Multiple sequence alignment - TraesCS3D01G385900

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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 TraesCS3D01G385900 chr3D 100.000 3209 0 0 1 3209 501330412 501333620 0.000000e+00 5927
1 TraesCS3D01G385900 chr3D 81.712 1285 113 68 233 1431 501412263 501413511 0.000000e+00 959
2 TraesCS3D01G385900 chr3D 88.395 810 66 9 1494 2277 501413641 501414448 0.000000e+00 950
3 TraesCS3D01G385900 chr3D 82.589 873 87 32 1442 2269 308985502 308984650 0.000000e+00 710
4 TraesCS3D01G385900 chr3D 89.753 283 16 3 1161 1431 308985876 308985595 1.830000e-92 350
5 TraesCS3D01G385900 chr3D 85.714 168 17 5 304 464 308987039 308986872 1.530000e-38 171
6 TraesCS3D01G385900 chr3A 91.298 2011 93 23 345 2327 640878804 640880760 0.000000e+00 2669
7 TraesCS3D01G385900 chr3A 89.216 816 56 14 1494 2277 640952202 640953017 0.000000e+00 990
8 TraesCS3D01G385900 chr3A 89.861 789 53 9 1494 2258 641012496 641013281 0.000000e+00 989
9 TraesCS3D01G385900 chr3A 83.655 881 75 36 1442 2269 428569928 428569064 0.000000e+00 765
10 TraesCS3D01G385900 chr3A 95.926 270 10 1 1164 1433 640951824 640952092 1.370000e-118 436
11 TraesCS3D01G385900 chr3A 95.926 270 10 1 1164 1433 641012118 641012386 1.370000e-118 436
12 TraesCS3D01G385900 chr3A 79.270 685 69 39 506 1147 640951121 640951775 8.290000e-111 411
13 TraesCS3D01G385900 chr3A 79.270 685 69 39 506 1147 641011415 641012069 8.290000e-111 411
14 TraesCS3D01G385900 chr3A 83.259 448 30 21 1007 1438 428570445 428570027 1.410000e-98 370
15 TraesCS3D01G385900 chr3A 83.110 373 29 12 4 349 640866927 640867292 3.110000e-80 309
16 TraesCS3D01G385900 chr3A 87.160 257 26 5 233 488 640950818 640951068 5.240000e-73 285
17 TraesCS3D01G385900 chr3A 87.160 257 26 5 233 488 641011112 641011362 5.240000e-73 285
18 TraesCS3D01G385900 chr3A 80.519 231 31 10 240 457 428571531 428571302 7.120000e-37 165
19 TraesCS3D01G385900 chr3B 91.051 1855 95 22 505 2333 663072894 663071085 0.000000e+00 2440
20 TraesCS3D01G385900 chr3B 88.481 790 62 12 1494 2258 663062000 663061215 0.000000e+00 928
21 TraesCS3D01G385900 chr3B 84.491 806 69 26 1515 2269 412596318 412597118 0.000000e+00 745
22 TraesCS3D01G385900 chr3B 90.210 286 23 3 228 512 663079747 663079466 5.060000e-98 368
23 TraesCS3D01G385900 chr3B 89.153 295 14 7 1155 1435 412595874 412596164 5.090000e-93 351
24 TraesCS3D01G385900 chr3B 97.884 189 4 0 1245 1433 663062316 663062128 8.580000e-86 327
25 TraesCS3D01G385900 chr3B 88.350 206 21 2 295 500 663065669 663065467 8.890000e-61 244
26 TraesCS3D01G385900 chr3B 84.568 162 16 5 304 457 412594356 412594516 5.540000e-33 152
27 TraesCS3D01G385900 chr4D 87.876 932 101 8 2288 3209 49166276 49165347 0.000000e+00 1085
28 TraesCS3D01G385900 chr5B 87.991 916 99 7 2303 3209 466192016 466192929 0.000000e+00 1072
29 TraesCS3D01G385900 chr5A 87.882 916 100 7 2303 3209 24794488 24793575 0.000000e+00 1066
30 TraesCS3D01G385900 chr5A 87.882 916 100 7 2303 3209 603438037 603438950 0.000000e+00 1066
31 TraesCS3D01G385900 chr4B 87.882 916 99 8 2303 3209 169589263 169588351 0.000000e+00 1066
32 TraesCS3D01G385900 chr4B 87.882 916 100 7 2303 3209 508554500 508553587 0.000000e+00 1066
33 TraesCS3D01G385900 chr2B 87.882 916 100 7 2303 3209 80106233 80107146 0.000000e+00 1066
34 TraesCS3D01G385900 chr1B 87.882 916 100 7 2303 3209 217206839 217205926 0.000000e+00 1066
35 TraesCS3D01G385900 chr1A 87.882 916 100 7 2303 3209 242695430 242694517 0.000000e+00 1066


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 TraesCS3D01G385900 chr3D 501330412 501333620 3208 False 5927.000000 5927 100.000000 1 3209 1 chr3D.!!$F1 3208
1 TraesCS3D01G385900 chr3D 501412263 501414448 2185 False 954.500000 959 85.053500 233 2277 2 chr3D.!!$F2 2044
2 TraesCS3D01G385900 chr3D 308984650 308987039 2389 True 410.333333 710 86.018667 304 2269 3 chr3D.!!$R1 1965
3 TraesCS3D01G385900 chr3A 640878804 640880760 1956 False 2669.000000 2669 91.298000 345 2327 1 chr3A.!!$F2 1982
4 TraesCS3D01G385900 chr3A 640950818 640953017 2199 False 530.500000 990 87.893000 233 2277 4 chr3A.!!$F3 2044
5 TraesCS3D01G385900 chr3A 641011112 641013281 2169 False 530.250000 989 88.054250 233 2258 4 chr3A.!!$F4 2025
6 TraesCS3D01G385900 chr3A 428569064 428571531 2467 True 433.333333 765 82.477667 240 2269 3 chr3A.!!$R1 2029
7 TraesCS3D01G385900 chr3B 663071085 663072894 1809 True 2440.000000 2440 91.051000 505 2333 1 chr3B.!!$R1 1828
8 TraesCS3D01G385900 chr3B 663061215 663065669 4454 True 499.666667 928 91.571667 295 2258 3 chr3B.!!$R3 1963
9 TraesCS3D01G385900 chr3B 412594356 412597118 2762 False 416.000000 745 86.070667 304 2269 3 chr3B.!!$F1 1965
10 TraesCS3D01G385900 chr4D 49165347 49166276 929 True 1085.000000 1085 87.876000 2288 3209 1 chr4D.!!$R1 921
11 TraesCS3D01G385900 chr5B 466192016 466192929 913 False 1072.000000 1072 87.991000 2303 3209 1 chr5B.!!$F1 906
12 TraesCS3D01G385900 chr5A 24793575 24794488 913 True 1066.000000 1066 87.882000 2303 3209 1 chr5A.!!$R1 906
13 TraesCS3D01G385900 chr5A 603438037 603438950 913 False 1066.000000 1066 87.882000 2303 3209 1 chr5A.!!$F1 906
14 TraesCS3D01G385900 chr4B 169588351 169589263 912 True 1066.000000 1066 87.882000 2303 3209 1 chr4B.!!$R1 906
15 TraesCS3D01G385900 chr4B 508553587 508554500 913 True 1066.000000 1066 87.882000 2303 3209 1 chr4B.!!$R2 906
