Multiple sequence alignment - TraesCS2D01G392900

Loading Multiple Alignment...

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 TraesCS2D01G392900 chr2D 100.000 3764 0 0 1 3764 500794605 500790842 0.000000e+00 6951.0
1 TraesCS2D01G392900 chr2A 94.442 2627 118 16 397 3008 646553578 646556191 0.000000e+00 4017.0
2 TraesCS2D01G392900 chr2A 93.456 596 35 4 3040 3631 646556310 646556905 0.000000e+00 881.0
3 TraesCS2D01G392900 chr2A 94.074 135 8 0 3627 3761 646557167 646557301 4.930000e-49 206.0
4 TraesCS2D01G392900 chr2B 93.901 1984 77 18 842 2804 588534317 588536277 0.000000e+00 2953.0
5 TraesCS2D01G392900 chr2B 87.273 770 62 15 2994 3762 588536852 588537586 0.000000e+00 846.0
6 TraesCS2D01G392900 chr2B 94.764 191 9 1 2784 2973 588536582 588536772 2.840000e-76 296.0
7 TraesCS2D01G392900 chr2B 87.500 168 18 2 569 736 249527566 249527402 1.380000e-44 191.0
8 TraesCS2D01G392900 chr2B 85.938 64 6 2 3281 3342 611057353 611057415 8.730000e-07 65.8
9 TraesCS2D01G392900 chr3D 90.062 161 14 1 569 729 91710770 91710928 1.370000e-49 207.0
10 TraesCS2D01G392900 chr3A 90.260 154 13 1 576 729 723464479 723464630 2.290000e-47 200.0
11 TraesCS2D01G392900 chr6B 89.375 160 13 3 575 732 372573669 372573826 8.250000e-47 198.0
12 TraesCS2D01G392900 chr6B 87.059 170 20 1 560 729 16269662 16269829 1.380000e-44 191.0
13 TraesCS2D01G392900 chr6B 83.178 107 12 6 3241 3343 158187045 158186941 4.000000e-15 93.5
14 TraesCS2D01G392900 chr7A 89.241 158 15 1 575 732 451519963 451519808 2.970000e-46 196.0
15 TraesCS2D01G392900 chr7A 78.689 244 30 13 232 455 40543413 40543654 3.920000e-30 143.0
16 TraesCS2D01G392900 chr7A 79.286 140 22 5 3181 3320 112141409 112141541 1.440000e-14 91.6
17 TraesCS2D01G392900 chr6D 87.647 170 19 1 563 732 256724158 256724325 2.970000e-46 196.0
18 TraesCS2D01G392900 chr6A 89.241 158 15 1 575 732 366035494 366035339 2.970000e-46 196.0
19 TraesCS2D01G392900 chr1D 78.776 245 30 13 232 455 29961481 29961238 1.090000e-30 145.0
20 TraesCS2D01G392900 chr1D 86.364 110 12 3 232 340 142674892 142674785 2.380000e-22 117.0
21 TraesCS2D01G392900 chr1D 76.494 251 35 10 227 457 19135333 19135087 8.540000e-22 115.0
22 TraesCS2D01G392900 chr1A 77.959 245 38 14 232 466 548569398 548569160 5.070000e-29 139.0
23 TraesCS2D01G392900 chr1A 76.984 252 37 13 225 457 90725933 90725684 1.420000e-24 124.0
24 TraesCS2D01G392900 chr7B 76.892 251 28 21 232 456 634053535 634053781 8.540000e-22 115.0
25 TraesCS2D01G392900 chr7B 87.368 95 9 2 226 319 423144878 423144970 5.140000e-19 106.0
26 TraesCS2D01G392900 chr7B 100.000 28 0 0 343 370 443083407 443083434 7.000000e-03 52.8
27 TraesCS2D01G392900 chr5D 76.735 245 31 9 232 455 322989778 322989539 3.070000e-21 113.0
28 TraesCS2D01G392900 chr7D 88.136 59 5 2 3287 3343 622195958 622195900 6.750000e-08 69.4


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 TraesCS2D01G392900 chr2D 500790842 500794605 3763 True 6951.000000 6951 100.000000 1 3764 1 chr2D.!!$R1 3763
1 TraesCS2D01G392900 chr2A 646553578 646557301 3723 False 1701.333333 4017 93.990667 397 3761 3 chr2A.!!$F1 3364
2 TraesCS2D01G392900 chr2B 588534317 588537586 3269 False 1365.000000 2953 91.979333 842 3762 3 chr2B.!!$F2 2920

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
365 366 0.323360 ATAAGCCAAAAGCCGGAGCA 60.323 50.0 5.05 0.0 45.47 4.26 F
369 370 0.531753 GCCAAAAGCCGGAGCAAAAA 60.532 50.0 5.05 0.0 43.56 1.94 F
1329 1347 0.603975 GCTCTGGACAACCTGACACC 60.604 60.0 0.00 0.0 38.81 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1777 1798 0.096454 GGTATGCGCCTCGTTGTTTC 59.904 55.0 4.18 0.0 0.00 2.78 R
2346 2374 1.557099 AGTGGATGCCGTAGAGTTCA 58.443 50.0 0.00 0.0 0.00 3.18 R
2841 3192 0.179145 AAAGCACCGGTCGTATCTCG 60.179 55.0 2.59 0.0 41.41 4.04 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
21 22 4.882671 GAAAGTGGCGACAATATCATGT 57.117 40.909 0.00 0.00 46.06 3.21
22 23 4.837567 GAAAGTGGCGACAATATCATGTC 58.162 43.478 0.00 0.00 46.06 3.06
36 37 2.251869 CATGTCGGCATGTTGTTCTG 57.748 50.000 21.80 0.00 45.48 3.02
37 38 1.805943 CATGTCGGCATGTTGTTCTGA 59.194 47.619 21.80 0.00 45.48 3.27
38 39 1.225855 TGTCGGCATGTTGTTCTGAC 58.774 50.000 0.00 0.00 36.82 3.51
39 40 1.225855 GTCGGCATGTTGTTCTGACA 58.774 50.000 0.00 0.00 36.43 3.58
40 41 1.195448 GTCGGCATGTTGTTCTGACAG 59.805 52.381 0.00 0.00 37.04 3.51
41 42 1.202639 TCGGCATGTTGTTCTGACAGT 60.203 47.619 1.59 0.00 37.04 3.55
42 43 2.036604 TCGGCATGTTGTTCTGACAGTA 59.963 45.455 1.59 0.00 37.04 2.74
43 44 2.413112 CGGCATGTTGTTCTGACAGTAG 59.587 50.000 1.59 0.00 37.04 2.57
44 45 3.403038 GGCATGTTGTTCTGACAGTAGT 58.597 45.455 1.59 0.00 37.04 2.73
45 46 4.566004 GGCATGTTGTTCTGACAGTAGTA 58.434 43.478 1.59 0.00 37.04 1.82
46 47 4.994852 GGCATGTTGTTCTGACAGTAGTAA 59.005 41.667 1.59 0.00 37.04 2.24
47 48 5.643777 GGCATGTTGTTCTGACAGTAGTAAT 59.356 40.000 1.59 0.00 37.04 1.89
