Multiple sequence alignment - TraesCS1D01G083200

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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 TraesCS1D01G083200 chr1D 100.000 3999 0 0 1 3999 66200713 66196715 0.000000e+00 7385
1 TraesCS1D01G083200 chr7D 98.799 3414 29 11 1 3407 108265486 108262078 0.000000e+00 6067
2 TraesCS1D01G083200 chr7D 98.389 3414 33 20 1 3407 108302406 108299008 0.000000e+00 5980
3 TraesCS1D01G083200 chr7D 98.037 3413 41 21 1 3407 21682203 21678811 0.000000e+00 5908
4 TraesCS1D01G083200 chr7D 98.007 602 4 1 3406 3999 108299067 108298466 0.000000e+00 1038
5 TraesCS1D01G083200 chr7D 97.508 602 7 1 3406 3999 108262137 108261536 0.000000e+00 1022
6 TraesCS1D01G083200 chr7D 96.828 599 10 2 3409 3999 21678867 21678270 0.000000e+00 992
7 TraesCS1D01G083200 chr5D 98.741 3415 25 16 1 3407 30634480 30631076 0.000000e+00 6052
8 TraesCS1D01G083200 chr5D 98.178 2031 27 8 1 2029 420310681 420308659 0.000000e+00 3537
9 TraesCS1D01G083200 chr5D 98.856 1399 11 3 2014 3407 420308643 420307245 0.000000e+00 2490
10 TraesCS1D01G083200 chr5D 97.342 602 8 1 3406 3999 30631135 30630534 0.000000e+00 1016
11 TraesCS1D01G083200 chr5D 96.705 607 7 4 3406 3999 420307304 420306698 0.000000e+00 998
12 TraesCS1D01G083200 chr2D 98.243 3414 42 13 1 3407 343143641 343140239 0.000000e+00 5956
13 TraesCS1D01G083200 chr2D 97.671 601 5 2 3408 3999 343140296 343139696 0.000000e+00 1024
14 TraesCS1D01G083200 chr6A 93.095 2766 134 43 679 3407 615412802 615410057 0.000000e+00 3997
15 TraesCS1D01G083200 chr6A 90.896 703 41 16 1 688 615413624 615412930 0.000000e+00 922
16 TraesCS1D01G083200 chr6A 92.308 130 9 1 3833 3962 615409753 615409625 2.450000e-42 183
17 TraesCS1D01G083200 chr3A 94.528 1864 80 20 679 2532 735465089 735466940 0.000000e+00 2857
18 TraesCS1D01G083200 chr3A 90.241 830 52 20 2595 3407 735466937 735467754 0.000000e+00 1057
19 TraesCS1D01G083200 chr3A 92.275 699 32 15 1 688 735464263 735464950 0.000000e+00 972
20 TraesCS1D01G083200 chr4B 86.574 2309 223 59 1158 3407 638493177 638490897 0.000000e+00 2466
21 TraesCS1D01G083200 chr4B 86.957 598 60 14 3411 3999 638490948 638490360 0.000000e+00 656
22 TraesCS1D01G083200 chr7B 86.352 2308 233 58 1158 3407 712608227 712610510 0.000000e+00 2442
23 TraesCS1D01G083200 chr7B 86.224 588 65 12 3411 3991 712610459 712611037 1.220000e-174 623
24 TraesCS1D01G083200 chr7B 87.366 372 40 7 679 1047 712607804 712608171 1.720000e-113 420
25 TraesCS1D01G083200 chr7B 83.632 446 47 18 3411 3846 733215321 733214892 2.900000e-106 396
26 TraesCS1D01G083200 chr1B 84.045 445 47 15 3411 3846 621584041 621583612 1.340000e-109 407


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 TraesCS1D01G083200 chr1D 66196715 66200713 3998 True 7385.000000 7385 100.000000 1 3999 1 chr1D.!!$R1 3998
1 TraesCS1D01G083200 chr7D 108261536 108265486 3950 True 3544.500000 6067 98.153500 1 3999 2 chr7D.!!$R2 3998
2 TraesCS1D01G083200 chr7D 108298466 108302406 3940 True 3509.000000 5980 98.198000 1 3999 2 chr7D.!!$R3 3998
