Multiple sequence alignment - TraesCS1A01G065100

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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 TraesCS1A01G065100 chr1A 100.000 3212 0 0 1 3212 47215447 47212236 0.000000e+00 5932
1 TraesCS1A01G065100 chr1A 87.474 479 51 7 958 1434 45799771 45799300 7.840000e-151 544
2 TraesCS1A01G065100 chr1A 78.571 168 24 2 235 395 45800917 45800755 2.040000e-17 100
3 TraesCS1A01G065100 chr1D 95.663 3136 74 22 102 3212 47333397 47330299 0.000000e+00 4981
4 TraesCS1A01G065100 chr1D 86.136 339 36 8 2439 2770 381308237 381308571 3.940000e-94 355
5 TraesCS1A01G065100 chr1B 94.710 3157 99 24 82 3212 67057614 67054500 0.000000e+00 4843
6 TraesCS1A01G065100 chr1B 87.834 337 34 6 2437 2770 511445462 511445794 3.890000e-104 388
7 TraesCS1A01G065100 chr5B 85.552 353 43 7 2439 2789 139411600 139411946 2.360000e-96 363
8 TraesCS1A01G065100 chr7D 84.958 359 44 6 2437 2788 483478680 483478325 3.940000e-94 355
9 TraesCS1A01G065100 chr7D 84.011 369 46 8 2435 2797 469841315 469840954 3.070000e-90 342
10 TraesCS1A01G065100 chr4B 84.958 359 44 8 2436 2789 99596354 99596707 3.940000e-94 355
11 TraesCS1A01G065100 chr7B 84.511 368 46 10 2435 2797 493524768 493524407 1.420000e-93 353


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 TraesCS1A01G065100 chr1A 47212236 47215447 3211 True 5932 5932 100.0000 1 3212 1 chr1A.!!$R1 3211
1 TraesCS1A01G065100 chr1A 45799300 45800917 1617 True 322 544 83.0225 235 1434 2 chr1A.!!$R2 1199
2 TraesCS1A01G065100 chr1D 47330299 47333397 3098 True 4981 4981 95.6630 102 3212 1 chr1D.!!$R1 3110
3 TraesCS1A01G065100 chr1B 67054500 67057614 3114 True 4843 4843 94.7100 82 3212 1 chr1B.!!$R1 3130

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
129 131 0.621609 TATTTTGGGACGGGGGAGTG 59.378 55.0 0.00 0.0 0.0 3.51 F
826 855 0.806868 ATGCTGACAATTGCTCCGTG 59.193 50.0 5.05 0.0 0.0 4.94 F
971 1476 2.832129 CCTGGAGTACTTAGTCTTGGCA 59.168 50.0 0.00 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 2425 2.568062 TCAGGATTAACTGGTTGCGGTA 59.432 45.455 0.00 0.0 38.98 4.02 R
2161 2667 1.093159 CCACCTTGATGAGCTTCAGC 58.907 55.000 0.00 0.0 42.49 4.26 R
2838 3350 3.128242 GGAAGTGCTACTTGTACTCGCTA 59.872 47.826 6.31 0.0 40.73 4.26 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
74 75 8.879759 TCAATTAAAGAAGGCTAATAACAGACG 58.120 33.333 0.00 0.00 0.00 4.18
75 76 7.787725 ATTAAAGAAGGCTAATAACAGACGG 57.212 36.000 0.00 0.00 0.00 4.79
76 77 5.416271 AAAGAAGGCTAATAACAGACGGA 57.584 39.130 0.00 0.00 0.00 4.69
77 78 5.416271 AAGAAGGCTAATAACAGACGGAA 57.584 39.130 0.00 0.00 0.00 4.30
78 79 5.416271 AGAAGGCTAATAACAGACGGAAA 57.584 39.130 0.00 0.00 0.00 3.13
79 80 5.420409 AGAAGGCTAATAACAGACGGAAAG 58.580 41.667 0.00 0.00 0.00 2.62