48 49 6.402550 GGCATGTTGTTCTGACAGTAGTAATG 60.403 42.308 1.59 0.00 37.04 1.90
49 50 6.402550 GCATGTTGTTCTGACAGTAGTAATGG 60.403 42.308 1.59 0.00 37.04 3.16
50 51 6.169557 TGTTGTTCTGACAGTAGTAATGGT 57.830 37.500 1.59 0.00 37.04 3.55
51 52 6.220930 TGTTGTTCTGACAGTAGTAATGGTC 58.779 40.000 1.59 0.00 37.04 4.02
52 53 5.055642 TGTTCTGACAGTAGTAATGGTCG 57.944 43.478 1.59 0.00 33.04 4.79
53 54 4.521639 TGTTCTGACAGTAGTAATGGTCGT 59.478 41.667 1.59 0.00 33.04 4.34
54 55 4.959596 TCTGACAGTAGTAATGGTCGTC 57.040 45.455 1.59 0.00 33.04 4.20
55 56 3.693085 TCTGACAGTAGTAATGGTCGTCC 59.307 47.826 1.59 0.00 33.04 4.79
56 57 2.421073 TGACAGTAGTAATGGTCGTCCG 59.579 50.000 2.24 0.00 36.30 4.79
57 58 1.747355 ACAGTAGTAATGGTCGTCCGG 59.253 52.381 0.00 0.00 36.30 5.14
58 59 1.747355 CAGTAGTAATGGTCGTCCGGT 59.253 52.381 0.00 0.00 36.30 5.28
59 60 1.747355 AGTAGTAATGGTCGTCCGGTG 59.253 52.381 0.00 0.00 36.30 4.94
60 61 1.105457 TAGTAATGGTCGTCCGGTGG 58.895 55.000 0.00 0.00 36.30 4.61
61 62 0.901580 AGTAATGGTCGTCCGGTGGT 60.902 55.000 0.00 0.00 36.30 4.16
62 63 0.459063 GTAATGGTCGTCCGGTGGTC 60.459 60.000 0.00 0.00 36.30 4.02
63 64 0.612732 TAATGGTCGTCCGGTGGTCT 60.613 55.000 0.00 0.00 36.30 3.85
64 65 0.612732 AATGGTCGTCCGGTGGTCTA 60.613 55.000 0.00 0.00 36.30 2.59
65 66 1.035932 ATGGTCGTCCGGTGGTCTAG 61.036 60.000 0.00 0.00 36.30 2.43
66 67 1.377725 GGTCGTCCGGTGGTCTAGA 60.378 63.158 0.00 0.00 0.00 2.43
67 68 0.962356 GGTCGTCCGGTGGTCTAGAA 60.962 60.000 0.00 0.00 0.00 2.10
68 69 0.883833 GTCGTCCGGTGGTCTAGAAA 59.116 55.000 0.00 0.00 0.00 2.52
69 70 1.475682 GTCGTCCGGTGGTCTAGAAAT 59.524 52.381 0.00 0.00 0.00 2.17
70 71 2.094338 GTCGTCCGGTGGTCTAGAAATT 60.094 50.000 0.00 0.00 0.00 1.82
71 72 2.564062 TCGTCCGGTGGTCTAGAAATTT 59.436 45.455 0.00 0.00 0.00 1.82
72 73 2.671396 CGTCCGGTGGTCTAGAAATTTG 59.329 50.000 0.00 0.00 0.00 2.32
73 74 3.615592 CGTCCGGTGGTCTAGAAATTTGA 60.616 47.826 0.00 0.00 0.00 2.69
74 75 4.514401 GTCCGGTGGTCTAGAAATTTGAT 58.486 43.478 0.00 0.00 0.00 2.57
75 76 4.332819 GTCCGGTGGTCTAGAAATTTGATG 59.667 45.833 0.00 0.00 0.00 3.07
76 77 4.019681 TCCGGTGGTCTAGAAATTTGATGT 60.020 41.667 0.00 0.00 0.00 3.06
77 78 5.188163 TCCGGTGGTCTAGAAATTTGATGTA 59.812 40.000 0.00 0.00 0.00 2.29
78 79 5.878116 CCGGTGGTCTAGAAATTTGATGTAA 59.122 40.000 0.00 0.00 0.00 2.41
79 80 6.542370 CCGGTGGTCTAGAAATTTGATGTAAT 59.458 38.462 0.00 0.00 0.00 1.89
80 81 7.067008 CCGGTGGTCTAGAAATTTGATGTAATT 59.933 37.037 0.00 0.00 0.00 1.40
81 82 8.458843 CGGTGGTCTAGAAATTTGATGTAATTT 58.541 33.333 0.00 0.00 39.68 1.82
99 100 9.777297 ATGTAATTTTTATTATGGTTGGGATGC 57.223 29.630 0.00 0.00 0.00 3.91
100 101 8.986991 TGTAATTTTTATTATGGTTGGGATGCT 58.013 29.630 0.00 0.00 0.00 3.79
101 102 9.830975 GTAATTTTTATTATGGTTGGGATGCTT 57.169 29.630 0.00 0.00 0.00 3.91
102 103 8.962884 AATTTTTATTATGGTTGGGATGCTTC 57.037 30.769 0.00 0.00 0.00 3.86
103 104 7.487822 TTTTTATTATGGTTGGGATGCTTCA 57.512 32.000 1.64 0.00 0.00 3.02
104 105 7.673641 TTTTATTATGGTTGGGATGCTTCAT 57.326 32.000 1.64 0.00 0.00 2.57
105 106 8.774546 TTTTATTATGGTTGGGATGCTTCATA 57.225 30.769 1.64 0.00 0.00 2.15
106 107 8.774546 TTTATTATGGTTGGGATGCTTCATAA 57.225 30.769 1.64 0.00 33.48 1.90
107 108 8.954834 TTATTATGGTTGGGATGCTTCATAAT 57.045 30.769 0.00 0.00 39.55 1.28
108 109 7.860649 ATTATGGTTGGGATGCTTCATAATT 57.139 32.000 1.64 0.00 35.53 1.40
109 110 7.673641 TTATGGTTGGGATGCTTCATAATTT 57.326 32.000 1.64 0.00 0.00 1.82
110 111 6.564557 ATGGTTGGGATGCTTCATAATTTT 57.435 33.333 1.64 0.00 0.00 1.82
111 112 5.732633 TGGTTGGGATGCTTCATAATTTTG 58.267 37.500 1.64 0.00 0.00 2.44
112 113 5.483231 TGGTTGGGATGCTTCATAATTTTGA 59.517 36.000 1.64 0.00 0.00 2.69
113 114 6.156602 TGGTTGGGATGCTTCATAATTTTGAT 59.843 34.615 0.00 0.00 0.00 2.57
114 115 6.480981 GGTTGGGATGCTTCATAATTTTGATG 59.519 38.462 0.00 3.80 0.00 3.07
115 116 7.267128 GTTGGGATGCTTCATAATTTTGATGA 58.733 34.615 13.57 1.39 0.00 2.92
116 117 7.421087 TGGGATGCTTCATAATTTTGATGAA 57.579 32.000 13.57 8.42 40.23 2.57
117 118 8.025270 TGGGATGCTTCATAATTTTGATGAAT 57.975 30.769 13.57 9.55 41.31 2.57
118 119 8.487848 TGGGATGCTTCATAATTTTGATGAATT 58.512 29.630 13.57 0.00 41.31 2.17
119 120 9.333724 GGGATGCTTCATAATTTTGATGAATTT 57.666 29.630 13.57 0.00 41.31 1.82
187 188 9.872757 ATAAAAGATTATTTGTTGTATACGCCG 57.127 29.630 0.00 0.00 0.00 6.46
188 189 6.913873 AAGATTATTTGTTGTATACGCCGT 57.086 33.333 0.00 0.00 0.00 5.68
189 190 6.520792 AGATTATTTGTTGTATACGCCGTC 57.479 37.500 0.00 0.00 0.00 4.79
190 191 6.044046 AGATTATTTGTTGTATACGCCGTCA 58.956 36.000 0.00 0.00 0.00 4.35
191 192 6.535865 AGATTATTTGTTGTATACGCCGTCAA 59.464 34.615 0.00 0.00 0.00 3.18
192 193 6.665474 TTATTTGTTGTATACGCCGTCAAT 57.335 33.333 0.00 0.00 0.00 2.57
193 194 5.554822 ATTTGTTGTATACGCCGTCAATT 57.445 34.783 0.00 0.00 0.00 2.32
194 195 4.587211 TTGTTGTATACGCCGTCAATTC 57.413 40.909 0.00 0.00 0.00 2.17
