Multiple sequence alignment - TraesCS7A01G133100

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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 TraesCS7A01G133100 chr7A 100.000 3949 0 0 1 3949 85421100 85425048 0.000000e+00 7293
1 TraesCS7A01G133100 chr7B 91.631 3047 190 26 229 3240 33546698 33549714 0.000000e+00 4154
2 TraesCS7A01G133100 chr7B 88.627 721 39 16 3237 3948 33549742 33550428 0.000000e+00 837
3 TraesCS7A01G133100 chr7B 83.305 587 66 26 963 1543 83559961 83560521 2.720000e-141 512
4 TraesCS7A01G133100 chr7D 94.707 2286 111 8 690 2972 83799638 83801916 0.000000e+00 3542
5 TraesCS7A01G133100 chr7D 90.818 501 36 8 3237 3733 83802318 83802812 0.000000e+00 662
6 TraesCS7A01G133100 chr7D 95.221 272 13 0 2969 3240 83802019 83802290 7.840000e-117 431
7 TraesCS7A01G133100 chr7D 90.152 132 12 1 3794 3925 83802836 83802966 1.890000e-38 171
8 TraesCS7A01G133100 chr1A 85.816 564 54 18 987 1543 175601944 175602488 3.420000e-160 575
9 TraesCS7A01G133100 chr3A 85.461 564 58 17 987 1543 408567098 408567644 2.060000e-157 566
10 TraesCS7A01G133100 chr1B 84.342 562 59 21 987 1543 687610407 687609870 1.260000e-144 523
11 TraesCS7A01G133100 chr3B 82.906 585 66 24 964 1543 27125905 27125350 2.740000e-136 496
12 TraesCS7A01G133100 chr1D 89.344 122 12 1 1 122 366849811 366849691 6.830000e-33 152
13 TraesCS7A01G133100 chr2A 90.110 91 8 1 3794 3884 497459491 497459402 2.490000e-22 117
14 TraesCS7A01G133100 chr2A 89.011 91 9 1 3794 3884 497472743 497472654 1.160000e-20 111


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 TraesCS7A01G133100 chr7A 85421100 85425048 3948 False 7293.0 7293 100.0000 1 3949 1 chr7A.!!$F1 3948
1 TraesCS7A01G133100 chr7B 33546698 33550428 3730 False 2495.5 4154 90.1290 229 3948 2 chr7B.!!$F2 3719
2 TraesCS7A01G133100 chr7B 83559961 83560521 560 False 512.0 512 83.3050 963 1543 1 chr7B.!!$F1 580
3 TraesCS7A01G133100 chr7D 83799638 83802966 3328 False 1201.5 3542 92.7245 690 3925 4 chr7D.!!$F1 3235
4 TraesCS7A01G133100 chr1A 175601944 175602488 544 False 575.0 575 85.8160 987 1543 1 chr1A.!!$F1 556
5 TraesCS7A01G133100 chr3A 408567098 408567644 546 False 566.0 566 85.4610 987 1543 1 chr3A.!!$F1 556
6 TraesCS7A01G133100 chr1B 687609870 687610407 537 True 523.0 523 84.3420 987 1543 1 chr1B.!!$R1 556
7 TraesCS7A01G133100 chr3B 27125350 27125905 555 True 496.0 496 82.9060 964 1543 1 chr3B.!!$R1 579

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
86 87 0.035317 ATGCTTCAGCGACAGAACCA 59.965 50.000 0.00 0.00 45.83 3.67 F
167 168 0.100503 GCACCAAACTGTTCGCTGTT 59.899 50.000 0.00 0.00 40.29 3.16 F
238 239 0.465460 AACACGGGCTGATTGTGTGT 60.465 50.000 0.00 0.00 45.48 3.72 F
950 971 0.684153 CATCCAGTCCCCCGCAAAAT 60.684 55.000 0.00 0.00 0.00 1.82 F
2762 2804 1.010125 CAACTGTTTGGTGGACGCG 60.010 57.895 3.53 3.53 0.00 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 1516 0.107831 GGGCACGGCATGGTTAGATA 59.892 55.000 0.00 0.00 0.0 1.98 R
1484 1517 1.152963 GGGCACGGCATGGTTAGAT 60.153 57.895 0.00 0.00 0.0 1.98 R
1670 1703 1.218316 GGAGACAAGGGCCGTGTAG 59.782 63.158 25.09 3.65 0.0 2.74 R
2909 2951 1.674817 CGCCCATCTTTTAGGTCACGT 60.675 52.381 0.00 0.00 0.0 4.49 R
3575 3762 2.504175 GGTCCATTAGTTAGGTGCCAGA 59.496 50.000 0.00 0.00 0.0 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.954927 CGCCCTCATTTCCTTCCTAC 58.045 55.000 0.00 0.00 0.00 3.18
20 21 1.486726 CGCCCTCATTTCCTTCCTACT 59.513 52.381 0.00 0.00 0.00 2.57
21 22 2.092914 CGCCCTCATTTCCTTCCTACTT 60.093 50.000 0.00 0.00 0.00 2.24
22 23 3.622455 CGCCCTCATTTCCTTCCTACTTT 60.622 47.826 0.00 0.00 0.00 2.66
23 24 4.344978 GCCCTCATTTCCTTCCTACTTTT 58.655 43.478 0.00 0.00 0.00 2.27
24 25 4.772624 GCCCTCATTTCCTTCCTACTTTTT 59.227 41.667 0.00 0.00 0.00 1.94
25 26 5.105716 GCCCTCATTTCCTTCCTACTTTTTC 60.106 44.000 0.00 0.00 0.00 2.29
26 27 6.249192 CCCTCATTTCCTTCCTACTTTTTCT 58.751 40.000 0.00 0.00 0.00 2.52
27 28 7.402862 CCCTCATTTCCTTCCTACTTTTTCTA 58.597 38.462 0.00 0.00 0.00 2.10
28 29 8.055790 CCCTCATTTCCTTCCTACTTTTTCTAT 58.944 37.037 0.00 0.00 0.00 1.98
29 30 9.467796 CCTCATTTCCTTCCTACTTTTTCTATT 57.532 33.333 0.00 0.00 0.00 1.73
32 33 9.774742 CATTTCCTTCCTACTTTTTCTATTTCG 57.225 33.333 0.00 0.00 0.00 3.46
33 34 9.734984 ATTTCCTTCCTACTTTTTCTATTTCGA 57.265 29.630 0.00 0.00 0.00 3.71
34 35 8.543862 TTCCTTCCTACTTTTTCTATTTCGAC 57.456 34.615 0.00 0.00 0.00 4.20
35 36 7.904205 TCCTTCCTACTTTTTCTATTTCGACT 58.096 34.615 0.00 0.00 0.00 4.18
36 37 9.028284 TCCTTCCTACTTTTTCTATTTCGACTA 57.972 33.333 0.00 0.00 0.00 2.59
37 38 9.819267 CCTTCCTACTTTTTCTATTTCGACTAT 57.181 33.333 0.00 0.00 0.00 2.12
39 40 8.644318 TCCTACTTTTTCTATTTCGACTATGC 57.356 34.615 0.00 0.00 0.00 3.14
40 41 7.434307 TCCTACTTTTTCTATTTCGACTATGCG 59.566 37.037 0.00 0.00 0.00 4.73
41 42 5.796813 ACTTTTTCTATTTCGACTATGCGC 58.203 37.500 0.00 0.00 0.00 6.09
42 43 5.581085 ACTTTTTCTATTTCGACTATGCGCT 59.419 36.000 9.73 0.00 0.00 5.92
43 44 6.755141 ACTTTTTCTATTTCGACTATGCGCTA 59.245 34.615 9.73 0.00 0.00 4.26
44 45 7.277098 ACTTTTTCTATTTCGACTATGCGCTAA 59.723 33.333 9.73 0.00 0.00 3.09
45 46 7.709269 TTTTCTATTTCGACTATGCGCTAAT 57.291 32.000 9.73 0.00 0.00 1.73
46 47 6.690704 TTCTATTTCGACTATGCGCTAATG 57.309 37.500 9.73 0.00 0.00 1.90
