Multiple sequence alignment - TraesCS3D01G155300

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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 TraesCS3D01G155300 chr3D 100.000 2641 0 0 1 2641 122454582 122457222 0.000000e+00 4878.0
1 TraesCS3D01G155300 chr3D 89.286 196 17 2 2449 2640 122516017 122516212 2.630000e-60 243.0
2 TraesCS3D01G155300 chr3A 90.673 2155 124 33 547 2640 128286748 128288886 0.000000e+00 2795.0
3 TraesCS3D01G155300 chr3A 94.296 561 17 9 1 553 128286167 128286720 0.000000e+00 845.0
4 TraesCS3D01G155300 chr3A 93.617 329 20 1 2313 2640 128290064 128290392 8.490000e-135 490.0
5 TraesCS3D01G155300 chr3B 91.765 1020 51 15 547 1557 174147211 174148206 0.000000e+00 1387.0
6 TraesCS3D01G155300 chr3B 92.843 503 25 7 1 503 174145430 174145921 0.000000e+00 719.0
7 TraesCS3D01G155300 chr3B 92.405 395 28 1 2246 2640 174149344 174149736 1.770000e-156 562.0
8 TraesCS3D01G155300 chr3B 86.765 408 35 6 1818 2213 174148941 174149341 1.120000e-118 436.0
9 TraesCS3D01G155300 chr3B 95.745 47 2 0 500 546 174147126 174147172 2.820000e-10 76.8


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 TraesCS3D01G155300 chr3D 122454582 122457222 2640 False 4878.000000 4878 100.0000 1 2641 1 chr3D.!!$F1 2640
1 TraesCS3D01G155300 chr3A 128286167 128290392 4225 False 1376.666667 2795 92.8620 1 2640 3 chr3A.!!$F1 2639
2 TraesCS3D01G155300 chr3B 174145430 174149736 4306 False 636.160000 1387 91.9046 1 2640 5 chr3B.!!$F1 2639

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
469 477 1.134075 CAGTGTTCGCTGCATCTGC 59.866 57.895 0.0 0.0 42.5 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2375 4168 0.178767 TTCGGTGATCCAGCCTCATG 59.821 55.0 0.0 0.0 0.0 3.07 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
39 40 1.801771 GCATTACAACACTGTGCCGTA 59.198 47.619 7.90 6.75 36.96 4.02
102 103 2.053244 GACTGGACCATCATCCTCCAT 58.947 52.381 0.00 0.00 39.75 3.41
127 128 2.174349 CCGAGAAGCGCAACAAGC 59.826 61.111 11.47 0.00 39.11 4.01
215 216 1.282930 ACGACGGCGAAGAAGAAAGC 61.283 55.000 22.49 0.00 41.64 3.51
405 406 4.794278 TTTCGGCTTATGACAGACAGTA 57.206 40.909 0.00 0.00 0.00 2.74
406 407 5.339008 TTTCGGCTTATGACAGACAGTAT 57.661 39.130 0.00 0.00 0.00 2.12
417 418 2.497675 ACAGACAGTATGCGGATTCTGT 59.502 45.455 25.11 25.11 41.49 3.41
436 443 5.820131 TCTGTTGTGCTCACTGTATTTTTG 58.180 37.500 1.47 0.00 0.00 2.44
469 477 1.134075 CAGTGTTCGCTGCATCTGC 59.866 57.895 0.00 0.00 42.50 4.26
511 1727 3.968649 TGGTTGGTCTTTAGTGGACTACA 59.031 43.478 0.00 0.00 34.47 2.74
