Multiple sequence alignment - TraesCS6D01G201400

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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 TraesCS6D01G201400 chr6D 100.000 6439 0 0 1 6439 283557000 283550562 0.000000e+00 11891.0
1 TraesCS6D01G201400 chr6D 84.906 424 54 9 1 424 3494292 3494705 2.780000e-113 420.0
2 TraesCS6D01G201400 chr6B 94.315 6069 220 37 422 6439 444543369 444537375 0.000000e+00 9180.0
3 TraesCS6D01G201400 chr6A 96.356 5489 123 29 422 5850 403325584 403320113 0.000000e+00 8957.0
4 TraesCS6D01G201400 chr6A 96.225 1881 66 3 3973 5850 403137085 403135207 0.000000e+00 3075.0
5 TraesCS6D01G201400 chr6A 96.000 200 7 1 6080 6279 403320112 403319914 2.240000e-84 324.0
6 TraesCS6D01G201400 chr6A 95.000 200 9 1 6080 6279 403135206 403135008 4.850000e-81 313.0
7 TraesCS6D01G201400 chr6A 91.463 164 13 1 6276 6439 403133064 403132902 2.340000e-54 224.0
8 TraesCS6D01G201400 chr7A 88.915 424 42 5 1 421 620844512 620844933 9.570000e-143 518.0
9 TraesCS6D01G201400 chr4A 87.646 429 48 4 1 424 487895312 487895740 1.610000e-135 494.0
10 TraesCS6D01G201400 chr4A 83.898 118 17 2 6151 6267 556231385 556231501 1.900000e-20 111.0
11 TraesCS6D01G201400 chr2A 86.878 442 39 11 1 427 90686198 90685761 1.620000e-130 477.0
12 TraesCS6D01G201400 chr2A 78.125 160 27 7 6055 6211 10998057 10998211 1.910000e-15 95.3
13 TraesCS6D01G201400 chr1B 86.301 438 41 7 1 424 117462074 117461642 5.880000e-125 459.0
14 TraesCS6D01G201400 chr1B 84.471 425 57 5 3 421 577207735 577207314 1.670000e-110 411.0
15 TraesCS6D01G201400 chr1B 82.178 303 49 5 3446 3744 24104939 24104638 8.280000e-64 255.0
16 TraesCS6D01G201400 chr1B 75.410 244 48 10 6029 6265 391135805 391135567 2.450000e-19 108.0
17 TraesCS6D01G201400 chr1B 97.059 34 1 0 6162 6195 486843997 486843964 2.510000e-04 58.4
18 TraesCS6D01G201400 chr1A 86.175 434 42 11 1 421 16421907 16422335 2.740000e-123 453.0
19 TraesCS6D01G201400 chr1A 83.544 395 46 11 2636 3012 98227448 98227055 1.030000e-92 351.0
20 TraesCS6D01G201400 chr1D 87.798 377 36 6 2636 3009 31413953 31413584 3.570000e-117 433.0
21 TraesCS6D01G201400 chr1D 83.846 390 49 10 2636 3012 79314497 79314109 6.140000e-95 359.0
22 TraesCS6D01G201400 chr1D 79.464 112 21 2 6148 6258 363616446 363616336 1.920000e-10 78.7
23 TraesCS6D01G201400 chr2B 84.651 430 50 11 1 421 405479236 405479658 1.290000e-111 414.0
24 TraesCS6D01G201400 chr2B 81.459 329 52 8 3421 3744 319356649 319356973 1.780000e-65 261.0
25 TraesCS6D01G201400 chr2B 76.955 243 42 13 6030 6265 773469949 773470184 6.780000e-25 126.0
26 TraesCS6D01G201400 chr5B 84.199 443 48 13 1 425 529271263 529271701 1.670000e-110 411.0
27 TraesCS6D01G201400 chr5B 76.923 208 41 5 6059 6265 352606536 352606737 1.900000e-20 111.0
28 TraesCS6D01G201400 chr5D 86.197 355 40 7 2630 2978 439979426 439979075 6.100000e-100 375.0
29 TraesCS6D01G201400 chr3D 84.890 364 44 6 2630 2982 510649354 510649717 2.210000e-94 357.0
30 TraesCS6D01G201400 chr3D 77.917 240 46 5 6030 6265 452980482 452980718 6.730000e-30 143.0
31 TraesCS6D01G201400 chr3D 79.817 109 17 3 6157 6265 456015121 456015224 2.490000e-09 75.0
32 TraesCS6D01G201400 chrUn 84.085 377 40 8 2644 3012 94876664 94877028 4.780000e-91 346.0
33 TraesCS6D01G201400 chrUn 81.299 385 63 9 2630 3013 8810792 8811168 2.920000e-78 303.0
34 TraesCS6D01G201400 chr2D 81.818 319 42 7 3438 3744 439661340 439661026 2.980000e-63 254.0
35 TraesCS6D01G201400 chr7B 77.576 165 33 4 6102 6265 1355708 1355547 5.310000e-16 97.1
36 TraesCS6D01G201400 chr4B 85.938 64 7 2 6133 6195 405355241 405355303 4.170000e-07 67.6


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 TraesCS6D01G201400 chr6D 283550562 283557000 6438 True 11891.0 11891 100.000000 1 6439 1 chr6D.!!$R1 6438
1 TraesCS6D01G201400 chr6B 444537375 444543369 5994 True 9180.0 9180 94.315000 422 6439 1 chr6B.!!$R1 6017
2 TraesCS6D01G201400 chr6A 403319914 403325584 5670 True 4640.5 8957 96.178000 422 6279 2 chr6A.!!$R2 5857
3 TraesCS6D01G201400 chr6A 403132902 403137085 4183 True 1204.0 3075 94.229333 3973 6439 3 chr6A.!!$R1 2466

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
324 325 0.099082 GCGGACACAAAACGGACAAA 59.901 50.000 0.00 0.00 0.00 2.83 F
366 367 0.394352 GGGCCGTCTGATTTGTCCAT 60.394 55.000 0.00 0.00 0.00 3.41 F
1544 1592 0.099436 GCATCTGTGGCCATTTCGTC 59.901 55.000 9.72 0.00 0.00 4.20 F
2568 2635 1.122019 ACTCACCTTGGCGTCCTCTT 61.122 55.000 0.00 0.00 0.00 2.85 F
2653 2720 4.603535 ACCCCAGCTTGGTGCACC 62.604 66.667 29.67 29.67 45.94 5.01 F
3728 3799 2.975193 CGTGTCAGTGCATCATTTTGTG 59.025 45.455 0.00 0.00 0.00 3.33 F
4548 4621 0.378257 CTGTTTGTTGCAGCTGTCGT 59.622 50.000 16.64 0.00 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 1576 0.396435 ACTGACGAAATGGCCACAGA 59.604 50.000 21.85 0.00 0.00 3.41 R
1692 1743 1.012486 GCTGCTGGCTGAAATTGCAC 61.012 55.000 3.72 0.00 38.06 4.57 R
2963 3034 2.027625 GCACCCACGCTACACTCAC 61.028 63.158 0.00 0.00 0.00 3.51 R
3652 3723 3.312697 ACAGCTTCGAAGGAAAACAAGAC 59.687 43.478 25.77 5.71 0.00 3.01 R
4421 4494 3.316029 CCACACTTCTGTCAAATGCTTCA 59.684 43.478 0.00 0.00 0.00 3.02 R
