Multiple sequence alignment - TraesCS3D01G325000

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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 TraesCS3D01G325000 chr3D 100.000 3155 0 0 1 3155 437780428 437777274 0.000000e+00 5827.0
1 TraesCS3D01G325000 chr3D 95.556 90 4 0 88 177 12881655 12881744 9.120000e-31 145.0
2 TraesCS3D01G325000 chr3D 100.000 32 0 0 478 509 437779920 437779889 3.400000e-05 60.2
3 TraesCS3D01G325000 chr3D 100.000 32 0 0 509 540 437779951 437779920 3.400000e-05 60.2
4 TraesCS3D01G325000 chr3B 94.899 2666 74 27 509 3155 572937403 572934781 0.000000e+00 4113.0
5 TraesCS3D01G325000 chr3B 88.015 267 29 2 243 509 572937635 572937372 2.360000e-81 313.0
6 TraesCS3D01G325000 chr3B 91.667 72 6 0 175 246 572937457 572937386 2.000000e-17 100.0
7 TraesCS3D01G325000 chr3A 94.771 2161 58 29 307 2444 575949696 575947568 0.000000e+00 3314.0
8 TraesCS3D01G325000 chr3A 92.533 683 24 13 2487 3155 575947566 575946897 0.000000e+00 953.0
9 TraesCS3D01G325000 chr1D 90.655 1038 92 5 1032 2067 406973064 406974098 0.000000e+00 1375.0
10 TraesCS3D01G325000 chr1A 90.462 1038 94 5 1032 2067 502677765 502678799 0.000000e+00 1363.0
11 TraesCS3D01G325000 chr1B 90.077 1038 98 5 1032 2067 547281831 547282865 0.000000e+00 1341.0
12 TraesCS3D01G325000 chr5A 84.328 938 124 20 1064 1985 308376760 308375830 0.000000e+00 896.0
13 TraesCS3D01G325000 chr5A 96.667 90 3 0 90 179 674574280 674574369 1.960000e-32 150.0
14 TraesCS3D01G325000 chr5D 83.767 961 135 17 1040 1985 243219947 243220901 0.000000e+00 891.0
15 TraesCS3D01G325000 chr5D 95.556 90 4 0 88 177 452693779 452693868 9.120000e-31 145.0
16 TraesCS3D01G325000 chr5B 83.974 936 129 18 1064 1984 255200455 255199526 0.000000e+00 878.0
17 TraesCS3D01G325000 chr7A 97.727 88 2 0 89 176 63791611 63791698 5.450000e-33 152.0
18 TraesCS3D01G325000 chr7A 92.000 100 7 1 81 180 726647411 726647313 4.240000e-29 139.0
19 TraesCS3D01G325000 chr4B 90.598 117 7 4 66 180 634342661 634342547 5.450000e-33 152.0
20 TraesCS3D01G325000 chr6B 93.939 99 4 2 79 176 679569158 679569255 7.050000e-32 148.0
21 TraesCS3D01G325000 chr2D 95.556 90 4 0 87 176 188886174 188886085 9.120000e-31 145.0
22 TraesCS3D01G325000 chr7B 92.079 101 6 2 82 180 569948409 569948509 1.180000e-29 141.0


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 TraesCS3D01G325000 chr3D 437777274 437780428 3154 True 1982.466667 5827 100.000 1 3155 3 chr3D.!!$R1 3154
1 TraesCS3D01G325000 chr3B 572934781 572937635 2854 True 1508.666667 4113 91.527 175 3155 3 chr3B.!!$R1 2980
2 TraesCS3D01G325000 chr3A 575946897 575949696 2799 True 2133.500000 3314 93.652 307 3155 2 chr3A.!!$R1 2848
3 TraesCS3D01G325000 chr1D 406973064 406974098 1034 False 1375.000000 1375 90.655 1032 2067 1 chr1D.!!$F1 1035
4 TraesCS3D01G325000 chr1A 502677765 502678799 1034 False 1363.000000 1363 90.462 1032 2067 1 chr1A.!!$F1 1035
5 TraesCS3D01G325000 chr1B 547281831 547282865 1034 False 1341.000000 1341 90.077 1032 2067 1 chr1B.!!$F1 1035
6 TraesCS3D01G325000 chr5A 308375830 308376760 930 True 896.000000 896 84.328 1064 1985 1 chr5A.!!$R1 921
7 TraesCS3D01G325000 chr5D 243219947 243220901 954 False 891.000000 891 83.767 1040 1985 1 chr5D.!!$F1 945
8 TraesCS3D01G325000 chr5B 255199526 255200455 929 True 878.000000 878 83.974 1064 1984 1 chr5B.!!$R1 920

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
259 260 0.030235 TCGTGAGTTGAGTGTGTCGG 59.970 55.0 0.0 0.0 0.0 4.79 F
840 846 0.396417 CAAGAAACCCACACCCACCA 60.396 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2119 0.313987 TGTTGGATCGGATCGGATCG 59.686 55.0 27.38 9.46 43.00 3.69 R
2377 2413 0.028505 ACTCGATGCAATGCGAATGC 59.971 50.0 0.00 1.61 44.08 3.56 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 2.722201 GGCCTCGGAGTCGGTGAAT 61.722 63.158 4.02 0.00 36.95 2.57
19 20 1.389609 GGCCTCGGAGTCGGTGAATA 61.390 60.000 4.02 0.00 36.95 1.75
20 21 0.030908 GCCTCGGAGTCGGTGAATAG 59.969 60.000 4.02 0.00 36.95 1.73
