Multiple sequence alignment - TraesCS6D01G105900

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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 TraesCS6D01G105900 chr6D 100.000 2147 0 0 1 2147 69198818 69196672 0.000000e+00 3965
1 TraesCS6D01G105900 chr6D 83.069 378 48 7 1245 1615 69218691 69218323 1.590000e-86 329
2 TraesCS6D01G105900 chr6D 91.192 193 16 1 1956 2147 69216593 69216401 5.880000e-66 261
3 TraesCS6D01G105900 chr6A 89.887 1414 86 22 374 1767 87299227 87297851 0.000000e+00 1766
4 TraesCS6D01G105900 chr6A 87.554 466 40 7 760 1224 360194569 360195017 6.790000e-145 523
5 TraesCS6D01G105900 chr6A 92.228 193 13 2 1956 2147 87300778 87300587 2.720000e-69 272
6 TraesCS6D01G105900 chr6A 91.192 193 15 2 1956 2147 87297564 87297373 5.880000e-66 261
7 TraesCS6D01G105900 chr6A 92.254 142 11 0 1771 1912 87297703 87297562 3.610000e-48 202
8 TraesCS6D01G105900 chr6A 86.066 122 13 1 1494 1615 87301281 87301164 6.220000e-26 128
9 TraesCS6D01G105900 chr6B 85.296 1333 77 33 374 1672 144274355 144273108 0.000000e+00 1266
10 TraesCS6D01G105900 chr6B 85.233 386 42 7 1239 1615 144276229 144275850 1.200000e-102 383
11 TraesCS6D01G105900 chr6B 83.959 293 37 4 1629 1913 144275745 144275455 2.720000e-69 272
12 TraesCS6D01G105900 chr6B 91.878 197 11 2 1956 2147 144272603 144272407 9.770000e-69 270
13 TraesCS6D01G105900 chr6B 88.060 201 13 5 1956 2147 144275458 144275260 5.960000e-56 228
14 TraesCS6D01G105900 chr6B 91.608 143 12 0 1771 1913 144272742 144272600 4.670000e-47 198
15 TraesCS6D01G105900 chr2D 84.426 732 49 27 760 1487 622711522 622712192 0.000000e+00 660
16 TraesCS6D01G105900 chr2D 90.164 427 22 8 810 1226 407453497 407453913 2.420000e-149 538
17 TraesCS6D01G105900 chr2D 91.597 357 24 4 1 352 545947605 545947250 2.480000e-134 488
18 TraesCS6D01G105900 chr2D 86.730 211 23 3 1279 1487 407453935 407454142 1.660000e-56 230
19 TraesCS6D01G105900 chr7D 91.737 472 24 6 760 1229 475101164 475100706 1.800000e-180 641
20 TraesCS6D01G105900 chr7D 93.388 363 19 3 1 361 66512750 66512391 1.130000e-147 532
21 TraesCS6D01G105900 chr7D 92.515 334 23 2 2 334 477407370 477407038 5.360000e-131 477
22 TraesCS6D01G105900 chr4A 83.197 732 67 25 760 1487 407814836 407815515 8.420000e-174 619
23 TraesCS6D01G105900 chr4A 92.938 354 23 2 1 353 893364 893716 4.090000e-142 514
24 TraesCS6D01G105900 chr4A 83.542 559 45 25 933 1487 657666627 657666112 1.490000e-131 479
25 TraesCS6D01G105900 chr3A 84.441 617 49 25 875 1487 152000825 152000252 4.000000e-157 564
26 TraesCS6D01G105900 chr4B 91.375 371 26 4 1 368 630020854 630020487 8.840000e-139 503
27 TraesCS6D01G105900 chr4B 92.625 339 21 4 2 338 439315566 439315902 3.200000e-133 484
28 TraesCS6D01G105900 chr5D 92.351 353 25 2 2 352 454020384 454020736 3.180000e-138 501
29 TraesCS6D01G105900 chr5D 93.114 334 21 2 2 334 438061798 438061466 2.480000e-134 488
30 TraesCS6D01G105900 chr5D 92.749 331 22 2 5 334 539581742 539581413 5.360000e-131 477
31 TraesCS6D01G105900 chr2A 87.668 446 35 6 760 1203 762023844 762024271 3.180000e-138 501
32 TraesCS6D01G105900 chr4D 91.281 367 25 3 810 1174 328704137 328703776 5.320000e-136 494
33 TraesCS6D01G105900 chr2B 87.220 446 37 6 760 1203 795408283 795408710 6.890000e-135 490
34 TraesCS6D01G105900 chr2B 86.528 193 20 4 1297 1487 795318392 795318204 7.770000e-50 207


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 TraesCS6D01G105900 chr6D 69196672 69198818 2146 True 3965.000000 3965 100.000000 1 2147 1 chr6D.!!$R1 2146
1 TraesCS6D01G105900 chr6D 69216401 69218691 2290 True 295.000000 329 87.130500 1245 2147 2 chr6D.!!$R2 902
2 TraesCS6D01G105900 chr6A 87297373 87301281 3908 True 525.800000 1766 90.325400 374 2147 5 chr6A.!!$R1 1773
3 TraesCS6D01G105900 chr6B 144272407 144276229 3822 True 436.166667 1266 87.672333 374 2147 6 chr6B.!!$R1 1773
4 TraesCS6D01G105900 chr2D 622711522 622712192 670 False 660.000000 660 84.426000 760 1487 1 chr2D.!!$F1 727
5 TraesCS6D01G105900 chr2D 407453497 407454142 645 False 384.000000 538 88.447000 810 1487 2 chr2D.!!$F2 677
6 TraesCS6D01G105900 chr4A 407814836 407815515 679 False 619.000000 619 83.197000 760 1487 1 chr4A.!!$F2 727
7 TraesCS6D01G105900 chr4A 657666112 657666627 515 True 479.000000 479 83.542000 933 1487 1 chr4A.!!$R1 554
8 TraesCS6D01G105900 chr3A 152000252 152000825 573 True 564.000000 564 84.441000 875 1487 1 chr3A.!!$R1 612

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
59 60 0.107165 GGACCTCCAACCACCATAGC 60.107 60.0 0.0 0.0 35.64 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1928 5781 0.109723 CCGTTCTTTCCACCCTCCAA 59.89 55.0 0.0 0.0 0.0 3.53 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 2.461163 CTCCATCCCCCATCTGAGG 58.539 63.158 0.00 0.00 0.00 3.86
20 21 0.574818 TCCATCCCCCATCTGAGGAT 59.425 55.000 0.00 0.00 41.16 3.24
21 22 0.990374 CCATCCCCCATCTGAGGATC 59.010 60.000 0.00 0.00 38.36 3.36
22 23 1.486556 CCATCCCCCATCTGAGGATCT 60.487 57.143 0.00 0.00 38.36 2.75
23 24 2.225727 CCATCCCCCATCTGAGGATCTA 60.226 54.545 0.00 0.00 38.36 1.98
24 25 3.524826 CATCCCCCATCTGAGGATCTAA 58.475 50.000 0.00 0.00 38.36 2.10
25 26 3.724966 TCCCCCATCTGAGGATCTAAA 57.275 47.619 0.00 0.00 34.92 1.85
26 27 4.234170 TCCCCCATCTGAGGATCTAAAT 57.766 45.455 0.00 0.00 34.92 1.40
