Multiple sequence alignment - TraesCS5A01G147700

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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 TraesCS5A01G147700 chr5A 100.000 2398 0 0 1 2398 325746578 325744181 0.000000e+00 4429
1 TraesCS5A01G147700 chr5B 88.314 1643 90 48 32 1618 273857652 273856056 0.000000e+00 1877
2 TraesCS5A01G147700 chr5B 88.403 457 17 11 1637 2076 273855987 273855550 3.530000e-143 518
3 TraesCS5A01G147700 chr5D 89.438 1193 55 37 879 2031 231632336 231633497 0.000000e+00 1439
4 TraesCS5A01G147700 chr5D 91.921 656 38 12 221 869 231631637 231632284 0.000000e+00 904
5 TraesCS5A01G147700 chr5D 89.644 309 23 4 2092 2398 446484462 446484763 3.740000e-103 385
6 TraesCS5A01G147700 chr5D 90.909 187 13 3 2092 2277 370300098 370299915 5.120000e-62 248
7 TraesCS5A01G147700 chr5D 92.248 129 10 0 43 171 231630709 231630837 1.460000e-42 183
8 TraesCS5A01G147700 chr2D 89.577 307 24 6 2094 2398 48380641 48380341 1.340000e-102 383
9 TraesCS5A01G147700 chr2D 91.667 228 14 5 2176 2398 423551492 423551265 6.440000e-81 311
10 TraesCS5A01G147700 chr7D 89.251 307 27 5 2094 2398 136241983 136241681 1.740000e-101 379
11 TraesCS5A01G147700 chr7D 86.751 317 24 14 2094 2398 29764073 29763763 1.060000e-88 337
12 TraesCS5A01G147700 chr7A 88.350 309 31 4 2092 2398 520912668 520912973 1.350000e-97 366
13 TraesCS5A01G147700 chr6A 87.948 307 30 7 2094 2398 531312330 531312029 2.930000e-94 355
14 TraesCS5A01G147700 chr4D 87.338 308 35 4 2092 2398 81902697 81902393 1.360000e-92 350
15 TraesCS5A01G147700 chr3D 86.916 321 24 7 2094 2398 250024403 250024721 6.350000e-91 344
16 TraesCS5A01G147700 chr6D 85.976 328 19 8 2094 2398 43472352 43472675 2.300000e-85 326


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 TraesCS5A01G147700 chr5A 325744181 325746578 2397 True 4429.0 4429 100.000000 1 2398 1 chr5A.!!$R1 2397
1 TraesCS5A01G147700 chr5B 273855550 273857652 2102 True 1197.5 1877 88.358500 32 2076 2 chr5B.!!$R1 2044
2 TraesCS5A01G147700 chr5D 231630709 231633497 2788 False 842.0 1439 91.202333 43 2031 3 chr5D.!!$F2 1988

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
465 1264 0.322648 TGCCTCCAGATGGATATGCG 59.677 55.0 1.15 0.0 44.46 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2266 3205 0.104304 AAGCCGTTTCTCGCCGATAT 59.896 50.0 0.0 0.0 38.35 1.63 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 8.202745 GGACTCATAGTTAAGTGGAAAATCAG 57.797 38.462 0.00 0.00 0.00 2.90
26 27 7.824779 GGACTCATAGTTAAGTGGAAAATCAGT 59.175 37.037 0.00 0.00 0.00 3.41
27 28 9.220767 GACTCATAGTTAAGTGGAAAATCAGTT 57.779 33.333 0.00 0.00 34.91 3.16
28 29 9.574516 ACTCATAGTTAAGTGGAAAATCAGTTT 57.425 29.630 0.00 0.00 33.01 2.66
49 50 9.257651 CAGTTTATTATACAACTAGGTAGGCAC 57.742 37.037 0.00 0.00 31.78 5.01
118 119 0.810031 ACCGGACGCATTCACATAGC 60.810 55.000 9.46 0.00 0.00 2.97
171 177 1.131638 ACACATCCACCGCTATCCAT 58.868 50.000 0.00 0.00 0.00 3.41
172 178 1.490490 ACACATCCACCGCTATCCATT 59.510 47.619 0.00 0.00 0.00 3.16
173 179 2.146342 CACATCCACCGCTATCCATTC 58.854 52.381 0.00 0.00 0.00 2.67
174 180 1.072331 ACATCCACCGCTATCCATTCC 59.928 52.381 0.00 0.00 0.00 3.01
175 181 1.072173 CATCCACCGCTATCCATTCCA 59.928 52.381 0.00 0.00 0.00 3.53
176 182 0.468226 TCCACCGCTATCCATTCCAC 59.532 55.000 0.00 0.00 0.00 4.02
177 183 0.535102 CCACCGCTATCCATTCCACC 60.535 60.000 0.00 0.00 0.00 4.61
178 184 0.880278 CACCGCTATCCATTCCACCG 60.880 60.000 0.00 0.00 0.00 4.94
179 185 1.335132 ACCGCTATCCATTCCACCGT 61.335 55.000 0.00 0.00 0.00 4.83
180 186 0.600255 CCGCTATCCATTCCACCGTC 60.600 60.000 0.00 0.00 0.00 4.79
181 187 0.389391 CGCTATCCATTCCACCGTCT 59.611 55.000 0.00 0.00 0.00 4.18
230 1002 5.122396 ACGGTCTAAATTTCTAGACGTACGT 59.878 40.000 23.04 23.04 45.95 3.57
312 1089 3.007940 CAGTGTTACCAGGAATCCACAGA 59.992 47.826 0.61 0.00 0.00 3.41
315 1092 4.080863 GTGTTACCAGGAATCCACAGAGAT 60.081 45.833 0.61 0.00 0.00 2.75
324 1104 6.705381 CAGGAATCCACAGAGATAATCAGAAC 59.295 42.308 0.61 0.00 0.00 3.01
326 1106 6.481644 GGAATCCACAGAGATAATCAGAACAC 59.518 42.308 0.00 0.00 0.00 3.32
329 1109 4.564372 CCACAGAGATAATCAGAACACACG 59.436 45.833 0.00 0.00 0.00 4.49
331 1111 3.241553 CAGAGATAATCAGAACACACGCG 59.758 47.826 3.53 3.53 0.00 6.01
333 1113 0.645355 ATAATCAGAACACACGCGCG 59.355 50.000 30.96 30.96 0.00 6.86
431 1225 3.701664 ACTTTCATCTCCATTTGGACCC 58.298 45.455 0.00 0.00 39.78 4.46
465 1264 0.322648 TGCCTCCAGATGGATATGCG 59.677 55.000 1.15 0.00 44.46 4.73
466 1265 0.392193 GCCTCCAGATGGATATGCGG 60.392 60.000 1.15 0.92 44.46 5.69
468 1267 1.066573 CCTCCAGATGGATATGCGGAC 60.067 57.143 1.15 0.00 44.46 4.79
469 1268 0.603065 TCCAGATGGATATGCGGACG 59.397 55.000 0.00 0.00 39.78 4.79
475 1274 0.753848 TGGATATGCGGACGGACAGA 60.754 55.000 0.00 0.00 0.00 3.41
489 1288 1.152902 ACAGACAGGCAAGCAAGCA 60.153 52.632 2.78 0.00 35.83 3.91
643 1447 2.101233 GTCGCGGCCTCTCCTTTTC 61.101 63.158 6.13 0.00 0.00 2.29
