Multiple sequence alignment - TraesCS3D01G450000

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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 TraesCS3D01G450000 chr3D 100.000 2519 0 0 1 2519 558283431 558280913 0.000000e+00 4652
1 TraesCS3D01G450000 chr3D 78.626 262 56 0 1127 1388 558292432 558292171 9.260000e-40 174
2 TraesCS3D01G450000 chr3A 93.742 2269 99 19 274 2519 694516042 694513794 0.000000e+00 3363
3 TraesCS3D01G450000 chr3A 79.498 239 49 0 1127 1365 694533839 694533601 1.200000e-38 171
4 TraesCS3D01G450000 chrUn 95.185 893 43 0 598 1490 461575821 461576713 0.000000e+00 1411
5 TraesCS3D01G450000 chrUn 97.826 644 12 2 1827 2469 443899939 443900581 0.000000e+00 1110
6 TraesCS3D01G450000 chrUn 92.353 340 15 3 1492 1824 443899514 443899849 8.160000e-130 473
7 TraesCS3D01G450000 chrUn 93.291 313 20 1 285 596 343438885 343439197 6.350000e-126 460
8 TraesCS3D01G450000 chrUn 84.766 256 36 3 26 279 343437213 343437467 1.160000e-63 254
9 TraesCS3D01G450000 chrUn 78.927 261 55 0 1128 1388 40742114 40741854 7.160000e-41 178
10 TraesCS3D01G450000 chrUn 78.927 261 55 0 1128 1388 40745791 40746051 7.160000e-41 178
11 TraesCS3D01G450000 chrUn 78.927 261 55 0 1128 1388 303401668 303401408 7.160000e-41 178
12 TraesCS3D01G450000 chrUn 97.674 43 1 0 2471 2513 407446194 407446236 9.660000e-10 75


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 TraesCS3D01G450000 chr3D 558280913 558283431 2518 True 4652.0 4652 100.0000 1 2519 1 chr3D.!!$R1 2518
1 TraesCS3D01G450000 chr3A 694513794 694516042 2248 True 3363.0 3363 93.7420 274 2519 1 chr3A.!!$R1 2245
2 TraesCS3D01G450000 chrUn 461575821 461576713 892 False 1411.0 1411 95.1850 598 1490 1 chrUn.!!$F3 892
3 TraesCS3D01G450000 chrUn 443899514 443900581 1067 False 791.5 1110 95.0895 1492 2469 2 chrUn.!!$F5 977
4 TraesCS3D01G450000 chrUn 343437213 343439197 1984 False 357.0 460 89.0285 26 596 2 chrUn.!!$F4 570

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
186 188 0.025513 GACTAGCGTCATTTGCAGCG 59.974 55.000 0.0 0.00 39.98 5.18 F
1159 2581 2.189499 GTGGGGCGGATCATGAAGC 61.189 63.158 0.0 6.05 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1172 2594 1.229209 TTCGAGACCTTGGCCTCCT 60.229 57.895 3.32 0.0 0.00 3.69 R
2142 3666 2.557924 TGCAGTGCAAATTCACCCTAAG 59.442 45.455 17.26 0.0 37.68 2.18 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
22 23 4.337060 CGAGTGGACGACGGCACA 62.337 66.667 1.63 0.00 35.09 4.57
23 24 2.430921 GAGTGGACGACGGCACAG 60.431 66.667 1.63 0.00 0.00 3.66
24 25 4.664677 AGTGGACGACGGCACAGC 62.665 66.667 1.63 0.00 0.00 4.40
