Multiple sequence alignment - TraesCS4B01G294100

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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 TraesCS4B01G294100 chr4B 100.000 2672 0 0 1 2672 579458672 579461343 0.000000e+00 4935
1 TraesCS4B01G294100 chr4B 84.541 207 26 4 1859 2059 9360432 9360638 1.620000e-47 200
2 TraesCS4B01G294100 chr4B 93.913 115 7 0 2054 2168 195373393 195373507 9.830000e-40 174
3 TraesCS4B01G294100 chr4B 93.913 115 7 0 2054 2168 507022025 507021911 9.830000e-40 174
4 TraesCS4B01G294100 chr4D 91.234 1734 78 15 1 1672 463918165 463919886 0.000000e+00 2292
5 TraesCS4B01G294100 chr4D 84.765 361 42 11 1708 2059 463919891 463920247 1.520000e-92 350
6 TraesCS4B01G294100 chr4D 78.689 366 56 16 2303 2657 465186875 465187229 9.630000e-55 224
7 TraesCS4B01G294100 chr4D 84.653 202 23 6 1865 2059 74153600 74153400 7.550000e-46 195
8 TraesCS4B01G294100 chr4D 80.297 269 39 12 2290 2557 74153295 74153040 9.760000e-45 191
9 TraesCS4B01G294100 chr4A 92.620 813 52 6 1005 1812 5982850 5983659 0.000000e+00 1162
10 TraesCS4B01G294100 chr4A 87.400 627 51 23 1 610 5984398 5983783 0.000000e+00 695
11 TraesCS4B01G294100 chr7B 79.521 376 64 7 2303 2672 619133028 619132660 3.410000e-64 255
12 TraesCS4B01G294100 chr7B 76.471 374 70 13 2309 2672 619142870 619142505 1.260000e-43 187
13 TraesCS4B01G294100 chr1A 78.261 414 63 14 2269 2664 290366895 290366491 9.560000e-60 241
14 TraesCS4B01G294100 chr1A 79.276 304 50 6 2309 2606 244547638 244547934 1.620000e-47 200
15 TraesCS4B01G294100 chr1A 84.058 207 24 7 1859 2059 293739516 293739719 9.760000e-45 191
16 TraesCS4B01G294100 chr1D 80.422 332 50 8 2298 2622 291804840 291804517 3.440000e-59 239
17 TraesCS4B01G294100 chr7A 79.167 360 49 18 2303 2656 674306983 674307322 2.680000e-55 226
18 TraesCS4B01G294100 chr6D 81.853 259 40 7 1807 2059 85631746 85632003 7.490000e-51 211
19 TraesCS4B01G294100 chr3D 79.375 320 48 14 2345 2657 334639204 334638896 2.700000e-50 209
20 TraesCS4B01G294100 chr5A 82.400 250 32 8 1817 2059 537132269 537132513 9.690000e-50 207
21 TraesCS4B01G294100 chr5A 86.243 189 20 4 1876 2059 635944980 635944793 1.620000e-47 200
22 TraesCS4B01G294100 chr5A 94.783 115 6 0 2054 2168 456183357 456183243 2.110000e-41 180
23 TraesCS4B01G294100 chr1B 86.096 187 18 6 1876 2057 334901502 334901685 7.550000e-46 195
24 TraesCS4B01G294100 chr1B 77.457 346 54 15 2339 2672 607313604 607313271 4.540000e-43 185
25 TraesCS4B01G294100 chr2A 84.058 207 26 5 1859 2059 7842396 7842191 2.710000e-45 193
26 TraesCS4B01G294100 chr5D 83.981 206 25 5 1859 2059 9209733 9209935 9.760000e-45 191
27 TraesCS4B01G294100 chr5B 97.297 111 3 0 2054 2164 61638 61528 3.510000e-44 189
28 TraesCS4B01G294100 chr2B 94.783 115 6 0 2054 2168 80850617 80850503 2.110000e-41 180
29 TraesCS4B01G294100 chr2B 91.935 124 10 0 2045 2168 473848408 473848531 9.830000e-40 174
30 TraesCS4B01G294100 chrUn 93.913 115 7 0 2054 2168 265597607 265597721 9.830000e-40 174
31 TraesCS4B01G294100 chrUn 93.913 115 7 0 2054 2168 276141594 276141480 9.830000e-40 174
32 TraesCS4B01G294100 chrUn 93.913 115 7 0 2054 2168 290791124 290791238 9.830000e-40 174


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 TraesCS4B01G294100 chr4B 579458672 579461343 2671 False 4935 4935 100.0000 1 2672 1 chr4B.!!$F3 2671
1 TraesCS4B01G294100 chr4D 463918165 463920247 2082 False 1321 2292 87.9995 1 2059 2 chr4D.!!$F2 2058
2 TraesCS4B01G294100 chr4A 5982850 5983659 809 False 1162 1162 92.6200 1005 1812 1 chr4A.!!$F1 807
3 TraesCS4B01G294100 chr4A 5983783 5984398 615 True 695 695 87.4000 1 610 1 chr4A.!!$R1 609

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
261 272 0.108585 AAGCTCTCGTTGGAAGCCAA 59.891 50.0 0.0 0.0 41.69 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1679 1751 0.399454 AGATGCAGGCATAGGCGATT 59.601 50.0 6.76 0.0 42.47 3.34 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
123 127 3.703001 AACTACATCAGGTTGTGGGAG 57.297 47.619 0.10 0.00 35.61 4.30
133 137 6.381498 TCAGGTTGTGGGAGTATATTTGAA 57.619 37.500 0.00 0.00 0.00 2.69
151 162 2.116238 GAACTGGGATGCCTGGTACTA 58.884 52.381 14.59 0.00 0.00 1.82
261 272 0.108585 AAGCTCTCGTTGGAAGCCAA 59.891 50.000 0.00 0.00 41.69 4.52
272 283 1.755783 GAAGCCAAGGCCCCATCAG 60.756 63.158 7.62 0.00 43.17 2.90
362 373 5.064452 CACTGTAATCATCTTGTCAAGAGCC 59.936 44.000 19.64 5.51 41.61 4.70
373 384 0.608640 TCAAGAGCCGTTTCTCCCTC 59.391 55.000 0.00 0.00 33.66 4.30
374 385 0.737715 CAAGAGCCGTTTCTCCCTCG 60.738 60.000 0.00 0.00 33.66 4.63
376 387 0.898789 AGAGCCGTTTCTCCCTCGAA 60.899 55.000 0.00 0.00 33.66 3.71
377 388 0.175989 GAGCCGTTTCTCCCTCGAAT 59.824 55.000 0.00 0.00 0.00 3.34
378 389 1.407979 GAGCCGTTTCTCCCTCGAATA 59.592 52.381 0.00 0.00 0.00 1.75
379 390 1.136500 AGCCGTTTCTCCCTCGAATAC 59.864 52.381 0.00 0.00 0.00 1.89
