Multiple sequence alignment - TraesCS3D01G494900

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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 TraesCS3D01G494900 chr3D 100.000 2567 0 0 1 2567 587419922 587422488 0.000000e+00 4741
1 TraesCS3D01G494900 chr3D 95.779 308 11 2 1 306 564204875 564205182 1.770000e-136 496
2 TraesCS3D01G494900 chr3B 90.929 1808 105 25 774 2567 784525044 784526806 0.000000e+00 2375
3 TraesCS3D01G494900 chr3B 90.768 1809 107 25 774 2567 784453906 784455669 0.000000e+00 2361
4 TraesCS3D01G494900 chr3B 95.218 481 12 3 303 781 784524379 784524850 0.000000e+00 750
5 TraesCS3D01G494900 chr3B 95.010 481 13 5 303 781 784453242 784453713 0.000000e+00 745
6 TraesCS3D01G494900 chr7B 80.401 1347 169 50 805 2086 133245834 133244518 0.000000e+00 937
7 TraesCS3D01G494900 chr7B 82.727 220 38 0 2281 2500 133244313 133244094 2.010000e-46 196
8 TraesCS3D01G494900 chr7D 80.312 1346 173 47 805 2086 168069816 168068499 0.000000e+00 933
9 TraesCS3D01G494900 chr7D 82.479 234 41 0 2281 2514 168068295 168068062 3.350000e-49 206
10 TraesCS3D01G494900 chr7A 79.911 1349 179 48 802 2086 170191604 170190284 0.000000e+00 905
11 TraesCS3D01G494900 chr7A 83.163 196 33 0 2305 2500 170190070 170189875 2.030000e-41 180
12 TraesCS3D01G494900 chr1D 96.417 307 9 2 1 305 205134390 205134696 2.950000e-139 505
13 TraesCS3D01G494900 chr1D 96.141 311 9 3 1 309 247505451 247505760 2.950000e-139 505
14 TraesCS3D01G494900 chr1D 96.417 307 9 2 1 305 451393091 451393397 2.950000e-139 505
15 TraesCS3D01G494900 chr1D 93.827 324 15 4 1 322 411531967 411532287 1.380000e-132 483
16 TraesCS3D01G494900 chr2D 95.541 314 12 2 1 312 73126565 73126878 3.810000e-138 501
17 TraesCS3D01G494900 chr6D 95.779 308 12 1 1 307 89225907 89225600 1.770000e-136 496
18 TraesCS3D01G494900 chr6D 95.765 307 11 2 1 305 28034735 28035041 6.380000e-136 494
19 TraesCS3D01G494900 chr4A 94.393 321 13 5 1 316 66588670 66588350 2.970000e-134 488


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 TraesCS3D01G494900 chr3D 587419922 587422488 2566 False 4741.0 4741 100.0000 1 2567 1 chr3D.!!$F2 2566
1 TraesCS3D01G494900 chr3B 784524379 784526806 2427 False 1562.5 2375 93.0735 303 2567 2 chr3B.!!$F2 2264
2 TraesCS3D01G494900 chr3B 784453242 784455669 2427 False 1553.0 2361 92.8890 303 2567 2 chr3B.!!$F1 2264
3 TraesCS3D01G494900 chr7B 133244094 133245834 1740 True 566.5 937 81.5640 805 2500 2 chr7B.!!$R1 1695
4 TraesCS3D01G494900 chr7D 168068062 168069816 1754 True 569.5 933 81.3955 805 2514 2 chr7D.!!$R1 1709
5 TraesCS3D01G494900 chr7A 170189875 170191604 1729 True 542.5 905 81.5370 802 2500 2 chr7A.!!$R1 1698

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
75 76 0.036875 GTATGTGGCTAGGATGGGGC 59.963 60.0 0.0 0.0 0.0 5.80 F
172 173 0.106819 GGGGTAGGAGTAGCGACAGA 60.107 60.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 1536 0.178953 AGCATGCTGGAAACAAGGGT 60.179 50.0 21.98 0.0 42.06 4.34 R
2135 2439 1.105457 TGGCATTGCAGTAATCAGGC 58.895 50.0 11.39 0.0 0.00 4.85 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
54 55 4.699522 GGCGTGTGACCCAGTCCC 62.700 72.222 0.00 0.00 0.00 4.46
56 57 4.373116 CGTGTGACCCAGTCCCGG 62.373 72.222 0.00 0.00 0.00 5.73
57 58 3.239253 GTGTGACCCAGTCCCGGT 61.239 66.667 0.00 0.00 35.88 5.28
58 59 1.909781 GTGTGACCCAGTCCCGGTA 60.910 63.158 0.00 0.00 32.27 4.02
59 60 1.079621 TGTGACCCAGTCCCGGTAT 59.920 57.895 0.00 0.00 32.27 2.73
60 61 1.261938 TGTGACCCAGTCCCGGTATG 61.262 60.000 0.00 0.00 32.27 2.39
61 62 1.079621 TGACCCAGTCCCGGTATGT 59.920 57.895 0.00 0.00 32.27 2.29
62 63 1.261938 TGACCCAGTCCCGGTATGTG 61.262 60.000 0.00 0.00 32.27 3.21
63 64 1.968050 GACCCAGTCCCGGTATGTGG 61.968 65.000 0.00 1.17 32.27 4.17
64 65 2.189521 CCAGTCCCGGTATGTGGC 59.810 66.667 0.00 0.00 0.00 5.01
65 66 2.367202 CCAGTCCCGGTATGTGGCT 61.367 63.158 0.00 0.00 0.00 4.75
66 67 1.046472 CCAGTCCCGGTATGTGGCTA 61.046 60.000 0.00 0.00 0.00 3.93
67 68 0.389391 CAGTCCCGGTATGTGGCTAG 59.611 60.000 0.00 0.00 0.00 3.42
68 69 0.759436 AGTCCCGGTATGTGGCTAGG 60.759 60.000 0.00 0.00 0.00 3.02
69 70 0.757935 GTCCCGGTATGTGGCTAGGA 60.758 60.000 0.00 0.00 0.00 2.94
70 71 0.190069 TCCCGGTATGTGGCTAGGAT 59.810 55.000 0.00 0.00 0.00 3.24
71 72 0.321671 CCCGGTATGTGGCTAGGATG 59.678 60.000 0.00 0.00 0.00 3.51
72 73 0.321671 CCGGTATGTGGCTAGGATGG 59.678 60.000 0.00 0.00 0.00 3.51
73 74 0.321671 CGGTATGTGGCTAGGATGGG 59.678 60.000 0.00 0.00 0.00 4.00
74 75 0.693049 GGTATGTGGCTAGGATGGGG 59.307 60.000 0.00 0.00 0.00 4.96
75 76 0.036875 GTATGTGGCTAGGATGGGGC 59.963 60.000 0.00 0.00 0.00 5.80
76 77 0.401250 TATGTGGCTAGGATGGGGCA 60.401 55.000 0.00 0.00 35.68 5.36
77 78 1.070127 ATGTGGCTAGGATGGGGCAT 61.070 55.000 0.00 0.00 40.00 4.40
78 79 1.073897 GTGGCTAGGATGGGGCATC 59.926 63.158 0.00 0.00 40.00 3.91
