Multiple sequence alignment - TraesCS6D01G075600

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 TraesCS6D01G075600 chr6D 100.000 2267 0 0 484 2750 39065789 39063523 0.000000e+00 4187
1 TraesCS6D01G075600 chr6D 100.000 162 0 0 1 162 39066272 39066111 1.600000e-77 300
2 TraesCS6D01G075600 chr4B 96.801 1688 48 4 484 2167 167378538 167376853 0.000000e+00 2813
3 TraesCS6D01G075600 chr4B 95.414 1330 54 5 522 1847 273959158 273960484 0.000000e+00 2111
4 TraesCS6D01G075600 chr4B 98.126 587 11 0 2164 2750 167376573 167375987 0.000000e+00 1024
5 TraesCS6D01G075600 chr6A 96.836 1675 43 7 502 2168 603905442 603907114 0.000000e+00 2791
6 TraesCS6D01G075600 chr6A 98.126 587 11 0 2164 2750 603907882 603908468 0.000000e+00 1024
7 TraesCS6D01G075600 chr3A 96.531 1643 38 6 532 2168 144697447 144699076 0.000000e+00 2700
8 TraesCS6D01G075600 chr3A 98.978 587 6 0 2164 2750 144699844 144700430 0.000000e+00 1051
9 TraesCS6D01G075600 chr3A 88.235 119 2 6 1 117 144696842 144696950 6.180000e-27 132
10 TraesCS6D01G075600 chr3A 100.000 69 0 0 1 69 126037689 126037757 7.990000e-26 128
11 TraesCS6D01G075600 chr7B 96.002 1651 59 5 522 2168 660101521 660103168 0.000000e+00 2676
12 TraesCS6D01G075600 chr7B 97.956 587 12 0 2164 2750 660103937 660104523 0.000000e+00 1018
13 TraesCS6D01G075600 chr1A 96.809 1598 31 6 578 2168 564160204 564158620 0.000000e+00 2651
14 TraesCS6D01G075600 chr1A 91.525 118 2 6 1 117 564160917 564160807 3.670000e-34 156
15 TraesCS6D01G075600 chr2B 96.229 1591 54 4 484 2070 311925697 311924109 0.000000e+00 2601
16 TraesCS6D01G075600 chr2B 97.956 587 12 0 2164 2750 311908511 311907925 0.000000e+00 1018
17 TraesCS6D01G075600 chr3B 95.273 1650 52 6 522 2168 228014553 228016179 0.000000e+00 2591
18 TraesCS6D01G075600 chr3B 98.126 587 10 1 2164 2750 228016948 228017533 0.000000e+00 1022
19 TraesCS6D01G075600 chr4A 95.733 1500 33 6 484 1977 147536216 147534742 0.000000e+00 2386
20 TraesCS6D01G075600 chr4A 98.288 584 10 0 2167 2750 147533807 147533224 0.000000e+00 1024
21 TraesCS6D01G075600 chr6B 96.623 1214 33 5 962 2168 18463701 18462489 0.000000e+00 2008
22 TraesCS6D01G075600 chr6B 96.293 1214 37 6 962 2168 18465676 18466888 0.000000e+00 1986
23 TraesCS6D01G075600 chr6B 97.785 587 13 0 2164 2750 18461720 18461134 0.000000e+00 1013
24 TraesCS6D01G075600 chr6B 95.150 433 21 0 484 916 18464103 18463671 0.000000e+00 684
25 TraesCS6D01G075600 chr7A 98.637 587 8 0 2164 2750 542716729 542717315 0.000000e+00 1040
26 TraesCS6D01G075600 chr7A 88.983 118 2 6 1 117 542713631 542713738 4.780000e-28 135
