Multiple sequence alignment - TraesCS5D01G401000

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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 TraesCS5D01G401000 chr5D 100.000 6202 0 0 1 6202 466220209 466226410 0.000000e+00 11454.0
1 TraesCS5D01G401000 chr5B 94.433 5982 184 58 292 6202 573216254 573222157 0.000000e+00 9064.0
2 TraesCS5D01G401000 chr5B 91.288 264 15 5 27 282 516028915 516028652 2.750000e-93 353.0
3 TraesCS5D01G401000 chr5A 95.520 5245 119 49 317 5516 586594580 586599753 0.000000e+00 8277.0
4 TraesCS5D01G401000 chr5A 96.019 628 18 6 5578 6202 586599783 586600406 0.000000e+00 1014.0
5 TraesCS5D01G401000 chr5A 97.500 40 0 1 1 39 481684704 481684743 4.010000e-07 67.6
6 TraesCS5D01G401000 chr5A 88.889 54 2 3 1 51 528555069 528555121 5.190000e-06 63.9
7 TraesCS5D01G401000 chr7D 93.462 260 8 3 27 277 474523106 474522847 1.630000e-100 377.0
8 TraesCS5D01G401000 chr7D 88.672 256 18 9 27 271 538668919 538668664 1.010000e-77 302.0
9 TraesCS5D01G401000 chr6D 91.603 262 11 6 27 277 115651350 115651089 9.890000e-93 351.0
10 TraesCS5D01G401000 chr6D 92.683 41 1 1 1 39 20833025 20833065 2.410000e-04 58.4
11 TraesCS5D01G401000 chr6D 87.037 54 3 3 1 51 56858890 56858838 2.410000e-04 58.4
12 TraesCS5D01G401000 chr3D 91.571 261 12 8 27 277 512748746 512749006 9.890000e-93 351.0
13 TraesCS5D01G401000 chr3D 88.889 54 2 3 1 51 278067502 278067450 5.190000e-06 63.9
14 TraesCS5D01G401000 chr2D 91.188 261 12 5 27 276 472444400 472444140 1.660000e-90 344.0
15 TraesCS5D01G401000 chr2D 91.860 86 7 0 1609 1694 199139691 199139776 3.040000e-23 121.0
16 TraesCS5D01G401000 chr2D 90.566 53 1 3 1 50 118249085 118249034 4.010000e-07 67.6
17 TraesCS5D01G401000 chr4D 91.085 258 15 6 27 277 453054284 453054028 5.950000e-90 342.0
18 TraesCS5D01G401000 chr1A 90.551 254 18 3 27 277 365535361 365535611 1.290000e-86 331.0
19 TraesCS5D01G401000 chr4A 87.023 262 23 6 27 277 190185382 190185121 1.020000e-72 285.0
20 TraesCS5D01G401000 chrUn 92.683 41 1 1 1 39 115109970 115110010 2.410000e-04 58.4


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 TraesCS5D01G401000 chr5D 466220209 466226410 6201 False 11454.0 11454 100.0000 1 6202 1 chr5D.!!$F1 6201
1 TraesCS5D01G401000 chr5B 573216254 573222157 5903 False 9064.0 9064 94.4330 292 6202 1 chr5B.!!$F1 5910
2 TraesCS5D01G401000 chr5A 586594580 586600406 5826 False 4645.5 8277 95.7695 317 6202 2 chr5A.!!$F3 5885

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
202 203 0.030235 GGGCGTCACACAAAAAGGTC 59.970 55.0 0.00 0.00 0.00 3.85 F
216 217 0.036765 AAGGTCAGCCGCGTGAAATA 60.037 50.0 4.92 0.00 40.50 1.40 F
268 269 0.108963 TCGTCCCCGGTCAAATTTGT 59.891 50.0 17.47 0.00 33.95 2.83 F
375 384 0.171007 AAGTGGCGCCATCGAAATTG 59.829 50.0 35.23 0.00 38.10 2.32 F
1761 1815 0.330604 AGCATGGTGAGGTCATTGCT 59.669 50.0 0.00 8.43 35.83 3.91 F
3073 3127 0.536006 AGCTCTGCAAGGTTGTCACC 60.536 55.0 0.00 0.00 44.67 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1491 1545 0.179000 AGATGGCGTAGAAGGGCTTG 59.821 55.000 0.00 0.00 0.00 4.01 R
2076 2130 0.829182 CCCACAGCTTCCTGCCTTTT 60.829 55.000 0.00 0.00 43.02 2.27 R
2457 2511 2.573462 TCCTGCTTCCAATAAGCTGTCT 59.427 45.455 10.74 0.00 43.38 3.41 R
2496 2550 0.389391 CACAGACAACCTCACCGAGT 59.611 55.000 0.00 0.00 0.00 4.18 R
3848 3904 2.235898 ACGGGTAAATTGCATGCCATTT 59.764 40.909 26.99 26.99 0.00 2.32 R
5210 5291 0.243907 CACATCTCGAGGACACCGTT 59.756 55.000 13.56 0.00 0.00 4.44 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 3.150335 CCTGAGAGCTAGGCGCCA 61.150 66.667 31.54 14.00 40.39 5.69
21 22 2.105930 CTGAGAGCTAGGCGCCAC 59.894 66.667 31.54 17.93 40.39 5.01
22 23 2.679996 TGAGAGCTAGGCGCCACA 60.680 61.111 31.54 15.42 40.39 4.17
23 24 2.202810 GAGAGCTAGGCGCCACAC 60.203 66.667 31.54 17.11 40.39 3.82
24 25 2.681778 AGAGCTAGGCGCCACACT 60.682 61.111 31.54 21.99 40.39 3.55
25 26 1.379977 AGAGCTAGGCGCCACACTA 60.380 57.895 31.54 11.42 40.39 2.74
26 27 0.757188 AGAGCTAGGCGCCACACTAT 60.757 55.000 31.54 16.52 40.39 2.12
27 28 0.959553 GAGCTAGGCGCCACACTATA 59.040 55.000 31.54 10.17 40.39 1.31
28 29 0.962489 AGCTAGGCGCCACACTATAG 59.038 55.000 31.54 20.65 40.39 1.31
29 30 0.674534 GCTAGGCGCCACACTATAGT 59.325 55.000 31.54 6.76 0.00 2.12
30 31 3.911323 AGCTAGGCGCCACACTATAGTG 61.911 54.545 31.54 27.66 45.25 2.74
39 40 2.598045 CACTATAGTGCAGCGCCTG 58.402 57.895 19.55 2.69 39.39 4.85
40 41 0.103026 CACTATAGTGCAGCGCCTGA 59.897 55.000 19.55 0.00 39.39 3.86
41 42 0.387202 ACTATAGTGCAGCGCCTGAG 59.613 55.000 2.29 0.00 32.44 3.35
42 43 0.670706 CTATAGTGCAGCGCCTGAGA 59.329 55.000 2.29 0.00 32.44 3.27
43 44 0.670706 TATAGTGCAGCGCCTGAGAG 59.329 55.000 2.29 0.00 32.44 3.20
44 45 2.641439 ATAGTGCAGCGCCTGAGAGC 62.641 60.000 2.29 0.00 39.42 4.09
53 54 3.150335 CCTGAGAGCTAGGCGCCA 61.150 66.667 31.54 14.00 40.39 5.69
54 55 2.105930 CTGAGAGCTAGGCGCCAC 59.894 66.667 31.54 17.93 40.39 5.01
55 56 2.679996 TGAGAGCTAGGCGCCACA 60.680 61.111 31.54 15.42 40.39 4.17
56 57 2.202810 GAGAGCTAGGCGCCACAC 60.203 66.667 31.54 17.11 40.39 3.82
57 58 2.681778 AGAGCTAGGCGCCACACT 60.682 61.111 31.54 21.99 40.39 3.55
58 59 1.379977 AGAGCTAGGCGCCACACTA 60.380 57.895 31.54 11.42 40.39 2.74
