Multiple sequence alignment - TraesCS6B01G377600

Loading Multiple Alignment...

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 TraesCS6B01G377600 chr6B 100.000 2369 0 0 1 2369 652698487 652696119 0.000000e+00 4375.0
1 TraesCS6B01G377600 chr3B 96.367 2367 84 2 2 2368 680396475 680394111 0.000000e+00 3893.0
2 TraesCS6B01G377600 chr3B 95.823 2370 93 6 2 2369 131914703 131912338 0.000000e+00 3823.0
3 TraesCS6B01G377600 chr3B 95.571 2371 87 7 1 2369 610990468 610992822 0.000000e+00 3781.0
4 TraesCS6B01G377600 chr3B 94.409 1556 74 5 809 2361 731968899 731967354 0.000000e+00 2379.0
5 TraesCS6B01G377600 chr3B 95.298 1425 64 3 1 1425 108523327 108521906 0.000000e+00 2257.0
6 TraesCS6B01G377600 chr4B 95.063 2370 87 7 1 2369 29155949 29158289 0.000000e+00 3701.0
7 TraesCS6B01G377600 chr4B 96.635 1367 45 1 1 1366 2417766 2416400 0.000000e+00 2268.0
8 TraesCS6B01G377600 chr4B 94.820 888 36 3 1483 2369 2416221 2415343 0.000000e+00 1376.0
9 TraesCS6B01G377600 chr2B 95.816 1434 59 1 1 1434 697785740 697787172 0.000000e+00 2314.0
10 TraesCS6B01G377600 chr2B 96.357 1400 50 1 1 1400 110633561 110632163 0.000000e+00 2302.0
11 TraesCS6B01G377600 chr2B 95.701 884 35 3 1487 2369 110631711 110630830 0.000000e+00 1419.0
12 TraesCS6B01G377600 chr2B 95.667 877 32 6 1496 2369 697787481 697788354 0.000000e+00 1404.0
13 TraesCS6B01G377600 chr7B 94.737 1406 69 5 1 1406 619813978 619812578 0.000000e+00 2182.0
14 TraesCS6B01G377600 chr1B 95.878 1310 51 2 2 1311 685388873 685390179 0.000000e+00 2117.0
15 TraesCS6B01G377600 chr1B 96.499 914 29 3 1457 2369 685400180 685401091 0.000000e+00 1507.0
16 TraesCS6B01G377600 chr1B 94.118 153 8 1 1310 1461 685391800 685391952 5.090000e-57 231.0
17 TraesCS6B01G377600 chr1D 91.443 1005 58 13 447 1432 266178810 266177815 0.000000e+00 1354.0
18 TraesCS6B01G377600 chr1D 95.665 346 14 1 94 439 266181516 266181172 2.660000e-154 555.0
19 TraesCS6B01G377600 chr6A 90.040 1004 70 8 447 1432 396917939 396918930 0.000000e+00 1273.0
20 TraesCS6B01G377600 chr1A 88.835 1030 77 13 427 1432 40279613 40280628 0.000000e+00 1230.0
21 TraesCS6B01G377600 chr1A 96.210 343 12 1 94 436 40278850 40279191 5.720000e-156 560.0
22 TraesCS6B01G377600 chr7A 97.455 393 10 0 1977 2369 14707878 14707486 0.000000e+00 671.0
23 TraesCS6B01G377600 chrUn 97.449 392 10 0 1978 2369 403682626 403683017 0.000000e+00 669.0
24 TraesCS6B01G377600 chr4D 94.752 343 17 1 94 436 17107586 17107927 1.250000e-147 532.0
25 TraesCS6B01G377600 chr4D 83.133 83 5 5 1436 1518 258736117 258736190 1.520000e-07 67.6
26 TraesCS6B01G377600 chr3A 89.855 69 6 1 1436 1504 623996158 623996225 1.170000e-13 87.9
27 TraesCS6B01G377600 chr3D 81.818 99 13 3 1436 1530 481278240 481278337 7.020000e-11 78.7


