Multiple sequence alignment - TraesCS7A01G252700

Loading Multiple Alignment...

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 TraesCS7A01G252700 chr7A 100.000 7914 0 0 1 7914 237524936 237517023 0.000000e+00 14615.0
1 TraesCS7A01G252700 chr7B 96.608 4186 108 15 2208 6367 173861562 173865739 0.000000e+00 6913.0
2 TraesCS7A01G252700 chr7B 91.282 1560 89 19 6373 7913 173865926 173867457 0.000000e+00 2084.0
3 TraesCS7A01G252700 chr7B 96.367 1101 35 2 928 2024 173860477 173861576 0.000000e+00 1807.0
4 TraesCS7A01G252700 chr7B 88.924 948 65 17 1 926 173859483 173860412 0.000000e+00 1133.0
5 TraesCS7A01G252700 chr7D 98.756 3778 43 3 2208 5983 224052184 224055959 0.000000e+00 6713.0
6 TraesCS7A01G252700 chr7D 96.053 2027 75 3 1 2022 224050170 224052196 0.000000e+00 3295.0
7 TraesCS7A01G252700 chr7D 93.271 1382 57 14 6539 7913 224056712 224058064 0.000000e+00 2004.0
8 TraesCS7A01G252700 chr7D 98.273 579 4 1 5968 6540 224055974 224056552 0.000000e+00 1009.0
9 TraesCS7A01G252700 chr5B 99.479 192 0 1 2018 2209 660145812 660145622 1.630000e-91 348.0
10 TraesCS7A01G252700 chr5B 83.186 226 37 1 5419 5643 460265959 460265734 1.040000e-48 206.0
11 TraesCS7A01G252700 chr5B 72.581 434 87 21 1136 1562 460270221 460269813 6.490000e-21 113.0
12 TraesCS7A01G252700 chr5A 100.000 186 0 0 2024 2209 585407171 585407356 2.110000e-90 344.0
13 TraesCS7A01G252700 chr5A 83.186 226 37 1 5419 5643 484079423 484079198 1.040000e-48 206.0
14 TraesCS7A01G252700 chr5A 73.853 436 87 21 1136 1562 484083349 484082932 1.780000e-31 148.0
15 TraesCS7A01G252700 chr1A 98.469 196 1 2 2013 2208 583789124 583789317 2.110000e-90 344.0
16 TraesCS7A01G252700 chr4D 98.462 195 2 1 2020 2214 478512181 478512374 7.600000e-90 342.0
17 TraesCS7A01G252700 chr4B 99.471 189 0 1 2024 2212 193970495 193970682 7.600000e-90 342.0
18 TraesCS7A01G252700 chr3B 98.953 191 2 0 2020 2210 277752207 277752397 7.600000e-90 342.0
19 TraesCS7A01G252700 chr2A 98.958 192 1 1 2020 2210 661716486 661716295 7.600000e-90 342.0
20 TraesCS7A01G252700 chr6A 97.959 196 2 2 2021 2216 127185173 127185366 9.840000e-89 339.0
21 TraesCS7A01G252700 chr6A 76.712 146 30 4 5501 5644 607954896 607955039 2.370000e-10 78.7
22 TraesCS7A01G252700 chr4A 97.015 201 4 2 2022 2222 477497657 477497855 3.540000e-88 337.0
23 TraesCS7A01G252700 chr5D 83.186 226 37 1 5419 5643 383776440 383776215 1.040000e-48 206.0
24 TraesCS7A01G252700 chr5D 73.333 435 91 19 1136 1562 383780720 383780303 3.850000e-28 137.0
25 TraesCS7A01G252700 chr6B 77.397 146 29 4 5501 5644 702828229 702828372 5.090000e-12 84.2
26 TraesCS7A01G252700 chr1B 76.821 151 29 6 5497 5644 655100496 655100349 6.580000e-11 80.5
27 TraesCS7A01G252700 chr6D 76.712 146 30 4 5501 5644 461357664 461357807 2.370000e-10 78.7


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 TraesCS7A01G252700 chr7A 237517023 237524936 7913 True 14615.00 14615 100.00000 1 7914 1 chr7A.!!$R1 7913
1 TraesCS7A01G252700 chr7B 173859483 173867457 7974 False 2984.25 6913 93.29525 1 7913 4 chr7B.!!$F1 7912
2 TraesCS7A01G252700 chr7D 224050170 224058064 7894 False 3255.25 6713 96.58825 1 7913 4 chr7D.!!$F1 7912

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
722 760 1.005332 TCATTTCCATTCGCCCCAAGA 59.995 47.619 0.00 0.0 0.00 3.02 F
2108 2213 0.177141 TGGGTCTATTGTACGCAGCC 59.823 55.000 0.00 0.0 35.18 4.85 F
2175 2280 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.0 44.78 4.85 F
2188 2293 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.0 38.40 4.00 F
2189 2294 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.0 41.70 3.66 F
2196 2301 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.0 0.00 3.61 F
2214 2319 1.676967 GGCTCCCCTTCTGCACTTG 60.677 63.158 0.00 0.0 0.00 3.16 F
2517 2622 1.887854 CCACATGATGTTGTCAAGCCA 59.112 47.619 0.00 0.0 40.97 4.75 F
2722 2827 2.038033 GTCAGTGGGGCAGTTGTTACTA 59.962 50.000 0.00 0.0 31.96 1.82 F
3001 3106 2.162809 CCAACACCCTTTTATACACCGC 59.837 50.000 0.00 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 2250 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.0 0.00 2.69 R
3280 3385 1.565067 AAGTTCGGGTCGGGAATAGT 58.435 50.000 0.00 0.0 0.00 2.12 R