91 92 4.469883 GCATCCGGCATGAGATGT 57.530 55.556 15.42 0.00 41.60 3.06
92 93 2.711711 GCATCCGGCATGAGATGTT 58.288 52.632 15.42 0.00 41.60 2.71
93 94 1.882912 GCATCCGGCATGAGATGTTA 58.117 50.000 15.42 0.00 41.60 2.41
94 95 1.802960 GCATCCGGCATGAGATGTTAG 59.197 52.381 15.42 0.00 41.60 2.34
95 96 2.420642 CATCCGGCATGAGATGTTAGG 58.579 52.381 0.00 0.00 36.06 2.69
96 97 1.788229 TCCGGCATGAGATGTTAGGA 58.212 50.000 0.00 0.00 0.00 2.94
97 98 2.329267 TCCGGCATGAGATGTTAGGAT 58.671 47.619 0.00 0.00 0.00 3.24
98 99 2.705658 TCCGGCATGAGATGTTAGGATT 59.294 45.455 0.00 0.00 0.00 3.01
99 100 3.136443 TCCGGCATGAGATGTTAGGATTT 59.864 43.478 0.00 0.00 0.00 2.17
100 101 3.251729 CCGGCATGAGATGTTAGGATTTG 59.748 47.826 0.00 0.00 0.00 2.32
101 102 3.251729 CGGCATGAGATGTTAGGATTTGG 59.748 47.826 0.00 0.00 0.00 3.28
102 103 4.210331 GGCATGAGATGTTAGGATTTGGT 58.790 43.478 0.00 0.00 0.00 3.67
103 104 4.037208 GGCATGAGATGTTAGGATTTGGTG 59.963 45.833 0.00 0.00 0.00 4.17
104 105 4.498682 GCATGAGATGTTAGGATTTGGTGC 60.499 45.833 0.00 0.00 0.00 5.01
105 106 3.270027 TGAGATGTTAGGATTTGGTGCG 58.730 45.455 0.00 0.00 0.00 5.34
106 107 3.055458 TGAGATGTTAGGATTTGGTGCGA 60.055 43.478 0.00 0.00 0.00 5.10
107 108 3.270877 AGATGTTAGGATTTGGTGCGAC 58.729 45.455 0.00 0.00 0.00 5.19
108 109 1.434555 TGTTAGGATTTGGTGCGACG 58.565 50.000 0.00 0.00 0.00 5.12
109 110 1.270412 TGTTAGGATTTGGTGCGACGT 60.270 47.619 0.00 0.00 0.00 4.34
110 111 1.392510 GTTAGGATTTGGTGCGACGTC 59.607 52.381 5.18 5.18 0.00 4.34
111 112 0.457166 TAGGATTTGGTGCGACGTCG 60.457 55.000 32.57 32.57 43.27 5.12
112 113 2.736682 GGATTTGGTGCGACGTCGG 61.737 63.158 36.13 19.71 40.23 4.79
113 114 2.025418 GATTTGGTGCGACGTCGGT 61.025 57.895 36.13 2.46 40.23 4.69
114 115 1.562575 GATTTGGTGCGACGTCGGTT 61.563 55.000 36.13 0.00 40.23 4.44
115 116 1.161563 ATTTGGTGCGACGTCGGTTT 61.162 50.000 36.13 0.00 40.23 3.27
116 117 2.037913 TTTGGTGCGACGTCGGTTTG 62.038 55.000 36.13 11.48 40.23 2.93
117 118 3.708734 GGTGCGACGTCGGTTTGG 61.709 66.667 36.13 10.72 40.23 3.28
118 119 2.963320 GTGCGACGTCGGTTTGGT 60.963 61.111 36.13 0.00 40.23 3.67
119 120 1.661197 GTGCGACGTCGGTTTGGTA 60.661 57.895 36.13 6.33 40.23 3.25
120 121 1.010419 GTGCGACGTCGGTTTGGTAT 61.010 55.000 36.13 0.00 40.23 2.73
121 122 0.319727 TGCGACGTCGGTTTGGTATT 60.320 50.000 36.13 0.00 40.23 1.89
122 123 1.067985 TGCGACGTCGGTTTGGTATTA 60.068 47.619 36.13 0.00 40.23 0.98
123 124 1.585214 GCGACGTCGGTTTGGTATTAG 59.415 52.381 36.13 6.97 40.23 1.73
124 125 2.187707 CGACGTCGGTTTGGTATTAGG 58.812 52.381 29.70 0.00 35.37 2.69
125 126 1.929169 GACGTCGGTTTGGTATTAGGC 59.071 52.381 0.00 0.00 0.00 3.93
126 127 1.551883 ACGTCGGTTTGGTATTAGGCT 59.448 47.619 0.00 0.00 0.00 4.58
127 128 2.199236 CGTCGGTTTGGTATTAGGCTC 58.801 52.381 0.00 0.00 0.00 4.70
128 129 2.199236 GTCGGTTTGGTATTAGGCTCG 58.801 52.381 0.00 0.00 0.00 5.03
129 130 1.137479 TCGGTTTGGTATTAGGCTCGG 59.863 52.381 0.00 0.00 0.00 4.63
130 131 1.137479 CGGTTTGGTATTAGGCTCGGA 59.863 52.381 0.00 0.00 0.00 4.55
131 132 2.558378 GGTTTGGTATTAGGCTCGGAC 58.442 52.381 0.00 0.00 0.00 4.79
132 133 2.093341 GGTTTGGTATTAGGCTCGGACA 60.093 50.000 0.00 0.00 0.00 4.02
133 134 3.433173 GGTTTGGTATTAGGCTCGGACAT 60.433 47.826 0.00 0.00 0.00 3.06
134 135 4.196971 GTTTGGTATTAGGCTCGGACATT 58.803 43.478 0.00 0.00 0.00 2.71
135 136 3.746045 TGGTATTAGGCTCGGACATTC 57.254 47.619 0.00 0.00 0.00 2.67
136 137 2.035449 TGGTATTAGGCTCGGACATTCG 59.965 50.000 0.00 0.00 0.00 3.34
137 138 2.609737 GGTATTAGGCTCGGACATTCGG 60.610 54.545 0.00 0.00 0.00 4.30
138 139 0.249911 ATTAGGCTCGGACATTCGGC 60.250 55.000 0.00 0.00 0.00 5.54
139 140 1.609635 TTAGGCTCGGACATTCGGCA 61.610 55.000 0.00 0.00 0.00 5.69
140 141 2.292794 TAGGCTCGGACATTCGGCAC 62.293 60.000 0.00 0.00 0.00 5.01
141 142 3.195698 GCTCGGACATTCGGCACC 61.196 66.667 0.00 0.00 0.00 5.01
142 143 2.264480 CTCGGACATTCGGCACCA 59.736 61.111 0.00 0.00 0.00 4.17
143 144 2.047655 TCGGACATTCGGCACCAC 60.048 61.111 0.00 0.00 0.00 4.16
144 145 2.047274 CGGACATTCGGCACCACT 60.047 61.111 0.00 0.00 0.00 4.00
145 146 2.390599 CGGACATTCGGCACCACTG 61.391 63.158 0.00 0.00 0.00 3.66
146 147 2.690778 GGACATTCGGCACCACTGC 61.691 63.158 0.00 0.00 43.41 4.40
147 148 1.965930 GACATTCGGCACCACTGCA 60.966 57.895 0.00 0.00 46.28 4.41
148 149 1.303561 ACATTCGGCACCACTGCAT 60.304 52.632 0.00 0.00 46.28 3.96
149 150 1.308069 ACATTCGGCACCACTGCATC 61.308 55.000 0.00 0.00 46.28 3.91
150 151 1.002257 ATTCGGCACCACTGCATCA 60.002 52.632 0.00 0.00 46.28 3.07
151 152 0.608856 ATTCGGCACCACTGCATCAA 60.609 50.000 0.00 0.00 46.28 2.57
152 153 1.236616 TTCGGCACCACTGCATCAAG 61.237 55.000 0.00 0.00 46.28 3.02
153 154 2.693762 CGGCACCACTGCATCAAGG 61.694 63.158 0.00 0.00 46.28 3.61
154 155 2.345760 GGCACCACTGCATCAAGGG 61.346 63.158 0.00 0.00 46.28 3.95
