Multiple sequence alignment - TraesCS1D01G145700

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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 TraesCS1D01G145700 chr1D 100.000 2465 0 0 1 2465 201058284 201055820 0.000000e+00 4553.0
1 TraesCS1D01G145700 chr1D 92.437 119 5 3 92 209 201057888 201057773 1.520000e-37 167.0
2 TraesCS1D01G145700 chr1D 92.437 119 5 3 397 512 201058193 201058076 1.520000e-37 167.0
3 TraesCS1D01G145700 chr1D 84.211 57 6 3 2069 2123 318133165 318133110 4.000000e-03 52.8
4 TraesCS1D01G145700 chr1A 97.494 2474 41 9 1 2465 254997672 254995211 0.000000e+00 4205.0
5 TraesCS1D01G145700 chr1A 92.437 119 5 2 92 209 254997276 254997161 1.520000e-37 167.0
6 TraesCS1D01G145700 chr1A 89.167 120 6 6 397 512 254997581 254997465 2.560000e-30 143.0
7 TraesCS1D01G145700 chr1B 93.275 1026 54 5 530 1543 288960763 288959741 0.000000e+00 1498.0
8 TraesCS1D01G145700 chr1B 92.248 387 26 4 1 385 288961144 288960760 1.670000e-151 545.0
9 TraesCS1D01G145700 chr1B 91.772 316 20 4 1563 1874 288959750 288959437 3.760000e-118 435.0
10 TraesCS1D01G145700 chr1B 88.153 287 27 4 2181 2465 288954290 288954009 3.930000e-88 335.0
11 TraesCS1D01G145700 chr1B 91.597 119 6 3 397 512 288961053 288960936 7.050000e-36 161.0
12 TraesCS1D01G145700 chr1B 82.639 144 13 4 1928 2059 288958581 288958438 1.550000e-22 117.0
13 TraesCS1D01G145700 chr5A 81.855 496 87 3 973 1465 675958368 675957873 4.900000e-112 414.0
14 TraesCS1D01G145700 chr4B 89.157 83 7 2 2061 2141 139763336 139763254 4.340000e-18 102.0
15 TraesCS1D01G145700 chr2D 88.372 86 8 2 2058 2141 615126524 615126609 4.340000e-18 102.0
16 TraesCS1D01G145700 chr7A 84.043 94 10 4 2051 2141 97912663 97912754 4.370000e-13 86.1
17 TraesCS1D01G145700 chr7D 93.333 45 2 1 2061 2104 447070922 447070878 5.690000e-07 65.8
18 TraesCS1D01G145700 chr6B 93.333 45 2 1 2057 2100 667156401 667156445 5.690000e-07 65.8
19 TraesCS1D01G145700 chr2A 91.111 45 3 1 2053 2096 74165885 74165929 2.650000e-05 60.2
20 TraesCS1D01G145700 chr5D 88.000 50 3 3 2063 2110 491432656 491432608 3.420000e-04 56.5


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 TraesCS1D01G145700 chr1D 201055820 201058284 2464 True 1629.0 4553 94.958000 1 2465 3 chr1D.!!$R2 2464
1 TraesCS1D01G145700 chr1A 254995211 254997672 2461 True 1505.0 4205 93.032667 1 2465 3 chr1A.!!$R1 2464
2 TraesCS1D01G145700 chr1B 288958438 288961144 2706 True 551.2 1498 90.306200 1 2059 5 chr1B.!!$R2 2058

