Multiple sequence alignment - TraesCS5D01G120900

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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 TraesCS5D01G120900 chr5D 100.000 3765 0 0 1 3765 172590604 172594368 0.000000e+00 6953
1 TraesCS5D01G120900 chr5D 97.067 341 9 1 1 340 52192281 52191941 1.170000e-159 573
2 TraesCS5D01G120900 chr5D 97.067 341 9 1 1 340 207708666 207708326 1.170000e-159 573
3 TraesCS5D01G120900 chr5D 97.067 341 9 1 1 340 264560015 264560355 1.170000e-159 573
4 TraesCS5D01G120900 chr5D 97.067 341 9 1 1 340 274654413 274654753 1.170000e-159 573
5 TraesCS5D01G120900 chr3B 95.502 3468 117 6 337 3765 422525308 422521841 0.000000e+00 5504
6 TraesCS5D01G120900 chr3B 95.212 3237 104 15 568 3765 589967431 589964207 0.000000e+00 5072
7 TraesCS5D01G120900 chr3B 89.655 232 24 0 339 570 589973163 589972932 2.840000e-76 296
8 TraesCS5D01G120900 chr3A 95.569 3453 119 24 338 3765 276940667 276944110 0.000000e+00 5498
9 TraesCS5D01G120900 chr6B 95.252 3475 115 18 330 3765 576574700 576571237 0.000000e+00 5457
10 TraesCS5D01G120900 chr6B 92.643 2297 135 17 1244 3507 436208032 436205737 0.000000e+00 3275
11 TraesCS5D01G120900 chr6B 92.593 594 38 4 339 926 467168881 467168288 0.000000e+00 848
12 TraesCS5D01G120900 chr6B 87.176 733 71 9 327 1054 162103204 162102490 0.000000e+00 811
13 TraesCS5D01G120900 chr6B 87.119 722 70 9 339 1054 516269707 516270411 0.000000e+00 797
14 TraesCS5D01G120900 chr6B 96.198 263 10 0 3503 3765 436205695 436205433 7.470000e-117 431
15 TraesCS5D01G120900 chr6B 84.496 129 13 4 1065 1187 356839598 356839471 1.840000e-23 121
16 TraesCS5D01G120900 chr5B 94.387 2904 108 14 339 3199 245670648 245667757 0.000000e+00 4409
17 TraesCS5D01G120900 chr5B 83.813 278 43 2 339 615 208769613 208769337 2.880000e-66 263
18 TraesCS5D01G120900 chr4B 92.153 2294 142 7 1249 3507 249881858 249884148 0.000000e+00 3205
19 TraesCS5D01G120900 chr6A 93.899 1557 83 8 1958 3507 233245045 233246596 0.000000e+00 2338
20 TraesCS5D01G120900 chr6A 95.437 263 12 0 3503 3765 233246638 233246900 1.620000e-113 420
21 TraesCS5D01G120900 chr2A 93.320 1557 94 6 1958 3507 499392375 499390822 0.000000e+00 2290
22 TraesCS5D01G120900 chr2A 95.112 491 23 1 1244 1734 499393191 499392702 0.000000e+00 773
23 TraesCS5D01G120900 chr2A 93.487 261 17 0 3505 3765 499390778 499390518 4.560000e-104 388
24 TraesCS5D01G120900 chr1D 89.733 711 43 15 1051 1731 195768708 195769418 0.000000e+00 881
25 TraesCS5D01G120900 chr1D 90.476 588 49 4 1766 2347 195769580 195770166 0.000000e+00 769
26 TraesCS5D01G120900 chr1D 97.361 341 8 1 1 340 53123526 53123186 2.520000e-161 579
27 TraesCS5D01G120900 chr1D 97.067 341 9 1 1 340 428026685 428026345 1.170000e-159 573
28 TraesCS5D01G120900 chr4A 95.817 526 21 1 335 859 371047842 371047317 0.000000e+00 848
29 TraesCS5D01G120900 chr4A 95.316 491 22 1 1244 1734 360502211 360502700 0.000000e+00 778
30 TraesCS5D01G120900 chr4A 96.198 263 10 0 3503 3765 360504697 360504959 7.470000e-117 431
31 TraesCS5D01G120900 chr1B 95.927 491 20 0 1244 1734 334537334 334536844 0.000000e+00 797
32 TraesCS5D01G120900 chr1B 89.456 588 55 4 1766 2347 269642819 269642233 0.000000e+00 736
33 TraesCS5D01G120900 chr6D 97.067 341 9 1 1 340 45238517 45238857 1.170000e-159 573
34 TraesCS5D01G120900 chr6D 97.067 341 9 1 1 340 340545789 340545449 1.170000e-159 573
35 TraesCS5D01G120900 chr4D 97.067 341 9 1 1 340 301487003 301486663 1.170000e-159 573
36 TraesCS5D01G120900 chr5A 89.789 284 18 9 779 1054 220457906 220457626 1.660000e-93 353
37 TraesCS5D01G120900 chr2B 86.392 316 36 7 732 1044 268009348 268009037 4.660000e-89 339
38 TraesCS5D01G120900 chr7D 83.692 325 33 10 1140 1449 436397064 436397383 4.760000e-74 289
39 TraesCS5D01G120900 chr7A 88.024 167 8 4 612 778 558249260 558249414 1.790000e-43 187
40 TraesCS5D01G120900 chr7B 84.375 128 9 7 1065 1184 571571389 571571265 8.550000e-22 115


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 TraesCS5D01G120900 chr5D 172590604 172594368 3764 False 6953.000000 6953 100.0000 1 3765 1 chr5D.!!$F1 3764
1 TraesCS5D01G120900 chr3B 422521841 422525308 3467 True 5504.000000 5504 95.5020 337 3765 1 chr3B.!!$R1 3428
2 TraesCS5D01G120900 chr3B 589964207 589967431 3224 True 5072.000000 5072 95.2120 568 3765 1 chr3B.!!$R2 3197
3 TraesCS5D01G120900 chr3A 276940667 276944110 3443 False 5498.000000 5498 95.5690 338 3765 1 chr3A.!!$F1 3427
4 TraesCS5D01G120900 chr6B 576571237 576574700 3463 True 5457.000000 5457 95.2520 330 3765 1 chr6B.!!$R4 3435
5 TraesCS5D01G120900 chr6B 436205433 436208032 2599 True 1853.000000 3275 94.4205 1244 3765 2 chr6B.!!$R5 2521
6 TraesCS5D01G120900 chr6B 467168288 467168881 593 True 848.000000 848 92.5930 339 926 1 chr6B.!!$R3 587
