Multiple sequence alignment - TraesCS7D01G146700

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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 TraesCS7D01G146700 chr7D 100.000 5064 0 0 1 5064 93792849 93787786 0.000000e+00 9352.0
1 TraesCS7D01G146700 chr7D 84.987 1512 197 29 1830 3329 606636159 606637652 0.000000e+00 1507.0
2 TraesCS7D01G146700 chr7D 99.339 605 1 1 1 605 90761527 90762128 0.000000e+00 1092.0
3 TraesCS7D01G146700 chr7D 82.891 339 44 12 3341 3672 606637774 606638105 4.960000e-75 292.0
4 TraesCS7D01G146700 chr7D 85.276 163 2 2 466 606 90748372 90748210 1.140000e-31 148.0
5 TraesCS7D01G146700 chr7D 85.185 162 2 2 466 605 93806355 93806516 4.090000e-31 147.0
6 TraesCS7D01G146700 chr7D 82.639 144 23 2 3923 4065 606638262 606638404 5.320000e-25 126.0
7 TraesCS7D01G146700 chr7B 95.102 4532 134 25 604 5064 47004229 46999715 0.000000e+00 7059.0
8 TraesCS7D01G146700 chr7B 85.545 1515 187 30 1828 3329 690754917 690753422 0.000000e+00 1555.0
9 TraesCS7D01G146700 chr7B 86.413 552 71 3 1278 1827 690755576 690755027 7.250000e-168 601.0
10 TraesCS7D01G146700 chr7B 83.776 339 41 12 3341 3672 690753285 690752954 4.920000e-80 309.0
11 TraesCS7D01G146700 chr7B 83.951 162 21 4 3930 4089 690752790 690752632 3.160000e-32 150.0
12 TraesCS7D01G146700 chr7A 96.269 3752 71 31 604 4336 96571058 96567357 0.000000e+00 6089.0
13 TraesCS7D01G146700 chr7A 85.461 1520 189 28 1823 3329 698679382 698677882 0.000000e+00 1554.0
14 TraesCS7D01G146700 chr7A 89.013 628 15 5 1 605 727614180 727614776 0.000000e+00 728.0
15 TraesCS7D01G146700 chr7A 95.599 409 18 0 4656 5064 96565718 96565310 0.000000e+00 656.0
16 TraesCS7D01G146700 chr7A 93.537 294 14 3 4332 4620 96566523 96566230 2.800000e-117 433.0
17 TraesCS7D01G146700 chr7A 84.524 336 44 7 3341 3672 698677753 698677422 4.890000e-85 326.0
18 TraesCS7D01G146700 chr7A 84.375 160 3 7 466 603 727609684 727609525 2.460000e-28 137.0
19 TraesCS7D01G146700 chr7A 83.333 144 22 2 3923 4065 698677265 698677123 1.140000e-26 132.0
20 TraesCS7D01G146700 chr6A 91.002 2145 177 16 1193 3329 591440013 591437877 0.000000e+00 2878.0
21 TraesCS7D01G146700 chr6A 86.501 363 47 2 3328 3689 591437777 591437416 1.020000e-106 398.0
22 TraesCS7D01G146700 chr6A 78.893 289 49 8 3790 4066 591437337 591437049 8.660000e-43 185.0
23 TraesCS7D01G146700 chr6A 73.834 493 93 23 3588 4066 591436502 591436032 4.060000e-36 163.0
24 TraesCS7D01G146700 chr6A 91.954 87 5 1 4325 4411 190660352 190660436 2.480000e-23 121.0
25 TraesCS7D01G146700 chr6A 91.954 87 5 1 4325 4411 190738275 190738359 2.480000e-23 121.0
26 TraesCS7D01G146700 chr6D 90.599 2170 184 20 1170 3329 443849968 443847809 0.000000e+00 2859.0
27 TraesCS7D01G146700 chr6D 87.017 362 45 2 3328 3688 443847722 443847362 1.700000e-109 407.0
28 TraesCS7D01G146700 chr6D 80.000 290 44 8 3790 4066 443847283 443846995 8.600000e-48 202.0
29 TraesCS7D01G146700 chr6B 90.443 2166 195 12 1170 3329 668250628 668248469 0.000000e+00 2843.0
30 TraesCS7D01G146700 chr6B 85.984 371 50 2 3328 3697 668248352 668247983 3.670000e-106 396.0
31 TraesCS7D01G146700 chr6B 78.746 287 49 8 3792 4066 668247903 668247617 1.120000e-41 182.0
32 TraesCS7D01G146700 chr1D 83.343 1801 257 38 1278 3052 349794640 349792857 0.000000e+00 1624.0
33 TraesCS7D01G146700 chr1D 92.857 84 6 0 4325 4408 489300066 489299983 6.890000e-24 122.0
34 TraesCS7D01G146700 chr1D 92.857 84 6 0 4325 4408 489432954 489432871 6.890000e-24 122.0
35 TraesCS7D01G146700 chr1D 82.099 162 7 3 466 605 227002681 227002520 8.910000e-23 119.0
36 TraesCS7D01G146700 chr1B 82.944 1800 266 36 1278 3052 471763388 471761605 0.000000e+00 1585.0
37 TraesCS7D01G146700 chr1A 82.879 1799 269 34 1278 3052 450096396 450094613 0.000000e+00 1580.0
38 TraesCS7D01G146700 chr1A 89.583 96 8 1 4325 4420 518662763 518662856 2.480000e-23 121.0
39 TraesCS7D01G146700 chr2A 94.586 628 12 2 1 606 22185305 22185932 0.000000e+00 952.0
40 TraesCS7D01G146700 chr2A 83.951 162 4 8 466 605 22181500 22181339 8.840000e-28 135.0
41 TraesCS7D01G146700 chr4B 80.639 563 91 14 2504 3051 586467286 586466727 2.180000e-113 420.0
42 TraesCS7D01G146700 chr3D 80.392 357 36 18 3 342 441245832 441245493 1.820000e-59 241.0
43 TraesCS7D01G146700 chrUn 85.185 162 2 2 466 605 477347766 477347605 4.090000e-31 147.0
44 TraesCS7D01G146700 chr3B 91.111 90 7 1 4325 4413 429973609 429973520 2.480000e-23 121.0
45 TraesCS7D01G146700 chr4A 81.988 161 8 7 466 605 608599782 608599942 3.200000e-22 117.0
46 TraesCS7D01G146700 chr4A 79.310 145 9 7 466 589 45372116 45372260 1.170000e-11 82.4
47 TraesCS7D01G146700 chr2B 88.542 96 9 2 4318 4413 483452948 483453041 1.150000e-21 115.0


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 TraesCS7D01G146700 chr7D 93787786 93792849 5063 True 9352.000000 9352 100.000000 1 5064 1 chr7D.!!$R2 5063
1 TraesCS7D01G146700 chr7D 90761527 90762128 601 False 1092.000000 1092 99.339000 1 605 1 chr7D.!!$F1 604
2 TraesCS7D01G146700 chr7D 606636159 606638404 2245 False 641.666667 1507 83.505667 1830 4065 3 chr7D.!!$F3 2235
3 TraesCS7D01G146700 chr7B 46999715 47004229 4514 True 7059.000000 7059 95.102000 604 5064 1 chr7B.!!$R1 4460
4 TraesCS7D01G146700 chr7B 690752632 690755576 2944 True 653.750000 1555 84.921250 1278 4089 4 chr7B.!!$R2 2811
5 TraesCS7D01G146700 chr7A 96565310 96571058 5748 True 2392.666667 6089 95.135000 604 5064 3 chr7A.!!$R2 4460
