Multiple sequence alignment - TraesCS1B01G415400

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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 TraesCS1B01G415400 chr1B 100.000 4102 0 0 602 4703 640558408 640554307 0.000000e+00 7576.0
1 TraesCS1B01G415400 chr1B 90.748 1524 90 16 3178 4679 640500883 640499389 0.000000e+00 1986.0
2 TraesCS1B01G415400 chr1B 85.347 1051 139 12 2627 3671 640566705 640567746 0.000000e+00 1074.0
3 TraesCS1B01G415400 chr1B 84.255 832 106 15 3069 3889 640568543 640569360 0.000000e+00 787.0
4 TraesCS1B01G415400 chr1B 100.000 266 0 0 1 266 640559009 640558744 4.230000e-135 492.0
5 TraesCS1B01G415400 chr1B 84.286 350 32 10 4196 4531 640497193 640496853 2.110000e-83 320.0
6 TraesCS1B01G415400 chr1B 84.899 298 28 6 3657 3938 640459434 640459138 7.700000e-73 285.0
7 TraesCS1B01G415400 chr1B 88.412 233 24 1 4443 4672 640483848 640483616 1.290000e-70 278.0
8 TraesCS1B01G415400 chr1B 83.893 298 30 7 3657 3938 640482220 640481925 7.760000e-68 268.0
9 TraesCS1B01G415400 chr1B 85.532 235 29 5 4442 4672 640460994 640460761 1.690000e-59 241.0
10 TraesCS1B01G415400 chr1B 80.208 288 39 6 4401 4680 640572241 640572518 2.870000e-47 200.0
11 TraesCS1B01G415400 chr1B 78.571 280 40 9 1830 2102 640501346 640501080 2.910000e-37 167.0
12 TraesCS1B01G415400 chr1B 78.417 278 44 12 4134 4405 640546239 640545972 2.910000e-37 167.0
13 TraesCS1B01G415400 chr1B 79.412 136 20 5 4080 4214 640459184 640459056 6.480000e-14 89.8
14 TraesCS1B01G415400 chr1B 78.261 138 17 12 4080 4214 640481971 640481844 5.050000e-10 76.8
15 TraesCS1B01G415400 chr1B 100.000 29 0 0 1944 1972 640501204 640501176 2.000000e-03 54.7
16 TraesCS1B01G415400 chr1D 94.930 3373 109 31 602 3961 464321931 464318608 0.000000e+00 5225.0
17 TraesCS1B01G415400 chr1D 88.467 711 61 12 3963 4665 464303372 464302675 0.000000e+00 839.0
18 TraesCS1B01G415400 chr1D 94.015 518 14 4 3437 3954 464311063 464310563 0.000000e+00 769.0
19 TraesCS1B01G415400 chr1D 91.304 460 31 4 2641 3099 464345298 464345749 1.860000e-173 619.0
20 TraesCS1B01G415400 chr1D 86.792 212 20 2 3601 3812 464288887 464288684 3.660000e-56 230.0
21 TraesCS1B01G415400 chr1D 84.977 213 21 7 4119 4320 464318640 464318428 6.170000e-49 206.0
22 TraesCS1B01G415400 chr1D 83.673 147 21 3 3963 4107 464318559 464318414 8.210000e-28 135.0
23 TraesCS1B01G415400 chr1D 90.625 96 7 2 4582 4677 464376655 464376748 4.940000e-25 126.0
24 TraesCS1B01G415400 chr1D 95.455 66 2 1 4614 4679 464301457 464301393 2.310000e-18 104.0
25 TraesCS1B01G415400 chr1A 95.991 3118 96 13 854 3961 556795734 556792636 0.000000e+00 5038.0
26 TraesCS1B01G415400 chr1A 87.978 732 69 13 3963 4679 556792589 556791862 0.000000e+00 846.0
27 TraesCS1B01G415400 chr1A 88.937 461 44 2 2639 3099 556802563 556803016 3.180000e-156 562.0
28 TraesCS1B01G415400 chr1A 89.583 96 9 1 4582 4677 556813679 556813773 2.300000e-23 121.0


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 TraesCS1B01G415400 chr1B 640554307 640559009 4702 True 4034.000000 7576 100.00000 1 4703 2 chr1B.!!$R5 4702
1 TraesCS1B01G415400 chr1B 640566705 640572518 5813 False 687.000000 1074 83.27000 2627 4680 3 chr1B.!!$F1 2053
2 TraesCS1B01G415400 chr1B 640496853 640501346 4493 True 631.925000 1986 88.40125 1830 4679 4 chr1B.!!$R4 2849
3 TraesCS1B01G415400 chr1B 640481844 640483848 2004 True 207.600000 278 83.52200 3657 4672 3 chr1B.!!$R3 1015
4 TraesCS1B01G415400 chr1B 640459056 640460994 1938 True 205.266667 285 83.28100 3657 4672 3 chr1B.!!$R2 1015
5 TraesCS1B01G415400 chr1D 464318414 464321931 3517 True 1855.333333 5225 87.86000 602 4320 3 chr1D.!!$R4 3718
6 TraesCS1B01G415400 chr1D 464310563 464311063 500 True 769.000000 769 94.01500 3437 3954 1 chr1D.!!$R2 517
7 TraesCS1B01G415400 chr1D 464301393 464303372 1979 True 471.500000 839 91.96100 3963 4679 2 chr1D.!!$R3 716
8 TraesCS1B01G415400 chr1A 556791862 556795734 3872 True 2942.000000 5038 91.98450 854 4679 2 chr1A.!!$R1 3825

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
156 157 0.106894 GGAAGGACGGCCATTAGAGG 59.893 60.000 11.69 0.0 36.29 3.69 F
157 158 0.106894 GAAGGACGGCCATTAGAGGG 59.893 60.000 11.69 0.0 36.29 4.30 F
802 804 0.110823 AACGACGCGAGCATTTTGAC 60.111 50.000 15.93 0.0 0.00 3.18 F
804 806 0.110867 CGACGCGAGCATTTTGACAA 60.111 50.000 15.93 0.0 0.00 3.18 F
