Multiple sequence alignment - TraesCS3A01G268600

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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 TraesCS3A01G268600 chr3A 100.000 3419 0 0 1 3419 494731190 494727772 0.000000e+00 6314.0
1 TraesCS3A01G268600 chr3A 93.396 212 13 1 1 211 669654786 669654997 2.560000e-81 313.0
2 TraesCS3A01G268600 chr3A 78.010 191 42 0 397 587 649716985 649716795 1.670000e-23 121.0
3 TraesCS3A01G268600 chr3A 95.238 42 2 0 1891 1932 494729191 494729150 2.200000e-07 67.6
4 TraesCS3A01G268600 chr3A 95.238 42 2 0 2000 2041 494729300 494729259 2.200000e-07 67.6
5 TraesCS3A01G268600 chr3B 96.850 1397 32 6 2034 3419 487049212 487047817 0.000000e+00 2326.0
6 TraesCS3A01G268600 chr3B 91.524 1640 77 18 397 1988 487050841 487049216 0.000000e+00 2202.0
7 TraesCS3A01G268600 chr3D 92.811 1391 73 13 2048 3419 373328585 373327203 0.000000e+00 1989.0
8 TraesCS3A01G268600 chr3D 89.375 1280 98 20 647 1913 373329987 373328733 0.000000e+00 1576.0
9 TraesCS3A01G268600 chr3D 93.365 211 14 0 1 211 132254798 132255008 2.560000e-81 313.0
10 TraesCS3A01G268600 chr3D 92.958 71 3 2 1915 1984 17441403 17441472 6.040000e-18 102.0
11 TraesCS3A01G268600 chr3D 90.278 72 7 0 1917 1988 284818406 284818335 1.010000e-15 95.3
12 TraesCS3A01G268600 chr7A 84.788 401 55 5 1 396 197659793 197659394 6.870000e-107 398.0
13 TraesCS3A01G268600 chr7A 93.243 74 5 0 1915 1988 48103080 48103153 3.610000e-20 110.0
14 TraesCS3A01G268600 chr7A 93.243 74 5 0 1915 1988 692371746 692371819 3.610000e-20 110.0
15 TraesCS3A01G268600 chr7A 93.243 74 5 0 1915 1988 692395592 692395665 3.610000e-20 110.0
16 TraesCS3A01G268600 chr4B 83.709 399 59 6 3 397 78331955 78331559 4.170000e-99 372.0
17 TraesCS3A01G268600 chr4B 92.063 63 5 0 1926 1988 110708228 110708166 4.700000e-14 89.8
18 TraesCS3A01G268600 chr1A 94.860 214 11 0 1 214 213777323 213777110 5.470000e-88 335.0
19 TraesCS3A01G268600 chr1A 91.667 72 6 0 1917 1988 188150855 188150926 2.170000e-17 100.0
20 TraesCS3A01G268600 chr1A 90.541 74 7 0 1915 1988 352174193 352174120 7.810000e-17 99.0
21 TraesCS3A01G268600 chr5D 93.458 214 14 0 1 214 113801653 113801440 5.510000e-83 318.0
22 TraesCS3A01G268600 chr5D 93.868 212 11 2 1 211 450878215 450878425 5.510000e-83 318.0
23 TraesCS3A01G268600 chr5D 82.432 222 34 4 397 615 543226668 543226449 4.500000e-44 189.0
24 TraesCS3A01G268600 chr5D 91.892 74 6 0 1915 1988 52281154 52281081 1.680000e-18 104.0
25 TraesCS3A01G268600 chr5D 89.333 75 6 2 1915 1988 472997440 472997513 3.630000e-15 93.5
26 TraesCS3A01G268600 chr5A 93.488 215 13 1 1 214 489635710 489635496 5.510000e-83 318.0
27 TraesCS3A01G268600 chr5A 95.767 189 7 1 210 397 167190199 167190387 1.540000e-78 303.0
28 TraesCS3A01G268600 chr4A 96.277 188 6 1 210 396 195566787 195566974 1.190000e-79 307.0
29 TraesCS3A01G268600 chr2A 96.277 188 5 2 210 396 180373237 180373423 1.190000e-79 307.0
30 TraesCS3A01G268600 chr6A 95.789 190 6 2 210 398 322813630 322813818 4.290000e-79 305.0
31 TraesCS3A01G268600 chr4D 95.745 188 6 2 210 396 60073388 60073574 5.540000e-78 302.0
32 TraesCS3A01G268600 chr4D 95.722 187 7 1 211 396 78437080 78437266 1.990000e-77 300.0
33 TraesCS3A01G268600 chr4D 87.838 74 9 0 1915 1988 302003479 302003406 1.690000e-13 87.9
34 TraesCS3A01G268600 chr2D 81.009 337 54 8 68 396 493042408 493042074 3.380000e-65 259.0
35 TraesCS3A01G268600 chr2D 84.375 224 29 4 397 615 262457106 262457328 7.430000e-52 215.0
36 TraesCS3A01G268600 chr2D 89.041 73 8 0 1915 1987 295175278 295175206 1.310000e-14 91.6
37 TraesCS3A01G268600 chr2B 86.486 222 26 3 397 615 286977423 286977203 1.230000e-59 241.0
38 TraesCS3A01G268600 chr2B 84.577 201 31 0 397 597 670442659 670442859 2.080000e-47 200.0
39 TraesCS3A01G268600 chr2B 84.080 201 31 1 397 597 641871631 641871432 3.480000e-45 193.0
40 TraesCS3A01G268600 chr7D 84.737 190 26 2 431 617 100235891 100235702 1.620000e-43 187.0
41 TraesCS3A01G268600 chr7D 93.548 62 4 0 1926 1987 514658895 514658834 3.630000e-15 93.5
42 TraesCS3A01G268600 chr7D 94.915 59 3 0 1926 1984 600224605 600224547 3.630000e-15 93.5
43 TraesCS3A01G268600 chr7D 88.571 70 8 0 1915 1984 337558893 337558962 6.080000e-13 86.1
44 TraesCS3A01G268600 chr1D 83.246 191 32 0 397 587 62423763 62423573 3.510000e-40 176.0
45 TraesCS3A01G268600 chr1D 93.243 74 5 0 1915 1988 128529111 128529184 3.610000e-20 110.0
46 TraesCS3A01G268600 chr1D 92.000 75 6 0 1914 1988 128530321 128530395 4.670000e-19 106.0
47 TraesCS3A01G268600 chr1D 89.189 74 4 1 1915 1988 381308588 381308657 4.700000e-14 89.8
48 TraesCS3A01G268600 chr1D 90.625 64 6 0 1925 1988 335590282 335590345 6.080000e-13 86.1
49 TraesCS3A01G268600 chr1D 90.476 63 6 0 1926 1988 100459002 100459064 2.190000e-12 84.2
50 TraesCS3A01G268600 chr1D 86.486 74 6 1 1915 1988 316618837 316618906 1.020000e-10 78.7
