Multiple sequence alignment - TraesCS6A01G073800

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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 TraesCS6A01G073800 chr6A 100.000 2720 0 0 680 3399 41599175 41601894 0.000000e+00 5024
1 TraesCS6A01G073800 chr6A 100.000 478 0 0 1 478 41598496 41598973 0.000000e+00 883
2 TraesCS6A01G073800 chr6A 97.479 357 9 0 8 364 571536605 571536961 8.060000e-171 610
3 TraesCS6A01G073800 chr7A 97.611 2721 55 6 680 3399 108111126 108108415 0.000000e+00 4656
4 TraesCS6A01G073800 chr7A 98.077 364 7 0 1 364 184624214 184623851 4.780000e-178 634
5 TraesCS6A01G073800 chr5A 97.649 2722 39 4 680 3399 560602068 560599370 0.000000e+00 4649
6 TraesCS6A01G073800 chr1D 97.668 2573 49 6 836 3399 416148330 416150900 0.000000e+00 4409
7 TraesCS6A01G073800 chr1D 94.595 148 8 0 680 827 416148063 416148210 2.640000e-56 230
8 TraesCS6A01G073800 chr2A 94.836 2750 100 14 680 3399 721617703 721614966 0.000000e+00 4253
9 TraesCS6A01G073800 chr3B 96.598 2557 77 6 849 3399 221136248 221133696 0.000000e+00 4231
10 TraesCS6A01G073800 chr3B 93.633 2733 149 14 680 3399 277022984 277025704 0.000000e+00 4060
11 TraesCS6A01G073800 chr3B 92.535 2063 124 11 680 2724 277018892 277020942 0.000000e+00 2929
12 TraesCS6A01G073800 chr3B 93.443 183 12 0 680 862 817347303 817347121 4.320000e-69 272
13 TraesCS6A01G073800 chr2B 93.624 2729 153 13 680 3399 75904892 75907608 0.000000e+00 4056
14 TraesCS6A01G073800 chr2B 99.176 364 3 0 1 364 177595258 177595621 0.000000e+00 656
15 TraesCS6A01G073800 chr1B 94.027 2260 117 12 1155 3399 123482818 123485074 0.000000e+00 3410
16 TraesCS6A01G073800 chr1B 98.356 365 6 0 1 365 675387013 675387377 2.860000e-180 641
17 TraesCS6A01G073800 chr1B 90.664 482 39 4 680 1160 123472282 123472758 1.330000e-178 636
18 TraesCS6A01G073800 chr3A 94.030 1876 82 14 680 2537 690719299 690721162 0.000000e+00 2817
19 TraesCS6A01G073800 chr3A 96.621 799 22 2 2606 3399 690721443 690722241 0.000000e+00 1321
20 TraesCS6A01G073800 chr3A 98.901 364 4 0 1 364 645356141 645356504 0.000000e+00 651
21 TraesCS6A01G073800 chr3A 98.630 365 5 0 1 365 728513460 728513824 0.000000e+00 647
22 TraesCS6A01G073800 chr4B 98.630 365 5 0 1 365 22185982 22185618 0.000000e+00 647
23 TraesCS6A01G073800 chr5B 98.626 364 5 0 1 364 9536591 9536954 0.000000e+00 645
24 TraesCS6A01G073800 chr5B 96.703 364 11 1 8 371 461406110 461405748 3.750000e-169 604
25 TraesCS6A01G073800 chr5B 95.556 90 4 0 367 456 690587970 690588059 9.830000e-31 145


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 TraesCS6A01G073800 chr6A 41598496 41601894 3398 False 2953.5 5024 100.0000 1 3399 2 chr6A.!!$F2 3398
1 TraesCS6A01G073800 chr7A 108108415 108111126 2711 True 4656.0 4656 97.6110 680 3399 1 chr7A.!!$R1 2719
2 TraesCS6A01G073800 chr5A 560599370 560602068 2698 True 4649.0 4649 97.6490 680 3399 1 chr5A.!!$R1 2719
3 TraesCS6A01G073800 chr1D 416148063 416150900 2837 False 2319.5 4409 96.1315 680 3399 2 chr1D.!!$F1 2719
4 TraesCS6A01G073800 chr2A 721614966 721617703 2737 True 4253.0 4253 94.8360 680 3399 1 chr2A.!!$R1 2719
5 TraesCS6A01G073800 chr3B 221133696 221136248 2552 True 4231.0 4231 96.5980 849 3399 1 chr3B.!!$R1 2550
6 TraesCS6A01G073800 chr3B 277018892 277025704 6812 False 3494.5 4060 93.0840 680 3399 2 chr3B.!!$F1 2719
7 TraesCS6A01G073800 chr2B 75904892 75907608 2716 False 4056.0 4056 93.6240 680 3399 1 chr2B.!!$F1 2719
8 TraesCS6A01G073800 chr1B 123482818 123485074 2256 False 3410.0 3410 94.0270 1155 3399 1 chr1B.!!$F2 2244
9 TraesCS6A01G073800 chr3A 690719299 690722241 2942 False 2069.0 2817 95.3255 680 3399 2 chr3A.!!$F3 2719

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
297 298 0.319405 ACGGGCTACTAGTTTTGCGT 59.681 50.000 0.00 0.0 0.00 5.24 F
298 299 1.270465 ACGGGCTACTAGTTTTGCGTT 60.270 47.619 0.00 0.0 0.00 4.84 F
299 300 1.802365 CGGGCTACTAGTTTTGCGTTT 59.198 47.619 0.00 0.0 0.00 3.60 F
1092 3252 2.203139 CAACCATGGCGGCGGATA 60.203 61.111 13.04 0.0 39.03 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1386 5598 1.172812 AAAGCAAGGAACCACGCCTC 61.173 55.000 0.0 0.0 33.76 4.70 R
2262 6491 3.614870 GCCCCAACAACAATTCAGATCAC 60.615 47.826 0.0 0.0 0.00 3.06 R
2323 6553 3.260380 AGATCTTGCTCAGTGTGTAGCTT 59.740 43.478 0.0 0.0 39.53 3.74 R
2934 7381 0.817013 CCACCACATACACATTGGCC 59.183 55.000 0.0 0.0 33.25 5.36 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 2.100605 AGGATCCAACGAAGAACAGC 57.899 50.000 15.82 0.00 0.00 4.40
20 21 1.347707 AGGATCCAACGAAGAACAGCA 59.652 47.619 15.82 0.00 0.00 4.41
21 22 1.734465 GGATCCAACGAAGAACAGCAG 59.266 52.381 6.95 0.00 0.00 4.24
22 23 1.129437 GATCCAACGAAGAACAGCAGC 59.871 52.381 0.00 0.00 0.00 5.25
23 24 1.205064 CCAACGAAGAACAGCAGCG 59.795 57.895 0.00 0.00 0.00 5.18
