Multiple sequence alignment - TraesCS1A01G353900

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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 TraesCS1A01G353900 chr1A 100.000 2753 0 0 1 2753 537071902 537074654 0.000000e+00 5084
1 TraesCS1A01G353900 chr1A 88.512 1828 195 11 130 1950 537081860 537083679 0.000000e+00 2198
2 TraesCS1A01G353900 chr1A 81.319 1622 278 21 123 1731 537090060 537091669 0.000000e+00 1293
3 TraesCS1A01G353900 chr1A 81.376 1541 262 19 206 1733 537085540 537087068 0.000000e+00 1232
4 TraesCS1A01G353900 chr1A 89.068 558 42 8 2195 2752 537083912 537084450 0.000000e+00 675
5 TraesCS1A01G353900 chr1A 99.219 128 1 0 1 128 537081893 537082020 5.930000e-57 231
6 TraesCS1A01G353900 chr1B 90.399 1979 156 17 123 2099 598701203 598699257 0.000000e+00 2571
7 TraesCS1A01G353900 chr1B 83.569 1625 245 15 123 1733 598698239 598696623 0.000000e+00 1502
8 TraesCS1A01G353900 chr1B 80.961 1623 282 24 123 1733 598693160 598691553 0.000000e+00 1260
9 TraesCS1A01G353900 chr1B 81.134 1622 254 28 128 1733 598688853 598687268 0.000000e+00 1253
10 TraesCS1A01G353900 chr1B 80.802 474 68 14 2196 2666 598699258 598698805 1.570000e-92 350
11 TraesCS1A01G353900 chr1B 94.400 125 7 0 4 128 598698196 598698072 2.800000e-45 193
12 TraesCS1A01G353900 chr1B 92.473 93 7 0 2082 2174 653831703 653831795 1.720000e-27 134
13 TraesCS1A01G353900 chr1D 91.535 1831 143 10 123 1950 441019208 441017387 0.000000e+00 2512
14 TraesCS1A01G353900 chr1D 89.663 1867 165 15 123 1984 441032982 441031139 0.000000e+00 2353
15 TraesCS1A01G353900 chr1D 80.718 1587 271 30 165 1731 441016616 441015045 0.000000e+00 1203
16 TraesCS1A01G353900 chr1D 86.941 559 51 11 2195 2753 441031006 441030470 2.340000e-170 608
17 TraesCS1A01G353900 chr1D 86.889 389 41 5 2195 2581 441017156 441016776 7.050000e-116 427
18 TraesCS1A01G353900 chr1D 92.000 125 10 0 4 128 441019165 441019041 2.820000e-40 176
19 TraesCS1A01G353900 chr1D 93.023 86 6 0 43 128 441008051 441007966 2.880000e-25 126
20 TraesCS1A01G353900 chr7A 97.468 79 1 1 2096 2174 133633157 133633234 1.720000e-27 134
21 TraesCS1A01G353900 chr6D 97.468 79 1 1 2096 2174 450262707 450262784 1.720000e-27 134
22 TraesCS1A01G353900 chr3D 97.468 79 1 1 2096 2174 141460849 141460772 1.720000e-27 134
23 TraesCS1A01G353900 chr3D 95.122 82 3 1 2093 2174 445035123 445035203 8.000000e-26 128
24 TraesCS1A01G353900 chr2D 97.468 79 1 1 2096 2174 391295405 391295328 1.720000e-27 134
25 TraesCS1A01G353900 chr5D 96.203 79 2 1 2096 2174 254342990 254343067 8.000000e-26 128
26 TraesCS1A01G353900 chr2A 94.118 85 4 1 2090 2174 444648281 444648364 8.000000e-26 128
27 TraesCS1A01G353900 chr6B 94.048 84 3 2 2091 2173 292229 292311 2.880000e-25 126


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 TraesCS1A01G353900 chr1A 537071902 537074654 2752 False 5084.000000 5084 100.000000 1 2753 1 chr1A.!!$F1 2752
1 TraesCS1A01G353900 chr1A 537081860 537091669 9809 False 1125.800000 2198 87.898800 1 2752 5 chr1A.!!$F2 2751
2 TraesCS1A01G353900 chr1B 598687268 598701203 13935 True 1188.166667 2571 85.210833 4 2666 6 chr1B.!!$R1 2662
3 TraesCS1A01G353900 chr1D 441030470 441032982 2512 True 1480.500000 2353 88.302000 123 2753 2 chr1D.!!$R3 2630
4 TraesCS1A01G353900 chr1D 441015045 441019208 4163 True 1079.500000 2512 87.785500 4 2581 4 chr1D.!!$R2 2577

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
826 861 0.106967 GGAGAGGGAACAAGCCATCC 60.107 60.0 0.0 0.0 39.48 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 2257 0.183252 GGACGGAGGGAGTACTAGCT 59.817 60.0 0.0 0.0 0.0 3.32 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
86 120 1.690985 GTAAGAGGCTGGGAGGGCT 60.691 63.158 0.00 0.00 44.87 5.19
87 121 1.082954 TAAGAGGCTGGGAGGGCTT 59.917 57.895 0.00 0.00 42.23 4.35
88 122 0.550147 TAAGAGGCTGGGAGGGCTTT 60.550 55.000 0.00 0.00 42.23 3.51
89 123 1.857638 AAGAGGCTGGGAGGGCTTTC 61.858 60.000 0.00 0.00 42.23 2.62
90 124 2.204213 AGGCTGGGAGGGCTTTCT 60.204 61.111 0.00 0.00 39.07 2.52
91 125 2.044551 GGCTGGGAGGGCTTTCTG 60.045 66.667 0.00 0.00 0.00 3.02
