Multiple sequence alignment - TraesCS4A01G032400

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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 TraesCS4A01G032400 chr4A 100.000 2366 0 0 1 2366 24864946 24862581 0.000000e+00 4370
1 TraesCS4A01G032400 chr7D 89.816 2062 195 9 103 2161 182612737 182610688 0.000000e+00 2630
2 TraesCS4A01G032400 chr7D 88.372 86 7 3 25 110 33813417 33813335 1.500000e-17 100
3 TraesCS4A01G032400 chr5D 89.704 2059 199 8 107 2161 108339556 108341605 0.000000e+00 2615
4 TraesCS4A01G032400 chr5D 88.378 2065 227 11 103 2161 430529954 430532011 0.000000e+00 2471
5 TraesCS4A01G032400 chr1A 89.148 2055 204 13 115 2161 561700296 561698253 0.000000e+00 2542
6 TraesCS4A01G032400 chr4D 88.766 2074 211 14 103 2168 23273968 23271909 0.000000e+00 2519
7 TraesCS4A01G032400 chr4D 88.415 2063 232 7 103 2161 35486786 35488845 0.000000e+00 2479
8 TraesCS4A01G032400 chr4D 85.648 216 6 13 2170 2366 442549134 442549343 1.110000e-48 204
9 TraesCS4A01G032400 chr2D 88.636 2068 222 9 103 2161 549979825 549981888 0.000000e+00 2505
10 TraesCS4A01G032400 chr2D 88.588 2068 214 12 111 2161 549504377 549506439 0.000000e+00 2492
11 TraesCS4A01G032400 chr3D 88.463 2063 222 11 103 2161 429313525 429311475 0.000000e+00 2477
12 TraesCS4A01G032400 chr5A 81.548 168 22 6 109 271 504238888 504238725 1.910000e-26 130


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 TraesCS4A01G032400 chr4A 24862581 24864946 2365 True 4370 4370 100.000 1 2366 1 chr4A.!!$R1 2365
1 TraesCS4A01G032400 chr7D 182610688 182612737 2049 True 2630 2630 89.816 103 2161 1 chr7D.!!$R2 2058
2 TraesCS4A01G032400 chr5D 108339556 108341605 2049 False 2615 2615 89.704 107 2161 1 chr5D.!!$F1 2054
3 TraesCS4A01G032400 chr5D 430529954 430532011 2057 False 2471 2471 88.378 103 2161 1 chr5D.!!$F2 2058
4 TraesCS4A01G032400 chr1A 561698253 561700296 2043 True 2542 2542 89.148 115 2161 1 chr1A.!!$R1 2046
5 TraesCS4A01G032400 chr4D 23271909 23273968 2059 True 2519 2519 88.766 103 2168 1 chr4D.!!$R1 2065
6 TraesCS4A01G032400 chr4D 35486786 35488845 2059 False 2479 2479 88.415 103 2161 1 chr4D.!!$F1 2058
7 TraesCS4A01G032400 chr2D 549979825 549981888 2063 False 2505 2505 88.636 103 2161 1 chr2D.!!$F2 2058
8 TraesCS4A01G032400 chr2D 549504377 549506439 2062 False 2492 2492 88.588 111 2161 1 chr2D.!!$F1 2050
9 TraesCS4A01G032400 chr3D 429311475 429313525 2050 True 2477 2477 88.463 103 2161 1 chr3D.!!$R1 2058

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
82 83 0.034863 GTGACCCATTTCCGGCCTAA 60.035 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 2009 0.106268 TCTTGGTCTTGGCTTTGGCA 60.106 50.0 0.0 0.0 40.87 4.92 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
26 27 1.247567 AAAAATGACCCAGCACTCCG 58.752 50.000 0.00 0.00 0.00 4.63
27 28 0.400213 AAAATGACCCAGCACTCCGA 59.600 50.000 0.00 0.00 0.00 4.55
28 29 0.321653 AAATGACCCAGCACTCCGAC 60.322 55.000 0.00 0.00 0.00 4.79
29 30 2.185310 AATGACCCAGCACTCCGACC 62.185 60.000 0.00 0.00 0.00 4.79
30 31 4.083862 GACCCAGCACTCCGACCC 62.084 72.222 0.00 0.00 0.00 4.46
31 32 4.954118 ACCCAGCACTCCGACCCA 62.954 66.667 0.00 0.00 0.00 4.51
32 33 3.636231 CCCAGCACTCCGACCCAA 61.636 66.667 0.00 0.00 0.00 4.12
33 34 2.429930 CCAGCACTCCGACCCAAA 59.570 61.111 0.00 0.00 0.00 3.28
34 35 1.966451 CCAGCACTCCGACCCAAAC 60.966 63.158 0.00 0.00 0.00 2.93
35 36 2.030562 AGCACTCCGACCCAAACG 59.969 61.111 0.00 0.00 0.00 3.60
45 46 4.160635 CCCAAACGGACGCGCATC 62.161 66.667 5.73 0.00 0.00 3.91
46 47 4.160635 CCAAACGGACGCGCATCC 62.161 66.667 13.66 13.66 35.16 3.51
64 65 3.884900 GCTTGGCGTTCGTATGGT 58.115 55.556 0.00 0.00 0.00 3.55
65 66 1.423845 GCTTGGCGTTCGTATGGTG 59.576 57.895 0.00 0.00 0.00 4.17
66 67 1.017177 GCTTGGCGTTCGTATGGTGA 61.017 55.000 0.00 0.00 0.00 4.02
67 68 0.719465 CTTGGCGTTCGTATGGTGAC 59.281 55.000 0.00 0.00 0.00 3.67
68 69 0.671163 TTGGCGTTCGTATGGTGACC 60.671 55.000 0.00 0.00 0.00 4.02
69 70 1.812507 GGCGTTCGTATGGTGACCC 60.813 63.158 0.00 0.00 0.00 4.46
78 79 2.034999 TGGTGACCCATTTCCGGC 59.965 61.111 0.00 0.00 35.17 6.13
79 80 2.754254 GGTGACCCATTTCCGGCC 60.754 66.667 0.00 0.00 0.00 6.13
80 81 2.355115 GTGACCCATTTCCGGCCT 59.645 61.111 0.00 0.00 0.00 5.19
81 82 1.605453 GTGACCCATTTCCGGCCTA 59.395 57.895 0.00 0.00 0.00 3.93
82 83 0.034863 GTGACCCATTTCCGGCCTAA 60.035 55.000 0.00 0.00 0.00 2.69
83 84 0.923358 TGACCCATTTCCGGCCTAAT 59.077 50.000 0.00 0.00 0.00 1.73
84 85 1.286553 TGACCCATTTCCGGCCTAATT 59.713 47.619 0.00 0.00 0.00 1.40
85 86 2.291930 TGACCCATTTCCGGCCTAATTT 60.292 45.455 0.00 0.00 0.00 1.82
86 87 2.764010 GACCCATTTCCGGCCTAATTTT 59.236 45.455 0.00 0.00 0.00 1.82