5038 5112 1.079127 CCGAGAACGTTGGCCTGAT 60.079 57.895 5.00 0.00 37.88 2.90 R
6375 8401 0.389817 CGCGGAGTCCAAATCAGACA 60.390 55.000 10.49 0.00 36.68 3.41 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 4.933064 GCGATCTCCTCCGGCGTG 62.933 72.222 6.01 0.00 0.00 5.34
19 20 4.933064 CGATCTCCTCCGGCGTGC 62.933 72.222 6.01 0.00 0.00 5.34
20 21 3.838271 GATCTCCTCCGGCGTGCA 61.838 66.667 6.01 0.00 0.00 4.57
21 22 4.148825 ATCTCCTCCGGCGTGCAC 62.149 66.667 6.82 6.82 0.00 4.57
23 24 4.803426 CTCCTCCGGCGTGCACTC 62.803 72.222 16.19 6.81 0.00 3.51
48 49 3.752339 GGCTTCCTTGGCGCCTTG 61.752 66.667 29.70 19.46 40.62 3.61
49 50 3.752339 GCTTCCTTGGCGCCTTGG 61.752 66.667 29.70 27.24 0.00 3.61
50 51 3.752339 CTTCCTTGGCGCCTTGGC 61.752 66.667 29.70 0.00 45.12 4.52
60 61 3.443925 GCCTTGGCCGCCTTCTTC 61.444 66.667 11.61 0.00 0.00 2.87
61 62 2.352805 CCTTGGCCGCCTTCTTCT 59.647 61.111 11.61 0.00 0.00 2.85
62 63 1.303643 CCTTGGCCGCCTTCTTCTT 60.304 57.895 11.61 0.00 0.00 2.52
63 64 1.308783 CCTTGGCCGCCTTCTTCTTC 61.309 60.000 11.61 0.00 0.00 2.87
64 65 0.606401 CTTGGCCGCCTTCTTCTTCA 60.606 55.000 11.61 0.00 0.00 3.02
65 66 0.889186 TTGGCCGCCTTCTTCTTCAC 60.889 55.000 11.61 0.00 0.00 3.18
66 67 2.041115 GGCCGCCTTCTTCTTCACC 61.041 63.158 0.71 0.00 0.00 4.02
67 68 1.003233 GCCGCCTTCTTCTTCACCT 60.003 57.895 0.00 0.00 0.00 4.00
68 69 0.606673 GCCGCCTTCTTCTTCACCTT 60.607 55.000 0.00 0.00 0.00 3.50
69 70 1.897560 CCGCCTTCTTCTTCACCTTT 58.102 50.000 0.00 0.00 0.00 3.11
70 71 1.807142 CCGCCTTCTTCTTCACCTTTC 59.193 52.381 0.00 0.00 0.00 2.62
71 72 2.551071 CCGCCTTCTTCTTCACCTTTCT 60.551 50.000 0.00 0.00 0.00 2.52
72 73 3.142174 CGCCTTCTTCTTCACCTTTCTT 58.858 45.455 0.00 0.00 0.00 2.52
73 74 3.058639 CGCCTTCTTCTTCACCTTTCTTG 60.059 47.826 0.00 0.00 0.00 3.02
74 75 3.254411 GCCTTCTTCTTCACCTTTCTTGG 59.746 47.826 0.00 0.00 0.00 3.61
75 76 3.254411 CCTTCTTCTTCACCTTTCTTGGC 59.746 47.826 0.00 0.00 0.00 4.52
76 77 2.494059 TCTTCTTCACCTTTCTTGGCG 58.506 47.619 0.00 0.00 0.00 5.69
77 78 1.537202 CTTCTTCACCTTTCTTGGCGG 59.463 52.381 0.00 0.00 0.00 6.13
78 79 0.250727 TCTTCACCTTTCTTGGCGGG 60.251 55.000 0.00 0.00 0.00 6.13
79 80 0.537371 CTTCACCTTTCTTGGCGGGT 60.537 55.000 0.00 0.00 0.00 5.28
80 81 0.536460 TTCACCTTTCTTGGCGGGTC 60.536 55.000 0.00 0.00 0.00 4.46
81 82 2.032071 ACCTTTCTTGGCGGGTCG 59.968 61.111 0.00 0.00 0.00 4.79
82 83 2.032071 CCTTTCTTGGCGGGTCGT 59.968 61.111 0.00 0.00 0.00 4.34
83 84 2.033194 CCTTTCTTGGCGGGTCGTC 61.033 63.158 0.00 0.00 0.00 4.20
84 85 2.356553 TTTCTTGGCGGGTCGTCG 60.357 61.111 0.00 0.00 32.50 5.12
85 86 3.869473 TTTCTTGGCGGGTCGTCGG 62.869 63.158 0.00 0.00 32.50 4.79
132 133 3.866582 GCCATGGACGGGGGAGAG 61.867 72.222 18.40 0.00 0.00 3.20
133 134 2.041922 CCATGGACGGGGGAGAGA 60.042 66.667 5.56 0.00 0.00 3.10
134 135 2.136878 CCATGGACGGGGGAGAGAG 61.137 68.421 5.56 0.00 0.00 3.20
135 136 2.136878 CATGGACGGGGGAGAGAGG 61.137 68.421 0.00 0.00 0.00 3.69
136 137 3.396822 ATGGACGGGGGAGAGAGGG 62.397 68.421 0.00 0.00 0.00 4.30
137 138 4.862823 GGACGGGGGAGAGAGGGG 62.863 77.778 0.00 0.00 0.00 4.79
138 139 4.862823 GACGGGGGAGAGAGGGGG 62.863 77.778 0.00 0.00 0.00 5.40
161 162 4.716977 GGAGGGACGTGGGAGGGT 62.717 72.222 0.00 0.00 0.00 4.34
162 163 2.606826 GAGGGACGTGGGAGGGTT 60.607 66.667 0.00 0.00 0.00 4.11
163 164 2.122099 AGGGACGTGGGAGGGTTT 60.122 61.111 0.00 0.00 0.00 3.27
164 165 2.033602 GGGACGTGGGAGGGTTTG 59.966 66.667 0.00 0.00 0.00 2.93
165 166 2.033602 GGACGTGGGAGGGTTTGG 59.966 66.667 0.00 0.00 0.00 3.28
166 167 2.033602 GACGTGGGAGGGTTTGGG 59.966 66.667 0.00 0.00 0.00 4.12
167 168 3.562732 GACGTGGGAGGGTTTGGGG 62.563 68.421 0.00 0.00 0.00 4.96
168 169 4.360405 CGTGGGAGGGTTTGGGGG 62.360 72.222 0.00 0.00 0.00 5.40
169 170 2.861974 GTGGGAGGGTTTGGGGGA 60.862 66.667 0.00 0.00 0.00 4.81
170 171 2.037128 TGGGAGGGTTTGGGGGAA 60.037 61.111 0.00 0.00 0.00 3.97
171 172 1.705450 TGGGAGGGTTTGGGGGAAA 60.705 57.895 0.00 0.00 0.00 3.13
172 173 1.083363 TGGGAGGGTTTGGGGGAAAT 61.083 55.000 0.00 0.00 0.00 2.17
173 174 0.617535 GGGAGGGTTTGGGGGAAATG 60.618 60.000 0.00 0.00 0.00 2.32
174 175 0.617535 GGAGGGTTTGGGGGAAATGG 60.618 60.000 0.00 0.00 0.00 3.16
175 176 0.617535 GAGGGTTTGGGGGAAATGGG 60.618 60.000 0.00 0.00 0.00 4.00
176 177 1.615124 GGGTTTGGGGGAAATGGGG 60.615 63.158 0.00 0.00 0.00 4.96
177 178 2.297895 GGTTTGGGGGAAATGGGGC 61.298 63.158 0.00 0.00 0.00 5.80
178 179 2.284258 TTTGGGGGAAATGGGGCG 60.284 61.111 0.00 0.00 0.00 6.13
179 180 3.167374 TTTGGGGGAAATGGGGCGT 62.167 57.895 0.00 0.00 0.00 5.68
180 181 3.895820 TTGGGGGAAATGGGGCGTG 62.896 63.158 0.00 0.00 0.00 5.34
199 200 3.267733 GGGGGTTGGTTTCTCCCA 58.732 61.111 0.00 0.00 42.71 4.37
200 201 1.228769 GGGGGTTGGTTTCTCCCAC 60.229 63.158 0.00 0.00 42.71 4.61
202 203 4.074647 GGTTGGTTTCTCCCACCG 57.925 61.111 0.00 0.00 41.27 4.94
203 204 1.452801 GGTTGGTTTCTCCCACCGA 59.547 57.895 0.00 0.00 41.27 4.69
204 205 0.887836 GGTTGGTTTCTCCCACCGAC 60.888 60.000 1.31 1.31 45.13 4.79
205 206 0.179040 GTTGGTTTCTCCCACCGACA 60.179 55.000 4.81 0.00 45.18 4.35
206 207 0.107831 TTGGTTTCTCCCACCGACAG 59.892 55.000 0.00 0.00 37.07 3.51