27 TraesCS6D01G075600 chr2D 93.827 162 3 1 1 162 618325345 618325191 1.270000e-58 237


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 TraesCS6D01G075600 chr6D 39063523 39066272 2749 True 2243.500000 4187 100.000000 1 2750 2 chr6D.!!$R1 2749
1 TraesCS6D01G075600 chr4B 273959158 273960484 1326 False 2111.000000 2111 95.414000 522 1847 1 chr4B.!!$F1 1325
2 TraesCS6D01G075600 chr4B 167375987 167378538 2551 True 1918.500000 2813 97.463500 484 2750 2 chr4B.!!$R1 2266
3 TraesCS6D01G075600 chr6A 603905442 603908468 3026 False 1907.500000 2791 97.481000 502 2750 2 chr6A.!!$F1 2248
4 TraesCS6D01G075600 chr3A 144696842 144700430 3588 False 1294.333333 2700 94.581333 1 2750 3 chr3A.!!$F2 2749
5 TraesCS6D01G075600 chr7B 660101521 660104523 3002 False 1847.000000 2676 96.979000 522 2750 2 chr7B.!!$F1 2228
6 TraesCS6D01G075600 chr1A 564158620 564160917 2297 True 1403.500000 2651 94.167000 1 2168 2 chr1A.!!$R1 2167
7 TraesCS6D01G075600 chr2B 311924109 311925697 1588 True 2601.000000 2601 96.229000 484 2070 1 chr2B.!!$R2 1586
8 TraesCS6D01G075600 chr2B 311907925 311908511 586 True 1018.000000 1018 97.956000 2164 2750 1 chr2B.!!$R1 586
9 TraesCS6D01G075600 chr3B 228014553 228017533 2980 False 1806.500000 2591 96.699500 522 2750 2 chr3B.!!$F1 2228
10 TraesCS6D01G075600 chr4A 147533224 147536216 2992 True 1705.000000 2386 97.010500 484 2750 2 chr4A.!!$R1 2266
11 TraesCS6D01G075600 chr6B 18465676 18466888 1212 False 1986.000000 1986 96.293000 962 2168 1 chr6B.!!$F1 1206
12 TraesCS6D01G075600 chr6B 18461134 18464103 2969 True 1235.000000 2008 96.519333 484 2750 3 chr6B.!!$R1 2266
13 TraesCS6D01G075600 chr7A 542713631 542717315 3684 False 587.500000 1040 93.810000 1 2750 2 chr7A.!!$F1 2749

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
161 163 0.391263 AACCTAGCGCAACACCTAGC 60.391 55.000 11.47 0.0 31.76 3.42 F
1364 2492 1.336795 GCATGGCCAACCTAACAACAC 60.337 52.381 10.96 0.0 36.63 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 2688 1.133668 TCATCCTCGCTCTCATCCTCA 60.134 52.381 0.0 0.0 0.0 3.86 R
2573 5256 2.835764 TCTCAGTTTTATGCCTACCCGT 59.164 45.455 0.0 0.0 0.0 5.28 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
32 33 6.937436 ACTATGACAGGAAAAGTCGTTTTT 57.063 33.333 0.00 1.13 41.59 1.94
95 97 3.744155 CCCCCTTCTTCTGCCCCC 61.744 72.222 0.00 0.00 0.00 5.40
96 98 4.115199 CCCCTTCTTCTGCCCCCG 62.115 72.222 0.00 0.00 0.00 5.73
97 99 3.009115 CCCTTCTTCTGCCCCCGA 61.009 66.667 0.00 0.00 0.00 5.14
