Multiple sequence alignment - TraesCS2D01G356400

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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 TraesCS2D01G356400 chr2D 100.000 4497 0 0 1 4497 458732288 458736784 0.000000e+00 8305.0
1 TraesCS2D01G356400 chr2D 88.609 992 93 11 896 1878 206239618 206240598 0.000000e+00 1188.0
2 TraesCS2D01G356400 chr2D 87.516 777 74 10 1879 2648 206240656 206241416 0.000000e+00 876.0
3 TraesCS2D01G356400 chr2D 81.053 760 98 23 2745 3490 206241417 206242144 8.450000e-157 564.0
4 TraesCS2D01G356400 chr2A 90.430 3166 199 55 563 3670 602122379 602125498 0.000000e+00 4072.0
5 TraesCS2D01G356400 chr2A 88.990 990 94 10 897 1878 277138919 277137937 0.000000e+00 1210.0
6 TraesCS2D01G356400 chr2A 86.028 773 79 12 1882 2648 277137876 277137127 0.000000e+00 802.0
7 TraesCS2D01G356400 chr2A 81.699 765 87 31 2745 3490 277137126 277136396 5.010000e-164 588.0
8 TraesCS2D01G356400 chr2A 82.789 337 21 15 14 345 602121771 602122075 2.670000e-67 267.0
9 TraesCS2D01G356400 chr2A 90.083 121 8 3 3806 3925 726600968 726601085 2.170000e-33 154.0
10 TraesCS2D01G356400 chr2A 81.553 103 11 5 408 510 602122289 602122383 1.340000e-10 78.7
11 TraesCS2D01G356400 chr2B 93.333 1890 96 17 699 2567 539703620 539705500 0.000000e+00 2765.0
12 TraesCS2D01G356400 chr2B 92.818 1448 66 12 2731 4154 539705500 539706933 0.000000e+00 2063.0
13 TraesCS2D01G356400 chr2B 87.078 1718 167 34 1796 3490 198423876 198425561 0.000000e+00 1892.0
14 TraesCS2D01G356400 chr2B 97.842 139 3 0 4359 4497 539706956 539707094 1.620000e-59 241.0
15 TraesCS2D01G356400 chr2B 87.000 100 7 2 128 227 539702631 539702724 1.710000e-19 108.0
16 TraesCS2D01G356400 chr6B 86.911 1719 168 34 1796 3490 384178670 384180355 0.000000e+00 1875.0
17 TraesCS2D01G356400 chr6B 100.000 28 0 0 3806 3833 706444818 706444791 8.000000e-03 52.8
18 TraesCS2D01G356400 chr6B 100.000 28 0 0 3806 3833 706529909 706529882 8.000000e-03 52.8
19 TraesCS2D01G356400 chrUn 88.117 993 96 12 896 1878 17537384 17538364 0.000000e+00 1160.0
20 TraesCS2D01G356400 chrUn 87.404 778 77 8 1879 2650 17538422 17539184 0.000000e+00 874.0
21 TraesCS2D01G356400 chrUn 81.003 758 99 23 2746 3490 17539184 17539909 1.090000e-155 560.0
22 TraesCS2D01G356400 chr5B 87.967 241 22 7 2459 2699 208767353 208767120 1.230000e-70 278.0
23 TraesCS2D01G356400 chr5B 82.061 262 24 10 3249 3490 392491310 392491568 7.630000e-48 202.0
24 TraesCS2D01G356400 chr1B 84.142 309 26 12 2491 2799 359604236 359604521 1.230000e-70 278.0
25 TraesCS2D01G356400 chr7B 82.524 309 22 13 2491 2799 353971054 353971330 4.490000e-60 243.0
26 TraesCS2D01G356400 chr4D 85.204 196 16 7 1515 1703 327056463 327056274 5.940000e-44 189.0
27 TraesCS2D01G356400 chr7D 84.932 146 10 5 3807 3941 585894256 585894400 2.180000e-28 137.0
28 TraesCS2D01G356400 chr3D 94.118 68 4 0 3806 3873 424591363 424591430 2.210000e-18 104.0
29 TraesCS2D01G356400 chr3B 96.000 50 2 0 3824 3873 554567001 554567050 1.040000e-11 82.4
30 TraesCS2D01G356400 chr6D 80.392 102 20 0 408 509 2368277 2368378 1.340000e-10 78.7
31 TraesCS2D01G356400 chr3A 84.000 75 12 0 417 491 712302719 712302793 6.240000e-09 73.1
32 TraesCS2D01G356400 chr4B 97.059 34 1 0 3903 3936 7878902 7878869 1.750000e-04 58.4


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 TraesCS2D01G356400 chr2D 458732288 458736784 4496 False 8305.000000 8305 100.000000 1 4497 1 chr2D.!!$F1 4496
1 TraesCS2D01G356400 chr2D 206239618 206242144 2526 False 876.000000 1188 85.726000 896 3490 3 chr2D.!!$F2 2594
2 TraesCS2D01G356400 chr2A 602121771 602125498 3727 False 1472.566667 4072 84.924000 14 3670 3 chr2A.!!$F2 3656
3 TraesCS2D01G356400 chr2A 277136396 277138919 2523 True 866.666667 1210 85.572333 897 3490 3 chr2A.!!$R1 2593
4 TraesCS2D01G356400 chr2B 198423876 198425561 1685 False 1892.000000 1892 87.078000 1796 3490 1 chr2B.!!$F1 1694
5 TraesCS2D01G356400 chr2B 539702631 539707094 4463 False 1294.250000 2765 92.748250 128 4497 4 chr2B.!!$F2 4369
6 TraesCS2D01G356400 chr6B 384178670 384180355 1685 False 1875.000000 1875 86.911000 1796 3490 1 chr6B.!!$F1 1694
7 TraesCS2D01G356400 chrUn 17537384 17539909 2525 False 864.666667 1160 85.508000 896 3490 3 chrUn.!!$F1 2594

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
465 869 0.247736 GAGGACGTCTGCATCCTTGT 59.752 55.000 16.46 0.0 45.74 3.16 F
886 1397 3.340814 TGGAGATTCAGTTGGCTCTTC 57.659 47.619 0.00 0.0 0.00 2.87 F
1885 2477 3.364621 GCGTTTAAATGTTGTCCTGCATG 59.635 43.478 9.12 0.0 0.00 4.06 F
2369 2970 3.455177 TGGGGTTACTTTGTCTGTGTGTA 59.545 43.478 0.00 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1627 2154 1.416480 GGTATGCACCTAGGACCCCC 61.416 65.000 17.98 3.53 42.11 5.40 R
