Multiple sequence alignment - TraesCS2A01G117700

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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 TraesCS2A01G117700 chr2A 100.000 1365 0 0 1 1365 67982793 67981429 0.000000e+00 2521
1 TraesCS2A01G117700 chr2A 100.000 1212 0 0 2018 3229 67980776 67979565 0.000000e+00 2239
2 TraesCS2A01G117700 chr2A 94.257 296 6 4 2934 3229 67714078 67713794 2.960000e-120 442
3 TraesCS2A01G117700 chr2D 93.201 1206 58 6 2038 3229 66868344 66869539 0.000000e+00 1751
4 TraesCS2A01G117700 chr2D 91.168 1053 59 14 295 1338 66866664 66867691 0.000000e+00 1399
5 TraesCS2A01G117700 chr2D 79.825 228 38 5 1139 1365 66867456 66867676 3.330000e-35 159
6 TraesCS2A01G117700 chr2D 79.781 183 34 3 1116 1296 66867510 66867691 2.610000e-26 130
7 TraesCS2A01G117700 chr2B 89.901 1218 81 22 2028 3229 104580731 104579540 0.000000e+00 1530
8 TraesCS2A01G117700 chr2B 92.128 1029 45 8 350 1365 104582300 104581295 0.000000e+00 1419
9 TraesCS2A01G117700 chr4A 88.995 418 34 9 2630 3045 509595716 509595309 1.030000e-139 507


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 TraesCS2A01G117700 chr2A 67979565 67982793 3228 True 2380.00 2521 100.00000 1 3229 2 chr2A.!!$R2 3228
1 TraesCS2A01G117700 chr2D 66866664 66869539 2875 False 859.75 1751 85.99375 295 3229 4 chr2D.!!$F1 2934
2 TraesCS2A01G117700 chr2B 104579540 104582300 2760 True 1474.50 1530 91.01450 350 3229 2 chr2B.!!$R1 2879

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
78 79 0.031994 GCAAAAAGCGCTTGGAGGAA 59.968 50.000 25.80 0.00 0.00 3.36 F
225 226 0.040942 CCCCATCCACCCATGAACAA 59.959 55.000 0.00 0.00 0.00 2.83 F
424 428 0.248377 AATCGTACTACGGCGCAGTC 60.248 55.000 18.55 7.74 42.81 3.51 F
435 439 0.807667 GGCGCAGTCGAGTTGATGAT 60.808 55.000 10.83 0.00 38.10 2.45 F
694 713 1.137086 CTCATTACTGGTACCGCTGCT 59.863 52.381 7.57 0.00 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1249 1276 0.542702 ATGGGTTCAGGTTTGGGCAG 60.543 55.000 0.00 0.00 0.00 4.85 R
2042 2069 2.040544 CGGTTCTGGCTTCGGCATT 61.041 57.895 0.00 0.00 43.96 3.56 R
2109 2615 2.562738 GCTCTGGTTTAGGCAATGGTTT 59.437 45.455 0.00 0.00 0.00 3.27 R
2210 2746 3.686241 CACATCAATTGTCAGTCATCGGT 59.314 43.478 5.13 0.00 36.00 4.69 R
2615 3160 1.213094 AAAACACACGCTCGAGACGG 61.213 55.000 25.38 18.49 34.00 4.79 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
25 26 3.726517 CGCAAGCCCCACACGAAG 61.727 66.667 0.00 0.00 0.00 3.79
26 27 3.365265 GCAAGCCCCACACGAAGG 61.365 66.667 0.00 0.00 0.00 3.46
27 28 2.429930 CAAGCCCCACACGAAGGA 59.570 61.111 0.00 0.00 0.00 3.36
28 29 1.672356 CAAGCCCCACACGAAGGAG 60.672 63.158 0.00 0.00 0.00 3.69
29 30 1.841556 AAGCCCCACACGAAGGAGA 60.842 57.895 0.00 0.00 0.00 3.71
30 31 1.415672 AAGCCCCACACGAAGGAGAA 61.416 55.000 0.00 0.00 0.00 2.87
31 32 1.072505 GCCCCACACGAAGGAGAAA 59.927 57.895 0.00 0.00 0.00 2.52
32 33 0.536460 GCCCCACACGAAGGAGAAAA 60.536 55.000 0.00 0.00 0.00 2.29
33 34 1.975660 CCCCACACGAAGGAGAAAAA 58.024 50.000 0.00 0.00 0.00 1.94
34 35 2.514803 CCCCACACGAAGGAGAAAAAT 58.485 47.619 0.00 0.00 0.00 1.82
35 36 2.228822 CCCCACACGAAGGAGAAAAATG 59.771 50.000 0.00 0.00 0.00 2.32
36 37 2.351738 CCCACACGAAGGAGAAAAATGC 60.352 50.000 0.00 0.00 0.00 3.56
37 38 2.293122 CCACACGAAGGAGAAAAATGCA 59.707 45.455 0.00 0.00 0.00 3.96
38 39 3.558505 CACACGAAGGAGAAAAATGCAG 58.441 45.455 0.00 0.00 0.00 4.41
39 40 2.030805 ACACGAAGGAGAAAAATGCAGC 60.031 45.455 0.00 0.00 0.00 5.25
40 41 2.030893 CACGAAGGAGAAAAATGCAGCA 60.031 45.455 0.00 0.00 0.00 4.41
41 42 2.622942 ACGAAGGAGAAAAATGCAGCAA 59.377 40.909 0.00 0.00 0.00 3.91
42 43 2.982470 CGAAGGAGAAAAATGCAGCAAC 59.018 45.455 0.00 0.00 0.00 4.17
43 44 3.550639 CGAAGGAGAAAAATGCAGCAACA 60.551 43.478 0.00 0.00 0.00 3.33
44 45 4.370917 GAAGGAGAAAAATGCAGCAACAA 58.629 39.130 0.00 0.00 0.00 2.83
45 46 4.405116 AGGAGAAAAATGCAGCAACAAA 57.595 36.364 0.00 0.00 0.00 2.83
46 47 4.374399 AGGAGAAAAATGCAGCAACAAAG 58.626 39.130 0.00 0.00 0.00 2.77
47 48 4.099881 AGGAGAAAAATGCAGCAACAAAGA 59.900 37.500 0.00 0.00 0.00 2.52
48 49 4.209911 GGAGAAAAATGCAGCAACAAAGAC 59.790 41.667 0.00 0.00 0.00 3.01
49 50 3.798337 AGAAAAATGCAGCAACAAAGACG 59.202 39.130 0.00 0.00 0.00 4.18
50 51 1.490621 AAATGCAGCAACAAAGACGC 58.509 45.000 0.00 0.00 0.00 5.19
51 52 0.670162 AATGCAGCAACAAAGACGCT 59.330 45.000 0.00 0.00 36.10 5.07
