Multiple sequence alignment - TraesCS5B01G225600

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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 TraesCS5B01G225600 chr5B 100.000 2657 0 0 1 2657 401075124 401072468 0.000000e+00 4907.0
1 TraesCS5B01G225600 chr5B 84.436 257 25 5 2 243 54841231 54840975 3.420000e-59 239.0
2 TraesCS5B01G225600 chr5B 88.000 200 18 3 1 198 494302745 494302550 5.720000e-57 231.0
3 TraesCS5B01G225600 chr5B 75.429 350 75 10 2203 2547 338665750 338666093 2.740000e-35 159.0
4 TraesCS5B01G225600 chr5A 84.062 1669 140 56 582 2183 442724561 442722952 0.000000e+00 1493.0
5 TraesCS5B01G225600 chr5A 93.898 295 12 2 235 523 442724853 442724559 8.730000e-120 440.0
6 TraesCS5B01G225600 chr5D 82.235 850 99 23 1846 2657 341578376 341577541 0.000000e+00 686.0
7 TraesCS5B01G225600 chr5D 83.967 736 61 27 657 1367 341579661 341578958 0.000000e+00 652.0
8 TraesCS5B01G225600 chr5D 95.078 386 8 5 1446 1821 341578832 341578448 4.900000e-167 597.0
9 TraesCS5B01G225600 chr5D 94.792 384 19 1 241 624 341580318 341579936 4.900000e-167 597.0
10 TraesCS5B01G225600 chr5D 100.000 35 0 0 623 657 341579709 341579675 6.140000e-07 65.8
11 TraesCS5B01G225600 chr6D 84.942 259 21 8 1 242 83062814 83062557 2.040000e-61 246.0
12 TraesCS5B01G225600 chr2B 89.055 201 18 2 1 198 69008141 69007942 2.040000e-61 246.0
13 TraesCS5B01G225600 chr7B 88.780 205 16 3 1 198 77427648 77427852 7.350000e-61 244.0
14 TraesCS5B01G225600 chr3B 88.500 200 18 3 1 198 807227830 807228026 1.230000e-58 237.0
15 TraesCS5B01G225600 chr7D 87.805 205 18 3 1 198 187249385 187249181 1.590000e-57 233.0
16 TraesCS5B01G225600 chr7D 88.000 200 20 2 1 198 619411077 619411274 1.590000e-57 233.0
17 TraesCS5B01G225600 chrUn 86.538 208 22 3 1 202 30132992 30133199 9.570000e-55 224.0
18 TraesCS5B01G225600 chr1D 75.648 193 44 3 2153 2344 204472000 204471810 2.820000e-15 93.5


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 TraesCS5B01G225600 chr5B 401072468 401075124 2656 True 4907.00 4907 100.0000 1 2657 1 chr5B.!!$R2 2656
1 TraesCS5B01G225600 chr5A 442722952 442724853 1901 True 966.50 1493 88.9800 235 2183 2 chr5A.!!$R1 1948
2 TraesCS5B01G225600 chr5D 341577541 341580318 2777 True 519.56 686 91.2144 241 2657 5 chr5D.!!$R1 2416

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
963 1231 0.035458 ACTACACTTCACTGGCCAGC 59.965 55.0 33.06 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 2772 0.036164 GAGTGTGGGCATGTGGTGTA 59.964 55.0 0.0 0.0 0.0 2.9 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
20 21 4.637489 CGAGGAGCGGCGATGGAG 62.637 72.222 12.98 0.00 36.03 3.86
21 22 3.219928 GAGGAGCGGCGATGGAGA 61.220 66.667 12.98 0.00 0.00 3.71
22 23 3.492311 GAGGAGCGGCGATGGAGAC 62.492 68.421 12.98 0.00 0.00 3.36
24 25 4.933064 GAGCGGCGATGGAGACGG 62.933 72.222 12.98 0.00 44.07 4.79
28 29 4.933064 GGCGATGGAGACGGCGAG 62.933 72.222 16.62 0.00 45.03 5.03
29 30 4.933064 GCGATGGAGACGGCGAGG 62.933 72.222 16.62 0.00 0.00 4.63
30 31 4.271816 CGATGGAGACGGCGAGGG 62.272 72.222 16.62 0.00 0.00 4.30
31 32 3.917760 GATGGAGACGGCGAGGGG 61.918 72.222 16.62 0.00 0.00 4.79
96 97 6.984740 TTAAACGAACTCATCAATGTTTGC 57.015 33.333 0.00 0.00 32.40 3.68
97 98 3.187478 ACGAACTCATCAATGTTTGCG 57.813 42.857 0.00 0.00 32.40 4.85
98 99 2.548057 ACGAACTCATCAATGTTTGCGT 59.452 40.909 0.00 0.00 32.40 5.24
99 100 3.003275 ACGAACTCATCAATGTTTGCGTT 59.997 39.130 0.00 0.00 32.40 4.84
100 101 4.212425 ACGAACTCATCAATGTTTGCGTTA 59.788 37.500 0.00 0.00 32.40 3.18
101 102 5.143660 CGAACTCATCAATGTTTGCGTTAA 58.856 37.500 0.00 0.00 0.00 2.01
102 103 5.623264 CGAACTCATCAATGTTTGCGTTAAA 59.377 36.000 0.00 0.00 0.00 1.52
103 104 6.305399 CGAACTCATCAATGTTTGCGTTAAAT 59.695 34.615 0.00 0.00 0.00 1.40
104 105 7.148983 CGAACTCATCAATGTTTGCGTTAAATT 60.149 33.333 0.00 0.00 0.00 1.82
105 106 7.945033 ACTCATCAATGTTTGCGTTAAATTT 57.055 28.000 0.00 0.00 0.00 1.82
106 107 9.469807 AACTCATCAATGTTTGCGTTAAATTTA 57.530 25.926 0.00 0.00 0.00 1.40
107 108 9.469807 ACTCATCAATGTTTGCGTTAAATTTAA 57.530 25.926 6.54 6.54 0.00 1.52
108 109 9.941991 CTCATCAATGTTTGCGTTAAATTTAAG 57.058 29.630 10.92 6.90 0.00 1.85
109 110 9.469807 TCATCAATGTTTGCGTTAAATTTAAGT 57.530 25.926 10.92 0.00 0.00 2.24
110 111 9.726034 CATCAATGTTTGCGTTAAATTTAAGTC 57.274 29.630 10.92 6.65 0.00 3.01
111 112 7.987486 TCAATGTTTGCGTTAAATTTAAGTCG 58.013 30.769 10.92 12.53 0.00 4.18
112 113 7.644551 TCAATGTTTGCGTTAAATTTAAGTCGT 59.355 29.630 10.92 0.00 0.00 4.34
113 114 8.893884 CAATGTTTGCGTTAAATTTAAGTCGTA 58.106 29.630 10.92 8.86 0.00 3.43
114 115 9.615295 AATGTTTGCGTTAAATTTAAGTCGTAT 57.385 25.926 10.92 0.00 0.00 3.06
115 116 9.615295 ATGTTTGCGTTAAATTTAAGTCGTATT 57.385 25.926 10.92 0.00 0.00 1.89
