Multiple sequence alignment - TraesCS5D01G210100

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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 TraesCS5D01G210100 chr5D 100.000 3556 0 0 1 3556 318463548 318459993 0.000000e+00 6567.0
1 TraesCS5D01G210100 chr5A 93.686 3310 146 25 290 3556 413052731 413049442 0.000000e+00 4896.0
2 TraesCS5D01G210100 chr5A 91.223 957 68 10 540 1486 413063735 413062785 0.000000e+00 1288.0
3 TraesCS5D01G210100 chr5A 89.130 46 4 1 2310 2355 709285898 709285854 4.960000e-04 56.5
4 TraesCS5D01G210100 chr5B 93.787 2189 97 21 1151 3316 368505374 368503202 0.000000e+00 3253.0
5 TraesCS5D01G210100 chr5B 92.717 865 46 11 298 1150 368506346 368505487 0.000000e+00 1232.0
6 TraesCS5D01G210100 chr7B 83.249 197 21 6 2293 2479 681749092 681749286 1.700000e-38 171.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G210100 chr5D 318459993 318463548 3555 True 6567.0 6567 100.000 1 3556 1 chr5D.!!$R1 3555
1 TraesCS5D01G210100 chr5A 413049442 413052731 3289 True 4896.0 4896 93.686 290 3556 1 chr5A.!!$R1 3266
2 TraesCS5D01G210100 chr5A 413062785 413063735 950 True 1288.0 1288 91.223 540 1486 1 chr5A.!!$R2 946
3 TraesCS5D01G210100 chr5B 368503202 368506346 3144 True 2242.5 3253 93.252 298 3316 2 chr5B.!!$R1 3018

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
25 26 0.107410 TCTTGTGACAAAGGCGGTGT 60.107 50.0 0.00 0.0 0.00 4.16 F
141 142 0.171231 GGACGAAGCCAAGCATTTCC 59.829 55.0 0.00 0.0 0.00 3.13 F
1517 1659 0.107654 AACGGCCACTCTATTCAGGC 60.108 55.0 2.24 0.0 46.28 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1517 1659 1.355971 GCCATTGCTTGCACTCATTG 58.644 50.000 0.0 0.0 33.53 2.82 R
1714 1856 2.040278 TGCCTCAACCTGTAAGCATTCT 59.960 45.455 0.0 0.0 0.00 2.40 R
3109 3281 0.830648 TGGTATTTCTCAGCCCCGAG 59.169 55.000 0.0 0.0 0.00 4.63 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
20 21 1.337703 TGTGCATCTTGTGACAAAGGC 59.662 47.619 0.00 5.00 0.00 4.35
21 22 0.592637 TGCATCTTGTGACAAAGGCG 59.407 50.000 0.00 0.00 0.00 5.52
22 23 0.109597 GCATCTTGTGACAAAGGCGG 60.110 55.000 0.00 0.00 0.00 6.13
23 24 1.238439 CATCTTGTGACAAAGGCGGT 58.762 50.000 0.00 0.00 0.00 5.68
24 25 1.069022 CATCTTGTGACAAAGGCGGTG 60.069 52.381 0.00 0.00 0.00 4.94
25 26 0.107410 TCTTGTGACAAAGGCGGTGT 60.107 50.000 0.00 0.00 0.00 4.16
26 27 0.738389 CTTGTGACAAAGGCGGTGTT 59.262 50.000 0.00 0.00 0.00 3.32
27 28 0.453793 TTGTGACAAAGGCGGTGTTG 59.546 50.000 0.00 0.00 0.00 3.33
28 29 1.299089 GTGACAAAGGCGGTGTTGC 60.299 57.895 0.00 0.00 0.00 4.17
29 30 1.750780 TGACAAAGGCGGTGTTGCA 60.751 52.632 0.00 0.00 36.28 4.08
30 31 1.315981 TGACAAAGGCGGTGTTGCAA 61.316 50.000 0.00 0.00 36.28 4.08
31 32 0.179124 GACAAAGGCGGTGTTGCAAA 60.179 50.000 0.00 0.00 36.28 3.68
43 44 2.611974 GTTGCAAACGAGTGTATGGG 57.388 50.000 0.00 0.00 36.92 4.00
44 45 1.877443 GTTGCAAACGAGTGTATGGGT 59.123 47.619 0.00 0.00 36.92 4.51
45 46 3.068560 GTTGCAAACGAGTGTATGGGTA 58.931 45.455 0.00 0.00 36.92 3.69
46 47 2.967362 TGCAAACGAGTGTATGGGTAG 58.033 47.619 0.00 0.00 0.00 3.18
47 48 2.277084 GCAAACGAGTGTATGGGTAGG 58.723 52.381 0.00 0.00 0.00 3.18
48 49 2.093869 GCAAACGAGTGTATGGGTAGGA 60.094 50.000 0.00 0.00 0.00 2.94
49 50 3.431766 GCAAACGAGTGTATGGGTAGGAT 60.432 47.826 0.00 0.00 0.00 3.24
50 51 4.766375 CAAACGAGTGTATGGGTAGGATT 58.234 43.478 0.00 0.00 0.00 3.01
51 52 4.402056 AACGAGTGTATGGGTAGGATTG 57.598 45.455 0.00 0.00 0.00 2.67
52 53 2.102588 ACGAGTGTATGGGTAGGATTGC 59.897 50.000 0.00 0.00 0.00 3.56
53 54 2.365617 CGAGTGTATGGGTAGGATTGCT 59.634 50.000 0.00 0.00 0.00 3.91
54 55 3.572682 CGAGTGTATGGGTAGGATTGCTA 59.427 47.826 0.00 0.00 0.00 3.49
55 56 4.558898 CGAGTGTATGGGTAGGATTGCTAC 60.559 50.000 6.79 6.79 0.00 3.58
56 57 4.295201 AGTGTATGGGTAGGATTGCTACA 58.705 43.478 16.00 0.00 0.00 2.74
57 58 4.101119 AGTGTATGGGTAGGATTGCTACAC 59.899 45.833 16.00 13.36 38.35 2.90
58 59 2.910688 ATGGGTAGGATTGCTACACG 57.089 50.000 16.00 0.00 33.67 4.49
59 60 1.563924 TGGGTAGGATTGCTACACGT 58.436 50.000 16.00 0.00 33.67 4.49
60 61 1.479323 TGGGTAGGATTGCTACACGTC 59.521 52.381 16.00 4.58 33.67 4.34
61 62 1.755380 GGGTAGGATTGCTACACGTCT 59.245 52.381 16.00 0.00 0.00 4.18
62 63 2.223758 GGGTAGGATTGCTACACGTCTC 60.224 54.545 16.00 0.00 0.00 3.36
63 64 2.426024 GGTAGGATTGCTACACGTCTCA 59.574 50.000 16.00 0.00 0.00 3.27
