Multiple sequence alignment - TraesCS5D01G325400

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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 TraesCS5D01G325400 chr5D 100.000 3194 0 0 1 3194 417042160 417038967 0.000000e+00 5899.0
1 TraesCS5D01G325400 chr5B 94.935 3218 80 28 13 3194 504308392 504305222 0.000000e+00 4963.0
2 TraesCS5D01G325400 chr5A 96.188 2361 59 15 854 3194 530302850 530300501 0.000000e+00 3832.0
3 TraesCS5D01G325400 chr5A 92.885 773 18 10 17 759 530304039 530303274 0.000000e+00 1088.0
4 TraesCS5D01G325400 chr5A 100.000 29 0 0 1878 1906 458281891 458281863 2.000000e-03 54.7
5 TraesCS5D01G325400 chr7A 86.628 172 23 0 1675 1846 282368854 282368683 1.170000e-44 191.0
6 TraesCS5D01G325400 chr7A 85.906 149 21 0 1300 1448 282369255 282369107 3.300000e-35 159.0
7 TraesCS5D01G325400 chr7A 100.000 28 0 0 351 378 631495295 631495268 6.000000e-03 52.8
8 TraesCS5D01G325400 chr7B 86.047 172 24 0 1675 1846 239363366 239363537 5.440000e-43 185.0
9 TraesCS5D01G325400 chr7B 85.906 149 21 0 1300 1448 239362965 239363113 3.300000e-35 159.0
10 TraesCS5D01G325400 chr3B 87.838 148 16 2 1297 1443 786970547 786970401 4.240000e-39 172.0
11 TraesCS5D01G325400 chr3D 87.162 148 17 2 1297 1443 588489275 588489129 1.970000e-37 167.0
12 TraesCS5D01G325400 chr7D 86.577 149 20 0 1300 1448 259840844 259840696 7.090000e-37 165.0
13 TraesCS5D01G325400 chr3A 86.486 148 18 2 1297 1443 718836820 718836674 9.170000e-36 161.0


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 TraesCS5D01G325400 chr5D 417038967 417042160 3193 True 5899 5899 100.0000 1 3194 1 chr5D.!!$R1 3193
1 TraesCS5D01G325400 chr5B 504305222 504308392 3170 True 4963 4963 94.9350 13 3194 1 chr5B.!!$R1 3181
2 TraesCS5D01G325400 chr5A 530300501 530304039 3538 True 2460 3832 94.5365 17 3194 2 chr5A.!!$R2 3177

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
124 125 0.041663 CGAAAGAAAAAGGCACGCGA 60.042 50.0 15.93 0.0 0.0 5.87 F
840 912 0.178935 CCTCCTCCCTCCTCATCCTC 60.179 65.0 0.00 0.0 0.0 3.71 F
841 913 0.859760 CTCCTCCCTCCTCATCCTCT 59.140 60.0 0.00 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1580 1978 1.298041 GGTTTTGCACCACGTCGTG 60.298 57.895 18.54 18.54 46.42 4.35 R
1658 2058 1.518572 GATCCCCTACACACGCACG 60.519 63.158 0.00 0.00 0.00 5.34 R
2806 3212 2.026157 GTCGCATGGCTCGATCGA 59.974 61.111 18.32 18.32 38.29 3.59 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
124 125 0.041663 CGAAAGAAAAAGGCACGCGA 60.042 50.000 15.93 0.00 0.00 5.87
458 486 0.462375 TCGTGGTACATTCCATCCGG 59.538 55.000 0.00 0.00 44.52 5.14
