Multiple sequence alignment - TraesCS4A01G264100

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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 TraesCS4A01G264100 chr4A 100.000 2711 0 0 1 2711 576577465 576574755 0.000000e+00 5007.0
1 TraesCS4A01G264100 chr4B 91.427 1703 69 32 493 2145 39288825 39290500 0.000000e+00 2265.0
2 TraesCS4A01G264100 chr4B 90.453 419 38 2 2195 2613 39290665 39291081 3.950000e-153 551.0
3 TraesCS4A01G264100 chrUn 91.837 1519 44 36 493 1960 61040620 61039131 0.000000e+00 2045.0
4 TraesCS4A01G264100 chrUn 88.086 512 50 6 2208 2711 61038902 61038394 5.000000e-167 597.0
5 TraesCS4A01G264100 chrUn 93.284 268 14 2 233 499 129564170 129563906 2.530000e-105 392.0
6 TraesCS4A01G264100 chr6A 94.757 267 11 1 230 496 129764946 129765209 1.940000e-111 412.0
7 TraesCS4A01G264100 chr5D 94.382 267 12 1 233 499 141427784 141428047 9.040000e-110 407.0
8 TraesCS4A01G264100 chr5D 97.143 35 1 0 1145 1179 342174903 342174937 2.920000e-05 60.2
9 TraesCS4A01G264100 chr7A 93.657 268 14 2 232 499 682182048 682181784 5.440000e-107 398.0
10 TraesCS4A01G264100 chr4D 93.585 265 14 2 233 497 78773929 78773668 2.530000e-105 392.0
11 TraesCS4A01G264100 chr3A 93.208 265 14 4 233 496 11970548 11970809 1.180000e-103 387.0
12 TraesCS4A01G264100 chr3A 92.565 269 16 2 228 496 65884310 65884046 1.520000e-102 383.0
13 TraesCS4A01G264100 chr3A 93.725 255 12 3 230 483 156231478 156231729 1.970000e-101 379.0
14 TraesCS4A01G264100 chr3A 94.024 251 12 2 233 483 156231733 156231980 7.090000e-101 377.0
15 TraesCS4A01G264100 chr5B 97.143 35 1 0 1145 1179 401667369 401667403 2.920000e-05 60.2
16 TraesCS4A01G264100 chr5A 97.143 35 1 0 1145 1179 443289172 443289206 2.920000e-05 60.2
17 TraesCS4A01G264100 chr1D 97.143 35 1 0 1518 1552 479540932 479540966 2.920000e-05 60.2
18 TraesCS4A01G264100 chr1B 97.143 35 1 0 1518 1552 667750384 667750418 2.920000e-05 60.2
19 TraesCS4A01G264100 chr1A 97.143 35 1 0 1518 1552 575808432 575808466 2.920000e-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 TraesCS4A01G264100 chr4A 576574755 576577465 2710 True 5007 5007 100.0000 1 2711 1 chr4A.!!$R1 2710
1 TraesCS4A01G264100 chr4B 39288825 39291081 2256 False 1408 2265 90.9400 493 2613 2 chr4B.!!$F1 2120
2 TraesCS4A01G264100 chrUn 61038394 61040620 2226 True 1321 2045 89.9615 493 2711 2 chrUn.!!$R2 2218
3 TraesCS4A01G264100 chr3A 156231478 156231980 502 False 378 379 93.8745 230 483 2 chr3A.!!$F2 253

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
95 96 0.036388 AATCGGGCGATCTGTTGTGT 60.036 50.0 0.0 0.0 33.08 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1809 1961 0.672401 GTCAAGAATCAACCGGCCGA 60.672 55.0 30.73 6.75 0.0 5.54 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
22 23 5.627499 TTGAAGAATCGTGAAGGAATTGG 57.373 39.130 0.00 0.00 0.00 3.16
23 24 4.905429 TGAAGAATCGTGAAGGAATTGGA 58.095 39.130 0.00 0.00 0.00 3.53
24 25 4.937620 TGAAGAATCGTGAAGGAATTGGAG 59.062 41.667 0.00 0.00 0.00 3.86
25 26 4.826274 AGAATCGTGAAGGAATTGGAGA 57.174 40.909 0.00 0.00 0.00 3.71
26 27 5.365021 AGAATCGTGAAGGAATTGGAGAT 57.635 39.130 0.00 0.00 0.00 2.75
27 28 5.363939 AGAATCGTGAAGGAATTGGAGATC 58.636 41.667 0.00 0.00 0.00 2.75
28 29 4.760530 ATCGTGAAGGAATTGGAGATCA 57.239 40.909 0.00 0.00 0.00 2.92
29 30 3.861840 TCGTGAAGGAATTGGAGATCAC 58.138 45.455 0.00 0.00 35.13 3.06
30 31 3.260632 TCGTGAAGGAATTGGAGATCACA 59.739 43.478 0.00 0.00 37.59 3.58
31 32 4.002982 CGTGAAGGAATTGGAGATCACAA 58.997 43.478 5.48 5.48 37.59 3.33
32 33 4.455533 CGTGAAGGAATTGGAGATCACAAA 59.544 41.667 6.90 0.00 37.59 2.83
33 34 5.048782 CGTGAAGGAATTGGAGATCACAAAA 60.049 40.000 6.90 0.00 37.59 2.44
34 35 6.514870 CGTGAAGGAATTGGAGATCACAAAAA 60.515 38.462 6.90 0.00 37.59 1.94
81 82 9.993454 ACATATCCAATCATATGATAGAATCGG 57.007 33.333 18.47 11.76 38.54 4.18
82 83 9.433153 CATATCCAATCATATGATAGAATCGGG 57.567 37.037 18.47 11.08 38.54 5.14
83 84 5.674525 TCCAATCATATGATAGAATCGGGC 58.325 41.667 18.47 0.00 33.73 6.13
84 85 4.509230 CCAATCATATGATAGAATCGGGCG 59.491 45.833 18.47 0.00 33.73 6.13
85 86 5.351458 CAATCATATGATAGAATCGGGCGA 58.649 41.667 18.47 0.00 33.73 5.54
86 87 5.798125 ATCATATGATAGAATCGGGCGAT 57.202 39.130 16.75 0.00 32.54 4.58
87 88 5.188327 TCATATGATAGAATCGGGCGATC 57.812 43.478 0.00 0.00 33.08 3.69
88 89 4.889995 TCATATGATAGAATCGGGCGATCT 59.110 41.667 0.00 0.00 33.08 2.75
89 90 3.516981 ATGATAGAATCGGGCGATCTG 57.483 47.619 0.00 0.00 33.08 2.90
