Multiple sequence alignment - TraesCS5A01G032500

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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 TraesCS5A01G032500 chr5A 100.000 6392 0 0 1 6392 29878796 29885187 0.000000e+00 11804
1 TraesCS5A01G032500 chr5A 89.844 896 54 14 1 872 29830114 29830996 0.000000e+00 1116
2 TraesCS5A01G032500 chr5A 90.670 418 37 2 1533 1949 630722179 630722595 7.240000e-154 555
3 TraesCS5A01G032500 chr5A 90.517 232 17 4 768 995 29829727 29829957 1.040000e-77 302
4 TraesCS5A01G032500 chr5A 81.818 264 29 11 1801 2063 513055269 513055024 3.020000e-48 204
5 TraesCS5A01G032500 chr5A 89.796 98 9 1 5549 5645 481203790 481203887 2.420000e-24 124
6 TraesCS5A01G032500 chr5A 85.484 124 11 4 1178 1296 630722062 630722183 8.700000e-24 122
7 TraesCS5A01G032500 chr5A 90.426 94 6 3 5544 5635 708410856 708410764 3.130000e-23 121
8 TraesCS5A01G032500 chr5B 88.872 5212 356 95 284 5400 35975224 35980306 0.000000e+00 6205
9 TraesCS5A01G032500 chr5B 86.404 228 23 5 5879 6099 38684279 38684505 6.400000e-60 243
10 TraesCS5A01G032500 chr5B 82.095 296 41 11 6098 6390 38684657 38684943 6.400000e-60 243
11 TraesCS5A01G032500 chr5B 88.649 185 10 4 5634 5814 35980425 35980602 1.400000e-51 215
12 TraesCS5A01G032500 chr5B 82.573 241 22 9 6169 6390 36070950 36071189 1.820000e-45 195
13 TraesCS5A01G032500 chr5B 95.556 90 4 0 5759 5848 38684102 38684191 1.860000e-30 145
14 TraesCS5A01G032500 chr5B 87.023 131 8 5 5428 5549 35980296 35980426 8.640000e-29 139
15 TraesCS5A01G032500 chr5B 78.922 204 22 12 8 195 35974863 35975061 1.130000e-22 119
16 TraesCS5A01G032500 chr5D 92.352 3635 168 49 1950 5537 41533972 41537543 0.000000e+00 5072
17 TraesCS5A01G032500 chr5D 89.398 1528 93 37 573 2073 41532390 41533875 0.000000e+00 1860
18 TraesCS5A01G032500 chr5D 90.635 299 24 3 6098 6392 41539095 41539393 1.670000e-105 394
19 TraesCS5A01G032500 chr5D 81.366 322 27 11 602 915 41530929 41531225 1.390000e-56 231
20 TraesCS5A01G032500 chr5D 88.095 168 10 4 5668 5831 41537569 41537730 2.350000e-44 191
21 TraesCS5A01G032500 chr5D 85.263 190 16 4 1801 1990 189932664 189932841 1.090000e-42 185
22 TraesCS5A01G032500 chr5D 75.000 448 84 13 188 616 41531346 41531784 1.420000e-41 182
23 TraesCS5A01G032500 chr5D 78.922 204 22 9 8 195 41531681 41531879 1.130000e-22 119
24 TraesCS5A01G032500 chr3B 83.945 436 57 6 3852 4280 651682046 651681617 7.720000e-109 405
25 TraesCS5A01G032500 chr3B 81.847 314 27 12 3370 3679 782437022 782436735 2.980000e-58 237
26 TraesCS5A01G032500 chr3B 81.529 314 28 11 3370 3679 651682366 651682079 1.390000e-56 231
27 TraesCS5A01G032500 chr3B 81.897 232 36 2 4055 4280 782471283 782471514 2.350000e-44 191
28 TraesCS5A01G032500 chr3B 88.776 98 9 2 5540 5635 50534569 50534666 1.130000e-22 119
29 TraesCS5A01G032500 chr3D 81.494 308 33 9 3376 3683 24664232 24664515 1.390000e-56 231
30 TraesCS5A01G032500 chr3D 91.304 92 6 2 5549 5639 146981121 146981031 2.420000e-24 124
31 TraesCS5A01G032500 chr4A 82.955 264 26 10 1801 2063 604531540 604531785 3.000000e-53 220
32 TraesCS5A01G032500 chr4A 80.617 227 40 4 3544 3769 708772318 708772095 8.520000e-39 172
33 TraesCS5A01G032500 chr4A 89.796 98 10 0 4057 4154 391389246 391389343 6.730000e-25 126
34 TraesCS5A01G032500 chr7A 82.197 264 27 12 1801 2063 61255238 61254994 6.490000e-50 209
35 TraesCS5A01G032500 chr7A 94.118 85 4 1 5549 5632 66643488 66643404 1.870000e-25 128
36 TraesCS5A01G032500 chr6A 82.197 264 28 10 1801 2063 75254037 75253792 6.490000e-50 209
37 TraesCS5A01G032500 chr7D 80.989 263 32 10 1801 2062 184648049 184647804 6.540000e-45 193
38 TraesCS5A01G032500 chr7D 79.339 242 34 6 2545 2783 627142848 627143076 8.580000e-34 156
39 TraesCS5A01G032500 chr1A 79.221 308 40 15 3376 3683 347780337 347780620 6.540000e-45 193
40 TraesCS5A01G032500 chrUn 78.662 314 39 18 3374 3683 75430528 75430817 3.940000e-42 183
41 TraesCS5A01G032500 chrUn 81.884 138 19 5 302 436 31638504 31638638 1.880000e-20 111
42 TraesCS5A01G032500 chr6B 79.623 265 34 13 1801 2063 148437877 148437631 8.520000e-39 172
43 TraesCS5A01G032500 chr6D 78.988 257 43 6 3537 3783 16150506 16150761 1.430000e-36 165
44 TraesCS5A01G032500 chr6D 91.304 92 7 1 5549 5639 65497086 65497177 2.420000e-24 124
45 TraesCS5A01G032500 chr6D 91.111 90 7 1 5549 5637 168293755 168293844 3.130000e-23 121
46 TraesCS5A01G032500 chr4B 91.837 98 8 0 4057 4154 150981492 150981589 3.110000e-28 137
