Multiple sequence alignment - TraesCS3B01G611000

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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 TraesCS3B01G611000 chr3B 100.000 3445 0 0 1 3445 829116291 829119735 0.000000e+00 6362
1 TraesCS3B01G611000 chr3B 99.634 3277 12 0 169 3445 813958507 813955231 0.000000e+00 5986
2 TraesCS3B01G611000 chr7B 99.878 3279 4 0 167 3445 204002752 204006030 0.000000e+00 6034
3 TraesCS3B01G611000 chr2A 99.238 3279 25 0 167 3445 713923488 713926766 0.000000e+00 5917
4 TraesCS3B01G611000 chr2A 98.935 2630 28 0 816 3445 39363907 39361278 0.000000e+00 4702
5 TraesCS3B01G611000 chr2A 98.741 556 7 0 167 722 39364444 39363889 0.000000e+00 989
6 TraesCS3B01G611000 chr3A 99.207 3279 25 1 167 3445 610424332 610421055 0.000000e+00 5910
7 TraesCS3B01G611000 chr3A 97.484 159 4 0 1 159 746265092 746265250 4.380000e-69 272
8 TraesCS3B01G611000 chr4A 98.721 3285 40 2 162 3445 586088084 586084801 0.000000e+00 5832
9 TraesCS3B01G611000 chr7D 97.543 3052 73 2 395 3445 237548457 237551507 0.000000e+00 5219
10 TraesCS3B01G611000 chr7D 96.296 189 7 0 167 355 237548280 237548468 9.280000e-81 311
11 TraesCS3B01G611000 chr5B 98.296 2523 42 1 924 3445 599616903 599614381 0.000000e+00 4420
12 TraesCS3B01G611000 chr5B 93.519 216 10 2 166 377 531864096 531864311 5.550000e-83 318
13 TraesCS3B01G611000 chr5B 91.781 73 6 0 858 930 531864453 531864525 6.080000e-18 102
14 TraesCS3B01G611000 chr3D 95.393 2518 115 1 929 3445 511280668 511278151 0.000000e+00 4006
15 TraesCS3B01G611000 chr3D 93.488 215 10 2 167 377 511281794 511281580 2.000000e-82 316
16 TraesCS3B01G611000 chr3D 97.484 159 4 0 1 159 611410827 611410985 4.380000e-69 272


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 TraesCS3B01G611000 chr3B 829116291 829119735 3444 False 6362.0 6362 100.0000 1 3445 1 chr3B.!!$F1 3444
1 TraesCS3B01G611000 chr3B 813955231 813958507 3276 True 5986.0 5986 99.6340 169 3445 1 chr3B.!!$R1 3276
2 TraesCS3B01G611000 chr7B 204002752 204006030 3278 False 6034.0 6034 99.8780 167 3445 1 chr7B.!!$F1 3278
3 TraesCS3B01G611000 chr2A 713923488 713926766 3278 False 5917.0 5917 99.2380 167 3445 1 chr2A.!!$F1 3278
4 TraesCS3B01G611000 chr2A 39361278 39364444 3166 True 2845.5 4702 98.8380 167 3445 2 chr2A.!!$R1 3278
5 TraesCS3B01G611000 chr3A 610421055 610424332 3277 True 5910.0 5910 99.2070 167 3445 1 chr3A.!!$R1 3278
6 TraesCS3B01G611000 chr4A 586084801 586088084 3283 True 5832.0 5832 98.7210 162 3445 1 chr4A.!!$R1 3283
7 TraesCS3B01G611000 chr7D 237548280 237551507 3227 False 2765.0 5219 96.9195 167 3445 2 chr7D.!!$F1 3278
8 TraesCS3B01G611000 chr5B 599614381 599616903 2522 True 4420.0 4420 98.2960 924 3445 1 chr5B.!!$R1 2521