47 48 5.161358 TCTATTTCGACTATGCGCTAATGG 58.839 41.667 9.73 0.00 0.00 3.16
48 49 2.148916 TTCGACTATGCGCTAATGGG 57.851 50.000 9.73 0.00 0.00 4.00
77 78 2.194800 TTAGTCGAGATGCTTCAGCG 57.805 50.000 2.07 5.59 45.83 5.18
78 79 1.379527 TAGTCGAGATGCTTCAGCGA 58.620 50.000 11.64 11.64 45.83 4.93
79 80 0.179150 AGTCGAGATGCTTCAGCGAC 60.179 55.000 26.15 26.15 44.91 5.19
80 81 0.456824 GTCGAGATGCTTCAGCGACA 60.457 55.000 27.38 7.32 44.42 4.35
81 82 0.179153 TCGAGATGCTTCAGCGACAG 60.179 55.000 11.64 0.00 45.83 3.51
82 83 0.179153 CGAGATGCTTCAGCGACAGA 60.179 55.000 8.53 0.00 45.83 3.41
83 84 1.733718 CGAGATGCTTCAGCGACAGAA 60.734 52.381 8.53 0.00 45.83 3.02
84 85 1.658095 GAGATGCTTCAGCGACAGAAC 59.342 52.381 2.07 0.00 45.83 3.01
85 86 0.723981 GATGCTTCAGCGACAGAACC 59.276 55.000 0.00 0.00 45.83 3.62
86 87 0.035317 ATGCTTCAGCGACAGAACCA 59.965 50.000 0.00 0.00 45.83 3.67
87 88 0.035317 TGCTTCAGCGACAGAACCAT 59.965 50.000 0.00 0.00 45.83 3.55
88 89 0.723981 GCTTCAGCGACAGAACCATC 59.276 55.000 0.00 0.00 0.00 3.51
89 90 0.994995 CTTCAGCGACAGAACCATCG 59.005 55.000 0.00 0.00 41.32 3.84
90 91 0.389817 TTCAGCGACAGAACCATCGG 60.390 55.000 0.00 0.00 38.78 4.18
91 92 3.377656 AGCGACAGAACCATCGGT 58.622 55.556 0.00 0.00 43.70 4.69
92 93 1.078759 CAGCGACAGAACCATCGGTC 61.079 60.000 0.00 0.00 46.49 4.79
93 94 1.215647 GCGACAGAACCATCGGTCT 59.784 57.895 7.35 0.00 45.23 3.85
94 95 0.802607 GCGACAGAACCATCGGTCTC 60.803 60.000 7.35 0.00 45.23 3.36
95 96 0.523546 CGACAGAACCATCGGTCTCG 60.524 60.000 7.35 0.00 45.23 4.04
96 97 0.526662 GACAGAACCATCGGTCTCGT 59.473 55.000 2.51 0.00 44.38 4.18
97 98 0.966920 ACAGAACCATCGGTCTCGTT 59.033 50.000 0.00 0.00 33.12 3.85
98 99 1.336887 ACAGAACCATCGGTCTCGTTG 60.337 52.381 0.00 0.00 33.12 4.10
99 100 1.067846 CAGAACCATCGGTCTCGTTGA 60.068 52.381 0.00 0.00 38.07 3.18
100 101 1.616865 AGAACCATCGGTCTCGTTGAA 59.383 47.619 0.00 0.00 38.07 2.69
101 102 2.233922 AGAACCATCGGTCTCGTTGAAT 59.766 45.455 0.00 0.00 38.07 2.57
102 103 2.010145 ACCATCGGTCTCGTTGAATG 57.990 50.000 0.00 0.00 38.07 2.67
103 104 0.652592 CCATCGGTCTCGTTGAATGC 59.347 55.000 0.00 0.00 38.07 3.56
104 105 0.298707 CATCGGTCTCGTTGAATGCG 59.701 55.000 0.00 0.00 38.07 4.73
105 106 0.172578 ATCGGTCTCGTTGAATGCGA 59.827 50.000 0.00 0.00 37.69 5.10
114 115 3.234386 TCGTTGAATGCGAGATATAGCG 58.766 45.455 0.00 0.00 35.87 4.26
120 121 3.955216 CGAGATATAGCGCTCGCG 58.045 61.111 16.34 10.04 45.97 5.87
130 131 3.081133 CGCTCGCGCTGTTGTTAT 58.919 55.556 5.56 0.00 0.00 1.89
131 132 1.013323 CGCTCGCGCTGTTGTTATC 60.013 57.895 5.56 0.00 0.00 1.75
132 133 1.348594 GCTCGCGCTGTTGTTATCC 59.651 57.895 5.56 0.00 0.00 2.59
133 134 1.358725 GCTCGCGCTGTTGTTATCCA 61.359 55.000 5.56 0.00 0.00 3.41
134 135 1.075542 CTCGCGCTGTTGTTATCCAA 58.924 50.000 5.56 0.00 0.00 3.53
135 136 1.463056 CTCGCGCTGTTGTTATCCAAA 59.537 47.619 5.56 0.00 34.07 3.28
136 137 1.874231 TCGCGCTGTTGTTATCCAAAA 59.126 42.857 5.56 0.00 34.07 2.44
137 138 2.290916 TCGCGCTGTTGTTATCCAAAAA 59.709 40.909 5.56 0.00 34.07 1.94
162 163 4.749245 AAGAATAGCACCAAACTGTTCG 57.251 40.909 0.00 0.00 39.45 3.95
163 164 2.484264 AGAATAGCACCAAACTGTTCGC 59.516 45.455 0.00 0.00 39.45 4.70
164 165 2.185004 ATAGCACCAAACTGTTCGCT 57.815 45.000 10.27 10.27 0.00 4.93
165 166 1.225855 TAGCACCAAACTGTTCGCTG 58.774 50.000 13.57 1.54 0.00 5.18
166 167 0.748005 AGCACCAAACTGTTCGCTGT 60.748 50.000 0.00 0.00 0.00 4.40
167 168 0.100503 GCACCAAACTGTTCGCTGTT 59.899 50.000 0.00 0.00 40.29 3.16
168 169 1.826327 CACCAAACTGTTCGCTGTTG 58.174 50.000 0.00 0.00 38.88 3.33
169 170 0.738389 ACCAAACTGTTCGCTGTTGG 59.262 50.000 5.39 5.39 38.88 3.77
170 171 0.738389 CCAAACTGTTCGCTGTTGGT 59.262 50.000 0.00 0.00 38.88 3.67
171 172 1.134175 CCAAACTGTTCGCTGTTGGTT 59.866 47.619 0.00 0.00 38.88 3.67
172 173 2.416701 CCAAACTGTTCGCTGTTGGTTT 60.417 45.455 0.00 0.00 38.88 3.27
173 174 3.249917 CAAACTGTTCGCTGTTGGTTTT 58.750 40.909 0.00 0.00 38.88 2.43
174 175 3.586100 AACTGTTCGCTGTTGGTTTTT 57.414 38.095 0.00 0.00 37.77 1.94
175 176 2.874849 ACTGTTCGCTGTTGGTTTTTG 58.125 42.857 0.00 0.00 0.00 2.44
176 177 2.230266 ACTGTTCGCTGTTGGTTTTTGT 59.770 40.909 0.00 0.00 0.00 2.83
177 178 2.598192 CTGTTCGCTGTTGGTTTTTGTG 59.402 45.455 0.00 0.00 0.00 3.33
178 179 2.029828 TGTTCGCTGTTGGTTTTTGTGT 60.030 40.909 0.00 0.00 0.00 3.72
179 180 3.190744 TGTTCGCTGTTGGTTTTTGTGTA 59.809 39.130 0.00 0.00 0.00 2.90
180 181 3.684103 TCGCTGTTGGTTTTTGTGTAG 57.316 42.857 0.00 0.00 0.00 2.74
181 182 2.116366 CGCTGTTGGTTTTTGTGTAGC 58.884 47.619 0.00 0.00 0.00 3.58
182 183 2.116366 GCTGTTGGTTTTTGTGTAGCG 58.884 47.619 0.00 0.00 0.00 4.26
183 184 2.116366 CTGTTGGTTTTTGTGTAGCGC 58.884 47.619 0.00 0.00 0.00 5.92
184 185 1.472878 TGTTGGTTTTTGTGTAGCGCA 59.527 42.857 11.47 0.00 0.00 6.09
196 197 4.335082 GTGTAGCGCACAACATAATGAA 57.665 40.909 11.47 0.00 46.91 2.57
197 198 4.717991 GTGTAGCGCACAACATAATGAAA 58.282 39.130 11.47 0.00 46.91 2.69
198 199 5.331902 GTGTAGCGCACAACATAATGAAAT 58.668 37.500 11.47 0.00 46.91 2.17
199 200 5.799936 GTGTAGCGCACAACATAATGAAATT 59.200 36.000 11.47 0.00 46.91 1.82
200 201 6.021468 GTGTAGCGCACAACATAATGAAATTC 60.021 38.462 11.47 0.00 46.91 2.17
201 202 4.097714 AGCGCACAACATAATGAAATTCG 58.902 39.130 11.47 0.00 37.87 3.34
202 203 4.094911 GCGCACAACATAATGAAATTCGA 58.905 39.130 0.30 0.00 37.87 3.71