47 TraesCS5A01G032500 chr2A 88.785 107 12 0 4057 4163 522248712 522248606 1.450000e-26 132
48 TraesCS5A01G032500 chr7B 90.816 98 8 1 4057 4154 68185412 68185316 5.200000e-26 130
49 TraesCS5A01G032500 chr3A 87.850 107 13 0 4057 4163 86562439 86562333 6.730000e-25 126
50 TraesCS5A01G032500 chr2D 89.796 98 9 1 5539 5635 217497001 217496904 2.420000e-24 124
51 TraesCS5A01G032500 chr1D 91.304 92 6 2 5545 5635 291087419 291087509 2.420000e-24 124


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 TraesCS5A01G032500 chr5A 29878796 29885187 6391 False 11804.000000 11804 100.000000 1 6392 1 chr5A.!!$F1 6391
1 TraesCS5A01G032500 chr5A 29829727 29830996 1269 False 709.000000 1116 90.180500 1 995 2 chr5A.!!$F3 994
2 TraesCS5A01G032500 chr5A 630722062 630722595 533 False 338.500000 555 88.077000 1178 1949 2 chr5A.!!$F4 771
3 TraesCS5A01G032500 chr5B 35974863 35980602 5739 False 1669.500000 6205 85.866500 8 5814 4 chr5B.!!$F2 5806
4 TraesCS5A01G032500 chr5B 38684102 38684943 841 False 210.333333 243 88.018333 5759 6390 3 chr5B.!!$F3 631
5 TraesCS5A01G032500 chr5D 41530929 41539393 8464 False 1149.857143 5072 85.109714 8 6392 7 chr5D.!!$F2 6384
6 TraesCS5A01G032500 chr3B 651681617 651682366 749 True 318.000000 405 82.737000 3370 4280 2 chr3B.!!$R2 910

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
44 790 0.390492 GCCTATGCCCAGCAAAATCC 59.610 55.000 0.00 0.00 43.62 3.01 F
443 1371 0.687354 ACTGTGTCGCCAAAGAGGAT 59.313 50.000 0.00 0.00 41.22 3.24 F
1113 2087 0.526662 AGACGGTGAAGATGTCCGAC 59.473 55.000 9.75 3.71 46.05 4.79 F
1114 2088 0.797249 GACGGTGAAGATGTCCGACG 60.797 60.000 9.75 0.00 46.05 5.12 F
1571 2596 1.012841 GCTTCAAGATTCGCCTCAGG 58.987 55.000 0.00 0.00 0.00 3.86 F
1580 2605 1.115467 TTCGCCTCAGGATTCTCCTC 58.885 55.000 0.00 0.00 45.66 3.71 F
2023 3057 1.321474 CACAGCAGTTGTTCCATGGT 58.679 50.000 12.58 0.00 38.16 3.55 F
3977 5243 1.263484 CACTTGCTGCAAGACTCACTG 59.737 52.381 40.04 25.75 43.42 3.66 F
4829 6105 0.331616 CCCAAAAAGGACCTCGGGAT 59.668 55.000 11.24 0.00 41.22 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1085 2059 0.388649 CTTCACCGTCTTCCTGACCG 60.389 60.000 0.00 0.00 42.49 4.79 R
2119 3372 0.533951 CCCAATCAGCAAGGGAAAGC 59.466 55.000 0.00 0.00 45.80 3.51 R
2617 3876 0.179032 TGCGTTCCTTTGCTTCCTCA 60.179 50.000 0.00 0.00 0.00 3.86 R
2817 4078 1.999735 TCAAAGTCGATCGCCATTGAC 59.000 47.619 12.18 3.62 42.12 3.18 R
3268 4529 1.152546 GCTTGGTTGGGACCCTGTT 60.153 57.895 13.00 0.00 45.92 3.16 R
3881 5147 8.673711 TCTTGTATATAAATCACCAGTGCAAAC 58.326 33.333 0.00 0.00 0.00 2.93 R
4141 5411 0.394938 TCACCCTGCTCGCAAAGTTA 59.605 50.000 0.00 0.00 0.00 2.24 R
4843 6119 0.179094 TTGTTGCTGTCCGAGAACGT 60.179 50.000 0.00 0.00 37.88 3.99 R
5803 7129 1.070843 CCGTTGTACACTGAACGCAAG 60.071 52.381 11.43 0.00 42.83 4.01 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
44 790 0.390492 GCCTATGCCCAGCAAAATCC 59.610 55.000 0.00 0.00 43.62 3.01
45 791 1.043022 CCTATGCCCAGCAAAATCCC 58.957 55.000 0.00 0.00 43.62 3.85
46 792 1.688942 CCTATGCCCAGCAAAATCCCA 60.689 52.381 0.00 0.00 43.62 4.37
47 793 2.322658 CTATGCCCAGCAAAATCCCAT 58.677 47.619 0.00 0.00 43.62 4.00
48 794 1.125633 ATGCCCAGCAAAATCCCATC 58.874 50.000 0.00 0.00 43.62 3.51
52 798 2.459644 CCCAGCAAAATCCCATCTCAA 58.540 47.619 0.00 0.00 0.00 3.02
133 895 5.046288 AGAATTCAATGAGGCTCTTAGGG 57.954 43.478 16.72 3.50 0.00 3.53
331 1167 4.424711 GCCCCACCATCGCCTTCA 62.425 66.667 0.00 0.00 0.00 3.02
346 1182 3.247056 TTCATTGGAGCCGGTGCGA 62.247 57.895 1.90 0.00 44.33 5.10
437 1365 1.133407 GGTTTTCACTGTGTCGCCAAA 59.867 47.619 7.79 0.00 0.00 3.28
443 1371 0.687354 ACTGTGTCGCCAAAGAGGAT 59.313 50.000 0.00 0.00 41.22 3.24
499 1437 7.625498 AGATTTAGGGGGTTCAAATTTTCAA 57.375 32.000 0.00 0.00 0.00 2.69
571 1509 2.753989 TGAATTGTGTTGACAGCACG 57.246 45.000 16.36 0.00 39.53 5.34
588 1526 6.630071 ACAGCACGGCAAAATCTAATAAATT 58.370 32.000 0.00 0.00 0.00 1.82
615 1553 1.001048 GCAGCACAGCAAAATCTCACA 60.001 47.619 0.00 0.00 0.00 3.58
616 1554 2.544277 GCAGCACAGCAAAATCTCACAA 60.544 45.455 0.00 0.00 0.00 3.33
622 1560 6.985645 AGCACAGCAAAATCTCACAAAAATTA 59.014 30.769 0.00 0.00 0.00 1.40
624 1562 8.284693 GCACAGCAAAATCTCACAAAAATTATT 58.715 29.630 0.00 0.00 0.00 1.40
640 1582 0.896923 TATTTTGGCAGCCCAGCAAG 59.103 50.000 9.64 0.00 43.37 4.01
911 1874 1.280998 TCCTCGATTCAAAACCCTCCC 59.719 52.381 0.00 0.00 0.00 4.30
