Multiple sequence alignment - TraesCS7A01G429600

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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 TraesCS7A01G429600 chr7A 100.000 2658 0 0 1 2658 624688936 624686279 0.000000e+00 4909
1 TraesCS7A01G429600 chr7B 96.000 1600 50 7 325 1917 585462568 585460976 0.000000e+00 2588
2 TraesCS7A01G429600 chr7B 95.332 557 23 2 2102 2655 585450596 585450040 0.000000e+00 881
3 TraesCS7A01G429600 chr7B 89.560 182 11 6 1921 2102 585460911 585460738 9.580000e-55 224
4 TraesCS7A01G429600 chr7D 96.859 1369 33 6 558 1917 541379777 541378410 0.000000e+00 2281
5 TraesCS7A01G429600 chr7D 94.526 274 13 2 2102 2374 541377858 541377586 3.160000e-114 422
6 TraesCS7A01G429600 chr7D 88.889 162 18 0 1925 2086 541378342 541378181 1.610000e-47 200
7 TraesCS7A01G429600 chr4D 93.373 332 15 4 1 325 435018807 435018476 3.980000e-133 484
8 TraesCS7A01G429600 chr2D 93.313 329 15 4 1 323 568879942 568879615 1.850000e-131 479
9 TraesCS7A01G429600 chr2D 93.030 330 16 4 1 324 112535065 112535393 2.390000e-130 475
10 TraesCS7A01G429600 chr2D 92.749 331 17 5 1 324 536469599 536469929 3.100000e-129 472
11 TraesCS7A01G429600 chr1A 93.072 332 13 7 2 325 475498564 475498893 6.660000e-131 477
12 TraesCS7A01G429600 chr3A 93.030 330 16 4 1 324 441083291 441082963 2.390000e-130 475
13 TraesCS7A01G429600 chr5D 92.814 334 13 7 1 325 120811322 120811653 8.610000e-130 473
14 TraesCS7A01G429600 chr5D 92.262 336 18 5 1 330 254482170 254481837 1.110000e-128 470
15 TraesCS7A01G429600 chr5B 92.771 332 14 6 1 323 275059739 275059409 3.100000e-129 472


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 TraesCS7A01G429600 chr7A 624686279 624688936 2657 True 4909.000000 4909 100.000000 1 2658 1 chr7A.!!$R1 2657
1 TraesCS7A01G429600 chr7B 585460738 585462568 1830 True 1406.000000 2588 92.780000 325 2102 2 chr7B.!!$R2 1777
2 TraesCS7A01G429600 chr7B 585450040 585450596 556 True 881.000000 881 95.332000 2102 2655 1 chr7B.!!$R1 553
3 TraesCS7A01G429600 chr7D 541377586 541379777 2191 True 967.666667 2281 93.424667 558 2374 3 chr7D.!!$R1 1816

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
262 263 0.035598 TCCGTGATTTTCTCCCGCAA 59.964 50.0 0.0 0.0 0.0 4.85 F
535 542 0.251916 CGTCATCCAAACAGCCCCTA 59.748 55.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1167 1179 2.110006 GCCAGCCTCCCGAGATTC 59.89 66.667 0.0 0.0 0.00 2.52 R
2419 2804 2.009774 ACGTAAAGGCTTGCAGCTATG 58.99 47.619 0.0 0.0 41.99 2.23 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 3.985410 CTGGAGGGAATTTGGCTCA 57.015 52.632 0.00 0.00 0.00 4.26
19 20 2.220653 CTGGAGGGAATTTGGCTCAA 57.779 50.000 0.00 0.00 0.00 3.02
20 21 2.097825 CTGGAGGGAATTTGGCTCAAG 58.902 52.381 0.00 0.00 0.00 3.02
21 22 1.272648 TGGAGGGAATTTGGCTCAAGG 60.273 52.381 0.00 0.00 0.00 3.61
22 23 1.272704 GGAGGGAATTTGGCTCAAGGT 60.273 52.381 0.00 0.00 0.00 3.50
23 24 1.821136 GAGGGAATTTGGCTCAAGGTG 59.179 52.381 0.00 0.00 0.00 4.00
24 25 0.897621 GGGAATTTGGCTCAAGGTGG 59.102 55.000 0.00 0.00 0.00 4.61
25 26 1.549950 GGGAATTTGGCTCAAGGTGGA 60.550 52.381 0.00 0.00 0.00 4.02
26 27 1.821136 GGAATTTGGCTCAAGGTGGAG 59.179 52.381 0.00 0.00 37.97 3.86
27 28 2.555227 GGAATTTGGCTCAAGGTGGAGA 60.555 50.000 0.00 0.00 37.05 3.71
28 29 3.359950 GAATTTGGCTCAAGGTGGAGAT 58.640 45.455 0.00 0.00 37.05 2.75
29 30 2.978156 TTTGGCTCAAGGTGGAGATT 57.022 45.000 0.00 0.00 37.05 2.40
30 31 2.205022 TTGGCTCAAGGTGGAGATTG 57.795 50.000 0.00 0.00 37.05 2.67
31 32 1.067295 TGGCTCAAGGTGGAGATTGT 58.933 50.000 0.00 0.00 37.05 2.71
32 33 1.425066 TGGCTCAAGGTGGAGATTGTT 59.575 47.619 0.00 0.00 37.05 2.83
33 34 2.642311 TGGCTCAAGGTGGAGATTGTTA 59.358 45.455 0.00 0.00 37.05 2.41
34 35 3.073798 TGGCTCAAGGTGGAGATTGTTAA 59.926 43.478 0.00 0.00 37.05 2.01
35 36 4.079253 GGCTCAAGGTGGAGATTGTTAAA 58.921 43.478 0.00 0.00 37.05 1.52
36 37 4.706962 GGCTCAAGGTGGAGATTGTTAAAT 59.293 41.667 0.00 0.00 37.05 1.40
37 38 5.185828 GGCTCAAGGTGGAGATTGTTAAATT 59.814 40.000 0.00 0.00 37.05 1.82
38 39 6.095377 GCTCAAGGTGGAGATTGTTAAATTG 58.905 40.000 0.00 0.00 37.05 2.32
39 40 6.294731 GCTCAAGGTGGAGATTGTTAAATTGT 60.295 38.462 0.00 0.00 37.05 2.71
40 41 6.980593 TCAAGGTGGAGATTGTTAAATTGTG 58.019 36.000 0.00 0.00 0.00 3.33
41 42 6.775142 TCAAGGTGGAGATTGTTAAATTGTGA 59.225 34.615 0.00 0.00 0.00 3.58
42 43 7.451255 TCAAGGTGGAGATTGTTAAATTGTGAT 59.549 33.333 0.00 0.00 0.00 3.06
43 44 7.396540 AGGTGGAGATTGTTAAATTGTGATC 57.603 36.000 0.00 0.00 0.00 2.92
44 45 6.378280 AGGTGGAGATTGTTAAATTGTGATCC 59.622 38.462 0.00 0.00 0.00 3.36
45 46 6.152661 GGTGGAGATTGTTAAATTGTGATCCA 59.847 38.462 0.00 0.00 0.00 3.41
46 47 7.309744 GGTGGAGATTGTTAAATTGTGATCCAA 60.310 37.037 0.00 0.00 35.06 3.53
47 48 8.087750 GTGGAGATTGTTAAATTGTGATCCAAA 58.912 33.333 0.00 0.00 36.44 3.28
48 49 8.814931 TGGAGATTGTTAAATTGTGATCCAAAT 58.185 29.630 1.49 0.00 36.44 2.32
