Multiple sequence alignment - TraesCS5D01G519700

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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 TraesCS5D01G519700 chr5D 100.000 3246 0 0 1513 4758 540289630 540286385 0.000000e+00 5995.0
1 TraesCS5D01G519700 chr5D 100.000 1272 0 0 1 1272 540291142 540289871 0.000000e+00 2350.0
2 TraesCS5D01G519700 chr5B 91.886 1824 117 16 1536 3346 682701239 682699434 0.000000e+00 2519.0
3 TraesCS5D01G519700 chr5B 91.693 638 27 6 3431 4068 682699410 682698799 0.000000e+00 861.0
4 TraesCS5D01G519700 chr5B 76.498 868 75 56 143 959 682704681 682703892 2.110000e-93 353.0
5 TraesCS5D01G519700 chr5B 86.081 273 30 4 966 1230 682703771 682703499 2.170000e-73 287.0
6 TraesCS5D01G519700 chr5B 80.000 390 32 13 4409 4758 682698309 682697926 3.680000e-61 246.0
7 TraesCS5D01G519700 chr5B 90.683 161 7 5 4067 4225 682698717 682698563 1.740000e-49 207.0
8 TraesCS5D01G519700 chr5B 97.297 74 2 0 4332 4405 27816094 27816167 5.000000e-25 126.0
9 TraesCS5D01G519700 chr5B 87.931 58 7 0 274 331 605783731 605783674 8.540000e-08 69.4
10 TraesCS5D01G519700 chr4A 93.548 1364 78 8 1835 3191 628331009 628329649 0.000000e+00 2023.0
11 TraesCS5D01G519700 chr4A 88.374 972 84 19 5 959 628334815 628333856 0.000000e+00 1142.0
12 TraesCS5D01G519700 chr4A 92.278 777 46 7 3395 4168 628329623 628328858 0.000000e+00 1090.0
13 TraesCS5D01G519700 chr4A 84.848 264 31 6 966 1220 628333759 628333496 1.700000e-64 257.0
14 TraesCS5D01G519700 chr7A 88.323 942 85 12 2286 3205 68888064 68889002 0.000000e+00 1107.0
15 TraesCS5D01G519700 chr7A 88.608 316 29 2 3431 3739 68889031 68889346 1.250000e-100 377.0
16 TraesCS5D01G519700 chr7A 83.471 121 14 2 998 1112 68885216 68885336 1.810000e-19 108.0
17 TraesCS5D01G519700 chr7A 90.541 74 6 1 4331 4404 310221565 310221637 3.920000e-16 97.1
18 TraesCS5D01G519700 chr7A 78.912 147 19 8 41 187 243777484 243777350 6.560000e-14 89.8
19 TraesCS5D01G519700 chr2D 87.759 964 92 11 2286 3231 614872129 614873084 0.000000e+00 1103.0
20 TraesCS5D01G519700 chr2D 86.364 308 35 2 3457 3757 614875281 614875588 3.550000e-86 329.0
21 TraesCS5D01G519700 chr2D 91.176 68 5 1 272 338 473721043 473721110 1.820000e-14 91.6
22 TraesCS5D01G519700 chr7D 87.979 940 84 12 2286 3205 64732827 64733757 0.000000e+00 1083.0
23 TraesCS5D01G519700 chr7D 87.975 316 31 2 3431 3739 64733785 64734100 2.710000e-97 366.0
24 TraesCS5D01G519700 chr7D 81.457 302 38 11 42 331 102552215 102552510 1.030000e-56 231.0
25 TraesCS5D01G519700 chr7D 79.402 301 36 18 45 331 128478092 128477804 6.290000e-44 189.0
26 TraesCS5D01G519700 chr7D 78.808 302 37 19 46 331 247308887 247308597 1.360000e-40 178.0
27 TraesCS5D01G519700 chr7D 95.294 85 4 0 4326 4410 78412226 78412142 8.310000e-28 135.0
28 TraesCS5D01G519700 chr7D 85.124 121 12 2 998 1112 64731403 64731523 8.360000e-23 119.0
29 TraesCS5D01G519700 chr7B 87.937 945 80 13 2286 3205 6371170 6372105 0.000000e+00 1083.0
30 TraesCS5D01G519700 chr7B 84.298 121 13 2 998 1112 6369914 6370034 3.890000e-21 113.0
31 TraesCS5D01G519700 chr4B 85.535 954 86 17 2286 3193 673190432 673189485 0.000000e+00 950.0
32 TraesCS5D01G519700 chr4B 87.423 326 33 3 3422 3739 673189454 673189129 7.520000e-98 368.0
33 TraesCS5D01G519700 chr5A 86.500 600 59 13 2347 2934 707643607 707644196 1.440000e-179 640.0
34 TraesCS5D01G519700 chr5A 80.841 214 31 7 46 258 429122185 429122389 4.930000e-35 159.0
35 TraesCS5D01G519700 chr5A 74.026 308 53 17 46 331 674360301 674360603 3.030000e-17 100.0
36 TraesCS5D01G519700 chr5A 82.759 87 15 0 3533 3619 707644715 707644801 1.420000e-10 78.7
37 TraesCS5D01G519700 chr3B 89.114 395 37 5 1947 2336 607811941 607811548 1.990000e-133 486.0
38 TraesCS5D01G519700 chrUn 84.483 406 39 9 2331 2718 99838361 99838760 3.480000e-101 379.0
39 TraesCS5D01G519700 chrUn 79.333 150 19 2 38 187 49220165 49220302 1.410000e-15 95.3
40 TraesCS5D01G519700 chr1D 81.457 302 37 12 44 330 118809109 118808812 3.700000e-56 230.0
41 TraesCS5D01G519700 chr1D 97.647 85 2 0 4326 4410 6193103 6193187 3.840000e-31 147.0
42 TraesCS5D01G519700 chr1D 79.333 150 19 2 38 187 68098128 68098265 1.410000e-15 95.3
43 TraesCS5D01G519700 chr1A 79.930 284 37 12 42 311 456341736 456342013 1.750000e-44 191.0
44 TraesCS5D01G519700 chr2B 89.815 108 11 0 2741 2848 749306151 749306258 6.420000e-29 139.0
45 TraesCS5D01G519700 chr6D 79.333 150 19 2 38 187 93284018 93284155 1.410000e-15 95.3
46 TraesCS5D01G519700 chr4D 79.333 150 19 2 38 187 391689874 391690011 1.410000e-15 95.3
47 TraesCS5D01G519700 chr3A 78.912 147 19 2 41 187 231278353 231278487 6.560000e-14 89.8
48 TraesCS5D01G519700 chr3A 79.310 145 16 7 197 330 690078493 690078634 6.560000e-14 89.8


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 TraesCS5D01G519700 chr5D 540286385 540291142 4757 True 4172.500000 5995 100.000000 1 4758 2 chr5D.!!$R1 4757
1 TraesCS5D01G519700 chr5B 682697926 682704681 6755 True 745.500000 2519 86.140167 143 4758 6 chr5B.!!$R2 4615
2 TraesCS5D01G519700 chr4A 628328858 628334815 5957 True 1128.000000 2023 89.762000 5 4168 4 chr4A.!!$R1 4163
3 TraesCS5D01G519700 chr7A 68885216 68889346 4130 False 530.666667 1107 86.800667 998 3739 3 chr7A.!!$F2 2741
