Multiple sequence alignment - TraesCS4A01G410900

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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 TraesCS4A01G410900 chr4A 100.000 1586 0 0 891 2476 683769209 683770794 0.000000e+00 2929.0
1 TraesCS4A01G410900 chr4A 100.000 421 0 0 1 421 683768319 683768739 0.000000e+00 778.0
2 TraesCS4A01G410900 chr4A 91.724 145 10 2 2051 2195 688269060 688268918 1.500000e-47 200.0
3 TraesCS4A01G410900 chr4A 96.552 116 4 0 2361 2476 137536960 137536845 2.510000e-45 193.0
4 TraesCS4A01G410900 chr4A 88.189 127 15 0 2350 2476 385719328 385719202 4.260000e-33 152.0
5 TraesCS4A01G410900 chr4D 91.794 1304 83 13 909 2195 477007011 477008307 0.000000e+00 1794.0
6 TraesCS4A01G410900 chr4D 93.315 359 8 8 64 421 477006271 477006614 1.310000e-142 516.0
7 TraesCS4A01G410900 chr4D 89.394 66 1 1 1 66 476884783 476884842 7.340000e-11 78.7
8 TraesCS4A01G410900 chr4B 91.621 1289 78 15 928 2195 601191936 601193215 0.000000e+00 1755.0
9 TraesCS4A01G410900 chr4B 90.988 344 14 9 79 421 601191510 601191837 4.860000e-122 448.0
10 TraesCS4A01G410900 chr4B 93.793 145 7 2 2051 2195 420713687 420713545 1.490000e-52 217.0
11 TraesCS4A01G410900 chr4B 90.476 84 7 1 2046 2129 601193993 601194075 2.600000e-20 110.0
12 TraesCS4A01G410900 chr1B 93.793 145 7 2 2051 2195 41251094 41250952 1.490000e-52 217.0
13 TraesCS4A01G410900 chr1B 93.333 120 7 1 2357 2476 377071834 377071716 2.530000e-40 176.0
14 TraesCS4A01G410900 chr1B 88.722 133 13 2 2344 2476 582910510 582910640 7.090000e-36 161.0
15 TraesCS4A01G410900 chr1B 86.207 145 13 6 2216 2358 41250901 41250762 1.530000e-32 150.0
16 TraesCS4A01G410900 chr7B 92.667 150 9 2 2046 2195 724776419 724776566 5.360000e-52 215.0
17 TraesCS4A01G410900 chr6B 93.662 142 7 2 2054 2195 165278752 165278613 6.940000e-51 211.0
18 TraesCS4A01G410900 chr6B 91.667 144 10 2 2052 2195 677435283 677435142 5.400000e-47 198.0
19 TraesCS4A01G410900 chr3A 96.667 120 4 0 2357 2476 395744513 395744394 1.500000e-47 200.0
20 TraesCS4A01G410900 chr2D 95.000 120 6 0 2357 2476 299898445 299898564 3.250000e-44 189.0
21 TraesCS4A01G410900 chr5B 92.857 126 8 1 2352 2476 534858248 534858123 5.440000e-42 182.0
22 TraesCS4A01G410900 chr6A 90.833 120 11 0 2357 2476 90084445 90084564 7.090000e-36 161.0
23 TraesCS4A01G410900 chr3D 90.000 120 12 0 2357 2476 466381006 466380887 3.300000e-34 156.0


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 TraesCS4A01G410900 chr4A 683768319 683770794 2475 False 1853.5 2929 100.000000 1 2476 2 chr4A.!!$F1 2475
1 TraesCS4A01G410900 chr4D 477006271 477008307 2036 False 1155.0 1794 92.554500 64 2195 2 chr4D.!!$F2 2131
2 TraesCS4A01G410900 chr4B 601191510 601194075 2565 False 771.0 1755 91.028333 79 2195 3 chr4B.!!$F1 2116

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
35 36 0.24912 TGCCGTATGTCCAGTCCAAG 59.751 55.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 1628 0.77681 TTCTCCCAGGCATTTCCACA 59.223 50.0 0.0 0.0 37.29 4.17 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
23 24 6.959639 ATGGAGTGAATATTTTTGCCGTAT 57.040 33.333 0.00 0.00 0.00 3.06
24 25 6.130298 TGGAGTGAATATTTTTGCCGTATG 57.870 37.500 0.00 0.00 0.00 2.39
25 26 5.650266 TGGAGTGAATATTTTTGCCGTATGT 59.350 36.000 0.00 0.00 0.00 2.29
26 27 6.183360 TGGAGTGAATATTTTTGCCGTATGTC 60.183 38.462 0.00 0.00 0.00 3.06
27 28 6.131544 AGTGAATATTTTTGCCGTATGTCC 57.868 37.500 0.00 0.00 0.00 4.02
28 29 5.650266 AGTGAATATTTTTGCCGTATGTCCA 59.350 36.000 0.00 0.00 0.00 4.02
29 30 5.971202 GTGAATATTTTTGCCGTATGTCCAG 59.029 40.000 0.00 0.00 0.00 3.86
30 31 5.650266 TGAATATTTTTGCCGTATGTCCAGT 59.350 36.000 0.00 0.00 0.00 4.00
31 32 5.751243 ATATTTTTGCCGTATGTCCAGTC 57.249 39.130 0.00 0.00 0.00 3.51
32 33 1.816074 TTTTGCCGTATGTCCAGTCC 58.184 50.000 0.00 0.00 0.00 3.85
33 34 0.687920 TTTGCCGTATGTCCAGTCCA 59.312 50.000 0.00 0.00 0.00 4.02
34 35 0.687920 TTGCCGTATGTCCAGTCCAA 59.312 50.000 0.00 0.00 0.00 3.53
35 36 0.249120 TGCCGTATGTCCAGTCCAAG 59.751 55.000 0.00 0.00 0.00 3.61
36 37 0.249398 GCCGTATGTCCAGTCCAAGT 59.751 55.000 0.00 0.00 0.00 3.16
