Multiple sequence alignment - TraesCS2D01G254600

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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 TraesCS2D01G254600 chr2D 100.000 5993 0 0 1 5993 306573735 306579727 0.000000e+00 11068
1 TraesCS2D01G254600 chr2D 94.356 5652 211 39 1 5586 497827111 497832720 0.000000e+00 8571
2 TraesCS2D01G254600 chr2D 92.289 5667 288 63 1 5584 229573749 229568149 0.000000e+00 7906
3 TraesCS2D01G254600 chr2D 95.620 4932 146 22 705 5586 32572677 32577588 0.000000e+00 7847
4 TraesCS2D01G254600 chr2D 94.998 3259 119 19 1 3225 344152958 344149710 0.000000e+00 5075
5 TraesCS2D01G254600 chr2D 95.456 2355 61 10 3257 5584 344149707 344147372 0.000000e+00 3714
6 TraesCS2D01G254600 chr2D 94.315 686 28 6 1 676 32571993 32572677 0.000000e+00 1040
7 TraesCS2D01G254600 chr2D 96.867 415 11 2 5580 5993 344147321 344146908 0.000000e+00 693
8 TraesCS2D01G254600 chr2D 96.860 414 11 2 5581 5993 32577638 32578050 0.000000e+00 691
9 TraesCS2D01G254600 chr2D 93.267 401 26 1 1 400 229571032 229570632 1.860000e-164 590
10 TraesCS2D01G254600 chr5D 95.604 5641 165 34 1 5584 172365071 172370685 0.000000e+00 8966
11 TraesCS2D01G254600 chr5D 94.581 5130 190 36 511 5586 164175893 164170798 0.000000e+00 7853
12 TraesCS2D01G254600 chr5D 95.664 3667 99 15 1252 4866 123741362 123737704 0.000000e+00 5836
13 TraesCS2D01G254600 chr5D 95.092 2771 88 8 2856 5586 172402605 172405367 0.000000e+00 4320
14 TraesCS2D01G254600 chr5D 94.315 2023 68 9 2856 4838 172515187 172517202 0.000000e+00 3055
15 TraesCS2D01G254600 chr5D 96.618 414 13 1 5580 5993 172370736 172371148 0.000000e+00 686
16 TraesCS2D01G254600 chr5D 96.394 416 13 1 5580 5993 172405417 172405832 0.000000e+00 684
17 TraesCS2D01G254600 chr5D 95.913 416 15 1 5580 5993 123735218 123734803 0.000000e+00 673
18 TraesCS2D01G254600 chr5D 86.755 604 54 18 2512 3099 308550466 308551059 0.000000e+00 649
19 TraesCS2D01G254600 chr1D 94.280 5542 231 39 1 5486 123209019 123203508 0.000000e+00 8399
20 TraesCS2D01G254600 chr1D 93.409 4597 203 38 1076 5586 123217298 123221880 0.000000e+00 6719
21 TraesCS2D01G254600 chr7D 93.451 5680 259 49 1 5586 292292135 292297795 0.000000e+00 8323
22 TraesCS2D01G254600 chr7D 91.581 2708 170 29 415 3093 413932867 413930189 0.000000e+00 3685
23 TraesCS2D01G254600 chr3D 93.156 5669 278 41 3 5586 178348906 178343263 0.000000e+00 8218
24 TraesCS2D01G254600 chr6A 92.898 5646 296 37 1 5585 340839484 340845085 0.000000e+00 8107