207 208 1.003718 GGTTTCTCCCACCGACAGG 60.004 63.158 0.00 0.00 45.13 4.00
208 209 1.671379 GTTTCTCCCACCGACAGGC 60.671 63.158 0.00 0.00 42.76 4.85
209 210 3.234630 TTTCTCCCACCGACAGGCG 62.235 63.158 0.00 0.00 42.76 5.52
225 226 3.636231 CGGGCCAGTGGAGGACAA 61.636 66.667 15.20 0.00 38.98 3.18
226 227 2.352805 GGGCCAGTGGAGGACAAG 59.647 66.667 15.20 0.00 38.98 3.16
227 228 2.360475 GGCCAGTGGAGGACAAGC 60.360 66.667 15.20 0.00 36.38 4.01
228 229 2.743928 GCCAGTGGAGGACAAGCG 60.744 66.667 15.20 0.00 0.00 4.68
229 230 2.743928 CCAGTGGAGGACAAGCGC 60.744 66.667 1.68 0.00 0.00 5.92
230 231 3.114616 CAGTGGAGGACAAGCGCG 61.115 66.667 0.00 0.00 0.00 6.86
264 265 4.719616 GCGCGCTGTCCGTTTCAC 62.720 66.667 26.67 0.00 39.71 3.18
265 266 4.072088 CGCGCTGTCCGTTTCACC 62.072 66.667 5.56 0.00 39.71 4.02
266 267 3.723348 GCGCTGTCCGTTTCACCC 61.723 66.667 0.00 0.00 39.71 4.61
267 268 3.047877 CGCTGTCCGTTTCACCCC 61.048 66.667 0.00 0.00 0.00 4.95
268 269 2.112297 GCTGTCCGTTTCACCCCA 59.888 61.111 0.00 0.00 0.00 4.96
269 270 1.527380 GCTGTCCGTTTCACCCCAA 60.527 57.895 0.00 0.00 0.00 4.12
270 271 1.104577 GCTGTCCGTTTCACCCCAAA 61.105 55.000 0.00 0.00 0.00 3.28
271 272 1.394618 CTGTCCGTTTCACCCCAAAA 58.605 50.000 0.00 0.00 0.00 2.44
272 273 1.066454 CTGTCCGTTTCACCCCAAAAC 59.934 52.381 0.00 0.00 34.09 2.43
273 274 0.386476 GTCCGTTTCACCCCAAAACC 59.614 55.000 0.00 0.00 33.93 3.27
274 275 1.102222 TCCGTTTCACCCCAAAACCG 61.102 55.000 0.00 0.00 33.93 4.44
275 276 1.360911 CGTTTCACCCCAAAACCGG 59.639 57.895 0.00 0.00 33.93 5.28
276 277 1.068417 GTTTCACCCCAAAACCGGC 59.932 57.895 0.00 0.00 31.80 6.13
277 278 2.491022 TTTCACCCCAAAACCGGCG 61.491 57.895 0.00 0.00 0.00 6.46
281 282 3.917760 CCCCAAAACCGGCGCAAA 61.918 61.111 10.83 0.00 0.00 3.68
282 283 2.660224 CCCAAAACCGGCGCAAAC 60.660 61.111 10.83 0.00 0.00 2.93
283 284 2.415426 CCAAAACCGGCGCAAACT 59.585 55.556 10.83 0.00 0.00 2.66
284 285 1.227118 CCAAAACCGGCGCAAACTT 60.227 52.632 10.83 0.00 0.00 2.66
285 286 1.486644 CCAAAACCGGCGCAAACTTG 61.487 55.000 10.83 5.62 0.00 3.16
286 287 1.227118 AAAACCGGCGCAAACTTGG 60.227 52.632 10.83 2.92 0.00 3.61
287 288 2.636778 AAAACCGGCGCAAACTTGGG 62.637 55.000 10.83 2.32 43.22 4.12
294 295 4.986708 GCAAACTTGGGCCGGGGA 62.987 66.667 2.18 0.00 0.00 4.81
295 296 2.037208 CAAACTTGGGCCGGGGAT 59.963 61.111 2.18 0.00 0.00 3.85
296 297 2.037208 AAACTTGGGCCGGGGATG 59.963 61.111 2.18 0.00 0.00 3.51
297 298 3.600410 AAACTTGGGCCGGGGATGG 62.600 63.158 2.18 0.00 0.00 3.51
303 304 4.055227 GGCCGGGGATGGGTCAAA 62.055 66.667 2.18 0.00 0.00 2.69
304 305 2.036572 GCCGGGGATGGGTCAAAA 59.963 61.111 2.18 0.00 0.00 2.44
305 306 2.052104 GCCGGGGATGGGTCAAAAG 61.052 63.158 2.18 0.00 0.00 2.27
306 307 2.052104 CCGGGGATGGGTCAAAAGC 61.052 63.158 0.00 0.00 0.00 3.51
307 308 2.406616 CGGGGATGGGTCAAAAGCG 61.407 63.158 0.00 0.00 0.00 4.68
308 309 2.052104 GGGGATGGGTCAAAAGCGG 61.052 63.158 0.00 0.00 0.00 5.52
309 310 1.001393 GGGATGGGTCAAAAGCGGA 60.001 57.895 0.00 0.00 0.00 5.54
310 311 1.313091 GGGATGGGTCAAAAGCGGAC 61.313 60.000 0.00 0.00 34.52 4.79
311 312 0.608035 GGATGGGTCAAAAGCGGACA 60.608 55.000 0.00 0.00 37.00 4.02
312 313 0.521735 GATGGGTCAAAAGCGGACAC 59.478 55.000 0.00 0.00 39.15 3.67
313 314 1.224870 TGGGTCAAAAGCGGACACA 59.775 52.632 2.39 2.39 45.86 3.72
314 315 0.394488 TGGGTCAAAAGCGGACACAA 60.394 50.000 3.82 0.00 45.13 3.33
315 316 0.741915 GGGTCAAAAGCGGACACAAA 59.258 50.000 0.00 0.00 38.56 2.83
316 317 1.135333 GGGTCAAAAGCGGACACAAAA 59.865 47.619 0.00 0.00 38.56 2.44
317 318 2.190161 GGTCAAAAGCGGACACAAAAC 58.810 47.619 0.00 0.00 37.00 2.43
318 319 1.843753 GTCAAAAGCGGACACAAAACG 59.156 47.619 0.00 0.00 35.36 3.60
319 320 1.196200 CAAAAGCGGACACAAAACGG 58.804 50.000 0.00 0.00 0.00 4.44
320 321 1.096416 AAAAGCGGACACAAAACGGA 58.904 45.000 0.00 0.00 0.00 4.69
321 322 0.379316 AAAGCGGACACAAAACGGAC 59.621 50.000 0.00 0.00 0.00 4.79
322 323 0.745128 AAGCGGACACAAAACGGACA 60.745 50.000 0.00 0.00 0.00 4.02
323 324 0.745128 AGCGGACACAAAACGGACAA 60.745 50.000 0.00 0.00 0.00 3.18
324 325 0.099082 GCGGACACAAAACGGACAAA 59.901 50.000 0.00 0.00 0.00 2.83
325 326 1.467713 GCGGACACAAAACGGACAAAA 60.468 47.619 0.00 0.00 0.00 2.44
326 327 2.446282 CGGACACAAAACGGACAAAAG 58.554 47.619 0.00 0.00 0.00 2.27
327 328 2.159490 CGGACACAAAACGGACAAAAGT 60.159 45.455 0.00 0.00 0.00 2.66
328 329 3.431856 GGACACAAAACGGACAAAAGTC 58.568 45.455 0.00 0.00 0.00 3.01
329 330 3.431856 GACACAAAACGGACAAAAGTCC 58.568 45.455 4.59 4.59 40.04 3.85
336 337 3.157922 GGACAAAAGTCCGTTTGCG 57.842 52.632 5.75 0.00 41.33 4.85
337 338 0.933047 GGACAAAAGTCCGTTTGCGC 60.933 55.000 0.00 0.00 41.33 6.09
338 339 0.933047 GACAAAAGTCCGTTTGCGCC 60.933 55.000 4.18 0.00 41.33 6.53
339 340 1.660264 CAAAAGTCCGTTTGCGCCC 60.660 57.895 4.18 0.00 36.67 6.13
340 341 3.189010 AAAAGTCCGTTTGCGCCCG 62.189 57.895 4.18 4.36 36.67 6.13
360 361 2.436646 CGCTGGGCCGTCTGATTT 60.437 61.111 0.00 0.00 0.00 2.17
361 362 2.753966 CGCTGGGCCGTCTGATTTG 61.754 63.158 0.00 0.00 0.00 2.32
362 363 1.675641 GCTGGGCCGTCTGATTTGT 60.676 57.895 0.00 0.00 0.00 2.83
