCGTTTGTTTACA 58.191 30.769 0.00 0.00 0.00 2.41
2282 3504 5.709966 ACAAATTTTCGCTTATCCAAGACC 58.290 37.500 0.00 0.00 33.20 3.85
2291 3514 4.092968 CGCTTATCCAAGACCACAAAGTAC 59.907 45.833 0.00 0.00 33.20 2.73
2301 3524 6.328641 AGACCACAAAGTACACACTACTAG 57.671 41.667 0.00 0.00 33.48 2.57
2380 3603 3.441222 CAGCAACTCTTATGGTCATGCAA 59.559 43.478 0.00 0.00 34.89 4.08
2384 3607 5.185454 CAACTCTTATGGTCATGCAACCTA 58.815 41.667 8.97 0.00 40.20 3.08
2397 3620 9.231297 GGTCATGCAACCTAATAATGTGTATAT 57.769 33.333 0.00 0.00 36.32 0.86
2481 3705 8.106247 TGTATGTTCCTTTTTGTGAGGTATTC 57.894 34.615 0.00 0.00 35.71 1.75
2486 3710 4.518970 TCCTTTTTGTGAGGTATTCTGCAC 59.481 41.667 0.00 0.00 35.71 4.57
2501 3725 9.855021 GGTATTCTGCACTGTTAAACAATTATT 57.145 29.630 0.00 0.00 0.00 1.40
2506 3730 6.276091 TGCACTGTTAAACAATTATTGTGCA 58.724 32.000 11.60 10.77 44.59 4.57
2660 3885 7.096884 ACAAAAGAAACAAAGAGGGTACTTC 57.903 36.000 0.00 0.00 0.00 3.01
2661 3886 6.183360 ACAAAAGAAACAAAGAGGGTACTTCG 60.183 38.462 0.00 0.00 0.00 3.79
2670 3895 7.049754 ACAAAGAGGGTACTTCGTTAGAAAAA 58.950 34.615 0.00 0.00 35.71 1.94
2698 3923 4.274459 GGCTGCACTTTGAGTATATGGAAG 59.726 45.833 0.50 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 73 3.071892 TCGGAGGTGGTATTGTTTTGACT 59.928 43.478 0.00 0.00 0.00 3.41
79 81 0.837272 ATGGGTCGGAGGTGGTATTG 59.163 55.000 0.00 0.00 0.00 1.90
81 83 1.219724 ACTATGGGTCGGAGGTGGTAT 59.780 52.381 0.00 0.00 0.00 2.73
87 89 2.361438 GACACTTACTATGGGTCGGAGG 59.639 54.545 0.00 0.00 0.00 4.30
94 96 2.961526 ACTGCGACACTTACTATGGG 57.038 50.000 0.00 0.00 0.00 4.00
100 102 3.064271 TGGTTCAAAACTGCGACACTTAC 59.936 43.478 0.00 0.00 0.00 2.34
121 123 1.581602 CGTTGTTTTGAACTGCGGTTG 59.418 47.619 17.49 0.00 35.58 3.77
154 156 1.722011 AACAAGTACGCCCTTCGATG 58.278 50.000 0.00 0.00 41.67 3.84
158 160 3.259902 CCTCTAAACAAGTACGCCCTTC 58.740 50.000 0.00 0.00 0.00 3.46
164 166 3.967332 TTCCCCCTCTAAACAAGTACG 57.033 47.619 0.00 0.00 0.00 3.67
427 969 4.060038 TGAGAAGATCATAAACTCCCGC 57.940 45.455 0.00 0.00 31.12 6.13
455 997 6.660521 TGTGATTCTTGTCATTATTTGCTCCT 59.339 34.615 0.00 0.00 0.00 3.69
597 1139 3.586470 TCCTTGTGGGCAAAGTTTCTA 57.414 42.857 0.00 0.00 33.73 2.10
797 1339 6.649141 CCAGTACAAGATAGTGTGCAGTTTAA 59.351 38.462 0.00 0.00 36.66 1.52
821 1363 1.277273 ACAACTTAAGGAGTACCGGCC 59.723 52.381 0.00 0.00 37.72 6.13
