Multiple sequence alignment - TraesCS6D01G236700

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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 TraesCS6D01G236700 chr6D 100.000 4109 0 0 1 4109 334229811 334225703 0.000000e+00 7589.0
1 TraesCS6D01G236700 chr6D 90.062 161 16 0 2178 2338 358326162 358326002 4.160000e-50 209.0
2 TraesCS6D01G236700 chr6D 82.857 210 30 6 2148 2354 378379475 378379269 2.520000e-42 183.0
3 TraesCS6D01G236700 chr6B 94.286 3815 133 33 293 4083 486222845 486226598 0.000000e+00 5758.0
4 TraesCS6D01G236700 chr6B 85.024 207 30 1 4 209 486167126 486167332 4.160000e-50 209.0
5 TraesCS6D01G236700 chr6B 85.859 198 26 2 2143 2338 539727743 539727546 4.160000e-50 209.0
6 TraesCS6D01G236700 chr6A 94.090 3841 104 44 283 4086 473577403 473573649 0.000000e+00 5722.0
7 TraesCS6D01G236700 chr6A 86.364 198 25 2 2143 2338 500083818 500083621 8.950000e-52 215.0
8 TraesCS6D01G236700 chr5D 89.918 486 23 10 688 1160 344617647 344618119 1.630000e-168 603.0
9 TraesCS6D01G236700 chr5D 85.993 307 19 10 861 1160 344616580 344616869 1.430000e-79 307.0
10 TraesCS6D01G236700 chr2D 79.160 595 92 23 2149 2728 512686870 512687447 2.320000e-102 383.0
11 TraesCS6D01G236700 chr2D 100.000 28 0 0 4036 4063 512688723 512688750 7.000000e-03 52.8
12 TraesCS6D01G236700 chr2A 79.027 596 91 25 2149 2728 656240947 656241524 1.080000e-100 377.0
13 TraesCS6D01G236700 chr2A 79.121 91 9 6 3982 4063 656242730 656242819 2.000000e-03 54.7
14 TraesCS6D01G236700 chr2B 78.319 595 91 26 2149 2728 602763481 602764052 2.350000e-92 350.0
15 TraesCS6D01G236700 chr2B 79.412 102 11 6 3982 4074 602765264 602765364 3.430000e-06 63.9
16 TraesCS6D01G236700 chr5A 86.207 58 5 3 283 340 680274876 680274930 4.440000e-05 60.2
17 TraesCS6D01G236700 chr7A 100.000 28 0 0 313 340 485196835 485196808 7.000000e-03 52.8


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 TraesCS6D01G236700 chr6D 334225703 334229811 4108 True 7589.00 7589 100.0000 1 4109 1 chr6D.!!$R1 4108
1 TraesCS6D01G236700 chr6B 486222845 486226598 3753 False 5758.00 5758 94.2860 293 4083 1 chr6B.!!$F2 3790
2 TraesCS6D01G236700 chr6A 473573649 473577403 3754 True 5722.00 5722 94.0900 283 4086 1 chr6A.!!$R1 3803
3 TraesCS6D01G236700 chr5D 344616580 344618119 1539 False 455.00 603 87.9555 688 1160 2 chr5D.!!$F1 472
4 TraesCS6D01G236700 chr2D 512686870 512688750 1880 False 217.90 383 89.5800 2149 4063 2 chr2D.!!$F1 1914
5 TraesCS6D01G236700 chr2A 656240947 656242819 1872 False 215.85 377 79.0740 2149 4063 2 chr2A.!!$F1 1914
6 TraesCS6D01G236700 chr2B 602763481 602765364 1883 False 206.95 350 78.8655 2149 4074 2 chr2B.!!$F1 1925

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
136 137 0.108207 GGATGTGGCTGATGAGGAGG 59.892 60.0 0.0 0.0 0.00 4.30 F
366 367 0.537188 CAAGCCGGTCAGTCCAGTAT 59.463 55.0 1.9 0.0 35.57 2.12 F
1965 2390 0.543410 TTCGTCAACAGGGGCTAGGA 60.543 55.0 0.0 0.0 0.00 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 2448 0.106868 GGGTTCGGGTTCCCATTAGG 60.107 60.0 8.70 0.00 42.95 2.69 R
2787 3254 0.535780 TGTTCTGAACCTGCTGCTGG 60.536 55.0 22.17 22.17 0.00 4.85 R
3768 4528 0.526524 GCACGCCTGCTACTCAGTAG 60.527 60.0 7.56 7.56 41.25 2.57 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
23 24 4.442375 GGAAGATACCGATCATGACGAT 57.558 45.455 16.06 4.88 36.91 3.73
24 25 4.169508 GGAAGATACCGATCATGACGATG 58.830 47.826 16.06 6.05 33.17 3.84
25 26 3.857549 AGATACCGATCATGACGATGG 57.142 47.619 16.06 10.06 33.17 3.51
27 28 3.441922 AGATACCGATCATGACGATGGAG 59.558 47.826 16.06 4.95 33.17 3.86
30 31 1.416373 CGATCATGACGATGGAGCAG 58.584 55.000 0.00 0.00 33.17 4.24
31 32 1.269465 CGATCATGACGATGGAGCAGT 60.269 52.381 0.00 0.00 33.17 4.40
33 34 2.014335 TCATGACGATGGAGCAGTTG 57.986 50.000 0.00 0.00 0.00 3.16
35 36 0.904649 ATGACGATGGAGCAGTTGGA 59.095 50.000 0.00 0.00 0.00 3.53
37 38 1.134699 TGACGATGGAGCAGTTGGATC 60.135 52.381 0.00 0.00 0.00 3.36
42 43 2.514824 GAGCAGTTGGATCCCGCC 60.515 66.667 9.90 0.00 0.00 6.13
43 44 4.473520 AGCAGTTGGATCCCGCCG 62.474 66.667 9.90 0.00 0.00 6.46
45 46 4.776322 CAGTTGGATCCCGCCGCA 62.776 66.667 9.90 0.00 0.00 5.69
46 47 4.473520 AGTTGGATCCCGCCGCAG 62.474 66.667 9.90 0.00 0.00 5.18
47 48 4.778143 GTTGGATCCCGCCGCAGT 62.778 66.667 9.90 0.00 0.00 4.40
48 49 4.776322 TTGGATCCCGCCGCAGTG 62.776 66.667 9.90 0.00 0.00 3.66
50 51 4.241555 GGATCCCGCCGCAGTGAT 62.242 66.667 0.00 0.00 0.00 3.06
52 53 3.445518 GATCCCGCCGCAGTGATGA 62.446 63.158 0.00 0.00 0.00 2.92
53 54 2.721971 GATCCCGCCGCAGTGATGAT 62.722 60.000 0.00 0.00 0.00 2.45
55 56 2.202919 CCGCCGCAGTGATGATCA 60.203 61.111 0.00 0.00 0.00 2.92
56 57 1.596203 CCGCCGCAGTGATGATCAT 60.596 57.895 8.25 8.25 0.00 2.45
57 58 0.319813 CCGCCGCAGTGATGATCATA 60.320 55.000 8.54 0.00 0.00 2.15
58 59 0.786581 CGCCGCAGTGATGATCATAC 59.213 55.000 8.54 7.58 0.00 2.39
59 60 0.786581 GCCGCAGTGATGATCATACG 59.213 55.000 8.54 7.73 0.00 3.06
