Multiple sequence alignment - TraesCS6A01G305900

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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 TraesCS6A01G305900 chr6A 100.000 2492 0 0 1 2492 539540414 539542905 0.000000e+00 4602
1 TraesCS6A01G305900 chr6A 98.607 2010 17 3 1 1999 81878342 81876333 0.000000e+00 3546
2 TraesCS6A01G305900 chr6A 98.205 2006 16 4 1 2001 68986029 68988019 0.000000e+00 3487
3 TraesCS6A01G305900 chr7A 99.250 1999 11 2 1 1995 594456846 594458844 0.000000e+00 3605
4 TraesCS6A01G305900 chr3B 99.149 1998 13 2 2 1995 217968232 217970229 0.000000e+00 3592
5 TraesCS6A01G305900 chr3B 99.100 1999 15 1 1 1996 220780301 220782299 0.000000e+00 3589
6 TraesCS6A01G305900 chr3B 98.799 1999 20 2 1 1995 217965040 217963042 0.000000e+00 3555
7 TraesCS6A01G305900 chr3B 98.351 2001 11 4 1 1997 565442175 565440193 0.000000e+00 3493
8 TraesCS6A01G305900 chr3B 91.026 390 15 4 1626 2000 636265023 636265407 2.210000e-140 508
9 TraesCS6A01G305900 chr3B 88.761 347 24 10 1992 2331 736356482 736356820 6.410000e-111 411
10 TraesCS6A01G305900 chr3B 90.323 279 13 7 1992 2263 779036678 779036407 1.100000e-93 353
11 TraesCS6A01G305900 chr1B 99.100 2000 14 2 1 1996 70692698 70690699 0.000000e+00 3591
12 TraesCS6A01G305900 chr1B 90.778 347 17 8 1992 2331 564310420 564310758 1.360000e-122 449
13 TraesCS6A01G305900 chr1A 98.449 1999 12 3 1 1995 394599115 394601098 0.000000e+00 3502
14 TraesCS6A01G305900 chr1A 89.546 507 23 13 1992 2491 47728262 47727779 1.270000e-172 616
15 TraesCS6A01G305900 chr4B 99.321 589 3 1 1408 1995 564142653 564143241 0.000000e+00 1064
16 TraesCS6A01G305900 chrUn 99.457 552 3 0 1408 1959 400615812 400616363 0.000000e+00 1003
17 TraesCS6A01G305900 chrUn 92.225 373 14 7 1992 2357 137885000 137885364 4.750000e-142 514
18 TraesCS6A01G305900 chrUn 83.212 411 14 20 2105 2492 24772439 24772817 2.390000e-85 326
19 TraesCS6A01G305900 chrUn 82.725 411 16 20 2105 2492 317331981 317332359 5.170000e-82 315
20 TraesCS6A01G305900 chrUn 86.154 130 10 6 2364 2492 374514059 374514181 1.550000e-27 134
21 TraesCS6A01G305900 chrUn 86.792 106 8 4 1992 2092 24772385 24772489 2.030000e-21 113
22 TraesCS6A01G305900 chrUn 86.792 106 8 4 1992 2092 317331927 317332031 2.030000e-21 113
23 TraesCS6A01G305900 chr3A 95.618 502 9 4 1992 2492 18085118 18084629 0.000000e+00 793
24 TraesCS6A01G305900 chr2D 94.809 366 16 3 1992 2357 19378925 19379287 3.600000e-158 568
25 TraesCS6A01G305900 chr2D 82.266 406 22 24 2105 2492 593430416 593430789 3.110000e-79 305
26 TraesCS6A01G305900 chr2D 87.597 129 9 5 2364 2492 116830094 116830215 2.580000e-30 143
27 TraesCS6A01G305900 chr2D 86.792 106 8 4 1992 2092 593430362 593430466 2.030000e-21 113
28 TraesCS6A01G305900 chr7B 89.685 349 19 7 1992 2331 692350589 692350249 1.770000e-116 429
29 TraesCS6A01G305900 chr4D 89.119 193 5 4 1179 1366 173129160 173129341 2.490000e-55 226
30 TraesCS6A01G305900 chr6D 87.597 129 9 5 2364 2492 39089954 39089833 2.580000e-30 143
31 TraesCS6A01G305900 chr7D 86.154 130 10 6 2364 2492 521349680 521349802 1.550000e-27 134


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 TraesCS6A01G305900 chr6A 539540414 539542905 2491 False 4602 4602 100.000 1 2492 1 chr6A.!!$F2 2491
1 TraesCS6A01G305900 chr6A 81876333 81878342 2009 True 3546 3546 98.607 1 1999 1 chr6A.!!$R1 1998
2 TraesCS6A01G305900 chr6A 68986029 68988019 1990 False 3487 3487 98.205 1 2001 1 chr6A.!!$F1 2000
3 TraesCS6A01G305900 chr7A 594456846 594458844 1998 False 3605 3605 99.250 1 1995 1 chr7A.!!$F1 1994
4 TraesCS6A01G305900 chr3B 217968232 217970229 1997 False 3592 3592 99.149 2 1995 1 chr3B.!!$F1 1993
5 TraesCS6A01G305900 chr3B 220780301 220782299 1998 False 3589 3589 99.100 1 1996 1 chr3B.!!$F2 1995
6 TraesCS6A01G305900 chr3B 217963042 217965040 1998 True 3555 3555 98.799 1 1995 1 chr3B.!!$R1 1994
7 TraesCS6A01G305900 chr3B 565440193 565442175 1982 True 3493 3493 98.351 1 1997 1 chr3B.!!$R2 1996
8 TraesCS6A01G305900 chr1B 70690699 70692698 1999 True 3591 3591 99.100 1 1996 1 chr1B.!!$R1 1995
9 TraesCS6A01G305900 chr1A 394599115 394601098 1983 False 3502 3502 98.449 1 1995 1 chr1A.!!$F1 1994
10 TraesCS6A01G305900 chr4B 564142653 564143241 588 False 1064 1064 99.321 1408 1995 1 chr4B.!!$F1 587
11 TraesCS6A01G305900 chrUn 400615812 400616363 551 False 1003 1003 99.457 1408 1959 1 chrUn.!!$F3 551

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
