Multiple sequence alignment - TraesCS4D01G185900

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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 TraesCS4D01G185900 chr4D 100.000 3344 0 0 1 3344 323602019 323605362 0.000000e+00 6176.0
1 TraesCS4D01G185900 chr4D 79.151 1060 181 24 1283 2331 323583319 323582289 0.000000e+00 697.0
2 TraesCS4D01G185900 chr4A 95.189 2785 94 13 582 3336 147654226 147651452 0.000000e+00 4364.0
3 TraesCS4D01G185900 chr4A 79.437 1065 169 35 1283 2331 148126606 148127636 0.000000e+00 708.0
4 TraesCS4D01G185900 chr4B 95.316 2455 73 10 278 2691 404123045 404125498 0.000000e+00 3858.0
5 TraesCS4D01G185900 chr4B 96.072 611 20 1 2738 3344 404125599 404126209 0.000000e+00 992.0
6 TraesCS4D01G185900 chr7D 90.016 1272 103 10 1070 2335 560892445 560893698 0.000000e+00 1624.0
7 TraesCS4D01G185900 chr7D 88.241 1063 92 11 1364 2426 560982799 560983828 0.000000e+00 1240.0
8 TraesCS4D01G185900 chr7D 92.446 278 21 0 1 278 608272181 608272458 6.720000e-107 398.0
9 TraesCS4D01G185900 chr7D 92.115 279 20 2 1 277 4651378 4651656 3.130000e-105 392.0
10 TraesCS4D01G185900 chr7A 89.119 1305 114 14 1052 2341 645038604 645039895 0.000000e+00 1598.0
11 TraesCS4D01G185900 chr7B 88.906 1298 116 19 1055 2338 608876491 608875208 0.000000e+00 1574.0
12 TraesCS4D01G185900 chr6D 92.857 280 17 3 1 277 327204222 327204501 1.440000e-108 403.0
13 TraesCS4D01G185900 chr6D 92.115 279 20 2 1 277 30580538 30580816 3.130000e-105 392.0
14 TraesCS4D01G185900 chr6D 75.641 156 23 12 2079 2225 376942209 376942358 2.790000e-06 63.9
15 TraesCS4D01G185900 chr3D 92.500 280 19 2 1 278 305633931 305633652 1.870000e-107 399.0
16 TraesCS4D01G185900 chr3D 92.473 279 19 2 1 277 20398396 20398674 6.720000e-107 398.0
17 TraesCS4D01G185900 chr1D 92.473 279 19 2 1 277 463059536 463059258 6.720000e-107 398.0
18 TraesCS4D01G185900 chr1D 91.844 282 20 3 1 279 475847125 475846844 1.120000e-104 390.0
19 TraesCS4D01G185900 chr2D 92.143 280 19 2 1 277 81323891 81324170 3.130000e-105 392.0
20 TraesCS4D01G185900 chr2B 77.432 257 40 11 1251 1505 773784332 773784572 1.620000e-28 137.0
21 TraesCS4D01G185900 chr1B 76.136 264 35 16 1251 1512 626036439 626036202 2.730000e-21 113.0
22 TraesCS4D01G185900 chr1A 80.882 136 21 5 1251 1384 474246680 474246812 5.900000e-18 102.0
23 TraesCS4D01G185900 chr6B 84.375 64 10 0 2162 2225 563130964 563131027 2.790000e-06 63.9
24 TraesCS4D01G185900 chr6A 85.714 56 8 0 2170 2225 518546573 518546628 3.600000e-05 60.2


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 TraesCS4D01G185900 chr4D 323602019 323605362 3343 False 6176 6176 100.000 1 3344 1 chr4D.!!$F1 3343
1 TraesCS4D01G185900 chr4D 323582289 323583319 1030 True 697 697 79.151 1283 2331 1 chr4D.!!$R1 1048
2 TraesCS4D01G185900 chr4A 147651452 147654226 2774 True 4364 4364 95.189 582 3336 1 chr4A.!!$R1 2754
3 TraesCS4D01G185900 chr4A 148126606 148127636 1030 False 708 708 79.437 1283 2331 1 chr4A.!!$F1 1048
4 TraesCS4D01G185900 chr4B 404123045 404126209 3164 False 2425 3858 95.694 278 3344 2 chr4B.!!$F1 3066
5 TraesCS4D01G185900 chr7D 560892445 560893698 1253 False 1624 1624 90.016 1070 2335 1 chr7D.!!$F2 1265
6 TraesCS4D01G185900 chr7D 560982799 560983828 1029 False 1240 1240 88.241 1364 2426 1 chr7D.!!$F3 1062
7 TraesCS4D01G185900 chr7A 645038604 645039895 1291 False 1598 1598 89.119 1052 2341 1 chr7A.!!$F1 1289
8 TraesCS4D01G185900 chr7B 608875208 608876491 1283 True 1574 1574 88.906 1055 2338 1 chr7B.!!$R1 1283

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
43 44 0.032815 GGCTGCTATTCTCTCCGGTC 59.967 60.0 0.00 0.0 0.0 4.79 F
106 107 0.105039 GACTGCCGGGGATGTTAGAG 59.895 60.0 2.18 0.0 0.0 2.43 F
107 108 0.325296 ACTGCCGGGGATGTTAGAGA 60.325 55.0 2.18 0.0 0.0 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1543 2.568623 AGTCCGCCTTGTTCTTGAAT 57.431 45.000 0.0 0.0 0.0 2.57 R
1736 1791 3.166490 TTCTTGGCGCCGTACACCA 62.166 57.895 23.9 0.0 0.0 4.17 R
2391 2446 3.434641 CGTGTTGCATGTTCTGATCTCTT 59.565 43.478 0.0 0.0 0.0 2.85 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
17 18 3.303189 ACTGCGGGAGGATGTCAG 58.697 61.111 0.51 0.00 0.00 3.51
18 19 2.202987 CTGCGGGAGGATGTCAGC 60.203 66.667 0.00 0.00 0.00 4.26
19 20 3.746949 CTGCGGGAGGATGTCAGCC 62.747 68.421 0.00 0.00 31.44 4.85
20 21 4.554036 GCGGGAGGATGTCAGCCC 62.554 72.222 2.75 0.00 37.21 5.19