51 TraesCS3A01G268600 chr6B 81.731 208 36 1 410 615 88328788 88328581 4.540000e-39 172.0
52 TraesCS3A01G268600 chr5B 93.243 74 5 0 1915 1988 55371038 55370965 3.610000e-20 110.0
53 TraesCS3A01G268600 chr1B 90.541 74 7 0 1915 1988 301273496 301273423 7.810000e-17 99.0
54 TraesCS3A01G268600 chrUn 92.063 63 5 0 1926 1988 3061895 3061957 4.700000e-14 89.8
55 TraesCS3A01G268600 chrUn 86.842 76 6 3 1915 1988 3062099 3062172 7.860000e-12 82.4
56 TraesCS3A01G268600 chrUn 90.323 62 6 0 1926 1987 31028452 31028391 7.860000e-12 82.4
57 TraesCS3A01G268600 chrUn 92.593 54 4 0 1926 1979 77899975 77900028 1.020000e-10 78.7
58 TraesCS3A01G268600 chrUn 85.135 74 11 0 1915 1988 126941247 126941320 3.660000e-10 76.8
59 TraesCS3A01G268600 chrUn 95.349 43 2 0 1937 1979 19227846 19227888 6.120000e-08 69.4
60 TraesCS3A01G268600 chr6D 90.476 63 6 0 1926 1988 317078802 317078864 2.190000e-12 84.2
61 TraesCS3A01G268600 chr6D 94.118 51 3 0 1938 1988 36072879 36072829 1.020000e-10 78.7
62 TraesCS3A01G268600 chr6D 88.889 63 7 0 1926 1988 361169366 361169428 1.020000e-10 78.7


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 TraesCS3A01G268600 chr3A 494727772 494731190 3418 True 2149.733333 6314 96.825333 1 3419 3 chr3A.!!$R2 3418
1 TraesCS3A01G268600 chr3B 487047817 487050841 3024 True 2264.000000 2326 94.187000 397 3419 2 chr3B.!!$R1 3022
2 TraesCS3A01G268600 chr3D 373327203 373329987 2784 True 1782.500000 1989 91.093000 647 3419 2 chr3D.!!$R2 2772

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
46 47 0.102481 GCGGCGGAACTTCTGATCTA 59.898 55.0 9.78 0.0 0.00 1.98 F
218 219 0.107703 CAGCTCTGGCCCGTTTGATA 60.108 55.0 0.00 0.0 39.73 2.15 F
1330 1370 0.389166 GAAGACAGCCAGACTCGGTG 60.389 60.0 0.00 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2144 0.408700 AACCAGTACTCCCTCCGTCT 59.591 55.00 0.0 0.0 0.00 4.18 R
2176 2278 5.772393 TCAAGGGCTCTGAAAACCTAATA 57.228 39.13 0.0 0.0 31.88 0.98 R
2963 3076 0.631753 CAGAGGAGGGTCAGGTAGGA 59.368 60.00 0.0 0.0 0.00 2.94 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
18 19 3.618171 GGTTTTCAGTGGCTACGGA 57.382 52.632 0.00 0.00 0.00 4.69
19 20 1.439679 GGTTTTCAGTGGCTACGGAG 58.560 55.000 2.98 0.00 32.65 4.63
42 43 4.735132 CGGCGGCGGAACTTCTGA 62.735 66.667 25.36 0.00 0.00 3.27
43 44 2.125106 GGCGGCGGAACTTCTGAT 60.125 61.111 9.78 0.00 0.00 2.90
44 45 2.174319 GGCGGCGGAACTTCTGATC 61.174 63.158 9.78 0.00 0.00 2.92
45 46 1.153549 GCGGCGGAACTTCTGATCT 60.154 57.895 9.78 0.00 0.00 2.75
46 47 0.102481 GCGGCGGAACTTCTGATCTA 59.898 55.000 9.78 0.00 0.00 1.98
47 48 1.866063 GCGGCGGAACTTCTGATCTAG 60.866 57.143 9.78 0.00 0.00 2.43
48 49 1.269309 CGGCGGAACTTCTGATCTAGG 60.269 57.143 0.00 0.00 0.00 3.02
49 50 1.757699 GGCGGAACTTCTGATCTAGGT 59.242 52.381 1.42 0.00 0.00 3.08
50 51 2.168728 GGCGGAACTTCTGATCTAGGTT 59.831 50.000 1.42 0.00 0.00 3.50
51 52 3.383825 GGCGGAACTTCTGATCTAGGTTA 59.616 47.826 1.42 0.00 0.00 2.85
52 53 4.142004 GGCGGAACTTCTGATCTAGGTTAA 60.142 45.833 1.42 0.00 0.00 2.01
53 54 5.453480 GGCGGAACTTCTGATCTAGGTTAAT 60.453 44.000 1.42 0.00 0.00 1.40
54 55 5.692654 GCGGAACTTCTGATCTAGGTTAATC 59.307 44.000 1.42 0.00 0.00 1.75
55 56 6.217294 CGGAACTTCTGATCTAGGTTAATCC 58.783 44.000 0.00 0.00 0.00 3.01
56 57 6.526526 GGAACTTCTGATCTAGGTTAATCCC 58.473 44.000 0.00 0.00 36.75 3.85
57 58 5.793030 ACTTCTGATCTAGGTTAATCCCG 57.207 43.478 0.00 0.00 36.75 5.14
58 59 5.455872 ACTTCTGATCTAGGTTAATCCCGA 58.544 41.667 0.00 0.00 36.75 5.14
59 60 5.897824 ACTTCTGATCTAGGTTAATCCCGAA 59.102 40.000 0.00 0.00 36.75 4.30
60 61 6.041069 ACTTCTGATCTAGGTTAATCCCGAAG 59.959 42.308 12.13 12.13 36.06 3.79
76 77 3.963383 CGAAGGGTTCCGGAATATTTG 57.037 47.619 22.04 14.67 0.00 2.32
77 78 2.616842 CGAAGGGTTCCGGAATATTTGG 59.383 50.000 22.04 11.83 0.00 3.28
78 79 3.683281 CGAAGGGTTCCGGAATATTTGGA 60.683 47.826 22.04 6.34 0.00 3.53
79 80 4.274978 GAAGGGTTCCGGAATATTTGGAA 58.725 43.478 22.04 15.43 39.38 3.53
80 81 4.325084 AGGGTTCCGGAATATTTGGAAA 57.675 40.909 22.04 0.00 43.01 3.13
81 82 4.878968 AGGGTTCCGGAATATTTGGAAAT 58.121 39.130 22.04 9.78 43.01 2.17
82 83 5.277250 AGGGTTCCGGAATATTTGGAAATT 58.723 37.500 22.04 9.27 43.01 1.82
83 84 5.724370 AGGGTTCCGGAATATTTGGAAATTT 59.276 36.000 22.04 0.00 43.01 1.82
84 85 6.898521 AGGGTTCCGGAATATTTGGAAATTTA 59.101 34.615 22.04 0.00 43.01 1.40
85 86 7.400627 AGGGTTCCGGAATATTTGGAAATTTAA 59.599 33.333 22.04 0.00 43.01 1.52
86 87 8.041919 GGGTTCCGGAATATTTGGAAATTTAAA 58.958 33.333 22.04 0.00 43.01 1.52
87 88 9.093970 GGTTCCGGAATATTTGGAAATTTAAAG 57.906 33.333 22.04 0.00 43.01 1.85
88 89 9.647797 GTTCCGGAATATTTGGAAATTTAAAGT 57.352 29.630 22.04 0.00 43.01 2.66
89 90 9.646427 TTCCGGAATATTTGGAAATTTAAAGTG 57.354 29.630 14.35 0.00 38.77 3.16
90 91 7.762159 TCCGGAATATTTGGAAATTTAAAGTGC 59.238 33.333 0.00 0.00 0.00 4.40
