Multiple sequence alignment - TraesCS5A01G204700

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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 TraesCS5A01G204700 chr5A 100.000 2707 0 0 1 2707 414300046 414297340 0.000000e+00 5000.0
1 TraesCS5A01G204700 chr5A 100.000 35 0 0 2187 2221 414297768 414297734 6.260000e-07 65.8
2 TraesCS5A01G204700 chr5A 100.000 35 0 0 2279 2313 414297860 414297826 6.260000e-07 65.8
3 TraesCS5A01G204700 chr5D 95.140 1893 73 14 349 2240 319734767 319732893 0.000000e+00 2968.0
4 TraesCS5A01G204700 chr5D 90.909 396 26 6 2314 2707 319732889 319732502 8.590000e-145 523.0
5 TraesCS5A01G204700 chr5B 95.351 1850 73 7 374 2221 370451807 370449969 0.000000e+00 2928.0
6 TraesCS5A01G204700 chr5B 91.457 398 22 8 2314 2707 370449954 370449565 1.100000e-148 536.0
7 TraesCS5A01G204700 chr4B 93.045 532 23 7 1705 2236 351298224 351298741 0.000000e+00 765.0
8 TraesCS5A01G204700 chr4B 92.628 529 27 7 1708 2236 257299752 257299236 0.000000e+00 750.0
9 TraesCS5A01G204700 chr4B 90.672 268 19 3 1969 2236 257273080 257272819 4.290000e-93 351.0
10 TraesCS5A01G204700 chr4B 95.745 47 2 0 2314 2360 257272816 257272770 2.890000e-10 76.8
11 TraesCS5A01G204700 chr4B 95.745 47 2 0 2314 2360 257299233 257299187 2.890000e-10 76.8
12 TraesCS5A01G204700 chr4B 97.619 42 1 0 2314 2355 351298744 351298785 3.740000e-09 73.1
13 TraesCS5A01G204700 chr4B 100.000 32 0 0 2286 2317 257272858 257272827 2.910000e-05 60.2
14 TraesCS5A01G204700 chr4B 100.000 32 0 0 2286 2317 257299275 257299244 2.910000e-05 60.2
15 TraesCS5A01G204700 chr2B 92.060 529 28 8 1708 2236 574921234 574920720 0.000000e+00 732.0
16 TraesCS5A01G204700 chr2B 97.561 41 1 0 2314 2354 574920717 574920677 1.340000e-08 71.3
17 TraesCS5A01G204700 chr2B 94.872 39 1 1 2286 2323 574920759 574920721 2.910000e-05 60.2
18 TraesCS5A01G204700 chr2D 92.363 419 11 3 1204 1622 321172353 321171956 6.500000e-161 577.0
19 TraesCS5A01G204700 chr2D 82.313 147 25 1 1 147 154189334 154189189 2.830000e-25 126.0
20 TraesCS5A01G204700 chr7A 86.014 143 19 1 1 143 43175246 43175387 4.670000e-33 152.0
21 TraesCS5A01G204700 chr7A 84.354 147 21 2 1 146 33493969 33494114 2.810000e-30 143.0
22 TraesCS5A01G204700 chr3A 85.714 140 17 3 7 145 424541503 424541366 7.810000e-31 145.0
23 TraesCS5A01G204700 chr1B 84.247 146 20 3 1 145 154631807 154631950 3.630000e-29 139.0
24 TraesCS5A01G204700 chr4D 83.217 143 23 1 1 143 41719931 41719790 2.190000e-26 130.0
25 TraesCS5A01G204700 chr4D 82.759 145 24 1 1 145 121480365 121480222 7.870000e-26 128.0
26 TraesCS5A01G204700 chr2A 82.759 145 24 1 1 145 667967894 667967751 7.870000e-26 128.0
27 TraesCS5A01G204700 chr4A 82.237 152 21 5 1 149 11776549 11776401 2.830000e-25 126.0


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 TraesCS5A01G204700 chr5A 414297340 414300046 2706 True 1710.533333 5000 100.000000 1 2707 3 chr5A.!!$R1 2706
1 TraesCS5A01G204700 chr5D 319732502 319734767 2265 True 1745.500000 2968 93.024500 349 2707 2 chr5D.!!$R1 2358
2 TraesCS5A01G204700 chr5B 370449565 370451807 2242 True 1732.000000 2928 93.404000 374 2707 2 chr5B.!!$R1 2333
3 TraesCS5A01G204700 chr4B 351298224 351298785 561 False 419.050000 765 95.332000 1705 2355 2 chr4B.!!$F1 650
4 TraesCS5A01G204700 chr4B 257299187 257299752 565 True 295.666667 750 96.124333 1708 2360 3 chr4B.!!$R2 652
5 TraesCS5A01G204700 chr2B 574920677 574921234 557 True 287.833333 732 94.831000 1708 2354 3 chr2B.!!$R1 646

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
257 258 0.0414 TGCGTTGAAATCTGTGCGTG 60.041 50.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 1909 0.178767 TCACAGCAGCACAGTCAACT 59.821 50.0 0.0 0.0 0.0 3.16 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
19 20 2.899303 AAATTGGACCGGGAATGAGT 57.101 45.000 6.32 0.00 0.00 3.41
20 21 2.420058 AATTGGACCGGGAATGAGTC 57.580 50.000 6.32 0.00 0.00 3.36
21 22 0.178068 ATTGGACCGGGAATGAGTCG 59.822 55.000 6.32 0.00 0.00 4.18
22 23 2.202892 GGACCGGGAATGAGTCGC 60.203 66.667 6.32 0.00 35.85 5.19
23 24 2.202892 GACCGGGAATGAGTCGCC 60.203 66.667 6.32 0.00 35.79 5.54
24 25 3.000819 ACCGGGAATGAGTCGCCA 61.001 61.111 6.32 0.00 35.79 5.69
25 26 2.311688 GACCGGGAATGAGTCGCCAT 62.312 60.000 6.32 0.00 35.79 4.40
26 27 1.889105 CCGGGAATGAGTCGCCATG 60.889 63.158 0.00 0.00 35.79 3.66
27 28 2.537560 CGGGAATGAGTCGCCATGC 61.538 63.158 0.00 0.00 35.79 4.06
38 39 2.258286 GCCATGCGGACACCAAAC 59.742 61.111 0.00 0.00 0.00 2.93
39 40 2.560861 CCATGCGGACACCAAACG 59.439 61.111 0.00 0.00 0.00 3.60
40 41 2.560861 CATGCGGACACCAAACGG 59.439 61.111 0.00 0.00 0.00 4.44
41 42 1.963855 CATGCGGACACCAAACGGA 60.964 57.895 0.00 0.00 0.00 4.69
42 43 1.964373 ATGCGGACACCAAACGGAC 60.964 57.895 0.00 0.00 0.00 4.79
43 44 3.708734 GCGGACACCAAACGGACG 61.709 66.667 0.00 0.00 0.00 4.79
44 45 3.708734 CGGACACCAAACGGACGC 61.709 66.667 0.00 0.00 0.00 5.19
45 46 3.708734 GGACACCAAACGGACGCG 61.709 66.667 3.53 3.53 0.00 6.01
46 47 4.364409 GACACCAAACGGACGCGC 62.364 66.667 5.73 0.00 0.00 6.86
57 58 4.117372 GACGCGCGTCCGTTTGAG 62.117 66.667 44.30 10.93 42.24 3.02
58 59 4.936823 ACGCGCGTCCGTTTGAGT 62.937 61.111 32.73 2.20 38.47 3.41
59 60 4.117372 CGCGCGTCCGTTTGAGTC 62.117 66.667 24.19 0.00 36.67 3.36
60 61 4.117372 GCGCGTCCGTTTGAGTCG 62.117 66.667 8.43 0.00 36.67 4.18
