Multiple sequence alignment - TraesCS6D01G293600

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 TraesCS6D01G293600 chr6D 100.000 3635 0 0 1 3635 404234599 404230965 0.000000e+00 6713
1 TraesCS6D01G293600 chr6A 96.854 3560 66 3 122 3635 550750204 550746645 0.000000e+00 5912
2 TraesCS6D01G293600 chrUn 95.219 2008 66 21 1 1990 78925967 78927962 0.000000e+00 3149
3 TraesCS6D01G293600 chrUn 96.884 1669 27 1 1992 3635 78928063 78929731 0.000000e+00 2771
4 TraesCS6D01G293600 chr1A 75.831 3008 630 66 213 3166 3503803 3500839 0.000000e+00 1437
5 TraesCS6D01G293600 chr1A 75.637 3021 623 82 205 3166 3491753 3488787 0.000000e+00 1397
6 TraesCS6D01G293600 chr1A 75.493 1065 234 20 147 1206 3582508 3581466 2.520000e-136 496
7 TraesCS6D01G293600 chr1A 74.847 1141 261 17 147 1281 3657363 3656243 9.070000e-136 494
8 TraesCS6D01G293600 chr1A 75.876 999 221 14 213 1208 3454727 3453746 3.260000e-135 492
9 TraesCS6D01G293600 chr1B 75.758 3003 630 60 213 3166 4591563 4588610 0.000000e+00 1423
10 TraesCS6D01G293600 chr1B 75.688 2978 635 63 237 3166 4114619 4117555 0.000000e+00 1406
11 TraesCS6D01G293600 chr1B 75.490 3011 647 61 207 3166 4095635 4098605 0.000000e+00 1387
12 TraesCS6D01G293600 chr1B 75.114 3070 675 59 144 3166 4150770 4153797 0.000000e+00 1354
13 TraesCS6D01G293600 chr1B 74.625 3070 683 64 149 3166 3964557 3967582 0.000000e+00 1266
14 TraesCS6D01G293600 chr1B 73.559 2984 692 65 236 3166 1819808 1816869 0.000000e+00 1050
15 TraesCS6D01G293600 chr1B 75.305 2134 457 46 1079 3166 4560726 4558617 0.000000e+00 957
16 TraesCS6D01G293600 chr1B 73.780 2479 574 47 737 3166 4824008 4821557 0.000000e+00 907
17 TraesCS6D01G293600 chr1B 71.378 1691 433 37 678 2342 4534296 4532631 9.460000e-106 394
18 TraesCS6D01G293600 chr1B 82.370 346 61 0 2821 3166 4842013 4841668 5.900000e-78 302
19 TraesCS6D01G293600 chr1D 75.342 3001 651 56 213 3166 621077 618119 0.000000e+00 1360


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 TraesCS6D01G293600 chr6D 404230965 404234599 3634 True 6713 6713 100.0000 1 3635 1 chr6D.!!$R1 3634
1 TraesCS6D01G293600 chr6A 550746645 550750204 3559 True 5912 5912 96.8540 122 3635 1 chr6A.!!$R1 3513
2 TraesCS6D01G293600 chrUn 78925967 78929731 3764 False 2960 3149 96.0515 1 3635 2 chrUn.!!$F1 3634
3 TraesCS6D01G293600 chr1A 3500839 3503803 2964 True 1437 1437 75.8310 213 3166 1 chr1A.!!$R3 2953