516 1732 6.770746 TGGTCTTTAGTGGACTACATAGAC 57.229 41.667 11.19 11.19 34.38 2.59
681 1935 7.789831 AGAGTATAGACCATGGAACTGGAATTA 59.210 37.037 21.47 1.68 39.73 1.40
683 1937 8.949421 AGTATAGACCATGGAACTGGAATTATT 58.051 33.333 21.47 0.00 39.73 1.40
735 1991 4.143073 TGAACAATTACGGCGTGTATTCAC 60.143 41.667 24.86 13.96 40.79 3.18
768 2024 9.836076 AAAATTTACAAGATAACTACGGAAAGC 57.164 29.630 0.00 0.00 0.00 3.51
769 2025 8.788325 AATTTACAAGATAACTACGGAAAGCT 57.212 30.769 0.00 0.00 0.00 3.74
778 2034 3.434309 ACTACGGAAAGCTGGTAGGTTA 58.566 45.455 14.95 0.00 38.32 2.85
836 2092 1.495878 GTGCACTATCCGCTCATCAG 58.504 55.000 10.32 0.00 0.00 2.90
842 2098 3.027412 ACTATCCGCTCATCAGTGTCTT 58.973 45.455 0.00 0.00 0.00 3.01
875 2131 2.033407 CCAAGTCGAATGATGACGATGC 60.033 50.000 0.00 0.00 41.24 3.91
1436 2711 8.263854 ACTAGTATTTTCTGGCTGGTATATGT 57.736 34.615 0.00 0.00 0.00 2.29
1437 2712 9.375974 ACTAGTATTTTCTGGCTGGTATATGTA 57.624 33.333 0.00 0.00 0.00 2.29
1557 2991 5.184096 TGTCTTTGTGGTTGCTTTGAACTTA 59.816 36.000 0.00 0.00 0.00 2.24
1573 3007 6.105657 TGAACTTAATCATGCACGTGTATG 57.894 37.500 32.88 32.88 39.12 2.39
1581 3015 3.316588 TCATGCACGTGTATGTTTTGGTT 59.683 39.130 35.26 5.71 38.89 3.67
1601 3035 4.935808 GGTTTCGGAGTTTGTGTATGATCT 59.064 41.667 0.00 0.00 0.00 2.75
1659 3095 6.684979 TGACAATATAAAAACGCGCAATACTG 59.315 34.615 5.73 0.00 0.00 2.74
1776 3214 8.161425 ACCACACATTAGTTACCAAGTTTAGAT 58.839 33.333 0.00 0.00 0.00 1.98
1783 3221 8.767478 TTAGTTACCAAGTTTAGATACTGCAC 57.233 34.615 0.00 0.00 0.00 4.57
1784 3222 6.765403 AGTTACCAAGTTTAGATACTGCACA 58.235 36.000 0.00 0.00 0.00 4.57
1785 3223 7.394816 AGTTACCAAGTTTAGATACTGCACAT 58.605 34.615 0.00 0.00 0.00 3.21
1786 3224 7.334421 AGTTACCAAGTTTAGATACTGCACATG 59.666 37.037 0.00 0.00 0.00 3.21
1787 3225 4.396166 ACCAAGTTTAGATACTGCACATGC 59.604 41.667 0.00 0.00 42.50 4.06
1818 3280 6.686630 CAGTAAAAACACAATAAGATGCCCA 58.313 36.000 0.00 0.00 0.00 5.36
1819 3281 6.586082 CAGTAAAAACACAATAAGATGCCCAC 59.414 38.462 0.00 0.00 0.00 4.61
1824 3584 3.507233 ACACAATAAGATGCCCACAACTG 59.493 43.478 0.00 0.00 0.00 3.16
1884 3644 4.673298 ACGCCATGGCACGAACGA 62.673 61.111 34.93 0.00 42.06 3.85
1901 3661 3.613527 AGCGAGATCAGCAGCTCA 58.386 55.556 14.27 0.00 34.48 4.26
1904 3664 0.459934 GCGAGATCAGCAGCTCAGTT 60.460 55.000 8.11 0.00 34.19 3.16
1939 3709 3.445096 CCCTCTTGGTCAATGATTTCCAC 59.555 47.826 0.00 0.00 0.00 4.02
1943 3713 2.874014 TGGTCAATGATTTCCACTGCA 58.126 42.857 0.00 0.00 0.00 4.41