466 477 3.631144 CATCAACGAACTGCATTTGTGT 58.369 40.909 0.00 0.00 34.89 3.72
486 509 8.837788 TTGTGTCAGGATATGATCATGTATTC 57.162 34.615 18.72 3.56 41.49 1.75
563 587 5.220912 GCTTCTGATACTAATGTTGCATGCA 60.221 40.000 18.46 18.46 0.00 3.96
654 691 9.939424 ATAGTTTACCAGAGTAATAGGAAGTCT 57.061 33.333 0.00 0.00 38.26 3.24
655 692 8.296211 AGTTTACCAGAGTAATAGGAAGTCTC 57.704 38.462 0.00 0.00 38.26 3.36
661 698 6.553100 CCAGAGTAATAGGAAGTCTCAAGGAT 59.447 42.308 0.00 0.00 0.00 3.24
662 699 7.432869 CAGAGTAATAGGAAGTCTCAAGGATG 58.567 42.308 0.00 0.00 0.00 3.51
677 714 9.167311 GTCTCAAGGATGTGTTAGAATATGTTT 57.833 33.333 0.00 0.00 0.00 2.83
684 721 9.341899 GGATGTGTTAGAATATGTTTGTGTTTC 57.658 33.333 0.00 0.00 0.00 2.78
698 735 7.476667 TGTTTGTGTTTCGATGAGTTTTATGT 58.523 30.769 0.00 0.00 0.00 2.29
704 741 7.321271 GTGTTTCGATGAGTTTTATGTTCTGTG 59.679 37.037 0.00 0.00 0.00 3.66
739 776 8.647256 AAGATTCCAAGAAGAGATTGAATGTT 57.353 30.769 0.00 0.00 0.00 2.71
794 831 2.165030 CCCTCCATCATCAAAAGTGTGC 59.835 50.000 0.00 0.00 0.00 4.57
797 834 4.421058 CTCCATCATCAAAAGTGTGCATG 58.579 43.478 0.00 0.00 0.00 4.06
862 899 4.262506 GCTACTCACCCTCACAGTAACTTT 60.263 45.833 0.00 0.00 0.00 2.66
871 908 4.999950 CCTCACAGTAACTTTGAAGCATCT 59.000 41.667 0.00 0.00 0.00 2.90
872 909 5.121454 CCTCACAGTAACTTTGAAGCATCTC 59.879 44.000 0.00 0.00 0.00 2.75
873 910 5.610398 TCACAGTAACTTTGAAGCATCTCA 58.390 37.500 0.00 0.00 0.00 3.27
899 936 0.185901 AGCTCCACAAAGCCCAAGAA 59.814 50.000 0.00 0.00 43.56 2.52
918 955 3.193479 AGAATACATGCTCGAGTGACACA 59.807 43.478 15.13 2.99 0.00 3.72
932 969 4.388485 AGTGACACACTGATTGCACATTA 58.612 39.130 8.59 0.00 43.63 1.90
950 987 5.074804 ACATTATATGTGCACATGAGCCAT 58.925 37.500 36.72 25.14 43.01 4.40
952 989 1.682740 TATGTGCACATGAGCCATGG 58.317 50.000 36.72 7.63 45.16 3.66
984 1028 3.128938 ACTGATCCTACGTACTGCAAGAC 59.871 47.826 0.00 0.00 37.43 3.01
985 1029 3.353557 TGATCCTACGTACTGCAAGACT 58.646 45.455 0.00 0.00 37.43 3.24
997 1045 5.073311 ACTGCAAGACTAGCGAATTCTAA 57.927 39.130 3.52 0.00 37.43 2.10
1007 1079 5.986135 ACTAGCGAATTCTAACCATGATCAC 59.014 40.000 0.00 0.00 0.00 3.06
1032 1104 1.472376 GGAGCCATCCTTTCTCTCGTG 60.472 57.143 0.00 0.00 42.94 4.35
1634 1706 4.181010 CAGGATCACCGGGCAGGG 62.181 72.222 6.32 0.00 46.96 4.45
1672 1744 2.753043 GCCTCGGTGGGTCGTAGA 60.753 66.667 0.00 0.00 36.00 2.59
1675 1747 1.077930 CTCGGTGGGTCGTAGAGGA 60.078 63.158 0.00 0.00 36.95 3.71
1676 1748 0.679002 CTCGGTGGGTCGTAGAGGAA 60.679 60.000 0.00 0.00 36.95 3.36
1679 1751 1.001181 CGGTGGGTCGTAGAGGAAAAA 59.999 52.381 0.00 0.00 36.95 1.94
1697 1773 1.242076 AAATCGCCTATGCCTGCATC 58.758 50.000 8.09 0.00 37.82 3.91
1703 1779 2.167281 CGCCTATGCCTGCATCTAGTAT 59.833 50.000 8.09 0.00 37.82 2.12
1704 1780 3.381590 CGCCTATGCCTGCATCTAGTATA 59.618 47.826 8.09 0.00 37.82 1.47
1705 1781 4.688021 GCCTATGCCTGCATCTAGTATAC 58.312 47.826 8.09 0.00 37.82 1.47
1720 1796 6.015918 TCTAGTATACTACTCGGCTACTCCT 58.984 44.000 8.59 0.00 40.14 3.69
1734 1810 6.774170 TCGGCTACTCCTTACATAATTACTCA 59.226 38.462 0.00 0.00 0.00 3.41
1835 1912 9.923143 TTATACATACTATCAAAAGGGATCGTG 57.077 33.333 0.00 0.00 0.00 4.35
1840 1917 1.153353 TCAAAAGGGATCGTGCGTTC 58.847 50.000 0.00 0.00 0.00 3.95
1841 1918 0.168128 CAAAAGGGATCGTGCGTTCC 59.832 55.000 11.92 11.92 34.21 3.62
1844 1921 0.953960 AAGGGATCGTGCGTTCCAAC 60.954 55.000 19.32 6.85 36.10 3.77
1845 1922 2.396157 GGGATCGTGCGTTCCAACC 61.396 63.158 19.32 3.33 36.10 3.77
1847 1924 1.735198 GATCGTGCGTTCCAACCGA 60.735 57.895 0.00 0.00 0.00 4.69
1851 1928 1.289109 CGTGCGTTCCAACCGAAGAT 61.289 55.000 0.00 0.00 0.00 2.40
1852 1929 0.872388 GTGCGTTCCAACCGAAGATT 59.128 50.000 0.00 0.00 0.00 2.40
1853 1930 1.265905 GTGCGTTCCAACCGAAGATTT 59.734 47.619 0.00 0.00 0.00 2.17
1854 1931 1.950909 TGCGTTCCAACCGAAGATTTT 59.049 42.857 0.00 0.00 0.00 1.82
1855 1932 2.359531 TGCGTTCCAACCGAAGATTTTT 59.640 40.909 0.00 0.00 0.00 1.94
1911 1990 5.535030 TGCTACATCACCGAGATACACTATT 59.465 40.000 0.00 0.00 34.43 1.73
1912 1991 6.713450 TGCTACATCACCGAGATACACTATTA 59.287 38.462 0.00 0.00 34.43 0.98
1913 1992 7.022384 GCTACATCACCGAGATACACTATTAC 58.978 42.308 0.00 0.00 34.43 1.89
1947 2030 8.855279 CGTGAAATAAACACTTTTTGAAACTCA 58.145 29.630 0.00 0.00 36.29 3.41
1955 2038 6.804677 ACACTTTTTGAAACTCATGCACATA 58.195 32.000 0.00 0.00 0.00 2.29
1970 2053 6.746822 TCATGCACATATTTGAAATCGTGAAC 59.253 34.615 18.87 7.42 0.00 3.18
2069 2152 9.886132 TGAAAATTTTATACTACTCCCTCTGTC 57.114 33.333 2.75 0.00 0.00 3.51
2070 2153 9.327628 GAAAATTTTATACTACTCCCTCTGTCC 57.672 37.037 2.75 0.00 0.00 4.02
2071 2154 6.651975 ATTTTATACTACTCCCTCTGTCCG 57.348 41.667 0.00 0.00 0.00 4.79
2072 2155 2.660670 ATACTACTCCCTCTGTCCGG 57.339 55.000 0.00 0.00 0.00 5.14
2073 2156 1.588239 TACTACTCCCTCTGTCCGGA 58.412 55.000 0.00 0.00 0.00 5.14
2074 2157 0.702902 ACTACTCCCTCTGTCCGGAA 59.297 55.000 5.23 0.00 0.00 4.30
2075 2158 1.288335 ACTACTCCCTCTGTCCGGAAT 59.712 52.381 5.23 0.00 0.00 3.01
