Multiple sequence alignment - TraesCS6B01G015200

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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 TraesCS6B01G015200 chr6B 100.000 4041 0 0 1 4041 9057063 9061103 0.000000e+00 7463.0
1 TraesCS6B01G015200 chr6B 89.368 1646 152 13 1598 3233 9034888 9036520 0.000000e+00 2049.0
2 TraesCS6B01G015200 chr6B 82.999 747 93 19 3293 4021 9036506 9037236 0.000000e+00 645.0
3 TraesCS6B01G015200 chr6B 83.735 664 78 19 2270 2919 9080345 9080992 5.780000e-168 601.0
4 TraesCS6B01G015200 chr6B 88.038 418 41 6 1748 2161 9079871 9080283 1.690000e-133 486.0
5 TraesCS6B01G015200 chr6B 81.395 602 70 20 468 1058 9034000 9034570 1.710000e-123 453.0
6 TraesCS6B01G015200 chr6B 90.476 105 10 0 3381 3485 214526805 214526701 5.450000e-29 139.0
7 TraesCS6B01G015200 chr6B 100.000 53 0 0 1079 1131 707195497 707195549 9.240000e-17 99.0
8 TraesCS6B01G015200 chr6A 92.487 1584 98 10 1661 3233 3773593 3772020 0.000000e+00 2246.0
9 TraesCS6B01G015200 chr6A 89.700 767 59 10 3293 4041 3772034 3771270 0.000000e+00 961.0
10 TraesCS6B01G015200 chr6A 83.866 657 82 14 2270 2919 3747034 3746395 4.470000e-169 604.0
11 TraesCS6B01G015200 chr6A 86.593 455 39 13 1723 2162 3747542 3747095 2.180000e-132 483.0
12 TraesCS6B01G015200 chr6A 78.431 612 67 23 478 1078 3774408 3773851 5.000000e-89 339.0
13 TraesCS6B01G015200 chr6A 81.597 288 44 3 610 897 3748437 3748159 3.140000e-56 230.0
14 TraesCS6B01G015200 chr6A 89.147 129 8 1 940 1062 3748082 3747954 5.410000e-34 156.0
15 TraesCS6B01G015200 chr6A 90.769 65 3 3 3231 3293 19834169 19834106 2.590000e-12 84.2
16 TraesCS6B01G015200 chr6D 90.737 1641 143 7 1598 3233 4722147 4720511 0.000000e+00 2180.0
17 TraesCS6B01G015200 chr6D 83.475 1059 132 22 1620 2654 3713433 3714472 0.000000e+00 946.0
18 TraesCS6B01G015200 chr6D 89.499 619 42 5 467 1064 3756604 3757220 0.000000e+00 761.0
19 TraesCS6B01G015200 chr6D 83.226 775 100 16 3293 4038 4720525 4719752 0.000000e+00 684.0
20 TraesCS6B01G015200 chr6D 88.224 535 50 5 555 1078 3712515 3713047 9.530000e-176 627.0
21 TraesCS6B01G015200 chr6D 83.683 668 85 12 2270 2917 3726982 3727645 3.450000e-170 608.0
22 TraesCS6B01G015200 chr6D 83.538 650 86 14 2270 2916 3740051 3740682 4.500000e-164 588.0
23 TraesCS6B01G015200 chr6D 85.210 453 47 11 1723 2161 3739543 3739989 7.970000e-122 448.0
24 TraesCS6B01G015200 chr6D 86.241 407 39 11 1 395 3756086 3756487 3.730000e-115 425.0
25 TraesCS6B01G015200 chr6D 80.000 525 68 20 468 987 4723059 4722567 1.790000e-93 353.0
26 TraesCS6B01G015200 chr6D 88.390 267 26 3 1896 2161 3726652 3726914 2.340000e-82 316.0
27 TraesCS6B01G015200 chr6D 82.007 289 47 3 610 897 3725645 3725929 1.450000e-59 241.0
28 TraesCS6B01G015200 chr6D 82.292 288 42 3 610 897 3738706 3738984 1.450000e-59 241.0
29 TraesCS6B01G015200 chr6D 89.759 166 16 1 1135 1300 3713036 3713200 1.140000e-50 211.0
30 TraesCS6B01G015200 chr6D 86.207 145 14 1 940 1078 3726006 3726150 7.000000e-33 152.0
31 TraesCS6B01G015200 chr6D 87.597 129 10 1 940 1062 3739061 3739189 1.170000e-30 145.0
32 TraesCS6B01G015200 chr6D 93.407 91 6 0 988 1078 4722530 4722440 7.050000e-28 135.0
33 TraesCS6B01G015200 chr6D 93.651 63 3 1 1393 1454 3726259 3726321 4.300000e-15 93.5
34 TraesCS6B01G015200 chr6D 93.443 61 2 2 3234 3293 349120377 349120436 5.560000e-14 89.8
