Multiple sequence alignment - TraesCS3B01G384700

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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 TraesCS3B01G384700 chr3B 100.000 2613 0 0 1 2613 605011844 605014456 0.000000e+00 4826.0
1 TraesCS3B01G384700 chr3D 90.794 1575 66 29 516 2024 457401367 457402928 0.000000e+00 2032.0
2 TraesCS3B01G384700 chr3D 91.503 612 35 12 2008 2613 457402946 457403546 0.000000e+00 826.0
3 TraesCS3B01G384700 chr3D 81.132 265 22 10 274 526 457400958 457401206 1.230000e-43 187.0
4 TraesCS3B01G384700 chr3A 87.358 1669 114 37 516 2119 600314896 600316532 0.000000e+00 1823.0
5 TraesCS3B01G384700 chr3A 90.619 501 36 7 2118 2613 600316613 600317107 0.000000e+00 654.0
6 TraesCS3B01G384700 chr3A 90.058 171 10 4 355 520 600314525 600314693 5.660000e-52 215.0
7 TraesCS3B01G384700 chr4D 92.593 54 3 1 119 172 56740938 56740886 2.790000e-10 76.8
8 TraesCS3B01G384700 chr4A 85.135 74 7 2 103 176 569867969 569867900 3.610000e-09 73.1
9 TraesCS3B01G384700 chr4A 84.000 75 8 3 103 177 593377520 593377590 4.670000e-08 69.4
10 TraesCS3B01G384700 chr4A 84.286 70 7 1 103 172 662286420 662286485 6.040000e-07 65.8
11 TraesCS3B01G384700 chr5A 82.759 87 8 4 89 175 613596510 613596589 1.300000e-08 71.3
12 TraesCS3B01G384700 chr4B 90.741 54 3 2 119 172 83310602 83310551 1.300000e-08 71.3
13 TraesCS3B01G384700 chr5D 85.507 69 6 1 108 176 456063691 456063627 4.670000e-08 69.4
14 TraesCS3B01G384700 chr7D 85.294 68 4 3 108 175 190083295 190083234 6.040000e-07 65.8
15 TraesCS3B01G384700 chr2B 84.507 71 5 3 108 177 632567394 632567329 6.040000e-07 65.8


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 TraesCS3B01G384700 chr3B 605011844 605014456 2612 False 4826.000000 4826 100.000000 1 2613 1 chr3B.!!$F1 2612
1 TraesCS3B01G384700 chr3D 457400958 457403546 2588 False 1015.000000 2032 87.809667 274 2613 3 chr3D.!!$F1 2339
2 TraesCS3B01G384700 chr3A 600314525 600317107 2582 False 897.333333 1823 89.345000 355 2613 3 chr3A.!!$F1 2258

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
947 1210 0.314302 CACGACTCCCTCGACAAAGT 59.686 55.0 0.0 0.0 46.14 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2460 2924 0.109412 GACTAACCCTCGTCACCGTG 60.109 60.0 0.0 0.0 35.01 4.94 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 3.798794 CCATTACCATTCTGGCCGA 57.201 52.632 0.00 0.00 42.67 5.54
19 20 2.051334 CCATTACCATTCTGGCCGAA 57.949 50.000 11.52 11.52 42.67 4.30
20 21 1.676006 CCATTACCATTCTGGCCGAAC 59.324 52.381 11.39 0.00 42.67 3.95
21 22 2.643551 CATTACCATTCTGGCCGAACT 58.356 47.619 11.39 2.10 42.67 3.01
22 23 2.396590 TTACCATTCTGGCCGAACTC 57.603 50.000 11.39 0.00 42.67 3.01
23 24 1.271856 TACCATTCTGGCCGAACTCA 58.728 50.000 11.39 0.00 42.67 3.41
24 25 0.400213 ACCATTCTGGCCGAACTCAA 59.600 50.000 11.39 0.00 42.67 3.02
25 26 1.202879 ACCATTCTGGCCGAACTCAAA 60.203 47.619 11.39 0.00 42.67 2.69
26 27 2.094675 CCATTCTGGCCGAACTCAAAT 58.905 47.619 11.39 0.00 33.72 2.32
27 28 2.493278 CCATTCTGGCCGAACTCAAATT 59.507 45.455 11.39 0.00 33.72 1.82
28 29 3.504863 CATTCTGGCCGAACTCAAATTG 58.495 45.455 11.39 2.44 33.72 2.32
29 30 2.270352 TCTGGCCGAACTCAAATTGT 57.730 45.000 0.00 0.00 0.00 2.71
30 31 2.582052 TCTGGCCGAACTCAAATTGTT 58.418 42.857 0.00 0.00 0.00 2.83
31 32 2.293122 TCTGGCCGAACTCAAATTGTTG 59.707 45.455 0.00 0.00 35.95 3.33
32 33 1.339610 TGGCCGAACTCAAATTGTTGG 59.660 47.619 0.00 0.00 35.29 3.77
33 34 1.418373 GCCGAACTCAAATTGTTGGC 58.582 50.000 0.00 0.00 35.87 4.52
34 35 1.269517 GCCGAACTCAAATTGTTGGCA 60.270 47.619 8.07 0.00 39.28 4.92
35 36 2.393764 CCGAACTCAAATTGTTGGCAC 58.606 47.619 0.00 0.00 35.29 5.01
36 37 2.034558 CCGAACTCAAATTGTTGGCACT 59.965 45.455 0.00 0.00 35.29 4.40
37 38 3.252215 CCGAACTCAAATTGTTGGCACTA 59.748 43.478 0.00 0.00 35.29 2.74
38 39 4.261405 CCGAACTCAAATTGTTGGCACTAA 60.261 41.667 0.00 0.00 35.29 2.24
39 40 4.911610 CGAACTCAAATTGTTGGCACTAAG 59.088 41.667 0.00 0.00 35.29 2.18
40 41 5.277779 CGAACTCAAATTGTTGGCACTAAGA 60.278 40.000 0.00 0.00 35.29 2.10
41 42 6.568462 CGAACTCAAATTGTTGGCACTAAGAT 60.568 38.462 0.00 0.00 35.29 2.40
42 43 7.360861 CGAACTCAAATTGTTGGCACTAAGATA 60.361 37.037 0.00 0.00 35.29 1.98
43 44 7.383102 ACTCAAATTGTTGGCACTAAGATAG 57.617 36.000 0.00 0.00 35.29 2.08
44 45 6.375455 ACTCAAATTGTTGGCACTAAGATAGG 59.625 38.462 0.00 0.00 35.29 2.57
45 46 6.245408 TCAAATTGTTGGCACTAAGATAGGT 58.755 36.000 0.00 0.00 35.29 3.08
46 47 6.719370 TCAAATTGTTGGCACTAAGATAGGTT 59.281 34.615 0.00 0.00 35.29 3.50
47 48 6.515272 AATTGTTGGCACTAAGATAGGTTG 57.485 37.500 0.00 0.00 0.00 3.77
48 49 3.950397 TGTTGGCACTAAGATAGGTTGG 58.050 45.455 0.00 0.00 0.00 3.77
49 50 3.329520 TGTTGGCACTAAGATAGGTTGGT 59.670 43.478 0.00 0.00 0.00 3.67
50 51 4.202524 TGTTGGCACTAAGATAGGTTGGTT 60.203 41.667 0.00 0.00 0.00 3.67
51 52 4.216411 TGGCACTAAGATAGGTTGGTTC 57.784 45.455 0.00 0.00 0.00 3.62
