Multiple sequence alignment - TraesCS2D01G338300

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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 TraesCS2D01G338300 chr2D 100.000 4551 0 0 1 4551 431919005 431923555 0.000000e+00 8405.0
1 TraesCS2D01G338300 chr2D 89.253 2075 135 39 2049 4088 433025028 433023007 0.000000e+00 2516.0
2 TraesCS2D01G338300 chr2D 89.674 552 25 8 616 1156 433026615 433026085 0.000000e+00 675.0
3 TraesCS2D01G338300 chr2D 92.079 404 24 5 4142 4544 433022686 433022290 3.070000e-156 562.0
4 TraesCS2D01G338300 chr2D 93.458 321 8 7 1166 1483 433025845 433025535 8.920000e-127 464.0
5 TraesCS2D01G338300 chr2D 86.269 386 21 15 263 638 433026906 433026543 1.540000e-104 390.0
6 TraesCS2D01G338300 chr2D 94.393 214 12 0 4133 4346 433022900 433022687 3.390000e-86 329.0
7 TraesCS2D01G338300 chr2D 99.160 119 1 0 1551 1669 433025435 433025317 9.920000e-52 215.0
8 TraesCS2D01G338300 chr2D 90.566 53 2 2 1785 1836 433025206 433025156 2.940000e-07 67.6
9 TraesCS2D01G338300 chr2D 86.441 59 6 2 3787 3844 433023400 433023343 3.800000e-06 63.9
10 TraesCS2D01G338300 chr2B 93.588 1965 86 24 2461 4398 511155508 511157459 0.000000e+00 2894.0
11 TraesCS2D01G338300 chr2B 87.028 1033 39 32 508 1483 511150827 511151821 0.000000e+00 1077.0
12 TraesCS2D01G338300 chr2B 86.966 445 14 11 1780 2214 511154596 511155006 1.150000e-125 460.0
13 TraesCS2D01G338300 chr2B 88.593 263 10 2 2201 2462 511155151 511155394 7.400000e-78 302.0
14 TraesCS2D01G338300 chr2B 96.104 154 4 2 4391 4544 511157424 511157575 2.720000e-62 250.0
15 TraesCS2D01G338300 chr2B 89.677 155 5 6 1603 1749 511154370 511154521 2.160000e-43 187.0
16 TraesCS2D01G338300 chr2B 91.406 128 10 1 1479 1605 511151970 511152097 1.680000e-39 174.0
17 TraesCS2D01G338300 chr2B 80.498 241 18 14 279 511 511150489 511150708 1.690000e-34 158.0
18 TraesCS2D01G338300 chr2B 95.349 43 2 0 3787 3829 511156746 511156788 8.170000e-08 69.4
19 TraesCS2D01G338300 chr2A 93.082 477 21 4 859 1333 554044735 554045201 0.000000e+00 688.0
20 TraesCS2D01G338300 chr2A 89.850 532 52 2 3023 3553 554075804 554076334 0.000000e+00 682.0
21 TraesCS2D01G338300 chr2A 82.991 535 37 28 1479 1988 554048675 554049180 6.990000e-118 435.0
22 TraesCS2D01G338300 chr2A 95.506 267 7 2 4133 4398 554076840 554077102 5.440000e-114 422.0
23 TraesCS2D01G338300 chr2A 89.836 305 18 5 310 601 554022731 554023035 3.320000e-101 379.0
24 TraesCS2D01G338300 chr2A 93.392 227 15 0 2461 2687 554072041 554072267 2.030000e-88 337.0
25 TraesCS2D01G338300 chr2A 91.667 228 13 3 3900 4124 554076573 554076797 1.230000e-80 311.0
26 TraesCS2D01G338300 chr2A 96.753 154 4 1 4391 4544 554077066 554077218 5.840000e-64 255.0
27 TraesCS2D01G338300 chr2A 86.957 230 13 6 593 820 554044516 554044730 4.550000e-60 243.0
28 TraesCS2D01G338300 chr2A 92.994 157 7 1 3638 3790 554076363 554076519 4.580000e-55 226.0
29 TraesCS2D01G338300 chr2A 95.935 123 5 0 2049 2171 554049303 554049425 2.780000e-47 200.0
30 TraesCS2D01G338300 chr2A 90.244 123 4 2 2261 2383 554050773 554050887 2.190000e-33 154.0
31 TraesCS2D01G338300 chr2A 90.909 99 8 1 2172 2269 554050402 554050500 1.030000e-26 132.0
32 TraesCS2D01G338300 chr2A 91.566 83 4 1 4465 4544 554378146 554378064 1.340000e-20 111.0
33 TraesCS2D01G338300 chr2A 89.011 91 7 1 4457 4544 554138545 554138635 4.810000e-20 110.0
34 TraesCS2D01G338300 chr2A 93.478 46 2 1 3784 3829 554076430 554076474 2.940000e-07 67.6
35 TraesCS2D01G338300 chr7D 88.104 269 25 7 1 265 168429955 168430220 3.420000e-81 313.0
36 TraesCS2D01G338300 chr7D 87.313 268 27 7 1 263 95116441 95116706 2.660000e-77 300.0
37 TraesCS2D01G338300 chr7D 87.218 266 28 5 1 263 166512075 166512337 9.570000e-77 298.0
38 TraesCS2D01G338300 chr6D 87.868 272 24 7 1 265 411248522 411248791 1.230000e-80 311.0
39 TraesCS2D01G338300 chr3D 87.970 266 27 4 1 263 499967195 499966932 4.420000e-80 309.0
40 TraesCS2D01G338300 chr3D 87.640 267 27 6 1 263 297681331 297681595 5.720000e-79 305.0
41 TraesCS2D01G338300 chr6B 87.640 267 29 4 1 263 41445070 41445336 1.590000e-79 307.0
42 TraesCS2D01G338300 chr1D 87.594 266 28 3 2 263 480866438 480866174 2.060000e-78 303.0
43 TraesCS2D01G338300 chr1B 87.266 267 26 6 1 263 368671579 368671317 9.570000e-77 298.0


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 TraesCS2D01G338300 chr2D 431919005 431923555 4550 False 8405.000000 8405 100.000000 1 4551 1 chr2D.!!$F1 4550
1 TraesCS2D01G338300 chr2D 433022290 433026906 4616 True 586.944444 2516 91.254778 263 4544 9 chr2D.!!$R1 4281
2 TraesCS2D01G338300 chr2B 511150489 511157575 7086 False 619.044444 2894 89.912111 279 4544 9 chr2B.!!$F1 4265
3 TraesCS2D01G338300 chr2A 554072041 554077218 5177 False 328.657143 682 93.377143 2461 4544 7 chr2A.!!$F4 2083
4 TraesCS2D01G338300 chr2A 554044516 554050887 6371 False 308.666667 688 90.019667 593 2383 6 chr2A.!!$F3 1790

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
231 232 0.032815 AAAATCCGGCCAACCAAACG 59.967 50.0 2.24 0.0 34.57 3.60 F
261 262 0.037419 ATTGTGCGGTGAAATTGGCC 60.037 50.0 0.00 0.0 0.00 5.36 F
732 872 0.101759 GCACTGCTATTACGACCGGA 59.898 55.0 9.46 0.0 0.00 5.14 F
