Multiple sequence alignment - TraesCS2D01G411400

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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 TraesCS2D01G411400 chr2D 100.000 2382 0 0 522 2903 526344798 526347179 0.000000e+00 4399
1 TraesCS2D01G411400 chr2D 100.000 169 0 0 1 169 526344277 526344445 2.170000e-81 313
2 TraesCS2D01G411400 chr2A 92.073 2460 82 32 525 2903 671281754 671284181 0.000000e+00 3358
3 TraesCS2D01G411400 chr2B 93.257 1572 53 21 525 2059 622656570 622658125 0.000000e+00 2266
4 TraesCS2D01G411400 chr2B 95.609 797 23 2 2107 2903 622673325 622674109 0.000000e+00 1267
5 TraesCS2D01G411400 chr6B 81.720 930 135 28 1001 1904 497216751 497215831 0.000000e+00 743
6 TraesCS2D01G411400 chr6B 81.325 166 28 3 2 166 707617343 707617180 6.530000e-27 132
7 TraesCS2D01G411400 chr6B 80.838 167 27 3 2 166 715074888 715074725 3.040000e-25 126
8 TraesCS2D01G411400 chr6D 85.634 710 86 12 1204 1901 325755903 325756608 0.000000e+00 732
9 TraesCS2D01G411400 chr6D 89.922 129 13 0 1001 1129 325755666 325755794 1.790000e-37 167
10 TraesCS2D01G411400 chr6A 85.112 712 89 13 1204 1901 464538143 464538851 0.000000e+00 712
11 TraesCS2D01G411400 chr6A 91.473 129 11 0 1001 1129 464537913 464538041 8.270000e-41 178
12 TraesCS2D01G411400 chr7D 85.870 276 39 0 1574 1849 433876570 433876845 7.870000e-76 294
13 TraesCS2D01G411400 chr7D 82.278 158 25 3 2 158 45887454 45887609 1.810000e-27 134
14 TraesCS2D01G411400 chr7D 81.325 166 28 3 2 166 1019826 1019663 6.530000e-27 132
15 TraesCS2D01G411400 chr7B 84.828 290 44 0 1574 1863 451289912 451290201 2.830000e-75 292
16 TraesCS2D01G411400 chr7A 85.612 278 40 0 1572 1849 484525275 484525552 2.830000e-75 292
17 TraesCS2D01G411400 chr3B 80.435 276 46 6 1579 1850 826725618 826725889 1.360000e-48 204
18 TraesCS2D01G411400 chr3B 82.911 158 24 3 2 158 804395177 804395022 3.900000e-29 139
19 TraesCS2D01G411400 chr4A 83.544 158 23 2 2 158 124811262 124811417 8.380000e-31 145
20 TraesCS2D01G411400 chr4B 82.278 158 25 3 2 158 27271889 27272044 1.810000e-27 134
21 TraesCS2D01G411400 chr1B 82.278 158 25 3 2 158 545278688 545278533 1.810000e-27 134
22 TraesCS2D01G411400 chr1A 82.550 149 23 3 11 158 458533280 458533134 8.440000e-26 128


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 TraesCS2D01G411400 chr2D 526344277 526347179 2902 False 2356.0 4399 100.0000 1 2903 2 chr2D.!!$F1 2902
1 TraesCS2D01G411400 chr2A 671281754 671284181 2427 False 3358.0 3358 92.0730 525 2903 1 chr2A.!!$F1 2378
2 TraesCS2D01G411400 chr2B 622656570 622658125 1555 False 2266.0 2266 93.2570 525 2059 1 chr2B.!!$F1 1534
3 TraesCS2D01G411400 chr2B 622673325 622674109 784 False 1267.0 1267 95.6090 2107 2903 1 chr2B.!!$F2 796
4 TraesCS2D01G411400 chr6B 497215831 497216751 920 True 743.0 743 81.7200 1001 1904 1 chr6B.!!$R1 903
5 TraesCS2D01G411400 chr6D 325755666 325756608 942 False 449.5 732 87.7780 1001 1901 2 chr6D.!!$F1 900
6 TraesCS2D01G411400 chr6A 464537913 464538851 938 False 445.0 712 88.2925 1001 1901 2 chr6A.!!$F1 900