61 62 1.490621 CGCAGTGATGATCATACGCA 58.509 50.000 8.54 0.00 0.00 5.24
62 63 2.064014 CGCAGTGATGATCATACGCAT 58.936 47.619 8.54 0.00 0.00 4.73
63 64 2.091744 CGCAGTGATGATCATACGCATC 59.908 50.000 8.54 0.00 40.92 3.91
64 65 3.062042 GCAGTGATGATCATACGCATCA 58.938 45.455 8.54 0.00 46.13 3.07
73 74 5.841810 TGATCATACGCATCATCTGTGTTA 58.158 37.500 0.00 0.00 46.34 2.41
74 75 5.922544 TGATCATACGCATCATCTGTGTTAG 59.077 40.000 0.00 0.00 46.34 2.34
75 76 4.620982 TCATACGCATCATCTGTGTTAGG 58.379 43.478 0.00 0.00 46.34 2.69
76 77 4.340950 TCATACGCATCATCTGTGTTAGGA 59.659 41.667 0.00 0.00 46.34 2.94
77 78 3.827008 ACGCATCATCTGTGTTAGGAT 57.173 42.857 0.00 0.00 46.34 3.24
78 79 3.461061 ACGCATCATCTGTGTTAGGATG 58.539 45.455 0.00 0.00 46.34 3.51
79 80 3.118629 ACGCATCATCTGTGTTAGGATGT 60.119 43.478 0.00 0.00 46.34 3.06
80 81 3.873361 CGCATCATCTGTGTTAGGATGTT 59.127 43.478 0.00 0.00 39.93 2.71
81 82 4.025396 CGCATCATCTGTGTTAGGATGTTC 60.025 45.833 0.00 0.00 39.93 3.18
82 83 4.877823 GCATCATCTGTGTTAGGATGTTCA 59.122 41.667 0.00 0.00 39.93 3.18
83 84 5.355071 GCATCATCTGTGTTAGGATGTTCAA 59.645 40.000 0.00 0.00 39.93 2.69
84 85 6.457934 GCATCATCTGTGTTAGGATGTTCAAG 60.458 42.308 0.00 0.00 39.93 3.02
87 88 2.749621 CTGTGTTAGGATGTTCAAGGGC 59.250 50.000 0.00 0.00 0.00 5.19
91 92 2.755103 GTTAGGATGTTCAAGGGCTTGG 59.245 50.000 0.00 0.00 40.78 3.61
92 93 0.613012 AGGATGTTCAAGGGCTTGGC 60.613 55.000 0.00 0.00 40.78 4.52
93 94 0.899717 GGATGTTCAAGGGCTTGGCA 60.900 55.000 0.00 0.00 40.78 4.92
94 95 0.529378 GATGTTCAAGGGCTTGGCAG 59.471 55.000 0.00 0.00 40.78 4.85
95 96 1.538687 ATGTTCAAGGGCTTGGCAGC 61.539 55.000 0.00 1.00 46.52 5.25
102 103 3.510846 GGCTTGGCAGCTCAGATG 58.489 61.111 8.45 0.00 46.44 2.90
104 105 0.679002 GGCTTGGCAGCTCAGATGAA 60.679 55.000 0.00 0.00 46.44 2.57
105 106 0.733729 GCTTGGCAGCTCAGATGAAG 59.266 55.000 0.00 0.00 43.51 3.02
107 108 2.008329 CTTGGCAGCTCAGATGAAGAC 58.992 52.381 0.00 0.00 0.00 3.01
108 109 0.978907 TGGCAGCTCAGATGAAGACA 59.021 50.000 0.00 0.00 0.00 3.41
109 110 1.348696 TGGCAGCTCAGATGAAGACAA 59.651 47.619 0.00 0.00 0.00 3.18
110 111 1.736681 GGCAGCTCAGATGAAGACAAC 59.263 52.381 0.00 0.00 0.00 3.32
111 112 1.736681 GCAGCTCAGATGAAGACAACC 59.263 52.381 0.00 0.00 0.00 3.77
114 115 2.094286 AGCTCAGATGAAGACAACCGAG 60.094 50.000 0.00 0.00 0.00 4.63
115 116 2.094494 GCTCAGATGAAGACAACCGAGA 60.094 50.000 0.00 0.00 0.00 4.04
116 117 3.615110 GCTCAGATGAAGACAACCGAGAA 60.615 47.826 0.00 0.00 0.00 2.87
117 118 4.172505 CTCAGATGAAGACAACCGAGAAG 58.827 47.826 0.00 0.00 0.00 2.85
119 120 3.056536 CAGATGAAGACAACCGAGAAGGA 60.057 47.826 0.00 0.00 45.00 3.36
120 121 3.772025 AGATGAAGACAACCGAGAAGGAT 59.228 43.478 0.00 0.00 45.00 3.24
121 122 3.319137 TGAAGACAACCGAGAAGGATG 57.681 47.619 0.00 0.00 46.99 3.51
125 126 2.471255 CAACCGAGAAGGATGTGGC 58.529 57.895 0.00 0.00 45.00 5.01
128 129 0.904865 ACCGAGAAGGATGTGGCTGA 60.905 55.000 0.00 0.00 45.00 4.26
129 130 0.467384 CCGAGAAGGATGTGGCTGAT 59.533 55.000 0.00 0.00 45.00 2.90
130 131 1.579698 CGAGAAGGATGTGGCTGATG 58.420 55.000 0.00 0.00 0.00 3.07
131 132 1.137675 CGAGAAGGATGTGGCTGATGA 59.862 52.381 0.00 0.00 0.00 2.92
132 133 2.802415 CGAGAAGGATGTGGCTGATGAG 60.802 54.545 0.00 0.00 0.00 2.90
134 135 1.487976 GAAGGATGTGGCTGATGAGGA 59.512 52.381 0.00 0.00 0.00 3.71
135 136 1.129917 AGGATGTGGCTGATGAGGAG 58.870 55.000 0.00 0.00 0.00 3.69
136 137 0.108207 GGATGTGGCTGATGAGGAGG 59.892 60.000 0.00 0.00 0.00 4.30
137 138 0.108207 GATGTGGCTGATGAGGAGGG 59.892 60.000 0.00 0.00 0.00 4.30
138 139 1.351080 ATGTGGCTGATGAGGAGGGG 61.351 60.000 0.00 0.00 0.00 4.79
139 140 3.092511 TGGCTGATGAGGAGGGGC 61.093 66.667 0.00 0.00 0.00 5.80
143 144 1.692042 CTGATGAGGAGGGGCTGGT 60.692 63.158 0.00 0.00 0.00 4.00
144 145 1.980784 CTGATGAGGAGGGGCTGGTG 61.981 65.000 0.00 0.00 0.00 4.17
145 146 1.690633 GATGAGGAGGGGCTGGTGA 60.691 63.158 0.00 0.00 0.00 4.02
158 159 2.262915 GGTGACAGGGTGAGCGAG 59.737 66.667 0.00 0.00 0.00 5.03
159 160 2.262915 GTGACAGGGTGAGCGAGG 59.737 66.667 0.00 0.00 0.00 4.63
160 161 2.117423 TGACAGGGTGAGCGAGGA 59.883 61.111 0.00 0.00 0.00 3.71
161 162 1.979155 TGACAGGGTGAGCGAGGAG 60.979 63.158 0.00 0.00 0.00 3.69
162 163 2.681778 ACAGGGTGAGCGAGGAGG 60.682 66.667 0.00 0.00 0.00 4.30
163 164 2.681778 CAGGGTGAGCGAGGAGGT 60.682 66.667 0.00 0.00 0.00 3.85
165 166 1.985116 AGGGTGAGCGAGGAGGTTC 60.985 63.158 0.00 0.00 0.00 3.62
166 167 2.182030 GGTGAGCGAGGAGGTTCG 59.818 66.667 0.00 0.00 43.23 3.95
167 168 2.182030 GTGAGCGAGGAGGTTCGG 59.818 66.667 0.00 0.00 40.79 4.30
168 169 2.035155 TGAGCGAGGAGGTTCGGA 59.965 61.111 0.00 0.00 40.79 4.55
169 170 2.341101 TGAGCGAGGAGGTTCGGAC 61.341 63.158 0.00 0.00 40.79 4.79
170 171 2.282958 AGCGAGGAGGTTCGGACA 60.283 61.111 0.00 0.00 40.79 4.02
172 173 1.737008 GCGAGGAGGTTCGGACAAC 60.737 63.158 0.00 0.00 40.79 3.32