90 91 2.239400 TGATAGAATCGGGCGATCTGT 58.761 47.619 0.00 0.00 33.08 3.41
91 92 2.628178 TGATAGAATCGGGCGATCTGTT 59.372 45.455 0.00 0.00 33.08 3.16
92 93 2.509052 TAGAATCGGGCGATCTGTTG 57.491 50.000 0.00 0.00 33.08 3.33
93 94 0.537188 AGAATCGGGCGATCTGTTGT 59.463 50.000 0.00 0.00 33.08 3.32
94 95 0.652592 GAATCGGGCGATCTGTTGTG 59.347 55.000 0.00 0.00 33.08 3.33
95 96 0.036388 AATCGGGCGATCTGTTGTGT 60.036 50.000 0.00 0.00 33.08 3.72
96 97 0.460284 ATCGGGCGATCTGTTGTGTC 60.460 55.000 0.00 0.00 0.00 3.67
97 98 1.079819 CGGGCGATCTGTTGTGTCT 60.080 57.895 0.00 0.00 0.00 3.41
98 99 1.354337 CGGGCGATCTGTTGTGTCTG 61.354 60.000 0.00 0.00 0.00 3.51
99 100 1.639298 GGGCGATCTGTTGTGTCTGC 61.639 60.000 0.00 0.00 0.00 4.26
100 101 0.671781 GGCGATCTGTTGTGTCTGCT 60.672 55.000 0.00 0.00 0.00 4.24
101 102 0.441533 GCGATCTGTTGTGTCTGCTG 59.558 55.000 0.00 0.00 0.00 4.41
102 103 1.936656 GCGATCTGTTGTGTCTGCTGA 60.937 52.381 0.00 0.00 0.00 4.26
103 104 2.407090 CGATCTGTTGTGTCTGCTGAA 58.593 47.619 0.00 0.00 0.00 3.02
104 105 2.998670 CGATCTGTTGTGTCTGCTGAAT 59.001 45.455 0.00 0.00 0.00 2.57
105 106 3.061831 CGATCTGTTGTGTCTGCTGAATC 59.938 47.826 0.00 0.00 0.00 2.52
106 107 2.407090 TCTGTTGTGTCTGCTGAATCG 58.593 47.619 0.00 0.00 0.00 3.34
107 108 0.867746 TGTTGTGTCTGCTGAATCGC 59.132 50.000 0.00 0.00 0.00 4.58
108 109 0.179240 GTTGTGTCTGCTGAATCGCG 60.179 55.000 0.00 0.00 0.00 5.87
109 110 1.900585 TTGTGTCTGCTGAATCGCGC 61.901 55.000 0.00 0.00 0.00 6.86
110 111 2.097038 GTGTCTGCTGAATCGCGCT 61.097 57.895 5.56 0.00 0.00 5.92
111 112 0.802222 GTGTCTGCTGAATCGCGCTA 60.802 55.000 5.56 0.00 0.00 4.26
112 113 0.526310 TGTCTGCTGAATCGCGCTAG 60.526 55.000 5.56 0.00 0.00 3.42
113 114 1.589993 TCTGCTGAATCGCGCTAGC 60.590 57.895 5.56 4.06 40.74 3.42
125 126 2.963499 CGCTAGCGCAAGAGATTCA 58.037 52.632 26.07 0.00 43.02 2.57
126 127 1.280982 CGCTAGCGCAAGAGATTCAA 58.719 50.000 26.07 0.00 43.02 2.69
127 128 1.257415 CGCTAGCGCAAGAGATTCAAG 59.743 52.381 26.07 0.00 43.02 3.02
128 129 2.544685 GCTAGCGCAAGAGATTCAAGA 58.455 47.619 11.47 0.00 43.02 3.02
129 130 2.932614 GCTAGCGCAAGAGATTCAAGAA 59.067 45.455 11.47 0.00 43.02 2.52
130 131 3.372206 GCTAGCGCAAGAGATTCAAGAAA 59.628 43.478 11.47 0.00 43.02 2.52
131 132 4.034975 GCTAGCGCAAGAGATTCAAGAAAT 59.965 41.667 11.47 0.00 43.02 2.17
132 133 4.352600 AGCGCAAGAGATTCAAGAAATG 57.647 40.909 11.47 0.00 43.02 2.32
133 134 3.755378 AGCGCAAGAGATTCAAGAAATGT 59.245 39.130 11.47 0.00 43.02 2.71
134 135 4.937620 AGCGCAAGAGATTCAAGAAATGTA 59.062 37.500 11.47 0.00 43.02 2.29
135 136 5.024555 GCGCAAGAGATTCAAGAAATGTAC 58.975 41.667 0.30 0.00 43.02 2.90
136 137 5.163814 GCGCAAGAGATTCAAGAAATGTACT 60.164 40.000 0.30 0.00 43.02 2.73
137 138 6.621596 GCGCAAGAGATTCAAGAAATGTACTT 60.622 38.462 0.30 0.00 43.02 2.24
138 139 7.413000 GCGCAAGAGATTCAAGAAATGTACTTA 60.413 37.037 0.30 0.00 43.02 2.24
139 140 8.113062 CGCAAGAGATTCAAGAAATGTACTTAG 58.887 37.037 0.00 0.00 43.02 2.18
140 141 8.940952 GCAAGAGATTCAAGAAATGTACTTAGT 58.059 33.333 0.00 0.00 0.00 2.24
143 144 9.868277 AGAGATTCAAGAAATGTACTTAGTCAG 57.132 33.333 0.00 0.00 0.00 3.51
144 145 8.485976 AGATTCAAGAAATGTACTTAGTCAGC 57.514 34.615 0.00 0.00 0.00 4.26
145 146 8.317679 AGATTCAAGAAATGTACTTAGTCAGCT 58.682 33.333 0.00 0.00 0.00 4.24
146 147 8.854614 ATTCAAGAAATGTACTTAGTCAGCTT 57.145 30.769 0.00 0.00 0.00 3.74
147 148 9.944376 ATTCAAGAAATGTACTTAGTCAGCTTA 57.056 29.630 0.00 0.00 0.00 3.09
148 149 9.944376 TTCAAGAAATGTACTTAGTCAGCTTAT 57.056 29.630 0.00 0.00 0.00 1.73
156 157 9.862371 ATGTACTTAGTCAGCTTATATATGCAC 57.138 33.333 19.48 11.50 0.00 4.57
157 158 8.856103 TGTACTTAGTCAGCTTATATATGCACA 58.144 33.333 19.48 10.46 0.00 4.57
158 159 9.862371 GTACTTAGTCAGCTTATATATGCACAT 57.138 33.333 19.48 7.70 0.00 3.21
163 164 8.768957 AGTCAGCTTATATATGCACATTACAG 57.231 34.615 19.48 0.00 0.00 2.74
164 165 8.370940 AGTCAGCTTATATATGCACATTACAGT 58.629 33.333 19.48 0.00 0.00 3.55
165 166 8.993121 GTCAGCTTATATATGCACATTACAGTT 58.007 33.333 19.48 0.00 0.00 3.16
175 176 9.840427 ATATGCACATTACAGTTAGTTTTCAAC 57.160 29.630 0.00 0.00 0.00 3.18
176 177 7.089770 TGCACATTACAGTTAGTTTTCAACA 57.910 32.000 0.00 0.00 0.00 3.33
177 178 6.970043 TGCACATTACAGTTAGTTTTCAACAC 59.030 34.615 0.00 0.00 0.00 3.32
178 179 6.970043 GCACATTACAGTTAGTTTTCAACACA 59.030 34.615 0.00 0.00 0.00 3.72
179 180 7.486551 GCACATTACAGTTAGTTTTCAACACAA 59.513 33.333 0.00 0.00 0.00 3.33
