Multiple sequence alignment - TraesCS2D01G282900

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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 TraesCS2D01G282900 chr2D 100.000 3919 0 0 1 3919 355688815 355684897 0.000000e+00 7238.0
1 TraesCS2D01G282900 chr2D 91.892 74 4 2 2617 2690 643314390 643314461 6.930000e-18 102.0
2 TraesCS2D01G282900 chr2D 95.745 47 0 1 3516 3562 355685255 355685211 1.510000e-09 75.0
3 TraesCS2D01G282900 chr2D 95.745 47 0 1 3561 3605 355685300 355685254 1.510000e-09 75.0
4 TraesCS2D01G282900 chr2D 97.674 43 1 0 2619 2661 413260014 413259972 1.510000e-09 75.0
5 TraesCS2D01G282900 chr2A 95.278 3113 77 26 824 3900 475881158 475878080 0.000000e+00 4870.0
6 TraesCS2D01G282900 chr2A 83.297 455 56 12 1 454 754043584 754044019 6.100000e-108 401.0
7 TraesCS2D01G282900 chr2A 95.745 47 1 1 3516 3562 475878420 475878375 1.510000e-09 75.0
8 TraesCS2D01G282900 chr2A 95.745 47 0 1 3561 3605 475878465 475878419 1.510000e-09 75.0
9 TraesCS2D01G282900 chr2B 93.681 2184 75 22 1418 3561 423668952 423666792 0.000000e+00 3210.0
10 TraesCS2D01G282900 chr2B 95.902 610 11 5 824 1419 423669622 423669013 0.000000e+00 976.0
11 TraesCS2D01G282900 chr2B 88.785 642 49 10 1 640 794550520 794551140 0.000000e+00 765.0
12 TraesCS2D01G282900 chr2B 92.486 346 23 2 3561 3904 423666837 423666493 3.520000e-135 492.0
13 TraesCS2D01G282900 chr2B 79.804 510 63 17 1 506 142948957 142949430 6.270000e-88 335.0
14 TraesCS2D01G282900 chr2B 100.000 44 0 0 2620 2663 115903419 115903462 9.030000e-12 82.4
15 TraesCS2D01G282900 chr4B 96.498 771 25 2 1 770 565089069 565088300 0.000000e+00 1273.0
16 TraesCS2D01G282900 chr7B 94.618 706 37 1 1 706 735034766 735034062 0.000000e+00 1092.0
17 TraesCS2D01G282900 chr7B 77.265 607 85 37 20 601 394833471 394832893 1.370000e-79 307.0
18 TraesCS2D01G282900 chr3B 80.946 803 98 26 2 790 762602492 762601731 5.640000e-163 584.0
19 TraesCS2D01G282900 chr3B 96.875 32 0 1 2661 2691 13772393 13772362 7.000000e-03 52.8
20 TraesCS2D01G282900 chr5B 87.632 380 46 1 1 379 55229765 55230144 1.290000e-119 440.0
21 TraesCS2D01G282900 chr5B 83.095 349 47 9 1 338 8025446 8025099 1.370000e-79 307.0
22 TraesCS2D01G282900 chr7D 83.848 421 66 2 1 419 244142614 244142194 2.190000e-107 399.0
23 TraesCS2D01G282900 chr7D 100.000 43 0 0 2619 2661 574037718 574037676 3.250000e-11 80.5
24 TraesCS2D01G282900 chr7A 82.673 202 35 0 157 358 448437540 448437339 3.110000e-41 180.0