912 1875 1.282157 CCTCGATTCAAAACCCTCCCT 59.718 52.381 0.00 0.00 0.00 4.20
944 1907 3.011789 CGACGAACTCGCGATCCG 61.012 66.667 10.36 15.88 44.43 4.18
952 1915 3.486252 CTCGCGATCCGTTCCTCCC 62.486 68.421 10.36 0.00 38.35 4.30
954 1917 3.155167 GCGATCCGTTCCTCCCCT 61.155 66.667 0.00 0.00 0.00 4.79
958 1929 0.691413 GATCCGTTCCTCCCCTCCTT 60.691 60.000 0.00 0.00 0.00 3.36
985 1956 1.057976 GCTTTCGCTTTCGCTCGAG 59.942 57.895 8.45 8.45 36.02 4.04
986 1957 1.618640 GCTTTCGCTTTCGCTCGAGT 61.619 55.000 15.13 0.00 36.02 4.18
987 1958 0.784778 CTTTCGCTTTCGCTCGAGTT 59.215 50.000 15.13 0.00 36.02 3.01
988 1959 0.782384 TTTCGCTTTCGCTCGAGTTC 59.218 50.000 15.13 0.00 36.02 3.01
989 1960 1.334992 TTCGCTTTCGCTCGAGTTCG 61.335 55.000 15.13 10.22 36.02 3.95
990 1961 2.178892 TCGCTTTCGCTCGAGTTCGA 62.179 55.000 15.13 12.58 46.44 3.71
1113 2087 0.526662 AGACGGTGAAGATGTCCGAC 59.473 55.000 9.75 3.71 46.05 4.79
1114 2088 0.797249 GACGGTGAAGATGTCCGACG 60.797 60.000 9.75 0.00 46.05 5.12
1157 2131 2.564975 CGTCAGCGAGGGTACGTT 59.435 61.111 0.00 0.00 41.33 3.99
1159 2133 1.881602 GTCAGCGAGGGTACGTTCT 59.118 57.895 0.00 0.00 35.59 3.01
1530 2534 4.554036 GGTGGAGGGGCGCAGATC 62.554 72.222 10.83 2.67 0.00 2.75
1571 2596 1.012841 GCTTCAAGATTCGCCTCAGG 58.987 55.000 0.00 0.00 0.00 3.86
1580 2605 1.115467 TTCGCCTCAGGATTCTCCTC 58.885 55.000 0.00 0.00 45.66 3.71
1621 2647 6.992715 GTGGTGGCTAGTATACAAATCAATCT 59.007 38.462 5.50 0.00 0.00 2.40
2023 3057 1.321474 CACAGCAGTTGTTCCATGGT 58.679 50.000 12.58 0.00 38.16 3.55
2134 3387 3.092301 GTTTAGGCTTTCCCTTGCTGAT 58.908 45.455 0.00 0.00 43.06 2.90
2143 3396 1.358787 TCCCTTGCTGATTGGGAACAT 59.641 47.619 0.00 0.00 46.06 2.71
2251 3504 6.234177 AGACCTGAGTGAGAAATTTAAGGTG 58.766 40.000 0.00 0.00 36.93 4.00
2303 3561 7.724305 TTTTACAGTACACTCTTAAGCTTGG 57.276 36.000 9.86 1.84 0.00 3.61
2360 3618 2.143122 CTGCAGGCGTTAAAGACAGAA 58.857 47.619 5.57 0.00 0.00 3.02
2369 3627 4.213482 GCGTTAAAGACAGAACACCAGATT 59.787 41.667 0.00 0.00 0.00 2.40
2430 3688 5.067023 TCAGATGCTACACAGATGACTACAG 59.933 44.000 0.00 0.00 0.00 2.74
2503 3762 7.923414 AGTTGTGTACTCTTCAGTTTTCTTT 57.077 32.000 0.00 0.00 33.62 2.52
2515 3774 9.490379 TCTTCAGTTTTCTTTTCTGTATCTACC 57.510 33.333 0.00 0.00 0.00 3.18
2519 3778 7.334671 CAGTTTTCTTTTCTGTATCTACCTCCC 59.665 40.741 0.00 0.00 0.00 4.30
2528 3787 5.195146 TCTGTATCTACCTCCCACTAAAGGA 59.805 44.000 0.00 0.00 36.46 3.36
2539 3798 4.586841 TCCCACTAAAGGAAACAAACATGG 59.413 41.667 0.00 0.00 0.00 3.66
2577 3836 3.825585 TCAACAGTGAGCCAATATGCAAA 59.174 39.130 0.00 0.00 0.00 3.68
2581 3840 5.172934 ACAGTGAGCCAATATGCAAATTTG 58.827 37.500 14.03 14.03 0.00 2.32
2647 3906 4.723248 CAAAGGAACGCAAGGATCTTTAC 58.277 43.478 0.00 0.00 46.39 2.01
2699 3958 8.275040 AGCTGGTTATTCTGGTATCAGTTTATT 58.725 33.333 2.20 0.00 41.59 1.40
2701 3960 8.657074 TGGTTATTCTGGTATCAGTTTATTCG 57.343 34.615 2.20 0.00 41.59 3.34
2712 3971 5.258685 TCAGTTTATTCGTTGTTACTGCG 57.741 39.130 0.00 0.00 34.49 5.18
2714 3973 5.636121 TCAGTTTATTCGTTGTTACTGCGAT 59.364 36.000 0.00 0.00 34.49 4.58
2724 3985 5.728049 CGTTGTTACTGCGATAAATTGACAG 59.272 40.000 0.00 0.00 0.00 3.51
2731 3992 5.105310 ACTGCGATAAATTGACAGTAGGACT 60.105 40.000 0.00 0.00 39.69 3.85
2735 3996 7.985184 TGCGATAAATTGACAGTAGGACTTAAT 59.015 33.333 0.00 0.00 0.00 1.40
2737 3998 9.314321 CGATAAATTGACAGTAGGACTTAATGT 57.686 33.333 0.00 0.00 42.81 2.71
2760 4021 4.215399 TGACTTGCACATTGCTTAGGTAAC 59.785 41.667 0.00 0.00 45.31 2.50
2769 4030 7.494625 GCACATTGCTTAGGTAACATAAGAGTA 59.505 37.037 6.66 0.00 40.96 2.59
2817 4078 1.462670 GAAGAAACAGCAGAAGGAGCG 59.537 52.381 0.00 0.00 37.01 5.03
2996 4257 9.113876 GTTCCTCATGTTTTTAACAGTTTATCG 57.886 33.333 0.00 0.00 45.95 2.92
3134 4395 7.595819 ACATTTACAATGGAAGGAACTGAAA 57.404 32.000 1.72 0.00 40.86 2.69
3881 5147 9.810545 TTTCAAACTTTCAAACCTTGGTTATAG 57.189 29.630 5.38 4.11 0.00 1.31
3897 5163 5.772672 TGGTTATAGTTTGCACTGGTGATTT 59.227 36.000 4.79 0.00 34.06 2.17
3944 5210 3.733443 ATTTGTCAAACTGGCAGGAAC 57.267 42.857 20.34 11.12 31.48 3.62
3977 5243 1.263484 CACTTGCTGCAAGACTCACTG 59.737 52.381 40.04 25.75 43.42 3.66
3991 5257 4.449068 AGACTCACTGAGTACGCAATTTTG 59.551 41.667 11.84 0.00 43.53 2.44
3994 5260 5.065988 ACTCACTGAGTACGCAATTTTGTTT 59.934 36.000 10.13 0.00 41.51 2.83
4013 5279 5.385198 TGTTTTCTTCTCCTTATGCTGGTT 58.615 37.500 0.00 0.00 0.00 3.67
4028 5294 5.643379 TGCTGGTTTGATTTGAACCTATC 57.357 39.130 7.45 0.00 45.39 2.08