87 88 3.955551 GACCCATTTCCGGCCTAATTTTA 59.044 43.478 0.00 0.00 0.00 1.52
88 89 4.354662 ACCCATTTCCGGCCTAATTTTAA 58.645 39.130 0.00 0.00 0.00 1.52
89 90 4.404394 ACCCATTTCCGGCCTAATTTTAAG 59.596 41.667 0.00 0.00 0.00 1.85
90 91 4.368315 CCATTTCCGGCCTAATTTTAAGC 58.632 43.478 0.00 0.00 0.00 3.09
91 92 4.368315 CATTTCCGGCCTAATTTTAAGCC 58.632 43.478 0.00 0.62 36.99 4.35
97 98 4.665833 GGCCTAATTTTAAGCCGGATTT 57.334 40.909 11.69 3.16 31.20 2.17
98 99 4.368315 GGCCTAATTTTAAGCCGGATTTG 58.632 43.478 11.69 0.00 31.20 2.32
99 100 3.802139 GCCTAATTTTAAGCCGGATTTGC 59.198 43.478 11.69 0.20 0.00 3.68
100 101 4.679372 GCCTAATTTTAAGCCGGATTTGCA 60.679 41.667 11.69 0.00 0.00 4.08
101 102 5.600696 CCTAATTTTAAGCCGGATTTGCAT 58.399 37.500 11.69 0.00 0.00 3.96
105 106 1.029408 TAAGCCGGATTTGCATGCGT 61.029 50.000 11.69 0.88 42.41 5.24
120 121 2.885861 CGTGCGCCTACTCCTCTT 59.114 61.111 4.18 0.00 0.00 2.85
126 127 2.798364 GCCTACTCCTCTTCCCGGC 61.798 68.421 0.00 0.00 0.00 6.13
128 129 1.075896 CTACTCCTCTTCCCGGCCT 60.076 63.158 0.00 0.00 0.00 5.19
131 132 4.377760 TCCTCTTCCCGGCCTCGT 62.378 66.667 0.00 0.00 33.95 4.18
154 156 2.045926 GGTAGCAGCCACCACCAG 60.046 66.667 4.93 0.00 36.01 4.00
159 161 2.839098 CAGCCACCACCAGTTCCT 59.161 61.111 0.00 0.00 0.00 3.36
169 171 2.225117 CCACCAGTTCCTCCATTTTCCT 60.225 50.000 0.00 0.00 0.00 3.36
170 172 3.500343 CACCAGTTCCTCCATTTTCCTT 58.500 45.455 0.00 0.00 0.00 3.36
213 225 2.733669 CCGCCCCACACCCGTTATA 61.734 63.158 0.00 0.00 0.00 0.98
216 228 0.542805 GCCCCACACCCGTTATAGAA 59.457 55.000 0.00 0.00 0.00 2.10
278 290 4.129737 CTCGTCCGGCGTCACCAT 62.130 66.667 16.00 0.00 42.13 3.55
424 436 2.758327 ACGCGAGGTATGAGGCCA 60.758 61.111 15.93 0.00 0.00 5.36
514 526 0.319125 GGAGGCGCTCTACATGCTAC 60.319 60.000 7.64 0.00 0.00 3.58
522 534 4.049186 CGCTCTACATGCTACGGTTAAAT 58.951 43.478 0.00 0.00 0.00 1.40
535 547 2.679639 CGGTTAAATCCTAGCCAGCACA 60.680 50.000 0.00 0.00 0.00 4.57
540 552 1.277580 ATCCTAGCCAGCACAGCCTT 61.278 55.000 0.00 0.00 0.00 4.35
595 608 1.672854 ATCGGCGTTTCCTCGGATGA 61.673 55.000 6.85 0.00 0.00 2.92
660 673 0.321298 GCTTCCACGTGTACCCACAT 60.321 55.000 15.65 0.00 41.93 3.21
663 676 2.387445 CCACGTGTACCCACATGCG 61.387 63.158 15.65 0.00 44.22 4.73
667 680 1.295423 GTGTACCCACATGCGTCCT 59.705 57.895 0.00 0.00 41.44 3.85
672 685 2.360350 CCACATGCGTCCTGCCTT 60.360 61.111 0.00 0.00 45.60 4.35
776 796 2.678580 TGGTGGCTCGTCATCCGA 60.679 61.111 0.00 0.00 45.00 4.55
841 861 1.525077 GACACCCGCAACCTGTTCA 60.525 57.895 0.00 0.00 0.00 3.18
895 915 1.895798 TGCAGAACCTCATCTTCGAGT 59.104 47.619 0.00 0.00 0.00 4.18
946 966 0.249868 CGAGACACAAAGCCAGGACA 60.250 55.000 0.00 0.00 0.00 4.02
951 971 2.281761 CAAAGCCAGGACAGCCGT 60.282 61.111 0.00 0.00 39.96 5.68
992 1012 1.122019 GGCTATGATCCCGACCAGGT 61.122 60.000 0.00 0.00 38.74 4.00
1015 1035 1.405933 CCTTCATGCGTGATCAGGTCA 60.406 52.381 15.84 14.22 33.56 4.02
1141 1161 4.577677 TCGCCAACCAAGCTGCCA 62.578 61.111 0.00 0.00 0.00 4.92
1215 1235 0.308993 ACAAGCTTCTTTGCGAGTGC 59.691 50.000 0.00 0.00 43.20 4.40
1237 1257 1.291877 GCGCGACATTGGACAAGACT 61.292 55.000 12.10 0.00 0.00 3.24
1302 1323 4.666655 CGTGTCCATCGAAAGTTTCATGAC 60.667 45.833 20.42 16.76 0.00 3.06
1344 1366 1.366111 AATTTATGAGCACGCGCGGT 61.366 50.000 35.22 18.51 45.49 5.68
1361 1383 1.269448 CGGTTGGGTGTCCATTTTCAG 59.731 52.381 0.00 0.00 43.63 3.02
1369 1391 2.493278 GTGTCCATTTTCAGGTGATGGG 59.507 50.000 2.12 0.00 40.55 4.00
1392 1414 4.502950 GGGGTGATTCAACAAGATTGCAAA 60.503 41.667 1.71 0.00 0.00 3.68
1428 1450 4.070552 GAGAGCGTCAAGGCCCGT 62.071 66.667 0.00 0.00 0.00 5.28
1471 1493 3.567164 GCAAGACATGGTATGCTAGCAAT 59.433 43.478 23.54 12.76 39.89 3.56
1512 1536 1.597742 AGTTCATGCTTGCGTGTTCT 58.402 45.000 13.58 10.37 0.00 3.01
1516 1540 4.036262 AGTTCATGCTTGCGTGTTCTTTTA 59.964 37.500 13.58 0.00 0.00 1.52
1517 1541 4.764679 TCATGCTTGCGTGTTCTTTTAT 57.235 36.364 13.58 0.00 0.00 1.40
1518 1542 4.475028 TCATGCTTGCGTGTTCTTTTATG 58.525 39.130 13.58 0.00 0.00 1.90
1588 1614 2.037641 GCTTTGGAGGCATTCAAGGTTT 59.962 45.455 3.30 0.00 0.00 3.27
1591 1617 5.741673 GCTTTGGAGGCATTCAAGGTTTAAA 60.742 40.000 3.30 0.00 0.00 1.52
1611 1637 1.032014 ACAACGGCAAGTGCTTCAAT 58.968 45.000 2.85 0.00 41.70 2.57
1707 1733 2.747855 GAAGCAAGCCGTGGAGGG 60.748 66.667 0.00 0.00 41.48 4.30
1785 1812 2.256591 GCGAGATGCGGCATCCAAT 61.257 57.895 33.01 19.13 41.36 3.16
1831 1858 5.469421 GGCATGATGAATAAGAAGGACTCAG 59.531 44.000 0.00 0.00 0.00 3.35
1870 1897 4.094887 GGCGTTTCATAGAAGAGCAAATGA 59.905 41.667 9.49 0.00 0.00 2.57
1875 1902 3.623060 TCATAGAAGAGCAAATGAACGCC 59.377 43.478 0.00 0.00 0.00 5.68
1882 1909 2.161855 AGCAAATGAACGCCTTCATGA 58.838 42.857 11.07 0.00 44.93 3.07
