Multiple sequence alignment - TraesCS2D01G516800

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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 TraesCS2D01G516800 chr2D 100.000 2668 0 0 1 2668 607965695 607963028 0.000000e+00 4927
1 TraesCS2D01G516800 chr2D 82.580 1969 239 50 412 2321 607942262 607940339 0.000000e+00 1640
2 TraesCS2D01G516800 chr2D 81.814 1952 295 35 405 2321 607973788 607971862 0.000000e+00 1583
3 TraesCS2D01G516800 chr2D 96.418 335 12 0 2334 2668 393213909 393214243 1.080000e-153 553
4 TraesCS2D01G516800 chr2B 93.155 2279 107 15 59 2321 741155278 741153033 0.000000e+00 3299
5 TraesCS2D01G516800 chr2B 81.668 1942 290 43 412 2315 741118739 741116826 0.000000e+00 1554
6 TraesCS2D01G516800 chr2B 79.474 1939 330 40 412 2315 741149077 741147172 0.000000e+00 1314
7 TraesCS2D01G516800 chr2B 79.059 1318 198 40 1033 2313 741022343 741021067 0.000000e+00 833
8 TraesCS2D01G516800 chr2B 77.614 1425 251 49 422 1818 741392039 741390655 0.000000e+00 802
9 TraesCS2D01G516800 chr2B 83.792 654 88 10 1677 2315 741385196 741384546 2.940000e-169 604
10 TraesCS2D01G516800 chr2B 95.370 324 15 0 2345 2668 81322245 81321922 1.420000e-142 516
11 TraesCS2D01G516800 chr2B 81.282 577 88 16 1754 2315 741390644 741390073 1.460000e-122 449
12 TraesCS2D01G516800 chr2B 90.774 336 29 2 412 747 741022729 741022396 5.240000e-122 448
13 TraesCS2D01G516800 chr2B 73.958 480 77 26 412 880 741372058 741371616 1.650000e-32 150
14 TraesCS2D01G516800 chr2A 91.003 1934 133 22 412 2321 739438698 739436782 0.000000e+00 2569
15 TraesCS2D01G516800 chr2A 75.901 1415 278 42 423 1818 739704136 739702766 0.000000e+00 665
16 TraesCS2D01G516800 chr2A 82.578 706 103 10 1623 2315 739688532 739687834 2.940000e-169 604
17 TraesCS2D01G516800 chr2A 81.942 659 104 9 412 1065 739691298 739690650 6.500000e-151 544
18 TraesCS2D01G516800 chr2A 82.669 577 80 16 1754 2315 739702755 739702184 6.630000e-136 494
19 TraesCS2D01G516800 chr2A 82.895 304 46 4 2016 2315 739451714 739451413 4.380000e-68 268
20 TraesCS2D01G516800 chr2A 82.895 152 26 0 1194 1345 739473413 739473262 1.290000e-28 137
21 TraesCS2D01G516800 chr7D 97.161 317 9 0 2352 2668 478336229 478336545 1.090000e-148 536
22 TraesCS2D01G516800 chr7D 95.611 319 14 0 2350 2668 36664235 36664553 1.830000e-141 512
23 TraesCS2D01G516800 chr3D 95.758 330 14 0 2339 2668 19544295 19544624 1.410000e-147 532
24 TraesCS2D01G516800 chr3A 93.519 324 20 1 2345 2668 728987118 728986796 5.170000e-132 481
25 TraesCS2D01G516800 chr4B 95.623 297 13 0 2369 2665 122312869 122313165 6.680000e-131 477
26 TraesCS2D01G516800 chr7A 91.667 324 24 3 2346 2668 654994560 654994239 1.880000e-121 446
27 TraesCS2D01G516800 chr6B 90.938 320 28 1 2349 2668 45521608 45521290 1.900000e-116 429


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 TraesCS2D01G516800 chr2D 607963028 607965695 2667 True 4927.0 4927 100.0000 1 2668 1 chr2D.!!$R2 2667
1 TraesCS2D01G516800 chr2D 607940339 607942262 1923 True 1640.0 1640 82.5800 412 2321 1 chr2D.!!$R1 1909
2 TraesCS2D01G516800 chr2D 607971862 607973788 1926 True 1583.0 1583 81.8140 405 2321 1 chr2D.!!$R3 1916
3 TraesCS2D01G516800 chr2B 741147172 741155278 8106 True 2306.5 3299 86.3145 59 2321 2 chr2B.!!$R6 2262
4 TraesCS2D01G516800 chr2B 741116826 741118739 1913 True 1554.0 1554 81.6680 412 2315 1 chr2B.!!$R2 1903
5 TraesCS2D01G516800 chr2B 741021067 741022729 1662 True 640.5 833 84.9165 412 2313 2 chr2B.!!$R5 1901
6 TraesCS2D01G516800 chr2B 741390073 741392039 1966 True 625.5 802 79.4480 422 2315 2 chr2B.!!$R7 1893
7 TraesCS2D01G516800 chr2B 741384546 741385196 650 True 604.0 604 83.7920 1677 2315 1 chr2B.!!$R4 638
8 TraesCS2D01G516800 chr2A 739436782 739438698 1916 True 2569.0 2569 91.0030 412 2321 1 chr2A.!!$R1 1909
9 TraesCS2D01G516800 chr2A 739702184 739704136 1952 True 579.5 665 79.2850 423 2315 2 chr2A.!!$R5 1892
10 TraesCS2D01G516800 chr2A 739687834 739691298 3464 True 574.0 604 82.2600 412 2315 2 chr2A.!!$R4 1903

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
54 55 1.004044 CTGTCCTTTCATGAGCCTGGT 59.996 52.381 0.0 0.0 0.0 4.00 F
975 999 1.070601 GGGCAAATTGTTTCACTGGCT 59.929 47.619 0.0 0.0 33.4 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1109 1150 0.169672 CAGCTGCAATGTGTGTAGGC 59.830 55.0 0.00 0.0 40.14 3.93 R
2491 10212 0.037590 CCCAAAGATCCACGGGAACA 59.962 55.0 5.19 0.0 41.62 3.18 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
24 25 7.383102 GGTGATGAATGATTAGTGAAGTTGT 57.617 36.000 0.00 0.00 0.00 3.32
25 26 8.492673 GGTGATGAATGATTAGTGAAGTTGTA 57.507 34.615 0.00 0.00 0.00 2.41
26 27 9.113838 GGTGATGAATGATTAGTGAAGTTGTAT 57.886 33.333 0.00 0.00 0.00 2.29
27 28 9.926751 GTGATGAATGATTAGTGAAGTTGTATG 57.073 33.333 0.00 0.00 0.00 2.39
28 29 9.671279 TGATGAATGATTAGTGAAGTTGTATGT 57.329 29.630 0.00 0.00 0.00 2.29
39 40 7.773149 AGTGAAGTTGTATGTATACTCTGTCC 58.227 38.462 4.17 0.00 34.41 4.02