4 TraesCS5D01G519700 chr2D 614872129 614875588 3459 False 716.000000 1103 87.061500 2286 3757 2 chr2D.!!$F2 1471
5 TraesCS5D01G519700 chr7D 64731403 64734100 2697 False 522.666667 1083 87.026000 998 3739 3 chr7D.!!$F2 2741
6 TraesCS5D01G519700 chr7B 6369914 6372105 2191 False 598.000000 1083 86.117500 998 3205 2 chr7B.!!$F1 2207
7 TraesCS5D01G519700 chr4B 673189129 673190432 1303 True 659.000000 950 86.479000 2286 3739 2 chr4B.!!$R1 1453
8 TraesCS5D01G519700 chr5A 707643607 707644801 1194 False 359.350000 640 84.629500 2347 3619 2 chr5A.!!$F3 1272

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
971 1157 0.614697 TCTCCGTGATCTTGGGCTCA 60.615 55.0 0.00 0.00 0.00 4.26 F
1579 5859 0.032217 CCAATGTACCCCCTTGCCAT 60.032 55.0 0.00 0.00 0.00 4.40 F
1791 6075 0.250513 GGTGACAGGAAGCCTAGGTG 59.749 60.0 11.31 2.43 29.64 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2488 7024 1.424493 GCGGCAGTCTGACATACAGC 61.424 60.000 10.88 7.25 45.38 4.40 R
3306 8044 4.142049 ACTTGTAACACCACAAAACATGGG 60.142 41.667 0.00 0.00 41.97 4.00 R
3778 10564 2.421424 GAGGGACAAGCTAACAGCATTG 59.579 50.000 0.38 5.17 45.56 2.82 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
28 29 4.733077 TTCTTTTCTGGGTTGGGTATGA 57.267 40.909 0.00 0.00 0.00 2.15
39 40 1.191535 TGGGTATGAGGGTCTTGACG 58.808 55.000 0.00 0.00 0.00 4.35
73 74 9.155975 CCTTTTGTTCATAGGATAGGAATATCG 57.844 37.037 0.00 0.00 43.72 2.92
121 122 6.765036 AGTGTGATGACATGTATCTCAATTCC 59.235 38.462 0.00 0.00 33.63 3.01
124 125 8.146412 TGTGATGACATGTATCTCAATTCCTAG 58.854 37.037 0.00 0.00 0.00 3.02
125 126 8.363390 GTGATGACATGTATCTCAATTCCTAGA 58.637 37.037 0.00 0.00 0.00 2.43
153 154 8.706492 AAAAATGAATGTCGTTTGATGCATAT 57.294 26.923 0.00 0.00 35.90 1.78
161 162 7.355332 TGTCGTTTGATGCATATGATATGAG 57.645 36.000 16.22 0.00 0.00 2.90
195 197 4.991153 GCCTAGGCTAATGCTTCTTTTT 57.009 40.909 27.17 0.00 39.59 1.94
267 285 4.200447 TCATTCCTACAACCCCCAAAAA 57.800 40.909 0.00 0.00 0.00 1.94
544 574 2.492090 CCCTTCGTCGGCTCTCAG 59.508 66.667 0.00 0.00 0.00 3.35
578 608 4.394712 GGCCTCCACCAGACCACG 62.395 72.222 0.00 0.00 0.00 4.94
687 735 3.710722 CGGCTCCACCCTCAGCTT 61.711 66.667 0.00 0.00 35.82 3.74
694 742 1.676967 CACCCTCAGCTTTCTGGCC 60.677 63.158 0.00 0.00 40.69 5.36
695 743 1.849823 ACCCTCAGCTTTCTGGCCT 60.850 57.895 3.32 0.00 40.69 5.19
726 774 2.033141 GCCAGTCAGCAGCCTTCA 59.967 61.111 0.00 0.00 0.00 3.02
819 870 1.774894 GCTCCCACCCAAGGTACACA 61.775 60.000 0.00 0.00 32.11 3.72
840 891 1.408683 CCTGCTGCCATTGCCTTACTA 60.409 52.381 0.00 0.00 36.33 1.82
844 895 2.480244 GCTGCCATTGCCTTACTAAAGC 60.480 50.000 0.00 0.00 36.33 3.51
846 897 4.199310 CTGCCATTGCCTTACTAAAGCTA 58.801 43.478 0.00 0.00 36.33 3.32
849 900 5.067674 TGCCATTGCCTTACTAAAGCTAATG 59.932 40.000 0.00 0.00 35.94 1.90
856 914 6.816640 TGCCTTACTAAAGCTAATGTACAGTG 59.183 38.462 5.98 0.00 0.00 3.66
860 918 6.037786 ACTAAAGCTAATGTACAGTGCAGA 57.962 37.500 5.98 0.00 0.00 4.26
881 952 7.110043 CAGATAGCTAATGATCTGCTCCATA 57.890 40.000 10.51 0.00 41.84 2.74
896 967 6.095860 TCTGCTCCATATTCATTTTCCACTTG 59.904 38.462 0.00 0.00 0.00 3.16
900 971 7.572523 TCCATATTCATTTTCCACTTGCTAG 57.427 36.000 0.00 0.00 0.00 3.42
919 990 8.554490 TTGCTAGAAGTCTAATTCTATCCCTT 57.446 34.615 0.00 0.00 40.18 3.95
923 994 7.757242 AGAAGTCTAATTCTATCCCTTTGGT 57.243 36.000 0.00 0.00 37.76 3.67
933 1005 4.715297 TCTATCCCTTTGGTACTTGGAGTC 59.285 45.833 0.00 0.00 0.00 3.36
934 1006 2.986050 TCCCTTTGGTACTTGGAGTCT 58.014 47.619 0.00 0.00 0.00 3.24
944 1016 0.689623 CTTGGAGTCTGAACAGGGCT 59.310 55.000 1.93 1.52 0.00 5.19
956 1028 2.206576 ACAGGGCTTCAACATTCTCC 57.793 50.000 0.00 0.00 0.00 3.71
959 1031 0.804989 GGGCTTCAACATTCTCCGTG 59.195 55.000 0.00 0.00 0.00 4.94
961 1033 2.359900 GGCTTCAACATTCTCCGTGAT 58.640 47.619 0.00 0.00 0.00 3.06
962 1034 2.352960 GGCTTCAACATTCTCCGTGATC 59.647 50.000 0.00 0.00 0.00 2.92
964 1036 3.686726 GCTTCAACATTCTCCGTGATCTT 59.313 43.478 0.00 0.00 0.00 2.40
968 1154 1.303309 CATTCTCCGTGATCTTGGGC 58.697 55.000 0.00 0.00 0.00 5.36
971 1157 0.614697 TCTCCGTGATCTTGGGCTCA 60.615 55.000 0.00 0.00 0.00 4.26
979 1166 1.194781 ATCTTGGGCTCACGGACTGT 61.195 55.000 0.00 0.00 0.00 3.55
991 1178 3.755628 GACTGTACCCAGGCGCGA 61.756 66.667 12.10 0.00 43.36 5.87
993 1180 4.814294 CTGTACCCAGGCGCGACC 62.814 72.222 9.25 10.36 34.90 4.79
1100 1293 2.865598 CGGGAGATGCTCATCCGCT 61.866 63.158 6.27 0.00 38.58 5.52
1113 1306 1.107114 ATCCGCTGTACAGGTGAGAG 58.893 55.000 23.95 0.40 0.00 3.20
1116 1319 0.457509 CGCTGTACAGGTGAGAGCAG 60.458 60.000 23.95 2.42 0.00 4.24
1145 1348 2.602211 CTCATCTCGTGTTGCAGATGAC 59.398 50.000 9.34 0.00 46.61 3.06
1148 1351 0.436150 CTCGTGTTGCAGATGACGTG 59.564 55.000 0.00 3.70 33.56 4.49
1151 1354 1.965930 TGTTGCAGATGACGTGCCC 60.966 57.895 0.00 0.00 40.43 5.36
1154 1357 0.537143 TTGCAGATGACGTGCCCTTT 60.537 50.000 0.00 0.00 40.43 3.11
1158 1361 1.741770 GATGACGTGCCCTTTCGCT 60.742 57.895 0.00 0.00 0.00 4.93
1159 1362 0.459585 GATGACGTGCCCTTTCGCTA 60.460 55.000 0.00 0.00 0.00 4.26
1161 1364 1.214589 GACGTGCCCTTTCGCTAGA 59.785 57.895 0.00 0.00 0.00 2.43
1165 1368 0.378610 GTGCCCTTTCGCTAGATTGC 59.621 55.000 0.00 0.00 0.00 3.56
1213 1421 2.369394 GCCTTGGATAGGTTGGTTCTG 58.631 52.381 0.00 0.00 46.61 3.02
