Multiple sequence alignment - TraesCS6B01G407400

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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 TraesCS6B01G407400 chr6B 100.000 3947 0 0 1 3947 681900680 681904626 0.000000e+00 7289
1 TraesCS6B01G407400 chr6B 94.051 2841 167 2 357 3196 521149624 521146785 0.000000e+00 4309
2 TraesCS6B01G407400 chr6B 95.543 359 13 2 1 356 542247771 542248129 4.420000e-159 571
3 TraesCS6B01G407400 chr6B 95.531 358 12 2 1 357 590873402 590873048 1.590000e-158 569
4 TraesCS6B01G407400 chr6B 89.447 199 16 2 3211 3408 681207942 681208136 3.050000e-61 246
5 TraesCS6B01G407400 chr6B 83.019 212 24 9 3401 3608 681209001 681209204 8.710000e-42 182
6 TraesCS6B01G407400 chr7D 95.119 2848 124 10 357 3201 550636005 550638840 0.000000e+00 4475
7 TraesCS6B01G407400 chr5D 94.831 2844 133 6 357 3199 350369413 350366583 0.000000e+00 4425
8 TraesCS6B01G407400 chr5D 94.480 2844 146 5 357 3199 41771246 41768413 0.000000e+00 4372
9 TraesCS6B01G407400 chr5D 93.987 2844 162 6 357 3198 134489637 134486801 0.000000e+00 4296
10 TraesCS6B01G407400 chr2B 94.491 2850 140 9 357 3201 511146791 511149628 0.000000e+00 4377
11 TraesCS6B01G407400 chr2B 95.531 358 10 4 1 357 249713703 249713351 5.720000e-158 568
12 TraesCS6B01G407400 chr5B 94.376 2845 152 6 357 3199 184289063 184291901 0.000000e+00 4361
13 TraesCS6B01G407400 chr5B 95.518 357 13 3 1 356 293850251 293850605 5.720000e-158 568
14 TraesCS6B01G407400 chr7B 94.275 2847 147 11 359 3198 244886055 244883218 0.000000e+00 4340
15 TraesCS6B01G407400 chr7B 94.175 2850 151 9 357 3202 377873080 377875918 0.000000e+00 4329
16 TraesCS6B01G407400 chr7B 96.328 354 9 3 4 356 529073222 529072872 2.640000e-161 579
17 TraesCS6B01G407400 chr7B 95.531 358 13 3 1 356 443753503 443753859 1.590000e-158 569
18 TraesCS6B01G407400 chr7B 95.265 359 13 3 1 358 730764248 730764603 2.060000e-157 566
19 TraesCS6B01G407400 chr7B 94.309 369 13 6 1 367 62332530 62332892 3.440000e-155 558
20 TraesCS6B01G407400 chr6A 89.615 597 37 14 3356 3946 595444607 595445184 0.000000e+00 736
21 TraesCS6B01G407400 chr6A 87.097 155 19 1 3211 3364 595443708 595443862 1.460000e-39 174
22 TraesCS6B01G407400 chr4B 95.506 356 15 1 1 356 398412710 398413064 5.720000e-158 568
23 TraesCS6B01G407400 chr6D 85.874 446 41 11 3214 3657 449780322 449780747 4.650000e-124 455


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 TraesCS6B01G407400 chr6B 681900680 681904626 3946 False 7289 7289 100.000 1 3947 1 chr6B.!!$F2 3946
1 TraesCS6B01G407400 chr6B 521146785 521149624 2839 True 4309 4309 94.051 357 3196 1 chr6B.!!$R1 2839
2 TraesCS6B01G407400 chr6B 681207942 681209204 1262 False 214 246 86.233 3211 3608 2 chr6B.!!$F3 397
3 TraesCS6B01G407400 chr7D 550636005 550638840 2835 False 4475 4475 95.119 357 3201 1 chr7D.!!$F1 2844
4 TraesCS6B01G407400 chr5D 350366583 350369413 2830 True 4425 4425 94.831 357 3199 1 chr5D.!!$R3 2842
5 TraesCS6B01G407400 chr5D 41768413 41771246 2833 True 4372 4372 94.480 357 3199 1 chr5D.!!$R1 2842
6 TraesCS6B01G407400 chr5D 134486801 134489637 2836 True 4296 4296 93.987 357 3198 1 chr5D.!!$R2 2841
7 TraesCS6B01G407400 chr2B 511146791 511149628 2837 False 4377 4377 94.491 357 3201 1 chr2B.!!$F1 2844
8 TraesCS6B01G407400 chr5B 184289063 184291901 2838 False 4361 4361 94.376 357 3199 1 chr5B.!!$F1 2842
9 TraesCS6B01G407400 chr7B 244883218 244886055 2837 True 4340 4340 94.275 359 3198 1 chr7B.!!$R1 2839
10 TraesCS6B01G407400 chr7B 377873080 377875918 2838 False 4329 4329 94.175 357 3202 1 chr7B.!!$F2 2845
11 TraesCS6B01G407400 chr6A 595443708 595445184 1476 False 455 736 88.356 3211 3946 2 chr6A.!!$F1 735

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
173 174 0.032952 TTCCGTTTGGACTCCGTCTG 59.967 55.0 0.00 0.0 46.45 3.51 F
362 363 0.033503 TGGAGACGTATCAGAGGGCA 60.034 55.0 12.92 0.0 0.00 5.36 F
1754 1780 0.178926 TTAGGACGACCCAAGGGACA 60.179 55.0 13.15 0.0 38.96 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 2125 0.110295 CACCCTGGGTCATGACAACA 59.890 55.0 26.47 21.7 31.02 3.33 R
2315 2341 0.167470 ACGTCGTCATCGTCATCGTT 59.833 50.0 0.00 0.0 36.85 3.85 R
3365 3400 0.030235 CATGCCGCCATTGATCTGTG 59.970 55.0 0.00 0.0 0.00 3.66 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
30 31 2.520982 CGAGGGGCCCACGAGATA 60.521 66.667 34.97 0.00 39.84 1.98
31 32 2.565645 CGAGGGGCCCACGAGATAG 61.566 68.421 34.97 6.23 39.84 2.08
32 33 2.122813 AGGGGCCCACGAGATAGG 60.123 66.667 27.72 0.00 0.00 2.57
34 35 3.242291 GGGCCCACGAGATAGGGG 61.242 72.222 19.95 0.00 45.58 4.79
37 38 4.301027 CCCACGAGATAGGGGCGC 62.301 72.222 0.00 0.00 41.58 6.53
38 39 4.647615 CCACGAGATAGGGGCGCG 62.648 72.222 0.00 0.00 34.71 6.86
68 69 3.474570 GAGCGTGCCCTCCATCCT 61.475 66.667 0.00 0.00 0.00 3.24
69 70 3.453070 GAGCGTGCCCTCCATCCTC 62.453 68.421 0.00 0.00 0.00 3.71
70 71 4.899239 GCGTGCCCTCCATCCTCG 62.899 72.222 0.00 0.00 0.00 4.63
71 72 3.461773 CGTGCCCTCCATCCTCGT 61.462 66.667 0.00 0.00 0.00 4.18
72 73 2.187946 GTGCCCTCCATCCTCGTG 59.812 66.667 0.00 0.00 0.00 4.35
73 74 3.083349 TGCCCTCCATCCTCGTGG 61.083 66.667 0.00 0.00 40.76 4.94
74 75 4.554036 GCCCTCCATCCTCGTGGC 62.554 72.222 0.00 0.00 39.19 5.01
75 76 3.866582 CCCTCCATCCTCGTGGCC 61.867 72.222 0.00 0.00 39.19 5.36
76 77 4.227134 CCTCCATCCTCGTGGCCG 62.227 72.222 0.00 0.00 39.19 6.13
