Multiple sequence alignment - TraesCS5B01G410000

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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 TraesCS5B01G410000 chr5B 100.000 2561 0 0 1 2561 585025484 585022924 0.000000e+00 4730
1 TraesCS5B01G410000 chr5D 92.115 2600 94 44 14 2561 477395079 477392539 0.000000e+00 3563
2 TraesCS5B01G410000 chr5D 88.065 310 18 7 1232 1541 7043680 7043390 1.460000e-92 350
3 TraesCS5B01G410000 chr5A 91.441 2103 99 30 494 2561 596581713 596579657 0.000000e+00 2811
4 TraesCS5B01G410000 chr5A 90.000 250 13 5 234 471 596582303 596582054 1.910000e-81 313
5 TraesCS5B01G410000 chr5A 84.324 185 13 9 14 184 596582508 596582326 1.580000e-37 167
6 TraesCS5B01G410000 chr1A 89.873 158 12 3 1233 1388 31028866 31028711 1.550000e-47 200
7 TraesCS5B01G410000 chr1A 94.783 115 5 1 1427 1541 31028712 31028599 7.280000e-41 178


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 TraesCS5B01G410000 chr5B 585022924 585025484 2560 True 4730 4730 100.000000 1 2561 1 chr5B.!!$R1 2560
1 TraesCS5B01G410000 chr5D 477392539 477395079 2540 True 3563 3563 92.115000 14 2561 1 chr5D.!!$R2 2547
2 TraesCS5B01G410000 chr5A 596579657 596582508 2851 True 1097 2811 88.588333 14 2561 3 chr5A.!!$R1 2547

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
256 284 0.034059 AGCTACGTGCAAGACAAGCT 59.966 50.0 17.57 17.57 45.94 3.74 F
1047 1425 0.246360 TTGACATGGACGCGATGACT 59.754 50.0 15.93 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1168 1549 0.041238 TCCTCCTCGTCCTCAACCAT 59.959 55.0 0.0 0.0 0.00 3.55 R
1906 2303 0.103572 ACGTCAACCTGCGTACTTGT 59.896 50.0 0.0 0.0 39.72 3.16 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
141 154 1.881973 CATTAGCGCATTGTAGCCCAT 59.118 47.619 11.47 0.00 0.00 4.00
184 203 2.302230 GCATGCACAACACAACGCC 61.302 57.895 14.21 0.00 0.00 5.68
185 204 1.661197 CATGCACAACACAACGCCC 60.661 57.895 0.00 0.00 0.00 6.13
186 205 2.124060 ATGCACAACACAACGCCCA 61.124 52.632 0.00 0.00 0.00 5.36
187 206 2.278531 GCACAACACAACGCCCAC 60.279 61.111 0.00 0.00 0.00 4.61
200 219 3.000819 CCCACGCCCTGGTAGTCA 61.001 66.667 0.00 0.00 38.60 3.41
201 220 2.589157 CCCACGCCCTGGTAGTCAA 61.589 63.158 0.00 0.00 38.60 3.18
202 221 1.079127 CCACGCCCTGGTAGTCAAG 60.079 63.158 0.00 0.00 34.90 3.02
203 222 1.741770 CACGCCCTGGTAGTCAAGC 60.742 63.158 0.00 0.00 0.00 4.01