92 126 2.759795 GCTGGGAGGGCTTTCTGT 59.240 61.111 0.00 0.00 0.00 3.41
93 127 1.075659 GCTGGGAGGGCTTTCTGTT 59.924 57.895 0.00 0.00 0.00 3.16
94 128 0.540597 GCTGGGAGGGCTTTCTGTTT 60.541 55.000 0.00 0.00 0.00 2.83
95 129 1.251251 CTGGGAGGGCTTTCTGTTTG 58.749 55.000 0.00 0.00 0.00 2.93
96 130 0.555769 TGGGAGGGCTTTCTGTTTGT 59.444 50.000 0.00 0.00 0.00 2.83
97 131 1.063266 TGGGAGGGCTTTCTGTTTGTT 60.063 47.619 0.00 0.00 0.00 2.83
98 132 2.039418 GGGAGGGCTTTCTGTTTGTTT 58.961 47.619 0.00 0.00 0.00 2.83
99 133 2.224042 GGGAGGGCTTTCTGTTTGTTTG 60.224 50.000 0.00 0.00 0.00 2.93
100 134 2.473816 GAGGGCTTTCTGTTTGTTTGC 58.526 47.619 0.00 0.00 0.00 3.68
101 135 1.202405 AGGGCTTTCTGTTTGTTTGCG 60.202 47.619 0.00 0.00 0.00 4.85
102 136 1.470805 GGGCTTTCTGTTTGTTTGCGT 60.471 47.619 0.00 0.00 0.00 5.24
103 137 2.267426 GGCTTTCTGTTTGTTTGCGTT 58.733 42.857 0.00 0.00 0.00 4.84
104 138 2.670905 GGCTTTCTGTTTGTTTGCGTTT 59.329 40.909 0.00 0.00 0.00 3.60
105 139 3.241963 GGCTTTCTGTTTGTTTGCGTTTC 60.242 43.478 0.00 0.00 0.00 2.78
106 140 3.366422 GCTTTCTGTTTGTTTGCGTTTCA 59.634 39.130 0.00 0.00 0.00 2.69
107 141 4.720946 GCTTTCTGTTTGTTTGCGTTTCAC 60.721 41.667 0.00 0.00 0.00 3.18
108 142 3.560902 TCTGTTTGTTTGCGTTTCACA 57.439 38.095 0.00 0.00 0.00 3.58
109 143 3.902150 TCTGTTTGTTTGCGTTTCACAA 58.098 36.364 0.00 0.00 0.00 3.33
110 144 4.489810 TCTGTTTGTTTGCGTTTCACAAT 58.510 34.783 0.00 0.00 30.64 2.71
111 145 4.325741 TCTGTTTGTTTGCGTTTCACAATG 59.674 37.500 0.00 0.00 30.64 2.82
112 146 3.369147 TGTTTGTTTGCGTTTCACAATGG 59.631 39.130 0.00 0.00 30.64 3.16
113 147 3.510388 TTGTTTGCGTTTCACAATGGA 57.490 38.095 0.00 0.00 0.00 3.41
114 148 3.510388 TGTTTGCGTTTCACAATGGAA 57.490 38.095 0.00 0.00 0.00 3.53
115 149 3.443037 TGTTTGCGTTTCACAATGGAAG 58.557 40.909 0.00 0.00 31.52 3.46
116 150 2.132740 TTGCGTTTCACAATGGAAGC 57.867 45.000 0.00 0.00 0.00 3.86
117 151 1.028130 TGCGTTTCACAATGGAAGCA 58.972 45.000 0.00 0.00 0.00 3.91
118 152 1.406898 TGCGTTTCACAATGGAAGCAA 59.593 42.857 0.00 0.00 28.69 3.91
119 153 2.035704 TGCGTTTCACAATGGAAGCAAT 59.964 40.909 0.00 0.00 28.69 3.56
120 154 2.663119 GCGTTTCACAATGGAAGCAATC 59.337 45.455 0.00 0.00 0.00 2.67
121 155 3.856638 GCGTTTCACAATGGAAGCAATCA 60.857 43.478 0.00 0.00 0.00 2.57
146 180 8.863049 CATTTCTGAAATTTATACCACACTTGC 58.137 33.333 12.74 0.00 0.00 4.01
161 195 1.423161 ACTTGCCCTTCTGAAGCTTCT 59.577 47.619 26.09 0.00 0.00 2.85
193 228 5.006649 TGTCAAAGTCATCGAGTCAACAAAG 59.993 40.000 0.00 0.00 0.00 2.77
309 344 3.885297 CTGTGGTTCTTGGTGATCTTGTT 59.115 43.478 0.00 0.00 0.00 2.83
430 465 3.673597 TCGAGGAGGCTGAGGGGT 61.674 66.667 0.00 0.00 0.00 4.95
432 467 2.039624 GAGGAGGCTGAGGGGTGA 59.960 66.667 0.00 0.00 0.00 4.02
462 497 1.814429 ACCGGGGGATGATACATCAA 58.186 50.000 6.32 0.00 40.69 2.57
591 626 2.430332 TCAATCCAATTTCAATCCGGCC 59.570 45.455 0.00 0.00 0.00 6.13
641 676 3.232213 TCAGATTGAGAGCACGGTAAC 57.768 47.619 0.00 0.00 0.00 2.50
697 732 1.755179 TCTTGGCCTAGAAAGCATGC 58.245 50.000 14.95 10.51 0.00 4.06
826 861 0.106967 GGAGAGGGAACAAGCCATCC 60.107 60.000 0.00 0.00 39.48 3.51
827 862 0.620556 GAGAGGGAACAAGCCATCCA 59.379 55.000 0.00 0.00 39.48 3.41
855 893 2.803451 CTACAAGCAGAGCTTCCGTAG 58.197 52.381 12.06 12.06 46.77 3.51
877 915 2.162681 GAAATGTGGGTGTCCTTCCAG 58.837 52.381 0.00 0.00 33.13 3.86
1155 1193 0.754217 GATGCATGCCACATGGGAGT 60.754 55.000 16.68 0.00 39.50 3.85
1170 1208 7.219322 CACATGGGAGTAAGATCATAATCACA 58.781 38.462 12.19 12.19 37.64 3.58
1185 1223 3.616956 ATCACAAGCCGATCAGAGAAA 57.383 42.857 0.00 0.00 0.00 2.52
1330 1368 2.306341 CATAGCCATGGAGATAGCCG 57.694 55.000 18.40 0.00 0.00 5.52
1409 1447 2.799017 TCTTAGTGCTCGGTTCTGGTA 58.201 47.619 0.00 0.00 0.00 3.25
1439 1477 4.087182 CTCAGACACCTTAGGGAGTACAA 58.913 47.826 2.32 0.00 36.57 2.41
1502 1540 5.308237 AGGAAGATCAGCCTCGGTATATTTT 59.692 40.000 0.00 0.00 0.00 1.82
1524 1562 1.948721 GCTTGGCTAAAAGGCGGCAT 61.949 55.000 13.08 0.00 44.78 4.40
1538 1576 1.871080 CGGCATGGTTCTGAGGATAC 58.129 55.000 0.00 0.00 0.00 2.24
1565 1603 5.066505 AGTTCCTTTTGCAAAGTAGTCACTG 59.933 40.000 12.41 0.00 34.36 3.66