989 1008 0.394565 GATCTCAATCCCCACCTCCG 59.605 60.000 0.00 0.0 0.00 4.63 F
1029 1048 1.152546 GCTCCTCCTCCTCCTCCTC 60.153 68.421 0.00 0.0 0.00 3.71 F
2854 2880 1.450531 GGAAAGCATCATGGCCCTCG 61.451 60.000 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 1894 0.110688 CGAACATGTGCGTCTGGTTG 60.111 55.000 18.56 0.0 0.00 3.77 R
1926 1945 1.375396 GGCCACATAGACACGCACA 60.375 57.895 0.00 0.0 0.00 4.57 R
2694 2719 0.318022 CATGTTGTGCTGCTTTCGCA 60.318 50.000 0.00 0.0 45.60 5.10 R
2824 2849 2.749076 TGATGCTTTCCAAGTCCATTCG 59.251 45.455 0.00 0.0 0.00 3.34 R
3246 3272 2.098117 GCTATGGTTGGTTCTCATGTGC 59.902 50.000 0.00 0.0 0.00 4.57 R
3399 4820 3.326747 GGAAAGCGCTCTGACTTTAGAA 58.673 45.455 12.06 0.0 36.28 2.10 R
3975 5459 0.473755 TCACTGAAAGAGCAGGGCAA 59.526 50.000 0.00 0.0 39.17 4.52 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
25 26 4.836125 TTGAGCAAATTCCTTCACTGAC 57.164 40.909 0.00 0.00 0.00 3.51
26 27 2.807967 TGAGCAAATTCCTTCACTGACG 59.192 45.455 0.00 0.00 0.00 4.35
28 29 3.476552 AGCAAATTCCTTCACTGACGAA 58.523 40.909 0.00 0.00 0.00 3.85
29 30 3.882888 AGCAAATTCCTTCACTGACGAAA 59.117 39.130 0.00 0.00 0.00 3.46
30 31 4.338118 AGCAAATTCCTTCACTGACGAAAA 59.662 37.500 0.00 0.00 0.00 2.29
31 32 5.040635 GCAAATTCCTTCACTGACGAAAAA 58.959 37.500 0.00 0.00 0.00 1.94
62 63 4.181309 CTCAAATAGGAGCCTCGGTATC 57.819 50.000 0.00 0.00 0.00 2.24
63 64 3.572642 TCAAATAGGAGCCTCGGTATCA 58.427 45.455 0.00 0.00 0.00 2.15
65 66 4.220821 TCAAATAGGAGCCTCGGTATCATC 59.779 45.833 0.00 0.00 0.00 2.92
66 67 1.822506 TAGGAGCCTCGGTATCATCG 58.177 55.000 0.00 0.00 0.00 3.84
68 69 0.241481 GGAGCCTCGGTATCATCGAC 59.759 60.000 0.00 0.00 32.86 4.20
70 71 1.081376 GCCTCGGTATCATCGACGG 60.081 63.158 0.00 0.00 32.86 4.79
71 72 1.512996 GCCTCGGTATCATCGACGGA 61.513 60.000 0.00 0.00 32.86 4.69
72 73 1.166129 CCTCGGTATCATCGACGGAT 58.834 55.000 6.64 6.64 32.86 4.18
74 75 1.130749 CTCGGTATCATCGACGGATCC 59.869 57.143 0.00 0.00 32.86 3.36
75 76 0.879090 CGGTATCATCGACGGATCCA 59.121 55.000 13.41 0.00 0.00 3.41
76 77 1.268625 CGGTATCATCGACGGATCCAA 59.731 52.381 13.41 0.00 0.00 3.53
77 78 2.287970 CGGTATCATCGACGGATCCAAA 60.288 50.000 13.41 0.00 0.00 3.28
78 79 3.614150 CGGTATCATCGACGGATCCAAAT 60.614 47.826 13.41 0.00 0.00 2.32
79 80 4.315803 GGTATCATCGACGGATCCAAATT 58.684 43.478 13.41 0.00 0.00 1.82
82 83 4.665833 TCATCGACGGATCCAAATTACT 57.334 40.909 13.41 0.00 0.00 2.24
84 85 4.808895 TCATCGACGGATCCAAATTACTTG 59.191 41.667 13.41 0.00 34.52 3.16
85 86 4.459390 TCGACGGATCCAAATTACTTGA 57.541 40.909 13.41 0.00 37.17 3.02
86 87 4.430007 TCGACGGATCCAAATTACTTGAG 58.570 43.478 13.41 0.00 37.17 3.02
87 88 3.001330 CGACGGATCCAAATTACTTGAGC 59.999 47.826 13.41 0.00 37.17 4.26
90 91 3.941483 CGGATCCAAATTACTTGAGCACT 59.059 43.478 13.41 0.00 37.17 4.40
91 92 4.396166 CGGATCCAAATTACTTGAGCACTT 59.604 41.667 13.41 0.00 37.17 3.16
92 93 5.447818 CGGATCCAAATTACTTGAGCACTTC 60.448 44.000 13.41 0.00 37.17 3.01
93 94 5.649831 GGATCCAAATTACTTGAGCACTTCT 59.350 40.000 6.95 0.00 37.17 2.85
94 95 6.183360 GGATCCAAATTACTTGAGCACTTCTC 60.183 42.308 6.95 0.00 42.23 2.87
95 96 5.869579 TCCAAATTACTTGAGCACTTCTCT 58.130 37.500 0.00 0.00 42.38 3.10
96 97 6.299141 TCCAAATTACTTGAGCACTTCTCTT 58.701 36.000 0.00 0.00 42.38 2.85
97 98 6.772716 TCCAAATTACTTGAGCACTTCTCTTT 59.227 34.615 0.00 0.00 42.38 2.52
100 101 6.793492 ATTACTTGAGCACTTCTCTTTGAC 57.207 37.500 0.00 0.00 42.38 3.18
101 102 4.414337 ACTTGAGCACTTCTCTTTGACT 57.586 40.909 0.00 0.00 42.38 3.41
102 103 5.537300 ACTTGAGCACTTCTCTTTGACTA 57.463 39.130 0.00 0.00 42.38 2.59
103 104 5.293560 ACTTGAGCACTTCTCTTTGACTAC 58.706 41.667 0.00 0.00 42.38 2.73
104 105 4.937201 TGAGCACTTCTCTTTGACTACA 57.063 40.909 0.00 0.00 42.38 2.74
109 110 6.349300 AGCACTTCTCTTTGACTACAAAAGA 58.651 36.000 0.00 0.00 43.92 2.52
110 111 6.823689 AGCACTTCTCTTTGACTACAAAAGAA 59.176 34.615 1.30 1.30 43.92 2.52
113 114 9.050601 CACTTCTCTTTGACTACAAAAGAAGAT 57.949 33.333 27.89 19.33 46.37 2.40
114 115 9.620259 ACTTCTCTTTGACTACAAAAGAAGATT 57.380 29.630 27.89 17.38 46.37 2.40
147 148 2.186532 AAAGAAGAAGGAAGGACGGC 57.813 50.000 0.00 0.00 0.00 5.68
148 149 0.325272 AAGAAGAAGGAAGGACGGCC 59.675 55.000 0.00 0.00 0.00 6.13
149 150 0.836400 AGAAGAAGGAAGGACGGCCA 60.836 55.000 11.69 0.00 36.29 5.36
150 151 0.253327 GAAGAAGGAAGGACGGCCAT 59.747 55.000 11.69 0.00 36.29 4.40
