Multiple sequence alignment - TraesCS3D01G110400

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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 TraesCS3D01G110400 chr3D 100.000 3458 0 0 1 3458 64182277 64185734 0.000000e+00 6386.0
1 TraesCS3D01G110400 chr3B 93.921 2780 106 21 733 3458 106416194 106418964 0.000000e+00 4139.0
2 TraesCS3D01G110400 chr3B 88.105 723 52 22 1 703 106415484 106416192 0.000000e+00 828.0
3 TraesCS3D01G110400 chr3B 100.000 29 0 0 44 72 434708795 434708767 2.000000e-03 54.7
4 TraesCS3D01G110400 chr3A 92.957 2073 89 9 930 2999 74360032 74362050 0.000000e+00 2966.0
5 TraesCS3D01G110400 chr3A 84.615 169 9 6 688 840 74359433 74359600 5.980000e-33 152.0
6 TraesCS3D01G110400 chr3A 86.131 137 10 4 1 137 74353266 74353393 4.650000e-29 139.0
7 TraesCS3D01G110400 chr5D 84.082 245 35 3 1848 2088 42036157 42036401 2.080000e-57 233.0
8 TraesCS3D01G110400 chr7A 85.417 144 16 4 417 555 670505672 670505529 1.000000e-30 145.0
9 TraesCS3D01G110400 chr6B 82.313 147 20 4 35 177 141650853 141650709 4.690000e-24 122.0
10 TraesCS3D01G110400 chr1D 77.095 179 28 11 329 502 7830174 7830344 1.320000e-14 91.6
11 TraesCS3D01G110400 chr2D 90.566 53 5 0 415 467 469374712 469374764 1.720000e-08 71.3
12 TraesCS3D01G110400 chr5B 87.500 56 7 0 608 663 356504690 356504635 8.010000e-07 65.8


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 TraesCS3D01G110400 chr3D 64182277 64185734 3457 False 6386.0 6386 100.000 1 3458 1 chr3D.!!$F1 3457
1 TraesCS3D01G110400 chr3B 106415484 106418964 3480 False 2483.5 4139 91.013 1 3458 2 chr3B.!!$F1 3457
2 TraesCS3D01G110400 chr3A 74359433 74362050 2617 False 1559.0 2966 88.786 688 2999 2 chr3A.!!$F2 2311

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
764 786 0.179124 GCCACCAACGTTCTTTTGCA 60.179 50.0 0.0 0.0 0.0 4.08 F
946 1336 0.684479 TCCTCATCTCACACCTCCCG 60.684 60.0 0.0 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2206 2625 0.035725 TCCAGCTGCAATGTCAGAGG 60.036 55.0 8.66 8.69 36.19 3.69 R
2904 3333 0.394899 GTGCAAGCTAAGCCCCAGAT 60.395 55.0 8.43 0.00 0.00 2.90 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
21 22 3.407209 AGATGATTACCACCATTCCCCT 58.593 45.455 0.00 0.00 0.00 4.79
22 23 3.793827 AGATGATTACCACCATTCCCCTT 59.206 43.478 0.00 0.00 0.00 3.95
24 25 2.243736 TGATTACCACCATTCCCCTTCC 59.756 50.000 0.00 0.00 0.00 3.46
