Multiple sequence alignment - TraesCS5D01G335300

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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 TraesCS5D01G335300 chr5D 100.000 3761 0 0 1 3761 424595908 424599668 0.000000e+00 6946.0
1 TraesCS5D01G335300 chr5D 98.529 68 0 1 58 124 379111034 379110967 6.600000e-23 119.0
2 TraesCS5D01G335300 chr5D 95.745 47 1 1 2899 2944 489897225 489897179 1.450000e-09 75.0
3 TraesCS5D01G335300 chr5B 94.697 2093 93 2 687 2761 513646745 513648837 0.000000e+00 3234.0
4 TraesCS5D01G335300 chr5B 95.172 2009 87 2 869 2867 513711315 513713323 0.000000e+00 3164.0
5 TraesCS5D01G335300 chr5B 84.599 1870 250 24 911 2763 137112813 137110965 0.000000e+00 1823.0
6 TraesCS5D01G335300 chr5B 94.693 358 12 4 349 704 513710222 513710574 1.970000e-152 549.0
7 TraesCS5D01G335300 chr5B 93.627 204 11 2 3237 3440 513713577 513713778 1.700000e-78 303.0
8 TraesCS5D01G335300 chr5B 92.188 192 12 3 125 315 237141585 237141774 6.190000e-68 268.0
9 TraesCS5D01G335300 chr5B 85.769 260 20 8 2949 3191 513713328 513713587 3.730000e-65 259.0
10 TraesCS5D01G335300 chr5B 81.395 258 30 11 2942 3191 513649058 513649305 1.070000e-45 195.0
11 TraesCS5D01G335300 chr5B 86.264 182 7 2 689 853 513710596 513710776 8.300000e-42 182.0
12 TraesCS5D01G335300 chr5B 87.898 157 8 2 3246 3401 513649850 513649996 1.390000e-39 174.0
13 TraesCS5D01G335300 chr5B 90.909 88 6 1 2792 2879 513648974 513649059 2.370000e-22 117.0
14 TraesCS5D01G335300 chr5B 72.201 259 56 15 3488 3740 516893041 516892793 8.720000e-07 65.8
15 TraesCS5D01G335300 chr5A 93.646 1983 108 9 911 2879 538348951 538350929 0.000000e+00 2948.0
16 TraesCS5D01G335300 chr5A 85.569 1774 237 17 1006 2763 138430586 138428816 0.000000e+00 1840.0
17 TraesCS5D01G335300 chr5A 84.848 792 85 14 2981 3761 538350958 538351725 0.000000e+00 765.0
18 TraesCS5D01G335300 chr5A 82.043 646 42 24 314 911 538348279 538348898 2.030000e-132 483.0
19 TraesCS5D01G335300 chr7D 82.763 1723 259 19 1064 2766 531977411 531975707 0.000000e+00 1502.0
20 TraesCS5D01G335300 chr7D 81.839 1729 291 15 1010 2719 193935002 193936726 0.000000e+00 1432.0
21 TraesCS5D01G335300 chr7D 92.965 199 10 4 123 319 385865286 385865090 1.710000e-73 287.0
22 TraesCS5D01G335300 chr7D 92.308 195 12 3 123 315 294651802 294651995 1.330000e-69 274.0
23 TraesCS5D01G335300 chr7D 91.282 195 14 3 123 315 6713781 6713588 2.880000e-66 263.0
24 TraesCS5D01G335300 chr7D 95.652 46 1 1 2899 2943 5023111 5023156 5.210000e-09 73.1
25 TraesCS5D01G335300 chr7B 82.733 1720 263 17 1064 2766 572507610 572505908 0.000000e+00 1500.0
26 TraesCS5D01G335300 chr7B 81.829 1695 285 16 1071 2746 34168300 34169990 0.000000e+00 1402.0
27 TraesCS5D01G335300 chr7B 88.583 254 18 6 58 308 692028958 692028713 7.900000e-77 298.0
28 TraesCS5D01G335300 chr7B 91.748 206 12 4 123 325 614919286 614919083 7.950000e-72 281.0
29 TraesCS5D01G335300 chr1D 82.072 1718 274 25 1067 2766 344284178 344285879 0.000000e+00 1435.0
30 TraesCS5D01G335300 chr1D 81.797 1736 289 21 1025 2742 344676221 344674495 0.000000e+00 1430.0
31 TraesCS5D01G335300 chr1A 80.682 1760 293 30 1025 2766 444421746 444420016 0.000000e+00 1323.0
32 TraesCS5D01G335300 chr1A 93.462 260 12 3 58 315 300931580 300931836 7.620000e-102 381.0
33 TraesCS5D01G335300 chr1A 100.000 57 0 0 3 59 300929508 300929564 5.140000e-19 106.0
34 TraesCS5D01G335300 chr7A 80.731 1095 191 14 1688 2766 612532264 612531174 0.000000e+00 835.0
35 TraesCS5D01G335300 chr7A 80.247 81 13 3 3272 3351 610204989 610205067 1.460000e-04 58.4
36 TraesCS5D01G335300 chr2D 92.308 195 12 3 123 315 151665803 151665996 1.330000e-69 274.0
37 TraesCS5D01G335300 chr2D 86.486 74 5 2 2875 2943 569256745 569256818 4.030000e-10 76.8
38 TraesCS5D01G335300 chr2D 95.745 47 1 1 2899 2944 36277579 36277533 1.450000e-09 75.0
39 TraesCS5D01G335300 chr2D 95.652 46 1 1 2899 2943 270473973 270473928 5.210000e-09 73.1
40 TraesCS5D01G335300 chr3B 89.952 209 15 5 123 328 814647441 814647646 8.010000e-67 265.0
41 TraesCS5D01G335300 chr6A 91.765 85 5 2 58 141 126640433 126640350 2.370000e-22 117.0
42 TraesCS5D01G335300 chr6A 97.727 44 1 0 2900 2943 435774295 435774338 4.030000e-10 76.8
43 TraesCS5D01G335300 chr6A 97.059 34 1 0 3202 3235 454846958 454846991 1.460000e-04 58.4
44 TraesCS5D01G335300 chr4A 97.015 67 2 0 58 124 108419058 108418992 3.070000e-21 113.0