16 TraesCS3D01G385900 chr2B 80106233 80107146 913 False 1066.000000 1066 87.882000 2303 3209 1 chr2B.!!$F1 906
17 TraesCS3D01G385900 chr1B 217205926 217206839 913 True 1066.000000 1066 87.882000 2303 3209 1 chr1B.!!$R1 906
18 TraesCS3D01G385900 chr1A 242694517 242695430 913 True 1066.000000 1066 87.882000 2303 3209 1 chr1A.!!$R1 906

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
118 119 0.102120 CCAAACCACGTGCACAACAT 59.898 50.0 18.64 0.0 0.00 2.71 F
1084 4300 0.248289 GAGGGATTTTGACGTCCGGA 59.752 55.0 14.12 0.0 35.28 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 5151 0.820871 CTCTTCCTCCTCCACTTCCG 59.179 60.0 0.00 0.00 0.00 4.30 R
2803 6348 0.606673 GTTGGCAGACTTGGAGTCCC 60.607 60.0 6.74 1.29 46.18 4.46 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
19 20 1.374560 ATTAAACGCCGCATAGTGCA 58.625 45.000 2.63 0.00 45.36 4.57
20 21 1.374560 TTAAACGCCGCATAGTGCAT 58.625 45.000 2.63 0.00 45.36 3.96
21 22 0.934496 TAAACGCCGCATAGTGCATC 59.066 50.000 2.63 0.00 45.36 3.91
22 23 1.024046 AAACGCCGCATAGTGCATCA 61.024 50.000 2.63 0.00 45.36 3.07
23 24 1.431488 AACGCCGCATAGTGCATCAG 61.431 55.000 2.63 0.00 45.36 2.90
24 25 2.635899 GCCGCATAGTGCATCAGC 59.364 61.111 2.63 0.00 45.36 4.26
25 26 2.901292 GCCGCATAGTGCATCAGCC 61.901 63.158 2.63 0.00 45.36 4.85
26 27 2.256591 CCGCATAGTGCATCAGCCC 61.257 63.158 2.63 0.00 45.36 5.19
27 28 1.524393 CGCATAGTGCATCAGCCCA 60.524 57.895 2.63 0.00 45.36 5.36
28 29 1.504647 CGCATAGTGCATCAGCCCAG 61.505 60.000 2.63 0.00 45.36 4.45
29 30 0.465097 GCATAGTGCATCAGCCCAGT 60.465 55.000 0.00 0.00 44.26 4.00
30 31 1.590932 CATAGTGCATCAGCCCAGTC 58.409 55.000 0.00 0.00 41.13 3.51
31 32 0.471617 ATAGTGCATCAGCCCAGTCC 59.528 55.000 0.00 0.00 41.13 3.85
32 33 0.909133 TAGTGCATCAGCCCAGTCCA 60.909 55.000 0.00 0.00 41.13 4.02
33 34 1.303561 GTGCATCAGCCCAGTCCAA 60.304 57.895 0.00 0.00 41.13 3.53
34 35 0.682209 GTGCATCAGCCCAGTCCAAT 60.682 55.000 0.00 0.00 41.13 3.16
35 36 0.681887 TGCATCAGCCCAGTCCAATG 60.682 55.000 0.00 0.00 41.13 2.82
36 37 2.012902 GCATCAGCCCAGTCCAATGC 62.013 60.000 0.00 0.00 33.53 3.56
37 38 0.681887 CATCAGCCCAGTCCAATGCA 60.682 55.000 0.00 0.00 0.00 3.96
38 39 0.395311 ATCAGCCCAGTCCAATGCAG 60.395 55.000 0.00 0.00 0.00 4.41
39 40 2.050350 CAGCCCAGTCCAATGCAGG 61.050 63.158 0.00 0.00 0.00 4.85
40 41 3.455469 GCCCAGTCCAATGCAGGC 61.455 66.667 0.00 0.00 0.00 4.85
41 42 2.036098 CCCAGTCCAATGCAGGCA 59.964 61.111 0.00 0.00 0.00 4.75
42 43 1.607178 CCCAGTCCAATGCAGGCAA 60.607 57.895 0.00 0.00 0.00 4.52
43 44 0.974010 CCCAGTCCAATGCAGGCAAT 60.974 55.000 0.00 0.00 0.00 3.56
44 45 0.458669 CCAGTCCAATGCAGGCAATC 59.541 55.000 0.00 0.00 0.00 2.67
45 46 1.179152 CAGTCCAATGCAGGCAATCA 58.821 50.000 0.00 0.00 0.00 2.57
46 47 1.546923 CAGTCCAATGCAGGCAATCAA 59.453 47.619 0.00 0.00 0.00 2.57
47 48 2.028839 CAGTCCAATGCAGGCAATCAAA 60.029 45.455 0.00 0.00 0.00 2.69
48 49 2.028748 AGTCCAATGCAGGCAATCAAAC 60.029 45.455 0.00 0.00 0.00 2.93
49 50 1.067706 TCCAATGCAGGCAATCAAACG 60.068 47.619 0.00 0.00 0.00 3.60
50 51 0.717224 CAATGCAGGCAATCAAACGC 59.283 50.000 0.00 0.00 0.00 4.84
51 52 0.317799 AATGCAGGCAATCAAACGCA 59.682 45.000 0.00 0.00 0.00 5.24
52 53 0.533491 ATGCAGGCAATCAAACGCAT 59.467 45.000 0.00 0.00 35.36 4.73
53 54 0.388778 TGCAGGCAATCAAACGCATG 60.389 50.000 0.00 0.00 42.55 4.06
54 55 1.079875 GCAGGCAATCAAACGCATGG 61.080 55.000 0.00 0.00 40.15 3.66
55 56 0.458889 CAGGCAATCAAACGCATGGG 60.459 55.000 8.44 8.44 36.33 4.00
56 57 1.153588 GGCAATCAAACGCATGGGG 60.154 57.895 14.94 0.00 0.00 4.96
57 58 1.603236 GGCAATCAAACGCATGGGGA 61.603 55.000 14.94 2.19 0.00 4.81
58 59 0.179129 GCAATCAAACGCATGGGGAG 60.179 55.000 14.94 3.54 0.00 4.30
59 60 0.457035 CAATCAAACGCATGGGGAGG 59.543 55.000 14.94 2.80 0.00 4.30
60 61 0.331278 AATCAAACGCATGGGGAGGA 59.669 50.000 14.94 8.18 0.00 3.71
61 62 0.107017 ATCAAACGCATGGGGAGGAG 60.107 55.000 14.94 0.00 0.00 3.69
62 63 1.002134 CAAACGCATGGGGAGGAGT 60.002 57.895 14.94 0.00 0.00 3.85
63 64 0.609131 CAAACGCATGGGGAGGAGTT 60.609 55.000 14.94 0.00 0.00 3.01
64 65 0.609131 AAACGCATGGGGAGGAGTTG 60.609 55.000 14.94 0.00 0.00 3.16
65 66 1.779061 AACGCATGGGGAGGAGTTGT 61.779 55.000 14.94 0.00 0.00 3.32
66 67 1.002134 CGCATGGGGAGGAGTTGTT 60.002 57.895 0.89 0.00 0.00 2.83
67 68 0.609131 CGCATGGGGAGGAGTTGTTT 60.609 55.000 0.89 0.00 0.00 2.83
68 69 1.632589 GCATGGGGAGGAGTTGTTTT 58.367 50.000 0.00 0.00 0.00 2.43
69 70 1.546029 GCATGGGGAGGAGTTGTTTTC 59.454 52.381 0.00 0.00 0.00 2.29
70 71 2.171003 CATGGGGAGGAGTTGTTTTCC 58.829 52.381 0.00 0.00 34.83 3.13
72 73 2.708759 TGGGGAGGAGTTGTTTTCCTA 58.291 47.619 0.00 0.00 45.00 2.94
73 74 3.057586 TGGGGAGGAGTTGTTTTCCTAA 58.942 45.455 0.00 0.00 45.00 2.69
74 75 3.660669 TGGGGAGGAGTTGTTTTCCTAAT 59.339 43.478 0.00 0.00 45.00 1.73
75 76 4.017126 GGGGAGGAGTTGTTTTCCTAATG 58.983 47.826 0.00 0.00 45.00 1.90
76 77 4.508584 GGGGAGGAGTTGTTTTCCTAATGT 60.509 45.833 0.00 0.00 45.00 2.71
77 78 5.280830 GGGGAGGAGTTGTTTTCCTAATGTA 60.281 44.000 0.00 0.00 45.00 2.29
78 79 6.424032 GGGAGGAGTTGTTTTCCTAATGTAT 58.576 40.000 0.00 0.00 45.00 2.29
79 80 7.366191 GGGGAGGAGTTGTTTTCCTAATGTATA 60.366 40.741 0.00 0.00 45.00 1.47
80 81 8.218488 GGGAGGAGTTGTTTTCCTAATGTATAT 58.782 37.037 0.00 0.00 45.00 0.86
81 82 9.057089 GGAGGAGTTGTTTTCCTAATGTATATG 57.943 37.037 0.00 0.00 45.00 1.78