294 295 4.656112 GGAGAGGATCAATCTAGGTTTCCA 59.344 45.833 8.8 0.0 37.82 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2293 2336 0.037734 ACCTTTTCCCCAACCTAGCG 59.962 55.0 0.0 0.0 0.0 4.26 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
294 295 4.656112 GGAGAGGATCAATCTAGGTTTCCA 59.344 45.833 8.80 0.00 37.82 3.53
434 435 9.301897 AGTTCTTTCCTATTGTAAGCAGAAATT 57.698 29.630 0.00 0.00 0.00 1.82
1269 1270 2.867333 ATGTCCGTCTGCACTACGCG 62.867 60.000 3.53 3.53 46.97 6.01
2001 2044 4.498009 CCGCCTTAAAAACATAGGATGCAG 60.498 45.833 0.00 0.00 0.00 4.41
2002 2045 4.096382 CGCCTTAAAAACATAGGATGCAGT 59.904 41.667 0.00 0.00 0.00 4.40
2003 2046 5.295787 CGCCTTAAAAACATAGGATGCAGTA 59.704 40.000 0.00 0.00 0.00 2.74
2004 2047 6.495706 GCCTTAAAAACATAGGATGCAGTAC 58.504 40.000 0.00 0.00 0.00 2.73
2005 2048 6.094881 GCCTTAAAAACATAGGATGCAGTACA 59.905 38.462 0.00 0.00 0.00 2.90
2006 2049 7.201821 GCCTTAAAAACATAGGATGCAGTACAT 60.202 37.037 0.00 0.00 43.54 2.29
2007 2050 8.686334 CCTTAAAAACATAGGATGCAGTACATT 58.314 33.333 0.00 0.00 39.84 2.71
2008 2051 9.507280 CTTAAAAACATAGGATGCAGTACATTG 57.493 33.333 0.00 0.00 39.84 2.82
2009 2052 7.466746 AAAAACATAGGATGCAGTACATTGT 57.533 32.000 0.00 0.00 39.84 2.71
2010 2053 6.441093 AAACATAGGATGCAGTACATTGTG 57.559 37.500 0.00 0.00 39.84 3.33
2011 2054 4.454678 ACATAGGATGCAGTACATTGTGG 58.545 43.478 0.00 0.00 39.84 4.17
2012 2055 4.080356 ACATAGGATGCAGTACATTGTGGT 60.080 41.667 0.00 0.00 39.84 4.16
2013 2056 3.439857 AGGATGCAGTACATTGTGGTT 57.560 42.857 0.00 0.00 39.84 3.67
2014 2057 3.084039 AGGATGCAGTACATTGTGGTTG 58.916 45.455 0.00 0.00 39.84 3.77
2015 2058 2.819608 GGATGCAGTACATTGTGGTTGT 59.180 45.455 0.00 0.00 39.84 3.32
2016 2059 3.255642 GGATGCAGTACATTGTGGTTGTT 59.744 43.478 0.00 0.00 39.84 2.83
2017 2060 3.706802 TGCAGTACATTGTGGTTGTTG 57.293 42.857 0.00 0.00 0.00 3.33
2018 2061 3.282885 TGCAGTACATTGTGGTTGTTGA 58.717 40.909 0.00 0.00 0.00 3.18
2019 2062 3.314913 TGCAGTACATTGTGGTTGTTGAG 59.685 43.478 0.00 0.00 0.00 3.02
2020 2063 3.304659 GCAGTACATTGTGGTTGTTGAGG 60.305 47.826 0.00 0.00 0.00 3.86
2021 2064 4.133820 CAGTACATTGTGGTTGTTGAGGA 58.866 43.478 0.00 0.00 0.00 3.71
2022 2065 4.578516 CAGTACATTGTGGTTGTTGAGGAA 59.421 41.667 0.00 0.00 0.00 3.36
2023 2066 4.578928 AGTACATTGTGGTTGTTGAGGAAC 59.421 41.667 0.00 0.00 0.00 3.62
2024 2067 2.357637 ACATTGTGGTTGTTGAGGAACG 59.642 45.455 0.00 0.00 34.49 3.95
2025 2068 1.384525 TTGTGGTTGTTGAGGAACGG 58.615 50.000 0.00 0.00 34.49 4.44
2026 2069 0.542333 TGTGGTTGTTGAGGAACGGA 59.458 50.000 0.00 0.00 34.49 4.69
2027 2070 1.226746 GTGGTTGTTGAGGAACGGAG 58.773 55.000 0.00 0.00 34.49 4.63
2028 2071 0.107831 TGGTTGTTGAGGAACGGAGG 59.892 55.000 0.00 0.00 34.49 4.30
2029 2072 1.235281 GGTTGTTGAGGAACGGAGGC 61.235 60.000 0.00 0.00 34.49 4.70
2030 2073 1.072505 TTGTTGAGGAACGGAGGCC 59.927 57.895 0.00 0.00 34.49 5.19
2042 2085 3.474570 GAGGCCGGACTGCTGGAT 61.475 66.667 19.29 0.00 43.76 3.41
2043 2086 3.746949 GAGGCCGGACTGCTGGATG 62.747 68.421 19.29 0.00 43.76 3.51
2044 2087 4.864334 GGCCGGACTGCTGGATGG 62.864 72.222 5.05 0.00 43.76 3.51
2045 2088 4.101448 GCCGGACTGCTGGATGGT 62.101 66.667 5.05 0.00 43.76 3.55
2046 2089 2.124983 CCGGACTGCTGGATGGTG 60.125 66.667 0.00 0.00 43.76 4.17
2047 2090 2.821366 CGGACTGCTGGATGGTGC 60.821 66.667 0.00 0.00 0.00 5.01
2048 2091 2.673523 GGACTGCTGGATGGTGCT 59.326 61.111 0.00 0.00 0.00 4.40
2049 2092 1.748122 GGACTGCTGGATGGTGCTG 60.748 63.158 0.00 0.00 0.00 4.41
2050 2093 2.360852 ACTGCTGGATGGTGCTGC 60.361 61.111 0.00 0.00 33.54 5.25
2051 2094 3.138798 CTGCTGGATGGTGCTGCC 61.139 66.667 0.00 0.00 32.02 4.85
2074 2117 4.779733 GCCAGGGAGGACCGAGGA 62.780 72.222 0.00 0.00 46.96 3.71
2075 2118 2.760385 CCAGGGAGGACCGAGGAC 60.760 72.222 0.00 0.00 46.96 3.85
2076 2119 3.141488 CAGGGAGGACCGAGGACG 61.141 72.222 0.00 0.00 46.96 4.79
2086 2129 4.135153 CGAGGACGGTGGCTGGAG 62.135 72.222 0.00 0.00 35.72 3.86
2087 2130 4.459089 GAGGACGGTGGCTGGAGC 62.459 72.222 0.00 0.00 41.14 4.70
2097 2140 4.154347 GCTGGAGCCTGGAGGTCG 62.154 72.222 0.00 0.00 44.30 4.79
2098 2141 4.154347 CTGGAGCCTGGAGGTCGC 62.154 72.222 0.00 0.00 44.30 5.19
2099 2142 4.704103 TGGAGCCTGGAGGTCGCT 62.704 66.667 0.00 0.00 44.30 4.93
2100 2143 4.154347 GGAGCCTGGAGGTCGCTG 62.154 72.222 0.00 0.00 44.30 5.18
2101 2144 4.828925 GAGCCTGGAGGTCGCTGC 62.829 72.222 0.00 0.00 37.57 5.25
2143 2186 4.394712 CGGAGGTGGACTGGTGGC 62.395 72.222 0.00 0.00 0.00 5.01
2144 2187 4.035102 GGAGGTGGACTGGTGGCC 62.035 72.222 0.00 0.00 0.00 5.36
2145 2188 2.930562 GAGGTGGACTGGTGGCCT 60.931 66.667 3.32 0.00 0.00 5.19
2146 2189 3.252284 AGGTGGACTGGTGGCCTG 61.252 66.667 3.32 0.00 0.00 4.85