25 TraesCS2D01G282900 chr7A 97.674 43 1 0 2619 2661 39288411 39288369 1.510000e-09 75.0
26 TraesCS2D01G282900 chr7A 100.000 29 0 0 3891 3919 386394958 386394986 2.000000e-03 54.7
27 TraesCS2D01G282900 chr7A 100.000 28 0 0 2664 2691 713877061 713877034 7.000000e-03 52.8
28 TraesCS2D01G282900 chr5A 92.647 68 3 1 2625 2690 608338089 608338156 3.220000e-16 97.1
29 TraesCS2D01G282900 chr4D 77.576 165 23 10 625 786 132931325 132931478 1.940000e-13 87.9
30 TraesCS2D01G282900 chr6A 94.000 50 2 1 2614 2663 594988189 594988237 1.510000e-09 75.0
31 TraesCS2D01G282900 chrUn 96.774 31 1 0 2661 2691 378256997 378257027 7.000000e-03 52.8


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 TraesCS2D01G282900 chr2D 355684897 355688815 3918 True 2462.666667 7238 97.163333 1 3919 3 chr2D.!!$R2 3918
1 TraesCS2D01G282900 chr2A 475878080 475881158 3078 True 1673.333333 4870 95.589333 824 3900 3 chr2A.!!$R1 3076
2 TraesCS2D01G282900 chr2B 423666493 423669622 3129 True 1559.333333 3210 94.023000 824 3904 3 chr2B.!!$R1 3080
3 TraesCS2D01G282900 chr2B 794550520 794551140 620 False 765.000000 765 88.785000 1 640 1 chr2B.!!$F3 639
4 TraesCS2D01G282900 chr4B 565088300 565089069 769 True 1273.000000 1273 96.498000 1 770 1 chr4B.!!$R1 769
5 TraesCS2D01G282900 chr7B 735034062 735034766 704 True 1092.000000 1092 94.618000 1 706 1 chr7B.!!$R2 705
6 TraesCS2D01G282900 chr7B 394832893 394833471 578 True 307.000000 307 77.265000 20 601 1 chr7B.!!$R1 581
7 TraesCS2D01G282900 chr3B 762601731 762602492 761 True 584.000000 584 80.946000 2 790 1 chr3B.!!$R2 788

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
729 791 0.597637 GCATACGTGGTGGGATCGAG 60.598 60.000 0.00 0.0 0.0 4.04 F
1416 1494 0.105964 CCGTGTGTGAACCTGAGGAA 59.894 55.000 4.99 0.0 0.0 3.36 F
2136 2293 2.738846 GTCGTTGAATGTCAGATGCACT 59.261 45.455 0.00 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2250 2408 1.748493 ACTTCAGGTTTGCAGCGAAAA 59.252 42.857 0.0 0.0 0.00 2.29 R
2254 2412 1.758783 GAAACTTCAGGTTTGCAGCG 58.241 50.000 0.0 0.0 46.77 5.18 R
3885 4076 1.133792 AGGGAGTAATTGGGAATGGCG 60.134 52.381 0.0 0.0 0.00 5.69 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
207 209 4.740822 GGATGCCCCGGTTGCAGT 62.741 66.667 19.14 9.19 42.92 4.40
298 300 3.745803 GCTGCTGGCTTCTGGCAC 61.746 66.667 0.00 0.00 44.10 5.01
495 548 3.023735 GATGGGAGGGGCAAGGGT 61.024 66.667 0.00 0.00 0.00 4.34
729 791 0.597637 GCATACGTGGTGGGATCGAG 60.598 60.000 0.00 0.00 0.00 4.04