91 92 7.547370 CCGGAATATTTGGAAATTTAAAGTGCA 59.453 33.333 0.00 0.00 0.00 4.57
92 93 8.930760 CGGAATATTTGGAAATTTAAAGTGCAA 58.069 29.630 0.00 0.75 0.00 4.08
97 98 7.784633 TTTGGAAATTTAAAGTGCAAAGAGG 57.215 32.000 13.79 0.00 30.41 3.69
98 99 5.852827 TGGAAATTTAAAGTGCAAAGAGGG 58.147 37.500 0.00 0.00 0.00 4.30
99 100 5.221621 TGGAAATTTAAAGTGCAAAGAGGGG 60.222 40.000 0.00 0.00 0.00 4.79
100 101 4.890158 AATTTAAAGTGCAAAGAGGGGG 57.110 40.909 0.00 0.00 0.00 5.40
128 129 2.978010 CACCGAGGTGGGCACAAC 60.978 66.667 14.19 0.00 44.64 3.32
129 130 4.265056 ACCGAGGTGGGCACAACC 62.265 66.667 0.00 0.00 44.64 3.77
138 139 2.361230 GGCACAACCCACCTAGGC 60.361 66.667 9.30 0.00 35.39 3.93
139 140 2.746277 GCACAACCCACCTAGGCG 60.746 66.667 9.30 0.00 35.39 5.52
140 141 2.746277 CACAACCCACCTAGGCGC 60.746 66.667 9.30 0.00 35.39 6.53
141 142 4.388499 ACAACCCACCTAGGCGCG 62.388 66.667 9.30 0.00 35.39 6.86
178 179 2.282462 CCTGGTGGGTTGTGCCTC 60.282 66.667 0.00 0.00 37.43 4.70
179 180 2.282462 CTGGTGGGTTGTGCCTCC 60.282 66.667 0.00 0.00 37.43 4.30
180 181 3.868200 CTGGTGGGTTGTGCCTCCC 62.868 68.421 0.00 0.00 43.67 4.30
181 182 3.580319 GGTGGGTTGTGCCTCCCT 61.580 66.667 0.00 0.00 43.74 4.20
182 183 2.520968 GTGGGTTGTGCCTCCCTT 59.479 61.111 0.00 0.00 43.74 3.95
183 184 1.903404 GTGGGTTGTGCCTCCCTTG 60.903 63.158 0.00 0.00 43.74 3.61
184 185 2.283173 GGGTTGTGCCTCCCTTGG 60.283 66.667 0.00 0.00 40.48 3.61
185 186 2.283173 GGTTGTGCCTCCCTTGGG 60.283 66.667 0.00 0.00 0.00 4.12
186 187 2.283173 GTTGTGCCTCCCTTGGGG 60.283 66.667 5.78 0.00 46.11 4.96
187 188 4.299796 TTGTGCCTCCCTTGGGGC 62.300 66.667 5.78 0.00 43.94 5.80
206 207 4.421515 CCCCCAGGTGCAGCTCTG 62.422 72.222 17.16 10.20 0.00 3.35
214 215 4.269523 TGCAGCTCTGGCCCGTTT 62.270 61.111 0.00 0.00 39.73 3.60
215 216 3.741476 GCAGCTCTGGCCCGTTTG 61.741 66.667 0.00 0.00 39.73 2.93
216 217 2.032528 CAGCTCTGGCCCGTTTGA 59.967 61.111 0.00 0.00 39.73 2.69
217 218 1.377725 CAGCTCTGGCCCGTTTGAT 60.378 57.895 0.00 0.00 39.73 2.57
218 219 0.107703 CAGCTCTGGCCCGTTTGATA 60.108 55.000 0.00 0.00 39.73 2.15
219 220 0.839946 AGCTCTGGCCCGTTTGATAT 59.160 50.000 0.00 0.00 39.73 1.63
220 221 1.212935 AGCTCTGGCCCGTTTGATATT 59.787 47.619 0.00 0.00 39.73 1.28
221 222 1.334869 GCTCTGGCCCGTTTGATATTG 59.665 52.381 0.00 0.00 0.00 1.90
222 223 2.917933 CTCTGGCCCGTTTGATATTGA 58.082 47.619 0.00 0.00 0.00 2.57
223 224 3.480470 CTCTGGCCCGTTTGATATTGAT 58.520 45.455 0.00 0.00 0.00 2.57
224 225 3.885297 CTCTGGCCCGTTTGATATTGATT 59.115 43.478 0.00 0.00 0.00 2.57
225 226 4.277476 TCTGGCCCGTTTGATATTGATTT 58.723 39.130 0.00 0.00 0.00 2.17
226 227 4.709397 TCTGGCCCGTTTGATATTGATTTT 59.291 37.500 0.00 0.00 0.00 1.82
227 228 5.186797 TCTGGCCCGTTTGATATTGATTTTT 59.813 36.000 0.00 0.00 0.00 1.94
272 273 4.988486 GCAACTGGCACTGCGCAC 62.988 66.667 5.66 0.00 45.17 5.34
273 274 3.282157 CAACTGGCACTGCGCACT 61.282 61.111 5.66 0.00 45.17 4.40
274 275 1.960763 CAACTGGCACTGCGCACTA 60.961 57.895 5.66 0.00 45.17 2.74
275 276 1.669115 AACTGGCACTGCGCACTAG 60.669 57.895 5.66 7.22 45.17 2.57
276 277 2.816958 CTGGCACTGCGCACTAGG 60.817 66.667 5.66 0.00 45.17 3.02
277 278 3.596066 CTGGCACTGCGCACTAGGT 62.596 63.158 5.66 0.00 45.17 3.08
278 279 2.815647 GGCACTGCGCACTAGGTC 60.816 66.667 5.66 0.00 45.17 3.85
279 280 2.048222 GCACTGCGCACTAGGTCA 60.048 61.111 5.66 0.00 41.79 4.02
280 281 1.667830 GCACTGCGCACTAGGTCAA 60.668 57.895 5.66 0.00 41.79 3.18
281 282 1.021390 GCACTGCGCACTAGGTCAAT 61.021 55.000 5.66 0.00 41.79 2.57
282 283 1.739035 GCACTGCGCACTAGGTCAATA 60.739 52.381 5.66 0.00 41.79 1.90
283 284 2.196749 CACTGCGCACTAGGTCAATAG 58.803 52.381 5.66 0.00 0.00 1.73
284 285 1.137086 ACTGCGCACTAGGTCAATAGG 59.863 52.381 5.66 0.00 0.00 2.57
285 286 1.137086 CTGCGCACTAGGTCAATAGGT 59.863 52.381 5.66 0.00 0.00 3.08
286 287 1.553248 TGCGCACTAGGTCAATAGGTT 59.447 47.619 5.66 0.00 0.00 3.50
287 288 2.761767 TGCGCACTAGGTCAATAGGTTA 59.238 45.455 5.66 0.00 0.00 2.85
288 289 3.181479 TGCGCACTAGGTCAATAGGTTAG 60.181 47.826 5.66 0.00 0.00 2.34
289 290 3.181478 GCGCACTAGGTCAATAGGTTAGT 60.181 47.826 0.30 0.00 0.00 2.24
290 291 4.608951 CGCACTAGGTCAATAGGTTAGTC 58.391 47.826 0.00 0.00 0.00 2.59
291 292 4.499357 CGCACTAGGTCAATAGGTTAGTCC 60.499 50.000 0.00 0.00 0.00 3.85
292 293 4.202233 GCACTAGGTCAATAGGTTAGTCCC 60.202 50.000 0.00 0.00 36.75 4.46
293 294 4.960469 CACTAGGTCAATAGGTTAGTCCCA 59.040 45.833 0.00 0.00 36.75 4.37
294 295 5.424252 CACTAGGTCAATAGGTTAGTCCCAA 59.576 44.000 0.00 0.00 36.75 4.12
295 296 6.027482 ACTAGGTCAATAGGTTAGTCCCAAA 58.973 40.000 0.00 0.00 36.75 3.28
296 297 5.853572 AGGTCAATAGGTTAGTCCCAAAA 57.146 39.130 0.00 0.00 36.75 2.44
297 298 6.208840 AGGTCAATAGGTTAGTCCCAAAAA 57.791 37.500 0.00 0.00 36.75 1.94
333 334 9.956720 AGTTGCTATAAAATGATTGTAAGCATC 57.043 29.630 10.74 10.26 33.21 3.91
