Multiple sequence alignment - TraesCS1D01G160400

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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 TraesCS1D01G160400 chr1D 100.000 4250 0 0 1 4250 226955549 226959798 0.000000e+00 7849
1 TraesCS1D01G160400 chr1D 97.499 3718 75 6 1 3714 57215366 57219069 0.000000e+00 6335
2 TraesCS1D01G160400 chr1D 98.079 1093 14 5 1 1088 318662297 318663387 0.000000e+00 1895
3 TraesCS1D01G160400 chr1D 87.763 523 33 19 3729 4250 299688039 299687547 2.200000e-162 582
4 TraesCS1D01G160400 chr1D 93.727 271 16 1 3725 3995 3133700 3133431 5.120000e-109 405
5 TraesCS1D01G160400 chr1D 98.889 90 1 0 3620 3709 318666813 318666902 1.220000e-35 161
6 TraesCS1D01G160400 chrUn 98.279 3719 48 6 1 3714 108982530 108986237 0.000000e+00 6499
7 TraesCS1D01G160400 chr7D 98.015 3728 55 8 1 3725 169476113 169479824 0.000000e+00 6457
8 TraesCS1D01G160400 chr7D 97.693 3727 62 7 1 3724 266878569 266882274 0.000000e+00 6384
9 TraesCS1D01G160400 chr7D 97.854 3541 58 7 187 3718 21762009 21765540 0.000000e+00 6102
10 TraesCS1D01G160400 chr7D 97.736 3534 63 7 187 3714 602023851 602020329 0.000000e+00 6067
11 TraesCS1D01G160400 chr7D 87.619 525 33 20 3727 4250 26654074 26653581 7.920000e-162 580
12 TraesCS1D01G160400 chr7D 93.210 324 19 3 3714 4036 165559825 165560146 1.380000e-129 473
13 TraesCS1D01G160400 chr7D 90.288 278 25 2 3716 3993 563202422 563202147 3.120000e-96 363
14 TraesCS1D01G160400 chr4D 97.663 3552 58 6 187 3714 51343676 51347226 0.000000e+00 6076
15 TraesCS1D01G160400 chr4D 87.954 523 32 4 3729 4250 5321835 5322327 4.730000e-164 588
16 TraesCS1D01G160400 chr3D 97.512 3537 70 7 187 3716 562383189 562379664 0.000000e+00 6028
17 TraesCS1D01G160400 chr3D 88.145 523 31 18 3729 4250 131802803 131802311 1.020000e-165 593
18 TraesCS1D01G160400 chr3D 87.572 523 34 19 3729 4250 609465815 609465323 1.020000e-160 577
19 TraesCS1D01G160400 chr3D 87.335 529 34 20 3725 4250 572917552 572918050 3.690000e-160 575
20 TraesCS1D01G160400 chr5D 98.450 2581 40 0 1135 3715 42563241 42565821 0.000000e+00 4545
21 TraesCS1D01G160400 chr5D 98.313 1067 15 1 1 1064 42562176 42563242 0.000000e+00 1868
22 TraesCS1D01G160400 chr5D 87.595 524 33 5 3729 4250 408089078 408088585 2.850000e-161 579
23 TraesCS1D01G160400 chr3B 91.519 507 34 7 3722 4223 758610926 758610424 0.000000e+00 689
24 TraesCS1D01G160400 chr3A 91.018 501 34 8 3727 4222 31920092 31919598 0.000000e+00 665
25 TraesCS1D01G160400 chr6A 91.224 490 37 6 3729 4215 557920358 557919872 0.000000e+00 662
26 TraesCS1D01G160400 chr6D 87.380 523 36 11 3728 4250 300902053 300902545 1.330000e-159 573
27 TraesCS1D01G160400 chr2D 93.421 380 22 3 3729 4107 124527394 124527017 1.030000e-155 560