645 1449 2.820037 GCGGCCTCTCCTTTTCCG 60.820 66.667 0.00 0.00 42.68 4.30
753 1557 1.730501 TTTGGAGCAGCTTCGATCTG 58.269 50.000 0.00 9.96 34.79 2.90
794 1598 3.171388 GACATCCCATCCCGCCCT 61.171 66.667 0.00 0.00 0.00 5.19
795 1599 3.171388 ACATCCCATCCCGCCCTC 61.171 66.667 0.00 0.00 0.00 4.30
796 1600 3.958860 CATCCCATCCCGCCCTCC 61.959 72.222 0.00 0.00 0.00 4.30
887 1727 5.164031 CGCGTCGCCTCTCTCTATATATATC 60.164 48.000 12.44 0.00 0.00 1.63
888 1728 5.697178 GCGTCGCCTCTCTCTATATATATCA 59.303 44.000 5.75 0.00 0.00 2.15
922 1769 3.186047 GTCGGTCGCACCATTCCG 61.186 66.667 6.21 0.00 38.47 4.30
954 1801 2.878406 ACACAAACAACCTCCGAATCAG 59.122 45.455 0.00 0.00 0.00 2.90
1024 1874 4.269523 TGAGCAACAGCCGCCCTT 62.270 61.111 0.00 0.00 0.00 3.95
1026 1876 3.909086 GAGCAACAGCCGCCCTTCT 62.909 63.158 0.00 0.00 0.00 2.85
1309 2159 1.202348 ACATCAAGAGCTGACGATCCG 60.202 52.381 0.00 0.00 36.69 4.18
1312 2162 3.417275 AAGAGCTGACGATCCGGCG 62.417 63.158 0.00 0.00 42.98 6.46
1344 2199 1.227497 GGCTCTTCTCTGATGCCGG 60.227 63.158 0.00 0.00 33.96 6.13
1355 2210 1.594862 CTGATGCCGGTCGATCTTTTC 59.405 52.381 1.90 0.00 0.00 2.29
1357 2212 2.280628 GATGCCGGTCGATCTTTTCTT 58.719 47.619 1.90 0.00 0.00 2.52
1358 2213 1.722011 TGCCGGTCGATCTTTTCTTC 58.278 50.000 1.90 0.00 0.00 2.87
1360 2215 2.289444 TGCCGGTCGATCTTTTCTTCTT 60.289 45.455 1.90 0.00 0.00 2.52
1361 2216 2.348971 GCCGGTCGATCTTTTCTTCTTC 59.651 50.000 1.90 0.00 0.00 2.87
1392 2247 1.661112 CTTGTGCTAGCTCGTTTAGGC 59.339 52.381 17.23 0.00 0.00 3.93
1395 2250 1.135333 GTGCTAGCTCGTTTAGGCTCT 59.865 52.381 17.23 0.00 39.65 4.09
1399 2254 2.671854 GCTCGTTTAGGCTCTGAGC 58.328 57.895 21.17 21.17 44.37 4.26
1507 2362 7.450634 TCTCTCGGGTATGCTAGTGTAAATTAT 59.549 37.037 0.00 0.00 0.00 1.28
1587 2444 1.269517 TGCGAATTGTTTTCCAGCACC 60.270 47.619 0.00 0.00 0.00 5.01
1602 2464 2.749044 ACCCTGCTGCATGCTTCG 60.749 61.111 20.33 8.48 43.37 3.79
1627 2546 4.625028 AGCTTTTTCTTGAGATGTTTGGC 58.375 39.130 0.00 0.00 0.00 4.52
1635 2554 3.986996 TGAGATGTTTGGCTCATCAGA 57.013 42.857 15.67 4.05 42.63 3.27
1636 2555 3.603532 TGAGATGTTTGGCTCATCAGAC 58.396 45.455 15.67 9.63 42.63 3.51
1637 2556 3.008266 TGAGATGTTTGGCTCATCAGACA 59.992 43.478 15.67 11.23 42.63 3.41
1638 2557 4.197750 GAGATGTTTGGCTCATCAGACAT 58.802 43.478 15.67 1.50 42.63 3.06
1639 2558 4.548991 GATGTTTGGCTCATCAGACATC 57.451 45.455 11.02 11.02 45.39 3.06
1640 2559 3.421919 TGTTTGGCTCATCAGACATCA 57.578 42.857 0.00 0.00 37.57 3.07
1641 2560 3.340928 TGTTTGGCTCATCAGACATCAG 58.659 45.455 0.00 0.00 37.57 2.90
1706 2626 8.755696 ATACTATAGTACAGTGTAGCGTAGTC 57.244 38.462 14.82 2.03 32.72 2.59
1707 2627 5.988561 ACTATAGTACAGTGTAGCGTAGTCC 59.011 44.000 2.75 0.00 0.00 3.85
1708 2628 3.347077 AGTACAGTGTAGCGTAGTCCT 57.653 47.619 2.39 0.00 0.00 3.85
1709 2629 4.478206 AGTACAGTGTAGCGTAGTCCTA 57.522 45.455 2.39 0.00 0.00 2.94
1710 2630 4.440880 AGTACAGTGTAGCGTAGTCCTAG 58.559 47.826 2.39 0.00 0.00 3.02
1711 2631 3.623906 ACAGTGTAGCGTAGTCCTAGA 57.376 47.619 0.00 0.00 0.00 2.43
1712 2632 4.153673 ACAGTGTAGCGTAGTCCTAGAT 57.846 45.455 0.00 0.00 0.00 1.98
1713 2633 4.525024 ACAGTGTAGCGTAGTCCTAGATT 58.475 43.478 0.00 0.00 0.00 2.40
1758 2678 2.048601 AGCTGGGAGATCTCAAGATGG 58.951 52.381 23.85 8.60 34.37 3.51
1780 2700 3.264450 GTCTTGGATCAAGGGAAGGAAGA 59.736 47.826 7.67 0.00 41.33 2.87
2040 2979 2.871216 TTCACCGGCGTGTCCAACAA 62.871 55.000 6.01 0.00 41.09 2.83
2041 2980 2.124653 ACCGGCGTGTCCAACAAA 60.125 55.556 6.01 0.00 34.01 2.83
2042 2981 2.330041 CCGGCGTGTCCAACAAAC 59.670 61.111 6.01 0.00 34.01 2.93
2052 2991 1.329599 GTCCAACAAACAGTCCGTGTC 59.670 52.381 0.00 0.00 39.03 3.67
2076 3015 1.285950 GCGTGGGCTCCTGTTTTTC 59.714 57.895 0.00 0.00 35.83 2.29
2077 3016 1.956802 CGTGGGCTCCTGTTTTTCC 59.043 57.895 0.00 0.00 0.00 3.13
2078 3017 0.821711 CGTGGGCTCCTGTTTTTCCA 60.822 55.000 0.00 0.00 0.00 3.53
2079 3018 1.408969 GTGGGCTCCTGTTTTTCCAA 58.591 50.000 0.00 0.00 0.00 3.53
2080 3019 1.068588 GTGGGCTCCTGTTTTTCCAAC 59.931 52.381 0.00 0.00 0.00 3.77
2081 3020 0.679505 GGGCTCCTGTTTTTCCAACC 59.320 55.000 0.00 0.00 0.00 3.77
2082 3021 1.408969 GGCTCCTGTTTTTCCAACCA 58.591 50.000 0.00 0.00 0.00 3.67
2083 3022 1.760029 GGCTCCTGTTTTTCCAACCAA 59.240 47.619 0.00 0.00 0.00 3.67
2084 3023 2.169561 GGCTCCTGTTTTTCCAACCAAA 59.830 45.455 0.00 0.00 0.00 3.28
2085 3024 3.194861 GCTCCTGTTTTTCCAACCAAAC 58.805 45.455 0.00 0.00 34.09 2.93
2086 3025 3.443976 CTCCTGTTTTTCCAACCAAACG 58.556 45.455 0.00 0.00 35.93 3.60
2087 3026 1.930503 CCTGTTTTTCCAACCAAACGC 59.069 47.619 0.00 0.00 35.93 4.84
2088 3027 1.586123 CTGTTTTTCCAACCAAACGCG 59.414 47.619 3.53 3.53 35.93 6.01
2089 3028 0.924777 GTTTTTCCAACCAAACGCGG 59.075 50.000 12.47 0.00 0.00 6.46
2090 3029 0.179108 TTTTTCCAACCAAACGCGGG 60.179 50.000 12.47 4.35 0.00 6.13
2091 3030 1.321074 TTTTCCAACCAAACGCGGGT 61.321 50.000 12.47 5.15 41.41 5.28
2092 3031 0.465097 TTTCCAACCAAACGCGGGTA 60.465 50.000 12.47 0.00 37.77 3.69
2093 3032 0.465097 TTCCAACCAAACGCGGGTAA 60.465 50.000 12.47 0.00 37.77 2.85