52 53 3.195661 GGCACTAAGATAGGTTGGTTCG 58.804 50.000 0.00 0.00 0.00 3.95
53 54 3.369157 GGCACTAAGATAGGTTGGTTCGT 60.369 47.826 0.00 0.00 0.00 3.85
54 55 3.864003 GCACTAAGATAGGTTGGTTCGTC 59.136 47.826 0.00 0.00 0.00 4.20
55 56 4.430908 CACTAAGATAGGTTGGTTCGTCC 58.569 47.826 0.00 0.00 0.00 4.79
56 57 4.081862 CACTAAGATAGGTTGGTTCGTCCA 60.082 45.833 0.00 0.00 45.60 4.02
57 58 4.715297 ACTAAGATAGGTTGGTTCGTCCAT 59.285 41.667 3.33 0.00 46.60 3.41
58 59 3.543680 AGATAGGTTGGTTCGTCCATG 57.456 47.619 3.33 0.00 46.60 3.66
59 60 2.838202 AGATAGGTTGGTTCGTCCATGT 59.162 45.455 3.33 0.00 46.60 3.21
60 61 4.028131 AGATAGGTTGGTTCGTCCATGTA 58.972 43.478 3.33 0.00 46.60 2.29
61 62 4.468510 AGATAGGTTGGTTCGTCCATGTAA 59.531 41.667 3.33 0.00 46.60 2.41
62 63 3.713826 AGGTTGGTTCGTCCATGTAAT 57.286 42.857 3.33 0.00 46.60 1.89
63 64 4.028993 AGGTTGGTTCGTCCATGTAATT 57.971 40.909 3.33 0.00 46.60 1.40
64 65 3.756434 AGGTTGGTTCGTCCATGTAATTG 59.244 43.478 3.33 0.00 46.60 2.32
65 66 3.754323 GGTTGGTTCGTCCATGTAATTGA 59.246 43.478 3.33 0.00 46.60 2.57
66 67 4.398044 GGTTGGTTCGTCCATGTAATTGAT 59.602 41.667 3.33 0.00 46.60 2.57
67 68 5.448632 GGTTGGTTCGTCCATGTAATTGATC 60.449 44.000 3.33 0.00 46.60 2.92
68 69 4.837972 TGGTTCGTCCATGTAATTGATCA 58.162 39.130 0.00 0.00 41.93 2.92
69 70 5.436175 TGGTTCGTCCATGTAATTGATCAT 58.564 37.500 0.00 0.00 41.93 2.45
70 71 5.527214 TGGTTCGTCCATGTAATTGATCATC 59.473 40.000 0.00 0.00 41.93 2.92
71 72 5.527214 GGTTCGTCCATGTAATTGATCATCA 59.473 40.000 0.00 0.00 35.97 3.07
72 73 6.422223 GTTCGTCCATGTAATTGATCATCAC 58.578 40.000 0.00 0.00 0.00 3.06
73 74 5.669477 TCGTCCATGTAATTGATCATCACA 58.331 37.500 0.00 1.47 0.00 3.58
74 75 6.290605 TCGTCCATGTAATTGATCATCACAT 58.709 36.000 0.00 3.95 0.00 3.21
75 76 6.424812 TCGTCCATGTAATTGATCATCACATC 59.575 38.462 12.11 4.31 0.00 3.06
76 77 6.203338 CGTCCATGTAATTGATCATCACATCA 59.797 38.462 12.11 2.64 0.00 3.07
77 78 7.358066 GTCCATGTAATTGATCATCACATCAC 58.642 38.462 12.11 9.38 32.28 3.06
78 79 7.012610 GTCCATGTAATTGATCATCACATCACA 59.987 37.037 12.11 0.21 32.28 3.58
79 80 7.722285 TCCATGTAATTGATCATCACATCACAT 59.278 33.333 12.11 2.30 32.28 3.21
80 81 8.021396 CCATGTAATTGATCATCACATCACATC 58.979 37.037 12.11 0.00 32.28 3.06
81 82 8.784043 CATGTAATTGATCATCACATCACATCT 58.216 33.333 12.11 0.00 32.28 2.90
82 83 8.741603 TGTAATTGATCATCACATCACATCTT 57.258 30.769 0.00 0.00 32.28 2.40
83 84 9.835389 TGTAATTGATCATCACATCACATCTTA 57.165 29.630 0.00 0.00 32.28 2.10
86 87 9.794719 AATTGATCATCACATCACATCTTATCT 57.205 29.630 0.00 0.00 32.28 1.98
87 88 9.794719 ATTGATCATCACATCACATCTTATCTT 57.205 29.630 0.00 0.00 32.28 2.40
89 90 9.702494 TGATCATCACATCACATCTTATCTTAC 57.298 33.333 0.00 0.00 0.00 2.34
90 91 9.926158 GATCATCACATCACATCTTATCTTACT 57.074 33.333 0.00 0.00 0.00 2.24
102 103 9.810545 ACATCTTATCTTACTAGAAGAAGTTGC 57.189 33.333 0.00 0.00 34.43 4.17
109 110 8.582657 TCTTACTAGAAGAAGTTGCTACATCT 57.417 34.615 0.00 0.07 33.97 2.90
110 111 8.462811 TCTTACTAGAAGAAGTTGCTACATCTG 58.537 37.037 6.80 0.00 32.94 2.90
111 112 6.597832 ACTAGAAGAAGTTGCTACATCTGT 57.402 37.500 6.80 1.26 32.94 3.41
112 113 6.998802 ACTAGAAGAAGTTGCTACATCTGTT 58.001 36.000 6.80 1.97 32.94 3.16
113 114 7.093992 ACTAGAAGAAGTTGCTACATCTGTTC 58.906 38.462 6.80 2.58 32.94 3.18
114 115 5.241662 AGAAGAAGTTGCTACATCTGTTCC 58.758 41.667 6.80 0.00 32.94 3.62
115 116 4.899352 AGAAGTTGCTACATCTGTTCCT 57.101 40.909 5.25 0.00 31.50 3.36
116 117 6.211584 AGAAGAAGTTGCTACATCTGTTCCTA 59.788 38.462 6.80 0.00 32.94 2.94
117 118 6.360370 AGAAGTTGCTACATCTGTTCCTAA 57.640 37.500 5.25 0.00 31.50 2.69
118 119 6.769512 AGAAGTTGCTACATCTGTTCCTAAA 58.230 36.000 5.25 0.00 31.50 1.85
119 120 7.398024 AGAAGTTGCTACATCTGTTCCTAAAT 58.602 34.615 5.25 0.00 31.50 1.40
120 121 8.540388 AGAAGTTGCTACATCTGTTCCTAAATA 58.460 33.333 5.25 0.00 31.50 1.40
121 122 9.331282 GAAGTTGCTACATCTGTTCCTAAATAT 57.669 33.333 0.13 0.00 0.00 1.28
126 127 9.982651 TGCTACATCTGTTCCTAAATATAAGTC 57.017 33.333 0.00 0.00 0.00 3.01
127 128 9.982651 GCTACATCTGTTCCTAAATATAAGTCA 57.017 33.333 0.00 0.00 0.00 3.41
162 163 9.352163 GTTTATGTAAATTGAACTGCAAAAACG 57.648 29.630 0.00 0.00 40.48 3.60
163 164 8.635877 TTATGTAAATTGAACTGCAAAAACGT 57.364 26.923 0.00 0.00 40.48 3.99
164 165 6.561945 TGTAAATTGAACTGCAAAAACGTC 57.438 33.333 0.00 0.00 40.48 4.34
165 166 6.326375 TGTAAATTGAACTGCAAAAACGTCT 58.674 32.000 0.00 0.00 40.48 4.18
166 167 6.809196 TGTAAATTGAACTGCAAAAACGTCTT 59.191 30.769 0.00 0.00 40.48 3.01
167 168 7.968956 TGTAAATTGAACTGCAAAAACGTCTTA 59.031 29.630 0.00 0.00 40.48 2.10
168 169 8.964150 GTAAATTGAACTGCAAAAACGTCTTAT 58.036 29.630 0.00 0.00 40.48 1.73
170 171 9.691362 AAATTGAACTGCAAAAACGTCTTATAT 57.309 25.926 0.00 0.00 40.48 0.86
171 172 9.691362 AATTGAACTGCAAAAACGTCTTATATT 57.309 25.926 0.00 0.00 40.48 1.28
174 175 9.820229 TGAACTGCAAAAACGTCTTATATTAAG 57.180 29.630 0.00 0.00 0.00 1.85
