Multiple sequence alignment - TraesCS2B01G479800

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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 TraesCS2B01G479800 chr2B 100.000 2441 0 0 1 2441 677220059 677217619 0.000000e+00 4508
1 TraesCS2B01G479800 chr2B 94.417 412 14 2 2037 2440 147497765 147498175 2.060000e-175 625
2 TraesCS2B01G479800 chr2B 94.161 411 14 2 2038 2440 787521448 787521040 3.450000e-173 617
3 TraesCS2B01G479800 chr2B 93.917 411 17 1 2038 2440 47691780 47691370 4.460000e-172 614
4 TraesCS2B01G479800 chr2B 93.431 411 19 1 2038 2440 47718166 47717756 9.660000e-169 603
5 TraesCS2B01G479800 chr2B 87.351 419 19 12 2034 2440 174799344 174799740 1.330000e-122 449
6 TraesCS2B01G479800 chr2D 94.035 2062 88 13 1 2035 565184148 565182095 0.000000e+00 3094
7 TraesCS2B01G479800 chr2D 85.227 440 34 15 2026 2441 139489995 139490427 8.070000e-115 424
8 TraesCS2B01G479800 chr2A 90.323 2077 104 39 1 2034 705785315 705783293 0.000000e+00 2632
9 TraesCS2B01G479800 chr4A 79.828 1398 182 52 423 1775 712966642 712965300 0.000000e+00 928
10 TraesCS2B01G479800 chr4A 93.917 411 17 1 2038 2440 743715059 743715469 4.460000e-172 614
11 TraesCS2B01G479800 chr7A 82.373 868 105 30 919 1775 20402174 20401344 0.000000e+00 712
12 TraesCS2B01G479800 chr7A 85.843 445 50 8 927 1362 20226161 20225721 6.150000e-126 460
13 TraesCS2B01G479800 chr1B 96.834 379 10 1 2062 2440 662561203 662561579 1.230000e-177 632
14 TraesCS2B01G479800 chr1B 93.431 411 19 1 2038 2440 392754448 392754038 9.660000e-169 603
15 TraesCS2B01G479800 chr7D 87.546 546 56 4 919 1462 20516221 20515686 2.670000e-174 621
16 TraesCS2B01G479800 chr7D 87.075 441 50 5 927 1362 20117609 20117171 2.180000e-135 492
17 TraesCS2B01G479800 chrUn 93.917 411 16 2 2038 2440 38374349 38374758 1.600000e-171 612
18 TraesCS2B01G479800 chrUn 93.416 243 8 2 2038 2272 75297779 75297537 1.070000e-93 353
19 TraesCS2B01G479800 chrUn 93.416 243 8 2 2038 2272 247945998 247945756 1.070000e-93 353
20 TraesCS2B01G479800 chr3B 93.447 412 15 2 2038 2441 800119521 800119928 3.470000e-168 601
21 TraesCS2B01G479800 chr7B 86.988 415 20 16 2037 2438 681788051 681787658 1.040000e-118 436


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 TraesCS2B01G479800 chr2B 677217619 677220059 2440 True 4508 4508 100.000 1 2441 1 chr2B.!!$R3 2440
1 TraesCS2B01G479800 chr2D 565182095 565184148 2053 True 3094 3094 94.035 1 2035 1 chr2D.!!$R1 2034
2 TraesCS2B01G479800 chr2A 705783293 705785315 2022 True 2632 2632 90.323 1 2034 1 chr2A.!!$R1 2033
3 TraesCS2B01G479800 chr4A 712965300 712966642 1342 True 928 928 79.828 423 1775 1 chr4A.!!$R1 1352
4 TraesCS2B01G479800 chr7A 20401344 20402174 830 True 712 712 82.373 919 1775 1 chr7A.!!$R2 856
5 TraesCS2B01G479800 chr7D 20515686 20516221 535 True 621 621 87.546 919 1462 1 chr7D.!!$R2 543

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
342 368 0.109132 GAATTGGGGCGCAAACTCTG 60.109 55.0 21.22 0.0 0.0 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2042 2121 0.108138 CCACACGGGAGAGATCAACC 60.108 60.0 0.0 0.0 40.01 3.77 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
35 36 0.609406 TCCATATCCGCCCTCTCTCG 60.609 60.000 0.00 0.00 0.00 4.04
61 62 2.431942 CGGAAAGGTACTGCGCGT 60.432 61.111 8.43 6.51 40.86 6.01
168 194 2.570334 CCCCCTCTAGGCCTCTCTA 58.430 63.158 9.68 0.00 0.00 2.43
174 200 3.430453 CCTCTAGGCCTCTCTATCCTTG 58.570 54.545 9.68 0.00 0.00 3.61
342 368 0.109132 GAATTGGGGCGCAAACTCTG 60.109 55.000 21.22 0.00 0.00 3.35
343 369 0.539438 AATTGGGGCGCAAACTCTGA 60.539 50.000 21.22 0.00 0.00 3.27
344 370 0.962356 ATTGGGGCGCAAACTCTGAG 60.962 55.000 21.22 2.45 0.00 3.35
428 455 1.303309 GCTATGCTGCAGTTACAGGG 58.697 55.000 16.64 3.45 38.16 4.45
480 507 2.483877 TGCAGAACAGCGGAAGTAATTG 59.516 45.455 0.00 0.00 37.31 2.32
516 545 7.663081 CAGATGAAATAGCCCAAAATAGCTAGA 59.337 37.037 0.00 0.00 44.36 2.43
526 555 5.827797 CCCAAAATAGCTAGATGTTGCCTTA 59.172 40.000 0.00 0.00 0.00 2.69
550 579 9.599866 TTATAGTTGAATCAGGTTGATAGTGTG 57.400 33.333 0.00 0.00 35.76 3.82
576 606 4.464597 TGTAGCAACCTTTCAAACTTGGTT 59.535 37.500 0.00 0.00 42.78 3.67
643 673 9.905713 TGGATGGATACTTTATATATTTCCTGC 57.094 33.333 0.00 0.00 37.61 4.85
663 701 2.030805 GCGCAAACATCAACTTCCTCTT 60.031 45.455 0.30 0.00 0.00 2.85
725 766 5.050091 CAGTACACTTTTCAAGATTGCTCGT 60.050 40.000 0.00 0.00 0.00 4.18
780 821 7.546250 TTGATGCCCTTGGTAATTTTCTTTA 57.454 32.000 0.00 0.00 0.00 1.85
965 1028 6.002704 AGAATGTTCATTTTCTCTCTGCAGT 58.997 36.000 14.67 0.00 0.00 4.40
1569 1646 4.693283 TCATGCTACACTTATGCAGTACC 58.307 43.478 0.00 0.00 40.18 3.34
1615 1692 8.644374 ACTAGAGATTATGGTAGATCAGAACC 57.356 38.462 0.00 0.00 36.24 3.62
1660 1737 1.066430 ACTGGTTGTGTTGTGACTCGT 60.066 47.619 0.00 0.00 0.00 4.18
