Multiple sequence alignment - TraesCS6B01G015200
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 pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
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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 primersListed 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. |
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Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.