Multiple sequence alignment - TraesCS7D01G337600

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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 TraesCS7D01G337600 chr7D 100.000 3386 0 0 604 3989 430929222 430925837 0.000000e+00 6253.0
1 TraesCS7D01G337600 chr7D 100.000 208 0 0 1 208 430929825 430929618 6.250000e-103 385.0
2 TraesCS7D01G337600 chr7A 93.880 3317 149 20 682 3987 501973916 501977189 0.000000e+00 4951.0
3 TraesCS7D01G337600 chr7B 95.564 3066 95 16 925 3989 448344780 448341755 0.000000e+00 4870.0
4 TraesCS7D01G337600 chr7B 90.553 561 33 4 1829 2388 623463264 623463805 0.000000e+00 725.0
5 TraesCS7D01G337600 chr7B 93.438 381 17 3 2712 3092 623471443 623471071 3.480000e-155 558.0
6 TraesCS7D01G337600 chr7B 95.038 262 13 0 2127 2388 623265400 623265661 2.870000e-111 412.0
7 TraesCS7D01G337600 chr7B 93.985 266 14 2 1829 2093 623264919 623265183 6.210000e-108 401.0
8 TraesCS7D01G337600 chr7B 94.737 247 11 1 2384 2628 623470226 623470472 2.250000e-102 383.0
9 TraesCS7D01G337600 chr7B 92.140 229 10 3 2864 3092 623266487 623266267 2.310000e-82 316.0
10 TraesCS7D01G337600 chr7B 94.904 157 8 0 2712 2868 623267973 623267817 3.080000e-61 246.0
11 TraesCS7D01G337600 chr1B 95.539 807 29 1 1829 2628 122922072 122922878 0.000000e+00 1284.0
12 TraesCS7D01G337600 chr1B 92.950 383 17 4 2712 3092 122923854 122923480 2.100000e-152 549.0
13 TraesCS7D01G337600 chr2B 71.895 612 108 56 1349 1928 791471278 791471857 7.000000e-23 119.0
14 TraesCS7D01G337600 chr2D 75.758 198 32 14 1739 1928 644375153 644374964 7.100000e-13 86.1
15 TraesCS7D01G337600 chr2A 73.962 265 45 20 1676 1928 769501551 769501299 7.100000e-13 86.1


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 TraesCS7D01G337600 chr7D 430925837 430929825 3988 True 3319.0 6253 100.0000 1 3989 2 chr7D.!!$R1 3988
1 TraesCS7D01G337600 chr7A 501973916 501977189 3273 False 4951.0 4951 93.8800 682 3987 1 chr7A.!!$F1 3305
2 TraesCS7D01G337600 chr7B 448341755 448344780 3025 True 4870.0 4870 95.5640 925 3989 1 chr7B.!!$R1 3064
3 TraesCS7D01G337600 chr7B 623463264 623463805 541 False 725.0 725 90.5530 1829 2388 1 chr7B.!!$F1 559
4 TraesCS7D01G337600 chr7B 623264919 623265661 742 False 406.5 412 94.5115 1829 2388 2 chr7B.!!$F3 559
5 TraesCS7D01G337600 chr7B 623266267 623267973 1706 True 281.0 316 93.5220 2712 3092 2 chr7B.!!$R3 380
6 TraesCS7D01G337600 chr1B 122922072 122922878 806 False 1284.0 1284 95.5390 1829 2628 1 chr1B.!!$F1 799

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
52 53 0.032540 CCCTGCACCTCTTGTTTTGC 59.967 55.0 0.0 0.0 35.45 3.68 F
205 206 0.035458 CAGGAGGTGGTGGAAGTGAC 59.965 60.0 0.0 0.0 0.00 3.67 F
206 207 0.104934 AGGAGGTGGTGGAAGTGACT 60.105 55.0 0.0 0.0 0.00 3.41 F
815 822 0.179032 AACCGTGTGAGGTGATTGCA 60.179 50.0 0.0 0.0 45.21 4.08 F
2083 2091 0.396435 TCTCACAACCAAGGCATCGT 59.604 50.0 0.0 0.0 0.00 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 1469 1.306970 GAAGGAGGAGGACCGGAGA 59.693 63.158 9.46 0.0 41.83 3.71 R
2142 2351 0.031314 ACTCATGTATCCGCGAGCAG 59.969 55.000 8.23 0.0 0.00 4.24 R
2253 2462 1.200760 TGTAGATGGTGCCCAGCAGT 61.201 55.000 11.32 0.0 43.12 4.40 R
2640 2856 0.102481 ATACCGACACCAGCGACATC 59.898 55.000 0.00 0.0 0.00 3.06 R
3963 5518 0.179073 CGGCTCCGTCAGAAATGGAT 60.179 55.000 0.00 0.0 42.37 3.41 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 4.289837 TCCCTTAGGTTTAGCCCTATCA 57.710 45.455 0.00 0.00 36.96 2.15
22 23 4.637600 TCCCTTAGGTTTAGCCCTATCAA 58.362 43.478 0.00 0.00 36.96 2.57
23 24 5.232347 TCCCTTAGGTTTAGCCCTATCAAT 58.768 41.667 0.00 0.00 36.96 2.57
24 25 5.309806 TCCCTTAGGTTTAGCCCTATCAATC 59.690 44.000 0.00 0.00 36.96 2.67
25 26 5.310857 CCCTTAGGTTTAGCCCTATCAATCT 59.689 44.000 0.00 0.00 36.96 2.40
26 27 6.183361 CCCTTAGGTTTAGCCCTATCAATCTT 60.183 42.308 0.00 0.00 36.96 2.40
27 28 6.937465 CCTTAGGTTTAGCCCTATCAATCTTC 59.063 42.308 0.00 0.00 36.96 2.87
28 29 4.962155 AGGTTTAGCCCTATCAATCTTCG 58.038 43.478 0.00 0.00 38.26 3.79
29 30 4.409247 AGGTTTAGCCCTATCAATCTTCGT 59.591 41.667 0.00 0.00 38.26 3.85
30 31 4.750598 GGTTTAGCCCTATCAATCTTCGTC 59.249 45.833 0.00 0.00 0.00 4.20
31 32 5.453480 GGTTTAGCCCTATCAATCTTCGTCT 60.453 44.000 0.00 0.00 0.00 4.18
32 33 5.871396 TTAGCCCTATCAATCTTCGTCTT 57.129 39.130 0.00 0.00 0.00 3.01
33 34 4.329462 AGCCCTATCAATCTTCGTCTTC 57.671 45.455 0.00 0.00 0.00 2.87
34 35 3.070302 AGCCCTATCAATCTTCGTCTTCC 59.930 47.826 0.00 0.00 0.00 3.46
35 36 3.804063 GCCCTATCAATCTTCGTCTTCCC 60.804 52.174 0.00 0.00 0.00 3.97
36 37 3.643792 CCCTATCAATCTTCGTCTTCCCT 59.356 47.826 0.00 0.00 0.00 4.20
37 38 4.502259 CCCTATCAATCTTCGTCTTCCCTG 60.502 50.000 0.00 0.00 0.00 4.45
38 39 2.386661 TCAATCTTCGTCTTCCCTGC 57.613 50.000 0.00 0.00 0.00 4.85
39 40 1.623311 TCAATCTTCGTCTTCCCTGCA 59.377 47.619 0.00 0.00 0.00 4.41
40 41 1.734465 CAATCTTCGTCTTCCCTGCAC 59.266 52.381 0.00 0.00 0.00 4.57
41 42 0.250513 ATCTTCGTCTTCCCTGCACC 59.749 55.000 0.00 0.00 0.00 5.01
42 43 0.832135 TCTTCGTCTTCCCTGCACCT 60.832 55.000 0.00 0.00 0.00 4.00