2190 9552 0.031449 GTACTCATCGAGCTCAGCCC 59.969 60.0 15.40 0.0 32.04 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 8440 0.249953 TTAACTCTTGGGCGCGTTCA 60.250 50.000 8.43 3.35 0.00 3.18 R
2190 9552 2.740055 GCAGGTGCACAGAGACGG 60.740 66.667 20.43 2.37 41.59 4.79 R
2441 10242 0.034670 AGGTTGCAGGGCAGATCTTC 60.035 55.000 0.00 0.00 40.61 2.87 R
4150 15401 0.105039 CAATCTACAGACGGAGCCCC 59.895 60.000 0.00 0.00 0.00 5.80 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 1.819905 AAACTGGGCCGTTTTGTGG 59.180 52.632 16.96 0.00 33.57 4.17
25 26 3.111939 CCGTTTTGTGGCCGTGAA 58.888 55.556 0.00 0.00 0.00 3.18
26 27 1.298788 CCGTTTTGTGGCCGTGAAC 60.299 57.895 0.00 0.00 0.00 3.18
27 28 1.298788 CGTTTTGTGGCCGTGAACC 60.299 57.895 0.00 0.00 0.00 3.62
28 29 1.066752 GTTTTGTGGCCGTGAACCC 59.933 57.895 0.00 0.00 0.00 4.11
29 30 1.379977 TTTTGTGGCCGTGAACCCA 60.380 52.632 0.00 0.00 0.00 4.51
30 31 0.970937 TTTTGTGGCCGTGAACCCAA 60.971 50.000 0.00 0.00 31.90 4.12
31 32 0.970937 TTTGTGGCCGTGAACCCAAA 60.971 50.000 0.00 0.00 31.90 3.28
32 33 1.668101 TTGTGGCCGTGAACCCAAAC 61.668 55.000 0.00 0.00 31.90 2.93
33 34 1.826487 GTGGCCGTGAACCCAAACT 60.826 57.895 0.00 0.00 31.90 2.66
34 35 1.076632 TGGCCGTGAACCCAAACTT 60.077 52.632 0.00 0.00 0.00 2.66
35 36 0.183014 TGGCCGTGAACCCAAACTTA 59.817 50.000 0.00 0.00 0.00 2.24
36 37 1.202952 TGGCCGTGAACCCAAACTTAT 60.203 47.619 0.00 0.00 0.00 1.73
37 38 2.040012 TGGCCGTGAACCCAAACTTATA 59.960 45.455 0.00 0.00 0.00 0.98
38 39 3.284617 GGCCGTGAACCCAAACTTATAT 58.715 45.455 0.00 0.00 0.00 0.86
39 40 3.697542 GGCCGTGAACCCAAACTTATATT 59.302 43.478 0.00 0.00 0.00 1.28
40 41 4.158949 GGCCGTGAACCCAAACTTATATTT 59.841 41.667 0.00 0.00 0.00 1.40
41 42 5.336929 GGCCGTGAACCCAAACTTATATTTT 60.337 40.000 0.00 0.00 0.00 1.82
42 43 6.127675 GGCCGTGAACCCAAACTTATATTTTA 60.128 38.462 0.00 0.00 0.00 1.52
43 44 7.417003 GGCCGTGAACCCAAACTTATATTTTAT 60.417 37.037 0.00 0.00 0.00 1.40
44 45 7.434013 GCCGTGAACCCAAACTTATATTTTATG 59.566 37.037 0.00 0.00 0.00 1.90
45 46 8.463607 CCGTGAACCCAAACTTATATTTTATGT 58.536 33.333 0.00 0.00 0.00 2.29
46 47 9.849166 CGTGAACCCAAACTTATATTTTATGTT 57.151 29.630 0.00 0.00 0.00 2.71
114 115 9.673454 AGTTTTTCTGTTATTTTAATCACGTCC 57.327 29.630 0.00 0.00 0.00 4.79
115 116 9.453325 GTTTTTCTGTTATTTTAATCACGTCCA 57.547 29.630 0.00 0.00 0.00 4.02
116 117 9.453325 TTTTTCTGTTATTTTAATCACGTCCAC 57.547 29.630 0.00 0.00 0.00 4.02
117 118 6.730960 TCTGTTATTTTAATCACGTCCACC 57.269 37.500 0.00 0.00 0.00 4.61
118 119 5.349270 TCTGTTATTTTAATCACGTCCACCG 59.651 40.000 0.00 0.00 44.03 4.94
119 120 4.392445 TGTTATTTTAATCACGTCCACCGG 59.608 41.667 0.00 0.00 42.24 5.28
120 121 2.835580 TTTTAATCACGTCCACCGGA 57.164 45.000 9.46 0.00 42.24 5.14
130 131 3.568000 TCCACCGGACATGATTTGG 57.432 52.632 9.46 1.94 0.00 3.28
131 132 0.034574 TCCACCGGACATGATTTGGG 60.035 55.000 9.46 0.00 0.00 4.12
132 133 1.037030 CCACCGGACATGATTTGGGG 61.037 60.000 9.46 0.00 0.00 4.96
133 134 0.323360 CACCGGACATGATTTGGGGT 60.323 55.000 9.46 0.00 0.00 4.95
134 135 0.323360 ACCGGACATGATTTGGGGTG 60.323 55.000 9.46 0.00 0.00 4.61
135 136 1.666209 CCGGACATGATTTGGGGTGC 61.666 60.000 0.00 0.00 0.00 5.01
136 137 1.809207 GGACATGATTTGGGGTGCG 59.191 57.895 0.00 0.00 0.00 5.34
137 138 1.666209 GGACATGATTTGGGGTGCGG 61.666 60.000 0.00 0.00 0.00 5.69
138 139 2.283472 GACATGATTTGGGGTGCGGC 62.283 60.000 0.00 0.00 0.00 6.53
139 140 2.759560 ATGATTTGGGGTGCGGCC 60.760 61.111 0.00 0.00 0.00 6.13
168 169 4.612412 GCACCCACGACCCAACGA 62.612 66.667 0.00 0.00 37.03 3.85
169 170 2.109387 CACCCACGACCCAACGAA 59.891 61.111 0.00 0.00 37.03 3.85
170 171 2.109593 ACCCACGACCCAACGAAC 59.890 61.111 0.00 0.00 37.03 3.95
171 172 2.109387 CCCACGACCCAACGAACA 59.891 61.111 0.00 0.00 37.03 3.18
172 173 1.959226 CCCACGACCCAACGAACAG 60.959 63.158 0.00 0.00 37.03 3.16
173 174 1.068417 CCACGACCCAACGAACAGA 59.932 57.895 0.00 0.00 37.03 3.41
174 175 0.531090 CCACGACCCAACGAACAGAA 60.531 55.000 0.00 0.00 37.03 3.02
175 176 0.859232 CACGACCCAACGAACAGAAG 59.141 55.000 0.00 0.00 37.03 2.85
176 177 0.878961 ACGACCCAACGAACAGAAGC 60.879 55.000 0.00 0.00 37.03 3.86
177 178 1.860078 GACCCAACGAACAGAAGCG 59.140 57.895 0.00 0.00 0.00 4.68
178 179 1.566018 GACCCAACGAACAGAAGCGG 61.566 60.000 0.00 0.00 0.00 5.52
179 180 1.301401 CCCAACGAACAGAAGCGGA 60.301 57.895 0.00 0.00 0.00 5.54
180 181 1.566018 CCCAACGAACAGAAGCGGAC 61.566 60.000 0.00 0.00 0.00 4.79
181 182 0.878523 CCAACGAACAGAAGCGGACA 60.879 55.000 0.00 0.00 0.00 4.02
182 183 1.148310 CAACGAACAGAAGCGGACAT 58.852 50.000 0.00 0.00 0.00 3.06
183 184 1.136252 CAACGAACAGAAGCGGACATG 60.136 52.381 0.00 0.00 0.00 3.21
184 185 0.670546 ACGAACAGAAGCGGACATGG 60.671 55.000 0.00 0.00 0.00 3.66
185 186 1.361668 CGAACAGAAGCGGACATGGG 61.362 60.000 0.00 0.00 0.00 4.00
186 187 1.648467 GAACAGAAGCGGACATGGGC 61.648 60.000 0.00 0.00 0.00 5.36
187 188 3.197790 CAGAAGCGGACATGGGCG 61.198 66.667 0.00 0.00 0.00 6.13
188 189 3.390521 AGAAGCGGACATGGGCGA 61.391 61.111 0.00 0.00 0.00 5.54
189 190 2.435938 GAAGCGGACATGGGCGAA 60.436 61.111 0.00 0.00 0.00 4.70
190 191 2.746277 AAGCGGACATGGGCGAAC 60.746 61.111 0.00 0.00 0.00 3.95
191 192 4.778143 AGCGGACATGGGCGAACC 62.778 66.667 0.00 0.00 40.81 3.62