1697 1775 1.308047 TGTGTTGTTGCGCTTCAGAT 58.692 45.000 9.73 0.00 0.00 2.90
1749 1827 8.786898 TCGATTCAAGATGAGTTTCAAAGAAAT 58.213 29.630 0.00 0.00 0.00 2.17
1820 1898 7.397221 TGGATACATGTTTCTTCTTGATCAGT 58.603 34.615 14.76 0.00 46.17 3.41
1947 2025 6.482308 TGCAGTTCCTAGTGTACTTTTTCTTC 59.518 38.462 0.00 0.00 0.00 2.87
1963 2041 8.791675 ACTTTTTCTTCATCTTTTTGGCAAAAA 58.208 25.926 30.03 30.03 37.99 1.94
2004 2082 2.758009 CAATGTGGCTTTCCTTTGTGG 58.242 47.619 0.00 0.00 37.10 4.17
2020 2099 1.411977 TGTGGCAAGGAAAATGTGGTG 59.588 47.619 0.00 0.00 0.00 4.17
2035 2114 0.890542 TGGTGCCTTGCTAGTTGCTG 60.891 55.000 0.00 0.00 43.37 4.41
2036 2115 0.890996 GGTGCCTTGCTAGTTGCTGT 60.891 55.000 0.00 0.00 43.37 4.40
2037 2116 0.954452 GTGCCTTGCTAGTTGCTGTT 59.046 50.000 0.00 0.00 43.37 3.16
2038 2117 0.953727 TGCCTTGCTAGTTGCTGTTG 59.046 50.000 0.00 0.00 43.37 3.33
2039 2118 0.954452 GCCTTGCTAGTTGCTGTTGT 59.046 50.000 0.00 0.00 43.37 3.32
2040 2119 1.338020 GCCTTGCTAGTTGCTGTTGTT 59.662 47.619 0.00 0.00 43.37 2.83
2041 2120 2.552315 GCCTTGCTAGTTGCTGTTGTTA 59.448 45.455 0.00 0.00 43.37 2.41
2042 2121 3.365364 GCCTTGCTAGTTGCTGTTGTTAG 60.365 47.826 0.00 0.00 43.37 2.34
2043 2122 3.189287 CCTTGCTAGTTGCTGTTGTTAGG 59.811 47.826 0.00 0.00 43.37 2.69
2044 2123 3.485463 TGCTAGTTGCTGTTGTTAGGT 57.515 42.857 0.00 0.00 43.37 3.08
2045 2124 3.815809 TGCTAGTTGCTGTTGTTAGGTT 58.184 40.909 0.00 0.00 43.37 3.50
2046 2125 3.563808 TGCTAGTTGCTGTTGTTAGGTTG 59.436 43.478 0.00 0.00 43.37 3.77
2047 2126 3.813166 GCTAGTTGCTGTTGTTAGGTTGA 59.187 43.478 0.00 0.00 38.95 3.18
2048 2127 4.455877 GCTAGTTGCTGTTGTTAGGTTGAT 59.544 41.667 0.00 0.00 38.95 2.57
2049 2128 5.390991 GCTAGTTGCTGTTGTTAGGTTGATC 60.391 44.000 0.00 0.00 38.95 2.92
2050 2129 4.718961 AGTTGCTGTTGTTAGGTTGATCT 58.281 39.130 0.00 0.00 0.00 2.75
2051 2130 4.757149 AGTTGCTGTTGTTAGGTTGATCTC 59.243 41.667 0.00 0.00 0.00 2.75
2052 2131 4.623932 TGCTGTTGTTAGGTTGATCTCT 57.376 40.909 0.00 0.00 0.00 3.10
2053 2132 4.569943 TGCTGTTGTTAGGTTGATCTCTC 58.430 43.478 0.00 0.00 0.00 3.20
2054 2133 3.935828 GCTGTTGTTAGGTTGATCTCTCC 59.064 47.826 0.00 0.00 0.00 3.71
2055 2134 4.508662 CTGTTGTTAGGTTGATCTCTCCC 58.491 47.826 0.00 0.00 0.00 4.30
2056 2135 3.056107 TGTTGTTAGGTTGATCTCTCCCG 60.056 47.826 0.00 0.00 0.00 5.14
2057 2136 2.816411 TGTTAGGTTGATCTCTCCCGT 58.184 47.619 0.00 0.00 0.00 5.28
2058 2137 2.496070 TGTTAGGTTGATCTCTCCCGTG 59.504 50.000 0.00 0.00 0.00 4.94
2059 2138 2.496470 GTTAGGTTGATCTCTCCCGTGT 59.504 50.000 0.00 0.00 0.00 4.49
2060 2139 0.898320 AGGTTGATCTCTCCCGTGTG 59.102 55.000 0.00 0.00 0.00 3.82
2061 2140 0.108138 GGTTGATCTCTCCCGTGTGG 60.108 60.000 0.00 0.00 0.00 4.17
2079 2158 3.728373 GCCCAACGGACCCCTGAT 61.728 66.667 0.00 0.00 0.00 2.90
2080 2159 2.590092 CCCAACGGACCCCTGATC 59.410 66.667 0.00 0.00 0.00 2.92
2081 2160 2.590092 CCAACGGACCCCTGATCC 59.410 66.667 0.00 0.00 0.00 3.36
2091 2170 3.933722 CCTGATCCGCGCCCTGAT 61.934 66.667 0.00 0.88 0.00 2.90
2092 2171 2.356793 CTGATCCGCGCCCTGATC 60.357 66.667 17.63 17.63 38.27 2.92
2093 2172 4.284860 TGATCCGCGCCCTGATCG 62.285 66.667 18.61 0.00 40.19 3.69
2111 2190 2.123468 GGGGCGCCCAACCATAAT 60.123 61.111 44.46 0.00 44.65 1.28
2112 2191 1.151908 GGGGCGCCCAACCATAATA 59.848 57.895 44.46 0.00 44.65 0.98
2113 2192 0.251608 GGGGCGCCCAACCATAATAT 60.252 55.000 44.46 0.00 44.65 1.28
2114 2193 0.887933 GGGCGCCCAACCATAATATG 59.112 55.000 40.73 0.00 35.81 1.78
2115 2194 2.497349 GGGCGCCCAACCATAATATGG 61.497 57.143 40.73 17.24 45.32 2.74
2125 2204 2.159382 CCATAATATGGTTGACGGGCC 58.841 52.381 11.07 0.00 45.54 5.80
2126 2205 2.159382 CATAATATGGTTGACGGGCCC 58.841 52.381 13.57 13.57 0.00 5.80
2127 2206 0.475044 TAATATGGTTGACGGGCCCC 59.525 55.000 18.66 2.97 0.00 5.80
2128 2207 1.286305 AATATGGTTGACGGGCCCCT 61.286 55.000 18.66 3.90 0.00 4.79
2129 2208 1.994885 ATATGGTTGACGGGCCCCTG 61.995 60.000 18.66 5.47 0.00 4.45
2142 2221 4.435436 CCCTGTCACGCAGCGCTA 62.435 66.667 16.61 0.00 43.71 4.26
2143 2222 3.181967 CCTGTCACGCAGCGCTAC 61.182 66.667 16.61 13.93 43.71 3.58
2144 2223 2.430751 CTGTCACGCAGCGCTACA 60.431 61.111 16.61 17.90 38.52 2.74
2145 2224 1.807165 CTGTCACGCAGCGCTACAT 60.807 57.895 16.61 0.00 38.52 2.29
2146 2225 0.525455 CTGTCACGCAGCGCTACATA 60.525 55.000 16.61 0.00 38.52 2.29
2147 2226 0.109039 TGTCACGCAGCGCTACATAA 60.109 50.000 16.61 0.00 0.00 1.90
2148 2227 0.996462 GTCACGCAGCGCTACATAAA 59.004 50.000 16.61 0.00 0.00 1.40
2149 2228 1.005975 GTCACGCAGCGCTACATAAAG 60.006 52.381 16.61 0.00 0.00 1.85
2150 2229 1.135228 TCACGCAGCGCTACATAAAGA 60.135 47.619 16.61 0.00 0.00 2.52
2151 2230 1.256376 CACGCAGCGCTACATAAAGAG 59.744 52.381 16.61 0.00 0.00 2.85
2152 2231 0.855349 CGCAGCGCTACATAAAGAGG 59.145 55.000 10.99 0.00 0.00 3.69
2153 2232 1.802880 CGCAGCGCTACATAAAGAGGT 60.803 52.381 10.99 0.00 0.00 3.85