62 63 3.774702 GCGTCCGTTTGAGTCGGC 61.775 66.667 0.00 0.00 46.49 5.54
63 64 3.467119 CGTCCGTTTGAGTCGGCG 61.467 66.667 0.00 0.00 46.49 6.46
64 65 3.774702 GTCCGTTTGAGTCGGCGC 61.775 66.667 0.00 0.00 46.49 6.53
67 68 3.698463 CGTTTGAGTCGGCGCGTT 61.698 61.111 8.43 0.00 0.00 4.84
68 69 2.127758 GTTTGAGTCGGCGCGTTG 60.128 61.111 8.43 0.00 0.00 4.10
69 70 3.342627 TTTGAGTCGGCGCGTTGG 61.343 61.111 8.43 0.00 0.00 3.77
70 71 3.793775 TTTGAGTCGGCGCGTTGGA 62.794 57.895 8.43 0.00 0.00 3.53
82 83 3.988459 CGTTGGACCGCCTTTTATG 57.012 52.632 0.00 0.00 34.31 1.90
83 84 1.161843 CGTTGGACCGCCTTTTATGT 58.838 50.000 0.00 0.00 34.31 2.29
84 85 1.129811 CGTTGGACCGCCTTTTATGTC 59.870 52.381 0.00 0.00 34.31 3.06
85 86 1.471287 GTTGGACCGCCTTTTATGTCC 59.529 52.381 0.00 0.00 45.99 4.02
86 87 2.390427 GGACCGCCTTTTATGTCCG 58.610 57.895 0.00 0.00 38.07 4.79
87 88 1.712018 GGACCGCCTTTTATGTCCGC 61.712 60.000 0.00 0.00 38.07 5.54
88 89 2.032185 GACCGCCTTTTATGTCCGCG 62.032 60.000 0.00 0.00 42.37 6.46
89 90 2.022762 CGCCTTTTATGTCCGCGC 59.977 61.111 0.00 0.00 36.02 6.86
90 91 2.407616 GCCTTTTATGTCCGCGCC 59.592 61.111 0.00 0.00 0.00 6.53
91 92 2.707039 CCTTTTATGTCCGCGCCG 59.293 61.111 0.00 0.00 0.00 6.46
92 93 1.812093 CCTTTTATGTCCGCGCCGA 60.812 57.895 0.00 0.00 0.00 5.54
93 94 1.347221 CTTTTATGTCCGCGCCGAC 59.653 57.895 20.04 20.04 0.00 4.79
94 95 2.032185 CTTTTATGTCCGCGCCGACC 62.032 60.000 23.06 8.48 31.35 4.79
95 96 2.510064 TTTTATGTCCGCGCCGACCT 62.510 55.000 23.06 16.92 31.35 3.85
96 97 3.709880 TTATGTCCGCGCCGACCTG 62.710 63.158 23.06 0.00 31.35 4.00
102 103 4.717629 CGCGCCGACCTGAACAGA 62.718 66.667 0.00 0.00 0.00 3.41
103 104 2.125512 GCGCCGACCTGAACAGAT 60.126 61.111 0.00 0.00 0.00 2.90
104 105 1.141019 GCGCCGACCTGAACAGATA 59.859 57.895 0.00 0.00 0.00 1.98
105 106 1.146358 GCGCCGACCTGAACAGATAC 61.146 60.000 0.00 0.00 0.00 2.24
106 107 0.527817 CGCCGACCTGAACAGATACC 60.528 60.000 3.19 0.00 0.00 2.73
107 108 0.535335 GCCGACCTGAACAGATACCA 59.465 55.000 3.19 0.00 0.00 3.25
108 109 1.471676 GCCGACCTGAACAGATACCAG 60.472 57.143 3.19 0.00 0.00 4.00
109 110 1.471676 CCGACCTGAACAGATACCAGC 60.472 57.143 3.19 0.00 0.00 4.85
110 111 1.204704 CGACCTGAACAGATACCAGCA 59.795 52.381 3.19 0.00 0.00 4.41
111 112 2.736719 CGACCTGAACAGATACCAGCAG 60.737 54.545 3.19 0.00 0.00 4.24
112 113 2.497675 GACCTGAACAGATACCAGCAGA 59.502 50.000 3.19 0.00 0.00 4.26
113 114 3.110705 ACCTGAACAGATACCAGCAGAT 58.889 45.455 3.19 0.00 0.00 2.90
114 115 3.118482 ACCTGAACAGATACCAGCAGATG 60.118 47.826 3.19 0.00 0.00 2.90
115 116 3.133542 CCTGAACAGATACCAGCAGATGA 59.866 47.826 3.19 0.00 0.00 2.92
116 117 4.383444 CCTGAACAGATACCAGCAGATGAA 60.383 45.833 3.19 0.00 0.00 2.57
117 118 5.164620 TGAACAGATACCAGCAGATGAAA 57.835 39.130 0.00 0.00 0.00 2.69
118 119 5.748402 TGAACAGATACCAGCAGATGAAAT 58.252 37.500 0.00 0.00 0.00 2.17
119 120 5.587443 TGAACAGATACCAGCAGATGAAATG 59.413 40.000 0.00 0.00 0.00 2.32
120 121 4.458397 ACAGATACCAGCAGATGAAATGG 58.542 43.478 0.00 0.00 38.83 3.16
121 122 3.819337 CAGATACCAGCAGATGAAATGGG 59.181 47.826 0.00 0.00 37.13 4.00
122 123 3.461085 AGATACCAGCAGATGAAATGGGT 59.539 43.478 0.00 0.00 37.13 4.51
123 124 2.134789 ACCAGCAGATGAAATGGGTC 57.865 50.000 0.00 0.00 37.13 4.46
124 125 1.019673 CCAGCAGATGAAATGGGTCG 58.980 55.000 0.00 0.00 0.00 4.79
125 126 0.379669 CAGCAGATGAAATGGGTCGC 59.620 55.000 0.00 0.00 0.00 5.19
126 127 0.749454 AGCAGATGAAATGGGTCGCC 60.749 55.000 0.00 0.00 0.00 5.54
127 128 1.728490 GCAGATGAAATGGGTCGCCC 61.728 60.000 7.87 7.87 45.71 6.13
139 140 1.934589 GGTCGCCCCATTAAAATTGC 58.065 50.000 0.00 0.00 0.00 3.56
140 141 1.480545 GGTCGCCCCATTAAAATTGCT 59.519 47.619 0.00 0.00 0.00 3.91
141 142 2.481276 GGTCGCCCCATTAAAATTGCTC 60.481 50.000 0.00 0.00 0.00 4.26
142 143 2.427095 GTCGCCCCATTAAAATTGCTCT 59.573 45.455 0.00 0.00 0.00 4.09
143 144 3.630312 GTCGCCCCATTAAAATTGCTCTA 59.370 43.478 0.00 0.00 0.00 2.43
144 145 4.097286 GTCGCCCCATTAAAATTGCTCTAA 59.903 41.667 0.00 0.00 0.00 2.10
145 146 4.707448 TCGCCCCATTAAAATTGCTCTAAA 59.293 37.500 0.00 0.00 0.00 1.85
146 147 5.362430 TCGCCCCATTAAAATTGCTCTAAAT 59.638 36.000 0.00 0.00 0.00 1.40
147 148 5.463061 CGCCCCATTAAAATTGCTCTAAATG 59.537 40.000 0.00 0.00 0.00 2.32
148 149 6.348498 GCCCCATTAAAATTGCTCTAAATGT 58.652 36.000 0.00 0.00 0.00 2.71
149 150 6.479990 GCCCCATTAAAATTGCTCTAAATGTC 59.520 38.462 0.00 0.00 0.00 3.06
150 151 6.697019 CCCCATTAAAATTGCTCTAAATGTCG 59.303 38.462 0.00 0.00 0.00 4.35
151 152 7.257722 CCCATTAAAATTGCTCTAAATGTCGT 58.742 34.615 0.00 0.00 0.00 4.34
152 153 7.432252 CCCATTAAAATTGCTCTAAATGTCGTC 59.568 37.037 0.00 0.00 0.00 4.20
153 154 8.184192 CCATTAAAATTGCTCTAAATGTCGTCT 58.816 33.333 0.00 0.00 0.00 4.18
154 155 9.214953 CATTAAAATTGCTCTAAATGTCGTCTC 57.785 33.333 0.00 0.00 0.00 3.36
155 156 8.547967 TTAAAATTGCTCTAAATGTCGTCTCT 57.452 30.769 0.00 0.00 0.00 3.10
156 157 6.654793 AAATTGCTCTAAATGTCGTCTCTC 57.345 37.500 0.00 0.00 0.00 3.20
157 158 4.783764 TTGCTCTAAATGTCGTCTCTCA 57.216 40.909 0.00 0.00 0.00 3.27
158 159 4.098055 TGCTCTAAATGTCGTCTCTCAC 57.902 45.455 0.00 0.00 0.00 3.51
159 160 3.759086 TGCTCTAAATGTCGTCTCTCACT 59.241 43.478 0.00 0.00 0.00 3.41
160 161 4.941873 TGCTCTAAATGTCGTCTCTCACTA 59.058 41.667 0.00 0.00 0.00 2.74
161 162 5.414765 TGCTCTAAATGTCGTCTCTCACTAA 59.585 40.000 0.00 0.00 0.00 2.24
162 163 6.072119 TGCTCTAAATGTCGTCTCTCACTAAA 60.072 38.462 0.00 0.00 0.00 1.85