24 25 1.439365 CAACGAAGAACAGCAGCGC 60.439 57.895 0.00 0.00 0.00 5.92
25 26 1.887242 AACGAAGAACAGCAGCGCA 60.887 52.632 11.47 0.00 0.00 6.09
26 27 1.835483 AACGAAGAACAGCAGCGCAG 61.835 55.000 11.47 1.31 0.00 5.18
27 28 2.866028 GAAGAACAGCAGCGCAGG 59.134 61.111 11.47 1.51 0.00 4.85
28 29 2.670934 AAGAACAGCAGCGCAGGG 60.671 61.111 11.47 0.00 0.00 4.45
29 30 4.711949 AGAACAGCAGCGCAGGGG 62.712 66.667 11.47 0.00 0.00 4.79
42 43 3.315949 AGGGGCGAACGGTGCTTA 61.316 61.111 0.00 0.00 0.00 3.09
43 44 2.124860 GGGGCGAACGGTGCTTAT 60.125 61.111 0.00 0.00 0.00 1.73
44 45 2.178235 GGGGCGAACGGTGCTTATC 61.178 63.158 0.00 0.00 0.00 1.75
45 46 2.178235 GGGCGAACGGTGCTTATCC 61.178 63.158 0.00 0.00 0.00 2.59
56 57 1.083489 TGCTTATCCGCACCTTTTCG 58.917 50.000 0.00 0.00 34.44 3.46
57 58 0.377203 GCTTATCCGCACCTTTTCGG 59.623 55.000 0.00 0.00 46.52 4.30
58 59 0.377203 CTTATCCGCACCTTTTCGGC 59.623 55.000 0.00 0.00 44.91 5.54
59 60 1.027792 TTATCCGCACCTTTTCGGCC 61.028 55.000 0.00 0.00 44.91 6.13
60 61 1.906105 TATCCGCACCTTTTCGGCCT 61.906 55.000 0.00 0.00 44.91 5.19
61 62 1.906105 ATCCGCACCTTTTCGGCCTA 61.906 55.000 0.00 0.00 44.91 3.93
62 63 2.396157 CCGCACCTTTTCGGCCTAC 61.396 63.158 0.00 0.00 39.14 3.18
63 64 2.736682 CGCACCTTTTCGGCCTACG 61.737 63.158 0.00 0.00 46.11 3.51
64 65 3.035576 GCACCTTTTCGGCCTACGC 62.036 63.158 0.00 0.00 43.86 4.42
74 75 4.770874 GCCTACGCCTGGCCGAAA 62.771 66.667 14.12 2.29 44.32 3.46
75 76 2.046700 CCTACGCCTGGCCGAAAA 60.047 61.111 14.12 0.00 0.00 2.29
76 77 2.106683 CCTACGCCTGGCCGAAAAG 61.107 63.158 14.12 0.00 0.00 2.27
77 78 2.744709 TACGCCTGGCCGAAAAGC 60.745 61.111 14.12 0.00 0.00 3.51
78 79 3.248446 TACGCCTGGCCGAAAAGCT 62.248 57.895 14.12 0.00 0.00 3.74
79 80 3.804193 CGCCTGGCCGAAAAGCTC 61.804 66.667 14.12 0.00 0.00 4.09
80 81 2.360475 GCCTGGCCGAAAAGCTCT 60.360 61.111 7.66 0.00 0.00 4.09
81 82 1.973812 GCCTGGCCGAAAAGCTCTT 60.974 57.895 7.66 0.00 0.00 2.85
82 83 1.927608 GCCTGGCCGAAAAGCTCTTC 61.928 60.000 7.66 0.00 0.00 2.87
83 84 1.639298 CCTGGCCGAAAAGCTCTTCG 61.639 60.000 15.27 15.27 46.12 3.79
88 89 3.102515 CGAAAAGCTCTTCGGTCGA 57.897 52.632 14.43 0.00 43.51 4.20
89 90 1.415374 CGAAAAGCTCTTCGGTCGAA 58.585 50.000 14.43 5.67 43.51 3.71
96 97 2.815647 CTTCGGTCGAAGCCTGGC 60.816 66.667 18.19 11.65 43.95 4.85
97 98 4.388499 TTCGGTCGAAGCCTGGCC 62.388 66.667 16.57 0.00 0.00 5.36
100 101 4.388499 GGTCGAAGCCTGGCCGAA 62.388 66.667 19.17 4.08 33.91 4.30
101 102 2.358247 GTCGAAGCCTGGCCGAAA 60.358 61.111 19.17 0.00 33.91 3.46
102 103 1.964373 GTCGAAGCCTGGCCGAAAA 60.964 57.895 19.17 0.00 33.91 2.29
103 104 1.671054 TCGAAGCCTGGCCGAAAAG 60.671 57.895 16.57 1.42 0.00 2.27
104 105 2.690778 CGAAGCCTGGCCGAAAAGG 61.691 63.158 16.57 2.35 44.97 3.11
113 114 2.870372 CCGAAAAGGCCAGCTTCG 59.130 61.111 20.74 20.74 41.18 3.79
114 115 2.870372 CGAAAAGGCCAGCTTCGG 59.130 61.111 20.22 7.20 38.57 4.30
115 116 1.966451 CGAAAAGGCCAGCTTCGGT 60.966 57.895 20.22 0.00 38.57 4.69
116 117 1.876664 GAAAAGGCCAGCTTCGGTC 59.123 57.895 5.01 0.00 0.00 4.79
117 118 0.889186 GAAAAGGCCAGCTTCGGTCA 60.889 55.000 5.01 0.00 30.91 4.02
118 119 1.172812 AAAAGGCCAGCTTCGGTCAC 61.173 55.000 5.01 0.00 30.91 3.67
119 120 3.553095 AAGGCCAGCTTCGGTCACC 62.553 63.158 5.01 0.00 30.91 4.02
130 131 4.589675 GGTCACCGGTGGGCCAAA 62.590 66.667 33.40 11.27 36.48 3.28
131 132 2.519780 GTCACCGGTGGGCCAAAA 60.520 61.111 33.40 10.46 36.48 2.44
132 133 2.128507 GTCACCGGTGGGCCAAAAA 61.129 57.895 33.40 9.64 36.48 1.94
133 134 2.128507 TCACCGGTGGGCCAAAAAC 61.129 57.895 33.40 0.00 36.48 2.43
134 135 3.220658 ACCGGTGGGCCAAAAACG 61.221 61.111 8.40 11.07 36.48 3.60
135 136 3.984749 CCGGTGGGCCAAAAACGG 61.985 66.667 20.63 20.63 35.01 4.44
144 145 1.007849 CCAAAAACGGCCCAGTTCG 60.008 57.895 0.00 0.00 32.43 3.95
145 146 1.007849 CAAAAACGGCCCAGTTCGG 60.008 57.895 0.00 0.00 32.43 4.30
152 153 4.475135 GCCCAGTTCGGCCTCCTC 62.475 72.222 0.00 0.00 43.66 3.71
153 154 4.148825 CCCAGTTCGGCCTCCTCG 62.149 72.222 0.00 0.00 0.00 4.63
154 155 4.821589 CCAGTTCGGCCTCCTCGC 62.822 72.222 0.00 0.00 0.00 5.03
155 156 4.069232 CAGTTCGGCCTCCTCGCA 62.069 66.667 0.00 0.00 0.00 5.10
156 157 4.070552 AGTTCGGCCTCCTCGCAC 62.071 66.667 0.00 0.00 0.00 5.34
162 163 4.821589 GCCTCCTCGCACCCGAAG 62.822 72.222 0.00 0.00 43.87 3.79
163 164 4.821589 CCTCCTCGCACCCGAAGC 62.822 72.222 0.00 0.00 43.87 3.86
164 165 3.764466 CTCCTCGCACCCGAAGCT 61.764 66.667 0.00 0.00 43.87 3.74
165 166 2.361992 TCCTCGCACCCGAAGCTA 60.362 61.111 0.00 0.00 43.87 3.32
166 167 2.202756 CCTCGCACCCGAAGCTAC 60.203 66.667 0.00 0.00 43.87 3.58
167 168 2.711922 CCTCGCACCCGAAGCTACT 61.712 63.158 0.00 0.00 43.87 2.57
168 169 1.381928 CCTCGCACCCGAAGCTACTA 61.382 60.000 0.00 0.00 43.87 1.82