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 TraesCS6B01G377600 chr6B 652696119 652698487 2368 True 4375.0 4375 100.0000 1 2369 1 chr6B.!!$R1 2368
1 TraesCS6B01G377600 chr3B 680394111 680396475 2364 True 3893.0 3893 96.3670 2 2368 1 chr3B.!!$R3 2366
2 TraesCS6B01G377600 chr3B 131912338 131914703 2365 True 3823.0 3823 95.8230 2 2369 1 chr3B.!!$R2 2367
3 TraesCS6B01G377600 chr3B 610990468 610992822 2354 False 3781.0 3781 95.5710 1 2369 1 chr3B.!!$F1 2368
4 TraesCS6B01G377600 chr3B 731967354 731968899 1545 True 2379.0 2379 94.4090 809 2361 1 chr3B.!!$R4 1552
5 TraesCS6B01G377600 chr3B 108521906 108523327 1421 True 2257.0 2257 95.2980 1 1425 1 chr3B.!!$R1 1424
6 TraesCS6B01G377600 chr4B 29155949 29158289 2340 False 3701.0 3701 95.0630 1 2369 1 chr4B.!!$F1 2368
7 TraesCS6B01G377600 chr4B 2415343 2417766 2423 True 1822.0 2268 95.7275 1 2369 2 chr4B.!!$R1 2368
8 TraesCS6B01G377600 chr2B 110630830 110633561 2731 True 1860.5 2302 96.0290 1 2369 2 chr2B.!!$R1 2368
9 TraesCS6B01G377600 chr2B 697785740 697788354 2614 False 1859.0 2314 95.7415 1 2369 2 chr2B.!!$F1 2368
10 TraesCS6B01G377600 chr7B 619812578 619813978 1400 True 2182.0 2182 94.7370 1 1406 1 chr7B.!!$R1 1405
11 TraesCS6B01G377600 chr1B 685400180 685401091 911 False 1507.0 1507 96.4990 1457 2369 1 chr1B.!!$F1 912
12 TraesCS6B01G377600 chr1B 685388873 685391952 3079 False 1174.0 2117 94.9980 2 1461 2 chr1B.!!$F2 1459
13 TraesCS6B01G377600 chr1D 266177815 266181516 3701 True 954.5 1354 93.5540 94 1432 2 chr1D.!!$R1 1338
14 TraesCS6B01G377600 chr6A 396917939 396918930 991 False 1273.0 1273 90.0400 447 1432 1 chr6A.!!$F1 985
15 TraesCS6B01G377600 chr1A 40278850 40280628 1778 False 895.0 1230 92.5225 94 1432 2 chr1A.!!$F1 1338


