Multiple sequence alignment - TraesCS2D01G264100

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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 TraesCS2D01G264100 chr2D 100.000 2250 0 0 1 2250 322925978 322928227 0 4156
1 TraesCS2D01G264100 chr2D 93.880 768 39 7 1486 2250 94865015 94864253 0 1151
2 TraesCS2D01G264100 chr2D 99.198 374 3 0 1 374 53912649 53912276 0 675
3 TraesCS2D01G264100 chr2D 98.663 374 5 0 1 374 637310942 637310569 0 664
4 TraesCS2D01G264100 chrUn 99.371 1112 5 2 375 1486 216518849 216519958 0 2013
5 TraesCS2D01G264100 chrUn 99.371 1112 4 3 375 1486 93409878 93410986 0 2012
6 TraesCS2D01G264100 chrUn 99.193 1115 7 2 375 1489 216521517 216520405 0 2008
7 TraesCS2D01G264100 chrUn 99.191 1112 7 2 375 1486 396205607 396206716 0 2002
8 TraesCS2D01G264100 chrUn 99.198 374 3 0 1 374 257941875 257942248 0 675
9 TraesCS2D01G264100 chrUn 99.198 374 3 0 1 374 412433226 412433599 0 675
10 TraesCS2D01G264100 chrUn 98.128 374 7 0 1 374 229499846 229500219 0 652
11 TraesCS2D01G264100 chr6D 99.283 1115 6 2 375 1489 168254679 168253567 0 2013
12 TraesCS2D01G264100 chr6D 99.281 1112 6 2 375 1486 168252011 168253120 0 2008
13 TraesCS2D01G264100 chr6D 94.524 767 35 4 1486 2250 386427592 386428353 0 1177
14 TraesCS2D01G264100 chr6D 94.524 767 33 5 1486 2250 386419446 386420205 0 1175
15 TraesCS2D01G264100 chr6D 94.018 769 36 8 1486 2250 334422853 334422091 0 1157
16 TraesCS2D01G264100 chr6D 98.128 374 7 0 1 374 283185175 283185548 0 652
17 TraesCS2D01G264100 chr5D 99.283 1115 6 2 375 1489 503217971 503216859 0 2013
18 TraesCS2D01G264100 chr5D 94.524 767 38 3 1486 2250 206125538 206126302 0 1181
19 TraesCS2D01G264100 chr5D 94.133 767 36 6 1486 2250 304708063 304708822 0 1158
20 TraesCS2D01G264100 chr3B 99.103 1115 8 2 375 1489 201526777 201525665 0 2002
21 TraesCS2D01G264100 chr1D 99.191 1113 6 3 375 1486 254398356 254399466 0 2002
22 TraesCS2D01G264100 chr1D 94.003 767 40 5 1486 2250 149882410 149883172 0 1157
23 TraesCS2D01G264100 chr3D 94.141 768 38 5 1486 2250 479573293 479572530 0 1162
24 TraesCS2D01G264100 chr3D 93.880 768 40 5 1487 2250 478400799 478400035 0 1151
25 TraesCS2D01G264100 chr3D 99.198 374 3 0 1 374 145421502 145421875 0 675
26 TraesCS2D01G264100 chr4D 99.198 374 3 0 1 374 123686726 123687099 0 675
27 TraesCS2D01G264100 chr1B 98.396 374 6 0 1 374 517083285 517083658 0 658


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 TraesCS2D01G264100 chr2D 322925978 322928227 2249 False 4156 4156 100.000 1 2250 1 chr2D.!!$F1 2249
1 TraesCS2D01G264100 chr2D 94864253 94865015 762 True 1151 1151 93.880 1486 2250 1 chr2D.!!$R2 764
2 TraesCS2D01G264100 chrUn 216518849 216519958 1109 False 2013 2013 99.371 375 1486 1 chrUn.!!$F2 1111
3 TraesCS2D01G264100 chrUn 93409878 93410986 1108 False 2012 2012 99.371 375 1486 1 chrUn.!!$F1 1111
4 TraesCS2D01G264100 chrUn 216520405 216521517 1112 True 2008 2008 99.193 375 1489 1 chrUn.!!$R1 1114
5 TraesCS2D01G264100 chrUn 396205607 396206716 1109 False 2002 2002 99.191 375 1486 1 chrUn.!!$F5 1111
6 TraesCS2D01G264100 chr6D 168253567 168254679 1112 True 2013 2013 99.283 375 1489 1 chr6D.!!$R1 1114
7 TraesCS2D01G264100 chr6D 168252011 168253120 1109 False 2008 2008 99.281 375 1486 1 chr6D.!!$F1 1111
8 TraesCS2D01G264100 chr6D 386427592 386428353 761 False 1177 1177 94.524 1486 2250 1 chr6D.!!$F4 764
9 TraesCS2D01G264100 chr6D 386419446 386420205 759 False 1175 1175 94.524 1486 2250 1 chr6D.!!$F3 764
10 TraesCS2D01G264100 chr6D 334422091 334422853 762 True 1157 1157 94.018 1486 2250 1 chr6D.!!$R2 764
11 TraesCS2D01G264100 chr5D 503216859 503217971 1112 True 2013 2013 99.283 375 1489 1 chr5D.!!$R1 1114
12 TraesCS2D01G264100 chr5D 206125538 206126302 764 False 1181 1181 94.524 1486 2250 1 chr5D.!!$F1 764
13 TraesCS2D01G264100 chr5D 304708063 304708822 759 False 1158 1158 94.133 1486 2250 1 chr5D.!!$F2 764
14 TraesCS2D01G264100 chr3B 201525665 201526777 1112 True 2002 2002 99.103 375 1489 1 chr3B.!!$R1 1114
15 TraesCS2D01G264100 chr1D 254398356 254399466 1110 False 2002 2002 99.191 375 1486 1 chr1D.!!$F2 1111
16 TraesCS2D01G264100 chr1D 149882410 149883172 762 False 1157 1157 94.003 1486 2250 1 chr1D.!!$F1 764
17 TraesCS2D01G264100 chr3D 479572530 479573293 763 True 1162 1162 94.141 1486 2250 1 chr3D.!!$R2 764
18 TraesCS2D01G264100 chr3D 478400035 478400799 764 True 1151 1151 93.880 1487 2250 1 chr3D.!!$R1 763

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
101 102 0.034059 AGCGATGGCGGATTTCCTAG 59.966 55.0 0.0 0.0 46.35 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1581 1583 1.101635 TGCCCGAGATTCGATCGTCT 61.102 55.0 15.94 11.59 43.74 4.18 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
21 22 2.731572 ACAGGAAGATTGGCAAGATGG 58.268 47.619 5.96 0.00 0.00 3.51
22 23 2.029623 CAGGAAGATTGGCAAGATGGG 58.970 52.381 5.96 0.00 0.00 4.00
23 24 1.063417 AGGAAGATTGGCAAGATGGGG 60.063 52.381 5.96 0.00 0.00 4.96
24 25 0.749049 GAAGATTGGCAAGATGGGGC 59.251 55.000 5.96 0.00 0.00 5.80
37 38 1.838611 ATGGGGCCATCATCCTTACT 58.161 50.000 4.39 0.00 29.42 2.24
38 39 0.846015 TGGGGCCATCATCCTTACTG 59.154 55.000 4.39 0.00 0.00 2.74
39 40 1.140312 GGGGCCATCATCCTTACTGA 58.860 55.000 4.39 0.00 0.00 3.41
40 41 1.072965 GGGGCCATCATCCTTACTGAG 59.927 57.143 4.39 0.00 0.00 3.35
41 42 1.771255 GGGCCATCATCCTTACTGAGT 59.229 52.381 4.39 0.00 0.00 3.41