21 22 1.676746 CCTCGGAGTCGGTGAATAGA 58.323 55.000 4.02 0.00 36.95 1.98
22 23 1.604755 CCTCGGAGTCGGTGAATAGAG 59.395 57.143 4.02 0.00 36.95 2.43
23 24 1.002251 CTCGGAGTCGGTGAATAGAGC 60.002 57.143 0.00 0.00 36.95 4.09
24 25 0.317103 CGGAGTCGGTGAATAGAGCG 60.317 60.000 0.00 0.00 38.19 5.03
25 26 0.595310 GGAGTCGGTGAATAGAGCGC 60.595 60.000 0.00 0.00 36.78 5.92
26 27 0.930742 GAGTCGGTGAATAGAGCGCG 60.931 60.000 0.00 0.00 36.78 6.86
27 28 1.944676 GTCGGTGAATAGAGCGCGG 60.945 63.158 8.83 0.00 36.78 6.46
28 29 2.116533 TCGGTGAATAGAGCGCGGA 61.117 57.895 8.83 0.00 36.78 5.54
29 30 1.007271 CGGTGAATAGAGCGCGGAT 60.007 57.895 8.83 0.00 0.00 4.18
30 31 1.278172 CGGTGAATAGAGCGCGGATG 61.278 60.000 8.83 0.00 0.00 3.51
31 32 0.946221 GGTGAATAGAGCGCGGATGG 60.946 60.000 8.83 0.00 0.00 3.51
32 33 0.032130 GTGAATAGAGCGCGGATGGA 59.968 55.000 8.83 0.00 0.00 3.41
33 34 0.315251 TGAATAGAGCGCGGATGGAG 59.685 55.000 8.83 0.00 0.00 3.86
34 35 0.389166 GAATAGAGCGCGGATGGAGG 60.389 60.000 8.83 0.00 0.00 4.30
35 36 2.441822 AATAGAGCGCGGATGGAGGC 62.442 60.000 8.83 0.00 0.00 4.70
56 57 4.473520 CTCATCCGCAACCCCGCT 62.474 66.667 0.00 0.00 0.00 5.52
57 58 4.776322 TCATCCGCAACCCCGCTG 62.776 66.667 0.00 0.00 0.00 5.18
80 81 4.899239 CCATCACGCCCGCTCTCC 62.899 72.222 0.00 0.00 0.00 3.71
81 82 3.842923 CATCACGCCCGCTCTCCT 61.843 66.667 0.00 0.00 0.00 3.69
82 83 3.532155 ATCACGCCCGCTCTCCTC 61.532 66.667 0.00 0.00 0.00 3.71
83 84 4.742649 TCACGCCCGCTCTCCTCT 62.743 66.667 0.00 0.00 0.00 3.69
84 85 4.504916 CACGCCCGCTCTCCTCTG 62.505 72.222 0.00 0.00 0.00 3.35
86 87 2.829003 CGCCCGCTCTCCTCTGTA 60.829 66.667 0.00 0.00 0.00 2.74
87 88 2.809010 GCCCGCTCTCCTCTGTAC 59.191 66.667 0.00 0.00 0.00 2.90
88 89 2.052690 GCCCGCTCTCCTCTGTACA 61.053 63.158 0.00 0.00 0.00 2.90
89 90 1.395826 GCCCGCTCTCCTCTGTACAT 61.396 60.000 0.00 0.00 0.00 2.29
90 91 0.387202 CCCGCTCTCCTCTGTACATG 59.613 60.000 0.00 0.00 0.00 3.21
91 92 1.107114 CCGCTCTCCTCTGTACATGT 58.893 55.000 2.69 2.69 0.00 3.21
92 93 1.202348 CCGCTCTCCTCTGTACATGTG 60.202 57.143 9.11 0.00 0.00 3.21
93 94 1.800655 CGCTCTCCTCTGTACATGTGC 60.801 57.143 9.11 8.01 0.00 4.57
94 95 1.480137 GCTCTCCTCTGTACATGTGCT 59.520 52.381 15.25 0.00 0.00 4.40
95 96 2.738000 GCTCTCCTCTGTACATGTGCTG 60.738 54.545 15.25 14.30 0.00 4.41
96 97 1.205655 TCTCCTCTGTACATGTGCTGC 59.794 52.381 15.25 0.00 0.00 5.25
97 98 0.250234 TCCTCTGTACATGTGCTGCC 59.750 55.000 15.25 0.00 0.00 4.85
98 99 0.251354 CCTCTGTACATGTGCTGCCT 59.749 55.000 15.25 0.00 0.00 4.75
99 100 1.649664 CTCTGTACATGTGCTGCCTC 58.350 55.000 15.25 0.00 0.00 4.70
100 101 0.250234 TCTGTACATGTGCTGCCTCC 59.750 55.000 15.25 0.00 0.00 4.30
101 102 1.079197 TGTACATGTGCTGCCTCCG 60.079 57.895 15.25 0.00 0.00 4.63
102 103 1.079127 GTACATGTGCTGCCTCCGT 60.079 57.895 9.11 0.00 0.00 4.69
103 104 0.174845 GTACATGTGCTGCCTCCGTA 59.825 55.000 9.11 0.00 0.00 4.02
104 105 0.899019 TACATGTGCTGCCTCCGTAA 59.101 50.000 9.11 0.00 0.00 3.18
105 106 0.036164 ACATGTGCTGCCTCCGTAAA 59.964 50.000 0.00 0.00 0.00 2.01
106 107 0.447801 CATGTGCTGCCTCCGTAAAC 59.552 55.000 0.00 0.00 0.00 2.01
107 108 0.324943 ATGTGCTGCCTCCGTAAACT 59.675 50.000 0.00 0.00 0.00 2.66
108 109 0.970640 TGTGCTGCCTCCGTAAACTA 59.029 50.000 0.00 0.00 0.00 2.24
109 110 1.345089 TGTGCTGCCTCCGTAAACTAA 59.655 47.619 0.00 0.00 0.00 2.24
110 111 2.027561 TGTGCTGCCTCCGTAAACTAAT 60.028 45.455 0.00 0.00 0.00 1.73
111 112 3.196039 TGTGCTGCCTCCGTAAACTAATA 59.804 43.478 0.00 0.00 0.00 0.98
112 113 4.141801 TGTGCTGCCTCCGTAAACTAATAT 60.142 41.667 0.00 0.00 0.00 1.28
113 114 5.069383 TGTGCTGCCTCCGTAAACTAATATA 59.931 40.000 0.00 0.00 0.00 0.86
114 115 5.987347 GTGCTGCCTCCGTAAACTAATATAA 59.013 40.000 0.00 0.00 0.00 0.98
115 116 6.145696 GTGCTGCCTCCGTAAACTAATATAAG 59.854 42.308 0.00 0.00 0.00 1.73
116 117 6.041182 TGCTGCCTCCGTAAACTAATATAAGA 59.959 38.462 0.00 0.00 0.00 2.10
117 118 6.586844 GCTGCCTCCGTAAACTAATATAAGAG 59.413 42.308 0.00 0.00 0.00 2.85
118 119 6.453092 TGCCTCCGTAAACTAATATAAGAGC 58.547 40.000 0.00 0.00 0.00 4.09