195 196 3.852286 TGTTGTATACGCCGTCAATTCT 58.148 40.909 0.00 0.00 0.00 2.40
196 197 3.615056 TGTTGTATACGCCGTCAATTCTG 59.385 43.478 0.00 0.00 0.00 3.02
197 198 3.513680 TGTATACGCCGTCAATTCTGT 57.486 42.857 0.00 0.00 0.00 3.41
198 199 4.635833 TGTATACGCCGTCAATTCTGTA 57.364 40.909 0.00 0.00 0.00 2.74
199 200 5.190992 TGTATACGCCGTCAATTCTGTAT 57.809 39.130 0.00 0.00 0.00 2.29
200 201 6.316440 TGTATACGCCGTCAATTCTGTATA 57.684 37.500 0.00 0.00 0.00 1.47
201 202 6.916440 TGTATACGCCGTCAATTCTGTATAT 58.084 36.000 0.00 0.00 30.27 0.86
202 203 8.042944 TGTATACGCCGTCAATTCTGTATATA 57.957 34.615 0.00 0.00 30.27 0.86
203 204 8.513774 TGTATACGCCGTCAATTCTGTATATAA 58.486 33.333 0.00 0.00 30.27 0.98
204 205 9.512435 GTATACGCCGTCAATTCTGTATATAAT 57.488 33.333 0.00 0.00 30.27 1.28
206 207 7.807687 ACGCCGTCAATTCTGTATATAATAC 57.192 36.000 0.00 0.00 0.00 1.89
207 208 7.600065 ACGCCGTCAATTCTGTATATAATACT 58.400 34.615 0.00 0.00 0.00 2.12
208 209 8.733458 ACGCCGTCAATTCTGTATATAATACTA 58.267 33.333 0.00 0.00 0.00 1.82
209 210 9.563898 CGCCGTCAATTCTGTATATAATACTAA 57.436 33.333 0.00 0.00 0.00 2.24
227 228 7.700022 ATACTAAGAGTCGGTCAGTTAAACT 57.300 36.000 0.00 0.00 0.00 2.66
228 229 8.798859 ATACTAAGAGTCGGTCAGTTAAACTA 57.201 34.615 0.00 0.00 0.00 2.24
229 230 7.516198 ACTAAGAGTCGGTCAGTTAAACTAA 57.484 36.000 0.00 0.00 0.00 2.24
230 231 8.120140 ACTAAGAGTCGGTCAGTTAAACTAAT 57.880 34.615 0.00 0.00 0.00 1.73
231 232 8.027771 ACTAAGAGTCGGTCAGTTAAACTAATG 58.972 37.037 0.00 0.00 0.00 1.90
232 233 5.169295 AGAGTCGGTCAGTTAAACTAATGC 58.831 41.667 0.00 0.00 0.00 3.56
233 234 4.251268 AGTCGGTCAGTTAAACTAATGCC 58.749 43.478 0.00 0.00 0.00 4.40
234 235 3.373130 GTCGGTCAGTTAAACTAATGCCC 59.627 47.826 0.00 0.00 0.00 5.36
235 236 3.262405 TCGGTCAGTTAAACTAATGCCCT 59.738 43.478 0.00 0.00 0.00 5.19
236 237 3.374058 CGGTCAGTTAAACTAATGCCCTG 59.626 47.826 0.00 0.00 0.00 4.45
237 238 4.332828 GGTCAGTTAAACTAATGCCCTGT 58.667 43.478 0.00 0.00 0.00 4.00
238 239 4.765339 GGTCAGTTAAACTAATGCCCTGTT 59.235 41.667 0.00 0.00 0.00 3.16
239 240 5.243060 GGTCAGTTAAACTAATGCCCTGTTT 59.757 40.000 0.00 0.00 37.60 2.83
240 241 6.149633 GTCAGTTAAACTAATGCCCTGTTTG 58.850 40.000 0.00 0.00 35.77 2.93
241 242 5.830991 TCAGTTAAACTAATGCCCTGTTTGT 59.169 36.000 0.00 0.00 35.77 2.83
242 243 6.322712 TCAGTTAAACTAATGCCCTGTTTGTT 59.677 34.615 0.00 0.00 35.77 2.83
243 244 6.983890 CAGTTAAACTAATGCCCTGTTTGTTT 59.016 34.615 0.00 0.00 37.88 2.83
244 245 6.983890 AGTTAAACTAATGCCCTGTTTGTTTG 59.016 34.615 8.09 0.00 36.03 2.93
245 246 4.335400 AACTAATGCCCTGTTTGTTTGG 57.665 40.909 0.00 0.00 0.00 3.28
246 247 2.632512 ACTAATGCCCTGTTTGTTTGGG 59.367 45.455 0.00 0.00 43.62 4.12
251 252 2.708216 CCCTGTTTGTTTGGGCTTTT 57.292 45.000 0.00 0.00 33.88 2.27
252 253 2.287769 CCCTGTTTGTTTGGGCTTTTG 58.712 47.619 0.00 0.00 33.88 2.44
253 254 1.670295 CCTGTTTGTTTGGGCTTTTGC 59.330 47.619 0.00 0.00 46.64 3.68
254 255 2.631267 CTGTTTGTTTGGGCTTTTGCT 58.369 42.857 0.00 0.00 46.54 3.91
255 256 3.009026 CTGTTTGTTTGGGCTTTTGCTT 58.991 40.909 0.00 0.00 46.54 3.91
256 257 3.006247 TGTTTGTTTGGGCTTTTGCTTC 58.994 40.909 0.00 0.00 46.54 3.86
257 258 3.270027 GTTTGTTTGGGCTTTTGCTTCT 58.730 40.909 0.00 0.00 46.54 2.85
258 259 2.600470 TGTTTGGGCTTTTGCTTCTG 57.400 45.000 0.00 0.00 46.54 3.02
259 260 1.220529 GTTTGGGCTTTTGCTTCTGC 58.779 50.000 0.00 0.00 46.54 4.26
260 261 1.122227 TTTGGGCTTTTGCTTCTGCT 58.878 45.000 0.00 0.00 46.54 4.24
261 262 1.122227 TTGGGCTTTTGCTTCTGCTT 58.878 45.000 0.00 0.00 46.54 3.91
262 263 1.122227 TGGGCTTTTGCTTCTGCTTT 58.878 45.000 0.00 0.00 46.54 3.51
263 264 1.485895 TGGGCTTTTGCTTCTGCTTTT 59.514 42.857 0.00 0.00 46.54 2.27
264 265 1.869132 GGGCTTTTGCTTCTGCTTTTG 59.131 47.619 0.00 0.00 46.54 2.44
265 266 1.262417 GGCTTTTGCTTCTGCTTTTGC 59.738 47.619 0.00 0.00 46.54 3.68
283 284 8.574196 GCTTTTGCATCTTTTCACTTAAGTAA 57.426 30.769 8.04 0.00 46.58 2.24
284 285 9.030301 GCTTTTGCATCTTTTCACTTAAGTAAA 57.970 29.630 8.04 5.63 46.58 2.01
318 319 8.435931 AAAAACCCTCCTAAATAGATGCTTTT 57.564 30.769 0.00 0.00 0.00 2.27
319 320 8.435931 AAAACCCTCCTAAATAGATGCTTTTT 57.564 30.769 0.00 0.00 0.00 1.94
336 337 2.797177 TTTTGGTTTGGCTTTTGGCT 57.203 40.000 0.00 0.00 46.20 4.75
337 338 2.797177 TTTGGTTTGGCTTTTGGCTT 57.203 40.000 0.00 0.00 46.20 4.35
338 339 3.914426 TTTGGTTTGGCTTTTGGCTTA 57.086 38.095 0.00 0.00 46.20 3.09
339 340 4.429854 TTTGGTTTGGCTTTTGGCTTAT 57.570 36.364 0.00 0.00 46.20 1.73
340 341 3.399440 TGGTTTGGCTTTTGGCTTATG 57.601 42.857 0.00 0.00 46.20 1.90
341 342 2.703007 TGGTTTGGCTTTTGGCTTATGT 59.297 40.909 0.00 0.00 46.20 2.29
342 343 3.135530 TGGTTTGGCTTTTGGCTTATGTT 59.864 39.130 0.00 0.00 46.20 2.71
343 344 3.498018 GGTTTGGCTTTTGGCTTATGTTG 59.502 43.478 0.00 0.00 46.20 3.33
344 345 3.399440 TTGGCTTTTGGCTTATGTTGG 57.601 42.857 0.00 0.00 46.20 3.77
