Multiple sequence alignment - TraesCS3D01G121000

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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 TraesCS3D01G121000 chr3D 100.000 5189 0 0 956 6144 76938868 76933680 0.000000e+00 9583.0
1 TraesCS3D01G121000 chr3D 100.000 714 0 0 1 714 76939823 76939110 0.000000e+00 1319.0
2 TraesCS3D01G121000 chr3D 93.478 92 6 0 4205 4296 57504476 57504567 2.990000e-28 137.0
3 TraesCS3D01G121000 chr3D 90.196 102 10 0 111 212 47776323 47776222 3.860000e-27 134.0
4 TraesCS3D01G121000 chr3D 87.302 63 6 1 4725 4785 612296027 612295965 3.070000e-08 71.3
5 TraesCS3D01G121000 chr3A 95.038 2116 66 13 2530 4639 91028700 91026618 0.000000e+00 3290.0
6 TraesCS3D01G121000 chr3A 92.960 1463 43 21 4723 6144 91026620 91025177 0.000000e+00 2076.0
7 TraesCS3D01G121000 chr3A 90.871 1424 81 29 991 2398 91030170 91028780 0.000000e+00 1864.0
8 TraesCS3D01G121000 chr3A 91.205 307 12 3 407 713 91031101 91030810 2.670000e-108 403.0
9 TraesCS3D01G121000 chr3A 90.909 220 19 1 1 220 91031662 91031444 1.670000e-75 294.0
10 TraesCS3D01G121000 chr3A 87.786 131 12 4 4723 4849 137577210 137577080 3.840000e-32 150.0
11 TraesCS3D01G121000 chr3A 91.667 96 8 0 4209 4304 569232141 569232236 3.860000e-27 134.0
12 TraesCS3D01G121000 chr3A 89.320 103 11 0 4205 4307 10305761 10305863 5.000000e-26 130.0
13 TraesCS3D01G121000 chr3A 79.221 154 21 7 4505 4649 718060375 718060526 5.070000e-16 97.1
14 TraesCS3D01G121000 chr3B 92.398 2118 91 25 2530 4639 123477044 123474989 0.000000e+00 2955.0
15 TraesCS3D01G121000 chr3B 91.994 1449 89 21 956 2398 123478551 123477124 0.000000e+00 2008.0
16 TraesCS3D01G121000 chr3B 89.047 1333 50 34 4830 6111 123474952 123473665 0.000000e+00 1565.0
17 TraesCS3D01G121000 chr3B 93.375 317 14 3 401 713 123478978 123478665 4.340000e-126 462.0
18 TraesCS3D01G121000 chr3B 88.398 362 31 7 1 356 123570018 123569662 5.690000e-115 425.0
19 TraesCS3D01G121000 chr3B 94.495 109 6 0 2426 2534 4149876 4149984 1.060000e-37 169.0
20 TraesCS3D01G121000 chr3B 94.495 109 6 0 2426 2534 4967902 4968010 1.060000e-37 169.0
21 TraesCS3D01G121000 chr3B 85.156 128 16 3 4515 4639 74334349 74334476 1.800000e-25 128.0
22 TraesCS3D01G121000 chr3B 82.979 94 10 5 4630 4722 252927633 252927721 5.110000e-11 80.5
23 TraesCS3D01G121000 chr3B 82.000 100 12 5 4630 4728 444685680 444685586 5.110000e-11 80.5
24 TraesCS3D01G121000 chr3B 100.000 33 0 0 2395 2427 123477073 123477041 1.850000e-05 62.1
25 TraesCS3D01G121000 chr7D 82.919 603 69 9 2577 3174 369910841 369911414 4.250000e-141 512.0
26 TraesCS3D01G121000 chr7D 83.794 506 51 13 2650 3154 65531121 65531596 9.390000e-123 451.0
27 TraesCS3D01G121000 chr7D 92.562 121 9 0 2422 2542 161297221 161297101 2.280000e-39 174.0