116 117 9.448294 TGTTTGCGTTAAATTTAAGTCGTATTT 57.552 25.926 10.92 0.00 0.00 1.40
117 118 9.702949 GTTTGCGTTAAATTTAAGTCGTATTTG 57.297 29.630 10.92 0.00 0.00 2.32
118 119 7.481768 TGCGTTAAATTTAAGTCGTATTTGC 57.518 32.000 10.92 5.40 0.00 3.68
119 120 6.246748 TGCGTTAAATTTAAGTCGTATTTGCG 59.753 34.615 10.92 8.07 0.00 4.85
120 121 6.602974 CGTTAAATTTAAGTCGTATTTGCGC 58.397 36.000 10.92 0.00 0.00 6.09
121 122 6.552908 CGTTAAATTTAAGTCGTATTTGCGCG 60.553 38.462 10.92 0.00 0.00 6.86
122 123 2.791417 TTTAAGTCGTATTTGCGCGG 57.209 45.000 8.83 0.00 0.00 6.46
123 124 0.370958 TTAAGTCGTATTTGCGCGGC 59.629 50.000 8.83 0.00 0.00 6.53
124 125 0.736672 TAAGTCGTATTTGCGCGGCA 60.737 50.000 8.83 3.20 34.90 5.69
125 126 1.366111 AAGTCGTATTTGCGCGGCAT 61.366 50.000 8.83 0.00 38.76 4.40
126 127 1.061887 GTCGTATTTGCGCGGCATT 59.938 52.632 8.83 0.29 38.76 3.56
127 128 0.923911 GTCGTATTTGCGCGGCATTC 60.924 55.000 8.83 0.00 38.76 2.67
128 129 1.061729 CGTATTTGCGCGGCATTCA 59.938 52.632 8.83 0.00 38.76 2.57
129 130 0.522286 CGTATTTGCGCGGCATTCAA 60.522 50.000 8.83 0.00 38.76 2.69
130 131 0.913876 GTATTTGCGCGGCATTCAAC 59.086 50.000 8.83 0.00 38.76 3.18
131 132 0.808125 TATTTGCGCGGCATTCAACT 59.192 45.000 8.83 0.00 38.76 3.16
132 133 0.038343 ATTTGCGCGGCATTCAACTT 60.038 45.000 8.83 0.00 38.76 2.66
133 134 0.249238 TTTGCGCGGCATTCAACTTT 60.249 45.000 8.83 0.00 38.76 2.66
134 135 0.249238 TTGCGCGGCATTCAACTTTT 60.249 45.000 8.83 0.00 38.76 2.27
135 136 0.249238 TGCGCGGCATTCAACTTTTT 60.249 45.000 8.83 0.00 31.71 1.94
136 137 0.434628 GCGCGGCATTCAACTTTTTC 59.565 50.000 8.83 0.00 0.00 2.29
137 138 1.764851 CGCGGCATTCAACTTTTTCA 58.235 45.000 0.00 0.00 0.00 2.69
138 139 2.123342 CGCGGCATTCAACTTTTTCAA 58.877 42.857 0.00 0.00 0.00 2.69
139 140 2.537625 CGCGGCATTCAACTTTTTCAAA 59.462 40.909 0.00 0.00 0.00 2.69
140 141 3.000724 CGCGGCATTCAACTTTTTCAAAA 59.999 39.130 0.00 0.00 0.00 2.44
141 142 4.493220 CGCGGCATTCAACTTTTTCAAAAA 60.493 37.500 0.00 0.00 0.00 1.94
157 158 3.015516 AAAAATGGACGCCACGACT 57.984 47.368 0.50 0.00 35.80 4.18
158 159 0.591170 AAAAATGGACGCCACGACTG 59.409 50.000 0.50 0.00 35.80 3.51
159 160 1.234615 AAAATGGACGCCACGACTGG 61.235 55.000 0.50 0.00 41.13 4.00
160 161 3.605749 AATGGACGCCACGACTGGG 62.606 63.158 0.50 0.00 38.13 4.45
201 202 2.046604 GGTTAGCACCGGTGGGTC 60.047 66.667 34.58 18.94 46.01 4.46
202 203 2.745037 GTTAGCACCGGTGGGTCA 59.255 61.111 34.58 10.92 46.01 4.02
203 204 1.670083 GTTAGCACCGGTGGGTCAC 60.670 63.158 34.58 18.18 46.01 3.67
204 205 3.229156 TTAGCACCGGTGGGTCACG 62.229 63.158 34.58 9.21 46.01 4.35
206 207 4.388499 GCACCGGTGGGTCACGAT 62.388 66.667 34.58 0.00 46.01 3.73
207 208 2.345991 CACCGGTGGGTCACGATT 59.654 61.111 27.57 0.00 46.01 3.34
208 209 1.302192 CACCGGTGGGTCACGATTT 60.302 57.895 27.57 0.00 46.01 2.17
209 210 0.887387 CACCGGTGGGTCACGATTTT 60.887 55.000 27.57 0.00 46.01 1.82
210 211 0.179012 ACCGGTGGGTCACGATTTTT 60.179 50.000 6.12 0.00 46.01 1.94
211 212 1.072015 ACCGGTGGGTCACGATTTTTA 59.928 47.619 6.12 0.00 46.01 1.52
212 213 1.735571 CCGGTGGGTCACGATTTTTAG 59.264 52.381 0.00 0.00 34.83 1.85
213 214 1.129811 CGGTGGGTCACGATTTTTAGC 59.870 52.381 0.00 0.00 34.83 3.09
214 215 1.471287 GGTGGGTCACGATTTTTAGCC 59.529 52.381 0.00 0.00 34.83 3.93
215 216 1.471287 GTGGGTCACGATTTTTAGCCC 59.529 52.381 0.00 0.00 35.37 5.19
216 217 1.353022 TGGGTCACGATTTTTAGCCCT 59.647 47.619 0.00 0.00 35.79 5.19
217 218 2.014857 GGGTCACGATTTTTAGCCCTC 58.985 52.381 0.00 0.00 0.00 4.30
218 219 2.014857 GGTCACGATTTTTAGCCCTCC 58.985 52.381 0.00 0.00 0.00 4.30
219 220 2.355818 GGTCACGATTTTTAGCCCTCCT 60.356 50.000 0.00 0.00 0.00 3.69
220 221 2.678336 GTCACGATTTTTAGCCCTCCTG 59.322 50.000 0.00 0.00 0.00 3.86
221 222 2.569853 TCACGATTTTTAGCCCTCCTGA 59.430 45.455 0.00 0.00 0.00 3.86
222 223 3.008594 TCACGATTTTTAGCCCTCCTGAA 59.991 43.478 0.00 0.00 0.00 3.02
223 224 3.756434 CACGATTTTTAGCCCTCCTGAAA 59.244 43.478 0.00 0.00 0.00 2.69
224 225 3.756963 ACGATTTTTAGCCCTCCTGAAAC 59.243 43.478 0.00 0.00 29.81 2.78
225 226 3.181510 CGATTTTTAGCCCTCCTGAAACG 60.182 47.826 0.00 0.00 29.81 3.60
226 227 2.194201 TTTTAGCCCTCCTGAAACGG 57.806 50.000 0.00 0.00 0.00 4.44
227 228 0.322187 TTTAGCCCTCCTGAAACGGC 60.322 55.000 0.00 0.00 41.96 5.68
228 229 2.930562 AGCCCTCCTGAAACGGCT 60.931 61.111 0.00 0.00 46.96 5.52
229 230 2.747855 GCCCTCCTGAAACGGCTG 60.748 66.667 0.00 0.00 38.41 4.85
230 231 2.045926 CCCTCCTGAAACGGCTGG 60.046 66.667 0.00 0.00 0.00 4.85
231 232 2.592993 CCCTCCTGAAACGGCTGGA 61.593 63.158 0.00 0.00 35.07 3.86
232 233 4.606071 CTCCTGAAACGGCTGGAG 57.394 61.111 11.59 11.59 44.20 3.86
233 234 4.208426 TCCTGAAACGGCTGGAGA 57.792 55.556 0.00 0.00 32.84 3.71