4141 5411 3.114558 CGAAACTCTCTGCTCGCTT 57.885 52.632 0.00 0.00 0.00 4.68
4210 5480 6.262273 GGAAACAAGTTGATGTTGGAGAACTA 59.738 38.462 10.54 0.00 42.49 2.24
4488 5764 3.441572 CGACTTCTTTCAGCATCCCATTT 59.558 43.478 0.00 0.00 0.00 2.32
4493 5769 6.494835 ACTTCTTTCAGCATCCCATTTTAACT 59.505 34.615 0.00 0.00 0.00 2.24
4494 5770 6.271488 TCTTTCAGCATCCCATTTTAACTG 57.729 37.500 0.00 0.00 0.00 3.16
4496 5772 3.429492 TCAGCATCCCATTTTAACTGCA 58.571 40.909 0.00 0.00 32.18 4.41
4497 5773 3.444742 TCAGCATCCCATTTTAACTGCAG 59.555 43.478 13.48 13.48 32.18 4.41
4498 5774 2.762327 AGCATCCCATTTTAACTGCAGG 59.238 45.455 19.93 0.00 32.18 4.85
4499 5775 2.497273 GCATCCCATTTTAACTGCAGGT 59.503 45.455 19.93 15.51 0.00 4.00
4500 5776 3.055891 GCATCCCATTTTAACTGCAGGTT 60.056 43.478 19.93 12.22 41.54 3.50
4501 5777 4.497300 CATCCCATTTTAACTGCAGGTTG 58.503 43.478 19.93 6.41 38.75 3.77
4502 5778 2.298729 TCCCATTTTAACTGCAGGTTGC 59.701 45.455 19.93 0.00 45.29 4.17
4778 6054 2.630098 TGTCAGAGAGGAACCTCAACAG 59.370 50.000 20.84 11.96 44.99 3.16
4827 6103 0.893727 CACCCAAAAAGGACCTCGGG 60.894 60.000 14.01 14.01 41.22 5.14
4828 6104 1.063654 ACCCAAAAAGGACCTCGGGA 61.064 55.000 19.96 0.00 41.22 5.14
4829 6105 0.331616 CCCAAAAAGGACCTCGGGAT 59.668 55.000 11.24 0.00 41.22 3.85
4839 6115 1.301244 CCTCGGGATGATGGCGAAG 60.301 63.158 0.00 0.00 0.00 3.79
4869 6145 1.279840 GGACAGCAACAACAGCGAC 59.720 57.895 0.00 0.00 37.01 5.19
4902 6178 1.521010 CCAGCTCATGTCTCTGGCG 60.521 63.158 14.33 0.00 40.63 5.69
5028 6307 3.120385 CGCAACTCGCTGATGCCA 61.120 61.111 5.31 0.00 40.75 4.92
5124 6409 4.845580 CCGCCATTGAGCTCGCCT 62.846 66.667 9.64 0.00 0.00 5.52
5127 6412 2.203126 CCATTGAGCTCGCCTCCC 60.203 66.667 9.64 0.00 39.98 4.30
5209 6497 1.699083 TGCAGAAGAAGGTGGTCATCA 59.301 47.619 0.00 0.00 0.00 3.07
5217 6505 4.408821 GTGGTCATCAGGCCGCCA 62.409 66.667 13.15 0.00 0.00 5.69
5219 6507 4.408821 GGTCATCAGGCCGCCACA 62.409 66.667 13.15 0.00 0.00 4.17
5403 6707 4.225717 TGGAACCACTGATGATGATGAAGA 59.774 41.667 0.00 0.00 0.00 2.87
5426 6730 2.274893 TCAGTCAGCTGAGCTCTGG 58.725 57.895 24.68 11.94 45.94 3.86
5437 6741 3.867600 GCTGAGCTCTGGTGATGAAGAAA 60.868 47.826 20.66 0.00 0.00 2.52
5438 6742 3.933955 CTGAGCTCTGGTGATGAAGAAAG 59.066 47.826 16.19 0.00 0.00 2.62
5439 6743 3.580022 TGAGCTCTGGTGATGAAGAAAGA 59.420 43.478 16.19 0.00 0.00 2.52
5547 6866 8.533569 TCTGGGTTTCTTCTTCTTTTATTTGT 57.466 30.769 0.00 0.00 0.00 2.83
5548 6867 8.977412 TCTGGGTTTCTTCTTCTTTTATTTGTT 58.023 29.630 0.00 0.00 0.00 2.83
5555 6874 9.862149 TTCTTCTTCTTTTATTTGTTACTCCCT 57.138 29.630 0.00 0.00 0.00 4.20
5556 6875 9.503399 TCTTCTTCTTTTATTTGTTACTCCCTC 57.497 33.333 0.00 0.00 0.00 4.30
5557 6876 7.900782 TCTTCTTTTATTTGTTACTCCCTCG 57.099 36.000 0.00 0.00 0.00 4.63
5558 6877 7.447594 TCTTCTTTTATTTGTTACTCCCTCGT 58.552 34.615 0.00 0.00 0.00 4.18
5559 6878 7.601508 TCTTCTTTTATTTGTTACTCCCTCGTC 59.398 37.037 0.00 0.00 0.00 4.20
5560 6879 6.168389 TCTTTTATTTGTTACTCCCTCGTCC 58.832 40.000 0.00 0.00 0.00 4.79
5561 6880 4.476628 TTATTTGTTACTCCCTCGTCCC 57.523 45.455 0.00 0.00 0.00 4.46
5562 6881 1.719529 TTTGTTACTCCCTCGTCCCA 58.280 50.000 0.00 0.00 0.00 4.37
5563 6882 1.946984 TTGTTACTCCCTCGTCCCAT 58.053 50.000 0.00 0.00 0.00 4.00
5564 6883 2.832643 TGTTACTCCCTCGTCCCATA 57.167 50.000 0.00 0.00 0.00 2.74
5565 6884 3.104519 TGTTACTCCCTCGTCCCATAA 57.895 47.619 0.00 0.00 0.00 1.90
5566 6885 3.649843 TGTTACTCCCTCGTCCCATAAT 58.350 45.455 0.00 0.00 0.00 1.28
5567 6886 4.806892 TGTTACTCCCTCGTCCCATAATA 58.193 43.478 0.00 0.00 0.00 0.98
5568 6887 5.399991 TGTTACTCCCTCGTCCCATAATAT 58.600 41.667 0.00 0.00 0.00 1.28
5569 6888 6.554784 TGTTACTCCCTCGTCCCATAATATA 58.445 40.000 0.00 0.00 0.00 0.86
5570 6889 7.011994 TGTTACTCCCTCGTCCCATAATATAA 58.988 38.462 0.00 0.00 0.00 0.98
5571 6890 7.177921 TGTTACTCCCTCGTCCCATAATATAAG 59.822 40.741 0.00 0.00 0.00 1.73
5572 6891 5.900437 ACTCCCTCGTCCCATAATATAAGA 58.100 41.667 0.00 0.00 0.00 2.10
5573 6892 6.320518 ACTCCCTCGTCCCATAATATAAGAA 58.679 40.000 0.00 0.00 0.00 2.52
5574 6893 6.210984 ACTCCCTCGTCCCATAATATAAGAAC 59.789 42.308 0.00 0.00 0.00 3.01
5575 6894 5.184479 TCCCTCGTCCCATAATATAAGAACG 59.816 44.000 0.00 0.00 0.00 3.95
5576 6895 5.047519 CCCTCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
5577 6896 6.453092 CCTCGTCCCATAATATAAGAACGTT 58.547 40.000 0.00 0.00 0.00 3.99