28 TraesCS1D01G160400 chr2D 86.085 539 41 21 3714 4250 579004705 579005211 2.230000e-152 549
29 TraesCS1D01G160400 chr7B 90.652 353 31 2 3719 4070 704641979 704642330 6.430000e-128 468
30 TraesCS1D01G160400 chr7B 89.916 357 33 3 3718 4073 45352994 45353348 1.390000e-124 457
31 TraesCS1D01G160400 chr7B 88.571 140 13 2 1 140 673956744 673956880 2.630000e-37 167
32 TraesCS1D01G160400 chr7B 87.097 124 8 1 1 124 673956539 673956654 2.670000e-27 134
33 TraesCS1D01G160400 chr2B 89.694 359 32 4 3714 4069 146819852 146820208 1.800000e-123 453
34 TraesCS1D01G160400 chr2B 97.500 200 4 1 1 199 442922991 442923190 1.460000e-89 340


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 TraesCS1D01G160400 chr1D 226955549 226959798 4249 False 7849.0 7849 100.0000 1 4250 1 chr1D.!!$F2 4249
1 TraesCS1D01G160400 chr1D 57215366 57219069 3703 False 6335.0 6335 97.4990 1 3714 1 chr1D.!!$F1 3713
2 TraesCS1D01G160400 chr1D 318662297 318666902 4605 False 1028.0 1895 98.4840 1 3709 2 chr1D.!!$F3 3708
3 TraesCS1D01G160400 chrUn 108982530 108986237 3707 False 6499.0 6499 98.2790 1 3714 1 chrUn.!!$F1 3713
4 TraesCS1D01G160400 chr7D 169476113 169479824 3711 False 6457.0 6457 98.0150 1 3725 1 chr7D.!!$F3 3724
5 TraesCS1D01G160400 chr7D 266878569 266882274 3705 False 6384.0 6384 97.6930 1 3724 1 chr7D.!!$F4 3723
6 TraesCS1D01G160400 chr7D 21762009 21765540 3531 False 6102.0 6102 97.8540 187 3718 1 chr7D.!!$F1 3531
7 TraesCS1D01G160400 chr7D 602020329 602023851 3522 True 6067.0 6067 97.7360 187 3714 1 chr7D.!!$R3 3527
8 TraesCS1D01G160400 chr4D 51343676 51347226 3550 False 6076.0 6076 97.6630 187 3714 1 chr4D.!!$F2 3527
9 TraesCS1D01G160400 chr3D 562379664 562383189 3525 True 6028.0 6028 97.5120 187 3716 1 chr3D.!!$R2 3529
10 TraesCS1D01G160400 chr5D 42562176 42565821 3645 False 3206.5 4545 98.3815 1 3715 2 chr5D.!!$F1 3714
11 TraesCS1D01G160400 chr3B 758610424 758610926 502 True 689.0 689 91.5190 3722 4223 1 chr3B.!!$R1 501
12 TraesCS1D01G160400 chr2D 579004705 579005211 506 False 549.0 549 86.0850 3714 4250 1 chr2D.!!$F1 536

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
882 890 0.687354 ACTGACGGTCATTGCCTCTT 59.313 50.000 11.86 0.00 0.00 2.85 F
1492 1626 2.288030 ACACAAAAGAAGAGCTGCATGC 60.288 45.455 11.82 11.82 43.29 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1922 2058 3.013533 TCCCATGCTACCTATATGCCCTA 59.986 47.826 0.00 0.00 0.0 3.53 R
3316 4163 0.753479 GAGTCTGGATCGAGGCCTCA 60.753 60.000 31.67 19.07 0.0 3.86 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
818 826 2.028930 CAGAGGCTCAAGTACCGAAAGT 60.029 50.000 18.26 0.00 0.00 2.66
882 890 0.687354 ACTGACGGTCATTGCCTCTT 59.313 50.000 11.86 0.00 0.00 2.85