80 81 4.820894 AGGCTAATAACAGACGGAAAGT 57.179 40.909 0.00 0.00 0.00 2.66
87 88 7.009357 GCTAATAACAGACGGAAAGTAGTTGAG 59.991 40.741 0.00 0.00 34.42 3.02
89 90 2.299297 ACAGACGGAAAGTAGTTGAGGG 59.701 50.000 0.00 0.00 0.00 4.30
92 93 1.900486 ACGGAAAGTAGTTGAGGGGAG 59.100 52.381 0.00 0.00 0.00 4.30
96 97 2.861147 AAGTAGTTGAGGGGAGCAAC 57.139 50.000 0.00 0.00 44.46 4.17
124 126 2.089201 GACACTTATTTTGGGACGGGG 58.911 52.381 0.00 0.00 0.00 5.73
129 131 0.621609 TATTTTGGGACGGGGGAGTG 59.378 55.000 0.00 0.00 0.00 3.51
132 134 3.549433 TTGGGACGGGGGAGTGCTA 62.549 63.158 0.00 0.00 32.80 3.49
133 135 3.155167 GGGACGGGGGAGTGCTAG 61.155 72.222 0.00 0.00 32.80 3.42
168 170 4.718774 TGTTAGGAGAGATCTGCTGGAAAT 59.281 41.667 13.50 0.00 44.59 2.17
421 430 1.371558 GGAGTTTCTGGTCGCCACT 59.628 57.895 0.00 0.00 0.00 4.00
490 499 3.244735 GCCCCCTTCTCCATATTTCTCTC 60.245 52.174 0.00 0.00 0.00 3.20
498 507 7.016465 CCTTCTCCATATTTCTCTCTTCCATCT 59.984 40.741 0.00 0.00 0.00 2.90
499 508 7.927683 TCTCCATATTTCTCTCTTCCATCTT 57.072 36.000 0.00 0.00 0.00 2.40
523 534 2.372172 CCATGGCCTAGGTTTAGGGTAG 59.628 54.545 11.31 0.00 45.66 3.18
576 587 4.051237 GTTTTCCAGTCTGCATTTGTTCC 58.949 43.478 0.00 0.00 0.00 3.62
628 639 9.342308 ACAATGTATGATGTCCTGGTTTAATAG 57.658 33.333 0.00 0.00 0.00 1.73
825 854 1.200716 CAATGCTGACAATTGCTCCGT 59.799 47.619 5.05 0.00 0.00 4.69
826 855 0.806868 ATGCTGACAATTGCTCCGTG 59.193 50.000 5.05 0.00 0.00 4.94
897 949 9.398170 CATAAATAAATGCTGAATTCGTAAGGG 57.602 33.333 0.04 0.00 38.47 3.95
932 984 4.038402 GCAATAGCTCCAAAGTTATGCCAT 59.962 41.667 0.00 0.00 37.91 4.40
971 1476 2.832129 CCTGGAGTACTTAGTCTTGGCA 59.168 50.000 0.00 0.00 0.00 4.92
1143 1649 3.304928 GCAATTTCTGGGACAACAGACAG 60.305 47.826 0.00 0.00 46.44 3.51
1347 1853 5.580022 AGACAGTTTTATGGCACCCTTTAT 58.420 37.500 0.00 0.00 0.00 1.40
1533 2039 3.028850 TCCCGACATTGGTCTAGTTAGG 58.971 50.000 0.00 0.00 42.05 2.69
1919 2425 3.327172 CCCATGTCCTATTCTCATCAGCT 59.673 47.826 0.00 0.00 0.00 4.24
2043 2549 3.955471 AGGATTCGAGGCAATTGAGAAA 58.045 40.909 10.34 0.00 0.00 2.52
2061 2567 5.818336 TGAGAAACGACTTTACACAATGGAA 59.182 36.000 0.00 0.00 0.00 3.53
2332 2838 7.900782 TTTATTGTAGTGACAGGAAACTAGC 57.099 36.000 0.00 0.00 40.21 3.42
2414 2921 3.248446 TTGTAGTGACAGGGGCGCC 62.248 63.158 21.18 21.18 36.76 6.53
2423 2930 2.284699 AGGGGCGCCTACTTCTGT 60.285 61.111 28.56 0.21 0.00 3.41
2433 2943 4.671766 GCGCCTACTTCTGTTGGTAAATTG 60.672 45.833 0.00 0.00 40.42 2.32
2508 3018 9.793252 ATATTTCAATGAGATTTAACTGTGTGC 57.207 29.630 0.00 0.00 0.00 4.57
2788 3300 9.939424 GTGGGGATAACTCTCTTAGGTATATAT 57.061 37.037 0.00 0.00 38.27 0.86
2838 3350 6.305272 TGATAAGAGAACTGGAGAAAGCAT 57.695 37.500 0.00 0.00 0.00 3.79