7 TraesCS5D01G120900 chr6B 162102490 162103204 714 True 811.000000 811 87.1760 327 1054 1 chr6B.!!$R1 727
8 TraesCS5D01G120900 chr6B 516269707 516270411 704 False 797.000000 797 87.1190 339 1054 1 chr6B.!!$F1 715
9 TraesCS5D01G120900 chr5B 245667757 245670648 2891 True 4409.000000 4409 94.3870 339 3199 1 chr5B.!!$R2 2860
10 TraesCS5D01G120900 chr4B 249881858 249884148 2290 False 3205.000000 3205 92.1530 1249 3507 1 chr4B.!!$F1 2258
11 TraesCS5D01G120900 chr6A 233245045 233246900 1855 False 1379.000000 2338 94.6680 1958 3765 2 chr6A.!!$F1 1807
12 TraesCS5D01G120900 chr2A 499390518 499393191 2673 True 1150.333333 2290 93.9730 1244 3765 3 chr2A.!!$R1 2521
13 TraesCS5D01G120900 chr1D 195768708 195770166 1458 False 825.000000 881 90.1045 1051 2347 2 chr1D.!!$F1 1296
14 TraesCS5D01G120900 chr4A 371047317 371047842 525 True 848.000000 848 95.8170 335 859 1 chr4A.!!$R1 524
15 TraesCS5D01G120900 chr4A 360502211 360504959 2748 False 604.500000 778 95.7570 1244 3765 2 chr4A.!!$F1 2521
16 TraesCS5D01G120900 chr1B 269642233 269642819 586 True 736.000000 736 89.4560 1766 2347 1 chr1B.!!$R1 581

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
69 70 0.039035 AGGGAAGGCCGTATTTGCAA 59.961 50.000 0.00 0.0 33.83 4.08 F
184 185 0.168788 CGCACACCATCATCACCAAC 59.831 55.000 0.00 0.0 0.00 3.77 F
186 187 1.470098 GCACACCATCATCACCAACTC 59.530 52.381 0.00 0.0 0.00 3.01 F
2314 2662 0.460987 GGACCTCTGGTTCGAGCATG 60.461 60.000 0.53 0.0 35.25 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1339 1358 6.132658 TGAAGCTGTGACTCTCTATTATCCT 58.867 40.000 0.00 0.00 0.00 3.24 R
2118 2465 1.466167 CGAGTTCCTCCAACAATGCTG 59.534 52.381 0.00 0.00 37.48 4.41 R
2317 2665 0.747644 TACAATCCGTGGCCATGCTG 60.748 55.000 20.27 17.05 0.00 4.41 R
3146 3512 1.997606 GCAACTCAAGTTATACGCCGT 59.002 47.619 0.00 0.00 36.32 5.68 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
31 32 9.448438 TGCATTTGTATGAGTAGTTTATCTTGT 57.552 29.630 0.00 0.00 33.37 3.16
32 33 9.708222 GCATTTGTATGAGTAGTTTATCTTGTG 57.292 33.333 0.00 0.00 33.37 3.33
37 38 9.462606 TGTATGAGTAGTTTATCTTGTGAGAGA 57.537 33.333 0.00 0.00 34.85 3.10
41 42 9.698309 TGAGTAGTTTATCTTGTGAGAGAAAAG 57.302 33.333 0.00 0.00 42.76 2.27
42 43 9.145865 GAGTAGTTTATCTTGTGAGAGAAAAGG 57.854 37.037 0.00 0.00 42.76 3.11
43 44 8.871125 AGTAGTTTATCTTGTGAGAGAAAAGGA 58.129 33.333 0.00 0.00 42.76 3.36
44 45 9.660180 GTAGTTTATCTTGTGAGAGAAAAGGAT 57.340 33.333 0.00 0.00 42.76 3.24
45 46 8.558973 AGTTTATCTTGTGAGAGAAAAGGATG 57.441 34.615 0.00 0.00 42.76 3.51
46 47 8.378565 AGTTTATCTTGTGAGAGAAAAGGATGA 58.621 33.333 0.00 0.00 42.76 2.92
47 48 9.003658 GTTTATCTTGTGAGAGAAAAGGATGAA 57.996 33.333 0.00 0.00 42.76 2.57
48 49 9.745018 TTTATCTTGTGAGAGAAAAGGATGAAT 57.255 29.630 0.00 0.00 39.44 2.57
49 50 7.627298 ATCTTGTGAGAGAAAAGGATGAATG 57.373 36.000 0.00 0.00 34.85 2.67
50 51 6.772605 TCTTGTGAGAGAAAAGGATGAATGA 58.227 36.000 0.00 0.00 0.00 2.57
51 52 6.877855 TCTTGTGAGAGAAAAGGATGAATGAG 59.122 38.462 0.00 0.00 0.00 2.90
52 53 5.494724 TGTGAGAGAAAAGGATGAATGAGG 58.505 41.667 0.00 0.00 0.00 3.86
53 54 4.880696 GTGAGAGAAAAGGATGAATGAGGG 59.119 45.833 0.00 0.00 0.00 4.30
54 55 4.784838 TGAGAGAAAAGGATGAATGAGGGA 59.215 41.667 0.00 0.00 0.00 4.20
55 56 5.251468 TGAGAGAAAAGGATGAATGAGGGAA 59.749 40.000 0.00 0.00 0.00 3.97
56 57 5.753716 AGAGAAAAGGATGAATGAGGGAAG 58.246 41.667 0.00 0.00 0.00 3.46
57 58 4.864726 AGAAAAGGATGAATGAGGGAAGG 58.135 43.478 0.00 0.00 0.00 3.46
58 59 2.744352 AAGGATGAATGAGGGAAGGC 57.256 50.000 0.00 0.00 0.00 4.35
59 60 0.849417 AGGATGAATGAGGGAAGGCC 59.151 55.000 0.00 0.00 0.00 5.19
60 61 0.536006 GGATGAATGAGGGAAGGCCG 60.536 60.000 0.00 0.00 33.83 6.13
61 62 0.181350 GATGAATGAGGGAAGGCCGT 59.819 55.000 0.00 0.00 33.83 5.68
62 63 1.416401 GATGAATGAGGGAAGGCCGTA 59.584 52.381 0.00 0.00 33.83 4.02
63 64 1.507140 TGAATGAGGGAAGGCCGTAT 58.493 50.000 0.00 0.00 33.83 3.06
64 65 1.843851 TGAATGAGGGAAGGCCGTATT 59.156 47.619 0.00 0.00 33.83 1.89
65 66 2.241176 TGAATGAGGGAAGGCCGTATTT 59.759 45.455 0.00 0.00 33.83 1.40
66 67 2.348411 ATGAGGGAAGGCCGTATTTG 57.652 50.000 0.00 0.00 33.83 2.32
67 68 0.393808 TGAGGGAAGGCCGTATTTGC 60.394 55.000 0.00 0.00 33.83 3.68
68 69 0.393808 GAGGGAAGGCCGTATTTGCA 60.394 55.000 0.00 0.00 33.83 4.08
69 70 0.039035 AGGGAAGGCCGTATTTGCAA 59.961 50.000 0.00 0.00 33.83 4.08
70 71 0.892063 GGGAAGGCCGTATTTGCAAA 59.108 50.000 15.44 15.44 33.83 3.68
71 72 1.403647 GGGAAGGCCGTATTTGCAAAC 60.404 52.381 15.41 2.12 33.83 2.93
72 73 1.613270 GAAGGCCGTATTTGCAAACG 58.387 50.000 15.41 15.25 38.80 3.60
73 74 0.955905 AAGGCCGTATTTGCAAACGT 59.044 45.000 15.41 1.77 37.40 3.99
74 75 0.239879 AGGCCGTATTTGCAAACGTG 59.760 50.000 15.41 10.31 37.40 4.49