52 53 0.670162 ATGCAGCAACAAAGACGCTT 59.330 45.000 0.00 0.00 32.48 4.68
53 54 0.248580 TGCAGCAACAAAGACGCTTG 60.249 50.000 0.00 0.00 32.48 4.01
54 55 0.248621 GCAGCAACAAAGACGCTTGT 60.249 50.000 0.00 0.00 41.31 3.16
56 57 2.111756 CAGCAACAAAGACGCTTGTTC 58.888 47.619 7.64 4.68 45.51 3.18
57 58 1.742831 AGCAACAAAGACGCTTGTTCA 59.257 42.857 7.64 0.00 45.51 3.18
58 59 2.163412 AGCAACAAAGACGCTTGTTCAA 59.837 40.909 7.64 0.00 45.51 2.69
59 60 2.531508 GCAACAAAGACGCTTGTTCAAG 59.468 45.455 8.04 8.04 45.51 3.02
60 61 2.475200 ACAAAGACGCTTGTTCAAGC 57.525 45.000 22.68 22.68 36.05 4.01
61 62 1.742831 ACAAAGACGCTTGTTCAAGCA 59.257 42.857 28.69 0.00 45.75 3.91
62 63 2.163412 ACAAAGACGCTTGTTCAAGCAA 59.837 40.909 28.69 0.00 45.75 3.91
63 64 3.178267 CAAAGACGCTTGTTCAAGCAAA 58.822 40.909 28.69 0.00 45.75 3.68
64 65 3.502191 AAGACGCTTGTTCAAGCAAAA 57.498 38.095 28.69 0.00 45.75 2.44
65 66 3.502191 AGACGCTTGTTCAAGCAAAAA 57.498 38.095 28.69 0.00 45.75 1.94
66 67 3.438360 AGACGCTTGTTCAAGCAAAAAG 58.562 40.909 28.69 18.07 45.75 2.27
67 68 1.926510 ACGCTTGTTCAAGCAAAAAGC 59.073 42.857 28.69 11.41 45.75 3.51
76 77 4.250080 GCAAAAAGCGCTTGGAGG 57.750 55.556 25.80 14.61 0.00 4.30
77 78 1.659794 GCAAAAAGCGCTTGGAGGA 59.340 52.632 25.80 0.00 0.00 3.71
78 79 0.031994 GCAAAAAGCGCTTGGAGGAA 59.968 50.000 25.80 0.00 0.00 3.36
79 80 1.337167 GCAAAAAGCGCTTGGAGGAAT 60.337 47.619 25.80 2.25 0.00 3.01
80 81 2.094752 GCAAAAAGCGCTTGGAGGAATA 60.095 45.455 25.80 0.00 0.00 1.75
81 82 3.429410 GCAAAAAGCGCTTGGAGGAATAT 60.429 43.478 25.80 0.49 0.00 1.28
82 83 4.354587 CAAAAAGCGCTTGGAGGAATATC 58.645 43.478 25.80 0.00 0.00 1.63
83 84 3.281727 AAAGCGCTTGGAGGAATATCA 57.718 42.857 25.80 0.00 0.00 2.15
84 85 3.281727 AAGCGCTTGGAGGAATATCAA 57.718 42.857 24.40 0.00 0.00 2.57
85 86 2.565841 AGCGCTTGGAGGAATATCAAC 58.434 47.619 2.64 0.00 0.00 3.18
86 87 2.092968 AGCGCTTGGAGGAATATCAACA 60.093 45.455 2.64 0.00 0.00 3.33
87 88 2.682856 GCGCTTGGAGGAATATCAACAA 59.317 45.455 0.00 0.00 0.00 2.83
88 89 3.128589 GCGCTTGGAGGAATATCAACAAA 59.871 43.478 0.00 0.00 0.00 2.83
89 90 4.380444 GCGCTTGGAGGAATATCAACAAAA 60.380 41.667 0.00 0.00 0.00 2.44
90 91 5.335127 CGCTTGGAGGAATATCAACAAAAG 58.665 41.667 0.00 0.00 0.00 2.27
91 92 5.105063 GCTTGGAGGAATATCAACAAAAGC 58.895 41.667 0.00 0.00 0.00 3.51
92 93 5.336690 GCTTGGAGGAATATCAACAAAAGCA 60.337 40.000 0.00 0.00 37.01 3.91
93 94 6.662865 TTGGAGGAATATCAACAAAAGCAA 57.337 33.333 0.00 0.00 0.00 3.91
94 95 6.855763 TGGAGGAATATCAACAAAAGCAAT 57.144 33.333 0.00 0.00 0.00 3.56
95 96 7.243604 TGGAGGAATATCAACAAAAGCAATT 57.756 32.000 0.00 0.00 0.00 2.32
96 97 7.322664 TGGAGGAATATCAACAAAAGCAATTC 58.677 34.615 0.00 0.00 0.00 2.17
97 98 7.178983 TGGAGGAATATCAACAAAAGCAATTCT 59.821 33.333 0.00 0.00 0.00 2.40
98 99 7.490402 GGAGGAATATCAACAAAAGCAATTCTG 59.510 37.037 0.00 0.00 0.00 3.02
131 132 3.067755 CGTGCGTACGTGACTTTTAAG 57.932 47.619 18.32 0.00 44.99 1.85
132 133 2.468777 CGTGCGTACGTGACTTTTAAGT 59.531 45.455 18.32 0.00 44.99 2.24
133 134 3.061006 CGTGCGTACGTGACTTTTAAGTT 60.061 43.478 18.32 0.00 44.99 2.66
134 135 4.548726 CGTGCGTACGTGACTTTTAAGTTT 60.549 41.667 18.32 0.00 44.99 2.66
135 136 5.257864 GTGCGTACGTGACTTTTAAGTTTT 58.742 37.500 17.90 0.00 39.88 2.43
136 137 6.410038 GTGCGTACGTGACTTTTAAGTTTTA 58.590 36.000 17.90 0.00 39.88 1.52
137 138 6.899243 GTGCGTACGTGACTTTTAAGTTTTAA 59.101 34.615 17.90 0.00 39.88 1.52
138 139 6.899243 TGCGTACGTGACTTTTAAGTTTTAAC 59.101 34.615 17.90 0.00 39.88 2.01
139 140 6.899243 GCGTACGTGACTTTTAAGTTTTAACA 59.101 34.615 17.90 0.00 39.88 2.41
140 141 7.109259 GCGTACGTGACTTTTAAGTTTTAACAG 59.891 37.037 17.90 0.00 39.88 3.16
141 142 7.580165 CGTACGTGACTTTTAAGTTTTAACAGG 59.420 37.037 7.22 0.00 39.88 4.00
142 143 7.381766 ACGTGACTTTTAAGTTTTAACAGGT 57.618 32.000 0.00 0.00 39.88 4.00
143 144 7.466805 ACGTGACTTTTAAGTTTTAACAGGTC 58.533 34.615 0.00 0.00 39.88 3.85
144 145 7.119553 ACGTGACTTTTAAGTTTTAACAGGTCA 59.880 33.333 0.00 0.00 39.88 4.02
145 146 7.964011 CGTGACTTTTAAGTTTTAACAGGTCAA 59.036 33.333 0.00 0.00 39.88 3.18
146 147 9.797556 GTGACTTTTAAGTTTTAACAGGTCAAT 57.202 29.630 0.00 0.00 39.88 2.57
154 155 8.871686 AAGTTTTAACAGGTCAATCAATCAAC 57.128 30.769 0.00 0.00 0.00 3.18
155 156 7.433680 AGTTTTAACAGGTCAATCAATCAACC 58.566 34.615 0.00 0.00 0.00 3.77