201 202 3.803886 GGCGAACCCATTACCGTC 58.196 61.111 0.00 0.00 0.00 4.79
202 203 1.816679 GGCGAACCCATTACCGTCC 60.817 63.158 0.00 0.00 0.00 4.79
203 204 1.816679 GCGAACCCATTACCGTCCC 60.817 63.158 0.00 0.00 0.00 4.46
204 205 1.597989 CGAACCCATTACCGTCCCA 59.402 57.895 0.00 0.00 0.00 4.37
205 206 0.036199 CGAACCCATTACCGTCCCAA 60.036 55.000 0.00 0.00 0.00 4.12
206 207 1.611148 CGAACCCATTACCGTCCCAAA 60.611 52.381 0.00 0.00 0.00 3.28
207 208 2.089201 GAACCCATTACCGTCCCAAAG 58.911 52.381 0.00 0.00 0.00 2.77
208 209 0.330267 ACCCATTACCGTCCCAAAGG 59.670 55.000 0.00 0.00 0.00 3.11
209 210 0.395173 CCCATTACCGTCCCAAAGGG 60.395 60.000 0.00 0.00 46.11 3.95
219 220 1.917872 TCCCAAAGGGACAAAATCCG 58.082 50.000 0.00 0.00 46.17 4.18
220 221 1.549037 TCCCAAAGGGACAAAATCCGG 60.549 52.381 0.00 0.00 46.17 5.14
226 227 1.589630 GGACAAAATCCGGCCAACC 59.410 57.895 2.24 0.00 37.88 3.77
227 228 1.182385 GGACAAAATCCGGCCAACCA 61.182 55.000 2.24 0.00 37.88 3.67
228 229 0.676736 GACAAAATCCGGCCAACCAA 59.323 50.000 2.24 0.00 34.57 3.67
229 230 1.069358 GACAAAATCCGGCCAACCAAA 59.931 47.619 2.24 0.00 34.57 3.28
230 231 1.202592 ACAAAATCCGGCCAACCAAAC 60.203 47.619 2.24 0.00 34.57 2.93
231 232 0.032815 AAAATCCGGCCAACCAAACG 59.967 50.000 2.24 0.00 34.57 3.60
232 233 1.110518 AAATCCGGCCAACCAAACGT 61.111 50.000 2.24 0.00 34.57 3.99
233 234 1.520600 AATCCGGCCAACCAAACGTC 61.521 55.000 2.24 0.00 34.57 4.34
234 235 3.666253 CCGGCCAACCAAACGTCC 61.666 66.667 2.24 0.00 34.57 4.79
235 236 4.020378 CGGCCAACCAAACGTCCG 62.020 66.667 2.24 0.00 34.57 4.79
236 237 2.903350 GGCCAACCAAACGTCCGT 60.903 61.111 0.00 0.00 35.26 4.69
237 238 2.483197 GGCCAACCAAACGTCCGTT 61.483 57.895 0.00 0.00 40.45 4.44
239 240 0.662085 GCCAACCAAACGTCCGTTTA 59.338 50.000 16.45 0.00 45.32 2.01
240 241 1.334329 GCCAACCAAACGTCCGTTTAG 60.334 52.381 16.45 12.44 45.32 1.85
241 242 1.264826 CCAACCAAACGTCCGTTTAGG 59.735 52.381 16.45 19.43 45.32 2.69
250 251 3.146783 TCCGTTTAGGATTGTGCGG 57.853 52.632 0.00 0.00 45.98 5.69
251 252 0.322322 TCCGTTTAGGATTGTGCGGT 59.678 50.000 0.00 0.00 45.98 5.68
252 253 0.446222 CCGTTTAGGATTGTGCGGTG 59.554 55.000 0.00 0.00 45.00 4.94
253 254 1.434555 CGTTTAGGATTGTGCGGTGA 58.565 50.000 0.00 0.00 0.00 4.02
254 255 1.801771 CGTTTAGGATTGTGCGGTGAA 59.198 47.619 0.00 0.00 0.00 3.18
255 256 2.224549 CGTTTAGGATTGTGCGGTGAAA 59.775 45.455 0.00 0.00 0.00 2.69
256 257 3.119990 CGTTTAGGATTGTGCGGTGAAAT 60.120 43.478 0.00 0.00 0.00 2.17
257 258 4.614993 CGTTTAGGATTGTGCGGTGAAATT 60.615 41.667 0.00 0.00 0.00 1.82
258 259 4.433186 TTAGGATTGTGCGGTGAAATTG 57.567 40.909 0.00 0.00 0.00 2.32
259 260 1.545582 AGGATTGTGCGGTGAAATTGG 59.454 47.619 0.00 0.00 0.00 3.16
260 261 1.349234 GATTGTGCGGTGAAATTGGC 58.651 50.000 0.00 0.00 0.00 4.52
261 262 0.037419 ATTGTGCGGTGAAATTGGCC 60.037 50.000 0.00 0.00 0.00 5.36
305 308 4.638865 ACTCTACCGATGTAATTTTTGCCC 59.361 41.667 0.00 0.00 0.00 5.36
307 310 3.866883 ACCGATGTAATTTTTGCCCTG 57.133 42.857 0.00 0.00 0.00 4.45
372 383 3.876914 TGGGAGCAAAGCAATACTAATCG 59.123 43.478 0.00 0.00 0.00 3.34
374 385 3.535860 GAGCAAAGCAATACTAATCGCG 58.464 45.455 0.00 0.00 0.00 5.87
387 398 3.638971 TCGCGCGTCGATCTCTAT 58.361 55.556 30.98 0.00 43.16 1.98
420 431 5.423610 AGTGAAGAGTTACATCAGCCTATGT 59.576 40.000 6.74 6.74 42.62 2.29
448 463 4.651778 AGCAACATGAGCTACTGGTTTTA 58.348 39.130 14.18 0.00 41.32 1.52
461 477 8.141909 AGCTACTGGTTTTATTTGAAGGAAAAC 58.858 33.333 7.73 7.73 40.65 2.43
470 486 4.846779 TTTGAAGGAAAACCGAATGAGG 57.153 40.909 0.00 0.00 37.30 3.86
480 496 3.983044 ACCGAATGAGGTAGCTTTTCT 57.017 42.857 13.40 0.00 43.89 2.52
484 500 4.003648 CGAATGAGGTAGCTTTTCTGGTT 58.996 43.478 13.40 0.00 0.00 3.67
514 652 2.859032 GCTAGACAGCCTACGTACATGC 60.859 54.545 0.00 0.00 42.37 4.06
545 683 0.481567 CCATTGCTCCCCATCCATCT 59.518 55.000 0.00 0.00 0.00 2.90
581 719 4.023279 GTGGTGATGACAAATGTTGCAGTA 60.023 41.667 0.00 0.00 0.00 2.74
582 720 4.023279 TGGTGATGACAAATGTTGCAGTAC 60.023 41.667 0.00 0.00 0.00 2.73
583 721 4.216257 GGTGATGACAAATGTTGCAGTACT 59.784 41.667 0.00 0.00 0.00 2.73
584 722 5.149273 GTGATGACAAATGTTGCAGTACTG 58.851 41.667 18.93 18.93 0.00 2.74
585 723 4.216042 TGATGACAAATGTTGCAGTACTGG 59.784 41.667 23.95 7.41 0.00 4.00
586 724 3.814625 TGACAAATGTTGCAGTACTGGA 58.185 40.909 23.95 19.25 0.00 3.86
587 725 3.814842 TGACAAATGTTGCAGTACTGGAG 59.185 43.478 23.95 10.83 31.08 3.86
588 726 2.554032 ACAAATGTTGCAGTACTGGAGC 59.446 45.455 23.95 22.74 33.12 4.70
589 727 1.442769 AATGTTGCAGTACTGGAGCG 58.557 50.000 23.95 0.00 35.08 5.03
590 728 0.391661 ATGTTGCAGTACTGGAGCGG 60.392 55.000 23.95 0.00 35.08 5.52
686 826 1.524355 CGGATATTGAAGTGCTCTGCG 59.476 52.381 0.00 0.00 0.00 5.18
727 867 3.435327 CCAAAGTTGCACTGCTATTACGA 59.565 43.478 1.98 0.00 0.00 3.43
728 868 4.394795 CAAAGTTGCACTGCTATTACGAC 58.605 43.478 1.98 0.00 0.00 4.34
729 869 2.618053 AGTTGCACTGCTATTACGACC 58.382 47.619 1.98 0.00 0.00 4.79
730 870 1.323534 GTTGCACTGCTATTACGACCG 59.676 52.381 1.98 0.00 0.00 4.79
731 871 0.179121 TGCACTGCTATTACGACCGG 60.179 55.000 0.00 0.00 0.00 5.28
732 872 0.101759 GCACTGCTATTACGACCGGA 59.898 55.000 9.46 0.00 0.00 5.14