9 TraesCS3B01G611000 chr3D 511278151 511281794 3643 True 2161.0 4006 94.4405 167 3445 2 chr3D.!!$R1 3278

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
24 25 0.036732 TTCATTCGAGGTTGCCTGCT 59.963 50.0 0.00 0.00 31.76 4.24 F
102 103 0.107703 AAATGCCGTGCTGCTAGCTA 60.108 50.0 17.23 1.31 42.97 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1150 1675 8.470002 GCTCAAATAATTCTTAACACCTTCCAT 58.530 33.333 0.00 0.0 0.00 3.41 R
3246 3771 1.544537 CGTGGATCCAGTTTTCCCACA 60.545 52.381 16.81 0.0 45.52 4.17 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
20 21 3.249687 ACCTTCATTCGAGGTTGCC 57.750 52.632 0.00 0.00 45.06 4.52
21 22 0.693049 ACCTTCATTCGAGGTTGCCT 59.307 50.000 0.00 0.00 45.06 4.75
22 23 1.089920 CCTTCATTCGAGGTTGCCTG 58.910 55.000 0.00 0.00 31.76 4.85
23 24 0.449388 CTTCATTCGAGGTTGCCTGC 59.551 55.000 0.00 0.00 31.76 4.85
24 25 0.036732 TTCATTCGAGGTTGCCTGCT 59.963 50.000 0.00 0.00 31.76 4.24
25 26 0.391661 TCATTCGAGGTTGCCTGCTC 60.392 55.000 0.00 0.00 31.76 4.26
26 27 0.674581 CATTCGAGGTTGCCTGCTCA 60.675 55.000 0.00 0.00 31.76 4.26
27 28 0.674895 ATTCGAGGTTGCCTGCTCAC 60.675 55.000 0.00 0.00 31.76 3.51
28 29 1.758440 TTCGAGGTTGCCTGCTCACT 61.758 55.000 0.00 0.00 31.76 3.41
29 30 1.739562 CGAGGTTGCCTGCTCACTC 60.740 63.158 0.00 0.00 31.76 3.51
30 31 1.676384 GAGGTTGCCTGCTCACTCT 59.324 57.895 0.00 0.00 31.76 3.24
31 32 0.673022 GAGGTTGCCTGCTCACTCTG 60.673 60.000 0.00 0.00 31.76 3.35
32 33 1.673665 GGTTGCCTGCTCACTCTGG 60.674 63.158 0.00 0.00 0.00 3.86
33 34 1.372683 GTTGCCTGCTCACTCTGGA 59.627 57.895 0.00 0.00 0.00 3.86
34 35 0.250467 GTTGCCTGCTCACTCTGGAA 60.250 55.000 0.00 0.00 0.00 3.53
35 36 0.694771 TTGCCTGCTCACTCTGGAAT 59.305 50.000 0.00 0.00 0.00 3.01
36 37 0.694771 TGCCTGCTCACTCTGGAATT 59.305 50.000 0.00 0.00 0.00 2.17
37 38 1.074405 TGCCTGCTCACTCTGGAATTT 59.926 47.619 0.00 0.00 0.00 1.82
38 39 2.305635 TGCCTGCTCACTCTGGAATTTA 59.694 45.455 0.00 0.00 0.00 1.40
39 40 3.054139 TGCCTGCTCACTCTGGAATTTAT 60.054 43.478 0.00 0.00 0.00 1.40
40 41 3.314635 GCCTGCTCACTCTGGAATTTATG 59.685 47.826 0.00 0.00 0.00 1.90
41 42 3.314635 CCTGCTCACTCTGGAATTTATGC 59.685 47.826 0.00 0.00 0.00 3.14
42 43 4.197750 CTGCTCACTCTGGAATTTATGCT 58.802 43.478 0.00 0.00 0.00 3.79
43 44 4.592942 TGCTCACTCTGGAATTTATGCTT 58.407 39.130 0.00 0.00 0.00 3.91
44 45 5.012239 TGCTCACTCTGGAATTTATGCTTT 58.988 37.500 0.00 0.00 0.00 3.51
45 46 5.477984 TGCTCACTCTGGAATTTATGCTTTT 59.522 36.000 0.00 0.00 0.00 2.27
46 47 6.032717 GCTCACTCTGGAATTTATGCTTTTC 58.967 40.000 0.00 0.00 0.00 2.29
47 48 6.515272 TCACTCTGGAATTTATGCTTTTCC 57.485 37.500 0.00 0.00 39.50 3.13
48 49 6.248433 TCACTCTGGAATTTATGCTTTTCCT 58.752 36.000 0.00 0.00 39.72 3.36