173 174 1.965219 CGAGGAGGTTCGGACAACT 59.035 57.895 0.00 0.00 36.95 3.16
175 176 1.542915 CGAGGAGGTTCGGACAACTAA 59.457 52.381 0.00 0.00 36.95 2.24
176 177 2.165845 CGAGGAGGTTCGGACAACTAAT 59.834 50.000 0.00 0.00 36.95 1.73
177 178 3.734293 CGAGGAGGTTCGGACAACTAATC 60.734 52.174 0.00 0.00 36.95 1.75
178 179 3.442076 AGGAGGTTCGGACAACTAATCT 58.558 45.455 0.00 0.00 0.00 2.40
179 180 3.195825 AGGAGGTTCGGACAACTAATCTG 59.804 47.826 0.00 0.00 0.00 2.90
180 181 3.522553 GAGGTTCGGACAACTAATCTGG 58.477 50.000 0.00 0.00 0.00 3.86
181 182 2.236395 AGGTTCGGACAACTAATCTGGG 59.764 50.000 0.00 0.00 0.00 4.45
183 184 3.522553 GTTCGGACAACTAATCTGGGAG 58.477 50.000 0.00 0.00 0.00 4.30
184 185 2.108168 TCGGACAACTAATCTGGGAGG 58.892 52.381 0.00 0.00 0.00 4.30
185 186 1.139058 CGGACAACTAATCTGGGAGGG 59.861 57.143 0.00 0.00 0.00 4.30
187 188 1.559682 GACAACTAATCTGGGAGGGCA 59.440 52.381 0.00 0.00 0.00 5.36
189 190 2.378547 ACAACTAATCTGGGAGGGCAAA 59.621 45.455 0.00 0.00 0.00 3.68
190 191 3.181423 ACAACTAATCTGGGAGGGCAAAA 60.181 43.478 0.00 0.00 0.00 2.44
191 192 3.825908 ACTAATCTGGGAGGGCAAAAA 57.174 42.857 0.00 0.00 0.00 1.94
193 194 4.687976 ACTAATCTGGGAGGGCAAAAATT 58.312 39.130 0.00 0.00 0.00 1.82
196 197 2.528564 TCTGGGAGGGCAAAAATTCTG 58.471 47.619 0.00 0.00 0.00 3.02
197 198 2.158325 TCTGGGAGGGCAAAAATTCTGT 60.158 45.455 0.00 0.00 0.00 3.41
198 199 2.634453 CTGGGAGGGCAAAAATTCTGTT 59.366 45.455 0.00 0.00 0.00 3.16
199 200 3.044894 TGGGAGGGCAAAAATTCTGTTT 58.955 40.909 0.00 0.00 0.00 2.83
200 201 3.457749 TGGGAGGGCAAAAATTCTGTTTT 59.542 39.130 0.00 0.00 0.00 2.43
201 202 4.065088 GGGAGGGCAAAAATTCTGTTTTC 58.935 43.478 0.00 0.00 0.00 2.29
203 204 5.368145 GGAGGGCAAAAATTCTGTTTTCTT 58.632 37.500 0.00 0.00 0.00 2.52
204 205 6.463755 GGGAGGGCAAAAATTCTGTTTTCTTA 60.464 38.462 0.00 0.00 0.00 2.10
205 206 6.423905 GGAGGGCAAAAATTCTGTTTTCTTAC 59.576 38.462 0.00 0.00 0.00 2.34
206 207 6.288294 AGGGCAAAAATTCTGTTTTCTTACC 58.712 36.000 0.00 0.00 0.00 2.85
207 208 6.099701 AGGGCAAAAATTCTGTTTTCTTACCT 59.900 34.615 0.00 0.00 0.00 3.08
208 209 6.202762 GGGCAAAAATTCTGTTTTCTTACCTG 59.797 38.462 0.00 0.00 0.00 4.00
210 211 7.494298 GGCAAAAATTCTGTTTTCTTACCTGAA 59.506 33.333 0.00 0.00 0.00 3.02
211 212 8.328146 GCAAAAATTCTGTTTTCTTACCTGAAC 58.672 33.333 0.00 0.00 0.00 3.18
213 214 9.586435 AAAAATTCTGTTTTCTTACCTGAACTG 57.414 29.630 0.00 0.00 0.00 3.16
214 215 5.751243 TTCTGTTTTCTTACCTGAACTGC 57.249 39.130 0.00 0.00 0.00 4.40
215 216 4.134563 TCTGTTTTCTTACCTGAACTGCC 58.865 43.478 0.00 0.00 0.00 4.85
218 219 1.344065 TTCTTACCTGAACTGCCGGA 58.656 50.000 5.05 0.00 0.00 5.14
219 220 1.568504 TCTTACCTGAACTGCCGGAT 58.431 50.000 5.05 0.00 0.00 4.18
220 221 1.906574 TCTTACCTGAACTGCCGGATT 59.093 47.619 5.05 0.00 0.00 3.01
221 222 2.009774 CTTACCTGAACTGCCGGATTG 58.990 52.381 5.05 0.00 0.00 2.67
223 224 0.981183 ACCTGAACTGCCGGATTGTA 59.019 50.000 5.05 0.00 0.00 2.41
224 225 1.349688 ACCTGAACTGCCGGATTGTAA 59.650 47.619 5.05 0.00 0.00 2.41
225 226 1.737793 CCTGAACTGCCGGATTGTAAC 59.262 52.381 5.05 0.00 0.00 2.50
228 229 3.417101 TGAACTGCCGGATTGTAACATT 58.583 40.909 5.05 0.00 0.00 2.71
229 230 3.823873 TGAACTGCCGGATTGTAACATTT 59.176 39.130 5.05 0.00 0.00 2.32
233 234 5.189928 ACTGCCGGATTGTAACATTTATGA 58.810 37.500 5.05 0.00 0.00 2.15
234 235 5.827797 ACTGCCGGATTGTAACATTTATGAT 59.172 36.000 5.05 0.00 0.00 2.45
235 236 6.017109 ACTGCCGGATTGTAACATTTATGATC 60.017 38.462 5.05 0.00 0.00 2.92
236 237 5.825151 TGCCGGATTGTAACATTTATGATCA 59.175 36.000 5.05 0.00 0.00 2.92
237 238 6.017192 TGCCGGATTGTAACATTTATGATCAG 60.017 38.462 5.05 0.00 0.00 2.90
238 239 6.568462 GCCGGATTGTAACATTTATGATCAGG 60.568 42.308 5.05 0.00 32.76 3.86
240 241 6.373779 GGATTGTAACATTTATGATCAGGCG 58.626 40.000 0.09 0.00 0.00 5.52
241 242 6.017109 GGATTGTAACATTTATGATCAGGCGT 60.017 38.462 0.09 0.00 0.00 5.68
244 245 5.877564 TGTAACATTTATGATCAGGCGTTCA 59.122 36.000 0.09 0.00 0.00 3.18
245 246 6.542005 TGTAACATTTATGATCAGGCGTTCAT 59.458 34.615 0.09 0.00 35.99 2.57
246 247 7.713073 TGTAACATTTATGATCAGGCGTTCATA 59.287 33.333 0.09 0.00 34.23 2.15
249 250 7.995289 ACATTTATGATCAGGCGTTCATAAAA 58.005 30.769 21.21 11.18 46.61 1.52
250 251 7.915397 ACATTTATGATCAGGCGTTCATAAAAC 59.085 33.333 21.21 0.00 46.61 2.43
251 252 7.624360 TTTATGATCAGGCGTTCATAAAACT 57.376 32.000 17.62 0.00 43.86 2.66
252 253 8.725405 TTTATGATCAGGCGTTCATAAAACTA 57.275 30.769 17.62 2.96 43.86 2.24
255 256 6.345298 TGATCAGGCGTTCATAAAACTATGA 58.655 36.000 0.00 0.00 34.91 2.15
256 257 6.821160 TGATCAGGCGTTCATAAAACTATGAA 59.179 34.615 3.93 3.93 42.29 2.57
267 268 7.653647 TCATAAAACTATGAACCGCTTTGTTT 58.346 30.769 0.00 0.00 33.89 2.83
270 271 4.237349 ACTATGAACCGCTTTGTTTTGG 57.763 40.909 0.00 0.00 0.00 3.28
272 273 3.535280 ATGAACCGCTTTGTTTTGGTT 57.465 38.095 0.00 0.00 46.90 3.67
276 277 3.320673 ACCGCTTTGTTTTGGTTTTGA 57.679 38.095 0.00 0.00 0.00 2.69
277 278 3.867857 ACCGCTTTGTTTTGGTTTTGAT 58.132 36.364 0.00 0.00 0.00 2.57