5578 6897 6.927381 CCTCGTCCCATAATATAAGAACGTTT 59.073 38.462 0.46 0.00 0.00 3.60
5579 6898 7.440255 CCTCGTCCCATAATATAAGAACGTTTT 59.560 37.037 0.46 0.00 0.00 2.43
5580 6899 8.721019 TCGTCCCATAATATAAGAACGTTTTT 57.279 30.769 9.22 9.22 0.00 1.94
5621 6940 6.644248 AAAAACGGCCTTATATTATGGGAC 57.356 37.500 0.00 0.00 0.00 4.46
5623 6942 2.901249 CGGCCTTATATTATGGGACGG 58.099 52.381 14.23 1.71 45.53 4.79
5624 6943 2.498481 CGGCCTTATATTATGGGACGGA 59.502 50.000 14.23 0.00 45.53 4.69
5625 6944 3.430374 CGGCCTTATATTATGGGACGGAG 60.430 52.174 14.23 0.00 45.53 4.63
5626 6945 3.118371 GGCCTTATATTATGGGACGGAGG 60.118 52.174 0.00 0.00 0.00 4.30
5627 6946 3.118371 GCCTTATATTATGGGACGGAGGG 60.118 52.174 0.00 0.00 0.00 4.30
5628 6947 4.359105 CCTTATATTATGGGACGGAGGGA 58.641 47.826 0.00 0.00 0.00 4.20
5629 6948 4.406003 CCTTATATTATGGGACGGAGGGAG 59.594 50.000 0.00 0.00 0.00 4.30
5661 6980 0.620556 AGATTTGGCGAGTGGTGGAT 59.379 50.000 0.00 0.00 0.00 3.41
5663 6982 0.620556 ATTTGGCGAGTGGTGGATCT 59.379 50.000 0.00 0.00 0.00 2.75
5740 7066 1.733526 GTTTGCAAGTGCTTCCGGT 59.266 52.632 0.00 0.00 42.66 5.28
5754 7080 2.234300 TCCGGTTTGAGTGTGAGAAC 57.766 50.000 0.00 0.00 0.00 3.01
5756 7082 1.867233 CCGGTTTGAGTGTGAGAACTG 59.133 52.381 0.00 0.00 0.00 3.16
5803 7129 4.925068 AGCATGTGAGTTGTGTTCTTTTC 58.075 39.130 0.00 0.00 0.00 2.29
5843 8073 3.325135 CGGGGGACTCAGCTCTTATATTT 59.675 47.826 0.00 0.00 0.00 1.40
5848 8078 5.994668 GGGACTCAGCTCTTATATTTTGAGG 59.005 44.000 4.56 0.00 37.08 3.86
5850 8080 6.704050 GGACTCAGCTCTTATATTTTGAGGTC 59.296 42.308 4.56 0.00 36.57 3.85
5854 8084 7.624549 TCAGCTCTTATATTTTGAGGTCAGTT 58.375 34.615 0.00 0.00 36.57 3.16
5855 8085 8.758829 TCAGCTCTTATATTTTGAGGTCAGTTA 58.241 33.333 0.00 0.00 36.57 2.24
5907 8250 3.949754 CAGAATGAGATGGCTGCCTTTTA 59.050 43.478 21.03 0.00 39.69 1.52
5968 8312 1.268386 GCGTGATGGAAGATGTGCATG 60.268 52.381 0.00 0.00 38.62 4.06
5977 8321 3.436704 GGAAGATGTGCATGTCGAAGAAA 59.563 43.478 0.00 0.00 39.69 2.52
5982 8326 3.210227 TGTGCATGTCGAAGAAAAAGGA 58.790 40.909 0.00 0.00 39.69 3.36
5989 8333 1.778484 TCGAAGAAAAAGGAAGGGGGT 59.222 47.619 0.00 0.00 0.00 4.95
6003 8349 2.765502 AGGGGGTGAGATTTAGAGACC 58.234 52.381 0.00 0.00 0.00 3.85
6045 8394 0.666374 GTTAGCAAAGCGGTGTTGGT 59.334 50.000 14.95 14.95 39.80 3.67
6049 8398 1.724582 GCAAAGCGGTGTTGGTGACT 61.725 55.000 10.16 0.00 0.00 3.41
6053 8402 2.561478 AGCGGTGTTGGTGACTAATT 57.439 45.000 0.00 0.00 0.00 1.40
6068 8417 8.383175 TGGTGACTAATTCAGAACCTAGATTTT 58.617 33.333 7.75 0.00 36.25 1.82
6103 8618 1.876156 CTTGGCGCAAGATTATCCCTC 59.124 52.381 10.83 0.00 43.42 4.30
6203 8718 2.683968 TGACAAGTACTGATTCGGTGC 58.316 47.619 8.44 7.00 0.00 5.01
6248 8763 0.890996 CTGAGAGGTGTTTGGTGGGC 60.891 60.000 0.00 0.00 0.00 5.36
6268 8783 2.841215 CGTAAGGGTGGAAAGTGACAA 58.159 47.619 0.00 0.00 0.00 3.18
6273 8788 3.909732 AGGGTGGAAAGTGACAATGAAA 58.090 40.909 0.00 0.00 0.00 2.69
6274 8789 4.285863 AGGGTGGAAAGTGACAATGAAAA 58.714 39.130 0.00 0.00 0.00 2.29
6276 8791 5.366477 AGGGTGGAAAGTGACAATGAAAAAT 59.634 36.000 0.00 0.00 0.00 1.82
6277 8792 6.553100 AGGGTGGAAAGTGACAATGAAAAATA 59.447 34.615 0.00 0.00 0.00 1.40
6278 8793 6.645003 GGGTGGAAAGTGACAATGAAAAATAC 59.355 38.462 0.00 0.00 0.00 1.89
6279 8794 7.433680 GGTGGAAAGTGACAATGAAAAATACT 58.566 34.615 0.00 0.00 0.00 2.12
6280 8795 7.595130 GGTGGAAAGTGACAATGAAAAATACTC 59.405 37.037 0.00 0.00 0.00 2.59
6312 8830 8.441312 AATGCATATTCAAATCCAAAACATCC 57.559 30.769 0.00 0.00 0.00 3.51
6328 8846 6.720012 AAACATCCGCATCCAAATTAAAAC 57.280 33.333 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.065926 TCTCCACGCTCTTGCATGAAT 60.066 47.619 0.00 0.00 33.80 2.57
1 2 0.321346 TCTCCACGCTCTTGCATGAA 59.679 50.000 0.00 0.00 33.80 2.57
2 3 0.108472 CTCTCCACGCTCTTGCATGA 60.108 55.000 0.00 1.92 33.80 3.07
44 790 8.755018 GTGTTGTCAACTAAATTTTTGAGATGG 58.245 33.333 16.45 0.00 32.40 3.51
45 791 9.299963 TGTGTTGTCAACTAAATTTTTGAGATG 57.700 29.630 16.45 0.00 32.40 2.90
46 792 9.868277 TTGTGTTGTCAACTAAATTTTTGAGAT 57.132 25.926 16.45 0.00 32.40 2.75
47 793 9.134734 GTTGTGTTGTCAACTAAATTTTTGAGA 57.865 29.630 16.45 2.68 42.76 3.27
48 794 8.920665 TGTTGTGTTGTCAACTAAATTTTTGAG 58.079 29.630 16.45 0.00 45.26 3.02
133 895 8.617809 TGTCGCTGAAATTAATAGGGAATAAAC 58.382 33.333 5.35 0.00 35.56 2.01
264 1065 0.537653 TATGGATTGAACGGTGCCGA 59.462 50.000 18.16 0.00 42.83 5.54
274 1075 0.478072 AATGGCGGCCTATGGATTGA 59.522 50.000 21.46 0.00 0.00 2.57