334 335 9.185192 GTTGCTATAAAATGATTGTAAGCATCC 57.815 33.333 10.74 4.77 33.21 3.51
335 336 8.462589 TGCTATAAAATGATTGTAAGCATCCA 57.537 30.769 7.62 0.00 33.21 3.41
336 337 8.911965 TGCTATAAAATGATTGTAAGCATCCAA 58.088 29.630 7.62 0.00 33.21 3.53
337 338 9.403110 GCTATAAAATGATTGTAAGCATCCAAG 57.597 33.333 0.00 0.00 33.21 3.61
341 342 8.712285 AAAATGATTGTAAGCATCCAAGAATG 57.288 30.769 0.00 0.00 33.21 2.67
342 343 7.649533 AATGATTGTAAGCATCCAAGAATGA 57.350 32.000 0.00 0.00 33.21 2.57
343 344 7.834881 ATGATTGTAAGCATCCAAGAATGAT 57.165 32.000 0.00 0.00 26.60 2.45
344 345 8.929260 ATGATTGTAAGCATCCAAGAATGATA 57.071 30.769 0.00 0.00 26.60 2.15
345 346 8.750515 TGATTGTAAGCATCCAAGAATGATAA 57.249 30.769 0.00 0.00 0.00 1.75
346 347 9.358406 TGATTGTAAGCATCCAAGAATGATAAT 57.642 29.630 0.00 0.00 0.00 1.28
354 355 8.910944 AGCATCCAAGAATGATAATATATTGGC 58.089 33.333 8.28 0.89 36.50 4.52
355 356 8.689061 GCATCCAAGAATGATAATATATTGGCA 58.311 33.333 8.28 6.41 36.50 4.92
358 359 9.978336 TCCAAGAATGATAATATATTGGCATGA 57.022 29.630 8.28 2.90 36.50 3.07
413 414 0.394192 CAAGGATGAGGGCGCAGATA 59.606 55.000 10.83 0.00 0.00 1.98
461 462 4.230502 ACATGGGTGATCCTATCCAACTTT 59.769 41.667 0.00 0.00 32.46 2.66
467 468 5.297776 GGTGATCCTATCCAACTTTCACATG 59.702 44.000 0.00 0.00 35.00 3.21
469 470 6.259608 GTGATCCTATCCAACTTTCACATGAG 59.740 42.308 0.00 0.00 33.84 2.90
478 479 4.021102 ACTTTCACATGAGAATCCGGTT 57.979 40.909 6.40 0.00 0.00 4.44
488 489 6.038603 ACATGAGAATCCGGTTATGTTTGATG 59.961 38.462 0.00 0.00 0.00 3.07
497 498 5.856455 CCGGTTATGTTTGATGAGTTTGTTC 59.144 40.000 0.00 0.00 0.00 3.18
502 503 9.121517 GTTATGTTTGATGAGTTTGTTCAGATG 57.878 33.333 0.00 0.00 0.00 2.90
533 534 5.940192 AATTCGGCATCGAGCAATTTATA 57.060 34.783 8.71 0.00 46.75 0.98
545 546 6.593770 TCGAGCAATTTATAAGCAGTTCAAGA 59.406 34.615 0.00 0.00 0.00 3.02
573 574 2.275318 GATTGAGCATCTATAGGCGGC 58.725 52.381 0.00 0.00 37.52 6.53
579 580 2.234908 AGCATCTATAGGCGGCTAAAGG 59.765 50.000 23.58 14.96 37.52 3.11
597 598 7.202066 GGCTAAAGGGGACAACTAGAACATATA 60.202 40.741 0.00 0.00 0.00 0.86
691 727 6.882610 TGAGATGCTATTGTTTGAGTTTGT 57.117 33.333 0.00 0.00 0.00 2.83
707 744 5.186021 TGAGTTTGTGGGCTCTTAAAAACAA 59.814 36.000 0.00 0.00 33.22 2.83
711 748 4.027437 TGTGGGCTCTTAAAAACAAAGGT 58.973 39.130 0.00 0.00 0.00 3.50
713 750 4.098807 GTGGGCTCTTAAAAACAAAGGTCA 59.901 41.667 0.00 0.00 0.00 4.02
716 753 6.551601 TGGGCTCTTAAAAACAAAGGTCAATA 59.448 34.615 0.00 0.00 0.00 1.90
733 770 8.331931 AGGTCAATATTTAGAGGACATGGTTA 57.668 34.615 0.00 0.00 0.00 2.85
741 778 4.000928 AGAGGACATGGTTAGATGACCT 57.999 45.455 4.52 4.52 46.88 3.85
747 784 5.364157 GGACATGGTTAGATGACCTACTTCT 59.636 44.000 0.00 0.00 40.47 2.85
793 830 1.852942 CGGATGAGTACAATGTCCGG 58.147 55.000 16.44 0.00 45.92 5.14
818 857 1.966451 GTGGGCTTGAAGACACCCG 60.966 63.158 0.00 0.00 46.02 5.28
845 884 7.606456 TGTGGAAGACATTATTAACTTCAGTCC 59.394 37.037 0.00 0.00 39.99 3.85
846 885 7.065923 GTGGAAGACATTATTAACTTCAGTCCC 59.934 40.741 0.00 0.00 39.99 4.46
931 971 3.522392 ACCTACTACTTCCCCGGATAG 57.478 52.381 0.73 0.00 0.00 2.08
1217 1257 1.134699 TCATCAGTGTCCGAGAATGCC 60.135 52.381 0.00 0.00 0.00 4.40
1234 1274 0.822121 GCCTTTCGTCAGGTGGGTTT 60.822 55.000 4.83 0.00 36.15 3.27
1244 1284 3.056328 GTGGGTTTGGAGCCTCGC 61.056 66.667 0.00 0.00 43.97 5.03
1276 1316 2.041265 TTGAGGAGGAGGGGGCTC 59.959 66.667 0.00 0.00 0.00 4.70
1330 1370 0.389166 GAAGACAGCCAGACTCGGTG 60.389 60.000 0.00 0.00 0.00 4.94
1452 1494 1.352687 GGCCTATCCCTTTCTCCATCC 59.647 57.143 0.00 0.00 0.00 3.51
1521 1568 1.613255 GGGGAATCGGTGCTTTGAGAA 60.613 52.381 0.00 0.00 0.00 2.87
1522 1569 2.369394 GGGAATCGGTGCTTTGAGAAT 58.631 47.619 0.00 0.00 0.00 2.40
1523 1570 2.755103 GGGAATCGGTGCTTTGAGAATT 59.245 45.455 0.00 0.00 0.00 2.17
1524 1571 3.428045 GGGAATCGGTGCTTTGAGAATTG 60.428 47.826 0.00 0.00 0.00 2.32
1525 1572 3.440173 GGAATCGGTGCTTTGAGAATTGA 59.560 43.478 0.00 0.00 0.00 2.57
1526 1573 4.437930 GGAATCGGTGCTTTGAGAATTGAG 60.438 45.833 0.00 0.00 0.00 3.02
1527 1574 3.401033 TCGGTGCTTTGAGAATTGAGA 57.599 42.857 0.00 0.00 0.00 3.27
1560 1615 3.096092 TGCTGTGTATGGGGGAATTTTC 58.904 45.455 0.00 0.00 0.00 2.29
1562 1617 3.706086 GCTGTGTATGGGGGAATTTTCAT 59.294 43.478 0.00 0.00 0.00 2.57
1568 1628 1.008206 TGGGGGAATTTTCATGGGAGG 59.992 52.381 0.00 0.00 0.00 4.30
1569 1629 1.692441 GGGGGAATTTTCATGGGAGGG 60.692 57.143 0.00 0.00 0.00 4.30
1596 1656 9.465985 GAGTAGACTCTATACTGCAAATTAACC 57.534 37.037 2.29 0.00 39.81 2.85
1599 1659 7.727181 AGACTCTATACTGCAAATTAACCGAT 58.273 34.615 0.00 0.00 0.00 4.18
1650 1710 8.482128 TGGTTTCTCCACTTGAAATACATTTTT 58.518 29.630 0.00 0.00 41.93 1.94
1835 1895 3.397955 AGGGGACAGAAGTAACAAACCAT 59.602 43.478 0.00 0.00 0.00 3.55
1853 1913 6.642707 AACCATCAAATTTAGTTTCCGTGA 57.357 33.333 0.00 0.00 0.00 4.35