43 44 0.390472 CTTCGTCTTCCCTGCACCTC 60.390 60.000 0.00 0.00 0.00 3.85
44 45 0.832135 TTCGTCTTCCCTGCACCTCT 60.832 55.000 0.00 0.00 0.00 3.69
45 46 0.832135 TCGTCTTCCCTGCACCTCTT 60.832 55.000 0.00 0.00 0.00 2.85
46 47 0.671781 CGTCTTCCCTGCACCTCTTG 60.672 60.000 0.00 0.00 0.00 3.02
47 48 0.398318 GTCTTCCCTGCACCTCTTGT 59.602 55.000 0.00 0.00 0.00 3.16
48 49 1.140312 TCTTCCCTGCACCTCTTGTT 58.860 50.000 0.00 0.00 0.00 2.83
49 50 1.494721 TCTTCCCTGCACCTCTTGTTT 59.505 47.619 0.00 0.00 0.00 2.83
50 51 2.091885 TCTTCCCTGCACCTCTTGTTTT 60.092 45.455 0.00 0.00 0.00 2.43
51 52 1.691196 TCCCTGCACCTCTTGTTTTG 58.309 50.000 0.00 0.00 0.00 2.44
52 53 0.032540 CCCTGCACCTCTTGTTTTGC 59.967 55.000 0.00 0.00 35.45 3.68
53 54 0.318107 CCTGCACCTCTTGTTTTGCG 60.318 55.000 0.00 0.00 37.82 4.85
54 55 0.381801 CTGCACCTCTTGTTTTGCGT 59.618 50.000 0.00 0.00 37.82 5.24
55 56 0.814457 TGCACCTCTTGTTTTGCGTT 59.186 45.000 0.00 0.00 37.82 4.84
56 57 1.203523 TGCACCTCTTGTTTTGCGTTT 59.796 42.857 0.00 0.00 37.82 3.60
57 58 1.587946 GCACCTCTTGTTTTGCGTTTG 59.412 47.619 0.00 0.00 0.00 2.93
58 59 1.587946 CACCTCTTGTTTTGCGTTTGC 59.412 47.619 0.00 0.00 43.20 3.68
59 60 1.476488 ACCTCTTGTTTTGCGTTTGCT 59.524 42.857 0.00 0.00 43.34 3.91
60 61 2.685897 ACCTCTTGTTTTGCGTTTGCTA 59.314 40.909 0.00 0.00 43.34 3.49
61 62 3.129638 ACCTCTTGTTTTGCGTTTGCTAA 59.870 39.130 0.00 0.00 43.34 3.09
62 63 4.109050 CCTCTTGTTTTGCGTTTGCTAAA 58.891 39.130 0.00 0.00 42.19 1.85
63 64 4.744631 CCTCTTGTTTTGCGTTTGCTAAAT 59.255 37.500 0.71 0.00 45.11 1.40
64 65 5.234116 CCTCTTGTTTTGCGTTTGCTAAATT 59.766 36.000 0.71 0.00 45.11 1.82
65 66 6.267500 TCTTGTTTTGCGTTTGCTAAATTC 57.733 33.333 0.71 0.00 45.11 2.17
66 67 5.807520 TCTTGTTTTGCGTTTGCTAAATTCA 59.192 32.000 0.71 0.00 45.11 2.57
67 68 5.633996 TGTTTTGCGTTTGCTAAATTCAG 57.366 34.783 0.71 0.00 45.11 3.02
68 69 4.505922 TGTTTTGCGTTTGCTAAATTCAGG 59.494 37.500 0.71 0.00 45.11 3.86
69 70 4.314740 TTTGCGTTTGCTAAATTCAGGT 57.685 36.364 0.00 0.00 43.34 4.00
70 71 3.281341 TGCGTTTGCTAAATTCAGGTG 57.719 42.857 0.00 0.00 43.34 4.00
71 72 1.985684 GCGTTTGCTAAATTCAGGTGC 59.014 47.619 0.00 0.00 38.39 5.01
72 73 2.351738 GCGTTTGCTAAATTCAGGTGCT 60.352 45.455 0.00 0.00 38.39 4.40
73 74 3.857010 GCGTTTGCTAAATTCAGGTGCTT 60.857 43.478 0.00 0.00 38.39 3.91
74 75 3.670055 CGTTTGCTAAATTCAGGTGCTTG 59.330 43.478 0.00 0.00 0.00 4.01
75 76 3.940209 TTGCTAAATTCAGGTGCTTGG 57.060 42.857 0.00 0.00 0.00 3.61
76 77 3.153369 TGCTAAATTCAGGTGCTTGGA 57.847 42.857 0.00 0.00 0.00 3.53
77 78 2.819608 TGCTAAATTCAGGTGCTTGGAC 59.180 45.455 0.00 0.00 0.00 4.02
78 79 2.819608 GCTAAATTCAGGTGCTTGGACA 59.180 45.455 0.00 0.00 0.00 4.02
79 80 3.445096 GCTAAATTCAGGTGCTTGGACAT 59.555 43.478 0.00 0.00 0.00 3.06
80 81 4.082026 GCTAAATTCAGGTGCTTGGACATT 60.082 41.667 0.00 0.00 0.00 2.71
81 82 4.961438 AAATTCAGGTGCTTGGACATTT 57.039 36.364 0.00 0.00 0.00 2.32
82 83 4.961438 AATTCAGGTGCTTGGACATTTT 57.039 36.364 0.00 0.00 0.00 1.82
83 84 4.961438 ATTCAGGTGCTTGGACATTTTT 57.039 36.364 0.00 0.00 0.00 1.94
84 85 6.418057 AATTCAGGTGCTTGGACATTTTTA 57.582 33.333 0.00 0.00 0.00 1.52
85 86 5.452078 TTCAGGTGCTTGGACATTTTTAG 57.548 39.130 0.00 0.00 0.00 1.85
86 87 3.826157 TCAGGTGCTTGGACATTTTTAGG 59.174 43.478 0.00 0.00 0.00 2.69
87 88 3.056607 CAGGTGCTTGGACATTTTTAGGG 60.057 47.826 0.00 0.00 0.00 3.53
88 89 2.353704 GGTGCTTGGACATTTTTAGGGC 60.354 50.000 0.00 0.00 0.00 5.19
89 90 1.543802 TGCTTGGACATTTTTAGGGCG 59.456 47.619 0.00 0.00 0.00 6.13
90 91 1.135112 GCTTGGACATTTTTAGGGCGG 60.135 52.381 0.00 0.00 0.00 6.13
91 92 0.892063 TTGGACATTTTTAGGGCGGC 59.108 50.000 0.00 0.00 0.00 6.53
92 93 0.251386 TGGACATTTTTAGGGCGGCA 60.251 50.000 12.47 0.00 0.00 5.69
93 94 0.172578 GGACATTTTTAGGGCGGCAC 59.827 55.000 12.47 0.00 0.00 5.01
94 95 1.173913 GACATTTTTAGGGCGGCACT 58.826 50.000 10.75 10.75 0.00 4.40
95 96 1.132453 GACATTTTTAGGGCGGCACTC 59.868 52.381 8.66 0.00 0.00 3.51
96 97 0.098728 CATTTTTAGGGCGGCACTCG 59.901 55.000 8.66 0.00 42.76 4.18
97 98 0.035820 ATTTTTAGGGCGGCACTCGA 60.036 50.000 8.66 0.00 42.43 4.04
98 99 0.035820 TTTTTAGGGCGGCACTCGAT 60.036 50.000 8.66 0.00 42.43 3.59
99 100 0.035820 TTTTAGGGCGGCACTCGATT 60.036 50.000 8.66 0.00 42.43 3.34
100 101 0.035820 TTTAGGGCGGCACTCGATTT 60.036 50.000 8.66 0.00 42.43 2.17
101 102 0.461339 TTAGGGCGGCACTCGATTTC 60.461 55.000 8.66 0.00 42.43 2.17
102 103 1.327690 TAGGGCGGCACTCGATTTCT 61.328 55.000 8.66 0.00 42.43 2.52
103 104 2.464459 GGGCGGCACTCGATTTCTG 61.464 63.158 12.47 0.00 42.43 3.02
104 105 2.401195 GCGGCACTCGATTTCTGC 59.599 61.111 0.00 0.00 42.43 4.26
105 106 2.103042 GCGGCACTCGATTTCTGCT 61.103 57.895 0.00 0.00 42.43 4.24
106 107 1.639298 GCGGCACTCGATTTCTGCTT 61.639 55.000 0.00 0.00 42.43 3.91
107 108 0.798776 CGGCACTCGATTTCTGCTTT 59.201 50.000 0.00 0.00 42.43 3.51
108 109 1.197721 CGGCACTCGATTTCTGCTTTT 59.802 47.619 0.00 0.00 42.43 2.27
109 110 2.726066 CGGCACTCGATTTCTGCTTTTC 60.726 50.000 0.00 0.00 42.43 2.29