6 TraesCS7D01G146700 chr7A 727614180 727614776 596 False 728.000000 728 89.013000 1 605 1 chr7A.!!$F1 604
7 TraesCS7D01G146700 chr7A 698677123 698679382 2259 True 670.666667 1554 84.439333 1823 4065 3 chr7A.!!$R3 2242
8 TraesCS7D01G146700 chr6A 591436032 591440013 3981 True 906.000000 2878 82.557500 1193 4066 4 chr6A.!!$R1 2873
9 TraesCS7D01G146700 chr6D 443846995 443849968 2973 True 1156.000000 2859 85.872000 1170 4066 3 chr6D.!!$R1 2896
10 TraesCS7D01G146700 chr6B 668247617 668250628 3011 True 1140.333333 2843 85.057667 1170 4066 3 chr6B.!!$R1 2896
11 TraesCS7D01G146700 chr1D 349792857 349794640 1783 True 1624.000000 1624 83.343000 1278 3052 1 chr1D.!!$R2 1774
12 TraesCS7D01G146700 chr1B 471761605 471763388 1783 True 1585.000000 1585 82.944000 1278 3052 1 chr1B.!!$R1 1774
13 TraesCS7D01G146700 chr1A 450094613 450096396 1783 True 1580.000000 1580 82.879000 1278 3052 1 chr1A.!!$R1 1774
14 TraesCS7D01G146700 chr2A 22185305 22185932 627 False 952.000000 952 94.586000 1 606 1 chr2A.!!$F1 605
15 TraesCS7D01G146700 chr4B 586466727 586467286 559 True 420.000000 420 80.639000 2504 3051 1 chr4B.!!$R1 547

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
412 413 0.100682 GCGAACTGAGCCGATGTAGA 59.899 55.0 0.00 0.00 0.00 2.59 F
462 463 0.108992 AGTCCGATAGCGCGTGAAAA 60.109 50.0 8.43 0.00 35.83 2.29 F
468 469 0.168128 ATAGCGCGTGAAAAACAGCC 59.832 50.0 8.43 0.00 33.83 4.85 F
504 505 0.250038 TGCAGCGATTGGAGCCTATC 60.250 55.0 1.51 1.51 34.64 2.08 F
572 573 0.250727 TCCGGGTTGCAAAGGAGAAG 60.251 55.0 13.56 0.00 0.00 2.85 F
574 575 0.537371 CGGGTTGCAAAGGAGAAGGT 60.537 55.0 0.00 0.00 0.00 3.50 F
1722 1743 0.613853 TCTTCTCGGGATCCACGGTT 60.614 55.0 15.23 0.00 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2172 2302 0.320771 GCACCATGTCCTTGTCGACT 60.321 55.000 17.92 0.00 33.70 4.18 R
3078 3226 0.529773 GCATGAACCCGAGCACGATA 60.530 55.000 4.70 0.00 42.66 2.92 R
3537 4093 1.198094 TCCCCTCCATGTCGCAGAAA 61.198 55.000 0.00 0.00 39.69 2.52 R
3712 4296 2.202298 CAATGGCGACGGCGAAAC 60.202 61.111 18.90 3.59 41.24 2.78 R
3713 4297 2.255172 AACAATGGCGACGGCGAAA 61.255 52.632 18.90 0.00 41.24 3.46 R
3715 4299 3.418913 CAACAATGGCGACGGCGA 61.419 61.111 18.90 0.00 41.24 5.54 R
4925 6990 0.037697 TTCGCGGTGAATACTGTGCT 60.038 50.000 6.13 0.00 42.20 4.40 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
130 131 0.523072 ATTAGCAAAGCACTGCACGG 59.477 50.000 12.01 0.00 45.18 4.94
131 132 0.533978 TTAGCAAAGCACTGCACGGA 60.534 50.000 12.01 0.00 45.18 4.69
132 133 0.533978 TAGCAAAGCACTGCACGGAA 60.534 50.000 12.01 0.00 45.18 4.30
133 134 1.370900 GCAAAGCACTGCACGGAAG 60.371 57.895 3.30 0.00 42.17 3.46
134 135 1.283793 CAAAGCACTGCACGGAAGG 59.716 57.895 3.30 0.00 0.00 3.46
135 136 1.148273 AAAGCACTGCACGGAAGGA 59.852 52.632 3.30 0.00 0.00 3.36
136 137 0.886490 AAAGCACTGCACGGAAGGAG 60.886 55.000 3.30 0.00 0.00 3.69
137 138 1.758440 AAGCACTGCACGGAAGGAGA 61.758 55.000 3.30 0.00 0.00 3.71
138 139 1.301716 GCACTGCACGGAAGGAGAA 60.302 57.895 0.00 0.00 0.00 2.87
139 140 1.294659 GCACTGCACGGAAGGAGAAG 61.295 60.000 0.00 0.00 0.00 2.85
140 141 0.318441 CACTGCACGGAAGGAGAAGA 59.682 55.000 0.74 0.00 0.00 2.87
141 142 0.605589 ACTGCACGGAAGGAGAAGAG 59.394 55.000 0.74 0.00 0.00 2.85
142 143 0.739112 CTGCACGGAAGGAGAAGAGC 60.739 60.000 0.00 0.00 0.00 4.09
143 144 1.188219 TGCACGGAAGGAGAAGAGCT 61.188 55.000 0.00 0.00 0.00 4.09
144 145 0.739112 GCACGGAAGGAGAAGAGCTG 60.739 60.000 0.00 0.00 0.00 4.24
145 146 0.108424 CACGGAAGGAGAAGAGCTGG 60.108 60.000 0.00 0.00 0.00 4.85
146 147 1.153469 CGGAAGGAGAAGAGCTGGC 60.153 63.158 0.00 0.00 0.00 4.85
147 148 1.223211 GGAAGGAGAAGAGCTGGCC 59.777 63.158 0.00 0.00 0.00 5.36
148 149 1.153469 GAAGGAGAAGAGCTGGCCG 60.153 63.158 0.00 0.00 0.00 6.13
149 150 2.585791 GAAGGAGAAGAGCTGGCCGG 62.586 65.000 7.41 7.41 0.00 6.13
150 151 4.168291 GGAGAAGAGCTGGCCGGG 62.168 72.222 15.02 1.86 0.00 5.73
151 152 4.168291 GAGAAGAGCTGGCCGGGG 62.168 72.222 15.02 0.00 0.00 5.73
152 153 4.722535 AGAAGAGCTGGCCGGGGA 62.723 66.667 15.02 0.00 0.00 4.81
153 154 3.717294 GAAGAGCTGGCCGGGGAA 61.717 66.667 15.02 0.00 0.00 3.97
154 155 3.256960 AAGAGCTGGCCGGGGAAA 61.257 61.111 15.02 0.00 0.00 3.13
155 156 2.558380 GAAGAGCTGGCCGGGGAAAT 62.558 60.000 15.02 0.00 0.00 2.17
156 157 2.043953 GAGCTGGCCGGGGAAATT 60.044 61.111 15.02 0.00 0.00 1.82
157 158 1.226262 GAGCTGGCCGGGGAAATTA 59.774 57.895 15.02 0.00 0.00 1.40
158 159 1.076995 AGCTGGCCGGGGAAATTAC 60.077 57.895 15.02 0.00 0.00 1.89
159 160 2.125326 GCTGGCCGGGGAAATTACC 61.125 63.158 15.02 0.00 0.00 2.85
160 161 1.613061 CTGGCCGGGGAAATTACCT 59.387 57.895 2.57 0.00 0.00 3.08
161 162 0.465642 CTGGCCGGGGAAATTACCTC 60.466 60.000 2.57 0.00 0.00 3.85
162 163 0.917333 TGGCCGGGGAAATTACCTCT 60.917 55.000 2.18 0.00 0.00 3.69
163 164 0.257905 GGCCGGGGAAATTACCTCTT 59.742 55.000 2.18 0.00 0.00 2.85
164 165 1.389555 GCCGGGGAAATTACCTCTTG 58.610 55.000 2.18 0.00 0.00 3.02
165 166 1.389555 CCGGGGAAATTACCTCTTGC 58.610 55.000 0.00 0.00 0.00 4.01
166 167 1.389555 CGGGGAAATTACCTCTTGCC 58.610 55.000 0.00 0.00 32.57 4.52
167 168 1.389555 GGGGAAATTACCTCTTGCCG 58.610 55.000 0.00 0.00 34.06 5.69
168 169 1.064979 GGGGAAATTACCTCTTGCCGA 60.065 52.381 0.00 0.00 34.06 5.54
169 170 2.014857 GGGAAATTACCTCTTGCCGAC 58.985 52.381 0.00 0.00 0.00 4.79