75 76 0.731174 GGCCGTATTTGCAAACGTGG 60.731 55.000 15.41 16.37 37.40 4.94
76 77 0.238817 GCCGTATTTGCAAACGTGGA 59.761 50.000 22.69 0.00 37.40 4.02
77 78 1.727857 GCCGTATTTGCAAACGTGGAG 60.728 52.381 22.69 10.17 37.40 3.86
78 79 1.801771 CCGTATTTGCAAACGTGGAGA 59.198 47.619 15.41 0.00 37.40 3.71
79 80 2.159707 CCGTATTTGCAAACGTGGAGAG 60.160 50.000 15.41 0.00 37.40 3.20
80 81 2.159707 CGTATTTGCAAACGTGGAGAGG 60.160 50.000 15.41 0.00 34.48 3.69
81 82 1.247567 ATTTGCAAACGTGGAGAGGG 58.752 50.000 15.41 0.00 0.00 4.30
82 83 0.821711 TTTGCAAACGTGGAGAGGGG 60.822 55.000 8.05 0.00 0.00 4.79
83 84 1.990160 TTGCAAACGTGGAGAGGGGT 61.990 55.000 0.00 0.00 0.00 4.95
84 85 1.966451 GCAAACGTGGAGAGGGGTG 60.966 63.158 0.00 0.00 0.00 4.61
85 86 1.450211 CAAACGTGGAGAGGGGTGT 59.550 57.895 0.00 0.00 0.00 4.16
86 87 0.884704 CAAACGTGGAGAGGGGTGTG 60.885 60.000 0.00 0.00 0.00 3.82
87 88 2.052047 AAACGTGGAGAGGGGTGTGG 62.052 60.000 0.00 0.00 0.00 4.17
88 89 2.923035 CGTGGAGAGGGGTGTGGT 60.923 66.667 0.00 0.00 0.00 4.16
89 90 1.608336 CGTGGAGAGGGGTGTGGTA 60.608 63.158 0.00 0.00 0.00 3.25
90 91 0.976073 CGTGGAGAGGGGTGTGGTAT 60.976 60.000 0.00 0.00 0.00 2.73
91 92 1.687054 CGTGGAGAGGGGTGTGGTATA 60.687 57.143 0.00 0.00 0.00 1.47
92 93 2.690840 GTGGAGAGGGGTGTGGTATAT 58.309 52.381 0.00 0.00 0.00 0.86
93 94 3.046374 GTGGAGAGGGGTGTGGTATATT 58.954 50.000 0.00 0.00 0.00 1.28
94 95 3.458487 GTGGAGAGGGGTGTGGTATATTT 59.542 47.826 0.00 0.00 0.00 1.40
95 96 4.079958 GTGGAGAGGGGTGTGGTATATTTT 60.080 45.833 0.00 0.00 0.00 1.82
96 97 4.542525 TGGAGAGGGGTGTGGTATATTTTT 59.457 41.667 0.00 0.00 0.00 1.94
97 98 4.887655 GGAGAGGGGTGTGGTATATTTTTG 59.112 45.833 0.00 0.00 0.00 2.44
98 99 4.278310 AGAGGGGTGTGGTATATTTTTGC 58.722 43.478 0.00 0.00 0.00 3.68
99 100 4.020543 GAGGGGTGTGGTATATTTTTGCA 58.979 43.478 0.00 0.00 0.00 4.08
100 101 4.421131 AGGGGTGTGGTATATTTTTGCAA 58.579 39.130 0.00 0.00 0.00 4.08
101 102 4.841246 AGGGGTGTGGTATATTTTTGCAAA 59.159 37.500 8.05 8.05 0.00 3.68
102 103 5.308237 AGGGGTGTGGTATATTTTTGCAAAA 59.692 36.000 20.46 20.46 0.00 2.44
103 104 6.012945 AGGGGTGTGGTATATTTTTGCAAAAT 60.013 34.615 24.39 16.25 0.00 1.82
104 105 6.657117 GGGGTGTGGTATATTTTTGCAAAATT 59.343 34.615 24.39 21.79 0.00 1.82
105 106 7.361628 GGGGTGTGGTATATTTTTGCAAAATTG 60.362 37.037 24.39 0.00 0.00 2.32
124 125 9.305925 CAAAATTGCCATAGTTTTCTTCCTATC 57.694 33.333 0.00 0.00 0.00 2.08
125 126 7.588497 AATTGCCATAGTTTTCTTCCTATCC 57.412 36.000 0.00 0.00 0.00 2.59
126 127 4.703897 TGCCATAGTTTTCTTCCTATCCG 58.296 43.478 0.00 0.00 0.00 4.18
127 128 4.163458 TGCCATAGTTTTCTTCCTATCCGT 59.837 41.667 0.00 0.00 0.00 4.69
128 129 5.123936 GCCATAGTTTTCTTCCTATCCGTT 58.876 41.667 0.00 0.00 0.00 4.44
129 130 6.126997 TGCCATAGTTTTCTTCCTATCCGTTA 60.127 38.462 0.00 0.00 0.00 3.18
130 131 6.424207 GCCATAGTTTTCTTCCTATCCGTTAG 59.576 42.308 0.00 0.00 0.00 2.34
131 132 7.686127 GCCATAGTTTTCTTCCTATCCGTTAGA 60.686 40.741 0.00 0.00 0.00 2.10
132 133 8.368668 CCATAGTTTTCTTCCTATCCGTTAGAT 58.631 37.037 0.00 0.00 39.15 1.98
141 142 8.900781 TCTTCCTATCCGTTAGATATAAATCCG 58.099 37.037 0.00 0.00 36.84 4.18
142 143 8.812513 TTCCTATCCGTTAGATATAAATCCGA 57.187 34.615 0.00 0.00 36.84 4.55
143 144 8.218338 TCCTATCCGTTAGATATAAATCCGAC 57.782 38.462 0.00 0.00 36.84 4.79
144 145 7.830697 TCCTATCCGTTAGATATAAATCCGACA 59.169 37.037 0.00 0.00 36.84 4.35
145 146 8.129840 CCTATCCGTTAGATATAAATCCGACAG 58.870 40.741 0.00 0.00 36.84 3.51
146 147 5.706916 TCCGTTAGATATAAATCCGACAGC 58.293 41.667 0.00 0.00 31.98 4.40
147 148 4.863131 CCGTTAGATATAAATCCGACAGCC 59.137 45.833 0.00 0.00 31.98 4.85
148 149 5.336531 CCGTTAGATATAAATCCGACAGCCT 60.337 44.000 0.00 0.00 31.98 4.58
149 150 6.127814 CCGTTAGATATAAATCCGACAGCCTA 60.128 42.308 0.00 0.00 31.98 3.93
150 151 7.416438 CCGTTAGATATAAATCCGACAGCCTAT 60.416 40.741 0.00 0.00 31.98 2.57
151 152 8.618677 CGTTAGATATAAATCCGACAGCCTATA 58.381 37.037 0.00 0.00 31.98 1.31
155 156 7.928706 AGATATAAATCCGACAGCCTATATTGC 59.071 37.037 0.00 0.00 31.98 3.56
156 157 3.769739 AATCCGACAGCCTATATTGCA 57.230 42.857 0.00 0.00 0.00 4.08
157 158 2.820059 TCCGACAGCCTATATTGCAG 57.180 50.000 0.00 0.00 0.00 4.41
158 159 1.344438 TCCGACAGCCTATATTGCAGG 59.656 52.381 0.00 0.00 36.16 4.85
159 160 1.344438 CCGACAGCCTATATTGCAGGA 59.656 52.381 0.00 0.00 34.91 3.86
160 161 2.027745 CCGACAGCCTATATTGCAGGAT 60.028 50.000 0.00 0.00 34.91 3.24
163 164 2.089980 CAGCCTATATTGCAGGATGGC 58.910 52.381 10.48 10.48 44.21 4.40
164 165 1.706866 AGCCTATATTGCAGGATGGCA 59.293 47.619 17.58 0.00 43.19 4.92
165 166 1.815003 GCCTATATTGCAGGATGGCAC 59.185 52.381 12.68 0.00 44.86 5.01
166 167 2.079158 CCTATATTGCAGGATGGCACG 58.921 52.381 0.00 0.00 44.86 5.34
167 168 1.466167 CTATATTGCAGGATGGCACGC 59.534 52.381 0.00 0.00 44.86 5.34