1891 1918 3.287867 ACGCCTTCATGAAGATCCAAT 57.712 42.857 32.49 11.72 40.79 3.16
1893 1920 3.208594 CGCCTTCATGAAGATCCAATGA 58.791 45.455 32.49 0.00 40.79 2.57
1914 1941 1.219124 GAGGCTTGAGATGGACGCA 59.781 57.895 0.00 0.00 0.00 5.24
1919 1948 1.202510 GCTTGAGATGGACGCAGAGAT 60.203 52.381 0.00 0.00 0.00 2.75
1920 1949 2.035193 GCTTGAGATGGACGCAGAGATA 59.965 50.000 0.00 0.00 0.00 1.98
1930 1959 0.654683 CGCAGAGATACAAGCCAAGC 59.345 55.000 0.00 0.00 0.00 4.01
1931 1960 1.742761 GCAGAGATACAAGCCAAGCA 58.257 50.000 0.00 0.00 0.00 3.91
1933 1962 1.669779 CAGAGATACAAGCCAAGCAGC 59.330 52.381 0.00 0.00 0.00 5.25
1953 1982 1.208052 CTTGAGATGGAGGCGGAGAAA 59.792 52.381 0.00 0.00 0.00 2.52
1965 1994 2.356135 GCGGAGAAACAAGCCAAGATA 58.644 47.619 0.00 0.00 0.00 1.98
1980 2009 4.159506 GCCAAGATATTAGAGATCGAGGCT 59.840 45.833 11.40 0.00 41.23 4.58
1986 2015 1.485124 TAGAGATCGAGGCTGCCAAA 58.515 50.000 22.65 5.75 0.00 3.28
1999 2028 0.106268 TGCCAAAGCCAAGACCAAGA 60.106 50.000 0.00 0.00 38.69 3.02
2005 2034 2.341846 AGCCAAGACCAAGACGAAAA 57.658 45.000 0.00 0.00 0.00 2.29
2025 2054 2.202743 GTGGCACTCGCGAGCATA 60.203 61.111 34.83 16.60 39.92 3.14
2038 2067 0.468226 GAGCATAATGACCGGGGTGA 59.532 55.000 6.32 0.00 0.00 4.02
2056 2085 4.530875 GGTGAAGATCATGAAGGTGGATT 58.469 43.478 0.00 0.00 0.00 3.01
2076 2105 1.068417 CAACACCGGGTCGTCAAGA 59.932 57.895 6.32 0.00 0.00 3.02
2098 2127 2.156051 GAGGCCGTGGTTCGAGAAGT 62.156 60.000 0.00 0.00 42.86 3.01
2105 2134 2.417719 GTGGTTCGAGAAGTTGCAGAT 58.582 47.619 0.00 0.00 0.00 2.90
2118 2147 4.002982 AGTTGCAGATCGACATGCTTAAA 58.997 39.130 20.62 7.71 42.98 1.52
2187 2217 3.460648 TCGAGAGAGCAGATGTCGA 57.539 52.632 1.79 1.79 39.77 4.20
2188 2218 1.960417 TCGAGAGAGCAGATGTCGAT 58.040 50.000 0.00 0.00 37.52 3.59
2189 2219 1.601430 TCGAGAGAGCAGATGTCGATG 59.399 52.381 0.00 0.00 37.52 3.84
2190 2220 1.601430 CGAGAGAGCAGATGTCGATGA 59.399 52.381 0.00 0.00 35.64 2.92
2191 2221 2.226200 CGAGAGAGCAGATGTCGATGAT 59.774 50.000 0.00 0.00 35.64 2.45
2192 2222 3.567530 GAGAGAGCAGATGTCGATGATG 58.432 50.000 0.00 0.00 0.00 3.07
2193 2223 3.220940 AGAGAGCAGATGTCGATGATGA 58.779 45.455 0.00 0.00 0.00 2.92
2194 2224 3.253921 AGAGAGCAGATGTCGATGATGAG 59.746 47.826 0.00 0.00 0.00 2.90
2195 2225 3.220940 AGAGCAGATGTCGATGATGAGA 58.779 45.455 0.00 0.00 0.00 3.27
2196 2226 3.827876 AGAGCAGATGTCGATGATGAGAT 59.172 43.478 0.00 0.00 0.00 2.75
2197 2227 4.281435 AGAGCAGATGTCGATGATGAGATT 59.719 41.667 0.00 0.00 0.00 2.40
2198 2228 4.558178 AGCAGATGTCGATGATGAGATTC 58.442 43.478 0.00 0.00 0.00 2.52
2199 2229 3.679025 GCAGATGTCGATGATGAGATTCC 59.321 47.826 0.00 0.00 0.00 3.01
2200 2230 3.919197 CAGATGTCGATGATGAGATTCCG 59.081 47.826 0.00 0.00 0.00 4.30
2201 2231 2.800881 TGTCGATGATGAGATTCCGG 57.199 50.000 0.00 0.00 0.00 5.14
2202 2232 1.341209 TGTCGATGATGAGATTCCGGG 59.659 52.381 0.00 0.00 0.00 5.73
2203 2233 0.318441 TCGATGATGAGATTCCGGGC 59.682 55.000 0.00 0.00 0.00 6.13
2204 2234 0.033920 CGATGATGAGATTCCGGGCA 59.966 55.000 0.00 0.00 0.00 5.36
2205 2235 1.805869 GATGATGAGATTCCGGGCAG 58.194 55.000 0.00 0.00 0.00 4.85
2206 2236 1.345741 GATGATGAGATTCCGGGCAGA 59.654 52.381 0.00 0.00 0.00 4.26
2207 2237 0.755079 TGATGAGATTCCGGGCAGAG 59.245 55.000 0.00 0.00 0.00 3.35
2208 2238 1.043816 GATGAGATTCCGGGCAGAGA 58.956 55.000 0.00 0.00 0.00 3.10
2209 2239 1.622811 GATGAGATTCCGGGCAGAGAT 59.377 52.381 0.00 0.00 0.00 2.75
2210 2240 1.500474 TGAGATTCCGGGCAGAGATT 58.500 50.000 0.00 0.00 0.00 2.40
2211 2241 1.139654 TGAGATTCCGGGCAGAGATTG 59.860 52.381 0.00 0.00 0.00 2.67
2212 2242 1.414181 GAGATTCCGGGCAGAGATTGA 59.586 52.381 0.00 0.00 0.00 2.57
2213 2243 2.038295 GAGATTCCGGGCAGAGATTGAT 59.962 50.000 0.00 0.00 0.00 2.57
2214 2244 2.149578 GATTCCGGGCAGAGATTGATG 58.850 52.381 0.00 0.00 0.00 3.07
2215 2245 1.203237 TTCCGGGCAGAGATTGATGA 58.797 50.000 0.00 0.00 0.00 2.92
2216 2246 0.755079 TCCGGGCAGAGATTGATGAG 59.245 55.000 0.00 0.00 0.00 2.90
2217 2247 0.755079 CCGGGCAGAGATTGATGAGA 59.245 55.000 0.00 0.00 0.00 3.27
2218 2248 1.347050 CCGGGCAGAGATTGATGAGAT 59.653 52.381 0.00 0.00 0.00 2.75
2219 2249 2.612471 CCGGGCAGAGATTGATGAGATC 60.612 54.545 0.00 0.00 0.00 2.75
2220 2250 2.036862 CGGGCAGAGATTGATGAGATCA 59.963 50.000 0.00 0.00 37.55 2.92
2221 2251 3.666274 GGGCAGAGATTGATGAGATCAG 58.334 50.000 0.00 0.00 40.94 2.90
2222 2252 3.068560 GGCAGAGATTGATGAGATCAGC 58.931 50.000 0.00 0.00 40.94 4.26
2223 2253 3.494573 GGCAGAGATTGATGAGATCAGCA 60.495 47.826 0.00 0.00 40.88 4.41
2224 2254 3.743911 GCAGAGATTGATGAGATCAGCAG 59.256 47.826 0.64 0.00 43.59 4.24
2225 2255 4.311606 CAGAGATTGATGAGATCAGCAGG 58.688 47.826 0.64 0.00 43.59 4.85