25 TraesCS2D01G254600 chr6A 92.787 3854 203 32 1784 5586 343800628 343796799 0.000000e+00 5507
26 TraesCS2D01G254600 chr6A 96.618 414 13 1 5581 5993 340845137 340845550 0.000000e+00 686
27 TraesCS2D01G254600 chr6A 87.309 457 47 6 2652 3098 81783796 81783341 4.140000e-141 512
28 TraesCS2D01G254600 chr3A 92.515 5665 324 39 1 5587 596208195 596202553 0.000000e+00 8021
29 TraesCS2D01G254600 chr3A 95.422 415 18 1 5580 5993 596202505 596202091 0.000000e+00 660
30 TraesCS2D01G254600 chr6D 94.479 4637 172 22 1021 5587 74708063 74703441 0.000000e+00 7068
31 TraesCS2D01G254600 chr6D 93.205 4739 244 28 1 4677 201618173 201622895 0.000000e+00 6896
32 TraesCS2D01G254600 chr6D 95.894 414 15 1 5580 5993 74703393 74702982 0.000000e+00 669
33 TraesCS2D01G254600 chrUn 94.510 1275 41 4 4339 5585 70709522 70710795 0.000000e+00 1940
34 TraesCS2D01G254600 chrUn 95.422 415 17 2 5580 5993 70710847 70711260 0.000000e+00 660


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 TraesCS2D01G254600 chr2D 306573735 306579727 5992 False 11068.000000 11068 100.000000 1 5993 1 chr2D.!!$F1 5992
1 TraesCS2D01G254600 chr2D 497827111 497832720 5609 False 8571.000000 8571 94.356000 1 5586 1 chr2D.!!$F2 5585
2 TraesCS2D01G254600 chr2D 229568149 229573749 5600 True 4248.000000 7906 92.778000 1 5584 2 chr2D.!!$R1 5583
3 TraesCS2D01G254600 chr2D 32571993 32578050 6057 False 3192.666667 7847 95.598333 1 5993 3 chr2D.!!$F3 5992
4 TraesCS2D01G254600 chr2D 344146908 344152958 6050 True 3160.666667 5075 95.773667 1 5993 3 chr2D.!!$R2 5992
5 TraesCS2D01G254600 chr5D 164170798 164175893 5095 True 7853.000000 7853 94.581000 511 5586 1 chr5D.!!$R1 5075
6 TraesCS2D01G254600 chr5D 172365071 172371148 6077 False 4826.000000 8966 96.111000 1 5993 2 chr5D.!!$F3 5992
7 TraesCS2D01G254600 chr5D 123734803 123741362 6559 True 3254.500000 5836 95.788500 1252 5993 2 chr5D.!!$R2 4741
8 TraesCS2D01G254600 chr5D 172515187 172517202 2015 False 3055.000000 3055 94.315000 2856 4838 1 chr5D.!!$F1 1982
9 TraesCS2D01G254600 chr5D 172402605 172405832 3227 False 2502.000000 4320 95.743000 2856 5993 2 chr5D.!!$F4 3137
10 TraesCS2D01G254600 chr5D 308550466 308551059 593 False 649.000000 649 86.755000 2512 3099 1 chr5D.!!$F2 587
11 TraesCS2D01G254600 chr1D 123203508 123209019 5511 True 8399.000000 8399 94.280000 1 5486 1 chr1D.!!$R1 5485
12 TraesCS2D01G254600 chr1D 123217298 123221880 4582 False 6719.000000 6719 93.409000 1076 5586 1 chr1D.!!$F1 4510
13 TraesCS2D01G254600 chr7D 292292135 292297795 5660 False 8323.000000 8323 93.451000 1 5586 1 chr7D.!!$F1 5585
