Multiple sequence alignment - TraesCS3D01G396500

Loading Multiple Alignment...

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 TraesCS3D01G396500 chr3D 100.000 5823 0 0 1 5823 511351746 511345924 0.000000e+00 10754
1 TraesCS3D01G396500 chr3D 93.084 882 34 17 1 862 384565000 384565874 0.000000e+00 1266
2 TraesCS3D01G396500 chr3D 92.405 869 43 16 1 857 29616439 29615582 0.000000e+00 1218
3 TraesCS3D01G396500 chr3D 92.246 877 38 15 1 857 512837790 512836924 0.000000e+00 1216
4 TraesCS3D01G396500 chr3D 92.032 866 32 17 1 861 519680917 519681750 0.000000e+00 1182
5 TraesCS3D01G396500 chr3D 86.656 652 31 20 243 866 590497072 590496449 0.000000e+00 671
6 TraesCS3D01G396500 chr3D 94.660 206 7 3 5120 5321 388314625 388314830 3.390000e-82 316
7 TraesCS3D01G396500 chr3B 95.856 4223 148 19 918 5130 672874085 672869880 0.000000e+00 6804
8 TraesCS3D01G396500 chr3B 91.949 708 42 13 162 857 785866889 785867593 0.000000e+00 977
9 TraesCS3D01G396500 chr3B 96.887 514 16 0 5310 5823 672869883 672869370 0.000000e+00 861
10 TraesCS3D01G396500 chr3A 96.527 3686 102 12 918 4583 647483013 647479334 0.000000e+00 6074
11 TraesCS3D01G396500 chr3A 96.538 491 17 0 5310 5800 647478777 647478287 0.000000e+00 813
12 TraesCS3D01G396500 chr3A 89.910 555 30 19 4580 5130 647479306 647478774 0.000000e+00 691
13 TraesCS3D01G396500 chr5B 93.227 3558 185 20 1148 4675 437800085 437803616 0.000000e+00 5184
14 TraesCS3D01G396500 chr5B 96.181 288 11 0 4679 4966 437805815 437806102 6.830000e-129 472
15 TraesCS3D01G396500 chr5B 97.906 191 2 1 5127 5315 2812595 2812405 4.350000e-86 329
16 TraesCS3D01G396500 chr2D 94.925 867 27 11 1 861 6096186 6097041 0.000000e+00 1341
17 TraesCS3D01G396500 chr2D 93.936 874 28 10 1 857 470155608 470156473 0.000000e+00 1297
18 TraesCS3D01G396500 chr2D 96.970 198 3 2 5127 5322 20189492 20189296 4.350000e-86 329
19 TraesCS3D01G396500 chr2D 97.906 191 2 1 5126 5314 26038968 26038778 4.350000e-86 329
20 TraesCS3D01G396500 chr2D 85.981 107 13 2 1493 1598 23158428 23158533 4.770000e-21 113
21 TraesCS3D01G396500 chr1D 93.537 882 31 10 1 861 340321947 340321071 0.000000e+00 1290
22 TraesCS3D01G396500 chr1D 97.917 192 2 1 5127 5316 93501169 93500978 1.210000e-86 331
23 TraesCS3D01G396500 chr5D 95.385 715 23 10 1 709 350679046 350679756 0.000000e+00 1129
24 TraesCS3D01G396500 chr5D 91.184 794 47 20 1 779 486860177 486859392 0.000000e+00 1057
25 TraesCS3D01G396500 chr5D 97.906 191 2 1 5129 5317 130661326 130661516 4.350000e-86 329
26 TraesCS3D01G396500 chr5D 96.429 196 4 2 5123 5316 486861195 486861389 2.620000e-83 320
27 TraesCS3D01G396500 chr7D 91.042 480 11 8 380 857 442687442 442687891 2.300000e-173 619
28 TraesCS3D01G396500 chr7D 98.413 189 1 1 5127 5313 161844388 161844576 1.210000e-86 331
29 TraesCS3D01G396500 chr4A 96.465 198 3 3 5117 5312 634457051 634457246 2.020000e-84 324
30 TraesCS3D01G396500 chr7A 88.136 236 17 10 635 861 516224257 516224490 2.670000e-68 270
31 TraesCS3D01G396500 chr7A 87.288 236 18 11 635 861 192572582 192572350 5.790000e-65 259
32 TraesCS3D01G396500 chr7A 86.441 236 21 10 635 861 211046245 211046012 1.250000e-61 248
33 TraesCS3D01G396500 chr5A 77.556 450 83 9 1247 1694 2888724 2889157 7.490000e-64 255
34 TraesCS3D01G396500 chr1A 86.325 234 20 9 635 861 252038680 252038908 1.620000e-60 244
35 TraesCS3D01G396500 chr6A 84.112 107 15 2 1493 1598 578686674 578686569 1.030000e-17 102


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 TraesCS3D01G396500 chr3D 511345924 511351746 5822 True 10754.0 10754 100.0000 1 5823 1 chr3D.!!$R2 5822
1 TraesCS3D01G396500 chr3D 384565000 384565874 874 False 1266.0 1266 93.0840 1 862 1 chr3D.!!$F1 861
2 TraesCS3D01G396500 chr3D 29615582 29616439 857 True 1218.0 1218 92.4050 1 857 1 chr3D.!!$R1 856
3 TraesCS3D01G396500 chr3D 512836924 512837790 866 True 1216.0 1216 92.2460 1 857 1 chr3D.!!$R3 856
4 TraesCS3D01G396500 chr3D 519680917 519681750 833 False 1182.0 1182 92.0320 1 861 1 chr3D.!!$F3 860
5 TraesCS3D01G396500 chr3D 590496449 590497072 623 True 671.0 671 86.6560 243 866 1 chr3D.!!$R4 623
6 TraesCS3D01G396500 chr3B 672869370 672874085 4715 True 3832.5 6804 96.3715 918 5823 2 chr3B.!!$R1 4905
7 TraesCS3D01G396500 chr3B 785866889 785867593 704 False 977.0 977 91.9490 162 857 1 chr3B.!!$F1 695
8 TraesCS3D01G396500 chr3A 647478287 647483013 4726 True 2526.0 6074 94.3250 918 5800 3 chr3A.!!$R1 4882
9 TraesCS3D01G396500 chr5B 437800085 437806102 6017 False 2828.0 5184 94.7040 1148 4966 2 chr5B.!!$F1 3818
10 TraesCS3D01G396500 chr2D 6096186 6097041 855 False 1341.0 1341 94.9250 1 861 1 chr2D.!!$F1 860