119 120 5.572126 GCCTCCGTAAACTAATATAAGAGCG 59.428 44.000 0.00 0.00 0.00 5.03
120 121 6.675987 CCTCCGTAAACTAATATAAGAGCGT 58.324 40.000 0.00 0.00 0.00 5.07
121 122 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
122 123 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
123 124 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
124 125 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
125 126 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
170 171 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
171 172 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
172 173 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
173 174 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
174 175 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
182 183 6.783708 AGTTTACAGAGGGAGTAGAATCTG 57.216 41.667 0.00 0.00 43.81 2.90
189 190 7.214467 CAGAGGGAGTAGAATCTGTAGAATC 57.786 44.000 0.00 0.00 35.52 2.52
190 191 6.208599 CAGAGGGAGTAGAATCTGTAGAATCC 59.791 46.154 0.00 0.00 35.52 3.01
191 192 5.074115 AGGGAGTAGAATCTGTAGAATCCG 58.926 45.833 0.00 0.00 0.00 4.18
192 193 4.828387 GGGAGTAGAATCTGTAGAATCCGT 59.172 45.833 0.00 0.00 0.00 4.69
193 194 6.002704 GGGAGTAGAATCTGTAGAATCCGTA 58.997 44.000 0.00 0.00 0.00 4.02
194 195 6.489361 GGGAGTAGAATCTGTAGAATCCGTAA 59.511 42.308 0.00 0.00 0.00 3.18
195 196 7.308710 GGGAGTAGAATCTGTAGAATCCGTAAG 60.309 44.444 0.00 0.00 0.00 2.34
196 197 7.444792 GGAGTAGAATCTGTAGAATCCGTAAGA 59.555 40.741 0.00 0.00 43.02 2.10
197 198 8.749026 AGTAGAATCTGTAGAATCCGTAAGAA 57.251 34.615 0.00 0.00 43.02 2.52
198 199 8.842280 AGTAGAATCTGTAGAATCCGTAAGAAG 58.158 37.037 0.00 0.00 43.02 2.85
199 200 7.045126 AGAATCTGTAGAATCCGTAAGAAGG 57.955 40.000 0.00 0.00 43.02 3.46
200 201 4.650754 TCTGTAGAATCCGTAAGAAGGC 57.349 45.455 0.00 0.00 43.02 4.35
201 202 3.066342 TCTGTAGAATCCGTAAGAAGGCG 59.934 47.826 0.00 0.00 43.02 5.52
203 204 0.179081 AGAATCCGTAAGAAGGCGGC 60.179 55.000 0.00 0.00 46.79 6.53
204 205 0.461339 GAATCCGTAAGAAGGCGGCA 60.461 55.000 13.08 0.00 46.79 5.69
205 206 0.180406 AATCCGTAAGAAGGCGGCAT 59.820 50.000 13.08 0.00 46.79 4.40
206 207 1.045407 ATCCGTAAGAAGGCGGCATA 58.955 50.000 13.08 0.00 46.79 3.14
207 208 0.825410 TCCGTAAGAAGGCGGCATAA 59.175 50.000 13.08 0.00 46.79 1.90
208 209 0.935196 CCGTAAGAAGGCGGCATAAC 59.065 55.000 13.08 0.69 41.53 1.89
209 210 1.472728 CCGTAAGAAGGCGGCATAACT 60.473 52.381 13.08 1.35 41.53 2.24
210 211 1.859080 CGTAAGAAGGCGGCATAACTC 59.141 52.381 13.08 0.00 43.02 3.01
211 212 2.737359 CGTAAGAAGGCGGCATAACTCA 60.737 50.000 13.08 0.00 43.02 3.41
212 213 2.489938 AAGAAGGCGGCATAACTCAA 57.510 45.000 13.08 0.00 0.00 3.02
213 214 2.029838 AGAAGGCGGCATAACTCAAG 57.970 50.000 13.08 0.00 0.00 3.02
214 215 0.378610 GAAGGCGGCATAACTCAAGC 59.621 55.000 13.08 0.00 0.00 4.01
215 216 0.322456 AAGGCGGCATAACTCAAGCA 60.322 50.000 13.08 0.00 0.00 3.91
216 217 1.026718 AGGCGGCATAACTCAAGCAC 61.027 55.000 13.08 0.00 0.00 4.40
217 218 1.026718 GGCGGCATAACTCAAGCACT 61.027 55.000 3.07 0.00 0.00 4.40
218 219 1.651987 GCGGCATAACTCAAGCACTA 58.348 50.000 0.00 0.00 0.00 2.74
219 220 1.594862 GCGGCATAACTCAAGCACTAG 59.405 52.381 0.00 0.00 0.00 2.57
220 221 2.893637 CGGCATAACTCAAGCACTAGT 58.106 47.619 0.00 0.00 0.00 2.57
221 222 2.860735 CGGCATAACTCAAGCACTAGTC 59.139 50.000 0.00 0.00 0.00 2.59
222 223 2.860735 GGCATAACTCAAGCACTAGTCG 59.139 50.000 0.00 0.00 0.00 4.18
223 224 3.428999 GGCATAACTCAAGCACTAGTCGA 60.429 47.826 0.00 0.00 0.00 4.20
224 225 3.794028 GCATAACTCAAGCACTAGTCGAG 59.206 47.826 0.00 0.00 0.00 4.04
225 226 4.438880 GCATAACTCAAGCACTAGTCGAGA 60.439 45.833 12.68 0.93 0.00 4.04
226 227 5.641709 CATAACTCAAGCACTAGTCGAGAA 58.358 41.667 12.68 4.04 0.00 2.87
227 228 4.585955 AACTCAAGCACTAGTCGAGAAA 57.414 40.909 12.68 0.00 0.00 2.52
228 229 4.585955 ACTCAAGCACTAGTCGAGAAAA 57.414 40.909 12.68 0.00 0.00 2.29
229 230 5.140747 ACTCAAGCACTAGTCGAGAAAAT 57.859 39.130 12.68 0.00 0.00 1.82
230 231 5.542779 ACTCAAGCACTAGTCGAGAAAATT 58.457 37.500 12.68 0.00 0.00 1.82