49 50 7.402054 TCACTCTGGAATTTATGCTTTTCCTA 58.598 34.615 0.00 0.00 39.72 2.94
50 51 7.336931 TCACTCTGGAATTTATGCTTTTCCTAC 59.663 37.037 0.00 0.00 39.72 3.18
51 52 7.121168 CACTCTGGAATTTATGCTTTTCCTACA 59.879 37.037 0.00 0.00 39.72 2.74
52 53 7.337942 ACTCTGGAATTTATGCTTTTCCTACAG 59.662 37.037 0.00 0.00 39.72 2.74
53 54 6.095440 TCTGGAATTTATGCTTTTCCTACAGC 59.905 38.462 0.00 0.00 39.72 4.40
54 55 5.951747 TGGAATTTATGCTTTTCCTACAGCT 59.048 36.000 0.00 0.00 39.72 4.24
55 56 7.116075 TGGAATTTATGCTTTTCCTACAGCTA 58.884 34.615 0.00 0.00 39.72 3.32
56 57 7.283127 TGGAATTTATGCTTTTCCTACAGCTAG 59.717 37.037 0.00 0.00 39.72 3.42
57 58 6.625873 ATTTATGCTTTTCCTACAGCTAGC 57.374 37.500 6.62 6.62 36.92 3.42
58 59 3.922171 ATGCTTTTCCTACAGCTAGCT 57.078 42.857 12.68 12.68 36.92 3.32
72 73 5.654317 CAGCTAGCTGTCTCATGTAAATG 57.346 43.478 32.46 6.51 39.10 2.32
73 74 4.025061 CAGCTAGCTGTCTCATGTAAATGC 60.025 45.833 32.46 0.00 39.10 3.56
74 75 3.873361 GCTAGCTGTCTCATGTAAATGCA 59.127 43.478 7.70 0.00 0.00 3.96
75 76 4.514441 GCTAGCTGTCTCATGTAAATGCAT 59.486 41.667 7.70 0.00 0.00 3.96
76 77 5.333952 GCTAGCTGTCTCATGTAAATGCATC 60.334 44.000 7.70 0.00 0.00 3.91
77 78 4.520179 AGCTGTCTCATGTAAATGCATCA 58.480 39.130 0.00 0.00 0.00 3.07
78 79 4.575236 AGCTGTCTCATGTAAATGCATCAG 59.425 41.667 0.00 0.00 0.00 2.90
79 80 4.261072 GCTGTCTCATGTAAATGCATCAGG 60.261 45.833 0.00 0.00 0.00 3.86
80 81 5.101648 TGTCTCATGTAAATGCATCAGGA 57.898 39.130 0.00 0.00 0.00 3.86
81 82 5.499313 TGTCTCATGTAAATGCATCAGGAA 58.501 37.500 0.00 0.00 0.00 3.36
82 83 5.587443 TGTCTCATGTAAATGCATCAGGAAG 59.413 40.000 0.00 0.00 0.00 3.46
83 84 5.819379 GTCTCATGTAAATGCATCAGGAAGA 59.181 40.000 0.00 0.00 0.00 2.87
84 85 6.317140 GTCTCATGTAAATGCATCAGGAAGAA 59.683 38.462 0.00 0.00 0.00 2.52
85 86 6.885918 TCTCATGTAAATGCATCAGGAAGAAA 59.114 34.615 0.00 0.00 0.00 2.52
86 87 7.558807 TCTCATGTAAATGCATCAGGAAGAAAT 59.441 33.333 0.00 0.00 0.00 2.17
87 88 7.485810 TCATGTAAATGCATCAGGAAGAAATG 58.514 34.615 0.00 0.00 0.00 2.32
88 89 5.653507 TGTAAATGCATCAGGAAGAAATGC 58.346 37.500 0.00 0.00 44.72 3.56
89 90 3.814005 AATGCATCAGGAAGAAATGCC 57.186 42.857 0.00 0.00 44.03 4.40
90 91 1.097232 TGCATCAGGAAGAAATGCCG 58.903 50.000 4.30 0.00 44.03 5.69
91 92 1.098050 GCATCAGGAAGAAATGCCGT 58.902 50.000 0.00 0.00 39.87 5.68
92 93 1.202222 GCATCAGGAAGAAATGCCGTG 60.202 52.381 0.00 0.00 39.87 4.94
93 94 1.098050 ATCAGGAAGAAATGCCGTGC 58.902 50.000 0.00 0.00 0.00 5.34
94 95 0.036732 TCAGGAAGAAATGCCGTGCT 59.963 50.000 0.00 0.00 0.00 4.40
95 96 0.169672 CAGGAAGAAATGCCGTGCTG 59.830 55.000 0.00 0.00 0.00 4.41
96 97 1.153958 GGAAGAAATGCCGTGCTGC 60.154 57.895 0.00 0.00 0.00 5.25