205 224 0.613853 ACGCCCTGGTAGTCAAGCTA 60.614 55.000 0.00 0.00 0.00 3.32
213 232 0.992802 GTAGTCAAGCTACGTGCAGC 59.007 55.000 0.00 0.00 45.94 5.25
214 233 0.108804 TAGTCAAGCTACGTGCAGCC 60.109 55.000 6.70 0.00 45.94 4.85
215 234 2.432456 TCAAGCTACGTGCAGCCG 60.432 61.111 6.70 0.00 45.94 5.52
216 235 4.152625 CAAGCTACGTGCAGCCGC 62.153 66.667 6.70 0.00 45.94 6.53
217 236 4.379243 AAGCTACGTGCAGCCGCT 62.379 61.111 6.70 0.00 45.94 5.52
218 237 4.803426 AGCTACGTGCAGCCGCTC 62.803 66.667 6.70 0.00 45.94 5.03
220 239 2.432456 CTACGTGCAGCCGCTCAA 60.432 61.111 0.00 0.00 39.64 3.02
221 240 2.027073 CTACGTGCAGCCGCTCAAA 61.027 57.895 0.00 0.00 39.64 2.69
222 241 1.565156 CTACGTGCAGCCGCTCAAAA 61.565 55.000 0.00 0.00 39.64 2.44
223 242 1.160946 TACGTGCAGCCGCTCAAAAA 61.161 50.000 0.00 0.00 39.64 1.94
256 284 0.034059 AGCTACGTGCAAGACAAGCT 59.966 50.000 17.57 17.57 45.94 3.74
317 345 4.208686 AGCCGCGAACGAGATCCC 62.209 66.667 8.23 0.00 43.93 3.85
436 485 4.195334 ACCCCAGCCATCGATGCC 62.195 66.667 20.25 9.38 0.00 4.40
475 524 7.352739 CCATTACTTCGCGATTAAGCTAAAAT 58.647 34.615 10.88 0.72 34.40 1.82
479 528 1.703490 CGCGATTAAGCTAAAATGCGC 59.297 47.619 0.00 0.00 37.79 6.09
509 876 0.324091 CACCCTACCTGGACCTACGT 60.324 60.000 0.00 0.00 38.35 3.57
727 1095 1.137479 CCGTAGAATCTTTACCCGCCA 59.863 52.381 0.00 0.00 0.00 5.69
742 1110 2.814410 GCCAAGAAGAAAAAGGCGC 58.186 52.632 0.00 0.00 35.42 6.53
972 1350 5.746721 GTCCTTCATTTGTTGTGGTTGTTAC 59.253 40.000 0.00 0.00 0.00 2.50
973 1351 5.654650 TCCTTCATTTGTTGTGGTTGTTACT 59.345 36.000 0.00 0.00 0.00 2.24
1047 1425 0.246360 TTGACATGGACGCGATGACT 59.754 50.000 15.93 0.00 0.00 3.41
1722 2114 2.983402 CATGCCATGCTACACTATGC 57.017 50.000 0.00 0.00 0.00 3.14
1723 2115 2.501261 CATGCCATGCTACACTATGCT 58.499 47.619 0.00 0.00 0.00 3.79
1724 2116 3.667360 CATGCCATGCTACACTATGCTA 58.333 45.455 0.00 0.00 0.00 3.49
1725 2117 3.391506 TGCCATGCTACACTATGCTAG 57.608 47.619 0.00 0.00 0.00 3.42
1768 2160 5.715434 TGACGTGTAGGCTGCATATATAA 57.285 39.130 8.93 0.00 0.00 0.98
1769 2161 6.280855 TGACGTGTAGGCTGCATATATAAT 57.719 37.500 8.93 0.00 0.00 1.28
1770 2162 6.697395 TGACGTGTAGGCTGCATATATAATT 58.303 36.000 8.93 0.00 0.00 1.40
1771 2163 7.832769 TGACGTGTAGGCTGCATATATAATTA 58.167 34.615 8.93 0.00 0.00 1.40
1772 2164 7.758076 TGACGTGTAGGCTGCATATATAATTAC 59.242 37.037 8.93 0.00 0.00 1.89