29 30 2.158019 ACCACCATTCCCCTTCCATTTT 60.158 45.455 0.00 0.00 0.00 1.82
91 94 7.500892 ACATTTTCGGTATATGCCAGAAACATA 59.499 33.333 20.56 12.28 33.93 2.29
102 105 6.176975 TGCCAGAAACATATTTTCTACACG 57.823 37.500 10.56 0.00 36.69 4.49
195 198 2.288729 TGCTCAATTCGTCTATGCATGC 59.711 45.455 11.82 11.82 0.00 4.06
198 201 4.056740 CTCAATTCGTCTATGCATGCTCT 58.943 43.478 20.33 8.90 0.00 4.09
199 202 4.053983 TCAATTCGTCTATGCATGCTCTC 58.946 43.478 20.33 4.26 0.00 3.20
203 206 2.366590 TCGTCTATGCATGCTCTCCATT 59.633 45.455 20.33 0.00 29.71 3.16
204 207 3.136763 CGTCTATGCATGCTCTCCATTT 58.863 45.455 20.33 0.00 29.71 2.32
207 210 5.517904 GTCTATGCATGCTCTCCATTTTTC 58.482 41.667 20.33 0.00 29.71 2.29
220 223 7.095857 GCTCTCCATTTTTCTCGTATACATCAG 60.096 40.741 3.32 0.00 0.00 2.90
602 623 3.443588 AAAAAGGCAGTGGCGTCC 58.556 55.556 11.51 0.00 42.47 4.79
686 707 3.185651 CGAGACATAGTCGCCCATG 57.814 57.895 0.00 0.00 37.67 3.66
705 726 3.499737 GCCGTCTGTCGCCCATTG 61.500 66.667 0.00 0.00 38.35 2.82
718 740 3.111442 CATTGTTTTGCGCGCCCC 61.111 61.111 30.77 13.91 0.00 5.80
719 741 4.371590 ATTGTTTTGCGCGCCCCC 62.372 61.111 30.77 14.29 0.00 5.40
764 786 0.179124 GCCACCAACGTTCTTTTGCA 60.179 50.000 0.00 0.00 0.00 4.08
889 952 1.597461 CAGTTTCCCTCCCGTCTCC 59.403 63.158 0.00 0.00 0.00 3.71
929 1319 4.673534 TTTAAATTTCGAACGCCTCTCC 57.326 40.909 0.00 0.00 0.00 3.71
930 1320 2.474410 AAATTTCGAACGCCTCTCCT 57.526 45.000 0.00 0.00 0.00 3.69
931 1321 2.011540 AATTTCGAACGCCTCTCCTC 57.988 50.000 0.00 0.00 0.00 3.71
946 1336 0.684479 TCCTCATCTCACACCTCCCG 60.684 60.000 0.00 0.00 0.00 5.14
958 1348 4.489771 CTCCCGCACCATCCACCC 62.490 72.222 0.00 0.00 0.00 4.61
966 1363 1.414919 GCACCATCCACCCGACTAATA 59.585 52.381 0.00 0.00 0.00 0.98
1145 1550 4.016706 CGTGCCCTTCCTCCCGTT 62.017 66.667 0.00 0.00 0.00 4.44
1587 1995 4.500116 GAGTGCTCCGGCTCCGTC 62.500 72.222 7.59 0.00 39.59 4.79
1762 2170 2.360801 ACAATTTCCAAGAACACCGGTG 59.639 45.455 32.83 32.83 0.00 4.94
1804 2215 2.409870 CCATGGCCTTCCGCAGTTC 61.410 63.158 3.32 0.00 40.31 3.01
2203 2622 4.029520 TGGTGTATGGCATGGCTAATTTT 58.970 39.130 21.08 1.27 0.00 1.82
2221 2640 3.648339 TTTTTCCTCTGACATTGCAGC 57.352 42.857 0.00 0.00 35.86 5.25
2289 2708 3.056313 GCGCTCACCCTTGAATGCC 62.056 63.158 0.00 0.00 0.00 4.40
2336 2755 3.012502 TCCCTTGTCAGGTACAGTCCTAT 59.987 47.826 0.00 0.00 39.87 2.57