733 873 1.864435 GCACTGCTATTACGACCGGAG 60.864 57.143 9.46 3.87 0.00 4.63
734 874 0.384669 ACTGCTATTACGACCGGAGC 59.615 55.000 9.46 5.03 0.00 4.70
735 875 0.669077 CTGCTATTACGACCGGAGCT 59.331 55.000 9.46 0.00 34.19 4.09
736 876 0.384309 TGCTATTACGACCGGAGCTG 59.616 55.000 9.46 0.00 34.19 4.24
761 911 1.832167 GTCCCCAAGCCAAGCAACA 60.832 57.895 0.00 0.00 0.00 3.33
762 912 1.075674 TCCCCAAGCCAAGCAACAA 60.076 52.632 0.00 0.00 0.00 2.83
763 913 0.471591 TCCCCAAGCCAAGCAACAAT 60.472 50.000 0.00 0.00 0.00 2.71
764 914 0.320946 CCCCAAGCCAAGCAACAATG 60.321 55.000 0.00 0.00 0.00 2.82
831 981 6.421801 AGTGAATGCATGTACAAAGAAAAAGC 59.578 34.615 0.00 0.00 0.00 3.51
839 989 7.471721 CATGTACAAAGAAAAAGCGATGGATA 58.528 34.615 0.00 0.00 0.00 2.59
881 1040 4.747265 ATTGCACATCCCCCATATAACT 57.253 40.909 0.00 0.00 0.00 2.24
882 1041 3.788227 TGCACATCCCCCATATAACTC 57.212 47.619 0.00 0.00 0.00 3.01
883 1042 3.052329 TGCACATCCCCCATATAACTCA 58.948 45.455 0.00 0.00 0.00 3.41
884 1043 3.181445 TGCACATCCCCCATATAACTCAC 60.181 47.826 0.00 0.00 0.00 3.51
885 1044 3.181445 GCACATCCCCCATATAACTCACA 60.181 47.826 0.00 0.00 0.00 3.58
886 1045 4.645535 CACATCCCCCATATAACTCACAG 58.354 47.826 0.00 0.00 0.00 3.66
887 1046 4.347876 CACATCCCCCATATAACTCACAGA 59.652 45.833 0.00 0.00 0.00 3.41
888 1047 4.594920 ACATCCCCCATATAACTCACAGAG 59.405 45.833 0.00 0.00 35.52 3.35
894 1058 5.070981 CCCCATATAACTCACAGAGTCACAT 59.929 44.000 0.00 0.00 42.59 3.21
943 1107 4.464008 CCATACATACAAAGAGCACCCAT 58.536 43.478 0.00 0.00 0.00 4.00
1174 1589 2.287668 GCTATCGCTTCCTATGTGTCGT 60.288 50.000 0.00 0.00 0.00 4.34
1204 1620 2.811317 GTCTTGGCTCCGAGCACG 60.811 66.667 21.76 9.23 44.75 5.34
1205 1621 3.303135 TCTTGGCTCCGAGCACGT 61.303 61.111 21.76 0.00 44.75 4.49
1294 1717 0.317479 CGTGTCCCGAGTTCTTTCCT 59.683 55.000 0.00 0.00 39.56 3.36
1295 1718 1.542915 CGTGTCCCGAGTTCTTTCCTA 59.457 52.381 0.00 0.00 39.56 2.94
1296 1719 2.415625 CGTGTCCCGAGTTCTTTCCTAG 60.416 54.545 0.00 0.00 39.56 3.02
1297 1720 2.561858 GTGTCCCGAGTTCTTTCCTAGT 59.438 50.000 0.00 0.00 0.00 2.57
1298 1721 3.006644 GTGTCCCGAGTTCTTTCCTAGTT 59.993 47.826 0.00 0.00 0.00 2.24
1299 1722 3.257624 TGTCCCGAGTTCTTTCCTAGTTC 59.742 47.826 0.00 0.00 0.00 3.01
1300 1723 2.830321 TCCCGAGTTCTTTCCTAGTTCC 59.170 50.000 0.00 0.00 0.00 3.62
1411 5091 7.174946 TCTCTCTCTCTCTCTCTGTTTTTCTTC 59.825 40.741 0.00 0.00 0.00 2.87
1420 5100 5.684704 TCTCTGTTTTTCTTCACCACATCT 58.315 37.500 0.00 0.00 0.00 2.90
1467 5150 3.810310 ATTTTTGGGCGTGTTTTGAGA 57.190 38.095 0.00 0.00 0.00 3.27
1498 5448 4.601857 AGTTGGAGAAGGGATTTGTCCTTA 59.398 41.667 4.94 0.00 46.73 2.69
1524 5474 4.557895 CGTGGGTTTTGGAGTATTGTTTCC 60.558 45.833 0.00 0.00 0.00 3.13
1531 5481 4.295141 TGGAGTATTGTTTCCGGTCAAT 57.705 40.909 19.43 19.43 36.22 2.57
1549 5501 5.163754 GGTCAATAAATTCAGTTGGTCGGAG 60.164 44.000 0.00 0.00 0.00 4.63
1691 7918 0.737715 GACGAGGATGTCCAGCACAC 60.738 60.000 1.30 0.00 38.04 3.82
1694 7921 1.841302 GAGGATGTCCAGCACACCCA 61.841 60.000 1.30 0.00 38.04 4.51
1757 8012 0.254178 AAAGCGATGGTCATGAGCCT 59.746 50.000 21.58 12.46 0.00 4.58
1820 8112 4.842292 GCACCTCGCATCTGATGA 57.158 55.556 21.30 0.34 41.79 2.92
1823 8115 1.329906 GCACCTCGCATCTGATGAAAG 59.670 52.381 21.30 15.26 41.79 2.62
1824 8116 2.625737 CACCTCGCATCTGATGAAAGT 58.374 47.619 21.30 9.10 0.00 2.66
1826 8118 2.234661 ACCTCGCATCTGATGAAAGTCA 59.765 45.455 21.30 0.00 0.00 3.41
1827 8119 3.118482 ACCTCGCATCTGATGAAAGTCAT 60.118 43.478 21.30 3.10 40.34 3.06
1828 8120 4.100035 ACCTCGCATCTGATGAAAGTCATA 59.900 41.667 21.30 0.00 37.20 2.15
1954 8255 0.737367 CTTGTCGAGGAATGCGAGCA 60.737 55.000 0.00 0.00 38.59 4.26
1955 8256 0.108186 TTGTCGAGGAATGCGAGCAT 60.108 50.000 4.52 4.52 38.59 3.79
1956 8257 0.807275 TGTCGAGGAATGCGAGCATG 60.807 55.000 11.64 0.00 38.59 4.06
1957 8258 1.884464 TCGAGGAATGCGAGCATGC 60.884 57.895 10.51 10.51 36.68 4.06
2012 8393 1.300697 AAGTCGTGCGAGTCAACCC 60.301 57.895 2.23 0.00 0.00 4.11
2013 8394 2.023414 AAGTCGTGCGAGTCAACCCA 62.023 55.000 2.23 0.00 0.00 4.51
2014 8395 2.022129 GTCGTGCGAGTCAACCCAG 61.022 63.158 0.00 0.00 0.00 4.45
2015 8396 2.197605 TCGTGCGAGTCAACCCAGA 61.198 57.895 0.00 0.00 0.00 3.86
2016 8397 1.734477 CGTGCGAGTCAACCCAGAG 60.734 63.158 0.00 0.00 0.00 3.35
2017 8398 1.367840 GTGCGAGTCAACCCAGAGT 59.632 57.895 0.00 0.00 0.00 3.24
2018 8399 0.667792 GTGCGAGTCAACCCAGAGTC 60.668 60.000 0.00 0.00 35.17 3.36
2020 8401 0.389166 GCGAGTCAACCCAGAGTCAG 60.389 60.000 0.00 0.00 37.75 3.51
2021 8402 1.248486 CGAGTCAACCCAGAGTCAGA 58.752 55.000 0.00 0.00 37.75 3.27
2022 8403 1.068194 CGAGTCAACCCAGAGTCAGAC 60.068 57.143 0.00 0.00 37.75 3.51
2023 8404 1.273886 GAGTCAACCCAGAGTCAGACC 59.726 57.143 0.00 0.00 37.79 3.85
2190 9552 0.031449 GTACTCATCGAGCTCAGCCC 59.969 60.000 15.40 0.00 32.04 5.19
2409 10210 3.821636 CTGGCCCAGCGCTATGAGG 62.822 68.421 10.99 7.15 37.74 3.86
2441 10242 1.855513 TAATCATCCGCCGGTTAACG 58.144 50.000 1.63 0.00 43.80 3.18
2610 10541 3.488778 TCGACCTCTATCTACTGGGAC 57.511 52.381 0.00 0.00 0.00 4.46
2612 10543 3.142951 CGACCTCTATCTACTGGGACTG 58.857 54.545 0.00 0.00 0.00 3.51
2693 13040 1.595382 GTCATTCCCGATGGGCGAG 60.595 63.158 0.00 0.00 43.94 5.03