156 157 5.621197 TTAACAGGTCAATCAATCAACCG 57.379 39.130 0.00 0.00 36.87 4.44
157 158 3.417069 ACAGGTCAATCAATCAACCGA 57.583 42.857 0.00 0.00 36.87 4.69
158 159 3.955471 ACAGGTCAATCAATCAACCGAT 58.045 40.909 0.00 0.00 36.87 4.18
159 160 3.941483 ACAGGTCAATCAATCAACCGATC 59.059 43.478 0.00 0.00 36.87 3.69
160 161 3.001634 CAGGTCAATCAATCAACCGATCG 59.998 47.826 8.51 8.51 36.87 3.69
161 162 3.118775 AGGTCAATCAATCAACCGATCGA 60.119 43.478 18.66 0.00 36.87 3.59
162 163 3.809832 GGTCAATCAATCAACCGATCGAT 59.190 43.478 18.66 0.00 25.70 3.59
163 164 4.084328 GGTCAATCAATCAACCGATCGATC 60.084 45.833 18.66 15.68 24.74 3.69
164 165 4.507756 GTCAATCAATCAACCGATCGATCA 59.492 41.667 24.40 5.53 24.74 2.92
165 166 5.006649 GTCAATCAATCAACCGATCGATCAA 59.993 40.000 24.40 5.22 24.74 2.57
166 167 5.759763 TCAATCAATCAACCGATCGATCAAT 59.240 36.000 24.40 9.28 24.74 2.57
167 168 6.928492 TCAATCAATCAACCGATCGATCAATA 59.072 34.615 24.40 5.88 24.74 1.90
168 169 6.712241 ATCAATCAACCGATCGATCAATAC 57.288 37.500 24.40 0.00 0.00 1.89
169 170 4.988540 TCAATCAACCGATCGATCAATACC 59.011 41.667 24.40 0.00 0.00 2.73
170 171 3.007979 TCAACCGATCGATCAATACCG 57.992 47.619 24.40 10.30 0.00 4.02
171 172 1.455786 CAACCGATCGATCAATACCGC 59.544 52.381 24.40 0.00 0.00 5.68
172 173 0.386858 ACCGATCGATCAATACCGCG 60.387 55.000 24.40 8.87 0.00 6.46
173 174 0.109919 CCGATCGATCAATACCGCGA 60.110 55.000 24.40 0.00 37.17 5.87
174 175 1.664874 CCGATCGATCAATACCGCGAA 60.665 52.381 24.40 0.00 36.28 4.70
175 176 1.382419 CGATCGATCAATACCGCGAAC 59.618 52.381 24.40 0.00 36.28 3.95
176 177 1.719780 GATCGATCAATACCGCGAACC 59.280 52.381 20.52 0.00 36.28 3.62
177 178 0.593008 TCGATCAATACCGCGAACCG 60.593 55.000 8.23 0.00 0.00 4.44
187 188 2.975799 GCGAACCGGACCAAGCAA 60.976 61.111 9.46 0.00 0.00 3.91
188 189 2.966309 GCGAACCGGACCAAGCAAG 61.966 63.158 9.46 0.00 0.00 4.01
189 190 2.954611 GAACCGGACCAAGCAAGC 59.045 61.111 9.46 0.00 0.00 4.01
190 191 2.966309 GAACCGGACCAAGCAAGCG 61.966 63.158 9.46 0.00 0.00 4.68
191 192 3.767630 AACCGGACCAAGCAAGCGT 62.768 57.895 9.46 0.00 0.00 5.07
192 193 3.423154 CCGGACCAAGCAAGCGTC 61.423 66.667 0.00 0.00 0.00 5.19
193 194 3.777925 CGGACCAAGCAAGCGTCG 61.778 66.667 0.00 0.00 0.00 5.12
194 195 3.423154 GGACCAAGCAAGCGTCGG 61.423 66.667 0.00 0.00 0.00 4.79
195 196 2.665185 GACCAAGCAAGCGTCGGT 60.665 61.111 0.00 0.00 0.00 4.69
196 197 2.665185 ACCAAGCAAGCGTCGGTC 60.665 61.111 0.00 0.00 0.00 4.79
197 198 3.777925 CCAAGCAAGCGTCGGTCG 61.778 66.667 0.00 0.00 43.12 4.79
198 199 3.777925 CAAGCAAGCGTCGGTCGG 61.778 66.667 0.00 0.00 40.26 4.79
220 221 4.900704 CGGCCCCATCCACCCATG 62.901 72.222 0.00 0.00 0.00 3.66
221 222 3.428664 GGCCCCATCCACCCATGA 61.429 66.667 0.00 0.00 0.00 3.07
222 223 2.689175 GCCCCATCCACCCATGAA 59.311 61.111 0.00 0.00 0.00 2.57
223 224 1.758122 GCCCCATCCACCCATGAAC 60.758 63.158 0.00 0.00 0.00 3.18
224 225 1.696686 CCCCATCCACCCATGAACA 59.303 57.895 0.00 0.00 0.00 3.18
225 226 0.040942 CCCCATCCACCCATGAACAA 59.959 55.000 0.00 0.00 0.00 2.83
226 227 1.343277 CCCCATCCACCCATGAACAAT 60.343 52.381 0.00 0.00 0.00 2.71
227 228 2.469952 CCCATCCACCCATGAACAATT 58.530 47.619 0.00 0.00 0.00 2.32
228 229 2.839425 CCCATCCACCCATGAACAATTT 59.161 45.455 0.00 0.00 0.00 1.82
229 230 3.118665 CCCATCCACCCATGAACAATTTC 60.119 47.826 0.00 0.00 0.00 2.17
230 231 3.514706 CCATCCACCCATGAACAATTTCA 59.485 43.478 0.00 0.00 45.93 2.69
231 232 4.020396 CCATCCACCCATGAACAATTTCAA 60.020 41.667 0.00 0.00 45.01 2.69
232 233 5.512749 CCATCCACCCATGAACAATTTCAAA 60.513 40.000 0.00 0.00 45.01 2.69
233 234 5.212532 TCCACCCATGAACAATTTCAAAG 57.787 39.130 0.00 0.00 45.01 2.77
234 235 3.747529 CCACCCATGAACAATTTCAAAGC 59.252 43.478 0.00 0.00 45.01 3.51
235 236 4.503643 CCACCCATGAACAATTTCAAAGCT 60.504 41.667 0.00 0.00 45.01 3.74
236 237 4.449743 CACCCATGAACAATTTCAAAGCTG 59.550 41.667 0.00 0.00 45.01 4.24
237 238 3.434299 CCCATGAACAATTTCAAAGCTGC 59.566 43.478 0.00 0.00 45.01 5.25
238 239 3.434299 CCATGAACAATTTCAAAGCTGCC 59.566 43.478 0.00 0.00 45.01 4.85
239 240 2.741612 TGAACAATTTCAAAGCTGCCG 58.258 42.857 0.00 0.00 38.87 5.69
240 241 2.360483 TGAACAATTTCAAAGCTGCCGA 59.640 40.909 0.00 0.00 38.87 5.54
241 242 3.005684 TGAACAATTTCAAAGCTGCCGAT 59.994 39.130 0.00 0.00 38.87 4.18
242 243 3.221964 ACAATTTCAAAGCTGCCGATC 57.778 42.857 0.00 0.00 0.00 3.69