180 181 9.515020 CACATTACAGTTAGTTTTCAACACAAT 57.485 29.630 0.00 0.00 0.00 2.71
181 182 9.515020 ACATTACAGTTAGTTTTCAACACAATG 57.485 29.630 0.00 0.00 32.58 2.82
182 183 7.979115 TTACAGTTAGTTTTCAACACAATGC 57.021 32.000 0.00 0.00 0.00 3.56
183 184 5.960113 ACAGTTAGTTTTCAACACAATGCA 58.040 33.333 0.00 0.00 0.00 3.96
184 185 6.572519 ACAGTTAGTTTTCAACACAATGCAT 58.427 32.000 0.00 0.00 0.00 3.96
185 186 7.041107 ACAGTTAGTTTTCAACACAATGCATT 58.959 30.769 5.99 5.99 0.00 3.56
186 187 7.222611 ACAGTTAGTTTTCAACACAATGCATTC 59.777 33.333 9.53 0.00 0.00 2.67
187 188 6.417635 AGTTAGTTTTCAACACAATGCATTCG 59.582 34.615 9.53 6.39 0.00 3.34
188 189 4.681744 AGTTTTCAACACAATGCATTCGT 58.318 34.783 9.53 7.09 0.00 3.85
189 190 4.503734 AGTTTTCAACACAATGCATTCGTG 59.496 37.500 26.53 26.53 36.70 4.35
190 191 3.978718 TTCAACACAATGCATTCGTGA 57.021 38.095 31.08 20.29 34.69 4.35
191 192 3.978718 TCAACACAATGCATTCGTGAA 57.021 38.095 31.08 20.00 34.69 3.18
192 193 3.887741 TCAACACAATGCATTCGTGAAG 58.112 40.909 31.08 24.65 34.69 3.02
193 194 3.314913 TCAACACAATGCATTCGTGAAGT 59.685 39.130 31.08 16.66 34.69 3.01
194 195 3.988379 ACACAATGCATTCGTGAAGTT 57.012 38.095 31.08 16.67 34.69 2.66
195 196 5.008118 TCAACACAATGCATTCGTGAAGTTA 59.992 36.000 31.08 17.36 34.69 2.24
196 197 4.783242 ACACAATGCATTCGTGAAGTTAC 58.217 39.130 31.08 0.00 34.69 2.50
197 198 4.274705 ACACAATGCATTCGTGAAGTTACA 59.725 37.500 31.08 0.00 34.69 2.41
198 199 5.048782 ACACAATGCATTCGTGAAGTTACAT 60.049 36.000 31.08 14.98 34.69 2.29
199 200 5.858049 CACAATGCATTCGTGAAGTTACATT 59.142 36.000 25.23 0.00 32.23 2.71
200 201 6.363088 CACAATGCATTCGTGAAGTTACATTT 59.637 34.615 25.23 0.00 32.23 2.32
201 202 6.363088 ACAATGCATTCGTGAAGTTACATTTG 59.637 34.615 9.53 0.00 0.00 2.32
202 203 5.431420 TGCATTCGTGAAGTTACATTTGT 57.569 34.783 0.00 0.00 0.00 2.83
203 204 5.826586 TGCATTCGTGAAGTTACATTTGTT 58.173 33.333 0.00 0.00 0.00 2.83
204 205 6.269315 TGCATTCGTGAAGTTACATTTGTTT 58.731 32.000 0.00 0.00 0.00 2.83
205 206 7.418408 TGCATTCGTGAAGTTACATTTGTTTA 58.582 30.769 0.00 0.00 0.00 2.01
206 207 8.079203 TGCATTCGTGAAGTTACATTTGTTTAT 58.921 29.630 0.00 0.00 0.00 1.40
207 208 8.365210 GCATTCGTGAAGTTACATTTGTTTATG 58.635 33.333 0.00 0.00 0.00 1.90
208 209 9.393249 CATTCGTGAAGTTACATTTGTTTATGT 57.607 29.630 0.00 0.00 41.43 2.29
221 222 9.709495 ACATTTGTTTATGTATCATGCTTTTGT 57.291 25.926 0.00 0.00 36.99 2.83
222 223 9.961266 CATTTGTTTATGTATCATGCTTTTGTG 57.039 29.630 0.00 0.00 0.00 3.33
223 224 9.709495 ATTTGTTTATGTATCATGCTTTTGTGT 57.291 25.926 0.00 0.00 0.00 3.72
242 243 4.400251 TGTGTATACAAAGTACTCCCTCCG 59.600 45.833 7.25 0.00 32.88 4.63
298 299 4.642429 AGTCAAGCCTCGTAAAGTTTGAT 58.358 39.130 0.00 0.00 32.56 2.57
302 303 5.705441 TCAAGCCTCGTAAAGTTTGATCAAT 59.295 36.000 9.40 0.00 0.00 2.57
366 367 2.486918 CATCAGTAGATGCGGCATGAA 58.513 47.619 21.98 4.89 44.61 2.57
371 372 5.122519 TCAGTAGATGCGGCATGAATTAAA 58.877 37.500 21.98 0.00 0.00 1.52
378 379 5.776519 TGCGGCATGAATTAAATTTTCAC 57.223 34.783 0.00 0.00 36.02 3.18
490 491 5.964958 TGCAGAGTAAAAAGGATCAAAGG 57.035 39.130 0.00 0.00 0.00 3.11
491 492 4.766891 TGCAGAGTAAAAAGGATCAAAGGG 59.233 41.667 0.00 0.00 0.00 3.95
717 805 3.951306 TGCAAGAATCAAGAACAACACG 58.049 40.909 0.00 0.00 0.00 4.49
764 852 3.825160 GAACTGCCGAGCCACCACA 62.825 63.158 0.00 0.00 0.00 4.17
768 856 2.904866 GCCGAGCCACCACAACAA 60.905 61.111 0.00 0.00 0.00 2.83
769 857 2.908073 GCCGAGCCACCACAACAAG 61.908 63.158 0.00 0.00 0.00 3.16
770 858 2.639286 CGAGCCACCACAACAAGC 59.361 61.111 0.00 0.00 0.00 4.01
771 859 1.893808 CGAGCCACCACAACAAGCT 60.894 57.895 0.00 0.00 36.25 3.74
772 860 1.447317 CGAGCCACCACAACAAGCTT 61.447 55.000 0.00 0.00 32.97 3.74
773 861 0.746659 GAGCCACCACAACAAGCTTT 59.253 50.000 0.00 0.00 32.97 3.51
774 862 0.461135 AGCCACCACAACAAGCTTTG 59.539 50.000 0.00 0.00 0.00 2.77
819 914 2.330216 ACCAGCAGTACTTCTTCCACT 58.670 47.619 0.00 0.00 0.00 4.00
820 915 3.507411 ACCAGCAGTACTTCTTCCACTA 58.493 45.455 0.00 0.00 0.00 2.74
821 916 3.258622 ACCAGCAGTACTTCTTCCACTAC 59.741 47.826 0.00 0.00 0.00 2.73
828 923 4.643784 AGTACTTCTTCCACTACATACCCG 59.356 45.833 0.00 0.00 0.00 5.28
903 998 1.120530 ACGGGCCACATAGTAGAAGG 58.879 55.000 4.39 0.00 0.00 3.46
930 1025 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
943 1038 4.078922 AGAGAGAGAGAGAGAGAGAGAGGA 60.079 50.000 0.00 0.00 0.00 3.71
945 1040 2.703007 AGAGAGAGAGAGAGAGAGGAGC 59.297 54.545 0.00 0.00 0.00 4.70