2393 2996 2.361757 CAACCATCAAGACAAACTGGCA 59.638 45.455 0.00 0.00 0.00 4.92 R
3235 3860 0.246635 TACAAGAGCCAGCGGAAGAC 59.753 55.000 0.00 0.00 0.00 3.01 R
4030 4693 0.106149 AGATACGATTTCACCGGCCC 59.894 55.000 0.00 0.00 0.00 5.80 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
53 56 7.814587 CAGATGTGTATCTTCTGTGTAAAGACA 59.185 37.037 0.00 0.00 41.71 3.41
106 112 4.143137 GCTTTCTCTCGCTCAAGAAAAGAG 60.143 45.833 0.00 0.00 40.09 2.85
138 144 6.260050 AGAAACGCAACATCAAAGAGTTAAGA 59.740 34.615 0.00 0.00 0.00 2.10
142 148 4.712763 CAACATCAAAGAGTTAAGACCGC 58.287 43.478 0.00 0.00 0.00 5.68
146 152 1.012486 AAAGAGTTAAGACCGCGGCG 61.012 55.000 28.58 16.78 0.00 6.46
169 175 3.364062 CTTCACAGGAAGCTACGTATCG 58.636 50.000 0.00 0.00 43.67 2.92
170 176 2.362736 TCACAGGAAGCTACGTATCGT 58.637 47.619 0.00 0.00 44.35 3.73
299 314 4.890306 GCTCCCTCCCTCCCTCCC 62.890 77.778 0.00 0.00 0.00 4.30
300 315 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
301 316 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
302 317 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
303 318 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
304 319 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
305 320 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
306 321 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
307 322 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
308 323 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
309 324 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
310 325 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
373 617 3.140814 GCCGATCTGGGTTTGGGC 61.141 66.667 5.87 0.00 38.63 5.36
465 869 0.247736 GAGGACGTCTGCATCCTTGT 59.752 55.000 16.46 0.00 45.74 3.16
467 871 0.247736 GGACGTCTGCATCCTTGTCT 59.752 55.000 16.46 0.00 31.75 3.41
545 949 4.081030 CTCGCGTTGGTGCTGCTG 62.081 66.667 5.77 0.00 0.00 4.41
549 953 4.034258 CGTTGGTGCTGCTGGCTG 62.034 66.667 0.00 0.00 42.39 4.85
550 954 4.353437 GTTGGTGCTGCTGGCTGC 62.353 66.667 15.66 15.66 42.39 5.25
614 1024 5.410746 TCTCTCTTGCTACAGATTTTTGCTG 59.589 40.000 0.00 0.00 39.26 4.41
620 1030 3.691609 GCTACAGATTTTTGCTGGCTAGT 59.308 43.478 0.00 0.00 37.69 2.57
622 1032 5.529060 GCTACAGATTTTTGCTGGCTAGTAT 59.471 40.000 0.00 0.00 37.69 2.12
672 1085 8.974060 ATCCTCAGAAGTACTGTTTGTTTTTA 57.026 30.769 0.00 0.00 45.86 1.52
685 1101 5.125739 TGTTTGTTTTTATGAGTTGACCGGT 59.874 36.000 6.92 6.92 0.00 5.28
701 1117 4.227538 GACCGGTACATCGATAATCAGTG 58.772 47.826 7.34 0.00 0.00 3.66
886 1397 3.340814 TGGAGATTCAGTTGGCTCTTC 57.659 47.619 0.00 0.00 0.00 2.87
941 1452 4.272504 CGCTCTTGGTGTTTTGTTCTTCTA 59.727 41.667 0.00 0.00 0.00 2.10
951 1462 7.803659 GGTGTTTTGTTCTTCTAATGCTACTTC 59.196 37.037 0.00 0.00 0.00 3.01
955 1466 9.950680 TTTTGTTCTTCTAATGCTACTTCTTTG 57.049 29.630 0.00 0.00 0.00 2.77
1012 1528 8.242053 CCCTGATGAATAAACATGAATATCTGC 58.758 37.037 0.00 0.00 0.00 4.26
1127 1643 9.655769 GTAATGTTATCTATGCATTTCACAGTG 57.344 33.333 3.54 0.00 34.97 3.66
1524 2051 6.070194 CCCTGTTTCTCTTTTCCTGGTATCTA 60.070 42.308 0.00 0.00 0.00 1.98
1600 2127 5.927689 TGCTCTTGAATTTTGGTAATGCAAG 59.072 36.000 10.62 10.62 34.23 4.01
1627 2154 9.926751 CTGCACTATGAATGACAAATTAGTAAG 57.073 33.333 0.00 0.00 0.00 2.34
1700 2229 7.751732 TGCTGCATTGTTCAGTAATACTAAAG 58.248 34.615 0.00 0.00 34.21 1.85
1714 2243 9.823647 AGTAATACTAAAGTGATTCATGGTCTG 57.176 33.333 0.00 0.00 0.00 3.51
1728 2257 6.293004 TCATGGTCTGAACAAAAAGGTTTT 57.707 33.333 0.00 0.00 0.00 2.43
1733 2262 9.758651 ATGGTCTGAACAAAAAGGTTTTTATAC 57.241 29.630 0.00 0.00 38.23 1.47
1885 2477 3.364621 GCGTTTAAATGTTGTCCTGCATG 59.635 43.478 9.12 0.00 0.00 4.06
1914 2506 5.067936 GTCTGGAAGCTATTAGCAGTACTGA 59.932 44.000 27.08 6.10 45.56 3.41
1932 2525 6.812160 AGTACTGATAGTTAAGGCTTTTCACG 59.188 38.462 4.45 0.00 0.00 4.35
1985 2578 6.245408 TGAAAGTAACCAATATGCTTCTGGT 58.755 36.000 1.54 1.54 45.50 4.00
2369 2970 3.455177 TGGGGTTACTTTGTCTGTGTGTA 59.545 43.478 0.00 0.00 0.00 2.90
2418 3021 4.501915 CCAGTTTGTCTTGATGGTTGCATT 60.502 41.667 0.00 0.00 0.00 3.56
2429 3032 6.106648 TGATGGTTGCATTGGAACATTTAA 57.893 33.333 20.58 3.45 39.30 1.52
2500 3107 9.625747 TTTATTCTTGCCATGTTATCTGTGATA 57.374 29.630 0.00 0.00 0.00 2.15
2526 3133 4.217836 TGCATGAAGCTTCTTCTCTCAT 57.782 40.909 26.09 8.44 45.94 2.90
2528 3135 5.008331 TGCATGAAGCTTCTTCTCTCATTT 58.992 37.500 26.09 0.00 45.94 2.32
2529 3136 5.106277 TGCATGAAGCTTCTTCTCTCATTTG 60.106 40.000 26.09 7.02 45.94 2.32
2597 3204 6.533819 TTTTATTACGGCTGATGGTTATCG 57.466 37.500 0.00 0.00 36.04 2.92