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
89 90 0.037326 TTCGATTCGCTCCAGTGCTT 60.037 50.0 0.0 0.0 0.0 3.91 F
116 117 0.182061 TCGCTAGGTGGTCTACGGAT 59.818 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1673 1.372748 GATCTCGCTGATGCCGGAG 60.373 63.158 5.05 0.0 35.14 4.63 R
2065 2202 1.674322 CGGGCCTCCACGAATTTGT 60.674 57.895 0.84 0.0 0.00 2.83 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
21 22 4.644103 GCTTCCCGTGTGTCTACTATAA 57.356 45.455 0.00 0.00 0.00 0.98
22 23 5.197682 GCTTCCCGTGTGTCTACTATAAT 57.802 43.478 0.00 0.00 0.00 1.28
23 24 6.323203 GCTTCCCGTGTGTCTACTATAATA 57.677 41.667 0.00 0.00 0.00 0.98
24 25 6.742109 GCTTCCCGTGTGTCTACTATAATAA 58.258 40.000 0.00 0.00 0.00 1.40
25 26 6.862090 GCTTCCCGTGTGTCTACTATAATAAG 59.138 42.308 0.00 0.00 0.00 1.73
26 27 7.469732 GCTTCCCGTGTGTCTACTATAATAAGT 60.470 40.741 0.00 0.00 0.00 2.24
27 28 7.886629 TCCCGTGTGTCTACTATAATAAGTT 57.113 36.000 0.00 0.00 0.00 2.66
28 29 8.297470 TCCCGTGTGTCTACTATAATAAGTTT 57.703 34.615 0.00 0.00 0.00 2.66
29 30 8.752187 TCCCGTGTGTCTACTATAATAAGTTTT 58.248 33.333 0.00 0.00 0.00 2.43
30 31 8.814235 CCCGTGTGTCTACTATAATAAGTTTTG 58.186 37.037 0.00 0.00 0.00 2.44
31 32 8.325997 CCGTGTGTCTACTATAATAAGTTTTGC 58.674 37.037 0.00 0.00 0.00 3.68
32 33 8.325997 CGTGTGTCTACTATAATAAGTTTTGCC 58.674 37.037 0.00 0.00 0.00 4.52
33 34 9.379791 GTGTGTCTACTATAATAAGTTTTGCCT 57.620 33.333 0.00 0.00 0.00 4.75
34 35 9.953565 TGTGTCTACTATAATAAGTTTTGCCTT 57.046 29.630 0.00 0.00 0.00 4.35
36 37 8.889717 TGTCTACTATAATAAGTTTTGCCTTGC 58.110 33.333 0.00 0.00 0.00 4.01
37 38 9.110502 GTCTACTATAATAAGTTTTGCCTTGCT 57.889 33.333 0.00 0.00 0.00 3.91
38 39 9.326413 TCTACTATAATAAGTTTTGCCTTGCTC 57.674 33.333 0.00 0.00 0.00 4.26
39 40 7.334844 ACTATAATAAGTTTTGCCTTGCTCC 57.665 36.000 0.00 0.00 0.00 4.70
40 41 3.575965 AATAAGTTTTGCCTTGCTCCG 57.424 42.857 0.00 0.00 0.00 4.63
41 42 2.264005 TAAGTTTTGCCTTGCTCCGA 57.736 45.000 0.00 0.00 0.00 4.55
42 43 1.398692 AAGTTTTGCCTTGCTCCGAA 58.601 45.000 0.00 0.00 0.00 4.30
43 44 0.668535 AGTTTTGCCTTGCTCCGAAC 59.331 50.000 0.00 0.00 0.00 3.95
44 45 0.660300 GTTTTGCCTTGCTCCGAACG 60.660 55.000 0.00 0.00 0.00 3.95
45 46 1.791103 TTTTGCCTTGCTCCGAACGG 61.791 55.000 6.94 6.94 0.00 4.44
46 47 4.697756 TGCCTTGCTCCGAACGGG 62.698 66.667 13.29 5.52 35.59 5.28
47 48 4.388499 GCCTTGCTCCGAACGGGA 62.388 66.667 13.29 0.00 44.68 5.14
54 55 4.304413 TCCGAACGGGAGGGGTGA 62.304 66.667 13.29 0.00 40.94 4.02
55 56 4.078516 CCGAACGGGAGGGGTGAC 62.079 72.222 5.25 0.00 38.47 3.67
56 57 4.430765 CGAACGGGAGGGGTGACG 62.431 72.222 0.00 0.00 0.00 4.35
57 58 2.993264 GAACGGGAGGGGTGACGA 60.993 66.667 0.00 0.00 0.00 4.20
58 59 2.284405 AACGGGAGGGGTGACGAT 60.284 61.111 0.00 0.00 0.00 3.73
59 60 1.000739 AACGGGAGGGGTGACGATA 59.999 57.895 0.00 0.00 0.00 2.92
60 61 1.041447 AACGGGAGGGGTGACGATAG 61.041 60.000 0.00 0.00 46.19 2.08
61 62 2.857744 CGGGAGGGGTGACGATAGC 61.858 68.421 0.00 0.00 42.67 2.97
62 63 2.728817 GGAGGGGTGACGATAGCG 59.271 66.667 0.00 0.00 44.79 4.26
63 64 2.728817 GAGGGGTGACGATAGCGG 59.271 66.667 4.97 0.00 43.17 5.52