49 50 9.657419 GGAGATTGTTAAATTGTGATCCAAATT 57.343 29.630 1.49 2.70 36.44 1.82
61 62 8.956533 TTGTGATCCAAATTCTATCGTATTGA 57.043 30.769 0.00 0.00 0.00 2.57
62 63 8.365399 TGTGATCCAAATTCTATCGTATTGAC 57.635 34.615 0.00 0.00 0.00 3.18
63 64 8.204160 TGTGATCCAAATTCTATCGTATTGACT 58.796 33.333 0.00 0.00 0.00 3.41
64 65 9.692749 GTGATCCAAATTCTATCGTATTGACTA 57.307 33.333 0.00 0.00 0.00 2.59
65 66 9.914131 TGATCCAAATTCTATCGTATTGACTAG 57.086 33.333 0.00 0.00 0.00 2.57
67 68 9.915629 ATCCAAATTCTATCGTATTGACTAGAC 57.084 33.333 0.00 0.00 0.00 2.59
68 69 8.074370 TCCAAATTCTATCGTATTGACTAGACG 58.926 37.037 0.00 0.00 37.93 4.18
69 70 7.861372 CCAAATTCTATCGTATTGACTAGACGT 59.139 37.037 0.00 0.00 37.81 4.34
70 71 9.874215 CAAATTCTATCGTATTGACTAGACGTA 57.126 33.333 0.00 0.00 37.81 3.57
87 88 2.554032 ACGTAGTATATACGGTGTGGGC 59.446 50.000 11.61 0.00 41.94 5.36
88 89 2.095059 CGTAGTATATACGGTGTGGGCC 60.095 54.545 7.23 0.00 37.29 5.80
89 90 2.393630 AGTATATACGGTGTGGGCCT 57.606 50.000 4.53 0.00 0.00 5.19
90 91 2.686119 AGTATATACGGTGTGGGCCTT 58.314 47.619 4.53 0.00 0.00 4.35
91 92 3.043418 AGTATATACGGTGTGGGCCTTT 58.957 45.455 4.53 0.00 0.00 3.11
92 93 2.341846 ATATACGGTGTGGGCCTTTG 57.658 50.000 4.53 0.00 0.00 2.77
93 94 0.393267 TATACGGTGTGGGCCTTTGC 60.393 55.000 4.53 0.00 0.00 3.68
94 95 5.909139 TATATACGGTGTGGGCCTTTGCG 62.909 52.174 4.53 0.00 38.85 4.85
96 97 3.223589 GGTGTGGGCCTTTGCGTT 61.224 61.111 4.53 0.00 38.85 4.84
97 98 2.027460 GTGTGGGCCTTTGCGTTG 59.973 61.111 4.53 0.00 38.85 4.10
98 99 3.222855 TGTGGGCCTTTGCGTTGG 61.223 61.111 4.53 0.00 38.85 3.77
99 100 3.223589 GTGGGCCTTTGCGTTGGT 61.224 61.111 4.53 0.00 38.85 3.67
100 101 1.899534 GTGGGCCTTTGCGTTGGTA 60.900 57.895 4.53 0.00 38.85 3.25
101 102 1.899534 TGGGCCTTTGCGTTGGTAC 60.900 57.895 4.53 0.00 38.85 3.34
102 103 2.632544 GGGCCTTTGCGTTGGTACC 61.633 63.158 4.43 4.43 38.85 3.34
103 104 2.559330 GCCTTTGCGTTGGTACCG 59.441 61.111 7.57 0.00 0.00 4.02
104 105 1.962306 GCCTTTGCGTTGGTACCGA 60.962 57.895 7.57 1.50 0.00 4.69
105 106 1.864176 CCTTTGCGTTGGTACCGAC 59.136 57.895 20.98 20.98 0.00 4.79
110 111 2.175566 CGTTGGTACCGACGCGTA 59.824 61.111 35.36 1.36 45.15 4.42
111 112 2.145905 CGTTGGTACCGACGCGTAC 61.146 63.158 35.36 6.52 45.15 3.67
113 114 2.321333 TTGGTACCGACGCGTACGA 61.321 57.895 25.30 10.88 43.93 3.43
114 115 2.021931 GGTACCGACGCGTACGAG 59.978 66.667 25.30 19.58 43.93 4.18
115 116 2.740714 GGTACCGACGCGTACGAGT 61.741 63.158 24.75 24.75 43.93 4.18
116 117 1.418342 GGTACCGACGCGTACGAGTA 61.418 60.000 24.55 21.29 43.93 2.59
117 118 0.314339 GTACCGACGCGTACGAGTAC 60.314 60.000 24.55 25.58 43.93 2.73
118 119 0.734597 TACCGACGCGTACGAGTACA 60.735 55.000 24.55 7.41 43.93 2.90
119 120 1.132436 CCGACGCGTACGAGTACAA 59.868 57.895 24.55 0.00 43.93 2.41
120 121 1.122419 CCGACGCGTACGAGTACAAC 61.122 60.000 24.55 11.19 43.93 3.32
121 122 0.179240 CGACGCGTACGAGTACAACT 60.179 55.000 24.55 0.42 43.93 3.16
122 123 1.518286 GACGCGTACGAGTACAACTC 58.482 55.000 24.55 7.54 43.93 3.01
134 135 5.819270 GAGTACAACTCGTTTACTTGTCC 57.181 43.478 0.00 0.00 35.28 4.02
135 136 5.526506 AGTACAACTCGTTTACTTGTCCT 57.473 39.130 0.00 0.00 30.76 3.85
136 137 5.527033 AGTACAACTCGTTTACTTGTCCTC 58.473 41.667 0.00 0.00 30.76 3.71
137 138 3.725490 ACAACTCGTTTACTTGTCCTCC 58.275 45.455 0.00 0.00 0.00 4.30
138 139 3.133362 ACAACTCGTTTACTTGTCCTCCA 59.867 43.478 0.00 0.00 0.00 3.86
139 140 4.124238 CAACTCGTTTACTTGTCCTCCAA 58.876 43.478 0.00 0.00 0.00 3.53
153 154 4.826274 TCCTCCAAGGACTCTTGTATTG 57.174 45.455 5.56 0.00 46.65 1.90
154 155 3.055094 TCCTCCAAGGACTCTTGTATTGC 60.055 47.826 5.56 0.00 46.65 3.56
155 156 3.274288 CTCCAAGGACTCTTGTATTGCC 58.726 50.000 5.56 0.00 46.65 4.52
156 157 2.026262 TCCAAGGACTCTTGTATTGCCC 60.026 50.000 5.56 0.00 46.65 5.36
157 158 2.025887 CCAAGGACTCTTGTATTGCCCT 60.026 50.000 5.56 0.00 46.65 5.19
158 159 3.274288 CAAGGACTCTTGTATTGCCCTC 58.726 50.000 0.00 0.00 43.92 4.30
159 160 2.839228 AGGACTCTTGTATTGCCCTCT 58.161 47.619 0.00 0.00 0.00 3.69
160 161 3.185455 AGGACTCTTGTATTGCCCTCTT 58.815 45.455 0.00 0.00 0.00 2.85
161 162 4.362677 AGGACTCTTGTATTGCCCTCTTA 58.637 43.478 0.00 0.00 0.00 2.10
162 163 4.971924 AGGACTCTTGTATTGCCCTCTTAT 59.028 41.667 0.00 0.00 0.00 1.73
163 164 6.143915 AGGACTCTTGTATTGCCCTCTTATA 58.856 40.000 0.00 0.00 0.00 0.98
164 165 6.789959 AGGACTCTTGTATTGCCCTCTTATAT 59.210 38.462 0.00 0.00 0.00 0.86
165 166 7.956315 AGGACTCTTGTATTGCCCTCTTATATA 59.044 37.037 0.00 0.00 0.00 0.86
166 167 8.035984 GGACTCTTGTATTGCCCTCTTATATAC 58.964 40.741 0.00 0.00 0.00 1.47
167 168 7.908453 ACTCTTGTATTGCCCTCTTATATACC 58.092 38.462 0.00 0.00 0.00 2.73
168 169 7.038231 ACTCTTGTATTGCCCTCTTATATACCC 60.038 40.741 0.00 0.00 0.00 3.69
169 170 6.214819 TCTTGTATTGCCCTCTTATATACCCC 59.785 42.308 0.00 0.00 0.00 4.95
170 171 5.416858 TGTATTGCCCTCTTATATACCCCA 58.583 41.667 0.00 0.00 0.00 4.96