1220 1428 5.261216 TGGATAGGTTGGTTCTGGAATTTC 58.739 41.667 0.00 0.00 0.00 2.17
1221 1429 4.645136 GGATAGGTTGGTTCTGGAATTTCC 59.355 45.833 8.59 8.59 36.96 3.13
1235 5489 6.712998 TCTGGAATTTCCGTAGTTTTGATTCA 59.287 34.615 10.79 0.00 40.17 2.57
1238 5492 8.455682 TGGAATTTCCGTAGTTTTGATTCATAC 58.544 33.333 10.79 0.00 40.17 2.39
1259 5513 7.990886 TCATACTGAATTGTTGAATAGTACCCC 59.009 37.037 0.00 0.00 0.00 4.95
1572 5852 2.666317 CCTTCAATCCAATGTACCCCC 58.334 52.381 0.00 0.00 0.00 5.40
1578 5858 1.143329 TCCAATGTACCCCCTTGCCA 61.143 55.000 0.00 0.00 0.00 4.92
1579 5859 0.032217 CCAATGTACCCCCTTGCCAT 60.032 55.000 0.00 0.00 0.00 4.40
1580 5860 1.622173 CCAATGTACCCCCTTGCCATT 60.622 52.381 0.00 0.00 0.00 3.16
1581 5861 2.187100 CAATGTACCCCCTTGCCATTT 58.813 47.619 0.00 0.00 0.00 2.32
1671 5953 3.071874 TCTGCTAAATTGTGGGACAGG 57.928 47.619 0.00 0.00 41.80 4.00
1677 5959 4.157840 GCTAAATTGTGGGACAGGGTTAAG 59.842 45.833 0.00 0.00 41.80 1.85
1679 5961 0.774908 TTGTGGGACAGGGTTAAGGG 59.225 55.000 0.00 0.00 41.80 3.95
1683 5965 2.042569 GTGGGACAGGGTTAAGGGAATT 59.957 50.000 0.00 0.00 41.80 2.17
1686 5968 4.167307 TGGGACAGGGTTAAGGGAATTATC 59.833 45.833 0.00 0.00 0.00 1.75
1689 5971 5.828328 GGACAGGGTTAAGGGAATTATCTTG 59.172 44.000 3.75 0.00 0.00 3.02
1690 5972 6.402981 ACAGGGTTAAGGGAATTATCTTGT 57.597 37.500 3.75 0.00 0.00 3.16
1693 5975 6.321435 CAGGGTTAAGGGAATTATCTTGTTCC 59.679 42.308 0.00 0.00 42.51 3.62
1694 5976 5.298527 GGGTTAAGGGAATTATCTTGTTCCG 59.701 44.000 0.00 0.00 43.84 4.30
1695 5977 5.884232 GGTTAAGGGAATTATCTTGTTCCGT 59.116 40.000 0.00 0.00 43.84 4.69
1696 5978 7.049754 GGTTAAGGGAATTATCTTGTTCCGTA 58.950 38.462 0.00 0.00 43.84 4.02
1697 5979 7.226128 GGTTAAGGGAATTATCTTGTTCCGTAG 59.774 40.741 0.00 0.00 43.84 3.51
1698 5980 4.704965 AGGGAATTATCTTGTTCCGTAGC 58.295 43.478 0.00 0.00 43.84 3.58
1699 5981 4.409247 AGGGAATTATCTTGTTCCGTAGCT 59.591 41.667 0.00 0.00 43.84 3.32
1700 5982 4.511826 GGGAATTATCTTGTTCCGTAGCTG 59.488 45.833 0.00 0.00 43.84 4.24
1701 5983 5.116882 GGAATTATCTTGTTCCGTAGCTGT 58.883 41.667 0.00 0.00 35.03 4.40
1702 5984 5.585047 GGAATTATCTTGTTCCGTAGCTGTT 59.415 40.000 0.00 0.00 35.03 3.16
1703 5985 6.093633 GGAATTATCTTGTTCCGTAGCTGTTT 59.906 38.462 0.00 0.00 35.03 2.83
1704 5986 7.361799 GGAATTATCTTGTTCCGTAGCTGTTTT 60.362 37.037 0.00 0.00 35.03 2.43
1705 5987 4.749245 ATCTTGTTCCGTAGCTGTTTTG 57.251 40.909 0.00 0.00 0.00 2.44
1744 6026 3.055819 ACATCATCTGTTCCGTAGCTGTT 60.056 43.478 0.00 0.00 32.90 3.16
1791 6075 0.250513 GGTGACAGGAAGCCTAGGTG 59.749 60.000 11.31 2.43 29.64 4.00
1795 6079 1.142748 CAGGAAGCCTAGGTGCTCG 59.857 63.158 11.31 0.00 41.80 5.03
1897 6426 8.501580 CACATTAGGAGATATAACAGCACAATG 58.498 37.037 0.00 0.00 0.00 2.82
1905 6434 9.929180 GAGATATAACAGCACAATGGTAGAATA 57.071 33.333 0.00 0.00 0.00 1.75
1912 6441 3.632145 GCACAATGGTAGAATAACCCCAG 59.368 47.826 0.00 0.00 38.90 4.45
1915 6444 5.714806 CACAATGGTAGAATAACCCCAGTTT 59.285 40.000 0.00 0.00 38.90 2.66
1961 6490 3.146618 ACGTGAGTCAATAACTAGGCG 57.853 47.619 0.00 0.00 44.19 5.52
1997 6526 4.320202 GCTATTTCTTTTCCAGTGCGTGAA 60.320 41.667 0.00 0.00 0.00 3.18
2084 6617 3.081804 GCTTGTGCAATAAGTACCACCT 58.918 45.455 12.10 0.00 37.38 4.00
2095 6628 9.099454 GCAATAAGTACCACCTATAATATCTGC 57.901 37.037 0.00 0.00 0.00 4.26
2108 6641 4.500499 AATATCTGCTTTCTGCCTGTCT 57.500 40.909 0.00 0.00 42.00 3.41
2140 6673 3.942115 GGACTCCATGGACTCTAAAAAGC 59.058 47.826 11.44 0.00 0.00 3.51
2142 6675 2.939103 CTCCATGGACTCTAAAAAGCGG 59.061 50.000 11.44 0.00 0.00 5.52
2153 6687 7.304919 ACTCTAAAAAGCGGCTATTAGTTTC 57.695 36.000 23.59 0.00 0.00 2.78
2155 6689 8.255905 ACTCTAAAAAGCGGCTATTAGTTTCTA 58.744 33.333 23.59 11.44 0.00 2.10
2165 6699 8.989980 GCGGCTATTAGTTTCTAGATGTATTTT 58.010 33.333 0.00 0.00 0.00 1.82
2239 6775 9.936759 TCTTAACAAAATTTGAACTGAAAACCT 57.063 25.926 13.19 0.00 0.00 3.50
2245 6781 5.930837 ATTTGAACTGAAAACCTGTTGGA 57.069 34.783 0.00 0.00 37.11 3.53
2295 6831 5.048224 CCTTTCAGTTGCTGTCATTCTGATT 60.048 40.000 0.00 0.00 35.31 2.57
2327 6863 9.997482 CTGTTTAGAAGTTTTTAGTAACTTGCA 57.003 29.630 6.49 0.00 45.68 4.08
2364 6900 4.693283 CAGAACTTGTGTGAAGGAGTGTA 58.307 43.478 0.00 0.00 0.00 2.90
2376 6912 4.469945 TGAAGGAGTGTAAGAATACAGGGG 59.530 45.833 0.00 0.00 42.54 4.79
2413 6949 0.837691 ATCAGCCACTGTCAGTCCCA 60.838 55.000 1.37 0.00 32.61 4.37
2420 6956 1.905215 CACTGTCAGTCCCAGGAGAAT 59.095 52.381 1.37 0.00 34.16 2.40
2435 6971 1.669779 GAGAATGACAGCACATCTGCC 59.330 52.381 0.00 0.00 46.76 4.85
2483 7019 2.095059 CCTTTACATGCAGTGGAAGCAC 60.095 50.000 0.00 0.00 45.95 4.40
2645 7194 7.169982 GGCTTGTATGTTGATGAGTGATACTAC 59.830 40.741 0.00 0.00 0.00 2.73
2657 7206 9.632807 GATGAGTGATACTACTATTTCACCATC 57.367 37.037 12.88 12.88 39.39 3.51
3218 7826 9.330063 TCCTACAGTATTTGATCTTTTGCTATG 57.670 33.333 0.00 0.00 0.00 2.23
3295 8033 4.223923 AGCTAGGCTCAACAATCTTGTAGT 59.776 41.667 0.00 0.00 35.28 2.73
3306 8044 9.997482 TCAACAATCTTGTAGTTGTTACTTTTC 57.003 29.630 3.50 0.00 44.27 2.29
3350 8107 8.650714 ACAAGTTAAATAAAAGATACGACGGAC 58.349 33.333 0.00 0.00 0.00 4.79
3367 8124 7.751047 CGACGGACGGAATATTATCATTAAT 57.249 36.000 0.00 0.00 38.46 1.40
3369 8126 7.253983 CGACGGACGGAATATTATCATTAATGG 60.254 40.741 15.36 0.00 38.46 3.16