37 38 1.739371 GCCGTATGTCCAGTCCAAGTC 60.739 57.143 0.00 0.00 0.00 3.01
38 39 1.134788 CCGTATGTCCAGTCCAAGTCC 60.135 57.143 0.00 0.00 0.00 3.85
39 40 1.548719 CGTATGTCCAGTCCAAGTCCA 59.451 52.381 0.00 0.00 0.00 4.02
40 41 2.028476 CGTATGTCCAGTCCAAGTCCAA 60.028 50.000 0.00 0.00 0.00 3.53
41 42 3.556213 CGTATGTCCAGTCCAAGTCCAAA 60.556 47.826 0.00 0.00 0.00 3.28
42 43 2.638480 TGTCCAGTCCAAGTCCAAAG 57.362 50.000 0.00 0.00 0.00 2.77
43 44 1.142870 TGTCCAGTCCAAGTCCAAAGG 59.857 52.381 0.00 0.00 0.00 3.11
44 45 1.420138 GTCCAGTCCAAGTCCAAAGGA 59.580 52.381 0.00 0.00 0.00 3.36
45 46 2.131854 TCCAGTCCAAGTCCAAAGGAA 58.868 47.619 0.00 0.00 31.38 3.36
46 47 2.512056 TCCAGTCCAAGTCCAAAGGAAA 59.488 45.455 0.00 0.00 31.38 3.13
47 48 3.140144 TCCAGTCCAAGTCCAAAGGAAAT 59.860 43.478 0.00 0.00 31.38 2.17
48 49 3.256631 CCAGTCCAAGTCCAAAGGAAATG 59.743 47.826 0.00 0.00 31.38 2.32
49 50 2.893489 AGTCCAAGTCCAAAGGAAATGC 59.107 45.455 0.00 0.00 31.38 3.56
50 51 2.627699 GTCCAAGTCCAAAGGAAATGCA 59.372 45.455 0.00 0.00 31.38 3.96
51 52 3.069443 GTCCAAGTCCAAAGGAAATGCAA 59.931 43.478 0.00 0.00 31.38 4.08
52 53 3.708631 TCCAAGTCCAAAGGAAATGCAAA 59.291 39.130 0.00 0.00 31.38 3.68
53 54 4.060205 CCAAGTCCAAAGGAAATGCAAAG 58.940 43.478 0.00 0.00 31.38 2.77
54 55 3.391506 AGTCCAAAGGAAATGCAAAGC 57.608 42.857 0.00 0.00 31.38 3.51
55 56 2.037641 AGTCCAAAGGAAATGCAAAGCC 59.962 45.455 0.00 0.00 31.38 4.35
56 57 1.347378 TCCAAAGGAAATGCAAAGCCC 59.653 47.619 0.00 0.00 0.00 5.19
57 58 1.431496 CAAAGGAAATGCAAAGCCCG 58.569 50.000 0.00 0.00 0.00 6.13
58 59 1.047801 AAAGGAAATGCAAAGCCCGT 58.952 45.000 0.00 0.00 0.00 5.28
59 60 1.047801 AAGGAAATGCAAAGCCCGTT 58.952 45.000 0.00 0.00 0.00 4.44
60 61 0.318120 AGGAAATGCAAAGCCCGTTG 59.682 50.000 0.00 0.00 0.00 4.10
61 62 0.316841 GGAAATGCAAAGCCCGTTGA 59.683 50.000 0.00 0.00 0.00 3.18
62 63 1.270041 GGAAATGCAAAGCCCGTTGAA 60.270 47.619 0.00 0.00 0.00 2.69
65 66 1.864565 ATGCAAAGCCCGTTGAAAAC 58.135 45.000 0.00 0.00 45.31 2.43
70 71 1.226746 AAGCCCGTTGAAAACTCTCG 58.773 50.000 0.00 0.00 46.99 4.04
92 93 4.544689 CCGCTGCGACGAGAGAGG 62.545 72.222 25.45 0.41 34.06 3.69
184 186 4.485834 CCGACGAATCCGGTGCGA 62.486 66.667 17.35 0.00 41.91 5.10
185 187 2.278596 CGACGAATCCGGTGCGAT 60.279 61.111 17.35 0.00 40.78 4.58
186 188 2.576893 CGACGAATCCGGTGCGATG 61.577 63.158 17.35 7.46 40.78 3.84
213 215 1.586422 GTGGTGGATCACGATGGATG 58.414 55.000 0.00 0.00 34.83 3.51
214 216 0.469494 TGGTGGATCACGATGGATGG 59.531 55.000 0.00 0.00 34.83 3.51
215 217 0.758734 GGTGGATCACGATGGATGGA 59.241 55.000 0.00 0.00 34.83 3.41
216 218 1.349026 GGTGGATCACGATGGATGGAT 59.651 52.381 0.00 0.00 34.83 3.41
234 236 2.573609 ATCGGCAGCAACGACTACCC 62.574 60.000 0.00 0.00 43.78 3.69
235 237 2.663196 GGCAGCAACGACTACCCT 59.337 61.111 0.00 0.00 0.00 4.34
236 238 1.741770 GGCAGCAACGACTACCCTG 60.742 63.158 0.00 0.00 0.00 4.45
239 241 2.436115 GCAACGACTACCCTGCCC 60.436 66.667 0.00 0.00 0.00 5.36
240 242 2.955881 GCAACGACTACCCTGCCCT 61.956 63.158 0.00 0.00 0.00 5.19
241 243 1.610554 GCAACGACTACCCTGCCCTA 61.611 60.000 0.00 0.00 0.00 3.53
315 317 2.283351 CCCGCTCCGTTTTAAATAGACG 59.717 50.000 4.32 4.32 36.61 4.18
405 407 2.024871 GTCTCCGACGCTCCATCG 59.975 66.667 0.00 0.00 39.33 3.84
907 909 4.427394 ATTCGTCGGCTGCTGATC 57.573 55.556 15.18 7.61 0.00 2.92
911 913 1.589993 CGTCGGCTGCTGATCGATT 60.590 57.895 15.18 0.00 35.35 3.34
912 914 1.815212 CGTCGGCTGCTGATCGATTG 61.815 60.000 15.18 0.00 35.35 2.67
914 916 1.522355 CGGCTGCTGATCGATTGGT 60.522 57.895 1.17 0.00 0.00 3.67
915 917 1.493950 CGGCTGCTGATCGATTGGTC 61.494 60.000 1.17 0.00 0.00 4.02
926 928 2.886587 CGATTGGTCGGTGGTTTTAC 57.113 50.000 0.00 0.00 44.00 2.01
965 967 3.386402 TGGTTTGGGGATTTGTTCTTGTC 59.614 43.478 0.00 0.00 0.00 3.18
1056 1058 2.673833 GACACCTTCGAGTACAGGTTG 58.326 52.381 3.70 3.53 40.85 3.77
1085 1087 1.152226 CCTAGCCCCTCCCGATCTT 60.152 63.158 0.00 0.00 0.00 2.40
1120 1137 1.759293 GCGGATCGCGAAACCCTAAC 61.759 60.000 23.30 11.38 44.55 2.34
1145 1162 0.390735 AACTAACACGGCCGATGTCC 60.391 55.000 35.90 0.00 0.00 4.02