169 170 0.669077 CTCGCACCCGAAGCTACTAT 59.331 55.000 0.00 0.00 43.87 2.12
170 171 1.067212 CTCGCACCCGAAGCTACTATT 59.933 52.381 0.00 0.00 43.87 1.73
171 172 1.479323 TCGCACCCGAAGCTACTATTT 59.521 47.619 0.00 0.00 41.17 1.40
172 173 2.093869 TCGCACCCGAAGCTACTATTTT 60.094 45.455 0.00 0.00 41.17 1.82
173 174 2.676342 CGCACCCGAAGCTACTATTTTT 59.324 45.455 0.00 0.00 36.29 1.94
174 175 3.485216 CGCACCCGAAGCTACTATTTTTG 60.485 47.826 0.00 0.00 36.29 2.44
175 176 3.181500 GCACCCGAAGCTACTATTTTTGG 60.181 47.826 0.00 0.00 0.00 3.28
176 177 3.014623 ACCCGAAGCTACTATTTTTGGC 58.985 45.455 0.00 0.00 0.00 4.52
177 178 2.357952 CCCGAAGCTACTATTTTTGGCC 59.642 50.000 0.00 0.00 0.00 5.36
178 179 2.031683 CCGAAGCTACTATTTTTGGCCG 59.968 50.000 0.00 0.00 0.00 6.13
179 180 2.538939 CGAAGCTACTATTTTTGGCCGC 60.539 50.000 0.00 0.00 0.00 6.53
180 181 1.014352 AGCTACTATTTTTGGCCGCG 58.986 50.000 0.00 0.00 0.00 6.46
181 182 0.591488 GCTACTATTTTTGGCCGCGC 60.591 55.000 0.00 0.00 0.00 6.86
199 200 3.213402 CCCCGCCAACAACGTGTT 61.213 61.111 0.00 0.00 42.08 3.32
200 201 2.776913 CCCCGCCAACAACGTGTTT 61.777 57.895 0.00 0.00 38.77 2.83
201 202 1.139947 CCCGCCAACAACGTGTTTT 59.860 52.632 0.00 0.00 38.77 2.43
202 203 0.868177 CCCGCCAACAACGTGTTTTC 60.868 55.000 0.00 0.00 38.77 2.29
203 204 1.197368 CCGCCAACAACGTGTTTTCG 61.197 55.000 0.00 2.21 38.77 3.46
204 205 1.197368 CGCCAACAACGTGTTTTCGG 61.197 55.000 0.00 0.00 38.77 4.30
205 206 1.476235 GCCAACAACGTGTTTTCGGC 61.476 55.000 11.81 11.81 38.77 5.54
206 207 0.868177 CCAACAACGTGTTTTCGGCC 60.868 55.000 0.00 0.00 38.77 6.13
207 208 0.868177 CAACAACGTGTTTTCGGCCC 60.868 55.000 0.00 0.00 38.77 5.80
208 209 1.313812 AACAACGTGTTTTCGGCCCA 61.314 50.000 0.00 0.00 37.26 5.36
209 210 1.313812 ACAACGTGTTTTCGGCCCAA 61.314 50.000 0.00 0.00 34.94 4.12
210 211 0.868177 CAACGTGTTTTCGGCCCAAC 60.868 55.000 0.00 0.00 34.94 3.77
211 212 2.007113 AACGTGTTTTCGGCCCAACC 62.007 55.000 0.00 0.00 34.94 3.77
212 213 2.482333 CGTGTTTTCGGCCCAACCA 61.482 57.895 0.00 0.00 39.03 3.67
213 214 1.066752 GTGTTTTCGGCCCAACCAC 59.933 57.895 0.00 0.00 39.03 4.16
214 215 2.333581 GTTTTCGGCCCAACCACG 59.666 61.111 0.00 0.00 39.03 4.94
215 216 2.907917 TTTTCGGCCCAACCACGG 60.908 61.111 0.00 0.00 39.03 4.94
222 223 2.907917 CCCAACCACGGCCGAAAA 60.908 61.111 35.90 0.00 0.00 2.29
223 224 2.642700 CCAACCACGGCCGAAAAG 59.357 61.111 35.90 18.96 0.00 2.27
224 225 2.050442 CAACCACGGCCGAAAAGC 60.050 61.111 35.90 0.00 0.00 3.51
240 241 2.436115 GCCTACTTCGGCCACACC 60.436 66.667 2.24 0.00 44.41 4.16
241 242 2.267961 CCTACTTCGGCCACACCC 59.732 66.667 2.24 0.00 33.26 4.61
242 243 2.291043 CCTACTTCGGCCACACCCT 61.291 63.158 2.24 0.00 33.26 4.34
243 244 1.079127 CTACTTCGGCCACACCCTG 60.079 63.158 2.24 0.00 33.26 4.45
244 245 2.521958 CTACTTCGGCCACACCCTGG 62.522 65.000 2.24 0.00 44.08 4.45
251 252 2.203422 CCACACCCTGGCCGAAAA 60.203 61.111 0.00 0.00 31.36 2.29
252 253 2.561037 CCACACCCTGGCCGAAAAC 61.561 63.158 0.00 0.00 31.36 2.43
253 254 1.528309 CACACCCTGGCCGAAAACT 60.528 57.895 0.00 0.00 0.00 2.66
254 255 1.528309 ACACCCTGGCCGAAAACTG 60.528 57.895 0.00 0.00 0.00 3.16
255 256 2.597510 ACCCTGGCCGAAAACTGC 60.598 61.111 0.00 0.00 0.00 4.40
256 257 3.373565 CCCTGGCCGAAAACTGCC 61.374 66.667 0.00 0.00 0.00 4.85
257 258 2.282462 CCTGGCCGAAAACTGCCT 60.282 61.111 0.00 0.00 0.00 4.75
258 259 1.903404 CCTGGCCGAAAACTGCCTT 60.903 57.895 0.00 0.00 0.00 4.35
259 260 1.463553 CCTGGCCGAAAACTGCCTTT 61.464 55.000 0.00 0.00 0.00 3.11
260 261 0.389025 CTGGCCGAAAACTGCCTTTT 59.611 50.000 0.00 0.00 34.56 2.27
261 262 0.387565 TGGCCGAAAACTGCCTTTTC 59.612 50.000 0.00 6.62 43.09 2.29
272 273 2.757077 CCTTTTCGGCCCACTCCT 59.243 61.111 0.00 0.00 0.00 3.69
273 274 1.675641 CCTTTTCGGCCCACTCCTG 60.676 63.158 0.00 0.00 0.00 3.86
274 275 1.675641 CTTTTCGGCCCACTCCTGG 60.676 63.158 0.00 0.00 37.29 4.45
294 295 1.636988 CCGACGGGCTACTAGTTTTG 58.363 55.000 5.81 0.00 0.00 2.44
295 296 0.997196 CGACGGGCTACTAGTTTTGC 59.003 55.000 0.00 3.63 0.00 3.68
296 297 0.997196 GACGGGCTACTAGTTTTGCG 59.003 55.000 0.00 0.00 0.00 4.85
297 298 0.319405 ACGGGCTACTAGTTTTGCGT 59.681 50.000 0.00 0.00 0.00 5.24
298 299 1.270465 ACGGGCTACTAGTTTTGCGTT 60.270 47.619 0.00 0.00 0.00 4.84
299 300 1.802365 CGGGCTACTAGTTTTGCGTTT 59.198 47.619 0.00 0.00 0.00 3.60
300 301 2.224784 CGGGCTACTAGTTTTGCGTTTT 59.775 45.455 0.00 0.00 0.00 2.43
301 302 3.666111 CGGGCTACTAGTTTTGCGTTTTC 60.666 47.826 0.00 0.00 0.00 2.29
302 303 3.501062 GGGCTACTAGTTTTGCGTTTTCT 59.499 43.478 0.00 0.00 0.00 2.52
303 304 4.023450 GGGCTACTAGTTTTGCGTTTTCTT 60.023 41.667 0.00 0.00 0.00 2.52
304 305 5.145059 GGCTACTAGTTTTGCGTTTTCTTC 58.855 41.667 0.00 0.00 0.00 2.87
305 306 5.277634 GGCTACTAGTTTTGCGTTTTCTTCA 60.278 40.000 0.00 0.00 0.00 3.02