77 78 4.899239 CTCCATCCTCGTGGCCGC 62.899 72.222 6.11 6.11 39.19 6.53
80 81 4.899239 CATCCTCGTGGCCGCCTC 62.899 72.222 11.56 6.14 0.00 4.70
84 85 4.514577 CTCGTGGCCGCCTCGATT 62.515 66.667 30.69 0.00 46.01 3.34
85 86 4.812476 TCGTGGCCGCCTCGATTG 62.812 66.667 27.99 5.27 43.13 2.67
88 89 4.408821 TGGCCGCCTCGATTGCTT 62.409 61.111 11.61 0.00 0.00 3.91
89 90 3.577313 GGCCGCCTCGATTGCTTC 61.577 66.667 0.71 0.00 0.00 3.86
90 91 2.512515 GCCGCCTCGATTGCTTCT 60.513 61.111 5.65 0.00 0.00 2.85
91 92 2.109126 GCCGCCTCGATTGCTTCTT 61.109 57.895 5.65 0.00 0.00 2.52
92 93 1.717937 CCGCCTCGATTGCTTCTTG 59.282 57.895 5.65 0.00 0.00 3.02
93 94 0.740868 CCGCCTCGATTGCTTCTTGA 60.741 55.000 5.65 0.00 0.00 3.02
94 95 0.371645 CGCCTCGATTGCTTCTTGAC 59.628 55.000 5.65 0.00 0.00 3.18
95 96 1.731720 GCCTCGATTGCTTCTTGACT 58.268 50.000 0.15 0.00 0.00 3.41
96 97 2.079925 GCCTCGATTGCTTCTTGACTT 58.920 47.619 0.15 0.00 0.00 3.01
97 98 2.159599 GCCTCGATTGCTTCTTGACTTG 60.160 50.000 0.15 0.00 0.00 3.16
98 99 2.159599 CCTCGATTGCTTCTTGACTTGC 60.160 50.000 0.00 0.00 0.00 4.01
99 100 2.481568 CTCGATTGCTTCTTGACTTGCA 59.518 45.455 0.00 0.00 0.00 4.08
100 101 2.224079 TCGATTGCTTCTTGACTTGCAC 59.776 45.455 0.00 0.00 35.01 4.57
101 102 2.225019 CGATTGCTTCTTGACTTGCACT 59.775 45.455 0.00 0.00 35.01 4.40
102 103 3.666374 CGATTGCTTCTTGACTTGCACTC 60.666 47.826 0.00 0.00 35.01 3.51
103 104 1.597742 TGCTTCTTGACTTGCACTCC 58.402 50.000 0.00 0.00 0.00 3.85
104 105 1.134128 TGCTTCTTGACTTGCACTCCA 60.134 47.619 0.00 0.00 0.00 3.86
105 106 1.949525 GCTTCTTGACTTGCACTCCAA 59.050 47.619 0.00 0.00 0.00 3.53
113 114 1.805869 CTTGCACTCCAAGTCCTCTG 58.194 55.000 0.00 0.00 44.74 3.35
114 115 0.397941 TTGCACTCCAAGTCCTCTGG 59.602 55.000 0.00 0.00 0.00 3.86
115 116 0.471780 TGCACTCCAAGTCCTCTGGA 60.472 55.000 0.00 0.00 0.00 3.86
116 117 0.908198 GCACTCCAAGTCCTCTGGAT 59.092 55.000 0.00 0.00 32.73 3.41
117 118 1.134551 GCACTCCAAGTCCTCTGGATC 60.135 57.143 0.00 0.00 32.73 3.36
118 119 2.182827 CACTCCAAGTCCTCTGGATCA 58.817 52.381 0.00 0.00 32.73 2.92
119 120 2.093764 CACTCCAAGTCCTCTGGATCAC 60.094 54.545 0.00 0.00 32.73 3.06
120 121 1.135915 CTCCAAGTCCTCTGGATCACG 59.864 57.143 0.00 0.00 32.73 4.35
121 122 0.898320 CCAAGTCCTCTGGATCACGT 59.102 55.000 0.00 0.00 32.73 4.49
122 123 1.276421 CCAAGTCCTCTGGATCACGTT 59.724 52.381 0.00 0.00 32.73 3.99
123 124 2.611518 CAAGTCCTCTGGATCACGTTC 58.388 52.381 0.00 0.00 32.73 3.95
124 125 0.811915 AGTCCTCTGGATCACGTTCG 59.188 55.000 0.00 0.00 32.73 3.95
125 126 0.526662 GTCCTCTGGATCACGTTCGT 59.473 55.000 0.00 0.00 32.73 3.85
126 127 1.067776 GTCCTCTGGATCACGTTCGTT 60.068 52.381 0.00 0.00 32.73 3.85
127 128 1.201647 TCCTCTGGATCACGTTCGTTC 59.798 52.381 0.00 0.00 0.00 3.95
128 129 1.630148 CTCTGGATCACGTTCGTTCC 58.370 55.000 8.55 8.55 0.00 3.62
129 130 0.963225 TCTGGATCACGTTCGTTCCA 59.037 50.000 15.01 15.01 36.81 3.53
130 131 1.341852 TCTGGATCACGTTCGTTCCAA 59.658 47.619 16.09 7.87 37.78 3.53
131 132 2.139917 CTGGATCACGTTCGTTCCAAA 58.860 47.619 16.09 0.27 37.78 3.28
132 133 2.546368 CTGGATCACGTTCGTTCCAAAA 59.454 45.455 16.09 0.00 37.78 2.44
133 134 2.943690 TGGATCACGTTCGTTCCAAAAA 59.056 40.909 13.92 0.00 35.38 1.94
134 135 3.566322 TGGATCACGTTCGTTCCAAAAAT 59.434 39.130 13.92 0.00 35.38 1.82
135 136 4.156182 GGATCACGTTCGTTCCAAAAATC 58.844 43.478 10.10 0.00 0.00 2.17
136 137 4.319911 GGATCACGTTCGTTCCAAAAATCA 60.320 41.667 10.10 0.00 0.00 2.57
137 138 4.822036 TCACGTTCGTTCCAAAAATCAT 57.178 36.364 0.00 0.00 0.00 2.45
138 139 4.532276 TCACGTTCGTTCCAAAAATCATG 58.468 39.130 0.00 0.00 0.00 3.07
139 140 3.119463 CACGTTCGTTCCAAAAATCATGC 59.881 43.478 0.00 0.00 0.00 4.06
140 141 3.004315 ACGTTCGTTCCAAAAATCATGCT 59.996 39.130 0.00 0.00 0.00 3.79
141 142 3.603770 CGTTCGTTCCAAAAATCATGCTC 59.396 43.478 0.00 0.00 0.00 4.26
142 143 3.848272 TCGTTCCAAAAATCATGCTCC 57.152 42.857 0.00 0.00 0.00 4.70
143 144 2.491693 TCGTTCCAAAAATCATGCTCCC 59.508 45.455 0.00 0.00 0.00 4.30
144 145 2.731968 CGTTCCAAAAATCATGCTCCCG 60.732 50.000 0.00 0.00 0.00 5.14
145 146 2.491693 GTTCCAAAAATCATGCTCCCGA 59.508 45.455 0.00 0.00 0.00 5.14
146 147 2.801483 TCCAAAAATCATGCTCCCGAA 58.199 42.857 0.00 0.00 0.00 4.30
147 148 2.754552 TCCAAAAATCATGCTCCCGAAG 59.245 45.455 0.00 0.00 0.00 3.79
163 164 2.928694 CGAAGGTTTCATTCCGTTTGG 58.071 47.619 0.00 0.00 0.00 3.28
164 165 2.550606 CGAAGGTTTCATTCCGTTTGGA 59.449 45.455 0.00 0.00 44.61 3.53
165 166 3.608474 CGAAGGTTTCATTCCGTTTGGAC 60.608 47.826 0.00 0.00 46.45 4.02
166 167 3.223674 AGGTTTCATTCCGTTTGGACT 57.776 42.857 0.00 0.00 46.45 3.85
167 168 3.146847 AGGTTTCATTCCGTTTGGACTC 58.853 45.455 0.00 0.00 46.45 3.36
168 169 2.228103 GGTTTCATTCCGTTTGGACTCC 59.772 50.000 0.00 0.00 46.45 3.85
169 170 1.803334 TTCATTCCGTTTGGACTCCG 58.197 50.000 0.00 0.00 46.45 4.63
170 171 0.682852 TCATTCCGTTTGGACTCCGT 59.317 50.000 0.00 0.00 46.45 4.69
171 172 1.076332 CATTCCGTTTGGACTCCGTC 58.924 55.000 0.00 0.00 46.45 4.79
172 173 0.974383 ATTCCGTTTGGACTCCGTCT 59.026 50.000 0.00 0.00 46.45 4.18
173 174 0.032952 TTCCGTTTGGACTCCGTCTG 59.967 55.000 0.00 0.00 46.45 3.51
174 175 0.824595 TCCGTTTGGACTCCGTCTGA 60.825 55.000 0.00 0.00 40.17 3.27
175 176 0.246635 CCGTTTGGACTCCGTCTGAT 59.753 55.000 0.00 0.00 37.49 2.90
176 177 1.475280 CCGTTTGGACTCCGTCTGATA 59.525 52.381 0.00 0.00 37.49 2.15