363 364 1.648467 GCTGGGCCGTCTGATTTGTC 61.648 60.000 0.00 0.00 0.00 3.18
364 365 1.002624 TGGGCCGTCTGATTTGTCC 60.003 57.895 0.00 0.00 0.00 4.02
365 366 1.002624 GGGCCGTCTGATTTGTCCA 60.003 57.895 0.00 0.00 0.00 4.02
366 367 0.394352 GGGCCGTCTGATTTGTCCAT 60.394 55.000 0.00 0.00 0.00 3.41
367 368 1.463674 GGCCGTCTGATTTGTCCATT 58.536 50.000 0.00 0.00 0.00 3.16
368 369 1.818674 GGCCGTCTGATTTGTCCATTT 59.181 47.619 0.00 0.00 0.00 2.32
369 370 2.231235 GGCCGTCTGATTTGTCCATTTT 59.769 45.455 0.00 0.00 0.00 1.82
370 371 3.442273 GGCCGTCTGATTTGTCCATTTTA 59.558 43.478 0.00 0.00 0.00 1.52
371 372 4.412207 GCCGTCTGATTTGTCCATTTTAC 58.588 43.478 0.00 0.00 0.00 2.01
372 373 4.674362 GCCGTCTGATTTGTCCATTTTACC 60.674 45.833 0.00 0.00 0.00 2.85
373 374 4.700213 CCGTCTGATTTGTCCATTTTACCT 59.300 41.667 0.00 0.00 0.00 3.08
374 375 5.183140 CCGTCTGATTTGTCCATTTTACCTT 59.817 40.000 0.00 0.00 0.00 3.50
375 376 6.373216 CCGTCTGATTTGTCCATTTTACCTTA 59.627 38.462 0.00 0.00 0.00 2.69
376 377 7.094549 CCGTCTGATTTGTCCATTTTACCTTAA 60.095 37.037 0.00 0.00 0.00 1.85
377 378 8.293867 CGTCTGATTTGTCCATTTTACCTTAAA 58.706 33.333 0.00 0.00 0.00 1.52
378 379 9.406828 GTCTGATTTGTCCATTTTACCTTAAAC 57.593 33.333 0.00 0.00 0.00 2.01
379 380 9.137459 TCTGATTTGTCCATTTTACCTTAAACA 57.863 29.630 0.00 0.00 0.00 2.83
380 381 9.410556 CTGATTTGTCCATTTTACCTTAAACAG 57.589 33.333 0.00 0.00 0.00 3.16
381 382 9.137459 TGATTTGTCCATTTTACCTTAAACAGA 57.863 29.630 0.00 0.00 0.00 3.41
382 383 9.406828 GATTTGTCCATTTTACCTTAAACAGAC 57.593 33.333 0.00 0.00 0.00 3.51
383 384 6.548441 TGTCCATTTTACCTTAAACAGACG 57.452 37.500 0.00 0.00 30.12 4.18
384 385 5.470777 TGTCCATTTTACCTTAAACAGACGG 59.529 40.000 0.00 0.00 30.12 4.79
385 386 5.005094 TCCATTTTACCTTAAACAGACGGG 58.995 41.667 0.00 0.00 0.00 5.28
386 387 4.157105 CCATTTTACCTTAAACAGACGGGG 59.843 45.833 0.00 0.00 0.00 5.73
387 388 4.703379 TTTTACCTTAAACAGACGGGGA 57.297 40.909 0.00 0.00 0.00 4.81
388 389 3.683365 TTACCTTAAACAGACGGGGAC 57.317 47.619 0.00 0.00 0.00 4.46
400 401 3.480133 GGGGACGGACAGGATGGG 61.480 72.222 0.00 0.00 43.62 4.00
401 402 3.480133 GGGACGGACAGGATGGGG 61.480 72.222 0.00 0.00 43.62 4.96
402 403 2.687566 GGACGGACAGGATGGGGT 60.688 66.667 0.00 0.00 43.62 4.95
403 404 2.584608 GACGGACAGGATGGGGTG 59.415 66.667 0.00 0.00 43.62 4.61
404 405 3.009115 ACGGACAGGATGGGGTGG 61.009 66.667 0.00 0.00 43.62 4.61
405 406 4.489771 CGGACAGGATGGGGTGGC 62.490 72.222 0.00 0.00 43.62 5.01
406 407 4.489771 GGACAGGATGGGGTGGCG 62.490 72.222 0.00 0.00 43.62 5.69
417 418 4.382320 GGTGGCGCGGTGGAGTTA 62.382 66.667 8.83 0.00 0.00 2.24
418 419 2.813908 GTGGCGCGGTGGAGTTAG 60.814 66.667 8.83 0.00 0.00 2.34
419 420 4.077184 TGGCGCGGTGGAGTTAGG 62.077 66.667 8.83 0.00 0.00 2.69
445 446 2.435693 GCCTATGGACTGGCGGACT 61.436 63.158 0.00 0.00 39.71 3.85
468 469 3.369546 AGGAAAATTCAACTGGCAACG 57.630 42.857 0.00 0.00 42.51 4.10
471 472 2.422276 AAATTCAACTGGCAACGAGC 57.578 45.000 0.00 0.00 44.65 5.03
536 538 0.984230 ATTCCGACTTGCAGGAAGGA 59.016 50.000 1.40 7.88 41.75 3.36
635 644 2.281761 CACACTGACCCCACAGCC 60.282 66.667 0.00 0.00 41.06 4.85
710 720 4.853142 TACCCGCGATGCTCCCCT 62.853 66.667 8.23 0.00 0.00 4.79
798 811 2.030562 CAACAACTCCCGCTCCGT 59.969 61.111 0.00 0.00 0.00 4.69
841 854 4.124970 AGTCTCCGCCCGATTTTTATTAC 58.875 43.478 0.00 0.00 0.00 1.89
842 855 3.060070 GTCTCCGCCCGATTTTTATTACG 60.060 47.826 0.00 0.00 0.00 3.18
843 856 2.211806 TCCGCCCGATTTTTATTACGG 58.788 47.619 0.00 0.00 44.16 4.02
844 857 2.158986 TCCGCCCGATTTTTATTACGGA 60.159 45.455 0.00 0.00 46.94 4.69
845 858 2.222445 CCGCCCGATTTTTATTACGGAG 59.778 50.000 0.00 0.00 46.94 4.63
846 859 2.349155 CGCCCGATTTTTATTACGGAGC 60.349 50.000 0.00 0.00 46.94 4.70
847 860 2.614983 GCCCGATTTTTATTACGGAGCA 59.385 45.455 0.00 0.00 46.94 4.26
848 861 3.547413 GCCCGATTTTTATTACGGAGCAC 60.547 47.826 0.00 0.00 46.94 4.40
849 862 3.002965 CCCGATTTTTATTACGGAGCACC 59.997 47.826 0.00 0.00 46.94 5.01
850 863 3.623960 CCGATTTTTATTACGGAGCACCA 59.376 43.478 0.00 0.00 46.94 4.17
851 864 4.274950 CCGATTTTTATTACGGAGCACCAT 59.725 41.667 0.00 0.00 46.94 3.55
902 932 2.227036 CCCAGAAGCACCCACCTCT 61.227 63.158 0.00 0.00 0.00 3.69
983 1013 4.366684 GCCTGGTGGAGGTTGGGG 62.367 72.222 0.00 0.00 44.97 4.96
1524 1572 3.935203 ACTTTGCATACTTCCGATCACAG 59.065 43.478 0.00 0.00 0.00 3.66
1528 1576 2.808202 GCATACTTCCGATCACAGGCAT 60.808 50.000 0.00 0.00 0.00 4.40
1531 1579 1.134580 ACTTCCGATCACAGGCATCTG 60.135 52.381 0.00 0.00 46.10 2.90
1544 1592 0.099436 GCATCTGTGGCCATTTCGTC 59.901 55.000 9.72 0.00 0.00 4.20
1545 1593 1.452110 CATCTGTGGCCATTTCGTCA 58.548 50.000 9.72 0.00 0.00 4.35
1692 1743 6.718388 TGATTTCAGCTTGTATTTCTATGCG 58.282 36.000 0.00 0.00 0.00 4.73
1790 1842 4.143137 GCAAAACTTCCGGTAATGCATTTG 60.143 41.667 18.75 6.93 38.60 2.32
1821 1873 5.092781 CGTAATTCAAAATTCCGGGAACTG 58.907 41.667 12.53 9.98 0.00 3.16
2068 2133 5.825593 TTGAGTTCCTTGGATAAGAGTGT 57.174 39.130 0.00 0.00 35.92 3.55
2310 2377 5.904984 ACTATGTAGCCAAATGGTATGGA 57.095 39.130 0.71 0.00 40.56 3.41
2568 2635 1.122019 ACTCACCTTGGCGTCCTCTT 61.122 55.000 0.00 0.00 0.00 2.85