1569 1607 1.593196 TGCAAAGTAGTCACTGCCAC 58.407 50.000 0.00 0.00 34.36 5.01
1575 1613 1.699634 AGTAGTCACTGCCACAATGGT 59.300 47.619 0.00 0.00 40.46 3.55
1594 1632 1.751927 CCTGCTTCTCATGGTGGGC 60.752 63.158 0.00 0.00 0.00 5.36
1609 1647 2.617021 GGTGGGCTTCCGAAGATAACAA 60.617 50.000 12.54 0.00 0.00 2.83
1612 1650 2.618709 GGGCTTCCGAAGATAACAATGG 59.381 50.000 12.54 0.00 0.00 3.16
1712 1750 2.915463 CGTACTACAGCTACACAACTGC 59.085 50.000 0.00 0.00 37.42 4.40
1732 1770 2.970324 GCGAGTTTGTCCGGCACA 60.970 61.111 0.00 0.00 0.00 4.57
1733 1771 2.954753 GCGAGTTTGTCCGGCACAG 61.955 63.158 0.00 0.00 35.97 3.66
1734 1772 2.946762 GAGTTTGTCCGGCACAGC 59.053 61.111 0.00 0.06 35.97 4.40
1799 1837 1.541147 CCGTGGTGACATTGCTTTGAT 59.459 47.619 0.00 0.00 46.14 2.57
1841 1881 1.135094 CTATGGACCATGGCTCACCT 58.865 55.000 17.73 0.00 36.63 4.00
1885 1925 3.445450 TGCTTTGCTGGTGTAAAAGTTGA 59.555 39.130 0.00 0.00 34.18 3.18
1888 1929 5.735922 GCTTTGCTGGTGTAAAAGTTGATGA 60.736 40.000 0.00 0.00 34.18 2.92
1889 1930 6.403866 TTTGCTGGTGTAAAAGTTGATGAT 57.596 33.333 0.00 0.00 0.00 2.45
1890 1931 7.517614 TTTGCTGGTGTAAAAGTTGATGATA 57.482 32.000 0.00 0.00 0.00 2.15
1891 1932 7.701539 TTGCTGGTGTAAAAGTTGATGATAT 57.298 32.000 0.00 0.00 0.00 1.63
1892 1933 7.701539 TGCTGGTGTAAAAGTTGATGATATT 57.298 32.000 0.00 0.00 0.00 1.28
1926 1974 4.179926 TCTGGTTCTTGACTCGATCTTG 57.820 45.455 0.00 0.00 0.00 3.02
1938 1986 7.436430 TGACTCGATCTTGTATGGAGTATAC 57.564 40.000 3.12 0.00 41.68 1.47
1942 1990 7.041030 ACTCGATCTTGTATGGAGTATACTGTG 60.041 40.741 10.90 0.00 41.82 3.66
1950 1998 7.295340 TGTATGGAGTATACTGTGACTGGTAT 58.705 38.462 10.90 6.90 41.82 2.73
1953 2001 4.215827 GGAGTATACTGTGACTGGTATCCG 59.784 50.000 10.90 0.00 31.98 4.18
1961 2098 4.476297 TGTGACTGGTATCCGGTACATAT 58.524 43.478 0.00 0.00 44.10 1.78
1968 2105 1.276622 ATCCGGTACATATGGCTCCC 58.723 55.000 7.80 0.27 0.00 4.30
1984 2121 2.355412 GCTCCCTAATTACCGGTTGTGT 60.355 50.000 15.04 0.00 0.00 3.72
1997 2157 4.399934 ACCGGTTGTGTTTGTAATCACTTT 59.600 37.500 0.00 0.00 35.82 2.66
2000 2160 5.276161 CGGTTGTGTTTGTAATCACTTTTGC 60.276 40.000 7.19 0.00 35.82 3.68
2001 2161 5.006261 GGTTGTGTTTGTAATCACTTTTGCC 59.994 40.000 7.19 0.00 35.82 4.52
2002 2162 5.330455 TGTGTTTGTAATCACTTTTGCCA 57.670 34.783 7.19 0.00 35.82 4.92
2019 2179 8.755977 ACTTTTGCCATCTTCATCTGAATAAAT 58.244 29.630 0.00 0.00 33.01 1.40
2029 2189 7.503566 TCTTCATCTGAATAAATAAGCCCTTGG 59.496 37.037 0.00 0.00 33.01 3.61
2043 2203 3.142174 GCCCTTGGCTAAGTAGCTAATG 58.858 50.000 9.16 7.05 46.38 1.90
2049 2209 6.258947 CCTTGGCTAAGTAGCTAATGTTTCTC 59.741 42.308 9.16 0.00 46.38 2.87
2054 2214 6.699642 GCTAAGTAGCTAATGTTTCTCCTCAG 59.300 42.308 0.00 0.00 45.62 3.35
2055 2215 6.859112 AAGTAGCTAATGTTTCTCCTCAGA 57.141 37.500 0.00 0.00 0.00 3.27
2059 2219 5.022787 AGCTAATGTTTCTCCTCAGACTCT 58.977 41.667 0.00 0.00 0.00 3.24
2060 2220 5.127031 AGCTAATGTTTCTCCTCAGACTCTC 59.873 44.000 0.00 0.00 0.00 3.20
2061 2221 5.127031 GCTAATGTTTCTCCTCAGACTCTCT 59.873 44.000 0.00 0.00 0.00 3.10
2096 2256 4.403752 TGTATAGAGCTGACACATCTTGCT 59.596 41.667 0.00 0.00 37.81 3.91
2097 2257 5.594317 TGTATAGAGCTGACACATCTTGCTA 59.406 40.000 0.00 0.00 36.15 3.49
2098 2258 3.523606 AGAGCTGACACATCTTGCTAG 57.476 47.619 0.00 0.00 36.15 3.42
2099 2259 1.932511 GAGCTGACACATCTTGCTAGC 59.067 52.381 8.10 8.10 36.15 3.42
2100 2260 1.554160 AGCTGACACATCTTGCTAGCT 59.446 47.619 17.23 0.00 40.93 3.32
2101 2261 2.762887 AGCTGACACATCTTGCTAGCTA 59.237 45.455 17.23 7.59 42.80 3.32
2102 2262 3.122297 GCTGACACATCTTGCTAGCTAG 58.878 50.000 18.70 18.70 35.56 3.42
2103 2263 3.430098 GCTGACACATCTTGCTAGCTAGT 60.430 47.826 22.75 9.99 35.56 2.57
2104 2264 4.202060 GCTGACACATCTTGCTAGCTAGTA 60.202 45.833 22.75 15.16 35.56 1.82
2105 2265 5.250235 TGACACATCTTGCTAGCTAGTAC 57.750 43.478 22.75 7.00 0.00 2.73
2106 2266 4.950475 TGACACATCTTGCTAGCTAGTACT 59.050 41.667 22.75 0.00 0.00 2.73
2107 2267 5.066634 TGACACATCTTGCTAGCTAGTACTC 59.933 44.000 22.75 12.91 0.00 2.59
2108 2268 4.339814 ACACATCTTGCTAGCTAGTACTCC 59.660 45.833 22.75 5.55 0.00 3.85