1264 1281 1.997606 CCCGTAAGATCGCGTTTTCTT 59.002 47.619 19.68 19.68 43.02 2.52
1270 1287 2.577763 GATCGCGTTTTCTTGCCGGG 62.578 60.000 5.77 0.00 36.08 5.73
1273 1290 2.951458 CGTTTTCTTGCCGGGTCC 59.049 61.111 2.18 0.00 0.00 4.46
1275 1292 1.895231 GTTTTCTTGCCGGGTCCGT 60.895 57.895 2.18 0.00 37.81 4.69
1284 1301 1.437986 CCGGGTCCGTTCTCTGATC 59.562 63.158 8.67 0.00 37.81 2.92
1295 1312 4.142816 CCGTTCTCTGATCTTGCGAAATTT 60.143 41.667 0.00 0.00 0.00 1.82
1296 1313 5.385617 CGTTCTCTGATCTTGCGAAATTTT 58.614 37.500 0.00 0.00 0.00 1.82
1299 1316 4.156556 TCTCTGATCTTGCGAAATTTTGGG 59.843 41.667 7.54 0.00 0.00 4.12
1585 1603 6.667848 TGGTTTGTCTGATCAGGATCTAGTTA 59.332 38.462 22.42 0.00 38.60 2.24
1628 1646 0.776810 TTGTGGAAATGCCTGGGAGA 59.223 50.000 0.00 0.00 37.63 3.71
1647 1665 5.054477 GGAGAAACTTGCAGTGTGTTAGTA 58.946 41.667 0.00 0.00 0.00 1.82
1648 1666 5.177696 GGAGAAACTTGCAGTGTGTTAGTAG 59.822 44.000 0.00 0.00 0.00 2.57
1649 1667 5.671493 AGAAACTTGCAGTGTGTTAGTAGT 58.329 37.500 0.00 0.00 0.00 2.73
1717 1735 4.344978 TGCTGGTACTGTCTGTAGATCTT 58.655 43.478 0.00 0.00 0.00 2.40
1740 1758 5.482006 TCCTGTGATGATCTGTTAGTGTTG 58.518 41.667 0.00 0.00 0.00 3.33
1779 1797 8.561536 TGTTATCTGGTTCCTTATGATTAGGA 57.438 34.615 0.00 0.00 40.01 2.94
1786 1804 9.535170 CTGGTTCCTTATGATTAGGAGTATAGA 57.465 37.037 0.07 0.00 42.51 1.98
1822 1841 5.416952 AGTGAATCTTATGTTTGCAAGAGGG 59.583 40.000 0.00 0.00 34.43 4.30
1863 1882 1.479730 TGAGCTATGCACTGTCCAGAG 59.520 52.381 0.40 0.00 0.00 3.35
1901 1920 2.741517 TGCACGTTTGGTACATCATCAG 59.258 45.455 0.00 0.00 39.30 2.90
1903 1922 1.999735 ACGTTTGGTACATCATCAGCG 59.000 47.619 0.00 0.00 39.30 5.18
1988 2007 5.395325 GATGTCCACATCTGTTAACATCG 57.605 43.478 9.13 3.27 46.88 3.84
2016 2035 4.207165 ACTGGTTGTGACACTGCTAATTT 58.793 39.130 7.20 0.00 0.00 1.82
2017 2036 5.373222 ACTGGTTGTGACACTGCTAATTTA 58.627 37.500 7.20 0.00 0.00 1.40
2019 2038 5.373222 TGGTTGTGACACTGCTAATTTACT 58.627 37.500 7.20 0.00 0.00 2.24
2052 2081 0.543749 CCTAGGAGGAACTTGCCCTG 59.456 60.000 1.05 0.00 41.55 4.45
2062 2091 3.129287 GGAACTTGCCCTGTGTTATCATG 59.871 47.826 0.00 0.00 0.00 3.07
2065 2094 0.998928 TGCCCTGTGTTATCATGGGT 59.001 50.000 13.16 0.00 40.09 4.51
2079 2108 4.574674 TCATGGGTACTCTTGAATGCTT 57.425 40.909 8.80 0.00 0.00 3.91
2082 2111 4.487714 TGGGTACTCTTGAATGCTTAGG 57.512 45.455 0.00 0.00 0.00 2.69
2084 2113 4.288626 TGGGTACTCTTGAATGCTTAGGTT 59.711 41.667 0.00 0.00 0.00 3.50
2085 2114 5.222048 TGGGTACTCTTGAATGCTTAGGTTT 60.222 40.000 0.00 0.00 0.00 3.27
2086 2115 5.710567 GGGTACTCTTGAATGCTTAGGTTTT 59.289 40.000 0.00 0.00 0.00 2.43
2091 2120 8.409358 ACTCTTGAATGCTTAGGTTTTTATGT 57.591 30.769 0.00 0.00 0.00 2.29
2099 2128 5.105797 TGCTTAGGTTTTTATGTGATGCTGG 60.106 40.000 0.00 0.00 0.00 4.85
2102 2131 5.897377 AGGTTTTTATGTGATGCTGGTAC 57.103 39.130 0.00 0.00 0.00 3.34
2125 2157 7.369803 ACAGTTGATAGAACTTGCTGTAATG 57.630 36.000 0.00 0.00 34.47 1.90
2132 2164 3.944015 AGAACTTGCTGTAATGATCTGCC 59.056 43.478 0.00 0.00 0.00 4.85
2135 2167 2.336945 TGCTGTAATGATCTGCCAGG 57.663 50.000 0.00 0.00 0.00 4.45
2157 2189 4.003648 GGATGTTGGTAGAACTTCCTGTG 58.996 47.826 10.66 0.00 39.80 3.66
2164 2196 4.021104 TGGTAGAACTTCCTGTGATGTCTG 60.021 45.833 0.00 0.00 0.00 3.51
2195 2227 9.083422 CTCACCTTTAGGATTATAGAGTGATGA 57.917 37.037 2.06 0.00 38.94 2.92
2199 2231 9.579768 CCTTTAGGATTATAGAGTGATGATTCG 57.420 37.037 0.00 0.00 37.39 3.34
2202 2234 9.914131 TTAGGATTATAGAGTGATGATTCGTTG 57.086 33.333 0.00 0.00 0.00 4.10
2204 2236 7.869937 AGGATTATAGAGTGATGATTCGTTGTG 59.130 37.037 0.00 0.00 0.00 3.33
2205 2237 7.116948 GGATTATAGAGTGATGATTCGTTGTGG 59.883 40.741 0.00 0.00 0.00 4.17
2215 2299 1.234821 TTCGTTGTGGATGCACTTCC 58.765 50.000 18.75 0.00 36.24 3.46
2227 2311 3.540314 TGCACTTCCTTTTGCATGTTT 57.460 38.095 0.00 0.00 43.79 2.83
2228 2312 3.196463 TGCACTTCCTTTTGCATGTTTG 58.804 40.909 0.00 0.00 43.79 2.93
2229 2313 2.545106 GCACTTCCTTTTGCATGTTTGG 59.455 45.455 0.00 0.00 38.68 3.28
2232 2316 4.744631 CACTTCCTTTTGCATGTTTGGTAC 59.255 41.667 0.00 0.00 0.00 3.34
2233 2317 4.404073 ACTTCCTTTTGCATGTTTGGTACA 59.596 37.500 0.00 0.00 41.97 2.90