786 850 2.215196 GCCGTCTACAAGTGTTTTCCA 58.785 47.619 0.00 0.00 0.00 3.53
787 851 2.812011 GCCGTCTACAAGTGTTTTCCAT 59.188 45.455 0.00 0.00 0.00 3.41
788 852 3.998341 GCCGTCTACAAGTGTTTTCCATA 59.002 43.478 0.00 0.00 0.00 2.74
789 853 4.634443 GCCGTCTACAAGTGTTTTCCATAT 59.366 41.667 0.00 0.00 0.00 1.78
790 854 5.123344 GCCGTCTACAAGTGTTTTCCATATT 59.877 40.000 0.00 0.00 0.00 1.28
791 855 6.349033 GCCGTCTACAAGTGTTTTCCATATTT 60.349 38.462 0.00 0.00 0.00 1.40
792 856 7.590279 CCGTCTACAAGTGTTTTCCATATTTT 58.410 34.615 0.00 0.00 0.00 1.82
793 857 8.079809 CCGTCTACAAGTGTTTTCCATATTTTT 58.920 33.333 0.00 0.00 0.00 1.94
813 877 5.596836 TTTTTGAGCAACTTTGGAGACAT 57.403 34.783 0.00 0.00 42.32 3.06
814 878 6.707440 TTTTTGAGCAACTTTGGAGACATA 57.293 33.333 0.00 0.00 42.32 2.29
815 879 6.899393 TTTTGAGCAACTTTGGAGACATAT 57.101 33.333 0.00 0.00 42.32 1.78
816 880 6.899393 TTTGAGCAACTTTGGAGACATATT 57.101 33.333 0.00 0.00 42.32 1.28
817 881 6.899393 TTGAGCAACTTTGGAGACATATTT 57.101 33.333 0.00 0.00 42.32 1.40
818 882 6.899393 TGAGCAACTTTGGAGACATATTTT 57.101 33.333 0.00 0.00 42.32 1.82
819 883 7.288810 TGAGCAACTTTGGAGACATATTTTT 57.711 32.000 0.00 0.00 42.32 1.94
1416 1494 0.105964 CCGTGTGTGAACCTGAGGAA 59.894 55.000 4.99 0.00 0.00 3.36
1503 1643 4.636206 GGGCCTATTTGAAACTAGTGAGTG 59.364 45.833 0.84 0.00 35.52 3.51
1884 2041 9.516314 GTTTCCACTTATATTAAAATCAGTGCC 57.484 33.333 0.00 0.00 32.00 5.01
1916 2073 3.959943 AGGTTCACATTTTGTTACGTGC 58.040 40.909 0.00 0.00 0.00 5.34
2136 2293 2.738846 GTCGTTGAATGTCAGATGCACT 59.261 45.455 0.00 0.00 0.00 4.40
2234 2392 8.774546 TTAAAATCCCATGACAAATATGCCTA 57.225 30.769 0.00 0.00 0.00 3.93
2238 2396 6.713762 TCCCATGACAAATATGCCTAAAAG 57.286 37.500 0.00 0.00 0.00 2.27
2287 2445 0.474660 AGTTTCCCAGACAGAGCCCT 60.475 55.000 0.00 0.00 0.00 5.19
2473 2631 9.191995 CTTTTGAATTTACCAAGGTTGATGTAC 57.808 33.333 0.00 0.00 0.00 2.90
2766 2925 7.021196 CCGTTCTTTTAATCCAGTAACATGTG 58.979 38.462 0.00 0.00 0.00 3.21
3056 3236 7.231317 ACCAGATCACTGTTACAAAATTGTGAT 59.769 33.333 14.25 14.25 40.88 3.06
3113 3294 1.075542 CGAGTGGCGTTAAATGCAGA 58.924 50.000 0.00 0.00 34.64 4.26
3169 3350 0.258774 GGACCCAACATGGCTATGGT 59.741 55.000 15.11 4.56 38.66 3.55
3180 3361 2.770447 TGGCTATGGTCATAACAGGGA 58.230 47.619 0.00 0.00 0.00 4.20
3211 3392 6.150396 TCTATTTTCTCTGAGGATTCGACC 57.850 41.667 4.59 0.00 0.00 4.79
3212 3393 3.611766 TTTTCTCTGAGGATTCGACCC 57.388 47.619 4.59 0.00 0.00 4.46
3458 3643 4.321718 CATGAGAGTTTCAGAGCCTTTGA 58.678 43.478 0.00 0.00 39.68 2.69