177 178 2.100916 CCGTTTGGACTCCGTCTGATAT 59.899 50.000 0.00 0.00 37.49 1.63
178 179 3.430374 CCGTTTGGACTCCGTCTGATATT 60.430 47.826 0.00 0.00 37.49 1.28
179 180 3.797256 CGTTTGGACTCCGTCTGATATTC 59.203 47.826 0.00 0.00 32.47 1.75
180 181 4.120589 GTTTGGACTCCGTCTGATATTCC 58.879 47.826 0.00 0.00 32.47 3.01
181 182 3.314307 TGGACTCCGTCTGATATTCCT 57.686 47.619 0.00 0.00 32.47 3.36
182 183 3.643237 TGGACTCCGTCTGATATTCCTT 58.357 45.455 0.00 0.00 32.47 3.36
183 184 4.030913 TGGACTCCGTCTGATATTCCTTT 58.969 43.478 0.00 0.00 32.47 3.11
184 185 4.469945 TGGACTCCGTCTGATATTCCTTTT 59.530 41.667 0.00 0.00 32.47 2.27
185 186 5.051153 GGACTCCGTCTGATATTCCTTTTC 58.949 45.833 0.00 0.00 32.47 2.29
186 187 5.163395 GGACTCCGTCTGATATTCCTTTTCT 60.163 44.000 0.00 0.00 32.47 2.52
187 188 6.301169 ACTCCGTCTGATATTCCTTTTCTT 57.699 37.500 0.00 0.00 0.00 2.52
188 189 6.342111 ACTCCGTCTGATATTCCTTTTCTTC 58.658 40.000 0.00 0.00 0.00 2.87
189 190 5.348986 TCCGTCTGATATTCCTTTTCTTCG 58.651 41.667 0.00 0.00 0.00 3.79
190 191 5.126545 TCCGTCTGATATTCCTTTTCTTCGA 59.873 40.000 0.00 0.00 0.00 3.71
191 192 5.810587 CCGTCTGATATTCCTTTTCTTCGAA 59.189 40.000 0.00 0.00 0.00 3.71
192 193 6.312918 CCGTCTGATATTCCTTTTCTTCGAAA 59.687 38.462 0.00 0.00 0.00 3.46
193 194 7.174082 CGTCTGATATTCCTTTTCTTCGAAAC 58.826 38.462 0.00 0.00 0.00 2.78
194 195 7.148639 CGTCTGATATTCCTTTTCTTCGAAACA 60.149 37.037 0.00 0.00 0.00 2.83
195 196 7.958025 GTCTGATATTCCTTTTCTTCGAAACAC 59.042 37.037 0.00 0.00 0.00 3.32
196 197 7.878127 TCTGATATTCCTTTTCTTCGAAACACT 59.122 33.333 0.00 0.00 0.00 3.55
197 198 7.806690 TGATATTCCTTTTCTTCGAAACACTG 58.193 34.615 0.00 0.00 0.00 3.66
198 199 7.659799 TGATATTCCTTTTCTTCGAAACACTGA 59.340 33.333 0.00 0.00 0.00 3.41
199 200 6.693315 ATTCCTTTTCTTCGAAACACTGAA 57.307 33.333 0.00 0.00 0.00 3.02
200 201 6.503589 TTCCTTTTCTTCGAAACACTGAAA 57.496 33.333 0.00 2.34 0.00 2.69
201 202 6.693315 TCCTTTTCTTCGAAACACTGAAAT 57.307 33.333 9.49 0.00 0.00 2.17
202 203 7.795482 TCCTTTTCTTCGAAACACTGAAATA 57.205 32.000 9.49 2.77 0.00 1.40
203 204 7.861630 TCCTTTTCTTCGAAACACTGAAATAG 58.138 34.615 9.49 9.48 0.00 1.73
204 205 7.041372 TCCTTTTCTTCGAAACACTGAAATAGG 60.041 37.037 18.83 18.83 32.66 2.57
205 206 5.607119 TTCTTCGAAACACTGAAATAGGC 57.393 39.130 0.00 0.00 0.00 3.93
206 207 4.637276 TCTTCGAAACACTGAAATAGGCA 58.363 39.130 0.00 0.00 0.00 4.75
207 208 5.060506 TCTTCGAAACACTGAAATAGGCAA 58.939 37.500 0.00 0.00 0.00 4.52
208 209 5.529430 TCTTCGAAACACTGAAATAGGCAAA 59.471 36.000 0.00 0.00 0.00 3.68
209 210 5.759506 TCGAAACACTGAAATAGGCAAAA 57.240 34.783 0.00 0.00 0.00 2.44
210 211 6.137794 TCGAAACACTGAAATAGGCAAAAA 57.862 33.333 0.00 0.00 0.00 1.94
230 231 1.981256 AAATAGCAATACGGGCTGGG 58.019 50.000 0.00 0.00 42.62 4.45
231 232 0.537371 AATAGCAATACGGGCTGGGC 60.537 55.000 0.00 0.00 42.62 5.36
241 242 4.176752 GGCTGGGCCTCCGGTTAG 62.177 72.222 4.53 0.00 46.69 2.34
242 243 3.400054 GCTGGGCCTCCGGTTAGT 61.400 66.667 4.53 0.00 41.53 2.24
243 244 2.062177 GCTGGGCCTCCGGTTAGTA 61.062 63.158 4.53 0.00 41.53 1.82
244 245 2.029307 GCTGGGCCTCCGGTTAGTAG 62.029 65.000 4.53 0.00 41.53 2.57
245 246 1.382146 TGGGCCTCCGGTTAGTAGG 60.382 63.158 4.53 0.51 35.24 3.18
246 247 1.382283 GGGCCTCCGGTTAGTAGGT 60.382 63.158 0.84 0.00 32.67 3.08
247 248 0.979709 GGGCCTCCGGTTAGTAGGTT 60.980 60.000 0.84 0.00 32.67 3.50
248 249 1.689258 GGGCCTCCGGTTAGTAGGTTA 60.689 57.143 0.84 0.00 32.67 2.85
249 250 1.685517 GGCCTCCGGTTAGTAGGTTAG 59.314 57.143 0.00 0.00 32.67 2.34
250 251 2.382882 GCCTCCGGTTAGTAGGTTAGT 58.617 52.381 0.00 0.00 32.67 2.24
251 252 2.360483 GCCTCCGGTTAGTAGGTTAGTC 59.640 54.545 0.00 0.00 32.67 2.59
252 253 2.954989 CCTCCGGTTAGTAGGTTAGTCC 59.045 54.545 0.00 0.00 0.00 3.85
253 254 2.954989 CTCCGGTTAGTAGGTTAGTCCC 59.045 54.545 0.00 0.00 36.75 4.46
254 255 2.311542 TCCGGTTAGTAGGTTAGTCCCA 59.688 50.000 0.00 0.00 36.75 4.37
255 256 3.099141 CCGGTTAGTAGGTTAGTCCCAA 58.901 50.000 0.00 0.00 36.75 4.12
256 257 3.515104 CCGGTTAGTAGGTTAGTCCCAAA 59.485 47.826 0.00 0.00 36.75 3.28
257 258 4.020307 CCGGTTAGTAGGTTAGTCCCAAAA 60.020 45.833 0.00 0.00 36.75 2.44
258 259 5.512921 CCGGTTAGTAGGTTAGTCCCAAAAA 60.513 44.000 0.00 0.00 36.75 1.94
259 260 6.175471 CGGTTAGTAGGTTAGTCCCAAAAAT 58.825 40.000 0.00 0.00 36.75 1.82
260 261 6.093082 CGGTTAGTAGGTTAGTCCCAAAAATG 59.907 42.308 0.00 0.00 36.75 2.32
261 262 7.170277 GGTTAGTAGGTTAGTCCCAAAAATGA 58.830 38.462 0.00 0.00 36.75 2.57
262 263 7.832685 GGTTAGTAGGTTAGTCCCAAAAATGAT 59.167 37.037 0.00 0.00 36.75 2.45
263 264 9.895138 GTTAGTAGGTTAGTCCCAAAAATGATA 57.105 33.333 0.00 0.00 36.75 2.15
285 286 9.688091 TGATATAAATGTGTAAAGTAAAGCCCA 57.312 29.630 0.00 0.00 0.00 5.36
291 292 7.768807 ATGTGTAAAGTAAAGCCCATAAACA 57.231 32.000 0.00 0.00 0.00 2.83
292 293 7.768807 TGTGTAAAGTAAAGCCCATAAACAT 57.231 32.000 0.00 0.00 0.00 2.71
293 294 7.822658 TGTGTAAAGTAAAGCCCATAAACATC 58.177 34.615 0.00 0.00 0.00 3.06
294 295 7.094118 TGTGTAAAGTAAAGCCCATAAACATCC 60.094 37.037 0.00 0.00 0.00 3.51
295 296 6.948886 TGTAAAGTAAAGCCCATAAACATCCA 59.051 34.615 0.00 0.00 0.00 3.41
296 297 6.926630 AAAGTAAAGCCCATAAACATCCAA 57.073 33.333 0.00 0.00 0.00 3.53
297 298 6.926630 AAGTAAAGCCCATAAACATCCAAA 57.073 33.333 0.00 0.00 0.00 3.28
298 299 6.926630 AGTAAAGCCCATAAACATCCAAAA 57.073 33.333 0.00 0.00 0.00 2.44