2076 2159 2.292323 ACTACTCCCTCTGTCCGGAATT 60.292 50.000 5.23 0.00 0.00 2.17
2077 2160 2.544844 ACTCCCTCTGTCCGGAATTA 57.455 50.000 5.23 0.00 0.00 1.40
2078 2161 2.108970 ACTCCCTCTGTCCGGAATTAC 58.891 52.381 5.23 0.00 0.00 1.89
2079 2162 2.292323 ACTCCCTCTGTCCGGAATTACT 60.292 50.000 5.23 0.00 0.00 2.24
2080 2163 2.766828 CTCCCTCTGTCCGGAATTACTT 59.233 50.000 5.23 0.00 0.00 2.24
2081 2164 2.500098 TCCCTCTGTCCGGAATTACTTG 59.500 50.000 5.23 0.00 0.00 3.16
2082 2165 2.236395 CCCTCTGTCCGGAATTACTTGT 59.764 50.000 5.23 0.00 0.00 3.16
2083 2166 3.522553 CCTCTGTCCGGAATTACTTGTC 58.477 50.000 5.23 0.00 0.00 3.18
2084 2167 3.056107 CCTCTGTCCGGAATTACTTGTCA 60.056 47.826 5.23 0.00 0.00 3.58
2085 2168 4.383118 CCTCTGTCCGGAATTACTTGTCAT 60.383 45.833 5.23 0.00 0.00 3.06
2086 2169 4.755411 TCTGTCCGGAATTACTTGTCATC 58.245 43.478 5.23 0.00 0.00 2.92
2087 2170 4.221924 TCTGTCCGGAATTACTTGTCATCA 59.778 41.667 5.23 0.00 0.00 3.07
2088 2171 4.900684 TGTCCGGAATTACTTGTCATCAA 58.099 39.130 5.23 0.00 0.00 2.57
2089 2172 5.309638 TGTCCGGAATTACTTGTCATCAAA 58.690 37.500 5.23 0.00 32.87 2.69
2090 2173 5.765677 TGTCCGGAATTACTTGTCATCAAAA 59.234 36.000 5.23 0.00 32.87 2.44
2091 2174 6.432783 TGTCCGGAATTACTTGTCATCAAAAT 59.567 34.615 5.23 0.00 32.87 1.82
2092 2175 6.747280 GTCCGGAATTACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
2093 2176 6.035843 CCGGAATTACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
2094 2177 6.127758 CCGGAATTACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
2095 2178 7.416664 CCGGAATTACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
2096 2179 7.433131 CGGAATTACTTGTCATCAAAATGGATG 59.567 37.037 0.00 0.00 44.78 3.51
2097 2180 8.253113 GGAATTACTTGTCATCAAAATGGATGT 58.747 33.333 0.00 0.00 44.00 3.06
2101 2184 9.685276 TTACTTGTCATCAAAATGGATGTATCT 57.315 29.630 0.00 0.00 44.00 1.98
2103 2186 9.334947 ACTTGTCATCAAAATGGATGTATCTAG 57.665 33.333 0.00 0.00 44.00 2.43
2104 2187 9.551734 CTTGTCATCAAAATGGATGTATCTAGA 57.448 33.333 0.00 0.00 44.00 2.43
2105 2188 9.904198 TTGTCATCAAAATGGATGTATCTAGAA 57.096 29.630 0.00 0.00 44.00 2.10
2106 2189 9.330063 TGTCATCAAAATGGATGTATCTAGAAC 57.670 33.333 0.00 0.00 44.00 3.01
2107 2190 9.553064 GTCATCAAAATGGATGTATCTAGAACT 57.447 33.333 0.00 0.00 44.00 3.01
2151 2234 9.865321 ATTCATTTCAATGACAAGTATTTCTGG 57.135 29.630 1.52 0.00 44.54 3.86
2152 2235 8.634335 TCATTTCAATGACAAGTATTTCTGGA 57.366 30.769 0.00 0.00 40.32 3.86
2153 2236 8.514594 TCATTTCAATGACAAGTATTTCTGGAC 58.485 33.333 0.00 0.00 40.32 4.02
2154 2237 6.480524 TTCAATGACAAGTATTTCTGGACG 57.519 37.500 0.00 0.00 0.00 4.79
2155 2238 4.935205 TCAATGACAAGTATTTCTGGACGG 59.065 41.667 0.00 0.00 0.00 4.79
2156 2239 4.819105 ATGACAAGTATTTCTGGACGGA 57.181 40.909 0.00 0.00 0.00 4.69
2157 2240 4.188247 TGACAAGTATTTCTGGACGGAG 57.812 45.455 0.00 0.00 0.00 4.63
2158 2241 3.056107 TGACAAGTATTTCTGGACGGAGG 60.056 47.826 0.00 0.00 0.00 4.30
2159 2242 2.236395 ACAAGTATTTCTGGACGGAGGG 59.764 50.000 0.00 0.00 0.00 4.30
2160 2243 2.500098 CAAGTATTTCTGGACGGAGGGA 59.500 50.000 0.00 0.00 0.00 4.20
2161 2244 2.389715 AGTATTTCTGGACGGAGGGAG 58.610 52.381 0.00 0.00 0.00 4.30
2162 2245 2.108970 GTATTTCTGGACGGAGGGAGT 58.891 52.381 0.00 0.00 0.00 3.85
2163 2246 2.544844 ATTTCTGGACGGAGGGAGTA 57.455 50.000 0.00 0.00 0.00 2.59
2164 2247 2.544844 TTTCTGGACGGAGGGAGTAT 57.455 50.000 0.00 0.00 0.00 2.12
2165 2248 2.544844 TTCTGGACGGAGGGAGTATT 57.455 50.000 0.00 0.00 0.00 1.89
2166 2249 3.675348 TTCTGGACGGAGGGAGTATTA 57.325 47.619 0.00 0.00 0.00 0.98
2167 2250 3.225177 TCTGGACGGAGGGAGTATTAG 57.775 52.381 0.00 0.00 0.00 1.73
2168 2251 1.614413 CTGGACGGAGGGAGTATTAGC 59.386 57.143 0.00 0.00 0.00 3.09
2169 2252 1.063492 TGGACGGAGGGAGTATTAGCA 60.063 52.381 0.00 0.00 0.00 3.49
2170 2253 2.037144 GGACGGAGGGAGTATTAGCAA 58.963 52.381 0.00 0.00 0.00 3.91
2171 2254 2.433239 GGACGGAGGGAGTATTAGCAAA 59.567 50.000 0.00 0.00 0.00 3.68
2172 2255 3.455327 GACGGAGGGAGTATTAGCAAAC 58.545 50.000 0.00 0.00 0.00 2.93
2173 2256 2.835764 ACGGAGGGAGTATTAGCAAACA 59.164 45.455 0.00 0.00 0.00 2.83
2174 2257 3.454812 ACGGAGGGAGTATTAGCAAACAT 59.545 43.478 0.00 0.00 0.00 2.71
2175 2258 4.080526 ACGGAGGGAGTATTAGCAAACATT 60.081 41.667 0.00 0.00 0.00 2.71
2176 2259 4.881850 CGGAGGGAGTATTAGCAAACATTT 59.118 41.667 0.00 0.00 0.00 2.32
2177 2260 5.357032 CGGAGGGAGTATTAGCAAACATTTT 59.643 40.000 0.00 0.00 0.00 1.82
2178 2261 6.458342 CGGAGGGAGTATTAGCAAACATTTTC 60.458 42.308 0.00 0.00 0.00 2.29
2179 2262 6.603599 GGAGGGAGTATTAGCAAACATTTTCT 59.396 38.462 0.00 0.00 0.00 2.52
2180 2263 7.773690 GGAGGGAGTATTAGCAAACATTTTCTA 59.226 37.037 0.00 0.00 0.00 2.10
2181 2264 9.174166 GAGGGAGTATTAGCAAACATTTTCTAA 57.826 33.333 0.05 0.05 32.16 2.10
2182 2265 9.528489 AGGGAGTATTAGCAAACATTTTCTAAA 57.472 29.630 1.48 0.00 31.57 1.85
2183 2266 9.569167 GGGAGTATTAGCAAACATTTTCTAAAC 57.431 33.333 1.48 2.62 31.57 2.01