322 1158 4.567318 GGCTCCAATGAAGGCGAT 57.433 55.556 0.00 0.00 0.00 4.58
380 1216 1.734465 GCCAACCTCTTCTTCACATCG 59.266 52.381 0.00 0.00 0.00 3.84
437 1365 2.765807 CCCCCTGCGTCATCCTCT 60.766 66.667 0.00 0.00 0.00 3.69
525 1463 1.851065 TTGCTGGGTAGAGCCATGCA 61.851 55.000 16.02 16.02 42.30 3.96
588 1526 0.248565 TTTGCTGTGCTGCCAACAAA 59.751 45.000 12.46 12.46 0.00 2.83
595 1533 1.001048 TGTGAGATTTTGCTGTGCTGC 60.001 47.619 0.00 0.00 0.00 5.25
615 1553 3.758023 GCTGGGCTGCCAAAATAATTTTT 59.242 39.130 22.05 0.00 35.41 1.94
616 1554 3.244840 TGCTGGGCTGCCAAAATAATTTT 60.245 39.130 22.05 0.00 0.00 1.82
622 1560 0.832983 TCTTGCTGGGCTGCCAAAAT 60.833 50.000 22.05 0.00 0.00 1.82
624 1562 1.228956 ATCTTGCTGGGCTGCCAAA 60.229 52.632 22.05 7.09 0.00 3.28
628 1570 1.077930 TGAGATCTTGCTGGGCTGC 60.078 57.895 0.00 0.00 0.00 5.25
633 1575 3.310774 CCGTAAATGTGAGATCTTGCTGG 59.689 47.826 0.00 0.00 0.00 4.85
640 1582 6.537301 TGAATTACCACCGTAAATGTGAGATC 59.463 38.462 0.00 0.00 37.97 2.75
944 1907 0.550393 AGGGAAAGGAGGGGAGGAAC 60.550 60.000 0.00 0.00 0.00 3.62
952 1915 0.615850 AAAGCGAGAGGGAAAGGAGG 59.384 55.000 0.00 0.00 0.00 4.30
954 1917 0.246635 CGAAAGCGAGAGGGAAAGGA 59.753 55.000 0.00 0.00 40.82 3.36
985 1956 0.101759 TCCATCGTCCGGATTCGAAC 59.898 55.000 19.51 0.00 39.45 3.95
986 1957 0.384309 CTCCATCGTCCGGATTCGAA 59.616 55.000 19.51 0.00 39.45 3.71
987 1958 1.452953 CCTCCATCGTCCGGATTCGA 61.453 60.000 18.17 18.17 40.28 3.71
988 1959 1.007271 CCTCCATCGTCCGGATTCG 60.007 63.158 7.81 7.98 31.28 3.34
989 1960 0.315568 CTCCTCCATCGTCCGGATTC 59.684 60.000 7.81 0.00 31.28 2.52
990 1961 1.115930 CCTCCTCCATCGTCCGGATT 61.116 60.000 7.81 0.00 31.28 3.01
1085 2059 0.388649 CTTCACCGTCTTCCTGACCG 60.389 60.000 0.00 0.00 42.49 4.79
1086 2060 0.966920 TCTTCACCGTCTTCCTGACC 59.033 55.000 0.00 0.00 42.49 4.02
1157 2131 2.393989 CTAGATCCGCTCGCGCAAGA 62.394 60.000 8.75 0.00 43.02 3.02
1159 2133 2.026157 CTAGATCCGCTCGCGCAA 59.974 61.111 8.75 0.00 38.24 4.85
1344 2348 2.646719 GTGTAGTCGGGCGTGTGA 59.353 61.111 0.00 0.00 0.00 3.58
1528 2532 1.896220 ACCTTGTCAATGTGCACGAT 58.104 45.000 13.13 4.14 0.00 3.73
1529 2533 2.535012 TACCTTGTCAATGTGCACGA 57.465 45.000 13.13 0.00 0.00 4.35
1530 2534 2.661709 CGTTACCTTGTCAATGTGCACG 60.662 50.000 13.13 8.01 0.00 5.34
1532 2536 1.876799 CCGTTACCTTGTCAATGTGCA 59.123 47.619 3.96 0.00 0.00 4.57
1571 2596 4.646572 AGGACAACAACAAGAGGAGAATC 58.353 43.478 0.00 0.00 0.00 2.52
1580 2605 2.099405 ACCACCAAGGACAACAACAAG 58.901 47.619 0.00 0.00 41.22 3.16
2023 3057 4.981806 AAAAGTCAGTTTGCTGCAACTA 57.018 36.364 15.72 0.00 42.29 2.24
2049 3301 9.507280 CCATTGTTTGATTACAGATGATACAAC 57.493 33.333 0.00 0.00 0.00 3.32
2052 3304 8.677300 ACACCATTGTTTGATTACAGATGATAC 58.323 33.333 0.00 0.00 28.43 2.24
2114 3367 2.969821 TCAGCAAGGGAAAGCCTAAA 57.030 45.000 0.00 0.00 0.00 1.85
2119 3372 0.533951 CCCAATCAGCAAGGGAAAGC 59.466 55.000 0.00 0.00 45.80 3.51
2134 3387 7.588512 CAAAAGTTTCACAAAAATGTTCCCAA 58.411 30.769 0.00 0.00 0.00 4.12
2143 3396 8.121708 GCATGAATAGCAAAAGTTTCACAAAAA 58.878 29.630 0.00 0.00 31.45 1.94
2260 3513 8.664211 TGTAAAAACAAACAAAAACTTGAGGT 57.336 26.923 0.00 0.00 0.00 3.85
2277 3530 8.068380 CCAAGCTTAAGAGTGTACTGTAAAAAC 58.932 37.037 6.67 0.00 0.00 2.43
2288 3541 2.370189 ACTCTGCCAAGCTTAAGAGTGT 59.630 45.455 26.02 14.71 45.82 3.55
2303 3561 3.433615 GTGTGTAAGTCCATTCACTCTGC 59.566 47.826 0.00 0.00 0.00 4.26
2360 3618 8.103948 CTGATTCTTTCAGTAAAATCTGGTGT 57.896 34.615 0.00 0.00 45.79 4.16
2398 3656 3.138304 TGTGTAGCATCTGACAAACACC 58.862 45.455 10.16 0.00 37.11 4.16
2430 3688 7.438757 TGCAAACATACCATATTGATGAATTGC 59.561 33.333 17.66 17.66 41.61 3.56
2503 3762 5.897824 CCTTTAGTGGGAGGTAGATACAGAA 59.102 44.000 0.00 0.00 0.00 3.02
2512 3771 5.104024 TGTTTGTTTCCTTTAGTGGGAGGTA 60.104 40.000 0.00 0.00 34.06 3.08
2515 3774 5.278957 CCATGTTTGTTTCCTTTAGTGGGAG 60.279 44.000 0.00 0.00 34.06 4.30
2519 3778 7.463469 GAAACCATGTTTGTTTCCTTTAGTG 57.537 36.000 12.48 0.00 43.59 2.74
2551 3810 4.802039 GCATATTGGCTCACTGTTGAAATG 59.198 41.667 0.00 0.00 0.00 2.32
2577 3836 7.895429 TCAGGTCCTTAAATTCAGATTCCAAAT 59.105 33.333 0.00 0.00 0.00 2.32
2581 3840 7.611855 TCTTTCAGGTCCTTAAATTCAGATTCC 59.388 37.037 0.00 0.00 0.00 3.01
2617 3876 0.179032 TGCGTTCCTTTGCTTCCTCA 60.179 50.000 0.00 0.00 0.00 3.86
2678 3937 9.916397 CAACGAATAAACTGATACCAGAATAAC 57.084 33.333 0.00 0.00 43.02 1.89
