Multiple sequence alignment - TraesCS6D01G224100

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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 TraesCS6D01G224100 chr6D 100.000 5283 0 0 1 5283 316100881 316095599 0.000000e+00 9756
1 TraesCS6D01G224100 chr6B 94.033 5346 209 52 1 5280 508607919 508613220 0.000000e+00 8004
2 TraesCS6D01G224100 chr6A 93.575 4809 165 59 1 4715 453908165 453903407 0.000000e+00 7036
3 TraesCS6D01G224100 chr6A 89.958 478 33 8 4705 5171 453902756 453902283 2.100000e-168 603
4 TraesCS6D01G224100 chr6A 79.412 340 51 11 1837 2161 410325059 410324724 6.890000e-54 222
5 TraesCS6D01G224100 chr2B 94.386 1336 57 6 1440 2765 199221956 199220629 0.000000e+00 2036
6 TraesCS6D01G224100 chr1B 93.848 1333 56 9 1440 2763 342128108 342126793 0.000000e+00 1984
7 TraesCS6D01G224100 chr5B 92.670 1337 75 7 1440 2765 356196768 356198092 0.000000e+00 1905
8 TraesCS6D01G224100 chr3A 80.415 337 49 9 1837 2161 23263237 23263568 1.900000e-59 241
9 TraesCS6D01G224100 chr5A 80.236 339 48 11 1837 2161 6661547 6661880 2.460000e-58 237
10 TraesCS6D01G224100 chr7A 79.762 336 53 9 1837 2161 121908266 121908597 4.120000e-56 230


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 TraesCS6D01G224100 chr6D 316095599 316100881 5282 True 9756.0 9756 100.0000 1 5283 1 chr6D.!!$R1 5282
1 TraesCS6D01G224100 chr6B 508607919 508613220 5301 False 8004.0 8004 94.0330 1 5280 1 chr6B.!!$F1 5279
2 TraesCS6D01G224100 chr6A 453902283 453908165 5882 True 3819.5 7036 91.7665 1 5171 2 chr6A.!!$R2 5170
3 TraesCS6D01G224100 chr2B 199220629 199221956 1327 True 2036.0 2036 94.3860 1440 2765 1 chr2B.!!$R1 1325
4 TraesCS6D01G224100 chr1B 342126793 342128108 1315 True 1984.0 1984 93.8480 1440 2763 1 chr1B.!!$R1 1323
5 TraesCS6D01G224100 chr5B 356196768 356198092 1324 False 1905.0 1905 92.6700 1440 2765 1 chr5B.!!$F1 1325

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
46 47 0.178964 CTGCCCCTGGAAAGTGGAAA 60.179 55.000 0.00 0.0 0.00 3.13 F
1430 1490 1.173043 GTGCCATTTCCATTCCACGA 58.827 50.000 0.00 0.0 0.00 4.35 F
1438 1498 1.153369 CCATTCCACGACGCAGGAT 60.153 57.895 10.06 0.0 33.10 3.24 F
2062 2133 1.377725 CTTCAAGCAGGGCGGTGAT 60.378 57.895 0.00 0.0 30.31 3.06 F
2359 2432 1.465794 AGCCTCTACCGAACTCTGTC 58.534 55.000 0.00 0.0 0.00 3.51 F
2447 2530 2.870411 AGTACGTTTTTGCACTGAGGTC 59.130 45.455 0.00 0.0 0.00 3.85 F
4158 4250 1.336795 GCTTGCAATGTTTAGCCCGTT 60.337 47.619 0.00 0.0 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 1498 0.250295 CAGCGGAAAACCAGAGTCCA 60.250 55.000 0.00 0.00 0.00 4.02 R