2201 2284 7.962934 TCTAAACAATTTTATTCAATCGGCG 57.037 32.000 0.00 0.00 0.00 6.46
2202 2285 7.753659 TCTAAACAATTTTATTCAATCGGCGA 58.246 30.769 13.87 13.87 0.00 5.54
2203 2286 6.869421 AAACAATTTTATTCAATCGGCGAG 57.131 33.333 17.22 2.16 0.00 5.03
2204 2287 5.560966 ACAATTTTATTCAATCGGCGAGT 57.439 34.783 17.22 10.73 0.00 4.18
2205 2288 6.671614 ACAATTTTATTCAATCGGCGAGTA 57.328 33.333 17.22 0.00 0.00 2.59
2206 2289 7.259290 ACAATTTTATTCAATCGGCGAGTAT 57.741 32.000 17.22 6.80 0.00 2.12
2207 2290 7.703328 ACAATTTTATTCAATCGGCGAGTATT 58.297 30.769 17.22 4.54 0.00 1.89
2208 2291 8.188139 ACAATTTTATTCAATCGGCGAGTATTT 58.812 29.630 17.22 0.88 0.00 1.40
2209 2292 9.658475 CAATTTTATTCAATCGGCGAGTATTTA 57.342 29.630 17.22 1.99 0.00 1.40
2213 2296 9.917129 TTTATTCAATCGGCGAGTATTTATAGA 57.083 29.630 17.22 1.00 0.00 1.98
2214 2297 9.917129 TTATTCAATCGGCGAGTATTTATAGAA 57.083 29.630 17.22 10.92 0.00 2.10
2216 2299 8.827177 TTCAATCGGCGAGTATTTATAGAATT 57.173 30.769 17.22 0.00 0.00 2.17
2217 2300 8.239681 TCAATCGGCGAGTATTTATAGAATTG 57.760 34.615 17.22 10.04 0.00 2.32
2218 2301 8.085909 TCAATCGGCGAGTATTTATAGAATTGA 58.914 33.333 17.22 12.28 0.00 2.57
2219 2302 7.813852 ATCGGCGAGTATTTATAGAATTGAC 57.186 36.000 17.22 0.00 0.00 3.18
2220 2303 5.854866 TCGGCGAGTATTTATAGAATTGACG 59.145 40.000 4.99 0.00 0.00 4.35
2221 2304 5.060569 CGGCGAGTATTTATAGAATTGACGG 59.939 44.000 0.00 0.00 0.00 4.79
2222 2305 6.154445 GGCGAGTATTTATAGAATTGACGGA 58.846 40.000 0.00 0.00 0.00 4.69
2223 2306 6.089150 GGCGAGTATTTATAGAATTGACGGAC 59.911 42.308 0.00 0.00 0.00 4.79
2224 2307 6.862090 GCGAGTATTTATAGAATTGACGGACT 59.138 38.462 0.00 0.00 0.00 3.85
2225 2308 7.381678 GCGAGTATTTATAGAATTGACGGACTT 59.618 37.037 0.00 0.00 0.00 3.01
2226 2309 9.245962 CGAGTATTTATAGAATTGACGGACTTT 57.754 33.333 0.00 0.00 0.00 2.66
2244 2327 2.535012 TTTTTGGAAATTGGCGGGAC 57.465 45.000 0.00 0.00 0.00 4.46
2245 2328 1.414158 TTTTGGAAATTGGCGGGACA 58.586 45.000 0.00 0.00 0.00 4.02
2246 2329 1.414158 TTTGGAAATTGGCGGGACAA 58.586 45.000 0.00 0.00 34.41 3.18
2247 2330 1.638529 TTGGAAATTGGCGGGACAAT 58.361 45.000 0.00 0.00 42.56 2.71
2372 2455 9.658799 TTTTTGAGTTAACAAACATTCCATGAA 57.341 25.926 8.61 0.00 39.08 2.57
2373 2456 9.829507 TTTTGAGTTAACAAACATTCCATGAAT 57.170 25.926 8.61 0.00 39.08 2.57
2403 2486 7.657023 AACTATTTAGTAAGTCCCGATCAGT 57.343 36.000 0.00 0.00 34.99 3.41
2404 2487 7.657023 ACTATTTAGTAAGTCCCGATCAGTT 57.343 36.000 0.00 0.00 34.13 3.16
2405 2488 8.075761 ACTATTTAGTAAGTCCCGATCAGTTT 57.924 34.615 0.00 0.00 34.13 2.66
2406 2489 8.537858 ACTATTTAGTAAGTCCCGATCAGTTTT 58.462 33.333 0.00 0.00 34.13 2.43
2407 2490 9.379791 CTATTTAGTAAGTCCCGATCAGTTTTT 57.620 33.333 0.00 0.00 0.00 1.94
2408 2491 7.429636 TTTAGTAAGTCCCGATCAGTTTTTG 57.570 36.000 0.00 0.00 0.00 2.44
2409 2492 5.223449 AGTAAGTCCCGATCAGTTTTTGA 57.777 39.130 0.00 0.00 40.85 2.69
2410 2493 5.617252 AGTAAGTCCCGATCAGTTTTTGAA 58.383 37.500 0.00 0.00 39.77 2.69
2411 2494 6.238648 AGTAAGTCCCGATCAGTTTTTGAAT 58.761 36.000 0.00 0.00 39.77 2.57
2412 2495 6.715264 AGTAAGTCCCGATCAGTTTTTGAATT 59.285 34.615 0.00 0.00 39.77 2.17
2413 2496 6.405278 AAGTCCCGATCAGTTTTTGAATTT 57.595 33.333 0.00 0.00 39.77 1.82
2414 2497 6.405278 AGTCCCGATCAGTTTTTGAATTTT 57.595 33.333 0.00 0.00 39.77 1.82
2415 2498 6.816136 AGTCCCGATCAGTTTTTGAATTTTT 58.184 32.000 0.00 0.00 39.77 1.94
2416 2499 7.947282 AGTCCCGATCAGTTTTTGAATTTTTA 58.053 30.769 0.00 0.00 39.77 1.52
2417 2500 8.082242 AGTCCCGATCAGTTTTTGAATTTTTAG 58.918 33.333 0.00 0.00 39.77 1.85
2418 2501 7.328493 GTCCCGATCAGTTTTTGAATTTTTAGG 59.672 37.037 0.00 0.00 39.77 2.69
2419 2502 7.231722 TCCCGATCAGTTTTTGAATTTTTAGGA 59.768 33.333 0.00 0.00 39.77 2.94
2420 2503 8.034804 CCCGATCAGTTTTTGAATTTTTAGGAT 58.965 33.333 0.00 0.00 39.77 3.24
2439 2522 9.504708 TTTAGGATATTTTTCCACTAACGAACA 57.495 29.630 0.00 0.00 38.32 3.18
2440 2523 9.675464 TTAGGATATTTTTCCACTAACGAACAT 57.325 29.630 0.00 0.00 38.32 2.71
2441 2524 8.575649 AGGATATTTTTCCACTAACGAACATT 57.424 30.769 0.00 0.00 38.32 2.71
2442 2525 9.020731 AGGATATTTTTCCACTAACGAACATTT 57.979 29.630 0.00 0.00 38.32 2.32
2443 2526 9.634163 GGATATTTTTCCACTAACGAACATTTT 57.366 29.630 0.00 0.00 35.72 1.82
2467 2550 9.840427 TTTTTGAATTGGCGAAATTTTGTTTAA 57.160 22.222 7.27 1.44 38.64 1.52
2471 2554 9.657121 TGAATTGGCGAAATTTTGTTTAATTTC 57.343 25.926 7.27 10.33 44.95 2.17
2545 2628 5.782893 TTTTTGATTTCCCGAACATCTGT 57.217 34.783 0.00 0.00 0.00 3.41
2546 2629 5.371115 TTTTGATTTCCCGAACATCTGTC 57.629 39.130 0.00 0.00 0.00 3.51
2547 2630 3.981071 TGATTTCCCGAACATCTGTCT 57.019 42.857 0.00 0.00 0.00 3.41
2548 2631 4.286297 TGATTTCCCGAACATCTGTCTT 57.714 40.909 0.00 0.00 0.00 3.01
2549 2632 5.414789 TGATTTCCCGAACATCTGTCTTA 57.585 39.130 0.00 0.00 0.00 2.10
2550 2633 5.989477 TGATTTCCCGAACATCTGTCTTAT 58.011 37.500 0.00 0.00 0.00 1.73