11 TraesCS3D01G396500 chr2D 470155608 470156473 865 False 1297.0 1297 93.9360 1 857 1 chr2D.!!$F3 856
12 TraesCS3D01G396500 chr1D 340321071 340321947 876 True 1290.0 1290 93.5370 1 861 1 chr1D.!!$R2 860
13 TraesCS3D01G396500 chr5D 350679046 350679756 710 False 1129.0 1129 95.3850 1 709 1 chr5D.!!$F2 708
14 TraesCS3D01G396500 chr5D 486859392 486860177 785 True 1057.0 1057 91.1840 1 779 1 chr5D.!!$R1 778

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
916 985 0.868406 GAAGAGCTGTCACAAACGGG 59.132 55.000 0.00 0.0 34.56 5.28 F
1750 1838 0.970937 TCTCCGCGAAACCCTCTGAT 60.971 55.000 8.23 0.0 0.00 2.90 F
2272 2387 0.388520 CAATCGGTGAGCTCGTGTCA 60.389 55.000 9.64 0.0 0.00 3.58 F
2324 2439 1.070105 GCCAACACCAGTCACCGTA 59.930 57.895 0.00 0.0 0.00 4.02 F
3784 3899 0.111639 GCACCCCACCAAACCTTCTA 59.888 55.000 0.00 0.0 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2254 2369 0.109086 CTGACACGAGCTCACCGATT 60.109 55.0 15.40 0.00 0.0 3.34 R
2585 2700 0.317160 TGTGCTCGATCCAGACGTTT 59.683 50.0 0.00 0.00 0.0 3.60 R
3167 3282 0.461339 AACCAGTTCAGTTCACGCGT 60.461 50.0 5.58 5.58 0.0 6.01 R
4308 4427 0.774276 TATGGTTGTGAACTGCCCCA 59.226 50.0 0.00 0.00 0.0 4.96 R
5117 7489 0.034089 ACACCCCCTTAAGAGCATGC 60.034 55.0 10.51 10.51 0.0 4.06 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
656 682 5.747951 TTTTGCAAAAACAATTAGCCCAG 57.252 34.783 21.94 0.00 0.00 4.45
887 956 6.566141 CAAATCATGCAGTACATTTGATCCA 58.434 36.000 13.34 0.00 38.12 3.41
888 957 6.778834 AATCATGCAGTACATTTGATCCAA 57.221 33.333 0.00 0.00 36.64 3.53
889 958 6.971726 ATCATGCAGTACATTTGATCCAAT 57.028 33.333 0.00 0.00 36.64 3.16
890 959 8.467963 AATCATGCAGTACATTTGATCCAATA 57.532 30.769 0.00 0.00 36.64 1.90
891 960 7.263100 TCATGCAGTACATTTGATCCAATAC 57.737 36.000 0.00 0.00 36.64 1.89
892 961 6.827762 TCATGCAGTACATTTGATCCAATACA 59.172 34.615 0.00 0.00 36.64 2.29
893 962 7.338957 TCATGCAGTACATTTGATCCAATACAA 59.661 33.333 0.00 0.00 36.64 2.41
894 963 7.087409 TGCAGTACATTTGATCCAATACAAG 57.913 36.000 0.00 0.00 0.00 3.16
895 964 5.973565 GCAGTACATTTGATCCAATACAAGC 59.026 40.000 0.00 0.00 0.00 4.01
896 965 6.404623 GCAGTACATTTGATCCAATACAAGCA 60.405 38.462 0.00 0.00 0.00 3.91
897 966 7.191551 CAGTACATTTGATCCAATACAAGCAG 58.808 38.462 0.00 0.00 0.00 4.24
898 967 7.066163 CAGTACATTTGATCCAATACAAGCAGA 59.934 37.037 0.00 0.00 0.00 4.26
899 968 6.839124 ACATTTGATCCAATACAAGCAGAA 57.161 33.333 0.00 0.00 0.00 3.02
900 969 6.860080 ACATTTGATCCAATACAAGCAGAAG 58.140 36.000 0.00 0.00 0.00 2.85
901 970 6.660521 ACATTTGATCCAATACAAGCAGAAGA 59.339 34.615 0.00 0.00 0.00 2.87
902 971 6.748333 TTTGATCCAATACAAGCAGAAGAG 57.252 37.500 0.00 0.00 0.00 2.85
903 972 4.194640 TGATCCAATACAAGCAGAAGAGC 58.805 43.478 0.00 0.00 0.00 4.09
905 974 3.603532 TCCAATACAAGCAGAAGAGCTG 58.396 45.455 0.00 0.00 45.89 4.24
906 975 3.008375 TCCAATACAAGCAGAAGAGCTGT 59.992 43.478 0.00 0.00 45.89 4.40
907 976 3.373439 CCAATACAAGCAGAAGAGCTGTC 59.627 47.826 0.00 0.00 45.89 3.51
908 977 3.969287 ATACAAGCAGAAGAGCTGTCA 57.031 42.857 0.00 0.00 45.89 3.58
909 978 1.876322 ACAAGCAGAAGAGCTGTCAC 58.124 50.000 0.00 0.00 45.89 3.67
910 979 1.139654 ACAAGCAGAAGAGCTGTCACA 59.860 47.619 0.00 0.00 45.89 3.58
911 980 2.216046 CAAGCAGAAGAGCTGTCACAA 58.784 47.619 0.00 0.00 45.89 3.33
912 981 2.615447 CAAGCAGAAGAGCTGTCACAAA 59.385 45.455 0.00 0.00 45.89 2.83
913 982 2.216898 AGCAGAAGAGCTGTCACAAAC 58.783 47.619 0.00 0.00 46.62 2.93
914 983 1.070309 GCAGAAGAGCTGTCACAAACG 60.070 52.381 0.00 0.00 46.62 3.60
915 984 1.528586 CAGAAGAGCTGTCACAAACGG 59.471 52.381 0.00 0.00 39.85 4.44
916 985 0.868406 GAAGAGCTGTCACAAACGGG 59.132 55.000 0.00 0.00 34.56 5.28
929 998 1.174078 AAACGGGGGCACGGTAAAAG 61.174 55.000 0.00 0.00 38.39 2.27
947 1016 4.373532 AAAGCAATTCAAATTTCGTGCG 57.626 36.364 0.00 0.00 0.00 5.34
1750 1838 0.970937 TCTCCGCGAAACCCTCTGAT 60.971 55.000 8.23 0.00 0.00 2.90
1808 1923 2.869233 AGATCTCTTCGAGAAGCTGC 57.131 50.000 7.91 0.00 42.27 5.25
1846 1961 4.410400 GCCAGTCCCAAGACCCCG 62.410 72.222 0.00 0.00 44.72 5.73
1945 2060 1.668151 GCGTTGTGTCCAGGTCTCC 60.668 63.158 0.00 0.00 0.00 3.71
1967 2082 4.020617 CTTCAGTGGGGCAGGCGA 62.021 66.667 0.00 0.00 0.00 5.54
2272 2387 0.388520 CAATCGGTGAGCTCGTGTCA 60.389 55.000 9.64 0.00 0.00 3.58
2324 2439 1.070105 GCCAACACCAGTCACCGTA 59.930 57.895 0.00 0.00 0.00 4.02
2524 2639 4.945246 TGCTTTATCTATCCCGTGAAGAC 58.055 43.478 0.00 0.00 0.00 3.01
2701 2816 6.403200 GCTTCTTACGATTGGCTCAAAATGTA 60.403 38.462 0.00 0.00 0.00 2.29
