Multiple sequence alignment - TraesCS2A01G005800

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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 TraesCS2A01G005800 chr2A 100.000 3555 0 0 1 3555 2741683 2738129 0.000000e+00 6565.0
1 TraesCS2A01G005800 chr2A 84.738 878 124 8 2592 3465 699978069 699977198 0.000000e+00 870.0
2 TraesCS2A01G005800 chr2A 91.667 84 4 3 215 297 621963457 621963538 2.900000e-21 113.0
3 TraesCS2A01G005800 chr2D 91.614 2683 192 19 324 2989 2929828 2932494 0.000000e+00 3677.0
4 TraesCS2A01G005800 chr2D 90.552 1069 97 4 2337 3404 2934146 2935211 0.000000e+00 1411.0
5 TraesCS2A01G005800 chr2D 86.813 910 111 8 2563 3466 386839719 386840625 0.000000e+00 1007.0
6 TraesCS2A01G005800 chr2D 94.318 88 4 1 3444 3530 2935217 2935304 2.230000e-27 134.0
7 TraesCS2A01G005800 chr2D 88.764 89 7 3 215 302 403216092 403216006 4.850000e-19 106.0
8 TraesCS2A01G005800 chr2B 91.562 2157 157 10 381 2529 7857383 7855244 0.000000e+00 2952.0
9 TraesCS2A01G005800 chr2B 89.199 1361 119 13 327 1659 7768071 7766711 0.000000e+00 1674.0
10 TraesCS2A01G005800 chr2B 90.231 778 59 3 1714 2491 7766713 7765953 0.000000e+00 1000.0
11 TraesCS2A01G005800 chr2B 91.026 78 7 0 2486 2563 7765422 7765345 4.850000e-19 106.0
12 TraesCS2A01G005800 chr6D 88.268 912 97 8 2564 3469 137122354 137121447 0.000000e+00 1083.0
13 TraesCS2A01G005800 chr6D 87.115 908 104 10 2562 3465 408146010 408146908 0.000000e+00 1016.0
14 TraesCS2A01G005800 chr1D 87.459 909 106 7 2563 3466 18806710 18805805 0.000000e+00 1040.0
15 TraesCS2A01G005800 chr1D 90.476 84 5 3 215 297 20653727 20653808 1.350000e-19 108.0
16 TraesCS2A01G005800 chr4D 87.444 892 104 7 2579 3466 431555291 431556178 0.000000e+00 1020.0
17 TraesCS2A01G005800 chr4D 87.332 892 105 7 2579 3466 431674418 431675305 0.000000e+00 1014.0
18 TraesCS2A01G005800 chr4D 87.220 892 106 7 2579 3466 431621056 431621943 0.000000e+00 1009.0
19 TraesCS2A01G005800 chr4D 89.888 89 6 3 215 302 301016486 301016572 1.040000e-20 111.0
20 TraesCS2A01G005800 chr5A 81.743 608 91 14 1925 2527 613579393 613579985 1.150000e-134 490.0
21 TraesCS2A01G005800 chr5A 90.476 84 5 3 215 297 110885182 110885101 1.350000e-19 108.0
22 TraesCS2A01G005800 chr5B 77.368 623 112 18 1925 2539 605996391 605996992 3.400000e-90 342.0
23 TraesCS2A01G005800 chr7D 91.667 84 4 3 215 297 89480727 89480646 2.900000e-21 113.0
24 TraesCS2A01G005800 chr7D 90.476 84 5 3 215 297 206601372 206601453 1.350000e-19 108.0
25 TraesCS2A01G005800 chr6A 90.476 84 5 3 215 297 351609303 351609384 1.350000e-19 108.0
26 TraesCS2A01G005800 chr6A 100.000 29 0 0 293 321 290737671 290737699 2.000000e-03 54.7
27 TraesCS2A01G005800 chr3D 88.764 89 7 3 215 302 236628896 236628810 4.850000e-19 106.0


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 TraesCS2A01G005800 chr2A 2738129 2741683 3554 True 6565.000000 6565 100.000000 1 3555 1 chr2A.!!$R1 3554
1 TraesCS2A01G005800 chr2A 699977198 699978069 871 True 870.000000 870 84.738000 2592 3465 1 chr2A.!!$R2 873
2 TraesCS2A01G005800 chr2D 2929828 2935304 5476 False 1740.666667 3677 92.161333 324 3530 3 chr2D.!!$F2 3206
3 TraesCS2A01G005800 chr2D 386839719 386840625 906 False 1007.000000 1007 86.813000 2563 3466 1 chr2D.!!$F1 903
4 TraesCS2A01G005800 chr2B 7855244 7857383 2139 True 2952.000000 2952 91.562000 381 2529 1 chr2B.!!$R1 2148
5 TraesCS2A01G005800 chr2B 7765345 7768071 2726 True 926.666667 1674 90.152000 327 2563 3 chr2B.!!$R2 2236
6 TraesCS2A01G005800 chr6D 137121447 137122354 907 True 1083.000000 1083 88.268000 2564 3469 1 chr6D.!!$R1 905
7 TraesCS2A01G005800 chr6D 408146010 408146908 898 False 1016.000000 1016 87.115000 2562 3465 1 chr6D.!!$F1 903
8 TraesCS2A01G005800 chr1D 18805805 18806710 905 True 1040.000000 1040 87.459000 2563 3466 1 chr1D.!!$R1 903
9 TraesCS2A01G005800 chr4D 431555291 431556178 887 False 1020.000000 1020 87.444000 2579 3466 1 chr4D.!!$F2 887
10 TraesCS2A01G005800 chr4D 431674418 431675305 887 False 1014.000000 1014 87.332000 2579 3466 1 chr4D.!!$F4 887
11 TraesCS2A01G005800 chr4D 431621056 431621943 887 False 1009.000000 1009 87.220000 2579 3466 1 chr4D.!!$F3 887
12 TraesCS2A01G005800 chr5A 613579393 613579985 592 False 490.000000 490 81.743000 1925 2527 1 chr5A.!!$F1 602
13 TraesCS2A01G005800 chr5B 605996391 605996992 601 False 342.000000 342 77.368000 1925 2539 1 chr5B.!!$F1 614

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
754 760 0.042581 TCAGGGGTGTGGCTAGATCA 59.957 55.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2746 5637 0.033228 TGGGCATTTTTGCTTCGTGG 59.967 50.0 0.0 0.0 34.73 4.94 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 4.566545 TCATTCGAAGAGCTGAGATCTC 57.433 45.455 16.21 16.21 38.43 2.75