2608 2691 1.984297 GTACCTTTTCTCACGCTCGAC 59.016 52.381 0.00 0.00 0.00 4.20 R
2916 3004 5.511363 TGAGTAAAAAGGACCAAAGGTTCA 58.489 37.500 0.00 0.00 35.25 3.18 R
3847 3939 3.508793 CCTCAGCATGTCCTGAAATGTTT 59.491 43.478 4.82 0.00 41.02 2.83 R
4158 4250 4.647424 ACAAATGGAAGACGAAGCAAAA 57.353 36.364 0.00 0.00 0.00 2.44 R
4220 4314 7.230108 ACATTTGTCTTCCTGATATATGCCAAG 59.770 37.037 0.00 0.00 31.86 3.61 R
5040 5831 0.522626 CATGATGCGCAACTTGGTCA 59.477 50.000 17.11 13.54 0.00 4.02 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
40 41 1.895238 CATTGCTGCCCCTGGAAAG 59.105 57.895 0.00 0.00 0.00 2.62
41 42 0.901580 CATTGCTGCCCCTGGAAAGT 60.902 55.000 0.00 0.00 0.00 2.66
42 43 0.901580 ATTGCTGCCCCTGGAAAGTG 60.902 55.000 0.00 0.00 0.00 3.16
43 44 2.677875 GCTGCCCCTGGAAAGTGG 60.678 66.667 0.00 0.00 0.00 4.00
44 45 3.170362 CTGCCCCTGGAAAGTGGA 58.830 61.111 0.00 0.00 0.00 4.02
45 46 1.460255 CTGCCCCTGGAAAGTGGAA 59.540 57.895 0.00 0.00 0.00 3.53
46 47 0.178964 CTGCCCCTGGAAAGTGGAAA 60.179 55.000 0.00 0.00 0.00 3.13
64 65 3.562505 GAAACTCACATTGCTTGCTCAG 58.437 45.455 0.00 0.00 0.00 3.35
82 83 4.616835 GCTCAGCCCAGAAACACAATAAAG 60.617 45.833 0.00 0.00 0.00 1.85
96 97 6.795399 ACACAATAAAGGTTTCACTCAGTTG 58.205 36.000 0.00 0.00 0.00 3.16
130 137 1.565759 ACATGGAAGCTTCAGGCCATA 59.434 47.619 27.02 5.30 39.01 2.74
136 143 2.478872 AGCTTCAGGCCATACTAGGA 57.521 50.000 5.01 0.00 43.05 2.94
426 469 9.075519 CAACAAATACTGCAATTATTCGTTGAT 57.924 29.630 18.45 2.37 32.62 2.57
573 617 2.151049 CTCAGTGGGCAAAGGCAAGC 62.151 60.000 0.00 0.00 43.71 4.01
815 870 9.447157 CATAAAATCACCAACCACCAATAAAAT 57.553 29.630 0.00 0.00 0.00 1.82
1119 1177 3.264450 CAGAAACCACCTCCTCCTATGTT 59.736 47.826 0.00 0.00 0.00 2.71
1120 1178 3.916989 AGAAACCACCTCCTCCTATGTTT 59.083 43.478 0.00 0.00 0.00 2.83
1140 1198 5.814705 TGTTTTCTTCCAATGCAAACGATTT 59.185 32.000 0.00 0.00 31.24 2.17
1430 1490 1.173043 GTGCCATTTCCATTCCACGA 58.827 50.000 0.00 0.00 0.00 4.35
1438 1498 1.153369 CCATTCCACGACGCAGGAT 60.153 57.895 10.06 0.00 33.10 3.24
1515 1575 6.986231 GGTTCAGGTTTGATCAGAATTTGTTT 59.014 34.615 0.00 0.00 32.27 2.83
1960 2031 3.135530 ACAAGGAGGCTGATAAGGTGATC 59.864 47.826 0.00 0.00 0.00 2.92
2059 2130 3.909086 GAGCTTCAAGCAGGGCGGT 62.909 63.158 13.10 0.00 45.56 5.68
2062 2133 1.377725 CTTCAAGCAGGGCGGTGAT 60.378 57.895 0.00 0.00 30.31 3.06