35 TraesCS6B01G015200 chr6D 95.238 42 2 0 3009 3050 3727719 3727760 2.610000e-07 67.6
36 TraesCS6B01G015200 chr6D 97.297 37 1 0 785 821 3725934 3725970 3.370000e-06 63.9
37 TraesCS6B01G015200 chr6D 97.297 37 1 0 785 821 3738989 3739025 3.370000e-06 63.9
38 TraesCS6B01G015200 chrUn 83.381 1059 135 24 1620 2654 306428645 306429686 0.000000e+00 942.0
39 TraesCS6B01G015200 chrUn 88.224 535 50 5 555 1078 306427727 306428259 9.530000e-176 627.0
40 TraesCS6B01G015200 chrUn 88.636 220 20 4 3367 3582 371790579 371790797 3.100000e-66 263.0
41 TraesCS6B01G015200 chrUn 89.759 166 16 1 1135 1300 306428248 306428412 1.140000e-50 211.0
42 TraesCS6B01G015200 chrUn 91.803 61 3 2 3234 3293 230053952 230054011 2.590000e-12 84.2
43 TraesCS6B01G015200 chrUn 91.803 61 3 2 3234 3293 399444343 399444284 2.590000e-12 84.2
44 TraesCS6B01G015200 chr1A 77.676 654 94 36 2283 2903 32261198 32261832 6.430000e-93 351.0
45 TraesCS6B01G015200 chr1A 81.586 353 48 11 1793 2132 32260846 32261194 3.980000e-70 276.0
46 TraesCS6B01G015200 chr1A 93.846 65 2 2 1068 1131 1197245 1197308 3.320000e-16 97.1
47 TraesCS6B01G015200 chr1A 98.113 53 0 1 1080 1132 25787736 25787787 1.550000e-14 91.6
48 TraesCS6B01G015200 chr1D 76.923 663 112 29 2283 2921 33639648 33640293 5.000000e-89 339.0
49 TraesCS6B01G015200 chr1D 82.906 351 46 8 1793 2132 33639297 33639644 1.820000e-78 303.0
50 TraesCS6B01G015200 chr1D 87.273 220 23 4 3367 3582 177261406 177261624 3.120000e-61 246.0
51 TraesCS6B01G015200 chr3D 88.636 220 20 4 3367 3582 158931033 158931251 3.100000e-66 263.0
52 TraesCS6B01G015200 chr3D 91.935 62 3 2 3234 3294 457703524 457703464 7.200000e-13 86.1
53 TraesCS6B01G015200 chr3D 91.803 61 3 2 3234 3293 115754404 115754345 2.590000e-12 84.2
54 TraesCS6B01G015200 chr1B 81.143 350 44 11 1793 2132 51106167 51106504 1.110000e-65 261.0
55 TraesCS6B01G015200 chr1B 93.578 109 6 1 1297 1405 359902145 359902038 1.160000e-35 161.0
56 TraesCS6B01G015200 chr1B 80.000 145 22 7 561 704 51105031 51105169 2.570000e-17 100.0
57 TraesCS6B01G015200 chr5D 88.235 221 19 6 3367 3582 432406889 432406671 1.440000e-64 257.0
58 TraesCS6B01G015200 chr5D 87.273 220 23 4 3367 3582 196431067 196431285 3.120000e-61 246.0
59 TraesCS6B01G015200 chr4A 86.818 220 24 2 3367 3582 310768179 310768397 1.450000e-59 241.0
60 TraesCS6B01G015200 chr4A 98.148 54 0 1 1078 1131 603716917 603716969 4.300000e-15 93.5
61 TraesCS6B01G015200 chr3B 86.818 220 23 3 3367 3582 702969561 702969344 1.450000e-59 241.0
62 TraesCS6B01G015200 chr3B 87.288 118 15 0 3367 3484 519146873 519146990 7.050000e-28 135.0
63 TraesCS6B01G015200 chr3B 98.246 57 0 1 1075 1131 655312076 655312131 9.240000e-17 99.0
64 TraesCS6B01G015200 chr3B 100.000 52 0 0 1080 1131 304655 304706 3.320000e-16 97.1
65 TraesCS6B01G015200 chr3B 89.286 56 4 2 3764 3818 42378837 42378891 7.250000e-08 69.4
66 TraesCS6B01G015200 chr4D 95.192 104 4 1 1297 1400 110080934 110081036 3.230000e-36 163.0
67 TraesCS6B01G015200 chr4D 91.803 61 3 2 3234 3293 477264611 477264552 2.590000e-12 84.2
68 TraesCS6B01G015200 chr4D 100.000 32 0 0 3584 3615 35780848 35780879 4.360000e-05 60.2
69 TraesCS6B01G015200 chr3A 96.000 100 4 0 1295 1394 109150963 109150864 3.230000e-36 163.0
70 TraesCS6B01G015200 chr3A 89.091 55 6 0 3764 3818 33998157 33998211 7.250000e-08 69.4
71 TraesCS6B01G015200 chr2A 95.192 104 4 1 1291 1394 101846921 101847023 3.230000e-36 163.0