2906 3021 2.827921 GGTTGCATTGACTTCAATCCCT 59.172 45.455 1.28 0.00 44.10 4.20
2910 3025 2.352960 GCATTGACTTCAATCCCTCGTC 59.647 50.000 1.28 0.00 44.10 4.20
2999 3114 5.423931 ACCTTCCTTCTTGGTCTCTATTCTC 59.576 44.000 0.00 0.00 37.07 2.87
3088 3203 4.036518 AGCAAGGTACTGAGGATGAGATT 58.963 43.478 0.00 0.00 40.86 2.40
3141 3256 1.118965 TCTGACCTTGGCGTGGAAGA 61.119 55.000 2.55 2.96 0.00 2.87
3148 3263 2.287608 CCTTGGCGTGGAAGACTTTTTC 60.288 50.000 0.00 0.00 0.00 2.29
3167 3282 1.076549 GGCAATGGACCTGTTGGGA 59.923 57.895 10.79 0.00 38.76 4.37
3362 3477 2.771089 TGAGTGTCACTTCCATGCTTC 58.229 47.619 7.00 0.00 0.00 3.86
3493 3608 8.798402 CAAAATTTACTACCCCTTTGTGTATGA 58.202 33.333 0.00 0.00 0.00 2.15
3576 3691 1.604378 CTTCAATCTGGCCCTCGGT 59.396 57.895 0.00 0.00 0.00 4.69
3703 3818 5.059833 CAGCTCCAACTAGTCAAGAACTTT 58.940 41.667 0.00 0.00 39.55 2.66
3781 3896 2.123033 GGCACCCCACCAAACCTT 60.123 61.111 0.00 0.00 0.00 3.50
3784 3899 0.111639 GCACCCCACCAAACCTTCTA 59.888 55.000 0.00 0.00 0.00 2.10
3959 4074 1.847328 TCGACAAGCCTACCAGATCA 58.153 50.000 0.00 0.00 0.00 2.92
4338 4462 8.072567 GCAGTTCACAACCATAAATAGATCATC 58.927 37.037 0.00 0.00 0.00 2.92
4370 4494 4.592942 ACTTGAGTGGTTGCATATGACAT 58.407 39.130 6.97 0.00 0.00 3.06
4490 4617 8.430801 AGAGATCTGATTGTTTGTAATACAGC 57.569 34.615 0.00 0.00 0.00 4.40
4633 4796 6.360618 AGGGGCAGAAATACATAAAGAAGAG 58.639 40.000 0.00 0.00 0.00 2.85
4702 7060 8.659925 AACTACTTCAGATTCATAATGCTGAG 57.340 34.615 0.00 0.00 38.48 3.35
4721 7080 5.673337 TGAGCTAACACTTGTGAAATGAC 57.327 39.130 7.83 0.00 0.00 3.06
4747 7106 6.258947 GTGTATCCTCTTTGAATGCTACTTCC 59.741 42.308 0.00 0.00 0.00 3.46
4749 7108 4.836825 TCCTCTTTGAATGCTACTTCCAG 58.163 43.478 0.00 0.00 0.00 3.86
4952 7311 4.997565 TCTCTTCAAGCCAAAACAGTTTG 58.002 39.130 0.00 0.00 43.26 2.93
4985 7344 8.722480 TTGGTGAGTCAAAATATGTCATAGAG 57.278 34.615 0.00 0.00 0.00 2.43
4986 7345 6.763135 TGGTGAGTCAAAATATGTCATAGAGC 59.237 38.462 0.00 0.00 0.00 4.09
4987 7346 6.763135 GGTGAGTCAAAATATGTCATAGAGCA 59.237 38.462 0.00 0.00 0.00 4.26
4988 7347 7.042187 GGTGAGTCAAAATATGTCATAGAGCAG 60.042 40.741 0.00 0.00 0.00 4.24
4989 7348 7.493971 GTGAGTCAAAATATGTCATAGAGCAGT 59.506 37.037 0.00 0.00 0.00 4.40
4990 7349 7.708322 TGAGTCAAAATATGTCATAGAGCAGTC 59.292 37.037 0.00 0.00 0.00 3.51
4991 7350 6.699204 AGTCAAAATATGTCATAGAGCAGTCG 59.301 38.462 0.00 0.00 0.00 4.18
4992 7351 5.463392 TCAAAATATGTCATAGAGCAGTCGC 59.537 40.000 0.00 0.00 38.99 5.19
4993 7352 4.590850 AATATGTCATAGAGCAGTCGCA 57.409 40.909 0.00 0.00 42.27 5.10
4994 7353 2.967599 ATGTCATAGAGCAGTCGCAA 57.032 45.000 0.00 0.00 42.27 4.85
4995 7354 2.741759 TGTCATAGAGCAGTCGCAAA 57.258 45.000 0.00 0.00 42.27 3.68
4996 7355 3.038788 TGTCATAGAGCAGTCGCAAAA 57.961 42.857 0.00 0.00 42.27 2.44
4997 7356 3.398406 TGTCATAGAGCAGTCGCAAAAA 58.602 40.909 0.00 0.00 42.27 1.94
5106 7478 5.996513 AGATTGCATATAGGTTCTGCTTCTG 59.003 40.000 0.00 0.00 36.84 3.02
5130 7502 3.944015 AGCTGTAAAGCATGCTCTTAAGG 59.056 43.478 22.93 15.89 37.25 2.69
5131 7503 3.065925 GCTGTAAAGCATGCTCTTAAGGG 59.934 47.826 22.93 13.94 34.41 3.95
5132 7504 3.620488 TGTAAAGCATGCTCTTAAGGGG 58.380 45.455 22.93 0.00 0.00 4.79
5133 7505 2.149973 AAAGCATGCTCTTAAGGGGG 57.850 50.000 22.93 0.00 0.00 5.40
5134 7506 1.002857 AAGCATGCTCTTAAGGGGGT 58.997 50.000 22.93 0.00 0.00 4.95
5135 7507 0.257039 AGCATGCTCTTAAGGGGGTG 59.743 55.000 16.30 0.01 0.00 4.61
5136 7508 0.034089 GCATGCTCTTAAGGGGGTGT 60.034 55.000 11.37 0.00 0.00 4.16
5137 7509 1.616994 GCATGCTCTTAAGGGGGTGTT 60.617 52.381 11.37 0.00 0.00 3.32
5138 7510 2.807676 CATGCTCTTAAGGGGGTGTTT 58.192 47.619 4.10 0.00 0.00 2.83
5139 7511 2.286365 TGCTCTTAAGGGGGTGTTTG 57.714 50.000 4.10 0.00 0.00 2.93
5140 7512 1.203001 TGCTCTTAAGGGGGTGTTTGG 60.203 52.381 4.10 0.00 0.00 3.28
5141 7513 1.203013 GCTCTTAAGGGGGTGTTTGGT 60.203 52.381 4.10 0.00 0.00 3.67
5142 7514 2.755208 GCTCTTAAGGGGGTGTTTGGTT 60.755 50.000 4.10 0.00 0.00 3.67
5143 7515 3.154710 CTCTTAAGGGGGTGTTTGGTTC 58.845 50.000 1.85 0.00 0.00 3.62
5144 7516 2.514582 TCTTAAGGGGGTGTTTGGTTCA 59.485 45.455 1.85 0.00 0.00 3.18
5145 7517 2.668144 TAAGGGGGTGTTTGGTTCAG 57.332 50.000 0.00 0.00 0.00 3.02
5146 7518 0.930726 AAGGGGGTGTTTGGTTCAGA 59.069 50.000 0.00 0.00 0.00 3.27
5147 7519 0.930726 AGGGGGTGTTTGGTTCAGAA 59.069 50.000 0.00 0.00 0.00 3.02
5148 7520 1.133482 AGGGGGTGTTTGGTTCAGAAG 60.133 52.381 0.00 0.00 0.00 2.85
5149 7521 1.411074 GGGGGTGTTTGGTTCAGAAGT 60.411 52.381 0.00 0.00 0.00 3.01
5150 7522 1.954382 GGGGTGTTTGGTTCAGAAGTC 59.046 52.381 0.00 0.00 0.00 3.01
5151 7523 1.954382 GGGTGTTTGGTTCAGAAGTCC 59.046 52.381 0.00 0.00 0.00 3.85