946 1041 2.435805 GAGAGAGAGAGAGAGAGGAGCA 59.564 54.545 0.00 0.00 0.00 4.26
952 1081 0.829990 GAGAGAGAGGAGCAAAGGGG 59.170 60.000 0.00 0.00 0.00 4.79
1179 1315 3.353836 CACCGCAACTTCCACCGG 61.354 66.667 0.00 0.00 45.80 5.28
1389 1537 2.280592 ACGCGGACCAAGTTCACC 60.281 61.111 12.47 0.00 0.00 4.02
1689 1837 1.376942 GGACGACGAGGAGGTGAGA 60.377 63.158 0.00 0.00 0.00 3.27
1711 1859 0.580578 CAGCGAGATGTGCATGTAGC 59.419 55.000 6.36 6.36 45.96 3.58
1770 1922 4.691216 GCTAGGCTGGGATAATTTAACTCG 59.309 45.833 0.00 0.00 0.00 4.18
1776 1928 6.238402 GGCTGGGATAATTTAACTCGTTCTTC 60.238 42.308 0.00 0.00 0.00 2.87
1783 1935 4.966850 TTTAACTCGTTCTTCTTCGCTG 57.033 40.909 0.00 0.00 0.00 5.18
1830 1982 0.953960 GGCCGGTTGATTCTTGACGT 60.954 55.000 1.90 0.00 0.00 4.34
1831 1983 0.872388 GCCGGTTGATTCTTGACGTT 59.128 50.000 1.90 0.00 0.00 3.99
1832 1984 1.399727 GCCGGTTGATTCTTGACGTTG 60.400 52.381 1.90 0.00 0.00 4.10
1833 1985 2.139917 CCGGTTGATTCTTGACGTTGA 58.860 47.619 0.00 0.00 0.00 3.18
1834 1986 2.157668 CCGGTTGATTCTTGACGTTGAG 59.842 50.000 0.00 0.00 0.00 3.02
1835 1987 3.057019 CGGTTGATTCTTGACGTTGAGA 58.943 45.455 0.00 0.00 0.00 3.27
1836 1988 3.679980 CGGTTGATTCTTGACGTTGAGAT 59.320 43.478 0.00 0.00 0.00 2.75
1837 1989 4.152402 CGGTTGATTCTTGACGTTGAGATT 59.848 41.667 0.00 0.00 0.00 2.40
1838 1990 5.347635 CGGTTGATTCTTGACGTTGAGATTA 59.652 40.000 0.00 0.00 0.00 1.75
1858 2010 9.478019 GAGATTAATTGTGTTTAACAGTGATCG 57.522 33.333 0.00 0.00 40.74 3.69
1859 2011 9.214957 AGATTAATTGTGTTTAACAGTGATCGA 57.785 29.630 0.00 0.00 40.74 3.59
1860 2012 9.988350 GATTAATTGTGTTTAACAGTGATCGAT 57.012 29.630 0.00 0.00 40.74 3.59
1861 2013 9.988350 ATTAATTGTGTTTAACAGTGATCGATC 57.012 29.630 18.72 18.72 40.74 3.69
1871 2023 5.798125 ACAGTGATCGATCCTAATGATGT 57.202 39.130 22.31 12.57 32.41 3.06
1881 2033 8.153479 TCGATCCTAATGATGTGTTATTTTGG 57.847 34.615 0.00 0.00 32.41 3.28
1883 2035 9.051679 CGATCCTAATGATGTGTTATTTTGGTA 57.948 33.333 0.00 0.00 32.41 3.25
1937 2089 2.338500 GAGGCTCGTGTCTTTACTTGG 58.662 52.381 0.00 0.00 0.00 3.61
1938 2090 1.692519 AGGCTCGTGTCTTTACTTGGT 59.307 47.619 0.00 0.00 0.00 3.67
1939 2091 2.895404 AGGCTCGTGTCTTTACTTGGTA 59.105 45.455 0.00 0.00 0.00 3.25
1957 2109 6.655003 ACTTGGTATACTTGATTGTCCACTTG 59.345 38.462 2.25 0.00 0.00 3.16
1969 2152 4.987408 TGTCCACTTGAAATGCATATGG 57.013 40.909 0.00 1.75 34.64 2.74
1970 2153 3.700539 TGTCCACTTGAAATGCATATGGG 59.299 43.478 0.00 0.00 34.29 4.00
1971 2154 2.694628 TCCACTTGAAATGCATATGGGC 59.305 45.455 0.00 0.00 34.29 5.36
1977 2171 5.834742 ACTTGAAATGCATATGGGCTATGAA 59.165 36.000 0.00 0.00 39.79 2.57
1978 2172 5.710513 TGAAATGCATATGGGCTATGAAC 57.289 39.130 0.00 0.00 39.79 3.18
1979 2173 5.387788 TGAAATGCATATGGGCTATGAACT 58.612 37.500 0.00 0.00 39.79 3.01
2009 2203 4.049546 TGAGCCATGCATGCTTAATTTC 57.950 40.909 21.69 10.01 39.69 2.17
2027 2221 9.626045 CTTAATTTCCCTTTGCACTTAGTTTAG 57.374 33.333 0.00 0.00 0.00 1.85
2036 2230 6.486253 TTGCACTTAGTTTAGCTTGATCTG 57.514 37.500 0.00 0.00 0.00 2.90
2100 2299 2.777832 ACTTGCTTGAGAAGGCTAGG 57.222 50.000 0.00 0.00 36.08 3.02
2112 2311 1.223763 GGCTAGGTTGCCCCACTAC 59.776 63.158 0.00 0.00 46.82 2.73
2127 2326 2.419297 CCACTACACTCCTCTGAATGGC 60.419 54.545 0.00 0.00 0.00 4.40
2150 2349 5.605327 CGGGACTCGCAATAAAAATATACG 58.395 41.667 0.00 0.00 0.00 3.06
2151 2350 5.176223 CGGGACTCGCAATAAAAATATACGT 59.824 40.000 0.00 0.00 0.00 3.57
2152 2351 6.363088 CGGGACTCGCAATAAAAATATACGTA 59.637 38.462 0.00 0.00 0.00 3.57
2153 2352 7.504818 GGGACTCGCAATAAAAATATACGTAC 58.495 38.462 0.00 0.00 0.00 3.67
2154 2353 7.383300 GGGACTCGCAATAAAAATATACGTACT 59.617 37.037 0.00 0.00 0.00 2.73
2155 2354 8.423215 GGACTCGCAATAAAAATATACGTACTC 58.577 37.037 0.00 0.00 0.00 2.59
2156 2355 8.290663 ACTCGCAATAAAAATATACGTACTCC 57.709 34.615 0.00 0.00 0.00 3.85
2157 2356 7.383300 ACTCGCAATAAAAATATACGTACTCCC 59.617 37.037 0.00 0.00 0.00 4.30
2158 2357 7.436118 TCGCAATAAAAATATACGTACTCCCT 58.564 34.615 0.00 0.00 0.00 4.20
2159 2358 7.927629 TCGCAATAAAAATATACGTACTCCCTT 59.072 33.333 0.00 0.00 0.00 3.95
2160 2359 8.553696 CGCAATAAAAATATACGTACTCCCTTT 58.446 33.333 0.00 0.00 0.00 3.11
2161 2360 9.874215 GCAATAAAAATATACGTACTCCCTTTC 57.126 33.333 0.00 0.00 0.00 2.62
2165 2364 8.585189 AAAAATATACGTACTCCCTTTCGATC 57.415 34.615 0.00 0.00 0.00 3.69
2166 2365 5.893897 ATATACGTACTCCCTTTCGATCC 57.106 43.478 0.00 0.00 0.00 3.36
2169 2457 3.559069 ACGTACTCCCTTTCGATCCATA 58.441 45.455 0.00 0.00 0.00 2.74