2551 2634 7.119709 TGATTTCCCGAACATCTGTCTTATA 57.880 36.000 0.00 0.00 0.00 0.98
2552 2635 7.561251 TGATTTCCCGAACATCTGTCTTATAA 58.439 34.615 0.00 0.00 0.00 0.98
2553 2636 8.044309 TGATTTCCCGAACATCTGTCTTATAAA 58.956 33.333 0.00 0.00 0.00 1.40
2554 2637 8.801882 ATTTCCCGAACATCTGTCTTATAAAA 57.198 30.769 0.00 0.00 0.00 1.52
2555 2638 8.801882 TTTCCCGAACATCTGTCTTATAAAAT 57.198 30.769 0.00 0.00 0.00 1.82
2556 2639 8.801882 TTCCCGAACATCTGTCTTATAAAATT 57.198 30.769 0.00 0.00 0.00 1.82
2557 2640 8.433421 TCCCGAACATCTGTCTTATAAAATTC 57.567 34.615 0.00 0.00 0.00 2.17
2558 2641 8.044309 TCCCGAACATCTGTCTTATAAAATTCA 58.956 33.333 0.00 0.00 0.00 2.57
2559 2642 8.673711 CCCGAACATCTGTCTTATAAAATTCAA 58.326 33.333 0.00 0.00 0.00 2.69
2600 2683 8.973835 TTCTTTTACAAAATCACGAACACTTT 57.026 26.923 0.00 0.00 0.00 2.66
2601 2684 8.973835 TCTTTTACAAAATCACGAACACTTTT 57.026 26.923 0.00 0.00 0.00 2.27
2607 2690 8.782533 ACAAAATCACGAACACTTTTAGAATC 57.217 30.769 0.00 0.00 0.00 2.52
2608 2691 7.860872 ACAAAATCACGAACACTTTTAGAATCC 59.139 33.333 0.00 0.00 0.00 3.01
2609 2692 7.504924 AAATCACGAACACTTTTAGAATCCA 57.495 32.000 0.00 0.00 0.00 3.41
2610 2693 5.917541 TCACGAACACTTTTAGAATCCAC 57.082 39.130 0.00 0.00 0.00 4.02
2611 2694 5.361427 TCACGAACACTTTTAGAATCCACA 58.639 37.500 0.00 0.00 0.00 4.17
2612 2695 5.818336 TCACGAACACTTTTAGAATCCACAA 59.182 36.000 0.00 0.00 0.00 3.33
2613 2696 6.316640 TCACGAACACTTTTAGAATCCACAAA 59.683 34.615 0.00 0.00 0.00 2.83
2614 2697 6.413818 CACGAACACTTTTAGAATCCACAAAC 59.586 38.462 0.00 0.00 0.00 2.93
2615 2698 6.094325 ACGAACACTTTTAGAATCCACAAACA 59.906 34.615 0.00 0.00 0.00 2.83
2616 2699 7.138736 CGAACACTTTTAGAATCCACAAACAT 58.861 34.615 0.00 0.00 0.00 2.71
2617 2700 7.647715 CGAACACTTTTAGAATCCACAAACATT 59.352 33.333 0.00 0.00 0.00 2.71
2618 2701 9.313118 GAACACTTTTAGAATCCACAAACATTT 57.687 29.630 0.00 0.00 0.00 2.32
2619 2702 9.665719 AACACTTTTAGAATCCACAAACATTTT 57.334 25.926 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 127 4.520492 CCAGGCATCCCAGTTCAAATATAC 59.480 45.833 0.00 0.00 0.00 1.47
133 137 2.496679 ATAGTACCAGGCATCCCAGT 57.503 50.000 0.00 0.00 0.00 4.00
151 162 3.149196 AGTCGCTGGAACATGTGAAAAT 58.851 40.909 0.00 0.00 38.20 1.82
362 373 2.953466 TGGTATTCGAGGGAGAAACG 57.047 50.000 0.00 0.00 33.43 3.60
373 384 4.688879 TGTTACAACAGCTCTTGGTATTCG 59.311 41.667 6.67 0.00 34.30 3.34
374 385 5.928153 GTGTTACAACAGCTCTTGGTATTC 58.072 41.667 6.67 0.00 40.05 1.75
439 450 3.745332 TGCAGTTCGTTGATGCATAAG 57.255 42.857 0.00 0.00 44.56 1.73
486 509 6.688637 TCCATCTTAAGCTTCATTCACATG 57.311 37.500 0.00 0.00 0.00 3.21
588 625 4.815308 TGGCATGGCATTGTAATAATTTGC 59.185 37.500 19.43 0.00 0.00 3.68
635 672 5.659079 CCTTGAGACTTCCTATTACTCTGGT 59.341 44.000 0.00 0.00 0.00 4.00
654 691 8.729756 CACAAACATATTCTAACACATCCTTGA 58.270 33.333 0.00 0.00 0.00 3.02
655 692 8.514594 ACACAAACATATTCTAACACATCCTTG 58.485 33.333 0.00 0.00 0.00 3.61
661 698 8.144155 TCGAAACACAAACATATTCTAACACA 57.856 30.769 0.00 0.00 0.00 3.72
662 699 9.051027 CATCGAAACACAAACATATTCTAACAC 57.949 33.333 0.00 0.00 0.00 3.32
677 714 7.011950 ACAGAACATAAAACTCATCGAAACACA 59.988 33.333 0.00 0.00 0.00 3.72
684 721 4.695455 ACCCACAGAACATAAAACTCATCG 59.305 41.667 0.00 0.00 0.00 3.84
695 732 5.930837 TCTTTTTGAAACCCACAGAACAT 57.069 34.783 0.00 0.00 0.00 2.71
698 735 5.423610 TGGAATCTTTTTGAAACCCACAGAA 59.576 36.000 0.00 0.00 0.00 3.02
704 741 6.816136 TCTTCTTGGAATCTTTTTGAAACCC 58.184 36.000 0.00 0.00 0.00 4.11
794 831 2.995283 TGCCTTGGAGAATGAGACATG 58.005 47.619 0.00 0.00 0.00 3.21
797 834 2.363683 CCTTGCCTTGGAGAATGAGAC 58.636 52.381 0.00 0.00 0.00 3.36
862 899 1.746171 GCTGGCAGATGAGATGCTTCA 60.746 52.381 20.86 0.00 43.35 3.02
871 908 0.401356 TTTGTGGAGCTGGCAGATGA 59.599 50.000 20.86 0.00 0.00 2.92
872 909 0.809385 CTTTGTGGAGCTGGCAGATG 59.191 55.000 20.86 0.00 0.00 2.90
873 910 0.964358 GCTTTGTGGAGCTGGCAGAT 60.964 55.000 20.86 13.42 39.57 2.90
899 936 2.493675 AGTGTGTCACTCGAGCATGTAT 59.506 45.455 13.61 0.00 41.21 2.29
932 969 2.235891 CCATGGCTCATGTGCACATAT 58.764 47.619 30.92 17.99 39.94 1.78
950 987 0.179702 GGATCAGTGATCAGCAGCCA 59.820 55.000 29.56 0.00 40.50 4.75
952 989 2.753296 GTAGGATCAGTGATCAGCAGC 58.247 52.381 29.56 14.92 40.50 5.25
984 1028 5.406780 GGTGATCATGGTTAGAATTCGCTAG 59.593 44.000 0.00 0.00 0.00 3.42
985 1029 5.297547 GGTGATCATGGTTAGAATTCGCTA 58.702 41.667 0.00 0.00 0.00 4.26
997 1045 1.524002 CTCCAGCGGTGATCATGGT 59.476 57.895 17.83 5.10 34.32 3.55
1007 1079 1.821332 GAAAGGATGGCTCCAGCGG 60.821 63.158 0.00 0.00 44.79 5.52
1032 1104 4.202202 ACGGTGGAGAAGAAGATGATCATC 60.202 45.833 25.42 25.42 38.09 2.92
1121 1193 1.597027 AGGCCGTTGAAGTGGAACG 60.597 57.895 0.00 0.00 45.86 3.95
1122 1194 1.949257 CAGGCCGTTGAAGTGGAAC 59.051 57.895 0.00 0.00 0.00 3.62
1123 1195 1.896660 GCAGGCCGTTGAAGTGGAA 60.897 57.895 0.00 0.00 0.00 3.53
1634 1706 1.372087 CCTTTGGATCCTCTGCACGC 61.372 60.000 14.23 0.00 0.00 5.34