306 307 6.371389 GCTACTAGTTTTGCGTTTTCTTCAT 58.629 36.000 0.00 0.00 0.00 2.57
307 308 6.856426 GCTACTAGTTTTGCGTTTTCTTCATT 59.144 34.615 0.00 0.00 0.00 2.57
308 309 7.059602 GCTACTAGTTTTGCGTTTTCTTCATTC 59.940 37.037 0.00 0.00 0.00 2.67
309 310 7.027778 ACTAGTTTTGCGTTTTCTTCATTCT 57.972 32.000 0.00 0.00 0.00 2.40
310 311 8.149973 ACTAGTTTTGCGTTTTCTTCATTCTA 57.850 30.769 0.00 0.00 0.00 2.10
311 312 8.068380 ACTAGTTTTGCGTTTTCTTCATTCTAC 58.932 33.333 0.00 0.00 0.00 2.59
312 313 5.907391 AGTTTTGCGTTTTCTTCATTCTACG 59.093 36.000 0.00 0.00 0.00 3.51
319 320 7.681125 CGTTTTCTTCATTCTACGCTATAGT 57.319 36.000 0.84 0.00 0.00 2.12
320 321 8.116624 CGTTTTCTTCATTCTACGCTATAGTT 57.883 34.615 0.84 0.00 0.00 2.24
321 322 8.592998 CGTTTTCTTCATTCTACGCTATAGTTT 58.407 33.333 0.84 0.00 0.00 2.66
322 323 9.903185 GTTTTCTTCATTCTACGCTATAGTTTC 57.097 33.333 0.84 0.00 0.00 2.78
323 324 8.644318 TTTCTTCATTCTACGCTATAGTTTCC 57.356 34.615 0.84 0.00 0.00 3.13
324 325 6.436261 TCTTCATTCTACGCTATAGTTTCCG 58.564 40.000 0.84 0.00 0.00 4.30
325 326 6.261603 TCTTCATTCTACGCTATAGTTTCCGA 59.738 38.462 0.84 0.00 0.00 4.55
326 327 6.381481 TCATTCTACGCTATAGTTTCCGAA 57.619 37.500 0.84 0.00 0.00 4.30
327 328 6.798482 TCATTCTACGCTATAGTTTCCGAAA 58.202 36.000 0.84 0.00 0.00 3.46
328 329 7.431249 TCATTCTACGCTATAGTTTCCGAAAT 58.569 34.615 0.84 0.00 0.00 2.17
329 330 7.924412 TCATTCTACGCTATAGTTTCCGAAATT 59.076 33.333 0.84 0.00 0.00 1.82
330 331 7.459394 TTCTACGCTATAGTTTCCGAAATTG 57.541 36.000 0.84 0.00 0.00 2.32
331 332 4.531659 ACGCTATAGTTTCCGAAATTGC 57.468 40.909 0.84 0.00 0.00 3.56
332 333 4.189231 ACGCTATAGTTTCCGAAATTGCT 58.811 39.130 0.84 0.00 0.00 3.91
333 334 5.353938 ACGCTATAGTTTCCGAAATTGCTA 58.646 37.500 0.84 0.00 0.00 3.49
334 335 5.233689 ACGCTATAGTTTCCGAAATTGCTAC 59.766 40.000 0.84 0.00 0.00 3.58
335 336 5.233476 CGCTATAGTTTCCGAAATTGCTACA 59.767 40.000 0.84 0.00 0.00 2.74
336 337 6.237996 CGCTATAGTTTCCGAAATTGCTACAA 60.238 38.462 0.84 0.00 0.00 2.41
337 338 7.469260 GCTATAGTTTCCGAAATTGCTACAAA 58.531 34.615 0.84 0.00 0.00 2.83
338 339 7.966204 GCTATAGTTTCCGAAATTGCTACAAAA 59.034 33.333 0.84 0.00 0.00 2.44
339 340 9.834628 CTATAGTTTCCGAAATTGCTACAAAAA 57.165 29.630 0.00 0.00 0.00 1.94
382 383 9.679661 AAAAATTCCAGTTATTTTGGACAAGTT 57.320 25.926 0.00 0.00 44.13 2.66
385 386 9.981114 AATTCCAGTTATTTTGGACAAGTTAAG 57.019 29.630 0.00 0.00 44.13 1.85
386 387 8.528044 TTCCAGTTATTTTGGACAAGTTAAGT 57.472 30.769 0.00 0.00 44.13 2.24
387 388 9.629878 TTCCAGTTATTTTGGACAAGTTAAGTA 57.370 29.630 0.00 0.00 44.13 2.24
388 389 9.629878 TCCAGTTATTTTGGACAAGTTAAGTAA 57.370 29.630 0.00 0.00 39.74 2.24
392 393 9.467258 GTTATTTTGGACAAGTTAAGTAAACCC 57.533 33.333 0.00 0.00 39.03 4.11
393 394 7.663043 ATTTTGGACAAGTTAAGTAAACCCA 57.337 32.000 0.00 0.00 39.03 4.51
394 395 7.477945 TTTTGGACAAGTTAAGTAAACCCAA 57.522 32.000 0.00 0.00 39.03 4.12
395 396 6.453926 TTGGACAAGTTAAGTAAACCCAAC 57.546 37.500 0.00 0.00 39.03 3.77
396 397 5.507637 TGGACAAGTTAAGTAAACCCAACA 58.492 37.500 0.00 0.00 39.03 3.33
397 398 5.591067 TGGACAAGTTAAGTAAACCCAACAG 59.409 40.000 0.00 0.00 39.03 3.16
398 399 5.824097 GGACAAGTTAAGTAAACCCAACAGA 59.176 40.000 0.00 0.00 39.03 3.41
399 400 6.238566 GGACAAGTTAAGTAAACCCAACAGAC 60.239 42.308 0.00 0.00 39.03 3.51
400 401 6.181908 ACAAGTTAAGTAAACCCAACAGACA 58.818 36.000 0.00 0.00 39.03 3.41
401 402 6.660094 ACAAGTTAAGTAAACCCAACAGACAA 59.340 34.615 0.00 0.00 39.03 3.18
402 403 7.177041 ACAAGTTAAGTAAACCCAACAGACAAA 59.823 33.333 0.00 0.00 39.03 2.83
403 404 7.891498 AGTTAAGTAAACCCAACAGACAAAT 57.109 32.000 0.00 0.00 39.03 2.32
404 405 7.937649 AGTTAAGTAAACCCAACAGACAAATC 58.062 34.615 0.00 0.00 39.03 2.17
405 406 7.778382 AGTTAAGTAAACCCAACAGACAAATCT 59.222 33.333 0.00 0.00 39.03 2.40
406 407 9.059260 GTTAAGTAAACCCAACAGACAAATCTA 57.941 33.333 0.00 0.00 30.21 1.98
407 408 9.802039 TTAAGTAAACCCAACAGACAAATCTAT 57.198 29.630 0.00 0.00 32.25 1.98
408 409 7.687941 AGTAAACCCAACAGACAAATCTATG 57.312 36.000 0.00 0.00 32.25 2.23
409 410 7.231467 AGTAAACCCAACAGACAAATCTATGT 58.769 34.615 0.00 0.00 32.25 2.29
410 411 8.380099 AGTAAACCCAACAGACAAATCTATGTA 58.620 33.333 0.00 0.00 32.25 2.29
411 412 9.005777 GTAAACCCAACAGACAAATCTATGTAA 57.994 33.333 0.00 0.00 32.25 2.41
412 413 8.650143 AAACCCAACAGACAAATCTATGTAAT 57.350 30.769 0.00 0.00 32.25 1.89
413 414 7.630242 ACCCAACAGACAAATCTATGTAATG 57.370 36.000 0.00 0.00 32.25 1.90
414 415 6.095440 ACCCAACAGACAAATCTATGTAATGC 59.905 38.462 0.00 0.00 32.25 3.56
415 416 6.095300 CCCAACAGACAAATCTATGTAATGCA 59.905 38.462 0.00 0.00 32.25 3.96
416 417 6.968904 CCAACAGACAAATCTATGTAATGCAC 59.031 38.462 0.00 0.00 32.25 4.57
417 418 7.148188 CCAACAGACAAATCTATGTAATGCACT 60.148 37.037 0.00 0.00 32.25 4.40
418 419 7.545362 ACAGACAAATCTATGTAATGCACTC 57.455 36.000 0.00 0.00 32.25 3.51