2109 2269 3.892588 ACATCTTGCTAGCTAGTACTCCC 59.107 47.826 22.75 4.84 0.00 4.30
2110 2270 3.955524 TCTTGCTAGCTAGTACTCCCT 57.044 47.619 22.75 0.00 0.00 4.20
2111 2271 3.822940 TCTTGCTAGCTAGTACTCCCTC 58.177 50.000 22.75 3.42 0.00 4.30
2112 2272 2.660670 TGCTAGCTAGTACTCCCTCC 57.339 55.000 21.62 2.71 0.00 4.30
2113 2273 1.202782 TGCTAGCTAGTACTCCCTCCG 60.203 57.143 21.62 0.00 0.00 4.63
2114 2274 1.202794 GCTAGCTAGTACTCCCTCCGT 60.203 57.143 21.62 0.00 0.00 4.69
2115 2275 2.769893 CTAGCTAGTACTCCCTCCGTC 58.230 57.143 12.92 0.00 0.00 4.79
2116 2276 0.183252 AGCTAGTACTCCCTCCGTCC 59.817 60.000 0.00 0.00 0.00 4.79
2117 2277 1.165284 GCTAGTACTCCCTCCGTCCG 61.165 65.000 0.00 0.00 0.00 4.79
2118 2278 1.153086 TAGTACTCCCTCCGTCCGC 60.153 63.158 0.00 0.00 0.00 5.54
2119 2279 1.913951 TAGTACTCCCTCCGTCCGCA 61.914 60.000 0.00 0.00 0.00 5.69
2120 2280 2.036098 TACTCCCTCCGTCCGCAA 59.964 61.111 0.00 0.00 0.00 4.85
2121 2281 1.607178 TACTCCCTCCGTCCGCAAA 60.607 57.895 0.00 0.00 0.00 3.68
2122 2282 1.186917 TACTCCCTCCGTCCGCAAAA 61.187 55.000 0.00 0.00 0.00 2.44
2123 2283 1.741770 CTCCCTCCGTCCGCAAAAG 60.742 63.158 0.00 0.00 0.00 2.27
2124 2284 3.431725 CCCTCCGTCCGCAAAAGC 61.432 66.667 0.00 0.00 0.00 3.51
2125 2285 2.358737 CCTCCGTCCGCAAAAGCT 60.359 61.111 0.00 0.00 0.00 3.74
2126 2286 1.966451 CCTCCGTCCGCAAAAGCTT 60.966 57.895 0.00 0.00 0.00 3.74
2127 2287 1.207593 CTCCGTCCGCAAAAGCTTG 59.792 57.895 0.00 0.00 35.49 4.01
2128 2288 1.507141 CTCCGTCCGCAAAAGCTTGT 61.507 55.000 0.00 0.00 34.79 3.16
2129 2289 1.082104 CCGTCCGCAAAAGCTTGTC 60.082 57.895 0.00 0.00 34.79 3.18
2130 2290 1.082104 CGTCCGCAAAAGCTTGTCC 60.082 57.895 0.00 0.00 34.79 4.02
2131 2291 1.285950 GTCCGCAAAAGCTTGTCCC 59.714 57.895 0.00 0.00 34.79 4.46
2132 2292 1.150536 TCCGCAAAAGCTTGTCCCT 59.849 52.632 0.00 0.00 34.79 4.20
2133 2293 0.889186 TCCGCAAAAGCTTGTCCCTC 60.889 55.000 0.00 0.00 34.79 4.30
2134 2294 1.172180 CCGCAAAAGCTTGTCCCTCA 61.172 55.000 0.00 0.00 34.79 3.86
2135 2295 0.667993 CGCAAAAGCTTGTCCCTCAA 59.332 50.000 0.00 0.00 34.79 3.02
2136 2296 1.066908 CGCAAAAGCTTGTCCCTCAAA 59.933 47.619 0.00 0.00 35.48 2.69
2137 2297 2.288395 CGCAAAAGCTTGTCCCTCAAAT 60.288 45.455 0.00 0.00 35.48 2.32
2138 2298 3.062042 GCAAAAGCTTGTCCCTCAAATG 58.938 45.455 0.00 0.00 35.48 2.32
2139 2299 3.656559 CAAAAGCTTGTCCCTCAAATGG 58.343 45.455 0.00 0.00 35.48 3.16
2140 2300 2.978156 AAGCTTGTCCCTCAAATGGA 57.022 45.000 0.00 0.00 35.48 3.41
2141 2301 3.463048 AAGCTTGTCCCTCAAATGGAT 57.537 42.857 0.00 0.00 35.48 3.41
2142 2302 2.731572 AGCTTGTCCCTCAAATGGATG 58.268 47.619 0.00 0.00 35.48 3.51
2143 2303 2.042162 AGCTTGTCCCTCAAATGGATGT 59.958 45.455 0.00 0.00 35.48 3.06
2144 2304 3.266772 AGCTTGTCCCTCAAATGGATGTA 59.733 43.478 0.00 0.00 35.48 2.29
2145 2305 4.079558 AGCTTGTCCCTCAAATGGATGTAT 60.080 41.667 0.00 0.00 35.48 2.29
2146 2306 4.276926 GCTTGTCCCTCAAATGGATGTATC 59.723 45.833 0.00 0.00 35.48 2.24
2147 2307 5.688807 CTTGTCCCTCAAATGGATGTATCT 58.311 41.667 0.00 0.00 35.48 1.98
2148 2308 6.688922 GCTTGTCCCTCAAATGGATGTATCTA 60.689 42.308 0.00 0.00 35.48 1.98
2149 2309 6.425210 TGTCCCTCAAATGGATGTATCTAG 57.575 41.667 0.00 0.00 33.65 2.43
2150 2310 5.221722 TGTCCCTCAAATGGATGTATCTAGC 60.222 44.000 0.00 0.00 33.65 3.42
2151 2311 4.907269 TCCCTCAAATGGATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
2152 2312 4.999950 CCCTCAAATGGATGTATCTAGCAC 59.000 45.833 0.00 0.00 0.00 4.40
2153 2313 4.999950 CCTCAAATGGATGTATCTAGCACC 59.000 45.833 0.00 0.00 0.00 5.01
2154 2314 5.455183 CCTCAAATGGATGTATCTAGCACCA 60.455 44.000 0.00 0.00 0.00 4.17
2155 2315 6.000246 TCAAATGGATGTATCTAGCACCAA 58.000 37.500 0.00 0.00 0.00 3.67
2156 2316 6.057533 TCAAATGGATGTATCTAGCACCAAG 58.942 40.000 0.00 0.00 0.00 3.61
2157 2317 5.636903 AATGGATGTATCTAGCACCAAGT 57.363 39.130 0.00 0.00 0.00 3.16
2158 2318 5.636903 ATGGATGTATCTAGCACCAAGTT 57.363 39.130 0.00 0.00 0.00 2.66
2159 2319 6.747414 ATGGATGTATCTAGCACCAAGTTA 57.253 37.500 0.00 0.00 0.00 2.24
2160 2320 6.161855 TGGATGTATCTAGCACCAAGTTAG 57.838 41.667 0.00 0.00 32.79 2.34