1773 2165 7.837863 ACGTGTAGGCTGCATATATAATTACT 58.162 34.615 8.93 0.00 0.00 2.24
1775 2167 9.797556 CGTGTAGGCTGCATATATAATTACTAA 57.202 33.333 8.93 0.00 0.00 2.24
1886 2283 1.078759 CGACTGATTCACCGCTCACC 61.079 60.000 0.00 0.00 0.00 4.02
1887 2284 1.078759 GACTGATTCACCGCTCACCG 61.079 60.000 0.00 0.00 0.00 4.94
1906 2303 1.144969 GTGACCAAAATGCTCGTCGA 58.855 50.000 0.00 0.00 0.00 4.20
1912 2309 2.734606 CCAAAATGCTCGTCGACAAGTA 59.265 45.455 17.16 6.55 0.00 2.24
1925 2322 0.103572 ACAAGTACGCAGGTTGACGT 59.896 50.000 0.00 0.00 45.85 4.34
1953 2351 5.872070 GGTCTCTCTGTTTTACTCTGGATTG 59.128 44.000 0.00 0.00 0.00 2.67
1966 2364 3.079578 TCTGGATTGTCTAACGTCGACT 58.920 45.455 14.70 0.00 32.70 4.18
1970 2368 0.386352 TTGTCTAACGTCGACTGCCG 60.386 55.000 14.70 2.42 40.25 5.69
1971 2369 1.208614 GTCTAACGTCGACTGCCGT 59.791 57.895 14.70 3.16 39.32 5.68
1972 2370 1.063951 GTCTAACGTCGACTGCCGTG 61.064 60.000 14.70 0.00 37.38 4.94
1973 2371 1.208358 CTAACGTCGACTGCCGTGA 59.792 57.895 14.70 0.00 37.38 4.35
1974 2372 0.793478 CTAACGTCGACTGCCGTGAG 60.793 60.000 14.70 5.12 37.38 3.51
1975 2373 1.229975 TAACGTCGACTGCCGTGAGA 61.230 55.000 14.70 0.00 37.38 3.27
1976 2374 2.202362 CGTCGACTGCCGTGAGAG 60.202 66.667 14.70 0.00 39.75 3.20
2122 2526 2.256117 ACCCGGTCTCTCTGTTTTTG 57.744 50.000 0.00 0.00 0.00 2.44
2124 2528 1.543429 CCCGGTCTCTCTGTTTTTGCT 60.543 52.381 0.00 0.00 0.00 3.91
2263 2667 0.946221 ACGTGAGCTTCTCCGCTTTG 60.946 55.000 0.00 0.00 41.08 2.77
2323 2727 4.155099 ACAGAGACAGATCACTGACTTACG 59.845 45.833 8.45 0.00 45.62 3.18
2324 2728 3.127895 AGAGACAGATCACTGACTTACGC 59.872 47.826 0.00 0.00 45.62 4.42
2336 2740 0.179029 ACTTACGCAGCAAAGGTGGT 60.179 50.000 8.88 0.00 35.28 4.16
2414 2819 1.274728 AGGGCAAGAGATATGCTAGCG 59.725 52.381 10.77 0.00 43.34 4.26
2415 2820 1.273606 GGGCAAGAGATATGCTAGCGA 59.726 52.381 10.77 0.15 43.34 4.93
2416 2821 2.605030 GGCAAGAGATATGCTAGCGAG 58.395 52.381 10.77 0.00 43.34 5.03
2450 2855 0.937304 TTGCAGTTCAACAGTCGCTC 59.063 50.000 0.00 0.00 0.00 5.03
2513 2920 1.774856 CCCCTAAACATAGTCCCCAGG 59.225 57.143 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.815308 ACTAGGATGCTATACGCCTATACG 59.185 45.833 0.00 0.00 38.05 3.06
6 7 6.204495 GGTACTAGGATGCTATACGCCTATAC 59.796 46.154 0.00 0.00 38.05 1.47
7 8 6.126681 TGGTACTAGGATGCTATACGCCTATA 60.127 42.308 0.00 0.00 38.05 1.31