278 279 3.868661 ACCGCTTTGTTTTGGTTTTGATC 59.131 39.130 0.00 0.00 0.00 2.92
279 280 3.060607 CCGCTTTGTTTTGGTTTTGATCG 60.061 43.478 0.00 0.00 0.00 3.69
280 281 3.060607 CGCTTTGTTTTGGTTTTGATCGG 60.061 43.478 0.00 0.00 0.00 4.18
281 282 4.116238 GCTTTGTTTTGGTTTTGATCGGA 58.884 39.130 0.00 0.00 0.00 4.55
283 284 5.923684 GCTTTGTTTTGGTTTTGATCGGATA 59.076 36.000 0.00 0.00 0.00 2.59
284 285 6.128929 GCTTTGTTTTGGTTTTGATCGGATAC 60.129 38.462 0.00 0.00 0.00 2.24
299 300 3.724295 GGATACGAACAACTGCACTTC 57.276 47.619 0.00 0.00 0.00 3.01
300 301 3.064207 GGATACGAACAACTGCACTTCA 58.936 45.455 0.00 0.00 0.00 3.02
366 367 0.537188 CAAGCCGGTCAGTCCAGTAT 59.463 55.000 1.90 0.00 35.57 2.12
371 372 2.933573 CCGGTCAGTCCAGTATCTACT 58.066 52.381 0.00 0.00 36.90 2.57
386 387 1.203063 TCTACTCTGCTCACACCCACT 60.203 52.381 0.00 0.00 0.00 4.00
387 388 0.969149 TACTCTGCTCACACCCACTG 59.031 55.000 0.00 0.00 0.00 3.66
388 389 1.004080 CTCTGCTCACACCCACTGG 60.004 63.158 0.00 0.00 37.80 4.00
389 390 2.670934 CTGCTCACACCCACTGGC 60.671 66.667 0.00 0.00 33.59 4.85
390 391 4.269523 TGCTCACACCCACTGGCC 62.270 66.667 0.00 0.00 33.59 5.36
391 392 4.269523 GCTCACACCCACTGGCCA 62.270 66.667 4.71 4.71 33.59 5.36
392 393 2.281761 CTCACACCCACTGGCCAC 60.282 66.667 0.00 0.00 33.59 5.01
473 474 2.043953 GTGGCCCCAAGGACCATC 60.044 66.667 0.00 0.00 42.80 3.51
488 489 1.227060 CATCACGCCGATCAGAGCA 60.227 57.895 0.00 0.00 29.21 4.26
640 643 1.860078 GCGACCAACGAAGGACAAG 59.140 57.895 4.96 0.00 45.77 3.16
677 683 4.441087 GTCGTTCATTCAGAAGGCAAAAAC 59.559 41.667 0.00 0.00 40.89 2.43
688 694 2.242043 AGGCAAAAACACATGCTAGCT 58.758 42.857 17.23 0.00 42.20 3.32
689 695 3.420893 AGGCAAAAACACATGCTAGCTA 58.579 40.909 17.23 2.58 42.20 3.32
690 696 3.191371 AGGCAAAAACACATGCTAGCTAC 59.809 43.478 17.23 0.00 42.20 3.58
691 697 3.501950 GCAAAAACACATGCTAGCTACC 58.498 45.455 17.23 0.00 39.46 3.18
1036 1431 1.340017 GGCACCAGGTAAGCTGATTGA 60.340 52.381 0.00 0.00 0.00 2.57
1053 1448 5.427378 TGATTGATGTTCATACGTGACCAT 58.573 37.500 0.00 0.00 39.81 3.55
1160 1560 3.244526 TGTTCTTGTGGATCTTGCTGCTA 60.245 43.478 0.00 0.00 0.00 3.49
1208 1609 1.112113 TCTACCGTGCCCTTGATCTC 58.888 55.000 0.00 0.00 0.00 2.75
1442 1850 2.325583 TAATCCTCGAAAGGCGCATT 57.674 45.000 10.83 5.20 43.02 3.56
1473 1893 1.860326 CACCGCTTTTCTTTGCCTTTG 59.140 47.619 0.00 0.00 0.00 2.77
1474 1894 1.480545 ACCGCTTTTCTTTGCCTTTGT 59.519 42.857 0.00 0.00 0.00 2.83
1475 1895 2.093711 ACCGCTTTTCTTTGCCTTTGTT 60.094 40.909 0.00 0.00 0.00 2.83
1476 1896 2.539688 CCGCTTTTCTTTGCCTTTGTTC 59.460 45.455 0.00 0.00 0.00 3.18
1477 1897 2.539688 CGCTTTTCTTTGCCTTTGTTCC 59.460 45.455 0.00 0.00 0.00 3.62
1478 1898 3.737972 CGCTTTTCTTTGCCTTTGTTCCT 60.738 43.478 0.00 0.00 0.00 3.36
1479 1899 3.557185 GCTTTTCTTTGCCTTTGTTCCTG 59.443 43.478 0.00 0.00 0.00 3.86
1480 1900 2.888834 TTCTTTGCCTTTGTTCCTGC 57.111 45.000 0.00 0.00 0.00 4.85
1481 1901 1.039856 TCTTTGCCTTTGTTCCTGCC 58.960 50.000 0.00 0.00 0.00 4.85
1482 1902 1.043022 CTTTGCCTTTGTTCCTGCCT 58.957 50.000 0.00 0.00 0.00 4.75
1483 1903 1.413812 CTTTGCCTTTGTTCCTGCCTT 59.586 47.619 0.00 0.00 0.00 4.35
1484 1904 1.494960 TTGCCTTTGTTCCTGCCTTT 58.505 45.000 0.00 0.00 0.00 3.11
1703 2126 5.715070 TCTCTCATCTTTTCGTCTCCTTTC 58.285 41.667 0.00 0.00 0.00 2.62
1889 2314 9.747293 CTTGGCTTATTACTAGTAGTTCTTACC 57.253 37.037 8.40 4.79 32.37 2.85
1965 2390 0.543410 TTCGTCAACAGGGGCTAGGA 60.543 55.000 0.00 0.00 0.00 2.94
2023 2448 7.066781 TGGAAACCCAAATCCTAATCCTAATC 58.933 38.462 0.00 0.00 36.64 1.75
2787 3254 1.589727 GCAGCAACACCAGCAACAC 60.590 57.895 0.00 0.00 0.00 3.32
2820 3287 3.842869 GAACATGCTCGGGTTCTCT 57.157 52.632 0.00 0.00 40.12 3.10
2821 3288 2.100605 GAACATGCTCGGGTTCTCTT 57.899 50.000 0.00 0.00 40.12 2.85
2932 3414 1.601419 CGAGGACTTGAAGCCGGGTA 61.601 60.000 6.57 0.00 0.00 3.69
2938 3420 1.349259 CTTGAAGCCGGGTACGAACG 61.349 60.000 6.57 0.00 44.60 3.95
3298 3849 4.779993 ACTGTTCTTGGTCTTCCTTCTT 57.220 40.909 0.00 0.00 34.23 2.52
3299 3850 5.888982 ACTGTTCTTGGTCTTCCTTCTTA 57.111 39.130 0.00 0.00 34.23 2.10
3448 4017 6.855836 TCCTTGTGTGAATTTCATATGAAGC 58.144 36.000 17.28 11.80 35.21 3.86
3640 4383 2.883386 GGAAGATTGGCATCATCACTCC 59.117 50.000 2.27 3.95 29.97 3.85
3682 4425 2.159653 GCATTGCTCTACAGTCGGTTTG 60.160 50.000 0.16 0.00 0.00 2.93
3683 4426 3.325870 CATTGCTCTACAGTCGGTTTGA 58.674 45.455 0.00 0.00 0.00 2.69
3754 4514 1.089920 GATCGGTTTGCTGTGCTGAT 58.910 50.000 0.00 0.00 0.00 2.90
3759 4519 2.675032 CGGTTTGCTGTGCTGATCTAGA 60.675 50.000 0.00 0.00 0.00 2.43
3760 4520 2.935201 GGTTTGCTGTGCTGATCTAGAG 59.065 50.000 0.00 0.00 0.00 2.43
3762 4522 1.117994 TGCTGTGCTGATCTAGAGGG 58.882 55.000 0.00 0.00 0.00 4.30
3763 4523 0.392336 GCTGTGCTGATCTAGAGGGG 59.608 60.000 0.00 0.00 0.00 4.79
3764 4524 2.031624 GCTGTGCTGATCTAGAGGGGA 61.032 57.143 0.00 0.00 0.00 4.81