2233 2304 2.205074 CGCGCTCTATCCAAACAGAAT 58.795 47.619 5.56 0.00 0.00 2.40
2359 2432 1.465794 AGCCTCTACCGAACTCTGTC 58.534 55.000 0.00 0.00 0.00 3.51
2447 2530 2.870411 AGTACGTTTTTGCACTGAGGTC 59.130 45.455 0.00 0.00 0.00 3.85
2583 2666 5.613329 ACAATGTTCAAGCACCATCAAATT 58.387 33.333 0.00 0.00 0.00 1.82
2608 2691 4.854399 TGTTGAAATCAGCGTAAAGTTGG 58.146 39.130 0.00 0.00 0.00 3.77
2683 2766 4.883354 GGGATGCCCAGAAGCCCG 62.883 72.222 0.00 0.00 44.65 6.13
3273 3361 6.566079 AGAATATGTTGGTCCTTGATGAGA 57.434 37.500 0.00 0.00 0.00 3.27
3753 3842 5.751243 AAATGTAGATTGGCGGTTGATAC 57.249 39.130 0.00 0.00 0.00 2.24
4158 4250 1.336795 GCTTGCAATGTTTAGCCCGTT 60.337 47.619 0.00 0.00 0.00 4.44
4390 4502 6.843208 TGATAGAAACACGTGTTCAAAAACA 58.157 32.000 32.36 23.01 43.06 2.83
4518 4635 7.299134 TGAATTGGGGGAGTAACTTTAAGAAA 58.701 34.615 0.00 0.00 0.00 2.52
4528 4645 9.244799 GGAGTAACTTTAAGAAAACATGTTTGG 57.755 33.333 23.93 10.68 32.36 3.28
4542 4659 8.831715 AAACATGTTTGGAAATCTAATGAACC 57.168 30.769 22.71 0.00 0.00 3.62
4722 5510 8.718102 TTGAAGAATTAGGTGTTCACTATAGC 57.282 34.615 0.00 0.00 0.00 2.97
4897 5688 5.276461 TGCTCATGACGGTATTAGATTGT 57.724 39.130 0.00 0.00 0.00 2.71
4908 5699 4.280174 GGTATTAGATTGTAGTCGGCTCCA 59.720 45.833 0.00 0.00 0.00 3.86
4934 5725 4.705110 AATAAGGGCTTGCAAAAAGGTT 57.295 36.364 0.00 0.00 0.00 3.50
4935 5726 2.620251 AAGGGCTTGCAAAAAGGTTC 57.380 45.000 0.00 0.00 0.00 3.62
5003 5794 7.495606 TCTTGCCTTTTCTTCTTTCAAATTTCC 59.504 33.333 0.00 0.00 0.00 3.13
5052 5843 9.515020 AATAATTTGTATATTGACCAAGTTGCG 57.485 29.630 0.00 0.00 0.00 4.85
5116 5917 6.723298 AGATCTTTACAGAGGAGTACATGG 57.277 41.667 0.00 0.00 30.36 3.66
5136 5937 7.110155 ACATGGTTGTCGTCCTAGAAATAAAT 58.890 34.615 0.00 0.00 0.00 1.40
5209 6013 1.789523 TGCCCCCATACTGAGTACTC 58.210 55.000 16.32 16.32 0.00 2.59
5228 6032 0.546747 CCCTGGTACTCCCAAGTCCA 60.547 60.000 0.00 0.00 44.65 4.02
5249 6053 6.098409 GTCCAGAAACATCTCCCTATAAGTCA 59.902 42.308 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.144913 TGAGTTTCCACTTTCCAGGGG 59.855 52.381 0.00 0.00 46.73 4.79
40 41 2.035066 AGCAAGCAATGTGAGTTTCCAC 59.965 45.455 0.00 0.00 37.55 4.02
41 42 2.294233 GAGCAAGCAATGTGAGTTTCCA 59.706 45.455 0.00 0.00 0.00 3.53
42 43 2.294233 TGAGCAAGCAATGTGAGTTTCC 59.706 45.455 0.00 0.00 0.00 3.13
43 44 3.562505 CTGAGCAAGCAATGTGAGTTTC 58.437 45.455 0.00 0.00 0.00 2.78
44 45 3.637998 CTGAGCAAGCAATGTGAGTTT 57.362 42.857 0.00 0.00 0.00 2.66
64 65 4.600692 AACCTTTATTGTGTTTCTGGGC 57.399 40.909 0.00 0.00 0.00 5.36