79 80 2.695646 GGCACGTCTTCGATTCGC 59.304 61.111 0.00 0.00 40.62 4.70
80 81 1.805945 GGCACGTCTTCGATTCGCT 60.806 57.895 0.00 0.00 40.62 4.93
81 82 1.626388 GCACGTCTTCGATTCGCTC 59.374 57.895 0.00 0.00 40.62 5.03
82 83 1.743855 GCACGTCTTCGATTCGCTCC 61.744 60.000 0.00 0.00 40.62 4.70
83 84 0.456142 CACGTCTTCGATTCGCTCCA 60.456 55.000 0.00 0.00 40.62 3.86
84 85 0.179161 ACGTCTTCGATTCGCTCCAG 60.179 55.000 0.00 0.00 40.62 3.86
85 86 0.179161 CGTCTTCGATTCGCTCCAGT 60.179 55.000 0.00 0.00 39.71 4.00
86 87 1.272781 GTCTTCGATTCGCTCCAGTG 58.727 55.000 0.00 0.00 0.00 3.66
87 88 0.458543 TCTTCGATTCGCTCCAGTGC 60.459 55.000 0.00 0.00 0.00 4.40
88 89 0.459237 CTTCGATTCGCTCCAGTGCT 60.459 55.000 0.00 0.00 0.00 4.40
89 90 0.037326 TTCGATTCGCTCCAGTGCTT 60.037 50.000 0.00 0.00 0.00 3.91
90 91 0.815095 TCGATTCGCTCCAGTGCTTA 59.185 50.000 0.00 0.00 0.00 3.09
91 92 1.409064 TCGATTCGCTCCAGTGCTTAT 59.591 47.619 0.00 0.00 0.00 1.73
92 93 2.621526 TCGATTCGCTCCAGTGCTTATA 59.378 45.455 0.00 0.00 0.00 0.98
93 94 3.255888 TCGATTCGCTCCAGTGCTTATAT 59.744 43.478 0.00 0.00 0.00 0.86
94 95 3.990469 CGATTCGCTCCAGTGCTTATATT 59.010 43.478 0.00 0.00 0.00 1.28
95 96 4.090642 CGATTCGCTCCAGTGCTTATATTC 59.909 45.833 0.00 0.00 0.00 1.75
96 97 3.013276 TCGCTCCAGTGCTTATATTCG 57.987 47.619 0.00 0.00 0.00 3.34
97 98 2.361119 TCGCTCCAGTGCTTATATTCGT 59.639 45.455 0.00 0.00 0.00 3.85
98 99 2.726760 CGCTCCAGTGCTTATATTCGTC 59.273 50.000 0.00 0.00 0.00 4.20
99 100 2.726760 GCTCCAGTGCTTATATTCGTCG 59.273 50.000 0.00 0.00 0.00 5.12
100 101 2.726760 CTCCAGTGCTTATATTCGTCGC 59.273 50.000 0.00 0.00 0.00 5.19
101 102 2.361119 TCCAGTGCTTATATTCGTCGCT 59.639 45.455 0.00 0.00 0.00 4.93
102 103 3.566742 TCCAGTGCTTATATTCGTCGCTA 59.433 43.478 0.00 0.00 0.00 4.26
103 104 3.914966 CCAGTGCTTATATTCGTCGCTAG 59.085 47.826 0.00 0.00 0.00 3.42
104 105 3.914966 CAGTGCTTATATTCGTCGCTAGG 59.085 47.826 0.00 0.00 0.00 3.02
105 106 3.568853 AGTGCTTATATTCGTCGCTAGGT 59.431 43.478 0.00 0.00 0.00 3.08
106 107 3.669122 GTGCTTATATTCGTCGCTAGGTG 59.331 47.826 0.00 0.00 0.00 4.00
107 108 3.243336 GCTTATATTCGTCGCTAGGTGG 58.757 50.000 0.00 0.00 0.00 4.61
108 109 3.305199 GCTTATATTCGTCGCTAGGTGGT 60.305 47.826 0.00 0.00 0.00 4.16
109 110 4.474113 CTTATATTCGTCGCTAGGTGGTC 58.526 47.826 0.00 0.00 0.00 4.02
110 111 2.048444 TATTCGTCGCTAGGTGGTCT 57.952 50.000 0.00 0.00 0.00 3.85
111 112 2.048444 ATTCGTCGCTAGGTGGTCTA 57.952 50.000 0.00 0.00 0.00 2.59
112 113 1.089920 TTCGTCGCTAGGTGGTCTAC 58.910 55.000 0.00 0.00 0.00 2.59
113 114 1.086067 TCGTCGCTAGGTGGTCTACG 61.086 60.000 0.00 0.00 0.00 3.51
114 115 1.726265 GTCGCTAGGTGGTCTACGG 59.274 63.158 0.00 0.00 0.00 4.02
115 116 0.745845 GTCGCTAGGTGGTCTACGGA 60.746 60.000 0.00 0.00 0.00 4.69
116 117 0.182061 TCGCTAGGTGGTCTACGGAT 59.818 55.000 0.00 0.00 0.00 4.18
117 118 0.592148 CGCTAGGTGGTCTACGGATC 59.408 60.000 0.00 0.00 0.00 3.36
118 119 1.814634 CGCTAGGTGGTCTACGGATCT 60.815 57.143 0.00 0.00 0.00 2.75
119 120 1.609555 GCTAGGTGGTCTACGGATCTG 59.390 57.143 0.00 0.00 0.00 2.90