3373 8130 8.883731 GGACGGAATATTATCATTAATGGACTG 58.116 37.037 15.36 6.16 30.64 3.51
3410 8182 5.045215 TCAGTTTACCTTACACACACTTCG 58.955 41.667 0.00 0.00 0.00 3.79
3412 8184 2.443887 TACCTTACACACACTTCGCC 57.556 50.000 0.00 0.00 0.00 5.54
3823 10609 2.154462 CAAGGTAACACAAGCAGAGGG 58.846 52.381 0.00 0.00 41.41 4.30
3829 10615 1.974875 CACAAGCAGAGGGCATGCA 60.975 57.895 21.36 0.00 44.83 3.96
3846 10632 3.546543 ATGCTGCCATGCCATGCC 61.547 61.111 0.00 0.00 0.00 4.40
3848 10634 3.546543 GCTGCCATGCCATGCCAT 61.547 61.111 0.00 0.00 0.00 4.40
3849 10635 2.421314 CTGCCATGCCATGCCATG 59.579 61.111 9.68 9.68 41.71 3.66
3850 10636 3.807631 CTGCCATGCCATGCCATGC 62.808 63.158 11.13 7.49 40.92 4.06
3853 10639 2.497293 CATGCCATGCCATGCGTT 59.503 55.556 3.39 0.00 36.52 4.84
3868 10654 1.888018 CGTTCCCAGAAGCTCGGTA 59.112 57.895 0.00 0.00 0.00 4.02
3874 10660 0.830648 CCAGAAGCTCGGTATTCCCA 59.169 55.000 0.00 0.00 0.00 4.37
3918 10704 1.139989 TCTTTCAGCGAAACTCAGCG 58.860 50.000 0.00 0.00 38.61 5.18
3931 10717 3.045601 ACTCAGCGTCTTGTTTATGCT 57.954 42.857 0.00 0.00 39.79 3.79
3964 10750 4.543590 TCTTGACCTCCTGATTTCTGTC 57.456 45.455 0.00 0.00 0.00 3.51
3965 10751 4.163427 TCTTGACCTCCTGATTTCTGTCT 58.837 43.478 0.00 0.00 0.00 3.41
3966 10752 3.969287 TGACCTCCTGATTTCTGTCTG 57.031 47.619 0.00 0.00 0.00 3.51
3967 10753 2.027745 TGACCTCCTGATTTCTGTCTGC 60.028 50.000 0.00 0.00 0.00 4.26
4028 10814 7.265693 GAAAAGGACATAATCTTTTTCGTGC 57.734 36.000 8.04 0.00 46.92 5.34
4110 10981 2.159170 AGACGAGATAACAGCCAGAAGC 60.159 50.000 0.00 0.00 44.25 3.86
4145 11016 4.469469 TCCTTGGGGAATTTTCAACTCT 57.531 40.909 0.00 0.00 38.93 3.24
4147 11018 3.259123 CCTTGGGGAATTTTCAACTCTGG 59.741 47.826 0.00 0.00 33.58 3.86
4154 11025 1.896220 TTTTCAACTCTGGCGCTCAT 58.104 45.000 7.64 0.00 0.00 2.90
4155 11026 1.896220 TTTCAACTCTGGCGCTCATT 58.104 45.000 7.64 0.00 0.00 2.57
4171 11042 5.693814 CGCTCATTTTTCTTCCCTATATGC 58.306 41.667 0.00 0.00 0.00 3.14
4178 11049 5.505181 TTTCTTCCCTATATGCCTGGATC 57.495 43.478 0.00 0.00 0.00 3.36
4220 11091 1.187567 ATTGGGCTGGACTGGTTTGC 61.188 55.000 0.00 0.00 0.00 3.68
4225 11096 1.941812 CTGGACTGGTTTGCACGTC 59.058 57.895 0.00 0.00 0.00 4.34
4227 11098 0.813610 TGGACTGGTTTGCACGTCTG 60.814 55.000 0.00 0.00 0.00 3.51
4228 11099 0.531974 GGACTGGTTTGCACGTCTGA 60.532 55.000 0.00 0.00 0.00 3.27
4229 11100 1.295792 GACTGGTTTGCACGTCTGAA 58.704 50.000 0.00 0.00 0.00 3.02
4230 11101 1.668751 GACTGGTTTGCACGTCTGAAA 59.331 47.619 0.00 0.00 0.00 2.69
4231 11102 1.670811 ACTGGTTTGCACGTCTGAAAG 59.329 47.619 0.00 0.00 0.00 2.62
4232 11103 0.380378 TGGTTTGCACGTCTGAAAGC 59.620 50.000 0.00 0.00 0.00 3.51
4233 11104 0.663153 GGTTTGCACGTCTGAAAGCT 59.337 50.000 0.00 0.00 0.00 3.74
4235 11106 1.330521 GTTTGCACGTCTGAAAGCTCA 59.669 47.619 0.00 0.00 0.00 4.26
4236 11107 0.937304 TTGCACGTCTGAAAGCTCAC 59.063 50.000 0.00 0.00 0.00 3.51
4237 11108 0.179086 TGCACGTCTGAAAGCTCACA 60.179 50.000 0.00 0.00 0.00 3.58
4238 11109 0.510359 GCACGTCTGAAAGCTCACAG 59.490 55.000 12.14 12.14 35.72 3.66
4239 11110 1.858091 CACGTCTGAAAGCTCACAGT 58.142 50.000 16.13 0.61 35.84 3.55
4240 11111 2.205074 CACGTCTGAAAGCTCACAGTT 58.795 47.619 16.13 0.00 35.84 3.16
4241 11112 2.033407 CACGTCTGAAAGCTCACAGTTG 60.033 50.000 16.13 12.90 35.84 3.16
4242 11113 2.205074 CGTCTGAAAGCTCACAGTTGT 58.795 47.619 16.13 0.00 35.84 3.32
4243 11114 2.609459 CGTCTGAAAGCTCACAGTTGTT 59.391 45.455 16.13 0.00 35.84 2.83
4244 11115 3.544834 CGTCTGAAAGCTCACAGTTGTTG 60.545 47.826 16.13 4.03 35.84 3.33
4245 11116 3.623060 GTCTGAAAGCTCACAGTTGTTGA 59.377 43.478 16.13 0.00 35.84 3.18
4246 11117 3.623060 TCTGAAAGCTCACAGTTGTTGAC 59.377 43.478 16.13 0.00 35.84 3.18
4248 11119 3.755905 TGAAAGCTCACAGTTGTTGACAA 59.244 39.130 0.00 0.00 0.00 3.18
4249 11120 4.398988 TGAAAGCTCACAGTTGTTGACAAT 59.601 37.500 0.00 0.00 38.24 2.71
4250 11121 4.989279 AAGCTCACAGTTGTTGACAATT 57.011 36.364 0.00 0.00 38.24 2.32
4251 11122 4.558538 AGCTCACAGTTGTTGACAATTC 57.441 40.909 0.00 0.00 38.24 2.17
4252 11123 3.947196 AGCTCACAGTTGTTGACAATTCA 59.053 39.130 0.00 0.00 38.24 2.57
4254 11125 4.601019 CTCACAGTTGTTGACAATTCACC 58.399 43.478 0.00 0.00 38.24 4.02
4258 11129 2.693074 AGTTGTTGACAATTCACCCCAC 59.307 45.455 0.00 0.00 38.24 4.61
4259 11130 2.693074 GTTGTTGACAATTCACCCCACT 59.307 45.455 0.00 0.00 38.24 4.00
4260 11131 2.582052 TGTTGACAATTCACCCCACTC 58.418 47.619 0.00 0.00 0.00 3.51
4261 11132 2.174639 TGTTGACAATTCACCCCACTCT 59.825 45.455 0.00 0.00 0.00 3.24
4262 11133 3.222603 GTTGACAATTCACCCCACTCTT 58.777 45.455 0.00 0.00 0.00 2.85
4264 11135 3.909732 TGACAATTCACCCCACTCTTTT 58.090 40.909 0.00 0.00 0.00 2.27
4266 11137 3.230976 ACAATTCACCCCACTCTTTTCC 58.769 45.455 0.00 0.00 0.00 3.13
4267 11138 3.117131 ACAATTCACCCCACTCTTTTCCT 60.117 43.478 0.00 0.00 0.00 3.36
4268 11139 2.656947 TTCACCCCACTCTTTTCCTG 57.343 50.000 0.00 0.00 0.00 3.86
4269 11140 1.518367 TCACCCCACTCTTTTCCTGT 58.482 50.000 0.00 0.00 0.00 4.00
4270 11141 1.420138 TCACCCCACTCTTTTCCTGTC 59.580 52.381 0.00 0.00 0.00 3.51
4271 11142 0.771755 ACCCCACTCTTTTCCTGTCC 59.228 55.000 0.00 0.00 0.00 4.02
4272 11143 0.771127 CCCCACTCTTTTCCTGTCCA 59.229 55.000 0.00 0.00 0.00 4.02
4277 11148 3.555966 CACTCTTTTCCTGTCCAACCTT 58.444 45.455 0.00 0.00 0.00 3.50
