Multiple sequence alignment - TraesCS2D01G427400

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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 TraesCS2D01G427400 chr2D 100.000 4710 0 0 1 4710 539431235 539426526 0.000000e+00 8698
1 TraesCS2D01G427400 chr2A 96.988 3187 65 17 673 3850 683015109 683011945 0.000000e+00 5325
2 TraesCS2D01G427400 chr2A 91.751 691 20 7 1 676 683019192 683018524 0.000000e+00 926
3 TraesCS2D01G427400 chr2B 94.146 3143 99 27 728 3852 643686207 643683132 0.000000e+00 4706
4 TraesCS2D01G427400 chr2B 92.035 113 9 0 3843 3955 601206951 601206839 4.880000e-35 159
5 TraesCS2D01G427400 chr7A 83.600 750 89 16 3969 4709 479671832 479671108 0.000000e+00 673
6 TraesCS2D01G427400 chr7A 91.818 110 9 0 3843 3952 61816026 61815917 2.270000e-33 154
7 TraesCS2D01G427400 chr4A 80.058 692 78 33 1522 2193 641401326 641401977 4.300000e-125 459
8 TraesCS2D01G427400 chr4A 86.930 329 25 9 994 1319 641400892 641401205 2.080000e-93 353
9 TraesCS2D01G427400 chr5D 83.037 507 49 21 1700 2193 530873539 530873057 4.360000e-115 425
10 TraesCS2D01G427400 chr5D 86.544 327 26 12 994 1320 530874122 530873814 1.250000e-90 344
11 TraesCS2D01G427400 chr5D 94.175 103 6 0 3849 3951 205794744 205794642 1.750000e-34 158
12 TraesCS2D01G427400 chr5D 90.909 110 9 1 3843 3951 125803453 125803562 3.800000e-31 147
13 TraesCS2D01G427400 chr5B 88.720 328 19 9 994 1318 670118217 670117905 7.390000e-103 385
14 TraesCS2D01G427400 chr5B 77.858 691 76 37 1523 2193 670117791 670117158 1.610000e-94 357
15 TraesCS2D01G427400 chr5B 87.705 122 14 1 3843 3964 191137868 191137748 1.770000e-29 141
16 TraesCS2D01G427400 chr6D 78.238 386 55 16 835 1217 439114489 439114848 2.210000e-53 220
17 TraesCS2D01G427400 chr1D 79.866 298 39 12 4416 4709 492371642 492371922 1.030000e-46 198
18 TraesCS2D01G427400 chr4D 93.519 108 7 0 3848 3955 177433202 177433309 1.360000e-35 161
19 TraesCS2D01G427400 chr4D 82.895 152 19 7 3814 3960 175795054 175794905 3.820000e-26 130
20 TraesCS2D01G427400 chr7B 92.453 106 7 1 3845 3950 478835138 478835034 2.940000e-32 150
21 TraesCS2D01G427400 chr6A 90.179 112 9 2 3845 3955 611563281 611563171 1.370000e-30 145


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 TraesCS2D01G427400 chr2D 539426526 539431235 4709 True 8698.0 8698 100.0000 1 4710 1 chr2D.!!$R1 4709
1 TraesCS2D01G427400 chr2A 683011945 683019192 7247 True 3125.5 5325 94.3695 1 3850 2 chr2A.!!$R1 3849
2 TraesCS2D01G427400 chr2B 643683132 643686207 3075 True 4706.0 4706 94.1460 728 3852 1 chr2B.!!$R2 3124
3 TraesCS2D01G427400 chr7A 479671108 479671832 724 True 673.0 673 83.6000 3969 4709 1 chr7A.!!$R2 740
4 TraesCS2D01G427400 chr4A 641400892 641401977 1085 False 406.0 459 83.4940 994 2193 2 chr4A.!!$F1 1199
5 TraesCS2D01G427400 chr5D 530873057 530874122 1065 True 384.5 425 84.7905 994 2193 2 chr5D.!!$R2 1199
6 TraesCS2D01G427400 chr5B 670117158 670118217 1059 True 371.0 385 83.2890 994 2193 2 chr5B.!!$R2 1199

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
234 235 0.103208 CTCCCCTCGTCTTTGATCCG 59.897 60.0 0.0 0.0 0.00 4.18 F
838 4276 0.332972 AAAATCAGGCCCACTCCTCC 59.667 55.0 0.0 0.0 33.25 4.30 F
839 4277 0.551131 AAATCAGGCCCACTCCTCCT 60.551 55.0 0.0 0.0 33.25 3.69 F
2632 6202 0.953960 AACCGACGATTGACCCAAGC 60.954 55.0 0.0 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 5624 0.895530 CCCGTGCTTACTCTTCCTCA 59.104 55.000 0.0 0.0 0.0 3.86 R
2619 6189 1.399440 CATCACTGCTTGGGTCAATCG 59.601 52.381 0.0 0.0 0.0 3.34 R
2832 6402 4.606210 ACTAGTCTTCCCTTCCTTCTCTC 58.394 47.826 0.0 0.0 0.0 3.20 R
4414 8002 0.034059 AAGCACACGGAGAGACAAGG 59.966 55.000 0.0 0.0 0.0 3.61 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
47 48 2.370281 AGACCGCACATACACTTCAG 57.630 50.000 0.00 0.00 0.00 3.02
50 51 1.695893 CCGCACATACACTTCAGCCG 61.696 60.000 0.00 0.00 0.00 5.52
190 191 4.377760 ACCCTCCCTTCTCGCCGA 62.378 66.667 0.00 0.00 0.00 5.54
215 216 2.420890 CTCTGGCCAGGAGATCGC 59.579 66.667 32.23 0.00 33.03 4.58
216 217 2.042537 TCTGGCCAGGAGATCGCT 60.043 61.111 32.23 0.00 0.00 4.93
217 218 2.086251 CTCTGGCCAGGAGATCGCTC 62.086 65.000 32.23 0.00 40.54 5.03
225 226 3.035727 GAGATCGCTCCCCTCGTC 58.964 66.667 0.00 0.00 35.01 4.20
226 227 1.527380 GAGATCGCTCCCCTCGTCT 60.527 63.158 0.00 0.00 35.01 4.18
227 228 1.076632 AGATCGCTCCCCTCGTCTT 60.077 57.895 0.00 0.00 0.00 3.01
228 229 0.684805 AGATCGCTCCCCTCGTCTTT 60.685 55.000 0.00 0.00 0.00 2.52
229 230 0.528684 GATCGCTCCCCTCGTCTTTG 60.529 60.000 0.00 0.00 0.00 2.77
230 231 0.970937 ATCGCTCCCCTCGTCTTTGA 60.971 55.000 0.00 0.00 0.00 2.69
231 232 0.970937 TCGCTCCCCTCGTCTTTGAT 60.971 55.000 0.00 0.00 0.00 2.57
232 233 0.528684 CGCTCCCCTCGTCTTTGATC 60.529 60.000 0.00 0.00 0.00 2.92
233 234 0.179070 GCTCCCCTCGTCTTTGATCC 60.179 60.000 0.00 0.00 0.00 3.36