170 171 1.664151 GGAAATTACCTCTTGCCGACG 59.336 52.381 0.00 0.00 0.00 5.12
171 172 1.062148 GAAATTACCTCTTGCCGACGC 59.938 52.381 0.00 0.00 0.00 5.19
172 173 1.082117 AATTACCTCTTGCCGACGCG 61.082 55.000 3.53 3.53 38.08 6.01
173 174 1.940883 ATTACCTCTTGCCGACGCGA 61.941 55.000 15.93 0.00 38.08 5.87
174 175 2.537792 TTACCTCTTGCCGACGCGAG 62.538 60.000 15.93 6.19 46.59 5.03
185 186 2.945984 ACGCGAGTTTGTGCCATG 59.054 55.556 15.93 0.00 46.40 3.66
186 187 2.176546 CGCGAGTTTGTGCCATGG 59.823 61.111 7.63 7.63 0.00 3.66
187 188 2.126346 GCGAGTTTGTGCCATGGC 60.126 61.111 30.54 30.54 42.35 4.40
188 189 2.568090 CGAGTTTGTGCCATGGCC 59.432 61.111 33.44 23.83 41.09 5.36
189 190 2.568090 GAGTTTGTGCCATGGCCG 59.432 61.111 33.44 0.00 41.09 6.13
190 191 2.990967 AGTTTGTGCCATGGCCGG 60.991 61.111 33.44 0.00 41.09 6.13
212 213 4.899239 GCGGATGCGACTCCAGGG 62.899 72.222 12.10 0.00 34.78 4.45
213 214 3.147595 CGGATGCGACTCCAGGGA 61.148 66.667 0.00 0.00 34.78 4.20
214 215 2.501610 GGATGCGACTCCAGGGAC 59.498 66.667 0.00 0.00 35.24 4.46
215 216 2.501610 GATGCGACTCCAGGGACC 59.498 66.667 0.00 0.00 0.00 4.46
216 217 3.432051 GATGCGACTCCAGGGACCG 62.432 68.421 0.00 2.15 0.00 4.79
359 360 3.477504 CACGACATTGTGCAAAGGG 57.522 52.632 0.00 0.00 32.31 3.95
360 361 0.667993 CACGACATTGTGCAAAGGGT 59.332 50.000 0.00 0.00 32.31 4.34
361 362 0.951558 ACGACATTGTGCAAAGGGTC 59.048 50.000 0.00 0.00 0.00 4.46
362 363 1.238439 CGACATTGTGCAAAGGGTCT 58.762 50.000 0.00 0.00 0.00 3.85
363 364 1.069022 CGACATTGTGCAAAGGGTCTG 60.069 52.381 0.00 0.33 0.00 3.51
364 365 1.270550 GACATTGTGCAAAGGGTCTGG 59.729 52.381 0.00 0.00 0.00 3.86
365 366 0.604578 CATTGTGCAAAGGGTCTGGG 59.395 55.000 0.00 0.00 0.00 4.45
366 367 0.482446 ATTGTGCAAAGGGTCTGGGA 59.518 50.000 0.00 0.00 0.00 4.37
367 368 0.178992 TTGTGCAAAGGGTCTGGGAG 60.179 55.000 0.00 0.00 0.00 4.30
368 369 1.973812 GTGCAAAGGGTCTGGGAGC 60.974 63.158 0.00 0.00 0.00 4.70
380 381 2.456627 TGGGAGCCAGGATAGATGC 58.543 57.895 0.00 0.00 0.00 3.91
381 382 0.104777 TGGGAGCCAGGATAGATGCT 60.105 55.000 0.00 0.00 36.62 3.79
384 385 2.747396 GAGCCAGGATAGATGCTCTG 57.253 55.000 0.00 0.00 45.21 3.35
385 386 1.969923 GAGCCAGGATAGATGCTCTGT 59.030 52.381 0.00 0.00 45.21 3.41
386 387 2.368221 GAGCCAGGATAGATGCTCTGTT 59.632 50.000 0.00 0.00 45.21 3.16
387 388 2.368221 AGCCAGGATAGATGCTCTGTTC 59.632 50.000 0.00 0.00 0.00 3.18
388 389 2.368221 GCCAGGATAGATGCTCTGTTCT 59.632 50.000 0.00 0.00 0.00 3.01
389 390 3.554752 GCCAGGATAGATGCTCTGTTCTC 60.555 52.174 0.00 0.00 0.00 2.87
390 391 3.896888 CCAGGATAGATGCTCTGTTCTCT 59.103 47.826 0.00 0.00 0.00 3.10
391 392 4.262121 CCAGGATAGATGCTCTGTTCTCTG 60.262 50.000 0.00 0.00 0.00 3.35
392 393 4.341806 CAGGATAGATGCTCTGTTCTCTGT 59.658 45.833 0.00 0.00 0.00 3.41
393 394 4.341806 AGGATAGATGCTCTGTTCTCTGTG 59.658 45.833 0.00 0.00 0.00 3.66
394 395 2.383368 AGATGCTCTGTTCTCTGTGC 57.617 50.000 0.00 0.00 34.33 4.57
395 396 0.997932 GATGCTCTGTTCTCTGTGCG 59.002 55.000 0.00 0.00 35.72 5.34
396 397 0.605083 ATGCTCTGTTCTCTGTGCGA 59.395 50.000 0.00 0.00 35.72 5.10
397 398 0.389025 TGCTCTGTTCTCTGTGCGAA 59.611 50.000 0.00 0.00 35.72 4.70
398 399 0.787183 GCTCTGTTCTCTGTGCGAAC 59.213 55.000 0.00 0.00 40.79 3.95
399 400 1.604185 GCTCTGTTCTCTGTGCGAACT 60.604 52.381 0.00 0.00 40.95 3.01
400 401 2.057316 CTCTGTTCTCTGTGCGAACTG 58.943 52.381 0.00 0.00 40.95 3.16
401 402 1.681264 TCTGTTCTCTGTGCGAACTGA 59.319 47.619 2.80 2.80 42.86 3.41
402 403 2.057316 CTGTTCTCTGTGCGAACTGAG 58.943 52.381 21.36 21.36 40.55 3.35
403 404 0.787183 GTTCTCTGTGCGAACTGAGC 59.213 55.000 22.30 8.56 38.14 4.26
404 405 0.319900 TTCTCTGTGCGAACTGAGCC 60.320 55.000 22.30 0.00 36.19 4.70
405 406 2.049156 TCTGTGCGAACTGAGCCG 60.049 61.111 0.00 0.00 0.00 5.52
406 407 2.049156 CTGTGCGAACTGAGCCGA 60.049 61.111 0.00 0.00 0.00 5.54
407 408 1.446792 CTGTGCGAACTGAGCCGAT 60.447 57.895 0.00 0.00 0.00 4.18
408 409 1.690283 CTGTGCGAACTGAGCCGATG 61.690 60.000 0.00 0.00 0.00 3.84
409 410 1.738099 GTGCGAACTGAGCCGATGT 60.738 57.895 0.00 0.00 0.00 3.06
410 411 0.457853 GTGCGAACTGAGCCGATGTA 60.458 55.000 0.00 0.00 0.00 2.29
411 412 0.179137 TGCGAACTGAGCCGATGTAG 60.179 55.000 0.00 0.00 0.00 2.74
412 413 0.100682 GCGAACTGAGCCGATGTAGA 59.899 55.000 0.00 0.00 0.00 2.59
413 414 1.862008 GCGAACTGAGCCGATGTAGAG 60.862 57.143 0.00 0.00 0.00 2.43
414 415 1.268794 CGAACTGAGCCGATGTAGAGG 60.269 57.143 0.00 0.00 0.00 3.69
421 422 3.976339 CCGATGTAGAGGCAAGGAG 57.024 57.895 0.00 0.00 0.00 3.69
422 423 0.249657 CCGATGTAGAGGCAAGGAGC 60.250 60.000 0.00 0.00 44.65 4.70
440 441 4.266070 CGAGCCGCGCTTAGCCTA 62.266 66.667 5.56 0.00 44.76 3.93
441 442 2.340443 GAGCCGCGCTTAGCCTAT 59.660 61.111 5.56 0.00 44.76 2.57
442 443 2.024319 GAGCCGCGCTTAGCCTATG 61.024 63.158 5.56 0.00 44.76 2.23
443 444 2.029073 GCCGCGCTTAGCCTATGA 59.971 61.111 5.56 0.00 44.76 2.15
444 445 2.024319 GCCGCGCTTAGCCTATGAG 61.024 63.158 5.56 0.00 44.76 2.90
445 446 1.364171 CCGCGCTTAGCCTATGAGT 59.636 57.895 5.56 0.00 44.76 3.41
446 447 0.664767 CCGCGCTTAGCCTATGAGTC 60.665 60.000 5.56 0.00 44.76 3.36
447 448 0.664767 CGCGCTTAGCCTATGAGTCC 60.665 60.000 5.56 0.00 44.76 3.85
448 449 0.664767 GCGCTTAGCCTATGAGTCCG 60.665 60.000 0.00 0.00 40.81 4.79
449 450 0.952280 CGCTTAGCCTATGAGTCCGA 59.048 55.000 0.00 0.00 0.00 4.55
450 451 1.542030 CGCTTAGCCTATGAGTCCGAT 59.458 52.381 0.00 0.00 0.00 4.18
451 452 2.747989 CGCTTAGCCTATGAGTCCGATA 59.252 50.000 0.00 0.00 0.00 2.92