2174 2462 3.325135 ACTCCCTTTCGATCCATACATCC 59.675 47.826 0.00 0.00 0.00 3.51
2175 2463 3.313791 TCCCTTTCGATCCATACATCCA 58.686 45.455 0.00 0.00 0.00 3.41
2184 2472 2.221169 TCCATACATCCATTTGAGCGC 58.779 47.619 0.00 0.00 0.00 5.92
2198 2486 3.111853 TGAGCGCCAAGTAATATGGAG 57.888 47.619 2.29 0.00 40.56 3.86
2201 2489 0.512952 CGCCAAGTAATATGGAGCGC 59.487 55.000 0.00 0.00 40.56 5.92
2227 2542 8.660435 CAGGGAGTATATGATTTTCCTTTCCTA 58.340 37.037 0.00 0.00 0.00 2.94
2250 2568 7.557719 CCTATGGAGTATTTGGTTCAGAACAAT 59.442 37.037 15.36 9.39 0.00 2.71
2401 2722 5.507650 CGGTCCAAGATAGGAAGTACTAAGC 60.508 48.000 0.00 0.00 39.92 3.09
2409 2730 2.576191 AGGAAGTACTAAGCCATGGCAA 59.424 45.455 37.18 23.65 44.88 4.52
2431 2752 6.366061 GCAATTTATTCCTGTGTTCCAAAGAC 59.634 38.462 0.00 0.00 0.00 3.01
2445 2766 1.734465 CAAAGACGCTGAGGGTTCATC 59.266 52.381 2.97 0.00 31.68 2.92
2473 2794 6.455360 TTTAATCCATTCTGATGAGCCAAC 57.545 37.500 0.00 0.00 35.16 3.77
2539 2860 2.683211 ATCTTTCAAACAGCCAGGGT 57.317 45.000 0.00 0.00 0.00 4.34
2550 2871 2.237392 ACAGCCAGGGTTATCACTTCTC 59.763 50.000 0.00 0.00 0.00 2.87
2598 2919 4.034410 GGTCCTCTTTTGGTCTCCTATCT 58.966 47.826 0.00 0.00 0.00 1.98
2603 2924 6.098982 TCCTCTTTTGGTCTCCTATCTCATTC 59.901 42.308 0.00 0.00 0.00 2.67
2617 2938 8.293157 TCCTATCTCATTCGATCGATAATATGC 58.707 37.037 20.18 0.00 0.00 3.14
2619 2940 5.273944 TCTCATTCGATCGATAATATGCGG 58.726 41.667 20.18 14.08 0.00 5.69
2620 2941 3.796717 TCATTCGATCGATAATATGCGGC 59.203 43.478 20.18 0.00 0.00 6.53
2622 2943 2.526077 TCGATCGATAATATGCGGCAC 58.474 47.619 15.15 0.00 0.00 5.01
2643 2964 7.803189 CGGCACCTGCAATTTTTACTTATATAG 59.197 37.037 0.00 0.00 44.36 1.31
2644 2965 8.082242 GGCACCTGCAATTTTTACTTATATAGG 58.918 37.037 0.00 0.00 44.36 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.312895 TCCAATTCCTTCACGATTCTTCAA 58.687 37.500 0.00 0.00 0.00 2.69
1 2 4.905429 TCCAATTCCTTCACGATTCTTCA 58.095 39.130 0.00 0.00 0.00 3.02
4 5 4.826274 TCTCCAATTCCTTCACGATTCT 57.174 40.909 0.00 0.00 0.00 2.40
5 6 5.007136 GTGATCTCCAATTCCTTCACGATTC 59.993 44.000 0.00 0.00 0.00 2.52
6 7 4.878397 GTGATCTCCAATTCCTTCACGATT 59.122 41.667 0.00 0.00 0.00 3.34
7 8 4.080919 TGTGATCTCCAATTCCTTCACGAT 60.081 41.667 0.00 0.00 37.01 3.73
8 9 3.260632 TGTGATCTCCAATTCCTTCACGA 59.739 43.478 0.00 0.00 37.01 4.35
9 10 3.599343 TGTGATCTCCAATTCCTTCACG 58.401 45.455 0.00 0.00 37.01 4.35
10 11 5.964958 TTTGTGATCTCCAATTCCTTCAC 57.035 39.130 0.00 0.00 35.27 3.18
11 12 6.975196 TTTTTGTGATCTCCAATTCCTTCA 57.025 33.333 0.00 0.00 0.00 3.02
55 56 9.993454 CCGATTCTATCATATGATTGGATATGT 57.007 33.333 22.84 1.52 37.51 2.29
56 57 9.433153 CCCGATTCTATCATATGATTGGATATG 57.567 37.037 22.84 15.37 37.57 1.78
57 58 8.099537 GCCCGATTCTATCATATGATTGGATAT 58.900 37.037 22.84 14.21 36.05 1.63
58 59 7.445121 GCCCGATTCTATCATATGATTGGATA 58.555 38.462 22.84 10.65 36.05 2.59
59 60 6.294473 GCCCGATTCTATCATATGATTGGAT 58.706 40.000 22.84 20.01 36.05 3.41
60 61 5.674525 GCCCGATTCTATCATATGATTGGA 58.325 41.667 22.84 16.19 36.05 3.53
61 62 4.509230 CGCCCGATTCTATCATATGATTGG 59.491 45.833 22.84 15.58 36.05 3.16
62 63 5.351458 TCGCCCGATTCTATCATATGATTG 58.649 41.667 22.84 20.10 36.05 2.67
63 64 5.598416 TCGCCCGATTCTATCATATGATT 57.402 39.130 22.84 5.42 36.05 2.57
64 65 5.538053 AGATCGCCCGATTCTATCATATGAT 59.462 40.000 21.50 21.50 35.40 2.45
65 66 4.889995 AGATCGCCCGATTCTATCATATGA 59.110 41.667 8.10 8.10 34.60 2.15
66 67 4.981054 CAGATCGCCCGATTCTATCATATG 59.019 45.833 4.53 0.00 34.60 1.78
67 68 4.646945 ACAGATCGCCCGATTCTATCATAT 59.353 41.667 4.53 0.00 34.60 1.78
68 69 4.017126 ACAGATCGCCCGATTCTATCATA 58.983 43.478 4.53 0.00 34.60 2.15
69 70 2.828520 ACAGATCGCCCGATTCTATCAT 59.171 45.455 4.53 0.00 34.60 2.45
70 71 2.239400 ACAGATCGCCCGATTCTATCA 58.761 47.619 4.53 0.00 34.60 2.15
71 72 2.989840 CAACAGATCGCCCGATTCTATC 59.010 50.000 4.53 0.00 34.60 2.08
72 73 2.365617 ACAACAGATCGCCCGATTCTAT 59.634 45.455 4.53 0.00 34.60 1.98
73 74 1.754803 ACAACAGATCGCCCGATTCTA 59.245 47.619 4.53 0.00 34.60 2.10
74 75 0.537188 ACAACAGATCGCCCGATTCT 59.463 50.000 4.53 1.50 34.60 2.40
75 76 0.652592 CACAACAGATCGCCCGATTC 59.347 55.000 4.53 0.00 34.60 2.52
76 77 0.036388 ACACAACAGATCGCCCGATT 60.036 50.000 4.53 0.00 34.60 3.34
77 78 0.460284 GACACAACAGATCGCCCGAT 60.460 55.000 2.39 2.39 37.59 4.18
78 79 1.080093 GACACAACAGATCGCCCGA 60.080 57.895 0.00 0.00 0.00 5.14