59 60 0.757188 AGAGCTAGGCGCCACACTAT 60.757 55.000 31.54 16.52 40.39 2.12
60 61 0.959553 GAGCTAGGCGCCACACTATA 59.040 55.000 31.54 10.17 40.39 1.31
61 62 0.962489 AGCTAGGCGCCACACTATAG 59.038 55.000 31.54 20.65 40.39 1.31
62 63 0.674534 GCTAGGCGCCACACTATAGT 59.325 55.000 31.54 6.76 0.00 2.12
63 64 3.911323 AGCTAGGCGCCACACTATAGTG 61.911 54.545 31.54 27.66 45.25 2.74
74 75 2.656085 CACTATAGTGCAGCGTCTAGC 58.344 52.381 19.55 0.00 42.13 3.42
76 77 3.608241 CACTATAGTGCAGCGTCTAGCTC 60.608 52.174 19.55 0.00 45.99 4.09
77 78 5.804604 CACTATAGTGCAGCGTCTAGCTCT 61.805 50.000 19.55 0.00 45.99 4.09
78 79 7.217041 CACTATAGTGCAGCGTCTAGCTCTT 62.217 48.000 19.55 0.00 45.99 2.85
79 80 7.942375 CACTATAGTGCAGCGTCTAGCTCTTA 61.942 46.154 19.55 0.00 45.99 2.10
80 81 9.616216 CACTATAGTGCAGCGTCTAGCTCTTAG 62.616 48.148 19.55 0.00 45.99 2.18
84 85 3.857638 GCGTCTAGCTCTTAGGCTC 57.142 57.895 0.00 0.00 42.97 4.70
85 86 1.314730 GCGTCTAGCTCTTAGGCTCT 58.685 55.000 0.00 0.00 42.97 4.09
86 87 1.001815 GCGTCTAGCTCTTAGGCTCTG 60.002 57.143 0.00 0.00 42.97 3.35
87 88 1.001815 CGTCTAGCTCTTAGGCTCTGC 60.002 57.143 0.00 0.00 42.97 4.26
88 89 2.028130 GTCTAGCTCTTAGGCTCTGCA 58.972 52.381 0.00 0.00 42.97 4.41
89 90 2.028130 TCTAGCTCTTAGGCTCTGCAC 58.972 52.381 0.00 0.00 42.97 4.57
90 91 1.753649 CTAGCTCTTAGGCTCTGCACA 59.246 52.381 0.00 0.00 42.97 4.57
91 92 0.979665 AGCTCTTAGGCTCTGCACAA 59.020 50.000 0.00 0.00 38.24 3.33
92 93 1.558756 AGCTCTTAGGCTCTGCACAAT 59.441 47.619 0.00 0.00 38.24 2.71
93 94 1.669779 GCTCTTAGGCTCTGCACAATG 59.330 52.381 0.00 0.00 0.00 2.82
94 95 2.679059 GCTCTTAGGCTCTGCACAATGA 60.679 50.000 0.00 0.00 0.00 2.57
95 96 2.935201 CTCTTAGGCTCTGCACAATGAC 59.065 50.000 0.00 0.00 0.00 3.06
96 97 2.568956 TCTTAGGCTCTGCACAATGACT 59.431 45.455 0.00 0.00 0.00 3.41
97 98 3.008375 TCTTAGGCTCTGCACAATGACTT 59.992 43.478 0.00 0.00 0.00 3.01
98 99 4.222810 TCTTAGGCTCTGCACAATGACTTA 59.777 41.667 0.00 0.00 0.00 2.24
99 100 2.983229 AGGCTCTGCACAATGACTTAG 58.017 47.619 0.00 0.00 0.00 2.18
100 101 1.399791 GGCTCTGCACAATGACTTAGC 59.600 52.381 0.00 0.00 0.00 3.09
101 102 2.079158 GCTCTGCACAATGACTTAGCA 58.921 47.619 0.00 0.00 0.00 3.49
102 103 2.485426 GCTCTGCACAATGACTTAGCAA 59.515 45.455 0.00 0.00 34.45 3.91
103 104 3.128242 GCTCTGCACAATGACTTAGCAAT 59.872 43.478 0.00 0.00 34.45 3.56
104 105 4.380233 GCTCTGCACAATGACTTAGCAATT 60.380 41.667 0.00 0.00 34.45 2.32
105 106 5.706916 CTCTGCACAATGACTTAGCAATTT 58.293 37.500 0.00 0.00 34.45 1.82
106 107 6.088016 TCTGCACAATGACTTAGCAATTTT 57.912 33.333 0.00 0.00 34.45 1.82
107 108 6.514947 TCTGCACAATGACTTAGCAATTTTT 58.485 32.000 0.00 0.00 34.45 1.94
108 109 7.656412 TCTGCACAATGACTTAGCAATTTTTA 58.344 30.769 0.00 0.00 34.45 1.52
109 110 7.809331 TCTGCACAATGACTTAGCAATTTTTAG 59.191 33.333 0.00 0.00 34.45 1.85
110 111 6.867816 TGCACAATGACTTAGCAATTTTTAGG 59.132 34.615 0.00 0.00 31.42 2.69
111 112 6.183360 GCACAATGACTTAGCAATTTTTAGGC 60.183 38.462 0.00 0.00 0.00 3.93
112 113 6.867816 CACAATGACTTAGCAATTTTTAGGCA 59.132 34.615 0.00 0.00 0.00 4.75
113 114 7.062605 CACAATGACTTAGCAATTTTTAGGCAG 59.937 37.037 0.00 0.00 0.00 4.85
114 115 6.840780 ATGACTTAGCAATTTTTAGGCAGT 57.159 33.333 0.00 0.00 0.00 4.40
115 116 6.254281 TGACTTAGCAATTTTTAGGCAGTC 57.746 37.500 0.00 0.00 33.59 3.51
116 117 6.003950 TGACTTAGCAATTTTTAGGCAGTCT 58.996 36.000 0.00 0.00 33.92 3.24
117 118 6.072508 TGACTTAGCAATTTTTAGGCAGTCTG 60.073 38.462 0.00 0.00 33.92 3.51
118 119 5.183904 ACTTAGCAATTTTTAGGCAGTCTGG 59.816 40.000 1.14 0.00 0.00 3.86
119 120 2.827921 AGCAATTTTTAGGCAGTCTGGG 59.172 45.455 1.14 0.00 0.00 4.45
120 121 2.094026 GCAATTTTTAGGCAGTCTGGGG 60.094 50.000 1.14 0.00 0.00 4.96
121 122 3.165071 CAATTTTTAGGCAGTCTGGGGT 58.835 45.455 1.14 0.00 0.00 4.95
122 123 2.286365 TTTTTAGGCAGTCTGGGGTG 57.714 50.000 1.14 0.00 0.00 4.61
123 124 0.251165 TTTTAGGCAGTCTGGGGTGC 60.251 55.000 1.14 0.00 39.08 5.01
124 125 1.422977 TTTAGGCAGTCTGGGGTGCA 61.423 55.000 1.14 0.00 41.75 4.57
125 126 1.422977 TTAGGCAGTCTGGGGTGCAA 61.423 55.000 1.14 0.00 41.75 4.08
126 127 2.124507 TAGGCAGTCTGGGGTGCAAC 62.125 60.000 1.14 0.00 41.75 4.17
127 128 3.357079 GCAGTCTGGGGTGCAACG 61.357 66.667 1.14 0.00 39.62 4.10
140 141 3.663176 CAACGCTGGCCAGGTGTG 61.663 66.667 33.46 21.87 0.00 3.82
141 142 4.189580 AACGCTGGCCAGGTGTGT 62.190 61.111 33.46 18.84 0.00 3.72
142 143 2.813726 AACGCTGGCCAGGTGTGTA 61.814 57.895 33.46 0.00 0.00 2.90
143 144 2.434884 CGCTGGCCAGGTGTGTAG 60.435 66.667 33.46 7.49 0.00 2.74
144 145 2.747855 GCTGGCCAGGTGTGTAGC 60.748 66.667 33.46 14.33 0.00 3.58
145 146 2.434884 CTGGCCAGGTGTGTAGCG 60.435 66.667 26.14 0.00 0.00 4.26
146 147 4.697756 TGGCCAGGTGTGTAGCGC 62.698 66.667 0.00 0.00 0.00 5.92
154 155 1.734163 GGTGTGTAGCGCCTATTTGT 58.266 50.000 2.29 0.00 44.20 2.83
155 156 1.396996 GGTGTGTAGCGCCTATTTGTG 59.603 52.381 2.29 0.00 44.20 3.33
156 157 2.343101 GTGTGTAGCGCCTATTTGTGA 58.657 47.619 2.29 0.00 0.00 3.58
157 158 2.348666 GTGTGTAGCGCCTATTTGTGAG 59.651 50.000 2.29 0.00 0.00 3.51
158 159 1.933853 GTGTAGCGCCTATTTGTGAGG 59.066 52.381 2.29 0.00 37.12 3.86
164 165 3.996825 CCTATTTGTGAGGCGTTGC 57.003 52.632 0.00 0.00 0.00 4.17
165 166 1.164411 CCTATTTGTGAGGCGTTGCA 58.836 50.000 0.00 0.00 0.00 4.08