27 28 3.912528 TCCCCCATCTGAGGATCTAAATG 59.087 47.826 0.00 0.00 34.92 2.32
30 31 4.263243 CCCCATCTGAGGATCTAAATGGAC 60.263 50.000 11.93 0.00 39.71 4.02
32 33 5.512749 CCCATCTGAGGATCTAAATGGACAG 60.513 48.000 11.93 0.00 39.71 3.51
33 34 5.071519 CCATCTGAGGATCTAAATGGACAGT 59.928 44.000 0.00 0.00 39.71 3.55
34 35 5.604758 TCTGAGGATCTAAATGGACAGTG 57.395 43.478 0.00 0.00 34.92 3.66
35 36 4.125703 CTGAGGATCTAAATGGACAGTGC 58.874 47.826 0.00 0.00 34.92 4.40
36 37 3.118261 TGAGGATCTAAATGGACAGTGCC 60.118 47.826 0.00 0.00 34.92 5.01
37 38 2.158900 AGGATCTAAATGGACAGTGCCG 60.159 50.000 0.00 0.00 0.00 5.69
38 39 2.158957 GGATCTAAATGGACAGTGCCGA 60.159 50.000 0.00 0.00 0.00 5.54
39 40 3.495100 GGATCTAAATGGACAGTGCCGAT 60.495 47.826 0.00 0.00 0.00 4.18
40 41 2.905075 TCTAAATGGACAGTGCCGATG 58.095 47.619 0.00 0.00 0.00 3.84
41 42 1.942657 CTAAATGGACAGTGCCGATGG 59.057 52.381 0.00 0.00 0.00 3.51
42 43 0.327924 AAATGGACAGTGCCGATGGA 59.672 50.000 0.00 0.00 0.00 3.41
43 44 0.392998 AATGGACAGTGCCGATGGAC 60.393 55.000 0.00 0.00 0.00 4.02
44 45 2.125106 GGACAGTGCCGATGGACC 60.125 66.667 0.00 0.00 0.00 4.46
45 46 2.660064 GGACAGTGCCGATGGACCT 61.660 63.158 0.00 0.00 0.00 3.85
46 47 1.153549 GACAGTGCCGATGGACCTC 60.154 63.158 0.00 0.00 0.00 3.85
47 48 2.187946 CAGTGCCGATGGACCTCC 59.812 66.667 0.00 0.00 0.00 4.30
57 58 3.503974 TGGACCTCCAACCACCATA 57.496 52.632 0.00 0.00 44.35 2.74
58 59 1.285280 TGGACCTCCAACCACCATAG 58.715 55.000 0.00 0.00 44.35 2.23
59 60 0.107165 GGACCTCCAACCACCATAGC 60.107 60.000 0.00 0.00 35.64 2.97
60 61 0.107165 GACCTCCAACCACCATAGCC 60.107 60.000 0.00 0.00 0.00 3.93
61 62 1.227383 CCTCCAACCACCATAGCCC 59.773 63.158 0.00 0.00 0.00 5.19
64 65 3.202001 CAACCACCATAGCCCGCG 61.202 66.667 0.00 0.00 0.00 6.46
65 66 3.395702 AACCACCATAGCCCGCGA 61.396 61.111 8.23 0.00 0.00 5.87
66 67 3.675619 AACCACCATAGCCCGCGAC 62.676 63.158 8.23 0.00 0.00 5.19
67 68 4.910585 CCACCATAGCCCGCGACC 62.911 72.222 8.23 0.00 0.00 4.79
70 71 4.647615 CCATAGCCCGCGACCTCG 62.648 72.222 8.23 0.00 43.27 4.63
71 72 3.592814 CATAGCCCGCGACCTCGA 61.593 66.667 8.23 0.00 43.02 4.04
78 79 2.052941 CGCGACCTCGACGAGATC 60.053 66.667 26.11 18.09 43.02 2.75
79 80 2.328639 GCGACCTCGACGAGATCC 59.671 66.667 26.11 9.03 43.02 3.36
80 81 2.627004 CGACCTCGACGAGATCCG 59.373 66.667 26.11 19.61 43.02 4.18
81 82 2.883468 CGACCTCGACGAGATCCGG 61.883 68.421 26.11 12.30 43.93 5.14
82 83 1.523258 GACCTCGACGAGATCCGGA 60.523 63.158 26.11 6.61 43.93 5.14
85 86 0.604243 CCTCGACGAGATCCGGAGAT 60.604 60.000 26.11 0.00 43.93 2.75
93 94 2.528134 GATCCGGAGATCCCCAACA 58.472 57.895 11.34 0.00 42.78 3.33
95 96 1.345715 ATCCGGAGATCCCCAACACC 61.346 60.000 11.34 0.00 0.00 4.16
96 97 2.186903 CGGAGATCCCCAACACCG 59.813 66.667 0.00 0.00 34.77 4.94
97 98 2.124695 GGAGATCCCCAACACCGC 60.125 66.667 0.00 0.00 0.00 5.68
98 99 2.670148 GGAGATCCCCAACACCGCT 61.670 63.158 0.00 0.00 0.00 5.52
99 100 1.450312 GAGATCCCCAACACCGCTG 60.450 63.158 0.00 0.00 0.00 5.18
101 102 4.740822 ATCCCCAACACCGCTGGC 62.741 66.667 0.00 0.00 32.10 4.85
106 107 2.662596 CAACACCGCTGGCTCCTA 59.337 61.111 0.00 0.00 0.00 2.94
107 108 1.448540 CAACACCGCTGGCTCCTAG 60.449 63.158 0.00 0.00 0.00 3.02
110 111 3.141488 ACCGCTGGCTCCTAGACG 61.141 66.667 0.00 0.00 0.00 4.18
111 112 2.829003 CCGCTGGCTCCTAGACGA 60.829 66.667 0.00 0.00 0.00 4.20
112 113 2.415608 CCGCTGGCTCCTAGACGAA 61.416 63.158 0.00 0.00 0.00 3.85
114 115 1.439644 GCTGGCTCCTAGACGAAGG 59.560 63.158 0.00 0.00 38.06 3.46
117 118 0.902984 TGGCTCCTAGACGAAGGCAA 60.903 55.000 7.75 0.00 41.91 4.52
118 119 0.249398 GGCTCCTAGACGAAGGCAAA 59.751 55.000 0.00 0.00 36.51 3.68
119 120 1.338769 GGCTCCTAGACGAAGGCAAAA 60.339 52.381 0.00 0.00 36.51 2.44
120 121 2.003301 GCTCCTAGACGAAGGCAAAAG 58.997 52.381 0.00 0.00 36.51 2.27
122 123 1.087501 CCTAGACGAAGGCAAAAGCC 58.912 55.000 0.00 0.00 0.00 4.35
124 125 2.003301 CTAGACGAAGGCAAAAGCCTC 58.997 52.381 9.77 3.07 39.63 4.70
125 126 0.951040 AGACGAAGGCAAAAGCCTCG 60.951 55.000 19.31 19.31 39.63 4.63
126 127 2.176792 CGAAGGCAAAAGCCTCGC 59.823 61.111 9.77 4.55 39.63 5.03
127 128 2.568612 GAAGGCAAAAGCCTCGCC 59.431 61.111 9.77 0.00 46.62 5.54
131 132 2.563427 GCAAAAGCCTCGCCTGAC 59.437 61.111 0.00 0.00 0.00 3.51
132 133 2.982744 GCAAAAGCCTCGCCTGACC 61.983 63.158 0.00 0.00 0.00 4.02
133 134 2.358737 AAAAGCCTCGCCTGACCG 60.359 61.111 0.00 0.00 0.00 4.79
155 156 2.663196 CGGAGCCCGGAGAAACTT 59.337 61.111 0.73 0.00 44.15 2.66
157 158 0.464452 CGGAGCCCGGAGAAACTTAT 59.536 55.000 0.73 0.00 44.15 1.73
158 159 1.134491 CGGAGCCCGGAGAAACTTATT 60.134 52.381 0.73 0.00 44.15 1.40
160 161 2.562635 GAGCCCGGAGAAACTTATTCC 58.437 52.381 0.73 0.00 0.00 3.01
168 169 5.278964 GGAGAAACTTATTCCGACACAAC 57.721 43.478 0.00 0.00 0.00 3.32
171 172 4.514066 AGAAACTTATTCCGACACAACACC 59.486 41.667 0.00 0.00 0.00 4.16
172 173 3.478857 ACTTATTCCGACACAACACCA 57.521 42.857 0.00 0.00 0.00 4.17
173 174 3.135994 ACTTATTCCGACACAACACCAC 58.864 45.455 0.00 0.00 0.00 4.16
174 175 2.172851 TATTCCGACACAACACCACC 57.827 50.000 0.00 0.00 0.00 4.61
175 176 0.882927 ATTCCGACACAACACCACCG 60.883 55.000 0.00 0.00 0.00 4.94
176 177 3.645975 CCGACACAACACCACCGC 61.646 66.667 0.00 0.00 0.00 5.68
177 178 2.892914 CGACACAACACCACCGCA 60.893 61.111 0.00 0.00 0.00 5.69
178 179 2.465299 CGACACAACACCACCGCAA 61.465 57.895 0.00 0.00 0.00 4.85