59 61 1.794864 CGACATCGACGACAGAGGT 59.205 57.895 0.00 0.00 43.02 3.85
68 70 1.300931 CGACAGAGGTGTGGTGGTG 60.301 63.158 0.00 0.00 36.88 4.17
70 72 2.324014 GACAGAGGTGTGGTGGTGCA 62.324 60.000 0.00 0.00 36.88 4.57
73 75 3.772853 GAGGTGTGGTGGTGCAGCA 62.773 63.158 15.99 15.99 39.63 4.41
96 98 3.636231 TGGTGTGAGGGCTTCCGG 61.636 66.667 0.00 0.00 35.17 5.14
132 134 4.856801 GCATGGTGGTCGGGCGAT 62.857 66.667 0.00 0.00 0.00 4.58
163 165 1.380524 CAGTCCGGTGAGTATCGACT 58.619 55.000 0.00 0.00 38.61 4.18
180 182 3.630769 TCGACTATGGACTAGCGTCATTT 59.369 43.478 0.00 0.00 42.05 2.32
185 187 0.375106 GGACTAGCGTCATTTGCAGC 59.625 55.000 0.00 0.00 42.05 5.25
186 188 0.025513 GACTAGCGTCATTTGCAGCG 59.974 55.000 0.00 0.00 39.98 5.18
229 231 7.147742 TGCATTGGAAAAATTATAGGTCTTCCC 60.148 37.037 0.00 0.00 32.94 3.97
302 1717 2.227194 GGTTGACAATCTTTCGGTGGT 58.773 47.619 0.00 0.00 0.00 4.16
305 1720 3.417069 TGACAATCTTTCGGTGGTCAT 57.583 42.857 0.00 0.00 30.99 3.06
438 1858 4.060205 AGCATCACCAAAATTTGCTTGTC 58.940 39.130 0.00 0.00 40.58 3.18
556 1976 5.486526 ACAAGCTTGTTGGATTGTTTTTCA 58.513 33.333 26.36 0.00 42.09 2.69
557 1977 5.936956 ACAAGCTTGTTGGATTGTTTTTCAA 59.063 32.000 26.36 0.00 42.09 2.69
558 1978 6.598850 ACAAGCTTGTTGGATTGTTTTTCAAT 59.401 30.769 26.36 0.00 42.09 2.57
560 1980 7.628769 AGCTTGTTGGATTGTTTTTCAATTT 57.371 28.000 0.00 0.00 45.49 1.82
586 2007 4.035324 TGCACCATTGTTGAAAATTTGCAG 59.965 37.500 0.00 0.00 33.82 4.41
620 2041 5.534207 TTGAGTGGACATTTTGCTCAAAT 57.466 34.783 0.00 0.00 41.41 2.32
662 2083 8.462811 TCAGCACTTGTAGTTAAAAATGTTCAA 58.537 29.630 0.00 0.00 0.00 2.69
714 2135 8.089115 AGCTAGTTGGATATTTTTAATCTCGC 57.911 34.615 0.00 0.00 0.00 5.03
715 2136 7.715249 AGCTAGTTGGATATTTTTAATCTCGCA 59.285 33.333 0.00 0.00 0.00 5.10
719 2140 5.129634 TGGATATTTTTAATCTCGCAGGCA 58.870 37.500 0.00 0.00 0.00 4.75
749 2171 8.760103 AATGTAACGGGCGTAATTTTTAAATT 57.240 26.923 5.82 5.82 41.24 1.82
811 2233 2.277084 GGGTCACGACATACATTCCAC 58.723 52.381 0.00 0.00 0.00 4.02
819 2241 6.706716 TCACGACATACATTCCACACTTTTTA 59.293 34.615 0.00 0.00 0.00 1.52
821 2243 7.533900 CACGACATACATTCCACACTTTTTAAG 59.466 37.037 0.00 0.00 0.00 1.85
958 2380 5.056894 GGCGTGACCGAACTATATATCTT 57.943 43.478 0.00 0.00 35.63 2.40
1159 2581 2.189499 GTGGGGCGGATCATGAAGC 61.189 63.158 0.00 6.05 0.00 3.86
1245 2667 0.732880 AGTTCATCGGCTTCGTCACG 60.733 55.000 0.00 0.00 35.06 4.35
1520 2942 2.243221 AGAAGCATGGCAGGGATTAACT 59.757 45.455 0.00 0.00 0.00 2.24
1576 3005 6.852664 AGTTGTTTCGATCTTCTTGTGTTTT 58.147 32.000 0.00 0.00 0.00 2.43
1598 3027 3.006644 TCGGTCTTCGATCTAGCTAGCTA 59.993 47.826 22.85 22.85 43.74 3.32