45 TraesCS5D01G335300 chr1B 97.727 44 1 0 2900 2943 668959991 668960034 4.030000e-10 76.8
46 TraesCS5D01G335300 chr4B 95.652 46 1 1 2899 2943 590440270 590440315 5.210000e-09 73.1
47 TraesCS5D01G335300 chr3D 89.831 59 2 3 2885 2943 524219734 524219788 5.210000e-09 73.1
48 TraesCS5D01G335300 chr2A 81.481 81 11 4 3272 3351 4013590 4013667 3.140000e-06 63.9
49 TraesCS5D01G335300 chr2A 80.247 81 13 3 3272 3351 238529870 238529948 1.460000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G335300 chr5D 424595908 424599668 3760 False 6946.000000 6946 100.000000 1 3761 1 chr5D.!!$F1 3760
1 TraesCS5D01G335300 chr5B 137110965 137112813 1848 True 1823.000000 1823 84.599000 911 2763 1 chr5B.!!$R1 1852
2 TraesCS5D01G335300 chr5B 513646745 513649996 3251 False 930.000000 3234 88.724750 687 3401 4 chr5B.!!$F2 2714
3 TraesCS5D01G335300 chr5B 513710222 513713778 3556 False 891.400000 3164 91.105000 349 3440 5 chr5B.!!$F3 3091
4 TraesCS5D01G335300 chr5A 138428816 138430586 1770 True 1840.000000 1840 85.569000 1006 2763 1 chr5A.!!$R1 1757
5 TraesCS5D01G335300 chr5A 538348279 538351725 3446 False 1398.666667 2948 86.845667 314 3761 3 chr5A.!!$F1 3447
6 TraesCS5D01G335300 chr7D 531975707 531977411 1704 True 1502.000000 1502 82.763000 1064 2766 1 chr7D.!!$R3 1702
7 TraesCS5D01G335300 chr7D 193935002 193936726 1724 False 1432.000000 1432 81.839000 1010 2719 1 chr7D.!!$F2 1709
8 TraesCS5D01G335300 chr7B 572505908 572507610 1702 True 1500.000000 1500 82.733000 1064 2766 1 chr7B.!!$R1 1702
9 TraesCS5D01G335300 chr7B 34168300 34169990 1690 False 1402.000000 1402 81.829000 1071 2746 1 chr7B.!!$F1 1675
10 TraesCS5D01G335300 chr1D 344284178 344285879 1701 False 1435.000000 1435 82.072000 1067 2766 1 chr1D.!!$F1 1699
11 TraesCS5D01G335300 chr1D 344674495 344676221 1726 True 1430.000000 1430 81.797000 1025 2742 1 chr1D.!!$R1 1717
12 TraesCS5D01G335300 chr1A 444420016 444421746 1730 True 1323.000000 1323 80.682000 1025 2766 1 chr1A.!!$R1 1741
13 TraesCS5D01G335300 chr1A 300929508 300931836 2328 False 243.500000 381 96.731000 3 315 2 chr1A.!!$F1 312
14 TraesCS5D01G335300 chr7A 612531174 612532264 1090 True 835.000000 835 80.731000 1688 2766 1 chr7A.!!$R1 1078

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
288 289 0.038801 GGTTTGCTCTCAGCCTTTGC 60.039 55.000 0.00 0.0 41.51 3.68 F
309 310 0.179084 CCATCGGCGTAACTGGTCAT 60.179 55.000 6.85 0.0 0.00 3.06 F
625 733 0.603975 GCCGGATGGATACCTGCTTC 60.604 60.000 5.05 0.0 37.49 3.86 F
729 875 0.759346 AGTTCGAAGCCTTGACCTGT 59.241 50.000 0.00 0.0 0.00 4.00 F
1593 2612 1.363080 GAGGATCGTAACTCCGGCC 59.637 63.158 0.00 0.0 37.88 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 3424 0.679002 GCATGGCCAGAGTCACATGT 60.679 55.000 13.05 0.0 41.94 3.21 R
2202 3961 1.976474 GAATGCCGGTGCCTTGGAA 60.976 57.895 1.90 0.0 36.33 3.53 R
2434 4193 0.650512 CCGTACTTATGCAACGCCAG 59.349 55.000 2.35 0.0 35.36 4.85 R
2689 4525 0.746204 GGCCTGCAGAAGTAGCCTTC 60.746 60.000 17.39 0.0 46.23 3.46 R
2944 4969 0.100503 GACGGCCCACAACATATTGC 59.899 55.000 0.00 0.0 39.66 3.56 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
59 60 8.424133 TCTCACTCTAATGTATACATTGCATGT 58.576 33.333 32.16 23.02 45.34 3.21
61 62 7.986889 TCACTCTAATGTATACATTGCATGTGT 59.013 33.333 32.16 22.61 45.34 3.72
62 63 9.260002 CACTCTAATGTATACATTGCATGTGTA 57.740 33.333 32.16 14.76 45.34 2.90
65 66 9.777297 TCTAATGTATACATTGCATGTGTATGT 57.223 29.630 32.16 16.93 45.34 2.29
68 69 8.681486 ATGTATACATTGCATGTGTATGTTCT 57.319 30.769 24.49 10.21 44.60 3.01
70 71 9.606631 TGTATACATTGCATGTGTATGTTCTAA 57.393 29.630 24.49 9.54 44.60 2.10
72 73 8.962884 ATACATTGCATGTGTATGTTCTAAGA 57.037 30.769 18.94 0.00 44.60 2.10
73 74 7.312657 ACATTGCATGTGTATGTTCTAAGAG 57.687 36.000 3.64 0.00 43.01 2.85
74 75 6.317140 ACATTGCATGTGTATGTTCTAAGAGG 59.683 38.462 3.64 0.00 43.01 3.69
76 77 5.664457 TGCATGTGTATGTTCTAAGAGGAG 58.336 41.667 0.00 0.00 36.65 3.69
79 80 5.073311 TGTGTATGTTCTAAGAGGAGCAC 57.927 43.478 0.00 0.00 29.89 4.40
80 81 4.526650 TGTGTATGTTCTAAGAGGAGCACA 59.473 41.667 0.00 0.00 29.89 4.57
81 82 5.011635 TGTGTATGTTCTAAGAGGAGCACAA 59.988 40.000 0.00 0.00 31.45 3.33
86 87 5.620206 TGTTCTAAGAGGAGCACAATTTCA 58.380 37.500 0.00 0.00 0.00 2.69
87 88 5.702670 TGTTCTAAGAGGAGCACAATTTCAG 59.297 40.000 0.00 0.00 0.00 3.02
89 90 6.114187 TCTAAGAGGAGCACAATTTCAGAA 57.886 37.500 0.00 0.00 0.00 3.02
90 91 6.169094 TCTAAGAGGAGCACAATTTCAGAAG 58.831 40.000 0.00 0.00 0.00 2.85