2154 2233 1.594862 GCAGCGCTACATAAAGAGGTG 59.405 52.381 10.99 0.00 44.45 4.00
2155 2234 2.205074 CAGCGCTACATAAAGAGGTGG 58.795 52.381 10.99 0.00 39.96 4.61
2156 2235 1.139058 AGCGCTACATAAAGAGGTGGG 59.861 52.381 8.99 0.00 0.00 4.61
2157 2236 1.810412 GCGCTACATAAAGAGGTGGGG 60.810 57.143 0.00 0.00 34.54 4.96
2158 2237 1.202651 CGCTACATAAAGAGGTGGGGG 60.203 57.143 0.00 0.00 28.97 5.40
2159 2238 1.477014 GCTACATAAAGAGGTGGGGGC 60.477 57.143 0.00 0.00 0.00 5.80
2160 2239 1.143073 CTACATAAAGAGGTGGGGGCC 59.857 57.143 0.00 0.00 0.00 5.80
2161 2240 1.152963 CATAAAGAGGTGGGGGCCG 60.153 63.158 0.00 0.00 0.00 6.13
2162 2241 2.383601 ATAAAGAGGTGGGGGCCGG 61.384 63.158 0.00 0.00 0.00 6.13
2186 2265 4.164252 GCAGTACGAGGTTCACCG 57.836 61.111 0.00 0.00 42.08 4.94
2187 2266 2.092882 GCAGTACGAGGTTCACCGC 61.093 63.158 0.00 0.00 42.08 5.68
2193 2272 3.723348 GAGGTTCACCGCGTTGCC 61.723 66.667 4.92 0.00 42.08 4.52
2194 2273 4.555709 AGGTTCACCGCGTTGCCA 62.556 61.111 4.92 0.00 42.08 4.92
2195 2274 4.025401 GGTTCACCGCGTTGCCAG 62.025 66.667 4.92 0.00 0.00 4.85
2196 2275 4.025401 GTTCACCGCGTTGCCAGG 62.025 66.667 4.92 0.00 0.00 4.45
2209 2288 3.646715 CCAGGCTCCCCACCGAAA 61.647 66.667 0.00 0.00 0.00 3.46
2210 2289 2.434331 CAGGCTCCCCACCGAAAA 59.566 61.111 0.00 0.00 0.00 2.29
2211 2290 1.971695 CAGGCTCCCCACCGAAAAC 60.972 63.158 0.00 0.00 0.00 2.43
2212 2291 2.154074 AGGCTCCCCACCGAAAACT 61.154 57.895 0.00 0.00 0.00 2.66
2213 2292 1.674651 GGCTCCCCACCGAAAACTC 60.675 63.158 0.00 0.00 0.00 3.01
2214 2293 1.674651 GCTCCCCACCGAAAACTCC 60.675 63.158 0.00 0.00 0.00 3.85
2215 2294 1.375523 CTCCCCACCGAAAACTCCG 60.376 63.158 0.00 0.00 0.00 4.63
2221 2300 4.382320 CCGAAAACTCCGGCCCGA 62.382 66.667 3.71 0.00 40.54 5.14
2222 2301 2.125269 CGAAAACTCCGGCCCGAT 60.125 61.111 3.71 0.00 0.00 4.18
2223 2302 2.171725 CGAAAACTCCGGCCCGATC 61.172 63.158 3.71 0.00 0.00 3.69
2224 2303 1.221021 GAAAACTCCGGCCCGATCT 59.779 57.895 3.71 0.00 0.00 2.75
2225 2304 0.462789 GAAAACTCCGGCCCGATCTA 59.537 55.000 3.71 0.00 0.00 1.98
2226 2305 0.464452 AAAACTCCGGCCCGATCTAG 59.536 55.000 3.71 0.00 0.00 2.43
2227 2306 1.400530 AAACTCCGGCCCGATCTAGG 61.401 60.000 3.71 0.00 0.00 3.02
2228 2307 2.203509 CTCCGGCCCGATCTAGGT 60.204 66.667 3.71 0.00 0.00 3.08
2229 2308 2.203451 TCCGGCCCGATCTAGGTC 60.203 66.667 3.71 0.00 0.00 3.85
2230 2309 2.203509 CCGGCCCGATCTAGGTCT 60.204 66.667 3.71 0.00 0.00 3.85
2231 2310 1.074423 CCGGCCCGATCTAGGTCTA 59.926 63.158 3.71 0.00 0.00 2.59
2232 2311 0.961358 CCGGCCCGATCTAGGTCTAG 60.961 65.000 3.71 0.00 34.56 2.43
2233 2312 1.587933 CGGCCCGATCTAGGTCTAGC 61.588 65.000 0.00 3.58 33.32 3.42
2234 2313 1.587933 GGCCCGATCTAGGTCTAGCG 61.588 65.000 0.62 0.00 33.32 4.26
2235 2314 1.877367 CCCGATCTAGGTCTAGCGC 59.123 63.158 0.00 0.00 33.32 5.92
2236 2315 0.606944 CCCGATCTAGGTCTAGCGCT 60.607 60.000 17.26 17.26 33.32 5.92
2237 2316 0.519519 CCGATCTAGGTCTAGCGCTG 59.480 60.000 22.90 10.49 33.32 5.18
2238 2317 1.514003 CGATCTAGGTCTAGCGCTGA 58.486 55.000 22.90 12.92 33.32 4.26
2239 2318 1.195900 CGATCTAGGTCTAGCGCTGAC 59.804 57.143 22.90 23.21 33.32 3.51
2240 2319 2.222886 GATCTAGGTCTAGCGCTGACA 58.777 52.381 28.66 16.23 36.26 3.58
2241 2320 1.669604 TCTAGGTCTAGCGCTGACAG 58.330 55.000 28.66 21.75 36.26 3.51
2242 2321 1.065345 TCTAGGTCTAGCGCTGACAGT 60.065 52.381 28.66 21.20 36.26 3.55
2243 2322 1.064803 CTAGGTCTAGCGCTGACAGTG 59.935 57.143 28.66 11.79 36.26 3.66
2244 2323 0.609406 AGGTCTAGCGCTGACAGTGA 60.609 55.000 28.66 13.65 36.26 3.41
2245 2324 0.456995 GGTCTAGCGCTGACAGTGAC 60.457 60.000 28.66 21.01 36.26 3.67
2246 2325 0.794981 GTCTAGCGCTGACAGTGACG 60.795 60.000 22.90 8.32 34.80 4.35
2247 2326 1.515088 CTAGCGCTGACAGTGACGG 60.515 63.158 22.90 0.00 0.00 4.79
2248 2327 2.874010 CTAGCGCTGACAGTGACGGG 62.874 65.000 22.90 2.74 0.00 5.28
2249 2328 4.357947 GCGCTGACAGTGACGGGA 62.358 66.667 20.12 0.00 0.00 5.14
2250 2329 2.338620 CGCTGACAGTGACGGGAA 59.661 61.111 10.62 0.00 0.00 3.97
2251 2330 1.734477 CGCTGACAGTGACGGGAAG 60.734 63.158 10.62 0.00 0.00 3.46
2252 2331 2.029844 GCTGACAGTGACGGGAAGC 61.030 63.158 3.99 0.00 0.00 3.86
2253 2332 1.668294 CTGACAGTGACGGGAAGCT 59.332 57.895 0.00 0.00 0.00 3.74
2254 2333 0.389166 CTGACAGTGACGGGAAGCTC 60.389 60.000 0.00 0.00 0.00 4.09
2255 2334 1.079750 GACAGTGACGGGAAGCTCC 60.080 63.158 0.00 0.00 35.23 4.70
2296 2375 4.864334 GCCGCCATCCACTCCCTG 62.864 72.222 0.00 0.00 0.00 4.45
2297 2376 4.864334 CCGCCATCCACTCCCTGC 62.864 72.222 0.00 0.00 0.00 4.85
2298 2377 4.864334 CGCCATCCACTCCCTGCC 62.864 72.222 0.00 0.00 0.00 4.85
2299 2378 3.731728 GCCATCCACTCCCTGCCA 61.732 66.667 0.00 0.00 0.00 4.92
2300 2379 3.065787 GCCATCCACTCCCTGCCAT 62.066 63.158 0.00 0.00 0.00 4.40
2301 2380 1.150081 CCATCCACTCCCTGCCATC 59.850 63.158 0.00 0.00 0.00 3.51