234 235 2.683916 TCCTGAAACGGCTGGAGAT 58.316 52.632 0.00 0.00 32.84 2.75
235 236 0.250234 TCCTGAAACGGCTGGAGATG 59.750 55.000 0.00 0.00 32.84 2.90
236 237 1.372087 CCTGAAACGGCTGGAGATGC 61.372 60.000 0.00 0.00 0.00 3.91
237 238 0.392193 CTGAAACGGCTGGAGATGCT 60.392 55.000 0.00 0.00 0.00 3.79
238 239 0.391661 TGAAACGGCTGGAGATGCTC 60.392 55.000 0.00 0.00 0.00 4.26
239 240 0.107945 GAAACGGCTGGAGATGCTCT 60.108 55.000 0.00 0.00 0.00 4.09
315 316 4.410400 GGCTCCCCACGTGAAGGG 62.410 72.222 19.30 20.04 46.36 3.95
325 326 3.443045 GTGAAGGGGCACATGCGG 61.443 66.667 0.00 0.00 43.26 5.69
531 537 3.083997 GGATCTGTGCCCGGGACT 61.084 66.667 29.31 3.74 0.00 3.85
564 570 2.125552 TCAATGCCAGAGCCGTCG 60.126 61.111 0.00 0.00 38.69 5.12
660 895 2.864114 CACCATGCAAGTGGGAGAG 58.136 57.895 11.02 0.00 43.77 3.20
824 1080 2.487762 TCTGCAATACTTGGCTTTTCCG 59.512 45.455 0.00 0.00 37.80 4.30
863 1123 8.271231 CGTTTTCACGGTATAAAATGTTCAAA 57.729 30.769 9.98 0.00 43.16 2.69
870 1130 9.458374 CACGGTATAAAATGTTCAAAACTTCTT 57.542 29.630 0.00 0.00 0.00 2.52
912 1173 7.579723 GCCTATAAATACGTCCTCAGATCCATT 60.580 40.741 0.00 0.00 0.00 3.16
951 1219 1.374758 GCCGCTGCTTCACTACACT 60.375 57.895 0.00 0.00 33.53 3.55
952 1220 0.951040 GCCGCTGCTTCACTACACTT 60.951 55.000 0.00 0.00 33.53 3.16
956 1224 2.760374 GCTGCTTCACTACACTTCACT 58.240 47.619 0.00 0.00 0.00 3.41
957 1225 2.478134 GCTGCTTCACTACACTTCACTG 59.522 50.000 0.00 0.00 0.00 3.66
963 1231 0.035458 ACTACACTTCACTGGCCAGC 59.965 55.000 33.06 0.00 0.00 4.85
980 1248 1.196354 CAGCGTCTTCTCTTTTGGCAG 59.804 52.381 0.00 0.00 0.00 4.85
987 1255 1.904865 CTCTTTTGGCAGCCCAGCA 60.905 57.895 9.64 0.00 43.37 4.41
1068 1336 1.065764 CGTCTCCATCATCGCCGAA 59.934 57.895 0.00 0.00 0.00 4.30
1156 1433 3.018856 TCTTGCTTGGGATGCTTACATG 58.981 45.455 0.00 0.00 36.35 3.21
1182 1459 2.772568 TTTGTGATCAGGTGTTTGCG 57.227 45.000 0.00 0.00 0.00 4.85
1188 1465 0.606401 ATCAGGTGTTTGCGTCAGGG 60.606 55.000 0.00 0.00 0.00 4.45
1191 1468 1.227853 GGTGTTTGCGTCAGGGACT 60.228 57.895 0.00 0.00 43.88 3.85
1235 1512 2.224066 ACCGAGTGAGCAAGGTATATGC 60.224 50.000 0.00 0.00 44.15 3.14
1245 1524 1.424638 AGGTATATGCTTCCACGGCT 58.575 50.000 0.00 0.00 0.00 5.52
1257 1536 1.369209 CACGGCTTTCTGTTGCACG 60.369 57.895 0.00 0.00 0.00 5.34
1262 1541 2.539953 CGGCTTTCTGTTGCACGTTTTA 60.540 45.455 0.00 0.00 0.00 1.52
1306 1586 3.690422 TGTTGCTGATCGTGTGTTTTTC 58.310 40.909 0.00 0.00 0.00 2.29
1346 1632 2.190488 CTTCAGGGAGGACAGGGCAC 62.190 65.000 0.00 0.00 0.00 5.01
1370 1656 4.645136 TCTCAAGATATACCGTGAGTTGCT 59.355 41.667 9.55 0.00 38.87 3.91
1385 1672 3.806380 AGTTGCTCTTCCTGCTCATATG 58.194 45.455 0.00 0.00 0.00 1.78
1403 1751 6.589135 TCATATGTGAATCTGAATCTGCTGT 58.411 36.000 1.90 0.00 0.00 4.40
1414 1762 1.446907 ATCTGCTGTTTTCGCCTGAG 58.553 50.000 0.00 0.00 0.00 3.35
1421 1774 3.814945 CTGTTTTCGCCTGAGATGAAAC 58.185 45.455 0.00 0.00 31.81 2.78
1444 1797 6.460781 ACGAAATGTAATGTGAGTTGGACTA 58.539 36.000 0.00 0.00 0.00 2.59
1461 1814 1.535462 ACTAGTTGTTGATGTTGCGGC 59.465 47.619 0.00 0.00 0.00 6.53
1640 1993 0.104672 TGGAAGACCAAGGAGGGACA 60.105 55.000 0.00 0.00 43.91 4.02
1662 2015 0.962356 CCAAGTGCCCCTAGTTGCAG 60.962 60.000 3.84 0.00 38.34 4.41
1842 2225 2.125832 CGCGGTTGTATCGTGGGT 60.126 61.111 0.00 0.00 34.88 4.51
1844 2227 1.689352 CGCGGTTGTATCGTGGGTTC 61.689 60.000 0.00 0.00 34.88 3.62
1847 2265 2.144730 CGGTTGTATCGTGGGTTCAAA 58.855 47.619 0.00 0.00 0.00 2.69
1896 2317 3.379650 ACGCAGTTGTTGTAGCACT 57.620 47.368 0.00 0.00 37.78 4.40
1912 2333 7.376435 TGTAGCACTACAATACACGTAGTAA 57.624 36.000 8.04 0.00 46.03 2.24
1962 2390 0.730265 GTCGTGTTGGTTGTTCTGCA 59.270 50.000 0.00 0.00 0.00 4.41
2090 2519 2.878406 CCTCAAAGAGCGACCTTTTCAA 59.122 45.455 0.00 0.00 34.41 2.69
2091 2520 3.058639 CCTCAAAGAGCGACCTTTTCAAG 60.059 47.826 0.00 0.00 34.41 3.02
2122 2560 2.356553 CGAAACCCGCGTCCAAGA 60.357 61.111 4.92 0.00 0.00 3.02
2132 2570 0.310543 GCGTCCAAGAATGCACACAA 59.689 50.000 0.00 0.00 0.00 3.33
2150 2588 8.363390 TGCACACAACCATCTTTATCAATAAAA 58.637 29.630 0.00 0.00 32.39 1.52
2184 2624 7.535489 ACAAATACGTAGATCAACCTAAAGC 57.465 36.000 0.08 0.00 0.00 3.51
2191 2631 5.463724 CGTAGATCAACCTAAAGCCATCTTC 59.536 44.000 0.00 0.00 0.00 2.87
2192 2632 5.441718 AGATCAACCTAAAGCCATCTTCA 57.558 39.130 0.00 0.00 0.00 3.02
2193 2633 5.189180 AGATCAACCTAAAGCCATCTTCAC 58.811 41.667 0.00 0.00 0.00 3.18
2194 2634 3.334691 TCAACCTAAAGCCATCTTCACG 58.665 45.455 0.00 0.00 0.00 4.35
2196 2636 1.906574 ACCTAAAGCCATCTTCACGGA 59.093 47.619 0.00 0.00 0.00 4.69
2198 2638 2.168521 CCTAAAGCCATCTTCACGGAGA 59.831 50.000 0.00 0.00 0.00 3.71
2207 2647 2.514803 TCTTCACGGAGATGTCTGTCA 58.485 47.619 0.33 0.00 40.62 3.58