156 157 1.679977 CACCACTGCATCAAGGGGG 60.680 63.158 0.00 0.00 45.91 5.40
157 158 2.162906 ACCACTGCATCAAGGGGGT 61.163 57.895 0.00 0.00 45.91 4.95
158 159 0.844661 ACCACTGCATCAAGGGGGTA 60.845 55.000 0.00 0.00 45.91 3.69
159 160 0.107017 CCACTGCATCAAGGGGGTAG 60.107 60.000 0.00 0.00 37.06 3.18
160 161 0.107017 CACTGCATCAAGGGGGTAGG 60.107 60.000 0.00 0.00 0.00 3.18
161 162 0.253160 ACTGCATCAAGGGGGTAGGA 60.253 55.000 0.00 0.00 0.00 2.94
162 163 0.471617 CTGCATCAAGGGGGTAGGAG 59.528 60.000 0.00 0.00 0.00 3.69
163 164 0.253160 TGCATCAAGGGGGTAGGAGT 60.253 55.000 0.00 0.00 0.00 3.85
164 165 1.009060 TGCATCAAGGGGGTAGGAGTA 59.991 52.381 0.00 0.00 0.00 2.59
165 166 1.694696 GCATCAAGGGGGTAGGAGTAG 59.305 57.143 0.00 0.00 0.00 2.57
166 167 1.694696 CATCAAGGGGGTAGGAGTAGC 59.305 57.143 0.00 0.00 0.00 3.58
167 168 0.396695 TCAAGGGGGTAGGAGTAGCG 60.397 60.000 0.00 0.00 0.00 4.26
168 169 0.396695 CAAGGGGGTAGGAGTAGCGA 60.397 60.000 0.00 0.00 0.00 4.93
169 170 0.396835 AAGGGGGTAGGAGTAGCGAC 60.397 60.000 0.00 0.00 0.00 5.19
170 171 1.076485 GGGGGTAGGAGTAGCGACA 60.076 63.158 0.00 0.00 0.00 4.35
171 172 1.108132 GGGGGTAGGAGTAGCGACAG 61.108 65.000 0.00 0.00 0.00 3.51
172 173 0.106819 GGGGTAGGAGTAGCGACAGA 60.107 60.000 0.00 0.00 0.00 3.41
173 174 1.479021 GGGGTAGGAGTAGCGACAGAT 60.479 57.143 0.00 0.00 0.00 2.90
174 175 1.609555 GGGTAGGAGTAGCGACAGATG 59.390 57.143 0.00 0.00 0.00 2.90
175 176 2.299521 GGTAGGAGTAGCGACAGATGT 58.700 52.381 0.00 0.00 0.00 3.06
176 177 2.688958 GGTAGGAGTAGCGACAGATGTT 59.311 50.000 0.00 0.00 0.00 2.71
177 178 2.949451 AGGAGTAGCGACAGATGTTG 57.051 50.000 0.00 0.00 0.00 3.33
186 187 2.477825 CGACAGATGTTGCCTAGATGG 58.522 52.381 0.00 0.00 39.35 3.51
187 188 2.159043 CGACAGATGTTGCCTAGATGGT 60.159 50.000 0.00 0.00 38.35 3.55
188 189 3.201290 GACAGATGTTGCCTAGATGGTG 58.799 50.000 0.00 0.00 38.35 4.17
189 190 2.092753 ACAGATGTTGCCTAGATGGTGG 60.093 50.000 0.00 0.00 38.35 4.61
195 196 3.393472 GCCTAGATGGTGGCTTCAG 57.607 57.895 0.00 0.00 45.26 3.02
196 197 0.179034 GCCTAGATGGTGGCTTCAGG 60.179 60.000 0.00 0.00 45.26 3.86
197 198 0.471617 CCTAGATGGTGGCTTCAGGG 59.528 60.000 0.00 0.00 0.00 4.45
198 199 1.207791 CTAGATGGTGGCTTCAGGGT 58.792 55.000 0.00 0.00 0.00 4.34
199 200 1.561542 CTAGATGGTGGCTTCAGGGTT 59.438 52.381 0.00 0.00 0.00 4.11
200 201 1.668826 AGATGGTGGCTTCAGGGTTA 58.331 50.000 0.00 0.00 0.00 2.85
201 202 1.282157 AGATGGTGGCTTCAGGGTTAC 59.718 52.381 0.00 0.00 0.00 2.50
202 203 1.282157 GATGGTGGCTTCAGGGTTACT 59.718 52.381 0.00 0.00 0.00 2.24
220 221 9.847224 AGGGTTACTGATGTATTATTTTGTAGG 57.153 33.333 0.00 0.00 0.00 3.18
221 222 9.623000 GGGTTACTGATGTATTATTTTGTAGGT 57.377 33.333 0.00 0.00 0.00 3.08
251 252 9.810545 TTGTGCTTAATAATTAATAAAGTGGCC 57.189 29.630 0.00 0.00 0.00 5.36
252 253 8.132362 TGTGCTTAATAATTAATAAAGTGGCCG 58.868 33.333 0.00 0.00 0.00 6.13
253 254 8.132995 GTGCTTAATAATTAATAAAGTGGCCGT 58.867 33.333 0.00 0.00 0.00 5.68
254 255 9.339850 TGCTTAATAATTAATAAAGTGGCCGTA 57.660 29.630 0.00 0.00 0.00 4.02
258 259 7.753309 ATAATTAATAAAGTGGCCGTATGCA 57.247 32.000 0.00 0.00 43.89 3.96
259 260 6.648879 AATTAATAAAGTGGCCGTATGCAT 57.351 33.333 3.79 3.79 43.89 3.96
260 261 5.682943 TTAATAAAGTGGCCGTATGCATC 57.317 39.130 0.19 0.00 43.89 3.91
261 262 1.577468 TAAAGTGGCCGTATGCATCG 58.423 50.000 0.19 7.03 43.89 3.84
262 263 0.392461 AAAGTGGCCGTATGCATCGT 60.392 50.000 0.19 0.00 43.89 3.73
263 264 0.810031 AAGTGGCCGTATGCATCGTC 60.810 55.000 0.19 0.00 43.89 4.20
264 265 2.108157 TGGCCGTATGCATCGTCC 59.892 61.111 0.19 7.07 43.89 4.79
265 266 2.108157 GGCCGTATGCATCGTCCA 59.892 61.111 0.19 0.00 43.89 4.02
266 267 1.956170 GGCCGTATGCATCGTCCAG 60.956 63.158 0.19 0.00 43.89 3.86
267 268 1.067416 GCCGTATGCATCGTCCAGA 59.933 57.895 0.19 0.00 40.77 3.86
268 269 0.319900 GCCGTATGCATCGTCCAGAT 60.320 55.000 0.19 0.00 41.01 2.90
276 277 1.445095 ATCGTCCAGATGCAGAGGC 59.555 57.895 0.00 0.00 38.36 4.70
277 278 2.037620 ATCGTCCAGATGCAGAGGCC 62.038 60.000 0.00 0.00 38.36 5.19
278 279 2.202987 GTCCAGATGCAGAGGCCG 60.203 66.667 0.00 0.00 40.13 6.13
279 280 3.473647 TCCAGATGCAGAGGCCGG 61.474 66.667 0.00 0.00 40.13 6.13
280 281 4.559063 CCAGATGCAGAGGCCGGG 62.559 72.222 2.18 0.00 40.13 5.73
281 282 4.559063 CAGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
283 284 4.864334 GATGCAGAGGCCGGGGTG 62.864 72.222 2.18 0.00 40.13 4.61
287 288 4.864334 CAGAGGCCGGGGTGCATC 62.864 72.222 2.18 0.00 42.12 3.91
293 294 3.411517 CCGGGGTGCATCCTCCTT 61.412 66.667 17.44 0.00 36.25 3.36
294 295 2.677228 CGGGGTGCATCCTCCTTT 59.323 61.111 17.44 0.00 36.25 3.11
295 296 1.000896 CGGGGTGCATCCTCCTTTT 60.001 57.895 17.44 0.00 36.25 2.27
296 297 1.032114 CGGGGTGCATCCTCCTTTTC 61.032 60.000 17.44 0.00 36.25 2.29
297 298 0.332972 GGGGTGCATCCTCCTTTTCT 59.667 55.000 17.44 0.00 36.25 2.52
