Multiple sequence alignment - TraesCS2D01G132800

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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 TraesCS2D01G132800 chr2D 100.000 2264 0 0 1 2264 78321033 78318770 0.000000e+00 4181.0
1 TraesCS2D01G132800 chr2D 96.224 980 35 2 1 979 583993890 583994868 0.000000e+00 1604.0
2 TraesCS2D01G132800 chr2D 95.582 996 41 2 1 994 400817448 400816454 0.000000e+00 1592.0
3 TraesCS2D01G132800 chr2D 92.105 1102 76 10 992 2088 152002051 152003146 0.000000e+00 1543.0
4 TraesCS2D01G132800 chr2D 90.563 1155 91 12 992 2136 632767126 632768272 0.000000e+00 1513.0
5 TraesCS2D01G132800 chr2D 94.444 72 3 1 2193 2264 476792429 476792499 2.380000e-20 110.0
6 TraesCS2D01G132800 chr1D 93.106 1146 71 6 995 2138 14673876 14672737 0.000000e+00 1672.0
7 TraesCS2D01G132800 chr1D 95.783 996 39 2 1 994 309964941 309965935 0.000000e+00 1604.0
8 TraesCS2D01G132800 chr1D 82.500 120 18 2 2146 2264 481985795 481985912 3.980000e-18 102.0
9 TraesCS2D01G132800 chr4D 96.382 995 34 2 1 994 321556025 321557018 0.000000e+00 1637.0
10 TraesCS2D01G132800 chr4D 96.100 1000 36 3 1 998 279288184 279289182 0.000000e+00 1628.0
11 TraesCS2D01G132800 chr4D 96.076 994 38 1 1 994 321609839 321610831 0.000000e+00 1618.0
12 TraesCS2D01G132800 chr7D 95.683 996 39 4 1 994 184434110 184435103 0.000000e+00 1598.0
13 TraesCS2D01G132800 chr7D 95.582 996 41 3 1 995 244822576 244823569 0.000000e+00 1592.0
14 TraesCS2D01G132800 chr6D 95.596 999 40 4 1 998 366782874 366781879 0.000000e+00 1598.0
15 TraesCS2D01G132800 chr6D 95.476 840 34 3 992 1828 377213197 377214035 0.000000e+00 1338.0
16 TraesCS2D01G132800 chr4B 90.026 1153 97 16 995 2138 467349046 467347903 0.000000e+00 1476.0
17 TraesCS2D01G132800 chr6B 89.895 1148 89 10 995 2138 281222422 281221298 0.000000e+00 1452.0
18 TraesCS2D01G132800 chr6B 89.529 764 62 9 1391 2138 126305887 126306648 0.000000e+00 952.0
19 TraesCS2D01G132800 chr6B 84.348 115 15 3 2023 2136 126306417 126306529 2.380000e-20 110.0
20 TraesCS2D01G132800 chr6B 91.667 72 6 0 2193 2264 126306839 126306910 1.430000e-17 100.0
21 TraesCS2D01G132800 chr3D 90.759 1093 68 10 992 2067 310407082 310408158 0.000000e+00 1428.0
22 TraesCS2D01G132800 chr5D 93.796 951 38 8 992 1936 520879598 520880533 0.000000e+00 1410.0
23 TraesCS2D01G132800 chr5B 95.667 854 34 2 992 1842 387879123 387879976 0.000000e+00 1369.0
24 TraesCS2D01G132800 chr6A 93.647 913 55 2 1226 2138 466347387 466348296 0.000000e+00 1362.0
25 TraesCS2D01G132800 chr6A 93.654 914 51 4 1226 2138 466391761 466392668 0.000000e+00 1360.0
26 TraesCS2D01G132800 chr6A 93.319 913 55 4 1226 2138 466149456 466150362 0.000000e+00 1343.0
27 TraesCS2D01G132800 chr6A 93.069 909 59 4 1226 2134 466153196 466154100 0.000000e+00 1327.0
28 TraesCS2D01G132800 chr3B 93.243 74 5 0 2048 2121 169644567 169644494 2.380000e-20 110.0
29 TraesCS2D01G132800 chr2B 84.848 66 6 4 1910 1973 717642525 717642462 1.880000e-06 63.9