82 83 8.451908 AGGAGTTGTTTTCCTAATGTATATGC 57.548 34.615 0.00 0.00 43.21 3.14
83 84 8.052748 AGGAGTTGTTTTCCTAATGTATATGCA 58.947 33.333 0.00 0.00 43.21 3.96
84 85 8.682710 GGAGTTGTTTTCCTAATGTATATGCAA 58.317 33.333 0.00 0.00 0.00 4.08
85 86 9.503427 GAGTTGTTTTCCTAATGTATATGCAAC 57.497 33.333 0.00 0.00 33.69 4.17
86 87 9.243105 AGTTGTTTTCCTAATGTATATGCAACT 57.757 29.630 0.00 0.00 37.43 3.16
87 88 9.503427 GTTGTTTTCCTAATGTATATGCAACTC 57.497 33.333 0.00 0.00 0.00 3.01
88 89 8.800370 TGTTTTCCTAATGTATATGCAACTCA 57.200 30.769 0.00 0.00 0.00 3.41
89 90 9.407380 TGTTTTCCTAATGTATATGCAACTCAT 57.593 29.630 0.00 0.00 39.17 2.90
93 94 8.722480 TCCTAATGTATATGCAACTCATATGC 57.278 34.615 0.00 6.80 45.42 3.14
101 102 2.358957 GCAACTCATATGCAGACACCA 58.641 47.619 0.00 0.00 43.29 4.17
102 103 2.749076 GCAACTCATATGCAGACACCAA 59.251 45.455 0.00 0.00 43.29 3.67
103 104 3.191162 GCAACTCATATGCAGACACCAAA 59.809 43.478 0.00 0.00 43.29 3.28
104 105 4.726416 CAACTCATATGCAGACACCAAAC 58.274 43.478 0.00 0.00 0.00 2.93
105 106 3.347216 ACTCATATGCAGACACCAAACC 58.653 45.455 0.00 0.00 0.00 3.27
106 107 3.244875 ACTCATATGCAGACACCAAACCA 60.245 43.478 0.00 0.00 0.00 3.67
107 108 3.081061 TCATATGCAGACACCAAACCAC 58.919 45.455 0.00 0.00 0.00 4.16
108 109 1.518325 TATGCAGACACCAAACCACG 58.482 50.000 0.00 0.00 0.00 4.94
109 110 0.465460 ATGCAGACACCAAACCACGT 60.465 50.000 0.00 0.00 0.00 4.49
110 111 1.355210 GCAGACACCAAACCACGTG 59.645 57.895 9.08 9.08 36.04 4.49
111 112 1.355210 CAGACACCAAACCACGTGC 59.645 57.895 10.91 0.00 33.09 5.34
112 113 1.078072 AGACACCAAACCACGTGCA 60.078 52.632 10.91 0.00 33.09 4.57
113 114 1.063488 GACACCAAACCACGTGCAC 59.937 57.895 10.91 6.82 33.09 4.57
114 115 1.649390 GACACCAAACCACGTGCACA 61.649 55.000 18.64 0.00 33.09 4.57
115 116 1.244697 ACACCAAACCACGTGCACAA 61.245 50.000 18.64 0.00 33.09 3.33
116 117 0.800300 CACCAAACCACGTGCACAAC 60.800 55.000 18.64 0.00 0.00 3.32
117 118 1.244697 ACCAAACCACGTGCACAACA 61.245 50.000 18.64 0.00 0.00 3.33
118 119 0.102120 CCAAACCACGTGCACAACAT 59.898 50.000 18.64 0.00 0.00 2.71
119 120 1.198767 CAAACCACGTGCACAACATG 58.801 50.000 18.64 8.90 41.41 3.21
121 122 0.814457 AACCACGTGCACAACATGTT 59.186 45.000 18.64 4.92 46.67 2.71
122 123 0.814457 ACCACGTGCACAACATGTTT 59.186 45.000 18.64 0.00 46.67 2.83
123 124 1.203523 ACCACGTGCACAACATGTTTT 59.796 42.857 18.64 0.00 46.67 2.43
124 125 1.851666 CCACGTGCACAACATGTTTTC 59.148 47.619 18.64 1.51 46.67 2.29
125 126 2.479389 CCACGTGCACAACATGTTTTCT 60.479 45.455 18.64 0.00 46.67 2.52
126 127 3.178267 CACGTGCACAACATGTTTTCTT 58.822 40.909 18.64 0.00 46.67 2.52
127 128 3.611986 CACGTGCACAACATGTTTTCTTT 59.388 39.130 18.64 0.00 46.67 2.52
128 129 4.091220 CACGTGCACAACATGTTTTCTTTT 59.909 37.500 18.64 0.00 46.67 2.27
129 130 4.688413 ACGTGCACAACATGTTTTCTTTTT 59.312 33.333 18.64 0.00 46.67 1.94
130 131 5.014483 CGTGCACAACATGTTTTCTTTTTG 58.986 37.500 18.64 0.00 0.00 2.44
131 132 4.787591 GTGCACAACATGTTTTCTTTTTGC 59.212 37.500 13.17 9.29 0.00 3.68
132 133 4.453478 TGCACAACATGTTTTCTTTTTGCA 59.547 33.333 8.77 11.56 0.00 4.08
133 134 5.123502 TGCACAACATGTTTTCTTTTTGCAT 59.876 32.000 8.77 0.00 0.00 3.96
134 135 5.452944 GCACAACATGTTTTCTTTTTGCATG 59.547 36.000 8.77 0.00 41.67 4.06
136 137 7.675870 GCACAACATGTTTTCTTTTTGCATGTA 60.676 33.333 8.77 0.00 46.17 2.29
137 138 8.336806 CACAACATGTTTTCTTTTTGCATGTAT 58.663 29.630 8.77 0.00 46.17 2.29
138 139 8.891720 ACAACATGTTTTCTTTTTGCATGTATT 58.108 25.926 8.77 0.00 46.17 1.89
139 140 9.372541 CAACATGTTTTCTTTTTGCATGTATTC 57.627 29.630 8.77 0.00 46.17 1.75
140 141 8.659925 ACATGTTTTCTTTTTGCATGTATTCA 57.340 26.923 6.68 0.00 45.40 2.57
141 142 9.107177 ACATGTTTTCTTTTTGCATGTATTCAA 57.893 25.926 6.68 0.00 45.40 2.69
144 145 9.322773 TGTTTTCTTTTTGCATGTATTCAATCA 57.677 25.926 0.00 0.00 0.00 2.57
147 148 9.708092 TTTCTTTTTGCATGTATTCAATCATCA 57.292 25.926 0.00 0.00 0.00 3.07
148 149 9.708092 TTCTTTTTGCATGTATTCAATCATCAA 57.292 25.926 0.00 0.00 0.00 2.57
149 150 9.878667 TCTTTTTGCATGTATTCAATCATCAAT 57.121 25.926 0.00 0.00 0.00 2.57
151 152 9.654663 TTTTTGCATGTATTCAATCATCAATCA 57.345 25.926 0.00 0.00 0.00 2.57
152 153 8.865590 TTTGCATGTATTCAATCATCAATCAG 57.134 30.769 0.00 0.00 0.00 2.90
153 154 6.443792 TGCATGTATTCAATCATCAATCAGC 58.556 36.000 0.00 0.00 0.00 4.26
154 155 5.862323 GCATGTATTCAATCATCAATCAGCC 59.138 40.000 0.00 0.00 0.00 4.85
155 156 6.516028 GCATGTATTCAATCATCAATCAGCCA 60.516 38.462 0.00 0.00 0.00 4.75
156 157 7.430441 CATGTATTCAATCATCAATCAGCCAA 58.570 34.615 0.00 0.00 0.00 4.52
157 158 7.034685 TGTATTCAATCATCAATCAGCCAAG 57.965 36.000 0.00 0.00 0.00 3.61
158 159 4.380841 TTCAATCATCAATCAGCCAAGC 57.619 40.909 0.00 0.00 0.00 4.01
159 160 3.628008 TCAATCATCAATCAGCCAAGCT 58.372 40.909 0.00 0.00 40.77 3.74
160 161 4.784177 TCAATCATCAATCAGCCAAGCTA 58.216 39.130 0.00 0.00 36.40 3.32
161 162 5.195185 TCAATCATCAATCAGCCAAGCTAA 58.805 37.500 0.00 0.00 36.40 3.09
162 163 5.653330 TCAATCATCAATCAGCCAAGCTAAA 59.347 36.000 0.00 0.00 36.40 1.85
163 164 4.970662 TCATCAATCAGCCAAGCTAAAC 57.029 40.909 0.00 0.00 36.40 2.01
164 165 4.592942 TCATCAATCAGCCAAGCTAAACT 58.407 39.130 0.00 0.00 36.40 2.66
165 166 4.637534 TCATCAATCAGCCAAGCTAAACTC 59.362 41.667 0.00 0.00 36.40 3.01
166 167 4.019792 TCAATCAGCCAAGCTAAACTCA 57.980 40.909 0.00 0.00 36.40 3.41
167 168 4.005650 TCAATCAGCCAAGCTAAACTCAG 58.994 43.478 0.00 0.00 36.40 3.35