2302 2381 1.638679 CCATCCACTCCCTGCCATCA 61.639 60.000 0.00 0.00 0.00 3.07
2303 2382 0.465097 CATCCACTCCCTGCCATCAC 60.465 60.000 0.00 0.00 0.00 3.06
2304 2383 1.639635 ATCCACTCCCTGCCATCACC 61.640 60.000 0.00 0.00 0.00 4.02
2305 2384 2.124983 CACTCCCTGCCATCACCG 60.125 66.667 0.00 0.00 0.00 4.94
2306 2385 3.402681 ACTCCCTGCCATCACCGG 61.403 66.667 0.00 0.00 0.00 5.28
2315 2394 4.386951 CATCACCGGCCACCGTCA 62.387 66.667 0.00 0.00 46.80 4.35
2316 2395 4.388499 ATCACCGGCCACCGTCAC 62.388 66.667 0.00 0.00 46.80 3.67
2340 2419 4.452733 CGGCACCGGGAGTTCCTC 62.453 72.222 6.32 0.00 35.95 3.71
2341 2420 3.319198 GGCACCGGGAGTTCCTCA 61.319 66.667 6.32 0.00 35.95 3.86
2342 2421 2.670148 GGCACCGGGAGTTCCTCAT 61.670 63.158 6.32 0.00 35.95 2.90
2343 2422 1.153349 GCACCGGGAGTTCCTCATC 60.153 63.158 6.32 0.00 35.95 2.92
2344 2423 1.522569 CACCGGGAGTTCCTCATCC 59.477 63.158 6.32 0.00 35.95 3.51
2345 2424 2.058595 ACCGGGAGTTCCTCATCCG 61.059 63.158 6.32 0.00 35.90 4.18
2346 2425 2.107141 CGGGAGTTCCTCATCCGC 59.893 66.667 0.00 0.00 36.38 5.54
2347 2426 2.721167 CGGGAGTTCCTCATCCGCA 61.721 63.158 0.00 0.00 36.38 5.69
2348 2427 1.153349 GGGAGTTCCTCATCCGCAC 60.153 63.158 0.00 0.00 36.38 5.34
2349 2428 1.153349 GGAGTTCCTCATCCGCACC 60.153 63.158 0.00 0.00 31.08 5.01
2350 2429 1.596934 GAGTTCCTCATCCGCACCA 59.403 57.895 0.00 0.00 0.00 4.17
2351 2430 0.460987 GAGTTCCTCATCCGCACCAG 60.461 60.000 0.00 0.00 0.00 4.00
2352 2431 1.450312 GTTCCTCATCCGCACCAGG 60.450 63.158 0.00 0.00 0.00 4.45
2353 2432 1.612146 TTCCTCATCCGCACCAGGA 60.612 57.895 0.00 0.00 45.54 3.86
2354 2433 1.617018 TTCCTCATCCGCACCAGGAG 61.617 60.000 0.00 0.00 44.55 3.69
2355 2434 2.060383 CCTCATCCGCACCAGGAGA 61.060 63.158 0.00 0.00 44.55 3.71
2356 2435 1.617018 CCTCATCCGCACCAGGAGAA 61.617 60.000 0.00 0.00 44.55 2.87
2357 2436 0.179089 CTCATCCGCACCAGGAGAAG 60.179 60.000 0.00 0.00 44.55 2.85
2358 2437 1.153289 CATCCGCACCAGGAGAAGG 60.153 63.158 0.00 0.00 44.55 3.46
2359 2438 1.613630 ATCCGCACCAGGAGAAGGT 60.614 57.895 0.00 0.00 44.55 3.50
2360 2439 0.325296 ATCCGCACCAGGAGAAGGTA 60.325 55.000 0.00 0.00 44.55 3.08
2361 2440 0.970937 TCCGCACCAGGAGAAGGTAG 60.971 60.000 0.00 0.00 37.23 3.18
2362 2441 1.517832 CGCACCAGGAGAAGGTAGG 59.482 63.158 0.00 0.00 37.23 3.18
2363 2442 1.258445 CGCACCAGGAGAAGGTAGGT 61.258 60.000 0.00 0.00 37.23 3.08
2364 2443 0.984995 GCACCAGGAGAAGGTAGGTT 59.015 55.000 0.00 0.00 37.23 3.50
2365 2444 1.066071 GCACCAGGAGAAGGTAGGTTC 60.066 57.143 0.00 0.00 37.23 3.62
2366 2445 2.257207 CACCAGGAGAAGGTAGGTTCA 58.743 52.381 0.00 0.00 37.23 3.18
2367 2446 2.028020 CACCAGGAGAAGGTAGGTTCAC 60.028 54.545 0.00 0.00 37.23 3.18
2368 2447 1.555533 CCAGGAGAAGGTAGGTTCACC 59.444 57.143 0.00 0.00 37.43 4.02
2369 2448 1.204941 CAGGAGAAGGTAGGTTCACCG 59.795 57.143 0.00 0.00 43.84 4.94
2370 2449 0.535797 GGAGAAGGTAGGTTCACCGG 59.464 60.000 0.00 0.00 43.84 5.28
2371 2450 1.553706 GAGAAGGTAGGTTCACCGGA 58.446 55.000 9.46 0.00 43.84 5.14
2372 2451 2.108970 GAGAAGGTAGGTTCACCGGAT 58.891 52.381 9.46 0.00 43.84 4.18
2373 2452 2.101082 GAGAAGGTAGGTTCACCGGATC 59.899 54.545 9.46 0.00 43.84 3.36
2374 2453 2.108970 GAAGGTAGGTTCACCGGATCT 58.891 52.381 9.46 0.00 43.84 2.75
2375 2454 1.777941 AGGTAGGTTCACCGGATCTC 58.222 55.000 9.46 0.00 43.84 2.75
2376 2455 0.751452 GGTAGGTTCACCGGATCTCC 59.249 60.000 9.46 5.35 42.08 3.71
2377 2456 1.688627 GGTAGGTTCACCGGATCTCCT 60.689 57.143 9.46 13.05 42.08 3.69
2378 2457 2.423947 GGTAGGTTCACCGGATCTCCTA 60.424 54.545 9.46 12.00 42.08 2.94
2379 2458 2.074729 AGGTTCACCGGATCTCCTAG 57.925 55.000 9.46 0.00 42.08 3.02
2380 2459 0.389757 GGTTCACCGGATCTCCTAGC 59.610 60.000 9.46 0.00 0.00 3.42
2381 2460 0.389757 GTTCACCGGATCTCCTAGCC 59.610 60.000 9.46 0.00 0.00 3.93
2382 2461 0.759436 TTCACCGGATCTCCTAGCCC 60.759 60.000 9.46 0.00 0.00 5.19
2383 2462 1.457643 CACCGGATCTCCTAGCCCA 60.458 63.158 9.46 0.00 0.00 5.36
2384 2463 1.457831 ACCGGATCTCCTAGCCCAC 60.458 63.158 9.46 0.00 0.00 4.61
2385 2464 1.152440 CCGGATCTCCTAGCCCACT 60.152 63.158 0.00 0.00 0.00 4.00
2386 2465 1.182385 CCGGATCTCCTAGCCCACTC 61.182 65.000 0.00 0.00 0.00 3.51
2387 2466 1.182385 CGGATCTCCTAGCCCACTCC 61.182 65.000 0.00 0.00 0.00 3.85
2388 2467 1.182385 GGATCTCCTAGCCCACTCCG 61.182 65.000 0.00 0.00 0.00 4.63
2389 2468 0.178987 GATCTCCTAGCCCACTCCGA 60.179 60.000 0.00 0.00 0.00 4.55
2390 2469 0.485099 ATCTCCTAGCCCACTCCGAT 59.515 55.000 0.00 0.00 0.00 4.18
2391 2470 0.178987 TCTCCTAGCCCACTCCGATC 60.179 60.000 0.00 0.00 0.00 3.69
2392 2471 0.178975 CTCCTAGCCCACTCCGATCT 60.179 60.000 0.00 0.00 0.00 2.75
2393 2472 1.074084 CTCCTAGCCCACTCCGATCTA 59.926 57.143 0.00 0.00 0.00 1.98
2394 2473 1.497716 TCCTAGCCCACTCCGATCTAA 59.502 52.381 0.00 0.00 0.00 2.10
2395 2474 1.889829 CCTAGCCCACTCCGATCTAAG 59.110 57.143 0.00 0.00 0.00 2.18