203 204 4.734854 GCGCACAACATAATGAAATTCGAT 59.265 37.500 0.30 0.00 37.87 3.59
204 205 5.331013 GCGCACAACATAATGAAATTCGATG 60.331 40.000 0.30 2.17 37.87 3.84
205 206 5.964751 CGCACAACATAATGAAATTCGATGA 59.035 36.000 8.64 0.00 37.87 2.92
206 207 6.468637 CGCACAACATAATGAAATTCGATGAA 59.531 34.615 8.64 0.00 37.87 2.57
207 208 7.008176 CGCACAACATAATGAAATTCGATGAAA 59.992 33.333 8.64 0.00 37.87 2.69
208 209 8.810427 GCACAACATAATGAAATTCGATGAAAT 58.190 29.630 8.64 0.00 37.87 2.17
235 236 2.507339 AAAAACACGGGCTGATTGTG 57.493 45.000 0.00 0.00 39.47 3.33
237 238 0.667993 AAACACGGGCTGATTGTGTG 59.332 50.000 0.00 0.00 45.48 3.82
238 239 0.465460 AACACGGGCTGATTGTGTGT 60.465 50.000 0.00 0.00 45.48 3.72
239 240 1.165907 ACACGGGCTGATTGTGTGTG 61.166 55.000 0.00 0.00 44.59 3.82
240 241 1.148273 ACGGGCTGATTGTGTGTGT 59.852 52.632 0.00 0.00 0.00 3.72
241 242 0.884704 ACGGGCTGATTGTGTGTGTC 60.885 55.000 0.00 0.00 0.00 3.67
242 243 1.868997 GGGCTGATTGTGTGTGTCG 59.131 57.895 0.00 0.00 0.00 4.35
243 244 1.577328 GGGCTGATTGTGTGTGTCGG 61.577 60.000 0.00 0.00 0.00 4.79
252 253 1.480545 TGTGTGTGTCGGATAGGATGG 59.519 52.381 0.00 0.00 0.00 3.51
256 257 3.383505 TGTGTGTCGGATAGGATGGTAAG 59.616 47.826 0.00 0.00 0.00 2.34
258 259 1.968493 TGTCGGATAGGATGGTAAGGC 59.032 52.381 0.00 0.00 0.00 4.35
259 260 1.275573 GTCGGATAGGATGGTAAGGCC 59.724 57.143 0.00 0.00 37.90 5.19
274 275 5.186797 TGGTAAGGCCATCATGTTAAAAAGG 59.813 40.000 5.01 0.00 43.61 3.11
277 278 4.623863 AGGCCATCATGTTAAAAAGGGAT 58.376 39.130 5.01 0.00 0.00 3.85
282 283 5.127519 CCATCATGTTAAAAAGGGATGAGCA 59.872 40.000 0.00 0.00 35.36 4.26
283 284 5.643379 TCATGTTAAAAAGGGATGAGCAC 57.357 39.130 0.00 0.00 0.00 4.40
286 287 6.211184 TCATGTTAAAAAGGGATGAGCACAAT 59.789 34.615 0.00 0.00 0.00 2.71
289 290 6.945435 TGTTAAAAAGGGATGAGCACAATAGA 59.055 34.615 0.00 0.00 0.00 1.98
291 292 6.521151 AAAAAGGGATGAGCACAATAGAAG 57.479 37.500 0.00 0.00 0.00 2.85
292 293 3.853355 AGGGATGAGCACAATAGAAGG 57.147 47.619 0.00 0.00 0.00 3.46
293 294 3.387962 AGGGATGAGCACAATAGAAGGA 58.612 45.455 0.00 0.00 0.00 3.36
309 310 5.391312 AGAAGGATTGCACATAACCAAAC 57.609 39.130 0.00 0.00 0.00 2.93
312 313 3.057596 AGGATTGCACATAACCAAACACG 60.058 43.478 0.00 0.00 0.00 4.49
314 315 4.083217 GGATTGCACATAACCAAACACGTA 60.083 41.667 0.00 0.00 0.00 3.57
331 332 6.307031 ACACGTATGTTTTACATTTGCTCA 57.693 33.333 0.00 0.00 39.88 4.26
336 337 6.092944 CGTATGTTTTACATTTGCTCACCCTA 59.907 38.462 0.00 0.00 39.88 3.53
340 341 7.206687 TGTTTTACATTTGCTCACCCTAAAAG 58.793 34.615 0.00 0.00 0.00 2.27
341 342 3.942130 ACATTTGCTCACCCTAAAAGC 57.058 42.857 0.00 0.00 36.56 3.51
360 361 1.477558 GCACATAGGCAGGCAGGTAAT 60.478 52.381 0.00 0.00 0.00 1.89
362 363 2.126882 ACATAGGCAGGCAGGTAATCA 58.873 47.619 0.00 0.00 0.00 2.57
367 368 1.474077 GGCAGGCAGGTAATCAAACAG 59.526 52.381 0.00 0.00 0.00 3.16
371 372 3.441572 CAGGCAGGTAATCAAACAGAAGG 59.558 47.826 0.00 0.00 0.00 3.46
376 377 5.449177 GCAGGTAATCAAACAGAAGGCATAC 60.449 44.000 0.00 0.00 0.00 2.39
383 384 6.839124 TCAAACAGAAGGCATACAAATGAT 57.161 33.333 0.00 0.00 34.84 2.45
391 392 7.332678 CAGAAGGCATACAAATGATCATCGATA 59.667 37.037 9.06 2.13 34.84 2.92
392 393 8.045507 AGAAGGCATACAAATGATCATCGATAT 58.954 33.333 9.06 4.41 34.84 1.63
393 394 7.549615 AGGCATACAAATGATCATCGATATG 57.450 36.000 9.06 15.98 34.84 1.78
409 410 7.976175 TCATCGATATGATACAGGCTATCAAAC 59.024 37.037 0.00 0.00 37.20 2.93
416 417 1.066143 ACAGGCTATCAAACGAGGTGG 60.066 52.381 0.00 0.00 0.00 4.61
418 419 1.906574 AGGCTATCAAACGAGGTGGAA 59.093 47.619 0.00 0.00 0.00 3.53
419 420 2.007608 GGCTATCAAACGAGGTGGAAC 58.992 52.381 0.00 0.00 0.00 3.62
420 421 2.614481 GGCTATCAAACGAGGTGGAACA 60.614 50.000 0.00 0.00 39.98 3.18
421 422 3.270877 GCTATCAAACGAGGTGGAACAT 58.729 45.455 0.00 0.00 44.52 2.71
422 423 3.063997 GCTATCAAACGAGGTGGAACATG 59.936 47.826 0.00 0.00 44.52 3.21
423 424 1.890876 TCAAACGAGGTGGAACATGG 58.109 50.000 0.00 0.00 44.52 3.66
425 426 0.893727 AAACGAGGTGGAACATGGGC 60.894 55.000 0.00 0.00 44.52 5.36
426 427 2.819595 CGAGGTGGAACATGGGCG 60.820 66.667 0.00 0.00 44.52 6.13
427 428 2.668632 GAGGTGGAACATGGGCGA 59.331 61.111 0.00 0.00 44.52 5.54
428 429 1.450312 GAGGTGGAACATGGGCGAG 60.450 63.158 0.00 0.00 44.52 5.03
429 430 1.899437 GAGGTGGAACATGGGCGAGA 61.899 60.000 0.00 0.00 44.52 4.04
466 468 2.274104 GGCTGAACCGGGCCATAA 59.726 61.111 13.93 0.00 46.84 1.90
493 495 6.935741 ACATTACGCCTAGAATTAATGCAA 57.064 33.333 13.11 0.00 35.99 4.08
503 505 6.873076 CCTAGAATTAATGCAAGCAACCAAAA 59.127 34.615 0.00 0.00 0.00 2.44
543 545 7.599245 ACTTTCTAAAGTGACGACATTTCCTAG 59.401 37.037 7.29 0.00 46.80 3.02
550 552 3.071479 GACGACATTTCCTAGCCAACAA 58.929 45.455 0.00 0.00 0.00 2.83
551 553 2.812011 ACGACATTTCCTAGCCAACAAC 59.188 45.455 0.00 0.00 0.00 3.32
555 557 3.569701 ACATTTCCTAGCCAACAACACAG 59.430 43.478 0.00 0.00 0.00 3.66
564 566 3.071602 AGCCAACAACACAGTACTCATCT 59.928 43.478 0.00 0.00 0.00 2.90
602 604 3.280295 CTCTCCGTAAGCTAGGACTTGA 58.720 50.000 1.80 0.00 32.33 3.02
617 619 3.003275 GGACTTGAAGCGTTGATGTGAAA 59.997 43.478 0.00 0.00 0.00 2.69
669 673 2.063266 TGAAAAGCGTAGTTGTAGCGG 58.937 47.619 0.00 0.00 35.78 5.52
670 674 2.288334 TGAAAAGCGTAGTTGTAGCGGA 60.288 45.455 0.00 0.00 35.78 5.54
671 675 2.443887 AAAGCGTAGTTGTAGCGGAA 57.556 45.000 0.00 0.00 35.78 4.30