98 100 2.378634 CCCTTCTTCTGCCCCCGAT 61.379 63.158 0.00 0.00 0.00 4.18
99 101 1.609783 CCTTCTTCTGCCCCCGATT 59.390 57.895 0.00 0.00 0.00 3.34
100 102 0.464554 CCTTCTTCTGCCCCCGATTC 60.465 60.000 0.00 0.00 0.00 2.52
101 103 0.543749 CTTCTTCTGCCCCCGATTCT 59.456 55.000 0.00 0.00 0.00 2.40
102 104 0.541863 TTCTTCTGCCCCCGATTCTC 59.458 55.000 0.00 0.00 0.00 2.87
103 105 1.147153 CTTCTGCCCCCGATTCTCC 59.853 63.158 0.00 0.00 0.00 3.71
104 106 2.330924 CTTCTGCCCCCGATTCTCCC 62.331 65.000 0.00 0.00 0.00 4.30
105 107 4.241555 CTGCCCCCGATTCTCCCG 62.242 72.222 0.00 0.00 0.00 5.14
107 109 4.237207 GCCCCCGATTCTCCCGTC 62.237 72.222 0.00 0.00 0.00 4.79
108 110 2.444140 CCCCCGATTCTCCCGTCT 60.444 66.667 0.00 0.00 0.00 4.18
109 111 2.499827 CCCCCGATTCTCCCGTCTC 61.500 68.421 0.00 0.00 0.00 3.36
153 155 1.135199 CGAGACCTAAACCTAGCGCAA 60.135 52.381 11.47 0.00 0.00 4.85
155 157 1.621814 AGACCTAAACCTAGCGCAACA 59.378 47.619 11.47 0.00 0.00 3.33
156 158 1.730612 GACCTAAACCTAGCGCAACAC 59.269 52.381 11.47 0.00 0.00 3.32
158 160 1.338769 CCTAAACCTAGCGCAACACCT 60.339 52.381 11.47 0.00 0.00 4.00
159 161 2.093869 CCTAAACCTAGCGCAACACCTA 60.094 50.000 11.47 0.00 0.00 3.08
160 162 2.094762 AAACCTAGCGCAACACCTAG 57.905 50.000 11.47 0.41 0.00 3.02
161 163 0.391263 AACCTAGCGCAACACCTAGC 60.391 55.000 11.47 0.00 31.76 3.42
780 1880 3.430098 GCTTGTCTAGATGGGTGAGTCAG 60.430 52.174 0.00 0.00 0.00 3.51
817 1917 4.600062 TGACAGAGTACTTAGAGATGGCA 58.400 43.478 0.00 0.00 0.00 4.92
844 1944 6.209589 TGAAGATTACTTAGAGATGGATCCCG 59.790 42.308 9.90 0.00 36.39 5.14
889 1989 7.221838 CACCTCTCTTCTAGATTTGTCGAAATC 59.778 40.741 0.00 2.20 45.50 2.17
952 2072 4.456911 TGCTGCAAAATCTGAACTTAGAGG 59.543 41.667 0.00 0.00 0.00 3.69
1364 2492 1.336795 GCATGGCCAACCTAACAACAC 60.337 52.381 10.96 0.00 36.63 3.32
1376 2504 4.821805 ACCTAACAACACAGAACAAGATGG 59.178 41.667 0.00 0.00 0.00 3.51
1551 2688 1.173043 CTGAGAGCGAGGTTGAGAGT 58.827 55.000 0.00 0.00 0.00 3.24
1615 2752 7.301420 AGTAGAGGAAGATGAGGAATATCACA 58.699 38.462 0.00 0.00 30.46 3.58
1875 3012 8.293867 GTGCACAGTAATGGTAATTTTCTAACA 58.706 33.333 13.17 0.00 0.00 2.41
2130 3267 6.639563 TCATGGAATCGACATCAACTCTAAA 58.360 36.000 0.00 0.00 0.00 1.85
2222 4905 5.425217 GGGTTGATTCTTCCCCACATAATTT 59.575 40.000 5.74 0.00 37.09 1.82
2573 5256 3.833650 TCCACCACTACTAAAATCCACGA 59.166 43.478 0.00 0.00 0.00 4.35
2657 5340 6.377146 CCAACACTTATGCCCTATTTGTAAGT 59.623 38.462 0.00 0.00 36.37 2.24
2659 5342 9.120538 CAACACTTATGCCCTATTTGTAAGTAT 57.879 33.333 0.00 0.00 34.75 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.036091 AGCGTGCTATAAAGAAGGGGTA 58.964 45.455 0.00 0.00 0.00 3.69