5028 5141 9.753674 ACATTATCCCTGAAATCAGAAGTTTTA 57.246 29.630 11.94 0.0 46.59 1.52 R
5152 5265 6.215636 ACAGGTATACTTCAACCCATTTCTCT 59.784 38.462 2.25 0.0 36.34 3.10 R
5654 5767 7.113965 GCAAATTCGTATCAAGCATTATTCTGG 59.886 37.037 0.00 0.0 0.00 3.86 R
5942 6066 5.695818 ACTGGCGATGTATTTTGTGTTTAC 58.304 37.500 0.00 0.0 0.00 2.01 R
6362 6523 4.725790 ACTGCCTTCAAATTTATCAGCC 57.274 40.909 0.00 0.0 0.00 4.85 R
6804 7315 5.817296 TGGGAAGATTAACTGATTCATCGTG 59.183 40.000 0.00 0.0 0.00 4.35 R
6828 7343 0.179009 TGGAGCTGAAGCAAAGCACT 60.179 50.000 4.90 0.0 43.37 4.40 R
7153 7669 0.382515 TTTTGCACACGGCTACCAAC 59.617 50.000 0.00 0.0 45.15 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 2.970974 GCACGACCCTCAAAGCAGC 61.971 63.158 0.00 0.00 0.00 5.25
153 154 2.168313 GAGAGAGGAGAAGGAAGGCTTG 59.832 54.545 3.46 0.00 0.00 4.01
208 209 2.579738 GGGGACTCGAGCTGGTTC 59.420 66.667 13.61 1.41 0.00 3.62
296 297 2.770475 GAGGGGAAGGAGGAGGCC 60.770 72.222 0.00 0.00 0.00 5.19
371 373 2.308690 GAGGCGTCAAGGTACCTATCT 58.691 52.381 16.67 6.57 30.95 1.98
372 374 3.484407 GAGGCGTCAAGGTACCTATCTA 58.516 50.000 16.67 0.00 30.95 1.98
375 394 3.193056 GGCGTCAAGGTACCTATCTATCC 59.807 52.174 16.67 8.90 0.00 2.59
397 416 1.821241 CTCTCTCGCTCTCGCTCTCG 61.821 65.000 0.00 0.00 35.26 4.04
401 420 4.936248 CGCTCTCGCTCTCGCTCG 62.936 72.222 0.00 0.00 35.26 5.03
403 422 3.572539 CTCTCGCTCTCGCTCGCT 61.573 66.667 0.00 0.00 35.26 4.93
404 423 3.506312 CTCTCGCTCTCGCTCGCTC 62.506 68.421 0.00 0.00 35.26 5.03
405 424 4.936248 CTCGCTCTCGCTCGCTCG 62.936 72.222 0.00 0.00 35.26 5.03
409 428 4.605967 CTCTCGCTCGCTCGCTCC 62.606 72.222 0.00 0.00 0.00 4.70
428 447 4.896482 GCTCCCTCTCCCGTATATAATCAT 59.104 45.833 0.00 0.00 0.00 2.45
523 543 3.980646 TTTTGTTGTGATTCGGAGGTG 57.019 42.857 0.00 0.00 0.00 4.00
624 651 5.566627 GCTCTTGCCTTTTAGGTGCAAATTA 60.567 40.000 0.00 0.00 43.69 1.40
696 734 3.191371 CCATTGCTTTAGGCTTCTCGTTT 59.809 43.478 0.00 0.00 42.39 3.60
701 739 4.817464 TGCTTTAGGCTTCTCGTTTACAAA 59.183 37.500 0.00 0.00 42.39 2.83
713 751 8.964420 TTCTCGTTTACAAATCATTTCCATTC 57.036 30.769 0.00 0.00 0.00 2.67
714 752 7.240674 TCTCGTTTACAAATCATTTCCATTCG 58.759 34.615 0.00 0.00 0.00 3.34
717 755 3.525268 ACAAATCATTTCCATTCGCCC 57.475 42.857 0.00 0.00 0.00 6.13
722 760 1.005332 TCATTTCCATTCGCCCCAAGA 59.995 47.619 0.00 0.00 0.00 3.02
756 794 5.645067 ACATTTTGCATCTTCGAGAGATTCA 59.355 36.000 7.20 6.61 42.55 2.57
760 798 3.950395 TGCATCTTCGAGAGATTCAGAGA 59.050 43.478 7.20 0.00 42.55 3.10
762 800 4.792704 GCATCTTCGAGAGATTCAGAGACC 60.793 50.000 7.20 0.00 42.55 3.85
784 823 1.749063 GGTACCTTAGCATGTTTGGGC 59.251 52.381 4.06 0.00 0.00 5.36
804 843 4.253685 GGCAGTCTTCTTGTATGCTGTTA 58.746 43.478 0.00 0.00 37.08 2.41
868 907 6.480981 ACTTTGGAAATCATTTGCTTCAACAG 59.519 34.615 3.04 0.00 31.65 3.16
1515 1617 2.833794 TCAACTCACAAGGAAGAACCG 58.166 47.619 0.00 0.00 44.74 4.44
1658 1760 6.459985 CCATTTTTCTGATCGATTATGTGCCA 60.460 38.462 0.00 0.00 0.00 4.92
1685 1787 2.419297 GGATGCTTGGTCTCTGTACCTG 60.419 54.545 0.00 0.00 40.44 4.00
1791 1896 3.084786 AGAAGTTGCAAATGAGCTACCC 58.915 45.455 0.00 0.00 40.37 3.69
1855 1960 4.520492 TGAAGGAAAATCAGCACTCCTTTC 59.480 41.667 3.84 0.00 46.08 2.62
1916 2021 2.281762 CGTTGGTTGCGCTAATCTAGTC 59.718 50.000 9.73 0.00 0.00 2.59
1999 2104 5.095490 GGCACTGAAAATATCTTTGGAACG 58.905 41.667 0.00 0.00 0.00 3.95
2032 2137 4.502962 GCACTTGCATAATAAAAAGGGCA 58.497 39.130 3.73 0.00 46.12 5.36
2033 2138 4.567959 GCACTTGCATAATAAAAAGGGCAG 59.432 41.667 3.73 0.00 46.12 4.85
2034 2139 4.567959 CACTTGCATAATAAAAAGGGCAGC 59.432 41.667 0.00 0.00 32.31 5.25
2035 2140 3.817709 TGCATAATAAAAAGGGCAGCC 57.182 42.857 1.26 1.26 0.00 4.85
2036 2141 2.433970 TGCATAATAAAAAGGGCAGCCC 59.566 45.455 24.90 24.90 45.90 5.19
2047 2152 2.045045 GCAGCCCCAGTGCATGTA 60.045 61.111 0.00 0.00 40.86 2.29
2048 2153 2.117156 GCAGCCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 40.86 2.74
2049 2154 2.117156 CAGCCCCAGTGCATGTAGC 61.117 63.158 0.00 0.00 45.96 3.58
2050 2155 2.273449 GCCCCAGTGCATGTAGCT 59.727 61.111 0.00 0.00 45.94 3.32
2051 2156 1.821332 GCCCCAGTGCATGTAGCTC 60.821 63.158 0.00 0.00 45.94 4.09
2052 2157 1.153086 CCCCAGTGCATGTAGCTCC 60.153 63.158 0.00 0.00 45.94 4.70