171 172 6.035973 TGTATTGCCCTCTTATATACCCCAT 58.964 40.000 0.00 0.00 0.00 4.00
172 173 4.927267 TTGCCCTCTTATATACCCCATG 57.073 45.455 0.00 0.00 0.00 3.66
173 174 3.881871 TGCCCTCTTATATACCCCATGT 58.118 45.455 0.00 0.00 0.00 3.21
174 175 5.031269 TGCCCTCTTATATACCCCATGTA 57.969 43.478 0.00 0.00 0.00 2.29
175 176 5.416858 TGCCCTCTTATATACCCCATGTAA 58.583 41.667 0.00 0.00 31.94 2.41
176 177 6.035973 TGCCCTCTTATATACCCCATGTAAT 58.964 40.000 0.00 0.00 31.94 1.89
177 178 6.157994 TGCCCTCTTATATACCCCATGTAATC 59.842 42.308 0.00 0.00 31.94 1.75
178 179 6.685620 GCCCTCTTATATACCCCATGTAATCG 60.686 46.154 0.00 0.00 31.94 3.34
179 180 6.281405 CCTCTTATATACCCCATGTAATCGC 58.719 44.000 0.00 0.00 31.94 4.58
180 181 6.127168 CCTCTTATATACCCCATGTAATCGCA 60.127 42.308 0.00 0.00 31.94 5.10
181 182 6.636705 TCTTATATACCCCATGTAATCGCAC 58.363 40.000 0.00 0.00 31.94 5.34
182 183 2.561478 ATACCCCATGTAATCGCACC 57.439 50.000 0.00 0.00 31.94 5.01
183 184 1.502690 TACCCCATGTAATCGCACCT 58.497 50.000 0.00 0.00 0.00 4.00
184 185 1.502690 ACCCCATGTAATCGCACCTA 58.497 50.000 0.00 0.00 0.00 3.08
185 186 1.841277 ACCCCATGTAATCGCACCTAA 59.159 47.619 0.00 0.00 0.00 2.69
186 187 2.240160 ACCCCATGTAATCGCACCTAAA 59.760 45.455 0.00 0.00 0.00 1.85
187 188 2.878406 CCCCATGTAATCGCACCTAAAG 59.122 50.000 0.00 0.00 0.00 1.85
188 189 3.433031 CCCCATGTAATCGCACCTAAAGA 60.433 47.826 0.00 0.00 0.00 2.52
189 190 3.560068 CCCATGTAATCGCACCTAAAGAC 59.440 47.826 0.00 0.00 0.00 3.01
190 191 3.245284 CCATGTAATCGCACCTAAAGACG 59.755 47.826 0.00 0.00 0.00 4.18
191 192 2.883574 TGTAATCGCACCTAAAGACGG 58.116 47.619 0.00 0.00 0.00 4.79
192 193 1.591619 GTAATCGCACCTAAAGACGGC 59.408 52.381 0.00 0.00 0.00 5.68
193 194 0.743345 AATCGCACCTAAAGACGGCC 60.743 55.000 0.00 0.00 0.00 6.13
194 195 1.614241 ATCGCACCTAAAGACGGCCT 61.614 55.000 0.00 0.00 0.00 5.19
195 196 2.100631 CGCACCTAAAGACGGCCTG 61.101 63.158 0.00 0.00 0.00 4.85
196 197 1.003718 GCACCTAAAGACGGCCTGT 60.004 57.895 0.00 0.00 0.00 4.00
209 210 3.114616 CCTGTCGCCTCGTGCTTG 61.115 66.667 0.00 0.00 38.05 4.01
210 211 2.356313 CTGTCGCCTCGTGCTTGT 60.356 61.111 0.00 0.00 38.05 3.16
211 212 1.080772 CTGTCGCCTCGTGCTTGTA 60.081 57.895 0.00 0.00 38.05 2.41
212 213 0.666274 CTGTCGCCTCGTGCTTGTAA 60.666 55.000 0.00 0.00 38.05 2.41
213 214 0.037697 TGTCGCCTCGTGCTTGTAAT 60.038 50.000 0.00 0.00 38.05 1.89
214 215 1.202817 TGTCGCCTCGTGCTTGTAATA 59.797 47.619 0.00 0.00 38.05 0.98
215 216 1.587034 GTCGCCTCGTGCTTGTAATAC 59.413 52.381 0.00 0.00 38.05 1.89
216 217 1.475280 TCGCCTCGTGCTTGTAATACT 59.525 47.619 0.00 0.00 38.05 2.12
217 218 1.852895 CGCCTCGTGCTTGTAATACTC 59.147 52.381 0.00 0.00 38.05 2.59
218 219 2.202566 GCCTCGTGCTTGTAATACTCC 58.797 52.381 0.00 0.00 36.87 3.85
219 220 2.159085 GCCTCGTGCTTGTAATACTCCT 60.159 50.000 0.00 0.00 36.87 3.69
220 221 3.707793 CCTCGTGCTTGTAATACTCCTC 58.292 50.000 0.00 0.00 0.00 3.71
221 222 3.130516 CCTCGTGCTTGTAATACTCCTCA 59.869 47.826 0.00 0.00 0.00 3.86
222 223 4.202161 CCTCGTGCTTGTAATACTCCTCAT 60.202 45.833 0.00 0.00 0.00 2.90
223 224 5.009710 CCTCGTGCTTGTAATACTCCTCATA 59.990 44.000 0.00 0.00 0.00 2.15
224 225 6.073327 TCGTGCTTGTAATACTCCTCATAG 57.927 41.667 0.00 0.00 0.00 2.23
225 226 5.593095 TCGTGCTTGTAATACTCCTCATAGT 59.407 40.000 0.00 0.00 0.00 2.12
226 227 5.687730 CGTGCTTGTAATACTCCTCATAGTG 59.312 44.000 0.00 0.00 0.00 2.74
227 228 6.459710 CGTGCTTGTAATACTCCTCATAGTGA 60.460 42.308 0.00 0.00 0.00 3.41
228 229 7.437748 GTGCTTGTAATACTCCTCATAGTGAT 58.562 38.462 0.00 0.00 0.00 3.06
229 230 7.928706 GTGCTTGTAATACTCCTCATAGTGATT 59.071 37.037 0.00 0.00 0.00 2.57
230 231 7.928167 TGCTTGTAATACTCCTCATAGTGATTG 59.072 37.037 0.00 0.00 0.00 2.67
231 232 7.095439 GCTTGTAATACTCCTCATAGTGATTGC 60.095 40.741 0.00 0.00 0.00 3.56
232 233 6.447162 TGTAATACTCCTCATAGTGATTGCG 58.553 40.000 0.00 0.00 0.00 4.85
233 234 2.231215 ACTCCTCATAGTGATTGCGC 57.769 50.000 0.00 0.00 0.00 6.09
234 235 1.202580 ACTCCTCATAGTGATTGCGCC 60.203 52.381 4.18 0.00 0.00 6.53
235 236 1.069823 CTCCTCATAGTGATTGCGCCT 59.930 52.381 4.18 0.00 0.00 5.52
236 237 1.486310 TCCTCATAGTGATTGCGCCTT 59.514 47.619 4.18 0.00 0.00 4.35
237 238 1.869767 CCTCATAGTGATTGCGCCTTC 59.130 52.381 4.18 1.68 0.00 3.46
238 239 1.524355 CTCATAGTGATTGCGCCTTCG 59.476 52.381 4.18 0.00 39.07 3.79
239 240 1.134818 TCATAGTGATTGCGCCTTCGT 60.135 47.619 4.18 0.00 38.14 3.85
240 241 1.665679 CATAGTGATTGCGCCTTCGTT 59.334 47.619 4.18 0.00 38.14 3.85
241 242 1.355971 TAGTGATTGCGCCTTCGTTC 58.644 50.000 4.18 0.00 38.14 3.95
242 243 1.225745 GTGATTGCGCCTTCGTTCG 60.226 57.895 4.18 0.00 38.14 3.95
243 244 1.666553 TGATTGCGCCTTCGTTCGT 60.667 52.632 4.18 0.00 38.14 3.85
244 245 1.058903 GATTGCGCCTTCGTTCGTC 59.941 57.895 4.18 0.00 38.14 4.20
245 246 2.292802 GATTGCGCCTTCGTTCGTCC 62.293 60.000 4.18 0.00 38.14 4.79