2235 2319 5.132897 TCCTTTTGCATGTTTGGTACATC 57.867 39.130 0.00 0.00 45.71 3.06
2236 2320 4.586421 TCCTTTTGCATGTTTGGTACATCA 59.414 37.500 0.00 0.00 45.71 3.07
2237 2321 5.069648 TCCTTTTGCATGTTTGGTACATCAA 59.930 36.000 0.00 0.00 45.71 2.57
2238 2322 5.177327 CCTTTTGCATGTTTGGTACATCAAC 59.823 40.000 0.00 0.00 45.71 3.18
2239 2323 3.932545 TGCATGTTTGGTACATCAACC 57.067 42.857 0.00 0.00 45.71 3.77
2240 2324 3.225940 TGCATGTTTGGTACATCAACCA 58.774 40.909 0.00 0.00 45.71 3.67
2263 2347 2.360165 CCTTGGATGGTTAGCATGAAGC 59.640 50.000 0.19 0.00 46.19 3.86
2275 2359 2.926165 GCATGAAGCAGTCAGTGTTTC 58.074 47.619 2.18 2.18 44.50 2.78
2281 2365 1.672881 AGCAGTCAGTGTTTCTTGTGC 59.327 47.619 0.00 0.00 0.00 4.57
2301 2385 2.688507 CGCTGTTGAATGTCCAGTACT 58.311 47.619 0.00 0.00 0.00 2.73
2302 2386 2.413112 CGCTGTTGAATGTCCAGTACTG 59.587 50.000 16.34 16.34 0.00 2.74
2304 2388 3.433615 GCTGTTGAATGTCCAGTACTGTC 59.566 47.826 21.18 12.09 0.00 3.51
2305 2389 4.800914 GCTGTTGAATGTCCAGTACTGTCT 60.801 45.833 21.18 0.97 0.00 3.41
2309 2393 6.929049 TGTTGAATGTCCAGTACTGTCTTAAG 59.071 38.462 21.18 5.25 0.00 1.85
2316 2400 6.497259 TGTCCAGTACTGTCTTAAGATTTCCT 59.503 38.462 21.18 0.00 0.00 3.36
2318 2402 8.192110 GTCCAGTACTGTCTTAAGATTTCCTAG 58.808 40.741 21.18 3.87 0.00 3.02
2335 2419 3.255888 TCCTAGGCTATATTGCTGTCACG 59.744 47.826 2.96 0.00 0.00 4.35
2337 2421 2.039418 AGGCTATATTGCTGTCACGGA 58.961 47.619 9.02 0.00 0.00 4.69
2338 2422 2.036475 AGGCTATATTGCTGTCACGGAG 59.964 50.000 9.02 0.00 0.00 4.63
2353 2437 4.569564 GTCACGGAGAGTAAAAACAACTGT 59.430 41.667 0.00 0.00 0.00 3.55
2354 2438 5.064325 GTCACGGAGAGTAAAAACAACTGTT 59.936 40.000 0.00 0.00 40.50 3.16
2355 2439 5.292589 TCACGGAGAGTAAAAACAACTGTTC 59.707 40.000 0.00 0.00 37.25 3.18
2356 2440 5.064198 CACGGAGAGTAAAAACAACTGTTCA 59.936 40.000 0.00 0.00 37.25 3.18
2357 2441 5.293569 ACGGAGAGTAAAAACAACTGTTCAG 59.706 40.000 0.00 0.00 37.25 3.02
2358 2442 5.277345 CGGAGAGTAAAAACAACTGTTCAGG 60.277 44.000 4.82 0.00 37.25 3.86
2359 2443 5.500645 AGAGTAAAAACAACTGTTCAGGC 57.499 39.130 4.82 0.00 37.25 4.85
2360 2444 4.338400 AGAGTAAAAACAACTGTTCAGGCC 59.662 41.667 0.00 0.00 37.25 5.19
2362 2446 1.119684 AAAACAACTGTTCAGGCCCC 58.880 50.000 0.00 0.00 37.25 5.80
2364 2448 2.113139 CAACTGTTCAGGCCCCGT 59.887 61.111 0.00 0.00 0.00 5.28
2365 2449 1.528309 CAACTGTTCAGGCCCCGTT 60.528 57.895 0.00 0.00 0.00 4.44
2367 2451 1.106944 AACTGTTCAGGCCCCGTTTG 61.107 55.000 0.00 0.00 0.00 2.93
2368 2452 1.228124 CTGTTCAGGCCCCGTTTGA 60.228 57.895 0.00 0.00 0.00 2.69
2371 2455 1.339631 TGTTCAGGCCCCGTTTGATAG 60.340 52.381 0.00 0.00 0.00 2.08
2372 2456 0.393808 TTCAGGCCCCGTTTGATAGC 60.394 55.000 0.00 0.00 0.00 2.97
2373 2457 1.077787 CAGGCCCCGTTTGATAGCA 60.078 57.895 0.00 0.00 0.00 3.49
2375 2459 0.039035 AGGCCCCGTTTGATAGCAAA 59.961 50.000 1.13 1.13 41.47 3.68
2376 2460 0.455815 GGCCCCGTTTGATAGCAAAG 59.544 55.000 6.36 1.51 44.12 2.77
2377 2461 1.173913 GCCCCGTTTGATAGCAAAGT 58.826 50.000 6.36 0.00 44.12 2.66
2378 2462 2.361789 GCCCCGTTTGATAGCAAAGTA 58.638 47.619 6.36 0.00 44.12 2.24
2381 2465 4.142249 GCCCCGTTTGATAGCAAAGTATTT 60.142 41.667 6.36 0.00 44.12 1.40
2383 2467 6.033966 CCCCGTTTGATAGCAAAGTATTTTC 58.966 40.000 6.36 0.00 44.12 2.29
2384 2468 6.127730 CCCCGTTTGATAGCAAAGTATTTTCT 60.128 38.462 6.36 0.00 44.12 2.52
2387 2471 9.834628 CCGTTTGATAGCAAAGTATTTTCTAAA 57.165 29.630 6.36 0.00 44.12 1.85
2408 2492 9.066892 TCTAAACATTTTGAGAATACTGCAGTT 57.933 29.630 27.06 7.94 0.00 3.16
2410 2494 8.947055 AAACATTTTGAGAATACTGCAGTTTT 57.053 26.923 27.06 23.44 0.00 2.43
2411 2495 8.947055 AACATTTTGAGAATACTGCAGTTTTT 57.053 26.923 27.06 18.80 0.00 1.94
2412 2496 8.356533 ACATTTTGAGAATACTGCAGTTTTTG 57.643 30.769 27.06 17.34 0.00 2.44
2420 2504 9.937175 GAGAATACTGCAGTTTTTGATATTACC 57.063 33.333 27.06 7.95 0.00 2.85
2421 2505 9.461312 AGAATACTGCAGTTTTTGATATTACCA 57.539 29.630 27.06 1.00 0.00 3.25
2444 2528 9.243105 ACCATAGTTTTATTTACAATGAGCTGT 57.757 29.630 0.00 0.00 0.00 4.40
2449 2533 8.730680 AGTTTTATTTACAATGAGCTGTTCGAT 58.269 29.630 0.00 0.00 0.00 3.59