928 936 6.540189 GCTGATAATTCTCCTTGCTTGAAGTA 59.460 38.462 0.00 0.00 0.00 2.24
1106 1240 2.746269 TGAGGTTAACGGTTTCTGACG 58.254 47.619 0.00 0.00 0.00 4.35
1219 1353 5.860716 GCTTCATGAGACTGAATTTTGTTCC 59.139 40.000 0.00 0.00 34.76 3.62
1387 1521 2.365293 GGAAAGTGTTGTGGAAAGGCAT 59.635 45.455 0.00 0.00 0.00 4.40
1492 1626 2.288030 ACACAAAAGAAGAGCTGCATGC 60.288 45.455 11.82 11.82 43.29 4.06
1714 1849 4.181578 GTTTCTATTAGCTGCGAGGAACA 58.818 43.478 0.00 0.00 29.29 3.18
1922 2058 9.570468 CTTAGGTAGGTTTTCTTTTTCTTAGGT 57.430 33.333 0.00 0.00 0.00 3.08
2062 2199 5.389859 TGGTATGATTTTGGAAGCAACAG 57.610 39.130 0.00 0.00 34.43 3.16
2634 2772 1.617357 ACCTCTGTGTTAACTCCGTCC 59.383 52.381 7.22 0.00 0.00 4.79
3316 4163 4.023291 GTCATTCAGGAGAAGAGAGGAGT 58.977 47.826 0.00 0.00 37.14 3.85
3486 4336 6.660521 TGCTTCCTTTTGTGATCATGTATCTT 59.339 34.615 0.00 0.00 35.45 2.40
3709 4721 0.168788 CATTGGCGCAACGAGTCATT 59.831 50.000 10.83 0.00 0.00 2.57
3719 4731 5.894807 GCGCAACGAGTCATTTAGTTTATAC 59.105 40.000 0.30 0.00 0.00 1.47
3780 4792 5.297547 CAGAGCACGTGTATTAATATGGGT 58.702 41.667 18.38 0.00 0.00 4.51
3795 4807 9.886132 ATTAATATGGGTGATCTAACGGATAAC 57.114 33.333 0.00 0.00 35.51 1.89
3816 4828 4.223144 ACAATAACTGGGCCTTTTTGAGT 58.777 39.130 4.53 0.00 0.00 3.41
3821 4833 2.038659 CTGGGCCTTTTTGAGTCCAAA 58.961 47.619 4.53 0.00 40.24 3.28
3943 4955 4.965200 AGCACTTCATTATAGAGGTCCC 57.035 45.455 0.00 0.00 0.00 4.46
3970 4982 5.412526 TCGTGCGTACTCTTTTGAATTTT 57.587 34.783 1.24 0.00 0.00 1.82
3976 4988 5.974751 GCGTACTCTTTTGAATTTTGGTTCA 59.025 36.000 0.00 0.00 36.38 3.18
4066 5107 4.609018 CCCTCGATCGCCGCCAAT 62.609 66.667 11.09 0.00 38.37 3.16
4067 5108 3.038417 CCTCGATCGCCGCCAATC 61.038 66.667 11.09 0.00 38.37 2.67
4068 5109 3.398134 CTCGATCGCCGCCAATCG 61.398 66.667 11.09 13.87 44.66 3.34
4086 5127 4.292178 CCTCTGGCGCCCTCGATC 62.292 72.222 26.77 0.00 38.10 3.69
4087 5128 4.637489 CTCTGGCGCCCTCGATCG 62.637 72.222 26.77 9.36 38.10 3.69
4130 5171 4.664677 ATCGCCGCCTATCGCACC 62.665 66.667 0.00 0.00 37.30 5.01
4193 5239 1.480212 ATCGCAAGTCACCCCACTCA 61.480 55.000 0.00 0.00 39.48 3.41
4200 5246 3.314331 CACCCCACTCAGGTCGCT 61.314 66.667 0.00 0.00 34.56 4.93
4238 5284 0.912486 AGCCGCTAATCCACTCCTTT 59.088 50.000 0.00 0.00 0.00 3.11
4239 5285 1.017387 GCCGCTAATCCACTCCTTTG 58.983 55.000 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 3.817084 CCGCATGATCACCACTCAATAAT 59.183 43.478 0.00 0.00 0.00 1.28
527 534 4.164221 AGTGATTAGATGGACCCAACGAAT 59.836 41.667 4.78 4.78 29.90 3.34
635 642 6.940298 CCTTGGTCAGAAAATTCAGTTACCTA 59.060 38.462 0.00 0.00 0.00 3.08
928 936 0.749454 GGGTTCTGCAGATCGGCAAT 60.749 55.000 21.00 0.00 44.40 3.56