82 84 0.543749 AGAATCGGGGGCAGAAGAAG 59.456 55.000 0.00 0.00 0.00 2.85
84 86 1.338136 GGAGAATCGGGGGCAGAAGA 61.338 60.000 0.00 0.00 34.37 2.87
85 87 1.147153 GGAGAATCGGGGGCAGAAG 59.853 63.158 0.00 0.00 34.37 2.85
86 88 2.375345 GGGAGAATCGGGGGCAGAA 61.375 63.158 0.00 0.00 34.37 3.02
87 89 2.768344 GGGAGAATCGGGGGCAGA 60.768 66.667 0.00 0.00 34.37 4.26
88 90 4.241555 CGGGAGAATCGGGGGCAG 62.242 72.222 0.00 0.00 34.37 4.85
90 92 4.237207 GACGGGAGAATCGGGGGC 62.237 72.222 0.00 0.00 34.37 5.80
91 93 2.444140 AGACGGGAGAATCGGGGG 60.444 66.667 0.00 0.00 34.37 5.40
92 94 2.499827 GGAGACGGGAGAATCGGGG 61.500 68.421 0.00 0.00 34.37 5.73
93 95 2.499827 GGGAGACGGGAGAATCGGG 61.500 68.421 0.00 0.00 34.37 5.14
94 96 2.499827 GGGGAGACGGGAGAATCGG 61.500 68.421 0.00 0.00 34.37 4.18
95 97 2.499827 GGGGGAGACGGGAGAATCG 61.500 68.421 0.00 0.00 34.37 3.34
96 98 3.552219 GGGGGAGACGGGAGAATC 58.448 66.667 0.00 0.00 0.00 2.52
780 1880 8.994170 AGTACTCTGTCAAATTTAAAGAAGAGC 58.006 33.333 12.10 0.00 34.58 4.09
817 1917 8.601546 GGGATCCATCTCTAAGTAATCTTCAAT 58.398 37.037 15.23 0.00 35.36 2.57
889 1989 8.567285 AATGAAACTCCTAAGTAATCTGTTGG 57.433 34.615 0.00 0.00 33.48 3.77
952 2072 2.170166 TGAGTTGCATTTGGGATCCAC 58.830 47.619 15.23 3.53 30.78 4.02
1348 2476 1.975660 TCTGTGTTGTTAGGTTGGCC 58.024 50.000 0.00 0.00 0.00 5.36
1364 2492 8.447924 AAGATAATCATCACCATCTTGTTCTG 57.552 34.615 0.00 0.00 36.60 3.02
1376 2504 3.876914 TGGGTTGCGAAGATAATCATCAC 59.123 43.478 0.00 0.00 33.21 3.06
1551 2688 1.133668 TCATCCTCGCTCTCATCCTCA 60.134 52.381 0.00 0.00 0.00 3.86
1743 2880 3.181501 TGCACTCTTTTCGGTGTCAAAAG 60.182 43.478 1.00 1.00 40.71 2.27
1744 2881 2.750166 TGCACTCTTTTCGGTGTCAAAA 59.250 40.909 0.00 0.00 36.03 2.44
1829 2966 4.574013 GCACTCATCTTCCATTGTAGAAGG 59.426 45.833 1.03 0.00 40.94 3.46
1875 3012 9.189156 ACCATAAATTAAGCACACATGAGTAAT 57.811 29.630 0.00 0.00 0.00 1.89
1897 3034 7.126733 AGTACTAGAGTAAAGACCATGACCAT 58.873 38.462 0.00 0.00 31.52 3.55
2130 3267 5.151454 AGCAGCTTACCCATATAGACTCTT 58.849 41.667 0.00 0.00 0.00 2.85
2222 4905 7.896811 TCTCTAGTCTTTGCATTCAACTTCTA 58.103 34.615 0.00 0.00 30.75 2.10
2573 5256 2.835764 TCTCAGTTTTATGCCTACCCGT 59.164 45.455 0.00 0.00 0.00 5.28
2657 5340 7.557724 CATTTATGCCAATGATGCCCATAATA 58.442 34.615 0.00 0.00 36.39 0.98
2659 5342 5.795972 CATTTATGCCAATGATGCCCATAA 58.204 37.500 0.00 0.00 36.39 1.90


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

AutoCloner maintained by Alex Coulton.