Multiple sequence alignment - TraesCS6D01G210500

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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 TraesCS6D01G210500 chr6D 100.000 2723 0 0 1 2723 296994555 296991833 0.000000e+00 5029.0
1 TraesCS6D01G210500 chr6D 88.140 742 68 13 997 1722 298399325 298398588 0.000000e+00 865.0
2 TraesCS6D01G210500 chr6D 87.752 743 65 19 996 1722 297489908 297489176 0.000000e+00 845.0
3 TraesCS6D01G210500 chr6D 87.076 766 60 24 996 1725 298207285 298206523 0.000000e+00 830.0
4 TraesCS6D01G210500 chr6D 87.015 747 64 23 993 1722 297407382 297406652 0.000000e+00 811.0
5 TraesCS6D01G210500 chr6D 93.238 281 14 1 719 994 297490226 297489946 2.520000e-110 409.0
6 TraesCS6D01G210500 chr6D 90.690 290 22 1 712 996 297407713 297407424 5.500000e-102 381.0
7 TraesCS6D01G210500 chr6D 90.421 261 15 7 219 474 297514301 297514046 4.340000e-88 335.0
8 TraesCS6D01G210500 chr6D 90.000 140 13 1 219 357 297429168 297429029 2.150000e-41 180.0
9 TraesCS6D01G210500 chr6D 93.333 120 7 1 393 512 297407827 297407709 2.790000e-40 176.0
10 TraesCS6D01G210500 chr6D 91.589 107 6 3 98 203 297463278 297463174 7.860000e-31 145.0
11 TraesCS6D01G210500 chr6D 93.846 65 3 1 919 982 298207396 298207332 2.230000e-16 97.1
12 TraesCS6D01G210500 chr6D 94.118 51 3 0 462 512 297490279 297490229 8.080000e-11 78.7
13 TraesCS6D01G210500 chr6B 91.569 1791 69 26 993 2723 461394687 461392919 0.000000e+00 2396.0
14 TraesCS6D01G210500 chr6B 87.190 765 59 23 997 1722 461961868 461961104 0.000000e+00 833.0
15 TraesCS6D01G210500 chr6B 86.239 763 69 24 996 1722 461848265 461847503 0.000000e+00 795.0
16 TraesCS6D01G210500 chr6B 95.636 275 10 2 723 996 461395002 461394729 8.950000e-120 440.0
17 TraesCS6D01G210500 chr6B 93.515 293 18 1 222 514 461395289 461394998 4.160000e-118 435.0
18 TraesCS6D01G210500 chr6B 93.846 65 3 1 919 982 461848380 461848316 2.230000e-16 97.1
19 TraesCS6D01G210500 chr6A 95.315 1046 40 6 993 2030 421463817 421464861 0.000000e+00 1652.0
20 TraesCS6D01G210500 chr6A 85.366 779 67 28 990 1725 421226054 421226828 0.000000e+00 763.0
21 TraesCS6D01G210500 chr6A 88.926 605 47 12 2124 2718 421466642 421467236 0.000000e+00 728.0
22 TraesCS6D01G210500 chr6A 93.471 291 17 2 219 509 421367318 421367606 5.390000e-117 431.0
23 TraesCS6D01G210500 chr6A 94.035 285 16 1 712 996 421463492 421463775 5.390000e-117 431.0
24 TraesCS6D01G210500 chr6A 94.393 214 11 1 296 509 421463281 421463493 7.270000e-86 327.0
25 TraesCS6D01G210500 chr6A 93.583 187 11 1 712 898 421367605 421367790 7.430000e-71 278.0
26 TraesCS6D01G210500 chr6A 88.372 129 14 1 587 714 590221655 590221783 1.310000e-33 154.0
27 TraesCS6D01G210500 chr6A 92.135 89 6 1 98 186 421457089 421457176 1.020000e-24 124.0
28 TraesCS6D01G210500 chr6A 93.846 65 3 1 919 982 421225949 421226013 2.230000e-16 97.1
29 TraesCS6D01G210500 chr5D 90.226 133 10 3 587 717 410369278 410369409 1.300000e-38 171.0
30 TraesCS6D01G210500 chr5D 94.231 52 1 2 1 50 550115474 550115423 8.080000e-11 78.7
31 TraesCS6D01G210500 chr5D 84.000 75 2 5 518 584 556876776 556876704 2.260000e-06 63.9
32 TraesCS6D01G210500 chr7A 88.406 138 15 1 587 723 202997106 202996969 6.030000e-37 165.0
33 TraesCS6D01G210500 chr7A 87.879 132 15 1 587 717 538498357 538498226 1.310000e-33 154.0
34 TraesCS6D01G210500 chr7A 96.226 53 1 1 1 52 91007797 91007849 4.830000e-13 86.1
35 TraesCS6D01G210500 chr7A 82.178 101 7 5 512 604 214871782 214871879 2.910000e-10 76.8
36 TraesCS6D01G210500 chr7D 89.313 131 13 1 586 716 84805248 84805119 2.170000e-36 163.0
37 TraesCS6D01G210500 chr7D 96.000 50 2 0 1 50 617508470 617508421 6.250000e-12 82.4
38 TraesCS6D01G210500 chr3D 88.462 130 14 1 587 715 575137833 575137962 3.630000e-34 156.0
39 TraesCS6D01G210500 chr5A 88.372 129 14 1 587 714 690549370 690549498 1.310000e-33 154.0
40 TraesCS6D01G210500 chr4A 88.372 129 14 1 587 714 238399279 238399407 1.310000e-33 154.0
41 TraesCS6D01G210500 chr4A 92.000 50 2 2 512 561 552816087 552816134 4.870000e-08 69.4
42 TraesCS6D01G210500 chr1B 86.765 136 16 2 587 721 610020137 610020003 1.690000e-32 150.0
43 TraesCS6D01G210500 chr7B 96.154 52 1 1 1 51 686615963 686615912 1.740000e-12 84.2
44 TraesCS6D01G210500 chr2B 96.154 52 1 1 1 51 732891789 732891840 1.740000e-12 84.2
45 TraesCS6D01G210500 chr2B 94.340 53 2 1 512 563 545233650 545233598 2.250000e-11 80.5
46 TraesCS6D01G210500 chr2D 91.803 61 2 2 1 59 21007729 21007670 6.250000e-12 82.4
47 TraesCS6D01G210500 chr4B 94.340 53 2 1 1 52 146466942 146466994 2.250000e-11 80.5