1676 1748 1.473258 TGCAGGCATAGGCGATTTTT 58.527 45.000 0.00 0.00 42.47 1.94
1679 1751 0.399454 AGATGCAGGCATAGGCGATT 59.601 50.000 6.76 0.00 42.47 3.34
1703 1779 4.760530 TGTAAGGAGTAGCCGAGTAGTA 57.239 45.455 0.00 0.00 43.43 1.82
1704 1780 3.641434 TGTAAGGAGTAGCCGAGTAGT 57.359 47.619 0.00 0.00 43.43 2.73
1705 1781 6.821031 ATTATGTAAGGAGTAGCCGAGTAG 57.179 41.667 0.00 0.00 43.43 2.57
1720 1796 8.192110 TGTCGTAGCACATGAGTAATTATGTAA 58.808 33.333 0.00 0.00 35.86 2.41
1734 1810 0.818296 GGACTCCTGTCGTAGCACAT 59.182 55.000 0.00 0.00 43.79 3.21
1821 1898 1.153353 GAACGCACGATCCCTTTTGA 58.847 50.000 0.00 0.00 0.00 2.69
1830 1907 1.289109 CTTCGGTTGGAACGCACGAT 61.289 55.000 0.00 0.00 33.26 3.73
1831 1908 1.952133 CTTCGGTTGGAACGCACGA 60.952 57.895 0.00 0.00 0.00 4.35
1835 1912 2.699251 AAAATCTTCGGTTGGAACGC 57.301 45.000 0.00 0.00 0.00 4.84
1854 1931 8.966868 GGTCATAACCTTGGAGAATATGAAAAA 58.033 33.333 0.00 0.00 42.80 1.94
1855 1932 8.112822 TGGTCATAACCTTGGAGAATATGAAAA 58.887 33.333 0.00 0.00 46.60 2.29
1856 1933 7.556275 GTGGTCATAACCTTGGAGAATATGAAA 59.444 37.037 0.00 0.00 46.60 2.69
1857 1934 7.054124 GTGGTCATAACCTTGGAGAATATGAA 58.946 38.462 0.00 0.00 46.60 2.57
1859 1936 6.356556 TGTGGTCATAACCTTGGAGAATATG 58.643 40.000 0.00 0.00 46.60 1.78
1860 1937 6.575244 TGTGGTCATAACCTTGGAGAATAT 57.425 37.500 0.00 0.00 46.60 1.28
1861 1938 6.575244 ATGTGGTCATAACCTTGGAGAATA 57.425 37.500 0.00 0.00 46.60 1.75
1862 1939 4.927267 TGTGGTCATAACCTTGGAGAAT 57.073 40.909 0.00 0.00 46.60 2.40
1863 1940 4.927267 ATGTGGTCATAACCTTGGAGAA 57.073 40.909 0.00 0.00 46.60 2.87
1864 1941 4.927267 AATGTGGTCATAACCTTGGAGA 57.073 40.909 0.00 0.00 46.60 3.71
1865 1942 5.713025 CAAAATGTGGTCATAACCTTGGAG 58.287 41.667 0.00 0.00 46.60 3.86
1866 1943 4.021544 GCAAAATGTGGTCATAACCTTGGA 60.022 41.667 0.00 0.00 46.60 3.53
1867 1944 4.021192 AGCAAAATGTGGTCATAACCTTGG 60.021 41.667 0.00 0.00 46.60 3.61
1868 1945 5.138125 AGCAAAATGTGGTCATAACCTTG 57.862 39.130 0.00 0.00 46.60 3.61
1869 1946 5.772672 TGTAGCAAAATGTGGTCATAACCTT 59.227 36.000 0.00 0.00 46.60 3.50
1870 1947 5.321102 TGTAGCAAAATGTGGTCATAACCT 58.679 37.500 0.00 0.00 46.60 3.50
1874 1953 5.356751 GGTGATGTAGCAAAATGTGGTCATA 59.643 40.000 0.00 0.00 39.22 2.15
1891 1970 6.771267 TGAGTAATAGTGTATCTCGGTGATGT 59.229 38.462 2.94 0.00 36.65 3.06
1912 1991 9.581099 AAAAGTGTTTATTTCACGAAATTGAGT 57.419 25.926 10.11 0.00 40.99 3.41
1929 2009 5.931146 TGTGCATGAGTTTCAAAAAGTGTTT 59.069 32.000 0.00 0.00 0.00 2.83
1931 2011 5.070770 TGTGCATGAGTTTCAAAAAGTGT 57.929 34.783 0.00 0.00 0.00 3.55
1932 2012 7.878477 ATATGTGCATGAGTTTCAAAAAGTG 57.122 32.000 0.00 0.00 0.00 3.16
1934 2014 8.980610 TCAAATATGTGCATGAGTTTCAAAAAG 58.019 29.630 0.00 0.00 0.00 2.27
1935 2015 8.883954 TCAAATATGTGCATGAGTTTCAAAAA 57.116 26.923 0.00 0.00 0.00 1.94
1936 2016 8.883954 TTCAAATATGTGCATGAGTTTCAAAA 57.116 26.923 0.00 0.00 0.00 2.44
1940 2023 7.485913 ACGATTTCAAATATGTGCATGAGTTTC 59.514 33.333 0.00 0.00 0.00 2.78
1942 2025 6.748658 CACGATTTCAAATATGTGCATGAGTT 59.251 34.615 0.00 0.00 0.00 3.01
1947 2030 6.619744 TGTTCACGATTTCAAATATGTGCAT 58.380 32.000 9.23 0.00 0.00 3.96
1984 2067 9.376075 TGCTTGAAAATTTGTAAAAGTGATCAA 57.624 25.926 0.00 0.00 0.00 2.57
2047 2130 6.041751 CCGGACAGAGGGAGTAGTATAAAATT 59.958 42.308 0.00 0.00 0.00 1.82
2059 2142 2.389715 AGTAATTCCGGACAGAGGGAG 58.610 52.381 1.83 0.00 33.01 4.30
2060 2143 2.500098 CAAGTAATTCCGGACAGAGGGA 59.500 50.000 1.83 0.00 0.00 4.20
2061 2144 2.236395 ACAAGTAATTCCGGACAGAGGG 59.764 50.000 1.83 0.00 0.00 4.30
2062 2145 3.056107 TGACAAGTAATTCCGGACAGAGG 60.056 47.826 1.83 0.00 0.00 3.69
2063 2146 4.188247 TGACAAGTAATTCCGGACAGAG 57.812 45.455 1.83 0.00 0.00 3.35
2064 2147 4.221924 TGATGACAAGTAATTCCGGACAGA 59.778 41.667 1.83 0.00 0.00 3.41
2065 2148 4.503910 TGATGACAAGTAATTCCGGACAG 58.496 43.478 1.83 0.00 0.00 3.51
2066 2149 4.545208 TGATGACAAGTAATTCCGGACA 57.455 40.909 1.83 0.00 0.00 4.02
2067 2150 5.873179 TTTGATGACAAGTAATTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
2068 2151 6.127758 CCATTTTGATGACAAGTAATTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
2069 2152 6.035843 CCATTTTGATGACAAGTAATTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
2070 2153 6.851609 TCCATTTTGATGACAAGTAATTCCG 58.148 36.000 0.00 0.00 37.32 4.30
2071 2154 8.253113 ACATCCATTTTGATGACAAGTAATTCC 58.747 33.333 7.93 0.00 43.94 3.01
2075 2158 9.685276 AGATACATCCATTTTGATGACAAGTAA 57.315 29.630 7.93 0.00 43.94 2.24
2077 2160 9.334947 CTAGATACATCCATTTTGATGACAAGT 57.665 33.333 7.93 0.00 43.94 3.16
2078 2161 9.551734 TCTAGATACATCCATTTTGATGACAAG 57.448 33.333 7.93 0.00 43.94 3.16
2079 2162 9.904198 TTCTAGATACATCCATTTTGATGACAA 57.096 29.630 7.93 0.00 43.94 3.18
2080 2163 9.330063 GTTCTAGATACATCCATTTTGATGACA 57.670 33.333 7.93 0.00 43.94 3.58
2081 2164 9.553064 AGTTCTAGATACATCCATTTTGATGAC 57.447 33.333 7.93 0.44 43.94 3.06