64 65 2.656560 AGGATTGCTACACGTCTCAC 57.343 50.000 0.00 0.00 0.00 3.51
66 67 1.135489 GGATTGCTACACGTCTCACGA 60.135 52.381 2.48 0.00 46.05 4.35
67 68 2.479730 GGATTGCTACACGTCTCACGAT 60.480 50.000 2.48 0.00 46.05 3.73
68 69 2.257974 TTGCTACACGTCTCACGATC 57.742 50.000 2.48 0.00 46.05 3.69
69 70 1.161843 TGCTACACGTCTCACGATCA 58.838 50.000 2.48 0.00 46.05 2.92
70 71 1.538075 TGCTACACGTCTCACGATCAA 59.462 47.619 2.48 0.00 46.05 2.57
71 72 2.030628 TGCTACACGTCTCACGATCAAA 60.031 45.455 2.48 0.00 46.05 2.69
72 73 2.984471 GCTACACGTCTCACGATCAAAA 59.016 45.455 2.48 0.00 46.05 2.44
73 74 3.612860 GCTACACGTCTCACGATCAAAAT 59.387 43.478 2.48 0.00 46.05 1.82
74 75 4.259451 GCTACACGTCTCACGATCAAAATC 60.259 45.833 2.48 0.00 46.05 2.17
75 76 3.914312 ACACGTCTCACGATCAAAATCT 58.086 40.909 2.48 0.00 46.05 2.40
76 77 3.675225 ACACGTCTCACGATCAAAATCTG 59.325 43.478 2.48 0.00 46.05 2.90
77 78 3.920412 CACGTCTCACGATCAAAATCTGA 59.080 43.478 2.48 0.00 46.05 3.27
88 89 4.149511 TCAAAATCTGATCATACCGCCA 57.850 40.909 0.00 0.00 0.00 5.69
89 90 4.717877 TCAAAATCTGATCATACCGCCAT 58.282 39.130 0.00 0.00 0.00 4.40
90 91 4.516321 TCAAAATCTGATCATACCGCCATG 59.484 41.667 0.00 0.00 0.00 3.66
91 92 2.775911 ATCTGATCATACCGCCATGG 57.224 50.000 7.63 7.63 46.41 3.66
92 93 1.715785 TCTGATCATACCGCCATGGA 58.284 50.000 18.40 0.00 42.00 3.41
93 94 1.620323 TCTGATCATACCGCCATGGAG 59.380 52.381 18.40 13.36 42.00 3.86
94 95 0.686789 TGATCATACCGCCATGGAGG 59.313 55.000 30.93 30.93 42.00 4.30
103 104 2.350895 CCATGGAGGCGGTTGACA 59.649 61.111 5.56 0.00 0.00 3.58
104 105 2.040544 CCATGGAGGCGGTTGACAC 61.041 63.158 5.56 0.00 0.00 3.67
105 106 2.047274 ATGGAGGCGGTTGACACG 60.047 61.111 0.00 0.00 0.00 4.49
114 115 3.276846 GTTGACACGCGCCCAGTT 61.277 61.111 5.73 0.00 0.00 3.16
115 116 1.957186 GTTGACACGCGCCCAGTTA 60.957 57.895 5.73 0.00 0.00 2.24
116 117 1.004320 TTGACACGCGCCCAGTTAT 60.004 52.632 5.73 0.00 0.00 1.89
117 118 1.017177 TTGACACGCGCCCAGTTATC 61.017 55.000 5.73 0.00 0.00 1.75
118 119 1.447140 GACACGCGCCCAGTTATCA 60.447 57.895 5.73 0.00 0.00 2.15
119 120 1.004320 ACACGCGCCCAGTTATCAA 60.004 52.632 5.73 0.00 0.00 2.57
120 121 0.392461 ACACGCGCCCAGTTATCAAT 60.392 50.000 5.73 0.00 0.00 2.57
121 122 0.304705 CACGCGCCCAGTTATCAATC 59.695 55.000 5.73 0.00 0.00 2.67
122 123 1.151777 ACGCGCCCAGTTATCAATCG 61.152 55.000 5.73 0.00 0.00 3.34
123 124 1.831389 CGCGCCCAGTTATCAATCGG 61.831 60.000 0.00 0.00 0.00 4.18
124 125 0.531974 GCGCCCAGTTATCAATCGGA 60.532 55.000 0.00 0.00 0.00 4.55
125 126 1.217882 CGCCCAGTTATCAATCGGAC 58.782 55.000 0.00 0.00 0.00 4.79
126 127 1.217882 GCCCAGTTATCAATCGGACG 58.782 55.000 0.00 0.00 0.00 4.79
127 128 1.202486 GCCCAGTTATCAATCGGACGA 60.202 52.381 0.00 0.00 0.00 4.20
128 129 2.740580 GCCCAGTTATCAATCGGACGAA 60.741 50.000 0.00 0.00 0.00 3.85
129 130 3.123804 CCCAGTTATCAATCGGACGAAG 58.876 50.000 0.00 0.00 0.00 3.79
130 131 2.540101 CCAGTTATCAATCGGACGAAGC 59.460 50.000 0.00 0.00 0.00 3.86
131 132 2.540101 CAGTTATCAATCGGACGAAGCC 59.460 50.000 0.00 0.00 0.00 4.35
132 133 2.167693 AGTTATCAATCGGACGAAGCCA 59.832 45.455 0.00 0.00 0.00 4.75
133 134 2.933906 GTTATCAATCGGACGAAGCCAA 59.066 45.455 0.00 0.00 0.00 4.52
134 135 1.656652 ATCAATCGGACGAAGCCAAG 58.343 50.000 0.00 0.00 0.00 3.61
135 136 1.019278 TCAATCGGACGAAGCCAAGC 61.019 55.000 0.00 0.00 0.00 4.01
136 137 1.003839 AATCGGACGAAGCCAAGCA 60.004 52.632 0.00 0.00 0.00 3.91
137 138 0.392998 AATCGGACGAAGCCAAGCAT 60.393 50.000 0.00 0.00 0.00 3.79
138 139 0.392998 ATCGGACGAAGCCAAGCATT 60.393 50.000 0.00 0.00 0.00 3.56
139 140 0.605319 TCGGACGAAGCCAAGCATTT 60.605 50.000 0.00 0.00 0.00 2.32
140 141 0.179189 CGGACGAAGCCAAGCATTTC 60.179 55.000 0.00 0.00 0.00 2.17
141 142 0.171231 GGACGAAGCCAAGCATTTCC 59.829 55.000 0.00 0.00 0.00 3.13
142 143 0.179189 GACGAAGCCAAGCATTTCCG 60.179 55.000 0.00 0.00 0.00 4.30
143 144 0.605319 ACGAAGCCAAGCATTTCCGA 60.605 50.000 0.00 0.00 0.00 4.55
144 145 0.521291 CGAAGCCAAGCATTTCCGAA 59.479 50.000 0.00 0.00 0.00 4.30
145 146 1.068610 CGAAGCCAAGCATTTCCGAAA 60.069 47.619 0.00 0.00 0.00 3.46
146 147 2.599659 GAAGCCAAGCATTTCCGAAAG 58.400 47.619 0.00 0.00 0.00 2.62
147 148 1.909700 AGCCAAGCATTTCCGAAAGA 58.090 45.000 0.00 0.00 0.00 2.52
148 149 2.238521 AGCCAAGCATTTCCGAAAGAA 58.761 42.857 0.00 0.00 0.00 2.52