452 453 3.181505 CGCTTAGCCTATGAGTCCGATAG 60.182 52.174 0.00 0.00 0.00 2.08
453 454 3.428316 GCTTAGCCTATGAGTCCGATAGC 60.428 52.174 0.00 0.00 0.00 2.97
454 455 1.169577 AGCCTATGAGTCCGATAGCG 58.830 55.000 0.00 0.00 37.24 4.26
455 456 0.456995 GCCTATGAGTCCGATAGCGC 60.457 60.000 0.00 0.00 35.83 5.92
456 457 0.179187 CCTATGAGTCCGATAGCGCG 60.179 60.000 0.00 0.00 35.83 6.86
457 458 0.517755 CTATGAGTCCGATAGCGCGT 59.482 55.000 8.43 0.00 35.83 6.01
458 459 0.237498 TATGAGTCCGATAGCGCGTG 59.763 55.000 8.43 0.00 35.83 5.34
459 460 1.444917 ATGAGTCCGATAGCGCGTGA 61.445 55.000 8.43 0.00 35.83 4.35
460 461 1.063649 GAGTCCGATAGCGCGTGAA 59.936 57.895 8.43 0.00 35.83 3.18
461 462 0.524816 GAGTCCGATAGCGCGTGAAA 60.525 55.000 8.43 0.00 35.83 2.69
462 463 0.108992 AGTCCGATAGCGCGTGAAAA 60.109 50.000 8.43 0.00 35.83 2.29
463 464 0.717224 GTCCGATAGCGCGTGAAAAA 59.283 50.000 8.43 0.00 35.83 1.94
464 465 0.717224 TCCGATAGCGCGTGAAAAAC 59.283 50.000 8.43 0.00 35.83 2.43
465 466 0.440758 CCGATAGCGCGTGAAAAACA 59.559 50.000 8.43 0.00 35.83 2.83
466 467 1.526986 CCGATAGCGCGTGAAAAACAG 60.527 52.381 8.43 0.00 35.83 3.16
467 468 1.524548 GATAGCGCGTGAAAAACAGC 58.475 50.000 8.43 0.00 33.61 4.40
468 469 0.168128 ATAGCGCGTGAAAAACAGCC 59.832 50.000 8.43 0.00 33.83 4.85
469 470 2.165362 TAGCGCGTGAAAAACAGCCG 62.165 55.000 8.43 0.00 33.83 5.52
470 471 2.629210 CGCGTGAAAAACAGCCGA 59.371 55.556 0.00 0.00 0.00 5.54
471 472 1.438710 CGCGTGAAAAACAGCCGAG 60.439 57.895 0.00 0.00 0.00 4.63
472 473 1.725973 GCGTGAAAAACAGCCGAGC 60.726 57.895 0.00 0.00 0.00 5.03
473 474 1.082104 CGTGAAAAACAGCCGAGCC 60.082 57.895 0.00 0.00 0.00 4.70
474 475 1.781025 CGTGAAAAACAGCCGAGCCA 61.781 55.000 0.00 0.00 0.00 4.75
475 476 0.598065 GTGAAAAACAGCCGAGCCAT 59.402 50.000 0.00 0.00 0.00 4.40
476 477 1.810151 GTGAAAAACAGCCGAGCCATA 59.190 47.619 0.00 0.00 0.00 2.74
477 478 1.810151 TGAAAAACAGCCGAGCCATAC 59.190 47.619 0.00 0.00 0.00 2.39
478 479 0.802494 AAAAACAGCCGAGCCATACG 59.198 50.000 0.00 0.00 0.00 3.06
479 480 1.644786 AAAACAGCCGAGCCATACGC 61.645 55.000 0.00 0.00 37.98 4.42
480 481 2.796483 AAACAGCCGAGCCATACGCA 62.796 55.000 0.00 0.00 41.38 5.24
481 482 2.280389 CAGCCGAGCCATACGCAT 60.280 61.111 0.00 0.00 41.38 4.73
482 483 2.280389 AGCCGAGCCATACGCATG 60.280 61.111 0.00 0.00 41.38 4.06
483 484 4.017877 GCCGAGCCATACGCATGC 62.018 66.667 7.91 7.91 41.38 4.06
484 485 3.705638 CCGAGCCATACGCATGCG 61.706 66.667 36.79 36.79 46.03 4.73
499 500 4.527157 GCGTGCAGCGATTGGAGC 62.527 66.667 11.94 0.00 44.77 4.70
500 501 3.869272 CGTGCAGCGATTGGAGCC 61.869 66.667 3.04 0.00 44.77 4.70
501 502 2.437359 GTGCAGCGATTGGAGCCT 60.437 61.111 0.00 0.00 34.64 4.58
502 503 1.153369 GTGCAGCGATTGGAGCCTA 60.153 57.895 0.00 0.00 34.64 3.93
503 504 0.533755 GTGCAGCGATTGGAGCCTAT 60.534 55.000 0.00 0.00 34.64 2.57
504 505 0.250038 TGCAGCGATTGGAGCCTATC 60.250 55.000 1.51 1.51 34.64 2.08
507 508 4.268687 CGATTGGAGCCTATCGCC 57.731 61.111 17.58 0.00 42.35 5.54
508 509 1.668294 CGATTGGAGCCTATCGCCT 59.332 57.895 17.58 0.00 42.35 5.52
509 510 0.668706 CGATTGGAGCCTATCGCCTG 60.669 60.000 17.58 0.00 42.35 4.85
510 511 0.321122 GATTGGAGCCTATCGCCTGG 60.321 60.000 0.00 0.00 38.78 4.45
511 512 1.772819 ATTGGAGCCTATCGCCTGGG 61.773 60.000 0.00 0.00 38.78 4.45
512 513 3.631046 GGAGCCTATCGCCTGGGG 61.631 72.222 4.03 4.03 38.78 4.96
513 514 4.321966 GAGCCTATCGCCTGGGGC 62.322 72.222 5.77 4.26 46.75 5.80
523 524 4.102113 CCTGGGGCAAAAGTGAGG 57.898 61.111 0.00 0.00 0.00 3.86
524 525 1.460255 CCTGGGGCAAAAGTGAGGA 59.540 57.895 0.00 0.00 0.00 3.71
525 526 0.610232 CCTGGGGCAAAAGTGAGGAG 60.610 60.000 0.00 0.00 0.00 3.69
526 527 0.610232 CTGGGGCAAAAGTGAGGAGG 60.610 60.000 0.00 0.00 0.00 4.30
527 528 1.979155 GGGGCAAAAGTGAGGAGGC 60.979 63.158 0.00 0.00 0.00 4.70
528 529 1.979155 GGGCAAAAGTGAGGAGGCC 60.979 63.158 0.00 0.00 40.63 5.19
529 530 2.335712 GGCAAAAGTGAGGAGGCCG 61.336 63.158 0.00 0.00 0.00 6.13
530 531 1.600916 GCAAAAGTGAGGAGGCCGT 60.601 57.895 0.00 0.00 0.00 5.68
531 532 1.856265 GCAAAAGTGAGGAGGCCGTG 61.856 60.000 0.00 0.00 0.00 4.94
532 533 1.600916 AAAAGTGAGGAGGCCGTGC 60.601 57.895 0.00 0.00 0.00 5.34
533 534 3.883744 AAAGTGAGGAGGCCGTGCG 62.884 63.158 0.00 0.00 0.00 5.34
535 536 4.148825 GTGAGGAGGCCGTGCGAT 62.149 66.667 0.00 0.00 0.00 4.58
536 537 4.147449 TGAGGAGGCCGTGCGATG 62.147 66.667 0.00 0.00 0.00 3.84
537 538 4.148825 GAGGAGGCCGTGCGATGT 62.149 66.667 0.00 0.00 0.00 3.06
538 539 4.148825 AGGAGGCCGTGCGATGTC 62.149 66.667 0.00 0.00 0.00 3.06
540 541 4.451150 GAGGCCGTGCGATGTCCA 62.451 66.667 0.00 0.00 0.00 4.02
541 542 4.457496 AGGCCGTGCGATGTCCAG 62.457 66.667 0.00 0.00 0.00 3.86
545 546 4.758251 CGTGCGATGTCCAGCCCA 62.758 66.667 0.00 0.00 0.00 5.36
546 547 2.821366 GTGCGATGTCCAGCCCAG 60.821 66.667 0.00 0.00 0.00 4.45
547 548 3.002583 TGCGATGTCCAGCCCAGA 61.003 61.111 0.00 0.00 0.00 3.86
548 549 2.369633 TGCGATGTCCAGCCCAGAT 61.370 57.895 0.00 0.00 0.00 2.90
549 550 1.890979 GCGATGTCCAGCCCAGATG 60.891 63.158 0.00 0.00 0.00 2.90
550 551 1.825341 CGATGTCCAGCCCAGATGA 59.175 57.895 0.00 0.00 0.00 2.92
551 552 0.531532 CGATGTCCAGCCCAGATGAC 60.532 60.000 0.00 0.00 0.00 3.06
552 553 0.531532 GATGTCCAGCCCAGATGACG 60.532 60.000 0.00 0.00 0.00 4.35
553 554 1.267574 ATGTCCAGCCCAGATGACGT 61.268 55.000 0.00 0.00 0.00 4.34
554 555 1.153549 GTCCAGCCCAGATGACGTC 60.154 63.158 9.11 9.11 0.00 4.34