4281 11152 0.469144 TTTCCTGTCCAACCTTGCCC 60.469 55.000 0.00 0.00 0.00 5.36
4284 11155 1.763770 CTGTCCAACCTTGCCCTCT 59.236 57.895 0.00 0.00 0.00 3.69
4285 11156 0.322008 CTGTCCAACCTTGCCCTCTC 60.322 60.000 0.00 0.00 0.00 3.20
4287 11158 1.463214 TCCAACCTTGCCCTCTCCA 60.463 57.895 0.00 0.00 0.00 3.86
4288 11159 1.303643 CCAACCTTGCCCTCTCCAC 60.304 63.158 0.00 0.00 0.00 4.02
4290 11161 2.539081 AACCTTGCCCTCTCCACCC 61.539 63.158 0.00 0.00 0.00 4.61
4291 11162 2.612115 CCTTGCCCTCTCCACCCT 60.612 66.667 0.00 0.00 0.00 4.34
4292 11163 2.674220 CCTTGCCCTCTCCACCCTC 61.674 68.421 0.00 0.00 0.00 4.30
4293 11164 1.920325 CTTGCCCTCTCCACCCTCA 60.920 63.158 0.00 0.00 0.00 3.86
4294 11165 1.463214 TTGCCCTCTCCACCCTCAA 60.463 57.895 0.00 0.00 0.00 3.02
4295 11166 1.779061 TTGCCCTCTCCACCCTCAAC 61.779 60.000 0.00 0.00 0.00 3.18
4296 11167 2.982130 CCCTCTCCACCCTCAACG 59.018 66.667 0.00 0.00 0.00 4.10
4297 11168 2.266055 CCTCTCCACCCTCAACGC 59.734 66.667 0.00 0.00 0.00 4.84
4298 11169 2.266055 CTCTCCACCCTCAACGCC 59.734 66.667 0.00 0.00 0.00 5.68
4299 11170 3.316573 CTCTCCACCCTCAACGCCC 62.317 68.421 0.00 0.00 0.00 6.13
4329 11265 2.109126 GCGATGGACCTGTTGGAGC 61.109 63.158 0.00 0.00 37.04 4.70
4331 11267 1.450312 GATGGACCTGTTGGAGCCG 60.450 63.158 0.00 0.00 35.28 5.52
4332 11268 2.876368 GATGGACCTGTTGGAGCCGG 62.876 65.000 0.00 0.00 35.28 6.13
4334 11270 4.021925 GACCTGTTGGAGCCGGCT 62.022 66.667 33.48 33.48 37.04 5.52
4335 11271 3.959991 GACCTGTTGGAGCCGGCTC 62.960 68.421 42.46 42.46 42.04 4.70
4348 11284 2.496817 GGCTCCTCTGCCGTACTG 59.503 66.667 0.00 0.00 43.74 2.74
4360 11296 1.447838 CGTACTGCATCCTGCCGTT 60.448 57.895 1.58 0.00 44.23 4.44
4361 11297 1.695893 CGTACTGCATCCTGCCGTTG 61.696 60.000 1.58 0.00 44.23 4.10
4362 11298 1.078497 TACTGCATCCTGCCGTTGG 60.078 57.895 1.58 0.00 44.23 3.77
4372 11308 3.414700 GCCGTTGGCTCACTGACG 61.415 66.667 0.00 0.00 46.69 4.35
4373 11309 3.414700 CCGTTGGCTCACTGACGC 61.415 66.667 0.00 0.00 34.41 5.19
4374 11310 3.767230 CGTTGGCTCACTGACGCG 61.767 66.667 3.53 3.53 0.00 6.01
4375 11311 2.661866 GTTGGCTCACTGACGCGT 60.662 61.111 13.85 13.85 0.00 6.01
4376 11312 2.661537 TTGGCTCACTGACGCGTG 60.662 61.111 20.70 5.54 36.25 5.34
4411 11347 2.360852 CAGTGGGCTGAGGGCAAG 60.361 66.667 0.00 0.00 45.28 4.01
4412 11348 4.357279 AGTGGGCTGAGGGCAAGC 62.357 66.667 0.00 0.00 44.01 4.01
4460 11404 3.489513 GGCCACCCGAGCCCTAAT 61.490 66.667 0.00 0.00 45.16 1.73
4468 11417 0.837272 CCGAGCCCTAATTCCTCCAA 59.163 55.000 0.00 0.00 0.00 3.53
4478 11427 4.938226 CCTAATTCCTCCAACAGTCTTGAC 59.062 45.833 0.00 0.00 0.00 3.18
4479 11428 2.930826 TTCCTCCAACAGTCTTGACC 57.069 50.000 0.00 0.00 0.00 4.02
4482 11431 1.271054 CCTCCAACAGTCTTGACCCAG 60.271 57.143 0.00 0.00 0.00 4.45
4504 11453 0.250770 AAAACCCCACTCGAAGCTCC 60.251 55.000 0.00 0.00 0.00 4.70
4505 11454 1.128188 AAACCCCACTCGAAGCTCCT 61.128 55.000 0.00 0.00 0.00 3.69
4506 11455 1.831652 AACCCCACTCGAAGCTCCTG 61.832 60.000 0.00 0.00 0.00 3.86
4507 11456 2.286523 CCCCACTCGAAGCTCCTGT 61.287 63.158 0.00 0.00 0.00 4.00
4555 11504 4.083862 GTCCCACACCGCCCTCTC 62.084 72.222 0.00 0.00 0.00 3.20
4568 11535 1.395826 CCCTCTCCACCCTCATCGTC 61.396 65.000 0.00 0.00 0.00 4.20
4576 11543 4.530857 CCTCATCGTCACCGCCCC 62.531 72.222 0.00 0.00 0.00 5.80
4592 11559 4.530857 CCCGCCCTCGTCACCATC 62.531 72.222 0.00 0.00 0.00 3.51
4594 11561 4.129737 CGCCCTCGTCACCATCGT 62.130 66.667 0.00 0.00 0.00 3.73
4595 11562 2.202756 GCCCTCGTCACCATCGTC 60.203 66.667 0.00 0.00 0.00 4.20
4616 11583 0.107214 TGGATCCGATTGAGGCCAAC 60.107 55.000 5.01 0.00 34.72 3.77
4622 11589 1.068333 CCGATTGAGGCCAACAACTTG 60.068 52.381 15.67 9.49 34.72 3.16
4638 11605 0.944311 CTTGTTCGTCGTCCCACTGG 60.944 60.000 0.00 0.00 0.00 4.00
4653 11636 2.847234 TGGACCCAACTCCGTGCT 60.847 61.111 0.00 0.00 32.22 4.40
4687 11670 1.729881 GATCAAACGGCTGGATGGC 59.270 57.895 0.00 0.00 37.94 4.40
4702 11685 0.390860 ATGGCGAAGGAAGGAGATCG 59.609 55.000 0.00 0.00 38.28 3.69
4732 11715 5.051240 GGCGCGGCAATATATATTAGTGTAC 60.051 44.000 29.32 0.00 0.00 2.90
4737 11720 9.314321 GCGGCAATATATATTAGTGTACATCTT 57.686 33.333 7.65 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.120377 ACCCTCATACCCAACCCAGA 59.880 55.000 0.00 0.00 0.00 3.86
20 21 1.191535 CGTCAAGACCCTCATACCCA 58.808 55.000 0.00 0.00 0.00 4.51
21 22 0.464452 CCGTCAAGACCCTCATACCC 59.536 60.000 0.00 0.00 0.00 3.69
25 26 1.187087 GTCTCCGTCAAGACCCTCAT 58.813 55.000 0.00 0.00 39.85 2.90
81 82 9.942850 TGTCATCACACTTTCTATGATTTTCTA 57.057 29.630 0.00 0.00 30.58 2.10
94 95 8.571461 AATTGAGATACATGTCATCACACTTT 57.429 30.769 0.00 3.80 34.48 2.66
241 251 3.596046 TGGGGGTTGTAGGAATGAATTCT 59.404 43.478 7.05 0.00 37.00 2.40
246 256 3.905493 TTTTGGGGGTTGTAGGAATGA 57.095 42.857 0.00 0.00 0.00 2.57
344 364 3.256960 GACCCTTGGGCTGGTGGA 61.257 66.667 5.46 0.00 34.20 4.02
348 368 4.410400 GACGGACCCTTGGGCTGG 62.410 72.222 5.46 0.00 42.59 4.85
430 460 2.247358 GAGATGGAGATGGGAGAGGAC 58.753 57.143 0.00 0.00 0.00 3.85
520 550 4.772231 CCGACGAAGGGGAGGGGA 62.772 72.222 0.00 0.00 0.00 4.81
523 553 3.839432 GAGCCGACGAAGGGGAGG 61.839 72.222 0.00 0.00 0.00 4.30
539 569 3.456365 GAGGCGGCTCTGCTGAGA 61.456 66.667 30.02 0.00 42.73 3.27
672 720 0.676151 CAGAAAGCTGAGGGTGGAGC 60.676 60.000 0.00 0.00 45.17 4.70