299 300 7.494922 AGTAAAGCCCATAAACATCCAAAAT 57.505 32.000 0.00 0.00 0.00 1.82
300 301 7.330262 AGTAAAGCCCATAAACATCCAAAATG 58.670 34.615 0.00 0.00 0.00 2.32
301 302 4.758773 AGCCCATAAACATCCAAAATGG 57.241 40.909 0.00 0.00 39.43 3.16
362 363 0.033503 TGGAGACGTATCAGAGGGCA 60.034 55.000 12.92 0.00 0.00 5.36
580 583 3.341043 CGGCGCATCTTCATCGGG 61.341 66.667 10.83 0.00 0.00 5.14
582 585 2.896854 GCGCATCTTCATCGGGCA 60.897 61.111 0.30 0.00 38.38 5.36
679 689 0.610232 GCCATGGCCTCTGTGAGTTT 60.610 55.000 27.24 0.00 34.56 2.66
773 783 7.201956 GGTTGATTAGTGGTCTGATCTATGAGT 60.202 40.741 0.00 0.00 37.51 3.41
774 784 7.517614 TGATTAGTGGTCTGATCTATGAGTC 57.482 40.000 0.00 0.00 37.51 3.36
818 828 2.243810 GGTTGCAATTTGTGGTAGGGA 58.756 47.619 0.59 0.00 0.00 4.20
926 938 5.186198 GTGATTTGTAGCTATTGGTGGTCT 58.814 41.667 0.00 0.00 0.00 3.85
1038 1050 5.993441 TGCTATGATAGTGATGAACCATGTG 59.007 40.000 0.92 0.00 0.00 3.21
1163 1176 0.320771 GTCAGGCCATTGTCGTGTCT 60.321 55.000 5.01 0.00 0.00 3.41
1190 1203 2.034558 CCAGTTTGCTCCATCGTTTGTT 59.965 45.455 0.00 0.00 0.00 2.83
1197 1210 1.726791 CTCCATCGTTTGTTGAGGACG 59.273 52.381 0.00 0.00 38.09 4.79
1261 1274 3.640967 GAGTCTGATTCCCTCTATGTGCT 59.359 47.826 0.00 0.00 0.00 4.40
1293 1318 1.194121 TGAGCCAACTCCTGCTGCTA 61.194 55.000 0.00 0.00 42.74 3.49
1294 1319 0.179936 GAGCCAACTCCTGCTGCTAT 59.820 55.000 0.00 0.00 38.11 2.97
1395 1420 1.667830 ATGTCCACGTTCGTGCTGG 60.668 57.895 18.14 6.87 35.03 4.85
1476 1502 0.934496 CTTGAACACCGTTGCGAAGA 59.066 50.000 0.00 0.00 0.00 2.87
1571 1597 2.265367 TGGATCCAAGTGTCCAAGCTA 58.735 47.619 13.46 0.00 41.36 3.32
1742 1768 5.179368 ACACATGTGTTTCATTCTTAGGACG 59.821 40.000 25.76 0.00 41.83 4.79
1754 1780 0.178926 TTAGGACGACCCAAGGGACA 60.179 55.000 13.15 0.00 38.96 4.02
1783 1809 2.488891 CCTCAACACACCCATCCAGAAA 60.489 50.000 0.00 0.00 0.00 2.52
1786 1812 4.588899 TCAACACACCCATCCAGAAATAG 58.411 43.478 0.00 0.00 0.00 1.73
1790 1816 4.289672 ACACACCCATCCAGAAATAGAACT 59.710 41.667 0.00 0.00 0.00 3.01
1801 1827 5.996513 CCAGAAATAGAACTAGATGCAGCAT 59.003 40.000 7.91 7.91 0.00 3.79
1802 1828 6.485984 CCAGAAATAGAACTAGATGCAGCATT 59.514 38.462 9.90 2.42 0.00 3.56
1837 1863 1.952367 GCTGGCAACTAGGAAGCATGT 60.952 52.381 0.00 0.00 34.01 3.21
1898 1924 3.622826 CCTGGGACACCGGACGTT 61.623 66.667 9.46 0.00 46.80 3.99
1970 1996 4.535781 CATTTGACCCCAACCATGATAGA 58.464 43.478 0.00 0.00 30.88 1.98
1991 2017 1.614449 AGAGGAAGAGAGGAGGCCTA 58.386 55.000 4.42 0.00 31.76 3.93
2355 2381 2.723273 ACATTTTGTGTAGCTAGGGCC 58.277 47.619 0.00 0.00 39.91 5.80
2500 2528 3.646637 AGGTAGTGCTAGGTTGAACTTGT 59.353 43.478 0.00 0.00 0.00 3.16
2516 2544 5.293324 TGAACTTGTTATGCCGTATGATCAC 59.707 40.000 0.00 0.00 0.00 3.06
2536 2564 3.003480 ACGCATGCTTTACTTCTCTTCC 58.997 45.455 17.13 0.00 0.00 3.46
2602 2631 4.039488 TCCATTGATTTGCTGCTTCAACTT 59.961 37.500 12.86 0.42 32.61 2.66
2640 2669 3.508793 GCTAGGGCAAGTGGTATATCGTA 59.491 47.826 0.00 0.00 38.54 3.43
2855 2884 0.966920 AAGGTGGATCGTCAGTTCGT 59.033 50.000 0.00 0.00 0.00 3.85
2893 2922 1.554617 TCATCATCTTCGCCCAGTTCA 59.445 47.619 0.00 0.00 0.00 3.18
2915 2944 1.134877 CACCATTGTTGTGTTGTGGCA 60.135 47.619 0.00 0.00 33.24 4.92
3053 3082 4.118410 CAGCCAACTAAACAAAATGCACA 58.882 39.130 0.00 0.00 0.00 4.57
3087 3116 1.789523 TGCAGGGACTAGGGATACAC 58.210 55.000 0.00 0.00 36.02 2.90
3201 3231 0.250597 GGAACCAAACACGCCCTAGT 60.251 55.000 0.00 0.00 0.00 2.57
3202 3232 1.002315 GGAACCAAACACGCCCTAGTA 59.998 52.381 0.00 0.00 0.00 1.82
3203 3233 2.344025 GAACCAAACACGCCCTAGTAG 58.656 52.381 0.00 0.00 0.00 2.57
3204 3234 1.636148 ACCAAACACGCCCTAGTAGA 58.364 50.000 0.00 0.00 0.00 2.59
3205 3235 2.185387 ACCAAACACGCCCTAGTAGAT 58.815 47.619 0.00 0.00 0.00 1.98
3206 3236 2.570302 ACCAAACACGCCCTAGTAGATT 59.430 45.455 0.00 0.00 0.00 2.40
3207 3237 2.936498 CCAAACACGCCCTAGTAGATTG 59.064 50.000 0.00 0.00 0.00 2.67
3208 3238 3.596214 CAAACACGCCCTAGTAGATTGT 58.404 45.455 0.00 0.00 0.00 2.71
3209 3239 3.521947 AACACGCCCTAGTAGATTGTC 57.478 47.619 0.00 0.00 0.00 3.18
3212 3242 3.451178 ACACGCCCTAGTAGATTGTCATT 59.549 43.478 0.00 0.00 0.00 2.57
3217 3247 5.675538 GCCCTAGTAGATTGTCATTGTCTT 58.324 41.667 0.00 0.00 0.00 3.01
3223 3253 6.169094 AGTAGATTGTCATTGTCTTGTGAGG 58.831 40.000 0.00 0.00 0.00 3.86
3227 3257 5.545063 TTGTCATTGTCTTGTGAGGTAGA 57.455 39.130 0.00 0.00 0.00 2.59
3233 3263 1.272769 GTCTTGTGAGGTAGAGGCGTT 59.727 52.381 0.00 0.00 0.00 4.84
3252 3283 4.436317 GCGTTAGTTCCGTTTGATATGCAA 60.436 41.667 0.00 0.00 33.88 4.08
3254 3285 5.732647 CGTTAGTTCCGTTTGATATGCAAAG 59.267 40.000 0.00 0.00 46.48 2.77
3295 3326 2.131183 GTATGCATCTGCCGAGTCTTC 58.869 52.381 0.19 0.00 41.18 2.87
3317 3352 6.471976 TCGAGAAAAACTGAATGACATGAG 57.528 37.500 0.00 0.00 0.00 2.90
3318 3353 5.084722 CGAGAAAAACTGAATGACATGAGC 58.915 41.667 0.00 0.00 0.00 4.26
3319 3354 5.382618 AGAAAAACTGAATGACATGAGCC 57.617 39.130 0.00 0.00 0.00 4.70
3320 3355 3.837213 AAAACTGAATGACATGAGCCG 57.163 42.857 0.00 0.00 0.00 5.52
3339 3374 4.941263 AGCCGTGCTTTTACTAATCATCAA 59.059 37.500 0.00 0.00 33.89 2.57
3364 3399 0.394352 AACGGATGGAATGGACTGCC 60.394 55.000 0.00 0.00 0.00 4.85
3365 3400 1.526917 CGGATGGAATGGACTGCCC 60.527 63.158 0.00 0.00 0.00 5.36
3449 5111 1.105759 GGGGAGATCAGTTGGCATGC 61.106 60.000 9.90 9.90 0.00 4.06