152 153 1.580059 AGAAGGAAGGACGGCCATTA 58.420 50.000 11.69 0.00 36.29 1.90
153 154 1.486726 AGAAGGAAGGACGGCCATTAG 59.513 52.381 11.69 0.00 36.29 1.73
155 156 1.123928 AGGAAGGACGGCCATTAGAG 58.876 55.000 11.69 0.00 36.29 2.43
156 157 0.106894 GGAAGGACGGCCATTAGAGG 59.893 60.000 11.69 0.00 36.29 3.69
157 158 0.106894 GAAGGACGGCCATTAGAGGG 59.893 60.000 11.69 0.00 36.29 4.30
158 159 0.326238 AAGGACGGCCATTAGAGGGA 60.326 55.000 11.69 0.00 36.29 4.20
159 160 0.760945 AGGACGGCCATTAGAGGGAG 60.761 60.000 11.69 0.00 36.29 4.30
162 163 1.056700 ACGGCCATTAGAGGGAGCAT 61.057 55.000 2.24 0.00 0.00 3.79
164 165 1.879796 CGGCCATTAGAGGGAGCATTC 60.880 57.143 2.24 0.00 0.00 2.67
166 167 2.225467 GCCATTAGAGGGAGCATTCAC 58.775 52.381 0.00 0.00 0.00 3.18
167 168 2.421952 GCCATTAGAGGGAGCATTCACA 60.422 50.000 0.00 0.00 0.00 3.58
168 169 3.474600 CCATTAGAGGGAGCATTCACAG 58.525 50.000 0.00 0.00 0.00 3.66
169 170 3.135348 CCATTAGAGGGAGCATTCACAGA 59.865 47.826 0.00 0.00 0.00 3.41
170 171 4.202440 CCATTAGAGGGAGCATTCACAGAT 60.202 45.833 0.00 0.00 0.00 2.90
172 173 5.441718 TTAGAGGGAGCATTCACAGATTT 57.558 39.130 0.00 0.00 0.00 2.17
173 174 3.618351 AGAGGGAGCATTCACAGATTTG 58.382 45.455 0.00 0.00 0.00 2.32
174 175 2.097825 AGGGAGCATTCACAGATTTGC 58.902 47.619 0.00 0.00 35.34 3.68
175 176 1.135721 GGGAGCATTCACAGATTTGCC 59.864 52.381 0.00 0.00 35.71 4.52
176 177 1.202222 GGAGCATTCACAGATTTGCCG 60.202 52.381 0.00 0.00 35.71 5.69
177 178 0.813184 AGCATTCACAGATTTGCCGG 59.187 50.000 0.00 0.00 35.71 6.13
178 179 0.527565 GCATTCACAGATTTGCCGGT 59.472 50.000 1.90 0.00 0.00 5.28
179 180 1.067635 GCATTCACAGATTTGCCGGTT 60.068 47.619 1.90 0.00 0.00 4.44
182 183 0.950836 TCACAGATTTGCCGGTTGTG 59.049 50.000 1.90 8.89 40.25 3.33
183 184 0.664166 CACAGATTTGCCGGTTGTGC 60.664 55.000 1.90 0.00 33.60 4.57
184 185 1.106351 ACAGATTTGCCGGTTGTGCA 61.106 50.000 1.90 0.00 36.84 4.57
200 201 2.061028 GTGCAACAAAGCCATTAGTGC 58.939 47.619 0.00 0.00 36.32 4.40
201 202 1.962807 TGCAACAAAGCCATTAGTGCT 59.037 42.857 0.00 0.00 41.89 4.40
203 204 3.057596 TGCAACAAAGCCATTAGTGCTAC 60.058 43.478 0.00 0.00 38.34 3.58
204 205 3.673323 GCAACAAAGCCATTAGTGCTACC 60.673 47.826 0.00 0.00 38.34 3.18
206 207 3.761897 ACAAAGCCATTAGTGCTACCAA 58.238 40.909 0.00 0.00 38.34 3.67
207 208 4.148838 ACAAAGCCATTAGTGCTACCAAA 58.851 39.130 0.00 0.00 38.34 3.28
208 209 4.772100 ACAAAGCCATTAGTGCTACCAAAT 59.228 37.500 0.00 0.00 38.34 2.32
209 210 5.949354 ACAAAGCCATTAGTGCTACCAAATA 59.051 36.000 0.00 0.00 38.34 1.40
212 213 6.451064 AGCCATTAGTGCTACCAAATAAAC 57.549 37.500 0.00 0.00 37.28 2.01
213 214 5.065988 AGCCATTAGTGCTACCAAATAAACG 59.934 40.000 0.00 0.00 37.28 3.60
215 216 5.163703 CCATTAGTGCTACCAAATAAACGCA 60.164 40.000 0.00 0.00 0.00 5.24
216 217 3.824414 AGTGCTACCAAATAAACGCAC 57.176 42.857 0.00 0.00 45.77 5.34
218 219 4.091453 GTGCTACCAAATAAACGCACAT 57.909 40.909 7.26 0.00 45.02 3.21
219 220 4.481463 GTGCTACCAAATAAACGCACATT 58.519 39.130 7.26 0.00 45.02 2.71
220 221 4.920927 GTGCTACCAAATAAACGCACATTT 59.079 37.500 7.26 0.00 45.02 2.32
221 222 5.060446 GTGCTACCAAATAAACGCACATTTC 59.940 40.000 7.26 0.00 45.02 2.17
222 223 5.157781 GCTACCAAATAAACGCACATTTCA 58.842 37.500 0.00 0.00 0.00 2.69
223 224 5.804979 GCTACCAAATAAACGCACATTTCAT 59.195 36.000 0.00 0.00 0.00 2.57
224 225 6.237542 GCTACCAAATAAACGCACATTTCATG 60.238 38.462 0.00 0.00 0.00 3.07
225 226 4.388469 ACCAAATAAACGCACATTTCATGC 59.612 37.500 0.00 0.00 39.81 4.06
227 228 3.865011 ATAAACGCACATTTCATGCCA 57.135 38.095 0.00 0.00 40.09 4.92
228 229 2.747396 AAACGCACATTTCATGCCAT 57.253 40.000 0.00 0.00 40.09 4.40
234 235 4.214119 ACGCACATTTCATGCCATATACTC 59.786 41.667 0.00 0.00 40.09 2.59
235 236 4.378770 CGCACATTTCATGCCATATACTCC 60.379 45.833 0.00 0.00 40.09 3.85
236 237 4.520111 GCACATTTCATGCCATATACTCCA 59.480 41.667 0.00 0.00 37.08 3.86
237 238 5.335426 GCACATTTCATGCCATATACTCCAG 60.335 44.000 0.00 0.00 37.08 3.86
238 239 5.766670 CACATTTCATGCCATATACTCCAGT 59.233 40.000 0.00 0.00 0.00 4.00
239 240 5.766670 ACATTTCATGCCATATACTCCAGTG 59.233 40.000 0.00 0.00 0.00 3.66
240 241 3.407424 TCATGCCATATACTCCAGTGC 57.593 47.619 0.00 0.00 0.00 4.40
241 242 2.705127 TCATGCCATATACTCCAGTGCA 59.295 45.455 0.00 0.00 0.00 4.57
244 245 1.876156 GCCATATACTCCAGTGCAAGC 59.124 52.381 0.00 0.00 0.00 4.01