40 41 7.616150 AGTGAAGTTGTATGTATACTCTGTCCT 59.384 37.037 4.17 0.00 34.41 3.85
41 42 8.251721 GTGAAGTTGTATGTATACTCTGTCCTT 58.748 37.037 4.17 0.46 34.41 3.36
42 43 8.812972 TGAAGTTGTATGTATACTCTGTCCTTT 58.187 33.333 4.17 0.00 34.41 3.11
43 44 9.303537 GAAGTTGTATGTATACTCTGTCCTTTC 57.696 37.037 4.17 0.00 34.41 2.62
44 45 8.362464 AGTTGTATGTATACTCTGTCCTTTCA 57.638 34.615 4.17 0.00 34.41 2.69
45 46 8.982723 AGTTGTATGTATACTCTGTCCTTTCAT 58.017 33.333 4.17 0.00 34.41 2.57
46 47 9.035607 GTTGTATGTATACTCTGTCCTTTCATG 57.964 37.037 4.17 0.00 34.41 3.07
47 48 8.533569 TGTATGTATACTCTGTCCTTTCATGA 57.466 34.615 4.17 0.00 34.41 3.07
48 49 8.633561 TGTATGTATACTCTGTCCTTTCATGAG 58.366 37.037 4.17 0.00 34.41 2.90
49 50 5.907207 TGTATACTCTGTCCTTTCATGAGC 58.093 41.667 4.17 0.00 0.00 4.26
50 51 2.777832 ACTCTGTCCTTTCATGAGCC 57.222 50.000 0.00 0.00 0.00 4.70
51 52 2.264455 ACTCTGTCCTTTCATGAGCCT 58.736 47.619 0.00 0.00 0.00 4.58
52 53 2.027377 ACTCTGTCCTTTCATGAGCCTG 60.027 50.000 0.00 0.00 0.00 4.85
53 54 1.280133 TCTGTCCTTTCATGAGCCTGG 59.720 52.381 0.00 0.00 0.00 4.45
54 55 1.004044 CTGTCCTTTCATGAGCCTGGT 59.996 52.381 0.00 0.00 0.00 4.00
55 56 2.237143 CTGTCCTTTCATGAGCCTGGTA 59.763 50.000 0.00 0.00 0.00 3.25
56 57 2.237143 TGTCCTTTCATGAGCCTGGTAG 59.763 50.000 0.00 0.00 0.00 3.18
57 58 2.237392 GTCCTTTCATGAGCCTGGTAGT 59.763 50.000 0.00 0.00 0.00 2.73
67 68 3.840666 TGAGCCTGGTAGTTTCTCAAGAT 59.159 43.478 0.00 0.00 31.62 2.40
68 69 5.023452 TGAGCCTGGTAGTTTCTCAAGATA 58.977 41.667 0.00 0.00 31.62 1.98
72 73 6.611642 AGCCTGGTAGTTTCTCAAGATACATA 59.388 38.462 0.00 0.00 0.00 2.29
77 78 8.758829 TGGTAGTTTCTCAAGATACATATGTGT 58.241 33.333 18.81 12.06 42.39 3.72
78 79 9.601217 GGTAGTTTCTCAAGATACATATGTGTT 57.399 33.333 18.81 5.74 39.77 3.32
85 86 6.582636 TCAAGATACATATGTGTTCCTGTCC 58.417 40.000 18.81 0.00 39.77 4.02
86 87 6.156083 TCAAGATACATATGTGTTCCTGTCCA 59.844 38.462 18.81 0.00 39.77 4.02
133 134 5.607477 TGACGTCCTTGTTAGAACTTGAAT 58.393 37.500 14.12 0.00 0.00 2.57
148 149 3.394635 GAATAGTCCCGGCCGGCAA 62.395 63.158 39.46 25.69 0.00 4.52
149 150 2.879813 GAATAGTCCCGGCCGGCAAA 62.880 60.000 39.46 22.91 0.00 3.68
150 151 2.487274 AATAGTCCCGGCCGGCAAAA 62.487 55.000 39.46 23.24 0.00 2.44
151 152 2.279037 ATAGTCCCGGCCGGCAAAAT 62.279 55.000 39.46 25.59 0.00 1.82
317 319 2.866762 GTCTCGTATTCCTGGCATGTTC 59.133 50.000 0.00 0.00 0.00 3.18
322 324 3.063997 CGTATTCCTGGCATGTTCTTGTC 59.936 47.826 0.00 0.00 0.00 3.18
323 325 2.957402 TTCCTGGCATGTTCTTGTCT 57.043 45.000 0.00 0.00 0.00 3.41
334 336 6.872020 GGCATGTTCTTGTCTGTAGTTAGTAA 59.128 38.462 0.00 0.00 0.00 2.24
337 339 9.692749 CATGTTCTTGTCTGTAGTTAGTAAGAA 57.307 33.333 0.00 0.00 33.74 2.52
338 340 9.915629 ATGTTCTTGTCTGTAGTTAGTAAGAAG 57.084 33.333 0.00 0.00 35.18 2.85
339 341 9.128404 TGTTCTTGTCTGTAGTTAGTAAGAAGA 57.872 33.333 0.00 0.00 35.18 2.87
340 342 9.962783 GTTCTTGTCTGTAGTTAGTAAGAAGAA 57.037 33.333 0.00 0.00 35.18 2.52
342 344 8.298140 TCTTGTCTGTAGTTAGTAAGAAGAAGC 58.702 37.037 0.00 0.00 0.00 3.86
343 345 7.762588 TGTCTGTAGTTAGTAAGAAGAAGCT 57.237 36.000 0.00 0.00 0.00 3.74
344 346 8.859236 TGTCTGTAGTTAGTAAGAAGAAGCTA 57.141 34.615 0.00 0.00 0.00 3.32
345 347 8.948145 TGTCTGTAGTTAGTAAGAAGAAGCTAG 58.052 37.037 0.00 0.00 0.00 3.42
346 348 7.911727 GTCTGTAGTTAGTAAGAAGAAGCTAGC 59.088 40.741 6.62 6.62 0.00 3.42
347 349 6.783162 TGTAGTTAGTAAGAAGAAGCTAGCG 58.217 40.000 9.55 0.00 0.00 4.26
348 350 5.251601 AGTTAGTAAGAAGAAGCTAGCGG 57.748 43.478 9.55 0.00 0.00 5.52
349 351 4.948621 AGTTAGTAAGAAGAAGCTAGCGGA 59.051 41.667 9.55 0.00 0.00 5.54
350 352 5.418209 AGTTAGTAAGAAGAAGCTAGCGGAA 59.582 40.000 9.55 0.00 0.00 4.30
351 353 4.379339 AGTAAGAAGAAGCTAGCGGAAG 57.621 45.455 9.55 0.00 0.00 3.46
352 354 4.017808 AGTAAGAAGAAGCTAGCGGAAGA 58.982 43.478 9.55 0.00 0.00 2.87
397 399 3.319122 GCAAAACCACTCACCATTTCTCT 59.681 43.478 0.00 0.00 0.00 3.10
398 400 4.202151 GCAAAACCACTCACCATTTCTCTT 60.202 41.667 0.00 0.00 0.00 2.85
655 666 2.094803 CAGCGAGTGTCTCATCTCAACT 60.095 50.000 0.00 0.00 0.00 3.16
662 673 6.570571 CGAGTGTCTCATCTCAACTTTTCCTA 60.571 42.308 0.00 0.00 0.00 2.94
930 954 2.544267 CGACCTCAGTTTCACTTGGTTC 59.456 50.000 0.00 0.00 34.12 3.62
974 998 1.202627 TGGGCAAATTGTTTCACTGGC 60.203 47.619 0.00 0.00 0.00 4.85
975 999 1.070601 GGGCAAATTGTTTCACTGGCT 59.929 47.619 0.00 0.00 33.40 4.75
1094 1135 8.806634 TCAAAAATTGCATATTCATAAACTCGC 58.193 29.630 0.00 0.00 0.00 5.03
1102 1143 1.570813 TCATAAACTCGCCTCGCATG 58.429 50.000 0.00 0.00 0.00 4.06
1107 1148 2.659897 CTCGCCTCGCATGCCTAC 60.660 66.667 13.15 0.00 0.00 3.18
1109 1150 2.963854 CGCCTCGCATGCCTACTG 60.964 66.667 13.15 0.00 0.00 2.74
1150 1195 5.125356 TGTTGAGAATCTCAGAAACTTGCA 58.875 37.500 13.11 2.00 41.75 4.08
1163 1208 6.094742 TCAGAAACTTGCAACAACTGAACATA 59.905 34.615 14.29 0.00 31.51 2.29
1240 1285 6.659242 CACCTAAAGATCCTAGATCTCTCCTC 59.341 46.154 7.53 0.00 0.00 3.71
1263 1308 4.279169 CCAATGACTTCGATGGGCATATTT 59.721 41.667 7.52 0.00 0.00 1.40