97 98 1.589716 GGAAGAAATGCCGTGCTGCT 61.590 55.000 0.00 0.00 0.00 4.24
98 99 1.086696 GAAGAAATGCCGTGCTGCTA 58.913 50.000 0.00 0.00 0.00 3.49
99 100 1.063174 GAAGAAATGCCGTGCTGCTAG 59.937 52.381 0.00 0.00 0.00 3.42
100 101 1.063166 GAAATGCCGTGCTGCTAGC 59.937 57.895 8.10 8.10 42.82 3.42
101 102 1.372087 GAAATGCCGTGCTGCTAGCT 61.372 55.000 17.23 0.00 42.97 3.32
102 103 0.107703 AAATGCCGTGCTGCTAGCTA 60.108 50.000 17.23 1.31 42.97 3.32
103 104 0.531532 AATGCCGTGCTGCTAGCTAG 60.532 55.000 16.84 16.84 42.97 3.42
115 116 3.682372 GCTAGCTAGCCATGTTCAAAC 57.318 47.619 31.67 2.80 43.39 2.93
116 117 2.356069 GCTAGCTAGCCATGTTCAAACC 59.644 50.000 31.67 2.60 43.39 3.27
117 118 1.453155 AGCTAGCCATGTTCAAACCG 58.547 50.000 12.13 0.00 0.00 4.44
118 119 1.003118 AGCTAGCCATGTTCAAACCGA 59.997 47.619 12.13 0.00 0.00 4.69
119 120 1.398390 GCTAGCCATGTTCAAACCGAG 59.602 52.381 2.29 0.00 0.00 4.63
120 121 2.935238 GCTAGCCATGTTCAAACCGAGA 60.935 50.000 2.29 0.00 0.00 4.04
121 122 2.496899 AGCCATGTTCAAACCGAGAT 57.503 45.000 0.00 0.00 0.00 2.75
122 123 2.795329 AGCCATGTTCAAACCGAGATT 58.205 42.857 0.00 0.00 0.00 2.40
123 124 2.489329 AGCCATGTTCAAACCGAGATTG 59.511 45.455 0.00 0.00 0.00 2.67
124 125 2.228822 GCCATGTTCAAACCGAGATTGT 59.771 45.455 0.00 0.00 0.00 2.71
125 126 3.305335 GCCATGTTCAAACCGAGATTGTT 60.305 43.478 0.00 0.00 0.00 2.83
126 127 4.795962 GCCATGTTCAAACCGAGATTGTTT 60.796 41.667 0.00 0.00 36.40 2.83
127 128 4.917415 CCATGTTCAAACCGAGATTGTTTC 59.083 41.667 0.00 0.00 33.82 2.78
128 129 5.507149 CCATGTTCAAACCGAGATTGTTTCA 60.507 40.000 0.00 0.00 33.82 2.69
129 130 5.568685 TGTTCAAACCGAGATTGTTTCAA 57.431 34.783 0.00 0.00 33.82 2.69
130 131 5.577835 TGTTCAAACCGAGATTGTTTCAAG 58.422 37.500 0.00 0.00 33.82 3.02
131 132 4.829064 TCAAACCGAGATTGTTTCAAGG 57.171 40.909 0.00 0.00 33.82 3.61
132 133 3.004315 TCAAACCGAGATTGTTTCAAGGC 59.996 43.478 0.00 0.00 33.82 4.35
133 134 2.568623 ACCGAGATTGTTTCAAGGCT 57.431 45.000 0.00 0.00 0.00 4.58
134 135 3.695830 ACCGAGATTGTTTCAAGGCTA 57.304 42.857 0.00 0.00 0.00 3.93
135 136 4.015872 ACCGAGATTGTTTCAAGGCTAA 57.984 40.909 0.00 0.00 0.00 3.09
136 137 3.751698 ACCGAGATTGTTTCAAGGCTAAC 59.248 43.478 0.00 0.00 0.00 2.34
137 138 3.127030 CCGAGATTGTTTCAAGGCTAACC 59.873 47.826 0.00 0.00 0.00 2.85
147 148 3.681473 GGCTAACCTTGCACCACC 58.319 61.111 0.00 0.00 0.00 4.61
148 149 1.977009 GGCTAACCTTGCACCACCC 60.977 63.158 0.00 0.00 0.00 4.61
149 150 1.228429 GCTAACCTTGCACCACCCA 60.228 57.895 0.00 0.00 0.00 4.51
150 151 1.524008 GCTAACCTTGCACCACCCAC 61.524 60.000 0.00 0.00 0.00 4.61
151 152 0.179004 CTAACCTTGCACCACCCACA 60.179 55.000 0.00 0.00 0.00 4.17
152 153 0.480690 TAACCTTGCACCACCCACAT 59.519 50.000 0.00 0.00 0.00 3.21