1918 1978 8.993121 AGTAAATCAAATGTCATATAAGCTCCG 58.007 33.333 0.00 0.00 0.00 4.63
1967 2068 5.346281 GGATGTATCTAGCACTGAAATACGC 59.654 44.000 0.00 0.00 0.00 4.42
1984 2085 8.590204 TGAAATACGCCTAGATACATCCATTTA 58.410 33.333 0.00 0.00 0.00 1.40
1988 2089 5.012148 ACGCCTAGATACATCCATTTAAGCT 59.988 40.000 0.00 0.00 0.00 3.74
1989 2090 5.578727 CGCCTAGATACATCCATTTAAGCTC 59.421 44.000 0.00 0.00 0.00 4.09
1991 2092 6.102663 CCTAGATACATCCATTTAAGCTCCG 58.897 44.000 0.00 0.00 0.00 4.63
1992 2093 5.552870 AGATACATCCATTTAAGCTCCGT 57.447 39.130 0.00 0.00 0.00 4.69
1993 2094 5.542779 AGATACATCCATTTAAGCTCCGTC 58.457 41.667 0.00 0.00 0.00 4.79
1994 2095 2.919228 ACATCCATTTAAGCTCCGTCC 58.081 47.619 0.00 0.00 0.00 4.79
1996 2097 2.691409 TCCATTTAAGCTCCGTCCTG 57.309 50.000 0.00 0.00 0.00 3.86
1998 2099 2.569853 TCCATTTAAGCTCCGTCCTGAA 59.430 45.455 0.00 0.00 0.00 3.02
1999 2100 3.199946 TCCATTTAAGCTCCGTCCTGAAT 59.800 43.478 0.00 0.00 0.00 2.57
2000 2101 3.947834 CCATTTAAGCTCCGTCCTGAATT 59.052 43.478 0.00 0.00 0.00 2.17
2001 2102 5.104693 TCCATTTAAGCTCCGTCCTGAATTA 60.105 40.000 0.00 0.00 0.00 1.40
2002 2103 5.237344 CCATTTAAGCTCCGTCCTGAATTAG 59.763 44.000 0.00 0.00 0.00 1.73
2004 2105 6.534475 TTTAAGCTCCGTCCTGAATTAGTA 57.466 37.500 0.00 0.00 0.00 1.82
2005 2106 6.534475 TTAAGCTCCGTCCTGAATTAGTAA 57.466 37.500 0.00 0.00 0.00 2.24
2006 2107 5.416271 AAGCTCCGTCCTGAATTAGTAAA 57.584 39.130 0.00 0.00 0.00 2.01
2007 2108 5.615925 AGCTCCGTCCTGAATTAGTAAAT 57.384 39.130 0.00 0.00 0.00 1.40
2008 2109 5.602628 AGCTCCGTCCTGAATTAGTAAATC 58.397 41.667 0.00 0.00 0.00 2.17
2011 2112 6.315393 GCTCCGTCCTGAATTAGTAAATCAAA 59.685 38.462 2.40 0.00 0.00 2.69
2012 2113 7.012421 GCTCCGTCCTGAATTAGTAAATCAAAT 59.988 37.037 2.40 0.00 0.00 2.32
2015 2116 8.122952 CCGTCCTGAATTAGTAAATCAAATGTC 58.877 37.037 2.40 0.00 0.00 3.06
2027 2128 8.993121 AGTAAATCAAATGTCATATAAGCTCCG 58.007 33.333 0.00 0.00 0.00 4.63
2028 2129 7.807977 AAATCAAATGTCATATAAGCTCCGT 57.192 32.000 0.00 0.00 0.00 4.69
2029 2130 7.426929 AATCAAATGTCATATAAGCTCCGTC 57.573 36.000 0.00 0.00 0.00 4.79
2030 2131 5.297547 TCAAATGTCATATAAGCTCCGTCC 58.702 41.667 0.00 0.00 0.00 4.79
2031 2132 5.070446 TCAAATGTCATATAAGCTCCGTCCT 59.930 40.000 0.00 0.00 0.00 3.85
2032 2133 4.527509 ATGTCATATAAGCTCCGTCCTG 57.472 45.455 0.00 0.00 0.00 3.86
2043 2144 2.093658 GCTCCGTCCTGAACTAATTCCA 60.094 50.000 0.00 0.00 33.49 3.53
2165 2267 4.492328 ATTGAGACCAAATGCCCTAAGCG 61.492 47.826 0.00 0.00 39.19 4.68
2686 2799 5.588246 TGCAGATATCTTCGGCTAGAGATAG 59.412 44.000 1.33 0.00 44.77 2.08
2700 2813 9.332502 CGGCTAGAGATAGTATGTTCAGTATAT 57.667 37.037 0.00 0.00 0.00 0.86
2777 2890 8.352942 ACATCTGTTTTCTTTTGTACTCCAATC 58.647 33.333 0.00 0.00 31.81 2.67
2793 2906 4.766375 TCCAATCAGAAAATACGACCCTC 58.234 43.478 0.00 0.00 0.00 4.30
2893 3006 5.071115 TGGTTTTAAGATTCCCTTGGTTTGG 59.929 40.000 0.00 0.00 36.34 3.28
2917 3030 9.391006 TGGTACCATTTTCATATCTTTACAGAC 57.609 33.333 11.60 0.00 0.00 3.51
3073 3187 4.079558 TCCTAGGAGGATTGTAACCGTACT 60.080 45.833 7.62 0.00 40.06 2.73
3096 3210 7.542025 ACTCCTATCTTTTCAATGCAATGAAC 58.458 34.615 16.70 0.00 38.95 3.18
3151 3266 6.648192 AGAGATGACATTTCTCTTAACTGGG 58.352 40.000 2.67 0.00 46.01 4.45
3159 3274 1.079825 TCTCTTAACTGGGGCCACCTA 59.920 52.381 0.20 0.00 41.11 3.08
3181 3296 8.603304 ACCTAAGACTGGTTCAATACTGTTTAT 58.397 33.333 0.00 0.00 33.34 1.40
3191 3312 4.924462 TCAATACTGTTTATGTCAACGCGA 59.076 37.500 15.93 0.00 0.00 5.87
3192 3313 4.835199 ATACTGTTTATGTCAACGCGAC 57.165 40.909 15.93 0.00 45.61 5.19
3215 3336 7.462462 CGACCTCGTTTGAAAAGTATTAGTAGC 60.462 40.741 0.00 0.00 34.11 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.439679 CTCCGTAGCCACTGAAAACC 58.560 55.000 0.00 0.00 0.00 3.27
1 2 0.796927 GCTCCGTAGCCACTGAAAAC 59.203 55.000 0.00 0.00 43.40 2.43
2 3 3.226884 GCTCCGTAGCCACTGAAAA 57.773 52.632 0.00 0.00 43.40 2.29
25 26 4.735132 TCAGAAGTTCCGCCGCCG 62.735 66.667 0.00 0.00 0.00 6.46
26 27 2.125106 ATCAGAAGTTCCGCCGCC 60.125 61.111 0.00 0.00 0.00 6.13
27 28 0.102481 TAGATCAGAAGTTCCGCCGC 59.898 55.000 0.00 0.00 0.00 6.53
28 29 1.269309 CCTAGATCAGAAGTTCCGCCG 60.269 57.143 0.00 0.00 0.00 6.46
29 30 1.757699 ACCTAGATCAGAAGTTCCGCC 59.242 52.381 0.00 0.00 0.00 6.13
30 31 3.528597 AACCTAGATCAGAAGTTCCGC 57.471 47.619 0.00 0.00 0.00 5.54
31 32 6.217294 GGATTAACCTAGATCAGAAGTTCCG 58.783 44.000 0.00 0.00 35.41 4.30
32 33 6.526526 GGGATTAACCTAGATCAGAAGTTCC 58.473 44.000 0.00 0.00 38.98 3.62
33 34 6.040616 TCGGGATTAACCTAGATCAGAAGTTC 59.959 42.308 0.00 0.00 38.98 3.01
34 35 5.897824 TCGGGATTAACCTAGATCAGAAGTT 59.102 40.000 0.00 0.00 38.98 2.66
35 36 5.455872 TCGGGATTAACCTAGATCAGAAGT 58.544 41.667 0.00 0.00 38.98 3.01
36 37 6.406692 TTCGGGATTAACCTAGATCAGAAG 57.593 41.667 0.00 0.00 38.98 2.85