345 346 2.324541 TGGCTTTTGGCTTATGTTGGT 58.675 42.857 0.00 0.00 46.20 3.67
346 347 3.501349 TGGCTTTTGGCTTATGTTGGTA 58.499 40.909 0.00 0.00 46.20 3.25
347 348 4.093011 TGGCTTTTGGCTTATGTTGGTAT 58.907 39.130 0.00 0.00 46.20 2.73
348 349 5.265191 TGGCTTTTGGCTTATGTTGGTATA 58.735 37.500 0.00 0.00 46.20 1.47
349 350 5.717178 TGGCTTTTGGCTTATGTTGGTATAA 59.283 36.000 0.00 0.00 46.20 0.98
350 351 6.127479 TGGCTTTTGGCTTATGTTGGTATAAG 60.127 38.462 0.00 0.00 46.20 1.73
361 362 1.757682 TGGTATAAGCCAAAAGCCGG 58.242 50.000 0.00 0.00 45.47 6.13
362 363 1.282447 TGGTATAAGCCAAAAGCCGGA 59.718 47.619 5.05 0.00 45.47 5.14
363 364 1.947456 GGTATAAGCCAAAAGCCGGAG 59.053 52.381 5.05 0.00 45.47 4.63
364 365 1.333931 GTATAAGCCAAAAGCCGGAGC 59.666 52.381 5.05 0.00 45.47 4.70
365 366 0.323360 ATAAGCCAAAAGCCGGAGCA 60.323 50.000 5.05 0.00 45.47 4.26
366 367 0.538516 TAAGCCAAAAGCCGGAGCAA 60.539 50.000 5.05 0.00 45.47 3.91
367 368 1.398958 AAGCCAAAAGCCGGAGCAAA 61.399 50.000 5.05 0.00 45.47 3.68
368 369 1.068921 GCCAAAAGCCGGAGCAAAA 59.931 52.632 5.05 0.00 43.56 2.44
369 370 0.531753 GCCAAAAGCCGGAGCAAAAA 60.532 50.000 5.05 0.00 43.56 1.94
370 371 1.501169 CCAAAAGCCGGAGCAAAAAG 58.499 50.000 5.05 0.00 43.56 2.27
371 372 0.861185 CAAAAGCCGGAGCAAAAAGC 59.139 50.000 5.05 0.00 43.56 3.51
385 386 5.330455 GCAAAAAGCCCTATTTAGAAGCT 57.670 39.130 0.00 0.00 37.23 3.74
386 387 5.724328 GCAAAAAGCCCTATTTAGAAGCTT 58.276 37.500 0.00 0.00 41.38 3.74
387 388 6.014242 AGCAAAAAGCCCTATTTAGAAGCTTT 60.014 34.615 15.79 15.79 45.76 3.51
390 391 6.918067 AAAGCCCTATTTAGAAGCTTTTGT 57.082 33.333 15.79 0.00 43.63 2.83
391 392 5.904362 AGCCCTATTTAGAAGCTTTTGTG 57.096 39.130 0.00 0.00 31.50 3.33
392 393 4.706962 AGCCCTATTTAGAAGCTTTTGTGG 59.293 41.667 0.00 0.00 31.50 4.17
393 394 4.678044 GCCCTATTTAGAAGCTTTTGTGGC 60.678 45.833 0.00 1.87 0.00 5.01
394 395 4.462483 CCCTATTTAGAAGCTTTTGTGGCA 59.538 41.667 0.00 0.00 0.00 4.92
395 396 5.047377 CCCTATTTAGAAGCTTTTGTGGCAA 60.047 40.000 0.00 0.00 0.00 4.52
439 440 4.470334 AAAAAGCAGAAGCAAAAGTCCA 57.530 36.364 0.00 0.00 45.49 4.02
440 441 3.722728 AAAGCAGAAGCAAAAGTCCAG 57.277 42.857 0.00 0.00 45.49 3.86
459 461 3.496870 CCAGACAAACAGGGCTTAAGAGT 60.497 47.826 6.67 0.00 0.00 3.24
502 504 8.385898 ACTCAAGTTTCGTAATATGTTTTCCA 57.614 30.769 0.00 0.00 0.00 3.53
530 532 6.155827 TCAAAATAGTGTGGCTAAAATGCAC 58.844 36.000 0.00 0.00 32.72 4.57
564 567 6.367969 ACGAGCGTCATTTACTCATAGTTTTT 59.632 34.615 0.00 0.00 0.00 1.94
639 642 8.523915 TTACATATGGAGCAAAATGAGTGAAT 57.476 30.769 7.80 0.00 0.00 2.57
641 644 6.832384 ACATATGGAGCAAAATGAGTGAATCT 59.168 34.615 7.80 0.00 0.00 2.40
642 645 7.994911 ACATATGGAGCAAAATGAGTGAATCTA 59.005 33.333 7.80 0.00 0.00 1.98
752 755 9.649167 GTATAATTTATTGCACCGACCTATAGT 57.351 33.333 0.00 0.00 0.00 2.12
760 763 2.287373 CACCGACCTATAGTCACGACTC 59.713 54.545 2.26 0.00 46.69 3.36
767 770 4.636648 ACCTATAGTCACGACTCAAGACTG 59.363 45.833 2.26 0.00 42.21 3.51
837 840 7.811117 TCATTTAGAGTAGAACTCCTAGCTC 57.189 40.000 3.49 0.00 46.18 4.09
888 892 3.610114 GCGTGCCATCATTTGCCTATAAG 60.610 47.826 0.00 0.00 0.00 1.73
934 951 2.410469 GGATCACATTGCAGCGGC 59.590 61.111 0.31 0.31 41.68 6.53
957 974 3.202906 GGCAATACTATCAAACAGCCGA 58.797 45.455 0.00 0.00 0.00 5.54
973 991 2.730672 CGAGCAGCAAGTACGCACC 61.731 63.158 0.00 0.00 0.00 5.01
1329 1347 0.603975 GCTCTGGACAACCTGACACC 60.604 60.000 0.00 0.00 38.81 4.16
1632 1650 0.876342 CGCCTCGGCCTCATTTCTAC 60.876 60.000 0.00 0.00 37.98 2.59
1660 1678 1.403780 GGATGAACTTCCGTACGTGCT 60.404 52.381 15.21 0.00 0.00 4.40
1755 1775 4.974275 TCGTACCGATCGAATCTTTCAATC 59.026 41.667 18.66 0.00 34.36 2.67
1777 1798 0.935196 GCCCGCTAATTAACCTGTCG 59.065 55.000 0.00 0.00 0.00 4.35
1851 1872 1.271543 TGACAGGCTAGCTGTTGCAAT 60.272 47.619 15.72 0.00 42.74 3.56
1852 1873 2.027285 TGACAGGCTAGCTGTTGCAATA 60.027 45.455 15.72 0.00 42.74 1.90
1854 1875 3.012518 ACAGGCTAGCTGTTGCAATAAG 58.987 45.455 15.72 5.00 42.74 1.73
1856 1877 2.239654 AGGCTAGCTGTTGCAATAAGGA 59.760 45.455 15.72 0.00 42.74 3.36
1936 1961 3.797256 CGCTAGCAAACTGATAGGTGTAC 59.203 47.826 16.45 0.00 36.89 2.90
1944 1969 6.603095 CAAACTGATAGGTGTACTTTTCTGC 58.397 40.000 0.00 0.00 0.00 4.26
2069 2097 1.509004 GGCGATATCGGAGAGCCTC 59.491 63.158 25.51 6.88 43.63 4.70
2297 2325 3.204827 GGCGCGCTGGTCATCAAT 61.205 61.111 32.29 0.00 0.00 2.57
2338 2366 6.097554 CAGGTATCCTTCTAGACAGACACAAT 59.902 42.308 0.00 0.00 0.00 2.71
2406 2434 2.386660 GCAGGCTCTGAGCAACGAC 61.387 63.158 28.95 12.70 44.75 4.34
2633 2661 4.409218 CGACCGCTTCCGACCGAA 62.409 66.667 0.00 0.00 36.29 4.30
2640 2668 1.736645 CTTCCGACCGAACGCATGT 60.737 57.895 0.00 0.00 0.00 3.21
2651 2679 0.179032 AACGCATGTTGGACTGTCCA 60.179 50.000 25.12 25.12 46.61 4.02
2723 2751 1.139989 CCGATGATGTGTCGCCATAC 58.860 55.000 0.00 0.00 37.75 2.39
2730 2758 1.520787 GTGTCGCCATACGGGAAGG 60.521 63.158 0.00 0.00 43.89 3.46