168 169 3.988976 ATCAGCCAAGCTAAACTCAGA 57.011 42.857 0.00 0.00 36.40 3.27
169 170 3.325293 TCAGCCAAGCTAAACTCAGAG 57.675 47.619 0.00 0.00 36.40 3.35
170 171 1.736681 CAGCCAAGCTAAACTCAGAGC 59.263 52.381 0.00 0.00 36.40 4.09
171 172 1.090728 GCCAAGCTAAACTCAGAGCC 58.909 55.000 0.00 0.00 39.65 4.70
172 173 1.611673 GCCAAGCTAAACTCAGAGCCA 60.612 52.381 0.00 0.00 39.65 4.75
173 174 2.943199 GCCAAGCTAAACTCAGAGCCAT 60.943 50.000 0.00 0.00 39.65 4.40
174 175 2.681848 CCAAGCTAAACTCAGAGCCATG 59.318 50.000 0.00 0.00 39.65 3.66
175 176 2.681848 CAAGCTAAACTCAGAGCCATGG 59.318 50.000 7.63 7.63 39.65 3.66
176 177 2.191400 AGCTAAACTCAGAGCCATGGA 58.809 47.619 18.40 0.00 39.65 3.41
177 178 2.776536 AGCTAAACTCAGAGCCATGGAT 59.223 45.455 18.40 10.08 39.65 3.41
178 179 2.877168 GCTAAACTCAGAGCCATGGATG 59.123 50.000 18.40 10.85 32.25 3.51
179 180 1.760192 AAACTCAGAGCCATGGATGC 58.240 50.000 18.40 3.39 0.00 3.91
180 181 0.622136 AACTCAGAGCCATGGATGCA 59.378 50.000 18.40 0.00 0.00 3.96
181 182 0.844660 ACTCAGAGCCATGGATGCAT 59.155 50.000 18.40 0.00 0.00 3.96
182 183 1.239347 CTCAGAGCCATGGATGCATG 58.761 55.000 18.40 19.49 0.00 4.06
264 268 2.717639 ATTGGGCTAGTGCTAGTTGG 57.282 50.000 7.90 0.00 39.59 3.77
268 272 2.907696 TGGGCTAGTGCTAGTTGGTAAA 59.092 45.455 7.90 0.00 39.59 2.01
269 273 3.055385 TGGGCTAGTGCTAGTTGGTAAAG 60.055 47.826 7.90 0.00 39.59 1.85
270 274 3.197116 GGGCTAGTGCTAGTTGGTAAAGA 59.803 47.826 7.90 0.00 39.59 2.52
272 276 4.182339 GCTAGTGCTAGTTGGTAAAGACC 58.818 47.826 7.90 0.00 39.58 3.85
294 303 4.323792 CCACATGGACATAAGGTGACTTCT 60.324 45.833 0.00 0.00 44.17 2.85
295 304 6.371885 CCACATGGACATAAGGTGACTTCTG 61.372 48.000 0.00 0.00 46.70 3.02
296 305 8.479122 CCACATGGACATAAGGTGACTTCTGA 62.479 46.154 0.00 0.00 44.83 3.27
334 343 1.814429 TGGAAACAGGGTCAAGGAGA 58.186 50.000 0.00 0.00 35.01 3.71
595 2936 3.569701 ACAAGGGAAGCATAGTGTTTGTG 59.430 43.478 0.00 0.00 0.00 3.33
610 2963 0.955428 TTGTGCAGTTGATCGAGGCC 60.955 55.000 0.00 0.00 0.00 5.19
642 2995 2.078849 ATCAACACAGTGCGATCGAA 57.921 45.000 21.57 5.06 0.00 3.71
649 3002 0.248825 CAGTGCGATCGAAGAGAGGG 60.249 60.000 21.57 0.00 43.63 4.30
727 3156 2.045926 ATGGTCGAGGCAGTTGGC 60.046 61.111 0.00 0.00 43.74 4.52
760 3189 3.010138 AGCTGGGTTTTGATGCTTAGGTA 59.990 43.478 0.00 0.00 0.00 3.08
761 3190 3.128764 GCTGGGTTTTGATGCTTAGGTAC 59.871 47.826 0.00 0.00 0.00 3.34
762 3191 3.340034 TGGGTTTTGATGCTTAGGTACG 58.660 45.455 0.00 0.00 0.00 3.67
764 3193 3.340928 GGTTTTGATGCTTAGGTACGGT 58.659 45.455 0.00 0.00 0.00 4.83
812 3268 2.033448 TGGTCGAAAAGGCGGCAT 59.967 55.556 13.08 0.00 37.68 4.40
904 3710 5.163642 CGCTACTAGTAGTGTGTGAAGGATT 60.164 44.000 28.04 0.00 38.50 3.01
957 3790 8.543774 GTCAATTATACTGTAAGCTCATCACAC 58.456 37.037 0.00 0.00 37.60 3.82
1059 4255 2.433446 CACCTGTCTGCCTGCCTT 59.567 61.111 0.00 0.00 0.00 4.35
1084 4300 0.248289 GAGGGATTTTGACGTCCGGA 59.752 55.000 14.12 0.00 35.28 5.14
1491 4921 7.609532 ACTTGCTTGAAAGAAATATCTGCTAGT 59.390 33.333 0.00 0.00 35.59 2.57
1691 5151 2.289694 ACGTGATGGCCAATATAGGAGC 60.290 50.000 10.96 0.00 0.00 4.70
1958 5418 1.821216 TCCCGTGATTTTGCTTCCTC 58.179 50.000 0.00 0.00 0.00 3.71
1961 5421 1.394917 CCGTGATTTTGCTTCCTCTCG 59.605 52.381 0.00 0.00 0.00 4.04
1971 5431 0.674581 CTTCCTCTCGCATTGCACCA 60.675 55.000 9.69 0.00 0.00 4.17
1980 5440 1.659233 CATTGCACCACCGCTTCAA 59.341 52.632 0.00 0.00 0.00 2.69
2006 5490 0.815615 CCTTCACCGCTATTGGCTCC 60.816 60.000 0.00 0.00 39.13 4.70
2010 5494 4.626081 CCGCTATTGGCTCCCGGG 62.626 72.222 16.85 16.85 39.13 5.73
2048 5532 2.370189 GAGCTATAGTCTGGCAATGGGT 59.630 50.000 0.84 0.00 32.85 4.51
2059 5546 1.077501 CAATGGGTGGAGCCGATGT 60.078 57.895 0.00 0.00 35.75 3.06
2061 5548 2.593468 AATGGGTGGAGCCGATGTCG 62.593 60.000 0.00 0.00 35.75 4.35
2083 5579 1.545706 AACCTTCGAGCAGACCTCCC 61.546 60.000 0.00 0.00 37.27 4.30
2084 5580 1.684049 CCTTCGAGCAGACCTCCCT 60.684 63.158 0.00 0.00 37.27 4.20
2307 5845 1.647545 AAGTCGGCACCATTGATGCG 61.648 55.000 0.00 0.00 44.37 4.73
2339 5877 2.760650 TGTATGTCATCGAGCAGTTCCT 59.239 45.455 0.00 0.00 0.00 3.36
2400 5938 9.993454 GAATAGGCTCATGAGATAATATGCATA 57.007 33.333 27.04 9.27 0.00 3.14
2406 5944 8.763356 GCTCATGAGATAATATGCATAGCTAAC 58.237 37.037 27.04 5.38 0.00 2.34
2483 6021 3.840991 TCGCTAAGCTCCCTAATTCCTA 58.159 45.455 0.00 0.00 0.00 2.94
2484 6022 4.220724 TCGCTAAGCTCCCTAATTCCTAA 58.779 43.478 0.00 0.00 0.00 2.69
2548 6087 0.033011 AGTAGAGGATGTCACCGCCT 60.033 55.000 0.00 0.00 34.73 5.52
2582 6121 2.868044 GCAGAACTCGAGAGCAAAGGAA 60.868 50.000 21.68 0.00 0.00 3.36
2600 6139 0.538746 AATCGCACGGAAAAGGGGTT 60.539 50.000 0.00 0.00 0.00 4.11
2627 6166 4.202182 GGTACTTCTGTCGCCAATATGGTA 60.202 45.833 0.00 0.00 40.46 3.25
2662 6201 0.486879 AATTCCCACAAGCCCAAGGA 59.513 50.000 0.00 0.00 0.00 3.36
2666 6205 1.132881 TCCCACAAGCCCAAGGAAAAT 60.133 47.619 0.00 0.00 0.00 1.82
2681 6220 8.317679 CCCAAGGAAAATAATTATGTCCAACAA 58.682 33.333 21.94 0.00 0.00 2.83
2710 6252 7.756614 ACCAACTTTAAGAAGGGTAAGAAGAT 58.243 34.615 0.00 0.00 37.19 2.40
2716 6258 9.377312 CTTTAAGAAGGGTAAGAAGATCTTCAG 57.623 37.037 31.79 14.59 41.84 3.02
2741 6286 0.034670 ACAAGGGAGATGGCTGCTTC 60.035 55.000 0.00 0.00 32.36 3.86
2799 6344 3.243401 CCCAAACAAGTACAAGAAGCCAC 60.243 47.826 0.00 0.00 0.00 5.01
2800 6345 3.380004 CCAAACAAGTACAAGAAGCCACA 59.620 43.478 0.00 0.00 0.00 4.17