166 167 1.135689 CCTATTTGTGAGGCGTTGCAC 60.136 52.381 0.00 0.00 35.63 4.57
167 168 1.535028 CTATTTGTGAGGCGTTGCACA 59.465 47.619 0.00 0.00 42.73 4.57
169 170 2.413677 TTGTGAGGCGTTGCACAAT 58.586 47.368 8.97 0.00 46.57 2.71
170 171 0.030504 TTGTGAGGCGTTGCACAATG 59.969 50.000 8.97 0.00 46.57 2.82
171 172 1.100463 TGTGAGGCGTTGCACAATGT 61.100 50.000 4.63 0.00 41.61 2.71
172 173 0.871722 GTGAGGCGTTGCACAATGTA 59.128 50.000 4.63 0.00 35.19 2.29
173 174 1.135972 GTGAGGCGTTGCACAATGTAG 60.136 52.381 4.63 0.00 35.19 2.74
174 175 1.156736 GAGGCGTTGCACAATGTAGT 58.843 50.000 4.63 0.00 0.00 2.73
175 176 0.874390 AGGCGTTGCACAATGTAGTG 59.126 50.000 4.63 0.00 42.37 2.74
176 177 0.591170 GGCGTTGCACAATGTAGTGT 59.409 50.000 4.63 0.00 41.52 3.55
182 183 1.501741 CACAATGTAGTGTGGCGCC 59.498 57.895 22.73 22.73 44.29 6.53
183 184 2.032634 ACAATGTAGTGTGGCGCCG 61.033 57.895 23.90 5.43 0.00 6.46
184 185 2.435938 AATGTAGTGTGGCGCCGG 60.436 61.111 23.90 0.00 0.00 6.13
185 186 3.969250 AATGTAGTGTGGCGCCGGG 62.969 63.158 23.90 0.00 0.00 5.73
197 198 3.587933 GCCGGGCGTCACACAAAA 61.588 61.111 1.81 0.00 0.00 2.44
198 199 3.111939 CCGGGCGTCACACAAAAA 58.888 55.556 0.00 0.00 0.00 1.94
199 200 1.008995 CCGGGCGTCACACAAAAAG 60.009 57.895 0.00 0.00 0.00 2.27
200 201 1.008995 CGGGCGTCACACAAAAAGG 60.009 57.895 0.00 0.00 0.00 3.11
201 202 1.720694 CGGGCGTCACACAAAAAGGT 61.721 55.000 0.00 0.00 0.00 3.50
202 203 0.030235 GGGCGTCACACAAAAAGGTC 59.970 55.000 0.00 0.00 0.00 3.85
203 204 0.736053 GGCGTCACACAAAAAGGTCA 59.264 50.000 0.00 0.00 0.00 4.02
204 205 1.268539 GGCGTCACACAAAAAGGTCAG 60.269 52.381 0.00 0.00 0.00 3.51
205 206 1.859998 GCGTCACACAAAAAGGTCAGC 60.860 52.381 0.00 0.00 0.00 4.26
206 207 1.268539 CGTCACACAAAAAGGTCAGCC 60.269 52.381 0.00 0.00 0.00 4.85
207 208 1.021202 TCACACAAAAAGGTCAGCCG 58.979 50.000 0.00 0.00 40.50 5.52
208 209 0.594796 CACACAAAAAGGTCAGCCGC 60.595 55.000 0.00 0.00 40.50 6.53
209 210 1.370414 CACAAAAAGGTCAGCCGCG 60.370 57.895 0.00 0.00 40.50 6.46
210 211 1.822186 ACAAAAAGGTCAGCCGCGT 60.822 52.632 4.92 0.00 40.50 6.01
211 212 1.370414 CAAAAAGGTCAGCCGCGTG 60.370 57.895 4.92 0.00 40.50 5.34
212 213 1.525077 AAAAAGGTCAGCCGCGTGA 60.525 52.632 4.92 0.00 40.50 4.35
213 214 1.098712 AAAAAGGTCAGCCGCGTGAA 61.099 50.000 4.92 0.00 40.50 3.18
214 215 1.098712 AAAAGGTCAGCCGCGTGAAA 61.099 50.000 4.92 0.00 40.50 2.69
215 216 0.889186 AAAGGTCAGCCGCGTGAAAT 60.889 50.000 4.92 0.00 40.50 2.17
216 217 0.036765 AAGGTCAGCCGCGTGAAATA 60.037 50.000 4.92 0.00 40.50 1.40
217 218 0.460284 AGGTCAGCCGCGTGAAATAG 60.460 55.000 4.92 0.00 40.50 1.73
218 219 0.739813 GGTCAGCCGCGTGAAATAGT 60.740 55.000 4.92 0.00 0.00 2.12
219 220 1.076332 GTCAGCCGCGTGAAATAGTT 58.924 50.000 4.92 0.00 0.00 2.24
220 221 1.463444 GTCAGCCGCGTGAAATAGTTT 59.537 47.619 4.92 0.00 0.00 2.66
221 222 1.730064 TCAGCCGCGTGAAATAGTTTC 59.270 47.619 4.92 0.00 40.08 2.78
222 223 1.463056 CAGCCGCGTGAAATAGTTTCA 59.537 47.619 4.92 1.24 46.68 2.69
232 233 5.917541 TGAAATAGTTTCACGGACAGTTC 57.082 39.130 1.24 0.00 44.21 3.01
233 234 5.361427 TGAAATAGTTTCACGGACAGTTCA 58.639 37.500 1.24 0.00 44.21 3.18
234 235 5.995282 TGAAATAGTTTCACGGACAGTTCAT 59.005 36.000 1.24 0.00 44.21 2.57
235 236 6.485313 TGAAATAGTTTCACGGACAGTTCATT 59.515 34.615 1.24 0.00 44.21 2.57
236 237 6.481954 AATAGTTTCACGGACAGTTCATTC 57.518 37.500 0.00 0.00 0.00 2.67
237 238 4.073293 AGTTTCACGGACAGTTCATTCT 57.927 40.909 0.00 0.00 0.00 2.40
238 239 3.809832 AGTTTCACGGACAGTTCATTCTG 59.190 43.478 0.00 0.00 40.80 3.02
240 241 2.754472 TCACGGACAGTTCATTCTGTG 58.246 47.619 4.06 4.48 46.81 3.66
242 243 3.685139 ACGGACAGTTCATTCTGTGAT 57.315 42.857 4.06 0.00 46.81 3.06
243 244 4.008074 ACGGACAGTTCATTCTGTGATT 57.992 40.909 4.06 0.00 46.81 2.57
244 245 4.389374 ACGGACAGTTCATTCTGTGATTT 58.611 39.130 4.06 0.00 46.81 2.17
245 246 4.214119 ACGGACAGTTCATTCTGTGATTTG 59.786 41.667 4.06 0.00 46.81 2.32
246 247 4.452114 CGGACAGTTCATTCTGTGATTTGA 59.548 41.667 4.06 0.00 46.81 2.69
247 248 5.122869 CGGACAGTTCATTCTGTGATTTGAT 59.877 40.000 4.06 0.00 46.81 2.57
248 249 6.348786 CGGACAGTTCATTCTGTGATTTGATT 60.349 38.462 4.06 0.00 46.81 2.57
249 250 7.373493 GGACAGTTCATTCTGTGATTTGATTT 58.627 34.615 4.06 0.00 46.81 2.17
250 251 7.540055 GGACAGTTCATTCTGTGATTTGATTTC 59.460 37.037 4.06 0.00 46.81 2.17
251 252 7.080099 ACAGTTCATTCTGTGATTTGATTTCG 58.920 34.615 0.00 0.00 45.40 3.46
252 253 7.080099 CAGTTCATTCTGTGATTTGATTTCGT 58.920 34.615 0.00 0.00 36.54 3.85
253 254 7.269937 CAGTTCATTCTGTGATTTGATTTCGTC 59.730 37.037 0.00 0.00 36.54 4.20
254 255 6.182039 TCATTCTGTGATTTGATTTCGTCC 57.818 37.500 0.00 0.00 0.00 4.79
255 256 5.123820 TCATTCTGTGATTTGATTTCGTCCC 59.876 40.000 0.00 0.00 0.00 4.46
256 257 3.343617 TCTGTGATTTGATTTCGTCCCC 58.656 45.455 0.00 0.00 0.00 4.81
257 258 2.080693 TGTGATTTGATTTCGTCCCCG 58.919 47.619 0.00 0.00 0.00 5.73
258 259 1.400494 GTGATTTGATTTCGTCCCCGG 59.600 52.381 0.00 0.00 33.95 5.73
259 260 1.003812 TGATTTGATTTCGTCCCCGGT 59.996 47.619 0.00 0.00 33.95 5.28
260 261 1.669265 GATTTGATTTCGTCCCCGGTC 59.331 52.381 0.00 0.00 33.95 4.79
261 262 0.397187 TTTGATTTCGTCCCCGGTCA 59.603 50.000 0.00 0.00 33.95 4.02