2053 2158 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.00 45.94 4.30
2054 2159 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
2055 2160 2.176273 CAGTGCATGTAGCTCCCGC 61.176 63.158 0.00 0.00 45.94 6.13
2057 2162 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2058 2163 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2059 2164 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2060 2165 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2063 2168 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2075 2180 4.785453 GCGCAGGGTCTGGGGAAG 62.785 72.222 0.30 0.00 43.28 3.46
2076 2181 4.101448 CGCAGGGTCTGGGGAAGG 62.101 72.222 4.35 0.00 40.11 3.46
2077 2182 3.732849 GCAGGGTCTGGGGAAGGG 61.733 72.222 0.00 0.00 31.21 3.95
2078 2183 2.204151 CAGGGTCTGGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
2079 2184 2.125225 AGGGTCTGGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
2080 2185 3.015753 GGGTCTGGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
2081 2186 3.400054 GGTCTGGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
2082 2187 2.284405 GTCTGGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
2083 2188 2.284405 TCTGGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
2084 2189 3.400054 CTGGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
2085 2190 4.257810 TGGGGAAGGGTCCGACCA 62.258 66.667 19.43 0.00 46.04 4.02
2086 2191 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
2087 2192 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2088 2193 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2089 2194 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2090 2195 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2091 2196 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2092 2197 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2093 2198 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2103 2208 3.934068 ACCACTTTGGGTCTATTGTACG 58.066 45.455 0.00 0.00 43.37 3.67
2104 2209 2.676342 CCACTTTGGGTCTATTGTACGC 59.324 50.000 0.00 0.00 32.67 4.42
2105 2210 3.331150 CACTTTGGGTCTATTGTACGCA 58.669 45.455 0.00 0.00 37.94 5.24
2106 2211 3.370978 CACTTTGGGTCTATTGTACGCAG 59.629 47.826 0.00 0.00 40.36 5.18
2107 2212 2.018542 TTGGGTCTATTGTACGCAGC 57.981 50.000 0.00 0.00 40.36 5.25
2108 2213 0.177141 TGGGTCTATTGTACGCAGCC 59.823 55.000 0.00 0.00 35.18 4.85
2109 2214 0.464452 GGGTCTATTGTACGCAGCCT 59.536 55.000 0.00 0.00 0.00 4.58
2110 2215 1.134491 GGGTCTATTGTACGCAGCCTT 60.134 52.381 0.00 0.00 0.00 4.35
2111 2216 2.629051 GGTCTATTGTACGCAGCCTTT 58.371 47.619 0.00 0.00 0.00 3.11
2112 2217 2.608090 GGTCTATTGTACGCAGCCTTTC 59.392 50.000 0.00 0.00 0.00 2.62
2113 2218 2.608090 GTCTATTGTACGCAGCCTTTCC 59.392 50.000 0.00 0.00 0.00 3.13
2114 2219 1.940613 CTATTGTACGCAGCCTTTCCC 59.059 52.381 0.00 0.00 0.00 3.97
2115 2220 0.328258 ATTGTACGCAGCCTTTCCCT 59.672 50.000 0.00 0.00 0.00 4.20
2116 2221 0.978151 TTGTACGCAGCCTTTCCCTA 59.022 50.000 0.00 0.00 0.00 3.53
2117 2222 0.248289 TGTACGCAGCCTTTCCCTAC 59.752 55.000 0.00 0.00 0.00 3.18
2118 2223 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2119 2224 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2120 2225 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2121 2226 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2122 2227 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2123 2228 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
2124 2229 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
2125 2230 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
2126 2231 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
2127 2232 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
2128 2233 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
2129 2234 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
2141 2246 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
2142 2247 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
2143 2248 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
2144 2249 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
2145 2250 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