3506 3696 7.984422 ACTTCTGTTCACATTCACATGATAA 57.016 32.000 0.00 0.00 34.11 1.75
3523 3713 5.128033 TGATAAAGGATTCCTGCCATTCA 57.872 39.130 5.84 3.36 32.13 2.57
3720 3911 4.944962 TGCATTTACGTCCAAAGATCAG 57.055 40.909 0.00 0.00 0.00 2.90
3744 3935 4.097714 CGGATCATCGAACAACCAATTTG 58.902 43.478 0.00 0.00 41.49 2.32
3773 3964 3.937706 AGTAGCTCATGTGAACAATCTGC 59.062 43.478 0.00 0.00 0.00 4.26
3775 3966 2.747989 AGCTCATGTGAACAATCTGCTG 59.252 45.455 0.00 0.00 0.00 4.41
3841 4032 6.662755 AGAATATGCTGACCAAATTCTACCA 58.337 36.000 0.00 0.00 35.64 3.25
3885 4076 5.048846 ACCTGATATGGTGTTCATAACCC 57.951 43.478 0.00 0.00 41.23 4.11
3904 4095 1.318576 CGCCATTCCCAATTACTCCC 58.681 55.000 0.00 0.00 0.00 4.30
3905 4096 1.133792 CGCCATTCCCAATTACTCCCT 60.134 52.381 0.00 0.00 0.00 4.20
3906 4097 2.587522 GCCATTCCCAATTACTCCCTC 58.412 52.381 0.00 0.00 0.00 4.30
3907 4098 2.175715 GCCATTCCCAATTACTCCCTCT 59.824 50.000 0.00 0.00 0.00 3.69
3908 4099 3.825328 CCATTCCCAATTACTCCCTCTG 58.175 50.000 0.00 0.00 0.00 3.35
3909 4100 3.203040 CCATTCCCAATTACTCCCTCTGT 59.797 47.826 0.00 0.00 0.00 3.41
3910 4101 4.455606 CATTCCCAATTACTCCCTCTGTC 58.544 47.826 0.00 0.00 0.00 3.51
3911 4102 2.478292 TCCCAATTACTCCCTCTGTCC 58.522 52.381 0.00 0.00 0.00 4.02
3912 4103 1.490910 CCCAATTACTCCCTCTGTCCC 59.509 57.143 0.00 0.00 0.00 4.46
3913 4104 2.196595 CCAATTACTCCCTCTGTCCCA 58.803 52.381 0.00 0.00 0.00 4.37
3914 4105 2.576191 CCAATTACTCCCTCTGTCCCAA 59.424 50.000 0.00 0.00 0.00 4.12
3915 4106 3.010138 CCAATTACTCCCTCTGTCCCAAA 59.990 47.826 0.00 0.00 0.00 3.28
3916 4107 4.508405 CCAATTACTCCCTCTGTCCCAAAA 60.508 45.833 0.00 0.00 0.00 2.44
3917 4108 5.264395 CAATTACTCCCTCTGTCCCAAAAT 58.736 41.667 0.00 0.00 0.00 1.82
3918 4109 6.423182 CAATTACTCCCTCTGTCCCAAAATA 58.577 40.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 137 0.892755 CATGCATTGTGCTGGAACCT 59.107 50.000 0.00 0.00 45.31 3.50
192 194 0.540830 TTTTACTGCAACCGGGGCAT 60.541 50.000 21.26 14.29 41.06 4.40
207 209 1.143277 TGGAACCACGAAGCCCTTTTA 59.857 47.619 0.00 0.00 0.00 1.52
298 300 2.745884 TGGAATCACGGCGGCAAG 60.746 61.111 13.24 0.00 0.00 4.01
495 548 2.115052 ATGGCCGCTCAACCAACA 59.885 55.556 0.00 0.00 39.96 3.33
791 855 5.596836 ATGTCTCCAAAGTTGCTCAAAAA 57.403 34.783 0.00 0.00 0.00 1.94
792 856 6.899393 ATATGTCTCCAAAGTTGCTCAAAA 57.101 33.333 0.00 0.00 0.00 2.44
793 857 6.899393 AATATGTCTCCAAAGTTGCTCAAA 57.101 33.333 0.00 0.00 0.00 2.69