168 169 0.466007 ATATTGCAGGATGGCACGCA 60.466 50.000 0.00 0.00 44.86 5.24
169 170 1.375853 TATTGCAGGATGGCACGCAC 61.376 55.000 0.00 0.00 44.86 5.34
170 171 3.991888 TATTGCAGGATGGCACGCACA 62.992 52.381 0.00 0.00 44.86 4.57
171 172 4.107051 GCAGGATGGCACGCACAC 62.107 66.667 0.00 0.00 35.86 3.82
172 173 3.434319 CAGGATGGCACGCACACC 61.434 66.667 0.00 0.00 0.00 4.16
173 174 3.952508 AGGATGGCACGCACACCA 61.953 61.111 0.00 0.00 41.06 4.17
176 177 2.033911 ATGGCACGCACACCATCA 59.966 55.556 0.00 0.00 43.26 3.07
177 178 1.378911 ATGGCACGCACACCATCAT 60.379 52.632 0.00 0.00 43.26 2.45
178 179 1.378882 ATGGCACGCACACCATCATC 61.379 55.000 0.00 0.00 43.26 2.92
179 180 2.039974 GGCACGCACACCATCATCA 61.040 57.895 0.00 0.00 0.00 3.07
180 181 1.135315 GCACGCACACCATCATCAC 59.865 57.895 0.00 0.00 0.00 3.06
181 182 1.796151 CACGCACACCATCATCACC 59.204 57.895 0.00 0.00 0.00 4.02
182 183 0.954938 CACGCACACCATCATCACCA 60.955 55.000 0.00 0.00 0.00 4.17
183 184 0.250684 ACGCACACCATCATCACCAA 60.251 50.000 0.00 0.00 0.00 3.67
184 185 0.168788 CGCACACCATCATCACCAAC 59.831 55.000 0.00 0.00 0.00 3.77
185 186 1.538047 GCACACCATCATCACCAACT 58.462 50.000 0.00 0.00 0.00 3.16
186 187 1.470098 GCACACCATCATCACCAACTC 59.530 52.381 0.00 0.00 0.00 3.01
187 188 2.877300 GCACACCATCATCACCAACTCT 60.877 50.000 0.00 0.00 0.00 3.24
188 189 2.745821 CACACCATCATCACCAACTCTG 59.254 50.000 0.00 0.00 0.00 3.35
189 190 2.373169 ACACCATCATCACCAACTCTGT 59.627 45.455 0.00 0.00 0.00 3.41
190 191 3.181440 ACACCATCATCACCAACTCTGTT 60.181 43.478 0.00 0.00 0.00 3.16
191 192 3.822735 CACCATCATCACCAACTCTGTTT 59.177 43.478 0.00 0.00 0.00 2.83
192 193 4.279169 CACCATCATCACCAACTCTGTTTT 59.721 41.667 0.00 0.00 0.00 2.43
193 194 4.520492 ACCATCATCACCAACTCTGTTTTC 59.480 41.667 0.00 0.00 0.00 2.29
194 195 4.763793 CCATCATCACCAACTCTGTTTTCT 59.236 41.667 0.00 0.00 0.00 2.52
195 196 5.939883 CCATCATCACCAACTCTGTTTTCTA 59.060 40.000 0.00 0.00 0.00 2.10
196 197 6.600822 CCATCATCACCAACTCTGTTTTCTAT 59.399 38.462 0.00 0.00 0.00 1.98
197 198 7.121759 CCATCATCACCAACTCTGTTTTCTATT 59.878 37.037 0.00 0.00 0.00 1.73
198 199 7.672983 TCATCACCAACTCTGTTTTCTATTC 57.327 36.000 0.00 0.00 0.00 1.75
199 200 6.655003 TCATCACCAACTCTGTTTTCTATTCC 59.345 38.462 0.00 0.00 0.00 3.01
200 201 5.313712 TCACCAACTCTGTTTTCTATTCCC 58.686 41.667 0.00 0.00 0.00 3.97
201 202 5.073144 TCACCAACTCTGTTTTCTATTCCCT 59.927 40.000 0.00 0.00 0.00 4.20
202 203 5.412904 CACCAACTCTGTTTTCTATTCCCTC 59.587 44.000 0.00 0.00 0.00 4.30
203 204 5.310857 ACCAACTCTGTTTTCTATTCCCTCT 59.689 40.000 0.00 0.00 0.00 3.69
204 205 5.645497 CCAACTCTGTTTTCTATTCCCTCTG 59.355 44.000 0.00 0.00 0.00 3.35
205 206 6.234177 CAACTCTGTTTTCTATTCCCTCTGT 58.766 40.000 0.00 0.00 0.00 3.41
206 207 6.441088 ACTCTGTTTTCTATTCCCTCTGTT 57.559 37.500 0.00 0.00 0.00 3.16
207 208 6.468543 ACTCTGTTTTCTATTCCCTCTGTTC 58.531 40.000 0.00 0.00 0.00 3.18
208 209 5.805728 TCTGTTTTCTATTCCCTCTGTTCC 58.194 41.667 0.00 0.00 0.00 3.62
209 210 5.548056 TCTGTTTTCTATTCCCTCTGTTCCT 59.452 40.000 0.00 0.00 0.00 3.36
210 211 6.729100 TCTGTTTTCTATTCCCTCTGTTCCTA 59.271 38.462 0.00 0.00 0.00 2.94
211 212 7.236847 TCTGTTTTCTATTCCCTCTGTTCCTAA 59.763 37.037 0.00 0.00 0.00 2.69
212 213 7.751646 TGTTTTCTATTCCCTCTGTTCCTAAA 58.248 34.615 0.00 0.00 0.00 1.85
213 214 8.390921 TGTTTTCTATTCCCTCTGTTCCTAAAT 58.609 33.333 0.00 0.00 0.00 1.40
214 215 9.901172 GTTTTCTATTCCCTCTGTTCCTAAATA 57.099 33.333 0.00 0.00 0.00 1.40
219 220 9.853177 CTATTCCCTCTGTTCCTAAATATTTGT 57.147 33.333 11.05 0.00 0.00 2.83
220 221 8.753497 ATTCCCTCTGTTCCTAAATATTTGTC 57.247 34.615 11.05 0.00 0.00 3.18
221 222 7.510675 TCCCTCTGTTCCTAAATATTTGTCT 57.489 36.000 11.05 0.00 0.00 3.41
222 223 7.928873 TCCCTCTGTTCCTAAATATTTGTCTT 58.071 34.615 11.05 0.00 0.00 3.01
223 224 8.390921 TCCCTCTGTTCCTAAATATTTGTCTTT 58.609 33.333 11.05 0.00 0.00 2.52
224 225 9.025041 CCCTCTGTTCCTAAATATTTGTCTTTT 57.975 33.333 11.05 0.00 0.00 2.27
242 243 9.787532 TTGTCTTTTTAGAGATTTCAACAAGTG 57.212 29.630 0.00 0.00 0.00 3.16
243 244 9.173021 TGTCTTTTTAGAGATTTCAACAAGTGA 57.827 29.630 0.00 0.00 0.00 3.41
244 245 9.439537 GTCTTTTTAGAGATTTCAACAAGTGAC 57.560 33.333 0.00 0.00 35.39 3.67
245 246 9.396022 TCTTTTTAGAGATTTCAACAAGTGACT 57.604 29.630 0.00 0.00 35.39 3.41
248 249 9.607988 TTTTAGAGATTTCAACAAGTGACTACA 57.392 29.630 0.00 0.00 35.39 2.74
249 250 9.778741 TTTAGAGATTTCAACAAGTGACTACAT 57.221 29.630 0.00 0.00 35.39 2.29
252 253 9.376075 AGAGATTTCAACAAGTGACTACATATG 57.624 33.333 0.00 0.00 35.39 1.78
253 254 8.498054 AGATTTCAACAAGTGACTACATATGG 57.502 34.615 7.80 0.00 35.39 2.74
254 255 8.321353 AGATTTCAACAAGTGACTACATATGGA 58.679 33.333 7.80 0.00 35.39 3.41
255 256 7.905604 TTTCAACAAGTGACTACATATGGAG 57.094 36.000 13.77 13.77 35.39 3.86