680 684 6.087820 GCGTAGTTGTAGCGGAAAATATAGAG 59.912 42.308 0.00 0.00 0.00 2.43
683 687 9.182933 GTAGTTGTAGCGGAAAATATAGAGAAG 57.817 37.037 0.00 0.00 0.00 2.85
685 689 5.539048 TGTAGCGGAAAATATAGAGAAGCC 58.461 41.667 0.00 0.00 0.00 4.35
689 693 6.827727 AGCGGAAAATATAGAGAAGCCTTTA 58.172 36.000 0.00 0.00 0.00 1.85
710 727 1.244019 ACTTGCCCGAGGATTGCAAC 61.244 55.000 0.00 0.00 39.86 4.17
714 731 1.750399 CCCGAGGATTGCAACCCTG 60.750 63.158 20.03 9.72 31.84 4.45
730 747 1.613437 CCCTGCAAATCAAACGAACCT 59.387 47.619 0.00 0.00 0.00 3.50
754 772 7.093902 CCTTAGAAAAAGAATTAGGGGTCCAAC 60.094 40.741 0.00 0.00 0.00 3.77
756 774 7.098845 AGAAAAAGAATTAGGGGTCCAACTA 57.901 36.000 0.00 0.00 0.00 2.24
769 787 5.130477 GGGGTCCAACTACTCTGAAATATCA 59.870 44.000 0.00 0.00 0.00 2.15
814 832 3.067461 TGGGTTCTTTGTATGCACAACAC 59.933 43.478 3.28 0.00 44.28 3.32
856 877 5.450688 GCGTCTTGATTACTGTACAGGAGAT 60.451 44.000 26.12 15.97 0.00 2.75
859 880 6.096987 GTCTTGATTACTGTACAGGAGATCCA 59.903 42.308 26.12 15.35 38.89 3.41
876 897 1.675310 CAATCCCAGGCGTTGCTCA 60.675 57.895 0.00 0.00 0.00 4.26
950 971 0.684153 CATCCAGTCCCCCGCAAAAT 60.684 55.000 0.00 0.00 0.00 1.82
963 984 3.012518 CCGCAAAATTCTCCATCACTCT 58.987 45.455 0.00 0.00 0.00 3.24
964 985 3.181503 CCGCAAAATTCTCCATCACTCTG 60.182 47.826 0.00 0.00 0.00 3.35
1670 1703 4.097361 GCCCCCAACCTCGAGTCC 62.097 72.222 12.31 0.00 0.00 3.85
1856 1889 2.737180 CTGGAGGATATGGCGCGT 59.263 61.111 8.43 0.00 0.00 6.01
1930 1963 2.355818 GGAAAGCAGGAAGGTAATCGGT 60.356 50.000 0.00 0.00 0.00 4.69
1931 1964 2.403252 AAGCAGGAAGGTAATCGGTG 57.597 50.000 0.00 0.00 0.00 4.94
1940 1973 4.743644 GGAAGGTAATCGGTGATAAGAACG 59.256 45.833 0.00 0.00 0.00 3.95
2075 2111 9.736023 AATTTATAGTTTATGCTTAGCAGTTGC 57.264 29.630 13.74 3.44 43.65 4.17
2079 2115 1.277326 TATGCTTAGCAGTTGCGTCG 58.723 50.000 13.74 0.00 43.65 5.12
2148 2190 6.982141 CCAACCTTTAGGAAAACCAAGTTTAC 59.018 38.462 2.06 0.00 35.08 2.01
2221 2263 4.685628 GGTATGTTTTCCGTCACGAAGTAA 59.314 41.667 0.00 0.00 41.61 2.24
2345 2387 7.882271 ACAATGAATTCTACTCTCAGAGCTTTT 59.118 33.333 0.00 0.00 32.04 2.27
2384 2426 4.226427 TGAGACAATGGAAAGCTGCTAT 57.774 40.909 0.90 0.00 0.00 2.97
2393 2435 4.655963 TGGAAAGCTGCTATGAGAAGTTT 58.344 39.130 0.90 0.00 0.00 2.66
2420 2462 4.392940 CATCTGGTATCTCCCCAAACATC 58.607 47.826 0.00 0.00 34.77 3.06
2447 2489 8.918202 AGACCTACAACATTTTACTTGATTCA 57.082 30.769 0.00 0.00 0.00 2.57
2690 2732 7.554476 AGGGCTGATCAAGTAAAGAAAATAGAC 59.446 37.037 0.00 0.00 0.00 2.59
2720 2762 8.064814 GTGTTAAGAGTTGTTGAGAATTCAGAC 58.935 37.037 8.44 3.77 34.15 3.51
2762 2804 1.010125 CAACTGTTTGGTGGACGCG 60.010 57.895 3.53 3.53 0.00 6.01
2774 2816 2.416260 GACGCGTATGGGAGGGTC 59.584 66.667 13.97 0.00 41.73 4.46
2909 2951 5.592688 TGATGATCATCGTGTTCAGTACCTA 59.407 40.000 26.52 5.07 40.63 3.08
2942 2984 2.968574 AGATGGGCGATCTACAGACAAT 59.031 45.455 10.53 0.00 39.88 2.71
3013 3161 5.471456 TCTCTGCATTTTTCTCCAAGAAGAC 59.529 40.000 0.00 0.00 35.37 3.01
3031 3179 1.659098 GACGGAATGACCTGCGTAAAG 59.341 52.381 0.00 0.00 43.88 1.85
3104 3252 4.222124 TGATGCCCTTAAGGAGAAACTC 57.778 45.455 23.74 10.48 38.24 3.01
3135 3284 4.338118 ACTGAATCAAACATTTGTCGGTGT 59.662 37.500 8.05 1.23 39.18 4.16
3144 3293 3.253188 ACATTTGTCGGTGTCAATTCAGG 59.747 43.478 0.00 0.00 0.00 3.86
3191 3340 8.796601 AAGTTCAACAGCTGAAGTACAGAACTG 61.797 40.741 23.35 0.00 45.31 3.16
3257 3437 1.202710 TCCAAACTGGCTTTGCGACTA 60.203 47.619 0.00 0.00 38.40 2.59
3264 3444 1.087501 GGCTTTGCGACTAAAGGGAG 58.912 55.000 8.61 0.00 37.96 4.30
3304 3484 1.488393 GAAGCCCTCCATCAGTAGCTT 59.512 52.381 0.00 0.00 40.72 3.74
3314 3494 3.181516 CCATCAGTAGCTTTGAGTTTCGC 60.182 47.826 0.00 0.00 0.00 4.70
3334 3514 4.327898 TCGCGACAATCAAATACAACTACC 59.672 41.667 3.71 0.00 0.00 3.18
3350 3530 2.192979 CCAGTGGTGTGCTGGTGT 59.807 61.111 0.00 0.00 46.22 4.16
3399 3580 4.808895 TGTGCCTTATGTATTGCTCTTACG 59.191 41.667 0.00 0.00 0.00 3.18
3403 3584 5.779922 CCTTATGTATTGCTCTTACGGCTA 58.220 41.667 0.00 0.00 0.00 3.93
3405 3586 6.311445 CCTTATGTATTGCTCTTACGGCTATG 59.689 42.308 0.00 0.00 0.00 2.23
3436 3617 3.962423 GTATGTCCTACTGACTTACGCC 58.038 50.000 0.00 0.00 44.75 5.68
3439 3620 2.629137 TGTCCTACTGACTTACGCCAAA 59.371 45.455 0.00 0.00 44.75 3.28
3440 3621 3.251571 GTCCTACTGACTTACGCCAAAG 58.748 50.000 0.00 0.00 41.03 2.77
3441 3622 3.057033 GTCCTACTGACTTACGCCAAAGA 60.057 47.826 0.00 0.00 41.03 2.52
3442 3623 3.767673 TCCTACTGACTTACGCCAAAGAT 59.232 43.478 0.00 0.00 0.00 2.40
3465 3648 8.313292 AGATTGGAGAGAAGCTTAATATGCTAG 58.687 37.037 0.00 0.00 40.22 3.42
3467 3650 5.175127 GGAGAGAAGCTTAATATGCTAGCC 58.825 45.833 13.29 0.00 40.22 3.93
3492 3675 8.567948 CCAAATCAAATGTTGTAGTGTTCTACT 58.432 33.333 6.89 0.00 44.74 2.57
3666 3853 8.458573 TTCAACAAAGGCTCTAAAGTTTATGA 57.541 30.769 0.00 0.00 0.00 2.15
3696 3883 1.511850 TGTGTGTGGAGCAATCTTCG 58.488 50.000 0.00 0.00 0.00 3.79
3733 3922 0.935196 GTCCGACCATTTATCGTGGC 59.065 55.000 0.00 0.00 40.49 5.01
3734 3923 0.179067 TCCGACCATTTATCGTGGCC 60.179 55.000 0.00 0.00 40.49 5.36
3735 3924 0.179056 CCGACCATTTATCGTGGCCT 60.179 55.000 3.32 0.00 40.49 5.19
3736 3925 1.663695 CGACCATTTATCGTGGCCTT 58.336 50.000 3.32 0.00 40.49 4.35
3737 3926 2.014128 CGACCATTTATCGTGGCCTTT 58.986 47.619 3.32 0.00 40.49 3.11