91 92 4.630644 AGAGGAGCACAATTTCAGAAGA 57.369 40.909 0.00 0.00 0.00 2.87
92 93 4.577875 AGAGGAGCACAATTTCAGAAGAG 58.422 43.478 0.00 0.00 0.00 2.85
93 94 4.041444 AGAGGAGCACAATTTCAGAAGAGT 59.959 41.667 0.00 0.00 0.00 3.24
94 95 5.247110 AGAGGAGCACAATTTCAGAAGAGTA 59.753 40.000 0.00 0.00 0.00 2.59
95 96 6.059787 AGGAGCACAATTTCAGAAGAGTAT 57.940 37.500 0.00 0.00 0.00 2.12
96 97 6.479884 AGGAGCACAATTTCAGAAGAGTATT 58.520 36.000 0.00 0.00 0.00 1.89
97 98 6.944862 AGGAGCACAATTTCAGAAGAGTATTT 59.055 34.615 0.00 0.00 0.00 1.40
98 99 7.449704 AGGAGCACAATTTCAGAAGAGTATTTT 59.550 33.333 0.00 0.00 0.00 1.82
99 100 8.084684 GGAGCACAATTTCAGAAGAGTATTTTT 58.915 33.333 0.00 0.00 0.00 1.94
127 128 8.970691 ATTTGAAGTGGTTTGATTTTCTATCG 57.029 30.769 0.00 0.00 0.00 2.92
128 129 7.737972 TTGAAGTGGTTTGATTTTCTATCGA 57.262 32.000 0.00 0.00 0.00 3.59
129 130 7.364522 TGAAGTGGTTTGATTTTCTATCGAG 57.635 36.000 0.00 0.00 0.00 4.04
130 131 7.158697 TGAAGTGGTTTGATTTTCTATCGAGA 58.841 34.615 0.00 0.00 0.00 4.04
131 132 6.969828 AGTGGTTTGATTTTCTATCGAGAC 57.030 37.500 0.00 0.00 0.00 3.36
132 133 6.702329 AGTGGTTTGATTTTCTATCGAGACT 58.298 36.000 0.00 0.00 0.00 3.24
133 134 7.162082 AGTGGTTTGATTTTCTATCGAGACTT 58.838 34.615 0.00 0.00 0.00 3.01
134 135 7.661847 AGTGGTTTGATTTTCTATCGAGACTTT 59.338 33.333 0.00 0.00 0.00 2.66
135 136 8.932791 GTGGTTTGATTTTCTATCGAGACTTTA 58.067 33.333 0.00 0.00 0.00 1.85
136 137 9.667107 TGGTTTGATTTTCTATCGAGACTTTAT 57.333 29.630 0.00 0.00 0.00 1.40
147 148 9.892130 TCTATCGAGACTTTATATCTAGCATCA 57.108 33.333 0.00 0.00 0.00 3.07
199 200 7.776618 AATAATCCTGTCCGTATGACTATCA 57.223 36.000 0.00 0.00 44.75 2.15
200 201 7.776618 ATAATCCTGTCCGTATGACTATCAA 57.223 36.000 0.00 0.00 44.75 2.57
201 202 4.913335 TCCTGTCCGTATGACTATCAAC 57.087 45.455 0.00 0.00 44.75 3.18
202 203 4.274978 TCCTGTCCGTATGACTATCAACA 58.725 43.478 0.00 0.00 44.75 3.33
203 204 4.707934 TCCTGTCCGTATGACTATCAACAA 59.292 41.667 0.00 0.00 44.75 2.83
204 205 5.362717 TCCTGTCCGTATGACTATCAACAAT 59.637 40.000 0.00 0.00 44.75 2.71
205 206 5.692204 CCTGTCCGTATGACTATCAACAATC 59.308 44.000 0.00 0.00 44.75 2.67
206 207 6.215495 TGTCCGTATGACTATCAACAATCA 57.785 37.500 0.00 0.00 44.75 2.57
207 208 6.816136 TGTCCGTATGACTATCAACAATCAT 58.184 36.000 0.00 0.00 44.75 2.45
210 211 8.082852 GTCCGTATGACTATCAACAATCATACT 58.917 37.037 16.83 0.00 46.15 2.12
238 239 9.739276 ATTTTCATATGTTTCCTTCTGTGTCTA 57.261 29.630 1.90 0.00 0.00 2.59
240 241 7.239763 TCATATGTTTCCTTCTGTGTCTACA 57.760 36.000 1.90 0.00 35.08 2.74
241 242 7.851228 TCATATGTTTCCTTCTGTGTCTACAT 58.149 34.615 1.90 0.00 35.97 2.29
246 247 8.918202 TGTTTCCTTCTGTGTCTACATATTTT 57.082 30.769 0.00 0.00 35.97 1.82
247 248 8.783093 TGTTTCCTTCTGTGTCTACATATTTTG 58.217 33.333 0.00 0.00 35.97 2.44
248 249 8.999431 GTTTCCTTCTGTGTCTACATATTTTGA 58.001 33.333 0.00 0.00 35.97 2.69
251 252 7.280876 TCCTTCTGTGTCTACATATTTTGATGC 59.719 37.037 0.00 0.00 35.97 3.91
252 253 7.066163 CCTTCTGTGTCTACATATTTTGATGCA 59.934 37.037 0.00 0.00 35.97 3.96
253 254 7.307493 TCTGTGTCTACATATTTTGATGCAC 57.693 36.000 0.00 0.00 35.97 4.57
254 255 6.878389 TCTGTGTCTACATATTTTGATGCACA 59.122 34.615 0.00 0.00 35.97 4.57
255 256 6.841119 TGTGTCTACATATTTTGATGCACAC 58.159 36.000 0.00 0.00 0.00 3.82
256 257 6.654582 TGTGTCTACATATTTTGATGCACACT 59.345 34.615 0.00 0.00 33.22 3.55
258 259 7.065085 GTGTCTACATATTTTGATGCACACTCT 59.935 37.037 0.00 0.00 0.00 3.24
259 260 7.607607 TGTCTACATATTTTGATGCACACTCTT 59.392 33.333 0.00 0.00 0.00 2.85
260 261 8.454106 GTCTACATATTTTGATGCACACTCTTT 58.546 33.333 0.00 0.00 0.00 2.52
261 262 8.668353 TCTACATATTTTGATGCACACTCTTTC 58.332 33.333 0.00 0.00 0.00 2.62
262 263 7.218228 ACATATTTTGATGCACACTCTTTCA 57.782 32.000 0.00 0.00 0.00 2.69
263 264 7.660112 ACATATTTTGATGCACACTCTTTCAA 58.340 30.769 0.00 0.00 0.00 2.69
264 265 8.308931 ACATATTTTGATGCACACTCTTTCAAT 58.691 29.630 0.00 0.00 0.00 2.57
265 266 9.791820 CATATTTTGATGCACACTCTTTCAATA 57.208 29.630 0.00 0.00 0.00 1.90
268 269 9.715121 ATTTTGATGCACACTCTTTCAATATTT 57.285 25.926 0.00 0.00 0.00 1.40
269 270 8.523523 TTTGATGCACACTCTTTCAATATTTG 57.476 30.769 0.00 0.00 0.00 2.32
270 271 6.623486 TGATGCACACTCTTTCAATATTTGG 58.377 36.000 0.00 0.00 0.00 3.28
271 272 6.209192 TGATGCACACTCTTTCAATATTTGGT 59.791 34.615 0.00 0.00 0.00 3.67
272 273 6.403866 TGCACACTCTTTCAATATTTGGTT 57.596 33.333 0.00 0.00 0.00 3.67