2226 2256 3.068560 GAGATTGATGAGATCAGCAGGC 58.931 50.000 0.64 0.00 43.59 4.85
2227 2257 2.438392 AGATTGATGAGATCAGCAGGCA 59.562 45.455 0.64 0.00 43.59 4.75
2228 2258 3.073209 AGATTGATGAGATCAGCAGGCAT 59.927 43.478 0.64 0.00 43.59 4.40
2229 2259 4.286291 AGATTGATGAGATCAGCAGGCATA 59.714 41.667 0.64 0.00 43.59 3.14
2230 2260 3.679824 TGATGAGATCAGCAGGCATAG 57.320 47.619 0.00 0.00 37.34 2.23
2231 2261 2.302157 TGATGAGATCAGCAGGCATAGG 59.698 50.000 0.00 0.00 37.34 2.57
2232 2262 1.054231 TGAGATCAGCAGGCATAGGG 58.946 55.000 0.00 0.00 0.00 3.53
2233 2263 0.324285 GAGATCAGCAGGCATAGGGG 59.676 60.000 0.00 0.00 0.00 4.79
2234 2264 0.104777 AGATCAGCAGGCATAGGGGA 60.105 55.000 0.00 0.00 0.00 4.81
2235 2265 0.990374 GATCAGCAGGCATAGGGGAT 59.010 55.000 0.00 0.00 0.00 3.85
2236 2266 1.353694 GATCAGCAGGCATAGGGGATT 59.646 52.381 0.00 0.00 0.00 3.01
2237 2267 1.225373 TCAGCAGGCATAGGGGATTT 58.775 50.000 0.00 0.00 0.00 2.17
2238 2268 1.143684 TCAGCAGGCATAGGGGATTTC 59.856 52.381 0.00 0.00 0.00 2.17
2239 2269 1.144503 CAGCAGGCATAGGGGATTTCT 59.855 52.381 0.00 0.00 0.00 2.52
2240 2270 1.423161 AGCAGGCATAGGGGATTTCTC 59.577 52.381 0.00 0.00 0.00 2.87
2241 2271 1.879796 GCAGGCATAGGGGATTTCTCG 60.880 57.143 0.00 0.00 0.00 4.04
2242 2272 1.059913 AGGCATAGGGGATTTCTCGG 58.940 55.000 0.00 0.00 0.00 4.63
2243 2273 0.036875 GGCATAGGGGATTTCTCGGG 59.963 60.000 0.00 0.00 0.00 5.14
2244 2274 1.056660 GCATAGGGGATTTCTCGGGA 58.943 55.000 0.00 0.00 0.00 5.14
2245 2275 1.420138 GCATAGGGGATTTCTCGGGAA 59.580 52.381 0.00 0.00 0.00 3.97
2246 2276 2.158667 GCATAGGGGATTTCTCGGGAAA 60.159 50.000 13.89 13.89 44.26 3.13
2247 2277 3.687264 GCATAGGGGATTTCTCGGGAAAA 60.687 47.826 15.66 0.00 43.51 2.29
2248 2278 4.532834 CATAGGGGATTTCTCGGGAAAAA 58.467 43.478 15.66 0.00 43.51 1.94
2266 2296 2.323999 AAAACAGGCATGGAATGGGA 57.676 45.000 2.31 0.00 46.86 4.37
2267 2297 1.856629 AAACAGGCATGGAATGGGAG 58.143 50.000 2.31 0.00 46.86 4.30
2268 2298 0.685458 AACAGGCATGGAATGGGAGC 60.685 55.000 2.31 0.00 46.86 4.70
2269 2299 1.831286 CAGGCATGGAATGGGAGCC 60.831 63.158 0.00 0.00 46.86 4.70
2270 2300 2.908940 GGCATGGAATGGGAGCCG 60.909 66.667 0.00 0.00 46.86 5.52
2271 2301 2.192979 GCATGGAATGGGAGCCGA 59.807 61.111 0.00 0.00 46.86 5.54
2272 2302 1.228367 GCATGGAATGGGAGCCGAT 60.228 57.895 0.00 0.00 46.86 4.18
2273 2303 0.825010 GCATGGAATGGGAGCCGATT 60.825 55.000 0.00 0.00 46.86 3.34
2274 2304 0.956633 CATGGAATGGGAGCCGATTG 59.043 55.000 1.28 0.00 41.79 2.67
2275 2305 0.846015 ATGGAATGGGAGCCGATTGA 59.154 50.000 1.28 0.00 0.00 2.57
2276 2306 0.181114 TGGAATGGGAGCCGATTGAG 59.819 55.000 1.28 0.00 0.00 3.02
2277 2307 1.169034 GGAATGGGAGCCGATTGAGC 61.169 60.000 1.28 0.00 0.00 4.26
2278 2308 1.502163 GAATGGGAGCCGATTGAGCG 61.502 60.000 1.28 0.00 34.64 5.03
2279 2309 1.971505 AATGGGAGCCGATTGAGCGA 61.972 55.000 0.00 0.00 34.64 4.93
2280 2310 1.971505 ATGGGAGCCGATTGAGCGAA 61.972 55.000 0.00 0.00 34.64 4.70
2281 2311 1.884926 GGGAGCCGATTGAGCGAAG 60.885 63.158 0.00 0.00 34.64 3.79
2282 2312 1.141881 GGAGCCGATTGAGCGAAGA 59.858 57.895 0.00 0.00 34.64 2.87
2283 2313 0.873743 GGAGCCGATTGAGCGAAGAG 60.874 60.000 0.00 0.00 34.64 2.85
2284 2314 0.101399 GAGCCGATTGAGCGAAGAGA 59.899 55.000 0.00 0.00 34.64 3.10
2285 2315 0.532573 AGCCGATTGAGCGAAGAGAA 59.467 50.000 0.00 0.00 34.64 2.87
2286 2316 1.066858 AGCCGATTGAGCGAAGAGAAA 60.067 47.619 0.00 0.00 34.64 2.52
2287 2317 1.325943 GCCGATTGAGCGAAGAGAAAG 59.674 52.381 0.00 0.00 0.00 2.62
2288 2318 2.881074 CCGATTGAGCGAAGAGAAAGA 58.119 47.619 0.00 0.00 0.00 2.52
2289 2319 3.452474 CCGATTGAGCGAAGAGAAAGAT 58.548 45.455 0.00 0.00 0.00 2.40
2290 2320 3.244814 CCGATTGAGCGAAGAGAAAGATG 59.755 47.826 0.00 0.00 0.00 2.90
2291 2321 3.862267 CGATTGAGCGAAGAGAAAGATGT 59.138 43.478 0.00 0.00 0.00 3.06
2292 2322 5.037385 CGATTGAGCGAAGAGAAAGATGTA 58.963 41.667 0.00 0.00 0.00 2.29
2293 2323 5.172951 CGATTGAGCGAAGAGAAAGATGTAG 59.827 44.000 0.00 0.00 0.00 2.74
2294 2324 5.644977 TTGAGCGAAGAGAAAGATGTAGA 57.355 39.130 0.00 0.00 0.00 2.59
2295 2325 5.242069 TGAGCGAAGAGAAAGATGTAGAG 57.758 43.478 0.00 0.00 0.00 2.43
2296 2326 4.944317 TGAGCGAAGAGAAAGATGTAGAGA 59.056 41.667 0.00 0.00 0.00 3.10
2297 2327 5.065859 TGAGCGAAGAGAAAGATGTAGAGAG 59.934 44.000 0.00 0.00 0.00 3.20
2298 2328 4.947388 AGCGAAGAGAAAGATGTAGAGAGT 59.053 41.667 0.00 0.00 0.00 3.24
2299 2329 5.034152 GCGAAGAGAAAGATGTAGAGAGTG 58.966 45.833 0.00 0.00 0.00 3.51
2300 2330 5.034152 CGAAGAGAAAGATGTAGAGAGTGC 58.966 45.833 0.00 0.00 0.00 4.40
2301 2331 4.630894 AGAGAAAGATGTAGAGAGTGCG 57.369 45.455 0.00 0.00 0.00 5.34
2302 2332 4.013728 AGAGAAAGATGTAGAGAGTGCGT 58.986 43.478 0.00 0.00 0.00 5.24
2303 2333 4.101942 GAGAAAGATGTAGAGAGTGCGTG 58.898 47.826 0.00 0.00 0.00 5.34
