Multiple sequence alignment - TraesCS2D01G081300

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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 TraesCS2D01G081300 chr2D 100.000 2192 0 0 1 2192 34993875 34996066 0.000000e+00 4048.0
1 TraesCS2D01G081300 chr2D 91.292 1424 121 3 771 2192 34987890 34989312 0.000000e+00 1940.0
2 TraesCS2D01G081300 chr2D 85.909 1249 176 0 929 2177 585477150 585475902 0.000000e+00 1332.0
3 TraesCS2D01G081300 chr2D 85.385 1259 176 8 929 2184 585517413 585516160 0.000000e+00 1299.0
4 TraesCS2D01G081300 chr2D 82.123 179 27 5 2 176 138704748 138704571 4.880000e-32 148.0
5 TraesCS2D01G081300 chr2B 96.809 2194 51 4 1 2192 57671693 57673869 0.000000e+00 3646.0
6 TraesCS2D01G081300 chr2B 90.871 1424 127 3 771 2192 57664395 57665817 0.000000e+00 1906.0
7 TraesCS2D01G081300 chr2B 85.308 1266 180 6 929 2190 706418483 706417220 0.000000e+00 1303.0
8 TraesCS2D01G081300 chr2B 84.507 1207 171 13 963 2157 425353460 425352258 0.000000e+00 1179.0
9 TraesCS2D01G081300 chr2A 90.413 1575 143 7 620 2192 38309019 38310587 0.000000e+00 2065.0
10 TraesCS2D01G081300 chr2A 85.691 1251 170 7 929 2177 719541278 719540035 0.000000e+00 1310.0
11 TraesCS2D01G081300 chr2A 80.663 181 27 6 4 176 716393006 716393186 1.370000e-27 134.0
12 TraesCS2D01G081300 chr4A 88.636 176 16 4 3 176 594144834 594145007 6.130000e-51 211.0
13 TraesCS2D01G081300 chr4A 89.286 56 3 3 612 666 534559107 534559160 1.400000e-07 67.6
14 TraesCS2D01G081300 chr7D 86.034 179 19 3 3 176 498416625 498416802 1.030000e-43 187.0
15 TraesCS2D01G081300 chr7D 86.310 168 19 3 1 164 118398472 118398305 1.730000e-41 180.0
16 TraesCS2D01G081300 chr4D 84.324 185 21 5 3 179 9304336 9304152 8.040000e-40 174.0
17 TraesCS2D01G081300 chr7A 83.146 178 25 3 2 176 63577965 63578140 8.100000e-35 158.0
18 TraesCS2D01G081300 chr5D 81.183 186 25 6 1 176 276452442 276452257 8.160000e-30 141.0
19 TraesCS2D01G081300 chr5A 91.803 61 4 1 611 671 11253291 11253232 1.390000e-12 84.2
20 TraesCS2D01G081300 chr6D 91.667 60 4 1 612 671 318784624 318784566 5.020000e-12 82.4
21 TraesCS2D01G081300 chr3D 85.938 64 9 0 604 667 591816030 591815967 3.900000e-08 69.4
22 TraesCS2D01G081300 chr5B 84.848 66 10 0 606 671 499600354 499600419 1.400000e-07 67.6
23 TraesCS2D01G081300 chr5B 85.075 67 9 1 606 671 500565291 500565225 1.400000e-07 67.6
24 TraesCS2D01G081300 chr3A 95.000 40 2 0 632 671 575609858 575609819 1.820000e-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 TraesCS2D01G081300 chr2D 34993875 34996066 2191 False 4048 4048 100.000 1 2192 1 chr2D.!!$F2 2191
1 TraesCS2D01G081300 chr2D 34987890 34989312 1422 False 1940 1940 91.292 771 2192 1 chr2D.!!$F1 1421
2 TraesCS2D01G081300 chr2D 585475902 585477150 1248 True 1332 1332 85.909 929 2177 1 chr2D.!!$R2 1248
3 TraesCS2D01G081300 chr2D 585516160 585517413 1253 True 1299 1299 85.385 929 2184 1 chr2D.!!$R3 1255
4 TraesCS2D01G081300 chr2B 57671693 57673869 2176 False 3646 3646 96.809 1 2192 1 chr2B.!!$F2 2191
5 TraesCS2D01G081300 chr2B 57664395 57665817 1422 False 1906 1906 90.871 771 2192 1 chr2B.!!$F1 1421
6 TraesCS2D01G081300 chr2B 706417220 706418483 1263 True 1303 1303 85.308 929 2190 1 chr2B.!!$R2 1261
7 TraesCS2D01G081300 chr2B 425352258 425353460 1202 True 1179 1179 84.507 963 2157 1 chr2B.!!$R1 1194
8 TraesCS2D01G081300 chr2A 38309019 38310587 1568 False 2065 2065 90.413 620 2192 1 chr2A.!!$F1 1572
9 TraesCS2D01G081300 chr2A 719540035 719541278 1243 True 1310 1310 85.691 929 2177 1 chr2A.!!$R1 1248