419 420 7.334090 ACAGACAAATCTATGTAATGCACTCT 58.666 34.615 0.00 0.00 32.25 3.24
420 421 8.478066 ACAGACAAATCTATGTAATGCACTCTA 58.522 33.333 0.00 0.00 32.25 2.43
421 422 9.317936 CAGACAAATCTATGTAATGCACTCTAA 57.682 33.333 0.00 0.00 32.25 2.10
422 423 9.319143 AGACAAATCTATGTAATGCACTCTAAC 57.681 33.333 0.00 0.00 32.57 2.34
423 424 9.319143 GACAAATCTATGTAATGCACTCTAACT 57.681 33.333 0.00 0.00 32.57 2.24
424 425 9.672673 ACAAATCTATGTAATGCACTCTAACTT 57.327 29.630 0.00 0.00 0.00 2.66
425 426 9.926751 CAAATCTATGTAATGCACTCTAACTTG 57.073 33.333 0.00 0.00 0.00 3.16
426 427 7.721286 ATCTATGTAATGCACTCTAACTTGC 57.279 36.000 0.00 0.00 39.33 4.01
427 428 6.878317 TCTATGTAATGCACTCTAACTTGCT 58.122 36.000 0.00 0.00 39.62 3.91
428 429 8.007405 TCTATGTAATGCACTCTAACTTGCTA 57.993 34.615 0.00 0.00 39.62 3.49
429 430 8.138074 TCTATGTAATGCACTCTAACTTGCTAG 58.862 37.037 0.00 0.00 39.62 3.42
430 431 5.419542 TGTAATGCACTCTAACTTGCTAGG 58.580 41.667 0.00 0.00 39.62 3.02
431 432 4.559862 AATGCACTCTAACTTGCTAGGT 57.440 40.909 0.00 0.00 39.62 3.08
432 433 5.677319 AATGCACTCTAACTTGCTAGGTA 57.323 39.130 0.00 0.00 39.62 3.08
433 434 5.878406 ATGCACTCTAACTTGCTAGGTAT 57.122 39.130 0.00 0.00 39.62 2.73
434 435 5.677319 TGCACTCTAACTTGCTAGGTATT 57.323 39.130 0.00 0.00 39.62 1.89
435 436 6.785337 TGCACTCTAACTTGCTAGGTATTA 57.215 37.500 0.00 0.00 39.62 0.98
436 437 7.177832 TGCACTCTAACTTGCTAGGTATTAA 57.822 36.000 0.00 0.00 39.62 1.40
437 438 7.617225 TGCACTCTAACTTGCTAGGTATTAAA 58.383 34.615 0.00 0.00 39.62 1.52
438 439 8.098286 TGCACTCTAACTTGCTAGGTATTAAAA 58.902 33.333 0.00 0.00 39.62 1.52
439 440 8.943002 GCACTCTAACTTGCTAGGTATTAAAAA 58.057 33.333 0.00 0.00 35.74 1.94
463 464 9.588096 AAAACCTTGTGTTCCTTTTCTATATCT 57.412 29.630 0.00 0.00 35.67 1.98
779 780 3.939066 ACTTAAACGCATCCTACTGCTT 58.061 40.909 0.00 0.00 40.06 3.91
1092 3252 2.203139 CAACCATGGCGGCGGATA 60.203 61.111 13.04 0.00 39.03 2.59
1386 5598 6.501781 GTCTCTGCATAGGAATCAATTTTGG 58.498 40.000 0.00 0.00 0.00 3.28
1672 5890 5.468409 TCATCGTTGATCTTACAAACTGCAA 59.532 36.000 0.00 0.00 0.00 4.08
1715 5935 6.876257 GCGGATTTATATTTCTCAGGTCAGAT 59.124 38.462 0.00 0.00 0.00 2.90
1808 6028 3.391665 ATCTTCCGCTGCCTTCCGG 62.392 63.158 0.00 0.00 45.64 5.14
1839 6059 3.836365 TTGGATGATGCGTGATTCCTA 57.164 42.857 0.00 0.00 0.00 2.94
1864 6084 7.129109 TCATTGAGTCTTCGATAAACCAAAC 57.871 36.000 0.00 0.00 0.00 2.93
2149 6378 8.936070 TTAAAATCGATCTTGATTTCCTCGTA 57.064 30.769 0.00 0.00 45.36 3.43
2262 6491 5.945784 TCTTCTATGTGTGGGATCCTTTTTG 59.054 40.000 12.58 0.00 0.00 2.44
2323 6553 7.174413 TCTACATGGATTTCAAGTTGGATGAA 58.826 34.615 2.34 0.00 35.11 2.57
2801 7248 6.034591 TCTACTAATTGCTGAACGCTAAGTC 58.965 40.000 0.00 0.00 40.11 3.01
3079 7526 3.576550 TGGCTCGGCTAATATGTCACATA 59.423 43.478 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.347707 TGCTGTTCTTCGTTGGATCCT 59.652 47.619 14.23 0.00 0.00 3.24
1 2 1.734465 CTGCTGTTCTTCGTTGGATCC 59.266 52.381 4.20 4.20 0.00 3.36
2 3 1.129437 GCTGCTGTTCTTCGTTGGATC 59.871 52.381 0.00 0.00 0.00 3.36
3 4 1.160137 GCTGCTGTTCTTCGTTGGAT 58.840 50.000 0.00 0.00 0.00 3.41
4 5 1.221466 CGCTGCTGTTCTTCGTTGGA 61.221 55.000 0.00 0.00 0.00 3.53
5 6 1.205064 CGCTGCTGTTCTTCGTTGG 59.795 57.895 0.00 0.00 0.00 3.77
6 7 1.439365 GCGCTGCTGTTCTTCGTTG 60.439 57.895 0.00 0.00 0.00 4.10
7 8 1.835483 CTGCGCTGCTGTTCTTCGTT 61.835 55.000 9.73 0.00 0.00 3.85
8 9 2.280119 TGCGCTGCTGTTCTTCGT 60.280 55.556 9.73 0.00 0.00 3.85
9 10 2.473378 CTGCGCTGCTGTTCTTCG 59.527 61.111 9.73 0.00 0.00 3.79
10 11 2.684843 CCCTGCGCTGCTGTTCTTC 61.685 63.158 9.73 0.00 0.00 2.87
11 12 2.670934 CCCTGCGCTGCTGTTCTT 60.671 61.111 9.73 0.00 0.00 2.52
12 13 4.711949 CCCCTGCGCTGCTGTTCT 62.712 66.667 9.73 0.00 0.00 3.01
24 25 2.869503 ATAAGCACCGTTCGCCCCTG 62.870 60.000 0.00 0.00 0.00 4.45
25 26 2.588856 GATAAGCACCGTTCGCCCCT 62.589 60.000 0.00 0.00 0.00 4.79
26 27 2.124860 ATAAGCACCGTTCGCCCC 60.125 61.111 0.00 0.00 0.00 5.80
27 28 2.178235 GGATAAGCACCGTTCGCCC 61.178 63.158 0.00 0.00 0.00 6.13
28 29 2.522638 CGGATAAGCACCGTTCGCC 61.523 63.158 0.00 0.00 44.57 5.54
29 30 3.003478 CGGATAAGCACCGTTCGC 58.997 61.111 0.00 0.00 44.57 4.70
37 38 1.083489 CGAAAAGGTGCGGATAAGCA 58.917 50.000 0.00 0.00 45.96 3.91
38 39 3.897819 CGAAAAGGTGCGGATAAGC 57.102 52.632 0.00 0.00 37.71 3.09
45 46 2.736682 CGTAGGCCGAAAAGGTGCG 61.737 63.158 0.00 0.00 43.70 5.34
46 47 3.035576 GCGTAGGCCGAAAAGGTGC 62.036 63.158 0.00 0.00 43.70 5.01
47 48 3.174788 GCGTAGGCCGAAAAGGTG 58.825 61.111 0.00 0.00 43.70 4.00
58 59 2.046700 TTTTCGGCCAGGCGTAGG 60.047 61.111 13.55 0.00 0.00 3.18
59 60 2.750888 GCTTTTCGGCCAGGCGTAG 61.751 63.158 13.55 10.29 0.00 3.51
60 61 2.744709 GCTTTTCGGCCAGGCGTA 60.745 61.111 13.55 0.61 0.00 4.42