14 TraesCS2D01G254600 chr7D 413930189 413932867 2678 True 3685.000000 3685 91.581000 415 3093 1 chr7D.!!$R1 2678
15 TraesCS2D01G254600 chr3D 178343263 178348906 5643 True 8218.000000 8218 93.156000 3 5586 1 chr3D.!!$R1 5583
16 TraesCS2D01G254600 chr6A 343796799 343800628 3829 True 5507.000000 5507 92.787000 1784 5586 1 chr6A.!!$R2 3802
17 TraesCS2D01G254600 chr6A 340839484 340845550 6066 False 4396.500000 8107 94.758000 1 5993 2 chr6A.!!$F1 5992
18 TraesCS2D01G254600 chr3A 596202091 596208195 6104 True 4340.500000 8021 93.968500 1 5993 2 chr3A.!!$R1 5992
19 TraesCS2D01G254600 chr6D 201618173 201622895 4722 False 6896.000000 6896 93.205000 1 4677 1 chr6D.!!$F1 4676
20 TraesCS2D01G254600 chr6D 74702982 74708063 5081 True 3868.500000 7068 95.186500 1021 5993 2 chr6D.!!$R1 4972
21 TraesCS2D01G254600 chrUn 70709522 70711260 1738 False 1300.000000 1940 94.966000 4339 5993 2 chrUn.!!$F1 1654

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
931 958 0.804364 GATCTGCACAAACCGCATCA 59.196 50.0 0.00 0.00 39.02 3.07 F
1946 1979 0.673437 TTAGTTTGCTTGCCCTGCAC 59.327 50.0 0.00 0.00 38.71 4.57 F
2597 2648 0.838122 AAGCAGTGCACTCCCCTACT 60.838 55.0 18.64 4.84 0.00 2.57 F
3712 3817 0.680618 CAGAGCCTCCTCATAGCAGG 59.319 60.0 0.00 0.00 40.68 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 2233 2.556622 CAAATTTAGGGGCGTTCACTGT 59.443 45.455 0.00 0.00 0.00 3.55 R
3015 3104 1.027792 GTTCCCGGTGTGTTGTGTGT 61.028 55.000 0.00 0.00 0.00 3.72 R
3968 4078 1.142748 GACGTCATGGAGCTCCCTG 59.857 63.158 29.95 28.42 35.38 4.45 R
5496 7412 3.076621 TCATTTCTACTGCTTGCACCAG 58.923 45.455 11.06 11.06 36.41 4.00 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
58 63 3.267233 AGGTGCATCCAGCCCCAA 61.267 61.111 0.00 0.00 44.14 4.12
200 206 3.869065 CGCCCAAATAAGTAACCAGAGA 58.131 45.455 0.00 0.00 0.00 3.10
931 958 0.804364 GATCTGCACAAACCGCATCA 59.196 50.000 0.00 0.00 39.02 3.07
958 985 3.461061 GAGATCATGCAGTTCATCCGAA 58.539 45.455 0.00 0.00 31.79 4.30
1312 1339 3.224007 AAACCCGCCCTCTGCCAAT 62.224 57.895 0.00 0.00 36.24 3.16
1361 1388 2.357517 CTTCCAACTGAGCGCCGT 60.358 61.111 2.29 0.00 0.00 5.68
1673 1705 2.263540 GGCAAAGGACGCCTACGA 59.736 61.111 0.00 0.00 46.56 3.43
1692 1724 3.065786 ACGAAGCGTACGAGATATGGAAA 59.934 43.478 21.65 0.00 38.73 3.13
1707 1739 1.492599 TGGAAACACATCACCCTCACA 59.507 47.619 0.00 0.00 33.40 3.58
1897 1930 6.539324 TGTTGTTTGCTTATGTATCGTTAGC 58.461 36.000 0.00 0.00 0.00 3.09
1941 1974 2.608016 GCTGAACTTAGTTTGCTTGCCC 60.608 50.000 13.71 0.00 0.00 5.36