3 TraesCS1D01G083200 chr7D 21678270 21682203 3933 True 3450.000000 5908 97.432500 1 3999 2 chr7D.!!$R1 3998
4 TraesCS1D01G083200 chr5D 30630534 30634480 3946 True 3534.000000 6052 98.041500 1 3999 2 chr5D.!!$R1 3998
5 TraesCS1D01G083200 chr5D 420306698 420310681 3983 True 2341.666667 3537 97.913000 1 3999 3 chr5D.!!$R2 3998
6 TraesCS1D01G083200 chr2D 343139696 343143641 3945 True 3490.000000 5956 97.957000 1 3999 2 chr2D.!!$R1 3998
7 TraesCS1D01G083200 chr6A 615409625 615413624 3999 True 1700.666667 3997 92.099667 1 3962 3 chr6A.!!$R1 3961
8 TraesCS1D01G083200 chr3A 735464263 735467754 3491 False 1628.666667 2857 92.348000 1 3407 3 chr3A.!!$F1 3406
9 TraesCS1D01G083200 chr4B 638490360 638493177 2817 True 1561.000000 2466 86.765500 1158 3999 2 chr4B.!!$R1 2841
10 TraesCS1D01G083200 chr7B 712607804 712611037 3233 False 1161.666667 2442 86.647333 679 3991 3 chr7B.!!$F1 3312

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
160 168 5.238432 TCAAAACACTGCGAATAATGTCAGT 59.762 36.000 0.0 0.0 40.08 3.41 F
1312 1497 2.890945 GGCACTAAACACCAACCAATCT 59.109 45.455 0.0 0.0 0.00 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1465 1660 2.091055 TCCCCCAAAACTTGAACATCCA 60.091 45.455 0.00 0.0 0.00 3.41 R
3389 3697 4.531659 AAAACAGTTTCTACGACACTGC 57.468 40.909 9.39 0.0 42.13 4.40 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
160 168 5.238432 TCAAAACACTGCGAATAATGTCAGT 59.762 36.000 0.00 0.0 40.08 3.41
351 367 9.455847 CCTTTTTCTTCTTCTTTTACATGACAG 57.544 33.333 0.00 0.0 0.00 3.51
1312 1497 2.890945 GGCACTAAACACCAACCAATCT 59.109 45.455 0.00 0.0 0.00 2.40
1525 1720 6.992715 GGTTCATGCTCTAGTATGGTAAACAT 59.007 38.462 8.00 0.0 43.68 2.71
1547 1742 4.072839 TGGCGGACAATTTATACAACACA 58.927 39.130 0.00 0.0 0.00 3.72
1589 1784 9.136323 ACTTCATCAAGTGGTAAAGAGAATTTT 57.864 29.630 0.00 0.0 41.64 1.82
2263 2496 5.475273 AAAGTGATCGTGTATGCTTCATG 57.525 39.130 0.00 0.0 0.00 3.07
2369 2620 3.772060 AAATGCAGATCTTCTTTCCGC 57.228 42.857 0.00 0.0 0.00 5.54
3390 3698 6.620678 TGAAAGCAAATCCAAGTTGTATAGC 58.379 36.000 1.45 0.3 0.00 2.97
3391 3699 6.208402 TGAAAGCAAATCCAAGTTGTATAGCA 59.792 34.615 1.45 0.0 0.00 3.49
3392 3700 5.824904 AGCAAATCCAAGTTGTATAGCAG 57.175 39.130 1.45 0.0 0.00 4.24
3393 3701 5.256474 AGCAAATCCAAGTTGTATAGCAGT 58.744 37.500 1.45 0.0 0.00 4.40
3394 3702 5.124457 AGCAAATCCAAGTTGTATAGCAGTG 59.876 40.000 1.45 0.0 0.00 3.66
3395 3703 5.106157 GCAAATCCAAGTTGTATAGCAGTGT 60.106 40.000 1.45 0.0 0.00 3.55
3396 3704 6.546395 CAAATCCAAGTTGTATAGCAGTGTC 58.454 40.000 1.45 0.0 0.00 3.67
3397 3705 3.845178 TCCAAGTTGTATAGCAGTGTCG 58.155 45.455 1.45 0.0 0.00 4.35
3398 3706 3.257375 TCCAAGTTGTATAGCAGTGTCGT 59.743 43.478 1.45 0.0 0.00 4.34
3399 3707 4.460034 TCCAAGTTGTATAGCAGTGTCGTA 59.540 41.667 1.45 0.0 0.00 3.43
3400 3708 4.798907 CCAAGTTGTATAGCAGTGTCGTAG 59.201 45.833 1.45 0.0 0.00 3.51
3401 3709 5.392703 CCAAGTTGTATAGCAGTGTCGTAGA 60.393 44.000 1.45 0.0 0.00 2.59
3402 3710 5.892160 AGTTGTATAGCAGTGTCGTAGAA 57.108 39.130 0.00 0.0 39.69 2.10
3403 3711 6.263516 AGTTGTATAGCAGTGTCGTAGAAA 57.736 37.500 0.00 0.0 39.69 2.52