3450 5112 1.105759 GGGAGATCAGTTGGCATGCC 61.106 60.000 30.54 30.54 0.00 4.40
3453 5115 1.337071 GAGATCAGTTGGCATGCCATG 59.663 52.381 38.78 32.54 46.64 3.66
3454 5116 0.387929 GATCAGTTGGCATGCCATGG 59.612 55.000 38.78 28.47 46.64 3.66
3455 5117 0.324923 ATCAGTTGGCATGCCATGGT 60.325 50.000 38.78 28.20 46.64 3.55
3456 5118 0.966875 TCAGTTGGCATGCCATGGTC 60.967 55.000 38.78 26.44 46.64 4.02
3473 5135 0.971386 GTCGTCAGGTCAACCCCTAA 59.029 55.000 0.00 0.00 36.42 2.69
3476 5138 2.640826 TCGTCAGGTCAACCCCTAATTT 59.359 45.455 0.00 0.00 36.42 1.82
3498 5160 5.994887 TTTTGTGCATATATGGGTACGAC 57.005 39.130 14.51 0.00 0.00 4.34
3499 5161 3.291809 TGTGCATATATGGGTACGACG 57.708 47.619 14.51 0.00 0.00 5.12
3500 5162 1.990563 GTGCATATATGGGTACGACGC 59.009 52.381 14.51 0.00 0.00 5.19
3501 5163 1.067425 TGCATATATGGGTACGACGCC 60.067 52.381 14.51 0.00 0.00 5.68
3539 5205 4.157958 CGTCTCCGTCCGTCCGAC 62.158 72.222 0.00 0.00 38.21 4.79
3554 5220 2.046314 GACCACACCATCCACGGG 60.046 66.667 0.00 0.00 0.00 5.28
3555 5221 4.344865 ACCACACCATCCACGGGC 62.345 66.667 0.00 0.00 0.00 6.13
3582 5248 2.372690 CGTGTACGCCAGTGAGTGC 61.373 63.158 0.00 0.00 0.00 4.40
3627 5293 4.510038 AACAGTTTGCTGCAGGAAATAG 57.490 40.909 32.02 27.33 46.30 1.73
3637 5303 5.221986 TGCTGCAGGAAATAGACATCCATAT 60.222 40.000 17.12 0.00 38.23 1.78
3638 5304 6.013466 TGCTGCAGGAAATAGACATCCATATA 60.013 38.462 17.12 0.00 38.23 0.86
3718 5384 3.753434 AGCGACGTCAGCTCCCTG 61.753 66.667 23.04 4.12 41.83 4.45
3771 5437 6.799925 GGTTGTTTGTAGATCACAATTTACCG 59.200 38.462 10.27 0.00 46.38 4.02
3910 5580 2.417586 GGCCATACGTTAGTCAACCAAC 59.582 50.000 0.00 0.00 0.00 3.77
3915 5585 5.106830 CCATACGTTAGTCAACCAACCTTTC 60.107 44.000 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.520982 TATCTCGTGGGCCCCTCG 60.521 66.667 22.27 23.69 41.16 4.63
14 15 2.210711 CCTATCTCGTGGGCCCCTC 61.211 68.421 22.27 11.95 0.00 4.30
15 16 2.122813 CCTATCTCGTGGGCCCCT 60.123 66.667 22.27 0.00 0.00 4.79
16 17 3.242291 CCCTATCTCGTGGGCCCC 61.242 72.222 22.27 10.05 36.61 5.80
17 18 3.242291 CCCCTATCTCGTGGGCCC 61.242 72.222 17.59 17.59 42.03 5.80
20 21 4.301027 GCGCCCCTATCTCGTGGG 62.301 72.222 0.00 0.00 42.98 4.61
21 22 4.647615 CGCGCCCCTATCTCGTGG 62.648 72.222 0.00 0.00 0.00 4.94
49 50 4.554036 GATGGAGGGCACGCTCCC 62.554 72.222 25.75 11.57 42.55 4.30
50 51 4.554036 GGATGGAGGGCACGCTCC 62.554 72.222 23.07 23.07 43.20 4.70
51 52 3.453070 GAGGATGGAGGGCACGCTC 62.453 68.421 6.18 6.18 0.00 5.03
52 53 3.474570 GAGGATGGAGGGCACGCT 61.475 66.667 0.00 0.00 0.00 5.07
53 54 4.899239 CGAGGATGGAGGGCACGC 62.899 72.222 0.00 0.00 0.00 5.34
54 55 3.461773 ACGAGGATGGAGGGCACG 61.462 66.667 0.00 0.00 0.00 5.34
55 56 2.187946 CACGAGGATGGAGGGCAC 59.812 66.667 0.00 0.00 0.00 5.01
56 57 3.083349 CCACGAGGATGGAGGGCA 61.083 66.667 0.00 0.00 43.02 5.36
57 58 4.554036 GCCACGAGGATGGAGGGC 62.554 72.222 1.86 0.00 43.02 5.19
58 59 3.866582 GGCCACGAGGATGGAGGG 61.867 72.222 1.86 0.00 43.02 4.30
59 60 4.227134 CGGCCACGAGGATGGAGG 62.227 72.222 2.24 0.00 43.02 4.30
60 61 4.899239 GCGGCCACGAGGATGGAG 62.899 72.222 2.24 0.00 43.02 3.86
63 64 4.899239 GAGGCGGCCACGAGGATG 62.899 72.222 23.09 0.00 44.60 3.51
71 72 4.408821 AAGCAATCGAGGCGGCCA 62.409 61.111 23.09 0.00 36.08 5.36
72 73 3.577313 GAAGCAATCGAGGCGGCC 61.577 66.667 12.11 12.11 36.08 6.13
73 74 2.109126 AAGAAGCAATCGAGGCGGC 61.109 57.895 0.00 0.00 36.08 6.53
74 75 0.740868 TCAAGAAGCAATCGAGGCGG 60.741 55.000 6.25 0.00 36.08 6.13
75 76 0.371645 GTCAAGAAGCAATCGAGGCG 59.628 55.000 6.25 0.00 36.08 5.52
76 77 1.731720 AGTCAAGAAGCAATCGAGGC 58.268 50.000 3.80 3.80 0.00 4.70
77 78 2.159599 GCAAGTCAAGAAGCAATCGAGG 60.160 50.000 0.00 0.00 0.00 4.63
78 79 2.481568 TGCAAGTCAAGAAGCAATCGAG 59.518 45.455 0.00 0.00 33.48 4.04
79 80 2.224079 GTGCAAGTCAAGAAGCAATCGA 59.776 45.455 0.00 0.00 38.91 3.59
80 81 2.225019 AGTGCAAGTCAAGAAGCAATCG 59.775 45.455 0.00 0.00 38.91 3.34
81 82 3.819537 GAGTGCAAGTCAAGAAGCAATC 58.180 45.455 0.00 0.00 43.33 2.67
82 83 2.555757 GGAGTGCAAGTCAAGAAGCAAT 59.444 45.455 0.00 0.00 38.29 3.56
83 84 1.949525 GGAGTGCAAGTCAAGAAGCAA 59.050 47.619 0.00 0.00 38.29 3.91
84 85 1.134128 TGGAGTGCAAGTCAAGAAGCA 60.134 47.619 0.00 0.00 38.29 3.91
85 86 1.597742 TGGAGTGCAAGTCAAGAAGC 58.402 50.000 0.00 0.00 38.29 3.86
86 87 3.209410 ACTTGGAGTGCAAGTCAAGAAG 58.791 45.455 22.87 12.84 38.37 2.85
87 88 3.281727 ACTTGGAGTGCAAGTCAAGAA 57.718 42.857 22.87 4.30 38.37 2.52
93 94 1.071385 CAGAGGACTTGGAGTGCAAGT 59.929 52.381 27.72 27.72 44.58 3.16
94 95 1.610102 CCAGAGGACTTGGAGTGCAAG 60.610 57.143 21.50 21.50 39.19 4.01
95 96 0.397941 CCAGAGGACTTGGAGTGCAA 59.602 55.000 0.00 0.00 39.19 4.08
96 97 0.471780 TCCAGAGGACTTGGAGTGCA 60.472 55.000 2.51 0.00 39.19 4.57
97 98 0.908198 ATCCAGAGGACTTGGAGTGC 59.092 55.000 0.19 0.00 36.76 4.40
98 99 2.093764 GTGATCCAGAGGACTTGGAGTG 60.094 54.545 0.19 0.00 32.98 3.51
99 100 2.183679 GTGATCCAGAGGACTTGGAGT 58.816 52.381 0.19 0.00 32.98 3.85
100 101 1.135915 CGTGATCCAGAGGACTTGGAG 59.864 57.143 0.19 0.00 32.98 3.86
101 102 1.186200 CGTGATCCAGAGGACTTGGA 58.814 55.000 0.00 0.00 32.98 3.53
102 103 0.898320 ACGTGATCCAGAGGACTTGG 59.102 55.000 0.00 0.00 32.98 3.61
103 104 2.611518 GAACGTGATCCAGAGGACTTG 58.388 52.381 0.00 0.00 32.98 3.16
104 105 1.202582 CGAACGTGATCCAGAGGACTT 59.797 52.381 0.00 0.00 32.98 3.01