2147 2190 4.351054 GGTGGACTGGTGGCCTGG 62.351 72.222 3.32 0.00 0.00 4.45
2207 2250 3.465403 CGAGGGCAGGGGAGTGAG 61.465 72.222 0.00 0.00 0.00 3.51
2208 2251 2.039624 GAGGGCAGGGGAGTGAGA 59.960 66.667 0.00 0.00 0.00 3.27
2209 2252 1.383803 GAGGGCAGGGGAGTGAGAT 60.384 63.158 0.00 0.00 0.00 2.75
2210 2253 1.692042 AGGGCAGGGGAGTGAGATG 60.692 63.158 0.00 0.00 0.00 2.90
2211 2254 2.750657 GGGCAGGGGAGTGAGATGG 61.751 68.421 0.00 0.00 0.00 3.51
2212 2255 1.997874 GGCAGGGGAGTGAGATGGT 60.998 63.158 0.00 0.00 0.00 3.55
2213 2256 1.524482 GCAGGGGAGTGAGATGGTC 59.476 63.158 0.00 0.00 0.00 4.02
2214 2257 1.819229 CAGGGGAGTGAGATGGTCG 59.181 63.158 0.00 0.00 0.00 4.79
2215 2258 1.381872 AGGGGAGTGAGATGGTCGG 60.382 63.158 0.00 0.00 0.00 4.79
2216 2259 1.381327 GGGGAGTGAGATGGTCGGA 60.381 63.158 0.00 0.00 0.00 4.55
2217 2260 0.760945 GGGGAGTGAGATGGTCGGAT 60.761 60.000 0.00 0.00 0.00 4.18
2218 2261 0.390860 GGGAGTGAGATGGTCGGATG 59.609 60.000 0.00 0.00 0.00 3.51
2219 2262 0.390860 GGAGTGAGATGGTCGGATGG 59.609 60.000 0.00 0.00 0.00 3.51
2220 2263 1.403814 GAGTGAGATGGTCGGATGGA 58.596 55.000 0.00 0.00 0.00 3.41
2221 2264 1.339610 GAGTGAGATGGTCGGATGGAG 59.660 57.143 0.00 0.00 0.00 3.86
2222 2265 0.390860 GTGAGATGGTCGGATGGAGG 59.609 60.000 0.00 0.00 0.00 4.30
2223 2266 0.760567 TGAGATGGTCGGATGGAGGG 60.761 60.000 0.00 0.00 0.00 4.30
2224 2267 1.460305 AGATGGTCGGATGGAGGGG 60.460 63.158 0.00 0.00 0.00 4.79
2225 2268 1.459539 GATGGTCGGATGGAGGGGA 60.460 63.158 0.00 0.00 0.00 4.81
2226 2269 1.460305 ATGGTCGGATGGAGGGGAG 60.460 63.158 0.00 0.00 0.00 4.30
2227 2270 2.844839 GGTCGGATGGAGGGGAGG 60.845 72.222 0.00 0.00 0.00 4.30
2228 2271 2.844839 GTCGGATGGAGGGGAGGG 60.845 72.222 0.00 0.00 0.00 4.30
2229 2272 4.172232 TCGGATGGAGGGGAGGGG 62.172 72.222 0.00 0.00 0.00 4.79
2230 2273 4.172232 CGGATGGAGGGGAGGGGA 62.172 72.222 0.00 0.00 0.00 4.81
2231 2274 2.122189 GGATGGAGGGGAGGGGAG 60.122 72.222 0.00 0.00 0.00 4.30
2232 2275 2.122189 GATGGAGGGGAGGGGAGG 60.122 72.222 0.00 0.00 0.00 4.30
2233 2276 3.795924 ATGGAGGGGAGGGGAGGG 61.796 72.222 0.00 0.00 0.00 4.30
2236 2279 4.179599 GAGGGGAGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
2240 2283 4.500826 GGAGGGGAGGGGAGGGAC 62.501 77.778 0.00 0.00 0.00 4.46
2241 2284 4.500826 GAGGGGAGGGGAGGGACC 62.501 77.778 0.00 0.00 38.08 4.46
2244 2287 4.862823 GGGAGGGGAGGGACCGAG 62.863 77.778 0.00 0.00 40.11 4.63
2245 2288 4.862823 GGAGGGGAGGGACCGAGG 62.863 77.778 0.00 0.00 40.11 4.63
2246 2289 4.862823 GAGGGGAGGGACCGAGGG 62.863 77.778 0.00 0.00 40.11 4.30
2248 2291 4.862823 GGGGAGGGACCGAGGGAG 62.863 77.778 0.00 0.00 40.11 4.30
2259 2302 3.535962 GAGGGAGCGGCAGGAGAG 61.536 72.222 1.45 0.00 0.00 3.20
2298 2341 4.334837 GCCTTCAGCTAGCGCTAG 57.665 61.111 34.98 34.98 46.99 3.42
2299 2342 1.300542 GCCTTCAGCTAGCGCTAGG 60.301 63.158 37.97 27.48 46.99 3.02
2300 2343 2.022240 GCCTTCAGCTAGCGCTAGGT 62.022 60.000 36.64 36.64 46.99 3.08
2301 2344 0.461961 CCTTCAGCTAGCGCTAGGTT 59.538 55.000 38.89 19.12 46.99 3.50
2302 2345 1.565305 CTTCAGCTAGCGCTAGGTTG 58.435 55.000 38.89 31.64 46.99 3.77
2303 2346 0.175760 TTCAGCTAGCGCTAGGTTGG 59.824 55.000 38.89 29.71 46.99 3.77
2304 2347 1.227380 CAGCTAGCGCTAGGTTGGG 60.227 63.158 38.89 26.74 46.99 4.12
2305 2348 2.109181 GCTAGCGCTAGGTTGGGG 59.891 66.667 37.97 18.07 33.87 4.96
2306 2349 2.432300 GCTAGCGCTAGGTTGGGGA 61.432 63.158 37.97 8.55 33.87 4.81
2307 2350 1.968050 GCTAGCGCTAGGTTGGGGAA 61.968 60.000 37.97 7.78 33.87 3.97
2308 2351 0.539986 CTAGCGCTAGGTTGGGGAAA 59.460 55.000 32.51 2.03 0.00 3.13
2309 2352 0.985760 TAGCGCTAGGTTGGGGAAAA 59.014 50.000 14.45 0.00 0.00 2.29
2310 2353 0.322546 AGCGCTAGGTTGGGGAAAAG 60.323 55.000 8.99 0.00 0.00 2.27
2311 2354 1.313091 GCGCTAGGTTGGGGAAAAGG 61.313 60.000 0.00 0.00 0.00 3.11
2312 2355 0.037734 CGCTAGGTTGGGGAAAAGGT 59.962 55.000 0.00 0.00 0.00 3.50
2313 2356 1.546998 CGCTAGGTTGGGGAAAAGGTT 60.547 52.381 0.00 0.00 0.00 3.50
2314 2357 2.290450 CGCTAGGTTGGGGAAAAGGTTA 60.290 50.000 0.00 0.00 0.00 2.85
2315 2358 3.353557 GCTAGGTTGGGGAAAAGGTTAG 58.646 50.000 0.00 0.00 0.00 2.34
2316 2359 3.009805 GCTAGGTTGGGGAAAAGGTTAGA 59.990 47.826 0.00 0.00 0.00 2.10
2317 2360 4.507869 GCTAGGTTGGGGAAAAGGTTAGAA 60.508 45.833 0.00 0.00 0.00 2.10
2318 2361 4.759793 AGGTTGGGGAAAAGGTTAGAAT 57.240 40.909 0.00 0.00 0.00 2.40
2319 2362 4.673968 AGGTTGGGGAAAAGGTTAGAATC 58.326 43.478 0.00 0.00 0.00 2.52
2320 2363 3.442625 GGTTGGGGAAAAGGTTAGAATCG 59.557 47.826 0.00 0.00 0.00 3.34
2321 2364 4.329392 GTTGGGGAAAAGGTTAGAATCGA 58.671 43.478 0.00 0.00 0.00 3.59