37 38 5.304614 CCTTCGGGATTAACCTAGATCAGAA 59.695 44.000 0.00 0.00 38.98 3.02
38 39 4.833380 CCTTCGGGATTAACCTAGATCAGA 59.167 45.833 0.00 0.00 38.98 3.27
39 40 5.140747 CCTTCGGGATTAACCTAGATCAG 57.859 47.826 0.00 0.00 38.98 2.90
55 56 2.616842 CAAATATTCCGGAACCCTTCGG 59.383 50.000 21.56 2.30 46.89 4.30
56 57 2.616842 CCAAATATTCCGGAACCCTTCG 59.383 50.000 21.56 6.70 0.00 3.79
57 58 3.893521 TCCAAATATTCCGGAACCCTTC 58.106 45.455 21.56 0.00 0.00 3.46
58 59 4.325084 TTCCAAATATTCCGGAACCCTT 57.675 40.909 21.56 10.41 33.88 3.95
59 60 4.325084 TTTCCAAATATTCCGGAACCCT 57.675 40.909 21.56 6.52 38.52 4.34
60 61 5.607939 AATTTCCAAATATTCCGGAACCC 57.392 39.130 21.56 0.00 38.52 4.11
61 62 9.093970 CTTTAAATTTCCAAATATTCCGGAACC 57.906 33.333 21.56 0.00 38.52 3.62
62 63 9.647797 ACTTTAAATTTCCAAATATTCCGGAAC 57.352 29.630 21.56 0.00 38.52 3.62
63 64 9.646427 CACTTTAAATTTCCAAATATTCCGGAA 57.354 29.630 21.37 21.37 37.03 4.30
64 65 7.762159 GCACTTTAAATTTCCAAATATTCCGGA 59.238 33.333 0.00 0.00 0.00 5.14
65 66 7.547370 TGCACTTTAAATTTCCAAATATTCCGG 59.453 33.333 0.00 0.00 0.00 5.14
66 67 8.472683 TGCACTTTAAATTTCCAAATATTCCG 57.527 30.769 0.00 0.00 0.00 4.30
71 72 9.487790 CCTCTTTGCACTTTAAATTTCCAAATA 57.512 29.630 0.00 0.00 0.00 1.40
72 73 7.445096 CCCTCTTTGCACTTTAAATTTCCAAAT 59.555 33.333 0.00 0.00 0.00 2.32
73 74 6.765512 CCCTCTTTGCACTTTAAATTTCCAAA 59.234 34.615 0.00 0.00 0.00 3.28
74 75 6.287525 CCCTCTTTGCACTTTAAATTTCCAA 58.712 36.000 0.00 0.00 0.00 3.53
75 76 5.221621 CCCCTCTTTGCACTTTAAATTTCCA 60.222 40.000 0.00 0.00 0.00 3.53
76 77 5.237815 CCCCTCTTTGCACTTTAAATTTCC 58.762 41.667 0.00 0.00 0.00 3.13
77 78 5.237815 CCCCCTCTTTGCACTTTAAATTTC 58.762 41.667 0.00 0.00 0.00 2.17
78 79 5.227569 CCCCCTCTTTGCACTTTAAATTT 57.772 39.130 0.00 0.00 0.00 1.82
79 80 4.890158 CCCCCTCTTTGCACTTTAAATT 57.110 40.909 0.00 0.00 0.00 1.82
111 112 2.978010 GTTGTGCCCACCTCGGTG 60.978 66.667 9.13 9.13 45.02 4.94
112 113 4.265056 GGTTGTGCCCACCTCGGT 62.265 66.667 0.00 0.00 0.00 4.69
121 122 2.361230 GCCTAGGTGGGTTGTGCC 60.361 66.667 11.31 0.00 36.00 5.01
122 123 2.746277 CGCCTAGGTGGGTTGTGC 60.746 66.667 15.00 0.00 36.00 4.57
123 124 2.746277 GCGCCTAGGTGGGTTGTG 60.746 66.667 23.60 0.00 36.00 3.33
124 125 4.388499 CGCGCCTAGGTGGGTTGT 62.388 66.667 26.83 0.00 36.00 3.32
161 162 2.282462 GAGGCACAACCCACCAGG 60.282 66.667 0.00 0.00 40.58 4.45
162 163 2.282462 GGAGGCACAACCCACCAG 60.282 66.667 0.00 0.00 40.58 4.00
163 164 3.897122 GGGAGGCACAACCCACCA 61.897 66.667 0.00 0.00 44.24 4.17
164 165 3.146828 AAGGGAGGCACAACCCACC 62.147 63.158 0.00 0.00 46.47 4.61
165 166 1.903404 CAAGGGAGGCACAACCCAC 60.903 63.158 0.00 0.00 46.47 4.61
166 167 2.520458 CAAGGGAGGCACAACCCA 59.480 61.111 0.00 0.00 46.47 4.51
167 168 2.283173 CCAAGGGAGGCACAACCC 60.283 66.667 0.00 0.00 44.94 4.11
168 169 2.283173 CCCAAGGGAGGCACAACC 60.283 66.667 0.00 0.00 37.50 3.77
189 190 4.421515 CAGAGCTGCACCTGGGGG 62.422 72.222 1.02 0.00 38.88 5.40
190 191 4.421515 CCAGAGCTGCACCTGGGG 62.422 72.222 24.51 0.00 44.68 4.96
197 198 4.269523 AAACGGGCCAGAGCTGCA 62.270 61.111 10.86 0.00 39.73 4.41
198 199 3.741476 CAAACGGGCCAGAGCTGC 61.741 66.667 10.86 0.00 39.73 5.25
199 200 0.107703 TATCAAACGGGCCAGAGCTG 60.108 55.000 10.86 3.60 39.73 4.24
200 201 0.839946 ATATCAAACGGGCCAGAGCT 59.160 50.000 10.86 0.00 39.73 4.09
201 202 1.334869 CAATATCAAACGGGCCAGAGC 59.665 52.381 10.86 0.00 38.76 4.09
202 203 2.917933 TCAATATCAAACGGGCCAGAG 58.082 47.619 10.86 0.00 0.00 3.35
203 204 3.576078 ATCAATATCAAACGGGCCAGA 57.424 42.857 10.86 0.00 0.00 3.86
204 205 4.654091 AAATCAATATCAAACGGGCCAG 57.346 40.909 4.39 1.85 0.00 4.85
205 206 5.413309 AAAAATCAATATCAAACGGGCCA 57.587 34.783 4.39 0.00 0.00 5.36
248 249 1.740043 GCAGTGCCAGTTGCTGTTTTT 60.740 47.619 2.85 0.00 42.00 1.94
249 250 0.179103 GCAGTGCCAGTTGCTGTTTT 60.179 50.000 2.85 0.00 42.00 2.43
250 251 1.438814 GCAGTGCCAGTTGCTGTTT 59.561 52.632 2.85 0.00 42.00 2.83
251 252 2.837883 CGCAGTGCCAGTTGCTGTT 61.838 57.895 10.11 0.00 42.00 3.16
252 253 3.282157 CGCAGTGCCAGTTGCTGT 61.282 61.111 10.11 0.00 42.00 4.40
253 254 4.695231 GCGCAGTGCCAGTTGCTG 62.695 66.667 10.11 0.00 42.00 4.41
255 256 4.988486 GTGCGCAGTGCCAGTTGC 62.988 66.667 12.22 7.28 45.60 4.17
256 257 1.904852 CTAGTGCGCAGTGCCAGTTG 61.905 60.000 27.70 8.69 45.60 3.16
257 258 1.669115 CTAGTGCGCAGTGCCAGTT 60.669 57.895 27.70 3.15 45.60 3.16
258 259 2.047844 CTAGTGCGCAGTGCCAGT 60.048 61.111 27.70 13.44 45.60 4.00
259 260 2.816958 CCTAGTGCGCAGTGCCAG 60.817 66.667 27.70 16.51 45.60 4.85
260 261 3.589654 GACCTAGTGCGCAGTGCCA 62.590 63.158 27.70 7.02 45.60 4.92
261 262 2.815647 GACCTAGTGCGCAGTGCC 60.816 66.667 27.70 7.91 45.60 5.01
262 263 1.021390 ATTGACCTAGTGCGCAGTGC 61.021 55.000 27.70 13.94 46.70 4.40
263 264 2.196749 CTATTGACCTAGTGCGCAGTG 58.803 52.381 27.70 14.29 0.00 3.66