42 43 2.173569 GGGCCATCATCCTTACTGAGTT 59.826 50.000 4.39 0.00 0.00 3.01
43 44 3.471680 GGCCATCATCCTTACTGAGTTC 58.528 50.000 0.00 0.00 0.00 3.01
44 45 3.126831 GCCATCATCCTTACTGAGTTCG 58.873 50.000 0.00 0.00 0.00 3.95
45 46 3.181475 GCCATCATCCTTACTGAGTTCGA 60.181 47.826 0.00 0.00 0.00 3.71
46 47 4.363999 CCATCATCCTTACTGAGTTCGAC 58.636 47.826 0.00 0.00 0.00 4.20
47 48 4.142160 CCATCATCCTTACTGAGTTCGACA 60.142 45.833 0.00 0.00 0.00 4.35
48 49 5.452496 CCATCATCCTTACTGAGTTCGACAT 60.452 44.000 0.00 0.00 0.00 3.06
49 50 5.661056 TCATCCTTACTGAGTTCGACATT 57.339 39.130 0.00 0.00 0.00 2.71
50 51 5.410924 TCATCCTTACTGAGTTCGACATTG 58.589 41.667 0.00 0.00 0.00 2.82
51 52 4.866508 TCCTTACTGAGTTCGACATTGT 57.133 40.909 0.00 0.00 0.00 2.71
52 53 4.556233 TCCTTACTGAGTTCGACATTGTG 58.444 43.478 0.00 0.00 0.00 3.33
53 54 4.038763 TCCTTACTGAGTTCGACATTGTGT 59.961 41.667 0.00 0.00 0.00 3.72
54 55 5.242171 TCCTTACTGAGTTCGACATTGTGTA 59.758 40.000 0.00 0.00 0.00 2.90
55 56 6.071560 TCCTTACTGAGTTCGACATTGTGTAT 60.072 38.462 0.00 0.00 0.00 2.29
56 57 6.035005 CCTTACTGAGTTCGACATTGTGTATG 59.965 42.308 0.00 0.00 40.26 2.39
57 58 3.679980 ACTGAGTTCGACATTGTGTATGC 59.320 43.478 0.00 0.00 37.81 3.14
58 59 2.666022 TGAGTTCGACATTGTGTATGCG 59.334 45.455 0.00 0.00 37.81 4.73
59 60 1.393539 AGTTCGACATTGTGTATGCGC 59.606 47.619 0.00 0.00 37.81 6.09
60 61 0.724549 TTCGACATTGTGTATGCGCC 59.275 50.000 4.18 0.00 37.81 6.53
61 62 1.012343 CGACATTGTGTATGCGCCG 60.012 57.895 4.18 0.00 37.81 6.46
62 63 1.297598 GACATTGTGTATGCGCCGC 60.298 57.895 4.18 0.00 37.81 6.53
63 64 1.976478 GACATTGTGTATGCGCCGCA 61.976 55.000 16.69 16.69 44.86 5.69
64 65 1.297819 CATTGTGTATGCGCCGCAG 60.298 57.895 19.64 0.00 43.65 5.18
65 66 1.449423 ATTGTGTATGCGCCGCAGA 60.449 52.632 19.64 11.05 43.65 4.26
66 67 1.024046 ATTGTGTATGCGCCGCAGAA 61.024 50.000 19.64 5.21 43.65 3.02
67 68 1.634757 TTGTGTATGCGCCGCAGAAG 61.635 55.000 19.64 0.00 43.65 2.85
68 69 2.511373 TGTATGCGCCGCAGAAGG 60.511 61.111 19.64 0.00 43.65 3.46
77 78 2.997899 CCGCAGAAGGCCATTAGAG 58.002 57.895 5.01 0.00 40.31 2.43
78 79 0.533755 CCGCAGAAGGCCATTAGAGG 60.534 60.000 5.01 0.00 40.31 3.69
79 80 0.533755 CGCAGAAGGCCATTAGAGGG 60.534 60.000 5.01 0.00 40.31 4.30
87 88 3.713902 CCATTAGAGGGCAAGCGAT 57.286 52.632 0.00 0.00 0.00 4.58
88 89 1.233019 CCATTAGAGGGCAAGCGATG 58.767 55.000 0.00 0.00 0.00 3.84
89 90 1.233019 CATTAGAGGGCAAGCGATGG 58.767 55.000 0.00 0.00 0.00 3.51
95 96 3.211963 GGCAAGCGATGGCGGATT 61.212 61.111 0.00 0.00 45.46 3.01
96 97 2.774799 GGCAAGCGATGGCGGATTT 61.775 57.895 0.00 0.00 45.46 2.17
97 98 1.298638 GCAAGCGATGGCGGATTTC 60.299 57.895 0.00 0.00 46.35 2.17
98 99 1.356624 CAAGCGATGGCGGATTTCC 59.643 57.895 0.00 0.00 46.35 3.13
99 100 1.097547 CAAGCGATGGCGGATTTCCT 61.098 55.000 0.00 0.00 46.35 3.36
100 101 0.468226 AAGCGATGGCGGATTTCCTA 59.532 50.000 0.00 0.00 46.35 2.94
101 102 0.034059 AGCGATGGCGGATTTCCTAG 59.966 55.000 0.00 0.00 46.35 3.02
102 103 1.569479 GCGATGGCGGATTTCCTAGC 61.569 60.000 0.00 0.00 38.16 3.42
103 104 0.249868 CGATGGCGGATTTCCTAGCA 60.250 55.000 0.00 0.00 0.00 3.49
104 105 1.517242 GATGGCGGATTTCCTAGCAG 58.483 55.000 0.00 0.00 0.00 4.24
105 106 0.536006 ATGGCGGATTTCCTAGCAGC 60.536 55.000 0.00 0.00 0.00 5.25
106 107 1.153168 GGCGGATTTCCTAGCAGCA 60.153 57.895 0.00 0.00 0.00 4.41
107 108 1.440145 GGCGGATTTCCTAGCAGCAC 61.440 60.000 0.00 0.00 0.00 4.40
108 109 0.744414 GCGGATTTCCTAGCAGCACA 60.744 55.000 0.00 0.00 0.00 4.57
109 110 1.959042 CGGATTTCCTAGCAGCACAT 58.041 50.000 0.00 0.00 0.00 3.21
110 111 1.869767 CGGATTTCCTAGCAGCACATC 59.130 52.381 0.00 0.00 0.00 3.06
111 112 2.742856 CGGATTTCCTAGCAGCACATCA 60.743 50.000 0.00 0.00 0.00 3.07
112 113 3.484407 GGATTTCCTAGCAGCACATCAT 58.516 45.455 0.00 0.00 0.00 2.45
113 114 4.645535 GGATTTCCTAGCAGCACATCATA 58.354 43.478 0.00 0.00 0.00 2.15
114 115 4.453819 GGATTTCCTAGCAGCACATCATAC 59.546 45.833 0.00 0.00 0.00 2.39
115 116 4.486125 TTTCCTAGCAGCACATCATACA 57.514 40.909 0.00 0.00 0.00 2.29
116 117 4.694760 TTCCTAGCAGCACATCATACAT 57.305 40.909 0.00 0.00 0.00 2.29
117 118 5.806654 TTCCTAGCAGCACATCATACATA 57.193 39.130 0.00 0.00 0.00 2.29
118 119 6.364568 TTCCTAGCAGCACATCATACATAT 57.635 37.500 0.00 0.00 0.00 1.78
119 120 6.364568 TCCTAGCAGCACATCATACATATT 57.635 37.500 0.00 0.00 0.00 1.28
120 121 6.772605 TCCTAGCAGCACATCATACATATTT 58.227 36.000 0.00 0.00 0.00 1.40
121 122 7.906327 TCCTAGCAGCACATCATACATATTTA 58.094 34.615 0.00 0.00 0.00 1.40
122 123 8.542926 TCCTAGCAGCACATCATACATATTTAT 58.457 33.333 0.00 0.00 0.00 1.40
123 124 9.822185 CCTAGCAGCACATCATACATATTTATA 57.178 33.333 0.00 0.00 0.00 0.98
126 127 9.159364 AGCAGCACATCATACATATTTATACAG 57.841 33.333 0.00 0.00 0.00 2.74
127 128 8.939929 GCAGCACATCATACATATTTATACAGT 58.060 33.333 0.00 0.00 0.00 3.55
160 161 1.679139 CCATGTATGGGATTGCACGT 58.321 50.000 2.87 0.00 44.31 4.49
161 162 2.844946 CCATGTATGGGATTGCACGTA 58.155 47.619 2.87 0.00 44.31 3.57
162 163 2.807967 CCATGTATGGGATTGCACGTAG 59.192 50.000 2.87 0.00 44.31 3.51
163 164 3.744214 CCATGTATGGGATTGCACGTAGT 60.744 47.826 2.87 0.00 43.68 2.73
164 165 3.173668 TGTATGGGATTGCACGTAGTC 57.826 47.619 0.00 0.00 41.61 2.59
165 166 2.159014 TGTATGGGATTGCACGTAGTCC 60.159 50.000 0.00 0.00 41.61 3.85
166 167 0.908910 ATGGGATTGCACGTAGTCCA 59.091 50.000 2.70 0.00 41.61 4.02
167 168 0.908910 TGGGATTGCACGTAGTCCAT 59.091 50.000 2.70 0.00 41.61 3.41