48 TraesCS6D01G210500 chr3A 94.340 53 2 1 1 52 100896711 100896763 2.250000e-11 80.5
49 TraesCS6D01G210500 chr1D 94.231 52 1 1 1 50 450038168 450038117 8.080000e-11 78.7


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 TraesCS6D01G210500 chr6D 296991833 296994555 2722 True 5029.000000 5029 100.000000 1 2723 1 chr6D.!!$R1 2722
1 TraesCS6D01G210500 chr6D 298398588 298399325 737 True 865.000000 865 88.140000 997 1722 1 chr6D.!!$R5 725
2 TraesCS6D01G210500 chr6D 298206523 298207396 873 True 463.550000 830 90.461000 919 1725 2 chr6D.!!$R8 806
3 TraesCS6D01G210500 chr6D 297406652 297407827 1175 True 456.000000 811 90.346000 393 1722 3 chr6D.!!$R6 1329
4 TraesCS6D01G210500 chr6D 297489176 297490279 1103 True 444.233333 845 91.702667 462 1722 3 chr6D.!!$R7 1260
5 TraesCS6D01G210500 chr6B 461392919 461395289 2370 True 1090.333333 2396 93.573333 222 2723 3 chr6B.!!$R2 2501
6 TraesCS6D01G210500 chr6B 461961104 461961868 764 True 833.000000 833 87.190000 997 1722 1 chr6B.!!$R1 725
7 TraesCS6D01G210500 chr6B 461847503 461848380 877 True 446.050000 795 90.042500 919 1722 2 chr6B.!!$R3 803
8 TraesCS6D01G210500 chr6A 421463281 421467236 3955 False 784.500000 1652 93.167250 296 2718 4 chr6A.!!$F5 2422
9 TraesCS6D01G210500 chr6A 421225949 421226828 879 False 430.050000 763 89.606000 919 1725 2 chr6A.!!$F3 806

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
523 524 0.106149 AACGTGCTCCTCCGTTTCTT 59.894 50.0 0.0 0.0 44.16 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 2039 0.541392 TGCTGGATGAACACCGCTAT 59.459 50.0 0.0 0.0 0.0 2.97 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
65 66 3.442950 AAAAACGAGCCGTAAACGC 57.557 47.368 0.62 0.00 39.99 4.84
66 67 0.939419 AAAAACGAGCCGTAAACGCT 59.061 45.000 0.62 0.00 39.99 5.07
67 68 0.233848 AAAACGAGCCGTAAACGCTG 59.766 50.000 0.62 0.00 39.99 5.18
68 69 1.562575 AAACGAGCCGTAAACGCTGG 61.563 55.000 0.62 2.76 39.99 4.85
69 70 3.186047 CGAGCCGTAAACGCTGGG 61.186 66.667 0.00 0.00 38.18 4.45
70 71 2.047560 GAGCCGTAAACGCTGGGT 60.048 61.111 0.00 0.00 38.18 4.51
71 72 2.047560 AGCCGTAAACGCTGGGTC 60.048 61.111 0.00 0.00 38.18 4.46
72 73 2.047560 GCCGTAAACGCTGGGTCT 60.048 61.111 0.00 0.00 38.18 3.85
73 74 2.098831 GCCGTAAACGCTGGGTCTC 61.099 63.158 0.00 0.00 38.18 3.36
74 75 1.590147 CCGTAAACGCTGGGTCTCT 59.410 57.895 0.00 0.00 38.18 3.10
75 76 0.458025 CCGTAAACGCTGGGTCTCTC 60.458 60.000 0.00 0.00 38.18 3.20
76 77 0.526662 CGTAAACGCTGGGTCTCTCT 59.473 55.000 0.00 0.00 0.00 3.10
77 78 1.067776 CGTAAACGCTGGGTCTCTCTT 60.068 52.381 0.00 0.00 0.00 2.85
78 79 2.609737 CGTAAACGCTGGGTCTCTCTTT 60.610 50.000 0.00 0.00 0.00 2.52
79 80 2.640316 AAACGCTGGGTCTCTCTTTT 57.360 45.000 0.00 0.00 0.00 2.27
80 81 2.640316 AACGCTGGGTCTCTCTTTTT 57.360 45.000 0.00 0.00 0.00 1.94
106 107 2.994186 TTTTAGGGATACGCTGGGTC 57.006 50.000 0.00 0.00 37.60 4.46
107 108 2.170012 TTTAGGGATACGCTGGGTCT 57.830 50.000 0.00 0.00 37.60 3.85
108 109 1.700955 TTAGGGATACGCTGGGTCTC 58.299 55.000 0.00 0.82 37.60 3.36
109 110 0.851469 TAGGGATACGCTGGGTCTCT 59.149 55.000 0.00 0.00 37.60 3.10
110 111 0.468400 AGGGATACGCTGGGTCTCTC 60.468 60.000 0.00 0.92 37.60 3.20
111 112 0.468400 GGGATACGCTGGGTCTCTCT 60.468 60.000 0.00 0.00 37.60 3.10
112 113 1.404843 GGATACGCTGGGTCTCTCTT 58.595 55.000 0.00 0.00 0.00 2.85
113 114 1.067821 GGATACGCTGGGTCTCTCTTG 59.932 57.143 0.00 0.00 0.00 3.02
114 115 1.067821 GATACGCTGGGTCTCTCTTGG 59.932 57.143 0.00 0.00 0.00 3.61
115 116 0.251653 TACGCTGGGTCTCTCTTGGT 60.252 55.000 0.00 0.00 0.00 3.67
116 117 1.122019 ACGCTGGGTCTCTCTTGGTT 61.122 55.000 0.00 0.00 0.00 3.67
117 118 0.671781 CGCTGGGTCTCTCTTGGTTG 60.672 60.000 0.00 0.00 0.00 3.77
118 119 0.687354 GCTGGGTCTCTCTTGGTTGA 59.313 55.000 0.00 0.00 0.00 3.18
119 120 1.072331 GCTGGGTCTCTCTTGGTTGAA 59.928 52.381 0.00 0.00 0.00 2.69
120 121 2.290577 GCTGGGTCTCTCTTGGTTGAAT 60.291 50.000 0.00 0.00 0.00 2.57
121 122 3.812167 GCTGGGTCTCTCTTGGTTGAATT 60.812 47.826 0.00 0.00 0.00 2.17
122 123 3.754965 TGGGTCTCTCTTGGTTGAATTG 58.245 45.455 0.00 0.00 0.00 2.32
123 124 3.138283 TGGGTCTCTCTTGGTTGAATTGT 59.862 43.478 0.00 0.00 0.00 2.71
124 125 4.145052 GGGTCTCTCTTGGTTGAATTGTT 58.855 43.478 0.00 0.00 0.00 2.83
125 126 4.216472 GGGTCTCTCTTGGTTGAATTGTTC 59.784 45.833 0.00 0.00 0.00 3.18
126 127 4.821805 GGTCTCTCTTGGTTGAATTGTTCA 59.178 41.667 0.00 0.00 38.04 3.18
127 128 5.049129 GGTCTCTCTTGGTTGAATTGTTCAG 60.049 44.000 0.00 0.00 41.38 3.02
128 129 5.529060 GTCTCTCTTGGTTGAATTGTTCAGT 59.471 40.000 0.00 0.00 41.38 3.41