179 180 1.063488 GACACAACACCACCGCAAC 59.937 57.895 0.00 0.00 0.00 4.17
180 181 2.024022 CACAACACCACCGCAACG 59.976 61.111 0.00 0.00 0.00 4.10
203 204 3.967715 GGCAACGTCTCCCTCAAC 58.032 61.111 0.00 0.00 0.00 3.18
204 205 1.671379 GGCAACGTCTCCCTCAACC 60.671 63.158 0.00 0.00 0.00 3.77
205 206 1.671379 GCAACGTCTCCCTCAACCC 60.671 63.158 0.00 0.00 0.00 4.11
207 208 1.263356 CAACGTCTCCCTCAACCCTA 58.737 55.000 0.00 0.00 0.00 3.53
208 209 1.621814 CAACGTCTCCCTCAACCCTAA 59.378 52.381 0.00 0.00 0.00 2.69
209 210 1.264295 ACGTCTCCCTCAACCCTAAC 58.736 55.000 0.00 0.00 0.00 2.34
210 211 0.535797 CGTCTCCCTCAACCCTAACC 59.464 60.000 0.00 0.00 0.00 2.85
211 212 0.910338 GTCTCCCTCAACCCTAACCC 59.090 60.000 0.00 0.00 0.00 4.11
212 213 0.797579 TCTCCCTCAACCCTAACCCT 59.202 55.000 0.00 0.00 0.00 4.34
213 214 2.013006 TCTCCCTCAACCCTAACCCTA 58.987 52.381 0.00 0.00 0.00 3.53
214 215 2.117051 CTCCCTCAACCCTAACCCTAC 58.883 57.143 0.00 0.00 0.00 3.18
215 216 1.210538 CCCTCAACCCTAACCCTACC 58.789 60.000 0.00 0.00 0.00 3.18
217 218 1.558294 CCTCAACCCTAACCCTACCAC 59.442 57.143 0.00 0.00 0.00 4.16
219 220 1.980036 TCAACCCTAACCCTACCACAC 59.020 52.381 0.00 0.00 0.00 3.82
220 221 1.700739 CAACCCTAACCCTACCACACA 59.299 52.381 0.00 0.00 0.00 3.72
221 222 1.355112 ACCCTAACCCTACCACACAC 58.645 55.000 0.00 0.00 0.00 3.82
223 224 0.616891 CCTAACCCTACCACACACCC 59.383 60.000 0.00 0.00 0.00 4.61
224 225 1.354101 CTAACCCTACCACACACCCA 58.646 55.000 0.00 0.00 0.00 4.51
225 226 1.002773 CTAACCCTACCACACACCCAC 59.997 57.143 0.00 0.00 0.00 4.61
227 228 1.846124 CCCTACCACACACCCACCT 60.846 63.158 0.00 0.00 0.00 4.00
228 229 0.545787 CCCTACCACACACCCACCTA 60.546 60.000 0.00 0.00 0.00 3.08
229 230 0.902531 CCTACCACACACCCACCTAG 59.097 60.000 0.00 0.00 0.00 3.02
230 231 0.249398 CTACCACACACCCACCTAGC 59.751 60.000 0.00 0.00 0.00 3.42
231 232 1.537814 TACCACACACCCACCTAGCG 61.538 60.000 0.00 0.00 0.00 4.26
232 233 2.579657 CCACACACCCACCTAGCGA 61.580 63.158 0.00 0.00 0.00 4.93
233 234 1.369692 CACACACCCACCTAGCGAA 59.630 57.895 0.00 0.00 0.00 4.70
234 235 0.949105 CACACACCCACCTAGCGAAC 60.949 60.000 0.00 0.00 0.00 3.95
236 237 0.670546 CACACCCACCTAGCGAACAG 60.671 60.000 0.00 0.00 0.00 3.16
237 238 0.830444 ACACCCACCTAGCGAACAGA 60.830 55.000 0.00 0.00 0.00 3.41
238 239 0.389948 CACCCACCTAGCGAACAGAC 60.390 60.000 0.00 0.00 0.00 3.51
240 241 1.218316 CCACCTAGCGAACAGACCC 59.782 63.158 0.00 0.00 0.00 4.46
241 242 1.153823 CACCTAGCGAACAGACCCG 60.154 63.158 0.00 0.00 0.00 5.28
242 243 1.303888 ACCTAGCGAACAGACCCGA 60.304 57.895 0.00 0.00 0.00 5.14
243 244 1.313812 ACCTAGCGAACAGACCCGAG 61.314 60.000 0.00 0.00 0.00 4.63
246 247 1.405821 CTAGCGAACAGACCCGAGATT 59.594 52.381 0.00 0.00 0.00 2.40
247 248 0.173708 AGCGAACAGACCCGAGATTC 59.826 55.000 0.00 0.00 0.00 2.52
248 249 0.806492 GCGAACAGACCCGAGATTCC 60.806 60.000 0.00 0.00 0.00 3.01
249 250 0.179108 CGAACAGACCCGAGATTCCC 60.179 60.000 0.00 0.00 0.00 3.97
250 251 0.178301 GAACAGACCCGAGATTCCCC 59.822 60.000 0.00 0.00 0.00 4.81
254 255 2.040779 ACCCGAGATTCCCCTCCC 60.041 66.667 0.00 0.00 0.00 4.30
255 256 2.287251 CCCGAGATTCCCCTCCCT 59.713 66.667 0.00 0.00 0.00 4.20
256 257 1.839296 CCCGAGATTCCCCTCCCTC 60.839 68.421 0.00 0.00 0.00 4.30
258 259 1.839296 CGAGATTCCCCTCCCTCCC 60.839 68.421 0.00 0.00 0.00 4.30
260 261 2.040779 GATTCCCCTCCCTCCCGT 60.041 66.667 0.00 0.00 0.00 5.28
262 263 4.772231 TTCCCCTCCCTCCCGTCG 62.772 72.222 0.00 0.00 0.00 5.12
283 284 3.760035 GAGCGGCCAACGGAGAGA 61.760 66.667 2.24 0.00 44.51 3.10
285 286 3.760035 GCGGCCAACGGAGAGAGA 61.760 66.667 2.24 0.00 44.51 3.10
286 287 2.492090 CGGCCAACGGAGAGAGAG 59.508 66.667 2.24 0.00 39.42 3.20
287 288 2.896443 GGCCAACGGAGAGAGAGG 59.104 66.667 0.00 0.00 0.00 3.69
288 289 2.726351 GGCCAACGGAGAGAGAGGG 61.726 68.421 0.00 0.00 0.00 4.30
291 292 0.533032 CCAACGGAGAGAGAGGGAAC 59.467 60.000 0.00 0.00 0.00 3.62
314 315 3.577313 GCGCGCAAGGAATCCCTC 61.577 66.667 29.10 0.00 43.48 4.30
315 316 2.187946 CGCGCAAGGAATCCCTCT 59.812 61.111 8.75 0.00 43.48 3.69
316 317 1.450312 CGCGCAAGGAATCCCTCTT 60.450 57.895 8.75 0.00 43.48 2.85
317 318 1.709147 CGCGCAAGGAATCCCTCTTG 61.709 60.000 8.75 0.00 43.48 3.02
318 319 1.379642 GCGCAAGGAATCCCTCTTGG 61.380 60.000 0.30 0.00 43.48 3.61
319 320 1.379642 CGCAAGGAATCCCTCTTGGC 61.380 60.000 0.00 0.00 43.48 4.52
322 323 0.922626 AAGGAATCCCTCTTGGCCTC 59.077 55.000 3.32 0.00 43.48 4.70
323 324 0.990818 AGGAATCCCTCTTGGCCTCC 60.991 60.000 3.32 0.00 38.86 4.30
324 325 0.990818 GGAATCCCTCTTGGCCTCCT 60.991 60.000 3.32 0.00 33.75 3.69
326 327 0.627986 AATCCCTCTTGGCCTCCTTG 59.372 55.000 3.32 0.00 0.00 3.61
327 328 0.253347 ATCCCTCTTGGCCTCCTTGA 60.253 55.000 3.32 0.00 0.00 3.02
329 330 0.182299 CCCTCTTGGCCTCCTTGATC 59.818 60.000 3.32 0.00 0.00 2.92
331 332 0.813210 CTCTTGGCCTCCTTGATCGC 60.813 60.000 3.32 0.00 0.00 4.58
332 333 1.821332 CTTGGCCTCCTTGATCGCC 60.821 63.158 3.32 0.50 41.99 5.54
334 335 0.980754 TTGGCCTCCTTGATCGCCTA 60.981 55.000 3.32 0.00 42.15 3.93
335 336 1.369321 GGCCTCCTTGATCGCCTAG 59.631 63.158 0.00 0.00 38.41 3.02
348 349 4.875561 ATCGCCTAGATCCTACTTTTCC 57.124 45.455 0.00 0.00 33.45 3.13
349 350 2.621998 TCGCCTAGATCCTACTTTTCCG 59.378 50.000 0.00 0.00 0.00 4.30
350 351 2.288273 CGCCTAGATCCTACTTTTCCGG 60.288 54.545 0.00 0.00 0.00 5.14