2600 3207 5.654603 ATTACGGCTGATGGTTATCGATA 57.345 39.130 0.00 0.00 36.04 2.92
2704 3316 5.681639 AGAAACAACTATACATGGCTACCC 58.318 41.667 0.00 0.00 0.00 3.69
2706 3318 5.710409 AACAACTATACATGGCTACCCTT 57.290 39.130 0.00 0.00 0.00 3.95
2707 3319 5.036117 ACAACTATACATGGCTACCCTTG 57.964 43.478 0.00 0.00 40.97 3.61
2812 3424 3.885297 ACTTTGTTGCAGTAGACATTGCT 59.115 39.130 0.00 0.00 40.87 3.91
2906 3523 4.184079 TCCTTCGCTGTAGGAAACTAAC 57.816 45.455 0.00 0.00 46.54 2.34
2928 3550 6.034161 ACTAGCTAAATACGACACCTGTTT 57.966 37.500 0.00 0.00 0.00 2.83
2942 3564 5.656480 ACACCTGTTTCATTTTGTAACACC 58.344 37.500 0.00 0.00 33.68 4.16
3235 3860 2.427410 GCTTCGTGCCAAGCAACG 60.427 61.111 7.15 0.00 46.93 4.10
3239 3864 1.092921 TTCGTGCCAAGCAACGTCTT 61.093 50.000 0.00 0.00 41.47 3.01
3241 3866 1.282875 GTGCCAAGCAACGTCTTCC 59.717 57.895 0.00 0.00 41.47 3.46
3247 3872 4.090057 GCAACGTCTTCCGCTGGC 62.090 66.667 0.00 0.00 41.42 4.85
3456 4097 2.454772 AGGAGAATTTTGGGGGTTTCCT 59.545 45.455 0.00 0.00 35.33 3.36
3457 4098 2.567169 GGAGAATTTTGGGGGTTTCCTG 59.433 50.000 0.00 0.00 35.33 3.86
3519 4162 0.803768 AGATCATCGCGTGTCACTGC 60.804 55.000 5.77 5.65 0.00 4.40
3598 4242 1.534595 GGATGGCATTGTTGTCGCATC 60.535 52.381 0.00 0.00 0.00 3.91
3600 4244 0.804364 TGGCATTGTTGTCGCATCTC 59.196 50.000 0.00 0.00 0.00 2.75
3608 4252 2.166254 TGTTGTCGCATCTCTCTGCATA 59.834 45.455 0.00 0.00 42.40 3.14
3679 4331 1.869754 CGACTGACTGGTGTGGACTTG 60.870 57.143 0.00 0.00 0.00 3.16
3880 4532 2.032549 GGCTGCACTTTACTGATATGCG 60.033 50.000 0.50 0.00 39.18 4.73
3965 4628 8.944029 CATGATATGGACCTATTCATGAAGAAC 58.056 37.037 14.54 4.02 39.49 3.01
3999 4662 3.953612 TGAAGTTCAGCCTCACACAAAAT 59.046 39.130 0.08 0.00 0.00 1.82
4030 4693 1.443802 GAGAAGCCAAAGGAAGACCG 58.556 55.000 0.00 0.00 41.83 4.79
4031 4694 0.036875 AGAAGCCAAAGGAAGACCGG 59.963 55.000 0.00 0.00 41.83 5.28
4032 4695 0.960861 GAAGCCAAAGGAAGACCGGG 60.961 60.000 6.32 0.00 41.83 5.73
4033 4696 3.062466 GCCAAAGGAAGACCGGGC 61.062 66.667 6.32 0.52 42.12 6.13
4034 4697 2.361230 CCAAAGGAAGACCGGGCC 60.361 66.667 1.76 0.00 41.83 5.80
4035 4698 2.746277 CAAAGGAAGACCGGGCCG 60.746 66.667 21.46 21.46 41.83 6.13
4119 4782 1.250328 TCAAGCTGCAACTTCCCATG 58.750 50.000 0.00 0.00 0.00 3.66
4125 4788 2.440409 CTGCAACTTCCCATGTAAGCT 58.560 47.619 5.24 0.00 0.00 3.74
4126 4789 3.609853 CTGCAACTTCCCATGTAAGCTA 58.390 45.455 5.24 0.00 0.00 3.32
4127 4790 4.009675 CTGCAACTTCCCATGTAAGCTAA 58.990 43.478 5.24 0.00 0.00 3.09
4128 4791 4.402829 TGCAACTTCCCATGTAAGCTAAA 58.597 39.130 5.24 0.00 0.00 1.85
4166 4829 9.628500 AAAAACCCCAAGCTATATTAACTCTAG 57.372 33.333 0.00 0.00 0.00 2.43
4167 4830 8.562949 AAACCCCAAGCTATATTAACTCTAGA 57.437 34.615 0.00 0.00 0.00 2.43
4169 4832 8.196378 ACCCCAAGCTATATTAACTCTAGAAG 57.804 38.462 0.00 0.00 0.00 2.85
4170 4833 7.235812 ACCCCAAGCTATATTAACTCTAGAAGG 59.764 40.741 0.00 0.00 0.00 3.46
4171 4834 7.100409 CCCAAGCTATATTAACTCTAGAAGGC 58.900 42.308 0.00 0.00 0.00 4.35
4173 4836 8.032451 CCAAGCTATATTAACTCTAGAAGGCTC 58.968 40.741 0.00 0.00 0.00 4.70
4174 4837 8.802267 CAAGCTATATTAACTCTAGAAGGCTCT 58.198 37.037 0.00 0.00 35.52 4.09
4183 4846 3.512033 CTAGAAGGCTCTAGCACGTTT 57.488 47.619 4.07 0.00 43.63 3.60
4184 4847 2.086054 AGAAGGCTCTAGCACGTTTG 57.914 50.000 4.07 0.00 44.36 2.93
4185 4848 1.618837 AGAAGGCTCTAGCACGTTTGA 59.381 47.619 4.07 0.00 44.36 2.69
4186 4849 1.996191 GAAGGCTCTAGCACGTTTGAG 59.004 52.381 4.07 0.00 44.36 3.02
4187 4850 0.247736 AGGCTCTAGCACGTTTGAGG 59.752 55.000 4.07 0.00 44.36 3.86
4188 4851 0.741221 GGCTCTAGCACGTTTGAGGG 60.741 60.000 4.07 0.00 44.36 4.30
4189 4852 0.741221 GCTCTAGCACGTTTGAGGGG 60.741 60.000 0.00 0.00 41.59 4.79
4190 4853 0.608640 CTCTAGCACGTTTGAGGGGT 59.391 55.000 0.00 0.00 0.00 4.95
4191 4854 1.002087 CTCTAGCACGTTTGAGGGGTT 59.998 52.381 0.00 0.00 0.00 4.11
4192 4855 1.156736 CTAGCACGTTTGAGGGGTTG 58.843 55.000 0.00 0.00 0.00 3.77
4193 4856 0.887387 TAGCACGTTTGAGGGGTTGC 60.887 55.000 0.00 0.00 0.00 4.17
4194 4857 2.485795 GCACGTTTGAGGGGTTGCA 61.486 57.895 0.00 0.00 0.00 4.08
4195 4858 1.805428 GCACGTTTGAGGGGTTGCAT 61.805 55.000 0.00 0.00 0.00 3.96
4196 4859 1.529226 CACGTTTGAGGGGTTGCATA 58.471 50.000 0.00 0.00 0.00 3.14
4197 4860 1.883275 CACGTTTGAGGGGTTGCATAA 59.117 47.619 0.00 0.00 0.00 1.90
4198 4861 2.095263 CACGTTTGAGGGGTTGCATAAG 60.095 50.000 0.00 0.00 0.00 1.73
4199 4862 2.224670 ACGTTTGAGGGGTTGCATAAGA 60.225 45.455 0.00 0.00 0.00 2.10
4200 4863 3.016736 CGTTTGAGGGGTTGCATAAGAT 58.983 45.455 0.00 0.00 0.00 2.40
4201 4864 3.181497 CGTTTGAGGGGTTGCATAAGATG 60.181 47.826 0.00 0.00 0.00 2.90
4202 4865 4.016444 GTTTGAGGGGTTGCATAAGATGA 58.984 43.478 0.00 0.00 0.00 2.92