120 121 2.748798 GCTAGGTGGTCTACGGATCTGA 60.749 54.545 9.00 0.00 0.00 3.27
121 122 2.526888 AGGTGGTCTACGGATCTGAA 57.473 50.000 9.00 0.00 0.00 3.02
122 123 3.033659 AGGTGGTCTACGGATCTGAAT 57.966 47.619 9.00 0.00 0.00 2.57
123 124 2.695666 AGGTGGTCTACGGATCTGAATG 59.304 50.000 9.00 0.00 0.00 2.67
124 125 2.431057 GGTGGTCTACGGATCTGAATGT 59.569 50.000 9.00 0.00 0.00 2.71
125 126 3.635373 GGTGGTCTACGGATCTGAATGTA 59.365 47.826 9.00 0.00 0.00 2.29
126 127 4.098960 GGTGGTCTACGGATCTGAATGTAA 59.901 45.833 9.00 0.00 0.00 2.41
127 128 5.282510 GTGGTCTACGGATCTGAATGTAAG 58.717 45.833 9.00 0.00 0.00 2.34
128 129 4.954202 TGGTCTACGGATCTGAATGTAAGT 59.046 41.667 9.00 0.00 0.00 2.24
129 130 5.421056 TGGTCTACGGATCTGAATGTAAGTT 59.579 40.000 9.00 0.00 0.00 2.66
130 131 6.070995 TGGTCTACGGATCTGAATGTAAGTTT 60.071 38.462 9.00 0.00 0.00 2.66
131 132 6.817140 GGTCTACGGATCTGAATGTAAGTTTT 59.183 38.462 9.00 0.00 0.00 2.43
132 133 7.010275 GGTCTACGGATCTGAATGTAAGTTTTC 59.990 40.741 9.00 0.00 0.00 2.29
133 134 7.760340 GTCTACGGATCTGAATGTAAGTTTTCT 59.240 37.037 9.00 0.00 0.00 2.52
134 135 8.311836 TCTACGGATCTGAATGTAAGTTTTCTT 58.688 33.333 9.00 0.00 43.24 2.52
135 136 7.745620 ACGGATCTGAATGTAAGTTTTCTTT 57.254 32.000 9.00 0.00 40.91 2.52
136 137 8.166422 ACGGATCTGAATGTAAGTTTTCTTTT 57.834 30.769 9.00 0.00 40.91 2.27
137 138 9.280174 ACGGATCTGAATGTAAGTTTTCTTTTA 57.720 29.630 9.00 0.00 40.91 1.52
138 139 9.543018 CGGATCTGAATGTAAGTTTTCTTTTAC 57.457 33.333 0.00 0.00 40.91 2.01
163 164 9.429359 ACTTCTATTGTTCTTTGTACTGAGATG 57.571 33.333 0.00 0.00 0.00 2.90
164 165 9.645059 CTTCTATTGTTCTTTGTACTGAGATGA 57.355 33.333 0.00 0.00 0.00 2.92
166 167 9.591792 TCTATTGTTCTTTGTACTGAGATGATG 57.408 33.333 0.00 0.00 0.00 3.07
167 168 6.486253 TTGTTCTTTGTACTGAGATGATGC 57.514 37.500 0.00 0.00 0.00 3.91
168 169 5.798132 TGTTCTTTGTACTGAGATGATGCT 58.202 37.500 0.00 0.00 0.00 3.79
591 595 5.446143 TTTCAATAAACGCAAGGACACAT 57.554 34.783 0.00 0.00 46.39 3.21
882 904 1.884464 CATCGGTGCCATCTCACGG 60.884 63.158 0.00 0.00 37.83 4.94
948 970 3.694072 AGTACTGTGATCAGAGCAGAGTC 59.306 47.826 20.88 12.88 43.76 3.36
972 994 3.971245 ACTCTTTAGCCTGAAGACCTG 57.029 47.619 0.00 0.00 0.00 4.00
973 995 3.511477 ACTCTTTAGCCTGAAGACCTGA 58.489 45.455 0.00 0.00 0.00 3.86
975 997 4.161377 ACTCTTTAGCCTGAAGACCTGATC 59.839 45.833 0.00 0.00 0.00 2.92
976 998 4.096681 TCTTTAGCCTGAAGACCTGATCA 58.903 43.478 0.00 0.00 0.00 2.92
977 999 3.895232 TTAGCCTGAAGACCTGATCAC 57.105 47.619 0.00 0.00 0.00 3.06
978 1000 1.649321 AGCCTGAAGACCTGATCACA 58.351 50.000 0.00 0.00 0.00 3.58
1527 1646 7.394816 ACAAGTACTCACTGGCTTTTATGTAT 58.605 34.615 0.00 0.00 34.36 2.29
1570 1692 2.440247 TCTCCGGCATCAGCGAGA 60.440 61.111 0.00 0.00 43.41 4.04
1931 2063 2.170817 GGATCCGAACCTAGCTTCCTTT 59.829 50.000 0.00 0.00 0.00 3.11
1942 2075 0.110010 GCTTCCTTTCTCGTTGCTGC 60.110 55.000 0.00 0.00 0.00 5.25
1947 2080 0.164647 CTTTCTCGTTGCTGCTTCCG 59.835 55.000 0.00 0.39 0.00 4.30
1975 2108 7.717568 TGTGTGAATTTCCCTTTTCGATTTTA 58.282 30.769 0.00 0.00 0.00 1.52
1976 2109 8.198109 TGTGTGAATTTCCCTTTTCGATTTTAA 58.802 29.630 0.00 0.00 0.00 1.52