2803 6348 1.195448 CAAGTACAAGAAGCCACAGCG 59.805 52.381 0.00 0.00 46.67 5.18
2837 6382 2.563620 TGCCAACATGATTGTGAGCAAT 59.436 40.909 0.00 0.00 46.99 3.56
2925 6471 2.517402 GGGTGGACACGGTGCAAA 60.517 61.111 8.30 0.00 35.32 3.68
2927 6473 0.606944 GGGTGGACACGGTGCAAATA 60.607 55.000 8.30 0.00 35.32 1.40
2932 6478 3.128589 GTGGACACGGTGCAAATATTCAT 59.871 43.478 8.30 0.00 35.32 2.57
2933 6479 3.128415 TGGACACGGTGCAAATATTCATG 59.872 43.478 8.30 0.00 29.43 3.07
2971 6517 8.912988 ACATTTCATTGTTTTCTTCTTACCAGA 58.087 29.630 0.00 0.00 0.00 3.86
2982 6528 2.481441 TCTTACCAGATCACAGGCCAT 58.519 47.619 5.01 0.00 0.00 4.40
2984 6530 1.878211 TACCAGATCACAGGCCATGA 58.122 50.000 5.01 9.15 0.00 3.07
2999 6545 2.146342 CCATGAGTCCGTATTGATGGC 58.854 52.381 0.00 0.00 0.00 4.40
3035 6581 2.291209 TCTGTTCATGGTGTTGGCAT 57.709 45.000 0.00 0.00 0.00 4.40
3043 6589 0.251121 TGGTGTTGGCATGGTCGATT 60.251 50.000 0.00 0.00 0.00 3.34
3086 6632 0.657840 GTGCAACTGAAGAACGTGCT 59.342 50.000 0.00 0.00 0.00 4.40
3090 6636 1.063912 CAACTGAAGAACGTGCTGCAA 59.936 47.619 5.49 0.00 0.00 4.08
3094 6640 1.221414 GAAGAACGTGCTGCAAGTCT 58.779 50.000 20.86 15.78 35.30 3.24
3096 6642 0.941463 AGAACGTGCTGCAAGTCTCG 60.941 55.000 20.86 14.11 35.30 4.04
3111 6657 2.503356 AGTCTCGGCCATCAAGAAGAAT 59.497 45.455 2.24 0.00 0.00 2.40
3115 6661 2.158900 TCGGCCATCAAGAAGAATCTCC 60.159 50.000 2.24 0.00 33.77 3.71
3132 6678 2.192263 CTCCTTAGTGGCTCCCTTCTT 58.808 52.381 0.00 0.00 35.26 2.52
3172 6718 9.635520 TTAAGTTGGTCTTCGAGTCTAATAAAG 57.364 33.333 0.00 0.00 37.56 1.85
3195 6741 7.224522 AGTAGTTGTTACGAACTATGGACTT 57.775 36.000 9.37 0.00 39.89 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.465097 ACTGGGCTGATGCACTATGC 60.465 55.000 0.00 0.00 44.40 3.14
11 12 1.590932 GACTGGGCTGATGCACTATG 58.409 55.000 0.00 0.00 44.40 2.23
12 13 0.471617 GGACTGGGCTGATGCACTAT 59.528 55.000 0.00 0.00 44.40 2.12
13 14 0.909133 TGGACTGGGCTGATGCACTA 60.909 55.000 0.00 0.00 44.40 2.74
14 15 1.782201 TTGGACTGGGCTGATGCACT 61.782 55.000 0.00 0.00 44.40 4.40
15 16 0.682209 ATTGGACTGGGCTGATGCAC 60.682 55.000 0.00 0.00 44.33 4.57
16 17 0.681887 CATTGGACTGGGCTGATGCA 60.682 55.000 0.00 0.00 41.91 3.96
17 18 2.012902 GCATTGGACTGGGCTGATGC 62.013 60.000 0.00 0.00 38.76 3.91
18 19 0.681887 TGCATTGGACTGGGCTGATG 60.682 55.000 0.00 0.00 0.00 3.07
19 20 0.395311 CTGCATTGGACTGGGCTGAT 60.395 55.000 0.00 0.00 0.00 2.90
20 21 1.001764 CTGCATTGGACTGGGCTGA 60.002 57.895 0.00 0.00 0.00 4.26
21 22 2.050350 CCTGCATTGGACTGGGCTG 61.050 63.158 0.00 0.00 0.00 4.85
22 23 2.357836 CCTGCATTGGACTGGGCT 59.642 61.111 0.00 0.00 0.00 5.19
23 24 3.455469 GCCTGCATTGGACTGGGC 61.455 66.667 0.00 0.00 0.00 5.36
24 25 0.974010 ATTGCCTGCATTGGACTGGG 60.974 55.000 0.00 0.00 0.00 4.45
25 26 0.458669 GATTGCCTGCATTGGACTGG 59.541 55.000 0.00 0.00 0.00 4.00
26 27 1.179152 TGATTGCCTGCATTGGACTG 58.821 50.000 0.00 0.00 0.00 3.51
27 28 1.927487 TTGATTGCCTGCATTGGACT 58.073 45.000 0.00 0.00 0.00 3.85
28 29 2.340337 GTTTGATTGCCTGCATTGGAC 58.660 47.619 0.00 0.00 0.00 4.02
29 30 1.067706 CGTTTGATTGCCTGCATTGGA 60.068 47.619 0.00 0.00 0.00 3.53
30 31 1.352114 CGTTTGATTGCCTGCATTGG 58.648 50.000 0.00 0.00 0.00 3.16
31 32 0.717224 GCGTTTGATTGCCTGCATTG 59.283 50.000 0.00 0.00 0.00 2.82
32 33 0.317799 TGCGTTTGATTGCCTGCATT 59.682 45.000 0.00 0.00 0.00 3.56
33 34 0.533491 ATGCGTTTGATTGCCTGCAT 59.467 45.000 0.00 0.00 38.16 3.96
34 35 0.388778 CATGCGTTTGATTGCCTGCA 60.389 50.000 0.00 0.00 36.69 4.41
35 36 1.079875 CCATGCGTTTGATTGCCTGC 61.080 55.000 0.00 0.00 0.00 4.85
36 37 0.458889 CCCATGCGTTTGATTGCCTG 60.459 55.000 0.00 0.00 0.00 4.85
37 38 1.606885 CCCCATGCGTTTGATTGCCT 61.607 55.000 0.00 0.00 0.00 4.75
38 39 1.153588 CCCCATGCGTTTGATTGCC 60.154 57.895 0.00 0.00 0.00 4.52
39 40 0.179129 CTCCCCATGCGTTTGATTGC 60.179 55.000 0.00 0.00 0.00 3.56
40 41 0.457035 CCTCCCCATGCGTTTGATTG 59.543 55.000 0.00 0.00 0.00 2.67
41 42 0.331278 TCCTCCCCATGCGTTTGATT 59.669 50.000 0.00 0.00 0.00 2.57
42 43 0.107017 CTCCTCCCCATGCGTTTGAT 60.107 55.000 0.00 0.00 0.00 2.57
43 44 1.299648 CTCCTCCCCATGCGTTTGA 59.700 57.895 0.00 0.00 0.00 2.69
44 45 0.609131 AACTCCTCCCCATGCGTTTG 60.609 55.000 0.00 0.00 0.00 2.93
45 46 0.609131 CAACTCCTCCCCATGCGTTT 60.609 55.000 0.00 0.00 0.00 3.60
46 47 1.002134 CAACTCCTCCCCATGCGTT 60.002 57.895 0.00 0.00 0.00 4.84
47 48 1.779061 AACAACTCCTCCCCATGCGT 61.779 55.000 0.00 0.00 0.00 5.24
48 49 0.609131 AAACAACTCCTCCCCATGCG 60.609 55.000 0.00 0.00 0.00 4.73
49 50 1.546029 GAAAACAACTCCTCCCCATGC 59.454 52.381 0.00 0.00 0.00 4.06
50 51 2.171003 GGAAAACAACTCCTCCCCATG 58.829 52.381 0.00 0.00 0.00 3.66
51 52 2.073776 AGGAAAACAACTCCTCCCCAT 58.926 47.619 0.00 0.00 39.16 4.00
52 53 1.529744 AGGAAAACAACTCCTCCCCA 58.470 50.000 0.00 0.00 39.16 4.96
53 54 3.801307 TTAGGAAAACAACTCCTCCCC 57.199 47.619 0.00 0.00 42.56 4.81
54 55 4.663334 ACATTAGGAAAACAACTCCTCCC 58.337 43.478 0.00 0.00 42.56 4.30
55 56 9.057089 CATATACATTAGGAAAACAACTCCTCC 57.943 37.037 0.00 0.00 42.56 4.30
56 57 8.560374 GCATATACATTAGGAAAACAACTCCTC 58.440 37.037 0.00 0.00 42.56 3.71
57 58 8.052748 TGCATATACATTAGGAAAACAACTCCT 58.947 33.333 0.00 0.00 45.56 3.69
58 59 8.220755 TGCATATACATTAGGAAAACAACTCC 57.779 34.615 0.00 0.00 0.00 3.85
59 60 9.503427 GTTGCATATACATTAGGAAAACAACTC 57.497 33.333 0.00 0.00 32.06 3.01