110 111 2.414691 GGCACTCGATTTCTGCTTTTCC 60.415 50.000 0.00 0.00 0.00 3.13
111 112 2.726066 GCACTCGATTTCTGCTTTTCCG 60.726 50.000 0.00 0.00 0.00 4.30
112 113 2.076863 ACTCGATTTCTGCTTTTCCGG 58.923 47.619 0.00 0.00 0.00 5.14
113 114 2.289444 ACTCGATTTCTGCTTTTCCGGA 60.289 45.455 0.00 0.00 0.00 5.14
114 115 2.346803 TCGATTTCTGCTTTTCCGGAG 58.653 47.619 3.34 0.00 0.00 4.63
134 135 3.402681 CGGAGGCAGGGGTGACAT 61.403 66.667 0.00 0.00 0.00 3.06
135 136 2.273449 GGAGGCAGGGGTGACATG 59.727 66.667 0.00 0.00 0.00 3.21
136 137 2.300967 GGAGGCAGGGGTGACATGA 61.301 63.158 0.00 0.00 0.00 3.07
137 138 1.222936 GAGGCAGGGGTGACATGAG 59.777 63.158 0.00 0.00 0.00 2.90
138 139 2.262774 GAGGCAGGGGTGACATGAGG 62.263 65.000 0.00 0.00 0.00 3.86
139 140 2.300967 GGCAGGGGTGACATGAGGA 61.301 63.158 0.00 0.00 0.00 3.71
140 141 1.222936 GCAGGGGTGACATGAGGAG 59.777 63.158 0.00 0.00 0.00 3.69
141 142 1.222936 CAGGGGTGACATGAGGAGC 59.777 63.158 0.00 0.00 0.00 4.70
142 143 2.187946 GGGGTGACATGAGGAGCG 59.812 66.667 0.00 0.00 0.00 5.03
143 144 2.187946 GGGTGACATGAGGAGCGG 59.812 66.667 0.00 0.00 0.00 5.52
144 145 2.512515 GGTGACATGAGGAGCGGC 60.513 66.667 0.00 0.00 0.00 6.53
145 146 2.265739 GTGACATGAGGAGCGGCA 59.734 61.111 0.00 0.00 0.00 5.69
146 147 1.812922 GTGACATGAGGAGCGGCAG 60.813 63.158 0.00 0.00 0.00 4.85
147 148 2.202987 GACATGAGGAGCGGCAGG 60.203 66.667 0.00 0.00 0.00 4.85
148 149 3.746949 GACATGAGGAGCGGCAGGG 62.747 68.421 0.00 0.00 0.00 4.45
149 150 3.473647 CATGAGGAGCGGCAGGGA 61.474 66.667 1.45 0.00 0.00 4.20
150 151 3.474570 ATGAGGAGCGGCAGGGAC 61.475 66.667 1.45 0.00 0.00 4.46
164 165 4.477975 GGACGAGCGTCGACCCTG 62.478 72.222 7.62 3.07 46.18 4.45
165 166 4.477975 GACGAGCGTCGACCCTGG 62.478 72.222 7.62 9.13 43.74 4.45
168 169 4.803426 GAGCGTCGACCCTGGCAG 62.803 72.222 7.62 7.75 0.00 4.85
171 172 4.436998 CGTCGACCCTGGCAGGAC 62.437 72.222 34.84 24.40 37.67 3.85
172 173 4.436998 GTCGACCCTGGCAGGACG 62.437 72.222 34.84 32.84 37.67 4.79
173 174 4.988716 TCGACCCTGGCAGGACGT 62.989 66.667 34.84 24.12 37.67 4.34
174 175 4.742201 CGACCCTGGCAGGACGTG 62.742 72.222 34.84 19.77 37.67 4.49
175 176 3.626924 GACCCTGGCAGGACGTGT 61.627 66.667 34.84 22.98 37.67 4.49
176 177 3.591254 GACCCTGGCAGGACGTGTC 62.591 68.421 34.84 26.42 37.67 3.67
177 178 4.742201 CCCTGGCAGGACGTGTCG 62.742 72.222 34.84 12.25 37.67 4.35
178 179 3.991051 CCTGGCAGGACGTGTCGT 61.991 66.667 29.96 0.00 45.10 4.34
179 180 2.734723 CTGGCAGGACGTGTCGTG 60.735 66.667 16.16 16.16 45.32 4.35
180 181 3.499929 CTGGCAGGACGTGTCGTGT 62.500 63.158 20.02 0.00 44.62 4.49
181 182 2.137425 CTGGCAGGACGTGTCGTGTA 62.137 60.000 20.02 11.20 44.62 2.90
182 183 1.731969 GGCAGGACGTGTCGTGTAC 60.732 63.158 20.02 12.05 44.62 2.90
183 184 2.078914 GCAGGACGTGTCGTGTACG 61.079 63.158 20.02 0.00 44.62 3.67
192 193 3.587095 TCGTGTACGAGCAGGAGG 58.413 61.111 2.55 0.00 44.22 4.30
193 194 1.303074 TCGTGTACGAGCAGGAGGT 60.303 57.895 2.55 0.00 44.22 3.85
194 195 1.154016 CGTGTACGAGCAGGAGGTG 60.154 63.158 0.00 0.00 43.02 4.00
195 196 1.215647 GTGTACGAGCAGGAGGTGG 59.784 63.158 0.00 0.00 0.00 4.61
196 197 1.228769 TGTACGAGCAGGAGGTGGT 60.229 57.895 0.00 0.00 40.54 4.16
197 198 1.215647 GTACGAGCAGGAGGTGGTG 59.784 63.158 0.00 0.00 36.87 4.17
198 199 1.982395 TACGAGCAGGAGGTGGTGG 60.982 63.158 0.00 0.00 36.87 4.61
199 200 2.435120 TACGAGCAGGAGGTGGTGGA 62.435 60.000 0.00 0.00 36.87 4.02
200 201 2.583441 CGAGCAGGAGGTGGTGGAA 61.583 63.158 0.00 0.00 36.87 3.53
201 202 1.298014 GAGCAGGAGGTGGTGGAAG 59.702 63.158 0.00 0.00 36.87 3.46
202 203 1.462238 AGCAGGAGGTGGTGGAAGT 60.462 57.895 0.00 0.00 34.82 3.01
203 204 1.302832 GCAGGAGGTGGTGGAAGTG 60.303 63.158 0.00 0.00 0.00 3.16
204 205 1.768684 GCAGGAGGTGGTGGAAGTGA 61.769 60.000 0.00 0.00 0.00 3.41
205 206 0.035458 CAGGAGGTGGTGGAAGTGAC 59.965 60.000 0.00 0.00 0.00 3.67
206 207 0.104934 AGGAGGTGGTGGAAGTGACT 60.105 55.000 0.00 0.00 0.00 3.41
207 208 0.321996 GGAGGTGGTGGAAGTGACTC 59.678 60.000 0.00 0.00 0.00 3.36
622 623 2.142356 TTGTTGCATATCAGGGTGGG 57.858 50.000 0.00 0.00 0.00 4.61
623 624 0.258484 TGTTGCATATCAGGGTGGGG 59.742 55.000 0.00 0.00 0.00 4.96
624 625 0.550914 GTTGCATATCAGGGTGGGGA 59.449 55.000 0.00 0.00 0.00 4.81
625 626 0.550914 TTGCATATCAGGGTGGGGAC 59.449 55.000 0.00 0.00 0.00 4.46
643 644 3.259625 GGGACCTCTATAGAGATGGTTGC 59.740 52.174 28.04 12.76 44.74 4.17
644 645 3.057174 GGACCTCTATAGAGATGGTTGCG 60.057 52.174 28.04 12.78 44.74 4.85
645 646 2.894126 ACCTCTATAGAGATGGTTGCGG 59.106 50.000 28.04 13.15 44.74 5.69
646 647 2.353208 CCTCTATAGAGATGGTTGCGGC 60.353 54.545 28.04 0.00 44.74 6.53
647 648 1.269723 TCTATAGAGATGGTTGCGGCG 59.730 52.381 0.51 0.51 0.00 6.46
648 649 0.317160 TATAGAGATGGTTGCGGCGG 59.683 55.000 9.78 0.00 0.00 6.13
649 650 2.996168 ATAGAGATGGTTGCGGCGGC 62.996 60.000 9.78 9.68 40.52 6.53
666 667 4.368808 CGGCAAGCAACGACGGTG 62.369 66.667 8.96 8.96 0.00 4.94
667 668 4.025401 GGCAAGCAACGACGGTGG 62.025 66.667 15.86 0.00 0.00 4.61
668 669 4.025401 GCAAGCAACGACGGTGGG 62.025 66.667 15.86 0.00 0.00 4.61