2396 2475 2.489255 CCTAGCCCACTCCGATCTAAGA 60.489 54.545 0.00 0.00 0.00 2.10
2397 2476 2.160721 AGCCCACTCCGATCTAAGAA 57.839 50.000 0.00 0.00 0.00 2.52
2398 2477 2.683768 AGCCCACTCCGATCTAAGAAT 58.316 47.619 0.00 0.00 0.00 2.40
2399 2478 2.630580 AGCCCACTCCGATCTAAGAATC 59.369 50.000 0.00 0.00 0.00 2.52
2400 2479 2.630580 GCCCACTCCGATCTAAGAATCT 59.369 50.000 0.00 0.00 0.00 2.40
2401 2480 3.827302 GCCCACTCCGATCTAAGAATCTA 59.173 47.826 0.00 0.00 0.00 1.98
2402 2481 4.464597 GCCCACTCCGATCTAAGAATCTAT 59.535 45.833 0.00 0.00 0.00 1.98
2403 2482 5.393678 GCCCACTCCGATCTAAGAATCTATC 60.394 48.000 0.00 0.00 0.00 2.08
2404 2483 5.712446 CCCACTCCGATCTAAGAATCTATCA 59.288 44.000 0.00 0.00 0.00 2.15
2405 2484 6.209589 CCCACTCCGATCTAAGAATCTATCAA 59.790 42.308 0.00 0.00 0.00 2.57
2406 2485 7.093552 CCCACTCCGATCTAAGAATCTATCAAT 60.094 40.741 0.00 0.00 0.00 2.57
2407 2486 7.758980 CCACTCCGATCTAAGAATCTATCAATG 59.241 40.741 0.00 0.00 0.00 2.82
2408 2487 7.758980 CACTCCGATCTAAGAATCTATCAATGG 59.241 40.741 0.00 0.00 0.00 3.16
2409 2488 7.453126 ACTCCGATCTAAGAATCTATCAATGGT 59.547 37.037 0.00 0.00 0.00 3.55
2410 2489 8.879427 TCCGATCTAAGAATCTATCAATGGTA 57.121 34.615 0.00 0.00 0.00 3.25
2411 2490 9.480861 TCCGATCTAAGAATCTATCAATGGTAT 57.519 33.333 0.00 0.00 0.00 2.73
2412 2491 9.743057 CCGATCTAAGAATCTATCAATGGTATC 57.257 37.037 0.00 0.00 0.00 2.24
2420 2499 8.703743 AGAATCTATCAATGGTATCAGATAGCC 58.296 37.037 15.60 8.99 39.66 3.93
2421 2500 7.984859 ATCTATCAATGGTATCAGATAGCCA 57.015 36.000 15.60 13.51 39.66 4.75
2422 2501 7.415592 TCTATCAATGGTATCAGATAGCCAG 57.584 40.000 15.60 6.87 39.66 4.85
2423 2502 7.184862 TCTATCAATGGTATCAGATAGCCAGA 58.815 38.462 15.60 11.20 39.66 3.86
2424 2503 6.887886 ATCAATGGTATCAGATAGCCAGAT 57.112 37.500 15.60 12.65 34.18 2.90
2425 2504 6.291648 TCAATGGTATCAGATAGCCAGATC 57.708 41.667 15.60 0.00 34.18 2.75
2426 2505 4.998671 ATGGTATCAGATAGCCAGATCG 57.001 45.455 15.60 0.00 34.18 3.69
2427 2506 3.092301 TGGTATCAGATAGCCAGATCGG 58.908 50.000 15.60 0.00 38.11 4.18
2428 2507 2.428890 GGTATCAGATAGCCAGATCGGG 59.571 54.545 7.64 7.64 34.06 5.14
2439 2518 3.760580 CCAGATCGGGCTAGAAGATTT 57.239 47.619 0.00 0.00 0.00 2.17
2440 2519 3.658709 CCAGATCGGGCTAGAAGATTTC 58.341 50.000 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 3.023591 GCACGCGCAGTACCTTTCC 62.024 63.158 5.73 0.00 38.36 3.13
61 62 1.539869 AGAGGGGAAGGAAGCAGCA 60.540 57.895 0.00 0.00 0.00 4.41
153 178 3.430453 CAAGGATAGAGAGGCCTAGAGG 58.570 54.545 4.42 0.00 38.53 3.69
168 194 1.767681 GCATCTGAGAGGACCAAGGAT 59.232 52.381 0.00 0.00 0.00 3.24
174 200 2.279120 CGCGCATCTGAGAGGACC 60.279 66.667 8.75 0.00 0.00 4.46
213 239 4.144681 CGCGCAACAGCAGCTCTC 62.145 66.667 8.75 0.00 36.85 3.20
237 263 2.336809 GAGATGACCTAGCGGCCG 59.663 66.667 24.05 24.05 0.00 6.13
342 368 3.555139 CAGATCGAGGTTCAAGATTGCTC 59.445 47.826 0.00 0.00 0.00 4.26
343 369 3.529533 CAGATCGAGGTTCAAGATTGCT 58.470 45.455 0.00 0.00 0.00 3.91
344 370 2.611292 CCAGATCGAGGTTCAAGATTGC 59.389 50.000 0.00 0.00 0.00 3.56
345 371 4.128925 TCCAGATCGAGGTTCAAGATTG 57.871 45.455 7.06 0.00 0.00 2.67
470 497 7.334421 TCATCTGCTTGAACTACAATTACTTCC 59.666 37.037 0.00 0.00 37.88 3.46
480 507 5.008118 GGGCTATTTCATCTGCTTGAACTAC 59.992 44.000 0.00 0.00 35.42 2.73
516 545 6.426587 ACCTGATTCAACTATAAGGCAACAT 58.573 36.000 0.00 0.00 41.41 2.71
526 555 7.624549 ACACACTATCAACCTGATTCAACTAT 58.375 34.615 0.00 0.00 38.26 2.12
550 579 5.273944 CAAGTTTGAAAGGTTGCTACAGAC 58.726 41.667 0.00 0.00 0.00 3.51
576 606 1.843206 TCCATACACAATGCTGCCCTA 59.157 47.619 0.00 0.00 33.92 3.53
643 673 3.003689 ACAAGAGGAAGTTGATGTTTGCG 59.996 43.478 0.00 0.00 0.00 4.85
663 701 4.394729 GGAGTGTTTCCAGAAATACCACA 58.605 43.478 14.17 0.00 46.01 4.17
687 725 3.377172 AGTGTACTGAAGCAAACAACCAC 59.623 43.478 0.00 0.00 0.00 4.16
780 821 8.267894 ACTCCAAAGACAAATATACTGCTGTAT 58.732 33.333 18.72 18.72 41.72 2.29
802 843 8.129211 GCAATAATCACCATAACTTAACACTCC 58.871 37.037 0.00 0.00 0.00 3.85
965 1028 4.041723 GCGCTAACAGCAAAGAAAGAAAA 58.958 39.130 0.00 0.00 42.58 2.29
1023 1086 3.734902 GCTCATTTATGGGTTCTTTGCCG 60.735 47.826 0.00 0.00 0.00 5.69
1569 1646 1.342555 TTACACGCGAGGATTCAACG 58.657 50.000 15.93 0.00 0.00 4.10
1612 1689 2.158871 TCTGCAGTTTACGAACAGGGTT 60.159 45.455 14.67 0.00 38.26 4.11
1615 1692 4.749245 AAATCTGCAGTTTACGAACAGG 57.251 40.909 14.67 0.00 38.26 4.00
1651 1728 0.927537 CAAAAGACGCACGAGTCACA 59.072 50.000 3.75 0.00 43.24 3.58
1652 1729 0.928229 ACAAAAGACGCACGAGTCAC 59.072 50.000 3.75 0.00 43.24 3.67
1660 1737 0.934496 CAACGGAGACAAAAGACGCA 59.066 50.000 0.00 0.00 0.00 5.24
1697 1775 3.819368 TGTCATCAACAGCCAGAAAAGA 58.181 40.909 0.00 0.00 32.81 2.52
1706 1784 3.811722 TCGAAACATGTCATCAACAGC 57.188 42.857 0.00 0.00 42.37 4.40