2653 2720 4.603535 ACCCCAGCTTGGTGCACC 62.604 66.667 29.67 29.67 45.94 5.01
2963 3034 5.827568 ATGTTTTGCTATGTTTTCTTGCG 57.172 34.783 0.00 0.00 0.00 4.85
3067 3138 6.575162 AATTAGGTTGACAAACTAGCTTGG 57.425 37.500 12.58 0.00 36.48 3.61
3652 3723 8.939929 GGTATGTTAGGATTCATGACATATGTG 58.060 37.037 14.43 0.00 36.11 3.21
3667 3738 6.241207 ACATATGTGTCTTGTTTTCCTTCG 57.759 37.500 7.78 0.00 31.41 3.79
3728 3799 2.975193 CGTGTCAGTGCATCATTTTGTG 59.025 45.455 0.00 0.00 0.00 3.33
4421 4494 6.860080 CATTGCTCCTGAAATGTACAGAAAT 58.140 36.000 0.33 0.00 35.09 2.17
4548 4621 0.378257 CTGTTTGTTGCAGCTGTCGT 59.622 50.000 16.64 0.00 0.00 4.34
4807 4880 7.013083 TCCCTCTTTACTCGTAGTCATATGTTC 59.987 40.741 1.90 0.00 0.00 3.18
4953 5026 2.403987 CTCGTAGGCAGGTCGTCG 59.596 66.667 0.00 0.00 0.00 5.12
5038 5112 0.698238 CTGGGATCCAACACCTTCCA 59.302 55.000 15.23 0.00 30.80 3.53
5724 5804 4.627467 TGTTTTTCCGAACACCAAAATGTG 59.373 37.500 0.00 0.00 42.05 3.21
5751 5831 5.838529 ACTGTACCTAATTTGTTGGTTTGC 58.161 37.500 0.00 0.00 35.48 3.68
5900 5980 4.358614 AGCAGAGGAGGAATATACCTAGGT 59.641 45.833 20.57 20.57 40.73 3.08
5965 6045 1.214589 CAGAGCAAAGCACATGCCC 59.785 57.895 0.00 0.00 44.91 5.36
6049 6129 5.664294 TGCGAAATCACTAGTTAAGGGTA 57.336 39.130 0.00 0.00 0.00 3.69
6050 6130 6.229936 TGCGAAATCACTAGTTAAGGGTAT 57.770 37.500 0.00 0.00 0.00 2.73
6051 6131 6.646267 TGCGAAATCACTAGTTAAGGGTATT 58.354 36.000 0.00 0.00 0.00 1.89
6052 6132 6.759827 TGCGAAATCACTAGTTAAGGGTATTC 59.240 38.462 0.00 0.00 0.00 1.75
6053 6133 6.985059 GCGAAATCACTAGTTAAGGGTATTCT 59.015 38.462 0.00 0.00 0.00 2.40
6059 6139 7.455058 TCACTAGTTAAGGGTATTCTTTGCAA 58.545 34.615 0.00 0.00 0.00 4.08
6070 6150 1.981256 TCTTTGCAAAGGTCACTCCC 58.019 50.000 33.01 0.00 36.67 4.30
6071 6151 1.214175 TCTTTGCAAAGGTCACTCCCA 59.786 47.619 33.01 12.48 36.67 4.37
6072 6152 1.338020 CTTTGCAAAGGTCACTCCCAC 59.662 52.381 28.12 0.00 36.75 4.61
6073 6153 0.467290 TTGCAAAGGTCACTCCCACC 60.467 55.000 0.00 0.00 36.75 4.61
6075 6155 0.690762 GCAAAGGTCACTCCCACCTA 59.309 55.000 0.00 0.00 44.03 3.08
6076 6156 1.610886 GCAAAGGTCACTCCCACCTAC 60.611 57.143 0.00 0.00 44.03 3.18
6077 6157 1.978580 CAAAGGTCACTCCCACCTACT 59.021 52.381 0.00 0.00 44.03 2.57
6078 6158 1.939980 AAGGTCACTCCCACCTACTC 58.060 55.000 0.00 0.00 44.03 2.59
6231 6311 2.549754 CTGTTGTGTTTCTCGCCTCAAT 59.450 45.455 0.00 0.00 0.00 2.57
6245 6325 9.832445 TTCTCGCCTCAATATCTTTTAAACTAT 57.168 29.630 0.00 0.00 0.00 2.12
6301 8327 4.740431 GGCTTTGCCGCGCCAAAT 62.740 61.111 16.13 0.00 45.59 2.32
6375 8401 1.741706 CTGGTTGCTCTTTCATGCGAT 59.258 47.619 0.00 0.00 0.00 4.58
6395 8421 0.108804 GTCTGATTTGGACTCCGCGA 60.109 55.000 8.23 0.00 0.00 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.752339 CCAAGGCGCCAAGGAAGC 61.752 66.667 31.54 0.00 0.00 3.86
33 34 3.752339 GCCAAGGCGCCAAGGAAG 61.752 66.667 33.48 16.07 0.00 3.46
43 44 3.443925 GAAGAAGGCGGCCAAGGC 61.444 66.667 23.09 1.52 41.06 4.35
44 45 1.303643 AAGAAGAAGGCGGCCAAGG 60.304 57.895 23.09 0.00 0.00 3.61
45 46 0.606401 TGAAGAAGAAGGCGGCCAAG 60.606 55.000 23.09 0.00 0.00 3.61
46 47 0.889186 GTGAAGAAGAAGGCGGCCAA 60.889 55.000 23.09 0.00 0.00 4.52
47 48 1.302511 GTGAAGAAGAAGGCGGCCA 60.303 57.895 23.09 0.00 0.00 5.36
48 49 2.041115 GGTGAAGAAGAAGGCGGCC 61.041 63.158 12.11 12.11 0.00 6.13
49 50 0.606673 AAGGTGAAGAAGAAGGCGGC 60.607 55.000 0.00 0.00 0.00 6.53
50 51 1.807142 GAAAGGTGAAGAAGAAGGCGG 59.193 52.381 0.00 0.00 0.00 6.13
51 52 2.772287 AGAAAGGTGAAGAAGAAGGCG 58.228 47.619 0.00 0.00 0.00 5.52
52 53 3.254411 CCAAGAAAGGTGAAGAAGAAGGC 59.746 47.826 0.00 0.00 0.00 4.35
53 54 3.254411 GCCAAGAAAGGTGAAGAAGAAGG 59.746 47.826 0.00 0.00 0.00 3.46
54 55 3.058639 CGCCAAGAAAGGTGAAGAAGAAG 60.059 47.826 0.00 0.00 41.75 2.85
55 56 2.878406 CGCCAAGAAAGGTGAAGAAGAA 59.122 45.455 0.00 0.00 41.75 2.52
56 57 2.494059 CGCCAAGAAAGGTGAAGAAGA 58.506 47.619 0.00 0.00 41.75 2.87
57 58 1.537202 CCGCCAAGAAAGGTGAAGAAG 59.463 52.381 0.00 0.00 41.75 2.85
58 59 1.604604 CCGCCAAGAAAGGTGAAGAA 58.395 50.000 0.00 0.00 41.75 2.52
59 60 0.250727 CCCGCCAAGAAAGGTGAAGA 60.251 55.000 0.00 0.00 41.75 2.87
60 61 0.537371 ACCCGCCAAGAAAGGTGAAG 60.537 55.000 0.00 0.00 41.75 3.02
61 62 0.536460 GACCCGCCAAGAAAGGTGAA 60.536 55.000 0.00 0.00 41.75 3.18
62 63 1.072505 GACCCGCCAAGAAAGGTGA 59.927 57.895 0.00 0.00 41.75 4.02
63 64 2.325082 CGACCCGCCAAGAAAGGTG 61.325 63.158 0.00 0.00 38.90 4.00
64 65 2.032071 CGACCCGCCAAGAAAGGT 59.968 61.111 0.00 0.00 34.57 3.50
65 66 2.032071 ACGACCCGCCAAGAAAGG 59.968 61.111 0.00 0.00 0.00 3.11
66 67 2.380410 CGACGACCCGCCAAGAAAG 61.380 63.158 0.00 0.00 0.00 2.62
67 68 2.356553 CGACGACCCGCCAAGAAA 60.357 61.111 0.00 0.00 0.00 2.52
68 69 4.367023 CCGACGACCCGCCAAGAA 62.367 66.667 0.00 0.00 0.00 2.52
115 116 3.866582 CTCTCCCCCGTCCATGGC 61.867 72.222 6.96 0.96 0.00 4.40
116 117 2.041922 TCTCTCCCCCGTCCATGG 60.042 66.667 4.97 4.97 0.00 3.66
117 118 2.136878 CCTCTCTCCCCCGTCCATG 61.137 68.421 0.00 0.00 0.00 3.66
118 119 2.283809 CCTCTCTCCCCCGTCCAT 59.716 66.667 0.00 0.00 0.00 3.41
119 120 4.075793 CCCTCTCTCCCCCGTCCA 62.076 72.222 0.00 0.00 0.00 4.02