794 858 6.899393 AAATATGTCTCCAAAGTTGCTCAA 57.101 33.333 0.00 0.00 0.00 3.02
795 859 6.899393 AAAATATGTCTCCAAAGTTGCTCA 57.101 33.333 0.00 0.00 0.00 4.26
822 886 7.395772 TCCAGCACCATTTATATGTCTCAAAAA 59.604 33.333 0.00 0.00 0.00 1.94
936 1000 0.527385 CTTAGCTCAGTCCTCGCAGC 60.527 60.000 0.00 0.00 0.00 5.25
937 1001 0.527385 GCTTAGCTCAGTCCTCGCAG 60.527 60.000 0.00 0.00 0.00 5.18
938 1002 0.967887 AGCTTAGCTCAGTCCTCGCA 60.968 55.000 0.00 0.00 30.62 5.10
939 1003 1.813192 AGCTTAGCTCAGTCCTCGC 59.187 57.895 0.00 0.00 30.62 5.03
1416 1494 8.429237 TGTACCATTGAAATGTCCCTAATTTT 57.571 30.769 2.55 0.00 34.60 1.82
1503 1643 9.523755 CTTGAGTCAGACAAGAAAAGGCACTTC 62.524 44.444 2.66 0.00 46.61 3.01
1884 2041 6.148811 ACAAAATGTGAACCTAGTAATCACGG 59.851 38.462 12.40 0.00 44.95 4.94
2136 2293 7.695055 TCTCATTCAAAATAGGTTACTTGGGA 58.305 34.615 0.00 0.00 0.00 4.37
2211 2369 7.673641 TTAGGCATATTTGTCATGGGATTTT 57.326 32.000 0.00 0.00 0.00 1.82
2217 2375 7.546358 TGTTCTTTTAGGCATATTTGTCATGG 58.454 34.615 0.00 0.00 0.00 3.66
2250 2408 1.748493 ACTTCAGGTTTGCAGCGAAAA 59.252 42.857 0.00 0.00 0.00 2.29
2254 2412 1.758783 GAAACTTCAGGTTTGCAGCG 58.241 50.000 0.00 0.00 46.77 5.18
2287 2445 7.975616 CAGAACCAAGACAAAGAAATGAAAGAA 59.024 33.333 0.00 0.00 0.00 2.52
2473 2631 3.811722 TGTTGCATTGCTCTAAAGACG 57.188 42.857 10.49 0.00 0.00 4.18
2551 2709 6.382919 AGTGATTGCTAGGGGTACTTAAAA 57.617 37.500 0.00 0.00 0.00 1.52
2766 2925 8.173130 CCTTACCAGAAAAATGTACGTTATGTC 58.827 37.037 0.00 0.00 0.00 3.06
2833 2992 4.096382 TGAGGAGTTTCAGCTGTTTGTTTC 59.904 41.667 14.67 5.51 0.00 2.78
3056 3236 2.772077 TAAGGGCAATACAGCACGAA 57.228 45.000 0.00 0.00 44.43 3.85
3113 3294 4.060205 ACGTGTTTCGGTTACTAGCAAAT 58.940 39.130 0.00 0.00 44.69 2.32
3458 3643 6.625532 AACATATTCTTTGGGCCATTCTTT 57.374 33.333 7.26 0.00 0.00 2.52
3506 3696 2.579860 AGAGTGAATGGCAGGAATCCTT 59.420 45.455 0.00 0.00 0.00 3.36
3523 3713 7.308830 GCATGAAGATGTTTCTTGGTTAAGAGT 60.309 37.037 0.00 0.00 42.34 3.24
3700 3891 4.492570 CGTCTGATCTTTGGACGTAAATGC 60.493 45.833 16.58 0.00 44.93 3.56
3720 3911 2.004583 TGGTTGTTCGATGATCCGTC 57.995 50.000 0.00 0.00 0.00 4.79
3744 3935 5.962433 TGTTCACATGAGCTACTAGTAACC 58.038 41.667 3.76 0.00 0.00 2.85
3775 3966 2.577911 GCCTGCGCAATTTCGAGC 60.578 61.111 13.05 1.99 34.03 5.03
3841 4032 8.793592 CAGGTATCTTTAACTTAAAGGTTGCTT 58.206 33.333 17.55 6.70 44.04 3.91
3885 4076 1.133792 AGGGAGTAATTGGGAATGGCG 60.134 52.381 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.