3738 3927 2.422127 CGACCATTTATCGTGGCCTTTT 59.578 45.455 3.32 0.00 40.49 2.27
3739 3928 3.119637 CGACCATTTATCGTGGCCTTTTT 60.120 43.478 3.32 0.00 40.49 1.94
3740 3929 4.095185 CGACCATTTATCGTGGCCTTTTTA 59.905 41.667 3.32 0.00 40.49 1.52
3741 3930 5.220970 CGACCATTTATCGTGGCCTTTTTAT 60.221 40.000 3.32 0.00 40.49 1.40
3742 3931 6.538945 ACCATTTATCGTGGCCTTTTTATT 57.461 33.333 3.32 0.00 40.49 1.40
3743 3932 6.941857 ACCATTTATCGTGGCCTTTTTATTT 58.058 32.000 3.32 0.00 40.49 1.40
3744 3933 8.068892 ACCATTTATCGTGGCCTTTTTATTTA 57.931 30.769 3.32 0.00 40.49 1.40
3745 3934 8.700973 ACCATTTATCGTGGCCTTTTTATTTAT 58.299 29.630 3.32 0.00 40.49 1.40
3746 3935 9.541143 CCATTTATCGTGGCCTTTTTATTTATT 57.459 29.630 3.32 0.00 0.00 1.40
3829 4018 3.583806 CAGCTCTGAGTTAACTGTGGAG 58.416 50.000 14.14 16.46 0.00 3.86
3844 4033 2.172505 TGTGGAGGTTCTCAGCTTTGAA 59.827 45.455 0.00 0.00 31.08 2.69
3895 4084 6.017400 TCTTCATGAATTCAGGTTTTCTGC 57.983 37.500 18.78 0.00 43.06 4.26
3908 4101 3.307242 GGTTTTCTGCGTCTAGTGCTATG 59.693 47.826 10.29 2.91 0.00 2.23
3917 4110 5.575606 TGCGTCTAGTGCTATGAACTAAAAC 59.424 40.000 10.29 0.00 29.96 2.43
3948 4141 7.864108 TGGTATTCTCCATAATTTGTCAGTG 57.136 36.000 0.00 0.00 31.96 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.249192 AGAAAAAGTAGGAAGGAAATGAGGG 58.751 40.000 0.00 0.00 0.00 4.30
6 7 9.774742 CGAAATAGAAAAAGTAGGAAGGAAATG 57.225 33.333 0.00 0.00 0.00 2.32
7 8 9.734984 TCGAAATAGAAAAAGTAGGAAGGAAAT 57.265 29.630 0.00 0.00 0.00 2.17
8 9 8.996271 GTCGAAATAGAAAAAGTAGGAAGGAAA 58.004 33.333 0.00 0.00 0.00 3.13
9 10 8.373220 AGTCGAAATAGAAAAAGTAGGAAGGAA 58.627 33.333 0.00 0.00 0.00 3.36
14 15 7.434307 CGCATAGTCGAAATAGAAAAAGTAGGA 59.566 37.037 0.00 0.00 0.00 2.94
16 17 7.043325 AGCGCATAGTCGAAATAGAAAAAGTAG 60.043 37.037 11.47 0.00 0.00 2.57
17 18 6.755141 AGCGCATAGTCGAAATAGAAAAAGTA 59.245 34.615 11.47 0.00 0.00 2.24
18 19 5.581085 AGCGCATAGTCGAAATAGAAAAAGT 59.419 36.000 11.47 0.00 0.00 2.66
19 20 6.037423 AGCGCATAGTCGAAATAGAAAAAG 57.963 37.500 11.47 0.00 0.00 2.27
20 21 7.528481 TTAGCGCATAGTCGAAATAGAAAAA 57.472 32.000 11.47 0.00 0.00 1.94
21 22 7.307160 CCATTAGCGCATAGTCGAAATAGAAAA 60.307 37.037 11.47 0.00 0.00 2.29
22 23 6.145534 CCATTAGCGCATAGTCGAAATAGAAA 59.854 38.462 11.47 0.00 0.00 2.52
23 24 5.633601 CCATTAGCGCATAGTCGAAATAGAA 59.366 40.000 11.47 0.00 0.00 2.10
24 25 5.161358 CCATTAGCGCATAGTCGAAATAGA 58.839 41.667 11.47 0.00 0.00 1.98
25 26 4.327357 CCCATTAGCGCATAGTCGAAATAG 59.673 45.833 11.47 0.00 0.00 1.73
26 27 4.242475 CCCATTAGCGCATAGTCGAAATA 58.758 43.478 11.47 0.00 0.00 1.40
27 28 3.067106 CCCATTAGCGCATAGTCGAAAT 58.933 45.455 11.47 0.00 0.00 2.17
28 29 2.479837 CCCATTAGCGCATAGTCGAAA 58.520 47.619 11.47 0.00 0.00 3.46
29 30 1.872237 GCCCATTAGCGCATAGTCGAA 60.872 52.381 11.47 0.00 0.00 3.71
30 31 0.319555 GCCCATTAGCGCATAGTCGA 60.320 55.000 11.47 0.00 0.00 4.20
31 32 0.599991 TGCCCATTAGCGCATAGTCG 60.600 55.000 11.47 0.00 34.65 4.18
32 33 1.151668 CTGCCCATTAGCGCATAGTC 58.848 55.000 11.47 0.00 33.78 2.59
33 34 0.758734 TCTGCCCATTAGCGCATAGT 59.241 50.000 11.47 0.00 33.78 2.12
34 35 1.151668 GTCTGCCCATTAGCGCATAG 58.848 55.000 11.47 0.00 33.78 2.23
35 36 0.250295 GGTCTGCCCATTAGCGCATA 60.250 55.000 11.47 0.00 33.78 3.14
36 37 1.526917 GGTCTGCCCATTAGCGCAT 60.527 57.895 11.47 0.00 33.78 4.73
37 38 2.124736 GGTCTGCCCATTAGCGCA 60.125 61.111 11.47 0.00 34.65 6.09
47 48 4.732106 CGACTAATCGGGTCTGCC 57.268 61.111 0.00 0.00 44.99 4.85
54 55 4.396289 GCTGAAGCATCTCGACTAATCGG 61.396 52.174 0.00 0.00 44.05 4.18
55 56 2.723658 GCTGAAGCATCTCGACTAATCG 59.276 50.000 0.00 0.00 44.72 3.34
56 57 2.723658 CGCTGAAGCATCTCGACTAATC 59.276 50.000 2.79 0.00 42.21 1.75
57 58 2.359214 TCGCTGAAGCATCTCGACTAAT 59.641 45.455 2.79 0.00 42.21 1.73
58 59 1.743394 TCGCTGAAGCATCTCGACTAA 59.257 47.619 2.79 0.00 42.21 2.24
59 60 1.064208 GTCGCTGAAGCATCTCGACTA 59.936 52.381 21.13 0.00 42.88 2.59
60 61 0.179150 GTCGCTGAAGCATCTCGACT 60.179 55.000 21.13 0.00 42.88 4.18
61 62 0.456824 TGTCGCTGAAGCATCTCGAC 60.457 55.000 21.41 21.41 44.57 4.20
62 63 0.179153 CTGTCGCTGAAGCATCTCGA 60.179 55.000 2.79 3.50 42.21 4.04
63 64 0.179153 TCTGTCGCTGAAGCATCTCG 60.179 55.000 2.79 0.00 42.21 4.04
64 65 1.658095 GTTCTGTCGCTGAAGCATCTC 59.342 52.381 2.79 0.00 42.21 2.75
65 66 1.674221 GGTTCTGTCGCTGAAGCATCT 60.674 52.381 17.10 0.00 42.21 2.90
66 67 0.723981 GGTTCTGTCGCTGAAGCATC 59.276 55.000 17.10 0.00 42.21 3.91
67 68 0.035317 TGGTTCTGTCGCTGAAGCAT 59.965 50.000 19.22 0.00 41.94 3.79
68 69 1.445518 TGGTTCTGTCGCTGAAGCA 59.554 52.632 19.22 19.22 43.54 3.91
69 70 0.723981 GATGGTTCTGTCGCTGAAGC 59.276 55.000 15.96 15.96 39.21 3.86
70 71 0.994995 CGATGGTTCTGTCGCTGAAG 59.005 55.000 0.79 0.00 0.00 3.02
71 72 0.389817 CCGATGGTTCTGTCGCTGAA 60.390 55.000 0.00 0.00 36.57 3.02
72 73 1.215382 CCGATGGTTCTGTCGCTGA 59.785 57.895 0.00 0.00 36.57 4.26
73 74 1.078759 GACCGATGGTTCTGTCGCTG 61.079 60.000 0.00 0.00 35.25 5.18
74 75 1.215647 GACCGATGGTTCTGTCGCT 59.784 57.895 0.00 0.00 35.25 4.93
75 76 0.802607 GAGACCGATGGTTCTGTCGC 60.803 60.000 0.00 0.00 40.06 5.19
76 77 0.523546 CGAGACCGATGGTTCTGTCG 60.524 60.000 0.00 0.00 40.06 4.35
77 78 0.526662 ACGAGACCGATGGTTCTGTC 59.473 55.000 0.00 0.00 35.25 3.51