2161 2321 5.661312 TGGATGTATCTAGCACCAAGTTAGT 59.339 40.000 0.00 0.00 33.25 2.24
2162 2322 5.986135 GGATGTATCTAGCACCAAGTTAGTG 59.014 44.000 0.00 0.00 38.30 2.74
2174 2334 6.810911 CACCAAGTTAGTGCTAGATACATCT 58.189 40.000 0.00 0.00 40.86 2.90
2175 2335 7.941919 CACCAAGTTAGTGCTAGATACATCTA 58.058 38.462 0.00 0.00 38.32 1.98
2189 2349 9.462174 CTAGATACATCTAGCTTTGTTTCTCAG 57.538 37.037 12.18 10.39 46.80 3.35
2190 2350 8.072321 AGATACATCTAGCTTTGTTTCTCAGA 57.928 34.615 0.00 0.00 31.28 3.27
2191 2351 8.535335 AGATACATCTAGCTTTGTTTCTCAGAA 58.465 33.333 0.00 0.00 31.28 3.02
2192 2352 8.715191 ATACATCTAGCTTTGTTTCTCAGAAG 57.285 34.615 0.00 0.00 0.00 2.85
2193 2353 5.936956 ACATCTAGCTTTGTTTCTCAGAAGG 59.063 40.000 0.00 0.00 0.00 3.46
2219 2379 6.921914 AGTACTAACATCTAGCGTTGTTTCT 58.078 36.000 0.00 3.97 37.29 2.52
2241 2403 6.827727 TCTAACTACTTGAGAAGCCTGTTTT 58.172 36.000 0.00 0.00 0.00 2.43
2289 2451 0.670854 GAGGGTGACGAAGGACAAGC 60.671 60.000 0.00 0.00 0.00 4.01
2291 2453 0.321653 GGGTGACGAAGGACAAGCAT 60.322 55.000 0.00 0.00 0.00 3.79
2305 2467 2.281345 GCATCCTGGGCATCCTCG 60.281 66.667 0.00 0.00 0.00 4.63
2306 2468 2.429058 CATCCTGGGCATCCTCGG 59.571 66.667 0.00 0.00 0.00 4.63
2334 2496 2.480932 CGCAGATTCTCAGAAGCAGCTA 60.481 50.000 16.82 0.00 0.00 3.32
2335 2497 2.865551 GCAGATTCTCAGAAGCAGCTAC 59.134 50.000 12.43 0.00 0.00 3.58
2369 2531 2.748058 ATCCTGCCGCGAAGTTTGGT 62.748 55.000 8.23 0.00 0.00 3.67
2382 2544 4.201970 CGAAGTTTGGTACTTTTCAGCCAA 60.202 41.667 0.00 0.00 47.00 4.52
2383 2545 5.656480 GAAGTTTGGTACTTTTCAGCCAAA 58.344 37.500 3.78 3.78 47.00 3.28
2399 2561 2.227865 GCCAAAAGATGCTGGTTAACGA 59.772 45.455 0.00 0.00 34.97 3.85
2406 2568 3.935203 AGATGCTGGTTAACGATGTCTTG 59.065 43.478 0.00 0.00 0.00 3.02
2407 2569 3.120321 TGCTGGTTAACGATGTCTTGT 57.880 42.857 0.00 0.00 0.00 3.16
2408 2570 4.260139 TGCTGGTTAACGATGTCTTGTA 57.740 40.909 0.00 0.00 0.00 2.41
2409 2571 3.991773 TGCTGGTTAACGATGTCTTGTAC 59.008 43.478 0.00 0.00 0.00 2.90
2410 2572 3.991773 GCTGGTTAACGATGTCTTGTACA 59.008 43.478 0.00 0.00 43.86 2.90
2669 2838 1.067060 GCTTCAAGTTTCCACCACACC 59.933 52.381 0.00 0.00 0.00 4.16
2672 2841 1.142060 TCAAGTTTCCACCACACCGAT 59.858 47.619 0.00 0.00 0.00 4.18
2688 2857 7.993183 ACCACACCGATCTTTATTAAATCAGAT 59.007 33.333 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.159377 TCAATGACTTTGAATGGTTCGC 57.841 40.909 1.46 0.00 41.38 4.70
1 2 5.049474 TGACTCAATGACTTTGAATGGTTCG 60.049 40.000 5.40 0.00 43.64 3.95
2 3 6.317789 TGACTCAATGACTTTGAATGGTTC 57.682 37.500 5.40 0.00 43.64 3.62
3 4 5.278660 GCTGACTCAATGACTTTGAATGGTT 60.279 40.000 5.40 0.00 43.64 3.67
4 5 4.217118 GCTGACTCAATGACTTTGAATGGT 59.783 41.667 5.40 0.85 43.64 3.55
86 120 4.299155 TGTGAAACGCAAACAAACAGAAA 58.701 34.783 0.00 0.00 42.39 2.52
87 121 3.902150 TGTGAAACGCAAACAAACAGAA 58.098 36.364 0.00 0.00 42.39 3.02
88 122 3.560902 TGTGAAACGCAAACAAACAGA 57.439 38.095 0.00 0.00 42.39 3.41
89 123 4.492247 CCATTGTGAAACGCAAACAAACAG 60.492 41.667 0.00 0.00 42.39 3.16
90 124 3.369147 CCATTGTGAAACGCAAACAAACA 59.631 39.130 0.00 0.00 42.39 2.83
91 125 3.614616 TCCATTGTGAAACGCAAACAAAC 59.385 39.130 0.00 0.00 42.39 2.93
92 126 3.849911 TCCATTGTGAAACGCAAACAAA 58.150 36.364 0.00 0.00 42.39 2.83
93 127 3.510388 TCCATTGTGAAACGCAAACAA 57.490 38.095 0.00 0.00 42.39 2.83
94 128 3.443037 CTTCCATTGTGAAACGCAAACA 58.557 40.909 0.00 0.00 42.39 2.83
95 129 2.218530 GCTTCCATTGTGAAACGCAAAC 59.781 45.455 0.00 0.00 42.39 2.93
96 130 2.159184 TGCTTCCATTGTGAAACGCAAA 60.159 40.909 0.00 0.00 42.39 3.68
97 131 1.406898 TGCTTCCATTGTGAAACGCAA 59.593 42.857 0.00 0.00 42.39 4.85
98 132 1.028130 TGCTTCCATTGTGAAACGCA 58.972 45.000 0.00 0.00 42.39 5.24
99 133 2.132740 TTGCTTCCATTGTGAAACGC 57.867 45.000 0.00 0.00 42.39 4.84
100 134 3.899734 TGATTGCTTCCATTGTGAAACG 58.100 40.909 0.00 0.00 42.39 3.60
101 135 6.647895 AGAAATGATTGCTTCCATTGTGAAAC 59.352 34.615 0.00 0.00 33.70 2.78
102 136 6.647481 CAGAAATGATTGCTTCCATTGTGAAA 59.353 34.615 0.00 0.00 33.70 2.69
103 137 6.015265 TCAGAAATGATTGCTTCCATTGTGAA 60.015 34.615 0.00 0.00 33.70 3.18