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 TraesCS2D01G132800 chr2D 78318770 78321033 2263 True 4181.000000 4181 100.000000 1 2264 1 chr2D.!!$R1 2263
1 TraesCS2D01G132800 chr2D 583993890 583994868 978 False 1604.000000 1604 96.224000 1 979 1 chr2D.!!$F3 978
2 TraesCS2D01G132800 chr2D 400816454 400817448 994 True 1592.000000 1592 95.582000 1 994 1 chr2D.!!$R2 993
3 TraesCS2D01G132800 chr2D 152002051 152003146 1095 False 1543.000000 1543 92.105000 992 2088 1 chr2D.!!$F1 1096
4 TraesCS2D01G132800 chr2D 632767126 632768272 1146 False 1513.000000 1513 90.563000 992 2136 1 chr2D.!!$F4 1144
5 TraesCS2D01G132800 chr1D 14672737 14673876 1139 True 1672.000000 1672 93.106000 995 2138 1 chr1D.!!$R1 1143
6 TraesCS2D01G132800 chr1D 309964941 309965935 994 False 1604.000000 1604 95.783000 1 994 1 chr1D.!!$F1 993
7 TraesCS2D01G132800 chr4D 321556025 321557018 993 False 1637.000000 1637 96.382000 1 994 1 chr4D.!!$F2 993
8 TraesCS2D01G132800 chr4D 279288184 279289182 998 False 1628.000000 1628 96.100000 1 998 1 chr4D.!!$F1 997
9 TraesCS2D01G132800 chr4D 321609839 321610831 992 False 1618.000000 1618 96.076000 1 994 1 chr4D.!!$F3 993
10 TraesCS2D01G132800 chr7D 184434110 184435103 993 False 1598.000000 1598 95.683000 1 994 1 chr7D.!!$F1 993
11 TraesCS2D01G132800 chr7D 244822576 244823569 993 False 1592.000000 1592 95.582000 1 995 1 chr7D.!!$F2 994
12 TraesCS2D01G132800 chr6D 366781879 366782874 995 True 1598.000000 1598 95.596000 1 998 1 chr6D.!!$R1 997
13 TraesCS2D01G132800 chr6D 377213197 377214035 838 False 1338.000000 1338 95.476000 992 1828 1 chr6D.!!$F1 836
14 TraesCS2D01G132800 chr4B 467347903 467349046 1143 True 1476.000000 1476 90.026000 995 2138 1 chr4B.!!$R1 1143
15 TraesCS2D01G132800 chr6B 281221298 281222422 1124 True 1452.000000 1452 89.895000 995 2138 1 chr6B.!!$R1 1143
16 TraesCS2D01G132800 chr6B 126305887 126306910 1023 False 387.333333 952 88.514667 1391 2264 3 chr6B.!!$F1 873
17 TraesCS2D01G132800 chr3D 310407082 310408158 1076 False 1428.000000 1428 90.759000 992 2067 1 chr3D.!!$F1 1075
18 TraesCS2D01G132800 chr5D 520879598 520880533 935 False 1410.000000 1410 93.796000 992 1936 1 chr5D.!!$F1 944
19 TraesCS2D01G132800 chr5B 387879123 387879976 853 False 1369.000000 1369 95.667000 992 1842 1 chr5B.!!$F1 850
20 TraesCS2D01G132800 chr6A 466347387 466348296 909 False 1362.000000 1362 93.647000 1226 2138 1 chr6A.!!$F1 912
21 TraesCS2D01G132800 chr6A 466391761 466392668 907 False 1360.000000 1360 93.654000 1226 2138 1 chr6A.!!$F2 912
22 TraesCS2D01G132800 chr6A 466149456 466154100 4644 False 1335.000000 1343 93.194000 1226 2138 2 chr6A.!!$F3 912

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
451 452 1.027792 AACTCAAACAACCCGCACGT 61.028 50.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 5227 0.323178 TCCTCCTCGCGTTACTTCCT 60.323 55.0 5.77 0.0 0.0 3.36 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
30 31 6.094048 CCCACAGTACAATATTGAAGTCTTGG 59.906 42.308 22.16 17.37 0.00 3.61
128 129 2.024414 GGCTCAATATTTGCCTTCCGT 58.976 47.619 17.51 0.00 43.05 4.69
