Multiple sequence alignment - TraesCS7D01G266800

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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 TraesCS7D01G266800 chr7D 100.000 3886 0 0 804 4689 249590126 249594011 0.000000e+00 7177
1 TraesCS7D01G266800 chr7D 100.000 448 0 0 1 448 249589323 249589770 0.000000e+00 828
2 TraesCS7D01G266800 chr7B 97.864 3277 54 7 835 4102 226576173 226579442 0.000000e+00 5650
3 TraesCS7D01G266800 chr7B 94.866 448 23 0 1 448 226575411 226575858 0.000000e+00 701
4 TraesCS7D01G266800 chr7B 92.776 263 12 6 4431 4689 226580226 226580485 1.590000e-99 374
5 TraesCS7D01G266800 chr7B 96.335 191 7 0 4100 4290 226579676 226579866 9.790000e-82 315
6 TraesCS7D01G266800 chr7B 95.876 97 4 0 4288 4384 226580132 226580228 1.750000e-34 158
7 TraesCS7D01G266800 chr7A 92.532 3187 127 48 813 3934 271635528 271632388 0.000000e+00 4464
8 TraesCS7D01G266800 chr7A 95.759 448 19 0 1 448 271636022 271635575 0.000000e+00 723
9 TraesCS7D01G266800 chr4B 93.377 302 19 1 1 302 652315886 652316186 3.330000e-121 446
10 TraesCS7D01G266800 chr2B 93.046 302 20 1 1 302 746592822 746593122 1.550000e-119 440
11 TraesCS7D01G266800 chr6B 91.391 302 24 2 1 302 87006811 87007110 3.380000e-111 412
12 TraesCS7D01G266800 chr5A 78.593 327 59 9 3364 3685 504872859 504873179 6.150000e-49 206


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 TraesCS7D01G266800 chr7D 249589323 249594011 4688 False 4002.5 7177 100.0000 1 4689 2 chr7D.!!$F1 4688
1 TraesCS7D01G266800 chr7B 226575411 226580485 5074 False 1439.6 5650 95.5434 1 4689 5 chr7B.!!$F1 4688
2 TraesCS7D01G266800 chr7A 271632388 271636022 3634 True 2593.5 4464 94.1455 1 3934 2 chr7A.!!$R1 3933

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
91 92 1.665916 CGGTATCCTCATGCTGGCG 60.666 63.158 0.0 0.0 0.00 5.69 F
355 356 2.995939 TGCAGATGAGAGCAAAAGTACG 59.004 45.455 0.0 0.0 37.90 3.67 F
1863 2109 3.381272 AGTGTCCATTTTGACCACAGTTG 59.619 43.478 0.0 0.0 34.25 3.16 F
2942 3218 1.000827 CAGTGCCTAGCGACCTCTATG 60.001 57.143 0.0 0.0 0.00 2.23 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1041 1281 0.329596 GGTCCCTTGCAATCTGGTCT 59.670 55.000 0.00 0.0 0.0 3.85 R
1880 2126 3.458857 TCCACTACTACCACCCAAACAAA 59.541 43.478 0.00 0.0 0.0 2.83 R
3523 3816 2.050836 TTGTGAAGGGCAGCGGAGAA 62.051 55.000 0.00 0.0 0.0 2.87 R
4026 4334 1.386533 GGTATCGAGAAGGACCGTCA 58.613 55.000 10.22 0.0 0.0 4.35 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