168 169 1.280710 TGGGATTGCACGTAGTCCATT 59.719 47.619 2.70 0.00 41.61 3.16
169 170 1.940613 GGGATTGCACGTAGTCCATTC 59.059 52.381 2.70 0.00 41.61 2.67
170 171 1.940613 GGATTGCACGTAGTCCATTCC 59.059 52.381 0.00 0.00 41.61 3.01
171 172 2.627945 GATTGCACGTAGTCCATTCCA 58.372 47.619 0.00 0.00 41.61 3.53
172 173 1.803334 TTGCACGTAGTCCATTCCAC 58.197 50.000 0.00 0.00 41.61 4.02
173 174 0.036765 TGCACGTAGTCCATTCCACC 60.037 55.000 0.00 0.00 41.61 4.61
174 175 0.249398 GCACGTAGTCCATTCCACCT 59.751 55.000 0.00 0.00 41.61 4.00
175 176 1.338769 GCACGTAGTCCATTCCACCTT 60.339 52.381 0.00 0.00 41.61 3.50
176 177 2.874457 GCACGTAGTCCATTCCACCTTT 60.874 50.000 0.00 0.00 41.61 3.11
177 178 3.618019 GCACGTAGTCCATTCCACCTTTA 60.618 47.826 0.00 0.00 41.61 1.85
178 179 4.766375 CACGTAGTCCATTCCACCTTTAT 58.234 43.478 0.00 0.00 41.61 1.40
179 180 4.809426 CACGTAGTCCATTCCACCTTTATC 59.191 45.833 0.00 0.00 41.61 1.75
180 181 4.715297 ACGTAGTCCATTCCACCTTTATCT 59.285 41.667 0.00 0.00 29.74 1.98
181 182 5.895534 ACGTAGTCCATTCCACCTTTATCTA 59.104 40.000 0.00 0.00 29.74 1.98
182 183 6.553852 ACGTAGTCCATTCCACCTTTATCTAT 59.446 38.462 0.00 0.00 29.74 1.98
183 184 7.091443 CGTAGTCCATTCCACCTTTATCTATC 58.909 42.308 0.00 0.00 0.00 2.08
184 185 7.039644 CGTAGTCCATTCCACCTTTATCTATCT 60.040 40.741 0.00 0.00 0.00 1.98
185 186 9.310449 GTAGTCCATTCCACCTTTATCTATCTA 57.690 37.037 0.00 0.00 0.00 1.98
186 187 8.429237 AGTCCATTCCACCTTTATCTATCTAG 57.571 38.462 0.00 0.00 0.00 2.43
187 188 7.456269 AGTCCATTCCACCTTTATCTATCTAGG 59.544 40.741 0.00 0.00 0.00 3.02
188 189 7.235812 GTCCATTCCACCTTTATCTATCTAGGT 59.764 40.741 0.00 0.00 41.58 3.08
189 190 7.794683 TCCATTCCACCTTTATCTATCTAGGTT 59.205 37.037 0.00 0.00 38.93 3.50
190 191 9.101325 CCATTCCACCTTTATCTATCTAGGTTA 57.899 37.037 0.00 0.00 38.93 2.85
193 194 8.896722 TCCACCTTTATCTATCTAGGTTATCC 57.103 38.462 0.00 0.00 38.93 2.59
195 196 9.327731 CCACCTTTATCTATCTAGGTTATCCTT 57.672 37.037 0.00 0.00 42.12 3.36
210 211 8.112016 AGGTTATCCTTCTTTCTTAACAAAGC 57.888 34.615 0.00 0.00 42.12 3.51
211 212 7.724061 AGGTTATCCTTCTTTCTTAACAAAGCA 59.276 33.333 0.00 0.00 42.12 3.91
212 213 8.023706 GGTTATCCTTCTTTCTTAACAAAGCAG 58.976 37.037 0.00 0.00 33.94 4.24
213 214 8.784043 GTTATCCTTCTTTCTTAACAAAGCAGA 58.216 33.333 4.83 0.31 30.63 4.26
214 215 7.823745 ATCCTTCTTTCTTAACAAAGCAGAA 57.176 32.000 4.83 0.00 30.63 3.02
215 216 7.823745 TCCTTCTTTCTTAACAAAGCAGAAT 57.176 32.000 4.83 0.00 30.63 2.40
216 217 7.651808 TCCTTCTTTCTTAACAAAGCAGAATG 58.348 34.615 4.83 0.00 30.63 2.67
217 218 7.285401 TCCTTCTTTCTTAACAAAGCAGAATGT 59.715 33.333 4.83 0.00 39.31 2.71
218 219 7.380602 CCTTCTTTCTTAACAAAGCAGAATGTG 59.619 37.037 4.83 0.00 39.31 3.21
219 220 7.566760 TCTTTCTTAACAAAGCAGAATGTGA 57.433 32.000 0.00 0.00 39.31 3.58
220 221 8.169977 TCTTTCTTAACAAAGCAGAATGTGAT 57.830 30.769 0.00 0.00 39.31 3.06
221 222 8.077991 TCTTTCTTAACAAAGCAGAATGTGATG 58.922 33.333 0.00 0.00 39.31 3.07
222 223 7.509141 TTCTTAACAAAGCAGAATGTGATGA 57.491 32.000 0.00 0.00 39.31 2.92
223 224 7.692460 TCTTAACAAAGCAGAATGTGATGAT 57.308 32.000 0.00 0.00 39.31 2.45
224 225 7.755591 TCTTAACAAAGCAGAATGTGATGATC 58.244 34.615 0.00 0.00 39.31 2.92
225 226 4.611310 ACAAAGCAGAATGTGATGATCG 57.389 40.909 0.00 0.00 39.31 3.69
226 227 4.256110 ACAAAGCAGAATGTGATGATCGA 58.744 39.130 0.00 0.00 39.31 3.59
227 228 4.880120 ACAAAGCAGAATGTGATGATCGAT 59.120 37.500 0.00 0.00 39.31 3.59
228 229 5.007430 ACAAAGCAGAATGTGATGATCGATC 59.993 40.000 18.72 18.72 39.31 3.69
229 230 3.661944 AGCAGAATGTGATGATCGATCC 58.338 45.455 22.31 8.72 39.31 3.36
230 231 2.740981 GCAGAATGTGATGATCGATCCC 59.259 50.000 22.31 14.28 39.31 3.85
231 232 3.556633 GCAGAATGTGATGATCGATCCCT 60.557 47.826 22.31 9.99 39.31 4.20
232 233 4.244066 CAGAATGTGATGATCGATCCCTC 58.756 47.826 22.31 18.05 0.00 4.30
233 234 4.021280 CAGAATGTGATGATCGATCCCTCT 60.021 45.833 22.31 9.88 0.00 3.69
234 235 5.184671 CAGAATGTGATGATCGATCCCTCTA 59.815 44.000 22.31 12.18 0.00 2.43
235 236 5.957168 AGAATGTGATGATCGATCCCTCTAT 59.043 40.000 22.31 8.84 0.00 1.98
236 237 6.440010 AGAATGTGATGATCGATCCCTCTATT 59.560 38.462 22.31 19.22 0.00 1.73
237 238 7.617329 AGAATGTGATGATCGATCCCTCTATTA 59.383 37.037 22.31 3.21 0.00 0.98
238 239 7.911130 ATGTGATGATCGATCCCTCTATTAT 57.089 36.000 22.31 6.63 0.00 1.28
239 240 7.105241 TGTGATGATCGATCCCTCTATTATG 57.895 40.000 22.31 0.00 0.00 1.90
240 241 6.097412 TGTGATGATCGATCCCTCTATTATGG 59.903 42.308 22.31 0.00 0.00 2.74
241 242 5.600069 TGATGATCGATCCCTCTATTATGGG 59.400 44.000 22.31 0.00 44.66 4.00
262 263 7.354751 TGGGATTTATGTTTATACCAAAGCC 57.645 36.000 6.36 6.36 35.03 4.35
263 264 7.129425 TGGGATTTATGTTTATACCAAAGCCT 58.871 34.615 11.66 0.00 35.61 4.58
264 265 7.286775 TGGGATTTATGTTTATACCAAAGCCTC 59.713 37.037 11.66 5.97 35.61 4.70
265 266 7.505923 GGGATTTATGTTTATACCAAAGCCTCT 59.494 37.037 11.66 0.00 35.61 3.69
266 267 9.569122 GGATTTATGTTTATACCAAAGCCTCTA 57.431 33.333 7.22 0.00 33.94 2.43
269 270 9.969001 TTTATGTTTATACCAAAGCCTCTACTT 57.031 29.630 0.00 0.00 0.00 2.24
270 271 9.969001 TTATGTTTATACCAAAGCCTCTACTTT 57.031 29.630 0.00 0.00 40.49 2.66
272 273 9.614792 ATGTTTATACCAAAGCCTCTACTTTAG 57.385 33.333 0.00 0.00 37.78 1.85
273 274 8.818860 TGTTTATACCAAAGCCTCTACTTTAGA 58.181 33.333 0.00 0.00 37.78 2.10
274 275 9.833917 GTTTATACCAAAGCCTCTACTTTAGAT 57.166 33.333 0.00 0.00 37.78 1.98
280 281 9.833917 ACCAAAGCCTCTACTTTAGATATTTAC 57.166 33.333 0.00 0.00 37.78 2.01