262 263 0.397187 TTGATTTCGTCCCCGGTCAA 59.603 50.000 0.00 0.00 32.30 3.18
263 264 0.397187 TGATTTCGTCCCCGGTCAAA 59.603 50.000 0.00 0.00 33.95 2.69
264 265 1.003812 TGATTTCGTCCCCGGTCAAAT 59.996 47.619 0.00 0.00 33.95 2.32
265 266 2.089201 GATTTCGTCCCCGGTCAAATT 58.911 47.619 0.00 0.00 33.95 1.82
266 267 1.984066 TTTCGTCCCCGGTCAAATTT 58.016 45.000 0.00 0.00 33.95 1.82
267 268 1.240256 TTCGTCCCCGGTCAAATTTG 58.760 50.000 12.15 12.15 33.95 2.32
268 269 0.108963 TCGTCCCCGGTCAAATTTGT 59.891 50.000 17.47 0.00 33.95 2.83
269 270 0.519961 CGTCCCCGGTCAAATTTGTC 59.480 55.000 17.47 12.07 0.00 3.18
270 271 1.611519 GTCCCCGGTCAAATTTGTCA 58.388 50.000 17.47 0.00 0.00 3.58
271 272 1.957877 GTCCCCGGTCAAATTTGTCAA 59.042 47.619 17.47 0.00 0.00 3.18
272 273 2.362717 GTCCCCGGTCAAATTTGTCAAA 59.637 45.455 17.47 0.00 0.00 2.69
273 274 3.006430 GTCCCCGGTCAAATTTGTCAAAT 59.994 43.478 17.47 4.91 0.00 2.32
274 275 3.643792 TCCCCGGTCAAATTTGTCAAATT 59.356 39.130 16.26 16.26 42.62 1.82
288 289 4.217754 GTCAAATTTGACGCCAAGTACA 57.782 40.909 29.94 0.00 46.80 2.90
289 290 3.972502 GTCAAATTTGACGCCAAGTACAC 59.027 43.478 29.94 8.66 46.80 2.90
290 291 3.880490 TCAAATTTGACGCCAAGTACACT 59.120 39.130 16.91 0.00 33.23 3.55
291 292 4.024387 TCAAATTTGACGCCAAGTACACTC 60.024 41.667 16.91 0.00 33.23 3.51
292 293 1.873698 TTTGACGCCAAGTACACTCC 58.126 50.000 0.00 0.00 33.23 3.85
293 294 0.319211 TTGACGCCAAGTACACTCCG 60.319 55.000 0.00 0.00 0.00 4.63
294 295 1.288127 GACGCCAAGTACACTCCGT 59.712 57.895 0.00 0.00 0.00 4.69
375 384 0.171007 AAGTGGCGCCATCGAAATTG 59.829 50.000 35.23 0.00 38.10 2.32
499 513 2.498726 CCTCTCTTGGCTCGCCTC 59.501 66.667 9.65 0.00 36.94 4.70
500 514 2.103934 CTCTCTTGGCTCGCCTCG 59.896 66.667 9.65 0.36 36.94 4.63
540 576 4.620937 GCCGCGTATCCCCCTTCC 62.621 72.222 4.92 0.00 0.00 3.46
541 577 3.937447 CCGCGTATCCCCCTTCCC 61.937 72.222 4.92 0.00 0.00 3.97
542 578 2.842936 CGCGTATCCCCCTTCCCT 60.843 66.667 0.00 0.00 0.00 4.20
543 579 2.440817 CGCGTATCCCCCTTCCCTT 61.441 63.158 0.00 0.00 0.00 3.95
703 745 2.362369 ATCGCTGTCCCACTCCCAG 61.362 63.158 0.00 0.00 0.00 4.45
704 746 3.314331 CGCTGTCCCACTCCCAGT 61.314 66.667 0.00 0.00 0.00 4.00
705 747 2.665603 GCTGTCCCACTCCCAGTC 59.334 66.667 0.00 0.00 0.00 3.51
706 748 2.960688 GCTGTCCCACTCCCAGTCC 61.961 68.421 0.00 0.00 0.00 3.85
707 749 2.203938 TGTCCCACTCCCAGTCCC 60.204 66.667 0.00 0.00 0.00 4.46
708 750 2.203938 GTCCCACTCCCAGTCCCA 60.204 66.667 0.00 0.00 0.00 4.37
870 918 1.759459 GATTCCCGCCGATTCCTCCT 61.759 60.000 0.00 0.00 0.00 3.69
871 919 1.759459 ATTCCCGCCGATTCCTCCTC 61.759 60.000 0.00 0.00 0.00 3.71
872 920 3.930012 CCCGCCGATTCCTCCTCC 61.930 72.222 0.00 0.00 0.00 4.30
1761 1815 0.330604 AGCATGGTGAGGTCATTGCT 59.669 50.000 0.00 8.43 35.83 3.91
1797 1851 2.421529 GGATTTGGAGCCGTATCTTGGT 60.422 50.000 0.00 0.00 0.00 3.67
1885 1939 3.286329 TGATATGTGATTGTGCTGCCT 57.714 42.857 0.00 0.00 0.00 4.75
1886 1940 3.208594 TGATATGTGATTGTGCTGCCTC 58.791 45.455 0.00 0.00 0.00 4.70
2037 2091 6.206829 TGATGTCGATCACTATAAACGAGGAT 59.793 38.462 0.00 0.00 33.40 3.24
2040 2094 6.081049 GTCGATCACTATAAACGAGGATGAG 58.919 44.000 0.00 0.00 33.82 2.90
2076 2130 3.640407 GGGAGTGACCAGCAGCCA 61.640 66.667 0.00 0.00 41.20 4.75
2256 2310 2.811317 CGCACGCAGACCCTTCTC 60.811 66.667 0.00 0.00 0.00 2.87
2415 2469 5.127845 AGGAGAGATAAAGAAGATTGTCGCA 59.872 40.000 0.00 0.00 0.00 5.10
2457 2511 4.311520 TGGCTCTACTGGACTAAGTACA 57.688 45.455 0.00 0.00 0.00 2.90
2786 2840 4.627467 AGATGAAGATGCTAACGACAACAC 59.373 41.667 0.00 0.00 0.00 3.32
3073 3127 0.536006 AGCTCTGCAAGGTTGTCACC 60.536 55.000 0.00 0.00 44.67 4.02
3260 3316 3.247442 TGTAGTCTTGATGGTTAACGCG 58.753 45.455 3.53 3.53 0.00 6.01
3392 3448 7.402862 ACTATGTTGCAATAGTAAAGAACCCT 58.597 34.615 10.35 0.00 40.74 4.34
3542 3598 6.604795 AGGTTTTCACTCTTCATGATTATGGG 59.395 38.462 0.00 0.00 34.97 4.00
3648 3704 4.887748 TGCTTTTGGTTTCTTCAACACAA 58.112 34.783 0.00 0.00 37.07 3.33
3848 3904 6.761312 TCGTCAAGAATTAAAGAACCCACTA 58.239 36.000 0.00 0.00 0.00 2.74
4069 4127 2.819608 CCCCAGTAAATTGTGTCTGTGG 59.180 50.000 0.00 0.00 0.00 4.17
4174 4247 8.632679 TGCAAATTCTTAGACATGAAAACTTCT 58.367 29.630 0.00 0.00 0.00 2.85
4234 4307 4.968259 TCACACAACAGTTTAGCATACCT 58.032 39.130 0.00 0.00 0.00 3.08
4253 4326 7.908601 GCATACCTTTTTCCATTTACTTCTACG 59.091 37.037 0.00 0.00 0.00 3.51
4501 4574 1.812235 CAGACTACTTGGCATGCACA 58.188 50.000 21.36 12.37 0.00 4.57
4682 4761 4.894784 TCAGAAGAACACATAGGGAACAC 58.105 43.478 0.00 0.00 0.00 3.32
4742 4823 4.681978 GGCGACTGCAAGACCGGT 62.682 66.667 6.92 6.92 45.35 5.28
4743 4824 2.260434 GCGACTGCAAGACCGGTA 59.740 61.111 7.34 0.00 42.15 4.02
4798 4879 3.675698 GTCAGCTTGTAAGTGACAGTAGC 59.324 47.826 15.79 0.00 40.74 3.58
4858 4939 4.660168 AGATTGCCTGATGAGTTTTCTGT 58.340 39.130 0.00 0.00 0.00 3.41
5210 5291 4.087182 AGAGTAACTTCTGAATCCCGACA 58.913 43.478 0.00 0.00 0.00 4.35
5255 5337 2.417257 GCCATTGATTGGGCTGCGA 61.417 57.895 0.00 0.00 46.55 5.10
5349 5432 1.988107 TGATGGTTGAGGAGGAGCTTT 59.012 47.619 0.00 0.00 0.00 3.51
5350 5433 2.376518 TGATGGTTGAGGAGGAGCTTTT 59.623 45.455 0.00 0.00 0.00 2.27
5424 5508 4.842139 ACGAGTGAGCGATGAATAAAAC 57.158 40.909 0.00 0.00 34.83 2.43