4203 4866 3.281727 TGAGGGGTTGCATAAGATGAC 57.718 47.619 0.00 0.00 0.00 3.06
4204 4867 2.575735 TGAGGGGTTGCATAAGATGACA 59.424 45.455 0.00 0.00 0.00 3.58
4205 4868 3.202818 TGAGGGGTTGCATAAGATGACAT 59.797 43.478 0.00 0.00 0.00 3.06
4206 4869 4.210331 GAGGGGTTGCATAAGATGACATT 58.790 43.478 0.00 0.00 0.00 2.71
4207 4870 4.613437 AGGGGTTGCATAAGATGACATTT 58.387 39.130 0.00 0.00 0.00 2.32
4208 4871 4.403432 AGGGGTTGCATAAGATGACATTTG 59.597 41.667 0.00 0.00 0.00 2.32
4209 4872 4.402155 GGGGTTGCATAAGATGACATTTGA 59.598 41.667 0.00 0.00 0.00 2.69
4210 4873 5.105392 GGGGTTGCATAAGATGACATTTGAA 60.105 40.000 0.00 0.00 0.00 2.69
4211 4874 6.038356 GGGTTGCATAAGATGACATTTGAAG 58.962 40.000 0.00 0.00 0.00 3.02
4212 4875 6.350445 GGGTTGCATAAGATGACATTTGAAGT 60.350 38.462 0.00 0.00 0.00 3.01
4213 4876 6.749118 GGTTGCATAAGATGACATTTGAAGTC 59.251 38.462 0.00 0.00 36.55 3.01
4223 4886 5.765176 TGACATTTGAAGTCAGCTTTCATG 58.235 37.500 0.30 0.51 40.80 3.07
4224 4887 4.553323 ACATTTGAAGTCAGCTTTCATGC 58.447 39.130 0.30 0.00 34.61 4.06
4225 4888 4.038282 ACATTTGAAGTCAGCTTTCATGCA 59.962 37.500 0.30 0.00 34.61 3.96
4226 4889 3.631145 TTGAAGTCAGCTTTCATGCAC 57.369 42.857 0.30 0.00 34.61 4.57
4227 4890 2.574450 TGAAGTCAGCTTTCATGCACA 58.426 42.857 0.00 0.00 34.61 4.57
4228 4891 2.950975 TGAAGTCAGCTTTCATGCACAA 59.049 40.909 0.00 0.00 34.61 3.33
4229 4892 3.243168 TGAAGTCAGCTTTCATGCACAAC 60.243 43.478 0.00 0.00 34.61 3.32
4230 4893 2.300433 AGTCAGCTTTCATGCACAACA 58.700 42.857 0.00 0.00 34.99 3.33
4231 4894 2.689471 AGTCAGCTTTCATGCACAACAA 59.311 40.909 0.00 0.00 34.99 2.83
4232 4895 3.130869 AGTCAGCTTTCATGCACAACAAA 59.869 39.130 0.00 0.00 34.99 2.83
4233 4896 3.243643 GTCAGCTTTCATGCACAACAAAC 59.756 43.478 0.00 0.00 34.99 2.93
4234 4897 2.216940 CAGCTTTCATGCACAACAAACG 59.783 45.455 0.00 0.00 34.99 3.60
4235 4898 2.098934 AGCTTTCATGCACAACAAACGA 59.901 40.909 0.00 0.00 34.99 3.85
4236 4899 3.052036 GCTTTCATGCACAACAAACGAT 58.948 40.909 0.00 0.00 0.00 3.73
4237 4900 4.023279 AGCTTTCATGCACAACAAACGATA 60.023 37.500 0.00 0.00 34.99 2.92
4238 4901 4.679197 GCTTTCATGCACAACAAACGATAA 59.321 37.500 0.00 0.00 0.00 1.75
4239 4902 5.164158 GCTTTCATGCACAACAAACGATAAG 60.164 40.000 0.00 0.00 0.00 1.73
4240 4903 5.431420 TTCATGCACAACAAACGATAAGT 57.569 34.783 0.00 0.00 0.00 2.24
4241 4904 4.782156 TCATGCACAACAAACGATAAGTG 58.218 39.130 0.00 0.00 0.00 3.16
4242 4905 4.513318 TCATGCACAACAAACGATAAGTGA 59.487 37.500 0.00 0.00 0.00 3.41
4243 4906 4.203950 TGCACAACAAACGATAAGTGAC 57.796 40.909 0.00 0.00 0.00 3.67
4244 4907 3.874543 TGCACAACAAACGATAAGTGACT 59.125 39.130 0.00 0.00 0.00 3.41
4245 4908 5.051153 TGCACAACAAACGATAAGTGACTA 58.949 37.500 0.00 0.00 0.00 2.59
4246 4909 5.176774 TGCACAACAAACGATAAGTGACTAG 59.823 40.000 0.00 0.00 0.00 2.57
4247 4910 5.609088 CACAACAAACGATAAGTGACTAGC 58.391 41.667 0.00 0.00 0.00 3.42
4248 4911 4.689345 ACAACAAACGATAAGTGACTAGCC 59.311 41.667 0.00 0.00 0.00 3.93
4249 4912 4.803098 ACAAACGATAAGTGACTAGCCT 57.197 40.909 0.00 0.00 0.00 4.58
4250 4913 5.909621 ACAAACGATAAGTGACTAGCCTA 57.090 39.130 0.00 0.00 0.00 3.93
4251 4914 6.276832 ACAAACGATAAGTGACTAGCCTAA 57.723 37.500 0.00 0.00 0.00 2.69
4252 4915 6.694447 ACAAACGATAAGTGACTAGCCTAAA 58.306 36.000 0.00 0.00 0.00 1.85
4253 4916 7.328737 ACAAACGATAAGTGACTAGCCTAAAT 58.671 34.615 0.00 0.00 0.00 1.40
4254 4917 7.822822 ACAAACGATAAGTGACTAGCCTAAATT 59.177 33.333 0.00 0.00 0.00 1.82
4255 4918 8.665685 CAAACGATAAGTGACTAGCCTAAATTT 58.334 33.333 0.00 0.00 0.00 1.82
4256 4919 7.772332 ACGATAAGTGACTAGCCTAAATTTG 57.228 36.000 0.00 0.00 0.00 2.32
4257 4920 7.553334 ACGATAAGTGACTAGCCTAAATTTGA 58.447 34.615 0.00 0.00 0.00 2.69
4258 4921 8.038944 ACGATAAGTGACTAGCCTAAATTTGAA 58.961 33.333 0.00 0.00 0.00 2.69
4259 4922 9.046296 CGATAAGTGACTAGCCTAAATTTGAAT 57.954 33.333 0.00 0.00 0.00 2.57
4263 4926 8.635765 AGTGACTAGCCTAAATTTGAATTTCA 57.364 30.769 0.00 0.00 39.24 2.69
4264 4927 9.077885 AGTGACTAGCCTAAATTTGAATTTCAA 57.922 29.630 7.74 7.74 39.24 2.69
4265 4928 9.860898 GTGACTAGCCTAAATTTGAATTTCAAT 57.139 29.630 12.39 1.30 39.24 2.57
4320 4983 8.862325 ATATAAATGTGGTCAAACTTCTGACA 57.138 30.769 6.12 0.00 46.31 3.58
4321 4984 5.913137 AAATGTGGTCAAACTTCTGACAA 57.087 34.783 6.12 0.00 46.31 3.18
4322 4985 5.913137 AATGTGGTCAAACTTCTGACAAA 57.087 34.783 6.12 0.00 46.31 2.83
4323 4986 5.913137 ATGTGGTCAAACTTCTGACAAAA 57.087 34.783 6.12 0.00 46.31 2.44
4324 4987 5.913137 TGTGGTCAAACTTCTGACAAAAT 57.087 34.783 6.12 0.00 46.31 1.82
4325 4988 5.649557 TGTGGTCAAACTTCTGACAAAATG 58.350 37.500 6.12 0.00 46.31 2.32
4326 4989 5.184864 TGTGGTCAAACTTCTGACAAAATGT 59.815 36.000 6.12 0.00 46.31 2.71