3765 4525 1.962807 CTGTGCTGATCTAGAGGGGAG 59.037 57.143 0.00 0.00 0.00 4.30
3766 4526 1.337118 GTGCTGATCTAGAGGGGAGG 58.663 60.000 0.00 0.00 0.00 4.30
3768 4528 1.191489 GCTGATCTAGAGGGGAGGCC 61.191 65.000 0.00 0.00 0.00 5.19
3769 4529 0.486879 CTGATCTAGAGGGGAGGCCT 59.513 60.000 3.86 3.86 0.00 5.19
3771 4531 1.429687 TGATCTAGAGGGGAGGCCTAC 59.570 57.143 6.36 6.36 0.00 3.18
3773 4533 0.854218 TCTAGAGGGGAGGCCTACTG 59.146 60.000 16.60 0.00 0.00 2.74
3774 4534 0.854218 CTAGAGGGGAGGCCTACTGA 59.146 60.000 16.60 0.00 0.00 3.41
3775 4535 0.854218 TAGAGGGGAGGCCTACTGAG 59.146 60.000 16.60 0.00 0.00 3.35
3953 4717 5.452078 TTTTTCCTTGCATACCTGTCAAG 57.548 39.130 0.00 0.00 36.81 3.02
4063 4836 2.436417 TCCAGCCATGAAAAGCACTAC 58.564 47.619 0.00 0.00 0.00 2.73
4086 4859 1.204941 GTAGGAGGAGAAAAGCAGCGA 59.795 52.381 0.00 0.00 0.00 4.93
4087 4860 0.248843 AGGAGGAGAAAAGCAGCGAG 59.751 55.000 0.00 0.00 0.00 5.03
4088 4861 0.036858 GGAGGAGAAAAGCAGCGAGT 60.037 55.000 0.00 0.00 0.00 4.18
4089 4862 1.609320 GGAGGAGAAAAGCAGCGAGTT 60.609 52.381 0.00 0.00 0.00 3.01
4090 4863 2.353803 GGAGGAGAAAAGCAGCGAGTTA 60.354 50.000 0.00 0.00 0.00 2.24
4091 4864 3.326747 GAGGAGAAAAGCAGCGAGTTAA 58.673 45.455 0.00 0.00 0.00 2.01
4092 4865 3.935828 GAGGAGAAAAGCAGCGAGTTAAT 59.064 43.478 0.00 0.00 0.00 1.40
4093 4866 4.327680 AGGAGAAAAGCAGCGAGTTAATT 58.672 39.130 0.00 0.00 0.00 1.40
4094 4867 5.488341 AGGAGAAAAGCAGCGAGTTAATTA 58.512 37.500 0.00 0.00 0.00 1.40
4095 4868 5.351740 AGGAGAAAAGCAGCGAGTTAATTAC 59.648 40.000 0.00 0.00 0.00 1.89
4096 4869 5.121768 GGAGAAAAGCAGCGAGTTAATTACA 59.878 40.000 0.00 0.00 0.00 2.41
4097 4870 5.928153 AGAAAAGCAGCGAGTTAATTACAC 58.072 37.500 0.00 0.00 0.00 2.90
4098 4871 5.701290 AGAAAAGCAGCGAGTTAATTACACT 59.299 36.000 0.00 0.00 0.00 3.55
4099 4872 6.872020 AGAAAAGCAGCGAGTTAATTACACTA 59.128 34.615 0.00 0.00 0.00 2.74
4100 4873 7.549488 AGAAAAGCAGCGAGTTAATTACACTAT 59.451 33.333 0.00 0.00 0.00 2.12
4101 4874 7.611213 AAAGCAGCGAGTTAATTACACTATT 57.389 32.000 0.00 0.00 0.00 1.73
4102 4875 8.712285 AAAGCAGCGAGTTAATTACACTATTA 57.288 30.769 0.00 0.00 0.00 0.98
4103 4876 8.712285 AAGCAGCGAGTTAATTACACTATTAA 57.288 30.769 0.00 0.00 0.00 1.40
4104 4877 8.888579 AGCAGCGAGTTAATTACACTATTAAT 57.111 30.769 0.00 0.00 33.79 1.40
4105 4878 9.976511 AGCAGCGAGTTAATTACACTATTAATA 57.023 29.630 0.00 0.00 33.79 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.194641 CATCGTCATGATCGGTATCTTCCG 61.195 50.000 14.72 0.00 41.11 4.30
2 3 3.917329 TCGTCATGATCGGTATCTTCC 57.083 47.619 14.72 0.00 32.93 3.46
6 7 3.763902 CTCCATCGTCATGATCGGTATC 58.236 50.000 14.72 0.00 34.13 2.24
8 9 1.269723 GCTCCATCGTCATGATCGGTA 59.730 52.381 14.72 1.33 34.13 4.02
10 11 0.032540 TGCTCCATCGTCATGATCGG 59.967 55.000 14.72 6.98 34.13 4.18
12 13 2.522836 ACTGCTCCATCGTCATGATC 57.477 50.000 0.00 0.00 34.13 2.92
15 16 1.012086 CCAACTGCTCCATCGTCATG 58.988 55.000 0.00 0.00 0.00 3.07
17 18 0.904649 ATCCAACTGCTCCATCGTCA 59.095 50.000 0.00 0.00 0.00 4.35
18 19 1.576356 GATCCAACTGCTCCATCGTC 58.424 55.000 0.00 0.00 0.00 4.20
21 22 0.533755 CGGGATCCAACTGCTCCATC 60.534 60.000 15.23 0.00 0.00 3.51
23 24 2.989639 CGGGATCCAACTGCTCCA 59.010 61.111 15.23 0.00 0.00 3.86
24 25 2.514824 GCGGGATCCAACTGCTCC 60.515 66.667 15.23 0.00 37.26 4.70
25 26 2.514824 GGCGGGATCCAACTGCTC 60.515 66.667 15.23 2.73 40.08 4.26
30 31 4.778143 ACTGCGGCGGGATCCAAC 62.778 66.667 15.23 4.20 0.00 3.77
31 32 4.776322 CACTGCGGCGGGATCCAA 62.776 66.667 15.23 0.00 0.00 3.53
33 34 4.241555 ATCACTGCGGCGGGATCC 62.242 66.667 14.26 1.92 0.00 3.36
35 36 2.721971 GATCATCACTGCGGCGGGAT 62.722 60.000 14.26 8.64 0.00 3.85
37 38 2.969238 GATCATCACTGCGGCGGG 60.969 66.667 14.26 2.36 0.00 6.13
39 40 0.786581 GTATGATCATCACTGCGGCG 59.213 55.000 12.53 0.51 0.00 6.46
40 41 0.786581 CGTATGATCATCACTGCGGC 59.213 55.000 12.53 0.00 0.00 6.53
42 43 1.490621 TGCGTATGATCATCACTGCG 58.509 50.000 12.53 5.79 0.00 5.18
43 44 3.062042 TGATGCGTATGATCATCACTGC 58.938 45.455 12.53 12.22 42.72 4.40
49 50 4.891260 ACACAGATGATGCGTATGATCAT 58.109 39.130 13.81 13.81 42.15 2.45
50 51 4.326504 ACACAGATGATGCGTATGATCA 57.673 40.909 14.60 0.00 30.34 2.92
52 53 5.011023 TCCTAACACAGATGATGCGTATGAT 59.989 40.000 0.00 0.00 0.00 2.45
53 54 4.340950 TCCTAACACAGATGATGCGTATGA 59.659 41.667 0.00 0.00 0.00 2.15
55 56 4.937201 TCCTAACACAGATGATGCGTAT 57.063 40.909 0.00 0.00 0.00 3.06
56 57 4.099419 ACATCCTAACACAGATGATGCGTA 59.901 41.667 6.98 0.00 42.04 4.42
57 58 3.118629 ACATCCTAACACAGATGATGCGT 60.119 43.478 6.98 0.00 42.04 5.24
58 59 3.461061 ACATCCTAACACAGATGATGCG 58.539 45.455 6.98 0.00 42.04 4.73
59 60 4.877823 TGAACATCCTAACACAGATGATGC 59.122 41.667 6.98 0.00 42.04 3.91
61 62 6.118170 CCTTGAACATCCTAACACAGATGAT 58.882 40.000 6.98 0.00 42.04 2.45
62 63 5.491070 CCTTGAACATCCTAACACAGATGA 58.509 41.667 6.98 0.00 42.04 2.92
63 64 4.637534 CCCTTGAACATCCTAACACAGATG 59.362 45.833 0.00 0.00 44.44 2.90