822 1364 2.756840 ACAACTTAAGGAGTACCGGC 57.243 50.000 0.00 0.00 37.72 6.13
823 1365 5.969423 TGATAACAACTTAAGGAGTACCGG 58.031 41.667 7.53 0.00 37.72 5.28
824 1366 7.465513 GCATTGATAACAACTTAAGGAGTACCG 60.466 40.741 7.53 0.00 37.72 4.02
966 1508 2.289002 GGTTTTGCTATCCAGATCTGCG 59.711 50.000 17.76 10.69 0.00 5.18
1279 1821 0.452585 GCACTGGTAGAGTCGTCCTC 59.547 60.000 7.84 0.00 40.80 3.71
1370 1912 5.163088 ACCTTGTTGTTATTCCTCTCCTTGT 60.163 40.000 0.00 0.00 0.00 3.16
1397 1939 1.336440 CTCTCACTGCTATGGAGACGG 59.664 57.143 0.00 0.00 34.24 4.79
1447 1989 4.216257 CGACAATTCCAAATCCTGTCTGTT 59.784 41.667 0.00 0.00 35.36 3.16
1512 2054 0.947244 GTTCATATGGCGAGGCAAGG 59.053 55.000 2.86 0.00 0.00 3.61
1536 2078 2.442236 TGGAATGATCAAGGAAGGCC 57.558 50.000 0.00 0.00 0.00 5.19
1634 2176 2.509964 ACCAGTCCTTGTTTCTTGAGGT 59.490 45.455 0.00 0.00 32.33 3.85
1678 2220 4.563976 GTGTGATGCAACATTTGGATTAGC 59.436 41.667 0.00 0.00 42.07 3.09
1740 2282 2.808543 AGCACACGAGTGGAAAAGAATC 59.191 45.455 14.90 0.00 45.98 2.52
1880 2430 3.810310 TTGGCCAACAACGAAGAATTT 57.190 38.095 16.05 0.00 33.18 1.82
2016 2566 8.280909 ACGTGAAAATTACAATTCAACATGAC 57.719 30.769 0.00 0.00 37.31 3.06
2084 2634 6.899393 AATTTTCTGCCACTGATCACTAAA 57.101 33.333 0.00 0.00 0.00 1.85
2227 2780 2.286833 ACGGATTAATTCGATGTTGCCG 59.713 45.455 22.83 13.12 41.72 5.69
2250 3472 7.806014 GGATAAGCGAAAATTTGTCTGTAAACA 59.194 33.333 0.00 0.00 0.00 2.83
2257 3479 6.349363 GGTCTTGGATAAGCGAAAATTTGTCT 60.349 38.462 0.00 0.00 33.82 3.41
2282 3504 6.976349 TGTTCACTAGTAGTGTGTACTTTGTG 59.024 38.462 25.83 1.40 46.03 3.33
2291 3514 6.073765 GGTTTGTCATGTTCACTAGTAGTGTG 60.074 42.308 25.83 17.97 46.03 3.82
2301 3524 0.385473 CGGCGGTTTGTCATGTTCAC 60.385 55.000 0.00 0.00 0.00 3.18
2397 3620 5.717078 ACTTGAGTTCTTGACACGGTATA 57.283 39.130 0.00 0.00 0.00 1.47
2441 3665 8.191534 AGGAACATACAAGTACTCAAGTTAGT 57.808 34.615 0.00 0.00 0.00 2.24
2452 3676 7.057894 ACCTCACAAAAAGGAACATACAAGTA 58.942 34.615 0.00 0.00 37.35 2.24
2454 3678 6.391227 ACCTCACAAAAAGGAACATACAAG 57.609 37.500 0.00 0.00 37.35 3.16
2481 3705 6.420306 TGCACAATAATTGTTTAACAGTGCAG 59.580 34.615 25.66 9.18 42.21 4.41
2660 3885 4.403453 GTGCAGCCACTATTTTTCTAACG 58.597 43.478 0.00 0.00 38.93 3.18


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

AutoCloner maintained by Alex Coulton.