22 23 3.083997 GGGAGGATGTCAGCCCGT 61.084 66.667 2.75 0.00 0.00 5.28
23 24 2.501610 GGAGGATGTCAGCCCGTC 59.498 66.667 2.75 0.00 0.00 4.79
24 25 2.105128 GAGGATGTCAGCCCGTCG 59.895 66.667 2.75 0.00 0.00 5.12
25 26 3.432051 GAGGATGTCAGCCCGTCGG 62.432 68.421 3.60 3.60 0.00 4.79
35 36 2.815308 CCCGTCGGCTGCTATTCT 59.185 61.111 5.50 0.00 0.00 2.40
36 37 1.300233 CCCGTCGGCTGCTATTCTC 60.300 63.158 5.50 0.00 0.00 2.87
37 38 1.736586 CCGTCGGCTGCTATTCTCT 59.263 57.895 0.00 0.00 0.00 3.10
38 39 0.318275 CCGTCGGCTGCTATTCTCTC 60.318 60.000 0.00 0.00 0.00 3.20
39 40 0.318275 CGTCGGCTGCTATTCTCTCC 60.318 60.000 0.00 0.00 0.00 3.71
40 41 0.318275 GTCGGCTGCTATTCTCTCCG 60.318 60.000 0.00 0.00 38.34 4.63
41 42 1.006805 CGGCTGCTATTCTCTCCGG 60.007 63.158 0.00 0.00 33.85 5.14
42 43 1.739338 CGGCTGCTATTCTCTCCGGT 61.739 60.000 0.00 0.00 33.85 5.28
43 44 0.032815 GGCTGCTATTCTCTCCGGTC 59.967 60.000 0.00 0.00 0.00 4.79
44 45 1.036707 GCTGCTATTCTCTCCGGTCT 58.963 55.000 0.00 0.00 0.00 3.85
45 46 1.269517 GCTGCTATTCTCTCCGGTCTG 60.270 57.143 0.00 0.00 0.00 3.51
46 47 2.302260 CTGCTATTCTCTCCGGTCTGA 58.698 52.381 0.00 0.00 0.00 3.27
47 48 2.025155 TGCTATTCTCTCCGGTCTGAC 58.975 52.381 0.00 0.00 0.00 3.51
48 49 1.338655 GCTATTCTCTCCGGTCTGACC 59.661 57.143 16.99 16.99 34.05 4.02
57 58 3.241177 GGTCTGACCGTTTGCGAC 58.759 61.111 11.71 0.00 41.33 5.19
67 68 1.643298 CGTTTGCGACGTTACTGTTG 58.357 50.000 4.46 0.00 46.49 3.33
68 69 1.005766 CGTTTGCGACGTTACTGTTGT 60.006 47.619 4.46 0.00 46.49 3.32
69 70 2.359598 GTTTGCGACGTTACTGTTGTG 58.640 47.619 0.00 0.00 0.00 3.33
70 71 1.642728 TTGCGACGTTACTGTTGTGT 58.357 45.000 0.00 0.00 0.00 3.72
71 72 0.924777 TGCGACGTTACTGTTGTGTG 59.075 50.000 0.00 0.00 0.00 3.82
72 73 0.382636 GCGACGTTACTGTTGTGTGC 60.383 55.000 0.00 0.00 0.00 4.57
73 74 0.111878 CGACGTTACTGTTGTGTGCG 60.112 55.000 0.00 0.00 0.00 5.34
74 75 1.202203 GACGTTACTGTTGTGTGCGA 58.798 50.000 0.00 0.00 0.00 5.10
75 76 0.925466 ACGTTACTGTTGTGTGCGAC 59.075 50.000 0.00 0.00 0.00 5.19
76 77 0.111878 CGTTACTGTTGTGTGCGACG 60.112 55.000 0.00 0.00 0.00 5.12
77 78 0.382636 GTTACTGTTGTGTGCGACGC 60.383 55.000 14.19 14.19 0.00 5.19
78 79 0.528901 TTACTGTTGTGTGCGACGCT 60.529 50.000 22.08 0.00 0.00 5.07
79 80 0.311477 TACTGTTGTGTGCGACGCTA 59.689 50.000 22.08 7.35 0.00 4.26
80 81 1.213094 ACTGTTGTGTGCGACGCTAC 61.213 55.000 22.08 19.16 35.48 3.58
81 82 1.886861 CTGTTGTGTGCGACGCTACC 61.887 60.000 22.08 9.43 34.34 3.18
82 83 2.731721 TTGTGTGCGACGCTACCG 60.732 61.111 22.08 0.00 41.14 4.02
89 90 2.350537 CGACGCTACCGCTACGAC 60.351 66.667 0.00 0.00 38.22 4.34
90 91 2.806856 CGACGCTACCGCTACGACT 61.807 63.158 0.00 0.00 38.22 4.18
91 92 1.297451 GACGCTACCGCTACGACTG 60.297 63.158 0.00 0.00 38.22 3.51
92 93 2.651232 CGCTACCGCTACGACTGC 60.651 66.667 0.00 0.00 0.00 4.40
93 94 2.278661 GCTACCGCTACGACTGCC 60.279 66.667 0.00 0.00 0.00 4.85
94 95 2.024305 CTACCGCTACGACTGCCG 59.976 66.667 0.00 0.00 45.44 5.69
95 96 3.465296 CTACCGCTACGACTGCCGG 62.465 68.421 0.00 0.00 43.93 6.13
99 100 3.537874 GCTACGACTGCCGGGGAT 61.538 66.667 2.18 0.00 43.93 3.85
100 101 2.417516 CTACGACTGCCGGGGATG 59.582 66.667 2.18 0.00 43.93 3.51
101 102 2.363276 TACGACTGCCGGGGATGT 60.363 61.111 2.18 0.00 43.93 3.06
102 103 1.956629 CTACGACTGCCGGGGATGTT 61.957 60.000 2.18 0.00 43.93 2.71
103 104 0.683828 TACGACTGCCGGGGATGTTA 60.684 55.000 2.18 0.00 43.93 2.41
104 105 1.227263 CGACTGCCGGGGATGTTAG 60.227 63.158 2.18 0.00 33.91 2.34
105 106 1.672854 CGACTGCCGGGGATGTTAGA 61.673 60.000 2.18 0.00 33.91 2.10
106 107 0.105039 GACTGCCGGGGATGTTAGAG 59.895 60.000 2.18 0.00 0.00 2.43
107 108 0.325296 ACTGCCGGGGATGTTAGAGA 60.325 55.000 2.18 0.00 0.00 3.10
108 109 1.051812 CTGCCGGGGATGTTAGAGAT 58.948 55.000 2.18 0.00 0.00 2.75
109 110 2.248248 CTGCCGGGGATGTTAGAGATA 58.752 52.381 2.18 0.00 0.00 1.98
110 111 2.834549 CTGCCGGGGATGTTAGAGATAT 59.165 50.000 2.18 0.00 0.00 1.63
111 112 4.023980 CTGCCGGGGATGTTAGAGATATA 58.976 47.826 2.18 0.00 0.00 0.86
112 113 4.620723 TGCCGGGGATGTTAGAGATATAT 58.379 43.478 2.18 0.00 0.00 0.86
113 114 5.030147 TGCCGGGGATGTTAGAGATATATT 58.970 41.667 2.18 0.00 0.00 1.28
114 115 5.487488 TGCCGGGGATGTTAGAGATATATTT 59.513 40.000 2.18 0.00 0.00 1.40
115 116 5.817816 GCCGGGGATGTTAGAGATATATTTG 59.182 44.000 2.18 0.00 0.00 2.32
116 117 6.349300 CCGGGGATGTTAGAGATATATTTGG 58.651 44.000 0.00 0.00 0.00 3.28