175 176 9.274065 GAACTGCAAAAACGTCTTATATTAAGG 57.726 33.333 0.00 0.00 0.00 2.69
176 177 8.556213 ACTGCAAAAACGTCTTATATTAAGGA 57.444 30.769 0.00 0.00 0.00 3.36
177 178 9.174166 ACTGCAAAAACGTCTTATATTAAGGAT 57.826 29.630 0.00 0.00 0.00 3.24
193 194 6.500589 TTAAGGATATTCAGGAACAGAGGG 57.499 41.667 0.00 0.00 0.00 4.30
194 195 4.014273 AGGATATTCAGGAACAGAGGGT 57.986 45.455 0.00 0.00 0.00 4.34
195 196 3.713764 AGGATATTCAGGAACAGAGGGTG 59.286 47.826 0.00 0.00 0.00 4.61
196 197 3.456277 GGATATTCAGGAACAGAGGGTGT 59.544 47.826 0.00 0.00 43.24 4.16
197 198 4.654262 GGATATTCAGGAACAGAGGGTGTA 59.346 45.833 0.00 0.00 39.03 2.90
198 199 3.983044 ATTCAGGAACAGAGGGTGTAC 57.017 47.619 0.00 0.00 39.03 2.90
199 200 2.696526 TCAGGAACAGAGGGTGTACT 57.303 50.000 0.00 0.00 39.03 2.73
200 201 3.820195 TCAGGAACAGAGGGTGTACTA 57.180 47.619 0.00 0.00 39.03 1.82
201 202 4.122337 TCAGGAACAGAGGGTGTACTAA 57.878 45.455 0.00 0.00 39.03 2.24
202 203 4.684724 TCAGGAACAGAGGGTGTACTAAT 58.315 43.478 0.00 0.00 39.03 1.73
203 204 5.091552 TCAGGAACAGAGGGTGTACTAATT 58.908 41.667 0.00 0.00 39.03 1.40
204 205 6.258354 TCAGGAACAGAGGGTGTACTAATTA 58.742 40.000 0.00 0.00 39.03 1.40
205 206 6.901300 TCAGGAACAGAGGGTGTACTAATTAT 59.099 38.462 0.00 0.00 39.03 1.28
206 207 8.063153 TCAGGAACAGAGGGTGTACTAATTATA 58.937 37.037 0.00 0.00 39.03 0.98
207 208 8.142551 CAGGAACAGAGGGTGTACTAATTATAC 58.857 40.741 0.00 0.00 39.03 1.47
208 209 7.014038 AGGAACAGAGGGTGTACTAATTATACG 59.986 40.741 0.00 0.00 39.03 3.06
209 210 6.081872 ACAGAGGGTGTACTAATTATACGC 57.918 41.667 0.00 8.75 37.75 4.42
210 211 5.595542 ACAGAGGGTGTACTAATTATACGCA 59.404 40.000 14.77 0.62 37.75 5.24
211 212 6.267014 ACAGAGGGTGTACTAATTATACGCAT 59.733 38.462 14.77 7.48 37.75 4.73
212 213 6.807230 CAGAGGGTGTACTAATTATACGCATC 59.193 42.308 14.77 12.59 37.25 3.91
213 214 6.492429 AGAGGGTGTACTAATTATACGCATCA 59.508 38.462 14.77 0.00 37.25 3.07
214 215 7.014905 AGAGGGTGTACTAATTATACGCATCAA 59.985 37.037 14.77 0.00 37.25 2.57
215 216 7.152645 AGGGTGTACTAATTATACGCATCAAG 58.847 38.462 14.77 0.00 37.25 3.02
216 217 6.927381 GGGTGTACTAATTATACGCATCAAGT 59.073 38.462 14.77 0.00 35.53 3.16
217 218 7.095774 GGGTGTACTAATTATACGCATCAAGTG 60.096 40.741 14.77 0.00 35.53 3.16
218 219 7.437267 GGTGTACTAATTATACGCATCAAGTGT 59.563 37.037 14.77 0.00 44.62 3.55
219 220 9.454585 GTGTACTAATTATACGCATCAAGTGTA 57.545 33.333 0.00 0.00 46.38 2.90
220 221 9.673454 TGTACTAATTATACGCATCAAGTGTAG 57.327 33.333 0.00 0.00 45.61 2.74
221 222 7.639162 ACTAATTATACGCATCAAGTGTAGC 57.361 36.000 0.00 0.00 45.61 3.58
222 223 7.434492 ACTAATTATACGCATCAAGTGTAGCT 58.566 34.615 0.00 0.00 45.61 3.32
223 224 7.926555 ACTAATTATACGCATCAAGTGTAGCTT 59.073 33.333 0.00 0.00 45.61 3.74
224 225 7.553881 AATTATACGCATCAAGTGTAGCTTT 57.446 32.000 0.00 0.00 45.61 3.51
225 226 8.657074 AATTATACGCATCAAGTGTAGCTTTA 57.343 30.769 0.00 0.00 45.61 1.85
226 227 8.833231 ATTATACGCATCAAGTGTAGCTTTAT 57.167 30.769 0.00 0.00 45.61 1.40
227 228 6.771188 ATACGCATCAAGTGTAGCTTTATC 57.229 37.500 0.00 0.00 45.61 1.75
228 229 3.551890 ACGCATCAAGTGTAGCTTTATCG 59.448 43.478 0.00 0.00 39.69 2.92
229 230 3.551890 CGCATCAAGTGTAGCTTTATCGT 59.448 43.478 0.00 0.00 34.69 3.73
230 231 4.317418 CGCATCAAGTGTAGCTTTATCGTC 60.317 45.833 0.00 0.00 34.69 4.20
231 232 4.806247 GCATCAAGTGTAGCTTTATCGTCT 59.194 41.667 0.00 0.00 34.69 4.18
232 233 5.051374 GCATCAAGTGTAGCTTTATCGTCTC 60.051 44.000 0.00 0.00 34.69 3.36
233 234 5.638596 TCAAGTGTAGCTTTATCGTCTCA 57.361 39.130 0.00 0.00 34.69 3.27
234 235 6.208988 TCAAGTGTAGCTTTATCGTCTCAT 57.791 37.500 0.00 0.00 34.69 2.90
235 236 6.266323 TCAAGTGTAGCTTTATCGTCTCATC 58.734 40.000 0.00 0.00 34.69 2.92
236 237 6.095580 TCAAGTGTAGCTTTATCGTCTCATCT 59.904 38.462 0.00 0.00 34.69 2.90
237 238 5.826586 AGTGTAGCTTTATCGTCTCATCTG 58.173 41.667 0.00 0.00 0.00 2.90
238 239 5.590663 AGTGTAGCTTTATCGTCTCATCTGA 59.409 40.000 0.00 0.00 0.00 3.27
239 240 6.264292 AGTGTAGCTTTATCGTCTCATCTGAT 59.736 38.462 0.00 0.00 0.00 2.90
240 241 6.920758 GTGTAGCTTTATCGTCTCATCTGATT 59.079 38.462 0.00 0.00 0.00 2.57
241 242 7.436673 GTGTAGCTTTATCGTCTCATCTGATTT 59.563 37.037 0.00 0.00 0.00 2.17
242 243 8.630037 TGTAGCTTTATCGTCTCATCTGATTTA 58.370 33.333 0.00 0.00 0.00 1.40
243 244 9.123709 GTAGCTTTATCGTCTCATCTGATTTAG 57.876 37.037 0.00 0.00 0.00 1.85
244 245 7.721402 AGCTTTATCGTCTCATCTGATTTAGT 58.279 34.615 0.00 0.00 0.00 2.24
245 246 8.851145 AGCTTTATCGTCTCATCTGATTTAGTA 58.149 33.333 0.00 0.00 0.00 1.82
246 247 8.907685 GCTTTATCGTCTCATCTGATTTAGTAC 58.092 37.037 0.00 0.00 0.00 2.73
251 252 8.678593 TCGTCTCATCTGATTTAGTACTATGT 57.321 34.615 2.79 0.00 0.00 2.29
252 253 8.560374 TCGTCTCATCTGATTTAGTACTATGTG 58.440 37.037 2.79 0.00 0.00 3.21
253 254 8.560374 CGTCTCATCTGATTTAGTACTATGTGA 58.440 37.037 2.79 2.24 0.00 3.58
264 265 9.959721 ATTTAGTACTATGTGAATTCACTTGGT 57.040 29.630 31.78 31.78 46.55 3.67