2743 13090 5.804639 ACATGAGCACAAGTATGTTTCCTA 58.195 37.500 0.00 0.00 37.82 2.94
2783 13130 8.745837 CATGTTTTGTTTAGTTCATCACTGTTC 58.254 33.333 0.00 0.00 35.97 3.18
2850 13197 6.266103 AGGAATACTTTTGGATGCCATACATG 59.734 38.462 0.00 0.00 39.84 3.21
2867 13214 9.062524 GCCATACATGTAATACAAATGACCTAA 57.937 33.333 10.14 0.00 0.00 2.69
2911 13258 7.747155 ATTTTGGCAATTGATTGAAATGTCA 57.253 28.000 10.34 0.00 40.14 3.58
2954 13302 7.537306 CACGTTTCCTGTTTAAATCCATAACAG 59.463 37.037 0.00 0.00 45.15 3.16
2981 13329 8.713708 TTTGAATCCCCAACTCATTTAGTTTA 57.286 30.769 0.00 0.00 46.61 2.01
2982 13330 8.713708 TTGAATCCCCAACTCATTTAGTTTAA 57.286 30.769 0.00 0.00 46.61 1.52
2983 13331 8.117813 TGAATCCCCAACTCATTTAGTTTAAC 57.882 34.615 0.00 0.00 46.61 2.01
3039 14198 8.453238 ACTGAGGTTACTAGTACTGTATGATG 57.547 38.462 5.39 0.00 0.00 3.07
3105 14264 0.467290 ACAATTTGGACGTGGCACCT 60.467 50.000 12.86 0.00 0.00 4.00
3303 14462 2.821366 CAGCTGGGGCGTCATGTC 60.821 66.667 5.57 0.00 44.37 3.06
3333 14492 2.092753 CCTTAGAAGCAGGCCTCAATGA 60.093 50.000 0.00 0.00 0.00 2.57
3502 14661 3.881688 CCTATGGAATGCCTGTTCTTGAG 59.118 47.826 0.00 0.00 34.31 3.02
3505 14664 1.615384 GGAATGCCTGTTCTTGAGCCT 60.615 52.381 0.00 0.00 0.00 4.58
3538 14697 0.419865 TGGACCAAGAGTATCCCCCA 59.580 55.000 0.00 0.00 33.66 4.96
3663 14827 3.154827 AGTCGATTTGGATTTGGTGGT 57.845 42.857 0.00 0.00 0.00 4.16
3698 14862 4.154195 GCCACATGTAAGTGTGTTTAGGAG 59.846 45.833 0.00 0.00 46.21 3.69
3870 15039 6.920569 ACTCGTATTCAGACTTGTTTTGTT 57.079 33.333 0.00 0.00 0.00 2.83
3936 15108 7.984422 TTCTGTCTACATCATCATGTGTTTT 57.016 32.000 0.00 0.00 43.54 2.43
4124 15340 1.349026 AGCTATGCACAGTCTGGTTGT 59.651 47.619 4.53 0.00 0.00 3.32
4128 15345 0.751277 TGCACAGTCTGGTTGTTGGG 60.751 55.000 4.53 0.00 0.00 4.12
4129 15346 1.455383 GCACAGTCTGGTTGTTGGGG 61.455 60.000 4.53 0.00 0.00 4.96
4131 15348 0.474184 ACAGTCTGGTTGTTGGGGAG 59.526 55.000 4.53 0.00 0.00 4.30
4135 15386 1.913419 GTCTGGTTGTTGGGGAGGATA 59.087 52.381 0.00 0.00 0.00 2.59
4149 15400 4.384465 GGGAGGATATTTGGGGAGGATAT 58.616 47.826 0.00 0.00 0.00 1.63
4150 15401 4.166919 GGGAGGATATTTGGGGAGGATATG 59.833 50.000 0.00 0.00 0.00 1.78
4159 15410 1.536662 GGAGGATATGGGGCTCCGT 60.537 63.158 1.07 1.07 36.62 4.69
4160 15411 1.545706 GGAGGATATGGGGCTCCGTC 61.546 65.000 0.00 0.00 36.62 4.79
4474 15965 5.213913 AGTATATACGCCGATGTTACGAG 57.786 43.478 7.23 0.00 35.09 4.18
4544 16035 9.467796 TCTGCTAGCATACATAGATACTGTTAT 57.532 33.333 19.72 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.819905 CCACAAAACGGCCCAGTTT 59.180 52.632 0.00 0.00 45.21 2.66
1 2 2.791868 GCCACAAAACGGCCCAGTT 61.792 57.895 0.00 0.00 44.22 3.16
2 3 3.223589 GCCACAAAACGGCCCAGT 61.224 61.111 0.00 0.00 44.22 4.00
8 9 1.298788 GTTCACGGCCACAAAACGG 60.299 57.895 2.24 0.00 0.00 4.44
9 10 1.298788 GGTTCACGGCCACAAAACG 60.299 57.895 2.24 0.00 0.00 3.60
10 11 1.066752 GGGTTCACGGCCACAAAAC 59.933 57.895 2.24 0.82 0.00 2.43
11 12 0.970937 TTGGGTTCACGGCCACAAAA 60.971 50.000 2.24 0.00 0.00 2.44
12 13 0.970937 TTTGGGTTCACGGCCACAAA 60.971 50.000 2.24 0.00 0.00 2.83
13 14 1.379977 TTTGGGTTCACGGCCACAA 60.380 52.632 2.24 0.00 0.00 3.33
14 15 2.122167 GTTTGGGTTCACGGCCACA 61.122 57.895 2.24 0.00 0.00 4.17
15 16 1.388837 AAGTTTGGGTTCACGGCCAC 61.389 55.000 2.24 0.00 0.00 5.01
16 17 0.183014 TAAGTTTGGGTTCACGGCCA 59.817 50.000 2.24 0.00 0.00 5.36
17 18 1.541379 ATAAGTTTGGGTTCACGGCC 58.459 50.000 0.00 0.00 0.00 6.13
18 19 4.976224 AATATAAGTTTGGGTTCACGGC 57.024 40.909 0.00 0.00 0.00 5.68
19 20 8.463607 ACATAAAATATAAGTTTGGGTTCACGG 58.536 33.333 0.00 0.00 0.00 4.94
20 21 9.849166 AACATAAAATATAAGTTTGGGTTCACG 57.151 29.630 0.00 0.00 0.00 4.35
88 89 9.673454 GGACGTGATTAAAATAACAGAAAAACT 57.327 29.630 0.00 0.00 0.00 2.66
89 90 9.453325 TGGACGTGATTAAAATAACAGAAAAAC 57.547 29.630 0.00 0.00 0.00 2.43
90 91 9.453325 GTGGACGTGATTAAAATAACAGAAAAA 57.547 29.630 0.00 0.00 0.00 1.94
91 92 8.077386 GGTGGACGTGATTAAAATAACAGAAAA 58.923 33.333 0.00 0.00 0.00 2.29
92 93 7.571613 CGGTGGACGTGATTAAAATAACAGAAA 60.572 37.037 0.00 0.00 37.93 2.52
93 94 6.128499 CGGTGGACGTGATTAAAATAACAGAA 60.128 38.462 0.00 0.00 37.93 3.02
94 95 5.349270 CGGTGGACGTGATTAAAATAACAGA 59.651 40.000 0.00 0.00 37.93 3.41
95 96 5.446741 CCGGTGGACGTGATTAAAATAACAG 60.447 44.000 0.00 0.00 42.24 3.16
96 97 4.392445 CCGGTGGACGTGATTAAAATAACA 59.608 41.667 0.00 0.00 42.24 2.41
97 98 4.630940 TCCGGTGGACGTGATTAAAATAAC 59.369 41.667 0.00 0.00 42.24 1.89
98 99 4.630940 GTCCGGTGGACGTGATTAAAATAA 59.369 41.667 0.00 0.00 43.14 1.40
99 100 4.183101 GTCCGGTGGACGTGATTAAAATA 58.817 43.478 0.00 0.00 43.14 1.40
100 101 3.004862 GTCCGGTGGACGTGATTAAAAT 58.995 45.455 0.00 0.00 43.14 1.82
101 102 2.415776 GTCCGGTGGACGTGATTAAAA 58.584 47.619 0.00 0.00 43.14 1.52
102 103 2.083167 GTCCGGTGGACGTGATTAAA 57.917 50.000 0.00 0.00 43.14 1.52
103 104 3.818586 GTCCGGTGGACGTGATTAA 57.181 52.632 0.00 0.00 43.14 1.40
112 113 0.034574 CCCAAATCATGTCCGGTGGA 60.035 55.000 0.00 0.00 0.00 4.02
113 114 1.037030 CCCCAAATCATGTCCGGTGG 61.037 60.000 0.00 0.00 0.00 4.61
114 115 0.323360 ACCCCAAATCATGTCCGGTG 60.323 55.000 0.00 0.00 0.00 4.94
115 116 0.323360 CACCCCAAATCATGTCCGGT 60.323 55.000 0.00 0.00 0.00 5.28