245 246 2.746142 GCCATATACTCCAGTGCAAGCA 60.746 50.000 0.00 0.00 0.00 3.91
246 247 3.136763 CCATATACTCCAGTGCAAGCAG 58.863 50.000 0.00 0.00 0.00 4.24
247 248 3.181462 CCATATACTCCAGTGCAAGCAGA 60.181 47.826 0.00 0.00 0.00 4.26
249 250 2.928801 TACTCCAGTGCAAGCAGAAA 57.071 45.000 0.00 0.00 0.00 2.52
250 251 2.057137 ACTCCAGTGCAAGCAGAAAA 57.943 45.000 0.00 0.00 0.00 2.29
251 252 2.590821 ACTCCAGTGCAAGCAGAAAAT 58.409 42.857 0.00 0.00 0.00 1.82
252 253 2.961062 ACTCCAGTGCAAGCAGAAAATT 59.039 40.909 0.00 0.00 0.00 1.82
253 254 4.144297 ACTCCAGTGCAAGCAGAAAATTA 58.856 39.130 0.00 0.00 0.00 1.40
254 255 4.584325 ACTCCAGTGCAAGCAGAAAATTAA 59.416 37.500 0.00 0.00 0.00 1.40
255 256 5.068987 ACTCCAGTGCAAGCAGAAAATTAAA 59.931 36.000 0.00 0.00 0.00 1.52
256 257 5.911752 TCCAGTGCAAGCAGAAAATTAAAA 58.088 33.333 0.00 0.00 0.00 1.52
645 646 5.525745 TGAGCAAGTTTATCGAGAAACACAA 59.474 36.000 30.79 13.56 41.00 3.33
653 654 1.135527 TCGAGAAACACAACGACACCT 59.864 47.619 0.00 0.00 0.00 4.00
678 679 5.659440 AATAACACCATGATGTTTCCACC 57.341 39.130 11.57 0.00 39.86 4.61
679 680 1.533625 ACACCATGATGTTTCCACCG 58.466 50.000 0.00 0.00 0.00 4.94
682 683 1.073125 ACCATGATGTTTCCACCGACA 59.927 47.619 0.00 0.00 0.00 4.35
687 688 1.659098 GATGTTTCCACCGACATCGAC 59.341 52.381 2.09 0.00 41.70 4.20
688 689 0.677288 TGTTTCCACCGACATCGACT 59.323 50.000 2.09 0.00 43.02 4.18
689 690 1.336517 TGTTTCCACCGACATCGACTC 60.337 52.381 2.09 0.00 43.02 3.36
690 691 0.963225 TTTCCACCGACATCGACTCA 59.037 50.000 2.09 0.00 43.02 3.41
691 692 1.182667 TTCCACCGACATCGACTCAT 58.817 50.000 2.09 0.00 43.02 2.90
692 693 1.182667 TCCACCGACATCGACTCATT 58.817 50.000 2.09 0.00 43.02 2.57
693 694 1.135112 TCCACCGACATCGACTCATTG 60.135 52.381 2.09 0.00 43.02 2.82
694 695 1.404181 CCACCGACATCGACTCATTGT 60.404 52.381 2.09 0.00 43.02 2.71
695 696 1.920574 CACCGACATCGACTCATTGTC 59.079 52.381 2.09 6.11 43.02 3.18
696 697 1.544246 ACCGACATCGACTCATTGTCA 59.456 47.619 14.56 0.00 45.60 3.58
698 699 2.159379 CCGACATCGACTCATTGTCAGA 60.159 50.000 14.56 0.00 45.60 3.27
713 714 8.492673 TCATTGTCAGACAAGTCAATATAACC 57.507 34.615 20.55 0.00 41.94 2.85
736 738 8.437360 ACCTTTTCTCAAATTTGGTCAAATTC 57.563 30.769 17.90 0.00 46.76 2.17
742 744 8.647143 TCTCAAATTTGGTCAAATTCAGAAAC 57.353 30.769 17.90 0.00 46.76 2.78
748 750 6.477053 TTGGTCAAATTCAGAAACCATTGA 57.523 33.333 5.43 3.47 39.61 2.57
752 754 6.642540 GGTCAAATTCAGAAACCATTGACTTC 59.357 38.462 21.45 11.09 43.66 3.01
753 755 7.202526 GTCAAATTCAGAAACCATTGACTTCA 58.797 34.615 18.18 0.00 41.92 3.02
754 756 7.380602 GTCAAATTCAGAAACCATTGACTTCAG 59.619 37.037 18.18 0.00 41.92 3.02
755 757 7.285172 TCAAATTCAGAAACCATTGACTTCAGA 59.715 33.333 0.00 0.00 0.00 3.27
757 759 5.034852 TCAGAAACCATTGACTTCAGACA 57.965 39.130 0.00 0.00 0.00 3.41
759 761 5.885352 TCAGAAACCATTGACTTCAGACAAA 59.115 36.000 0.00 0.00 33.89 2.83
760 762 6.376864 TCAGAAACCATTGACTTCAGACAAAA 59.623 34.615 0.00 0.00 33.89 2.44
761 763 6.473455 CAGAAACCATTGACTTCAGACAAAAC 59.527 38.462 0.00 0.00 33.89 2.43
762 764 6.378280 AGAAACCATTGACTTCAGACAAAACT 59.622 34.615 0.00 0.00 33.89 2.66
764 766 7.639113 AACCATTGACTTCAGACAAAACTTA 57.361 32.000 0.00 0.00 33.89 2.24
766 768 8.918202 ACCATTGACTTCAGACAAAACTTATA 57.082 30.769 0.00 0.00 33.89 0.98
769 771 7.416154 TTGACTTCAGACAAAACTTATACGG 57.584 36.000 0.00 0.00 0.00 4.02
780 782 5.632244 AAACTTATACGGGTCGCATTTTT 57.368 34.783 0.00 0.00 0.00 1.94
785 787 7.022979 ACTTATACGGGTCGCATTTTTAAAAC 58.977 34.615 0.00 0.00 0.00 2.43
788 790 2.653113 CGGGTCGCATTTTTAAAACGAC 59.347 45.455 23.73 23.73 44.16 4.34
802 804 0.110823 AACGACGCGAGCATTTTGAC 60.111 50.000 15.93 0.00 0.00 3.18
804 806 0.110867 CGACGCGAGCATTTTGACAA 60.111 50.000 15.93 0.00 0.00 3.18
805 807 1.658931 CGACGCGAGCATTTTGACAAA 60.659 47.619 15.93 0.00 0.00 2.83
807 809 2.786578 GACGCGAGCATTTTGACAAAAA 59.213 40.909 15.93 1.33 39.53 1.94
868 877 1.222567 ATTCCCCATCTACCACCACC 58.777 55.000 0.00 0.00 0.00 4.61
869 878 1.268992 TTCCCCATCTACCACCACCG 61.269 60.000 0.00 0.00 0.00 4.94
903 912 2.238144 CCCCACATCACAGAGAGTCAAT 59.762 50.000 0.00 0.00 0.00 2.57
912 921 1.484240 CAGAGAGTCAATCCCCTGTCC 59.516 57.143 0.00 0.00 0.00 4.02
985 1004 1.813102 AGGAGATCTCAATCCCCACC 58.187 55.000 23.85 4.17 32.28 4.61
986 1005 1.296523 AGGAGATCTCAATCCCCACCT 59.703 52.381 23.85 6.53 32.28 4.00
989 1008 0.394565 GATCTCAATCCCCACCTCCG 59.605 60.000 0.00 0.00 0.00 4.63