1998 3776 9.059260 GTAAACTTGTTTCTGGTAGTCCATAAA 57.941 33.333 1.72 0.00 43.43 1.40
2007 3785 4.400120 TGGTAGTCCATAAAACCCAACAC 58.600 43.478 0.00 0.00 39.03 3.32
2010 3788 3.558033 AGTCCATAAAACCCAACACGTT 58.442 40.909 0.00 0.00 0.00 3.99
2012 3790 2.034812 TCCATAAAACCCAACACGTTGC 59.965 45.455 4.34 0.00 39.16 4.17
2013 3791 2.223829 CCATAAAACCCAACACGTTGCA 60.224 45.455 4.34 0.00 39.16 4.08
2014 3792 3.448686 CATAAAACCCAACACGTTGCAA 58.551 40.909 4.34 0.00 39.16 4.08
2015 3793 2.457366 AAAACCCAACACGTTGCAAA 57.543 40.000 0.00 0.00 39.16 3.68
2016 3794 2.457366 AAACCCAACACGTTGCAAAA 57.543 40.000 0.00 0.00 39.16 2.44
2074 3865 5.008118 GCCTCAATAAAGACCTATCAGCAAC 59.992 44.000 0.00 0.00 0.00 4.17
2128 3920 3.430556 TCACATACGACCAAATCAACACG 59.569 43.478 0.00 0.00 0.00 4.49
2156 3948 6.653020 ACATGATGGCTAAGTCACATTTAGA 58.347 36.000 0.00 0.00 31.26 2.10
2158 3950 7.611467 ACATGATGGCTAAGTCACATTTAGAAA 59.389 33.333 0.00 0.00 31.26 2.52
2198 3990 8.441608 CACACAAAACACAAAGATCAAAATCAA 58.558 29.630 0.00 0.00 34.07 2.57
2217 4009 1.648504 AGGCCATTACGCTTACGAAC 58.351 50.000 5.01 0.00 43.93 3.95
2222 4014 2.997986 CCATTACGCTTACGAACTTGGT 59.002 45.455 0.00 0.00 43.93 3.67
2230 4023 0.319211 TACGAACTTGGTCACCGCTG 60.319 55.000 0.00 0.00 0.00 5.18
2249 4042 3.186409 GCTGACAAACGAGCACAAATAGA 59.814 43.478 0.00 0.00 35.15 1.98
2254 4047 3.389687 AACGAGCACAAATAGATTGCG 57.610 42.857 0.00 0.00 43.13 4.85
2302 4095 2.210961 CTCTAGGACGCGACACATCTA 58.789 52.381 15.93 2.41 0.00 1.98
2318 4111 7.113658 ACACATCTATGAACTTGGTAGTAGG 57.886 40.000 0.00 0.00 33.17 3.18
2375 4168 3.066760 ACTGTAAAACAACCAGAAGCAGC 59.933 43.478 0.00 0.00 0.00 5.25
2456 4249 2.173569 AGTGCCAGTTCTCCAACTCTTT 59.826 45.455 0.00 0.00 41.24 2.52
2479 4272 2.408050 GAGACAGCACACGTTGAAGAT 58.592 47.619 0.00 0.00 0.00 2.40
2560 4353 4.518211 ACAAAACAGAGAAAGAGGAGCATG 59.482 41.667 0.00 0.00 0.00 4.06
2640 4433 2.170607 CAAATGTGGAGGACGGATAGGT 59.829 50.000 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.016627 GTAATGCTGGCGCTGAATCA 58.983 50.000 7.64 0.00 36.97 2.57
39 40 3.834813 TGCAGACCTGACTCACTATTCTT 59.165 43.478 0.47 0.00 0.00 2.52
102 103 3.064987 GCGCTTCTCGGAGTGGCTA 62.065 63.158 17.31 0.00 38.94 3.93
127 128 1.239968 GCCAGTGCCTCCTTGTTCAG 61.240 60.000 0.00 0.00 0.00 3.02
215 216 2.256764 CGATCGGATCGCCCTCTG 59.743 66.667 25.34 0.23 46.55 3.35
322 323 2.441375 TGTTCAAGTCTCCACCATCCAA 59.559 45.455 0.00 0.00 0.00 3.53
405 406 1.089920 GAGCACAACAGAATCCGCAT 58.910 50.000 0.00 0.00 0.00 4.73