256 257 5.419542 TCAACAAGTGACTACATATGGAGC 58.580 41.667 15.30 8.47 0.00 4.70
257 258 5.046663 TCAACAAGTGACTACATATGGAGCA 60.047 40.000 15.30 10.95 0.00 4.26
258 259 5.420725 ACAAGTGACTACATATGGAGCAA 57.579 39.130 15.30 0.16 0.00 3.91
259 260 5.804639 ACAAGTGACTACATATGGAGCAAA 58.195 37.500 15.30 0.00 0.00 3.68
260 261 6.237901 ACAAGTGACTACATATGGAGCAAAA 58.762 36.000 15.30 0.00 0.00 2.44
261 262 6.886459 ACAAGTGACTACATATGGAGCAAAAT 59.114 34.615 15.30 0.00 0.00 1.82
262 263 8.046708 ACAAGTGACTACATATGGAGCAAAATA 58.953 33.333 15.30 0.00 0.00 1.40
263 264 8.892723 CAAGTGACTACATATGGAGCAAAATAA 58.107 33.333 15.30 0.00 0.00 1.40
264 265 8.668510 AGTGACTACATATGGAGCAAAATAAG 57.331 34.615 15.30 0.00 0.00 1.73
265 266 8.267894 AGTGACTACATATGGAGCAAAATAAGT 58.732 33.333 15.30 0.00 0.00 2.24
266 267 8.338259 GTGACTACATATGGAGCAAAATAAGTG 58.662 37.037 15.30 0.00 0.00 3.16
267 268 8.264347 TGACTACATATGGAGCAAAATAAGTGA 58.736 33.333 15.30 0.00 0.00 3.41
268 269 9.109393 GACTACATATGGAGCAAAATAAGTGAA 57.891 33.333 15.30 0.00 0.00 3.18
269 270 9.632638 ACTACATATGGAGCAAAATAAGTGAAT 57.367 29.630 15.30 0.00 0.00 2.57
271 272 8.757982 ACATATGGAGCAAAATAAGTGAATCT 57.242 30.769 7.80 0.00 0.00 2.40
272 273 9.851686 ACATATGGAGCAAAATAAGTGAATCTA 57.148 29.630 7.80 0.00 0.00 1.98
274 275 9.851686 ATATGGAGCAAAATAAGTGAATCTACA 57.148 29.630 0.00 0.00 0.00 2.74
275 276 7.377766 TGGAGCAAAATAAGTGAATCTACAC 57.622 36.000 0.00 0.00 40.60 2.90
318 319 5.353394 ACATTCGTATGTGGTAGTCCATT 57.647 39.130 6.89 0.00 46.20 3.16
319 320 5.741011 ACATTCGTATGTGGTAGTCCATTT 58.259 37.500 6.89 0.00 46.20 2.32
320 321 5.584649 ACATTCGTATGTGGTAGTCCATTTG 59.415 40.000 6.89 0.00 46.20 2.32
321 322 5.408880 TTCGTATGTGGTAGTCCATTTGA 57.591 39.130 0.00 0.00 46.20 2.69
322 323 5.408880 TCGTATGTGGTAGTCCATTTGAA 57.591 39.130 0.00 0.00 46.20 2.69
323 324 5.795972 TCGTATGTGGTAGTCCATTTGAAA 58.204 37.500 0.00 0.00 46.20 2.69
324 325 6.411376 TCGTATGTGGTAGTCCATTTGAAAT 58.589 36.000 0.00 0.00 46.20 2.17
325 326 6.537301 TCGTATGTGGTAGTCCATTTGAAATC 59.463 38.462 0.00 0.00 46.20 2.17
367 368 5.693769 ACAATAAAGAGGCTAGCCAACTA 57.306 39.130 34.70 19.59 38.92 2.24
713 728 3.302347 CTCACTCCCTCGCCACACC 62.302 68.421 0.00 0.00 0.00 4.16
1339 1358 9.880157 GGTACAGAGTTTATGGTTACTGAAATA 57.120 33.333 0.00 0.00 0.00 1.40
1698 1747 7.492524 CCATGTCTATGCAGTCTTTCTAACTA 58.507 38.462 0.00 0.00 32.79 2.24
2118 2465 2.184579 CTCCTCGAACGGGGAAGC 59.815 66.667 16.58 0.00 45.40 3.86
2309 2657 1.001974 CATTGTGGACCTCTGGTTCGA 59.998 52.381 0.00 0.00 35.25 3.71
2310 2658 0.679505 TTGTGGACCTCTGGTTCGAG 59.320 55.000 0.00 0.00 35.25 4.04
2311 2659 1.079750 GTGGACCTCTGGTTCGAGC 60.080 63.158 0.00 0.00 35.25 5.03
2312 2660 1.533033 TGGACCTCTGGTTCGAGCA 60.533 57.895 0.53 0.00 35.25 4.26
2313 2661 0.904865 TGGACCTCTGGTTCGAGCAT 60.905 55.000 0.53 0.00 35.25 3.79
2314 2662 0.460987 GGACCTCTGGTTCGAGCATG 60.461 60.000 0.53 0.00 35.25 4.06
2315 2663 0.460987 GACCTCTGGTTCGAGCATGG 60.461 60.000 0.53 0.00 35.25 3.66
2316 2664 1.817099 CCTCTGGTTCGAGCATGGC 60.817 63.158 0.53 0.00 0.00 4.40
2317 2665 1.817099 CTCTGGTTCGAGCATGGCC 60.817 63.158 0.00 0.00 0.00 5.36
2395 2753 0.464870 CAGATCCTCTGTGCTCCCTG 59.535 60.000 0.00 0.00 39.58 4.45
2864 3223 5.136816 TGCGTGTACAAATCTTACAGGTA 57.863 39.130 0.00 0.00 37.55 3.08
3188 3554 4.996758 GCCTACAAATGATTTTGCCAGTTT 59.003 37.500 0.00 0.00 45.01 2.66
3447 3814 6.494893 TTACATGCTAACTTGCTGGTTTAG 57.505 37.500 0.00 0.00 0.00 1.85
3718 4132 0.519077 GCTCGAGGTTTGCTTCCTTG 59.481 55.000 15.58 0.00 37.71 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.448438 ACAAGATAAACTACTCATACAAATGCA 57.552 29.630 0.00 0.00 32.76 3.96
6 7 9.708222 CACAAGATAAACTACTCATACAAATGC 57.292 33.333 0.00 0.00 32.76 3.56
11 12 9.462606 TCTCTCACAAGATAAACTACTCATACA 57.537 33.333 0.00 0.00 0.00 2.29
15 16 9.698309 CTTTTCTCTCACAAGATAAACTACTCA 57.302 33.333 0.00 0.00 30.02 3.41
16 17 9.145865 CCTTTTCTCTCACAAGATAAACTACTC 57.854 37.037 0.00 0.00 30.02 2.59
17 18 8.871125 TCCTTTTCTCTCACAAGATAAACTACT 58.129 33.333 0.00 0.00 30.02 2.57
18 19 9.660180 ATCCTTTTCTCTCACAAGATAAACTAC 57.340 33.333 0.00 0.00 30.02 2.73
19 20 9.658799 CATCCTTTTCTCTCACAAGATAAACTA 57.341 33.333 0.00 0.00 30.02 2.24
20 21 8.378565 TCATCCTTTTCTCTCACAAGATAAACT 58.621 33.333 0.00 0.00 30.02 2.66
21 22 8.553459 TCATCCTTTTCTCTCACAAGATAAAC 57.447 34.615 0.00 0.00 30.02 2.01
22 23 9.745018 ATTCATCCTTTTCTCTCACAAGATAAA 57.255 29.630 0.00 0.00 0.00 1.40
23 24 9.170734 CATTCATCCTTTTCTCTCACAAGATAA 57.829 33.333 0.00 0.00 0.00 1.75
24 25 8.542926 TCATTCATCCTTTTCTCTCACAAGATA 58.457 33.333 0.00 0.00 0.00 1.98
25 26 7.400439 TCATTCATCCTTTTCTCTCACAAGAT 58.600 34.615 0.00 0.00 0.00 2.40
