Multiple sequence alignment - TraesCS7A01G095400

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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 TraesCS7A01G095400 chr7A 100.000 4104 0 0 855 4958 58232995 58237098 0.000000e+00 7579.0
1 TraesCS7A01G095400 chr7A 100.000 618 0 0 1 618 58232141 58232758 0.000000e+00 1142.0
2 TraesCS7A01G095400 chr7A 80.171 585 83 25 3359 3928 83292208 83291642 1.660000e-109 407.0
3 TraesCS7A01G095400 chr7A 85.677 384 52 1 1696 2079 83298825 83298445 7.730000e-108 401.0
4 TraesCS7A01G095400 chr7A 82.057 457 61 8 2222 2678 83298280 83297845 2.180000e-98 370.0
5 TraesCS7A01G095400 chr7A 87.043 301 39 0 1215 1515 83299210 83298910 1.710000e-89 340.0
6 TraesCS7A01G095400 chr7D 92.000 2750 154 23 1566 4307 54760605 54757914 0.000000e+00 3799.0
7 TraesCS7A01G095400 chr7D 92.522 789 47 7 859 1636 54761280 54760493 0.000000e+00 1120.0
8 TraesCS7A01G095400 chr7D 87.264 636 31 14 1 615 54762074 54761468 0.000000e+00 680.0
9 TraesCS7A01G095400 chr7D 79.198 1048 163 38 2801 3820 80714238 80713218 0.000000e+00 676.0
10 TraesCS7A01G095400 chr7D 86.473 621 45 17 4300 4891 54757674 54757064 0.000000e+00 645.0
11 TraesCS7A01G095400 chr7D 86.645 307 41 0 1215 1521 80715769 80715463 1.710000e-89 340.0
12 TraesCS7A01G095400 chr7D 92.647 68 5 0 4891 4958 54757034 54756967 1.140000e-16 99.0
13 TraesCS7A01G095400 chr4A 91.751 2376 157 19 1608 3976 670886798 670889141 0.000000e+00 3265.0
14 TraesCS7A01G095400 chr4A 92.510 761 41 12 856 1611 670886139 670886888 0.000000e+00 1075.0
15 TraesCS7A01G095400 chr4A 84.330 485 68 7 1015 1498 670942177 670942654 7.520000e-128 468.0
16 TraesCS7A01G095400 chr4A 85.854 410 58 0 2211 2620 670943329 670943738 2.120000e-118 436.0
17 TraesCS7A01G095400 chr4A 85.854 410 51 6 1689 2096 670942701 670943105 3.550000e-116 429.0
18 TraesCS7A01G095400 chr4A 86.103 331 24 12 4009 4339 670925054 670925362 2.210000e-88 337.0
19 TraesCS7A01G095400 chr4A 82.927 123 7 4 506 615 670885828 670885949 1.140000e-16 99.0
20 TraesCS7A01G095400 chr4A 100.000 34 0 0 273 306 606584322 606584289 4.140000e-06 63.9
21 TraesCS7A01G095400 chr6A 87.949 390 44 3 1696 2085 585971745 585972131 1.630000e-124 457.0
22 TraesCS7A01G095400 chr6A 85.556 450 48 5 1083 1516 585971120 585971568 5.850000e-124 455.0
23 TraesCS7A01G095400 chr6A 94.737 95 5 0 3355 3449 585973437 585973531 1.110000e-31 148.0
24 TraesCS7A01G095400 chrUn 82.752 516 71 7 3355 3870 108752198 108751701 1.270000e-120 444.0
25 TraesCS7A01G095400 chrUn 88.764 356 35 3 1697 2051 108746461 108746812 9.860000e-117 431.0
26 TraesCS7A01G095400 chrUn 83.971 418 59 3 2800 3209 108795245 108794828 1.290000e-105 394.0
27 TraesCS7A01G095400 chrUn 82.243 428 68 7 2252 2678 108747117 108747537 3.650000e-96 363.0
28 TraesCS7A01G095400 chrUn 85.065 308 43 3 1206 1513 108618599 108618903 1.340000e-80 311.0
29 TraesCS7A01G095400 chrUn 97.059 34 1 0 273 306 332851764 332851731 1.930000e-04 58.4
30 TraesCS7A01G095400 chr4B 86.616 396 49 2 1689 2084 665302209 665301818 7.620000e-118 435.0
31 TraesCS7A01G095400 chr4B 79.769 173 34 1 3656 3828 665300752 665300581 1.870000e-24 124.0
32 TraesCS7A01G095400 chr5A 85.930 398 52 2 1689 2086 704975083 704974690 5.930000e-114 422.0
33 TraesCS7A01G095400 chr5A 81.589 516 77 10 3355 3870 704950506 704951003 1.280000e-110 411.0
34 TraesCS7A01G095400 chr5A 83.447 441 63 3 2243 2682 705144081 705144512 7.730000e-108 401.0
35 TraesCS7A01G095400 chr5A 79.899 592 75 25 3348 3917 705146561 705147130 1.290000e-105 394.0
36 TraesCS7A01G095400 chr5A 81.647 425 70 8 2255 2678 704974426 704974009 3.670000e-91 346.0
37 TraesCS7A01G095400 chr5A 79.060 468 67 6 3355 3822 680216871 680216435 4.850000e-75 292.0
38 TraesCS7A01G095400 chr2D 84.527 433 56 5 2251 2682 584759225 584759647 7.680000e-113 418.0
39 TraesCS7A01G095400 chr7B 85.938 384 51 2 1696 2079 28062205 28061825 1.660000e-109 407.0
40 TraesCS7A01G095400 chr7B 79.167 600 94 25 3359 3944 28060144 28059562 2.160000e-103 387.0
41 TraesCS7A01G095400 chr7B 87.055 309 38 2 1215 1522 28062590 28062283 1.020000e-91 348.0
42 TraesCS7A01G095400 chr7B 84.641 306 38 6 2373 2678 28061157 28060861 3.750000e-76 296.0
43 TraesCS7A01G095400 chr7B 97.059 34 1 0 273 306 613240173 613240140 1.930000e-04 58.4
44 TraesCS7A01G095400 chr4D 82.051 468 66 7 3355 3822 499457956 499457507 2.800000e-102 383.0
45 TraesCS7A01G095400 chr4D 82.100 419 66 5 2810 3228 499458510 499458101 2.840000e-92 350.0
46 TraesCS7A01G095400 chr4D 81.542 428 67 2 2251 2678 499459039 499458624 4.750000e-90 342.0
47 TraesCS7A01G095400 chr3B 84.295 312 45 2 1204 1513 818314503 818314812 8.070000e-78 302.0
48 TraesCS7A01G095400 chr6D 100.000 34 0 0 273 306 355436620 355436653 4.140000e-06 63.9
49 TraesCS7A01G095400 chr1B 100.000 34 0 0 273 306 423640269 423640236 4.140000e-06 63.9
50 TraesCS7A01G095400 chr1B 97.059 34 1 0 273 306 29975403 29975370 1.930000e-04 58.4
51 TraesCS7A01G095400 chr1B 97.059 34 1 0 273 306 614972548 614972581 1.930000e-04 58.4
52 TraesCS7A01G095400 chr5D 97.059 34 1 0 273 306 134782126 134782159 1.930000e-04 58.4