79 80 1.079819 AGACACAACAGATCGCCCG 60.080 57.895 0.00 0.00 0.00 6.13
80 81 1.639298 GCAGACACAACAGATCGCCC 61.639 60.000 0.00 0.00 0.00 6.13
81 82 0.671781 AGCAGACACAACAGATCGCC 60.672 55.000 0.00 0.00 0.00 5.54
82 83 0.441533 CAGCAGACACAACAGATCGC 59.558 55.000 0.00 0.00 0.00 4.58
83 84 2.070262 TCAGCAGACACAACAGATCG 57.930 50.000 0.00 0.00 0.00 3.69
84 85 3.061831 CGATTCAGCAGACACAACAGATC 59.938 47.826 0.00 0.00 0.00 2.75
85 86 2.998670 CGATTCAGCAGACACAACAGAT 59.001 45.455 0.00 0.00 0.00 2.90
86 87 2.407090 CGATTCAGCAGACACAACAGA 58.593 47.619 0.00 0.00 0.00 3.41
87 88 1.136141 GCGATTCAGCAGACACAACAG 60.136 52.381 0.00 0.00 37.05 3.16
88 89 0.867746 GCGATTCAGCAGACACAACA 59.132 50.000 0.00 0.00 37.05 3.33
89 90 0.179240 CGCGATTCAGCAGACACAAC 60.179 55.000 0.00 0.00 36.85 3.32
90 91 1.900585 GCGCGATTCAGCAGACACAA 61.901 55.000 12.10 0.00 36.85 3.33
91 92 2.382746 GCGCGATTCAGCAGACACA 61.383 57.895 12.10 0.00 36.85 3.72
92 93 0.802222 TAGCGCGATTCAGCAGACAC 60.802 55.000 12.10 0.00 36.85 3.67
93 94 0.526310 CTAGCGCGATTCAGCAGACA 60.526 55.000 12.10 0.00 36.85 3.41
94 95 1.816214 GCTAGCGCGATTCAGCAGAC 61.816 60.000 12.10 0.00 36.85 3.51
95 96 1.589993 GCTAGCGCGATTCAGCAGA 60.590 57.895 12.10 0.00 36.85 4.26
96 97 2.926855 GCTAGCGCGATTCAGCAG 59.073 61.111 12.10 0.00 36.85 4.24
108 109 2.544685 TCTTGAATCTCTTGCGCTAGC 58.455 47.619 14.31 4.06 45.41 3.42
109 110 5.064452 ACATTTCTTGAATCTCTTGCGCTAG 59.936 40.000 12.92 12.92 0.00 3.42
110 111 4.937620 ACATTTCTTGAATCTCTTGCGCTA 59.062 37.500 9.73 0.00 0.00 4.26
111 112 3.755378 ACATTTCTTGAATCTCTTGCGCT 59.245 39.130 9.73 0.00 0.00 5.92
112 113 4.088823 ACATTTCTTGAATCTCTTGCGC 57.911 40.909 0.00 0.00 0.00 6.09
113 114 6.414408 AGTACATTTCTTGAATCTCTTGCG 57.586 37.500 0.00 0.00 0.00 4.85
114 115 8.940952 ACTAAGTACATTTCTTGAATCTCTTGC 58.059 33.333 0.00 0.00 0.00 4.01
117 118 9.868277 CTGACTAAGTACATTTCTTGAATCTCT 57.132 33.333 0.00 0.00 0.00 3.10
118 119 8.599774 GCTGACTAAGTACATTTCTTGAATCTC 58.400 37.037 0.00 0.00 0.00 2.75
119 120 8.317679 AGCTGACTAAGTACATTTCTTGAATCT 58.682 33.333 0.00 0.00 0.00 2.40
120 121 8.485976 AGCTGACTAAGTACATTTCTTGAATC 57.514 34.615 0.00 0.00 0.00 2.52
121 122 8.854614 AAGCTGACTAAGTACATTTCTTGAAT 57.145 30.769 0.00 0.00 0.00 2.57
122 123 9.944376 ATAAGCTGACTAAGTACATTTCTTGAA 57.056 29.630 0.00 0.00 0.00 2.69
130 131 9.862371 GTGCATATATAAGCTGACTAAGTACAT 57.138 33.333 10.99 0.00 0.00 2.29
131 132 8.856103 TGTGCATATATAAGCTGACTAAGTACA 58.144 33.333 10.99 1.65 0.00 2.90
132 133 9.862371 ATGTGCATATATAAGCTGACTAAGTAC 57.138 33.333 10.99 0.00 0.00 2.73
137 138 9.860898 CTGTAATGTGCATATATAAGCTGACTA 57.139 33.333 10.99 0.00 0.00 2.59
138 139 8.370940 ACTGTAATGTGCATATATAAGCTGACT 58.629 33.333 10.99 0.00 0.00 3.41
139 140 8.539770 ACTGTAATGTGCATATATAAGCTGAC 57.460 34.615 10.99 3.08 0.00 3.51
149 150 9.840427 GTTGAAAACTAACTGTAATGTGCATAT 57.160 29.630 0.00 0.00 45.32 1.78
168 169 4.676546 TCACGAATGCATTGTGTTGAAAA 58.323 34.783 26.68 13.71 35.20 2.29
169 170 4.298744 TCACGAATGCATTGTGTTGAAA 57.701 36.364 26.68 14.18 35.20 2.69
170 171 3.978718 TCACGAATGCATTGTGTTGAA 57.021 38.095 26.68 14.43 35.20 2.69
171 172 3.314913 ACTTCACGAATGCATTGTGTTGA 59.685 39.130 26.68 17.31 35.20 3.18
172 173 3.631144 ACTTCACGAATGCATTGTGTTG 58.369 40.909 26.68 23.12 35.20 3.33
173 174 3.988379 ACTTCACGAATGCATTGTGTT 57.012 38.095 26.68 16.81 35.20 3.32
174 175 3.988379 AACTTCACGAATGCATTGTGT 57.012 38.095 26.68 19.08 35.20 3.72
175 176 4.782156 TGTAACTTCACGAATGCATTGTG 58.218 39.130 18.59 22.34 34.96 3.33
176 177 5.627499 ATGTAACTTCACGAATGCATTGT 57.373 34.783 18.59 12.29 0.00 2.71
177 178 6.363088 ACAAATGTAACTTCACGAATGCATTG 59.637 34.615 18.59 11.63 0.00 2.82
178 179 6.446318 ACAAATGTAACTTCACGAATGCATT 58.554 32.000 12.83 12.83 0.00 3.56
179 180 6.012658 ACAAATGTAACTTCACGAATGCAT 57.987 33.333 0.00 0.00 0.00 3.96
180 181 5.431420 ACAAATGTAACTTCACGAATGCA 57.569 34.783 0.00 0.00 0.00 3.96
181 182 6.747659 AAACAAATGTAACTTCACGAATGC 57.252 33.333 0.00 0.00 0.00 3.56
182 183 9.393249 ACATAAACAAATGTAACTTCACGAATG 57.607 29.630 0.00 0.00 38.31 2.67
195 196 9.709495 ACAAAAGCATGATACATAAACAAATGT 57.291 25.926 0.00 0.00 42.62 2.71
196 197 9.961266 CACAAAAGCATGATACATAAACAAATG 57.039 29.630 0.00 0.00 0.00 2.32
197 198 9.709495 ACACAAAAGCATGATACATAAACAAAT 57.291 25.926 0.00 0.00 0.00 2.32
218 219 5.105635 CGGAGGGAGTACTTTGTATACACAA 60.106 44.000 4.68 3.04 42.93 3.33
219 220 4.400251 CGGAGGGAGTACTTTGTATACACA 59.600 45.833 4.68 0.00 0.00 3.72