104 138 5.477637 TCAGAAATGATTGCTTCCATTGTGA 59.522 36.000 0.00 0.00 33.70 3.58
105 139 5.716094 TCAGAAATGATTGCTTCCATTGTG 58.284 37.500 0.00 0.00 33.70 3.33
106 140 5.988310 TCAGAAATGATTGCTTCCATTGT 57.012 34.783 0.00 0.00 33.70 2.71
107 141 7.843490 ATTTCAGAAATGATTGCTTCCATTG 57.157 32.000 7.64 0.00 33.70 2.82
108 142 8.857694 AAATTTCAGAAATGATTGCTTCCATT 57.142 26.923 9.24 0.00 34.75 3.16
114 148 9.807649 GTGGTATAAATTTCAGAAATGATTGCT 57.192 29.630 9.24 0.00 0.00 3.91
115 149 9.585099 TGTGGTATAAATTTCAGAAATGATTGC 57.415 29.630 9.24 1.45 0.00 3.56
120 154 8.863049 GCAAGTGTGGTATAAATTTCAGAAATG 58.137 33.333 9.24 0.00 0.00 2.32
121 155 8.034804 GGCAAGTGTGGTATAAATTTCAGAAAT 58.965 33.333 2.20 2.20 0.00 2.17
146 180 2.865492 GCCAGAAGCTTCAGAAGGG 58.135 57.895 27.57 19.43 38.99 3.95
193 228 5.049398 TCTGAGCTCGAAAGACTTAAGAC 57.951 43.478 10.09 2.62 35.39 3.01
290 325 3.221771 CCAACAAGATCACCAAGAACCA 58.778 45.455 0.00 0.00 0.00 3.67
309 344 2.297315 CACGAAGGATATAGCTCTGCCA 59.703 50.000 0.00 0.00 0.00 4.92
430 465 0.536233 CCCCGGTTTGTGACACATCA 60.536 55.000 9.55 0.00 0.00 3.07
432 467 1.228429 CCCCCGGTTTGTGACACAT 60.228 57.895 9.55 0.00 0.00 3.21
462 497 1.358402 CTCTCGCATCGTGCTAGCT 59.642 57.895 17.23 0.00 42.25 3.32
641 676 4.676723 GCTCCTGACTGCTTACTCTAACAG 60.677 50.000 0.00 0.00 36.22 3.16
668 703 2.038557 TCTAGGCCAAGAACAACCTGTC 59.961 50.000 5.01 0.00 33.60 3.51
697 732 6.506500 AGCAAACTCCTTCATATCAACAAG 57.493 37.500 0.00 0.00 0.00 3.16
855 893 1.545841 GAAGGACACCCACATTTCCC 58.454 55.000 0.00 0.00 33.88 3.97
877 915 4.236935 CCAACATATGCAGAACCAACAAC 58.763 43.478 1.58 0.00 0.00 3.32
893 931 2.107204 ACAAGAGTGCTCTTCCCAACAT 59.893 45.455 11.15 0.00 46.13 2.71
945 983 3.823304 GCAAGATCAAGGAGAAGTGGTTT 59.177 43.478 0.00 0.00 0.00 3.27
948 986 3.055240 AGAGCAAGATCAAGGAGAAGTGG 60.055 47.826 0.00 0.00 0.00 4.00
1155 1193 6.758254 TGATCGGCTTGTGATTATGATCTTA 58.242 36.000 0.00 0.00 33.64 2.10
1170 1208 1.677217 GCCACTTTCTCTGATCGGCTT 60.677 52.381 0.00 0.00 35.17 4.35
1185 1223 0.550914 TTGTTCCAAGACTGGCCACT 59.449 50.000 0.00 0.00 43.17 4.00
1224 1262 8.779354 ACCAGTAAGCTTCTTTAGACAAATAG 57.221 34.615 0.00 0.00 0.00 1.73
1330 1368 9.685828 GTATAAGAAAGATCCACACATCTCTAC 57.314 37.037 0.00 0.00 31.44 2.59
1367 1405 3.325293 TTTCTCTCAGTAAGGCAGCAG 57.675 47.619 0.00 0.00 0.00 4.24
1409 1447 1.807814 AAGGTGTCTGAGAACCCTGT 58.192 50.000 9.27 0.00 37.13 4.00
1439 1477 7.335422 CACCTAACAACAAGATATTCTTCTGCT 59.665 37.037 0.00 0.00 33.78 4.24
1502 1540 0.960364 CCGCCTTTTAGCCAAGCTCA 60.960 55.000 0.00 0.00 40.44 4.26
1524 1562 5.590818 AGGAACTTAGTATCCTCAGAACCA 58.409 41.667 9.29 0.00 42.44 3.67
1538 1576 7.012421 AGTGACTACTTTGCAAAAGGAACTTAG 59.988 37.037 13.84 0.18 40.88 2.18
1549 1587 1.946768 GTGGCAGTGACTACTTTGCAA 59.053 47.619 0.00 0.00 34.07 4.08
1555 1593 1.699634 ACCATTGTGGCAGTGACTACT 59.300 47.619 0.00 0.00 42.67 2.57
1565 1603 0.610232 AGAAGCAGGACCATTGTGGC 60.610 55.000 0.00 0.00 42.67 5.01
1569 1607 2.022195 CCATGAGAAGCAGGACCATTG 58.978 52.381 0.00 0.00 0.00 2.82
1575 1613 1.993653 CCCACCATGAGAAGCAGGA 59.006 57.895 0.00 0.00 0.00 3.86
1594 1632 4.513442 TCCACCATTGTTATCTTCGGAAG 58.487 43.478 11.54 11.54 0.00 3.46
1609 1647 0.979665 CCGGATAGCAGATCCACCAT 59.020 55.000 15.72 0.00 38.08 3.55
1612 1650 0.601311 GTGCCGGATAGCAGATCCAC 60.601 60.000 5.05 8.83 45.14 4.02
1648 1686 4.152647 GACAAGACCTCAAATTTTCCCCT 58.847 43.478 0.00 0.00 0.00 4.79
1712 1750 2.250939 TGCCGGACAAACTCGCAAG 61.251 57.895 5.05 0.00 0.00 4.01
1732 1770 3.632333 TCTATGCTGTGGTACTACTGCT 58.368 45.455 31.07 22.01 43.37 4.24
1733 1771 4.038042 TCATCTATGCTGTGGTACTACTGC 59.962 45.833 27.08 27.08 43.30 4.40
1734 1772 5.774498 TCATCTATGCTGTGGTACTACTG 57.226 43.478 10.95 11.10 0.00 2.74
1799 1837 5.130477 AGACAAGAAGAGAACCACCAGTAAA 59.870 40.000 0.00 0.00 0.00 2.01
1841 1881 4.916041 AGGAAGTCTCATCAACCAATCA 57.084 40.909 0.00 0.00 0.00 2.57
1849 1889 2.816087 GCAAAGCAAGGAAGTCTCATCA 59.184 45.455 0.00 0.00 0.00 3.07
1892 1933 9.793259 AGTCAAGAACCAGATCAACTTAAATAA 57.207 29.630 0.00 0.00 0.00 1.40
1926 1974 7.094291 GGATACCAGTCACAGTATACTCCATAC 60.094 44.444 1.26 0.00 39.99 2.39