2841 3192 1.633774 TCTCCCTGACCTTGACACTC 58.366 55.000 0.00 0.00 0.00 3.51
2928 3282 1.103803 GTCCACCGAGCTGTCTATCA 58.896 55.000 0.00 0.00 0.00 2.15
3020 3539 4.230745 ACGTAACTATTTTGCCAGGGAT 57.769 40.909 0.00 0.00 0.00 3.85
3066 3585 1.202428 GCCGAGGATACCTTCTGTCAC 60.202 57.143 0.00 0.00 31.76 3.67
3179 3699 2.037511 TGTATGAGGATGATGCGCATGA 59.962 45.455 30.76 22.10 37.34 3.07
3184 3704 3.181494 TGAGGATGATGCGCATGAAAAAG 60.181 43.478 30.76 0.00 37.34 2.27
3279 3799 4.798387 GCGAACCATTGTGTATTGATTTCC 59.202 41.667 0.00 0.00 0.00 3.13
3302 3822 5.392380 CCTTTAGCGAGACATTGCTCAAAAT 60.392 40.000 0.00 0.00 43.03 1.82
3326 3846 1.402984 ATAGCGTGCTATTAGCGGAGC 60.403 52.381 16.81 16.81 46.26 4.70
3366 3889 4.271696 TGATGATCCAACGACAAGTTCT 57.728 40.909 0.00 0.00 42.02 3.01
3596 4119 2.744202 GTGAGTGAGAATTGGACGCATT 59.256 45.455 0.00 0.00 0.00 3.56
3678 4467 3.449737 CGCCTAGATAATATTCCCGGGAA 59.550 47.826 37.24 37.24 38.59 3.97
3694 4483 2.713877 GGGAATACCGCACTAACCAAA 58.286 47.619 0.00 0.00 36.97 3.28
3750 4539 8.581253 AAATCGGGAAAATTCTCAACTATCTT 57.419 30.769 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.837567 GACATGATATTGTCGCCACTTTC 58.162 43.478 0.00 0.00 36.93 2.62
1 2 4.882671 GACATGATATTGTCGCCACTTT 57.117 40.909 0.00 0.00 36.93 2.66
18 19 1.806542 GTCAGAACAACATGCCGACAT 59.193 47.619 0.00 0.00 36.79 3.06
19 20 1.225855 GTCAGAACAACATGCCGACA 58.774 50.000 0.00 0.00 0.00 4.35
20 21 1.195448 CTGTCAGAACAACATGCCGAC 59.805 52.381 0.00 0.00 34.24 4.79
21 22 1.202639 ACTGTCAGAACAACATGCCGA 60.203 47.619 6.91 0.00 34.24 5.54
22 23 1.229428 ACTGTCAGAACAACATGCCG 58.771 50.000 6.91 0.00 34.24 5.69
23 24 3.403038 ACTACTGTCAGAACAACATGCC 58.597 45.455 6.91 0.00 34.24 4.40
24 25 6.402550 CCATTACTACTGTCAGAACAACATGC 60.403 42.308 6.91 0.00 34.24 4.06
25 26 6.650807 ACCATTACTACTGTCAGAACAACATG 59.349 38.462 6.91 0.00 34.24 3.21
26 27 6.769512 ACCATTACTACTGTCAGAACAACAT 58.230 36.000 6.91 0.00 34.24 2.71
27 28 6.169557 ACCATTACTACTGTCAGAACAACA 57.830 37.500 6.91 0.00 34.24 3.33
28 29 5.345202 CGACCATTACTACTGTCAGAACAAC 59.655 44.000 6.91 0.00 34.24 3.32
29 30 5.010314 ACGACCATTACTACTGTCAGAACAA 59.990 40.000 6.91 0.00 34.24 2.83
30 31 4.521639 ACGACCATTACTACTGTCAGAACA 59.478 41.667 6.91 0.00 0.00 3.18
31 32 5.056894 ACGACCATTACTACTGTCAGAAC 57.943 43.478 6.91 0.00 0.00 3.01
32 33 4.157289 GGACGACCATTACTACTGTCAGAA 59.843 45.833 6.91 0.00 35.97 3.02
33 34 3.693085 GGACGACCATTACTACTGTCAGA 59.307 47.826 6.91 0.00 35.97 3.27
34 35 3.487042 CGGACGACCATTACTACTGTCAG 60.487 52.174 4.48 0.00 35.59 3.51
35 36 2.421073 CGGACGACCATTACTACTGTCA 59.579 50.000 4.48 0.00 35.59 3.58
36 37 2.223433 CCGGACGACCATTACTACTGTC 60.223 54.545 0.00 0.00 35.59 3.51
37 38 1.747355 CCGGACGACCATTACTACTGT 59.253 52.381 0.00 0.00 35.59 3.55
38 39 1.747355 ACCGGACGACCATTACTACTG 59.253 52.381 9.46 0.00 35.59 2.74
39 40 1.747355 CACCGGACGACCATTACTACT 59.253 52.381 9.46 0.00 35.59 2.57
40 41 1.202336 CCACCGGACGACCATTACTAC 60.202 57.143 9.46 0.00 35.59 2.73
41 42 1.105457 CCACCGGACGACCATTACTA 58.895 55.000 9.46 0.00 35.59 1.82
42 43 0.901580 ACCACCGGACGACCATTACT 60.902 55.000 9.46 0.00 35.59 2.24
43 44 0.459063 GACCACCGGACGACCATTAC 60.459 60.000 9.46 0.00 35.59 1.89
44 45 0.612732 AGACCACCGGACGACCATTA 60.613 55.000 9.46 0.00 35.59 1.90
45 46 0.612732 TAGACCACCGGACGACCATT 60.613 55.000 9.46 0.00 35.59 3.16
46 47 1.000521 TAGACCACCGGACGACCAT 60.001 57.895 9.46 0.00 35.59 3.55
47 48 1.676635 CTAGACCACCGGACGACCA 60.677 63.158 9.46 0.00 35.59 4.02
48 49 0.962356 TTCTAGACCACCGGACGACC 60.962 60.000 9.46 0.00 0.00 4.79
49 50 0.883833 TTTCTAGACCACCGGACGAC 59.116 55.000 9.46 0.00 0.00 4.34
50 51 1.843368 ATTTCTAGACCACCGGACGA 58.157 50.000 9.46 0.00 0.00 4.20
51 52 2.667473 AATTTCTAGACCACCGGACG 57.333 50.000 9.46 0.00 0.00 4.79
52 53 3.934068 TCAAATTTCTAGACCACCGGAC 58.066 45.455 9.46 0.00 0.00 4.79
53 54 4.019681 ACATCAAATTTCTAGACCACCGGA 60.020 41.667 9.46 0.00 0.00 5.14
54 55 4.261801 ACATCAAATTTCTAGACCACCGG 58.738 43.478 0.00 0.00 0.00 5.28
55 56 6.978343 TTACATCAAATTTCTAGACCACCG 57.022 37.500 0.00 0.00 0.00 4.94
73 74 9.777297 GCATCCCAACCATAATAAAAATTACAT 57.223 29.630 0.00 0.00 0.00 2.29
74 75 8.986991 AGCATCCCAACCATAATAAAAATTACA 58.013 29.630 0.00 0.00 0.00 2.41
75 76 9.830975 AAGCATCCCAACCATAATAAAAATTAC 57.169 29.630 0.00 0.00 0.00 1.89
77 78 8.547173 TGAAGCATCCCAACCATAATAAAAATT 58.453 29.630 0.00 0.00 0.00 1.82
78 79 8.088463 TGAAGCATCCCAACCATAATAAAAAT 57.912 30.769 0.00 0.00 0.00 1.82
79 80 7.487822 TGAAGCATCCCAACCATAATAAAAA 57.512 32.000 0.00 0.00 0.00 1.94
80 81 7.673641 ATGAAGCATCCCAACCATAATAAAA 57.326 32.000 0.00 0.00 0.00 1.52
81 82 8.774546 TTATGAAGCATCCCAACCATAATAAA 57.225 30.769 0.00 0.00 0.00 1.40
82 83 8.954834 ATTATGAAGCATCCCAACCATAATAA 57.045 30.769 0.00 0.00 36.21 1.40