2219 9940 2.960819 ACTAAGGAAGCAACGCTACTG 58.039 47.619 0.00 0.00 38.25 2.74
2262 9983 1.051812 CGCTAACTGGATCCCTGGAT 58.948 55.000 9.90 0.00 37.59 3.41
2263 9984 1.417890 CGCTAACTGGATCCCTGGATT 59.582 52.381 9.90 0.00 34.60 3.01
2315 10036 3.420904 CGTATCGACATACACATGAACCG 59.579 47.826 0.00 0.00 35.44 4.44
2318 10039 4.023739 TCGACATACACATGAACCGTAG 57.976 45.455 0.00 0.00 35.96 3.51
2321 10042 4.119862 GACATACACATGAACCGTAGCAT 58.880 43.478 0.00 0.00 35.96 3.79
2322 10043 3.871006 ACATACACATGAACCGTAGCATG 59.129 43.478 0.00 10.98 45.56 4.06
2323 10044 1.086696 ACACATGAACCGTAGCATGC 58.913 50.000 10.51 10.51 44.30 4.06
2324 10045 0.378257 CACATGAACCGTAGCATGCC 59.622 55.000 15.66 0.00 44.30 4.40
2325 10046 0.035534 ACATGAACCGTAGCATGCCA 60.036 50.000 15.66 3.22 44.30 4.92
2326 10047 1.093972 CATGAACCGTAGCATGCCAA 58.906 50.000 15.66 0.00 35.93 4.52
2327 10048 1.472082 CATGAACCGTAGCATGCCAAA 59.528 47.619 15.66 0.00 35.93 3.28
2328 10049 1.832883 TGAACCGTAGCATGCCAAAT 58.167 45.000 15.66 0.00 0.00 2.32
2329 10050 2.166829 TGAACCGTAGCATGCCAAATT 58.833 42.857 15.66 2.55 0.00 1.82
2330 10051 2.560542 TGAACCGTAGCATGCCAAATTT 59.439 40.909 15.66 2.30 0.00 1.82
2331 10052 2.652941 ACCGTAGCATGCCAAATTTG 57.347 45.000 15.66 11.40 0.00 2.32
2332 10053 1.892474 ACCGTAGCATGCCAAATTTGT 59.108 42.857 15.66 0.00 0.00 2.83
2333 10054 2.094752 ACCGTAGCATGCCAAATTTGTC 60.095 45.455 15.66 4.74 0.00 3.18
2334 10055 2.529151 CGTAGCATGCCAAATTTGTCC 58.471 47.619 15.66 8.07 0.00 4.02
2335 10056 2.094803 CGTAGCATGCCAAATTTGTCCA 60.095 45.455 15.66 13.09 0.00 4.02
2336 10057 2.460757 AGCATGCCAAATTTGTCCAC 57.539 45.000 15.66 4.44 0.00 4.02
2337 10058 1.002315 AGCATGCCAAATTTGTCCACC 59.998 47.619 15.66 8.35 0.00 4.61
2338 10059 1.270732 GCATGCCAAATTTGTCCACCA 60.271 47.619 16.73 6.36 0.00 4.17
2339 10060 2.690786 CATGCCAAATTTGTCCACCAG 58.309 47.619 16.73 1.11 0.00 4.00
2340 10061 1.047002 TGCCAAATTTGTCCACCAGG 58.953 50.000 16.73 0.22 0.00 4.45
2341 10062 0.321346 GCCAAATTTGTCCACCAGGG 59.679 55.000 16.73 0.00 34.83 4.45
2342 10063 0.321346 CCAAATTTGTCCACCAGGGC 59.679 55.000 16.73 0.00 41.04 5.19
2343 10064 1.341080 CAAATTTGTCCACCAGGGCT 58.659 50.000 10.15 0.00 41.31 5.19
2344 10065 1.001181 CAAATTTGTCCACCAGGGCTG 59.999 52.381 10.15 0.00 41.31 4.85
2345 10066 0.482446 AATTTGTCCACCAGGGCTGA 59.518 50.000 0.00 0.00 41.31 4.26
2346 10067 0.482446 ATTTGTCCACCAGGGCTGAA 59.518 50.000 0.00 0.00 41.31 3.02
2347 10068 0.260230 TTTGTCCACCAGGGCTGAAA 59.740 50.000 0.00 0.00 41.31 2.69
2348 10069 0.260230 TTGTCCACCAGGGCTGAAAA 59.740 50.000 0.00 0.00 41.31 2.29
2349 10070 0.467290 TGTCCACCAGGGCTGAAAAC 60.467 55.000 0.00 0.00 41.31 2.43
2350 10071 0.178990 GTCCACCAGGGCTGAAAACT 60.179 55.000 0.00 0.00 36.28 2.66
2351 10072 0.178992 TCCACCAGGGCTGAAAACTG 60.179 55.000 0.00 0.00 36.21 3.16
2352 10073 1.662044 CACCAGGGCTGAAAACTGC 59.338 57.895 0.00 0.00 0.00 4.40
2353 10074 1.531602 ACCAGGGCTGAAAACTGCC 60.532 57.895 9.11 9.11 0.00 4.85
2354 10075 2.278330 CCAGGGCTGAAAACTGCCC 61.278 63.158 23.17 23.17 42.47 5.36
2355 10076 2.118294 AGGGCTGAAAACTGCCCC 59.882 61.111 25.60 8.10 43.11 5.80
2356 10077 2.997315 GGGCTGAAAACTGCCCCC 60.997 66.667 21.08 0.00 36.55 5.40
2357 10078 3.373565 GGCTGAAAACTGCCCCCG 61.374 66.667 0.00 0.00 0.00 5.73
2358 10079 4.056125 GCTGAAAACTGCCCCCGC 62.056 66.667 0.00 0.00 0.00 6.13
2359 10080 3.737172 CTGAAAACTGCCCCCGCG 61.737 66.667 0.00 0.00 38.08 6.46
2360 10081 4.572571 TGAAAACTGCCCCCGCGT 62.573 61.111 4.92 0.00 38.08 6.01
2361 10082 3.733960 GAAAACTGCCCCCGCGTC 61.734 66.667 4.92 0.00 38.08 5.19
2378 10099 4.803426 CGTCTGCCTGGGCGACTC 62.803 72.222 22.97 9.15 45.51 3.36
2379 10100 4.803426 GTCTGCCTGGGCGACTCG 62.803 72.222 20.51 0.00 45.51 4.18
2399 10120 3.186047 CGGCGCTCGATCCGTTTT 61.186 61.111 7.64 0.00 42.43 2.43
2400 10121 2.736682 CGGCGCTCGATCCGTTTTT 61.737 57.895 7.64 0.00 42.43 1.94
2414 10135 2.665854 TTTTTCCGGCGTCGTCCC 60.666 61.111 9.28 0.00 33.95 4.46
2415 10136 3.167822 TTTTTCCGGCGTCGTCCCT 62.168 57.895 9.28 0.00 33.95 4.20
2416 10137 3.869473 TTTTCCGGCGTCGTCCCTG 62.869 63.158 9.28 0.00 33.95 4.45
2424 10145 4.681978 GTCGTCCCTGTGCGCCTT 62.682 66.667 4.18 0.00 0.00 4.35
2425 10146 4.373116 TCGTCCCTGTGCGCCTTC 62.373 66.667 4.18 0.00 0.00 3.46
2430 10151 4.785453 CCTGTGCGCCTTCCCCTC 62.785 72.222 4.18 0.00 0.00 4.30
2501 10222 2.033602 GGGGTTCTGTTCCCGTGG 59.966 66.667 0.00 0.00 45.46 4.94
2502 10223 2.522367 GGGGTTCTGTTCCCGTGGA 61.522 63.158 0.00 0.00 45.46 4.02
2503 10224 1.683441 GGGTTCTGTTCCCGTGGAT 59.317 57.895 0.00 0.00 35.27 3.41
2504 10225 0.392595 GGGTTCTGTTCCCGTGGATC 60.393 60.000 0.00 0.00 35.27 3.36
2505 10226 0.613777 GGTTCTGTTCCCGTGGATCT 59.386 55.000 0.00 0.00 0.00 2.75
2506 10227 1.003233 GGTTCTGTTCCCGTGGATCTT 59.997 52.381 0.00 0.00 0.00 2.40
2507 10228 2.552373 GGTTCTGTTCCCGTGGATCTTT 60.552 50.000 0.00 0.00 0.00 2.52
2508 10229 2.472695 TCTGTTCCCGTGGATCTTTG 57.527 50.000 0.00 0.00 0.00 2.77