162 163 7.789273 TTCCGAAAGAAAAATGTAGTACACA 57.211 32.000 4.80 0.00 42.69 3.72
163 164 7.181143 TCCGAAAGAAAAATGTAGTACACAC 57.819 36.000 4.80 0.00 40.86 3.82
164 165 6.987992 TCCGAAAGAAAAATGTAGTACACACT 59.012 34.615 4.80 0.00 40.86 3.55
165 166 8.143193 TCCGAAAGAAAAATGTAGTACACACTA 58.857 33.333 4.80 0.00 40.86 2.74
166 167 8.767085 CCGAAAGAAAAATGTAGTACACACTAA 58.233 33.333 4.80 0.00 40.86 2.24
212 213 9.794719 ATTAGCCTAAAAATCCCTGTTATAGTC 57.205 33.333 0.00 0.00 0.00 2.59
213 214 6.602278 AGCCTAAAAATCCCTGTTATAGTCC 58.398 40.000 0.00 0.00 0.00 3.85
214 215 5.768662 GCCTAAAAATCCCTGTTATAGTCCC 59.231 44.000 0.00 0.00 0.00 4.46
215 216 6.636336 GCCTAAAAATCCCTGTTATAGTCCCA 60.636 42.308 0.00 0.00 0.00 4.37
216 217 6.771267 CCTAAAAATCCCTGTTATAGTCCCAC 59.229 42.308 0.00 0.00 0.00 4.61
217 218 4.790718 AAATCCCTGTTATAGTCCCACC 57.209 45.455 0.00 0.00 0.00 4.61
218 219 1.784358 TCCCTGTTATAGTCCCACCG 58.216 55.000 0.00 0.00 0.00 4.94
219 220 1.007479 TCCCTGTTATAGTCCCACCGT 59.993 52.381 0.00 0.00 0.00 4.83
220 221 1.835531 CCCTGTTATAGTCCCACCGTT 59.164 52.381 0.00 0.00 0.00 4.44
221 222 2.237893 CCCTGTTATAGTCCCACCGTTT 59.762 50.000 0.00 0.00 0.00 3.60
222 223 3.528532 CCTGTTATAGTCCCACCGTTTC 58.471 50.000 0.00 0.00 0.00 2.78
223 224 3.055675 CCTGTTATAGTCCCACCGTTTCA 60.056 47.826 0.00 0.00 0.00 2.69
224 225 4.383770 CCTGTTATAGTCCCACCGTTTCAT 60.384 45.833 0.00 0.00 0.00 2.57
225 226 5.163385 CCTGTTATAGTCCCACCGTTTCATA 60.163 44.000 0.00 0.00 0.00 2.15
226 227 6.297080 TGTTATAGTCCCACCGTTTCATAA 57.703 37.500 0.00 0.00 0.00 1.90
227 228 6.891388 TGTTATAGTCCCACCGTTTCATAAT 58.109 36.000 0.00 0.00 0.00 1.28
228 229 7.340256 TGTTATAGTCCCACCGTTTCATAATT 58.660 34.615 0.00 0.00 0.00 1.40
229 230 7.830201 TGTTATAGTCCCACCGTTTCATAATTT 59.170 33.333 0.00 0.00 0.00 1.82
230 231 6.693315 ATAGTCCCACCGTTTCATAATTTG 57.307 37.500 0.00 0.00 0.00 2.32
231 232 4.658063 AGTCCCACCGTTTCATAATTTGA 58.342 39.130 0.00 0.00 0.00 2.69
232 233 5.261216 AGTCCCACCGTTTCATAATTTGAT 58.739 37.500 0.00 0.00 33.34 2.57
233 234 6.419791 AGTCCCACCGTTTCATAATTTGATA 58.580 36.000 0.00 0.00 33.34 2.15
234 235 6.887545 AGTCCCACCGTTTCATAATTTGATAA 59.112 34.615 0.00 0.00 33.34 1.75
235 236 6.970613 GTCCCACCGTTTCATAATTTGATAAC 59.029 38.462 0.00 0.00 33.34 1.89
236 237 6.659668 TCCCACCGTTTCATAATTTGATAACA 59.340 34.615 0.00 0.00 33.34 2.41
237 238 6.750039 CCCACCGTTTCATAATTTGATAACAC 59.250 38.462 0.00 0.00 33.34 3.32
238 239 7.309177 CCACCGTTTCATAATTTGATAACACA 58.691 34.615 0.00 0.00 33.34 3.72
239 240 7.973388 CCACCGTTTCATAATTTGATAACACAT 59.027 33.333 0.00 0.00 33.34 3.21
240 241 9.352784 CACCGTTTCATAATTTGATAACACATT 57.647 29.630 0.00 0.00 33.34 2.71
241 242 9.921637 ACCGTTTCATAATTTGATAACACATTT 57.078 25.926 0.00 0.00 33.34 2.32
250 251 7.733402 ATTTGATAACACATTTTTGCAAGCT 57.267 28.000 0.00 0.00 0.00 3.74
251 252 8.830201 ATTTGATAACACATTTTTGCAAGCTA 57.170 26.923 0.00 0.00 0.00 3.32
252 253 8.830201 TTTGATAACACATTTTTGCAAGCTAT 57.170 26.923 0.00 0.00 0.00 2.97
253 254 9.920133 TTTGATAACACATTTTTGCAAGCTATA 57.080 25.926 0.00 0.00 0.00 1.31
260 261 8.859156 ACACATTTTTGCAAGCTATATAAAACG 58.141 29.630 0.00 0.00 0.00 3.60
261 262 8.859156 CACATTTTTGCAAGCTATATAAAACGT 58.141 29.630 0.00 0.00 0.00 3.99
262 263 9.072294 ACATTTTTGCAAGCTATATAAAACGTC 57.928 29.630 0.00 0.00 0.00 4.34
263 264 9.289303 CATTTTTGCAAGCTATATAAAACGTCT 57.711 29.630 0.00 0.00 0.00 4.18
264 265 9.855021 ATTTTTGCAAGCTATATAAAACGTCTT 57.145 25.926 0.00 0.00 0.00 3.01
293 294 9.971922 ATTATCACCTTCAAAGAAAAAGTCTTG 57.028 29.630 0.00 0.00 46.36 3.02
324 325 5.067805 GCCCTCGGAGTCAAAATTCATATTT 59.932 40.000 4.02 0.00 35.49 1.40
346 347 1.413767 CGGTTCCGTCTTCAGCATCG 61.414 60.000 2.82 0.00 0.00 3.84
475 476 1.527370 GCGGCTCCCAGTCCTAATT 59.473 57.895 0.00 0.00 0.00 1.40
476 477 0.756903 GCGGCTCCCAGTCCTAATTA 59.243 55.000 0.00 0.00 0.00 1.40
512 513 3.724914 GACAGCGGCTCCCAGTAGC 62.725 68.421 0.00 0.00 41.99 3.58
554 568 1.080538 GACTCCCACTACCCACCCT 59.919 63.158 0.00 0.00 0.00 4.34
562 576 0.252558 ACTACCCACCCTACCCACAG 60.253 60.000 0.00 0.00 0.00 3.66
573 588 1.833055 TACCCACAGACCCATCCCCT 61.833 60.000 0.00 0.00 0.00 4.79
802 821 1.375523 CGTTCTGGAAGGAACCCGG 60.376 63.158 0.00 0.00 41.58 5.73