248 249 3.467119 CGCCTTCGTTCGTCCGTG 61.467 66.667 0.00 0.00 0.00 4.94
249 250 2.049802 GCCTTCGTTCGTCCGTGA 60.050 61.111 0.00 0.00 0.00 4.35
250 251 1.445582 GCCTTCGTTCGTCCGTGAT 60.446 57.895 0.00 0.00 0.00 3.06
251 252 1.012486 GCCTTCGTTCGTCCGTGATT 61.012 55.000 0.00 0.00 0.00 2.57
252 253 1.425412 CCTTCGTTCGTCCGTGATTT 58.575 50.000 0.00 0.00 0.00 2.17
253 254 1.796459 CCTTCGTTCGTCCGTGATTTT 59.204 47.619 0.00 0.00 0.00 1.82
254 255 2.159881 CCTTCGTTCGTCCGTGATTTTC 60.160 50.000 0.00 0.00 0.00 2.29
255 256 2.427232 TCGTTCGTCCGTGATTTTCT 57.573 45.000 0.00 0.00 0.00 2.52
256 257 2.322161 TCGTTCGTCCGTGATTTTCTC 58.678 47.619 0.00 0.00 0.00 2.87
257 258 1.389106 CGTTCGTCCGTGATTTTCTCC 59.611 52.381 0.00 0.00 0.00 3.71
258 259 1.730612 GTTCGTCCGTGATTTTCTCCC 59.269 52.381 0.00 0.00 0.00 4.30
259 260 0.108992 TCGTCCGTGATTTTCTCCCG 60.109 55.000 0.00 0.00 0.00 5.14
260 261 1.693083 CGTCCGTGATTTTCTCCCGC 61.693 60.000 0.00 0.00 0.00 6.13
261 262 0.672401 GTCCGTGATTTTCTCCCGCA 60.672 55.000 0.00 0.00 0.00 5.69
262 263 0.035598 TCCGTGATTTTCTCCCGCAA 59.964 50.000 0.00 0.00 0.00 4.85
263 264 0.447801 CCGTGATTTTCTCCCGCAAG 59.552 55.000 0.00 0.00 0.00 4.01
275 276 4.364817 CGCAAGGGTTTCCACGTA 57.635 55.556 0.00 0.00 34.83 3.57
276 277 2.619362 CGCAAGGGTTTCCACGTAA 58.381 52.632 0.00 0.00 34.83 3.18
277 278 0.945813 CGCAAGGGTTTCCACGTAAA 59.054 50.000 0.00 0.00 34.83 2.01
278 279 1.334243 CGCAAGGGTTTCCACGTAAAA 59.666 47.619 0.00 0.00 34.83 1.52
279 280 2.223525 CGCAAGGGTTTCCACGTAAAAA 60.224 45.455 0.00 0.00 34.83 1.94
280 281 3.551250 CGCAAGGGTTTCCACGTAAAAAT 60.551 43.478 0.00 0.00 34.83 1.82
281 282 3.985279 GCAAGGGTTTCCACGTAAAAATC 59.015 43.478 0.00 0.00 34.83 2.17
282 283 4.552355 CAAGGGTTTCCACGTAAAAATCC 58.448 43.478 13.64 13.64 36.14 3.01
283 284 2.815503 AGGGTTTCCACGTAAAAATCCG 59.184 45.455 14.93 0.00 40.02 4.18
284 285 2.553602 GGGTTTCCACGTAAAAATCCGT 59.446 45.455 8.01 0.00 37.90 4.69
291 292 4.563524 CACGTAAAAATCCGTGTCTCTC 57.436 45.455 4.17 0.00 46.87 3.20
292 293 4.235360 CACGTAAAAATCCGTGTCTCTCT 58.765 43.478 4.17 0.00 46.87 3.10
293 294 5.396484 CACGTAAAAATCCGTGTCTCTCTA 58.604 41.667 4.17 0.00 46.87 2.43
294 295 6.034591 CACGTAAAAATCCGTGTCTCTCTAT 58.965 40.000 4.17 0.00 46.87 1.98
295 296 6.196724 CACGTAAAAATCCGTGTCTCTCTATC 59.803 42.308 4.17 0.00 46.87 2.08
296 297 6.095160 ACGTAAAAATCCGTGTCTCTCTATCT 59.905 38.462 0.00 0.00 35.69 1.98
297 298 6.633634 CGTAAAAATCCGTGTCTCTCTATCTC 59.366 42.308 0.00 0.00 0.00 2.75
298 299 6.531503 AAAAATCCGTGTCTCTCTATCTCA 57.468 37.500 0.00 0.00 0.00 3.27
299 300 6.723298 AAAATCCGTGTCTCTCTATCTCAT 57.277 37.500 0.00 0.00 0.00 2.90
300 301 6.723298 AAATCCGTGTCTCTCTATCTCATT 57.277 37.500 0.00 0.00 0.00 2.57
301 302 6.723298 AATCCGTGTCTCTCTATCTCATTT 57.277 37.500 0.00 0.00 0.00 2.32
302 303 7.825331 AATCCGTGTCTCTCTATCTCATTTA 57.175 36.000 0.00 0.00 0.00 1.40
303 304 8.415950 AATCCGTGTCTCTCTATCTCATTTAT 57.584 34.615 0.00 0.00 0.00 1.40
304 305 7.825331 TCCGTGTCTCTCTATCTCATTTATT 57.175 36.000 0.00 0.00 0.00 1.40
305 306 8.239038 TCCGTGTCTCTCTATCTCATTTATTT 57.761 34.615 0.00 0.00 0.00 1.40
306 307 8.353684 TCCGTGTCTCTCTATCTCATTTATTTC 58.646 37.037 0.00 0.00 0.00 2.17
307 308 8.356657 CCGTGTCTCTCTATCTCATTTATTTCT 58.643 37.037 0.00 0.00 0.00 2.52
308 309 9.393249 CGTGTCTCTCTATCTCATTTATTTCTC 57.607 37.037 0.00 0.00 0.00 2.87
309 310 9.393249 GTGTCTCTCTATCTCATTTATTTCTCG 57.607 37.037 0.00 0.00 0.00 4.04
310 311 9.126151 TGTCTCTCTATCTCATTTATTTCTCGT 57.874 33.333 0.00 0.00 0.00 4.18
311 312 9.959749 GTCTCTCTATCTCATTTATTTCTCGTT 57.040 33.333 0.00 0.00 0.00 3.85
329 330 6.869695 TCTCGTTATTATCTAACAACAGCCA 58.130 36.000 0.00 0.00 0.00 4.75
331 332 8.635328 TCTCGTTATTATCTAACAACAGCCATA 58.365 33.333 0.00 0.00 0.00 2.74
352 353 0.686224 CCTGCCCTGCCAATTTTTCA 59.314 50.000 0.00 0.00 0.00 2.69
382 383 1.270199 TGCTACCGCAACCTTCGTTTA 60.270 47.619 0.00 0.00 44.62 2.01
400 401 2.820059 TAGATCAGCGCCGATGAATT 57.180 45.000 9.85 3.00 29.85 2.17
424 425 1.967066 ACCATGCCAATTTTTCGGTCA 59.033 42.857 0.00 0.00 0.00 4.02
426 427 2.029110 CCATGCCAATTTTTCGGTCAGT 60.029 45.455 0.00 0.00 0.00 3.41
473 480 2.622962 CGGGGTGGCGAAAACCTTC 61.623 63.158 0.00 0.00 37.85 3.46
535 542 0.251916 CGTCATCCAAACAGCCCCTA 59.748 55.000 0.00 0.00 0.00 3.53
539 546 3.136626 GTCATCCAAACAGCCCCTATAGT 59.863 47.826 0.00 0.00 0.00 2.12
611 620 2.376695 AATGGGCATAGCTCTTGCAT 57.623 45.000 19.71 6.32 41.95 3.96
960 972 4.550076 AGAAGACATAGCAAGAGCAAGT 57.450 40.909 0.00 0.00 45.49 3.16
1120 1132 2.203983 TCTCTTGCAGGGCCTCCA 60.204 61.111 0.95 0.00 34.83 3.86
1167 1179 1.431440 CGGAGACCTCGAGCTGAAG 59.569 63.158 6.99 0.00 0.00 3.02
1178 1190 1.268999 CGAGCTGAAGAATCTCGGGAG 60.269 57.143 0.00 0.00 44.06 4.30
1346 1358 8.642935 TCAAGGTAACCATCAATTAAACATCA 57.357 30.769 0.00 0.00 37.17 3.07
1683 1695 9.981114 AATGATACGAGTCATGTTCATGTAATA 57.019 29.630 11.73 1.82 38.76 0.98