2304 2334 2.285827 AAGATGTAGAGAGTGCGTGC 57.714 50.000 0.00 0.00 0.00 5.34
2305 2335 0.099613 AGATGTAGAGAGTGCGTGCG 59.900 55.000 0.00 0.00 0.00 5.34
2306 2336 0.179161 GATGTAGAGAGTGCGTGCGT 60.179 55.000 0.00 0.00 0.00 5.24
2307 2337 0.456824 ATGTAGAGAGTGCGTGCGTG 60.457 55.000 0.00 0.00 0.00 5.34
2308 2338 2.126463 TAGAGAGTGCGTGCGTGC 60.126 61.111 0.00 0.00 0.00 5.34
2309 2339 3.946305 TAGAGAGTGCGTGCGTGCG 62.946 63.158 0.00 0.00 37.81 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.202879 TCGGAGTGCTGGGTCATTTTT 60.203 47.619 0.00 0.00 0.00 1.94
8 9 0.400213 TCGGAGTGCTGGGTCATTTT 59.600 50.000 0.00 0.00 0.00 1.82
9 10 0.321653 GTCGGAGTGCTGGGTCATTT 60.322 55.000 0.00 0.00 0.00 2.32
10 11 1.296715 GTCGGAGTGCTGGGTCATT 59.703 57.895 0.00 0.00 0.00 2.57
11 12 2.660064 GGTCGGAGTGCTGGGTCAT 61.660 63.158 0.00 0.00 0.00 3.06
12 13 3.311110 GGTCGGAGTGCTGGGTCA 61.311 66.667 0.00 0.00 0.00 4.02
13 14 4.083862 GGGTCGGAGTGCTGGGTC 62.084 72.222 0.00 0.00 0.00 4.46
14 15 4.954118 TGGGTCGGAGTGCTGGGT 62.954 66.667 0.00 0.00 0.00 4.51
15 16 3.190738 TTTGGGTCGGAGTGCTGGG 62.191 63.158 0.00 0.00 0.00 4.45
16 17 1.966451 GTTTGGGTCGGAGTGCTGG 60.966 63.158 0.00 0.00 0.00 4.85
17 18 2.317609 CGTTTGGGTCGGAGTGCTG 61.318 63.158 0.00 0.00 0.00 4.41
18 19 2.030562 CGTTTGGGTCGGAGTGCT 59.969 61.111 0.00 0.00 0.00 4.40
28 29 4.160635 GATGCGCGTCCGTTTGGG 62.161 66.667 19.11 0.00 36.67 4.12
29 30 4.160635 GGATGCGCGTCCGTTTGG 62.161 66.667 31.62 0.00 36.67 3.28
47 48 1.017177 TCACCATACGAACGCCAAGC 61.017 55.000 0.00 0.00 0.00 4.01
48 49 0.719465 GTCACCATACGAACGCCAAG 59.281 55.000 0.00 0.00 0.00 3.61
49 50 0.671163 GGTCACCATACGAACGCCAA 60.671 55.000 0.00 0.00 0.00 4.52
50 51 1.079681 GGTCACCATACGAACGCCA 60.080 57.895 0.00 0.00 0.00 5.69
51 52 1.812507 GGGTCACCATACGAACGCC 60.813 63.158 0.00 0.00 36.50 5.68
52 53 1.079681 TGGGTCACCATACGAACGC 60.080 57.895 0.00 0.00 43.37 4.84
62 63 1.917336 TAGGCCGGAAATGGGTCACC 61.917 60.000 5.05 0.00 37.24 4.02
63 64 0.034863 TTAGGCCGGAAATGGGTCAC 60.035 55.000 5.05 0.00 0.00 3.67
64 65 0.923358 ATTAGGCCGGAAATGGGTCA 59.077 50.000 5.05 0.00 0.00 4.02
65 66 2.067365 AATTAGGCCGGAAATGGGTC 57.933 50.000 5.05 0.00 0.00 4.46
66 67 2.543037 AAATTAGGCCGGAAATGGGT 57.457 45.000 5.05 0.00 0.00 4.51
67 68 4.739436 GCTTAAAATTAGGCCGGAAATGGG 60.739 45.833 5.05 0.00 30.38 4.00
68 69 4.368315 GCTTAAAATTAGGCCGGAAATGG 58.632 43.478 5.05 0.00 30.38 3.16
69 70 4.368315 GGCTTAAAATTAGGCCGGAAATG 58.632 43.478 5.05 0.00 44.40 2.32
70 71 4.665833 GGCTTAAAATTAGGCCGGAAAT 57.334 40.909 5.05 0.00 44.40 2.17
77 78 3.802139 GCAAATCCGGCTTAAAATTAGGC 59.198 43.478 0.00 0.00 35.27 3.93
78 79 5.004922 TGCAAATCCGGCTTAAAATTAGG 57.995 39.130 0.00 0.00 0.00 2.69
79 80 5.050837 GCATGCAAATCCGGCTTAAAATTAG 60.051 40.000 14.21 0.00 0.00 1.73
80 81 4.808364 GCATGCAAATCCGGCTTAAAATTA 59.192 37.500 14.21 0.00 0.00 1.40
81 82 3.622612 GCATGCAAATCCGGCTTAAAATT 59.377 39.130 14.21 0.00 0.00 1.82
82 83 3.197265 GCATGCAAATCCGGCTTAAAAT 58.803 40.909 14.21 0.00 0.00 1.82
83 84 2.615869 GCATGCAAATCCGGCTTAAAA 58.384 42.857 14.21 0.00 0.00 1.52
84 85 1.468908 CGCATGCAAATCCGGCTTAAA 60.469 47.619 19.57 0.00 0.00 1.52
85 86 0.100325 CGCATGCAAATCCGGCTTAA 59.900 50.000 19.57 0.00 0.00 1.85
86 87 1.029408 ACGCATGCAAATCCGGCTTA 61.029 50.000 19.57 0.00 0.00 3.09
87 88 2.342650 ACGCATGCAAATCCGGCTT 61.343 52.632 19.57 0.00 0.00 4.35
88 89 2.751436 ACGCATGCAAATCCGGCT 60.751 55.556 19.57 0.00 0.00 5.52
89 90 2.580326 CACGCATGCAAATCCGGC 60.580 61.111 19.57 0.00 0.00 6.13
99 100 3.264897 GGAGTAGGCGCACGCATG 61.265 66.667 17.69 0.00 44.11 4.06
100 101 3.432051 GAGGAGTAGGCGCACGCAT 62.432 63.158 17.69 12.82 44.11 4.73
101 102 4.129737 GAGGAGTAGGCGCACGCA 62.130 66.667 17.69 0.00 44.11 5.24
105 106 2.058595 GGGAAGAGGAGTAGGCGCA 61.059 63.158 10.83 0.00 0.00 6.09
126 127 3.109612 CTGCTACCGACCGACGAGG 62.110 68.421 0.00 0.00 45.77 4.63
128 129 3.807538 GCTGCTACCGACCGACGA 61.808 66.667 0.00 0.00 45.77 4.20
131 132 3.755628 GTGGCTGCTACCGACCGA 61.756 66.667 4.63 0.00 0.00 4.69
140 141 2.113986 GAACTGGTGGTGGCTGCT 59.886 61.111 0.00 0.00 0.00 4.24
154 156 5.297547 GGTTTTGAAGGAAAATGGAGGAAC 58.702 41.667 0.00 0.00 35.96 3.62
159 161 3.901222 GGAGGGTTTTGAAGGAAAATGGA 59.099 43.478 0.00 0.00 35.96 3.41
169 171 2.116556 GGGCGGGAGGGTTTTGAA 59.883 61.111 0.00 0.00 0.00 2.69
170 172 4.338710 CGGGCGGGAGGGTTTTGA 62.339 66.667 0.00 0.00 0.00 2.69
208 219 3.004524 AGGTCGATGGCGTCTTCTATAAC 59.995 47.826 5.00 0.00 38.98 1.89
209 220 3.220110 AGGTCGATGGCGTCTTCTATAA 58.780 45.455 5.00 0.00 38.98 0.98
210 221 2.812591 GAGGTCGATGGCGTCTTCTATA 59.187 50.000 5.00 0.00 38.98 1.31