265 266 9.787435 TTTAGTACTATGTGAATTCACTTGGTT 57.213 29.630 33.23 23.96 46.55 3.67
266 267 9.787435 TTAGTACTATGTGAATTCACTTGGTTT 57.213 29.630 33.23 26.13 46.55 3.27
267 268 8.691661 AGTACTATGTGAATTCACTTGGTTTT 57.308 30.769 33.23 23.57 46.55 2.43
268 269 9.131791 AGTACTATGTGAATTCACTTGGTTTTT 57.868 29.630 33.23 21.88 46.55 1.94
298 300 3.019799 TGGTTCTCTCGATCTAAGCCT 57.980 47.619 0.00 0.00 0.00 4.58
315 317 1.106285 CCTAGGGCATTTGCTTCACC 58.894 55.000 0.00 0.00 41.70 4.02
327 334 1.071987 CTTCACCTGGCTCTGCACA 59.928 57.895 0.00 0.00 0.00 4.57
341 348 3.070429 CTGCACAACAGTGGTTCTTTC 57.930 47.619 0.00 0.00 41.86 2.62
342 349 1.748493 TGCACAACAGTGGTTCTTTCC 59.252 47.619 0.00 0.00 34.21 3.13
343 350 1.748493 GCACAACAGTGGTTCTTTCCA 59.252 47.619 0.00 0.00 34.21 3.53
344 351 2.362077 GCACAACAGTGGTTCTTTCCAT 59.638 45.455 0.00 0.00 39.81 3.41
345 352 3.550842 GCACAACAGTGGTTCTTTCCATC 60.551 47.826 0.00 0.00 39.81 3.51
346 353 3.885297 CACAACAGTGGTTCTTTCCATCT 59.115 43.478 0.00 0.00 39.81 2.90
347 354 3.885297 ACAACAGTGGTTCTTTCCATCTG 59.115 43.478 0.00 0.00 39.81 2.90
348 355 4.136796 CAACAGTGGTTCTTTCCATCTGA 58.863 43.478 16.03 0.00 39.81 3.27
349 356 3.744660 ACAGTGGTTCTTTCCATCTGAC 58.255 45.455 16.03 0.00 39.81 3.51
350 357 3.077359 CAGTGGTTCTTTCCATCTGACC 58.923 50.000 0.00 0.00 39.81 4.02
351 358 2.982488 AGTGGTTCTTTCCATCTGACCT 59.018 45.455 0.00 0.00 39.81 3.85
352 359 3.077359 GTGGTTCTTTCCATCTGACCTG 58.923 50.000 0.00 0.00 39.81 4.00
353 360 2.978978 TGGTTCTTTCCATCTGACCTGA 59.021 45.455 0.00 0.00 31.96 3.86
469 480 2.256158 CCGCACGTCACGACCTTA 59.744 61.111 2.91 0.00 0.00 2.69
471 482 1.081641 CGCACGTCACGACCTTAGT 60.082 57.895 2.91 0.00 0.00 2.24
472 483 0.662374 CGCACGTCACGACCTTAGTT 60.662 55.000 2.91 0.00 0.00 2.24
479 496 5.005586 CACGTCACGACCTTAGTTACAAAAA 59.994 40.000 2.91 0.00 0.00 1.94
635 886 4.152625 GCGACACATGGCACGCTC 62.153 66.667 19.55 0.00 46.06 5.03
636 887 3.490759 CGACACATGGCACGCTCC 61.491 66.667 0.00 0.00 0.00 4.70
637 888 3.490759 GACACATGGCACGCTCCG 61.491 66.667 0.00 0.00 0.00 4.63
638 889 3.932580 GACACATGGCACGCTCCGA 62.933 63.158 0.00 0.00 0.00 4.55
739 992 1.088340 CCGCAATGGTCAGAGCAGAG 61.088 60.000 8.56 4.24 0.00 3.35
924 1187 1.004862 GCTCTTTTTAGCCCCCACTCT 59.995 52.381 0.00 0.00 36.45 3.24
926 1189 1.633945 TCTTTTTAGCCCCCACTCTCC 59.366 52.381 0.00 0.00 0.00 3.71
932 1195 4.715130 CCCCCACTCTCCCCACGA 62.715 72.222 0.00 0.00 0.00 4.35
933 1196 3.391382 CCCCACTCTCCCCACGAC 61.391 72.222 0.00 0.00 0.00 4.34
934 1197 2.283966 CCCACTCTCCCCACGACT 60.284 66.667 0.00 0.00 0.00 4.18
936 1199 2.352032 CCACTCTCCCCACGACTCC 61.352 68.421 0.00 0.00 0.00 3.85
938 1201 2.360980 CTCTCCCCACGACTCCCT 59.639 66.667 0.00 0.00 0.00 4.20
942 1205 3.450115 CCCCACGACTCCCTCGAC 61.450 72.222 0.00 0.00 46.14 4.20
943 1206 2.675423 CCCACGACTCCCTCGACA 60.675 66.667 0.00 0.00 46.14 4.35
944 1207 2.273179 CCCACGACTCCCTCGACAA 61.273 63.158 0.00 0.00 46.14 3.18
945 1208 1.663739 CCACGACTCCCTCGACAAA 59.336 57.895 0.00 0.00 46.14 2.83
946 1209 0.388649 CCACGACTCCCTCGACAAAG 60.389 60.000 0.00 0.00 46.14 2.77
947 1210 0.314302 CACGACTCCCTCGACAAAGT 59.686 55.000 0.00 0.00 46.14 2.66
978 1269 1.137825 GACTCCGACCAAGAGCTCG 59.862 63.158 8.37 0.00 34.56 5.03
994 1285 3.094058 CGAGCGCCGATCATCGTC 61.094 66.667 2.29 0.00 41.76 4.20
1018 1320 0.035056 CATGGTGAGGTCCAACTCCC 60.035 60.000 0.00 0.00 41.09 4.30
1079 1393 2.509964 GGTACCTTCCACTTCCATCCAT 59.490 50.000 4.06 0.00 0.00 3.41
1141 1459 2.820059 TTGGCGATTCATAGCTCGAT 57.180 45.000 0.00 0.00 37.05 3.59
1144 1462 3.466836 TGGCGATTCATAGCTCGATTTT 58.533 40.909 0.00 0.00 37.05 1.82
1145 1463 3.494626 TGGCGATTCATAGCTCGATTTTC 59.505 43.478 0.00 0.00 37.05 2.29
1361 1681 3.706373 GGACCTGGCGCCTCTTCA 61.706 66.667 29.70 5.44 0.00 3.02
1597 1923 2.801631 CGATCCCCCTCCTGCTGAC 61.802 68.421 0.00 0.00 0.00 3.51
1657 1994 8.149647 TGCTGAATTTTGTTCCTTTGTTCATAT 58.850 29.630 0.00 0.00 0.00 1.78
1666 2003 6.775142 TGTTCCTTTGTTCATATTGGAAGACA 59.225 34.615 0.00 0.00 34.73 3.41
1726 2063 8.161425 ACTATAGTTTTTGTGTCCTGGTAATGT 58.839 33.333 0.00 0.00 0.00 2.71
1765 2102 6.036470 GCAATTTTGAGCCACCTAGTATTTC 58.964 40.000 0.00 0.00 0.00 2.17
1802 2140 3.525268 AGCTTTCTGTGTGGGTTTTTG 57.475 42.857 0.00 0.00 0.00 2.44
1914 2252 7.201758 GGCTGACAAGATAAATTCATGTGATGA 60.202 37.037 0.00 0.00 36.45 2.92
1975 2318 0.721718 GTCAACTCGCTGGGAATTCG 59.278 55.000 0.00 0.00 0.00 3.34
2019 2362 1.376553 GCAGTCAAGGCTCCAGGTC 60.377 63.158 0.00 0.00 0.00 3.85
2058 2435 4.600062 ACCCCAGTTAATCAGTTGGATTC 58.400 43.478 0.00 0.00 42.62 2.52
2059 2439 4.044065 ACCCCAGTTAATCAGTTGGATTCA 59.956 41.667 0.00 0.00 42.62 2.57
2064 2444 6.406177 CCAGTTAATCAGTTGGATTCAATGGG 60.406 42.308 8.90 0.00 45.19 4.00
2065 2445 6.377996 CAGTTAATCAGTTGGATTCAATGGGA 59.622 38.462 0.00 0.00 42.62 4.37
2066 2446 6.378280 AGTTAATCAGTTGGATTCAATGGGAC 59.622 38.462 0.00 0.00 42.62 4.46