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
241 242 0.251916 CCTATTCGGTGGTTCAGCCA 59.748 55.0 0.0 0.0 46.95 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 1826 0.462047 GTATCCCTCTGTGGTTGGCG 60.462 60.0 0.0 0.0 0.0 5.69 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
240 241 0.252197 ACCTATTCGGTGGTTCAGCC 59.748 55.000 0.00 0.0 46.80 4.85
241 242 0.251916 CCTATTCGGTGGTTCAGCCA 59.748 55.000 0.00 0.0 46.95 4.75
317 318 4.848357 CCCATTAAGGATGTTGAGTCTGT 58.152 43.478 0.00 0.0 41.22 3.41
331 332 8.408043 TGTTGAGTCTGTCATGGAAAAATTAT 57.592 30.769 0.00 0.0 34.17 1.28
336 337 6.438425 AGTCTGTCATGGAAAAATTATGCCTT 59.562 34.615 0.00 0.0 0.00 4.35
364 365 9.989296 TTCCTTTTTCATTTATAGGAGGAATGA 57.011 29.630 0.00 0.0 37.19 2.57
402 403 6.744822 TCCCTTACCTAAAGACACCATACTA 58.255 40.000 0.00 0.0 37.38 1.82
404 405 7.289317 TCCCTTACCTAAAGACACCATACTATG 59.711 40.741 0.00 0.0 37.38 2.23
512 513 2.163613 ACATGAACATCGCGAGTCACTA 59.836 45.455 16.66 0.0 0.00 2.74
567 568 8.906867 CATTAAGAATTGTCCTAACCATGACAT 58.093 33.333 0.00 0.0 40.88 3.06
577 578 5.887598 TCCTAACCATGACATTGAAGAATGG 59.112 40.000 0.00 0.0 43.00 3.16
812 813 5.144100 ACAACAATGTGAGGGGTTTTATCA 58.856 37.500 0.00 0.0 38.69 2.15
1025 1026 0.833287 ATCGGTGGGTCAATCCTCAG 59.167 55.000 0.00 0.0 36.25 3.35
1824 1826 1.215423 AGGCCCACATAACAAGATCCC 59.785 52.381 0.00 0.0 0.00 3.85
1834 1836 1.303236 CAAGATCCCGCCAACCACA 60.303 57.895 0.00 0.0 0.00 4.17
1941 1945 2.026449 AGGGAAACAAGATGAGAGCCAG 60.026 50.000 0.00 0.0 0.00 4.85
2037 2049 1.001406 AGTCTTCCTTTCTCTGCGTGG 59.999 52.381 0.00 0.0 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 5.747951 CAAAAAGGTTAAGCATTTTGGCA 57.252 34.783 27.80 0.00 39.75 4.92
193 194 2.819608 GGACCAGATTAAGCAAGTGCAA 59.180 45.455 6.00 0.00 45.16 4.08
246 247 9.860898 GAAGTATGTAGATGCATATATGTGTCA 57.139 33.333 14.14 4.47 34.35 3.58
248 249 9.866798 CAGAAGTATGTAGATGCATATATGTGT 57.133 33.333 14.14 3.40 34.35 3.72
249 250 8.815189 GCAGAAGTATGTAGATGCATATATGTG 58.185 37.037 14.14 0.00 34.35 3.21
250 251 8.534496 TGCAGAAGTATGTAGATGCATATATGT 58.466 33.333 14.14 0.00 38.64 2.29
331 332 8.875168 TCCTATAAATGAAAAAGGAAAAAGGCA 58.125 29.630 0.00 0.00 33.45 4.75
483 484 4.242475 TCGCGATGTTCATGTCTAAAACT 58.758 39.130 3.71 0.00 0.00 2.66
512 513 6.767902 TCTTTATTCTCTGTCAAACAAGCACT 59.232 34.615 0.00 0.00 0.00 4.40
567 568 6.795144 AATACATGATTGGCCATTCTTCAA 57.205 33.333 24.22 8.23 0.00 2.69
577 578 9.347240 AGGAGCATTATATAATACATGATTGGC 57.653 33.333 7.65 4.47 0.00 4.52
812 813 7.936847 TGGCATATCCGACTATTATTGAAACTT 59.063 33.333 0.00 0.00 37.80 2.66
1025 1026 4.464008 TCCTTCTGCAATATTGTCCATCC 58.536 43.478 16.61 0.00 0.00 3.51
1201 1202 1.227943 CACTACCGATGGCCATGGG 60.228 63.158 37.30 37.30 41.74 4.00
1330 1331 2.615447 CAATCATGGGTGTCGAAGGATG 59.385 50.000 0.00 0.00 0.00 3.51
1503 1504 5.883180 ACTAGTTACCTGACACTCTCTTCT 58.117 41.667 0.00 0.00 0.00 2.85
1824 1826 0.462047 GTATCCCTCTGTGGTTGGCG 60.462 60.000 0.00 0.00 0.00 5.69
1834 1836 7.093245 GGTCTTTCTAAAAGACAGTATCCCTCT 60.093 40.741 25.57 0.00 46.31 3.69
1941 1945 8.391106 GTTGACCTAACAACATATCATGTCTTC 58.609 37.037 0.00 0.00 46.19 2.87
2037 2049 7.010830 GCTTCCATCAAGAAAATAATGAAAGCC 59.989 37.037 0.00 0.00 32.36 4.35


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

AutoCloner maintained by Alex Coulton.