2504 2923 0.685785 TTTGGCTCTTGTGGGTTGCA 60.686 50.000 0.00 0.00 0.00 4.08
2519 2938 2.143122 GTTGCAACTGAACCGATGAGA 58.857 47.619 22.36 0.00 0.00 3.27
2763 3187 4.342092 CCCTTGTGTATTTGATTCCATCCC 59.658 45.833 0.00 0.00 0.00 3.85
2777 3201 6.677965 TGATTCCATCCCATATAGCCTTGATA 59.322 38.462 0.00 0.00 0.00 2.15
2784 3208 8.878211 CATCCCATATAGCCTTGATAGATATGT 58.122 37.037 0.00 0.00 31.40 2.29
2804 3233 9.880064 GATATGTCAAATTGTTGATGATCTCAG 57.120 33.333 0.00 0.00 45.38 3.35
2871 3300 7.611855 CCTAGAACCACCAATAGTTTCTGAAAT 59.388 37.037 6.06 0.00 0.00 2.17
2872 3301 7.219484 AGAACCACCAATAGTTTCTGAAATG 57.781 36.000 6.06 0.58 0.00 2.32
2884 3313 2.507484 TCTGAAATGCCACCTGACTTG 58.493 47.619 0.00 0.00 0.00 3.16
2904 3333 2.897326 TGTGTAGTCTTTGCCTCAGCTA 59.103 45.455 0.00 0.00 40.80 3.32
2917 3346 1.001860 CTCAGCTATCTGGGGCTTAGC 59.998 57.143 0.00 0.00 40.69 3.09
2934 3363 2.119801 AGCTTGCACCCTAGTTGATG 57.880 50.000 0.00 0.00 0.00 3.07
2990 3419 7.910162 ACATTGCTATGTTTGATAAATCGTGAC 59.090 33.333 8.03 0.00 42.29 3.67
3019 3448 8.871686 AAATAGTTTGTGTTTTCATGAAGACC 57.128 30.769 22.40 15.34 0.00 3.85
3054 3483 8.669946 AAACCAAAACCCATGTTATGTAAAAG 57.330 30.769 0.00 0.00 33.30 2.27
3120 3549 5.032846 TCCATAACAAAGGGAGTGATCTCT 58.967 41.667 0.00 0.00 40.29 3.10
3265 3694 6.658816 AGCTCAGATCTGTAGATACGATTCAT 59.341 38.462 21.92 0.00 34.37 2.57
3273 3702 6.776116 TCTGTAGATACGATTCATGGTAGGTT 59.224 38.462 0.00 0.00 0.00 3.50
3274 3703 7.940688 TCTGTAGATACGATTCATGGTAGGTTA 59.059 37.037 0.00 0.00 0.00 2.85
3381 3810 4.741321 TGCAATTCAATCTTTCATCCCC 57.259 40.909 0.00 0.00 0.00 4.81
3382 3811 3.451902 TGCAATTCAATCTTTCATCCCCC 59.548 43.478 0.00 0.00 0.00 5.40
3383 3812 3.451902 GCAATTCAATCTTTCATCCCCCA 59.548 43.478 0.00 0.00 0.00 4.96
3384 3813 4.442472 GCAATTCAATCTTTCATCCCCCAG 60.442 45.833 0.00 0.00 0.00 4.45
3385 3814 4.614967 ATTCAATCTTTCATCCCCCAGT 57.385 40.909 0.00 0.00 0.00 4.00
3386 3815 3.652057 TCAATCTTTCATCCCCCAGTC 57.348 47.619 0.00 0.00 0.00 3.51
3449 3878 9.314321 AGTTAAATACTCATTAATCGACCTGTG 57.686 33.333 0.00 0.00 28.23 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.252535 AAATGGAAGGGGAATGGTGG 57.747 50.000 0.00 0.00 0.00 4.61
55 56 9.414295 GCATATACCGAAAATGTATAGTGTGTA 57.586 33.333 0.00 0.00 35.31 2.90
56 57 7.386848 GGCATATACCGAAAATGTATAGTGTGT 59.613 37.037 0.00 0.00 35.31 3.72
57 58 7.386573 TGGCATATACCGAAAATGTATAGTGTG 59.613 37.037 0.00 0.00 35.31 3.82