669 670 3.353836 CAAGCAACGACGGTGGGG 61.354 66.667 15.86 0.00 0.00 4.96
670 671 4.636435 AAGCAACGACGGTGGGGG 62.636 66.667 15.86 0.00 0.00 5.40
673 674 4.388499 CAACGACGGTGGGGGAGG 62.388 72.222 4.57 0.00 0.00 4.30
674 675 4.948080 AACGACGGTGGGGGAGGT 62.948 66.667 0.00 0.00 0.00 3.85
675 676 4.948080 ACGACGGTGGGGGAGGTT 62.948 66.667 0.00 0.00 0.00 3.50
676 677 4.388499 CGACGGTGGGGGAGGTTG 62.388 72.222 0.00 0.00 0.00 3.77
677 678 2.926242 GACGGTGGGGGAGGTTGA 60.926 66.667 0.00 0.00 0.00 3.18
678 679 2.204090 ACGGTGGGGGAGGTTGAT 60.204 61.111 0.00 0.00 0.00 2.57
679 680 2.272146 CGGTGGGGGAGGTTGATG 59.728 66.667 0.00 0.00 0.00 3.07
680 681 2.683475 GGTGGGGGAGGTTGATGG 59.317 66.667 0.00 0.00 0.00 3.51
686 687 2.597903 GGAGGTTGATGGGAGGGC 59.402 66.667 0.00 0.00 0.00 5.19
736 737 2.122189 GGGGGAGAGGGGATCCAG 60.122 72.222 15.23 0.00 38.70 3.86
739 740 3.237741 GGAGAGGGGATCCAGGCG 61.238 72.222 15.23 0.00 36.79 5.52
740 741 2.123251 GAGAGGGGATCCAGGCGA 60.123 66.667 15.23 0.00 34.83 5.54
744 745 2.113986 GGGGATCCAGGCGATTGG 59.886 66.667 15.23 0.00 39.70 3.16
775 776 1.027357 GGGCGAATGCATGATGAAGT 58.973 50.000 0.00 0.00 45.35 3.01
793 794 7.445402 TGATGAAGTAGAAAGAAAGGTTGAAGG 59.555 37.037 0.00 0.00 0.00 3.46
799 800 4.645136 AGAAAGAAAGGTTGAAGGTGAACC 59.355 41.667 0.00 0.00 42.91 3.62
815 822 0.179032 AACCGTGTGAGGTGATTGCA 60.179 50.000 0.00 0.00 45.21 4.08
818 825 1.676916 CCGTGTGAGGTGATTGCAGAT 60.677 52.381 0.00 0.00 0.00 2.90
827 834 2.100252 GGTGATTGCAGATGTTGGATGG 59.900 50.000 0.00 0.00 0.00 3.51
839 846 3.861797 GGATGGTGATCCGGCGGT 61.862 66.667 27.32 13.58 39.04 5.68
889 896 1.083489 TTTCACAAATAGGCGCTCCG 58.917 50.000 7.64 0.00 37.47 4.63
938 945 5.391950 CCCATTAATTTTGTCTCACTCCACG 60.392 44.000 0.00 0.00 0.00 4.94
988 995 3.181470 CCAAAAGGTACAACCAAACCCTG 60.181 47.826 0.00 0.00 41.95 4.45
991 998 3.895704 AGGTACAACCAAACCCTGAAT 57.104 42.857 0.00 0.00 41.95 2.57
1075 1083 5.222484 CCCTATCTACATTACCACCCCTCTA 60.222 48.000 0.00 0.00 0.00 2.43
1177 1185 1.215382 CCTGACAATGCCGACGAGA 59.785 57.895 0.00 0.00 0.00 4.04
1190 1198 0.674534 GACGAGACTTCACCACCACT 59.325 55.000 0.00 0.00 0.00 4.00
1410 1418 1.433471 CACGCTGCTCGACATCCTA 59.567 57.895 5.98 0.00 41.67 2.94
1461 1469 4.749310 CTGCTCAACTCGGCGCCT 62.749 66.667 26.68 1.82 0.00 5.52
2083 2091 0.396435 TCTCACAACCAAGGCATCGT 59.604 50.000 0.00 0.00 0.00 3.73
2142 2351 1.866925 GCTGTTGTGTACTTCGCCC 59.133 57.895 0.00 0.00 0.00 6.13
2202 2411 0.459585 CGTGGAAGGTGGTGTATCGG 60.460 60.000 0.00 0.00 0.00 4.18
2253 2462 2.571757 GCTGTGATCGTCGGGACA 59.428 61.111 0.00 0.00 0.00 4.02
2289 2498 1.523711 CATCAACGCCGGCTATGGT 60.524 57.895 26.68 16.68 0.00 3.55
2382 2591 2.050351 CTGCCGACGTTCGTCACT 60.050 61.111 21.94 0.00 38.40 3.41
2640 2856 4.280494 CCGGACTACATCGCGGGG 62.280 72.222 6.13 0.36 37.45 5.73
2658 2874 1.509463 GATGTCGCTGGTGTCGGTA 59.491 57.895 0.00 0.00 0.00 4.02
2685 2901 0.173708 CCGGGTTCTTCCTCTTCTCG 59.826 60.000 0.00 0.00 36.25 4.04
2694 2910 2.233305 TCCTCTTCTCGGGCTACTTT 57.767 50.000 0.00 0.00 0.00 2.66
2841 3057 2.780094 CGCCGGAGATGAGTGCTCT 61.780 63.158 5.05 0.00 32.98 4.09
2991 4541 1.079543 CAGAGCCAAGAGGTGACCG 60.080 63.158 0.00 0.00 37.19 4.79
3013 4563 4.209080 CGTTGATCGATCCATGAATTTCGA 59.791 41.667 22.31 3.02 43.82 3.71
3016 4566 5.359756 TGATCGATCCATGAATTTCGACTT 58.640 37.500 22.31 0.00 42.66 3.01
3032 4583 5.426689 TCGACTTCTCCCTTACTACACTA 57.573 43.478 0.00 0.00 0.00 2.74
3033 4584 5.181748 TCGACTTCTCCCTTACTACACTAC 58.818 45.833 0.00 0.00 0.00 2.73
3034 4585 4.940046 CGACTTCTCCCTTACTACACTACA 59.060 45.833 0.00 0.00 0.00 2.74
3035 4586 5.163774 CGACTTCTCCCTTACTACACTACAC 60.164 48.000 0.00 0.00 0.00 2.90
3036 4587 5.890049 ACTTCTCCCTTACTACACTACACT 58.110 41.667 0.00 0.00 0.00 3.55
3037 4588 7.025520 ACTTCTCCCTTACTACACTACACTA 57.974 40.000 0.00 0.00 0.00 2.74
3038 4589 7.111466 ACTTCTCCCTTACTACACTACACTAG 58.889 42.308 0.00 0.00 0.00 2.57
3039 4590 5.435291 TCTCCCTTACTACACTACACTAGC 58.565 45.833 0.00 0.00 0.00 3.42
3040 4591 5.191323 TCTCCCTTACTACACTACACTAGCT 59.809 44.000 0.00 0.00 0.00 3.32
3116 4667 2.936498 GTGCATGCGACAGTTAAGGTAT 59.064 45.455 14.09 0.00 0.00 2.73
3162 4713 6.168389 CAGAGTGGTTAACCGGTAATTAAGT 58.832 40.000 19.65 2.37 39.43 2.24
3248 4800 8.964476 TGGATAATAAACAGTGAGAATTCTCC 57.036 34.615 28.40 20.25 42.20 3.71
3260 4812 3.028850 AGAATTCTCCACATGCCATTGG 58.971 45.455 0.88 0.00 0.00 3.16
3461 5013 2.367894 TGAATGTTTTGAATGCCTGGCA 59.632 40.909 25.65 25.65 44.86 4.92
3481 5033 3.438360 CAATGGCCGTCTTTTAAGCATC 58.562 45.455 0.00 0.00 0.00 3.91
3658 5210 7.933033 AGTTGTGCAATTTCAGTATTCCAATTT 59.067 29.630 0.00 0.00 0.00 1.82
3801 5354 3.189287 AGTTTGATTTGACCACTGATCGC 59.811 43.478 0.00 0.00 0.00 4.58
3816 5369 2.487762 TGATCGCCAAAACTCAATCACC 59.512 45.455 0.00 0.00 0.00 4.02
3855 5410 8.217778 GCGCTTCTCTATATGATAGAAACAAAC 58.782 37.037 0.00 0.00 0.00 2.93
3961 5516 0.322008 CTGACCCTCCTGGCAAAGTC 60.322 60.000 0.00 0.00 37.83 3.01