555 556 2.187946 CCAGCCCAGATGACGTCC 59.812 66.667 14.12 0.00 0.00 4.79
556 557 2.202797 CAGCCCAGATGACGTCCG 60.203 66.667 14.12 0.00 0.00 4.79
557 558 3.461773 AGCCCAGATGACGTCCGG 61.462 66.667 14.12 8.20 0.00 5.14
558 559 4.530857 GCCCAGATGACGTCCGGG 62.531 72.222 19.72 19.72 46.01 5.73
559 560 3.075005 CCCAGATGACGTCCGGGT 61.075 66.667 14.12 0.00 39.41 5.28
560 561 2.656069 CCCAGATGACGTCCGGGTT 61.656 63.158 14.12 0.00 39.41 4.11
561 562 1.447838 CCAGATGACGTCCGGGTTG 60.448 63.158 14.12 4.53 0.00 3.77
562 563 2.100631 CAGATGACGTCCGGGTTGC 61.101 63.158 14.12 0.00 0.00 4.17
563 564 2.047655 GATGACGTCCGGGTTGCA 60.048 61.111 14.12 0.00 0.00 4.08
564 565 1.669760 GATGACGTCCGGGTTGCAA 60.670 57.895 14.12 0.00 0.00 4.08
565 566 1.228003 ATGACGTCCGGGTTGCAAA 60.228 52.632 14.12 0.00 0.00 3.68
566 567 1.234615 ATGACGTCCGGGTTGCAAAG 61.235 55.000 14.12 0.00 0.00 2.77
567 568 2.593436 ACGTCCGGGTTGCAAAGG 60.593 61.111 0.00 5.56 0.00 3.11
568 569 2.281208 CGTCCGGGTTGCAAAGGA 60.281 61.111 13.56 13.56 0.00 3.36
569 570 2.325082 CGTCCGGGTTGCAAAGGAG 61.325 63.158 16.83 9.53 32.82 3.69
570 571 1.072505 GTCCGGGTTGCAAAGGAGA 59.927 57.895 16.83 3.59 32.82 3.71
571 572 0.536460 GTCCGGGTTGCAAAGGAGAA 60.536 55.000 16.83 0.00 32.82 2.87
572 573 0.250727 TCCGGGTTGCAAAGGAGAAG 60.251 55.000 13.56 0.00 0.00 2.85
573 574 1.244019 CCGGGTTGCAAAGGAGAAGG 61.244 60.000 0.00 0.00 0.00 3.46
574 575 0.537371 CGGGTTGCAAAGGAGAAGGT 60.537 55.000 0.00 0.00 0.00 3.50
575 576 1.704641 GGGTTGCAAAGGAGAAGGTT 58.295 50.000 0.00 0.00 0.00 3.50
576 577 2.039418 GGGTTGCAAAGGAGAAGGTTT 58.961 47.619 0.00 0.00 0.00 3.27
577 578 2.224042 GGGTTGCAAAGGAGAAGGTTTG 60.224 50.000 0.00 0.00 36.84 2.93
589 590 4.880899 GGTTTGCAACCGGTATGC 57.119 55.556 25.46 25.46 42.62 3.14
795 804 1.373121 GAGCTATAAGACGGCGGCC 60.373 63.158 10.28 9.54 0.00 6.13
1119 1136 1.353103 CATTGATCCGCCTTCACGC 59.647 57.895 0.00 0.00 0.00 5.34
1142 1160 1.135546 CGTGCGCATTGGGTTGATTTA 60.136 47.619 15.91 0.00 0.00 1.40
1353 1371 1.184970 TGGAGATCGCCGCCATCATA 61.185 55.000 11.16 0.00 39.94 2.15
1713 1734 1.682684 GCAGGAGGTCTTCTCGGGA 60.683 63.158 0.00 0.00 43.34 5.14
1722 1743 0.613853 TCTTCTCGGGATCCACGGTT 60.614 55.000 15.23 0.00 0.00 4.44
2172 2302 2.583441 CGAGGTGTGCTCCAAGGGA 61.583 63.158 0.00 0.00 0.00 4.20
2422 2558 1.479730 TCATCGAGCTCTGCAAGATGT 59.520 47.619 20.87 0.00 45.62 3.06
3537 4093 2.890371 GTGTACGCCGACTGGGAT 59.110 61.111 0.00 0.00 38.47 3.85
3909 4511 3.074999 GCTCCGACCTCCTCAGCAG 62.075 68.421 0.00 0.00 0.00 4.24
3912 4514 2.125753 CGACCTCCTCAGCAGCAC 60.126 66.667 0.00 0.00 0.00 4.40
3913 4515 2.267324 GACCTCCTCAGCAGCACC 59.733 66.667 0.00 0.00 0.00 5.01
4030 4632 0.543277 TCAAGCAGAAGGGCATCGAT 59.457 50.000 0.00 0.00 35.83 3.59
4213 4901 3.218453 TCTCTCTACTGCTGCATAGGTC 58.782 50.000 1.31 0.00 0.00 3.85
4236 4924 5.655974 TCTTCTTGTGCTCTCTATCTGACAT 59.344 40.000 0.00 0.00 0.00 3.06
4323 5881 2.339418 CTCTTGCTTCTCTCACTGCTG 58.661 52.381 0.00 0.00 0.00 4.41
4353 5912 7.813627 CCTCCCTAAACTAATATAAGAGCGTTC 59.186 40.741 0.00 0.00 0.00 3.95
4446 6030 2.790433 TGCACCTCCTACATCCAAAAC 58.210 47.619 0.00 0.00 0.00 2.43
4553 6138 5.924254 TCACATCTACCTACACAAAAACTCG 59.076 40.000 0.00 0.00 0.00 4.18
4565 6151 5.008316 ACACAAAAACTCGTAAACCTCATCC 59.992 40.000 0.00 0.00 0.00 3.51
4597 6183 5.236911 GGTTTACAGAAACACGATGGTACAA 59.763 40.000 0.00 0.00 44.64 2.41
4757 6821 5.683302 CACGACATCCATAGCGATATATGTC 59.317 44.000 19.63 19.63 39.71 3.06
4860 6924 2.679837 CAATTGCACTGAAGGTATCGCT 59.320 45.455 0.00 0.00 0.00 4.93
4893 6958 3.634910 GGTCTCTCCAACTCTCTGATACC 59.365 52.174 0.00 0.00 35.97 2.73
4898 6963 4.339530 TCTCCAACTCTCTGATACCAATCG 59.660 45.833 0.00 0.00 34.60 3.34
4905 6970 5.179742 ACTCTCTGATACCAATCGTACGATC 59.820 44.000 29.51 17.80 34.60 3.69
4925 6990 4.135747 TCGCATGGTAGAATGAATCACA 57.864 40.909 0.00 0.00 0.00 3.58
4926 6991 4.122046 TCGCATGGTAGAATGAATCACAG 58.878 43.478 0.00 0.00 0.00 3.66
4927 6992 3.303593 CGCATGGTAGAATGAATCACAGC 60.304 47.826 0.00 0.00 0.00 4.40
4930 6995 4.284829 TGGTAGAATGAATCACAGCACA 57.715 40.909 0.00 0.00 0.00 4.57
4980 7045 2.290514 CCAGCAGGTGAATTCAGAAGGA 60.291 50.000 8.80 0.00 0.00 3.36
5049 7114 4.252073 CAGCTAATCCATGATACAGGAGC 58.748 47.826 0.00 0.00 37.34 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 1.153469 CGGCCAGCTCTTCTCCTTC 60.153 63.158 2.24 0.00 0.00 3.46
131 132 2.664081 CCGGCCAGCTCTTCTCCTT 61.664 63.158 2.24 0.00 0.00 3.36
132 133 3.080121 CCGGCCAGCTCTTCTCCT 61.080 66.667 2.24 0.00 0.00 3.69
133 134 4.168291 CCCGGCCAGCTCTTCTCC 62.168 72.222 2.24 0.00 0.00 3.71
134 135 4.168291 CCCCGGCCAGCTCTTCTC 62.168 72.222 2.24 0.00 0.00 2.87
135 136 4.722535 TCCCCGGCCAGCTCTTCT 62.723 66.667 2.24 0.00 0.00 2.85
136 137 2.558380 ATTTCCCCGGCCAGCTCTTC 62.558 60.000 2.24 0.00 0.00 2.87
137 138 2.155197 AATTTCCCCGGCCAGCTCTT 62.155 55.000 2.24 0.00 0.00 2.85
138 139 1.279025 TAATTTCCCCGGCCAGCTCT 61.279 55.000 2.24 0.00 0.00 4.09
139 140 1.101635 GTAATTTCCCCGGCCAGCTC 61.102 60.000 2.24 0.00 0.00 4.09
140 141 1.076995 GTAATTTCCCCGGCCAGCT 60.077 57.895 2.24 0.00 0.00 4.24
141 142 2.125326 GGTAATTTCCCCGGCCAGC 61.125 63.158 2.24 0.00 0.00 4.85
142 143 0.465642 GAGGTAATTTCCCCGGCCAG 60.466 60.000 2.24 0.00 0.00 4.85
143 144 0.917333 AGAGGTAATTTCCCCGGCCA 60.917 55.000 2.24 0.00 0.00 5.36
144 145 0.257905 AAGAGGTAATTTCCCCGGCC 59.742 55.000 0.00 0.00 0.00 6.13