72 TraesCS6B01G015200 chr2A 88.189 127 10 4 1278 1402 660286754 660286877 3.250000e-31 147.0
73 TraesCS6B01G015200 chr2A 100.000 51 0 0 1081 1131 43282766 43282716 1.200000e-15 95.3
74 TraesCS6B01G015200 chr7B 94.286 105 5 1 1290 1394 562993169 562993066 4.180000e-35 159.0
75 TraesCS6B01G015200 chr7B 91.935 62 2 3 3235 3295 158380268 158380327 2.590000e-12 84.2
76 TraesCS6B01G015200 chr2B 94.286 105 5 1 1294 1398 230532419 230532522 4.180000e-35 159.0
77 TraesCS6B01G015200 chr2B 90.000 120 9 3 1293 1411 601206843 601206960 7.000000e-33 152.0
78 TraesCS6B01G015200 chr4B 90.435 115 11 0 1289 1403 646855887 646856001 7.000000e-33 152.0
79 TraesCS6B01G015200 chr7A 100.000 54 0 0 1078 1131 724297048 724297101 2.570000e-17 100.0
80 TraesCS6B01G015200 chr7A 100.000 53 0 0 1079 1131 594698076 594698024 9.240000e-17 99.0
81 TraesCS6B01G015200 chr7D 93.220 59 2 2 3236 3293 39581133 39581076 7.200000e-13 86.1


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 TraesCS6B01G015200 chr6B 9057063 9061103 4040 False 7463.000000 7463 100.000000 1 4041 1 chr6B.!!$F1 4040
1 TraesCS6B01G015200 chr6B 9034000 9037236 3236 False 1049.000000 2049 84.587333 468 4021 3 chr6B.!!$F3 3553
2 TraesCS6B01G015200 chr6B 9079871 9080992 1121 False 543.500000 601 85.886500 1748 2919 2 chr6B.!!$F4 1171
3 TraesCS6B01G015200 chr6A 3771270 3774408 3138 True 1182.000000 2246 86.872667 478 4041 3 chr6A.!!$R3 3563
4 TraesCS6B01G015200 chr6A 3746395 3748437 2042 True 368.250000 604 85.300750 610 2919 4 chr6A.!!$R2 2309
5 TraesCS6B01G015200 chr6D 4719752 4723059 3307 True 838.000000 2180 86.842500 468 4038 4 chr6D.!!$R1 3570
6 TraesCS6B01G015200 chr6D 3712515 3714472 1957 False 594.666667 946 87.152667 555 2654 3 chr6D.!!$F2 2099
7 TraesCS6B01G015200 chr6D 3756086 3757220 1134 False 593.000000 761 87.870000 1 1064 2 chr6D.!!$F5 1063
8 TraesCS6B01G015200 chr6D 3738706 3740682 1976 False 297.180000 588 87.186800 610 2916 5 chr6D.!!$F4 2306
9 TraesCS6B01G015200 chr6D 3725645 3727760 2115 False 220.285714 608 89.496143 610 3050 7 chr6D.!!$F3 2440
10 TraesCS6B01G015200 chrUn 306427727 306429686 1959 False 593.333333 942 87.121333 555 2654 3 chrUn.!!$F3 2099
11 TraesCS6B01G015200 chr1A 32260846 32261832 986 False 313.500000 351 79.631000 1793 2903 2 chr1A.!!$F3 1110
12 TraesCS6B01G015200 chr1D 33639297 33640293 996 False 321.000000 339 79.914500 1793 2921 2 chr1D.!!$F2 1128


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
167 174 0.601576 TTTGACATGGTCCGGACACG 60.602 55.000 34.4 23.34 40.55 4.49 F
175 182 0.957395 GGTCCGGACACGTCTGTAGA 60.957 60.000 34.4 0.00 38.78 2.59 F
416 443 1.112113 AACTGTCACCTGTGAGTCGT 58.888 50.000 0.0 0.00 40.75 4.34 F
1508 1717 1.134431 CCCCCACCAGCATATTTTTGC 60.134 52.381 0.0 0.00 43.09 3.68 F
1557 1766 0.042731 TCTTCCTCGTCCCCCAATCT 59.957 55.000 0.0 0.00 0.00 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1377 1585 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.0 0.00 0.0 0.00 4.12 R
1538 1747 0.042731 AGATTGGGGGACGAGGAAGA 59.957 55.0 0.00 0.0 0.00 2.87 R
1550 1759 0.936691 AATTGGGGGAGGAGATTGGG 59.063 55.0 0.00 0.0 0.00 4.12 R
2929 3397 0.106819 GCAGTGGCATCCCTGAATCT 60.107 55.0 7.69 0.0 40.72 2.40 R
3235 3704 0.449786 CAAAACGATGCATACGGCCA 59.550 50.0 18.34 0.0 43.89 5.36 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.