Multiple sequence alignment - TraesCS1D01G313500

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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 TraesCS1D01G313500 chr1D 100.000 2336 0 0 1 2336 408846509 408848844 0.000000e+00 4314.0
1 TraesCS1D01G313500 chr5D 92.985 1682 100 16 1 1677 311901583 311903251 0.000000e+00 2436.0
2 TraesCS1D01G313500 chr5D 92.308 78 6 0 2084 2161 70203296 70203373 6.820000e-21 111.0
3 TraesCS1D01G313500 chr5D 82.558 86 11 4 2121 2203 24091139 24091223 3.220000e-09 73.1
4 TraesCS1D01G313500 chr5A 93.113 1394 88 7 291 1682 35638352 35636965 0.000000e+00 2036.0
5 TraesCS1D01G313500 chr5A 87.847 1695 185 19 1 1683 621007974 621006289 0.000000e+00 1969.0
6 TraesCS1D01G313500 chr5A 85.865 1705 208 29 1 1683 648908923 648907230 0.000000e+00 1783.0
7 TraesCS1D01G313500 chr5A 85.561 651 77 16 1047 1687 599774849 599774206 0.000000e+00 665.0
8 TraesCS1D01G313500 chr5A 85.891 567 63 16 1131 1687 599772693 599772134 2.590000e-164 588.0
9 TraesCS1D01G313500 chr5A 85.538 567 65 16 1131 1687 599772003 599771444 5.600000e-161 577.0
10 TraesCS1D01G313500 chr5A 92.208 77 6 0 2079 2155 384946924 384947000 2.450000e-20 110.0
11 TraesCS1D01G313500 chr5A 94.118 51 3 0 2032 2082 689226 689276 6.920000e-11 78.7
12 TraesCS1D01G313500 chr5A 91.489 47 4 0 2043 2089 470161873 470161827 5.390000e-07 65.8
13 TraesCS1D01G313500 chr7A 87.544 1694 190 19 1 1682 149312249 149310565 0.000000e+00 1940.0
14 TraesCS1D01G313500 chr7A 91.892 148 9 3 1536 1682 490968511 490968656 1.090000e-48 204.0
15 TraesCS1D01G313500 chr7A 87.117 163 19 2 1520 1682 40953660 40953820 1.430000e-42 183.0
16 TraesCS1D01G313500 chr4A 87.433 1679 192 17 9 1681 163215661 163213996 0.000000e+00 1914.0
17 TraesCS1D01G313500 chr4A 86.052 1692 185 28 7 1682 477027584 477025928 0.000000e+00 1770.0
18 TraesCS1D01G313500 chr4A 86.286 1050 139 5 1 1046 89694029 89692981 0.000000e+00 1136.0
19 TraesCS1D01G313500 chr4A 86.503 652 71 16 1040 1682 89684263 89683620 0.000000e+00 701.0
20 TraesCS1D01G313500 chr4A 86.462 325 31 13 1364 1682 60355726 60355409 6.180000e-91 344.0
21 TraesCS1D01G313500 chr4D 85.418 1351 193 4 6 1353 348704395 348703046 0.000000e+00 1400.0
22 TraesCS1D01G313500 chr1B 80.717 1338 244 13 6 1336 16951751 16953081 0.000000e+00 1029.0
23 TraesCS1D01G313500 chr1B 91.026 78 7 0 2084 2161 327343926 327343849 3.170000e-19 106.0
24 TraesCS1D01G313500 chr1B 85.542 83 8 4 2079 2161 121774695 121774617 1.490000e-12 84.2
25 TraesCS1D01G313500 chr3A 75.242 1341 290 36 5 1324 523688554 523687235 1.190000e-167 599.0
26 TraesCS1D01G313500 chr1A 86.506 415 36 15 1674 2081 73091745 73092146 2.760000e-119 438.0
27 TraesCS1D01G313500 chr6D 89.683 252 16 4 1674 1916 469119377 469119627 1.740000e-81 313.0
28 TraesCS1D01G313500 chr6D 90.184 163 12 3 1920 2080 469119775 469119935 2.350000e-50 209.0
29 TraesCS1D01G313500 chr6D 88.525 61 5 2 2023 2082 42085249 42085308 3.220000e-09 73.1
30 TraesCS1D01G313500 chr6D 89.655 58 5 1 2024 2080 356746875 356746932 3.220000e-09 73.1
31 TraesCS1D01G313500 chr6D 83.784 74 7 4 2023 2091 450272268 450272341 5.390000e-07 65.8
32 TraesCS1D01G313500 chr3D 84.375 192 24 6 1499 1686 264427782 264427593 1.430000e-42 183.0
33 TraesCS1D01G313500 chr3D 78.462 130 24 2 191 318 136729301 136729174 5.350000e-12 82.4
34 TraesCS1D01G313500 chr7B 93.902 82 5 0 2079 2160 362036544 362036463 8.760000e-25 124.0
35 TraesCS1D01G313500 chr7B 91.667 72 6 0 2085 2156 437874334 437874263 1.480000e-17 100.0
36 TraesCS1D01G313500 chr7D 92.405 79 6 0 2082 2160 289250833 289250755 1.900000e-21 113.0
37 TraesCS1D01G313500 chr7D 93.878 49 3 0 2032 2080 64414388 64414340 8.950000e-10 75.0
38 TraesCS1D01G313500 chr6B 92.208 77 6 0 2085 2161 432482394 432482318 2.450000e-20 110.0
39 TraesCS1D01G313500 chr6B 89.655 58 3 2 2023 2080 276750700 276750754 1.160000e-08 71.3
40 TraesCS1D01G313500 chr6A 85.542 83 8 3 2079 2161 53880028 53880106 1.490000e-12 84.2
41 TraesCS1D01G313500 chr6A 86.486 74 10 0 191 264 503934558 503934631 5.350000e-12 82.4
42 TraesCS1D01G313500 chr6A 78.400 125 21 4 191 312 133819771 133819892 2.490000e-10 76.8
43 TraesCS1D01G313500 chr2D 88.333 60 5 2 2023 2080 637029922 637029981 1.160000e-08 71.3


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 TraesCS1D01G313500 chr1D 408846509 408848844 2335 False 4314 4314 100.000000 1 2336 1 chr1D.!!$F1 2335
1 TraesCS1D01G313500 chr5D 311901583 311903251 1668 False 2436 2436 92.985000 1 1677 1 chr5D.!!$F3 1676
2 TraesCS1D01G313500 chr5A 35636965 35638352 1387 True 2036 2036 93.113000 291 1682 1 chr5A.!!$R1 1391
3 TraesCS1D01G313500 chr5A 621006289 621007974 1685 True 1969 1969 87.847000 1 1683 1 chr5A.!!$R3 1682
4 TraesCS1D01G313500 chr5A 648907230 648908923 1693 True 1783 1783 85.865000 1 1683 1 chr5A.!!$R4 1682
5 TraesCS1D01G313500 chr5A 599771444 599774849 3405 True 610 665 85.663333 1047 1687 3 chr5A.!!$R5 640
6 TraesCS1D01G313500 chr7A 149310565 149312249 1684 True 1940 1940 87.544000 1 1682 1 chr7A.!!$R1 1681
7 TraesCS1D01G313500 chr4A 163213996 163215661 1665 True 1914 1914 87.433000 9 1681 1 chr4A.!!$R4 1672