1749 1827 6.210078 CCTTAACATTTCAGTGCGGTAAAAA 58.790 36.000 0.00 0.00 0.00 1.94
1966 2044 9.695526 GCCACATTGCATAATCTATGAATAAAA 57.304 29.630 0.92 0.00 38.45 1.52
2004 2082 0.681175 AGGCACCACATTTTCCTTGC 59.319 50.000 0.00 0.00 0.00 4.01
2035 2114 3.056035 ACGGGAGAGATCAACCTAACAAC 60.056 47.826 0.00 0.00 0.00 3.32
2036 2115 3.056107 CACGGGAGAGATCAACCTAACAA 60.056 47.826 0.00 0.00 0.00 2.83
2037 2116 2.496070 CACGGGAGAGATCAACCTAACA 59.504 50.000 0.00 0.00 0.00 2.41
2038 2117 2.496470 ACACGGGAGAGATCAACCTAAC 59.504 50.000 0.00 0.00 0.00 2.34
2039 2118 2.496070 CACACGGGAGAGATCAACCTAA 59.504 50.000 0.00 0.00 0.00 2.69
2040 2119 2.100197 CACACGGGAGAGATCAACCTA 58.900 52.381 0.00 0.00 0.00 3.08
2041 2120 0.898320 CACACGGGAGAGATCAACCT 59.102 55.000 0.00 0.00 0.00 3.50
2042 2121 0.108138 CCACACGGGAGAGATCAACC 60.108 60.000 0.00 0.00 40.01 3.77
2043 2122 3.442996 CCACACGGGAGAGATCAAC 57.557 57.895 0.00 0.00 40.01 3.18
2062 2141 3.699134 GATCAGGGGTCCGTTGGGC 62.699 68.421 0.00 0.00 0.00 5.36
2063 2142 2.590092 GATCAGGGGTCCGTTGGG 59.410 66.667 0.00 0.00 0.00 4.12
2064 2143 2.590092 GGATCAGGGGTCCGTTGG 59.410 66.667 0.00 0.00 0.00 3.77
2074 2153 3.873026 GATCAGGGCGCGGATCAGG 62.873 68.421 29.84 3.02 39.71 3.86
2075 2154 2.356793 GATCAGGGCGCGGATCAG 60.357 66.667 29.84 4.90 39.71 2.90
2076 2155 4.284860 CGATCAGGGCGCGGATCA 62.285 66.667 32.07 4.24 39.88 2.92
2094 2173 0.251608 ATATTATGGTTGGGCGCCCC 60.252 55.000 41.75 27.38 45.71 5.80
2095 2174 0.887933 CATATTATGGTTGGGCGCCC 59.112 55.000 39.40 39.40 0.00 6.13
2096 2175 0.887933 CCATATTATGGTTGGGCGCC 59.112 55.000 21.18 21.18 45.54 6.53
2106 2185 2.159382 GGGCCCGTCAACCATATTATG 58.841 52.381 5.69 0.00 0.00 1.90
2107 2186 1.074889 GGGGCCCGTCAACCATATTAT 59.925 52.381 17.79 0.00 0.00 1.28
2108 2187 0.475044 GGGGCCCGTCAACCATATTA 59.525 55.000 17.79 0.00 0.00 0.98
2109 2188 1.229076 GGGGCCCGTCAACCATATT 59.771 57.895 17.79 0.00 0.00 1.28
2110 2189 1.696314 AGGGGCCCGTCAACCATAT 60.696 57.895 18.95 0.00 0.00 1.78
2111 2190 2.285818 AGGGGCCCGTCAACCATA 60.286 61.111 18.95 0.00 0.00 2.74
2112 2191 4.047125 CAGGGGCCCGTCAACCAT 62.047 66.667 18.95 0.00 0.00 3.55
2114 2193 4.717313 GACAGGGGCCCGTCAACC 62.717 72.222 30.08 12.98 31.22 3.77
2115 2194 3.948719 TGACAGGGGCCCGTCAAC 61.949 66.667 33.24 19.43 35.45 3.18
2116 2195 3.948719 GTGACAGGGGCCCGTCAA 61.949 66.667 35.33 23.44 38.19 3.18
2128 2207 0.109039 TTATGTAGCGCTGCGTGACA 60.109 50.000 27.69 25.34 0.00 3.58
2129 2208 0.996462 TTTATGTAGCGCTGCGTGAC 59.004 50.000 27.69 20.33 0.00 3.67
2130 2209 1.135228 TCTTTATGTAGCGCTGCGTGA 60.135 47.619 27.69 18.51 0.00 4.35
2131 2210 1.256376 CTCTTTATGTAGCGCTGCGTG 59.744 52.381 27.69 13.04 0.00 5.34
2132 2211 1.560923 CTCTTTATGTAGCGCTGCGT 58.439 50.000 23.71 23.71 0.00 5.24
2133 2212 0.855349 CCTCTTTATGTAGCGCTGCG 59.145 55.000 22.90 19.17 0.00 5.18
2134 2213 1.594862 CACCTCTTTATGTAGCGCTGC 59.405 52.381 22.90 21.06 0.00 5.25
2135 2214 2.205074 CCACCTCTTTATGTAGCGCTG 58.795 52.381 22.90 0.17 0.00 5.18
2136 2215 1.139058 CCCACCTCTTTATGTAGCGCT 59.861 52.381 17.26 17.26 0.00 5.92
2137 2216 1.583054 CCCACCTCTTTATGTAGCGC 58.417 55.000 0.00 0.00 0.00 5.92
2138 2217 1.202651 CCCCCACCTCTTTATGTAGCG 60.203 57.143 0.00 0.00 0.00 4.26
2139 2218 1.477014 GCCCCCACCTCTTTATGTAGC 60.477 57.143 0.00 0.00 0.00 3.58
2140 2219 1.143073 GGCCCCCACCTCTTTATGTAG 59.857 57.143 0.00 0.00 0.00 2.74
2141 2220 1.218844 GGCCCCCACCTCTTTATGTA 58.781 55.000 0.00 0.00 0.00 2.29
2142 2221 1.921869 CGGCCCCCACCTCTTTATGT 61.922 60.000 0.00 0.00 0.00 2.29
2143 2222 1.152963 CGGCCCCCACCTCTTTATG 60.153 63.158 0.00 0.00 0.00 1.90
2144 2223 2.383601 CCGGCCCCCACCTCTTTAT 61.384 63.158 0.00 0.00 0.00 1.40
2145 2224 3.012722 CCGGCCCCCACCTCTTTA 61.013 66.667 0.00 0.00 0.00 1.85
2163 2242 3.909258 AACCTCGTACTGCGTGCCG 62.909 63.158 0.00 0.00 42.13 5.69
2164 2243 2.048503 AACCTCGTACTGCGTGCC 60.049 61.111 0.00 0.00 42.13 5.01
2165 2244 1.372499 TGAACCTCGTACTGCGTGC 60.372 57.895 0.00 0.00 42.13 5.34
2166 2245 1.007336 GGTGAACCTCGTACTGCGTG 61.007 60.000 0.00 0.00 42.13 5.34
2167 2246 1.288127 GGTGAACCTCGTACTGCGT 59.712 57.895 0.00 0.00 42.13 5.24
2168 2247 1.800315 CGGTGAACCTCGTACTGCG 60.800 63.158 0.00 0.00 43.01 5.18
2169 2248 2.092882 GCGGTGAACCTCGTACTGC 61.093 63.158 0.00 0.00 39.24 4.40
2170 2249 1.800315 CGCGGTGAACCTCGTACTG 60.800 63.158 0.00 0.00 39.22 2.74
2171 2250 2.564975 CGCGGTGAACCTCGTACT 59.435 61.111 0.00 0.00 39.22 2.73
2176 2255 3.723348 GGCAACGCGGTGAACCTC 61.723 66.667 31.65 9.59 0.00 3.85
2177 2256 4.555709 TGGCAACGCGGTGAACCT 62.556 61.111 31.65 0.00 42.51 3.50
2178 2257 4.025401 CTGGCAACGCGGTGAACC 62.025 66.667 31.65 21.40 42.51 3.62
2179 2258 4.025401 CCTGGCAACGCGGTGAAC 62.025 66.667 31.65 20.39 42.51 3.18
2192 2271 3.204467 TTTTCGGTGGGGAGCCTGG 62.204 63.158 0.00 0.00 0.00 4.45