1029 1048 1.152546 GCTCCTCCTCCTCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
1613 1632 3.710722 CGCCAACCTCTCCAGCCT 61.711 66.667 0.00 0.00 0.00 4.58
1788 1807 2.046217 GGCGGGAGGAACTTCACC 60.046 66.667 0.00 0.00 41.55 4.02
1812 1831 3.461773 GGCCTCAGGTCGCTGCTA 61.462 66.667 0.00 0.00 0.00 3.49
1814 1833 1.520342 GCCTCAGGTCGCTGCTAAG 60.520 63.158 0.00 0.00 0.00 2.18
1875 1894 3.934962 GCCTCCTCGCTGGGGATC 61.935 72.222 0.00 0.00 39.16 3.36
2031 2056 2.027385 GGCTTCTGGGATCACAATTCC 58.973 52.381 0.00 0.00 0.00 3.01
2185 2210 1.966451 GCAGGGTTGGTCTGGAACG 60.966 63.158 0.00 0.00 33.16 3.95
2199 2224 1.581447 GAACGCCAGCCTGAAAAGG 59.419 57.895 0.00 0.00 0.00 3.11
2277 2302 7.959175 TGAAGTACAACTACACTAAGGTTGAT 58.041 34.615 11.21 0.54 41.71 2.57
2535 2560 4.859798 GTCAGCTACAATATCCGCTATGTC 59.140 45.833 0.00 0.00 0.00 3.06
2549 2574 1.817911 TATGTCGGGCGTTGGTCACA 61.818 55.000 0.00 0.00 0.00 3.58
2622 2647 4.751431 GGCTCCTTGTGCCTGATT 57.249 55.556 0.00 0.00 46.38 2.57
2673 2698 6.915300 CCTCAGACTGTAAGATTCTGATAACG 59.085 42.308 1.59 0.00 42.80 3.18
2694 2719 2.093235 GGCTCACTTTGCTAGTCTGGAT 60.093 50.000 0.00 0.00 33.85 3.41
2824 2849 4.500375 GCCAAGTGGAAGAATCAATATGGC 60.500 45.833 0.18 0.00 42.26 4.40
2854 2880 1.450531 GGAAAGCATCATGGCCCTCG 61.451 60.000 0.00 0.00 0.00 4.63
2961 2987 2.070890 CTATGCTTGTCGTGCTCGCG 62.071 60.000 0.00 0.00 36.96 5.87
3246 3272 4.034048 GGTGGAGTTATAACAGCGATTGTG 59.966 45.833 17.65 0.00 40.74 3.33
3277 3306 2.846206 ACCAACCATAGCAGAAGGATGA 59.154 45.455 0.00 0.00 0.00 2.92
3399 4820 3.262660 TCATCCTGAATGTGTTCTCAGCT 59.737 43.478 0.00 0.00 38.19 4.24
3435 4856 3.005367 CGCTTTCCCCTGTGTTTTACATT 59.995 43.478 0.00 0.00 38.92 2.71
3812 5244 4.943705 CCTGATGGATGAATATTTACCCCG 59.056 45.833 0.00 0.00 34.57 5.73
3833 5266 0.829333 ATTGGTGCTTGTTTGTGGCA 59.171 45.000 0.00 0.00 0.00 4.92
3882 5321 2.503895 AGGAAACCAGATCAGGCAAG 57.496 50.000 3.64 0.00 0.00 4.01
3957 5396 5.812286 TGGTTTACCTTCCCTGTTATTCTC 58.188 41.667 0.00 0.00 36.82 2.87
3961 5400 6.855763 TTACCTTCCCTGTTATTCTCGTAA 57.144 37.500 0.00 0.00 0.00 3.18
3973 5457 8.176814 TGTTATTCTCGTAACGTTGGAATTAG 57.823 34.615 11.99 0.11 37.37 1.73
3975 5459 8.650714 GTTATTCTCGTAACGTTGGAATTAGTT 58.349 33.333 11.99 0.00 0.00 2.24
3979 5465 4.083908 TCGTAACGTTGGAATTAGTTTGCC 60.084 41.667 11.99 0.00 0.00 4.52
4014 5501 0.383124 GCTCTGCGTTTTCGTGTGTC 60.383 55.000 0.00 0.00 46.03 3.67
4019 5506 0.027586 GCGTTTTCGTGTGTCTGCTT 59.972 50.000 0.00 0.00 46.03 3.91
4044 5531 1.495878 CGTATGCATCTGAGACCTGC 58.504 55.000 0.19 1.22 36.45 4.85
4045 5532 1.871408 CGTATGCATCTGAGACCTGCC 60.871 57.143 0.19 0.00 35.02 4.85
4048 5535 1.153208 GCATCTGAGACCTGCCCTG 60.153 63.158 0.00 0.00 0.00 4.45
4116 5606 8.181904 TGATTCCTTTTCCTATTGCCATAATC 57.818 34.615 0.00 0.00 0.00 1.75
4188 5682 0.899717 GCCAAGGTGGATTTCTGCCA 60.900 55.000 0.00 0.00 40.96 4.92
4275 5796 2.090400 TGCATCTGAGAACTGTCTGC 57.910 50.000 0.00 0.00 32.80 4.26
4306 5828 5.104485 ACTGTTTTCCTACCCATCCATAGTC 60.104 44.000 0.00 0.00 0.00 2.59
4348 5870 2.833943 TGAGATGCCTGTTCAGCTCTAA 59.166 45.455 9.87 0.00 46.43 2.10
4521 8602 5.013704 TCCTATTTGTTAAAGCCACTCCTCA 59.986 40.000 0.00 0.00 0.00 3.86
4526 8607 2.450609 TAAAGCCACTCCTCAACGTC 57.549 50.000 0.00 0.00 0.00 4.34
4622 9980 5.578005 TCACTAAGTCGGCATATATAGGC 57.422 43.478 10.90 10.90 0.00 3.93
4636 10000 9.468532 GGCATATATAGGCTTCAAAAGAAAAAG 57.531 33.333 18.06 0.00 32.84 2.27
4680 10044 1.079503 CAACCGAGACTTGCTTAGGC 58.920 55.000 0.00 0.00 39.26 3.93
4685 10060 2.468831 CGAGACTTGCTTAGGCTGATC 58.531 52.381 0.00 0.00 44.50 2.92
4696 10071 5.061853 GCTTAGGCTGATCATCATCAAGAA 58.938 41.667 0.00 0.00 38.63 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.025963 GTCAGTGAAGGAATTTGCTCAAATAG 58.974 38.462 8.11 0.00 39.88 1.73
2 3 5.563475 CGTCAGTGAAGGAATTTGCTCAAAT 60.563 40.000 0.00 2.24 42.35 2.32
3 4 4.261155 CGTCAGTGAAGGAATTTGCTCAAA 60.261 41.667 0.00 0.00 34.46 2.69
4 5 3.250762 CGTCAGTGAAGGAATTTGCTCAA 59.749 43.478 0.00 0.00 0.00 3.02
6 7 3.067106 TCGTCAGTGAAGGAATTTGCTC 58.933 45.455 6.22 0.00 0.00 4.26
7 8 3.126001 TCGTCAGTGAAGGAATTTGCT 57.874 42.857 6.22 0.00 0.00 3.91
8 9 3.896648 TTCGTCAGTGAAGGAATTTGC 57.103 42.857 6.22 0.00 0.00 3.68
43 44 4.499183 GATGATACCGAGGCTCCTATTTG 58.501 47.826 9.32 0.00 0.00 2.32
