Multiple sequence alignment - TraesCS1D01G071600

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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 TraesCS1D01G071600 chr1D 100.000 2177 0 0 1 2177 51916503 51918679 0.000000e+00 4021.0
1 TraesCS1D01G071600 chr6D 97.368 2204 29 3 1 2177 389254921 389252720 0.000000e+00 3722.0
2 TraesCS1D01G071600 chr6D 98.526 1968 26 2 1 1967 389250126 389248161 0.000000e+00 3470.0
3 TraesCS1D01G071600 chr3A 97.323 2204 29 5 1 2177 66007380 66009580 0.000000e+00 3716.0
4 TraesCS1D01G071600 chr5D 97.232 2204 31 4 1 2177 503238778 503236578 0.000000e+00 3705.0
5 TraesCS1D01G071600 chr5D 97.268 2196 30 4 9 2177 503243019 503240827 0.000000e+00 3696.0
6 TraesCS1D01G071600 chr5D 96.127 1291 22 3 915 2177 503232335 503231045 0.000000e+00 2082.0
7 TraesCS1D01G071600 chr5D 94.932 809 14 2 1396 2177 503227069 503226261 0.000000e+00 1242.0
8 TraesCS1D01G071600 chrUn 96.916 2205 35 5 1 2177 216508366 216510565 0.000000e+00 3664.0
9 TraesCS1D01G071600 chrUn 96.618 1449 22 2 756 2177 397077306 397078754 0.000000e+00 2379.0
10 TraesCS1D01G071600 chrUn 97.685 216 5 0 1962 2177 286273033 286272818 2.640000e-99 372.0
11 TraesCS1D01G071600 chr3B 96.868 2203 41 2 1 2177 201537272 201535072 0.000000e+00 3661.0
12 TraesCS1D01G071600 chr3D 98.323 1968 29 3 1 1967 589265771 589267735 0.000000e+00 3448.0
13 TraesCS1D01G071600 chr3D 95.438 1666 46 5 538 2177 48687483 48689144 0.000000e+00 2628.0
14 TraesCS1D01G071600 chr7B 98.412 1952 28 2 1 1951 662724156 662722207 0.000000e+00 3430.0
15 TraesCS1D01G071600 chr6A 95.678 995 15 3 1210 2177 608869208 608870201 0.000000e+00 1574.0
16 TraesCS1D01G071600 chr7A 95.281 996 20 2 1209 2177 46416286 46415291 0.000000e+00 1554.0
17 TraesCS1D01G071600 chr2B 100.000 29 0 0 1939 1967 521300143 521300171 1.000000e-03 54.7


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 TraesCS1D01G071600 chr1D 51916503 51918679 2176 False 4021.0 4021 100.0000 1 2177 1 chr1D.!!$F1 2176
1 TraesCS1D01G071600 chr6D 389248161 389254921 6760 True 3596.0 3722 97.9470 1 2177 2 chr6D.!!$R1 2176
2 TraesCS1D01G071600 chr3A 66007380 66009580 2200 False 3716.0 3716 97.3230 1 2177 1 chr3A.!!$F1 2176
3 TraesCS1D01G071600 chr5D 503236578 503243019 6441 True 3700.5 3705 97.2500 1 2177 2 chr5D.!!$R2 2176
4 TraesCS1D01G071600 chr5D 503226261 503232335 6074 True 1662.0 2082 95.5295 915 2177 2 chr5D.!!$R1 1262
5 TraesCS1D01G071600 chrUn 216508366 216510565 2199 False 3664.0 3664 96.9160 1 2177 1 chrUn.!!$F1 2176
6 TraesCS1D01G071600 chrUn 397077306 397078754 1448 False 2379.0 2379 96.6180 756 2177 1 chrUn.!!$F2 1421