5152 7524 2.422945 GGGTGTTTGGTTCAGAAGTCCT 60.423 50.000 0.00 0.00 0.00 3.85
5153 7525 3.181448 GGGTGTTTGGTTCAGAAGTCCTA 60.181 47.826 0.00 0.00 0.00 2.94
5154 7526 4.065789 GGTGTTTGGTTCAGAAGTCCTAG 58.934 47.826 0.00 0.00 0.00 3.02
5155 7527 4.065789 GTGTTTGGTTCAGAAGTCCTAGG 58.934 47.826 0.82 0.82 0.00 3.02
5156 7528 3.971305 TGTTTGGTTCAGAAGTCCTAGGA 59.029 43.478 7.62 7.62 0.00 2.94
5157 7529 4.202326 TGTTTGGTTCAGAAGTCCTAGGAC 60.202 45.833 31.29 31.29 44.86 3.85
5215 7587 8.217131 CTCTAGTAGAGTCTTTTTCTAGTCCC 57.783 42.308 17.70 0.00 37.57 4.46
5216 7588 7.931046 TCTAGTAGAGTCTTTTTCTAGTCCCT 58.069 38.462 0.00 0.00 33.84 4.20
5217 7589 6.844097 AGTAGAGTCTTTTTCTAGTCCCTG 57.156 41.667 0.00 0.00 0.00 4.45
5218 7590 6.316513 AGTAGAGTCTTTTTCTAGTCCCTGT 58.683 40.000 0.00 0.00 0.00 4.00
5219 7591 7.468496 AGTAGAGTCTTTTTCTAGTCCCTGTA 58.532 38.462 0.00 0.00 0.00 2.74
5220 7592 6.844097 AGAGTCTTTTTCTAGTCCCTGTAG 57.156 41.667 0.00 0.00 0.00 2.74
5221 7593 6.553857 AGAGTCTTTTTCTAGTCCCTGTAGA 58.446 40.000 0.00 0.00 0.00 2.59
5222 7594 7.011382 AGAGTCTTTTTCTAGTCCCTGTAGAA 58.989 38.462 0.00 0.00 35.21 2.10
5223 7595 7.509659 AGAGTCTTTTTCTAGTCCCTGTAGAAA 59.490 37.037 1.96 1.96 42.24 2.52
5229 7601 5.997384 TCTAGTCCCTGTAGAAAAAGTCC 57.003 43.478 0.00 0.00 0.00 3.85
5230 7602 4.776308 TCTAGTCCCTGTAGAAAAAGTCCC 59.224 45.833 0.00 0.00 0.00 4.46
5231 7603 3.599348 AGTCCCTGTAGAAAAAGTCCCT 58.401 45.455 0.00 0.00 0.00 4.20
5232 7604 3.583526 AGTCCCTGTAGAAAAAGTCCCTC 59.416 47.826 0.00 0.00 0.00 4.30
5233 7605 2.910977 TCCCTGTAGAAAAAGTCCCTCC 59.089 50.000 0.00 0.00 0.00 4.30
5234 7606 2.026169 CCCTGTAGAAAAAGTCCCTCCC 60.026 54.545 0.00 0.00 0.00 4.30
5235 7607 2.354805 CCTGTAGAAAAAGTCCCTCCCG 60.355 54.545 0.00 0.00 0.00 5.14
5236 7608 2.302157 CTGTAGAAAAAGTCCCTCCCGT 59.698 50.000 0.00 0.00 0.00 5.28
5237 7609 2.707257 TGTAGAAAAAGTCCCTCCCGTT 59.293 45.455 0.00 0.00 0.00 4.44
5238 7610 3.136992 TGTAGAAAAAGTCCCTCCCGTTT 59.863 43.478 0.00 0.00 0.00 3.60
5239 7611 2.583143 AGAAAAAGTCCCTCCCGTTTG 58.417 47.619 0.00 0.00 0.00 2.93
5240 7612 1.611977 GAAAAAGTCCCTCCCGTTTGG 59.388 52.381 0.00 0.00 0.00 3.28
5241 7613 0.554305 AAAAGTCCCTCCCGTTTGGT 59.446 50.000 0.00 0.00 34.77 3.67
5242 7614 0.554305 AAAGTCCCTCCCGTTTGGTT 59.446 50.000 0.00 0.00 34.77 3.67
5243 7615 0.109913 AAGTCCCTCCCGTTTGGTTC 59.890 55.000 0.00 0.00 34.77 3.62
5244 7616 1.303074 GTCCCTCCCGTTTGGTTCC 60.303 63.158 0.00 0.00 34.77 3.62
5245 7617 1.462627 TCCCTCCCGTTTGGTTCCT 60.463 57.895 0.00 0.00 34.77 3.36
5246 7618 0.178897 TCCCTCCCGTTTGGTTCCTA 60.179 55.000 0.00 0.00 34.77 2.94
5247 7619 0.252197 CCCTCCCGTTTGGTTCCTAG 59.748 60.000 0.00 0.00 34.77 3.02
5248 7620 0.252197 CCTCCCGTTTGGTTCCTAGG 59.748 60.000 0.82 0.82 34.77 3.02
5249 7621 0.252197 CTCCCGTTTGGTTCCTAGGG 59.748 60.000 9.46 0.00 40.16 3.53
5250 7622 0.178897 TCCCGTTTGGTTCCTAGGGA 60.179 55.000 9.46 0.00 44.85 4.20
5251 7623 0.035725 CCCGTTTGGTTCCTAGGGAC 60.036 60.000 12.35 12.35 41.26 4.46
5252 7624 0.981943 CCGTTTGGTTCCTAGGGACT 59.018 55.000 20.08 0.00 46.37 3.85
5253 7625 1.350019 CCGTTTGGTTCCTAGGGACTT 59.650 52.381 20.08 0.00 41.75 3.01
5254 7626 2.224695 CCGTTTGGTTCCTAGGGACTTT 60.225 50.000 20.08 0.00 41.75 2.66
5255 7627 3.483421 CGTTTGGTTCCTAGGGACTTTT 58.517 45.455 20.08 0.00 41.75 2.27
5256 7628 3.887110 CGTTTGGTTCCTAGGGACTTTTT 59.113 43.478 20.08 0.00 41.75 1.94
5257 7629 5.065235 CGTTTGGTTCCTAGGGACTTTTTA 58.935 41.667 20.08 0.00 41.75 1.52
5258 7630 5.180680 CGTTTGGTTCCTAGGGACTTTTTAG 59.819 44.000 20.08 4.22 41.75 1.85
5259 7631 4.921644 TGGTTCCTAGGGACTTTTTAGG 57.078 45.455 20.08 0.00 41.75 2.69
5260 7632 3.590182 TGGTTCCTAGGGACTTTTTAGGG 59.410 47.826 20.08 0.00 41.75 3.53
5261 7633 3.848377 GGTTCCTAGGGACTTTTTAGGGA 59.152 47.826 20.08 0.00 41.75 4.20
5262 7634 4.324099 GGTTCCTAGGGACTTTTTAGGGAC 60.324 50.000 20.08 0.45 40.79 4.46
5263 7635 4.431158 TCCTAGGGACTTTTTAGGGACT 57.569 45.455 9.46 0.00 41.75 3.85
5264 7636 4.771338 TCCTAGGGACTTTTTAGGGACTT 58.229 43.478 9.46 0.00 39.49 3.01
5265 7637 5.167921 TCCTAGGGACTTTTTAGGGACTTT 58.832 41.667 9.46 0.00 39.49 2.66
5266 7638 5.613973 TCCTAGGGACTTTTTAGGGACTTTT 59.386 40.000 9.46 0.00 39.49 2.27
5267 7639 6.103649 TCCTAGGGACTTTTTAGGGACTTTTT 59.896 38.462 9.46 0.00 39.49 1.94
5268 7640 6.433404 CCTAGGGACTTTTTAGGGACTTTTTC 59.567 42.308 0.00 0.00 39.49 2.29
5269 7641 6.027025 AGGGACTTTTTAGGGACTTTTTCT 57.973 37.500 0.00 0.00 34.75 2.52
5270 7642 7.157947 AGGGACTTTTTAGGGACTTTTTCTA 57.842 36.000 0.00 0.00 34.75 2.10