220 221 4.929781 CGGAGGGAGTACTTTGTATACAC 58.070 47.826 4.68 0.00 0.00 2.90
242 243 7.781548 TCTTATATGCGAACTAAAAAGGACC 57.218 36.000 0.00 0.00 0.00 4.46
274 275 4.510340 TCAAACTTTACGAGGCTTGACTTC 59.490 41.667 9.20 0.00 30.70 3.01
483 484 3.719268 TGTGCATGTACTCCCTTTGAT 57.281 42.857 15.25 0.00 0.00 2.57
485 486 2.684881 GGATGTGCATGTACTCCCTTTG 59.315 50.000 15.25 0.00 0.00 2.77
486 487 2.578021 AGGATGTGCATGTACTCCCTTT 59.422 45.455 20.55 7.42 0.00 3.11
488 489 1.885049 AGGATGTGCATGTACTCCCT 58.115 50.000 20.55 18.93 0.00 4.20
489 490 3.838244 TTAGGATGTGCATGTACTCCC 57.162 47.619 20.55 17.50 0.00 4.30
490 491 5.405571 CGTATTTAGGATGTGCATGTACTCC 59.594 44.000 15.25 17.00 0.00 3.85
491 492 6.144080 GTCGTATTTAGGATGTGCATGTACTC 59.856 42.308 15.25 9.59 0.00 2.59
649 735 1.907255 GGTGTAGGGGTACTGCTTCTT 59.093 52.381 0.00 0.00 32.41 2.52
659 745 1.228337 GCGTTTTGGGTGTAGGGGT 60.228 57.895 0.00 0.00 0.00 4.95
717 805 0.861837 CGAGATGGTAGATTTGCCGC 59.138 55.000 0.00 0.00 0.00 6.53
761 849 3.047796 GAGATGTGCAAAGCTTGTTGTG 58.952 45.455 0.00 0.00 0.00 3.33
764 852 2.035066 GTGGAGATGTGCAAAGCTTGTT 59.965 45.455 0.00 0.00 0.00 2.83
768 856 2.211250 ATGTGGAGATGTGCAAAGCT 57.789 45.000 0.00 0.00 0.00 3.74
769 857 4.357142 CATAATGTGGAGATGTGCAAAGC 58.643 43.478 0.00 0.00 0.00 3.51
770 858 4.097437 AGCATAATGTGGAGATGTGCAAAG 59.903 41.667 0.00 0.00 33.80 2.77
771 859 4.018490 AGCATAATGTGGAGATGTGCAAA 58.982 39.130 0.00 0.00 33.80 3.68
772 860 3.623703 AGCATAATGTGGAGATGTGCAA 58.376 40.909 0.00 0.00 33.80 4.08
773 861 3.286329 AGCATAATGTGGAGATGTGCA 57.714 42.857 0.00 0.00 33.80 4.57
774 862 3.628942 TCAAGCATAATGTGGAGATGTGC 59.371 43.478 0.00 0.00 0.00 4.57
819 914 2.863132 AAGTTTGTGCCGGGTATGTA 57.137 45.000 2.18 0.00 0.00 2.29
820 915 2.224572 TGTAAGTTTGTGCCGGGTATGT 60.225 45.455 2.18 0.00 0.00 2.29
821 916 2.418628 CTGTAAGTTTGTGCCGGGTATG 59.581 50.000 2.18 0.00 0.00 2.39
828 923 1.807142 GAGGAGCTGTAAGTTTGTGCC 59.193 52.381 0.00 0.00 35.30 5.01
903 998 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
930 1025 2.624029 CCCTTTGCTCCTCTCTCTCTCT 60.624 54.545 0.00 0.00 0.00 3.10
943 1038 1.747444 TCTTCCTCTTCCCCTTTGCT 58.253 50.000 0.00 0.00 0.00 3.91
945 1040 4.331108 CTTCTTCTTCCTCTTCCCCTTTG 58.669 47.826 0.00 0.00 0.00 2.77
946 1041 3.332187 CCTTCTTCTTCCTCTTCCCCTTT 59.668 47.826 0.00 0.00 0.00 3.11
952 1081 4.278975 TCTTGCCTTCTTCTTCCTCTTC 57.721 45.455 0.00 0.00 0.00 2.87
1035 1171 0.905337 GGCACTCCCTGTACACCTCT 60.905 60.000 0.00 0.00 0.00 3.69
1689 1837 1.818363 CATGCACATCTCGCTGCCT 60.818 57.895 0.00 0.00 31.97 4.75
1711 1859 4.506886 ACACGTAGGAAGAAGAGAACTG 57.493 45.455 0.00 0.00 0.00 3.16
1715 1863 4.008330 CCACTACACGTAGGAAGAAGAGA 58.992 47.826 8.97 0.00 37.49 3.10
1716 1864 3.128938 CCCACTACACGTAGGAAGAAGAG 59.871 52.174 8.97 0.00 37.49 2.85
1722 1870 2.104967 CCATCCCACTACACGTAGGAA 58.895 52.381 8.97 0.00 36.97 3.36
1770 1922 4.434857 CCGAAGAAATCAGCGAAGAAGAAC 60.435 45.833 0.00 0.00 0.00 3.01
1776 1928 1.078709 TGCCGAAGAAATCAGCGAAG 58.921 50.000 0.00 0.00 33.96 3.79
1809 1961 0.672401 GTCAAGAATCAACCGGCCGA 60.672 55.000 30.73 6.75 0.00 5.54
1810 1962 1.794222 GTCAAGAATCAACCGGCCG 59.206 57.895 21.04 21.04 0.00 6.13
1811 1963 0.953960 ACGTCAAGAATCAACCGGCC 60.954 55.000 0.00 0.00 0.00 6.13
1812 1964 0.872388 AACGTCAAGAATCAACCGGC 59.128 50.000 0.00 0.00 0.00 6.13
1832 1984 9.478019 CGATCACTGTTAAACACAATTAATCTC 57.522 33.333 0.00 0.00 33.87 2.75
1833 1985 9.214957 TCGATCACTGTTAAACACAATTAATCT 57.785 29.630 0.00 0.00 33.87 2.40
1834 1986 9.988350 ATCGATCACTGTTAAACACAATTAATC 57.012 29.630 0.00 0.00 33.87 1.75
1835 1987 9.988350 GATCGATCACTGTTAAACACAATTAAT 57.012 29.630 20.52 0.00 33.87 1.40
1836 1988 8.447833 GGATCGATCACTGTTAAACACAATTAA 58.552 33.333 25.93 0.00 33.87 1.40
1837 1989 7.822334 AGGATCGATCACTGTTAAACACAATTA 59.178 33.333 25.93 0.00 33.87 1.40
1838 1990 6.655003 AGGATCGATCACTGTTAAACACAATT 59.345 34.615 25.93 0.00 33.87 2.32
1890 2042 8.430801 TTTGAGGGTAACAACAAAATCAATTG 57.569 30.769 0.00 0.00 39.10 2.32
1937 2089 7.698130 GCATTTCAAGTGGACAATCAAGTATAC 59.302 37.037 0.00 0.00 0.00 1.47
1938 2090 7.392953 TGCATTTCAAGTGGACAATCAAGTATA 59.607 33.333 0.00 0.00 0.00 1.47
1939 2091 6.209192 TGCATTTCAAGTGGACAATCAAGTAT 59.791 34.615 0.00 0.00 0.00 2.12
1957 2109 5.972107 AGTTCATAGCCCATATGCATTTC 57.028 39.130 3.54 0.00 41.04 2.17
1969 2152 5.467063 GGCTCATTTGTACTAGTTCATAGCC 59.533 44.000 19.90 19.90 38.00 3.93