2217 2657 4.096682 GGAGATGTCTGTCACTACACCTAC 59.903 50.000 0.00 0.00 0.00 3.18
2220 2660 4.848562 TGTCTGTCACTACACCTACAAG 57.151 45.455 0.00 0.00 0.00 3.16
2227 2667 7.231925 TCTGTCACTACACCTACAAGTTTGATA 59.768 37.037 0.00 0.00 0.00 2.15
2228 2668 7.375834 TGTCACTACACCTACAAGTTTGATAG 58.624 38.462 0.00 0.00 0.00 2.08
2230 2670 7.328737 GTCACTACACCTACAAGTTTGATAGTG 59.671 40.741 0.00 0.00 33.93 2.74
2233 2673 6.169557 ACACCTACAAGTTTGATAGTGTGA 57.830 37.500 13.48 0.00 36.96 3.58
2237 2677 6.495872 ACCTACAAGTTTGATAGTGTGACCTA 59.504 38.462 0.00 0.00 0.00 3.08
2244 2684 5.401531 TTGATAGTGTGACCTAACCTCAC 57.598 43.478 0.00 0.00 38.86 3.51
2256 2696 1.459450 AACCTCACACCAACACACAC 58.541 50.000 0.00 0.00 0.00 3.82
2257 2697 0.393808 ACCTCACACCAACACACACC 60.394 55.000 0.00 0.00 0.00 4.16
2258 2698 0.393673 CCTCACACCAACACACACCA 60.394 55.000 0.00 0.00 0.00 4.17
2268 2708 4.041567 ACCAACACACACCATCTAATCTGA 59.958 41.667 0.00 0.00 0.00 3.27
2290 2730 1.244019 GCCTCACCAAGCCGTTTCAT 61.244 55.000 0.00 0.00 0.00 2.57
2294 2734 1.072489 TCACCAAGCCGTTTCATGGTA 59.928 47.619 0.00 0.00 44.12 3.25
2296 2736 2.095263 CACCAAGCCGTTTCATGGTAAG 60.095 50.000 0.00 0.00 44.12 2.34
2346 2786 0.547954 TAGGGTACACCACATGCCCA 60.548 55.000 0.00 0.00 43.89 5.36
2347 2787 1.677633 GGGTACACCACATGCCCAC 60.678 63.158 0.00 0.00 39.13 4.61
2348 2788 1.074072 GGTACACCACATGCCCACA 59.926 57.895 0.00 0.00 35.64 4.17
2353 2793 1.073722 ACCACATGCCCACACTCTG 59.926 57.895 0.00 0.00 0.00 3.35
2356 2796 0.675837 CACATGCCCACACTCTGGAG 60.676 60.000 0.00 0.00 43.95 3.86
2360 2800 2.217038 GCCCACACTCTGGAGTCCA 61.217 63.158 12.40 12.40 43.95 4.02
2366 2806 2.279069 ACTCTGGAGTCCACTGCCG 61.279 63.158 8.12 0.00 36.92 5.69
2387 2827 1.955080 ACATCTTCCGTCGTCCTATCC 59.045 52.381 0.00 0.00 0.00 2.59
2409 2849 0.404040 GGGAGGGACCAACACATTGA 59.596 55.000 0.00 0.00 38.15 2.57
2415 2855 2.306847 GGACCAACACATTGACCTTGT 58.693 47.619 0.00 0.00 38.15 3.16
2424 2865 2.042979 ACATTGACCTTGTAGGCCCAAT 59.957 45.455 0.00 0.00 40.35 3.16
2425 2866 2.990740 TTGACCTTGTAGGCCCAATT 57.009 45.000 0.00 0.00 39.63 2.32
2428 2869 2.092323 GACCTTGTAGGCCCAATTGTC 58.908 52.381 0.00 4.15 39.63 3.18
2434 2875 0.108520 TAGGCCCAATTGTCGTCGAC 60.109 55.000 18.51 18.51 0.00 4.20
2436 2877 2.025418 GCCCAATTGTCGTCGACGT 61.025 57.895 34.40 15.32 40.80 4.34
2439 2880 0.708370 CCAATTGTCGTCGACGTCAG 59.292 55.000 34.40 22.65 38.47 3.51
2440 2881 0.091344 CAATTGTCGTCGACGTCAGC 59.909 55.000 34.40 22.76 38.47 4.26
2441 2882 0.318360 AATTGTCGTCGACGTCAGCA 60.318 50.000 34.40 24.72 38.47 4.41
2442 2883 0.109272 ATTGTCGTCGACGTCAGCAT 60.109 50.000 34.40 23.23 38.47 3.79
2443 2884 1.001745 TTGTCGTCGACGTCAGCATG 61.002 55.000 34.40 7.16 38.47 4.06
2444 2885 1.154282 GTCGTCGACGTCAGCATGA 60.154 57.895 34.40 12.61 39.98 3.07
2461 2902 1.317613 TGATGTCAAACAGCACCACC 58.682 50.000 0.00 0.00 39.86 4.61
2465 2906 1.133823 TGTCAAACAGCACCACCATCT 60.134 47.619 0.00 0.00 0.00 2.90
2474 2915 4.465512 CCACCATCTTGCGTGCGC 62.466 66.667 9.85 9.85 42.35 6.09
2484 2925 3.814268 GCGTGCGCCCATCAACAT 61.814 61.111 4.18 0.00 34.56 2.71
2496 2937 1.607148 CATCAACATGCATCCATCGCT 59.393 47.619 0.00 0.00 0.00 4.93
2507 2948 1.142748 CCATCGCTGAGACTCCACC 59.857 63.158 0.00 0.00 0.00 4.61
2539 2981 2.827190 AGACCCGCTGCGTCGATA 60.827 61.111 21.59 0.00 35.33 2.92
2552 2994 2.041966 CGTCGATACGGTAGATGCAAC 58.958 52.381 0.00 0.00 45.50 4.17
2555 2997 2.686405 TCGATACGGTAGATGCAACACT 59.314 45.455 0.00 0.00 0.00 3.55
2568 3010 1.517242 CAACACTGCTCCACCTCTTC 58.483 55.000 0.00 0.00 0.00 2.87
2569 3011 0.398318 AACACTGCTCCACCTCTTCC 59.602 55.000 0.00 0.00 0.00 3.46
2571 3013 1.159664 ACTGCTCCACCTCTTCCCT 59.840 57.895 0.00 0.00 0.00 4.20
2573 3015 1.613630 TGCTCCACCTCTTCCCTCC 60.614 63.158 0.00 0.00 0.00 4.30
2574 3016 1.613630 GCTCCACCTCTTCCCTCCA 60.614 63.158 0.00 0.00 0.00 3.86
2575 3017 1.621672 GCTCCACCTCTTCCCTCCAG 61.622 65.000 0.00 0.00 0.00 3.86
2576 3018 1.613630 TCCACCTCTTCCCTCCAGC 60.614 63.158 0.00 0.00 0.00 4.85
2577 3019 2.674220 CCACCTCTTCCCTCCAGCC 61.674 68.421 0.00 0.00 0.00 4.85
2578 3020 1.920325 CACCTCTTCCCTCCAGCCA 60.920 63.158 0.00 0.00 0.00 4.75
2579 3021 1.614824 ACCTCTTCCCTCCAGCCAG 60.615 63.158 0.00 0.00 0.00 4.85
2580 3022 2.588989 CTCTTCCCTCCAGCCAGC 59.411 66.667 0.00 0.00 0.00 4.85
2583 3038 1.210204 TCTTCCCTCCAGCCAGCAAT 61.210 55.000 0.00 0.00 0.00 3.56
2613 3068 0.528470 GAGGGAGGACGACACTGAAG 59.472 60.000 0.00 0.00 0.00 3.02
2617 3072 0.667792 GAGGACGACACTGAAGGCAC 60.668 60.000 0.00 0.00 0.00 5.01
2632 3087 2.401967 GCACTGCCACCATCTGATC 58.598 57.895 0.00 0.00 0.00 2.92
2634 3089 1.139654 GCACTGCCACCATCTGATCTA 59.860 52.381 0.00 0.00 0.00 1.98