281 282 8.979574 CCAAAGCCTCTACTTTAGATATTTACG 58.020 37.037 0.00 0.00 37.78 3.18
282 283 8.488764 CAAAGCCTCTACTTTAGATATTTACGC 58.511 37.037 0.00 0.00 37.78 4.42
283 284 7.527568 AGCCTCTACTTTAGATATTTACGCT 57.472 36.000 0.00 0.00 33.66 5.07
284 285 7.371936 AGCCTCTACTTTAGATATTTACGCTG 58.628 38.462 0.00 0.00 33.66 5.18
285 286 7.230913 AGCCTCTACTTTAGATATTTACGCTGA 59.769 37.037 0.00 0.00 33.66 4.26
286 287 8.030106 GCCTCTACTTTAGATATTTACGCTGAT 58.970 37.037 0.00 0.00 33.66 2.90
287 288 9.347934 CCTCTACTTTAGATATTTACGCTGATG 57.652 37.037 0.00 0.00 33.66 3.07
291 292 8.594881 ACTTTAGATATTTACGCTGATGAAGG 57.405 34.615 0.00 0.00 0.00 3.46
292 293 8.421784 ACTTTAGATATTTACGCTGATGAAGGA 58.578 33.333 0.00 0.00 0.00 3.36
293 294 9.261180 CTTTAGATATTTACGCTGATGAAGGAA 57.739 33.333 0.00 0.00 0.00 3.36
294 295 9.607988 TTTAGATATTTACGCTGATGAAGGAAA 57.392 29.630 0.00 0.00 0.00 3.13
295 296 7.721286 AGATATTTACGCTGATGAAGGAAAG 57.279 36.000 0.00 0.00 0.00 2.62
296 297 4.622701 ATTTACGCTGATGAAGGAAAGC 57.377 40.909 0.00 0.00 0.00 3.51
297 298 2.024176 TACGCTGATGAAGGAAAGCC 57.976 50.000 0.00 0.00 31.84 4.35
312 313 6.189036 AGGAAAGCCTTGTTAAAGACTACT 57.811 37.500 0.00 0.00 43.90 2.57
313 314 7.312415 AGGAAAGCCTTGTTAAAGACTACTA 57.688 36.000 0.00 0.00 43.90 1.82
314 315 7.160049 AGGAAAGCCTTGTTAAAGACTACTAC 58.840 38.462 0.00 0.00 43.90 2.73
315 316 7.016366 AGGAAAGCCTTGTTAAAGACTACTACT 59.984 37.037 0.00 0.00 43.90 2.57
316 317 7.660617 GGAAAGCCTTGTTAAAGACTACTACTT 59.339 37.037 0.00 0.00 35.19 2.24
317 318 8.975663 AAAGCCTTGTTAAAGACTACTACTTT 57.024 30.769 0.00 0.00 40.13 2.66
318 319 8.975663 AAGCCTTGTTAAAGACTACTACTTTT 57.024 30.769 0.00 0.00 38.34 2.27
319 320 8.379457 AGCCTTGTTAAAGACTACTACTTTTG 57.621 34.615 0.00 0.00 38.34 2.44
320 321 8.208903 AGCCTTGTTAAAGACTACTACTTTTGA 58.791 33.333 0.00 0.00 38.34 2.69
321 322 8.281194 GCCTTGTTAAAGACTACTACTTTTGAC 58.719 37.037 0.00 0.00 38.34 3.18
322 323 9.543783 CCTTGTTAAAGACTACTACTTTTGACT 57.456 33.333 0.00 0.00 38.34 3.41
325 326 9.538508 TGTTAAAGACTACTACTTTTGACTTCC 57.461 33.333 0.00 0.00 38.34 3.46
326 327 9.761504 GTTAAAGACTACTACTTTTGACTTCCT 57.238 33.333 0.00 0.00 38.34 3.36
329 330 9.682465 AAAGACTACTACTTTTGACTTCCTTTT 57.318 29.630 0.00 0.00 34.50 2.27
330 331 9.682465 AAGACTACTACTTTTGACTTCCTTTTT 57.318 29.630 0.00 0.00 0.00 1.94
331 332 9.327628 AGACTACTACTTTTGACTTCCTTTTTC 57.672 33.333 0.00 0.00 0.00 2.29
332 333 8.139521 ACTACTACTTTTGACTTCCTTTTTCG 57.860 34.615 0.00 0.00 0.00 3.46
333 334 6.997239 ACTACTTTTGACTTCCTTTTTCGT 57.003 33.333 0.00 0.00 0.00 3.85
334 335 9.252962 CTACTACTTTTGACTTCCTTTTTCGTA 57.747 33.333 0.00 0.00 0.00 3.43
335 336 7.913423 ACTACTTTTGACTTCCTTTTTCGTAC 58.087 34.615 0.00 0.00 0.00 3.67
336 337 6.997239 ACTTTTGACTTCCTTTTTCGTACT 57.003 33.333 0.00 0.00 0.00 2.73
337 338 7.012959 ACTTTTGACTTCCTTTTTCGTACTC 57.987 36.000 0.00 0.00 0.00 2.59
338 339 6.822170 ACTTTTGACTTCCTTTTTCGTACTCT 59.178 34.615 0.00 0.00 0.00 3.24
339 340 7.336176 ACTTTTGACTTCCTTTTTCGTACTCTT 59.664 33.333 0.00 0.00 0.00 2.85
340 341 6.839820 TTGACTTCCTTTTTCGTACTCTTC 57.160 37.500 0.00 0.00 0.00 2.87
341 342 6.158023 TGACTTCCTTTTTCGTACTCTTCT 57.842 37.500 0.00 0.00 0.00 2.85
342 343 6.579865 TGACTTCCTTTTTCGTACTCTTCTT 58.420 36.000 0.00 0.00 0.00 2.52
343 344 7.046033 TGACTTCCTTTTTCGTACTCTTCTTT 58.954 34.615 0.00 0.00 0.00 2.52
344 345 7.224167 TGACTTCCTTTTTCGTACTCTTCTTTC 59.776 37.037 0.00 0.00 0.00 2.62
345 346 7.046033 ACTTCCTTTTTCGTACTCTTCTTTCA 58.954 34.615 0.00 0.00 0.00 2.69
346 347 7.715686 ACTTCCTTTTTCGTACTCTTCTTTCAT 59.284 33.333 0.00 0.00 0.00 2.57
347 348 7.653767 TCCTTTTTCGTACTCTTCTTTCATC 57.346 36.000 0.00 0.00 0.00 2.92
348 349 6.649557 TCCTTTTTCGTACTCTTCTTTCATCC 59.350 38.462 0.00 0.00 0.00 3.51
349 350 6.651225 CCTTTTTCGTACTCTTCTTTCATCCT 59.349 38.462 0.00 0.00 0.00 3.24
350 351 7.148557 CCTTTTTCGTACTCTTCTTTCATCCTC 60.149 40.741 0.00 0.00 0.00 3.71
351 352 4.985538 TCGTACTCTTCTTTCATCCTCC 57.014 45.455 0.00 0.00 0.00 4.30
352 353 4.601084 TCGTACTCTTCTTTCATCCTCCT 58.399 43.478 0.00 0.00 0.00 3.69
353 354 5.017490 TCGTACTCTTCTTTCATCCTCCTT 58.983 41.667 0.00 0.00 0.00 3.36
354 355 6.185511 TCGTACTCTTCTTTCATCCTCCTTA 58.814 40.000 0.00 0.00 0.00 2.69
355 356 6.095160 TCGTACTCTTCTTTCATCCTCCTTAC 59.905 42.308 0.00 0.00 0.00 2.34
356 357 5.685520 ACTCTTCTTTCATCCTCCTTACC 57.314 43.478 0.00 0.00 0.00 2.85
357 358 5.094387 ACTCTTCTTTCATCCTCCTTACCA 58.906 41.667 0.00 0.00 0.00 3.25
358 359 5.188751 ACTCTTCTTTCATCCTCCTTACCAG 59.811 44.000 0.00 0.00 0.00 4.00
359 360 5.342017 TCTTCTTTCATCCTCCTTACCAGA 58.658 41.667 0.00 0.00 0.00 3.86
360 361 5.785423 TCTTCTTTCATCCTCCTTACCAGAA 59.215 40.000 0.00 0.00 0.00 3.02
361 362 5.422214 TCTTTCATCCTCCTTACCAGAAC 57.578 43.478 0.00 0.00 0.00 3.01
362 363 3.887621 TTCATCCTCCTTACCAGAACG 57.112 47.619 0.00 0.00 0.00 3.95
363 364 1.480954 TCATCCTCCTTACCAGAACGC 59.519 52.381 0.00 0.00 0.00 4.84
364 365 0.831307 ATCCTCCTTACCAGAACGCC 59.169 55.000 0.00 0.00 0.00 5.68
365 366 0.252103 TCCTCCTTACCAGAACGCCT 60.252 55.000 0.00 0.00 0.00 5.52
366 367 0.613777 CCTCCTTACCAGAACGCCTT 59.386 55.000 0.00 0.00 0.00 4.35
367 368 1.003233 CCTCCTTACCAGAACGCCTTT 59.997 52.381 0.00 0.00 0.00 3.11
368 369 2.347731 CTCCTTACCAGAACGCCTTTC 58.652 52.381 0.00 0.00 33.95 2.62
369 370 1.002773 TCCTTACCAGAACGCCTTTCC 59.997 52.381 0.00 0.00 34.32 3.13