129 130 5.528690 TCTCTCTTGGTTGAATTGTTCAGTG 59.471 40.000 0.00 0.00 41.38 3.66
130 131 5.436175 TCTCTTGGTTGAATTGTTCAGTGA 58.564 37.500 0.00 0.00 41.38 3.41
131 132 5.528690 TCTCTTGGTTGAATTGTTCAGTGAG 59.471 40.000 0.00 0.00 41.38 3.51
132 133 4.580167 TCTTGGTTGAATTGTTCAGTGAGG 59.420 41.667 0.00 0.00 41.38 3.86
133 134 2.622942 TGGTTGAATTGTTCAGTGAGGC 59.377 45.455 0.00 0.00 41.38 4.70
134 135 2.887152 GGTTGAATTGTTCAGTGAGGCT 59.113 45.455 0.00 0.00 41.38 4.58
135 136 3.319122 GGTTGAATTGTTCAGTGAGGCTT 59.681 43.478 0.00 0.00 41.38 4.35
136 137 4.540824 GTTGAATTGTTCAGTGAGGCTTC 58.459 43.478 0.00 0.00 41.38 3.86
137 138 2.807967 TGAATTGTTCAGTGAGGCTTCG 59.192 45.455 0.00 0.00 34.08 3.79
138 139 2.839486 ATTGTTCAGTGAGGCTTCGA 57.161 45.000 0.00 0.00 0.00 3.71
139 140 1.865865 TTGTTCAGTGAGGCTTCGAC 58.134 50.000 0.00 0.00 0.00 4.20
140 141 0.318699 TGTTCAGTGAGGCTTCGACG 60.319 55.000 0.00 0.00 0.00 5.12
141 142 1.009389 GTTCAGTGAGGCTTCGACGG 61.009 60.000 0.00 0.00 0.00 4.79
142 143 2.765250 TTCAGTGAGGCTTCGACGGC 62.765 60.000 7.44 7.44 0.00 5.68
143 144 4.421479 AGTGAGGCTTCGACGGCG 62.421 66.667 2.87 2.87 39.35 6.46
162 163 1.421485 CGTCCATCGCAAGTGAAGC 59.579 57.895 0.00 0.00 39.48 3.86
185 186 4.047059 GACCCCGCGACGTCTTGA 62.047 66.667 14.70 0.00 0.00 3.02
186 187 3.352338 GACCCCGCGACGTCTTGAT 62.352 63.158 14.70 0.00 0.00 2.57
187 188 1.996786 GACCCCGCGACGTCTTGATA 61.997 60.000 14.70 0.00 0.00 2.15
188 189 1.140161 CCCCGCGACGTCTTGATAA 59.860 57.895 14.70 0.00 0.00 1.75
189 190 0.458889 CCCCGCGACGTCTTGATAAA 60.459 55.000 14.70 0.00 0.00 1.40
190 191 0.921347 CCCGCGACGTCTTGATAAAG 59.079 55.000 14.70 0.00 0.00 1.85
191 192 1.468565 CCCGCGACGTCTTGATAAAGA 60.469 52.381 14.70 0.00 0.00 2.52
192 193 1.582502 CCGCGACGTCTTGATAAAGAC 59.417 52.381 14.70 12.47 44.28 3.01
193 194 1.582502 CGCGACGTCTTGATAAAGACC 59.417 52.381 16.10 3.68 44.75 3.85
194 195 2.731341 CGCGACGTCTTGATAAAGACCT 60.731 50.000 16.10 5.83 44.75 3.85
195 196 3.486375 CGCGACGTCTTGATAAAGACCTA 60.486 47.826 16.10 0.00 44.75 3.08
196 197 4.418392 GCGACGTCTTGATAAAGACCTAA 58.582 43.478 16.10 0.00 44.75 2.69
197 198 4.264849 GCGACGTCTTGATAAAGACCTAAC 59.735 45.833 16.10 5.61 44.75 2.34
198 199 5.396484 CGACGTCTTGATAAAGACCTAACA 58.604 41.667 16.10 0.00 44.75 2.41
199 200 6.034591 CGACGTCTTGATAAAGACCTAACAT 58.965 40.000 16.10 0.00 44.75 2.71
200 201 6.020599 CGACGTCTTGATAAAGACCTAACATG 60.021 42.308 16.10 4.22 44.75 3.21
201 202 5.581085 ACGTCTTGATAAAGACCTAACATGC 59.419 40.000 16.10 0.00 44.75 4.06
202 203 5.812642 CGTCTTGATAAAGACCTAACATGCT 59.187 40.000 16.10 0.00 44.75 3.79
203 204 6.978659 CGTCTTGATAAAGACCTAACATGCTA 59.021 38.462 16.10 0.00 44.75 3.49
204 205 7.168302 CGTCTTGATAAAGACCTAACATGCTAG 59.832 40.741 16.10 0.00 44.75 3.42
205 206 8.198109 GTCTTGATAAAGACCTAACATGCTAGA 58.802 37.037 11.53 0.00 42.47 2.43
206 207 8.417106 TCTTGATAAAGACCTAACATGCTAGAG 58.583 37.037 4.66 0.00 0.00 2.43
207 208 7.898014 TGATAAAGACCTAACATGCTAGAGA 57.102 36.000 4.66 0.00 0.00 3.10
208 209 7.946207 TGATAAAGACCTAACATGCTAGAGAG 58.054 38.462 4.66 0.00 0.00 3.20
209 210 7.780271 TGATAAAGACCTAACATGCTAGAGAGA 59.220 37.037 4.66 0.00 0.00 3.10
210 211 6.463995 AAAGACCTAACATGCTAGAGAGAG 57.536 41.667 4.66 0.00 0.00 3.20
211 212 3.888930 AGACCTAACATGCTAGAGAGAGC 59.111 47.826 4.66 0.00 43.16 4.09
212 213 3.888930 GACCTAACATGCTAGAGAGAGCT 59.111 47.826 4.66 0.00 43.27 4.09
213 214 5.055265 ACCTAACATGCTAGAGAGAGCTA 57.945 43.478 4.66 0.00 43.27 3.32
214 215 5.450453 ACCTAACATGCTAGAGAGAGCTAA 58.550 41.667 4.66 0.00 43.27 3.09
215 216 5.534654 ACCTAACATGCTAGAGAGAGCTAAG 59.465 44.000 4.66 0.00 43.27 2.18
216 217 4.320608 AACATGCTAGAGAGAGCTAAGC 57.679 45.455 0.00 0.00 43.27 3.09
217 218 3.565307 ACATGCTAGAGAGAGCTAAGCT 58.435 45.455 0.00 0.00 43.27 3.74
218 219 3.318839 ACATGCTAGAGAGAGCTAAGCTG 59.681 47.826 0.00 0.00 43.27 4.24
219 220 3.011566 TGCTAGAGAGAGCTAAGCTGT 57.988 47.619 0.00 0.00 43.27 4.40
220 221 3.360867 TGCTAGAGAGAGCTAAGCTGTT 58.639 45.455 0.00 0.00 43.27 3.16
251 252 5.755861 GTGCTCACAGTCTAAGAAAGAAAGT 59.244 40.000 0.00 0.00 35.47 2.66
253 254 6.258727 TGCTCACAGTCTAAGAAAGAAAGTTG 59.741 38.462 0.00 0.00 35.47 3.16
256 257 6.480320 TCACAGTCTAAGAAAGAAAGTTGAGC 59.520 38.462 0.00 0.00 35.47 4.26
352 353 6.896021 TTATTCACCAATAACCGGAAACAA 57.104 33.333 9.46 0.00 30.74 2.83
358 359 4.585162 ACCAATAACCGGAAACAATTGTGA 59.415 37.500 12.82 0.00 0.00 3.58
448 449 2.693762 GCACACACGCATGCCTGAT 61.694 57.895 21.37 7.80 35.73 2.90