163 164 6.251801 GCTCTAAATGTCGTCTCTCACTAAAC 59.748 42.308 0.00 0.00 0.00 2.01
164 165 6.312487 TCTAAATGTCGTCTCTCACTAAACG 58.688 40.000 0.00 0.00 36.50 3.60
165 166 2.327081 TGTCGTCTCTCACTAAACGC 57.673 50.000 0.00 0.00 35.22 4.84
166 167 1.605232 TGTCGTCTCTCACTAAACGCA 59.395 47.619 0.00 0.00 35.22 5.24
167 168 1.977412 GTCGTCTCTCACTAAACGCAC 59.023 52.381 0.00 0.00 35.22 5.34
168 169 0.975544 CGTCTCTCACTAAACGCACG 59.024 55.000 0.00 0.00 0.00 5.34
169 170 0.708918 GTCTCTCACTAAACGCACGC 59.291 55.000 0.00 0.00 0.00 5.34
170 171 0.388134 TCTCTCACTAAACGCACGCC 60.388 55.000 0.00 0.00 0.00 5.68
171 172 1.674611 CTCTCACTAAACGCACGCCG 61.675 60.000 0.00 0.00 44.21 6.46
172 173 2.726691 CTCACTAAACGCACGCCGG 61.727 63.158 0.00 0.00 42.52 6.13
173 174 2.735478 CACTAAACGCACGCCGGA 60.735 61.111 5.05 0.00 42.52 5.14
174 175 2.029369 ACTAAACGCACGCCGGAA 59.971 55.556 5.05 0.00 42.52 4.30
175 176 1.375013 ACTAAACGCACGCCGGAAT 60.375 52.632 5.05 0.00 42.52 3.01
176 177 1.060308 CTAAACGCACGCCGGAATG 59.940 57.895 5.05 2.60 42.52 2.67
177 178 2.896428 CTAAACGCACGCCGGAATGC 62.896 60.000 17.91 17.91 42.52 3.56
180 181 4.397090 CGCACGCCGGAATGCAAA 62.397 61.111 24.79 0.00 42.17 3.68
181 182 2.049618 GCACGCCGGAATGCAAAA 60.050 55.556 21.71 0.00 41.65 2.44
182 183 1.663074 GCACGCCGGAATGCAAAAA 60.663 52.632 21.71 0.00 41.65 1.94
206 207 9.634163 AAAAATATCCAGAAAAATACGAACACC 57.366 29.630 0.00 0.00 0.00 4.16
207 208 4.939509 ATCCAGAAAAATACGAACACCG 57.060 40.909 0.00 0.00 45.44 4.94
208 209 3.068560 TCCAGAAAAATACGAACACCGG 58.931 45.455 0.00 0.00 43.93 5.28
209 210 2.413634 CCAGAAAAATACGAACACCGGC 60.414 50.000 0.00 0.00 43.93 6.13
210 211 1.808343 AGAAAAATACGAACACCGGCC 59.192 47.619 0.00 0.00 43.93 6.13
211 212 1.536331 GAAAAATACGAACACCGGCCA 59.464 47.619 0.00 0.00 43.93 5.36
212 213 1.161843 AAAATACGAACACCGGCCAG 58.838 50.000 0.00 0.00 43.93 4.85
214 215 2.530958 AATACGAACACCGGCCAGGG 62.531 60.000 16.44 2.18 46.96 4.45
216 217 3.697747 CGAACACCGGCCAGGGTA 61.698 66.667 16.44 0.00 46.96 3.69
217 218 2.267961 GAACACCGGCCAGGGTAG 59.732 66.667 16.44 7.80 46.96 3.18
218 219 3.325201 GAACACCGGCCAGGGTAGG 62.325 68.421 16.44 4.66 46.96 3.18
219 220 3.857521 AACACCGGCCAGGGTAGGA 62.858 63.158 16.44 0.00 46.96 2.94
220 221 3.782443 CACCGGCCAGGGTAGGAC 61.782 72.222 16.44 0.00 46.96 3.85
221 222 4.007323 ACCGGCCAGGGTAGGACT 62.007 66.667 16.44 0.00 46.96 3.85
222 223 3.155167 CCGGCCAGGGTAGGACTC 61.155 72.222 2.24 0.00 33.12 3.36
223 224 2.042843 CGGCCAGGGTAGGACTCT 60.043 66.667 2.24 0.00 33.12 3.24
224 225 2.427245 CGGCCAGGGTAGGACTCTG 61.427 68.421 2.24 0.00 46.17 3.35
231 232 3.474798 AGGGTAGGACTCTGATGAACA 57.525 47.619 0.00 0.00 0.00 3.18
232 233 3.370104 AGGGTAGGACTCTGATGAACAG 58.630 50.000 0.00 0.00 46.97 3.16
233 234 2.432510 GGGTAGGACTCTGATGAACAGG 59.567 54.545 0.00 0.00 45.76 4.00
234 235 3.100671 GGTAGGACTCTGATGAACAGGT 58.899 50.000 0.00 0.00 45.76 4.00
235 236 3.131400 GGTAGGACTCTGATGAACAGGTC 59.869 52.174 0.00 0.00 45.76 3.85
236 237 2.894731 AGGACTCTGATGAACAGGTCA 58.105 47.619 11.29 0.00 45.76 4.02
237 238 2.564947 AGGACTCTGATGAACAGGTCAC 59.435 50.000 11.29 0.00 45.76 3.67
238 239 2.564947 GGACTCTGATGAACAGGTCACT 59.435 50.000 11.29 0.00 45.76 3.41
249 250 2.601481 CAGGTCACTGCGTTGAAATC 57.399 50.000 0.00 0.00 38.01 2.17
250 251 2.146342 CAGGTCACTGCGTTGAAATCT 58.854 47.619 0.00 0.00 38.01 2.40
251 252 2.096069 CAGGTCACTGCGTTGAAATCTG 60.096 50.000 0.00 0.00 38.01 2.90
252 253 1.873591 GGTCACTGCGTTGAAATCTGT 59.126 47.619 0.00 0.00 0.00 3.41
253 254 2.349817 GGTCACTGCGTTGAAATCTGTG 60.350 50.000 0.00 0.00 0.00 3.66
254 255 1.264020 TCACTGCGTTGAAATCTGTGC 59.736 47.619 0.00 0.00 32.18 4.57
255 256 0.235665 ACTGCGTTGAAATCTGTGCG 59.764 50.000 0.00 0.00 0.00 5.34
256 257 0.235665 CTGCGTTGAAATCTGTGCGT 59.764 50.000 0.00 0.00 0.00 5.24
257 258 0.041400 TGCGTTGAAATCTGTGCGTG 60.041 50.000 0.00 0.00 0.00 5.34
258 259 0.725784 GCGTTGAAATCTGTGCGTGG 60.726 55.000 0.00 0.00 0.00 4.94
259 260 0.725784 CGTTGAAATCTGTGCGTGGC 60.726 55.000 0.00 0.00 0.00 5.01
260 261 0.387239 GTTGAAATCTGTGCGTGGCC 60.387 55.000 0.00 0.00 0.00 5.36
261 262 1.851021 TTGAAATCTGTGCGTGGCCG 61.851 55.000 0.00 0.00 37.07 6.13
262 263 2.281484 AAATCTGTGCGTGGCCGT 60.281 55.556 0.00 0.00 36.15 5.68
263 264 1.004320 AAATCTGTGCGTGGCCGTA 60.004 52.632 0.00 0.00 36.15 4.02
264 265 1.019278 AAATCTGTGCGTGGCCGTAG 61.019 55.000 0.00 0.00 36.15 3.51
283 284 2.006772 GCTTACGAGGCACCATTCG 58.993 57.895 0.00 0.00 42.26 3.34
284 285 1.429148 GCTTACGAGGCACCATTCGG 61.429 60.000 0.00 0.00 40.93 4.30
286 287 1.135527 CTTACGAGGCACCATTCGGTA 59.864 52.381 0.00 0.00 46.94 4.02
287 288 1.184431 TACGAGGCACCATTCGGTAA 58.816 50.000 0.00 0.00 46.94 2.85
288 289 0.322322 ACGAGGCACCATTCGGTAAA 59.678 50.000 0.00 0.00 46.94 2.01
289 290 1.270947 ACGAGGCACCATTCGGTAAAA 60.271 47.619 0.00 0.00 46.94 1.52
290 291 1.807742 CGAGGCACCATTCGGTAAAAA 59.192 47.619 0.00 0.00 46.94 1.94
306 307 1.534729 AAAAAGTGGATCAGACCCGC 58.465 50.000 0.00 0.00 34.52 6.13
307 308 0.673644 AAAAGTGGATCAGACCCGCG 60.674 55.000 0.00 0.00 39.10 6.46
308 309 2.521958 AAAGTGGATCAGACCCGCGG 62.522 60.000 21.04 21.04 39.10 6.46
309 310 3.458163 GTGGATCAGACCCGCGGA 61.458 66.667 30.73 6.25 0.00 5.54
310 311 3.147595 TGGATCAGACCCGCGGAG 61.148 66.667 30.73 19.69 0.00 4.63