234 235 0.103208 CTCCCCTCGTCTTTGATCCG 59.897 60.000 0.00 0.00 0.00 4.18
235 236 1.144057 CCCCTCGTCTTTGATCCGG 59.856 63.158 0.00 0.00 0.00 5.14
356 358 2.046285 GTGCGCTTGGCCCAACTAT 61.046 57.895 9.73 0.00 42.61 2.12
366 368 1.477558 GGCCCAACTATGATGGTCCAG 60.478 57.143 0.00 0.00 36.00 3.86
391 393 0.755327 GGACTTGTGGTGCCAGGTTT 60.755 55.000 0.00 0.00 0.00 3.27
409 411 2.643933 TTGACACATCGAGCTCTCTG 57.356 50.000 12.85 11.18 0.00 3.35
416 418 1.603802 CATCGAGCTCTCTGACTCTCC 59.396 57.143 12.85 0.00 0.00 3.71
472 474 3.809832 ACACGGCTAAATCATGCTATGAC 59.190 43.478 1.65 0.00 43.01 3.06
527 529 1.337260 GGCGCTCGATATGGAAGACAT 60.337 52.381 7.64 0.00 43.68 3.06
583 585 1.885887 TGTTTCCTTTTCGCCATCCTG 59.114 47.619 0.00 0.00 0.00 3.86
586 588 1.533625 TCCTTTTCGCCATCCTGTTG 58.466 50.000 0.00 0.00 0.00 3.33
824 4262 3.579232 CCGCCGCGGGGTAAAATC 61.579 66.667 36.12 12.98 44.15 2.17
825 4263 2.820479 CGCCGCGGGGTAAAATCA 60.820 61.111 32.15 0.00 34.97 2.57
826 4264 2.819552 CGCCGCGGGGTAAAATCAG 61.820 63.158 32.15 0.00 34.97 2.90
827 4265 2.478033 GCCGCGGGGTAAAATCAGG 61.478 63.158 29.38 0.00 34.97 3.86
828 4266 2.478033 CCGCGGGGTAAAATCAGGC 61.478 63.158 20.10 0.00 0.00 4.85
829 4267 2.478033 CGCGGGGTAAAATCAGGCC 61.478 63.158 0.00 0.00 0.00 5.19
830 4268 2.125326 GCGGGGTAAAATCAGGCCC 61.125 63.158 0.00 0.00 40.35 5.80
831 4269 1.304952 CGGGGTAAAATCAGGCCCA 59.695 57.895 0.00 0.00 42.79 5.36
832 4270 1.035385 CGGGGTAAAATCAGGCCCAC 61.035 60.000 0.00 0.00 42.79 4.61
833 4271 0.335019 GGGGTAAAATCAGGCCCACT 59.665 55.000 0.00 0.00 42.79 4.00
834 4272 1.685180 GGGGTAAAATCAGGCCCACTC 60.685 57.143 0.00 0.00 42.79 3.51
835 4273 1.685180 GGGTAAAATCAGGCCCACTCC 60.685 57.143 0.00 0.00 40.76 3.85
836 4274 1.285078 GGTAAAATCAGGCCCACTCCT 59.715 52.381 0.00 0.00 36.78 3.69
837 4275 2.644676 GTAAAATCAGGCCCACTCCTC 58.355 52.381 0.00 0.00 33.25 3.71
838 4276 0.332972 AAAATCAGGCCCACTCCTCC 59.667 55.000 0.00 0.00 33.25 4.30
839 4277 0.551131 AAATCAGGCCCACTCCTCCT 60.551 55.000 0.00 0.00 33.25 3.69
840 4278 0.985490 AATCAGGCCCACTCCTCCTC 60.985 60.000 0.00 0.00 33.25 3.71
841 4279 2.905676 ATCAGGCCCACTCCTCCTCC 62.906 65.000 0.00 0.00 33.25 4.30
842 4280 3.288381 AGGCCCACTCCTCCTCCT 61.288 66.667 0.00 0.00 0.00 3.69
843 4281 2.766229 GGCCCACTCCTCCTCCTC 60.766 72.222 0.00 0.00 0.00 3.71
914 4365 2.597217 CCCCGCAGAAAAGCCACA 60.597 61.111 0.00 0.00 0.00 4.17
1020 4471 2.171725 GTACAACGGCATCGGGCTC 61.172 63.158 0.23 0.00 44.01 4.70
1429 4910 7.859325 TGCTCATACCCTTTTCTGTTTATAC 57.141 36.000 0.00 0.00 0.00 1.47
1430 4911 7.630082 TGCTCATACCCTTTTCTGTTTATACT 58.370 34.615 0.00 0.00 0.00 2.12
1431 4912 7.552687 TGCTCATACCCTTTTCTGTTTATACTG 59.447 37.037 0.00 0.00 0.00 2.74
1453 4934 8.988546 ACTGTATCTCTGTATCTGTCAGTTAT 57.011 34.615 0.00 0.00 34.86 1.89
1473 4954 8.299570 CAGTTATCCTTTTGCTATGTGAAAACT 58.700 33.333 0.00 0.00 0.00 2.66
1519 5001 2.270527 GTTGGAGAGGAGGCCAGC 59.729 66.667 5.01 0.00 35.23 4.85
1673 5212 2.239402 TGAAGTATAAACCCCCGGTTCC 59.761 50.000 0.00 0.00 46.20 3.62
2058 5624 3.645687 AGGAAGAGTCAGAGCAGAAGTTT 59.354 43.478 0.00 0.00 0.00 2.66
2619 6189 2.896168 TCATTCCCGTGATAAACCGAC 58.104 47.619 0.00 0.00 0.00 4.79
2632 6202 0.953960 AACCGACGATTGACCCAAGC 60.954 55.000 0.00 0.00 0.00 4.01
2832 6402 6.757897 TGATAAGGAAGCACCAAAACATAG 57.242 37.500 2.96 0.00 42.04 2.23
3226 6805 4.582240 AGGAAAGAGTTGGAGAAGCAAAAG 59.418 41.667 0.00 0.00 0.00 2.27
3361 6940 0.678048 AACATGAGCGGAGGAAAGGC 60.678 55.000 0.00 0.00 0.00 4.35
3363 6942 3.391665 ATGAGCGGAGGAAAGGCGG 62.392 63.158 0.00 0.00 0.00 6.13
3530 7109 5.476945 AGGTATGACCCAAATTCAAACAGAC 59.523 40.000 0.00 0.00 39.75 3.51
3594 7173 1.402259 CGGTCGACACAGAGCTAGATT 59.598 52.381 18.91 0.00 36.57 2.40
3815 7395 9.176181 ACATTTTTACGTTTGTGTTAATGCTAG 57.824 29.630 0.00 0.00 0.00 3.42
3862 7442 7.922699 AGTCCTAATATATATTCCCTCTGCC 57.077 40.000 11.28 0.00 0.00 4.85
3863 7443 6.847036 AGTCCTAATATATATTCCCTCTGCCC 59.153 42.308 11.28 0.00 0.00 5.36
3864 7444 6.043358 GTCCTAATATATATTCCCTCTGCCCC 59.957 46.154 11.28 0.00 0.00 5.80
3865 7445 5.911178 CCTAATATATATTCCCTCTGCCCCA 59.089 44.000 11.28 0.00 0.00 4.96
3866 7446 6.389869 CCTAATATATATTCCCTCTGCCCCAA 59.610 42.308 11.28 0.00 0.00 4.12
3867 7447 6.734918 AATATATATTCCCTCTGCCCCAAA 57.265 37.500 1.91 0.00 0.00 3.28
3868 7448 6.734918 ATATATATTCCCTCTGCCCCAAAA 57.265 37.500 0.00 0.00 0.00 2.44
3869 7449 3.999764 ATATTCCCTCTGCCCCAAAAT 57.000 42.857 0.00 0.00 0.00 1.82
3870 7450 6.734918 ATATATTCCCTCTGCCCCAAAATA 57.265 37.500 0.00 0.00 0.00 1.40
3871 7451 3.774842 ATTCCCTCTGCCCCAAAATAA 57.225 42.857 0.00 0.00 0.00 1.40
3872 7452 2.826674 TCCCTCTGCCCCAAAATAAG 57.173 50.000 0.00 0.00 0.00 1.73
3873 7453 2.000048 TCCCTCTGCCCCAAAATAAGT 59.000 47.619 0.00 0.00 0.00 2.24
3874 7454 2.102578 CCCTCTGCCCCAAAATAAGTG 58.897 52.381 0.00 0.00 0.00 3.16