2699 3958 5.405873 TGTCAATTTATCGCAGTAACAACGA 59.594 36.000 0.00 0.00 40.53 3.85
2701 3960 6.599437 ACTGTCAATTTATCGCAGTAACAAC 58.401 36.000 0.00 0.00 38.46 3.32
2714 3973 9.431887 GTCACATTAAGTCCTACTGTCAATTTA 57.568 33.333 0.00 0.00 0.00 1.40
2724 3985 5.532025 GTGCAAGTCACATTAAGTCCTAC 57.468 43.478 0.00 0.00 44.98 3.18
2760 4021 4.550831 CGACAGCGGCAAAATACTCTTATG 60.551 45.833 1.45 0.00 0.00 1.90
2817 4078 1.999735 TCAAAGTCGATCGCCATTGAC 59.000 47.619 12.18 3.62 42.12 3.18
2895 4156 5.182001 AGGGTTGAAGACTGAATCGAATTTG 59.818 40.000 0.00 0.00 0.00 2.32
3134 4395 1.823610 GTAGTTAACCCCTCGAGCACT 59.176 52.381 6.99 4.15 0.00 4.40
3175 4436 2.160205 TGTCTGTCCTTGACTACTCGG 58.840 52.381 0.00 0.00 35.63 4.63
3268 4529 1.152546 GCTTGGTTGGGACCCTGTT 60.153 57.895 13.00 0.00 45.92 3.16
3881 5147 8.673711 TCTTGTATATAAATCACCAGTGCAAAC 58.326 33.333 0.00 0.00 0.00 2.93
3928 5194 1.967319 TGAGTTCCTGCCAGTTTGAC 58.033 50.000 0.00 0.00 0.00 3.18
3944 5210 4.386424 GCAGCAAGTGCGTTAACTTTGAG 61.386 47.826 3.71 2.21 43.99 3.02
3977 5243 6.359883 GGAGAAGAAAACAAAATTGCGTACTC 59.640 38.462 0.00 0.00 0.00 2.59
3991 5257 5.966742 AACCAGCATAAGGAGAAGAAAAC 57.033 39.130 0.00 0.00 0.00 2.43
3994 5260 5.241403 TCAAACCAGCATAAGGAGAAGAA 57.759 39.130 0.00 0.00 0.00 2.52
4028 5294 7.657336 ACACACATTATCACCAAAACTAAAGG 58.343 34.615 0.00 0.00 0.00 3.11
4141 5411 0.394938 TCACCCTGCTCGCAAAGTTA 59.605 50.000 0.00 0.00 0.00 2.24
4237 5513 0.548031 TGGATTAGCAGGAAGGGCAG 59.452 55.000 0.00 0.00 0.00 4.85
4499 5775 0.035036 CCATGGTGGTTGCAATGCAA 59.965 50.000 17.55 17.55 46.80 4.08
4500 5776 1.672320 CCATGGTGGTTGCAATGCA 59.328 52.632 2.72 2.72 36.47 3.96
4501 5777 1.742510 GCCATGGTGGTTGCAATGC 60.743 57.895 14.67 0.00 40.46 3.56
4502 5778 0.390603 CAGCCATGGTGGTTGCAATG 60.391 55.000 14.67 0.00 41.73 2.82
4503 5779 0.542467 TCAGCCATGGTGGTTGCAAT 60.542 50.000 14.67 0.00 46.67 3.56
4707 5983 2.987547 TTGAGGCCTTGCTGCTGC 60.988 61.111 6.77 8.89 40.20 5.25
4710 5986 1.593296 CTTCCTTGAGGCCTTGCTGC 61.593 60.000 6.77 0.00 34.44 5.25
4711 5987 0.037303 TCTTCCTTGAGGCCTTGCTG 59.963 55.000 6.77 0.00 34.44 4.41
4717 5993 2.155279 GTTGTTCTCTTCCTTGAGGCC 58.845 52.381 0.00 0.00 34.98 5.19
4778 6054 2.512515 GCGGTCTCTCCATGGTGC 60.513 66.667 12.58 2.25 35.57 5.01
4827 6103 0.807667 ACGTCTGCTTCGCCATCATC 60.808 55.000 0.00 0.00 0.00 2.92
4828 6104 0.391661 AACGTCTGCTTCGCCATCAT 60.392 50.000 0.00 0.00 0.00 2.45
4829 6105 1.005037 AACGTCTGCTTCGCCATCA 60.005 52.632 0.00 0.00 0.00 3.07
4839 6115 2.089349 GCTGTCCGAGAACGTCTGC 61.089 63.158 0.00 0.00 37.88 4.26
4843 6119 0.179094 TTGTTGCTGTCCGAGAACGT 60.179 50.000 0.00 0.00 37.88 3.99
4848 6124 1.571460 GCTGTTGTTGCTGTCCGAG 59.429 57.895 0.00 0.00 0.00 4.63
4869 6145 1.160137 GCTGGTTGAAGCTGTAGGTG 58.840 55.000 3.35 0.00 40.20 4.00
4902 6178 1.258445 TGGCGTTCTCCTTCTCCTCC 61.258 60.000 0.00 0.00 0.00 4.30
4947 6226 2.811317 CCGTTGCAGAGCGAGACC 60.811 66.667 8.60 0.00 0.00 3.85
5349 6640 4.947147 TCCCTGTTGTGCACGCCC 62.947 66.667 13.13 2.70 0.00 6.13
5426 6730 8.801715 GATCTACAGATCTCTTTCTTCATCAC 57.198 38.462 11.25 0.00 45.60 3.06
5547 6866 7.472741 TCTTATATTATGGGACGAGGGAGTAA 58.527 38.462 0.00 0.00 0.00 2.24
5548 6867 7.036154 TCTTATATTATGGGACGAGGGAGTA 57.964 40.000 0.00 0.00 0.00 2.59
5549 6868 5.900437 TCTTATATTATGGGACGAGGGAGT 58.100 41.667 0.00 0.00 0.00 3.85
5550 6869 6.625300 CGTTCTTATATTATGGGACGAGGGAG 60.625 46.154 0.00 0.00 0.00 4.30
5551 6870 5.184479 CGTTCTTATATTATGGGACGAGGGA 59.816 44.000 0.00 0.00 0.00 4.20
5552 6871 5.047519 ACGTTCTTATATTATGGGACGAGGG 60.048 44.000 14.76 0.00 0.00 4.30
5553 6872 6.022163 ACGTTCTTATATTATGGGACGAGG 57.978 41.667 14.76 0.00 0.00 4.63
5554 6873 7.941795 AAACGTTCTTATATTATGGGACGAG 57.058 36.000 0.00 0.00 0.00 4.18
5555 6874 8.721019 AAAAACGTTCTTATATTATGGGACGA 57.279 30.769 0.00 0.00 0.00 4.20
5598 6917 5.239963 CGTCCCATAATATAAGGCCGTTTTT 59.760 40.000 0.00 0.00 0.00 1.94
5599 6918 4.758165 CGTCCCATAATATAAGGCCGTTTT 59.242 41.667 0.00 0.00 0.00 2.43
5600 6919 4.320870 CGTCCCATAATATAAGGCCGTTT 58.679 43.478 0.00 0.00 0.00 3.60
5601 6920 3.307199 CCGTCCCATAATATAAGGCCGTT 60.307 47.826 0.00 0.00 0.00 4.44
5602 6921 2.235402 CCGTCCCATAATATAAGGCCGT 59.765 50.000 0.00 0.00 0.00 5.68
5603 6922 2.498481 TCCGTCCCATAATATAAGGCCG 59.502 50.000 0.00 0.00 0.00 6.13
5604 6923 3.118371 CCTCCGTCCCATAATATAAGGCC 60.118 52.174 0.00 0.00 0.00 5.19
5605 6924 3.118371 CCCTCCGTCCCATAATATAAGGC 60.118 52.174 0.00 0.00 0.00 4.35