243 244 2.094545 ACAATTTCAAAGCTGCCGATCC 60.095 45.455 0.00 0.00 0.00 3.36
244 245 1.838112 ATTTCAAAGCTGCCGATCCA 58.162 45.000 0.00 0.00 0.00 3.41
245 246 1.838112 TTTCAAAGCTGCCGATCCAT 58.162 45.000 0.00 0.00 0.00 3.41
246 247 1.097232 TTCAAAGCTGCCGATCCATG 58.903 50.000 0.00 0.00 0.00 3.66
247 248 0.749091 TCAAAGCTGCCGATCCATGG 60.749 55.000 4.97 4.97 0.00 3.66
254 255 2.814604 CCGATCCATGGCTCGACA 59.185 61.111 33.60 5.23 36.04 4.35
255 256 1.300465 CCGATCCATGGCTCGACAG 60.300 63.158 33.60 16.93 36.04 3.51
256 257 1.300465 CGATCCATGGCTCGACAGG 60.300 63.158 29.53 2.70 36.04 4.00
257 258 1.596477 GATCCATGGCTCGACAGGC 60.596 63.158 6.96 0.00 45.76 4.85
310 311 2.030958 GTACGCAACGGGTTCAGGG 61.031 63.158 0.00 0.00 0.00 4.45
314 315 4.636435 CAACGGGTTCAGGGCGGT 62.636 66.667 0.00 0.00 0.00 5.68
315 316 2.924101 AACGGGTTCAGGGCGGTA 60.924 61.111 0.00 0.00 0.00 4.02
316 317 3.244281 AACGGGTTCAGGGCGGTAC 62.244 63.158 0.00 0.00 0.00 3.34
334 337 2.978824 GGGTTGAGCTCGTGCCTA 59.021 61.111 9.64 0.00 40.80 3.93
339 342 0.898326 TTGAGCTCGTGCCTACCTGA 60.898 55.000 9.64 0.00 40.80 3.86
348 351 1.116536 TGCCTACCTGACGACCACAA 61.117 55.000 0.00 0.00 0.00 3.33
352 355 2.224209 CCTACCTGACGACCACAACTTT 60.224 50.000 0.00 0.00 0.00 2.66
360 363 3.396560 ACGACCACAACTTTAGCTTACC 58.603 45.455 0.00 0.00 0.00 2.85
366 369 4.691216 CCACAACTTTAGCTTACCTCTGTC 59.309 45.833 0.00 0.00 0.00 3.51
376 380 3.619038 GCTTACCTCTGTCCGAAAATCTG 59.381 47.826 0.00 0.00 0.00 2.90
378 382 5.623824 GCTTACCTCTGTCCGAAAATCTGTA 60.624 44.000 0.00 0.00 0.00 2.74
424 428 0.248377 AATCGTACTACGGCGCAGTC 60.248 55.000 18.55 7.74 42.81 3.51
433 437 3.084579 GGCGCAGTCGAGTTGATG 58.915 61.111 10.83 0.00 38.10 3.07
434 438 1.446099 GGCGCAGTCGAGTTGATGA 60.446 57.895 10.83 0.00 38.10 2.92
435 439 0.807667 GGCGCAGTCGAGTTGATGAT 60.808 55.000 10.83 0.00 38.10 2.45
683 702 2.455032 CGCGGTCTCTTCTCATTACTG 58.545 52.381 0.00 0.00 0.00 2.74
687 706 4.734108 GCGGTCTCTTCTCATTACTGGTAC 60.734 50.000 0.00 0.00 0.00 3.34
688 707 4.202030 CGGTCTCTTCTCATTACTGGTACC 60.202 50.000 4.43 4.43 0.00 3.34
689 708 4.202030 GGTCTCTTCTCATTACTGGTACCG 60.202 50.000 7.57 4.79 0.00 4.02
694 713 1.137086 CTCATTACTGGTACCGCTGCT 59.863 52.381 7.57 0.00 0.00 4.24
733 752 4.785453 GCGGGAGGAAGGTGCAGG 62.785 72.222 0.00 0.00 0.00 4.85
755 774 3.329386 CGGCAGATGAAAAGTTGAGAGA 58.671 45.455 0.00 0.00 0.00 3.10
840 859 2.115910 TCCTGGCCTGCTTGGTTG 59.884 61.111 3.32 0.00 38.35 3.77
844 863 2.598394 GGCCTGCTTGGTTGCTCA 60.598 61.111 0.00 0.00 38.35 4.26
962 986 1.795768 TTAGAAGCGGTGAAGCACAG 58.204 50.000 0.00 0.00 40.15 3.66
985 1009 2.575993 GCAAGAGCTGCGAGAGGA 59.424 61.111 0.00 0.00 42.37 3.71
1233 1260 1.799933 AACCTGAACCCATGCCAAAA 58.200 45.000 0.00 0.00 0.00 2.44
1249 1276 2.087646 CAAAACCAGAGCCTAAGCCTC 58.912 52.381 0.00 0.00 41.25 4.70
1293 1320 2.045926 CCAGAGCCCAAACCGGAG 60.046 66.667 9.46 0.00 36.56 4.63
1345 1372 3.580604 AAGCCTGAGCCCAAGCCTG 62.581 63.158 0.00 0.00 41.25 4.85
2109 2615 1.500783 AAAGCCAGAGCCTAAGCCCA 61.501 55.000 0.00 0.00 41.25 5.36
2156 2692 1.490490 CCTGAACCTATGCCTAAGCCA 59.510 52.381 0.00 0.00 38.69 4.75
2309 2852 6.649155 TGTGCTATTTCTAGAATAAGTGGCA 58.351 36.000 5.89 9.71 0.00 4.92
2320 2863 4.838986 AGAATAAGTGGCATAGTATCCGGT 59.161 41.667 0.00 0.00 0.00 5.28
2400 2945 0.184692 TCTGTTGTTCCATGCACCCA 59.815 50.000 0.00 0.00 0.00 4.51
2416 2961 5.147767 TGCACCCATGATGAGTACTACTAT 58.852 41.667 0.00 0.00 0.00 2.12
2418 2963 6.159988 GCACCCATGATGAGTACTACTATTC 58.840 44.000 0.00 0.00 0.00 1.75
2468 3013 2.000429 TCATCTGTGCACATGACTCG 58.000 50.000 22.00 7.65 0.00 4.18
2485 3030 3.378339 ACTCGGTTGTTCTTTCGTGTAG 58.622 45.455 0.00 0.00 0.00 2.74
2486 3031 3.067180 ACTCGGTTGTTCTTTCGTGTAGA 59.933 43.478 0.00 0.00 0.00 2.59
2563 3108 7.147976 GCAGTCTATGTTGTTTTCCTTTTGAT 58.852 34.615 0.00 0.00 0.00 2.57
2581 3126 2.285977 GATTTATTTCGCCTCGTGGGT 58.714 47.619 5.54 0.00 37.43 4.51
2615 3160 1.132500 CCCCTATTCCTCCACTGGAC 58.868 60.000 0.00 0.00 35.58 4.02
2624 3169 1.649390 CTCCACTGGACCGTCTCGAG 61.649 65.000 5.93 5.93 0.00 4.04
2625 3170 2.179517 CACTGGACCGTCTCGAGC 59.820 66.667 7.81 1.89 0.00 5.03
2753 3300 2.203584 AGAGATGTGCAGAATTCCCCT 58.796 47.619 0.65 0.00 0.00 4.79
2762 3309 3.392616 TGCAGAATTCCCCTAGAATCCTC 59.607 47.826 0.65 0.00 44.75 3.71