8 TraesCS1D01G313500 chr4A 477025928 477027584 1656 True 1770 1770 86.052000 7 1682 1 chr4A.!!$R5 1675
9 TraesCS1D01G313500 chr4A 89692981 89694029 1048 True 1136 1136 86.286000 1 1046 1 chr4A.!!$R3 1045
10 TraesCS1D01G313500 chr4A 89683620 89684263 643 True 701 701 86.503000 1040 1682 1 chr4A.!!$R2 642
11 TraesCS1D01G313500 chr4D 348703046 348704395 1349 True 1400 1400 85.418000 6 1353 1 chr4D.!!$R1 1347
12 TraesCS1D01G313500 chr1B 16951751 16953081 1330 False 1029 1029 80.717000 6 1336 1 chr1B.!!$F1 1330
13 TraesCS1D01G313500 chr3A 523687235 523688554 1319 True 599 599 75.242000 5 1324 1 chr3A.!!$R1 1319
14 TraesCS1D01G313500 chr6D 469119377 469119935 558 False 261 313 89.933500 1674 2080 2 chr6D.!!$F4 406

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
265 269 1.150536 GGGCTGGGTGTGAAAGACA 59.849 57.895 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1916 4712 0.166161 TCGACGACTCGCTTCTCTTG 59.834 55.0 0.0 0.0 39.96 3.02 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
265 269 1.150536 GGGCTGGGTGTGAAAGACA 59.849 57.895 0.00 0.00 0.00 3.41
620 625 4.956075 TGCTAGTGGAGATATGTTCAGACA 59.044 41.667 0.00 0.00 40.71 3.41
753 758 6.668645 AGGCAAATACACCACTAAATCCATA 58.331 36.000 0.00 0.00 0.00 2.74
959 965 9.232473 AGAAACTTATCTACATTTGTTCTTCCC 57.768 33.333 0.00 0.00 0.00 3.97
1102 1108 2.669744 TTTCACCATGGGGCTGGCAA 62.670 55.000 18.09 0.00 40.15 4.52
1208 2596 5.297527 TCAATGCTTGTATGCACCTATCTTG 59.702 40.000 0.00 0.00 46.33 3.02
1279 3357 3.055891 TGCGATGATTCTGAAGGAGAACA 60.056 43.478 0.00 0.00 43.71 3.18
1385 4162 0.035439 GCCTTTTGGAGTGATCGGGA 60.035 55.000 0.00 0.00 44.07 5.14
1421 4202 3.068590 CACTTGGAAGCATTTTGTGGAGT 59.931 43.478 0.00 0.00 0.00 3.85
1422 4203 3.319122 ACTTGGAAGCATTTTGTGGAGTC 59.681 43.478 0.00 0.00 0.00 3.36
1424 4205 2.886523 TGGAAGCATTTTGTGGAGTCTG 59.113 45.455 0.00 0.00 0.00 3.51
1425 4206 2.887152 GGAAGCATTTTGTGGAGTCTGT 59.113 45.455 0.00 0.00 0.00 3.41
1458 4241 6.320164 TGTTCTACATAACTGTGTTGCCTTTT 59.680 34.615 0.00 0.00 36.79 2.27
1459 4242 6.312399 TCTACATAACTGTGTTGCCTTTTG 57.688 37.500 0.00 0.00 36.79 2.44
1460 4243 6.058833 TCTACATAACTGTGTTGCCTTTTGA 58.941 36.000 0.00 0.00 36.79 2.69
1461 4244 5.590530 ACATAACTGTGTTGCCTTTTGAA 57.409 34.783 0.00 0.00 33.22 2.69
1497 4283 2.870411 GTCTGAACTTAGTTTGGTGCGT 59.130 45.455 0.00 0.00 0.00 5.24
1531 4317 1.172180 TGCTTCAGGGTTTTCGCCTG 61.172 55.000 0.00 0.00 38.63 4.85
1599 4385 4.363991 AGTGCTTGATCTCACTTTTCCT 57.636 40.909 9.13 0.00 40.32 3.36
1641 4427 3.373130 GGAACTGGCTGTATTTCCGTTAC 59.627 47.826 0.00 0.00 0.00 2.50
1810 4606 5.643348 TGTTCACATAGGCAGATTGTAGTTG 59.357 40.000 0.00 0.00 0.00 3.16
1842 4638 9.577003 CTAGTTAGACATTTTACGTCACAAAAC 57.423 33.333 0.00 0.00 35.77 2.43
1854 4650 5.607477 ACGTCACAAAACATTCTCTTCCTA 58.393 37.500 0.00 0.00 0.00 2.94
1888 4684 6.509418 TGCCATACTAAAACTTCAATCCAC 57.491 37.500 0.00 0.00 0.00 4.02
1894 4690 6.187727 ACTAAAACTTCAATCCACTCTCCA 57.812 37.500 0.00 0.00 0.00 3.86
1900 4696 0.393537 CAATCCACTCTCCAGCACCC 60.394 60.000 0.00 0.00 0.00 4.61
1916 4712 0.601057 ACCCCGCAAGCACAATTTAC 59.399 50.000 0.00 0.00 0.00 2.01
1917 4713 0.600557 CCCCGCAAGCACAATTTACA 59.399 50.000 0.00 0.00 0.00 2.41
1918 4714 1.000283 CCCCGCAAGCACAATTTACAA 60.000 47.619 0.00 0.00 0.00 2.41
1948 4888 2.028294 AGTCGTCGAGAGGAGACTGTAA 60.028 50.000 0.00 0.00 44.43 2.41
1958 4898 1.665161 GGAGACTGTAACACGTCCACG 60.665 57.143 0.00 0.00 46.33 4.94
1979 4920 1.102154 CCACCTCGGCAATGCAATTA 58.898 50.000 7.79 0.00 32.46 1.40
1995 4936 6.299805 TGCAATTACAGAGAAGGTATGTCT 57.700 37.500 0.00 0.00 30.24 3.41
1996 4937 6.711277 TGCAATTACAGAGAAGGTATGTCTT 58.289 36.000 0.00 0.00 26.83 3.01
2033 4974 8.815565 TTGATACTATCAAAATTAAGTGGCCA 57.184 30.769 0.00 0.00 45.57 5.36
2071 5013 0.684479 GGCCCCCAAAATCTCAGGAC 60.684 60.000 0.00 0.00 0.00 3.85
2093 5035 4.640855 CCTGTCGGTGTCGTGCGT 62.641 66.667 0.00 0.00 37.69 5.24
2094 5036 2.657296 CTGTCGGTGTCGTGCGTT 60.657 61.111 0.00 0.00 37.69 4.84
2095 5037 2.927618 CTGTCGGTGTCGTGCGTTG 61.928 63.158 0.00 0.00 37.69 4.10
2096 5038 3.698463 GTCGGTGTCGTGCGTTGG 61.698 66.667 0.00 0.00 37.69 3.77
2097 5039 4.953868 TCGGTGTCGTGCGTTGGG 62.954 66.667 0.00 0.00 37.69 4.12
2099 5041 3.645975 GGTGTCGTGCGTTGGGTG 61.646 66.667 0.00 0.00 0.00 4.61
2100 5042 3.645975 GTGTCGTGCGTTGGGTGG 61.646 66.667 0.00 0.00 0.00 4.61
2101 5043 4.164087 TGTCGTGCGTTGGGTGGT 62.164 61.111 0.00 0.00 0.00 4.16
2102 5044 2.898343 GTCGTGCGTTGGGTGGTT 60.898 61.111 0.00 0.00 0.00 3.67
2103 5045 2.897846 TCGTGCGTTGGGTGGTTG 60.898 61.111 0.00 0.00 0.00 3.77
2104 5046 3.959975 CGTGCGTTGGGTGGTTGG 61.960 66.667 0.00 0.00 0.00 3.77
2105 5047 2.831284 GTGCGTTGGGTGGTTGGT 60.831 61.111 0.00 0.00 0.00 3.67
2106 5048 2.043852 TGCGTTGGGTGGTTGGTT 60.044 55.556 0.00 0.00 0.00 3.67
2107 5049 2.415426 GCGTTGGGTGGTTGGTTG 59.585 61.111 0.00 0.00 0.00 3.77
2108 5050 2.419739 GCGTTGGGTGGTTGGTTGT 61.420 57.895 0.00 0.00 0.00 3.32
2109 5051 1.102222 GCGTTGGGTGGTTGGTTGTA 61.102 55.000 0.00 0.00 0.00 2.41
2110 5052 1.611519 CGTTGGGTGGTTGGTTGTAT 58.388 50.000 0.00 0.00 0.00 2.29