61 62 4.643387 AGCTTTTCGGCCAGGCGT 62.643 61.111 13.55 0.00 0.00 5.68
62 63 3.804193 GAGCTTTTCGGCCAGGCG 61.804 66.667 5.00 7.36 0.00 5.52
63 64 1.927608 GAAGAGCTTTTCGGCCAGGC 61.928 60.000 1.26 1.26 0.00 4.85
64 65 1.639298 CGAAGAGCTTTTCGGCCAGG 61.639 60.000 26.87 2.66 44.56 4.45
65 66 1.790387 CGAAGAGCTTTTCGGCCAG 59.210 57.895 26.87 3.33 44.56 4.85
66 67 3.966215 CGAAGAGCTTTTCGGCCA 58.034 55.556 26.87 0.00 44.56 5.36
80 81 4.388499 GGCCAGGCTTCGACCGAA 62.388 66.667 12.43 4.72 33.69 4.30
83 84 3.894547 TTTCGGCCAGGCTTCGACC 62.895 63.158 12.43 0.00 32.39 4.79
84 85 1.912371 CTTTTCGGCCAGGCTTCGAC 61.912 60.000 12.43 0.00 32.39 4.20
85 86 1.671054 CTTTTCGGCCAGGCTTCGA 60.671 57.895 12.43 10.26 0.00 3.71
86 87 2.690778 CCTTTTCGGCCAGGCTTCG 61.691 63.158 12.43 7.66 0.00 3.79
87 88 3.278157 CCTTTTCGGCCAGGCTTC 58.722 61.111 12.43 0.00 0.00 3.86
96 97 2.870372 CGAAGCTGGCCTTTTCGG 59.130 61.111 21.35 9.12 39.82 4.30
97 98 1.912371 GACCGAAGCTGGCCTTTTCG 61.912 60.000 21.83 21.83 42.31 3.46
98 99 0.889186 TGACCGAAGCTGGCCTTTTC 60.889 55.000 3.32 4.33 32.78 2.29
99 100 1.150536 TGACCGAAGCTGGCCTTTT 59.849 52.632 3.32 0.00 32.78 2.27
100 101 1.600916 GTGACCGAAGCTGGCCTTT 60.601 57.895 3.32 0.00 32.78 3.11
101 102 2.032681 GTGACCGAAGCTGGCCTT 59.967 61.111 3.32 0.00 36.19 4.35
102 103 4.021925 GGTGACCGAAGCTGGCCT 62.022 66.667 3.32 0.00 0.00 5.19
113 114 4.589675 TTTGGCCCACCGGTGACC 62.590 66.667 36.07 32.32 39.70 4.02
114 115 2.128507 TTTTTGGCCCACCGGTGAC 61.129 57.895 36.07 25.37 39.70 3.67
115 116 2.128507 GTTTTTGGCCCACCGGTGA 61.129 57.895 36.07 13.42 39.70 4.02
116 117 2.419620 GTTTTTGGCCCACCGGTG 59.580 61.111 28.26 28.26 39.70 4.94
117 118 3.220658 CGTTTTTGGCCCACCGGT 61.221 61.111 0.00 0.00 39.70 5.28
118 119 3.984749 CCGTTTTTGGCCCACCGG 61.985 66.667 0.00 0.00 39.70 5.28
126 127 1.007849 CGAACTGGGCCGTTTTTGG 60.008 57.895 13.50 3.06 0.00 3.28
127 128 1.007849 CCGAACTGGGCCGTTTTTG 60.008 57.895 13.50 4.04 0.00 2.44
128 129 3.439008 CCGAACTGGGCCGTTTTT 58.561 55.556 13.50 0.00 0.00 1.94
136 137 4.148825 CGAGGAGGCCGAACTGGG 62.149 72.222 0.00 0.00 38.63 4.45
137 138 4.821589 GCGAGGAGGCCGAACTGG 62.822 72.222 0.00 0.00 42.50 4.00
138 139 4.069232 TGCGAGGAGGCCGAACTG 62.069 66.667 0.00 0.00 0.00 3.16
139 140 4.070552 GTGCGAGGAGGCCGAACT 62.071 66.667 0.00 0.00 33.01 3.01
145 146 4.821589 CTTCGGGTGCGAGGAGGC 62.822 72.222 0.00 0.00 0.00 4.70
146 147 4.821589 GCTTCGGGTGCGAGGAGG 62.822 72.222 0.00 0.00 0.00 4.30
147 148 2.415608 TAGCTTCGGGTGCGAGGAG 61.416 63.158 0.00 0.00 35.28 3.69
148 149 2.361992 TAGCTTCGGGTGCGAGGA 60.362 61.111 0.00 0.00 35.28 3.71
149 150 1.381928 TAGTAGCTTCGGGTGCGAGG 61.382 60.000 0.00 0.00 33.43 4.63
150 151 0.669077 ATAGTAGCTTCGGGTGCGAG 59.331 55.000 0.00 0.00 33.43 5.03
151 152 1.108776 AATAGTAGCTTCGGGTGCGA 58.891 50.000 0.00 0.00 33.43 5.10
152 153 1.935933 AAATAGTAGCTTCGGGTGCG 58.064 50.000 0.00 0.00 33.43 5.34
153 154 3.181500 CCAAAAATAGTAGCTTCGGGTGC 60.181 47.826 0.00 0.00 0.00 5.01
154 155 3.181500 GCCAAAAATAGTAGCTTCGGGTG 60.181 47.826 0.00 0.00 0.00 4.61
155 156 3.014623 GCCAAAAATAGTAGCTTCGGGT 58.985 45.455 0.00 0.00 0.00 5.28
156 157 2.357952 GGCCAAAAATAGTAGCTTCGGG 59.642 50.000 0.00 0.00 0.00 5.14
157 158 2.031683 CGGCCAAAAATAGTAGCTTCGG 59.968 50.000 2.24 0.00 0.00 4.30
158 159 2.538939 GCGGCCAAAAATAGTAGCTTCG 60.539 50.000 2.24 0.00 0.00 3.79
159 160 2.538939 CGCGGCCAAAAATAGTAGCTTC 60.539 50.000 2.24 0.00 0.00 3.86
160 161 1.400494 CGCGGCCAAAAATAGTAGCTT 59.600 47.619 2.24 0.00 0.00 3.74
161 162 1.014352 CGCGGCCAAAAATAGTAGCT 58.986 50.000 2.24 0.00 0.00 3.32
162 163 0.591488 GCGCGGCCAAAAATAGTAGC 60.591 55.000 8.83 0.00 0.00 3.58
163 164 3.526825 GCGCGGCCAAAAATAGTAG 57.473 52.632 8.83 0.00 0.00 2.57
182 183 2.286127 AAAACACGTTGTTGGCGGGG 62.286 55.000 4.51 0.00 40.14 5.73
183 184 0.868177 GAAAACACGTTGTTGGCGGG 60.868 55.000 4.51 0.00 40.14 6.13
184 185 1.197368 CGAAAACACGTTGTTGGCGG 61.197 55.000 4.51 0.00 40.14 6.13
185 186 1.197368 CCGAAAACACGTTGTTGGCG 61.197 55.000 4.51 9.85 40.14 5.69
186 187 1.476235 GCCGAAAACACGTTGTTGGC 61.476 55.000 14.31 14.31 46.83 4.52
187 188 0.868177 GGCCGAAAACACGTTGTTGG 60.868 55.000 2.32 2.32 40.14 3.77
188 189 0.868177 GGGCCGAAAACACGTTGTTG 60.868 55.000 0.00 0.00 40.14 3.33
189 190 1.313812 TGGGCCGAAAACACGTTGTT 61.314 50.000 0.00 0.00 43.41 2.83
190 191 1.313812 TTGGGCCGAAAACACGTTGT 61.314 50.000 0.00 0.00 0.00 3.32
191 192 0.868177 GTTGGGCCGAAAACACGTTG 60.868 55.000 0.01 0.00 0.00 4.10
192 193 1.434287 GTTGGGCCGAAAACACGTT 59.566 52.632 0.01 0.00 0.00 3.99
193 194 2.483197 GGTTGGGCCGAAAACACGT 61.483 57.895 0.01 0.00 0.00 4.49
194 195 2.333581 GGTTGGGCCGAAAACACG 59.666 61.111 0.01 0.00 0.00 4.49
195 196 1.066752 GTGGTTGGGCCGAAAACAC 59.933 57.895 18.86 18.86 38.01 3.32