273 274 6.815089 TGCACACTCTTTCAATATTTGGTTT 58.185 32.000 0.00 0.00 0.00 3.27
274 275 6.700960 TGCACACTCTTTCAATATTTGGTTTG 59.299 34.615 0.00 0.00 0.00 2.93
275 276 6.346838 GCACACTCTTTCAATATTTGGTTTGC 60.347 38.462 0.00 0.00 0.00 3.68
276 277 6.925165 CACACTCTTTCAATATTTGGTTTGCT 59.075 34.615 0.00 0.00 0.00 3.91
277 278 7.115378 CACACTCTTTCAATATTTGGTTTGCTC 59.885 37.037 0.00 0.00 0.00 4.26
278 279 7.014615 ACACTCTTTCAATATTTGGTTTGCTCT 59.985 33.333 0.00 0.00 0.00 4.09
279 280 7.540055 CACTCTTTCAATATTTGGTTTGCTCTC 59.460 37.037 0.00 0.00 0.00 3.20
280 281 7.231317 ACTCTTTCAATATTTGGTTTGCTCTCA 59.769 33.333 0.00 0.00 0.00 3.27
281 282 7.596494 TCTTTCAATATTTGGTTTGCTCTCAG 58.404 34.615 0.00 0.00 0.00 3.35
282 283 5.314923 TCAATATTTGGTTTGCTCTCAGC 57.685 39.130 0.00 0.00 42.82 4.26
283 284 4.158394 TCAATATTTGGTTTGCTCTCAGCC 59.842 41.667 0.00 0.00 41.51 4.85
284 285 2.299326 ATTTGGTTTGCTCTCAGCCT 57.701 45.000 0.00 0.00 41.51 4.58
285 286 2.071778 TTTGGTTTGCTCTCAGCCTT 57.928 45.000 0.00 0.00 41.51 4.35
286 287 2.071778 TTGGTTTGCTCTCAGCCTTT 57.928 45.000 0.00 0.00 41.51 3.11
287 288 1.321474 TGGTTTGCTCTCAGCCTTTG 58.679 50.000 0.00 0.00 41.51 2.77
288 289 0.038801 GGTTTGCTCTCAGCCTTTGC 60.039 55.000 0.00 0.00 41.51 3.68
289 290 0.386478 GTTTGCTCTCAGCCTTTGCG 60.386 55.000 0.00 0.00 41.51 4.85
290 291 2.133742 TTTGCTCTCAGCCTTTGCGC 62.134 55.000 0.00 0.00 41.51 6.09
291 292 3.808656 GCTCTCAGCCTTTGCGCC 61.809 66.667 4.18 0.00 44.33 6.53
292 293 2.359107 CTCTCAGCCTTTGCGCCA 60.359 61.111 4.18 0.00 44.33 5.69
293 294 1.748122 CTCTCAGCCTTTGCGCCAT 60.748 57.895 4.18 0.00 44.33 4.40
294 295 1.712977 CTCTCAGCCTTTGCGCCATC 61.713 60.000 4.18 0.00 44.33 3.51
295 296 3.104602 CTCAGCCTTTGCGCCATCG 62.105 63.158 4.18 0.00 44.33 3.84
296 297 4.183686 CAGCCTTTGCGCCATCGG 62.184 66.667 4.18 0.72 44.33 4.18
306 307 2.125269 GCCATCGGCGTAACTGGT 60.125 61.111 6.85 0.00 39.62 4.00
307 308 2.171725 GCCATCGGCGTAACTGGTC 61.172 63.158 6.85 3.57 39.62 4.02
308 309 1.216977 CCATCGGCGTAACTGGTCA 59.783 57.895 6.85 0.00 0.00 4.02
309 310 0.179084 CCATCGGCGTAACTGGTCAT 60.179 55.000 6.85 0.00 0.00 3.06
310 311 1.209128 CATCGGCGTAACTGGTCATC 58.791 55.000 6.85 0.00 0.00 2.92
311 312 1.112113 ATCGGCGTAACTGGTCATCT 58.888 50.000 6.85 0.00 0.00 2.90
312 313 1.753930 TCGGCGTAACTGGTCATCTA 58.246 50.000 6.85 0.00 0.00 1.98
319 320 5.690857 GGCGTAACTGGTCATCTAGTTAATC 59.309 44.000 5.93 2.51 44.77 1.75
326 327 7.501844 ACTGGTCATCTAGTTAATCTAAAGCC 58.498 38.462 0.00 0.00 31.36 4.35
327 328 6.827727 TGGTCATCTAGTTAATCTAAAGCCC 58.172 40.000 0.00 0.00 0.00 5.19
331 332 5.272283 TCTAGTTAATCTAAAGCCCGGTG 57.728 43.478 0.00 0.00 0.00 4.94
340 341 2.730129 AAAGCCCGGTGGATGCCTTT 62.730 55.000 0.00 0.00 0.00 3.11
454 552 0.618458 TGCAACCACCCAGATCCTAC 59.382 55.000 0.00 0.00 0.00 3.18
455 553 0.618458 GCAACCACCCAGATCCTACA 59.382 55.000 0.00 0.00 0.00 2.74
483 581 4.388378 AGACCTTAGAGGATAACGTTGC 57.612 45.455 11.99 2.52 37.67 4.17
509 607 3.426159 CGAAGTTTTTGGCGATACATGCT 60.426 43.478 0.00 0.00 0.00 3.79
621 729 2.632996 TCTAAAGCCGGATGGATACCTG 59.367 50.000 5.05 0.00 37.49 4.00
625 733 0.603975 GCCGGATGGATACCTGCTTC 60.604 60.000 5.05 0.00 37.49 3.86
628 736 2.158755 CCGGATGGATACCTGCTTCTTT 60.159 50.000 0.00 0.00 37.49 2.52
630 738 3.947834 CGGATGGATACCTGCTTCTTTTT 59.052 43.478 0.00 0.00 0.00 1.94
729 875 0.759346 AGTTCGAAGCCTTGACCTGT 59.241 50.000 0.00 0.00 0.00 4.00
811 975 1.510623 GAAACACAGCTCGCATGCG 60.511 57.895 33.61 33.61 41.35 4.73
862 1383 1.671261 CGCACAGCTAGCTTCTCTGTT 60.671 52.381 16.46 0.00 38.85 3.16
972 1733 3.077359 GCTTGTCTCTGTTGGCTACAAT 58.923 45.455 2.94 0.00 39.13 2.71
1057 1916 1.480137 TGGAAAGTTTGCTGGTGGTTG 59.520 47.619 8.67 0.00 0.00 3.77
1593 2612 1.363080 GAGGATCGTAACTCCGGCC 59.637 63.158 0.00 0.00 37.88 6.13
1692 3424 2.761195 CGTCCTCGGCGTCATCTCA 61.761 63.158 6.85 0.00 0.00 3.27
2415 4174 3.261216 CGTGCGCATGCCGATGTA 61.261 61.111 18.03 0.00 41.78 2.29
2425 4184 1.589196 GCCGATGTAGTGGACGAGC 60.589 63.158 0.00 0.00 0.00 5.03
2797 4821 0.673644 GAGCCGTACATTGCACCACT 60.674 55.000 0.00 0.00 0.00 4.00
2895 4920 9.778741 ATGTGAACTACTCATTCTGTTAAGAAA 57.221 29.630 0.00 0.00 45.44 2.52
2896 4921 9.778741 TGTGAACTACTCATTCTGTTAAGAAAT 57.221 29.630 0.00 0.00 45.44 2.17
2937 4962 8.664211 AAAGCTCTTATATTTCTTTACCGAGG 57.336 34.615 0.00 0.00 0.00 4.63
2938 4963 6.760291 AGCTCTTATATTTCTTTACCGAGGG 58.240 40.000 0.00 0.00 0.00 4.30