83 84 8.954834 AATTATGAAGCATCCCAACCATAATA 57.045 30.769 0.00 0.00 36.66 0.98
84 85 7.860649 AATTATGAAGCATCCCAACCATAAT 57.139 32.000 0.00 0.00 38.24 1.28
85 86 7.673641 AAATTATGAAGCATCCCAACCATAA 57.326 32.000 0.00 0.00 33.01 1.90
86 87 7.344093 TCAAAATTATGAAGCATCCCAACCATA 59.656 33.333 0.00 0.00 0.00 2.74
87 88 6.156602 TCAAAATTATGAAGCATCCCAACCAT 59.843 34.615 0.00 0.00 0.00 3.55
88 89 5.483231 TCAAAATTATGAAGCATCCCAACCA 59.517 36.000 0.00 0.00 0.00 3.67
89 90 5.976458 TCAAAATTATGAAGCATCCCAACC 58.024 37.500 0.00 0.00 0.00 3.77
90 91 7.267128 TCATCAAAATTATGAAGCATCCCAAC 58.733 34.615 0.00 0.00 32.06 3.77
91 92 7.421087 TCATCAAAATTATGAAGCATCCCAA 57.579 32.000 0.00 0.00 32.06 4.12
92 93 7.421087 TTCATCAAAATTATGAAGCATCCCA 57.579 32.000 0.00 0.00 38.19 4.37
93 94 8.897872 AATTCATCAAAATTATGAAGCATCCC 57.102 30.769 7.87 0.00 44.27 3.85
161 162 9.872757 CGGCGTATACAACAAATAATCTTTTAT 57.127 29.630 0.00 0.00 0.00 1.40
162 163 8.881743 ACGGCGTATACAACAAATAATCTTTTA 58.118 29.630 12.58 0.00 0.00 1.52
163 164 7.754625 ACGGCGTATACAACAAATAATCTTTT 58.245 30.769 12.58 0.00 0.00 2.27
164 165 7.064847 TGACGGCGTATACAACAAATAATCTTT 59.935 33.333 14.74 0.00 0.00 2.52
165 166 6.535865 TGACGGCGTATACAACAAATAATCTT 59.464 34.615 14.74 0.00 0.00 2.40
166 167 6.044046 TGACGGCGTATACAACAAATAATCT 58.956 36.000 14.74 0.00 0.00 2.40
167 168 6.276611 TGACGGCGTATACAACAAATAATC 57.723 37.500 14.74 0.00 0.00 1.75
168 169 6.665474 TTGACGGCGTATACAACAAATAAT 57.335 33.333 14.74 0.00 0.00 1.28
169 170 6.665474 ATTGACGGCGTATACAACAAATAA 57.335 33.333 14.74 0.00 0.00 1.40
170 171 6.535865 AGAATTGACGGCGTATACAACAAATA 59.464 34.615 14.74 0.00 0.00 1.40
171 172 5.353123 AGAATTGACGGCGTATACAACAAAT 59.647 36.000 14.74 4.69 0.00 2.32
172 173 4.691685 AGAATTGACGGCGTATACAACAAA 59.308 37.500 14.74 0.00 0.00 2.83
173 174 4.092237 CAGAATTGACGGCGTATACAACAA 59.908 41.667 14.74 12.54 0.00 2.83
174 175 3.615056 CAGAATTGACGGCGTATACAACA 59.385 43.478 14.74 1.81 0.00 3.33
175 176 3.615496 ACAGAATTGACGGCGTATACAAC 59.385 43.478 14.74 0.00 0.00 3.32
176 177 3.852286 ACAGAATTGACGGCGTATACAA 58.148 40.909 14.74 14.18 0.00 2.41
177 178 3.513680 ACAGAATTGACGGCGTATACA 57.486 42.857 14.74 3.64 0.00 2.29
178 179 8.900511 TTATATACAGAATTGACGGCGTATAC 57.099 34.615 14.74 0.18 0.00 1.47
180 181 9.512435 GTATTATATACAGAATTGACGGCGTAT 57.488 33.333 14.74 0.00 0.00 3.06
181 182 8.733458 AGTATTATATACAGAATTGACGGCGTA 58.267 33.333 14.74 0.00 0.00 4.42
182 183 7.600065 AGTATTATATACAGAATTGACGGCGT 58.400 34.615 14.65 14.65 0.00 5.68
183 184 9.563898 TTAGTATTATATACAGAATTGACGGCG 57.436 33.333 4.80 4.80 0.00 6.46
201 202 9.236006 AGTTTAACTGACCGACTCTTAGTATTA 57.764 33.333 0.00 0.00 0.00 0.98
202 203 8.120140 AGTTTAACTGACCGACTCTTAGTATT 57.880 34.615 0.00 0.00 0.00 1.89
203 204 7.700022 AGTTTAACTGACCGACTCTTAGTAT 57.300 36.000 0.00 0.00 0.00 2.12
204 205 8.621532 TTAGTTTAACTGACCGACTCTTAGTA 57.378 34.615 8.00 0.00 0.00 1.82
205 206 7.516198 TTAGTTTAACTGACCGACTCTTAGT 57.484 36.000 8.00 0.00 0.00 2.24
206 207 7.009357 GCATTAGTTTAACTGACCGACTCTTAG 59.991 40.741 8.00 0.00 0.00 2.18
207 208 6.810182 GCATTAGTTTAACTGACCGACTCTTA 59.190 38.462 8.00 0.00 0.00 2.10
208 209 5.638234 GCATTAGTTTAACTGACCGACTCTT 59.362 40.000 8.00 0.00 0.00 2.85
209 210 5.169295 GCATTAGTTTAACTGACCGACTCT 58.831 41.667 8.00 0.00 0.00 3.24
210 211 4.329256 GGCATTAGTTTAACTGACCGACTC 59.671 45.833 8.00 0.00 0.00 3.36
211 212 4.251268 GGCATTAGTTTAACTGACCGACT 58.749 43.478 8.00 0.00 0.00 4.18
212 213 3.373130 GGGCATTAGTTTAACTGACCGAC 59.627 47.826 8.00 0.00 0.00 4.79
213 214 3.262405 AGGGCATTAGTTTAACTGACCGA 59.738 43.478 8.00 0.00 41.93 4.69
214 215 3.374058 CAGGGCATTAGTTTAACTGACCG 59.626 47.826 8.00 0.00 41.93 4.79
215 216 4.332828 ACAGGGCATTAGTTTAACTGACC 58.667 43.478 8.00 3.68 37.03 4.02
216 217 5.959618 AACAGGGCATTAGTTTAACTGAC 57.040 39.130 8.00 0.00 0.00 3.51
217 218 5.830991 ACAAACAGGGCATTAGTTTAACTGA 59.169 36.000 8.00 0.00 34.03 3.41
218 219 6.084326 ACAAACAGGGCATTAGTTTAACTG 57.916 37.500 8.00 0.00 34.03 3.16
219 220 6.724893 AACAAACAGGGCATTAGTTTAACT 57.275 33.333 2.32 2.32 34.03 2.24
220 221 6.201997 CCAAACAAACAGGGCATTAGTTTAAC 59.798 38.462 0.00 0.00 34.03 2.01
221 222 6.284459 CCAAACAAACAGGGCATTAGTTTAA 58.716 36.000 0.00 0.00 34.03 1.52
222 223 5.221541 CCCAAACAAACAGGGCATTAGTTTA 60.222 40.000 0.00 0.00 35.44 2.01
223 224 4.444164 CCCAAACAAACAGGGCATTAGTTT 60.444 41.667 0.00 0.00 35.44 2.66
224 225 3.070878 CCCAAACAAACAGGGCATTAGTT 59.929 43.478 0.00 0.00 35.44 2.24
225 226 2.632512 CCCAAACAAACAGGGCATTAGT 59.367 45.455 0.00 0.00 35.44 2.24
226 227 3.317603 CCCAAACAAACAGGGCATTAG 57.682 47.619 0.00 0.00 35.44 1.73
232 233 2.287769 CAAAAGCCCAAACAAACAGGG 58.712 47.619 0.00 0.00 45.68 4.45
233 234 1.670295 GCAAAAGCCCAAACAAACAGG 59.330 47.619 0.00 0.00 0.00 4.00
234 235 2.631267 AGCAAAAGCCCAAACAAACAG 58.369 42.857 0.00 0.00 0.00 3.16