835 856 0.455633 GCGTTGCAGCTGGAAGATTG 60.456 55.000 22.03 12.28 34.07 2.67
844 867 3.250762 CAGCTGGAAGATTGTTTCACGAA 59.749 43.478 5.57 0.00 34.07 3.85
855 878 9.840427 AAGATTGTTTCACGAATTCGATATTTT 57.160 25.926 33.05 7.74 43.02 1.82
856 879 9.490663 AGATTGTTTCACGAATTCGATATTTTC 57.509 29.630 33.05 17.91 43.02 2.29
857 880 8.614994 ATTGTTTCACGAATTCGATATTTTCC 57.385 30.769 33.05 13.06 43.02 3.13
858 881 6.244999 TGTTTCACGAATTCGATATTTTCCG 58.755 36.000 33.05 4.55 43.02 4.30
881 905 6.742718 CCGACAATCATGTATGAACTGTTTTC 59.257 38.462 11.79 0.73 40.74 2.29
896 920 0.321298 TTTTCAGTAGCGGGCCTGAC 60.321 55.000 18.31 5.35 37.43 3.51
967 994 0.877743 GACCTGAGTTTGCTTGGAGC 59.122 55.000 0.00 0.00 42.82 4.70
982 1009 2.203907 AGCAGCCTGGTGAGGTCT 60.204 61.111 0.00 0.00 42.15 3.85
995 1022 2.093235 GTGAGGTCTTATGCTGCCTTCT 60.093 50.000 0.00 0.00 0.00 2.85
1150 1177 4.166144 CCCAAGGTACACCCTCTCAAATAT 59.834 45.833 0.00 0.00 45.47 1.28
1154 1290 7.365652 CCAAGGTACACCCTCTCAAATATAGTT 60.366 40.741 0.00 0.00 45.47 2.24
1155 1291 7.750947 AGGTACACCCTCTCAAATATAGTTT 57.249 36.000 0.00 0.00 40.71 2.66
1158 1298 9.322773 GGTACACCCTCTCAAATATAGTTTTAC 57.677 37.037 0.00 0.00 0.00 2.01
1262 1404 0.324943 TCAGGTTTCCTACAGCAGCC 59.675 55.000 0.00 0.00 29.64 4.85
1363 1505 4.325472 CGAGTATAACCAGACGGAACAAAC 59.675 45.833 0.00 0.00 35.59 2.93
1364 1506 5.217978 AGTATAACCAGACGGAACAAACA 57.782 39.130 0.00 0.00 35.59 2.83
1517 1659 0.107654 AACGGCCACTCTATTCAGGC 60.108 55.000 2.24 0.00 46.28 4.85
1683 1825 5.627367 TGTGCTATTTTTAATTGTGCGTCAC 59.373 36.000 3.44 3.44 34.56 3.67
1700 1842 4.421948 CGTCACCTTACATACTGGACTTC 58.578 47.826 0.00 0.00 0.00 3.01
1805 1947 5.129320 TCAGTCCATCATGTGTATAGCAACT 59.871 40.000 0.00 0.00 0.00 3.16
2208 2350 4.073200 GCATTGCCAGGTGGGTGC 62.073 66.667 0.00 0.00 39.65 5.01
2336 2478 3.756963 GCGTTCCCTTTTCTAATGGAAGT 59.243 43.478 0.00 0.00 38.30 3.01
2417 2559 8.107095 ACTCAGGTTAAGCTTTTGGATATTACA 58.893 33.333 3.20 0.00 0.00 2.41
2430 2572 9.851686 TTTTGGATATTACAGCTATCTCACAAT 57.148 29.630 0.00 0.00 0.00 2.71
2537 2679 4.785346 ACCAGATATGTGGAATGAGCTT 57.215 40.909 24.90 0.00 40.44 3.74
2574 2716 8.414778 AGATTTAGTACCTGTATACTGCACTTC 58.585 37.037 15.53 10.23 36.09 3.01
2764 2906 6.749923 AGCATTCTTTCCAGTGTATTTCTC 57.250 37.500 0.00 0.00 0.00 2.87
2979 3150 5.419760 GTGGAACTTTTGGTTGAGTCTAC 57.580 43.478 0.00 0.00 38.41 2.59
2980 3151 4.879545 GTGGAACTTTTGGTTGAGTCTACA 59.120 41.667 7.04 0.00 38.41 2.74
2999 3171 4.510167 ACATCCCCAAACCTCTTATCAG 57.490 45.455 0.00 0.00 0.00 2.90
3103 3275 1.676529 CTCAGGCTTGCTCCAATCATG 59.323 52.381 0.00 0.00 0.00 3.07
3240 3413 3.392285 AGGATTTGGCAAAGCTTCCTTTT 59.608 39.130 25.32 6.81 39.20 2.27
3327 3504 7.190871 TCGACGTTGAAGCTTTTATTTTTCTT 58.809 30.769 2.05 0.00 0.00 2.52
3352 3529 8.626917 TTACTATAAAAATGGTACTCCCTGGA 57.373 34.615 0.00 0.00 0.00 3.86
3353 3530 7.707467 ACTATAAAAATGGTACTCCCTGGAT 57.293 36.000 0.00 0.00 0.00 3.41
3354 3531 7.746703 ACTATAAAAATGGTACTCCCTGGATC 58.253 38.462 0.00 0.00 0.00 3.36
3397 3575 7.873719 TTTCTTTACTGTGAAAATGGACAGA 57.126 32.000 0.00 0.00 41.90 3.41
3408 3586 2.953466 ATGGACAGATTTGCATGTGC 57.047 45.000 3.01 3.01 38.16 4.57
3475 3653 8.462016 GTTTGACCAAAGTGCTATATGATCTTT 58.538 33.333 0.00 0.00 0.00 2.52
3478 3656 9.851686 TGACCAAAGTGCTATATGATCTTTTAT 57.148 29.630 0.00 0.00 0.00 1.40
3541 3719 4.326504 AAAGTGGAGCTTTTGGTTGATG 57.673 40.909 0.00 0.00 44.41 3.07
3542 3720 2.949447 AGTGGAGCTTTTGGTTGATGT 58.051 42.857 0.00 0.00 0.00 3.06
3552 3730 2.867287 TGGTTGATGTTTGTGCACAG 57.133 45.000 20.59 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.337703 GCCTTTGTCACAAGATGCACA 59.662 47.619 0.00 0.00 0.00 4.57
1 2 1.664016 CGCCTTTGTCACAAGATGCAC 60.664 52.381 8.25 0.00 0.00 4.57
2 3 0.592637 CGCCTTTGTCACAAGATGCA 59.407 50.000 8.25 0.00 0.00 3.96
3 4 0.109597 CCGCCTTTGTCACAAGATGC 60.110 55.000 0.00 0.00 0.00 3.91
4 5 1.069022 CACCGCCTTTGTCACAAGATG 60.069 52.381 0.00 0.00 0.00 2.90
5 6 1.238439 CACCGCCTTTGTCACAAGAT 58.762 50.000 0.00 0.00 0.00 2.40
6 7 0.107410 ACACCGCCTTTGTCACAAGA 60.107 50.000 0.00 0.00 0.00 3.02
7 8 0.738389 AACACCGCCTTTGTCACAAG 59.262 50.000 0.00 0.00 0.00 3.16
8 9 0.453793 CAACACCGCCTTTGTCACAA 59.546 50.000 0.00 0.00 0.00 3.33