8 9 5.131784 GGTACTAGGATGCTATACGCCTAT 58.868 45.833 0.00 0.00 38.05 2.57
9 10 4.019051 TGGTACTAGGATGCTATACGCCTA 60.019 45.833 0.00 0.00 38.05 3.93
10 11 3.245158 TGGTACTAGGATGCTATACGCCT 60.245 47.826 0.00 0.00 38.05 5.52
11 12 3.087031 TGGTACTAGGATGCTATACGCC 58.913 50.000 0.00 0.00 38.05 5.68
12 13 3.425892 CGTGGTACTAGGATGCTATACGC 60.426 52.174 0.00 0.00 39.77 4.42
78 79 9.214957 CGTACATAGGCATGGATAAATCTTTAA 57.785 33.333 0.00 0.00 36.39 1.52
79 80 8.372459 ACGTACATAGGCATGGATAAATCTTTA 58.628 33.333 0.00 0.00 36.39 1.85
80 81 7.224297 ACGTACATAGGCATGGATAAATCTTT 58.776 34.615 0.00 0.00 36.39 2.52
81 82 6.769512 ACGTACATAGGCATGGATAAATCTT 58.230 36.000 0.00 0.00 36.39 2.40
87 88 7.178805 TGGTAAATACGTACATAGGCATGGATA 59.821 37.037 0.00 0.00 36.39 2.59
141 154 2.139917 GTCACGATGCCACTTACACAA 58.860 47.619 0.00 0.00 0.00 3.33
185 204 1.741770 GCTTGACTACCAGGGCGTG 60.742 63.158 0.00 0.00 0.00 5.34
186 205 0.613853 TAGCTTGACTACCAGGGCGT 60.614 55.000 0.00 0.00 33.00 5.68
187 206 0.179108 GTAGCTTGACTACCAGGGCG 60.179 60.000 0.00 0.00 44.80 6.13
188 207 3.762674 GTAGCTTGACTACCAGGGC 57.237 57.895 0.00 0.00 44.80 5.19
194 213 0.992802 GCTGCACGTAGCTTGACTAC 59.007 55.000 3.01 0.00 46.70 2.73
195 214 0.108804 GGCTGCACGTAGCTTGACTA 60.109 55.000 10.03 0.00 45.94 2.59
197 216 2.730672 CGGCTGCACGTAGCTTGAC 61.731 63.158 10.03 5.20 45.94 3.18
198 217 2.432456 CGGCTGCACGTAGCTTGA 60.432 61.111 10.03 0.00 45.94 3.02
200 219 4.379243 AGCGGCTGCACGTAGCTT 62.379 61.111 21.93 0.00 46.23 3.74
201 220 4.803426 GAGCGGCTGCACGTAGCT 62.803 66.667 21.93 3.75 46.23 3.32
203 222 1.565156 TTTTGAGCGGCTGCACGTAG 61.565 55.000 21.93 0.00 46.23 3.51
205 224 2.477176 TTTTTGAGCGGCTGCACGT 61.477 52.632 21.93 0.00 46.23 4.49
206 225 2.331098 TTTTTGAGCGGCTGCACG 59.669 55.556 21.93 3.97 46.23 5.34
224 243 3.188667 GCACGTAGCTAGCTTTCCTTTTT 59.811 43.478 24.88 0.00 41.15 1.94
225 244 2.742589 GCACGTAGCTAGCTTTCCTTTT 59.257 45.455 24.88 0.00 41.15 2.27
226 245 2.289444 TGCACGTAGCTAGCTTTCCTTT 60.289 45.455 24.88 0.00 45.94 3.11
227 246 1.275291 TGCACGTAGCTAGCTTTCCTT 59.725 47.619 24.88 0.00 45.94 3.36
228 247 0.895530 TGCACGTAGCTAGCTTTCCT 59.104 50.000 24.88 0.00 45.94 3.36
229 248 1.661112 CTTGCACGTAGCTAGCTTTCC 59.339 52.381 24.88 10.45 45.94 3.13
230 249 2.345942 GTCTTGCACGTAGCTAGCTTTC 59.654 50.000 24.88 15.27 44.32 2.62