1917 1932 5.882557 ACGGTGCATTTCTCTTTCATCTTAT 59.117 36.000 0.00 0.00 0.00 1.73
1942 2018 1.802636 GACGTTATGGGACGGACGA 59.197 57.895 0.00 0.00 46.77 4.20
1955 2031 4.460505 GGACGGACGAAGTACAAATTTTG 58.539 43.478 7.59 7.59 45.67 2.44
1956 2032 3.880610 ACGGACGAAGTACAAATTTTGC 58.119 40.909 9.04 0.00 45.67 3.68
2384 2769 7.451501 TGCAGACTCATCAAAATAACATCAA 57.548 32.000 0.00 0.00 0.00 2.57
2460 2845 1.978782 GATAAACAGTTTGCGTGCTGC 59.021 47.619 8.93 0.00 46.70 5.25
2485 2870 5.925971 TCATCCAGTATGAGCCATTGGCG 62.926 52.174 21.60 5.81 43.33 5.69
2554 2941 2.969950 AGCTCGGTACTAATAATGCCCA 59.030 45.455 0.00 0.00 0.00 5.36
2575 2962 0.754217 ATTGATCTTGCGGGCATGCT 60.754 50.000 18.92 0.00 35.36 3.79
2595 2982 3.305094 GCTGCAATTCAACAATTGGATCG 59.695 43.478 10.83 0.00 45.96 3.69
2639 3026 1.850998 GATAGGGTTAGGGCCAGGTTT 59.149 52.381 6.18 0.00 0.00 3.27
2655 3042 4.142293 CCAGGTTTACCTAGACTAACCGAC 60.142 50.000 0.14 0.00 46.65 4.79
2656 3043 4.460382 CAGGTTTACCTAGACTAACCGACA 59.540 45.833 0.14 0.00 46.65 4.35
2657 3044 4.460731 AGGTTTACCTAGACTAACCGACAC 59.539 45.833 0.00 0.00 46.48 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.097825 CTTGAGCCAAATTCCCTCCAG 58.902 52.381 0.00 0.00 0.00 3.86
1 2 1.272648 CCTTGAGCCAAATTCCCTCCA 60.273 52.381 0.00 0.00 0.00 3.86
2 3 1.272704 ACCTTGAGCCAAATTCCCTCC 60.273 52.381 0.00 0.00 0.00 4.30
3 4 1.821136 CACCTTGAGCCAAATTCCCTC 59.179 52.381 0.00 0.00 0.00 4.30
4 5 1.550869 CCACCTTGAGCCAAATTCCCT 60.551 52.381 0.00 0.00 0.00 4.20
5 6 0.897621 CCACCTTGAGCCAAATTCCC 59.102 55.000 0.00 0.00 0.00 3.97
6 7 1.821136 CTCCACCTTGAGCCAAATTCC 59.179 52.381 0.00 0.00 0.00 3.01
7 8 2.795329 TCTCCACCTTGAGCCAAATTC 58.205 47.619 0.00 0.00 32.22 2.17
8 9 2.978156 TCTCCACCTTGAGCCAAATT 57.022 45.000 0.00 0.00 32.22 1.82
9 10 3.094572 CAATCTCCACCTTGAGCCAAAT 58.905 45.455 0.00 0.00 32.22 2.32
10 11 2.158475 ACAATCTCCACCTTGAGCCAAA 60.158 45.455 0.00 0.00 32.22 3.28
11 12 1.425066 ACAATCTCCACCTTGAGCCAA 59.575 47.619 0.00 0.00 32.22 4.52
12 13 1.067295 ACAATCTCCACCTTGAGCCA 58.933 50.000 0.00 0.00 32.22 4.75
13 14 2.206576 AACAATCTCCACCTTGAGCC 57.793 50.000 0.00 0.00 32.22 4.70
14 15 5.904362 ATTTAACAATCTCCACCTTGAGC 57.096 39.130 0.00 0.00 32.22 4.26
15 16 7.040478 TCACAATTTAACAATCTCCACCTTGAG 60.040 37.037 0.00 0.00 0.00 3.02
16 17 6.775142 TCACAATTTAACAATCTCCACCTTGA 59.225 34.615 0.00 0.00 0.00 3.02
17 18 6.980593 TCACAATTTAACAATCTCCACCTTG 58.019 36.000 0.00 0.00 0.00 3.61
18 19 7.093771 GGATCACAATTTAACAATCTCCACCTT 60.094 37.037 0.00 0.00 0.00 3.50
19 20 6.378280 GGATCACAATTTAACAATCTCCACCT 59.622 38.462 0.00 0.00 0.00 4.00
20 21 6.152661 TGGATCACAATTTAACAATCTCCACC 59.847 38.462 0.00 0.00 0.00 4.61
21 22 7.156876 TGGATCACAATTTAACAATCTCCAC 57.843 36.000 0.00 0.00 0.00 4.02
22 23 7.773489 TTGGATCACAATTTAACAATCTCCA 57.227 32.000 0.00 0.00 33.18 3.86
23 24 9.657419 AATTTGGATCACAATTTAACAATCTCC 57.343 29.630 0.00 0.00 39.21 3.71
35 36 9.559732 TCAATACGATAGAATTTGGATCACAAT 57.440 29.630 0.00 0.00 38.35 2.71
36 37 8.826710 GTCAATACGATAGAATTTGGATCACAA 58.173 33.333 0.00 0.00 41.38 3.33
37 38 8.204160 AGTCAATACGATAGAATTTGGATCACA 58.796 33.333 0.00 0.00 41.38 3.58
38 39 8.594881 AGTCAATACGATAGAATTTGGATCAC 57.405 34.615 0.00 0.00 41.38 3.06
39 40 9.914131 CTAGTCAATACGATAGAATTTGGATCA 57.086 33.333 0.00 0.00 41.38 2.92
41 42 9.915629 GTCTAGTCAATACGATAGAATTTGGAT 57.084 33.333 0.00 0.00 41.38 3.41
42 43 8.074370 CGTCTAGTCAATACGATAGAATTTGGA 58.926 37.037 0.00 0.00 38.89 3.53
43 44 7.861372 ACGTCTAGTCAATACGATAGAATTTGG 59.139 37.037 7.80 0.00 39.80 3.28
44 45 8.783999 ACGTCTAGTCAATACGATAGAATTTG 57.216 34.615 7.80 0.00 39.80 2.32
46 47 9.270640 ACTACGTCTAGTCAATACGATAGAATT 57.729 33.333 7.80 0.00 39.80 2.17
47 48 8.830201 ACTACGTCTAGTCAATACGATAGAAT 57.170 34.615 7.80 0.00 39.80 2.40
48 49 9.920133 ATACTACGTCTAGTCAATACGATAGAA 57.080 33.333 7.80 0.00 39.80 2.10
53 54 9.278734 CGTATATACTACGTCTAGTCAATACGA 57.721 37.037 24.23 0.63 44.93 3.43
54 55 8.527488 CCGTATATACTACGTCTAGTCAATACG 58.473 40.741 22.98 22.98 43.71 3.06
55 56 9.360093 ACCGTATATACTACGTCTAGTCAATAC 57.640 37.037 11.05 2.57 39.09 1.89
56 57 9.358872 CACCGTATATACTACGTCTAGTCAATA 57.641 37.037 11.05 0.00 39.09 1.90
57 58 7.875041 ACACCGTATATACTACGTCTAGTCAAT 59.125 37.037 11.05 0.00 39.09 2.57
58 59 7.169813 CACACCGTATATACTACGTCTAGTCAA 59.830 40.741 11.05 0.00 39.09 3.18
59 60 6.642540 CACACCGTATATACTACGTCTAGTCA 59.357 42.308 11.05 0.00 39.09 3.41
60 61 6.090088 CCACACCGTATATACTACGTCTAGTC 59.910 46.154 11.05 0.00 39.09 2.59
61 62 5.928839 CCACACCGTATATACTACGTCTAGT 59.071 44.000 11.05 0.00 39.09 2.57
62 63 5.349817 CCCACACCGTATATACTACGTCTAG 59.650 48.000 11.05 0.00 39.09 2.43
63 64 5.237815 CCCACACCGTATATACTACGTCTA 58.762 45.833 11.05 0.00 39.09 2.59
64 65 4.067896 CCCACACCGTATATACTACGTCT 58.932 47.826 11.05 0.00 39.09 4.18