9 10 1.999071 GCAACACCGCCTTTGTCACA 61.999 55.000 0.00 0.00 0.00 3.58
10 11 1.299089 GCAACACCGCCTTTGTCAC 60.299 57.895 0.00 0.00 0.00 3.67
11 12 1.315981 TTGCAACACCGCCTTTGTCA 61.316 50.000 0.00 0.00 0.00 3.58
12 13 0.179124 TTTGCAACACCGCCTTTGTC 60.179 50.000 0.00 0.00 0.00 3.18
13 14 0.459411 GTTTGCAACACCGCCTTTGT 60.459 50.000 0.00 0.00 0.00 2.83
14 15 1.478622 CGTTTGCAACACCGCCTTTG 61.479 55.000 0.00 0.00 0.00 2.77
15 16 1.226831 CGTTTGCAACACCGCCTTT 60.227 52.632 0.00 0.00 0.00 3.11
16 17 2.058829 CTCGTTTGCAACACCGCCTT 62.059 55.000 0.00 0.00 0.00 4.35
17 18 2.515057 TCGTTTGCAACACCGCCT 60.515 55.556 0.00 0.00 0.00 5.52
18 19 2.051345 CTCGTTTGCAACACCGCC 60.051 61.111 0.00 0.00 0.00 6.13
19 20 1.654137 CACTCGTTTGCAACACCGC 60.654 57.895 0.00 0.00 0.00 5.68
20 21 0.931702 TACACTCGTTTGCAACACCG 59.068 50.000 0.00 1.94 0.00 4.94
21 22 2.350388 CCATACACTCGTTTGCAACACC 60.350 50.000 0.00 0.00 0.00 4.16
22 23 2.350388 CCCATACACTCGTTTGCAACAC 60.350 50.000 0.00 0.00 0.00 3.32
23 24 1.876799 CCCATACACTCGTTTGCAACA 59.123 47.619 0.00 0.00 0.00 3.33
24 25 1.877443 ACCCATACACTCGTTTGCAAC 59.123 47.619 0.00 0.00 0.00 4.17
25 26 2.264005 ACCCATACACTCGTTTGCAA 57.736 45.000 0.00 0.00 0.00 4.08
26 27 2.354303 CCTACCCATACACTCGTTTGCA 60.354 50.000 0.00 0.00 0.00 4.08
27 28 2.093869 TCCTACCCATACACTCGTTTGC 60.094 50.000 0.00 0.00 0.00 3.68
28 29 3.880047 TCCTACCCATACACTCGTTTG 57.120 47.619 0.00 0.00 0.00 2.93
29 30 4.766375 CAATCCTACCCATACACTCGTTT 58.234 43.478 0.00 0.00 0.00 3.60
30 31 3.431766 GCAATCCTACCCATACACTCGTT 60.432 47.826 0.00 0.00 0.00 3.85
31 32 2.102588 GCAATCCTACCCATACACTCGT 59.897 50.000 0.00 0.00 0.00 4.18
32 33 2.365617 AGCAATCCTACCCATACACTCG 59.634 50.000 0.00 0.00 0.00 4.18
33 34 4.344102 TGTAGCAATCCTACCCATACACTC 59.656 45.833 0.00 0.00 44.77 3.51
34 35 4.101119 GTGTAGCAATCCTACCCATACACT 59.899 45.833 0.00 0.00 44.77 3.55
35 36 4.377897 GTGTAGCAATCCTACCCATACAC 58.622 47.826 0.00 0.00 44.77 2.90
36 37 3.069016 CGTGTAGCAATCCTACCCATACA 59.931 47.826 0.00 0.00 44.77 2.29
37 38 3.069158 ACGTGTAGCAATCCTACCCATAC 59.931 47.826 0.00 0.00 44.77 2.39
38 39 3.302161 ACGTGTAGCAATCCTACCCATA 58.698 45.455 0.00 0.00 44.77 2.74
39 40 2.102588 GACGTGTAGCAATCCTACCCAT 59.897 50.000 0.00 0.00 44.77 4.00
40 41 1.479323 GACGTGTAGCAATCCTACCCA 59.521 52.381 0.00 0.00 44.77 4.51
41 42 1.755380 AGACGTGTAGCAATCCTACCC 59.245 52.381 0.00 0.00 44.77 3.69
42 43 2.426024 TGAGACGTGTAGCAATCCTACC 59.574 50.000 0.00 0.00 44.77 3.18
43 44 3.436496 GTGAGACGTGTAGCAATCCTAC 58.564 50.000 0.00 0.00 45.44 3.18
44 45 2.096980 CGTGAGACGTGTAGCAATCCTA 59.903 50.000 0.00 0.00 36.74 2.94
45 46 1.135373 CGTGAGACGTGTAGCAATCCT 60.135 52.381 0.00 0.00 36.74 3.24
46 47 1.135489 TCGTGAGACGTGTAGCAATCC 60.135 52.381 0.00 0.00 43.14 3.01
47 48 2.257974 TCGTGAGACGTGTAGCAATC 57.742 50.000 0.00 0.00 43.14 2.67
48 49 2.163613 TGATCGTGAGACGTGTAGCAAT 59.836 45.455 0.00 0.00 46.97 3.56
49 50 1.538075 TGATCGTGAGACGTGTAGCAA 59.462 47.619 0.00 0.00 46.97 3.91
50 51 1.161843 TGATCGTGAGACGTGTAGCA 58.838 50.000 0.00 0.00 46.97 3.49
51 52 2.257974 TTGATCGTGAGACGTGTAGC 57.742 50.000 0.00 0.00 46.97 3.58
52 53 5.003872 CAGATTTTGATCGTGAGACGTGTAG 59.996 44.000 0.00 0.00 46.97 2.74
53 54 4.857037 CAGATTTTGATCGTGAGACGTGTA 59.143 41.667 0.00 0.00 46.97 2.90
54 55 3.675225 CAGATTTTGATCGTGAGACGTGT 59.325 43.478 0.00 0.00 46.97 4.49
55 56 3.920412 TCAGATTTTGATCGTGAGACGTG 59.080 43.478 0.00 0.00 46.97 4.49
56 57 4.174411 TCAGATTTTGATCGTGAGACGT 57.826 40.909 0.00 0.00 46.97 4.34
66 67 9.806305 TCCATGGCGGTATGATCAGATTTTGAT 62.806 40.741 6.96 0.00 41.94 2.57
67 68 4.149511 TGGCGGTATGATCAGATTTTGA 57.850 40.909 0.09 0.00 40.85 2.69
68 69 4.320714 CCATGGCGGTATGATCAGATTTTG 60.321 45.833 0.00 0.00 0.00 2.44
69 70 3.822735 CCATGGCGGTATGATCAGATTTT 59.177 43.478 0.00 0.00 0.00 1.82
70 71 3.072915 TCCATGGCGGTATGATCAGATTT 59.927 43.478 6.96 0.00 35.57 2.17
71 72 2.639347 TCCATGGCGGTATGATCAGATT 59.361 45.455 6.96 0.00 35.57 2.40
72 73 2.235650 CTCCATGGCGGTATGATCAGAT 59.764 50.000 6.96 0.00 35.57 2.90
73 74 1.620323 CTCCATGGCGGTATGATCAGA 59.380 52.381 6.96 0.00 35.57 3.27
74 75 1.338484 CCTCCATGGCGGTATGATCAG 60.338 57.143 13.01 0.00 35.57 2.90
75 76 0.686789 CCTCCATGGCGGTATGATCA 59.313 55.000 13.01 0.00 35.57 2.92
76 77 3.540211 CCTCCATGGCGGTATGATC 57.460 57.895 13.01 0.00 35.57 2.92