2111 5053 1.268352 CGTTGGGTGGTTGGTTGTATG 59.732 52.381 0.00 0.00 0.00 2.39
2112 5054 1.000394 GTTGGGTGGTTGGTTGTATGC 60.000 52.381 0.00 0.00 0.00 3.14
2113 5055 0.186143 TGGGTGGTTGGTTGTATGCA 59.814 50.000 0.00 0.00 0.00 3.96
2114 5056 1.203112 TGGGTGGTTGGTTGTATGCAT 60.203 47.619 3.79 3.79 0.00 3.96
2115 5057 1.204467 GGGTGGTTGGTTGTATGCATG 59.796 52.381 10.16 0.00 0.00 4.06
2116 5058 2.166829 GGTGGTTGGTTGTATGCATGA 58.833 47.619 10.16 0.00 0.00 3.07
2117 5059 2.760092 GGTGGTTGGTTGTATGCATGAT 59.240 45.455 10.16 0.00 0.00 2.45
2118 5060 3.181487 GGTGGTTGGTTGTATGCATGATC 60.181 47.826 10.16 0.33 0.00 2.92
2119 5061 2.682352 TGGTTGGTTGTATGCATGATCG 59.318 45.455 10.16 0.00 0.00 3.69
2120 5062 2.682856 GGTTGGTTGTATGCATGATCGT 59.317 45.455 10.16 0.00 0.00 3.73
2121 5063 3.128589 GGTTGGTTGTATGCATGATCGTT 59.871 43.478 10.16 0.00 0.00 3.85
2122 5064 4.097714 GTTGGTTGTATGCATGATCGTTG 58.902 43.478 10.16 0.00 0.00 4.10
2123 5065 2.097304 TGGTTGTATGCATGATCGTTGC 59.903 45.455 10.16 12.26 40.55 4.17
2124 5066 2.355756 GGTTGTATGCATGATCGTTGCT 59.644 45.455 10.16 8.86 40.77 3.91
2125 5067 3.181497 GGTTGTATGCATGATCGTTGCTT 60.181 43.478 10.16 14.80 40.77 3.91
2126 5068 4.414852 GTTGTATGCATGATCGTTGCTTT 58.585 39.130 10.16 10.28 40.77 3.51
2127 5069 5.448496 GGTTGTATGCATGATCGTTGCTTTA 60.448 40.000 10.16 9.52 40.77 1.85
2128 5070 6.201517 GTTGTATGCATGATCGTTGCTTTAT 58.798 36.000 10.16 8.70 40.77 1.40
2129 5071 7.351981 GTTGTATGCATGATCGTTGCTTTATA 58.648 34.615 10.16 7.92 40.77 0.98
2130 5072 7.671495 TGTATGCATGATCGTTGCTTTATAT 57.329 32.000 10.16 8.14 40.77 0.86
2131 5073 8.770438 TGTATGCATGATCGTTGCTTTATATA 57.230 30.769 10.16 7.37 40.77 0.86
2132 5074 9.382275 TGTATGCATGATCGTTGCTTTATATAT 57.618 29.630 10.16 7.04 40.77 0.86
2146 5088 6.730960 CTTTATATATAAAGCGGGGCGAAA 57.269 37.500 25.10 1.66 41.69 3.46
2147 5089 6.730960 TTTATATATAAAGCGGGGCGAAAG 57.269 37.500 12.90 0.00 0.00 2.62
2148 5090 1.892209 ATATAAAGCGGGGCGAAAGG 58.108 50.000 0.00 0.00 0.00 3.11
2162 5104 3.891056 CGAAAGGCTTTTTCGGTAAGT 57.109 42.857 14.66 0.00 45.17 2.24
2163 5105 3.551551 CGAAAGGCTTTTTCGGTAAGTG 58.448 45.455 14.66 1.02 45.17 3.16
2164 5106 3.608474 CGAAAGGCTTTTTCGGTAAGTGG 60.608 47.826 14.66 0.00 45.17 4.00
2165 5107 2.651382 AGGCTTTTTCGGTAAGTGGT 57.349 45.000 0.00 0.00 0.00 4.16
2166 5108 2.501261 AGGCTTTTTCGGTAAGTGGTC 58.499 47.619 0.00 0.00 0.00 4.02
2167 5109 1.538512 GGCTTTTTCGGTAAGTGGTCC 59.461 52.381 0.00 0.00 0.00 4.46
2168 5110 2.223745 GCTTTTTCGGTAAGTGGTCCA 58.776 47.619 0.00 0.00 0.00 4.02
2169 5111 2.225727 GCTTTTTCGGTAAGTGGTCCAG 59.774 50.000 0.00 0.00 0.00 3.86
2170 5112 3.735591 CTTTTTCGGTAAGTGGTCCAGA 58.264 45.455 0.00 0.00 0.00 3.86
2171 5113 3.842007 TTTTCGGTAAGTGGTCCAGAA 57.158 42.857 0.00 0.00 0.00 3.02
2172 5114 2.825861 TTCGGTAAGTGGTCCAGAAC 57.174 50.000 0.00 0.00 0.00 3.01
2173 5115 2.005370 TCGGTAAGTGGTCCAGAACT 57.995 50.000 0.00 0.00 0.00 3.01
2174 5116 3.159213 TCGGTAAGTGGTCCAGAACTA 57.841 47.619 0.00 0.00 0.00 2.24
2175 5117 3.499338 TCGGTAAGTGGTCCAGAACTAA 58.501 45.455 0.00 0.00 0.00 2.24
2176 5118 4.091549 TCGGTAAGTGGTCCAGAACTAAT 58.908 43.478 0.00 0.00 0.00 1.73
2177 5119 4.081862 TCGGTAAGTGGTCCAGAACTAATG 60.082 45.833 0.00 0.00 0.00 1.90
2178 5120 3.939592 GGTAAGTGGTCCAGAACTAATGC 59.060 47.826 0.00 0.00 0.00 3.56
2179 5121 4.323562 GGTAAGTGGTCCAGAACTAATGCT 60.324 45.833 0.00 0.00 0.00 3.79
2180 5122 3.618690 AGTGGTCCAGAACTAATGCTC 57.381 47.619 0.00 0.00 0.00 4.26
2181 5123 3.177228 AGTGGTCCAGAACTAATGCTCT 58.823 45.455 0.00 0.00 0.00 4.09
2182 5124 3.055530 AGTGGTCCAGAACTAATGCTCTG 60.056 47.826 0.00 0.00 39.06 3.35
2183 5125 2.906389 TGGTCCAGAACTAATGCTCTGT 59.094 45.455 0.00 0.00 37.89 3.41
2184 5126 3.327757 TGGTCCAGAACTAATGCTCTGTT 59.672 43.478 0.00 0.00 37.89 3.16
2185 5127 4.202461 TGGTCCAGAACTAATGCTCTGTTT 60.202 41.667 0.00 0.00 37.89 2.83
2186 5128 4.762251 GGTCCAGAACTAATGCTCTGTTTT 59.238 41.667 0.00 0.00 37.89 2.43
2187 5129 5.335191 GGTCCAGAACTAATGCTCTGTTTTG 60.335 44.000 0.00 0.00 37.89 2.44
2188 5130 5.470098 GTCCAGAACTAATGCTCTGTTTTGA 59.530 40.000 0.00 0.00 37.89 2.69
2189 5131 5.702670 TCCAGAACTAATGCTCTGTTTTGAG 59.297 40.000 0.00 0.00 37.89 3.02
2190 5132 5.702670 CCAGAACTAATGCTCTGTTTTGAGA 59.297 40.000 0.00 0.00 37.89 3.27
2191 5133 6.373774 CCAGAACTAATGCTCTGTTTTGAGAT 59.626 38.462 0.00 0.00 37.89 2.75
2192 5134 7.550551 CCAGAACTAATGCTCTGTTTTGAGATA 59.449 37.037 0.00 0.00 37.89 1.98
2193 5135 8.939929 CAGAACTAATGCTCTGTTTTGAGATAA 58.060 33.333 0.00 0.00 35.38 1.75
2194 5136 9.160496 AGAACTAATGCTCTGTTTTGAGATAAG 57.840 33.333 0.00 0.00 36.23 1.73
2195 5137 9.155975 GAACTAATGCTCTGTTTTGAGATAAGA 57.844 33.333 0.00 0.00 36.23 2.10
2196 5138 9.507329 AACTAATGCTCTGTTTTGAGATAAGAA 57.493 29.630 0.00 0.00 36.23 2.52
2197 5139 9.160496 ACTAATGCTCTGTTTTGAGATAAGAAG 57.840 33.333 0.00 0.00 36.23 2.85
2198 5140 9.376075 CTAATGCTCTGTTTTGAGATAAGAAGA 57.624 33.333 0.00 0.00 36.23 2.87
2199 5141 7.846644 ATGCTCTGTTTTGAGATAAGAAGAG 57.153 36.000 0.00 0.00 36.23 2.85
2200 5142 6.169094 TGCTCTGTTTTGAGATAAGAAGAGG 58.831 40.000 0.00 0.00 36.23 3.69
2201 5143 5.584251 GCTCTGTTTTGAGATAAGAAGAGGG 59.416 44.000 0.00 0.00 36.23 4.30