2094 3033 0.885596 TCCAACCAAACGCGGGTAAG 60.886 55.000 12.47 4.82 37.77 2.34
2095 3034 0.885596 CCAACCAAACGCGGGTAAGA 60.886 55.000 12.47 0.00 37.77 2.10
2096 3035 0.515564 CAACCAAACGCGGGTAAGAG 59.484 55.000 12.47 0.00 37.77 2.85
2097 3036 1.232621 AACCAAACGCGGGTAAGAGC 61.233 55.000 12.47 0.00 37.77 4.09
2098 3037 1.669760 CCAAACGCGGGTAAGAGCA 60.670 57.895 12.47 0.00 0.00 4.26
2099 3038 1.024579 CCAAACGCGGGTAAGAGCAT 61.025 55.000 12.47 0.00 0.00 3.79
2100 3039 0.373716 CAAACGCGGGTAAGAGCATC 59.626 55.000 12.47 0.00 0.00 3.91
2111 3050 2.107953 GAGCATCTCCAGCCGTCC 59.892 66.667 0.00 0.00 0.00 4.79
2112 3051 3.781770 GAGCATCTCCAGCCGTCCG 62.782 68.421 0.00 0.00 0.00 4.79
2113 3052 4.148825 GCATCTCCAGCCGTCCGT 62.149 66.667 0.00 0.00 0.00 4.69
2114 3053 2.105128 CATCTCCAGCCGTCCGTC 59.895 66.667 0.00 0.00 0.00 4.79
2115 3054 3.148279 ATCTCCAGCCGTCCGTCC 61.148 66.667 0.00 0.00 0.00 4.79
2139 3078 1.264288 CGGAGGAGGCATAAAAATCGC 59.736 52.381 0.00 0.00 0.00 4.58
2140 3079 1.609072 GGAGGAGGCATAAAAATCGCC 59.391 52.381 0.00 0.00 46.62 5.54
2143 3082 4.319249 GGCATAAAAATCGCCGCC 57.681 55.556 0.00 0.00 35.79 6.13
2144 3083 1.733526 GGCATAAAAATCGCCGCCT 59.266 52.632 0.00 0.00 35.79 5.52
2145 3084 0.948678 GGCATAAAAATCGCCGCCTA 59.051 50.000 0.00 0.00 35.79 3.93
2146 3085 1.335496 GGCATAAAAATCGCCGCCTAA 59.665 47.619 0.00 0.00 35.79 2.69
2147 3086 2.604614 GGCATAAAAATCGCCGCCTAAG 60.605 50.000 0.00 0.00 35.79 2.18
2148 3087 2.604614 GCATAAAAATCGCCGCCTAAGG 60.605 50.000 0.00 0.00 0.00 2.69
2149 3088 1.670791 TAAAAATCGCCGCCTAAGGG 58.329 50.000 0.00 0.00 0.00 3.95
2166 3105 4.587189 GCGAGCCGGCGGTAGAAT 62.587 66.667 28.82 8.64 0.00 2.40
2167 3106 3.036577 CGAGCCGGCGGTAGAATA 58.963 61.111 28.82 0.00 0.00 1.75
2168 3107 1.081376 CGAGCCGGCGGTAGAATAG 60.081 63.158 28.82 8.43 0.00 1.73
2169 3108 1.289380 GAGCCGGCGGTAGAATAGG 59.711 63.158 28.82 0.00 0.00 2.57
2170 3109 2.357154 GCCGGCGGTAGAATAGGC 60.357 66.667 28.82 5.42 37.61 3.93
2172 3111 2.733593 CGGCGGTAGAATAGGCGC 60.734 66.667 0.00 0.00 46.03 6.53
2173 3112 2.735237 GGCGGTAGAATAGGCGCT 59.265 61.111 7.64 0.00 0.00 5.92
2174 3113 1.859427 CGGCGGTAGAATAGGCGCTA 61.859 60.000 7.64 0.00 46.03 4.26
2175 3114 0.109226 GGCGGTAGAATAGGCGCTAG 60.109 60.000 7.64 0.00 0.00 3.42
2176 3115 0.109226 GCGGTAGAATAGGCGCTAGG 60.109 60.000 7.64 0.00 0.00 3.02
2177 3116 0.526662 CGGTAGAATAGGCGCTAGGG 59.473 60.000 7.64 1.65 0.00 3.53
2178 3117 0.896226 GGTAGAATAGGCGCTAGGGG 59.104 60.000 7.64 0.00 0.00 4.79
2179 3118 1.630223 GTAGAATAGGCGCTAGGGGT 58.370 55.000 7.64 0.00 0.00 4.95
2180 3119 1.272769 GTAGAATAGGCGCTAGGGGTG 59.727 57.143 7.64 0.00 0.00 4.61
2181 3120 1.122019 AGAATAGGCGCTAGGGGTGG 61.122 60.000 7.64 0.00 0.00 4.61
2182 3121 1.384082 AATAGGCGCTAGGGGTGGT 60.384 57.895 7.64 0.00 0.00 4.16
2183 3122 0.986550 AATAGGCGCTAGGGGTGGTT 60.987 55.000 7.64 0.00 0.00 3.67
2184 3123 1.696097 ATAGGCGCTAGGGGTGGTTG 61.696 60.000 7.64 0.00 0.00 3.77
2185 3124 4.796495 GGCGCTAGGGGTGGTTGG 62.796 72.222 7.64 0.00 0.00 3.77
2186 3125 4.796495 GCGCTAGGGGTGGTTGGG 62.796 72.222 9.09 0.00 0.00 4.12
2187 3126 4.796495 CGCTAGGGGTGGTTGGGC 62.796 72.222 0.00 0.00 0.00 5.36
2188 3127 3.657350 GCTAGGGGTGGTTGGGCA 61.657 66.667 0.00 0.00 0.00 5.36
2189 3128 2.996330 GCTAGGGGTGGTTGGGCAT 61.996 63.158 0.00 0.00 0.00 4.40
2190 3129 1.227383 CTAGGGGTGGTTGGGCATC 59.773 63.158 0.00 0.00 0.00 3.91
2191 3130 2.284515 CTAGGGGTGGTTGGGCATCC 62.285 65.000 0.00 0.00 0.00 3.51
2192 3131 3.991318 GGGGTGGTTGGGCATCCA 61.991 66.667 0.00 0.00 42.25 3.41
2193 3132 2.362889 GGGTGGTTGGGCATCCAG 60.363 66.667 0.00 0.00 45.04 3.86
2194 3133 3.070576 GGTGGTTGGGCATCCAGC 61.071 66.667 7.90 7.90 45.04 4.85
2195 3134 2.036256 GTGGTTGGGCATCCAGCT 59.964 61.111 0.00 0.00 45.04 4.24
2196 3135 2.036098 TGGTTGGGCATCCAGCTG 59.964 61.111 6.78 6.78 45.04 4.24
2197 3136 2.036256 GGTTGGGCATCCAGCTGT 59.964 61.111 13.81 0.00 45.04 4.40
2198 3137 2.048603 GGTTGGGCATCCAGCTGTC 61.049 63.158 13.81 0.00 45.04 3.51
2199 3138 2.046023 TTGGGCATCCAGCTGTCG 60.046 61.111 13.81 1.18 45.04 4.35
2200 3139 4.783621 TGGGCATCCAGCTGTCGC 62.784 66.667 13.81 11.60 44.79 5.19
2202 3141 2.894387 GGCATCCAGCTGTCGCTC 60.894 66.667 13.81 2.98 45.15 5.03
2203 3142 2.186384 GCATCCAGCTGTCGCTCT 59.814 61.111 13.81 0.00 45.15 4.09
2204 3143 1.882167 GCATCCAGCTGTCGCTCTC 60.882 63.158 13.81 0.00 45.15 3.20
2205 3144 1.514553 CATCCAGCTGTCGCTCTCA 59.485 57.895 13.81 0.00 45.15 3.27
2206 3145 0.528033 CATCCAGCTGTCGCTCTCAG 60.528 60.000 13.81 0.00 45.15 3.35
2207 3146 1.674764 ATCCAGCTGTCGCTCTCAGG 61.675 60.000 13.81 0.00 45.15 3.86
2208 3147 2.508887 CAGCTGTCGCTCTCAGGC 60.509 66.667 5.25 0.00 45.15 4.85
2216 3155 2.653702 GCTCTCAGGCGCCGATAT 59.346 61.111 23.20 0.00 0.00 1.63
2217 3156 1.445238 GCTCTCAGGCGCCGATATC 60.445 63.158 23.20 6.33 0.00 1.63
2218 3157 1.154131 CTCTCAGGCGCCGATATCG 60.154 63.158 23.20 18.31 39.44 2.92