5271 7643 7.232188 AGGGACTTTTTAGGGACTTTTTCTAG 58.768 38.462 0.00 0.00 34.75 2.43
5272 7644 7.002879 GGGACTTTTTAGGGACTTTTTCTAGT 58.997 38.462 0.00 0.00 41.75 2.57
5273 7645 7.174599 GGGACTTTTTAGGGACTTTTTCTAGTC 59.825 40.741 0.00 0.00 43.05 2.59
5274 7646 7.937942 GGACTTTTTAGGGACTTTTTCTAGTCT 59.062 37.037 0.00 0.00 43.26 3.24
5275 7647 8.905660 ACTTTTTAGGGACTTTTTCTAGTCTC 57.094 34.615 0.00 0.00 44.42 3.36
5281 7653 6.211587 GGGACTTTTTCTAGTCTCTAGGAC 57.788 45.833 0.00 3.84 41.50 3.85
5302 7674 5.828747 GACTAAAAAGTCCCTGAACCAAAC 58.171 41.667 0.00 0.00 32.97 2.93
5303 7675 5.265989 ACTAAAAAGTCCCTGAACCAAACA 58.734 37.500 0.00 0.00 0.00 2.83
5304 7676 4.465632 AAAAAGTCCCTGAACCAAACAC 57.534 40.909 0.00 0.00 0.00 3.32
5305 7677 2.067365 AAGTCCCTGAACCAAACACC 57.933 50.000 0.00 0.00 0.00 4.16
5306 7678 0.185175 AGTCCCTGAACCAAACACCC 59.815 55.000 0.00 0.00 0.00 4.61
5307 7679 0.826256 GTCCCTGAACCAAACACCCC 60.826 60.000 0.00 0.00 0.00 4.95
5308 7680 1.533033 CCCTGAACCAAACACCCCC 60.533 63.158 0.00 0.00 0.00 5.40
5309 7681 1.541672 CCTGAACCAAACACCCCCT 59.458 57.895 0.00 0.00 0.00 4.79
5310 7682 0.774908 CCTGAACCAAACACCCCCTA 59.225 55.000 0.00 0.00 0.00 3.53
5311 7683 1.146152 CCTGAACCAAACACCCCCTAA 59.854 52.381 0.00 0.00 0.00 2.69
5312 7684 2.514803 CTGAACCAAACACCCCCTAAG 58.485 52.381 0.00 0.00 0.00 2.18
5346 7718 7.724506 CCGATATATAGGGTATAGCAAGAGGAA 59.275 40.741 4.02 0.00 0.00 3.36
5455 7827 6.884280 ATGTGCTAAACTATTTATGCCCTC 57.116 37.500 0.00 0.00 0.00 4.30
5609 7981 1.856802 TCATTCAGACATCCATCGCG 58.143 50.000 0.00 0.00 0.00 5.87
5619 7991 1.136169 CATCCATCGCGTGTGCATATG 60.136 52.381 5.77 0.00 42.97 1.78
5695 8067 6.401474 CCGATTTGAATATGTCTAATCAGGCG 60.401 42.308 15.15 0.00 44.19 5.52
5794 8166 5.648178 TTTGATAACACAATGCATGCTCT 57.352 34.783 20.33 3.10 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
201 205 5.086104 AGCAACCAATCATACTTACGTCT 57.914 39.130 0.00 0.00 0.00 4.18
205 209 8.082242 ACAAAAAGAGCAACCAATCATACTTAC 58.918 33.333 0.00 0.00 0.00 2.34
863 932 6.566141 TGGATCAAATGTACTGCATGATTTG 58.434 36.000 0.00 2.88 37.96 2.32
864 933 6.778834 TGGATCAAATGTACTGCATGATTT 57.221 33.333 0.00 0.00 37.96 2.17
867 936 6.827762 TGTATTGGATCAAATGTACTGCATGA 59.172 34.615 5.52 0.00 37.96 3.07
868 937 7.030075 TGTATTGGATCAAATGTACTGCATG 57.970 36.000 5.52 0.00 37.96 4.06
869 938 7.643569 TTGTATTGGATCAAATGTACTGCAT 57.356 32.000 5.52 0.00 40.03 3.96
870 939 6.404623 GCTTGTATTGGATCAAATGTACTGCA 60.405 38.462 5.52 0.00 0.00 4.41
871 940 5.973565 GCTTGTATTGGATCAAATGTACTGC 59.026 40.000 5.52 2.96 0.00 4.40
872 941 7.066163 TCTGCTTGTATTGGATCAAATGTACTG 59.934 37.037 5.52 0.00 0.00 2.74
873 942 7.112122 TCTGCTTGTATTGGATCAAATGTACT 58.888 34.615 5.52 0.00 0.00 2.73
874 943 7.320443 TCTGCTTGTATTGGATCAAATGTAC 57.680 36.000 5.52 0.00 0.00 2.90
875 944 7.828717 TCTTCTGCTTGTATTGGATCAAATGTA 59.171 33.333 5.52 0.00 0.00 2.29
876 945 6.660521 TCTTCTGCTTGTATTGGATCAAATGT 59.339 34.615 5.52 0.00 0.00 2.71
877 946 7.092137 TCTTCTGCTTGTATTGGATCAAATG 57.908 36.000 5.52 0.00 0.00 2.32
878 947 6.183360 GCTCTTCTGCTTGTATTGGATCAAAT 60.183 38.462 0.00 0.00 0.00 2.32
879 948 5.124457 GCTCTTCTGCTTGTATTGGATCAAA 59.876 40.000 0.00 0.00 0.00 2.69
880 949 4.637534 GCTCTTCTGCTTGTATTGGATCAA 59.362 41.667 0.00 0.00 0.00 2.57
881 950 4.080695 AGCTCTTCTGCTTGTATTGGATCA 60.081 41.667 0.00 0.00 40.93 2.92
882 951 4.272991 CAGCTCTTCTGCTTGTATTGGATC 59.727 45.833 0.00 0.00 41.98 3.36
883 952 4.197750 CAGCTCTTCTGCTTGTATTGGAT 58.802 43.478 0.00 0.00 41.98 3.41
884 953 3.008375 ACAGCTCTTCTGCTTGTATTGGA 59.992 43.478 0.00 0.00 46.76 3.53
885 954 3.341823 ACAGCTCTTCTGCTTGTATTGG 58.658 45.455 0.00 0.00 46.76 3.16
886 955 3.999001 TGACAGCTCTTCTGCTTGTATTG 59.001 43.478 0.00 0.00 46.76 1.90
887 956 3.999663 GTGACAGCTCTTCTGCTTGTATT 59.000 43.478 0.00 0.00 46.76 1.89
888 957 3.007290 TGTGACAGCTCTTCTGCTTGTAT 59.993 43.478 0.00 0.00 46.76 2.29
889 958 2.365293 TGTGACAGCTCTTCTGCTTGTA 59.635 45.455 0.00 0.00 46.76 2.41
890 959 1.139654 TGTGACAGCTCTTCTGCTTGT 59.860 47.619 0.00 0.00 46.76 3.16
891 960 1.875009 TGTGACAGCTCTTCTGCTTG 58.125 50.000 0.00 0.00 46.76 4.01
892 961 2.615912 GTTTGTGACAGCTCTTCTGCTT 59.384 45.455 0.00 0.00 46.76 3.91
893 962 2.216898 GTTTGTGACAGCTCTTCTGCT 58.783 47.619 0.00 0.00 46.76 4.24
894 963 1.070309 CGTTTGTGACAGCTCTTCTGC 60.070 52.381 0.00 0.00 46.76 4.26
896 965 1.541233 CCCGTTTGTGACAGCTCTTCT 60.541 52.381 0.00 0.00 0.00 2.85
897 966 0.868406 CCCGTTTGTGACAGCTCTTC 59.132 55.000 0.00 0.00 0.00 2.87
898 967 0.535102 CCCCGTTTGTGACAGCTCTT 60.535 55.000 0.00 0.00 0.00 2.85