231 250 2.288825 TGTCTTGCACGTAGCTAGCTTT 60.289 45.455 24.88 4.85 44.32 3.51
232 251 1.272490 TGTCTTGCACGTAGCTAGCTT 59.728 47.619 24.88 1.07 44.32 3.74
242 261 1.202568 CACGAGCTTGTCTTGCACG 59.797 57.895 2.72 4.28 46.58 5.34
243 262 0.233332 GACACGAGCTTGTCTTGCAC 59.767 55.000 2.72 0.00 42.36 4.57
244 263 0.880278 GGACACGAGCTTGTCTTGCA 60.880 55.000 16.19 0.00 44.63 4.08
264 292 2.032634 GCACGATCAACAGCGGGAA 61.033 57.895 0.00 0.00 36.77 3.97
436 485 2.994387 TAATGGCCGCGAGATGCTGG 62.994 60.000 8.23 0.00 43.27 4.85
705 1073 1.861971 CGGGTAAAGATTCTACGGCC 58.138 55.000 0.00 0.00 0.00 6.13
727 1095 2.693074 TCTTTGGCGCCTTTTTCTTCTT 59.307 40.909 29.70 0.00 0.00 2.52
742 1110 2.275380 CCCCGGTGGCTTTCTTTGG 61.275 63.158 0.00 0.00 0.00 3.28
972 1350 6.986817 TCTTTCTTTCTCCTGACACTTAACAG 59.013 38.462 0.00 0.00 0.00 3.16
973 1351 6.884832 TCTTTCTTTCTCCTGACACTTAACA 58.115 36.000 0.00 0.00 0.00 2.41
1168 1549 0.041238 TCCTCCTCGTCCTCAACCAT 59.959 55.000 0.00 0.00 0.00 3.55
1173 1554 2.438614 CGCTCCTCCTCGTCCTCA 60.439 66.667 0.00 0.00 0.00 3.86
1603 1984 2.951269 ACGTATGTGACTCCGTCCA 58.049 52.632 0.00 0.00 0.00 4.02
1612 1993 6.675971 GTTCCAAAACTTTCACACGTATGTGA 60.676 38.462 21.82 8.59 45.87 3.58
1613 1994 5.454232 GTTCCAAAACTTTCACACGTATGTG 59.546 40.000 13.64 13.64 43.44 3.21
1614 1995 5.575019 GTTCCAAAACTTTCACACGTATGT 58.425 37.500 0.00 0.00 34.08 2.29
1615 1996 4.668837 CGTTCCAAAACTTTCACACGTATG 59.331 41.667 0.00 0.00 32.95 2.39
1616 1997 4.260866 CCGTTCCAAAACTTTCACACGTAT 60.261 41.667 0.00 0.00 32.95 3.06
1617 1998 3.063725 CCGTTCCAAAACTTTCACACGTA 59.936 43.478 0.00 0.00 32.95 3.57
1716 2108 1.400530 GCACGGGTCCCTAGCATAGT 61.401 60.000 14.67 0.00 36.82 2.12
1717 2109 1.115930 AGCACGGGTCCCTAGCATAG 61.116 60.000 19.94 0.24 38.80 2.23
1718 2110 0.689745 AAGCACGGGTCCCTAGCATA 60.690 55.000 19.94 0.00 0.00 3.14
1719 2111 0.689745 TAAGCACGGGTCCCTAGCAT 60.690 55.000 19.94 12.64 0.00 3.79
1720 2112 0.689745 ATAAGCACGGGTCCCTAGCA 60.690 55.000 19.94 4.54 0.00 3.49
1721 2113 0.468648 AATAAGCACGGGTCCCTAGC 59.531 55.000 6.29 9.83 0.00 3.42
1722 2114 3.277142 AAAATAAGCACGGGTCCCTAG 57.723 47.619 6.29 0.00 0.00 3.02
1723 2115 3.776417 ACTAAAATAAGCACGGGTCCCTA 59.224 43.478 6.29 0.00 0.00 3.53
1724 2116 2.574824 ACTAAAATAAGCACGGGTCCCT 59.425 45.455 6.29 0.00 0.00 4.20