86 87 2.040544 GTGTCAACCGCCTCCATGG 61.041 63.158 4.97 4.97 39.35 3.66
87 88 2.390599 CGTGTCAACCGCCTCCATG 61.391 63.158 0.00 0.00 0.00 3.66
88 89 2.047274 CGTGTCAACCGCCTCCAT 60.047 61.111 0.00 0.00 0.00 3.41
89 90 4.980805 GCGTGTCAACCGCCTCCA 62.981 66.667 0.00 0.00 45.20 3.86
97 98 1.296056 ATAACTGGGCGCGTGTCAAC 61.296 55.000 8.43 0.00 0.00 3.18
98 99 1.004320 ATAACTGGGCGCGTGTCAA 60.004 52.632 8.43 0.00 0.00 3.18
99 100 1.447140 GATAACTGGGCGCGTGTCA 60.447 57.895 8.43 2.82 0.00 3.58
100 101 1.017177 TTGATAACTGGGCGCGTGTC 61.017 55.000 8.43 0.00 0.00 3.67
101 102 0.392461 ATTGATAACTGGGCGCGTGT 60.392 50.000 8.43 0.00 0.00 4.49
102 103 0.304705 GATTGATAACTGGGCGCGTG 59.695 55.000 8.43 0.00 0.00 5.34
103 104 1.151777 CGATTGATAACTGGGCGCGT 61.152 55.000 8.43 0.00 0.00 6.01
104 105 1.564622 CGATTGATAACTGGGCGCG 59.435 57.895 0.00 0.00 0.00 6.86
105 106 0.531974 TCCGATTGATAACTGGGCGC 60.532 55.000 0.00 0.00 0.00 6.53
106 107 1.217882 GTCCGATTGATAACTGGGCG 58.782 55.000 0.00 0.00 0.00 6.13
107 108 1.202486 TCGTCCGATTGATAACTGGGC 60.202 52.381 0.00 0.00 0.00 5.36
108 109 2.882927 TCGTCCGATTGATAACTGGG 57.117 50.000 0.00 0.00 0.00 4.45
109 110 2.540101 GCTTCGTCCGATTGATAACTGG 59.460 50.000 0.00 0.00 0.00 4.00
110 111 2.540101 GGCTTCGTCCGATTGATAACTG 59.460 50.000 0.00 0.00 0.00 3.16
111 112 2.167693 TGGCTTCGTCCGATTGATAACT 59.832 45.455 0.00 0.00 0.00 2.24
112 113 2.546778 TGGCTTCGTCCGATTGATAAC 58.453 47.619 0.00 0.00 0.00 1.89
113 114 2.971660 TGGCTTCGTCCGATTGATAA 57.028 45.000 0.00 0.00 0.00 1.75
114 115 2.821546 CTTGGCTTCGTCCGATTGATA 58.178 47.619 0.00 0.00 0.00 2.15
115 116 1.656652 CTTGGCTTCGTCCGATTGAT 58.343 50.000 0.00 0.00 0.00 2.57
116 117 1.019278 GCTTGGCTTCGTCCGATTGA 61.019 55.000 0.00 0.00 0.00 2.57
117 118 1.298157 TGCTTGGCTTCGTCCGATTG 61.298 55.000 0.00 0.00 0.00 2.67
118 119 0.392998 ATGCTTGGCTTCGTCCGATT 60.393 50.000 0.00 0.00 0.00 3.34
119 120 0.392998 AATGCTTGGCTTCGTCCGAT 60.393 50.000 0.00 0.00 0.00 4.18
120 121 0.605319 AAATGCTTGGCTTCGTCCGA 60.605 50.000 0.00 0.00 0.00 4.55
121 122 0.179189 GAAATGCTTGGCTTCGTCCG 60.179 55.000 0.00 0.00 0.00 4.79
122 123 0.171231 GGAAATGCTTGGCTTCGTCC 59.829 55.000 0.00 0.00 0.00 4.79
123 124 0.179189 CGGAAATGCTTGGCTTCGTC 60.179 55.000 0.00 0.00 0.00 4.20
124 125 0.605319 TCGGAAATGCTTGGCTTCGT 60.605 50.000 0.00 0.00 0.00 3.85
125 126 0.521291 TTCGGAAATGCTTGGCTTCG 59.479 50.000 0.00 0.00 0.00 3.79
126 127 2.228822 TCTTTCGGAAATGCTTGGCTTC 59.771 45.455 3.24 0.00 0.00 3.86
127 128 2.238521 TCTTTCGGAAATGCTTGGCTT 58.761 42.857 3.24 0.00 0.00 4.35
128 129 1.909700 TCTTTCGGAAATGCTTGGCT 58.090 45.000 3.24 0.00 0.00 4.75
129 130 2.723124 TTCTTTCGGAAATGCTTGGC 57.277 45.000 3.24 0.00 0.00 4.52
130 131 5.466393 ACATTTTTCTTTCGGAAATGCTTGG 59.534 36.000 3.24 0.00 42.63 3.61
131 132 6.529463 ACATTTTTCTTTCGGAAATGCTTG 57.471 33.333 3.24 1.21 42.63 4.01
132 133 7.433680 ACTACATTTTTCTTTCGGAAATGCTT 58.566 30.769 3.24 0.00 42.63 3.91
133 134 6.981722 ACTACATTTTTCTTTCGGAAATGCT 58.018 32.000 3.24 0.51 42.63 3.79
134 135 7.806014 TGTACTACATTTTTCTTTCGGAAATGC 59.194 33.333 3.24 0.00 42.63 3.56
135 136 9.113876 GTGTACTACATTTTTCTTTCGGAAATG 57.886 33.333 3.24 1.08 42.63 2.32
136 137 8.842280 TGTGTACTACATTTTTCTTTCGGAAAT 58.158 29.630 3.24 0.00 37.79 2.17
137 138 8.124199 GTGTGTACTACATTTTTCTTTCGGAAA 58.876 33.333 2.78 2.78 42.24 3.13
138 139 7.496591 AGTGTGTACTACATTTTTCTTTCGGAA 59.503 33.333 0.00 0.00 42.24 4.30
139 140 6.987992 AGTGTGTACTACATTTTTCTTTCGGA 59.012 34.615 0.00 0.00 42.24 4.55
140 141 7.186021 AGTGTGTACTACATTTTTCTTTCGG 57.814 36.000 0.00 0.00 42.24 4.30
186 187 9.794719 GACTATAACAGGGATTTTTAGGCTAAT 57.205 33.333 7.96 0.00 0.00 1.73
187 188 8.215736 GGACTATAACAGGGATTTTTAGGCTAA 58.784 37.037 2.04 2.04 0.00 3.09
188 189 7.202158 GGGACTATAACAGGGATTTTTAGGCTA 60.202 40.741 0.00 0.00 0.00 3.93
189 190 6.410504 GGGACTATAACAGGGATTTTTAGGCT 60.411 42.308 0.00 0.00 0.00 4.58
190 191 5.768662 GGGACTATAACAGGGATTTTTAGGC 59.231 44.000 0.00 0.00 0.00 3.93
191 192 6.771267 GTGGGACTATAACAGGGATTTTTAGG 59.229 42.308 0.00 0.00 0.00 2.69
192 193 6.771267 GGTGGGACTATAACAGGGATTTTTAG 59.229 42.308 0.00 0.00 0.00 1.85
193 194 6.633127 CGGTGGGACTATAACAGGGATTTTTA 60.633 42.308 0.00 0.00 0.00 1.52