5430 5514 7.955324 CGAGTGAGCGATGAATAAAACTAAAAA 59.045 33.333 0.00 0.00 0.00 1.94
5453 5537 2.980586 TGTGCTTGTGTTTTTCGATCG 58.019 42.857 9.36 9.36 0.00 3.69
5469 5553 2.159240 CGATCGATTCTCAGGTGGTTGA 60.159 50.000 10.26 0.00 0.00 3.18
5480 5564 3.077359 CAGGTGGTTGAGAATTCAGACC 58.923 50.000 8.44 12.20 36.18 3.85
5504 5588 6.403418 CCTTCAGTCTGATTTGAGATTCTTGC 60.403 42.308 2.68 0.00 0.00 4.01
5516 5600 6.309712 TGAGATTCTTGCTCTTCTGTTTTG 57.690 37.500 0.00 0.00 33.57 2.44
5517 5601 6.057533 TGAGATTCTTGCTCTTCTGTTTTGA 58.942 36.000 0.00 0.00 33.57 2.69
5518 5602 6.204301 TGAGATTCTTGCTCTTCTGTTTTGAG 59.796 38.462 0.00 0.00 33.57 3.02
5519 5603 5.472820 AGATTCTTGCTCTTCTGTTTTGAGG 59.527 40.000 0.00 0.00 0.00 3.86
5520 5604 4.422073 TCTTGCTCTTCTGTTTTGAGGA 57.578 40.909 0.00 0.00 0.00 3.71
5522 5606 5.192927 TCTTGCTCTTCTGTTTTGAGGAAA 58.807 37.500 0.00 0.00 37.62 3.13
5523 5607 5.829924 TCTTGCTCTTCTGTTTTGAGGAAAT 59.170 36.000 0.00 0.00 37.62 2.17
5524 5608 6.322201 TCTTGCTCTTCTGTTTTGAGGAAATT 59.678 34.615 0.00 0.00 37.62 1.82
5525 5609 6.076981 TGCTCTTCTGTTTTGAGGAAATTC 57.923 37.500 0.00 0.00 0.00 2.17
5526 5610 5.829924 TGCTCTTCTGTTTTGAGGAAATTCT 59.170 36.000 0.00 0.00 0.00 2.40
5527 5611 6.148264 GCTCTTCTGTTTTGAGGAAATTCTG 58.852 40.000 0.00 0.00 0.00 3.02
5528 5612 6.238869 GCTCTTCTGTTTTGAGGAAATTCTGT 60.239 38.462 0.00 0.00 0.00 3.41
5529 5613 7.645058 TCTTCTGTTTTGAGGAAATTCTGTT 57.355 32.000 0.00 0.00 0.00 3.16
5531 5615 8.531146 TCTTCTGTTTTGAGGAAATTCTGTTTT 58.469 29.630 0.00 0.00 0.00 2.43
5532 5616 9.154847 CTTCTGTTTTGAGGAAATTCTGTTTTT 57.845 29.630 0.00 0.00 0.00 1.94
5585 5694 5.376756 TTTTTGTGAGGGGTTACTACACT 57.623 39.130 0.00 0.00 33.41 3.55
5586 5695 5.376756 TTTTGTGAGGGGTTACTACACTT 57.623 39.130 0.00 0.00 33.41 3.16
5587 5696 6.497624 TTTTGTGAGGGGTTACTACACTTA 57.502 37.500 0.00 0.00 33.41 2.24
5588 5697 6.691255 TTTGTGAGGGGTTACTACACTTAT 57.309 37.500 0.00 0.00 33.41 1.73
5589 5698 7.795534 TTTGTGAGGGGTTACTACACTTATA 57.204 36.000 0.00 0.00 33.41 0.98
5590 5699 7.983166 TTGTGAGGGGTTACTACACTTATAT 57.017 36.000 0.00 0.00 33.41 0.86
5591 5700 9.491406 TTTGTGAGGGGTTACTACACTTATATA 57.509 33.333 0.00 0.00 33.41 0.86
5592 5701 9.664777 TTGTGAGGGGTTACTACACTTATATAT 57.335 33.333 0.00 0.00 33.41 0.86
5593 5702 9.085645 TGTGAGGGGTTACTACACTTATATATG 57.914 37.037 0.00 0.00 33.41 1.78
5594 5703 9.305555 GTGAGGGGTTACTACACTTATATATGA 57.694 37.037 2.80 0.00 0.00 2.15
5595 5704 9.886337 TGAGGGGTTACTACACTTATATATGAA 57.114 33.333 2.80 0.00 0.00 2.57
5676 5785 2.101917 GCCCATTAGACACTAGCCGTTA 59.898 50.000 0.00 0.00 0.00 3.18
6038 6149 0.815734 TACCAGAACTACTGCGCCTC 59.184 55.000 4.18 0.00 44.52 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.696521 CACTATAGTGTGGCGCCTAGCTC 62.697 56.522 29.70 17.44 42.44 4.09
9 10 3.911323 CACTATAGTGTGGCGCCTAGCT 61.911 54.545 29.70 22.74 42.44 3.32
10 11 1.603172 CACTATAGTGTGGCGCCTAGC 60.603 57.143 29.70 17.93 42.25 3.42
11 12 2.423926 CACTATAGTGTGGCGCCTAG 57.576 55.000 29.70 21.10 40.96 3.02
22 23 0.387202 CTCAGGCGCTGCACTATAGT 59.613 55.000 7.64 0.00 0.00 2.12
23 24 0.670706 TCTCAGGCGCTGCACTATAG 59.329 55.000 7.64 0.00 0.00 1.31
24 25 0.670706 CTCTCAGGCGCTGCACTATA 59.329 55.000 7.64 0.00 0.00 1.31
25 26 1.440893 CTCTCAGGCGCTGCACTAT 59.559 57.895 7.64 0.00 0.00 2.12
26 27 2.888111 CTCTCAGGCGCTGCACTA 59.112 61.111 7.64 0.00 0.00 2.74
27 28 4.756458 GCTCTCAGGCGCTGCACT 62.756 66.667 7.64 0.00 0.00 4.40
28 29 3.362399 TAGCTCTCAGGCGCTGCAC 62.362 63.158 7.64 0.00 37.05 4.57
29 30 3.070576 TAGCTCTCAGGCGCTGCA 61.071 61.111 7.64 0.00 37.05 4.41
30 31 2.279385 CTAGCTCTCAGGCGCTGC 60.279 66.667 7.64 2.66 37.05 5.25
31 32 2.416678 CCTAGCTCTCAGGCGCTG 59.583 66.667 7.64 3.67 37.05 5.18
41 42 5.696521 CACTATAGTGTGGCGCCTAGCTC 62.697 56.522 29.70 17.44 42.44 4.09
42 43 3.911323 CACTATAGTGTGGCGCCTAGCT 61.911 54.545 29.70 22.74 42.44 3.32
43 44 1.603172 CACTATAGTGTGGCGCCTAGC 60.603 57.143 29.70 17.93 42.25 3.42
44 45 2.423926 CACTATAGTGTGGCGCCTAG 57.576 55.000 29.70 21.10 40.96 3.02
52 53 4.092764 GCTAGACGCTGCACTATAGTGTG 61.093 52.174 28.95 22.81 40.91 3.82
53 54 2.033550 GCTAGACGCTGCACTATAGTGT 59.966 50.000 28.95 12.82 40.91 3.55
54 55 2.656085 GCTAGACGCTGCACTATAGTG 58.344 52.381 25.68 25.68 41.37 2.74
66 67 1.001815 CAGAGCCTAAGAGCTAGACGC 60.002 57.143 0.00 0.00 45.15 5.19
67 68 1.001815 GCAGAGCCTAAGAGCTAGACG 60.002 57.143 0.00 0.00 45.15 4.18
68 69 2.028130 TGCAGAGCCTAAGAGCTAGAC 58.972 52.381 0.00 0.00 45.15 2.59
69 70 2.028130 GTGCAGAGCCTAAGAGCTAGA 58.972 52.381 0.00 0.00 45.15 2.43
70 71 1.753649 TGTGCAGAGCCTAAGAGCTAG 59.246 52.381 0.00 0.00 45.15 3.42
71 72 1.852633 TGTGCAGAGCCTAAGAGCTA 58.147 50.000 0.00 0.00 45.15 3.32
73 74 1.669779 CATTGTGCAGAGCCTAAGAGC 59.330 52.381 0.00 0.00 0.00 4.09
74 75 2.935201 GTCATTGTGCAGAGCCTAAGAG 59.065 50.000 0.00 0.00 0.00 2.85
75 76 2.568956 AGTCATTGTGCAGAGCCTAAGA 59.431 45.455 0.00 0.00 0.00 2.10
76 77 2.983229 AGTCATTGTGCAGAGCCTAAG 58.017 47.619 0.00 0.00 0.00 2.18
77 78 3.423539 AAGTCATTGTGCAGAGCCTAA 57.576 42.857 0.00 0.00 0.00 2.69
78 79 3.679917 GCTAAGTCATTGTGCAGAGCCTA 60.680 47.826 0.00 0.00 0.00 3.93
79 80 2.938756 GCTAAGTCATTGTGCAGAGCCT 60.939 50.000 0.00 0.00 0.00 4.58