298 299 1.564348 GGGGTGCATCCTCCTTTTCTA 59.436 52.381 17.44 0.00 36.25 2.10
299 300 2.025321 GGGGTGCATCCTCCTTTTCTAA 60.025 50.000 17.44 0.00 36.25 2.10
300 301 3.563479 GGGGTGCATCCTCCTTTTCTAAA 60.563 47.826 17.44 0.00 36.25 1.85
301 302 4.086457 GGGTGCATCCTCCTTTTCTAAAA 58.914 43.478 9.39 0.00 36.25 1.52
302 303 4.526650 GGGTGCATCCTCCTTTTCTAAAAA 59.473 41.667 9.39 0.00 36.25 1.94
340 341 7.116075 TCCAGATTAATCGATGGGAAAAAGAA 58.884 34.615 18.76 0.61 33.45 2.52
341 342 7.779798 TCCAGATTAATCGATGGGAAAAAGAAT 59.220 33.333 18.76 0.00 33.45 2.40
342 343 8.416329 CCAGATTAATCGATGGGAAAAAGAATT 58.584 33.333 13.55 0.00 0.00 2.17
399 400 1.063717 AGGTGGCACCCCAATGATTAG 60.064 52.381 32.30 0.00 44.33 1.73
475 478 5.405797 TGCATATATCTTCATCAGCTCGTC 58.594 41.667 0.00 0.00 0.00 4.20
500 503 2.040145 TCCAATCAACATGGTGAGCAGA 59.960 45.455 19.98 11.94 39.09 4.26
517 520 3.636300 AGCAGATGTTACTTGCCAAACAA 59.364 39.130 4.15 0.00 38.95 2.83
521 524 6.215121 CAGATGTTACTTGCCAAACAATGAA 58.785 36.000 0.00 0.00 38.95 2.57
529 532 6.825610 ACTTGCCAAACAATGAATTAAGGAA 58.174 32.000 0.00 0.00 37.72 3.36
530 533 7.278875 ACTTGCCAAACAATGAATTAAGGAAA 58.721 30.769 0.00 0.00 37.72 3.13
531 534 7.772757 ACTTGCCAAACAATGAATTAAGGAAAA 59.227 29.630 0.00 0.00 37.72 2.29
532 535 8.688747 TTGCCAAACAATGAATTAAGGAAAAT 57.311 26.923 0.00 0.00 31.73 1.82
533 536 9.784531 TTGCCAAACAATGAATTAAGGAAAATA 57.215 25.926 0.00 0.00 31.73 1.40
707 710 5.243426 ACCTGTAAACACAACACACAATC 57.757 39.130 0.00 0.00 0.00 2.67
730 733 7.062749 TCTTAAGTGCAAGTAGAAGGAGAAA 57.937 36.000 1.63 0.00 0.00 2.52
754 757 4.457257 ACCCACAAAACAACAAAAATGGTG 59.543 37.500 0.00 0.00 0.00 4.17
789 993 9.206690 TCCACTATGAGAAGATACTTCTGAATT 57.793 33.333 16.97 0.24 30.72 2.17
814 1018 4.439289 GGGCATTGATAAGAGAAAGCACAC 60.439 45.833 0.00 0.00 0.00 3.82
845 1049 5.356751 ACAAATATTGTGCGCTGGAATCTAA 59.643 36.000 9.73 0.00 43.48 2.10
847 1051 5.869753 ATATTGTGCGCTGGAATCTAATC 57.130 39.130 9.73 0.00 0.00 1.75
975 1180 6.128742 GCATTTGTTTCAACATTCCACAGATC 60.129 38.462 0.00 0.00 38.95 2.75
976 1181 5.452078 TTGTTTCAACATTCCACAGATCC 57.548 39.130 0.00 0.00 38.95 3.36
998 1203 4.040217 CCCACAATCCCAAGAAATCAACAA 59.960 41.667 0.00 0.00 0.00 2.83
1041 1246 1.081840 GCTTTGTGACTGCTTCGGC 60.082 57.895 0.00 0.00 42.19 5.54
1046 1251 1.014044 TGTGACTGCTTCGGCGATTC 61.014 55.000 11.76 6.16 45.37 2.52
1071 1276 2.361438 CACCTGTACGGAGAACTATCCC 59.639 54.545 2.31 0.00 35.82 3.85
1087 1292 0.820226 TCCCTCATGCTCTTCTCACG 59.180 55.000 0.00 0.00 0.00 4.35
1100 1305 1.153647 CTCACGCGTCCTTATGGCA 60.154 57.895 9.86 0.00 0.00 4.92
1103 1308 1.139989 CACGCGTCCTTATGGCATAG 58.860 55.000 9.86 2.56 0.00 2.23
1110 1315 3.490348 GTCCTTATGGCATAGGCATTGT 58.510 45.455 10.89 0.00 46.61 2.71
1126 1331 4.709886 GGCATTGTGGGGTTTATAAGACTT 59.290 41.667 0.00 0.00 0.00 3.01
1150 1355 5.750547 TCATTTCACTTACATCTCGATGCTC 59.249 40.000 6.81 0.00 42.39 4.26
1157 1363 6.479990 CACTTACATCTCGATGCTCCATTTTA 59.520 38.462 6.81 0.00 42.39 1.52
1159 1365 8.367911 ACTTACATCTCGATGCTCCATTTTATA 58.632 33.333 6.81 0.00 42.39 0.98
1160 1366 9.208022 CTTACATCTCGATGCTCCATTTTATAA 57.792 33.333 6.81 0.00 42.39 0.98
1161 1367 9.554395 TTACATCTCGATGCTCCATTTTATAAA 57.446 29.630 6.81 0.00 42.39 1.40
1162 1368 8.450578 ACATCTCGATGCTCCATTTTATAAAA 57.549 30.769 12.85 12.85 42.39 1.52
1163 1369 8.902806 ACATCTCGATGCTCCATTTTATAAAAA 58.097 29.630 14.35 0.00 42.39 1.94
1220 1426 1.272928 TGCCCCTGCATTACATTTGGA 60.273 47.619 0.00 0.00 44.23 3.53
1229 1435 2.645730 TTACATTTGGACGCATTGCC 57.354 45.000 2.41 0.00 0.00 4.52
1272 1479 9.224267 GTTCATCATGTATGTGCTTCCTTATAT 57.776 33.333 0.00 0.00 36.89 0.86
1281 1488 4.037690 GTGCTTCCTTATATTTTGCGCTG 58.962 43.478 9.73 0.00 0.00 5.18
1323 1536 4.165180 TGCCCATATCTTGTTGGCTAACTA 59.835 41.667 14.47 5.69 42.62 2.24
1363 1576 1.901591 CATGCATGGGACCCTGTATC 58.098 55.000 19.40 0.00 0.00 2.24
1442 1655 1.807226 GGGCGCAATACAACTTCCC 59.193 57.895 10.83 0.00 0.00 3.97
1556 1769 4.762289 ACATGTCCAAAGGTATCTCTCC 57.238 45.455 0.00 0.00 0.00 3.71
1557 1770 4.366267 ACATGTCCAAAGGTATCTCTCCT 58.634 43.478 0.00 0.00 36.81 3.69
1558 1771 4.785376 ACATGTCCAAAGGTATCTCTCCTT 59.215 41.667 0.00 0.00 45.84 3.36
1613 1826 6.270156 ACATTGATGTTCACAATACATGCA 57.730 33.333 0.00 0.00 37.90 3.96
2014 2288 8.798859 AAATGTAATGACTCATTAGTTCAGCT 57.201 30.769 11.15 0.00 37.06 4.24
2135 2439 9.906660 TTTTGTAAAGTTATGCTATCCACAAAG 57.093 29.630 0.00 0.00 35.51 2.77
2157 2461 3.617045 GCCTGATTACTGCAATGCCAAAA 60.617 43.478 1.53 0.00 0.00 2.44
2158 2462 4.178540 CCTGATTACTGCAATGCCAAAAG 58.821 43.478 1.53 0.00 0.00 2.27
2176 2480 4.734398 AAAGTGCACACAGGAATTCAAA 57.266 36.364 21.04 0.00 0.00 2.69
2215 2519 7.718525 TGTCCTAATAAACAAAAGAAACACCC 58.281 34.615 0.00 0.00 0.00 4.61