1938 1986 2.097036 TGTACCGGATACCAGTCACAG 58.903 52.381 9.46 0.00 32.16 3.66
1942 1990 3.368116 GCCATATGTACCGGATACCAGTC 60.368 52.174 9.46 0.00 32.16 3.51
1950 1998 0.190069 AGGGAGCCATATGTACCGGA 59.810 55.000 9.46 0.00 0.00 5.14
1953 2001 5.626116 CGGTAATTAGGGAGCCATATGTACC 60.626 48.000 1.24 9.24 0.00 3.34
1961 2098 1.210967 CAACCGGTAATTAGGGAGCCA 59.789 52.381 8.00 0.00 0.00 4.75
1968 2105 7.747357 GTGATTACAAACACAACCGGTAATTAG 59.253 37.037 8.00 0.00 35.46 1.73
1984 2121 7.048629 TGAAGATGGCAAAAGTGATTACAAA 57.951 32.000 0.00 0.00 0.00 2.83
1997 2157 8.355169 GCTTATTTATTCAGATGAAGATGGCAA 58.645 33.333 0.00 0.00 37.48 4.52
2000 2160 7.668886 AGGGCTTATTTATTCAGATGAAGATGG 59.331 37.037 1.32 0.00 37.48 3.51
2001 2161 8.632906 AGGGCTTATTTATTCAGATGAAGATG 57.367 34.615 1.32 0.00 37.48 2.90
2002 2162 9.075678 CAAGGGCTTATTTATTCAGATGAAGAT 57.924 33.333 1.32 0.00 37.48 2.40
2040 2200 6.432403 AAAGAGAGTCTGAGGAGAAACATT 57.568 37.500 0.00 0.00 0.00 2.71
2066 2226 8.531982 AGATGTGTCAGCTCTATACAAAAAGTA 58.468 33.333 0.12 0.00 37.06 2.24
2071 2231 5.582269 GCAAGATGTGTCAGCTCTATACAAA 59.418 40.000 0.12 0.00 0.00 2.83
2072 2232 5.105187 AGCAAGATGTGTCAGCTCTATACAA 60.105 40.000 0.12 0.00 34.26 2.41
2079 2239 1.932511 GCTAGCAAGATGTGTCAGCTC 59.067 52.381 10.63 0.00 38.44 4.09
2088 2248 4.148838 AGGGAGTACTAGCTAGCAAGATG 58.851 47.826 20.91 4.30 0.00 2.90
2096 2256 1.419387 GGACGGAGGGAGTACTAGCTA 59.581 57.143 0.00 0.00 0.00 3.32
2097 2257 0.183252 GGACGGAGGGAGTACTAGCT 59.817 60.000 0.00 0.00 0.00 3.32
2098 2258 1.165284 CGGACGGAGGGAGTACTAGC 61.165 65.000 0.00 0.00 0.00 3.42
2099 2259 1.165284 GCGGACGGAGGGAGTACTAG 61.165 65.000 0.00 0.00 0.00 2.57
2100 2260 1.153086 GCGGACGGAGGGAGTACTA 60.153 63.158 0.00 0.00 0.00 1.82
2101 2261 2.439883 GCGGACGGAGGGAGTACT 60.440 66.667 0.00 0.00 0.00 2.73
2102 2262 1.880819 TTTGCGGACGGAGGGAGTAC 61.881 60.000 0.00 0.00 0.00 2.73
2103 2263 1.186917 TTTTGCGGACGGAGGGAGTA 61.187 55.000 0.00 0.00 0.00 2.59
2104 2264 2.450479 CTTTTGCGGACGGAGGGAGT 62.450 60.000 0.00 0.00 0.00 3.85
2105 2265 1.741770 CTTTTGCGGACGGAGGGAG 60.742 63.158 0.00 0.00 0.00 4.30
2106 2266 2.345991 CTTTTGCGGACGGAGGGA 59.654 61.111 0.00 0.00 0.00 4.20
2107 2267 3.431725 GCTTTTGCGGACGGAGGG 61.432 66.667 0.00 0.00 34.86 4.30
2117 2277 7.535624 ATCCATTTGAGGGACAAGCTTTTGC 62.536 44.000 0.00 0.00 40.94 3.68
2118 2278 3.321682 TCCATTTGAGGGACAAGCTTTTG 59.678 43.478 0.00 0.00 39.77 2.44
2119 2279 3.575805 TCCATTTGAGGGACAAGCTTTT 58.424 40.909 0.00 0.00 39.77 2.27
2120 2280 3.243359 TCCATTTGAGGGACAAGCTTT 57.757 42.857 0.00 0.00 39.77 3.51
2121 2281 2.978156 TCCATTTGAGGGACAAGCTT 57.022 45.000 0.00 0.00 39.77 3.74
2122 2282 2.042162 ACATCCATTTGAGGGACAAGCT 59.958 45.455 0.00 0.00 39.77 3.74
2123 2283 2.450476 ACATCCATTTGAGGGACAAGC 58.550 47.619 0.00 0.00 39.77 4.01
2124 2284 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
2125 2285 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
2126 2286 5.221722 GCTAGATACATCCATTTGAGGGACA 60.222 44.000 0.00 0.00 37.23 4.02
2127 2287 5.221722 TGCTAGATACATCCATTTGAGGGAC 60.222 44.000 0.00 0.00 37.23 4.46
2128 2288 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
2129 2289 4.999950 GTGCTAGATACATCCATTTGAGGG 59.000 45.833 0.00 0.00 0.00 4.30
2130 2290 4.999950 GGTGCTAGATACATCCATTTGAGG 59.000 45.833 0.00 0.00 0.00 3.86
2131 2291 5.614308 TGGTGCTAGATACATCCATTTGAG 58.386 41.667 0.00 0.00 0.00 3.02
2132 2292 5.628797 TGGTGCTAGATACATCCATTTGA 57.371 39.130 0.00 0.00 0.00 2.69
2133 2293 5.824624 ACTTGGTGCTAGATACATCCATTTG 59.175 40.000 0.00 0.00 0.00 2.32
2134 2294 6.006275 ACTTGGTGCTAGATACATCCATTT 57.994 37.500 0.00 0.00 0.00 2.32
2135 2295 5.636903 ACTTGGTGCTAGATACATCCATT 57.363 39.130 0.00 0.00 0.00 3.16
2136 2296 5.636903 AACTTGGTGCTAGATACATCCAT 57.363 39.130 0.00 0.00 0.00 3.41
2137 2297 5.661312 ACTAACTTGGTGCTAGATACATCCA 59.339 40.000 0.00 0.00 0.00 3.41
2138 2298 5.986135 CACTAACTTGGTGCTAGATACATCC 59.014 44.000 0.00 0.00 0.00 3.51
2149 2309 7.470147 TAGATGTATCTAGCACTAACTTGGTGC 60.470 40.741 19.67 19.67 46.34 5.01