351 352 2.037381 GCCTAGATCCTACTTTTCCGGG 59.963 54.545 0.00 0.00 0.00 5.73
353 354 3.069729 CCTAGATCCTACTTTTCCGGGTG 59.930 52.174 0.00 0.00 0.00 4.61
354 355 1.209747 AGATCCTACTTTTCCGGGTGC 59.790 52.381 0.00 0.00 0.00 5.01
355 356 0.107848 ATCCTACTTTTCCGGGTGCG 60.108 55.000 0.00 0.00 0.00 5.34
356 357 1.186917 TCCTACTTTTCCGGGTGCGA 61.187 55.000 0.00 0.00 0.00 5.10
357 358 0.739813 CCTACTTTTCCGGGTGCGAG 60.740 60.000 0.00 0.00 0.00 5.03
359 360 3.788766 CTTTTCCGGGTGCGAGCG 61.789 66.667 0.00 0.00 0.00 5.03
360 361 4.612412 TTTTCCGGGTGCGAGCGT 62.612 61.111 0.00 0.00 0.00 5.07
361 362 4.612412 TTTCCGGGTGCGAGCGTT 62.612 61.111 0.00 0.00 0.00 4.84
366 367 3.712881 GGGTGCGAGCGTTGTCAC 61.713 66.667 0.00 0.00 0.00 3.67
375 376 2.029073 CGTTGTCACGCAGGAGGT 59.971 61.111 0.00 0.00 40.18 3.85
376 377 1.287815 CGTTGTCACGCAGGAGGTA 59.712 57.895 0.00 0.00 40.18 3.08
377 378 0.319211 CGTTGTCACGCAGGAGGTAA 60.319 55.000 0.00 0.00 40.18 2.85
378 379 1.870580 CGTTGTCACGCAGGAGGTAAA 60.871 52.381 0.00 0.00 40.18 2.01
380 381 1.873698 TGTCACGCAGGAGGTAAAAC 58.126 50.000 0.00 0.00 0.00 2.43
381 382 1.154197 GTCACGCAGGAGGTAAAACC 58.846 55.000 0.00 0.00 38.99 3.27
383 384 0.872388 CACGCAGGAGGTAAAACCAC 59.128 55.000 0.00 0.00 41.95 4.16
384 385 0.601841 ACGCAGGAGGTAAAACCACG 60.602 55.000 0.00 0.00 41.95 4.94
385 386 1.296056 CGCAGGAGGTAAAACCACGG 61.296 60.000 0.00 0.00 41.95 4.94
386 387 0.958876 GCAGGAGGTAAAACCACGGG 60.959 60.000 0.00 0.00 41.95 5.28
388 389 1.073548 GGAGGTAAAACCACGGGCA 59.926 57.895 0.00 0.00 41.95 5.36
389 390 1.239296 GGAGGTAAAACCACGGGCAC 61.239 60.000 0.00 0.00 41.95 5.01
406 2405 1.397190 GCACGTCGTTGTCAATGTCAG 60.397 52.381 0.00 1.16 0.00 3.51
455 2460 3.686726 GGTTCCTGCTAATCACTTGTGAG 59.313 47.826 9.39 0.00 0.00 3.51
456 2461 4.319177 GTTCCTGCTAATCACTTGTGAGT 58.681 43.478 9.39 9.04 36.25 3.41
457 2462 4.623932 TCCTGCTAATCACTTGTGAGTT 57.376 40.909 8.97 6.41 32.54 3.01
458 2463 4.318332 TCCTGCTAATCACTTGTGAGTTG 58.682 43.478 8.97 8.39 32.54 3.16
459 2464 4.067896 CCTGCTAATCACTTGTGAGTTGT 58.932 43.478 8.97 0.00 32.54 3.32
460 2465 4.083643 CCTGCTAATCACTTGTGAGTTGTG 60.084 45.833 8.97 5.35 32.54 3.33
461 2466 4.702831 TGCTAATCACTTGTGAGTTGTGA 58.297 39.130 8.97 0.00 43.53 3.58
538 2554 8.582437 CCACTAAATCATGATTGGATAATGCTT 58.418 33.333 21.39 4.61 0.00 3.91
540 2556 8.800332 ACTAAATCATGATTGGATAATGCTTCC 58.200 33.333 21.39 0.00 0.00 3.46
545 2561 3.316029 TGATTGGATAATGCTTCCGCTTG 59.684 43.478 0.00 0.00 35.94 4.01
550 2566 2.192664 TAATGCTTCCGCTTGTCCAA 57.807 45.000 0.00 0.00 36.97 3.53
566 2582 2.126071 AACACGTGGCGATCTCCG 60.126 61.111 21.57 0.00 42.21 4.63
573 2589 2.125106 GGCGATCTCCGGTTTGCT 60.125 61.111 0.00 0.00 39.04 3.91
575 2591 2.517450 GCGATCTCCGGTTTGCTCG 61.517 63.158 0.00 7.48 39.04 5.03
618 2634 1.379576 GCAAGGCTGGCAAGGAGAT 60.380 57.895 9.55 0.00 0.00 2.75
682 2698 0.465705 GATCAAGGAGCCGATGGTGA 59.534 55.000 0.00 0.00 0.00 4.02
880 2911 1.530323 CGGTTCCCGGTCTTCATTTT 58.470 50.000 0.00 0.00 44.15 1.82
883 2914 2.626266 GGTTCCCGGTCTTCATTTTGTT 59.374 45.455 0.00 0.00 0.00 2.83
885 2916 4.278919 GGTTCCCGGTCTTCATTTTGTTTA 59.721 41.667 0.00 0.00 0.00 2.01
889 2920 5.770663 TCCCGGTCTTCATTTTGTTTATTCA 59.229 36.000 0.00 0.00 0.00 2.57
890 2921 6.265649 TCCCGGTCTTCATTTTGTTTATTCAA 59.734 34.615 0.00 0.00 0.00 2.69
1003 3054 2.757314 GAGCAAGGAAAGGAAAGGATGG 59.243 50.000 0.00 0.00 0.00 3.51
1314 3369 1.139853 GATTACCCTCCCTGCTCTGTG 59.860 57.143 0.00 0.00 0.00 3.66
1324 3379 2.082231 CCTGCTCTGTGTCCTGAAATG 58.918 52.381 0.00 0.00 0.00 2.32
1468 3529 9.262358 GTGTATTAGGGAGAACTGATACATTTC 57.738 37.037 12.06 0.00 45.57 2.17
1553 3623 7.696981 AGGCATTACATAGATGATGGATTCTT 58.303 34.615 0.00 0.00 40.18 2.52
1594 3664 7.426929 AGCTAGTCATGGCTTATTAATTTCG 57.573 36.000 4.49 0.00 41.01 3.46
1615 3685 4.899457 TCGGATACAATTGTCAGGAGGTAT 59.101 41.667 15.85 0.00 0.00 2.73
1617 3687 6.055588 CGGATACAATTGTCAGGAGGTATTT 58.944 40.000 15.85 0.00 0.00 1.40
1682 3853 2.047061 CCCGATCACCCTGAATTCCTA 58.953 52.381 2.27 0.00 0.00 2.94
1703 3874 9.540538 TTCCTAAATGAAACATTCCCTTTGATA 57.459 29.630 0.00 0.00 0.00 2.15
1710 3881 8.243961 TGAAACATTCCCTTTGATACTTTTGA 57.756 30.769 0.00 0.00 0.00 2.69
1712 3883 9.196552 GAAACATTCCCTTTGATACTTTTGAAG 57.803 33.333 0.00 0.00 0.00 3.02
1720 3891 7.229506 CCCTTTGATACTTTTGAAGTCTTCACT 59.770 37.037 14.98 1.33 41.77 3.41
1721 3892 8.072567 CCTTTGATACTTTTGAAGTCTTCACTG 58.927 37.037 14.98 10.19 41.77 3.66
1746 5269 0.035056 GTGGCACCAGCTGGAATAGT 60.035 55.000 39.19 13.98 41.70 2.12
1748 5271 1.098050 GGCACCAGCTGGAATAGTTG 58.902 55.000 39.19 25.09 41.70 3.16
1764 5287 6.484977 GGAATAGTTGGTCCTGAAGATCATTC 59.515 42.308 0.00 0.00 34.86 2.67
1767 5290 1.134401 TGGTCCTGAAGATCATTCGCC 60.134 52.381 0.00 0.00 27.56 5.54
1769 5292 2.365617 GGTCCTGAAGATCATTCGCCTA 59.634 50.000 0.00 0.00 0.00 3.93
1849 5702 7.352739 ACTTGTGTAGATTGTTCGAAAATGTC 58.647 34.615 0.00 0.00 0.00 3.06
1853 5706 5.642063 TGTAGATTGTTCGAAAATGTCCCTC 59.358 40.000 0.00 0.00 0.00 4.30
1913 5766 2.171870 TCAAGTGGGAAGAACGGTTTCT 59.828 45.455 0.00 0.00 44.53 2.52
1946 5799 1.975660 TTTGGAGGGTGGAAAGAACG 58.024 50.000 0.00 0.00 0.00 3.95
1947 5800 0.109723 TTGGAGGGTGGAAAGAACGG 59.890 55.000 0.00 0.00 0.00 4.44
1948 5801 1.057851 TGGAGGGTGGAAAGAACGGT 61.058 55.000 0.00 0.00 0.00 4.83