3962 5517 1.059584 TGACCCTCCTGGCAAAGTCA 61.060 55.000 5.07 5.07 37.83 3.41
3963 5518 0.110486 GACCCTCCTGGCAAAGTCAA 59.890 55.000 0.00 0.00 37.83 3.18
3964 5519 0.779997 ACCCTCCTGGCAAAGTCAAT 59.220 50.000 0.00 0.00 37.83 2.57
3965 5520 1.272147 ACCCTCCTGGCAAAGTCAATC 60.272 52.381 0.00 0.00 37.83 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.289837 TGATAGGGCTAAACCTAAGGGA 57.710 45.455 0.00 0.00 45.69 4.20
1 2 5.310857 AGATTGATAGGGCTAAACCTAAGGG 59.689 44.000 0.00 0.00 45.69 3.95
2 3 6.441088 AGATTGATAGGGCTAAACCTAAGG 57.559 41.667 0.00 0.00 45.69 2.69
3 4 6.647067 CGAAGATTGATAGGGCTAAACCTAAG 59.353 42.308 0.00 0.00 45.69 2.18
4 5 6.099269 ACGAAGATTGATAGGGCTAAACCTAA 59.901 38.462 0.00 0.00 45.69 2.69
5 6 5.601313 ACGAAGATTGATAGGGCTAAACCTA 59.399 40.000 0.00 0.00 46.55 3.08
6 7 4.409247 ACGAAGATTGATAGGGCTAAACCT 59.591 41.667 0.00 0.00 44.75 3.50
7 8 4.704965 ACGAAGATTGATAGGGCTAAACC 58.295 43.478 0.00 0.00 37.93 3.27
8 9 5.602628 AGACGAAGATTGATAGGGCTAAAC 58.397 41.667 0.00 0.00 0.00 2.01
9 10 5.871396 AGACGAAGATTGATAGGGCTAAA 57.129 39.130 0.00 0.00 0.00 1.85
10 11 5.221461 GGAAGACGAAGATTGATAGGGCTAA 60.221 44.000 0.00 0.00 0.00 3.09
11 12 4.281182 GGAAGACGAAGATTGATAGGGCTA 59.719 45.833 0.00 0.00 0.00 3.93
12 13 3.070302 GGAAGACGAAGATTGATAGGGCT 59.930 47.826 0.00 0.00 0.00 5.19
13 14 3.394719 GGAAGACGAAGATTGATAGGGC 58.605 50.000 0.00 0.00 0.00 5.19
14 15 3.643792 AGGGAAGACGAAGATTGATAGGG 59.356 47.826 0.00 0.00 0.00 3.53
15 16 4.626042 CAGGGAAGACGAAGATTGATAGG 58.374 47.826 0.00 0.00 0.00 2.57
16 17 4.054671 GCAGGGAAGACGAAGATTGATAG 58.945 47.826 0.00 0.00 0.00 2.08
17 18 3.450817 TGCAGGGAAGACGAAGATTGATA 59.549 43.478 0.00 0.00 0.00 2.15
18 19 2.237143 TGCAGGGAAGACGAAGATTGAT 59.763 45.455 0.00 0.00 0.00 2.57
19 20 1.623311 TGCAGGGAAGACGAAGATTGA 59.377 47.619 0.00 0.00 0.00 2.57
20 21 1.734465 GTGCAGGGAAGACGAAGATTG 59.266 52.381 0.00 0.00 0.00 2.67
21 22 1.339151 GGTGCAGGGAAGACGAAGATT 60.339 52.381 0.00 0.00 0.00 2.40
22 23 0.250513 GGTGCAGGGAAGACGAAGAT 59.749 55.000 0.00 0.00 0.00 2.40
23 24 0.832135 AGGTGCAGGGAAGACGAAGA 60.832 55.000 0.00 0.00 0.00 2.87
24 25 0.390472 GAGGTGCAGGGAAGACGAAG 60.390 60.000 0.00 0.00 0.00 3.79
25 26 0.832135 AGAGGTGCAGGGAAGACGAA 60.832 55.000 0.00 0.00 0.00 3.85
26 27 0.832135 AAGAGGTGCAGGGAAGACGA 60.832 55.000 0.00 0.00 0.00 4.20
27 28 0.671781 CAAGAGGTGCAGGGAAGACG 60.672 60.000 0.00 0.00 0.00 4.18
28 29 0.398318 ACAAGAGGTGCAGGGAAGAC 59.602 55.000 0.00 0.00 0.00 3.01
29 30 1.140312 AACAAGAGGTGCAGGGAAGA 58.860 50.000 0.00 0.00 0.00 2.87
30 31 1.986882 AAACAAGAGGTGCAGGGAAG 58.013 50.000 0.00 0.00 0.00 3.46
31 32 2.031120 CAAAACAAGAGGTGCAGGGAA 58.969 47.619 0.00 0.00 0.00 3.97
32 33 1.691196 CAAAACAAGAGGTGCAGGGA 58.309 50.000 0.00 0.00 0.00 4.20
33 34 0.032540 GCAAAACAAGAGGTGCAGGG 59.967 55.000 0.00 0.00 36.97 4.45
34 35 0.318107 CGCAAAACAAGAGGTGCAGG 60.318 55.000 0.00 0.00 36.80 4.85
35 36 0.381801 ACGCAAAACAAGAGGTGCAG 59.618 50.000 0.00 0.00 36.80 4.41
36 37 0.814457 AACGCAAAACAAGAGGTGCA 59.186 45.000 0.00 0.00 36.80 4.57
37 38 1.587946 CAAACGCAAAACAAGAGGTGC 59.412 47.619 0.00 0.00 0.00 5.01
38 39 1.587946 GCAAACGCAAAACAAGAGGTG 59.412 47.619 0.00 0.00 0.00 4.00
39 40 1.476488 AGCAAACGCAAAACAAGAGGT 59.524 42.857 0.00 0.00 0.00 3.85
40 41 2.208326 AGCAAACGCAAAACAAGAGG 57.792 45.000 0.00 0.00 0.00 3.69
41 42 5.888412 ATTTAGCAAACGCAAAACAAGAG 57.112 34.783 0.00 0.00 0.00 2.85
42 43 5.807520 TGAATTTAGCAAACGCAAAACAAGA 59.192 32.000 0.00 0.00 0.00 3.02
43 44 6.030379 TGAATTTAGCAAACGCAAAACAAG 57.970 33.333 0.00 0.00 0.00 3.16
44 45 5.006165 CCTGAATTTAGCAAACGCAAAACAA 59.994 36.000 0.00 0.00 0.00 2.83
45 46 4.505922 CCTGAATTTAGCAAACGCAAAACA 59.494 37.500 0.00 0.00 0.00 2.83
46 47 4.506288 ACCTGAATTTAGCAAACGCAAAAC 59.494 37.500 0.00 0.00 0.00 2.43
47 48 4.505922 CACCTGAATTTAGCAAACGCAAAA 59.494 37.500 0.00 0.00 0.00 2.44
48 49 4.047822 CACCTGAATTTAGCAAACGCAAA 58.952 39.130 0.00 0.00 0.00 3.68
49 50 3.637432 CACCTGAATTTAGCAAACGCAA 58.363 40.909 0.00 0.00 0.00 4.85
50 51 2.606795 GCACCTGAATTTAGCAAACGCA 60.607 45.455 0.00 0.00 0.00 5.24
51 52 1.985684 GCACCTGAATTTAGCAAACGC 59.014 47.619 0.00 0.00 0.00 4.84
52 53 3.559238 AGCACCTGAATTTAGCAAACG 57.441 42.857 0.00 0.00 0.00 3.60
53 54 3.989817 CCAAGCACCTGAATTTAGCAAAC 59.010 43.478 0.00 0.00 0.00 2.93
54 55 3.894427 TCCAAGCACCTGAATTTAGCAAA 59.106 39.130 0.00 0.00 0.00 3.68
55 56 3.255642 GTCCAAGCACCTGAATTTAGCAA 59.744 43.478 0.00 0.00 0.00 3.91
56 57 2.819608 GTCCAAGCACCTGAATTTAGCA 59.180 45.455 0.00 0.00 0.00 3.49
57 58 2.819608 TGTCCAAGCACCTGAATTTAGC 59.180 45.455 0.00 0.00 0.00 3.09
58 59 5.649782 AATGTCCAAGCACCTGAATTTAG 57.350 39.130 0.00 0.00 0.00 1.85
59 60 6.418057 AAAATGTCCAAGCACCTGAATTTA 57.582 33.333 0.00 0.00 0.00 1.40
60 61 4.961438 AAATGTCCAAGCACCTGAATTT 57.039 36.364 0.00 0.00 0.00 1.82
61 62 4.961438 AAAATGTCCAAGCACCTGAATT 57.039 36.364 0.00 0.00 0.00 2.17
62 63 4.961438 AAAAATGTCCAAGCACCTGAAT 57.039 36.364 0.00 0.00 0.00 2.57