7 TraesCS1D01G071600 chr3B 201535072 201537272 2200 True 3661.0 3661 96.8680 1 2177 1 chr3B.!!$R1 2176
8 TraesCS1D01G071600 chr3D 589265771 589267735 1964 False 3448.0 3448 98.3230 1 1967 1 chr3D.!!$F2 1966
9 TraesCS1D01G071600 chr3D 48687483 48689144 1661 False 2628.0 2628 95.4380 538 2177 1 chr3D.!!$F1 1639
10 TraesCS1D01G071600 chr7B 662722207 662724156 1949 True 3430.0 3430 98.4120 1 1951 1 chr7B.!!$R1 1950
11 TraesCS1D01G071600 chr6A 608869208 608870201 993 False 1574.0 1574 95.6780 1210 2177 1 chr6A.!!$F1 967
12 TraesCS1D01G071600 chr7A 46415291 46416286 995 True 1554.0 1554 95.2810 1209 2177 1 chr7A.!!$R1 968

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
39 40 0.631212 CCCCAAGGGCAGGTTCTTAT 59.369 55.0 0.0 0.0 35.35 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1259 5512 0.667487 CGTGATGAACTGTCGGCACT 60.667 55.0 0.0 0.0 31.67 4.4 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
39 40 0.631212 CCCCAAGGGCAGGTTCTTAT 59.369 55.000 0.00 0.00 35.35 1.73
47 48 1.669265 GGCAGGTTCTTATGCGTTACC 59.331 52.381 0.00 0.00 43.49 2.85
69 70 2.549282 CGTTCGCCACTGGAAACG 59.451 61.111 16.93 16.93 37.17 3.60
79 80 1.228124 CTGGAAACGCCACTTCCCA 60.228 57.895 4.20 0.00 43.33 4.37
127 128 0.674581 CAGCGTTCATCCTGAGCCAA 60.675 55.000 0.00 0.00 0.00 4.52
477 4727 5.986135 CGTCCCATCGAGAAAGAGAATTAAT 59.014 40.000 0.00 0.00 0.00 1.40
891 5141 7.391554 CCATTCAAGAGTTTCTATCTGTTTCCA 59.608 37.037 0.00 0.00 0.00 3.53
892 5142 7.730364 TTCAAGAGTTTCTATCTGTTTCCAC 57.270 36.000 0.00 0.00 0.00 4.02
893 5143 5.926542 TCAAGAGTTTCTATCTGTTTCCACG 59.073 40.000 0.00 0.00 0.00 4.94
894 5144 4.246458 AGAGTTTCTATCTGTTTCCACGC 58.754 43.478 0.00 0.00 0.00 5.34
897 5147 1.568504 TCTATCTGTTTCCACGCCCT 58.431 50.000 0.00 0.00 0.00 5.19
901 5151 1.314730 TCTGTTTCCACGCCCTTTTC 58.685 50.000 0.00 0.00 0.00 2.29
902 5152 1.133915 TCTGTTTCCACGCCCTTTTCT 60.134 47.619 0.00 0.00 0.00 2.52
904 5154 1.407258 TGTTTCCACGCCCTTTTCTTG 59.593 47.619 0.00 0.00 0.00 3.02
905 5155 1.679153 GTTTCCACGCCCTTTTCTTGA 59.321 47.619 0.00 0.00 0.00 3.02
906 5156 1.604604 TTCCACGCCCTTTTCTTGAG 58.395 50.000 0.00 0.00 0.00 3.02
907 5157 0.762418 TCCACGCCCTTTTCTTGAGA 59.238 50.000 0.00 0.00 0.00 3.27
908 5158 0.875059 CCACGCCCTTTTCTTGAGAC 59.125 55.000 0.00 0.00 0.00 3.36
910 5160 0.765510 ACGCCCTTTTCTTGAGACCT 59.234 50.000 0.00 0.00 0.00 3.85
911 5161 1.270893 ACGCCCTTTTCTTGAGACCTC 60.271 52.381 0.00 0.00 0.00 3.85
912 5162 1.443802 GCCCTTTTCTTGAGACCTCG 58.556 55.000 0.00 0.00 0.00 4.63
913 5163 1.002087 GCCCTTTTCTTGAGACCTCGA 59.998 52.381 0.00 0.00 0.00 4.04
916 5166 3.498777 CCCTTTTCTTGAGACCTCGAAAC 59.501 47.826 0.00 0.00 0.00 2.78