78 79 0.966920 AACGAGACCGATGGTTCTGT 59.033 50.000 0.00 0.00 35.25 3.41
79 80 1.067846 TCAACGAGACCGATGGTTCTG 60.068 52.381 0.00 0.00 38.80 3.02
80 81 1.254026 TCAACGAGACCGATGGTTCT 58.746 50.000 0.00 0.00 38.80 3.01
81 82 2.074547 TTCAACGAGACCGATGGTTC 57.925 50.000 0.00 0.00 38.80 3.62
82 83 2.346803 CATTCAACGAGACCGATGGTT 58.653 47.619 0.00 0.00 38.80 3.67
83 84 2.007049 GCATTCAACGAGACCGATGGT 61.007 52.381 0.00 0.00 38.80 3.55
84 85 0.652592 GCATTCAACGAGACCGATGG 59.347 55.000 0.00 0.00 38.80 3.51
85 86 0.298707 CGCATTCAACGAGACCGATG 59.701 55.000 0.00 0.00 39.51 3.84
86 87 0.172578 TCGCATTCAACGAGACCGAT 59.827 50.000 0.00 0.00 39.50 4.18
87 88 1.582461 TCGCATTCAACGAGACCGA 59.418 52.632 0.00 0.00 39.50 4.69
88 89 4.162640 TCGCATTCAACGAGACCG 57.837 55.556 0.00 0.00 42.50 4.79
93 94 3.234386 CGCTATATCTCGCATTCAACGA 58.766 45.455 0.00 0.00 38.02 3.85
94 95 3.608211 CGCTATATCTCGCATTCAACG 57.392 47.619 0.00 0.00 0.00 4.10
114 115 2.857934 TTGGATAACAACAGCGCGAGC 61.858 52.381 12.10 1.63 46.61 5.03
115 116 1.075542 TTGGATAACAACAGCGCGAG 58.924 50.000 12.10 3.23 33.18 5.03
116 117 1.514003 TTTGGATAACAACAGCGCGA 58.486 45.000 12.10 0.00 39.19 5.87
117 118 2.323939 TTTTGGATAACAACAGCGCG 57.676 45.000 0.00 0.00 39.19 6.86
138 139 5.977129 CGAACAGTTTGGTGCTATTCTTTTT 59.023 36.000 0.00 0.00 0.00 1.94
139 140 5.519722 CGAACAGTTTGGTGCTATTCTTTT 58.480 37.500 0.00 0.00 0.00 2.27
140 141 4.556699 GCGAACAGTTTGGTGCTATTCTTT 60.557 41.667 2.53 0.00 0.00 2.52
141 142 3.058224 GCGAACAGTTTGGTGCTATTCTT 60.058 43.478 2.53 0.00 0.00 2.52
142 143 2.484264 GCGAACAGTTTGGTGCTATTCT 59.516 45.455 2.53 0.00 0.00 2.40
143 144 2.484264 AGCGAACAGTTTGGTGCTATTC 59.516 45.455 4.31 0.00 0.00 1.75
144 145 2.226437 CAGCGAACAGTTTGGTGCTATT 59.774 45.455 17.84 0.00 35.94 1.73
145 146 1.806542 CAGCGAACAGTTTGGTGCTAT 59.193 47.619 17.84 0.00 35.94 2.97
146 147 1.225855 CAGCGAACAGTTTGGTGCTA 58.774 50.000 17.84 0.00 35.94 3.49
147 148 0.748005 ACAGCGAACAGTTTGGTGCT 60.748 50.000 26.35 14.43 44.45 4.40
148 149 0.100503 AACAGCGAACAGTTTGGTGC 59.899 50.000 26.35 11.40 44.45 5.01
149 150 1.533756 CCAACAGCGAACAGTTTGGTG 60.534 52.381 25.26 25.26 45.71 4.17
150 151 0.738389 CCAACAGCGAACAGTTTGGT 59.262 50.000 0.00 0.00 0.00 3.67
151 152 0.738389 ACCAACAGCGAACAGTTTGG 59.262 50.000 2.53 0.51 0.00 3.28
152 153 2.559998 AACCAACAGCGAACAGTTTG 57.440 45.000 0.00 0.00 0.00 2.93
153 154 3.586100 AAAACCAACAGCGAACAGTTT 57.414 38.095 0.00 0.00 0.00 2.66
154 155 3.249917 CAAAAACCAACAGCGAACAGTT 58.750 40.909 0.00 0.00 0.00 3.16
155 156 2.230266 ACAAAAACCAACAGCGAACAGT 59.770 40.909 0.00 0.00 0.00 3.55
156 157 2.598192 CACAAAAACCAACAGCGAACAG 59.402 45.455 0.00 0.00 0.00 3.16
157 158 2.029828 ACACAAAAACCAACAGCGAACA 60.030 40.909 0.00 0.00 0.00 3.18
158 159 2.601804 ACACAAAAACCAACAGCGAAC 58.398 42.857 0.00 0.00 0.00 3.95
159 160 3.732471 GCTACACAAAAACCAACAGCGAA 60.732 43.478 0.00 0.00 0.00 4.70
160 161 2.223386 GCTACACAAAAACCAACAGCGA 60.223 45.455 0.00 0.00 0.00 4.93
161 162 2.116366 GCTACACAAAAACCAACAGCG 58.884 47.619 0.00 0.00 0.00 5.18
162 163 2.116366 CGCTACACAAAAACCAACAGC 58.884 47.619 0.00 0.00 0.00 4.40
163 164 2.116366 GCGCTACACAAAAACCAACAG 58.884 47.619 0.00 0.00 0.00 3.16
164 165 1.472878 TGCGCTACACAAAAACCAACA 59.527 42.857 9.73 0.00 0.00 3.33
165 166 2.196295 TGCGCTACACAAAAACCAAC 57.804 45.000 9.73 0.00 0.00 3.77
176 177 5.559427 ATTTCATTATGTTGTGCGCTACA 57.441 34.783 16.56 16.56 37.56 2.74
177 178 5.169561 CGAATTTCATTATGTTGTGCGCTAC 59.830 40.000 9.73 4.82 0.00 3.58
178 179 5.064071 TCGAATTTCATTATGTTGTGCGCTA 59.936 36.000 9.73 0.00 0.00 4.26
179 180 4.097714 CGAATTTCATTATGTTGTGCGCT 58.902 39.130 9.73 0.00 0.00 5.92
180 181 4.094911 TCGAATTTCATTATGTTGTGCGC 58.905 39.130 0.00 0.00 0.00 6.09
181 182 5.964751 TCATCGAATTTCATTATGTTGTGCG 59.035 36.000 0.00 0.00 0.00 5.34
182 183 7.739022 TTCATCGAATTTCATTATGTTGTGC 57.261 32.000 0.00 0.00 0.00 4.57
216 217 1.754226 ACACAATCAGCCCGTGTTTTT 59.246 42.857 0.00 0.00 40.91 1.94
217 218 1.066908 CACACAATCAGCCCGTGTTTT 59.933 47.619 0.00 0.00 41.79 2.43
218 219 0.667993 CACACAATCAGCCCGTGTTT 59.332 50.000 0.00 0.00 41.79 2.83
219 220 0.465460 ACACACAATCAGCCCGTGTT 60.465 50.000 0.00 0.00 41.79 3.32
220 221 1.148273 ACACACAATCAGCCCGTGT 59.852 52.632 0.00 0.00 44.45 4.49
221 222 1.165907 ACACACACAATCAGCCCGTG 61.166 55.000 0.00 0.00 36.70 4.94
222 223 0.884704 GACACACACAATCAGCCCGT 60.885 55.000 0.00 0.00 0.00 5.28
223 224 1.868997 GACACACACAATCAGCCCG 59.131 57.895 0.00 0.00 0.00 6.13
224 225 1.577328 CCGACACACACAATCAGCCC 61.577 60.000 0.00 0.00 0.00 5.19
225 226 0.602638 TCCGACACACACAATCAGCC 60.603 55.000 0.00 0.00 0.00 4.85
226 227 1.442769 ATCCGACACACACAATCAGC 58.557 50.000 0.00 0.00 0.00 4.26
227 228 3.119137 TCCTATCCGACACACACAATCAG 60.119 47.826 0.00 0.00 0.00 2.90
228 229 2.829120 TCCTATCCGACACACACAATCA 59.171 45.455 0.00 0.00 0.00 2.57
229 230 3.520290 TCCTATCCGACACACACAATC 57.480 47.619 0.00 0.00 0.00 2.67
230 231 3.432186 CCATCCTATCCGACACACACAAT 60.432 47.826 0.00 0.00 0.00 2.71
231 232 2.093711 CCATCCTATCCGACACACACAA 60.094 50.000 0.00 0.00 0.00 3.33
232 233 1.480545 CCATCCTATCCGACACACACA 59.519 52.381 0.00 0.00 0.00 3.72
233 234 1.480954 ACCATCCTATCCGACACACAC 59.519 52.381 0.00 0.00 0.00 3.82
234 235 1.860641 ACCATCCTATCCGACACACA 58.139 50.000 0.00 0.00 0.00 3.72