4 TraesCS6D01G293600 chr1A 3488787 3491753 2966 True 1397 1397 75.6370 205 3166 1 chr1A.!!$R2 2961
5 TraesCS6D01G293600 chr1A 3581466 3582508 1042 True 496 496 75.4930 147 1206 1 chr1A.!!$R4 1059
6 TraesCS6D01G293600 chr1A 3656243 3657363 1120 True 494 494 74.8470 147 1281 1 chr1A.!!$R5 1134
7 TraesCS6D01G293600 chr1A 3453746 3454727 981 True 492 492 75.8760 213 1208 1 chr1A.!!$R1 995
8 TraesCS6D01G293600 chr1B 4588610 4591563 2953 True 1423 1423 75.7580 213 3166 1 chr1B.!!$R4 2953
9 TraesCS6D01G293600 chr1B 4114619 4117555 2936 False 1406 1406 75.6880 237 3166 1 chr1B.!!$F3 2929
10 TraesCS6D01G293600 chr1B 4095635 4098605 2970 False 1387 1387 75.4900 207 3166 1 chr1B.!!$F2 2959
11 TraesCS6D01G293600 chr1B 4150770 4153797 3027 False 1354 1354 75.1140 144 3166 1 chr1B.!!$F4 3022
12 TraesCS6D01G293600 chr1B 3964557 3967582 3025 False 1266 1266 74.6250 149 3166 1 chr1B.!!$F1 3017
13 TraesCS6D01G293600 chr1B 1816869 1819808 2939 True 1050 1050 73.5590 236 3166 1 chr1B.!!$R1 2930
14 TraesCS6D01G293600 chr1B 4558617 4560726 2109 True 957 957 75.3050 1079 3166 1 chr1B.!!$R3 2087
15 TraesCS6D01G293600 chr1B 4821557 4824008 2451 True 907 907 73.7800 737 3166 1 chr1B.!!$R5 2429
16 TraesCS6D01G293600 chr1B 4532631 4534296 1665 True 394 394 71.3780 678 2342 1 chr1B.!!$R2 1664
17 TraesCS6D01G293600 chr1D 618119 621077 2958 True 1360 1360 75.3420 213 3166 1 chr1D.!!$R1 2953

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
187 217 0.693049 CACCCCTGCTCTACCTTTGT 59.307 55.000 0.00 0.0 0.00 2.83 F
188 218 0.693049 ACCCCTGCTCTACCTTTGTG 59.307 55.000 0.00 0.0 0.00 3.33 F
193 223 2.039084 CCTGCTCTACCTTTGTGTCCTT 59.961 50.000 0.00 0.0 0.00 3.36 F
197 227 3.494398 GCTCTACCTTTGTGTCCTTGTCA 60.494 47.826 0.00 0.0 0.00 3.58 F
345 375 4.394712 CTCCTGGCGGGACACCAC 62.395 72.222 12.08 0.0 34.53 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 1376 3.513515 GGAGGTTCACCAAATTGCCAATA 59.486 43.478 0.00 0.00 38.89 1.90 R
1616 1648 4.532126 TCTTTAAGCTCCATGGAACTGAGA 59.468 41.667 18.36 17.13 0.00 3.27 R
2483 2620 1.547372 CAAGAACAATTGGCAGGAGGG 59.453 52.381 10.83 0.00 0.00 4.30 R
2632 2769 7.443272 CCTGATAATGTCATCAAATGCTAGTCA 59.557 37.037 0.00 0.00 35.97 3.41 R
2676 2838 4.072131 GCCTTGTAGACTTTTCCATGTCA 58.928 43.478 0.00 0.00 35.81 3.58 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
33 34 2.494870 GCAATGAAACCCTGAGAGCAAT 59.505 45.455 0.00 0.00 0.00 3.56
37 38 2.309755 TGAAACCCTGAGAGCAATGGAT 59.690 45.455 0.00 0.00 0.00 3.41