2806 3353 7.912250 CACTGTATTTTCAGGATTCTAATGTGC 59.088 37.037 0.00 0.00 39.48 4.57
2808 3355 6.597672 TGTATTTTCAGGATTCTAATGTGCGT 59.402 34.615 0.00 0.00 0.00 5.24
2823 3370 2.622962 GCGTACCCACCAGCAAACC 61.623 63.158 0.00 0.00 0.00 3.27
2824 3371 1.072505 CGTACCCACCAGCAAACCT 59.927 57.895 0.00 0.00 0.00 3.50
2825 3372 0.953960 CGTACCCACCAGCAAACCTC 60.954 60.000 0.00 0.00 0.00 3.85
2826 3373 0.608308 GTACCCACCAGCAAACCTCC 60.608 60.000 0.00 0.00 0.00 4.30
2827 3374 1.785353 TACCCACCAGCAAACCTCCC 61.785 60.000 0.00 0.00 0.00 4.30
2828 3375 2.520458 CCACCAGCAAACCTCCCA 59.480 61.111 0.00 0.00 0.00 4.37
2866 3413 2.120909 GCATGCCCAACGCCATACT 61.121 57.895 6.36 0.00 36.24 2.12
2886 3433 1.698506 AAATCCCGCTTTCCACACAA 58.301 45.000 0.00 0.00 0.00 3.33
2943 3493 1.191535 CAGTTCCACACGATCCCCTA 58.808 55.000 0.00 0.00 0.00 3.53
2955 3505 2.820787 CGATCCCCTACCTAGATGACAC 59.179 54.545 0.00 0.00 0.00 3.67
3015 3566 8.534954 AGTATAGTACTGCTTAGATTTCACCA 57.465 34.615 5.39 0.00 37.69 4.17
3143 3694 7.575720 CGGTCTACAATATAGCACATGAGATCA 60.576 40.741 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.726517 CTTCGTGTGGGGCTTGCG 61.727 66.667 0.00 0.00 0.00 4.85
9 10 3.365265 CCTTCGTGTGGGGCTTGC 61.365 66.667 0.00 0.00 0.00 4.01
10 11 1.672356 CTCCTTCGTGTGGGGCTTG 60.672 63.158 0.00 0.00 0.00 4.01
11 12 1.415672 TTCTCCTTCGTGTGGGGCTT 61.416 55.000 0.00 0.00 0.00 4.35
12 13 1.415672 TTTCTCCTTCGTGTGGGGCT 61.416 55.000 0.00 0.00 0.00 5.19
13 14 0.536460 TTTTCTCCTTCGTGTGGGGC 60.536 55.000 0.00 0.00 0.00 5.80
14 15 1.975660 TTTTTCTCCTTCGTGTGGGG 58.024 50.000 0.00 0.00 0.00 4.96
15 16 2.351738 GCATTTTTCTCCTTCGTGTGGG 60.352 50.000 0.00 0.00 0.00 4.61
16 17 2.293122 TGCATTTTTCTCCTTCGTGTGG 59.707 45.455 0.00 0.00 0.00 4.17
17 18 3.558505 CTGCATTTTTCTCCTTCGTGTG 58.441 45.455 0.00 0.00 0.00 3.82
18 19 2.030805 GCTGCATTTTTCTCCTTCGTGT 60.031 45.455 0.00 0.00 0.00 4.49
19 20 2.030893 TGCTGCATTTTTCTCCTTCGTG 60.031 45.455 0.00 0.00 0.00 4.35
20 21 2.229792 TGCTGCATTTTTCTCCTTCGT 58.770 42.857 0.00 0.00 0.00 3.85
21 22 2.982470 GTTGCTGCATTTTTCTCCTTCG 59.018 45.455 1.84 0.00 0.00 3.79
22 23 3.981211 TGTTGCTGCATTTTTCTCCTTC 58.019 40.909 1.84 0.00 0.00 3.46
23 24 4.405116 TTGTTGCTGCATTTTTCTCCTT 57.595 36.364 1.84 0.00 0.00 3.36
24 25 4.099881 TCTTTGTTGCTGCATTTTTCTCCT 59.900 37.500 1.84 0.00 0.00 3.69
25 26 4.209911 GTCTTTGTTGCTGCATTTTTCTCC 59.790 41.667 1.84 0.00 0.00 3.71
26 27 4.085415 CGTCTTTGTTGCTGCATTTTTCTC 60.085 41.667 1.84 0.00 0.00 2.87
27 28 3.798337 CGTCTTTGTTGCTGCATTTTTCT 59.202 39.130 1.84 0.00 0.00 2.52
28 29 3.602265 GCGTCTTTGTTGCTGCATTTTTC 60.602 43.478 1.84 0.00 0.00 2.29
29 30 2.284952 GCGTCTTTGTTGCTGCATTTTT 59.715 40.909 1.84 0.00 0.00 1.94
30 31 1.860326 GCGTCTTTGTTGCTGCATTTT 59.140 42.857 1.84 0.00 0.00 1.82
31 32 1.067516 AGCGTCTTTGTTGCTGCATTT 59.932 42.857 1.84 0.00 37.62 2.32
32 33 0.670162 AGCGTCTTTGTTGCTGCATT 59.330 45.000 1.84 0.00 37.62 3.56
33 34 0.670162 AAGCGTCTTTGTTGCTGCAT 59.330 45.000 1.84 0.00 39.30 3.96
34 35 0.248580 CAAGCGTCTTTGTTGCTGCA 60.249 50.000 0.00 0.00 39.30 4.41
35 36 0.248621 ACAAGCGTCTTTGTTGCTGC 60.249 50.000 0.00 0.00 38.05 5.25
36 37 2.193306 AACAAGCGTCTTTGTTGCTG 57.807 45.000 11.99 0.00 46.44 4.41
50 51 2.195922 AGCGCTTTTTGCTTGAACAAG 58.804 42.857 2.64 9.82 40.48 3.16
51 52 2.292103 AGCGCTTTTTGCTTGAACAA 57.708 40.000 2.64 0.00 40.48 2.83
58 59 0.823356 TCCTCCAAGCGCTTTTTGCT 60.823 50.000 22.51 0.00 46.68 3.91
59 60 0.031994 TTCCTCCAAGCGCTTTTTGC 59.968 50.000 22.51 0.00 38.57 3.68
60 61 2.730550 ATTCCTCCAAGCGCTTTTTG 57.269 45.000 22.51 10.65 0.00 2.44
61 62 4.016444 TGATATTCCTCCAAGCGCTTTTT 58.984 39.130 22.51 0.00 0.00 1.94
62 63 3.620488 TGATATTCCTCCAAGCGCTTTT 58.380 40.909 22.51 0.00 0.00 2.27
63 64 3.281727 TGATATTCCTCCAAGCGCTTT 57.718 42.857 22.51 6.71 0.00 3.51
64 65 2.945668 GTTGATATTCCTCCAAGCGCTT 59.054 45.455 18.98 18.98 0.00 4.68
65 66 2.092968 TGTTGATATTCCTCCAAGCGCT 60.093 45.455 2.64 2.64 0.00 5.92
66 67 2.288666 TGTTGATATTCCTCCAAGCGC 58.711 47.619 0.00 0.00 0.00 5.92
67 68 4.963276 TTTGTTGATATTCCTCCAAGCG 57.037 40.909 0.00 0.00 0.00 4.68
68 69 5.105063 GCTTTTGTTGATATTCCTCCAAGC 58.895 41.667 0.00 0.00 0.00 4.01
69 70 6.271488 TGCTTTTGTTGATATTCCTCCAAG 57.729 37.500 0.00 0.00 0.00 3.61
70 71 6.662865 TTGCTTTTGTTGATATTCCTCCAA 57.337 33.333 0.00 0.00 0.00 3.53