917 5167 4.127171 CCTTTTCTTGAGACCTCGAAACA 58.873 43.478 0.00 0.00 0.00 2.83
918 5168 4.757149 CCTTTTCTTGAGACCTCGAAACAT 59.243 41.667 0.00 0.00 0.00 2.71
1327 5580 8.235905 GGATCGGTAACTAATAGTGCTACTAAG 58.764 40.741 0.00 0.00 33.89 2.18
1434 5687 7.427989 TCTGTATACTTTCCCCGTTCTATTT 57.572 36.000 4.17 0.00 0.00 1.40
1485 5738 7.013369 TCGGATCATATAGATATCCCTTCAACG 59.987 40.741 0.00 0.00 37.00 4.10
1529 5782 3.005554 CTCGAATGACTCACCAAAGCAT 58.994 45.455 0.00 0.00 0.00 3.79
1636 5889 4.801330 ATTCGGGATTTTTCTTGGGAAC 57.199 40.909 0.00 0.00 0.00 3.62
1801 6055 6.969993 AATAAGTCGAAGATAGAAGAGCCT 57.030 37.500 0.00 0.00 40.67 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.030862 GAACGGGTGGGTAACGCA 59.969 61.111 0.00 0.00 41.73 5.24
69 70 0.804989 CAAGTCGAATGGGAAGTGGC 59.195 55.000 0.00 0.00 0.00 5.01
79 80 3.501828 TGCTTAACACATGCAAGTCGAAT 59.498 39.130 0.00 0.00 34.59 3.34
127 128 4.892345 TGAATCTCATGGAGAGTTCGATCT 59.108 41.667 0.00 0.00 42.26 2.75
168 169 5.790593 TGCTTTGTCTACGAATAAGGAAGT 58.209 37.500 0.00 0.00 0.00 3.01
477 4727 1.341976 GCCCCTTTGCCTTAGGATTCA 60.342 52.381 0.69 0.00 34.56 2.57
842 5092 6.269769 TGGAAATTGAAAAGAAATGTAGCCCT 59.730 34.615 0.00 0.00 0.00 5.19
891 5141 0.765510 AGGTCTCAAGAAAAGGGCGT 59.234 50.000 0.00 0.00 0.00 5.68
892 5142 1.443802 GAGGTCTCAAGAAAAGGGCG 58.556 55.000 0.00 0.00 0.00 6.13
893 5143 1.002087 TCGAGGTCTCAAGAAAAGGGC 59.998 52.381 0.00 0.00 0.00 5.19
894 5144 3.402628 TTCGAGGTCTCAAGAAAAGGG 57.597 47.619 0.00 0.00 0.00 3.95
897 5147 5.364778 TCATGTTTCGAGGTCTCAAGAAAA 58.635 37.500 0.00 0.00 34.86 2.29
901 5151 3.257393 CCTCATGTTTCGAGGTCTCAAG 58.743 50.000 0.00 0.00 44.35 3.02
902 5152 3.319137 CCTCATGTTTCGAGGTCTCAA 57.681 47.619 0.00 0.00 44.35 3.02
910 5160 7.386851 AGAAGTAATTTCTCCTCATGTTTCGA 58.613 34.615 0.00 0.00 42.54 3.71
911 5161 7.602517 AGAAGTAATTTCTCCTCATGTTTCG 57.397 36.000 0.00 0.00 42.54 3.46
1259 5512 0.667487 CGTGATGAACTGTCGGCACT 60.667 55.000 0.00 0.00 31.67 4.40
1434 5687 1.038681 TGCATAAGACCCGCGGTAGA 61.039 55.000 26.12 4.53 35.25 2.59
1485 5738 5.525378 AGATCTTTTCGATGACCTATGTTGC 59.475 40.000 0.00 0.00 30.84 4.17
1512 5765 4.560108 GCTTTCATGCTTTGGTGAGTCATT 60.560 41.667 0.00 0.00 0.00 2.57
1514 5767 2.294233 GCTTTCATGCTTTGGTGAGTCA 59.706 45.455 0.00 0.00 0.00 3.41
1529 5782 6.071391 GGAATCCATTTTCTAACTGGCTTTCA 60.071 38.462 0.00 0.00 0.00 2.69
1636 5889 4.462483 TCCATTCCAATTTCTTCCCGAAAG 59.538 41.667 0.00 0.00 44.29 2.62
1801 6055 9.312904 AGTTTCCATTTCTTCATTTGGAATCTA 57.687 29.630 10.77 0.00 45.14 1.98
2064 6885 1.568504 TTCACCTCATACGGCTCCTT 58.431 50.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.