60 61 9.243105 AGTTGCATATACATTAGGAAAACAACT 57.757 29.630 0.00 0.00 38.32 3.16
61 62 9.503427 GAGTTGCATATACATTAGGAAAACAAC 57.497 33.333 0.00 0.00 34.28 3.32
62 63 9.237187 TGAGTTGCATATACATTAGGAAAACAA 57.763 29.630 0.00 0.00 0.00 2.83
63 64 8.800370 TGAGTTGCATATACATTAGGAAAACA 57.200 30.769 0.00 0.00 0.00 2.83
67 68 9.166173 GCATATGAGTTGCATATACATTAGGAA 57.834 33.333 6.97 0.00 46.03 3.36
68 69 8.320617 TGCATATGAGTTGCATATACATTAGGA 58.679 33.333 6.97 0.00 46.03 2.94
69 70 8.496707 TGCATATGAGTTGCATATACATTAGG 57.503 34.615 6.97 0.00 46.03 2.69
81 82 2.358957 TGGTGTCTGCATATGAGTTGC 58.641 47.619 6.97 0.00 40.55 4.17
82 83 4.379813 GGTTTGGTGTCTGCATATGAGTTG 60.380 45.833 6.97 0.00 0.00 3.16
83 84 3.758554 GGTTTGGTGTCTGCATATGAGTT 59.241 43.478 6.97 0.00 0.00 3.01
84 85 3.244875 TGGTTTGGTGTCTGCATATGAGT 60.245 43.478 6.97 0.00 0.00 3.41
85 86 3.127548 GTGGTTTGGTGTCTGCATATGAG 59.872 47.826 6.97 1.43 0.00 2.90
86 87 3.081061 GTGGTTTGGTGTCTGCATATGA 58.919 45.455 6.97 0.00 0.00 2.15
87 88 2.159531 CGTGGTTTGGTGTCTGCATATG 60.160 50.000 0.00 0.00 0.00 1.78
88 89 2.083774 CGTGGTTTGGTGTCTGCATAT 58.916 47.619 0.00 0.00 0.00 1.78
89 90 1.202710 ACGTGGTTTGGTGTCTGCATA 60.203 47.619 0.00 0.00 0.00 3.14
90 91 0.465460 ACGTGGTTTGGTGTCTGCAT 60.465 50.000 0.00 0.00 0.00 3.96
91 92 1.078072 ACGTGGTTTGGTGTCTGCA 60.078 52.632 0.00 0.00 0.00 4.41
92 93 1.355210 CACGTGGTTTGGTGTCTGC 59.645 57.895 7.95 0.00 0.00 4.26
93 94 1.355210 GCACGTGGTTTGGTGTCTG 59.645 57.895 18.88 0.00 36.54 3.51
94 95 1.078072 TGCACGTGGTTTGGTGTCT 60.078 52.632 18.88 0.00 36.54 3.41
95 96 1.063488 GTGCACGTGGTTTGGTGTC 59.937 57.895 18.88 0.00 36.54 3.67
96 97 1.244697 TTGTGCACGTGGTTTGGTGT 61.245 50.000 18.88 0.00 36.54 4.16
97 98 0.800300 GTTGTGCACGTGGTTTGGTG 60.800 55.000 18.88 0.00 37.22 4.17
98 99 1.244697 TGTTGTGCACGTGGTTTGGT 61.245 50.000 18.88 0.00 0.00 3.67
99 100 0.102120 ATGTTGTGCACGTGGTTTGG 59.898 50.000 18.88 0.00 0.00 3.28
100 101 1.198767 CATGTTGTGCACGTGGTTTG 58.801 50.000 18.88 1.26 38.60 2.93
101 102 0.814457 ACATGTTGTGCACGTGGTTT 59.186 45.000 18.88 0.00 45.66 3.27
102 103 0.814457 AACATGTTGTGCACGTGGTT 59.186 45.000 18.88 7.20 39.54 3.67
103 104 0.814457 AAACATGTTGTGCACGTGGT 59.186 45.000 18.88 4.20 44.99 4.16
104 105 1.851666 GAAAACATGTTGTGCACGTGG 59.148 47.619 18.88 0.00 45.66 4.94
105 106 2.796304 AGAAAACATGTTGTGCACGTG 58.204 42.857 12.82 12.28 46.65 4.49
106 107 3.502191 AAGAAAACATGTTGTGCACGT 57.498 38.095 12.82 0.00 0.00 4.49
107 108 4.838665 AAAAGAAAACATGTTGTGCACG 57.161 36.364 12.82 0.00 0.00 5.34
108 109 4.787591 GCAAAAAGAAAACATGTTGTGCAC 59.212 37.500 12.82 10.75 30.68 4.57
109 110 4.453478 TGCAAAAAGAAAACATGTTGTGCA 59.547 33.333 12.82 9.28 35.24 4.57
110 111 4.967437 TGCAAAAAGAAAACATGTTGTGC 58.033 34.783 12.82 6.51 30.85 4.57
111 112 6.544622 ACATGCAAAAAGAAAACATGTTGTG 58.455 32.000 12.82 0.00 46.80 3.33
112 113 6.740411 ACATGCAAAAAGAAAACATGTTGT 57.260 29.167 12.82 6.37 46.80 3.32
113 114 9.372541 GAATACATGCAAAAAGAAAACATGTTG 57.627 29.630 12.82 0.00 46.80 3.33
114 115 9.107177 TGAATACATGCAAAAAGAAAACATGTT 57.893 25.926 4.92 4.92 46.80 2.71
118 119 9.322773 TGATTGAATACATGCAAAAAGAAAACA 57.677 25.926 0.00 0.00 0.00 2.83
121 122 9.708092 TGATGATTGAATACATGCAAAAAGAAA 57.292 25.926 0.00 0.00 0.00 2.52
122 123 9.708092 TTGATGATTGAATACATGCAAAAAGAA 57.292 25.926 0.00 0.00 0.00 2.52
123 124 9.878667 ATTGATGATTGAATACATGCAAAAAGA 57.121 25.926 0.00 0.00 0.00 2.52
125 126 9.654663 TGATTGATGATTGAATACATGCAAAAA 57.345 25.926 0.00 0.00 0.00 1.94
126 127 9.308318 CTGATTGATGATTGAATACATGCAAAA 57.692 29.630 0.00 0.00 0.00 2.44
127 128 7.436970 GCTGATTGATGATTGAATACATGCAAA 59.563 33.333 0.00 0.00 0.00 3.68
128 129 6.921307 GCTGATTGATGATTGAATACATGCAA 59.079 34.615 0.00 0.00 0.00 4.08
129 130 6.443792 GCTGATTGATGATTGAATACATGCA 58.556 36.000 0.00 0.00 0.00 3.96
130 131 5.862323 GGCTGATTGATGATTGAATACATGC 59.138 40.000 0.00 0.00 0.00 4.06
131 132 6.977213 TGGCTGATTGATGATTGAATACATG 58.023 36.000 0.00 0.00 0.00 3.21
132 133 7.591421 TTGGCTGATTGATGATTGAATACAT 57.409 32.000 0.00 0.00 0.00 2.29
133 134 6.460537 GCTTGGCTGATTGATGATTGAATACA 60.461 38.462 0.00 0.00 0.00 2.29
134 135 5.919141 GCTTGGCTGATTGATGATTGAATAC 59.081 40.000 0.00 0.00 0.00 1.89
135 136 5.831525 AGCTTGGCTGATTGATGATTGAATA 59.168 36.000 0.00 0.00 37.57 1.75
136 137 4.649674 AGCTTGGCTGATTGATGATTGAAT 59.350 37.500 0.00 0.00 37.57 2.57
137 138 4.021229 AGCTTGGCTGATTGATGATTGAA 58.979 39.130 0.00 0.00 37.57 2.69
138 139 3.628008 AGCTTGGCTGATTGATGATTGA 58.372 40.909 0.00 0.00 37.57 2.57
139 140 5.509716 TTAGCTTGGCTGATTGATGATTG 57.490 39.130 0.00 0.00 40.10 2.67
140 141 5.655532 AGTTTAGCTTGGCTGATTGATGATT 59.344 36.000 0.00 0.00 40.10 2.57
141 142 5.198965 AGTTTAGCTTGGCTGATTGATGAT 58.801 37.500 0.00 0.00 40.10 2.45
142 143 4.592942 AGTTTAGCTTGGCTGATTGATGA 58.407 39.130 0.00 0.00 40.10 2.92
143 144 4.397103 TGAGTTTAGCTTGGCTGATTGATG 59.603 41.667 0.00 0.00 40.10 3.07
144 145 4.592942 TGAGTTTAGCTTGGCTGATTGAT 58.407 39.130 0.00 0.00 40.10 2.57
145 146 4.005650 CTGAGTTTAGCTTGGCTGATTGA 58.994 43.478 0.00 0.00 40.10 2.57
146 147 4.005650 TCTGAGTTTAGCTTGGCTGATTG 58.994 43.478 0.00 0.00 40.10 2.67
147 148 4.260170 CTCTGAGTTTAGCTTGGCTGATT 58.740 43.478 0.00 0.00 40.10 2.57
148 149 3.871485 CTCTGAGTTTAGCTTGGCTGAT 58.129 45.455 0.00 0.00 40.10 2.90