1977 2110 9.203421 GTGTGAATTTCCCTTTTCGATTTTAAT 57.797 29.630 0.00 0.00 0.00 1.40
1978 2111 9.771534 TGTGAATTTCCCTTTTCGATTTTAATT 57.228 25.926 0.00 0.00 0.00 1.40
1993 2126 9.893634 TCGATTTTAATTTACAGAATCCACCTA 57.106 29.630 0.00 0.00 0.00 3.08
2059 2196 3.549221 GGTTCTGCGTTTTTCCGAAATCA 60.549 43.478 0.00 0.00 0.00 2.57
2065 2202 3.978217 GCGTTTTTCCGAAATCATTGTGA 59.022 39.130 0.00 0.00 0.00 3.58
2082 2219 0.608035 TGACAAATTCGTGGAGGCCC 60.608 55.000 0.00 0.00 0.00 5.80
2084 2221 1.674322 CAAATTCGTGGAGGCCCGT 60.674 57.895 0.00 0.00 34.29 5.28
2085 2222 1.074248 AAATTCGTGGAGGCCCGTT 59.926 52.632 0.00 0.00 34.29 4.44
2086 2223 1.241315 AAATTCGTGGAGGCCCGTTG 61.241 55.000 0.00 0.00 34.29 4.10
2135 2293 3.122971 GGAAACTACCGTGGCGCC 61.123 66.667 22.73 22.73 0.00 6.53
2213 2371 1.649321 ACTCCTCAGCAGTTCATCCA 58.351 50.000 0.00 0.00 0.00 3.41
2229 2387 1.559368 TCCATGCAAATTCCCCTGTG 58.441 50.000 0.00 0.00 0.00 3.66
2496 2655 1.074319 TACTAACCGCGCGCTTCTTG 61.074 55.000 30.48 17.94 0.00 3.02
2693 2852 4.404098 GGTGTCCCGACCGCCATT 62.404 66.667 0.00 0.00 0.00 3.16
2781 2940 1.365699 CCAGGTACGTGCATTACCAC 58.634 55.000 22.83 4.76 41.48 4.16
2798 2957 1.069204 CCACCGATCGATCACTTCCAT 59.931 52.381 24.40 0.00 0.00 3.41
2809 2976 7.361457 TCGATCACTTCCATTATTCCTAGTT 57.639 36.000 0.00 0.00 0.00 2.24
2850 3017 0.865111 CCCGTGTGTGTGTGTATGTG 59.135 55.000 0.00 0.00 0.00 3.21
2854 3021 3.117046 CGTGTGTGTGTGTATGTGTGTA 58.883 45.455 0.00 0.00 0.00 2.90
2856 3023 4.143410 CGTGTGTGTGTGTATGTGTGTATC 60.143 45.833 0.00 0.00 0.00 2.24
2858 3025 4.987912 TGTGTGTGTGTATGTGTGTATCTG 59.012 41.667 0.00 0.00 0.00 2.90
2864 3031 2.501316 TGTATGTGTGTATCTGCAGGCT 59.499 45.455 15.13 4.32 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.644103 TTATAGTAGACACACGGGAAGC 57.356 45.455 0.00 0.00 0.00 3.86
1 2 7.938715 ACTTATTATAGTAGACACACGGGAAG 58.061 38.462 0.00 0.00 0.00 3.46
2 3 7.886629 ACTTATTATAGTAGACACACGGGAA 57.113 36.000 0.00 0.00 0.00 3.97
3 4 7.886629 AACTTATTATAGTAGACACACGGGA 57.113 36.000 0.00 0.00 0.00 5.14
4 5 8.814235 CAAAACTTATTATAGTAGACACACGGG 58.186 37.037 0.00 0.00 0.00 5.28
5 6 8.325997 GCAAAACTTATTATAGTAGACACACGG 58.674 37.037 0.00 0.00 0.00 4.94
6 7 8.325997 GGCAAAACTTATTATAGTAGACACACG 58.674 37.037 0.00 0.00 0.00 4.49
7 8 9.379791 AGGCAAAACTTATTATAGTAGACACAC 57.620 33.333 0.00 0.00 0.00 3.82
8 9 9.953565 AAGGCAAAACTTATTATAGTAGACACA 57.046 29.630 0.00 0.00 0.00 3.72
10 11 8.889717 GCAAGGCAAAACTTATTATAGTAGACA 58.110 33.333 0.00 0.00 0.00 3.41
11 12 9.110502 AGCAAGGCAAAACTTATTATAGTAGAC 57.889 33.333 0.00 0.00 0.00 2.59
12 13 9.326413 GAGCAAGGCAAAACTTATTATAGTAGA 57.674 33.333 0.00 0.00 0.00 2.59
13 14 8.560374 GGAGCAAGGCAAAACTTATTATAGTAG 58.440 37.037 0.00 0.00 0.00 2.57
14 15 7.225931 CGGAGCAAGGCAAAACTTATTATAGTA 59.774 37.037 0.00 0.00 0.00 1.82
15 16 6.038271 CGGAGCAAGGCAAAACTTATTATAGT 59.962 38.462 0.00 0.00 0.00 2.12
16 17 6.260050 TCGGAGCAAGGCAAAACTTATTATAG 59.740 38.462 0.00 0.00 0.00 1.31
17 18 6.116806 TCGGAGCAAGGCAAAACTTATTATA 58.883 36.000 0.00 0.00 0.00 0.98