479 480 9.751542 CAAACTTTTGTACTTAGAGAGAGAAGA 57.248 33.333 0.00 0.00 33.59 2.87
509 510 0.381801 ACAAGGAAGCAAGCAACGTG 59.618 50.000 0.00 0.00 0.00 4.49
520 521 2.251642 GCAACGTGCTCCTCCGTTT 61.252 57.895 0.00 0.00 44.16 3.60
521 522 1.860078 CAACGTGCTCCTCCGTTTC 59.140 57.895 0.00 0.00 44.16 2.78
522 523 0.600255 CAACGTGCTCCTCCGTTTCT 60.600 55.000 0.00 0.00 44.16 2.52
523 524 0.106149 AACGTGCTCCTCCGTTTCTT 59.894 50.000 0.00 0.00 44.16 2.52
524 525 0.106149 ACGTGCTCCTCCGTTTCTTT 59.894 50.000 0.00 0.00 32.50 2.52
525 526 1.342174 ACGTGCTCCTCCGTTTCTTTA 59.658 47.619 0.00 0.00 32.50 1.85
526 527 2.224113 ACGTGCTCCTCCGTTTCTTTAA 60.224 45.455 0.00 0.00 32.50 1.52
527 528 2.412089 CGTGCTCCTCCGTTTCTTTAAG 59.588 50.000 0.00 0.00 0.00 1.85
528 529 3.400255 GTGCTCCTCCGTTTCTTTAAGT 58.600 45.455 0.00 0.00 0.00 2.24
529 530 3.432592 GTGCTCCTCCGTTTCTTTAAGTC 59.567 47.826 0.00 0.00 0.00 3.01
530 531 3.323979 TGCTCCTCCGTTTCTTTAAGTCT 59.676 43.478 0.00 0.00 0.00 3.24
531 532 3.680458 GCTCCTCCGTTTCTTTAAGTCTG 59.320 47.826 0.00 0.00 0.00 3.51
532 533 3.660865 TCCTCCGTTTCTTTAAGTCTGC 58.339 45.455 0.00 0.00 0.00 4.26
533 534 3.070446 TCCTCCGTTTCTTTAAGTCTGCA 59.930 43.478 0.00 0.00 0.00 4.41
534 535 4.003648 CCTCCGTTTCTTTAAGTCTGCAT 58.996 43.478 0.00 0.00 0.00 3.96
535 536 5.046878 TCCTCCGTTTCTTTAAGTCTGCATA 60.047 40.000 0.00 0.00 0.00 3.14
536 537 5.817816 CCTCCGTTTCTTTAAGTCTGCATAT 59.182 40.000 0.00 0.00 0.00 1.78
537 538 6.984474 CCTCCGTTTCTTTAAGTCTGCATATA 59.016 38.462 0.00 0.00 0.00 0.86
538 539 7.494625 CCTCCGTTTCTTTAAGTCTGCATATAA 59.505 37.037 0.00 0.00 0.00 0.98
539 540 8.420374 TCCGTTTCTTTAAGTCTGCATATAAG 57.580 34.615 0.00 0.00 0.00 1.73
540 541 8.255206 TCCGTTTCTTTAAGTCTGCATATAAGA 58.745 33.333 0.00 0.00 0.00 2.10
541 542 9.046296 CCGTTTCTTTAAGTCTGCATATAAGAT 57.954 33.333 0.00 0.00 0.00 2.40
607 608 9.764363 AAAGTATCACGCATCTTCTAATATTGA 57.236 29.630 0.00 0.00 0.00 2.57
608 609 9.935241 AAGTATCACGCATCTTCTAATATTGAT 57.065 29.630 0.00 0.00 0.00 2.57
609 610 9.935241 AGTATCACGCATCTTCTAATATTGATT 57.065 29.630 0.00 0.00 0.00 2.57
612 613 8.661352 TCACGCATCTTCTAATATTGATTTCA 57.339 30.769 0.00 0.00 0.00 2.69
613 614 9.276590 TCACGCATCTTCTAATATTGATTTCAT 57.723 29.630 0.00 0.00 0.00 2.57
637 638 9.941664 CATAGTGTGAATGTTGATATCTTTTCC 57.058 33.333 3.98 0.00 0.00 3.13
638 639 9.911788 ATAGTGTGAATGTTGATATCTTTTCCT 57.088 29.630 3.98 0.00 0.00 3.36
640 641 9.167311 AGTGTGAATGTTGATATCTTTTCCTAC 57.833 33.333 3.98 4.53 0.00 3.18
641 642 8.116753 GTGTGAATGTTGATATCTTTTCCTACG 58.883 37.037 3.98 0.00 0.00 3.51
642 643 8.038351 TGTGAATGTTGATATCTTTTCCTACGA 58.962 33.333 3.98 0.00 0.00 3.43
643 644 8.879759 GTGAATGTTGATATCTTTTCCTACGAA 58.120 33.333 3.98 0.00 0.00 3.85
644 645 9.098355 TGAATGTTGATATCTTTTCCTACGAAG 57.902 33.333 3.98 0.00 0.00 3.79
646 647 9.449719 AATGTTGATATCTTTTCCTACGAAGTT 57.550 29.630 3.98 0.00 37.78 2.66
648 649 9.582431 TGTTGATATCTTTTCCTACGAAGTTAG 57.418 33.333 3.98 0.00 37.78 2.34
649 650 9.583765 GTTGATATCTTTTCCTACGAAGTTAGT 57.416 33.333 3.98 0.00 37.78 2.24
650 651 9.798994 TTGATATCTTTTCCTACGAAGTTAGTC 57.201 33.333 3.98 0.00 37.78 2.59
651 652 8.963725 TGATATCTTTTCCTACGAAGTTAGTCA 58.036 33.333 3.98 0.00 37.78 3.41
652 653 9.798994 GATATCTTTTCCTACGAAGTTAGTCAA 57.201 33.333 0.00 0.00 37.78 3.18
654 655 7.704789 TCTTTTCCTACGAAGTTAGTCAAAC 57.295 36.000 0.00 0.00 37.78 2.93
688 689 9.787532 AATTTGATTTTGACCAGATGTTATACG 57.212 29.630 0.00 0.00 0.00 3.06
689 690 6.358118 TGATTTTGACCAGATGTTATACGC 57.642 37.500 0.00 0.00 0.00 4.42
690 691 5.877564 TGATTTTGACCAGATGTTATACGCA 59.122 36.000 0.00 0.00 0.00 5.24
691 692 6.372937 TGATTTTGACCAGATGTTATACGCAA 59.627 34.615 0.00 0.00 0.00 4.85
692 693 6.561737 TTTTGACCAGATGTTATACGCAAA 57.438 33.333 0.00 0.00 0.00 3.68
693 694 5.539582 TTGACCAGATGTTATACGCAAAC 57.460 39.130 0.00 0.00 0.00 2.93
694 695 4.827692 TGACCAGATGTTATACGCAAACT 58.172 39.130 0.00 0.00 0.00 2.66
695 696 5.968254 TGACCAGATGTTATACGCAAACTA 58.032 37.500 0.00 0.00 0.00 2.24
696 697 6.399743 TGACCAGATGTTATACGCAAACTAA 58.600 36.000 0.00 0.00 0.00 2.24
697 698 6.874664 TGACCAGATGTTATACGCAAACTAAA 59.125 34.615 0.00 0.00 0.00 1.85
698 699 7.388224 TGACCAGATGTTATACGCAAACTAAAA 59.612 33.333 0.00 0.00 0.00 1.52
699 700 8.101654 ACCAGATGTTATACGCAAACTAAAAA 57.898 30.769 0.00 0.00 0.00 1.94
747 748 9.565213 GACTCCATCATTCAAACAATAGAAAAG 57.435 33.333 0.00 0.00 0.00 2.27
749 750 7.322664 TCCATCATTCAAACAATAGAAAAGGC 58.677 34.615 0.00 0.00 0.00 4.35
774 776 3.965347 ACTACCACTTGGATATAACGCCT 59.035 43.478 1.14 0.00 38.94 5.52