2228 3167 3.474806 CGATATCGGCCCATTCGC 58.525 61.111 17.51 0.00 35.37 4.70
2229 3168 2.444624 CGATATCGGCCCATTCGCG 61.445 63.158 17.51 0.00 35.37 5.87
2230 3169 2.047274 ATATCGGCCCATTCGCGG 60.047 61.111 6.13 0.00 0.00 6.46
2231 3170 4.980805 TATCGGCCCATTCGCGGC 62.981 66.667 6.13 0.00 46.29 6.53
2237 3176 3.443045 CCCATTCGCGGCTGCTTT 61.443 61.111 17.03 0.00 39.65 3.51
2238 3177 2.568090 CCATTCGCGGCTGCTTTT 59.432 55.556 17.03 0.00 39.65 2.27
2239 3178 1.514873 CCATTCGCGGCTGCTTTTC 60.515 57.895 17.03 0.00 39.65 2.29
2240 3179 1.864750 CATTCGCGGCTGCTTTTCG 60.865 57.895 17.03 0.00 39.65 3.46
2241 3180 3.039202 ATTCGCGGCTGCTTTTCGG 62.039 57.895 17.03 0.00 39.65 4.30
2247 3186 2.672996 GCTGCTTTTCGGCCCAGA 60.673 61.111 8.45 0.00 41.25 3.86
2248 3187 2.048603 GCTGCTTTTCGGCCCAGAT 61.049 57.895 8.45 0.00 41.25 2.90
2249 3188 0.748005 GCTGCTTTTCGGCCCAGATA 60.748 55.000 8.45 0.00 41.25 1.98
2250 3189 1.750193 CTGCTTTTCGGCCCAGATAA 58.250 50.000 0.00 0.00 0.00 1.75
2251 3190 2.091541 CTGCTTTTCGGCCCAGATAAA 58.908 47.619 0.00 0.00 0.00 1.40
2252 3191 2.689983 CTGCTTTTCGGCCCAGATAAAT 59.310 45.455 0.00 0.00 0.00 1.40
2253 3192 3.882888 CTGCTTTTCGGCCCAGATAAATA 59.117 43.478 0.00 0.00 0.00 1.40
2254 3193 3.882888 TGCTTTTCGGCCCAGATAAATAG 59.117 43.478 0.00 0.00 0.00 1.73
2255 3194 4.134563 GCTTTTCGGCCCAGATAAATAGA 58.865 43.478 0.00 0.00 0.00 1.98
2256 3195 4.578928 GCTTTTCGGCCCAGATAAATAGAA 59.421 41.667 0.00 0.00 0.00 2.10
2257 3196 5.067283 GCTTTTCGGCCCAGATAAATAGAAA 59.933 40.000 0.00 0.00 0.00 2.52
2258 3197 6.405397 GCTTTTCGGCCCAGATAAATAGAAAA 60.405 38.462 0.00 2.48 35.77 2.29
2259 3198 7.654022 TTTTCGGCCCAGATAAATAGAAAAT 57.346 32.000 0.00 0.00 33.28 1.82
2260 3199 6.633500 TTCGGCCCAGATAAATAGAAAATG 57.367 37.500 0.00 0.00 0.00 2.32
2261 3200 5.070001 TCGGCCCAGATAAATAGAAAATGG 58.930 41.667 0.00 0.00 0.00 3.16
2262 3201 4.321230 CGGCCCAGATAAATAGAAAATGGC 60.321 45.833 0.00 0.00 34.46 4.40
2263 3202 4.021104 GGCCCAGATAAATAGAAAATGGCC 60.021 45.833 0.00 0.00 46.90 5.36
2264 3203 4.021104 GCCCAGATAAATAGAAAATGGCCC 60.021 45.833 0.00 0.00 0.00 5.80
2265 3204 4.218417 CCCAGATAAATAGAAAATGGCCCG 59.782 45.833 0.00 0.00 0.00 6.13
2266 3205 5.070001 CCAGATAAATAGAAAATGGCCCGA 58.930 41.667 0.00 0.00 0.00 5.14
2267 3206 5.711976 CCAGATAAATAGAAAATGGCCCGAT 59.288 40.000 0.00 0.00 0.00 4.18
2268 3207 6.884295 CCAGATAAATAGAAAATGGCCCGATA 59.116 38.462 0.00 0.00 0.00 2.92
2269 3208 7.557719 CCAGATAAATAGAAAATGGCCCGATAT 59.442 37.037 0.00 0.00 0.00 1.63
2270 3209 8.616076 CAGATAAATAGAAAATGGCCCGATATC 58.384 37.037 0.00 0.00 0.00 1.63
2271 3210 5.880054 AAATAGAAAATGGCCCGATATCG 57.120 39.130 18.31 18.31 39.44 2.92
2282 3221 2.421131 CGATATCGGCGAGAAACGG 58.579 57.895 17.22 0.00 42.83 4.44
2292 3231 3.419815 GCGAGAAACGGCTTATATTCG 57.580 47.619 0.00 0.00 42.83 3.34
2293 3232 2.155155 GCGAGAAACGGCTTATATTCGG 59.845 50.000 0.00 0.00 42.83 4.30
2294 3233 2.155155 CGAGAAACGGCTTATATTCGGC 59.845 50.000 0.00 0.00 38.46 5.54
2298 3237 2.150424 CGGCTTATATTCGGCGTGG 58.850 57.895 6.85 0.00 43.15 4.94
2299 3238 0.599204 CGGCTTATATTCGGCGTGGT 60.599 55.000 6.85 0.00 43.15 4.16
2300 3239 1.589803 GGCTTATATTCGGCGTGGTT 58.410 50.000 6.85 0.00 0.00 3.67
2301 3240 1.529865 GGCTTATATTCGGCGTGGTTC 59.470 52.381 6.85 0.00 0.00 3.62
2302 3241 1.191647 GCTTATATTCGGCGTGGTTCG 59.808 52.381 6.85 0.00 43.12 3.95
2303 3242 1.790623 CTTATATTCGGCGTGGTTCGG 59.209 52.381 6.85 0.00 40.26 4.30
2304 3243 0.746063 TATATTCGGCGTGGTTCGGT 59.254 50.000 6.85 0.00 40.26 4.69
2305 3244 0.808453 ATATTCGGCGTGGTTCGGTG 60.808 55.000 6.85 0.00 40.26 4.94
2306 3245 2.157305 TATTCGGCGTGGTTCGGTGT 62.157 55.000 6.85 0.00 40.26 4.16
2307 3246 2.999739 ATTCGGCGTGGTTCGGTGTT 63.000 55.000 6.85 0.00 40.26 3.32
2308 3247 4.007940 CGGCGTGGTTCGGTGTTG 62.008 66.667 0.00 0.00 40.26 3.33
2309 3248 2.589442 GGCGTGGTTCGGTGTTGA 60.589 61.111 0.00 0.00 40.26 3.18
2310 3249 2.181521 GGCGTGGTTCGGTGTTGAA 61.182 57.895 0.00 0.00 40.26 2.69
2311 3250 1.512156 GGCGTGGTTCGGTGTTGAAT 61.512 55.000 0.00 0.00 40.26 2.57
2312 3251 0.309612 GCGTGGTTCGGTGTTGAATT 59.690 50.000 0.00 0.00 40.26 2.17
2313 3252 1.924191 GCGTGGTTCGGTGTTGAATTG 60.924 52.381 0.00 0.00 40.26 2.32
2314 3253 1.332375 CGTGGTTCGGTGTTGAATTGT 59.668 47.619 0.00 0.00 35.71 2.71
2315 3254 2.601266 CGTGGTTCGGTGTTGAATTGTC 60.601 50.000 0.00 0.00 35.71 3.18
2316 3255 2.356382 GTGGTTCGGTGTTGAATTGTCA 59.644 45.455 0.00 0.00 0.00 3.58
2317 3256 3.017442 TGGTTCGGTGTTGAATTGTCAA 58.983 40.909 0.00 0.00 41.57 3.18
2353 3292 7.757941 TTTTTATCACATGGTTCATCACAGA 57.242 32.000 0.00 0.00 0.00 3.41
2354 3293 7.757941 TTTTATCACATGGTTCATCACAGAA 57.242 32.000 0.00 0.00 0.00 3.02
2355 3294 7.757941 TTTATCACATGGTTCATCACAGAAA 57.242 32.000 0.00 0.00 0.00 2.52
2356 3295 7.757941 TTATCACATGGTTCATCACAGAAAA 57.242 32.000 0.00 0.00 0.00 2.29
2357 3296 6.845758 ATCACATGGTTCATCACAGAAAAT 57.154 33.333 0.00 0.00 0.00 1.82
2358 3297 6.258230 TCACATGGTTCATCACAGAAAATC 57.742 37.500 0.00 0.00 0.00 2.17