2509 10230 1.003118 TCTGTTCCCGTGGATCTTTGG 59.997 52.381 0.00 0.00 0.00 3.28
2510 10231 0.037590 TGTTCCCGTGGATCTTTGGG 59.962 55.000 9.58 9.58 43.36 4.12
2511 10232 1.001393 TTCCCGTGGATCTTTGGGC 60.001 57.895 10.67 0.00 41.65 5.36
2512 10233 1.784301 TTCCCGTGGATCTTTGGGCA 61.784 55.000 10.67 0.00 41.65 5.36
2513 10234 1.304052 CCCGTGGATCTTTGGGCAA 60.304 57.895 4.17 0.00 34.25 4.52
2514 10235 1.595093 CCCGTGGATCTTTGGGCAAC 61.595 60.000 4.17 0.00 34.25 4.17
2515 10236 1.501741 CGTGGATCTTTGGGCAACG 59.498 57.895 0.00 0.00 37.60 4.10
2516 10237 1.234615 CGTGGATCTTTGGGCAACGT 61.235 55.000 0.00 0.00 37.60 3.99
2517 10238 0.240945 GTGGATCTTTGGGCAACGTG 59.759 55.000 0.00 0.00 37.60 4.49
2518 10239 0.179004 TGGATCTTTGGGCAACGTGT 60.179 50.000 0.00 0.00 37.60 4.49
2519 10240 0.958822 GGATCTTTGGGCAACGTGTT 59.041 50.000 0.00 0.00 37.60 3.32
2520 10241 1.068541 GGATCTTTGGGCAACGTGTTC 60.069 52.381 0.00 0.00 37.60 3.18
2521 10242 0.591170 ATCTTTGGGCAACGTGTTCG 59.409 50.000 0.00 0.00 43.34 3.95
2522 10243 0.462225 TCTTTGGGCAACGTGTTCGA 60.462 50.000 0.00 0.00 40.62 3.71
2523 10244 0.316689 CTTTGGGCAACGTGTTCGAC 60.317 55.000 0.00 0.00 40.62 4.20
2533 10254 3.401577 GTGTTCGACGAGATGCAGA 57.598 52.632 0.00 0.00 0.00 4.26
2534 10255 1.914634 GTGTTCGACGAGATGCAGAT 58.085 50.000 0.00 0.00 0.00 2.90
2535 10256 1.585668 GTGTTCGACGAGATGCAGATG 59.414 52.381 0.00 0.00 0.00 2.90
2536 10257 1.203928 GTTCGACGAGATGCAGATGG 58.796 55.000 0.00 0.00 0.00 3.51
2537 10258 0.528466 TTCGACGAGATGCAGATGGC 60.528 55.000 0.00 0.00 45.13 4.40
2557 10278 2.281761 CTGGCGGCTGTGAAGGTT 60.282 61.111 11.43 0.00 0.00 3.50
2558 10279 2.594303 TGGCGGCTGTGAAGGTTG 60.594 61.111 11.43 0.00 0.00 3.77
2559 10280 2.281484 GGCGGCTGTGAAGGTTGA 60.281 61.111 0.00 0.00 0.00 3.18
2560 10281 1.675641 GGCGGCTGTGAAGGTTGAT 60.676 57.895 0.00 0.00 0.00 2.57
2561 10282 1.503542 GCGGCTGTGAAGGTTGATG 59.496 57.895 0.00 0.00 0.00 3.07
2562 10283 1.503542 CGGCTGTGAAGGTTGATGC 59.496 57.895 0.00 0.00 0.00 3.91
2563 10284 0.957395 CGGCTGTGAAGGTTGATGCT 60.957 55.000 0.00 0.00 0.00 3.79
2564 10285 0.524862 GGCTGTGAAGGTTGATGCTG 59.475 55.000 0.00 0.00 0.00 4.41
2565 10286 0.109412 GCTGTGAAGGTTGATGCTGC 60.109 55.000 0.00 0.00 0.00 5.25
2566 10287 1.241165 CTGTGAAGGTTGATGCTGCA 58.759 50.000 4.13 4.13 0.00 4.41
2567 10288 1.199327 CTGTGAAGGTTGATGCTGCAG 59.801 52.381 10.11 10.11 0.00 4.41
2568 10289 0.109412 GTGAAGGTTGATGCTGCAGC 60.109 55.000 31.89 31.89 42.50 5.25
2569 10290 1.136147 GAAGGTTGATGCTGCAGCG 59.864 57.895 32.11 0.52 45.83 5.18
2570 10291 2.262471 GAAGGTTGATGCTGCAGCGG 62.262 60.000 32.11 0.00 45.83 5.52
2571 10292 4.487412 GGTTGATGCTGCAGCGGC 62.487 66.667 32.11 25.60 45.83 6.53
2591 10312 3.900892 CTCCGGCGCTCCACGTAT 61.901 66.667 7.64 0.00 46.11 3.06
2592 10313 3.825833 CTCCGGCGCTCCACGTATC 62.826 68.421 7.64 0.00 46.11 2.24
2593 10314 3.900892 CCGGCGCTCCACGTATCT 61.901 66.667 7.64 0.00 46.11 1.98
2594 10315 2.655364 CGGCGCTCCACGTATCTG 60.655 66.667 7.64 0.00 46.11 2.90
2595 10316 2.279517 GGCGCTCCACGTATCTGG 60.280 66.667 7.64 0.00 46.11 3.86
2596 10317 2.962253 GCGCTCCACGTATCTGGC 60.962 66.667 0.00 0.00 46.11 4.85
2597 10318 2.655364 CGCTCCACGTATCTGGCG 60.655 66.667 0.00 0.00 36.87 5.69
2598 10319 2.279517 GCTCCACGTATCTGGCGG 60.280 66.667 0.00 0.00 0.00 6.13
2599 10320 2.782222 GCTCCACGTATCTGGCGGA 61.782 63.158 0.00 0.00 0.00 5.54
2600 10321 1.813859 CTCCACGTATCTGGCGGAA 59.186 57.895 0.00 0.00 0.00 4.30
2601 10322 0.249073 CTCCACGTATCTGGCGGAAG 60.249 60.000 0.00 0.00 0.00 3.46
2621 10342 3.771216 AGCATGGCTTGGGATAATTAGG 58.229 45.455 2.33 0.00 33.89 2.69
2622 10343 3.140895 AGCATGGCTTGGGATAATTAGGT 59.859 43.478 2.33 0.00 33.89 3.08
2623 10344 3.507622 GCATGGCTTGGGATAATTAGGTC 59.492 47.826 2.33 0.00 0.00 3.85
2624 10345 3.485463 TGGCTTGGGATAATTAGGTCG 57.515 47.619 0.00 0.00 0.00 4.79
2625 10346 2.105821 TGGCTTGGGATAATTAGGTCGG 59.894 50.000 0.00 0.00 0.00 4.79
2626 10347 2.152016 GCTTGGGATAATTAGGTCGGC 58.848 52.381 0.00 0.00 0.00 5.54
2627 10348 2.486548 GCTTGGGATAATTAGGTCGGCA 60.487 50.000 0.00 0.00 0.00 5.69
2628 10349 3.810743 GCTTGGGATAATTAGGTCGGCAT 60.811 47.826 0.00 0.00 0.00 4.40
2629 10350 3.695830 TGGGATAATTAGGTCGGCATC 57.304 47.619 0.00 0.00 0.00 3.91
2630 10351 2.976185 TGGGATAATTAGGTCGGCATCA 59.024 45.455 0.00 0.00 0.00 3.07
2631 10352 3.587061 TGGGATAATTAGGTCGGCATCAT 59.413 43.478 0.00 0.00 0.00 2.45
2632 10353 3.941483 GGGATAATTAGGTCGGCATCATG 59.059 47.826 0.00 0.00 0.00 3.07
2633 10354 3.941483 GGATAATTAGGTCGGCATCATGG 59.059 47.826 0.00 0.00 0.00 3.66
2634 10355 4.323485 GGATAATTAGGTCGGCATCATGGA 60.323 45.833 0.00 0.00 0.00 3.41
2635 10356 2.550830 ATTAGGTCGGCATCATGGAC 57.449 50.000 0.00 0.00 0.00 4.02
2636 10357 0.104120 TTAGGTCGGCATCATGGACG 59.896 55.000 0.00 0.00 41.81 4.79
2637 10358 2.363711 TAGGTCGGCATCATGGACGC 62.364 60.000 0.00 0.00 39.74 5.19
2638 10359 2.202932 GTCGGCATCATGGACGCT 60.203 61.111 0.00 0.00 39.74 5.07