22 23 3.317711 TCATTCGAAGAGCTGAGATCTCC 59.682 47.826 20.03 5.58 38.43 3.71
23 24 2.727123 TCGAAGAGCTGAGATCTCCT 57.273 50.000 20.03 10.58 0.00 3.69
24 25 3.847671 TCGAAGAGCTGAGATCTCCTA 57.152 47.619 20.03 1.25 0.00 2.94
25 26 4.157849 TCGAAGAGCTGAGATCTCCTAA 57.842 45.455 20.03 0.48 0.00 2.69
26 27 4.527944 TCGAAGAGCTGAGATCTCCTAAA 58.472 43.478 20.03 0.10 0.00 1.85
27 28 4.578516 TCGAAGAGCTGAGATCTCCTAAAG 59.421 45.833 20.03 11.39 0.00 1.85
28 29 4.261572 CGAAGAGCTGAGATCTCCTAAAGG 60.262 50.000 20.03 4.75 0.00 3.11
29 30 4.534647 AGAGCTGAGATCTCCTAAAGGA 57.465 45.455 20.03 0.00 43.08 3.36
30 31 4.877773 AGAGCTGAGATCTCCTAAAGGAA 58.122 43.478 20.03 0.00 44.91 3.36
31 32 5.276440 AGAGCTGAGATCTCCTAAAGGAAA 58.724 41.667 20.03 0.00 44.91 3.13
32 33 5.723887 AGAGCTGAGATCTCCTAAAGGAAAA 59.276 40.000 20.03 0.00 44.91 2.29
33 34 6.214412 AGAGCTGAGATCTCCTAAAGGAAAAA 59.786 38.462 20.03 0.00 44.91 1.94
34 35 6.967897 AGCTGAGATCTCCTAAAGGAAAAAT 58.032 36.000 20.03 0.00 44.91 1.82
35 36 7.409358 AGCTGAGATCTCCTAAAGGAAAAATT 58.591 34.615 20.03 0.00 44.91 1.82
36 37 8.552296 AGCTGAGATCTCCTAAAGGAAAAATTA 58.448 33.333 20.03 0.00 44.91 1.40
37 38 8.835439 GCTGAGATCTCCTAAAGGAAAAATTAG 58.165 37.037 20.03 5.82 44.91 1.73
38 39 8.738645 TGAGATCTCCTAAAGGAAAAATTAGC 57.261 34.615 20.03 0.00 44.91 3.09
39 40 8.552296 TGAGATCTCCTAAAGGAAAAATTAGCT 58.448 33.333 20.03 0.00 44.91 3.32
41 42 9.839817 AGATCTCCTAAAGGAAAAATTAGCTAC 57.160 33.333 0.00 0.00 44.91 3.58
42 43 9.839817 GATCTCCTAAAGGAAAAATTAGCTACT 57.160 33.333 0.00 0.00 44.91 2.57
43 44 9.839817 ATCTCCTAAAGGAAAAATTAGCTACTC 57.160 33.333 0.00 0.00 44.91 2.59
44 45 8.265764 TCTCCTAAAGGAAAAATTAGCTACTCC 58.734 37.037 0.00 0.00 44.91 3.85
45 46 7.344134 TCCTAAAGGAAAAATTAGCTACTCCC 58.656 38.462 0.00 0.00 42.18 4.30
46 47 7.184022 TCCTAAAGGAAAAATTAGCTACTCCCT 59.816 37.037 0.00 0.00 42.18 4.20
47 48 7.499563 CCTAAAGGAAAAATTAGCTACTCCCTC 59.500 40.741 0.00 0.00 37.39 4.30
48 49 5.375283 AGGAAAAATTAGCTACTCCCTCC 57.625 43.478 0.00 0.00 0.00 4.30
49 50 4.788617 AGGAAAAATTAGCTACTCCCTCCA 59.211 41.667 11.16 0.00 0.00 3.86
50 51 4.882427 GGAAAAATTAGCTACTCCCTCCAC 59.118 45.833 0.00 0.00 0.00 4.02
51 52 4.505324 AAAATTAGCTACTCCCTCCACC 57.495 45.455 0.00 0.00 0.00 4.61
52 53 3.423058 AATTAGCTACTCCCTCCACCT 57.577 47.619 0.00 0.00 0.00 4.00
53 54 2.942604 TTAGCTACTCCCTCCACCTT 57.057 50.000 0.00 0.00 0.00 3.50
54 55 2.942604 TAGCTACTCCCTCCACCTTT 57.057 50.000 0.00 0.00 0.00 3.11
55 56 1.574263 AGCTACTCCCTCCACCTTTC 58.426 55.000 0.00 0.00 0.00 2.62
56 57 1.079658 AGCTACTCCCTCCACCTTTCT 59.920 52.381 0.00 0.00 0.00 2.52
57 58 2.315155 AGCTACTCCCTCCACCTTTCTA 59.685 50.000 0.00 0.00 0.00 2.10
58 59 3.051727 AGCTACTCCCTCCACCTTTCTAT 60.052 47.826 0.00 0.00 0.00 1.98
59 60 3.070302 GCTACTCCCTCCACCTTTCTATG 59.930 52.174 0.00 0.00 0.00 2.23
60 61 2.482494 ACTCCCTCCACCTTTCTATGG 58.518 52.381 0.00 0.00 37.32 2.74
61 62 1.141858 CTCCCTCCACCTTTCTATGGC 59.858 57.143 0.00 0.00 35.81 4.40
62 63 0.183731 CCCTCCACCTTTCTATGGCC 59.816 60.000 0.00 0.00 35.81 5.36
63 64 1.216990 CCTCCACCTTTCTATGGCCT 58.783 55.000 3.32 0.00 35.81 5.19
64 65 2.408565 CCTCCACCTTTCTATGGCCTA 58.591 52.381 3.32 0.00 35.81 3.93
65 66 2.777692 CCTCCACCTTTCTATGGCCTAA 59.222 50.000 3.32 0.00 35.81 2.69
66 67 3.395941 CCTCCACCTTTCTATGGCCTAAT 59.604 47.826 3.32 0.00 35.81 1.73
67 68 4.392940 CTCCACCTTTCTATGGCCTAATG 58.607 47.826 3.32 0.00 35.81 1.90
68 69 2.887152 CCACCTTTCTATGGCCTAATGC 59.113 50.000 3.32 0.00 40.16 3.56
69 70 3.554934 CACCTTTCTATGGCCTAATGCA 58.445 45.455 3.32 0.00 43.89 3.96
70 71 4.147321 CACCTTTCTATGGCCTAATGCAT 58.853 43.478 3.32 0.00 43.89 3.96
71 72 4.586001 CACCTTTCTATGGCCTAATGCATT 59.414 41.667 17.56 17.56 43.89 3.56
72 73 5.069516 CACCTTTCTATGGCCTAATGCATTT 59.930 40.000 18.75 0.21 43.89 2.32
73 74 5.662657 ACCTTTCTATGGCCTAATGCATTTT 59.337 36.000 18.75 0.00 43.89 1.82
74 75 6.156775 ACCTTTCTATGGCCTAATGCATTTTT 59.843 34.615 18.75 0.00 43.89 1.94
106 107 7.751768 GCCTCTGGCTATTCTAAATGTAAAT 57.248 36.000 0.73 0.00 46.69 1.40
107 108 8.848474 GCCTCTGGCTATTCTAAATGTAAATA 57.152 34.615 0.73 0.00 46.69 1.40
108 109 9.284968 GCCTCTGGCTATTCTAAATGTAAATAA 57.715 33.333 0.73 0.00 46.69 1.40
180 181 8.589335 AATATTAGACACTGCATTAGGTAACG 57.411 34.615 0.00 0.00 46.39 3.18
181 182 3.247006 AGACACTGCATTAGGTAACGG 57.753 47.619 0.00 0.00 46.39 4.44
182 183 2.829720 AGACACTGCATTAGGTAACGGA 59.170 45.455 0.00 0.00 46.39 4.69
183 184 3.451178 AGACACTGCATTAGGTAACGGAT 59.549 43.478 0.00 0.00 46.39 4.18
184 185 3.531538 ACACTGCATTAGGTAACGGATG 58.468 45.455 0.00 0.00 46.39 3.51
185 186 2.872245 CACTGCATTAGGTAACGGATGG 59.128 50.000 0.00 0.00 46.39 3.51
186 187 2.158813 ACTGCATTAGGTAACGGATGGG 60.159 50.000 0.00 0.00 46.39 4.00