406 407 0.250252 TGAGCACAACAGAATCCGCA 60.250 50.000 0.00 0.00 0.00 5.69
417 418 6.714810 ACTATCCAAAAATACAGTGAGCACAA 59.285 34.615 0.00 0.00 0.00 3.33
436 443 1.282157 ACACTGCCCCTTCAACTATCC 59.718 52.381 0.00 0.00 0.00 2.59
466 474 7.816031 ACCAAATAAAGATCAGAAAACATGCAG 59.184 33.333 0.00 0.00 0.00 4.41
467 475 7.669427 ACCAAATAAAGATCAGAAAACATGCA 58.331 30.769 0.00 0.00 0.00 3.96
468 476 8.437742 CAACCAAATAAAGATCAGAAAACATGC 58.562 33.333 0.00 0.00 0.00 4.06
469 477 8.928733 CCAACCAAATAAAGATCAGAAAACATG 58.071 33.333 0.00 0.00 0.00 3.21
470 478 8.650490 ACCAACCAAATAAAGATCAGAAAACAT 58.350 29.630 0.00 0.00 0.00 2.71
471 479 8.017418 ACCAACCAAATAAAGATCAGAAAACA 57.983 30.769 0.00 0.00 0.00 2.83
474 482 8.477419 AAGACCAACCAAATAAAGATCAGAAA 57.523 30.769 0.00 0.00 0.00 2.52
511 1727 7.343057 TCACCTTGACATGAATCTACAGTCTAT 59.657 37.037 0.00 0.00 0.00 1.98
700 1954 7.906010 CGCCGTAATTGTTCACAAAATATCTAA 59.094 33.333 0.00 0.00 39.55 2.10
701 1955 7.064847 ACGCCGTAATTGTTCACAAAATATCTA 59.935 33.333 0.00 0.00 39.55 1.98
836 2092 7.117812 TCGACTTGGAATTATTTCTCAAGACAC 59.882 37.037 22.00 15.55 39.71 3.67
842 2098 8.615211 CATCATTCGACTTGGAATTATTTCTCA 58.385 33.333 0.00 0.00 34.50 3.27
875 2131 1.336125 GTCGGATAAGGTCTACCACGG 59.664 57.143 1.26 0.00 38.89 4.94
969 2232 1.301558 GAGGCAGAGATGGCGATGG 60.302 63.158 0.00 0.00 39.53 3.51
1015 2288 1.449246 AGTGCGATCTGCTTGCCTC 60.449 57.895 10.16 0.00 46.63 4.70
1392 2665 6.868622 ACTAGTACTAGCAAAGGATGACAAG 58.131 40.000 26.54 3.47 36.66 3.16
1423 2698 6.596621 TGCAAACTTATACATATACCAGCCA 58.403 36.000 0.00 0.00 0.00 4.75
1557 2991 4.022416 ACCAAAACATACACGTGCATGATT 60.022 37.500 30.64 23.28 0.00 2.57
1573 3007 3.840468 ACACAAACTCCGAAACCAAAAC 58.160 40.909 0.00 0.00 0.00 2.43
1581 3015 5.408299 CACAAGATCATACACAAACTCCGAA 59.592 40.000 0.00 0.00 0.00 4.30
1635 3069 6.685403 ACAGTATTGCGCGTTTTTATATTGTC 59.315 34.615 8.43 0.00 0.00 3.18
1636 3070 6.548171 ACAGTATTGCGCGTTTTTATATTGT 58.452 32.000 8.43 8.75 0.00 2.71
1637 3071 7.428183 AGAACAGTATTGCGCGTTTTTATATTG 59.572 33.333 8.43 8.18 0.00 1.90
1639 3073 7.011828 AGAACAGTATTGCGCGTTTTTATAT 57.988 32.000 8.43 0.00 0.00 0.86
1640 3074 6.411630 AGAACAGTATTGCGCGTTTTTATA 57.588 33.333 8.43 0.00 0.00 0.98
1690 3126 8.576442 CCACATGTTGACCTTCTTTATAAAGTT 58.424 33.333 21.69 7.79 37.31 2.66
1691 3127 7.942341 TCCACATGTTGACCTTCTTTATAAAGT 59.058 33.333 21.69 6.35 37.31 2.66
1692 3128 8.335532 TCCACATGTTGACCTTCTTTATAAAG 57.664 34.615 17.60 17.60 37.36 1.85
1693 3129 8.698973 TTCCACATGTTGACCTTCTTTATAAA 57.301 30.769 0.00 0.00 0.00 1.40