1946 1979 0.673437 TTAGTTTGCTTGCCCTGCAC 59.327 50.000 0.00 0.00 38.71 4.57
2194 2233 5.406767 AAGTTTACACATACGCAACGAAA 57.593 34.783 0.00 0.00 0.00 3.46
2597 2648 0.838122 AAGCAGTGCACTCCCCTACT 60.838 55.000 18.64 4.84 0.00 2.57
2978 3067 3.067106 CGCTTATAAACAGATCGGGCAT 58.933 45.455 0.00 0.00 0.00 4.40
3015 3104 3.332485 AGGTGGAACTAAACATTAGGCCA 59.668 43.478 5.01 8.83 36.74 5.36
3024 3115 2.356665 ACATTAGGCCACACACAACA 57.643 45.000 5.01 0.00 0.00 3.33
3385 3481 4.333926 AGTCTCGCTAAAATGAAGAATGCC 59.666 41.667 0.00 0.00 0.00 4.40
3457 3553 7.969536 TGAAAGAACTCCATCAAGAAACTAG 57.030 36.000 0.00 0.00 0.00 2.57
3560 3656 3.181528 CGTGGACGTACGCAATTATGTTT 60.182 43.478 16.72 0.00 37.24 2.83
3638 3743 2.162319 TCTGACAGTTGCGTGCATAA 57.838 45.000 1.59 0.00 0.00 1.90
3680 3785 1.134788 AGGACACGACATTCCGGATTC 60.135 52.381 4.15 1.04 36.95 2.52
3712 3817 0.680618 CAGAGCCTCCTCATAGCAGG 59.319 60.000 0.00 0.00 40.68 4.85
3714 3819 1.149711 AGAGCCTCCTCATAGCAGGAT 59.850 52.381 0.00 0.00 42.02 3.24
3758 3865 2.279037 AAAACAGAGCCCCACCACGT 62.279 55.000 0.00 0.00 0.00 4.49
3980 4095 0.983378 GGTACACCAGGGAGCTCCAT 60.983 60.000 33.29 25.66 38.24 3.41
4041 4156 1.679139 CACAAGCAAGGGTGAAGACA 58.321 50.000 0.00 0.00 37.18 3.41
4140 4255 0.600255 GCACTACGTGAAGCCACAGT 60.600 55.000 0.00 0.00 43.34 3.55
4224 4341 7.168302 CAGCTAAAGACAGGTCAGAATATAACG 59.832 40.741 1.84 0.00 0.00 3.18
4940 6805 2.774234 CCATACTCTGTGGGGATTCTGT 59.226 50.000 0.00 0.00 32.98 3.41
4950 6815 3.890527 GGATTCTGTCCACTGCCAT 57.109 52.632 0.00 0.00 46.96 4.40
5339 7225 9.787435 TTAGTTTGTGTTAGAACAAGTATCCAT 57.213 29.630 0.00 0.00 40.93 3.41
5496 7412 1.192534 GTTCAGTGCAGTACTCAACGC 59.807 52.381 0.00 0.00 37.60 4.84
5746 7720 9.269108 CTTAAATGTAAGTCATGCAGTCCGCAT 62.269 40.741 0.00 0.00 45.35 4.73
5830 7804 1.472201 CGTGCAGCACAGGACTATGAT 60.472 52.381 25.19 0.00 36.20 2.45
5932 7909 3.152341 AGAAATATGCTACCCATGCAGC 58.848 45.455 0.00 5.50 44.04 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 56 1.229082 TACGAGACTGGTTGGGGCT 60.229 57.895 0.00 0.00 0.00 5.19
58 63 2.940527 GCAGACCTACTACGAGACTGGT 60.941 54.545 0.00 0.00 0.00 4.00
200 206 3.284449 GGCGGCCGTGTTGAACTT 61.284 61.111 28.70 0.00 0.00 2.66
228 234 1.213094 CGCGCCCGACCTGTTTATAG 61.213 60.000 0.00 0.00 36.29 1.31
256 262 0.834687 TGTTTAGTCCCACCTCGCCT 60.835 55.000 0.00 0.00 0.00 5.52
698 722 2.922740 TTGGTTAGAGTTCCGCACTT 57.077 45.000 0.00 0.00 35.01 3.16
931 958 2.159000 TGAACTGCATGATCTCGCTGAT 60.159 45.455 16.61 8.05 38.27 2.90