2067 2447 4.598036 ATCAGTTGGATTCAATGGGACT 57.402 40.909 0.00 0.00 35.10 3.85
2086 2466 5.535030 GGGACTAGAAACACCATTTTTCTGT 59.465 40.000 0.00 4.36 42.15 3.41
2092 2472 6.706295 AGAAACACCATTTTTCTGTTCCAAA 58.294 32.000 0.00 0.00 40.93 3.28
2114 2495 6.453926 AAAAATTGGATATGCAAAATGCCC 57.546 33.333 14.00 0.00 44.23 5.36
2122 2584 5.405269 GGATATGCAAAATGCCCGTTATTTC 59.595 40.000 0.00 0.00 44.23 2.17
2129 2591 4.718940 AATGCCCGTTATTTCCTTTCTG 57.281 40.909 0.00 0.00 0.00 3.02
2134 2596 3.254657 CCCGTTATTTCCTTTCTGTGCAA 59.745 43.478 0.00 0.00 0.00 4.08
2140 2602 4.572985 TTTCCTTTCTGTGCAATGAGTG 57.427 40.909 0.00 0.00 0.00 3.51
2153 2615 5.575606 GTGCAATGAGTGAATCTGGAAATTG 59.424 40.000 0.00 0.00 0.00 2.32
2230 2692 6.415573 AGTACAAATGTCAGTTTCCCCTATC 58.584 40.000 0.00 0.00 0.00 2.08
2231 2693 5.520748 ACAAATGTCAGTTTCCCCTATCT 57.479 39.130 0.00 0.00 0.00 1.98
2373 2837 3.754965 TGCTTCAAGTGGCTATTGAGTT 58.245 40.909 5.37 0.00 37.91 3.01
2460 2924 4.746309 TCATGCCCTGCACCTGCC 62.746 66.667 0.00 0.00 43.04 4.85
2516 2980 1.693606 CCAACCTCCAACCTGCAAAAT 59.306 47.619 0.00 0.00 0.00 1.82
2519 2983 3.525800 ACCTCCAACCTGCAAAATAGT 57.474 42.857 0.00 0.00 0.00 2.12
2520 2984 3.844640 ACCTCCAACCTGCAAAATAGTT 58.155 40.909 0.00 0.00 0.00 2.24
2522 2986 5.390387 ACCTCCAACCTGCAAAATAGTTAA 58.610 37.500 0.00 0.00 0.00 2.01
2525 2990 5.778862 TCCAACCTGCAAAATAGTTAAAGC 58.221 37.500 0.00 0.00 0.00 3.51
2535 3000 9.920133 TGCAAAATAGTTAAAGCATTTGATGTA 57.080 25.926 0.00 0.00 39.63 2.29
2546 3011 7.801547 AAGCATTTGATGTAAGATTGAAACG 57.198 32.000 0.00 0.00 0.00 3.60
2548 3013 6.071952 AGCATTTGATGTAAGATTGAAACGGT 60.072 34.615 0.00 0.00 0.00 4.83
2551 3016 6.869315 TTGATGTAAGATTGAAACGGTTCA 57.131 33.333 12.93 12.93 42.12 3.18
2556 3021 7.129109 TGTAAGATTGAAACGGTTCATTCTC 57.871 36.000 30.44 22.33 46.43 2.87
2582 3047 7.359598 CGGACAGAATTTTCTCAGTTTAGTGAG 60.360 40.741 8.04 8.04 44.71 3.51
2595 3060 8.319143 TCAGTTTAGTGAGTAACTATTTTGGC 57.681 34.615 0.00 0.00 41.10 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.057315 ACAATTTGAGTTCGGCCAGAATG 60.057 43.478 2.24 3.74 41.49 2.67
8 9 3.157087 ACAATTTGAGTTCGGCCAGAAT 58.843 40.909 2.24 0.00 41.49 2.40
9 10 2.582052 ACAATTTGAGTTCGGCCAGAA 58.418 42.857 2.24 4.57 36.31 3.02
10 11 2.270352 ACAATTTGAGTTCGGCCAGA 57.730 45.000 2.24 0.00 0.00 3.86
11 12 2.607771 CCAACAATTTGAGTTCGGCCAG 60.608 50.000 2.24 0.00 34.24 4.85
12 13 1.339610 CCAACAATTTGAGTTCGGCCA 59.660 47.619 2.24 0.00 34.24 5.36
13 14 1.934849 GCCAACAATTTGAGTTCGGCC 60.935 52.381 2.79 0.00 34.24 6.13
14 15 1.269517 TGCCAACAATTTGAGTTCGGC 60.270 47.619 2.79 7.66 38.79 5.54
15 16 2.034558 AGTGCCAACAATTTGAGTTCGG 59.965 45.455 2.79 0.00 34.24 4.30
16 17 3.354089 AGTGCCAACAATTTGAGTTCG 57.646 42.857 2.79 0.00 34.24 3.95
17 18 6.072112 TCTTAGTGCCAACAATTTGAGTTC 57.928 37.500 2.79 0.00 34.24 3.01
18 19 6.655078 ATCTTAGTGCCAACAATTTGAGTT 57.345 33.333 2.79 0.00 34.24 3.01
19 20 6.375455 CCTATCTTAGTGCCAACAATTTGAGT 59.625 38.462 2.79 0.00 34.24 3.41
20 21 6.375455 ACCTATCTTAGTGCCAACAATTTGAG 59.625 38.462 2.79 0.00 34.24 3.02
21 22 6.245408 ACCTATCTTAGTGCCAACAATTTGA 58.755 36.000 2.79 0.00 34.24 2.69
22 23 6.515272 ACCTATCTTAGTGCCAACAATTTG 57.485 37.500 0.00 0.00 0.00 2.32
23 24 6.071391 CCAACCTATCTTAGTGCCAACAATTT 60.071 38.462 0.00 0.00 0.00 1.82
24 25 5.418840 CCAACCTATCTTAGTGCCAACAATT 59.581 40.000 0.00 0.00 0.00 2.32
25 26 4.949856 CCAACCTATCTTAGTGCCAACAAT 59.050 41.667 0.00 0.00 0.00 2.71
26 27 4.202524 ACCAACCTATCTTAGTGCCAACAA 60.203 41.667 0.00 0.00 0.00 2.83
27 28 3.329520 ACCAACCTATCTTAGTGCCAACA 59.670 43.478 0.00 0.00 0.00 3.33
28 29 3.951663 ACCAACCTATCTTAGTGCCAAC 58.048 45.455 0.00 0.00 0.00 3.77
29 30 4.585879 GAACCAACCTATCTTAGTGCCAA 58.414 43.478 0.00 0.00 0.00 4.52
30 31 3.369052 CGAACCAACCTATCTTAGTGCCA 60.369 47.826 0.00 0.00 0.00 4.92
31 32 3.195661 CGAACCAACCTATCTTAGTGCC 58.804 50.000 0.00 0.00 0.00 5.01
32 33 3.858247 ACGAACCAACCTATCTTAGTGC 58.142 45.455 0.00 0.00 0.00 4.40
33 34 4.081862 TGGACGAACCAACCTATCTTAGTG 60.082 45.833 3.90 0.00 46.75 2.74
34 35 4.091549 TGGACGAACCAACCTATCTTAGT 58.908 43.478 3.90 0.00 46.75 2.24
35 36 4.730949 TGGACGAACCAACCTATCTTAG 57.269 45.455 3.90 0.00 46.75 2.18
47 48 5.527214 TGATGATCAATTACATGGACGAACC 59.473 40.000 0.00 0.00 39.54 3.62
48 49 6.037062 TGTGATGATCAATTACATGGACGAAC 59.963 38.462 0.00 0.00 30.26 3.95
49 50 6.112058 TGTGATGATCAATTACATGGACGAA 58.888 36.000 0.00 0.00 30.26 3.85
50 51 5.669477 TGTGATGATCAATTACATGGACGA 58.331 37.500 0.00 0.00 30.26 4.20
51 52 5.989551 TGTGATGATCAATTACATGGACG 57.010 39.130 0.00 0.00 30.26 4.79
52 53 7.012610 TGTGATGTGATGATCAATTACATGGAC 59.987 37.037 20.64 17.15 43.52 4.02
53 54 7.055378 TGTGATGTGATGATCAATTACATGGA 58.945 34.615 20.64 9.49 43.52 3.41
54 55 7.266922 TGTGATGTGATGATCAATTACATGG 57.733 36.000 20.64 0.00 43.52 3.66