1696 3132 7.451255 TGAATTCCACATGTTGACCTTCTTTAT 59.549 33.333 16.28 0.00 0.00 1.40
1697 3133 6.775142 TGAATTCCACATGTTGACCTTCTTTA 59.225 34.615 16.28 0.00 0.00 1.85
1698 3134 5.598005 TGAATTCCACATGTTGACCTTCTTT 59.402 36.000 16.28 1.19 0.00 2.52
1715 3151 2.681344 GTTGGATGTACGGGTGAATTCC 59.319 50.000 2.27 0.00 0.00 3.01
1786 3224 2.741612 TGTGTTTTTACTGCATGCTGC 58.258 42.857 22.92 7.47 45.29 5.25
1787 3225 6.862608 TCTTATTGTGTTTTTACTGCATGCTG 59.137 34.615 21.60 21.60 0.00 4.41
1788 3226 6.980593 TCTTATTGTGTTTTTACTGCATGCT 58.019 32.000 20.33 1.26 0.00 3.79
1789 3227 7.669098 CATCTTATTGTGTTTTTACTGCATGC 58.331 34.615 11.82 11.82 0.00 4.06
1797 3235 6.656632 TGTGGGCATCTTATTGTGTTTTTA 57.343 33.333 0.00 0.00 0.00 1.52
1884 3644 1.321805 ACTGAGCTGCTGATCTCGCT 61.322 55.000 7.01 4.24 35.03 4.93
1970 3748 6.285990 TGGACTACCAGAAACAAGTTTACTC 58.714 40.000 0.00 0.00 41.77 2.59
1998 3776 2.682155 ATTTTGCAACGTGTTGGGTT 57.318 40.000 14.07 0.00 40.74 4.11
2074 3865 1.065854 ACCTCTTTCAATGAGCTCCGG 60.066 52.381 12.15 0.00 0.00 5.14
2128 3920 4.507710 TGTGACTTAGCCATCATGTTCTC 58.492 43.478 0.00 0.00 0.00 2.87
2160 3952 1.565156 TTTGTGTGATGCTCGGACGC 61.565 55.000 0.00 0.00 0.00 5.19
2165 3957 2.753989 TGTGTTTTGTGTGATGCTCG 57.246 45.000 0.00 0.00 0.00 5.03
2198 3990 1.206371 AGTTCGTAAGCGTAATGGCCT 59.794 47.619 3.32 0.00 39.49 5.19
2222 4014 1.954146 GCTCGTTTGTCAGCGGTGA 60.954 57.895 14.39 14.39 0.00 4.02
2230 4023 4.554973 GCAATCTATTTGTGCTCGTTTGTC 59.445 41.667 0.00 0.00 37.65 3.18
2234 4027 3.000041 TCGCAATCTATTTGTGCTCGTT 59.000 40.909 0.00 0.00 43.98 3.85
2249 4042 7.655328 TCAAAATTAAAACCTTCATGTCGCAAT 59.345 29.630 0.00 0.00 0.00 3.56
2254 4047 8.576442 TCCTCTCAAAATTAAAACCTTCATGTC 58.424 33.333 0.00 0.00 0.00 3.06
2293 4086 7.068348 TCCTACTACCAAGTTCATAGATGTGTC 59.932 40.741 0.00 0.00 37.15 3.67
2302 4095 4.470304 GGGTTCTCCTACTACCAAGTTCAT 59.530 45.833 0.00 0.00 37.15 2.57
2318 4111 5.878406 TTCCAGATTGATAGAGGGTTCTC 57.122 43.478 0.00 0.00 40.25 2.87
2375 4168 0.178767 TTCGGTGATCCAGCCTCATG 59.821 55.000 0.00 0.00 0.00 3.07
2456 4249 1.324383 TCAACGTGTGCTGTCTCCTA 58.676 50.000 0.00 0.00 0.00 2.94
2463 4256 1.462283 CTGGATCTTCAACGTGTGCTG 59.538 52.381 0.00 0.00 0.00 4.41
2479 4272 8.343787 ACTTTTCCTTAATAATTGGGATCTGGA 58.656 33.333 0.00 0.00 0.00 3.86
2560 4353 0.394762 TGGCATGGTGGCTCATCTTC 60.395 55.000 5.12 0.00 44.10 2.87


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

AutoCloner maintained by Alex Coulton.