120 121 4.862823 CCCCTCTCTCCCCCGTCC 62.863 77.778 0.00 0.00 0.00 4.79
121 122 4.862823 CCCCCTCTCTCCCCCGTC 62.863 77.778 0.00 0.00 0.00 4.79
144 145 4.716977 ACCCTCCCACGTCCCTCC 62.717 72.222 0.00 0.00 0.00 4.30
145 146 2.222013 AAACCCTCCCACGTCCCTC 61.222 63.158 0.00 0.00 0.00 4.30
146 147 2.122099 AAACCCTCCCACGTCCCT 60.122 61.111 0.00 0.00 0.00 4.20
147 148 2.033602 CAAACCCTCCCACGTCCC 59.966 66.667 0.00 0.00 0.00 4.46
148 149 2.033602 CCAAACCCTCCCACGTCC 59.966 66.667 0.00 0.00 0.00 4.79
149 150 2.033602 CCCAAACCCTCCCACGTC 59.966 66.667 0.00 0.00 0.00 4.34
150 151 3.576259 CCCCAAACCCTCCCACGT 61.576 66.667 0.00 0.00 0.00 4.49
151 152 4.360405 CCCCCAAACCCTCCCACG 62.360 72.222 0.00 0.00 0.00 4.94
152 153 2.026208 TTTCCCCCAAACCCTCCCAC 62.026 60.000 0.00 0.00 0.00 4.61
153 154 1.083363 ATTTCCCCCAAACCCTCCCA 61.083 55.000 0.00 0.00 0.00 4.37
154 155 0.617535 CATTTCCCCCAAACCCTCCC 60.618 60.000 0.00 0.00 0.00 4.30
155 156 0.617535 CCATTTCCCCCAAACCCTCC 60.618 60.000 0.00 0.00 0.00 4.30
156 157 0.617535 CCCATTTCCCCCAAACCCTC 60.618 60.000 0.00 0.00 0.00 4.30
157 158 1.473844 CCCATTTCCCCCAAACCCT 59.526 57.895 0.00 0.00 0.00 4.34
158 159 1.615124 CCCCATTTCCCCCAAACCC 60.615 63.158 0.00 0.00 0.00 4.11
159 160 2.297895 GCCCCATTTCCCCCAAACC 61.298 63.158 0.00 0.00 0.00 3.27
160 161 2.655073 CGCCCCATTTCCCCCAAAC 61.655 63.158 0.00 0.00 0.00 2.93
161 162 2.284258 CGCCCCATTTCCCCCAAA 60.284 61.111 0.00 0.00 0.00 3.28
162 163 3.595758 ACGCCCCATTTCCCCCAA 61.596 61.111 0.00 0.00 0.00 4.12
163 164 4.374584 CACGCCCCATTTCCCCCA 62.375 66.667 0.00 0.00 0.00 4.96
182 183 1.228769 GTGGGAGAAACCAACCCCC 60.229 63.158 0.00 0.00 43.34 5.40
183 184 4.513777 GTGGGAGAAACCAACCCC 57.486 61.111 0.00 0.00 43.34 4.95
186 187 0.179040 TGTCGGTGGGAGAAACCAAC 60.179 55.000 0.00 0.00 44.95 3.77
187 188 0.107831 CTGTCGGTGGGAGAAACCAA 59.892 55.000 0.00 0.00 43.34 3.67
188 189 1.752198 CTGTCGGTGGGAGAAACCA 59.248 57.895 0.00 0.00 41.20 3.67
189 190 1.003718 CCTGTCGGTGGGAGAAACC 60.004 63.158 0.00 0.00 38.08 3.27
190 191 1.671379 GCCTGTCGGTGGGAGAAAC 60.671 63.158 0.00 0.00 0.00 2.78
191 192 2.747686 GCCTGTCGGTGGGAGAAA 59.252 61.111 0.00 0.00 0.00 2.52
192 193 3.691342 CGCCTGTCGGTGGGAGAA 61.691 66.667 0.00 0.00 37.15 2.87
208 209 3.612247 CTTGTCCTCCACTGGCCCG 62.612 68.421 0.00 0.00 0.00 6.13
209 210 2.352805 CTTGTCCTCCACTGGCCC 59.647 66.667 0.00 0.00 0.00 5.80
210 211 2.360475 GCTTGTCCTCCACTGGCC 60.360 66.667 0.00 0.00 0.00 5.36
211 212 2.743928 CGCTTGTCCTCCACTGGC 60.744 66.667 0.00 0.00 0.00 4.85
212 213 2.743928 GCGCTTGTCCTCCACTGG 60.744 66.667 0.00 0.00 0.00 4.00
213 214 3.114616 CGCGCTTGTCCTCCACTG 61.115 66.667 5.56 0.00 0.00 3.66
247 248 4.719616 GTGAAACGGACAGCGCGC 62.720 66.667 26.66 26.66 0.00 6.86
248 249 4.072088 GGTGAAACGGACAGCGCG 62.072 66.667 0.00 0.00 38.12 6.86
249 250 3.723348 GGGTGAAACGGACAGCGC 61.723 66.667 0.00 0.00 38.12 5.92
250 251 3.047877 GGGGTGAAACGGACAGCG 61.048 66.667 0.00 0.00 38.12 5.18
251 252 1.104577 TTTGGGGTGAAACGGACAGC 61.105 55.000 0.00 0.00 38.12 4.40
252 253 1.066454 GTTTTGGGGTGAAACGGACAG 59.934 52.381 0.00 0.00 38.12 3.51
253 254 1.104630 GTTTTGGGGTGAAACGGACA 58.895 50.000 0.00 0.00 38.12 4.02
254 255 0.386476 GGTTTTGGGGTGAAACGGAC 59.614 55.000 0.00 0.00 37.76 4.79
255 256 1.102222 CGGTTTTGGGGTGAAACGGA 61.102 55.000 0.00 0.00 38.71 4.69
256 257 1.360911 CGGTTTTGGGGTGAAACGG 59.639 57.895 0.00 0.00 37.76 4.44
257 258 1.360911 CCGGTTTTGGGGTGAAACG 59.639 57.895 0.00 0.00 37.76 3.60
258 259 1.068417 GCCGGTTTTGGGGTGAAAC 59.932 57.895 1.90 0.00 36.51 2.78
259 260 2.491022 CGCCGGTTTTGGGGTGAAA 61.491 57.895 1.90 0.00 37.20 2.69
260 261 2.907917 CGCCGGTTTTGGGGTGAA 60.908 61.111 1.90 0.00 37.20 3.18
264 265 3.917760 TTTGCGCCGGTTTTGGGG 61.918 61.111 4.18 0.00 44.36 4.96
265 266 2.636778 AAGTTTGCGCCGGTTTTGGG 62.637 55.000 4.18 0.00 0.00 4.12
266 267 1.227118 AAGTTTGCGCCGGTTTTGG 60.227 52.632 4.18 0.00 0.00 3.28
267 268 1.486644 CCAAGTTTGCGCCGGTTTTG 61.487 55.000 4.18 3.33 0.00 2.44
268 269 1.227118 CCAAGTTTGCGCCGGTTTT 60.227 52.632 4.18 0.00 0.00 2.43
269 270 2.415426 CCAAGTTTGCGCCGGTTT 59.585 55.556 4.18 0.00 0.00 3.27
270 271 3.601685 CCCAAGTTTGCGCCGGTT 61.602 61.111 4.18 0.00 0.00 4.44
277 278 4.986708 TCCCCGGCCCAAGTTTGC 62.987 66.667 0.00 0.00 0.00 3.68
278 279 2.037208 ATCCCCGGCCCAAGTTTG 59.963 61.111 0.00 0.00 0.00 2.93
279 280 2.037208 CATCCCCGGCCCAAGTTT 59.963 61.111 0.00 0.00 0.00 2.66
280 281 4.060667 CCATCCCCGGCCCAAGTT 62.061 66.667 0.00 0.00 0.00 2.66
286 287 3.593771 TTTTGACCCATCCCCGGCC 62.594 63.158 0.00 0.00 0.00 6.13
287 288 2.036572 TTTTGACCCATCCCCGGC 59.963 61.111 0.00 0.00 0.00 6.13
288 289 2.052104 GCTTTTGACCCATCCCCGG 61.052 63.158 0.00 0.00 0.00 5.73
289 290 2.406616 CGCTTTTGACCCATCCCCG 61.407 63.158 0.00 0.00 0.00 5.73
290 291 2.052104 CCGCTTTTGACCCATCCCC 61.052 63.158 0.00 0.00 0.00 4.81
291 292 1.001393 TCCGCTTTTGACCCATCCC 60.001 57.895 0.00 0.00 0.00 3.85
292 293 0.608035 TGTCCGCTTTTGACCCATCC 60.608 55.000 0.00 0.00 31.60 3.51
293 294 0.521735 GTGTCCGCTTTTGACCCATC 59.478 55.000 0.00 0.00 31.60 3.51
294 295 0.179004 TGTGTCCGCTTTTGACCCAT 60.179 50.000 0.00 0.00 31.60 4.00