781 783 4.750098 ACTTGGATATAACGCCTCAATTCG 59.250 41.667 0.00 0.00 0.00 3.34
905 912 0.692476 AATCTACACAGCACCAGCCA 59.308 50.000 0.00 0.00 43.56 4.75
908 915 1.207089 TCTACACAGCACCAGCCATAC 59.793 52.381 0.00 0.00 43.56 2.39
1032 1137 2.989253 TGCTGCGAGAAGACGGGA 60.989 61.111 0.00 0.00 0.00 5.14
1350 1455 0.523966 ACCTCAAGAAGCGACTCGAG 59.476 55.000 11.84 11.84 0.00 4.04
1490 1628 2.884207 GTCGTCCGCCACCGATTC 60.884 66.667 0.00 0.00 35.30 2.52
1569 1713 3.611970 TGAAGACAGTTTTTGGTCGGAA 58.388 40.909 0.00 0.00 39.01 4.30
1598 1742 3.371063 GACGGTGGACAGCTCCGA 61.371 66.667 16.85 0.00 46.05 4.55
1698 1848 1.610038 CTGTTCATGCAAGCTGGTGAA 59.390 47.619 0.00 0.00 0.00 3.18
1773 1924 7.554118 AGTTTCTTGTTCATTTCTTGTCTCTCA 59.446 33.333 0.00 0.00 0.00 3.27
1808 1959 8.732746 AAAATCTTTGGCATATACTACTTCGT 57.267 30.769 0.00 0.00 0.00 3.85
1853 2018 2.484264 CCTGTAAAACGGAAGAGCTTGG 59.516 50.000 0.00 0.00 0.00 3.61
1862 2027 1.075536 GGAAGAGCTTGGGAAGGGAAA 59.924 52.381 0.00 0.00 0.00 3.13
1874 2039 5.326069 TGGGAAGGGAAAAATAATCGTTCA 58.674 37.500 0.00 0.00 0.00 3.18
2059 2255 1.003233 GTGGAGGGGTGAAGTTGTAGG 59.997 57.143 0.00 0.00 0.00 3.18
2136 3994 0.813184 CGTCCGTTAGGTAAGCTGGA 59.187 55.000 0.00 0.00 39.05 3.86
2141 3999 2.618053 CGTTAGGTAAGCTGGAGGTTG 58.382 52.381 1.30 0.00 37.00 3.77
2185 4043 3.257624 AGTCACTAAGTAGGGAACAACGG 59.742 47.826 0.00 0.00 37.51 4.44
2186 4044 3.256631 GTCACTAAGTAGGGAACAACGGA 59.743 47.826 0.00 0.00 37.51 4.69
2187 4045 3.508793 TCACTAAGTAGGGAACAACGGAG 59.491 47.826 0.00 0.00 31.65 4.63
2188 4046 4.994099 TCACTAAGTAGGGAACAACGGAGT 60.994 45.833 0.00 0.00 35.41 3.85
2189 4047 4.460382 CACTAAGTAGGGAACAACGGAGTA 59.540 45.833 0.00 0.00 45.00 2.59
2190 4048 4.704057 ACTAAGTAGGGAACAACGGAGTAG 59.296 45.833 0.00 0.00 45.00 2.57
2191 4049 3.166560 AGTAGGGAACAACGGAGTAGT 57.833 47.619 0.00 0.00 45.00 2.73
2192 4050 2.824341 AGTAGGGAACAACGGAGTAGTG 59.176 50.000 0.00 0.00 45.00 2.74
2193 4051 1.713297 AGGGAACAACGGAGTAGTGT 58.287 50.000 0.00 0.00 45.00 3.55
2194 4052 1.617357 AGGGAACAACGGAGTAGTGTC 59.383 52.381 0.00 0.00 45.00 3.67
2195 4053 1.342174 GGGAACAACGGAGTAGTGTCA 59.658 52.381 0.00 0.00 45.00 3.58
2228 4086 2.502142 TGTGGCTACCTCGACTAGAA 57.498 50.000 0.00 0.00 0.00 2.10
2284 4142 4.100498 ACGATCGGGTGGACTTATTGTAAT 59.900 41.667 20.98 0.00 0.00 1.89
2290 4148 5.875910 CGGGTGGACTTATTGTAATTGTGTA 59.124 40.000 0.00 0.00 0.00 2.90
2400 4258 7.425224 TTGGTTAAAGGAAAAGTGAAATCCA 57.575 32.000 0.00 0.00 35.62 3.41
2572 4435 4.643784 TCCCCTGCGTGTTTTTAAAACTTA 59.356 37.500 19.39 0.00 0.00 2.24
2683 4554 7.901889 GCATACATGATTACAAGCTAATCATCG 59.098 37.037 16.80 14.68 46.05 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 0.939419 AGCGTTTACGGCTCGTTTTT 59.061 45.000 5.57 0.00 41.54 1.94
48 49 0.233848 CAGCGTTTACGGCTCGTTTT 59.766 50.000 5.57 0.00 41.54 2.43
49 50 1.562575 CCAGCGTTTACGGCTCGTTT 61.563 55.000 5.57 0.00 41.54 3.60
50 51 2.025418 CCAGCGTTTACGGCTCGTT 61.025 57.895 5.57 0.00 41.54 3.85
51 52 2.431942 CCAGCGTTTACGGCTCGT 60.432 61.111 4.29 5.58 44.35 4.18
52 53 3.186047 CCCAGCGTTTACGGCTCG 61.186 66.667 4.29 0.00 40.23 5.03
53 54 2.047560 ACCCAGCGTTTACGGCTC 60.048 61.111 4.29 0.00 40.23 4.70
54 55 2.047560 GACCCAGCGTTTACGGCT 60.048 61.111 4.29 0.00 40.23 5.52
55 56 2.047560 AGACCCAGCGTTTACGGC 60.048 61.111 4.29 0.00 40.23 5.68
56 57 0.458025 GAGAGACCCAGCGTTTACGG 60.458 60.000 4.29 0.00 40.23 4.02
57 58 0.526662 AGAGAGACCCAGCGTTTACG 59.473 55.000 0.00 0.00 43.27 3.18
58 59 2.745515 AAGAGAGACCCAGCGTTTAC 57.254 50.000 0.00 0.00 0.00 2.01
59 60 3.764237 AAAAGAGAGACCCAGCGTTTA 57.236 42.857 0.00 0.00 0.00 2.01
60 61 2.640316 AAAAGAGAGACCCAGCGTTT 57.360 45.000 0.00 0.00 0.00 3.60
61 62 2.640316 AAAAAGAGAGACCCAGCGTT 57.360 45.000 0.00 0.00 0.00 4.84
86 87 2.841881 AGACCCAGCGTATCCCTAAAAA 59.158 45.455 0.00 0.00 0.00 1.94
87 88 2.433239 GAGACCCAGCGTATCCCTAAAA 59.567 50.000 0.00 0.00 0.00 1.52
88 89 2.037144 GAGACCCAGCGTATCCCTAAA 58.963 52.381 0.00 0.00 0.00 1.85
89 90 1.217183 AGAGACCCAGCGTATCCCTAA 59.783 52.381 0.00 0.00 32.84 2.69
90 91 0.851469 AGAGACCCAGCGTATCCCTA 59.149 55.000 0.00 0.00 32.84 3.53
91 92 0.468400 GAGAGACCCAGCGTATCCCT 60.468 60.000 0.00 0.00 32.84 4.20
92 93 0.468400 AGAGAGACCCAGCGTATCCC 60.468 60.000 0.00 0.00 32.84 3.85
93 94 1.067821 CAAGAGAGACCCAGCGTATCC 59.932 57.143 0.00 0.00 32.84 2.59
94 95 1.067821 CCAAGAGAGACCCAGCGTATC 59.932 57.143 0.00 0.00 32.56 2.24
95 96 1.115467 CCAAGAGAGACCCAGCGTAT 58.885 55.000 0.00 0.00 0.00 3.06