264 265 1.137086 CCTATTGACCTAGTGCGCAGT 59.863 52.381 23.25 23.25 0.00 4.40
265 266 1.137086 ACCTATTGACCTAGTGCGCAG 59.863 52.381 12.22 0.12 0.00 5.18
266 267 1.191535 ACCTATTGACCTAGTGCGCA 58.808 50.000 5.66 5.66 0.00 6.09
267 268 2.311124 AACCTATTGACCTAGTGCGC 57.689 50.000 0.00 0.00 0.00 6.09
268 269 4.499357 GGACTAACCTATTGACCTAGTGCG 60.499 50.000 0.00 0.00 35.41 5.34
269 270 4.202233 GGGACTAACCTATTGACCTAGTGC 60.202 50.000 0.00 0.00 38.98 4.40
270 271 4.960469 TGGGACTAACCTATTGACCTAGTG 59.040 45.833 0.00 0.00 38.98 2.74
271 272 5.216665 TGGGACTAACCTATTGACCTAGT 57.783 43.478 0.00 0.00 38.98 2.57
272 273 6.555463 TTTGGGACTAACCTATTGACCTAG 57.445 41.667 0.00 0.00 38.98 3.02
273 274 6.956102 TTTTGGGACTAACCTATTGACCTA 57.044 37.500 0.00 0.00 38.98 3.08
274 275 5.853572 TTTTGGGACTAACCTATTGACCT 57.146 39.130 0.00 0.00 38.98 3.85
307 308 9.956720 GATGCTTACAATCATTTTATAGCAACT 57.043 29.630 0.00 0.00 40.33 3.16
308 309 9.185192 GGATGCTTACAATCATTTTATAGCAAC 57.815 33.333 0.00 0.00 40.33 4.17
309 310 8.911965 TGGATGCTTACAATCATTTTATAGCAA 58.088 29.630 0.00 0.00 40.33 3.91
310 311 8.462589 TGGATGCTTACAATCATTTTATAGCA 57.537 30.769 0.00 0.00 41.08 3.49
311 312 9.403110 CTTGGATGCTTACAATCATTTTATAGC 57.597 33.333 0.00 0.00 0.00 2.97
315 316 9.806203 CATTCTTGGATGCTTACAATCATTTTA 57.194 29.630 0.00 0.00 0.00 1.52
316 317 8.533657 TCATTCTTGGATGCTTACAATCATTTT 58.466 29.630 0.00 0.00 0.00 1.82
317 318 8.070034 TCATTCTTGGATGCTTACAATCATTT 57.930 30.769 0.00 0.00 0.00 2.32
318 319 7.649533 TCATTCTTGGATGCTTACAATCATT 57.350 32.000 0.00 0.00 0.00 2.57
319 320 7.834881 ATCATTCTTGGATGCTTACAATCAT 57.165 32.000 0.00 0.00 0.00 2.45
320 321 8.750515 TTATCATTCTTGGATGCTTACAATCA 57.249 30.769 0.00 0.00 0.00 2.57
328 329 8.910944 GCCAATATATTATCATTCTTGGATGCT 58.089 33.333 0.00 0.00 34.88 3.79
329 330 8.689061 TGCCAATATATTATCATTCTTGGATGC 58.311 33.333 0.00 0.00 34.88 3.91
332 333 9.978336 TCATGCCAATATATTATCATTCTTGGA 57.022 29.630 0.00 0.00 34.88 3.53
364 365 9.836076 CGTCTCCAACGTATCTATAATTTATGA 57.164 33.333 0.00 0.00 46.42 2.15
381 382 4.363999 CTCATCCTTGATACGTCTCCAAC 58.636 47.826 0.00 0.00 0.00 3.77
382 383 3.384789 CCTCATCCTTGATACGTCTCCAA 59.615 47.826 0.00 0.00 0.00 3.53
383 384 2.959030 CCTCATCCTTGATACGTCTCCA 59.041 50.000 0.00 0.00 0.00 3.86
384 385 2.297597 CCCTCATCCTTGATACGTCTCC 59.702 54.545 0.00 0.00 0.00 3.71
385 386 2.288518 GCCCTCATCCTTGATACGTCTC 60.289 54.545 0.00 0.00 0.00 3.36
386 387 1.689273 GCCCTCATCCTTGATACGTCT 59.311 52.381 0.00 0.00 0.00 4.18
387 388 1.603172 CGCCCTCATCCTTGATACGTC 60.603 57.143 0.00 0.00 0.00 4.34
388 389 0.389391 CGCCCTCATCCTTGATACGT 59.611 55.000 0.00 0.00 0.00 3.57
389 390 0.946221 GCGCCCTCATCCTTGATACG 60.946 60.000 0.00 0.00 0.00 3.06
390 391 0.106708 TGCGCCCTCATCCTTGATAC 59.893 55.000 4.18 0.00 0.00 2.24
391 392 0.394192 CTGCGCCCTCATCCTTGATA 59.606 55.000 4.18 0.00 0.00 2.15
392 393 1.147824 CTGCGCCCTCATCCTTGAT 59.852 57.895 4.18 0.00 0.00 2.57
393 394 1.340399 ATCTGCGCCCTCATCCTTGA 61.340 55.000 4.18 0.00 0.00 3.02
394 395 0.394192 TATCTGCGCCCTCATCCTTG 59.606 55.000 4.18 0.00 0.00 3.61
395 396 1.356124 ATATCTGCGCCCTCATCCTT 58.644 50.000 4.18 0.00 0.00 3.36
413 414 2.493278 CAAATTTCAGACCTCCGGCAAT 59.507 45.455 0.00 0.00 0.00 3.56
421 422 4.768968 CCCATGTTCTCAAATTTCAGACCT 59.231 41.667 0.00 0.00 0.00 3.85
428 429 5.336102 AGGATCACCCATGTTCTCAAATTT 58.664 37.500 0.00 0.00 37.41 1.82
461 462 4.753516 ACATAACCGGATTCTCATGTGA 57.246 40.909 9.46 0.00 0.00 3.58
467 468 5.817816 ACTCATCAAACATAACCGGATTCTC 59.182 40.000 9.46 0.00 0.00 2.87
469 470 6.436843 AACTCATCAAACATAACCGGATTC 57.563 37.500 9.46 0.00 0.00 2.52
478 479 7.040548 TGCATCTGAACAAACTCATCAAACATA 60.041 33.333 0.00 0.00 0.00 2.29
488 489 5.112220 TGTTGATGCATCTGAACAAACTC 57.888 39.130 26.32 3.29 0.00 3.01
497 498 2.855963 GCCGAATTTGTTGATGCATCTG 59.144 45.455 26.32 6.02 0.00 2.90
502 503 1.847999 CGATGCCGAATTTGTTGATGC 59.152 47.619 0.00 0.00 38.22 3.91
533 534 7.719483 TCAATCAAATCTTTCTTGAACTGCTT 58.281 30.769 0.00 0.00 36.43 3.91
545 546 7.094890 CGCCTATAGATGCTCAATCAAATCTTT 60.095 37.037 0.00 0.00 37.81 2.52
579 580 9.444600 TCAACTTTTATATGTTCTAGTTGTCCC 57.555 33.333 0.00 0.00 41.76 4.46
691 727 4.282496 TGACCTTTGTTTTTAAGAGCCCA 58.718 39.130 0.00 0.00 0.00 5.36
707 744 7.213178 ACCATGTCCTCTAAATATTGACCTT 57.787 36.000 0.00 0.00 0.00 3.50
716 753 6.617371 AGGTCATCTAACCATGTCCTCTAAAT 59.383 38.462 0.00 0.00 37.67 1.40
733 770 6.191315 ACAGTGATACAGAAGTAGGTCATCT 58.809 40.000 0.00 0.00 32.86 2.90
779 816 2.081462 CCCAAACCGGACATTGTACTC 58.919 52.381 9.46 0.00 36.56 2.59
793 830 0.469144 TCTTCAAGCCCACCCCAAAC 60.469 55.000 0.00 0.00 0.00 2.93
818 857 8.324163 ACTGAAGTTAATAATGTCTTCCACAC 57.676 34.615 0.00 0.00 38.04 3.82
845 884 0.320374 TTGCACTAAGACGGGACTGG 59.680 55.000 0.00 0.00 0.00 4.00