2939 4964 6.553852 AGCTCTTATATTTCTTTACCGAGGGA 59.446 38.462 0.00 0.00 0.00 4.20
2940 4965 6.869388 GCTCTTATATTTCTTTACCGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
2941 4966 7.471679 GCTCTTATATTTCTTTACCGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
2942 4967 9.075678 CTCTTATATTTCTTTACCGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
2943 4968 9.075678 TCTTATATTTCTTTACCGAGGGAGTAG 57.924 37.037 0.00 0.00 0.00 2.57
2944 4969 6.667558 ATATTTCTTTACCGAGGGAGTAGG 57.332 41.667 0.00 0.00 0.00 3.18
2945 4970 1.772836 TCTTTACCGAGGGAGTAGGC 58.227 55.000 0.00 0.00 0.00 3.93
2976 5001 3.261951 CCGTCGCCACTATTGCCG 61.262 66.667 0.00 0.00 0.00 5.69
3044 5092 2.645838 ATACTTTGCGAGCCATCCAT 57.354 45.000 0.00 0.00 0.00 3.41
3045 5093 3.769739 ATACTTTGCGAGCCATCCATA 57.230 42.857 0.00 0.00 0.00 2.74
3049 5097 3.181455 ACTTTGCGAGCCATCCATATGTA 60.181 43.478 1.24 0.00 0.00 2.29
3073 5121 2.151202 CGGTTGAATGTTGTAGCCTGT 58.849 47.619 0.00 0.00 0.00 4.00
3080 5128 2.004583 TGTTGTAGCCTGTCGTATGC 57.995 50.000 0.00 0.00 0.00 3.14
3181 5280 9.807921 TTATTGGAGGAAAGATGAGTTTTAAGT 57.192 29.630 0.00 0.00 0.00 2.24
3183 5282 8.848474 TTGGAGGAAAGATGAGTTTTAAGTAG 57.152 34.615 0.00 0.00 0.00 2.57
3184 5283 8.202461 TGGAGGAAAGATGAGTTTTAAGTAGA 57.798 34.615 0.00 0.00 0.00 2.59
3185 5284 8.656806 TGGAGGAAAGATGAGTTTTAAGTAGAA 58.343 33.333 0.00 0.00 0.00 2.10
3186 5285 9.503399 GGAGGAAAGATGAGTTTTAAGTAGAAA 57.497 33.333 0.00 0.00 0.00 2.52
3217 5316 7.739022 TTTTCGTGAATATGCAAAGCTTATG 57.261 32.000 0.00 1.67 30.99 1.90
3218 5317 6.435430 TTCGTGAATATGCAAAGCTTATGT 57.565 33.333 0.00 0.00 30.99 2.29
3219 5318 7.546778 TTCGTGAATATGCAAAGCTTATGTA 57.453 32.000 0.00 0.47 30.99 2.29
3220 5319 7.728847 TCGTGAATATGCAAAGCTTATGTAT 57.271 32.000 0.00 8.23 30.99 2.29
3221 5320 7.796838 TCGTGAATATGCAAAGCTTATGTATC 58.203 34.615 0.00 0.00 30.99 2.24
3222 5321 7.657354 TCGTGAATATGCAAAGCTTATGTATCT 59.343 33.333 0.00 0.00 30.99 1.98
3223 5322 8.285394 CGTGAATATGCAAAGCTTATGTATCTT 58.715 33.333 0.00 4.98 30.99 2.40
3224 5323 9.956720 GTGAATATGCAAAGCTTATGTATCTTT 57.043 29.630 0.00 4.07 30.99 2.52
3391 6036 6.767902 TCTCTAATTGCGATTTTAGCCATTCT 59.232 34.615 4.06 0.00 33.07 2.40
3481 6126 3.201290 CAGTTGTAGCATCCTTAGCAGG 58.799 50.000 0.00 0.00 42.50 4.85
3511 6156 0.887387 TTGCAACAAGGCCTACGACC 60.887 55.000 5.16 0.00 0.00 4.79
3527 6172 8.472413 GGCCTACGACCATATATTAAGTATCAA 58.528 37.037 0.00 0.00 0.00 2.57
3596 6241 2.253513 ACGGGAGTGCCAAAATTCG 58.746 52.632 0.08 0.00 44.82 3.34
3601 6246 2.095212 GGGAGTGCCAAAATTCGTCTTC 60.095 50.000 0.00 0.00 35.15 2.87
3603 6248 2.552315 GAGTGCCAAAATTCGTCTTCCA 59.448 45.455 0.00 0.00 0.00 3.53
3615 6260 0.678048 GTCTTCCACCTGCATCCACC 60.678 60.000 0.00 0.00 0.00 4.61
3617 6262 3.266686 TTCCACCTGCATCCACCGG 62.267 63.158 0.00 0.00 0.00 5.28
3636 6281 3.568686 GGTGCGCCGTGAACATAA 58.431 55.556 4.18 0.00 0.00 1.90
3711 6356 4.538746 AGGAACTTGTAGAAGTAGTGGC 57.461 45.455 5.58 0.00 41.87 5.01
3718 6363 2.029623 GTAGAAGTAGTGGCCGGATCA 58.970 52.381 5.05 0.00 0.00 2.92
3722 6367 0.467474 AGTAGTGGCCGGATCATCGA 60.467 55.000 5.05 0.00 0.00 3.59
3724 6369 0.603065 TAGTGGCCGGATCATCGATG 59.397 55.000 19.61 19.61 0.00 3.84
3725 6370 2.031012 TGGCCGGATCATCGATGC 59.969 61.111 20.81 7.57 0.00 3.91
3727 6372 1.376424 GGCCGGATCATCGATGCAT 60.376 57.895 20.81 14.22 30.72 3.96
3742 6387 1.302033 GCATACCAGGAGATGCCGG 60.302 63.158 16.23 0.00 42.18 6.13
3745 6390 1.762522 ATACCAGGAGATGCCGGCAG 61.763 60.000 35.36 21.15 43.43 4.85
3746 6391 4.559063 CCAGGAGATGCCGGCAGG 62.559 72.222 35.36 24.67 43.43 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 5.738619 TTGTGCTCCTCTTAGAACATACA 57.261 39.130 0.00 0.00 34.91 2.29
61 62 7.394016 TGAAATTGTGCTCCTCTTAGAACATA 58.606 34.615 0.00 0.00 34.91 2.29
62 63 6.240894 TGAAATTGTGCTCCTCTTAGAACAT 58.759 36.000 0.00 0.00 34.91 2.71
63 64 5.620206 TGAAATTGTGCTCCTCTTAGAACA 58.380 37.500 0.00 0.00 32.94 3.18
64 65 5.934625 TCTGAAATTGTGCTCCTCTTAGAAC 59.065 40.000 0.00 0.00 0.00 3.01
65 66 6.114187 TCTGAAATTGTGCTCCTCTTAGAA 57.886 37.500 0.00 0.00 0.00 2.10
66 67 5.745312 TCTGAAATTGTGCTCCTCTTAGA 57.255 39.130 0.00 0.00 0.00 2.10
67 68 6.169094 TCTTCTGAAATTGTGCTCCTCTTAG 58.831 40.000 0.00 0.00 0.00 2.18
68 69 6.114187 TCTTCTGAAATTGTGCTCCTCTTA 57.886 37.500 0.00 0.00 0.00 2.10
70 71 4.041444 ACTCTTCTGAAATTGTGCTCCTCT 59.959 41.667 0.00 0.00 0.00 3.69