116 117 1.666209 GCACCCCAAATCATGTCCGG 61.666 60.000 0.00 0.00 0.00 5.14
117 118 1.809207 GCACCCCAAATCATGTCCG 59.191 57.895 0.00 0.00 0.00 4.79
118 119 1.666209 CCGCACCCCAAATCATGTCC 61.666 60.000 0.00 0.00 0.00 4.02
119 120 1.809207 CCGCACCCCAAATCATGTC 59.191 57.895 0.00 0.00 0.00 3.06
120 121 2.350458 GCCGCACCCCAAATCATGT 61.350 57.895 0.00 0.00 0.00 3.21
121 122 2.495866 GCCGCACCCCAAATCATG 59.504 61.111 0.00 0.00 0.00 3.07
122 123 2.759560 GGCCGCACCCCAAATCAT 60.760 61.111 0.00 0.00 0.00 2.45
151 152 4.612412 TCGTTGGGTCGTGGGTGC 62.612 66.667 0.00 0.00 0.00 5.01
152 153 2.109387 TTCGTTGGGTCGTGGGTG 59.891 61.111 0.00 0.00 0.00 4.61
153 154 2.109593 GTTCGTTGGGTCGTGGGT 59.890 61.111 0.00 0.00 0.00 4.51
154 155 1.959226 CTGTTCGTTGGGTCGTGGG 60.959 63.158 0.00 0.00 0.00 4.61
155 156 0.531090 TTCTGTTCGTTGGGTCGTGG 60.531 55.000 0.00 0.00 0.00 4.94
156 157 0.859232 CTTCTGTTCGTTGGGTCGTG 59.141 55.000 0.00 0.00 0.00 4.35
157 158 0.878961 GCTTCTGTTCGTTGGGTCGT 60.879 55.000 0.00 0.00 0.00 4.34
158 159 1.860078 GCTTCTGTTCGTTGGGTCG 59.140 57.895 0.00 0.00 0.00 4.79
159 160 1.566018 CCGCTTCTGTTCGTTGGGTC 61.566 60.000 0.00 0.00 0.00 4.46
160 161 1.597027 CCGCTTCTGTTCGTTGGGT 60.597 57.895 0.00 0.00 0.00 4.51
161 162 1.301401 TCCGCTTCTGTTCGTTGGG 60.301 57.895 0.00 0.00 0.00 4.12
162 163 0.878523 TGTCCGCTTCTGTTCGTTGG 60.879 55.000 0.00 0.00 0.00 3.77
163 164 1.136252 CATGTCCGCTTCTGTTCGTTG 60.136 52.381 0.00 0.00 0.00 4.10
164 165 1.148310 CATGTCCGCTTCTGTTCGTT 58.852 50.000 0.00 0.00 0.00 3.85
165 166 0.670546 CCATGTCCGCTTCTGTTCGT 60.671 55.000 0.00 0.00 0.00 3.85
166 167 1.361668 CCCATGTCCGCTTCTGTTCG 61.362 60.000 0.00 0.00 0.00 3.95
167 168 1.648467 GCCCATGTCCGCTTCTGTTC 61.648 60.000 0.00 0.00 0.00 3.18
168 169 1.675641 GCCCATGTCCGCTTCTGTT 60.676 57.895 0.00 0.00 0.00 3.16
169 170 2.045926 GCCCATGTCCGCTTCTGT 60.046 61.111 0.00 0.00 0.00 3.41
170 171 3.197790 CGCCCATGTCCGCTTCTG 61.198 66.667 0.00 0.00 0.00 3.02
171 172 2.954684 TTCGCCCATGTCCGCTTCT 61.955 57.895 0.00 0.00 0.00 2.85
172 173 2.435938 TTCGCCCATGTCCGCTTC 60.436 61.111 0.00 0.00 0.00 3.86
173 174 2.746277 GTTCGCCCATGTCCGCTT 60.746 61.111 0.00 0.00 0.00 4.68
174 175 4.778143 GGTTCGCCCATGTCCGCT 62.778 66.667 0.00 0.00 0.00 5.52
184 185 1.816679 GGACGGTAATGGGTTCGCC 60.817 63.158 0.00 0.00 0.00 5.54
185 186 1.816679 GGGACGGTAATGGGTTCGC 60.817 63.158 0.00 0.00 0.00 4.70
186 187 0.036199 TTGGGACGGTAATGGGTTCG 60.036 55.000 0.00 0.00 0.00 3.95
187 188 2.089201 CTTTGGGACGGTAATGGGTTC 58.911 52.381 0.00 0.00 0.00 3.62
188 189 1.272258 CCTTTGGGACGGTAATGGGTT 60.272 52.381 0.00 0.00 33.58 4.11
189 190 0.330267 CCTTTGGGACGGTAATGGGT 59.670 55.000 0.00 0.00 33.58 4.51
190 191 2.805060 TCCCTTTGGGACGGTAATGGG 61.805 57.143 0.42 6.72 46.17 4.00
191 192 0.621609 TCCCTTTGGGACGGTAATGG 59.378 55.000 0.42 0.00 46.17 3.16
201 202 0.894835 CCGGATTTTGTCCCTTTGGG 59.105 55.000 0.00 0.00 44.77 4.12
202 203 0.246360 GCCGGATTTTGTCCCTTTGG 59.754 55.000 5.05 0.00 44.77 3.28
203 204 0.246360 GGCCGGATTTTGTCCCTTTG 59.754 55.000 5.05 0.00 44.77 2.77
204 205 0.178947 TGGCCGGATTTTGTCCCTTT 60.179 50.000 5.05 0.00 44.77 3.11
205 206 0.178947 TTGGCCGGATTTTGTCCCTT 60.179 50.000 5.05 0.00 44.77 3.95
206 207 0.898326 GTTGGCCGGATTTTGTCCCT 60.898 55.000 5.05 0.00 44.77 4.20
207 208 1.589630 GTTGGCCGGATTTTGTCCC 59.410 57.895 5.05 0.00 44.77 4.46
208 209 1.182385 TGGTTGGCCGGATTTTGTCC 61.182 55.000 5.05 0.00 44.10 4.02
209 210 0.676736 TTGGTTGGCCGGATTTTGTC 59.323 50.000 5.05 0.00 37.67 3.18
210 211 1.123928 TTTGGTTGGCCGGATTTTGT 58.876 45.000 5.05 0.00 37.67 2.83
211 212 1.507562 GTTTGGTTGGCCGGATTTTG 58.492 50.000 5.05 0.00 37.67 2.44
212 213 0.032815 CGTTTGGTTGGCCGGATTTT 59.967 50.000 5.05 0.00 37.67 1.82
213 214 1.110518 ACGTTTGGTTGGCCGGATTT 61.111 50.000 5.05 0.00 37.67 2.17
214 215 1.520600 GACGTTTGGTTGGCCGGATT 61.521 55.000 5.05 0.00 37.67 3.01
215 216 1.969589 GACGTTTGGTTGGCCGGAT 60.970 57.895 5.05 0.00 37.67 4.18
216 217 2.592287 GACGTTTGGTTGGCCGGA 60.592 61.111 5.05 0.00 37.67 5.14
217 218 3.666253 GGACGTTTGGTTGGCCGG 61.666 66.667 0.00 0.00 37.67 6.13
218 219 4.020378 CGGACGTTTGGTTGGCCG 62.020 66.667 0.00 0.00 37.67 6.13
219 220 2.007113 AAACGGACGTTTGGTTGGCC 62.007 55.000 20.42 0.00 45.34 5.36
220 221 0.662085 TAAACGGACGTTTGGTTGGC 59.338 50.000 27.19 0.00 46.34 4.52
221 222 1.264826 CCTAAACGGACGTTTGGTTGG 59.735 52.381 27.19 19.70 46.34 3.77
222 223 2.211806 TCCTAAACGGACGTTTGGTTG 58.788 47.619 27.19 15.32 46.34 3.77
223 224 2.618442 TCCTAAACGGACGTTTGGTT 57.382 45.000 27.19 8.59 46.34 3.67
224 225 2.809696 CAATCCTAAACGGACGTTTGGT 59.190 45.455 27.19 10.97 46.80 3.67
225 226 2.809696 ACAATCCTAAACGGACGTTTGG 59.190 45.455 27.19 24.35 46.80 3.28
226 227 3.805823 CACAATCCTAAACGGACGTTTG 58.194 45.455 27.19 18.09 46.80 2.93
227 228 2.224784 GCACAATCCTAAACGGACGTTT 59.775 45.455 23.69 23.69 46.80 3.60
228 229 1.802365 GCACAATCCTAAACGGACGTT 59.198 47.619 3.99 3.99 46.80 3.99
229 230 1.435577 GCACAATCCTAAACGGACGT 58.564 50.000 0.00 0.00 46.80 4.34
230 231 0.368907 CGCACAATCCTAAACGGACG 59.631 55.000 0.00 0.00 46.80 4.79
231 232 0.725117 CCGCACAATCCTAAACGGAC 59.275 55.000 0.00 0.00 46.80 4.79