64 65 4.848357 CCCTTGAACATCCTAACACAGAT 58.152 43.478 0.00 0.00 0.00 2.90
68 69 3.073274 AGCCCTTGAACATCCTAACAC 57.927 47.619 0.00 0.00 0.00 3.32
70 71 2.755103 CCAAGCCCTTGAACATCCTAAC 59.245 50.000 9.50 0.00 42.93 2.34
71 72 2.883888 GCCAAGCCCTTGAACATCCTAA 60.884 50.000 9.50 0.00 42.93 2.69
73 74 0.613012 GCCAAGCCCTTGAACATCCT 60.613 55.000 9.50 0.00 42.93 3.24
74 75 0.899717 TGCCAAGCCCTTGAACATCC 60.900 55.000 9.50 0.00 42.93 3.51
75 76 0.529378 CTGCCAAGCCCTTGAACATC 59.471 55.000 9.50 0.00 42.93 3.06
76 77 1.538687 GCTGCCAAGCCCTTGAACAT 61.539 55.000 9.50 0.00 44.22 2.71
77 78 2.202395 GCTGCCAAGCCCTTGAACA 61.202 57.895 9.50 6.57 44.22 3.18
78 79 2.653115 GCTGCCAAGCCCTTGAAC 59.347 61.111 9.50 2.50 44.22 3.18
87 88 2.008329 GTCTTCATCTGAGCTGCCAAG 58.992 52.381 0.00 0.00 0.00 3.61
91 92 1.736681 GGTTGTCTTCATCTGAGCTGC 59.263 52.381 0.00 0.00 0.00 5.25
92 93 1.998315 CGGTTGTCTTCATCTGAGCTG 59.002 52.381 0.00 0.00 0.00 4.24
93 94 1.895798 TCGGTTGTCTTCATCTGAGCT 59.104 47.619 0.00 0.00 0.00 4.09
94 95 2.094494 TCTCGGTTGTCTTCATCTGAGC 60.094 50.000 9.11 0.00 42.21 4.26
95 96 3.857549 TCTCGGTTGTCTTCATCTGAG 57.142 47.619 8.13 8.13 43.07 3.35
97 98 3.056536 TCCTTCTCGGTTGTCTTCATCTG 60.057 47.826 0.00 0.00 0.00 2.90
98 99 3.165875 TCCTTCTCGGTTGTCTTCATCT 58.834 45.455 0.00 0.00 0.00 2.90
101 102 2.632996 ACATCCTTCTCGGTTGTCTTCA 59.367 45.455 0.00 0.00 40.86 3.02
102 103 2.996621 CACATCCTTCTCGGTTGTCTTC 59.003 50.000 0.00 0.00 42.47 2.87
104 105 1.276421 CCACATCCTTCTCGGTTGTCT 59.724 52.381 0.00 0.00 42.47 3.41
105 106 1.726853 CCACATCCTTCTCGGTTGTC 58.273 55.000 0.00 0.00 42.47 3.18
107 108 0.036010 AGCCACATCCTTCTCGGTTG 60.036 55.000 0.00 0.00 38.27 3.77
108 109 0.036010 CAGCCACATCCTTCTCGGTT 60.036 55.000 0.00 0.00 0.00 4.44
109 110 0.904865 TCAGCCACATCCTTCTCGGT 60.905 55.000 0.00 0.00 0.00 4.69
110 111 0.467384 ATCAGCCACATCCTTCTCGG 59.533 55.000 0.00 0.00 0.00 4.63
111 112 1.137675 TCATCAGCCACATCCTTCTCG 59.862 52.381 0.00 0.00 0.00 4.04
114 115 1.487976 TCCTCATCAGCCACATCCTTC 59.512 52.381 0.00 0.00 0.00 3.46
115 116 1.489649 CTCCTCATCAGCCACATCCTT 59.510 52.381 0.00 0.00 0.00 3.36
116 117 1.129917 CTCCTCATCAGCCACATCCT 58.870 55.000 0.00 0.00 0.00 3.24
117 118 0.108207 CCTCCTCATCAGCCACATCC 59.892 60.000 0.00 0.00 0.00 3.51
118 119 0.108207 CCCTCCTCATCAGCCACATC 59.892 60.000 0.00 0.00 0.00 3.06
119 120 1.351080 CCCCTCCTCATCAGCCACAT 61.351 60.000 0.00 0.00 0.00 3.21
120 121 1.997311 CCCCTCCTCATCAGCCACA 60.997 63.158 0.00 0.00 0.00 4.17
121 122 2.914289 CCCCTCCTCATCAGCCAC 59.086 66.667 0.00 0.00 0.00 5.01
125 126 1.692042 ACCAGCCCCTCCTCATCAG 60.692 63.158 0.00 0.00 0.00 2.90
128 129 1.997874 GTCACCAGCCCCTCCTCAT 60.998 63.158 0.00 0.00 0.00 2.90
129 130 2.607750 GTCACCAGCCCCTCCTCA 60.608 66.667 0.00 0.00 0.00 3.86
130 131 2.607750 TGTCACCAGCCCCTCCTC 60.608 66.667 0.00 0.00 0.00 3.71
131 132 2.608988 CTGTCACCAGCCCCTCCT 60.609 66.667 0.00 0.00 0.00 3.69
132 133 3.721706 CCTGTCACCAGCCCCTCC 61.722 72.222 0.00 0.00 37.38 4.30
134 135 4.599500 ACCCTGTCACCAGCCCCT 62.599 66.667 0.00 0.00 37.38 4.79
135 136 4.351054 CACCCTGTCACCAGCCCC 62.351 72.222 0.00 0.00 37.38 5.80
136 137 3.249189 TCACCCTGTCACCAGCCC 61.249 66.667 0.00 0.00 37.38 5.19
137 138 2.348998 CTCACCCTGTCACCAGCC 59.651 66.667 0.00 0.00 37.38 4.85
138 139 2.359230 GCTCACCCTGTCACCAGC 60.359 66.667 0.00 0.00 37.38 4.85
139 140 2.047844 CGCTCACCCTGTCACCAG 60.048 66.667 0.00 0.00 38.50 4.00
143 144 1.979155 CTCCTCGCTCACCCTGTCA 60.979 63.158 0.00 0.00 0.00 3.58
144 145 2.716017 CCTCCTCGCTCACCCTGTC 61.716 68.421 0.00 0.00 0.00 3.51
145 146 2.681778 CCTCCTCGCTCACCCTGT 60.682 66.667 0.00 0.00 0.00 4.00
150 151 2.182030 CCGAACCTCCTCGCTCAC 59.818 66.667 0.00 0.00 37.51 3.51
151 152 2.035155 TCCGAACCTCCTCGCTCA 59.965 61.111 0.00 0.00 37.51 4.26
152 153 1.874345 TTGTCCGAACCTCCTCGCTC 61.874 60.000 0.00 0.00 37.51 5.03
153 154 1.906824 TTGTCCGAACCTCCTCGCT 60.907 57.895 0.00 0.00 37.51 4.93
154 155 1.737008 GTTGTCCGAACCTCCTCGC 60.737 63.158 0.00 0.00 37.51 5.03
155 156 1.171308 TAGTTGTCCGAACCTCCTCG 58.829 55.000 0.00 0.00 38.58 4.63
158 159 3.522553 CAGATTAGTTGTCCGAACCTCC 58.477 50.000 0.00 0.00 0.00 4.30
159 160 3.522553 CCAGATTAGTTGTCCGAACCTC 58.477 50.000 0.00 0.00 0.00 3.85
160 161 2.236395 CCCAGATTAGTTGTCCGAACCT 59.764 50.000 0.00 0.00 0.00 3.50
161 162 2.235402 TCCCAGATTAGTTGTCCGAACC 59.765 50.000 0.00 0.00 0.00 3.62
162 163 3.522553 CTCCCAGATTAGTTGTCCGAAC 58.477 50.000 0.00 0.00 0.00 3.95
163 164 2.500098 CCTCCCAGATTAGTTGTCCGAA 59.500 50.000 0.00 0.00 0.00 4.30
165 166 1.139058 CCCTCCCAGATTAGTTGTCCG 59.861 57.143 0.00 0.00 0.00 4.79
166 167 1.134068 GCCCTCCCAGATTAGTTGTCC 60.134 57.143 0.00 0.00 0.00 4.02
167 168 1.559682 TGCCCTCCCAGATTAGTTGTC 59.440 52.381 0.00 0.00 0.00 3.18
168 169 1.668826 TGCCCTCCCAGATTAGTTGT 58.331 50.000 0.00 0.00 0.00 3.32