71 72 6.855763 ATTGCTTTTGTTGATATTCCTCCA 57.144 33.333 0.00 0.00 0.00 3.86
72 73 7.490402 CAGAATTGCTTTTGTTGATATTCCTCC 59.510 37.037 0.00 0.00 0.00 4.30
73 74 7.009907 GCAGAATTGCTTTTGTTGATATTCCTC 59.990 37.037 0.00 0.00 46.95 3.71
74 75 6.815142 GCAGAATTGCTTTTGTTGATATTCCT 59.185 34.615 0.00 0.00 46.95 3.36
75 76 6.997222 GCAGAATTGCTTTTGTTGATATTCC 58.003 36.000 0.00 0.00 46.95 3.01
110 111 5.162446 ACTTAAAAGTCACGTACGCACGC 62.162 47.826 16.72 3.35 43.22 5.34
111 112 2.468777 ACTTAAAAGTCACGTACGCACG 59.531 45.455 16.72 6.64 44.33 5.34
112 113 4.442350 AACTTAAAAGTCACGTACGCAC 57.558 40.909 16.72 12.51 38.57 5.34
113 114 5.467902 AAAACTTAAAAGTCACGTACGCA 57.532 34.783 16.72 0.00 38.57 5.24
114 115 6.899243 TGTTAAAACTTAAAAGTCACGTACGC 59.101 34.615 16.72 0.00 38.57 4.42
115 116 7.580165 CCTGTTAAAACTTAAAAGTCACGTACG 59.420 37.037 15.01 15.01 38.57 3.67
116 117 8.390354 ACCTGTTAAAACTTAAAAGTCACGTAC 58.610 33.333 0.00 0.00 38.57 3.67
117 118 8.491331 ACCTGTTAAAACTTAAAAGTCACGTA 57.509 30.769 0.00 0.00 38.57 3.57
118 119 7.119553 TGACCTGTTAAAACTTAAAAGTCACGT 59.880 33.333 0.00 0.00 38.57 4.49
119 120 7.465989 TGACCTGTTAAAACTTAAAAGTCACG 58.534 34.615 0.00 0.00 38.57 4.35
120 121 9.797556 ATTGACCTGTTAAAACTTAAAAGTCAC 57.202 29.630 0.00 0.00 38.57 3.67
128 129 9.959749 GTTGATTGATTGACCTGTTAAAACTTA 57.040 29.630 0.00 0.00 0.00 2.24
129 130 7.926018 GGTTGATTGATTGACCTGTTAAAACTT 59.074 33.333 0.00 0.00 0.00 2.66
130 131 7.433680 GGTTGATTGATTGACCTGTTAAAACT 58.566 34.615 0.00 0.00 0.00 2.66
131 132 6.362283 CGGTTGATTGATTGACCTGTTAAAAC 59.638 38.462 0.00 0.00 0.00 2.43
132 133 6.263392 TCGGTTGATTGATTGACCTGTTAAAA 59.737 34.615 0.00 0.00 0.00 1.52
133 134 5.765677 TCGGTTGATTGATTGACCTGTTAAA 59.234 36.000 0.00 0.00 0.00 1.52
134 135 5.309638 TCGGTTGATTGATTGACCTGTTAA 58.690 37.500 0.00 0.00 0.00 2.01
135 136 4.900684 TCGGTTGATTGATTGACCTGTTA 58.099 39.130 0.00 0.00 0.00 2.41
136 137 3.750371 TCGGTTGATTGATTGACCTGTT 58.250 40.909 0.00 0.00 0.00 3.16
137 138 3.417069 TCGGTTGATTGATTGACCTGT 57.583 42.857 0.00 0.00 0.00 4.00
138 139 3.001634 CGATCGGTTGATTGATTGACCTG 59.998 47.826 7.38 0.00 38.12 4.00
139 140 3.118775 TCGATCGGTTGATTGATTGACCT 60.119 43.478 16.41 0.00 39.60 3.85
140 141 3.194861 TCGATCGGTTGATTGATTGACC 58.805 45.455 16.41 0.00 39.60 4.02
146 147 4.988540 GGTATTGATCGATCGGTTGATTGA 59.011 41.667 20.03 0.00 46.58 2.57
147 148 4.143326 CGGTATTGATCGATCGGTTGATTG 60.143 45.833 20.03 2.90 37.34 2.67
148 149 3.987868 CGGTATTGATCGATCGGTTGATT 59.012 43.478 20.03 2.20 34.09 2.57
149 150 3.575630 CGGTATTGATCGATCGGTTGAT 58.424 45.455 20.03 8.82 37.60 2.57
150 151 2.860971 GCGGTATTGATCGATCGGTTGA 60.861 50.000 20.03 0.72 0.00 3.18
151 152 1.455786 GCGGTATTGATCGATCGGTTG 59.544 52.381 20.03 8.95 0.00 3.77
152 153 1.779569 GCGGTATTGATCGATCGGTT 58.220 50.000 20.03 9.88 0.00 4.44
153 154 0.386858 CGCGGTATTGATCGATCGGT 60.387 55.000 20.03 8.34 0.00 4.69
154 155 0.109919 TCGCGGTATTGATCGATCGG 60.110 55.000 20.03 6.50 0.00 4.18
155 156 1.382419 GTTCGCGGTATTGATCGATCG 59.618 52.381 20.03 9.36 0.00 3.69
156 157 1.719780 GGTTCGCGGTATTGATCGATC 59.280 52.381 18.72 18.72 0.00 3.69
157 158 1.779569 GGTTCGCGGTATTGATCGAT 58.220 50.000 6.13 0.00 0.00 3.59
158 159 0.593008 CGGTTCGCGGTATTGATCGA 60.593 55.000 6.13 0.00 0.00 3.59
159 160 1.545614 CCGGTTCGCGGTATTGATCG 61.546 60.000 6.13 0.00 0.00 3.69
160 161 0.249155 TCCGGTTCGCGGTATTGATC 60.249 55.000 6.13 0.00 0.00 2.92
161 162 0.529119 GTCCGGTTCGCGGTATTGAT 60.529 55.000 6.13 0.00 0.00 2.57
162 163 1.153784 GTCCGGTTCGCGGTATTGA 60.154 57.895 6.13 0.00 0.00 2.57
163 164 2.169146 GGTCCGGTTCGCGGTATTG 61.169 63.158 6.13 0.00 0.00 1.90
164 165 2.169937 TTGGTCCGGTTCGCGGTATT 62.170 55.000 6.13 0.00 0.00 1.89
165 166 2.567564 CTTGGTCCGGTTCGCGGTAT 62.568 60.000 6.13 0.00 0.00 2.73
166 167 3.285523 CTTGGTCCGGTTCGCGGTA 62.286 63.158 6.13 0.00 0.00 4.02
167 168 4.675029 CTTGGTCCGGTTCGCGGT 62.675 66.667 6.13 0.00 0.00 5.68
170 171 2.966309 CTTGCTTGGTCCGGTTCGC 61.966 63.158 0.00 0.00 0.00 4.70
171 172 2.966309 GCTTGCTTGGTCCGGTTCG 61.966 63.158 0.00 0.00 0.00 3.95
172 173 2.954611 GCTTGCTTGGTCCGGTTC 59.045 61.111 0.00 0.00 0.00 3.62
173 174 2.978010 CGCTTGCTTGGTCCGGTT 60.978 61.111 0.00 0.00 0.00 4.44
174 175 4.250305 ACGCTTGCTTGGTCCGGT 62.250 61.111 0.00 0.00 0.00 5.28