80 81 1.399791 GCTAAGTCATTGTGCAGAGCC 59.600 52.381 0.00 0.00 0.00 4.70
81 82 2.079158 TGCTAAGTCATTGTGCAGAGC 58.921 47.619 0.00 0.00 0.00 4.09
82 83 4.959596 ATTGCTAAGTCATTGTGCAGAG 57.040 40.909 0.00 0.00 33.13 3.35
83 84 5.710513 AAATTGCTAAGTCATTGTGCAGA 57.289 34.783 0.00 0.00 33.13 4.26
84 85 6.774354 AAAAATTGCTAAGTCATTGTGCAG 57.226 33.333 0.00 0.00 33.13 4.41
85 86 6.867816 CCTAAAAATTGCTAAGTCATTGTGCA 59.132 34.615 0.00 0.00 0.00 4.57
86 87 6.183360 GCCTAAAAATTGCTAAGTCATTGTGC 60.183 38.462 0.00 0.00 0.00 4.57
87 88 6.867816 TGCCTAAAAATTGCTAAGTCATTGTG 59.132 34.615 0.00 0.00 0.00 3.33
88 89 6.991938 TGCCTAAAAATTGCTAAGTCATTGT 58.008 32.000 0.00 0.00 0.00 2.71
89 90 7.092716 ACTGCCTAAAAATTGCTAAGTCATTG 58.907 34.615 0.00 0.00 0.00 2.82
90 91 7.177392 AGACTGCCTAAAAATTGCTAAGTCATT 59.823 33.333 0.00 0.00 33.10 2.57
91 92 6.660949 AGACTGCCTAAAAATTGCTAAGTCAT 59.339 34.615 0.00 0.00 33.10 3.06
92 93 6.003950 AGACTGCCTAAAAATTGCTAAGTCA 58.996 36.000 0.00 0.00 33.10 3.41
93 94 6.317857 CAGACTGCCTAAAAATTGCTAAGTC 58.682 40.000 0.00 0.00 31.68 3.01
94 95 5.183904 CCAGACTGCCTAAAAATTGCTAAGT 59.816 40.000 0.00 0.00 0.00 2.24
95 96 5.393461 CCCAGACTGCCTAAAAATTGCTAAG 60.393 44.000 0.00 0.00 0.00 2.18
96 97 4.462483 CCCAGACTGCCTAAAAATTGCTAA 59.538 41.667 0.00 0.00 0.00 3.09
97 98 4.016444 CCCAGACTGCCTAAAAATTGCTA 58.984 43.478 0.00 0.00 0.00 3.49
98 99 2.827921 CCCAGACTGCCTAAAAATTGCT 59.172 45.455 0.00 0.00 0.00 3.91
99 100 2.094026 CCCCAGACTGCCTAAAAATTGC 60.094 50.000 0.00 0.00 0.00 3.56
100 101 3.056607 CACCCCAGACTGCCTAAAAATTG 60.057 47.826 0.00 0.00 0.00 2.32
101 102 3.165071 CACCCCAGACTGCCTAAAAATT 58.835 45.455 0.00 0.00 0.00 1.82
102 103 2.807676 CACCCCAGACTGCCTAAAAAT 58.192 47.619 0.00 0.00 0.00 1.82
103 104 1.821666 GCACCCCAGACTGCCTAAAAA 60.822 52.381 0.00 0.00 0.00 1.94
104 105 0.251165 GCACCCCAGACTGCCTAAAA 60.251 55.000 0.00 0.00 0.00 1.52
105 106 1.378762 GCACCCCAGACTGCCTAAA 59.621 57.895 0.00 0.00 0.00 1.85
106 107 1.422977 TTGCACCCCAGACTGCCTAA 61.423 55.000 0.00 0.00 31.97 2.69
107 108 1.845664 TTGCACCCCAGACTGCCTA 60.846 57.895 0.00 0.00 31.97 3.93
108 109 3.177884 TTGCACCCCAGACTGCCT 61.178 61.111 0.00 0.00 31.97 4.75
109 110 2.985847 GTTGCACCCCAGACTGCC 60.986 66.667 0.00 0.00 31.97 4.85
110 111 3.357079 CGTTGCACCCCAGACTGC 61.357 66.667 0.00 0.00 0.00 4.40
111 112 3.357079 GCGTTGCACCCCAGACTG 61.357 66.667 0.00 0.00 0.00 3.51
112 113 3.560251 AGCGTTGCACCCCAGACT 61.560 61.111 0.00 0.00 0.00 3.24
113 114 3.357079 CAGCGTTGCACCCCAGAC 61.357 66.667 0.00 0.00 0.00 3.51
114 115 4.641645 CCAGCGTTGCACCCCAGA 62.642 66.667 0.00 0.00 0.00 3.86
123 124 3.663176 CACACCTGGCCAGCGTTG 61.663 66.667 28.39 23.48 0.00 4.10
124 125 2.731691 CTACACACCTGGCCAGCGTT 62.732 60.000 28.39 17.03 0.00 4.84
125 126 3.238497 TACACACCTGGCCAGCGT 61.238 61.111 28.39 22.43 0.00 5.07
126 127 2.434884 CTACACACCTGGCCAGCG 60.435 66.667 28.39 21.74 0.00 5.18
127 128 2.747855 GCTACACACCTGGCCAGC 60.748 66.667 28.39 10.68 0.00 4.85
128 129 2.434884 CGCTACACACCTGGCCAG 60.435 66.667 26.87 26.87 0.00 4.85
129 130 4.697756 GCGCTACACACCTGGCCA 62.698 66.667 4.71 4.71 0.00 5.36
131 132 2.311688 ATAGGCGCTACACACCTGGC 62.312 60.000 7.64 0.00 34.92 4.85
132 133 0.178068 AATAGGCGCTACACACCTGG 59.822 55.000 7.64 0.00 34.92 4.45
133 134 1.665679 CAAATAGGCGCTACACACCTG 59.334 52.381 7.64 0.00 34.92 4.00
134 135 1.278127 ACAAATAGGCGCTACACACCT 59.722 47.619 7.64 0.00 37.61 4.00
135 136 1.396996 CACAAATAGGCGCTACACACC 59.603 52.381 7.64 0.00 0.00 4.16
136 137 2.343101 TCACAAATAGGCGCTACACAC 58.657 47.619 7.64 0.00 0.00 3.82
137 138 2.616960 CTCACAAATAGGCGCTACACA 58.383 47.619 7.64 0.00 0.00 3.72
138 139 1.933853 CCTCACAAATAGGCGCTACAC 59.066 52.381 7.64 0.00 0.00 2.90
139 140 2.309528 CCTCACAAATAGGCGCTACA 57.690 50.000 7.64 0.00 0.00 2.74
146 147 1.135689 GTGCAACGCCTCACAAATAGG 60.136 52.381 0.00 0.00 37.17 2.57
147 148 1.535028 TGTGCAACGCCTCACAAATAG 59.465 47.619 0.00 0.00 42.39 1.73
148 149 1.598882 TGTGCAACGCCTCACAAATA 58.401 45.000 0.00 0.00 42.39 1.40
149 150 0.743688 TTGTGCAACGCCTCACAAAT 59.256 45.000 12.52 0.00 46.40 2.32
150 151 2.184323 TTGTGCAACGCCTCACAAA 58.816 47.368 12.52 0.66 46.40 2.83
151 152 3.911137 TTGTGCAACGCCTCACAA 58.089 50.000 11.33 11.33 46.97 3.33
152 153 1.100463 ACATTGTGCAACGCCTCACA 61.100 50.000 0.00 0.86 42.39 3.58
153 154 0.871722 TACATTGTGCAACGCCTCAC 59.128 50.000 0.00 0.00 42.39 3.51
154 155 1.155889 CTACATTGTGCAACGCCTCA 58.844 50.000 0.00 0.00 42.39 3.86
155 156 1.135972 CACTACATTGTGCAACGCCTC 60.136 52.381 0.00 0.00 42.39 4.70
156 157 0.874390 CACTACATTGTGCAACGCCT 59.126 50.000 0.00 0.00 42.39 5.52
157 158 0.591170 ACACTACATTGTGCAACGCC 59.409 50.000 0.00 0.00 42.39 5.68
158 159 1.662876 CCACACTACATTGTGCAACGC 60.663 52.381 0.00 0.00 44.79 4.84
159 160 1.662876 GCCACACTACATTGTGCAACG 60.663 52.381 0.00 0.00 44.79 4.10
160 161 1.662876 CGCCACACTACATTGTGCAAC 60.663 52.381 0.00 0.00 44.79 4.17
161 162 0.590682 CGCCACACTACATTGTGCAA 59.409 50.000 0.00 0.00 44.79 4.08
162 163 1.851021 GCGCCACACTACATTGTGCA 61.851 55.000 0.00 0.00 44.79 4.57
163 164 1.154225 GCGCCACACTACATTGTGC 60.154 57.895 0.00 0.00 44.79 4.57