117 118 6.349300 CGGGGATGTTAGAGATATATTTGGG 58.651 44.000 0.00 0.00 0.00 4.12
118 119 6.070194 CGGGGATGTTAGAGATATATTTGGGT 60.070 42.308 0.00 0.00 0.00 4.51
119 120 7.528881 CGGGGATGTTAGAGATATATTTGGGTT 60.529 40.741 0.00 0.00 0.00 4.11
120 121 8.832735 GGGGATGTTAGAGATATATTTGGGTTA 58.167 37.037 0.00 0.00 0.00 2.85
121 122 9.668497 GGGATGTTAGAGATATATTTGGGTTAC 57.332 37.037 0.00 0.00 0.00 2.50
135 136 9.984590 ATATTTGGGTTACTTGTATTTGGTAGT 57.015 29.630 0.00 0.00 0.00 2.73
136 137 7.748691 TTTGGGTTACTTGTATTTGGTAGTC 57.251 36.000 0.00 0.00 0.00 2.59
137 138 6.691255 TGGGTTACTTGTATTTGGTAGTCT 57.309 37.500 0.00 0.00 0.00 3.24
138 139 7.795534 TGGGTTACTTGTATTTGGTAGTCTA 57.204 36.000 0.00 0.00 0.00 2.59
139 140 7.844009 TGGGTTACTTGTATTTGGTAGTCTAG 58.156 38.462 0.00 0.00 0.00 2.43
140 141 7.093201 TGGGTTACTTGTATTTGGTAGTCTAGG 60.093 40.741 0.00 0.00 0.00 3.02
141 142 7.124750 GGGTTACTTGTATTTGGTAGTCTAGGA 59.875 40.741 0.00 0.00 0.00 2.94
142 143 8.702819 GGTTACTTGTATTTGGTAGTCTAGGAT 58.297 37.037 0.00 0.00 0.00 3.24
146 147 8.603304 ACTTGTATTTGGTAGTCTAGGATTTGT 58.397 33.333 0.00 0.00 0.00 2.83
153 154 7.989947 TGGTAGTCTAGGATTTGTAATCCTT 57.010 36.000 22.19 9.96 45.78 3.36
154 155 8.019656 TGGTAGTCTAGGATTTGTAATCCTTC 57.980 38.462 22.19 14.35 45.78 3.46
155 156 7.844779 TGGTAGTCTAGGATTTGTAATCCTTCT 59.155 37.037 22.19 18.84 45.78 2.85
156 157 8.361889 GGTAGTCTAGGATTTGTAATCCTTCTC 58.638 40.741 22.19 13.82 45.78 2.87
157 158 7.368198 AGTCTAGGATTTGTAATCCTTCTCC 57.632 40.000 22.19 10.81 45.78 3.71
158 159 7.136203 AGTCTAGGATTTGTAATCCTTCTCCT 58.864 38.462 22.19 12.40 45.78 3.69
159 160 8.290277 AGTCTAGGATTTGTAATCCTTCTCCTA 58.710 37.037 22.19 6.31 45.78 2.94
160 161 8.361889 GTCTAGGATTTGTAATCCTTCTCCTAC 58.638 40.741 22.19 10.56 45.78 3.18
161 162 6.502074 AGGATTTGTAATCCTTCTCCTACC 57.498 41.667 13.83 0.00 45.78 3.18
162 163 6.213525 AGGATTTGTAATCCTTCTCCTACCT 58.786 40.000 13.83 0.00 45.78 3.08
163 164 6.678857 AGGATTTGTAATCCTTCTCCTACCTT 59.321 38.462 13.83 0.00 45.78 3.50
164 165 7.849904 AGGATTTGTAATCCTTCTCCTACCTTA 59.150 37.037 13.83 0.00 45.78 2.69
165 166 8.661345 GGATTTGTAATCCTTCTCCTACCTTAT 58.339 37.037 10.48 0.00 35.36 1.73
166 167 9.713713 GATTTGTAATCCTTCTCCTACCTTATC 57.286 37.037 0.00 0.00 0.00 1.75
167 168 8.855804 TTTGTAATCCTTCTCCTACCTTATCT 57.144 34.615 0.00 0.00 0.00 1.98
168 169 8.855804 TTGTAATCCTTCTCCTACCTTATCTT 57.144 34.615 0.00 0.00 0.00 2.40
169 170 8.480133 TGTAATCCTTCTCCTACCTTATCTTC 57.520 38.462 0.00 0.00 0.00 2.87
170 171 8.065627 TGTAATCCTTCTCCTACCTTATCTTCA 58.934 37.037 0.00 0.00 0.00 3.02
171 172 7.610580 AATCCTTCTCCTACCTTATCTTCAG 57.389 40.000 0.00 0.00 0.00 3.02
172 173 5.459505 TCCTTCTCCTACCTTATCTTCAGG 58.540 45.833 0.00 0.00 37.45 3.86
173 174 5.195960 TCCTTCTCCTACCTTATCTTCAGGA 59.804 44.000 0.00 0.00 35.14 3.86
177 178 5.068215 TCCTACCTTATCTTCAGGAGAGG 57.932 47.826 0.00 0.00 37.93 3.69
178 179 3.576550 CCTACCTTATCTTCAGGAGAGGC 59.423 52.174 0.00 0.00 37.93 4.70
179 180 3.413105 ACCTTATCTTCAGGAGAGGCT 57.587 47.619 0.00 0.00 37.93 4.58
180 181 3.730269 ACCTTATCTTCAGGAGAGGCTT 58.270 45.455 0.00 0.00 37.93 4.35
181 182 3.709141 ACCTTATCTTCAGGAGAGGCTTC 59.291 47.826 0.00 0.00 37.93 3.86
182 183 3.966665 CCTTATCTTCAGGAGAGGCTTCT 59.033 47.826 0.00 0.00 37.93 2.85
183 184 4.408596 CCTTATCTTCAGGAGAGGCTTCTT 59.591 45.833 0.00 0.00 37.93 2.52
184 185 5.600484 CCTTATCTTCAGGAGAGGCTTCTTA 59.400 44.000 0.00 0.00 37.93 2.10
185 186 6.462347 CCTTATCTTCAGGAGAGGCTTCTTAC 60.462 46.154 0.00 0.00 37.93 2.34
186 187 3.100671 TCTTCAGGAGAGGCTTCTTACC 58.899 50.000 0.00 0.00 32.53 2.85
187 188 1.867363 TCAGGAGAGGCTTCTTACCC 58.133 55.000 0.00 0.00 32.53 3.69
188 189 1.362932 TCAGGAGAGGCTTCTTACCCT 59.637 52.381 0.00 0.00 32.53 4.34
189 190 1.760029 CAGGAGAGGCTTCTTACCCTC 59.240 57.143 0.00 0.00 46.39 4.30
194 195 3.653835 GAGGCTTCTTACCCTCCAAAT 57.346 47.619 0.00 0.00 41.42 2.32
195 196 3.546724 GAGGCTTCTTACCCTCCAAATC 58.453 50.000 0.00 0.00 41.42 2.17
196 197 3.193782 AGGCTTCTTACCCTCCAAATCT 58.806 45.455 0.00 0.00 0.00 2.40
197 198 3.593780 AGGCTTCTTACCCTCCAAATCTT 59.406 43.478 0.00 0.00 0.00 2.40
198 199 3.696548 GGCTTCTTACCCTCCAAATCTTG 59.303 47.826 0.00 0.00 0.00 3.02
199 200 4.336280 GCTTCTTACCCTCCAAATCTTGT 58.664 43.478 0.00 0.00 0.00 3.16
200 201 5.497474 GCTTCTTACCCTCCAAATCTTGTA 58.503 41.667 0.00 0.00 0.00 2.41