459 487 0.531974 CGTGGTACATTCCATCCGGG 60.532 60.000 0.00 0.00 44.52 5.73
460 488 0.179029 GTGGTACATTCCATCCGGGG 60.179 60.000 0.00 0.00 44.52 5.73
461 489 1.228154 GGTACATTCCATCCGGGGC 60.228 63.158 0.00 0.00 37.22 5.80
462 490 1.597027 GTACATTCCATCCGGGGCG 60.597 63.158 0.00 0.00 37.22 6.13
602 645 2.684104 CCTCACTCCCTCCCTCGA 59.316 66.667 0.00 0.00 0.00 4.04
609 652 2.681778 CCCTCCCTCGACTGTGCT 60.682 66.667 0.00 0.00 0.00 4.40
658 723 6.525629 TCCAAACTTGTTTAGAGAGAGAAGG 58.474 40.000 0.00 0.00 0.00 3.46
659 724 6.326583 TCCAAACTTGTTTAGAGAGAGAAGGA 59.673 38.462 0.00 0.00 0.00 3.36
660 725 6.648725 CCAAACTTGTTTAGAGAGAGAAGGAG 59.351 42.308 0.00 0.00 0.00 3.69
661 726 7.437748 CAAACTTGTTTAGAGAGAGAAGGAGA 58.562 38.462 0.00 0.00 0.00 3.71
819 884 1.010795 TCCTCATCTCCACCTCCTCA 58.989 55.000 0.00 0.00 0.00 3.86
820 885 1.118838 CCTCATCTCCACCTCCTCAC 58.881 60.000 0.00 0.00 0.00 3.51
823 888 0.326048 CATCTCCACCTCCTCACCCT 60.326 60.000 0.00 0.00 0.00 4.34
835 907 1.862138 TCACCCTCCTCCCTCCTCA 60.862 63.158 0.00 0.00 0.00 3.86
836 908 1.231751 TCACCCTCCTCCCTCCTCAT 61.232 60.000 0.00 0.00 0.00 2.90
838 910 1.152139 CCCTCCTCCCTCCTCATCC 60.152 68.421 0.00 0.00 0.00 3.51
839 911 1.673928 CCCTCCTCCCTCCTCATCCT 61.674 65.000 0.00 0.00 0.00 3.24
840 912 0.178935 CCTCCTCCCTCCTCATCCTC 60.179 65.000 0.00 0.00 0.00 3.71
841 913 0.859760 CTCCTCCCTCCTCATCCTCT 59.140 60.000 0.00 0.00 0.00 3.69
842 914 1.220236 CTCCTCCCTCCTCATCCTCTT 59.780 57.143 0.00 0.00 0.00 2.85
843 915 1.219213 TCCTCCCTCCTCATCCTCTTC 59.781 57.143 0.00 0.00 0.00 2.87
844 916 1.715785 CTCCCTCCTCATCCTCTTCC 58.284 60.000 0.00 0.00 0.00 3.46
849 921 2.046292 CTCCTCATCCTCTTCCCTTCC 58.954 57.143 0.00 0.00 0.00 3.46
868 1262 2.363795 TTCCCATCGACGAGGCCT 60.364 61.111 3.86 3.86 0.00 5.19
1254 1652 1.841103 GGCATCCTCCTCCTCCTCC 60.841 68.421 0.00 0.00 0.00 4.30
1577 1975 6.945218 CCTCCTCAGGTACGTACTATATACT 58.055 44.000 24.07 9.60 34.60 2.12
1580 1978 7.841956 TCCTCAGGTACGTACTATATACTACC 58.158 42.308 24.07 7.18 0.00 3.18
1581 1979 7.454694 TCCTCAGGTACGTACTATATACTACCA 59.545 40.741 24.07 0.63 0.00 3.25
1582 1980 7.547370 CCTCAGGTACGTACTATATACTACCAC 59.453 44.444 24.07 3.91 0.00 4.16
1583 1981 7.090808 TCAGGTACGTACTATATACTACCACG 58.909 42.308 24.07 3.28 0.00 4.94
1616 2014 1.207791 CCTACACCTTCCATGCCTCT 58.792 55.000 0.00 0.00 0.00 3.69
1653 2053 3.443976 ACGCTAAAACCTGTGCTTTTTG 58.556 40.909 0.00 0.00 0.00 2.44
1658 2058 2.008752 AACCTGTGCTTTTTGTGTGC 57.991 45.000 0.00 0.00 0.00 4.57
2259 2659 6.037830 GCTTAATGAGGCACCGTAATTTAGAA 59.962 38.462 0.00 0.00 0.00 2.10