194 195 5.516044 GGTGGGACTATAACAGGGATTTTT 58.484 41.667 0.00 0.00 0.00 1.94
195 196 4.384868 CGGTGGGACTATAACAGGGATTTT 60.385 45.833 0.00 0.00 0.00 1.82
196 197 3.135895 CGGTGGGACTATAACAGGGATTT 59.864 47.826 0.00 0.00 0.00 2.17
197 198 2.704065 CGGTGGGACTATAACAGGGATT 59.296 50.000 0.00 0.00 0.00 3.01
198 199 2.326428 CGGTGGGACTATAACAGGGAT 58.674 52.381 0.00 0.00 0.00 3.85
199 200 1.007479 ACGGTGGGACTATAACAGGGA 59.993 52.381 0.00 0.00 0.00 4.20
200 201 1.492764 ACGGTGGGACTATAACAGGG 58.507 55.000 0.00 0.00 0.00 4.45
201 202 3.055675 TGAAACGGTGGGACTATAACAGG 60.056 47.826 0.00 0.00 0.00 4.00
202 203 4.196626 TGAAACGGTGGGACTATAACAG 57.803 45.455 0.00 0.00 0.00 3.16
203 204 4.829872 ATGAAACGGTGGGACTATAACA 57.170 40.909 0.00 0.00 0.00 2.41
204 205 7.797038 AATTATGAAACGGTGGGACTATAAC 57.203 36.000 0.00 0.00 0.00 1.89
205 206 8.047911 TCAAATTATGAAACGGTGGGACTATAA 58.952 33.333 0.00 0.00 34.30 0.98
206 207 7.566569 TCAAATTATGAAACGGTGGGACTATA 58.433 34.615 0.00 0.00 34.30 1.31
207 208 6.419791 TCAAATTATGAAACGGTGGGACTAT 58.580 36.000 0.00 0.00 34.30 2.12
208 209 5.806818 TCAAATTATGAAACGGTGGGACTA 58.193 37.500 0.00 0.00 34.30 2.59
209 210 4.658063 TCAAATTATGAAACGGTGGGACT 58.342 39.130 0.00 0.00 34.30 3.85
210 211 5.576447 ATCAAATTATGAAACGGTGGGAC 57.424 39.130 0.00 0.00 42.54 4.46
211 212 6.659668 TGTTATCAAATTATGAAACGGTGGGA 59.340 34.615 0.00 0.00 42.54 4.37
212 213 6.750039 GTGTTATCAAATTATGAAACGGTGGG 59.250 38.462 0.00 0.00 42.54 4.61
213 214 7.309177 TGTGTTATCAAATTATGAAACGGTGG 58.691 34.615 0.00 0.00 42.54 4.61
214 215 8.909708 ATGTGTTATCAAATTATGAAACGGTG 57.090 30.769 0.00 0.00 42.54 4.94
215 216 9.921637 AAATGTGTTATCAAATTATGAAACGGT 57.078 25.926 0.00 0.00 42.54 4.83
224 225 9.270640 AGCTTGCAAAAATGTGTTATCAAATTA 57.729 25.926 0.00 0.00 31.89 1.40
225 226 8.156994 AGCTTGCAAAAATGTGTTATCAAATT 57.843 26.923 0.00 0.00 33.37 1.82
226 227 7.733402 AGCTTGCAAAAATGTGTTATCAAAT 57.267 28.000 0.00 0.00 0.00 2.32
227 228 8.830201 ATAGCTTGCAAAAATGTGTTATCAAA 57.170 26.923 0.00 0.00 0.00 2.69
234 235 8.859156 CGTTTTATATAGCTTGCAAAAATGTGT 58.141 29.630 0.00 0.00 0.00 3.72
235 236 8.859156 ACGTTTTATATAGCTTGCAAAAATGTG 58.141 29.630 15.35 0.00 35.72 3.21
236 237 8.980143 ACGTTTTATATAGCTTGCAAAAATGT 57.020 26.923 0.00 4.42 33.50 2.71
237 238 9.289303 AGACGTTTTATATAGCTTGCAAAAATG 57.711 29.630 0.00 3.78 0.00 2.32
238 239 9.855021 AAGACGTTTTATATAGCTTGCAAAAAT 57.145 25.926 0.00 0.00 0.00 1.82
267 268 9.971922 CAAGACTTTTTCTTTGAAGGTGATAAT 57.028 29.630 0.00 0.00 42.37 1.28
268 269 8.966868 ACAAGACTTTTTCTTTGAAGGTGATAA 58.033 29.630 0.00 0.00 42.37 1.75
269 270 8.519799 ACAAGACTTTTTCTTTGAAGGTGATA 57.480 30.769 0.00 0.00 42.37 2.15
270 271 7.410120 ACAAGACTTTTTCTTTGAAGGTGAT 57.590 32.000 0.00 0.00 42.37 3.06
271 272 6.834168 ACAAGACTTTTTCTTTGAAGGTGA 57.166 33.333 0.00 0.00 42.37 4.02
276 277 9.691362 GGCATAATACAAGACTTTTTCTTTGAA 57.309 29.630 0.00 0.00 42.37 2.69
277 278 8.303876 GGGCATAATACAAGACTTTTTCTTTGA 58.696 33.333 0.00 0.00 42.37 2.69
278 279 8.306761 AGGGCATAATACAAGACTTTTTCTTTG 58.693 33.333 0.00 0.00 42.37 2.77
279 280 8.422577 AGGGCATAATACAAGACTTTTTCTTT 57.577 30.769 0.00 0.00 42.37 2.52
280 281 7.148239 CGAGGGCATAATACAAGACTTTTTCTT 60.148 37.037 0.00 0.00 46.29 2.52
281 282 6.316390 CGAGGGCATAATACAAGACTTTTTCT 59.684 38.462 0.00 0.00 35.32 2.52
282 283 6.458342 CCGAGGGCATAATACAAGACTTTTTC 60.458 42.308 0.00 0.00 0.00 2.29
283 284 5.357032 CCGAGGGCATAATACAAGACTTTTT 59.643 40.000 0.00 0.00 0.00 1.94
284 285 4.881850 CCGAGGGCATAATACAAGACTTTT 59.118 41.667 0.00 0.00 0.00 2.27
285 286 4.163458 TCCGAGGGCATAATACAAGACTTT 59.837 41.667 0.00 0.00 0.00 2.66
286 287 3.709653 TCCGAGGGCATAATACAAGACTT 59.290 43.478 0.00 0.00 0.00 3.01
287 288 3.305720 TCCGAGGGCATAATACAAGACT 58.694 45.455 0.00 0.00 0.00 3.24
288 289 3.069729 ACTCCGAGGGCATAATACAAGAC 59.930 47.826 0.00 0.00 0.00 3.01
293 294 3.746045 TTGACTCCGAGGGCATAATAC 57.254 47.619 0.00 0.00 0.00 1.89
332 333 1.519455 GTCCCGATGCTGAAGACGG 60.519 63.158 0.00 0.00 44.16 4.79
338 339 3.458163 GGACGGTCCCGATGCTGA 61.458 66.667 16.55 0.00 42.83 4.26
471 472 2.810410 GCGGGCGGGGAGGTAATTA 61.810 63.158 0.00 0.00 0.00 1.40
554 568 1.307517 GGGGATGGGTCTGTGGGTA 60.308 63.158 0.00 0.00 0.00 3.69
562 576 1.077716 CGTGGAAAGGGGATGGGTC 60.078 63.158 0.00 0.00 0.00 4.46