65 66 3.365364 GCCCACACCGTATATACTACGTC 60.365 52.174 11.05 0.00 39.09 4.34
66 67 2.554032 GCCCACACCGTATATACTACGT 59.446 50.000 11.05 0.00 39.09 3.57
67 68 2.095059 GGCCCACACCGTATATACTACG 60.095 54.545 11.05 0.48 40.30 3.51
68 69 3.160269 AGGCCCACACCGTATATACTAC 58.840 50.000 11.05 0.00 33.69 2.73
69 70 3.530928 AGGCCCACACCGTATATACTA 57.469 47.619 11.05 0.00 33.69 1.82
70 71 2.393630 AGGCCCACACCGTATATACT 57.606 50.000 11.05 0.00 33.69 2.12
71 72 3.135994 CAAAGGCCCACACCGTATATAC 58.864 50.000 0.00 2.53 33.69 1.47
72 73 2.485835 GCAAAGGCCCACACCGTATATA 60.486 50.000 0.00 0.00 33.69 0.86
73 74 1.749286 GCAAAGGCCCACACCGTATAT 60.749 52.381 0.00 0.00 33.69 0.86
74 75 0.393267 GCAAAGGCCCACACCGTATA 60.393 55.000 0.00 0.00 33.69 1.47
75 76 1.677633 GCAAAGGCCCACACCGTAT 60.678 57.895 0.00 0.00 33.69 3.06
76 77 2.281900 GCAAAGGCCCACACCGTA 60.282 61.111 0.00 0.00 33.69 4.02
79 80 3.223589 AACGCAAAGGCCCACACC 61.224 61.111 0.00 0.00 36.38 4.16
80 81 2.027460 CAACGCAAAGGCCCACAC 59.973 61.111 0.00 0.00 36.38 3.82
81 82 2.626255 TACCAACGCAAAGGCCCACA 62.626 55.000 0.00 0.00 36.38 4.17
82 83 1.899534 TACCAACGCAAAGGCCCAC 60.900 57.895 0.00 0.00 36.38 4.61
83 84 1.899534 GTACCAACGCAAAGGCCCA 60.900 57.895 0.00 0.00 36.38 5.36
84 85 2.632544 GGTACCAACGCAAAGGCCC 61.633 63.158 7.15 0.00 36.38 5.80
85 86 2.959372 GGTACCAACGCAAAGGCC 59.041 61.111 7.15 0.00 36.38 5.19
86 87 1.962306 TCGGTACCAACGCAAAGGC 60.962 57.895 13.54 0.00 0.00 4.35
87 88 1.864176 GTCGGTACCAACGCAAAGG 59.136 57.895 13.54 0.00 0.00 3.11
88 89 1.489824 CGTCGGTACCAACGCAAAG 59.510 57.895 13.28 0.00 31.48 2.77
89 90 3.627714 CGTCGGTACCAACGCAAA 58.372 55.556 13.28 0.00 31.48 3.68
93 94 2.145905 GTACGCGTCGGTACCAACG 61.146 63.158 21.11 21.11 41.68 4.10
94 95 2.145905 CGTACGCGTCGGTACCAAC 61.146 63.158 18.63 4.42 39.65 3.77
95 96 2.175566 CGTACGCGTCGGTACCAA 59.824 61.111 18.63 0.00 39.65 3.67
96 97 2.739704 CTCGTACGCGTCGGTACCA 61.740 63.158 18.63 0.00 39.65 3.25
97 98 1.418342 TACTCGTACGCGTCGGTACC 61.418 60.000 18.63 0.16 39.65 3.34
98 99 0.314339 GTACTCGTACGCGTCGGTAC 60.314 60.000 18.63 23.99 39.47 3.34
99 100 0.734597 TGTACTCGTACGCGTCGGTA 60.735 55.000 18.63 18.38 38.85 4.02
100 101 1.565156 TTGTACTCGTACGCGTCGGT 61.565 55.000 18.63 19.29 38.85 4.69
101 102 1.122419 GTTGTACTCGTACGCGTCGG 61.122 60.000 18.63 9.43 38.85 4.79
102 103 0.179240 AGTTGTACTCGTACGCGTCG 60.179 55.000 18.63 19.59 38.85 5.12
103 104 1.518286 GAGTTGTACTCGTACGCGTC 58.482 55.000 18.63 6.85 35.28 5.19
104 105 3.664930 GAGTTGTACTCGTACGCGT 57.335 52.632 19.17 19.17 35.28 6.01
117 118 3.724374 TGGAGGACAAGTAAACGAGTTG 58.276 45.455 0.00 0.00 43.22 3.16
118 119 4.411256 TTGGAGGACAAGTAAACGAGTT 57.589 40.909 0.00 0.00 33.18 3.01
138 139 3.185455 AGAGGGCAATACAAGAGTCCTT 58.815 45.455 0.00 0.00 0.00 3.36
139 140 2.839228 AGAGGGCAATACAAGAGTCCT 58.161 47.619 0.00 0.00 0.00 3.85
140 141 3.636153 AAGAGGGCAATACAAGAGTCC 57.364 47.619 0.00 0.00 0.00 3.85
141 142 8.035984 GGTATATAAGAGGGCAATACAAGAGTC 58.964 40.741 0.00 0.00 0.00 3.36
142 143 7.038231 GGGTATATAAGAGGGCAATACAAGAGT 60.038 40.741 0.00 0.00 0.00 3.24
143 144 7.331791 GGGTATATAAGAGGGCAATACAAGAG 58.668 42.308 0.00 0.00 0.00 2.85
144 145 6.214819 GGGGTATATAAGAGGGCAATACAAGA 59.785 42.308 0.00 0.00 0.00 3.02
145 146 6.012858 TGGGGTATATAAGAGGGCAATACAAG 60.013 42.308 0.00 0.00 0.00 3.16
146 147 5.852807 TGGGGTATATAAGAGGGCAATACAA 59.147 40.000 0.00 0.00 0.00 2.41
147 148 5.416858 TGGGGTATATAAGAGGGCAATACA 58.583 41.667 0.00 0.00 0.00 2.29
148 149 6.069615 ACATGGGGTATATAAGAGGGCAATAC 60.070 42.308 0.00 0.00 0.00 1.89
149 150 6.035973 ACATGGGGTATATAAGAGGGCAATA 58.964 40.000 0.00 0.00 0.00 1.90
150 151 4.857933 ACATGGGGTATATAAGAGGGCAAT 59.142 41.667 0.00 0.00 0.00 3.56
151 152 4.247814 ACATGGGGTATATAAGAGGGCAA 58.752 43.478 0.00 0.00 0.00 4.52
152 153 3.881871 ACATGGGGTATATAAGAGGGCA 58.118 45.455 0.00 0.00 0.00 5.36
153 154 6.576778 ATTACATGGGGTATATAAGAGGGC 57.423 41.667 0.00 0.00 0.00 5.19
154 155 6.685620 GCGATTACATGGGGTATATAAGAGGG 60.686 46.154 0.00 0.00 0.00 4.30
155 156 6.127168 TGCGATTACATGGGGTATATAAGAGG 60.127 42.308 0.00 0.00 0.00 3.69
156 157 6.757010 GTGCGATTACATGGGGTATATAAGAG 59.243 42.308 0.00 0.00 0.00 2.85
157 158 6.351541 GGTGCGATTACATGGGGTATATAAGA 60.352 42.308 0.00 0.00 0.00 2.10
158 159 5.815740 GGTGCGATTACATGGGGTATATAAG 59.184 44.000 0.00 0.00 0.00 1.73
159 160 5.486063 AGGTGCGATTACATGGGGTATATAA 59.514 40.000 0.00 0.00 0.00 0.98
160 161 5.027460 AGGTGCGATTACATGGGGTATATA 58.973 41.667 0.00 0.00 0.00 0.86
161 162 3.844211 AGGTGCGATTACATGGGGTATAT 59.156 43.478 0.00 0.00 0.00 0.86
162 163 3.244582 AGGTGCGATTACATGGGGTATA 58.755 45.455 0.00 0.00 0.00 1.47
163 164 2.054799 AGGTGCGATTACATGGGGTAT 58.945 47.619 0.00 0.00 0.00 2.73
164 165 1.502690 AGGTGCGATTACATGGGGTA 58.497 50.000 0.00 0.00 0.00 3.69