711 759 2.389020 CGCTGAAGGCTGCTGACTG 61.389 63.158 0.00 0.00 39.13 3.51
723 771 4.069232 CCTCCGTGCCTCGCTGAA 62.069 66.667 0.00 0.00 38.35 3.02
802 853 1.420532 GGTGTGTACCTTGGGTGGGA 61.421 60.000 0.00 0.00 43.97 4.37
819 870 0.967380 GTAAGGCAATGGCAGCAGGT 60.967 55.000 10.05 0.00 43.71 4.00
824 875 3.019564 AGCTTTAGTAAGGCAATGGCAG 58.980 45.455 18.12 0.00 43.71 4.85
840 891 5.525378 GCTATCTGCACTGTACATTAGCTTT 59.475 40.000 13.29 3.95 42.31 3.51
844 895 8.084684 TCATTAGCTATCTGCACTGTACATTAG 58.915 37.037 0.00 0.00 45.94 1.73
846 897 6.820335 TCATTAGCTATCTGCACTGTACATT 58.180 36.000 0.00 0.00 45.94 2.71
849 900 6.585702 CAGATCATTAGCTATCTGCACTGTAC 59.414 42.308 10.51 0.00 41.80 2.90
860 918 8.087303 TGAATATGGAGCAGATCATTAGCTAT 57.913 34.615 0.00 0.00 39.02 2.97
881 952 6.944862 AGACTTCTAGCAAGTGGAAAATGAAT 59.055 34.615 10.94 0.00 0.00 2.57
890 961 7.870445 GGATAGAATTAGACTTCTAGCAAGTGG 59.130 40.741 10.94 0.00 42.94 4.00
896 967 7.875554 CCAAAGGGATAGAATTAGACTTCTAGC 59.124 40.741 1.51 1.51 41.30 3.42
900 971 8.706521 AGTACCAAAGGGATAGAATTAGACTTC 58.293 37.037 0.00 0.00 38.05 3.01
919 990 3.071023 CCTGTTCAGACTCCAAGTACCAA 59.929 47.826 1.00 0.00 0.00 3.67
923 994 1.623811 GCCCTGTTCAGACTCCAAGTA 59.376 52.381 1.00 0.00 0.00 2.24
933 1005 3.152341 AGAATGTTGAAGCCCTGTTCAG 58.848 45.455 0.00 0.00 37.72 3.02
934 1006 3.149196 GAGAATGTTGAAGCCCTGTTCA 58.851 45.455 0.00 0.00 34.56 3.18
944 1016 4.002982 CCAAGATCACGGAGAATGTTGAA 58.997 43.478 0.00 0.00 32.63 2.69
959 1031 0.460987 CAGTCCGTGAGCCCAAGATC 60.461 60.000 0.00 0.00 0.00 2.75
961 1033 0.541063 TACAGTCCGTGAGCCCAAGA 60.541 55.000 0.00 0.00 0.00 3.02
962 1034 0.389948 GTACAGTCCGTGAGCCCAAG 60.390 60.000 0.00 0.00 0.00 3.61
964 1036 2.280552 GGTACAGTCCGTGAGCCCA 61.281 63.158 0.00 0.00 0.00 5.36
968 1154 1.890894 CCTGGGTACAGTCCGTGAG 59.109 63.158 0.00 0.00 43.36 3.51
971 1157 3.379445 CGCCTGGGTACAGTCCGT 61.379 66.667 0.00 0.00 43.36 4.69
1023 1210 1.095600 GAAGGGAAGCCAATCGAACC 58.904 55.000 0.00 0.00 0.00 3.62
1100 1293 2.598565 AGAACTGCTCTCACCTGTACA 58.401 47.619 0.00 0.00 0.00 2.90
1113 1306 2.665537 CACGAGATGAGTCAAGAACTGC 59.334 50.000 0.00 0.00 38.74 4.40
1116 1319 3.120854 GCAACACGAGATGAGTCAAGAAC 60.121 47.826 0.00 0.00 0.00 3.01
1145 1348 0.652592 CAATCTAGCGAAAGGGCACG 59.347 55.000 0.00 0.00 34.64 5.34
1148 1351 1.776034 CGGCAATCTAGCGAAAGGGC 61.776 60.000 0.00 0.00 34.64 5.19
1151 1354 4.795970 ATAAACGGCAATCTAGCGAAAG 57.204 40.909 0.00 0.00 34.64 2.62
1154 1357 4.873827 AGAAAATAAACGGCAATCTAGCGA 59.126 37.500 0.00 0.00 34.64 4.93
1203 1411 2.235891 ACGGAAATTCCAGAACCAACC 58.764 47.619 13.04 0.00 35.91 3.77
1213 1421 8.674607 AGTATGAATCAAAACTACGGAAATTCC 58.325 33.333 0.99 0.99 0.00 3.01
1235 5489 7.993183 CAGGGGTACTATTCAACAATTCAGTAT 59.007 37.037 0.00 0.00 0.00 2.12
1238 5492 6.414732 TCAGGGGTACTATTCAACAATTCAG 58.585 40.000 0.00 0.00 0.00 3.02
1551 5831 2.666317 GGGGTACATTGGATTGAAGGG 58.334 52.381 0.00 0.00 0.00 3.95
1564 5844 3.767309 AATAAATGGCAAGGGGGTACA 57.233 42.857 0.00 0.00 0.00 2.90
1629 5911 8.883954 CAGAATCTAATCAACTGCATCTAGAA 57.116 34.615 0.00 0.00 0.00 2.10
1645 5927 6.480763 TGTCCCACAATTTAGCAGAATCTAA 58.519 36.000 0.00 0.00 0.00 2.10
1671 5953 5.884232 ACGGAACAAGATAATTCCCTTAACC 59.116 40.000 0.00 0.00 41.26 2.85
1677 5959 4.511826 CAGCTACGGAACAAGATAATTCCC 59.488 45.833 0.00 0.00 41.26 3.97
1679 5961 6.663944 AACAGCTACGGAACAAGATAATTC 57.336 37.500 0.00 0.00 0.00 2.17
1683 5965 5.178623 CACAAAACAGCTACGGAACAAGATA 59.821 40.000 0.00 0.00 0.00 1.98
1686 5968 3.311322 TCACAAAACAGCTACGGAACAAG 59.689 43.478 0.00 0.00 0.00 3.16
1689 5971 3.810373 CATCACAAAACAGCTACGGAAC 58.190 45.455 0.00 0.00 0.00 3.62
1690 5972 2.225491 GCATCACAAAACAGCTACGGAA 59.775 45.455 0.00 0.00 0.00 4.30
1693 5975 1.194547 ACGCATCACAAAACAGCTACG 59.805 47.619 0.00 0.00 0.00 3.51
1694 5976 2.969443 ACGCATCACAAAACAGCTAC 57.031 45.000 0.00 0.00 0.00 3.58
1695 5977 3.626977 CAAACGCATCACAAAACAGCTA 58.373 40.909 0.00 0.00 0.00 3.32
1696 5978 2.462889 CAAACGCATCACAAAACAGCT 58.537 42.857 0.00 0.00 0.00 4.24
1697 5979 1.071305 GCAAACGCATCACAAAACAGC 60.071 47.619 0.00 0.00 0.00 4.40
1698 5980 2.462889 AGCAAACGCATCACAAAACAG 58.537 42.857 0.00 0.00 0.00 3.16
1699 5981 2.575694 AGCAAACGCATCACAAAACA 57.424 40.000 0.00 0.00 0.00 2.83
1700 5982 2.597272 GCAAGCAAACGCATCACAAAAC 60.597 45.455 0.00 0.00 0.00 2.43
1701 5983 1.592081 GCAAGCAAACGCATCACAAAA 59.408 42.857 0.00 0.00 0.00 2.44
1702 5984 1.207390 GCAAGCAAACGCATCACAAA 58.793 45.000 0.00 0.00 0.00 2.83
1703 5985 0.101939 TGCAAGCAAACGCATCACAA 59.898 45.000 0.00 0.00 31.95 3.33
1704 5986 0.594540 GTGCAAGCAAACGCATCACA 60.595 50.000 0.00 0.00 40.89 3.58
1705 5987 0.594540 TGTGCAAGCAAACGCATCAC 60.595 50.000 0.00 0.00 40.89 3.06
1744 6026 1.581934 CTTCGACTGGCTGTCACAAA 58.418 50.000 21.99 12.58 45.60 2.83
1754 6036 3.972227 CCAGGTTGCTTCGACTGG 58.028 61.111 3.39 3.39 43.87 4.00
1762 6044 2.833913 CCTGTCACCCCAGGTTGCT 61.834 63.158 0.00 0.00 45.81 3.91
1791 6075 4.889832 ATCCTGAAATTTGATCACGAGC 57.110 40.909 0.00 0.00 0.00 5.03
1795 6079 8.514594 TGTTCTTGTATCCTGAAATTTGATCAC 58.485 33.333 0.00 0.00 0.00 3.06
1870 6399 6.524734 TGTGCTGTTATATCTCCTAATGTGG 58.475 40.000 0.00 0.00 0.00 4.17