105 106 0.811915 CGAACGTGATCCAGAGGACT 59.188 55.000 0.00 0.00 32.98 3.85
106 107 0.526662 ACGAACGTGATCCAGAGGAC 59.473 55.000 0.00 0.00 32.98 3.85
107 108 1.201647 GAACGAACGTGATCCAGAGGA 59.798 52.381 0.00 0.00 35.55 3.71
108 109 1.630148 GAACGAACGTGATCCAGAGG 58.370 55.000 0.00 0.00 0.00 3.69
109 110 1.067846 TGGAACGAACGTGATCCAGAG 60.068 52.381 14.19 0.00 37.05 3.35
110 111 0.963225 TGGAACGAACGTGATCCAGA 59.037 50.000 14.19 0.00 37.05 3.86
111 112 1.790755 TTGGAACGAACGTGATCCAG 58.209 50.000 16.50 0.00 42.55 3.86
112 113 2.242047 TTTGGAACGAACGTGATCCA 57.758 45.000 14.19 14.19 40.10 3.41
113 114 3.612472 TTTTTGGAACGAACGTGATCC 57.388 42.857 10.07 10.07 0.00 3.36
114 115 4.778904 TGATTTTTGGAACGAACGTGATC 58.221 39.130 0.00 0.00 0.00 2.92
115 116 4.822036 TGATTTTTGGAACGAACGTGAT 57.178 36.364 0.00 0.00 0.00 3.06
116 117 4.532276 CATGATTTTTGGAACGAACGTGA 58.468 39.130 0.00 0.00 0.00 4.35
117 118 3.119463 GCATGATTTTTGGAACGAACGTG 59.881 43.478 0.00 0.00 0.00 4.49
118 119 3.004315 AGCATGATTTTTGGAACGAACGT 59.996 39.130 0.00 0.00 0.00 3.99
119 120 3.564511 AGCATGATTTTTGGAACGAACG 58.435 40.909 0.00 0.00 0.00 3.95
120 121 3.920412 GGAGCATGATTTTTGGAACGAAC 59.080 43.478 0.00 0.00 0.00 3.95
121 122 3.056891 GGGAGCATGATTTTTGGAACGAA 60.057 43.478 0.00 0.00 0.00 3.85
122 123 2.491693 GGGAGCATGATTTTTGGAACGA 59.508 45.455 0.00 0.00 0.00 3.85
123 124 2.731968 CGGGAGCATGATTTTTGGAACG 60.732 50.000 0.00 0.00 0.00 3.95
124 125 2.491693 TCGGGAGCATGATTTTTGGAAC 59.508 45.455 0.00 0.00 0.00 3.62
125 126 2.801483 TCGGGAGCATGATTTTTGGAA 58.199 42.857 0.00 0.00 0.00 3.53
126 127 2.505650 TCGGGAGCATGATTTTTGGA 57.494 45.000 0.00 0.00 0.00 3.53
127 128 2.159198 CCTTCGGGAGCATGATTTTTGG 60.159 50.000 0.00 0.00 37.25 3.28
128 129 2.493278 ACCTTCGGGAGCATGATTTTTG 59.507 45.455 0.00 0.00 38.77 2.44
129 130 2.807676 ACCTTCGGGAGCATGATTTTT 58.192 42.857 0.00 0.00 38.77 1.94
130 131 2.514458 ACCTTCGGGAGCATGATTTT 57.486 45.000 0.00 0.00 38.77 1.82
131 132 2.514458 AACCTTCGGGAGCATGATTT 57.486 45.000 0.00 0.00 38.77 2.17
132 133 2.290896 TGAAACCTTCGGGAGCATGATT 60.291 45.455 0.00 0.00 38.77 2.57
133 134 1.281867 TGAAACCTTCGGGAGCATGAT 59.718 47.619 0.00 0.00 38.77 2.45
134 135 0.690192 TGAAACCTTCGGGAGCATGA 59.310 50.000 0.00 0.00 38.77 3.07
135 136 1.755179 ATGAAACCTTCGGGAGCATG 58.245 50.000 0.00 0.00 38.77 4.06
136 137 2.369394 GAATGAAACCTTCGGGAGCAT 58.631 47.619 0.00 0.00 38.77 3.79
137 138 1.613255 GGAATGAAACCTTCGGGAGCA 60.613 52.381 0.00 0.00 38.77 4.26
138 139 1.095600 GGAATGAAACCTTCGGGAGC 58.904 55.000 0.00 0.00 38.77 4.70
139 140 1.338769 ACGGAATGAAACCTTCGGGAG 60.339 52.381 0.00 0.00 38.77 4.30
140 141 0.688487 ACGGAATGAAACCTTCGGGA 59.312 50.000 0.00 0.00 38.77 5.14
141 142 1.530323 AACGGAATGAAACCTTCGGG 58.470 50.000 0.00 0.00 41.87 5.14
142 143 2.351350 CCAAACGGAATGAAACCTTCGG 60.351 50.000 0.00 0.00 0.00 4.30
143 144 2.550606 TCCAAACGGAATGAAACCTTCG 59.449 45.455 0.00 0.00 0.00 3.79
144 145 3.568430 AGTCCAAACGGAATGAAACCTTC 59.432 43.478 0.00 0.00 33.16 3.46
145 146 3.562182 AGTCCAAACGGAATGAAACCTT 58.438 40.909 0.00 0.00 33.16 3.50
146 147 3.146847 GAGTCCAAACGGAATGAAACCT 58.853 45.455 0.00 0.00 33.16 3.50
147 148 2.228103 GGAGTCCAAACGGAATGAAACC 59.772 50.000 3.60 0.00 33.16 3.27
148 149 2.095919 CGGAGTCCAAACGGAATGAAAC 60.096 50.000 10.49 0.00 33.16 2.78
149 150 2.147958 CGGAGTCCAAACGGAATGAAA 58.852 47.619 10.49 0.00 33.16 2.69
150 151 1.071071 ACGGAGTCCAAACGGAATGAA 59.929 47.619 10.49 0.00 29.74 2.57
151 152 0.682852 ACGGAGTCCAAACGGAATGA 59.317 50.000 10.49 0.00 29.74 2.57
152 153 3.226884 ACGGAGTCCAAACGGAATG 57.773 52.632 10.49 0.00 29.74 2.67
165 166 5.460419 CGAAGAAAAGGAATATCAGACGGAG 59.540 44.000 0.00 0.00 0.00 4.63
166 167 5.126545 TCGAAGAAAAGGAATATCAGACGGA 59.873 40.000 0.00 0.00 0.00 4.69
167 168 5.348986 TCGAAGAAAAGGAATATCAGACGG 58.651 41.667 0.00 0.00 0.00 4.79
168 169 6.887376 TTCGAAGAAAAGGAATATCAGACG 57.113 37.500 0.00 0.00 45.90 4.18
169 170 7.958025 GTGTTTCGAAGAAAAGGAATATCAGAC 59.042 37.037 0.00 0.00 45.90 3.51
170 171 7.878127 AGTGTTTCGAAGAAAAGGAATATCAGA 59.122 33.333 0.00 0.00 45.90 3.27
171 172 7.959651 CAGTGTTTCGAAGAAAAGGAATATCAG 59.040 37.037 0.00 0.00 45.90 2.90
172 173 7.659799 TCAGTGTTTCGAAGAAAAGGAATATCA 59.340 33.333 0.00 0.00 45.90 2.15
173 174 8.029642 TCAGTGTTTCGAAGAAAAGGAATATC 57.970 34.615 0.00 0.00 45.90 1.63
174 175 7.979444 TCAGTGTTTCGAAGAAAAGGAATAT 57.021 32.000 0.00 0.00 45.90 1.28
175 176 7.795482 TTCAGTGTTTCGAAGAAAAGGAATA 57.205 32.000 0.00 0.00 45.90 1.75
176 177 6.693315 TTCAGTGTTTCGAAGAAAAGGAAT 57.307 33.333 0.00 0.00 45.90 3.01
177 178 6.503589 TTTCAGTGTTTCGAAGAAAAGGAA 57.496 33.333 6.96 2.71 45.90 3.36
178 179 6.693315 ATTTCAGTGTTTCGAAGAAAAGGA 57.307 33.333 11.92 0.00 45.90 3.36
179 180 7.078228 CCTATTTCAGTGTTTCGAAGAAAAGG 58.922 38.462 11.92 13.94 45.90 3.11
180 181 6.578919 GCCTATTTCAGTGTTTCGAAGAAAAG 59.421 38.462 11.92 10.48 45.90 2.27
181 182 6.038825 TGCCTATTTCAGTGTTTCGAAGAAAA 59.961 34.615 11.92 3.47 45.90 2.29
182 183 5.529430 TGCCTATTTCAGTGTTTCGAAGAAA 59.471 36.000 10.72 10.72 45.90 2.52
183 184 5.060506 TGCCTATTTCAGTGTTTCGAAGAA 58.939 37.500 0.00 0.00 45.90 2.52
184 185 4.637276 TGCCTATTTCAGTGTTTCGAAGA 58.363 39.130 0.00 0.00 0.00 2.87
185 186 5.356882 TTGCCTATTTCAGTGTTTCGAAG 57.643 39.130 0.00 0.00 0.00 3.79