231 232 6.688578 ACTCAAGCACTAGTCGAGAAAATTA 58.311 36.000 12.68 0.00 0.00 1.40
232 233 6.809196 ACTCAAGCACTAGTCGAGAAAATTAG 59.191 38.462 12.68 0.00 0.00 1.73
233 234 6.100004 TCAAGCACTAGTCGAGAAAATTAGG 58.900 40.000 0.00 0.00 0.00 2.69
234 235 4.434520 AGCACTAGTCGAGAAAATTAGGC 58.565 43.478 0.00 0.00 0.00 3.93
235 236 4.081642 AGCACTAGTCGAGAAAATTAGGCA 60.082 41.667 0.00 0.00 0.00 4.75
236 237 4.033014 GCACTAGTCGAGAAAATTAGGCAC 59.967 45.833 0.00 0.00 0.00 5.01
237 238 5.411781 CACTAGTCGAGAAAATTAGGCACT 58.588 41.667 0.00 0.00 46.37 4.40
238 239 5.289675 CACTAGTCGAGAAAATTAGGCACTG 59.710 44.000 0.00 0.00 41.52 3.66
239 240 3.600388 AGTCGAGAAAATTAGGCACTGG 58.400 45.455 0.00 0.00 41.52 4.00
240 241 3.008049 AGTCGAGAAAATTAGGCACTGGT 59.992 43.478 0.00 0.00 41.52 4.00
241 242 3.371285 GTCGAGAAAATTAGGCACTGGTC 59.629 47.826 0.00 0.00 41.52 4.02
242 243 2.348666 CGAGAAAATTAGGCACTGGTCG 59.651 50.000 0.00 0.00 41.52 4.79
243 244 3.335579 GAGAAAATTAGGCACTGGTCGT 58.664 45.455 0.00 0.00 41.52 4.34
244 245 3.074412 AGAAAATTAGGCACTGGTCGTG 58.926 45.455 0.00 0.00 46.58 4.35
245 246 2.851263 AAATTAGGCACTGGTCGTGA 57.149 45.000 0.00 0.00 46.81 4.35
246 247 2.386661 AATTAGGCACTGGTCGTGAG 57.613 50.000 0.00 0.00 46.81 3.51
247 248 1.267121 ATTAGGCACTGGTCGTGAGT 58.733 50.000 0.00 0.00 46.81 3.41
248 249 1.045407 TTAGGCACTGGTCGTGAGTT 58.955 50.000 0.00 0.00 46.81 3.01
249 250 0.317160 TAGGCACTGGTCGTGAGTTG 59.683 55.000 0.00 0.00 46.81 3.16
250 251 1.069090 GGCACTGGTCGTGAGTTGA 59.931 57.895 0.00 0.00 46.81 3.18
251 252 0.946221 GGCACTGGTCGTGAGTTGAG 60.946 60.000 0.00 0.00 46.81 3.02
252 253 0.249489 GCACTGGTCGTGAGTTGAGT 60.249 55.000 0.00 0.00 46.81 3.41
253 254 1.491670 CACTGGTCGTGAGTTGAGTG 58.508 55.000 0.00 0.00 46.81 3.51
254 255 1.112113 ACTGGTCGTGAGTTGAGTGT 58.888 50.000 0.00 0.00 0.00 3.55
255 256 1.202417 ACTGGTCGTGAGTTGAGTGTG 60.202 52.381 0.00 0.00 0.00 3.82
256 257 0.821517 TGGTCGTGAGTTGAGTGTGT 59.178 50.000 0.00 0.00 0.00 3.72
257 258 1.202371 TGGTCGTGAGTTGAGTGTGTC 60.202 52.381 0.00 0.00 0.00 3.67
258 259 1.121240 GTCGTGAGTTGAGTGTGTCG 58.879 55.000 0.00 0.00 0.00 4.35
259 260 0.030235 TCGTGAGTTGAGTGTGTCGG 59.970 55.000 0.00 0.00 0.00 4.79
260 261 0.939577 CGTGAGTTGAGTGTGTCGGG 60.940 60.000 0.00 0.00 0.00 5.14
281 282 3.691609 GGAAAATGGAGATGAGCTCGTTT 59.308 43.478 10.42 3.87 44.91 3.60
289 290 1.841302 ATGAGCTCGTTTGCCCCTCA 61.841 55.000 9.64 0.00 37.01 3.86
291 292 2.281484 GCTCGTTTGCCCCTCACA 60.281 61.111 0.00 0.00 0.00 3.58
292 293 2.617274 GCTCGTTTGCCCCTCACAC 61.617 63.158 0.00 0.00 0.00 3.82
332 333 1.079197 TGGCACCACAGTAGATGCG 60.079 57.895 0.00 0.00 39.02 4.73
335 336 1.815421 CACCACAGTAGATGCGCCC 60.815 63.158 4.18 0.00 0.00 6.13
357 358 2.593468 ATCCGTGCAACCAGATCCGG 62.593 60.000 0.00 0.00 36.83 5.14
359 360 2.359850 GTGCAACCAGATCCGGCA 60.360 61.111 0.00 0.00 0.00 5.69
388 389 3.047877 GTCCGCTGGGAAACACGG 61.048 66.667 0.00 0.00 46.08 4.94
421 422 4.709886 GGCCAACTAGTTAACATTTCCCAT 59.290 41.667 8.04 0.00 0.00 4.00
442 443 6.992715 CCCATTTAGAATCTGTAGAATCCGTT 59.007 38.462 0.00 0.00 0.00 4.44
451 452 6.726490 TCTGTAGAATCCGTTAATAGGCTT 57.274 37.500 0.00 0.00 0.00 4.35
463 464 5.803967 CGTTAATAGGCTTCGTAACTCAAGT 59.196 40.000 0.00 0.00 0.00 3.16
468 469 8.868635 AATAGGCTTCGTAACTCAAGTATTAC 57.131 34.615 0.00 0.00 0.00 1.89
496 497 2.604046 ATTAGGCACTGGTCGTGATC 57.396 50.000 0.00 0.00 46.81 2.92
498 499 0.963856 TAGGCACTGGTCGTGATCGT 60.964 55.000 0.00 0.00 46.81 3.73
560 561 1.158434 TTTCCCGTGGAAATGTACGC 58.842 50.000 12.41 0.00 45.42 4.42
708 711 0.745128 CCCGCCCTATAAAACACGCA 60.745 55.000 0.00 0.00 0.00 5.24
709 712 0.655733 CCGCCCTATAAAACACGCAG 59.344 55.000 0.00 0.00 0.00 5.18
839 845 1.112916 CCAAGAAACCCACACCCACC 61.113 60.000 0.00 0.00 0.00 4.61
840 846 0.396417 CAAGAAACCCACACCCACCA 60.396 55.000 0.00 0.00 0.00 4.17
842 848 1.076632 GAAACCCACACCCACCACA 60.077 57.895 0.00 0.00 0.00 4.17
843 849 1.380650 AAACCCACACCCACCACAC 60.381 57.895 0.00 0.00 0.00 3.82