54 55 3.508793 CCAAAGACCAAGATGCTTGATGT 59.491 43.478 8.64 0.00 0.00 3.06
74 75 2.093783 GTCATGTTAGTTCTTTCGCCCG 59.906 50.000 0.00 0.00 0.00 6.13
91 92 1.665916 CGGTATCCTCATGCTGGCG 60.666 63.158 0.00 0.00 0.00 5.69
149 150 5.119931 TCATTTGACAATGTTGCCTACAC 57.880 39.130 0.00 0.00 40.78 2.90
278 279 5.118990 ACTATGCAGAATTTATCACAGCGT 58.881 37.500 0.00 0.00 0.00 5.07
327 328 4.910195 TGTATGCTTCTGTTCTGAACCAT 58.090 39.130 17.26 14.17 0.00 3.55
355 356 2.995939 TGCAGATGAGAGCAAAAGTACG 59.004 45.455 0.00 0.00 37.90 3.67
380 381 3.600388 ACAGAAGGATCATCCAACGAAC 58.400 45.455 6.42 0.00 39.61 3.95
948 1188 5.163581 GGCAGATTCATTGATACTTGCACTT 60.164 40.000 12.12 0.00 0.00 3.16
949 1189 6.327934 GCAGATTCATTGATACTTGCACTTT 58.672 36.000 0.00 0.00 0.00 2.66
950 1190 7.415541 GGCAGATTCATTGATACTTGCACTTTA 60.416 37.037 12.12 0.00 0.00 1.85
951 1191 7.970061 GCAGATTCATTGATACTTGCACTTTAA 59.030 33.333 0.00 0.00 0.00 1.52
1292 1533 6.088016 TCTGCTGTTTATTTTTGCTGACAT 57.912 33.333 0.00 0.00 0.00 3.06
1316 1557 9.778993 CATTGACCTAATTGTCTTATCAACTTG 57.221 33.333 0.00 0.00 36.21 3.16
1766 2012 6.246420 AGAACTGTGGATTCGAATTTCAAG 57.754 37.500 12.81 10.53 0.00 3.02
1863 2109 3.381272 AGTGTCCATTTTGACCACAGTTG 59.619 43.478 0.00 0.00 34.25 3.16
1880 2126 3.562557 CAGTTGCTACAGGTTTTACGGTT 59.437 43.478 0.13 0.00 0.00 4.44
2096 2344 7.654520 TCGTTTACTATTCTTGCTACACAGTTT 59.345 33.333 0.00 0.00 0.00 2.66
2130 2378 2.707849 CCTGTGGAGCCTGCAATGC 61.708 63.158 0.00 0.00 0.00 3.56
2747 3011 5.104444 CCTGTCTAGGGACTACAGACTTCTA 60.104 48.000 9.49 0.00 45.16 2.10
2942 3218 1.000827 CAGTGCCTAGCGACCTCTATG 60.001 57.143 0.00 0.00 0.00 2.23
2955 3231 2.499289 ACCTCTATGAGTGGTCAAGCTG 59.501 50.000 0.00 0.00 37.53 4.24
3153 3434 4.214332 GTCTTTAGGAAGCCACTTCAACAG 59.786 45.833 9.38 0.65 41.77 3.16
3523 3816 5.009631 TGCTGCTGTGTAAGTTAAATCCAT 58.990 37.500 0.00 0.00 0.00 3.41
3529 3822 6.456988 GCTGTGTAAGTTAAATCCATTCTCCG 60.457 42.308 0.00 0.00 0.00 4.63
3761 4063 9.634021 TTGGCATTGGTTTTATATAGTCATACA 57.366 29.630 0.00 0.00 0.00 2.29
3859 4167 5.853936 TGCATGTTACTGTATATGGAGACC 58.146 41.667 11.90 0.00 0.00 3.85
3998 4306 4.703897 AGAGAAAAATTCACTCACCGTCA 58.296 39.130 0.00 0.00 33.69 4.35
3999 4307 5.123227 AGAGAAAAATTCACTCACCGTCAA 58.877 37.500 0.00 0.00 33.69 3.18
4009 4317 6.073327 TCACTCACCGTCAATGTATCTATC 57.927 41.667 0.00 0.00 0.00 2.08
4026 4334 1.821216 ATCGCGGAATTCACTTTGGT 58.179 45.000 6.13 0.00 0.00 3.67
4060 4368 6.061441 TCTCGATACCCTAAATACGGTTGTA 58.939 40.000 0.00 0.00 33.36 2.41