2216 2520 7.342284 TGTCCTAATAAACAAAAGAAACACCCA 59.658 33.333 0.00 0.00 0.00 4.51
2229 2533 4.893524 AGAAACACCCAGGAAAAGGTTTAG 59.106 41.667 0.00 0.00 32.72 1.85
2240 2544 4.510386 GGAAAAGGTTTAGTCCAGGGGAAT 60.510 45.833 0.00 0.00 31.38 3.01
2241 2545 4.759793 AAAGGTTTAGTCCAGGGGAATT 57.240 40.909 0.00 0.00 31.38 2.17
2243 2547 2.993863 AGGTTTAGTCCAGGGGAATTGT 59.006 45.455 0.00 0.00 31.38 2.71
2267 2571 4.689612 TGTACCTCAAATATGCTCCTCC 57.310 45.455 0.00 0.00 0.00 4.30
2292 2614 8.616076 CCTCCATTTCTTACTTGCTATACAAAG 58.384 37.037 0.00 0.00 37.96 2.77
2311 2633 2.043227 AGCATACTCCACTAGAAGGCC 58.957 52.381 0.00 0.00 0.00 5.19
2316 2638 2.769209 ACTCCACTAGAAGGCCATGAT 58.231 47.619 5.01 0.00 0.00 2.45
2319 2641 3.114606 TCCACTAGAAGGCCATGATTCA 58.885 45.455 5.01 0.00 0.00 2.57
2322 2645 4.891756 CCACTAGAAGGCCATGATTCAAAT 59.108 41.667 5.01 0.00 0.00 2.32
2348 2671 8.058667 TGTGCTCAAAGATCAAACAATATCAT 57.941 30.769 0.00 0.00 0.00 2.45
2352 2675 7.646922 GCTCAAAGATCAAACAATATCATGGTC 59.353 37.037 0.00 0.00 0.00 4.02
2366 2689 1.404391 CATGGTCCTCTGATTTGCAGC 59.596 52.381 0.00 0.00 44.52 5.25
2426 2749 1.257743 TGGGTTCCGTTCTCTCTGAG 58.742 55.000 0.00 0.00 0.00 3.35
2439 2762 6.263392 CGTTCTCTCTGAGGATATAAGACCAA 59.737 42.308 4.59 0.00 0.00 3.67
2496 2819 6.575083 ATCTTTCGATCTTTATCACACACG 57.425 37.500 0.00 0.00 31.93 4.49
2514 2837 2.079158 ACGTTGTCAGCTGATTCCATG 58.921 47.619 21.47 11.65 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 4.699522 GGGACTGGGTCACACGCC 62.700 72.222 0.14 0.00 35.79 5.68
39 40 4.373116 CCGGGACTGGGTCACACG 62.373 72.222 0.00 0.00 35.39 4.49
40 41 1.262640 ATACCGGGACTGGGTCACAC 61.263 60.000 6.32 0.00 35.39 3.82
41 42 1.079621 ATACCGGGACTGGGTCACA 59.920 57.895 6.32 0.00 35.39 3.58
42 43 1.262640 ACATACCGGGACTGGGTCAC 61.263 60.000 6.32 0.00 38.99 3.67
43 44 1.079621 ACATACCGGGACTGGGTCA 59.920 57.895 6.32 0.00 38.99 4.02
44 45 1.520666 CACATACCGGGACTGGGTC 59.479 63.158 6.32 0.00 38.99 4.46
45 46 1.993391 CCACATACCGGGACTGGGT 60.993 63.158 6.32 0.00 41.62 4.51
46 47 2.908015 CCACATACCGGGACTGGG 59.092 66.667 6.32 0.13 0.00 4.45
47 48 1.046472 TAGCCACATACCGGGACTGG 61.046 60.000 6.32 7.19 0.00 4.00
48 49 0.389391 CTAGCCACATACCGGGACTG 59.611 60.000 6.32 2.05 0.00 3.51
49 50 0.759436 CCTAGCCACATACCGGGACT 60.759 60.000 6.32 0.00 0.00 3.85
50 51 0.757935 TCCTAGCCACATACCGGGAC 60.758 60.000 6.32 0.00 0.00 4.46
51 52 0.190069 ATCCTAGCCACATACCGGGA 59.810 55.000 6.32 0.00 0.00 5.14
52 53 0.321671 CATCCTAGCCACATACCGGG 59.678 60.000 6.32 0.00 0.00 5.73
53 54 0.321671 CCATCCTAGCCACATACCGG 59.678 60.000 0.00 0.00 0.00 5.28
54 55 0.321671 CCCATCCTAGCCACATACCG 59.678 60.000 0.00 0.00 0.00 4.02
55 56 0.693049 CCCCATCCTAGCCACATACC 59.307 60.000 0.00 0.00 0.00 2.73
56 57 0.036875 GCCCCATCCTAGCCACATAC 59.963 60.000 0.00 0.00 0.00 2.39
57 58 0.401250 TGCCCCATCCTAGCCACATA 60.401 55.000 0.00 0.00 0.00 2.29
58 59 1.070127 ATGCCCCATCCTAGCCACAT 61.070 55.000 0.00 0.00 0.00 3.21
59 60 1.697394 ATGCCCCATCCTAGCCACA 60.697 57.895 0.00 0.00 0.00 4.17
60 61 1.073897 GATGCCCCATCCTAGCCAC 59.926 63.158 0.00 0.00 35.07 5.01
61 62 3.580084 GATGCCCCATCCTAGCCA 58.420 61.111 0.00 0.00 35.07 4.75
68 69 2.987547 CATGCCGGATGCCCCATC 60.988 66.667 5.05 0.00 39.87 3.51
69 70 3.500949 TCATGCCGGATGCCCCAT 61.501 61.111 5.05 0.00 40.16 4.00
70 71 4.193893 CTCATGCCGGATGCCCCA 62.194 66.667 5.05 0.00 40.16 4.96
71 72 3.201707 ATCTCATGCCGGATGCCCC 62.202 63.158 5.05 0.00 40.16 5.80
72 73 1.970114 CATCTCATGCCGGATGCCC 60.970 63.158 5.05 0.00 40.16 5.36
73 74 0.820891 AACATCTCATGCCGGATGCC 60.821 55.000 5.05 0.00 41.93 4.40
74 75 1.802960 CTAACATCTCATGCCGGATGC 59.197 52.381 5.05 0.00 41.93 3.91
75 76 2.037641 TCCTAACATCTCATGCCGGATG 59.962 50.000 5.05 6.59 43.30 3.51
76 77 2.329267 TCCTAACATCTCATGCCGGAT 58.671 47.619 5.05 0.00 0.00 4.18
77 78 1.788229 TCCTAACATCTCATGCCGGA 58.212 50.000 5.05 0.00 0.00 5.14
78 79 2.847327 ATCCTAACATCTCATGCCGG 57.153 50.000 0.00 0.00 0.00 6.13
79 80 3.251729 CCAAATCCTAACATCTCATGCCG 59.748 47.826 0.00 0.00 0.00 5.69
80 81 4.037208 CACCAAATCCTAACATCTCATGCC 59.963 45.833 0.00 0.00 0.00 4.40
81 82 4.498682 GCACCAAATCCTAACATCTCATGC 60.499 45.833 0.00 0.00 0.00 4.06
82 83 4.260907 CGCACCAAATCCTAACATCTCATG 60.261 45.833 0.00 0.00 0.00 3.07
83 84 3.879295 CGCACCAAATCCTAACATCTCAT 59.121 43.478 0.00 0.00 0.00 2.90
84 85 3.055458 TCGCACCAAATCCTAACATCTCA 60.055 43.478 0.00 0.00 0.00 3.27
85 86 3.309954 GTCGCACCAAATCCTAACATCTC 59.690 47.826 0.00 0.00 0.00 2.75
86 87 3.270877 GTCGCACCAAATCCTAACATCT 58.729 45.455 0.00 0.00 0.00 2.90
87 88 2.030457 CGTCGCACCAAATCCTAACATC 59.970 50.000 0.00 0.00 0.00 3.06
88 89 2.006888 CGTCGCACCAAATCCTAACAT 58.993 47.619 0.00 0.00 0.00 2.71
89 90 1.270412 ACGTCGCACCAAATCCTAACA 60.270 47.619 0.00 0.00 0.00 2.41