186 187 5.759506 TTTGCCTATTTCAGTGTTTCGAA 57.240 34.783 0.00 0.00 0.00 3.71
187 188 5.759506 TTTTGCCTATTTCAGTGTTTCGA 57.240 34.783 0.00 0.00 0.00 3.71
209 210 2.693074 CCCAGCCCGTATTGCTATTTTT 59.307 45.455 0.00 0.00 36.81 1.94
210 211 2.306847 CCCAGCCCGTATTGCTATTTT 58.693 47.619 0.00 0.00 36.81 1.82
211 212 1.981256 CCCAGCCCGTATTGCTATTT 58.019 50.000 0.00 0.00 36.81 1.40
212 213 0.537371 GCCCAGCCCGTATTGCTATT 60.537 55.000 0.00 0.00 36.81 1.73
213 214 1.073199 GCCCAGCCCGTATTGCTAT 59.927 57.895 0.00 0.00 36.81 2.97
214 215 2.508928 GCCCAGCCCGTATTGCTA 59.491 61.111 0.00 0.00 36.81 3.49
215 216 4.506255 GGCCCAGCCCGTATTGCT 62.506 66.667 0.00 0.00 44.06 3.91
230 231 4.805044 GGACTAACCTACTAACCGGAGGC 61.805 56.522 9.46 0.00 44.44 4.70
231 232 2.954989 GGACTAACCTACTAACCGGAGG 59.045 54.545 9.46 6.51 45.59 4.30
232 233 2.954989 GGGACTAACCTACTAACCGGAG 59.045 54.545 9.46 0.00 38.98 4.63
233 234 2.311542 TGGGACTAACCTACTAACCGGA 59.688 50.000 9.46 0.00 38.98 5.14
234 235 2.738743 TGGGACTAACCTACTAACCGG 58.261 52.381 0.00 0.00 38.98 5.28
235 236 4.806640 TTTGGGACTAACCTACTAACCG 57.193 45.455 0.00 0.00 38.98 4.44
236 237 7.170277 TCATTTTTGGGACTAACCTACTAACC 58.830 38.462 0.00 0.00 38.98 2.85
237 238 8.803397 ATCATTTTTGGGACTAACCTACTAAC 57.197 34.615 0.00 0.00 38.98 2.34
259 260 9.688091 TGGGCTTTACTTTACACATTTATATCA 57.312 29.630 0.00 0.00 0.00 2.15
265 266 8.643324 TGTTTATGGGCTTTACTTTACACATTT 58.357 29.630 0.00 0.00 0.00 2.32
266 267 8.184304 TGTTTATGGGCTTTACTTTACACATT 57.816 30.769 0.00 0.00 0.00 2.71
267 268 7.768807 TGTTTATGGGCTTTACTTTACACAT 57.231 32.000 0.00 0.00 0.00 3.21
268 269 7.094118 GGATGTTTATGGGCTTTACTTTACACA 60.094 37.037 0.00 0.00 0.00 3.72
269 270 7.094118 TGGATGTTTATGGGCTTTACTTTACAC 60.094 37.037 0.00 0.00 0.00 2.90
270 271 6.948886 TGGATGTTTATGGGCTTTACTTTACA 59.051 34.615 0.00 0.00 0.00 2.41
271 272 7.399245 TGGATGTTTATGGGCTTTACTTTAC 57.601 36.000 0.00 0.00 0.00 2.01
272 273 8.423906 TTTGGATGTTTATGGGCTTTACTTTA 57.576 30.769 0.00 0.00 0.00 1.85
273 274 6.926630 TTGGATGTTTATGGGCTTTACTTT 57.073 33.333 0.00 0.00 0.00 2.66
274 275 6.926630 TTTGGATGTTTATGGGCTTTACTT 57.073 33.333 0.00 0.00 0.00 2.24
275 276 6.926630 TTTTGGATGTTTATGGGCTTTACT 57.073 33.333 0.00 0.00 0.00 2.24
276 277 6.538381 CCATTTTGGATGTTTATGGGCTTTAC 59.462 38.462 0.00 0.00 40.96 2.01
277 278 6.441924 TCCATTTTGGATGTTTATGGGCTTTA 59.558 34.615 0.00 0.00 42.67 1.85
278 279 5.250313 TCCATTTTGGATGTTTATGGGCTTT 59.750 36.000 0.00 0.00 42.67 3.51
279 280 4.782156 TCCATTTTGGATGTTTATGGGCTT 59.218 37.500 0.00 0.00 42.67 4.35
280 281 4.360889 TCCATTTTGGATGTTTATGGGCT 58.639 39.130 0.00 0.00 42.67 5.19
281 282 4.751767 TCCATTTTGGATGTTTATGGGC 57.248 40.909 0.00 0.00 42.67 5.36
324 325 9.027129 CGTCTCCAACGTATCTATAATTTTTGA 57.973 33.333 0.00 0.00 46.42 2.69
341 342 1.202428 GCCCTCTGATACGTCTCCAAC 60.202 57.143 0.00 0.00 0.00 3.77
342 343 1.112113 GCCCTCTGATACGTCTCCAA 58.888 55.000 0.00 0.00 0.00 3.53
343 344 0.033503 TGCCCTCTGATACGTCTCCA 60.034 55.000 0.00 0.00 0.00 3.86
344 345 1.112113 TTGCCCTCTGATACGTCTCC 58.888 55.000 0.00 0.00 0.00 3.71
345 346 1.534175 CGTTGCCCTCTGATACGTCTC 60.534 57.143 0.00 0.00 0.00 3.36
346 347 0.456221 CGTTGCCCTCTGATACGTCT 59.544 55.000 0.00 0.00 0.00 4.18
347 348 1.146358 GCGTTGCCCTCTGATACGTC 61.146 60.000 0.00 0.00 34.89 4.34
348 349 1.153628 GCGTTGCCCTCTGATACGT 60.154 57.895 0.00 0.00 34.89 3.57
349 350 2.230940 CGCGTTGCCCTCTGATACG 61.231 63.158 0.00 0.00 35.48 3.06
350 351 2.526120 GCGCGTTGCCCTCTGATAC 61.526 63.158 8.43 0.00 37.76 2.24
351 352 2.202878 GCGCGTTGCCCTCTGATA 60.203 61.111 8.43 0.00 37.76 2.15
362 363 4.436998 CGAGGGGAGAAGCGCGTT 62.437 66.667 8.43 0.00 0.00 4.84
390 391 4.263209 CGAGCTCGCGCCATCTCT 62.263 66.667 25.07 0.00 36.60 3.10
649 659 2.423898 GCCATGGCTGCAGCTTGAT 61.424 57.895 35.82 22.48 41.70 2.57
679 689 3.780850 GGAACAGAGAGAAAGGGGGATTA 59.219 47.826 0.00 0.00 0.00 1.75
721 731 4.202305 GCATCTAGATCAAACCCTAGCTGT 60.202 45.833 1.03 0.00 33.82 4.40
773 783 3.138304 GCATAGCAACCAACCATATCGA 58.862 45.455 0.00 0.00 0.00 3.59
774 784 3.058708 CAGCATAGCAACCAACCATATCG 60.059 47.826 0.00 0.00 0.00 2.92
818 828 5.371526 CCTACCACATGCTTGAACATCTAT 58.628 41.667 6.60 0.00 0.00 1.98
926 938 8.841300 TCTACAACAAACAACATGCTACAAATA 58.159 29.630 0.00 0.00 0.00 1.40
1057 1070 4.080807 ACACAACATACCGGACAATCCATA 60.081 41.667 9.46 0.00 35.91 2.74
1163 1176 0.111061 ATGGAGCAAACTGGCTGTCA 59.889 50.000 0.00 0.00 45.99 3.58
1190 1203 3.147595 ATAGGCTGCGCGTCCTCA 61.148 61.111 21.39 10.33 34.02 3.86
1197 1210 2.427540 ATCTCGGACATAGGCTGCGC 62.428 60.000 0.00 0.00 0.00 6.09
1476 1502 1.202651 CCCACAGAACTCGAACACCTT 60.203 52.381 0.00 0.00 0.00 3.50
1571 1597 1.219393 GGCGCTGCTAAGGTCTCTT 59.781 57.895 7.64 0.00 37.03 2.85
1742 1768 0.765510 AACTCAGTGTCCCTTGGGTC 59.234 55.000 5.51 0.52 0.00 4.46
1783 1809 8.814931 AGAAGATAATGCTGCATCTAGTTCTAT 58.185 33.333 16.55 7.94 31.25 1.98
1786 1812 6.368516 GGAGAAGATAATGCTGCATCTAGTTC 59.631 42.308 16.55 15.44 31.25 3.01
1790 1816 6.430962 AAGGAGAAGATAATGCTGCATCTA 57.569 37.500 16.55 10.68 31.25 1.98
1970 1996 1.080329 AGGCCTCCTCTCTTCCTCTTT 59.920 52.381 0.00 0.00 0.00 2.52
1991 2017 4.305524 AGACATTGATCTCCTCCTCCATT 58.694 43.478 0.00 0.00 0.00 3.16