3875 7455 2.557452 CCCTCTGCCCCAAAATAAGTGT 60.557 50.000 0.00 0.00 0.00 3.55
3876 7456 2.755103 CCTCTGCCCCAAAATAAGTGTC 59.245 50.000 0.00 0.00 0.00 3.67
3877 7457 3.562176 CCTCTGCCCCAAAATAAGTGTCT 60.562 47.826 0.00 0.00 0.00 3.41
3878 7458 3.686016 TCTGCCCCAAAATAAGTGTCTC 58.314 45.455 0.00 0.00 0.00 3.36
3879 7459 3.073798 TCTGCCCCAAAATAAGTGTCTCA 59.926 43.478 0.00 0.00 0.00 3.27
3880 7460 3.826157 CTGCCCCAAAATAAGTGTCTCAA 59.174 43.478 0.00 0.00 0.00 3.02
3881 7461 3.572255 TGCCCCAAAATAAGTGTCTCAAC 59.428 43.478 0.00 0.00 0.00 3.18
3882 7462 3.826729 GCCCCAAAATAAGTGTCTCAACT 59.173 43.478 0.00 0.00 0.00 3.16
3883 7463 4.280929 GCCCCAAAATAAGTGTCTCAACTT 59.719 41.667 0.00 0.00 42.89 2.66
3884 7464 5.221441 GCCCCAAAATAAGTGTCTCAACTTT 60.221 40.000 0.00 0.00 40.77 2.66
3885 7465 6.015772 GCCCCAAAATAAGTGTCTCAACTTTA 60.016 38.462 0.00 0.00 40.77 1.85
3886 7466 7.593825 CCCCAAAATAAGTGTCTCAACTTTAG 58.406 38.462 0.00 0.00 40.77 1.85
3887 7467 7.230712 CCCCAAAATAAGTGTCTCAACTTTAGT 59.769 37.037 0.00 0.00 40.77 2.24
3888 7468 9.280174 CCCAAAATAAGTGTCTCAACTTTAGTA 57.720 33.333 0.00 0.00 40.77 1.82
3897 7477 9.174166 AGTGTCTCAACTTTAGTACAATTTTGT 57.826 29.630 1.08 1.08 44.86 2.83
3923 7503 8.015185 ACTAACCTTAGTACAAAGTTGAGACA 57.985 34.615 0.00 0.00 41.92 3.41
3924 7504 7.924947 ACTAACCTTAGTACAAAGTTGAGACAC 59.075 37.037 0.00 0.00 41.92 3.67
3925 7505 6.481434 ACCTTAGTACAAAGTTGAGACACT 57.519 37.500 0.00 0.00 0.00 3.55
3926 7506 6.885922 ACCTTAGTACAAAGTTGAGACACTT 58.114 36.000 0.00 0.00 38.74 3.16
3927 7507 8.015185 ACCTTAGTACAAAGTTGAGACACTTA 57.985 34.615 0.00 0.00 35.87 2.24
3928 7508 8.648693 ACCTTAGTACAAAGTTGAGACACTTAT 58.351 33.333 0.00 0.00 35.87 1.73
3929 7509 9.490379 CCTTAGTACAAAGTTGAGACACTTATT 57.510 33.333 0.00 0.00 35.87 1.40
3933 7513 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
3934 7514 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
3935 7515 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
3936 7516 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
3937 7517 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
3938 7518 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
3939 7519 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
3940 7520 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
3941 7521 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3942 7522 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
3943 7523 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3944 7524 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
3945 7525 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
3946 7526 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3947 7527 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
3948 7528 1.961133 TTTGGGACGGAGGGAGTATT 58.039 50.000 0.00 0.00 0.00 1.89
3949 7529 2.852714 TTGGGACGGAGGGAGTATTA 57.147 50.000 0.00 0.00 0.00 0.98
3950 7530 3.339713 TTGGGACGGAGGGAGTATTAT 57.660 47.619 0.00 0.00 0.00 1.28
3951 7531 4.474303 TTGGGACGGAGGGAGTATTATA 57.526 45.455 0.00 0.00 0.00 0.98
3952 7532 4.687262 TGGGACGGAGGGAGTATTATAT 57.313 45.455 0.00 0.00 0.00 0.86
3953 7533 5.801720 TGGGACGGAGGGAGTATTATATA 57.198 43.478 0.00 0.00 0.00 0.86
3954 7534 6.156554 TGGGACGGAGGGAGTATTATATAA 57.843 41.667 0.00 0.00 0.00 0.98
3955 7535 6.748969 TGGGACGGAGGGAGTATTATATAAT 58.251 40.000 12.51 12.51 0.00 1.28
3956 7536 6.837568 TGGGACGGAGGGAGTATTATATAATC 59.162 42.308 11.28 4.44 0.00 1.75
3957 7537 7.068061 GGGACGGAGGGAGTATTATATAATCT 58.932 42.308 11.28 8.72 0.00 2.40
3958 7538 7.231115 GGGACGGAGGGAGTATTATATAATCTC 59.769 44.444 11.28 15.41 0.00 2.75
3959 7539 8.000127 GGACGGAGGGAGTATTATATAATCTCT 59.000 40.741 21.43 16.78 0.00 3.10
3960 7540 8.983702 ACGGAGGGAGTATTATATAATCTCTC 57.016 38.462 20.65 20.65 0.00 3.20
3961 7541 7.716123 ACGGAGGGAGTATTATATAATCTCTCG 59.284 40.741 21.43 19.66 31.50 4.04
3962 7542 7.308109 CGGAGGGAGTATTATATAATCTCTCGC 60.308 44.444 27.32 27.32 38.44 5.03
3963 7543 7.502895 GGAGGGAGTATTATATAATCTCTCGCA 59.497 40.741 30.93 11.35 39.33 5.10
3964 7544 8.458573 AGGGAGTATTATATAATCTCTCGCAG 57.541 38.462 30.93 0.00 39.33 5.18
3965 7545 8.056400 AGGGAGTATTATATAATCTCTCGCAGT 58.944 37.037 30.93 21.19 39.33 4.40
3966 7546 8.132362 GGGAGTATTATATAATCTCTCGCAGTG 58.868 40.741 28.30 0.00 38.28 3.66
3967 7547 7.646130 GGAGTATTATATAATCTCTCGCAGTGC 59.354 40.741 21.43 4.58 32.59 4.40
4004 7584 1.078426 GACGTGGGGAATGGGAGTG 60.078 63.158 0.00 0.00 0.00 3.51
4017 7598 0.832135 GGGAGTGACAGGGTGTGAGA 60.832 60.000 0.00 0.00 0.00 3.27
4023 7604 2.808543 GTGACAGGGTGTGAGATTCAAC 59.191 50.000 0.00 0.00 0.00 3.18
4032 7613 2.301583 TGTGAGATTCAACGTCCCATGA 59.698 45.455 0.00 0.00 0.00 3.07
4039 7620 2.432444 TCAACGTCCCATGATTGGTTC 58.568 47.619 0.00 0.00 41.91 3.62
4045 7626 3.621214 CGTCCCATGATTGGTTCAGGTAA 60.621 47.826 0.00 0.00 41.91 2.85