165 166 1.502690 TAGGTGCGATTACATGGGGT 58.497 50.000 0.00 0.00 0.00 4.95
166 167 2.631160 TTAGGTGCGATTACATGGGG 57.369 50.000 0.00 0.00 0.00 4.96
167 168 3.560068 GTCTTTAGGTGCGATTACATGGG 59.440 47.826 0.00 0.00 0.00 4.00
168 169 3.245284 CGTCTTTAGGTGCGATTACATGG 59.755 47.826 0.00 0.00 0.00 3.66
169 170 3.245284 CCGTCTTTAGGTGCGATTACATG 59.755 47.826 0.00 0.00 0.00 3.21
170 171 3.454375 CCGTCTTTAGGTGCGATTACAT 58.546 45.455 0.00 0.00 0.00 2.29
171 172 2.883574 CCGTCTTTAGGTGCGATTACA 58.116 47.619 0.00 0.00 0.00 2.41
172 173 1.591619 GCCGTCTTTAGGTGCGATTAC 59.408 52.381 0.00 0.00 0.00 1.89
173 174 1.472026 GGCCGTCTTTAGGTGCGATTA 60.472 52.381 0.00 0.00 0.00 1.75
174 175 0.743345 GGCCGTCTTTAGGTGCGATT 60.743 55.000 0.00 0.00 0.00 3.34
175 176 1.153429 GGCCGTCTTTAGGTGCGAT 60.153 57.895 0.00 0.00 0.00 4.58
176 177 2.263540 GGCCGTCTTTAGGTGCGA 59.736 61.111 0.00 0.00 0.00 5.10
177 178 2.100631 CAGGCCGTCTTTAGGTGCG 61.101 63.158 0.00 0.00 0.00 5.34
178 179 1.003718 ACAGGCCGTCTTTAGGTGC 60.004 57.895 0.00 0.00 0.00 5.01
179 180 0.736325 CGACAGGCCGTCTTTAGGTG 60.736 60.000 20.38 4.08 42.98 4.00
180 181 1.590147 CGACAGGCCGTCTTTAGGT 59.410 57.895 20.38 2.10 42.98 3.08
181 182 1.810030 GCGACAGGCCGTCTTTAGG 60.810 63.158 20.38 9.49 42.98 2.69
182 183 3.782042 GCGACAGGCCGTCTTTAG 58.218 61.111 20.38 9.77 42.98 1.85
198 199 2.159085 AGGAGTATTACAAGCACGAGGC 60.159 50.000 0.00 0.00 45.30 4.70
199 200 3.130516 TGAGGAGTATTACAAGCACGAGG 59.869 47.826 0.00 0.00 0.00 4.63
200 201 4.371855 TGAGGAGTATTACAAGCACGAG 57.628 45.455 0.00 0.00 0.00 4.18
201 202 5.593095 ACTATGAGGAGTATTACAAGCACGA 59.407 40.000 0.00 0.00 0.00 4.35
202 203 5.687730 CACTATGAGGAGTATTACAAGCACG 59.312 44.000 0.00 0.00 0.00 5.34
203 204 6.806751 TCACTATGAGGAGTATTACAAGCAC 58.193 40.000 0.00 0.00 0.00 4.40
204 205 7.603180 ATCACTATGAGGAGTATTACAAGCA 57.397 36.000 0.00 0.00 0.00 3.91
205 206 7.095439 GCAATCACTATGAGGAGTATTACAAGC 60.095 40.741 0.00 0.00 0.00 4.01
206 207 7.115520 CGCAATCACTATGAGGAGTATTACAAG 59.884 40.741 0.00 0.00 0.00 3.16
207 208 6.923508 CGCAATCACTATGAGGAGTATTACAA 59.076 38.462 0.00 0.00 0.00 2.41
208 209 6.447162 CGCAATCACTATGAGGAGTATTACA 58.553 40.000 0.00 0.00 0.00 2.41
209 210 5.346281 GCGCAATCACTATGAGGAGTATTAC 59.654 44.000 0.30 0.00 0.00 1.89
210 211 5.470368 GCGCAATCACTATGAGGAGTATTA 58.530 41.667 0.30 0.00 0.00 0.98
211 212 4.310769 GCGCAATCACTATGAGGAGTATT 58.689 43.478 0.30 0.00 0.00 1.89
212 213 3.306364 GGCGCAATCACTATGAGGAGTAT 60.306 47.826 10.83 0.00 0.00 2.12
213 214 2.035961 GGCGCAATCACTATGAGGAGTA 59.964 50.000 10.83 0.00 0.00 2.59
214 215 1.202580 GGCGCAATCACTATGAGGAGT 60.203 52.381 10.83 0.00 0.00 3.85
215 216 1.069823 AGGCGCAATCACTATGAGGAG 59.930 52.381 10.83 0.00 0.00 3.69
216 217 1.123077 AGGCGCAATCACTATGAGGA 58.877 50.000 10.83 0.00 0.00 3.71
217 218 1.869767 GAAGGCGCAATCACTATGAGG 59.130 52.381 10.83 0.00 0.00 3.86
218 219 1.524355 CGAAGGCGCAATCACTATGAG 59.476 52.381 10.83 0.00 0.00 2.90
219 220 1.134818 ACGAAGGCGCAATCACTATGA 60.135 47.619 10.83 0.00 42.48 2.15
220 221 1.290203 ACGAAGGCGCAATCACTATG 58.710 50.000 10.83 0.00 42.48 2.23
221 222 1.933853 GAACGAAGGCGCAATCACTAT 59.066 47.619 10.83 0.00 42.48 2.12
222 223 1.355971 GAACGAAGGCGCAATCACTA 58.644 50.000 10.83 0.00 42.48 2.74
223 224 1.626654 CGAACGAAGGCGCAATCACT 61.627 55.000 10.83 0.00 42.48 3.41
224 225 1.225745 CGAACGAAGGCGCAATCAC 60.226 57.895 10.83 0.00 42.48 3.06
225 226 1.623081 GACGAACGAAGGCGCAATCA 61.623 55.000 10.83 0.00 42.48 2.57
226 227 1.058903 GACGAACGAAGGCGCAATC 59.941 57.895 10.83 5.56 42.48 2.67
227 228 2.388232 GGACGAACGAAGGCGCAAT 61.388 57.895 10.83 0.00 42.48 3.56
228 229 3.039588 GGACGAACGAAGGCGCAA 61.040 61.111 10.83 0.00 42.48 4.85
231 232 3.467119 CACGGACGAACGAAGGCG 61.467 66.667 10.16 0.00 44.79 5.52
232 233 1.012486 AATCACGGACGAACGAAGGC 61.012 55.000 10.16 0.00 37.61 4.35
233 234 1.425412 AAATCACGGACGAACGAAGG 58.575 50.000 10.16 0.85 37.61 3.46
234 235 2.729882 AGAAAATCACGGACGAACGAAG 59.270 45.455 10.16 3.28 37.61 3.79
235 236 2.727798 GAGAAAATCACGGACGAACGAA 59.272 45.455 10.16 0.00 37.61 3.85
236 237 2.322161 GAGAAAATCACGGACGAACGA 58.678 47.619 10.16 0.00 37.61 3.85
237 238 1.389106 GGAGAAAATCACGGACGAACG 59.611 52.381 0.00 0.00 40.31 3.95
238 239 1.730612 GGGAGAAAATCACGGACGAAC 59.269 52.381 0.00 0.00 0.00 3.95
239 240 2.088950 GGGAGAAAATCACGGACGAA 57.911 50.000 0.00 0.00 0.00 3.85
240 241 3.826637 GGGAGAAAATCACGGACGA 57.173 52.632 0.00 0.00 0.00 4.20
257 258 0.885596 TTACGTGGAAACCCTTGCGG 60.886 55.000 0.00 0.00 37.81 5.69
258 259 0.945813 TTTACGTGGAAACCCTTGCG 59.054 50.000 0.00 0.00 0.00 4.85
259 260 3.439895 TTTTTACGTGGAAACCCTTGC 57.560 42.857 0.00 0.00 0.00 4.01
260 261 4.552355 GGATTTTTACGTGGAAACCCTTG 58.448 43.478 0.00 0.00 0.00 3.61
261 262 3.253921 CGGATTTTTACGTGGAAACCCTT 59.746 43.478 0.00 0.00 0.00 3.95
