Multiple sequence alignment - TraesCS7B01G320300

Loading Multiple Alignment...

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 TraesCS7B01G320300 chr7B 100.000 6965 0 0 1 6965 570481154 570474190 0 12863
1 TraesCS7B01G320300 chr1B 98.637 6968 85 10 1 6965 419953947 419960907 0 12333
2 TraesCS7B01G320300 chr1B 98.407 6969 93 15 1 6965 65600596 65593642 0 12238
3 TraesCS7B01G320300 chr1B 98.251 6975 103 18 1 6965 167986969 167980004 0 12187
4 TraesCS7B01G320300 chr1A 98.622 6968 87 8 1 6965 521305226 521312187 0 12327
5 TraesCS7B01G320300 chr1A 98.166 6979 104 23 1 6965 531033311 531040279 0 12157
6 TraesCS7B01G320300 chr6A 98.180 6977 105 21 1 6962 90756943 90763912 0 12161
7 TraesCS7B01G320300 chr5B 98.177 6968 112 14 1 6965 158883263 158890218 0 12150
8 TraesCS7B01G320300 chr5B 98.036 6977 115 20 1 6965 474303102 474310068 0 12105


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 TraesCS7B01G320300 chr7B 570474190 570481154 6964 True 12863 12863 100.000 1 6965 1 chr7B.!!$R1 6964
1 TraesCS7B01G320300 chr1B 419953947 419960907 6960 False 12333 12333 98.637 1 6965 1 chr1B.!!$F1 6964
2 TraesCS7B01G320300 chr1B 65593642 65600596 6954 True 12238 12238 98.407 1 6965 1 chr1B.!!$R1 6964
3 TraesCS7B01G320300 chr1B 167980004 167986969 6965 True 12187 12187 98.251 1 6965 1 chr1B.!!$R2 6964
4 TraesCS7B01G320300 chr1A 521305226 521312187 6961 False 12327 12327 98.622 1 6965 1 chr1A.!!$F1 6964
5 TraesCS7B01G320300 chr1A 531033311 531040279 6968 False 12157 12157 98.166 1 6965 1 chr1A.!!$F2 6964
6 TraesCS7B01G320300 chr6A 90756943 90763912 6969 False 12161 12161 98.180 1 6962 1 chr6A.!!$F1 6961
7 TraesCS7B01G320300 chr5B 158883263 158890218 6955 False 12150 12150 98.177 1 6965 1 chr5B.!!$F1 6964
8 TraesCS7B01G320300 chr5B 474303102 474310068 6966 False 12105 12105 98.036 1 6965 1 chr5B.!!$F2 6964