845 851 4.596585 CCCACACCCACCACACCC 62.597 72.222 0.00 0.00 0.00 4.61
846 852 4.947147 CCACACCCACCACACCCG 62.947 72.222 0.00 0.00 0.00 5.28
887 904 2.445654 CCAGCCTCCTCCTCCTCC 60.446 72.222 0.00 0.00 0.00 4.30
1001 1021 4.575973 GCCGGAGCAGCCATCCAT 62.576 66.667 5.05 0.00 39.53 3.41
1002 1022 2.593725 CCGGAGCAGCCATCCATG 60.594 66.667 0.00 0.00 36.57 3.66
2088 2119 1.252175 TAGAGCCGCTCATCTCATCC 58.748 55.000 22.29 0.00 32.06 3.51
2258 2294 7.178274 AGGCAAATAAATACAGGAAACATGACA 59.822 33.333 0.00 0.00 0.00 3.58
2377 2413 6.406370 TCATCATCTTTGTACCAGTACCAAG 58.594 40.000 13.08 13.08 39.06 3.61
2378 2414 4.575885 TCATCTTTGTACCAGTACCAAGC 58.424 43.478 14.03 0.00 38.17 4.01
2379 2415 4.041075 TCATCTTTGTACCAGTACCAAGCA 59.959 41.667 14.03 6.63 38.17 3.91
2380 2416 4.634012 TCTTTGTACCAGTACCAAGCAT 57.366 40.909 14.03 0.00 38.17 3.79
2381 2417 4.980573 TCTTTGTACCAGTACCAAGCATT 58.019 39.130 14.03 0.00 38.17 3.56
2382 2418 5.001232 TCTTTGTACCAGTACCAAGCATTC 58.999 41.667 14.03 0.00 38.17 2.67
2399 2435 3.538780 CATTCGCATTGCATCGAGTAAG 58.461 45.455 9.69 0.00 36.02 2.34
2471 2509 8.788409 AAAGATTCAATTTTCGAAACTGTCTC 57.212 30.769 10.79 11.29 0.00 3.36
2472 2510 7.736447 AGATTCAATTTTCGAAACTGTCTCT 57.264 32.000 10.79 12.99 0.00 3.10
2473 2511 8.159344 AGATTCAATTTTCGAAACTGTCTCTT 57.841 30.769 10.79 0.00 0.00 2.85
2509 2551 1.099879 TTACTCCTCCTCGCGCCTAC 61.100 60.000 0.00 0.00 0.00 3.18
2560 2602 0.035152 TGCCATCACTGCTTGGGTAG 60.035 55.000 0.00 0.00 33.40 3.18
2942 2998 1.308069 GGCATGTGCACCGAGTCAAT 61.308 55.000 15.69 0.00 44.36 2.57
3018 3074 1.835483 CTGCCGACAGTTGCACACTC 61.835 60.000 0.00 0.00 39.22 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.030908 CTATTCACCGACTCCGAGGC 59.969 60.000 0.00 0.00 38.22 4.70
2 3 1.604755 CTCTATTCACCGACTCCGAGG 59.395 57.143 0.00 0.00 38.22 4.63
3 4 1.002251 GCTCTATTCACCGACTCCGAG 60.002 57.143 0.00 0.00 38.22 4.63
4 5 1.022735 GCTCTATTCACCGACTCCGA 58.977 55.000 0.00 0.00 38.22 4.55
5 6 0.317103 CGCTCTATTCACCGACTCCG 60.317 60.000 0.00 0.00 0.00 4.63
6 7 0.595310 GCGCTCTATTCACCGACTCC 60.595 60.000 0.00 0.00 0.00 3.85
9 10 1.944676 CCGCGCTCTATTCACCGAC 60.945 63.158 5.56 0.00 0.00 4.79
11 12 1.007271 ATCCGCGCTCTATTCACCG 60.007 57.895 5.56 0.00 0.00 4.94
12 13 0.946221 CCATCCGCGCTCTATTCACC 60.946 60.000 5.56 0.00 0.00 4.02
14 15 0.315251 CTCCATCCGCGCTCTATTCA 59.685 55.000 5.56 0.00 0.00 2.57
15 16 0.389166 CCTCCATCCGCGCTCTATTC 60.389 60.000 5.56 0.00 0.00 1.75
16 17 1.668294 CCTCCATCCGCGCTCTATT 59.332 57.895 5.56 0.00 0.00 1.73
18 19 3.606662 GCCTCCATCCGCGCTCTA 61.607 66.667 5.56 0.00 0.00 2.43
39 40 4.473520 AGCGGGGTTGCGGATGAG 62.474 66.667 0.00 0.00 40.67 2.90
40 41 4.776322 CAGCGGGGTTGCGGATGA 62.776 66.667 0.00 0.00 40.67 2.92
63 64 4.899239 GGAGAGCGGGCGTGATGG 62.899 72.222 0.00 0.00 0.00 3.51
64 65 3.781770 GAGGAGAGCGGGCGTGATG 62.782 68.421 0.00 0.00 0.00 3.07
65 66 3.532155 GAGGAGAGCGGGCGTGAT 61.532 66.667 0.00 0.00 0.00 3.06
66 67 4.742649 AGAGGAGAGCGGGCGTGA 62.743 66.667 0.00 0.00 0.00 4.35
67 68 4.504916 CAGAGGAGAGCGGGCGTG 62.505 72.222 0.00 0.00 0.00 5.34
68 69 3.640257 TACAGAGGAGAGCGGGCGT 62.640 63.158 0.00 0.00 0.00 5.68
69 70 2.829003 TACAGAGGAGAGCGGGCG 60.829 66.667 0.00 0.00 0.00 6.13
70 71 1.395826 ATGTACAGAGGAGAGCGGGC 61.396 60.000 0.33 0.00 0.00 6.13
71 72 0.387202 CATGTACAGAGGAGAGCGGG 59.613 60.000 0.33 0.00 0.00 6.13
72 73 1.107114 ACATGTACAGAGGAGAGCGG 58.893 55.000 0.00 0.00 0.00 5.52
73 74 1.800655 GCACATGTACAGAGGAGAGCG 60.801 57.143 0.00 0.00 0.00 5.03
74 75 1.480137 AGCACATGTACAGAGGAGAGC 59.520 52.381 0.00 0.00 0.00 4.09
75 76 2.738000 GCAGCACATGTACAGAGGAGAG 60.738 54.545 0.00 0.00 0.00 3.20
76 77 1.205655 GCAGCACATGTACAGAGGAGA 59.794 52.381 0.00 0.00 0.00 3.71
77 78 1.649664 GCAGCACATGTACAGAGGAG 58.350 55.000 0.00 0.00 0.00 3.69
78 79 0.250234 GGCAGCACATGTACAGAGGA 59.750 55.000 0.00 0.00 0.00 3.71
79 80 0.251354 AGGCAGCACATGTACAGAGG 59.749 55.000 0.00 0.00 0.00 3.69
80 81 1.649664 GAGGCAGCACATGTACAGAG 58.350 55.000 0.00 0.00 0.00 3.35