2452 2536 2.907910 ACAATGAGCTGTTCGATTGC 57.092 45.000 0.00 0.00 32.36 3.56
2453 2537 1.470098 ACAATGAGCTGTTCGATTGCC 59.530 47.619 0.00 0.00 32.36 4.52
2455 2539 1.709147 ATGAGCTGTTCGATTGCCGC 61.709 55.000 0.00 0.00 38.37 6.53
2457 2541 1.639298 GAGCTGTTCGATTGCCGCTT 61.639 55.000 0.00 0.00 38.37 4.68
2458 2542 0.391130 AGCTGTTCGATTGCCGCTTA 60.391 50.000 0.00 0.00 38.37 3.09
2459 2543 0.446222 GCTGTTCGATTGCCGCTTAA 59.554 50.000 0.00 0.00 38.37 1.85
2460 2544 1.135803 GCTGTTCGATTGCCGCTTAAA 60.136 47.619 0.00 0.00 38.37 1.52
2461 2545 2.667171 GCTGTTCGATTGCCGCTTAAAA 60.667 45.455 0.00 0.00 38.37 1.52
2462 2546 2.908626 CTGTTCGATTGCCGCTTAAAAC 59.091 45.455 0.00 0.00 38.37 2.43
2463 2547 2.550606 TGTTCGATTGCCGCTTAAAACT 59.449 40.909 0.00 0.00 38.37 2.66
2464 2548 2.892373 TCGATTGCCGCTTAAAACTG 57.108 45.000 0.00 0.00 38.37 3.16
2465 2549 2.147958 TCGATTGCCGCTTAAAACTGT 58.852 42.857 0.00 0.00 38.37 3.55
2466 2550 2.550606 TCGATTGCCGCTTAAAACTGTT 59.449 40.909 0.00 0.00 38.37 3.16
2467 2551 2.656422 CGATTGCCGCTTAAAACTGTTG 59.344 45.455 0.00 0.00 0.00 3.33
2470 2554 8.811913 TCGATTGCCGCTTAAAACTGTTGTTT 62.812 38.462 0.00 0.00 41.99 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.321181 ACATACGGCAAAAATATTCACTCCAT 59.679 34.615 0.00 0.00 0.00 3.41
1 2 5.650266 ACATACGGCAAAAATATTCACTCCA 59.350 36.000 0.00 0.00 0.00 3.86
2 3 6.131544 ACATACGGCAAAAATATTCACTCC 57.868 37.500 0.00 0.00 0.00 3.85
3 4 6.183360 TGGACATACGGCAAAAATATTCACTC 60.183 38.462 0.00 0.00 0.00 3.51
4 5 5.650266 TGGACATACGGCAAAAATATTCACT 59.350 36.000 0.00 0.00 0.00 3.41
5 6 5.885881 TGGACATACGGCAAAAATATTCAC 58.114 37.500 0.00 0.00 0.00 3.18
6 7 5.650266 ACTGGACATACGGCAAAAATATTCA 59.350 36.000 0.00 0.00 0.00 2.57
7 8 6.131544 ACTGGACATACGGCAAAAATATTC 57.868 37.500 0.00 0.00 0.00 1.75
8 9 5.067283 GGACTGGACATACGGCAAAAATATT 59.933 40.000 0.00 0.00 0.00 1.28
9 10 4.578928 GGACTGGACATACGGCAAAAATAT 59.421 41.667 0.00 0.00 0.00 1.28
10 11 3.942748 GGACTGGACATACGGCAAAAATA 59.057 43.478 0.00 0.00 0.00 1.40
11 12 2.752903 GGACTGGACATACGGCAAAAAT 59.247 45.455 0.00 0.00 0.00 1.82
12 13 2.156098 GGACTGGACATACGGCAAAAA 58.844 47.619 0.00 0.00 0.00 1.94
13 14 1.072489 TGGACTGGACATACGGCAAAA 59.928 47.619 0.00 0.00 0.00 2.44
14 15 0.687920 TGGACTGGACATACGGCAAA 59.312 50.000 0.00 0.00 0.00 3.68
15 16 0.687920 TTGGACTGGACATACGGCAA 59.312 50.000 0.00 0.00 0.00 4.52
16 17 0.249120 CTTGGACTGGACATACGGCA 59.751 55.000 0.00 0.00 0.00 5.69
17 18 0.249398 ACTTGGACTGGACATACGGC 59.751 55.000 0.00 0.00 0.00 5.68
18 19 1.134788 GGACTTGGACTGGACATACGG 60.135 57.143 0.00 0.00 0.00 4.02
19 20 1.548719 TGGACTTGGACTGGACATACG 59.451 52.381 0.00 0.00 0.00 3.06
20 21 3.695830 TTGGACTTGGACTGGACATAC 57.304 47.619 0.00 0.00 0.00 2.39
21 22 3.009033 CCTTTGGACTTGGACTGGACATA 59.991 47.826 0.00 0.00 0.00 2.29
22 23 2.224867 CCTTTGGACTTGGACTGGACAT 60.225 50.000 0.00 0.00 0.00 3.06
23 24 1.142870 CCTTTGGACTTGGACTGGACA 59.857 52.381 0.00 0.00 0.00 4.02
24 25 1.420138 TCCTTTGGACTTGGACTGGAC 59.580 52.381 0.00 0.00 0.00 4.02
25 26 1.814429 TCCTTTGGACTTGGACTGGA 58.186 50.000 0.00 0.00 0.00 3.86
26 27 2.656947 TTCCTTTGGACTTGGACTGG 57.343 50.000 0.00 0.00 0.00 4.00
27 28 3.305608 GCATTTCCTTTGGACTTGGACTG 60.306 47.826 0.00 0.00 0.00 3.51
28 29 2.893489 GCATTTCCTTTGGACTTGGACT 59.107 45.455 0.00 0.00 0.00 3.85
29 30 2.627699 TGCATTTCCTTTGGACTTGGAC 59.372 45.455 0.00 0.00 0.00 4.02
30 31 2.956132 TGCATTTCCTTTGGACTTGGA 58.044 42.857 0.00 0.00 0.00 3.53
31 32 3.749665 TTGCATTTCCTTTGGACTTGG 57.250 42.857 0.00 0.00 0.00 3.61
32 33 3.495753 GCTTTGCATTTCCTTTGGACTTG 59.504 43.478 0.00 0.00 0.00 3.16
33 34 3.494924 GGCTTTGCATTTCCTTTGGACTT 60.495 43.478 0.00 0.00 0.00 3.01
34 35 2.037641 GGCTTTGCATTTCCTTTGGACT 59.962 45.455 0.00 0.00 0.00 3.85
35 36 2.416747 GGCTTTGCATTTCCTTTGGAC 58.583 47.619 0.00 0.00 0.00 4.02
36 37 1.347378 GGGCTTTGCATTTCCTTTGGA 59.653 47.619 0.00 0.00 0.00 3.53
37 38 1.812235 GGGCTTTGCATTTCCTTTGG 58.188 50.000 0.00 0.00 0.00 3.28
38 39 1.270252 ACGGGCTTTGCATTTCCTTTG 60.270 47.619 0.00 0.00 0.00 2.77