175 176 3.423154 GACGCTTGCTTGGTCCGG 61.423 66.667 0.00 0.00 0.00 5.14
176 177 3.777925 CGACGCTTGCTTGGTCCG 61.778 66.667 0.00 0.00 0.00 4.79
177 178 3.423154 CCGACGCTTGCTTGGTCC 61.423 66.667 0.00 0.00 0.00 4.46
178 179 2.665185 ACCGACGCTTGCTTGGTC 60.665 61.111 0.00 0.00 0.00 4.02
179 180 2.665185 GACCGACGCTTGCTTGGT 60.665 61.111 0.00 4.45 35.14 3.67
180 181 3.777925 CGACCGACGCTTGCTTGG 61.778 66.667 0.00 0.00 34.51 3.61
181 182 3.777925 CCGACCGACGCTTGCTTG 61.778 66.667 0.00 0.00 41.07 4.01
182 183 4.295119 ACCGACCGACGCTTGCTT 62.295 61.111 0.00 0.00 41.07 3.91
183 184 4.719369 GACCGACCGACGCTTGCT 62.719 66.667 0.00 0.00 41.07 3.91
203 204 4.900704 CATGGGTGGATGGGGCCG 62.901 72.222 0.00 0.00 0.00 6.13
204 205 3.007684 TTCATGGGTGGATGGGGCC 62.008 63.158 0.00 0.00 0.00 5.80
205 206 1.758122 GTTCATGGGTGGATGGGGC 60.758 63.158 0.00 0.00 0.00 5.80
206 207 0.040942 TTGTTCATGGGTGGATGGGG 59.959 55.000 0.00 0.00 0.00 4.96
207 208 2.163810 ATTGTTCATGGGTGGATGGG 57.836 50.000 0.00 0.00 0.00 4.00
208 209 3.514706 TGAAATTGTTCATGGGTGGATGG 59.485 43.478 0.00 0.00 38.88 3.51
209 210 4.804868 TGAAATTGTTCATGGGTGGATG 57.195 40.909 0.00 0.00 38.88 3.51
210 211 5.797051 CTTTGAAATTGTTCATGGGTGGAT 58.203 37.500 0.00 0.00 43.29 3.41
211 212 4.502950 GCTTTGAAATTGTTCATGGGTGGA 60.503 41.667 0.00 0.00 43.29 4.02
212 213 3.747529 GCTTTGAAATTGTTCATGGGTGG 59.252 43.478 0.00 0.00 43.29 4.61
213 214 4.449743 CAGCTTTGAAATTGTTCATGGGTG 59.550 41.667 0.00 0.00 43.29 4.61
214 215 4.634199 CAGCTTTGAAATTGTTCATGGGT 58.366 39.130 0.00 0.00 43.29 4.51
215 216 3.434299 GCAGCTTTGAAATTGTTCATGGG 59.566 43.478 0.00 0.00 43.29 4.00
216 217 3.434299 GGCAGCTTTGAAATTGTTCATGG 59.566 43.478 0.00 0.00 43.29 3.66
217 218 3.122278 CGGCAGCTTTGAAATTGTTCATG 59.878 43.478 0.00 0.00 43.29 3.07
218 219 3.005684 TCGGCAGCTTTGAAATTGTTCAT 59.994 39.130 0.00 0.00 43.29 2.57
219 220 2.360483 TCGGCAGCTTTGAAATTGTTCA 59.640 40.909 0.00 0.00 42.12 3.18
220 221 3.011949 TCGGCAGCTTTGAAATTGTTC 57.988 42.857 0.00 0.00 0.00 3.18
221 222 3.578688 GATCGGCAGCTTTGAAATTGTT 58.421 40.909 0.00 0.00 0.00 2.83
222 223 2.094545 GGATCGGCAGCTTTGAAATTGT 60.095 45.455 0.00 0.00 0.00 2.71
223 224 2.094597 TGGATCGGCAGCTTTGAAATTG 60.095 45.455 0.00 0.00 0.00 2.32
224 225 2.170166 TGGATCGGCAGCTTTGAAATT 58.830 42.857 0.00 0.00 0.00 1.82
225 226 1.838112 TGGATCGGCAGCTTTGAAAT 58.162 45.000 0.00 0.00 0.00 2.17
226 227 1.473677 CATGGATCGGCAGCTTTGAAA 59.526 47.619 0.00 0.00 0.00 2.69
227 228 1.097232 CATGGATCGGCAGCTTTGAA 58.903 50.000 0.00 0.00 0.00 2.69
228 229 0.749091 CCATGGATCGGCAGCTTTGA 60.749 55.000 5.56 0.00 0.00 2.69
229 230 1.731700 CCATGGATCGGCAGCTTTG 59.268 57.895 5.56 0.00 0.00 2.77
230 231 4.247781 CCATGGATCGGCAGCTTT 57.752 55.556 5.56 0.00 0.00 3.51
239 240 1.596477 GCCTGTCGAGCCATGGATC 60.596 63.158 20.38 20.38 0.00 3.36
240 241 2.507944 GCCTGTCGAGCCATGGAT 59.492 61.111 18.40 10.08 0.00 3.41
241 242 4.147449 CGCCTGTCGAGCCATGGA 62.147 66.667 18.40 0.00 41.67 3.41
292 293 2.030958 CCCTGAACCCGTTGCGTAC 61.031 63.158 0.00 0.00 0.00 3.67
293 294 2.344500 CCCTGAACCCGTTGCGTA 59.656 61.111 0.00 0.00 0.00 4.42
307 308 3.387947 CTCAACCCGTACCGCCCT 61.388 66.667 0.00 0.00 0.00 5.19
310 311 2.508663 GAGCTCAACCCGTACCGC 60.509 66.667 9.40 0.00 0.00 5.68
313 314 2.092882 GCACGAGCTCAACCCGTAC 61.093 63.158 15.40 0.00 37.91 3.67
314 315 2.260434 GCACGAGCTCAACCCGTA 59.740 61.111 15.40 0.00 37.91 4.02
315 316 4.681978 GGCACGAGCTCAACCCGT 62.682 66.667 15.40 2.61 41.70 5.28
316 317 3.001902 TAGGCACGAGCTCAACCCG 62.002 63.158 15.40 1.87 41.70 5.28
317 318 1.448013 GTAGGCACGAGCTCAACCC 60.448 63.158 15.40 9.84 41.70 4.11
318 319 1.448013 GGTAGGCACGAGCTCAACC 60.448 63.158 15.40 11.41 41.70 3.77
319 320 0.737715 CAGGTAGGCACGAGCTCAAC 60.738 60.000 15.40 1.52 40.38 3.18
320 321 0.898326 TCAGGTAGGCACGAGCTCAA 60.898 55.000 15.40 0.00 40.38 3.02
322 323 1.139947 GTCAGGTAGGCACGAGCTC 59.860 63.158 2.73 2.73 40.38 4.09
323 324 2.701780 CGTCAGGTAGGCACGAGCT 61.702 63.158 4.48 0.00 43.78 4.09
325 326 1.136984 GTCGTCAGGTAGGCACGAG 59.863 63.158 0.00 0.00 42.90 4.18
330 333 0.669625 GTTGTGGTCGTCAGGTAGGC 60.670 60.000 0.00 0.00 0.00 3.93
331 334 0.966920 AGTTGTGGTCGTCAGGTAGG 59.033 55.000 0.00 0.00 0.00 3.18
334 337 2.805657 GCTAAAGTTGTGGTCGTCAGGT 60.806 50.000 0.00 0.00 0.00 4.00