96 97 0.251653 ACCAAGAGAGACCCAGCGTA 60.252 55.000 0.00 0.00 0.00 4.42
97 98 1.122019 AACCAAGAGAGACCCAGCGT 61.122 55.000 0.00 0.00 0.00 5.07
98 99 0.671781 CAACCAAGAGAGACCCAGCG 60.672 60.000 0.00 0.00 0.00 5.18
99 100 0.687354 TCAACCAAGAGAGACCCAGC 59.313 55.000 0.00 0.00 0.00 4.85
100 101 3.710209 ATTCAACCAAGAGAGACCCAG 57.290 47.619 0.00 0.00 0.00 4.45
101 102 3.138283 ACAATTCAACCAAGAGAGACCCA 59.862 43.478 0.00 0.00 0.00 4.51
102 103 3.756117 ACAATTCAACCAAGAGAGACCC 58.244 45.455 0.00 0.00 0.00 4.46
103 104 4.821805 TGAACAATTCAACCAAGAGAGACC 59.178 41.667 0.00 0.00 36.59 3.85
104 105 5.529060 ACTGAACAATTCAACCAAGAGAGAC 59.471 40.000 0.00 0.00 39.58 3.36
105 106 5.528690 CACTGAACAATTCAACCAAGAGAGA 59.471 40.000 0.00 0.00 39.58 3.10
106 107 5.528690 TCACTGAACAATTCAACCAAGAGAG 59.471 40.000 0.00 0.00 39.58 3.20
107 108 5.436175 TCACTGAACAATTCAACCAAGAGA 58.564 37.500 0.00 0.00 39.58 3.10
108 109 5.278169 CCTCACTGAACAATTCAACCAAGAG 60.278 44.000 0.00 0.00 39.58 2.85
109 110 4.580167 CCTCACTGAACAATTCAACCAAGA 59.420 41.667 0.00 0.00 39.58 3.02
110 111 4.794003 GCCTCACTGAACAATTCAACCAAG 60.794 45.833 0.00 0.00 39.58 3.61
111 112 3.068024 GCCTCACTGAACAATTCAACCAA 59.932 43.478 0.00 0.00 39.58 3.67
112 113 2.622942 GCCTCACTGAACAATTCAACCA 59.377 45.455 0.00 0.00 39.58 3.67
113 114 2.887152 AGCCTCACTGAACAATTCAACC 59.113 45.455 0.00 0.00 39.58 3.77
114 115 4.540824 GAAGCCTCACTGAACAATTCAAC 58.459 43.478 0.00 0.00 39.58 3.18
115 116 3.250762 CGAAGCCTCACTGAACAATTCAA 59.749 43.478 0.00 0.00 39.58 2.69
116 117 2.807967 CGAAGCCTCACTGAACAATTCA 59.192 45.455 0.00 0.00 38.17 2.57
117 118 3.067106 TCGAAGCCTCACTGAACAATTC 58.933 45.455 0.00 0.00 0.00 2.17
118 119 2.808543 GTCGAAGCCTCACTGAACAATT 59.191 45.455 0.00 0.00 0.00 2.32
119 120 2.417719 GTCGAAGCCTCACTGAACAAT 58.582 47.619 0.00 0.00 0.00 2.71
120 121 1.865865 GTCGAAGCCTCACTGAACAA 58.134 50.000 0.00 0.00 0.00 2.83
121 122 0.318699 CGTCGAAGCCTCACTGAACA 60.319 55.000 0.00 0.00 0.00 3.18
122 123 1.009389 CCGTCGAAGCCTCACTGAAC 61.009 60.000 0.00 0.00 0.00 3.18
123 124 1.289066 CCGTCGAAGCCTCACTGAA 59.711 57.895 0.00 0.00 0.00 3.02
124 125 2.962569 CCGTCGAAGCCTCACTGA 59.037 61.111 0.00 0.00 0.00 3.41
125 126 2.811317 GCCGTCGAAGCCTCACTG 60.811 66.667 0.00 0.00 0.00 3.66
126 127 4.421479 CGCCGTCGAAGCCTCACT 62.421 66.667 0.00 0.00 38.10 3.41
144 145 1.421485 GCTTCACTTGCGATGGACG 59.579 57.895 0.00 0.00 45.66 4.79
152 153 3.345808 TCCGTGCGCTTCACTTGC 61.346 61.111 9.73 0.00 43.46 4.01
153 154 2.551270 GTCCGTGCGCTTCACTTG 59.449 61.111 9.73 0.00 43.46 3.16
154 155 2.665185 GGTCCGTGCGCTTCACTT 60.665 61.111 9.73 0.00 43.46 3.16
155 156 4.681978 GGGTCCGTGCGCTTCACT 62.682 66.667 9.73 0.00 43.46 3.41
168 169 1.996786 TATCAAGACGTCGCGGGGTC 61.997 60.000 18.60 18.60 0.00 4.46
169 170 1.597797 TTATCAAGACGTCGCGGGGT 61.598 55.000 10.46 4.09 0.00 4.95
170 171 0.458889 TTTATCAAGACGTCGCGGGG 60.459 55.000 10.46 0.00 0.00 5.73
171 172 0.921347 CTTTATCAAGACGTCGCGGG 59.079 55.000 10.46 0.44 30.57 6.13
172 173 1.904144 TCTTTATCAAGACGTCGCGG 58.096 50.000 10.46 3.82 33.80 6.46
180 181 8.306313 TCTAGCATGTTAGGTCTTTATCAAGA 57.694 34.615 15.63 0.00 36.62 3.02
181 182 8.417106 TCTCTAGCATGTTAGGTCTTTATCAAG 58.583 37.037 15.63 3.19 0.00 3.02
182 183 8.306313 TCTCTAGCATGTTAGGTCTTTATCAA 57.694 34.615 15.63 0.00 0.00 2.57
183 184 7.780271 TCTCTCTAGCATGTTAGGTCTTTATCA 59.220 37.037 15.63 0.00 0.00 2.15
184 185 8.172352 TCTCTCTAGCATGTTAGGTCTTTATC 57.828 38.462 15.63 0.00 0.00 1.75
185 186 7.255801 GCTCTCTCTAGCATGTTAGGTCTTTAT 60.256 40.741 15.63 0.00 42.30 1.40
186 187 6.039941 GCTCTCTCTAGCATGTTAGGTCTTTA 59.960 42.308 15.63 0.00 42.30 1.85
187 188 5.163457 GCTCTCTCTAGCATGTTAGGTCTTT 60.163 44.000 15.63 0.00 42.30 2.52
188 189 4.340950 GCTCTCTCTAGCATGTTAGGTCTT 59.659 45.833 15.63 0.00 42.30 3.01
189 190 3.888930 GCTCTCTCTAGCATGTTAGGTCT 59.111 47.826 15.63 0.00 42.30 3.85
190 191 3.888930 AGCTCTCTCTAGCATGTTAGGTC 59.111 47.826 15.63 1.18 45.30 3.85
191 192 3.909732 AGCTCTCTCTAGCATGTTAGGT 58.090 45.455 15.63 0.00 45.30 3.08
192 193 5.564651 GCTTAGCTCTCTCTAGCATGTTAGG 60.565 48.000 15.63 7.54 45.30 2.69
193 194 5.241506 AGCTTAGCTCTCTCTAGCATGTTAG 59.758 44.000 10.15 10.15 45.30 2.34
194 195 5.009510 CAGCTTAGCTCTCTCTAGCATGTTA 59.990 44.000 2.68 0.00 45.30 2.41
195 196 3.960102 AGCTTAGCTCTCTCTAGCATGTT 59.040 43.478 0.00 0.00 45.30 2.71
196 197 3.318839 CAGCTTAGCTCTCTCTAGCATGT 59.681 47.826 2.68 0.00 45.30 3.21
197 198 3.318839 ACAGCTTAGCTCTCTCTAGCATG 59.681 47.826 2.68 0.00 45.30 4.06