1725 2117 2.995283 ACTAAAATAAGCACGGGTCCC 58.005 47.619 0.00 0.00 0.00 4.46
1778 2170 9.645059 CGGATATTCATTCATTCATGTAGTAGT 57.355 33.333 0.00 0.00 0.00 2.73
1779 2171 9.645059 ACGGATATTCATTCATTCATGTAGTAG 57.355 33.333 0.00 0.00 0.00 2.57
1797 2190 8.429641 AGTAATTTACATCAGGTGACGGATATT 58.570 33.333 9.15 0.00 43.75 1.28
1800 2193 6.235231 AGTAATTTACATCAGGTGACGGAT 57.765 37.500 9.15 0.00 46.69 4.18
1850 2247 2.508663 GGGCTCTTCACGTACGGC 60.509 66.667 21.06 11.68 0.00 5.68
1886 2283 0.179250 CGACGAGCATTTTGGTCACG 60.179 55.000 7.39 7.82 44.51 4.35
1887 2284 1.136336 GTCGACGAGCATTTTGGTCAC 60.136 52.381 0.00 0.65 44.51 3.67
1906 2303 0.103572 ACGTCAACCTGCGTACTTGT 59.896 50.000 0.00 0.00 39.72 3.16
1925 2322 4.458295 CAGAGTAAAACAGAGAGACCGGTA 59.542 45.833 7.34 0.00 0.00 4.02
1953 2351 4.053067 CGGCAGTCGACGTTAGAC 57.947 61.111 10.46 14.73 39.51 2.59
1966 2364 2.640302 GCTCTCACCTCTCACGGCA 61.640 63.158 0.00 0.00 0.00 5.69
1970 2368 2.167487 CCTAAAGGCTCTCACCTCTCAC 59.833 54.545 0.00 0.00 39.93 3.51
1971 2369 2.461695 CCTAAAGGCTCTCACCTCTCA 58.538 52.381 0.00 0.00 39.93 3.27
2083 2487 3.269347 GTCAACCTGCGCACACGT 61.269 61.111 5.66 0.00 42.83 4.49
2085 2489 1.952133 TACGTCAACCTGCGCACAC 60.952 57.895 5.66 0.00 0.00 3.82
2122 2526 2.418628 TGCACCGTTAAATAAGCAGAGC 59.581 45.455 0.00 0.00 0.00 4.09
2124 2528 4.094294 GTCATGCACCGTTAAATAAGCAGA 59.906 41.667 0.00 0.00 35.26 4.26
2205 2609 5.105146 CCAGGATATCCGATAGAAAAGAGGG 60.105 48.000 16.21 0.39 42.08 4.30
2263 2667 3.754850 ACGGCCTATACTTTGTTTTCACC 59.245 43.478 0.00 0.00 0.00 4.02
2276 2680 5.305902 TCAAATTCTATCACCACGGCCTATA 59.694 40.000 0.00 0.00 0.00 1.31
2323 2727 1.598130 AGTCGACCACCTTTGCTGC 60.598 57.895 13.01 0.00 0.00 5.25
2324 2728 1.230635 CCAGTCGACCACCTTTGCTG 61.231 60.000 13.01 0.00 0.00 4.41
2414 2819 5.233988 ACTGCAACATCAAGTCTTCTACTC 58.766 41.667 0.00 0.00 37.50 2.59
2415 2820 5.220710 ACTGCAACATCAAGTCTTCTACT 57.779 39.130 0.00 0.00 41.49 2.57
2416 2821 5.466728 TGAACTGCAACATCAAGTCTTCTAC 59.533 40.000 0.00 0.00 0.00 2.59
2446 2851 2.149578 GATCAATGGAATCTGGGAGCG 58.850 52.381 0.00 0.00 0.00 5.03
2450 2855 5.075493 CCCTTTAGATCAATGGAATCTGGG 58.925 45.833 0.00 0.00 34.08 4.45
2513 2920 2.293170 CCTCTAAAAGCTGCTTAGGGC 58.707 52.381 16.31 0.00 42.22 5.19


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

AutoCloner maintained by Alex Coulton.