46 47 3.054875 TGAGAGCAATGGATAACTGCACT 60.055 43.478 0.00 0.00 39.30 4.40
47 48 3.539604 AGAGCAATGGATAACTGCACTC 58.460 45.455 0.00 0.00 38.58 3.51
49 50 3.944015 GAGCAATGGATAACTGCACTCTT 59.056 43.478 0.00 0.00 38.58 2.85
50 51 3.693085 AGCAATGGATAACTGCACTCTTG 59.307 43.478 0.00 0.00 38.58 3.02
51 52 3.441572 GCAATGGATAACTGCACTCTTGT 59.558 43.478 0.00 0.00 36.09 3.16
52 53 4.635765 GCAATGGATAACTGCACTCTTGTA 59.364 41.667 0.00 0.00 36.09 2.41
53 54 5.447818 GCAATGGATAACTGCACTCTTGTAC 60.448 44.000 0.00 0.00 36.09 2.90
54 55 5.683876 ATGGATAACTGCACTCTTGTACT 57.316 39.130 0.00 0.00 0.00 2.73
55 56 6.791867 ATGGATAACTGCACTCTTGTACTA 57.208 37.500 0.00 0.00 0.00 1.82
56 57 6.208988 TGGATAACTGCACTCTTGTACTAG 57.791 41.667 0.00 0.00 0.00 2.57
57 58 5.715279 TGGATAACTGCACTCTTGTACTAGT 59.285 40.000 0.00 0.00 0.00 2.57
59 60 7.148120 TGGATAACTGCACTCTTGTACTAGTAC 60.148 40.741 23.58 23.58 36.63 2.73
93 117 1.340405 CCATACCCTGAGCAAGCACTT 60.340 52.381 0.00 0.00 0.00 3.16
94 118 2.012673 CATACCCTGAGCAAGCACTTC 58.987 52.381 0.00 0.00 0.00 3.01
100 124 2.542411 CCTGAGCAAGCACTTCAAACAC 60.542 50.000 0.00 0.00 0.00 3.32
103 127 2.355756 GAGCAAGCACTTCAAACACTCA 59.644 45.455 0.00 0.00 0.00 3.41
104 128 2.098117 AGCAAGCACTTCAAACACTCAC 59.902 45.455 0.00 0.00 0.00 3.51
105 129 2.159393 GCAAGCACTTCAAACACTCACA 60.159 45.455 0.00 0.00 0.00 3.58
106 130 3.489738 GCAAGCACTTCAAACACTCACAT 60.490 43.478 0.00 0.00 0.00 3.21
107 131 4.285292 CAAGCACTTCAAACACTCACATC 58.715 43.478 0.00 0.00 0.00 3.06
108 132 3.813443 AGCACTTCAAACACTCACATCT 58.187 40.909 0.00 0.00 0.00 2.90
109 133 3.812053 AGCACTTCAAACACTCACATCTC 59.188 43.478 0.00 0.00 0.00 2.75
110 134 3.812053 GCACTTCAAACACTCACATCTCT 59.188 43.478 0.00 0.00 0.00 3.10
111 135 4.991056 GCACTTCAAACACTCACATCTCTA 59.009 41.667 0.00 0.00 0.00 2.43
112 136 5.119898 GCACTTCAAACACTCACATCTCTAG 59.880 44.000 0.00 0.00 0.00 2.43
113 137 6.450545 CACTTCAAACACTCACATCTCTAGA 58.549 40.000 0.00 0.00 0.00 2.43
114 138 6.585702 CACTTCAAACACTCACATCTCTAGAG 59.414 42.308 13.98 13.98 35.56 2.43
115 139 5.065704 TCAAACACTCACATCTCTAGAGC 57.934 43.478 15.35 0.00 32.71 4.09
116 140 4.769488 TCAAACACTCACATCTCTAGAGCT 59.231 41.667 15.35 1.95 32.71 4.09
117 141 5.946377 TCAAACACTCACATCTCTAGAGCTA 59.054 40.000 15.35 0.00 32.71 3.32
118 142 5.828299 AACACTCACATCTCTAGAGCTAC 57.172 43.478 15.35 0.00 32.71 3.58