4049 7630 4.099881 CCCATGATTGGTTCAGGTAAATGG 59.900 45.833 0.00 0.00 41.91 3.16
4059 7640 5.656416 GGTTCAGGTAAATGGGAATTCATCA 59.344 40.000 7.93 5.52 0.00 3.07
4070 7651 2.244769 GGAATTCATCAGGGAAGGGGAA 59.755 50.000 7.93 0.00 0.00 3.97
4071 7652 3.116977 GGAATTCATCAGGGAAGGGGAAT 60.117 47.826 7.93 0.00 0.00 3.01
4082 7663 3.033909 GGAAGGGGAATGGGAATTTGAG 58.966 50.000 0.00 0.00 0.00 3.02
4095 7676 3.496331 GAATTTGAGGGTGAAACTCCCA 58.504 45.455 10.77 0.00 39.04 4.37
4108 7689 1.799933 ACTCCCACAGATCTCATCCC 58.200 55.000 0.00 0.00 0.00 3.85
4109 7690 1.293458 ACTCCCACAGATCTCATCCCT 59.707 52.381 0.00 0.00 0.00 4.20
4130 7711 2.124411 GGTAGGGGCAGGTAATTGAGA 58.876 52.381 0.00 0.00 0.00 3.27
4148 7729 1.196012 GACGAGGGAGAGGGAATTGT 58.804 55.000 0.00 0.00 0.00 2.71
4154 7735 0.681243 GGAGAGGGAATTGTGTGGCC 60.681 60.000 0.00 0.00 0.00 5.36
4155 7736 0.329596 GAGAGGGAATTGTGTGGCCT 59.670 55.000 3.32 0.00 0.00 5.19
4156 7737 0.779997 AGAGGGAATTGTGTGGCCTT 59.220 50.000 3.32 0.00 0.00 4.35
4157 7738 1.147817 AGAGGGAATTGTGTGGCCTTT 59.852 47.619 3.32 0.00 0.00 3.11
4158 7739 1.970640 GAGGGAATTGTGTGGCCTTTT 59.029 47.619 3.32 0.00 0.00 2.27
4181 7762 3.575805 TCTTTTGAAAATGCCCCTCTGT 58.424 40.909 0.00 0.00 0.00 3.41
4184 7765 1.533625 TGAAAATGCCCCTCTGTTCG 58.466 50.000 0.00 0.00 0.00 3.95
4193 7774 0.107831 CCCTCTGTTCGTTCCCAACA 59.892 55.000 0.00 0.00 32.75 3.33
4198 7779 1.961793 TGTTCGTTCCCAACAGAAGG 58.038 50.000 0.00 0.00 33.86 3.46
4202 7783 1.202879 TCGTTCCCAACAGAAGGCAAT 60.203 47.619 0.00 0.00 32.87 3.56
4203 7784 1.068333 CGTTCCCAACAGAAGGCAATG 60.068 52.381 0.00 0.00 0.00 2.82
4207 7788 1.969923 CCCAACAGAAGGCAATGGAAA 59.030 47.619 0.00 0.00 32.82 3.13
4208 7789 2.368221 CCCAACAGAAGGCAATGGAAAA 59.632 45.455 0.00 0.00 32.82 2.29
4209 7790 3.392882 CCAACAGAAGGCAATGGAAAAC 58.607 45.455 0.00 0.00 32.82 2.43
4210 7791 3.392882 CAACAGAAGGCAATGGAAAACC 58.607 45.455 0.00 0.00 0.00 3.27
4211 7792 2.676748 ACAGAAGGCAATGGAAAACCA 58.323 42.857 0.00 0.00 0.00 3.67
4212 7793 2.629617 ACAGAAGGCAATGGAAAACCAG 59.370 45.455 0.00 0.00 0.00 4.00
4213 7794 1.620323 AGAAGGCAATGGAAAACCAGC 59.380 47.619 0.00 0.00 0.00 4.85
4214 7795 0.318120 AAGGCAATGGAAAACCAGCG 59.682 50.000 0.00 0.00 0.00 5.18
4222 7810 4.806640 ATGGAAAACCAGCGAAAATCAT 57.193 36.364 0.00 0.00 0.00 2.45
4231 7819 5.821204 ACCAGCGAAAATCATTGCTAATAC 58.179 37.500 0.00 0.00 37.99 1.89
4233 7821 4.376861 CAGCGAAAATCATTGCTAATACGC 59.623 41.667 0.00 0.00 37.99 4.42
4243 7831 2.215196 TGCTAATACGCGGGAAAATCC 58.785 47.619 12.47 0.00 35.23 3.01
4253 7841 3.566322 CGCGGGAAAATCCATTGGTTATA 59.434 43.478 0.00 0.00 38.64 0.98
4255 7843 4.825085 GCGGGAAAATCCATTGGTTATAGA 59.175 41.667 1.86 0.00 38.64 1.98
4258 7846 7.148239 GCGGGAAAATCCATTGGTTATAGATAG 60.148 40.741 1.86 0.00 38.64 2.08
4264 7852 6.904463 TCCATTGGTTATAGATAGTACGCA 57.096 37.500 1.86 0.00 0.00 5.24
4265 7853 7.476540 TCCATTGGTTATAGATAGTACGCAT 57.523 36.000 1.86 0.00 0.00 4.73
4267 7855 6.535150 CCATTGGTTATAGATAGTACGCATGG 59.465 42.308 0.00 0.00 0.00 3.66
4270 7858 6.920817 TGGTTATAGATAGTACGCATGGAAG 58.079 40.000 0.00 0.00 0.00 3.46
4318 7906 2.276827 GACAGCAGGTGCGATTGATGT 61.277 52.381 0.00 4.97 45.59 3.06
4319 7907 1.066215 ACAGCAGGTGCGATTGATGTA 60.066 47.619 0.00 0.00 41.63 2.29
4322 7910 2.487934 GCAGGTGCGATTGATGTAGAT 58.512 47.619 0.00 0.00 0.00 1.98
4323 7911 2.478134 GCAGGTGCGATTGATGTAGATC 59.522 50.000 0.00 0.00 0.00 2.75
4334 7922 7.038659 CGATTGATGTAGATCTATTCCCCTTC 58.961 42.308 5.57 1.63 0.00 3.46
4343 7931 9.114952 GTAGATCTATTCCCCTTCTTTTCTTTG 57.885 37.037 5.57 0.00 0.00 2.77
4344 7932 7.703755 AGATCTATTCCCCTTCTTTTCTTTGT 58.296 34.615 0.00 0.00 0.00 2.83
4346 7934 8.727100 ATCTATTCCCCTTCTTTTCTTTGTTT 57.273 30.769 0.00 0.00 0.00 2.83
4347 7935 7.951591 TCTATTCCCCTTCTTTTCTTTGTTTG 58.048 34.615 0.00 0.00 0.00 2.93
4362 7950 8.947304 TTCTTTGTTTGTTCATTTTCTTTTGC 57.053 26.923 0.00 0.00 0.00 3.68
4370 7958 8.665643 TTGTTCATTTTCTTTTGCAGATTGAT 57.334 26.923 0.00 0.00 0.00 2.57
4371 7959 9.761504 TTGTTCATTTTCTTTTGCAGATTGATA 57.238 25.926 0.00 0.00 0.00 2.15
4372 7960 9.414295 TGTTCATTTTCTTTTGCAGATTGATAG 57.586 29.630 0.00 0.00 0.00 2.08
4373 7961 8.378421 GTTCATTTTCTTTTGCAGATTGATAGC 58.622 33.333 0.00 0.00 0.00 2.97
4374 7962 7.037438 TCATTTTCTTTTGCAGATTGATAGCC 58.963 34.615 0.00 0.00 0.00 3.93
4375 7963 5.981088 TTTCTTTTGCAGATTGATAGCCA 57.019 34.783 0.00 0.00 0.00 4.75
4376 7964 5.571784 TTCTTTTGCAGATTGATAGCCAG 57.428 39.130 0.00 0.00 0.00 4.85
4377 7965 4.592942 TCTTTTGCAGATTGATAGCCAGT 58.407 39.130 0.00 0.00 0.00 4.00
4378 7966 5.012239 TCTTTTGCAGATTGATAGCCAGTT 58.988 37.500 0.00 0.00 0.00 3.16
4382 7970 2.810852 GCAGATTGATAGCCAGTTAGCC 59.189 50.000 0.00 0.00 0.00 3.93
4405 7993 2.352030 CCAAAAGGCTGCATGTGTGTAG 60.352 50.000 0.50 0.00 40.58 2.74
