Multiple sequence alignment - TraesCS1B01G051500

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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 TraesCS1B01G051500 chr1B 100.000 2315 0 0 1 2315 31660985 31663299 0 4276
1 TraesCS1B01G051500 chr1B 92.719 1346 95 3 1 1345 41706535 41705192 0 1940
2 TraesCS1B01G051500 chr1B 94.650 972 49 3 1345 2315 336299057 336300026 0 1504
3 TraesCS1B01G051500 chr1B 94.547 972 49 4 1345 2315 51675749 51674781 0 1498
4 TraesCS1B01G051500 chr1B 94.342 972 53 2 1345 2315 650613434 650614404 0 1489
5 TraesCS1B01G051500 chr7B 96.731 1346 41 3 1 1345 722949211 722947868 0 2239
6 TraesCS1B01G051500 chr7B 94.456 974 49 5 1345 2315 188571858 188572829 0 1495
7 TraesCS1B01G051500 chr6B 94.056 1346 77 3 1 1345 564308497 564309840 0 2039
8 TraesCS1B01G051500 chr6B 92.725 1347 90 3 1 1346 12073172 12071833 0 1938
9 TraesCS1B01G051500 chr6B 94.758 973 47 4 1345 2315 594795091 594796061 0 1511
10 TraesCS1B01G051500 chr6B 94.347 973 50 5 1345 2315 166843871 166842902 0 1487
11 TraesCS1B01G051500 chr3B 93.328 1349 87 3 1 1347 571018235 571019582 0 1989
12 TraesCS1B01G051500 chr3B 89.325 1349 137 6 1 1346 808035094 808036438 0 1687
13 TraesCS1B01G051500 chr3B 95.576 972 40 3 1345 2315 747119175 747118206 0 1554
14 TraesCS1B01G051500 chr3B 95.062 972 45 3 1345 2315 623167931 623166962 0 1526
15 TraesCS1B01G051500 chr3B 94.342 972 51 4 1345 2315 565232406 565231438 0 1487
16 TraesCS1B01G051500 chr7A 92.051 1346 104 3 1 1345 29988489 29987146 0 1890
17 TraesCS1B01G051500 chr7D 86.637 1347 169 10 1 1343 139749775 139748436 0 1480
18 TraesCS1B01G051500 chr4D 86.509 1349 176 6 1 1346 482768186 482769531 0 1478


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 TraesCS1B01G051500 chr1B 31660985 31663299 2314 False 4276 4276 100.000 1 2315 1 chr1B.!!$F1 2314
1 TraesCS1B01G051500 chr1B 41705192 41706535 1343 True 1940 1940 92.719 1 1345 1 chr1B.!!$R1 1344
2 TraesCS1B01G051500 chr1B 336299057 336300026 969 False 1504 1504 94.650 1345 2315 1 chr1B.!!$F2 970
3 TraesCS1B01G051500 chr1B 51674781 51675749 968 True 1498 1498 94.547 1345 2315 1 chr1B.!!$R2 970
4 TraesCS1B01G051500 chr1B 650613434 650614404 970 False 1489 1489 94.342 1345 2315 1 chr1B.!!$F3 970
5 TraesCS1B01G051500 chr7B 722947868 722949211 1343 True 2239 2239 96.731 1 1345 1 chr7B.!!$R1 1344
6 TraesCS1B01G051500 chr7B 188571858 188572829 971 False 1495 1495 94.456 1345 2315 1 chr7B.!!$F1 970
7 TraesCS1B01G051500 chr6B 564308497 564309840 1343 False 2039 2039 94.056 1 1345 1 chr6B.!!$F1 1344
8 TraesCS1B01G051500 chr6B 12071833 12073172 1339 True 1938 1938 92.725 1 1346 1 chr6B.!!$R1 1345
9 TraesCS1B01G051500 chr6B 594795091 594796061 970 False 1511 1511 94.758 1345 2315 1 chr6B.!!$F2 970
10 TraesCS1B01G051500 chr6B 166842902 166843871 969 True 1487 1487 94.347 1345 2315 1 chr6B.!!$R2 970
11 TraesCS1B01G051500 chr3B 571018235 571019582 1347 False 1989 1989 93.328 1 1347 1 chr3B.!!$F1 1346
12 TraesCS1B01G051500 chr3B 808035094 808036438 1344 False 1687 1687 89.325 1 1346 1 chr3B.!!$F2 1345
13 TraesCS1B01G051500 chr3B 747118206 747119175 969 True 1554 1554 95.576 1345 2315 1 chr3B.!!$R3 970
14 TraesCS1B01G051500 chr3B 623166962 623167931 969 True 1526 1526 95.062 1345 2315 1 chr3B.!!$R2 970
15 TraesCS1B01G051500 chr3B 565231438 565232406 968 True 1487 1487 94.342 1345 2315 1 chr3B.!!$R1 970
16 TraesCS1B01G051500 chr7A 29987146 29988489 1343 True 1890 1890 92.051 1 1345 1 chr7A.!!$R1 1344
17 TraesCS1B01G051500 chr7D 139748436 139749775 1339 True 1480 1480 86.637 1 1343 1 chr7D.!!$R1 1342
18 TraesCS1B01G051500 chr4D 482768186 482769531 1345 False 1478 1478 86.509 1 1346 1 chr4D.!!$F1 1345