899 968 1.071471 CCCCGTTTGTGACAGCTCT 59.929 57.895 0.00 0.00 0.00 4.09
900 969 1.966451 CCCCCGTTTGTGACAGCTC 60.966 63.158 0.00 0.00 0.00 4.09
901 970 2.113139 CCCCCGTTTGTGACAGCT 59.887 61.111 0.00 0.00 0.00 4.24
902 971 3.670377 GCCCCCGTTTGTGACAGC 61.670 66.667 0.00 0.00 0.00 4.40
903 972 2.203280 TGCCCCCGTTTGTGACAG 60.203 61.111 0.00 0.00 0.00 3.51
904 973 2.517402 GTGCCCCCGTTTGTGACA 60.517 61.111 0.00 0.00 0.00 3.58
905 974 3.656045 CGTGCCCCCGTTTGTGAC 61.656 66.667 0.00 0.00 0.00 3.67
906 975 4.939368 CCGTGCCCCCGTTTGTGA 62.939 66.667 0.00 0.00 0.00 3.58
907 976 3.828694 TACCGTGCCCCCGTTTGTG 62.829 63.158 0.00 0.00 0.00 3.33
908 977 2.621517 TTTACCGTGCCCCCGTTTGT 62.622 55.000 0.00 0.00 0.00 2.83
909 978 1.453762 TTTTACCGTGCCCCCGTTTG 61.454 55.000 0.00 0.00 0.00 2.93
910 979 1.152798 TTTTACCGTGCCCCCGTTT 60.153 52.632 0.00 0.00 0.00 3.60
911 980 1.601477 CTTTTACCGTGCCCCCGTT 60.601 57.895 0.00 0.00 0.00 4.44
912 981 2.032987 CTTTTACCGTGCCCCCGT 59.967 61.111 0.00 0.00 0.00 5.28
913 982 3.436924 GCTTTTACCGTGCCCCCG 61.437 66.667 0.00 0.00 0.00 5.73
914 983 1.254975 ATTGCTTTTACCGTGCCCCC 61.255 55.000 0.00 0.00 0.00 5.40
915 984 0.606096 AATTGCTTTTACCGTGCCCC 59.394 50.000 0.00 0.00 0.00 5.80
916 985 1.271102 TGAATTGCTTTTACCGTGCCC 59.729 47.619 0.00 0.00 0.00 5.36
929 998 1.720852 AGCGCACGAAATTTGAATTGC 59.279 42.857 11.47 0.00 0.00 3.56
947 1016 2.585153 GGAACGGGAGGAGGAAGC 59.415 66.667 0.00 0.00 0.00 3.86
1068 1144 1.152652 GGGGAGAGCTCGGAGATCA 60.153 63.158 23.67 0.00 31.99 2.92
1846 1961 1.475682 CCCTTTTGCTGCTGGAGATTC 59.524 52.381 0.00 0.00 0.00 2.52
1945 2060 3.933048 CTGCCCCACTGAAGCCCTG 62.933 68.421 0.00 0.00 0.00 4.45
1967 2082 2.434884 CATGCTCGGGTGCTCGTT 60.435 61.111 0.00 0.00 0.00 3.85
2254 2369 0.109086 CTGACACGAGCTCACCGATT 60.109 55.000 15.40 0.00 0.00 3.34
2272 2387 1.305297 TGCGACCACCCTCTCATCT 60.305 57.895 0.00 0.00 0.00 2.90
2308 2423 1.935300 GCTCTACGGTGACTGGTGTTG 60.935 57.143 0.00 0.00 0.00 3.33
2391 2506 6.185852 TCAGCAAGAAATCACATGTACATG 57.814 37.500 29.97 29.97 44.15 3.21
2400 2515 2.161211 GTCAGCCTCAGCAAGAAATCAC 59.839 50.000 0.00 0.00 43.56 3.06
2461 2576 6.429078 AGTCCGCACATATATCGTAGTTCTTA 59.571 38.462 0.00 0.00 0.00 2.10
2585 2700 0.317160 TGTGCTCGATCCAGACGTTT 59.683 50.000 0.00 0.00 0.00 3.60
2701 2816 5.126067 GCATTGTGTTCCACCTACAGATAT 58.874 41.667 0.00 0.00 32.73 1.63
2906 3021 1.899814 AGTTGTGAGCATTAGGGACGA 59.100 47.619 0.00 0.00 0.00 4.20
2910 3025 3.875727 CTCATGAGTTGTGAGCATTAGGG 59.124 47.826 14.95 0.00 36.95 3.53
2999 3114 1.526917 CTGGCATAGGCTTTCCGGG 60.527 63.158 0.00 0.00 40.87 5.73
3088 3203 1.463831 GCACGTCTCGAGTACTTCAGA 59.536 52.381 13.13 0.00 0.00 3.27
3141 3256 1.613437 CAGGTCCATTGCCGAAAAAGT 59.387 47.619 0.00 0.00 0.00 2.66
3148 3263 2.342650 CCCAACAGGTCCATTGCCG 61.343 63.158 0.00 0.00 0.00 5.69
3167 3282 0.461339 AACCAGTTCAGTTCACGCGT 60.461 50.000 5.58 5.58 0.00 6.01
3493 3608 8.652290 AGTAGAGAAAACTGAACCACTTTAGAT 58.348 33.333 0.00 0.00 0.00 1.98
3614 3729 7.741554 AGGAGTAGAAGGTATGAAGAAACAT 57.258 36.000 0.00 0.00 0.00 2.71
3781 3896 5.241403 TCAGGGAAAATTCAGCAACTAGA 57.759 39.130 0.00 0.00 0.00 2.43
3784 3899 3.575687 CCTTCAGGGAAAATTCAGCAACT 59.424 43.478 0.00 0.00 37.23 3.16
3959 4074 2.238144 CACCATCTCTCAGTCCAACCAT 59.762 50.000 0.00 0.00 0.00 3.55
4308 4427 0.774276 TATGGTTGTGAACTGCCCCA 59.226 50.000 0.00 0.00 0.00 4.96
4338 4462 4.091509 GCAACCACTCAAGTACATAACTCG 59.908 45.833 0.00 0.00 37.50 4.18
4404 4528 7.924412 GGTTACTATCGACAAAGAATCCACATA 59.076 37.037 0.00 0.00 0.00 2.29
4490 4617 6.435904 TCCAGTAGGTTCCCAAATTAATGTTG 59.564 38.462 0.00 0.00 35.89 3.33
4702 7060 4.211389 CACGTCATTTCACAAGTGTTAGC 58.789 43.478 0.00 0.00 0.00 3.09
4721 7080 5.352284 AGTAGCATTCAAAGAGGATACACG 58.648 41.667 0.00 0.00 41.41 4.49
4747 7106 8.025445 GGCAATAGGATATTCATAGCAAAACTG 58.975 37.037 0.00 0.00 0.00 3.16
4749 7108 8.115490 AGGCAATAGGATATTCATAGCAAAAC 57.885 34.615 0.00 0.00 0.00 2.43
4997 7356 5.105997 GCAGTGCCTTCTCTATGACATTTTT 60.106 40.000 2.85 0.00 0.00 1.94
4998 7357 4.397417 GCAGTGCCTTCTCTATGACATTTT 59.603 41.667 2.85 0.00 0.00 1.82
4999 7358 3.944015 GCAGTGCCTTCTCTATGACATTT 59.056 43.478 2.85 0.00 0.00 2.32
5000 7359 3.054875 TGCAGTGCCTTCTCTATGACATT 60.055 43.478 13.72 0.00 0.00 2.71
5001 7360 2.502947 TGCAGTGCCTTCTCTATGACAT 59.497 45.455 13.72 0.00 0.00 3.06
5002 7361 1.901833 TGCAGTGCCTTCTCTATGACA 59.098 47.619 13.72 0.00 0.00 3.58
5003 7362 2.680312 TGCAGTGCCTTCTCTATGAC 57.320 50.000 13.72 0.00 0.00 3.06
5004 7363 3.198417 TGAATGCAGTGCCTTCTCTATGA 59.802 43.478 26.68 8.96 34.98 2.15