4327 4990 6.099341 GTGGTCAAACTTCTGACAAAATGTT 58.901 36.000 6.12 0.00 46.31 2.71
4328 4991 7.094162 TGTGGTCAAACTTCTGACAAAATGTTA 60.094 33.333 6.12 0.00 46.31 2.41
4329 4992 7.757624 GTGGTCAAACTTCTGACAAAATGTTAA 59.242 33.333 6.12 0.00 46.31 2.01
4330 4993 8.474025 TGGTCAAACTTCTGACAAAATGTTAAT 58.526 29.630 6.12 0.00 46.31 1.40
4331 4994 9.959749 GGTCAAACTTCTGACAAAATGTTAATA 57.040 29.630 6.12 0.00 46.31 0.98
4334 4997 8.915654 CAAACTTCTGACAAAATGTTAATAGGC 58.084 33.333 0.00 0.00 0.00 3.93
4335 4998 6.842163 ACTTCTGACAAAATGTTAATAGGCG 58.158 36.000 0.00 0.00 0.00 5.52
4336 4999 5.811399 TCTGACAAAATGTTAATAGGCGG 57.189 39.130 0.00 0.00 0.00 6.13
4337 5000 5.492895 TCTGACAAAATGTTAATAGGCGGA 58.507 37.500 0.00 0.00 0.00 5.54
4338 5001 5.584649 TCTGACAAAATGTTAATAGGCGGAG 59.415 40.000 0.00 0.00 0.00 4.63
4339 5002 5.492895 TGACAAAATGTTAATAGGCGGAGA 58.507 37.500 0.00 0.00 0.00 3.71
4340 5003 5.584649 TGACAAAATGTTAATAGGCGGAGAG 59.415 40.000 0.00 0.00 0.00 3.20
4341 5004 5.741011 ACAAAATGTTAATAGGCGGAGAGA 58.259 37.500 0.00 0.00 0.00 3.10
4342 5005 5.817816 ACAAAATGTTAATAGGCGGAGAGAG 59.182 40.000 0.00 0.00 0.00 3.20
4343 5006 5.871396 AAATGTTAATAGGCGGAGAGAGA 57.129 39.130 0.00 0.00 0.00 3.10
4344 5007 5.871396 AATGTTAATAGGCGGAGAGAGAA 57.129 39.130 0.00 0.00 0.00 2.87
4345 5008 5.871396 ATGTTAATAGGCGGAGAGAGAAA 57.129 39.130 0.00 0.00 0.00 2.52
4346 5009 5.670792 TGTTAATAGGCGGAGAGAGAAAA 57.329 39.130 0.00 0.00 0.00 2.29
4347 5010 6.045072 TGTTAATAGGCGGAGAGAGAAAAA 57.955 37.500 0.00 0.00 0.00 1.94
4426 5089 0.392706 ACAGCATCGTGGACACAAGA 59.607 50.000 3.12 0.00 39.38 3.02
4427 5090 1.202639 ACAGCATCGTGGACACAAGAA 60.203 47.619 3.12 0.00 38.56 2.52
4428 5091 1.195448 CAGCATCGTGGACACAAGAAC 59.805 52.381 3.12 0.00 38.56 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.983592 CCTGCGGGGCGTTTCTTT 60.984 61.111 2.57 0.00 0.00 2.52
17 18 1.676678 TACACATCTGGAGGCTCCGC 61.677 60.000 27.58 6.44 40.17 5.54
79 82 0.036952 TTGAGCGAGAGAAAGCTGGG 60.037 55.000 0.00 0.00 44.69 4.45
106 112 5.694674 TTGATGTTGCGTTTCTTGTTTTC 57.305 34.783 0.00 0.00 0.00 2.29
142 148 3.121030 CTTCCTGTGAAGCCGCCG 61.121 66.667 0.00 0.00 41.45 6.46
149 155 2.751259 ACGATACGTAGCTTCCTGTGAA 59.249 45.455 9.44 0.00 38.73 3.18
150 156 2.353889 GACGATACGTAGCTTCCTGTGA 59.646 50.000 9.44 0.00 41.37 3.58
152 158 2.355132 CTGACGATACGTAGCTTCCTGT 59.645 50.000 13.86 1.68 41.37 4.00
155 161 2.353889 TGTCTGACGATACGTAGCTTCC 59.646 50.000 13.86 0.87 41.37 3.46
157 163 3.063725 GTCTGTCTGACGATACGTAGCTT 59.936 47.826 9.44 0.00 41.37 3.74
158 164 2.608546 GTCTGTCTGACGATACGTAGCT 59.391 50.000 9.44 0.00 41.37 3.32
159 165 2.971607 GTCTGTCTGACGATACGTAGC 58.028 52.381 0.00 0.00 41.37 3.58
169 175 2.433318 GGGCGCTGTCTGTCTGAC 60.433 66.667 7.64 0.00 45.54 3.51
170 176 2.038814 TTTGGGCGCTGTCTGTCTGA 62.039 55.000 7.64 0.00 0.00 3.27
216 224 4.796231 CTAGCGCCGGTTGCTCGT 62.796 66.667 23.79 6.47 42.85 4.18
229 237 2.508436 GGAAGGGGAGCAGCTAGC 59.492 66.667 6.62 6.62 46.19 3.42
230 238 1.383803 AGGGAAGGGGAGCAGCTAG 60.384 63.158 0.00 0.00 0.00 3.42
231 239 1.383248 GAGGGAAGGGGAGCAGCTA 60.383 63.158 0.00 0.00 0.00 3.32
232 240 2.690510 GAGGGAAGGGGAGCAGCT 60.691 66.667 0.00 0.00 0.00 4.24
233 241 3.803162 GGAGGGAAGGGGAGCAGC 61.803 72.222 0.00 0.00 0.00 5.25
234 242 3.093172 GGGAGGGAAGGGGAGCAG 61.093 72.222 0.00 0.00 0.00 4.24
295 310 2.018086 AGAGGAGGGAGGGAGGGAG 61.018 68.421 0.00 0.00 0.00 4.30
296 311 2.133201 AGAGGAGGGAGGGAGGGA 59.867 66.667 0.00 0.00 0.00 4.20
297 312 2.188215 AACAGAGGAGGGAGGGAGGG 62.188 65.000 0.00 0.00 0.00 4.30
298 313 0.252927 AAACAGAGGAGGGAGGGAGG 60.253 60.000 0.00 0.00 0.00 4.30
299 314 1.557371 GAAAACAGAGGAGGGAGGGAG 59.443 57.143 0.00 0.00 0.00 4.30
300 315 1.152271 AGAAAACAGAGGAGGGAGGGA 59.848 52.381 0.00 0.00 0.00 4.20
301 316 1.280421 CAGAAAACAGAGGAGGGAGGG 59.720 57.143 0.00 0.00 0.00 4.30
302 317 1.981495 ACAGAAAACAGAGGAGGGAGG 59.019 52.381 0.00 0.00 0.00 4.30
303 318 3.055747 GGTACAGAAAACAGAGGAGGGAG 60.056 52.174 0.00 0.00 0.00 4.30
304 319 2.904434 GGTACAGAAAACAGAGGAGGGA 59.096 50.000 0.00 0.00 0.00 4.20
305 320 2.353803 CGGTACAGAAAACAGAGGAGGG 60.354 54.545 0.00 0.00 0.00 4.30
306 321 2.931320 GCGGTACAGAAAACAGAGGAGG 60.931 54.545 0.00 0.00 0.00 4.30
307 322 2.288825 TGCGGTACAGAAAACAGAGGAG 60.289 50.000 0.00 0.00 0.00 3.69
308 323 1.689813 TGCGGTACAGAAAACAGAGGA 59.310 47.619 0.00 0.00 0.00 3.71
309 324 1.798813 GTGCGGTACAGAAAACAGAGG 59.201 52.381 0.00 0.00 0.00 3.69
310 325 1.798813 GGTGCGGTACAGAAAACAGAG 59.201 52.381 0.00 0.00 0.00 3.35
351 366 3.659089 AAACCCAGATCGGCGGTCG 62.659 63.158 15.35 9.63 40.90 4.79
352 367 2.106683 CAAACCCAGATCGGCGGTC 61.107 63.158 13.27 13.27 0.00 4.79