1970 2153 6.049149 TGGCTCATTTGTACTAGTTCATAGC 58.951 40.000 0.00 8.99 34.56 2.97
1971 2154 7.307632 GCATGGCTCATTTGTACTAGTTCATAG 60.308 40.741 0.00 0.00 37.53 2.23
1977 2171 4.220693 TGCATGGCTCATTTGTACTAGT 57.779 40.909 0.00 0.00 0.00 2.57
1978 2172 4.556104 GCATGCATGGCTCATTTGTACTAG 60.556 45.833 27.34 0.00 0.00 2.57
1979 2173 3.316029 GCATGCATGGCTCATTTGTACTA 59.684 43.478 27.34 0.00 0.00 1.82
2009 2203 4.518970 TCAAGCTAAACTAAGTGCAAAGGG 59.481 41.667 0.00 0.00 0.00 3.95
2027 2221 1.339438 TGAGTCCTTGCCAGATCAAGC 60.339 52.381 0.00 0.00 41.47 4.01
2036 2230 5.415701 TGAATAAACTCAATGAGTCCTTGCC 59.584 40.000 17.02 5.68 42.59 4.52
2100 2299 0.036294 GAGGAGTGTAGTGGGGCAAC 60.036 60.000 0.00 0.00 0.00 4.17
2105 2304 2.169352 CCATTCAGAGGAGTGTAGTGGG 59.831 54.545 0.00 0.00 0.00 4.61
2112 2311 1.153289 CCCGCCATTCAGAGGAGTG 60.153 63.158 0.00 0.00 0.00 3.51
2127 2326 5.176223 ACGTATATTTTTATTGCGAGTCCCG 59.824 40.000 0.00 0.00 42.21 5.14
2139 2338 9.683069 GATCGAAAGGGAGTACGTATATTTTTA 57.317 33.333 0.00 0.00 0.00 1.52
2145 2344 4.717877 TGGATCGAAAGGGAGTACGTATA 58.282 43.478 0.00 0.00 0.00 1.47
2147 2346 3.003394 TGGATCGAAAGGGAGTACGTA 57.997 47.619 0.00 0.00 0.00 3.57
2149 2348 3.317149 TGTATGGATCGAAAGGGAGTACG 59.683 47.826 0.00 0.00 0.00 3.67
2150 2349 4.931661 TGTATGGATCGAAAGGGAGTAC 57.068 45.455 0.00 0.00 0.00 2.73
2151 2350 4.527038 GGATGTATGGATCGAAAGGGAGTA 59.473 45.833 0.00 0.00 0.00 2.59
2152 2351 3.325135 GGATGTATGGATCGAAAGGGAGT 59.675 47.826 0.00 0.00 0.00 3.85
2153 2352 3.324846 TGGATGTATGGATCGAAAGGGAG 59.675 47.826 0.00 0.00 0.00 4.30
2154 2353 3.313791 TGGATGTATGGATCGAAAGGGA 58.686 45.455 0.00 0.00 0.00 4.20
2155 2354 3.769739 TGGATGTATGGATCGAAAGGG 57.230 47.619 0.00 0.00 0.00 3.95
2156 2355 5.764686 TCAAATGGATGTATGGATCGAAAGG 59.235 40.000 0.00 0.00 0.00 3.11
2157 2356 6.567321 GCTCAAATGGATGTATGGATCGAAAG 60.567 42.308 0.00 0.00 0.00 2.62
2158 2357 5.239306 GCTCAAATGGATGTATGGATCGAAA 59.761 40.000 0.00 0.00 0.00 3.46
2159 2358 4.756642 GCTCAAATGGATGTATGGATCGAA 59.243 41.667 0.00 0.00 0.00 3.71
2160 2359 4.318332 GCTCAAATGGATGTATGGATCGA 58.682 43.478 0.00 0.00 0.00 3.59
2161 2360 3.124128 CGCTCAAATGGATGTATGGATCG 59.876 47.826 0.00 0.00 0.00 3.69
2162 2361 3.120060 GCGCTCAAATGGATGTATGGATC 60.120 47.826 0.00 0.00 0.00 3.36
2163 2362 2.816087 GCGCTCAAATGGATGTATGGAT 59.184 45.455 0.00 0.00 0.00 3.41
2164 2363 2.221169 GCGCTCAAATGGATGTATGGA 58.779 47.619 0.00 0.00 0.00 3.41
2165 2364 1.267806 GGCGCTCAAATGGATGTATGG 59.732 52.381 7.64 0.00 0.00 2.74
2166 2365 1.948834 TGGCGCTCAAATGGATGTATG 59.051 47.619 7.64 0.00 0.00 2.39
2169 2457 0.813184 CTTGGCGCTCAAATGGATGT 59.187 50.000 7.64 0.00 34.56 3.06
2174 2462 4.275689 TCCATATTACTTGGCGCTCAAATG 59.724 41.667 7.64 9.72 34.56 2.32
2175 2463 4.460263 TCCATATTACTTGGCGCTCAAAT 58.540 39.130 7.64 2.29 34.56 2.32
2184 2472 2.146342 CCTGCGCTCCATATTACTTGG 58.854 52.381 9.73 0.00 35.45 3.61
2198 2486 3.437049 GGAAAATCATATACTCCCTGCGC 59.563 47.826 0.00 0.00 0.00 6.09
2201 2489 7.521669 AGGAAAGGAAAATCATATACTCCCTG 58.478 38.462 0.00 0.00 0.00 4.45
2227 2542 7.451255 TCAATTGTTCTGAACCAAATACTCCAT 59.549 33.333 17.26 0.00 0.00 3.41
2250 2568 9.927668 GGAGAATAATGAATTTTGGAAGTTCAA 57.072 29.630 5.01 0.00 35.70 2.69
2271 2589 9.798994 GAAAATCTGAATTAGTACGTAGGAGAA 57.201 33.333 0.00 0.00 0.00 2.87
2273 2591 9.804758 AAGAAAATCTGAATTAGTACGTAGGAG 57.195 33.333 0.00 0.00 0.00 3.69
2375 2696 4.607239 AGTACTTCCTATCTTGGACCGAA 58.393 43.478 0.00 0.00 35.58 4.30
2401 2722 4.741321 ACACAGGAATAAATTGCCATGG 57.259 40.909 7.63 7.63 0.00 3.66
2409 2730 5.335661 GCGTCTTTGGAACACAGGAATAAAT 60.336 40.000 0.00 0.00 39.29 1.40
2431 2752 1.742761 AACATGATGAACCCTCAGCG 58.257 50.000 0.00 0.00 41.04 5.18
2445 2766 6.921857 GGCTCATCAGAATGGATTAAAACATG 59.078 38.462 0.00 0.00 36.16 3.21
2473 2794 5.808540 CACAAATCAGGCTGTTTGGAATATG 59.191 40.000 29.01 20.32 39.12 1.78
2550 2871 5.527214 TGTGGCTGTCTGGAAAATATATTCG 59.473 40.000 0.00 0.00 0.00 3.34
2598 2919 3.796717 GCCGCATATTATCGATCGAATGA 59.203 43.478 24.60 14.17 0.00 2.57
2603 2924 1.588404 GGTGCCGCATATTATCGATCG 59.412 52.381 9.36 9.36 0.00 3.69
2617 2938 2.723124 AGTAAAAATTGCAGGTGCCG 57.277 45.000 0.00 0.00 41.18 5.69
2619 2940 8.630037 ACCTATATAAGTAAAAATTGCAGGTGC 58.370 33.333 0.00 0.00 42.50 5.01


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

AutoCloner maintained by Alex Coulton.