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
36 37 0.842635 TTTGGGGTTGCAGCCATTTT 59.157 45.000 22.07 0.0 37.54 1.82 F
612 617 2.009774 GCCACATACACGCTCTTGAAT 58.990 47.619 0.00 0.0 0.00 2.57 F
1943 1954 0.687354 AGAAGGGTTGTCGTCTGCAT 59.313 50.000 0.00 0.0 0.00 3.96 F
2383 2396 5.407502 GCCTACTCACAAGTTTGTTGTTTT 58.592 37.500 0.00 0.0 39.91 2.43 F
4282 4309 0.322277 ACTCTGATGCAAGTGGCTGG 60.322 55.000 0.00 0.0 45.15 4.85 F
4827 4854 0.320771 GACCGGAGCACAACTGATGT 60.321 55.000 9.46 0.0 45.34 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1310 1320 0.449388 GCAGCTCCCTTTTGATCGTG 59.551 55.000 0.00 0.0 0.00 4.35 R
2383 2396 2.741985 CGCTGATGGTCCACGCAA 60.742 61.111 0.00 0.0 0.00 4.85 R
2760 2777 0.317770 CGCCTGTGCACGAAAACAAT 60.318 50.000 13.13 0.0 37.32 2.71 R
4299 4326 3.260632 TGTTGTTCTAGCCTGCACATCTA 59.739 43.478 0.00 0.0 0.00 1.98 R
5400 5427 1.896220 ATGTCGTCACATGGCAGTTT 58.104 45.000 0.00 0.0 42.05 2.66 R
6738 6776 0.878523 GTCAGTGTGCACGGCAACTA 60.879 55.000 13.13 0.0 41.47 2.24 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
36 37 0.842635 TTTGGGGTTGCAGCCATTTT 59.157 45.000 22.07 0.00 37.54 1.82
140 142 2.143122 GCAGACTGTGACGAAATTGGA 58.857 47.619 3.99 0.00 0.00 3.53
612 617 2.009774 GCCACATACACGCTCTTGAAT 58.990 47.619 0.00 0.00 0.00 2.57
1007 1015 2.158856 CCTACATCAGCAGAATGGCTCA 60.159 50.000 0.00 0.00 43.68 4.26
1154 1162 5.500234 TGTTATTTGTTGGCAGCTAGATCT 58.500 37.500 0.00 0.00 0.00 2.75
1310 1320 4.911610 CCGTGTTGATTGACAAATTCACTC 59.088 41.667 0.00 0.00 40.36 3.51
1492 1502 3.071479 GGAATCCGTGTTCTGCACTTTA 58.929 45.455 0.00 0.00 45.57 1.85
1526 1536 4.395959 GGACATATCAAAGTCCCGTACA 57.604 45.455 0.00 0.00 46.79 2.90
1776 1787 1.602377 ACTGCTAGTGTTTTCGTTGCC 59.398 47.619 0.00 0.00 0.00 4.52
1943 1954 0.687354 AGAAGGGTTGTCGTCTGCAT 59.313 50.000 0.00 0.00 0.00 3.96
2135 2147 5.940617 ACCTTCATATTAGCATGGCAACTA 58.059 37.500 0.00 0.00 37.61 2.24
2223 2235 6.291648 TGGATCATACATTATCCTGCTCTC 57.708 41.667 0.00 0.00 41.94 3.20
2383 2396 5.407502 GCCTACTCACAAGTTTGTTGTTTT 58.592 37.500 0.00 0.00 39.91 2.43
2760 2777 4.688021 GGGTGTTGTTTTGTTGATGCTTA 58.312 39.130 0.00 0.00 0.00 3.09
3398 3416 0.396435 TCCTTCCATCTGTTGCGTGT 59.604 50.000 0.00 0.00 0.00 4.49
4000 4024 2.126882 CTCATGACCCCCTTACATGGA 58.873 52.381 0.00 0.00 40.86 3.41
4031 4056 6.255670 CCAGCTTTTTCCACTTGTTTTTAGTC 59.744 38.462 0.00 0.00 0.00 2.59
4282 4309 0.322277 ACTCTGATGCAAGTGGCTGG 60.322 55.000 0.00 0.00 45.15 4.85
4390 4417 6.317140 CAGCTGAAATATTGCCAACTCTTCTA 59.683 38.462 8.42 0.00 0.00 2.10
4803 4830 6.647895 GCAAAAATCAATGTGATGGAGAAACT 59.352 34.615 0.00 0.00 37.15 2.66
4827 4854 0.320771 GACCGGAGCACAACTGATGT 60.321 55.000 9.46 0.00 45.34 3.06
4871 4898 3.068691 CAGAGGAACGCCCGGAGA 61.069 66.667 0.73 0.00 40.87 3.71
4924 4951 2.353889 CAGCATAAATCTGCGCACTTCT 59.646 45.455 5.66 0.00 46.86 2.85