353 368 2.046314 CAAACCCAGATCGGCGGT 60.046 61.111 7.21 0.00 0.00 5.68
354 369 2.824041 CCAAACCCAGATCGGCGG 60.824 66.667 7.21 0.00 0.00 6.13
453 857 0.251354 GAGGCAGACAAGGATGCAGA 59.749 55.000 0.00 0.00 44.37 4.26
489 893 2.555547 GCAGCATGATAACGGCCCC 61.556 63.158 0.00 0.00 39.69 5.80
497 901 1.538849 CGGTGTAGCAGCAGCATGATA 60.539 52.381 3.17 0.00 45.49 2.15
498 902 0.812811 CGGTGTAGCAGCAGCATGAT 60.813 55.000 3.17 0.00 45.49 2.45
501 905 2.821366 GCGGTGTAGCAGCAGCAT 60.821 61.111 3.17 0.00 45.49 3.79
528 932 4.081030 CAGCAGCACCAACGCGAG 62.081 66.667 15.93 4.40 36.85 5.03
644 1057 9.574516 AAAACAAACAGTACTTCTGAGGATAAT 57.425 29.630 0.00 0.00 46.27 1.28
645 1058 8.974060 AAAACAAACAGTACTTCTGAGGATAA 57.026 30.769 0.00 0.00 46.27 1.75
672 1085 2.097036 TCGATGTACCGGTCAACTCAT 58.903 47.619 12.40 9.55 0.00 2.90
685 1101 6.089249 ACTGATGCACTGATTATCGATGTA 57.911 37.500 8.54 0.00 0.00 2.29
701 1117 2.227388 CCCTCACTCAACAAACTGATGC 59.773 50.000 0.00 0.00 0.00 3.91
781 1278 3.607741 ACTCCTCAAATGCACTCATCTG 58.392 45.455 0.00 0.00 31.27 2.90
791 1288 2.289694 ACTCCAACCGACTCCTCAAATG 60.290 50.000 0.00 0.00 0.00 2.32
829 1340 5.197451 AGAGTCACTACAGAAGATACCCTG 58.803 45.833 0.00 0.00 36.53 4.45
834 1345 7.615757 TCATTTGGAGAGTCACTACAGAAGATA 59.384 37.037 0.00 0.00 40.91 1.98
1012 1528 1.012086 CGACATGGTGCCTGAAGATG 58.988 55.000 0.00 0.00 0.00 2.90
1127 1643 2.636830 AGATGTTGTGATACCAGCTGC 58.363 47.619 8.66 0.00 0.00 5.25
1454 1979 7.638444 TCCCTTTGATTTCATCAGGTACAATA 58.362 34.615 0.00 0.00 40.94 1.90
1600 2127 6.789262 ACTAATTTGTCATTCATAGTGCAGC 58.211 36.000 0.00 0.00 0.00 5.25
1610 2137 5.593095 GGACCCCCTTACTAATTTGTCATTC 59.407 44.000 0.00 0.00 0.00 2.67
1627 2154 1.416480 GGTATGCACCTAGGACCCCC 61.416 65.000 17.98 3.53 42.11 5.40
1650 2177 7.391148 TCCTTCAAATATGTAAAGGTTCAGC 57.609 36.000 0.00 0.00 39.45 4.26
1782 2311 6.695429 AGCATGACTACTCATATGTACATGG 58.305 40.000 18.81 10.45 35.17 3.66
1885 2477 5.163499 ACTGCTAATAGCTTCCAGACTACAC 60.163 44.000 13.88 0.00 42.97 2.90
1914 2506 4.324267 ACAGCGTGAAAAGCCTTAACTAT 58.676 39.130 0.00 0.00 44.61 2.12
1932 2525 7.700656 ACACACAAAGTAAAACTAATGAACAGC 59.299 33.333 1.23 0.00 0.00 4.40
2016 2609 3.755378 AGCTTTAATGTCTTGTGCTCCAG 59.245 43.478 0.00 0.00 0.00 3.86
2246 2840 3.569701 TCCCTTTGATGCACAAGAACTTC 59.430 43.478 0.00 0.00 39.77 3.01
2355 2953 9.333497 CAATAACATTCATACACACAGACAAAG 57.667 33.333 0.00 0.00 0.00 2.77
2359 2957 8.668353 ACATCAATAACATTCATACACACAGAC 58.332 33.333 0.00 0.00 0.00 3.51
2393 2996 2.361757 CAACCATCAAGACAAACTGGCA 59.638 45.455 0.00 0.00 0.00 4.92
2418 3021 3.192422 CGCCACCTCAATTAAATGTTCCA 59.808 43.478 0.00 0.00 0.00 3.53
2429 3032 3.297134 AACCAATATCGCCACCTCAAT 57.703 42.857 0.00 0.00 0.00 2.57
2472 3079 8.970020 TCACAGATAACATGGCAAGAATAAAAT 58.030 29.630 0.00 0.00 0.00 1.82
2500 3107 6.015688 TGAGAGAAGAAGCTTCATGCAAAATT 60.016 34.615 27.57 10.84 45.94 1.82
2575 3182 5.845103 TCGATAACCATCAGCCGTAATAAA 58.155 37.500 0.00 0.00 0.00 1.40
2582 3189 4.338400 TCCTATATCGATAACCATCAGCCG 59.662 45.833 9.61 0.00 0.00 5.52
2597 3204 6.874288 AATTGCAGACAAAGCTCCTATATC 57.126 37.500 0.00 0.00 39.77 1.63
2600 3207 7.651027 ATTAAATTGCAGACAAAGCTCCTAT 57.349 32.000 0.00 0.00 39.77 2.57
2666 3278 7.266922 AGTTGTTTCTTTGCGACCTTTATTA 57.733 32.000 0.00 0.00 0.00 0.98
2812 3424 3.958147 TCACTCACAACAAGAGTCCACTA 59.042 43.478 0.00 0.00 44.11 2.74
2906 3523 6.097356 TGAAACAGGTGTCGTATTTAGCTAG 58.903 40.000 0.00 0.00 0.00 3.42
2928 3550 9.804758 ATAAAAAGAAACGGTGTTACAAAATGA 57.195 25.926 0.00 0.00 0.00 2.57
2966 3591 6.484540 CATTCAAGAATCAGGAGTTTGATCG 58.515 40.000 0.00 0.00 36.81 3.69
3235 3860 0.246635 TACAAGAGCCAGCGGAAGAC 59.753 55.000 0.00 0.00 0.00 3.01
3239 3864 1.123077 ATCATACAAGAGCCAGCGGA 58.877 50.000 0.00 0.00 0.00 5.54
3241 3866 3.127548 ACAAAATCATACAAGAGCCAGCG 59.872 43.478 0.00 0.00 0.00 5.18
3247 3872 7.482743 GCACATACACACAAAATCATACAAGAG 59.517 37.037 0.00 0.00 0.00 2.85
3598 4242 4.021894 GGTACCACCTATGTATGCAGAGAG 60.022 50.000 7.15 0.18 36.10 3.20
3600 4244 4.258702 GGTACCACCTATGTATGCAGAG 57.741 50.000 7.15 0.00 34.73 3.35
3679 4331 1.134610 CCTGCAAATTTCTGGCATCCC 60.135 52.381 2.51 0.00 36.87 3.85
3737 4389 1.275573 GTTTCGCTGGACCCTCTTACT 59.724 52.381 0.00 0.00 0.00 2.24
3859 4511 2.032549 CGCATATCAGTAAAGTGCAGCC 60.033 50.000 0.00 0.00 35.63 4.85
3880 4532 5.415415 ACAACGTATATCAGTCCGTCTAC 57.585 43.478 0.00 0.00 32.30 2.59
3965 4628 3.364366 GCTGAACTTCACAGGTTGATTCG 60.364 47.826 0.00 0.00 36.09 3.34
3999 4662 1.423541 TGGCTTCTCCACTGGCTTAAA 59.576 47.619 0.00 0.00 40.72 1.52
4030 4693 0.106149 AGATACGATTTCACCGGCCC 59.894 55.000 0.00 0.00 0.00 5.80