55 56 8.784043 AGATGTGATGTGATGATCAATTACATG 58.216 33.333 20.93 0.00 43.52 3.21
56 57 8.919777 AGATGTGATGTGATGATCAATTACAT 57.080 30.769 18.38 18.38 45.49 2.29
57 58 8.741603 AAGATGTGATGTGATGATCAATTACA 57.258 30.769 0.00 6.00 38.95 2.41
60 61 9.794719 AGATAAGATGTGATGTGATGATCAATT 57.205 29.630 0.00 0.00 34.11 2.32
61 62 9.794719 AAGATAAGATGTGATGTGATGATCAAT 57.205 29.630 0.00 0.00 34.11 2.57
63 64 9.702494 GTAAGATAAGATGTGATGTGATGATCA 57.298 33.333 0.00 0.00 0.00 2.92
64 65 9.926158 AGTAAGATAAGATGTGATGTGATGATC 57.074 33.333 0.00 0.00 0.00 2.92
76 77 9.810545 GCAACTTCTTCTAGTAAGATAAGATGT 57.189 33.333 8.55 6.02 34.17 3.06
83 84 9.196139 AGATGTAGCAACTTCTTCTAGTAAGAT 57.804 33.333 8.55 0.00 36.91 2.40
84 85 8.462811 CAGATGTAGCAACTTCTTCTAGTAAGA 58.537 37.037 8.55 5.30 37.87 2.10
85 86 8.247562 ACAGATGTAGCAACTTCTTCTAGTAAG 58.752 37.037 0.00 0.00 37.87 2.34
86 87 8.123639 ACAGATGTAGCAACTTCTTCTAGTAA 57.876 34.615 0.00 0.00 37.87 2.24
87 88 7.704578 ACAGATGTAGCAACTTCTTCTAGTA 57.295 36.000 0.00 0.00 37.87 1.82
88 89 6.597832 ACAGATGTAGCAACTTCTTCTAGT 57.402 37.500 0.00 0.00 37.87 2.57
89 90 6.533367 GGAACAGATGTAGCAACTTCTTCTAG 59.467 42.308 0.00 0.00 37.87 2.43
90 91 6.211584 AGGAACAGATGTAGCAACTTCTTCTA 59.788 38.462 0.00 0.00 37.87 2.10
91 92 5.012561 AGGAACAGATGTAGCAACTTCTTCT 59.987 40.000 0.00 0.00 37.87 2.85
92 93 5.241662 AGGAACAGATGTAGCAACTTCTTC 58.758 41.667 0.00 0.00 37.87 2.87
93 94 5.234466 AGGAACAGATGTAGCAACTTCTT 57.766 39.130 0.00 0.00 37.87 2.52
94 95 4.899352 AGGAACAGATGTAGCAACTTCT 57.101 40.909 0.00 0.00 39.91 2.85
95 96 7.617041 ATTTAGGAACAGATGTAGCAACTTC 57.383 36.000 0.00 0.00 0.00 3.01
100 101 9.982651 GACTTATATTTAGGAACAGATGTAGCA 57.017 33.333 0.00 0.00 0.00 3.49
101 102 9.982651 TGACTTATATTTAGGAACAGATGTAGC 57.017 33.333 0.00 0.00 0.00 3.58
136 137 9.352163 CGTTTTTGCAGTTCAATTTACATAAAC 57.648 29.630 0.00 0.00 34.12 2.01
137 138 9.088512 ACGTTTTTGCAGTTCAATTTACATAAA 57.911 25.926 0.00 0.00 34.12 1.40
138 139 8.635877 ACGTTTTTGCAGTTCAATTTACATAA 57.364 26.923 0.00 0.00 34.12 1.90
139 140 8.132362 AGACGTTTTTGCAGTTCAATTTACATA 58.868 29.630 0.00 0.00 34.12 2.29
140 141 6.978080 AGACGTTTTTGCAGTTCAATTTACAT 59.022 30.769 0.00 0.00 34.12 2.29
141 142 6.326375 AGACGTTTTTGCAGTTCAATTTACA 58.674 32.000 0.00 0.00 34.12 2.41
142 143 6.806120 AGACGTTTTTGCAGTTCAATTTAC 57.194 33.333 0.00 0.00 34.12 2.01
144 145 9.691362 ATATAAGACGTTTTTGCAGTTCAATTT 57.309 25.926 0.00 0.00 34.12 1.82
145 146 9.691362 AATATAAGACGTTTTTGCAGTTCAATT 57.309 25.926 0.00 0.00 34.12 2.32
148 149 9.820229 CTTAATATAAGACGTTTTTGCAGTTCA 57.180 29.630 0.00 0.00 0.00 3.18
149 150 9.274065 CCTTAATATAAGACGTTTTTGCAGTTC 57.726 33.333 0.00 0.00 0.00 3.01
150 151 9.005777 TCCTTAATATAAGACGTTTTTGCAGTT 57.994 29.630 0.00 0.00 0.00 3.16
151 152 8.556213 TCCTTAATATAAGACGTTTTTGCAGT 57.444 30.769 0.00 0.00 0.00 4.40
167 168 8.830741 CCCTCTGTTCCTGAATATCCTTAATAT 58.169 37.037 0.00 0.00 31.56 1.28
168 169 7.794683 ACCCTCTGTTCCTGAATATCCTTAATA 59.205 37.037 0.00 0.00 0.00 0.98
169 170 6.621514 ACCCTCTGTTCCTGAATATCCTTAAT 59.378 38.462 0.00 0.00 0.00 1.40
170 171 5.970640 ACCCTCTGTTCCTGAATATCCTTAA 59.029 40.000 0.00 0.00 0.00 1.85
171 172 5.366768 CACCCTCTGTTCCTGAATATCCTTA 59.633 44.000 0.00 0.00 0.00 2.69
172 173 4.164988 CACCCTCTGTTCCTGAATATCCTT 59.835 45.833 0.00 0.00 0.00 3.36
173 174 3.713764 CACCCTCTGTTCCTGAATATCCT 59.286 47.826 0.00 0.00 0.00 3.24
174 175 3.456277 ACACCCTCTGTTCCTGAATATCC 59.544 47.826 0.00 0.00 0.00 2.59
175 176 4.762289 ACACCCTCTGTTCCTGAATATC 57.238 45.455 0.00 0.00 0.00 1.63
176 177 5.281314 AGTACACCCTCTGTTCCTGAATAT 58.719 41.667 0.00 0.00 33.91 1.28
177 178 4.684724 AGTACACCCTCTGTTCCTGAATA 58.315 43.478 0.00 0.00 33.91 1.75
178 179 3.521727 AGTACACCCTCTGTTCCTGAAT 58.478 45.455 0.00 0.00 33.91 2.57
179 180 2.972348 AGTACACCCTCTGTTCCTGAA 58.028 47.619 0.00 0.00 33.91 3.02
180 181 2.696526 AGTACACCCTCTGTTCCTGA 57.303 50.000 0.00 0.00 33.91 3.86
181 182 5.422214 AATTAGTACACCCTCTGTTCCTG 57.578 43.478 0.00 0.00 33.91 3.86
182 183 7.014038 CGTATAATTAGTACACCCTCTGTTCCT 59.986 40.741 0.00 0.00 33.91 3.36
183 184 7.144000 CGTATAATTAGTACACCCTCTGTTCC 58.856 42.308 0.00 0.00 33.91 3.62
184 185 6.640092 GCGTATAATTAGTACACCCTCTGTTC 59.360 42.308 0.00 0.00 33.91 3.18
185 186 6.097270 TGCGTATAATTAGTACACCCTCTGTT 59.903 38.462 0.00 0.00 33.91 3.16
186 187 5.595542 TGCGTATAATTAGTACACCCTCTGT 59.404 40.000 0.00 0.00 36.82 3.41
187 188 6.080648 TGCGTATAATTAGTACACCCTCTG 57.919 41.667 0.00 0.00 0.00 3.35
188 189 6.492429 TGATGCGTATAATTAGTACACCCTCT 59.508 38.462 0.00 0.00 0.00 3.69
189 190 6.684686 TGATGCGTATAATTAGTACACCCTC 58.315 40.000 0.00 0.00 0.00 4.30
190 191 6.659745 TGATGCGTATAATTAGTACACCCT 57.340 37.500 0.00 0.00 0.00 4.34
191 192 6.927381 ACTTGATGCGTATAATTAGTACACCC 59.073 38.462 0.00 0.00 0.00 4.61
192 193 7.437267 ACACTTGATGCGTATAATTAGTACACC 59.563 37.037 0.00 0.00 0.00 4.16