28 TraesCS3D01G121000 chr7D 93.805 113 6 1 2422 2533 83801908 83802020 1.060000e-37 169.0
29 TraesCS3D01G121000 chr1D 84.690 516 50 12 2642 3154 378101946 378102435 7.160000e-134 488.0
30 TraesCS3D01G121000 chr1D 94.444 108 6 0 2426 2533 475814991 475815098 3.810000e-37 167.0
31 TraesCS3D01G121000 chr1D 89.524 105 11 0 108 212 300057995 300058099 3.860000e-27 134.0
32 TraesCS3D01G121000 chr7A 85.507 345 41 7 2577 2916 410410556 410410896 9.800000e-93 351.0
33 TraesCS3D01G121000 chr7A 90.291 103 10 0 4205 4307 180659512 180659614 1.070000e-27 135.0
34 TraesCS3D01G121000 chr7A 84.252 127 17 2 4723 4846 561386376 561386250 3.010000e-23 121.0
35 TraesCS3D01G121000 chr1A 95.536 112 5 0 2425 2536 19894865 19894976 4.890000e-41 180.0
36 TraesCS3D01G121000 chr1A 87.629 97 9 1 3826 3922 549045583 549045490 6.510000e-20 110.0
37 TraesCS3D01G121000 chr2D 95.370 108 5 0 2426 2533 194731001 194731108 8.190000e-39 172.0
38 TraesCS3D01G121000 chr2D 89.423 104 11 0 4204 4307 388818864 388818761 1.390000e-26 132.0
39 TraesCS3D01G121000 chr2D 86.517 89 9 2 4638 4726 591982750 591982665 1.820000e-15 95.3
40 TraesCS3D01G121000 chr2D 86.517 89 9 2 4638 4726 591997454 591997369 1.820000e-15 95.3
41 TraesCS3D01G121000 chrUn 91.667 120 7 2 2414 2533 74611450 74611566 4.930000e-36 163.0
42 TraesCS3D01G121000 chrUn 86.517 89 9 2 4638 4726 418303944 418304029 1.820000e-15 95.3
43 TraesCS3D01G121000 chr6A 92.920 113 7 1 2425 2536 205107072 205107184 4.930000e-36 163.0
44 TraesCS3D01G121000 chr6A 86.667 105 14 0 108 212 58322936 58322832 3.890000e-22 117.0
45 TraesCS3D01G121000 chr6A 86.667 105 14 0 108 212 478851357 478851461 3.890000e-22 117.0
46 TraesCS3D01G121000 chr1B 88.489 139 11 5 4505 4639 349756621 349756484 4.930000e-36 163.0
47 TraesCS3D01G121000 chr1B 79.747 79 14 2 4725 4801 638884422 638884344 8.600000e-04 56.5
48 TraesCS3D01G121000 chr7B 87.770 139 13 4 4505 4639 2475571 2475709 6.370000e-35 159.0
49 TraesCS3D01G121000 chr7B 89.623 106 9 1 4204 4307 83912862 83912757 3.860000e-27 134.0
50 TraesCS3D01G121000 chr7B 90.625 96 6 2 4631 4726 334772959 334772867 2.330000e-24 124.0
51 TraesCS3D01G121000 chr7B 92.857 42 3 0 4687 4728 678540767 678540726 1.850000e-05 62.1
52 TraesCS3D01G121000 chr5D 90.385 104 10 0 4204 4307 282007011 282007114 2.990000e-28 137.0
53 TraesCS3D01G121000 chr5D 89.524 105 11 0 108 212 505989401 505989505 3.860000e-27 134.0
54 TraesCS3D01G121000 chr5A 84.286 140 18 4 4504 4639 573080505 573080366 3.860000e-27 134.0
55 TraesCS3D01G121000 chr5A 86.792 106 13 1 108 212 374578121 374578226 3.890000e-22 117.0
56 TraesCS3D01G121000 chr5A 81.119 143 22 3 4707 4846 41376109 41376249 6.510000e-20 110.0