2639 10360 1.815421 GTCGGCATCATGGACGCTT 60.815 57.895 0.00 0.00 39.74 4.68
2640 10361 1.815003 TCGGCATCATGGACGCTTG 60.815 57.895 0.00 0.00 39.74 4.01
2641 10362 2.108514 CGGCATCATGGACGCTTGT 61.109 57.895 0.00 0.00 29.38 3.16
2642 10363 0.809636 CGGCATCATGGACGCTTGTA 60.810 55.000 0.00 0.00 29.38 2.41
2643 10364 1.378531 GGCATCATGGACGCTTGTAA 58.621 50.000 0.00 0.00 0.00 2.41
2644 10365 1.064060 GGCATCATGGACGCTTGTAAC 59.936 52.381 0.00 0.00 0.00 2.50
2645 10366 1.267532 GCATCATGGACGCTTGTAACG 60.268 52.381 0.00 0.00 0.00 3.18
2646 10367 1.006832 ATCATGGACGCTTGTAACGC 58.993 50.000 0.00 0.00 0.00 4.84
2647 10368 0.319986 TCATGGACGCTTGTAACGCA 60.320 50.000 0.00 0.00 0.00 5.24
2648 10369 0.095245 CATGGACGCTTGTAACGCAG 59.905 55.000 0.00 0.00 0.00 5.18
2650 10371 0.942410 TGGACGCTTGTAACGCAGTC 60.942 55.000 0.00 0.00 45.00 3.51
2651 10372 0.942410 GGACGCTTGTAACGCAGTCA 60.942 55.000 0.00 0.00 45.00 3.41
2652 10373 1.068474 GACGCTTGTAACGCAGTCAT 58.932 50.000 0.00 0.00 45.00 3.06
2653 10374 1.059264 GACGCTTGTAACGCAGTCATC 59.941 52.381 0.00 0.00 45.00 2.92
2654 10375 1.336887 ACGCTTGTAACGCAGTCATCT 60.337 47.619 0.00 0.00 45.00 2.90
2655 10376 1.726791 CGCTTGTAACGCAGTCATCTT 59.273 47.619 0.00 0.00 45.00 2.40
2656 10377 2.222596 CGCTTGTAACGCAGTCATCTTC 60.223 50.000 0.00 0.00 45.00 2.87
2657 10378 2.222596 GCTTGTAACGCAGTCATCTTCG 60.223 50.000 0.00 0.00 45.00 3.79
2658 10379 2.717580 TGTAACGCAGTCATCTTCGT 57.282 45.000 0.00 0.00 45.00 3.85
2661 10382 3.886044 ACGCAGTCATCTTCGTTGA 57.114 47.368 0.00 0.00 40.17 3.18
2662 10383 1.419374 ACGCAGTCATCTTCGTTGAC 58.581 50.000 0.00 0.00 40.17 3.18
2663 10384 1.269569 ACGCAGTCATCTTCGTTGACA 60.270 47.619 6.59 0.00 44.73 3.58
2664 10385 1.388093 CGCAGTCATCTTCGTTGACAG 59.612 52.381 6.59 0.00 44.73 3.51
2665 10386 1.728971 GCAGTCATCTTCGTTGACAGG 59.271 52.381 6.59 0.18 44.73 4.00
2666 10387 2.610479 GCAGTCATCTTCGTTGACAGGA 60.610 50.000 6.59 0.00 44.73 3.86
2667 10388 2.989840 CAGTCATCTTCGTTGACAGGAC 59.010 50.000 6.59 0.00 44.73 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.926751 CATACAACTTCACTAATCATTCATCAC 57.073 33.333 0.00 0.00 0.00 3.06
2 3 9.671279 ACATACAACTTCACTAATCATTCATCA 57.329 29.630 0.00 0.00 0.00 3.07
13 14 8.900781 GGACAGAGTATACATACAACTTCACTA 58.099 37.037 5.50 0.00 35.74 2.74
14 15 7.616150 AGGACAGAGTATACATACAACTTCACT 59.384 37.037 5.50 0.00 35.74 3.41
15 16 7.773149 AGGACAGAGTATACATACAACTTCAC 58.227 38.462 5.50 0.00 35.74 3.18
16 17 7.956328 AGGACAGAGTATACATACAACTTCA 57.044 36.000 5.50 0.00 35.74 3.02
17 18 9.303537 GAAAGGACAGAGTATACATACAACTTC 57.696 37.037 5.50 0.00 35.74 3.01
18 19 8.812972 TGAAAGGACAGAGTATACATACAACTT 58.187 33.333 5.50 0.38 35.74 2.66
19 20 8.362464 TGAAAGGACAGAGTATACATACAACT 57.638 34.615 5.50 0.00 35.74 3.16
20 21 9.035607 CATGAAAGGACAGAGTATACATACAAC 57.964 37.037 5.50 0.00 35.74 3.32
21 22 8.977412 TCATGAAAGGACAGAGTATACATACAA 58.023 33.333 5.50 0.00 35.74 2.41
22 23 8.533569 TCATGAAAGGACAGAGTATACATACA 57.466 34.615 5.50 0.00 35.74 2.29
23 24 7.596995 GCTCATGAAAGGACAGAGTATACATAC 59.403 40.741 5.50 0.00 0.00 2.39
24 25 7.255977 GGCTCATGAAAGGACAGAGTATACATA 60.256 40.741 5.50 0.00 0.00 2.29
25 26 6.463614 GGCTCATGAAAGGACAGAGTATACAT 60.464 42.308 5.50 0.00 0.00 2.29
26 27 5.163405 GGCTCATGAAAGGACAGAGTATACA 60.163 44.000 5.50 0.00 0.00 2.29
27 28 5.069781 AGGCTCATGAAAGGACAGAGTATAC 59.930 44.000 0.00 0.00 0.00 1.47
28 29 5.069648 CAGGCTCATGAAAGGACAGAGTATA 59.930 44.000 0.00 0.00 0.00 1.47
29 30 4.036518 AGGCTCATGAAAGGACAGAGTAT 58.963 43.478 0.00 0.00 0.00 2.12
30 31 3.196469 CAGGCTCATGAAAGGACAGAGTA 59.804 47.826 0.00 0.00 0.00 2.59
31 32 2.027377 CAGGCTCATGAAAGGACAGAGT 60.027 50.000 0.00 0.00 0.00 3.24
32 33 2.630158 CAGGCTCATGAAAGGACAGAG 58.370 52.381 0.00 0.00 0.00 3.35
33 34 1.280133 CCAGGCTCATGAAAGGACAGA 59.720 52.381 0.00 0.00 0.00 3.41
34 35 1.004044 ACCAGGCTCATGAAAGGACAG 59.996 52.381 0.00 0.00 0.00 3.51
35 36 1.067295 ACCAGGCTCATGAAAGGACA 58.933 50.000 0.00 0.00 0.00 4.02
36 37 2.237392 ACTACCAGGCTCATGAAAGGAC 59.763 50.000 0.00 0.00 0.00 3.85
37 38 2.551270 ACTACCAGGCTCATGAAAGGA 58.449 47.619 0.00 0.00 0.00 3.36
38 39 3.356529 AACTACCAGGCTCATGAAAGG 57.643 47.619 0.00 0.00 0.00 3.11
39 40 4.583871 AGAAACTACCAGGCTCATGAAAG 58.416 43.478 0.00 0.00 0.00 2.62
40 41 4.041567 TGAGAAACTACCAGGCTCATGAAA 59.958 41.667 0.00 0.00 31.24 2.69
41 42 3.582647 TGAGAAACTACCAGGCTCATGAA 59.417 43.478 0.00 0.00 31.24 2.57
42 43 3.173151 TGAGAAACTACCAGGCTCATGA 58.827 45.455 0.00 0.00 31.24 3.07
43 44 3.616956 TGAGAAACTACCAGGCTCATG 57.383 47.619 0.00 0.00 31.24 3.07
44 45 3.840666 TCTTGAGAAACTACCAGGCTCAT 59.159 43.478 0.00 0.00 35.73 2.90
45 46 3.239449 TCTTGAGAAACTACCAGGCTCA 58.761 45.455 0.00 0.00 34.11 4.26
46 47 3.963428 TCTTGAGAAACTACCAGGCTC 57.037 47.619 0.00 0.00 0.00 4.70
47 48 4.777896 TGTATCTTGAGAAACTACCAGGCT 59.222 41.667 0.00 0.00 0.00 4.58
48 49 5.086104 TGTATCTTGAGAAACTACCAGGC 57.914 43.478 0.00 0.00 0.00 4.85