295 296 0.394488 TTGTGTCCGCTTTTGACCCA 60.394 50.000 0.00 0.00 31.60 4.51
296 297 0.741915 TTTGTGTCCGCTTTTGACCC 59.258 50.000 0.00 0.00 31.60 4.46
297 298 2.190161 GTTTTGTGTCCGCTTTTGACC 58.810 47.619 0.00 0.00 31.60 4.02
298 299 1.843753 CGTTTTGTGTCCGCTTTTGAC 59.156 47.619 0.00 0.00 0.00 3.18
299 300 1.202200 CCGTTTTGTGTCCGCTTTTGA 60.202 47.619 0.00 0.00 0.00 2.69
300 301 1.196200 CCGTTTTGTGTCCGCTTTTG 58.804 50.000 0.00 0.00 0.00 2.44
301 302 1.096416 TCCGTTTTGTGTCCGCTTTT 58.904 45.000 0.00 0.00 0.00 2.27
302 303 0.379316 GTCCGTTTTGTGTCCGCTTT 59.621 50.000 0.00 0.00 0.00 3.51
303 304 0.745128 TGTCCGTTTTGTGTCCGCTT 60.745 50.000 0.00 0.00 0.00 4.68
304 305 0.745128 TTGTCCGTTTTGTGTCCGCT 60.745 50.000 0.00 0.00 0.00 5.52
305 306 0.099082 TTTGTCCGTTTTGTGTCCGC 59.901 50.000 0.00 0.00 0.00 5.54
306 307 2.159490 ACTTTTGTCCGTTTTGTGTCCG 60.159 45.455 0.00 0.00 0.00 4.79
307 308 3.431856 GACTTTTGTCCGTTTTGTGTCC 58.568 45.455 0.00 0.00 43.37 4.02
320 321 1.065109 GGCGCAAACGGACTTTTGT 59.935 52.632 10.83 0.00 38.51 2.83
321 322 1.660264 GGGCGCAAACGGACTTTTG 60.660 57.895 10.83 0.00 40.57 2.44
322 323 2.725641 GGGCGCAAACGGACTTTT 59.274 55.556 10.83 0.00 40.57 2.27
323 324 3.656045 CGGGCGCAAACGGACTTT 61.656 61.111 10.83 0.00 40.57 2.66
343 344 2.436646 AAATCAGACGGCCCAGCG 60.437 61.111 0.00 0.00 0.00 5.18
344 345 1.648467 GACAAATCAGACGGCCCAGC 61.648 60.000 0.00 0.00 0.00 4.85
345 346 1.026718 GGACAAATCAGACGGCCCAG 61.027 60.000 0.00 0.00 0.00 4.45
346 347 1.002624 GGACAAATCAGACGGCCCA 60.003 57.895 0.00 0.00 0.00 5.36
347 348 0.394352 ATGGACAAATCAGACGGCCC 60.394 55.000 0.00 0.00 0.00 5.80
348 349 1.463674 AATGGACAAATCAGACGGCC 58.536 50.000 0.00 0.00 0.00 6.13
349 350 3.575965 AAAATGGACAAATCAGACGGC 57.424 42.857 0.00 0.00 0.00 5.68
350 351 4.700213 AGGTAAAATGGACAAATCAGACGG 59.300 41.667 0.00 0.00 0.00 4.79
351 352 5.880054 AGGTAAAATGGACAAATCAGACG 57.120 39.130 0.00 0.00 0.00 4.18
352 353 9.406828 GTTTAAGGTAAAATGGACAAATCAGAC 57.593 33.333 0.00 0.00 0.00 3.51
353 354 9.137459 TGTTTAAGGTAAAATGGACAAATCAGA 57.863 29.630 0.00 0.00 0.00 3.27
354 355 9.410556 CTGTTTAAGGTAAAATGGACAAATCAG 57.589 33.333 0.00 0.00 0.00 2.90
355 356 9.137459 TCTGTTTAAGGTAAAATGGACAAATCA 57.863 29.630 0.00 0.00 0.00 2.57
356 357 9.406828 GTCTGTTTAAGGTAAAATGGACAAATC 57.593 33.333 0.00 0.00 0.00 2.17
357 358 8.079809 CGTCTGTTTAAGGTAAAATGGACAAAT 58.920 33.333 0.00 0.00 0.00 2.32
358 359 7.419204 CGTCTGTTTAAGGTAAAATGGACAAA 58.581 34.615 0.00 0.00 0.00 2.83
359 360 6.016943 CCGTCTGTTTAAGGTAAAATGGACAA 60.017 38.462 0.00 0.00 0.00 3.18
360 361 5.470777 CCGTCTGTTTAAGGTAAAATGGACA 59.529 40.000 0.00 0.00 0.00 4.02
361 362 5.106436 CCCGTCTGTTTAAGGTAAAATGGAC 60.106 44.000 0.00 0.00 0.00 4.02
362 363 5.005094 CCCGTCTGTTTAAGGTAAAATGGA 58.995 41.667 0.00 0.00 0.00 3.41
363 364 4.157105 CCCCGTCTGTTTAAGGTAAAATGG 59.843 45.833 0.00 0.00 0.00 3.16
364 365 5.005094 TCCCCGTCTGTTTAAGGTAAAATG 58.995 41.667 0.00 0.00 0.00 2.32
365 366 5.005740 GTCCCCGTCTGTTTAAGGTAAAAT 58.994 41.667 0.00 0.00 0.00 1.82
366 367 4.388485 GTCCCCGTCTGTTTAAGGTAAAA 58.612 43.478 0.00 0.00 0.00 1.52
367 368 3.554752 CGTCCCCGTCTGTTTAAGGTAAA 60.555 47.826 0.00 0.00 0.00 2.01
368 369 2.029110 CGTCCCCGTCTGTTTAAGGTAA 60.029 50.000 0.00 0.00 0.00 2.85
369 370 1.545582 CGTCCCCGTCTGTTTAAGGTA 59.454 52.381 0.00 0.00 0.00 3.08
370 371 0.319405 CGTCCCCGTCTGTTTAAGGT 59.681 55.000 0.00 0.00 0.00 3.50
371 372 0.390735 CCGTCCCCGTCTGTTTAAGG 60.391 60.000 0.00 0.00 0.00 2.69
372 373 0.604578 TCCGTCCCCGTCTGTTTAAG 59.395 55.000 0.00 0.00 0.00 1.85
373 374 0.318120 GTCCGTCCCCGTCTGTTTAA 59.682 55.000 0.00 0.00 0.00 1.52
374 375 0.827089 TGTCCGTCCCCGTCTGTTTA 60.827 55.000 0.00 0.00 0.00 2.01
375 376 2.095978 CTGTCCGTCCCCGTCTGTTT 62.096 60.000 0.00 0.00 0.00 2.83
376 377 2.522436 TGTCCGTCCCCGTCTGTT 60.522 61.111 0.00 0.00 0.00 3.16
377 378 2.989824 CTGTCCGTCCCCGTCTGT 60.990 66.667 0.00 0.00 0.00 3.41
378 379 3.760035 CCTGTCCGTCCCCGTCTG 61.760 72.222 0.00 0.00 0.00 3.51
379 380 3.298300 ATCCTGTCCGTCCCCGTCT 62.298 63.158 0.00 0.00 0.00 4.18
380 381 2.758737 ATCCTGTCCGTCCCCGTC 60.759 66.667 0.00 0.00 0.00 4.79
381 382 3.075005 CATCCTGTCCGTCCCCGT 61.075 66.667 0.00 0.00 0.00 5.28
382 383 3.849951 CCATCCTGTCCGTCCCCG 61.850 72.222 0.00 0.00 0.00 5.73
383 384 3.480133 CCCATCCTGTCCGTCCCC 61.480 72.222 0.00 0.00 0.00 4.81
384 385 3.480133 CCCCATCCTGTCCGTCCC 61.480 72.222 0.00 0.00 0.00 4.46
385 386 2.687566 ACCCCATCCTGTCCGTCC 60.688 66.667 0.00 0.00 0.00 4.79
386 387 2.584608 CACCCCATCCTGTCCGTC 59.415 66.667 0.00 0.00 0.00 4.79
387 388 3.009115 CCACCCCATCCTGTCCGT 61.009 66.667 0.00 0.00 0.00 4.69
388 389 4.489771 GCCACCCCATCCTGTCCG 62.490 72.222 0.00 0.00 0.00 4.79
389 390 4.489771 CGCCACCCCATCCTGTCC 62.490 72.222 0.00 0.00 0.00 4.02
400 401 4.382320 TAACTCCACCGCGCCACC 62.382 66.667 0.00 0.00 0.00 4.61
401 402 2.813908 CTAACTCCACCGCGCCAC 60.814 66.667 0.00 0.00 0.00 5.01
402 403 4.077184 CCTAACTCCACCGCGCCA 62.077 66.667 0.00 0.00 0.00 5.69
404 405 2.567564 TAAGCCTAACTCCACCGCGC 62.568 60.000 0.00 0.00 0.00 6.86