198 199 3.565307 ACAGCTTAGCTCTCTCTAGCAT 58.435 45.455 2.68 0.00 45.30 3.79
199 200 3.011566 ACAGCTTAGCTCTCTCTAGCA 57.988 47.619 2.68 0.00 45.30 3.49
200 201 5.108385 CTAACAGCTTAGCTCTCTCTAGC 57.892 47.826 2.68 0.00 43.11 3.42
211 212 1.373570 GCACCCTGCTAACAGCTTAG 58.626 55.000 0.00 0.00 42.97 2.18
212 213 3.551259 GCACCCTGCTAACAGCTTA 57.449 52.632 0.00 0.00 42.97 3.09
213 214 4.404691 GCACCCTGCTAACAGCTT 57.595 55.556 0.00 0.00 42.97 3.74
225 226 3.006967 TCTTTCTTAGACTGTGAGCACCC 59.993 47.826 0.00 0.00 0.00 4.61
232 233 6.481644 AGCTCAACTTTCTTTCTTAGACTGTG 59.518 38.462 0.00 0.00 30.90 3.66
235 236 6.587273 ACAGCTCAACTTTCTTTCTTAGACT 58.413 36.000 0.00 0.00 30.90 3.24
237 238 8.958119 TTAACAGCTCAACTTTCTTTCTTAGA 57.042 30.769 0.00 0.00 0.00 2.10
251 252 5.065914 AGACAGCTTCATTTAACAGCTCAA 58.934 37.500 0.00 0.00 42.15 3.02
253 254 6.917217 ATAGACAGCTTCATTTAACAGCTC 57.083 37.500 0.00 0.00 42.15 4.09
256 257 8.939929 TCTTGAATAGACAGCTTCATTTAACAG 58.060 33.333 0.00 0.00 31.83 3.16
277 278 9.021807 AGCATACTACTGTAGTTTAGTTCTTGA 57.978 33.333 24.09 4.22 40.14 3.02
379 380 2.102252 GGTGATGTGCTTTTGGTTCCAA 59.898 45.455 0.00 0.00 0.00 3.53
479 480 1.544246 GCTTCCTTGTTTATTGCCCGT 59.456 47.619 0.00 0.00 0.00 5.28
509 510 3.680458 CAGACTTAAAGAAACGGAGGAGC 59.320 47.826 0.00 0.00 0.00 4.70
514 515 8.255206 TCTTATATGCAGACTTAAAGAAACGGA 58.745 33.333 0.00 0.00 0.00 4.69
515 516 8.420374 TCTTATATGCAGACTTAAAGAAACGG 57.580 34.615 0.00 0.00 0.00 4.44
581 582 9.764363 TCAATATTAGAAGATGCGTGATACTTT 57.236 29.630 0.00 0.00 0.00 2.66
582 583 9.935241 ATCAATATTAGAAGATGCGTGATACTT 57.065 29.630 0.00 0.00 0.00 2.24
583 584 9.935241 AATCAATATTAGAAGATGCGTGATACT 57.065 29.630 0.00 0.00 0.00 2.12
586 587 9.276590 TGAAATCAATATTAGAAGATGCGTGAT 57.723 29.630 0.00 0.00 0.00 3.06
587 588 8.661352 TGAAATCAATATTAGAAGATGCGTGA 57.339 30.769 0.00 0.00 0.00 4.35
611 612 9.941664 GGAAAAGATATCAACATTCACACTATG 57.058 33.333 5.32 0.00 0.00 2.23
612 613 9.911788 AGGAAAAGATATCAACATTCACACTAT 57.088 29.630 5.32 0.00 0.00 2.12
614 615 9.167311 GTAGGAAAAGATATCAACATTCACACT 57.833 33.333 5.32 0.63 0.00 3.55
615 616 8.116753 CGTAGGAAAAGATATCAACATTCACAC 58.883 37.037 5.32 4.86 0.00 3.82
616 617 8.038351 TCGTAGGAAAAGATATCAACATTCACA 58.962 33.333 5.32 0.00 0.00 3.58
617 618 8.420374 TCGTAGGAAAAGATATCAACATTCAC 57.580 34.615 5.32 0.00 0.00 3.18
618 619 9.098355 CTTCGTAGGAAAAGATATCAACATTCA 57.902 33.333 5.32 0.00 0.00 2.57
619 620 9.099454 ACTTCGTAGGAAAAGATATCAACATTC 57.901 33.333 5.32 3.78 0.00 2.67
620 621 9.449719 AACTTCGTAGGAAAAGATATCAACATT 57.550 29.630 5.32 0.00 0.00 2.71
622 623 9.582431 CTAACTTCGTAGGAAAAGATATCAACA 57.418 33.333 5.32 0.00 0.00 3.33
623 624 9.583765 ACTAACTTCGTAGGAAAAGATATCAAC 57.416 33.333 5.32 0.00 0.00 3.18
624 625 9.798994 GACTAACTTCGTAGGAAAAGATATCAA 57.201 33.333 5.32 0.00 0.00 2.57
625 626 8.963725 TGACTAACTTCGTAGGAAAAGATATCA 58.036 33.333 5.32 0.00 0.00 2.15
626 627 9.798994 TTGACTAACTTCGTAGGAAAAGATATC 57.201 33.333 0.00 0.00 0.00 1.63
628 629 9.415544 GTTTGACTAACTTCGTAGGAAAAGATA 57.584 33.333 0.00 0.00 33.79 1.98
629 630 8.148999 AGTTTGACTAACTTCGTAGGAAAAGAT 58.851 33.333 0.00 0.00 44.73 2.40
630 631 7.495055 AGTTTGACTAACTTCGTAGGAAAAGA 58.505 34.615 0.00 0.00 44.73 2.52
631 632 7.710766 AGTTTGACTAACTTCGTAGGAAAAG 57.289 36.000 0.00 0.81 44.73 2.27
662 663 9.787532 CGTATAACATCTGGTCAAAATCAAATT 57.212 29.630 0.00 0.00 0.00 1.82
663 664 7.915397 GCGTATAACATCTGGTCAAAATCAAAT 59.085 33.333 0.00 0.00 0.00 2.32
664 665 7.094592 TGCGTATAACATCTGGTCAAAATCAAA 60.095 33.333 0.00 0.00 0.00 2.69
665 666 6.372937 TGCGTATAACATCTGGTCAAAATCAA 59.627 34.615 0.00 0.00 0.00 2.57
666 667 5.877564 TGCGTATAACATCTGGTCAAAATCA 59.122 36.000 0.00 0.00 0.00 2.57
667 668 6.358118 TGCGTATAACATCTGGTCAAAATC 57.642 37.500 0.00 0.00 0.00 2.17
668 669 6.751514 TTGCGTATAACATCTGGTCAAAAT 57.248 33.333 0.00 0.00 0.00 1.82
669 670 6.205853 AGTTTGCGTATAACATCTGGTCAAAA 59.794 34.615 0.00 0.00 0.00 2.44
670 671 5.703592 AGTTTGCGTATAACATCTGGTCAAA 59.296 36.000 0.00 0.00 0.00 2.69
671 672 5.242434 AGTTTGCGTATAACATCTGGTCAA 58.758 37.500 0.00 0.00 0.00 3.18
672 673 4.827692 AGTTTGCGTATAACATCTGGTCA 58.172 39.130 0.00 0.00 0.00 4.02
673 674 6.897259 TTAGTTTGCGTATAACATCTGGTC 57.103 37.500 0.00 0.00 0.00 4.02
674 675 7.675962 TTTTAGTTTGCGTATAACATCTGGT 57.324 32.000 0.00 0.00 0.00 4.00
698 699 7.072076 AGTCCATATAATACTCCCTCCGTTTTT 59.928 37.037 0.00 0.00 0.00 1.94
699 700 6.557633 AGTCCATATAATACTCCCTCCGTTTT 59.442 38.462 0.00 0.00 0.00 2.43
700 701 6.082707 AGTCCATATAATACTCCCTCCGTTT 58.917 40.000 0.00 0.00 0.00 3.60