1949 5802 0.109913 GGAGGGTGGAAAGAACGGTT 59.890 55.000 0.00 0.00 0.00 4.44
1950 5803 1.478105 GGAGGGTGGAAAGAACGGTTT 60.478 52.381 0.00 0.00 0.00 3.27
1951 5804 1.878088 GAGGGTGGAAAGAACGGTTTC 59.122 52.381 0.00 0.00 35.95 2.78
1952 5805 1.213430 AGGGTGGAAAGAACGGTTTCA 59.787 47.619 0.00 0.00 38.05 2.69
1953 5806 2.158519 AGGGTGGAAAGAACGGTTTCAT 60.159 45.455 0.00 0.00 38.05 2.57
1954 5807 2.228103 GGGTGGAAAGAACGGTTTCATC 59.772 50.000 0.00 0.00 38.05 2.92
1955 5808 3.146847 GGTGGAAAGAACGGTTTCATCT 58.853 45.455 0.00 0.00 38.05 2.90
1956 5809 3.568430 GGTGGAAAGAACGGTTTCATCTT 59.432 43.478 0.00 0.00 38.05 2.40
1957 5810 4.037565 GGTGGAAAGAACGGTTTCATCTTT 59.962 41.667 5.47 5.47 43.93 2.52
2047 5900 7.709947 AGCCATAATGACATGTTCAGTTAATG 58.290 34.615 0.00 1.53 37.77 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.104777 TCCTCAGATGGGGGATGGAG 60.105 60.000 0.00 0.00 0.00 3.86
2 3 0.990374 GATCCTCAGATGGGGGATGG 59.010 60.000 0.00 0.00 39.63 3.51
3 4 2.041824 AGATCCTCAGATGGGGGATG 57.958 55.000 0.00 0.00 39.63 3.51
6 7 3.009916 CCATTTAGATCCTCAGATGGGGG 59.990 52.174 0.00 0.00 32.38 5.40
7 8 3.912528 TCCATTTAGATCCTCAGATGGGG 59.087 47.826 0.00 0.00 35.79 4.96
8 9 4.349048 TGTCCATTTAGATCCTCAGATGGG 59.651 45.833 8.44 0.00 35.79 4.00
9 10 5.071519 ACTGTCCATTTAGATCCTCAGATGG 59.928 44.000 0.00 0.00 36.29 3.51
10 11 5.990386 CACTGTCCATTTAGATCCTCAGATG 59.010 44.000 0.00 0.00 30.90 2.90
11 12 5.454471 GCACTGTCCATTTAGATCCTCAGAT 60.454 44.000 0.00 0.00 34.57 2.90
13 14 4.125703 GCACTGTCCATTTAGATCCTCAG 58.874 47.826 0.00 0.00 0.00 3.35
14 15 3.118261 GGCACTGTCCATTTAGATCCTCA 60.118 47.826 0.00 0.00 0.00 3.86
15 16 3.471680 GGCACTGTCCATTTAGATCCTC 58.528 50.000 0.00 0.00 0.00 3.71
16 17 2.158900 CGGCACTGTCCATTTAGATCCT 60.159 50.000 0.00 0.00 0.00 3.24
18 19 3.179443 TCGGCACTGTCCATTTAGATC 57.821 47.619 0.00 0.00 0.00 2.75
20 21 2.419990 CCATCGGCACTGTCCATTTAGA 60.420 50.000 0.00 0.00 0.00 2.10
21 22 1.942657 CCATCGGCACTGTCCATTTAG 59.057 52.381 0.00 0.00 0.00 1.85
22 23 1.557371 TCCATCGGCACTGTCCATTTA 59.443 47.619 0.00 0.00 0.00 1.40
23 24 0.327924 TCCATCGGCACTGTCCATTT 59.672 50.000 0.00 0.00 0.00 2.32
24 25 0.392998 GTCCATCGGCACTGTCCATT 60.393 55.000 0.00 0.00 0.00 3.16
25 26 1.221840 GTCCATCGGCACTGTCCAT 59.778 57.895 0.00 0.00 0.00 3.41
26 27 2.662596 GTCCATCGGCACTGTCCA 59.337 61.111 0.00 0.00 0.00 4.02
27 28 2.125106 GGTCCATCGGCACTGTCC 60.125 66.667 0.00 0.00 0.00 4.02
30 31 2.184020 TTGGAGGTCCATCGGCACTG 62.184 60.000 0.00 0.00 46.97 3.66
32 33 1.745489 GTTGGAGGTCCATCGGCAC 60.745 63.158 0.00 0.00 46.97 5.01
33 34 2.668632 GTTGGAGGTCCATCGGCA 59.331 61.111 0.00 0.00 46.97 5.69
34 35 2.124695 GGTTGGAGGTCCATCGGC 60.125 66.667 0.00 0.00 46.97 5.54
35 36 1.078426 GTGGTTGGAGGTCCATCGG 60.078 63.158 0.00 0.00 46.97 4.18
36 37 1.078426 GGTGGTTGGAGGTCCATCG 60.078 63.158 0.00 0.00 46.97 3.84
37 38 0.625849 ATGGTGGTTGGAGGTCCATC 59.374 55.000 0.00 0.00 46.97 3.51
38 39 1.846439 CTATGGTGGTTGGAGGTCCAT 59.154 52.381 0.00 0.00 46.97 3.41
39 40 1.285280 CTATGGTGGTTGGAGGTCCA 58.715 55.000 0.00 0.00 45.94 4.02
40 41 0.107165 GCTATGGTGGTTGGAGGTCC 60.107 60.000 0.00 0.00 0.00 4.46
41 42 0.107165 GGCTATGGTGGTTGGAGGTC 60.107 60.000 0.00 0.00 0.00 3.85
42 43 1.571773 GGGCTATGGTGGTTGGAGGT 61.572 60.000 0.00 0.00 0.00 3.85
43 44 1.227383 GGGCTATGGTGGTTGGAGG 59.773 63.158 0.00 0.00 0.00 4.30
44 45 1.153168 CGGGCTATGGTGGTTGGAG 60.153 63.158 0.00 0.00 0.00 3.86
45 46 2.994699 CGGGCTATGGTGGTTGGA 59.005 61.111 0.00 0.00 0.00 3.53
46 47 2.828549 GCGGGCTATGGTGGTTGG 60.829 66.667 0.00 0.00 0.00 3.77
47 48 3.202001 CGCGGGCTATGGTGGTTG 61.202 66.667 0.00 0.00 0.00 3.77
49 50 4.157120 GTCGCGGGCTATGGTGGT 62.157 66.667 6.13 0.00 0.00 4.16
51 52 3.792053 GAGGTCGCGGGCTATGGTG 62.792 68.421 6.13 0.00 0.00 4.17
52 53 3.537874 GAGGTCGCGGGCTATGGT 61.538 66.667 6.13 0.00 0.00 3.55
53 54 4.647615 CGAGGTCGCGGGCTATGG 62.648 72.222 6.13 0.00 0.00 2.74
54 55 3.592814 TCGAGGTCGCGGGCTATG 61.593 66.667 6.13 0.00 39.60 2.23
55 56 3.593794 GTCGAGGTCGCGGGCTAT 61.594 66.667 6.13 0.00 39.60 2.97
60 61 3.509296 GATCTCGTCGAGGTCGCGG 62.509 68.421 19.18 0.00 38.60 6.46
61 62 2.052941 GATCTCGTCGAGGTCGCG 60.053 66.667 19.18 0.00 39.60 5.87
64 65 1.500512 CTCCGGATCTCGTCGAGGTC 61.501 65.000 24.49 24.49 38.93 3.85
65 66 1.524165 CTCCGGATCTCGTCGAGGT 60.524 63.158 21.63 15.70 37.11 3.85
66 67 0.604243 ATCTCCGGATCTCGTCGAGG 60.604 60.000 21.63 6.77 37.11 4.63
67 68 0.793861 GATCTCCGGATCTCGTCGAG 59.206 60.000 16.33 16.33 43.55 4.04
70 71 2.259281 GGGATCTCCGGATCTCGTC 58.741 63.158 3.57 0.00 45.53 4.20
71 72 4.504112 GGGATCTCCGGATCTCGT 57.496 61.111 3.57 0.00 45.53 4.18
73 74 0.682292 GTTGGGGATCTCCGGATCTC 59.318 60.000 3.57 0.00 46.01 2.75
74 75 0.031111 TGTTGGGGATCTCCGGATCT 60.031 55.000 3.57 0.00 45.53 2.75
75 76 0.106894 GTGTTGGGGATCTCCGGATC 59.893 60.000 3.57 0.00 45.51 3.36
76 77 1.345715 GGTGTTGGGGATCTCCGGAT 61.346 60.000 3.57 0.00 36.71 4.18
78 79 2.590092 GGTGTTGGGGATCTCCGG 59.410 66.667 7.25 0.00 36.71 5.14
79 80 2.186903 CGGTGTTGGGGATCTCCG 59.813 66.667 7.25 0.17 36.71 4.63
80 81 2.124695 GCGGTGTTGGGGATCTCC 60.125 66.667 3.99 3.99 0.00 3.71
81 82 1.450312 CAGCGGTGTTGGGGATCTC 60.450 63.158 6.41 0.00 0.00 2.75
82 83 2.671070 CAGCGGTGTTGGGGATCT 59.329 61.111 6.41 0.00 0.00 2.75
88 89 2.859273 CTAGGAGCCAGCGGTGTTGG 62.859 65.000 14.40 0.00 36.98 3.77