2202 5144 6.575254 GCTCTGTTTTGAGATAAGAAGAGGGA 60.575 42.308 0.00 0.00 36.23 4.20
2203 5145 6.702329 TCTGTTTTGAGATAAGAAGAGGGAC 58.298 40.000 0.00 0.00 0.00 4.46
2204 5146 6.270000 TCTGTTTTGAGATAAGAAGAGGGACA 59.730 38.462 0.00 0.00 0.00 4.02
2205 5147 6.467677 TGTTTTGAGATAAGAAGAGGGACAG 58.532 40.000 0.00 0.00 0.00 3.51
2206 5148 6.270000 TGTTTTGAGATAAGAAGAGGGACAGA 59.730 38.462 0.00 0.00 0.00 3.41
2207 5149 7.038017 TGTTTTGAGATAAGAAGAGGGACAGAT 60.038 37.037 0.00 0.00 0.00 2.90
2208 5150 7.502060 TTTGAGATAAGAAGAGGGACAGATT 57.498 36.000 0.00 0.00 0.00 2.40
2209 5151 8.609617 TTTGAGATAAGAAGAGGGACAGATTA 57.390 34.615 0.00 0.00 0.00 1.75
2210 5152 8.609617 TTGAGATAAGAAGAGGGACAGATTAA 57.390 34.615 0.00 0.00 0.00 1.40
2211 5153 8.789767 TGAGATAAGAAGAGGGACAGATTAAT 57.210 34.615 0.00 0.00 0.00 1.40
2212 5154 9.883293 TGAGATAAGAAGAGGGACAGATTAATA 57.117 33.333 0.00 0.00 0.00 0.98
2215 5157 9.796120 GATAAGAAGAGGGACAGATTAATATCG 57.204 37.037 0.00 0.00 35.85 2.92
2216 5158 6.597832 AGAAGAGGGACAGATTAATATCGG 57.402 41.667 0.00 0.00 35.85 4.18
2217 5159 6.078664 AGAAGAGGGACAGATTAATATCGGT 58.921 40.000 0.00 0.00 41.09 4.69
2218 5160 5.730296 AGAGGGACAGATTAATATCGGTG 57.270 43.478 0.00 0.00 38.96 4.94
2219 5161 4.021016 AGAGGGACAGATTAATATCGGTGC 60.021 45.833 0.00 0.00 43.20 5.01
2220 5162 3.904339 AGGGACAGATTAATATCGGTGCT 59.096 43.478 9.03 0.00 43.36 4.40
2221 5163 3.997021 GGGACAGATTAATATCGGTGCTG 59.003 47.826 9.03 0.00 43.36 4.41
2222 5164 3.997021 GGACAGATTAATATCGGTGCTGG 59.003 47.826 0.00 0.00 41.62 4.85
2223 5165 3.403038 ACAGATTAATATCGGTGCTGGC 58.597 45.455 0.00 0.00 37.72 4.85
2224 5166 3.181455 ACAGATTAATATCGGTGCTGGCA 60.181 43.478 0.00 0.00 37.72 4.92
2225 5167 4.005650 CAGATTAATATCGGTGCTGGCAT 58.994 43.478 0.00 0.00 35.85 4.40
2226 5168 5.178061 CAGATTAATATCGGTGCTGGCATA 58.822 41.667 0.00 0.00 35.85 3.14
2227 5169 5.643348 CAGATTAATATCGGTGCTGGCATAA 59.357 40.000 0.00 0.00 35.85 1.90
2228 5170 5.877012 AGATTAATATCGGTGCTGGCATAAG 59.123 40.000 0.00 0.00 35.85 1.73
2229 5171 3.492102 AATATCGGTGCTGGCATAAGT 57.508 42.857 0.00 0.00 0.00 2.24
2230 5172 4.617253 AATATCGGTGCTGGCATAAGTA 57.383 40.909 0.00 0.00 0.00 2.24
2231 5173 4.617253 ATATCGGTGCTGGCATAAGTAA 57.383 40.909 0.00 0.00 0.00 2.24
2232 5174 2.309528 TCGGTGCTGGCATAAGTAAG 57.690 50.000 0.00 0.00 0.00 2.34
2233 5175 1.828595 TCGGTGCTGGCATAAGTAAGA 59.171 47.619 0.00 0.00 0.00 2.10
2234 5176 2.235155 TCGGTGCTGGCATAAGTAAGAA 59.765 45.455 0.00 0.00 0.00 2.52
2235 5177 2.609459 CGGTGCTGGCATAAGTAAGAAG 59.391 50.000 0.00 0.00 0.00 2.85
2236 5178 3.610911 GGTGCTGGCATAAGTAAGAAGT 58.389 45.455 0.00 0.00 0.00 3.01
2237 5179 4.010349 GGTGCTGGCATAAGTAAGAAGTT 58.990 43.478 0.00 0.00 0.00 2.66
2238 5180 4.095036 GGTGCTGGCATAAGTAAGAAGTTC 59.905 45.833 0.00 0.00 0.00 3.01
2239 5181 4.938226 GTGCTGGCATAAGTAAGAAGTTCT 59.062 41.667 0.00 0.00 0.00 3.01
2240 5182 6.106673 GTGCTGGCATAAGTAAGAAGTTCTA 58.893 40.000 5.65 0.00 0.00 2.10
2241 5183 6.256757 GTGCTGGCATAAGTAAGAAGTTCTAG 59.743 42.308 5.65 0.00 0.00 2.43
2242 5184 5.235401 GCTGGCATAAGTAAGAAGTTCTAGC 59.765 44.000 5.65 3.60 0.00 3.42
2243 5185 6.294361 TGGCATAAGTAAGAAGTTCTAGCA 57.706 37.500 5.65 0.00 0.00 3.49
2244 5186 6.707290 TGGCATAAGTAAGAAGTTCTAGCAA 58.293 36.000 5.65 0.00 0.00 3.91
2245 5187 7.165485 TGGCATAAGTAAGAAGTTCTAGCAAA 58.835 34.615 5.65 0.00 0.00 3.68
2246 5188 7.663905 TGGCATAAGTAAGAAGTTCTAGCAAAA 59.336 33.333 5.65 0.00 0.00 2.44
2247 5189 8.178313 GGCATAAGTAAGAAGTTCTAGCAAAAG 58.822 37.037 5.65 0.00 0.00 2.27
2248 5190 8.722394 GCATAAGTAAGAAGTTCTAGCAAAAGT 58.278 33.333 5.65 0.00 0.00 2.66
2251 5193 8.507524 AAGTAAGAAGTTCTAGCAAAAGTTGT 57.492 30.769 5.65 0.00 0.00 3.32
2252 5194 9.609346 AAGTAAGAAGTTCTAGCAAAAGTTGTA 57.391 29.630 5.65 0.00 0.00 2.41
2253 5195 9.609346 AGTAAGAAGTTCTAGCAAAAGTTGTAA 57.391 29.630 5.65 0.00 0.00 2.41
2256 5198 7.875971 AGAAGTTCTAGCAAAAGTTGTAATGG 58.124 34.615 2.75 0.00 0.00 3.16
2257 5199 7.719633 AGAAGTTCTAGCAAAAGTTGTAATGGA 59.280 33.333 2.75 0.00 0.00 3.41
2258 5200 7.817418 AGTTCTAGCAAAAGTTGTAATGGAA 57.183 32.000 0.00 0.00 0.00 3.53
2259 5201 8.232913 AGTTCTAGCAAAAGTTGTAATGGAAA 57.767 30.769 0.00 0.00 0.00 3.13
2260 5202 8.691797 AGTTCTAGCAAAAGTTGTAATGGAAAA 58.308 29.630 0.00 0.00 0.00 2.29
2261 5203 9.308318 GTTCTAGCAAAAGTTGTAATGGAAAAA 57.692 29.630 0.00 0.00 0.00 1.94
2262 5204 9.528018 TTCTAGCAAAAGTTGTAATGGAAAAAG 57.472 29.630 0.00 0.00 0.00 2.27
2263 5205 8.691797 TCTAGCAAAAGTTGTAATGGAAAAAGT 58.308 29.630 0.00 0.00 0.00 2.66
2264 5206 9.959749 CTAGCAAAAGTTGTAATGGAAAAAGTA 57.040 29.630 0.00 0.00 0.00 2.24
2272 5214 9.802039 AGTTGTAATGGAAAAAGTATAAGGTCA 57.198 29.630 0.00 0.00 0.00 4.02
2274 5216 8.801882 TGTAATGGAAAAAGTATAAGGTCAGG 57.198 34.615 0.00 0.00 0.00 3.86
2275 5217 8.387813 TGTAATGGAAAAAGTATAAGGTCAGGT 58.612 33.333 0.00 0.00 0.00 4.00
2276 5218 7.939784 AATGGAAAAAGTATAAGGTCAGGTC 57.060 36.000 0.00 0.00 0.00 3.85
2277 5219 6.697641 TGGAAAAAGTATAAGGTCAGGTCT 57.302 37.500 0.00 0.00 0.00 3.85
2278 5220 6.708285 TGGAAAAAGTATAAGGTCAGGTCTC 58.292 40.000 0.00 0.00 0.00 3.36