1106 1240 3.999001 AGCTGCGGTAAGGTAAGTTTAAC 59.001 43.478 0.00 0.00 0.00 2.01
1108 1242 3.967332 AGCTGCGGTAAGGTAAGTTTA 57.033 42.857 0.00 0.00 0.00 2.01
1194 1328 5.382618 ACAAAATTCAGTCTCATGAAGCC 57.617 39.130 0.00 0.00 42.20 4.35
1219 1353 0.603065 GGCTTGGCTGGTTTTACCTG 59.397 55.000 0.00 0.00 39.58 4.00
1387 1521 7.385778 AGAACAACACAACTACAAAAGCTTA 57.614 32.000 0.00 0.00 0.00 3.09
1492 1626 7.663493 AGAAGAAACTCCAGGAGAAACAAATAG 59.337 37.037 24.45 0.00 33.32 1.73
1668 1803 4.008330 CCATGAGAGAACTGTTCTGCAAT 58.992 43.478 26.47 13.58 40.87 3.56
1714 1849 3.760684 CTCAAGACAAAAGCTAGCCCAAT 59.239 43.478 12.13 0.00 0.00 3.16
1922 2058 3.013533 TCCCATGCTACCTATATGCCCTA 59.986 47.826 0.00 0.00 0.00 3.53
1979 2116 9.416284 ACATCCGAAAATAAGTACCCAAATATT 57.584 29.630 0.00 0.00 0.00 1.28
2634 2772 3.277142 ACCTTAATTGGCCTAGAACCG 57.723 47.619 3.32 0.00 0.00 4.44
3316 4163 0.753479 GAGTCTGGATCGAGGCCTCA 60.753 60.000 31.67 19.07 0.00 3.86
3486 4336 4.575885 CCTTTTCTCACCGGATCTAACAA 58.424 43.478 9.46 0.00 0.00 2.83
3572 4422 4.722279 ACAAAGGAAGTAGATAGGAAGGGG 59.278 45.833 0.00 0.00 0.00 4.79
3628 4640 5.464030 TCAGACACCCAAGTCTTTACTAC 57.536 43.478 0.00 0.00 46.26 2.73
3719 4731 7.708752 TGCACTGTAAAATTTCCCAACTTTTAG 59.291 33.333 0.00 0.00 0.00 1.85
3740 4752 5.760253 GTGCTCTGGTGTATTATAATGCACT 59.240 40.000 32.23 4.08 46.81 4.40
3772 4784 7.311092 TGTTATCCGTTAGATCACCCATATT 57.689 36.000 0.00 0.00 36.33 1.28
3780 4792 7.214381 CCCAGTTATTGTTATCCGTTAGATCA 58.786 38.462 0.00 0.00 36.33 2.92
3793 4805 4.653801 ACTCAAAAAGGCCCAGTTATTGTT 59.346 37.500 0.00 0.00 0.00 2.83
3795 4807 4.809673 GACTCAAAAAGGCCCAGTTATTG 58.190 43.478 0.00 0.00 0.00 1.90
3816 4828 8.411991 AAATTTAGGTCGAAAATACCTTTGGA 57.588 30.769 0.00 0.00 45.26 3.53
3846 4858 7.092137 ACCTAATTTGGCCGATTAAAAGTAC 57.908 36.000 5.79 0.00 0.00 2.73
3847 4859 6.319405 GGACCTAATTTGGCCGATTAAAAGTA 59.681 38.462 5.79 3.45 0.00 2.24
3849 4861 5.126384 TGGACCTAATTTGGCCGATTAAAAG 59.874 40.000 5.79 6.98 0.00 2.27
3850 4862 5.017490 TGGACCTAATTTGGCCGATTAAAA 58.983 37.500 5.79 0.89 0.00 1.52
3862 4874 4.102681 CGAGAATACCCCTGGACCTAATTT 59.897 45.833 0.00 0.00 0.00 1.82
3943 4955 3.612423 TCAAAAGAGTACGCACGATGATG 59.388 43.478 0.00 0.00 0.00 3.07
3970 4982 1.595929 GGACGAACCGCTTGAACCA 60.596 57.895 0.00 0.00 0.00 3.67
4069 5110 4.292178 GATCGAGGGCGCCAGAGG 62.292 72.222 30.85 14.26 37.46 3.69
4070 5111 4.637489 CGATCGAGGGCGCCAGAG 62.637 72.222 30.85 18.19 37.46 3.35
4130 5171 3.834799 GAGGGGTAGACACGGCGG 61.835 72.222 13.24 2.35 0.00 6.13
4200 5246 2.184322 GTCGGAAGATCTGGCGCA 59.816 61.111 10.83 0.00 45.19 6.09


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

AutoCloner maintained by Alex Coulton.