2125 2208 9.865321 CCAGAAATACTTGTCATTGAAATGAAT 57.135 29.630 7.29 0.00 46.13 2.57
2126 2209 9.076781 TCCAGAAATACTTGTCATTGAAATGAA 57.923 29.630 7.29 0.00 46.13 2.57
2127 2210 8.514594 GTCCAGAAATACTTGTCATTGAAATGA 58.485 33.333 1.55 1.55 42.78 2.57
2128 2211 7.482743 CGTCCAGAAATACTTGTCATTGAAATG 59.517 37.037 0.00 0.00 37.75 2.32
2129 2212 7.362056 CCGTCCAGAAATACTTGTCATTGAAAT 60.362 37.037 0.00 0.00 0.00 2.17
2130 2213 6.072728 CCGTCCAGAAATACTTGTCATTGAAA 60.073 38.462 0.00 0.00 0.00 2.69
2131 2214 5.411361 CCGTCCAGAAATACTTGTCATTGAA 59.589 40.000 0.00 0.00 0.00 2.69
2132 2215 4.935205 CCGTCCAGAAATACTTGTCATTGA 59.065 41.667 0.00 0.00 0.00 2.57
2133 2216 4.935205 TCCGTCCAGAAATACTTGTCATTG 59.065 41.667 0.00 0.00 0.00 2.82
2134 2217 5.160607 TCCGTCCAGAAATACTTGTCATT 57.839 39.130 0.00 0.00 0.00 2.57
2135 2218 4.383118 CCTCCGTCCAGAAATACTTGTCAT 60.383 45.833 0.00 0.00 0.00 3.06
2136 2219 3.056107 CCTCCGTCCAGAAATACTTGTCA 60.056 47.826 0.00 0.00 0.00 3.58
2137 2220 3.522553 CCTCCGTCCAGAAATACTTGTC 58.477 50.000 0.00 0.00 0.00 3.18
2138 2221 2.236395 CCCTCCGTCCAGAAATACTTGT 59.764 50.000 0.00 0.00 0.00 3.16
2139 2222 2.500098 TCCCTCCGTCCAGAAATACTTG 59.500 50.000 0.00 0.00 0.00 3.16
2140 2223 2.766828 CTCCCTCCGTCCAGAAATACTT 59.233 50.000 0.00 0.00 0.00 2.24
2141 2224 2.292323 ACTCCCTCCGTCCAGAAATACT 60.292 50.000 0.00 0.00 0.00 2.12
2142 2225 2.108970 ACTCCCTCCGTCCAGAAATAC 58.891 52.381 0.00 0.00 0.00 1.89
2143 2226 2.544844 ACTCCCTCCGTCCAGAAATA 57.455 50.000 0.00 0.00 0.00 1.40
2144 2227 2.544844 TACTCCCTCCGTCCAGAAAT 57.455 50.000 0.00 0.00 0.00 2.17
2145 2228 2.544844 ATACTCCCTCCGTCCAGAAA 57.455 50.000 0.00 0.00 0.00 2.52
2146 2229 2.544844 AATACTCCCTCCGTCCAGAA 57.455 50.000 0.00 0.00 0.00 3.02
2147 2230 2.752154 GCTAATACTCCCTCCGTCCAGA 60.752 54.545 0.00 0.00 0.00 3.86
2148 2231 1.614413 GCTAATACTCCCTCCGTCCAG 59.386 57.143 0.00 0.00 0.00 3.86
2149 2232 1.063492 TGCTAATACTCCCTCCGTCCA 60.063 52.381 0.00 0.00 0.00 4.02
2150 2233 1.700955 TGCTAATACTCCCTCCGTCC 58.299 55.000 0.00 0.00 0.00 4.79
2151 2234 3.118884 TGTTTGCTAATACTCCCTCCGTC 60.119 47.826 0.00 0.00 0.00 4.79
2152 2235 2.835764 TGTTTGCTAATACTCCCTCCGT 59.164 45.455 0.00 0.00 0.00 4.69
2153 2236 3.536956 TGTTTGCTAATACTCCCTCCG 57.463 47.619 0.00 0.00 0.00 4.63
2154 2237 6.603599 AGAAAATGTTTGCTAATACTCCCTCC 59.396 38.462 0.00 0.00 0.00 4.30
2155 2238 7.631717 AGAAAATGTTTGCTAATACTCCCTC 57.368 36.000 0.00 0.00 0.00 4.30
2156 2239 9.528489 TTTAGAAAATGTTTGCTAATACTCCCT 57.472 29.630 6.74 0.00 37.94 4.20
2157 2240 9.569167 GTTTAGAAAATGTTTGCTAATACTCCC 57.431 33.333 6.74 0.00 37.94 4.30
2175 2258 8.855279 CGCCGATTGAATAAAATTGTTTAGAAA 58.145 29.630 0.00 0.00 32.76 2.52
2176 2259 8.237949 TCGCCGATTGAATAAAATTGTTTAGAA 58.762 29.630 0.00 0.00 32.76 2.10
2177 2260 7.753659 TCGCCGATTGAATAAAATTGTTTAGA 58.246 30.769 0.00 0.00 32.76 2.10
2178 2261 7.696453 ACTCGCCGATTGAATAAAATTGTTTAG 59.304 33.333 0.00 0.00 32.76 1.85
2179 2262 7.531716 ACTCGCCGATTGAATAAAATTGTTTA 58.468 30.769 0.00 0.00 33.76 2.01
2180 2263 6.386654 ACTCGCCGATTGAATAAAATTGTTT 58.613 32.000 0.00 0.00 0.00 2.83
2181 2264 5.949735 ACTCGCCGATTGAATAAAATTGTT 58.050 33.333 0.00 0.00 0.00 2.83
2182 2265 5.560966 ACTCGCCGATTGAATAAAATTGT 57.439 34.783 0.00 0.00 0.00 2.71
2183 2266 8.560576 AAATACTCGCCGATTGAATAAAATTG 57.439 30.769 0.00 0.00 0.00 2.32
2187 2270 9.917129 TCTATAAATACTCGCCGATTGAATAAA 57.083 29.630 0.00 0.00 0.00 1.40
2188 2271 9.917129 TTCTATAAATACTCGCCGATTGAATAA 57.083 29.630 0.00 0.00 0.00 1.40
2190 2273 9.436957 AATTCTATAAATACTCGCCGATTGAAT 57.563 29.630 0.00 0.00 0.00 2.57
2191 2274 8.708742 CAATTCTATAAATACTCGCCGATTGAA 58.291 33.333 0.00 0.00 0.00 2.69
2192 2275 8.085909 TCAATTCTATAAATACTCGCCGATTGA 58.914 33.333 0.00 0.00 0.00 2.57
2193 2276 8.162880 GTCAATTCTATAAATACTCGCCGATTG 58.837 37.037 0.00 0.00 0.00 2.67
2194 2277 7.061905 CGTCAATTCTATAAATACTCGCCGATT 59.938 37.037 0.00 0.00 0.00 3.34
2195 2278 6.527023 CGTCAATTCTATAAATACTCGCCGAT 59.473 38.462 0.00 0.00 0.00 4.18
2196 2279 5.854866 CGTCAATTCTATAAATACTCGCCGA 59.145 40.000 0.00 0.00 0.00 5.54
2197 2280 5.060569 CCGTCAATTCTATAAATACTCGCCG 59.939 44.000 0.00 0.00 0.00 6.46
2198 2281 6.089150 GTCCGTCAATTCTATAAATACTCGCC 59.911 42.308 0.00 0.00 0.00 5.54
2199 2282 6.862090 AGTCCGTCAATTCTATAAATACTCGC 59.138 38.462 0.00 0.00 0.00 5.03
2200 2283 8.798748 AAGTCCGTCAATTCTATAAATACTCG 57.201 34.615 0.00 0.00 0.00 4.18
2225 2308 1.762957 TGTCCCGCCAATTTCCAAAAA 59.237 42.857 0.00 0.00 0.00 1.94
2226 2309 1.414158 TGTCCCGCCAATTTCCAAAA 58.586 45.000 0.00 0.00 0.00 2.44
2227 2310 1.414158 TTGTCCCGCCAATTTCCAAA 58.586 45.000 0.00 0.00 0.00 3.28
2228 2311 1.638529 ATTGTCCCGCCAATTTCCAA 58.361 45.000 0.00 0.00 31.01 3.53
2229 2312 1.638529 AATTGTCCCGCCAATTTCCA 58.361 45.000 0.00 0.00 41.11 3.53
2230 2313 2.760634 AAATTGTCCCGCCAATTTCC 57.239 45.000 10.85 0.00 46.73 3.13