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 TraesCS7A01G095400 chr7A 58232141 58237098 4957 False 4360.500000 7579 100.000000 1 4958 2 chr7A.!!$F1 4957
1 TraesCS7A01G095400 chr7A 83291642 83292208 566 True 407.000000 407 80.171000 3359 3928 1 chr7A.!!$R1 569
2 TraesCS7A01G095400 chr7A 83297845 83299210 1365 True 370.333333 401 84.925667 1215 2678 3 chr7A.!!$R2 1463
3 TraesCS7A01G095400 chr7D 54756967 54762074 5107 True 1268.600000 3799 90.181200 1 4958 5 chr7D.!!$R1 4957
4 TraesCS7A01G095400 chr7D 80713218 80715769 2551 True 508.000000 676 82.921500 1215 3820 2 chr7D.!!$R2 2605
5 TraesCS7A01G095400 chr4A 670885828 670889141 3313 False 1479.666667 3265 89.062667 506 3976 3 chr4A.!!$F2 3470
6 TraesCS7A01G095400 chr4A 670942177 670943738 1561 False 444.333333 468 85.346000 1015 2620 3 chr4A.!!$F3 1605
7 TraesCS7A01G095400 chr6A 585971120 585973531 2411 False 353.333333 457 89.414000 1083 3449 3 chr6A.!!$F1 2366
8 TraesCS7A01G095400 chrUn 108746461 108747537 1076 False 397.000000 431 85.503500 1697 2678 2 chrUn.!!$F2 981
9 TraesCS7A01G095400 chr4B 665300581 665302209 1628 True 279.500000 435 83.192500 1689 3828 2 chr4B.!!$R1 2139
10 TraesCS7A01G095400 chr5A 705144081 705147130 3049 False 397.500000 401 81.673000 2243 3917 2 chr5A.!!$F2 1674
11 TraesCS7A01G095400 chr5A 704974009 704975083 1074 True 384.000000 422 83.788500 1689 2678 2 chr5A.!!$R2 989
12 TraesCS7A01G095400 chr7B 28059562 28062590 3028 True 359.500000 407 84.200250 1215 3944 4 chr7B.!!$R2 2729
13 TraesCS7A01G095400 chr4D 499457507 499459039 1532 True 358.333333 383 81.897667 2251 3822 3 chr4D.!!$R1 1571


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
592 621 0.036010 AGCCATTCCGTCCTCTGTTG 60.036 55.000 0.00 0.00 0.00 3.33 F
1119 1166 0.036164 TGTGGAAGTGGCGCAAGTAT 59.964 50.000 10.83 0.00 41.68 2.12 F
1664 1813 0.034089 ATGGAGAAAGCCGGGGAAAG 60.034 55.000 2.18 0.00 0.00 2.62 F
2069 2254 1.376942 CTGGCTTGGTGCTCCTCAG 60.377 63.158 6.34 3.51 42.39 3.35 F
2756 3594 0.820226 AAGCTGCTGCGTCTATCTGA 59.180 50.000 1.35 0.00 45.42 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 1707 0.034089 CTTTCCCCGGCTTTCTCCAT 60.034 55.0 0.00 0.0 0.00 3.41 R
2069 2254 0.097674 CTTCGCCTGTAGCACAATGC 59.902 55.0 0.00 0.0 45.46 3.56 R
2737 3575 0.820226 TCAGATAGACGCAGCAGCTT 59.180 50.0 0.00 0.0 39.10 3.74 R
3282 5533 0.831307 ATCCTAGGGGCTCGAACAAC 59.169 55.0 9.46 0.0 0.00 3.32 R
4392 6992 0.033208 TCATCACCCCCTTGCATTCC 60.033 55.0 0.00 0.0 0.00 3.01 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.