63 64 4.280677 CCTAAAAATGTCCAAGCACCTGAA 59.719 41.667 0.00 0.00 0.00 3.02
64 65 3.826157 CCTAAAAATGTCCAAGCACCTGA 59.174 43.478 0.00 0.00 0.00 3.86
65 66 3.056607 CCCTAAAAATGTCCAAGCACCTG 60.057 47.826 0.00 0.00 0.00 4.00
66 67 3.165071 CCCTAAAAATGTCCAAGCACCT 58.835 45.455 0.00 0.00 0.00 4.00
67 68 2.353704 GCCCTAAAAATGTCCAAGCACC 60.354 50.000 0.00 0.00 0.00 5.01
68 69 2.671070 CGCCCTAAAAATGTCCAAGCAC 60.671 50.000 0.00 0.00 0.00 4.40
69 70 1.543802 CGCCCTAAAAATGTCCAAGCA 59.456 47.619 0.00 0.00 0.00 3.91
70 71 1.135112 CCGCCCTAAAAATGTCCAAGC 60.135 52.381 0.00 0.00 0.00 4.01
71 72 1.135112 GCCGCCCTAAAAATGTCCAAG 60.135 52.381 0.00 0.00 0.00 3.61
72 73 0.892063 GCCGCCCTAAAAATGTCCAA 59.108 50.000 0.00 0.00 0.00 3.53
73 74 0.251386 TGCCGCCCTAAAAATGTCCA 60.251 50.000 0.00 0.00 0.00 4.02
74 75 0.172578 GTGCCGCCCTAAAAATGTCC 59.827 55.000 0.00 0.00 0.00 4.02
75 76 1.132453 GAGTGCCGCCCTAAAAATGTC 59.868 52.381 0.00 0.00 0.00 3.06
76 77 1.173913 GAGTGCCGCCCTAAAAATGT 58.826 50.000 0.00 0.00 0.00 2.71
77 78 0.098728 CGAGTGCCGCCCTAAAAATG 59.901 55.000 0.00 0.00 0.00 2.32
78 79 0.035820 TCGAGTGCCGCCCTAAAAAT 60.036 50.000 0.00 0.00 38.37 1.82
79 80 0.035820 ATCGAGTGCCGCCCTAAAAA 60.036 50.000 0.00 0.00 38.37 1.94
80 81 0.035820 AATCGAGTGCCGCCCTAAAA 60.036 50.000 0.00 0.00 38.37 1.52
81 82 0.035820 AAATCGAGTGCCGCCCTAAA 60.036 50.000 0.00 0.00 38.37 1.85
82 83 0.461339 GAAATCGAGTGCCGCCCTAA 60.461 55.000 0.00 0.00 38.37 2.69
83 84 1.143183 GAAATCGAGTGCCGCCCTA 59.857 57.895 0.00 0.00 38.37 3.53
84 85 2.125106 GAAATCGAGTGCCGCCCT 60.125 61.111 0.00 0.00 38.37 5.19
85 86 2.125106 AGAAATCGAGTGCCGCCC 60.125 61.111 0.00 0.00 38.37 6.13
86 87 3.093278 CAGAAATCGAGTGCCGCC 58.907 61.111 0.00 0.00 38.37 6.13
87 88 1.639298 AAGCAGAAATCGAGTGCCGC 61.639 55.000 7.90 0.00 37.98 6.53
88 89 0.798776 AAAGCAGAAATCGAGTGCCG 59.201 50.000 7.90 0.00 37.98 5.69
89 90 2.414691 GGAAAAGCAGAAATCGAGTGCC 60.415 50.000 7.90 0.00 37.98 5.01
90 91 2.726066 CGGAAAAGCAGAAATCGAGTGC 60.726 50.000 0.00 0.00 37.48 4.40
91 92 2.159653 CCGGAAAAGCAGAAATCGAGTG 60.160 50.000 0.00 0.00 0.00 3.51
92 93 2.076863 CCGGAAAAGCAGAAATCGAGT 58.923 47.619 0.00 0.00 0.00 4.18
93 94 2.346803 TCCGGAAAAGCAGAAATCGAG 58.653 47.619 0.00 0.00 0.00 4.04
94 95 2.346803 CTCCGGAAAAGCAGAAATCGA 58.653 47.619 5.23 0.00 0.00 3.59
95 96 1.398390 CCTCCGGAAAAGCAGAAATCG 59.602 52.381 5.23 0.00 0.00 3.34
96 97 1.133216 GCCTCCGGAAAAGCAGAAATC 59.867 52.381 5.23 0.00 0.00 2.17
97 98 1.177401 GCCTCCGGAAAAGCAGAAAT 58.823 50.000 5.23 0.00 0.00 2.17
98 99 0.893727 GGCCTCCGGAAAAGCAGAAA 60.894 55.000 19.18 0.00 0.00 2.52
99 100 1.303317 GGCCTCCGGAAAAGCAGAA 60.303 57.895 19.18 0.00 0.00 3.02
100 101 2.351276 GGCCTCCGGAAAAGCAGA 59.649 61.111 19.18 0.00 0.00 4.26
101 102 3.127533 CGGCCTCCGGAAAAGCAG 61.128 66.667 19.18 13.10 44.15 4.24
117 118 3.402681 ATGTCACCCCTGCCTCCG 61.403 66.667 0.00 0.00 0.00 4.63
118 119 2.262774 CTCATGTCACCCCTGCCTCC 62.263 65.000 0.00 0.00 0.00 4.30
119 120 1.222936 CTCATGTCACCCCTGCCTC 59.777 63.158 0.00 0.00 0.00 4.70
120 121 2.304056 CCTCATGTCACCCCTGCCT 61.304 63.158 0.00 0.00 0.00 4.75
121 122 2.262774 CTCCTCATGTCACCCCTGCC 62.263 65.000 0.00 0.00 0.00 4.85
122 123 1.222936 CTCCTCATGTCACCCCTGC 59.777 63.158 0.00 0.00 0.00 4.85
123 124 1.222936 GCTCCTCATGTCACCCCTG 59.777 63.158 0.00 0.00 0.00 4.45
124 125 2.362369 CGCTCCTCATGTCACCCCT 61.362 63.158 0.00 0.00 0.00 4.79
125 126 2.187946 CGCTCCTCATGTCACCCC 59.812 66.667 0.00 0.00 0.00 4.95
126 127 2.187946 CCGCTCCTCATGTCACCC 59.812 66.667 0.00 0.00 0.00 4.61
127 128 2.512515 GCCGCTCCTCATGTCACC 60.513 66.667 0.00 0.00 0.00 4.02
128 129 1.812922 CTGCCGCTCCTCATGTCAC 60.813 63.158 0.00 0.00 0.00 3.67
129 130 2.580815 CTGCCGCTCCTCATGTCA 59.419 61.111 0.00 0.00 0.00 3.58
130 131 2.202987 CCTGCCGCTCCTCATGTC 60.203 66.667 0.00 0.00 0.00 3.06
131 132 3.790437 CCCTGCCGCTCCTCATGT 61.790 66.667 0.00 0.00 0.00 3.21
132 133 3.473647 TCCCTGCCGCTCCTCATG 61.474 66.667 0.00 0.00 0.00 3.07
133 134 3.474570 GTCCCTGCCGCTCCTCAT 61.475 66.667 0.00 0.00 0.00 2.90
144 145 4.477975 GGTCGACGCTCGTCCCTG 62.478 72.222 15.64 3.58 41.14 4.45
147 148 4.477975 CAGGGTCGACGCTCGTCC 62.478 72.222 30.05 14.62 45.10 4.79
148 149 4.477975 CCAGGGTCGACGCTCGTC 62.478 72.222 30.05 11.97 41.35 4.20
151 152 4.803426 CTGCCAGGGTCGACGCTC 62.803 72.222 30.05 20.66 37.00 5.03
154 155 4.436998 GTCCTGCCAGGGTCGACG 62.437 72.222 11.68 0.00 35.59 5.12
155 156 4.436998 CGTCCTGCCAGGGTCGAC 62.437 72.222 19.10 7.13 36.06 4.20
156 157 4.988716 ACGTCCTGCCAGGGTCGA 62.989 66.667 26.50 1.35 36.91 4.20
157 158 4.742201 CACGTCCTGCCAGGGTCG 62.742 72.222 21.09 21.09 38.38 4.79
158 159 3.591254 GACACGTCCTGCCAGGGTC 62.591 68.421 11.68 6.51 35.59 4.46
159 160 3.626924 GACACGTCCTGCCAGGGT 61.627 66.667 11.68 0.00 35.59 4.34
160 161 4.742201 CGACACGTCCTGCCAGGG 62.742 72.222 11.68 0.00 35.59 4.45
161 162 3.991051 ACGACACGTCCTGCCAGG 61.991 66.667 3.69 3.69 33.69 4.45
162 163 2.137425 TACACGACACGTCCTGCCAG 62.137 60.000 0.00 0.00 38.32 4.85