2346 2429 9.658799 TTCATGGAATGTTTGTTAACTCAAAAA 57.341 25.926 7.22 0.00 46.80 1.94
2347 2430 9.829507 ATTCATGGAATGTTTGTTAACTCAAAA 57.170 25.926 7.22 0.00 46.80 2.44
2348 2431 9.258826 CATTCATGGAATGTTTGTTAACTCAAA 57.741 29.630 7.22 0.00 46.80 2.69
2349 2432 8.637099 TCATTCATGGAATGTTTGTTAACTCAA 58.363 29.630 16.10 0.00 46.48 3.02
2350 2433 8.175925 TCATTCATGGAATGTTTGTTAACTCA 57.824 30.769 16.10 4.40 46.48 3.41
2351 2434 9.643693 ATTCATTCATGGAATGTTTGTTAACTC 57.356 29.630 16.10 0.00 46.48 3.01
2377 2460 9.193806 ACTGATCGGGACTTACTAAATAGTTTA 57.806 33.333 6.47 0.00 37.73 2.01
2378 2461 8.075761 ACTGATCGGGACTTACTAAATAGTTT 57.924 34.615 6.47 0.00 37.73 2.66
2379 2462 7.657023 ACTGATCGGGACTTACTAAATAGTT 57.343 36.000 6.47 0.00 37.73 2.24
2380 2463 7.657023 AACTGATCGGGACTTACTAAATAGT 57.343 36.000 6.47 0.00 40.24 2.12
2381 2464 8.943909 AAAACTGATCGGGACTTACTAAATAG 57.056 34.615 6.47 0.00 0.00 1.73
2382 2465 9.158233 CAAAAACTGATCGGGACTTACTAAATA 57.842 33.333 6.47 0.00 0.00 1.40
2383 2466 7.881232 TCAAAAACTGATCGGGACTTACTAAAT 59.119 33.333 6.47 0.00 0.00 1.40
2384 2467 7.218614 TCAAAAACTGATCGGGACTTACTAAA 58.781 34.615 6.47 0.00 0.00 1.85
2385 2468 6.761312 TCAAAAACTGATCGGGACTTACTAA 58.239 36.000 6.47 0.00 0.00 2.24
2386 2469 6.349243 TCAAAAACTGATCGGGACTTACTA 57.651 37.500 6.47 0.00 0.00 1.82
2387 2470 5.223449 TCAAAAACTGATCGGGACTTACT 57.777 39.130 6.47 0.00 0.00 2.24
2388 2471 5.934935 TTCAAAAACTGATCGGGACTTAC 57.065 39.130 6.47 0.00 32.78 2.34
2389 2472 7.519032 AAATTCAAAAACTGATCGGGACTTA 57.481 32.000 6.47 0.00 32.78 2.24
2390 2473 6.405278 AAATTCAAAAACTGATCGGGACTT 57.595 33.333 6.47 0.00 32.78 3.01
2391 2474 6.405278 AAAATTCAAAAACTGATCGGGACT 57.595 33.333 6.47 0.00 32.78 3.85
2392 2475 7.328493 CCTAAAAATTCAAAAACTGATCGGGAC 59.672 37.037 6.47 0.00 32.78 4.46
2393 2476 7.231722 TCCTAAAAATTCAAAAACTGATCGGGA 59.768 33.333 6.47 0.00 32.78 5.14
2394 2477 7.375053 TCCTAAAAATTCAAAAACTGATCGGG 58.625 34.615 6.47 0.00 32.78 5.14
2395 2478 8.986477 ATCCTAAAAATTCAAAAACTGATCGG 57.014 30.769 0.00 0.00 32.78 4.18
2413 2496 9.504708 TGTTCGTTAGTGGAAAAATATCCTAAA 57.495 29.630 0.00 0.00 40.35 1.85
2414 2497 9.675464 ATGTTCGTTAGTGGAAAAATATCCTAA 57.325 29.630 0.00 0.00 40.35 2.69
2415 2498 9.675464 AATGTTCGTTAGTGGAAAAATATCCTA 57.325 29.630 0.00 0.00 40.35 2.94
2416 2499 8.575649 AATGTTCGTTAGTGGAAAAATATCCT 57.424 30.769 0.00 0.00 40.35 3.24
2417 2500 9.634163 AAAATGTTCGTTAGTGGAAAAATATCC 57.366 29.630 0.00 0.00 40.10 2.59
2441 2524 9.840427 TTAAACAAAATTTCGCCAATTCAAAAA 57.160 22.222 0.00 0.00 33.60 1.94
2445 2528 9.657121 GAAATTAAACAAAATTTCGCCAATTCA 57.343 25.926 6.36 0.00 42.68 2.57
2523 2606 5.534654 AGACAGATGTTCGGGAAATCAAAAA 59.465 36.000 0.00 0.00 0.00 1.94
2524 2607 5.070001 AGACAGATGTTCGGGAAATCAAAA 58.930 37.500 0.00 0.00 0.00 2.44
2525 2608 4.651778 AGACAGATGTTCGGGAAATCAAA 58.348 39.130 0.00 0.00 0.00 2.69
2526 2609 4.286297 AGACAGATGTTCGGGAAATCAA 57.714 40.909 0.00 0.00 0.00 2.57
2527 2610 3.981071 AGACAGATGTTCGGGAAATCA 57.019 42.857 0.00 0.00 0.00 2.57
2528 2611 8.433421 TTTATAAGACAGATGTTCGGGAAATC 57.567 34.615 0.00 0.00 0.00 2.17
2529 2612 8.801882 TTTTATAAGACAGATGTTCGGGAAAT 57.198 30.769 0.00 0.00 0.00 2.17
2530 2613 8.801882 ATTTTATAAGACAGATGTTCGGGAAA 57.198 30.769 0.00 0.00 0.00 3.13
2531 2614 8.801882 AATTTTATAAGACAGATGTTCGGGAA 57.198 30.769 0.00 0.00 0.00 3.97
2532 2615 8.044309 TGAATTTTATAAGACAGATGTTCGGGA 58.956 33.333 0.00 0.00 0.00 5.14
2533 2616 8.208718 TGAATTTTATAAGACAGATGTTCGGG 57.791 34.615 0.00 0.00 0.00 5.14
2574 2657 9.581099 AAAGTGTTCGTGATTTTGTAAAAGAAT 57.419 25.926 0.00 0.00 0.00 2.40
2575 2658 8.973835 AAAGTGTTCGTGATTTTGTAAAAGAA 57.026 26.923 0.00 0.00 0.00 2.52
2576 2659 8.973835 AAAAGTGTTCGTGATTTTGTAAAAGA 57.026 26.923 0.00 0.00 0.00 2.52
2581 2664 9.872757 GATTCTAAAAGTGTTCGTGATTTTGTA 57.127 29.630 0.00 0.00 0.00 2.41
2582 2665 7.860872 GGATTCTAAAAGTGTTCGTGATTTTGT 59.139 33.333 0.00 0.00 0.00 2.83
2583 2666 7.860373 TGGATTCTAAAAGTGTTCGTGATTTTG 59.140 33.333 0.00 0.00 0.00 2.44
2584 2667 7.860872 GTGGATTCTAAAAGTGTTCGTGATTTT 59.139 33.333 0.00 0.00 0.00 1.82
2585 2668 7.012894 TGTGGATTCTAAAAGTGTTCGTGATTT 59.987 33.333 0.00 0.00 0.00 2.17
2586 2669 6.485313 TGTGGATTCTAAAAGTGTTCGTGATT 59.515 34.615 0.00 0.00 0.00 2.57
2587 2670 5.995282 TGTGGATTCTAAAAGTGTTCGTGAT 59.005 36.000 0.00 0.00 0.00 3.06
2588 2671 5.361427 TGTGGATTCTAAAAGTGTTCGTGA 58.639 37.500 0.00 0.00 0.00 4.35
2589 2672 5.666969 TGTGGATTCTAAAAGTGTTCGTG 57.333 39.130 0.00 0.00 0.00 4.35
2590 2673 6.094325 TGTTTGTGGATTCTAAAAGTGTTCGT 59.906 34.615 0.00 0.00 0.00 3.85
2591 2674 6.491394 TGTTTGTGGATTCTAAAAGTGTTCG 58.509 36.000 0.00 0.00 0.00 3.95
2592 2675 8.871686 AATGTTTGTGGATTCTAAAAGTGTTC 57.128 30.769 0.00 0.00 0.00 3.18
2593 2676 9.665719 AAAATGTTTGTGGATTCTAAAAGTGTT 57.334 25.926 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.