2359 3298 5.769162 TCACATGGTTCATCACAGAAAATCA 59.231 36.000 0.00 0.00 0.00 2.57
2360 3299 6.264970 TCACATGGTTCATCACAGAAAATCAA 59.735 34.615 0.00 0.00 0.00 2.57
2361 3300 6.924612 CACATGGTTCATCACAGAAAATCAAA 59.075 34.615 0.00 0.00 0.00 2.69
2362 3301 7.601130 CACATGGTTCATCACAGAAAATCAAAT 59.399 33.333 0.00 0.00 0.00 2.32
2363 3302 8.805175 ACATGGTTCATCACAGAAAATCAAATA 58.195 29.630 0.00 0.00 0.00 1.40
2364 3303 9.642327 CATGGTTCATCACAGAAAATCAAATAA 57.358 29.630 0.00 0.00 0.00 1.40
2389 3328 9.638239 AATTCAATAAATAGTGCAACGACAAAT 57.362 25.926 0.00 0.00 45.86 2.32
2391 3330 9.767684 TTCAATAAATAGTGCAACGACAAATAG 57.232 29.630 0.00 0.00 45.86 1.73
2392 3331 8.941977 TCAATAAATAGTGCAACGACAAATAGT 58.058 29.630 0.00 0.00 45.86 2.12
2393 3332 9.554724 CAATAAATAGTGCAACGACAAATAGTT 57.445 29.630 0.00 0.00 45.86 2.24
2394 3333 9.769093 AATAAATAGTGCAACGACAAATAGTTC 57.231 29.630 0.00 0.00 45.86 3.01
2395 3334 6.795098 AATAGTGCAACGACAAATAGTTCA 57.205 33.333 0.00 0.00 45.86 3.18
2396 3335 6.795098 ATAGTGCAACGACAAATAGTTCAA 57.205 33.333 0.00 0.00 45.86 2.69
2397 3336 5.689383 AGTGCAACGACAAATAGTTCAAT 57.311 34.783 0.00 0.00 45.86 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.824779 ACTGATTTTCCACTTAACTATGAGTCC 59.175 37.037 0.00 0.00 0.00 3.85
1 2 8.779354 ACTGATTTTCCACTTAACTATGAGTC 57.221 34.615 0.00 0.00 0.00 3.36
2 3 9.574516 AAACTGATTTTCCACTTAACTATGAGT 57.425 29.630 0.00 0.00 0.00 3.41
22 23 9.204337 TGCCTACCTAGTTGTATAATAAACTGA 57.796 33.333 6.88 0.00 37.23 3.41
23 24 9.257651 GTGCCTACCTAGTTGTATAATAAACTG 57.742 37.037 6.88 0.00 37.23 3.16
24 25 8.984855 TGTGCCTACCTAGTTGTATAATAAACT 58.015 33.333 0.00 0.00 39.82 2.66
25 26 9.038803 GTGTGCCTACCTAGTTGTATAATAAAC 57.961 37.037 0.00 0.00 0.00 2.01
26 27 8.984855 AGTGTGCCTACCTAGTTGTATAATAAA 58.015 33.333 0.00 0.00 0.00 1.40
27 28 8.543293 AGTGTGCCTACCTAGTTGTATAATAA 57.457 34.615 0.00 0.00 0.00 1.40
28 29 8.418662 CAAGTGTGCCTACCTAGTTGTATAATA 58.581 37.037 0.00 0.00 0.00 0.98
29 30 7.272978 CAAGTGTGCCTACCTAGTTGTATAAT 58.727 38.462 0.00 0.00 0.00 1.28
30 31 6.636705 CAAGTGTGCCTACCTAGTTGTATAA 58.363 40.000 0.00 0.00 0.00 0.98
49 50 2.075338 GAAAGAGAGAGCCTGCAAGTG 58.925 52.381 0.00 0.00 0.00 3.16
105 106 0.028505 GCACCTGCTATGTGAATGCG 59.971 55.000 5.24 0.00 35.74 4.73
171 177 1.301401 CCGAGCAAAGACGGTGGAA 60.301 57.895 0.00 0.00 43.53 3.53
172 178 2.342279 CCGAGCAAAGACGGTGGA 59.658 61.111 0.00 0.00 43.53 4.02
177 183 4.394712 AGGGGCCGAGCAAAGACG 62.395 66.667 0.00 0.00 0.00 4.18
178 184 2.436824 GAGGGGCCGAGCAAAGAC 60.437 66.667 0.00 0.00 0.00 3.01
179 185 3.717294 GGAGGGGCCGAGCAAAGA 61.717 66.667 0.00 0.00 0.00 2.52
180 186 4.803908 GGGAGGGGCCGAGCAAAG 62.804 72.222 0.00 0.00 37.63 2.77
230 1002 6.604396 AGGTTGATGATGAAGATATTGTGCAA 59.396 34.615 0.00 0.00 0.00 4.08
312 1089 1.927174 GCGCGTGTGTTCTGATTATCT 59.073 47.619 8.43 0.00 0.00 1.98
315 1092 1.951181 GCGCGCGTGTGTTCTGATTA 61.951 55.000 32.35 0.00 0.00 1.75
364 1150 5.581874 CACAGCAAAAAGGTTCATCAAAAGT 59.418 36.000 0.00 0.00 0.00 2.66
440 1234 0.911045 TCCATCTGGAGGCAGCTCAA 60.911 55.000 0.00 0.00 39.78 3.02
465 1264 1.374758 CTTGCCTGTCTGTCCGTCC 60.375 63.158 0.00 0.00 0.00 4.79
466 1265 2.029844 GCTTGCCTGTCTGTCCGTC 61.030 63.158 0.00 0.00 0.00 4.79
468 1267 1.572085 CTTGCTTGCCTGTCTGTCCG 61.572 60.000 0.00 0.00 0.00 4.79
469 1268 1.860484 GCTTGCTTGCCTGTCTGTCC 61.860 60.000 0.00 0.00 0.00 4.02
475 1274 2.732658 GCTTGCTTGCTTGCCTGT 59.267 55.556 0.00 0.00 0.00 4.00
489 1288 0.321298 ACAAGGACGCGTATTGGCTT 60.321 50.000 29.38 14.03 0.00 4.35
637 1441 4.065789 AGCTGAAAGAAGTACGGAAAAGG 58.934 43.478 0.00 0.00 34.07 3.11
643 1447 7.707035 AGTTATGATTAGCTGAAAGAAGTACGG 59.293 37.037 0.00 0.00 34.07 4.02
645 1449 8.747666 CGAGTTATGATTAGCTGAAAGAAGTAC 58.252 37.037 0.00 0.00 34.07 2.73
700 1504 3.904800 TGCATGGCTACTAGTTTAGCA 57.095 42.857 17.34 9.63 45.52 3.49
869 1673 8.224720 AGAGGGTTGATATATATAGAGAGAGGC 58.775 40.741 0.00 0.00 0.00 4.70
870 1674 9.793259 GAGAGGGTTGATATATATAGAGAGAGG 57.207 40.741 0.00 0.00 0.00 3.69
887 1727 2.266055 GGAGCACGGAGAGGGTTG 59.734 66.667 0.00 0.00 0.00 3.77
888 1728 3.382832 CGGAGCACGGAGAGGGTT 61.383 66.667 0.00 0.00 39.42 4.11
954 1801 4.668289 GACGAGAAGAGGAGAAGTTGATC 58.332 47.826 0.00 0.00 0.00 2.92
1024 1874 1.682684 GGAGGCAGAGGAACCGAGA 60.683 63.158 0.00 0.00 0.00 4.04
1026 1876 1.682684 GAGGAGGCAGAGGAACCGA 60.683 63.158 0.00 0.00 0.00 4.69
1029 1879 1.216710 CACGAGGAGGCAGAGGAAC 59.783 63.158 0.00 0.00 0.00 3.62
1344 2199 7.883229 AGAAGAAGAAGAAGAAAAGATCGAC 57.117 36.000 0.00 0.00 0.00 4.20
1355 2210 5.990996 AGCACAAGAGAAGAAGAAGAAGAAG 59.009 40.000 0.00 0.00 0.00 2.85
1357 2212 5.543507 AGCACAAGAGAAGAAGAAGAAGA 57.456 39.130 0.00 0.00 0.00 2.87
1358 2213 5.348451 GCTAGCACAAGAGAAGAAGAAGAAG 59.652 44.000 10.63 0.00 0.00 2.85
1360 2215 4.526262 AGCTAGCACAAGAGAAGAAGAAGA 59.474 41.667 18.83 0.00 0.00 2.87
1361 2216 4.819769 AGCTAGCACAAGAGAAGAAGAAG 58.180 43.478 18.83 0.00 0.00 2.85