2639 3094 2.324541 GCCACCATCTGATCTAGGAGT 58.675 52.381 0.00 0.00 0.00 3.85
2644 3099 3.164268 CCATCTGATCTAGGAGTCCCAG 58.836 54.545 5.25 0.83 33.88 4.45
2646 3101 4.510748 CCATCTGATCTAGGAGTCCCAGAT 60.511 50.000 18.81 18.81 40.69 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.637489 CTCCATCGCCGCTCCTCG 62.637 72.222 0.00 0.00 38.08 4.63
4 5 3.219928 TCTCCATCGCCGCTCCTC 61.220 66.667 0.00 0.00 0.00 3.71
5 6 3.532155 GTCTCCATCGCCGCTCCT 61.532 66.667 0.00 0.00 0.00 3.69
6 7 4.933064 CGTCTCCATCGCCGCTCC 62.933 72.222 0.00 0.00 0.00 4.70
7 8 4.933064 CCGTCTCCATCGCCGCTC 62.933 72.222 0.00 0.00 0.00 5.03
11 12 4.933064 CTCGCCGTCTCCATCGCC 62.933 72.222 0.00 0.00 0.00 5.54
12 13 4.933064 CCTCGCCGTCTCCATCGC 62.933 72.222 0.00 0.00 0.00 4.58
13 14 4.271816 CCCTCGCCGTCTCCATCG 62.272 72.222 0.00 0.00 0.00 3.84
14 15 3.917760 CCCCTCGCCGTCTCCATC 61.918 72.222 0.00 0.00 0.00 3.51
29 30 2.454336 AAAACTAATAGGGGCTGCCC 57.546 50.000 29.93 29.93 44.51 5.36
70 71 8.487176 GCAAACATTGATGAGTTCGTTTAAATT 58.513 29.630 0.00 0.00 0.00 1.82
71 72 7.148983 CGCAAACATTGATGAGTTCGTTTAAAT 60.149 33.333 0.00 0.00 0.00 1.40
72 73 6.141527 CGCAAACATTGATGAGTTCGTTTAAA 59.858 34.615 0.00 0.00 0.00 1.52
73 74 5.623264 CGCAAACATTGATGAGTTCGTTTAA 59.377 36.000 0.00 0.00 0.00 1.52
74 75 5.143660 CGCAAACATTGATGAGTTCGTTTA 58.856 37.500 0.00 0.00 0.00 2.01
75 76 3.974401 CGCAAACATTGATGAGTTCGTTT 59.026 39.130 0.00 0.00 0.00 3.60
76 77 3.003275 ACGCAAACATTGATGAGTTCGTT 59.997 39.130 0.00 0.00 0.00 3.85
77 78 2.548057 ACGCAAACATTGATGAGTTCGT 59.452 40.909 0.00 0.30 0.00 3.85
78 79 3.187478 ACGCAAACATTGATGAGTTCG 57.813 42.857 0.00 0.00 0.00 3.95
79 80 6.984740 TTTAACGCAAACATTGATGAGTTC 57.015 33.333 15.13 0.00 39.66 3.01
80 81 7.945033 AATTTAACGCAAACATTGATGAGTT 57.055 28.000 15.66 15.66 41.42 3.01
81 82 7.945033 AAATTTAACGCAAACATTGATGAGT 57.055 28.000 0.00 0.00 0.00 3.41
82 83 9.941991 CTTAAATTTAACGCAAACATTGATGAG 57.058 29.630 6.54 0.00 0.00 2.90
83 84 9.469807 ACTTAAATTTAACGCAAACATTGATGA 57.530 25.926 6.54 0.00 0.00 2.92
84 85 9.726034 GACTTAAATTTAACGCAAACATTGATG 57.274 29.630 6.54 0.00 0.00 3.07
85 86 8.635124 CGACTTAAATTTAACGCAAACATTGAT 58.365 29.630 6.54 0.00 0.00 2.57
86 87 7.644551 ACGACTTAAATTTAACGCAAACATTGA 59.355 29.630 16.50 0.00 0.00 2.57
87 88 7.769766 ACGACTTAAATTTAACGCAAACATTG 58.230 30.769 16.50 3.86 0.00 2.82
88 89 7.917720 ACGACTTAAATTTAACGCAAACATT 57.082 28.000 16.50 0.00 0.00 2.71
89 90 9.615295 AATACGACTTAAATTTAACGCAAACAT 57.385 25.926 16.50 3.98 0.00 2.71
90 91 9.448294 AAATACGACTTAAATTTAACGCAAACA 57.552 25.926 16.50 3.26 0.00 2.83
91 92 9.702949 CAAATACGACTTAAATTTAACGCAAAC 57.297 29.630 16.50 2.82 0.00 2.93
92 93 8.418681 GCAAATACGACTTAAATTTAACGCAAA 58.581 29.630 16.50 7.06 0.00 3.68
93 94 7.201165 CGCAAATACGACTTAAATTTAACGCAA 60.201 33.333 16.50 8.88 34.06 4.85
94 95 6.246748 CGCAAATACGACTTAAATTTAACGCA 59.753 34.615 16.50 8.08 34.06 5.24
95 96 6.602974 CGCAAATACGACTTAAATTTAACGC 58.397 36.000 16.50 7.64 34.06 4.84
96 97 6.552908 CGCGCAAATACGACTTAAATTTAACG 60.553 38.462 8.75 15.49 34.06 3.18
97 98 6.290180 CCGCGCAAATACGACTTAAATTTAAC 60.290 38.462 8.75 0.00 34.06 2.01
98 99 5.733572 CCGCGCAAATACGACTTAAATTTAA 59.266 36.000 8.75 10.16 34.06 1.52
99 100 5.257108 CCGCGCAAATACGACTTAAATTTA 58.743 37.500 8.75 0.00 34.06 1.40
100 101 4.092816 CCGCGCAAATACGACTTAAATTT 58.907 39.130 8.75 0.00 34.06 1.82
101 102 3.676540 CCGCGCAAATACGACTTAAATT 58.323 40.909 8.75 0.00 34.06 1.82
102 103 2.538132 GCCGCGCAAATACGACTTAAAT 60.538 45.455 8.75 0.00 34.06 1.40
103 104 1.201943 GCCGCGCAAATACGACTTAAA 60.202 47.619 8.75 0.00 34.06 1.52
104 105 0.370958 GCCGCGCAAATACGACTTAA 59.629 50.000 8.75 0.00 34.06 1.85
105 106 0.736672 TGCCGCGCAAATACGACTTA 60.737 50.000 8.75 0.00 34.76 2.24
106 107 1.366111 ATGCCGCGCAAATACGACTT 61.366 50.000 8.75 0.00 43.62 3.01
107 108 1.366111 AATGCCGCGCAAATACGACT 61.366 50.000 8.75 0.00 43.62 4.18
108 109 0.923911 GAATGCCGCGCAAATACGAC 60.924 55.000 8.75 0.00 43.62 4.34
109 110 1.350319 GAATGCCGCGCAAATACGA 59.650 52.632 8.75 0.00 43.62 3.43
110 111 0.522286 TTGAATGCCGCGCAAATACG 60.522 50.000 8.75 0.00 43.62 3.06
111 112 0.913876 GTTGAATGCCGCGCAAATAC 59.086 50.000 8.75 0.00 43.62 1.89
112 113 0.808125 AGTTGAATGCCGCGCAAATA 59.192 45.000 8.75 0.00 43.62 1.40
113 114 0.038343 AAGTTGAATGCCGCGCAAAT 60.038 45.000 8.75 0.00 43.62 2.32
114 115 0.249238 AAAGTTGAATGCCGCGCAAA 60.249 45.000 8.75 0.00 43.62 3.68
115 116 0.249238 AAAAGTTGAATGCCGCGCAA 60.249 45.000 8.75 0.00 43.62 4.85
116 117 0.249238 AAAAAGTTGAATGCCGCGCA 60.249 45.000 8.75 2.46 44.86 6.09
117 118 0.434628 GAAAAAGTTGAATGCCGCGC 59.565 50.000 0.00 0.00 0.00 6.86