81 82 0.250234 GGAGGCAGCACATGTACAGA 59.750 55.000 0.00 0.00 0.00 3.41
82 83 1.086067 CGGAGGCAGCACATGTACAG 61.086 60.000 0.00 0.00 0.00 2.74
83 84 1.079197 CGGAGGCAGCACATGTACA 60.079 57.895 0.00 0.00 0.00 2.90
84 85 0.174845 TACGGAGGCAGCACATGTAC 59.825 55.000 0.00 0.00 0.00 2.90
85 86 0.899019 TTACGGAGGCAGCACATGTA 59.101 50.000 0.00 0.00 0.00 2.29
86 87 0.036164 TTTACGGAGGCAGCACATGT 59.964 50.000 0.00 0.00 0.00 3.21
87 88 0.447801 GTTTACGGAGGCAGCACATG 59.552 55.000 0.00 0.00 0.00 3.21
88 89 0.324943 AGTTTACGGAGGCAGCACAT 59.675 50.000 0.00 0.00 0.00 3.21
89 90 0.970640 TAGTTTACGGAGGCAGCACA 59.029 50.000 0.00 0.00 0.00 4.57
90 91 2.088950 TTAGTTTACGGAGGCAGCAC 57.911 50.000 0.00 0.00 0.00 4.40
91 92 4.682778 ATATTAGTTTACGGAGGCAGCA 57.317 40.909 0.00 0.00 0.00 4.41
92 93 6.453092 TCTTATATTAGTTTACGGAGGCAGC 58.547 40.000 0.00 0.00 0.00 5.25
93 94 6.586844 GCTCTTATATTAGTTTACGGAGGCAG 59.413 42.308 0.00 0.00 0.00 4.85
94 95 6.453092 GCTCTTATATTAGTTTACGGAGGCA 58.547 40.000 0.00 0.00 0.00 4.75
95 96 5.572126 CGCTCTTATATTAGTTTACGGAGGC 59.428 44.000 0.00 0.00 0.00 4.70
96 97 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
97 98 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
98 99 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
99 100 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
144 145 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
145 146 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
146 147 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
147 148 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
148 149 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
156 157 8.919145 CAGATTCTACTCCCTCTGTAAACTAAT 58.081 37.037 0.00 0.00 32.35 1.73
157 158 7.894364 ACAGATTCTACTCCCTCTGTAAACTAA 59.106 37.037 2.40 0.00 44.80 2.24
158 159 7.411808 ACAGATTCTACTCCCTCTGTAAACTA 58.588 38.462 2.40 0.00 44.80 2.24
159 160 6.257586 ACAGATTCTACTCCCTCTGTAAACT 58.742 40.000 2.40 0.00 44.80 2.66
160 161 6.532988 ACAGATTCTACTCCCTCTGTAAAC 57.467 41.667 2.40 0.00 44.80 2.01
161 162 7.640313 TCTACAGATTCTACTCCCTCTGTAAA 58.360 38.462 11.20 0.00 45.55 2.01
162 163 7.209340 TCTACAGATTCTACTCCCTCTGTAA 57.791 40.000 11.20 2.69 45.55 2.41
163 164 6.826632 TCTACAGATTCTACTCCCTCTGTA 57.173 41.667 10.00 10.00 44.80 2.74
165 166 6.208599 GGATTCTACAGATTCTACTCCCTCTG 59.791 46.154 0.00 0.00 40.71 3.35
166 167 6.311735 GGATTCTACAGATTCTACTCCCTCT 58.688 44.000 0.00 0.00 0.00 3.69
167 168 5.182380 CGGATTCTACAGATTCTACTCCCTC 59.818 48.000 0.00 0.00 0.00 4.30
168 169 5.074115 CGGATTCTACAGATTCTACTCCCT 58.926 45.833 0.00 0.00 0.00 4.20
169 170 4.828387 ACGGATTCTACAGATTCTACTCCC 59.172 45.833 0.00 0.00 0.00 4.30
170 171 7.444792 TCTTACGGATTCTACAGATTCTACTCC 59.555 40.741 0.00 0.00 0.00 3.85
171 172 8.380743 TCTTACGGATTCTACAGATTCTACTC 57.619 38.462 0.00 0.00 0.00 2.59
172 173 8.749026 TTCTTACGGATTCTACAGATTCTACT 57.251 34.615 0.00 0.00 0.00 2.57
173 174 8.077386 CCTTCTTACGGATTCTACAGATTCTAC 58.923 40.741 0.00 0.00 0.00 2.59
174 175 7.255520 GCCTTCTTACGGATTCTACAGATTCTA 60.256 40.741 0.00 0.00 0.00 2.10
175 176 6.461788 GCCTTCTTACGGATTCTACAGATTCT 60.462 42.308 0.00 0.00 0.00 2.40
176 177 5.692654 GCCTTCTTACGGATTCTACAGATTC 59.307 44.000 0.00 0.00 0.00 2.52
177 178 5.602628 GCCTTCTTACGGATTCTACAGATT 58.397 41.667 0.00 0.00 0.00 2.40
178 179 4.261656 CGCCTTCTTACGGATTCTACAGAT 60.262 45.833 0.00 0.00 0.00 2.90
179 180 3.066342 CGCCTTCTTACGGATTCTACAGA 59.934 47.826 0.00 0.00 0.00 3.41
180 181 3.372954 CGCCTTCTTACGGATTCTACAG 58.627 50.000 0.00 0.00 0.00 2.74
181 182 3.431922 CGCCTTCTTACGGATTCTACA 57.568 47.619 0.00 0.00 0.00 2.74
190 191 1.859080 GAGTTATGCCGCCTTCTTACG 59.141 52.381 0.00 0.00 0.00 3.18
191 192 2.901249 TGAGTTATGCCGCCTTCTTAC 58.099 47.619 0.00 0.00 0.00 2.34
192 193 3.531538 CTTGAGTTATGCCGCCTTCTTA 58.468 45.455 0.00 0.00 0.00 2.10
193 194 2.359900 CTTGAGTTATGCCGCCTTCTT 58.640 47.619 0.00 0.00 0.00 2.52
194 195 2.014068 GCTTGAGTTATGCCGCCTTCT 61.014 52.381 0.00 0.00 0.00 2.85