1635 3064 5.049267 TGCTATGTTCGGTTCCTACAAAAAC 60.049 40.000 0.00 0.00 0.00 2.43
1642 3071 2.287368 GGTTCCTACAAAAACTGCACCG 60.287 50.000 0.00 0.00 0.00 4.94
1742 3177 9.866798 TGTATTAATTGTTTTTAGCATGCATGA 57.133 25.926 30.64 7.50 0.00 3.07
1806 3243 7.750229 TTTGTTTGCTGTCAGAATAATCTCT 57.250 32.000 3.32 0.00 32.03 3.10
1808 3245 9.453572 TTTGTTTGCTGTCAGAATAATCTCTAT 57.546 29.630 3.32 0.00 32.03 1.98
2142 3666 2.084546 AGCTCAAAAGGGCATCGTAAC 58.915 47.619 0.00 0.00 0.00 2.50
2192 3716 2.552743 GTTTGTAGGGACCACTTCTTGC 59.447 50.000 0.00 0.00 0.00 4.01
2440 3964 3.054878 GCATGCAGTGAGGTTCTTTTTG 58.945 45.455 14.21 0.00 0.00 2.44
2481 4005 2.690778 GCGCTTGTAAGGGTGCCTG 61.691 63.158 0.00 0.00 40.70 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.337060 TGTGCCGTCGTCCACTCG 62.337 66.667 12.56 0.00 33.26 4.18
6 7 2.430921 CTGTGCCGTCGTCCACTC 60.431 66.667 12.56 0.00 33.26 3.51
7 8 4.664677 GCTGTGCCGTCGTCCACT 62.665 66.667 12.56 0.00 33.26 4.00
35 36 4.124351 TCGTCGATGTCGCCCACC 62.124 66.667 4.21 0.00 39.60 4.61
37 38 3.336715 CTGTCGTCGATGTCGCCCA 62.337 63.158 4.21 0.00 39.60 5.36
52 53 2.329539 CTGCACCACCACACCTCTGT 62.330 60.000 0.00 0.00 0.00 3.41
53 54 1.598962 CTGCACCACCACACCTCTG 60.599 63.158 0.00 0.00 0.00 3.35
54 55 2.831770 CTGCACCACCACACCTCT 59.168 61.111 0.00 0.00 0.00 3.69
70 72 4.320456 CTCACACCACCGCCTGCT 62.320 66.667 0.00 0.00 0.00 4.24
79 81 3.636231 CCGGAAGCCCTCACACCA 61.636 66.667 0.00 0.00 0.00 4.17
130 132 4.778143 ACTGCCGCCCGACCAATC 62.778 66.667 0.00 0.00 0.00 2.67
143 145 0.248539 GTCGATACTCACCGGACTGC 60.249 60.000 9.46 0.00 0.00 4.40
144 146 1.380524 AGTCGATACTCACCGGACTG 58.619 55.000 9.46 0.00 0.00 3.51
145 147 2.996249 TAGTCGATACTCACCGGACT 57.004 50.000 9.46 0.00 37.15 3.85
152 154 3.995048 CGCTAGTCCATAGTCGATACTCA 59.005 47.826 0.00 0.00 37.15 3.41
163 165 3.457234 CTGCAAATGACGCTAGTCCATA 58.543 45.455 0.00 0.00 46.51 2.74
189 191 2.223249 CCAATGCATACCACGTTAGCAC 60.223 50.000 0.00 0.00 38.12 4.40
196 198 7.594758 CCTATAATTTTTCCAATGCATACCACG 59.405 37.037 0.00 0.00 0.00 4.94
204 206 7.210174 GGGAAGACCTATAATTTTTCCAATGC 58.790 38.462 3.77 0.00 36.63 3.56
229 231 4.047395 ACCCCTTCTTCCCCTATATAGAGG 59.953 50.000 11.53 7.68 36.23 3.69
275 277 4.549458 CGAAAGATTGTCAACCAGCAATT 58.451 39.130 0.00 0.00 35.69 2.32
277 279 2.293122 CCGAAAGATTGTCAACCAGCAA 59.707 45.455 0.00 0.00 0.00 3.91
302 1717 5.177326 GGGCATGTATTTTGAGCAAAATGA 58.823 37.500 24.06 14.45 46.80 2.57
305 1720 4.613925 TGGGCATGTATTTTGAGCAAAA 57.386 36.364 10.43 10.43 43.48 2.44
317 1732 1.905894 TGCAGAGTACTTGGGCATGTA 59.094 47.619 11.53 0.00 0.00 2.29