118 119 1.764851 TGAAAAAGTTGAATGCCGCG 58.235 45.000 0.00 0.00 0.00 6.46
119 120 4.528531 TTTTGAAAAAGTTGAATGCCGC 57.471 36.364 0.00 0.00 0.00 6.53
139 140 0.591170 CAGTCGTGGCGTCCATTTTT 59.409 50.000 1.90 0.00 35.28 1.94
140 141 1.234615 CCAGTCGTGGCGTCCATTTT 61.235 55.000 1.90 0.00 36.89 1.82
141 142 1.671054 CCAGTCGTGGCGTCCATTT 60.671 57.895 1.90 0.00 36.89 2.32
142 143 2.047274 CCAGTCGTGGCGTCCATT 60.047 61.111 1.90 0.00 36.89 3.16
143 144 4.082523 CCCAGTCGTGGCGTCCAT 62.083 66.667 1.90 0.00 43.44 3.41
180 181 4.690719 CACCGGTGCTAACCCGCA 62.691 66.667 24.02 0.00 44.42 5.69
182 183 4.770874 CCCACCGGTGCTAACCCG 62.771 72.222 29.75 13.27 44.42 5.28
183 184 3.617143 GACCCACCGGTGCTAACCC 62.617 68.421 29.75 10.12 44.88 4.11
184 185 2.046604 GACCCACCGGTGCTAACC 60.047 66.667 29.75 11.52 44.88 2.85
185 186 1.670083 GTGACCCACCGGTGCTAAC 60.670 63.158 29.75 18.75 44.88 2.34
186 187 2.745037 GTGACCCACCGGTGCTAA 59.255 61.111 29.75 11.11 44.88 3.09
187 188 3.687102 CGTGACCCACCGGTGCTA 61.687 66.667 29.75 11.41 44.88 3.49
189 190 3.894547 AATCGTGACCCACCGGTGC 62.895 63.158 29.75 16.21 44.88 5.01
190 191 0.887387 AAAATCGTGACCCACCGGTG 60.887 55.000 28.26 28.26 44.88 4.94
192 193 1.735571 CTAAAAATCGTGACCCACCGG 59.264 52.381 0.00 0.00 0.00 5.28
193 194 1.129811 GCTAAAAATCGTGACCCACCG 59.870 52.381 0.00 0.00 0.00 4.94
194 195 1.471287 GGCTAAAAATCGTGACCCACC 59.529 52.381 0.00 0.00 0.00 4.61
195 196 1.471287 GGGCTAAAAATCGTGACCCAC 59.529 52.381 0.00 0.00 35.84 4.61
196 197 1.353022 AGGGCTAAAAATCGTGACCCA 59.647 47.619 0.00 0.00 38.39 4.51
197 198 2.014857 GAGGGCTAAAAATCGTGACCC 58.985 52.381 0.00 0.00 36.04 4.46
198 199 2.014857 GGAGGGCTAAAAATCGTGACC 58.985 52.381 0.00 0.00 0.00 4.02
199 200 2.678336 CAGGAGGGCTAAAAATCGTGAC 59.322 50.000 0.00 0.00 31.02 3.67
200 201 2.569853 TCAGGAGGGCTAAAAATCGTGA 59.430 45.455 0.00 0.00 35.04 4.35
201 202 2.985896 TCAGGAGGGCTAAAAATCGTG 58.014 47.619 0.00 0.00 0.00 4.35
202 203 3.713826 TTCAGGAGGGCTAAAAATCGT 57.286 42.857 0.00 0.00 0.00 3.73
203 204 3.181510 CGTTTCAGGAGGGCTAAAAATCG 60.182 47.826 0.00 0.00 0.00 3.34
204 205 3.128764 CCGTTTCAGGAGGGCTAAAAATC 59.871 47.826 0.00 0.00 0.00 2.17
205 206 3.089284 CCGTTTCAGGAGGGCTAAAAAT 58.911 45.455 0.00 0.00 0.00 1.82
206 207 2.510613 CCGTTTCAGGAGGGCTAAAAA 58.489 47.619 0.00 0.00 0.00 1.94
207 208 1.884928 GCCGTTTCAGGAGGGCTAAAA 60.885 52.381 1.66 0.00 44.90 1.52
208 209 0.322187 GCCGTTTCAGGAGGGCTAAA 60.322 55.000 1.66 0.00 44.90 1.85
209 210 1.298667 GCCGTTTCAGGAGGGCTAA 59.701 57.895 1.66 0.00 44.90 3.09
210 211 2.987125 GCCGTTTCAGGAGGGCTA 59.013 61.111 1.66 0.00 44.90 3.93
213 214 2.045926 CCAGCCGTTTCAGGAGGG 60.046 66.667 0.00 0.00 0.00 4.30
214 215 1.078848 CTCCAGCCGTTTCAGGAGG 60.079 63.158 0.00 0.00 43.07 4.30
215 216 4.606071 CTCCAGCCGTTTCAGGAG 57.394 61.111 0.00 0.00 41.43 3.69
216 217 0.250234 CATCTCCAGCCGTTTCAGGA 59.750 55.000 0.00 0.00 0.00 3.86
217 218 1.372087 GCATCTCCAGCCGTTTCAGG 61.372 60.000 0.00 0.00 0.00 3.86
218 219 0.392193 AGCATCTCCAGCCGTTTCAG 60.392 55.000 0.00 0.00 0.00 3.02
219 220 0.391661 GAGCATCTCCAGCCGTTTCA 60.392 55.000 0.00 0.00 0.00 2.69
220 221 2.388347 GAGCATCTCCAGCCGTTTC 58.612 57.895 0.00 0.00 0.00 2.78
221 222 4.625800 GAGCATCTCCAGCCGTTT 57.374 55.556 0.00 0.00 0.00 3.60
232 233 5.810587 TCGTGGTAGAATTTGTAAGAGCATC 59.189 40.000 0.00 0.00 0.00 3.91
233 234 5.730550 TCGTGGTAGAATTTGTAAGAGCAT 58.269 37.500 0.00 0.00 0.00 3.79
234 235 5.047590 TCTCGTGGTAGAATTTGTAAGAGCA 60.048 40.000 0.00 0.00 0.00 4.26
235 236 5.408356 TCTCGTGGTAGAATTTGTAAGAGC 58.592 41.667 0.00 0.00 0.00 4.09
236 237 5.517054 GCTCTCGTGGTAGAATTTGTAAGAG 59.483 44.000 0.00 0.00 0.00 2.85
237 238 5.185249 AGCTCTCGTGGTAGAATTTGTAAGA 59.815 40.000 0.00 0.00 0.00 2.10
238 239 5.411781 AGCTCTCGTGGTAGAATTTGTAAG 58.588 41.667 0.00 0.00 0.00 2.34
239 240 5.401531 AGCTCTCGTGGTAGAATTTGTAA 57.598 39.130 0.00 0.00 0.00 2.41
264 265 0.032130 AGCAAAAGTCGCGAGTGAGA 59.968 50.000 18.79 0.00 0.00 3.27
537 543 1.202114 TCTGGCATTGACGGAATTTGC 59.798 47.619 0.00 0.00 0.00 3.68
590 596 3.572255 AGACTAGGAATAGTGCTAGCTGC 59.428 47.826 17.32 8.97 46.83 5.25
603 610 7.390013 TCAGAGTATAAGGCTAGACTAGGAA 57.610 40.000 11.48 0.00 29.60 3.36
657 892 5.523588 TCTTCTCTCTCTCTCTCTCTCTCT 58.476 45.833 0.00 0.00 0.00 3.10
658 893 5.860941 TCTTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
659 894 6.821616 AATCTTCTCTCTCTCTCTCTCTCT 57.178 41.667 0.00 0.00 0.00 3.10
660 895 7.172361 GCTTAATCTTCTCTCTCTCTCTCTCTC 59.828 44.444 0.00 0.00 0.00 3.20
733 984 3.144506 GCCATGTTCATCCCATCTACAG 58.855 50.000 0.00 0.00 0.00 2.74
734 985 2.509131 TGCCATGTTCATCCCATCTACA 59.491 45.455 0.00 0.00 0.00 2.74