163 164 2.194889 TACACGACACGTCCTGCCA 61.195 57.895 0.00 0.00 38.32 4.92
164 165 1.731969 GTACACGACACGTCCTGCC 60.732 63.158 0.00 0.00 38.32 4.85
165 166 2.078914 CGTACACGACACGTCCTGC 61.079 63.158 0.00 0.00 43.02 4.85
166 167 0.452287 CTCGTACACGACACGTCCTG 60.452 60.000 0.00 0.00 44.22 3.86
167 168 1.864862 CTCGTACACGACACGTCCT 59.135 57.895 0.00 0.00 44.22 3.85
168 169 1.795177 GCTCGTACACGACACGTCC 60.795 63.158 0.00 0.00 44.22 4.79
169 170 1.058590 CTGCTCGTACACGACACGTC 61.059 60.000 0.00 0.00 44.22 4.34
170 171 1.082300 CTGCTCGTACACGACACGT 60.082 57.895 0.00 0.00 44.22 4.49
171 172 1.796355 CCTGCTCGTACACGACACG 60.796 63.158 0.00 0.00 44.22 4.49
172 173 0.454620 CTCCTGCTCGTACACGACAC 60.455 60.000 0.00 0.00 44.22 3.67
173 174 1.583495 CCTCCTGCTCGTACACGACA 61.583 60.000 0.00 4.01 44.22 4.35
174 175 1.136984 CCTCCTGCTCGTACACGAC 59.863 63.158 0.00 0.00 44.22 4.34
176 177 1.154016 CACCTCCTGCTCGTACACG 60.154 63.158 0.00 0.00 41.45 4.49
177 178 1.215647 CCACCTCCTGCTCGTACAC 59.784 63.158 0.00 0.00 0.00 2.90
178 179 1.228769 ACCACCTCCTGCTCGTACA 60.229 57.895 0.00 0.00 0.00 2.90
179 180 1.215647 CACCACCTCCTGCTCGTAC 59.784 63.158 0.00 0.00 0.00 3.67
180 181 1.982395 CCACCACCTCCTGCTCGTA 60.982 63.158 0.00 0.00 0.00 3.43
181 182 3.314331 CCACCACCTCCTGCTCGT 61.314 66.667 0.00 0.00 0.00 4.18
182 183 2.513026 CTTCCACCACCTCCTGCTCG 62.513 65.000 0.00 0.00 0.00 5.03
183 184 1.298014 CTTCCACCACCTCCTGCTC 59.702 63.158 0.00 0.00 0.00 4.26
184 185 1.462238 ACTTCCACCACCTCCTGCT 60.462 57.895 0.00 0.00 0.00 4.24
185 186 1.302832 CACTTCCACCACCTCCTGC 60.303 63.158 0.00 0.00 0.00 4.85
186 187 0.035458 GTCACTTCCACCACCTCCTG 59.965 60.000 0.00 0.00 0.00 3.86
187 188 0.104934 AGTCACTTCCACCACCTCCT 60.105 55.000 0.00 0.00 0.00 3.69
188 189 0.321996 GAGTCACTTCCACCACCTCC 59.678 60.000 0.00 0.00 0.00 4.30
189 190 3.917072 GAGTCACTTCCACCACCTC 57.083 57.895 0.00 0.00 0.00 3.85
603 604 1.341877 CCCCACCCTGATATGCAACAA 60.342 52.381 0.00 0.00 0.00 2.83
604 605 0.258484 CCCCACCCTGATATGCAACA 59.742 55.000 0.00 0.00 0.00 3.33
605 606 0.550914 TCCCCACCCTGATATGCAAC 59.449 55.000 0.00 0.00 0.00 4.17
606 607 0.550914 GTCCCCACCCTGATATGCAA 59.449 55.000 0.00 0.00 0.00 4.08
607 608 1.352622 GGTCCCCACCCTGATATGCA 61.353 60.000 0.00 0.00 36.54 3.96
608 609 1.062488 AGGTCCCCACCCTGATATGC 61.062 60.000 0.00 0.00 45.12 3.14
609 610 1.059913 GAGGTCCCCACCCTGATATG 58.940 60.000 0.00 0.00 45.12 1.78
610 611 0.952659 AGAGGTCCCCACCCTGATAT 59.047 55.000 0.00 0.00 45.12 1.63
611 612 1.627847 TAGAGGTCCCCACCCTGATA 58.372 55.000 0.00 0.00 45.12 2.15
612 613 0.952659 ATAGAGGTCCCCACCCTGAT 59.047 55.000 0.00 0.00 45.12 2.90
613 614 1.503784 CTATAGAGGTCCCCACCCTGA 59.496 57.143 0.00 0.00 45.12 3.86
614 615 1.503784 TCTATAGAGGTCCCCACCCTG 59.496 57.143 0.00 0.00 45.12 4.45
615 616 1.790157 CTCTATAGAGGTCCCCACCCT 59.210 57.143 20.37 0.00 45.12 4.34
616 617 1.787676 TCTCTATAGAGGTCCCCACCC 59.212 57.143 26.02 0.00 45.12 4.61
617 618 3.436243 CATCTCTATAGAGGTCCCCACC 58.564 54.545 26.02 0.00 44.19 4.61
618 619 3.181416 ACCATCTCTATAGAGGTCCCCAC 60.181 52.174 26.02 0.00 42.30 4.61
619 620 3.072086 ACCATCTCTATAGAGGTCCCCA 58.928 50.000 26.02 9.14 42.30 4.96
620 621 3.835395 CAACCATCTCTATAGAGGTCCCC 59.165 52.174 26.02 0.00 42.30 4.81
621 622 3.259625 GCAACCATCTCTATAGAGGTCCC 59.740 52.174 26.02 10.50 42.30 4.46
622 623 3.057174 CGCAACCATCTCTATAGAGGTCC 60.057 52.174 26.02 12.68 42.30 4.46
623 624 3.057174 CCGCAACCATCTCTATAGAGGTC 60.057 52.174 26.02 8.87 42.30 3.85
624 625 2.894126 CCGCAACCATCTCTATAGAGGT 59.106 50.000 26.02 18.92 42.30 3.85
625 626 2.353208 GCCGCAACCATCTCTATAGAGG 60.353 54.545 26.02 15.71 42.30 3.69
626 627 2.669670 CGCCGCAACCATCTCTATAGAG 60.670 54.545 21.81 21.81 43.36 2.43
627 628 1.269723 CGCCGCAACCATCTCTATAGA 59.730 52.381 1.69 1.69 35.80 1.98
628 629 1.670087 CCGCCGCAACCATCTCTATAG 60.670 57.143 0.00 0.00 0.00 1.31
629 630 0.317160 CCGCCGCAACCATCTCTATA 59.683 55.000 0.00 0.00 0.00 1.31
630 631 1.069765 CCGCCGCAACCATCTCTAT 59.930 57.895 0.00 0.00 0.00 1.98
631 632 2.499205 CCGCCGCAACCATCTCTA 59.501 61.111 0.00 0.00 0.00 2.43
649 650 4.368808 CACCGTCGTTGCTTGCCG 62.369 66.667 0.00 0.00 0.00 5.69
650 651 4.025401 CCACCGTCGTTGCTTGCC 62.025 66.667 0.00 0.00 0.00 4.52
651 652 4.025401 CCCACCGTCGTTGCTTGC 62.025 66.667 0.00 0.00 0.00 4.01
652 653 3.353836 CCCCACCGTCGTTGCTTG 61.354 66.667 0.00 0.00 0.00 4.01
653 654 4.636435 CCCCCACCGTCGTTGCTT 62.636 66.667 0.00 0.00 0.00 3.91
656 657 4.388499 CCTCCCCCACCGTCGTTG 62.388 72.222 0.00 0.00 0.00 4.10
657 658 4.948080 ACCTCCCCCACCGTCGTT 62.948 66.667 0.00 0.00 0.00 3.85
658 659 4.948080 AACCTCCCCCACCGTCGT 62.948 66.667 0.00 0.00 0.00 4.34
659 660 4.388499 CAACCTCCCCCACCGTCG 62.388 72.222 0.00 0.00 0.00 5.12
660 661 2.298661 ATCAACCTCCCCCACCGTC 61.299 63.158 0.00 0.00 0.00 4.79
661 662 2.204090 ATCAACCTCCCCCACCGT 60.204 61.111 0.00 0.00 0.00 4.83
662 663 2.272146 CATCAACCTCCCCCACCG 59.728 66.667 0.00 0.00 0.00 4.94