164 165 1.501741 GGCGCCACACTACATTGTG 59.498 57.895 24.80 0.00 45.57 3.33
165 166 2.032634 CGGCGCCACACTACATTGT 61.033 57.895 28.98 0.00 0.00 2.71
166 167 2.749865 CCGGCGCCACACTACATTG 61.750 63.158 28.98 5.35 0.00 2.82
167 168 2.435938 CCGGCGCCACACTACATT 60.436 61.111 28.98 0.00 0.00 2.71
168 169 4.467084 CCCGGCGCCACACTACAT 62.467 66.667 28.98 0.00 0.00 2.29
180 181 2.999363 CTTTTTGTGTGACGCCCGGC 62.999 60.000 0.00 0.00 0.00 6.13
181 182 1.008995 CTTTTTGTGTGACGCCCGG 60.009 57.895 0.00 0.00 0.00 5.73
182 183 1.008995 CCTTTTTGTGTGACGCCCG 60.009 57.895 0.00 0.00 0.00 6.13
183 184 0.030235 GACCTTTTTGTGTGACGCCC 59.970 55.000 0.00 0.00 0.00 6.13
184 185 0.736053 TGACCTTTTTGTGTGACGCC 59.264 50.000 0.00 0.00 0.00 5.68
185 186 1.859998 GCTGACCTTTTTGTGTGACGC 60.860 52.381 0.00 0.00 0.00 5.19
186 187 1.268539 GGCTGACCTTTTTGTGTGACG 60.269 52.381 0.00 0.00 0.00 4.35
187 188 1.268539 CGGCTGACCTTTTTGTGTGAC 60.269 52.381 0.00 0.00 0.00 3.67
188 189 1.021202 CGGCTGACCTTTTTGTGTGA 58.979 50.000 0.00 0.00 0.00 3.58
189 190 0.594796 GCGGCTGACCTTTTTGTGTG 60.595 55.000 0.00 0.00 0.00 3.82
190 191 1.733526 GCGGCTGACCTTTTTGTGT 59.266 52.632 0.00 0.00 0.00 3.72
191 192 1.370414 CGCGGCTGACCTTTTTGTG 60.370 57.895 0.00 0.00 0.00 3.33
192 193 1.822186 ACGCGGCTGACCTTTTTGT 60.822 52.632 12.47 0.00 0.00 2.83
193 194 1.370414 CACGCGGCTGACCTTTTTG 60.370 57.895 12.47 0.00 0.00 2.44
194 195 1.098712 TTCACGCGGCTGACCTTTTT 61.099 50.000 12.47 0.00 0.00 1.94
195 196 1.098712 TTTCACGCGGCTGACCTTTT 61.099 50.000 12.47 0.00 0.00 2.27
196 197 0.889186 ATTTCACGCGGCTGACCTTT 60.889 50.000 12.47 0.00 0.00 3.11
197 198 0.036765 TATTTCACGCGGCTGACCTT 60.037 50.000 12.47 0.00 0.00 3.50
198 199 0.460284 CTATTTCACGCGGCTGACCT 60.460 55.000 12.47 0.00 0.00 3.85
199 200 0.739813 ACTATTTCACGCGGCTGACC 60.740 55.000 12.47 0.00 0.00 4.02
200 201 1.076332 AACTATTTCACGCGGCTGAC 58.924 50.000 12.47 0.00 0.00 3.51
201 202 1.730064 GAAACTATTTCACGCGGCTGA 59.270 47.619 12.47 2.44 39.45 4.26
202 203 1.463056 TGAAACTATTTCACGCGGCTG 59.537 47.619 12.47 0.00 44.21 4.85
203 204 1.803334 TGAAACTATTTCACGCGGCT 58.197 45.000 12.47 0.00 44.21 5.52
210 211 5.361427 TGAACTGTCCGTGAAACTATTTCA 58.639 37.500 0.00 0.00 46.68 2.69
211 212 5.917541 TGAACTGTCCGTGAAACTATTTC 57.082 39.130 0.00 0.00 40.08 2.17
212 213 6.710744 AGAATGAACTGTCCGTGAAACTATTT 59.289 34.615 0.00 0.00 31.75 1.40
213 214 6.147821 CAGAATGAACTGTCCGTGAAACTATT 59.852 38.462 0.00 0.00 39.69 1.73
214 215 5.639506 CAGAATGAACTGTCCGTGAAACTAT 59.360 40.000 0.00 0.00 39.69 2.12
215 216 4.988540 CAGAATGAACTGTCCGTGAAACTA 59.011 41.667 0.00 0.00 39.69 2.24
216 217 3.809832 CAGAATGAACTGTCCGTGAAACT 59.190 43.478 0.00 0.00 39.69 2.66
217 218 3.560068 ACAGAATGAACTGTCCGTGAAAC 59.440 43.478 0.00 0.00 46.36 2.78
218 219 3.804036 ACAGAATGAACTGTCCGTGAAA 58.196 40.909 0.00 0.00 46.36 2.69
219 220 3.469008 ACAGAATGAACTGTCCGTGAA 57.531 42.857 0.00 0.00 46.36 3.18
227 228 7.080099 ACGAAATCAAATCACAGAATGAACTG 58.920 34.615 0.00 0.00 41.93 3.16
228 229 7.206981 ACGAAATCAAATCACAGAATGAACT 57.793 32.000 0.00 0.00 41.93 3.01
229 230 6.524586 GGACGAAATCAAATCACAGAATGAAC 59.475 38.462 0.00 0.00 41.93 3.18
230 231 6.349280 GGGACGAAATCAAATCACAGAATGAA 60.349 38.462 0.00 0.00 41.93 2.57
231 232 5.123820 GGGACGAAATCAAATCACAGAATGA 59.876 40.000 0.00 0.00 43.13 2.57
232 233 5.335127 GGGACGAAATCAAATCACAGAATG 58.665 41.667 0.00 0.00 46.00 2.67
233 234 4.399303 GGGGACGAAATCAAATCACAGAAT 59.601 41.667 0.00 0.00 0.00 2.40
234 235 3.756434 GGGGACGAAATCAAATCACAGAA 59.244 43.478 0.00 0.00 0.00 3.02
235 236 3.343617 GGGGACGAAATCAAATCACAGA 58.656 45.455 0.00 0.00 0.00 3.41
236 237 3.764885 GGGGACGAAATCAAATCACAG 57.235 47.619 0.00 0.00 0.00 3.66
250 251 7.736912 AATTTGACAAATTTGACCGGGGACG 62.737 44.000 24.64 0.00 45.60 4.79
251 252 1.611519 TGACAAATTTGACCGGGGAC 58.388 50.000 24.64 0.00 0.00 4.46
252 253 2.366640 TTGACAAATTTGACCGGGGA 57.633 45.000 24.64 0.00 0.00 4.81
253 254 3.676291 ATTTGACAAATTTGACCGGGG 57.324 42.857 24.64 0.00 0.00 5.73
268 269 3.880490 AGTGTACTTGGCGTCAAATTTGA 59.120 39.130 16.91 16.91 31.77 2.69
269 270 4.219033 GAGTGTACTTGGCGTCAAATTTG 58.781 43.478 12.15 12.15 31.77 2.32
270 271 3.252458 GGAGTGTACTTGGCGTCAAATTT 59.748 43.478 3.10 0.00 31.77 1.82
271 272 2.812011 GGAGTGTACTTGGCGTCAAATT 59.188 45.455 3.10 0.00 31.77 1.82
272 273 2.423577 GGAGTGTACTTGGCGTCAAAT 58.576 47.619 3.10 0.00 31.77 2.32
273 274 1.870580 CGGAGTGTACTTGGCGTCAAA 60.871 52.381 3.10 0.00 31.77 2.69
274 275 0.319211 CGGAGTGTACTTGGCGTCAA 60.319 55.000 0.91 0.91 0.00 3.18
275 276 1.287815 CGGAGTGTACTTGGCGTCA 59.712 57.895 0.00 0.00 0.00 4.35
276 277 0.523072 TACGGAGTGTACTTGGCGTC 59.477 55.000 0.00 0.00 45.73 5.19
277 278 0.524862 CTACGGAGTGTACTTGGCGT 59.475 55.000 0.00 0.00 45.73 5.68
278 279 0.806868 TCTACGGAGTGTACTTGGCG 59.193 55.000 0.00 0.00 45.73 5.69
279 280 2.541178 CGATCTACGGAGTGTACTTGGC 60.541 54.545 0.00 0.00 45.73 4.52
280 281 2.541178 GCGATCTACGGAGTGTACTTGG 60.541 54.545 0.00 0.00 45.73 3.61
281 282 2.096980 TGCGATCTACGGAGTGTACTTG 59.903 50.000 0.00 0.00 45.73 3.16
282 283 2.362736 TGCGATCTACGGAGTGTACTT 58.637 47.619 0.00 0.00 45.73 2.24
283 284 2.034104 TGCGATCTACGGAGTGTACT 57.966 50.000 0.00 0.00 45.73 2.73