201 202 5.354513 GCTTCTTACCCTCCAAATCTTGTAC 59.645 44.000 0.00 0.00 0.00 2.90
202 203 6.697641 TTCTTACCCTCCAAATCTTGTACT 57.302 37.500 0.00 0.00 0.00 2.73
203 204 6.295719 TCTTACCCTCCAAATCTTGTACTC 57.704 41.667 0.00 0.00 0.00 2.59
204 205 5.783360 TCTTACCCTCCAAATCTTGTACTCA 59.217 40.000 0.00 0.00 0.00 3.41
205 206 4.993705 ACCCTCCAAATCTTGTACTCAA 57.006 40.909 0.00 0.00 0.00 3.02
206 207 5.520748 ACCCTCCAAATCTTGTACTCAAT 57.479 39.130 0.00 0.00 32.82 2.57
207 208 6.636454 ACCCTCCAAATCTTGTACTCAATA 57.364 37.500 0.00 0.00 32.82 1.90
208 209 7.213178 ACCCTCCAAATCTTGTACTCAATAT 57.787 36.000 0.00 0.00 32.82 1.28
209 210 8.331931 ACCCTCCAAATCTTGTACTCAATATA 57.668 34.615 0.00 0.00 32.82 0.86
210 211 8.949421 ACCCTCCAAATCTTGTACTCAATATAT 58.051 33.333 0.00 0.00 32.82 0.86
217 218 9.640963 AAATCTTGTACTCAATATATACTCGCC 57.359 33.333 0.00 0.00 32.82 5.54
218 219 7.154435 TCTTGTACTCAATATATACTCGCCC 57.846 40.000 0.00 0.00 32.82 6.13
219 220 6.946583 TCTTGTACTCAATATATACTCGCCCT 59.053 38.462 0.00 0.00 32.82 5.19
220 221 6.754702 TGTACTCAATATATACTCGCCCTC 57.245 41.667 0.00 0.00 0.00 4.30
221 222 4.966965 ACTCAATATATACTCGCCCTCG 57.033 45.455 0.00 0.00 0.00 4.63
222 223 4.586884 ACTCAATATATACTCGCCCTCGA 58.413 43.478 0.00 0.00 43.28 4.04
239 240 5.420409 CCCTCGAGGCTTAATAATACATCC 58.580 45.833 26.87 0.00 0.00 3.51
240 241 5.046591 CCCTCGAGGCTTAATAATACATCCA 60.047 44.000 26.87 0.00 0.00 3.41
241 242 6.352222 CCCTCGAGGCTTAATAATACATCCAT 60.352 42.308 26.87 0.00 0.00 3.41
242 243 6.758886 CCTCGAGGCTTAATAATACATCCATC 59.241 42.308 20.67 0.00 0.00 3.51
243 244 7.239763 TCGAGGCTTAATAATACATCCATCA 57.760 36.000 0.00 0.00 0.00 3.07
244 245 7.851228 TCGAGGCTTAATAATACATCCATCAT 58.149 34.615 0.00 0.00 0.00 2.45
245 246 8.977412 TCGAGGCTTAATAATACATCCATCATA 58.023 33.333 0.00 0.00 0.00 2.15
246 247 9.770097 CGAGGCTTAATAATACATCCATCATAT 57.230 33.333 0.00 0.00 0.00 1.78
252 253 9.898152 TTAATAATACATCCATCATATTCCGCA 57.102 29.630 0.00 0.00 0.00 5.69
253 254 8.806429 AATAATACATCCATCATATTCCGCAA 57.194 30.769 0.00 0.00 0.00 4.85
254 255 6.500684 AATACATCCATCATATTCCGCAAC 57.499 37.500 0.00 0.00 0.00 4.17
255 256 3.819368 ACATCCATCATATTCCGCAACA 58.181 40.909 0.00 0.00 0.00 3.33
256 257 4.206375 ACATCCATCATATTCCGCAACAA 58.794 39.130 0.00 0.00 0.00 2.83
257 258 4.828939 ACATCCATCATATTCCGCAACAAT 59.171 37.500 0.00 0.00 0.00 2.71
258 259 5.048504 ACATCCATCATATTCCGCAACAATC 60.049 40.000 0.00 0.00 0.00 2.67
259 260 3.820467 TCCATCATATTCCGCAACAATCC 59.180 43.478 0.00 0.00 0.00 3.01
260 261 3.057315 CCATCATATTCCGCAACAATCCC 60.057 47.826 0.00 0.00 0.00 3.85
261 262 3.576078 TCATATTCCGCAACAATCCCT 57.424 42.857 0.00 0.00 0.00 4.20
262 263 3.476552 TCATATTCCGCAACAATCCCTC 58.523 45.455 0.00 0.00 0.00 4.30
263 264 3.136443 TCATATTCCGCAACAATCCCTCT 59.864 43.478 0.00 0.00 0.00 3.69
264 265 2.044123 ATTCCGCAACAATCCCTCTC 57.956 50.000 0.00 0.00 0.00 3.20
265 266 0.984230 TTCCGCAACAATCCCTCTCT 59.016 50.000 0.00 0.00 0.00 3.10
266 267 0.537188 TCCGCAACAATCCCTCTCTC 59.463 55.000 0.00 0.00 0.00 3.20
267 268 0.462759 CCGCAACAATCCCTCTCTCC 60.463 60.000 0.00 0.00 0.00 3.71
268 269 0.462759 CGCAACAATCCCTCTCTCCC 60.463 60.000 0.00 0.00 0.00 4.30
269 270 0.915364 GCAACAATCCCTCTCTCCCT 59.085 55.000 0.00 0.00 0.00 4.20
270 271 1.283321 GCAACAATCCCTCTCTCCCTT 59.717 52.381 0.00 0.00 0.00 3.95
271 272 2.682269 GCAACAATCCCTCTCTCCCTTC 60.682 54.545 0.00 0.00 0.00 3.46
272 273 1.886422 ACAATCCCTCTCTCCCTTCC 58.114 55.000 0.00 0.00 0.00 3.46
273 274 1.081174 ACAATCCCTCTCTCCCTTCCA 59.919 52.381 0.00 0.00 0.00 3.53
274 275 2.200081 CAATCCCTCTCTCCCTTCCAA 58.800 52.381 0.00 0.00 0.00 3.53
275 276 1.886422 ATCCCTCTCTCCCTTCCAAC 58.114 55.000 0.00 0.00 0.00 3.77
276 277 0.491823 TCCCTCTCTCCCTTCCAACA 59.508 55.000 0.00 0.00 0.00 3.33
312 313 7.099120 GCAAAATGTGGTTGATCTAGGAAAAT 58.901 34.615 0.00 0.00 0.00 1.82
372 373 4.574674 ATGATTGCTTCCTACCAAGACA 57.425 40.909 0.00 0.00 0.00 3.41
388 389 3.340814 AGACAAAGTCCAAGCGATGAT 57.659 42.857 0.00 0.00 32.18 2.45
425 426 4.580580 CACCTTCTTTCAGTACAAAGGCTT 59.419 41.667 0.00 0.00 40.12 4.35
488 500 4.735369 TGTGAAGGTTATGTTGGGACATT 58.265 39.130 0.00 0.00 43.92 2.71
493 505 3.852578 AGGTTATGTTGGGACATTCTCCT 59.147 43.478 0.00 1.87 43.92 3.69
506 518 2.743636 TTCTCCTCGTGTGGATTGTC 57.256 50.000 0.00 0.00 35.30 3.18