943 970 0.108186 TCGCTTCGGATGAACTGCAT 60.108 50.000 0.00 0.00 40.77 3.96
1312 1339 2.151202 GTGTTTCTTGCCGATGGAGAA 58.849 47.619 0.00 0.00 0.00 2.87
1361 1388 1.305201 GAAGACGGTGCACCTTTCAA 58.695 50.000 32.28 0.00 0.00 2.69
1547 1579 2.278792 CGTCGATGAGCATGCCGA 60.279 61.111 15.66 13.49 0.00 5.54
1673 1705 4.110482 GTGTTTCCATATCTCGTACGCTT 58.890 43.478 11.24 0.00 0.00 4.68
1692 1724 0.397941 CCTGTGTGAGGGTGATGTGT 59.602 55.000 0.00 0.00 38.36 3.72
1897 1930 5.675970 CAAAAGCAAATGATCACAAGCAAG 58.324 37.500 14.98 1.71 0.00 4.01
1941 1974 5.798434 CACATCATTACAAGTGATTGTGCAG 59.202 40.000 3.95 0.00 34.21 4.41
1946 1979 8.908678 CAAAGTTCACATCATTACAAGTGATTG 58.091 33.333 0.00 0.00 40.32 2.67
2194 2233 2.556622 CAAATTTAGGGGCGTTCACTGT 59.443 45.455 0.00 0.00 0.00 3.55
2767 2835 4.746115 CACATGTGGTGGTCAATTTTTCTG 59.254 41.667 18.51 0.00 44.04 3.02
2912 3001 5.098663 ACTCCTCTGGTTACTTATTTGGGA 58.901 41.667 0.00 0.00 0.00 4.37
2999 3088 4.465886 TGTGTGTGGCCTAATGTTTAGTT 58.534 39.130 3.32 0.00 0.00 2.24
3015 3104 1.027792 GTTCCCGGTGTGTTGTGTGT 61.028 55.000 0.00 0.00 0.00 3.72
3328 3424 5.002516 AGAAGGAGAACTGCATTTCAGAAG 58.997 41.667 17.88 0.00 45.72 2.85
3385 3481 3.496884 TGCTTTGCTTAACTAACAGGACG 59.503 43.478 0.00 0.00 0.00 4.79
3680 3785 1.298859 GGCTCTGTTAGTGCGTTGGG 61.299 60.000 0.00 0.00 35.71 4.12
3712 3817 2.164624 ACGTGGCAACTACAGAGAGATC 59.835 50.000 0.00 0.00 37.61 2.75
3714 3819 1.617322 ACGTGGCAACTACAGAGAGA 58.383 50.000 0.00 0.00 37.61 3.10
3758 3865 3.324108 GGTGGAGCGGGGTGGTAA 61.324 66.667 0.00 0.00 0.00 2.85
3968 4078 1.142748 GACGTCATGGAGCTCCCTG 59.857 63.158 29.95 28.42 35.38 4.45
3980 4095 3.359523 CCGTGGAGGTCGACGTCA 61.360 66.667 32.23 19.22 44.69 4.35
4140 4255 2.959484 GCTGGAGCACTACTGCCCA 61.959 63.158 0.45 0.00 45.53 5.36
4147 4262 1.609072 CTACGCATAGCTGGAGCACTA 59.391 52.381 0.00 0.00 45.16 2.74
4262 4379 4.909696 TGGCGATTGAAGTGAAGAAAAA 57.090 36.364 0.00 0.00 0.00 1.94
4313 4430 5.862323 GTCAATGAATTCATATGCCATGCTC 59.138 40.000 21.00 7.73 35.10 4.26
4860 5007 5.363580 TGTAGTGAATGTCTATCATCCTGCA 59.636 40.000 0.00 0.00 35.48 4.41
4940 6805 4.854173 TGATAAGCTTTTATGGCAGTGGA 58.146 39.130 3.20 0.00 0.00 4.02
5259 7145 5.105957 ACTGTGACACATAAGCAAACAACAA 60.106 36.000 9.11 0.00 0.00 2.83
5496 7412 3.076621 TCATTTCTACTGCTTGCACCAG 58.923 45.455 11.06 11.06 36.41 4.00
5717 7691 7.224753 CGGACTGCATGACTTACATTTAAGTAT 59.775 37.037 4.27 0.00 46.67 2.12


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

AutoCloner maintained by Alex Coulton.