4414 8002 2.095110 TGCATGTGTGTAGCAATGCTTC 60.095 45.455 14.85 9.33 40.44 3.86
4425 8013 1.742268 GCAATGCTTCCTTGTCTCTCC 59.258 52.381 0.00 0.00 0.00 3.71
4435 8023 0.464036 TTGTCTCTCCGTGTGCTTGT 59.536 50.000 0.00 0.00 0.00 3.16
4439 8027 2.475487 GTCTCTCCGTGTGCTTGTTAAC 59.525 50.000 0.00 0.00 0.00 2.01
4444 8032 2.097791 TCCGTGTGCTTGTTAACAAACC 59.902 45.455 20.89 14.98 35.15 3.27
4446 8034 3.502920 CGTGTGCTTGTTAACAAACCAA 58.497 40.909 20.89 6.02 35.15 3.67
4449 8037 4.867608 GTGTGCTTGTTAACAAACCAATGT 59.132 37.500 20.89 0.00 35.15 2.71
4454 8042 5.752955 GCTTGTTAACAAACCAATGTGTGAT 59.247 36.000 20.89 0.00 33.62 3.06
4457 8045 9.474920 CTTGTTAACAAACCAATGTGTGATTAT 57.525 29.630 20.89 0.00 33.62 1.28
4458 8046 8.809159 TGTTAACAAACCAATGTGTGATTATG 57.191 30.769 5.64 0.00 33.62 1.90
4487 8075 9.554395 TCACATTGTTGTAGATAAAGTGAAAGA 57.446 29.630 0.00 0.00 35.22 2.52
4500 8088 5.747951 AAGTGAAAGAGAGCAAGAGTTTG 57.252 39.130 0.00 0.00 37.36 2.93
4512 8100 6.995091 AGAGCAAGAGTTTGAAACTAGATTGT 59.005 34.615 21.14 13.34 43.03 2.71
4513 8101 6.963796 AGCAAGAGTTTGAAACTAGATTGTG 58.036 36.000 21.14 11.74 43.03 3.33
4537 8125 6.425114 TGAGTGCAAAACTAAGTCTGAGAATC 59.575 38.462 0.00 0.00 40.07 2.52
4538 8126 5.406780 AGTGCAAAACTAAGTCTGAGAATCG 59.593 40.000 0.00 0.00 37.36 3.34
4539 8127 5.177696 GTGCAAAACTAAGTCTGAGAATCGT 59.822 40.000 0.00 0.00 38.61 3.73
4540 8128 6.365247 GTGCAAAACTAAGTCTGAGAATCGTA 59.635 38.462 0.00 0.00 38.61 3.43
4541 8129 7.063544 GTGCAAAACTAAGTCTGAGAATCGTAT 59.936 37.037 0.00 0.00 38.61 3.06
4542 8130 7.063426 TGCAAAACTAAGTCTGAGAATCGTATG 59.937 37.037 0.00 0.00 38.61 2.39
4557 8146 5.856126 ATCGTATGGTGTGTTAGTTTGTG 57.144 39.130 0.00 0.00 0.00 3.33
4560 8149 3.988379 ATGGTGTGTTAGTTTGTGCTG 57.012 42.857 0.00 0.00 0.00 4.41
4561 8150 1.403679 TGGTGTGTTAGTTTGTGCTGC 59.596 47.619 0.00 0.00 0.00 5.25
4575 8164 2.053627 GTGCTGCATGTGCTTAAACAC 58.946 47.619 5.27 1.93 42.66 3.32
4586 8175 2.995939 TGCTTAAACACGATCAGAGCTG 59.004 45.455 0.00 0.00 0.00 4.24
4587 8176 2.222908 GCTTAAACACGATCAGAGCTGC 60.223 50.000 0.00 0.00 0.00 5.25
4588 8177 1.629013 TAAACACGATCAGAGCTGCG 58.371 50.000 0.00 0.00 0.00 5.18
4589 8178 1.016130 AAACACGATCAGAGCTGCGG 61.016 55.000 0.00 0.00 0.00 5.69
4604 8193 1.063469 CTGCGGGCCGTGTTTAATTAG 59.937 52.381 28.82 8.13 0.00 1.73
4659 8248 9.958180 TTTCATGTCTTAATTCACATTCTCCTA 57.042 29.630 0.00 0.00 30.48 2.94
4698 8287 5.473066 AATCCCTTTCAATCACCAAACAG 57.527 39.130 0.00 0.00 0.00 3.16
4709 8298 0.114364 ACCAAACAGGGGAATGGGAC 59.886 55.000 0.00 0.00 43.89 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.179081 GTCTACTGACGAATGGGCCC 60.179 60.000 17.59 17.59 33.15 5.80
47 48 3.315191 ACATGCTCCATAAAATACACGGC 59.685 43.478 0.00 0.00 0.00 5.68
50 51 5.127031 ACCCAACATGCTCCATAAAATACAC 59.873 40.000 0.00 0.00 0.00 2.90
56 57 1.824230 GCACCCAACATGCTCCATAAA 59.176 47.619 0.00 0.00 40.08 1.40
140 141 1.745890 CACTCCGGTGGTGAGTTCA 59.254 57.895 19.99 0.00 41.02 3.18
215 216 0.103208 CGGATCAAAGACGAGGGGAG 59.897 60.000 0.00 0.00 0.00 4.30
216 217 1.327690 CCGGATCAAAGACGAGGGGA 61.328 60.000 0.00 0.00 0.00 4.81
217 218 1.144057 CCGGATCAAAGACGAGGGG 59.856 63.158 0.00 0.00 0.00 4.79
218 219 0.460284 CACCGGATCAAAGACGAGGG 60.460 60.000 9.46 0.00 0.00 4.30
219 220 1.084370 GCACCGGATCAAAGACGAGG 61.084 60.000 9.46 0.00 0.00 4.63
220 221 1.084370 GGCACCGGATCAAAGACGAG 61.084 60.000 9.46 0.00 0.00 4.18
221 222 1.079405 GGCACCGGATCAAAGACGA 60.079 57.895 9.46 0.00 0.00 4.20
222 223 2.106683 GGGCACCGGATCAAAGACG 61.107 63.158 9.46 0.00 40.86 4.18
223 224 3.905249 GGGCACCGGATCAAAGAC 58.095 61.111 9.46 0.00 40.86 3.01
356 358 3.367288 TCCACGTACTGGACCATCA 57.633 52.632 9.25 0.00 44.99 3.07
366 368 1.226030 GGCACCACAAGTCCACGTAC 61.226 60.000 0.00 0.00 0.00 3.67
391 393 1.470494 GTCAGAGAGCTCGATGTGTCA 59.530 52.381 17.37 0.17 34.09 3.58
409 411 1.475403 TGAAGGATGTCGGGAGAGTC 58.525 55.000 0.00 0.00 41.26 3.36
416 418 1.439353 CCGCCATTGAAGGATGTCGG 61.439 60.000 0.00 0.00 41.38 4.79
472 474 3.005898 CATCCGGCGAACGTCATG 58.994 61.111 9.30 0.00 42.24 3.07
527 529 2.609747 AGGGCAGAACTACTCAGTCAA 58.390 47.619 0.00 0.00 32.29 3.18
583 585 6.124759 GTGTTACACAGAATTCGTACACAAC 58.875 40.000 10.96 13.04 34.08 3.32
586 588 4.746115 TGGTGTTACACAGAATTCGTACAC 59.254 41.667 17.67 17.32 35.86 2.90
635 650 6.406370 TCCCGCGAATCTTTCATTGATATAT 58.594 36.000 8.23 0.00 0.00 0.86
636 651 5.789521 TCCCGCGAATCTTTCATTGATATA 58.210 37.500 8.23 0.00 0.00 0.86
676 692 9.673454 GTTTCAAACGAGGTAGTATTTTTGATT 57.327 29.630 0.00 0.00 34.03 2.57
824 4262 3.086600 GGAGGAGGAGTGGGCCTG 61.087 72.222 4.53 0.00 38.73 4.85
825 4263 3.288381 AGGAGGAGGAGTGGGCCT 61.288 66.667 4.53 0.00 42.17 5.19
826 4264 2.766229 GAGGAGGAGGAGTGGGCC 60.766 72.222 0.00 0.00 0.00 5.80
827 4265 2.766229 GGAGGAGGAGGAGTGGGC 60.766 72.222 0.00 0.00 0.00 5.36