262 263 2.815503 CGGATTTTTACGTGGAAACCCT 59.184 45.455 0.00 0.00 0.00 4.34
263 264 2.553602 ACGGATTTTTACGTGGAAACCC 59.446 45.455 0.00 0.00 42.39 4.11
264 265 3.902261 ACGGATTTTTACGTGGAAACC 57.098 42.857 0.00 0.00 42.39 3.27
271 272 4.516365 AGAGAGACACGGATTTTTACGT 57.484 40.909 0.00 0.00 45.25 3.57
272 273 6.496571 AGATAGAGAGACACGGATTTTTACG 58.503 40.000 0.00 0.00 0.00 3.18
273 274 7.481642 TGAGATAGAGAGACACGGATTTTTAC 58.518 38.462 0.00 0.00 0.00 2.01
274 275 7.640597 TGAGATAGAGAGACACGGATTTTTA 57.359 36.000 0.00 0.00 0.00 1.52
275 276 6.531503 TGAGATAGAGAGACACGGATTTTT 57.468 37.500 0.00 0.00 0.00 1.94
276 277 6.723298 ATGAGATAGAGAGACACGGATTTT 57.277 37.500 0.00 0.00 0.00 1.82
277 278 6.723298 AATGAGATAGAGAGACACGGATTT 57.277 37.500 0.00 0.00 0.00 2.17
278 279 6.723298 AAATGAGATAGAGAGACACGGATT 57.277 37.500 0.00 0.00 0.00 3.01
279 280 8.415950 AATAAATGAGATAGAGAGACACGGAT 57.584 34.615 0.00 0.00 0.00 4.18
280 281 7.825331 AATAAATGAGATAGAGAGACACGGA 57.175 36.000 0.00 0.00 0.00 4.69
281 282 8.356657 AGAAATAAATGAGATAGAGAGACACGG 58.643 37.037 0.00 0.00 0.00 4.94
282 283 9.393249 GAGAAATAAATGAGATAGAGAGACACG 57.607 37.037 0.00 0.00 0.00 4.49
283 284 9.393249 CGAGAAATAAATGAGATAGAGAGACAC 57.607 37.037 0.00 0.00 0.00 3.67
284 285 9.126151 ACGAGAAATAAATGAGATAGAGAGACA 57.874 33.333 0.00 0.00 0.00 3.41
285 286 9.959749 AACGAGAAATAAATGAGATAGAGAGAC 57.040 33.333 0.00 0.00 0.00 3.36
302 303 8.827677 GGCTGTTGTTAGATAATAACGAGAAAT 58.172 33.333 7.44 0.00 39.29 2.17
303 304 7.820386 TGGCTGTTGTTAGATAATAACGAGAAA 59.180 33.333 7.44 0.00 39.29 2.52
304 305 7.324935 TGGCTGTTGTTAGATAATAACGAGAA 58.675 34.615 7.44 0.00 39.29 2.87
305 306 6.869695 TGGCTGTTGTTAGATAATAACGAGA 58.130 36.000 7.44 0.00 39.29 4.04
306 307 7.715265 ATGGCTGTTGTTAGATAATAACGAG 57.285 36.000 7.44 7.20 39.29 4.18
307 308 7.384115 GCTATGGCTGTTGTTAGATAATAACGA 59.616 37.037 0.00 0.00 39.29 3.85
308 309 7.360101 GGCTATGGCTGTTGTTAGATAATAACG 60.360 40.741 0.00 4.64 36.45 3.18
309 310 7.661847 AGGCTATGGCTGTTGTTAGATAATAAC 59.338 37.037 0.00 5.54 36.97 1.89
310 311 7.745717 AGGCTATGGCTGTTGTTAGATAATAA 58.254 34.615 0.00 0.00 36.97 1.40
311 312 7.316393 AGGCTATGGCTGTTGTTAGATAATA 57.684 36.000 0.00 0.00 36.97 0.98
312 313 6.192970 AGGCTATGGCTGTTGTTAGATAAT 57.807 37.500 0.00 0.00 36.97 1.28
313 314 5.630415 AGGCTATGGCTGTTGTTAGATAA 57.370 39.130 0.00 0.00 36.97 1.75
329 330 0.031817 AAATTGGCAGGGCAGGCTAT 60.032 50.000 4.52 0.00 34.73 2.97
331 332 1.129431 AAAAATTGGCAGGGCAGGCT 61.129 50.000 4.52 0.00 34.73 4.58
352 353 1.080705 GCGGTAGCAGTCAACGACT 60.081 57.895 0.00 0.00 44.44 4.18
369 370 2.222819 CGCTGATCTAAACGAAGGTTGC 60.223 50.000 0.00 0.00 36.25 4.17
378 379 1.852942 TCATCGGCGCTGATCTAAAC 58.147 50.000 28.64 0.00 0.00 2.01
382 383 1.224075 CAATTCATCGGCGCTGATCT 58.776 50.000 28.64 13.56 0.00 2.75
424 425 1.439679 GCGGAAAATCTGAACGGACT 58.560 50.000 0.00 0.00 0.00 3.85
426 427 0.675522 GGGCGGAAAATCTGAACGGA 60.676 55.000 0.00 0.00 0.00 4.69
535 542 4.348168 AGTCGCCATTTATGAGGGAACTAT 59.652 41.667 0.00 0.00 44.43 2.12
539 546 2.771943 AGAGTCGCCATTTATGAGGGAA 59.228 45.455 0.00 0.00 0.00 3.97
600 609 6.183360 CCATTCTTTTTACGATGCAAGAGCTA 60.183 38.462 0.00 0.00 42.74 3.32
611 620 4.280436 TCTCCAGCCATTCTTTTTACGA 57.720 40.909 0.00 0.00 0.00 3.43
960 972 2.749621 GGCTTCTAGCTTGCTTGCTTTA 59.250 45.455 9.11 0.00 43.74 1.85
1120 1132 3.626924 AGGCGCGTCCTTCTGGTT 61.627 61.111 7.31 0.00 44.75 3.67
1153 1165 3.078594 GAGATTCTTCAGCTCGAGGTC 57.921 52.381 15.54 1.30 0.00 3.85
1167 1179 2.110006 GCCAGCCTCCCGAGATTC 59.890 66.667 0.00 0.00 0.00 2.52
1683 1695 5.394224 CGCTATATTACAAGGGTCGGATGAT 60.394 44.000 0.00 0.00 0.00 2.45
2048 2124 5.343307 AAACAAGGTATGCCATTGAATCC 57.657 39.130 15.31 0.00 37.19 3.01
2138 2521 5.059161 CGTCATCCACCATTATGAACATCT 58.941 41.667 0.00 0.00 34.06 2.90
2148 2531 2.124736 CCGCCGTCATCCACCATT 60.125 61.111 0.00 0.00 0.00 3.16
2279 2664 6.769341 CAGGTCATTCATAAGTCATGATCCAA 59.231 38.462 0.00 0.00 43.26 3.53
2281 2666 6.528321 TCAGGTCATTCATAAGTCATGATCC 58.472 40.000 0.00 0.00 43.26 3.36
2384 2769 3.950395 GCTGCCTTCCTTCTGAATTGTAT 59.050 43.478 0.00 0.00 31.06 2.29
2419 2804 2.009774 ACGTAAAGGCTTGCAGCTATG 58.990 47.619 0.00 0.00 41.99 2.23
2460 2845 4.217767 CCAATGGCTCATACTGGATGATTG 59.782 45.833 2.40 5.12 43.78 2.67
2462 2847 3.813240 GCCAATGGCTCATACTGGATGAT 60.813 47.826 18.47 0.00 46.69 2.45
2485 2870 5.106118 GGCTCTTGGTTCTTCCTATTTTCAC 60.106 44.000 0.00 0.00 37.07 3.18
2554 2941 1.315690 CATGCCCGCAAGATCAATCT 58.684 50.000 0.00 0.00 43.02 2.40
2575 2962 3.056678 AGCGATCCAATTGTTGAATTGCA 60.057 39.130 4.43 0.00 44.95 4.08
2578 2965 5.359009 AGATCAGCGATCCAATTGTTGAATT 59.641 36.000 4.43 0.00 39.66 2.17
2586 2973 1.875576 GCCGAGATCAGCGATCCAATT 60.876 52.381 12.81 0.00 39.66 2.32


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

AutoCloner maintained by Alex Coulton.