4061 4369 6.716628 TCTCGATACCCTAAATACGGTTGTAT 59.283 38.462 0.00 0.00 43.14 2.29
4090 4398 5.049405 CACTTTGGTCATGGTACTTCTCAAC 60.049 44.000 0.00 0.00 0.00 3.18
4094 4402 3.432252 GGTCATGGTACTTCTCAACAACG 59.568 47.826 0.00 0.00 0.00 4.10
4159 4703 2.960384 TCACTTTAGTCACGGTCCTTCA 59.040 45.455 0.00 0.00 0.00 3.02
4216 4760 5.549347 AGCATCTATAATCAGAGCCACAAG 58.451 41.667 0.00 0.00 0.00 3.16
4228 4772 2.996734 CACAAGGCCGCCCCAAAT 60.997 61.111 5.55 0.00 35.39 2.32
4330 5142 2.599281 TCCGGAAGTGACTCGCCA 60.599 61.111 0.00 0.00 0.00 5.69
4334 5146 1.156736 CGGAAGTGACTCGCCAAATT 58.843 50.000 5.48 0.00 0.00 1.82
4366 5178 1.065273 GCTTCGCATTGCCATCCAG 59.935 57.895 2.41 0.00 0.00 3.86
4395 5207 4.324991 GGACACCGGCGGGAGTTT 62.325 66.667 31.78 5.31 37.24 2.66
4396 5208 3.047877 GACACCGGCGGGAGTTTG 61.048 66.667 31.78 20.92 37.24 2.93
4397 5209 3.524648 GACACCGGCGGGAGTTTGA 62.525 63.158 31.78 0.00 37.24 2.69
4398 5210 2.742372 CACCGGCGGGAGTTTGAG 60.742 66.667 31.78 1.05 36.97 3.02
4399 5211 3.239253 ACCGGCGGGAGTTTGAGT 61.239 61.111 31.78 1.72 36.97 3.41
4400 5212 2.032071 CCGGCGGGAGTTTGAGTT 59.968 61.111 20.56 0.00 34.06 3.01
4401 5213 2.033194 CCGGCGGGAGTTTGAGTTC 61.033 63.158 20.56 0.00 34.06 3.01
4402 5214 2.033194 CGGCGGGAGTTTGAGTTCC 61.033 63.158 0.00 0.00 0.00 3.62
4403 5215 2.033194 GGCGGGAGTTTGAGTTCCG 61.033 63.158 0.00 0.00 43.13 4.30
4404 5216 3.562635 CGGGAGTTTGAGTTCCGC 58.437 61.111 0.00 0.00 34.17 5.54
4405 5217 2.033194 CGGGAGTTTGAGTTCCGCC 61.033 63.158 0.00 0.00 34.17 6.13
4406 5218 2.033194 GGGAGTTTGAGTTCCGCCG 61.033 63.158 0.00 0.00 34.17 6.46
4407 5219 2.677979 GGAGTTTGAGTTCCGCCGC 61.678 63.158 0.00 0.00 0.00 6.53
4408 5220 2.668550 AGTTTGAGTTCCGCCGCC 60.669 61.111 0.00 0.00 0.00 6.13
4409 5221 2.975799 GTTTGAGTTCCGCCGCCA 60.976 61.111 0.00 0.00 0.00 5.69
4410 5222 2.668212 TTTGAGTTCCGCCGCCAG 60.668 61.111 0.00 0.00 0.00 4.85
4422 5234 4.803426 CGCCAGCTCCTCCGTGTC 62.803 72.222 0.00 0.00 0.00 3.67
4423 5235 4.459089 GCCAGCTCCTCCGTGTCC 62.459 72.222 0.00 0.00 0.00 4.02
4424 5236 3.775654 CCAGCTCCTCCGTGTCCC 61.776 72.222 0.00 0.00 0.00 4.46
4425 5237 4.135153 CAGCTCCTCCGTGTCCCG 62.135 72.222 0.00 0.00 0.00 5.14
4485 5297 1.150567 CCGCTCCAGATTCGAAGCAG 61.151 60.000 16.78 7.58 34.39 4.24
4531 5344 3.977244 CAACACCGCCCAGGCAAC 61.977 66.667 9.78 0.00 46.52 4.17
4605 5419 3.268103 AAGGCCGCCCGTCTCAATT 62.268 57.895 5.55 0.00 35.76 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 2.343101 CGGGCGAAAGAACTAACATGA 58.657 47.619 0.00 0.00 0.00 3.07