519 534 5.005779 GTGTGGATTGTCACGAGATATGAAC 59.994 44.000 0.00 0.00 40.31 3.18
555 570 0.336048 AGCCCATATGTGCACCCTTT 59.664 50.000 15.69 0.00 0.00 3.11
563 587 0.820871 TGTGCACCCTTTTTGTCCAC 59.179 50.000 15.69 0.00 0.00 4.02
612 636 7.068103 TCCATATACAAACATCCATGGTGAAAC 59.932 37.037 12.58 0.00 35.49 2.78
634 663 4.106197 CCGCTACAGTGAAAACTAGCTAG 58.894 47.826 19.44 19.44 0.00 3.42
771 801 2.046285 GGGCACATGCACCTACCAC 61.046 63.158 6.15 0.00 44.36 4.16
956 993 0.933097 GGTGCAGCGTCATAGTCATG 59.067 55.000 0.00 0.00 0.00 3.07
1942 1997 4.373116 CGGCGCTGGTGTACCTGT 62.373 66.667 8.83 0.00 37.30 4.00
2350 2405 0.535335 CGCCAAGCCCTAGTGTCTAA 59.465 55.000 0.00 0.00 0.00 2.10
2391 2446 4.638421 GGATTGGTTTGGATATGAACGTGA 59.362 41.667 0.00 0.00 0.00 4.35
2405 2460 5.139435 TGAACGTGAAGAGATCAGAACAT 57.861 39.130 0.00 0.00 39.19 2.71
2437 2492 7.170998 ACGTCCTACTTTACAGACAAGATTTTG 59.829 37.037 0.00 0.00 40.24 2.44
2471 2526 0.747255 AGATGTAGCTGTAGCCACCG 59.253 55.000 0.00 0.00 43.38 4.94
2472 2527 0.876342 GATGTAGCTGTAGCCACCGC 60.876 60.000 0.00 0.00 43.38 5.68
2473 2528 2.202892 GTAGCTGTAGCCACCGCC 60.203 66.667 0.00 0.00 43.38 6.13
2474 2529 2.682136 TAGCTGTAGCCACCGCCA 60.682 61.111 0.00 0.00 43.38 5.69
2475 2530 3.014085 TAGCTGTAGCCACCGCCAC 62.014 63.158 0.00 0.00 43.38 5.01
2526 2592 0.528924 TCAAATGGATGCTGCTGTGC 59.471 50.000 0.00 0.00 0.00 4.57
2554 2620 2.907910 ACGCATGCTTCATTCTTCAC 57.092 45.000 17.13 0.00 0.00 3.18
2580 2646 2.591066 CGAGAGCAACAGAAAGCTTG 57.409 50.000 0.00 0.00 42.04 4.01
2652 2729 2.437281 AGAGTGGCAGGATGAATACTGG 59.563 50.000 4.70 0.00 39.21 4.00
2876 3035 4.571176 GGAATAAAGACTGTTCGATCACCC 59.429 45.833 0.00 0.00 0.00 4.61
2963 3122 3.938963 TCTCTAATCAACCACATTTCCGC 59.061 43.478 0.00 0.00 0.00 5.54
2974 3133 4.162698 ACCACATTTCCGCTACATTACCTA 59.837 41.667 0.00 0.00 0.00 3.08
2987 3146 6.015603 GCTACATTACCTACCCTAACTACCAG 60.016 46.154 0.00 0.00 0.00 4.00
3205 3372 7.229306 TGTTCAGACACTTTCATCAGCTTTATT 59.771 33.333 0.00 0.00 0.00 1.40
3302 3469 5.661458 TCATAGTTTGTCCGGAGATCTTTC 58.339 41.667 3.06 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.023949 GCTGACATCCTCCCGCAGT 62.024 63.158 0.00 0.00 0.00 4.40
1 2 2.202987 GCTGACATCCTCCCGCAG 60.203 66.667 0.00 0.00 0.00 5.18
2 3 3.785859 GGCTGACATCCTCCCGCA 61.786 66.667 0.00 0.00 0.00 5.69
3 4 4.554036 GGGCTGACATCCTCCCGC 62.554 72.222 0.00 0.00 0.00 6.13
5 6 3.083997 ACGGGCTGACATCCTCCC 61.084 66.667 0.00 0.00 35.42 4.30
6 7 2.501610 GACGGGCTGACATCCTCC 59.498 66.667 0.00 0.00 0.00 4.30
7 8 2.105128 CGACGGGCTGACATCCTC 59.895 66.667 0.00 0.00 0.00 3.71
8 9 3.461773 CCGACGGGCTGACATCCT 61.462 66.667 5.81 0.00 0.00 3.24
18 19 1.300233 GAGAATAGCAGCCGACGGG 60.300 63.158 17.22 0.14 0.00 5.28
19 20 0.318275 GAGAGAATAGCAGCCGACGG 60.318 60.000 10.29 10.29 0.00 4.79
20 21 0.318275 GGAGAGAATAGCAGCCGACG 60.318 60.000 0.00 0.00 0.00 5.12
21 22 0.318275 CGGAGAGAATAGCAGCCGAC 60.318 60.000 0.00 0.00 41.11 4.79
22 23 1.456196 CCGGAGAGAATAGCAGCCGA 61.456 60.000 0.00 0.00 41.11 5.54
23 24 1.006805 CCGGAGAGAATAGCAGCCG 60.007 63.158 0.00 0.00 38.54 5.52
24 25 0.032815 GACCGGAGAGAATAGCAGCC 59.967 60.000 9.46 0.00 0.00 4.85
25 26 1.036707 AGACCGGAGAGAATAGCAGC 58.963 55.000 9.46 0.00 0.00 5.25
26 27 2.034053 GTCAGACCGGAGAGAATAGCAG 59.966 54.545 9.46 0.00 0.00 4.24
27 28 2.025155 GTCAGACCGGAGAGAATAGCA 58.975 52.381 9.46 0.00 0.00 3.49
28 29 1.338655 GGTCAGACCGGAGAGAATAGC 59.661 57.143 9.46 0.00 0.00 2.97
40 41 3.241177 GTCGCAAACGGTCAGACC 58.759 61.111 9.92 9.92 40.63 3.85
49 50 2.222863 ACACAACAGTAACGTCGCAAAC 60.223 45.455 0.00 0.00 0.00 2.93
50 51 2.001159 ACACAACAGTAACGTCGCAAA 58.999 42.857 0.00 0.00 0.00 3.68
51 52 1.325037 CACACAACAGTAACGTCGCAA 59.675 47.619 0.00 0.00 0.00 4.85
52 53 0.924777 CACACAACAGTAACGTCGCA 59.075 50.000 0.00 0.00 0.00 5.10
53 54 0.382636 GCACACAACAGTAACGTCGC 60.383 55.000 0.00 0.00 0.00 5.19
54 55 0.111878 CGCACACAACAGTAACGTCG 60.112 55.000 0.00 0.00 0.00 5.12
55 56 1.071698 GTCGCACACAACAGTAACGTC 60.072 52.381 0.00 0.00 0.00 4.34
56 57 0.925466 GTCGCACACAACAGTAACGT 59.075 50.000 0.00 0.00 0.00 3.99
57 58 0.111878 CGTCGCACACAACAGTAACG 60.112 55.000 0.00 0.00 0.00 3.18
58 59 0.382636 GCGTCGCACACAACAGTAAC 60.383 55.000 13.44 0.00 0.00 2.50
59 60 0.528901 AGCGTCGCACACAACAGTAA 60.529 50.000 21.09 0.00 0.00 2.24
60 61 0.311477 TAGCGTCGCACACAACAGTA 59.689 50.000 21.09 0.00 0.00 2.74