2146 2251 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
2147 2252 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
2148 2253 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
2149 2254 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
2150 2255 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
2151 2256 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
2152 2257 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
2153 2258 1.235724 GTTTCCAGGACTTGAACCCG 58.764 55.000 0.00 0.00 0.00 5.28
2154 2259 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
2155 2260 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
2156 2261 0.761323 TCCAGGACTTGAACCCGTGA 60.761 55.000 0.00 0.00 0.00 4.35
2157 2262 0.602905 CCAGGACTTGAACCCGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
2158 2263 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
2159 2264 0.763223 AGGACTTGAACCCGTGACCT 60.763 55.000 0.00 0.00 0.00 3.85
2160 2265 0.320508 GGACTTGAACCCGTGACCTC 60.321 60.000 0.00 0.00 0.00 3.85
2161 2266 0.391597 GACTTGAACCCGTGACCTCA 59.608 55.000 0.00 0.00 0.00 3.86
2162 2267 1.002087 GACTTGAACCCGTGACCTCAT 59.998 52.381 0.00 0.00 0.00 2.90
2163 2268 1.270839 ACTTGAACCCGTGACCTCATG 60.271 52.381 0.00 0.00 0.00 3.07
2174 2279 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2175 2280 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2176 2281 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2177 2282 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
2178 2283 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
2179 2284 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
2180 2285 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
2181 2286 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
2182 2287 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
2183 2288 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
2184 2289 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
2185 2290 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
2186 2291 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
2187 2292 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
2188 2293 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
2189 2294 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
2193 2298 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
2194 2299 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
2195 2300 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
2196 2301 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
2197 2302 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
2198 2303 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
2199 2304 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
2200 2305 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
2212 2317 2.204059 AGGCTCCCCTTCTGCACT 60.204 61.111 0.00 0.00 38.74 4.40
2213 2318 1.849823 AGGCTCCCCTTCTGCACTT 60.850 57.895 0.00 0.00 38.74 3.16
2214 2319 1.676967 GGCTCCCCTTCTGCACTTG 60.677 63.158 0.00 0.00 0.00 3.16
2215 2320 2.338785 GCTCCCCTTCTGCACTTGC 61.339 63.158 0.00 0.00 42.50 4.01
2312 2417 7.116519 CACATGCAAATGAATGTTGACATTACA 59.883 33.333 9.19 9.47 41.43 2.41
2517 2622 1.887854 CCACATGATGTTGTCAAGCCA 59.112 47.619 0.00 0.00 40.97 4.75
2722 2827 2.038033 GTCAGTGGGGCAGTTGTTACTA 59.962 50.000 0.00 0.00 31.96 1.82
3001 3106 2.162809 CCAACACCCTTTTATACACCGC 59.837 50.000 0.00 0.00 0.00 5.68
3280 3385 2.283821 GGGTTCCCATGCAGCCAA 60.284 61.111 2.59 0.00 0.00 4.52
4022 4127 3.739300 CAGCAGAAATTGGAAAACTGCAG 59.261 43.478 13.48 13.48 46.10 4.41
5028 5141 7.050377 CAGTTAAATATGGTGTCCAGTCAGAT 58.950 38.462 0.00 0.00 36.75 2.90
5151 5264 9.427821 AAGAGAGCTAGAGTAATCAGGAAATTA 57.572 33.333 0.00 0.00 0.00 1.40
5152 5265 9.427821 AGAGAGCTAGAGTAATCAGGAAATTAA 57.572 33.333 0.00 0.00 0.00 1.40
5213 5326 8.268850 ACGTGAGAACATTATATTTTTCTGCT 57.731 30.769 0.00 0.00 0.00 4.24
5380 5493 4.039730 GCCATAGTATCTGATGTGTCCTGT 59.960 45.833 0.00 0.00 0.00 4.00
5654 5767 4.254492 GTTATTCAGGTGGGTTCAGACTC 58.746 47.826 0.00 0.00 0.00 3.36
5874 5987 8.949177 AGGTGAAATTATTTGCAATTTGATTCC 58.051 29.630 0.00 0.00 38.04 3.01