193 194 8.348983 ACACTTGATGCGTATAATTAGTACAC 57.651 34.615 0.00 0.00 0.00 2.90
194 195 9.673454 CTACACTTGATGCGTATAATTAGTACA 57.327 33.333 0.00 0.00 0.00 2.90
195 196 8.636843 GCTACACTTGATGCGTATAATTAGTAC 58.363 37.037 0.00 0.00 0.00 2.73
196 197 8.573885 AGCTACACTTGATGCGTATAATTAGTA 58.426 33.333 0.00 0.00 0.00 1.82
197 198 7.434492 AGCTACACTTGATGCGTATAATTAGT 58.566 34.615 0.00 0.00 0.00 2.24
198 199 7.875316 AGCTACACTTGATGCGTATAATTAG 57.125 36.000 0.00 0.00 0.00 1.73
199 200 8.657074 AAAGCTACACTTGATGCGTATAATTA 57.343 30.769 0.00 0.00 39.09 1.40
200 201 7.553881 AAAGCTACACTTGATGCGTATAATT 57.446 32.000 0.00 0.00 39.09 1.40
201 202 8.833231 ATAAAGCTACACTTGATGCGTATAAT 57.167 30.769 0.00 0.00 39.09 1.28
202 203 7.114388 CGATAAAGCTACACTTGATGCGTATAA 59.886 37.037 0.00 0.00 39.09 0.98
203 204 6.581166 CGATAAAGCTACACTTGATGCGTATA 59.419 38.462 0.00 0.00 39.09 1.47
204 205 5.402568 CGATAAAGCTACACTTGATGCGTAT 59.597 40.000 0.00 0.00 39.09 3.06
205 206 4.738252 CGATAAAGCTACACTTGATGCGTA 59.262 41.667 0.00 0.00 39.09 4.42
206 207 3.551890 CGATAAAGCTACACTTGATGCGT 59.448 43.478 0.00 0.00 39.09 5.24
207 208 3.551890 ACGATAAAGCTACACTTGATGCG 59.448 43.478 0.00 0.00 39.09 4.73
208 209 4.806247 AGACGATAAAGCTACACTTGATGC 59.194 41.667 0.00 0.00 39.09 3.91
209 210 6.036470 TGAGACGATAAAGCTACACTTGATG 58.964 40.000 0.00 0.00 39.09 3.07
210 211 6.208988 TGAGACGATAAAGCTACACTTGAT 57.791 37.500 0.00 0.00 39.09 2.57
211 212 5.638596 TGAGACGATAAAGCTACACTTGA 57.361 39.130 0.00 0.00 39.09 3.02
212 213 6.198029 CAGATGAGACGATAAAGCTACACTTG 59.802 42.308 0.00 0.00 39.09 3.16
213 214 6.095580 TCAGATGAGACGATAAAGCTACACTT 59.904 38.462 0.00 0.00 41.70 3.16
214 215 5.590663 TCAGATGAGACGATAAAGCTACACT 59.409 40.000 0.00 0.00 0.00 3.55
215 216 5.822278 TCAGATGAGACGATAAAGCTACAC 58.178 41.667 0.00 0.00 0.00 2.90
216 217 6.641169 ATCAGATGAGACGATAAAGCTACA 57.359 37.500 0.00 0.00 0.00 2.74
217 218 7.938563 AAATCAGATGAGACGATAAAGCTAC 57.061 36.000 0.00 0.00 0.00 3.58
218 219 8.851145 ACTAAATCAGATGAGACGATAAAGCTA 58.149 33.333 0.00 0.00 0.00 3.32
219 220 7.721402 ACTAAATCAGATGAGACGATAAAGCT 58.279 34.615 0.00 0.00 0.00 3.74
220 221 7.938563 ACTAAATCAGATGAGACGATAAAGC 57.061 36.000 0.00 0.00 0.00 3.51
225 226 9.290988 ACATAGTACTAAATCAGATGAGACGAT 57.709 33.333 6.70 0.00 0.00 3.73
226 227 8.560374 CACATAGTACTAAATCAGATGAGACGA 58.440 37.037 6.70 0.00 0.00 4.20
227 228 8.560374 TCACATAGTACTAAATCAGATGAGACG 58.440 37.037 6.70 0.00 0.00 4.18
265 266 6.285224 TCGAGAGAACCATGTCTGTTAAAAA 58.715 36.000 0.00 0.00 37.03 1.94
266 267 5.849510 TCGAGAGAACCATGTCTGTTAAAA 58.150 37.500 0.00 0.00 37.03 1.52
267 268 5.462530 TCGAGAGAACCATGTCTGTTAAA 57.537 39.130 0.00 0.00 37.03 1.52
298 300 1.616725 CCAGGTGAAGCAAATGCCCTA 60.617 52.381 0.94 0.00 43.38 3.53
327 334 4.137543 GTCAGATGGAAAGAACCACTGTT 58.862 43.478 0.00 0.00 43.03 3.16
333 340 3.261897 TCTCAGGTCAGATGGAAAGAACC 59.738 47.826 0.00 0.00 0.00 3.62
338 345 4.161189 GTCAGATCTCAGGTCAGATGGAAA 59.839 45.833 0.00 0.00 32.94 3.13
339 346 3.703556 GTCAGATCTCAGGTCAGATGGAA 59.296 47.826 0.00 0.00 32.94 3.53
340 347 3.295093 GTCAGATCTCAGGTCAGATGGA 58.705 50.000 0.00 0.00 32.94 3.41
341 348 2.364970 GGTCAGATCTCAGGTCAGATGG 59.635 54.545 0.00 0.00 32.94 3.51
342 349 3.029570 TGGTCAGATCTCAGGTCAGATG 58.970 50.000 0.00 0.00 32.94 2.90
343 350 3.395054 TGGTCAGATCTCAGGTCAGAT 57.605 47.619 0.00 0.00 35.70 2.90
344 351 2.907458 TGGTCAGATCTCAGGTCAGA 57.093 50.000 0.00 0.00 0.00 3.27
345 352 4.214310 AGTATGGTCAGATCTCAGGTCAG 58.786 47.826 0.00 0.00 0.00 3.51
346 353 4.256983 AGTATGGTCAGATCTCAGGTCA 57.743 45.455 0.00 0.00 0.00 4.02
347 354 4.404073 ACAAGTATGGTCAGATCTCAGGTC 59.596 45.833 0.00 0.00 0.00 3.85
348 355 4.161189 CACAAGTATGGTCAGATCTCAGGT 59.839 45.833 0.00 0.00 0.00 4.00
349 356 4.442612 CCACAAGTATGGTCAGATCTCAGG 60.443 50.000 0.00 0.00 34.77 3.86
350 357 4.403752 TCCACAAGTATGGTCAGATCTCAG 59.596 45.833 0.00 0.00 40.95 3.35
351 358 4.352893 TCCACAAGTATGGTCAGATCTCA 58.647 43.478 0.00 0.00 40.95 3.27
352 359 5.344743 TTCCACAAGTATGGTCAGATCTC 57.655 43.478 0.00 0.00 40.95 2.75
353 360 5.664908 AGATTCCACAAGTATGGTCAGATCT 59.335 40.000 0.00 0.00 40.95 2.75
468 479 2.291190 GTGCGCTGGGTTTTTGTAACTA 59.709 45.455 9.73 0.00 0.00 2.24
469 480 1.066454 GTGCGCTGGGTTTTTGTAACT 59.934 47.619 9.73 0.00 0.00 2.24
471 482 0.386113 GGTGCGCTGGGTTTTTGTAA 59.614 50.000 9.73 0.00 0.00 2.41
472 483 1.787057 CGGTGCGCTGGGTTTTTGTA 61.787 55.000 9.73 0.00 0.00 2.41
761 1014 2.035237 AATTAATCGGGAGCGCCGGA 62.035 55.000 18.62 18.62 46.07 5.14
931 1194 0.966920 TCCACTTTGTCGAGGGAGTC 59.033 55.000 0.00 0.00 0.00 3.36
932 1195 1.070289 GTTCCACTTTGTCGAGGGAGT 59.930 52.381 0.00 0.00 0.00 3.85
933 1196 1.797025 GTTCCACTTTGTCGAGGGAG 58.203 55.000 0.00 0.00 0.00 4.30
934 1197 0.032952 CGTTCCACTTTGTCGAGGGA 59.967 55.000 0.00 0.00 0.00 4.20
936 1199 0.600255 AGCGTTCCACTTTGTCGAGG 60.600 55.000 0.00 0.00 0.00 4.63