1392 2247 1.668294 ACCAGTCGGTTGCTCAGAG 59.332 57.895 0.00 0.00 46.31 3.35
1462 2317 2.489329 AGAAAATCATTGTGGAGGCACG 59.511 45.455 0.00 0.00 0.00 5.34
1514 2369 8.766476 ACAAGCAGGAGTATATCAGCAATATAT 58.234 33.333 3.11 0.00 35.69 0.86
1515 2370 8.138928 ACAAGCAGGAGTATATCAGCAATATA 57.861 34.615 0.00 0.00 34.07 0.86
1534 2389 5.974725 TGTGGTGTACATCACATTACAAGCA 60.975 40.000 32.98 11.45 46.52 3.91
1555 2410 7.320324 GGAAAACAATTCGCACGTATATATGTG 59.680 37.037 24.85 24.85 44.10 3.21
1556 2411 7.011576 TGGAAAACAATTCGCACGTATATATGT 59.988 33.333 1.51 1.51 0.00 2.29
1557 2412 7.348956 TGGAAAACAATTCGCACGTATATATG 58.651 34.615 0.12 0.12 0.00 1.78
1558 2413 7.485418 TGGAAAACAATTCGCACGTATATAT 57.515 32.000 0.00 0.00 0.00 0.86
1559 2414 6.510478 GCTGGAAAACAATTCGCACGTATATA 60.510 38.462 0.00 0.00 0.00 0.86
1560 2415 5.729454 GCTGGAAAACAATTCGCACGTATAT 60.729 40.000 0.00 0.00 0.00 0.86
1561 2416 4.436317 GCTGGAAAACAATTCGCACGTATA 60.436 41.667 0.00 0.00 0.00 1.47
1562 2417 3.669557 GCTGGAAAACAATTCGCACGTAT 60.670 43.478 0.00 0.00 0.00 3.06
1602 2464 6.529477 GCCAAACATCTCAAGAAAAAGCTATC 59.471 38.462 0.00 0.00 0.00 2.08
1627 2546 5.163540 TGACTGATCACTGATGTCTGATGAG 60.164 44.000 11.87 0.00 35.09 2.90
1700 2620 9.941325 TTTCTATACTAGGAATCTAGGACTACG 57.059 37.037 0.00 0.00 45.50 3.51
1733 2653 2.856760 TGAGATCTCCCAGCTTACCT 57.143 50.000 20.03 0.00 0.00 3.08
1758 2678 3.264450 TCTTCCTTCCCTTGATCCAAGAC 59.736 47.826 8.16 0.00 43.42 3.01
1780 2700 3.144193 CCTCTCGCGCTCTTCCCT 61.144 66.667 5.56 0.00 0.00 4.20
1875 2795 2.279985 TTACGCGTTGAACGGCCA 60.280 55.556 20.78 0.00 42.82 5.36
1933 2872 1.151668 CTTTGCTACGCTCTTGCTGT 58.848 50.000 0.00 0.00 36.97 4.40
1959 2898 4.719369 ACGGCTTCACGCGTCTCC 62.719 66.667 9.86 7.17 40.44 3.71
2040 2979 2.522436 TCGGGGACACGGACTGTT 60.522 61.111 0.00 0.00 31.03 3.16
2041 2980 2.989824 CTCGGGGACACGGACTGT 60.990 66.667 0.00 0.00 34.96 3.55
2042 2981 4.436998 GCTCGGGGACACGGACTG 62.437 72.222 0.00 0.00 0.00 3.51
2067 3006 1.930503 GCGTTTGGTTGGAAAAACAGG 59.069 47.619 0.00 0.00 36.31 4.00
2076 3015 0.885596 TCTTACCCGCGTTTGGTTGG 60.886 55.000 10.83 2.19 37.31 3.77
2077 3016 0.515564 CTCTTACCCGCGTTTGGTTG 59.484 55.000 10.83 5.36 37.31 3.77
2078 3017 1.232621 GCTCTTACCCGCGTTTGGTT 61.233 55.000 10.83 0.00 37.31 3.67
2079 3018 1.670083 GCTCTTACCCGCGTTTGGT 60.670 57.895 4.92 8.20 39.97 3.67
2080 3019 1.024579 ATGCTCTTACCCGCGTTTGG 61.025 55.000 4.92 0.90 0.00 3.28
2081 3020 0.373716 GATGCTCTTACCCGCGTTTG 59.626 55.000 4.92 0.00 0.00 2.93
2082 3021 0.249398 AGATGCTCTTACCCGCGTTT 59.751 50.000 4.92 0.00 0.00 3.60
2083 3022 0.179108 GAGATGCTCTTACCCGCGTT 60.179 55.000 4.92 0.00 0.00 4.84
2084 3023 1.437986 GAGATGCTCTTACCCGCGT 59.562 57.895 4.92 0.00 0.00 6.01
2085 3024 1.300233 GGAGATGCTCTTACCCGCG 60.300 63.158 0.00 0.00 0.00 6.46
2086 3025 0.249657 CTGGAGATGCTCTTACCCGC 60.250 60.000 0.00 0.00 0.00 6.13
2087 3026 0.249657 GCTGGAGATGCTCTTACCCG 60.250 60.000 0.00 0.00 0.00 5.28
2088 3027 0.107643 GGCTGGAGATGCTCTTACCC 59.892 60.000 0.00 0.00 0.00 3.69
2089 3028 0.249657 CGGCTGGAGATGCTCTTACC 60.250 60.000 0.00 0.00 0.00 2.85
2090 3029 0.461961 ACGGCTGGAGATGCTCTTAC 59.538 55.000 0.00 0.00 0.00 2.34
2091 3030 0.747255 GACGGCTGGAGATGCTCTTA 59.253 55.000 0.00 0.00 0.00 2.10
2092 3031 1.519719 GACGGCTGGAGATGCTCTT 59.480 57.895 0.00 0.00 0.00 2.85
2093 3032 2.430610 GGACGGCTGGAGATGCTCT 61.431 63.158 0.00 0.00 0.00 4.09
2094 3033 2.107953 GGACGGCTGGAGATGCTC 59.892 66.667 0.00 0.00 0.00 4.26
2095 3034 3.842923 CGGACGGCTGGAGATGCT 61.843 66.667 0.00 0.00 0.00 3.79
2096 3035 4.148825 ACGGACGGCTGGAGATGC 62.149 66.667 0.04 0.00 0.00 3.91
2097 3036 2.105128 GACGGACGGCTGGAGATG 59.895 66.667 0.04 0.00 0.00 2.90
2098 3037 3.148279 GGACGGACGGCTGGAGAT 61.148 66.667 0.04 0.00 0.00 2.75
2115 3054 1.641552 TTTTATGCCTCCTCCGGGGG 61.642 60.000 16.89 16.89 35.33 5.40
2116 3055 0.257616 TTTTTATGCCTCCTCCGGGG 59.742 55.000 0.00 0.00 0.00 5.73
2117 3056 2.230660 GATTTTTATGCCTCCTCCGGG 58.769 52.381 0.00 0.00 0.00 5.73
2118 3057 1.873591 CGATTTTTATGCCTCCTCCGG 59.126 52.381 0.00 0.00 0.00 5.14
2119 3058 1.264288 GCGATTTTTATGCCTCCTCCG 59.736 52.381 0.00 0.00 0.00 4.63
2120 3059 1.609072 GGCGATTTTTATGCCTCCTCC 59.391 52.381 0.00 0.00 45.40 4.30
2121 3060 1.264288 CGGCGATTTTTATGCCTCCTC 59.736 52.381 0.00 0.00 46.67 3.71
2122 3061 1.308998 CGGCGATTTTTATGCCTCCT 58.691 50.000 0.00 0.00 46.67 3.69
2123 3062 0.317854 GCGGCGATTTTTATGCCTCC 60.318 55.000 12.98 0.00 46.67 4.30
2124 3063 0.317854 GGCGGCGATTTTTATGCCTC 60.318 55.000 12.98 0.00 46.67 4.70
2125 3064 1.733526 GGCGGCGATTTTTATGCCT 59.266 52.632 12.98 0.00 46.67 4.75
2126 3065 0.948678 TAGGCGGCGATTTTTATGCC 59.051 50.000 12.98 0.00 45.39 4.40
2127 3066 2.604614 CCTTAGGCGGCGATTTTTATGC 60.605 50.000 12.98 0.00 0.00 3.14
2128 3067 2.031157 CCCTTAGGCGGCGATTTTTATG 60.031 50.000 12.98 0.00 0.00 1.90
2129 3068 2.227194 CCCTTAGGCGGCGATTTTTAT 58.773 47.619 12.98 0.00 0.00 1.40