2322 2365 4.216411 TGGGGAAAAGGTTAGAATCGAG 57.784 45.455 0.00 0.00 0.00 4.04
2323 2366 3.054655 TGGGGAAAAGGTTAGAATCGAGG 60.055 47.826 0.00 0.00 0.00 4.63
2324 2367 3.199289 GGGGAAAAGGTTAGAATCGAGGA 59.801 47.826 0.00 0.00 0.00 3.71
2325 2368 4.324022 GGGGAAAAGGTTAGAATCGAGGAA 60.324 45.833 0.00 0.00 0.00 3.36
2326 2369 4.876679 GGGAAAAGGTTAGAATCGAGGAAG 59.123 45.833 0.00 0.00 0.00 3.46
2327 2370 4.876679 GGAAAAGGTTAGAATCGAGGAAGG 59.123 45.833 0.00 0.00 0.00 3.46
2328 2371 4.489306 AAAGGTTAGAATCGAGGAAGGG 57.511 45.455 0.00 0.00 0.00 3.95
2329 2372 3.399952 AGGTTAGAATCGAGGAAGGGA 57.600 47.619 0.00 0.00 0.00 4.20
2330 2373 3.721021 AGGTTAGAATCGAGGAAGGGAA 58.279 45.455 0.00 0.00 0.00 3.97
2331 2374 4.101856 AGGTTAGAATCGAGGAAGGGAAA 58.898 43.478 0.00 0.00 0.00 3.13
2332 2375 4.722279 AGGTTAGAATCGAGGAAGGGAAAT 59.278 41.667 0.00 0.00 0.00 2.17
2333 2376 4.816925 GGTTAGAATCGAGGAAGGGAAATG 59.183 45.833 0.00 0.00 0.00 2.32
2334 2377 5.396436 GGTTAGAATCGAGGAAGGGAAATGA 60.396 44.000 0.00 0.00 0.00 2.57
2335 2378 4.143986 AGAATCGAGGAAGGGAAATGAC 57.856 45.455 0.00 0.00 0.00 3.06
2336 2379 2.604046 ATCGAGGAAGGGAAATGACG 57.396 50.000 0.00 0.00 0.00 4.35
2337 2380 1.263356 TCGAGGAAGGGAAATGACGT 58.737 50.000 0.00 0.00 0.00 4.34
2338 2381 1.067142 TCGAGGAAGGGAAATGACGTG 60.067 52.381 0.00 0.00 0.00 4.49
2339 2382 1.087501 GAGGAAGGGAAATGACGTGC 58.912 55.000 0.00 0.00 0.00 5.34
2340 2383 0.693049 AGGAAGGGAAATGACGTGCT 59.307 50.000 0.00 0.00 0.00 4.40
2341 2384 1.073923 AGGAAGGGAAATGACGTGCTT 59.926 47.619 0.00 0.00 0.00 3.91
2342 2385 2.304761 AGGAAGGGAAATGACGTGCTTA 59.695 45.455 0.00 0.00 0.00 3.09
2343 2386 2.678336 GGAAGGGAAATGACGTGCTTAG 59.322 50.000 0.00 0.00 0.00 2.18
2344 2387 2.403252 AGGGAAATGACGTGCTTAGG 57.597 50.000 0.00 0.00 0.00 2.69
2345 2388 0.733150 GGGAAATGACGTGCTTAGGC 59.267 55.000 0.00 0.00 39.26 3.93
2346 2389 0.373716 GGAAATGACGTGCTTAGGCG 59.626 55.000 0.00 0.00 42.25 5.52
2347 2390 0.373716 GAAATGACGTGCTTAGGCGG 59.626 55.000 0.00 0.00 42.25 6.13
2348 2391 0.321298 AAATGACGTGCTTAGGCGGT 60.321 50.000 0.00 0.00 42.25 5.68
2349 2392 0.739813 AATGACGTGCTTAGGCGGTC 60.740 55.000 12.16 12.16 41.61 4.79
2350 2393 2.879462 GACGTGCTTAGGCGGTCG 60.879 66.667 0.00 6.29 42.25 4.79
2351 2394 4.430765 ACGTGCTTAGGCGGTCGG 62.431 66.667 11.77 0.00 42.25 4.79
2360 2403 3.976758 GGCGGTCGGCTACTTTTT 58.023 55.556 9.67 0.00 42.94 1.94
2376 2419 1.572447 TTTTTGGCTACTCGCACGC 59.428 52.632 0.00 0.00 41.67 5.34
2377 2420 1.847890 TTTTTGGCTACTCGCACGCC 61.848 55.000 0.00 0.00 44.02 5.68
2378 2421 2.725203 TTTTGGCTACTCGCACGCCT 62.725 55.000 0.00 0.00 44.09 5.52
2379 2422 1.879737 TTTGGCTACTCGCACGCCTA 61.880 55.000 0.00 0.00 44.09 3.93
2380 2423 1.879737 TTGGCTACTCGCACGCCTAA 61.880 55.000 0.00 0.00 44.09 2.69
2381 2424 1.877165 GGCTACTCGCACGCCTAAC 60.877 63.158 0.00 0.00 40.62 2.34
2382 2425 1.877165 GCTACTCGCACGCCTAACC 60.877 63.158 0.00 0.00 38.92 2.85
2383 2426 1.509463 CTACTCGCACGCCTAACCA 59.491 57.895 0.00 0.00 0.00 3.67
2384 2427 0.525668 CTACTCGCACGCCTAACCAG 60.526 60.000 0.00 0.00 0.00 4.00
2385 2428 0.961857 TACTCGCACGCCTAACCAGA 60.962 55.000 0.00 0.00 0.00 3.86
2386 2429 1.805945 CTCGCACGCCTAACCAGAC 60.806 63.158 0.00 0.00 0.00 3.51
2387 2430 2.048597 CGCACGCCTAACCAGACA 60.049 61.111 0.00 0.00 0.00 3.41
2388 2431 2.380410 CGCACGCCTAACCAGACAC 61.380 63.158 0.00 0.00 0.00 3.67
2389 2432 2.033194 GCACGCCTAACCAGACACC 61.033 63.158 0.00 0.00 0.00 4.16
2390 2433 1.736645 CACGCCTAACCAGACACCG 60.737 63.158 0.00 0.00 0.00 4.94
2391 2434 2.813908 CGCCTAACCAGACACCGC 60.814 66.667 0.00 0.00 0.00 5.68
2392 2435 2.813908 GCCTAACCAGACACCGCG 60.814 66.667 0.00 0.00 0.00 6.46
2393 2436 2.654877 CCTAACCAGACACCGCGT 59.345 61.111 4.92 0.00 0.00 6.01
2394 2437 1.445582 CCTAACCAGACACCGCGTC 60.446 63.158 4.92 0.00 45.77 5.19
2401 2444 3.545481 GACACCGCGTCGCTCATG 61.545 66.667 16.36 12.53 34.19 3.07
2402 2445 4.357947 ACACCGCGTCGCTCATGT 62.358 61.111 16.36 13.17 0.00 3.21
2403 2446 3.545481 CACCGCGTCGCTCATGTC 61.545 66.667 16.36 0.00 0.00 3.06
2404 2447 3.749064 ACCGCGTCGCTCATGTCT 61.749 61.111 16.36 0.00 0.00 3.41
2405 2448 3.250323 CCGCGTCGCTCATGTCTG 61.250 66.667 16.36 0.00 0.00 3.51
2406 2449 3.250323 CGCGTCGCTCATGTCTGG 61.250 66.667 16.36 0.00 0.00 3.86
2407 2450 2.125912 GCGTCGCTCATGTCTGGT 60.126 61.111 10.68 0.00 0.00 4.00
2408 2451 1.138883 GCGTCGCTCATGTCTGGTA 59.861 57.895 10.68 0.00 0.00 3.25
2409 2452 1.140407 GCGTCGCTCATGTCTGGTAC 61.140 60.000 10.68 0.00 0.00 3.34
2410 2453 0.525668 CGTCGCTCATGTCTGGTACC 60.526 60.000 4.43 4.43 0.00 3.34