71 72 4.322567 ACTCTTCTGAAATTGTGCTCCTC 58.677 43.478 0.00 0.00 0.00 3.71
72 73 4.363991 ACTCTTCTGAAATTGTGCTCCT 57.636 40.909 0.00 0.00 0.00 3.69
73 74 6.749923 AATACTCTTCTGAAATTGTGCTCC 57.250 37.500 0.00 0.00 0.00 4.70
102 103 8.792633 TCGATAGAAAATCAAACCACTTCAAAT 58.207 29.630 0.00 0.00 46.15 2.32
103 104 8.160521 TCGATAGAAAATCAAACCACTTCAAA 57.839 30.769 0.00 0.00 46.15 2.69
104 105 7.737972 TCGATAGAAAATCAAACCACTTCAA 57.262 32.000 0.00 0.00 46.15 2.69
216 217 7.239763 TGTAGACACAGAAGGAAACATATGA 57.760 36.000 10.38 0.00 0.00 2.15
217 218 9.770097 ATATGTAGACACAGAAGGAAACATATG 57.230 33.333 0.00 0.00 37.70 1.78
222 223 8.999431 TCAAAATATGTAGACACAGAAGGAAAC 58.001 33.333 0.00 0.00 38.30 2.78
224 225 9.166173 CATCAAAATATGTAGACACAGAAGGAA 57.834 33.333 0.00 0.00 38.30 3.36
227 228 7.907045 GTGCATCAAAATATGTAGACACAGAAG 59.093 37.037 0.00 0.00 38.30 2.85
228 229 7.390162 TGTGCATCAAAATATGTAGACACAGAA 59.610 33.333 0.00 0.00 38.30 3.02
229 230 6.878389 TGTGCATCAAAATATGTAGACACAGA 59.122 34.615 0.00 0.00 38.30 3.41
233 234 7.105588 AGAGTGTGCATCAAAATATGTAGACA 58.894 34.615 0.00 0.00 37.93 3.41
234 235 7.545362 AGAGTGTGCATCAAAATATGTAGAC 57.455 36.000 0.00 0.00 36.44 2.59
236 237 8.453320 TGAAAGAGTGTGCATCAAAATATGTAG 58.547 33.333 0.00 0.00 0.00 2.74
238 239 7.218228 TGAAAGAGTGTGCATCAAAATATGT 57.782 32.000 0.00 0.00 0.00 2.29
245 246 7.092079 CCAAATATTGAAAGAGTGTGCATCAA 58.908 34.615 0.00 0.00 34.80 2.57
246 247 6.209192 ACCAAATATTGAAAGAGTGTGCATCA 59.791 34.615 0.00 0.00 0.00 3.07
247 248 6.624423 ACCAAATATTGAAAGAGTGTGCATC 58.376 36.000 0.00 0.00 0.00 3.91
248 249 6.594788 ACCAAATATTGAAAGAGTGTGCAT 57.405 33.333 0.00 0.00 0.00 3.96
251 252 6.925165 AGCAAACCAAATATTGAAAGAGTGTG 59.075 34.615 0.00 0.00 0.00 3.82
252 253 7.014615 AGAGCAAACCAAATATTGAAAGAGTGT 59.985 33.333 0.00 0.00 0.00 3.55
253 254 7.373493 AGAGCAAACCAAATATTGAAAGAGTG 58.627 34.615 0.00 0.00 0.00 3.51
254 255 7.231317 TGAGAGCAAACCAAATATTGAAAGAGT 59.769 33.333 0.00 0.00 0.00 3.24
255 256 7.596494 TGAGAGCAAACCAAATATTGAAAGAG 58.404 34.615 0.00 0.00 0.00 2.85
256 257 7.523293 TGAGAGCAAACCAAATATTGAAAGA 57.477 32.000 0.00 0.00 0.00 2.52
258 259 6.158598 GCTGAGAGCAAACCAAATATTGAAA 58.841 36.000 0.00 0.00 41.89 2.69
259 260 5.336690 GGCTGAGAGCAAACCAAATATTGAA 60.337 40.000 0.00 0.00 44.75 2.69
260 261 4.158394 GGCTGAGAGCAAACCAAATATTGA 59.842 41.667 0.00 0.00 44.75 2.57
261 262 4.159135 AGGCTGAGAGCAAACCAAATATTG 59.841 41.667 0.00 0.00 44.75 1.90
262 263 4.347607 AGGCTGAGAGCAAACCAAATATT 58.652 39.130 0.00 0.00 44.75 1.28
263 264 3.973425 AGGCTGAGAGCAAACCAAATAT 58.027 40.909 0.00 0.00 44.75 1.28
264 265 3.439857 AGGCTGAGAGCAAACCAAATA 57.560 42.857 0.00 0.00 44.75 1.40
265 266 2.299326 AGGCTGAGAGCAAACCAAAT 57.701 45.000 0.00 0.00 44.75 2.32
266 267 2.071778 AAGGCTGAGAGCAAACCAAA 57.928 45.000 0.00 0.00 44.75 3.28
267 268 1.682854 CAAAGGCTGAGAGCAAACCAA 59.317 47.619 0.00 0.00 44.75 3.67
268 269 1.321474 CAAAGGCTGAGAGCAAACCA 58.679 50.000 0.00 0.00 44.75 3.67
269 270 0.038801 GCAAAGGCTGAGAGCAAACC 60.039 55.000 0.00 0.00 44.75 3.27
270 271 0.386478 CGCAAAGGCTGAGAGCAAAC 60.386 55.000 0.00 0.00 44.75 2.93
271 272 1.951510 CGCAAAGGCTGAGAGCAAA 59.048 52.632 0.00 0.00 44.75 3.68
272 273 2.620112 GCGCAAAGGCTGAGAGCAA 61.620 57.895 0.30 0.00 44.75 3.91
273 274 3.052082 GCGCAAAGGCTGAGAGCA 61.052 61.111 0.30 0.00 44.75 4.26
274 275 3.808656 GGCGCAAAGGCTGAGAGC 61.809 66.667 10.83 6.62 42.90 4.09
275 276 1.712977 GATGGCGCAAAGGCTGAGAG 61.713 60.000 10.83 0.00 46.88 3.20
276 277 1.746615 GATGGCGCAAAGGCTGAGA 60.747 57.895 10.83 0.00 46.88 3.27
277 278 2.796651 GATGGCGCAAAGGCTGAG 59.203 61.111 10.83 0.00 46.88 3.35
278 279 3.126879 CGATGGCGCAAAGGCTGA 61.127 61.111 10.83 0.00 46.88 4.26
279 280 4.183686 CCGATGGCGCAAAGGCTG 62.184 66.667 10.83 0.00 46.88 4.85
289 290 2.125269 ACCAGTTACGCCGATGGC 60.125 61.111 0.00 0.00 46.75 4.40
290 291 0.179084 ATGACCAGTTACGCCGATGG 60.179 55.000 0.00 0.00 38.83 3.51
291 292 1.202417 AGATGACCAGTTACGCCGATG 60.202 52.381 0.00 0.00 0.00 3.84
292 293 1.112113 AGATGACCAGTTACGCCGAT 58.888 50.000 0.00 0.00 0.00 4.18
293 294 1.674441 CTAGATGACCAGTTACGCCGA 59.326 52.381 0.00 0.00 0.00 5.54
294 295 1.404391 ACTAGATGACCAGTTACGCCG 59.596 52.381 0.00 0.00 0.00 6.46
295 296 3.521947 AACTAGATGACCAGTTACGCC 57.478 47.619 0.00 0.00 33.29 5.68
296 297 6.505272 AGATTAACTAGATGACCAGTTACGC 58.495 40.000 0.00 0.00 37.06 4.42