196 197 2.482333 CGTGGTTGGGCCGAAAACA 61.482 57.895 0.01 2.04 41.21 2.83
197 198 2.333581 CGTGGTTGGGCCGAAAAC 59.666 61.111 0.01 3.79 41.21 2.43
198 199 2.907917 CCGTGGTTGGGCCGAAAA 60.908 61.111 0.01 0.00 41.21 2.29
205 206 2.907917 TTTTCGGCCGTGGTTGGG 60.908 61.111 27.15 0.00 0.00 4.12
206 207 2.642700 CTTTTCGGCCGTGGTTGG 59.357 61.111 27.15 8.06 0.00 3.77
207 208 2.050442 GCTTTTCGGCCGTGGTTG 60.050 61.111 27.15 13.66 0.00 3.77
208 209 3.292159 GGCTTTTCGGCCGTGGTT 61.292 61.111 27.15 0.00 42.82 3.67
224 225 2.267961 GGGTGTGGCCGAAGTAGG 59.732 66.667 0.00 0.00 38.44 3.18
225 226 1.079127 CAGGGTGTGGCCGAAGTAG 60.079 63.158 0.00 0.00 38.44 2.57
226 227 2.589157 CCAGGGTGTGGCCGAAGTA 61.589 63.158 0.00 0.00 40.39 2.24
227 228 3.953775 CCAGGGTGTGGCCGAAGT 61.954 66.667 0.00 0.00 40.39 3.01
235 236 1.528309 AGTTTTCGGCCAGGGTGTG 60.528 57.895 2.24 0.00 0.00 3.82
236 237 1.528309 CAGTTTTCGGCCAGGGTGT 60.528 57.895 2.24 0.00 0.00 4.16
237 238 2.919494 GCAGTTTTCGGCCAGGGTG 61.919 63.158 2.24 0.00 35.07 4.61
238 239 2.597510 GCAGTTTTCGGCCAGGGT 60.598 61.111 2.24 0.00 35.07 4.34
255 256 1.675641 CAGGAGTGGGCCGAAAAGG 60.676 63.158 0.00 0.00 44.97 3.11
256 257 1.675641 CCAGGAGTGGGCCGAAAAG 60.676 63.158 0.00 0.00 40.67 2.27
257 258 2.434331 CCAGGAGTGGGCCGAAAA 59.566 61.111 0.00 0.00 40.67 2.29
258 259 4.344865 GCCAGGAGTGGGCCGAAA 62.345 66.667 0.00 0.00 45.87 3.46
275 276 1.636988 CAAAACTAGTAGCCCGTCGG 58.363 55.000 3.60 3.60 0.00 4.79
276 277 0.997196 GCAAAACTAGTAGCCCGTCG 59.003 55.000 0.00 0.00 0.00 5.12
277 278 0.997196 CGCAAAACTAGTAGCCCGTC 59.003 55.000 0.00 0.00 0.00 4.79
278 279 0.319405 ACGCAAAACTAGTAGCCCGT 59.681 50.000 0.00 0.62 0.00 5.28
279 280 1.435577 AACGCAAAACTAGTAGCCCG 58.564 50.000 0.00 0.00 0.00 6.13
280 281 3.501062 AGAAAACGCAAAACTAGTAGCCC 59.499 43.478 0.00 0.00 0.00 5.19
281 282 4.744136 AGAAAACGCAAAACTAGTAGCC 57.256 40.909 0.00 0.00 0.00 3.93
282 283 5.744490 TGAAGAAAACGCAAAACTAGTAGC 58.256 37.500 0.00 0.00 0.00 3.58
283 284 8.283291 AGAATGAAGAAAACGCAAAACTAGTAG 58.717 33.333 0.00 0.00 0.00 2.57
284 285 8.149973 AGAATGAAGAAAACGCAAAACTAGTA 57.850 30.769 0.00 0.00 0.00 1.82
285 286 7.027778 AGAATGAAGAAAACGCAAAACTAGT 57.972 32.000 0.00 0.00 0.00 2.57
286 287 7.266335 CGTAGAATGAAGAAAACGCAAAACTAG 59.734 37.037 0.00 0.00 0.00 2.57
287 288 7.067116 CGTAGAATGAAGAAAACGCAAAACTA 58.933 34.615 0.00 0.00 0.00 2.24
288 289 5.907391 CGTAGAATGAAGAAAACGCAAAACT 59.093 36.000 0.00 0.00 0.00 2.66
289 290 6.111862 CGTAGAATGAAGAAAACGCAAAAC 57.888 37.500 0.00 0.00 0.00 2.43
295 296 7.681125 ACTATAGCGTAGAATGAAGAAAACG 57.319 36.000 0.00 0.00 0.00 3.60
296 297 9.903185 GAAACTATAGCGTAGAATGAAGAAAAC 57.097 33.333 0.00 0.00 0.00 2.43
297 298 9.095065 GGAAACTATAGCGTAGAATGAAGAAAA 57.905 33.333 0.00 0.00 0.00 2.29
298 299 7.434307 CGGAAACTATAGCGTAGAATGAAGAAA 59.566 37.037 0.00 0.00 0.00 2.52
299 300 6.916387 CGGAAACTATAGCGTAGAATGAAGAA 59.084 38.462 0.00 0.00 0.00 2.52
300 301 6.261603 TCGGAAACTATAGCGTAGAATGAAGA 59.738 38.462 0.00 0.00 0.00 2.87
301 302 6.436261 TCGGAAACTATAGCGTAGAATGAAG 58.564 40.000 0.00 0.00 0.00 3.02
302 303 6.381481 TCGGAAACTATAGCGTAGAATGAA 57.619 37.500 0.00 0.00 0.00 2.57
303 304 6.381481 TTCGGAAACTATAGCGTAGAATGA 57.619 37.500 0.00 0.00 0.00 2.57
304 305 7.639162 ATTTCGGAAACTATAGCGTAGAATG 57.361 36.000 5.12 0.00 0.00 2.67
305 306 7.307219 GCAATTTCGGAAACTATAGCGTAGAAT 60.307 37.037 5.12 0.00 0.00 2.40
306 307 6.019318 GCAATTTCGGAAACTATAGCGTAGAA 60.019 38.462 5.12 0.00 0.00 2.10
307 308 5.461078 GCAATTTCGGAAACTATAGCGTAGA 59.539 40.000 5.12 0.00 0.00 2.59
308 309 5.462398 AGCAATTTCGGAAACTATAGCGTAG 59.538 40.000 5.12 0.00 0.00 3.51
309 310 5.353938 AGCAATTTCGGAAACTATAGCGTA 58.646 37.500 5.12 0.00 0.00 4.42
310 311 4.189231 AGCAATTTCGGAAACTATAGCGT 58.811 39.130 5.12 0.00 0.00 5.07
311 312 4.795970 AGCAATTTCGGAAACTATAGCG 57.204 40.909 5.12 0.00 0.00 4.26
312 313 6.598753 TGTAGCAATTTCGGAAACTATAGC 57.401 37.500 5.12 5.94 0.00 2.97
313 314 9.834628 TTTTTGTAGCAATTTCGGAAACTATAG 57.165 29.630 5.12 0.00 0.00 1.31
356 357 9.679661 AACTTGTCCAAAATAACTGGAATTTTT 57.320 25.926 0.00 0.00 44.55 1.94
359 360 9.981114 CTTAACTTGTCCAAAATAACTGGAATT 57.019 29.630 0.00 0.00 44.55 2.17
360 361 9.143155 ACTTAACTTGTCCAAAATAACTGGAAT 57.857 29.630 0.00 0.00 44.55 3.01
361 362 8.528044 ACTTAACTTGTCCAAAATAACTGGAA 57.472 30.769 0.00 0.00 44.55 3.53
362 363 9.629878 TTACTTAACTTGTCCAAAATAACTGGA 57.370 29.630 0.00 0.00 40.77 3.86
366 367 9.467258 GGGTTTACTTAACTTGTCCAAAATAAC 57.533 33.333 0.00 0.00 36.93 1.89
367 368 9.198475 TGGGTTTACTTAACTTGTCCAAAATAA 57.802 29.630 0.00 0.00 36.93 1.40
368 369 8.763984 TGGGTTTACTTAACTTGTCCAAAATA 57.236 30.769 0.00 0.00 36.93 1.40
369 370 7.663043 TGGGTTTACTTAACTTGTCCAAAAT 57.337 32.000 0.00 0.00 36.93 1.82