153 154 0.480690 AACCTTGCACCACCCACATA 59.519 50.000 0.00 0.00 0.00 2.29
154 155 0.704076 ACCTTGCACCACCCACATAT 59.296 50.000 0.00 0.00 0.00 1.78
155 156 1.919654 ACCTTGCACCACCCACATATA 59.080 47.619 0.00 0.00 0.00 0.86
156 157 2.513738 ACCTTGCACCACCCACATATAT 59.486 45.455 0.00 0.00 0.00 0.86
157 158 2.886523 CCTTGCACCACCCACATATATG 59.113 50.000 11.29 11.29 0.00 1.78
158 159 3.554934 CTTGCACCACCCACATATATGT 58.445 45.455 12.75 12.75 42.84 2.29
159 160 4.445592 CCTTGCACCACCCACATATATGTA 60.446 45.833 17.86 0.00 39.39 2.29
160 161 4.079980 TGCACCACCCACATATATGTAC 57.920 45.455 17.86 2.22 39.39 2.90
161 162 3.456277 TGCACCACCCACATATATGTACA 59.544 43.478 17.86 0.00 39.39 2.90
162 163 4.103943 TGCACCACCCACATATATGTACAT 59.896 41.667 17.86 13.93 39.39 2.29
163 164 5.308237 TGCACCACCCACATATATGTACATA 59.692 40.000 17.86 17.65 39.39 2.29
164 165 6.012945 TGCACCACCCACATATATGTACATAT 60.013 38.462 27.09 27.09 39.39 1.78
165 166 7.181125 TGCACCACCCACATATATGTACATATA 59.819 37.037 29.08 29.08 39.39 0.86
1150 1675 7.894708 TGACTTGATGCCAAATGAAATTAAGA 58.105 30.769 0.00 0.00 33.67 2.10
3246 3771 1.158904 TCCGGGATCATAGACCCTCT 58.841 55.000 0.00 0.00 43.57 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.468914 GGCAACCTCGAATGAAGGTTC 59.531 52.381 4.60 1.46 43.32 3.62
1 2 1.073923 AGGCAACCTCGAATGAAGGTT 59.926 47.619 1.73 1.73 45.76 3.50
3 4 1.089920 CAGGCAACCTCGAATGAAGG 58.910 55.000 0.00 0.00 37.17 3.46
4 5 0.449388 GCAGGCAACCTCGAATGAAG 59.551 55.000 0.00 0.00 37.17 3.02
5 6 0.036732 AGCAGGCAACCTCGAATGAA 59.963 50.000 0.00 0.00 37.17 2.57
6 7 0.391661 GAGCAGGCAACCTCGAATGA 60.392 55.000 0.00 0.00 37.17 2.57
7 8 0.674581 TGAGCAGGCAACCTCGAATG 60.675 55.000 0.00 0.00 37.17 2.67
8 9 0.674895 GTGAGCAGGCAACCTCGAAT 60.675 55.000 0.00 0.00 37.17 3.34
9 10 1.301716 GTGAGCAGGCAACCTCGAA 60.302 57.895 0.00 0.00 37.17 3.71
10 11 2.159819 GAGTGAGCAGGCAACCTCGA 62.160 60.000 0.00 0.00 37.17 4.04
11 12 1.739562 GAGTGAGCAGGCAACCTCG 60.740 63.158 0.00 0.00 37.17 4.63
12 13 0.673022 CAGAGTGAGCAGGCAACCTC 60.673 60.000 0.00 0.00 37.17 3.85
13 14 1.374190 CAGAGTGAGCAGGCAACCT 59.626 57.895 0.00 0.00 37.17 3.50
14 15 1.673665 CCAGAGTGAGCAGGCAACC 60.674 63.158 0.00 0.00 37.17 3.77
15 16 0.250467 TTCCAGAGTGAGCAGGCAAC 60.250 55.000 0.00 0.00 0.00 4.17
16 17 0.694771 ATTCCAGAGTGAGCAGGCAA 59.305 50.000 0.00 0.00 0.00 4.52
17 18 0.694771 AATTCCAGAGTGAGCAGGCA 59.305 50.000 0.00 0.00 0.00 4.75
18 19 1.831580 AAATTCCAGAGTGAGCAGGC 58.168 50.000 0.00 0.00 0.00 4.85
19 20 3.314635 GCATAAATTCCAGAGTGAGCAGG 59.685 47.826 0.00 0.00 0.00 4.85
20 21 4.197750 AGCATAAATTCCAGAGTGAGCAG 58.802 43.478 0.00 0.00 0.00 4.24
21 22 4.226427 AGCATAAATTCCAGAGTGAGCA 57.774 40.909 0.00 0.00 0.00 4.26