90 91 1.392510 GACGTCGCACCAAATCCTAAC 59.607 52.381 0.00 0.00 0.00 2.34
91 92 1.717194 GACGTCGCACCAAATCCTAA 58.283 50.000 0.00 0.00 0.00 2.69
92 93 0.457166 CGACGTCGCACCAAATCCTA 60.457 55.000 26.59 0.00 0.00 2.94
93 94 1.736645 CGACGTCGCACCAAATCCT 60.737 57.895 26.59 0.00 0.00 3.24
94 95 2.736682 CCGACGTCGCACCAAATCC 61.737 63.158 31.73 0.00 38.18 3.01
95 96 1.562575 AACCGACGTCGCACCAAATC 61.563 55.000 31.73 0.00 38.18 2.17
96 97 1.161563 AAACCGACGTCGCACCAAAT 61.162 50.000 31.73 10.22 38.18 2.32
97 98 1.814586 AAACCGACGTCGCACCAAA 60.815 52.632 31.73 0.00 38.18 3.28
98 99 2.202905 AAACCGACGTCGCACCAA 60.203 55.556 31.73 0.00 38.18 3.67
99 100 2.962786 CAAACCGACGTCGCACCA 60.963 61.111 31.73 0.00 38.18 4.17
100 101 3.708734 CCAAACCGACGTCGCACC 61.709 66.667 31.73 0.00 38.18 5.01
101 102 1.010419 ATACCAAACCGACGTCGCAC 61.010 55.000 31.73 0.00 38.18 5.34
102 103 0.319727 AATACCAAACCGACGTCGCA 60.320 50.000 31.73 10.32 38.18 5.10
103 104 1.585214 CTAATACCAAACCGACGTCGC 59.415 52.381 31.73 0.00 38.18 5.19
104 105 2.187707 CCTAATACCAAACCGACGTCG 58.812 52.381 30.33 30.33 39.44 5.12
105 106 1.929169 GCCTAATACCAAACCGACGTC 59.071 52.381 5.18 5.18 0.00 4.34
106 107 1.551883 AGCCTAATACCAAACCGACGT 59.448 47.619 0.00 0.00 0.00 4.34
107 108 2.199236 GAGCCTAATACCAAACCGACG 58.801 52.381 0.00 0.00 0.00 5.12
108 109 2.199236 CGAGCCTAATACCAAACCGAC 58.801 52.381 0.00 0.00 0.00 4.79
109 110 1.137479 CCGAGCCTAATACCAAACCGA 59.863 52.381 0.00 0.00 0.00 4.69
110 111 1.137479 TCCGAGCCTAATACCAAACCG 59.863 52.381 0.00 0.00 0.00 4.44
111 112 2.093341 TGTCCGAGCCTAATACCAAACC 60.093 50.000 0.00 0.00 0.00 3.27
112 113 3.255969 TGTCCGAGCCTAATACCAAAC 57.744 47.619 0.00 0.00 0.00 2.93
113 114 4.448210 GAATGTCCGAGCCTAATACCAAA 58.552 43.478 0.00 0.00 0.00 3.28
114 115 3.491964 CGAATGTCCGAGCCTAATACCAA 60.492 47.826 0.00 0.00 0.00 3.67
115 116 2.035449 CGAATGTCCGAGCCTAATACCA 59.965 50.000 0.00 0.00 0.00 3.25
116 117 2.609737 CCGAATGTCCGAGCCTAATACC 60.610 54.545 0.00 0.00 0.00 2.73
117 118 2.673833 CCGAATGTCCGAGCCTAATAC 58.326 52.381 0.00 0.00 0.00 1.89
118 119 1.000506 GCCGAATGTCCGAGCCTAATA 59.999 52.381 0.00 0.00 0.00 0.98
119 120 0.249911 GCCGAATGTCCGAGCCTAAT 60.250 55.000 0.00 0.00 0.00 1.73
120 121 1.143183 GCCGAATGTCCGAGCCTAA 59.857 57.895 0.00 0.00 0.00 2.69
121 122 2.055633 TGCCGAATGTCCGAGCCTA 61.056 57.895 0.00 0.00 0.00 3.93
122 123 3.390521 TGCCGAATGTCCGAGCCT 61.391 61.111 0.00 0.00 0.00 4.58
123 124 3.195698 GTGCCGAATGTCCGAGCC 61.196 66.667 0.00 0.00 0.00 4.70
124 125 3.195698 GGTGCCGAATGTCCGAGC 61.196 66.667 0.00 0.00 0.00 5.03
125 126 2.100631 GTGGTGCCGAATGTCCGAG 61.101 63.158 0.00 0.00 0.00 4.63
126 127 2.047655 GTGGTGCCGAATGTCCGA 60.048 61.111 0.00 0.00 0.00 4.55
127 128 2.047274 AGTGGTGCCGAATGTCCG 60.047 61.111 0.00 0.00 0.00 4.79
128 129 2.690778 GCAGTGGTGCCGAATGTCC 61.691 63.158 0.00 0.00 44.72 4.02
129 130 2.870372 GCAGTGGTGCCGAATGTC 59.130 61.111 0.00 0.00 44.72 3.06
138 139 1.679977 CCCCCTTGATGCAGTGGTG 60.680 63.158 0.00 0.00 0.00 4.17
139 140 0.844661 TACCCCCTTGATGCAGTGGT 60.845 55.000 0.00 0.00 0.00 4.16
140 141 0.107017 CTACCCCCTTGATGCAGTGG 60.107 60.000 0.00 0.00 0.00 4.00
141 142 0.107017 CCTACCCCCTTGATGCAGTG 60.107 60.000 0.00 0.00 0.00 3.66
142 143 0.253160 TCCTACCCCCTTGATGCAGT 60.253 55.000 0.00 0.00 0.00 4.40
143 144 0.471617 CTCCTACCCCCTTGATGCAG 59.528 60.000 0.00 0.00 0.00 4.41
144 145 0.253160 ACTCCTACCCCCTTGATGCA 60.253 55.000 0.00 0.00 0.00 3.96
145 146 1.694696 CTACTCCTACCCCCTTGATGC 59.305 57.143 0.00 0.00 0.00 3.91
146 147 1.694696 GCTACTCCTACCCCCTTGATG 59.305 57.143 0.00 0.00 0.00 3.07
147 148 1.758123 CGCTACTCCTACCCCCTTGAT 60.758 57.143 0.00 0.00 0.00 2.57
148 149 0.396695 CGCTACTCCTACCCCCTTGA 60.397 60.000 0.00 0.00 0.00 3.02
149 150 0.396695 TCGCTACTCCTACCCCCTTG 60.397 60.000 0.00 0.00 0.00 3.61
150 151 0.396835 GTCGCTACTCCTACCCCCTT 60.397 60.000 0.00 0.00 0.00 3.95
151 152 1.229643 GTCGCTACTCCTACCCCCT 59.770 63.158 0.00 0.00 0.00 4.79
152 153 1.076485 TGTCGCTACTCCTACCCCC 60.076 63.158 0.00 0.00 0.00 5.40
153 154 0.106819 TCTGTCGCTACTCCTACCCC 60.107 60.000 0.00 0.00 0.00 4.95
154 155 1.609555 CATCTGTCGCTACTCCTACCC 59.390 57.143 0.00 0.00 0.00 3.69
155 156 2.299521 ACATCTGTCGCTACTCCTACC 58.700 52.381 0.00 0.00 0.00 3.18
156 157 3.696898 CAACATCTGTCGCTACTCCTAC 58.303 50.000 0.00 0.00 0.00 3.18
157 158 2.099263 GCAACATCTGTCGCTACTCCTA 59.901 50.000 0.00 0.00 0.00 2.94
158 159 1.134965 GCAACATCTGTCGCTACTCCT 60.135 52.381 0.00 0.00 0.00 3.69
159 160 1.281899 GCAACATCTGTCGCTACTCC 58.718 55.000 0.00 0.00 0.00 3.85
160 161 1.134965 AGGCAACATCTGTCGCTACTC 60.135 52.381 0.00 0.00 41.41 2.59
161 162 0.898320 AGGCAACATCTGTCGCTACT 59.102 50.000 0.00 0.00 41.41 2.57