2411 2454 0.530744 GTCGCTCATGTCTGGTACCA 59.469 55.000 15.39 15.39 0.00 3.25
2412 2455 1.067142 GTCGCTCATGTCTGGTACCAA 60.067 52.381 17.11 0.82 0.00 3.67
2413 2456 1.204704 TCGCTCATGTCTGGTACCAAG 59.795 52.381 17.11 10.31 0.00 3.61
2414 2457 1.373570 GCTCATGTCTGGTACCAAGC 58.626 55.000 17.11 16.57 0.00 4.01
2415 2458 1.645034 CTCATGTCTGGTACCAAGCG 58.355 55.000 17.11 4.53 0.00 4.68
2416 2459 0.973632 TCATGTCTGGTACCAAGCGT 59.026 50.000 17.11 9.94 0.00 5.07
2417 2460 1.078709 CATGTCTGGTACCAAGCGTG 58.921 55.000 17.11 17.52 0.00 5.34
2432 2475 4.586235 GTGGCTGCCTGGGTGTGT 62.586 66.667 21.03 0.00 0.00 3.72
2433 2476 4.269523 TGGCTGCCTGGGTGTGTC 62.270 66.667 21.03 0.00 0.00 3.67
2434 2477 3.958860 GGCTGCCTGGGTGTGTCT 61.959 66.667 12.43 0.00 0.00 3.41
2435 2478 2.670934 GCTGCCTGGGTGTGTCTG 60.671 66.667 0.00 0.00 0.00 3.51
2436 2479 2.033141 CTGCCTGGGTGTGTCTGG 59.967 66.667 0.00 0.00 0.00 3.86
2437 2480 3.557903 CTGCCTGGGTGTGTCTGGG 62.558 68.421 0.00 0.00 0.00 4.45
2439 2482 3.252284 CCTGGGTGTGTCTGGGCT 61.252 66.667 0.00 0.00 0.00 5.19
2440 2483 2.348998 CTGGGTGTGTCTGGGCTC 59.651 66.667 0.00 0.00 0.00 4.70
2441 2484 2.447572 TGGGTGTGTCTGGGCTCA 60.448 61.111 0.00 0.00 0.00 4.26
2442 2485 1.845627 CTGGGTGTGTCTGGGCTCAT 61.846 60.000 0.00 0.00 0.00 2.90
2443 2486 1.377725 GGGTGTGTCTGGGCTCATG 60.378 63.158 0.00 0.00 0.00 3.07
2444 2487 1.377725 GGTGTGTCTGGGCTCATGG 60.378 63.158 0.00 0.00 0.00 3.66
2445 2488 1.377725 GTGTGTCTGGGCTCATGGG 60.378 63.158 0.00 0.00 0.00 4.00
2446 2489 2.439156 GTGTCTGGGCTCATGGGC 60.439 66.667 9.80 9.80 40.05 5.36
2462 2505 2.663196 GCCAACGGCCTAGTCACT 59.337 61.111 0.00 0.00 44.06 3.41
2463 2506 1.448013 GCCAACGGCCTAGTCACTC 60.448 63.158 0.00 0.00 44.06 3.51
2464 2507 1.889530 GCCAACGGCCTAGTCACTCT 61.890 60.000 0.00 0.00 44.06 3.24
2465 2508 0.608640 CCAACGGCCTAGTCACTCTT 59.391 55.000 0.00 0.00 0.00 2.85
2466 2509 1.002087 CCAACGGCCTAGTCACTCTTT 59.998 52.381 0.00 0.00 0.00 2.52
2467 2510 2.232941 CCAACGGCCTAGTCACTCTTTA 59.767 50.000 0.00 0.00 0.00 1.85
2468 2511 3.118738 CCAACGGCCTAGTCACTCTTTAT 60.119 47.826 0.00 0.00 0.00 1.40
2469 2512 4.098960 CCAACGGCCTAGTCACTCTTTATA 59.901 45.833 0.00 0.00 0.00 0.98
2470 2513 5.221461 CCAACGGCCTAGTCACTCTTTATAT 60.221 44.000 0.00 0.00 0.00 0.86
2471 2514 6.281405 CAACGGCCTAGTCACTCTTTATATT 58.719 40.000 0.00 0.00 0.00 1.28
2472 2515 7.431249 CAACGGCCTAGTCACTCTTTATATTA 58.569 38.462 0.00 0.00 0.00 0.98
2473 2516 6.979465 ACGGCCTAGTCACTCTTTATATTAC 58.021 40.000 0.00 0.00 0.00 1.89
2474 2517 6.015603 ACGGCCTAGTCACTCTTTATATTACC 60.016 42.308 0.00 0.00 0.00 2.85
2475 2518 6.208994 CGGCCTAGTCACTCTTTATATTACCT 59.791 42.308 0.00 0.00 0.00 3.08
2476 2519 7.255871 CGGCCTAGTCACTCTTTATATTACCTT 60.256 40.741 0.00 0.00 0.00 3.50
2477 2520 9.086758 GGCCTAGTCACTCTTTATATTACCTTA 57.913 37.037 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
294 295 5.738118 CAATGGTTGCTTGTTTTGTTGAT 57.262 34.783 0.00 0.00 0.00 2.57
434 435 2.106511 GCTCCCCAACTAAGGCATCATA 59.893 50.000 0.00 0.00 0.00 2.15
768 769 4.337836 TGAAGCACAAAGACTAACAATGCA 59.662 37.500 0.00 0.00 34.03 3.96
1269 1270 2.260481 GTTGTAGTAGGTCTCTTGCGC 58.740 52.381 0.00 0.00 0.00 6.09
2001 2044 4.553938 CGTTCCTCAACAACCACAATGTAC 60.554 45.833 0.00 0.00 32.14 2.90
2002 2045 3.562141 CGTTCCTCAACAACCACAATGTA 59.438 43.478 0.00 0.00 32.14 2.29
2003 2046 2.357637 CGTTCCTCAACAACCACAATGT 59.642 45.455 0.00 0.00 32.14 2.71
2004 2047 2.287547 CCGTTCCTCAACAACCACAATG 60.288 50.000 0.00 0.00 32.14 2.82
2005 2048 1.953686 CCGTTCCTCAACAACCACAAT 59.046 47.619 0.00 0.00 32.14 2.71
2006 2049 1.065345 TCCGTTCCTCAACAACCACAA 60.065 47.619 0.00 0.00 32.14 3.33
2007 2050 0.542333 TCCGTTCCTCAACAACCACA 59.458 50.000 0.00 0.00 32.14 4.17
2008 2051 1.226746 CTCCGTTCCTCAACAACCAC 58.773 55.000 0.00 0.00 32.14 4.16
2009 2052 0.107831 CCTCCGTTCCTCAACAACCA 59.892 55.000 0.00 0.00 32.14 3.67
2010 2053 1.235281 GCCTCCGTTCCTCAACAACC 61.235 60.000 0.00 0.00 32.14 3.77
2011 2054 1.235281 GGCCTCCGTTCCTCAACAAC 61.235 60.000 0.00 0.00 32.14 3.32
2012 2055 1.072505 GGCCTCCGTTCCTCAACAA 59.927 57.895 0.00 0.00 32.14 2.83
2013 2056 2.747686 GGCCTCCGTTCCTCAACA 59.252 61.111 0.00 0.00 32.14 3.33
2014 2057 2.434359 CGGCCTCCGTTCCTCAAC 60.434 66.667 0.00 0.00 42.73 3.18
2015 2058 3.702048 CCGGCCTCCGTTCCTCAA 61.702 66.667 0.00 0.00 46.80 3.02
2016 2059 4.689549 TCCGGCCTCCGTTCCTCA 62.690 66.667 0.00 0.00 46.80 3.86
2017 2060 4.144703 GTCCGGCCTCCGTTCCTC 62.145 72.222 0.00 0.00 46.80 3.71