145 146 1.389555 CAAGAGGTAATTTCCCCGGC 58.610 55.000 0.00 0.00 0.00 6.13
146 147 1.389555 GCAAGAGGTAATTTCCCCGG 58.610 55.000 0.00 0.00 0.00 5.73
147 148 1.389555 GGCAAGAGGTAATTTCCCCG 58.610 55.000 0.00 0.00 0.00 5.73
148 149 1.064979 TCGGCAAGAGGTAATTTCCCC 60.065 52.381 0.00 0.00 0.00 4.81
149 150 2.014857 GTCGGCAAGAGGTAATTTCCC 58.985 52.381 0.00 0.00 0.00 3.97
150 151 1.664151 CGTCGGCAAGAGGTAATTTCC 59.336 52.381 0.00 0.00 0.00 3.13
151 152 1.062148 GCGTCGGCAAGAGGTAATTTC 59.938 52.381 0.00 0.00 39.62 2.17
152 153 1.084289 GCGTCGGCAAGAGGTAATTT 58.916 50.000 0.00 0.00 39.62 1.82
153 154 1.082117 CGCGTCGGCAAGAGGTAATT 61.082 55.000 0.00 0.00 39.92 1.40
154 155 1.518572 CGCGTCGGCAAGAGGTAAT 60.519 57.895 0.00 0.00 39.92 1.89
155 156 2.126228 CGCGTCGGCAAGAGGTAA 60.126 61.111 0.00 0.00 39.92 2.85
156 157 3.047718 CTCGCGTCGGCAAGAGGTA 62.048 63.158 5.77 0.00 39.92 3.08
157 158 4.421479 CTCGCGTCGGCAAGAGGT 62.421 66.667 5.77 0.00 39.92 3.85
158 159 3.916392 AACTCGCGTCGGCAAGAGG 62.916 63.158 5.77 0.00 39.92 3.69
159 160 2.022129 AAACTCGCGTCGGCAAGAG 61.022 57.895 5.77 7.13 39.92 2.85
160 161 2.028484 AAACTCGCGTCGGCAAGA 59.972 55.556 5.77 0.00 39.92 3.02
161 162 2.170985 CAAACTCGCGTCGGCAAG 59.829 61.111 5.77 0.00 39.92 4.01
162 163 2.586635 ACAAACTCGCGTCGGCAA 60.587 55.556 5.77 0.00 39.92 4.52
163 164 3.334751 CACAAACTCGCGTCGGCA 61.335 61.111 5.77 0.00 39.92 5.69
164 165 4.719616 GCACAAACTCGCGTCGGC 62.720 66.667 5.77 0.00 0.00 5.54
165 166 4.072088 GGCACAAACTCGCGTCGG 62.072 66.667 5.77 0.00 0.00 4.79
166 167 3.334751 TGGCACAAACTCGCGTCG 61.335 61.111 5.77 0.58 31.92 5.12
192 193 2.125552 TGGAGTCGCATCCGCAAG 60.126 61.111 1.89 0.00 42.77 4.01
193 194 2.125552 CTGGAGTCGCATCCGCAA 60.126 61.111 1.89 0.00 42.77 4.85
194 195 4.147449 CCTGGAGTCGCATCCGCA 62.147 66.667 0.00 0.00 42.77 5.69
195 196 4.899239 CCCTGGAGTCGCATCCGC 62.899 72.222 0.00 0.00 42.77 5.54
196 197 3.147595 TCCCTGGAGTCGCATCCG 61.148 66.667 0.00 0.00 42.77 4.18
197 198 2.501610 GTCCCTGGAGTCGCATCC 59.498 66.667 0.00 0.00 40.03 3.51
198 199 2.501610 GGTCCCTGGAGTCGCATC 59.498 66.667 0.00 0.00 0.00 3.91
199 200 3.461773 CGGTCCCTGGAGTCGCAT 61.462 66.667 0.00 0.00 0.00 4.73
335 336 4.444024 CACAATGTCGTGCCGCCG 62.444 66.667 0.00 0.00 0.00 6.46
341 342 0.667993 ACCCTTTGCACAATGTCGTG 59.332 50.000 0.00 0.00 40.00 4.35
342 343 0.951558 GACCCTTTGCACAATGTCGT 59.048 50.000 0.00 0.00 0.00 4.34
343 344 1.069022 CAGACCCTTTGCACAATGTCG 60.069 52.381 0.00 0.00 0.00 4.35
344 345 1.270550 CCAGACCCTTTGCACAATGTC 59.729 52.381 0.00 0.00 0.00 3.06
345 346 1.331214 CCAGACCCTTTGCACAATGT 58.669 50.000 0.00 0.00 0.00 2.71
346 347 0.604578 CCCAGACCCTTTGCACAATG 59.395 55.000 0.00 0.00 0.00 2.82
347 348 0.482446 TCCCAGACCCTTTGCACAAT 59.518 50.000 0.00 0.00 0.00 2.71
348 349 0.178992 CTCCCAGACCCTTTGCACAA 60.179 55.000 0.00 0.00 0.00 3.33
349 350 1.455849 CTCCCAGACCCTTTGCACA 59.544 57.895 0.00 0.00 0.00 4.57
350 351 1.973812 GCTCCCAGACCCTTTGCAC 60.974 63.158 0.00 0.00 0.00 4.57
351 352 2.436109 GCTCCCAGACCCTTTGCA 59.564 61.111 0.00 0.00 0.00 4.08
352 353 2.361737 GGCTCCCAGACCCTTTGC 60.362 66.667 0.00 0.00 0.00 3.68
353 354 3.170362 TGGCTCCCAGACCCTTTG 58.830 61.111 0.00 0.00 0.00 2.77
362 363 0.104777 AGCATCTATCCTGGCTCCCA 60.105 55.000 0.00 0.00 28.71 4.37
363 364 0.612744 GAGCATCTATCCTGGCTCCC 59.387 60.000 0.00 0.00 45.31 4.30
376 377 0.997932 CGCACAGAGAACAGAGCATC 59.002 55.000 0.00 0.00 0.00 3.91
377 378 0.605083 TCGCACAGAGAACAGAGCAT 59.395 50.000 0.00 0.00 0.00 3.79
378 379 0.389025 TTCGCACAGAGAACAGAGCA 59.611 50.000 0.00 0.00 0.00 4.26
379 380 0.787183 GTTCGCACAGAGAACAGAGC 59.213 55.000 8.43 0.00 45.21 4.09
384 385 0.787183 GCTCAGTTCGCACAGAGAAC 59.213 55.000 11.55 5.64 45.97 3.01
385 386 0.319900 GGCTCAGTTCGCACAGAGAA 60.320 55.000 11.55 0.00 38.54 2.87
386 387 1.290324 GGCTCAGTTCGCACAGAGA 59.710 57.895 11.55 0.00 38.54 3.10
387 388 2.091112 CGGCTCAGTTCGCACAGAG 61.091 63.158 3.30 3.30 39.12 3.35
388 389 1.877576 ATCGGCTCAGTTCGCACAGA 61.878 55.000 0.00 0.00 0.00 3.41
389 390 1.446792 ATCGGCTCAGTTCGCACAG 60.447 57.895 0.00 0.00 0.00 3.66
390 391 1.737735 CATCGGCTCAGTTCGCACA 60.738 57.895 0.00 0.00 0.00 4.57
391 392 0.457853 TACATCGGCTCAGTTCGCAC 60.458 55.000 0.00 0.00 0.00 5.34
392 393 0.179137 CTACATCGGCTCAGTTCGCA 60.179 55.000 0.00 0.00 0.00 5.10
393 394 0.100682 TCTACATCGGCTCAGTTCGC 59.899 55.000 0.00 0.00 0.00 4.70
394 395 1.268794 CCTCTACATCGGCTCAGTTCG 60.269 57.143 0.00 0.00 0.00 3.95
395 396 1.537135 GCCTCTACATCGGCTCAGTTC 60.537 57.143 0.00 0.00 42.98 3.01
396 397 0.461961 GCCTCTACATCGGCTCAGTT 59.538 55.000 0.00 0.00 42.98 3.16
397 398 0.684479 TGCCTCTACATCGGCTCAGT 60.684 55.000 0.00 0.00 46.42 3.41
398 399 0.461548 TTGCCTCTACATCGGCTCAG 59.538 55.000 0.00 0.00 46.42 3.35
399 400 0.461548 CTTGCCTCTACATCGGCTCA 59.538 55.000 0.00 0.00 46.42 4.26
400 401 0.249657 CCTTGCCTCTACATCGGCTC 60.250 60.000 0.00 0.00 46.42 4.70
401 402 0.687757 TCCTTGCCTCTACATCGGCT 60.688 55.000 0.00 0.00 46.42 5.52
402 403 0.249657 CTCCTTGCCTCTACATCGGC 60.250 60.000 0.00 0.00 46.46 5.54
403 404 0.249657 GCTCCTTGCCTCTACATCGG 60.250 60.000 0.00 0.00 35.15 4.18
404 405 3.280920 GCTCCTTGCCTCTACATCG 57.719 57.895 0.00 0.00 35.15 3.84
423 424 3.559657 ATAGGCTAAGCGCGGCTCG 62.560 63.158 12.88 0.00 38.25 5.03
424 425 2.024319 CATAGGCTAAGCGCGGCTC 61.024 63.158 12.88 7.92 38.25 4.70