300 301 7.988028 GGCTTTAGATTAACTAGATGACCAGTT 59.012 37.037 0.00 0.00 38.50 3.16
301 302 7.419172 GGGCTTTAGATTAACTAGATGACCAGT 60.419 40.741 0.00 0.00 32.30 4.00
302 303 6.931840 GGGCTTTAGATTAACTAGATGACCAG 59.068 42.308 0.00 0.00 32.30 4.00
303 304 6.462487 CGGGCTTTAGATTAACTAGATGACCA 60.462 42.308 0.00 0.00 32.30 4.02
304 305 5.927115 CGGGCTTTAGATTAACTAGATGACC 59.073 44.000 0.00 0.00 32.30 4.02
305 306 5.927115 CCGGGCTTTAGATTAACTAGATGAC 59.073 44.000 0.00 0.00 32.30 3.06
306 307 5.601313 ACCGGGCTTTAGATTAACTAGATGA 59.399 40.000 6.32 0.00 32.30 2.92
307 308 5.696724 CACCGGGCTTTAGATTAACTAGATG 59.303 44.000 6.32 0.00 32.30 2.90
308 309 5.221661 CCACCGGGCTTTAGATTAACTAGAT 60.222 44.000 6.32 0.00 32.30 1.98
309 310 4.100498 CCACCGGGCTTTAGATTAACTAGA 59.900 45.833 6.32 0.00 32.30 2.43
310 311 4.100498 TCCACCGGGCTTTAGATTAACTAG 59.900 45.833 6.32 0.00 32.30 2.57
311 312 4.032310 TCCACCGGGCTTTAGATTAACTA 58.968 43.478 6.32 0.00 0.00 2.24
312 313 2.841881 TCCACCGGGCTTTAGATTAACT 59.158 45.455 6.32 0.00 0.00 2.24
319 320 1.823899 GGCATCCACCGGGCTTTAG 60.824 63.158 6.32 0.00 0.00 1.85
483 581 2.969443 ATCGCCAAAAACTTCGTCAG 57.031 45.000 0.00 0.00 0.00 3.51
509 607 9.936329 AATGATTTTCCTAATAAGGGCTAAAGA 57.064 29.630 0.00 0.00 43.84 2.52
652 760 4.502282 GCGTTCATTGTGTGTTTTTCATCA 59.498 37.500 0.00 0.00 0.00 3.07
729 875 4.532834 AGCTGTCTTTTTCTGGGTTGTTA 58.467 39.130 0.00 0.00 0.00 2.41
972 1733 0.703488 TGATGATTGGTTGCCTGGGA 59.297 50.000 0.00 0.00 0.00 4.37
1692 3424 0.679002 GCATGGCCAGAGTCACATGT 60.679 55.000 13.05 0.00 41.94 3.21
2202 3961 1.976474 GAATGCCGGTGCCTTGGAA 60.976 57.895 1.90 0.00 36.33 3.53
2349 4108 6.316390 GGTAAAAGATGATGTCGACTCCAATT 59.684 38.462 17.92 10.43 0.00 2.32
2355 4114 3.446161 TCCGGTAAAAGATGATGTCGACT 59.554 43.478 17.92 1.84 0.00 4.18
2415 4174 2.673341 TGCTCGAGCTCGTCCACT 60.673 61.111 35.27 0.00 42.66 4.00
2425 4184 3.485431 CAACGCCAGCTGCTCGAG 61.485 66.667 26.11 8.45 38.05 4.04
2434 4193 0.650512 CCGTACTTATGCAACGCCAG 59.349 55.000 2.35 0.00 35.36 4.85
2689 4525 0.746204 GGCCTGCAGAAGTAGCCTTC 60.746 60.000 17.39 0.00 46.23 3.46
2797 4821 0.472471 ACAAGCAACCGGAAAGGAGA 59.528 50.000 9.46 0.00 45.00 3.71
2911 4936 9.110502 CCTCGGTAAAGAAATATAAGAGCTTTT 57.889 33.333 0.00 0.00 31.85 2.27
2912 4937 7.715686 CCCTCGGTAAAGAAATATAAGAGCTTT 59.284 37.037 0.00 0.00 33.76 3.51
2913 4938 7.070821 TCCCTCGGTAAAGAAATATAAGAGCTT 59.929 37.037 0.00 0.00 0.00 3.74
2914 4939 6.553852 TCCCTCGGTAAAGAAATATAAGAGCT 59.446 38.462 0.00 0.00 0.00 4.09
2915 4940 6.756221 TCCCTCGGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
2916 4941 7.953752 ACTCCCTCGGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
2917 4942 7.909485 ACTCCCTCGGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
2918 4943 8.305317 CCTACTCCCTCGGTAAAGAAATATAAG 58.695 40.741 0.00 0.00 0.00 1.73
2919 4944 7.256083 GCCTACTCCCTCGGTAAAGAAATATAA 60.256 40.741 0.00 0.00 0.00 0.98
2920 4945 6.210185 GCCTACTCCCTCGGTAAAGAAATATA 59.790 42.308 0.00 0.00 0.00 0.86
2921 4946 5.011840 GCCTACTCCCTCGGTAAAGAAATAT 59.988 44.000 0.00 0.00 0.00 1.28
2922 4947 4.343239 GCCTACTCCCTCGGTAAAGAAATA 59.657 45.833 0.00 0.00 0.00 1.40
2923 4948 3.134262 GCCTACTCCCTCGGTAAAGAAAT 59.866 47.826 0.00 0.00 0.00 2.17
2924 4949 2.498885 GCCTACTCCCTCGGTAAAGAAA 59.501 50.000 0.00 0.00 0.00 2.52
2925 4950 2.105766 GCCTACTCCCTCGGTAAAGAA 58.894 52.381 0.00 0.00 0.00 2.52
2926 4951 1.006281 TGCCTACTCCCTCGGTAAAGA 59.994 52.381 0.00 0.00 0.00 2.52
2927 4952 1.481871 TGCCTACTCCCTCGGTAAAG 58.518 55.000 0.00 0.00 0.00 1.85
2928 4953 1.941377 TTGCCTACTCCCTCGGTAAA 58.059 50.000 0.00 0.00 0.00 2.01
2929 4954 2.170012 ATTGCCTACTCCCTCGGTAA 57.830 50.000 0.00 0.00 0.00 2.85
2930 4955 3.162666 CATATTGCCTACTCCCTCGGTA 58.837 50.000 0.00 0.00 0.00 4.02
2931 4956 1.971357 CATATTGCCTACTCCCTCGGT 59.029 52.381 0.00 0.00 0.00 4.69
2932 4957 1.971357 ACATATTGCCTACTCCCTCGG 59.029 52.381 0.00 0.00 0.00 4.63
2933 4958 3.181465 ACAACATATTGCCTACTCCCTCG 60.181 47.826 0.00 0.00 39.66 4.63
2934 4959 4.130118 CACAACATATTGCCTACTCCCTC 58.870 47.826 0.00 0.00 39.66 4.30
2935 4960 3.117888 CCACAACATATTGCCTACTCCCT 60.118 47.826 0.00 0.00 39.66 4.20
2936 4961 3.214328 CCACAACATATTGCCTACTCCC 58.786 50.000 0.00 0.00 39.66 4.30
2937 4962 3.214328 CCCACAACATATTGCCTACTCC 58.786 50.000 0.00 0.00 39.66 3.85
2938 4963 2.618709 GCCCACAACATATTGCCTACTC 59.381 50.000 0.00 0.00 39.66 2.59