195 196 0.378610 GCTTGAGTTATGCCGCCTTC 59.621 55.000 0.00 0.00 0.00 3.46
196 197 0.322456 TGCTTGAGTTATGCCGCCTT 60.322 50.000 0.00 0.00 0.00 4.35
197 198 1.026718 GTGCTTGAGTTATGCCGCCT 61.027 55.000 0.00 0.00 0.00 5.52
198 199 1.026718 AGTGCTTGAGTTATGCCGCC 61.027 55.000 0.00 0.00 0.00 6.13
199 200 1.594862 CTAGTGCTTGAGTTATGCCGC 59.405 52.381 0.00 0.00 0.00 6.53
200 201 2.860735 GACTAGTGCTTGAGTTATGCCG 59.139 50.000 0.00 0.00 0.00 5.69
201 202 2.860735 CGACTAGTGCTTGAGTTATGCC 59.139 50.000 0.00 0.00 0.00 4.40
202 203 3.770666 TCGACTAGTGCTTGAGTTATGC 58.229 45.455 0.00 0.00 0.00 3.14
203 204 5.236655 TCTCGACTAGTGCTTGAGTTATG 57.763 43.478 0.00 0.00 0.00 1.90
204 205 5.899120 TTCTCGACTAGTGCTTGAGTTAT 57.101 39.130 0.00 0.00 0.00 1.89
205 206 5.700722 TTTCTCGACTAGTGCTTGAGTTA 57.299 39.130 0.00 0.00 0.00 2.24
206 207 4.585955 TTTCTCGACTAGTGCTTGAGTT 57.414 40.909 0.00 0.00 0.00 3.01
207 208 4.585955 TTTTCTCGACTAGTGCTTGAGT 57.414 40.909 0.00 0.00 0.00 3.41
208 209 6.254589 CCTAATTTTCTCGACTAGTGCTTGAG 59.745 42.308 0.00 2.38 0.00 3.02
209 210 6.100004 CCTAATTTTCTCGACTAGTGCTTGA 58.900 40.000 0.00 0.00 0.00 3.02
210 211 5.220491 GCCTAATTTTCTCGACTAGTGCTTG 60.220 44.000 0.00 0.00 0.00 4.01
211 212 4.870991 GCCTAATTTTCTCGACTAGTGCTT 59.129 41.667 0.00 0.00 0.00 3.91
212 213 4.081642 TGCCTAATTTTCTCGACTAGTGCT 60.082 41.667 0.00 0.00 0.00 4.40
213 214 4.033014 GTGCCTAATTTTCTCGACTAGTGC 59.967 45.833 0.00 0.00 0.00 4.40
214 215 5.289675 CAGTGCCTAATTTTCTCGACTAGTG 59.710 44.000 0.00 0.00 0.00 2.74
215 216 5.411781 CAGTGCCTAATTTTCTCGACTAGT 58.588 41.667 0.00 0.00 0.00 2.57
216 217 4.806247 CCAGTGCCTAATTTTCTCGACTAG 59.194 45.833 0.00 0.00 0.00 2.57
217 218 4.222145 ACCAGTGCCTAATTTTCTCGACTA 59.778 41.667 0.00 0.00 0.00 2.59
218 219 3.008049 ACCAGTGCCTAATTTTCTCGACT 59.992 43.478 0.00 0.00 0.00 4.18
219 220 3.335579 ACCAGTGCCTAATTTTCTCGAC 58.664 45.455 0.00 0.00 0.00 4.20
220 221 3.596214 GACCAGTGCCTAATTTTCTCGA 58.404 45.455 0.00 0.00 0.00 4.04
221 222 2.348666 CGACCAGTGCCTAATTTTCTCG 59.651 50.000 0.00 0.00 0.00 4.04
222 223 3.125316 CACGACCAGTGCCTAATTTTCTC 59.875 47.826 0.00 0.00 44.72 2.87
223 224 3.074412 CACGACCAGTGCCTAATTTTCT 58.926 45.455 0.00 0.00 44.72 2.52
224 225 3.471495 CACGACCAGTGCCTAATTTTC 57.529 47.619 0.00 0.00 44.72 2.29
235 236 1.112113 ACACTCAACTCACGACCAGT 58.888 50.000 0.00 0.00 0.00 4.00
236 237 1.202417 ACACACTCAACTCACGACCAG 60.202 52.381 0.00 0.00 0.00 4.00
237 238 0.821517 ACACACTCAACTCACGACCA 59.178 50.000 0.00 0.00 0.00 4.02
238 239 1.488527 GACACACTCAACTCACGACC 58.511 55.000 0.00 0.00 0.00 4.79
239 240 1.121240 CGACACACTCAACTCACGAC 58.879 55.000 0.00 0.00 0.00 4.34
240 241 0.030235 CCGACACACTCAACTCACGA 59.970 55.000 0.00 0.00 0.00 4.35
241 242 0.939577 CCCGACACACTCAACTCACG 60.940 60.000 0.00 0.00 0.00 4.35
242 243 0.387929 TCCCGACACACTCAACTCAC 59.612 55.000 0.00 0.00 0.00 3.51
243 244 1.116308 TTCCCGACACACTCAACTCA 58.884 50.000 0.00 0.00 0.00 3.41
244 245 2.234300 TTTCCCGACACACTCAACTC 57.766 50.000 0.00 0.00 0.00 3.01
245 246 2.702592 TTTTCCCGACACACTCAACT 57.297 45.000 0.00 0.00 0.00 3.16
246 247 2.031157 CCATTTTCCCGACACACTCAAC 60.031 50.000 0.00 0.00 0.00 3.18
247 248 2.158740 TCCATTTTCCCGACACACTCAA 60.159 45.455 0.00 0.00 0.00 3.02
248 249 1.418264 TCCATTTTCCCGACACACTCA 59.582 47.619 0.00 0.00 0.00 3.41
249 250 2.076863 CTCCATTTTCCCGACACACTC 58.923 52.381 0.00 0.00 0.00 3.51
250 251 1.697432 TCTCCATTTTCCCGACACACT 59.303 47.619 0.00 0.00 0.00 3.55
251 252 2.178912 TCTCCATTTTCCCGACACAC 57.821 50.000 0.00 0.00 0.00 3.82
252 253 2.304470 TCATCTCCATTTTCCCGACACA 59.696 45.455 0.00 0.00 0.00 3.72
253 254 2.939103 CTCATCTCCATTTTCCCGACAC 59.061 50.000 0.00 0.00 0.00 3.67
254 255 2.680805 GCTCATCTCCATTTTCCCGACA 60.681 50.000 0.00 0.00 0.00 4.35
255 256 1.943340 GCTCATCTCCATTTTCCCGAC 59.057 52.381 0.00 0.00 0.00 4.79
256 257 1.839994 AGCTCATCTCCATTTTCCCGA 59.160 47.619 0.00 0.00 0.00 5.14
257 258 2.216898 GAGCTCATCTCCATTTTCCCG 58.783 52.381 9.40 0.00 35.77 5.14