45 46 2.755655 CGATGATACCGAGGCTCCTATT 59.244 50.000 9.32 0.00 0.00 1.73
46 47 2.026169 TCGATGATACCGAGGCTCCTAT 60.026 50.000 9.32 4.01 0.00 2.57
48 49 0.110678 TCGATGATACCGAGGCTCCT 59.889 55.000 9.32 0.00 0.00 3.69
51 52 1.516365 CCGTCGATGATACCGAGGCT 61.516 60.000 6.11 0.00 39.63 4.58
52 53 1.081376 CCGTCGATGATACCGAGGC 60.081 63.158 6.11 0.00 39.63 4.70
53 54 1.130749 GATCCGTCGATGATACCGAGG 59.869 57.143 6.11 0.00 40.35 4.63
54 55 1.130749 GGATCCGTCGATGATACCGAG 59.869 57.143 6.11 0.00 36.66 4.63
57 58 3.380479 TTTGGATCCGTCGATGATACC 57.620 47.619 6.11 6.60 0.00 2.73
58 59 6.157211 AGTAATTTGGATCCGTCGATGATAC 58.843 40.000 6.11 4.69 0.00 2.24
59 60 6.340962 AGTAATTTGGATCCGTCGATGATA 57.659 37.500 6.11 0.00 0.00 2.15
60 61 5.215252 AGTAATTTGGATCCGTCGATGAT 57.785 39.130 6.11 2.92 0.00 2.45
62 63 4.808895 TCAAGTAATTTGGATCCGTCGATG 59.191 41.667 7.39 0.00 37.39 3.84
63 64 5.018539 TCAAGTAATTTGGATCCGTCGAT 57.981 39.130 7.39 0.00 37.39 3.59
65 66 3.001330 GCTCAAGTAATTTGGATCCGTCG 59.999 47.826 7.39 0.00 37.39 5.12
66 67 3.938963 TGCTCAAGTAATTTGGATCCGTC 59.061 43.478 7.39 0.00 37.39 4.79
68 69 3.941483 AGTGCTCAAGTAATTTGGATCCG 59.059 43.478 7.39 0.00 37.39 4.18
70 71 6.597280 AGAGAAGTGCTCAAGTAATTTGGATC 59.403 38.462 0.00 0.00 46.45 3.36
71 72 6.479884 AGAGAAGTGCTCAAGTAATTTGGAT 58.520 36.000 0.00 0.00 46.45 3.41
72 73 5.869579 AGAGAAGTGCTCAAGTAATTTGGA 58.130 37.500 0.00 0.00 46.45 3.53
74 75 7.589221 GTCAAAGAGAAGTGCTCAAGTAATTTG 59.411 37.037 0.00 1.72 46.45 2.32
75 76 7.500559 AGTCAAAGAGAAGTGCTCAAGTAATTT 59.499 33.333 0.00 0.00 46.45 1.82
76 77 6.995091 AGTCAAAGAGAAGTGCTCAAGTAATT 59.005 34.615 0.00 0.00 46.45 1.40
77 78 6.529220 AGTCAAAGAGAAGTGCTCAAGTAAT 58.471 36.000 0.00 0.00 46.45 1.89
78 79 5.918608 AGTCAAAGAGAAGTGCTCAAGTAA 58.081 37.500 0.00 0.00 46.45 2.24
79 80 5.537300 AGTCAAAGAGAAGTGCTCAAGTA 57.463 39.130 0.00 0.00 46.45 2.24
82 83 5.276461 TGTAGTCAAAGAGAAGTGCTCAA 57.724 39.130 0.00 0.00 46.45 3.02
84 85 6.480320 TCTTTTGTAGTCAAAGAGAAGTGCTC 59.520 38.462 0.00 0.00 43.17 4.26
85 86 6.349300 TCTTTTGTAGTCAAAGAGAAGTGCT 58.651 36.000 0.00 0.00 43.17 4.40
86 87 6.604735 TCTTTTGTAGTCAAAGAGAAGTGC 57.395 37.500 0.00 0.00 43.17 4.40
87 88 8.425577 TCTTCTTTTGTAGTCAAAGAGAAGTG 57.574 34.615 23.74 13.82 44.71 3.16
128 129 1.271434 GGCCGTCCTTCCTTCTTCTTT 60.271 52.381 0.00 0.00 0.00 2.52
131 132 0.253327 ATGGCCGTCCTTCCTTCTTC 59.747 55.000 0.00 0.00 0.00 2.87
132 133 0.698818 AATGGCCGTCCTTCCTTCTT 59.301 50.000 0.00 0.00 0.00 2.52
133 134 1.486726 CTAATGGCCGTCCTTCCTTCT 59.513 52.381 0.00 0.00 0.00 2.85
134 135 1.485066 TCTAATGGCCGTCCTTCCTTC 59.515 52.381 0.00 0.00 0.00 3.46
135 136 1.486726 CTCTAATGGCCGTCCTTCCTT 59.513 52.381 0.00 0.00 0.00 3.36
136 137 1.123928 CTCTAATGGCCGTCCTTCCT 58.876 55.000 0.00 0.00 0.00 3.36
137 138 0.106894 CCTCTAATGGCCGTCCTTCC 59.893 60.000 0.00 0.00 0.00 3.46
138 139 0.106894 CCCTCTAATGGCCGTCCTTC 59.893 60.000 0.00 0.00 0.00 3.46
139 140 0.326238 TCCCTCTAATGGCCGTCCTT 60.326 55.000 0.00 0.00 0.00 3.36
140 141 0.760945 CTCCCTCTAATGGCCGTCCT 60.761 60.000 0.00 0.00 0.00 3.85
142 143 1.069935 GCTCCCTCTAATGGCCGTC 59.930 63.158 0.00 0.00 0.00 4.79
144 145 0.109342 AATGCTCCCTCTAATGGCCG 59.891 55.000 0.00 0.00 0.00 6.13
146 147 2.225467 GTGAATGCTCCCTCTAATGGC 58.775 52.381 0.00 0.00 0.00 4.40
147 148 3.135348 TCTGTGAATGCTCCCTCTAATGG 59.865 47.826 0.00 0.00 0.00 3.16
148 149 4.412796 TCTGTGAATGCTCCCTCTAATG 57.587 45.455 0.00 0.00 0.00 1.90
149 150 5.643421 AATCTGTGAATGCTCCCTCTAAT 57.357 39.130 0.00 0.00 0.00 1.73
150 151 5.188434 CAAATCTGTGAATGCTCCCTCTAA 58.812 41.667 0.00 0.00 0.00 2.10
152 153 3.618351 CAAATCTGTGAATGCTCCCTCT 58.382 45.455 0.00 0.00 0.00 3.69
153 154 2.098770 GCAAATCTGTGAATGCTCCCTC 59.901 50.000 0.00 0.00 35.93 4.30
155 156 1.135721 GGCAAATCTGTGAATGCTCCC 59.864 52.381 0.00 0.00 38.79 4.30
156 157 1.202222 CGGCAAATCTGTGAATGCTCC 60.202 52.381 0.00 0.00 38.79 4.70
157 158 1.202222 CCGGCAAATCTGTGAATGCTC 60.202 52.381 0.00 0.00 38.79 4.26
158 159 0.813184 CCGGCAAATCTGTGAATGCT 59.187 50.000 0.00 0.00 38.79 3.79
159 160 0.527565 ACCGGCAAATCTGTGAATGC 59.472 50.000 0.00 0.00 38.06 3.56
162 163 1.336440 CACAACCGGCAAATCTGTGAA 59.664 47.619 0.00 0.00 39.80 3.18
164 165 0.664166 GCACAACCGGCAAATCTGTG 60.664 55.000 0.00 7.18 40.26 3.66