2099 2125 0.110295 CACCCTGGGTCATGACAACA 59.890 55.000 26.47 21.70 31.02 3.33
2252 2278 1.819288 TCACAGGCAGCACTACTCTAC 59.181 52.381 0.00 0.00 0.00 2.59
2301 2327 2.537792 ATCGTTGTCGTCGTCGCCAT 62.538 55.000 0.00 0.00 38.33 4.40
2315 2341 0.167470 ACGTCGTCATCGTCATCGTT 59.833 50.000 0.00 0.00 36.85 3.85
2500 2528 2.517650 TGCGTGATCATACGGCATAA 57.482 45.000 0.00 0.00 43.87 1.90
2516 2544 2.029728 CGGAAGAGAAGTAAAGCATGCG 59.970 50.000 13.01 0.00 0.00 4.73
2536 2564 2.916716 GCACACAAACAATAATGGAGCG 59.083 45.455 0.00 0.00 0.00 5.03
2602 2631 3.084039 CCTAGCAATGCACAAGAGGAAA 58.916 45.455 8.35 0.00 0.00 3.13
2635 2664 3.243771 GGAACCTCACCGATGAATACGAT 60.244 47.826 0.00 0.00 33.30 3.73
2636 2665 2.100252 GGAACCTCACCGATGAATACGA 59.900 50.000 0.00 0.00 33.30 3.43
2640 2669 1.210478 CCTGGAACCTCACCGATGAAT 59.790 52.381 0.00 0.00 33.30 2.57
2893 2922 2.224018 GCCACAACACAACAATGGTGAT 60.224 45.455 4.82 0.00 39.88 3.06
2915 2944 2.636830 GATCACAGCTAGCACACCAAT 58.363 47.619 18.83 2.26 0.00 3.16
3039 3068 7.179338 AGGTAATACCCATGTGCATTTTGTTTA 59.821 33.333 5.71 0.00 39.75 2.01
3053 3082 4.042934 GTCCCTGCATTAGGTAATACCCAT 59.957 45.833 5.71 0.00 45.80 4.00
3142 3172 2.877097 TTGCATAGCCTTCTCAACCA 57.123 45.000 0.00 0.00 0.00 3.67
3201 3231 6.114187 ACCTCACAAGACAATGACAATCTA 57.886 37.500 0.00 0.00 0.00 1.98
3202 3232 4.978099 ACCTCACAAGACAATGACAATCT 58.022 39.130 0.00 0.00 0.00 2.40
3203 3233 6.166279 TCTACCTCACAAGACAATGACAATC 58.834 40.000 0.00 0.00 0.00 2.67
3204 3234 6.114187 TCTACCTCACAAGACAATGACAAT 57.886 37.500 0.00 0.00 0.00 2.71
3205 3235 5.511373 CCTCTACCTCACAAGACAATGACAA 60.511 44.000 0.00 0.00 0.00 3.18
3206 3236 4.021104 CCTCTACCTCACAAGACAATGACA 60.021 45.833 0.00 0.00 0.00 3.58
3207 3237 4.499183 CCTCTACCTCACAAGACAATGAC 58.501 47.826 0.00 0.00 0.00 3.06
3208 3238 3.055819 GCCTCTACCTCACAAGACAATGA 60.056 47.826 0.00 0.00 0.00 2.57
3209 3239 3.265791 GCCTCTACCTCACAAGACAATG 58.734 50.000 0.00 0.00 0.00 2.82
3212 3242 0.888619 CGCCTCTACCTCACAAGACA 59.111 55.000 0.00 0.00 0.00 3.41
3217 3247 2.211250 ACTAACGCCTCTACCTCACA 57.789 50.000 0.00 0.00 0.00 3.58
3223 3253 2.643933 AACGGAACTAACGCCTCTAC 57.356 50.000 0.00 0.00 34.00 2.59
3227 3257 2.467566 ATCAAACGGAACTAACGCCT 57.532 45.000 0.00 0.00 34.00 5.52
3233 3263 4.201773 CGCTTTGCATATCAAACGGAACTA 60.202 41.667 0.00 0.00 39.58 2.24
3254 3285 1.269448 TGAATTCCAAGCCAAAGTCGC 59.731 47.619 2.27 0.00 0.00 5.19
3295 3326 5.084722 GCTCATGTCATTCAGTTTTTCTCG 58.915 41.667 0.00 0.00 0.00 4.04
3317 3352 4.875544 TGATGATTAGTAAAAGCACGGC 57.124 40.909 0.00 0.00 0.00 5.68
3318 3353 5.163764 TGCTTGATGATTAGTAAAAGCACGG 60.164 40.000 12.72 0.82 43.57 4.94
3319 3354 5.868257 TGCTTGATGATTAGTAAAAGCACG 58.132 37.500 12.72 2.00 43.57 5.34
3320 3355 7.076842 TCTGCTTGATGATTAGTAAAAGCAC 57.923 36.000 12.72 0.00 43.57 4.40
3339 3374 1.281867 TCCATTCCATCCGTTTCTGCT 59.718 47.619 0.00 0.00 0.00 4.24
3364 3399 1.105167 ATGCCGCCATTGATCTGTGG 61.105 55.000 11.28 11.28 38.55 4.17
3365 3400 0.030235 CATGCCGCCATTGATCTGTG 59.970 55.000 0.00 0.00 0.00 3.66
3366 3401 0.107066 TCATGCCGCCATTGATCTGT 60.107 50.000 0.00 0.00 0.00 3.41
3367 3402 0.591659 CTCATGCCGCCATTGATCTG 59.408 55.000 0.00 0.00 0.00 2.90
3449 5111 0.673644 GGTTGACCTGACGACCATGG 60.674 60.000 11.19 11.19 42.26 3.66
3450 5112 0.673644 GGGTTGACCTGACGACCATG 60.674 60.000 8.05 0.00 43.92 3.66
3453 5115 0.901580 TAGGGGTTGACCTGACGACC 60.902 60.000 0.00 0.00 42.02 4.79
3454 5116 0.971386 TTAGGGGTTGACCTGACGAC 59.029 55.000 0.00 0.00 42.02 4.34
3455 5117 1.946984 ATTAGGGGTTGACCTGACGA 58.053 50.000 0.00 0.00 42.02 4.20
3456 5118 2.781681 AATTAGGGGTTGACCTGACG 57.218 50.000 0.00 0.00 42.02 4.35
3476 5138 4.508492 CGTCGTACCCATATATGCACAAAA 59.492 41.667 7.24 0.00 0.00 2.44
3490 5152 2.493501 GGAAGAGGCGTCGTACCC 59.506 66.667 0.00 0.00 0.00 3.69
3491 5153 1.602327 AAGGGAAGAGGCGTCGTACC 61.602 60.000 14.98 14.98 35.41 3.34
3492 5154 0.245813 AAAGGGAAGAGGCGTCGTAC 59.754 55.000 0.00 0.00 0.00 3.67
3493 5155 0.529378 GAAAGGGAAGAGGCGTCGTA 59.471 55.000 0.00 0.00 0.00 3.43
3494 5156 1.292541 GAAAGGGAAGAGGCGTCGT 59.707 57.895 0.00 0.00 0.00 4.34
3495 5157 1.448013 GGAAAGGGAAGAGGCGTCG 60.448 63.158 0.00 0.00 0.00 5.12
3496 5158 1.078356 GGGAAAGGGAAGAGGCGTC 60.078 63.158 0.00 0.00 0.00 5.19
3498 5160 2.125106 CGGGAAAGGGAAGAGGCG 60.125 66.667 0.00 0.00 0.00 5.52
3499 5161 0.960861 CAACGGGAAAGGGAAGAGGC 60.961 60.000 0.00 0.00 0.00 4.70
3500 5162 0.322546 CCAACGGGAAAGGGAAGAGG 60.323 60.000 0.00 0.00 35.59 3.69
3501 5163 0.690762 TCCAACGGGAAAGGGAAGAG 59.309 55.000 0.00 0.00 41.32 2.85
3564 5230 2.372690 GCACTCACTGGCGTACACG 61.373 63.158 0.00 0.00 43.27 4.49
3582 5248 3.885297 CCCTCCTGTAAACCTGCAATATG 59.115 47.826 0.00 0.00 0.00 1.78
3666 5332 7.598869 GGACCATTTGGACAAGAAGTTTTTATC 59.401 37.037 3.01 0.00 38.94 1.75
3667 5333 7.441836 GGACCATTTGGACAAGAAGTTTTTAT 58.558 34.615 3.01 0.00 38.94 1.40
3718 5384 8.394877 TGTCGTTGTCAATGAAAATATATCCAC 58.605 33.333 9.08 0.00 0.00 4.02
3827 5493 9.967346 TTTAAGACAACTAATATGGATCGAGAG 57.033 33.333 0.00 0.00 0.00 3.20
3867 5534 3.281727 TTGGCCTGTCTTGATACATCC 57.718 47.619 3.32 0.00 0.00 3.51
3897 5565 5.183014 CTTGGAAAGGTTGGTTGACTAAC 57.817 43.478 2.17 2.17 41.27 2.34


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

AutoCloner maintained by Alex Coulton.