22 23 5.573337 AAAGCATAAATTCCAGAGTGAGC 57.427 39.130 0.00 0.00 0.00 4.26
23 24 6.376581 AGGAAAAGCATAAATTCCAGAGTGAG 59.623 38.462 6.55 0.00 44.08 3.51
24 25 6.248433 AGGAAAAGCATAAATTCCAGAGTGA 58.752 36.000 6.55 0.00 44.08 3.41
25 26 6.521151 AGGAAAAGCATAAATTCCAGAGTG 57.479 37.500 6.55 0.00 44.08 3.51
26 27 7.175104 TGTAGGAAAAGCATAAATTCCAGAGT 58.825 34.615 6.55 0.00 44.08 3.24
27 28 7.630242 TGTAGGAAAAGCATAAATTCCAGAG 57.370 36.000 6.55 0.00 44.08 3.35
28 29 6.095440 GCTGTAGGAAAAGCATAAATTCCAGA 59.905 38.462 6.55 0.00 44.08 3.86
29 30 6.096001 AGCTGTAGGAAAAGCATAAATTCCAG 59.904 38.462 6.55 0.00 44.08 3.86
30 31 5.951747 AGCTGTAGGAAAAGCATAAATTCCA 59.048 36.000 6.55 0.00 44.08 3.53
31 32 6.456795 AGCTGTAGGAAAAGCATAAATTCC 57.543 37.500 0.00 0.00 42.06 3.01
32 33 7.012799 AGCTAGCTGTAGGAAAAGCATAAATTC 59.987 37.037 18.57 0.00 42.06 2.17
33 34 6.830838 AGCTAGCTGTAGGAAAAGCATAAATT 59.169 34.615 18.57 0.00 42.06 1.82
34 35 6.261826 CAGCTAGCTGTAGGAAAAGCATAAAT 59.738 38.462 32.46 0.00 42.06 1.40
35 36 5.586243 CAGCTAGCTGTAGGAAAAGCATAAA 59.414 40.000 32.46 0.00 42.06 1.40
36 37 5.118990 CAGCTAGCTGTAGGAAAAGCATAA 58.881 41.667 32.46 0.00 42.06 1.90
37 38 4.697514 CAGCTAGCTGTAGGAAAAGCATA 58.302 43.478 32.46 0.00 42.06 3.14
38 39 3.539604 CAGCTAGCTGTAGGAAAAGCAT 58.460 45.455 32.46 0.00 42.06 3.79
39 40 2.977914 CAGCTAGCTGTAGGAAAAGCA 58.022 47.619 32.46 0.00 42.06 3.91
46 47 8.422462 CATTTACATGAGACAGCTAGCTGTAGG 61.422 44.444 42.33 31.84 43.92 3.18
47 48 6.420306 CATTTACATGAGACAGCTAGCTGTAG 59.580 42.308 42.33 30.50 43.92 2.74
48 49 6.276091 CATTTACATGAGACAGCTAGCTGTA 58.724 40.000 42.33 30.48 43.92 2.74
49 50 5.114780 CATTTACATGAGACAGCTAGCTGT 58.885 41.667 42.88 42.88 45.29 4.40
50 51 4.025061 GCATTTACATGAGACAGCTAGCTG 60.025 45.833 37.27 37.27 40.16 4.24
51 52 4.125703 GCATTTACATGAGACAGCTAGCT 58.874 43.478 12.68 12.68 31.07 3.32
52 53 3.873361 TGCATTTACATGAGACAGCTAGC 59.127 43.478 6.62 6.62 31.07 3.42
53 54 5.756833 TGATGCATTTACATGAGACAGCTAG 59.243 40.000 0.00 0.00 31.07 3.42
54 55 5.673514 TGATGCATTTACATGAGACAGCTA 58.326 37.500 0.00 0.00 31.07 3.32
55 56 4.520179 TGATGCATTTACATGAGACAGCT 58.480 39.130 0.00 0.00 31.07 4.24
56 57 4.261072 CCTGATGCATTTACATGAGACAGC 60.261 45.833 0.00 0.00 33.61 4.40
57 58 5.121105 TCCTGATGCATTTACATGAGACAG 58.879 41.667 0.00 0.00 33.61 3.51
58 59 5.101648 TCCTGATGCATTTACATGAGACA 57.898 39.130 0.00 0.00 33.61 3.41
59 60 5.819379 TCTTCCTGATGCATTTACATGAGAC 59.181 40.000 0.00 0.00 33.61 3.36
60 61 5.993055 TCTTCCTGATGCATTTACATGAGA 58.007 37.500 0.00 0.00 33.61 3.27
61 62 6.688637 TTCTTCCTGATGCATTTACATGAG 57.311 37.500 0.00 0.00 31.81 2.90