57 TraesCS3D01G121000 chr5A 89.130 92 5 4 4638 4728 44998154 44998067 6.510000e-20 110.0
58 TraesCS3D01G121000 chr5A 100.000 28 0 0 3790 3817 111595004 111594977 1.100000e-02 52.8
59 TraesCS3D01G121000 chr2A 87.619 105 13 0 108 212 300328604 300328708 8.360000e-24 122.0
60 TraesCS3D01G121000 chr2A 79.592 147 22 6 4702 4846 699805523 699805663 1.410000e-16 99.0
61 TraesCS3D01G121000 chr6D 86.486 111 12 3 4505 4613 53884257 53884366 1.080000e-22 119.0
62 TraesCS3D01G121000 chr4A 82.482 137 21 3 4506 4639 437488131 437487995 3.890000e-22 117.0
63 TraesCS3D01G121000 chr4A 83.721 86 9 4 4637 4722 715190210 715190290 6.600000e-10 76.8
64 TraesCS3D01G121000 chr4A 85.000 60 6 3 4741 4798 733451018 733451076 2.390000e-04 58.4
65 TraesCS3D01G121000 chr6B 82.707 133 19 4 4723 4851 234148167 234148035 1.400000e-21 115.0
66 TraesCS3D01G121000 chr2B 82.540 126 20 2 4723 4846 614246210 614246335 6.510000e-20 110.0
67 TraesCS3D01G121000 chr2B 100.000 28 0 0 3790 3817 725623408 725623381 1.100000e-02 52.8
68 TraesCS3D01G121000 chr4D 95.833 48 1 1 4631 4678 282196995 282196949 6.600000e-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 TraesCS3D01G121000 chr3D 76933680 76939823 6143 True 5451.00 9583 100.0000 1 6144 2 chr3D.!!$R3 6143
1 TraesCS3D01G121000 chr3A 91025177 91031662 6485 True 1585.40 3290 92.1966 1 6144 5 chr3A.!!$R2 6143
2 TraesCS3D01G121000 chr3B 123473665 123478978 5313 True 1410.42 2955 93.3628 401 6111 5 chr3B.!!$R3 5710
3 TraesCS3D01G121000 chr7D 369910841 369911414 573 False 512.00 512 82.9190 2577 3174 1 chr7D.!!$F3 597


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
503 737 0.040157 CACAACCGTGGATGCTGTTG 60.040 55.0 11.26 11.26 42.8 3.33 F
623 869 0.095589 CCTTCGTCTCGTCTCTCGTG 59.904 60.0 0.00 0.00 40.8 4.35 F
1331 1953 0.459585 GCCACCGATTAGTTCAGCGA 60.460 55.0 0.00 0.00 0.0 4.93 F
2731 3422 0.171231 GCGGCAATCTTTCCAAGGAC 59.829 55.0 0.00 0.00 0.0 3.85 F
3252 3947 0.745845 GTCAGAGATTGCACCGCCAT 60.746 55.0 0.00 0.00 0.0 4.40 F
4090 4809 0.534412 AGCTCCAAGATGTCGGACTG 59.466 55.0 9.88 0.00 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1391 2013 0.234106 CTAATCAAGCATGAGCCGCG 59.766 55.000 0.00 0.00 43.56 6.46 R
2211 2848 1.086634 CGAGGAAGCAGCTAAGCCAC 61.087 60.000 0.00 0.00 34.23 5.01 R
3053 3748 2.121506 TCTGGGAACAAGGGGCCT 60.122 61.111 0.84 0.00 42.06 5.19 R
3922 4638 0.105964 TGGTTGCCAGCTGGGTAAAA 60.106 50.000 33.46 9.56 43.32 1.52 R
4321 5044 1.327303 AGATCAGGAGAAGCGCCTAG 58.673 55.000 2.29 0.00 31.11 3.02 R
5655 6418 0.108945 GCTGCTGTTGGGAATTCTGC 60.109 55.000 5.23 2.03 0.00 4.26 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)



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AutoCloner maintained by Alex Coulton.