1887 6416 4.270008 GGGTTATTCTACCATTGTGCTGT 58.730 43.478 0.00 0.00 40.09 4.40
1897 6426 7.764141 TGTTTAAAACTGGGGTTATTCTACC 57.236 36.000 0.00 0.00 34.90 3.18
1941 6470 2.751259 TCGCCTAGTTATTGACTCACGT 59.249 45.455 0.00 0.00 39.86 4.49
1942 6471 3.106672 GTCGCCTAGTTATTGACTCACG 58.893 50.000 0.00 0.00 39.86 4.35
1945 6474 3.445857 GGTGTCGCCTAGTTATTGACTC 58.554 50.000 0.00 0.00 39.86 3.36
1961 6490 5.948992 AAGAAATAGCTTTCACAGGTGTC 57.051 39.130 0.00 0.00 42.71 3.67
1973 6502 3.189287 CACGCACTGGAAAAGAAATAGCT 59.811 43.478 0.00 0.00 0.00 3.32
2074 6605 9.160412 AGAAAGCAGATATTATAGGTGGTACTT 57.840 33.333 0.00 0.00 0.00 2.24
2119 6652 3.619038 CGCTTTTTAGAGTCCATGGAGTC 59.381 47.826 33.90 33.90 43.06 3.36
2124 6657 2.359900 AGCCGCTTTTTAGAGTCCATG 58.640 47.619 0.00 0.00 0.00 3.66
2238 6774 6.514947 TGAACAAATTTCAGGAATCCAACAG 58.485 36.000 0.61 0.00 0.00 3.16
2239 6775 6.477053 TGAACAAATTTCAGGAATCCAACA 57.523 33.333 0.61 0.00 0.00 3.33
2245 6781 8.737168 TCGATAGATGAACAAATTTCAGGAAT 57.263 30.769 0.00 0.00 42.67 3.01
2315 6851 7.549134 CAGGTTGATCACTATGCAAGTTACTAA 59.451 37.037 0.00 0.00 35.76 2.24
2317 6853 5.877012 CAGGTTGATCACTATGCAAGTTACT 59.123 40.000 0.00 0.00 35.76 2.24
2327 6863 4.833478 AGTTCTGCAGGTTGATCACTAT 57.167 40.909 15.13 0.00 0.00 2.12
2329 6865 3.144506 CAAGTTCTGCAGGTTGATCACT 58.855 45.455 15.13 2.28 0.00 3.41
2364 6900 6.402981 ACTTCCAATAACCCCTGTATTCTT 57.597 37.500 0.00 0.00 0.00 2.52
2376 6912 6.318648 TGGCTGATGATGTTACTTCCAATAAC 59.681 38.462 0.00 0.00 33.85 1.89
2413 6949 3.263489 CAGATGTGCTGTCATTCTCCT 57.737 47.619 0.00 0.00 39.85 3.69
2435 6971 2.800544 CTGTGTGTACCAAGAACTTCCG 59.199 50.000 0.00 0.00 0.00 4.30
2483 7019 2.417933 GCAGTCTGACATACAGCTTTGG 59.582 50.000 10.88 0.00 45.38 3.28
2488 7024 1.424493 GCGGCAGTCTGACATACAGC 61.424 60.000 10.88 7.25 45.38 4.40
2645 7194 6.586344 AGTGGTAGTCATGATGGTGAAATAG 58.414 40.000 0.00 0.00 0.00 1.73
2657 7206 6.701145 AGACATGTAGTAGTGGTAGTCATG 57.299 41.667 0.00 0.00 37.68 3.07
2944 7524 6.481313 TGATGCTGCTGAGTAAGATATCAAAC 59.519 38.462 5.32 2.50 0.00 2.93
3218 7826 7.658982 TGCAGGATAGATCTTGTATGAATGAAC 59.341 37.037 0.00 0.00 36.40 3.18
3295 8033 6.109359 CCACAAAACATGGGAAAAGTAACAA 58.891 36.000 0.00 0.00 32.54 2.83
3306 8044 4.142049 ACTTGTAACACCACAAAACATGGG 60.142 41.667 0.00 0.00 41.97 4.00
3358 8115 9.283768 ACGCAATTATTCAGTCCATTAATGATA 57.716 29.630 17.23 2.92 0.00 2.15
3359 8116 8.169977 ACGCAATTATTCAGTCCATTAATGAT 57.830 30.769 17.23 3.87 0.00 2.45
3360 8117 7.498900 AGACGCAATTATTCAGTCCATTAATGA 59.501 33.333 17.23 0.46 32.70 2.57
3361 8118 7.642669 AGACGCAATTATTCAGTCCATTAATG 58.357 34.615 8.58 8.58 32.70 1.90
3362 8119 7.807977 AGACGCAATTATTCAGTCCATTAAT 57.192 32.000 5.93 0.00 32.70 1.40
3363 8120 7.335673 TGAAGACGCAATTATTCAGTCCATTAA 59.664 33.333 5.93 0.00 32.70 1.40
3364 8121 6.821160 TGAAGACGCAATTATTCAGTCCATTA 59.179 34.615 5.93 0.00 32.70 1.90
3367 8124 4.574892 TGAAGACGCAATTATTCAGTCCA 58.425 39.130 5.93 0.00 32.70 4.02
3373 8130 7.073342 AGGTAAACTGAAGACGCAATTATTC 57.927 36.000 0.00 0.00 0.00 1.75
3382 8139 5.045215 TGTGTGTAAGGTAAACTGAAGACG 58.955 41.667 0.00 0.00 0.00 4.18
3778 10564 2.421424 GAGGGACAAGCTAACAGCATTG 59.579 50.000 0.38 5.17 45.56 2.82
3846 10632 1.699656 CGAGCTTCTGGGAACGCATG 61.700 60.000 0.00 0.00 0.00 4.06
3847 10633 1.448540 CGAGCTTCTGGGAACGCAT 60.449 57.895 0.00 0.00 0.00 4.73
3848 10634 2.048222 CGAGCTTCTGGGAACGCA 60.048 61.111 0.00 0.00 0.00 5.24
3849 10635 2.221906 TACCGAGCTTCTGGGAACGC 62.222 60.000 1.86 0.00 33.49 4.84
3850 10636 0.460311 ATACCGAGCTTCTGGGAACG 59.540 55.000 1.86 0.00 33.49 3.95
3853 10639 1.120530 GGAATACCGAGCTTCTGGGA 58.879 55.000 1.86 0.00 33.49 4.37
3868 10654 0.031111 TCCTGATCGGTCCTGGGAAT 60.031 55.000 0.00 0.00 0.00 3.01
3874 10660 0.613777 GGTTTGTCCTGATCGGTCCT 59.386 55.000 0.00 0.00 0.00 3.85
3918 10704 7.145932 ACCAAAGATACAGCATAAACAAGAC 57.854 36.000 0.00 0.00 0.00 3.01
4059 10845 7.041098 ACTGCAATGCTAGGTTTATATAAGCAC 60.041 37.037 6.82 0.91 45.18 4.40
4110 10981 5.509498 TCCCCAAGGAACTGAAATTCATAG 58.491 41.667 0.00 0.00 40.08 2.23
4145 11016 0.887933 GGGAAGAAAAATGAGCGCCA 59.112 50.000 2.29 1.52 0.00 5.69
4147 11018 5.693814 CATATAGGGAAGAAAAATGAGCGC 58.306 41.667 0.00 0.00 0.00 5.92
4154 11025 5.725551 TCCAGGCATATAGGGAAGAAAAA 57.274 39.130 0.00 0.00 0.00 1.94
4155 11026 5.372363 TGATCCAGGCATATAGGGAAGAAAA 59.628 40.000 0.00 0.00 32.25 2.29
4178 11049 3.760151 ACGGGCATCCATCATTATGAATG 59.240 43.478 0.00 0.03 40.28 2.67
4220 11091 1.858091 ACTGTGAGCTTTCAGACGTG 58.142 50.000 20.60 1.47 35.84 4.49
4225 11096 3.374988 TGTCAACAACTGTGAGCTTTCAG 59.625 43.478 14.65 14.65 37.65 3.02
4227 11098 4.355543 TTGTCAACAACTGTGAGCTTTC 57.644 40.909 0.00 0.00 0.00 2.62
4228 11099 4.989279 ATTGTCAACAACTGTGAGCTTT 57.011 36.364 0.00 0.00 38.86 3.51
4229 11100 4.398988 TGAATTGTCAACAACTGTGAGCTT 59.601 37.500 0.00 0.00 38.86 3.74
4230 11101 3.947196 TGAATTGTCAACAACTGTGAGCT 59.053 39.130 0.00 0.00 38.86 4.09
4231 11102 4.037690 GTGAATTGTCAACAACTGTGAGC 58.962 43.478 0.00 0.00 38.86 4.26
4232 11103 4.498009 GGGTGAATTGTCAACAACTGTGAG 60.498 45.833 0.00 0.00 43.92 3.51
4233 11104 3.380004 GGGTGAATTGTCAACAACTGTGA 59.620 43.478 0.00 0.00 43.92 3.58
4235 11106 2.693074 GGGGTGAATTGTCAACAACTGT 59.307 45.455 0.00 0.00 43.92 3.55