2279 5221 6.500751 TGGAAAAAGTATAAGGTCAGGTCTCT 59.499 38.462 0.00 0.00 0.00 3.10
2280 5222 7.676893 TGGAAAAAGTATAAGGTCAGGTCTCTA 59.323 37.037 0.00 0.00 0.00 2.43
2281 5223 8.198778 GGAAAAAGTATAAGGTCAGGTCTCTAG 58.801 40.741 0.00 0.00 0.00 2.43
2282 5224 6.718522 AAAGTATAAGGTCAGGTCTCTAGC 57.281 41.667 0.00 0.00 0.00 3.42
2283 5225 5.390087 AGTATAAGGTCAGGTCTCTAGCA 57.610 43.478 0.00 0.00 0.00 3.49
2284 5226 5.767670 AGTATAAGGTCAGGTCTCTAGCAA 58.232 41.667 0.00 0.00 0.00 3.91
2285 5227 6.377912 AGTATAAGGTCAGGTCTCTAGCAAT 58.622 40.000 0.00 0.00 0.00 3.56
2286 5228 6.841755 AGTATAAGGTCAGGTCTCTAGCAATT 59.158 38.462 0.00 0.00 0.00 2.32
2287 5229 4.917906 AAGGTCAGGTCTCTAGCAATTT 57.082 40.909 0.00 0.00 0.00 1.82
2288 5230 4.479786 AGGTCAGGTCTCTAGCAATTTC 57.520 45.455 0.00 0.00 0.00 2.17
2289 5231 3.840666 AGGTCAGGTCTCTAGCAATTTCA 59.159 43.478 0.00 0.00 0.00 2.69
2290 5232 4.472833 AGGTCAGGTCTCTAGCAATTTCAT 59.527 41.667 0.00 0.00 0.00 2.57
2291 5233 4.574013 GGTCAGGTCTCTAGCAATTTCATG 59.426 45.833 0.00 0.00 0.00 3.07
2292 5234 4.034975 GTCAGGTCTCTAGCAATTTCATGC 59.965 45.833 0.00 0.00 46.78 4.06
2306 5248 7.745015 GCAATTTCATGCTTGACAATATTTGT 58.255 30.769 1.02 0.00 44.13 2.83
2307 5249 8.871862 GCAATTTCATGCTTGACAATATTTGTA 58.128 29.630 1.02 0.00 42.73 2.41
2309 5251 9.926158 AATTTCATGCTTGACAATATTTGTACA 57.074 25.926 1.02 0.00 45.52 2.90
2310 5252 8.741101 TTTCATGCTTGACAATATTTGTACAC 57.259 30.769 1.02 0.00 45.52 2.90
2311 5253 7.446001 TCATGCTTGACAATATTTGTACACA 57.554 32.000 0.00 0.00 45.52 3.72
2312 5254 7.304735 TCATGCTTGACAATATTTGTACACAC 58.695 34.615 0.00 0.00 45.52 3.82
2313 5255 6.625873 TGCTTGACAATATTTGTACACACA 57.374 33.333 0.00 0.00 45.52 3.72
2314 5256 6.434596 TGCTTGACAATATTTGTACACACAC 58.565 36.000 0.00 0.00 45.52 3.82
2315 5257 5.563751 GCTTGACAATATTTGTACACACACG 59.436 40.000 0.00 0.00 45.52 4.49
2316 5258 5.024768 TGACAATATTTGTACACACACGC 57.975 39.130 0.00 0.00 45.52 5.34
2317 5259 4.060288 ACAATATTTGTACACACACGCG 57.940 40.909 3.53 3.53 43.27 6.01
2318 5260 2.798834 ATATTTGTACACACACGCGC 57.201 45.000 5.73 0.00 33.30 6.86
2319 5261 0.435388 TATTTGTACACACACGCGCG 59.565 50.000 30.96 30.96 33.30 6.86
2320 5262 1.492319 ATTTGTACACACACGCGCGT 61.492 50.000 32.73 32.73 33.30 6.01
2330 5272 4.072913 ACGCGCGTGAAGTATGAG 57.927 55.556 37.37 0.93 0.00 2.90
2331 5273 1.504900 ACGCGCGTGAAGTATGAGA 59.495 52.632 37.37 0.00 0.00 3.27
2332 5274 0.100682 ACGCGCGTGAAGTATGAGAT 59.899 50.000 37.37 4.40 0.00 2.75
2333 5275 0.772926 CGCGCGTGAAGTATGAGATC 59.227 55.000 24.19 0.00 0.00 2.75
2334 5276 0.772926 GCGCGTGAAGTATGAGATCG 59.227 55.000 8.43 0.00 0.00 3.69
2335 5277 1.860399 GCGCGTGAAGTATGAGATCGT 60.860 52.381 8.43 0.00 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 67 4.646572 AGAGGGATGAGTTCAACAAAGTC 58.353 43.478 0.00 0.00 37.75 3.01
265 269 8.641498 AAAAGTGAGATATTCTGTTTGTGGAT 57.359 30.769 0.00 0.00 0.00 3.41
320 324 1.434513 ATCTTGCCACAACCCCTCCA 61.435 55.000 0.00 0.00 0.00 3.86
528 532 3.181434 TGAACAAGGCTGGATAAGTGGTT 60.181 43.478 0.00 0.00 0.00 3.67
530 534 3.012518 CTGAACAAGGCTGGATAAGTGG 58.987 50.000 0.00 0.00 0.00 4.00
753 758 8.752187 GCAAGATCTCTCTCCAGATAAGAATAT 58.248 37.037 0.00 0.00 32.94 1.28
959 965 0.400213 TACCCTTGCCACTGGACAAG 59.600 55.000 18.32 18.32 42.35 3.16
1065 1071 4.023291 TGAAATATTGTTCCCCTTGAGGC 58.977 43.478 0.00 0.00 0.00 4.70
1089 1095 2.165167 CATATAGTTGCCAGCCCCATG 58.835 52.381 0.00 0.00 0.00 3.66
1102 1108 5.582950 TTCCAAATAGCCCAGCATATAGT 57.417 39.130 0.00 0.00 0.00 2.12
1279 3357 4.202243 GCAGAGCCTCATCATCTCTTTAGT 60.202 45.833 0.00 0.00 35.19 2.24
1353 4127 3.966665 TCCAAAAGGCTTCCAAATGACTT 59.033 39.130 0.00 0.00 0.00 3.01
1385 4162 3.162666 TCCAAGTGTCTTGGTATCTCGT 58.837 45.455 22.50 0.00 40.40 4.18
1421 4202 9.208022 CAGTTATGTAGAACATCAGAAAACAGA 57.792 33.333 0.00 0.00 39.88 3.41
1422 4203 8.993121 ACAGTTATGTAGAACATCAGAAAACAG 58.007 33.333 0.00 0.00 39.88 3.16
1424 4205 8.774586 ACACAGTTATGTAGAACATCAGAAAAC 58.225 33.333 0.00 0.00 39.88 2.43
1425 4206 8.902540 ACACAGTTATGTAGAACATCAGAAAA 57.097 30.769 0.00 0.00 39.88 2.29
1458 4241 2.308570 AGACCACATTACAGCCCATTCA 59.691 45.455 0.00 0.00 0.00 2.57
1459 4242 2.684881 CAGACCACATTACAGCCCATTC 59.315 50.000 0.00 0.00 0.00 2.67
1460 4243 2.308570 TCAGACCACATTACAGCCCATT 59.691 45.455 0.00 0.00 0.00 3.16
1461 4244 1.915489 TCAGACCACATTACAGCCCAT 59.085 47.619 0.00 0.00 0.00 4.00
1497 4283 0.743688 AAGCACCATCAACACGCAAA 59.256 45.000 0.00 0.00 0.00 3.68
1531 4317 0.725117 CAATCGAAACGCCCACTACC 59.275 55.000 0.00 0.00 0.00 3.18
1555 4341 2.116125 GGAAACCTGCTGTGGGCT 59.884 61.111 0.00 0.00 42.39 5.19
1578 4364 4.041444 AGAGGAAAAGTGAGATCAAGCACT 59.959 41.667 9.31 9.31 46.59 4.40
1597 4383 4.321230 CCGAATTCAAACAAGGGAAAGAGG 60.321 45.833 6.22 0.00 0.00 3.69
1599 4385 4.465886 TCCGAATTCAAACAAGGGAAAGA 58.534 39.130 6.22 0.00 0.00 2.52
1641 4427 6.992123 GGCTAATCCCCTTTCCATTAAAAATG 59.008 38.462 0.00 0.00 0.00 2.32
1775 4571 7.011950 TCTGCCTATGTGAACATATTTAAACCG 59.988 37.037 3.70 0.00 38.09 4.44
1810 4606 7.274904 TGACGTAAAATGTCTAACTAGCATGAC 59.725 37.037 0.00 0.00 35.24 3.06
1865 4661 6.245408 AGTGGATTGAAGTTTTAGTATGGCA 58.755 36.000 0.00 0.00 0.00 4.92