235 236 3.243771 CCTTACCATCCTATCCGACACAC 60.244 52.174 0.00 0.00 0.00 3.82
236 237 2.963101 CCTTACCATCCTATCCGACACA 59.037 50.000 0.00 0.00 0.00 3.72
237 238 2.288886 GCCTTACCATCCTATCCGACAC 60.289 54.545 0.00 0.00 0.00 3.67
238 239 1.968493 GCCTTACCATCCTATCCGACA 59.032 52.381 0.00 0.00 0.00 4.35
239 240 1.275573 GGCCTTACCATCCTATCCGAC 59.724 57.143 0.00 0.00 38.86 4.79
240 241 1.132977 TGGCCTTACCATCCTATCCGA 60.133 52.381 3.32 0.00 46.36 4.55
241 242 1.348064 TGGCCTTACCATCCTATCCG 58.652 55.000 3.32 0.00 46.36 4.18
252 253 5.420739 TCCCTTTTTAACATGATGGCCTTAC 59.579 40.000 3.32 0.00 0.00 2.34
256 257 4.405358 TCATCCCTTTTTAACATGATGGCC 59.595 41.667 0.00 0.00 32.49 5.36
258 259 5.127519 TGCTCATCCCTTTTTAACATGATGG 59.872 40.000 0.00 0.00 32.49 3.51
259 260 6.038356 GTGCTCATCCCTTTTTAACATGATG 58.962 40.000 0.00 0.00 0.00 3.07
260 261 5.716228 TGTGCTCATCCCTTTTTAACATGAT 59.284 36.000 0.00 0.00 0.00 2.45
268 269 5.420104 CCTTCTATTGTGCTCATCCCTTTTT 59.580 40.000 0.00 0.00 0.00 1.94
274 275 4.023365 GCAATCCTTCTATTGTGCTCATCC 60.023 45.833 0.00 0.00 38.78 3.51
277 278 3.691118 GTGCAATCCTTCTATTGTGCTCA 59.309 43.478 0.00 0.00 38.78 4.26
282 283 6.186957 TGGTTATGTGCAATCCTTCTATTGT 58.813 36.000 0.00 0.00 38.78 2.71
283 284 6.698008 TGGTTATGTGCAATCCTTCTATTG 57.302 37.500 0.00 0.00 39.41 1.90
286 287 6.007076 TGTTTGGTTATGTGCAATCCTTCTA 58.993 36.000 0.00 0.00 0.00 2.10
289 290 4.558496 CGTGTTTGGTTATGTGCAATCCTT 60.558 41.667 0.00 0.00 0.00 3.36
291 292 3.241701 CGTGTTTGGTTATGTGCAATCC 58.758 45.455 0.00 0.00 0.00 3.01
292 293 3.896122 ACGTGTTTGGTTATGTGCAATC 58.104 40.909 0.00 0.00 0.00 2.67
293 294 5.048364 ACATACGTGTTTGGTTATGTGCAAT 60.048 36.000 0.00 0.00 34.01 3.56
309 310 5.567534 GGTGAGCAAATGTAAAACATACGTG 59.432 40.000 0.00 0.00 37.97 4.49
312 313 6.267496 AGGGTGAGCAAATGTAAAACATAC 57.733 37.500 0.00 0.00 37.97 2.39
314 315 6.909550 TTAGGGTGAGCAAATGTAAAACAT 57.090 33.333 0.00 0.00 41.31 2.71
321 322 3.005791 GTGCTTTTAGGGTGAGCAAATGT 59.994 43.478 0.00 0.00 46.77 2.71
325 326 2.356665 TGTGCTTTTAGGGTGAGCAA 57.643 45.000 0.00 0.00 46.77 3.91
331 332 2.357154 CCTGCCTATGTGCTTTTAGGGT 60.357 50.000 8.03 0.00 36.32 4.34
336 337 1.180029 CTGCCTGCCTATGTGCTTTT 58.820 50.000 0.00 0.00 0.00 2.27
340 341 0.107214 TTACCTGCCTGCCTATGTGC 60.107 55.000 0.00 0.00 0.00 4.57
341 342 2.158769 TGATTACCTGCCTGCCTATGTG 60.159 50.000 0.00 0.00 0.00 3.21
360 361 6.433716 TGATCATTTGTATGCCTTCTGTTTGA 59.566 34.615 0.00 0.00 0.00 2.69
362 363 6.839124 TGATCATTTGTATGCCTTCTGTTT 57.161 33.333 0.00 0.00 0.00 2.83
367 368 5.929697 TCGATGATCATTTGTATGCCTTC 57.070 39.130 10.14 0.00 0.00 3.46
383 384 7.645058 TTGATAGCCTGTATCATATCGATGA 57.355 36.000 8.54 0.00 46.13 2.92
391 392 4.345257 ACCTCGTTTGATAGCCTGTATCAT 59.655 41.667 0.00 0.00 34.34 2.45
392 393 3.704566 ACCTCGTTTGATAGCCTGTATCA 59.295 43.478 0.00 0.00 32.63 2.15
393 394 4.051922 CACCTCGTTTGATAGCCTGTATC 58.948 47.826 0.00 0.00 0.00 2.24
400 401 2.695359 TGTTCCACCTCGTTTGATAGC 58.305 47.619 0.00 0.00 0.00 2.97
402 403 3.605634 CCATGTTCCACCTCGTTTGATA 58.394 45.455 0.00 0.00 0.00 2.15
409 410 2.819595 CGCCCATGTTCCACCTCG 60.820 66.667 0.00 0.00 0.00 4.63
460 462 5.962433 TCTAGGCGTAATGTATCTTATGGC 58.038 41.667 0.00 2.41 41.21 4.40
466 468 8.094548 TGCATTAATTCTAGGCGTAATGTATCT 58.905 33.333 15.51 0.00 36.66 1.98
507 509 8.365647 TCGTCACTTTAGAAAGTCTTAAAGGAT 58.634 33.333 4.66 0.00 45.65 3.24
508 510 7.650903 GTCGTCACTTTAGAAAGTCTTAAAGGA 59.349 37.037 4.66 0.00 45.65 3.36
510 512 8.348983 TGTCGTCACTTTAGAAAGTCTTAAAG 57.651 34.615 4.66 5.22 45.65 1.85
511 513 8.882415 ATGTCGTCACTTTAGAAAGTCTTAAA 57.118 30.769 4.66 0.00 45.65 1.52
531 533 2.811431 TGTTGTTGGCTAGGAAATGTCG 59.189 45.455 0.00 0.00 0.00 4.35
533 535 3.561143 TGTGTTGTTGGCTAGGAAATGT 58.439 40.909 0.00 0.00 0.00 2.71
535 537 3.832527 ACTGTGTTGTTGGCTAGGAAAT 58.167 40.909 0.00 0.00 0.00 2.17
543 545 3.187227 CAGATGAGTACTGTGTTGTTGGC 59.813 47.826 0.00 0.00 0.00 4.52
550 552 9.026121 AGTTAATCTTACAGATGAGTACTGTGT 57.974 33.333 0.00 0.97 46.15 3.72
574 576 5.997129 GTCCTAGCTTACGGAGAGTATTAGT 59.003 44.000 0.00 0.00 34.88 2.24
579 581 4.080695 TCAAGTCCTAGCTTACGGAGAGTA 60.081 45.833 0.00 0.00 0.00 2.59
584 586 2.165845 GCTTCAAGTCCTAGCTTACGGA 59.834 50.000 0.00 0.00 32.26 4.69
585 587 2.541556 GCTTCAAGTCCTAGCTTACGG 58.458 52.381 0.00 0.00 32.26 4.02
586 588 2.186076 CGCTTCAAGTCCTAGCTTACG 58.814 52.381 0.00 0.00 32.80 3.18
587 589 3.233684 ACGCTTCAAGTCCTAGCTTAC 57.766 47.619 0.00 0.00 32.80 2.34
591 593 2.080286 TCAACGCTTCAAGTCCTAGC 57.920 50.000 0.00 0.00 0.00 3.42
602 604 9.139174 CCTTATAAAAATTTCACATCAACGCTT 57.861 29.630 0.00 0.00 0.00 4.68
646 650 4.026804 CCGCTACAACTACGCTTTTCATAG 60.027 45.833 0.00 0.00 0.00 2.23
655 659 5.916883 TCTATATTTTCCGCTACAACTACGC 59.083 40.000 0.00 0.00 0.00 4.42
657 661 9.182933 CTTCTCTATATTTTCCGCTACAACTAC 57.817 37.037 0.00 0.00 0.00 2.73
663 667 5.785243 AGGCTTCTCTATATTTTCCGCTAC 58.215 41.667 0.00 0.00 0.00 3.58
671 675 8.687242 GGCAAGTTTAAAGGCTTCTCTATATTT 58.313 33.333 0.00 0.00 0.00 1.40
680 684 1.883926 TCGGGCAAGTTTAAAGGCTTC 59.116 47.619 0.00 0.00 0.00 3.86
683 687 0.526211 CCTCGGGCAAGTTTAAAGGC 59.474 55.000 0.00 0.00 0.00 4.35
685 689 3.673323 GCAATCCTCGGGCAAGTTTAAAG 60.673 47.826 0.00 0.00 0.00 1.85