39 40 1.047801 ACGGGCTTTGCATTTCCTTT 58.952 45.000 0.00 0.00 0.00 3.11
40 41 1.047801 AACGGGCTTTGCATTTCCTT 58.952 45.000 0.00 0.00 0.00 3.36
41 42 0.318120 CAACGGGCTTTGCATTTCCT 59.682 50.000 0.00 0.00 0.00 3.36
42 43 0.316841 TCAACGGGCTTTGCATTTCC 59.683 50.000 0.00 0.00 0.00 3.13
43 44 2.147436 TTCAACGGGCTTTGCATTTC 57.853 45.000 0.00 0.00 0.00 2.17
44 45 2.611225 TTTCAACGGGCTTTGCATTT 57.389 40.000 0.00 0.00 0.00 2.32
45 46 2.158971 AGTTTTCAACGGGCTTTGCATT 60.159 40.909 0.00 0.00 36.23 3.56
46 47 1.412343 AGTTTTCAACGGGCTTTGCAT 59.588 42.857 0.00 0.00 36.23 3.96
47 48 0.820871 AGTTTTCAACGGGCTTTGCA 59.179 45.000 0.00 0.00 36.23 4.08
48 49 1.067060 AGAGTTTTCAACGGGCTTTGC 59.933 47.619 0.00 0.00 36.23 3.68
49 50 2.602217 CGAGAGTTTTCAACGGGCTTTG 60.602 50.000 0.00 0.00 36.23 2.77
50 51 1.602377 CGAGAGTTTTCAACGGGCTTT 59.398 47.619 0.00 0.00 36.23 3.51
51 52 1.226746 CGAGAGTTTTCAACGGGCTT 58.773 50.000 0.00 0.00 36.23 4.35
52 53 0.602905 CCGAGAGTTTTCAACGGGCT 60.603 55.000 0.00 0.00 39.82 5.19
53 54 1.866925 CCGAGAGTTTTCAACGGGC 59.133 57.895 0.00 0.00 39.82 6.13
54 55 0.602905 AGCCGAGAGTTTTCAACGGG 60.603 55.000 0.00 0.00 41.97 5.28
55 56 0.790814 GAGCCGAGAGTTTTCAACGG 59.209 55.000 0.00 0.00 43.37 4.44
56 57 0.790814 GGAGCCGAGAGTTTTCAACG 59.209 55.000 0.00 0.00 36.23 4.10
57 58 1.157585 GGGAGCCGAGAGTTTTCAAC 58.842 55.000 0.00 0.00 0.00 3.18
58 59 3.625745 GGGAGCCGAGAGTTTTCAA 57.374 52.632 0.00 0.00 0.00 2.69
92 93 1.265454 ACCGTTGGGTCTCCATCTCC 61.265 60.000 0.00 0.00 46.01 3.71
145 147 3.670377 GTGGGCTGGGTTTCGTGC 61.670 66.667 0.00 0.00 0.00 5.34
146 148 3.353836 CGTGGGCTGGGTTTCGTG 61.354 66.667 0.00 0.00 0.00 4.35
184 186 0.107456 GATCCACCACCTCATCGCAT 59.893 55.000 0.00 0.00 0.00 4.73
185 187 1.264045 TGATCCACCACCTCATCGCA 61.264 55.000 0.00 0.00 0.00 5.10
186 188 0.811616 GTGATCCACCACCTCATCGC 60.812 60.000 0.00 0.00 0.00 4.58
213 215 1.141019 TAGTCGTTGCTGCCGATCC 59.859 57.895 4.41 0.00 36.62 3.36
214 216 1.146358 GGTAGTCGTTGCTGCCGATC 61.146 60.000 4.41 0.13 36.62 3.69
215 217 1.153628 GGTAGTCGTTGCTGCCGAT 60.154 57.895 4.41 0.00 36.62 4.18
216 218 2.260434 GGTAGTCGTTGCTGCCGA 59.740 61.111 0.00 0.00 31.90 5.54
892 894 2.004808 AATCGATCAGCAGCCGACGA 62.005 55.000 0.00 5.98 35.02 4.20
893 895 1.589993 AATCGATCAGCAGCCGACG 60.590 57.895 0.00 0.00 35.02 5.12
895 897 1.227350 CCAATCGATCAGCAGCCGA 60.227 57.895 0.00 0.00 36.72 5.54
911 913 0.033781 CCGAGTAAAACCACCGACCA 59.966 55.000 0.00 0.00 0.00 4.02
912 914 0.318120 TCCGAGTAAAACCACCGACC 59.682 55.000 0.00 0.00 0.00 4.79
914 916 3.405823 AAATCCGAGTAAAACCACCGA 57.594 42.857 0.00 0.00 0.00 4.69
915 917 4.214758 AGAAAAATCCGAGTAAAACCACCG 59.785 41.667 0.00 0.00 0.00 4.94
919 921 7.328493 CCATTTCAGAAAAATCCGAGTAAAACC 59.672 37.037 0.00 0.00 0.00 3.27
920 922 7.865889 ACCATTTCAGAAAAATCCGAGTAAAAC 59.134 33.333 0.00 0.00 0.00 2.43
921 923 7.947282 ACCATTTCAGAAAAATCCGAGTAAAA 58.053 30.769 0.00 0.00 0.00 1.52
923 925 7.519032 AACCATTTCAGAAAAATCCGAGTAA 57.481 32.000 0.00 0.00 0.00 2.24
924 926 7.367285 CAAACCATTTCAGAAAAATCCGAGTA 58.633 34.615 0.00 0.00 0.00 2.59
925 927 6.215845 CAAACCATTTCAGAAAAATCCGAGT 58.784 36.000 0.00 0.00 0.00 4.18
926 928 5.634859 CCAAACCATTTCAGAAAAATCCGAG 59.365 40.000 0.00 0.00 0.00 4.63
965 967 4.637489 CTCGATCGAGGCCCTGCG 62.637 72.222 32.81 9.62 38.51 5.18
1107 1124 4.488879 AGTTAGTTAGTTAGGGTTTCGCG 58.511 43.478 0.00 0.00 0.00 5.87
1120 1137 3.492421 TCGGCCGTGTTAGTTAGTTAG 57.508 47.619 27.15 0.00 0.00 2.34
1264 1281 3.691342 CAGAGAACGGACCCGGCA 61.691 66.667 13.43 0.00 44.69 5.69
1270 1287 1.135373 TCGCAAGATCAGAGAACGGAC 60.135 52.381 0.00 0.00 45.01 4.79
1352 1369 4.323477 GCGTAGTGCACCCACCCA 62.323 66.667 14.63 0.00 45.45 4.51
1610 1628 0.776810 TTCTCCCAGGCATTTCCACA 59.223 50.000 0.00 0.00 37.29 4.17
1647 1665 8.007742 AGAGTATCCAGGATAATAACACAGACT 58.992 37.037 11.06 2.37 33.66 3.24
1648 1666 8.184304 AGAGTATCCAGGATAATAACACAGAC 57.816 38.462 11.06 0.00 33.66 3.51
1649 1667 8.642432 CAAGAGTATCCAGGATAATAACACAGA 58.358 37.037 11.06 0.00 33.66 3.41
1717 1735 5.245977 TCAACACTAACAGATCATCACAGGA 59.754 40.000 0.00 0.00 0.00 3.86