62 63 7.485810 CATTTCTTCCTGATGCATTTACATGA 58.514 34.615 0.00 0.00 31.07 3.07
63 64 6.200286 GCATTTCTTCCTGATGCATTTACATG 59.800 38.462 0.00 0.00 44.18 3.21
64 65 6.278363 GCATTTCTTCCTGATGCATTTACAT 58.722 36.000 0.00 0.00 44.18 2.29
65 66 5.394443 GGCATTTCTTCCTGATGCATTTACA 60.394 40.000 0.00 0.00 46.01 2.41
66 67 5.045872 GGCATTTCTTCCTGATGCATTTAC 58.954 41.667 0.00 0.00 46.01 2.01
67 68 4.202040 CGGCATTTCTTCCTGATGCATTTA 60.202 41.667 0.00 0.00 46.01 1.40
68 69 3.429822 CGGCATTTCTTCCTGATGCATTT 60.430 43.478 0.00 0.00 46.01 2.32
69 70 2.100252 CGGCATTTCTTCCTGATGCATT 59.900 45.455 0.00 0.00 46.01 3.56
70 71 1.679680 CGGCATTTCTTCCTGATGCAT 59.320 47.619 0.00 0.00 46.01 3.96
71 72 1.097232 CGGCATTTCTTCCTGATGCA 58.903 50.000 9.42 0.00 46.01 3.96
72 73 1.098050 ACGGCATTTCTTCCTGATGC 58.902 50.000 0.00 0.00 44.06 3.91
73 74 1.202222 GCACGGCATTTCTTCCTGATG 60.202 52.381 0.00 0.00 0.00 3.07
74 75 1.098050 GCACGGCATTTCTTCCTGAT 58.902 50.000 0.00 0.00 0.00 2.90
75 76 0.036732 AGCACGGCATTTCTTCCTGA 59.963 50.000 0.00 0.00 0.00 3.86
76 77 0.169672 CAGCACGGCATTTCTTCCTG 59.830 55.000 0.00 0.00 0.00 3.86
77 78 1.589716 GCAGCACGGCATTTCTTCCT 61.590 55.000 0.00 0.00 0.00 3.36
78 79 1.153958 GCAGCACGGCATTTCTTCC 60.154 57.895 0.00 0.00 0.00 3.46
79 80 1.063174 CTAGCAGCACGGCATTTCTTC 59.937 52.381 0.00 0.00 35.83 2.87
80 81 1.089920 CTAGCAGCACGGCATTTCTT 58.910 50.000 0.00 0.00 35.83 2.52
81 82 1.372087 GCTAGCAGCACGGCATTTCT 61.372 55.000 10.63 0.00 41.89 2.52
82 83 1.063166 GCTAGCAGCACGGCATTTC 59.937 57.895 10.63 0.00 41.89 2.17
83 84 0.107703 TAGCTAGCAGCACGGCATTT 60.108 50.000 18.83 0.00 45.56 2.32
84 85 0.531532 CTAGCTAGCAGCACGGCATT 60.532 55.000 18.83 0.00 45.56 3.56
85 86 1.068753 CTAGCTAGCAGCACGGCAT 59.931 57.895 18.83 0.00 45.56 4.40
86 87 2.496341 CTAGCTAGCAGCACGGCA 59.504 61.111 18.83 0.00 45.56 5.69
96 97 2.609459 CGGTTTGAACATGGCTAGCTAG 59.391 50.000 16.84 16.84 0.00 3.42
97 98 2.235155 TCGGTTTGAACATGGCTAGCTA 59.765 45.455 15.72 9.47 0.00 3.32
98 99 1.003118 TCGGTTTGAACATGGCTAGCT 59.997 47.619 15.72 0.00 0.00 3.32
99 100 1.398390 CTCGGTTTGAACATGGCTAGC 59.602 52.381 6.04 6.04 0.00 3.42
100 101 2.972625 TCTCGGTTTGAACATGGCTAG 58.027 47.619 0.00 0.00 0.00 3.42
101 102 3.627395 ATCTCGGTTTGAACATGGCTA 57.373 42.857 0.00 0.00 0.00 3.93
102 103 2.489329 CAATCTCGGTTTGAACATGGCT 59.511 45.455 0.00 0.00 0.00 4.75
103 104 2.228822 ACAATCTCGGTTTGAACATGGC 59.771 45.455 0.00 0.00 0.00 4.40
104 105 4.503741 AACAATCTCGGTTTGAACATGG 57.496 40.909 0.00 0.00 0.00 3.66
105 106 5.518812 TGAAACAATCTCGGTTTGAACATG 58.481 37.500 0.00 0.00 38.50 3.21
106 107 5.766150 TGAAACAATCTCGGTTTGAACAT 57.234 34.783 0.00 0.00 38.50 2.71
107 108 5.449862 CCTTGAAACAATCTCGGTTTGAACA 60.450 40.000 0.00 0.00 38.50 3.18