2455 2856 6.426937 TCTTGATTTTCCTGGTACTTCTTTCG 59.573 38.462 0.00 0.00 0.00 3.46
2517 2918 4.829064 ACTTTTACCACGACGTACTACA 57.171 40.909 0.00 0.00 0.00 2.74
2615 3019 0.104487 GCGCCCTAGAAACCTAGTCC 59.896 60.000 0.00 0.00 33.44 3.85
2616 3020 0.751452 CGCCCTAGAAACCTAGTCCC 59.249 60.000 0.00 0.00 33.44 4.46
2703 3107 5.066764 GTGGTTCTGTTAGTTTTGTGGCTAA 59.933 40.000 0.00 0.00 0.00 3.09
2745 3149 7.291566 ACTAGTAGGAGTGAGCTATTGTATGT 58.708 38.462 1.45 0.00 0.00 2.29
2883 3289 2.320781 GAGCTTAGCAGGTATGAGGGA 58.679 52.381 7.07 0.00 0.00 4.20
2899 3305 4.785301 TGAGGGAGAATGATTGATTGGTC 58.215 43.478 0.00 0.00 0.00 4.02
2917 3325 1.075542 TCGCGCATTCATCTCGTTTT 58.924 45.000 8.75 0.00 0.00 2.43
2960 3368 8.614346 CATGAACTTGTTGATTTGTTTTTCCAT 58.386 29.630 0.00 0.00 0.00 3.41
2968 3376 8.260818 TGTTGATTTGTTTTTCCATCACCTTAA 58.739 29.630 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.338126 ATCACGGTCGTGGTCTCGC 62.338 63.158 21.05 0.00 45.43 5.03
9 10 2.875485 ATCACGGTCGTGGTCTCG 59.125 61.111 21.05 0.00 45.43 4.04
15 16 1.139816 CCATCGTGATCACGGTCGTG 61.140 60.000 39.34 30.43 46.40 4.35
23 24 1.134699 GGCTTCACTCCATCGTGATCA 60.135 52.381 0.00 0.00 42.91 2.92
229 237 2.287644 GCAATTTGTTGCTTGGTTGGTC 59.712 45.455 5.93 0.00 44.15 4.02
373 381 1.817099 GAATCCAGCTGCCTCCACG 60.817 63.158 8.66 0.00 0.00 4.94
374 382 1.452833 GGAATCCAGCTGCCTCCAC 60.453 63.158 8.66 0.00 0.00 4.02
375 383 3.001514 GGAATCCAGCTGCCTCCA 58.998 61.111 8.66 0.00 0.00 3.86
376 384 2.203126 CGGAATCCAGCTGCCTCC 60.203 66.667 8.66 12.12 0.00 4.30
377 385 2.203126 CCGGAATCCAGCTGCCTC 60.203 66.667 8.66 3.75 0.00 4.70
602 645 1.033746 AGCACAAGCACAAGCACAGT 61.034 50.000 0.00 0.00 45.49 3.55
609 652 0.179132 CAGCACAAGCACAAGCACAA 60.179 50.000 0.00 0.00 45.49 3.33
658 723 4.173924 GCCCTGCCTGCTCCTCTC 62.174 72.222 0.00 0.00 0.00 3.20
660 725 1.987807 TATTGCCCTGCCTGCTCCTC 61.988 60.000 0.00 0.00 0.00 3.71
661 726 1.574526 TTATTGCCCTGCCTGCTCCT 61.575 55.000 0.00 0.00 0.00 3.69
778 843 0.949105 AGTAAAAGTCCGCGTGGCAG 60.949 55.000 11.05 0.00 34.14 4.85
819 884 1.629297 GATGAGGAGGGAGGAGGGT 59.371 63.158 0.00 0.00 0.00 4.34
820 885 1.152139 GGATGAGGAGGGAGGAGGG 60.152 68.421 0.00 0.00 0.00 4.30
823 888 1.219213 GAAGAGGATGAGGAGGGAGGA 59.781 57.143 0.00 0.00 0.00 3.71
835 907 1.629464 GGGAAGGGAAGGGAAGAGGAT 60.629 57.143 0.00 0.00 0.00 3.24
836 908 0.253207 GGGAAGGGAAGGGAAGAGGA 60.253 60.000 0.00 0.00 0.00 3.71
838 910 1.492599 GATGGGAAGGGAAGGGAAGAG 59.507 57.143 0.00 0.00 0.00 2.85
839 911 1.596496 GATGGGAAGGGAAGGGAAGA 58.404 55.000 0.00 0.00 0.00 2.87
840 912 0.181350 CGATGGGAAGGGAAGGGAAG 59.819 60.000 0.00 0.00 0.00 3.46