370 371 1.003233 CCTTACCAGAACGCCTTTCCT 59.997 52.381 0.00 0.00 34.32 3.36
371 372 2.076863 CTTACCAGAACGCCTTTCCTG 58.923 52.381 0.00 0.00 34.32 3.86
372 373 0.323629 TACCAGAACGCCTTTCCTGG 59.676 55.000 0.00 0.00 37.98 4.45
373 374 1.073199 CCAGAACGCCTTTCCTGGT 59.927 57.895 0.00 0.00 34.32 4.00
1226 1228 7.669722 ACATAGAATGCCACTCTTTAAAAAGGA 59.330 33.333 2.77 0.00 36.67 3.36
1577 1579 4.580995 ACGAGACTGAACTAGGTATGATGG 59.419 45.833 0.00 0.00 0.00 3.51
1704 1706 3.435457 CCAATATGAGCATCCAGGTTCCA 60.435 47.826 0.00 0.00 0.00 3.53
1732 1734 4.120589 GGTTATTGACCGAAGATCTGTCC 58.879 47.826 0.00 0.00 39.00 4.02
1855 1858 1.638529 GGAGTCCCGGATGAGATCAT 58.361 55.000 0.73 0.00 39.70 2.45
1858 1861 1.051812 GTCCCGGATGAGATCATGGT 58.948 55.000 0.73 0.00 36.57 3.55
1875 1878 4.571577 TCATGGTCATGAAGAGGAGTCTCT 60.572 45.833 10.83 0.00 44.14 3.10
1988 1991 0.459063 GAGTTACGGGAATTCGCCGT 60.459 55.000 30.57 30.57 42.53 5.68
2051 2059 3.579302 CCTCAAGGGGTGGCCACA 61.579 66.667 35.78 14.57 0.00 4.17
2052 2060 2.282462 CTCAAGGGGTGGCCACAC 60.282 66.667 35.78 33.56 46.97 3.82
2209 2220 2.628559 CCTAGTAGGATTCCCCACACCA 60.629 54.545 11.09 0.00 37.67 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.371917 CCCATCTTGCCAATCTTCCTGTA 60.372 47.826 0.00 0.00 0.00 2.74
1 2 2.622452 CCCATCTTGCCAATCTTCCTGT 60.622 50.000 0.00 0.00 0.00 4.00
2 3 2.029623 CCCATCTTGCCAATCTTCCTG 58.970 52.381 0.00 0.00 0.00 3.86
3 4 1.063417 CCCCATCTTGCCAATCTTCCT 60.063 52.381 0.00 0.00 0.00 3.36
4 5 1.406903 CCCCATCTTGCCAATCTTCC 58.593 55.000 0.00 0.00 0.00 3.46
5 6 0.749049 GCCCCATCTTGCCAATCTTC 59.251 55.000 0.00 0.00 0.00 2.87
6 7 2.906268 GCCCCATCTTGCCAATCTT 58.094 52.632 0.00 0.00 0.00 2.40
7 8 4.692930 GCCCCATCTTGCCAATCT 57.307 55.556 0.00 0.00 0.00 2.40
18 19 1.426598 CAGTAAGGATGATGGCCCCAT 59.573 52.381 0.00 3.40 39.69 4.00
19 20 0.846015 CAGTAAGGATGATGGCCCCA 59.154 55.000 0.00 0.00 0.00 4.96
20 21 1.072965 CTCAGTAAGGATGATGGCCCC 59.927 57.143 0.00 0.00 0.00 5.80
21 22 1.771255 ACTCAGTAAGGATGATGGCCC 59.229 52.381 0.00 0.00 0.00 5.80
22 23 3.471680 GAACTCAGTAAGGATGATGGCC 58.528 50.000 0.00 0.00 0.00 5.36
23 24 3.126831 CGAACTCAGTAAGGATGATGGC 58.873 50.000 0.00 0.00 0.00 4.40
24 25 4.142160 TGTCGAACTCAGTAAGGATGATGG 60.142 45.833 0.00 0.00 0.00 3.51
25 26 4.998788 TGTCGAACTCAGTAAGGATGATG 58.001 43.478 0.00 0.00 0.00 3.07
26 27 5.860941 ATGTCGAACTCAGTAAGGATGAT 57.139 39.130 0.00 0.00 0.00 2.45
27 28 5.047306 ACAATGTCGAACTCAGTAAGGATGA 60.047 40.000 0.00 0.00 0.00 2.92
28 29 5.062683 CACAATGTCGAACTCAGTAAGGATG 59.937 44.000 0.00 0.00 0.00 3.51
29 30 5.171476 CACAATGTCGAACTCAGTAAGGAT 58.829 41.667 0.00 0.00 0.00 3.24
30 31 4.038763 ACACAATGTCGAACTCAGTAAGGA 59.961 41.667 0.00 0.00 0.00 3.36
31 32 4.307432 ACACAATGTCGAACTCAGTAAGG 58.693 43.478 0.00 0.00 0.00 2.69
32 33 6.454318 GCATACACAATGTCGAACTCAGTAAG 60.454 42.308 0.00 0.00 37.93 2.34
33 34 5.347635 GCATACACAATGTCGAACTCAGTAA 59.652 40.000 0.00 0.00 37.93 2.24
34 35 4.862574 GCATACACAATGTCGAACTCAGTA 59.137 41.667 0.00 0.00 37.93 2.74
35 36 3.679980 GCATACACAATGTCGAACTCAGT 59.320 43.478 0.00 0.00 37.93 3.41
36 37 3.241773 CGCATACACAATGTCGAACTCAG 60.242 47.826 0.00 0.00 37.32 3.35
37 38 2.666022 CGCATACACAATGTCGAACTCA 59.334 45.455 0.00 0.00 37.32 3.41
38 39 2.534939 GCGCATACACAATGTCGAACTC 60.535 50.000 0.30 0.00 37.32 3.01
39 40 1.393539 GCGCATACACAATGTCGAACT 59.606 47.619 0.30 0.00 37.32 3.01
40 41 1.529010 GGCGCATACACAATGTCGAAC 60.529 52.381 10.83 0.00 37.32 3.95
41 42 0.724549 GGCGCATACACAATGTCGAA 59.275 50.000 10.83 0.00 37.32 3.71
42 43 1.417577 CGGCGCATACACAATGTCGA 61.418 55.000 10.83 0.00 37.32 4.20
43 44 1.012343 CGGCGCATACACAATGTCG 60.012 57.895 10.83 0.00 37.93 4.35
44 45 1.297598 GCGGCGCATACACAATGTC 60.298 57.895 29.21 0.00 37.93 3.06
45 46 1.980951 CTGCGGCGCATACACAATGT 61.981 55.000 36.35 0.00 38.13 2.71
46 47 1.297819 CTGCGGCGCATACACAATG 60.298 57.895 36.35 17.23 38.13 2.82
47 48 1.024046 TTCTGCGGCGCATACACAAT 61.024 50.000 36.35 0.00 38.13 2.71
48 49 1.634757 CTTCTGCGGCGCATACACAA 61.635 55.000 36.35 20.02 38.13 3.33
49 50 2.047750 TTCTGCGGCGCATACACA 60.048 55.556 36.35 14.47 38.13 3.72
50 51 2.703409 CTTCTGCGGCGCATACAC 59.297 61.111 36.35 3.60 38.13 2.90
51 52 2.511373 CCTTCTGCGGCGCATACA 60.511 61.111 36.35 19.35 38.13 2.29
52 53 3.941836 GCCTTCTGCGGCGCATAC 61.942 66.667 36.35 18.41 40.79 2.39
59 60 0.533755 CCTCTAATGGCCTTCTGCGG 60.534 60.000 3.32 0.00 42.61 5.69
60 61 0.533755 CCCTCTAATGGCCTTCTGCG 60.534 60.000 3.32 0.00 42.61 5.18
61 62 0.821301 GCCCTCTAATGGCCTTCTGC 60.821 60.000 3.32 0.00 43.33 4.26
62 63 3.410960 GCCCTCTAATGGCCTTCTG 57.589 57.895 3.32 0.00 43.33 3.02
69 70 1.233019 CATCGCTTGCCCTCTAATGG 58.767 55.000 0.00 0.00 0.00 3.16
70 71 1.233019 CCATCGCTTGCCCTCTAATG 58.767 55.000 0.00 0.00 0.00 1.90
71 72 0.536006 GCCATCGCTTGCCCTCTAAT 60.536 55.000 0.00 0.00 0.00 1.73
72 73 1.153168 GCCATCGCTTGCCCTCTAA 60.153 57.895 0.00 0.00 0.00 2.10
73 74 2.505982 GCCATCGCTTGCCCTCTA 59.494 61.111 0.00 0.00 0.00 2.43
74 75 4.845580 CGCCATCGCTTGCCCTCT 62.846 66.667 0.00 0.00 0.00 3.69
78 79 2.668261 GAAATCCGCCATCGCTTGCC 62.668 60.000 0.00 0.00 0.00 4.52
79 80 1.298638 GAAATCCGCCATCGCTTGC 60.299 57.895 0.00 0.00 0.00 4.01
80 81 1.097547 AGGAAATCCGCCATCGCTTG 61.098 55.000 0.00 0.00 42.08 4.01
81 82 0.468226 TAGGAAATCCGCCATCGCTT 59.532 50.000 0.00 0.00 42.08 4.68
82 83 0.034059 CTAGGAAATCCGCCATCGCT 59.966 55.000 0.00 0.00 42.08 4.93