258 259 2.216898 CGAGCTCATCTCCATTTTCCC 58.783 52.381 15.40 0.00 38.62 3.97
259 260 2.911484 ACGAGCTCATCTCCATTTTCC 58.089 47.619 15.40 0.00 38.62 3.13
260 261 4.656041 CAAACGAGCTCATCTCCATTTTC 58.344 43.478 15.40 0.00 38.62 2.29
281 282 4.308458 CCGTTCGTGTGAGGGGCA 62.308 66.667 0.00 0.00 0.00 5.36
319 320 1.522355 CTGGGCGCATCTACTGTGG 60.522 63.158 10.83 0.00 35.82 4.17
320 321 0.105593 ATCTGGGCGCATCTACTGTG 59.894 55.000 10.83 0.00 38.45 3.66
332 333 3.134127 GGTTGCACGGATCTGGGC 61.134 66.667 22.46 22.46 0.00 5.36
335 336 1.293924 GATCTGGTTGCACGGATCTG 58.706 55.000 15.55 0.00 45.55 2.90
357 358 3.488090 GGACGCACTTACCGCTGC 61.488 66.667 0.00 0.00 0.00 5.25
388 389 2.501261 ACTAGTTGGCCTCGGTTTTTC 58.499 47.619 3.32 0.00 0.00 2.29
400 401 9.238368 TCTAAATGGGAAATGTTAACTAGTTGG 57.762 33.333 18.56 0.00 0.00 3.77
442 443 9.956720 GTAATACTTGAGTTACGAAGCCTATTA 57.043 33.333 0.00 0.00 0.00 0.98
445 446 7.466455 CGAGTAATACTTGAGTTACGAAGCCTA 60.466 40.741 1.36 0.00 36.25 3.93
463 464 6.984474 CCAGTGCCTAATTTTCTCGAGTAATA 59.016 38.462 13.13 0.00 0.00 0.98
468 469 3.600388 ACCAGTGCCTAATTTTCTCGAG 58.400 45.455 5.93 5.93 0.00 4.04
496 497 3.865745 CAGTGCCTAATCCTTCACTTACG 59.134 47.826 0.00 0.00 37.66 3.18
498 499 3.844211 ACCAGTGCCTAATCCTTCACTTA 59.156 43.478 0.00 0.00 37.66 2.24
722 725 1.002134 CGTGGAGAATGGGGTGCTT 60.002 57.895 0.00 0.00 0.00 3.91
766 769 1.641677 GTGTTGTGTCACACGCTCC 59.358 57.895 4.80 0.00 37.90 4.70
817 823 1.463553 GGGTGTGGGTTTCTTGGCAG 61.464 60.000 0.00 0.00 0.00 4.85
839 845 0.107831 TTTTGGAGAGGACGGGTGTG 59.892 55.000 0.00 0.00 0.00 3.82
840 846 1.003233 GATTTTGGAGAGGACGGGTGT 59.997 52.381 0.00 0.00 0.00 4.16
842 848 0.618981 GGATTTTGGAGAGGACGGGT 59.381 55.000 0.00 0.00 0.00 5.28
843 849 0.107165 GGGATTTTGGAGAGGACGGG 60.107 60.000 0.00 0.00 0.00 5.28
845 851 0.107165 GGGGGATTTTGGAGAGGACG 60.107 60.000 0.00 0.00 0.00 4.79
846 852 0.999712 TGGGGGATTTTGGAGAGGAC 59.000 55.000 0.00 0.00 0.00 3.85
887 904 2.206536 GCGGATCTGGGAGGAGGAG 61.207 68.421 3.14 0.00 0.00 3.69
2088 2119 0.313987 TGTTGGATCGGATCGGATCG 59.686 55.000 27.38 9.46 43.00 3.69
2165 2196 8.461222 TCATCAAACATGTAAGGATCACATTTC 58.539 33.333 0.00 0.00 34.39 2.17
2258 2294 1.300542 CACGCCCGGCACAAAAATT 60.301 52.632 10.77 0.00 0.00 1.82
2336 2372 8.754230 AGATGATGATGATACAATAGACAACG 57.246 34.615 0.00 0.00 0.00 4.10
2367 2403 1.382522 ATGCGAATGCTTGGTACTGG 58.617 50.000 0.00 0.00 43.34 4.00
2368 2404 2.789208 CAATGCGAATGCTTGGTACTG 58.211 47.619 0.00 0.00 43.34 2.74
2377 2413 0.028505 ACTCGATGCAATGCGAATGC 59.971 50.000 0.00 1.61 44.08 3.56
2378 2414 3.001634 ACTTACTCGATGCAATGCGAATG 59.998 43.478 0.00 3.78 35.95 2.67
2379 2415 3.198068 ACTTACTCGATGCAATGCGAAT 58.802 40.909 0.00 4.15 35.95 3.34
2380 2416 2.616960 ACTTACTCGATGCAATGCGAA 58.383 42.857 0.00 0.00 35.95 4.70
2381 2417 2.293677 ACTTACTCGATGCAATGCGA 57.706 45.000 0.00 8.94 35.01 5.10
2382 2418 2.537529 CCAACTTACTCGATGCAATGCG 60.538 50.000 0.00 0.00 0.00 4.73
2399 2435 1.359848 CACATCTCTACGGCACCAAC 58.640 55.000 0.00 0.00 0.00 3.77
2446 2482 8.624776 AGAGACAGTTTCGAAAATTGAATCTTT 58.375 29.630 23.03 12.64 0.00 2.52
2448 2484 7.736447 AGAGACAGTTTCGAAAATTGAATCT 57.264 32.000 23.03 20.37 0.00 2.40
2449 2485 8.070171 TCAAGAGACAGTTTCGAAAATTGAATC 58.930 33.333 23.03 19.11 0.00 2.52
2450 2486 7.930217 TCAAGAGACAGTTTCGAAAATTGAAT 58.070 30.769 23.03 13.99 0.00 2.57
2473 2511 9.396022 GGAGGAGTAAATAAACATCAAGATTCA 57.604 33.333 0.00 0.00 0.00 2.57
2509 2551 3.003689 GCGTCCAACATCCCATCATAAAG 59.996 47.826 0.00 0.00 0.00 1.85
2560 2602 5.169295 AGCAACCGTAGACTCACTTAAATC 58.831 41.667 0.00 0.00 0.00 2.17
2823 2873 7.721402 AGTCCTACACTTAATTAGCAGATCTG 58.279 38.462 18.84 18.84 26.56 2.90
2865 2915 2.722094 TGGAACATGTATTGAGGCACC 58.278 47.619 0.00 0.00 0.00 5.01
2942 2998 0.948678 GCACCGCCAGTACAAGAAAA 59.051 50.000 0.00 0.00 0.00 2.29
3018 3074 0.108329 AGGGTTGATTCCGTAGTGCG 60.108 55.000 0.00 0.00 40.95 5.34


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

AutoCloner maintained by Alex Coulton.