62 63 8.995220 GTTTCTGGCATATACCGAAAATGTATA 58.005 33.333 11.25 0.00 35.52 1.47
63 64 7.500892 TGTTTCTGGCATATACCGAAAATGTAT 59.499 33.333 11.25 0.00 35.52 2.29
170 173 6.661669 CATGCATAGACGAATTGAGCATAAA 58.338 36.000 0.00 0.00 39.00 1.40
171 174 5.334337 GCATGCATAGACGAATTGAGCATAA 60.334 40.000 14.21 0.00 39.00 1.90
176 179 4.056740 AGAGCATGCATAGACGAATTGAG 58.943 43.478 21.98 0.00 0.00 3.02
183 186 2.452295 ATGGAGAGCATGCATAGACG 57.548 50.000 21.98 0.00 38.35 4.18
186 189 5.560375 CGAGAAAAATGGAGAGCATGCATAG 60.560 44.000 21.98 0.00 39.36 2.23
195 198 7.383572 CCTGATGTATACGAGAAAAATGGAGAG 59.616 40.741 0.00 0.00 0.00 3.20
198 201 7.119709 TCCTGATGTATACGAGAAAAATGGA 57.880 36.000 0.00 0.00 0.00 3.41
199 202 7.786178 TTCCTGATGTATACGAGAAAAATGG 57.214 36.000 0.00 0.00 0.00 3.16
204 207 8.988934 GCAAATATTCCTGATGTATACGAGAAA 58.011 33.333 0.00 0.00 0.00 2.52
207 210 7.600375 ACAGCAAATATTCCTGATGTATACGAG 59.400 37.037 17.95 0.00 40.22 4.18
261 264 9.454585 AAAATGTGTATGATAAAATGCTGATCG 57.545 29.630 0.00 0.00 0.00 3.69
372 377 9.797556 CTGAAGAAAGATCATCATGCATTTTTA 57.202 29.630 0.00 0.00 33.21 1.52
388 393 8.251026 ACGATATACAATGTGTCTGAAGAAAGA 58.749 33.333 0.00 0.00 0.00 2.52
764 786 1.545706 GGAGAGGAAGAAGCCACCGT 61.546 60.000 0.00 0.00 0.00 4.83
907 970 4.758165 AGGAGAGGCGTTCGAAATTTAAAA 59.242 37.500 0.00 0.00 0.00 1.52
929 1319 1.142748 GCGGGAGGTGTGAGATGAG 59.857 63.158 0.00 0.00 0.00 2.90
930 1320 1.609210 TGCGGGAGGTGTGAGATGA 60.609 57.895 0.00 0.00 0.00 2.92
931 1321 1.448540 GTGCGGGAGGTGTGAGATG 60.449 63.158 0.00 0.00 0.00 2.90
946 1336 0.180406 ATTAGTCGGGTGGATGGTGC 59.820 55.000 0.00 0.00 0.00 5.01
958 1348 1.336887 CCAGATGCGGGGTATTAGTCG 60.337 57.143 0.00 0.00 0.00 4.18
1145 1550 1.453379 CTCCGCGGGAAGTAGAGGA 60.453 63.158 27.83 0.00 0.00 3.71
1804 2215 6.968131 TTAGACCAGAATGAAACGAATGAG 57.032 37.500 0.00 0.00 39.69 2.90
1989 2408 3.532896 GGAATCACCGCAGAACTCA 57.467 52.632 0.00 0.00 0.00 3.41
2046 2465 0.400213 TCGGGTGGCTGTTGAAGAAT 59.600 50.000 0.00 0.00 0.00 2.40
2203 2622 2.156917 CAGCTGCAATGTCAGAGGAAA 58.843 47.619 0.00 0.00 36.19 3.13
2206 2625 0.035725 TCCAGCTGCAATGTCAGAGG 60.036 55.000 8.66 8.69 36.19 3.69
2221 2640 1.479709 ATCAGGAACCTCGAGTCCAG 58.520 55.000 20.73 14.43 0.00 3.86
2336 2755 3.785859 GGACCATCCTCCGCAGCA 61.786 66.667 0.00 0.00 32.53 4.41