4031 4694 2.401351 GTAGATACGATTTCACCGGCC 58.599 52.381 0.00 0.00 0.00 6.13
4164 4827 2.823747 TCAAACGTGCTAGAGCCTTCTA 59.176 45.455 0.00 0.00 41.18 2.10
4166 4829 1.996191 CTCAAACGTGCTAGAGCCTTC 59.004 52.381 0.00 0.00 41.18 3.46
4167 4830 1.338200 CCTCAAACGTGCTAGAGCCTT 60.338 52.381 0.00 0.00 41.18 4.35
4169 4832 0.741221 CCCTCAAACGTGCTAGAGCC 60.741 60.000 0.00 0.00 41.18 4.70
4170 4833 0.741221 CCCCTCAAACGTGCTAGAGC 60.741 60.000 0.00 0.00 42.50 4.09
4171 4834 0.608640 ACCCCTCAAACGTGCTAGAG 59.391 55.000 0.00 0.00 0.00 2.43
4173 4836 1.156736 CAACCCCTCAAACGTGCTAG 58.843 55.000 0.00 0.00 0.00 3.42
4174 4837 0.887387 GCAACCCCTCAAACGTGCTA 60.887 55.000 0.00 0.00 0.00 3.49
4176 4839 1.805428 ATGCAACCCCTCAAACGTGC 61.805 55.000 0.00 0.00 0.00 5.34
4177 4840 1.529226 TATGCAACCCCTCAAACGTG 58.471 50.000 0.00 0.00 0.00 4.49
4178 4841 2.159382 CTTATGCAACCCCTCAAACGT 58.841 47.619 0.00 0.00 0.00 3.99
4179 4842 2.432444 TCTTATGCAACCCCTCAAACG 58.568 47.619 0.00 0.00 0.00 3.60
4180 4843 4.016444 TCATCTTATGCAACCCCTCAAAC 58.984 43.478 0.00 0.00 0.00 2.93
4181 4844 4.016444 GTCATCTTATGCAACCCCTCAAA 58.984 43.478 0.00 0.00 0.00 2.69
4182 4845 3.010027 TGTCATCTTATGCAACCCCTCAA 59.990 43.478 0.00 0.00 0.00 3.02
4183 4846 2.575735 TGTCATCTTATGCAACCCCTCA 59.424 45.455 0.00 0.00 0.00 3.86
4184 4847 3.281727 TGTCATCTTATGCAACCCCTC 57.718 47.619 0.00 0.00 0.00 4.30
4185 4848 3.959495 ATGTCATCTTATGCAACCCCT 57.041 42.857 0.00 0.00 0.00 4.79
4186 4849 4.402155 TCAAATGTCATCTTATGCAACCCC 59.598 41.667 0.00 0.00 0.00 4.95
4187 4850 5.581126 TCAAATGTCATCTTATGCAACCC 57.419 39.130 0.00 0.00 0.00 4.11
4188 4851 6.624423 ACTTCAAATGTCATCTTATGCAACC 58.376 36.000 0.00 0.00 0.00 3.77
4189 4852 7.307694 TGACTTCAAATGTCATCTTATGCAAC 58.692 34.615 0.00 0.00 39.23 4.17
4190 4853 7.451501 TGACTTCAAATGTCATCTTATGCAA 57.548 32.000 0.00 0.00 39.23 4.08
4191 4854 6.403964 GCTGACTTCAAATGTCATCTTATGCA 60.404 38.462 0.00 0.00 42.57 3.96
4192 4855 5.970023 GCTGACTTCAAATGTCATCTTATGC 59.030 40.000 0.00 0.00 42.57 3.14
4193 4856 7.317842 AGCTGACTTCAAATGTCATCTTATG 57.682 36.000 0.00 0.00 42.57 1.90
4194 4857 7.934855 AAGCTGACTTCAAATGTCATCTTAT 57.065 32.000 10.07 0.00 44.11 1.73
4195 4858 7.445096 TGAAAGCTGACTTCAAATGTCATCTTA 59.555 33.333 11.57 0.00 44.72 2.10
4196 4859 6.263842 TGAAAGCTGACTTCAAATGTCATCTT 59.736 34.615 7.02 7.02 46.28 2.40
4197 4860 5.766670 TGAAAGCTGACTTCAAATGTCATCT 59.233 36.000 0.00 0.00 42.57 2.90
4198 4861 6.005583 TGAAAGCTGACTTCAAATGTCATC 57.994 37.500 0.00 0.00 42.57 2.92
4199 4862 6.387465 CATGAAAGCTGACTTCAAATGTCAT 58.613 36.000 3.54 0.00 42.57 3.06
4200 4863 5.765176 CATGAAAGCTGACTTCAAATGTCA 58.235 37.500 3.54 0.00 41.48 3.58
4201 4864 4.620184 GCATGAAAGCTGACTTCAAATGTC 59.380 41.667 3.54 0.00 34.05 3.06
4202 4865 4.038282 TGCATGAAAGCTGACTTCAAATGT 59.962 37.500 3.54 0.00 34.05 2.71
4203 4866 4.384846 GTGCATGAAAGCTGACTTCAAATG 59.615 41.667 3.54 0.68 34.05 2.32
4204 4867 4.038282 TGTGCATGAAAGCTGACTTCAAAT 59.962 37.500 3.54 0.00 34.05 2.32
4205 4868 3.380954 TGTGCATGAAAGCTGACTTCAAA 59.619 39.130 3.54 0.00 34.05 2.69
4206 4869 2.950975 TGTGCATGAAAGCTGACTTCAA 59.049 40.909 3.54 0.00 34.05 2.69
4207 4870 2.574450 TGTGCATGAAAGCTGACTTCA 58.426 42.857 0.00 1.93 34.05 3.02
4208 4871 3.243168 TGTTGTGCATGAAAGCTGACTTC 60.243 43.478 0.00 0.00 34.05 3.01
4209 4872 2.689471 TGTTGTGCATGAAAGCTGACTT 59.311 40.909 0.00 0.00 37.90 3.01
4210 4873 2.300433 TGTTGTGCATGAAAGCTGACT 58.700 42.857 0.00 0.00 34.99 3.41
4211 4874 2.780065 TGTTGTGCATGAAAGCTGAC 57.220 45.000 0.00 0.00 34.99 3.51
4212 4875 3.446799 GTTTGTTGTGCATGAAAGCTGA 58.553 40.909 0.00 0.00 34.99 4.26
4213 4876 2.216940 CGTTTGTTGTGCATGAAAGCTG 59.783 45.455 0.00 0.00 34.99 4.24
4214 4877 2.098934 TCGTTTGTTGTGCATGAAAGCT 59.901 40.909 0.00 0.00 34.99 3.74
4215 4878 2.458951 TCGTTTGTTGTGCATGAAAGC 58.541 42.857 0.00 0.00 0.00 3.51
4216 4879 5.914635 ACTTATCGTTTGTTGTGCATGAAAG 59.085 36.000 0.00 0.00 0.00 2.62
4217 4880 5.685068 CACTTATCGTTTGTTGTGCATGAAA 59.315 36.000 0.00 0.00 0.00 2.69
4218 4881 5.008118 TCACTTATCGTTTGTTGTGCATGAA 59.992 36.000 0.00 0.00 0.00 2.57
4219 4882 4.513318 TCACTTATCGTTTGTTGTGCATGA 59.487 37.500 0.00 0.00 0.00 3.07
4220 4883 4.612614 GTCACTTATCGTTTGTTGTGCATG 59.387 41.667 0.00 0.00 0.00 4.06
4221 4884 4.515191 AGTCACTTATCGTTTGTTGTGCAT 59.485 37.500 0.00 0.00 0.00 3.96
4222 4885 3.874543 AGTCACTTATCGTTTGTTGTGCA 59.125 39.130 0.00 0.00 0.00 4.57
4223 4886 4.468095 AGTCACTTATCGTTTGTTGTGC 57.532 40.909 0.00 0.00 0.00 4.57
4224 4887 5.389516 GGCTAGTCACTTATCGTTTGTTGTG 60.390 44.000 0.00 0.00 0.00 3.33
4225 4888 4.689345 GGCTAGTCACTTATCGTTTGTTGT 59.311 41.667 0.00 0.00 0.00 3.32