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
797 801 0.804989 GGCGATTCCAACAGTCCTTG 59.195 55.0 0.0 0.0 34.01 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2239 2251 0.552848 CCTATGGTGCCCTCCATGTT 59.447 55.0 11.13 0.0 46.27 2.71 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
55 56 2.410262 CGTCTCAATCGTGTTTCTGCAC 60.410 50.000 0.00 0.0 36.12 4.57
58 59 3.876914 TCTCAATCGTGTTTCTGCACTTT 59.123 39.130 0.00 0.0 37.24 2.66
174 177 5.021033 AGACAGCGATCTGATTTCATCTT 57.979 39.130 0.00 0.0 42.95 2.40
291 294 4.373116 GTCAGCGAGCGGTTCCCA 62.373 66.667 0.00 0.0 0.00 4.37
337 340 1.069204 GCATCAGTCCCGCAGAAGATA 59.931 52.381 0.00 0.0 0.00 1.98
368 371 3.307339 GGCATGGCAAGTTATTTTGGGAA 60.307 43.478 15.47 0.0 0.00 3.97
384 387 1.173913 GGAATTTTACCCACGCAGCT 58.826 50.000 0.00 0.0 0.00 4.24
511 514 1.585267 TTTGGTTGCAGATGCGCGAT 61.585 50.000 12.10 0.0 45.83 4.58
598 601 7.425577 TCTGTGTAGAGTTTCAAATGATGTG 57.574 36.000 0.00 0.0 0.00 3.21
727 730 9.151471 GACAGTTATTACAACTCAATCAAGCTA 57.849 33.333 0.00 0.0 0.00 3.32
735 738 2.568956 ACTCAATCAAGCTAGCTGGTCA 59.431 45.455 20.16 0.0 0.00 4.02
743 746 5.201243 TCAAGCTAGCTGGTCATTACTCTA 58.799 41.667 20.16 0.0 0.00 2.43
797 801 0.804989 GGCGATTCCAACAGTCCTTG 59.195 55.000 0.00 0.0 34.01 3.61
894 898 1.270518 CCAGCCATCGGATAACTCAGG 60.271 57.143 0.00 0.0 0.00 3.86
929 933 0.940126 GTTGCGCGATCATCAAGGAT 59.060 50.000 12.10 0.0 0.00 3.24
955 959 7.730084 AGATCATATTTGCAGCTTACAGAGTA 58.270 34.615 0.00 0.0 0.00 2.59
1081 1086 0.973632 TTCTGAAGCCTTGGCGAGTA 59.026 50.000 5.95 0.0 0.00 2.59
1337 1342 2.474410 AAACTCCCTTTACTCCGCAG 57.526 50.000 0.00 0.0 0.00 5.18
1423 1428 7.819900 AGTAAAAAGCTTCAGTAGTGTGATAGG 59.180 37.037 0.00 0.0 0.00 2.57
1460 1465 3.265737 TCAACCATTGGTGCAGTAGGTAT 59.734 43.478 9.62 0.0 35.34 2.73
1580 1586 3.055819 AGCACACACGAGAATATTCACCT 60.056 43.478 17.56 0.0 0.00 4.00
1584 1590 4.021456 ACACACGAGAATATTCACCTCACA 60.021 41.667 17.56 0.0 0.00 3.58
1652 1658 1.204146 AGTGTAGGGGATCGCAACAT 58.796 50.000 16.65 6.9 0.00 2.71
1766 1772 1.504359 CGCTTGACGTTCCCTTTACA 58.496 50.000 0.00 0.0 36.87 2.41
1767 1773 1.459592 CGCTTGACGTTCCCTTTACAG 59.540 52.381 0.00 0.0 36.87 2.74
1793 1800 9.871238 GAGAACAAGTATGAAATAGAAGTACCA 57.129 33.333 0.00 0.0 0.00 3.25
1819 1827 2.890945 GGTGTTGTTGGATAGGTTTGCT 59.109 45.455 0.00 0.0 0.00 3.91
2056 2066 1.137872 CGGAACTCTAGCAAGCATCCT 59.862 52.381 0.00 0.0 0.00 3.24
2066 2076 4.130286 AGCAAGCATCCTCAACTACTAC 57.870 45.455 0.00 0.0 0.00 2.73
2068 2078 4.020218 AGCAAGCATCCTCAACTACTACAA 60.020 41.667 0.00 0.0 0.00 2.41
2109 2119 7.297614 ACCCAACCATAGCATTAAAGTATCAT 58.702 34.615 0.00 0.0 0.00 2.45
2119 2130 6.897413 AGCATTAAAGTATCATGTCCCCTTTT 59.103 34.615 0.00 0.0 0.00 2.27
2131 2142 2.128535 TCCCCTTTTATCCCATACGCA 58.871 47.619 0.00 0.0 0.00 5.24