83 84 1.569479 GCTAGGAAATCCGCCATCGC 61.569 60.000 0.00 0.00 42.08 4.58
84 85 0.249868 TGCTAGGAAATCCGCCATCG 60.250 55.000 0.00 0.00 42.08 3.84
85 86 1.517242 CTGCTAGGAAATCCGCCATC 58.483 55.000 0.00 0.00 42.08 3.51
86 87 0.536006 GCTGCTAGGAAATCCGCCAT 60.536 55.000 0.00 0.00 42.08 4.40
87 88 1.153168 GCTGCTAGGAAATCCGCCA 60.153 57.895 0.00 0.00 42.08 5.69
88 89 1.153168 TGCTGCTAGGAAATCCGCC 60.153 57.895 0.00 0.00 42.08 6.13
89 90 0.744414 TGTGCTGCTAGGAAATCCGC 60.744 55.000 0.00 0.00 42.08 5.54
90 91 1.869767 GATGTGCTGCTAGGAAATCCG 59.130 52.381 0.00 0.00 42.08 4.18
91 92 2.923121 TGATGTGCTGCTAGGAAATCC 58.077 47.619 0.00 0.00 30.06 3.01
92 93 5.059161 TGTATGATGTGCTGCTAGGAAATC 58.941 41.667 0.00 0.00 31.63 2.17
93 94 5.039920 TGTATGATGTGCTGCTAGGAAAT 57.960 39.130 0.00 0.00 0.00 2.17
94 95 4.486125 TGTATGATGTGCTGCTAGGAAA 57.514 40.909 0.00 0.00 0.00 3.13
95 96 4.694760 ATGTATGATGTGCTGCTAGGAA 57.305 40.909 0.00 0.00 0.00 3.36
96 97 6.364568 AATATGTATGATGTGCTGCTAGGA 57.635 37.500 0.00 0.00 0.00 2.94
97 98 8.728337 ATAAATATGTATGATGTGCTGCTAGG 57.272 34.615 0.00 0.00 0.00 3.02
100 101 9.159364 CTGTATAAATATGTATGATGTGCTGCT 57.841 33.333 0.00 0.00 0.00 4.24
101 102 8.939929 ACTGTATAAATATGTATGATGTGCTGC 58.060 33.333 0.00 0.00 0.00 5.25
142 143 3.466836 ACTACGTGCAATCCCATACATG 58.533 45.455 0.00 0.00 0.00 3.21
143 144 3.494398 GGACTACGTGCAATCCCATACAT 60.494 47.826 0.00 0.00 0.00 2.29
144 145 2.159014 GGACTACGTGCAATCCCATACA 60.159 50.000 0.00 0.00 0.00 2.29
145 146 2.159014 TGGACTACGTGCAATCCCATAC 60.159 50.000 0.00 0.00 29.43 2.39
146 147 2.112190 TGGACTACGTGCAATCCCATA 58.888 47.619 0.00 0.00 29.43 2.74
147 148 0.908910 TGGACTACGTGCAATCCCAT 59.091 50.000 0.00 0.00 29.43 4.00
148 149 0.908910 ATGGACTACGTGCAATCCCA 59.091 50.000 0.00 0.00 37.44 4.37
149 150 1.940613 GAATGGACTACGTGCAATCCC 59.059 52.381 0.00 0.00 37.44 3.85
150 151 1.940613 GGAATGGACTACGTGCAATCC 59.059 52.381 6.81 6.81 44.19 3.01
151 152 2.351726 GTGGAATGGACTACGTGCAATC 59.648 50.000 0.00 0.00 37.44 2.67
152 153 2.356135 GTGGAATGGACTACGTGCAAT 58.644 47.619 0.00 0.00 37.44 3.56
153 154 1.609580 GGTGGAATGGACTACGTGCAA 60.610 52.381 0.00 0.00 37.44 4.08
154 155 0.036765 GGTGGAATGGACTACGTGCA 60.037 55.000 0.00 0.00 38.41 4.57
155 156 0.249398 AGGTGGAATGGACTACGTGC 59.751 55.000 0.00 0.00 0.00 5.34
156 157 2.762535 AAGGTGGAATGGACTACGTG 57.237 50.000 0.00 0.00 0.00 4.49
157 158 4.715297 AGATAAAGGTGGAATGGACTACGT 59.285 41.667 0.00 0.00 0.00 3.57
158 159 5.277857 AGATAAAGGTGGAATGGACTACG 57.722 43.478 0.00 0.00 0.00 3.51
159 160 8.196378 AGATAGATAAAGGTGGAATGGACTAC 57.804 38.462 0.00 0.00 0.00 2.73
160 161 9.535170 CTAGATAGATAAAGGTGGAATGGACTA 57.465 37.037 0.00 0.00 0.00 2.59
161 162 7.456269 CCTAGATAGATAAAGGTGGAATGGACT 59.544 40.741 0.00 0.00 0.00 3.85
162 163 7.235812 ACCTAGATAGATAAAGGTGGAATGGAC 59.764 40.741 0.00 0.00 40.83 4.02
163 164 7.313731 ACCTAGATAGATAAAGGTGGAATGGA 58.686 38.462 0.00 0.00 40.83 3.41
164 165 7.560796 ACCTAGATAGATAAAGGTGGAATGG 57.439 40.000 0.00 0.00 40.83 3.16
167 168 9.322769 GGATAACCTAGATAGATAAAGGTGGAA 57.677 37.037 0.00 0.00 41.51 3.53
168 169 8.689054 AGGATAACCTAGATAGATAAAGGTGGA 58.311 37.037 0.00 0.00 45.83 4.02
169 170 8.903059 AGGATAACCTAGATAGATAAAGGTGG 57.097 38.462 0.00 0.00 45.83 4.61
184 185 9.227777 GCTTTGTTAAGAAAGAAGGATAACCTA 57.772 33.333 24.85 0.00 38.67 3.08
185 186 7.724061 TGCTTTGTTAAGAAAGAAGGATAACCT 59.276 33.333 24.85 0.00 39.43 3.50
186 187 7.882179 TGCTTTGTTAAGAAAGAAGGATAACC 58.118 34.615 24.85 7.65 35.30 2.85
187 188 8.784043 TCTGCTTTGTTAAGAAAGAAGGATAAC 58.216 33.333 25.46 9.60 38.65 1.89
188 189 8.918202 TCTGCTTTGTTAAGAAAGAAGGATAA 57.082 30.769 25.46 9.72 38.65 1.75
189 190 8.918202 TTCTGCTTTGTTAAGAAAGAAGGATA 57.082 30.769 25.46 13.27 38.65 2.59
190 191 7.823745 TTCTGCTTTGTTAAGAAAGAAGGAT 57.176 32.000 25.46 0.00 38.65 3.24
191 192 7.285401 ACATTCTGCTTTGTTAAGAAAGAAGGA 59.715 33.333 25.46 20.63 38.65 3.36
192 193 7.380602 CACATTCTGCTTTGTTAAGAAAGAAGG 59.619 37.037 25.46 16.54 38.65 3.46
193 194 8.131100 TCACATTCTGCTTTGTTAAGAAAGAAG 58.869 33.333 24.85 23.33 39.26 2.85
194 195 7.995289 TCACATTCTGCTTTGTTAAGAAAGAA 58.005 30.769 24.85 15.88 38.68 2.52
195 196 7.566760 TCACATTCTGCTTTGTTAAGAAAGA 57.433 32.000 24.85 11.49 35.30 2.52
196 197 8.077991 TCATCACATTCTGCTTTGTTAAGAAAG 58.922 33.333 18.28 18.28 33.86 2.62
197 198 7.939782 TCATCACATTCTGCTTTGTTAAGAAA 58.060 30.769 0.00 0.00 33.86 2.52
198 199 7.509141 TCATCACATTCTGCTTTGTTAAGAA 57.491 32.000 0.00 0.00 34.61 2.52
199 200 7.413328 CGATCATCACATTCTGCTTTGTTAAGA 60.413 37.037 0.00 0.00 32.92 2.10
200 201 6.685828 CGATCATCACATTCTGCTTTGTTAAG 59.314 38.462 0.00 0.00 34.36 1.85
201 202 6.371271 TCGATCATCACATTCTGCTTTGTTAA 59.629 34.615 0.00 0.00 0.00 2.01
202 203 5.874261 TCGATCATCACATTCTGCTTTGTTA 59.126 36.000 0.00 0.00 0.00 2.41
203 204 4.696877 TCGATCATCACATTCTGCTTTGTT 59.303 37.500 0.00 0.00 0.00 2.83
204 205 4.256110 TCGATCATCACATTCTGCTTTGT 58.744 39.130 0.00 0.00 0.00 2.83
205 206 4.870221 TCGATCATCACATTCTGCTTTG 57.130 40.909 0.00 0.00 0.00 2.77
206 207 4.514441 GGATCGATCATCACATTCTGCTTT 59.486 41.667 25.93 0.00 32.33 3.51
207 208 4.063689 GGATCGATCATCACATTCTGCTT 58.936 43.478 25.93 0.00 32.33 3.91
208 209 3.556633 GGGATCGATCATCACATTCTGCT 60.557 47.826 25.93 0.00 34.60 4.24
209 210 2.740981 GGGATCGATCATCACATTCTGC 59.259 50.000 25.93 4.71 34.60 4.26