1740 1758 5.355350 ACCAGATAACAGTAAAGCAAGCATC 59.645 40.000 0.00 0.00 0.00 3.91
1786 1804 9.896645 AACATAAGATTCACTATCACATGAACT 57.103 29.630 0.00 0.00 37.64 3.01
1813 1832 2.044650 GCTCCATGCCCTCTTGCA 60.045 61.111 0.00 0.00 46.94 4.08
1822 1841 5.593968 TCATTCATAACAAATGCTCCATGC 58.406 37.500 0.00 0.00 43.25 4.06
1841 1860 2.502947 TCTGGACAGTGCATAGCTCATT 59.497 45.455 0.00 0.00 0.00 2.57
1863 1882 3.658757 TGCAAAGGAGGTGCATTTTAC 57.341 42.857 0.00 0.00 46.76 2.01
1901 1920 4.683832 ACTTCAGACTAACATGATACCGC 58.316 43.478 0.00 0.00 0.00 5.68
1903 1922 6.631016 TGTGACTTCAGACTAACATGATACC 58.369 40.000 0.00 0.00 0.00 2.73
1977 1996 3.807622 ACCAGTGTTGACGATGTTAACAG 59.192 43.478 14.65 3.88 41.38 3.16
2010 2029 6.375455 AGGCATTTCCTCACACAGTAAATTAG 59.625 38.462 0.00 0.00 43.20 1.73
2016 2035 3.197766 CCTAGGCATTTCCTCACACAGTA 59.802 47.826 0.00 0.00 43.20 2.74
2017 2036 2.026822 CCTAGGCATTTCCTCACACAGT 60.027 50.000 0.00 0.00 43.20 3.55
2019 2038 2.237143 CTCCTAGGCATTTCCTCACACA 59.763 50.000 2.96 0.00 43.20 3.72
2023 2042 2.505819 GTTCCTCCTAGGCATTTCCTCA 59.494 50.000 2.96 0.00 43.20 3.86
2036 2055 1.062488 ACACAGGGCAAGTTCCTCCT 61.062 55.000 0.00 0.00 31.06 3.69
2052 2081 6.238484 GCATTCAAGAGTACCCATGATAACAC 60.238 42.308 0.00 0.00 0.00 3.32
2062 2091 4.489306 ACCTAAGCATTCAAGAGTACCC 57.511 45.455 0.00 0.00 0.00 3.69
2065 2094 9.515226 ACATAAAAACCTAAGCATTCAAGAGTA 57.485 29.630 0.00 0.00 0.00 2.59
2079 2108 6.477253 TGTACCAGCATCACATAAAAACCTA 58.523 36.000 0.00 0.00 0.00 3.08
2082 2111 6.254281 ACTGTACCAGCATCACATAAAAAC 57.746 37.500 0.00 0.00 34.37 2.43
2084 2113 6.000840 TCAACTGTACCAGCATCACATAAAA 58.999 36.000 0.00 0.00 34.37 1.52
2085 2114 5.555966 TCAACTGTACCAGCATCACATAAA 58.444 37.500 0.00 0.00 34.37 1.40
2086 2115 5.159273 TCAACTGTACCAGCATCACATAA 57.841 39.130 0.00 0.00 34.37 1.90
2091 2120 5.187772 AGTTCTATCAACTGTACCAGCATCA 59.812 40.000 0.00 0.00 34.37 3.07
2099 2128 7.884816 TTACAGCAAGTTCTATCAACTGTAC 57.115 36.000 0.00 0.00 38.48 2.90
2102 2131 7.601073 TCATTACAGCAAGTTCTATCAACTG 57.399 36.000 0.00 0.00 0.00 3.16
2104 2133 8.333908 CAGATCATTACAGCAAGTTCTATCAAC 58.666 37.037 0.00 0.00 0.00 3.18
2106 2135 6.481313 GCAGATCATTACAGCAAGTTCTATCA 59.519 38.462 0.00 0.00 0.00 2.15
2107 2136 6.073331 GGCAGATCATTACAGCAAGTTCTATC 60.073 42.308 0.00 0.00 0.00 2.08
2108 2137 5.762218 GGCAGATCATTACAGCAAGTTCTAT 59.238 40.000 0.00 0.00 0.00 1.98
2110 2139 3.944015 GGCAGATCATTACAGCAAGTTCT 59.056 43.478 0.00 0.00 0.00 3.01
2112 2141 3.689347 TGGCAGATCATTACAGCAAGTT 58.311 40.909 0.00 0.00 0.00 2.66
2114 2143 2.617308 CCTGGCAGATCATTACAGCAAG 59.383 50.000 17.94 0.00 0.00 4.01
2115 2144 2.646930 CCTGGCAGATCATTACAGCAA 58.353 47.619 17.94 0.00 0.00 3.91
2116 2145 1.134007 CCCTGGCAGATCATTACAGCA 60.134 52.381 17.94 0.00 0.00 4.41
2117 2146 1.141657 TCCCTGGCAGATCATTACAGC 59.858 52.381 17.94 0.00 0.00 4.40
2125 2157 0.257039 ACCAACATCCCTGGCAGATC 59.743 55.000 17.94 0.00 37.48 2.75
2132 2164 3.264450 AGGAAGTTCTACCAACATCCCTG 59.736 47.826 2.25 0.00 38.43 4.45
2135 2167 4.003648 CACAGGAAGTTCTACCAACATCC 58.996 47.826 2.25 1.31 38.06 3.51
2195 2227 1.812571 GGAAGTGCATCCACAACGAAT 59.187 47.619 1.24 0.00 44.53 3.34
2197 2229 0.396435 AGGAAGTGCATCCACAACGA 59.604 50.000 9.02 0.00 44.53 3.85
2198 2230 1.238439 AAGGAAGTGCATCCACAACG 58.762 50.000 9.02 0.00 44.53 4.10
2199 2231 3.383761 CAAAAGGAAGTGCATCCACAAC 58.616 45.455 9.02 0.00 44.53 3.32
2201 2233 1.340889 GCAAAAGGAAGTGCATCCACA 59.659 47.619 9.02 0.00 44.53 4.17
2202 2234 1.340889 TGCAAAAGGAAGTGCATCCAC 59.659 47.619 9.02 0.00 45.52 4.02
2227 2311 2.870175 CCAAGGTTGGTTGATGTACCA 58.130 47.619 0.09 0.00 46.23 3.25
2228 2312 3.443681 CATCCAAGGTTGGTTGATGTACC 59.556 47.826 12.68 0.00 46.25 3.34
2229 2313 3.443681 CCATCCAAGGTTGGTTGATGTAC 59.556 47.826 17.81 0.00 46.25 2.90
2232 2316 2.528564 ACCATCCAAGGTTGGTTGATG 58.471 47.619 17.81 10.42 46.25 3.07
2233 2317 2.999185 ACCATCCAAGGTTGGTTGAT 57.001 45.000 17.81 1.62 46.25 2.57
2241 2325 3.624777 CTTCATGCTAACCATCCAAGGT 58.375 45.455 0.00 0.00 45.91 3.50