2018 2061 4.698625 AGTCCGGCCTCCGTTCCT 62.699 66.667 0.00 0.00 46.80 3.36
2019 2062 4.452733 CAGTCCGGCCTCCGTTCC 62.453 72.222 0.00 0.00 46.80 3.62
2025 2068 3.474570 ATCCAGCAGTCCGGCCTC 61.475 66.667 0.00 0.00 0.00 4.70
2026 2069 3.790437 CATCCAGCAGTCCGGCCT 61.790 66.667 0.00 0.00 0.00 5.19
2027 2070 4.864334 CCATCCAGCAGTCCGGCC 62.864 72.222 0.00 0.00 0.00 6.13
2028 2071 4.101448 ACCATCCAGCAGTCCGGC 62.101 66.667 0.00 0.00 0.00 6.13
2029 2072 2.124983 CACCATCCAGCAGTCCGG 60.125 66.667 0.00 0.00 0.00 5.14
2030 2073 2.821366 GCACCATCCAGCAGTCCG 60.821 66.667 0.00 0.00 0.00 4.79
2031 2074 1.748122 CAGCACCATCCAGCAGTCC 60.748 63.158 0.00 0.00 0.00 3.85
2032 2075 2.404995 GCAGCACCATCCAGCAGTC 61.405 63.158 0.00 0.00 0.00 3.51
2033 2076 2.360852 GCAGCACCATCCAGCAGT 60.361 61.111 0.00 0.00 0.00 4.40
2034 2077 3.138798 GGCAGCACCATCCAGCAG 61.139 66.667 0.00 0.00 38.86 4.24
2057 2100 4.779733 TCCTCGGTCCTCCCTGGC 62.780 72.222 0.00 0.00 35.26 4.85
2058 2101 2.760385 GTCCTCGGTCCTCCCTGG 60.760 72.222 0.00 0.00 37.10 4.45
2059 2102 3.141488 CGTCCTCGGTCCTCCCTG 61.141 72.222 0.00 0.00 0.00 4.45
2069 2112 4.135153 CTCCAGCCACCGTCCTCG 62.135 72.222 0.00 0.00 0.00 4.63
2070 2113 4.459089 GCTCCAGCCACCGTCCTC 62.459 72.222 0.00 0.00 34.31 3.71
2080 2123 4.154347 CGACCTCCAGGCTCCAGC 62.154 72.222 0.00 0.00 39.32 4.85
2081 2124 4.154347 GCGACCTCCAGGCTCCAG 62.154 72.222 0.00 0.00 39.32 3.86
2082 2125 4.704103 AGCGACCTCCAGGCTCCA 62.704 66.667 0.00 0.00 39.32 3.86
2083 2126 4.154347 CAGCGACCTCCAGGCTCC 62.154 72.222 0.00 0.00 39.32 4.70
2084 2127 4.828925 GCAGCGACCTCCAGGCTC 62.829 72.222 0.00 0.00 39.32 4.70
2121 2164 3.775654 CAGTCCACCTCCGGCCTC 61.776 72.222 0.00 0.00 0.00 4.70
2124 2167 4.394712 CACCAGTCCACCTCCGGC 62.395 72.222 0.00 0.00 0.00 6.13
2125 2168 3.706373 CCACCAGTCCACCTCCGG 61.706 72.222 0.00 0.00 0.00 5.14
2126 2169 4.394712 GCCACCAGTCCACCTCCG 62.395 72.222 0.00 0.00 0.00 4.63
2127 2170 4.035102 GGCCACCAGTCCACCTCC 62.035 72.222 0.00 0.00 0.00 4.30
2128 2171 2.930562 AGGCCACCAGTCCACCTC 60.931 66.667 5.01 0.00 0.00 3.85
2129 2172 3.252284 CAGGCCACCAGTCCACCT 61.252 66.667 5.01 0.00 0.00 4.00
2130 2173 4.351054 CCAGGCCACCAGTCCACC 62.351 72.222 5.01 0.00 0.00 4.61
2190 2233 3.465403 CTCACTCCCCTGCCCTCG 61.465 72.222 0.00 0.00 0.00 4.63
2191 2234 1.383803 ATCTCACTCCCCTGCCCTC 60.384 63.158 0.00 0.00 0.00 4.30
2192 2235 1.692042 CATCTCACTCCCCTGCCCT 60.692 63.158 0.00 0.00 0.00 5.19
2193 2236 2.750657 CCATCTCACTCCCCTGCCC 61.751 68.421 0.00 0.00 0.00 5.36
2194 2237 1.977293 GACCATCTCACTCCCCTGCC 61.977 65.000 0.00 0.00 0.00 4.85
2195 2238 1.524482 GACCATCTCACTCCCCTGC 59.476 63.158 0.00 0.00 0.00 4.85
2196 2239 1.680522 CCGACCATCTCACTCCCCTG 61.681 65.000 0.00 0.00 0.00 4.45
2197 2240 1.381872 CCGACCATCTCACTCCCCT 60.382 63.158 0.00 0.00 0.00 4.79
2198 2241 0.760945 ATCCGACCATCTCACTCCCC 60.761 60.000 0.00 0.00 0.00 4.81
2199 2242 0.390860 CATCCGACCATCTCACTCCC 59.609 60.000 0.00 0.00 0.00 4.30
2200 2243 0.390860 CCATCCGACCATCTCACTCC 59.609 60.000 0.00 0.00 0.00 3.85
2201 2244 1.339610 CTCCATCCGACCATCTCACTC 59.660 57.143 0.00 0.00 0.00 3.51
2202 2245 1.407936 CTCCATCCGACCATCTCACT 58.592 55.000 0.00 0.00 0.00 3.41
2203 2246 0.390860 CCTCCATCCGACCATCTCAC 59.609 60.000 0.00 0.00 0.00 3.51
2204 2247 0.760567 CCCTCCATCCGACCATCTCA 60.761 60.000 0.00 0.00 0.00 3.27
2205 2248 1.476007 CCCCTCCATCCGACCATCTC 61.476 65.000 0.00 0.00 0.00 2.75
2206 2249 1.460305 CCCCTCCATCCGACCATCT 60.460 63.158 0.00 0.00 0.00 2.90
2207 2250 1.459539 TCCCCTCCATCCGACCATC 60.460 63.158 0.00 0.00 0.00 3.51
2208 2251 1.460305 CTCCCCTCCATCCGACCAT 60.460 63.158 0.00 0.00 0.00 3.55
2209 2252 2.041922 CTCCCCTCCATCCGACCA 60.042 66.667 0.00 0.00 0.00 4.02
2210 2253 2.844839 CCTCCCCTCCATCCGACC 60.845 72.222 0.00 0.00 0.00 4.79
2211 2254 2.844839 CCCTCCCCTCCATCCGAC 60.845 72.222 0.00 0.00 0.00 4.79
2212 2255 4.172232 CCCCTCCCCTCCATCCGA 62.172 72.222 0.00 0.00 0.00 4.55
2213 2256 4.172232 TCCCCTCCCCTCCATCCG 62.172 72.222 0.00 0.00 0.00 4.18
2214 2257 2.122189 CTCCCCTCCCCTCCATCC 60.122 72.222 0.00 0.00 0.00 3.51
2215 2258 2.122189 CCTCCCCTCCCCTCCATC 60.122 72.222 0.00 0.00 0.00 3.51
2216 2259 3.795924 CCCTCCCCTCCCCTCCAT 61.796 72.222 0.00 0.00 0.00 3.41
2219 2262 4.179599 CTCCCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
2223 2266 4.500826 GTCCCTCCCCTCCCCTCC 62.501 77.778 0.00 0.00 0.00 4.30
2224 2267 4.500826 GGTCCCTCCCCTCCCCTC 62.501 77.778 0.00 0.00 0.00 4.30
2227 2270 4.862823 CTCGGTCCCTCCCCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