5005 7364 3.538591 TGAATGCAGTGCCTTCTCTATG 58.461 45.455 26.68 0.00 34.98 2.23
5006 7365 3.920231 TGAATGCAGTGCCTTCTCTAT 57.080 42.857 26.68 5.49 34.98 1.98
5007 7366 3.538591 CATGAATGCAGTGCCTTCTCTA 58.461 45.455 26.68 12.62 34.98 2.43
5008 7367 2.366533 CATGAATGCAGTGCCTTCTCT 58.633 47.619 26.68 15.36 34.98 3.10
5009 7368 2.846039 CATGAATGCAGTGCCTTCTC 57.154 50.000 26.68 13.23 34.98 2.87
5117 7489 0.034089 ACACCCCCTTAAGAGCATGC 60.034 55.000 10.51 10.51 0.00 4.06
5130 7502 1.954382 GACTTCTGAACCAAACACCCC 59.046 52.381 0.00 0.00 0.00 4.95
5131 7503 1.954382 GGACTTCTGAACCAAACACCC 59.046 52.381 0.00 0.00 0.00 4.61
5132 7504 2.932261 AGGACTTCTGAACCAAACACC 58.068 47.619 0.58 0.00 0.00 4.16
5133 7505 4.065789 CCTAGGACTTCTGAACCAAACAC 58.934 47.826 1.05 0.00 0.00 3.32
5134 7506 3.971305 TCCTAGGACTTCTGAACCAAACA 59.029 43.478 7.62 0.00 0.00 2.83
5135 7507 4.316645 GTCCTAGGACTTCTGAACCAAAC 58.683 47.826 31.12 3.26 41.57 2.93
5136 7508 4.618920 GTCCTAGGACTTCTGAACCAAA 57.381 45.455 31.12 0.00 41.57 3.28
5190 7562 8.050930 AGGGACTAGAAAAAGACTCTACTAGAG 58.949 40.741 11.06 11.06 42.94 2.43
5191 7563 7.830201 CAGGGACTAGAAAAAGACTCTACTAGA 59.170 40.741 0.00 0.00 36.02 2.43
5192 7564 7.612633 ACAGGGACTAGAAAAAGACTCTACTAG 59.387 40.741 0.00 0.00 36.02 2.57
5193 7565 7.468496 ACAGGGACTAGAAAAAGACTCTACTA 58.532 38.462 0.00 0.00 36.02 1.82
5194 7566 6.316513 ACAGGGACTAGAAAAAGACTCTACT 58.683 40.000 0.00 0.00 36.02 2.57
5195 7567 6.593268 ACAGGGACTAGAAAAAGACTCTAC 57.407 41.667 0.00 0.00 36.02 2.59
5196 7568 7.696981 TCTACAGGGACTAGAAAAAGACTCTA 58.303 38.462 0.00 0.00 36.02 2.43
5197 7569 6.553857 TCTACAGGGACTAGAAAAAGACTCT 58.446 40.000 0.00 0.00 36.02 3.24
5198 7570 6.837471 TCTACAGGGACTAGAAAAAGACTC 57.163 41.667 0.00 0.00 36.02 3.36
5199 7571 7.613551 TTTCTACAGGGACTAGAAAAAGACT 57.386 36.000 0.00 0.00 37.31 3.24
5200 7572 8.672823 TTTTTCTACAGGGACTAGAAAAAGAC 57.327 34.615 16.61 0.00 46.05 3.01
5204 7576 7.222161 GGACTTTTTCTACAGGGACTAGAAAA 58.778 38.462 0.00 8.58 43.60 2.29
5205 7577 6.239800 GGGACTTTTTCTACAGGGACTAGAAA 60.240 42.308 0.00 0.00 38.08 2.52
5206 7578 5.247792 GGGACTTTTTCTACAGGGACTAGAA 59.752 44.000 0.00 0.00 36.02 2.10
5207 7579 4.776308 GGGACTTTTTCTACAGGGACTAGA 59.224 45.833 0.00 0.00 36.02 2.43
5208 7580 4.778427 AGGGACTTTTTCTACAGGGACTAG 59.222 45.833 0.00 0.00 28.08 2.57
5209 7581 4.759953 AGGGACTTTTTCTACAGGGACTA 58.240 43.478 0.00 0.00 28.08 2.59
5210 7582 3.583526 GAGGGACTTTTTCTACAGGGACT 59.416 47.826 0.00 0.00 41.55 3.85
5211 7583 3.307550 GGAGGGACTTTTTCTACAGGGAC 60.308 52.174 0.00 0.00 41.55 4.46
5212 7584 2.910977 GGAGGGACTTTTTCTACAGGGA 59.089 50.000 0.00 0.00 41.55 4.20
5213 7585 2.026169 GGGAGGGACTTTTTCTACAGGG 60.026 54.545 0.00 0.00 41.55 4.45
5214 7586 2.354805 CGGGAGGGACTTTTTCTACAGG 60.355 54.545 0.00 0.00 41.55 4.00
5215 7587 2.302157 ACGGGAGGGACTTTTTCTACAG 59.698 50.000 0.00 0.00 41.55 2.74
5216 7588 2.332117 ACGGGAGGGACTTTTTCTACA 58.668 47.619 0.00 0.00 41.55 2.74
5217 7589 3.413846 AACGGGAGGGACTTTTTCTAC 57.586 47.619 0.00 0.00 41.55 2.59
5218 7590 3.497227 CCAAACGGGAGGGACTTTTTCTA 60.497 47.826 0.00 0.00 41.55 2.10
5219 7591 2.583143 CAAACGGGAGGGACTTTTTCT 58.417 47.619 0.00 0.00 41.55 2.52
5220 7592 1.611977 CCAAACGGGAGGGACTTTTTC 59.388 52.381 0.00 0.00 41.55 2.29
5221 7593 1.063492 ACCAAACGGGAGGGACTTTTT 60.063 47.619 0.00 0.00 41.55 1.94
5222 7594 0.554305 ACCAAACGGGAGGGACTTTT 59.446 50.000 0.00 0.00 41.55 2.27
5223 7595 0.554305 AACCAAACGGGAGGGACTTT 59.446 50.000 0.00 0.00 41.55 2.66
5224 7596 0.109913 GAACCAAACGGGAGGGACTT 59.890 55.000 0.00 0.00 41.55 3.01
5226 7598 1.303074 GGAACCAAACGGGAGGGAC 60.303 63.158 0.00 0.00 41.15 4.46
5227 7599 0.178897 TAGGAACCAAACGGGAGGGA 60.179 55.000 0.00 0.00 41.15 4.20
5228 7600 0.252197 CTAGGAACCAAACGGGAGGG 59.748 60.000 0.00 0.00 41.15 4.30
5229 7601 0.252197 CCTAGGAACCAAACGGGAGG 59.748 60.000 1.05 0.00 41.15 4.30
5230 7602 0.252197 CCCTAGGAACCAAACGGGAG 59.748 60.000 11.48 0.00 41.15 4.30
5231 7603 0.178897 TCCCTAGGAACCAAACGGGA 60.179 55.000 11.48 0.00 41.15 5.14
5232 7604 0.035725 GTCCCTAGGAACCAAACGGG 60.036 60.000 11.48 0.00 44.81 5.28
5233 7605 0.981943 AGTCCCTAGGAACCAAACGG 59.018 55.000 11.48 0.00 31.38 4.44
5234 7606 2.853235 AAGTCCCTAGGAACCAAACG 57.147 50.000 11.48 0.00 31.38 3.60
5235 7607 5.475909 CCTAAAAAGTCCCTAGGAACCAAAC 59.524 44.000 11.48 0.00 35.17 2.93
5236 7608 5.458508 CCCTAAAAAGTCCCTAGGAACCAAA 60.459 44.000 11.48 0.00 35.17 3.28
5237 7609 4.043686 CCCTAAAAAGTCCCTAGGAACCAA 59.956 45.833 11.48 0.00 35.17 3.67
5238 7610 3.590182 CCCTAAAAAGTCCCTAGGAACCA 59.410 47.826 11.48 0.00 35.17 3.67