187 188 1.142060 TGCATTAGGTAACGGATGGGG 59.858 52.381 0.00 0.00 46.39 4.96
188 189 1.142262 GCATTAGGTAACGGATGGGGT 59.858 52.381 0.00 0.00 46.39 4.95
189 190 2.846193 CATTAGGTAACGGATGGGGTG 58.154 52.381 0.00 0.00 46.39 4.61
190 191 1.955451 TTAGGTAACGGATGGGGTGT 58.045 50.000 0.00 0.00 46.39 4.16
191 192 2.844654 TAGGTAACGGATGGGGTGTA 57.155 50.000 0.00 0.00 46.39 2.90
192 193 1.955451 AGGTAACGGATGGGGTGTAA 58.045 50.000 0.00 0.00 46.39 2.41
193 194 2.268107 AGGTAACGGATGGGGTGTAAA 58.732 47.619 0.00 0.00 46.39 2.01
194 195 2.848071 AGGTAACGGATGGGGTGTAAAT 59.152 45.455 0.00 0.00 46.39 1.40
195 196 3.267551 AGGTAACGGATGGGGTGTAAATT 59.732 43.478 0.00 0.00 46.39 1.82
196 197 4.018490 GGTAACGGATGGGGTGTAAATTT 58.982 43.478 0.00 0.00 0.00 1.82
197 198 4.463539 GGTAACGGATGGGGTGTAAATTTT 59.536 41.667 0.00 0.00 0.00 1.82
198 199 4.529109 AACGGATGGGGTGTAAATTTTG 57.471 40.909 0.00 0.00 0.00 2.44
199 200 3.502356 ACGGATGGGGTGTAAATTTTGT 58.498 40.909 0.00 0.00 0.00 2.83
200 201 3.257127 ACGGATGGGGTGTAAATTTTGTG 59.743 43.478 0.00 0.00 0.00 3.33
201 202 3.508012 CGGATGGGGTGTAAATTTTGTGA 59.492 43.478 0.00 0.00 0.00 3.58
202 203 4.380444 CGGATGGGGTGTAAATTTTGTGAG 60.380 45.833 0.00 0.00 0.00 3.51
203 204 4.770010 GGATGGGGTGTAAATTTTGTGAGA 59.230 41.667 0.00 0.00 0.00 3.27
204 205 5.105756 GGATGGGGTGTAAATTTTGTGAGAG 60.106 44.000 0.00 0.00 0.00 3.20
205 206 3.572255 TGGGGTGTAAATTTTGTGAGAGC 59.428 43.478 0.00 0.00 0.00 4.09
206 207 3.056821 GGGGTGTAAATTTTGTGAGAGCC 60.057 47.826 0.00 0.00 0.00 4.70
207 208 3.572255 GGGTGTAAATTTTGTGAGAGCCA 59.428 43.478 0.00 0.00 0.00 4.75
208 209 4.546570 GGTGTAAATTTTGTGAGAGCCAC 58.453 43.478 0.00 0.00 45.88 5.01
209 210 4.278419 GGTGTAAATTTTGTGAGAGCCACT 59.722 41.667 0.00 0.00 45.86 4.00
210 211 5.221244 GGTGTAAATTTTGTGAGAGCCACTT 60.221 40.000 0.00 0.00 45.86 3.16
211 212 5.687285 GTGTAAATTTTGTGAGAGCCACTTG 59.313 40.000 0.00 0.00 45.86 3.16
212 213 5.359576 TGTAAATTTTGTGAGAGCCACTTGT 59.640 36.000 0.00 0.00 45.86 3.16
213 214 4.574599 AATTTTGTGAGAGCCACTTGTC 57.425 40.909 0.00 0.00 45.86 3.18
214 215 1.581934 TTTGTGAGAGCCACTTGTCG 58.418 50.000 0.00 0.00 45.86 4.35
215 216 0.464036 TTGTGAGAGCCACTTGTCGT 59.536 50.000 0.00 0.00 45.86 4.34
216 217 0.249447 TGTGAGAGCCACTTGTCGTG 60.249 55.000 0.00 0.00 45.86 4.35
217 218 0.249489 GTGAGAGCCACTTGTCGTGT 60.249 55.000 0.00 0.00 42.20 4.49
218 219 1.000607 GTGAGAGCCACTTGTCGTGTA 60.001 52.381 0.00 0.00 42.20 2.90
219 220 1.684450 TGAGAGCCACTTGTCGTGTAA 59.316 47.619 0.00 0.00 42.20 2.41
220 221 2.299013 TGAGAGCCACTTGTCGTGTAAT 59.701 45.455 0.00 0.00 42.20 1.89
221 222 3.244078 TGAGAGCCACTTGTCGTGTAATT 60.244 43.478 0.00 0.00 42.20 1.40
222 223 3.740115 AGAGCCACTTGTCGTGTAATTT 58.260 40.909 0.00 0.00 42.20 1.82
223 224 3.498397 AGAGCCACTTGTCGTGTAATTTG 59.502 43.478 0.00 0.00 42.20 2.32
224 225 2.031157 AGCCACTTGTCGTGTAATTTGC 60.031 45.455 0.00 0.00 42.20 3.68
225 226 2.287308 GCCACTTGTCGTGTAATTTGCA 60.287 45.455 0.00 0.00 42.20 4.08
226 227 3.611530 GCCACTTGTCGTGTAATTTGCAT 60.612 43.478 0.00 0.00 42.20 3.96
227 228 3.913763 CCACTTGTCGTGTAATTTGCATG 59.086 43.478 0.69 0.69 42.20 4.06
228 229 4.536065 CACTTGTCGTGTAATTTGCATGT 58.464 39.130 6.59 0.00 38.84 3.21
229 230 4.612614 CACTTGTCGTGTAATTTGCATGTC 59.387 41.667 6.59 2.58 38.84 3.06
230 231 4.274705 ACTTGTCGTGTAATTTGCATGTCA 59.725 37.500 6.59 4.92 0.00 3.58
231 232 5.048782 ACTTGTCGTGTAATTTGCATGTCAT 60.049 36.000 7.26 0.00 0.00 3.06
232 233 6.148645 ACTTGTCGTGTAATTTGCATGTCATA 59.851 34.615 7.26 0.00 0.00 2.15
233 234 6.676237 TGTCGTGTAATTTGCATGTCATAT 57.324 33.333 6.59 0.00 0.00 1.78
234 235 7.778470 TGTCGTGTAATTTGCATGTCATATA 57.222 32.000 6.59 0.00 0.00 0.86
235 236 8.376889 TGTCGTGTAATTTGCATGTCATATAT 57.623 30.769 6.59 0.00 0.00 0.86
236 237 8.835439 TGTCGTGTAATTTGCATGTCATATATT 58.165 29.630 6.59 0.00 0.00 1.28
248 249 9.723601 TGCATGTCATATATTATTGCTCTAACA 57.276 29.630 0.00 0.00 0.00 2.41
249 250 9.979270 GCATGTCATATATTATTGCTCTAACAC 57.021 33.333 0.00 0.00 0.00 3.32
275 276 8.804743 CATGATCAATGTTAGTCTCAAAAATGC 58.195 33.333 0.00 0.00 0.00 3.56
276 277 7.884257 TGATCAATGTTAGTCTCAAAAATGCA 58.116 30.769 0.00 0.00 0.00 3.96
277 278 8.525316 TGATCAATGTTAGTCTCAAAAATGCAT 58.475 29.630 0.00 0.00 0.00 3.96
278 279 9.362539 GATCAATGTTAGTCTCAAAAATGCATT 57.637 29.630 5.99 5.99 0.00 3.56
280 281 9.844790 TCAATGTTAGTCTCAAAAATGCATTAG 57.155 29.630 13.39 6.48 0.00 1.73
281 282 9.079833 CAATGTTAGTCTCAAAAATGCATTAGG 57.920 33.333 13.39 5.49 0.00 2.69
282 283 6.620678 TGTTAGTCTCAAAAATGCATTAGGC 58.379 36.000 13.39 7.92 45.13 3.93
283 284 4.725790 AGTCTCAAAAATGCATTAGGCC 57.274 40.909 13.39 0.00 43.89 5.19
284 285 3.448660 AGTCTCAAAAATGCATTAGGCCC 59.551 43.478 13.39 0.00 43.89 5.80
285 286 3.195396 GTCTCAAAAATGCATTAGGCCCA 59.805 43.478 13.39 0.00 43.89 5.36