65 66 5.983118 GTGAAACCTTTATTGTGTTTCTGGG 59.017 40.000 13.50 0.00 45.02 4.45
82 83 3.319122 AGATTTGCCAACTGAGTGAAACC 59.681 43.478 0.00 0.00 37.80 3.27
96 97 4.498682 GCTTCCATGTCATACAGATTTGCC 60.499 45.833 0.00 0.00 0.00 4.52
260 303 5.965922 ACCCAGTTATTGCTTGCTTTAATC 58.034 37.500 0.00 0.00 0.00 1.75
426 469 2.633967 TGCCCTTTCGTTGGTACTCTTA 59.366 45.455 0.00 0.00 0.00 2.10
528 572 7.690952 AAACGTAAAAGGCCATAGTGATTAA 57.309 32.000 5.01 0.00 0.00 1.40
573 617 1.730501 AGTGAGATCATGTTGCCACG 58.269 50.000 0.00 0.00 0.00 4.94
595 639 4.389077 CCAGAAAAATTCGAGCGTAAGAGT 59.611 41.667 0.00 0.00 34.78 3.24
815 870 8.928448 ACAGCACTCTTCCTTTATCTAATCATA 58.072 33.333 0.00 0.00 0.00 2.15
1119 1177 5.627367 CGTAAATCGTTTGCATTGGAAGAAA 59.373 36.000 0.00 0.00 34.52 2.52
1120 1178 5.049336 TCGTAAATCGTTTGCATTGGAAGAA 60.049 36.000 0.00 0.00 40.80 2.52
1306 1366 5.516339 CACAAGAATTCAGTTCAACCAACAC 59.484 40.000 8.44 0.00 39.39 3.32
1307 1367 5.649557 CACAAGAATTCAGTTCAACCAACA 58.350 37.500 8.44 0.00 39.39 3.33
1430 1490 1.194781 AACCAGAGTCCATCCTGCGT 61.195 55.000 0.00 0.00 0.00 5.24
1438 1498 0.250295 CAGCGGAAAACCAGAGTCCA 60.250 55.000 0.00 0.00 0.00 4.02
1468 1528 3.763902 TCGATCTTCTTCAAGAGCTTCG 58.236 45.455 8.05 8.05 42.05 3.79
1515 1575 4.624015 ACGTCGTCTTGACCTGAAAAATA 58.376 39.130 0.00 0.00 45.23 1.40
1624 1693 8.588472 TGAAGAATCCTGGAGTATGTATGTATG 58.412 37.037 1.52 0.00 0.00 2.39
1928 1999 2.050144 AGCCTCCTTGTTGAACTGAGA 58.950 47.619 10.25 0.00 0.00 3.27
1960 2031 2.704572 ACCTTGAGCTTCATTTCCTCG 58.295 47.619 0.00 0.00 0.00 4.63
2233 2304 8.353684 TCAGGTTTCTAAATAAACATGCGAAAA 58.646 29.630 8.73 0.00 45.79 2.29
2416 2497 5.457473 GTGCAAAAACGTACTGCAAAGTATT 59.543 36.000 17.54 0.00 46.91 1.89
2417 2498 4.973663 GTGCAAAAACGTACTGCAAAGTAT 59.026 37.500 17.54 0.00 46.91 2.12
2418 2499 4.095185 AGTGCAAAAACGTACTGCAAAGTA 59.905 37.500 17.54 0.00 46.91 2.24
2419 2500 3.119637 AGTGCAAAAACGTACTGCAAAGT 60.120 39.130 17.54 6.19 46.91 2.66
2420 2501 3.240401 CAGTGCAAAAACGTACTGCAAAG 59.760 43.478 17.54 11.01 46.91 2.77
2421 2502 3.119814 TCAGTGCAAAAACGTACTGCAAA 60.120 39.130 17.54 6.90 46.91 3.68
2422 2503 2.420372 TCAGTGCAAAAACGTACTGCAA 59.580 40.909 17.54 3.70 46.91 4.08
2423 2504 2.010497 TCAGTGCAAAAACGTACTGCA 58.990 42.857 13.34 13.34 45.83 4.41
2447 2530 6.589830 AGTATTTGCAAGACTATAGCAACG 57.410 37.500 12.92 0.00 46.69 4.10
2533 2616 8.645110 CCTATTTCCCATATTTGCTCTTTTCAT 58.355 33.333 0.00 0.00 0.00 2.57