405 406 0.527817 CTAAGCCTAACTCCACCGCG 60.528 60.000 0.00 0.00 0.00 6.46
406 407 0.810426 GCTAAGCCTAACTCCACCGC 60.810 60.000 0.00 0.00 0.00 5.68
407 408 0.535335 TGCTAAGCCTAACTCCACCG 59.465 55.000 0.00 0.00 0.00 4.94
408 409 1.744114 GCTGCTAAGCCTAACTCCACC 60.744 57.143 0.00 0.00 44.22 4.61
409 410 1.657822 GCTGCTAAGCCTAACTCCAC 58.342 55.000 0.00 0.00 44.22 4.02
420 421 2.540265 CCAGTCCATAGGCTGCTAAG 57.460 55.000 0.00 0.00 0.00 2.18
441 442 5.010617 TGCCAGTTGAATTTTCCTTTAGTCC 59.989 40.000 0.00 0.00 0.00 3.85
445 446 5.067936 TCGTTGCCAGTTGAATTTTCCTTTA 59.932 36.000 0.00 0.00 0.00 1.85
485 487 4.316645 TCGTCTAGCTGAATATCTAGCGT 58.683 43.478 0.00 0.00 44.43 5.07
656 665 5.368989 ACCTGAGTTCAAAAGGTTAGAGTG 58.631 41.667 0.00 0.00 41.65 3.51
710 720 1.518774 GGAATAACCGCCGGTGAGA 59.481 57.895 18.79 0.00 35.34 3.27
798 811 0.036732 GAGATGGTGACCAGTGGCAA 59.963 55.000 11.23 0.00 36.75 4.52
849 862 3.585990 GATTGGGCGTGGGCGATG 61.586 66.667 0.00 0.00 41.24 3.84
850 863 3.420206 ATGATTGGGCGTGGGCGAT 62.420 57.895 0.00 0.00 41.24 4.58
851 864 4.108299 ATGATTGGGCGTGGGCGA 62.108 61.111 0.00 0.00 41.24 5.54
1439 1487 2.480802 GAGAGAAGAAAGTTGGGCGAAC 59.519 50.000 3.99 3.99 34.40 3.95
1528 1576 0.396435 ACTGACGAAATGGCCACAGA 59.604 50.000 21.85 0.00 0.00 3.41
1531 1579 1.210155 GCACTGACGAAATGGCCAC 59.790 57.895 8.16 0.00 0.00 5.01
1535 1583 4.418013 TGTAATTGCACTGACGAAATGG 57.582 40.909 0.00 0.00 0.00 3.16
1544 1592 6.752351 ACTCTTAGTACGATGTAATTGCACTG 59.248 38.462 0.00 0.00 35.13 3.66
1545 1593 6.864342 ACTCTTAGTACGATGTAATTGCACT 58.136 36.000 0.00 0.00 37.98 4.40
1692 1743 1.012486 GCTGCTGGCTGAAATTGCAC 61.012 55.000 3.72 0.00 38.06 4.57
1745 1797 3.766591 CTCCTCTTGCTCTGAGAAGGTTA 59.233 47.826 9.28 0.00 33.68 2.85
1790 1842 8.588789 CCCGGAATTTTGAATTACGAAAATAAC 58.411 33.333 17.10 0.00 37.53 1.89
1814 1866 4.390264 AGCAAGAGTTAAGAACAGTTCCC 58.610 43.478 9.85 0.00 0.00 3.97
2310 2377 7.444183 TCAAGTATCTTCACGAAAACTTTGGAT 59.556 33.333 0.00 0.00 32.62 3.41
2653 2720 4.673298 TGCGTGGGTGTAGCGTGG 62.673 66.667 0.00 0.00 0.00 4.94
2707 2774 7.847711 TTTGTTCATAATCCTTCCCAGAAAA 57.152 32.000 0.00 0.00 0.00 2.29
2711 2778 6.780457 ACATTTGTTCATAATCCTTCCCAG 57.220 37.500 0.00 0.00 0.00 4.45
2963 3034 2.027625 GCACCCACGCTACACTCAC 61.028 63.158 0.00 0.00 0.00 3.51
3050 3121 4.814771 ACTGTACCAAGCTAGTTTGTCAAC 59.185 41.667 16.87 11.98 0.00 3.18
3062 3133 5.526111 TGTTTAGACTGAAACTGTACCAAGC 59.474 40.000 0.00 0.00 39.57 4.01
3067 3138 8.880750 AGAAAACTGTTTAGACTGAAACTGTAC 58.119 33.333 6.16 0.00 45.30 2.90
3119 3190 5.700373 TGATAAGCAAAGCCCAAAATCAAAC 59.300 36.000 0.00 0.00 0.00 2.93
3652 3723 3.312697 ACAGCTTCGAAGGAAAACAAGAC 59.687 43.478 25.77 5.71 0.00 3.01
3667 3738 6.595716 ACAGTTCAAATGGTAGATACAGCTTC 59.404 38.462 0.00 0.00 0.00 3.86
3728 3799 8.287503 AGAAAATAAACTTATTGTCACGTGACC 58.712 33.333 38.12 23.86 44.15 4.02
4421 4494 3.316029 CCACACTTCTGTCAAATGCTTCA 59.684 43.478 0.00 0.00 0.00 3.02
4548 4621 5.929415 TGTGCTCATTTGAATTACGTACTGA 59.071 36.000 0.00 0.00 0.00 3.41
4807 4880 3.187227 ACAGAATGCAAAAGCTACTCACG 59.813 43.478 0.00 0.00 42.53 4.35
5038 5112 1.079127 CCGAGAACGTTGGCCTGAT 60.079 57.895 5.00 0.00 37.88 2.90
5724 5804 3.126343 CCAACAAATTAGGTACAGTCGCC 59.874 47.826 0.00 0.00 0.00 5.54
5937 6017 3.000773 GTGCTTTGCTCTGTTTTGTTTCG 60.001 43.478 0.00 0.00 0.00 3.46
6049 6129 2.893489 GGGAGTGACCTTTGCAAAGAAT 59.107 45.455 35.25 24.23 38.28 2.40
6050 6130 2.306847 GGGAGTGACCTTTGCAAAGAA 58.693 47.619 35.25 19.81 38.28 2.52
6051 6131 1.214175 TGGGAGTGACCTTTGCAAAGA 59.786 47.619 35.25 16.76 38.28 2.52
6052 6132 1.338020 GTGGGAGTGACCTTTGCAAAG 59.662 52.381 28.69 28.69 38.98 2.77
6053 6133 1.398692 GTGGGAGTGACCTTTGCAAA 58.601 50.000 12.14 12.14 38.98 3.68
6059 6139 1.433592 AGAGTAGGTGGGAGTGACCTT 59.566 52.381 0.00 0.00 41.31 3.50
6071 6151 4.102524 TCATTTGTCACCACAAGAGTAGGT 59.897 41.667 0.00 0.00 43.54 3.08
6072 6152 4.452455 GTCATTTGTCACCACAAGAGTAGG 59.548 45.833 0.00 0.00 43.54 3.18
6073 6153 4.150627 CGTCATTTGTCACCACAAGAGTAG 59.849 45.833 0.00 0.00 43.54 2.57
6074 6154 4.055360 CGTCATTTGTCACCACAAGAGTA 58.945 43.478 0.00 0.00 43.54 2.59
6075 6155 2.872245 CGTCATTTGTCACCACAAGAGT 59.128 45.455 0.00 0.00 43.54 3.24
6076 6156 2.349817 GCGTCATTTGTCACCACAAGAG 60.350 50.000 0.00 0.00 43.54 2.85
6077 6157 1.601903 GCGTCATTTGTCACCACAAGA 59.398 47.619 0.00 0.00 43.54 3.02
6078 6158 1.333308 TGCGTCATTTGTCACCACAAG 59.667 47.619 0.00 0.00 43.54 3.16
6129 6209 7.425606 TGAATCTAGGAAAAGAGCACAAAAAC 58.574 34.615 0.00 0.00 0.00 2.43
6245 6325 5.069781 GCCCCAAACTTATTAACATGGCATA 59.930 40.000 0.00 0.00 35.30 3.14
6274 6354 4.118584 GCAAAGCCATGAAGGGGT 57.881 55.556 0.00 0.00 41.27 4.95
6299 8325 3.582120 CCGGCACCGCGCATTATT 61.582 61.111 8.75 0.00 45.17 1.40
6344 8370 2.279851 CAACCAGTGTCGTCGCCA 60.280 61.111 0.00 0.00 0.00 5.69
6349 8375 1.134521 TGAAAGAGCAACCAGTGTCGT 60.135 47.619 0.00 0.00 0.00 4.34
6375 8401 0.389817 CGCGGAGTCCAAATCAGACA 60.390 55.000 10.49 0.00 36.68 3.41


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

AutoCloner maintained by Alex Coulton.