290 291 3.120105 CCAGCTGCGATCTACGGA 58.880 61.111 8.66 0.00 42.83 4.69
291 292 2.659897 GCCAGCTGCGATCTACGG 60.660 66.667 8.66 0.00 42.83 4.02
292 293 2.659897 GGCCAGCTGCGATCTACG 60.660 66.667 8.66 0.00 42.61 3.51
293 294 2.659897 CGGCCAGCTGCGATCTAC 60.660 66.667 8.66 0.00 42.61 2.59
294 295 3.916544 CCGGCCAGCTGCGATCTA 61.917 66.667 8.66 0.00 42.61 1.98
333 334 6.317789 TGATCGGAATAATTGAAGAATGGC 57.682 37.500 0.00 0.00 0.00 4.40
375 384 2.202878 TAATGCACGAGCTCGGCC 60.203 61.111 36.93 26.76 44.95 6.13
399 408 2.454832 CTTCCCCGCAAGAGCTGACA 62.455 60.000 0.00 0.00 43.02 3.58
532 568 2.998949 CGAAGGAAGGGAAGGGGG 59.001 66.667 0.00 0.00 0.00 5.40
540 576 1.139947 GTCGGAGAGCGAAGGAAGG 59.860 63.158 0.00 0.00 36.95 3.46
541 577 1.226435 CGTCGGAGAGCGAAGGAAG 60.226 63.158 0.00 0.00 36.95 3.46
542 578 2.875485 CGTCGGAGAGCGAAGGAA 59.125 61.111 0.00 0.00 36.95 3.36
543 579 3.812019 GCGTCGGAGAGCGAAGGA 61.812 66.667 0.00 0.00 36.95 3.36
870 918 4.440829 GAGGGGCAAATGGGCGGA 62.441 66.667 0.00 0.00 44.56 5.54
1131 1185 1.139095 GGAGTAGTCGAAGTGGCGG 59.861 63.158 0.00 0.00 0.00 6.13
1491 1545 0.179000 AGATGGCGTAGAAGGGCTTG 59.821 55.000 0.00 0.00 0.00 4.01
1584 1638 3.744719 TACGACTTGAGCGCGCCT 61.745 61.111 30.33 15.76 0.00 5.52
1645 1699 2.352805 CAGGGAGAGGTTGCCACC 59.647 66.667 0.00 0.00 44.67 4.61
1761 1815 0.904865 AATCCGACCTCCTGCACTCA 60.905 55.000 0.00 0.00 0.00 3.41
1797 1851 2.214216 AGTTGCCGGGTAGTGCAGA 61.214 57.895 2.18 0.00 38.95 4.26
1885 1939 3.606595 CTGAATGAGCTTCACAGGAGA 57.393 47.619 0.00 0.00 38.97 3.71
2037 2091 2.023598 AGTGTCTCCATCCTCATCCTCA 60.024 50.000 0.00 0.00 0.00 3.86
2040 2094 1.415659 CCAGTGTCTCCATCCTCATCC 59.584 57.143 0.00 0.00 0.00 3.51
2076 2130 0.829182 CCCACAGCTTCCTGCCTTTT 60.829 55.000 0.00 0.00 43.02 2.27
2448 2502 6.852420 TCCAATAAGCTGTCTGTACTTAGT 57.148 37.500 0.00 0.00 29.96 2.24
2457 2511 2.573462 TCCTGCTTCCAATAAGCTGTCT 59.427 45.455 10.74 0.00 43.38 3.41
2496 2550 0.389391 CACAGACAACCTCACCGAGT 59.611 55.000 0.00 0.00 0.00 4.18
2786 2840 3.054878 GCTTCAACAATTGACCTTGCAG 58.945 45.455 13.59 7.43 39.87 4.41
3073 3127 5.972107 AAAAGGACCAGATTCAAGACATG 57.028 39.130 0.00 0.00 0.00 3.21
3260 3316 3.450578 TGAAAGGTCACGACTACAACAC 58.549 45.455 0.00 0.00 0.00 3.32
3392 3448 9.744125 ATAAATATAGGGGGTATGAGCTCATTA 57.256 33.333 32.94 18.62 37.76 1.90
3542 3598 5.705905 AGTAACTTGATCTTTTACCCTGCAC 59.294 40.000 0.00 0.00 0.00 4.57
3648 3704 4.400251 CAGTGATTCCATGTACTTGCCATT 59.600 41.667 3.24 0.00 0.00 3.16
3689 3745 3.776969 TGATCTTACCCTCAGCATCTGTT 59.223 43.478 0.00 0.00 32.61 3.16
3848 3904 2.235898 ACGGGTAAATTGCATGCCATTT 59.764 40.909 26.99 26.99 0.00 2.32
4041 4099 6.432783 CAGACACAATTTACTGGGGTTAATGA 59.567 38.462 0.00 0.00 0.00 2.57
4044 4102 5.533154 CACAGACACAATTTACTGGGGTTAA 59.467 40.000 0.00 0.00 35.08 2.01
4069 4127 7.602517 ATTAGTAGTTTCAGTTCTGCATCAC 57.397 36.000 0.00 0.00 0.00 3.06
4299 4372 7.611467 TGTTCATCTCCATGTAGCTGTAAAAAT 59.389 33.333 0.00 0.00 0.00 1.82
4501 4574 2.084546 GCTGGCCGAGTAAATTGAAGT 58.915 47.619 0.00 0.00 0.00 3.01
4682 4761 6.452090 GCTGTACACGTAAAATAAGTGTCTCG 60.452 42.308 11.39 4.37 45.89 4.04
4742 4823 2.039787 TGAGTGGCCGGGATGGTA 59.960 61.111 2.18 0.00 41.21 3.25
4743 4824 3.402681 CTGAGTGGCCGGGATGGT 61.403 66.667 2.18 0.00 41.21 3.55
4858 4939 6.631971 TTTCAGTTAAGTGACATTGCATCA 57.368 33.333 12.62 0.00 0.00 3.07
5090 5171 1.226717 CGCTTCTCGGAGGTACTGC 60.227 63.158 4.96 2.49 45.89 4.40
5210 5291 0.243907 CACATCTCGAGGACACCGTT 59.756 55.000 13.56 0.00 0.00 4.44
5250 5332 1.211190 GGGCTTGCTCTTTTCGCAG 59.789 57.895 0.00 0.00 38.80 5.18
5255 5337 1.051008 CCCAAAGGGCTTGCTCTTTT 58.949 50.000 16.79 1.63 35.35 2.27
5326 5408 1.407989 GCTCCTCCTCAACCATCAAGG 60.408 57.143 0.00 0.00 45.67 3.61
5424 5508 8.963130 TCGAAAAACACAAGCACATATTTTTAG 58.037 29.630 0.00 0.00 31.33 1.85
5430 5514 5.121611 TCGATCGAAAAACACAAGCACATAT 59.878 36.000 16.99 0.00 0.00 1.78
5480 5564 6.372103 AGCAAGAATCTCAAATCAGACTGAAG 59.628 38.462 9.70 2.28 0.00 3.02
5504 5588 7.269477 ACAGAATTTCCTCAAAACAGAAGAG 57.731 36.000 0.00 0.00 0.00 2.85
5563 5672 5.376756 AGTGTAGTAACCCCTCACAAAAA 57.623 39.130 0.00 0.00 0.00 1.94
5564 5673 5.376756 AAGTGTAGTAACCCCTCACAAAA 57.623 39.130 0.00 0.00 0.00 2.44
5565 5674 6.691255 ATAAGTGTAGTAACCCCTCACAAA 57.309 37.500 0.00 0.00 0.00 2.83
5566 5675 7.983166 ATATAAGTGTAGTAACCCCTCACAA 57.017 36.000 0.00 0.00 0.00 3.33
5567 5676 9.085645 CATATATAAGTGTAGTAACCCCTCACA 57.914 37.037 0.00 0.00 0.00 3.58
5568 5677 9.305555 TCATATATAAGTGTAGTAACCCCTCAC 57.694 37.037 0.00 0.00 0.00 3.51
5569 5678 9.886337 TTCATATATAAGTGTAGTAACCCCTCA 57.114 33.333 0.00 0.00 0.00 3.86
5590 5699 9.352784 CGCATGGTTTATTTTCTTTTCTTCATA 57.647 29.630 0.00 0.00 0.00 2.15
5591 5700 7.872483 ACGCATGGTTTATTTTCTTTTCTTCAT 59.128 29.630 0.00 0.00 0.00 2.57
5592 5701 7.206687 ACGCATGGTTTATTTTCTTTTCTTCA 58.793 30.769 0.00 0.00 0.00 3.02
5593 5702 7.637709 ACGCATGGTTTATTTTCTTTTCTTC 57.362 32.000 0.00 0.00 0.00 2.87
5594 5703 8.432110 AAACGCATGGTTTATTTTCTTTTCTT 57.568 26.923 9.66 0.00 46.76 2.52


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

AutoCloner maintained by Alex Coulton.