735 986 3.213206 TGCCATGTTCATCCCATCTAC 57.787 47.619 0.00 0.00 0.00 2.59
736 987 3.395273 TCATGCCATGTTCATCCCATCTA 59.605 43.478 4.31 0.00 0.00 1.98
737 988 2.176148 TCATGCCATGTTCATCCCATCT 59.824 45.455 4.31 0.00 0.00 2.90
860 1120 8.971321 CAATAGGTGTTGATTCAAGAAGTTTTG 58.029 33.333 0.00 0.00 0.00 2.44
863 1123 6.294731 GGCAATAGGTGTTGATTCAAGAAGTT 60.295 38.462 0.00 0.00 0.00 2.66
870 1130 8.995027 ATTTATAGGCAATAGGTGTTGATTCA 57.005 30.769 0.00 0.00 0.00 2.57
876 1137 6.932960 GGACGTATTTATAGGCAATAGGTGTT 59.067 38.462 5.66 0.00 36.05 3.32
912 1173 2.853542 TGGGCTGGGCAGAGTGAA 60.854 61.111 0.00 0.00 0.00 3.18
951 1219 1.301716 GAAGACGCTGGCCAGTGAA 60.302 57.895 44.69 6.40 41.24 3.18
952 1220 2.159819 GAGAAGACGCTGGCCAGTGA 62.160 60.000 44.69 6.85 41.24 3.41
956 1224 0.108585 AAAAGAGAAGACGCTGGCCA 59.891 50.000 4.71 4.71 0.00 5.36
957 1225 0.519077 CAAAAGAGAAGACGCTGGCC 59.481 55.000 0.00 0.00 0.00 5.36
963 1231 0.519077 GGCTGCCAAAAGAGAAGACG 59.481 55.000 15.17 0.00 0.00 4.18
987 1255 1.290009 GGCCATTTTGCTGAAGCGT 59.710 52.632 0.00 0.00 45.83 5.07
1047 1315 2.106938 GCGATGATGGAGACGGCA 59.893 61.111 0.00 0.00 0.00 5.69
1068 1336 2.301296 CACCAGAGATCTCACCTTGTGT 59.699 50.000 24.39 10.64 34.79 3.72
1109 1379 1.227409 TTTGGCTTCTCGTCGTGCA 60.227 52.632 0.00 0.00 0.00 4.57
1110 1380 1.204312 GTTTGGCTTCTCGTCGTGC 59.796 57.895 0.00 0.00 0.00 5.34
1114 1384 1.192534 CGAACAGTTTGGCTTCTCGTC 59.807 52.381 0.00 0.00 0.00 4.20
1116 1386 1.192534 GACGAACAGTTTGGCTTCTCG 59.807 52.381 5.48 0.00 0.00 4.04
1156 1433 4.989279 ACACCTGATCACAAAATATGCC 57.011 40.909 0.00 0.00 0.00 4.40
1182 1459 1.552337 TCATGCTCTTCAGTCCCTGAC 59.448 52.381 0.00 0.00 40.46 3.51
1188 1465 5.466058 CACATTATCCTCATGCTCTTCAGTC 59.534 44.000 0.00 0.00 0.00 3.51
1191 1468 5.363562 ACACATTATCCTCATGCTCTTCA 57.636 39.130 0.00 0.00 0.00 3.02
1235 1512 0.040067 GCAACAGAAAGCCGTGGAAG 60.040 55.000 0.00 0.00 0.00 3.46
1245 1524 6.613233 TCTCTTTTAAAACGTGCAACAGAAA 58.387 32.000 0.00 0.00 35.74 2.52
1262 1541 7.646884 ACAGATCTATCCCCAAAATCTCTTTT 58.353 34.615 0.00 0.00 34.90 2.27
1306 1586 6.428159 TGAAGAAAGAATTCGGAAAGGAGAAG 59.572 38.462 0.00 0.00 40.63 2.85
1346 1632 4.979197 GCAACTCACGGTATATCTTGAGAG 59.021 45.833 22.53 15.69 38.19 3.20
1370 1656 5.364735 TCAGATTCACATATGAGCAGGAAGA 59.635 40.000 10.38 0.00 35.83 2.87
1385 1672 5.084722 CGAAAACAGCAGATTCAGATTCAC 58.915 41.667 0.00 0.00 0.00 3.18
1403 1751 2.761559 TCGTTTCATCTCAGGCGAAAA 58.238 42.857 0.00 0.00 30.91 2.29
1414 1762 7.271223 CCAACTCACATTACATTTCGTTTCATC 59.729 37.037 0.00 0.00 0.00 2.92
1421 1774 5.862924 AGTCCAACTCACATTACATTTCG 57.137 39.130 0.00 0.00 0.00 3.46
1444 1797 1.282570 CGCCGCAACATCAACAACT 59.717 52.632 0.00 0.00 0.00 3.16
1640 1993 1.465387 AACTAGGGGCACTTGGGGT 60.465 57.895 0.00 0.00 0.00 4.95
1662 2015 2.125106 AACGGCGAGGCAGAATCC 60.125 61.111 16.62 0.00 0.00 3.01
1847 2265 1.402194 CCAACGTGCAACAAACTGTGT 60.402 47.619 0.00 0.00 44.64 3.72
1904 2325 8.213518 TCTTAGGATTACACGATTTACTACGT 57.786 34.615 0.00 0.00 43.50 3.57
1912 2333 5.069251 CCCACTCTCTTAGGATTACACGATT 59.931 44.000 0.00 0.00 0.00 3.34
1921 2342 1.403687 GCGCCCCACTCTCTTAGGAT 61.404 60.000 0.00 0.00 0.00 3.24
1962 2390 1.800655 GCGTCATCTCGAATGCAGAGT 60.801 52.381 0.00 0.00 37.07 3.24
1970 2398 2.488355 GACCGGCGTCATCTCGAA 59.512 61.111 6.01 0.00 38.99 3.71
2041 2469 2.813474 CCGGCGCATCTCGTTTCA 60.813 61.111 10.83 0.00 41.07 2.69
2101 2530 4.368543 GGACGCGGGTTTCGACCT 62.369 66.667 12.47 0.00 42.43 3.85
2105 2534 1.296056 ATTCTTGGACGCGGGTTTCG 61.296 55.000 12.47 0.00 42.76 3.46
2113 2542 4.847255 GTGTGCATTCTTGGACGC 57.153 55.556 0.00 0.00 46.33 5.19
2122 2560 5.981088 TGATAAAGATGGTTGTGTGCATT 57.019 34.783 0.00 0.00 0.00 3.56
2150 2588 8.771920 TGATCTACGTATTTGTTTTGTCAGAT 57.228 30.769 0.00 0.00 0.00 2.90
2168 2606 6.258947 GTGAAGATGGCTTTAGGTTGATCTAC 59.741 42.308 0.00 0.00 33.61 2.59
2191 2631 2.488153 TGTAGTGACAGACATCTCCGTG 59.512 50.000 0.00 0.00 0.00 4.94
2192 2632 2.488545 GTGTAGTGACAGACATCTCCGT 59.511 50.000 0.00 0.00 35.82 4.69
2193 2633 2.159366 GGTGTAGTGACAGACATCTCCG 60.159 54.545 0.00 0.00 35.82 4.63
2194 2634 3.093057 AGGTGTAGTGACAGACATCTCC 58.907 50.000 0.00 0.00 31.16 3.71
2196 2636 4.663334 TGTAGGTGTAGTGACAGACATCT 58.337 43.478 8.24 8.24 40.19 2.90
2198 2638 4.833380 ACTTGTAGGTGTAGTGACAGACAT 59.167 41.667 0.00 0.00 35.82 3.06
2202 2642 5.597806 TCAAACTTGTAGGTGTAGTGACAG 58.402 41.667 0.00 0.00 35.82 3.51
2207 2647 7.014905 TCACACTATCAAACTTGTAGGTGTAGT 59.985 37.037 12.58 0.00 35.35 2.73
2217 2657 6.231211 AGGTTAGGTCACACTATCAAACTTG 58.769 40.000 0.00 0.00 0.00 3.16
2220 2660 5.638234 GTGAGGTTAGGTCACACTATCAAAC 59.362 44.000 0.00 0.00 43.30 2.93