2583 2666 7.081349 CCAACTTTACGCTGATTTCAACAATA 58.919 34.615 0.00 0.00 0.00 1.90
2608 2691 1.984297 GTACCTTTTCTCACGCTCGAC 59.016 52.381 0.00 0.00 0.00 4.20
2916 3004 5.511363 TGAGTAAAAAGGACCAAAGGTTCA 58.489 37.500 0.00 0.00 35.25 3.18
2925 3013 8.080417 GGAACAATTTACTGAGTAAAAAGGACC 58.920 37.037 20.27 16.25 40.62 4.46
3590 3678 5.657499 CAGAAAAAGAACGAACAGTAGACG 58.343 41.667 0.00 0.00 0.00 4.18
3753 3842 7.163001 AGTTAACCTAGGTTTAGTACTTCGG 57.837 40.000 31.47 0.00 39.31 4.30
3846 3938 4.021719 CCTCAGCATGTCCTGAAATGTTTT 60.022 41.667 4.82 0.00 41.02 2.43
3847 3939 3.508793 CCTCAGCATGTCCTGAAATGTTT 59.491 43.478 4.82 0.00 41.02 2.83
4158 4250 4.647424 ACAAATGGAAGACGAAGCAAAA 57.353 36.364 0.00 0.00 0.00 2.44
4220 4314 7.230108 ACATTTGTCTTCCTGATATATGCCAAG 59.770 37.037 0.00 0.00 31.86 3.61
4481 4593 3.395607 CCCCCAATTCAGAGATATGTGGA 59.604 47.826 0.00 0.00 0.00 4.02
4518 4635 7.961351 TGGTTCATTAGATTTCCAAACATGTT 58.039 30.769 4.92 4.92 0.00 2.71
4528 4645 4.494855 GCGTCAGCTGGTTCATTAGATTTC 60.495 45.833 15.13 0.00 41.01 2.17
4542 4659 1.028330 AATGGTCCATGCGTCAGCTG 61.028 55.000 7.63 7.63 45.42 4.24
4632 4749 9.862585 CTTTAGTTGCATATTTTTGTGTTTTCC 57.137 29.630 0.00 0.00 0.00 3.13
4672 4799 6.804677 AGTAATTTGTGCATTGTTCTTGTGA 58.195 32.000 0.00 0.00 0.00 3.58
4897 5688 4.100498 CCCTTATTTTAGTGGAGCCGACTA 59.900 45.833 0.00 0.00 0.00 2.59
4908 5699 6.183361 ACCTTTTTGCAAGCCCTTATTTTAGT 60.183 34.615 0.00 0.00 0.00 2.24
4934 5725 0.458543 GCTCGAGAAGTGCAATCGGA 60.459 55.000 18.75 5.24 39.04 4.55
4935 5726 0.459237 AGCTCGAGAAGTGCAATCGG 60.459 55.000 18.75 4.80 41.47 4.18
5040 5831 0.522626 CATGATGCGCAACTTGGTCA 59.477 50.000 17.11 13.54 0.00 4.02
5052 5843 3.517602 ACACATGCATGTTTCATGATGC 58.482 40.909 29.48 11.31 42.84 3.91
5100 5891 3.442625 CGACAACCATGTACTCCTCTGTA 59.557 47.826 0.00 0.00 40.74 2.74
5101 5892 2.231478 CGACAACCATGTACTCCTCTGT 59.769 50.000 0.00 0.00 40.74 3.41
5102 5893 2.231478 ACGACAACCATGTACTCCTCTG 59.769 50.000 0.00 0.00 40.74 3.35
5103 5894 2.492484 GACGACAACCATGTACTCCTCT 59.508 50.000 0.00 0.00 40.74 3.69
5104 5895 2.416972 GGACGACAACCATGTACTCCTC 60.417 54.545 0.00 0.00 40.74 3.71
5136 5937 7.732222 AAAGGTTATCTGCCATCCATTTTTA 57.268 32.000 0.00 0.00 0.00 1.52
5188 5992 2.300437 GAGTACTCAGTATGGGGGCATC 59.700 54.545 18.20 0.00 44.94 3.91
5228 6032 7.921041 TCATGACTTATAGGGAGATGTTTCT 57.079 36.000 0.00 0.00 33.88 2.52


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

AutoCloner maintained by Alex Coulton.