309 310 9.821662 GGTTGCTTTTATACGGATATGAAATAC 57.178 33.333 0.00 0.00 28.90 1.89
451 452 1.027792 AACTCAAACAACCCGCACGT 61.028 50.000 0.00 0.00 0.00 4.49
511 512 3.443045 CGGCTTCCGGCAGCAAAT 61.443 61.111 27.35 0.00 44.15 2.32
604 605 2.091541 TGATTTTCTGGGATTCACCGC 58.908 47.619 0.00 0.00 40.11 5.68
714 715 4.591498 GTGTGGGATGTACATACCTATGGA 59.409 45.833 32.60 13.62 42.54 3.41
788 789 1.376812 GGGATTCACCGTGTGGGAC 60.377 63.158 0.00 0.00 40.75 4.46
926 929 1.768684 ATCGCCCACACTCACTTGGT 61.769 55.000 0.00 0.00 0.00 3.67
932 935 1.227556 ACACTCACTTGGTGACGGC 60.228 57.895 0.00 0.00 37.67 5.68
1131 1134 1.577328 CGCCATGTTGGTGTGGAGAC 61.577 60.000 0.00 0.00 42.85 3.36
1137 1140 1.339247 TGTTGGTGTGGAGACGTTTGT 60.339 47.619 0.00 0.00 0.00 2.83
1148 1151 3.493873 GGAGACGTTTGTAAGGTGAAGGT 60.494 47.826 0.00 0.00 0.00 3.50
1272 1275 4.098960 CCACCGGTATGCTAGAGAAGTAAA 59.901 45.833 6.87 0.00 0.00 2.01
1320 5064 9.970395 CAACACTAACATCCATTTTATATGCAT 57.030 29.630 3.79 3.79 0.00 3.96
1483 5227 3.020274 CGTCAGAAAGAGAGGATGGAGA 58.980 50.000 0.00 0.00 0.00 3.71
1544 5288 1.304952 CTCGTGAGGAGGAGAGGGT 59.695 63.158 0.00 0.00 39.22 4.34
1822 5570 5.179045 AGTTTGTCAGCAATTTCTGTGAG 57.821 39.130 4.99 0.00 35.63 3.51
1828 5576 3.565482 TCAGCAATTTCTGTGAGTTGTCC 59.435 43.478 4.99 0.00 35.63 4.02
1836 5584 2.948979 TCTGTGAGTTGTCCGCAATTTT 59.051 40.909 0.00 0.00 36.92 1.82
1927 5754 2.264794 CTACCGCCACACACCCTC 59.735 66.667 0.00 0.00 0.00 4.30
1940 5767 4.832608 CCCTCGCGGTAGGTTGCC 62.833 72.222 6.13 0.00 34.56 4.52
1941 5768 4.077184 CCTCGCGGTAGGTTGCCA 62.077 66.667 6.13 0.00 31.46 4.92
1942 5769 2.047655 CTCGCGGTAGGTTGCCAA 60.048 61.111 6.13 0.00 0.00 4.52
1952 5779 4.486887 GTTGCCAAACCCTACCGT 57.513 55.556 0.00 0.00 0.00 4.83
2126 5962 0.106918 ACGAGAAAAAGCACCACCCA 60.107 50.000 0.00 0.00 0.00 4.51
2140 5976 2.045340 CCCAGGCGGTAGGGTTTG 60.045 66.667 0.00 0.00 40.34 2.93
2141 5977 2.598787 CCCAGGCGGTAGGGTTTGA 61.599 63.158 0.00 0.00 40.34 2.69
2156 6120 3.949885 TTGACCCGGCTCTAGCGGA 62.950 63.158 10.75 0.00 43.02 5.54
2162 6126 1.826921 CGGCTCTAGCGGAAGGGTA 60.827 63.158 3.61 0.00 43.02 3.69
2189 6161 3.879892 ACAAAGGAAGTTCTCTGTTCTGC 59.120 43.478 2.25 0.00 0.00 4.26
2190 6162 3.845781 AAGGAAGTTCTCTGTTCTGCA 57.154 42.857 2.25 0.00 0.00 4.41
2191 6163 3.118905 AGGAAGTTCTCTGTTCTGCAC 57.881 47.619 2.25 0.00 0.00 4.57
2195 6167 4.997395 GGAAGTTCTCTGTTCTGCACAATA 59.003 41.667 2.25 0.00 33.87 1.90
2256 6228 8.724229 CAAATATTAGGATGATCATCTCGCAAA 58.276 33.333 29.85 18.42 37.92 3.68
2257 6229 7.840342 ATATTAGGATGATCATCTCGCAAAC 57.160 36.000 29.85 14.78 37.92 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.608283 CCCAACCTTCGTCCTCTTCAC 60.608 57.143 0.00 0.00 0.00 3.18
128 129 3.072915 TCTCATCTGGGAAACTGCAGAAA 59.927 43.478 23.35 0.00 33.28 2.52
309 310 7.925993 TGATATTTCTTATAAAACACGCCAGG 58.074 34.615 0.00 0.00 0.00 4.45
451 452 4.682860 CGAACACGCCTACTTTCTAGAAAA 59.317 41.667 18.25 4.55 0.00 2.29