311 312 3.917760 GGATCAGACCCGCGGAGG 61.918 72.222 30.73 14.21 40.63 4.30
312 313 4.593864 GATCAGACCCGCGGAGGC 62.594 72.222 30.73 19.81 39.21 4.70
335 336 2.045340 CCCGACAAAGGGCCGAAT 60.045 61.111 0.00 0.00 45.72 3.34
336 337 1.677633 CCCGACAAAGGGCCGAATT 60.678 57.895 0.00 0.00 45.72 2.17
337 338 1.654023 CCCGACAAAGGGCCGAATTC 61.654 60.000 0.00 0.00 45.72 2.17
338 339 0.676782 CCGACAAAGGGCCGAATTCT 60.677 55.000 3.52 0.00 0.00 2.40
339 340 1.406341 CCGACAAAGGGCCGAATTCTA 60.406 52.381 3.52 0.00 0.00 2.10
340 341 2.561569 CGACAAAGGGCCGAATTCTAT 58.438 47.619 3.52 0.00 0.00 1.98
341 342 3.493699 CCGACAAAGGGCCGAATTCTATA 60.494 47.826 3.52 0.00 0.00 1.31
342 343 4.315803 CGACAAAGGGCCGAATTCTATAT 58.684 43.478 3.52 0.00 0.00 0.86
343 344 4.389077 CGACAAAGGGCCGAATTCTATATC 59.611 45.833 3.52 0.00 0.00 1.63
344 345 5.552178 GACAAAGGGCCGAATTCTATATCT 58.448 41.667 3.52 0.00 0.00 1.98
345 346 5.308825 ACAAAGGGCCGAATTCTATATCTG 58.691 41.667 3.52 0.00 0.00 2.90
346 347 5.163195 ACAAAGGGCCGAATTCTATATCTGT 60.163 40.000 3.52 0.00 0.00 3.41
347 348 6.042781 ACAAAGGGCCGAATTCTATATCTGTA 59.957 38.462 3.52 0.00 0.00 2.74
348 349 6.681729 AAGGGCCGAATTCTATATCTGTAA 57.318 37.500 3.52 0.00 0.00 2.41
349 350 6.681729 AGGGCCGAATTCTATATCTGTAAA 57.318 37.500 3.52 0.00 0.00 2.01
350 351 7.074653 AGGGCCGAATTCTATATCTGTAAAA 57.925 36.000 3.52 0.00 0.00 1.52
351 352 7.690256 AGGGCCGAATTCTATATCTGTAAAAT 58.310 34.615 3.52 0.00 0.00 1.82
352 353 8.822805 AGGGCCGAATTCTATATCTGTAAAATA 58.177 33.333 3.52 0.00 0.00 1.40
353 354 9.444600 GGGCCGAATTCTATATCTGTAAAATAA 57.555 33.333 3.52 0.00 0.00 1.40
393 394 6.296026 TCCTGTATTGTTTATATGGACAGCC 58.704 40.000 0.00 0.00 33.17 4.85
641 644 3.733960 CGCACGAGTCTCCGTCCA 61.734 66.667 0.00 0.00 41.29 4.02
692 695 3.503748 GGAAAGCTGCATTTATATCGGCT 59.496 43.478 1.02 0.00 43.63 5.52
694 697 2.430465 AGCTGCATTTATATCGGCTGG 58.570 47.619 1.02 0.00 40.59 4.85
871 875 1.074775 TTATCTACTGCCCCCGCCT 60.075 57.895 0.00 0.00 0.00 5.52
873 877 0.693092 TATCTACTGCCCCCGCCTTT 60.693 55.000 0.00 0.00 0.00 3.11
957 961 4.814294 CCCGCACTGTAGCCCGAC 62.814 72.222 0.00 0.00 0.00 4.79
1071 1075 3.202151 AGGTGAGTTTCTCCCAGTTTTGA 59.798 43.478 0.00 0.00 30.62 2.69
1083 1087 1.599071 CAGTTTTGACGCTCTGCTTCA 59.401 47.619 0.00 0.00 35.10 3.02
1114 1118 4.918129 TAGATTCGTCGGCGGCGC 62.918 66.667 30.91 26.17 38.89 6.53
1124 1128 3.517140 GGCGGCGCATCATTTCCA 61.517 61.111 34.36 0.00 0.00 3.53
1132 1136 2.674747 GCGCATCATTTCCATGTTTGGT 60.675 45.455 0.30 0.00 44.06 3.67
1133 1137 3.428725 GCGCATCATTTCCATGTTTGGTA 60.429 43.478 0.30 0.00 44.06 3.25
1134 1138 4.104776 CGCATCATTTCCATGTTTGGTAC 58.895 43.478 0.00 0.00 44.06 3.34
1194 1198 2.695147 TGCTTCTCCTCGCAGATGATTA 59.305 45.455 0.00 0.00 33.89 1.75
1612 1616 2.294078 CCTCCTCGGCCAAGAAGGT 61.294 63.158 2.24 0.00 40.61 3.50
1727 1731 2.758089 CCTGCGTGCTGATGCCTTC 61.758 63.158 0.00 0.00 38.71 3.46
1905 1909 6.369615 GGATGTTTTTAGCTTCGGTTGTAGTA 59.630 38.462 0.00 0.00 0.00 1.82
1906 1910 6.774354 TGTTTTTAGCTTCGGTTGTAGTAG 57.226 37.500 0.00 0.00 0.00 2.57
1907 1911 6.282930 TGTTTTTAGCTTCGGTTGTAGTAGT 58.717 36.000 0.00 0.00 0.00 2.73
2010 2014 3.692593 GTCCTGTTGTTGTGTACTTGGTT 59.307 43.478 0.00 0.00 0.00 3.67
2018 2022 0.865769 GTGTACTTGGTTGCTGTCCG 59.134 55.000 0.00 0.00 0.00 4.79
2020 2024 1.302192 TACTTGGTTGCTGTCCGCC 60.302 57.895 0.00 0.00 38.05 6.13
2192 2196 6.369890 CACTTCCAGGTATACATGCATCATAC 59.630 42.308 12.01 15.30 0.00 2.39
2193 2197 6.270927 ACTTCCAGGTATACATGCATCATACT 59.729 38.462 19.92 9.35 0.00 2.12
2194 2198 7.454694 ACTTCCAGGTATACATGCATCATACTA 59.545 37.037 19.92 7.67 0.00 1.82
2244 2248 5.537300 TTTACAGATGCATCCTAGACTCC 57.463 43.478 23.06 0.00 0.00 3.85
2245 2249 3.326946 ACAGATGCATCCTAGACTCCT 57.673 47.619 23.06 0.00 0.00 3.69
2246 2250 4.461450 ACAGATGCATCCTAGACTCCTA 57.539 45.455 23.06 0.00 0.00 2.94
2247 2251 4.406456 ACAGATGCATCCTAGACTCCTAG 58.594 47.826 23.06 2.03 41.58 3.02
2248 2252 4.141041 ACAGATGCATCCTAGACTCCTAGT 60.141 45.833 23.06 0.00 40.57 2.57
2249 2253 5.073827 ACAGATGCATCCTAGACTCCTAGTA 59.926 44.000 23.06 0.00 40.57 1.82
2250 2254 6.007076 CAGATGCATCCTAGACTCCTAGTAA 58.993 44.000 23.06 0.00 40.57 2.24
2251 2255 6.491745 CAGATGCATCCTAGACTCCTAGTAAA 59.508 42.308 23.06 0.00 40.57 2.01
2252 2256 7.014711 CAGATGCATCCTAGACTCCTAGTAAAA 59.985 40.741 23.06 0.00 40.57 1.52
2253 2257 7.732593 AGATGCATCCTAGACTCCTAGTAAAAT 59.267 37.037 23.06 0.00 40.57 1.82
2254 2258 7.055667 TGCATCCTAGACTCCTAGTAAAATG 57.944 40.000 0.00 0.00 40.57 2.32
2255 2259 6.611642 TGCATCCTAGACTCCTAGTAAAATGT 59.388 38.462 0.00 0.00 40.57 2.71
2256 2260 7.783119 TGCATCCTAGACTCCTAGTAAAATGTA 59.217 37.037 0.00 0.00 40.57 2.29
2257 2261 8.639761 GCATCCTAGACTCCTAGTAAAATGTAA 58.360 37.037 0.00 0.00 40.57 2.41
2258 2262 9.968870 CATCCTAGACTCCTAGTAAAATGTAAC 57.031 37.037 0.00 0.00 40.57 2.50
2259 2263 9.710818 ATCCTAGACTCCTAGTAAAATGTAACA 57.289 33.333 0.00 0.00 40.57 2.41
2260 2264 9.710818 TCCTAGACTCCTAGTAAAATGTAACAT 57.289 33.333 0.00 0.00 40.57 2.71
2393 2399 4.890581 ACTGGCCAGTGTTCTACTCTATAG 59.109 45.833 37.39 6.35 40.75 1.31
2428 2434 8.813643 AATAGTCTATTGTATAAACACTCGCC 57.186 34.615 4.22 0.00 34.61 5.54
2429 2435 6.466885 AGTCTATTGTATAAACACTCGCCT 57.533 37.500 0.00 0.00 34.61 5.52