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
885 3273 0.034756 CATGGTGACGTCCTGGTTCA 59.965 55.0 14.12 2.81 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 6125 2.004583 TGAATTAAGCACCGTCGGAG 57.995 50.0 20.51 12.0 0.0 4.63 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
54 55 6.642733 TTTGGGGATAGAAGAAGAAGACAT 57.357 37.500 0.00 0.00 0.00 3.06
588 2958 4.292186 ACAACACCTATCAATGCTCAGT 57.708 40.909 0.00 0.00 0.00 3.41
683 3066 7.492344 GGAATTATACAAGGAATTGTGCCAAAG 59.508 37.037 3.95 0.00 36.44 2.77
811 3199 2.917713 AGAGAAGAAGCAGAGGAGGA 57.082 50.000 0.00 0.00 0.00 3.71
885 3273 0.034756 CATGGTGACGTCCTGGTTCA 59.965 55.000 14.12 2.81 0.00 3.18
918 3306 0.489567 AAGGGGGTCAGACAGAGAGT 59.510 55.000 2.17 0.00 0.00 3.24
948 3336 1.268066 AAGACGAGGGGAGGAGAAAC 58.732 55.000 0.00 0.00 0.00 2.78
968 3359 2.505819 ACGGATTCATACCTTTGAGCCT 59.494 45.455 0.00 0.00 0.00 4.58
982 3373 3.741476 GCCTTGCGGTTGGAGCTG 61.741 66.667 0.00 0.00 35.28 4.24
989 3380 1.589716 GCGGTTGGAGCTGCTCATTT 61.590 55.000 28.95 0.00 37.74 2.32
1154 3545 2.093106 AGGCAGAGACGACGAACTAAT 58.907 47.619 0.00 0.00 0.00 1.73
1434 5470 1.343789 CCATGAGATGAGCGGATCTGT 59.656 52.381 2.89 0.00 32.57 3.41
1440 5476 4.899239 GAGCGGATCTGTGCGGGG 62.899 72.222 2.89 0.00 39.80 5.73
1567 5968 1.618030 GCTCTGAGGGAGGGAGAGA 59.382 63.158 6.83 0.00 42.08 3.10
1722 6125 2.438434 CCGTTGGATCTGGGTGCC 60.438 66.667 0.00 0.00 0.00 5.01
1792 6195 0.733150 GAACGCAGTATCCCCTTTGC 59.267 55.000 0.00 0.00 45.00 3.68
2138 6546 7.926555 ACATCTTGGAATAGTAAACAGTATCGG 59.073 37.037 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 4.645535 AGTTTTCTCATAACTGCTGCTGA 58.354 39.130 13.69 0.90 34.68 4.26
247 249 9.685276 ACCTGATTGTTCTCATTCATTATTGTA 57.315 29.630 0.00 0.00 34.75 2.41
400 415 2.816087 AGTGCTTCATAAGTGTTGCTGG 59.184 45.455 0.00 0.00 0.00 4.85
588 2958 2.831526 TCTGTGTATCAAGGTGCAGCTA 59.168 45.455 20.51 4.58 0.00 3.32
683 3066 9.113876 GTATTTTAGGCATGATTAAATACGTGC 57.886 33.333 0.00 13.00 44.94 5.34
811 3199 1.208165 GGAGGGACACCATGGACCTT 61.208 60.000 21.47 14.62 39.49 3.50
885 3273 3.521531 GACCCCCTTCTCATCTCTCTTTT 59.478 47.826 0.00 0.00 0.00 2.27
918 3306 2.038557 CCCCTCGTCTTTTCTTCTTCCA 59.961 50.000 0.00 0.00 0.00 3.53
948 3336 3.199880 AGGCTCAAAGGTATGAATCCG 57.800 47.619 0.00 0.00 31.16 4.18
968 3359 2.669569 GAGCAGCTCCAACCGCAA 60.670 61.111 11.84 0.00 0.00 4.85
982 3373 4.133796 GGGCCGTGGCAAATGAGC 62.134 66.667 13.76 0.00 44.11 4.26
1006 3397 2.108970 GTTCTCGGGATTCCTACCACT 58.891 52.381 2.01 0.00 0.00 4.00
1154 3545 3.307691 CCTCACAGCCATTCCTAACTTCA 60.308 47.826 0.00 0.00 0.00 3.02
1366 5402 1.383664 CCTCCCTGCCTCTGGATCA 60.384 63.158 0.00 0.00 0.00 2.92
1547 5948 2.235602 CTCTCCCTCCCTCAGAGCCA 62.236 65.000 0.00 0.00 41.74 4.75
1550 5951 0.465460 CGTCTCTCCCTCCCTCAGAG 60.465 65.000 0.00 0.00 42.83 3.35
1722 6125 2.004583 TGAATTAAGCACCGTCGGAG 57.995 50.000 20.51 12.00 0.00 4.63
2083 6491 8.725148 ACTTTTGCAGAGTATAAAGAACTCATG 58.275 33.333 12.12 0.00 44.77 3.07
2277 6689 7.244898 CCATTTGGTCAATTGTGCATTAAATG 58.755 34.615 5.13 13.16 34.50 2.32



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

AutoCloner maintained by Alex Coulton.