61 62 1.066752 TAGCGTCGCACACAACAGT 59.933 52.632 21.09 0.00 0.00 3.55
62 63 1.487231 GTAGCGTCGCACACAACAG 59.513 57.895 21.09 0.00 0.00 3.16
63 64 1.952133 GGTAGCGTCGCACACAACA 60.952 57.895 21.09 0.00 0.00 3.33
64 65 2.851104 GGTAGCGTCGCACACAAC 59.149 61.111 21.09 8.82 0.00 3.32
65 66 2.731721 CGGTAGCGTCGCACACAA 60.732 61.111 21.09 0.00 0.00 3.33
76 77 2.278661 GGCAGTCGTAGCGGTAGC 60.279 66.667 0.00 0.00 45.58 3.58
77 78 2.024305 CGGCAGTCGTAGCGGTAG 59.976 66.667 0.00 0.00 0.00 3.18
78 79 3.511595 CCGGCAGTCGTAGCGGTA 61.512 66.667 0.00 0.00 37.11 4.02
82 83 3.537874 ATCCCCGGCAGTCGTAGC 61.538 66.667 0.00 0.00 37.11 3.58
83 84 1.956629 AACATCCCCGGCAGTCGTAG 61.957 60.000 0.00 0.00 37.11 3.51
84 85 0.683828 TAACATCCCCGGCAGTCGTA 60.684 55.000 0.00 0.00 37.11 3.43
85 86 1.956629 CTAACATCCCCGGCAGTCGT 61.957 60.000 0.00 0.00 37.11 4.34
86 87 1.227263 CTAACATCCCCGGCAGTCG 60.227 63.158 0.00 0.00 38.88 4.18
87 88 0.105039 CTCTAACATCCCCGGCAGTC 59.895 60.000 0.00 0.00 0.00 3.51
88 89 0.325296 TCTCTAACATCCCCGGCAGT 60.325 55.000 0.00 0.00 0.00 4.40
89 90 1.051812 ATCTCTAACATCCCCGGCAG 58.948 55.000 0.00 0.00 0.00 4.85
90 91 2.391926 TATCTCTAACATCCCCGGCA 57.608 50.000 0.00 0.00 0.00 5.69
91 92 5.615925 AATATATCTCTAACATCCCCGGC 57.384 43.478 0.00 0.00 0.00 6.13
92 93 6.349300 CCAAATATATCTCTAACATCCCCGG 58.651 44.000 0.00 0.00 0.00 5.73
93 94 6.070194 ACCCAAATATATCTCTAACATCCCCG 60.070 42.308 0.00 0.00 0.00 5.73
94 95 7.272144 ACCCAAATATATCTCTAACATCCCC 57.728 40.000 0.00 0.00 0.00 4.81
95 96 9.668497 GTAACCCAAATATATCTCTAACATCCC 57.332 37.037 0.00 0.00 0.00 3.85
109 110 9.984590 ACTACCAAATACAAGTAACCCAAATAT 57.015 29.630 0.00 0.00 0.00 1.28
110 111 9.452287 GACTACCAAATACAAGTAACCCAAATA 57.548 33.333 0.00 0.00 0.00 1.40
111 112 8.168058 AGACTACCAAATACAAGTAACCCAAAT 58.832 33.333 0.00 0.00 0.00 2.32
112 113 7.519927 AGACTACCAAATACAAGTAACCCAAA 58.480 34.615 0.00 0.00 0.00 3.28
113 114 7.081857 AGACTACCAAATACAAGTAACCCAA 57.918 36.000 0.00 0.00 0.00 4.12
114 115 6.691255 AGACTACCAAATACAAGTAACCCA 57.309 37.500 0.00 0.00 0.00 4.51
115 116 7.124750 TCCTAGACTACCAAATACAAGTAACCC 59.875 40.741 0.00 0.00 0.00 4.11
116 117 8.071177 TCCTAGACTACCAAATACAAGTAACC 57.929 38.462 0.00 0.00 0.00 2.85
120 121 8.603304 ACAAATCCTAGACTACCAAATACAAGT 58.397 33.333 0.00 0.00 0.00 3.16
126 127 9.004231 AGGATTACAAATCCTAGACTACCAAAT 57.996 33.333 17.59 0.00 46.11 2.32
127 128 8.388656 AGGATTACAAATCCTAGACTACCAAA 57.611 34.615 17.59 0.00 46.11 3.28
128 129 7.989947 AGGATTACAAATCCTAGACTACCAA 57.010 36.000 17.59 0.00 46.11 3.67
139 140 6.502074 AGGTAGGAGAAGGATTACAAATCC 57.498 41.667 10.15 10.15 38.47 3.01
140 141 9.713713 GATAAGGTAGGAGAAGGATTACAAATC 57.286 37.037 0.00 0.00 0.00 2.17
141 142 9.453830 AGATAAGGTAGGAGAAGGATTACAAAT 57.546 33.333 0.00 0.00 0.00 2.32
142 143 8.855804 AGATAAGGTAGGAGAAGGATTACAAA 57.144 34.615 0.00 0.00 0.00 2.83
143 144 8.855804 AAGATAAGGTAGGAGAAGGATTACAA 57.144 34.615 0.00 0.00 0.00 2.41
144 145 8.065627 TGAAGATAAGGTAGGAGAAGGATTACA 58.934 37.037 0.00 0.00 0.00 2.41
145 146 8.480133 TGAAGATAAGGTAGGAGAAGGATTAC 57.520 38.462 0.00 0.00 0.00 1.89
146 147 7.730784 CCTGAAGATAAGGTAGGAGAAGGATTA 59.269 40.741 0.00 0.00 0.00 1.75
147 148 6.556874 CCTGAAGATAAGGTAGGAGAAGGATT 59.443 42.308 0.00 0.00 0.00 3.01
148 149 6.081356 CCTGAAGATAAGGTAGGAGAAGGAT 58.919 44.000 0.00 0.00 0.00 3.24
149 150 5.195960 TCCTGAAGATAAGGTAGGAGAAGGA 59.804 44.000 0.00 0.00 36.14 3.36
150 151 5.459505 TCCTGAAGATAAGGTAGGAGAAGG 58.540 45.833 0.00 0.00 36.14 3.46
155 156 4.693058 GCCTCTCCTGAAGATAAGGTAGGA 60.693 50.000 14.05 0.00 39.47 2.94
156 157 3.576550 GCCTCTCCTGAAGATAAGGTAGG 59.423 52.174 8.41 8.41 39.79 3.18
157 158 4.479158 AGCCTCTCCTGAAGATAAGGTAG 58.521 47.826 0.00 0.00 36.14 3.18
158 159 4.544564 AGCCTCTCCTGAAGATAAGGTA 57.455 45.455 0.00 0.00 36.14 3.08
159 160 3.413105 AGCCTCTCCTGAAGATAAGGT 57.587 47.619 0.00 0.00 36.14 3.50
160 161 3.966665 AGAAGCCTCTCCTGAAGATAAGG 59.033 47.826 0.00 0.00 32.19 2.69
161 162 5.612725 AAGAAGCCTCTCCTGAAGATAAG 57.387 43.478 0.00 0.00 32.19 1.73
162 163 5.364157 GGTAAGAAGCCTCTCCTGAAGATAA 59.636 44.000 0.00 0.00 32.19 1.75
163 164 4.896482 GGTAAGAAGCCTCTCCTGAAGATA 59.104 45.833 0.00 0.00 32.19 1.98
164 165 3.709141 GGTAAGAAGCCTCTCCTGAAGAT 59.291 47.826 0.00 0.00 32.19 2.40
165 166 3.100671 GGTAAGAAGCCTCTCCTGAAGA 58.899 50.000 0.00 0.00 0.00 2.87