5606 6925 4.359105 TCCCTCCGTCCCATAATATAAGG 58.641 47.826 0.00 0.00 0.00 2.69
5607 6926 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
5608 6927 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
5609 6928 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
5610 6929 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
5611 6930 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
5612 6931 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
5613 6932 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
5614 6933 2.969950 CAAATACTCCCTCCGTCCCATA 59.030 50.000 0.00 0.00 0.00 2.74
5615 6934 1.768870 CAAATACTCCCTCCGTCCCAT 59.231 52.381 0.00 0.00 0.00 4.00
5616 6935 1.200519 CAAATACTCCCTCCGTCCCA 58.799 55.000 0.00 0.00 0.00 4.37
5617 6936 1.201424 ACAAATACTCCCTCCGTCCC 58.799 55.000 0.00 0.00 0.00 4.46
5618 6937 4.684484 ATAACAAATACTCCCTCCGTCC 57.316 45.455 0.00 0.00 0.00 4.79
5619 6938 6.489361 TCTCTATAACAAATACTCCCTCCGTC 59.511 42.308 0.00 0.00 0.00 4.79
5620 6939 6.371278 TCTCTATAACAAATACTCCCTCCGT 58.629 40.000 0.00 0.00 0.00 4.69
5621 6940 6.896021 TCTCTATAACAAATACTCCCTCCG 57.104 41.667 0.00 0.00 0.00 4.63
5622 6941 9.495572 CAAATCTCTATAACAAATACTCCCTCC 57.504 37.037 0.00 0.00 0.00 4.30
5623 6942 9.495572 CCAAATCTCTATAACAAATACTCCCTC 57.504 37.037 0.00 0.00 0.00 4.30
5624 6943 7.939588 GCCAAATCTCTATAACAAATACTCCCT 59.060 37.037 0.00 0.00 0.00 4.20
5625 6944 7.095187 CGCCAAATCTCTATAACAAATACTCCC 60.095 40.741 0.00 0.00 0.00 4.30
5626 6945 7.656137 TCGCCAAATCTCTATAACAAATACTCC 59.344 37.037 0.00 0.00 0.00 3.85
5627 6946 8.589335 TCGCCAAATCTCTATAACAAATACTC 57.411 34.615 0.00 0.00 0.00 2.59
5628 6947 8.204836 ACTCGCCAAATCTCTATAACAAATACT 58.795 33.333 0.00 0.00 0.00 2.12
5629 6948 8.276325 CACTCGCCAAATCTCTATAACAAATAC 58.724 37.037 0.00 0.00 0.00 1.89
5663 6982 3.421919 TGACATTTCATCTGACAGCCA 57.578 42.857 0.00 0.00 0.00 4.75
5740 7066 5.127845 AGACTTCTCAGTTCTCACACTCAAA 59.872 40.000 0.00 0.00 31.22 2.69
5754 7080 7.581213 ACTGAGGATGTATAAGACTTCTCAG 57.419 40.000 18.96 18.96 39.74 3.35
5756 7082 9.959749 CTTAACTGAGGATGTATAAGACTTCTC 57.040 37.037 0.00 0.00 33.65 2.87
5803 7129 1.070843 CCGTTGTACACTGAACGCAAG 60.071 52.381 11.43 0.00 42.83 4.01
5843 8073 5.428253 GACTGCCATAATAACTGACCTCAA 58.572 41.667 0.00 0.00 0.00 3.02
5848 8078 5.796350 AAACGACTGCCATAATAACTGAC 57.204 39.130 0.00 0.00 0.00 3.51
5850 8080 6.176975 TGAAAACGACTGCCATAATAACTG 57.823 37.500 0.00 0.00 0.00 3.16
5854 8084 6.607689 CAACTTGAAAACGACTGCCATAATA 58.392 36.000 0.00 0.00 0.00 0.98
5855 8085 5.460646 CAACTTGAAAACGACTGCCATAAT 58.539 37.500 0.00 0.00 0.00 1.28
5896 8239 1.648467 CTCCGCACTAAAAGGCAGCC 61.648 60.000 1.84 1.84 0.00 4.85
5907 8250 2.224233 CCAAGATCATCATCTCCGCACT 60.224 50.000 0.00 0.00 38.55 4.40
5968 8312 2.160205 CCCCCTTCCTTTTTCTTCGAC 58.840 52.381 0.00 0.00 0.00 4.20
5977 8321 4.183916 TCTAAATCTCACCCCCTTCCTTT 58.816 43.478 0.00 0.00 0.00 3.11
5982 8326 3.116174 GGTCTCTAAATCTCACCCCCTT 58.884 50.000 0.00 0.00 0.00 3.95
6022 8371 3.057876 CCAACACCGCTTTGCTAACATAA 60.058 43.478 0.00 0.00 0.00 1.90
6024 8373 1.269448 CCAACACCGCTTTGCTAACAT 59.731 47.619 0.00 0.00 0.00 2.71
6029 8378 1.453015 TCACCAACACCGCTTTGCT 60.453 52.632 0.00 0.00 0.00 3.91
6053 8402 5.064707 GCGCACATAAAAATCTAGGTTCTGA 59.935 40.000 0.30 0.00 0.00 3.27
6068 8417 1.295357 CCAAGGACACGCGCACATAA 61.295 55.000 5.73 0.00 0.00 1.90
6070 8419 3.049674 CCAAGGACACGCGCACAT 61.050 61.111 5.73 0.00 0.00 3.21
6103 8618 3.496331 GAGAGGATTAGAGGGGAGTGAG 58.504 54.545 0.00 0.00 0.00 3.51
6248 8763 2.536761 TGTCACTTTCCACCCTTACG 57.463 50.000 0.00 0.00 0.00 3.18
6277 8792 8.411683 GGATTTGAATATGCATTTTCTCAGAGT 58.588 33.333 24.32 9.68 0.00 3.24
6278 8793 8.410912 TGGATTTGAATATGCATTTTCTCAGAG 58.589 33.333 24.32 0.00 0.00 3.35
6279 8794 8.296211 TGGATTTGAATATGCATTTTCTCAGA 57.704 30.769 24.32 10.57 0.00 3.27
6280 8795 8.936070 TTGGATTTGAATATGCATTTTCTCAG 57.064 30.769 24.32 0.00 0.00 3.35
6298 8816 2.830923 TGGATGCGGATGTTTTGGATTT 59.169 40.909 0.00 0.00 0.00 2.17
6312 8830 5.220378 CCATTTCCGTTTTAATTTGGATGCG 60.220 40.000 0.00 0.00 0.00 4.73
6328 8846 6.204688 TCGGATATCTTTCAATTCCATTTCCG 59.795 38.462 2.05 0.00 38.61 4.30
6366 8886 6.198216 ACTTGTGTGCAAAATTTATTCGTGTC 59.802 34.615 0.00 0.00 33.73 3.67


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

AutoCloner maintained by Alex Coulton.