49 50 8.424918 ACATATGTATCTTGAGAAACTACCAGG 58.575 37.037 6.56 0.00 0.00 4.45
50 51 9.254133 CACATATGTATCTTGAGAAACTACCAG 57.746 37.037 8.32 0.00 0.00 4.00
51 52 8.758829 ACACATATGTATCTTGAGAAACTACCA 58.241 33.333 8.32 0.00 37.26 3.25
52 53 9.601217 AACACATATGTATCTTGAGAAACTACC 57.399 33.333 8.32 0.00 38.45 3.18
54 55 9.817809 GGAACACATATGTATCTTGAGAAACTA 57.182 33.333 8.32 0.00 38.45 2.24
55 56 8.543774 AGGAACACATATGTATCTTGAGAAACT 58.456 33.333 8.32 0.00 38.45 2.66
56 57 8.607459 CAGGAACACATATGTATCTTGAGAAAC 58.393 37.037 19.82 5.02 38.45 2.78
57 58 8.321353 ACAGGAACACATATGTATCTTGAGAAA 58.679 33.333 26.27 0.00 38.45 2.52
85 86 1.613437 GGGTCCAAGTCCAACAATGTG 59.387 52.381 0.00 0.00 0.00 3.21
86 87 1.480498 GGGGTCCAAGTCCAACAATGT 60.480 52.381 0.00 0.00 0.00 2.71
133 134 1.624479 TATTTTGCCGGCCGGGACTA 61.624 55.000 43.31 30.73 38.47 2.59
148 149 0.105964 TAGTCGCAGCCGGCATATTT 59.894 50.000 31.54 11.86 42.67 1.40
149 150 0.321671 ATAGTCGCAGCCGGCATATT 59.678 50.000 31.54 4.11 42.67 1.28
150 151 0.321671 AATAGTCGCAGCCGGCATAT 59.678 50.000 31.54 13.16 42.67 1.78
151 152 0.599991 CAATAGTCGCAGCCGGCATA 60.600 55.000 31.54 11.36 42.67 3.14
216 218 7.999679 TCAATCATTCATCCTCCACAATAAAC 58.000 34.615 0.00 0.00 0.00 2.01
220 222 6.370453 TCATCAATCATTCATCCTCCACAAT 58.630 36.000 0.00 0.00 0.00 2.71
317 319 8.301002 AGCTTCTTCTTACTAACTACAGACAAG 58.699 37.037 0.00 0.00 0.00 3.16
322 324 6.908284 CGCTAGCTTCTTCTTACTAACTACAG 59.092 42.308 13.93 0.00 0.00 2.74
323 325 6.183360 CCGCTAGCTTCTTCTTACTAACTACA 60.183 42.308 13.93 0.00 0.00 2.74
334 336 5.599999 TTTATCTTCCGCTAGCTTCTTCT 57.400 39.130 13.93 0.00 0.00 2.85
337 339 4.123506 GCTTTTATCTTCCGCTAGCTTCT 58.876 43.478 13.93 0.00 0.00 2.85
338 340 3.871594 TGCTTTTATCTTCCGCTAGCTTC 59.128 43.478 13.93 0.00 0.00 3.86
339 341 3.873910 TGCTTTTATCTTCCGCTAGCTT 58.126 40.909 13.93 0.00 0.00 3.74
340 342 3.543680 TGCTTTTATCTTCCGCTAGCT 57.456 42.857 13.93 0.00 0.00 3.32
341 343 4.592179 CTTTGCTTTTATCTTCCGCTAGC 58.408 43.478 4.06 4.06 0.00 3.42
342 344 4.496507 GGCTTTGCTTTTATCTTCCGCTAG 60.497 45.833 0.00 0.00 0.00 3.42
343 345 3.377172 GGCTTTGCTTTTATCTTCCGCTA 59.623 43.478 0.00 0.00 0.00 4.26
344 346 2.164422 GGCTTTGCTTTTATCTTCCGCT 59.836 45.455 0.00 0.00 0.00 5.52
345 347 2.164422 AGGCTTTGCTTTTATCTTCCGC 59.836 45.455 0.00 0.00 0.00 5.54
346 348 3.762779 CAGGCTTTGCTTTTATCTTCCG 58.237 45.455 0.00 0.00 0.00 4.30
376 378 5.507985 GGAAGAGAAATGGTGAGTGGTTTTG 60.508 44.000 0.00 0.00 0.00 2.44
662 673 8.768397 TCCCTTCTGAATTAGTTACACATACAT 58.232 33.333 0.00 0.00 0.00 2.29
974 998 4.386049 CGTTACCAGTGAGAGCTAAAACAG 59.614 45.833 0.00 0.00 0.00 3.16
975 999 4.304110 CGTTACCAGTGAGAGCTAAAACA 58.696 43.478 0.00 0.00 0.00 2.83
1102 1143 2.009774 CAATGTGTGTAGGCAGTAGGC 58.990 52.381 0.00 0.00 43.74 3.93
1109 1150 0.169672 CAGCTGCAATGTGTGTAGGC 59.830 55.000 0.00 0.00 40.14 3.93
1150 1195 6.543831 GCTATTCCCAGATATGTTCAGTTGTT 59.456 38.462 0.00 0.00 0.00 2.83
1163 1208 1.417890 CCGTCCAAGCTATTCCCAGAT 59.582 52.381 0.00 0.00 0.00 2.90
1240 1285 1.683943 ATGCCCATCGAAGTCATTGG 58.316 50.000 0.00 0.00 0.00 3.16
1263 1308 2.105477 GCCCTGAGAATGAGCCTATTGA 59.895 50.000 0.00 0.00 0.00 2.57
1752 3520 5.956642 ACTCTCGTAGGTTCTGAAGATTTC 58.043 41.667 0.00 0.00 0.00 2.17
2126 3977 1.193650 TCTAAACGATGTTGTGTGCGC 59.806 47.619 0.00 0.00 0.00 6.09
2219 9940 6.651225 CGAGTTATTCCCAAGATTTAGATCCC 59.349 42.308 0.00 0.00 32.44 3.85
2262 9983 6.613699 AGAAGATTGGGTATGCCATATTGAA 58.386 36.000 1.04 0.00 36.17 2.69
2263 9984 6.044754 AGAGAAGATTGGGTATGCCATATTGA 59.955 38.462 1.04 0.00 36.17 2.57
2315 10036 3.253230 GTGGACAAATTTGGCATGCTAC 58.747 45.455 25.05 11.54 38.18 3.58
2318 10039 1.270732 TGGTGGACAAATTTGGCATGC 60.271 47.619 25.05 9.90 38.18 4.06
2321 10042 1.047002 CCTGGTGGACAAATTTGGCA 58.953 50.000 25.05 9.02 38.18 4.92
2322 10043 0.321346 CCCTGGTGGACAAATTTGGC 59.679 55.000 21.74 19.16 35.39 4.52
2323 10044 0.321346 GCCCTGGTGGACAAATTTGG 59.679 55.000 21.74 4.79 35.39 3.28
2324 10045 1.001181 CAGCCCTGGTGGACAAATTTG 59.999 52.381 16.67 16.67 35.39 2.32
2325 10046 1.133199 TCAGCCCTGGTGGACAAATTT 60.133 47.619 0.00 0.00 35.39 1.82
2326 10047 0.482446 TCAGCCCTGGTGGACAAATT 59.518 50.000 0.00 0.00 35.39 1.82
2327 10048 0.482446 TTCAGCCCTGGTGGACAAAT 59.518 50.000 0.00 0.00 35.39 2.32
2328 10049 0.260230 TTTCAGCCCTGGTGGACAAA 59.740 50.000 0.00 0.00 35.39 2.83
2329 10050 0.260230 TTTTCAGCCCTGGTGGACAA 59.740 50.000 0.00 0.00 35.39 3.18
2330 10051 0.467290 GTTTTCAGCCCTGGTGGACA 60.467 55.000 0.00 0.00 35.39 4.02
2331 10052 0.178990 AGTTTTCAGCCCTGGTGGAC 60.179 55.000 0.00 0.00 35.39 4.02
2332 10053 0.178992 CAGTTTTCAGCCCTGGTGGA 60.179 55.000 0.00 0.00 35.39 4.02
2333 10054 1.809567 GCAGTTTTCAGCCCTGGTGG 61.810 60.000 0.00 0.00 37.09 4.61
2334 10055 1.662044 GCAGTTTTCAGCCCTGGTG 59.338 57.895 0.00 0.00 0.00 4.17
2335 10056 1.531602 GGCAGTTTTCAGCCCTGGT 60.532 57.895 0.00 0.00 45.11 4.00
2336 10057 3.369921 GGCAGTTTTCAGCCCTGG 58.630 61.111 0.00 0.00 45.11 4.45