2130 3069 1.670791 CCCTTAGGCGGCGATTTTTA 58.329 50.000 12.98 0.00 0.00 1.52
2131 3070 2.489040 CCCTTAGGCGGCGATTTTT 58.511 52.632 12.98 0.00 0.00 1.94
2132 3071 4.235731 CCCTTAGGCGGCGATTTT 57.764 55.556 12.98 0.00 0.00 1.82
2149 3088 3.203546 TATTCTACCGCCGGCTCGC 62.204 63.158 26.68 0.00 0.00 5.03
2150 3089 1.081376 CTATTCTACCGCCGGCTCG 60.081 63.158 26.68 17.01 0.00 5.03
2151 3090 1.289380 CCTATTCTACCGCCGGCTC 59.711 63.158 26.68 0.00 0.00 4.70
2152 3091 2.868986 GCCTATTCTACCGCCGGCT 61.869 63.158 26.68 9.55 34.80 5.52
2153 3092 2.357154 GCCTATTCTACCGCCGGC 60.357 66.667 19.07 19.07 0.00 6.13
2154 3093 2.049433 CGCCTATTCTACCGCCGG 60.049 66.667 0.00 0.00 0.00 6.13
2155 3094 1.859427 TAGCGCCTATTCTACCGCCG 61.859 60.000 2.29 0.00 46.90 6.46
2156 3095 0.109226 CTAGCGCCTATTCTACCGCC 60.109 60.000 2.29 0.00 46.90 6.13
2157 3096 0.109226 CCTAGCGCCTATTCTACCGC 60.109 60.000 2.29 0.00 46.14 5.68
2158 3097 0.526662 CCCTAGCGCCTATTCTACCG 59.473 60.000 2.29 0.00 0.00 4.02
2159 3098 0.896226 CCCCTAGCGCCTATTCTACC 59.104 60.000 2.29 0.00 0.00 3.18
2160 3099 1.272769 CACCCCTAGCGCCTATTCTAC 59.727 57.143 2.29 0.00 0.00 2.59
2161 3100 1.629043 CACCCCTAGCGCCTATTCTA 58.371 55.000 2.29 0.00 0.00 2.10
2162 3101 1.122019 CCACCCCTAGCGCCTATTCT 61.122 60.000 2.29 0.00 0.00 2.40
2163 3102 1.371558 CCACCCCTAGCGCCTATTC 59.628 63.158 2.29 0.00 0.00 1.75
2164 3103 0.986550 AACCACCCCTAGCGCCTATT 60.987 55.000 2.29 0.00 0.00 1.73
2165 3104 1.384082 AACCACCCCTAGCGCCTAT 60.384 57.895 2.29 0.00 0.00 2.57
2166 3105 2.039951 AACCACCCCTAGCGCCTA 59.960 61.111 2.29 0.00 0.00 3.93
2167 3106 3.717294 CAACCACCCCTAGCGCCT 61.717 66.667 2.29 0.00 0.00 5.52
2168 3107 4.796495 CCAACCACCCCTAGCGCC 62.796 72.222 2.29 0.00 0.00 6.53
2169 3108 4.796495 CCCAACCACCCCTAGCGC 62.796 72.222 0.00 0.00 0.00 5.92
2170 3109 4.796495 GCCCAACCACCCCTAGCG 62.796 72.222 0.00 0.00 0.00 4.26
2171 3110 2.911221 GATGCCCAACCACCCCTAGC 62.911 65.000 0.00 0.00 0.00 3.42
2172 3111 1.227383 GATGCCCAACCACCCCTAG 59.773 63.158 0.00 0.00 0.00 3.02
2173 3112 2.313427 GGATGCCCAACCACCCCTA 61.313 63.158 0.00 0.00 0.00 3.53
2174 3113 3.672503 GGATGCCCAACCACCCCT 61.673 66.667 0.00 0.00 0.00 4.79
2175 3114 3.963124 CTGGATGCCCAACCACCCC 62.963 68.421 0.00 0.00 42.98 4.95
2176 3115 2.362889 CTGGATGCCCAACCACCC 60.363 66.667 0.00 0.00 42.98 4.61
2177 3116 3.070576 GCTGGATGCCCAACCACC 61.071 66.667 0.00 0.00 42.98 4.61
2178 3117 2.036256 AGCTGGATGCCCAACCAC 59.964 61.111 0.00 0.00 42.98 4.16
2179 3118 2.036098 CAGCTGGATGCCCAACCA 59.964 61.111 5.57 0.00 42.98 3.67
2180 3119 2.036256 ACAGCTGGATGCCCAACC 59.964 61.111 19.93 0.00 42.98 3.77
2181 3120 2.401766 CGACAGCTGGATGCCCAAC 61.402 63.158 19.93 0.00 42.98 3.77
2182 3121 2.046023 CGACAGCTGGATGCCCAA 60.046 61.111 19.93 0.00 42.98 4.12
2183 3122 4.783621 GCGACAGCTGGATGCCCA 62.784 66.667 19.93 0.00 44.23 5.36
2199 3138 1.445238 GATATCGGCGCCTGAGAGC 60.445 63.158 26.68 19.00 38.21 4.09
2200 3139 1.154131 CGATATCGGCGCCTGAGAG 60.154 63.158 26.68 8.63 35.37 3.20
2201 3140 2.954611 CGATATCGGCGCCTGAGA 59.045 61.111 26.68 20.39 35.37 3.27
2211 3150 2.444624 CGCGAATGGGCCGATATCG 61.445 63.158 18.31 18.31 39.44 2.92
2212 3151 2.100631 CCGCGAATGGGCCGATATC 61.101 63.158 8.23 0.49 0.00 1.63
2213 3152 2.047274 CCGCGAATGGGCCGATAT 60.047 61.111 8.23 0.00 0.00 1.63
2214 3153 4.980805 GCCGCGAATGGGCCGATA 62.981 66.667 8.23 0.00 44.97 2.92
2220 3159 2.872337 GAAAAGCAGCCGCGAATGGG 62.872 60.000 8.23 0.00 45.49 4.00
2221 3160 1.514873 GAAAAGCAGCCGCGAATGG 60.515 57.895 8.23 0.00 45.49 3.16
2222 3161 1.864750 CGAAAAGCAGCCGCGAATG 60.865 57.895 8.23 6.96 45.49 2.67
2223 3162 2.480555 CGAAAAGCAGCCGCGAAT 59.519 55.556 8.23 0.00 45.49 3.34
2224 3163 3.722295 CCGAAAAGCAGCCGCGAA 61.722 61.111 8.23 0.00 45.49 4.70
2229 3168 3.752339 CTGGGCCGAAAAGCAGCC 61.752 66.667 0.00 0.00 46.37 4.85
2230 3169 0.748005 TATCTGGGCCGAAAAGCAGC 60.748 55.000 0.00 0.00 0.00 5.25
2231 3170 1.750193 TTATCTGGGCCGAAAAGCAG 58.250 50.000 0.00 0.00 0.00 4.24
2232 3171 2.208132 TTTATCTGGGCCGAAAAGCA 57.792 45.000 0.00 0.00 0.00 3.91
2233 3172 4.134563 TCTATTTATCTGGGCCGAAAAGC 58.865 43.478 0.00 0.00 0.00 3.51
2234 3173 6.693315 TTTCTATTTATCTGGGCCGAAAAG 57.307 37.500 0.00 0.00 0.00 2.27
2235 3174 7.417342 CCATTTTCTATTTATCTGGGCCGAAAA 60.417 37.037 10.96 10.96 34.77 2.29
2236 3175 6.040391 CCATTTTCTATTTATCTGGGCCGAAA 59.960 38.462 0.00 0.00 0.00 3.46
2237 3176 5.534654 CCATTTTCTATTTATCTGGGCCGAA 59.465 40.000 0.00 0.00 0.00 4.30
2238 3177 5.070001 CCATTTTCTATTTATCTGGGCCGA 58.930 41.667 0.00 0.00 0.00 5.54
2239 3178 4.321230 GCCATTTTCTATTTATCTGGGCCG 60.321 45.833 0.00 0.00 0.00 6.13
2240 3179 5.139435 GCCATTTTCTATTTATCTGGGCC 57.861 43.478 0.00 0.00 0.00 5.80
2241 3180 4.021104 GGGCCATTTTCTATTTATCTGGGC 60.021 45.833 4.39 3.85 44.52 5.36
2242 3181 4.218417 CGGGCCATTTTCTATTTATCTGGG 59.782 45.833 4.39 0.00 0.00 4.45
2243 3182 5.070001 TCGGGCCATTTTCTATTTATCTGG 58.930 41.667 4.39 0.00 0.00 3.86