1873 4669 5.003804 GCTGGAGAGTGGATTGAAGTTTTA 58.996 41.667 0.00 0.00 0.00 1.52
1885 4681 4.087892 CGGGGTGCTGGAGAGTGG 62.088 72.222 0.00 0.00 0.00 4.00
1888 4684 3.965539 CTTGCGGGGTGCTGGAGAG 62.966 68.421 0.00 0.00 46.63 3.20
1894 4690 4.892965 TTGTGCTTGCGGGGTGCT 62.893 61.111 0.00 0.00 46.63 4.40
1900 4696 3.058293 TCTCTTGTAAATTGTGCTTGCGG 60.058 43.478 0.00 0.00 0.00 5.69
1904 4700 4.515191 TCGCTTCTCTTGTAAATTGTGCTT 59.485 37.500 0.00 0.00 0.00 3.91
1916 4712 0.166161 TCGACGACTCGCTTCTCTTG 59.834 55.000 0.00 0.00 39.96 3.02
1917 4713 0.444651 CTCGACGACTCGCTTCTCTT 59.555 55.000 0.00 0.00 39.96 2.85
1918 4714 0.390078 TCTCGACGACTCGCTTCTCT 60.390 55.000 0.00 0.00 39.96 3.10
1972 4913 6.299805 AGACATACCTTCTCTGTAATTGCA 57.700 37.500 0.00 0.00 0.00 4.08
2009 4950 8.815565 TTGGCCACTTAATTTTGATAGTATCA 57.184 30.769 3.88 8.84 37.55 2.15
2033 4974 2.678479 GCCCGGGGCGAAAATTTAATTT 60.678 45.455 24.63 0.00 39.62 1.82
2036 4977 1.891616 GCCCGGGGCGAAAATTTAA 59.108 52.632 24.63 0.00 39.62 1.52
2056 4998 0.394352 CCCGGTCCTGAGATTTTGGG 60.394 60.000 0.00 0.00 0.00 4.12
2080 5022 4.953868 CCCAACGCACGACACCGA 62.954 66.667 0.00 0.00 39.50 4.69
2082 5024 3.645975 CACCCAACGCACGACACC 61.646 66.667 0.00 0.00 0.00 4.16
2083 5025 3.645975 CCACCCAACGCACGACAC 61.646 66.667 0.00 0.00 0.00 3.67
2084 5026 3.683966 AACCACCCAACGCACGACA 62.684 57.895 0.00 0.00 0.00 4.35
2085 5027 2.898343 AACCACCCAACGCACGAC 60.898 61.111 0.00 0.00 0.00 4.34
2086 5028 2.897846 CAACCACCCAACGCACGA 60.898 61.111 0.00 0.00 0.00 4.35
2087 5029 3.959975 CCAACCACCCAACGCACG 61.960 66.667 0.00 0.00 0.00 5.34
2088 5030 2.419739 AACCAACCACCCAACGCAC 61.420 57.895 0.00 0.00 0.00 5.34
2089 5031 2.043852 AACCAACCACCCAACGCA 60.044 55.556 0.00 0.00 0.00 5.24
2090 5032 1.102222 TACAACCAACCACCCAACGC 61.102 55.000 0.00 0.00 0.00 4.84
2091 5033 1.268352 CATACAACCAACCACCCAACG 59.732 52.381 0.00 0.00 0.00 4.10
2092 5034 1.000394 GCATACAACCAACCACCCAAC 60.000 52.381 0.00 0.00 0.00 3.77
2093 5035 1.333177 GCATACAACCAACCACCCAA 58.667 50.000 0.00 0.00 0.00 4.12
2094 5036 0.186143 TGCATACAACCAACCACCCA 59.814 50.000 0.00 0.00 0.00 4.51
2095 5037 1.204467 CATGCATACAACCAACCACCC 59.796 52.381 0.00 0.00 0.00 4.61
2096 5038 2.166829 TCATGCATACAACCAACCACC 58.833 47.619 0.00 0.00 0.00 4.61
2097 5039 3.487376 CGATCATGCATACAACCAACCAC 60.487 47.826 0.00 0.00 0.00 4.16
2098 5040 2.682352 CGATCATGCATACAACCAACCA 59.318 45.455 0.00 0.00 0.00 3.67
2099 5041 2.682856 ACGATCATGCATACAACCAACC 59.317 45.455 0.00 0.00 0.00 3.77
2100 5042 4.097714 CAACGATCATGCATACAACCAAC 58.902 43.478 0.00 0.00 0.00 3.77
2101 5043 3.427368 GCAACGATCATGCATACAACCAA 60.427 43.478 13.94 0.00 43.29 3.67
2102 5044 2.097304 GCAACGATCATGCATACAACCA 59.903 45.455 13.94 0.00 43.29 3.67
2103 5045 2.355756 AGCAACGATCATGCATACAACC 59.644 45.455 19.29 0.00 46.22 3.77
2104 5046 3.680642 AGCAACGATCATGCATACAAC 57.319 42.857 19.29 0.00 46.22 3.32
2105 5047 4.700268 AAAGCAACGATCATGCATACAA 57.300 36.364 19.29 0.00 46.22 2.41
2106 5048 7.671495 ATATAAAGCAACGATCATGCATACA 57.329 32.000 19.29 5.40 46.22 2.29
2124 5066 5.644636 CCTTTCGCCCCGCTTTATATATAAA 59.355 40.000 15.47 15.47 0.00 1.40
2125 5067 5.180271 CCTTTCGCCCCGCTTTATATATAA 58.820 41.667 0.81 0.81 0.00 0.98
2126 5068 4.761975 CCTTTCGCCCCGCTTTATATATA 58.238 43.478 0.00 0.00 0.00 0.86
2127 5069 3.606687 CCTTTCGCCCCGCTTTATATAT 58.393 45.455 0.00 0.00 0.00 0.86
2128 5070 2.872842 GCCTTTCGCCCCGCTTTATATA 60.873 50.000 0.00 0.00 0.00 0.86
2129 5071 1.892209 CCTTTCGCCCCGCTTTATAT 58.108 50.000 0.00 0.00 0.00 0.86
2130 5072 0.816421 GCCTTTCGCCCCGCTTTATA 60.816 55.000 0.00 0.00 0.00 0.98
2131 5073 2.119029 GCCTTTCGCCCCGCTTTAT 61.119 57.895 0.00 0.00 0.00 1.40
2132 5074 2.748647 GCCTTTCGCCCCGCTTTA 60.749 61.111 0.00 0.00 0.00 1.85
2133 5075 4.660938 AGCCTTTCGCCCCGCTTT 62.661 61.111 0.00 0.00 38.78 3.51
2134 5076 4.660938 AAGCCTTTCGCCCCGCTT 62.661 61.111 0.00 0.00 38.78 4.68
2135 5077 4.660938 AAAGCCTTTCGCCCCGCT 62.661 61.111 0.00 0.00 38.78 5.52
2136 5078 3.220999 AAAAAGCCTTTCGCCCCGC 62.221 57.895 0.00 0.00 38.78 6.13
2137 5079 1.080772 GAAAAAGCCTTTCGCCCCG 60.081 57.895 0.00 0.00 38.78 5.73
2138 5080 1.080772 CGAAAAAGCCTTTCGCCCC 60.081 57.895 15.72 0.00 43.52 5.80
2139 5081 1.080772 CCGAAAAAGCCTTTCGCCC 60.081 57.895 20.34 0.00 46.89 6.13
2140 5082 0.876399 TACCGAAAAAGCCTTTCGCC 59.124 50.000 20.34 0.00 46.89 5.54
2141 5083 2.031420 ACTTACCGAAAAAGCCTTTCGC 60.031 45.455 20.34 0.00 46.89 4.70
2143 5085 3.317149 ACCACTTACCGAAAAAGCCTTTC 59.683 43.478 0.00 0.00 0.00 2.62
2144 5086 3.293337 ACCACTTACCGAAAAAGCCTTT 58.707 40.909 0.00 0.00 0.00 3.11
2145 5087 2.882761 GACCACTTACCGAAAAAGCCTT 59.117 45.455 0.00 0.00 0.00 4.35
2146 5088 2.501261 GACCACTTACCGAAAAAGCCT 58.499 47.619 0.00 0.00 0.00 4.58
2147 5089 1.538512 GGACCACTTACCGAAAAAGCC 59.461 52.381 0.00 0.00 0.00 4.35
2148 5090 2.223745 TGGACCACTTACCGAAAAAGC 58.776 47.619 0.00 0.00 0.00 3.51
2149 5091 3.735591 TCTGGACCACTTACCGAAAAAG 58.264 45.455 0.00 0.00 0.00 2.27
2150 5092 3.842007 TCTGGACCACTTACCGAAAAA 57.158 42.857 0.00 0.00 0.00 1.94