108 109 4.976116 CCTTGAAACAATCTCGGTTTGAAC 59.024 41.667 0.00 0.00 38.50 3.18
109 110 4.499019 GCCTTGAAACAATCTCGGTTTGAA 60.499 41.667 0.00 0.00 38.50 2.69
110 111 3.004315 GCCTTGAAACAATCTCGGTTTGA 59.996 43.478 0.00 0.00 38.50 2.69
111 112 3.004734 AGCCTTGAAACAATCTCGGTTTG 59.995 43.478 0.00 0.00 38.50 2.93
112 113 3.222603 AGCCTTGAAACAATCTCGGTTT 58.777 40.909 0.00 0.00 40.91 3.27
113 114 2.863809 AGCCTTGAAACAATCTCGGTT 58.136 42.857 0.00 0.00 0.00 4.44
114 115 2.568623 AGCCTTGAAACAATCTCGGT 57.431 45.000 0.00 0.00 0.00 4.69
115 116 3.127030 GGTTAGCCTTGAAACAATCTCGG 59.873 47.826 0.00 0.00 0.00 4.63
116 117 4.003648 AGGTTAGCCTTGAAACAATCTCG 58.996 43.478 0.00 0.00 44.18 4.04
130 131 1.977009 GGGTGGTGCAAGGTTAGCC 60.977 63.158 0.00 0.00 0.00 3.93
131 132 1.228429 TGGGTGGTGCAAGGTTAGC 60.228 57.895 0.00 0.00 0.00 3.09
132 133 0.179004 TGTGGGTGGTGCAAGGTTAG 60.179 55.000 0.00 0.00 0.00 2.34
133 134 0.480690 ATGTGGGTGGTGCAAGGTTA 59.519 50.000 0.00 0.00 0.00 2.85
134 135 0.480690 TATGTGGGTGGTGCAAGGTT 59.519 50.000 0.00 0.00 0.00 3.50
135 136 0.704076 ATATGTGGGTGGTGCAAGGT 59.296 50.000 0.00 0.00 0.00 3.50
136 137 2.727123 TATATGTGGGTGGTGCAAGG 57.273 50.000 0.00 0.00 0.00 3.61
137 138 3.554934 ACATATATGTGGGTGGTGCAAG 58.445 45.455 17.60 0.00 40.03 4.01
138 139 3.660970 ACATATATGTGGGTGGTGCAA 57.339 42.857 17.60 0.00 40.03 4.08
139 140 3.456277 TGTACATATATGTGGGTGGTGCA 59.544 43.478 25.48 6.32 41.89 4.57
140 141 4.079980 TGTACATATATGTGGGTGGTGC 57.920 45.455 25.48 3.89 41.89 5.01
155 156 9.836864 CATATACAGCCCAACATATATGTACAT 57.163 33.333 18.56 13.93 40.80 2.29
156 157 8.821817 ACATATACAGCCCAACATATATGTACA 58.178 33.333 18.56 0.00 44.04 2.90
157 158 9.098355 CACATATACAGCCCAACATATATGTAC 57.902 37.037 18.56 8.95 44.04 2.90
158 159 8.821817 ACACATATACAGCCCAACATATATGTA 58.178 33.333 18.56 1.10 44.04 2.29
159 160 7.607607 CACACATATACAGCCCAACATATATGT 59.392 37.037 12.75 12.75 45.55 2.29
160 161 7.823799 TCACACATATACAGCCCAACATATATG 59.176 37.037 11.29 11.29 41.05 1.78
161 162 7.917003 TCACACATATACAGCCCAACATATAT 58.083 34.615 0.00 0.00 0.00 0.86
162 163 7.309770 TCACACATATACAGCCCAACATATA 57.690 36.000 0.00 0.00 0.00 0.86
163 164 6.186420 TCACACATATACAGCCCAACATAT 57.814 37.500 0.00 0.00 0.00 1.78
164 165 5.622346 TCACACATATACAGCCCAACATA 57.378 39.130 0.00 0.00 0.00 2.29
165 166 4.502105 TCACACATATACAGCCCAACAT 57.498 40.909 0.00 0.00 0.00 2.71
1150 1675 8.470002 GCTCAAATAATTCTTAACACCTTCCAT 58.530 33.333 0.00 0.00 0.00 3.41
3246 3771 1.544537 CGTGGATCCAGTTTTCCCACA 60.545 52.381 16.81 0.00 45.52 4.17


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

AutoCloner maintained by Alex Coulton.