286 287 4.032310 TCTCAAAAATGCATTAGGCCCAT 58.968 39.130 13.39 0.00 43.89 4.00
287 288 5.068987 GTCTCAAAAATGCATTAGGCCCATA 59.931 40.000 13.39 0.00 43.89 2.74
288 289 5.840149 TCTCAAAAATGCATTAGGCCCATAT 59.160 36.000 13.39 0.00 43.89 1.78
289 290 7.009550 TCTCAAAAATGCATTAGGCCCATATA 58.990 34.615 13.39 0.00 43.89 0.86
290 291 7.675195 TCTCAAAAATGCATTAGGCCCATATAT 59.325 33.333 13.39 0.00 43.89 0.86
291 292 8.891985 TCAAAAATGCATTAGGCCCATATATA 57.108 30.769 13.39 0.00 43.89 0.86
292 293 9.491406 TCAAAAATGCATTAGGCCCATATATAT 57.509 29.630 13.39 0.00 43.89 0.86
293 294 9.537192 CAAAAATGCATTAGGCCCATATATATG 57.463 33.333 13.39 14.78 43.89 1.78
294 295 9.491406 AAAAATGCATTAGGCCCATATATATGA 57.509 29.630 21.97 3.48 43.89 2.15
295 296 9.664777 AAAATGCATTAGGCCCATATATATGAT 57.335 29.630 21.97 5.57 43.89 2.45
296 297 8.645814 AATGCATTAGGCCCATATATATGATG 57.354 34.615 21.97 16.44 43.89 3.07
297 298 7.391388 TGCATTAGGCCCATATATATGATGA 57.609 36.000 21.97 4.72 43.89 2.92
298 299 7.814356 TGCATTAGGCCCATATATATGATGAA 58.186 34.615 21.97 9.63 43.89 2.57
299 300 8.450434 TGCATTAGGCCCATATATATGATGAAT 58.550 33.333 21.97 11.47 43.89 2.57
300 301 9.964354 GCATTAGGCCCATATATATGATGAATA 57.036 33.333 21.97 7.23 34.28 1.75
339 340 1.558167 TACTTGGAGGATGGCGGCAA 61.558 55.000 18.31 0.00 0.00 4.52
359 360 2.048877 CCGGCAAAAGCAAGCAGG 60.049 61.111 0.00 0.00 39.60 4.85
368 369 1.422161 AAGCAAGCAGGAGAGGGTGT 61.422 55.000 0.00 0.00 0.00 4.16
369 370 0.545309 AGCAAGCAGGAGAGGGTGTA 60.545 55.000 0.00 0.00 0.00 2.90
370 371 0.391793 GCAAGCAGGAGAGGGTGTAC 60.392 60.000 0.00 0.00 0.00 2.90
372 373 1.066573 CAAGCAGGAGAGGGTGTACTG 60.067 57.143 0.00 0.00 0.00 2.74
375 380 0.534412 CAGGAGAGGGTGTACTGCTG 59.466 60.000 0.00 0.00 43.53 4.41
398 403 2.609002 TGCTGCTGCTATACGAACAATG 59.391 45.455 17.00 0.00 40.48 2.82
429 434 8.976986 AAAACAATAAGAGAAGCAGCTAAATG 57.023 30.769 0.00 0.00 0.00 2.32
444 449 6.566376 GCAGCTAAATGTTTTGGAAACCAATG 60.566 38.462 4.03 0.00 43.55 2.82
523 528 5.290386 AGTTCAAGTAAGAGAAACGGTCAG 58.710 41.667 0.00 0.00 0.00 3.51
601 606 3.596214 GGAGCTCACTCGTGGATAAAAA 58.404 45.455 17.19 0.00 44.48 1.94
612 617 7.114811 CACTCGTGGATAAAAATCAACCAAAAG 59.885 37.037 0.00 0.00 32.32 2.27
614 619 6.265649 TCGTGGATAAAAATCAACCAAAAGGA 59.734 34.615 0.00 0.00 32.32 3.36
615 620 6.926272 CGTGGATAAAAATCAACCAAAAGGAA 59.074 34.615 0.00 0.00 32.32 3.36
616 621 7.602265 CGTGGATAAAAATCAACCAAAAGGAAT 59.398 33.333 0.00 0.00 32.32 3.01
617 622 8.720562 GTGGATAAAAATCAACCAAAAGGAATG 58.279 33.333 0.00 0.00 32.32 2.67
622 628 2.865079 TCAACCAAAAGGAATGCCGTA 58.135 42.857 0.00 0.00 39.96 4.02
702 708 7.224949 GGACATTATTTACAGGCTTCTAGACAC 59.775 40.741 0.00 0.00 0.00 3.67
735 741 6.618287 TCAAACTTCTGAACGTGATTTGAT 57.382 33.333 0.00 0.00 31.51 2.57
736 742 6.658831 TCAAACTTCTGAACGTGATTTGATC 58.341 36.000 0.00 0.00 31.51 2.92
754 760 0.042581 TCAGGGGTGTGGCTAGATCA 59.957 55.000 0.00 0.00 0.00 2.92
757 763 2.301296 CAGGGGTGTGGCTAGATCATAG 59.699 54.545 0.00 0.00 0.00 2.23
759 765 2.706190 GGGGTGTGGCTAGATCATAGTT 59.294 50.000 0.00 0.00 0.00 2.24
768 783 5.300539 TGGCTAGATCATAGTTGACTGAGAC 59.699 44.000 0.00 0.00 33.85 3.36
769 784 5.534654 GGCTAGATCATAGTTGACTGAGACT 59.465 44.000 0.00 0.00 33.85 3.24
770 785 6.040391 GGCTAGATCATAGTTGACTGAGACTT 59.960 42.308 0.00 0.00 33.85 3.01
771 786 7.229707 GGCTAGATCATAGTTGACTGAGACTTA 59.770 40.741 0.00 0.00 33.85 2.24
772 787 8.625651 GCTAGATCATAGTTGACTGAGACTTAA 58.374 37.037 0.00 0.00 33.85 1.85
775 790 9.194972 AGATCATAGTTGACTGAGACTTAATCA 57.805 33.333 0.00 0.00 33.85 2.57
776 791 9.809096 GATCATAGTTGACTGAGACTTAATCAA 57.191 33.333 0.00 0.00 33.85 2.57
779 794 9.429359 CATAGTTGACTGAGACTTAATCAAGTT 57.571 33.333 4.37 0.00 45.18 2.66
789 804 9.832445 TGAGACTTAATCAAGTTTTAGTCAAGT 57.168 29.630 10.71 0.00 45.18 3.16
813 829 9.793259 AGTGAGAAAACATATAAAGGAGAACAA 57.207 29.630 0.00 0.00 0.00 2.83
907 930 2.304761 TCTGAGGTTTAGCAATCCCGTT 59.695 45.455 0.00 0.00 0.00 4.44
908 931 2.420022 CTGAGGTTTAGCAATCCCGTTG 59.580 50.000 0.00 0.00 40.90 4.10
910 933 2.418976 GAGGTTTAGCAATCCCGTTGAC 59.581 50.000 0.00 0.00 40.37 3.18
911 934 2.039879 AGGTTTAGCAATCCCGTTGACT 59.960 45.455 0.00 0.00 40.37 3.41
940 963 2.895680 GCTCTCTGCGATCCACCA 59.104 61.111 0.00 0.00 0.00 4.17
985 1010 3.551890 CGTGGTCATTCGATGTAAAGAGG 59.448 47.826 0.00 0.00 0.00 3.69
998 1023 3.876914 TGTAAAGAGGCACACACAAGAAG 59.123 43.478 0.00 0.00 0.00 2.85
1035 1060 1.466025 TACCGTTGCTCTGGTCCGTT 61.466 55.000 0.00 0.00 39.70 4.44
1037 1062 2.946762 GTTGCTCTGGTCCGTTGC 59.053 61.111 0.00 0.00 0.00 4.17
1051 1076 0.944386 CGTTGCCCCCTTAATCATCG 59.056 55.000 0.00 0.00 0.00 3.84
1170 1195 4.393155 TTCCTGCTGTCGCGCCAT 62.393 61.111 0.00 0.00 39.65 4.40