26 27 6.772605 TCATTCATCCTTTTCTCTCACAAGA 58.227 36.000 0.00 0.00 0.00 3.02
27 28 6.093771 CCTCATTCATCCTTTTCTCTCACAAG 59.906 42.308 0.00 0.00 0.00 3.16
28 29 5.942236 CCTCATTCATCCTTTTCTCTCACAA 59.058 40.000 0.00 0.00 0.00 3.33
29 30 5.494724 CCTCATTCATCCTTTTCTCTCACA 58.505 41.667 0.00 0.00 0.00 3.58
30 31 4.880696 CCCTCATTCATCCTTTTCTCTCAC 59.119 45.833 0.00 0.00 0.00 3.51
31 32 4.784838 TCCCTCATTCATCCTTTTCTCTCA 59.215 41.667 0.00 0.00 0.00 3.27
32 33 5.365021 TCCCTCATTCATCCTTTTCTCTC 57.635 43.478 0.00 0.00 0.00 3.20
33 34 5.339861 CCTTCCCTCATTCATCCTTTTCTCT 60.340 44.000 0.00 0.00 0.00 3.10
34 35 4.886489 CCTTCCCTCATTCATCCTTTTCTC 59.114 45.833 0.00 0.00 0.00 2.87
35 36 4.864726 CCTTCCCTCATTCATCCTTTTCT 58.135 43.478 0.00 0.00 0.00 2.52
36 37 3.382865 GCCTTCCCTCATTCATCCTTTTC 59.617 47.826 0.00 0.00 0.00 2.29
37 38 3.369175 GCCTTCCCTCATTCATCCTTTT 58.631 45.455 0.00 0.00 0.00 2.27
38 39 2.358615 GGCCTTCCCTCATTCATCCTTT 60.359 50.000 0.00 0.00 0.00 3.11
39 40 1.216427 GGCCTTCCCTCATTCATCCTT 59.784 52.381 0.00 0.00 0.00 3.36
40 41 0.849417 GGCCTTCCCTCATTCATCCT 59.151 55.000 0.00 0.00 0.00 3.24
41 42 0.536006 CGGCCTTCCCTCATTCATCC 60.536 60.000 0.00 0.00 0.00 3.51
42 43 0.181350 ACGGCCTTCCCTCATTCATC 59.819 55.000 0.00 0.00 0.00 2.92
43 44 1.507140 TACGGCCTTCCCTCATTCAT 58.493 50.000 0.00 0.00 0.00 2.57
44 45 1.507140 ATACGGCCTTCCCTCATTCA 58.493 50.000 0.00 0.00 0.00 2.57
45 46 2.618709 CAAATACGGCCTTCCCTCATTC 59.381 50.000 0.00 0.00 0.00 2.67
46 47 2.654863 CAAATACGGCCTTCCCTCATT 58.345 47.619 0.00 0.00 0.00 2.57
47 48 1.750682 GCAAATACGGCCTTCCCTCAT 60.751 52.381 0.00 0.00 0.00 2.90
48 49 0.393808 GCAAATACGGCCTTCCCTCA 60.394 55.000 0.00 0.00 0.00 3.86
49 50 0.393808 TGCAAATACGGCCTTCCCTC 60.394 55.000 0.00 0.00 0.00 4.30
50 51 0.039035 TTGCAAATACGGCCTTCCCT 59.961 50.000 0.00 0.00 0.00 4.20
51 52 0.892063 TTTGCAAATACGGCCTTCCC 59.108 50.000 8.05 0.00 0.00 3.97
52 53 1.731098 CGTTTGCAAATACGGCCTTCC 60.731 52.381 16.21 0.00 34.30 3.46
53 54 1.068816 ACGTTTGCAAATACGGCCTTC 60.069 47.619 23.35 4.89 41.81 3.46
54 55 0.955905 ACGTTTGCAAATACGGCCTT 59.044 45.000 23.35 4.11 41.81 4.35
55 56 0.239879 CACGTTTGCAAATACGGCCT 59.760 50.000 23.35 4.43 41.81 5.19
56 57 0.731174 CCACGTTTGCAAATACGGCC 60.731 55.000 23.35 6.84 41.81 6.13
57 58 0.238817 TCCACGTTTGCAAATACGGC 59.761 50.000 23.35 7.50 41.81 5.68
58 59 1.801771 TCTCCACGTTTGCAAATACGG 59.198 47.619 23.35 18.73 41.81 4.02
59 60 2.159707 CCTCTCCACGTTTGCAAATACG 60.160 50.000 19.33 19.33 43.08 3.06
60 61 2.161609 CCCTCTCCACGTTTGCAAATAC 59.838 50.000 16.21 2.86 0.00 1.89
61 62 2.432444 CCCTCTCCACGTTTGCAAATA 58.568 47.619 16.21 0.00 0.00 1.40
62 63 1.247567 CCCTCTCCACGTTTGCAAAT 58.752 50.000 16.21 0.00 0.00 2.32
63 64 0.821711 CCCCTCTCCACGTTTGCAAA 60.822 55.000 8.05 8.05 0.00 3.68
64 65 1.228124 CCCCTCTCCACGTTTGCAA 60.228 57.895 0.00 0.00 0.00 4.08
65 66 2.429930 CCCCTCTCCACGTTTGCA 59.570 61.111 0.00 0.00 0.00 4.08
66 67 1.966451 CACCCCTCTCCACGTTTGC 60.966 63.158 0.00 0.00 0.00 3.68
67 68 0.884704 CACACCCCTCTCCACGTTTG 60.885 60.000 0.00 0.00 0.00 2.93
68 69 1.450211 CACACCCCTCTCCACGTTT 59.550 57.895 0.00 0.00 0.00 3.60
69 70 2.516888 CCACACCCCTCTCCACGTT 61.517 63.158 0.00 0.00 0.00 3.99
70 71 2.376225 TACCACACCCCTCTCCACGT 62.376 60.000 0.00 0.00 0.00 4.49
71 72 0.976073 ATACCACACCCCTCTCCACG 60.976 60.000 0.00 0.00 0.00 4.94
72 73 2.170012 TATACCACACCCCTCTCCAC 57.830 55.000 0.00 0.00 0.00 4.02
73 74 3.431411 AATATACCACACCCCTCTCCA 57.569 47.619 0.00 0.00 0.00 3.86
74 75 4.790718 AAAATATACCACACCCCTCTCC 57.209 45.455 0.00 0.00 0.00 3.71
75 76 4.338400 GCAAAAATATACCACACCCCTCTC 59.662 45.833 0.00 0.00 0.00 3.20
76 77 4.264172 TGCAAAAATATACCACACCCCTCT 60.264 41.667 0.00 0.00 0.00 3.69
77 78 4.020543 TGCAAAAATATACCACACCCCTC 58.979 43.478 0.00 0.00 0.00 4.30
78 79 4.054359 TGCAAAAATATACCACACCCCT 57.946 40.909 0.00 0.00 0.00 4.79
79 80 4.810191 TTGCAAAAATATACCACACCCC 57.190 40.909 0.00 0.00 0.00 4.95
80 81 7.525759 CAATTTTGCAAAAATATACCACACCC 58.474 34.615 27.10 0.00 0.00 4.61
98 99 9.305925 GATAGGAAGAAAACTATGGCAATTTTG 57.694 33.333 10.93 0.00 30.43 2.44
99 100 8.478066 GGATAGGAAGAAAACTATGGCAATTTT 58.522 33.333 7.07 7.07 30.43 1.82
100 101 7.201821 CGGATAGGAAGAAAACTATGGCAATTT 60.202 37.037 0.00 0.00 30.43 1.82
101 102 6.263168 CGGATAGGAAGAAAACTATGGCAATT 59.737 38.462 0.00 0.00 30.43 2.32
102 103 5.765182 CGGATAGGAAGAAAACTATGGCAAT 59.235 40.000 0.00 0.00 30.43 3.56
103 104 5.123227 CGGATAGGAAGAAAACTATGGCAA 58.877 41.667 0.00 0.00 30.43 4.52
104 105 4.163458 ACGGATAGGAAGAAAACTATGGCA 59.837 41.667 0.00 0.00 30.43 4.92
105 106 4.704965 ACGGATAGGAAGAAAACTATGGC 58.295 43.478 0.00 0.00 30.43 4.40
106 107 7.723324 TCTAACGGATAGGAAGAAAACTATGG 58.277 38.462 0.00 0.00 30.43 2.74