2885 3415 8.491958 CCACAACCTAGTAGGGTTAATCTTATT 58.508 37.037 20.54 0.00 46.58 1.40
2915 3445 5.046376 TGAGCTTAATCCAGATGAAGTCACA 60.046 40.000 6.61 2.46 32.82 3.58
3150 3680 5.300752 CAATCTATGGACGGCAATCTTAGT 58.699 41.667 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 8.879759 CGTCTGTTATTAGCCTTCTTTAATTGA 58.120 33.333 0.00 0.00 0.00 2.57
49 50 8.122952 CCGTCTGTTATTAGCCTTCTTTAATTG 58.877 37.037 0.00 0.00 0.00 2.32
50 51 8.044908 TCCGTCTGTTATTAGCCTTCTTTAATT 58.955 33.333 0.00 0.00 0.00 1.40
51 52 7.562135 TCCGTCTGTTATTAGCCTTCTTTAAT 58.438 34.615 0.00 0.00 0.00 1.40
52 53 6.938507 TCCGTCTGTTATTAGCCTTCTTTAA 58.061 36.000 0.00 0.00 0.00 1.52
53 54 6.534475 TCCGTCTGTTATTAGCCTTCTTTA 57.466 37.500 0.00 0.00 0.00 1.85
54 55 5.416271 TCCGTCTGTTATTAGCCTTCTTT 57.584 39.130 0.00 0.00 0.00 2.52
55 56 5.416271 TTCCGTCTGTTATTAGCCTTCTT 57.584 39.130 0.00 0.00 0.00 2.52
56 57 5.046520 ACTTTCCGTCTGTTATTAGCCTTCT 60.047 40.000 0.00 0.00 0.00 2.85
57 58 5.176592 ACTTTCCGTCTGTTATTAGCCTTC 58.823 41.667 0.00 0.00 0.00 3.46
58 59 5.161943 ACTTTCCGTCTGTTATTAGCCTT 57.838 39.130 0.00 0.00 0.00 4.35
59 60 4.820894 ACTTTCCGTCTGTTATTAGCCT 57.179 40.909 0.00 0.00 0.00 4.58
60 61 5.658468 ACTACTTTCCGTCTGTTATTAGCC 58.342 41.667 0.00 0.00 0.00 3.93
61 62 6.810182 TCAACTACTTTCCGTCTGTTATTAGC 59.190 38.462 0.00 0.00 0.00 3.09
62 63 7.488471 CCTCAACTACTTTCCGTCTGTTATTAG 59.512 40.741 0.00 0.00 0.00 1.73
63 64 7.318141 CCTCAACTACTTTCCGTCTGTTATTA 58.682 38.462 0.00 0.00 0.00 0.98
64 65 6.164176 CCTCAACTACTTTCCGTCTGTTATT 58.836 40.000 0.00 0.00 0.00 1.40
65 66 5.337330 CCCTCAACTACTTTCCGTCTGTTAT 60.337 44.000 0.00 0.00 0.00 1.89
66 67 4.021719 CCCTCAACTACTTTCCGTCTGTTA 60.022 45.833 0.00 0.00 0.00 2.41
67 68 3.244112 CCCTCAACTACTTTCCGTCTGTT 60.244 47.826 0.00 0.00 0.00 3.16
68 69 2.299297 CCCTCAACTACTTTCCGTCTGT 59.701 50.000 0.00 0.00 0.00 3.41
69 70 2.353803 CCCCTCAACTACTTTCCGTCTG 60.354 54.545 0.00 0.00 0.00 3.51
70 71 1.900486 CCCCTCAACTACTTTCCGTCT 59.100 52.381 0.00 0.00 0.00 4.18
71 72 1.897802 TCCCCTCAACTACTTTCCGTC 59.102 52.381 0.00 0.00 0.00 4.79
72 73 1.900486 CTCCCCTCAACTACTTTCCGT 59.100 52.381 0.00 0.00 0.00 4.69
73 74 1.405661 GCTCCCCTCAACTACTTTCCG 60.406 57.143 0.00 0.00 0.00 4.30
74 75 1.628846 TGCTCCCCTCAACTACTTTCC 59.371 52.381 0.00 0.00 0.00 3.13
75 76 3.075148 GTTGCTCCCCTCAACTACTTTC 58.925 50.000 0.00 0.00 40.31 2.62
76 77 3.141767 GTTGCTCCCCTCAACTACTTT 57.858 47.619 0.00 0.00 40.31 2.66
77 78 2.861147 GTTGCTCCCCTCAACTACTT 57.139 50.000 0.00 0.00 40.31 2.24
87 88 0.591659 GTCGTGAAAAGTTGCTCCCC 59.408 55.000 0.00 0.00 0.00 4.81
89 90 1.940613 AGTGTCGTGAAAAGTTGCTCC 59.059 47.619 0.00 0.00 0.00 4.70
92 93 6.291585 CCAAAATAAGTGTCGTGAAAAGTTGC 60.292 38.462 0.00 0.00 0.00 4.17