1217 1242 2.431601 GCTCTCTCGCAAGCACGT 60.432 61.111 0.00 0.00 38.42 4.49
1278 1303 2.780094 CGTCTCATCTGCCGAGGCT 61.780 63.158 15.75 0.00 42.51 4.58
1495 1528 3.371097 GAGGTCGCCGCCTTGATCA 62.371 63.158 1.75 0.00 39.34 2.92
1641 1680 1.956170 CGAGTTCCTGCACGTGCTT 60.956 57.895 37.59 17.83 42.66 3.91
1650 1689 3.403057 CACGTGCTTGACCGGTCG 61.403 66.667 28.70 18.90 0.00 4.79
1700 1739 1.283905 TGACCTCTACCCATCGTCAGA 59.716 52.381 0.00 0.00 0.00 3.27
1857 1896 2.526873 AGGGTGCAGAAGGACGGT 60.527 61.111 0.00 0.00 36.89 4.83
2106 2149 2.030027 ACTTGGTGATCAGGGAGACA 57.970 50.000 0.00 0.00 0.00 3.41
2113 2156 0.179000 GATCAGGGAGACATTGCGGT 59.821 55.000 0.00 0.00 0.00 5.68
2140 2183 1.745489 CCGTTGCCCTTCCTGCTAC 60.745 63.158 0.00 0.00 0.00 3.58
2141 2184 1.745489 CGTTGCCCTTCCTGCTACC 60.745 63.158 0.00 0.00 32.01 3.18
2142 2185 1.378762 GTTGCCCTTCCTGCTACCA 59.621 57.895 0.00 0.00 0.00 3.25
2143 2186 0.960861 GTTGCCCTTCCTGCTACCAC 60.961 60.000 0.00 0.00 0.00 4.16
2144 2187 2.125106 GCCCTTCCTGCTACCACG 60.125 66.667 0.00 0.00 0.00 4.94
2145 2188 2.584608 CCCTTCCTGCTACCACGG 59.415 66.667 0.00 0.00 0.00 4.94
2146 2189 2.291043 CCCTTCCTGCTACCACGGT 61.291 63.158 0.00 0.00 0.00 4.83
2213 2256 1.900486 CCGAGGGTACAAAGGTTCTCT 59.100 52.381 0.00 0.00 0.00 3.10
2294 2337 1.099689 GGAGAGGTTCGAGGAGAGTG 58.900 60.000 0.00 0.00 0.00 3.51
2297 2340 1.228894 AGGTTCGAGGAGAGTGGCA 60.229 57.895 0.00 0.00 0.00 4.92
2335 2384 2.499685 GGCGGCCACTTCGAGTAT 59.500 61.111 15.62 0.00 0.00 2.12
2577 5466 2.433239 AGGTTTAGGACGCCGATAACAT 59.567 45.455 0.00 0.00 0.00 2.71
2605 5496 2.355986 TGGCATTAGACGTCCGCCT 61.356 57.895 26.44 8.50 43.38 5.52
2648 5539 1.692173 GGAGGCAACCTATACGGGCA 61.692 60.000 0.00 0.00 36.97 5.36
2682 5573 9.256477 GACGAACATTAGAATTGTCCATACATA 57.744 33.333 0.00 0.00 34.97 2.29
2734 5625 7.106239 CCCAACAAGTACTACTCATCTTCATT 58.894 38.462 0.00 0.00 0.00 2.57
2737 5628 9.208022 CAACAAGTACTACTCATCTTCATTTCA 57.792 33.333 0.00 0.00 0.00 2.69
2746 5637 2.617250 TCTTCATTTCATGCGTGTGC 57.383 45.000 5.68 0.00 43.20 4.57
2794 5687 2.770699 ACGCAGCTACGTTAGGTATC 57.229 50.000 6.06 0.00 45.75 2.24
2799 5693 0.588252 GCTACGTTAGGTATCCGCGA 59.412 55.000 8.23 0.00 0.00 5.87
2830 5724 2.537560 GCTGCCATCCGGAATGACG 61.538 63.158 9.01 0.00 37.59 4.35
2927 5823 7.116075 TGCCATGTCTAATTTATGGTAGTTGT 58.884 34.615 0.00 0.00 42.60 3.32
2931 5827 6.399743 TGTCTAATTTATGGTAGTTGTCGCA 58.600 36.000 0.00 0.00 0.00 5.10
2937 5833 7.618502 ATTTATGGTAGTTGTCGCATGTAAA 57.381 32.000 0.00 0.00 0.00 2.01
2997 5893 5.312895 ACATATGGTCAAACAGTAGTTGCA 58.687 37.500 7.80 0.00 38.17 4.08
2998 5894 5.945784 ACATATGGTCAAACAGTAGTTGCAT 59.054 36.000 7.80 0.00 38.17 3.96
3004 5900 5.008217 GGTCAAACAGTAGTTGCATTGTGTA 59.992 40.000 0.00 0.00 38.17 2.90
3008 5904 8.194104 TCAAACAGTAGTTGCATTGTGTATTTT 58.806 29.630 0.00 0.00 38.17 1.82
3021 5917 7.630513 GCATTGTGTATTTTACCTAGTTGCCAT 60.631 37.037 0.00 0.00 0.00 4.40
3026 5922 6.717540 TGTATTTTACCTAGTTGCCATGTGTT 59.282 34.615 0.00 0.00 0.00 3.32
3033 5929 2.318908 AGTTGCCATGTGTTGTCCAAT 58.681 42.857 0.00 0.00 0.00 3.16
3038 5934 4.085009 TGCCATGTGTTGTCCAATCATAA 58.915 39.130 0.00 0.00 0.00 1.90
3090 5986 4.657013 TGTATGTTTATCTGGTTGCCACA 58.343 39.130 0.00 0.00 0.00 4.17
3094 5990 4.013728 TGTTTATCTGGTTGCCACATACC 58.986 43.478 0.00 0.00 34.93 2.73
3096 5992 0.998928 ATCTGGTTGCCACATACCCA 59.001 50.000 0.00 0.00 33.34 4.51
3100 5996 1.203112 TGGTTGCCACATACCCACAAT 60.203 47.619 0.00 0.00 33.34 2.71
3247 6143 2.434359 GCGTGGACTAGGTGGTGC 60.434 66.667 0.00 0.00 0.00 5.01
3289 6185 2.901840 CCACACAACGCAGCTGGT 60.902 61.111 17.12 8.98 0.00 4.00
3314 6211 2.112928 ATGTTGCAGGGCGTGTGA 59.887 55.556 9.16 0.00 0.00 3.58
3374 6271 1.512734 GCATGCGAAAACTGCCTCG 60.513 57.895 0.00 0.00 38.11 4.63
3389 6286 1.608025 GCCTCGGTGTGTCAAGATTCA 60.608 52.381 0.00 0.00 0.00 2.57
3419 6316 1.141665 CTGGACGATGATCCACGCA 59.858 57.895 8.22 0.49 44.14 5.24
3421 6318 0.530431 TGGACGATGATCCACGCATG 60.530 55.000 8.22 0.00 44.14 4.06
3422 6319 0.530650 GGACGATGATCCACGCATGT 60.531 55.000 8.22 0.00 38.77 3.21
3423 6320 0.578683 GACGATGATCCACGCATGTG 59.421 55.000 4.30 4.30 46.00 3.21
3469 6371 7.132213 CACATATGGGCGTTAGTATTTTTGAG 58.868 38.462 7.80 0.00 0.00 3.02
3530 6433 1.137675 TCTGCGGATCATGGAACTGAG 59.862 52.381 0.00 0.00 0.00 3.35
3531 6434 0.462581 TGCGGATCATGGAACTGAGC 60.463 55.000 0.00 0.00 0.00 4.26
3532 6435 1.493950 GCGGATCATGGAACTGAGCG 61.494 60.000 0.00 0.00 32.35 5.03
3533 6436 0.103026 CGGATCATGGAACTGAGCGA 59.897 55.000 0.00 0.00 32.35 4.93
3534 6437 1.269988 CGGATCATGGAACTGAGCGAT 60.270 52.381 0.00 0.00 32.35 4.58
3535 6438 2.029918 CGGATCATGGAACTGAGCGATA 60.030 50.000 0.00 0.00 32.35 2.92
3536 6439 3.367806 CGGATCATGGAACTGAGCGATAT 60.368 47.826 0.00 0.00 32.35 1.63