938 1201 0.599204 GGAGCGTTCCACTTTGTCGA 60.599 55.000 14.14 0.00 43.45 4.20
942 1205 2.325082 CGGGGAGCGTTCCACTTTG 61.325 63.158 19.09 0.00 45.38 2.77
943 1206 2.032071 CGGGGAGCGTTCCACTTT 59.968 61.111 19.09 0.00 45.38 2.66
944 1207 2.920912 TCGGGGAGCGTTCCACTT 60.921 61.111 19.09 0.00 45.38 3.16
945 1208 3.692406 GTCGGGGAGCGTTCCACT 61.692 66.667 19.09 0.00 45.38 4.00
946 1209 3.644399 GAGTCGGGGAGCGTTCCAC 62.644 68.421 20.67 16.22 45.98 4.02
947 1210 3.379445 GAGTCGGGGAGCGTTCCA 61.379 66.667 20.67 0.00 45.98 3.53
967 1258 4.443266 GGCGCTCGAGCTCTTGGT 62.443 66.667 32.88 0.00 39.32 3.67
989 1280 1.676678 CCTCACCATGGACGGACGAT 61.677 60.000 21.47 0.00 0.00 3.73
994 1285 1.836999 TTGGACCTCACCATGGACGG 61.837 60.000 21.47 17.03 39.82 4.79
1018 1320 0.380378 GAGGAGTAGCAGCTGTCGAG 59.620 60.000 16.64 0.00 0.00 4.04
1068 1370 0.257039 GTGGAGGCATGGATGGAAGT 59.743 55.000 0.00 0.00 0.00 3.01
1079 1393 2.583441 CGGTGGAGAAGTGGAGGCA 61.583 63.158 0.00 0.00 0.00 4.75
1114 1432 4.214971 AGCTATGAATCGCCAATCATTGAC 59.785 41.667 0.00 0.00 37.46 3.18
1115 1433 4.392047 AGCTATGAATCGCCAATCATTGA 58.608 39.130 0.00 0.00 37.46 2.57
1128 1446 9.512435 CAAATGAAAGAAAATCGAGCTATGAAT 57.488 29.630 0.00 0.00 0.00 2.57
1141 1459 4.992319 CCATCAGCAGCAAATGAAAGAAAA 59.008 37.500 8.27 0.00 0.00 2.29
1144 1462 2.094390 GCCATCAGCAGCAAATGAAAGA 60.094 45.455 8.27 0.00 42.97 2.52
1145 1463 2.268298 GCCATCAGCAGCAAATGAAAG 58.732 47.619 8.27 0.00 42.97 2.62
1222 1542 1.523938 GTACTTGGAGCCGATGCCC 60.524 63.158 0.00 0.00 38.69 5.36
1528 1854 3.300013 AGGTAGTTCCTGCGCCTC 58.700 61.111 4.18 0.00 46.19 4.70
1546 1872 4.957684 AGCGCGCCGATCCTGATG 62.958 66.667 30.33 0.00 0.00 3.07
1585 1911 2.612115 AAGGGGTCAGCAGGAGGG 60.612 66.667 0.00 0.00 0.00 4.30
1597 1923 8.859090 GTCATATCATATCATAGAGAGAAGGGG 58.141 40.741 0.00 0.00 0.00 4.79
1657 1994 1.352083 CTCTGGGGTCTGTCTTCCAA 58.648 55.000 0.00 0.00 0.00 3.53
1666 2003 2.057922 ACACATCAAACTCTGGGGTCT 58.942 47.619 0.00 0.00 0.00 3.85
1726 2063 2.512692 ATTGCAACCATGGCTCACTA 57.487 45.000 13.04 0.00 0.00 2.74
1765 2102 7.066766 ACAGAAAGCTAGAATTAAGCCATTGAG 59.933 37.037 8.31 3.49 41.02 3.02
1935 2278 8.454106 GTTGACTGCATACAAGAACTGATATTT 58.546 33.333 6.05 0.00 0.00 1.40
1937 2280 7.334090 AGTTGACTGCATACAAGAACTGATAT 58.666 34.615 6.05 0.00 0.00 1.63
1938 2281 6.701340 AGTTGACTGCATACAAGAACTGATA 58.299 36.000 6.05 0.00 0.00 2.15
1975 2318 4.220602 ACCTTAATGTTGTGCTCCAATTCC 59.779 41.667 0.00 0.00 35.02 3.01
2019 2362 1.453155 GGTACTGGTTGCATGGACTG 58.547 55.000 0.00 0.00 0.00 3.51
2058 2435 5.982890 AAATGGTGTTTCTAGTCCCATTG 57.017 39.130 3.20 0.00 43.30 2.82
2059 2439 6.782494 AGAAAAATGGTGTTTCTAGTCCCATT 59.218 34.615 0.00 0.00 45.39 3.16
2064 2444 7.139392 GGAACAGAAAAATGGTGTTTCTAGTC 58.861 38.462 0.00 1.31 42.15 2.59
2065 2445 6.605594 TGGAACAGAAAAATGGTGTTTCTAGT 59.394 34.615 0.00 0.00 42.15 2.57
2066 2446 7.038154 TGGAACAGAAAAATGGTGTTTCTAG 57.962 36.000 0.00 0.00 42.15 2.43
2067 2447 7.411486 TTGGAACAGAAAAATGGTGTTTCTA 57.589 32.000 0.00 0.00 42.15 2.10
2114 2495 5.698832 TCATTGCACAGAAAGGAAATAACG 58.301 37.500 0.00 0.00 0.00 3.18
2122 2584 4.458295 AGATTCACTCATTGCACAGAAAGG 59.542 41.667 0.00 0.00 0.00 3.11
2129 2591 4.771590 TTTCCAGATTCACTCATTGCAC 57.228 40.909 0.00 0.00 0.00 4.57
2134 2596 8.105829 AGAAGTACAATTTCCAGATTCACTCAT 58.894 33.333 0.00 0.00 0.00 2.90
2303 2765 7.447374 TCATATTCACCGTTTTCACATTCTT 57.553 32.000 0.00 0.00 0.00 2.52
2305 2767 8.687824 AAATCATATTCACCGTTTTCACATTC 57.312 30.769 0.00 0.00 0.00 2.67
2306 2768 9.139174 GAAAATCATATTCACCGTTTTCACATT 57.861 29.630 0.00 0.00 36.25 2.71
2307 2769 7.484641 CGAAAATCATATTCACCGTTTTCACAT 59.515 33.333 0.00 0.00 36.09 3.21
2310 2772 6.904498 ACGAAAATCATATTCACCGTTTTCA 58.096 32.000 0.00 0.00 36.09 2.69
2311 2773 8.173130 ACTACGAAAATCATATTCACCGTTTTC 58.827 33.333 0.00 0.00 34.14 2.29
2373 2837 1.003839 GAAGGACACACCGATGCCA 60.004 57.895 0.00 0.00 44.74 4.92
2460 2924 0.109412 GACTAACCCTCGTCACCGTG 60.109 60.000 0.00 0.00 35.01 4.94
2520 2984 9.340695 CGTTTCAATCTTACATCAAATGCTTTA 57.659 29.630 0.00 0.00 0.00 1.85
2522 2986 6.808212 CCGTTTCAATCTTACATCAAATGCTT 59.192 34.615 0.00 0.00 0.00 3.91
2525 2990 7.807433 TGAACCGTTTCAATCTTACATCAAATG 59.193 33.333 0.00 0.00 38.87 2.32
2540 3005 2.224090 TGTCCGAGAATGAACCGTTTCA 60.224 45.455 0.00 0.00 45.93 2.69
2556 3021 6.423905 TCACTAAACTGAGAAAATTCTGTCCG 59.576 38.462 0.00 0.00 37.73 4.79
2572 3037 7.156673 TCGCCAAAATAGTTACTCACTAAACT 58.843 34.615 0.00 0.00 41.56 2.66
2573 3038 7.355332 TCGCCAAAATAGTTACTCACTAAAC 57.645 36.000 0.00 0.00 41.56 2.01
2582 3047 3.119743 GGTGGGTTCGCCAAAATAGTTAC 60.120 47.826 0.00 0.00 42.90 2.50
2593 3058 3.282374 ATGGGAAGGTGGGTTCGCC 62.282 63.158 0.00 0.00 43.69 5.54
2595 3060 4.319133 CATGGGAAGGTGGGTTCG 57.681 61.111 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.