2150 2310 6.810911 AGATGTATCTAGCACTAACTTGGTG 58.189 40.000 0.97 0.97 34.85 4.17
2151 2311 8.172352 CTAGATGTATCTAGCACTAACTTGGT 57.828 38.462 14.14 0.00 46.80 3.67
2164 2324 9.190317 TCTGAGAAACAAAGCTAGATGTATCTA 57.810 33.333 0.00 1.95 38.32 1.98
2165 2325 8.072321 TCTGAGAAACAAAGCTAGATGTATCT 57.928 34.615 0.00 0.00 40.86 1.98
2166 2326 8.709386 TTCTGAGAAACAAAGCTAGATGTATC 57.291 34.615 0.00 0.00 0.00 2.24
2167 2327 7.768120 CCTTCTGAGAAACAAAGCTAGATGTAT 59.232 37.037 0.00 0.00 0.00 2.29
2168 2328 7.099764 CCTTCTGAGAAACAAAGCTAGATGTA 58.900 38.462 0.00 0.00 0.00 2.29
2169 2329 5.936956 CCTTCTGAGAAACAAAGCTAGATGT 59.063 40.000 0.00 0.00 0.00 3.06
2170 2330 5.936956 ACCTTCTGAGAAACAAAGCTAGATG 59.063 40.000 0.00 0.00 0.00 2.90
2171 2331 6.120507 ACCTTCTGAGAAACAAAGCTAGAT 57.879 37.500 0.00 0.00 0.00 1.98
2172 2332 5.552870 ACCTTCTGAGAAACAAAGCTAGA 57.447 39.130 0.00 0.00 0.00 2.43
2173 2333 6.459923 ACTACCTTCTGAGAAACAAAGCTAG 58.540 40.000 0.00 0.00 0.00 3.42
2174 2334 6.420913 ACTACCTTCTGAGAAACAAAGCTA 57.579 37.500 0.00 0.00 0.00 3.32
2175 2335 5.297569 ACTACCTTCTGAGAAACAAAGCT 57.702 39.130 0.00 0.00 0.00 3.74
2176 2336 6.224584 AGTACTACCTTCTGAGAAACAAAGC 58.775 40.000 0.00 0.00 0.00 3.51
2177 2337 9.194271 GTTAGTACTACCTTCTGAGAAACAAAG 57.806 37.037 0.91 0.00 0.00 2.77
2178 2338 8.698210 TGTTAGTACTACCTTCTGAGAAACAAA 58.302 33.333 0.91 0.00 0.00 2.83
2179 2339 8.241497 TGTTAGTACTACCTTCTGAGAAACAA 57.759 34.615 0.91 0.00 0.00 2.83
2180 2340 7.828508 TGTTAGTACTACCTTCTGAGAAACA 57.171 36.000 0.91 0.00 0.00 2.83
2181 2341 8.741841 AGATGTTAGTACTACCTTCTGAGAAAC 58.258 37.037 13.08 3.22 0.00 2.78
2182 2342 8.880991 AGATGTTAGTACTACCTTCTGAGAAA 57.119 34.615 13.08 0.00 0.00 2.52
2183 2343 9.616156 CTAGATGTTAGTACTACCTTCTGAGAA 57.384 37.037 19.83 0.00 0.00 2.87
2184 2344 7.716123 GCTAGATGTTAGTACTACCTTCTGAGA 59.284 40.741 19.83 5.56 0.00 3.27
2185 2345 7.307514 CGCTAGATGTTAGTACTACCTTCTGAG 60.308 44.444 19.83 14.93 0.00 3.35
2186 2346 6.482641 CGCTAGATGTTAGTACTACCTTCTGA 59.517 42.308 19.83 8.27 0.00 3.27
2187 2347 6.260493 ACGCTAGATGTTAGTACTACCTTCTG 59.740 42.308 19.83 13.20 0.00 3.02
2188 2348 6.355747 ACGCTAGATGTTAGTACTACCTTCT 58.644 40.000 16.63 16.63 0.00 2.85
2189 2349 6.616774 ACGCTAGATGTTAGTACTACCTTC 57.383 41.667 0.91 3.70 0.00 3.46
2190 2350 6.376581 ACAACGCTAGATGTTAGTACTACCTT 59.623 38.462 0.91 0.00 28.35 3.50
2191 2351 5.884792 ACAACGCTAGATGTTAGTACTACCT 59.115 40.000 0.91 0.87 28.35 3.08
2192 2352 6.129053 ACAACGCTAGATGTTAGTACTACC 57.871 41.667 0.91 0.00 28.35 3.18
2193 2353 7.967303 AGAAACAACGCTAGATGTTAGTACTAC 59.033 37.037 0.91 0.00 41.56 2.73
2219 2379 6.354130 ACAAAACAGGCTTCTCAAGTAGTTA 58.646 36.000 0.00 0.00 0.00 2.24
2241 2403 1.538946 CGCCGTCGTTCGTGTAAACA 61.539 55.000 0.00 0.00 37.94 2.83
2260 2422 1.217779 GTCACCCTCTCTGAGCAGC 59.782 63.158 0.00 0.00 0.00 5.25
2289 2451 2.429058 CCGAGGATGCCCAGGATG 59.571 66.667 0.00 0.00 35.38 3.51
2305 2467 2.590007 AGAATCTGCGCCGATGCC 60.590 61.111 15.38 10.19 0.00 4.40
2306 2468 1.829349 CTGAGAATCTGCGCCGATGC 61.829 60.000 15.38 13.46 34.92 3.91
2382 2544 4.579869 AGACATCGTTAACCAGCATCTTT 58.420 39.130 0.00 0.00 0.00 2.52
2383 2545 4.207891 AGACATCGTTAACCAGCATCTT 57.792 40.909 0.00 0.00 0.00 2.40
2384 2546 3.895232 AGACATCGTTAACCAGCATCT 57.105 42.857 0.00 0.00 0.00 2.90
2406 2568 6.583050 GTGAGTGATGTTGTCTTCTACTGTAC 59.417 42.308 0.00 0.00 0.00 2.90
2407 2569 6.264518 TGTGAGTGATGTTGTCTTCTACTGTA 59.735 38.462 0.00 0.00 0.00 2.74
2408 2570 5.069119 TGTGAGTGATGTTGTCTTCTACTGT 59.931 40.000 0.00 0.00 0.00 3.55
2409 2571 5.403766 GTGTGAGTGATGTTGTCTTCTACTG 59.596 44.000 0.00 0.00 0.00 2.74
2410 2572 5.533482 GTGTGAGTGATGTTGTCTTCTACT 58.467 41.667 0.00 0.00 0.00 2.57
2443 2605 0.868406 GGTTGCCTGAACTGAACTCG 59.132 55.000 0.00 0.00 34.66 4.18
2701 2870 7.812309 TGTTATGACAGACGAAAAGTATCTG 57.188 36.000 0.00 0.00 44.49 2.90
2731 2900 1.452145 TTGACCCAGCCAACGAAAGC 61.452 55.000 0.00 0.00 0.00 3.51
2733 2902 1.698506 ATTTGACCCAGCCAACGAAA 58.301 45.000 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.