2341 10062 4.056125 GCGGGGGCAGTTTTCAGC 62.056 66.667 0.00 0.00 0.00 4.26
2342 10063 3.737172 CGCGGGGGCAGTTTTCAG 61.737 66.667 0.00 0.00 0.00 3.02
2343 10064 4.572571 ACGCGGGGGCAGTTTTCA 62.573 61.111 12.47 0.00 0.00 2.69
2344 10065 3.733960 GACGCGGGGGCAGTTTTC 61.734 66.667 12.47 0.00 0.00 2.29
2361 10082 4.803426 GAGTCGCCCAGGCAGACG 62.803 72.222 20.20 5.97 43.64 4.18
2362 10083 4.803426 CGAGTCGCCCAGGCAGAC 62.803 72.222 19.35 19.35 41.35 3.51
2383 10104 3.174788 AAAAACGGATCGAGCGCC 58.825 55.556 2.29 0.00 0.00 6.53
2397 10118 2.665854 GGGACGACGCCGGAAAAA 60.666 61.111 5.05 0.00 40.78 1.94
2398 10119 3.618750 AGGGACGACGCCGGAAAA 61.619 61.111 5.05 0.00 40.78 2.29
2399 10120 4.367023 CAGGGACGACGCCGGAAA 62.367 66.667 5.05 0.00 40.78 3.13
2407 10128 4.681978 AAGGCGCACAGGGACGAC 62.682 66.667 10.83 0.00 37.66 4.34
2408 10129 4.373116 GAAGGCGCACAGGGACGA 62.373 66.667 10.83 0.00 0.00 4.20
2413 10134 4.785453 GAGGGGAAGGCGCACAGG 62.785 72.222 10.83 0.00 0.00 4.00
2484 10205 1.848886 ATCCACGGGAACAGAACCCC 61.849 60.000 0.00 0.00 44.09 4.95
2485 10206 0.392595 GATCCACGGGAACAGAACCC 60.393 60.000 0.00 0.00 43.57 4.11
2486 10207 0.613777 AGATCCACGGGAACAGAACC 59.386 55.000 0.00 0.00 34.34 3.62
2487 10208 2.474410 AAGATCCACGGGAACAGAAC 57.526 50.000 0.00 0.00 34.34 3.01
2488 10209 2.552155 CCAAAGATCCACGGGAACAGAA 60.552 50.000 0.00 0.00 34.34 3.02
2489 10210 1.003118 CCAAAGATCCACGGGAACAGA 59.997 52.381 0.00 0.00 34.34 3.41
2490 10211 1.453155 CCAAAGATCCACGGGAACAG 58.547 55.000 0.00 0.00 34.34 3.16
2491 10212 0.037590 CCCAAAGATCCACGGGAACA 59.962 55.000 5.19 0.00 41.62 3.18
2492 10213 1.313091 GCCCAAAGATCCACGGGAAC 61.313 60.000 13.77 0.00 41.62 3.62
2493 10214 1.001393 GCCCAAAGATCCACGGGAA 60.001 57.895 13.77 0.00 41.62 3.97
2494 10215 1.784301 TTGCCCAAAGATCCACGGGA 61.784 55.000 13.77 0.00 41.62 5.14
2495 10216 1.304052 TTGCCCAAAGATCCACGGG 60.304 57.895 6.57 6.57 42.03 5.28
2496 10217 1.883021 GTTGCCCAAAGATCCACGG 59.117 57.895 0.00 0.00 0.00 4.94
2497 10218 1.234615 ACGTTGCCCAAAGATCCACG 61.235 55.000 1.09 0.00 0.00 4.94
2498 10219 0.240945 CACGTTGCCCAAAGATCCAC 59.759 55.000 1.09 0.00 0.00 4.02
2499 10220 0.179004 ACACGTTGCCCAAAGATCCA 60.179 50.000 1.09 0.00 0.00 3.41
2500 10221 0.958822 AACACGTTGCCCAAAGATCC 59.041 50.000 1.09 0.00 0.00 3.36
2501 10222 1.399727 CGAACACGTTGCCCAAAGATC 60.400 52.381 1.09 0.00 0.00 2.75
2502 10223 0.591170 CGAACACGTTGCCCAAAGAT 59.409 50.000 1.09 0.00 0.00 2.40
2503 10224 0.462225 TCGAACACGTTGCCCAAAGA 60.462 50.000 1.09 0.00 0.00 2.52
2504 10225 0.316689 GTCGAACACGTTGCCCAAAG 60.317 55.000 0.00 0.00 0.00 2.77
2505 10226 1.722677 GTCGAACACGTTGCCCAAA 59.277 52.632 0.00 0.00 0.00 3.28
2506 10227 2.526993 CGTCGAACACGTTGCCCAA 61.527 57.895 0.00 0.00 44.07 4.12
2507 10228 2.962786 CGTCGAACACGTTGCCCA 60.963 61.111 0.00 0.00 44.07 5.36
2515 10236 1.585668 CATCTGCATCTCGTCGAACAC 59.414 52.381 0.00 0.00 0.00 3.32
2516 10237 1.469767 CCATCTGCATCTCGTCGAACA 60.470 52.381 0.00 0.00 0.00 3.18
2517 10238 1.203928 CCATCTGCATCTCGTCGAAC 58.796 55.000 0.00 0.00 0.00 3.95
2518 10239 0.528466 GCCATCTGCATCTCGTCGAA 60.528 55.000 0.00 0.00 40.77 3.71
2519 10240 1.066422 GCCATCTGCATCTCGTCGA 59.934 57.895 0.00 0.00 40.77 4.20
2520 10241 2.298629 CGCCATCTGCATCTCGTCG 61.299 63.158 0.00 0.00 41.33 5.12
2521 10242 1.953138 CCGCCATCTGCATCTCGTC 60.953 63.158 0.00 0.00 41.33 4.20
2522 10243 2.107750 CCGCCATCTGCATCTCGT 59.892 61.111 0.00 0.00 41.33 4.18
2523 10244 3.344215 GCCGCCATCTGCATCTCG 61.344 66.667 0.00 0.00 41.33 4.04
2524 10245 2.110627 AGCCGCCATCTGCATCTC 59.889 61.111 0.00 0.00 41.33 2.75
2525 10246 2.203167 CAGCCGCCATCTGCATCT 60.203 61.111 0.00 0.00 41.33 2.90
2526 10247 3.285215 CCAGCCGCCATCTGCATC 61.285 66.667 0.00 0.00 41.33 3.91
2540 10261 2.281761 AACCTTCACAGCCGCCAG 60.282 61.111 0.00 0.00 0.00 4.85
2541 10262 2.410322 ATCAACCTTCACAGCCGCCA 62.410 55.000 0.00 0.00 0.00 5.69
2542 10263 1.675641 ATCAACCTTCACAGCCGCC 60.676 57.895 0.00 0.00 0.00 6.13
2543 10264 1.503542 CATCAACCTTCACAGCCGC 59.496 57.895 0.00 0.00 0.00 6.53
2544 10265 0.957395 AGCATCAACCTTCACAGCCG 60.957 55.000 0.00 0.00 0.00 5.52
2545 10266 0.524862 CAGCATCAACCTTCACAGCC 59.475 55.000 0.00 0.00 0.00 4.85
2546 10267 0.109412 GCAGCATCAACCTTCACAGC 60.109 55.000 0.00 0.00 0.00 4.40
2547 10268 1.199327 CTGCAGCATCAACCTTCACAG 59.801 52.381 0.00 0.00 0.00 3.66
2548 10269 1.241165 CTGCAGCATCAACCTTCACA 58.759 50.000 0.00 0.00 0.00 3.58
2549 10270 0.109412 GCTGCAGCATCAACCTTCAC 60.109 55.000 33.36 0.00 41.59 3.18
2550 10271 1.579964 CGCTGCAGCATCAACCTTCA 61.580 55.000 36.03 0.00 42.21 3.02
2551 10272 1.136147 CGCTGCAGCATCAACCTTC 59.864 57.895 36.03 5.05 42.21 3.46
2552 10273 2.338015 CCGCTGCAGCATCAACCTT 61.338 57.895 36.03 0.00 42.21 3.50
2553 10274 2.749044 CCGCTGCAGCATCAACCT 60.749 61.111 36.03 0.00 42.21 3.50
2554 10275 4.487412 GCCGCTGCAGCATCAACC 62.487 66.667 36.03 14.32 42.21 3.77