210 211 4.021280 AGAGGGATCGATCATCACATTCTG 60.021 45.833 25.93 0.00 37.39 3.02
211 212 4.158786 AGAGGGATCGATCATCACATTCT 58.841 43.478 25.93 13.59 37.39 2.40
212 213 4.533919 AGAGGGATCGATCATCACATTC 57.466 45.455 25.93 11.83 37.39 2.67
213 214 6.617782 AATAGAGGGATCGATCATCACATT 57.382 37.500 25.93 19.69 37.39 2.71
214 215 7.201983 CCATAATAGAGGGATCGATCATCACAT 60.202 40.741 25.93 15.97 37.39 3.21
215 216 6.097412 CCATAATAGAGGGATCGATCATCACA 59.903 42.308 25.93 14.66 37.39 3.58
216 217 6.511416 CCATAATAGAGGGATCGATCATCAC 58.489 44.000 25.93 15.41 34.68 3.06
217 218 6.721704 CCATAATAGAGGGATCGATCATCA 57.278 41.667 25.93 13.66 32.33 3.07
236 237 9.084533 GGCTTTGGTATAAACATAAATCCCATA 57.915 33.333 0.00 0.00 0.00 2.74
237 238 7.789349 AGGCTTTGGTATAAACATAAATCCCAT 59.211 33.333 0.00 0.00 0.00 4.00
238 239 7.129425 AGGCTTTGGTATAAACATAAATCCCA 58.871 34.615 0.00 0.00 0.00 4.37
239 240 7.505923 AGAGGCTTTGGTATAAACATAAATCCC 59.494 37.037 0.00 0.00 0.00 3.85
240 241 8.465273 AGAGGCTTTGGTATAAACATAAATCC 57.535 34.615 0.00 0.00 0.00 3.01
243 244 9.969001 AAGTAGAGGCTTTGGTATAAACATAAA 57.031 29.630 0.00 0.00 0.00 1.40
244 245 9.969001 AAAGTAGAGGCTTTGGTATAAACATAA 57.031 29.630 0.00 0.00 37.31 1.90
246 247 9.614792 CTAAAGTAGAGGCTTTGGTATAAACAT 57.385 33.333 0.00 0.00 38.89 2.71
247 248 8.818860 TCTAAAGTAGAGGCTTTGGTATAAACA 58.181 33.333 0.00 0.00 38.89 2.83
248 249 9.833917 ATCTAAAGTAGAGGCTTTGGTATAAAC 57.166 33.333 0.00 0.00 38.89 2.01
254 255 9.833917 GTAAATATCTAAAGTAGAGGCTTTGGT 57.166 33.333 0.00 0.00 38.89 3.67
255 256 8.979574 CGTAAATATCTAAAGTAGAGGCTTTGG 58.020 37.037 0.00 0.00 38.89 3.28
256 257 8.488764 GCGTAAATATCTAAAGTAGAGGCTTTG 58.511 37.037 0.00 0.00 38.89 2.77
257 258 8.422566 AGCGTAAATATCTAAAGTAGAGGCTTT 58.577 33.333 0.00 0.00 41.13 3.51
258 259 7.868415 CAGCGTAAATATCTAAAGTAGAGGCTT 59.132 37.037 0.00 0.00 38.38 4.35
259 260 7.230913 TCAGCGTAAATATCTAAAGTAGAGGCT 59.769 37.037 0.00 0.00 38.38 4.58
260 261 7.368833 TCAGCGTAAATATCTAAAGTAGAGGC 58.631 38.462 0.00 0.00 38.38 4.70
261 262 9.347934 CATCAGCGTAAATATCTAAAGTAGAGG 57.652 37.037 0.00 0.00 38.38 3.69
265 266 9.692749 CCTTCATCAGCGTAAATATCTAAAGTA 57.307 33.333 0.00 0.00 0.00 2.24
266 267 8.421784 TCCTTCATCAGCGTAAATATCTAAAGT 58.578 33.333 0.00 0.00 0.00 2.66
267 268 8.818141 TCCTTCATCAGCGTAAATATCTAAAG 57.182 34.615 0.00 0.00 0.00 1.85
268 269 9.607988 TTTCCTTCATCAGCGTAAATATCTAAA 57.392 29.630 0.00 0.00 0.00 1.85
269 270 9.261180 CTTTCCTTCATCAGCGTAAATATCTAA 57.739 33.333 0.00 0.00 0.00 2.10
270 271 7.385205 GCTTTCCTTCATCAGCGTAAATATCTA 59.615 37.037 0.00 0.00 0.00 1.98
271 272 6.203723 GCTTTCCTTCATCAGCGTAAATATCT 59.796 38.462 0.00 0.00 0.00 1.98
272 273 6.366630 GCTTTCCTTCATCAGCGTAAATATC 58.633 40.000 0.00 0.00 0.00 1.63
273 274 5.239525 GGCTTTCCTTCATCAGCGTAAATAT 59.760 40.000 0.00 0.00 32.68 1.28
274 275 4.574828 GGCTTTCCTTCATCAGCGTAAATA 59.425 41.667 0.00 0.00 32.68 1.40
275 276 3.378427 GGCTTTCCTTCATCAGCGTAAAT 59.622 43.478 0.00 0.00 32.68 1.40
276 277 2.747446 GGCTTTCCTTCATCAGCGTAAA 59.253 45.455 0.00 0.00 32.68 2.01
277 278 2.027192 AGGCTTTCCTTCATCAGCGTAA 60.027 45.455 0.00 0.00 40.66 3.18
278 279 1.555075 AGGCTTTCCTTCATCAGCGTA 59.445 47.619 0.00 0.00 40.66 4.42
279 280 0.326264 AGGCTTTCCTTCATCAGCGT 59.674 50.000 0.00 0.00 40.66 5.07
280 281 3.165606 AGGCTTTCCTTCATCAGCG 57.834 52.632 0.00 0.00 40.66 5.18
289 290 6.189036 AGTAGTCTTTAACAAGGCTTTCCT 57.811 37.500 0.00 0.00 42.76 3.36
290 291 7.160049 AGTAGTAGTCTTTAACAAGGCTTTCC 58.840 38.462 0.00 0.00 42.76 3.13
291 292 8.604640 AAGTAGTAGTCTTTAACAAGGCTTTC 57.395 34.615 0.00 0.00 42.76 2.62
292 293 8.975663 AAAGTAGTAGTCTTTAACAAGGCTTT 57.024 30.769 0.00 0.00 42.76 3.51
293 294 8.837389 CAAAAGTAGTAGTCTTTAACAAGGCTT 58.163 33.333 0.00 0.00 42.76 4.35
295 296 8.281194 GTCAAAAGTAGTAGTCTTTAACAAGGC 58.719 37.037 0.00 0.00 34.59 4.35
296 297 9.543783 AGTCAAAAGTAGTAGTCTTTAACAAGG 57.456 33.333 0.00 0.00 34.59 3.61
299 300 9.538508 GGAAGTCAAAAGTAGTAGTCTTTAACA 57.461 33.333 0.00 0.00 34.59 2.41
300 301 9.761504 AGGAAGTCAAAAGTAGTAGTCTTTAAC 57.238 33.333 0.00 0.00 34.59 2.01
303 304 9.682465 AAAAGGAAGTCAAAAGTAGTAGTCTTT 57.318 29.630 0.00 0.00 36.81 2.52
304 305 9.682465 AAAAAGGAAGTCAAAAGTAGTAGTCTT 57.318 29.630 0.00 0.00 0.00 3.01
305 306 9.327628 GAAAAAGGAAGTCAAAAGTAGTAGTCT 57.672 33.333 0.00 0.00 0.00 3.24
306 307 8.274248 CGAAAAAGGAAGTCAAAAGTAGTAGTC 58.726 37.037 0.00 0.00 0.00 2.59
307 308 7.767659 ACGAAAAAGGAAGTCAAAAGTAGTAGT 59.232 33.333 0.00 0.00 0.00 2.73
308 309 8.139521 ACGAAAAAGGAAGTCAAAAGTAGTAG 57.860 34.615 0.00 0.00 0.00 2.57
309 310 9.034544 GTACGAAAAAGGAAGTCAAAAGTAGTA 57.965 33.333 0.00 0.00 0.00 1.82
310 311 6.997239 ACGAAAAAGGAAGTCAAAAGTAGT 57.003 33.333 0.00 0.00 0.00 2.73
311 312 8.139521 AGTACGAAAAAGGAAGTCAAAAGTAG 57.860 34.615 0.00 0.00 0.00 2.57
312 313 7.983484 AGAGTACGAAAAAGGAAGTCAAAAGTA 59.017 33.333 0.00 0.00 0.00 2.24
313 314 6.822170 AGAGTACGAAAAAGGAAGTCAAAAGT 59.178 34.615 0.00 0.00 0.00 2.66
314 315 7.247929 AGAGTACGAAAAAGGAAGTCAAAAG 57.752 36.000 0.00 0.00 0.00 2.27
315 316 7.551617 AGAAGAGTACGAAAAAGGAAGTCAAAA 59.448 33.333 0.00 0.00 0.00 2.44
316 317 7.046033 AGAAGAGTACGAAAAAGGAAGTCAAA 58.954 34.615 0.00 0.00 0.00 2.69
317 318 6.579865 AGAAGAGTACGAAAAAGGAAGTCAA 58.420 36.000 0.00 0.00 0.00 3.18
318 319 6.158023 AGAAGAGTACGAAAAAGGAAGTCA 57.842 37.500 0.00 0.00 0.00 3.41