235 236 2.777832 AGCAAAAGCCCAAACAAACA 57.222 40.000 0.00 0.00 0.00 2.83
236 237 3.063861 CAGAAGCAAAAGCCCAAACAAAC 59.936 43.478 0.00 0.00 0.00 2.93
237 238 3.269178 CAGAAGCAAAAGCCCAAACAAA 58.731 40.909 0.00 0.00 0.00 2.83
238 239 2.903798 CAGAAGCAAAAGCCCAAACAA 58.096 42.857 0.00 0.00 0.00 2.83
239 240 1.473080 GCAGAAGCAAAAGCCCAAACA 60.473 47.619 0.00 0.00 41.58 2.83
240 241 1.202568 AGCAGAAGCAAAAGCCCAAAC 60.203 47.619 0.00 0.00 45.49 2.93
241 242 1.122227 AGCAGAAGCAAAAGCCCAAA 58.878 45.000 0.00 0.00 45.49 3.28
242 243 1.122227 AAGCAGAAGCAAAAGCCCAA 58.878 45.000 0.00 0.00 45.49 4.12
243 244 1.122227 AAAGCAGAAGCAAAAGCCCA 58.878 45.000 0.00 0.00 45.49 5.36
244 245 1.869132 CAAAAGCAGAAGCAAAAGCCC 59.131 47.619 0.00 0.00 45.49 5.19
245 246 1.262417 GCAAAAGCAGAAGCAAAAGCC 59.738 47.619 0.00 0.00 45.49 4.35
246 247 1.935199 TGCAAAAGCAGAAGCAAAAGC 59.065 42.857 0.00 0.00 45.49 3.51
247 248 4.056050 AGATGCAAAAGCAGAAGCAAAAG 58.944 39.130 0.00 0.00 45.49 2.27
248 249 4.062677 AGATGCAAAAGCAGAAGCAAAA 57.937 36.364 0.00 0.00 45.49 2.44
249 250 3.738830 AGATGCAAAAGCAGAAGCAAA 57.261 38.095 0.00 0.00 45.49 3.68
250 251 3.738830 AAGATGCAAAAGCAGAAGCAA 57.261 38.095 0.00 0.00 45.49 3.91
251 252 3.738830 AAAGATGCAAAAGCAGAAGCA 57.261 38.095 0.00 0.00 45.49 3.91
252 253 4.053295 TGAAAAGATGCAAAAGCAGAAGC 58.947 39.130 0.00 0.00 42.56 3.86
253 254 5.287226 AGTGAAAAGATGCAAAAGCAGAAG 58.713 37.500 0.00 0.00 0.00 2.85
254 255 5.266733 AGTGAAAAGATGCAAAAGCAGAA 57.733 34.783 0.00 0.00 0.00 3.02
255 256 4.924305 AGTGAAAAGATGCAAAAGCAGA 57.076 36.364 0.00 0.00 0.00 4.26
256 257 6.698766 ACTTAAGTGAAAAGATGCAAAAGCAG 59.301 34.615 7.48 0.00 0.00 4.24
257 258 6.572519 ACTTAAGTGAAAAGATGCAAAAGCA 58.427 32.000 7.48 0.00 0.00 3.91
258 259 8.574196 TTACTTAAGTGAAAAGATGCAAAAGC 57.426 30.769 18.56 0.00 0.00 3.51
293 294 8.435931 AAAAGCATCTATTTAGGAGGGTTTTT 57.564 30.769 10.80 0.00 45.81 1.94
316 317 3.078891 AGCCAAAAGCCAAACCAAAAA 57.921 38.095 0.00 0.00 45.47 1.94
317 318 2.797177 AGCCAAAAGCCAAACCAAAA 57.203 40.000 0.00 0.00 45.47 2.44
318 319 2.797177 AAGCCAAAAGCCAAACCAAA 57.203 40.000 0.00 0.00 45.47 3.28
319 320 3.135530 ACATAAGCCAAAAGCCAAACCAA 59.864 39.130 0.00 0.00 45.47 3.67
320 321 2.703007 ACATAAGCCAAAAGCCAAACCA 59.297 40.909 0.00 0.00 45.47 3.67
321 322 3.401033 ACATAAGCCAAAAGCCAAACC 57.599 42.857 0.00 0.00 45.47 3.27
322 323 3.498018 CCAACATAAGCCAAAAGCCAAAC 59.502 43.478 0.00 0.00 45.47 2.93
323 324 3.135530 ACCAACATAAGCCAAAAGCCAAA 59.864 39.130 0.00 0.00 45.47 3.28
324 325 2.703007 ACCAACATAAGCCAAAAGCCAA 59.297 40.909 0.00 0.00 45.47 4.52
325 326 2.324541 ACCAACATAAGCCAAAAGCCA 58.675 42.857 0.00 0.00 45.47 4.75
326 327 4.736126 ATACCAACATAAGCCAAAAGCC 57.264 40.909 0.00 0.00 45.47 4.35
342 343 1.282447 TCCGGCTTTTGGCTTATACCA 59.718 47.619 0.00 0.00 43.55 3.25
343 344 1.947456 CTCCGGCTTTTGGCTTATACC 59.053 52.381 0.00 0.00 43.55 2.73
344 345 1.333931 GCTCCGGCTTTTGGCTTATAC 59.666 52.381 0.00 0.00 43.55 1.47
345 346 1.065053 TGCTCCGGCTTTTGGCTTATA 60.065 47.619 0.00 0.00 43.55 0.98
346 347 0.323360 TGCTCCGGCTTTTGGCTTAT 60.323 50.000 0.00 0.00 43.55 1.73
347 348 0.538516 TTGCTCCGGCTTTTGGCTTA 60.539 50.000 0.00 0.00 43.55 3.09
348 349 1.398958 TTTGCTCCGGCTTTTGGCTT 61.399 50.000 0.00 0.00 43.55 4.35
349 350 1.398958 TTTTGCTCCGGCTTTTGGCT 61.399 50.000 0.00 0.00 43.55 4.75
350 351 0.531753 TTTTTGCTCCGGCTTTTGGC 60.532 50.000 0.00 0.00 39.59 4.52
351 352 1.501169 CTTTTTGCTCCGGCTTTTGG 58.499 50.000 0.00 0.00 39.59 3.28
352 353 0.861185 GCTTTTTGCTCCGGCTTTTG 59.139 50.000 0.00 0.00 39.59 2.44
353 354 0.249868 GGCTTTTTGCTCCGGCTTTT 60.250 50.000 0.00 0.00 42.39 2.27
354 355 1.367471 GGCTTTTTGCTCCGGCTTT 59.633 52.632 0.00 0.00 42.39 3.51
355 356 2.574018 GGGCTTTTTGCTCCGGCTT 61.574 57.895 0.00 0.00 42.39 4.35
356 357 2.137177 TAGGGCTTTTTGCTCCGGCT 62.137 55.000 0.00 0.00 45.11 5.52
357 358 1.037579 ATAGGGCTTTTTGCTCCGGC 61.038 55.000 0.00 0.00 45.11 6.13
358 359 1.474330 AATAGGGCTTTTTGCTCCGG 58.526 50.000 0.00 0.00 45.11 5.14
359 360 3.945285 TCTAAATAGGGCTTTTTGCTCCG 59.055 43.478 0.00 0.00 45.11 4.63
360 361 5.679894 GCTTCTAAATAGGGCTTTTTGCTCC 60.680 44.000 0.00 0.00 45.11 4.70
361 362 5.126222 AGCTTCTAAATAGGGCTTTTTGCTC 59.874 40.000 0.00 0.00 44.10 4.26
362 363 5.019470 AGCTTCTAAATAGGGCTTTTTGCT 58.981 37.500 0.00 0.00 42.39 3.91
363 364 5.330455 AGCTTCTAAATAGGGCTTTTTGC 57.670 39.130 0.00 0.00 41.94 3.68
364 365 7.657354 ACAAAAGCTTCTAAATAGGGCTTTTTG 59.343 33.333 25.57 23.03 46.59 2.44
365 366 7.657354 CACAAAAGCTTCTAAATAGGGCTTTTT 59.343 33.333 25.57 19.38 46.59 1.94
367 368 6.295292 CCACAAAAGCTTCTAAATAGGGCTTT 60.295 38.462 18.87 18.87 45.08 3.51
368 369 5.185828 CCACAAAAGCTTCTAAATAGGGCTT 59.814 40.000 0.00 12.36 41.02 4.35
369 370 4.706962 CCACAAAAGCTTCTAAATAGGGCT 59.293 41.667 0.00 4.04 35.53 5.19