2230 2670 2.158871 TGTTGGTGTGAGGTTAGGTCAC 60.159 50.000 0.00 0.00 43.97 3.67
2233 2673 1.841277 TGTGTTGGTGTGAGGTTAGGT 59.159 47.619 0.00 0.00 0.00 3.08
2237 2677 1.459450 GTGTGTGTTGGTGTGAGGTT 58.541 50.000 0.00 0.00 0.00 3.50
2244 2684 4.154737 CAGATTAGATGGTGTGTGTTGGTG 59.845 45.833 0.00 0.00 0.00 4.17
2257 2697 3.072038 TGGTGAGGCCATCAGATTAGATG 59.928 47.826 5.01 0.00 43.61 2.90
2258 2698 3.321039 TGGTGAGGCCATCAGATTAGAT 58.679 45.455 5.01 0.00 43.61 1.98
2286 2726 0.901827 TGCTCTCGGCTTACCATGAA 59.098 50.000 0.00 0.00 42.39 2.57
2290 2730 1.203994 GTTAGTGCTCTCGGCTTACCA 59.796 52.381 0.00 0.00 42.39 3.25
2294 2734 0.247736 CCAGTTAGTGCTCTCGGCTT 59.752 55.000 0.00 0.00 42.39 4.35
2296 2736 0.458716 GACCAGTTAGTGCTCTCGGC 60.459 60.000 0.00 0.00 42.22 5.54
2324 2764 2.297701 GGCATGTGGTGTACCCTAATG 58.702 52.381 0.00 1.68 34.29 1.90
2325 2765 1.214424 GGGCATGTGGTGTACCCTAAT 59.786 52.381 0.00 0.00 37.59 1.73
2330 2770 1.074072 TGTGGGCATGTGGTGTACC 59.926 57.895 0.00 0.00 0.00 3.34
2332 2772 0.036164 GAGTGTGGGCATGTGGTGTA 59.964 55.000 0.00 0.00 0.00 2.90
2333 2773 1.228245 GAGTGTGGGCATGTGGTGT 60.228 57.895 0.00 0.00 0.00 4.16
2346 2786 1.476007 GGCAGTGGACTCCAGAGTGT 61.476 60.000 4.74 0.00 42.66 3.55
2347 2787 1.294780 GGCAGTGGACTCCAGAGTG 59.705 63.158 4.74 0.00 42.66 3.51
2348 2788 2.279069 CGGCAGTGGACTCCAGAGT 61.279 63.158 0.00 0.00 45.84 3.24
2353 2793 1.153549 GATGTCGGCAGTGGACTCC 60.154 63.158 0.00 0.00 35.45 3.85
2356 2796 0.741221 GGAAGATGTCGGCAGTGGAC 60.741 60.000 0.00 0.00 34.99 4.02
2360 2800 1.215647 GACGGAAGATGTCGGCAGT 59.784 57.895 0.00 0.00 34.05 4.40
2366 2806 2.030981 GGATAGGACGACGGAAGATGTC 60.031 54.545 0.00 0.00 37.79 3.06
2387 2827 1.553690 ATGTGTTGGTCCCTCCCGAG 61.554 60.000 0.00 0.00 34.77 4.63
2398 2838 2.228822 GCCTACAAGGTCAATGTGTTGG 59.771 50.000 0.00 0.00 40.00 3.77
2409 2849 1.613255 CGACAATTGGGCCTACAAGGT 60.613 52.381 10.83 2.11 37.80 3.50
2415 2855 0.108520 GTCGACGACAATTGGGCCTA 60.109 55.000 22.66 0.00 32.09 3.93
2424 2865 1.001745 CATGCTGACGTCGACGACAA 61.002 55.000 41.52 27.35 42.55 3.18
2425 2866 1.442017 CATGCTGACGTCGACGACA 60.442 57.895 41.52 37.21 43.02 4.35
2428 2869 0.798389 ACATCATGCTGACGTCGACG 60.798 55.000 34.58 34.58 46.33 5.12
2434 2875 2.726989 GCTGTTTGACATCATGCTGACG 60.727 50.000 3.02 0.00 0.00 4.35
2436 2877 2.227149 GTGCTGTTTGACATCATGCTGA 59.773 45.455 3.02 0.00 0.00 4.26
2439 2880 1.270274 TGGTGCTGTTTGACATCATGC 59.730 47.619 0.00 0.00 0.00 4.06
2440 2881 2.352030 GGTGGTGCTGTTTGACATCATG 60.352 50.000 0.00 0.00 0.00 3.07
2441 2882 1.888512 GGTGGTGCTGTTTGACATCAT 59.111 47.619 0.00 0.00 0.00 2.45
2442 2883 1.317613 GGTGGTGCTGTTTGACATCA 58.682 50.000 0.00 0.00 0.00 3.07
2443 2884 1.317613 TGGTGGTGCTGTTTGACATC 58.682 50.000 0.00 0.00 0.00 3.06
2444 2885 1.888512 GATGGTGGTGCTGTTTGACAT 59.111 47.619 0.00 0.00 0.00 3.06
2445 2886 1.133823 AGATGGTGGTGCTGTTTGACA 60.134 47.619 0.00 0.00 0.00 3.58
2446 2887 1.609208 AGATGGTGGTGCTGTTTGAC 58.391 50.000 0.00 0.00 0.00 3.18
2447 2888 1.955778 CAAGATGGTGGTGCTGTTTGA 59.044 47.619 0.00 0.00 0.00 2.69
2448 2889 1.603678 GCAAGATGGTGGTGCTGTTTG 60.604 52.381 0.00 0.00 35.36 2.93
2449 2890 0.675633 GCAAGATGGTGGTGCTGTTT 59.324 50.000 0.00 0.00 35.36 2.83
2454 2895 2.562912 CACGCAAGATGGTGGTGC 59.437 61.111 0.00 0.00 43.62 5.01
2456 2897 3.049674 CGCACGCAAGATGGTGGT 61.050 61.111 0.00 0.00 43.62 4.16
2461 2902 3.459378 GATGGGCGCACGCAAGATG 62.459 63.158 17.69 0.00 42.66 2.90
2465 2906 4.036804 GTTGATGGGCGCACGCAA 62.037 61.111 17.69 12.11 42.66 4.85
2474 2915 1.268625 CGATGGATGCATGTTGATGGG 59.731 52.381 2.46 0.00 0.00 4.00
2484 2925 0.103755 GAGTCTCAGCGATGGATGCA 59.896 55.000 0.00 0.00 33.85 3.96
2496 2937 1.480212 AATGGCGTGGTGGAGTCTCA 61.480 55.000 1.47 0.00 0.00 3.27
2535 2977 2.789339 CAGTGTTGCATCTACCGTATCG 59.211 50.000 0.00 0.00 0.00 2.92
2552 2994 1.197430 AGGGAAGAGGTGGAGCAGTG 61.197 60.000 0.00 0.00 0.00 3.66
2555 2997 1.613630 GGAGGGAAGAGGTGGAGCA 60.614 63.158 0.00 0.00 0.00 4.26
2559 3001 2.674220 GGCTGGAGGGAAGAGGTGG 61.674 68.421 0.00 0.00 0.00 4.61
2568 3010 1.107538 CATCATTGCTGGCTGGAGGG 61.108 60.000 0.00 0.00 0.00 4.30
2569 3011 1.735376 GCATCATTGCTGGCTGGAGG 61.735 60.000 0.00 0.00 45.77 4.30
2571 3013 3.929002 GCATCATTGCTGGCTGGA 58.071 55.556 0.00 0.00 45.77 3.86
2580 3022 1.954382 CTCCCTCATGGTGCATCATTG 59.046 52.381 10.51 6.23 34.77 2.82
2583 3038 0.621280 TCCTCCCTCATGGTGCATCA 60.621 55.000 0.00 0.00 34.77 3.07
2593 3048 0.178973 TTCAGTGTCGTCCTCCCTCA 60.179 55.000 0.00 0.00 0.00 3.86
2617 3072 2.299582 CTCCTAGATCAGATGGTGGCAG 59.700 54.545 0.00 0.00 0.00 4.85
2623 3078 3.164268 CTGGGACTCCTAGATCAGATGG 58.836 54.545 2.11 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.