511 512 0.466555 AGGTGGCCTAACGCAAACAA 60.467 50.000 3.32 0.00 40.31 2.83
604 605 3.278367 CGTAGGTATGTACATCCCACG 57.722 52.381 18.71 20.06 0.00 4.94
714 715 4.772100 ACGGTGAATCCCAGAAATCATTTT 59.228 37.500 0.00 0.00 0.00 1.82
788 789 6.371548 CCCAATCATTTCCATAGGTATGTACG 59.628 42.308 0.00 0.00 31.82 3.67
926 929 0.669318 GACGACATTTGGAGCCGTCA 60.669 55.000 0.00 0.00 45.98 4.35
932 935 1.011968 TTCCGCGACGACATTTGGAG 61.012 55.000 8.23 0.00 0.00 3.86
1131 1134 2.546789 GGACACCTTCACCTTACAAACG 59.453 50.000 0.00 0.00 0.00 3.60
1148 1151 0.032952 CTTCTTTCGGTCGGTGGACA 59.967 55.000 0.00 0.00 45.28 4.02
1272 1275 6.707440 TGACACACATTTTGGAGTAACATT 57.293 33.333 0.00 0.00 0.00 2.71
1320 5064 0.975556 TGCATAGAGGAGGCGGTGAA 60.976 55.000 0.00 0.00 37.80 3.18
1483 5227 0.323178 TCCTCCTCGCGTTACTTCCT 60.323 55.000 5.77 0.00 0.00 3.36
1544 5288 2.226437 CGAGCCTTTGCAAGCTTTCTTA 59.774 45.455 13.77 0.00 40.11 2.10
1822 5570 4.047822 TCATCACAAAAATTGCGGACAAC 58.952 39.130 0.00 0.00 38.99 3.32
1867 5656 4.898265 CCTCTGTTCTATCCCTCATCTCAA 59.102 45.833 0.00 0.00 0.00 3.02
1927 5754 2.559330 GTTTGGCAACCTACCGCG 59.441 61.111 0.00 0.00 0.00 6.46
1940 5767 0.391263 GGCTCTGACGGTAGGGTTTG 60.391 60.000 0.00 0.00 0.00 2.93
1941 5768 1.551019 GGGCTCTGACGGTAGGGTTT 61.551 60.000 0.00 0.00 0.00 3.27
1942 5769 1.988406 GGGCTCTGACGGTAGGGTT 60.988 63.158 0.00 0.00 0.00 4.11
1984 5816 3.316868 GGGGTTGATTTTCTTCGTCACAA 59.683 43.478 0.00 0.00 0.00 3.33
2045 5878 2.116238 GTAGGATCCTGCAACCTACCA 58.884 52.381 25.28 0.00 45.85 3.25
2126 5962 3.075186 GGTCAAACCCTACCGCCT 58.925 61.111 0.00 0.00 30.04 5.52
2138 5974 3.458163 CCGCTAGAGCCGGGTCAA 61.458 66.667 33.52 0.00 37.91 3.18
2139 5975 3.949885 TTCCGCTAGAGCCGGGTCA 62.950 63.158 33.52 18.87 37.91 4.02
2140 5976 3.140225 CTTCCGCTAGAGCCGGGTC 62.140 68.421 26.17 26.17 37.91 4.46
2141 5977 3.148279 CTTCCGCTAGAGCCGGGT 61.148 66.667 5.45 5.45 37.91 5.28
2144 5980 1.389609 TTACCCTTCCGCTAGAGCCG 61.390 60.000 0.00 0.00 37.91 5.52
2145 5981 0.828677 TTTACCCTTCCGCTAGAGCC 59.171 55.000 0.00 0.00 37.91 4.70
2146 5982 2.685850 TTTTACCCTTCCGCTAGAGC 57.314 50.000 0.00 0.00 37.78 4.09
2168 6132 3.879295 TGCAGAACAGAGAACTTCCTTTG 59.121 43.478 0.00 0.00 0.00 2.77
2170 6134 3.118261 TGTGCAGAACAGAGAACTTCCTT 60.118 43.478 0.00 0.00 33.78 3.36
2176 6140 7.834068 TCTAATATTGTGCAGAACAGAGAAC 57.166 36.000 0.00 0.00 40.74 3.01
2177 6141 8.886719 CATTCTAATATTGTGCAGAACAGAGAA 58.113 33.333 0.00 6.49 40.74 2.87
2178 6142 8.260114 TCATTCTAATATTGTGCAGAACAGAGA 58.740 33.333 0.00 0.00 40.74 3.10
2179 6143 8.429493 TCATTCTAATATTGTGCAGAACAGAG 57.571 34.615 0.00 0.00 40.74 3.35
2180 6144 8.969260 ATCATTCTAATATTGTGCAGAACAGA 57.031 30.769 0.00 0.00 40.74 3.41
2208 6180 7.496346 TTGATAGAAGTGGATAGAAGTGGTT 57.504 36.000 0.00 0.00 0.00 3.67
2209 6181 7.496346 TTTGATAGAAGTGGATAGAAGTGGT 57.504 36.000 0.00 0.00 0.00 4.16
2240 6212 4.808077 ATGTGTTTGCGAGATGATCATC 57.192 40.909 25.42 25.42 38.09 2.92


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

AutoCloner maintained by Alex Coulton.