2248 2332 3.276857 CTGACTGCTTCATGCTAACCAT 58.723 45.455 0.00 0.00 43.37 3.55
2249 2333 2.038952 ACTGACTGCTTCATGCTAACCA 59.961 45.455 0.00 0.00 43.37 3.67
2250 2334 2.417933 CACTGACTGCTTCATGCTAACC 59.582 50.000 0.00 0.00 43.37 2.85
2263 2347 1.595489 GCGCACAAGAAACACTGACTG 60.595 52.381 0.30 0.00 0.00 3.51
2269 2353 1.191096 CAACAGCGCACAAGAAACAC 58.809 50.000 11.47 0.00 0.00 3.32
2275 2359 1.664016 GGACATTCAACAGCGCACAAG 60.664 52.381 11.47 0.00 0.00 3.16
2281 2365 2.413112 CAGTACTGGACATTCAACAGCG 59.587 50.000 15.49 0.00 35.70 5.18
2302 2386 9.157104 GCAATATAGCCTAGGAAATCTTAAGAC 57.843 37.037 14.75 0.00 0.00 3.01
2304 2388 9.160496 CAGCAATATAGCCTAGGAAATCTTAAG 57.840 37.037 14.75 0.00 34.23 1.85
2305 2389 8.660435 ACAGCAATATAGCCTAGGAAATCTTAA 58.340 33.333 14.75 0.00 34.23 1.85
2309 2393 6.370166 GTGACAGCAATATAGCCTAGGAAATC 59.630 42.308 14.75 0.00 34.23 2.17
2316 2400 3.227614 TCCGTGACAGCAATATAGCCTA 58.772 45.455 0.00 0.00 34.23 3.93
2318 2402 2.035961 TCTCCGTGACAGCAATATAGCC 59.964 50.000 0.00 0.00 34.23 3.93
2335 2419 5.505819 GCCTGAACAGTTGTTTTTACTCTCC 60.506 44.000 0.00 0.00 38.56 3.71
2337 2421 4.338400 GGCCTGAACAGTTGTTTTTACTCT 59.662 41.667 0.00 0.00 38.56 3.24
2338 2422 4.499188 GGGCCTGAACAGTTGTTTTTACTC 60.499 45.833 0.84 0.00 38.56 2.59
2353 2437 0.393808 GCTATCAAACGGGGCCTGAA 60.394 55.000 21.81 1.39 0.00 3.02
2354 2438 1.223487 GCTATCAAACGGGGCCTGA 59.777 57.895 21.81 7.64 0.00 3.86
2355 2439 0.679640 TTGCTATCAAACGGGGCCTG 60.680 55.000 11.83 11.83 0.00 4.85
2356 2440 0.039035 TTTGCTATCAAACGGGGCCT 59.961 50.000 0.84 0.00 37.28 5.19
2357 2441 0.455815 CTTTGCTATCAAACGGGGCC 59.544 55.000 0.00 0.00 37.28 5.80
2358 2442 1.173913 ACTTTGCTATCAAACGGGGC 58.826 50.000 0.00 0.00 37.28 5.80
2359 2443 5.576447 AAATACTTTGCTATCAAACGGGG 57.424 39.130 0.00 0.00 37.28 5.73
2360 2444 6.852664 AGAAAATACTTTGCTATCAAACGGG 58.147 36.000 0.00 0.00 37.28 5.28
2381 2465 9.066892 ACTGCAGTATTCTCAAAATGTTTAGAA 57.933 29.630 20.16 0.00 32.81 2.10
2383 2467 9.683069 AAACTGCAGTATTCTCAAAATGTTTAG 57.317 29.630 22.01 0.00 0.00 1.85
2387 2471 8.196771 TCAAAAACTGCAGTATTCTCAAAATGT 58.803 29.630 22.01 0.00 0.00 2.71
2388 2472 8.578308 TCAAAAACTGCAGTATTCTCAAAATG 57.422 30.769 22.01 7.82 0.00 2.32
2394 2478 9.937175 GGTAATATCAAAAACTGCAGTATTCTC 57.063 33.333 22.01 10.36 0.00 2.87
2395 2479 9.461312 TGGTAATATCAAAAACTGCAGTATTCT 57.539 29.630 22.01 0.19 0.00 2.40
2399 2483 9.899661 ACTATGGTAATATCAAAAACTGCAGTA 57.100 29.630 22.01 3.84 0.00 2.74
2400 2484 8.807948 ACTATGGTAATATCAAAAACTGCAGT 57.192 30.769 15.25 15.25 0.00 4.40
2418 2502 9.243105 ACAGCTCATTGTAAATAAAACTATGGT 57.757 29.630 0.00 0.00 32.95 3.55
2421 2505 9.988350 CGAACAGCTCATTGTAAATAAAACTAT 57.012 29.630 0.00 0.00 0.00 2.12
2422 2506 9.210329 TCGAACAGCTCATTGTAAATAAAACTA 57.790 29.630 0.00 0.00 0.00 2.24
2423 2507 8.094798 TCGAACAGCTCATTGTAAATAAAACT 57.905 30.769 0.00 0.00 0.00 2.66
2424 2508 8.895932 ATCGAACAGCTCATTGTAAATAAAAC 57.104 30.769 0.00 0.00 0.00 2.43
2427 2511 6.966632 GCAATCGAACAGCTCATTGTAAATAA 59.033 34.615 0.00 0.00 31.00 1.40
2428 2512 6.458206 GGCAATCGAACAGCTCATTGTAAATA 60.458 38.462 6.98 0.00 31.00 1.40
2431 2515 3.126858 GGCAATCGAACAGCTCATTGTAA 59.873 43.478 6.98 0.00 31.00 2.41
2432 2516 2.677836 GGCAATCGAACAGCTCATTGTA 59.322 45.455 6.98 0.00 31.00 2.41
2433 2517 1.470098 GGCAATCGAACAGCTCATTGT 59.530 47.619 6.98 0.00 31.00 2.71
2434 2518 1.530441 CGGCAATCGAACAGCTCATTG 60.530 52.381 6.98 0.00 42.43 2.82
2435 2519 0.729116 CGGCAATCGAACAGCTCATT 59.271 50.000 6.98 0.00 42.43 2.57
2437 2521 2.390599 GCGGCAATCGAACAGCTCA 61.391 57.895 0.00 0.00 42.43 4.26
2438 2522 1.639298 AAGCGGCAATCGAACAGCTC 61.639 55.000 1.45 2.97 42.43 4.09
2440 2524 0.446222 TTAAGCGGCAATCGAACAGC 59.554 50.000 1.45 0.00 42.43 4.40
2441 2525 2.892373 TTTAAGCGGCAATCGAACAG 57.108 45.000 1.45 0.00 42.43 3.16
2444 2528 2.550606 ACAGTTTTAAGCGGCAATCGAA 59.449 40.909 1.45 0.00 42.43 3.71
2446 2530 2.611974 ACAGTTTTAAGCGGCAATCG 57.388 45.000 1.45 0.00 42.76 3.34
2449 2533 3.512033 AACAACAGTTTTAAGCGGCAA 57.488 38.095 1.45 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.