213 225 1.810532 GAGGTCGATGGCGTCTTCT 59.189 57.895 5.00 0.00 38.98 2.85
216 228 2.437895 TCGAGGTCGATGGCGTCT 60.438 61.111 5.00 0.00 44.22 4.18
282 294 2.043953 GGCTTGCCTTTCCCGGAT 60.044 61.111 0.73 0.00 0.00 4.18
356 368 0.803768 CGACTCTCTTGCCCGATGTG 60.804 60.000 0.00 0.00 0.00 3.21
360 372 2.341101 GGTCGACTCTCTTGCCCGA 61.341 63.158 16.46 0.00 0.00 5.14
369 381 1.075698 TCCTTCCTCTTGGTCGACTCT 59.924 52.381 16.46 0.00 34.23 3.24
415 427 4.529219 CTGCGCGGTGGCCTCATA 62.529 66.667 8.83 0.00 35.02 2.15
454 466 1.972198 CGTTGGTGACCTCCTGCTA 59.028 57.895 2.11 0.00 0.00 3.49
514 526 1.940613 GTGCTGGCTAGGATTTAACCG 59.059 52.381 0.00 0.00 34.73 4.44
522 534 1.903877 GAAGGCTGTGCTGGCTAGGA 61.904 60.000 0.00 0.00 42.20 2.94
535 547 2.048127 GACGGCGTTGAGAAGGCT 60.048 61.111 16.19 0.00 41.72 4.58
595 608 4.778143 GGGCGAGTCGGGCAACAT 62.778 66.667 15.52 0.00 39.74 2.71
637 650 2.652530 GTACACGTGGAAGCCGGA 59.347 61.111 21.57 0.00 0.00 5.14
660 673 4.697756 CCGGAAAGGCAGGACGCA 62.698 66.667 0.00 0.00 45.17 5.24
663 676 3.327404 TCCCCGGAAAGGCAGGAC 61.327 66.667 0.73 0.00 39.21 3.85
667 680 4.344865 GCACTCCCCGGAAAGGCA 62.345 66.667 0.73 0.00 39.21 4.75
755 768 4.101448 ATGACGAGCCACCAGCCC 62.101 66.667 0.00 0.00 45.47 5.19
826 846 1.528309 CCTTGAACAGGTTGCGGGT 60.528 57.895 0.00 0.00 37.99 5.28
841 861 4.296265 GGCGAACGACATTCCCTT 57.704 55.556 0.00 0.00 33.26 3.95
913 933 1.301423 GTCTCGTCAGGATCGTAGCT 58.699 55.000 0.00 0.00 0.00 3.32
992 1012 0.745486 CTGATCACGCATGAAGGCCA 60.745 55.000 5.01 0.00 38.69 5.36
1015 1035 4.148825 GCCGTCCAGGTCGATGCT 62.149 66.667 7.77 0.00 43.70 3.79
1137 1157 1.596934 CTTCGGCTTAGGACTGGCA 59.403 57.895 0.00 0.00 0.00 4.92
1141 1161 2.167398 TTGCGCTTCGGCTTAGGACT 62.167 55.000 9.73 0.00 39.13 3.85
1188 1208 1.507141 AAAGAAGCTTGTCCACGGCG 61.507 55.000 2.10 4.80 0.00 6.46
1193 1213 1.229428 CTCGCAAAGAAGCTTGTCCA 58.771 50.000 2.10 0.00 0.00 4.02
1215 1235 2.244436 CTTGTCCAATGTCGCGCCAG 62.244 60.000 0.00 0.00 0.00 4.85
1221 1241 2.455674 TGGAGTCTTGTCCAATGTCG 57.544 50.000 0.00 0.00 44.01 4.35
1260 1281 6.294286 GGACACGAATCCAAAAGGTTGAATAA 60.294 38.462 5.04 0.00 38.77 1.40
1261 1282 5.182380 GGACACGAATCCAAAAGGTTGAATA 59.818 40.000 5.04 0.00 38.77 1.75
1287 1308 1.872388 TGCGGTCATGAAACTTTCGA 58.128 45.000 0.00 0.00 0.00 3.71
1291 1312 3.214328 ACTTCTTGCGGTCATGAAACTT 58.786 40.909 0.00 0.00 36.38 2.66
1302 1323 1.515521 AAGGCGGAAACTTCTTGCGG 61.516 55.000 0.72 0.00 33.80 5.69
1369 1391 2.562298 TGCAATCTTGTTGAATCACCCC 59.438 45.455 0.00 0.00 0.00 4.95
1392 1414 1.748493 TCAAGAGTGGCGCAAAACTTT 59.252 42.857 10.83 1.70 0.00 2.66
1471 1493 0.400213 ATGACACAAAAGAGGGCGGA 59.600 50.000 0.00 0.00 0.00 5.54
1512 1536 8.192743 AGCATATGGGCAAATGATACATAAAA 57.807 30.769 4.56 0.00 35.83 1.52
1516 1540 5.568023 GCAAGCATATGGGCAAATGATACAT 60.568 40.000 4.56 0.00 35.83 2.29
1517 1541 4.262121 GCAAGCATATGGGCAAATGATACA 60.262 41.667 4.56 0.00 35.83 2.29
1518 1542 4.240096 GCAAGCATATGGGCAAATGATAC 58.760 43.478 4.56 0.00 35.83 2.24
1588 1614 2.423892 TGAAGCACTTGCCGTTGTTTTA 59.576 40.909 0.00 0.00 43.38 1.52
1591 1617 0.814457 TTGAAGCACTTGCCGTTGTT 59.186 45.000 0.00 0.00 43.38 2.83
1611 1637 1.203001 ACCCGAAAGCAATGGGAAAGA 60.203 47.619 9.94 0.00 46.41 2.52
1690 1716 2.747855 CCCTCCACGGCTTGCTTC 60.748 66.667 0.00 0.00 0.00 3.86
1795 1822 5.894298 TTCATCATGCCCTCTATACTTGT 57.106 39.130 0.00 0.00 0.00 3.16
1803 1830 4.662179 TCCTTCTTATTCATCATGCCCTCT 59.338 41.667 0.00 0.00 0.00 3.69
1856 1883 3.334583 AGGCGTTCATTTGCTCTTCTA 57.665 42.857 0.00 0.00 0.00 2.10
1870 1897 2.787473 TGGATCTTCATGAAGGCGTT 57.213 45.000 30.33 15.74 38.88 4.84
1875 1902 5.531659 CCTCCTTCATTGGATCTTCATGAAG 59.468 44.000 26.56 26.56 44.51 3.02
1882 1909 3.267812 TCAAGCCTCCTTCATTGGATCTT 59.732 43.478 0.00 0.00 35.30 2.40
1891 1918 1.556911 GTCCATCTCAAGCCTCCTTCA 59.443 52.381 0.00 0.00 0.00 3.02
1893 1920 0.539051 CGTCCATCTCAAGCCTCCTT 59.461 55.000 0.00 0.00 0.00 3.36
1914 1941 1.558756 AGCTGCTTGGCTTGTATCTCT 59.441 47.619 0.00 0.00 39.86 3.10
1930 1959 1.523258 CCGCCTCCATCTCAAGCTG 60.523 63.158 0.00 0.00 0.00 4.24
1931 1960 1.684386 CTCCGCCTCCATCTCAAGCT 61.684 60.000 0.00 0.00 0.00 3.74
1933 1962 0.826715 TTCTCCGCCTCCATCTCAAG 59.173 55.000 0.00 0.00 0.00 3.02
1935 1964 0.537188 GTTTCTCCGCCTCCATCTCA 59.463 55.000 0.00 0.00 0.00 3.27
1939 1968 0.678048 GCTTGTTTCTCCGCCTCCAT 60.678 55.000 0.00 0.00 0.00 3.41
1953 1982 6.295011 CCTCGATCTCTAATATCTTGGCTTGT 60.295 42.308 0.00 0.00 0.00 3.16
1965 1994 1.709578 TGGCAGCCTCGATCTCTAAT 58.290 50.000 14.15 0.00 0.00 1.73
1980 2009 0.106268 TCTTGGTCTTGGCTTTGGCA 60.106 50.000 0.00 0.00 40.87 4.92