2430 2436 7.578310 AGTCTATTGTATAAACACTCGCCTA 57.422 36.000 0.00 0.00 34.61 3.93
2431 2437 8.179509 AGTCTATTGTATAAACACTCGCCTAT 57.820 34.615 0.00 0.00 34.61 2.57
2433 2439 9.903682 GTCTATTGTATAAACACTCGCCTATTA 57.096 33.333 0.00 0.00 34.61 0.98
2436 2442 6.720112 TGTATAAACACTCGCCTATTAGGT 57.280 37.500 11.38 0.00 37.80 3.08
2437 2443 7.822161 TGTATAAACACTCGCCTATTAGGTA 57.178 36.000 11.38 0.00 37.80 3.08
2438 2444 8.413309 TGTATAAACACTCGCCTATTAGGTAT 57.587 34.615 11.38 1.94 37.80 2.73
2439 2445 9.519191 TGTATAAACACTCGCCTATTAGGTATA 57.481 33.333 11.38 1.09 37.80 1.47
2451 2457 6.688578 CCTATTAGGTATACGTGCTTCATGT 58.311 40.000 8.32 0.00 37.38 3.21
2468 2474 6.197842 GCTTCATGTTTAGCATTGTAGCAATC 59.802 38.462 10.79 0.00 37.35 2.67
2469 2475 6.756299 TCATGTTTAGCATTGTAGCAATCA 57.244 33.333 0.00 0.00 35.19 2.57
2480 2486 6.197842 GCATTGTAGCAATCAGAATTAACTGC 59.802 38.462 0.00 0.00 37.75 4.40
2506 2512 9.814899 CCAATCTACTTCTGCATATAGGAATAG 57.185 37.037 0.00 0.00 0.00 1.73
2518 2524 7.545615 TGCATATAGGAATAGCGTTCATAACAG 59.454 37.037 7.11 1.36 0.00 3.16
2541 2547 5.882557 AGTTGTCGCTTTGGAATTATCTGAT 59.117 36.000 0.00 0.00 0.00 2.90
2554 2560 9.208022 TGGAATTATCTGATAATCTACTTTGCG 57.792 33.333 20.06 0.00 34.50 4.85
2586 2592 2.093306 TTGCTCACCATGTTCCGTAG 57.907 50.000 0.00 0.00 0.00 3.51
2590 2596 2.094390 GCTCACCATGTTCCGTAGTACA 60.094 50.000 0.38 0.00 0.00 2.90
2618 2624 1.271325 TGGGATTGCACTGATCGTTGT 60.271 47.619 0.00 0.00 0.00 3.32
2633 2639 5.580691 TGATCGTTGTAAGCTAATCTGGTTG 59.419 40.000 0.00 0.00 0.00 3.77
2663 2669 3.728221 GCATATAGCTGTCGATAGATGCG 59.272 47.826 13.99 0.00 43.81 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.014085 GCGACTCATTCCCGGTCCA 62.014 63.158 0.00 0.00 0.00 4.02
5 6 2.202892 GCGACTCATTCCCGGTCC 60.203 66.667 0.00 0.00 0.00 4.46
6 7 2.202892 GGCGACTCATTCCCGGTC 60.203 66.667 0.00 0.00 0.00 4.79
7 8 2.367202 ATGGCGACTCATTCCCGGT 61.367 57.895 0.00 0.00 0.00 5.28
8 9 1.889105 CATGGCGACTCATTCCCGG 60.889 63.158 0.00 0.00 0.00 5.73
9 10 2.537560 GCATGGCGACTCATTCCCG 61.538 63.158 0.00 0.00 0.00 5.14
10 11 3.425422 GCATGGCGACTCATTCCC 58.575 61.111 0.00 0.00 0.00 3.97
21 22 2.258286 GTTTGGTGTCCGCATGGC 59.742 61.111 0.00 0.00 34.14 4.40
22 23 2.560861 CGTTTGGTGTCCGCATGG 59.439 61.111 0.00 0.00 0.00 3.66
23 24 1.963855 TCCGTTTGGTGTCCGCATG 60.964 57.895 0.00 0.00 36.30 4.06
24 25 1.964373 GTCCGTTTGGTGTCCGCAT 60.964 57.895 0.00 0.00 36.30 4.73
25 26 2.589442 GTCCGTTTGGTGTCCGCA 60.589 61.111 0.00 0.00 36.30 5.69
26 27 3.708734 CGTCCGTTTGGTGTCCGC 61.709 66.667 0.00 0.00 36.30 5.54
27 28 3.708734 GCGTCCGTTTGGTGTCCG 61.709 66.667 0.00 0.00 36.30 4.79
28 29 3.708734 CGCGTCCGTTTGGTGTCC 61.709 66.667 0.00 0.00 36.30 4.02
29 30 4.364409 GCGCGTCCGTTTGGTGTC 62.364 66.667 8.43 0.00 36.67 3.67
40 41 4.117372 CTCAAACGGACGCGCGTC 62.117 66.667 45.60 45.60 43.87 5.19
41 42 4.936823 ACTCAAACGGACGCGCGT 62.937 61.111 38.52 38.52 0.00 6.01
42 43 4.117372 GACTCAAACGGACGCGCG 62.117 66.667 30.96 30.96 0.00 6.86
43 44 4.117372 CGACTCAAACGGACGCGC 62.117 66.667 5.73 0.00 0.00 6.86
50 51 3.698463 AACGCGCCGACTCAAACG 61.698 61.111 5.73 0.00 0.00 3.60
51 52 2.127758 CAACGCGCCGACTCAAAC 60.128 61.111 5.73 0.00 0.00 2.93
52 53 3.342627 CCAACGCGCCGACTCAAA 61.343 61.111 5.73 0.00 0.00 2.69
53 54 4.287781 TCCAACGCGCCGACTCAA 62.288 61.111 5.73 0.00 0.00 3.02
64 65 1.129811 GACATAAAAGGCGGTCCAACG 59.870 52.381 0.00 0.00 33.74 4.10
65 66 2.913777 GACATAAAAGGCGGTCCAAC 57.086 50.000 0.00 0.00 33.74 3.77
68 69 1.712018 GCGGACATAAAAGGCGGTCC 61.712 60.000 0.00 0.00 44.97 4.46
69 70 1.719709 GCGGACATAAAAGGCGGTC 59.280 57.895 0.00 0.00 0.00 4.79
70 71 2.104253 CGCGGACATAAAAGGCGGT 61.104 57.895 0.00 0.00 42.86 5.68
71 72 2.707039 CGCGGACATAAAAGGCGG 59.293 61.111 0.00 0.00 42.86 6.13
73 74 2.407616 GGCGCGGACATAAAAGGC 59.592 61.111 8.83 0.00 0.00 4.35
74 75 1.812093 TCGGCGCGGACATAAAAGG 60.812 57.895 14.27 0.00 0.00 3.11
75 76 1.347221 GTCGGCGCGGACATAAAAG 59.653 57.895 34.74 3.49 36.91 2.27
76 77 2.101835 GGTCGGCGCGGACATAAAA 61.102 57.895 38.05 8.18 38.70 1.52
77 78 2.509786 GGTCGGCGCGGACATAAA 60.510 61.111 38.05 8.89 38.70 1.40
78 79 3.454573 AGGTCGGCGCGGACATAA 61.455 61.111 38.05 9.60 38.70 1.90
79 80 4.201679 CAGGTCGGCGCGGACATA 62.202 66.667 38.05 9.97 38.70 2.29
85 86 2.607668 TATCTGTTCAGGTCGGCGCG 62.608 60.000 0.00 0.00 0.00 6.86
86 87 1.141019 TATCTGTTCAGGTCGGCGC 59.859 57.895 0.00 0.00 0.00 6.53
87 88 0.527817 GGTATCTGTTCAGGTCGGCG 60.528 60.000 0.00 0.00 0.00 6.46
88 89 0.535335 TGGTATCTGTTCAGGTCGGC 59.465 55.000 0.00 0.00 0.00 5.54
89 90 1.471676 GCTGGTATCTGTTCAGGTCGG 60.472 57.143 0.00 0.00 0.00 4.79
90 91 1.204704 TGCTGGTATCTGTTCAGGTCG 59.795 52.381 0.00 0.00 0.00 4.79
91 92 2.497675 TCTGCTGGTATCTGTTCAGGTC 59.502 50.000 0.00 0.00 0.00 3.85
92 93 2.540383 TCTGCTGGTATCTGTTCAGGT 58.460 47.619 0.00 0.00 0.00 4.00
93 94 3.133542 TCATCTGCTGGTATCTGTTCAGG 59.866 47.826 0.00 0.00 0.00 3.86
94 95 4.397481 TCATCTGCTGGTATCTGTTCAG 57.603 45.455 0.00 0.00 0.00 3.02
95 96 4.824479 TTCATCTGCTGGTATCTGTTCA 57.176 40.909 0.00 0.00 0.00 3.18
96 97 5.008415 CCATTTCATCTGCTGGTATCTGTTC 59.992 44.000 0.00 0.00 0.00 3.18
97 98 4.885907 CCATTTCATCTGCTGGTATCTGTT 59.114 41.667 0.00 0.00 0.00 3.16
98 99 4.458397 CCATTTCATCTGCTGGTATCTGT 58.542 43.478 0.00 0.00 0.00 3.41
99 100 3.819337 CCCATTTCATCTGCTGGTATCTG 59.181 47.826 0.00 0.00 0.00 2.90