689 693 0.539438 TGCAATCCTCGGGCAAGTTT 60.539 50.000 0.00 0.00 34.05 2.66
710 727 1.613437 AGGTTCGTTTGATTTGCAGGG 59.387 47.619 0.00 0.00 0.00 4.45
714 731 7.434013 TCTTTTTCTAAGGTTCGTTTGATTTGC 59.566 33.333 0.00 0.00 0.00 3.68
730 747 7.532199 AGTTGGACCCCTAATTCTTTTTCTAA 58.468 34.615 0.00 0.00 0.00 2.10
769 787 9.889128 CCCATTGGTTCAAAGTAATTTTCATAT 57.111 29.630 1.20 0.00 0.00 1.78
856 877 2.361104 GCAACGCCTGGGATTGGA 60.361 61.111 0.00 0.00 0.00 3.53
859 880 0.749454 GATGAGCAACGCCTGGGATT 60.749 55.000 0.00 0.00 0.00 3.01
876 897 1.676678 CCGTGGACCGTCTGATGGAT 61.677 60.000 22.36 6.80 33.66 3.41
950 971 0.247460 CGGTGCAGAGTGATGGAGAA 59.753 55.000 0.00 0.00 0.00 2.87
1054 1076 2.738521 CGTTGACGTGCTGAGGGG 60.739 66.667 0.00 0.00 34.11 4.79
1449 1482 2.262915 GTGACCGAGGAGCTGTGG 59.737 66.667 0.00 0.00 0.00 4.17
1481 1514 1.070134 GGCACGGCATGGTTAGATAGA 59.930 52.381 0.00 0.00 0.00 1.98
1482 1515 1.512926 GGCACGGCATGGTTAGATAG 58.487 55.000 0.00 0.00 0.00 2.08
1483 1516 0.107831 GGGCACGGCATGGTTAGATA 59.892 55.000 0.00 0.00 0.00 1.98
1484 1517 1.152963 GGGCACGGCATGGTTAGAT 60.153 57.895 0.00 0.00 0.00 1.98
1670 1703 1.218316 GGAGACAAGGGCCGTGTAG 59.782 63.158 25.09 3.65 0.00 2.74
2075 2111 5.062183 TGAACAGATATTTGAAGAAGCGACG 59.938 40.000 0.00 0.00 0.00 5.12
2079 2115 8.725148 TCTTTCTGAACAGATATTTGAAGAAGC 58.275 33.333 5.34 0.00 37.29 3.86
2221 2263 8.139989 GCAAATGATGAAACCTCATTAGCTTAT 58.860 33.333 0.00 0.00 42.60 1.73
2345 2387 2.234661 CTCAATCTGACCACTGCTACCA 59.765 50.000 0.00 0.00 0.00 3.25
2384 2426 2.373169 ACCAGATGCCTGAAACTTCTCA 59.627 45.455 0.00 0.00 43.02 3.27
2393 2435 1.722034 GGGAGATACCAGATGCCTGA 58.278 55.000 0.00 0.00 43.02 3.86
2420 2462 9.612620 GAATCAAGTAAAATGTTGTAGGTCTTG 57.387 33.333 0.00 0.00 33.48 3.02
2690 2732 6.662414 TTCTCAACAACTCTTAACACTGTG 57.338 37.500 6.19 6.19 0.00 3.66
2720 2762 6.860539 TGAAAAACACAATATCCAACGTGATG 59.139 34.615 0.00 0.00 33.56 3.07
2762 2804 3.925090 CGCCCGACCCTCCCATAC 61.925 72.222 0.00 0.00 0.00 2.39
2774 2816 1.953138 CATCTCTGCTAAGCGCCCG 60.953 63.158 2.29 0.00 38.05 6.13
2783 2825 2.170187 GAGAACATCCCACATCTCTGCT 59.830 50.000 0.00 0.00 36.29 4.24
2909 2951 1.674817 CGCCCATCTTTTAGGTCACGT 60.675 52.381 0.00 0.00 0.00 4.49
3013 3161 1.006832 CCTTTACGCAGGTCATTCCG 58.993 55.000 0.00 0.00 41.99 4.30
3104 3252 7.132213 ACAAATGTTTGATTCAGTAACACTCG 58.868 34.615 12.09 1.87 40.55 4.18
3135 3284 4.703379 AAATTTTGTGCCCCTGAATTGA 57.297 36.364 0.00 0.00 0.00 2.57
3159 3308 5.918608 ACTTCAGCTGTTGAACTTCTAAGA 58.081 37.500 14.67 0.00 40.82 2.10
3191 3340 0.956633 TCCGACATATGCTACCCGAC 59.043 55.000 1.58 0.00 0.00 4.79
3194 3343 2.496070 TGCTATCCGACATATGCTACCC 59.504 50.000 1.58 0.00 0.00 3.69
3223 3372 4.648762 CCAGTTTGGATGCCATAACCATAA 59.351 41.667 0.00 0.00 40.96 1.90
3257 3437 1.981495 CTCTCTTGTCCACCTCCCTTT 59.019 52.381 0.00 0.00 0.00 3.11
3264 3444 4.021102 TCAAATTCCTCTCTTGTCCACC 57.979 45.455 0.00 0.00 0.00 4.61
3304 3484 3.953874 TTTGATTGTCGCGAAACTCAA 57.046 38.095 23.57 23.57 0.00 3.02
3314 3494 6.402118 CCACTGGTAGTTGTATTTGATTGTCG 60.402 42.308 0.00 0.00 0.00 4.35
3334 3514 1.153188 TGACACCAGCACACCACTG 60.153 57.895 0.00 0.00 34.82 3.66
3350 3530 3.181462 ACACAGCACAATCTGAAGAGTGA 60.181 43.478 14.19 0.00 42.16 3.41
3399 3580 3.329386 ACATACGATGTCATGCATAGCC 58.671 45.455 0.00 0.00 39.92 3.93
3436 3617 8.074972 GCATATTAAGCTTCTCTCCAATCTTTG 58.925 37.037 0.00 0.00 0.00 2.77
3439 3620 7.077050 AGCATATTAAGCTTCTCTCCAATCT 57.923 36.000 0.00 0.00 39.87 2.40
3440 3621 7.064490 GCTAGCATATTAAGCTTCTCTCCAATC 59.936 40.741 10.63 0.00 43.25 2.67
3441 3622 6.878389 GCTAGCATATTAAGCTTCTCTCCAAT 59.122 38.462 10.63 0.00 43.25 3.16
3442 3623 6.226787 GCTAGCATATTAAGCTTCTCTCCAA 58.773 40.000 10.63 0.00 43.25 3.53
3465 3648 6.215845 AGAACACTACAACATTTGATTTGGC 58.784 36.000 0.00 0.00 0.00 4.52
3575 3762 2.504175 GGTCCATTAGTTAGGTGCCAGA 59.496 50.000 0.00 0.00 0.00 3.86
3666 3853 4.771577 TGCTCCACACACAATATTCCATTT 59.228 37.500 0.00 0.00 0.00 2.32
3696 3883 3.180782 CGGACGGCAATTTAAACAAACAC 59.819 43.478 0.00 0.00 0.00 3.32
3746 3935 9.838339 TTTAAAAATAATGCCTCCACTCAAAAA 57.162 25.926 0.00 0.00 0.00 1.94
3747 3936 9.487790 CTTTAAAAATAATGCCTCCACTCAAAA 57.512 29.630 0.00 0.00 0.00 2.44
3748 3937 8.646900 ACTTTAAAAATAATGCCTCCACTCAAA 58.353 29.630 0.00 0.00 0.00 2.69
3749 3938 8.189119 ACTTTAAAAATAATGCCTCCACTCAA 57.811 30.769 0.00 0.00 0.00 3.02
3750 3939 7.775053 ACTTTAAAAATAATGCCTCCACTCA 57.225 32.000 0.00 0.00 0.00 3.41
3751 3940 9.952188 GATACTTTAAAAATAATGCCTCCACTC 57.048 33.333 0.00 0.00 0.00 3.51
3752 3941 9.474313 TGATACTTTAAAAATAATGCCTCCACT 57.526 29.630 0.00 0.00 0.00 4.00
3844 4033 9.305925 CTTTGTAGCTTCTTTGAGTTGATTTTT 57.694 29.630 0.00 0.00 0.00 1.94
3848 4037 6.006759 GCTTTGTAGCTTCTTTGAGTTGAT 57.993 37.500 0.00 0.00 44.27 2.57
3849 4038 5.424121 GCTTTGTAGCTTCTTTGAGTTGA 57.576 39.130 0.00 0.00 44.27 3.18
3895 4084 6.025896 TCGTTTTAGTTCATAGCACTAGACG 58.974 40.000 0.00 10.33 38.33 4.18
3908 4101 8.815189 GGAGAATACCAATACTCGTTTTAGTTC 58.185 37.037 0.00 0.00 0.00 3.01
3917 4110 9.273016 ACAAATTATGGAGAATACCAATACTCG 57.727 33.333 0.00 0.00 43.47 4.18


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

AutoCloner maintained by Alex Coulton.