1986 2015 2.341846 TTTTCGTCTTGGTCTTGGCT 57.658 45.000 0.00 0.00 0.00 4.75
2005 2034 3.044305 GCTCGCGAGTGCCACTTT 61.044 61.111 34.46 0.00 44.29 2.66
2025 2054 1.285280 TGATCTTCACCCCGGTCATT 58.715 50.000 0.00 0.00 0.00 2.57
2038 2067 6.012113 TGTTGAAATCCACCTTCATGATCTT 58.988 36.000 0.00 0.00 32.98 2.40
2056 2085 0.531090 CTTGACGACCCGGTGTTGAA 60.531 55.000 15.00 3.02 32.21 2.69
2066 2095 1.014564 CGGCCTCTTTCTTGACGACC 61.015 60.000 0.00 0.00 0.00 4.79
2076 2105 1.004918 CTCGAACCACGGCCTCTTT 60.005 57.895 0.00 0.00 42.82 2.52
2098 2127 5.565592 AATTTAAGCATGTCGATCTGCAA 57.434 34.783 20.08 9.39 40.88 4.08
2105 2134 3.302434 GTCGTCGAATTTAAGCATGTCGA 59.698 43.478 0.00 0.00 38.32 4.20
2118 2147 4.042398 CCATAAATCACTCGTCGTCGAAT 58.958 43.478 6.19 0.00 45.61 3.34
2161 2191 0.950836 CTGCTCTCTCGATCCGACAT 59.049 55.000 0.00 0.00 0.00 3.06
2163 2193 1.069296 CATCTGCTCTCTCGATCCGAC 60.069 57.143 0.00 0.00 0.00 4.79
2165 2195 0.950836 ACATCTGCTCTCTCGATCCG 59.049 55.000 0.00 0.00 0.00 4.18
2166 2196 1.069296 CGACATCTGCTCTCTCGATCC 60.069 57.143 0.00 0.00 0.00 3.36
2167 2197 1.870402 TCGACATCTGCTCTCTCGATC 59.130 52.381 0.00 0.00 0.00 3.69
2168 2198 1.960417 TCGACATCTGCTCTCTCGAT 58.040 50.000 0.00 0.00 0.00 3.59
2169 2199 1.601430 CATCGACATCTGCTCTCTCGA 59.399 52.381 0.00 0.00 37.74 4.04
2170 2200 1.601430 TCATCGACATCTGCTCTCTCG 59.399 52.381 0.00 0.00 0.00 4.04
2171 2201 3.252944 TCATCATCGACATCTGCTCTCTC 59.747 47.826 0.00 0.00 0.00 3.20
2172 2202 3.220940 TCATCATCGACATCTGCTCTCT 58.779 45.455 0.00 0.00 0.00 3.10
2173 2203 3.252944 TCTCATCATCGACATCTGCTCTC 59.747 47.826 0.00 0.00 0.00 3.20
2174 2204 3.220940 TCTCATCATCGACATCTGCTCT 58.779 45.455 0.00 0.00 0.00 4.09
2175 2205 3.639716 TCTCATCATCGACATCTGCTC 57.360 47.619 0.00 0.00 0.00 4.26
2176 2206 4.558178 GAATCTCATCATCGACATCTGCT 58.442 43.478 0.00 0.00 0.00 4.24
2177 2207 3.679025 GGAATCTCATCATCGACATCTGC 59.321 47.826 0.00 0.00 0.00 4.26
2178 2208 3.919197 CGGAATCTCATCATCGACATCTG 59.081 47.826 0.00 0.00 0.00 2.90
2179 2209 3.056962 CCGGAATCTCATCATCGACATCT 60.057 47.826 0.00 0.00 0.00 2.90
2180 2210 3.249091 CCGGAATCTCATCATCGACATC 58.751 50.000 0.00 0.00 0.00 3.06
2181 2211 2.028658 CCCGGAATCTCATCATCGACAT 60.029 50.000 0.73 0.00 0.00 3.06
2182 2212 1.341209 CCCGGAATCTCATCATCGACA 59.659 52.381 0.73 0.00 0.00 4.35
2183 2213 1.937108 GCCCGGAATCTCATCATCGAC 60.937 57.143 0.73 0.00 0.00 4.20
2184 2214 0.318441 GCCCGGAATCTCATCATCGA 59.682 55.000 0.73 0.00 0.00 3.59
2185 2215 0.033920 TGCCCGGAATCTCATCATCG 59.966 55.000 0.73 0.00 0.00 3.84
2186 2216 1.345741 TCTGCCCGGAATCTCATCATC 59.654 52.381 0.73 0.00 0.00 2.92
2187 2217 1.347050 CTCTGCCCGGAATCTCATCAT 59.653 52.381 0.73 0.00 0.00 2.45
2188 2218 0.755079 CTCTGCCCGGAATCTCATCA 59.245 55.000 0.73 0.00 0.00 3.07
2189 2219 1.043816 TCTCTGCCCGGAATCTCATC 58.956 55.000 0.73 0.00 0.00 2.92
2190 2220 1.727062 ATCTCTGCCCGGAATCTCAT 58.273 50.000 0.73 0.00 0.00 2.90
2191 2221 1.139654 CAATCTCTGCCCGGAATCTCA 59.860 52.381 0.73 0.00 0.00 3.27
2192 2222 1.414181 TCAATCTCTGCCCGGAATCTC 59.586 52.381 0.73 0.00 0.00 2.75
2193 2223 1.500474 TCAATCTCTGCCCGGAATCT 58.500 50.000 0.73 0.00 0.00 2.40
2194 2224 2.149578 CATCAATCTCTGCCCGGAATC 58.850 52.381 0.73 0.00 0.00 2.52
2195 2225 1.770658 TCATCAATCTCTGCCCGGAAT 59.229 47.619 0.73 0.00 0.00 3.01
2196 2226 1.139654 CTCATCAATCTCTGCCCGGAA 59.860 52.381 0.73 0.00 0.00 4.30
2197 2227 0.755079 CTCATCAATCTCTGCCCGGA 59.245 55.000 0.73 0.00 0.00 5.14
2198 2228 0.755079 TCTCATCAATCTCTGCCCGG 59.245 55.000 0.00 0.00 0.00 5.73
2199 2229 2.036862 TGATCTCATCAATCTCTGCCCG 59.963 50.000 0.00 0.00 36.11 6.13
2200 2230 3.666274 CTGATCTCATCAATCTCTGCCC 58.334 50.000 0.00 0.00 39.11 5.36
2201 2231 3.068560 GCTGATCTCATCAATCTCTGCC 58.931 50.000 0.00 0.00 39.11 4.85
2202 2232 3.729966 TGCTGATCTCATCAATCTCTGC 58.270 45.455 0.00 0.00 39.11 4.26
2203 2233 4.311606 CCTGCTGATCTCATCAATCTCTG 58.688 47.826 0.00 0.00 39.11 3.35
2204 2234 3.244284 GCCTGCTGATCTCATCAATCTCT 60.244 47.826 0.00 0.00 39.11 3.10
2205 2235 3.068560 GCCTGCTGATCTCATCAATCTC 58.931 50.000 0.00 0.00 39.11 2.75
2206 2236 2.438392 TGCCTGCTGATCTCATCAATCT 59.562 45.455 0.00 0.00 39.11 2.40
2207 2237 2.847441 TGCCTGCTGATCTCATCAATC 58.153 47.619 0.00 0.00 39.11 2.67
2208 2238 3.510531 ATGCCTGCTGATCTCATCAAT 57.489 42.857 0.00 0.00 39.11 2.57
2209 2239 3.244457 CCTATGCCTGCTGATCTCATCAA 60.244 47.826 0.00 0.00 39.11 2.57
2210 2240 2.302157 CCTATGCCTGCTGATCTCATCA 59.698 50.000 0.00 0.00 37.76 3.07
2211 2241 2.354906 CCCTATGCCTGCTGATCTCATC 60.355 54.545 0.00 0.00 0.00 2.92
2212 2242 1.629353 CCCTATGCCTGCTGATCTCAT 59.371 52.381 0.00 0.00 0.00 2.90
2213 2243 1.054231 CCCTATGCCTGCTGATCTCA 58.946 55.000 0.00 0.00 0.00 3.27