18 19 4.947388 TCGGAGCAAGGCAAAACTTATTAT 59.053 37.500 0.00 0.00 0.00 1.28
19 20 4.328536 TCGGAGCAAGGCAAAACTTATTA 58.671 39.130 0.00 0.00 0.00 0.98
20 21 3.153919 TCGGAGCAAGGCAAAACTTATT 58.846 40.909 0.00 0.00 0.00 1.40
21 22 2.790433 TCGGAGCAAGGCAAAACTTAT 58.210 42.857 0.00 0.00 0.00 1.73
22 23 2.264005 TCGGAGCAAGGCAAAACTTA 57.736 45.000 0.00 0.00 0.00 2.24
23 24 1.067060 GTTCGGAGCAAGGCAAAACTT 59.933 47.619 0.00 0.00 0.00 2.66
24 25 0.668535 GTTCGGAGCAAGGCAAAACT 59.331 50.000 0.00 0.00 0.00 2.66
25 26 0.660300 CGTTCGGAGCAAGGCAAAAC 60.660 55.000 0.00 0.00 0.00 2.43
26 27 1.652012 CGTTCGGAGCAAGGCAAAA 59.348 52.632 0.00 0.00 0.00 2.44
27 28 2.258013 CCGTTCGGAGCAAGGCAAA 61.258 57.895 5.19 0.00 0.00 3.68
28 29 2.668212 CCGTTCGGAGCAAGGCAA 60.668 61.111 5.19 0.00 0.00 4.52
29 30 4.697756 CCCGTTCGGAGCAAGGCA 62.698 66.667 13.08 0.00 0.00 4.75
30 31 4.388499 TCCCGTTCGGAGCAAGGC 62.388 66.667 13.08 0.00 34.86 4.35
37 38 4.304413 TCACCCCTCCCGTTCGGA 62.304 66.667 13.08 0.00 38.83 4.55
38 39 4.078516 GTCACCCCTCCCGTTCGG 62.079 72.222 4.08 4.08 0.00 4.30
39 40 4.430765 CGTCACCCCTCCCGTTCG 62.431 72.222 0.00 0.00 0.00 3.95
40 41 1.039233 TATCGTCACCCCTCCCGTTC 61.039 60.000 0.00 0.00 0.00 3.95
41 42 1.000739 TATCGTCACCCCTCCCGTT 59.999 57.895 0.00 0.00 0.00 4.44
42 43 1.455217 CTATCGTCACCCCTCCCGT 60.455 63.158 0.00 0.00 0.00 5.28
43 44 2.857744 GCTATCGTCACCCCTCCCG 61.858 68.421 0.00 0.00 0.00 5.14
44 45 2.857744 CGCTATCGTCACCCCTCCC 61.858 68.421 0.00 0.00 0.00 4.30
45 46 2.728817 CGCTATCGTCACCCCTCC 59.271 66.667 0.00 0.00 0.00 4.30
46 47 2.728817 CCGCTATCGTCACCCCTC 59.271 66.667 0.00 0.00 0.00 4.30
47 48 3.537874 GCCGCTATCGTCACCCCT 61.538 66.667 0.00 0.00 0.00 4.79
48 49 3.845259 TGCCGCTATCGTCACCCC 61.845 66.667 0.00 0.00 0.00 4.95
49 50 2.585247 GTGCCGCTATCGTCACCC 60.585 66.667 0.00 0.00 38.49 4.61
50 51 2.954868 CGTGCCGCTATCGTCACC 60.955 66.667 0.00 0.00 41.01 4.02
51 52 2.202570 ACGTGCCGCTATCGTCAC 60.203 61.111 0.00 0.00 40.72 3.67
54 55 1.226603 GAAGACGTGCCGCTATCGT 60.227 57.895 0.00 8.11 40.49 3.73
55 56 2.286559 CGAAGACGTGCCGCTATCG 61.287 63.158 0.00 0.00 34.56 2.92
56 57 0.317938 ATCGAAGACGTGCCGCTATC 60.318 55.000 0.00 0.00 42.51 2.08
57 58 0.102481 AATCGAAGACGTGCCGCTAT 59.898 50.000 0.00 0.00 42.51 2.97
58 59 0.524816 GAATCGAAGACGTGCCGCTA 60.525 55.000 0.00 0.00 42.51 4.26
59 60 1.805945 GAATCGAAGACGTGCCGCT 60.806 57.895 0.00 0.00 42.51 5.52
60 61 2.695646 GAATCGAAGACGTGCCGC 59.304 61.111 0.00 0.00 42.51 6.53
61 62 2.987593 CGAATCGAAGACGTGCCG 59.012 61.111 0.00 0.00 42.51 5.69
62 63 1.743855 GAGCGAATCGAAGACGTGCC 61.744 60.000 6.91 0.00 42.51 5.01
63 64 1.626388 GAGCGAATCGAAGACGTGC 59.374 57.895 6.91 0.00 42.51 5.34
64 65 0.456142 TGGAGCGAATCGAAGACGTG 60.456 55.000 6.91 0.00 42.51 4.49
65 66 0.179161 CTGGAGCGAATCGAAGACGT 60.179 55.000 6.91 0.00 42.51 4.34
66 67 0.179161 ACTGGAGCGAATCGAAGACG 60.179 55.000 6.91 0.00 42.51 4.18
67 68 1.272781 CACTGGAGCGAATCGAAGAC 58.727 55.000 6.91 0.00 42.51 3.01