2193 2272 1.971695 GTTTTCGGTGGGGAGCCTG 60.972 63.158 0.00 0.00 0.00 4.85
2194 2273 2.125766 GAGTTTTCGGTGGGGAGCCT 62.126 60.000 0.00 0.00 0.00 4.58
2195 2274 1.674651 GAGTTTTCGGTGGGGAGCC 60.675 63.158 0.00 0.00 0.00 4.70
2196 2275 1.674651 GGAGTTTTCGGTGGGGAGC 60.675 63.158 0.00 0.00 0.00 4.70
2197 2276 1.375523 CGGAGTTTTCGGTGGGGAG 60.376 63.158 0.00 0.00 0.00 4.30
2198 2277 2.745037 CGGAGTTTTCGGTGGGGA 59.255 61.111 0.00 0.00 0.00 4.81
2199 2278 2.359478 CCGGAGTTTTCGGTGGGG 60.359 66.667 0.00 0.00 42.33 4.96
2205 2284 2.125269 ATCGGGCCGGAGTTTTCG 60.125 61.111 27.98 3.18 0.00 3.46
2206 2285 0.462789 TAGATCGGGCCGGAGTTTTC 59.537 55.000 27.98 10.90 0.00 2.29
2207 2286 0.464452 CTAGATCGGGCCGGAGTTTT 59.536 55.000 27.98 8.68 0.00 2.43
2208 2287 1.400530 CCTAGATCGGGCCGGAGTTT 61.401 60.000 27.98 10.39 0.00 2.66
2209 2288 1.833049 CCTAGATCGGGCCGGAGTT 60.833 63.158 27.98 11.98 0.00 3.01
2210 2289 2.203509 CCTAGATCGGGCCGGAGT 60.204 66.667 27.98 12.83 0.00 3.85
2211 2290 2.203509 ACCTAGATCGGGCCGGAG 60.204 66.667 27.98 17.30 0.00 4.63
2212 2291 1.421346 TAGACCTAGATCGGGCCGGA 61.421 60.000 27.98 16.21 29.81 5.14
2213 2292 0.961358 CTAGACCTAGATCGGGCCGG 60.961 65.000 27.98 11.36 35.21 6.13
2214 2293 1.587933 GCTAGACCTAGATCGGGCCG 61.588 65.000 22.51 22.51 35.21 6.13
2215 2294 1.587933 CGCTAGACCTAGATCGGGCC 61.588 65.000 8.16 0.00 35.21 5.80
2216 2295 1.877367 CGCTAGACCTAGATCGGGC 59.123 63.158 8.16 0.00 35.21 6.13
2217 2296 0.606944 AGCGCTAGACCTAGATCGGG 60.607 60.000 8.99 6.28 35.21 5.14
2218 2297 0.519519 CAGCGCTAGACCTAGATCGG 59.480 60.000 10.99 0.00 35.21 4.18
2219 2298 1.195900 GTCAGCGCTAGACCTAGATCG 59.804 57.143 21.86 3.19 35.21 3.69
2220 2299 2.222886 TGTCAGCGCTAGACCTAGATC 58.777 52.381 26.34 9.60 35.21 2.75
2221 2300 2.226330 CTGTCAGCGCTAGACCTAGAT 58.774 52.381 26.34 0.00 35.21 1.98
2222 2301 1.065345 ACTGTCAGCGCTAGACCTAGA 60.065 52.381 26.34 11.35 35.21 2.43
2223 2302 1.064803 CACTGTCAGCGCTAGACCTAG 59.935 57.143 26.34 21.75 35.15 3.02
2224 2303 1.095600 CACTGTCAGCGCTAGACCTA 58.904 55.000 26.34 14.58 35.15 3.08
2225 2304 0.609406 TCACTGTCAGCGCTAGACCT 60.609 55.000 26.34 15.00 35.15 3.85
2226 2305 0.456995 GTCACTGTCAGCGCTAGACC 60.457 60.000 26.34 13.74 35.15 3.85
2227 2306 0.794981 CGTCACTGTCAGCGCTAGAC 60.795 60.000 24.18 24.18 36.55 2.59
2228 2307 1.502190 CGTCACTGTCAGCGCTAGA 59.498 57.895 10.99 7.62 0.00 2.43
2229 2308 1.515088 CCGTCACTGTCAGCGCTAG 60.515 63.158 10.99 6.91 0.00 3.42
2230 2309 2.566529 CCGTCACTGTCAGCGCTA 59.433 61.111 10.99 0.00 0.00 4.26
2231 2310 4.363990 CCCGTCACTGTCAGCGCT 62.364 66.667 2.64 2.64 0.00 5.92
2232 2311 3.858868 TTCCCGTCACTGTCAGCGC 62.859 63.158 0.00 0.00 0.00 5.92
2233 2312 1.734477 CTTCCCGTCACTGTCAGCG 60.734 63.158 0.00 0.00 0.00 5.18
2234 2313 2.029844 GCTTCCCGTCACTGTCAGC 61.030 63.158 0.00 0.00 0.00 4.26
2235 2314 0.389166 GAGCTTCCCGTCACTGTCAG 60.389 60.000 0.00 0.00 0.00 3.51
2236 2315 1.666011 GAGCTTCCCGTCACTGTCA 59.334 57.895 0.00 0.00 0.00 3.58
2237 2316 1.079750 GGAGCTTCCCGTCACTGTC 60.080 63.158 0.00 0.00 0.00 3.51
2238 2317 2.932234 CGGAGCTTCCCGTCACTGT 61.932 63.158 5.70 0.00 44.23 3.55
2239 2318 2.125912 CGGAGCTTCCCGTCACTG 60.126 66.667 5.70 0.00 44.23 3.66
2279 2358 4.864334 CAGGGAGTGGATGGCGGC 62.864 72.222 0.00 0.00 0.00 6.53
2280 2359 4.864334 GCAGGGAGTGGATGGCGG 62.864 72.222 0.00 0.00 0.00 6.13
2281 2360 4.864334 GGCAGGGAGTGGATGGCG 62.864 72.222 0.00 0.00 0.00 5.69
2282 2361 2.972892 GATGGCAGGGAGTGGATGGC 62.973 65.000 0.00 0.00 39.75 4.40
2283 2362 1.150081 GATGGCAGGGAGTGGATGG 59.850 63.158 0.00 0.00 0.00 3.51
2284 2363 0.465097 GTGATGGCAGGGAGTGGATG 60.465 60.000 0.00 0.00 0.00 3.51
2285 2364 1.639635 GGTGATGGCAGGGAGTGGAT 61.640 60.000 0.00 0.00 0.00 3.41
2286 2365 2.300967 GGTGATGGCAGGGAGTGGA 61.301 63.158 0.00 0.00 0.00 4.02
2287 2366 2.273449 GGTGATGGCAGGGAGTGG 59.727 66.667 0.00 0.00 0.00 4.00
2288 2367 2.124983 CGGTGATGGCAGGGAGTG 60.125 66.667 0.00 0.00 0.00 3.51
2289 2368 3.402681 CCGGTGATGGCAGGGAGT 61.403 66.667 0.00 0.00 0.00 3.85
2334 2413 1.450312 CCTGGTGCGGATGAGGAAC 60.450 63.158 0.00 0.00 0.00 3.62
2335 2414 1.612146 TCCTGGTGCGGATGAGGAA 60.612 57.895 4.64 0.00 31.43 3.36
2336 2415 2.038813 TCCTGGTGCGGATGAGGA 59.961 61.111 3.15 3.15 31.93 3.71
2337 2416 1.617018 TTCTCCTGGTGCGGATGAGG 61.617 60.000 0.00 0.00 31.43 3.86
2338 2417 0.179089 CTTCTCCTGGTGCGGATGAG 60.179 60.000 0.00 0.00 31.43 2.90
2339 2418 1.617018 CCTTCTCCTGGTGCGGATGA 61.617 60.000 0.00 0.00 31.43 2.92
2340 2419 1.153289 CCTTCTCCTGGTGCGGATG 60.153 63.158 0.00 0.00 31.43 3.51
2341 2420 0.325296 TACCTTCTCCTGGTGCGGAT 60.325 55.000 9.79 0.49 38.42 4.18
2342 2421 0.970937 CTACCTTCTCCTGGTGCGGA 60.971 60.000 9.79 0.00 38.42 5.54
2343 2422 1.517832 CTACCTTCTCCTGGTGCGG 59.482 63.158 0.00 0.00 38.42 5.69