4226 4889 4.929808 AGGCTAGTCACTTATCGTTTGTTG 59.070 41.667 0.00 0.00 0.00 3.33
4227 4890 5.148651 AGGCTAGTCACTTATCGTTTGTT 57.851 39.130 0.00 0.00 0.00 2.83
4228 4891 4.803098 AGGCTAGTCACTTATCGTTTGT 57.197 40.909 0.00 0.00 0.00 2.83
4229 4892 7.772332 ATTTAGGCTAGTCACTTATCGTTTG 57.228 36.000 0.00 0.00 0.00 2.93
4230 4893 8.665685 CAAATTTAGGCTAGTCACTTATCGTTT 58.334 33.333 0.00 0.00 0.00 3.60
4231 4894 8.038944 TCAAATTTAGGCTAGTCACTTATCGTT 58.961 33.333 0.00 0.00 0.00 3.85
4232 4895 7.553334 TCAAATTTAGGCTAGTCACTTATCGT 58.447 34.615 0.00 0.00 0.00 3.73
4233 4896 8.420374 TTCAAATTTAGGCTAGTCACTTATCG 57.580 34.615 0.00 0.00 0.00 2.92
4237 4900 9.077885 TGAAATTCAAATTTAGGCTAGTCACTT 57.922 29.630 0.00 0.00 38.64 3.16
4238 4901 8.635765 TGAAATTCAAATTTAGGCTAGTCACT 57.364 30.769 0.00 0.00 38.64 3.41
4239 4902 9.860898 ATTGAAATTCAAATTTAGGCTAGTCAC 57.139 29.630 12.75 0.00 40.12 3.67
4294 4957 9.295825 TGTCAGAAGTTTGACCACATTTATATT 57.704 29.630 12.59 0.00 45.40 1.28
4295 4958 8.862325 TGTCAGAAGTTTGACCACATTTATAT 57.138 30.769 12.59 0.00 45.40 0.86
4296 4959 8.684386 TTGTCAGAAGTTTGACCACATTTATA 57.316 30.769 12.59 0.00 45.40 0.98
4297 4960 7.581213 TTGTCAGAAGTTTGACCACATTTAT 57.419 32.000 12.59 0.00 45.40 1.40
4298 4961 7.397892 TTTGTCAGAAGTTTGACCACATTTA 57.602 32.000 12.59 0.00 45.40 1.40
4299 4962 5.913137 TTGTCAGAAGTTTGACCACATTT 57.087 34.783 12.59 0.00 45.40 2.32
4300 4963 5.913137 TTTGTCAGAAGTTTGACCACATT 57.087 34.783 12.59 0.00 45.40 2.71
4301 4964 5.913137 TTTTGTCAGAAGTTTGACCACAT 57.087 34.783 12.59 0.00 45.40 3.21
4302 4965 5.184864 ACATTTTGTCAGAAGTTTGACCACA 59.815 36.000 12.59 0.80 45.40 4.17
4303 4966 5.650543 ACATTTTGTCAGAAGTTTGACCAC 58.349 37.500 12.59 0.00 45.40 4.16
4304 4967 5.913137 ACATTTTGTCAGAAGTTTGACCA 57.087 34.783 12.59 3.23 45.40 4.02
4305 4968 8.871686 ATTAACATTTTGTCAGAAGTTTGACC 57.128 30.769 12.59 1.18 45.40 4.02
4308 4971 8.915654 GCCTATTAACATTTTGTCAGAAGTTTG 58.084 33.333 0.00 0.00 0.00 2.93
4309 4972 7.807907 CGCCTATTAACATTTTGTCAGAAGTTT 59.192 33.333 0.00 0.00 0.00 2.66
4310 4973 7.305474 CGCCTATTAACATTTTGTCAGAAGTT 58.695 34.615 0.00 0.00 0.00 2.66
4311 4974 6.128007 CCGCCTATTAACATTTTGTCAGAAGT 60.128 38.462 0.00 0.00 0.00 3.01
4312 4975 6.093495 TCCGCCTATTAACATTTTGTCAGAAG 59.907 38.462 0.00 0.00 0.00 2.85
4313 4976 5.941058 TCCGCCTATTAACATTTTGTCAGAA 59.059 36.000 0.00 0.00 0.00 3.02
4314 4977 5.492895 TCCGCCTATTAACATTTTGTCAGA 58.507 37.500 0.00 0.00 0.00 3.27
4315 4978 5.584649 TCTCCGCCTATTAACATTTTGTCAG 59.415 40.000 0.00 0.00 0.00 3.51
4316 4979 5.492895 TCTCCGCCTATTAACATTTTGTCA 58.507 37.500 0.00 0.00 0.00 3.58
4317 4980 5.815740 TCTCTCCGCCTATTAACATTTTGTC 59.184 40.000 0.00 0.00 0.00 3.18
4318 4981 5.741011 TCTCTCCGCCTATTAACATTTTGT 58.259 37.500 0.00 0.00 0.00 2.83
4319 4982 6.049149 TCTCTCTCCGCCTATTAACATTTTG 58.951 40.000 0.00 0.00 0.00 2.44
4320 4983 6.235231 TCTCTCTCCGCCTATTAACATTTT 57.765 37.500 0.00 0.00 0.00 1.82
4321 4984 5.871396 TCTCTCTCCGCCTATTAACATTT 57.129 39.130 0.00 0.00 0.00 2.32
4322 4985 5.871396 TTCTCTCTCCGCCTATTAACATT 57.129 39.130 0.00 0.00 0.00 2.71
4323 4986 5.871396 TTTCTCTCTCCGCCTATTAACAT 57.129 39.130 0.00 0.00 0.00 2.71
4324 4987 5.670792 TTTTCTCTCTCCGCCTATTAACA 57.329 39.130 0.00 0.00 0.00 2.41
4345 5008 5.209818 TGACATGACTACCTCTCGTTTTT 57.790 39.130 0.00 0.00 0.00 1.94
4346 5009 4.866508 TGACATGACTACCTCTCGTTTT 57.133 40.909 0.00 0.00 0.00 2.43
4347 5010 5.407407 AATGACATGACTACCTCTCGTTT 57.593 39.130 0.00 0.00 0.00 3.60
4348 5011 5.448768 CGTAATGACATGACTACCTCTCGTT 60.449 44.000 0.00 0.00 0.00 3.85
4349 5012 4.035324 CGTAATGACATGACTACCTCTCGT 59.965 45.833 0.00 0.00 0.00 4.18
4350 5013 4.272748 TCGTAATGACATGACTACCTCTCG 59.727 45.833 0.00 0.00 0.00 4.04
4351 5014 5.527951 TCTCGTAATGACATGACTACCTCTC 59.472 44.000 0.00 0.00 0.00 3.20
4352 5015 5.437946 TCTCGTAATGACATGACTACCTCT 58.562 41.667 0.00 0.00 0.00 3.69
4353 5016 5.527951 TCTCTCGTAATGACATGACTACCTC 59.472 44.000 0.00 0.00 0.00 3.85
4354 5017 5.437946 TCTCTCGTAATGACATGACTACCT 58.562 41.667 0.00 0.00 0.00 3.08
4355 5018 5.752892 TCTCTCGTAATGACATGACTACC 57.247 43.478 0.00 0.00 0.00 3.18
4356 5019 7.017498 TCTTCTCTCGTAATGACATGACTAC 57.983 40.000 0.00 0.00 0.00 2.73
4357 5020 6.238511 GCTCTTCTCTCGTAATGACATGACTA 60.239 42.308 0.00 0.00 0.00 2.59
4426 5089 0.526662 AACGCGGATCTTCTCGAGTT 59.473 50.000 12.47 5.63 42.57 3.01
4427 5090 0.099082 GAACGCGGATCTTCTCGAGT 59.901 55.000 12.47 0.00 40.77 4.18
4428 5091 0.378962 AGAACGCGGATCTTCTCGAG 59.621 55.000 12.47 5.93 0.00 4.04


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

AutoCloner maintained by Alex Coulton.