5875 5988 8.728833 GGTGAAATTATTTGCAATTTGATTCCA 58.271 29.630 0.00 0.00 38.04 3.53
5903 6016 6.259829 TCTTTTGCCAAATTCTAAAAAGTGCC 59.740 34.615 0.00 0.00 38.42 5.01
5942 6066 3.393089 AAACTGACTGAGTGGCTGTAG 57.607 47.619 0.00 0.00 34.60 2.74
6346 6505 2.995258 CGCAATGTTTCCATCCCTTTTG 59.005 45.455 0.00 0.00 0.00 2.44
6745 7256 5.296035 GGAAGTACACCTATGGCAAACATAC 59.704 44.000 0.00 0.00 41.03 2.39
6804 7315 4.045783 GCCTCTTGAACTAGCGATACTTC 58.954 47.826 0.00 0.00 0.00 3.01
6818 7329 4.504461 GCGATACTTCACGATGAATCAGTT 59.496 41.667 0.00 0.00 35.59 3.16
6828 7343 5.817296 CACGATGAATCAGTTAATCTTCCCA 59.183 40.000 0.00 0.00 0.00 4.37
6850 7365 0.240411 GCTTTGCTTCAGCTCCAGTG 59.760 55.000 0.00 0.00 42.66 3.66
6852 7367 1.952296 CTTTGCTTCAGCTCCAGTGTT 59.048 47.619 0.00 0.00 42.66 3.32
6865 7380 4.574828 GCTCCAGTGTTTTGAAGTGTCTTA 59.425 41.667 0.00 0.00 0.00 2.10
6867 7382 6.238759 GCTCCAGTGTTTTGAAGTGTCTTAAT 60.239 38.462 0.00 0.00 0.00 1.40
6869 7384 8.740123 TCCAGTGTTTTGAAGTGTCTTAATTA 57.260 30.769 0.00 0.00 0.00 1.40
6870 7385 9.179909 TCCAGTGTTTTGAAGTGTCTTAATTAA 57.820 29.630 0.00 0.00 0.00 1.40
6910 7425 2.583593 GATGCCGAGTGCGACTCC 60.584 66.667 9.71 0.34 42.12 3.85
6913 7428 1.729470 ATGCCGAGTGCGACTCCTAG 61.729 60.000 9.71 0.00 42.12 3.02
6916 7431 2.407428 CGAGTGCGACTCCTAGGCA 61.407 63.158 2.96 0.00 42.12 4.75
6917 7432 1.729470 CGAGTGCGACTCCTAGGCAT 61.729 60.000 2.96 0.00 42.12 4.40
6918 7433 0.461961 GAGTGCGACTCCTAGGCATT 59.538 55.000 2.96 0.00 39.28 3.56
6921 7436 0.975556 TGCGACTCCTAGGCATTGGA 60.976 55.000 2.96 0.79 0.00 3.53
6962 7477 5.867716 CCAAATTCATCAGCAAGGAAGAAAG 59.132 40.000 0.00 0.00 29.52 2.62
7003 7518 4.862018 GTGCTTCAAAGTGCTAACAAAACA 59.138 37.500 0.00 0.00 0.00 2.83
7033 7549 5.428253 TCCAGCAAGGAAGATTGTACATAC 58.572 41.667 0.00 0.00 45.65 2.39
7043 7559 5.779806 AGATTGTACATACGTGACTTTGC 57.220 39.130 0.00 0.00 0.00 3.68
7152 7668 5.947566 TGTGCTTATCCACACTGTACTAGTA 59.052 40.000 0.00 0.00 40.55 1.82
7153 7669 6.095021 TGTGCTTATCCACACTGTACTAGTAG 59.905 42.308 1.87 0.00 40.55 2.57
7154 7670 6.095160 GTGCTTATCCACACTGTACTAGTAGT 59.905 42.308 8.14 8.14 37.60 2.73
7183 7699 5.588648 AGCCGTGTGCAAAATATGTATAGTT 59.411 36.000 0.00 0.00 44.83 2.24
7288 7806 4.527944 TCCAGTTGTGTGGTAAAACATCA 58.472 39.130 0.00 0.00 38.88 3.07
7297 7815 6.092748 GTGTGGTAAAACATCATCCATTCAC 58.907 40.000 0.00 0.00 31.49 3.18
7398 7921 6.751425 TGCAAAAATATTATTCCACGCTGAAG 59.249 34.615 0.00 0.00 0.00 3.02
7401 7924 9.139174 CAAAAATATTATTCCACGCTGAAGTTT 57.861 29.630 0.00 0.00 0.00 2.66
7404 7927 4.742438 TTATTCCACGCTGAAGTTTGAC 57.258 40.909 0.00 0.00 0.00 3.18
7439 7962 3.481903 CGTGCGTGCTGTAGGCTG 61.482 66.667 11.45 1.22 40.72 4.85
7440 7963 2.357517 GTGCGTGCTGTAGGCTGT 60.358 61.111 11.45 0.00 40.72 4.40
7441 7964 1.080093 GTGCGTGCTGTAGGCTGTA 60.080 57.895 11.45 0.00 40.72 2.74
7442 7965 0.669318 GTGCGTGCTGTAGGCTGTAA 60.669 55.000 11.45 0.00 40.72 2.41
7913 8436 3.395702 TACCGCCGCTTCATGGGT 61.396 61.111 0.00 0.00 34.81 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 0.873743 CGCCGATCTTCTCCTTCTGC 60.874 60.000 0.00 0.00 0.00 4.26
195 196 0.892063 GGAGAAGAACCAGCTCGAGT 59.108 55.000 15.13 0.00 0.00 4.18
268 269 1.934341 TTCCCCTCTCCCTCCTCGA 60.934 63.158 0.00 0.00 0.00 4.04
346 348 0.458025 GTACCTTGACGCCTCCGAAG 60.458 60.000 0.00 0.00 38.29 3.79
347 349 1.588082 GTACCTTGACGCCTCCGAA 59.412 57.895 0.00 0.00 38.29 4.30
371 373 1.001520 CGAGAGCGAGAGAGAGGGATA 59.998 57.143 0.00 0.00 40.82 2.59
372 374 0.250295 CGAGAGCGAGAGAGAGGGAT 60.250 60.000 0.00 0.00 40.82 3.85
397 416 4.264638 GAGAGGGAGCGAGCGAGC 62.265 72.222 0.00 0.00 37.41 5.03
401 420 3.928339 TATACGGGAGAGGGAGCGAGC 62.928 61.905 0.00 0.00 0.00 5.03
402 421 0.036448 TATACGGGAGAGGGAGCGAG 59.964 60.000 0.00 0.00 0.00 5.03
403 422 0.697079 ATATACGGGAGAGGGAGCGA 59.303 55.000 0.00 0.00 0.00 4.93
404 423 2.414994 TATATACGGGAGAGGGAGCG 57.585 55.000 0.00 0.00 0.00 5.03
405 424 4.279145 TGATTATATACGGGAGAGGGAGC 58.721 47.826 0.00 0.00 0.00 4.70
406 425 5.221342 GCATGATTATATACGGGAGAGGGAG 60.221 48.000 0.00 0.00 0.00 4.30
407 426 4.649674 GCATGATTATATACGGGAGAGGGA 59.350 45.833 0.00 0.00 0.00 4.20