417 1837 3.808726 TGACAAGCAAATTTTGGTGATGC 59.191 39.130 14.09 7.29 41.89 3.91
424 1844 9.094459 CGAAATATTGTTGACAAGCAAATTTTG 57.906 29.630 4.72 4.72 39.47 2.44
425 1845 9.039870 TCGAAATATTGTTGACAAGCAAATTTT 57.960 25.926 2.77 8.98 39.47 1.82
438 1858 6.707711 CAAAATGGCCATCGAAATATTGTTG 58.292 36.000 21.08 1.84 0.00 3.33
515 1935 8.567948 CAAGCTTGTTGAATAGAAAGTAAAGGA 58.432 33.333 18.65 0.00 0.00 3.36
555 1975 5.926214 TTCAACAATGGTGCATCAAATTG 57.074 34.783 2.42 7.84 36.35 2.32
556 1976 6.939132 TTTTCAACAATGGTGCATCAAATT 57.061 29.167 2.42 0.00 0.00 1.82
557 1977 7.513371 AATTTTCAACAATGGTGCATCAAAT 57.487 28.000 2.42 0.00 0.00 2.32
558 1978 6.939132 AATTTTCAACAATGGTGCATCAAA 57.061 29.167 2.42 0.00 0.00 2.69
560 1980 5.277876 GCAAATTTTCAACAATGGTGCATCA 60.278 36.000 0.00 0.00 32.17 3.07
586 2007 4.016444 TGTCCACTCAAAGATTATTGGCC 58.984 43.478 0.00 0.00 0.00 5.36
620 2041 4.278419 AGTGCTGAGTACATGCGTATATCA 59.722 41.667 3.02 0.00 0.00 2.15
631 2052 8.556194 CATTTTTAACTACAAGTGCTGAGTACA 58.444 33.333 3.02 0.00 0.00 2.90
714 2135 3.443976 GCCCGTTACATTTATTTGCCTG 58.556 45.455 0.00 0.00 0.00 4.85
715 2136 2.098443 CGCCCGTTACATTTATTTGCCT 59.902 45.455 0.00 0.00 0.00 4.75
719 2140 8.760103 AAAAATTACGCCCGTTACATTTATTT 57.240 26.923 0.00 0.00 0.00 1.40
749 2171 8.720562 CATGCTGGTAAATGATTCGTCATTATA 58.279 33.333 4.28 0.00 39.18 0.98
754 2176 3.627123 CCATGCTGGTAAATGATTCGTCA 59.373 43.478 0.00 0.00 31.35 4.35
770 2192 0.250901 GTTGTCCACCACTCCATGCT 60.251 55.000 0.00 0.00 0.00 3.79
773 2195 0.401738 CCAGTTGTCCACCACTCCAT 59.598 55.000 0.00 0.00 0.00 3.41
811 2233 9.107367 CTTTTATCTCGTTCTGCTTAAAAAGTG 57.893 33.333 0.00 0.00 30.57 3.16
819 2241 4.455877 CCCAACTTTTATCTCGTTCTGCTT 59.544 41.667 0.00 0.00 0.00 3.91
821 2243 3.751698 ACCCAACTTTTATCTCGTTCTGC 59.248 43.478 0.00 0.00 0.00 4.26
901 2323 3.278574 GCACTGGTACTCATATTGCCAA 58.721 45.455 0.00 0.00 0.00 4.52
1172 2594 1.229209 TTCGAGACCTTGGCCTCCT 60.229 57.895 3.32 0.00 0.00 3.69
1576 3005 4.322877 ATAGCTAGCTAGATCGAAGACCGA 60.323 45.833 27.42 3.60 40.77 4.69
1635 3064 3.932710 ACAATAGTACAATGTCGGTGCAG 59.067 43.478 0.00 0.00 0.00 4.41
1667 3096 7.009631 GCAGGTACATATCGATTGCATTAGTAG 59.990 40.741 1.71 0.00 0.00 2.57
1850 3373 5.297527 CAGGTGTGCTAATCATTCTGCATTA 59.702 40.000 1.93 0.00 37.76 1.90
2142 3666 2.557924 TGCAGTGCAAATTCACCCTAAG 59.442 45.455 17.26 0.00 37.68 2.18
2192 3716 6.796785 ATATGAAAAGGGGAAGGAATTGTG 57.203 37.500 0.00 0.00 0.00 3.33
2404 3928 4.336153 ACTGCATGCGAACATCATCATTAA 59.664 37.500 14.09 0.00 32.87 1.40
2440 3964 3.194272 GAGTGGGCGGTGTTTGTGC 62.194 63.158 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.