4236 11107 2.692557 TGGGGTGAATTGTCAACAACTG 59.307 45.455 0.00 0.00 43.92 3.16
4237 11108 2.693074 GTGGGGTGAATTGTCAACAACT 59.307 45.455 0.00 0.00 43.92 3.16
4238 11109 2.693074 AGTGGGGTGAATTGTCAACAAC 59.307 45.455 0.00 0.00 43.92 3.32
4239 11110 2.955660 GAGTGGGGTGAATTGTCAACAA 59.044 45.455 0.00 0.00 43.92 2.83
4240 11111 2.174639 AGAGTGGGGTGAATTGTCAACA 59.825 45.455 0.00 0.00 43.92 3.33
4241 11112 2.863809 AGAGTGGGGTGAATTGTCAAC 58.136 47.619 0.00 0.00 41.13 3.18
4242 11113 3.593442 AAGAGTGGGGTGAATTGTCAA 57.407 42.857 0.00 0.00 34.87 3.18
4243 11114 3.593442 AAAGAGTGGGGTGAATTGTCA 57.407 42.857 0.00 0.00 0.00 3.58
4244 11115 3.255888 GGAAAAGAGTGGGGTGAATTGTC 59.744 47.826 0.00 0.00 0.00 3.18
4245 11116 3.117131 AGGAAAAGAGTGGGGTGAATTGT 60.117 43.478 0.00 0.00 0.00 2.71
4246 11117 3.256631 CAGGAAAAGAGTGGGGTGAATTG 59.743 47.826 0.00 0.00 0.00 2.32
4248 11119 2.447047 ACAGGAAAAGAGTGGGGTGAAT 59.553 45.455 0.00 0.00 0.00 2.57
4249 11120 1.850345 ACAGGAAAAGAGTGGGGTGAA 59.150 47.619 0.00 0.00 0.00 3.18
4250 11121 1.420138 GACAGGAAAAGAGTGGGGTGA 59.580 52.381 0.00 0.00 0.00 4.02
4251 11122 1.545651 GGACAGGAAAAGAGTGGGGTG 60.546 57.143 0.00 0.00 0.00 4.61
4252 11123 0.771755 GGACAGGAAAAGAGTGGGGT 59.228 55.000 0.00 0.00 0.00 4.95
4254 11125 2.230660 GTTGGACAGGAAAAGAGTGGG 58.769 52.381 0.00 0.00 0.00 4.61
4258 11129 2.294512 GCAAGGTTGGACAGGAAAAGAG 59.705 50.000 0.00 0.00 0.00 2.85
4259 11130 2.306847 GCAAGGTTGGACAGGAAAAGA 58.693 47.619 0.00 0.00 0.00 2.52
4260 11131 1.341209 GGCAAGGTTGGACAGGAAAAG 59.659 52.381 0.00 0.00 0.00 2.27
4261 11132 1.408969 GGCAAGGTTGGACAGGAAAA 58.591 50.000 0.00 0.00 0.00 2.29
4262 11133 0.469144 GGGCAAGGTTGGACAGGAAA 60.469 55.000 0.00 0.00 0.00 3.13
4264 11135 1.774217 AGGGCAAGGTTGGACAGGA 60.774 57.895 0.00 0.00 0.00 3.86
4266 11137 0.322008 GAGAGGGCAAGGTTGGACAG 60.322 60.000 0.00 0.00 0.00 3.51
4267 11138 1.761174 GAGAGGGCAAGGTTGGACA 59.239 57.895 0.00 0.00 0.00 4.02
4268 11139 1.002011 GGAGAGGGCAAGGTTGGAC 60.002 63.158 0.00 0.00 0.00 4.02
4269 11140 1.463214 TGGAGAGGGCAAGGTTGGA 60.463 57.895 0.00 0.00 0.00 3.53
4270 11141 1.303643 GTGGAGAGGGCAAGGTTGG 60.304 63.158 0.00 0.00 0.00 3.77
4271 11142 1.303643 GGTGGAGAGGGCAAGGTTG 60.304 63.158 0.00 0.00 0.00 3.77
4272 11143 2.539081 GGGTGGAGAGGGCAAGGTT 61.539 63.158 0.00 0.00 0.00 3.50
4277 11148 2.206900 TTGAGGGTGGAGAGGGCA 59.793 61.111 0.00 0.00 0.00 5.36
4281 11152 2.266055 GGCGTTGAGGGTGGAGAG 59.734 66.667 0.00 0.00 0.00 3.20
4284 11155 2.852075 AAGGGCGTTGAGGGTGGA 60.852 61.111 0.00 0.00 0.00 4.02
4285 11156 2.672996 CAAGGGCGTTGAGGGTGG 60.673 66.667 14.44 0.00 38.60 4.61
4287 11158 4.660938 GGCAAGGGCGTTGAGGGT 62.661 66.667 22.92 0.00 42.47 4.34
4311 11247 2.109126 GCTCCAACAGGTCCATCGC 61.109 63.158 0.00 0.00 0.00 4.58
4313 11249 1.450312 CGGCTCCAACAGGTCCATC 60.450 63.158 0.00 0.00 0.00 3.51
4332 11268 2.202810 GCAGTACGGCAGAGGAGC 60.203 66.667 13.42 0.00 0.00 4.70
4333 11269 3.288484 TGCAGTACGGCAGAGGAG 58.712 61.111 17.06 0.00 39.25 3.69
4360 11296 4.662961 CCACGCGTCAGTGAGCCA 62.663 66.667 9.86 0.00 44.43 4.75
4394 11330 2.360852 CTTGCCCTCAGCCCACTG 60.361 66.667 0.00 0.00 45.95 3.66
4459 11403 2.040412 GGGTCAAGACTGTTGGAGGAAT 59.960 50.000 0.00 0.00 0.00 3.01
4460 11404 1.420138 GGGTCAAGACTGTTGGAGGAA 59.580 52.381 0.00 0.00 0.00 3.36
4478 11427 0.889186 CGAGTGGGGTTTTGACTGGG 60.889 60.000 0.00 0.00 0.00 4.45
4479 11428 0.107831 TCGAGTGGGGTTTTGACTGG 59.892 55.000 0.00 0.00 0.00 4.00
4482 11431 0.591659 GCTTCGAGTGGGGTTTTGAC 59.408 55.000 0.00 0.00 0.00 3.18
4513 11462 2.292828 AAGAGTGGGGGTGAATTGTG 57.707 50.000 0.00 0.00 0.00 3.33
4525 11474 0.310854 GTGGGACGCAAAAAGAGTGG 59.689 55.000 0.00 0.00 39.55 4.00
4526 11475 3.845625 GTGGGACGCAAAAAGAGTG 57.154 52.632 0.00 0.00 39.55 3.51
4576 11543 4.873129 CGATGGTGACGAGGGCGG 62.873 72.222 0.00 0.00 43.17 6.13
4578 11545 2.202756 GACGATGGTGACGAGGGC 60.203 66.667 0.00 0.00 34.70 5.19
4592 11559 1.788258 CCTCAATCGGATCCATGACG 58.212 55.000 13.41 3.54 0.00 4.35
4594 11561 0.397941 GGCCTCAATCGGATCCATGA 59.602 55.000 13.41 11.66 0.00 3.07
4595 11562 0.109153 TGGCCTCAATCGGATCCATG 59.891 55.000 13.41 7.68 0.00 3.66
4603 11570 1.608590 ACAAGTTGTTGGCCTCAATCG 59.391 47.619 14.80 9.97 38.07 3.34
4605 11572 2.034558 CGAACAAGTTGTTGGCCTCAAT 59.965 45.455 25.46 0.00 41.28 2.57
4607 11574 1.021202 CGAACAAGTTGTTGGCCTCA 58.979 50.000 25.46 0.00 41.28 3.86
4616 11583 0.580104 GTGGGACGACGAACAAGTTG 59.420 55.000 0.00 0.00 0.00 3.16
4622 11589 3.045142 TCCAGTGGGACGACGAAC 58.955 61.111 9.92 0.00 38.64 3.95
4638 11605 1.021390 CATCAGCACGGAGTTGGGTC 61.021 60.000 0.00 0.00 41.61 4.46
4642 11609 2.159476 CCAATTCATCAGCACGGAGTTG 60.159 50.000 0.00 0.00 41.61 3.16
4653 11636 4.486125 TTGATCGTCTCCCAATTCATCA 57.514 40.909 0.00 0.00 0.00 3.07
4687 11670 0.528684 GCACCGATCTCCTTCCTTCG 60.529 60.000 0.00 0.00 0.00 3.79
4688 11671 0.528684 CGCACCGATCTCCTTCCTTC 60.529 60.000 0.00 0.00 0.00 3.46
4689 11672 1.517832 CGCACCGATCTCCTTCCTT 59.482 57.895 0.00 0.00 0.00 3.36
4690 11673 2.427245 CCGCACCGATCTCCTTCCT 61.427 63.158 0.00 0.00 0.00 3.36
4691 11674 2.107141 CCGCACCGATCTCCTTCC 59.893 66.667 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.