663 664 2.683475 CCATCAACCTCCCCCACC 59.317 66.667 0.00 0.00 0.00 4.61
664 665 1.926426 CTCCCATCAACCTCCCCCAC 61.926 65.000 0.00 0.00 0.00 4.61
665 666 1.619363 CTCCCATCAACCTCCCCCA 60.619 63.158 0.00 0.00 0.00 4.96
666 667 2.386935 CCTCCCATCAACCTCCCCC 61.387 68.421 0.00 0.00 0.00 5.40
667 668 2.386935 CCCTCCCATCAACCTCCCC 61.387 68.421 0.00 0.00 0.00 4.81
668 669 3.061905 GCCCTCCCATCAACCTCCC 62.062 68.421 0.00 0.00 0.00 4.30
669 670 2.597903 GCCCTCCCATCAACCTCC 59.402 66.667 0.00 0.00 0.00 4.30
670 671 2.190578 CGCCCTCCCATCAACCTC 59.809 66.667 0.00 0.00 0.00 3.85
671 672 2.285368 TCGCCCTCCCATCAACCT 60.285 61.111 0.00 0.00 0.00 3.50
672 673 2.190578 CTCGCCCTCCCATCAACC 59.809 66.667 0.00 0.00 0.00 3.77
673 674 2.190578 CCTCGCCCTCCCATCAAC 59.809 66.667 0.00 0.00 0.00 3.18
674 675 3.797353 GCCTCGCCCTCCCATCAA 61.797 66.667 0.00 0.00 0.00 2.57
698 699 4.135153 AGCTAGTGGGCGCTGTCG 62.135 66.667 7.64 0.00 34.69 4.35
719 720 2.122189 CTGGATCCCCTCTCCCCC 60.122 72.222 9.90 0.00 31.32 5.40
720 721 2.122189 CCTGGATCCCCTCTCCCC 60.122 72.222 9.90 0.00 31.32 4.81
726 727 2.455565 CCAATCGCCTGGATCCCCT 61.456 63.158 9.90 0.00 38.96 4.79
755 756 0.040692 CTTCATCATGCATTCGCCCG 60.041 55.000 0.00 0.00 37.32 6.13
775 776 5.826208 GGTTCACCTTCAACCTTTCTTTCTA 59.174 40.000 0.00 0.00 40.33 2.10
793 794 1.531149 CAATCACCTCACACGGTTCAC 59.469 52.381 0.00 0.00 34.29 3.18
799 800 1.395954 CATCTGCAATCACCTCACACG 59.604 52.381 0.00 0.00 0.00 4.49
827 834 1.238625 TTTTTGGACCGCCGGATCAC 61.239 55.000 11.71 0.00 36.79 3.06
853 860 3.485743 GTGAAAACAAACTTGGCGTCATC 59.514 43.478 0.00 0.00 0.00 2.92
858 865 4.856115 ATTTGTGAAAACAAACTTGGCG 57.144 36.364 6.19 0.00 41.63 5.69
864 871 4.048504 AGCGCCTATTTGTGAAAACAAAC 58.951 39.130 2.29 0.00 41.63 2.93
883 890 6.539649 TTCTGAAAAATAATATCCGGAGCG 57.460 37.500 11.34 0.00 0.00 5.03
889 896 9.045223 GGGTGCAATTTCTGAAAAATAATATCC 57.955 33.333 6.95 3.43 0.00 2.59
938 945 1.519455 CCGAATGAGAGCGTGGACC 60.519 63.158 0.00 0.00 0.00 4.46
988 995 7.380602 GTGAATTAGCCACATTGCTGATAATTC 59.619 37.037 19.51 19.51 42.77 2.17
991 998 5.067674 GGTGAATTAGCCACATTGCTGATAA 59.932 40.000 0.00 0.00 42.77 1.75
1177 1185 3.117888 ACATTCTTGAGTGGTGGTGAAGT 60.118 43.478 0.00 0.00 0.00 3.01
1190 1198 4.456280 AGCTCGTACATGACATTCTTGA 57.544 40.909 0.00 0.00 0.00 3.02
1264 1272 2.582436 CCTTAAGAGCCGCCCGAA 59.418 61.111 3.36 0.00 0.00 4.30
1461 1469 1.306970 GAAGGAGGAGGACCGGAGA 59.693 63.158 9.46 0.00 41.83 3.71
1827 1835 1.376466 GTGGATGGACAGCACCACT 59.624 57.895 0.00 0.00 46.14 4.00
2083 2091 2.897207 CCTGTGGCGGTCCGAATA 59.103 61.111 17.49 0.00 34.14 1.75
2125 2334 1.148310 CAGGGCGAAGTACACAACAG 58.852 55.000 0.00 0.00 0.00 3.16
2129 2338 1.292223 GAGCAGGGCGAAGTACACA 59.708 57.895 0.00 0.00 0.00 3.72
2142 2351 0.031314 ACTCATGTATCCGCGAGCAG 59.969 55.000 8.23 0.00 0.00 4.24
2253 2462 1.200760 TGTAGATGGTGCCCAGCAGT 61.201 55.000 11.32 0.00 43.12 4.40
2640 2856 0.102481 ATACCGACACCAGCGACATC 59.898 55.000 0.00 0.00 0.00 3.06
2658 2874 3.682292 GAAGAACCCGGCCAGCGAT 62.682 63.158 2.24 0.00 0.00 4.58
2685 2901 1.810030 CCGCGACAGAAAGTAGCCC 60.810 63.158 8.23 0.00 44.85 5.19
2694 2910 3.749064 GTGCTCTCCCGCGACAGA 61.749 66.667 8.23 7.29 0.00 3.41
2832 3048 1.979155 CCCCGTCTCAGAGCACTCA 60.979 63.158 0.00 0.00 0.00 3.41
2970 4520 0.908198 GTCACCTCTTGGCTCTGGAT 59.092 55.000 0.00 0.00 36.63 3.41
2991 4541 5.235186 AGTCGAAATTCATGGATCGATCAAC 59.765 40.000 25.93 10.89 44.90 3.18
3013 4563 5.890049 AGTGTAGTGTAGTAAGGGAGAAGT 58.110 41.667 0.00 0.00 0.00 3.01
3016 4566 5.191323 AGCTAGTGTAGTGTAGTAAGGGAGA 59.809 44.000 0.00 0.00 0.00 3.71
3116 4667 3.058293 GTCGATGAACTTTGACATTGGCA 60.058 43.478 0.00 0.00 34.02 4.92
3248 4800 4.158209 TGAGTTCATAACCAATGGCATGTG 59.842 41.667 0.00 1.66 36.15 3.21
3260 4812 7.331934 TGCTACAGACAGAATTGAGTTCATAAC 59.668 37.037 0.00 0.00 39.39 1.89
3461 5013 2.427095 GGATGCTTAAAAGACGGCCATT 59.573 45.455 2.24 0.00 0.00 3.16
3481 5033 2.589798 TAATCGCACTACCCTTTCGG 57.410 50.000 0.00 0.00 37.81 4.30
3630 5182 6.446318 TGGAATACTGAAATTGCACAACTTC 58.554 36.000 0.00 0.00 32.95 3.01
3650 5202 6.775629 AGACAACAGTTAGCCTAAAATTGGAA 59.224 34.615 7.92 0.00 0.00 3.53
3658 5210 9.871238 CTTAAGATTAGACAACAGTTAGCCTAA 57.129 33.333 0.00 0.00 0.00 2.69
3801 5354 5.302823 AGGAGAAAAGGTGATTGAGTTTTGG 59.697 40.000 0.00 0.00 0.00 3.28
3816 5369 4.249661 AGAGAAGCGCTTAAGGAGAAAAG 58.750 43.478 25.11 0.00 0.00 2.27
3861 5416 8.530311 CCATGATCAGATAGCTAACTTACTGAT 58.470 37.037 20.02 20.02 43.57 2.90
3961 5516 1.672881 GGCTCCGTCAGAAATGGATTG 59.327 52.381 0.00 0.00 42.37 2.67
3962 5517 1.743772 CGGCTCCGTCAGAAATGGATT 60.744 52.381 0.00 0.00 42.37 3.01
3963 5518 0.179073 CGGCTCCGTCAGAAATGGAT 60.179 55.000 0.00 0.00 42.37 3.41
3964 5519 1.218047 CGGCTCCGTCAGAAATGGA 59.782 57.895 0.00 0.00 40.99 3.41
3965 5520 2.464459 GCGGCTCCGTCAGAAATGG 61.464 63.158 10.24 0.00 42.09 3.16


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

AutoCloner maintained by Alex Coulton.