100 101 3.461085 ACCCATTTCATCTGCTGGTATCT 59.539 43.478 0.00 0.00 0.00 1.98
101 102 3.817647 GACCCATTTCATCTGCTGGTATC 59.182 47.826 0.00 0.00 0.00 2.24
102 103 3.745480 CGACCCATTTCATCTGCTGGTAT 60.745 47.826 0.00 0.00 0.00 2.73
103 104 2.419990 CGACCCATTTCATCTGCTGGTA 60.420 50.000 0.00 0.00 0.00 3.25
104 105 1.679944 CGACCCATTTCATCTGCTGGT 60.680 52.381 0.00 0.00 0.00 4.00
105 106 1.019673 CGACCCATTTCATCTGCTGG 58.980 55.000 0.00 0.00 0.00 4.85
106 107 0.379669 GCGACCCATTTCATCTGCTG 59.620 55.000 0.00 0.00 0.00 4.41
107 108 0.749454 GGCGACCCATTTCATCTGCT 60.749 55.000 0.00 0.00 0.00 4.24
108 109 1.729881 GGCGACCCATTTCATCTGC 59.270 57.895 0.00 0.00 0.00 4.26
121 122 2.427095 AGAGCAATTTTAATGGGGCGAC 59.573 45.455 0.00 0.00 0.00 5.19
122 123 2.733956 AGAGCAATTTTAATGGGGCGA 58.266 42.857 0.00 0.00 0.00 5.54
123 124 4.647424 TTAGAGCAATTTTAATGGGGCG 57.353 40.909 0.00 0.00 0.00 6.13
124 125 6.348498 ACATTTAGAGCAATTTTAATGGGGC 58.652 36.000 0.00 0.00 0.00 5.80
125 126 6.697019 CGACATTTAGAGCAATTTTAATGGGG 59.303 38.462 0.00 0.00 0.00 4.96
126 127 7.257722 ACGACATTTAGAGCAATTTTAATGGG 58.742 34.615 0.00 0.00 0.00 4.00
127 128 8.184192 AGACGACATTTAGAGCAATTTTAATGG 58.816 33.333 0.00 0.00 0.00 3.16
128 129 9.214953 GAGACGACATTTAGAGCAATTTTAATG 57.785 33.333 0.00 0.00 0.00 1.90
129 130 9.167311 AGAGACGACATTTAGAGCAATTTTAAT 57.833 29.630 0.00 0.00 0.00 1.40
130 131 8.547967 AGAGACGACATTTAGAGCAATTTTAA 57.452 30.769 0.00 0.00 0.00 1.52
131 132 7.817478 TGAGAGACGACATTTAGAGCAATTTTA 59.183 33.333 0.00 0.00 0.00 1.52
132 133 6.650807 TGAGAGACGACATTTAGAGCAATTTT 59.349 34.615 0.00 0.00 0.00 1.82
133 134 6.091441 GTGAGAGACGACATTTAGAGCAATTT 59.909 38.462 0.00 0.00 0.00 1.82
134 135 5.578727 GTGAGAGACGACATTTAGAGCAATT 59.421 40.000 0.00 0.00 0.00 2.32
135 136 5.105554 AGTGAGAGACGACATTTAGAGCAAT 60.106 40.000 0.00 0.00 0.00 3.56
136 137 4.218635 AGTGAGAGACGACATTTAGAGCAA 59.781 41.667 0.00 0.00 0.00 3.91
137 138 3.759086 AGTGAGAGACGACATTTAGAGCA 59.241 43.478 0.00 0.00 0.00 4.26
138 139 4.364415 AGTGAGAGACGACATTTAGAGC 57.636 45.455 0.00 0.00 0.00 4.09
139 140 6.466413 CGTTTAGTGAGAGACGACATTTAGAG 59.534 42.308 0.00 0.00 37.69 2.43
140 141 6.312487 CGTTTAGTGAGAGACGACATTTAGA 58.688 40.000 0.00 0.00 37.69 2.10
141 142 5.003590 GCGTTTAGTGAGAGACGACATTTAG 59.996 44.000 0.00 0.00 37.69 1.85
142 143 4.855388 GCGTTTAGTGAGAGACGACATTTA 59.145 41.667 0.00 0.00 37.69 1.40
143 144 3.673809 GCGTTTAGTGAGAGACGACATTT 59.326 43.478 0.00 0.00 37.69 2.32
144 145 3.243336 GCGTTTAGTGAGAGACGACATT 58.757 45.455 0.00 0.00 37.69 2.71
145 146 2.228103 TGCGTTTAGTGAGAGACGACAT 59.772 45.455 0.00 0.00 37.69 3.06
146 147 1.605232 TGCGTTTAGTGAGAGACGACA 59.395 47.619 0.00 0.00 37.69 4.35
147 148 1.977412 GTGCGTTTAGTGAGAGACGAC 59.023 52.381 0.00 0.00 37.69 4.34
148 149 1.399343 CGTGCGTTTAGTGAGAGACGA 60.399 52.381 0.00 0.00 37.69 4.20
149 150 0.975544 CGTGCGTTTAGTGAGAGACG 59.024 55.000 0.00 0.00 38.45 4.18
150 151 0.708918 GCGTGCGTTTAGTGAGAGAC 59.291 55.000 0.00 0.00 0.00 3.36
151 152 0.388134 GGCGTGCGTTTAGTGAGAGA 60.388 55.000 0.00 0.00 0.00 3.10
152 153 1.674611 CGGCGTGCGTTTAGTGAGAG 61.675 60.000 0.00 0.00 0.00 3.20
153 154 1.731613 CGGCGTGCGTTTAGTGAGA 60.732 57.895 0.00 0.00 0.00 3.27
154 155 2.726691 CCGGCGTGCGTTTAGTGAG 61.727 63.158 6.01 0.00 0.00 3.51
155 156 2.696409 TTCCGGCGTGCGTTTAGTGA 62.696 55.000 6.01 0.00 0.00 3.41
156 157 1.632046 ATTCCGGCGTGCGTTTAGTG 61.632 55.000 6.01 0.00 0.00 2.74
157 158 1.375013 ATTCCGGCGTGCGTTTAGT 60.375 52.632 6.01 0.00 0.00 2.24
158 159 1.060308 CATTCCGGCGTGCGTTTAG 59.940 57.895 6.01 0.00 0.00 1.85
159 160 3.029564 GCATTCCGGCGTGCGTTTA 62.030 57.895 13.85 0.00 0.00 2.01
160 161 4.398598 GCATTCCGGCGTGCGTTT 62.399 61.111 13.85 0.00 0.00 3.60
163 164 3.888079 TTTTGCATTCCGGCGTGCG 62.888 57.895 20.92 0.00 44.11 5.34
164 165 1.663074 TTTTTGCATTCCGGCGTGC 60.663 52.632 19.99 19.99 41.61 5.34
165 166 4.643733 TTTTTGCATTCCGGCGTG 57.356 50.000 6.01 0.00 36.28 5.34
180 181 9.634163 GGTGTTCGTATTTTTCTGGATATTTTT 57.366 29.630 0.00 0.00 0.00 1.94
181 182 7.966204 CGGTGTTCGTATTTTTCTGGATATTTT 59.034 33.333 0.00 0.00 0.00 1.82
182 183 7.414762 CCGGTGTTCGTATTTTTCTGGATATTT 60.415 37.037 0.00 0.00 37.11 1.40
183 184 6.037830 CCGGTGTTCGTATTTTTCTGGATATT 59.962 38.462 0.00 0.00 37.11 1.28
184 185 5.526111 CCGGTGTTCGTATTTTTCTGGATAT 59.474 40.000 0.00 0.00 37.11 1.63
185 186 4.871557 CCGGTGTTCGTATTTTTCTGGATA 59.128 41.667 0.00 0.00 37.11 2.59
186 187 3.687698 CCGGTGTTCGTATTTTTCTGGAT 59.312 43.478 0.00 0.00 37.11 3.41
187 188 3.068560 CCGGTGTTCGTATTTTTCTGGA 58.931 45.455 0.00 0.00 37.11 3.86
188 189 2.413634 GCCGGTGTTCGTATTTTTCTGG 60.414 50.000 1.90 0.00 37.11 3.86
189 190 2.413634 GGCCGGTGTTCGTATTTTTCTG 60.414 50.000 1.90 0.00 37.11 3.02
190 191 1.808343 GGCCGGTGTTCGTATTTTTCT 59.192 47.619 1.90 0.00 37.11 2.52
191 192 1.536331 TGGCCGGTGTTCGTATTTTTC 59.464 47.619 1.90 0.00 37.11 2.29
192 193 1.538075 CTGGCCGGTGTTCGTATTTTT 59.462 47.619 2.29 0.00 37.11 1.94
193 194 1.161843 CTGGCCGGTGTTCGTATTTT 58.838 50.000 2.29 0.00 37.11 1.82
194 195 0.675522 CCTGGCCGGTGTTCGTATTT 60.676 55.000 11.58 0.00 37.11 1.40
195 196 1.078708 CCTGGCCGGTGTTCGTATT 60.079 57.895 11.58 0.00 37.11 1.89
196 197 2.582436 CCTGGCCGGTGTTCGTAT 59.418 61.111 11.58 0.00 37.11 3.06