149 150 2.613977 GCTCTGAGTTTAGCTTGGCTGA 60.614 50.000 6.53 0.00 40.10 4.26
150 151 1.736681 GCTCTGAGTTTAGCTTGGCTG 59.263 52.381 6.53 0.00 40.10 4.85
151 152 1.339535 GGCTCTGAGTTTAGCTTGGCT 60.340 52.381 6.53 0.00 43.41 4.75
152 153 1.090728 GGCTCTGAGTTTAGCTTGGC 58.909 55.000 6.53 0.00 38.80 4.52
153 154 2.479566 TGGCTCTGAGTTTAGCTTGG 57.520 50.000 6.53 0.00 38.80 3.61
154 155 2.681848 CCATGGCTCTGAGTTTAGCTTG 59.318 50.000 0.00 0.00 38.80 4.01
155 156 2.573462 TCCATGGCTCTGAGTTTAGCTT 59.427 45.455 6.96 0.00 38.80 3.74
156 157 2.191400 TCCATGGCTCTGAGTTTAGCT 58.809 47.619 6.96 0.00 38.80 3.32
157 158 2.698855 TCCATGGCTCTGAGTTTAGC 57.301 50.000 6.96 0.00 38.03 3.09
158 159 2.877168 GCATCCATGGCTCTGAGTTTAG 59.123 50.000 6.96 0.00 0.00 1.85
159 160 2.239402 TGCATCCATGGCTCTGAGTTTA 59.761 45.455 6.96 0.00 0.00 2.01
160 161 1.005097 TGCATCCATGGCTCTGAGTTT 59.995 47.619 6.96 0.00 0.00 2.66
161 162 0.622136 TGCATCCATGGCTCTGAGTT 59.378 50.000 6.96 0.00 0.00 3.01
162 163 0.844660 ATGCATCCATGGCTCTGAGT 59.155 50.000 6.96 0.00 0.00 3.41
163 164 1.239347 CATGCATCCATGGCTCTGAG 58.761 55.000 6.96 0.00 44.07 3.35
164 165 3.414486 CATGCATCCATGGCTCTGA 57.586 52.632 6.96 0.00 44.07 3.27
171 172 1.116308 TTTGCCTCCATGCATCCATG 58.884 50.000 0.00 0.00 46.70 3.66
172 173 1.868713 TTTTGCCTCCATGCATCCAT 58.131 45.000 0.00 0.00 41.70 3.41
173 174 1.642112 TTTTTGCCTCCATGCATCCA 58.358 45.000 0.00 0.00 41.70 3.41
189 190 6.430000 ACTGATTAGTTACCTGCATCGTTTTT 59.570 34.615 0.00 0.00 31.66 1.94
190 191 5.938125 ACTGATTAGTTACCTGCATCGTTTT 59.062 36.000 0.00 0.00 31.66 2.43
191 192 5.488341 ACTGATTAGTTACCTGCATCGTTT 58.512 37.500 0.00 0.00 31.66 3.60
192 193 5.086104 ACTGATTAGTTACCTGCATCGTT 57.914 39.130 0.00 0.00 31.66 3.85
193 194 4.441634 GGACTGATTAGTTACCTGCATCGT 60.442 45.833 0.00 0.00 37.25 3.73
194 195 4.051922 GGACTGATTAGTTACCTGCATCG 58.948 47.826 0.00 0.00 37.25 3.84
195 196 5.053145 CAGGACTGATTAGTTACCTGCATC 58.947 45.833 11.12 0.00 40.17 3.91
196 197 4.716784 TCAGGACTGATTAGTTACCTGCAT 59.283 41.667 16.48 0.00 43.54 3.96
197 198 4.093743 TCAGGACTGATTAGTTACCTGCA 58.906 43.478 16.48 6.85 43.54 4.41
198 199 4.737855 TCAGGACTGATTAGTTACCTGC 57.262 45.455 16.48 0.00 43.54 4.85
199 200 6.287589 ACTTCAGGACTGATTAGTTACCTG 57.712 41.667 15.58 15.58 44.47 4.00
200 201 8.611051 ATTACTTCAGGACTGATTAGTTACCT 57.389 34.615 10.84 0.00 39.64 3.08
210 211 9.399797 TCGTACTAATAATTACTTCAGGACTGA 57.600 33.333 0.00 0.00 37.91 3.41
211 212 9.448294 GTCGTACTAATAATTACTTCAGGACTG 57.552 37.037 0.00 0.00 0.00 3.51
212 213 9.182214 TGTCGTACTAATAATTACTTCAGGACT 57.818 33.333 0.00 0.00 0.00 3.85
213 214 9.962783 ATGTCGTACTAATAATTACTTCAGGAC 57.037 33.333 0.00 0.00 0.00 3.85
215 216 9.961265 TGATGTCGTACTAATAATTACTTCAGG 57.039 33.333 0.00 0.00 0.00 3.86
225 226 8.995220 GCCCAATAATTGATGTCGTACTAATAA 58.005 33.333 0.00 0.00 0.00 1.40
226 227 8.372459 AGCCCAATAATTGATGTCGTACTAATA 58.628 33.333 0.00 0.00 0.00 0.98
227 228 7.224297 AGCCCAATAATTGATGTCGTACTAAT 58.776 34.615 0.00 0.00 0.00 1.73
228 229 6.588204 AGCCCAATAATTGATGTCGTACTAA 58.412 36.000 0.00 0.00 0.00 2.24
229 230 6.169557 AGCCCAATAATTGATGTCGTACTA 57.830 37.500 0.00 0.00 0.00 1.82
230 231 5.036117 AGCCCAATAATTGATGTCGTACT 57.964 39.130 0.00 0.00 0.00 2.73
231 232 5.989777 ACTAGCCCAATAATTGATGTCGTAC 59.010 40.000 0.00 0.00 0.00 3.67
235 236 4.823989 AGCACTAGCCCAATAATTGATGTC 59.176 41.667 0.00 0.00 43.56 3.06
249 250 4.182339 GTCTTTACCAACTAGCACTAGCC 58.818 47.826 4.58 0.00 43.56 3.93
264 268 5.354234 CACCTTATGTCCATGTGGTCTTTAC 59.646 44.000 0.00 0.00 36.34 2.01
268 272 3.055094 GTCACCTTATGTCCATGTGGTCT 60.055 47.826 0.00 0.00 36.34 3.85
269 273 3.055094 AGTCACCTTATGTCCATGTGGTC 60.055 47.826 0.00 0.00 36.34 4.02
270 274 2.912956 AGTCACCTTATGTCCATGTGGT 59.087 45.455 0.00 1.75 36.34 4.16
272 276 4.633126 CAGAAGTCACCTTATGTCCATGTG 59.367 45.833 0.00 0.00 35.62 3.21
282 291 5.884322 TGTACCTAGTCAGAAGTCACCTTA 58.116 41.667 0.00 0.00 0.00 2.69
294 303 4.080015 CCAAAATGGGGATGTACCTAGTCA 60.080 45.833 0.00 0.00 38.98 3.41
295 304 4.165372 TCCAAAATGGGGATGTACCTAGTC 59.835 45.833 0.00 0.00 38.32 2.59
296 305 4.116113 TCCAAAATGGGGATGTACCTAGT 58.884 43.478 0.00 0.00 38.32 2.57
297 306 4.788925 TCCAAAATGGGGATGTACCTAG 57.211 45.455 0.00 0.00 38.32 3.02
298 307 5.222358 TGTTTCCAAAATGGGGATGTACCTA 60.222 40.000 0.00 0.00 38.32 3.08
301 310 4.081697 CCTGTTTCCAAAATGGGGATGTAC 60.082 45.833 0.00 0.00 38.32 2.90
351 366 3.793144 CTCCTCGCGTTTGGCTGC 61.793 66.667 5.77 0.00 40.44 5.25
376 391 2.983592 GAACAACCGGGGCCAGTG 60.984 66.667 6.32 0.00 0.00 3.66
595 2936 2.315246 GATGGCCTCGATCAACTGC 58.685 57.895 3.32 0.00 0.00 4.40
610 2963 4.209911 ACTGTGTTGATAATGCGATCGATG 59.790 41.667 21.57 0.00 0.00 3.84
642 2995 2.043450 CTGCCCTCGTCCCTCTCT 60.043 66.667 0.00 0.00 0.00 3.10
760 3189 4.072131 ACAGTGCAGAAAATGATAACCGT 58.928 39.130 0.00 0.00 0.00 4.83
761 3190 4.685169 ACAGTGCAGAAAATGATAACCG 57.315 40.909 0.00 0.00 0.00 4.44
762 3191 5.048083 TCCAACAGTGCAGAAAATGATAACC 60.048 40.000 0.00 0.00 0.00 2.85
764 3193 5.335897 GCTCCAACAGTGCAGAAAATGATAA 60.336 40.000 0.00 0.00 35.02 1.75
812 3268 7.226523 CGTTCTGGTGATATATCATTGAAACCA 59.773 37.037 18.18 16.79 39.30 3.67
852 3645 1.213296 GATCCCCAGCCTTCTTGGTA 58.787 55.000 0.00 0.00 38.35 3.25
853 3646 1.915078 CGATCCCCAGCCTTCTTGGT 61.915 60.000 0.00 0.00 38.35 3.67