96 97 5.912955 GTCCCAAAATAAGTGTCGTGAAAAG 59.087 40.000 0.00 0.00 0.00 2.27
98 99 4.024725 CGTCCCAAAATAAGTGTCGTGAAA 60.025 41.667 0.00 0.00 0.00 2.69
100 101 3.061322 CGTCCCAAAATAAGTGTCGTGA 58.939 45.455 0.00 0.00 0.00 4.35
144 146 3.713003 TCCAGCAGATCTCTCCTAACAA 58.287 45.455 0.00 0.00 0.00 2.83
145 147 3.388552 TCCAGCAGATCTCTCCTAACA 57.611 47.619 0.00 0.00 0.00 2.41
147 149 5.397221 CCAATTTCCAGCAGATCTCTCCTAA 60.397 44.000 0.00 0.00 0.00 2.69
148 150 4.102210 CCAATTTCCAGCAGATCTCTCCTA 59.898 45.833 0.00 0.00 0.00 2.94
152 154 3.779183 TCTCCAATTTCCAGCAGATCTCT 59.221 43.478 0.00 0.00 0.00 3.10
421 430 3.744719 CGACGGCTCGACCTTGGA 61.745 66.667 1.50 0.00 43.06 3.53
490 499 1.064166 AGGCCATGGTCAAGATGGAAG 60.064 52.381 20.74 0.00 42.81 3.46
498 507 2.241176 CCTAAACCTAGGCCATGGTCAA 59.759 50.000 20.74 9.75 38.50 3.18
499 508 1.843851 CCTAAACCTAGGCCATGGTCA 59.156 52.381 20.74 3.57 38.50 4.02
596 607 7.050377 ACCAGGACATCATACATTGTTCTTAG 58.950 38.462 0.00 0.00 28.93 2.18
628 639 5.346011 GGAATTTCGCTTGGATTTCAACTTC 59.654 40.000 0.00 0.00 0.00 3.01
825 854 5.089434 AGATGATGTGTATAGGATGAGGCA 58.911 41.667 0.00 0.00 0.00 4.75
826 855 5.674052 AGATGATGTGTATAGGATGAGGC 57.326 43.478 0.00 0.00 0.00 4.70
897 949 4.142403 TGGAGCTATTGCACAGTAATTTGC 60.142 41.667 1.12 0.00 42.74 3.68
932 984 5.884322 TCCAGGTAACAGTTACTCACTAGA 58.116 41.667 20.54 7.56 41.41 2.43
1143 1649 8.140628 TGACAGAACTGATCATATAGCTCTTTC 58.859 37.037 8.87 0.00 0.00 2.62
1533 2039 8.553459 TGAGATCAACTTCAGTTTTAAGATCC 57.447 34.615 11.43 6.66 35.80 3.36
1919 2425 2.568062 TCAGGATTAACTGGTTGCGGTA 59.432 45.455 0.00 0.00 38.98 4.02
2043 2549 5.365619 AGAACTTCCATTGTGTAAAGTCGT 58.634 37.500 0.00 0.00 30.99 4.34
2061 2567 7.888021 TCTGAAGATAAGACTGAGAAGAGAACT 59.112 37.037 0.00 0.00 0.00 3.01
2161 2667 1.093159 CCACCTTGATGAGCTTCAGC 58.907 55.000 0.00 0.00 42.49 4.26
2433 2943 4.863131 CGCGGGGTATCATCTAGTTTATTC 59.137 45.833 0.00 0.00 0.00 1.75
2791 3303 8.766476 TCAATCAAACTCTCCTCATCTTATCTT 58.234 33.333 0.00 0.00 0.00 2.40
2796 3308 8.766476 TCTTATCAATCAAACTCTCCTCATCTT 58.234 33.333 0.00 0.00 0.00 2.40
2797 3309 8.316497 TCTTATCAATCAAACTCTCCTCATCT 57.684 34.615 0.00 0.00 0.00 2.90
2798 3310 8.420222 TCTCTTATCAATCAAACTCTCCTCATC 58.580 37.037 0.00 0.00 0.00 2.92
2838 3350 3.128242 GGAAGTGCTACTTGTACTCGCTA 59.872 47.826 6.31 0.00 40.73 4.26
2885 3415 6.499106 TCATCTGGATTAAGCTCACCATTA 57.501 37.500 0.00 0.00 0.00 1.90
2890 3420 5.293079 GTGACTTCATCTGGATTAAGCTCAC 59.707 44.000 15.44 15.44 32.70 3.51
3150 3680 2.345880 GATCGCCTTCCGCTACCGAA 62.346 60.000 0.00 0.00 36.29 4.30


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

AutoCloner maintained by Alex Coulton.