2214 2244 0.324285 CCCCTATGCCTGCTGATCTC 59.676 60.000 0.00 0.00 0.00 2.75
2215 2245 0.104777 TCCCCTATGCCTGCTGATCT 60.105 55.000 0.00 0.00 0.00 2.75
2216 2246 0.990374 ATCCCCTATGCCTGCTGATC 59.010 55.000 0.00 0.00 0.00 2.92
2217 2247 1.453633 AATCCCCTATGCCTGCTGAT 58.546 50.000 0.00 0.00 0.00 2.90
2218 2248 1.143684 GAAATCCCCTATGCCTGCTGA 59.856 52.381 0.00 0.00 0.00 4.26
2219 2249 1.144503 AGAAATCCCCTATGCCTGCTG 59.855 52.381 0.00 0.00 0.00 4.41
2220 2250 1.423161 GAGAAATCCCCTATGCCTGCT 59.577 52.381 0.00 0.00 0.00 4.24
2221 2251 1.879796 CGAGAAATCCCCTATGCCTGC 60.880 57.143 0.00 0.00 0.00 4.85
2222 2252 1.271054 CCGAGAAATCCCCTATGCCTG 60.271 57.143 0.00 0.00 0.00 4.85
2223 2253 1.059913 CCGAGAAATCCCCTATGCCT 58.940 55.000 0.00 0.00 0.00 4.75
2224 2254 0.036875 CCCGAGAAATCCCCTATGCC 59.963 60.000 0.00 0.00 0.00 4.40
2225 2255 1.056660 TCCCGAGAAATCCCCTATGC 58.943 55.000 0.00 0.00 0.00 3.14
2226 2256 3.857157 TTTCCCGAGAAATCCCCTATG 57.143 47.619 0.00 0.00 37.07 2.23
2227 2257 4.873724 TTTTTCCCGAGAAATCCCCTAT 57.126 40.909 0.00 0.00 41.55 2.57
2246 2276 2.568509 CTCCCATTCCATGCCTGTTTTT 59.431 45.455 0.00 0.00 0.00 1.94
2247 2277 2.181975 CTCCCATTCCATGCCTGTTTT 58.818 47.619 0.00 0.00 0.00 2.43
2248 2278 1.856629 CTCCCATTCCATGCCTGTTT 58.143 50.000 0.00 0.00 0.00 2.83
2249 2279 0.685458 GCTCCCATTCCATGCCTGTT 60.685 55.000 0.00 0.00 0.00 3.16
2250 2280 1.076485 GCTCCCATTCCATGCCTGT 60.076 57.895 0.00 0.00 0.00 4.00
2251 2281 1.831286 GGCTCCCATTCCATGCCTG 60.831 63.158 0.00 0.00 40.36 4.85
2252 2282 2.605299 GGCTCCCATTCCATGCCT 59.395 61.111 0.00 0.00 40.36 4.75
2253 2283 2.703675 ATCGGCTCCCATTCCATGCC 62.704 60.000 0.00 0.00 40.14 4.40
2254 2284 0.825010 AATCGGCTCCCATTCCATGC 60.825 55.000 0.00 0.00 0.00 4.06
2255 2285 0.956633 CAATCGGCTCCCATTCCATG 59.043 55.000 0.00 0.00 0.00 3.66
2256 2286 0.846015 TCAATCGGCTCCCATTCCAT 59.154 50.000 0.00 0.00 0.00 3.41
2257 2287 0.181114 CTCAATCGGCTCCCATTCCA 59.819 55.000 0.00 0.00 0.00 3.53
2258 2288 1.169034 GCTCAATCGGCTCCCATTCC 61.169 60.000 0.00 0.00 0.00 3.01
2259 2289 1.502163 CGCTCAATCGGCTCCCATTC 61.502 60.000 0.00 0.00 0.00 2.67
2260 2290 1.524621 CGCTCAATCGGCTCCCATT 60.525 57.895 0.00 0.00 0.00 3.16
2261 2291 1.971505 TTCGCTCAATCGGCTCCCAT 61.972 55.000 0.00 0.00 0.00 4.00
2262 2292 2.578163 CTTCGCTCAATCGGCTCCCA 62.578 60.000 0.00 0.00 0.00 4.37
2263 2293 1.884926 CTTCGCTCAATCGGCTCCC 60.885 63.158 0.00 0.00 0.00 4.30
2264 2294 0.873743 CTCTTCGCTCAATCGGCTCC 60.874 60.000 0.00 0.00 0.00 4.70
2265 2295 0.101399 TCTCTTCGCTCAATCGGCTC 59.899 55.000 0.00 0.00 0.00 4.70
2266 2296 0.532573 TTCTCTTCGCTCAATCGGCT 59.467 50.000 0.00 0.00 0.00 5.52
2267 2297 1.325943 CTTTCTCTTCGCTCAATCGGC 59.674 52.381 0.00 0.00 0.00 5.54
2268 2298 2.881074 TCTTTCTCTTCGCTCAATCGG 58.119 47.619 0.00 0.00 0.00 4.18
2269 2299 3.862267 ACATCTTTCTCTTCGCTCAATCG 59.138 43.478 0.00 0.00 0.00 3.34
2270 2300 6.269315 TCTACATCTTTCTCTTCGCTCAATC 58.731 40.000 0.00 0.00 0.00 2.67
2271 2301 6.096141 TCTCTACATCTTTCTCTTCGCTCAAT 59.904 38.462 0.00 0.00 0.00 2.57
2272 2302 5.416013 TCTCTACATCTTTCTCTTCGCTCAA 59.584 40.000 0.00 0.00 0.00 3.02
2273 2303 4.944317 TCTCTACATCTTTCTCTTCGCTCA 59.056 41.667 0.00 0.00 0.00 4.26
2274 2304 5.065988 ACTCTCTACATCTTTCTCTTCGCTC 59.934 44.000 0.00 0.00 0.00 5.03
2275 2305 4.947388 ACTCTCTACATCTTTCTCTTCGCT 59.053 41.667 0.00 0.00 0.00 4.93
2276 2306 5.034152 CACTCTCTACATCTTTCTCTTCGC 58.966 45.833 0.00 0.00 0.00 4.70
2277 2307 5.034152 GCACTCTCTACATCTTTCTCTTCG 58.966 45.833 0.00 0.00 0.00 3.79
2278 2308 5.034152 CGCACTCTCTACATCTTTCTCTTC 58.966 45.833 0.00 0.00 0.00 2.87
2279 2309 4.461081 ACGCACTCTCTACATCTTTCTCTT 59.539 41.667 0.00 0.00 0.00 2.85
2280 2310 4.013728 ACGCACTCTCTACATCTTTCTCT 58.986 43.478 0.00 0.00 0.00 3.10
2281 2311 4.101942 CACGCACTCTCTACATCTTTCTC 58.898 47.826 0.00 0.00 0.00 2.87
2282 2312 3.674682 GCACGCACTCTCTACATCTTTCT 60.675 47.826 0.00 0.00 0.00 2.52
2283 2313 2.600867 GCACGCACTCTCTACATCTTTC 59.399 50.000 0.00 0.00 0.00 2.62
2284 2314 2.611518 GCACGCACTCTCTACATCTTT 58.388 47.619 0.00 0.00 0.00 2.52
2285 2315 1.468224 CGCACGCACTCTCTACATCTT 60.468 52.381 0.00 0.00 0.00 2.40
2286 2316 0.099613 CGCACGCACTCTCTACATCT 59.900 55.000 0.00 0.00 0.00 2.90
2287 2317 0.179161 ACGCACGCACTCTCTACATC 60.179 55.000 0.00 0.00 0.00 3.06
2288 2318 0.456824 CACGCACGCACTCTCTACAT 60.457 55.000 0.00 0.00 0.00 2.29
2289 2319 1.081442 CACGCACGCACTCTCTACA 60.081 57.895 0.00 0.00 0.00 2.74
2290 2320 2.437343 GCACGCACGCACTCTCTAC 61.437 63.158 0.00 0.00 0.00 2.59
2291 2321 2.126463 GCACGCACGCACTCTCTA 60.126 61.111 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.