4989 5016 1.470098 GATTGTCATGAAAGCTGCGGT 59.530 47.619 0.00 0.00 0.00 5.68
5400 5427 1.469335 GGGTCCTCACTTGTGACGGA 61.469 60.000 13.81 13.81 0.00 4.69
5554 5581 3.765511 AGTTGCTGTCACATGGCAAATAT 59.234 39.130 6.05 0.00 45.49 1.28
5952 5984 4.322080 AGTTTATCGCATGATCGAGGAA 57.678 40.909 0.00 0.00 42.14 3.36
5953 5985 4.302455 AGTTTATCGCATGATCGAGGAAG 58.698 43.478 0.00 0.00 42.14 3.46
5962 5994 1.065926 TGATCGAGGAAGCAGCATTGT 60.066 47.619 0.00 0.00 0.00 2.71
6533 6570 3.378911 TGCGCCGACAAGATAATCATA 57.621 42.857 4.18 0.00 0.00 2.15
6738 6776 3.555586 GGCAGAAGTTTTCATGTGGCAAT 60.556 43.478 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.804544 CCCTTACAATTCTCGCGCGA 60.805 55.000 32.60 32.60 0.00 5.87
140 142 8.914654 CACATTTGTTCACGTTCAATCATATTT 58.085 29.630 0.00 0.00 0.00 1.40
420 425 0.322906 TTGCCACACACCTGTTCACA 60.323 50.000 0.00 0.00 0.00 3.58
1214 1224 7.546778 AAAAACAAACACAAAAGTGTTGAGT 57.453 28.000 13.96 12.58 45.64 3.41
1310 1320 0.449388 GCAGCTCCCTTTTGATCGTG 59.551 55.000 0.00 0.00 0.00 4.35
1526 1536 8.251383 TCTTCCTCGATCTCATTATTAACCTT 57.749 34.615 0.00 0.00 0.00 3.50
1776 1787 5.621228 CGTCAGAAATCAAAACGGAAGAAAG 59.379 40.000 0.00 0.00 0.00 2.62
2135 2147 5.394663 GCAGTTGTCATCCTACTGTGATAGT 60.395 44.000 0.00 0.00 40.99 2.12
2383 2396 2.741985 CGCTGATGGTCCACGCAA 60.742 61.111 0.00 0.00 0.00 4.85
2488 2501 4.597404 TGTCAAATTTGTAAGCATGCCA 57.403 36.364 15.66 1.92 0.00 4.92
2760 2777 0.317770 CGCCTGTGCACGAAAACAAT 60.318 50.000 13.13 0.00 37.32 2.71
3034 3051 1.748493 TCATCGTCATCGGTGTCATCA 59.252 47.619 0.00 0.00 46.73 3.07
3705 3725 9.108284 GAAGGAAGAAATCATTTGGAAAAACAA 57.892 29.630 0.00 0.00 30.89 2.83
4000 4024 4.709886 ACAAGTGGAAAAAGCTGGTAGTTT 59.290 37.500 0.00 0.00 0.00 2.66
4031 4056 9.142515 TGTTTGCAATGATAGAAGCATTAAAAG 57.857 29.630 0.00 0.00 36.80 2.27
4299 4326 3.260632 TGTTGTTCTAGCCTGCACATCTA 59.739 43.478 0.00 0.00 0.00 1.98
4803 4830 1.891919 GTTGTGCTCCGGTCTTGCA 60.892 57.895 0.00 5.70 0.00 4.08
4827 4854 2.925706 TGCCCGGCTTGACACCTA 60.926 61.111 11.61 0.00 0.00 3.08
4924 4951 0.824109 CGACATTGACTGGGAGCCTA 59.176 55.000 0.00 0.00 0.00 3.93
4989 5016 0.874175 CGTGTTGTCAGCGGTCTCAA 60.874 55.000 0.00 0.00 0.00 3.02
5400 5427 1.896220 ATGTCGTCACATGGCAGTTT 58.104 45.000 0.00 0.00 42.05 2.66
5554 5581 4.314961 CAGTTGCCATGTGTACTGAACTA 58.685 43.478 10.99 0.00 40.24 2.24
5952 5984 2.093235 GGAACTCCTCTACAATGCTGCT 60.093 50.000 0.00 0.00 0.00 4.24
5953 5985 2.093235 AGGAACTCCTCTACAATGCTGC 60.093 50.000 0.00 0.00 44.77 5.25
6094 6126 2.232941 TGAATTCGGGCTCGTAGTCTTT 59.767 45.455 14.04 0.00 33.24 2.52
6533 6570 2.928801 TGCAGGTCACACTGTAATGT 57.071 45.000 0.00 0.00 40.59 2.71
6738 6776 0.878523 GTCAGTGTGCACGGCAACTA 60.879 55.000 13.13 0.00 41.47 2.24


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

AutoCloner maintained by Alex Coulton.