68 69 0.458543 GCACTGGAGCGAATCGAAGA 60.459 55.000 6.91 0.00 45.75 2.87
69 70 0.459237 AGCACTGGAGCGAATCGAAG 60.459 55.000 6.91 0.03 40.15 3.79
70 71 0.037326 AAGCACTGGAGCGAATCGAA 60.037 50.000 6.91 0.00 40.15 3.71
71 72 0.815095 TAAGCACTGGAGCGAATCGA 59.185 50.000 6.91 0.00 40.15 3.59
72 73 1.858091 ATAAGCACTGGAGCGAATCG 58.142 50.000 0.00 0.00 40.15 3.34
73 74 4.090642 CGAATATAAGCACTGGAGCGAATC 59.909 45.833 0.00 0.00 40.15 2.52
74 75 3.990469 CGAATATAAGCACTGGAGCGAAT 59.010 43.478 0.00 0.00 40.15 3.34
75 76 3.181479 ACGAATATAAGCACTGGAGCGAA 60.181 43.478 0.00 0.00 40.15 4.70
76 77 2.361119 ACGAATATAAGCACTGGAGCGA 59.639 45.455 0.00 0.00 40.15 4.93
77 78 2.726760 GACGAATATAAGCACTGGAGCG 59.273 50.000 0.00 0.00 40.15 5.03
78 79 2.726760 CGACGAATATAAGCACTGGAGC 59.273 50.000 0.00 0.00 0.00 4.70
79 80 2.726760 GCGACGAATATAAGCACTGGAG 59.273 50.000 0.00 0.00 0.00 3.86
80 81 2.361119 AGCGACGAATATAAGCACTGGA 59.639 45.455 0.00 0.00 0.00 3.86
81 82 2.743938 AGCGACGAATATAAGCACTGG 58.256 47.619 0.00 0.00 0.00 4.00
82 83 3.914966 CCTAGCGACGAATATAAGCACTG 59.085 47.826 0.00 0.00 0.00 3.66
83 84 3.568853 ACCTAGCGACGAATATAAGCACT 59.431 43.478 0.00 0.00 0.00 4.40
84 85 3.669122 CACCTAGCGACGAATATAAGCAC 59.331 47.826 0.00 0.00 0.00 4.40
85 86 3.305131 CCACCTAGCGACGAATATAAGCA 60.305 47.826 0.00 0.00 0.00 3.91
86 87 3.243336 CCACCTAGCGACGAATATAAGC 58.757 50.000 0.00 0.00 0.00 3.09
87 88 4.215827 AGACCACCTAGCGACGAATATAAG 59.784 45.833 0.00 0.00 0.00 1.73
88 89 4.139786 AGACCACCTAGCGACGAATATAA 58.860 43.478 0.00 0.00 0.00 0.98
89 90 3.748083 AGACCACCTAGCGACGAATATA 58.252 45.455 0.00 0.00 0.00 0.86
90 91 2.584236 AGACCACCTAGCGACGAATAT 58.416 47.619 0.00 0.00 0.00 1.28
91 92 2.048444 AGACCACCTAGCGACGAATA 57.952 50.000 0.00 0.00 0.00 1.75
92 93 1.674962 GTAGACCACCTAGCGACGAAT 59.325 52.381 0.00 0.00 0.00 3.34
93 94 1.089920 GTAGACCACCTAGCGACGAA 58.910 55.000 0.00 0.00 0.00 3.85
94 95 1.086067 CGTAGACCACCTAGCGACGA 61.086 60.000 0.00 0.00 0.00 4.20
95 96 1.351012 CGTAGACCACCTAGCGACG 59.649 63.158 0.00 0.00 0.00 5.12
96 97 0.745845 TCCGTAGACCACCTAGCGAC 60.746 60.000 0.00 0.00 0.00 5.19
97 98 0.182061 ATCCGTAGACCACCTAGCGA 59.818 55.000 0.00 0.00 0.00 4.93
98 99 0.592148 GATCCGTAGACCACCTAGCG 59.408 60.000 0.00 0.00 0.00 4.26
99 100 1.609555 CAGATCCGTAGACCACCTAGC 59.390 57.143 0.00 0.00 0.00 3.42
100 101 3.210232 TCAGATCCGTAGACCACCTAG 57.790 52.381 0.00 0.00 0.00 3.02
101 102 3.657398 TTCAGATCCGTAGACCACCTA 57.343 47.619 0.00 0.00 0.00 3.08
102 103 2.526888 TTCAGATCCGTAGACCACCT 57.473 50.000 0.00 0.00 0.00 4.00
103 104 2.431057 ACATTCAGATCCGTAGACCACC 59.569 50.000 0.00 0.00 0.00 4.61
104 105 3.802948 ACATTCAGATCCGTAGACCAC 57.197 47.619 0.00 0.00 0.00 4.16
105 106 4.954202 ACTTACATTCAGATCCGTAGACCA 59.046 41.667 0.00 0.00 0.00 4.02
106 107 5.517322 ACTTACATTCAGATCCGTAGACC 57.483 43.478 0.00 0.00 0.00 3.85
107 108 7.760340 AGAAAACTTACATTCAGATCCGTAGAC 59.240 37.037 0.00 0.00 0.00 2.59
108 109 7.837863 AGAAAACTTACATTCAGATCCGTAGA 58.162 34.615 0.00 0.00 0.00 2.59
109 110 8.480643 AAGAAAACTTACATTCAGATCCGTAG 57.519 34.615 0.00 0.00 0.00 3.51