2555 10276 3.740397 TGCCGCTGCAGCATCAAC 61.740 61.111 36.03 20.38 44.23 3.18
2574 10295 3.825833 GATACGTGGAGCGCCGGAG 62.826 68.421 5.05 1.55 46.11 4.63
2575 10296 3.896133 GATACGTGGAGCGCCGGA 61.896 66.667 5.05 0.00 46.11 5.14
2576 10297 3.900892 AGATACGTGGAGCGCCGG 61.901 66.667 2.29 0.00 46.11 6.13
2577 10298 2.655364 CAGATACGTGGAGCGCCG 60.655 66.667 2.29 2.21 46.11 6.46
2578 10299 2.279517 CCAGATACGTGGAGCGCC 60.280 66.667 2.29 0.00 46.11 6.53
2579 10300 2.962253 GCCAGATACGTGGAGCGC 60.962 66.667 0.00 0.00 46.11 5.92
2581 10302 2.279517 CCGCCAGATACGTGGAGC 60.280 66.667 0.00 0.00 40.44 4.70
2582 10303 0.249073 CTTCCGCCAGATACGTGGAG 60.249 60.000 0.00 0.00 40.84 3.86
2583 10304 1.813859 CTTCCGCCAGATACGTGGA 59.186 57.895 0.00 0.00 40.44 4.02
2584 10305 1.883084 GCTTCCGCCAGATACGTGG 60.883 63.158 0.00 0.00 41.01 4.94
2585 10306 0.530650 ATGCTTCCGCCAGATACGTG 60.531 55.000 0.00 0.00 34.43 4.49
2586 10307 0.530650 CATGCTTCCGCCAGATACGT 60.531 55.000 0.00 0.00 34.43 3.57
2587 10308 1.224069 CCATGCTTCCGCCAGATACG 61.224 60.000 0.00 0.00 34.43 3.06
2588 10309 1.510480 GCCATGCTTCCGCCAGATAC 61.510 60.000 0.00 0.00 34.43 2.24
2589 10310 1.227943 GCCATGCTTCCGCCAGATA 60.228 57.895 0.00 0.00 34.43 1.98
2590 10311 2.517875 GCCATGCTTCCGCCAGAT 60.518 61.111 0.00 0.00 34.43 2.90
2591 10312 3.272364 AAGCCATGCTTCCGCCAGA 62.272 57.895 0.00 0.00 46.77 3.86
2592 10313 2.753043 AAGCCATGCTTCCGCCAG 60.753 61.111 0.00 0.00 46.77 4.85
2593 10314 3.063704 CAAGCCATGCTTCCGCCA 61.064 61.111 0.00 0.00 46.77 5.69
2594 10315 3.830192 CCAAGCCATGCTTCCGCC 61.830 66.667 0.00 0.00 46.77 6.13
2595 10316 3.830192 CCCAAGCCATGCTTCCGC 61.830 66.667 0.00 0.00 46.77 5.54
2596 10317 0.179020 TATCCCAAGCCATGCTTCCG 60.179 55.000 0.00 0.00 46.77 4.30
2597 10318 2.071778 TTATCCCAAGCCATGCTTCC 57.928 50.000 0.00 0.00 46.77 3.46
2598 10319 4.219288 CCTAATTATCCCAAGCCATGCTTC 59.781 45.833 0.00 0.00 46.77 3.86
2600 10321 3.140895 ACCTAATTATCCCAAGCCATGCT 59.859 43.478 0.00 0.00 42.56 3.79
2601 10322 3.500343 ACCTAATTATCCCAAGCCATGC 58.500 45.455 0.00 0.00 0.00 4.06
2602 10323 3.753272 CGACCTAATTATCCCAAGCCATG 59.247 47.826 0.00 0.00 0.00 3.66
2603 10324 3.244911 CCGACCTAATTATCCCAAGCCAT 60.245 47.826 0.00 0.00 0.00 4.40
2604 10325 2.105821 CCGACCTAATTATCCCAAGCCA 59.894 50.000 0.00 0.00 0.00 4.75
2605 10326 2.779506 CCGACCTAATTATCCCAAGCC 58.220 52.381 0.00 0.00 0.00 4.35
2606 10327 2.152016 GCCGACCTAATTATCCCAAGC 58.848 52.381 0.00 0.00 0.00 4.01
2607 10328 3.485463 TGCCGACCTAATTATCCCAAG 57.515 47.619 0.00 0.00 0.00 3.61
2608 10329 3.392947 TGATGCCGACCTAATTATCCCAA 59.607 43.478 0.00 0.00 0.00 4.12
2609 10330 2.976185 TGATGCCGACCTAATTATCCCA 59.024 45.455 0.00 0.00 0.00 4.37
2610 10331 3.695830 TGATGCCGACCTAATTATCCC 57.304 47.619 0.00 0.00 0.00 3.85
2611 10332 3.941483 CCATGATGCCGACCTAATTATCC 59.059 47.826 0.00 0.00 0.00 2.59
2612 10333 4.631813 GTCCATGATGCCGACCTAATTATC 59.368 45.833 0.00 0.00 0.00 1.75
2613 10334 4.579869 GTCCATGATGCCGACCTAATTAT 58.420 43.478 0.00 0.00 0.00 1.28
2614 10335 3.554129 CGTCCATGATGCCGACCTAATTA 60.554 47.826 0.00 0.00 0.00 1.40
2615 10336 2.806745 CGTCCATGATGCCGACCTAATT 60.807 50.000 0.00 0.00 0.00 1.40
2616 10337 1.270305 CGTCCATGATGCCGACCTAAT 60.270 52.381 0.00 0.00 0.00 1.73
2617 10338 0.104120 CGTCCATGATGCCGACCTAA 59.896 55.000 0.00 0.00 0.00 2.69
2618 10339 1.739667 CGTCCATGATGCCGACCTA 59.260 57.895 0.00 0.00 0.00 3.08
2619 10340 2.501128 CGTCCATGATGCCGACCT 59.499 61.111 0.00 0.00 0.00 3.85
2620 10341 3.272334 GCGTCCATGATGCCGACC 61.272 66.667 6.87 0.00 38.50 4.79
2621 10342 1.815421 AAGCGTCCATGATGCCGAC 60.815 57.895 4.74 0.21 44.75 4.79
2622 10343 1.815003 CAAGCGTCCATGATGCCGA 60.815 57.895 4.74 0.00 44.75 5.54
2623 10344 0.809636 TACAAGCGTCCATGATGCCG 60.810 55.000 4.74 0.00 44.75 5.69
2624 10345 1.064060 GTTACAAGCGTCCATGATGCC 59.936 52.381 4.74 0.00 44.75 4.40
2625 10346 1.267532 CGTTACAAGCGTCCATGATGC 60.268 52.381 0.00 0.01 44.07 3.91
2626 10347 1.267532 GCGTTACAAGCGTCCATGATG 60.268 52.381 0.00 0.00 0.00 3.07
2627 10348 1.006832 GCGTTACAAGCGTCCATGAT 58.993 50.000 0.00 0.00 0.00 2.45
2628 10349 0.319986 TGCGTTACAAGCGTCCATGA 60.320 50.000 0.00 0.00 37.44 3.07
2629 10350 0.095245 CTGCGTTACAAGCGTCCATG 59.905 55.000 0.00 0.00 37.44 3.66
2630 10351 0.320421 ACTGCGTTACAAGCGTCCAT 60.320 50.000 0.00 0.00 37.44 3.41
2631 10352 0.942410 GACTGCGTTACAAGCGTCCA 60.942 55.000 0.00 0.00 37.44 4.02
2632 10353 0.942410 TGACTGCGTTACAAGCGTCC 60.942 55.000 9.33 0.00 37.35 4.79
2633 10354 1.059264 GATGACTGCGTTACAAGCGTC 59.941 52.381 6.35 6.35 38.04 5.19
2634 10355 1.068474 GATGACTGCGTTACAAGCGT 58.932 50.000 0.00 0.00 37.44 5.07
2635 10356 1.350193 AGATGACTGCGTTACAAGCG 58.650 50.000 0.00 0.00 37.44 4.68
2636 10357 2.222596 CGAAGATGACTGCGTTACAAGC 60.223 50.000 0.00 0.00 40.05 4.01
2637 10358 3.624726 CGAAGATGACTGCGTTACAAG 57.375 47.619 0.00 0.00 40.05 3.16


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

AutoCloner maintained by Alex Coulton.