3537 6440 3.931468 GGATCATGGAACTGAGCGATATG 59.069 47.826 0.00 0.00 32.35 1.78
3538 6441 3.391506 TCATGGAACTGAGCGATATGG 57.608 47.619 0.00 0.00 0.00 2.74
3539 6442 2.700371 TCATGGAACTGAGCGATATGGT 59.300 45.455 0.00 0.00 0.00 3.55
3540 6443 2.602257 TGGAACTGAGCGATATGGTG 57.398 50.000 0.00 0.00 0.00 4.17
3541 6444 1.831106 TGGAACTGAGCGATATGGTGT 59.169 47.619 0.00 0.00 0.00 4.16
3542 6445 3.028130 TGGAACTGAGCGATATGGTGTA 58.972 45.455 0.00 0.00 0.00 2.90
3543 6446 3.449377 TGGAACTGAGCGATATGGTGTAA 59.551 43.478 0.00 0.00 0.00 2.41
3544 6447 3.802685 GGAACTGAGCGATATGGTGTAAC 59.197 47.826 0.00 0.00 0.00 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.565307 AGGAGATCTCAGCTCTTCGAAT 58.435 45.455 23.85 0.00 32.98 3.34
3 4 3.011566 AGGAGATCTCAGCTCTTCGAA 57.988 47.619 23.85 0.00 32.98 3.71
4 5 2.727123 AGGAGATCTCAGCTCTTCGA 57.273 50.000 23.85 0.00 32.98 3.71
5 6 4.261572 CCTTTAGGAGATCTCAGCTCTTCG 60.262 50.000 23.85 4.63 37.39 3.79
6 7 4.892934 TCCTTTAGGAGATCTCAGCTCTTC 59.107 45.833 23.85 5.00 39.78 2.87
7 8 4.877773 TCCTTTAGGAGATCTCAGCTCTT 58.122 43.478 23.85 4.98 39.78 2.85
8 9 4.534647 TCCTTTAGGAGATCTCAGCTCT 57.465 45.455 23.85 13.71 39.78 4.09
9 10 5.606348 TTTCCTTTAGGAGATCTCAGCTC 57.394 43.478 23.85 6.82 46.36 4.09
10 11 6.380079 TTTTTCCTTTAGGAGATCTCAGCT 57.620 37.500 23.85 14.73 46.36 4.24
11 12 7.637631 AATTTTTCCTTTAGGAGATCTCAGC 57.362 36.000 23.85 7.92 46.36 4.26
12 13 8.835439 GCTAATTTTTCCTTTAGGAGATCTCAG 58.165 37.037 23.85 12.28 46.36 3.35
13 14 8.552296 AGCTAATTTTTCCTTTAGGAGATCTCA 58.448 33.333 23.85 1.54 46.36 3.27
14 15 8.972458 AGCTAATTTTTCCTTTAGGAGATCTC 57.028 34.615 14.75 14.75 46.36 2.75
15 16 9.839817 GTAGCTAATTTTTCCTTTAGGAGATCT 57.160 33.333 0.00 0.00 46.36 2.75
16 17 9.839817 AGTAGCTAATTTTTCCTTTAGGAGATC 57.160 33.333 0.00 0.00 46.36 2.75
17 18 9.839817 GAGTAGCTAATTTTTCCTTTAGGAGAT 57.160 33.333 0.00 0.00 46.36 2.75
18 19 8.265764 GGAGTAGCTAATTTTTCCTTTAGGAGA 58.734 37.037 0.00 0.00 46.36 3.71
19 20 7.499563 GGGAGTAGCTAATTTTTCCTTTAGGAG 59.500 40.741 0.00 0.00 46.36 3.69
20 21 7.184022 AGGGAGTAGCTAATTTTTCCTTTAGGA 59.816 37.037 0.00 0.00 43.73 2.94
21 22 7.347252 AGGGAGTAGCTAATTTTTCCTTTAGG 58.653 38.462 0.00 0.00 0.00 2.69
22 23 7.499563 GGAGGGAGTAGCTAATTTTTCCTTTAG 59.500 40.741 0.00 0.00 0.00 1.85
23 24 7.037153 TGGAGGGAGTAGCTAATTTTTCCTTTA 60.037 37.037 15.24 4.75 0.00 1.85
24 25 6.188407 GGAGGGAGTAGCTAATTTTTCCTTT 58.812 40.000 0.00 0.00 0.00 3.11
25 26 5.253096 TGGAGGGAGTAGCTAATTTTTCCTT 59.747 40.000 15.24 6.94 0.00 3.36
26 27 4.788617 TGGAGGGAGTAGCTAATTTTTCCT 59.211 41.667 15.24 11.06 0.00 3.36
27 28 4.882427 GTGGAGGGAGTAGCTAATTTTTCC 59.118 45.833 0.00 3.58 0.00 3.13
28 29 4.882427 GGTGGAGGGAGTAGCTAATTTTTC 59.118 45.833 0.00 0.00 0.00 2.29
29 30 4.540502 AGGTGGAGGGAGTAGCTAATTTTT 59.459 41.667 0.00 0.00 0.00 1.94
30 31 4.112331 AGGTGGAGGGAGTAGCTAATTTT 58.888 43.478 0.00 0.00 0.00 1.82
31 32 3.737263 AGGTGGAGGGAGTAGCTAATTT 58.263 45.455 0.00 0.00 0.00 1.82
32 33 3.423058 AGGTGGAGGGAGTAGCTAATT 57.577 47.619 0.00 0.00 0.00 1.40
33 34 3.423058 AAGGTGGAGGGAGTAGCTAAT 57.577 47.619 0.00 0.00 0.00 1.73
34 35 2.942604 AAGGTGGAGGGAGTAGCTAA 57.057 50.000 0.00 0.00 0.00 3.09
35 36 2.315155 AGAAAGGTGGAGGGAGTAGCTA 59.685 50.000 0.00 0.00 0.00 3.32
36 37 1.079658 AGAAAGGTGGAGGGAGTAGCT 59.920 52.381 0.00 0.00 0.00 3.32
37 38 1.574263 AGAAAGGTGGAGGGAGTAGC 58.426 55.000 0.00 0.00 0.00 3.58
38 39 3.643792 CCATAGAAAGGTGGAGGGAGTAG 59.356 52.174 0.00 0.00 37.72 2.57
39 40 3.654273 CCATAGAAAGGTGGAGGGAGTA 58.346 50.000 0.00 0.00 37.72 2.59
40 41 2.482494 CCATAGAAAGGTGGAGGGAGT 58.518 52.381 0.00 0.00 37.72 3.85
41 42 1.141858 GCCATAGAAAGGTGGAGGGAG 59.858 57.143 0.00 0.00 37.72 4.30
42 43 1.213296 GCCATAGAAAGGTGGAGGGA 58.787 55.000 0.00 0.00 37.72 4.20
43 44 0.183731 GGCCATAGAAAGGTGGAGGG 59.816 60.000 0.00 0.00 37.72 4.30
44 45 1.216990 AGGCCATAGAAAGGTGGAGG 58.783 55.000 5.01 0.00 37.72 4.30
45 46 4.392940 CATTAGGCCATAGAAAGGTGGAG 58.607 47.826 5.01 0.00 37.72 3.86
46 47 3.435026 GCATTAGGCCATAGAAAGGTGGA 60.435 47.826 5.01 0.00 37.72 4.02
47 48 2.887152 GCATTAGGCCATAGAAAGGTGG 59.113 50.000 5.01 0.00 38.55 4.61
48 49 3.554934 TGCATTAGGCCATAGAAAGGTG 58.445 45.455 5.01 0.00 43.89 4.00
49 50 3.951563 TGCATTAGGCCATAGAAAGGT 57.048 42.857 5.01 0.00 43.89 3.50
50 51 5.796424 AAATGCATTAGGCCATAGAAAGG 57.204 39.130 13.39 0.00 43.89 3.11
154 155 9.042008 CGTTACCTAATGCAGTGTCTAATATTT 57.958 33.333 0.00 0.00 0.00 1.40
155 156 7.656137 CCGTTACCTAATGCAGTGTCTAATATT 59.344 37.037 0.00 0.00 0.00 1.28
156 157 7.014905 TCCGTTACCTAATGCAGTGTCTAATAT 59.985 37.037 0.00 0.00 0.00 1.28
157 158 6.321945 TCCGTTACCTAATGCAGTGTCTAATA 59.678 38.462 0.00 0.00 0.00 0.98
158 159 5.128171 TCCGTTACCTAATGCAGTGTCTAAT 59.872 40.000 0.00 0.00 0.00 1.73