2170 2182 3.065371 GGGTTTGTGTTTCAGTCACTCAG 59.935 47.826 0.00 0.0 36.83 3.35
2179 2191 0.037303 CAGTCACTCAGGCAACCCAT 59.963 55.000 0.00 0.0 37.17 4.00
2235 2247 2.492025 AGTGGGAATCCCTCATGCTTA 58.508 47.619 20.55 0.0 45.70 3.09
2239 2251 4.707776 GGGAATCCCTCATGCTTACGCA 62.708 54.545 11.95 0.0 45.44 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.074967 AGCCTTTTGGGGTGATCGA 58.925 52.632 0.00 0.0 45.16 3.59
55 56 2.639065 TGCCCCGTTAGCATCTAAAAG 58.361 47.619 0.00 0.0 34.69 2.27
174 177 2.421388 CCACACTTCTCTGGAAACCACA 60.421 50.000 0.00 0.0 0.00 4.17
308 311 1.544093 CGGGACTGATGCTTGCCATAT 60.544 52.381 0.00 0.0 33.29 1.78
337 340 2.446435 ACTTGCCATGCCGTAATCTTT 58.554 42.857 0.00 0.0 0.00 2.52
368 371 0.881118 CACAGCTGCGTGGGTAAAAT 59.119 50.000 15.27 0.0 33.05 1.82
384 387 4.994907 ATATGACGTAGCACCTTACACA 57.005 40.909 0.00 0.0 0.00 3.72
486 489 2.159338 CGCATCTGCAACCAAATAGCTT 60.159 45.455 0.00 0.0 42.21 3.74
511 514 2.063979 CGGTGGGAGTGGCCATCTA 61.064 63.158 9.72 0.0 38.95 1.98
727 730 3.319405 CGTCCATAGAGTAATGACCAGCT 59.681 47.826 0.00 0.0 0.00 4.24
743 746 7.996098 TTTTTCCTTTTAGAATCTCGTCCAT 57.004 32.000 0.00 0.0 0.00 3.41
797 801 1.065126 AGGTGCATGGTCCTTTCTAGC 60.065 52.381 0.00 0.0 0.00 3.42
878 882 0.035458 GCCCCTGAGTTATCCGATGG 59.965 60.000 0.00 0.0 0.00 3.51
929 933 7.730084 ACTCTGTAAGCTGCAAATATGATCTA 58.270 34.615 1.02 0.0 0.00 1.98
955 959 1.535860 GCGTTGTTGCAGTGGAACAAT 60.536 47.619 35.53 0.0 43.34 2.71
1081 1086 5.478233 CGAGTTAGAGCATCGCTAGATAT 57.522 43.478 0.00 0.0 39.88 1.63
1580 1586 1.327690 GCCGGGGAGTCATAGTGTGA 61.328 60.000 2.18 0.0 0.00 3.58
1584 1590 1.905512 GTTGCCGGGGAGTCATAGT 59.094 57.895 2.18 0.0 0.00 2.12
1652 1658 7.115378 GGTTCGACACTCTTACTTATCGAAAAA 59.885 37.037 8.30 0.0 46.48 1.94
1767 1773 9.871238 TGGTACTTCTATTTCATACTTGTTCTC 57.129 33.333 0.00 0.0 0.00 2.87
1792 1799 4.843728 ACCTATCCAACAACACCTACATG 58.156 43.478 0.00 0.0 0.00 3.21
1793 1800 5.514500 AACCTATCCAACAACACCTACAT 57.486 39.130 0.00 0.0 0.00 2.29
2036 2046 1.137872 AGGATGCTTGCTAGAGTTCCG 59.862 52.381 0.00 0.0 0.00 4.30
2066 2076 7.934120 TGGTTGGGTTTTACCTTAATGAATTTG 59.066 33.333 0.00 0.0 38.64 2.32
2068 2078 7.619512 TGGTTGGGTTTTACCTTAATGAATT 57.380 32.000 0.00 0.0 38.64 2.17
2109 2119 2.158726 GCGTATGGGATAAAAGGGGACA 60.159 50.000 0.00 0.0 0.00 4.02
2119 2130 2.645802 GGGTTGTTTGCGTATGGGATA 58.354 47.619 0.00 0.0 0.00 2.59
2170 2182 3.568007 TGATTCGCTTATAATGGGTTGCC 59.432 43.478 0.00 0.0 0.00 4.52
2179 2191 6.583427 GCAATGCATTCATGATTCGCTTATAA 59.417 34.615 9.53 0.0 32.23 0.98
2235 2247 2.672996 GTGCCCTCCATGTTGCGT 60.673 61.111 0.00 0.0 0.00 5.24
2239 2251 0.552848 CCTATGGTGCCCTCCATGTT 59.447 55.000 11.13 0.0 46.27 2.71


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

AutoCloner maintained by Alex Coulton.