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
246 249 1.282157 GCATCTACAGTGGGTTTCCCT 59.718 52.381 6.38 0.0 45.7 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2767 4.571984 TCTTTCAATGATATCGTGTGCTGG 59.428 41.667 0.0 0.0 0.0 4.85 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
246 249 1.282157 GCATCTACAGTGGGTTTCCCT 59.718 52.381 6.38 0.00 45.70 4.20
314 317 5.757850 ATCTTGGATCGGCTTTGTATTTC 57.242 39.130 0.00 0.00 0.00 2.17
477 482 8.470805 TGACAAGCCAAGTAACTTAATGAAAAA 58.529 29.630 0.00 0.00 0.00 1.94
526 531 8.792633 TGTATCTTTGGAAAAACAATACAGGAG 58.207 33.333 0.00 0.00 0.00 3.69
625 638 4.039852 TCTGACTGCTTGTAACCACATGTA 59.960 41.667 0.00 0.00 33.76 2.29
955 972 8.871686 AAATTCGTTGAAAACTCTGCTAATTT 57.128 26.923 0.00 0.00 46.99 1.82
1561 1578 1.909302 TGTGGGAGAAGATGGGAGTTC 59.091 52.381 0.00 0.00 0.00 3.01
1677 1695 7.239143 TGATCTCTTCCATGGGAGATATTTCAT 59.761 37.037 23.65 8.52 45.72 2.57
1944 2767 9.455847 GCTAATTCTATTTGATGGAATGAACAC 57.544 33.333 1.09 0.00 39.21 3.32
1958 2781 2.616960 TGAACACCAGCACACGATATC 58.383 47.619 0.00 0.00 0.00 1.63
1959 2782 2.028567 TGAACACCAGCACACGATATCA 60.029 45.455 3.12 0.00 0.00 2.15
1960 2783 2.988010 ACACCAGCACACGATATCAT 57.012 45.000 3.12 0.00 0.00 2.45
1961 2784 3.266510 ACACCAGCACACGATATCATT 57.733 42.857 3.12 0.00 0.00 2.57
1962 2785 2.938451 ACACCAGCACACGATATCATTG 59.062 45.455 3.12 1.74 0.00 2.82
1963 2786 3.197265 CACCAGCACACGATATCATTGA 58.803 45.455 3.12 0.00 0.00 2.57
1964 2787 3.622612 CACCAGCACACGATATCATTGAA 59.377 43.478 3.12 0.00 0.00 2.69
1965 2788 4.094739 CACCAGCACACGATATCATTGAAA 59.905 41.667 3.12 0.00 0.00 2.69
1966 2789 4.333649 ACCAGCACACGATATCATTGAAAG 59.666 41.667 3.12 0.00 0.00 2.62
1967 2790 4.571984 CCAGCACACGATATCATTGAAAGA 59.428 41.667 3.12 0.00 0.00 2.52
1968 2791 5.277202 CCAGCACACGATATCATTGAAAGAG 60.277 44.000 3.12 0.00 0.00 2.85
1969 2792 5.521372 CAGCACACGATATCATTGAAAGAGA 59.479 40.000 3.12 0.00 0.00 3.10
1970 2793 6.036408 CAGCACACGATATCATTGAAAGAGAA 59.964 38.462 3.12 0.00 0.00 2.87
1971 2794 6.257411 AGCACACGATATCATTGAAAGAGAAG 59.743 38.462 3.12 0.00 0.00 2.85
2084 2933 4.755123 CCCTCTGTTCAAAATACTTGTCGT 59.245 41.667 0.00 0.00 0.00 4.34
2204 3053 0.608130 GTTCCAAGGGAATGGCCAAC 59.392 55.000 10.96 7.21 44.04 3.77
2311 3160 6.189859 AGATTTGGGATTTACAATCAGCTCA 58.810 36.000 0.00 0.00 0.00 4.26
2347 3196 7.448748 ACCTAAAATCTCGCACAGTAAATTT 57.551 32.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