74 75 0.320247 CTCGCCAGCATGAGGATACC 60.320 60.000 8.66 0.00 39.69 2.73
91 92 2.157738 ACACCTGCATCTTTCTTGCTC 58.842 47.619 0.00 0.00 40.77 4.26
149 150 4.633126 CCTACATCAACAATGTCAGTCAGG 59.367 45.833 0.00 0.00 45.78 3.86
278 279 7.931407 TGACATAGTAAAGAAGTTGAGCAGAAA 59.069 33.333 0.00 0.00 0.00 2.52
355 356 4.695455 TCGTTGGATGATCCTTCTGTTTTC 59.305 41.667 13.44 0.00 37.46 2.29
380 381 1.296715 CTGGAGGAACCCCTTGACG 59.703 63.158 0.00 0.00 44.53 4.35
825 826 7.789202 ATCAATAGGATAGTCAGCATGTACT 57.211 36.000 0.00 0.00 33.31 2.73
902 1141 5.331902 CCACAGGCAGAATTATGTAAAACG 58.668 41.667 1.46 0.00 0.00 3.60
1041 1281 0.329596 GGTCCCTTGCAATCTGGTCT 59.670 55.000 0.00 0.00 0.00 3.85
1292 1533 9.739276 ATCAAGTTGATAAGACAATTAGGTCAA 57.261 29.630 16.85 0.00 36.42 3.18
1316 1557 6.107901 ACATAGCAGGATCCTAAGTCAATC 57.892 41.667 15.67 0.00 0.00 2.67
1321 1562 3.900601 CTGGACATAGCAGGATCCTAAGT 59.099 47.826 15.67 8.62 32.06 2.24
1514 1760 4.430137 AGCACATCAAGCAAGTTGTATG 57.570 40.909 4.48 4.36 37.43 2.39
1766 2012 8.279103 GCAAGTATATATCAGCTCAAAACAGAC 58.721 37.037 0.00 0.00 0.00 3.51
1863 2109 4.556942 ACAAAACCGTAAAACCTGTAGC 57.443 40.909 0.00 0.00 0.00 3.58
1880 2126 3.458857 TCCACTACTACCACCCAAACAAA 59.541 43.478 0.00 0.00 0.00 2.83
1990 2238 5.050490 AGCATACAAAGAGCATAACCTACG 58.950 41.667 0.00 0.00 0.00 3.51
2130 2378 8.501580 CATTATATTCATGAACACTAGGCACAG 58.498 37.037 11.07 0.00 0.00 3.66
2566 2830 0.482446 ACTTCCCATGGAACTGGCAA 59.518 50.000 15.22 0.00 36.71 4.52
2942 3218 6.631962 AGTAAATACTACAGCTTGACCACTC 58.368 40.000 0.00 0.00 34.13 3.51
3055 3332 6.791867 ACAGTGCAGATAGACCAGTTATTA 57.208 37.500 0.00 0.00 0.00 0.98
3523 3816 2.050836 TTGTGAAGGGCAGCGGAGAA 62.051 55.000 0.00 0.00 0.00 2.87
3547 3840 4.023707 GGTCAAATAAGCATCAAGGGATCG 60.024 45.833 0.00 0.00 0.00 3.69
3859 4167 4.750098 AGAAACAAAGTGGACGATACACAG 59.250 41.667 10.43 4.14 41.21 3.66
3998 4306 5.784177 AGTGAATTCCGCGATAGATACATT 58.216 37.500 8.23 0.00 39.76 2.71
3999 4307 5.392767 AGTGAATTCCGCGATAGATACAT 57.607 39.130 8.23 0.00 39.76 2.29
4026 4334 1.386533 GGTATCGAGAAGGACCGTCA 58.613 55.000 10.22 0.00 0.00 4.35
4060 4368 8.109634 AGAAGTACCATGACCAAAGTGAATTAT 58.890 33.333 0.00 0.00 0.00 1.28
4061 4369 7.458397 AGAAGTACCATGACCAAAGTGAATTA 58.542 34.615 0.00 0.00 0.00 1.40
4090 4398 7.754069 TGACCGTATTTAGGTATTTACGTTG 57.246 36.000 0.00 0.00 43.01 4.10