319 320 7.224167 TGAAAGAAGAGTACGAAAAAGGAAGTC 59.776 37.037 0.00 0.00 0.00 3.01
320 321 7.046033 TGAAAGAAGAGTACGAAAAAGGAAGT 58.954 34.615 0.00 0.00 0.00 3.01
321 322 7.478520 TGAAAGAAGAGTACGAAAAAGGAAG 57.521 36.000 0.00 0.00 0.00 3.46
322 323 7.172703 GGATGAAAGAAGAGTACGAAAAAGGAA 59.827 37.037 0.00 0.00 0.00 3.36
323 324 6.649557 GGATGAAAGAAGAGTACGAAAAAGGA 59.350 38.462 0.00 0.00 0.00 3.36
324 325 6.651225 AGGATGAAAGAAGAGTACGAAAAAGG 59.349 38.462 0.00 0.00 0.00 3.11
325 326 7.148557 GGAGGATGAAAGAAGAGTACGAAAAAG 60.149 40.741 0.00 0.00 0.00 2.27
326 327 6.649557 GGAGGATGAAAGAAGAGTACGAAAAA 59.350 38.462 0.00 0.00 0.00 1.94
327 328 6.014499 AGGAGGATGAAAGAAGAGTACGAAAA 60.014 38.462 0.00 0.00 0.00 2.29
328 329 5.480772 AGGAGGATGAAAGAAGAGTACGAAA 59.519 40.000 0.00 0.00 0.00 3.46
329 330 5.017490 AGGAGGATGAAAGAAGAGTACGAA 58.983 41.667 0.00 0.00 0.00 3.85
330 331 4.601084 AGGAGGATGAAAGAAGAGTACGA 58.399 43.478 0.00 0.00 0.00 3.43
331 332 4.993029 AGGAGGATGAAAGAAGAGTACG 57.007 45.455 0.00 0.00 0.00 3.67
332 333 6.154706 TGGTAAGGAGGATGAAAGAAGAGTAC 59.845 42.308 0.00 0.00 0.00 2.73
333 334 6.261435 TGGTAAGGAGGATGAAAGAAGAGTA 58.739 40.000 0.00 0.00 0.00 2.59
334 335 5.094387 TGGTAAGGAGGATGAAAGAAGAGT 58.906 41.667 0.00 0.00 0.00 3.24
335 336 5.423610 TCTGGTAAGGAGGATGAAAGAAGAG 59.576 44.000 0.00 0.00 0.00 2.85
336 337 5.342017 TCTGGTAAGGAGGATGAAAGAAGA 58.658 41.667 0.00 0.00 0.00 2.87
337 338 5.683876 TCTGGTAAGGAGGATGAAAGAAG 57.316 43.478 0.00 0.00 0.00 2.85
338 339 5.568825 CGTTCTGGTAAGGAGGATGAAAGAA 60.569 44.000 0.00 0.00 0.00 2.52
339 340 4.081642 CGTTCTGGTAAGGAGGATGAAAGA 60.082 45.833 0.00 0.00 0.00 2.52
340 341 4.184629 CGTTCTGGTAAGGAGGATGAAAG 58.815 47.826 0.00 0.00 0.00 2.62
341 342 3.618997 GCGTTCTGGTAAGGAGGATGAAA 60.619 47.826 0.00 0.00 0.00 2.69
342 343 2.093658 GCGTTCTGGTAAGGAGGATGAA 60.094 50.000 0.00 0.00 0.00 2.57
343 344 1.480954 GCGTTCTGGTAAGGAGGATGA 59.519 52.381 0.00 0.00 0.00 2.92
344 345 1.473434 GGCGTTCTGGTAAGGAGGATG 60.473 57.143 0.00 0.00 0.00 3.51
345 346 0.831307 GGCGTTCTGGTAAGGAGGAT 59.169 55.000 0.00 0.00 0.00 3.24
346 347 0.252103 AGGCGTTCTGGTAAGGAGGA 60.252 55.000 0.00 0.00 0.00 3.71
347 348 0.613777 AAGGCGTTCTGGTAAGGAGG 59.386 55.000 0.00 0.00 0.00 4.30
348 349 2.347731 GAAAGGCGTTCTGGTAAGGAG 58.652 52.381 5.89 0.00 33.03 3.69
349 350 1.002773 GGAAAGGCGTTCTGGTAAGGA 59.997 52.381 12.77 0.00 36.40 3.36
350 351 1.003233 AGGAAAGGCGTTCTGGTAAGG 59.997 52.381 12.77 0.00 36.40 2.69
351 352 2.076863 CAGGAAAGGCGTTCTGGTAAG 58.923 52.381 12.77 0.00 36.40 2.34
352 353 1.271163 CCAGGAAAGGCGTTCTGGTAA 60.271 52.381 15.34 0.00 36.40 2.85
353 354 0.323629 CCAGGAAAGGCGTTCTGGTA 59.676 55.000 15.34 0.00 36.40 3.25
354 355 1.073199 CCAGGAAAGGCGTTCTGGT 59.927 57.895 15.34 0.00 36.40 4.00
355 356 1.073199 ACCAGGAAAGGCGTTCTGG 59.927 57.895 19.80 19.80 39.00 3.86
356 357 0.250295 TCACCAGGAAAGGCGTTCTG 60.250 55.000 12.77 8.83 36.40 3.02
357 358 0.693049 ATCACCAGGAAAGGCGTTCT 59.307 50.000 12.77 0.00 36.40 3.01
358 359 1.468914 GAATCACCAGGAAAGGCGTTC 59.531 52.381 4.47 4.47 35.28 3.95
359 360 1.534729 GAATCACCAGGAAAGGCGTT 58.465 50.000 0.00 0.00 0.00 4.84
360 361 0.673644 CGAATCACCAGGAAAGGCGT 60.674 55.000 0.00 0.00 0.00 5.68
361 362 1.369091 CCGAATCACCAGGAAAGGCG 61.369 60.000 0.00 0.00 0.00 5.52
362 363 1.657751 GCCGAATCACCAGGAAAGGC 61.658 60.000 0.00 0.00 36.63 4.35
363 364 0.322456 TGCCGAATCACCAGGAAAGG 60.322 55.000 0.00 0.00 0.00 3.11
364 365 1.089920 CTGCCGAATCACCAGGAAAG 58.910 55.000 0.00 0.00 0.00 2.62
365 366 0.690192 TCTGCCGAATCACCAGGAAA 59.310 50.000 0.00 0.00 0.00 3.13
366 367 0.911769 ATCTGCCGAATCACCAGGAA 59.088 50.000 0.00 0.00 0.00 3.36
367 368 0.911769 AATCTGCCGAATCACCAGGA 59.088 50.000 0.00 0.00 0.00 3.86
368 369 1.402968 CAAATCTGCCGAATCACCAGG 59.597 52.381 0.00 0.00 0.00 4.45
369 370 1.402968 CCAAATCTGCCGAATCACCAG 59.597 52.381 0.00 0.00 0.00 4.00
370 371 1.004161 TCCAAATCTGCCGAATCACCA 59.996 47.619 0.00 0.00 0.00 4.17
371 372 1.750193 TCCAAATCTGCCGAATCACC 58.250 50.000 0.00 0.00 0.00 4.02
372 373 3.243201 GGAATCCAAATCTGCCGAATCAC 60.243 47.826 0.00 0.00 0.00 3.06
373 374 2.951642 GGAATCCAAATCTGCCGAATCA 59.048 45.455 0.00 0.00 0.00 2.57
444 445 4.781934 TGACGATCTCTAGACAGATGGAA 58.218 43.478 9.91 0.00 32.94 3.53
1088 1090 3.118261 GGATGTAGCCAAGTGGATCAAGA 60.118 47.826 0.18 0.00 37.39 3.02
1262 1264 4.832248 TGATGAGCTACAAAAGGATTCGT 58.168 39.130 0.00 0.00 0.00 3.85
1560 1562 6.513556 CGTCTGTACCATCATACCTAGTTCAG 60.514 46.154 0.00 0.00 0.00 3.02
1577 1579 2.349627 CCCGAGATTCGATCGTCTGTAC 60.350 54.545 15.94 3.31 43.74 2.90
1581 1583 1.101635 TGCCCGAGATTCGATCGTCT 61.102 55.000 15.94 11.59 43.74 4.18
1722 1724 1.482593 GACATGACCGGGACAGATCTT 59.517 52.381 6.32 0.00 0.00 2.40
1727 1729 1.182667 TGTAGACATGACCGGGACAG 58.817 55.000 6.32 2.98 0.00 3.51
1732 1734 4.554919 CGAGAACTATGTAGACATGACCGG 60.555 50.000 0.00 0.00 37.15 5.28
1799 1801 8.703336 CGGTACATCAAATCACATAACTCATAG 58.297 37.037 0.00 0.00 0.00 2.23
1875 1878 3.872511 TCTTTACGTCTCGGCCATTTA 57.127 42.857 2.24 0.00 0.00 1.40
1988 1991 2.047769 TTAAGGCCCACTACTTCCCA 57.952 50.000 0.00 0.00 0.00 4.37
2101 2112 0.340208 GGAGGGGAGAAGGAAGGAGA 59.660 60.000 0.00 0.00 0.00 3.71
2102 2113 0.341609 AGGAGGGGAGAAGGAAGGAG 59.658 60.000 0.00 0.00 0.00 3.69
2230 2243 2.125225 GGGGAGGGAAGAGGTGGT 59.875 66.667 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.