89 90 1.448540 CTAGGAGCCAGCGGTGTTG 60.449 63.158 14.40 0.00 0.00 3.33
90 91 1.609501 TCTAGGAGCCAGCGGTGTT 60.610 57.895 14.40 0.75 0.00 3.32
92 93 2.496817 GTCTAGGAGCCAGCGGTG 59.503 66.667 7.86 7.86 0.00 4.94
93 94 3.141488 CGTCTAGGAGCCAGCGGT 61.141 66.667 0.00 0.00 0.00 5.68
95 96 1.064946 CTTCGTCTAGGAGCCAGCG 59.935 63.158 0.00 0.00 0.00 5.18
96 97 1.439644 CCTTCGTCTAGGAGCCAGC 59.560 63.158 0.00 0.00 37.50 4.85
97 98 1.323271 TGCCTTCGTCTAGGAGCCAG 61.323 60.000 5.39 0.00 37.50 4.85
98 99 0.902984 TTGCCTTCGTCTAGGAGCCA 60.903 55.000 5.39 0.00 37.50 4.75
99 100 0.249398 TTTGCCTTCGTCTAGGAGCC 59.751 55.000 5.39 0.00 37.50 4.70
101 102 2.003301 GCTTTTGCCTTCGTCTAGGAG 58.997 52.381 5.39 0.00 37.50 3.69
114 115 2.563427 GTCAGGCGAGGCTTTTGC 59.437 61.111 0.00 0.00 46.64 3.68
134 135 3.291101 TTTCTCCGGGCTCCGTTCG 62.291 63.158 0.00 0.00 46.80 3.95
135 136 1.740664 GTTTCTCCGGGCTCCGTTC 60.741 63.158 0.00 0.00 46.80 3.95
136 137 1.765597 AAGTTTCTCCGGGCTCCGTT 61.766 55.000 0.00 0.00 46.80 4.44
137 138 0.901580 TAAGTTTCTCCGGGCTCCGT 60.902 55.000 0.00 0.00 46.80 4.69
139 140 2.562635 GAATAAGTTTCTCCGGGCTCC 58.437 52.381 0.00 0.00 0.00 4.70
140 141 2.562635 GGAATAAGTTTCTCCGGGCTC 58.437 52.381 0.00 0.00 0.00 4.70
141 142 1.134491 CGGAATAAGTTTCTCCGGGCT 60.134 52.381 14.53 0.00 46.66 5.19
142 143 1.296727 CGGAATAAGTTTCTCCGGGC 58.703 55.000 14.53 0.00 46.66 6.13
146 147 4.753107 TGTTGTGTCGGAATAAGTTTCTCC 59.247 41.667 0.00 0.00 0.00 3.71
147 148 5.333875 GGTGTTGTGTCGGAATAAGTTTCTC 60.334 44.000 0.00 0.00 0.00 2.87
148 149 4.514066 GGTGTTGTGTCGGAATAAGTTTCT 59.486 41.667 0.00 0.00 0.00 2.52
149 150 4.273969 TGGTGTTGTGTCGGAATAAGTTTC 59.726 41.667 0.00 0.00 0.00 2.78
152 153 3.135994 GTGGTGTTGTGTCGGAATAAGT 58.864 45.455 0.00 0.00 0.00 2.24
153 154 2.482721 GGTGGTGTTGTGTCGGAATAAG 59.517 50.000 0.00 0.00 0.00 1.73
154 155 2.496111 GGTGGTGTTGTGTCGGAATAA 58.504 47.619 0.00 0.00 0.00 1.40
155 156 1.605968 CGGTGGTGTTGTGTCGGAATA 60.606 52.381 0.00 0.00 0.00 1.75
157 158 1.521906 CGGTGGTGTTGTGTCGGAA 60.522 57.895 0.00 0.00 0.00 4.30
158 159 2.107343 CGGTGGTGTTGTGTCGGA 59.893 61.111 0.00 0.00 0.00 4.55
160 161 2.465299 TTGCGGTGGTGTTGTGTCG 61.465 57.895 0.00 0.00 0.00 4.35
161 162 1.063488 GTTGCGGTGGTGTTGTGTC 59.937 57.895 0.00 0.00 0.00 3.67
163 164 2.024022 CGTTGCGGTGGTGTTGTG 59.976 61.111 0.00 0.00 0.00 3.33
164 165 3.206246 CCGTTGCGGTGGTGTTGT 61.206 61.111 0.00 0.00 42.73 3.32
182 183 3.358076 GAGGGAGACGTTGCCGAGG 62.358 68.421 0.00 0.00 43.23 4.63
183 184 2.154798 TTGAGGGAGACGTTGCCGAG 62.155 60.000 0.00 0.00 43.23 4.63
184 185 2.204461 TTGAGGGAGACGTTGCCGA 61.204 57.895 0.00 0.00 43.23 5.54
185 186 2.027625 GTTGAGGGAGACGTTGCCG 61.028 63.158 0.00 0.00 43.23 5.69
186 187 1.671379 GGTTGAGGGAGACGTTGCC 60.671 63.158 0.00 0.00 37.61 4.52
187 188 1.671379 GGGTTGAGGGAGACGTTGC 60.671 63.158 0.00 0.00 0.00 4.17
188 189 1.263356 TAGGGTTGAGGGAGACGTTG 58.737 55.000 0.00 0.00 0.00 4.10
190 191 1.264295 GTTAGGGTTGAGGGAGACGT 58.736 55.000 0.00 0.00 0.00 4.34
191 192 0.535797 GGTTAGGGTTGAGGGAGACG 59.464 60.000 0.00 0.00 0.00 4.18
192 193 0.910338 GGGTTAGGGTTGAGGGAGAC 59.090 60.000 0.00 0.00 0.00 3.36
193 194 0.797579 AGGGTTAGGGTTGAGGGAGA 59.202 55.000 0.00 0.00 0.00 3.71
194 195 2.117051 GTAGGGTTAGGGTTGAGGGAG 58.883 57.143 0.00 0.00 0.00 4.30
195 196 1.274011 GGTAGGGTTAGGGTTGAGGGA 60.274 57.143 0.00 0.00 0.00 4.20
196 197 1.210538 GGTAGGGTTAGGGTTGAGGG 58.789 60.000 0.00 0.00 0.00 4.30
198 199 2.027469 GTGTGGTAGGGTTAGGGTTGAG 60.027 54.545 0.00 0.00 0.00 3.02
199 200 1.980036 GTGTGGTAGGGTTAGGGTTGA 59.020 52.381 0.00 0.00 0.00 3.18
200 201 1.700739 TGTGTGGTAGGGTTAGGGTTG 59.299 52.381 0.00 0.00 0.00 3.77
201 202 1.701292 GTGTGTGGTAGGGTTAGGGTT 59.299 52.381 0.00 0.00 0.00 4.11
203 204 0.616891 GGTGTGTGGTAGGGTTAGGG 59.383 60.000 0.00 0.00 0.00 3.53
204 205 0.616891 GGGTGTGTGGTAGGGTTAGG 59.383 60.000 0.00 0.00 0.00 2.69
205 206 1.002773 GTGGGTGTGTGGTAGGGTTAG 59.997 57.143 0.00 0.00 0.00 2.34
207 208 1.712000 GGTGGGTGTGTGGTAGGGTT 61.712 60.000 0.00 0.00 0.00 4.11
208 209 2.151388 GGTGGGTGTGTGGTAGGGT 61.151 63.158 0.00 0.00 0.00 4.34
209 210 0.545787 TAGGTGGGTGTGTGGTAGGG 60.546 60.000 0.00 0.00 0.00 3.53
210 211 0.902531 CTAGGTGGGTGTGTGGTAGG 59.097 60.000 0.00 0.00 0.00 3.18
211 212 0.249398 GCTAGGTGGGTGTGTGGTAG 59.751 60.000 0.00 0.00 0.00 3.18
212 213 1.537814 CGCTAGGTGGGTGTGTGGTA 61.538 60.000 0.00 0.00 0.00 3.25
213 214 2.879233 CGCTAGGTGGGTGTGTGGT 61.879 63.158 0.00 0.00 0.00 4.16
214 215 2.047274 CGCTAGGTGGGTGTGTGG 60.047 66.667 0.00 0.00 0.00 4.17
215 216 0.949105 GTTCGCTAGGTGGGTGTGTG 60.949 60.000 0.00 0.00 0.00 3.82
217 218 0.670546 CTGTTCGCTAGGTGGGTGTG 60.671 60.000 0.00 0.00 0.00 3.82
219 220 0.389948 GTCTGTTCGCTAGGTGGGTG 60.390 60.000 0.00 0.00 0.00 4.61
220 221 1.542187 GGTCTGTTCGCTAGGTGGGT 61.542 60.000 0.00 0.00 0.00 4.51
221 222 1.218316 GGTCTGTTCGCTAGGTGGG 59.782 63.158 0.00 0.00 0.00 4.61
223 224 1.153823 CGGGTCTGTTCGCTAGGTG 60.154 63.158 0.00 0.00 0.00 4.00
224 225 1.303888 TCGGGTCTGTTCGCTAGGT 60.304 57.895 0.00 0.00 0.00 3.08
225 226 1.030488 TCTCGGGTCTGTTCGCTAGG 61.030 60.000 0.00 0.00 0.00 3.02
227 228 1.404391 GAATCTCGGGTCTGTTCGCTA 59.596 52.381 0.00 0.00 0.00 4.26
228 229 0.173708 GAATCTCGGGTCTGTTCGCT 59.826 55.000 0.00 0.00 0.00 4.93