169 170 2.806945 TTGCCCTCCCAGATTAGTTG 57.193 50.000 0.00 0.00 0.00 3.16
170 171 3.825908 TTTTGCCCTCCCAGATTAGTT 57.174 42.857 0.00 0.00 0.00 2.24
172 173 4.958581 AGAATTTTTGCCCTCCCAGATTAG 59.041 41.667 0.00 0.00 0.00 1.73
173 174 4.711355 CAGAATTTTTGCCCTCCCAGATTA 59.289 41.667 0.00 0.00 0.00 1.75
175 176 3.102204 CAGAATTTTTGCCCTCCCAGAT 58.898 45.455 0.00 0.00 0.00 2.90
176 177 2.158325 ACAGAATTTTTGCCCTCCCAGA 60.158 45.455 0.00 0.00 0.00 3.86
177 178 2.250924 ACAGAATTTTTGCCCTCCCAG 58.749 47.619 0.00 0.00 0.00 4.45
178 179 2.397044 ACAGAATTTTTGCCCTCCCA 57.603 45.000 0.00 0.00 0.00 4.37
179 180 3.769739 AAACAGAATTTTTGCCCTCCC 57.230 42.857 0.00 0.00 0.00 4.30
180 181 4.960938 AGAAAACAGAATTTTTGCCCTCC 58.039 39.130 0.00 0.00 0.00 4.30
181 182 6.423905 GGTAAGAAAACAGAATTTTTGCCCTC 59.576 38.462 0.00 0.00 0.00 4.30
183 184 6.202762 CAGGTAAGAAAACAGAATTTTTGCCC 59.797 38.462 0.00 0.00 0.00 5.36
184 185 6.983890 TCAGGTAAGAAAACAGAATTTTTGCC 59.016 34.615 0.00 0.00 0.00 4.52
185 186 8.328146 GTTCAGGTAAGAAAACAGAATTTTTGC 58.672 33.333 0.00 0.00 0.00 3.68
187 188 9.586435 CAGTTCAGGTAAGAAAACAGAATTTTT 57.414 29.630 0.00 0.00 0.00 1.94
189 190 7.203218 GCAGTTCAGGTAAGAAAACAGAATTT 58.797 34.615 0.00 0.00 0.00 1.82
190 191 6.239036 GGCAGTTCAGGTAAGAAAACAGAATT 60.239 38.462 0.00 0.00 0.00 2.17
191 192 5.241728 GGCAGTTCAGGTAAGAAAACAGAAT 59.758 40.000 0.00 0.00 0.00 2.40
193 194 4.134563 GGCAGTTCAGGTAAGAAAACAGA 58.865 43.478 0.00 0.00 0.00 3.41
196 197 2.225727 CCGGCAGTTCAGGTAAGAAAAC 59.774 50.000 0.00 0.00 0.00 2.43
197 198 2.105134 TCCGGCAGTTCAGGTAAGAAAA 59.895 45.455 0.00 0.00 0.00 2.29
198 199 1.695242 TCCGGCAGTTCAGGTAAGAAA 59.305 47.619 0.00 0.00 0.00 2.52
199 200 1.344065 TCCGGCAGTTCAGGTAAGAA 58.656 50.000 0.00 0.00 0.00 2.52
200 201 1.568504 ATCCGGCAGTTCAGGTAAGA 58.431 50.000 0.00 0.00 0.00 2.10
201 202 2.009774 CAATCCGGCAGTTCAGGTAAG 58.990 52.381 0.00 0.00 0.00 2.34
203 204 0.981183 ACAATCCGGCAGTTCAGGTA 59.019 50.000 0.00 0.00 0.00 3.08
204 205 0.981183 TACAATCCGGCAGTTCAGGT 59.019 50.000 0.00 0.00 0.00 4.00
205 206 1.737793 GTTACAATCCGGCAGTTCAGG 59.262 52.381 0.00 0.00 0.00 3.86
206 207 2.422597 TGTTACAATCCGGCAGTTCAG 58.577 47.619 0.00 0.00 0.00 3.02
207 208 2.552599 TGTTACAATCCGGCAGTTCA 57.447 45.000 0.00 0.00 0.00 3.18
208 209 4.434713 AAATGTTACAATCCGGCAGTTC 57.565 40.909 0.00 0.00 0.00 3.01
210 211 5.189928 TCATAAATGTTACAATCCGGCAGT 58.810 37.500 0.00 0.00 0.00 4.40
211 212 5.749596 TCATAAATGTTACAATCCGGCAG 57.250 39.130 0.00 0.00 0.00 4.85
213 214 6.312399 TGATCATAAATGTTACAATCCGGC 57.688 37.500 0.00 0.00 0.00 6.13
214 215 6.568462 GCCTGATCATAAATGTTACAATCCGG 60.568 42.308 0.00 0.00 0.00 5.14
215 216 6.373779 GCCTGATCATAAATGTTACAATCCG 58.626 40.000 0.00 0.00 0.00 4.18
218 219 6.942532 ACGCCTGATCATAAATGTTACAAT 57.057 33.333 0.00 0.00 0.00 2.71
219 220 6.372937 TGAACGCCTGATCATAAATGTTACAA 59.627 34.615 0.00 0.00 0.00 2.41
220 221 5.877564 TGAACGCCTGATCATAAATGTTACA 59.122 36.000 0.00 0.00 0.00 2.41
221 222 6.358118 TGAACGCCTGATCATAAATGTTAC 57.642 37.500 0.00 0.00 0.00 2.50
223 224 7.566760 TTATGAACGCCTGATCATAAATGTT 57.433 32.000 0.00 0.00 43.01 2.71
224 225 7.566760 TTTATGAACGCCTGATCATAAATGT 57.433 32.000 13.88 0.00 46.31 2.71
228 229 8.773645 CATAGTTTTATGAACGCCTGATCATAA 58.226 33.333 0.00 4.56 43.76 1.90
229 230 8.147704 TCATAGTTTTATGAACGCCTGATCATA 58.852 33.333 0.00 0.00 42.00 2.15
244 245 7.383843 CCAAAACAAAGCGGTTCATAGTTTTAT 59.616 33.333 21.31 8.27 36.35 1.40
245 246 6.697892 CCAAAACAAAGCGGTTCATAGTTTTA 59.302 34.615 21.31 0.00 36.35 1.52
246 247 5.522097 CCAAAACAAAGCGGTTCATAGTTTT 59.478 36.000 18.54 18.54 37.97 2.43
248 249 4.098807 ACCAAAACAAAGCGGTTCATAGTT 59.901 37.500 0.00 1.07 0.00 2.24
249 250 3.634910 ACCAAAACAAAGCGGTTCATAGT 59.365 39.130 0.00 0.00 0.00 2.12
250 251 4.237349 ACCAAAACAAAGCGGTTCATAG 57.763 40.909 0.00 0.00 0.00 2.23
251 252 4.657436 AACCAAAACAAAGCGGTTCATA 57.343 36.364 0.00 0.00 37.12 2.15
252 253 3.535280 AACCAAAACAAAGCGGTTCAT 57.465 38.095 0.00 0.00 37.12 2.57
255 256 3.665190 TCAAAACCAAAACAAAGCGGTT 58.335 36.364 0.00 0.00 43.55 4.44
256 257 3.320673 TCAAAACCAAAACAAAGCGGT 57.679 38.095 0.00 0.00 0.00 5.68
258 259 3.060607 CCGATCAAAACCAAAACAAAGCG 60.061 43.478 0.00 0.00 0.00 4.68
260 261 6.087555 CGTATCCGATCAAAACCAAAACAAAG 59.912 38.462 0.00 0.00 35.63 2.77
262 263 5.238868 TCGTATCCGATCAAAACCAAAACAA 59.761 36.000 0.00 0.00 38.40 2.83
263 264 4.755629 TCGTATCCGATCAAAACCAAAACA 59.244 37.500 0.00 0.00 38.40 2.83
264 265 5.285798 TCGTATCCGATCAAAACCAAAAC 57.714 39.130 0.00 0.00 38.40 2.43
267 268 4.316645 TGTTCGTATCCGATCAAAACCAA 58.683 39.130 0.00 0.00 43.80 3.67
276 277 2.094182 AGTGCAGTTGTTCGTATCCGAT 60.094 45.455 0.00 0.00 43.80 4.18
277 278 1.271379 AGTGCAGTTGTTCGTATCCGA 59.729 47.619 0.00 0.00 42.41 4.55
278 279 1.710013 AGTGCAGTTGTTCGTATCCG 58.290 50.000 0.00 0.00 0.00 4.18
279 280 3.064207 TGAAGTGCAGTTGTTCGTATCC 58.936 45.455 12.53 0.00 0.00 2.59