110 111 8.842358 AAAGAAAACTTACATTCAGATCCGTA 57.158 30.769 0.00 0.00 0.00 4.02
111 112 7.745620 AAAGAAAACTTACATTCAGATCCGT 57.254 32.000 0.00 0.00 0.00 4.69
112 113 9.543018 GTAAAAGAAAACTTACATTCAGATCCG 57.457 33.333 0.00 0.00 0.00 4.18
137 138 9.429359 CATCTCAGTACAAAGAACAATAGAAGT 57.571 33.333 0.00 0.00 0.00 3.01
138 139 9.645059 TCATCTCAGTACAAAGAACAATAGAAG 57.355 33.333 0.00 0.00 0.00 2.85
140 141 9.591792 CATCATCTCAGTACAAAGAACAATAGA 57.408 33.333 0.00 0.00 0.00 1.98
141 142 8.333908 GCATCATCTCAGTACAAAGAACAATAG 58.666 37.037 0.00 0.00 0.00 1.73
142 143 8.043113 AGCATCATCTCAGTACAAAGAACAATA 58.957 33.333 0.00 0.00 0.00 1.90
143 144 6.883217 AGCATCATCTCAGTACAAAGAACAAT 59.117 34.615 0.00 0.00 0.00 2.71
144 145 6.233434 AGCATCATCTCAGTACAAAGAACAA 58.767 36.000 0.00 0.00 0.00 2.83
145 146 5.798132 AGCATCATCTCAGTACAAAGAACA 58.202 37.500 0.00 0.00 0.00 3.18
591 595 7.334421 GCTGATGAACTGTTTTCTATGTAAGGA 59.666 37.037 0.00 0.00 0.00 3.36
684 689 0.940126 GCAGGAGCCACGTTATGATG 59.060 55.000 0.00 0.00 33.58 3.07
868 890 1.045407 TATACCCGTGAGATGGCACC 58.955 55.000 0.00 0.00 35.37 5.01
882 904 7.023197 TCTAATTTGGCGCTCTTTTTATACC 57.977 36.000 7.64 0.00 0.00 2.73
948 970 3.254892 GTCTTCAGGCTAAAGAGTTCGG 58.745 50.000 0.00 0.00 33.57 4.30
972 994 4.384247 CACTCGACTGTTTTCTCTGTGATC 59.616 45.833 0.00 0.00 0.00 2.92
973 995 4.302455 CACTCGACTGTTTTCTCTGTGAT 58.698 43.478 0.00 0.00 0.00 3.06
975 997 2.219674 GCACTCGACTGTTTTCTCTGTG 59.780 50.000 0.00 0.00 0.00 3.66
976 998 2.159099 TGCACTCGACTGTTTTCTCTGT 60.159 45.455 0.00 0.00 0.00 3.41
977 999 2.473816 TGCACTCGACTGTTTTCTCTG 58.526 47.619 0.00 0.00 0.00 3.35
978 1000 2.890808 TGCACTCGACTGTTTTCTCT 57.109 45.000 0.00 0.00 0.00 3.10
1554 1673 1.372748 GATCTCGCTGATGCCGGAG 60.373 63.158 5.05 0.00 35.14 4.63
1570 1692 2.501128 CATCACCACGCCCTCGAT 59.499 61.111 0.00 0.00 39.41 3.59
1942 2075 2.351738 GGGAAATTCACACAAGCGGAAG 60.352 50.000 0.00 0.00 0.00 3.46
1947 2080 3.735746 CGAAAAGGGAAATTCACACAAGC 59.264 43.478 0.00 0.00 0.00 4.01
2016 2153 2.535984 CGTTCATGTAAGATCGAGTGGC 59.464 50.000 0.00 0.00 33.72 5.01
2059 2196 2.228822 GCCTCCACGAATTTGTCACAAT 59.771 45.455 0.00 0.00 0.00 2.71
2065 2202 1.674322 CGGGCCTCCACGAATTTGT 60.674 57.895 0.84 0.00 0.00 2.83
2082 2219 3.814268 CCCGCTCCAATGGCAACG 61.814 66.667 0.00 0.00 42.51 4.10
2213 2371 3.390639 TGAAAACACAGGGGAATTTGCAT 59.609 39.130 0.00 0.00 0.00 3.96
2229 2387 1.222115 ACTCTCGGCGCAGTGAAAAC 61.222 55.000 10.83 0.00 0.00 2.43
2496 2655 1.379044 CTGGCAGACACATTCCCCC 60.379 63.158 9.42 0.00 0.00 5.40
2781 2940 4.627467 GGAATAATGGAAGTGATCGATCGG 59.373 45.833 20.03 0.00 0.00 4.18
2809 2976 2.224314 CGCGAGCACTCTGAGATGTATA 59.776 50.000 12.44 0.00 0.00 1.47
2844 3011 2.868583 CAGCCTGCAGATACACACATAC 59.131 50.000 17.39 0.00 0.00 2.39
2850 3017 2.093216 GCACAGCCTGCAGATACAC 58.907 57.895 17.39 0.00 46.29 2.90
2864 3031 3.047718 GATCCTCGTCGTCGGCACA 62.048 63.158 1.55 0.00 37.69 4.57


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

AutoCloner maintained by Alex Coulton.