166 167 1.659233 TGCACAACCGGCAAATCTG 59.341 52.632 0.00 0.00 38.54 2.90
167 168 4.172625 TGCACAACCGGCAAATCT 57.827 50.000 0.00 0.00 38.54 2.40
172 173 1.140589 CTTTGTTGCACAACCGGCA 59.859 52.632 0.00 0.00 37.90 5.69
173 174 2.237066 GCTTTGTTGCACAACCGGC 61.237 57.895 0.00 8.43 37.90 6.13
174 175 1.591327 GGCTTTGTTGCACAACCGG 60.591 57.895 10.82 0.00 37.90 5.28
175 176 0.249405 ATGGCTTTGTTGCACAACCG 60.249 50.000 10.82 1.47 37.90 4.44
176 177 1.952193 AATGGCTTTGTTGCACAACC 58.048 45.000 10.82 0.00 37.90 3.77
177 178 3.490526 CACTAATGGCTTTGTTGCACAAC 59.509 43.478 6.57 6.57 37.90 3.32
178 179 3.715495 CACTAATGGCTTTGTTGCACAA 58.285 40.909 0.00 0.00 36.11 3.33
179 180 2.545532 GCACTAATGGCTTTGTTGCACA 60.546 45.455 12.82 0.00 34.04 4.57
182 183 2.730550 AGCACTAATGGCTTTGTTGC 57.269 45.000 10.81 10.81 38.81 4.17
183 184 3.505680 TGGTAGCACTAATGGCTTTGTTG 59.494 43.478 0.00 0.00 42.62 3.33
184 185 3.761897 TGGTAGCACTAATGGCTTTGTT 58.238 40.909 0.00 0.00 42.62 2.83
186 187 4.782019 TTTGGTAGCACTAATGGCTTTG 57.218 40.909 0.00 0.00 42.62 2.77
187 188 7.320399 GTTTATTTGGTAGCACTAATGGCTTT 58.680 34.615 0.00 0.00 42.62 3.51
189 190 5.065988 CGTTTATTTGGTAGCACTAATGGCT 59.934 40.000 0.00 0.00 45.18 4.75
190 191 5.270853 CGTTTATTTGGTAGCACTAATGGC 58.729 41.667 0.00 0.00 0.00 4.40
191 192 5.163703 TGCGTTTATTTGGTAGCACTAATGG 60.164 40.000 0.00 0.00 0.00 3.16
192 193 5.874831 TGCGTTTATTTGGTAGCACTAATG 58.125 37.500 0.00 0.00 0.00 1.90
198 199 4.775058 AATGTGCGTTTATTTGGTAGCA 57.225 36.364 0.00 0.00 0.00 3.49
199 200 5.157781 TGAAATGTGCGTTTATTTGGTAGC 58.842 37.500 0.00 0.00 0.00 3.58
200 201 7.208379 CATGAAATGTGCGTTTATTTGGTAG 57.792 36.000 0.00 0.00 40.20 3.18
218 219 4.136796 GCACTGGAGTATATGGCATGAAA 58.863 43.478 10.98 0.00 0.00 2.69
219 220 3.136260 TGCACTGGAGTATATGGCATGAA 59.864 43.478 10.98 0.00 0.00 2.57
220 221 2.705127 TGCACTGGAGTATATGGCATGA 59.295 45.455 10.98 0.00 0.00 3.07
221 222 3.130280 TGCACTGGAGTATATGGCATG 57.870 47.619 10.98 0.00 0.00 4.06
222 223 3.748083 CTTGCACTGGAGTATATGGCAT 58.252 45.455 4.88 4.88 0.00 4.40
223 224 2.746142 GCTTGCACTGGAGTATATGGCA 60.746 50.000 0.00 0.00 0.00 4.92
224 225 1.876156 GCTTGCACTGGAGTATATGGC 59.124 52.381 0.00 0.00 0.00 4.40
225 226 3.136763 CTGCTTGCACTGGAGTATATGG 58.863 50.000 0.00 0.00 0.00 2.74
227 228 4.760530 TTCTGCTTGCACTGGAGTATAT 57.239 40.909 7.17 0.00 0.00 0.86
228 229 4.551702 TTTCTGCTTGCACTGGAGTATA 57.448 40.909 7.17 0.00 0.00 1.47
234 235 6.601741 TTTTTAATTTTCTGCTTGCACTGG 57.398 33.333 0.00 0.00 0.00 4.00
619 620 6.037720 TGTGTTTCTCGATAAACTTGCTCAAA 59.962 34.615 22.22 2.38 39.57 2.69
645 646 4.020928 TCATGGTGTTATTACAGGTGTCGT 60.021 41.667 0.00 0.00 34.24 4.34
653 654 6.151985 GGTGGAAACATCATGGTGTTATTACA 59.848 38.462 24.17 13.99 46.14 2.41
687 688 8.607459 GGTTATATTGACTTGTCTGACAATGAG 58.393 37.037 22.28 13.98 37.48 2.90
688 689 8.321353 AGGTTATATTGACTTGTCTGACAATGA 58.679 33.333 22.28 9.93 37.48 2.57
689 690 8.498054 AGGTTATATTGACTTGTCTGACAATG 57.502 34.615 22.28 17.63 37.48 2.82
690 691 9.520515 AAAGGTTATATTGACTTGTCTGACAAT 57.479 29.630 22.28 13.05 37.48 2.71
691 692 8.918202 AAAGGTTATATTGACTTGTCTGACAA 57.082 30.769 20.95 20.95 36.54 3.18
692 693 8.918202 AAAAGGTTATATTGACTTGTCTGACA 57.082 30.769 6.36 6.36 0.00 3.58
693 694 9.220767 AGAAAAGGTTATATTGACTTGTCTGAC 57.779 33.333 0.00 0.00 36.45 3.51
694 695 9.436957 GAGAAAAGGTTATATTGACTTGTCTGA 57.563 33.333 9.22 0.00 37.58 3.27
695 696 9.219603 TGAGAAAAGGTTATATTGACTTGTCTG 57.780 33.333 9.22 0.00 37.58 3.51
696 697 9.793259 TTGAGAAAAGGTTATATTGACTTGTCT 57.207 29.630 0.00 0.00 39.55 3.41
727 729 6.089249 AGTCAATGGTTTCTGAATTTGACC 57.911 37.500 20.34 13.58 0.00 4.02
729 731 7.285172 TCTGAAGTCAATGGTTTCTGAATTTGA 59.715 33.333 0.00 0.00 30.57 2.69
730 732 7.380602 GTCTGAAGTCAATGGTTTCTGAATTTG 59.619 37.037 8.06 0.00 30.57 2.32
731 733 7.068593 TGTCTGAAGTCAATGGTTTCTGAATTT 59.931 33.333 8.06 0.00 30.57 1.82
732 734 6.547141 TGTCTGAAGTCAATGGTTTCTGAATT 59.453 34.615 8.06 0.00 32.91 2.17
736 738 5.756195 TTGTCTGAAGTCAATGGTTTCTG 57.244 39.130 0.94 0.83 0.00 3.02
742 744 7.957484 CGTATAAGTTTTGTCTGAAGTCAATGG 59.043 37.037 0.00 0.00 0.00 3.16
748 750 5.861727 ACCCGTATAAGTTTTGTCTGAAGT 58.138 37.500 0.00 0.00 0.00 3.01
752 754 3.061697 GCGACCCGTATAAGTTTTGTCTG 59.938 47.826 0.00 0.00 0.00 3.51
753 755 3.256558 GCGACCCGTATAAGTTTTGTCT 58.743 45.455 0.00 0.00 0.00 3.41