2151 5093 3.135167 AGTTCTGGACCACTTACCGAAAA 59.865 43.478 0.00 0.00 0.00 2.29
2152 5094 2.701951 AGTTCTGGACCACTTACCGAAA 59.298 45.455 0.00 0.00 0.00 3.46
2153 5095 2.322658 AGTTCTGGACCACTTACCGAA 58.677 47.619 0.00 0.00 0.00 4.30
2154 5096 2.005370 AGTTCTGGACCACTTACCGA 57.995 50.000 0.00 0.00 0.00 4.69
2155 5097 3.947910 TTAGTTCTGGACCACTTACCG 57.052 47.619 0.00 0.00 0.00 4.02
2156 5098 3.939592 GCATTAGTTCTGGACCACTTACC 59.060 47.826 0.00 0.00 0.00 2.85
2157 5099 4.833390 AGCATTAGTTCTGGACCACTTAC 58.167 43.478 0.00 0.00 0.00 2.34
2158 5100 4.777896 AGAGCATTAGTTCTGGACCACTTA 59.222 41.667 0.00 0.00 33.72 2.24
2159 5101 3.584848 AGAGCATTAGTTCTGGACCACTT 59.415 43.478 0.00 0.00 33.72 3.16
2160 5102 3.055530 CAGAGCATTAGTTCTGGACCACT 60.056 47.826 0.00 0.00 45.92 4.00
2161 5103 3.265791 CAGAGCATTAGTTCTGGACCAC 58.734 50.000 0.00 0.00 45.92 4.16
2162 5104 3.616956 CAGAGCATTAGTTCTGGACCA 57.383 47.619 0.00 0.00 45.92 4.02
2168 5110 9.160496 CTTATCTCAAAACAGAGCATTAGTTCT 57.840 33.333 0.00 0.00 35.51 3.01
2169 5111 9.155975 TCTTATCTCAAAACAGAGCATTAGTTC 57.844 33.333 0.00 0.00 35.59 3.01
2170 5112 9.507329 TTCTTATCTCAAAACAGAGCATTAGTT 57.493 29.630 0.00 0.00 35.59 2.24
2171 5113 9.160496 CTTCTTATCTCAAAACAGAGCATTAGT 57.840 33.333 0.00 0.00 35.59 2.24
2172 5114 9.376075 TCTTCTTATCTCAAAACAGAGCATTAG 57.624 33.333 0.00 0.00 35.59 1.73
2173 5115 9.376075 CTCTTCTTATCTCAAAACAGAGCATTA 57.624 33.333 0.00 0.00 35.59 1.90
2174 5116 7.336427 CCTCTTCTTATCTCAAAACAGAGCATT 59.664 37.037 0.00 0.00 35.59 3.56
2175 5117 6.822676 CCTCTTCTTATCTCAAAACAGAGCAT 59.177 38.462 0.00 0.00 35.59 3.79
2176 5118 6.169094 CCTCTTCTTATCTCAAAACAGAGCA 58.831 40.000 0.00 0.00 35.59 4.26
2177 5119 5.584251 CCCTCTTCTTATCTCAAAACAGAGC 59.416 44.000 0.00 0.00 35.59 4.09
2178 5120 6.816140 GTCCCTCTTCTTATCTCAAAACAGAG 59.184 42.308 0.00 0.00 36.97 3.35
2179 5121 6.270000 TGTCCCTCTTCTTATCTCAAAACAGA 59.730 38.462 0.00 0.00 0.00 3.41
2180 5122 6.467677 TGTCCCTCTTCTTATCTCAAAACAG 58.532 40.000 0.00 0.00 0.00 3.16
2181 5123 6.270000 TCTGTCCCTCTTCTTATCTCAAAACA 59.730 38.462 0.00 0.00 0.00 2.83
2182 5124 6.702329 TCTGTCCCTCTTCTTATCTCAAAAC 58.298 40.000 0.00 0.00 0.00 2.43
2183 5125 6.935240 TCTGTCCCTCTTCTTATCTCAAAA 57.065 37.500 0.00 0.00 0.00 2.44
2184 5126 7.502060 AATCTGTCCCTCTTCTTATCTCAAA 57.498 36.000 0.00 0.00 0.00 2.69
2185 5127 8.609617 TTAATCTGTCCCTCTTCTTATCTCAA 57.390 34.615 0.00 0.00 0.00 3.02
2186 5128 8.789767 ATTAATCTGTCCCTCTTCTTATCTCA 57.210 34.615 0.00 0.00 0.00 3.27
2189 5131 9.796120 CGATATTAATCTGTCCCTCTTCTTATC 57.204 37.037 0.00 0.00 0.00 1.75
2190 5132 8.754080 CCGATATTAATCTGTCCCTCTTCTTAT 58.246 37.037 0.00 0.00 0.00 1.73
2191 5133 7.728981 ACCGATATTAATCTGTCCCTCTTCTTA 59.271 37.037 0.00 0.00 0.00 2.10
2192 5134 6.555360 ACCGATATTAATCTGTCCCTCTTCTT 59.445 38.462 0.00 0.00 0.00 2.52
2193 5135 6.015010 CACCGATATTAATCTGTCCCTCTTCT 60.015 42.308 0.00 0.00 28.10 2.85
2194 5136 6.159988 CACCGATATTAATCTGTCCCTCTTC 58.840 44.000 0.00 0.00 28.10 2.87
2195 5137 5.511545 GCACCGATATTAATCTGTCCCTCTT 60.512 44.000 0.00 0.00 28.10 2.85
2196 5138 4.021016 GCACCGATATTAATCTGTCCCTCT 60.021 45.833 0.00 0.00 28.10 3.69
2197 5139 4.021016 AGCACCGATATTAATCTGTCCCTC 60.021 45.833 0.00 0.00 28.10 4.30
2198 5140 3.904339 AGCACCGATATTAATCTGTCCCT 59.096 43.478 0.00 0.00 28.10 4.20
2199 5141 3.997021 CAGCACCGATATTAATCTGTCCC 59.003 47.826 0.00 0.00 28.10 4.46
2200 5142 3.997021 CCAGCACCGATATTAATCTGTCC 59.003 47.826 0.00 0.00 28.10 4.02
2201 5143 3.433615 GCCAGCACCGATATTAATCTGTC 59.566 47.826 0.00 0.00 28.10 3.51
2202 5144 3.181455 TGCCAGCACCGATATTAATCTGT 60.181 43.478 0.00 0.00 30.46 3.41
2203 5145 3.402110 TGCCAGCACCGATATTAATCTG 58.598 45.455 0.00 0.00 0.00 2.90
2204 5146 3.769739 TGCCAGCACCGATATTAATCT 57.230 42.857 0.00 0.00 0.00 2.40
2205 5147 5.643777 ACTTATGCCAGCACCGATATTAATC 59.356 40.000 0.00 0.00 0.00 1.75
2206 5148 5.560724 ACTTATGCCAGCACCGATATTAAT 58.439 37.500 0.00 0.00 0.00 1.40
2207 5149 4.968259 ACTTATGCCAGCACCGATATTAA 58.032 39.130 0.00 0.00 0.00 1.40
2208 5150 4.617253 ACTTATGCCAGCACCGATATTA 57.383 40.909 0.00 0.00 0.00 0.98
2209 5151 3.492102 ACTTATGCCAGCACCGATATT 57.508 42.857 0.00 0.00 0.00 1.28
2210 5152 4.283467 TCTTACTTATGCCAGCACCGATAT 59.717 41.667 0.00 0.00 0.00 1.63
2211 5153 3.639561 TCTTACTTATGCCAGCACCGATA 59.360 43.478 0.00 0.00 0.00 2.92
2212 5154 2.434336 TCTTACTTATGCCAGCACCGAT 59.566 45.455 0.00 0.00 0.00 4.18
2213 5155 1.828595 TCTTACTTATGCCAGCACCGA 59.171 47.619 0.00 0.00 0.00 4.69
2214 5156 2.309528 TCTTACTTATGCCAGCACCG 57.690 50.000 0.00 0.00 0.00 4.94
2215 5157 3.610911 ACTTCTTACTTATGCCAGCACC 58.389 45.455 0.00 0.00 0.00 5.01
2216 5158 4.938226 AGAACTTCTTACTTATGCCAGCAC 59.062 41.667 0.00 0.00 0.00 4.40
2217 5159 5.165961 AGAACTTCTTACTTATGCCAGCA 57.834 39.130 0.00 0.00 0.00 4.41
2218 5160 5.235401 GCTAGAACTTCTTACTTATGCCAGC 59.765 44.000 0.00 0.00 0.00 4.85
2219 5161 6.341316 TGCTAGAACTTCTTACTTATGCCAG 58.659 40.000 0.00 0.00 0.00 4.85
2220 5162 6.294361 TGCTAGAACTTCTTACTTATGCCA 57.706 37.500 0.00 0.00 0.00 4.92
2221 5163 7.611213 TTTGCTAGAACTTCTTACTTATGCC 57.389 36.000 0.00 0.00 0.00 4.40
2222 5164 8.722394 ACTTTTGCTAGAACTTCTTACTTATGC 58.278 33.333 0.00 0.00 0.00 3.14