280 281 4.313522 CTGAAGTGCAGTTGTTCGTATC 57.686 45.455 12.53 0.00 39.85 2.24
292 293 9.613428 AGCAATAATATAGTAAACTGAAGTGCA 57.387 29.630 0.00 0.00 0.00 4.57
311 312 8.476447 TCCTTCATTTCAAATGCATAGCAATAA 58.524 29.630 5.12 0.00 43.62 1.40
326 327 2.305927 GGACTCCACCTCCTTCATTTCA 59.694 50.000 0.00 0.00 0.00 2.69
366 367 1.203063 AGTGGGTGTGAGCAGAGTAGA 60.203 52.381 0.00 0.00 0.00 2.59
371 372 3.150949 CCAGTGGGTGTGAGCAGA 58.849 61.111 0.00 0.00 0.00 4.26
386 387 1.974957 TCTAGTGTTTAGCAGTGGCCA 59.025 47.619 0.00 0.00 42.56 5.36
387 388 2.762535 TCTAGTGTTTAGCAGTGGCC 57.237 50.000 0.00 0.00 42.56 5.36
388 389 3.813166 TGTTTCTAGTGTTTAGCAGTGGC 59.187 43.478 0.00 0.00 41.61 5.01
389 390 4.814234 TGTGTTTCTAGTGTTTAGCAGTGG 59.186 41.667 0.00 0.00 32.14 4.00
390 391 5.523916 AGTGTGTTTCTAGTGTTTAGCAGTG 59.476 40.000 0.00 0.00 32.14 3.66
391 392 5.523916 CAGTGTGTTTCTAGTGTTTAGCAGT 59.476 40.000 0.00 0.00 34.61 4.40
392 393 5.050091 CCAGTGTGTTTCTAGTGTTTAGCAG 60.050 44.000 0.00 0.00 0.00 4.24
473 474 3.260483 GCTGCTCTGATCGGCGTG 61.260 66.667 6.85 0.00 0.00 5.34
514 516 2.685100 GGTGAGAAACTAGTCAACCCG 58.315 52.381 0.00 0.00 0.00 5.28
566 568 4.508124 TGTTTTGTGTTGTTGCGAGTTTTT 59.492 33.333 0.00 0.00 0.00 1.94
659 665 4.998671 TGTGTTTTTGCCTTCTGAATGA 57.001 36.364 0.00 0.00 0.00 2.57
677 683 1.212616 GCTTCGGTAGCTAGCATGTG 58.787 55.000 21.99 10.05 46.77 3.21
952 1347 1.952990 TGCTCAACAAAAATCCTCGCA 59.047 42.857 0.00 0.00 0.00 5.10
1053 1448 4.409574 TGTTGTAGTAACCTGGGTTTGAGA 59.590 41.667 10.42 0.00 39.31 3.27
1128 1528 1.466167 CCACAAGAACAGAAGCCATCG 59.534 52.381 0.00 0.00 0.00 3.84
1160 1560 2.154462 CGACCAAGAAGGCAAGAACAT 58.846 47.619 0.00 0.00 43.14 2.71
1208 1609 2.859273 ATCAGGGAAAGCGAGCGTGG 62.859 60.000 0.00 0.00 0.00 4.94
1290 1691 0.954449 ATGCATAGATCTGCGCCAGC 60.954 55.000 4.18 0.00 45.30 4.85
1473 1893 5.257262 AGGATAAGAAAGAAAGGCAGGAAC 58.743 41.667 0.00 0.00 0.00 3.62
1474 1894 5.520748 AGGATAAGAAAGAAAGGCAGGAA 57.479 39.130 0.00 0.00 0.00 3.36
1475 1895 5.520748 AAGGATAAGAAAGAAAGGCAGGA 57.479 39.130 0.00 0.00 0.00 3.86
1476 1896 5.126222 GGAAAGGATAAGAAAGAAAGGCAGG 59.874 44.000 0.00 0.00 0.00 4.85
1477 1897 5.126222 GGGAAAGGATAAGAAAGAAAGGCAG 59.874 44.000 0.00 0.00 0.00 4.85
1478 1898 5.016831 GGGAAAGGATAAGAAAGAAAGGCA 58.983 41.667 0.00 0.00 0.00 4.75
1479 1899 4.402793 GGGGAAAGGATAAGAAAGAAAGGC 59.597 45.833 0.00 0.00 0.00 4.35
1480 1900 5.832221 AGGGGAAAGGATAAGAAAGAAAGG 58.168 41.667 0.00 0.00 0.00 3.11
1481 1901 6.485171 TGAGGGGAAAGGATAAGAAAGAAAG 58.515 40.000 0.00 0.00 0.00 2.62
1482 1902 6.463053 TGAGGGGAAAGGATAAGAAAGAAA 57.537 37.500 0.00 0.00 0.00 2.52
1483 1903 6.353951 GGATGAGGGGAAAGGATAAGAAAGAA 60.354 42.308 0.00 0.00 0.00 2.52
1484 1904 5.132816 GGATGAGGGGAAAGGATAAGAAAGA 59.867 44.000 0.00 0.00 0.00 2.52
1889 2314 2.874701 CAAATCCTCGATGTTAGGGCAG 59.125 50.000 0.00 0.00 34.66 4.85
1965 2390 1.599047 CTCCATGGGCTTCACGAGT 59.401 57.895 13.02 0.00 0.00 4.18
2023 2448 0.106868 GGGTTCGGGTTCCCATTAGG 60.107 60.000 8.70 0.00 42.95 2.69
2787 3254 0.535780 TGTTCTGAACCTGCTGCTGG 60.536 55.000 22.17 22.17 0.00 4.85
2820 3287 1.460689 ACCTCCTCCCGTGTCCAAA 60.461 57.895 0.00 0.00 0.00 3.28
2821 3288 2.203182 ACCTCCTCCCGTGTCCAA 59.797 61.111 0.00 0.00 0.00 3.53
2940 3422 2.352805 CTTGCACCTCCTCCACCC 59.647 66.667 0.00 0.00 0.00 4.61
3096 3623 1.195442 TGCCATCCTACCACGAACCA 61.195 55.000 0.00 0.00 0.00 3.67
3299 3850 9.612066 ACATGAACAAAACACCAAGAAATTAAT 57.388 25.926 0.00 0.00 0.00 1.40
3448 4017 3.308053 CCGTGCAGATTCTACATGAACAG 59.692 47.826 7.56 0.00 37.52 3.16
3640 4383 2.791560 CGTTGAGTGTTGACTGACTGAG 59.208 50.000 0.00 0.00 30.16 3.35
3682 4425 1.070445 AGCCTGCACAGTGTGTCTC 59.930 57.895 23.73 8.63 35.75 3.36
3683 4426 1.227764 CAGCCTGCACAGTGTGTCT 60.228 57.895 23.73 12.96 35.75 3.41
3754 4514 0.854218 CAGTAGGCCTCCCCTCTAGA 59.146 60.000 9.68 0.00 44.96 2.43
3760 4520 1.116536 GCTACTCAGTAGGCCTCCCC 61.117 65.000 9.68 0.00 36.71 4.81
3762 4522 1.036707 CTGCTACTCAGTAGGCCTCC 58.963 60.000 9.68 0.00 36.71 4.30
3763 4523 1.036707 CCTGCTACTCAGTAGGCCTC 58.963 60.000 9.68 0.21 46.12 4.70
3764 4524 3.215671 CCTGCTACTCAGTAGGCCT 57.784 57.895 11.78 11.78 46.12 5.19
3768 4528 0.526524 GCACGCCTGCTACTCAGTAG 60.527 60.000 7.56 7.56 41.25 2.57
3769 4529 1.511305 GCACGCCTGCTACTCAGTA 59.489 57.895 0.00 0.00 41.25 2.74
3787 4547 9.398170 ACGATGTAAATGAACAAATCAAGAAAG 57.602 29.630 0.00 0.00 42.54 2.62
3937 4698 6.286758 AGATATGTCTTGACAGGTATGCAAG 58.713 40.000 9.39 0.00 39.68 4.01
3938 4699 6.239217 AGATATGTCTTGACAGGTATGCAA 57.761 37.500 9.39 0.00 0.00 4.08
3953 4717 3.325135 CACAAGGAGGGGGTAGATATGTC 59.675 52.174 0.00 0.00 0.00 3.06
4023 4788 4.017222 TGGAAGATTCTTTGGGATGATGGT 60.017 41.667 0.00 0.00 0.00 3.55
4063 4836 0.902531 TGCTTTTCTCCTCCTACCGG 59.097 55.000 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.