162 163 2.099263 TCTAGGCAACATCTGTCGCTAC 59.901 50.000 0.00 0.00 41.41 3.58
163 164 2.375146 TCTAGGCAACATCTGTCGCTA 58.625 47.619 0.00 0.00 41.41 4.26
164 165 1.186200 TCTAGGCAACATCTGTCGCT 58.814 50.000 0.00 0.00 41.41 4.93
165 166 1.863454 CATCTAGGCAACATCTGTCGC 59.137 52.381 0.00 0.00 41.41 5.19
166 167 2.159043 ACCATCTAGGCAACATCTGTCG 60.159 50.000 0.00 0.00 43.14 4.35
167 168 3.201290 CACCATCTAGGCAACATCTGTC 58.799 50.000 0.00 0.00 43.14 3.51
168 169 2.092753 CCACCATCTAGGCAACATCTGT 60.093 50.000 0.00 0.00 43.14 3.41
169 170 2.569059 CCACCATCTAGGCAACATCTG 58.431 52.381 0.00 0.00 43.14 2.90
178 179 0.471617 CCCTGAAGCCACCATCTAGG 59.528 60.000 0.00 0.00 45.67 3.02
179 180 1.207791 ACCCTGAAGCCACCATCTAG 58.792 55.000 0.00 0.00 0.00 2.43
180 181 1.668826 AACCCTGAAGCCACCATCTA 58.331 50.000 0.00 0.00 0.00 1.98
181 182 1.282157 GTAACCCTGAAGCCACCATCT 59.718 52.381 0.00 0.00 0.00 2.90
182 183 1.282157 AGTAACCCTGAAGCCACCATC 59.718 52.381 0.00 0.00 0.00 3.51
183 184 1.004745 CAGTAACCCTGAAGCCACCAT 59.995 52.381 0.00 0.00 44.49 3.55
184 185 0.400213 CAGTAACCCTGAAGCCACCA 59.600 55.000 0.00 0.00 44.49 4.17
185 186 3.249687 CAGTAACCCTGAAGCCACC 57.750 57.895 0.00 0.00 44.49 4.61
194 195 9.847224 CCTACAAAATAATACATCAGTAACCCT 57.153 33.333 0.00 0.00 33.13 4.34
195 196 9.623000 ACCTACAAAATAATACATCAGTAACCC 57.377 33.333 0.00 0.00 33.13 4.11
225 226 9.810545 GGCCACTTTATTAATTATTAAGCACAA 57.189 29.630 0.00 0.00 0.00 3.33
226 227 8.132362 CGGCCACTTTATTAATTATTAAGCACA 58.868 33.333 2.24 0.00 0.00 4.57
227 228 8.132995 ACGGCCACTTTATTAATTATTAAGCAC 58.867 33.333 2.24 0.00 0.00 4.40
228 229 8.228035 ACGGCCACTTTATTAATTATTAAGCA 57.772 30.769 2.24 0.00 0.00 3.91
232 233 9.286170 TGCATACGGCCACTTTATTAATTATTA 57.714 29.630 2.24 0.00 43.89 0.98
233 234 8.172352 TGCATACGGCCACTTTATTAATTATT 57.828 30.769 2.24 0.00 43.89 1.40
234 235 7.753309 TGCATACGGCCACTTTATTAATTAT 57.247 32.000 2.24 0.00 43.89 1.28
235 236 7.360522 CGATGCATACGGCCACTTTATTAATTA 60.361 37.037 2.24 0.00 43.89 1.40
236 237 6.567701 CGATGCATACGGCCACTTTATTAATT 60.568 38.462 2.24 0.00 43.89 1.40
237 238 5.106712 CGATGCATACGGCCACTTTATTAAT 60.107 40.000 2.24 0.00 43.89 1.40
238 239 4.212425 CGATGCATACGGCCACTTTATTAA 59.788 41.667 2.24 0.00 43.89 1.40
239 240 3.743911 CGATGCATACGGCCACTTTATTA 59.256 43.478 2.24 0.00 43.89 0.98
240 241 2.548057 CGATGCATACGGCCACTTTATT 59.452 45.455 2.24 0.00 43.89 1.40
241 242 2.143122 CGATGCATACGGCCACTTTAT 58.857 47.619 2.24 0.00 43.89 1.40
242 243 1.134640 ACGATGCATACGGCCACTTTA 60.135 47.619 18.34 0.00 43.89 1.85
243 244 0.392461 ACGATGCATACGGCCACTTT 60.392 50.000 18.34 0.00 43.89 2.66
244 245 0.810031 GACGATGCATACGGCCACTT 60.810 55.000 18.34 0.00 43.89 3.16
245 246 1.227263 GACGATGCATACGGCCACT 60.227 57.895 18.34 0.00 43.89 4.00
246 247 3.319904 GACGATGCATACGGCCAC 58.680 61.111 18.34 7.20 43.89 5.01
249 250 0.319900 ATCTGGACGATGCATACGGC 60.320 55.000 18.34 16.22 45.13 5.68
250 251 1.422388 CATCTGGACGATGCATACGG 58.578 55.000 18.34 6.85 42.75 4.02
258 259 1.445095 GCCTCTGCATCTGGACGAT 59.555 57.895 0.00 0.00 37.47 3.73
259 260 2.725312 GGCCTCTGCATCTGGACGA 61.725 63.158 0.00 0.00 40.13 4.20
260 261 2.202987 GGCCTCTGCATCTGGACG 60.203 66.667 0.00 0.00 40.13 4.79
261 262 2.202987 CGGCCTCTGCATCTGGAC 60.203 66.667 0.00 0.35 40.13 4.02
262 263 3.473647 CCGGCCTCTGCATCTGGA 61.474 66.667 0.00 0.00 40.13 3.86
263 264 4.559063 CCCGGCCTCTGCATCTGG 62.559 72.222 0.00 0.00 40.13 3.86
264 265 4.559063 CCCCGGCCTCTGCATCTG 62.559 72.222 0.00 0.00 40.13 2.90
266 267 4.864334 CACCCCGGCCTCTGCATC 62.864 72.222 0.00 0.00 40.13 3.91
270 271 4.864334 GATGCACCCCGGCCTCTG 62.864 72.222 0.00 0.00 0.00 3.35
276 277 2.499303 AAAAGGAGGATGCACCCCGG 62.499 60.000 0.00 0.00 40.05 5.73
277 278 1.000896 AAAAGGAGGATGCACCCCG 60.001 57.895 0.00 0.00 40.05 5.73
278 279 0.332972 AGAAAAGGAGGATGCACCCC 59.667 55.000 0.00 0.00 40.05 4.95
279 280 3.366052 TTAGAAAAGGAGGATGCACCC 57.634 47.619 0.00 0.00 40.05 4.61
280 281 5.722021 TTTTTAGAAAAGGAGGATGCACC 57.278 39.130 0.00 0.00 39.35 5.01
422 423 3.378742 TCATCGGCTTGTTCTCTCTCTAC 59.621 47.826 0.00 0.00 0.00 2.59
475 478 4.178540 GCTCACCATGTTGATTGGAATTG 58.821 43.478 0.00 0.00 37.69 2.32
500 503 9.206870 CTTAATTCATTGTTTGGCAAGTAACAT 57.793 29.630 0.00 0.00 40.86 2.71
529 532 9.362151 TGGTACAGTTGATCCTTTTTCTTATTT 57.638 29.630 0.00 0.00 0.00 1.40
530 533 8.793592 GTGGTACAGTTGATCCTTTTTCTTATT 58.206 33.333 0.00 0.00 41.80 1.40
531 534 7.393515 GGTGGTACAGTTGATCCTTTTTCTTAT 59.606 37.037 0.00 0.00 41.80 1.73
532 535 6.713450 GGTGGTACAGTTGATCCTTTTTCTTA 59.287 38.462 0.00 0.00 41.80 2.10
533 536 5.535030 GGTGGTACAGTTGATCCTTTTTCTT 59.465 40.000 0.00 0.00 41.80 2.52
541 544 4.023193 CAGTTTTGGTGGTACAGTTGATCC 60.023 45.833 0.00 0.00 41.80 3.36
581 584 2.730090 CGATCAGCATTTGACAAGTGGC 60.730 50.000 12.08 6.31 38.99 5.01