115 116 8.900781 CGGATTTATATCTAACGGATAGGAAGA 58.099 37.037 0.00 0.00 39.89 2.87
116 117 8.900781 TCGGATTTATATCTAACGGATAGGAAG 58.099 37.037 0.00 0.00 39.89 3.46
117 118 8.680903 GTCGGATTTATATCTAACGGATAGGAA 58.319 37.037 0.00 0.00 39.89 3.36
118 119 7.830697 TGTCGGATTTATATCTAACGGATAGGA 59.169 37.037 0.00 0.00 39.89 2.94
119 120 7.993101 TGTCGGATTTATATCTAACGGATAGG 58.007 38.462 0.00 0.00 39.89 2.57
120 121 7.644551 GCTGTCGGATTTATATCTAACGGATAG 59.355 40.741 9.67 0.00 39.89 2.08
121 122 7.415989 GGCTGTCGGATTTATATCTAACGGATA 60.416 40.741 9.67 0.00 40.69 2.59
122 123 6.331061 GCTGTCGGATTTATATCTAACGGAT 58.669 40.000 9.67 0.00 38.38 4.18
123 124 5.336213 GGCTGTCGGATTTATATCTAACGGA 60.336 44.000 9.67 0.00 0.00 4.69
124 125 4.863131 GGCTGTCGGATTTATATCTAACGG 59.137 45.833 0.00 0.00 0.00 4.44
125 126 5.710984 AGGCTGTCGGATTTATATCTAACG 58.289 41.667 0.00 0.00 0.00 3.18
129 130 7.928706 GCAATATAGGCTGTCGGATTTATATCT 59.071 37.037 0.00 0.00 0.00 1.98
130 131 7.710907 TGCAATATAGGCTGTCGGATTTATATC 59.289 37.037 0.00 0.00 0.00 1.63
131 132 7.564793 TGCAATATAGGCTGTCGGATTTATAT 58.435 34.615 0.00 0.00 0.00 0.86
132 133 6.941857 TGCAATATAGGCTGTCGGATTTATA 58.058 36.000 0.00 0.00 0.00 0.98
133 134 5.804639 TGCAATATAGGCTGTCGGATTTAT 58.195 37.500 0.00 0.00 0.00 1.40
134 135 5.222079 TGCAATATAGGCTGTCGGATTTA 57.778 39.130 0.00 0.00 0.00 1.40
135 136 4.067896 CTGCAATATAGGCTGTCGGATTT 58.932 43.478 0.00 0.00 0.00 2.17
136 137 3.557898 CCTGCAATATAGGCTGTCGGATT 60.558 47.826 0.00 0.00 0.00 3.01
137 138 2.027745 CCTGCAATATAGGCTGTCGGAT 60.028 50.000 0.00 0.00 0.00 4.18
138 139 1.344438 CCTGCAATATAGGCTGTCGGA 59.656 52.381 0.00 0.00 0.00 4.55
139 140 1.344438 TCCTGCAATATAGGCTGTCGG 59.656 52.381 0.00 0.00 35.23 4.79
140 141 2.820059 TCCTGCAATATAGGCTGTCG 57.180 50.000 0.00 0.00 35.23 4.35
141 142 3.341823 CCATCCTGCAATATAGGCTGTC 58.658 50.000 0.00 0.00 35.23 3.51
142 143 2.553904 GCCATCCTGCAATATAGGCTGT 60.554 50.000 0.00 0.00 37.67 4.40
143 144 2.089980 GCCATCCTGCAATATAGGCTG 58.910 52.381 0.00 0.00 37.67 4.85
144 145 1.706866 TGCCATCCTGCAATATAGGCT 59.293 47.619 15.13 0.00 41.12 4.58
145 146 1.815003 GTGCCATCCTGCAATATAGGC 59.185 52.381 9.23 9.23 44.11 3.93
146 147 2.079158 CGTGCCATCCTGCAATATAGG 58.921 52.381 0.00 0.00 44.11 2.57
147 148 1.466167 GCGTGCCATCCTGCAATATAG 59.534 52.381 0.00 0.00 44.11 1.31
148 149 1.202746 TGCGTGCCATCCTGCAATATA 60.203 47.619 0.00 0.00 44.11 0.86
149 150 0.466007 TGCGTGCCATCCTGCAATAT 60.466 50.000 0.00 0.00 44.11 1.28
150 151 1.077858 TGCGTGCCATCCTGCAATA 60.078 52.632 0.00 0.00 44.11 1.90
151 152 2.361483 TGCGTGCCATCCTGCAAT 60.361 55.556 0.00 0.00 44.11 3.56
152 153 3.364441 GTGCGTGCCATCCTGCAA 61.364 61.111 0.00 0.00 44.11 4.08
153 154 4.639906 TGTGCGTGCCATCCTGCA 62.640 61.111 0.00 0.00 39.37 4.41
154 155 4.107051 GTGTGCGTGCCATCCTGC 62.107 66.667 0.00 0.00 0.00 4.85
155 156 3.434319 GGTGTGCGTGCCATCCTG 61.434 66.667 0.00 0.00 0.00 3.86
156 157 3.272364 ATGGTGTGCGTGCCATCCT 62.272 57.895 0.60 0.00 41.24 3.24
157 158 2.751436 ATGGTGTGCGTGCCATCC 60.751 61.111 0.60 0.00 41.24 3.51
160 161 2.033911 ATGATGGTGTGCGTGCCA 59.966 55.556 0.00 0.00 39.33 4.92
161 162 2.039974 TGATGATGGTGTGCGTGCC 61.040 57.895 0.00 0.00 0.00 5.01
162 163 1.135315 GTGATGATGGTGTGCGTGC 59.865 57.895 0.00 0.00 0.00 5.34
163 164 0.954938 TGGTGATGATGGTGTGCGTG 60.955 55.000 0.00 0.00 0.00 5.34
164 165 0.250684 TTGGTGATGATGGTGTGCGT 60.251 50.000 0.00 0.00 0.00 5.24
165 166 0.168788 GTTGGTGATGATGGTGTGCG 59.831 55.000 0.00 0.00 0.00 5.34
166 167 1.470098 GAGTTGGTGATGATGGTGTGC 59.530 52.381 0.00 0.00 0.00 4.57
167 168 2.745821 CAGAGTTGGTGATGATGGTGTG 59.254 50.000 0.00 0.00 0.00 3.82
168 169 2.373169 ACAGAGTTGGTGATGATGGTGT 59.627 45.455 0.00 0.00 0.00 4.16
169 170 3.063510 ACAGAGTTGGTGATGATGGTG 57.936 47.619 0.00 0.00 0.00 4.17
170 171 3.795688 AACAGAGTTGGTGATGATGGT 57.204 42.857 0.00 0.00 0.00 3.55
171 172 4.763793 AGAAAACAGAGTTGGTGATGATGG 59.236 41.667 0.00 0.00 0.00 3.51
172 173 5.954296 AGAAAACAGAGTTGGTGATGATG 57.046 39.130 0.00 0.00 0.00 3.07
173 174 7.337942 GGAATAGAAAACAGAGTTGGTGATGAT 59.662 37.037 0.00 0.00 0.00 2.45
174 175 6.655003 GGAATAGAAAACAGAGTTGGTGATGA 59.345 38.462 0.00 0.00 0.00 2.92
175 176 6.127897 GGGAATAGAAAACAGAGTTGGTGATG 60.128 42.308 0.00 0.00 0.00 3.07
176 177 5.946377 GGGAATAGAAAACAGAGTTGGTGAT 59.054 40.000 0.00 0.00 0.00 3.06
177 178 5.073144 AGGGAATAGAAAACAGAGTTGGTGA 59.927 40.000 0.00 0.00 0.00 4.02
178 179 5.316987 AGGGAATAGAAAACAGAGTTGGTG 58.683 41.667 0.00 0.00 0.00 4.17
179 180 5.310857 AGAGGGAATAGAAAACAGAGTTGGT 59.689 40.000 0.00 0.00 0.00 3.67
180 181 5.645497 CAGAGGGAATAGAAAACAGAGTTGG 59.355 44.000 0.00 0.00 0.00 3.77
181 182 6.234177 ACAGAGGGAATAGAAAACAGAGTTG 58.766 40.000 0.00 0.00 0.00 3.16