197 198 3.697747 CCCTGGCCGGTGTTCGTA 61.698 66.667 11.58 0.00 37.11 3.43
199 200 3.659089 CTACCCTGGCCGGTGTTCG 62.659 68.421 11.58 0.00 36.56 3.95
200 201 2.267961 CTACCCTGGCCGGTGTTC 59.732 66.667 11.58 0.00 36.56 3.18
201 202 3.327404 CCTACCCTGGCCGGTGTT 61.327 66.667 11.58 0.00 36.56 3.32
202 203 4.326227 TCCTACCCTGGCCGGTGT 62.326 66.667 11.58 8.09 36.56 4.16
203 204 3.782443 GTCCTACCCTGGCCGGTG 61.782 72.222 11.58 0.24 36.56 4.94
204 205 3.978410 GAGTCCTACCCTGGCCGGT 62.978 68.421 11.58 9.37 40.13 5.28
205 206 3.155167 GAGTCCTACCCTGGCCGG 61.155 72.222 3.88 3.88 0.00 6.13
206 207 2.042843 AGAGTCCTACCCTGGCCG 60.043 66.667 0.00 0.00 0.00 6.13
207 208 0.399233 ATCAGAGTCCTACCCTGGCC 60.399 60.000 0.00 0.00 0.00 5.36
208 209 0.755686 CATCAGAGTCCTACCCTGGC 59.244 60.000 0.00 0.00 0.00 4.85
209 210 2.432510 GTTCATCAGAGTCCTACCCTGG 59.567 54.545 0.00 0.00 0.00 4.45
210 211 3.099905 TGTTCATCAGAGTCCTACCCTG 58.900 50.000 0.00 0.00 0.00 4.45
211 212 3.370104 CTGTTCATCAGAGTCCTACCCT 58.630 50.000 0.00 0.00 46.27 4.34
212 213 2.432510 CCTGTTCATCAGAGTCCTACCC 59.567 54.545 0.00 0.00 46.27 3.69
213 214 3.100671 ACCTGTTCATCAGAGTCCTACC 58.899 50.000 0.00 0.00 46.27 3.18
214 215 3.764434 TGACCTGTTCATCAGAGTCCTAC 59.236 47.826 11.07 0.00 46.27 3.18
215 216 3.764434 GTGACCTGTTCATCAGAGTCCTA 59.236 47.826 11.07 0.00 46.27 2.94
216 217 2.564947 GTGACCTGTTCATCAGAGTCCT 59.435 50.000 11.07 0.00 46.27 3.85
217 218 2.564947 AGTGACCTGTTCATCAGAGTCC 59.435 50.000 11.07 5.94 46.27 3.85
218 219 3.583806 CAGTGACCTGTTCATCAGAGTC 58.416 50.000 0.00 0.00 46.27 3.36
219 220 2.289320 GCAGTGACCTGTTCATCAGAGT 60.289 50.000 0.00 0.00 46.27 3.24
220 221 2.344950 GCAGTGACCTGTTCATCAGAG 58.655 52.381 0.00 0.00 46.27 3.35
221 222 1.337167 CGCAGTGACCTGTTCATCAGA 60.337 52.381 0.00 0.00 46.27 3.27
222 223 1.073964 CGCAGTGACCTGTTCATCAG 58.926 55.000 0.00 0.00 41.02 2.90
223 224 0.392706 ACGCAGTGACCTGTTCATCA 59.607 50.000 0.00 0.00 42.51 3.07
224 225 1.195448 CAACGCAGTGACCTGTTCATC 59.805 52.381 0.00 0.00 45.00 2.92
225 226 1.202639 TCAACGCAGTGACCTGTTCAT 60.203 47.619 0.00 0.00 45.00 2.57
226 227 0.176910 TCAACGCAGTGACCTGTTCA 59.823 50.000 0.00 0.00 45.00 3.18
227 228 1.295792 TTCAACGCAGTGACCTGTTC 58.704 50.000 0.00 0.00 45.00 3.18
228 229 1.745232 TTTCAACGCAGTGACCTGTT 58.255 45.000 0.00 0.00 45.00 3.16
229 230 1.873591 GATTTCAACGCAGTGACCTGT 59.126 47.619 0.00 0.00 45.00 4.00
230 231 2.096069 CAGATTTCAACGCAGTGACCTG 60.096 50.000 0.00 0.00 45.00 4.00
231 232 2.146342 CAGATTTCAACGCAGTGACCT 58.854 47.619 0.00 0.00 45.00 3.85
232 233 1.873591 ACAGATTTCAACGCAGTGACC 59.126 47.619 0.00 0.00 45.00 4.02
233 234 2.908634 CACAGATTTCAACGCAGTGAC 58.091 47.619 0.00 0.00 45.00 3.67
234 235 1.264020 GCACAGATTTCAACGCAGTGA 59.736 47.619 0.00 0.00 45.00 3.41
235 236 1.678360 GCACAGATTTCAACGCAGTG 58.322 50.000 0.00 0.00 45.00 3.66
237 238 0.235665 ACGCACAGATTTCAACGCAG 59.764 50.000 0.00 0.00 0.00 5.18
238 239 0.041400 CACGCACAGATTTCAACGCA 60.041 50.000 0.00 0.00 0.00 5.24
239 240 0.725784 CCACGCACAGATTTCAACGC 60.726 55.000 0.00 0.00 0.00 4.84
240 241 0.725784 GCCACGCACAGATTTCAACG 60.726 55.000 0.00 0.00 0.00 4.10
241 242 0.387239 GGCCACGCACAGATTTCAAC 60.387 55.000 0.00 0.00 0.00 3.18
242 243 1.851021 CGGCCACGCACAGATTTCAA 61.851 55.000 2.24 0.00 0.00 2.69
243 244 2.324330 CGGCCACGCACAGATTTCA 61.324 57.895 2.24 0.00 0.00 2.69
244 245 1.017177 TACGGCCACGCACAGATTTC 61.017 55.000 2.24 0.00 46.04 2.17
245 246 1.004320 TACGGCCACGCACAGATTT 60.004 52.632 2.24 0.00 46.04 2.17
246 247 1.447838 CTACGGCCACGCACAGATT 60.448 57.895 2.24 0.00 46.04 2.40
247 248 2.184322 CTACGGCCACGCACAGAT 59.816 61.111 2.24 0.00 46.04 2.90
248 249 4.063967 CCTACGGCCACGCACAGA 62.064 66.667 2.24 0.00 46.04 3.41
261 262 0.464452 ATGGTGCCTCGTAAGCCTAC 59.536 55.000 0.00 0.00 37.18 3.18
262 263 1.138266 GAATGGTGCCTCGTAAGCCTA 59.862 52.381 0.00 0.00 37.18 3.93
263 264 0.107654 GAATGGTGCCTCGTAAGCCT 60.108 55.000 0.00 0.00 37.18 4.58
264 265 1.429148 CGAATGGTGCCTCGTAAGCC 61.429 60.000 0.00 0.00 37.18 4.35
265 266 1.429148 CCGAATGGTGCCTCGTAAGC 61.429 60.000 0.00 0.00 33.17 3.09
266 267 2.677971 CCGAATGGTGCCTCGTAAG 58.322 57.895 0.00 0.00 33.17 2.34
267 268 4.924019 CCGAATGGTGCCTCGTAA 57.076 55.556 0.00 0.00 33.17 3.18
287 288 1.534729 GCGGGTCTGATCCACTTTTT 58.465 50.000 7.88 0.00 0.00 1.94
288 289 0.673644 CGCGGGTCTGATCCACTTTT 60.674 55.000 7.88 0.00 0.00 2.27
289 290 1.079127 CGCGGGTCTGATCCACTTT 60.079 57.895 7.88 0.00 0.00 2.66
290 291 2.579201 CGCGGGTCTGATCCACTT 59.421 61.111 7.88 0.00 0.00 3.16
291 292 3.461773 CCGCGGGTCTGATCCACT 61.462 66.667 20.10 0.00 0.00 4.00
292 293 3.432051 CTCCGCGGGTCTGATCCAC 62.432 68.421 27.83 0.00 0.00 4.02
293 294 3.147595 CTCCGCGGGTCTGATCCA 61.148 66.667 27.83 0.26 0.00 3.41
294 295 3.917760 CCTCCGCGGGTCTGATCC 61.918 72.222 27.83 0.00 0.00 3.36
295 296 4.593864 GCCTCCGCGGGTCTGATC 62.594 72.222 27.83 4.00 0.00 2.92
312 313 4.778143 CCCTTTGTCGGGCTCGGG 62.778 72.222 5.94 0.00 37.41 5.14
319 320 0.676782 AGAATTCGGCCCTTTGTCGG 60.677 55.000 0.00 0.00 0.00 4.79
320 321 2.018542 TAGAATTCGGCCCTTTGTCG 57.981 50.000 0.00 0.00 0.00 4.35
321 322 5.409826 CAGATATAGAATTCGGCCCTTTGTC 59.590 44.000 0.00 0.00 0.00 3.18
322 323 5.163195 ACAGATATAGAATTCGGCCCTTTGT 60.163 40.000 0.00 0.00 0.00 2.83
323 324 5.308825 ACAGATATAGAATTCGGCCCTTTG 58.691 41.667 0.00 0.00 0.00 2.77