841 913 0.252974 TCGATGGGAAGGGAAGGGAA 60.253 55.000 0.00 0.00 0.00 3.97
842 914 0.981277 GTCGATGGGAAGGGAAGGGA 60.981 60.000 0.00 0.00 0.00 4.20
843 915 1.527370 GTCGATGGGAAGGGAAGGG 59.473 63.158 0.00 0.00 0.00 3.95
844 916 1.144057 CGTCGATGGGAAGGGAAGG 59.856 63.158 0.00 0.00 0.00 3.46
849 921 2.107141 GCCTCGTCGATGGGAAGG 59.893 66.667 5.94 6.28 0.00 3.46
1377 1775 3.565214 TGGGTGGAGCAGGCGAAA 61.565 61.111 0.00 0.00 0.00 3.46
1580 1978 1.298041 GGTTTTGCACCACGTCGTG 60.298 57.895 18.54 18.54 46.42 4.35
1581 1979 3.103875 GGTTTTGCACCACGTCGT 58.896 55.556 0.00 0.00 46.42 4.34
1616 2014 1.806461 GCGTCAGATCCGGGAGCATA 61.806 60.000 15.64 0.00 0.00 3.14
1653 2053 2.544359 CTACACACGCACGCACAC 59.456 61.111 0.00 0.00 0.00 3.82
1658 2058 1.518572 GATCCCCTACACACGCACG 60.519 63.158 0.00 0.00 0.00 5.34
2259 2659 2.039613 CTCCCAAGAAGAGCTGGAAAGT 59.960 50.000 0.00 0.00 0.00 2.66
2394 2794 4.009675 TGTCAATTGAAGATCCGGAAAGG 58.990 43.478 9.01 0.00 42.97 3.11
2517 2918 8.206867 TGTGCAAGACAGATAAATAGAAGCTAT 58.793 33.333 0.00 0.00 0.00 2.97
2615 3019 2.618053 CACGAGCTACCAAGTAAAGGG 58.382 52.381 0.00 0.00 0.00 3.95
2616 3020 2.232941 TCCACGAGCTACCAAGTAAAGG 59.767 50.000 0.00 0.00 0.00 3.11
2715 3119 8.852135 ACAATAGCTCACTCCTACTAGTAAATC 58.148 37.037 3.76 0.00 0.00 2.17
2719 3123 8.438373 ACATACAATAGCTCACTCCTACTAGTA 58.562 37.037 1.89 1.89 0.00 1.82
2720 3124 7.291566 ACATACAATAGCTCACTCCTACTAGT 58.708 38.462 0.00 0.00 0.00 2.57
2721 3125 7.753309 ACATACAATAGCTCACTCCTACTAG 57.247 40.000 0.00 0.00 0.00 2.57
2722 3126 7.778382 TGAACATACAATAGCTCACTCCTACTA 59.222 37.037 0.00 0.00 0.00 1.82
2723 3127 6.607600 TGAACATACAATAGCTCACTCCTACT 59.392 38.462 0.00 0.00 0.00 2.57
2724 3128 6.806751 TGAACATACAATAGCTCACTCCTAC 58.193 40.000 0.00 0.00 0.00 3.18
2745 3149 2.199208 TGCATTCCTCTCTCCCATGAA 58.801 47.619 0.00 0.00 0.00 2.57
2806 3212 2.026157 GTCGCATGGCTCGATCGA 59.974 61.111 18.32 18.32 38.29 3.59
2883 3289 1.331756 GCGCGACCAATCAATCATTCT 59.668 47.619 12.10 0.00 0.00 2.40
2899 3305 1.882198 AAAAACGAGATGAATGCGCG 58.118 45.000 0.00 0.00 34.71 6.86
2917 3325 5.716228 AGTTCATGCCATAGATGACCAAAAA 59.284 36.000 0.00 0.00 29.39 1.94
2922 3330 4.202441 ACAAGTTCATGCCATAGATGACC 58.798 43.478 0.00 0.00 29.39 4.02
3019 3430 7.612668 ACTTCATCATTTCTTGTGAGATGAG 57.387 36.000 0.00 0.00 43.82 2.90
3082 3496 5.450592 TTGAAATGAACTGCAATGCTACA 57.549 34.783 6.82 1.91 0.00 2.74
3086 3500 5.408356 AGAGATTGAAATGAACTGCAATGC 58.592 37.500 0.00 0.00 31.65 3.56


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

AutoCloner maintained by Alex Coulton.