408 427 4.499865 CGCATGATTATATACGGGAGAGGG 60.500 50.000 0.00 0.00 0.00 4.30
409 428 4.338400 TCGCATGATTATATACGGGAGAGG 59.662 45.833 0.00 0.00 0.00 3.69
410 429 5.274718 GTCGCATGATTATATACGGGAGAG 58.725 45.833 0.00 0.00 0.00 3.20
411 430 4.097437 GGTCGCATGATTATATACGGGAGA 59.903 45.833 0.00 0.00 0.00 3.71
428 447 3.462483 TTTTGTTCTAGTGAGGTCGCA 57.538 42.857 0.00 0.00 0.00 5.10
523 543 2.892425 CGACGCCCTCAATCCTGC 60.892 66.667 0.00 0.00 0.00 4.85
696 734 3.383185 GGGGCGAATGGAAATGATTTGTA 59.617 43.478 0.00 0.00 0.00 2.41
701 739 2.034124 CTTGGGGCGAATGGAAATGAT 58.966 47.619 0.00 0.00 0.00 2.45
713 751 1.812571 GTGGCATTATATCTTGGGGCG 59.187 52.381 0.00 0.00 0.00 6.13
714 752 2.875296 TGTGGCATTATATCTTGGGGC 58.125 47.619 0.00 0.00 0.00 5.80
717 755 6.282167 TGCAAAATGTGGCATTATATCTTGG 58.718 36.000 0.00 0.00 34.58 3.61
756 794 2.921834 TGCTAAGGTACCAGGTCTCT 57.078 50.000 15.94 0.00 0.00 3.10
760 798 3.561313 CCAAACATGCTAAGGTACCAGGT 60.561 47.826 15.94 0.00 0.00 4.00
762 800 3.016736 CCCAAACATGCTAAGGTACCAG 58.983 50.000 15.94 4.61 0.00 4.00
868 907 5.689383 TCAACAGGCAACAGAATAAGTTC 57.311 39.130 0.00 0.00 41.41 3.01
1026 1128 4.529731 GCCCCTGCCCCTCCAATC 62.530 72.222 0.00 0.00 0.00 2.67
1515 1617 5.622346 ACCTTGGAGACTTATCATCTTCC 57.378 43.478 0.00 0.00 0.00 3.46
1628 1730 8.408601 ACATAATCGATCAGAAAAATGGAAAGG 58.591 33.333 0.00 0.00 0.00 3.11
1658 1760 0.908198 GAGACCAAGCATCCCTGAGT 59.092 55.000 0.00 0.00 0.00 3.41
1791 1896 7.677454 TTGGCTGATATTGATATAAGCACAG 57.323 36.000 17.92 7.22 45.32 3.66
1855 1960 6.018016 CCAAACAAAAGCCAACCATTTCTAAG 60.018 38.462 0.00 0.00 0.00 2.18
1896 2001 3.259064 TGACTAGATTAGCGCAACCAAC 58.741 45.455 11.47 0.00 0.00 3.77
2024 2129 2.203684 CACTGGGGCTGCCCTTTT 60.204 61.111 34.99 17.53 44.66 2.27
2029 2134 3.643595 TACATGCACTGGGGCTGCC 62.644 63.158 11.05 11.05 33.36 4.85
2030 2135 2.045045 TACATGCACTGGGGCTGC 60.045 61.111 0.00 0.00 35.03 5.25
2031 2136 2.117156 GCTACATGCACTGGGGCTG 61.117 63.158 0.00 0.00 42.31 4.85
2032 2137 2.262774 GAGCTACATGCACTGGGGCT 62.263 60.000 13.29 13.29 45.94 5.19
2033 2138 1.821332 GAGCTACATGCACTGGGGC 60.821 63.158 0.00 0.00 45.94 5.80
2034 2139 1.153086 GGAGCTACATGCACTGGGG 60.153 63.158 0.00 0.00 45.94 4.96
2035 2140 1.153086 GGGAGCTACATGCACTGGG 60.153 63.158 0.00 0.00 45.94 4.45
2036 2141 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
2037 2142 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
2058 2163 4.785453 CTTCCCCAGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
2059 2164 4.101448 CCTTCCCCAGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
2060 2165 3.732849 CCCTTCCCCAGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
2061 2166 2.204151 ACCCTTCCCCAGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
2062 2167 2.125225 GACCCTTCCCCAGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
2063 2168 3.015753 GGACCCTTCCCCAGACCC 61.016 72.222 0.00 0.00 35.57 4.46
2064 2169 3.400054 CGGACCCTTCCCCAGACC 61.400 72.222 0.00 0.00 38.99 3.85
2065 2170 2.284405 TCGGACCCTTCCCCAGAC 60.284 66.667 0.00 0.00 38.99 3.51
2066 2171 2.284405 GTCGGACCCTTCCCCAGA 60.284 66.667 0.00 0.00 38.99 3.86
2067 2172 3.400054 GGTCGGACCCTTCCCCAG 61.400 72.222 16.55 0.00 38.99 4.45
2068 2173 4.257810 TGGTCGGACCCTTCCCCA 62.258 66.667 23.81 0.69 38.99 4.96
2069 2174 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
2070 2175 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2071 2176 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2072 2177 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2073 2178 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2074 2179 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2075 2180 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2076 2181 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2077 2182 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2082 2187 3.867216 GCGTACAATAGACCCAAAGTGGT 60.867 47.826 0.00 0.00 42.79 4.16
2083 2188 2.676342 GCGTACAATAGACCCAAAGTGG 59.324 50.000 0.00 0.00 37.25 4.00
2084 2189 3.331150 TGCGTACAATAGACCCAAAGTG 58.669 45.455 0.00 0.00 0.00 3.16
2085 2190 3.596214 CTGCGTACAATAGACCCAAAGT 58.404 45.455 0.00 0.00 0.00 2.66