233 234 0.446222 CACCGCACAATCCTAAACGG 59.554 55.000 0.00 0.00 45.86 4.44
234 235 1.434555 TCACCGCACAATCCTAAACG 58.565 50.000 0.00 0.00 0.00 3.60
235 236 3.907894 TTTCACCGCACAATCCTAAAC 57.092 42.857 0.00 0.00 0.00 2.01
236 237 4.321601 CCAATTTCACCGCACAATCCTAAA 60.322 41.667 0.00 0.00 0.00 1.85
237 238 3.192422 CCAATTTCACCGCACAATCCTAA 59.808 43.478 0.00 0.00 0.00 2.69
238 239 2.752354 CCAATTTCACCGCACAATCCTA 59.248 45.455 0.00 0.00 0.00 2.94
239 240 1.545582 CCAATTTCACCGCACAATCCT 59.454 47.619 0.00 0.00 0.00 3.24
240 241 1.994916 CCAATTTCACCGCACAATCC 58.005 50.000 0.00 0.00 0.00 3.01
241 242 1.349234 GCCAATTTCACCGCACAATC 58.651 50.000 0.00 0.00 0.00 2.67
242 243 0.037419 GGCCAATTTCACCGCACAAT 60.037 50.000 0.00 0.00 0.00 2.71
243 244 1.112315 AGGCCAATTTCACCGCACAA 61.112 50.000 5.01 0.00 0.00 3.33
244 245 0.250945 TAGGCCAATTTCACCGCACA 60.251 50.000 5.01 0.00 0.00 4.57
245 246 0.885196 TTAGGCCAATTTCACCGCAC 59.115 50.000 5.01 0.00 0.00 5.34
246 247 0.885196 GTTAGGCCAATTTCACCGCA 59.115 50.000 5.01 0.00 0.00 5.69
247 248 1.173913 AGTTAGGCCAATTTCACCGC 58.826 50.000 5.01 0.00 0.00 5.68
248 249 3.506067 AGAAAGTTAGGCCAATTTCACCG 59.494 43.478 15.72 0.00 34.77 4.94
249 250 4.379499 CGAGAAAGTTAGGCCAATTTCACC 60.379 45.833 15.72 7.98 34.77 4.02
250 251 4.723248 CGAGAAAGTTAGGCCAATTTCAC 58.277 43.478 15.72 9.95 34.77 3.18
251 252 3.190535 GCGAGAAAGTTAGGCCAATTTCA 59.809 43.478 15.72 0.00 34.77 2.69
252 253 3.190535 TGCGAGAAAGTTAGGCCAATTTC 59.809 43.478 5.01 6.71 32.95 2.17
253 254 3.153919 TGCGAGAAAGTTAGGCCAATTT 58.846 40.909 5.01 0.00 0.00 1.82
254 255 2.790433 TGCGAGAAAGTTAGGCCAATT 58.210 42.857 5.01 0.00 0.00 2.32
255 256 2.489938 TGCGAGAAAGTTAGGCCAAT 57.510 45.000 5.01 0.00 0.00 3.16
256 257 2.264005 TTGCGAGAAAGTTAGGCCAA 57.736 45.000 5.01 0.00 0.00 4.52
257 258 2.264005 TTTGCGAGAAAGTTAGGCCA 57.736 45.000 5.01 0.00 0.00 5.36
258 259 2.552743 AGTTTTGCGAGAAAGTTAGGCC 59.447 45.455 0.00 0.00 0.00 5.19
259 260 3.898517 AGTTTTGCGAGAAAGTTAGGC 57.101 42.857 0.00 0.00 0.00 3.93
260 261 6.956047 AGTAAAGTTTTGCGAGAAAGTTAGG 58.044 36.000 0.00 0.00 33.14 2.69
261 262 7.852516 AGAGTAAAGTTTTGCGAGAAAGTTAG 58.147 34.615 0.00 0.00 33.14 2.34
307 310 2.564458 CCGGCGCTGGTAAAAACC 59.436 61.111 27.83 0.00 0.00 3.27
372 383 0.453615 CTCCATAGAGATCGACGCGC 60.454 60.000 5.73 0.00 43.39 6.86
374 385 0.453615 CGCTCCATAGAGATCGACGC 60.454 60.000 0.00 0.00 43.39 5.19
387 398 1.758440 AACTCTTCACTGGCGCTCCA 61.758 55.000 7.64 0.00 40.85 3.86
448 463 4.832823 ACCTCATTCGGTTTTCCTTCAAAT 59.167 37.500 0.00 0.00 37.95 2.32
461 477 2.939103 CCAGAAAAGCTACCTCATTCGG 59.061 50.000 0.00 0.00 0.00 4.30
463 479 4.396478 GGAACCAGAAAAGCTACCTCATTC 59.604 45.833 0.00 0.00 0.00 2.67
484 500 2.759973 CTGTCTAGCAGCGGGGGA 60.760 66.667 1.97 0.00 38.52 4.81
545 683 1.419381 TCACCACTTGTCAGCTGGTA 58.581 50.000 15.13 0.00 34.49 3.25
581 719 1.992277 AATCTGCCTCCGCTCCAGT 60.992 57.895 0.00 0.00 35.36 4.00
582 720 1.523258 CAATCTGCCTCCGCTCCAG 60.523 63.158 0.00 0.00 35.36 3.86
583 721 2.586245 CAATCTGCCTCCGCTCCA 59.414 61.111 0.00 0.00 35.36 3.86
584 722 2.899339 GCAATCTGCCTCCGCTCC 60.899 66.667 0.00 0.00 37.42 4.70
686 826 2.809601 CGGTAGGCACGTCACAGC 60.810 66.667 0.00 0.00 0.00 4.40
727 867 1.043673 GGACTATGGTCAGCTCCGGT 61.044 60.000 11.67 0.00 43.77 5.28
728 868 1.742768 GGACTATGGTCAGCTCCGG 59.257 63.158 11.67 0.00 43.77 5.14
729 869 1.742768 GGGACTATGGTCAGCTCCG 59.257 63.158 11.67 0.00 43.77 4.63
730 870 0.691078 TGGGGACTATGGTCAGCTCC 60.691 60.000 11.67 7.25 43.77 4.70
731 871 1.139853 CTTGGGGACTATGGTCAGCTC 59.860 57.143 11.67 0.00 43.77 4.09
732 872 1.207791 CTTGGGGACTATGGTCAGCT 58.792 55.000 11.67 0.00 43.77 4.24
733 873 0.464554 GCTTGGGGACTATGGTCAGC 60.465 60.000 11.67 7.46 43.77 4.26
734 874 0.181350 GGCTTGGGGACTATGGTCAG 59.819 60.000 11.67 0.89 43.77 3.51
735 875 0.548926 TGGCTTGGGGACTATGGTCA 60.549 55.000 11.67 0.00 43.77 4.02
736 876 0.623723 TTGGCTTGGGGACTATGGTC 59.376 55.000 0.00 0.00 41.43 4.02
761 911 4.675510 CATTCAAAGAAGCCATACGCATT 58.324 39.130 0.00 0.00 41.38 3.56
762 912 3.489738 GCATTCAAAGAAGCCATACGCAT 60.490 43.478 0.00 0.00 41.38 4.73
763 913 2.159393 GCATTCAAAGAAGCCATACGCA 60.159 45.455 0.00 0.00 41.38 5.24
764 914 2.454055 GCATTCAAAGAAGCCATACGC 58.546 47.619 0.00 0.00 37.98 4.42
765 915 2.095853 ACGCATTCAAAGAAGCCATACG 59.904 45.455 0.00 0.00 0.00 3.06
767 917 3.126858 GTGACGCATTCAAAGAAGCCATA 59.873 43.478 0.00 0.00 35.39 2.74
768 918 2.095059 GTGACGCATTCAAAGAAGCCAT 60.095 45.455 0.00 0.00 35.39 4.40
769 919 1.266718 GTGACGCATTCAAAGAAGCCA 59.733 47.619 0.00 0.00 35.39 4.75
770 920 1.266718 TGTGACGCATTCAAAGAAGCC 59.733 47.619 0.00 0.00 35.39 4.35
773 923 1.946081 TGCTGTGACGCATTCAAAGAA 59.054 42.857 6.68 0.00 41.77 2.52
881 1040 2.417243 CCATACGCATGTGACTCTGTGA 60.417 50.000 14.43 0.00 0.00 3.58
882 1041 1.929169 CCATACGCATGTGACTCTGTG 59.071 52.381 14.43 0.00 0.00 3.66
883 1042 1.740380 GCCATACGCATGTGACTCTGT 60.740 52.381 14.43 0.00 37.47 3.41
884 1043 0.933097 GCCATACGCATGTGACTCTG 59.067 55.000 14.43 4.44 37.47 3.35
885 1044 0.826715 AGCCATACGCATGTGACTCT 59.173 50.000 14.43 0.00 41.38 3.24
886 1045 1.594862 GAAGCCATACGCATGTGACTC 59.405 52.381 14.43 0.00 41.38 3.36