425 426 2.029666 CATAGGCTAAGCGCGGCT 59.970 61.111 8.83 16.50 42.56 5.52
426 427 2.024319 CTCATAGGCTAAGCGCGGC 61.024 63.158 8.83 8.21 40.44 6.53
427 428 0.664767 GACTCATAGGCTAAGCGCGG 60.665 60.000 8.83 0.00 40.44 6.46
428 429 0.664767 GGACTCATAGGCTAAGCGCG 60.665 60.000 0.00 0.00 40.44 6.86
429 430 0.664767 CGGACTCATAGGCTAAGCGC 60.665 60.000 0.00 0.00 38.13 5.92
430 431 0.952280 TCGGACTCATAGGCTAAGCG 59.048 55.000 0.00 0.00 0.00 4.68
431 432 3.428316 GCTATCGGACTCATAGGCTAAGC 60.428 52.174 0.00 0.00 0.00 3.09
432 433 3.181505 CGCTATCGGACTCATAGGCTAAG 60.182 52.174 0.00 0.00 0.00 2.18
433 434 2.747989 CGCTATCGGACTCATAGGCTAA 59.252 50.000 0.00 0.00 0.00 3.09
434 435 2.357075 CGCTATCGGACTCATAGGCTA 58.643 52.381 0.00 0.00 0.00 3.93
435 436 1.169577 CGCTATCGGACTCATAGGCT 58.830 55.000 0.00 0.00 0.00 4.58
436 437 0.456995 GCGCTATCGGACTCATAGGC 60.457 60.000 0.00 0.00 35.95 3.93
437 438 0.179187 CGCGCTATCGGACTCATAGG 60.179 60.000 5.56 0.00 35.95 2.57
438 439 0.517755 ACGCGCTATCGGACTCATAG 59.482 55.000 5.73 0.00 35.95 2.23
439 440 0.237498 CACGCGCTATCGGACTCATA 59.763 55.000 5.73 0.00 35.95 2.15
440 441 1.008424 CACGCGCTATCGGACTCAT 60.008 57.895 5.73 0.00 35.95 2.90
441 442 1.650314 TTCACGCGCTATCGGACTCA 61.650 55.000 5.73 0.00 35.95 3.41
442 443 0.524816 TTTCACGCGCTATCGGACTC 60.525 55.000 5.73 0.00 35.95 3.36
443 444 0.108992 TTTTCACGCGCTATCGGACT 60.109 50.000 5.73 0.00 35.95 3.85
444 445 0.717224 TTTTTCACGCGCTATCGGAC 59.283 50.000 5.73 0.00 35.95 4.79
445 446 0.717224 GTTTTTCACGCGCTATCGGA 59.283 50.000 5.73 0.00 35.95 4.55
446 447 0.440758 TGTTTTTCACGCGCTATCGG 59.559 50.000 5.73 0.00 35.95 4.18
447 448 1.785881 CTGTTTTTCACGCGCTATCG 58.214 50.000 5.73 0.00 39.07 2.92
448 449 1.524548 GCTGTTTTTCACGCGCTATC 58.475 50.000 5.73 0.00 0.00 2.08
449 450 0.168128 GGCTGTTTTTCACGCGCTAT 59.832 50.000 5.73 0.00 0.00 2.97
450 451 1.572447 GGCTGTTTTTCACGCGCTA 59.428 52.632 5.73 0.00 0.00 4.26
451 452 2.331451 GGCTGTTTTTCACGCGCT 59.669 55.556 5.73 0.00 0.00 5.92
452 453 3.091022 CGGCTGTTTTTCACGCGC 61.091 61.111 5.73 0.00 0.00 6.86
453 454 1.438710 CTCGGCTGTTTTTCACGCG 60.439 57.895 3.53 3.53 0.00 6.01
454 455 1.725973 GCTCGGCTGTTTTTCACGC 60.726 57.895 0.00 0.00 0.00 5.34
455 456 1.082104 GGCTCGGCTGTTTTTCACG 60.082 57.895 0.00 0.00 0.00 4.35
456 457 0.598065 ATGGCTCGGCTGTTTTTCAC 59.402 50.000 0.00 0.00 0.00 3.18
457 458 1.810151 GTATGGCTCGGCTGTTTTTCA 59.190 47.619 0.00 0.00 0.00 2.69
458 459 1.202031 CGTATGGCTCGGCTGTTTTTC 60.202 52.381 0.00 0.00 0.00 2.29
459 460 0.802494 CGTATGGCTCGGCTGTTTTT 59.198 50.000 0.00 0.00 0.00 1.94
460 461 1.644786 GCGTATGGCTCGGCTGTTTT 61.645 55.000 0.00 0.00 39.11 2.43
461 462 2.106683 GCGTATGGCTCGGCTGTTT 61.107 57.895 0.00 0.00 39.11 2.83
462 463 2.511600 GCGTATGGCTCGGCTGTT 60.512 61.111 0.00 0.00 39.11 3.16
463 464 3.094062 ATGCGTATGGCTCGGCTGT 62.094 57.895 0.00 0.00 44.05 4.40
464 465 2.280389 ATGCGTATGGCTCGGCTG 60.280 61.111 0.00 0.00 44.05 4.85
465 466 2.280389 CATGCGTATGGCTCGGCT 60.280 61.111 5.47 0.00 44.05 5.52
466 467 4.017877 GCATGCGTATGGCTCGGC 62.018 66.667 15.54 0.00 44.05 5.54
467 468 3.705638 CGCATGCGTATGGCTCGG 61.706 66.667 31.33 0.00 44.05 4.63
479 480 2.277692 CCAATCGCTGCACGCATG 60.278 61.111 0.00 0.00 43.23 4.06
480 481 2.436469 TCCAATCGCTGCACGCAT 60.436 55.556 0.00 0.17 43.23 4.73
481 482 3.120385 CTCCAATCGCTGCACGCA 61.120 61.111 0.00 0.00 43.23 5.24
482 483 4.527157 GCTCCAATCGCTGCACGC 62.527 66.667 0.00 1.51 43.23 5.34
483 484 2.906182 TAGGCTCCAATCGCTGCACG 62.906 60.000 0.00 2.79 45.62 5.34
484 485 0.533755 ATAGGCTCCAATCGCTGCAC 60.534 55.000 0.00 0.00 0.00 4.57
485 486 0.250038 GATAGGCTCCAATCGCTGCA 60.250 55.000 0.00 0.00 0.00 4.41
486 487 1.287730 CGATAGGCTCCAATCGCTGC 61.288 60.000 5.32 0.00 38.61 5.25
487 488 2.819667 CGATAGGCTCCAATCGCTG 58.180 57.895 5.32 0.00 38.61 5.18
506 507 0.610232 CTCCTCACTTTTGCCCCAGG 60.610 60.000 0.00 0.00 0.00 4.45
507 508 0.610232 CCTCCTCACTTTTGCCCCAG 60.610 60.000 0.00 0.00 0.00 4.45
508 509 1.460255 CCTCCTCACTTTTGCCCCA 59.540 57.895 0.00 0.00 0.00 4.96
509 510 1.979155 GCCTCCTCACTTTTGCCCC 60.979 63.158 0.00 0.00 0.00 5.80
510 511 1.979155 GGCCTCCTCACTTTTGCCC 60.979 63.158 0.00 0.00 32.74 5.36
511 512 2.335712 CGGCCTCCTCACTTTTGCC 61.336 63.158 0.00 0.00 35.55 4.52
512 513 1.600916 ACGGCCTCCTCACTTTTGC 60.601 57.895 0.00 0.00 0.00 3.68
513 514 1.856265 GCACGGCCTCCTCACTTTTG 61.856 60.000 0.00 0.00 0.00 2.44
514 515 1.600916 GCACGGCCTCCTCACTTTT 60.601 57.895 0.00 0.00 0.00 2.27
515 516 2.032681 GCACGGCCTCCTCACTTT 59.967 61.111 0.00 0.00 0.00 2.66
516 517 4.379243 CGCACGGCCTCCTCACTT 62.379 66.667 0.00 0.00 0.00 3.16
518 519 4.148825 ATCGCACGGCCTCCTCAC 62.149 66.667 0.00 0.00 0.00 3.51
519 520 4.147449 CATCGCACGGCCTCCTCA 62.147 66.667 0.00 0.00 0.00 3.86
520 521 4.148825 ACATCGCACGGCCTCCTC 62.149 66.667 0.00 0.00 0.00 3.71
521 522 4.148825 GACATCGCACGGCCTCCT 62.149 66.667 0.00 0.00 0.00 3.69
523 524 4.451150 TGGACATCGCACGGCCTC 62.451 66.667 0.00 0.00 0.00 4.70
524 525 4.457496 CTGGACATCGCACGGCCT 62.457 66.667 0.00 0.00 0.00 5.19
528 529 4.758251 TGGGCTGGACATCGCACG 62.758 66.667 0.00 0.00 30.50 5.34
529 530 2.599645 ATCTGGGCTGGACATCGCAC 62.600 60.000 0.00 0.00 0.00 5.34
530 531 2.369633 ATCTGGGCTGGACATCGCA 61.370 57.895 0.00 0.00 0.00 5.10
531 532 1.890979 CATCTGGGCTGGACATCGC 60.891 63.158 0.00 0.00 0.00 4.58