2086 2191 2.351726 GCTGCGTACAATAGACCCAAAG 59.648 50.000 0.00 0.00 0.00 2.77
2087 2192 2.352388 GCTGCGTACAATAGACCCAAA 58.648 47.619 0.00 0.00 0.00 3.28
2088 2193 1.406341 GGCTGCGTACAATAGACCCAA 60.406 52.381 0.00 0.00 0.00 4.12
2089 2194 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.000 0.00 0.00 0.00 4.51
2090 2195 0.464452 AGGCTGCGTACAATAGACCC 59.536 55.000 0.00 0.00 0.00 4.46
2091 2196 2.311124 AAGGCTGCGTACAATAGACC 57.689 50.000 0.00 0.00 0.00 3.85
2092 2197 2.608090 GGAAAGGCTGCGTACAATAGAC 59.392 50.000 0.00 0.00 0.00 2.59
2093 2198 2.419574 GGGAAAGGCTGCGTACAATAGA 60.420 50.000 0.00 0.00 0.00 1.98
2094 2199 1.940613 GGGAAAGGCTGCGTACAATAG 59.059 52.381 0.00 0.00 0.00 1.73
2095 2200 1.557832 AGGGAAAGGCTGCGTACAATA 59.442 47.619 0.00 0.00 0.00 1.90
2096 2201 0.328258 AGGGAAAGGCTGCGTACAAT 59.672 50.000 0.00 0.00 0.00 2.71
2097 2202 0.978151 TAGGGAAAGGCTGCGTACAA 59.022 50.000 0.00 0.00 0.00 2.41
2098 2203 0.248289 GTAGGGAAAGGCTGCGTACA 59.752 55.000 0.00 0.00 36.89 2.90
2099 2204 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2100 2205 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2101 2206 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2102 2207 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2103 2208 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2104 2209 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
2105 2210 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
2106 2211 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
2107 2212 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
2108 2213 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
2109 2214 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
2110 2215 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
2111 2216 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
2112 2217 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
2113 2218 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
2114 2219 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
2115 2220 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
2116 2221 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
2117 2222 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
2118 2223 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
2119 2224 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
2133 2238 1.476110 CGGGTTCAAGTCCTGGAAACA 60.476 52.381 0.00 0.00 32.36 2.83
2134 2239 1.235724 CGGGTTCAAGTCCTGGAAAC 58.764 55.000 0.00 0.00 0.00 2.78
2135 2240 0.841289 ACGGGTTCAAGTCCTGGAAA 59.159 50.000 0.00 0.00 35.79 3.13
2136 2241 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
2137 2242 0.761323 TCACGGGTTCAAGTCCTGGA 60.761 55.000 0.00 0.00 35.79 3.86
2138 2243 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
2139 2244 0.602905 GGTCACGGGTTCAAGTCCTG 60.603 60.000 0.00 0.00 37.36 3.86
2140 2245 0.763223 AGGTCACGGGTTCAAGTCCT 60.763 55.000 0.00 0.00 0.00 3.85
2141 2246 0.320508 GAGGTCACGGGTTCAAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
2142 2247 0.391597 TGAGGTCACGGGTTCAAGTC 59.608 55.000 0.00 0.00 0.00 3.01
2143 2248 1.056660 ATGAGGTCACGGGTTCAAGT 58.943 50.000 0.00 0.00 0.00 3.16
2144 2249 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
2145 2250 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.00 0.00 2.69
2146 2251 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
2147 2252 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
2157 2262 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2158 2263 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2159 2264 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
2160 2265 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
2161 2266 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
2162 2267 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
2163 2268 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
2164 2269 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
2165 2270 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
2166 2271 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
2167 2272 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
2168 2273 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