2344 2423 1.258445 ACCTACCTTCTCCTGGTGCG 61.258 60.000 0.00 0.00 38.42 5.34
2345 2424 0.984995 AACCTACCTTCTCCTGGTGC 59.015 55.000 0.00 0.00 38.42 5.01
2346 2425 2.028020 GTGAACCTACCTTCTCCTGGTG 60.028 54.545 0.00 0.00 38.42 4.17
2347 2426 2.258109 GTGAACCTACCTTCTCCTGGT 58.742 52.381 0.00 0.00 41.28 4.00
2348 2427 1.555533 GGTGAACCTACCTTCTCCTGG 59.444 57.143 0.00 0.00 37.74 4.45
2349 2428 1.204941 CGGTGAACCTACCTTCTCCTG 59.795 57.143 0.00 0.00 38.62 3.86
2350 2429 1.558233 CGGTGAACCTACCTTCTCCT 58.442 55.000 0.00 0.00 38.62 3.69
2351 2430 0.535797 CCGGTGAACCTACCTTCTCC 59.464 60.000 0.00 0.00 38.62 3.71
2352 2431 1.553706 TCCGGTGAACCTACCTTCTC 58.446 55.000 0.00 0.00 38.62 2.87
2353 2432 2.108970 GATCCGGTGAACCTACCTTCT 58.891 52.381 0.00 0.00 38.62 2.85
2354 2433 2.101082 GAGATCCGGTGAACCTACCTTC 59.899 54.545 0.00 0.00 38.62 3.46
2355 2434 2.108970 GAGATCCGGTGAACCTACCTT 58.891 52.381 0.00 0.00 38.62 3.50
2356 2435 1.688627 GGAGATCCGGTGAACCTACCT 60.689 57.143 0.00 0.00 38.62 3.08
2357 2436 0.751452 GGAGATCCGGTGAACCTACC 59.249 60.000 0.00 0.00 37.37 3.18
2358 2437 1.777941 AGGAGATCCGGTGAACCTAC 58.222 55.000 0.00 0.00 42.08 3.18
2359 2438 2.752154 GCTAGGAGATCCGGTGAACCTA 60.752 54.545 0.00 10.26 42.08 3.08
2360 2439 2.030045 GCTAGGAGATCCGGTGAACCT 61.030 57.143 0.00 9.62 42.08 3.50
2361 2440 0.389757 GCTAGGAGATCCGGTGAACC 59.610 60.000 0.00 1.64 42.08 3.62
2362 2441 0.389757 GGCTAGGAGATCCGGTGAAC 59.610 60.000 0.00 0.00 42.08 3.18
2363 2442 0.759436 GGGCTAGGAGATCCGGTGAA 60.759 60.000 0.00 0.00 42.08 3.18
2364 2443 1.152525 GGGCTAGGAGATCCGGTGA 60.153 63.158 0.00 0.00 42.08 4.02
2365 2444 1.457643 TGGGCTAGGAGATCCGGTG 60.458 63.158 0.00 0.00 42.08 4.94
2366 2445 1.457831 GTGGGCTAGGAGATCCGGT 60.458 63.158 0.00 0.00 42.08 5.28
2367 2446 1.152440 AGTGGGCTAGGAGATCCGG 60.152 63.158 0.00 0.00 42.08 5.14
2368 2447 1.182385 GGAGTGGGCTAGGAGATCCG 61.182 65.000 0.00 0.00 42.08 4.18
2369 2448 1.182385 CGGAGTGGGCTAGGAGATCC 61.182 65.000 0.00 0.00 0.00 3.36
2370 2449 0.178987 TCGGAGTGGGCTAGGAGATC 60.179 60.000 0.00 0.00 0.00 2.75
2371 2450 0.485099 ATCGGAGTGGGCTAGGAGAT 59.515 55.000 0.00 0.00 0.00 2.75
2372 2451 0.178987 GATCGGAGTGGGCTAGGAGA 60.179 60.000 0.00 0.00 0.00 3.71
2373 2452 0.178975 AGATCGGAGTGGGCTAGGAG 60.179 60.000 0.00 0.00 0.00 3.69
2374 2453 1.146452 TAGATCGGAGTGGGCTAGGA 58.854 55.000 0.00 0.00 0.00 2.94
2375 2454 1.889829 CTTAGATCGGAGTGGGCTAGG 59.110 57.143 0.00 0.00 0.00 3.02
2376 2455 2.865079 TCTTAGATCGGAGTGGGCTAG 58.135 52.381 0.00 0.00 0.00 3.42
2377 2456 3.308035 TTCTTAGATCGGAGTGGGCTA 57.692 47.619 0.00 0.00 0.00 3.93
2378 2457 2.160721 TTCTTAGATCGGAGTGGGCT 57.839 50.000 0.00 0.00 0.00 5.19
2379 2458 2.630580 AGATTCTTAGATCGGAGTGGGC 59.369 50.000 0.00 0.00 0.00 5.36
2380 2459 5.712446 TGATAGATTCTTAGATCGGAGTGGG 59.288 44.000 0.00 0.00 0.00 4.61
2381 2460 6.825944 TGATAGATTCTTAGATCGGAGTGG 57.174 41.667 0.00 0.00 0.00 4.00
2382 2461 7.758980 CCATTGATAGATTCTTAGATCGGAGTG 59.241 40.741 0.00 0.00 0.00 3.51
2383 2462 7.453126 ACCATTGATAGATTCTTAGATCGGAGT 59.547 37.037 0.00 0.00 0.00 3.85
2384 2463 7.835822 ACCATTGATAGATTCTTAGATCGGAG 58.164 38.462 0.00 0.00 0.00 4.63
2385 2464 7.782897 ACCATTGATAGATTCTTAGATCGGA 57.217 36.000 0.00 0.00 0.00 4.55
2386 2465 9.743057 GATACCATTGATAGATTCTTAGATCGG 57.257 37.037 0.00 0.00 0.00 4.18
2394 2473 8.703743 GGCTATCTGATACCATTGATAGATTCT 58.296 37.037 11.56 0.00 40.18 2.40
2395 2474 8.481314 TGGCTATCTGATACCATTGATAGATTC 58.519 37.037 11.56 3.23 40.18 2.52
2396 2475 8.384693 TGGCTATCTGATACCATTGATAGATT 57.615 34.615 11.56 0.00 40.18 2.40
2397 2476 7.843252 TCTGGCTATCTGATACCATTGATAGAT 59.157 37.037 14.92 0.00 40.18 1.98
2398 2477 7.184862 TCTGGCTATCTGATACCATTGATAGA 58.815 38.462 14.92 8.38 40.18 1.98
2399 2478 7.415592 TCTGGCTATCTGATACCATTGATAG 57.584 40.000 14.92 0.00 40.51 2.08
2400 2479 7.201857 CGATCTGGCTATCTGATACCATTGATA 60.202 40.741 14.92 0.00 34.74 2.15
2401 2480 6.406737 CGATCTGGCTATCTGATACCATTGAT 60.407 42.308 14.92 14.43 34.74 2.57
2402 2481 5.105595 CGATCTGGCTATCTGATACCATTGA 60.106 44.000 14.92 11.71 34.74 2.57
2403 2482 5.107824 CGATCTGGCTATCTGATACCATTG 58.892 45.833 14.92 8.30 34.74 2.82
2404 2483 4.161189 CCGATCTGGCTATCTGATACCATT 59.839 45.833 14.92 9.01 34.74 3.16
2405 2484 3.703556 CCGATCTGGCTATCTGATACCAT 59.296 47.826 14.92 6.05 34.74 3.55
2406 2485 3.092301 CCGATCTGGCTATCTGATACCA 58.908 50.000 14.23 14.23 34.74 3.25
2407 2486 2.428890 CCCGATCTGGCTATCTGATACC 59.571 54.545 0.00 1.96 34.74 2.73
2408 2487 3.791973 CCCGATCTGGCTATCTGATAC 57.208 52.381 0.00 0.00 34.74 2.24
2419 2498 3.658709 GAAATCTTCTAGCCCGATCTGG 58.341 50.000 0.00 0.00 37.55 3.86


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

AutoCloner maintained by Alex Coulton.