532 533 0.531532 GTCATCTGGGCTGGACATCG 60.532 60.000 0.00 0.00 0.00 3.84
533 534 0.531532 CGTCATCTGGGCTGGACATC 60.532 60.000 0.00 0.00 0.00 3.06
534 535 1.267574 ACGTCATCTGGGCTGGACAT 61.268 55.000 0.00 0.00 0.00 3.06
535 536 1.888436 GACGTCATCTGGGCTGGACA 61.888 60.000 11.55 0.00 0.00 4.02
536 537 1.153549 GACGTCATCTGGGCTGGAC 60.154 63.158 11.55 0.00 0.00 4.02
537 538 2.359169 GGACGTCATCTGGGCTGGA 61.359 63.158 18.91 0.00 0.00 3.86
538 539 2.187946 GGACGTCATCTGGGCTGG 59.812 66.667 18.91 0.00 0.00 4.85
539 540 2.202797 CGGACGTCATCTGGGCTG 60.203 66.667 18.91 0.00 0.00 4.85
544 545 2.100631 GCAACCCGGACGTCATCTG 61.101 63.158 18.91 7.83 0.00 2.90
545 546 2.107041 TTGCAACCCGGACGTCATCT 62.107 55.000 18.91 0.00 0.00 2.90
546 547 1.231958 TTTGCAACCCGGACGTCATC 61.232 55.000 18.91 0.00 0.00 2.92
547 548 1.228003 TTTGCAACCCGGACGTCAT 60.228 52.632 18.91 0.00 0.00 3.06
548 549 1.890041 CTTTGCAACCCGGACGTCA 60.890 57.895 18.91 0.00 0.00 4.35
549 550 2.613506 CCTTTGCAACCCGGACGTC 61.614 63.158 7.13 7.13 0.00 4.34
550 551 2.593436 CCTTTGCAACCCGGACGT 60.593 61.111 0.73 0.00 0.00 4.34
551 552 2.281208 TCCTTTGCAACCCGGACG 60.281 61.111 0.73 0.00 0.00 4.79
552 553 0.536460 TTCTCCTTTGCAACCCGGAC 60.536 55.000 0.73 0.00 0.00 4.79
553 554 0.250727 CTTCTCCTTTGCAACCCGGA 60.251 55.000 0.73 4.84 0.00 5.14
554 555 1.244019 CCTTCTCCTTTGCAACCCGG 61.244 60.000 0.00 0.00 0.00 5.73
555 556 0.537371 ACCTTCTCCTTTGCAACCCG 60.537 55.000 0.00 0.00 0.00 5.28
556 557 1.704641 AACCTTCTCCTTTGCAACCC 58.295 50.000 0.00 0.00 0.00 4.11
557 558 3.097877 CAAACCTTCTCCTTTGCAACC 57.902 47.619 0.00 0.00 0.00 3.77
577 578 1.373590 ATTCCGTGCATACCGGTTGC 61.374 55.000 25.46 25.46 45.63 4.17
578 579 1.091537 AATTCCGTGCATACCGGTTG 58.908 50.000 15.04 12.49 45.63 3.77
579 580 1.828979 AAATTCCGTGCATACCGGTT 58.171 45.000 15.04 0.00 45.63 4.44
580 581 1.828979 AAAATTCCGTGCATACCGGT 58.171 45.000 13.98 13.98 45.63 5.28
581 582 2.931512 AAAAATTCCGTGCATACCGG 57.068 45.000 7.88 7.88 46.83 5.28
598 599 2.328639 GCGTTCGGCGTGGAAAAA 59.671 55.556 6.85 0.00 43.66 1.94
599 600 3.652000 GGCGTTCGGCGTGGAAAA 61.652 61.111 6.85 0.00 44.92 2.29
1086 1103 3.266510 TCAATGGAGGAACGGAATGAG 57.733 47.619 0.00 0.00 0.00 2.90
1089 1106 2.485479 CGGATCAATGGAGGAACGGAAT 60.485 50.000 0.00 0.00 0.00 3.01
1092 1109 1.160329 GCGGATCAATGGAGGAACGG 61.160 60.000 0.00 0.00 0.00 4.44
1094 1111 0.181350 AGGCGGATCAATGGAGGAAC 59.819 55.000 0.00 0.00 0.00 3.62
1119 1136 3.055719 AACCCAATGCGCACGAGG 61.056 61.111 14.90 16.48 0.00 4.63
1126 1144 4.492247 CGCAAATTAAATCAACCCAATGCG 60.492 41.667 0.00 0.00 45.22 4.73
1134 1152 7.290118 ACTGCAAAATCGCAAATTAAATCAAC 58.710 30.769 0.00 0.00 42.45 3.18
1142 1160 2.979813 GTCGACTGCAAAATCGCAAATT 59.020 40.909 8.70 0.00 42.45 1.82
1713 1734 1.077716 GCCCTGCTTAACCGTGGAT 60.078 57.895 0.00 0.00 0.00 3.41
1722 1743 2.754254 TCGAGCTCGCCCTGCTTA 60.754 61.111 30.97 8.61 41.30 3.09
2040 2170 2.044650 ATGCGCTTGGTGATGGCT 60.045 55.556 9.73 0.00 0.00 4.75
2172 2302 0.320771 GCACCATGTCCTTGTCGACT 60.321 55.000 17.92 0.00 33.70 4.18
3078 3226 0.529773 GCATGAACCCGAGCACGATA 60.530 55.000 4.70 0.00 42.66 2.92
3537 4093 1.198094 TCCCCTCCATGTCGCAGAAA 61.198 55.000 0.00 0.00 39.69 2.52
3709 4293 4.912485 TGGCGACGGCGAAACCAA 62.912 61.111 18.90 0.00 41.24 3.67
3712 4296 2.202298 CAATGGCGACGGCGAAAC 60.202 61.111 18.90 3.59 41.24 2.78
3713 4297 2.255172 AACAATGGCGACGGCGAAA 61.255 52.632 18.90 0.00 41.24 3.46
3715 4299 3.418913 CAACAATGGCGACGGCGA 61.419 61.111 18.90 0.00 41.24 5.54
4030 4632 1.299850 CTGCGGAATGGCGTCGATA 60.300 57.895 0.00 0.00 35.06 2.92
4117 4796 1.133407 GAAAACCACGCAACACAAGGA 59.867 47.619 0.00 0.00 0.00 3.36
4118 4797 1.135257 TGAAAACCACGCAACACAAGG 60.135 47.619 0.00 0.00 0.00 3.61
4213 4901 5.321959 TGTCAGATAGAGAGCACAAGAAG 57.678 43.478 0.00 0.00 0.00 2.85
4236 4924 7.247456 TCCCACACACTTGTATTACAGATAA 57.753 36.000 0.00 0.00 33.30 1.75
4323 5881 7.579916 GCTCTTATATTAGTTTAGGGAGGGAGC 60.580 44.444 0.00 0.00 33.61 4.70
4392 5955 5.476950 TCATAGTACCCCCTCTGTAAAGA 57.523 43.478 0.00 0.00 0.00 2.52
4399 5962 3.780850 CCAGTTTTCATAGTACCCCCTCT 59.219 47.826 0.00 0.00 0.00 3.69
4446 6030 9.617975 GTTCATTCATTTGAAAAGTAGAAGAGG 57.382 33.333 0.00 0.00 37.36 3.69
4553 6138 2.436173 CCTGAGGAGGGATGAGGTTTAC 59.564 54.545 0.00 0.00 35.40 2.01
4565 6151 4.065789 GTGTTTCTGTAAACCTGAGGAGG 58.934 47.826 4.99 0.00 43.66 4.30
4757 6821 0.452987 AGCATGCACGGCAAATAGTG 59.547 50.000 21.98 0.00 43.62 2.74
4885 6949 3.364664 GCGATCGTACGATTGGTATCAGA 60.365 47.826 35.15 7.40 36.71 3.27
4893 6958 1.487482 ACCATGCGATCGTACGATTG 58.513 50.000 32.32 32.32 38.66 2.67
4898 6963 3.897325 TCATTCTACCATGCGATCGTAC 58.103 45.455 17.81 0.88 0.00 3.67
4905 6970 3.303593 GCTGTGATTCATTCTACCATGCG 60.304 47.826 0.00 0.00 0.00 4.73
4925 6990 0.037697 TTCGCGGTGAATACTGTGCT 60.038 50.000 6.13 0.00 42.20 4.40
4926 6991 0.370273 CTTCGCGGTGAATACTGTGC 59.630 55.000 6.13 0.00 42.20 4.57
4927 6992 0.370273 GCTTCGCGGTGAATACTGTG 59.630 55.000 6.13 0.00 43.50 3.66
4930 6995 0.249398 AAGGCTTCGCGGTGAATACT 59.751 50.000 6.13 3.54 35.63 2.12
4952 7017 2.826777 ATTCACCTGCTGGAAGGCGG 62.827 60.000 17.64 0.00 41.46 6.13
4980 7045 7.816031 GTGATTTCCAGTGATGAAAACATGATT 59.184 33.333 0.00 0.00 37.02 2.57


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

AutoCloner maintained by Alex Coulton.