166 167 2.169561 GGGTAAGAAGCCTCTCCTGAAG 59.830 54.545 0.00 0.00 40.33 3.02
167 168 2.188817 GGGTAAGAAGCCTCTCCTGAA 58.811 52.381 0.00 0.00 40.33 3.02
168 169 1.867363 GGGTAAGAAGCCTCTCCTGA 58.133 55.000 0.00 0.00 40.33 3.86
176 177 3.653835 AGATTTGGAGGGTAAGAAGCC 57.346 47.619 0.00 0.00 44.09 4.35
177 178 4.336280 ACAAGATTTGGAGGGTAAGAAGC 58.664 43.478 0.00 0.00 34.12 3.86
178 179 6.712276 AGTACAAGATTTGGAGGGTAAGAAG 58.288 40.000 0.00 0.00 34.12 2.85
179 180 6.271391 TGAGTACAAGATTTGGAGGGTAAGAA 59.729 38.462 0.00 0.00 34.12 2.52
180 181 5.783360 TGAGTACAAGATTTGGAGGGTAAGA 59.217 40.000 0.00 0.00 34.12 2.10
181 182 6.049955 TGAGTACAAGATTTGGAGGGTAAG 57.950 41.667 0.00 0.00 34.12 2.34
182 183 6.442541 TTGAGTACAAGATTTGGAGGGTAA 57.557 37.500 0.00 0.00 34.12 2.85
183 184 6.636454 ATTGAGTACAAGATTTGGAGGGTA 57.364 37.500 0.00 0.00 39.46 3.69
184 185 4.993705 TTGAGTACAAGATTTGGAGGGT 57.006 40.909 0.00 0.00 34.12 4.34
191 192 9.640963 GGCGAGTATATATTGAGTACAAGATTT 57.359 33.333 0.00 0.00 38.59 2.17
192 193 8.251721 GGGCGAGTATATATTGAGTACAAGATT 58.748 37.037 0.00 0.00 38.59 2.40
193 194 7.616150 AGGGCGAGTATATATTGAGTACAAGAT 59.384 37.037 0.00 0.00 40.38 2.40
194 195 6.946583 AGGGCGAGTATATATTGAGTACAAGA 59.053 38.462 0.00 0.00 39.46 3.02
195 196 7.159322 AGGGCGAGTATATATTGAGTACAAG 57.841 40.000 0.00 0.00 39.46 3.16
196 197 6.128090 CGAGGGCGAGTATATATTGAGTACAA 60.128 42.308 0.00 0.00 40.82 2.41
197 198 5.353400 CGAGGGCGAGTATATATTGAGTACA 59.647 44.000 0.00 0.00 40.82 2.90
198 199 5.583854 TCGAGGGCGAGTATATATTGAGTAC 59.416 44.000 0.00 0.00 42.51 2.73
199 200 5.737860 TCGAGGGCGAGTATATATTGAGTA 58.262 41.667 0.00 0.00 42.51 2.59
200 201 4.586884 TCGAGGGCGAGTATATATTGAGT 58.413 43.478 0.00 0.00 42.51 3.41
216 217 5.046591 TGGATGTATTATTAAGCCTCGAGGG 60.047 44.000 32.06 14.53 35.18 4.30
217 218 6.037786 TGGATGTATTATTAAGCCTCGAGG 57.962 41.667 27.83 27.83 38.53 4.63
218 219 7.323420 TGATGGATGTATTATTAAGCCTCGAG 58.677 38.462 5.13 5.13 0.00 4.04
219 220 7.239763 TGATGGATGTATTATTAAGCCTCGA 57.760 36.000 0.00 0.00 0.00 4.04
220 221 9.770097 ATATGATGGATGTATTATTAAGCCTCG 57.230 33.333 0.00 0.00 0.00 4.63
226 227 9.898152 TGCGGAATATGATGGATGTATTATTAA 57.102 29.630 0.00 0.00 0.00 1.40
227 228 9.898152 TTGCGGAATATGATGGATGTATTATTA 57.102 29.630 0.00 0.00 0.00 0.98
228 229 8.677300 GTTGCGGAATATGATGGATGTATTATT 58.323 33.333 0.00 0.00 0.00 1.40
229 230 7.828717 TGTTGCGGAATATGATGGATGTATTAT 59.171 33.333 0.00 0.00 0.00 1.28
230 231 7.164803 TGTTGCGGAATATGATGGATGTATTA 58.835 34.615 0.00 0.00 0.00 0.98
231 232 6.003326 TGTTGCGGAATATGATGGATGTATT 58.997 36.000 0.00 0.00 0.00 1.89
232 233 5.559770 TGTTGCGGAATATGATGGATGTAT 58.440 37.500 0.00 0.00 0.00 2.29
233 234 4.967036 TGTTGCGGAATATGATGGATGTA 58.033 39.130 0.00 0.00 0.00 2.29
234 235 3.819368 TGTTGCGGAATATGATGGATGT 58.181 40.909 0.00 0.00 0.00 3.06
235 236 4.834357 TTGTTGCGGAATATGATGGATG 57.166 40.909 0.00 0.00 0.00 3.51
236 237 4.460382 GGATTGTTGCGGAATATGATGGAT 59.540 41.667 0.00 0.00 0.00 3.41
237 238 3.820467 GGATTGTTGCGGAATATGATGGA 59.180 43.478 0.00 0.00 0.00 3.41
238 239 3.057315 GGGATTGTTGCGGAATATGATGG 60.057 47.826 0.00 0.00 0.00 3.51
239 240 3.822735 AGGGATTGTTGCGGAATATGATG 59.177 43.478 0.00 0.00 0.00 3.07
240 241 4.074970 GAGGGATTGTTGCGGAATATGAT 58.925 43.478 0.00 0.00 0.00 2.45
241 242 3.136443 AGAGGGATTGTTGCGGAATATGA 59.864 43.478 0.00 0.00 0.00 2.15
242 243 3.480470 AGAGGGATTGTTGCGGAATATG 58.520 45.455 0.00 0.00 0.00 1.78
243 244 3.392616 AGAGAGGGATTGTTGCGGAATAT 59.607 43.478 0.00 0.00 0.00 1.28
244 245 2.771943 AGAGAGGGATTGTTGCGGAATA 59.228 45.455 0.00 0.00 0.00 1.75
245 246 1.561542 AGAGAGGGATTGTTGCGGAAT 59.438 47.619 0.00 0.00 0.00 3.01
246 247 0.984230 AGAGAGGGATTGTTGCGGAA 59.016 50.000 0.00 0.00 0.00 4.30
247 248 0.537188 GAGAGAGGGATTGTTGCGGA 59.463 55.000 0.00 0.00 0.00 5.54
248 249 0.462759 GGAGAGAGGGATTGTTGCGG 60.463 60.000 0.00 0.00 0.00 5.69
249 250 0.462759 GGGAGAGAGGGATTGTTGCG 60.463 60.000 0.00 0.00 0.00 4.85
250 251 0.915364 AGGGAGAGAGGGATTGTTGC 59.085 55.000 0.00 0.00 0.00 4.17
251 252 2.092699 GGAAGGGAGAGAGGGATTGTTG 60.093 54.545 0.00 0.00 0.00 3.33
252 253 2.200955 GGAAGGGAGAGAGGGATTGTT 58.799 52.381 0.00 0.00 0.00 2.83
253 254 1.081174 TGGAAGGGAGAGAGGGATTGT 59.919 52.381 0.00 0.00 0.00 2.71
254 255 1.885049 TGGAAGGGAGAGAGGGATTG 58.115 55.000 0.00 0.00 0.00 2.67