159 160 4.463539 TCCGTTACCTAATGCAGTGTCTAA 59.536 41.667 0.00 0.00 0.00 2.10
160 161 4.018490 TCCGTTACCTAATGCAGTGTCTA 58.982 43.478 0.00 0.00 0.00 2.59
161 162 2.829720 TCCGTTACCTAATGCAGTGTCT 59.170 45.455 0.00 0.00 0.00 3.41
162 163 3.241067 TCCGTTACCTAATGCAGTGTC 57.759 47.619 0.00 0.00 0.00 3.67
163 164 3.531538 CATCCGTTACCTAATGCAGTGT 58.468 45.455 0.00 0.00 0.00 3.55
164 165 2.872245 CCATCCGTTACCTAATGCAGTG 59.128 50.000 0.00 0.00 0.00 3.66
165 166 2.158813 CCCATCCGTTACCTAATGCAGT 60.159 50.000 0.00 0.00 0.00 4.40
166 167 2.494059 CCCATCCGTTACCTAATGCAG 58.506 52.381 0.00 0.00 0.00 4.41
167 168 1.142060 CCCCATCCGTTACCTAATGCA 59.858 52.381 0.00 0.00 0.00 3.96
168 169 1.142262 ACCCCATCCGTTACCTAATGC 59.858 52.381 0.00 0.00 0.00 3.56
169 170 2.171870 ACACCCCATCCGTTACCTAATG 59.828 50.000 0.00 0.00 0.00 1.90
170 171 2.484602 ACACCCCATCCGTTACCTAAT 58.515 47.619 0.00 0.00 0.00 1.73
171 172 1.955451 ACACCCCATCCGTTACCTAA 58.045 50.000 0.00 0.00 0.00 2.69
172 173 2.844654 TACACCCCATCCGTTACCTA 57.155 50.000 0.00 0.00 0.00 3.08
173 174 1.955451 TTACACCCCATCCGTTACCT 58.045 50.000 0.00 0.00 0.00 3.08
174 175 2.785540 TTTACACCCCATCCGTTACC 57.214 50.000 0.00 0.00 0.00 2.85
175 176 5.047872 ACAAAATTTACACCCCATCCGTTAC 60.048 40.000 0.00 0.00 0.00 2.50
176 177 5.047943 CACAAAATTTACACCCCATCCGTTA 60.048 40.000 0.00 0.00 0.00 3.18
177 178 3.898741 ACAAAATTTACACCCCATCCGTT 59.101 39.130 0.00 0.00 0.00 4.44
178 179 3.257127 CACAAAATTTACACCCCATCCGT 59.743 43.478 0.00 0.00 0.00 4.69
179 180 3.508012 TCACAAAATTTACACCCCATCCG 59.492 43.478 0.00 0.00 0.00 4.18
180 181 4.770010 TCTCACAAAATTTACACCCCATCC 59.230 41.667 0.00 0.00 0.00 3.51
181 182 5.622233 GCTCTCACAAAATTTACACCCCATC 60.622 44.000 0.00 0.00 0.00 3.51
182 183 4.220602 GCTCTCACAAAATTTACACCCCAT 59.779 41.667 0.00 0.00 0.00 4.00
183 184 3.572255 GCTCTCACAAAATTTACACCCCA 59.428 43.478 0.00 0.00 0.00 4.96
184 185 3.056821 GGCTCTCACAAAATTTACACCCC 60.057 47.826 0.00 0.00 0.00 4.95
185 186 3.572255 TGGCTCTCACAAAATTTACACCC 59.428 43.478 0.00 0.00 0.00 4.61
186 187 4.546570 GTGGCTCTCACAAAATTTACACC 58.453 43.478 0.00 0.00 45.39 4.16
198 199 2.522060 CACGACAAGTGGCTCTCAC 58.478 57.895 0.00 0.00 46.77 3.51
207 208 4.274705 TGACATGCAAATTACACGACAAGT 59.725 37.500 0.00 0.00 0.00 3.16
208 209 4.782156 TGACATGCAAATTACACGACAAG 58.218 39.130 0.00 0.00 0.00 3.16
209 210 4.820284 TGACATGCAAATTACACGACAA 57.180 36.364 0.00 0.00 0.00 3.18
210 211 6.676237 ATATGACATGCAAATTACACGACA 57.324 33.333 0.00 0.00 0.00 4.35
222 223 9.723601 TGTTAGAGCAATAATATATGACATGCA 57.276 29.630 10.78 0.00 34.89 3.96
223 224 9.979270 GTGTTAGAGCAATAATATATGACATGC 57.021 33.333 0.00 2.62 0.00 4.06
234 235 9.128404 ACATTGATCATGTGTTAGAGCAATAAT 57.872 29.630 0.00 0.00 45.78 1.28
235 236 8.510243 ACATTGATCATGTGTTAGAGCAATAA 57.490 30.769 0.00 0.00 45.78 1.40
236 237 8.510243 AACATTGATCATGTGTTAGAGCAATA 57.490 30.769 19.62 0.00 45.78 1.90
238 239 6.822667 AACATTGATCATGTGTTAGAGCAA 57.177 33.333 19.62 0.00 46.23 3.91
244 245 9.500785 TTTGAGACTAACATTGATCATGTGTTA 57.499 29.630 22.56 22.56 46.23 2.41
245 246 7.984422 TTGAGACTAACATTGATCATGTGTT 57.016 32.000 22.70 22.70 46.23 3.32
246 247 7.984422 TTTGAGACTAACATTGATCATGTGT 57.016 32.000 10.32 9.25 46.23 3.72
247 248 9.850628 ATTTTTGAGACTAACATTGATCATGTG 57.149 29.630 10.32 8.71 46.23 3.21
249 250 8.804743 GCATTTTTGAGACTAACATTGATCATG 58.195 33.333 0.00 0.00 39.07 3.07
250 251 8.525316 TGCATTTTTGAGACTAACATTGATCAT 58.475 29.630 0.00 0.00 0.00 2.45
251 252 7.884257 TGCATTTTTGAGACTAACATTGATCA 58.116 30.769 0.00 0.00 0.00 2.92
252 253 8.922058 ATGCATTTTTGAGACTAACATTGATC 57.078 30.769 0.00 0.00 0.00 2.92
254 255 9.844790 CTAATGCATTTTTGAGACTAACATTGA 57.155 29.630 18.75 0.00 0.00 2.57
255 256 9.079833 CCTAATGCATTTTTGAGACTAACATTG 57.920 33.333 18.75 0.00 0.00 2.82
256 257 7.761249 GCCTAATGCATTTTTGAGACTAACATT 59.239 33.333 18.75 0.00 40.77 2.71
257 258 7.260603 GCCTAATGCATTTTTGAGACTAACAT 58.739 34.615 18.75 0.00 40.77 2.71
258 259 6.350110 GGCCTAATGCATTTTTGAGACTAACA 60.350 38.462 18.75 0.00 43.89 2.41
259 260 6.036470 GGCCTAATGCATTTTTGAGACTAAC 58.964 40.000 18.75 0.00 43.89 2.34
260 261 5.127031 GGGCCTAATGCATTTTTGAGACTAA 59.873 40.000 18.75 0.00 43.89 2.24
261 262 4.644685 GGGCCTAATGCATTTTTGAGACTA 59.355 41.667 18.75 0.00 43.89 2.59
262 263 3.448660 GGGCCTAATGCATTTTTGAGACT 59.551 43.478 18.75 0.00 43.89 3.24
263 264 3.195396 TGGGCCTAATGCATTTTTGAGAC 59.805 43.478 18.75 0.68 43.89 3.36
264 265 3.439154 TGGGCCTAATGCATTTTTGAGA 58.561 40.909 18.75 0.00 43.89 3.27
265 266 3.891422 TGGGCCTAATGCATTTTTGAG 57.109 42.857 18.75 8.61 43.89 3.02
266 267 7.795534 ATATATGGGCCTAATGCATTTTTGA 57.204 32.000 18.75 0.00 43.89 2.69
267 268 9.537192 CATATATATGGGCCTAATGCATTTTTG 57.463 33.333 18.75 7.65 43.89 2.44