2228 2271 4.862823 CCTCGGTCCCTCCCCTCC 62.863 77.778 0.00 0.00 0.00 4.30
2229 2272 4.862823 CCCTCGGTCCCTCCCCTC 62.863 77.778 0.00 0.00 0.00 4.30
2231 2274 4.862823 CTCCCTCGGTCCCTCCCC 62.863 77.778 0.00 0.00 0.00 4.81
2242 2285 3.535962 CTCTCCTGCCGCTCCCTC 61.536 72.222 0.00 0.00 0.00 4.30
2288 2331 1.968050 TTCCCCAACCTAGCGCTAGC 61.968 60.000 34.26 4.06 45.58 3.42
2289 2332 0.539986 TTTCCCCAACCTAGCGCTAG 59.460 55.000 33.03 33.03 0.00 3.42
2290 2333 0.985760 TTTTCCCCAACCTAGCGCTA 59.014 50.000 17.75 17.75 0.00 4.26
2291 2334 0.322546 CTTTTCCCCAACCTAGCGCT 60.323 55.000 17.26 17.26 0.00 5.92
2292 2335 1.313091 CCTTTTCCCCAACCTAGCGC 61.313 60.000 0.00 0.00 0.00 5.92
2293 2336 0.037734 ACCTTTTCCCCAACCTAGCG 59.962 55.000 0.00 0.00 0.00 4.26
2294 2337 2.304221 AACCTTTTCCCCAACCTAGC 57.696 50.000 0.00 0.00 0.00 3.42
2295 2338 4.921644 TCTAACCTTTTCCCCAACCTAG 57.078 45.455 0.00 0.00 0.00 3.02
2296 2339 5.572066 CGATTCTAACCTTTTCCCCAACCTA 60.572 44.000 0.00 0.00 0.00 3.08
2297 2340 4.673968 GATTCTAACCTTTTCCCCAACCT 58.326 43.478 0.00 0.00 0.00 3.50
2298 2341 3.442625 CGATTCTAACCTTTTCCCCAACC 59.557 47.826 0.00 0.00 0.00 3.77
2299 2342 4.329392 TCGATTCTAACCTTTTCCCCAAC 58.671 43.478 0.00 0.00 0.00 3.77
2300 2343 4.566907 CCTCGATTCTAACCTTTTCCCCAA 60.567 45.833 0.00 0.00 0.00 4.12
2301 2344 3.054655 CCTCGATTCTAACCTTTTCCCCA 60.055 47.826 0.00 0.00 0.00 4.96
2302 2345 3.199289 TCCTCGATTCTAACCTTTTCCCC 59.801 47.826 0.00 0.00 0.00 4.81
2303 2346 4.482952 TCCTCGATTCTAACCTTTTCCC 57.517 45.455 0.00 0.00 0.00 3.97
2304 2347 4.876679 CCTTCCTCGATTCTAACCTTTTCC 59.123 45.833 0.00 0.00 0.00 3.13
2305 2348 4.876679 CCCTTCCTCGATTCTAACCTTTTC 59.123 45.833 0.00 0.00 0.00 2.29
2306 2349 4.534897 TCCCTTCCTCGATTCTAACCTTTT 59.465 41.667 0.00 0.00 0.00 2.27
2307 2350 4.101856 TCCCTTCCTCGATTCTAACCTTT 58.898 43.478 0.00 0.00 0.00 3.11
2308 2351 3.721021 TCCCTTCCTCGATTCTAACCTT 58.279 45.455 0.00 0.00 0.00 3.50
2309 2352 3.399952 TCCCTTCCTCGATTCTAACCT 57.600 47.619 0.00 0.00 0.00 3.50
2310 2353 4.482952 TTTCCCTTCCTCGATTCTAACC 57.517 45.455 0.00 0.00 0.00 2.85
2311 2354 5.524281 GTCATTTCCCTTCCTCGATTCTAAC 59.476 44.000 0.00 0.00 0.00 2.34
2312 2355 5.671493 GTCATTTCCCTTCCTCGATTCTAA 58.329 41.667 0.00 0.00 0.00 2.10
2313 2356 4.202121 CGTCATTTCCCTTCCTCGATTCTA 60.202 45.833 0.00 0.00 0.00 2.10
2314 2357 3.430929 CGTCATTTCCCTTCCTCGATTCT 60.431 47.826 0.00 0.00 0.00 2.40
2315 2358 2.866762 CGTCATTTCCCTTCCTCGATTC 59.133 50.000 0.00 0.00 0.00 2.52
2316 2359 2.236395 ACGTCATTTCCCTTCCTCGATT 59.764 45.455 0.00 0.00 0.00 3.34
2317 2360 1.831736 ACGTCATTTCCCTTCCTCGAT 59.168 47.619 0.00 0.00 0.00 3.59
2318 2361 1.067142 CACGTCATTTCCCTTCCTCGA 60.067 52.381 0.00 0.00 0.00 4.04
2319 2362 1.359848 CACGTCATTTCCCTTCCTCG 58.640 55.000 0.00 0.00 0.00 4.63
2320 2363 1.087501 GCACGTCATTTCCCTTCCTC 58.912 55.000 0.00 0.00 0.00 3.71
2321 2364 0.693049 AGCACGTCATTTCCCTTCCT 59.307 50.000 0.00 0.00 0.00 3.36
2322 2365 1.534729 AAGCACGTCATTTCCCTTCC 58.465 50.000 0.00 0.00 0.00 3.46
2323 2366 2.678336 CCTAAGCACGTCATTTCCCTTC 59.322 50.000 0.00 0.00 0.00 3.46
2324 2367 2.711542 CCTAAGCACGTCATTTCCCTT 58.288 47.619 0.00 0.00 0.00 3.95
2325 2368 1.679032 GCCTAAGCACGTCATTTCCCT 60.679 52.381 0.00 0.00 39.53 4.20
2326 2369 0.733150 GCCTAAGCACGTCATTTCCC 59.267 55.000 0.00 0.00 39.53 3.97
2327 2370 0.373716 CGCCTAAGCACGTCATTTCC 59.626 55.000 0.00 0.00 39.83 3.13
2328 2371 0.373716 CCGCCTAAGCACGTCATTTC 59.626 55.000 0.00 0.00 39.83 2.17
2329 2372 0.321298 ACCGCCTAAGCACGTCATTT 60.321 50.000 0.00 0.00 39.83 2.32
2330 2373 0.739813 GACCGCCTAAGCACGTCATT 60.740 55.000 0.00 0.00 37.69 2.57
2331 2374 1.153628 GACCGCCTAAGCACGTCAT 60.154 57.895 0.00 0.00 37.69 3.06
2332 2375 2.260434 GACCGCCTAAGCACGTCA 59.740 61.111 0.00 0.00 37.69 4.35
2333 2376 2.879462 CGACCGCCTAAGCACGTC 60.879 66.667 0.00 0.00 39.83 4.34
2334 2377 4.430765 CCGACCGCCTAAGCACGT 62.431 66.667 0.00 0.00 39.83 4.49
2336 2379 3.072486 TAGCCGACCGCCTAAGCAC 62.072 63.158 0.00 0.00 39.83 4.40
2337 2380 2.756691 TAGCCGACCGCCTAAGCA 60.757 61.111 0.00 0.00 39.83 3.91
2338 2381 2.279318 GTAGCCGACCGCCTAAGC 60.279 66.667 0.00 0.00 38.78 3.09
2339 2382 0.175073 AAAGTAGCCGACCGCCTAAG 59.825 55.000 0.00 0.00 38.78 2.18
2340 2383 0.609662 AAAAGTAGCCGACCGCCTAA 59.390 50.000 0.00 0.00 38.78 2.69
2341 2384 0.609662 AAAAAGTAGCCGACCGCCTA 59.390 50.000 0.00 0.00 38.78 3.93
2342 2385 1.373812 AAAAAGTAGCCGACCGCCT 59.626 52.632 0.00 0.00 38.78 5.52
2343 2386 3.976758 AAAAAGTAGCCGACCGCC 58.023 55.556 0.00 0.00 38.78 6.13