3677 3997 7.288852 TGTTCTTTTGTTTCTATCATTTCCCCA 59.711 33.333 0.00 0.0 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 168 2.409012 TCAACGCGCTTCTTGTAATCA 58.591 42.857 5.73 0.00 0.00 2.57
351 367 2.059541 GTTGCTTATCGTCTATCCCGC 58.940 52.381 0.00 0.00 0.00 6.13
828 993 3.994392 AGCAAGCGAGAAACGAAAGATAA 59.006 39.130 0.00 0.00 45.77 1.75
833 1000 1.865865 AGAGCAAGCGAGAAACGAAA 58.134 45.000 0.00 0.00 45.77 3.46
1312 1497 8.640063 TTTACATGTAGGTAGTCACTTACAGA 57.360 34.615 5.56 0.00 46.58 3.41
1412 1605 7.636259 CACAATTTATGGTTAGTTTGTGTGG 57.364 36.000 0.00 0.00 39.20 4.17
1465 1660 2.091055 TCCCCCAAAACTTGAACATCCA 60.091 45.455 0.00 0.00 0.00 3.41
1525 1720 4.072839 TGTGTTGTATAAATTGTCCGCCA 58.927 39.130 0.00 0.00 0.00 5.69
1547 1742 6.359804 TGATGAAGTGCCTAATGATAGCTTT 58.640 36.000 0.00 0.00 0.00 3.51
3389 3697 4.531659 AAAACAGTTTCTACGACACTGC 57.468 40.909 9.39 0.00 42.13 4.40
3422 3730 7.598493 GCTATACAACTTGGATTTGCTTTCAAA 59.402 33.333 0.00 0.00 45.24 2.69
3423 3731 7.090173 GCTATACAACTTGGATTTGCTTTCAA 58.910 34.615 0.00 0.00 0.00 2.69
3424 3732 6.208402 TGCTATACAACTTGGATTTGCTTTCA 59.792 34.615 10.91 0.00 0.00 2.69
3425 3733 6.620678 TGCTATACAACTTGGATTTGCTTTC 58.379 36.000 10.91 0.00 0.00 2.62
3426 3734 6.209391 ACTGCTATACAACTTGGATTTGCTTT 59.791 34.615 10.91 0.00 0.00 3.51
3427 3735 5.711976 ACTGCTATACAACTTGGATTTGCTT 59.288 36.000 10.91 0.18 0.00 3.91
3428 3736 5.124457 CACTGCTATACAACTTGGATTTGCT 59.876 40.000 10.91 0.00 0.00 3.91
3429 3737 5.106157 ACACTGCTATACAACTTGGATTTGC 60.106 40.000 0.00 0.00 0.00 3.68
3430 3738 6.500684 ACACTGCTATACAACTTGGATTTG 57.499 37.500 0.00 0.00 0.00 2.32
3431 3739 5.351465 CGACACTGCTATACAACTTGGATTT 59.649 40.000 0.00 0.00 0.00 2.17
3432 3740 4.870426 CGACACTGCTATACAACTTGGATT 59.130 41.667 0.00 0.00 0.00 3.01
3433 3741 4.081642 ACGACACTGCTATACAACTTGGAT 60.082 41.667 0.00 0.00 0.00 3.41
3434 3742 3.257375 ACGACACTGCTATACAACTTGGA 59.743 43.478 0.00 0.00 0.00 3.53
3435 3743 3.585862 ACGACACTGCTATACAACTTGG 58.414 45.455 0.00 0.00 0.00 3.61
3436 3744 5.637809 TCTACGACACTGCTATACAACTTG 58.362 41.667 0.00 0.00 0.00 3.16
3437 3745 5.892160 TCTACGACACTGCTATACAACTT 57.108 39.130 0.00 0.00 0.00 2.66
3438 3746 5.892160 TTCTACGACACTGCTATACAACT 57.108 39.130 0.00 0.00 0.00 3.16
3439 3747 6.033619 CAGTTTCTACGACACTGCTATACAAC 59.966 42.308 0.00 0.00 34.37 3.32
3440 3748 6.090783 CAGTTTCTACGACACTGCTATACAA 58.909 40.000 0.00 0.00 34.37 2.41
3441 3749 5.392703 CCAGTTTCTACGACACTGCTATACA 60.393 44.000 4.97 0.00 38.55 2.29
3442 3750 5.035443 CCAGTTTCTACGACACTGCTATAC 58.965 45.833 4.97 0.00 38.55 1.47
3443 3751 4.703575 ACCAGTTTCTACGACACTGCTATA 59.296 41.667 4.97 0.00 38.55 1.31
3444 3752 3.510360 ACCAGTTTCTACGACACTGCTAT 59.490 43.478 4.97 0.00 38.55 2.97
3445 3753 2.889045 ACCAGTTTCTACGACACTGCTA 59.111 45.455 4.97 0.00 38.55 3.49
3446 3754 1.687123 ACCAGTTTCTACGACACTGCT 59.313 47.619 4.97 0.00 38.55 4.24
3677 3997 3.030291 TCCTGCACCAAAGAAATGTTGT 58.970 40.909 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.