119 143 5.110814 ACACTCACATCTCTAGAGCTACT 57.889 43.478 15.35 0.00 32.71 2.57
125 149 5.104067 TCACATCTCTAGAGCTACTACCCAA 60.104 44.000 15.35 0.00 0.00 4.12
187 217 0.693049 CACCCCTGCTCTACCTTTGT 59.307 55.000 0.00 0.00 0.00 2.83
188 218 0.693049 ACCCCTGCTCTACCTTTGTG 59.307 55.000 0.00 0.00 0.00 3.33
193 223 2.039084 CCTGCTCTACCTTTGTGTCCTT 59.961 50.000 0.00 0.00 0.00 3.36
197 227 3.494398 GCTCTACCTTTGTGTCCTTGTCA 60.494 47.826 0.00 0.00 0.00 3.58
345 375 4.394712 CTCCTGGCGGGACACCAC 62.395 72.222 12.08 0.00 34.53 4.16
686 716 6.414732 TCCTTCAATAACCTAACAGGACATG 58.585 40.000 0.00 0.00 37.67 3.21
730 760 7.327975 ACCTGACGATGTTGATTTATCTTGTA 58.672 34.615 0.00 0.00 0.00 2.41
999 1030 6.044404 TCCCTTTCTCCATATCCAATCTAACC 59.956 42.308 0.00 0.00 0.00 2.85
1616 1648 9.671279 TGTAATGTCTCTGAATATGTTCAATGT 57.329 29.630 6.35 0.00 43.39 2.71
2483 2620 7.806014 TCGCCATAAACAAAAGATACAAAGTTC 59.194 33.333 0.00 0.00 0.00 3.01
2632 2769 7.015487 TGTTCTCTGTTTGGAATTTTGATGGAT 59.985 33.333 0.00 0.00 0.00 3.41
2676 2838 5.549742 TCAGGGCAACAGAAAATTTTGAT 57.450 34.783 8.47 0.00 39.74 2.57
3436 3618 5.665459 ACAGAGCCATATACTCTTGTCAAC 58.335 41.667 4.99 0.00 41.79 3.18
3437 3619 5.187772 ACAGAGCCATATACTCTTGTCAACA 59.812 40.000 4.99 0.00 41.79 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.899717 TCAGGGTTTCATTGCAGGGC 60.900 55.000 0.00 0.00 0.00 5.19
33 34 5.715279 ACTAGTACAAGAGTGCAGTTATCCA 59.285 40.000 0.00 0.00 32.20 3.41
37 38 7.879677 TGTAGTACTAGTACAAGAGTGCAGTTA 59.120 37.037 29.87 10.12 38.48 2.24
49 50 8.510283 TGGGGGTTAATATGTAGTACTAGTACA 58.490 37.037 29.87 16.28 38.28 2.90
50 51 8.940397 TGGGGGTTAATATGTAGTACTAGTAC 57.060 38.462 23.03 23.03 36.35 2.73
52 53 9.539194 GTATGGGGGTTAATATGTAGTACTAGT 57.461 37.037 1.87 0.00 0.00 2.57
53 54 8.975295 GGTATGGGGGTTAATATGTAGTACTAG 58.025 40.741 1.87 0.00 0.00 2.57
54 55 7.900784 GGGTATGGGGGTTAATATGTAGTACTA 59.099 40.741 0.00 0.00 0.00 1.82
55 56 6.732390 GGGTATGGGGGTTAATATGTAGTACT 59.268 42.308 0.00 0.00 0.00 2.73
56 57 6.732390 AGGGTATGGGGGTTAATATGTAGTAC 59.268 42.308 0.00 0.00 0.00 2.73
57 58 6.731919 CAGGGTATGGGGGTTAATATGTAGTA 59.268 42.308 0.00 0.00 0.00 1.82
59 60 5.788533 TCAGGGTATGGGGGTTAATATGTAG 59.211 44.000 0.00 0.00 0.00 2.74
71 95 1.152881 GCTTGCTCAGGGTATGGGG 60.153 63.158 0.00 0.00 0.00 4.96
93 117 4.769488 AGCTCTAGAGATGTGAGTGTTTGA 59.231 41.667 24.24 0.00 0.00 2.69
94 118 5.070770 AGCTCTAGAGATGTGAGTGTTTG 57.929 43.478 24.24 0.00 0.00 2.93