828 4266 1.075600 GAGGAGGAGGAGGAGTGGG 60.076 68.421 0.00 0.00 0.00 4.61
829 4267 1.075600 GGAGGAGGAGGAGGAGTGG 60.076 68.421 0.00 0.00 0.00 4.00
830 4268 0.106217 GAGGAGGAGGAGGAGGAGTG 60.106 65.000 0.00 0.00 0.00 3.51
831 4269 1.293683 GGAGGAGGAGGAGGAGGAGT 61.294 65.000 0.00 0.00 0.00 3.85
832 4270 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
833 4271 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
834 4272 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
835 4273 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
836 4274 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
837 4275 0.998945 AGAGGAGGAGGAGGAGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
838 4276 0.478507 GAGAGGAGGAGGAGGAGGAG 59.521 65.000 0.00 0.00 0.00 3.69
839 4277 0.996762 GGAGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
840 4278 1.541672 GGAGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
841 4279 1.541672 GGGAGAGGAGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
842 4280 2.387772 CGGGAGAGGAGGAGGAGGA 61.388 68.421 0.00 0.00 0.00 3.71
843 4281 2.197324 CGGGAGAGGAGGAGGAGG 59.803 72.222 0.00 0.00 0.00 4.30
914 4365 4.324991 GGAGCGGGTTGGGTTCGT 62.325 66.667 0.00 0.00 0.00 3.85
1429 4910 8.511321 GGATAACTGACAGATACAGAGATACAG 58.489 40.741 10.08 0.00 38.55 2.74
1430 4911 8.221251 AGGATAACTGACAGATACAGAGATACA 58.779 37.037 10.08 0.00 38.55 2.29
1431 4912 8.630054 AGGATAACTGACAGATACAGAGATAC 57.370 38.462 10.08 0.00 38.55 2.24
1450 4931 8.177119 ACAGTTTTCACATAGCAAAAGGATAA 57.823 30.769 0.00 0.00 0.00 1.75
1453 4934 5.592282 TGACAGTTTTCACATAGCAAAAGGA 59.408 36.000 0.00 0.00 0.00 3.36
1473 4954 6.472016 TCACATAGCAAAAGGATAACTGACA 58.528 36.000 0.00 0.00 0.00 3.58
1519 5001 3.829886 ACTGCACATGGACGTATTTTG 57.170 42.857 0.00 0.00 0.00 2.44
1639 5171 7.662669 GGGTTTATACTTCACTAGGAACAACAA 59.337 37.037 0.00 0.00 0.00 2.83
1673 5212 2.462456 TAACACAAGCAGGAGCAGAG 57.538 50.000 0.00 0.00 45.49 3.35
2058 5624 0.895530 CCCGTGCTTACTCTTCCTCA 59.104 55.000 0.00 0.00 0.00 3.86
2440 6010 3.328382 TCATCTTTAGAACCGTGGTGG 57.672 47.619 0.00 0.00 46.41 4.61
2619 6189 1.399440 CATCACTGCTTGGGTCAATCG 59.601 52.381 0.00 0.00 0.00 3.34
2632 6202 8.872845 GGCCTTTTGTTTTTATATTCATCACTG 58.127 33.333 0.00 0.00 0.00 3.66
2832 6402 4.606210 ACTAGTCTTCCCTTCCTTCTCTC 58.394 47.826 0.00 0.00 0.00 3.20
3226 6805 0.681564 TCCTCTCTTCCTCCAGACGC 60.682 60.000 0.00 0.00 0.00 5.19
3361 6940 2.342650 CCTTTCCACACCATGCCCG 61.343 63.158 0.00 0.00 0.00 6.13
3363 6942 1.076549 TCCCTTTCCACACCATGCC 59.923 57.895 0.00 0.00 0.00 4.40
3530 7109 5.297776 GGTCCCTGTTTTCATCATCACTATG 59.702 44.000 0.00 0.00 0.00 2.23
3594 7173 6.544931 CCTCTTTGAATCATGGCTATCTGAAA 59.455 38.462 0.00 0.00 0.00 2.69
3815 7395 5.847111 AAAGGTCAAACCACCTAAAAGAC 57.153 39.130 0.00 0.00 46.97 3.01
3852 7432 2.381961 ACTTATTTTGGGGCAGAGGGAA 59.618 45.455 0.00 0.00 0.00 3.97
3853 7433 2.000048 ACTTATTTTGGGGCAGAGGGA 59.000 47.619 0.00 0.00 0.00 4.20
3854 7434 2.102578 CACTTATTTTGGGGCAGAGGG 58.897 52.381 0.00 0.00 0.00 4.30
3855 7435 2.755103 GACACTTATTTTGGGGCAGAGG 59.245 50.000 0.00 0.00 0.00 3.69
3856 7436 3.690460 AGACACTTATTTTGGGGCAGAG 58.310 45.455 0.00 0.00 0.00 3.35
3857 7437 3.073798 TGAGACACTTATTTTGGGGCAGA 59.926 43.478 0.00 0.00 0.00 4.26
3858 7438 3.420893 TGAGACACTTATTTTGGGGCAG 58.579 45.455 0.00 0.00 0.00 4.85
3859 7439 3.517296 TGAGACACTTATTTTGGGGCA 57.483 42.857 0.00 0.00 0.00 5.36
3860 7440 3.826729 AGTTGAGACACTTATTTTGGGGC 59.173 43.478 0.00 0.00 0.00 5.80
3861 7441 6.405278 AAAGTTGAGACACTTATTTTGGGG 57.595 37.500 0.00 0.00 35.87 4.96
3862 7442 8.166422 ACTAAAGTTGAGACACTTATTTTGGG 57.834 34.615 0.00 0.00 35.87 4.12
3871 7451 9.174166 ACAAAATTGTACTAAAGTTGAGACACT 57.826 29.630 0.00 0.00 40.16 3.55
3897 7477 9.135189 TGTCTCAACTTTGTACTAAGGTTAGTA 57.865 33.333 19.08 5.64 43.36 1.82
3898 7478 7.924947 GTGTCTCAACTTTGTACTAAGGTTAGT 59.075 37.037 19.08 7.52 45.39 2.24
3899 7479 8.142551 AGTGTCTCAACTTTGTACTAAGGTTAG 58.857 37.037 19.08 14.11 36.82 2.34
3900 7480 8.015185 AGTGTCTCAACTTTGTACTAAGGTTA 57.985 34.615 19.08 5.55 0.00 2.85
3901 7481 6.885922 AGTGTCTCAACTTTGTACTAAGGTT 58.114 36.000 19.08 9.89 0.00 3.50
3902 7482 6.481434 AGTGTCTCAACTTTGTACTAAGGT 57.519 37.500 19.08 11.48 0.00 3.50
3903 7483 9.490379 AATAAGTGTCTCAACTTTGTACTAAGG 57.510 33.333 19.08 4.85 40.77 2.69
3907 7487 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
3908 7488 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
3909 7489 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
3910 7490 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
3911 7491 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
3912 7492 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
3913 7493 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
3914 7494 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