802 821 3.542629 AACGCGCAAAAGCTGAGGC 62.543 57.895 5.73 0.00 39.06 4.70
824 843 3.896648 TTCGTGAAACAATCTTCCAGC 57.103 42.857 0.00 0.00 35.74 4.85
825 844 5.082059 CGAATTCGTGAAACAATCTTCCAG 58.918 41.667 19.67 0.00 35.74 3.86
830 849 9.490663 GAAAATATCGAATTCGTGAAACAATCT 57.509 29.630 25.93 2.09 40.80 2.40
835 856 6.407181 GTCGGAAAATATCGAATTCGTGAAAC 59.593 38.462 25.93 12.81 40.80 2.78
844 867 7.496529 ACATGATTGTCGGAAAATATCGAAT 57.503 32.000 0.00 0.00 37.14 3.34
855 878 5.084818 ACAGTTCATACATGATTGTCGGA 57.915 39.130 0.00 0.00 37.28 4.55
856 879 5.801350 AACAGTTCATACATGATTGTCGG 57.199 39.130 0.00 0.00 35.37 4.79
857 880 7.297391 TGAAAACAGTTCATACATGATTGTCG 58.703 34.615 0.00 0.00 35.37 4.35
858 881 8.292448 ACTGAAAACAGTTCATACATGATTGTC 58.708 33.333 0.00 0.69 35.37 3.18
881 905 2.685387 GATCGTCAGGCCCGCTACTG 62.685 65.000 0.00 0.00 36.07 2.74
967 994 1.745141 GCATAAGACCTCACCAGGCTG 60.745 57.143 7.75 7.75 45.05 4.85
982 1009 2.773661 TCATCCTGAGAAGGCAGCATAA 59.226 45.455 0.00 0.00 34.56 1.90
995 1022 0.400213 AACACCGCCTTTCATCCTGA 59.600 50.000 0.00 0.00 0.00 3.86
1150 1177 6.989659 AGTAACAGCTAGCACAGTAAAACTA 58.010 36.000 18.83 0.00 0.00 2.24
1154 1290 6.285224 TCAAAGTAACAGCTAGCACAGTAAA 58.715 36.000 18.83 2.13 0.00 2.01
1155 1291 5.849510 TCAAAGTAACAGCTAGCACAGTAA 58.150 37.500 18.83 0.00 0.00 2.24
1158 1298 5.625251 CAATCAAAGTAACAGCTAGCACAG 58.375 41.667 18.83 8.89 0.00 3.66
1172 1313 2.839486 TCTGAGTCGGCAATCAAAGT 57.161 45.000 0.00 0.00 0.00 2.66
1262 1404 8.781196 CATTATCTCCAATATGTTCCAGTTCAG 58.219 37.037 0.00 0.00 0.00 3.02
1517 1659 1.355971 GCCATTGCTTGCACTCATTG 58.644 50.000 0.00 0.00 33.53 2.82
1541 1683 3.057596 TCATTCGACAAGCCCACATTTTC 60.058 43.478 0.00 0.00 0.00 2.29
1613 1755 3.405831 TGAAAACTCAGGCATCTCACAG 58.594 45.455 0.00 0.00 0.00 3.66
1673 1815 3.322369 CAGTATGTAAGGTGACGCACAA 58.678 45.455 11.20 0.00 35.86 3.33
1683 1825 8.311836 TGTTAGAAAGAAGTCCAGTATGTAAGG 58.688 37.037 0.00 0.00 0.00 2.69
1714 1856 2.040278 TGCCTCAACCTGTAAGCATTCT 59.960 45.455 0.00 0.00 0.00 2.40
1728 1870 5.789643 AAAGCAAGAGTTTTATGCCTCAA 57.210 34.783 0.00 0.00 40.93 3.02
1805 1947 2.270858 TCTGGGCTGTATTTACCACCA 58.729 47.619 0.00 0.00 0.00 4.17
2098 2240 5.754890 GCATACAATTCCCAATGATTTCCAC 59.245 40.000 0.00 0.00 0.00 4.02
2208 2350 0.095935 CGGCTTGCGAGTTCTGAATG 59.904 55.000 2.14 0.00 0.00 2.67
2336 2478 2.573009 TGAATGATCCTGCAAGACCTCA 59.427 45.455 0.00 0.00 34.07 3.86
2430 2572 1.412710 GATGTGCCCCTCATCTCGTAA 59.587 52.381 0.00 0.00 38.72 3.18
2537 2679 6.166279 CAGGTACTAAATCTGTGCAAAGAGA 58.834 40.000 13.14 3.24 36.02 3.10
2574 2716 2.291540 TGGGAGGAAAATGCCCTTACTG 60.292 50.000 0.00 0.00 42.52 2.74
2764 2906 5.123227 TGAAACGGGGCTAAGAATATGAAG 58.877 41.667 0.00 0.00 0.00 3.02
2821 2970 2.269241 GCCTGGGGAGCACTACAC 59.731 66.667 0.00 0.00 0.00 2.90
2877 3036 3.382865 TGCTGCACATTGTAAACTGGAAA 59.617 39.130 0.00 0.00 0.00 3.13
2949 3120 9.143155 ACTCAACCAAAAGTTCCACTTTATATT 57.857 29.630 2.36 0.00 46.78 1.28
2978 3149 3.852578 ACTGATAAGAGGTTTGGGGATGT 59.147 43.478 0.00 0.00 0.00 3.06
2979 3150 4.202441 CACTGATAAGAGGTTTGGGGATG 58.798 47.826 0.00 0.00 0.00 3.51
2980 3151 3.852578 ACACTGATAAGAGGTTTGGGGAT 59.147 43.478 0.00 0.00 0.00 3.85
3032 3204 2.241160 TCAAGGAAGTAGTACGGTGCA 58.759 47.619 0.00 0.00 0.00 4.57
3109 3281 0.830648 TGGTATTTCTCAGCCCCGAG 59.169 55.000 0.00 0.00 0.00 4.63
3191 3364 3.508762 GCTTCAGATTGATGCTTGGTTG 58.491 45.455 9.02 0.00 42.26 3.77
3240 3413 4.625028 CAATCTGAACCGAGCTATGATGA 58.375 43.478 0.00 0.00 0.00 2.92
3327 3504 8.626917 TCCAGGGAGTACCATTTTTATAGTAA 57.373 34.615 0.00 0.00 43.89 2.24
3447 3625 8.486210 AGATCATATAGCACTTTGGTCAAACTA 58.514 33.333 0.00 0.00 0.00 2.24
3475 3653 8.701908 AGAAGGATCCACGTTATACAGTATAA 57.298 34.615 15.82 8.72 0.00 0.98
3478 3656 7.414222 AAAGAAGGATCCACGTTATACAGTA 57.586 36.000 15.82 0.00 0.00 2.74
3479 3657 5.934402 AAGAAGGATCCACGTTATACAGT 57.066 39.130 15.82 0.00 0.00 3.55
3480 3658 7.119262 ACAAAAAGAAGGATCCACGTTATACAG 59.881 37.037 15.82 0.00 0.00 2.74
3481 3659 6.938030 ACAAAAAGAAGGATCCACGTTATACA 59.062 34.615 15.82 0.00 0.00 2.29
3482 3660 7.118680 TCACAAAAAGAAGGATCCACGTTATAC 59.881 37.037 15.82 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.