2225 5167 9.609346 ACAACTTTTGCTAGAACTTCTTACTTA 57.391 29.630 0.00 0.00 0.00 2.24
2226 5168 8.507524 ACAACTTTTGCTAGAACTTCTTACTT 57.492 30.769 0.00 0.00 0.00 2.24
2227 5169 9.609346 TTACAACTTTTGCTAGAACTTCTTACT 57.391 29.630 0.00 0.00 0.00 2.24
2230 5172 8.352942 CCATTACAACTTTTGCTAGAACTTCTT 58.647 33.333 0.00 0.00 0.00 2.52
2231 5173 7.719633 TCCATTACAACTTTTGCTAGAACTTCT 59.280 33.333 0.00 0.00 0.00 2.85
2232 5174 7.871853 TCCATTACAACTTTTGCTAGAACTTC 58.128 34.615 0.00 0.00 0.00 3.01
2233 5175 7.817418 TCCATTACAACTTTTGCTAGAACTT 57.183 32.000 0.00 0.00 0.00 2.66
2234 5176 7.817418 TTCCATTACAACTTTTGCTAGAACT 57.183 32.000 0.00 0.00 0.00 3.01
2235 5177 8.865590 TTTTCCATTACAACTTTTGCTAGAAC 57.134 30.769 0.00 0.00 0.00 3.01
2236 5178 9.528018 CTTTTTCCATTACAACTTTTGCTAGAA 57.472 29.630 0.00 0.00 0.00 2.10
2237 5179 8.691797 ACTTTTTCCATTACAACTTTTGCTAGA 58.308 29.630 0.00 0.00 0.00 2.43
2238 5180 8.871686 ACTTTTTCCATTACAACTTTTGCTAG 57.128 30.769 0.00 0.00 0.00 3.42
2246 5188 9.802039 TGACCTTATACTTTTTCCATTACAACT 57.198 29.630 0.00 0.00 0.00 3.16
2248 5190 9.238368 CCTGACCTTATACTTTTTCCATTACAA 57.762 33.333 0.00 0.00 0.00 2.41
2249 5191 8.387813 ACCTGACCTTATACTTTTTCCATTACA 58.612 33.333 0.00 0.00 0.00 2.41
2250 5192 8.803397 ACCTGACCTTATACTTTTTCCATTAC 57.197 34.615 0.00 0.00 0.00 1.89
2251 5193 8.832735 AGACCTGACCTTATACTTTTTCCATTA 58.167 33.333 0.00 0.00 0.00 1.90
2252 5194 7.699878 AGACCTGACCTTATACTTTTTCCATT 58.300 34.615 0.00 0.00 0.00 3.16
2253 5195 7.182930 AGAGACCTGACCTTATACTTTTTCCAT 59.817 37.037 0.00 0.00 0.00 3.41
2254 5196 6.500751 AGAGACCTGACCTTATACTTTTTCCA 59.499 38.462 0.00 0.00 0.00 3.53
2255 5197 6.948589 AGAGACCTGACCTTATACTTTTTCC 58.051 40.000 0.00 0.00 0.00 3.13
2256 5198 7.707464 GCTAGAGACCTGACCTTATACTTTTTC 59.293 40.741 0.00 0.00 0.00 2.29
2257 5199 7.180408 TGCTAGAGACCTGACCTTATACTTTTT 59.820 37.037 0.00 0.00 0.00 1.94
2258 5200 6.668283 TGCTAGAGACCTGACCTTATACTTTT 59.332 38.462 0.00 0.00 0.00 2.27
2259 5201 6.195700 TGCTAGAGACCTGACCTTATACTTT 58.804 40.000 0.00 0.00 0.00 2.66
2260 5202 5.767670 TGCTAGAGACCTGACCTTATACTT 58.232 41.667 0.00 0.00 0.00 2.24
2261 5203 5.390087 TGCTAGAGACCTGACCTTATACT 57.610 43.478 0.00 0.00 0.00 2.12
2262 5204 6.658188 ATTGCTAGAGACCTGACCTTATAC 57.342 41.667 0.00 0.00 0.00 1.47
2263 5205 7.344612 TGAAATTGCTAGAGACCTGACCTTATA 59.655 37.037 0.00 0.00 0.00 0.98
2264 5206 6.156949 TGAAATTGCTAGAGACCTGACCTTAT 59.843 38.462 0.00 0.00 0.00 1.73
2265 5207 5.483937 TGAAATTGCTAGAGACCTGACCTTA 59.516 40.000 0.00 0.00 0.00 2.69
2266 5208 4.287067 TGAAATTGCTAGAGACCTGACCTT 59.713 41.667 0.00 0.00 0.00 3.50
2267 5209 3.840666 TGAAATTGCTAGAGACCTGACCT 59.159 43.478 0.00 0.00 0.00 3.85
2268 5210 4.207891 TGAAATTGCTAGAGACCTGACC 57.792 45.455 0.00 0.00 0.00 4.02
2269 5211 4.034975 GCATGAAATTGCTAGAGACCTGAC 59.965 45.833 0.00 0.00 39.57 3.51
2270 5212 4.194640 GCATGAAATTGCTAGAGACCTGA 58.805 43.478 0.00 0.00 39.57 3.86
2271 5213 4.548991 GCATGAAATTGCTAGAGACCTG 57.451 45.455 0.00 0.00 39.57 4.00
2281 5223 7.745015 ACAAATATTGTCAAGCATGAAATTGC 58.255 30.769 0.00 0.00 40.56 3.56
2283 5225 9.926158 TGTACAAATATTGTCAAGCATGAAATT 57.074 25.926 0.00 0.00 44.12 1.82
2284 5226 9.357652 GTGTACAAATATTGTCAAGCATGAAAT 57.642 29.630 0.00 0.00 44.12 2.17
2285 5227 8.355913 TGTGTACAAATATTGTCAAGCATGAAA 58.644 29.630 0.00 0.00 44.12 2.69
2286 5228 7.807433 GTGTGTACAAATATTGTCAAGCATGAA 59.193 33.333 0.00 0.00 44.12 2.57
2287 5229 7.040823 TGTGTGTACAAATATTGTCAAGCATGA 60.041 33.333 0.00 0.00 44.12 3.07
2288 5230 7.060979 GTGTGTGTACAAATATTGTCAAGCATG 59.939 37.037 0.00 0.00 44.12 4.06
2289 5231 7.083858 GTGTGTGTACAAATATTGTCAAGCAT 58.916 34.615 0.00 0.00 44.12 3.79
2290 5232 6.434596 GTGTGTGTACAAATATTGTCAAGCA 58.565 36.000 0.00 0.00 44.12 3.91
2291 5233 5.563751 CGTGTGTGTACAAATATTGTCAAGC 59.436 40.000 0.00 0.00 44.12 4.01
2292 5234 5.563751 GCGTGTGTGTACAAATATTGTCAAG 59.436 40.000 0.00 0.00 44.12 3.02
2293 5235 5.444983 GCGTGTGTGTACAAATATTGTCAA 58.555 37.500 0.00 0.00 44.12 3.18
2294 5236 4.376514 CGCGTGTGTGTACAAATATTGTCA 60.377 41.667 0.00 0.00 44.12 3.58
2295 5237 4.079028 CGCGTGTGTGTACAAATATTGTC 58.921 43.478 0.00 0.00 44.12 3.18
2297 5239 2.837878 GCGCGTGTGTGTACAAATATTG 59.162 45.455 8.43 0.00 38.82 1.90
2298 5240 2.473212 CGCGCGTGTGTGTACAAATATT 60.473 45.455 24.19 0.00 38.82 1.28
2299 5241 1.059979 CGCGCGTGTGTGTACAAATAT 59.940 47.619 24.19 0.00 38.82 1.28
2300 5242 0.435388 CGCGCGTGTGTGTACAAATA 59.565 50.000 24.19 0.00 38.82 1.40
2301 5243 1.203065 CGCGCGTGTGTGTACAAAT 59.797 52.632 24.19 0.00 38.82 2.32
2302 5244 2.165940 ACGCGCGTGTGTGTACAAA 61.166 52.632 37.37 0.00 38.82 2.83
2303 5245 2.582772 ACGCGCGTGTGTGTACAA 60.583 55.556 37.37 0.00 38.82 2.41
2313 5255 0.100682 ATCTCATACTTCACGCGCGT 59.899 50.000 32.73 32.73 0.00 6.01
2314 5256 0.772926 GATCTCATACTTCACGCGCG 59.227 55.000 30.96 30.96 0.00 6.86
2315 5257 0.772926 CGATCTCATACTTCACGCGC 59.227 55.000 5.73 0.00 0.00 6.86
2316 5258 2.106750 ACGATCTCATACTTCACGCG 57.893 50.000 3.53 3.53 0.00 6.01


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

AutoCloner maintained by Alex Coulton.