2939 4964 2.654863 GCCCACAACATATTGCCTACT 58.345 47.619 0.00 0.00 39.66 2.57
2940 4965 1.681264 GGCCCACAACATATTGCCTAC 59.319 52.381 0.00 0.00 39.66 3.18
2941 4966 1.748939 CGGCCCACAACATATTGCCTA 60.749 52.381 0.00 0.00 39.66 3.93
2942 4967 1.037030 CGGCCCACAACATATTGCCT 61.037 55.000 0.00 0.00 39.66 4.75
2943 4968 1.319614 ACGGCCCACAACATATTGCC 61.320 55.000 0.00 0.00 39.66 4.52
2944 4969 0.100503 GACGGCCCACAACATATTGC 59.899 55.000 0.00 0.00 39.66 3.56
2945 4970 0.376852 CGACGGCCCACAACATATTG 59.623 55.000 0.00 0.00 41.98 1.90
3013 5050 5.121071 TCGCAAAGTATAATTGACGAACG 57.879 39.130 7.75 0.00 35.24 3.95
3017 5054 3.308595 TGGCTCGCAAAGTATAATTGACG 59.691 43.478 4.19 3.32 0.00 4.35
3073 5121 7.264947 TGAAAGATCTACATCAAAGCATACGA 58.735 34.615 0.00 0.00 0.00 3.43
3109 5162 6.790319 ACACTTTTATGGGGAAATCTACTGT 58.210 36.000 0.00 0.00 0.00 3.55
3128 5184 7.347222 TCTGGTATAAACTGATCCCATACACTT 59.653 37.037 0.00 0.00 0.00 3.16
3129 5185 6.844388 TCTGGTATAAACTGATCCCATACACT 59.156 38.462 0.00 0.00 0.00 3.55
3150 5206 6.599445 ACTCATCTTTCCTCCAATAATCTGG 58.401 40.000 0.00 0.00 37.87 3.86
3192 5291 7.812191 ACATAAGCTTTGCATATTCACGAAAAA 59.188 29.630 3.20 0.00 0.00 1.94
3193 5292 7.312154 ACATAAGCTTTGCATATTCACGAAAA 58.688 30.769 3.20 0.00 0.00 2.29
3194 5293 6.851609 ACATAAGCTTTGCATATTCACGAAA 58.148 32.000 3.20 0.00 0.00 3.46
3195 5294 6.435430 ACATAAGCTTTGCATATTCACGAA 57.565 33.333 3.20 0.00 0.00 3.85
3196 5295 7.657354 AGATACATAAGCTTTGCATATTCACGA 59.343 33.333 3.20 0.00 0.00 4.35
3197 5296 7.800767 AGATACATAAGCTTTGCATATTCACG 58.199 34.615 3.20 0.00 0.00 4.35
3198 5297 9.956720 AAAGATACATAAGCTTTGCATATTCAC 57.043 29.630 3.20 0.00 31.21 3.18
3228 5327 9.393786 AGCCCATCTAATTTTCTACCTCTATTA 57.606 33.333 0.00 0.00 0.00 0.98
3229 5328 8.160106 CAGCCCATCTAATTTTCTACCTCTATT 58.840 37.037 0.00 0.00 0.00 1.73
3230 5329 7.256835 CCAGCCCATCTAATTTTCTACCTCTAT 60.257 40.741 0.00 0.00 0.00 1.98
3231 5330 6.043243 CCAGCCCATCTAATTTTCTACCTCTA 59.957 42.308 0.00 0.00 0.00 2.43
3232 5331 5.163152 CCAGCCCATCTAATTTTCTACCTCT 60.163 44.000 0.00 0.00 0.00 3.69
3233 5332 5.066593 CCAGCCCATCTAATTTTCTACCTC 58.933 45.833 0.00 0.00 0.00 3.85
3234 5333 4.478686 ACCAGCCCATCTAATTTTCTACCT 59.521 41.667 0.00 0.00 0.00 3.08
3235 5334 4.793201 ACCAGCCCATCTAATTTTCTACC 58.207 43.478 0.00 0.00 0.00 3.18
3251 5896 2.092375 AGGATAACCAAAGCTACCAGCC 60.092 50.000 0.00 0.00 39.50 4.85
3454 6099 1.352352 AGGATGCTACAACTGCCTTGT 59.648 47.619 2.70 2.70 45.57 3.16
3457 6102 2.420687 GCTAAGGATGCTACAACTGCCT 60.421 50.000 0.00 0.00 0.00 4.75
3458 6103 1.943340 GCTAAGGATGCTACAACTGCC 59.057 52.381 0.00 0.00 0.00 4.85
3489 6134 2.025155 TCGTAGGCCTTGTTGCAAAAA 58.975 42.857 12.58 0.00 0.00 1.94
3490 6135 1.335496 GTCGTAGGCCTTGTTGCAAAA 59.665 47.619 12.58 0.00 0.00 2.44
3491 6136 0.948678 GTCGTAGGCCTTGTTGCAAA 59.051 50.000 12.58 0.00 0.00 3.68
3492 6137 2.624169 GTCGTAGGCCTTGTTGCAA 58.376 52.632 12.58 0.00 0.00 4.08
3493 6138 4.371975 GTCGTAGGCCTTGTTGCA 57.628 55.556 12.58 0.00 0.00 4.08
3567 6212 2.639065 GCACTCCCGTGGATTTGAATA 58.361 47.619 0.00 0.00 41.51 1.75
3579 6224 0.168128 GACGAATTTTGGCACTCCCG 59.832 55.000 0.00 0.00 35.87 5.14
3580 6225 1.534729 AGACGAATTTTGGCACTCCC 58.465 50.000 0.00 0.00 0.00 4.30
3596 6241 0.678048 GGTGGATGCAGGTGGAAGAC 60.678 60.000 0.00 0.00 0.00 3.01
3621 6266 0.371989 CGAATTATGTTCACGGCGCA 59.628 50.000 10.83 0.00 0.00 6.09
3624 6269 2.602217 GGCATCGAATTATGTTCACGGC 60.602 50.000 0.00 0.00 0.00 5.68
3636 6281 3.295734 CCATGAGACGGCATCGAAT 57.704 52.632 0.00 0.00 40.11 3.34
3682 6327 8.712103 ACTACTTCTACAAGTTCCTAGGTTTTT 58.288 33.333 9.08 0.00 40.16 1.94
3683 6328 8.148999 CACTACTTCTACAAGTTCCTAGGTTTT 58.851 37.037 9.08 0.00 40.16 2.43
3702 6347 0.389391 CGATGATCCGGCCACTACTT 59.611 55.000 2.24 0.00 0.00 2.24
3705 6350 0.603065 CATCGATGATCCGGCCACTA 59.397 55.000 21.02 0.00 0.00 2.74
3711 6356 1.066929 TGGTATGCATCGATGATCCGG 60.067 52.381 29.20 0.00 0.00 5.14
3718 6363 2.354503 GCATCTCCTGGTATGCATCGAT 60.355 50.000 22.91 0.00 46.19 3.59
3724 6369 1.302033 CCGGCATCTCCTGGTATGC 60.302 63.158 20.99 20.99 46.20 3.14
3725 6370 1.302033 GCCGGCATCTCCTGGTATG 60.302 63.158 24.80 7.23 33.09 2.39
3727 6372 2.364973 TGCCGGCATCTCCTGGTA 60.365 61.111 29.03 0.00 33.09 3.25
3742 6387 1.503542 CCTCACAAATCGCACCTGC 59.496 57.895 0.00 0.00 37.78 4.85


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

AutoCloner maintained by Alex Coulton.