3915 7495 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
3916 7496 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3917 7497 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
3918 7498 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
3919 7499 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
3920 7500 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
3921 7501 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
3922 7502 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3923 7503 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3924 7504 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3925 7505 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3926 7506 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3927 7507 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3928 7508 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
3929 7509 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
3930 7510 2.852714 TAATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
3931 7511 4.687262 ATATAATACTCCCTCCGTCCCA 57.313 45.455 0.00 0.00 0.00 4.37
3932 7512 7.068061 AGATTATATAATACTCCCTCCGTCCC 58.932 42.308 7.97 0.00 0.00 4.46
3933 7513 8.000127 AGAGATTATATAATACTCCCTCCGTCC 59.000 40.741 20.07 3.92 0.00 4.79
3934 7514 8.983702 AGAGATTATATAATACTCCCTCCGTC 57.016 38.462 20.07 4.67 0.00 4.79
3935 7515 7.716123 CGAGAGATTATATAATACTCCCTCCGT 59.284 40.741 22.54 10.86 31.56 4.69
3936 7516 7.308109 GCGAGAGATTATATAATACTCCCTCCG 60.308 44.444 22.54 19.55 31.56 4.63
3937 7517 7.502895 TGCGAGAGATTATATAATACTCCCTCC 59.497 40.741 22.54 14.93 31.56 4.30
3938 7518 8.453238 TGCGAGAGATTATATAATACTCCCTC 57.547 38.462 22.54 17.34 31.56 4.30
3939 7519 8.056400 ACTGCGAGAGATTATATAATACTCCCT 58.944 37.037 22.54 12.05 31.56 4.20
3940 7520 8.132362 CACTGCGAGAGATTATATAATACTCCC 58.868 40.741 22.54 18.27 31.56 4.30
3941 7521 7.646130 GCACTGCGAGAGATTATATAATACTCC 59.354 40.741 22.54 18.38 31.56 3.85
3942 7522 8.555166 GCACTGCGAGAGATTATATAATACTC 57.445 38.462 20.62 20.62 0.00 2.59
3961 7541 2.027460 CCCAACCAAACGCACTGC 59.973 61.111 0.00 0.00 0.00 4.40
3962 7542 2.727544 CCCCAACCAAACGCACTG 59.272 61.111 0.00 0.00 0.00 3.66
3963 7543 2.520741 CCCCCAACCAAACGCACT 60.521 61.111 0.00 0.00 0.00 4.40
3964 7544 2.519780 TCCCCCAACCAAACGCAC 60.520 61.111 0.00 0.00 0.00 5.34
3965 7545 1.706995 TACTCCCCCAACCAAACGCA 61.707 55.000 0.00 0.00 0.00 5.24
3966 7546 0.958876 CTACTCCCCCAACCAAACGC 60.959 60.000 0.00 0.00 0.00 4.84
3967 7547 0.322187 CCTACTCCCCCAACCAAACG 60.322 60.000 0.00 0.00 0.00 3.60
4004 7584 2.069273 CGTTGAATCTCACACCCTGTC 58.931 52.381 0.00 0.00 0.00 3.51
4032 7613 6.022315 TGAATTCCCATTTACCTGAACCAAT 58.978 36.000 2.27 0.00 0.00 3.16
4039 7620 4.586001 CCCTGATGAATTCCCATTTACCTG 59.414 45.833 2.27 0.00 0.00 4.00
4045 7626 3.374540 CCCTTCCCTGATGAATTCCCATT 60.375 47.826 2.27 0.00 0.00 3.16
4049 7630 1.852965 TCCCCTTCCCTGATGAATTCC 59.147 52.381 2.27 0.00 0.00 3.01
4059 7640 1.711684 AATTCCCATTCCCCTTCCCT 58.288 50.000 0.00 0.00 0.00 4.20
4070 7651 4.089361 GAGTTTCACCCTCAAATTCCCAT 58.911 43.478 0.00 0.00 0.00 4.00
4071 7652 3.496331 GAGTTTCACCCTCAAATTCCCA 58.504 45.455 0.00 0.00 0.00 4.37
4082 7663 1.630878 AGATCTGTGGGAGTTTCACCC 59.369 52.381 0.00 0.00 46.87 4.61
4095 7676 2.969628 CCTACCAGGGATGAGATCTGT 58.030 52.381 0.00 0.00 0.00 3.41
4108 7689 1.843851 TCAATTACCTGCCCCTACCAG 59.156 52.381 0.00 0.00 0.00 4.00
4109 7690 1.843851 CTCAATTACCTGCCCCTACCA 59.156 52.381 0.00 0.00 0.00 3.25
4130 7711 0.905357 CACAATTCCCTCTCCCTCGT 59.095 55.000 0.00 0.00 0.00 4.18
4156 7737 5.821995 CAGAGGGGCATTTTCAAAAGAAAAA 59.178 36.000 7.38 0.00 37.55 1.94
4157 7738 5.104569 ACAGAGGGGCATTTTCAAAAGAAAA 60.105 36.000 5.93 5.93 38.26 2.29
4158 7739 4.408596 ACAGAGGGGCATTTTCAAAAGAAA 59.591 37.500 0.00 0.00 0.00 2.52
4161 7742 4.309933 GAACAGAGGGGCATTTTCAAAAG 58.690 43.478 0.00 0.00 0.00 2.27
4166 7747 1.534729 ACGAACAGAGGGGCATTTTC 58.465 50.000 0.00 0.00 0.00 2.29
4181 7762 0.181587 TGCCTTCTGTTGGGAACGAA 59.818 50.000 0.00 0.00 0.00 3.85
4184 7765 1.273327 CCATTGCCTTCTGTTGGGAAC 59.727 52.381 0.00 0.00 37.72 3.62
4203 7784 3.123453 GCAATGATTTTCGCTGGTTTTCC 59.877 43.478 0.00 0.00 41.14 3.13
4207 7788 4.782019 TTAGCAATGATTTTCGCTGGTT 57.218 36.364 0.00 0.00 35.93 3.67
4208 7789 4.989279 ATTAGCAATGATTTTCGCTGGT 57.011 36.364 0.00 0.00 35.93 4.00
4209 7790 4.905866 CGTATTAGCAATGATTTTCGCTGG 59.094 41.667 0.00 0.00 35.93 4.85
4210 7791 4.376861 GCGTATTAGCAATGATTTTCGCTG 59.623 41.667 0.00 0.00 37.55 5.18
4211 7792 4.527564 GCGTATTAGCAATGATTTTCGCT 58.472 39.130 0.00 0.00 37.55 4.93
4212 7793 3.354920 CGCGTATTAGCAATGATTTTCGC 59.645 43.478 0.00 0.00 36.85 4.70
4213 7794 3.900116 CCGCGTATTAGCAATGATTTTCG 59.100 43.478 4.92 0.00 36.85 3.46
4214 7795 4.024387 TCCCGCGTATTAGCAATGATTTTC 60.024 41.667 4.92 0.00 36.85 2.29