324 325 5.568620 ACAGATATAGAATTCGGCCCTTT 57.431 39.130 0.00 0.00 0.00 3.11
325 326 6.681729 TTACAGATATAGAATTCGGCCCTT 57.318 37.500 0.00 0.00 0.00 3.95
326 327 6.681729 TTTACAGATATAGAATTCGGCCCT 57.318 37.500 0.00 0.00 0.00 5.19
327 328 7.923414 ATTTTACAGATATAGAATTCGGCCC 57.077 36.000 0.00 0.00 0.00 5.80
369 370 6.296026 GGCTGTCCATATAAACAATACAGGA 58.704 40.000 0.00 0.00 34.77 3.86
372 373 5.060506 CGGGCTGTCCATATAAACAATACA 58.939 41.667 0.00 0.00 34.36 2.29
373 374 4.083484 GCGGGCTGTCCATATAAACAATAC 60.083 45.833 0.00 0.00 34.36 1.89
630 633 3.681835 GTGCGGTGGACGGAGACT 61.682 66.667 0.00 0.00 45.97 3.24
641 644 1.151777 CGCCTTTATCGATGTGCGGT 61.152 55.000 18.65 0.00 41.33 5.68
692 695 2.084610 CAGACGAATCTGCAGTTCCA 57.915 50.000 14.67 0.00 45.83 3.53
752 756 1.885157 CCGCGTAGGTTAGTGTCCA 59.115 57.895 4.92 0.00 34.51 4.02
755 759 2.575461 GGCCGCGTAGGTTAGTGT 59.425 61.111 4.92 0.00 43.70 3.55
756 760 2.202837 GGGCCGCGTAGGTTAGTG 60.203 66.667 4.92 0.00 43.70 2.74
871 875 2.687566 GGGGGAGGAGGCGAGAAA 60.688 66.667 0.00 0.00 0.00 2.52
1071 1075 2.358003 GGCACTGAAGCAGAGCGT 60.358 61.111 9.98 0.00 46.15 5.07
1114 1118 7.864108 TCTAGTACCAAACATGGAAATGATG 57.136 36.000 1.10 0.00 0.00 3.07
1124 1128 6.206042 AGGAGAAGGATCTAGTACCAAACAT 58.794 40.000 9.72 0.00 35.54 2.71
1132 1136 3.223435 CGGCAAGGAGAAGGATCTAGTA 58.777 50.000 0.00 0.00 35.54 1.82
1133 1137 2.035632 CGGCAAGGAGAAGGATCTAGT 58.964 52.381 0.00 0.00 35.54 2.57
1134 1138 1.342819 CCGGCAAGGAGAAGGATCTAG 59.657 57.143 0.00 0.00 45.00 2.43
1507 1511 3.727258 CGGCCATGGGGTCCTTGA 61.727 66.667 15.13 0.00 34.31 3.02
1508 1512 3.727258 TCGGCCATGGGGTCCTTG 61.727 66.667 15.13 0.00 34.31 3.61
1612 1616 3.691342 CCTCCGTGGCGACCTTGA 61.691 66.667 0.00 0.00 0.00 3.02
1727 1731 0.248661 CAGCGAGATACACAGACCGG 60.249 60.000 0.00 0.00 0.00 5.28
1841 1845 5.974158 CACACTCATCTCGATTAGGTTACAG 59.026 44.000 0.00 0.00 0.00 2.74
1905 1909 0.178767 TCACAGCAGCACAGTCAACT 59.821 50.000 0.00 0.00 0.00 3.16
1906 1910 0.585357 CTCACAGCAGCACAGTCAAC 59.415 55.000 0.00 0.00 0.00 3.18
1907 1911 0.178767 ACTCACAGCAGCACAGTCAA 59.821 50.000 0.00 0.00 0.00 3.18
1946 1950 2.421952 GGAAGCAACAGAGATGGCCATA 60.422 50.000 20.84 0.00 0.00 2.74
1949 1953 1.372087 CGGAAGCAACAGAGATGGCC 61.372 60.000 0.00 0.00 0.00 5.36
2018 2022 1.372087 CGATCAAGAACAGGCCAGGC 61.372 60.000 5.01 1.26 0.00 4.85
2020 2024 1.081892 CACGATCAAGAACAGGCCAG 58.918 55.000 5.01 0.00 0.00 4.85
2221 2225 5.843421 AGGAGTCTAGGATGCATCTGTAAAT 59.157 40.000 25.28 9.14 0.00 1.40
2222 2226 5.211973 AGGAGTCTAGGATGCATCTGTAAA 58.788 41.667 25.28 2.84 0.00 2.01
2223 2227 4.809193 AGGAGTCTAGGATGCATCTGTAA 58.191 43.478 25.28 7.38 0.00 2.41
2301 2305 9.013229 CCACCATGCTATGTAAATATGTTATGT 57.987 33.333 0.00 0.00 0.00 2.29
2302 2306 7.970061 GCCACCATGCTATGTAAATATGTTATG 59.030 37.037 0.00 0.00 0.00 1.90
2303 2307 7.890127 AGCCACCATGCTATGTAAATATGTTAT 59.110 33.333 0.00 0.00 40.56 1.89
2304 2308 7.230747 AGCCACCATGCTATGTAAATATGTTA 58.769 34.615 0.00 0.00 40.56 2.41
2305 2309 6.070656 AGCCACCATGCTATGTAAATATGTT 58.929 36.000 0.00 0.00 40.56 2.71
2306 2310 5.634118 AGCCACCATGCTATGTAAATATGT 58.366 37.500 0.00 0.00 40.56 2.29
2307 2311 6.881065 ACTAGCCACCATGCTATGTAAATATG 59.119 38.462 0.00 0.00 42.63 1.78
2308 2312 7.020827 ACTAGCCACCATGCTATGTAAATAT 57.979 36.000 0.00 0.00 42.63 1.28
2309 2313 6.270000 AGACTAGCCACCATGCTATGTAAATA 59.730 38.462 0.00 0.00 42.63 1.40
2310 2314 5.072329 AGACTAGCCACCATGCTATGTAAAT 59.928 40.000 0.00 0.00 42.63 1.40
2311 2315 4.408921 AGACTAGCCACCATGCTATGTAAA 59.591 41.667 0.00 0.00 42.63 2.01
2312 2316 3.967326 AGACTAGCCACCATGCTATGTAA 59.033 43.478 0.00 0.00 42.63 2.41
2404 2410 8.179509 AGGCGAGTGTTTATACAATAGACTAT 57.820 34.615 0.74 0.00 40.76 2.12
2426 2432 5.130292 TGAAGCACGTATACCTAATAGGC 57.870 43.478 6.17 0.00 39.63 3.93
2428 2434 8.589335 AAACATGAAGCACGTATACCTAATAG 57.411 34.615 0.00 0.00 0.00 1.73
2429 2435 9.687210 CTAAACATGAAGCACGTATACCTAATA 57.313 33.333 0.00 0.00 0.00 0.98
2430 2436 7.170998 GCTAAACATGAAGCACGTATACCTAAT 59.829 37.037 0.00 0.00 38.63 1.73
2431 2437 6.477688 GCTAAACATGAAGCACGTATACCTAA 59.522 38.462 0.00 0.00 38.63 2.69
2433 2439 4.809426 GCTAAACATGAAGCACGTATACCT 59.191 41.667 0.00 0.00 38.63 3.08
2434 2440 4.569162 TGCTAAACATGAAGCACGTATACC 59.431 41.667 15.00 0.00 43.56 2.73
2451 2457 9.787532 GTTAATTCTGATTGCTACAATGCTAAA 57.212 29.630 0.00 0.00 0.00 1.85
2468 2474 7.678218 GCAGAAGTAGATTGGCAGTTAATTCTG 60.678 40.741 24.60 24.60 44.56 3.02
2469 2475 6.317391 GCAGAAGTAGATTGGCAGTTAATTCT 59.683 38.462 10.06 10.06 32.56 2.40
2480 2486 9.814899 CTATTCCTATATGCAGAAGTAGATTGG 57.185 37.037 0.00 0.00 0.00 3.16
2506 2512 1.459592 AGCGACAACTGTTATGAACGC 59.540 47.619 15.35 15.35 42.26 4.84
2518 2524 5.545658 TCAGATAATTCCAAAGCGACAAC 57.454 39.130 0.00 0.00 0.00 3.32
2570 2576 3.861276 TGTACTACGGAACATGGTGAG 57.139 47.619 0.00 0.00 0.00 3.51
2581 2587 5.723672 ATCCCAAGTATGATGTACTACGG 57.276 43.478 0.00 0.00 0.00 4.02
2586 2592 5.008019 CAGTGCAATCCCAAGTATGATGTAC 59.992 44.000 0.00 0.00 0.00 2.90
2590 2596 4.508551 TCAGTGCAATCCCAAGTATGAT 57.491 40.909 0.00 0.00 0.00 2.45
2618 2624 6.012658 CAAACTTGCAACCAGATTAGCTTA 57.987 37.500 0.00 0.00 0.00 3.09
2663 2669 3.254166 ACTGCAACATTTCACCATCAGAC 59.746 43.478 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.