229 230 0.806492 GGAATCTCGGGTCTGTTCGC 60.806 60.000 0.00 0.00 0.00 4.70
230 231 0.179108 GGGAATCTCGGGTCTGTTCG 60.179 60.000 0.00 0.00 0.00 3.95
231 232 0.178301 GGGGAATCTCGGGTCTGTTC 59.822 60.000 0.00 0.00 0.00 3.18
232 233 0.252742 AGGGGAATCTCGGGTCTGTT 60.253 55.000 0.00 0.00 0.00 3.16
233 234 0.688087 GAGGGGAATCTCGGGTCTGT 60.688 60.000 0.00 0.00 0.00 3.41
234 235 1.403687 GGAGGGGAATCTCGGGTCTG 61.404 65.000 0.00 0.00 34.74 3.51
236 237 2.141448 GGGAGGGGAATCTCGGGTC 61.141 68.421 0.00 0.00 34.74 4.46
237 238 2.040779 GGGAGGGGAATCTCGGGT 60.041 66.667 0.00 0.00 34.74 5.28
238 239 1.839296 GAGGGAGGGGAATCTCGGG 60.839 68.421 0.00 0.00 34.74 5.14
240 241 1.839296 GGGAGGGAGGGGAATCTCG 60.839 68.421 0.00 0.00 34.74 4.04
241 242 1.839296 CGGGAGGGAGGGGAATCTC 60.839 68.421 0.00 0.00 0.00 2.75
242 243 2.287251 CGGGAGGGAGGGGAATCT 59.713 66.667 0.00 0.00 0.00 2.40
243 244 2.040779 ACGGGAGGGAGGGGAATC 60.041 66.667 0.00 0.00 0.00 2.52
266 267 3.708220 CTCTCTCCGTTGGCCGCTC 62.708 68.421 0.00 0.00 34.38 5.03
267 268 3.764466 CTCTCTCCGTTGGCCGCT 61.764 66.667 0.00 0.00 34.38 5.52
269 270 2.492090 CTCTCTCTCCGTTGGCCG 59.508 66.667 0.00 0.00 0.00 6.13
271 272 1.258445 TTCCCTCTCTCTCCGTTGGC 61.258 60.000 0.00 0.00 0.00 4.52
274 275 0.114560 TGGTTCCCTCTCTCTCCGTT 59.885 55.000 0.00 0.00 0.00 4.44
275 276 0.323908 CTGGTTCCCTCTCTCTCCGT 60.324 60.000 0.00 0.00 0.00 4.69
276 277 1.671901 GCTGGTTCCCTCTCTCTCCG 61.672 65.000 0.00 0.00 0.00 4.63
277 278 1.671901 CGCTGGTTCCCTCTCTCTCC 61.672 65.000 0.00 0.00 0.00 3.71
278 279 1.671901 CCGCTGGTTCCCTCTCTCTC 61.672 65.000 0.00 0.00 0.00 3.20
279 280 1.684049 CCGCTGGTTCCCTCTCTCT 60.684 63.158 0.00 0.00 0.00 3.10
280 281 2.896443 CCGCTGGTTCCCTCTCTC 59.104 66.667 0.00 0.00 0.00 3.20
281 282 3.394836 GCCGCTGGTTCCCTCTCT 61.395 66.667 0.00 0.00 0.00 3.10
297 298 3.577313 GAGGGATTCCTTGCGCGC 61.577 66.667 27.26 27.26 45.05 6.86
298 299 1.450312 AAGAGGGATTCCTTGCGCG 60.450 57.895 0.00 0.00 45.05 6.86
301 302 1.039785 GGCCAAGAGGGATTCCTTGC 61.040 60.000 0.00 0.00 45.05 4.01
302 303 0.627986 AGGCCAAGAGGGATTCCTTG 59.372 55.000 5.01 0.00 45.05 3.61
303 304 0.922626 GAGGCCAAGAGGGATTCCTT 59.077 55.000 5.01 0.00 45.05 3.36
305 306 0.990818 AGGAGGCCAAGAGGGATTCC 60.991 60.000 5.01 0.00 40.01 3.01
306 307 0.922626 AAGGAGGCCAAGAGGGATTC 59.077 55.000 5.01 0.00 40.01 2.52
307 308 0.627986 CAAGGAGGCCAAGAGGGATT 59.372 55.000 5.01 0.00 40.01 3.01
309 310 0.253347 ATCAAGGAGGCCAAGAGGGA 60.253 55.000 5.01 0.00 40.01 4.20
310 311 0.182299 GATCAAGGAGGCCAAGAGGG 59.818 60.000 5.01 0.00 40.85 4.30
311 312 0.179062 CGATCAAGGAGGCCAAGAGG 60.179 60.000 5.01 0.00 38.23 3.69
312 313 0.813210 GCGATCAAGGAGGCCAAGAG 60.813 60.000 5.01 0.00 0.00 2.85
313 314 1.221840 GCGATCAAGGAGGCCAAGA 59.778 57.895 5.01 0.00 0.00 3.02
314 315 1.821332 GGCGATCAAGGAGGCCAAG 60.821 63.158 5.01 0.00 44.91 3.61
315 316 2.272146 GGCGATCAAGGAGGCCAA 59.728 61.111 5.01 0.00 44.91 4.52
317 318 1.115930 TCTAGGCGATCAAGGAGGCC 61.116 60.000 0.00 0.00 45.91 5.19
318 319 0.972883 ATCTAGGCGATCAAGGAGGC 59.027 55.000 0.00 0.00 0.00 4.70
326 327 4.616373 CGGAAAAGTAGGATCTAGGCGATC 60.616 50.000 0.00 0.00 46.37 3.69
327 328 3.256136 CGGAAAAGTAGGATCTAGGCGAT 59.744 47.826 0.00 0.00 34.25 4.58
329 330 2.288273 CCGGAAAAGTAGGATCTAGGCG 60.288 54.545 0.00 0.00 0.00 5.52
331 332 3.069729 CACCCGGAAAAGTAGGATCTAGG 59.930 52.174 0.73 0.00 0.00 3.02
332 333 3.492829 GCACCCGGAAAAGTAGGATCTAG 60.493 52.174 0.73 0.00 0.00 2.43
334 335 1.209747 GCACCCGGAAAAGTAGGATCT 59.790 52.381 0.73 0.00 0.00 2.75
335 336 1.664873 GCACCCGGAAAAGTAGGATC 58.335 55.000 0.73 0.00 0.00 3.36
338 339 0.739813 CTCGCACCCGGAAAAGTAGG 60.740 60.000 0.73 0.00 34.56 3.18
339 340 1.359459 GCTCGCACCCGGAAAAGTAG 61.359 60.000 0.73 0.00 34.56 2.57
340 341 1.375013 GCTCGCACCCGGAAAAGTA 60.375 57.895 0.73 0.00 34.56 2.24
341 342 2.668550 GCTCGCACCCGGAAAAGT 60.669 61.111 0.73 0.00 34.56 2.66
343 344 4.612412 ACGCTCGCACCCGGAAAA 62.612 61.111 0.73 0.00 34.56 2.29
349 350 3.712881 GTGACAACGCTCGCACCC 61.713 66.667 0.00 0.00 0.00 4.61
350 351 4.059459 CGTGACAACGCTCGCACC 62.059 66.667 0.00 0.00 43.98 5.01
359 360 1.873698 TTTACCTCCTGCGTGACAAC 58.126 50.000 0.00 0.00 0.00 3.32
360 361 2.215196 GTTTTACCTCCTGCGTGACAA 58.785 47.619 0.00 0.00 0.00 3.18
361 362 1.541670 GGTTTTACCTCCTGCGTGACA 60.542 52.381 0.00 0.00 34.73 3.58
362 363 1.154197 GGTTTTACCTCCTGCGTGAC 58.846 55.000 0.00 0.00 34.73 3.67
363 364 0.759959 TGGTTTTACCTCCTGCGTGA 59.240 50.000 0.00 0.00 39.58 4.35
366 367 1.296056 CCGTGGTTTTACCTCCTGCG 61.296 60.000 0.00 0.00 39.58 5.18
367 368 0.958876 CCCGTGGTTTTACCTCCTGC 60.959 60.000 0.00 0.00 39.58 4.85
368 369 0.958876 GCCCGTGGTTTTACCTCCTG 60.959 60.000 0.00 0.00 39.58 3.86
369 370 1.377612 GCCCGTGGTTTTACCTCCT 59.622 57.895 0.00 0.00 39.58 3.69
370 371 1.073548 TGCCCGTGGTTTTACCTCC 59.926 57.895 0.00 0.00 39.58 4.30
373 374 2.948323 CGTGCCCGTGGTTTTACC 59.052 61.111 0.00 0.00 39.22 2.85
383 384 2.314647 ATTGACAACGACGTGCCCG 61.315 57.895 0.00 0.00 40.83 6.13
384 385 1.206578 CATTGACAACGACGTGCCC 59.793 57.895 0.00 0.00 0.00 5.36
385 386 0.110823 GACATTGACAACGACGTGCC 60.111 55.000 0.00 0.00 0.00 5.01
386 387 0.579630 TGACATTGACAACGACGTGC 59.420 50.000 0.00 0.00 0.00 5.34
388 389 1.067974 TCCTGACATTGACAACGACGT 59.932 47.619 0.00 0.00 0.00 4.34