4222 7810 2.614983 GGATTTTCCCGCGTATTAGCAA 59.385 45.455 4.92 0.00 36.85 3.91
4231 7819 0.530288 AACCAATGGATTTTCCCGCG 59.470 50.000 6.16 0.00 35.03 6.46
4233 7821 7.883311 ACTATCTATAACCAATGGATTTTCCCG 59.117 37.037 6.16 0.00 37.09 5.14
4243 7831 7.320399 TCCATGCGTACTATCTATAACCAATG 58.680 38.462 0.00 0.00 0.00 2.82
4253 7841 3.567397 AGGACTTCCATGCGTACTATCT 58.433 45.455 0.00 0.00 38.89 1.98
4255 7843 4.471548 ACTAGGACTTCCATGCGTACTAT 58.528 43.478 0.00 0.00 38.89 2.12
4258 7846 4.644103 TTACTAGGACTTCCATGCGTAC 57.356 45.455 0.00 0.00 38.89 3.67
4261 7849 4.592485 AGATTACTAGGACTTCCATGCG 57.408 45.455 0.00 0.00 38.89 4.73
4264 7852 8.013667 AGATGGTAAGATTACTAGGACTTCCAT 58.986 37.037 0.00 0.00 35.37 3.41
4265 7853 7.363031 AGATGGTAAGATTACTAGGACTTCCA 58.637 38.462 0.00 0.00 34.65 3.53
4270 7858 9.930693 CCAATTAGATGGTAAGATTACTAGGAC 57.069 37.037 0.00 0.00 35.65 3.85
4294 7882 2.395988 AATCGCACCTGCTGTCACCA 62.396 55.000 0.00 0.00 39.32 4.17
4300 7888 1.596260 CTACATCAATCGCACCTGCTG 59.404 52.381 0.00 0.00 39.32 4.41
4313 7901 7.937700 AAAGAAGGGGAATAGATCTACATCA 57.062 36.000 4.10 0.00 0.00 3.07
4318 7906 8.836735 ACAAAGAAAAGAAGGGGAATAGATCTA 58.163 33.333 4.57 4.57 0.00 1.98
4319 7907 7.703755 ACAAAGAAAAGAAGGGGAATAGATCT 58.296 34.615 0.00 0.00 0.00 2.75
4322 7910 7.563556 ACAAACAAAGAAAAGAAGGGGAATAGA 59.436 33.333 0.00 0.00 0.00 1.98
4323 7911 7.726216 ACAAACAAAGAAAAGAAGGGGAATAG 58.274 34.615 0.00 0.00 0.00 1.73
4343 7931 8.389603 TCAATCTGCAAAAGAAAATGAACAAAC 58.610 29.630 0.00 0.00 38.79 2.93
4344 7932 8.489990 TCAATCTGCAAAAGAAAATGAACAAA 57.510 26.923 0.00 0.00 38.79 2.83
4346 7934 9.414295 CTATCAATCTGCAAAAGAAAATGAACA 57.586 29.630 0.00 0.00 38.79 3.18
4347 7935 8.378421 GCTATCAATCTGCAAAAGAAAATGAAC 58.622 33.333 0.00 0.00 38.79 3.18
4362 7950 3.812053 GTGGCTAACTGGCTATCAATCTG 59.188 47.826 0.00 0.00 42.34 2.90
4370 7958 2.554344 CCTTTTGGTGGCTAACTGGCTA 60.554 50.000 0.00 0.00 42.34 3.93
4371 7959 1.620822 CTTTTGGTGGCTAACTGGCT 58.379 50.000 0.00 0.00 42.34 4.75
4372 7960 0.603065 CCTTTTGGTGGCTAACTGGC 59.397 55.000 0.00 0.00 42.18 4.85
4373 7961 0.603065 GCCTTTTGGTGGCTAACTGG 59.397 55.000 0.00 0.00 46.38 4.00
4382 7970 0.390124 ACACATGCAGCCTTTTGGTG 59.610 50.000 0.00 0.00 45.40 4.17
4405 7993 1.742268 GGAGAGACAAGGAAGCATTGC 59.258 52.381 0.00 0.00 36.28 3.56
4410 7998 0.318762 ACACGGAGAGACAAGGAAGC 59.681 55.000 0.00 0.00 0.00 3.86
4414 8002 0.034059 AAGCACACGGAGAGACAAGG 59.966 55.000 0.00 0.00 0.00 3.61
4425 8013 3.138205 TGGTTTGTTAACAAGCACACG 57.862 42.857 28.91 0.00 38.57 4.49
4457 8045 9.500785 TCACTTTATCTACAACAATGTGATTCA 57.499 29.630 0.00 0.00 40.84 2.57
4466 8054 7.931407 TGCTCTCTTTCACTTTATCTACAACAA 59.069 33.333 0.00 0.00 0.00 2.83
4471 8059 8.032451 ACTCTTGCTCTCTTTCACTTTATCTAC 58.968 37.037 0.00 0.00 0.00 2.59
4474 8062 7.665561 AACTCTTGCTCTCTTTCACTTTATC 57.334 36.000 0.00 0.00 0.00 1.75
4477 8065 5.882557 TCAAACTCTTGCTCTCTTTCACTTT 59.117 36.000 0.00 0.00 32.14 2.66
4481 8069 5.882557 AGTTTCAAACTCTTGCTCTCTTTCA 59.117 36.000 0.00 0.00 37.02 2.69
4482 8070 6.370433 AGTTTCAAACTCTTGCTCTCTTTC 57.630 37.500 0.00 0.00 37.02 2.62
4486 8074 7.172361 ACAATCTAGTTTCAAACTCTTGCTCTC 59.828 37.037 5.92 0.00 41.77 3.20
4487 8075 6.995091 ACAATCTAGTTTCAAACTCTTGCTCT 59.005 34.615 5.92 0.00 41.77 4.09
4500 8088 6.729187 AGTTTTGCACTCACAATCTAGTTTC 58.271 36.000 0.00 0.00 0.00 2.78
4512 8100 5.276461 TCTCAGACTTAGTTTTGCACTCA 57.724 39.130 0.00 0.00 36.88 3.41
4513 8101 6.400515 CGATTCTCAGACTTAGTTTTGCACTC 60.401 42.308 0.00 0.00 36.88 3.51
4537 8125 3.496884 AGCACAAACTAACACACCATACG 59.503 43.478 0.00 0.00 0.00 3.06
4538 8126 4.783242 CAGCACAAACTAACACACCATAC 58.217 43.478 0.00 0.00 0.00 2.39
4539 8127 3.252215 GCAGCACAAACTAACACACCATA 59.748 43.478 0.00 0.00 0.00 2.74
4540 8128 2.034558 GCAGCACAAACTAACACACCAT 59.965 45.455 0.00 0.00 0.00 3.55
4541 8129 1.403679 GCAGCACAAACTAACACACCA 59.596 47.619 0.00 0.00 0.00 4.17
4542 8130 1.403679 TGCAGCACAAACTAACACACC 59.596 47.619 0.00 0.00 0.00 4.16
4557 8146 1.069296 TCGTGTTTAAGCACATGCAGC 60.069 47.619 20.48 2.68 45.16 5.25
4560 8149 3.125146 TCTGATCGTGTTTAAGCACATGC 59.875 43.478 20.48 9.95 39.19 4.06
4561 8150 4.726021 GCTCTGATCGTGTTTAAGCACATG 60.726 45.833 20.48 8.01 39.19 3.21
4586 8175 1.063027 GTCTAATTAAACACGGCCCGC 59.937 52.381 1.23 0.00 0.00 6.13
4587 8176 2.624636 AGTCTAATTAAACACGGCCCG 58.375 47.619 0.00 0.00 0.00 6.13
4588 8177 6.499234 TTTTAGTCTAATTAAACACGGCCC 57.501 37.500 0.00 0.00 0.00 5.80
4589 8178 9.659830 CATATTTTAGTCTAATTAAACACGGCC 57.340 33.333 0.00 0.00 0.00 6.13
4667 8256 6.830838 GGTGATTGAAAGGGATTTCTAGTGAT 59.169 38.462 2.75 0.00 32.39 3.06
4679 8268 2.299867 CCCTGTTTGGTGATTGAAAGGG 59.700 50.000 0.00 0.00 37.38 3.95


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

AutoCloner maintained by Alex Coulton.