2244 3183 6.824305 ATCGGGCCATTTTCTATTTATCTG 57.176 37.500 4.39 0.00 0.00 2.90
2245 3184 7.495934 CGATATCGGGCCATTTTCTATTTATCT 59.504 37.037 17.51 0.00 35.37 1.98
2246 3185 7.630924 CGATATCGGGCCATTTTCTATTTATC 58.369 38.462 17.51 0.00 35.37 1.75
2247 3186 7.553881 CGATATCGGGCCATTTTCTATTTAT 57.446 36.000 17.51 0.00 35.37 1.40
2248 3187 6.978343 CGATATCGGGCCATTTTCTATTTA 57.022 37.500 17.51 0.00 35.37 1.40
2249 3188 5.880054 CGATATCGGGCCATTTTCTATTT 57.120 39.130 17.51 0.00 35.37 1.40
2264 3203 1.606350 GCCGTTTCTCGCCGATATCG 61.606 60.000 18.31 18.31 38.35 2.92
2265 3204 0.318784 AGCCGTTTCTCGCCGATATC 60.319 55.000 0.00 0.00 38.35 1.63
2266 3205 0.104304 AAGCCGTTTCTCGCCGATAT 59.896 50.000 0.00 0.00 38.35 1.63
2267 3206 0.740149 TAAGCCGTTTCTCGCCGATA 59.260 50.000 0.00 0.00 38.35 2.92
2268 3207 0.104304 ATAAGCCGTTTCTCGCCGAT 59.896 50.000 0.00 0.00 38.35 4.18
2269 3208 0.740149 TATAAGCCGTTTCTCGCCGA 59.260 50.000 0.00 0.00 38.35 5.54
2270 3209 1.779569 ATATAAGCCGTTTCTCGCCG 58.220 50.000 0.00 0.00 38.35 6.46
2271 3210 2.155155 CGAATATAAGCCGTTTCTCGCC 59.845 50.000 0.00 0.00 38.35 5.54
2272 3211 2.155155 CCGAATATAAGCCGTTTCTCGC 59.845 50.000 0.00 0.00 38.35 5.03
2273 3212 2.155155 GCCGAATATAAGCCGTTTCTCG 59.845 50.000 0.00 0.00 39.52 4.04
2274 3213 2.155155 CGCCGAATATAAGCCGTTTCTC 59.845 50.000 0.00 0.00 0.00 2.87
2275 3214 2.132762 CGCCGAATATAAGCCGTTTCT 58.867 47.619 0.00 0.00 0.00 2.52
2276 3215 1.862827 ACGCCGAATATAAGCCGTTTC 59.137 47.619 0.00 0.00 0.00 2.78
2277 3216 1.595794 CACGCCGAATATAAGCCGTTT 59.404 47.619 0.00 0.00 0.00 3.60
2278 3217 1.214367 CACGCCGAATATAAGCCGTT 58.786 50.000 0.00 0.00 0.00 4.44
2279 3218 0.599204 CCACGCCGAATATAAGCCGT 60.599 55.000 0.00 0.00 0.00 5.68
2280 3219 0.599204 ACCACGCCGAATATAAGCCG 60.599 55.000 0.00 0.00 0.00 5.52
2281 3220 1.529865 GAACCACGCCGAATATAAGCC 59.470 52.381 0.00 0.00 0.00 4.35
2282 3221 1.191647 CGAACCACGCCGAATATAAGC 59.808 52.381 0.00 0.00 34.51 3.09
2283 3222 1.790623 CCGAACCACGCCGAATATAAG 59.209 52.381 0.00 0.00 41.07 1.73
2284 3223 1.136695 ACCGAACCACGCCGAATATAA 59.863 47.619 0.00 0.00 41.07 0.98
2285 3224 0.746063 ACCGAACCACGCCGAATATA 59.254 50.000 0.00 0.00 41.07 0.86
2286 3225 0.808453 CACCGAACCACGCCGAATAT 60.808 55.000 0.00 0.00 41.07 1.28
2287 3226 1.446445 CACCGAACCACGCCGAATA 60.446 57.895 0.00 0.00 41.07 1.75
2288 3227 2.740826 CACCGAACCACGCCGAAT 60.741 61.111 0.00 0.00 41.07 3.34
2289 3228 3.736732 AACACCGAACCACGCCGAA 62.737 57.895 0.00 0.00 41.07 4.30
2290 3229 4.224274 AACACCGAACCACGCCGA 62.224 61.111 0.00 0.00 41.07 5.54
2291 3230 4.007940 CAACACCGAACCACGCCG 62.008 66.667 0.00 0.00 41.07 6.46
2292 3231 1.512156 ATTCAACACCGAACCACGCC 61.512 55.000 0.00 0.00 41.07 5.68
2293 3232 0.309612 AATTCAACACCGAACCACGC 59.690 50.000 0.00 0.00 41.07 5.34
2294 3233 1.332375 ACAATTCAACACCGAACCACG 59.668 47.619 0.00 0.00 42.18 4.94
2295 3234 2.356382 TGACAATTCAACACCGAACCAC 59.644 45.455 0.00 0.00 0.00 4.16
2296 3235 2.644676 TGACAATTCAACACCGAACCA 58.355 42.857 0.00 0.00 0.00 3.67
2297 3236 3.701532 TTGACAATTCAACACCGAACC 57.298 42.857 0.00 0.00 36.79 3.62
2329 3268 7.757941 TCTGTGATGAACCATGTGATAAAAA 57.242 32.000 0.00 0.00 0.00 1.94
2330 3269 7.757941 TTCTGTGATGAACCATGTGATAAAA 57.242 32.000 0.00 0.00 0.00 1.52
2331 3270 7.757941 TTTCTGTGATGAACCATGTGATAAA 57.242 32.000 0.00 0.00 0.00 1.40
2332 3271 7.757941 TTTTCTGTGATGAACCATGTGATAA 57.242 32.000 0.00 0.00 0.00 1.75
2333 3272 7.611079 TGATTTTCTGTGATGAACCATGTGATA 59.389 33.333 0.00 0.00 0.00 2.15
2334 3273 6.434965 TGATTTTCTGTGATGAACCATGTGAT 59.565 34.615 0.00 0.00 0.00 3.06
2335 3274 5.769162 TGATTTTCTGTGATGAACCATGTGA 59.231 36.000 0.00 0.00 0.00 3.58
2336 3275 6.016213 TGATTTTCTGTGATGAACCATGTG 57.984 37.500 0.00 0.00 0.00 3.21
2337 3276 6.653526 TTGATTTTCTGTGATGAACCATGT 57.346 33.333 0.00 0.00 0.00 3.21
2338 3277 9.642327 TTATTTGATTTTCTGTGATGAACCATG 57.358 29.630 0.00 0.00 0.00 3.66
2363 3302 9.638239 ATTTGTCGTTGCACTATTTATTGAATT 57.362 25.926 0.00 0.00 0.00 2.17
2365 3304 9.767684 CTATTTGTCGTTGCACTATTTATTGAA 57.232 29.630 0.00 0.00 0.00 2.69
2366 3305 8.941977 ACTATTTGTCGTTGCACTATTTATTGA 58.058 29.630 0.00 0.00 0.00 2.57
2367 3306 9.554724 AACTATTTGTCGTTGCACTATTTATTG 57.445 29.630 0.00 0.00 0.00 1.90
2368 3307 9.769093 GAACTATTTGTCGTTGCACTATTTATT 57.231 29.630 0.00 0.00 0.00 1.40
2369 3308 8.941977 TGAACTATTTGTCGTTGCACTATTTAT 58.058 29.630 0.00 0.00 0.00 1.40
2370 3309 8.312896 TGAACTATTTGTCGTTGCACTATTTA 57.687 30.769 0.00 0.00 0.00 1.40
2371 3310 7.197071 TGAACTATTTGTCGTTGCACTATTT 57.803 32.000 0.00 0.00 0.00 1.40
2372 3311 6.795098 TGAACTATTTGTCGTTGCACTATT 57.205 33.333 0.00 0.00 0.00 1.73
2373 3312 6.795098 TTGAACTATTTGTCGTTGCACTAT 57.205 33.333 0.00 0.00 0.00 2.12
2374 3313 6.795098 ATTGAACTATTTGTCGTTGCACTA 57.205 33.333 0.00 0.00 0.00 2.74
2375 3314 5.689383 ATTGAACTATTTGTCGTTGCACT 57.311 34.783 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.