754 756 2.995258 TGCGACCCGTATAAGTTTTGTC 59.005 45.455 0.00 0.00 0.00 3.18
755 757 3.042871 TGCGACCCGTATAAGTTTTGT 57.957 42.857 0.00 0.00 0.00 2.83
757 759 5.632244 AAAATGCGACCCGTATAAGTTTT 57.368 34.783 0.00 0.00 31.12 2.43
759 761 6.740411 TTAAAAATGCGACCCGTATAAGTT 57.260 33.333 0.00 0.00 31.12 2.66
760 762 6.740411 TTTAAAAATGCGACCCGTATAAGT 57.260 33.333 0.00 0.00 31.12 2.24
761 763 6.193228 CGTTTTAAAAATGCGACCCGTATAAG 59.807 38.462 1.31 0.00 31.12 1.73
762 764 6.020372 CGTTTTAAAAATGCGACCCGTATAA 58.980 36.000 1.31 0.00 31.12 0.98
764 766 4.153835 TCGTTTTAAAAATGCGACCCGTAT 59.846 37.500 1.31 0.00 32.95 3.06
766 768 2.290093 TCGTTTTAAAAATGCGACCCGT 59.710 40.909 1.31 0.00 0.00 5.28
769 771 2.087905 GCGTCGTTTTAAAAATGCGACC 59.912 45.455 24.78 17.89 46.02 4.79
780 782 2.221286 TCAAAATGCTCGCGTCGTTTTA 59.779 40.909 22.92 14.21 33.00 1.52
785 787 0.110867 TTGTCAAAATGCTCGCGTCG 60.111 50.000 5.77 0.00 0.00 5.12
788 790 5.685195 ATATTTTTGTCAAAATGCTCGCG 57.315 34.783 11.44 0.00 41.77 5.87
829 831 9.027202 GGGGAATTTTACCTCACTTTTATGTTA 57.973 33.333 0.00 0.00 0.00 2.41
835 844 6.322931 AGATGGGGAATTTTACCTCACTTTT 58.677 36.000 0.00 0.00 40.94 2.27
985 1004 3.197790 CATTGGTGAGGCGCGGAG 61.198 66.667 8.83 0.00 0.00 4.63
986 1005 4.776322 CCATTGGTGAGGCGCGGA 62.776 66.667 8.83 0.00 0.00 5.54
1029 1048 2.203126 GCCCGGATCAGGAGCAAG 60.203 66.667 14.13 0.00 0.00 4.01
1078 1097 3.075005 GCAGTGGGCGGAGTAGGA 61.075 66.667 0.00 0.00 0.00 2.94
1875 1894 0.110688 CGAACATGTGCGTCTGGTTG 60.111 55.000 18.56 0.00 0.00 3.77
1926 1945 1.375396 GGCCACATAGACACGCACA 60.375 57.895 0.00 0.00 0.00 4.57
2031 2056 5.404946 CATCCTTTCAAGCATAACCTGTTG 58.595 41.667 0.00 0.00 0.00 3.33
2185 2210 1.979155 GGTCCCTTTTCAGGCTGGC 60.979 63.158 15.73 0.00 39.20 4.85
2277 2302 3.756434 GCTTGTAATACTTGGTTGCCTCA 59.244 43.478 0.00 0.00 0.00 3.86
2535 2560 4.025401 GCTTGTGACCAACGCCCG 62.025 66.667 0.00 0.00 0.00 6.13
2549 2574 0.388659 TTGCCGCTGAAATGTTGCTT 59.611 45.000 0.00 0.00 0.00 3.91
2622 2647 1.338294 ACATTAACCCGTCGACATGCA 60.338 47.619 17.16 0.00 0.00 3.96
2673 2698 1.276421 TCCAGACTAGCAAAGTGAGCC 59.724 52.381 0.00 0.00 39.07 4.70
2694 2719 0.318022 CATGTTGTGCTGCTTTCGCA 60.318 50.000 0.00 0.00 45.60 5.10
2824 2849 2.749076 TGATGCTTTCCAAGTCCATTCG 59.251 45.455 0.00 0.00 0.00 3.34
3246 3272 2.098117 GCTATGGTTGGTTCTCATGTGC 59.902 50.000 0.00 0.00 0.00 4.57
3399 4820 3.326747 GGAAAGCGCTCTGACTTTAGAA 58.673 45.455 12.06 0.00 36.28 2.10
3856 5295 4.655963 CCTGATCTGGTTTCCTTCTTTCA 58.344 43.478 10.40 0.00 0.00 2.69
3882 5321 3.399330 TGTGAATCAAGAACCGAACCTC 58.601 45.455 0.00 0.00 0.00 3.85
3957 5396 4.153256 GGCAAACTAATTCCAACGTTACG 58.847 43.478 0.00 2.19 0.00 3.18
3961 5400 2.556622 CAGGGCAAACTAATTCCAACGT 59.443 45.455 0.00 0.00 0.00 3.99
3973 5457 1.000938 CACTGAAAGAGCAGGGCAAAC 60.001 52.381 0.00 0.00 40.20 2.93
3975 5459 0.473755 TCACTGAAAGAGCAGGGCAA 59.526 50.000 0.00 0.00 39.17 4.52
4019 5506 3.490933 GGTCTCAGATGCATACGCTACAA 60.491 47.826 0.00 0.00 39.64 2.41
4044 5531 4.962155 AGAAAAACACTAGACAGACAGGG 58.038 43.478 0.00 0.00 0.00 4.45
4045 5532 7.378966 TGATAGAAAAACACTAGACAGACAGG 58.621 38.462 0.00 0.00 0.00 4.00
4048 5535 8.035394 TGGATGATAGAAAAACACTAGACAGAC 58.965 37.037 0.00 0.00 0.00 3.51
4116 5606 1.415289 GGAGGGTAAACCATAGACCGG 59.585 57.143 0.00 0.00 43.89 5.28
4172 5665 0.962356 CGCTGGCAGAAATCCACCTT 60.962 55.000 20.86 0.00 0.00 3.50
4188 5682 5.730568 GCAGATTAATTCCAACGAATTCGCT 60.731 40.000 27.03 13.29 43.79 4.93
4275 5796 3.581332 TGGGTAGGAAAACAGTAGACAGG 59.419 47.826 0.00 0.00 0.00 4.00
4306 5828 4.081254 TCAGATGGACCAATGAGTCAAGAG 60.081 45.833 0.00 0.00 38.59 2.85
4316 5838 2.133520 AGGCATCTCAGATGGACCAAT 58.866 47.619 16.70 0.00 0.00 3.16
4348 5870 8.020777 TGACATTATCCAAACCAATGCATATT 57.979 30.769 0.00 0.00 33.82 1.28
4521 8602 7.276218 TGAAAATCTTTATTCGGTATCGACGTT 59.724 33.333 0.00 0.00 45.92 3.99
4526 8607 7.855904 CCCTTTGAAAATCTTTATTCGGTATCG 59.144 37.037 0.00 0.00 37.82 2.92
4546 8635 2.958355 TGAAAGCTCAACCTTCCCTTTG 59.042 45.455 0.00 0.00 0.00 2.77
4622 9980 9.423061 TCTGGTCTTTTTCTTTTTCTTTTGAAG 57.577 29.630 0.00 0.00 39.88 3.02
4636 10000 8.571336 TGAATCTTCATTCTTCTGGTCTTTTTC 58.429 33.333 0.00 0.00 39.49 2.29


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

AutoCloner maintained by Alex Coulton.