4094 4402 8.985805 CCTTGATGACCGTATTTAGGTATTTAC 58.014 37.037 0.00 0.00 43.01 2.01
4184 4728 7.754924 GCTCTGATTATAGATGCTCTAAGACAC 59.245 40.741 0.00 0.00 31.96 3.67
4216 4760 3.451894 CAGACATTTGGGGCGGCC 61.452 66.667 22.00 22.00 0.00 6.13
4228 4772 2.611800 ATCCAGGCAGCCCAGACA 60.612 61.111 8.22 0.00 0.00 3.41
4274 4818 2.335011 GTCGTTTGGGCTGGTTGC 59.665 61.111 0.00 0.00 41.94 4.17
4330 5142 2.317530 GCTCCAGCTCGTCCTAATTT 57.682 50.000 0.00 0.00 38.21 1.82
4357 5169 4.758251 CACGACCGCTGGATGGCA 62.758 66.667 0.00 0.00 0.00 4.92
4381 5193 2.742372 CTCAAACTCCCGCCGGTG 60.742 66.667 8.42 8.42 0.00 4.94
4382 5194 2.726822 GAACTCAAACTCCCGCCGGT 62.727 60.000 1.90 0.00 0.00 5.28
4383 5195 2.032071 AACTCAAACTCCCGCCGG 59.968 61.111 0.00 0.00 0.00 6.13
4384 5196 2.033194 GGAACTCAAACTCCCGCCG 61.033 63.158 0.00 0.00 0.00 6.46
4385 5197 2.033194 CGGAACTCAAACTCCCGCC 61.033 63.158 0.00 0.00 33.47 6.13
4386 5198 3.562635 CGGAACTCAAACTCCCGC 58.437 61.111 0.00 0.00 33.47 6.13
4387 5199 2.033194 GGCGGAACTCAAACTCCCG 61.033 63.158 0.00 0.00 42.74 5.14
4388 5200 2.033194 CGGCGGAACTCAAACTCCC 61.033 63.158 0.00 0.00 0.00 4.30
4389 5201 2.677979 GCGGCGGAACTCAAACTCC 61.678 63.158 9.78 0.00 0.00 3.85
4390 5202 2.677979 GGCGGCGGAACTCAAACTC 61.678 63.158 9.78 0.00 0.00 3.01
4391 5203 2.668550 GGCGGCGGAACTCAAACT 60.669 61.111 9.78 0.00 0.00 2.66
4392 5204 2.966309 CTGGCGGCGGAACTCAAAC 61.966 63.158 13.52 0.00 0.00 2.93
4393 5205 2.668212 CTGGCGGCGGAACTCAAA 60.668 61.111 13.52 0.00 0.00 2.69
4405 5217 4.803426 GACACGGAGGAGCTGGCG 62.803 72.222 0.00 0.00 0.00 5.69
4406 5218 4.459089 GGACACGGAGGAGCTGGC 62.459 72.222 0.00 0.00 0.00 4.85
4407 5219 3.775654 GGGACACGGAGGAGCTGG 61.776 72.222 0.00 0.00 0.00 4.85
4408 5220 4.135153 CGGGACACGGAGGAGCTG 62.135 72.222 0.00 0.00 39.42 4.24
4459 5271 3.376935 AATCTGGAGCGGTGCCGAG 62.377 63.158 15.45 2.79 42.83 4.63
4494 5306 1.994463 CACCAGAGGGGAAGGGAAG 59.006 63.158 0.00 0.00 41.15 3.46
4495 5307 2.231380 GCACCAGAGGGGAAGGGAA 61.231 63.158 0.00 0.00 41.15 3.97
4530 5343 3.066814 GGCACGAGTACCCCGAGT 61.067 66.667 11.54 0.00 0.00 4.18
4531 5344 2.754658 AGGCACGAGTACCCCGAG 60.755 66.667 11.54 5.50 0.00 4.63
4532 5345 3.066190 CAGGCACGAGTACCCCGA 61.066 66.667 11.54 0.00 0.00 5.14
4534 5347 4.814294 CGCAGGCACGAGTACCCC 62.814 72.222 0.00 0.00 34.06 4.95
4573 5387 2.125512 CCTTGGCCTTCGACTCCG 60.126 66.667 3.32 0.00 37.07 4.63


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

AutoCloner maintained by Alex Coulton.