255 256 2.200955 GTTGGAAGGGAGAGAGGGATT 58.799 52.381 0.00 0.00 0.00 3.01
256 257 1.081174 TGTTGGAAGGGAGAGAGGGAT 59.919 52.381 0.00 0.00 0.00 3.85
257 258 0.491823 TGTTGGAAGGGAGAGAGGGA 59.508 55.000 0.00 0.00 0.00 4.20
258 259 1.362224 TTGTTGGAAGGGAGAGAGGG 58.638 55.000 0.00 0.00 0.00 4.30
259 260 3.149981 GTTTTGTTGGAAGGGAGAGAGG 58.850 50.000 0.00 0.00 0.00 3.69
260 261 3.820557 TGTTTTGTTGGAAGGGAGAGAG 58.179 45.455 0.00 0.00 0.00 3.20
261 262 3.943671 TGTTTTGTTGGAAGGGAGAGA 57.056 42.857 0.00 0.00 0.00 3.10
262 263 4.829492 AGATTGTTTTGTTGGAAGGGAGAG 59.171 41.667 0.00 0.00 0.00 3.20
263 264 4.803452 AGATTGTTTTGTTGGAAGGGAGA 58.197 39.130 0.00 0.00 0.00 3.71
264 265 4.320494 CGAGATTGTTTTGTTGGAAGGGAG 60.320 45.833 0.00 0.00 0.00 4.30
265 266 3.568007 CGAGATTGTTTTGTTGGAAGGGA 59.432 43.478 0.00 0.00 0.00 4.20
266 267 3.857010 GCGAGATTGTTTTGTTGGAAGGG 60.857 47.826 0.00 0.00 0.00 3.95
267 268 3.243367 TGCGAGATTGTTTTGTTGGAAGG 60.243 43.478 0.00 0.00 0.00 3.46
268 269 3.963665 TGCGAGATTGTTTTGTTGGAAG 58.036 40.909 0.00 0.00 0.00 3.46
269 270 4.377839 TTGCGAGATTGTTTTGTTGGAA 57.622 36.364 0.00 0.00 0.00 3.53
270 271 4.377839 TTTGCGAGATTGTTTTGTTGGA 57.622 36.364 0.00 0.00 0.00 3.53
271 272 5.006552 ACATTTTGCGAGATTGTTTTGTTGG 59.993 36.000 0.00 0.00 0.00 3.77
272 273 5.897518 CACATTTTGCGAGATTGTTTTGTTG 59.102 36.000 0.00 0.00 0.00 3.33
273 274 5.006552 CCACATTTTGCGAGATTGTTTTGTT 59.993 36.000 0.00 0.00 0.00 2.83
274 275 4.507388 CCACATTTTGCGAGATTGTTTTGT 59.493 37.500 0.00 0.00 0.00 2.83
275 276 4.507388 ACCACATTTTGCGAGATTGTTTTG 59.493 37.500 0.00 0.00 0.00 2.44
276 277 4.692228 ACCACATTTTGCGAGATTGTTTT 58.308 34.783 0.00 0.00 0.00 2.43
372 373 1.656652 CGGATCATCGCTTGGACTTT 58.343 50.000 0.00 0.00 0.00 2.66
388 389 2.571653 AGAAGGTGATTTGTCATCCGGA 59.428 45.455 6.61 6.61 0.00 5.14
425 426 2.912771 ACGAACATGTGTTGTCCTTCA 58.087 42.857 0.00 0.00 37.68 3.02
449 450 0.613260 ACAGCTCGGATTAGCCAACA 59.387 50.000 0.00 0.00 43.86 3.33
488 500 1.272490 GTGACAATCCACACGAGGAGA 59.728 52.381 0.00 0.00 41.90 3.71
506 518 4.909696 AGGTCTCTGTTCATATCTCGTG 57.090 45.455 0.00 0.00 0.00 4.35
519 534 1.410882 GGCTGCCTAACTAGGTCTCTG 59.589 57.143 12.43 0.00 45.42 3.35
542 557 2.950781 TGGACAAAAAGGGTGCACATA 58.049 42.857 20.43 0.00 31.34 2.29
555 570 2.076100 CGATTGCTAGCTGTGGACAAA 58.924 47.619 17.23 0.00 0.00 2.83
563 587 1.520494 ATGGATGCGATTGCTAGCTG 58.480 50.000 17.23 4.44 43.34 4.24
612 636 2.960819 AGCTAGTTTTCACTGTAGCGG 58.039 47.619 0.00 0.00 38.98 5.52
634 663 1.987770 CAAATGCTGTCGTTGCAATCC 59.012 47.619 0.59 0.00 44.01 3.01
771 801 5.399301 GCAAGTAGTTGTGCACATGTAAAAG 59.601 40.000 22.39 10.33 40.58 2.27
799 829 2.125188 GCTCCTGCACTCCTGCTC 60.125 66.667 0.00 0.00 44.57 4.26
956 993 0.723129 CGCGCTCGACTACTCTATGC 60.723 60.000 5.56 0.00 38.10 3.14
1053 1090 4.680237 TCGGCCGACACTTGCTGG 62.680 66.667 27.28 0.00 34.57 4.85
1488 1543 2.568623 AGTCCGCCTTGTTCTTGAAT 57.431 45.000 0.00 0.00 0.00 2.57
1736 1791 3.166490 TTCTTGGCGCCGTACACCA 62.166 57.895 23.90 0.00 0.00 4.17
2391 2446 3.434641 CGTGTTGCATGTTCTGATCTCTT 59.565 43.478 0.00 0.00 0.00 2.85
2405 2460 3.068448 TCTGTAAAGTAGGACGTGTTGCA 59.932 43.478 0.00 0.00 0.00 4.08
2437 2492 8.842280 ACAGCTACATCTTACATAGTCTTAGAC 58.158 37.037 3.85 3.85 0.00 2.59
2442 2497 6.207810 GGCTACAGCTACATCTTACATAGTCT 59.792 42.308 0.54 0.00 41.70 3.24
2471 2526 4.022416 TGACTTACATTTCACAATGGTGGC 60.022 41.667 0.00 0.00 43.82 5.01
2472 2527 5.703978 TGACTTACATTTCACAATGGTGG 57.296 39.130 0.00 0.00 43.82 4.61
2473 2528 6.680810 ACATGACTTACATTTCACAATGGTG 58.319 36.000 0.00 0.00 43.82 4.17
2474 2529 6.899393 ACATGACTTACATTTCACAATGGT 57.101 33.333 0.00 0.00 43.82 3.55
2475 2530 8.514594 ACTAACATGACTTACATTTCACAATGG 58.485 33.333 0.00 0.00 43.82 3.16
2526 2592 0.917259 GAAGCATGCGTACGAGTGAG 59.083 55.000 21.65 4.37 0.00 3.51
2554 2620 1.447489 CTGTTGCTCTCGCTGGAGG 60.447 63.158 5.24 0.00 40.85 4.30
2580 2646 1.086696 TGCCGTCTGAAATAAGCTGC 58.913 50.000 0.00 0.00 0.00 5.25
2876 3035 7.739022 TTCATTTTATATTGCTGTTGCGAAG 57.261 32.000 0.00 0.00 43.34 3.79
2963 3122 6.492772 CCTGGTAGTTAGGGTAGGTAATGTAG 59.507 46.154 0.00 0.00 0.00 2.74
2974 3133 6.800223 AGTCTATATCCTGGTAGTTAGGGT 57.200 41.667 0.00 0.00 35.96 4.34
3205 3372 8.114331 ACTGAGCTTTTTGTCATTATCATTGA 57.886 30.769 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.