846 885 2.069273 CTTTGCACTAAGACGGGACTG 58.931 52.381 0.00 0.00 0.00 3.51
931 971 2.802816 GTCAGTGCCGATGATGTTATCC 59.197 50.000 0.00 0.00 0.00 2.59
1206 1246 3.436001 GACGAAAGGCATTCTCGGA 57.564 52.632 15.99 0.00 40.66 4.55
1217 1257 0.951558 CCAAACCCACCTGACGAAAG 59.048 55.000 0.00 0.00 0.00 2.62
1321 1361 1.075698 TCCCTCTTCTTCACCGAGTCT 59.924 52.381 0.00 0.00 0.00 3.24
1330 1370 1.178276 TCTGACGCTCCCTCTTCTTC 58.822 55.000 0.00 0.00 0.00 2.87
1435 1477 5.131809 ACTTGAAGGATGGAGAAAGGGATAG 59.868 44.000 0.00 0.00 0.00 2.08
1452 1494 8.871686 AAGTATTTTAGTGGCAAAACTTGAAG 57.128 30.769 0.00 0.00 30.57 3.02
1560 1615 1.219213 AGAGTCTACTCCCCTCCCATG 59.781 57.143 6.50 0.00 43.88 3.66
1562 1617 2.298619 TAGAGTCTACTCCCCTCCCA 57.701 55.000 6.50 0.00 43.88 4.37
1568 1628 6.658188 ATTTGCAGTATAGAGTCTACTCCC 57.342 41.667 0.85 0.00 43.88 4.30
1569 1629 9.465985 GTTAATTTGCAGTATAGAGTCTACTCC 57.534 37.037 0.85 0.00 43.88 3.85
1650 1710 4.644498 TCAGAATGACAGAATGCAACTCA 58.356 39.130 0.00 0.00 42.56 3.41
1835 1895 5.984926 AGTACGTCACGGAAACTAAATTTGA 59.015 36.000 0.35 0.00 0.00 2.69
1853 1913 8.008513 ACACCTATTATTCAGATGAAGTACGT 57.991 34.615 1.32 0.00 37.48 3.57
1913 1973 2.930682 GTCAACTAATTCAGGACGGAGC 59.069 50.000 0.00 0.00 0.00 4.70
1918 1978 6.564125 CGTTTGAGTGTCAACTAATTCAGGAC 60.564 42.308 0.00 0.00 35.89 3.85
1967 2068 6.102663 CGGAGCTTAAATGGATGTATCTAGG 58.897 44.000 0.00 0.00 0.00 3.02
1984 2085 5.416271 TTTACTAATTCAGGACGGAGCTT 57.584 39.130 0.00 0.00 0.00 3.74
1988 2089 7.827236 ACATTTGATTTACTAATTCAGGACGGA 59.173 33.333 0.00 0.00 0.00 4.69
1989 2090 7.985476 ACATTTGATTTACTAATTCAGGACGG 58.015 34.615 0.00 0.00 0.00 4.79
2001 2102 8.993121 CGGAGCTTATATGACATTTGATTTACT 58.007 33.333 0.00 0.00 0.00 2.24
2002 2103 8.774586 ACGGAGCTTATATGACATTTGATTTAC 58.225 33.333 0.00 0.00 0.00 2.01
2004 2105 7.041098 GGACGGAGCTTATATGACATTTGATTT 60.041 37.037 0.00 0.00 0.00 2.17
2005 2106 6.428159 GGACGGAGCTTATATGACATTTGATT 59.572 38.462 0.00 0.00 0.00 2.57
2006 2107 5.934625 GGACGGAGCTTATATGACATTTGAT 59.065 40.000 0.00 0.00 0.00 2.57
2007 2108 5.070446 AGGACGGAGCTTATATGACATTTGA 59.930 40.000 0.00 0.00 0.00 2.69
2008 2109 5.178252 CAGGACGGAGCTTATATGACATTTG 59.822 44.000 0.00 0.00 0.00 2.32
2011 2112 4.152647 TCAGGACGGAGCTTATATGACAT 58.847 43.478 0.00 0.00 0.00 3.06
2012 2113 3.562182 TCAGGACGGAGCTTATATGACA 58.438 45.455 0.00 0.00 0.00 3.58
2015 2116 4.592485 AGTTCAGGACGGAGCTTATATG 57.408 45.455 0.00 0.00 0.00 1.78
2017 2118 6.239232 GGAATTAGTTCAGGACGGAGCTTATA 60.239 42.308 0.03 0.00 36.01 0.98
2018 2119 5.453480 GGAATTAGTTCAGGACGGAGCTTAT 60.453 44.000 0.03 0.00 36.01 1.73
2019 2120 4.142004 GGAATTAGTTCAGGACGGAGCTTA 60.142 45.833 0.03 0.00 36.01 3.09
2020 2121 3.369576 GGAATTAGTTCAGGACGGAGCTT 60.370 47.826 0.03 0.00 36.01 3.74
2021 2122 2.168728 GGAATTAGTTCAGGACGGAGCT 59.831 50.000 0.03 0.00 36.01 4.09
2022 2123 2.093658 TGGAATTAGTTCAGGACGGAGC 60.094 50.000 0.03 0.00 36.01 4.70
2023 2124 3.447586 TCTGGAATTAGTTCAGGACGGAG 59.552 47.826 0.03 0.00 36.01 4.63
2024 2125 3.194968 GTCTGGAATTAGTTCAGGACGGA 59.805 47.826 0.03 0.00 36.01 4.69
2025 2126 3.522553 GTCTGGAATTAGTTCAGGACGG 58.477 50.000 0.03 0.00 36.01 4.79
2026 2127 3.179830 CGTCTGGAATTAGTTCAGGACG 58.820 50.000 20.74 20.74 44.99 4.79
2027 2128 3.194968 TCCGTCTGGAATTAGTTCAGGAC 59.805 47.826 0.03 6.44 42.85 3.85
2028 2129 3.437213 TCCGTCTGGAATTAGTTCAGGA 58.563 45.455 0.03 0.00 42.85 3.86
2029 2130 3.430929 CCTCCGTCTGGAATTAGTTCAGG 60.431 52.174 0.03 0.00 45.87 3.86
2030 2131 3.430929 CCCTCCGTCTGGAATTAGTTCAG 60.431 52.174 0.03 0.00 45.87 3.02
2031 2132 2.500098 CCCTCCGTCTGGAATTAGTTCA 59.500 50.000 0.03 0.00 45.87 3.18
2032 2133 2.764572 TCCCTCCGTCTGGAATTAGTTC 59.235 50.000 0.00 0.00 45.87 3.01
2043 2144 0.408700 AACCAGTACTCCCTCCGTCT 59.591 55.000 0.00 0.00 0.00 4.18
2176 2278 5.772393 TCAAGGGCTCTGAAAACCTAATA 57.228 39.130 0.00 0.00 31.88 0.98
2700 2813 9.488762 TGGAAGAAGGTAATGAGAGAAAGTATA 57.511 33.333 0.00 0.00 0.00 1.47
2777 2890 4.927425 TCTTTTCGAGGGTCGTATTTTCTG 59.073 41.667 0.00 0.00 41.35 3.02
2793 2906 8.979574 GGAAGGATTATACTGTATGTCTTTTCG 58.020 37.037 10.51 0.00 0.00 3.46
2917 3030 7.707035 GTCTAATACAAGTTCACTAGGGTCATG 59.293 40.741 0.00 0.00 0.00 3.07
2963 3076 0.631753 CAGAGGAGGGTCAGGTAGGA 59.368 60.000 0.00 0.00 0.00 2.94
3073 3187 6.404623 CGGTTCATTGCATTGAAAAGATAGGA 60.405 38.462 21.99 0.00 37.36 2.94
3151 3266 0.690762 TGAACCAGTCTTAGGTGGCC 59.309 55.000 0.00 0.00 39.86 5.36
3159 3274 7.936847 TGACATAAACAGTATTGAACCAGTCTT 59.063 33.333 0.00 0.00 0.00 3.01
3191 3312 7.156673 TGCTACTAATACTTTTCAAACGAGGT 58.843 34.615 0.00 0.00 0.00 3.85
3192 3313 7.331193 ACTGCTACTAATACTTTTCAAACGAGG 59.669 37.037 0.00 0.00 0.00 4.63
3215 3336 8.710551 CATCTACTACTACCACGACTATTACTG 58.289 40.741 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.