370 371 4.678044 GCCACAAAAGCTTCTAAATAGGGC 60.678 45.833 0.00 1.87 0.00 5.19
371 372 4.462483 TGCCACAAAAGCTTCTAAATAGGG 59.538 41.667 0.00 0.00 0.00 3.53
372 373 5.643379 TGCCACAAAAGCTTCTAAATAGG 57.357 39.130 0.00 0.00 0.00 2.57
373 374 8.538409 AAATTGCCACAAAAGCTTCTAAATAG 57.462 30.769 0.00 0.00 0.00 1.73
374 375 8.772705 CAAAATTGCCACAAAAGCTTCTAAATA 58.227 29.630 0.00 0.00 0.00 1.40
375 376 7.641760 CAAAATTGCCACAAAAGCTTCTAAAT 58.358 30.769 0.00 0.00 0.00 1.40
376 377 7.014092 CAAAATTGCCACAAAAGCTTCTAAA 57.986 32.000 0.00 0.00 0.00 1.85
377 378 6.601741 CAAAATTGCCACAAAAGCTTCTAA 57.398 33.333 0.00 0.00 0.00 2.10
418 419 4.160252 TCTGGACTTTTGCTTCTGCTTTTT 59.840 37.500 0.00 0.00 40.48 1.94
430 431 2.223805 GCCCTGTTTGTCTGGACTTTTG 60.224 50.000 2.38 0.00 37.33 2.44
435 436 2.561478 TAAGCCCTGTTTGTCTGGAC 57.439 50.000 0.00 0.00 37.33 4.02
436 437 2.708861 TCTTAAGCCCTGTTTGTCTGGA 59.291 45.455 0.00 0.00 37.33 3.86
439 440 5.071923 AGTTACTCTTAAGCCCTGTTTGTCT 59.928 40.000 0.00 0.00 0.00 3.41
440 441 5.306394 AGTTACTCTTAAGCCCTGTTTGTC 58.694 41.667 0.00 0.00 0.00 3.18
502 504 8.720562 GCATTTTAGCCACACTATTTTGAAAAT 58.279 29.630 8.35 8.35 0.00 1.82
508 510 5.478407 GGTGCATTTTAGCCACACTATTTT 58.522 37.500 0.00 0.00 0.00 1.82
530 532 3.041940 GACGCTCGTGGTTGTGGG 61.042 66.667 0.00 0.00 0.00 4.61
611 614 7.229306 TCACTCATTTTGCTCCATATGTAATCC 59.771 37.037 1.24 0.00 0.00 3.01
612 615 8.158169 TCACTCATTTTGCTCCATATGTAATC 57.842 34.615 1.24 0.00 0.00 1.75
617 620 7.273320 AGATTCACTCATTTTGCTCCATATG 57.727 36.000 0.00 0.00 0.00 1.78
621 624 7.280876 GTGTATAGATTCACTCATTTTGCTCCA 59.719 37.037 0.00 0.00 0.00 3.86
623 626 8.430801 AGTGTATAGATTCACTCATTTTGCTC 57.569 34.615 0.00 0.00 40.28 4.26
718 721 6.303839 GGTGCAATAAATTATACTCCCTCCA 58.696 40.000 0.00 0.00 0.00 3.86
722 725 5.180680 GGTCGGTGCAATAAATTATACTCCC 59.819 44.000 0.00 0.00 0.00 4.30
752 755 0.959553 GGACCAGTCTTGAGTCGTGA 59.040 55.000 0.00 0.00 0.00 4.35
760 763 5.308825 ACTTGAGTTATTGGACCAGTCTTG 58.691 41.667 0.00 0.00 0.00 3.02
812 815 7.307751 CGAGCTAGGAGTTCTACTCTAAATGAG 60.308 44.444 6.77 0.00 44.46 2.90
820 823 5.870978 CCTATACGAGCTAGGAGTTCTACTC 59.129 48.000 0.00 0.00 44.32 2.59
837 840 6.370718 ACAAAGAACCTTTTAGCACCTATACG 59.629 38.462 0.00 0.00 0.00 3.06
934 951 3.002656 CGGCTGTTTGATAGTATTGCCAG 59.997 47.826 0.00 0.00 39.09 4.85
957 974 1.961277 GTGGTGCGTACTTGCTGCT 60.961 57.895 3.01 0.00 35.36 4.24
973 991 4.649088 TGTCTAGGAATGGTACGATGTG 57.351 45.455 0.00 0.00 0.00 3.21
1180 1198 4.222847 GATGGCCTCGACGACCCC 62.223 72.222 3.32 0.00 0.00 4.95
1316 1334 1.444250 TGACCGGTGTCAGGTTGTC 59.556 57.895 14.63 0.00 46.40 3.18
1329 1347 2.385315 CTACATACGCAGTGATGACCG 58.615 52.381 0.00 0.00 45.73 4.79
1615 1633 0.249489 CGGTAGAAATGAGGCCGAGG 60.249 60.000 0.00 0.00 44.57 4.63
1632 1650 1.726853 GGAAGTTCATCCTGACACGG 58.273 55.000 5.01 0.00 36.50 4.94
1660 1678 4.980573 ACTTAATTAGTTGGTGACCAGCA 58.019 39.130 20.62 0.79 37.20 4.41
1755 1775 1.147600 AGGTTAATTAGCGGGCCGG 59.852 57.895 29.48 9.71 0.00 6.13
1777 1798 0.096454 GGTATGCGCCTCGTTGTTTC 59.904 55.000 4.18 0.00 0.00 2.78
2042 2070 1.662608 CGATATCGCCTCCAGCAGT 59.337 57.895 12.95 0.00 44.04 4.40
2297 2325 1.831106 ACCTGCAGTTGATCACCGATA 59.169 47.619 13.81 0.00 0.00 2.92
2338 2366 2.101750 TGCCGTAGAGTTCAGTTCACAA 59.898 45.455 0.00 0.00 0.00 3.33
2346 2374 1.557099 AGTGGATGCCGTAGAGTTCA 58.443 50.000 0.00 0.00 0.00 3.18
2348 2376 2.159282 CGTTAGTGGATGCCGTAGAGTT 60.159 50.000 0.00 0.00 0.00 3.01
2406 2434 0.872021 GGAGCACGCTCTTGTATCGG 60.872 60.000 17.99 0.00 42.38 4.18
2633 2661 1.449782 TGGACAGTCCAACATGCGT 59.550 52.632 20.84 0.00 45.00 5.24
2723 2751 0.391793 GTCTTTCAGAGGCCTTCCCG 60.392 60.000 6.77 0.00 39.21 5.14
2841 3192 0.179145 AAAGCACCGGTCGTATCTCG 60.179 55.000 2.59 0.00 41.41 4.04
2914 3268 4.793071 CACTTAGATGATAGACAGCTCGG 58.207 47.826 0.00 0.00 41.75 4.63
3020 3539 2.496871 CCCACAAGCATATCAAAGCCAA 59.503 45.455 0.00 0.00 0.00 4.52
3066 3585 7.096844 CGATAGATTGATAGTGAACAACGTCAG 60.097 40.741 0.00 0.00 39.76 3.51
3167 3687 7.493320 ACAATATTTCTTTTTCATGCGCATCAT 59.507 29.630 22.51 0.00 35.31 2.45
3201 3721 5.236478 GGATTTTAAGAGCTGCGCTATGTTA 59.764 40.000 9.73 0.63 39.88 2.41
3262 3782 7.471721 TCGCTAAAGGAAATCAATACACAATG 58.528 34.615 0.00 0.00 0.00 2.82
3271 3791 5.391950 GCAATGTCTCGCTAAAGGAAATCAA 60.392 40.000 0.00 0.00 0.00 2.57
3279 3799 4.668576 TTTGAGCAATGTCTCGCTAAAG 57.331 40.909 0.00 0.00 38.99 1.85
3302 3822 2.415491 CCGCTAATAGCACGCTATAGCA 60.415 50.000 23.99 4.83 42.58 3.49
3366 3889 8.392612 ACGAACTCTTCTTTTTCGAAATTGTAA 58.607 29.630 12.12 1.93 43.83 2.41
3678 4467 3.508012 TGCATTTTTGGTTAGTGCGGTAT 59.492 39.130 0.00 0.00 38.58 2.73
3694 4483 6.013984 ACTTCCAATGGAAAGAATCTGCATTT 60.014 34.615 16.30 0.00 41.54 2.32


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

AutoCloner maintained by Alex Coulton.