246 249 2.010670 CGAGTTCAACGCACCAACA 58.989 52.632 0.00 0.00 0.00 3.33
314 317 3.181487 CCCTTTCCATTGAAGCATAACGG 60.181 47.826 0.00 0.00 0.00 4.44
521 526 4.467795 TGAACCTTCTGGAACTATCTCCTG 59.532 45.833 0.00 0.00 36.35 3.86
526 531 5.745227 TCCAATGAACCTTCTGGAACTATC 58.255 41.667 0.00 0.00 37.04 2.08
901 917 6.651755 AAAAATTGCAAGACAACTCAACAG 57.348 33.333 4.94 0.00 42.27 3.16
955 972 6.480651 TGCAGTAAACACGAGAGTTTAAATGA 59.519 34.615 18.56 9.48 46.40 2.57
1561 1578 6.373774 AGCTCAGTAAGGATCAACAATTGAAG 59.626 38.462 13.59 3.96 43.95 3.02
1567 1584 5.012046 TGAAGAGCTCAGTAAGGATCAACAA 59.988 40.000 17.77 0.00 0.00 2.83
1677 1695 8.514594 CAAGCTCAGAAGTAACATTATTTTCCA 58.485 33.333 0.00 0.00 0.00 3.53
1944 2767 4.571984 TCTTTCAATGATATCGTGTGCTGG 59.428 41.667 0.00 0.00 0.00 4.85
1958 2781 6.592994 TGAGTATGACTGCTTCTCTTTCAATG 59.407 38.462 0.00 0.00 0.00 2.82
1959 2782 6.705302 TGAGTATGACTGCTTCTCTTTCAAT 58.295 36.000 0.00 0.00 0.00 2.57
1960 2783 6.101650 TGAGTATGACTGCTTCTCTTTCAA 57.898 37.500 0.00 0.00 0.00 2.69
1961 2784 5.728637 TGAGTATGACTGCTTCTCTTTCA 57.271 39.130 0.00 0.00 0.00 2.69
1962 2785 5.928839 TGTTGAGTATGACTGCTTCTCTTTC 59.071 40.000 0.00 0.00 0.00 2.62
1963 2786 5.858381 TGTTGAGTATGACTGCTTCTCTTT 58.142 37.500 0.00 0.00 0.00 2.52
1964 2787 5.244851 TCTGTTGAGTATGACTGCTTCTCTT 59.755 40.000 0.00 0.00 0.00 2.85
1965 2788 4.769488 TCTGTTGAGTATGACTGCTTCTCT 59.231 41.667 0.00 0.00 0.00 3.10
1966 2789 5.065704 TCTGTTGAGTATGACTGCTTCTC 57.934 43.478 0.00 0.00 0.00 2.87
1967 2790 5.674052 ATCTGTTGAGTATGACTGCTTCT 57.326 39.130 0.00 0.00 0.00 2.85
1968 2791 7.518052 GCAATATCTGTTGAGTATGACTGCTTC 60.518 40.741 0.00 0.00 0.00 3.86
1969 2792 6.259608 GCAATATCTGTTGAGTATGACTGCTT 59.740 38.462 0.00 0.00 0.00 3.91
1970 2793 5.757320 GCAATATCTGTTGAGTATGACTGCT 59.243 40.000 0.00 0.00 0.00 4.24
1971 2794 5.049818 GGCAATATCTGTTGAGTATGACTGC 60.050 44.000 0.00 0.00 0.00 4.40
2059 2908 5.468746 CGACAAGTATTTTGAACAGAGGGAA 59.531 40.000 0.00 0.00 0.00 3.97
2084 2933 7.846644 TTCAGTTAAGTTCGAACTAAAACCA 57.153 32.000 32.20 23.76 38.57 3.67
2204 3053 8.294954 TCTAACTCTAAATTCCTACTCTGGTG 57.705 38.462 0.00 0.00 0.00 4.17
2311 3160 6.116126 CGAGATTTTAGGTTCAGATTTCCCT 58.884 40.000 0.00 0.00 0.00 4.20
2374 3223 7.074653 ACAGTACCTTGTTCTTGAGGAAATA 57.925 36.000 0.00 0.00 36.84 1.40


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

AutoCloner maintained by Alex Coulton.