701 702 5.652324 AGTCCATATAATACTCCCTCCGTT 58.348 41.667 0.00 0.00 0.00 4.44
702 703 5.262804 GAGTCCATATAATACTCCCTCCGT 58.737 45.833 0.00 0.00 34.79 4.69
703 704 5.838531 GAGTCCATATAATACTCCCTCCG 57.161 47.826 0.00 0.00 34.79 4.63
713 714 9.645128 TTGTTTGAATGATGGAGTCCATATAAT 57.355 29.630 24.89 15.26 45.26 1.28
714 715 9.645128 ATTGTTTGAATGATGGAGTCCATATAA 57.355 29.630 24.89 13.66 45.26 0.98
716 717 9.293404 CTATTGTTTGAATGATGGAGTCCATAT 57.707 33.333 24.89 13.84 45.26 1.78
717 718 8.493607 TCTATTGTTTGAATGATGGAGTCCATA 58.506 33.333 24.89 13.24 45.26 2.74
732 733 6.016610 GGTAGTGTGCCTTTTCTATTGTTTGA 60.017 38.462 0.00 0.00 0.00 2.69
747 748 3.560636 ATATCCAAGTGGTAGTGTGCC 57.439 47.619 0.00 0.00 36.34 5.01
749 750 4.506654 GCGTTATATCCAAGTGGTAGTGTG 59.493 45.833 0.00 0.00 36.34 3.82
774 776 1.533731 GACAAAACGAGGGCGAATTGA 59.466 47.619 0.00 0.00 41.64 2.57
781 783 1.452145 TTGGCTGACAAAACGAGGGC 61.452 55.000 0.00 0.00 35.79 5.19
905 912 3.230134 CCTGAGCTGCTAGGAAGAGTAT 58.770 50.000 15.72 0.00 36.11 2.12
908 915 0.104671 GCCTGAGCTGCTAGGAAGAG 59.895 60.000 21.62 5.68 36.11 2.85
1014 1119 2.811317 CCCGTCTTCTCGCAGCAC 60.811 66.667 0.00 0.00 0.00 4.40
1032 1137 3.322466 CACGGGCCCCTCTTGAGT 61.322 66.667 18.66 2.65 0.00 3.41
1350 1455 2.126031 GACGGCTTGGAGGACGAC 60.126 66.667 0.00 0.00 40.66 4.34
1392 1500 3.741476 GCCACAGGCTTCTTGGCG 61.741 66.667 14.09 0.00 46.11 5.69
1569 1713 1.172180 CCACCGTCATTGCCAGTGTT 61.172 55.000 0.00 0.00 0.00 3.32
1698 1848 4.348863 AATCTGAGACAAACTCTGCACT 57.651 40.909 0.00 0.00 45.13 4.40
1796 1947 8.692710 ACCAAATGATCAGAACGAAGTAGTATA 58.307 33.333 0.09 0.00 45.00 1.47
1797 1948 7.492669 CACCAAATGATCAGAACGAAGTAGTAT 59.507 37.037 0.09 0.00 45.00 2.12
1798 1949 6.811665 CACCAAATGATCAGAACGAAGTAGTA 59.188 38.462 0.09 0.00 45.00 1.82
1799 1950 5.639506 CACCAAATGATCAGAACGAAGTAGT 59.360 40.000 0.09 0.00 45.00 2.73
1800 1951 5.063944 CCACCAAATGATCAGAACGAAGTAG 59.936 44.000 0.09 0.00 45.00 2.57
1801 1952 4.935205 CCACCAAATGATCAGAACGAAGTA 59.065 41.667 0.09 0.00 45.00 2.24
1803 1954 3.127548 CCCACCAAATGATCAGAACGAAG 59.872 47.826 0.09 0.00 0.00 3.79
1804 1955 3.081061 CCCACCAAATGATCAGAACGAA 58.919 45.455 0.09 0.00 0.00 3.85
1805 1956 2.039746 ACCCACCAAATGATCAGAACGA 59.960 45.455 0.09 0.00 0.00 3.85
1806 1957 2.162208 CACCCACCAAATGATCAGAACG 59.838 50.000 0.09 0.00 0.00 3.95
1807 1958 3.157087 ACACCCACCAAATGATCAGAAC 58.843 45.455 0.09 0.00 0.00 3.01
1808 1959 3.524095 ACACCCACCAAATGATCAGAA 57.476 42.857 0.09 0.00 0.00 3.02
1853 2018 7.139392 GCTATGAACGATTATTTTTCCCTTCC 58.861 38.462 0.00 0.00 0.00 3.46
1862 2027 5.583061 TGAACACCGCTATGAACGATTATTT 59.417 36.000 0.00 0.00 0.00 1.40
1874 2039 0.541392 TGCTGGATGAACACCGCTAT 59.459 50.000 0.00 0.00 0.00 2.97
1912 2077 6.019779 ACAACAAAGAAGTTTGCAACACTA 57.980 33.333 0.00 0.00 46.13 2.74
2059 2255 1.172812 GGTCACTGGGGAAAGCACAC 61.173 60.000 0.00 0.00 0.00 3.82
2125 3983 0.984995 GGACAACCTCCAGCTTACCT 59.015 55.000 0.00 0.00 39.21 3.08
2136 3994 3.382083 AAAACTTCACCTGGACAACCT 57.618 42.857 0.00 0.00 37.04 3.50
2141 3999 4.712122 TTGACAAAAACTTCACCTGGAC 57.288 40.909 0.00 0.00 0.00 4.02
2144 4002 5.572896 GTGACTTTGACAAAAACTTCACCTG 59.427 40.000 14.77 0.08 30.47 4.00
2185 4043 6.604735 AACACAAACTCAATGACACTACTC 57.395 37.500 0.00 0.00 0.00 2.59
2186 4044 6.374333 ACAAACACAAACTCAATGACACTACT 59.626 34.615 0.00 0.00 0.00 2.57
2187 4045 6.468956 CACAAACACAAACTCAATGACACTAC 59.531 38.462 0.00 0.00 0.00 2.73
2188 4046 6.404184 CCACAAACACAAACTCAATGACACTA 60.404 38.462 0.00 0.00 0.00 2.74
2189 4047 5.401550 CACAAACACAAACTCAATGACACT 58.598 37.500 0.00 0.00 0.00 3.55
2190 4048 4.562394 CCACAAACACAAACTCAATGACAC 59.438 41.667 0.00 0.00 0.00 3.67
2191 4049 4.742417 CCACAAACACAAACTCAATGACA 58.258 39.130 0.00 0.00 0.00 3.58
2192 4050 3.551485 GCCACAAACACAAACTCAATGAC 59.449 43.478 0.00 0.00 0.00 3.06
2193 4051 3.446873 AGCCACAAACACAAACTCAATGA 59.553 39.130 0.00 0.00 0.00 2.57
2194 4052 3.784338 AGCCACAAACACAAACTCAATG 58.216 40.909 0.00 0.00 0.00 2.82
2195 4053 4.202111 GGTAGCCACAAACACAAACTCAAT 60.202 41.667 0.00 0.00 0.00 2.57
2228 4086 3.290948 TGCACCCTAAAACAAGACACT 57.709 42.857 0.00 0.00 0.00 3.55
2415 4273 6.960431 CGTCAATCAAATGTTTTGTTTTTGCT 59.040 30.769 0.39 0.00 31.88 3.91
2429 4287 1.135527 CTGCCATGGCGTCAATCAAAT 59.864 47.619 30.87 0.00 45.51 2.32
2683 4554 1.982073 GCCAACAGCACGATGTAGGC 61.982 60.000 0.00 0.00 42.97 3.93


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

AutoCloner maintained by Alex Coulton.