100 124 5.001232 GGGTAGTAGCTCTAGAGATGTGAG 58.999 50.000 24.24 0.00 0.00 3.51
103 127 5.134661 GTTGGGTAGTAGCTCTAGAGATGT 58.865 45.833 24.24 11.52 0.00 3.06
104 128 5.009210 GTGTTGGGTAGTAGCTCTAGAGATG 59.991 48.000 24.24 0.00 0.00 2.90
105 129 5.134661 GTGTTGGGTAGTAGCTCTAGAGAT 58.865 45.833 24.24 20.12 0.00 2.75
106 130 4.018688 TGTGTTGGGTAGTAGCTCTAGAGA 60.019 45.833 24.24 0.00 0.00 3.10
107 131 4.096682 GTGTGTTGGGTAGTAGCTCTAGAG 59.903 50.000 15.85 15.85 0.00 2.43
108 132 4.015084 GTGTGTTGGGTAGTAGCTCTAGA 58.985 47.826 0.00 0.00 0.00 2.43
109 133 3.181499 CGTGTGTTGGGTAGTAGCTCTAG 60.181 52.174 0.00 0.00 0.00 2.43
110 134 2.751259 CGTGTGTTGGGTAGTAGCTCTA 59.249 50.000 0.00 0.00 0.00 2.43
111 135 1.544691 CGTGTGTTGGGTAGTAGCTCT 59.455 52.381 0.00 0.00 0.00 4.09
112 136 1.542915 TCGTGTGTTGGGTAGTAGCTC 59.457 52.381 0.00 0.00 0.00 4.09
113 137 1.544691 CTCGTGTGTTGGGTAGTAGCT 59.455 52.381 0.00 0.00 0.00 3.32
114 138 1.542915 TCTCGTGTGTTGGGTAGTAGC 59.457 52.381 0.00 0.00 0.00 3.58
115 139 3.572584 GTTCTCGTGTGTTGGGTAGTAG 58.427 50.000 0.00 0.00 0.00 2.57
116 140 2.297033 GGTTCTCGTGTGTTGGGTAGTA 59.703 50.000 0.00 0.00 0.00 1.82
117 141 1.069668 GGTTCTCGTGTGTTGGGTAGT 59.930 52.381 0.00 0.00 0.00 2.73
118 142 1.069513 TGGTTCTCGTGTGTTGGGTAG 59.930 52.381 0.00 0.00 0.00 3.18
119 143 1.069513 CTGGTTCTCGTGTGTTGGGTA 59.930 52.381 0.00 0.00 0.00 3.69
125 149 0.392706 TGCATCTGGTTCTCGTGTGT 59.607 50.000 0.00 0.00 0.00 3.72
187 217 2.812836 ATGATGGCATGACAAGGACA 57.187 45.000 4.70 4.35 32.31 4.02
197 227 3.047115 AGAGAAGGAGACATGATGGCAT 58.953 45.455 0.00 0.00 34.29 4.40
686 716 3.851128 GCCTAGGGACGCAGGGAC 61.851 72.222 11.72 0.00 36.21 4.46
999 1030 6.021074 CGACGAGAGAGAGTTCATTTAACATG 60.021 42.308 0.00 0.00 40.83 3.21
1344 1376 3.513515 GGAGGTTCACCAAATTGCCAATA 59.486 43.478 0.00 0.00 38.89 1.90
1616 1648 4.532126 TCTTTAAGCTCCATGGAACTGAGA 59.468 41.667 18.36 17.13 0.00 3.27
2483 2620 1.547372 CAAGAACAATTGGCAGGAGGG 59.453 52.381 10.83 0.00 0.00 4.30
2632 2769 7.443272 CCTGATAATGTCATCAAATGCTAGTCA 59.557 37.037 0.00 0.00 35.97 3.41
2676 2838 4.072131 GCCTTGTAGACTTTTCCATGTCA 58.928 43.478 0.00 0.00 35.81 3.58
3209 3371 6.348540 GCTATGGAACCATAAAAGCGGATAAG 60.349 42.308 13.51 2.31 38.30 1.73
3436 3618 1.336795 GGCCGTTGGTCCAAGATTTTG 60.337 52.381 3.96 0.00 0.00 2.44
3437 3619 0.966179 GGCCGTTGGTCCAAGATTTT 59.034 50.000 3.96 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.