339 342 3.070590 AGGTAAGCTAAAGTTGTGGTCGT 59.929 43.478 0.00 0.00 0.00 4.34
348 351 3.428532 TCGGACAGAGGTAAGCTAAAGT 58.571 45.455 0.00 0.00 0.00 2.66
352 355 4.710375 AGATTTTCGGACAGAGGTAAGCTA 59.290 41.667 0.00 0.00 0.00 3.32
360 363 4.177026 CCTGTACAGATTTTCGGACAGAG 58.823 47.826 24.68 0.00 37.14 3.35
366 369 1.398390 GCAGCCTGTACAGATTTTCGG 59.602 52.381 24.68 7.57 0.00 4.30
376 380 2.416893 GAGCTTTTACTGCAGCCTGTAC 59.583 50.000 15.27 0.00 36.62 2.90
378 382 1.528129 GAGCTTTTACTGCAGCCTGT 58.472 50.000 15.27 0.00 36.62 4.00
424 428 1.325640 CTTGACGGCATCATCAACTCG 59.674 52.381 0.00 0.00 37.11 4.18
433 437 2.467826 GCCTCAGCTTGACGGCATC 61.468 63.158 0.00 0.00 39.14 3.91
434 438 2.437359 GCCTCAGCTTGACGGCAT 60.437 61.111 0.00 0.00 39.14 4.40
556 568 0.532862 CCATGTCGGGGATTTCTCCG 60.533 60.000 12.75 12.75 46.89 4.63
733 752 1.806542 TCTCAACTTTTCATCTGCCGC 59.193 47.619 0.00 0.00 0.00 6.53
755 774 0.981277 CCGGGTGGATCAGGTTACCT 60.981 60.000 0.00 0.00 37.49 3.08
826 845 2.598394 GAGCAACCAAGCAGGCCA 60.598 61.111 5.01 0.00 43.14 5.36
828 847 2.960170 CTGAGCAACCAAGCAGGC 59.040 61.111 0.00 0.00 43.14 4.85
840 859 2.298610 GGTGGTTTTATAGGGCTGAGC 58.701 52.381 0.00 0.00 0.00 4.26
844 863 1.688750 TGGGGTGGTTTTATAGGGCT 58.311 50.000 0.00 0.00 0.00 5.19
983 1007 1.451028 ATTGCTGCTCGCTCCTTCC 60.451 57.895 0.00 0.00 40.11 3.46
984 1008 1.712977 CCATTGCTGCTCGCTCCTTC 61.713 60.000 0.00 0.00 40.11 3.46
985 1009 1.748122 CCATTGCTGCTCGCTCCTT 60.748 57.895 0.00 0.00 40.11 3.36
1249 1276 0.542702 ATGGGTTCAGGTTTGGGCAG 60.543 55.000 0.00 0.00 0.00 4.85
1345 1372 2.046285 CAGGTTTGGGCATCGGGTC 61.046 63.158 0.00 0.00 0.00 4.46
2042 2069 2.040544 CGGTTCTGGCTTCGGCATT 61.041 57.895 0.00 0.00 43.96 3.56
2109 2615 2.562738 GCTCTGGTTTAGGCAATGGTTT 59.437 45.455 0.00 0.00 0.00 3.27
2210 2746 3.686241 CACATCAATTGTCAGTCATCGGT 59.314 43.478 5.13 0.00 36.00 4.69
2213 2749 7.493645 TGAGTATCACATCAATTGTCAGTCATC 59.506 37.037 5.13 0.00 42.56 2.92
2309 2852 5.585445 CACTATCTCGCTAACCGGATACTAT 59.415 44.000 9.46 0.00 37.59 2.12
2320 2863 4.853924 TGCATCATCACTATCTCGCTAA 57.146 40.909 0.00 0.00 0.00 3.09
2416 2961 7.026562 CCAACACGCAAATGATAATTACAGAA 58.973 34.615 0.00 0.00 0.00 3.02
2418 2963 6.321717 ACCAACACGCAAATGATAATTACAG 58.678 36.000 0.00 0.00 0.00 2.74
2468 3013 6.149504 GTGTATCTACACGAAAGAACAACC 57.850 41.667 4.84 0.00 45.87 3.77
2485 3030 6.526325 TGCAAACGAATAAAAGCATGTGTATC 59.474 34.615 0.00 0.00 0.00 2.24
2486 3031 6.385843 TGCAAACGAATAAAAGCATGTGTAT 58.614 32.000 0.00 0.00 0.00 2.29
2563 3108 1.444836 CACCCACGAGGCGAAATAAA 58.555 50.000 0.00 0.00 40.58 1.40
2581 3126 4.365111 GGGCATGTCCAGGGTGCA 62.365 66.667 12.68 0.00 40.53 4.57
2615 3160 1.213094 AAAACACACGCTCGAGACGG 61.213 55.000 25.38 18.49 34.00 4.79
2726 3273 7.285401 GGGGAATTCTGCACATCTCTATTTTTA 59.715 37.037 5.23 0.00 0.00 1.52
2732 3279 3.387962 AGGGGAATTCTGCACATCTCTA 58.612 45.455 5.23 0.00 0.00 2.43
2744 3291 6.126623 ACAAAGAGAGGATTCTAGGGGAATTC 60.127 42.308 0.00 0.00 43.90 2.17
2753 3300 5.584913 ACTGAGGACAAAGAGAGGATTCTA 58.415 41.667 0.00 0.00 32.53 2.10
2806 3353 0.953960 GAGGTTTGCTGGTGGGTACG 60.954 60.000 0.00 0.00 0.00 3.67
2808 3355 1.765074 GGAGGTTTGCTGGTGGGTA 59.235 57.895 0.00 0.00 0.00 3.69
2823 3370 1.139853 GATGTTAGCTGGGAGTGGGAG 59.860 57.143 0.00 0.00 0.00 4.30
2824 3371 1.204146 GATGTTAGCTGGGAGTGGGA 58.796 55.000 0.00 0.00 0.00 4.37
2825 3372 1.207791 AGATGTTAGCTGGGAGTGGG 58.792 55.000 0.00 0.00 0.00 4.61
2826 3373 2.766263 TGTAGATGTTAGCTGGGAGTGG 59.234 50.000 0.00 0.00 0.00 4.00
2827 3374 3.739519 GCTGTAGATGTTAGCTGGGAGTG 60.740 52.174 0.00 0.00 34.70 3.51
2828 3375 2.432510 GCTGTAGATGTTAGCTGGGAGT 59.567 50.000 0.00 0.00 34.70 3.85
2866 3413 2.570415 TGTGTGGAAAGCGGGATTTA 57.430 45.000 0.00 0.00 0.00 1.40
2925 3475 1.192428 GTAGGGGATCGTGTGGAACT 58.808 55.000 0.00 0.00 38.04 3.01
2932 3482 2.820787 GTCATCTAGGTAGGGGATCGTG 59.179 54.545 0.00 0.00 0.00 4.35
2994 3545 7.093509 TGTCATGGTGAAATCTAAGCAGTACTA 60.094 37.037 0.00 0.00 0.00 1.82
3015 3566 3.254166 ACTCTGAAAAATGCGCTTGTCAT 59.746 39.130 9.73 0.00 0.00 3.06
3082 3633 7.877612 TGGCTATCTGTACATTGTGGTTATATG 59.122 37.037 0.00 0.00 0.00 1.78
3143 3694 2.696707 TGTTGAACCGTCCAAGAGTACT 59.303 45.455 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.