2169 2274 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
2170 2275 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
2171 2276 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
2176 2281 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
2177 2282 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
2178 2283 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
2179 2284 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
2180 2285 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
2181 2286 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
2182 2287 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
2190 2295 3.721706 AGAAGGGGAGCCTTGGCG 61.722 66.667 5.95 0.00 0.00 5.69
2191 2296 2.044551 CAGAAGGGGAGCCTTGGC 60.045 66.667 2.97 2.97 0.00 4.52
2192 2297 2.044551 GCAGAAGGGGAGCCTTGG 60.045 66.667 0.00 0.00 0.00 3.61
2193 2298 1.676967 GTGCAGAAGGGGAGCCTTG 60.677 63.158 0.00 0.00 0.00 3.61
2194 2299 1.430369 AAGTGCAGAAGGGGAGCCTT 61.430 55.000 0.00 0.00 0.00 4.35
2195 2300 1.849823 AAGTGCAGAAGGGGAGCCT 60.850 57.895 0.00 0.00 0.00 4.58
2196 2301 1.676967 CAAGTGCAGAAGGGGAGCC 60.677 63.158 0.00 0.00 0.00 4.70
2197 2302 2.338785 GCAAGTGCAGAAGGGGAGC 61.339 63.158 0.00 0.00 41.59 4.70
2198 2303 3.993535 GCAAGTGCAGAAGGGGAG 58.006 61.111 0.00 0.00 41.59 4.30
2517 2622 4.007659 GTGTCCACGAATTTAACCCTGAT 58.992 43.478 0.00 0.00 0.00 2.90
2526 2631 2.370849 AGGTACAGGTGTCCACGAATTT 59.629 45.455 0.00 0.00 0.00 1.82
2722 2827 4.757149 GCTAGAGTCCACAACATCAAGTTT 59.243 41.667 0.00 0.00 38.74 2.66
3001 3106 7.954835 TGATAATATGGGCTTCCAAAAGAATG 58.045 34.615 0.00 0.00 44.86 2.67
3280 3385 1.565067 AAGTTCGGGTCGGGAATAGT 58.435 50.000 0.00 0.00 0.00 2.12
5028 5141 9.753674 ACATTATCCCTGAAATCAGAAGTTTTA 57.246 29.630 11.94 0.00 46.59 1.52
5151 5264 7.112779 CAGGTATACTTCAACCCATTTCTCTT 58.887 38.462 2.25 0.00 36.34 2.85
5152 5265 6.215636 ACAGGTATACTTCAACCCATTTCTCT 59.784 38.462 2.25 0.00 36.34 3.10
5654 5767 7.113965 GCAAATTCGTATCAAGCATTATTCTGG 59.886 37.037 0.00 0.00 0.00 3.86
5942 6066 5.695818 ACTGGCGATGTATTTTGTGTTTAC 58.304 37.500 0.00 0.00 0.00 2.01
6362 6523 4.725790 ACTGCCTTCAAATTTATCAGCC 57.274 40.909 0.00 0.00 0.00 4.85
6804 7315 5.817296 TGGGAAGATTAACTGATTCATCGTG 59.183 40.000 0.00 0.00 0.00 4.35
6818 7329 3.439857 AGCAAAGCACTGGGAAGATTA 57.560 42.857 0.00 0.00 0.00 1.75
6828 7343 0.179009 TGGAGCTGAAGCAAAGCACT 60.179 50.000 4.90 0.00 43.37 4.40
6910 7425 2.592861 GGCGCCTCCAATGCCTAG 60.593 66.667 22.15 0.00 45.40 3.02
6916 7431 2.044946 GGTTGAGGCGCCTCCAAT 60.045 61.111 44.85 19.99 42.09 3.16
6917 7432 4.344865 GGGTTGAGGCGCCTCCAA 62.345 66.667 44.85 35.07 42.09 3.53
6933 7448 1.321805 TGCTGATGAATTTGGCGGGG 61.322 55.000 0.00 0.00 0.00 5.73
6938 7453 5.395682 TTCTTCCTTGCTGATGAATTTGG 57.604 39.130 0.00 0.00 0.00 3.28
6962 7477 1.303091 ACCGCGGTTCCAAGTTATGC 61.303 55.000 28.70 0.00 0.00 3.14
7043 7559 1.482593 CACCTCCCTACACTGCCTAAG 59.517 57.143 0.00 0.00 0.00 2.18
7152 7668 0.464735 TTTGCACACGGCTACCAACT 60.465 50.000 0.00 0.00 45.15 3.16
7153 7669 0.382515 TTTTGCACACGGCTACCAAC 59.617 50.000 0.00 0.00 45.15 3.77
7154 7670 1.323412 ATTTTGCACACGGCTACCAA 58.677 45.000 0.00 0.00 45.15 3.67
7183 7699 2.158534 ACATACAAGCCAAACCACTGGA 60.159 45.455 0.71 0.00 38.96 3.86
7297 7815 6.040878 GCCATTTTCTTCTCATTCAATCCAG 58.959 40.000 0.00 0.00 0.00 3.86
7306 7824 4.038271 TCACAGGCCATTTTCTTCTCAT 57.962 40.909 5.01 0.00 0.00 2.90
7311 7829 5.876460 GCAATAAATCACAGGCCATTTTCTT 59.124 36.000 5.01 0.00 0.00 2.52
7351 7870 7.867752 TGCATGAAGGTTTTTGTTACTACTAC 58.132 34.615 0.00 0.00 0.00 2.73
7352 7871 8.453238 TTGCATGAAGGTTTTTGTTACTACTA 57.547 30.769 0.00 0.00 0.00 1.82
7353 7872 6.952773 TGCATGAAGGTTTTTGTTACTACT 57.047 33.333 0.00 0.00 0.00 2.57
7364 7883 9.956640 TGGAATAATATTTTTGCATGAAGGTTT 57.043 25.926 8.39 0.00 0.00 3.27
7398 7921 1.680735 TGGATTGCCACACAGTCAAAC 59.319 47.619 0.00 0.00 39.92 2.93
7460 7983 1.021968 GCGGCAATATCGAAGGGTTT 58.978 50.000 0.00 0.00 0.00 3.27
7539 8062 4.933064 CGAGGAGATGGGCGACGC 62.933 72.222 12.43 12.43 0.00 5.19


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

AutoCloner maintained by Alex Coulton.