707 710 7.308049 GGTTTTCTCCTTCTACTTGCACTTAAG 60.308 40.741 0.00 0.00 0.00 1.85
730 733 5.048434 CACCATTTTTGTTGTTTTGTGGGTT 60.048 36.000 0.00 0.00 0.00 4.11
754 757 3.827008 TCTCATAGTGGATTCCAGTGC 57.173 47.619 21.17 3.64 37.77 4.40
789 993 4.158394 GTGCTTTCTCTTATCAATGCCCAA 59.842 41.667 0.00 0.00 0.00 4.12
814 1018 2.916716 GCGCACAATATTTGTTGTCTGG 59.083 45.455 0.30 0.00 43.23 3.86
847 1051 5.352569 CCTTTGTTTACAGGTATCTGCTCAG 59.647 44.000 1.90 0.00 44.59 3.35
961 1166 3.524095 TTGTGGGATCTGTGGAATGTT 57.476 42.857 0.00 0.00 0.00 2.71
963 1168 2.954318 GGATTGTGGGATCTGTGGAATG 59.046 50.000 0.00 0.00 0.00 2.67
975 1180 3.577848 TGTTGATTTCTTGGGATTGTGGG 59.422 43.478 0.00 0.00 0.00 4.61
976 1181 4.870123 TGTTGATTTCTTGGGATTGTGG 57.130 40.909 0.00 0.00 0.00 4.17
998 1203 0.850100 TGACCACTTCCCCAACATGT 59.150 50.000 0.00 0.00 0.00 3.21
1041 1246 1.876714 CGTACAGGTGCCGGAATCG 60.877 63.158 5.05 0.00 0.00 3.34
1046 1251 2.642254 TTCTCCGTACAGGTGCCGG 61.642 63.158 0.00 0.00 43.03 6.13
1071 1276 0.457509 ACGCGTGAGAAGAGCATGAG 60.458 55.000 12.93 0.00 0.00 2.90
1087 1292 0.250295 TGCCTATGCCATAAGGACGC 60.250 55.000 4.88 0.00 36.89 5.19
1100 1305 6.068670 GTCTTATAAACCCCACAATGCCTAT 58.931 40.000 0.00 0.00 0.00 2.57
1103 1308 4.278310 AGTCTTATAAACCCCACAATGCC 58.722 43.478 0.00 0.00 0.00 4.40
1110 1315 7.466804 AGTGAAATGAAGTCTTATAAACCCCA 58.533 34.615 0.00 0.00 0.00 4.96
1126 1331 5.664457 AGCATCGAGATGTAAGTGAAATGA 58.336 37.500 13.79 0.00 40.80 2.57
1163 1369 5.861787 GCAACCTGTAACATTAGCGATTTTT 59.138 36.000 0.00 0.00 0.00 1.94
1164 1370 5.183140 AGCAACCTGTAACATTAGCGATTTT 59.817 36.000 0.00 0.00 0.00 1.82
1165 1371 4.700213 AGCAACCTGTAACATTAGCGATTT 59.300 37.500 0.00 0.00 0.00 2.17
1166 1372 4.261801 AGCAACCTGTAACATTAGCGATT 58.738 39.130 0.00 0.00 0.00 3.34
1167 1373 3.873910 AGCAACCTGTAACATTAGCGAT 58.126 40.909 0.00 0.00 0.00 4.58
1168 1374 3.328382 AGCAACCTGTAACATTAGCGA 57.672 42.857 0.00 0.00 0.00 4.93
1169 1375 3.435327 TCAAGCAACCTGTAACATTAGCG 59.565 43.478 0.00 0.00 0.00 4.26
1179 1385 1.750778 CCAACAAGTCAAGCAACCTGT 59.249 47.619 0.00 0.00 0.00 4.00
1220 1426 2.281484 ACAACCTCGGCAATGCGT 60.281 55.556 0.00 0.00 0.00 5.24
1229 1435 2.095978 AACCTCCGTCCACAACCTCG 62.096 60.000 0.00 0.00 0.00 4.63
1272 1479 1.876497 GCTTGATCCCCAGCGCAAAA 61.876 55.000 11.47 0.00 0.00 2.44
1305 1518 6.069615 ACAAGGGTAGTTAGCCAACAAGATAT 60.070 38.462 9.81 0.00 46.03 1.63
1306 1519 5.249852 ACAAGGGTAGTTAGCCAACAAGATA 59.750 40.000 9.81 0.00 46.03 1.98
1323 1536 0.178953 AGCATGCTGGAAACAAGGGT 60.179 50.000 21.98 0.00 42.06 4.34
1363 1576 1.742750 GCCTACGGACCCTAGCAAAAG 60.743 57.143 0.00 0.00 0.00 2.27
1428 1641 2.092323 GACCCTGGGAAGTTGTATTGC 58.908 52.381 22.23 0.00 0.00 3.56
1654 1868 1.394917 CTTTCCGTCATCTTTCCTGCG 59.605 52.381 0.00 0.00 0.00 5.18
1994 2260 7.123397 ACTGAGAGCTGAACTAATGAGTCATTA 59.877 37.037 21.50 21.50 35.54 1.90
2044 2318 9.202273 GATGATGTCTTATCCTTAAGTAAGCAG 57.798 37.037 0.97 0.00 36.87 4.24
2129 2433 3.921119 TTGCAGTAATCAGGCTTTGTG 57.079 42.857 0.00 0.00 0.00 3.33
2135 2439 1.105457 TGGCATTGCAGTAATCAGGC 58.895 50.000 11.39 0.00 0.00 4.85
2157 2461 7.176515 TGTTATATTTGAATTCCTGTGTGCACT 59.823 33.333 19.41 0.00 0.00 4.40
2158 2462 7.312154 TGTTATATTTGAATTCCTGTGTGCAC 58.688 34.615 10.75 10.75 0.00 4.57
2215 2519 3.421844 CCCTGGACTAAACCTTTTCCTG 58.578 50.000 0.00 0.00 0.00 3.86
2216 2520 2.378886 CCCCTGGACTAAACCTTTTCCT 59.621 50.000 0.00 0.00 0.00 3.36
2229 2533 4.079958 AGGTACAATACAATTCCCCTGGAC 60.080 45.833 0.00 0.00 0.00 4.02
2240 2544 7.573710 AGGAGCATATTTGAGGTACAATACAA 58.426 34.615 0.00 0.00 38.36 2.41
2241 2545 7.136822 AGGAGCATATTTGAGGTACAATACA 57.863 36.000 0.00 0.00 38.36 2.29
2243 2547 6.558775 AGGAGGAGCATATTTGAGGTACAATA 59.441 38.462 0.00 0.00 38.36 1.90
2267 2571 8.125448 GCTTTGTATAGCAAGTAAGAAATGGAG 58.875 37.037 0.00 0.00 40.89 3.86
2292 2614 1.762957 TGGCCTTCTAGTGGAGTATGC 59.237 52.381 3.32 0.00 0.00 3.14
2303 2625 5.394443 GCACAATTTGAATCATGGCCTTCTA 60.394 40.000 3.32 0.00 0.00 2.10
2311 2633 7.544217 TGATCTTTGAGCACAATTTGAATCATG 59.456 33.333 2.79 0.00 35.85 3.07
2316 2638 7.040494 TGTTTGATCTTTGAGCACAATTTGAA 58.960 30.769 2.79 0.00 35.85 2.69
2319 2641 9.715121 ATATTGTTTGATCTTTGAGCACAATTT 57.285 25.926 0.00 0.00 31.01 1.82
2322 2645 7.884257 TGATATTGTTTGATCTTTGAGCACAA 58.116 30.769 0.00 0.00 0.00 3.33
2348 2671 0.694771 AGCTGCAAATCAGAGGACCA 59.305 50.000 1.02 0.00 45.72 4.02
2352 2675 3.257469 TGACTAGCTGCAAATCAGAGG 57.743 47.619 1.02 0.00 45.72 3.69
2400 2723 0.400213 AGAACGGAACCCATGAGCAA 59.600 50.000 0.00 0.00 0.00 3.91
2496 2819 4.479619 GAAACATGGAATCAGCTGACAAC 58.520 43.478 20.97 12.31 0.00 3.32
2514 2837 0.106967 GCATGGAGGAGGGAGGAAAC 60.107 60.000 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.