182 183 6.441088 ACAGAGGGAATAGAAAACAGAGTT 57.559 37.500 0.00 0.00 0.00 3.01
183 184 6.441088 AACAGAGGGAATAGAAAACAGAGT 57.559 37.500 0.00 0.00 0.00 3.24
184 185 5.877564 GGAACAGAGGGAATAGAAAACAGAG 59.122 44.000 0.00 0.00 0.00 3.35
185 186 5.548056 AGGAACAGAGGGAATAGAAAACAGA 59.452 40.000 0.00 0.00 0.00 3.41
186 187 5.810095 AGGAACAGAGGGAATAGAAAACAG 58.190 41.667 0.00 0.00 0.00 3.16
187 188 5.843019 AGGAACAGAGGGAATAGAAAACA 57.157 39.130 0.00 0.00 0.00 2.83
188 189 8.809468 ATTTAGGAACAGAGGGAATAGAAAAC 57.191 34.615 0.00 0.00 0.00 2.43
193 194 9.853177 ACAAATATTTAGGAACAGAGGGAATAG 57.147 33.333 0.00 0.00 0.00 1.73
194 195 9.847224 GACAAATATTTAGGAACAGAGGGAATA 57.153 33.333 0.00 0.00 0.00 1.75
195 196 8.560903 AGACAAATATTTAGGAACAGAGGGAAT 58.439 33.333 0.00 0.00 0.00 3.01
196 197 7.928873 AGACAAATATTTAGGAACAGAGGGAA 58.071 34.615 0.00 0.00 0.00 3.97
197 198 7.510675 AGACAAATATTTAGGAACAGAGGGA 57.489 36.000 0.00 0.00 0.00 4.20
198 199 8.581253 AAAGACAAATATTTAGGAACAGAGGG 57.419 34.615 0.00 0.00 0.00 4.30
216 217 9.787532 CACTTGTTGAAATCTCTAAAAAGACAA 57.212 29.630 0.00 0.00 0.00 3.18
217 218 9.173021 TCACTTGTTGAAATCTCTAAAAAGACA 57.827 29.630 0.00 0.00 0.00 3.41
218 219 9.439537 GTCACTTGTTGAAATCTCTAAAAAGAC 57.560 33.333 0.00 0.00 35.39 3.01
219 220 9.396022 AGTCACTTGTTGAAATCTCTAAAAAGA 57.604 29.630 0.00 0.00 35.39 2.52
222 223 9.607988 TGTAGTCACTTGTTGAAATCTCTAAAA 57.392 29.630 0.00 0.00 35.39 1.52
223 224 9.778741 ATGTAGTCACTTGTTGAAATCTCTAAA 57.221 29.630 0.00 0.00 35.39 1.85
226 227 9.376075 CATATGTAGTCACTTGTTGAAATCTCT 57.624 33.333 0.00 0.00 35.39 3.10
227 228 8.607459 CCATATGTAGTCACTTGTTGAAATCTC 58.393 37.037 1.24 0.00 35.39 2.75
228 229 8.321353 TCCATATGTAGTCACTTGTTGAAATCT 58.679 33.333 1.24 0.00 35.39 2.40
229 230 8.492673 TCCATATGTAGTCACTTGTTGAAATC 57.507 34.615 1.24 0.00 35.39 2.17
230 231 7.066284 GCTCCATATGTAGTCACTTGTTGAAAT 59.934 37.037 1.24 0.00 35.39 2.17
231 232 6.371548 GCTCCATATGTAGTCACTTGTTGAAA 59.628 38.462 1.24 0.00 35.39 2.69
232 233 5.874810 GCTCCATATGTAGTCACTTGTTGAA 59.125 40.000 1.24 0.00 35.39 2.69
233 234 5.046663 TGCTCCATATGTAGTCACTTGTTGA 60.047 40.000 1.24 0.00 0.00 3.18
234 235 5.178061 TGCTCCATATGTAGTCACTTGTTG 58.822 41.667 1.24 0.00 0.00 3.33
235 236 5.420725 TGCTCCATATGTAGTCACTTGTT 57.579 39.130 1.24 0.00 0.00 2.83
236 237 5.420725 TTGCTCCATATGTAGTCACTTGT 57.579 39.130 1.24 0.00 0.00 3.16
237 238 6.741992 TTTTGCTCCATATGTAGTCACTTG 57.258 37.500 1.24 0.00 0.00 3.16
238 239 9.113838 CTTATTTTGCTCCATATGTAGTCACTT 57.886 33.333 1.24 0.00 0.00 3.16
239 240 8.267894 ACTTATTTTGCTCCATATGTAGTCACT 58.732 33.333 1.24 0.00 0.00 3.41
240 241 8.338259 CACTTATTTTGCTCCATATGTAGTCAC 58.662 37.037 1.24 0.00 0.00 3.67
241 242 8.264347 TCACTTATTTTGCTCCATATGTAGTCA 58.736 33.333 1.24 0.00 0.00 3.41
242 243 8.662781 TCACTTATTTTGCTCCATATGTAGTC 57.337 34.615 1.24 0.00 0.00 2.59
243 244 9.632638 ATTCACTTATTTTGCTCCATATGTAGT 57.367 29.630 1.24 0.00 0.00 2.73
245 246 9.851686 AGATTCACTTATTTTGCTCCATATGTA 57.148 29.630 1.24 0.00 0.00 2.29
246 247 8.757982 AGATTCACTTATTTTGCTCCATATGT 57.242 30.769 1.24 0.00 0.00 2.29
248 249 9.851686 TGTAGATTCACTTATTTTGCTCCATAT 57.148 29.630 0.00 0.00 0.00 1.78
249 250 9.109393 GTGTAGATTCACTTATTTTGCTCCATA 57.891 33.333 0.00 0.00 35.68 2.74
250 251 7.831193 AGTGTAGATTCACTTATTTTGCTCCAT 59.169 33.333 0.00 0.00 44.92 3.41
251 252 7.168219 AGTGTAGATTCACTTATTTTGCTCCA 58.832 34.615 0.00 0.00 44.92 3.86
252 253 7.550906 AGAGTGTAGATTCACTTATTTTGCTCC 59.449 37.037 0.98 0.00 46.81 4.70
253 254 8.485976 AGAGTGTAGATTCACTTATTTTGCTC 57.514 34.615 0.98 0.00 46.81 4.26
254 255 9.944376 TTAGAGTGTAGATTCACTTATTTTGCT 57.056 29.630 0.98 0.00 46.81 3.91
713 728 2.105128 GAGGGAGATGGTGCGACG 59.895 66.667 0.00 0.00 0.00 5.12
833 851 1.827399 GACCCGAGGACCTTGCAAGA 61.827 60.000 28.05 0.00 0.00 3.02
1277 1296 7.718314 AGATCTCATAAATGCACATACACATGT 59.282 33.333 0.00 0.00 46.58 3.21
1339 1358 6.132658 TGAAGCTGTGACTCTCTATTATCCT 58.867 40.000 0.00 0.00 0.00 3.24
1698 1747 6.796785 AGCCATAAACCTAGAAATTGCATT 57.203 33.333 0.00 0.00 0.00 3.56
2118 2465 1.466167 CGAGTTCCTCCAACAATGCTG 59.534 52.381 0.00 0.00 37.48 4.41
2316 2664 2.440796 AATCCGTGGCCATGCTGG 60.441 61.111 20.27 14.10 41.55 4.85
2317 2665 0.747644 TACAATCCGTGGCCATGCTG 60.748 55.000 20.27 17.05 0.00 4.41
3146 3512 1.997606 GCAACTCAAGTTATACGCCGT 59.002 47.619 0.00 0.00 36.32 5.68
3188 3554 6.428771 CCCTTGGTTATTCTAAGTTTTCGTCA 59.571 38.462 0.00 0.00 33.61 4.35
3447 3814 8.747538 ATTTCCTATATTCCACACACCTAAAC 57.252 34.615 0.00 0.00 0.00 2.01
3533 3946 5.288232 TCAGTTTGCAAGTTCAAAATTGACG 59.712 36.000 7.08 0.00 37.65 4.35


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

AutoCloner maintained by Alex Coulton.