389 390 1.778334 TCCTGACATTGACAACGACG 58.222 50.000 0.00 0.00 0.00 5.12
406 2405 1.067582 CGTACAAGCGAGGGGATCC 59.932 63.158 1.92 1.92 0.00 3.36
435 2434 4.623932 ACTCACAAGTGATTAGCAGGAA 57.376 40.909 3.01 0.00 39.13 3.36
438 2437 4.751600 TCACAACTCACAAGTGATTAGCAG 59.248 41.667 3.01 0.00 39.13 4.24
455 2460 0.730265 TTGGACAAGTGCGTCACAAC 59.270 50.000 11.58 1.80 37.66 3.32
456 2461 1.454201 TTTGGACAAGTGCGTCACAA 58.546 45.000 11.58 0.00 37.66 3.33
457 2462 1.601903 GATTTGGACAAGTGCGTCACA 59.398 47.619 11.58 0.00 37.66 3.58
458 2463 1.069227 GGATTTGGACAAGTGCGTCAC 60.069 52.381 2.28 2.28 37.66 3.67
459 2464 1.234821 GGATTTGGACAAGTGCGTCA 58.765 50.000 0.00 0.00 37.66 4.35
460 2465 1.234821 TGGATTTGGACAAGTGCGTC 58.765 50.000 0.00 0.00 35.03 5.19
461 2466 1.686355 TTGGATTTGGACAAGTGCGT 58.314 45.000 0.00 0.00 0.00 5.24
538 2554 1.885388 CACGTGTTGGACAAGCGGA 60.885 57.895 7.58 0.00 30.59 5.54
550 2566 4.129737 CCGGAGATCGCCACGTGT 62.130 66.667 16.29 0.00 37.59 4.49
563 2579 1.300620 CTCACACGAGCAAACCGGA 60.301 57.895 9.46 0.00 31.00 5.14
566 2582 2.946762 GCCTCACACGAGCAAACC 59.053 61.111 0.00 0.00 38.00 3.27
573 2589 4.794439 CCGCATCGCCTCACACGA 62.794 66.667 0.00 0.00 44.75 4.35
575 2591 3.188786 GTCCGCATCGCCTCACAC 61.189 66.667 0.00 0.00 0.00 3.82
618 2634 3.055530 TGTTTTCTTCTTGCTTTTGCCCA 60.056 39.130 0.00 0.00 46.87 5.36
890 2921 2.364972 ACACCTAGCCTGCAGTTTTT 57.635 45.000 13.81 0.00 0.00 1.94
1017 3068 4.467084 ACCATGTACGCCGCCAGG 62.467 66.667 0.00 0.00 41.62 4.45
1203 3257 7.039434 TCAGAGAAACTAGAGCAGAAGATTCAA 60.039 37.037 0.00 0.00 0.00 2.69
1259 3313 2.912967 GCAATCGCTTGATGTCACAAAG 59.087 45.455 2.58 0.00 34.04 2.77
1267 3321 0.247814 GTGTCCGCAATCGCTTGATG 60.248 55.000 2.58 0.00 34.04 3.07
1314 3369 4.179579 GCCGGCGCATTTCAGGAC 62.180 66.667 12.58 0.00 34.03 3.85
1324 3379 0.661020 AATTAACACATAGCCGGCGC 59.339 50.000 23.20 0.00 0.00 6.53
1468 3529 1.417890 ACTGACAGAAGTGACTTGGGG 59.582 52.381 10.08 0.00 0.00 4.96
1594 3664 6.238759 GCAAATACCTCCTGACAATTGTATCC 60.239 42.308 11.95 0.00 0.00 2.59
1615 3685 7.659799 TCAGTTTTAGCACAGTAGATTAGCAAA 59.340 33.333 0.00 0.00 0.00 3.68
1617 3687 6.697395 TCAGTTTTAGCACAGTAGATTAGCA 58.303 36.000 0.00 0.00 0.00 3.49
1659 3830 2.284515 AATTCAGGGTGATCGGGGCC 62.285 60.000 0.00 0.00 0.00 5.80
1672 3843 8.071177 AGGGAATGTTTCATTTAGGAATTCAG 57.929 34.615 7.93 0.00 0.00 3.02
1703 3874 5.734720 TGAGACAGTGAAGACTTCAAAAGT 58.265 37.500 19.32 16.58 46.38 2.66
1720 3891 2.142761 AGCTGGTGCCACTGAGACA 61.143 57.895 0.00 0.00 40.80 3.41
1721 3892 1.670406 CAGCTGGTGCCACTGAGAC 60.670 63.158 5.57 0.00 40.80 3.36
1746 5269 2.632377 GCGAATGATCTTCAGGACCAA 58.368 47.619 0.00 0.00 0.00 3.67
1748 5271 1.139853 AGGCGAATGATCTTCAGGACC 59.860 52.381 0.00 0.00 0.00 4.46
1749 5272 2.611225 AGGCGAATGATCTTCAGGAC 57.389 50.000 0.00 0.00 0.00 3.85
1841 5694 5.181245 TGAAAAGATGACGAGGGACATTTTC 59.819 40.000 0.00 0.00 31.58 2.29
1849 5702 3.059352 AGGTTGAAAAGATGACGAGGG 57.941 47.619 0.00 0.00 0.00 4.30
1853 5706 9.893305 AATTAAAGTAAGGTTGAAAAGATGACG 57.107 29.630 0.00 0.00 0.00 4.35
1925 5778 2.691011 CGTTCTTTCCACCCTCCAAAAA 59.309 45.455 0.00 0.00 0.00 1.94
1926 5779 2.303175 CGTTCTTTCCACCCTCCAAAA 58.697 47.619 0.00 0.00 0.00 2.44
1927 5780 1.477923 CCGTTCTTTCCACCCTCCAAA 60.478 52.381 0.00 0.00 0.00 3.28
1928 5781 0.109723 CCGTTCTTTCCACCCTCCAA 59.890 55.000 0.00 0.00 0.00 3.53
1929 5782 1.057851 ACCGTTCTTTCCACCCTCCA 61.058 55.000 0.00 0.00 0.00 3.86
1930 5783 0.109913 AACCGTTCTTTCCACCCTCC 59.890 55.000 0.00 0.00 0.00 4.30
1931 5784 1.878088 GAAACCGTTCTTTCCACCCTC 59.122 52.381 0.00 0.00 0.00 4.30
1932 5785 1.213430 TGAAACCGTTCTTTCCACCCT 59.787 47.619 0.00 0.00 34.60 4.34
1933 5786 1.682740 TGAAACCGTTCTTTCCACCC 58.317 50.000 0.00 0.00 34.60 4.61
1934 5787 3.146847 AGATGAAACCGTTCTTTCCACC 58.853 45.455 0.00 0.00 34.60 4.61
1935 5788 4.830826 AAGATGAAACCGTTCTTTCCAC 57.169 40.909 0.00 0.00 34.60 4.02
1936 5789 5.432885 GAAAGATGAAACCGTTCTTTCCA 57.567 39.130 11.67 0.00 44.81 3.53
1939 5792 5.222631 GCATGAAAGATGAAACCGTTCTTT 58.777 37.500 0.00 0.00 41.20 2.52
1940 5793 4.321230 GGCATGAAAGATGAAACCGTTCTT 60.321 41.667 0.00 0.00 34.60 2.52
1941 5794 3.191371 GGCATGAAAGATGAAACCGTTCT 59.809 43.478 0.00 0.00 34.60 3.01
1942 5795 3.057596 TGGCATGAAAGATGAAACCGTTC 60.058 43.478 0.00 0.00 0.00 3.95
1943 5796 2.890311 TGGCATGAAAGATGAAACCGTT 59.110 40.909 0.00 0.00 0.00 4.44
1944 5797 2.513753 TGGCATGAAAGATGAAACCGT 58.486 42.857 0.00 0.00 0.00 4.83
1945 5798 3.788333 ATGGCATGAAAGATGAAACCG 57.212 42.857 0.00 0.00 0.00 4.44
1946 5799 3.619929 GCAATGGCATGAAAGATGAAACC 59.380 43.478 0.00 0.00 40.72 3.27
1947 5800 4.501071 AGCAATGGCATGAAAGATGAAAC 58.499 39.130 0.00 0.00 44.61 2.78
1948 5801 4.811969 AGCAATGGCATGAAAGATGAAA 57.188 36.364 0.00 0.00 44.61 2.69
1949 5802 4.221041 TCAAGCAATGGCATGAAAGATGAA 59.779 37.500 0.00 0.00 44.02 2.57
1950 5803 3.764972 TCAAGCAATGGCATGAAAGATGA 59.235 39.130 0.00 0.00 44.02 2.92
1951 5804 4.118093 TCAAGCAATGGCATGAAAGATG 57.882 40.909 0.00 0.00 44.02 2.90
2055 5908 5.810080 AAGAAGTTACTAGTCAGGCAAGT 57.190 39.130 0.00 0.00 0.00 3.16
2111 5964 3.434309 AGAAGCAACAGGGCAAACATAT 58.566 40.909 0.00 0.00 35.83 1.78


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

AutoCloner maintained by Alex Coulton.