2504 2923 5.923733 ATAAGAGTCTCATCGGTTCAGTT 57.076 39.130 1.94 0.00 0.00 3.16
2519 2938 6.758886 GCTCAATAGTAGCACACAATAAGAGT 59.241 38.462 0.00 0.00 39.83 3.24
2777 3201 9.623000 TGAGATCATCAACAATTTGACATATCT 57.377 29.630 2.79 3.97 44.66 1.98
2784 3208 5.416639 CCCACTGAGATCATCAACAATTTGA 59.583 40.000 2.79 0.00 45.93 2.69
2789 3218 4.849813 ATCCCACTGAGATCATCAACAA 57.150 40.909 0.00 0.00 37.52 2.83
2833 3262 4.657039 GGTGGTTCTAGGTATGTCCCATTA 59.343 45.833 0.00 0.00 36.75 1.90
2841 3270 7.495934 CAGAAACTATTGGTGGTTCTAGGTATG 59.504 40.741 0.00 0.00 0.00 2.39
2871 3300 1.128200 ACTACACAAGTCAGGTGGCA 58.872 50.000 0.00 0.00 40.54 4.92
2884 3313 2.464157 AGCTGAGGCAAAGACTACAC 57.536 50.000 0.00 0.00 41.70 2.90
2892 3321 0.548031 CCCCAGATAGCTGAGGCAAA 59.452 55.000 10.19 0.00 45.17 3.68
2904 3333 0.394899 GTGCAAGCTAAGCCCCAGAT 60.395 55.000 8.43 0.00 0.00 2.90
2912 3341 3.334583 TCAACTAGGGTGCAAGCTAAG 57.665 47.619 0.00 0.00 0.00 2.18
2913 3342 3.009033 ACATCAACTAGGGTGCAAGCTAA 59.991 43.478 0.00 0.00 0.00 3.09
2914 3343 2.571653 ACATCAACTAGGGTGCAAGCTA 59.428 45.455 0.00 0.00 0.00 3.32
2934 3363 5.009610 TCCACTTCAAAAGATAACCAAGCAC 59.990 40.000 0.00 0.00 0.00 4.40
3047 3476 7.261325 TCACATTTTGTTAAGCAGCTTTTACA 58.739 30.769 14.29 14.91 0.00 2.41
3054 3483 7.412137 AAATCTTCACATTTTGTTAAGCAGC 57.588 32.000 0.00 0.00 33.02 5.25
3138 3567 9.841880 GAGTACAGAAGATTGATATGCGTAATA 57.158 33.333 0.00 0.00 0.00 0.98
3143 3572 6.364706 GGAAGAGTACAGAAGATTGATATGCG 59.635 42.308 0.00 0.00 0.00 4.73
3149 3578 6.267699 TCAGTTGGAAGAGTACAGAAGATTGA 59.732 38.462 0.00 0.00 0.00 2.57
3223 3652 6.643388 TCTGAGCTTCATCTAATTGCAACTA 58.357 36.000 0.00 0.00 0.00 2.24
3323 3752 5.449107 AATGCAGCACTCATTTGGATATC 57.551 39.130 0.00 0.00 30.60 1.63
3374 3803 1.612146 TCTTGCGACTGGGGGATGA 60.612 57.895 0.00 0.00 0.00 2.92
3381 3810 1.012086 CATCATGGTCTTGCGACTGG 58.988 55.000 0.00 0.00 40.10 4.00
3382 3811 1.012086 CCATCATGGTCTTGCGACTG 58.988 55.000 0.00 0.00 40.10 3.51
3383 3812 0.904649 TCCATCATGGTCTTGCGACT 59.095 50.000 2.79 0.00 39.03 4.18
3384 3813 1.009829 GTCCATCATGGTCTTGCGAC 58.990 55.000 2.79 0.00 39.03 5.19
3385 3814 0.612744 TGTCCATCATGGTCTTGCGA 59.387 50.000 2.79 0.00 39.03 5.10
3386 3815 1.452110 TTGTCCATCATGGTCTTGCG 58.548 50.000 2.79 0.00 39.03 4.85


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

AutoCloner maintained by Alex Coulton.