887 1046 1.066215 TGAAGCCATACGCATGTGACT 60.066 47.619 14.43 0.00 41.38 3.41
888 1047 1.328680 CTGAAGCCATACGCATGTGAC 59.671 52.381 14.43 0.00 41.38 3.67
894 1058 1.001974 ACTGAACTGAAGCCATACGCA 59.998 47.619 0.00 0.00 41.38 5.24
943 1107 5.221762 GCACCACTAGAGAGTAGAGAGGATA 60.222 48.000 0.00 0.00 33.32 2.59
980 1165 4.103103 GAAACCAAGCGGCGAGGC 62.103 66.667 12.98 0.00 34.57 4.70
1033 1218 1.002134 CTCCATGTCCAAGCGGGTT 60.002 57.895 0.00 0.00 38.11 4.11
1117 1302 1.272092 TGCTCCACCCTGATTTTCTGG 60.272 52.381 0.00 0.00 35.51 3.86
1174 1589 1.271054 GCCAAGACAAGAGGAAGCAGA 60.271 52.381 0.00 0.00 0.00 4.26
1204 1620 3.351416 GGACCAAACGCCGACCAC 61.351 66.667 0.00 0.00 0.00 4.16
1205 1621 3.524648 GAGGACCAAACGCCGACCA 62.525 63.158 0.00 0.00 0.00 4.02
1294 1717 2.934570 GCCGGACGTGTGGGAACTA 61.935 63.158 5.05 0.00 0.00 2.24
1295 1718 4.309950 GCCGGACGTGTGGGAACT 62.310 66.667 5.05 0.00 0.00 3.01
1377 5035 2.037772 GAGAGAGAGAGAGAGATCCGCT 59.962 54.545 0.00 0.00 0.00 5.52
1411 5091 1.872952 TGCAGAAAACGAGATGTGGTG 59.127 47.619 0.00 0.00 0.00 4.17
1420 5100 4.561213 CGTGATATGTACTGCAGAAAACGA 59.439 41.667 23.35 7.92 34.96 3.85
1467 5150 2.716424 TCCCTTCTCCAACTCCAACAAT 59.284 45.455 0.00 0.00 0.00 2.71
1524 5474 4.436852 CCGACCAACTGAATTTATTGACCG 60.437 45.833 0.00 0.00 0.00 4.79
1531 5481 5.106317 GCATTTCTCCGACCAACTGAATTTA 60.106 40.000 0.00 0.00 0.00 1.40
1595 5547 1.227793 GGCTGGGATGCTGTAGCTC 60.228 63.158 5.38 0.83 42.66 4.09
1722 7949 3.192954 TTTTCGCTTGCACGGCCTG 62.193 57.895 0.00 0.00 0.00 4.85
1725 7960 3.099574 GCTTTTCGCTTGCACGGC 61.100 61.111 0.00 0.00 35.14 5.68
1783 8075 1.135972 CATGGCAAACGAGAAGTTCCG 60.136 52.381 10.87 10.87 43.37 4.30
1820 8112 1.959042 CGCAGGAGCCATATGACTTT 58.041 50.000 3.65 0.00 37.52 2.66
1823 8115 1.227645 TGCGCAGGAGCCATATGAC 60.228 57.895 5.66 0.00 37.52 3.06
1824 8116 1.227645 GTGCGCAGGAGCCATATGA 60.228 57.895 12.22 0.00 37.52 2.15
1826 8118 2.280389 CGTGCGCAGGAGCCATAT 60.280 61.111 25.09 0.00 37.52 1.78
1827 8119 4.529219 CCGTGCGCAGGAGCCATA 62.529 66.667 30.22 0.00 37.52 2.74
1858 8150 2.279120 GGAGGCGACGAGATGCAG 60.279 66.667 0.00 0.00 0.00 4.41
1896 8188 2.638354 TTCGCCGGCCGTAGAGAAA 61.638 57.895 26.12 6.47 38.35 2.52
1954 8255 0.319900 GAGGTCGCCGACATATGCAT 60.320 55.000 20.08 3.79 33.68 3.96
1955 8256 1.067416 GAGGTCGCCGACATATGCA 59.933 57.895 20.08 0.00 33.68 3.96
1956 8257 2.016704 CGAGGTCGCCGACATATGC 61.017 63.158 20.08 0.57 33.68 3.14
1957 8258 0.589708 TACGAGGTCGCCGACATATG 59.410 55.000 20.08 10.63 44.43 1.78
1958 8259 0.590195 GTACGAGGTCGCCGACATAT 59.410 55.000 20.08 6.48 44.43 1.78
1959 8260 0.462581 AGTACGAGGTCGCCGACATA 60.463 55.000 20.08 2.76 44.43 2.29
2059 8440 0.249953 TTAACTCTTGGGCGCGTTCA 60.250 50.000 8.43 3.35 0.00 3.18
2190 9552 2.740055 GCAGGTGCACAGAGACGG 60.740 66.667 20.43 2.37 41.59 4.79
2409 10210 4.386230 CGGATGATTATTCGCACGAAATC 58.614 43.478 9.80 9.60 37.69 2.17
2441 10242 0.034670 AGGTTGCAGGGCAGATCTTC 60.035 55.000 0.00 0.00 40.61 2.87
2610 10541 0.464013 CCATCCAGCTGCCTTCTCAG 60.464 60.000 8.66 0.00 37.15 3.35
2612 10543 1.823041 GCCATCCAGCTGCCTTCTC 60.823 63.158 8.66 0.00 0.00 2.87
2642 10573 3.992427 GAGAAGGTGTAAAACGGTACCAG 59.008 47.826 13.54 7.45 35.66 4.00
2693 13040 7.201965 CCCCCATCAAACCTATAATTTACAACC 60.202 40.741 0.00 0.00 0.00 3.77
2743 13090 8.800370 AAACAAAACATGTATTGAAAAAGGGT 57.200 26.923 0.00 0.00 42.99 4.34
2783 13130 6.147164 ACTTTCAATACACGAGTACAACATGG 59.853 38.462 0.00 0.00 31.96 3.66
2822 13169 4.671831 TGGCATCCAAAAGTATTCCTGAA 58.328 39.130 0.00 0.00 0.00 3.02
2823 13170 4.314522 TGGCATCCAAAAGTATTCCTGA 57.685 40.909 0.00 0.00 0.00 3.86
2954 13302 6.993079 ACTAAATGAGTTGGGGATTCAAAAC 58.007 36.000 0.00 0.00 33.13 2.43
3039 14198 1.978617 CCACCCATGTCAACCCTGC 60.979 63.158 0.00 0.00 0.00 4.85
3333 14492 2.573462 TCTCTGGTTCTTAGCAAGCCAT 59.427 45.455 0.00 0.00 0.00 4.40
3502 14661 2.182842 CAGCGGTATGAAGCCAGGC 61.183 63.158 1.84 1.84 0.00 4.85
3505 14664 1.220749 GTCCAGCGGTATGAAGCCA 59.779 57.895 0.00 0.00 0.00 4.75
3538 14697 2.240667 AGTGCCTGCTCACCAATTATCT 59.759 45.455 0.00 0.00 37.68 1.98
3629 14793 7.092716 TCCAAATCGACTTAAACAGTAGTACC 58.907 38.462 0.00 0.00 35.01 3.34
3698 14862 1.298859 ACGGCCGAGCTGTCAAATTC 61.299 55.000 35.90 0.00 45.94 2.17
4124 15340 2.143602 CTCCCCAAATATCCTCCCCAA 58.856 52.381 0.00 0.00 0.00 4.12
4128 15345 4.166919 CCATATCCTCCCCAAATATCCTCC 59.833 50.000 0.00 0.00 0.00 4.30
4129 15346 4.166919 CCCATATCCTCCCCAAATATCCTC 59.833 50.000 0.00 0.00 0.00 3.71
4131 15348 3.205282 CCCCATATCCTCCCCAAATATCC 59.795 52.174 0.00 0.00 0.00 2.59
4135 15386 0.786435 GCCCCATATCCTCCCCAAAT 59.214 55.000 0.00 0.00 0.00 2.32
4149 15400 0.325296 AATCTACAGACGGAGCCCCA 60.325 55.000 0.00 0.00 0.00 4.96
4150 15401 0.105039 CAATCTACAGACGGAGCCCC 59.895 60.000 0.00 0.00 0.00 5.80
4159 15410 4.610333 TGGGAGCTTAGACAATCTACAGA 58.390 43.478 0.00 0.00 0.00 3.41
4160 15411 4.404073 ACTGGGAGCTTAGACAATCTACAG 59.596 45.833 0.00 0.00 0.00 2.74
4448 15939 8.419076 TCGTAACATCGGCGTATATACTATTA 57.581 34.615 6.85 0.00 0.00 0.98
4474 15965 2.420022 CCTGCCACATTTACTGCTACAC 59.580 50.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.