5239 7611 3.848377 TCCCTAAAAAGTCCCTAGGAACC 59.152 47.826 11.48 0.00 35.17 3.62
5240 7612 4.535294 AGTCCCTAAAAAGTCCCTAGGAAC 59.465 45.833 11.48 0.00 35.17 3.62
5241 7613 4.771338 AGTCCCTAAAAAGTCCCTAGGAA 58.229 43.478 11.48 0.00 35.17 3.36
5242 7614 4.431158 AGTCCCTAAAAAGTCCCTAGGA 57.569 45.455 11.48 0.00 35.17 2.94
5243 7615 5.516059 AAAGTCCCTAAAAAGTCCCTAGG 57.484 43.478 0.06 0.06 33.30 3.02
5244 7616 7.232188 AGAAAAAGTCCCTAAAAAGTCCCTAG 58.768 38.462 0.00 0.00 0.00 3.02
5245 7617 7.157947 AGAAAAAGTCCCTAAAAAGTCCCTA 57.842 36.000 0.00 0.00 0.00 3.53
5246 7618 6.027025 AGAAAAAGTCCCTAAAAAGTCCCT 57.973 37.500 0.00 0.00 0.00 4.20
5247 7619 7.002879 ACTAGAAAAAGTCCCTAAAAAGTCCC 58.997 38.462 0.00 0.00 0.00 4.46
5248 7620 7.937942 AGACTAGAAAAAGTCCCTAAAAAGTCC 59.062 37.037 0.00 0.00 45.86 3.85
5249 7621 8.905660 AGACTAGAAAAAGTCCCTAAAAAGTC 57.094 34.615 0.00 0.00 45.86 3.01
5250 7622 8.715842 AGAGACTAGAAAAAGTCCCTAAAAAGT 58.284 33.333 0.00 0.00 45.86 2.66
5253 7625 8.813951 CCTAGAGACTAGAAAAAGTCCCTAAAA 58.186 37.037 0.00 0.00 45.86 1.52
5254 7626 8.175431 TCCTAGAGACTAGAAAAAGTCCCTAAA 58.825 37.037 0.00 0.00 45.86 1.85
5255 7627 7.614974 GTCCTAGAGACTAGAAAAAGTCCCTAA 59.385 40.741 0.00 0.00 45.86 2.69
5256 7628 7.118060 GTCCTAGAGACTAGAAAAAGTCCCTA 58.882 42.308 0.00 0.00 45.86 3.53
5257 7629 5.953548 GTCCTAGAGACTAGAAAAAGTCCCT 59.046 44.000 0.00 0.00 45.86 4.20
5258 7630 6.211587 GTCCTAGAGACTAGAAAAAGTCCC 57.788 45.833 0.00 0.00 45.86 4.46
5279 7651 5.358725 TGTTTGGTTCAGGGACTTTTTAGTC 59.641 40.000 0.00 0.00 34.60 2.59
5280 7652 5.126545 GTGTTTGGTTCAGGGACTTTTTAGT 59.873 40.000 0.00 0.00 34.60 2.24
5281 7653 5.451381 GGTGTTTGGTTCAGGGACTTTTTAG 60.451 44.000 0.00 0.00 34.60 1.85
5282 7654 4.403113 GGTGTTTGGTTCAGGGACTTTTTA 59.597 41.667 0.00 0.00 34.60 1.52
5283 7655 3.196901 GGTGTTTGGTTCAGGGACTTTTT 59.803 43.478 0.00 0.00 34.60 1.94
5284 7656 2.764010 GGTGTTTGGTTCAGGGACTTTT 59.236 45.455 0.00 0.00 34.60 2.27
5285 7657 2.384828 GGTGTTTGGTTCAGGGACTTT 58.615 47.619 0.00 0.00 34.60 2.66
5286 7658 1.411074 GGGTGTTTGGTTCAGGGACTT 60.411 52.381 0.00 0.00 34.60 3.01
5287 7659 0.185175 GGGTGTTTGGTTCAGGGACT 59.815 55.000 0.00 0.00 43.88 3.85
5288 7660 0.826256 GGGGTGTTTGGTTCAGGGAC 60.826 60.000 0.00 0.00 0.00 4.46
5289 7661 1.539665 GGGGTGTTTGGTTCAGGGA 59.460 57.895 0.00 0.00 0.00 4.20
5290 7662 1.533033 GGGGGTGTTTGGTTCAGGG 60.533 63.158 0.00 0.00 0.00 4.45
5291 7663 0.774908 TAGGGGGTGTTTGGTTCAGG 59.225 55.000 0.00 0.00 0.00 3.86
5292 7664 2.158519 ACTTAGGGGGTGTTTGGTTCAG 60.159 50.000 0.00 0.00 0.00 3.02
5293 7665 1.854280 ACTTAGGGGGTGTTTGGTTCA 59.146 47.619 0.00 0.00 0.00 3.18
5294 7666 2.670019 ACTTAGGGGGTGTTTGGTTC 57.330 50.000 0.00 0.00 0.00 3.62
5295 7667 3.723154 TCTTACTTAGGGGGTGTTTGGTT 59.277 43.478 0.00 0.00 0.00 3.67
5296 7668 3.329277 TCTTACTTAGGGGGTGTTTGGT 58.671 45.455 0.00 0.00 0.00 3.67
5297 7669 4.270008 CATCTTACTTAGGGGGTGTTTGG 58.730 47.826 0.00 0.00 0.00 3.28
5298 7670 3.694566 GCATCTTACTTAGGGGGTGTTTG 59.305 47.826 0.00 0.00 0.00 2.93
5299 7671 3.308904 GGCATCTTACTTAGGGGGTGTTT 60.309 47.826 0.00 0.00 0.00 2.83
5300 7672 2.241430 GGCATCTTACTTAGGGGGTGTT 59.759 50.000 0.00 0.00 0.00 3.32
5301 7673 1.844497 GGCATCTTACTTAGGGGGTGT 59.156 52.381 0.00 0.00 0.00 4.16
5302 7674 1.202651 CGGCATCTTACTTAGGGGGTG 60.203 57.143 0.00 0.00 0.00 4.61
5303 7675 1.129058 CGGCATCTTACTTAGGGGGT 58.871 55.000 0.00 0.00 0.00 4.95
5304 7676 1.420430 TCGGCATCTTACTTAGGGGG 58.580 55.000 0.00 0.00 0.00 5.40
5305 7677 6.732896 ATATATCGGCATCTTACTTAGGGG 57.267 41.667 0.00 0.00 0.00 4.79
5306 7678 7.039644 CCCTATATATCGGCATCTTACTTAGGG 60.040 44.444 0.00 0.00 36.18 3.53
5307 7679 7.506261 ACCCTATATATCGGCATCTTACTTAGG 59.494 40.741 0.00 0.00 0.00 2.69
5308 7680 8.466617 ACCCTATATATCGGCATCTTACTTAG 57.533 38.462 0.00 0.00 0.00 2.18
5311 7683 9.742144 CTATACCCTATATATCGGCATCTTACT 57.258 37.037 0.00 0.00 0.00 2.24
5312 7684 8.460428 GCTATACCCTATATATCGGCATCTTAC 58.540 40.741 0.00 0.00 0.00 2.34
5346 7718 7.649533 TCCTCATGAATGCTCATAACAAAAT 57.350 32.000 0.00 0.00 40.49 1.82
5455 7827 2.602933 CCAAGCACGGCATCAATTATCG 60.603 50.000 0.00 0.00 0.00 2.92
5619 7991 3.070734 TGGAATGATAGCTTCCTCTCTGC 59.929 47.826 0.00 0.00 42.27 4.26
5695 8067 7.506114 TGATTAAAGGGACACTATACCATGTC 58.494 38.462 0.00 0.00 43.75 3.06
5780 8152 2.475685 CGAACTCAGAGCATGCATTGTG 60.476 50.000 21.98 18.78 0.00 3.33
5794 8166 3.629855 TGCCTTGAAATGTTTCGAACTCA 59.370 39.130 0.00 0.47 40.01 3.41


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

AutoCloner maintained by Alex Coulton.