854 3647 1.153086 CGATCCCCAGCCTTCTTGG 60.153 63.158 0.00 0.00 39.35 3.61
855 3648 0.471617 ATCGATCCCCAGCCTTCTTG 59.528 55.000 0.00 0.00 0.00 3.02
904 3710 1.760029 GGGCTTGGAAAACTGGACAAA 59.240 47.619 0.00 0.00 0.00 2.83
957 3790 4.741676 CGCCTAAACTAATACTGTAACCCG 59.258 45.833 0.00 0.00 0.00 5.28
1059 4255 3.818773 GGACGTCAAAATCCCTCAAAAGA 59.181 43.478 18.91 0.00 0.00 2.52
1084 4300 3.372241 GCTCCCTCTACTCTAACTCACCT 60.372 52.174 0.00 0.00 0.00 4.00
1491 4921 4.081309 ACCTCACCGTAGCAAATTAAGCTA 60.081 41.667 8.09 8.09 43.25 3.32
1593 5026 4.435436 ACGATGCGCGGCAGAAGA 62.435 61.111 8.83 0.00 43.65 2.87
1691 5151 0.820871 CTCTTCCTCCTCCACTTCCG 59.179 60.000 0.00 0.00 0.00 4.30
1937 5397 1.886542 AGGAAGCAAAATCACGGGAAC 59.113 47.619 0.00 0.00 0.00 3.62
1958 5418 4.465512 GCGGTGGTGCAATGCGAG 62.466 66.667 0.00 0.00 34.15 5.03
1961 5421 2.126346 GAAGCGGTGGTGCAATGC 60.126 61.111 0.00 0.00 37.31 3.56
1986 5458 4.637771 GCCAATAGCGGTGAAGGT 57.362 55.556 0.00 0.00 0.00 3.50
2033 5517 0.911769 CTCCACCCATTGCCAGACTA 59.088 55.000 0.00 0.00 0.00 2.59
2059 5546 2.048222 CTGCTCGAAGGTTGGCGA 60.048 61.111 0.00 0.00 35.01 5.54
2061 5548 2.035442 GGTCTGCTCGAAGGTTGGC 61.035 63.158 0.00 0.00 0.00 4.52
2083 5579 4.463879 CTGCACCCCGGAGCTCAG 62.464 72.222 17.19 12.02 33.00 3.35
2288 5820 1.647545 CGCATCAATGGTGCCGACTT 61.648 55.000 13.41 0.00 39.39 3.01
2290 5822 2.404789 CGCATCAATGGTGCCGAC 59.595 61.111 13.41 0.00 39.39 4.79
2292 5824 3.891400 CCCGCATCAATGGTGCCG 61.891 66.667 13.41 6.37 39.39 5.69
2301 5839 2.839632 ATCTCGCTCCCCGCATCA 60.840 61.111 0.00 0.00 39.08 3.07
2307 5845 1.040646 TGACATACATCTCGCTCCCC 58.959 55.000 0.00 0.00 0.00 4.81
2339 5877 5.231357 CGATTCTCGACCATTTTGTAATCGA 59.769 40.000 8.05 0.00 44.24 3.59
2361 5899 4.404394 TGAGCCTATTCCAATACAGAACGA 59.596 41.667 0.00 0.00 0.00 3.85
2377 5915 7.289549 AGCTATGCATATTATCTCATGAGCCTA 59.710 37.037 18.36 9.06 0.00 3.93
2406 5944 2.520979 CACTTAGGAAGTTCGAGCTCG 58.479 52.381 30.03 30.03 40.46 5.03
2412 5950 4.863131 AGTAATTCGCACTTAGGAAGTTCG 59.137 41.667 5.25 5.25 46.93 3.95
2415 5953 5.681695 GCCTAGTAATTCGCACTTAGGAAGT 60.682 44.000 0.00 0.00 44.06 3.01
2447 5985 1.081906 GCGATTATGCATGCCGTGG 60.082 57.895 16.68 0.58 34.15 4.94
2449 5987 1.800586 CTTAGCGATTATGCATGCCGT 59.199 47.619 16.68 6.58 37.31 5.68
2453 5991 2.417933 GGGAGCTTAGCGATTATGCATG 59.582 50.000 10.16 0.00 35.47 4.06
2483 6021 4.953579 TCAAAGTGGTAGCAAAGTTCCTTT 59.046 37.500 0.00 0.00 33.58 3.11
2484 6022 4.532834 TCAAAGTGGTAGCAAAGTTCCTT 58.467 39.130 0.00 0.00 0.00 3.36
2503 6041 2.542020 TCACGCCTCTGATGTTTCAA 57.458 45.000 0.00 0.00 0.00 2.69
2548 6087 3.722147 GAGTTCTGCTCAACACTCAGAA 58.278 45.455 0.00 0.00 43.58 3.02
2582 6121 1.074248 AACCCCTTTTCCGTGCGAT 59.926 52.632 0.00 0.00 0.00 4.58
2600 6139 1.334160 TGGCGACAGAAGTACCTTCA 58.666 50.000 6.74 0.00 42.37 3.02
2627 6166 4.043310 TGGGAATTGAAGTTCCTCTGATGT 59.957 41.667 0.00 0.00 45.62 3.06
2681 6220 9.871175 TTCTTACCCTTCTTAAAGTTGGTATTT 57.129 29.630 0.00 0.00 32.59 1.40
2688 6227 9.727859 GAAGATCTTCTTACCCTTCTTAAAGTT 57.272 33.333 25.26 0.00 36.73 2.66
2710 6252 3.587498 TCTCCCTTGTTCTTCCTGAAGA 58.413 45.455 5.50 5.50 44.94 2.87
2716 6258 1.283321 AGCCATCTCCCTTGTTCTTCC 59.717 52.381 0.00 0.00 0.00 3.46
2727 6269 1.093159 CAAGTGAAGCAGCCATCTCC 58.907 55.000 0.00 0.00 0.00 3.71
2728 6270 1.467734 CACAAGTGAAGCAGCCATCTC 59.532 52.381 0.00 0.00 0.00 2.75
2729 6271 1.531423 CACAAGTGAAGCAGCCATCT 58.469 50.000 0.00 0.00 0.00 2.90
2741 6286 1.226746 GTTCCTCCGAACCACAAGTG 58.773 55.000 0.00 0.00 42.26 3.16
2799 6344 1.079543 CAGACTTGGAGTCCCGCTG 60.080 63.158 6.74 5.09 46.18 5.18
2800 6345 2.948720 GCAGACTTGGAGTCCCGCT 61.949 63.158 6.74 0.00 46.18 5.52
2803 6348 0.606673 GTTGGCAGACTTGGAGTCCC 60.607 60.000 6.74 1.29 46.18 4.46
2837 6382 3.202818 ACCCAGATGCACCATTCTCATTA 59.797 43.478 0.00 0.00 0.00 1.90
2879 6424 3.486875 CGGTGGACTGACAAACTGAAAAC 60.487 47.826 0.00 0.00 0.00 2.43
2925 6471 4.325972 TGTCAGCACACACACATGAATAT 58.674 39.130 0.00 0.00 0.00 1.28
2927 6473 2.574450 TGTCAGCACACACACATGAAT 58.426 42.857 0.00 0.00 0.00 2.57
2932 6478 2.363683 TGAAATGTCAGCACACACACA 58.636 42.857 0.00 0.00 34.48 3.72
2933 6479 3.631145 ATGAAATGTCAGCACACACAC 57.369 42.857 0.00 0.00 37.14 3.82
2971 6517 1.267574 ACGGACTCATGGCCTGTGAT 61.268 55.000 3.32 0.00 0.00 3.06
2982 6528 1.107945 TCGCCATCAATACGGACTCA 58.892 50.000 0.00 0.00 0.00 3.41
2984 6530 2.483876 CATTCGCCATCAATACGGACT 58.516 47.619 0.00 0.00 0.00 3.85
2999 6545 1.016130 AGAAGCACTCGCACCATTCG 61.016 55.000 0.00 0.00 42.27 3.34
3086 6632 0.674581 CTTGATGGCCGAGACTTGCA 60.675 55.000 0.00 0.00 0.00 4.08
3090 6636 1.561643 TCTTCTTGATGGCCGAGACT 58.438 50.000 0.00 0.00 35.06 3.24
3094 6640 2.158900 GGAGATTCTTCTTGATGGCCGA 60.159 50.000 0.00 0.00 30.30 5.54
3096 6642 3.574354 AGGAGATTCTTCTTGATGGCC 57.426 47.619 0.00 0.00 30.30 5.36
3111 6657 1.362932 AGAAGGGAGCCACTAAGGAGA 59.637 52.381 0.00 0.00 41.22 3.71
3115 6661 3.425162 ACAAAGAAGGGAGCCACTAAG 57.575 47.619 0.00 0.00 0.00 2.18
3132 6678 4.349930 ACCAACTTAAGCCCTTCTCTACAA 59.650 41.667 1.29 0.00 0.00 2.41
3145 6691 9.635520 TTTATTAGACTCGAAGACCAACTTAAG 57.364 33.333 0.00 0.00 39.13 1.85
3172 6718 7.880059 AAAGTCCATAGTTCGTAACAACTAC 57.120 36.000 0.00 0.00 40.80 2.73


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

AutoCloner maintained by Alex Coulton.