370 371 7.039223 TGTTGGGTTTACTTAACTTGTCCAAAA 60.039 33.333 0.00 0.00 36.63 2.44
371 372 6.436532 TGTTGGGTTTACTTAACTTGTCCAAA 59.563 34.615 0.00 0.00 36.63 3.28
372 373 5.950549 TGTTGGGTTTACTTAACTTGTCCAA 59.049 36.000 0.00 0.00 34.19 3.53
373 374 5.507637 TGTTGGGTTTACTTAACTTGTCCA 58.492 37.500 0.00 0.00 36.93 4.02
374 375 5.824097 TCTGTTGGGTTTACTTAACTTGTCC 59.176 40.000 0.00 0.00 36.93 4.02
375 376 6.316890 TGTCTGTTGGGTTTACTTAACTTGTC 59.683 38.462 0.00 0.00 36.93 3.18
376 377 6.181908 TGTCTGTTGGGTTTACTTAACTTGT 58.818 36.000 0.00 0.00 36.93 3.16
377 378 6.687081 TGTCTGTTGGGTTTACTTAACTTG 57.313 37.500 0.00 0.00 36.93 3.16
378 379 7.706100 TTTGTCTGTTGGGTTTACTTAACTT 57.294 32.000 0.00 0.00 36.93 2.66
379 380 7.778382 AGATTTGTCTGTTGGGTTTACTTAACT 59.222 33.333 0.00 0.00 36.93 2.24
380 381 7.937649 AGATTTGTCTGTTGGGTTTACTTAAC 58.062 34.615 0.00 0.00 35.94 2.01
381 382 9.802039 ATAGATTTGTCTGTTGGGTTTACTTAA 57.198 29.630 0.00 0.00 0.00 1.85
382 383 9.226606 CATAGATTTGTCTGTTGGGTTTACTTA 57.773 33.333 0.00 0.00 0.00 2.24
383 384 7.724061 ACATAGATTTGTCTGTTGGGTTTACTT 59.276 33.333 0.00 0.00 0.00 2.24
384 385 7.231467 ACATAGATTTGTCTGTTGGGTTTACT 58.769 34.615 0.00 0.00 0.00 2.24
385 386 7.448748 ACATAGATTTGTCTGTTGGGTTTAC 57.551 36.000 0.00 0.00 0.00 2.01
386 387 9.747898 ATTACATAGATTTGTCTGTTGGGTTTA 57.252 29.630 0.00 0.00 0.00 2.01
387 388 8.522830 CATTACATAGATTTGTCTGTTGGGTTT 58.477 33.333 0.00 0.00 0.00 3.27
388 389 7.362920 GCATTACATAGATTTGTCTGTTGGGTT 60.363 37.037 0.00 0.00 0.00 4.11
389 390 6.095440 GCATTACATAGATTTGTCTGTTGGGT 59.905 38.462 0.00 0.00 0.00 4.51
390 391 6.095300 TGCATTACATAGATTTGTCTGTTGGG 59.905 38.462 0.00 0.00 0.00 4.12
391 392 6.968904 GTGCATTACATAGATTTGTCTGTTGG 59.031 38.462 0.00 0.00 0.00 3.77
392 393 7.755591 AGTGCATTACATAGATTTGTCTGTTG 58.244 34.615 0.00 0.00 0.00 3.33
393 394 7.826252 AGAGTGCATTACATAGATTTGTCTGTT 59.174 33.333 0.00 0.00 0.00 3.16
394 395 7.334090 AGAGTGCATTACATAGATTTGTCTGT 58.666 34.615 0.00 0.00 0.00 3.41
395 396 7.783090 AGAGTGCATTACATAGATTTGTCTG 57.217 36.000 0.00 0.00 0.00 3.51
396 397 9.319143 GTTAGAGTGCATTACATAGATTTGTCT 57.681 33.333 0.00 0.00 0.00 3.41
397 398 9.319143 AGTTAGAGTGCATTACATAGATTTGTC 57.681 33.333 0.00 0.00 0.00 3.18
398 399 9.672673 AAGTTAGAGTGCATTACATAGATTTGT 57.327 29.630 0.00 0.00 0.00 2.83
399 400 9.926751 CAAGTTAGAGTGCATTACATAGATTTG 57.073 33.333 0.00 0.00 0.00 2.32
400 401 8.616076 GCAAGTTAGAGTGCATTACATAGATTT 58.384 33.333 0.00 0.00 40.58 2.17
401 402 7.989741 AGCAAGTTAGAGTGCATTACATAGATT 59.010 33.333 0.00 0.00 43.42 2.40
402 403 7.504403 AGCAAGTTAGAGTGCATTACATAGAT 58.496 34.615 0.00 0.00 43.42 1.98
403 404 6.878317 AGCAAGTTAGAGTGCATTACATAGA 58.122 36.000 0.00 0.00 43.42 1.98
404 405 7.383572 CCTAGCAAGTTAGAGTGCATTACATAG 59.616 40.741 0.00 0.00 43.42 2.23
405 406 7.147724 ACCTAGCAAGTTAGAGTGCATTACATA 60.148 37.037 0.00 0.00 43.42 2.29
406 407 6.051717 CCTAGCAAGTTAGAGTGCATTACAT 58.948 40.000 0.00 0.00 43.42 2.29
407 408 5.046591 ACCTAGCAAGTTAGAGTGCATTACA 60.047 40.000 0.00 0.00 43.42 2.41
408 409 5.420409 ACCTAGCAAGTTAGAGTGCATTAC 58.580 41.667 0.00 0.00 43.42 1.89
409 410 5.677319 ACCTAGCAAGTTAGAGTGCATTA 57.323 39.130 0.00 0.00 43.42 1.90
410 411 4.559862 ACCTAGCAAGTTAGAGTGCATT 57.440 40.909 0.00 0.00 43.42 3.56
411 412 5.878406 ATACCTAGCAAGTTAGAGTGCAT 57.122 39.130 0.00 0.00 43.42 3.96
412 413 5.677319 AATACCTAGCAAGTTAGAGTGCA 57.323 39.130 0.00 0.00 43.42 4.57
413 414 8.488651 TTTTAATACCTAGCAAGTTAGAGTGC 57.511 34.615 0.00 0.00 41.22 4.40
437 438 9.588096 AGATATAGAAAAGGAACACAAGGTTTT 57.412 29.630 0.00 0.00 40.63 2.43
693 694 5.126699 TGTGTGGTTTTAGGGGACTTTAA 57.873 39.130 0.00 0.00 43.67 1.52
698 699 2.651382 ACTGTGTGGTTTTAGGGGAC 57.349 50.000 0.00 0.00 0.00 4.46
779 780 9.747898 GGATTGTTACCCCATTGATGTAATATA 57.252 33.333 0.00 0.00 0.00 0.86
869 3029 1.693152 GGGGATTAGGGGACGTGGAC 61.693 65.000 0.00 0.00 0.00 4.02
1386 5598 1.172812 AAAGCAAGGAACCACGCCTC 61.173 55.000 0.00 0.00 33.76 4.70
1808 6028 4.685628 ACGCATCATCCAAACAAAATTGAC 59.314 37.500 0.00 0.00 31.84 3.18
1839 6059 7.390440 TGTTTGGTTTATCGAAGACTCAATGAT 59.610 33.333 0.00 0.00 42.51 2.45
2149 6378 4.653801 TGCACATATACAGATACAGGTGGT 59.346 41.667 0.00 0.00 0.00 4.16
2262 6491 3.614870 GCCCCAACAACAATTCAGATCAC 60.615 47.826 0.00 0.00 0.00 3.06
2323 6553 3.260380 AGATCTTGCTCAGTGTGTAGCTT 59.740 43.478 0.00 0.00 39.53 3.74
2801 7248 6.144854 CCCACAGAACAATGCATTATATTCG 58.855 40.000 12.53 13.43 0.00 3.34
2934 7381 0.817013 CCACCACATACACATTGGCC 59.183 55.000 0.00 0.00 33.25 5.36
3079 7526 1.153289 GGTGCGATGCATGGTCTCT 60.153 57.895 2.46 0.00 41.91 3.10
3300 7752 7.588497 AATCTTGAATACTAATTTCTGGGCC 57.412 36.000 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.