2365 2408 0.525668 CTGGTTAGGCGTGCGAGTAG 60.526 60.000 0.00 0.00 0.00 2.57
2366 2409 0.961857 TCTGGTTAGGCGTGCGAGTA 60.962 55.000 0.00 0.00 0.00 2.59
2367 2410 2.261671 CTGGTTAGGCGTGCGAGT 59.738 61.111 0.00 0.00 0.00 4.18
2368 2411 1.805945 GTCTGGTTAGGCGTGCGAG 60.806 63.158 0.00 0.00 0.00 5.03
2369 2412 2.260434 GTCTGGTTAGGCGTGCGA 59.740 61.111 0.00 0.00 0.00 5.10
2370 2413 2.048597 TGTCTGGTTAGGCGTGCG 60.049 61.111 0.00 0.00 0.00 5.34
2371 2414 2.033194 GGTGTCTGGTTAGGCGTGC 61.033 63.158 0.00 0.00 0.00 5.34
2372 2415 1.736645 CGGTGTCTGGTTAGGCGTG 60.737 63.158 0.00 0.00 0.00 5.34
2373 2416 2.654877 CGGTGTCTGGTTAGGCGT 59.345 61.111 0.00 0.00 0.00 5.68
2374 2417 2.813908 GCGGTGTCTGGTTAGGCG 60.814 66.667 0.00 0.00 0.00 5.52
2375 2418 2.813908 CGCGGTGTCTGGTTAGGC 60.814 66.667 0.00 0.00 0.00 3.93
2376 2419 1.445582 GACGCGGTGTCTGGTTAGG 60.446 63.158 12.47 0.00 44.58 2.69
2377 2420 1.800315 CGACGCGGTGTCTGGTTAG 60.800 63.158 18.51 0.00 45.87 2.34
2378 2421 2.256158 CGACGCGGTGTCTGGTTA 59.744 61.111 18.51 0.00 45.87 2.85
2382 2425 3.971453 ATGAGCGACGCGGTGTCTG 62.971 63.158 18.51 13.02 45.87 3.51
2383 2426 3.749064 ATGAGCGACGCGGTGTCT 61.749 61.111 18.51 0.94 45.87 3.41
2384 2427 3.545481 CATGAGCGACGCGGTGTC 61.545 66.667 15.18 11.58 44.53 3.67
2385 2428 4.357947 ACATGAGCGACGCGGTGT 62.358 61.111 15.18 16.74 37.83 4.16
2386 2429 3.545481 GACATGAGCGACGCGGTG 61.545 66.667 15.18 16.10 37.83 4.94
2387 2430 3.749064 AGACATGAGCGACGCGGT 61.749 61.111 15.18 11.45 41.33 5.68
2388 2431 3.250323 CAGACATGAGCGACGCGG 61.250 66.667 15.18 8.17 0.00 6.46
2389 2432 2.592623 TACCAGACATGAGCGACGCG 62.593 60.000 15.18 3.53 0.00 6.01
2390 2433 1.138883 TACCAGACATGAGCGACGC 59.861 57.895 13.03 13.03 0.00 5.19
2391 2434 0.525668 GGTACCAGACATGAGCGACG 60.526 60.000 7.15 0.00 0.00 5.12
2392 2435 0.530744 TGGTACCAGACATGAGCGAC 59.469 55.000 11.60 0.00 0.00 5.19
2393 2436 1.204704 CTTGGTACCAGACATGAGCGA 59.795 52.381 15.65 0.00 0.00 4.93
2394 2437 1.645034 CTTGGTACCAGACATGAGCG 58.355 55.000 15.65 0.00 0.00 5.03
2395 2438 1.373570 GCTTGGTACCAGACATGAGC 58.626 55.000 15.65 15.95 0.00 4.26
2396 2439 1.066858 ACGCTTGGTACCAGACATGAG 60.067 52.381 15.65 9.65 0.00 2.90
2397 2440 0.973632 ACGCTTGGTACCAGACATGA 59.026 50.000 15.65 0.00 0.00 3.07
2398 2441 1.078709 CACGCTTGGTACCAGACATG 58.921 55.000 15.65 6.31 0.00 3.21
2399 2442 0.036388 CCACGCTTGGTACCAGACAT 60.036 55.000 15.65 0.00 38.23 3.06
2400 2443 1.369692 CCACGCTTGGTACCAGACA 59.630 57.895 15.65 0.00 38.23 3.41
2401 2444 2.033194 GCCACGCTTGGTACCAGAC 61.033 63.158 15.65 10.30 45.98 3.51
2402 2445 2.214216 AGCCACGCTTGGTACCAGA 61.214 57.895 15.65 5.69 45.98 3.86
2403 2446 2.034879 CAGCCACGCTTGGTACCAG 61.035 63.158 15.65 10.56 45.98 4.00
2404 2447 2.031919 CAGCCACGCTTGGTACCA 59.968 61.111 11.60 11.60 45.98 3.25
2405 2448 3.431725 GCAGCCACGCTTGGTACC 61.432 66.667 11.38 4.43 45.98 3.34
2406 2449 3.431725 GGCAGCCACGCTTGGTAC 61.432 66.667 11.38 0.61 45.98 3.34
2407 2450 3.636231 AGGCAGCCACGCTTGGTA 61.636 61.111 15.80 0.00 45.98 3.25
2415 2458 4.586235 ACACACCCAGGCAGCCAC 62.586 66.667 15.80 0.00 0.00 5.01
2416 2459 4.269523 GACACACCCAGGCAGCCA 62.270 66.667 15.80 0.00 0.00 4.75
2417 2460 3.958860 AGACACACCCAGGCAGCC 61.959 66.667 1.84 1.84 0.00 4.85
2418 2461 2.670934 CAGACACACCCAGGCAGC 60.671 66.667 0.00 0.00 0.00 5.25
2419 2462 2.033141 CCAGACACACCCAGGCAG 59.967 66.667 0.00 0.00 0.00 4.85
2420 2463 3.569210 CCCAGACACACCCAGGCA 61.569 66.667 0.00 0.00 0.00 4.75
2422 2465 3.252284 AGCCCAGACACACCCAGG 61.252 66.667 0.00 0.00 0.00 4.45
2423 2466 1.845627 ATGAGCCCAGACACACCCAG 61.846 60.000 0.00 0.00 0.00 4.45
2424 2467 1.847506 ATGAGCCCAGACACACCCA 60.848 57.895 0.00 0.00 0.00 4.51
2425 2468 1.377725 CATGAGCCCAGACACACCC 60.378 63.158 0.00 0.00 0.00 4.61
2426 2469 1.377725 CCATGAGCCCAGACACACC 60.378 63.158 0.00 0.00 0.00 4.16
2427 2470 1.377725 CCCATGAGCCCAGACACAC 60.378 63.158 0.00 0.00 0.00 3.82
2428 2471 3.080641 CCCATGAGCCCAGACACA 58.919 61.111 0.00 0.00 0.00 3.72
2429 2472 2.439156 GCCCATGAGCCCAGACAC 60.439 66.667 0.00 0.00 0.00 3.67
2446 2489 0.608640 AAGAGTGACTAGGCCGTTGG 59.391 55.000 0.00 0.00 0.00 3.77
2447 2490 2.457366 AAAGAGTGACTAGGCCGTTG 57.543 50.000 0.00 0.00 0.00 4.10
2448 2491 6.481434 AATATAAAGAGTGACTAGGCCGTT 57.519 37.500 0.00 0.00 0.00 4.44
2449 2492 6.015603 GGTAATATAAAGAGTGACTAGGCCGT 60.016 42.308 0.00 0.00 0.00 5.68
2450 2493 6.208994 AGGTAATATAAAGAGTGACTAGGCCG 59.791 42.308 0.00 0.00 0.00 6.13
2451 2494 7.541916 AGGTAATATAAAGAGTGACTAGGCC 57.458 40.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.