268 269 9.491406 TCATATATATGGGCCTAATGCATTTTT 57.509 29.630 18.75 0.00 35.50 1.94
269 270 9.664777 ATCATATATATGGGCCTAATGCATTTT 57.335 29.630 18.75 0.00 35.50 1.82
270 271 9.085645 CATCATATATATGGGCCTAATGCATTT 57.914 33.333 18.75 0.00 35.50 2.32
271 272 8.450434 TCATCATATATATGGGCCTAATGCATT 58.550 33.333 20.18 17.56 35.50 3.56
272 273 7.992295 TCATCATATATATGGGCCTAATGCAT 58.008 34.615 20.18 0.00 35.50 3.96
273 274 7.391388 TCATCATATATATGGGCCTAATGCA 57.609 36.000 20.18 0.00 35.50 3.96
274 275 8.874744 ATTCATCATATATATGGGCCTAATGC 57.125 34.615 20.18 0.00 34.50 3.56
303 304 8.467598 CCTCCAAGTACGCATATATATAGTGTT 58.532 37.037 13.12 5.85 0.00 3.32
304 305 7.832685 TCCTCCAAGTACGCATATATATAGTGT 59.167 37.037 11.26 12.04 0.00 3.55
305 306 8.221965 TCCTCCAAGTACGCATATATATAGTG 57.778 38.462 11.26 8.07 0.00 2.74
306 307 8.851145 CATCCTCCAAGTACGCATATATATAGT 58.149 37.037 0.00 2.06 0.00 2.12
307 308 8.300286 CCATCCTCCAAGTACGCATATATATAG 58.700 40.741 0.00 0.00 0.00 1.31
308 309 7.255836 GCCATCCTCCAAGTACGCATATATATA 60.256 40.741 0.00 0.00 0.00 0.86
309 310 6.463049 GCCATCCTCCAAGTACGCATATATAT 60.463 42.308 0.00 0.00 0.00 0.86
310 311 5.163447 GCCATCCTCCAAGTACGCATATATA 60.163 44.000 0.00 0.00 0.00 0.86
311 312 4.383118 GCCATCCTCCAAGTACGCATATAT 60.383 45.833 0.00 0.00 0.00 0.86
312 313 3.056107 GCCATCCTCCAAGTACGCATATA 60.056 47.826 0.00 0.00 0.00 0.86
313 314 2.289694 GCCATCCTCCAAGTACGCATAT 60.290 50.000 0.00 0.00 0.00 1.78
314 315 1.070134 GCCATCCTCCAAGTACGCATA 59.930 52.381 0.00 0.00 0.00 3.14
315 316 0.179045 GCCATCCTCCAAGTACGCAT 60.179 55.000 0.00 0.00 0.00 4.73
316 317 1.220749 GCCATCCTCCAAGTACGCA 59.779 57.895 0.00 0.00 0.00 5.24
317 318 1.883084 CGCCATCCTCCAAGTACGC 60.883 63.158 0.00 0.00 0.00 4.42
318 319 1.227263 CCGCCATCCTCCAAGTACG 60.227 63.158 0.00 0.00 0.00 3.67
319 320 1.523938 GCCGCCATCCTCCAAGTAC 60.524 63.158 0.00 0.00 0.00 2.73
320 321 1.558167 TTGCCGCCATCCTCCAAGTA 61.558 55.000 0.00 0.00 0.00 2.24
321 322 2.424842 TTTGCCGCCATCCTCCAAGT 62.425 55.000 0.00 0.00 0.00 3.16
322 323 1.660560 CTTTGCCGCCATCCTCCAAG 61.661 60.000 0.00 0.00 0.00 3.61
323 324 1.678635 CTTTGCCGCCATCCTCCAA 60.679 57.895 0.00 0.00 0.00 3.53
324 325 2.045045 CTTTGCCGCCATCCTCCA 60.045 61.111 0.00 0.00 0.00 3.86
325 326 3.521796 GCTTTGCCGCCATCCTCC 61.522 66.667 0.00 0.00 0.00 4.30
339 340 2.029518 GCTTGCTTTTGCCGGCTT 59.970 55.556 29.70 0.00 46.87 4.35
359 360 0.108424 CAGCAGCAGTACACCCTCTC 60.108 60.000 0.00 0.00 0.00 3.20
375 380 0.579156 GTTCGTATAGCAGCAGCAGC 59.421 55.000 3.17 0.46 45.49 5.25
398 403 7.018235 GCTGCTTCTCTTATTGTTTTAGTGTC 58.982 38.462 0.00 0.00 0.00 3.67
523 528 1.181098 AGCAGCCATGGTGGTCAAAC 61.181 55.000 14.67 0.00 40.46 2.93
587 592 6.642707 TTTGGTTGATTTTTATCCACGAGT 57.357 33.333 0.00 0.00 0.00 4.18
601 606 2.247358 ACGGCATTCCTTTTGGTTGAT 58.753 42.857 0.00 0.00 41.38 2.57
612 617 3.563808 TGCAATAATGTCTACGGCATTCC 59.436 43.478 0.00 0.00 37.65 3.01
614 619 3.565482 CCTGCAATAATGTCTACGGCATT 59.435 43.478 0.00 0.00 39.55 3.56
615 620 3.141398 CCTGCAATAATGTCTACGGCAT 58.859 45.455 0.00 0.00 0.00 4.40
616 621 2.560504 CCTGCAATAATGTCTACGGCA 58.439 47.619 0.00 0.00 0.00 5.69
617 622 1.264288 GCCTGCAATAATGTCTACGGC 59.736 52.381 0.00 0.00 0.00 5.68
622 628 4.512944 CGTTATCAGCCTGCAATAATGTCT 59.487 41.667 0.00 0.00 0.00 3.41
702 708 4.829064 TCAGAAGTTTGAAACAATCGGG 57.171 40.909 11.02 6.56 0.00 5.14
735 741 0.042581 TGATCTAGCCACACCCCTGA 59.957 55.000 0.00 0.00 0.00 3.86
736 742 1.135094 ATGATCTAGCCACACCCCTG 58.865 55.000 0.00 0.00 0.00 4.45
739 745 3.388024 TCAACTATGATCTAGCCACACCC 59.612 47.826 0.00 0.00 0.00 4.61
759 765 9.477484 GACTAAAACTTGATTAAGTCTCAGTCA 57.523 33.333 21.04 0.00 46.14 3.41
771 786 9.788960 GTTTTCTCACTTGACTAAAACTTGATT 57.211 29.630 13.28 0.00 34.85 2.57
772 787 8.956426 TGTTTTCTCACTTGACTAAAACTTGAT 58.044 29.630 17.70 0.00 36.62 2.57
773 788 8.330466 TGTTTTCTCACTTGACTAAAACTTGA 57.670 30.769 17.70 4.56 36.62 3.02
846 868 7.027760 GTCGATGCTATATTCGTGGAATCTTA 58.972 38.462 0.00 0.00 36.74 2.10
853 875 6.150318 AGTTTAGTCGATGCTATATTCGTGG 58.850 40.000 0.00 0.00 36.74 4.94
907 930 5.639506 GCAGAGAGCTGTTGTTTATTAGTCA 59.360 40.000 0.00 0.00 44.17 3.41
908 931 5.220303 CGCAGAGAGCTGTTGTTTATTAGTC 60.220 44.000 0.00 0.00 44.17 2.59
910 933 4.864806 TCGCAGAGAGCTGTTGTTTATTAG 59.135 41.667 0.00 0.00 44.17 1.73
911 934 4.816392 TCGCAGAGAGCTGTTGTTTATTA 58.184 39.130 0.00 0.00 44.17 0.98
940 963 5.220854 CGTCCTGAATTTAAATGGCTCGATT 60.221 40.000 0.39 0.00 0.00 3.34
985 1010 2.351157 GCTCCATTCTTCTTGTGTGTGC 60.351 50.000 0.00 0.00 0.00 4.57
998 1023 0.107508 TAGTGCTGCAGGCTCCATTC 60.108 55.000 17.12 0.00 42.39 2.67
1017 1042 2.803817 AACGGACCAGAGCAACGGT 61.804 57.895 0.00 0.00 38.56 4.83
1035 1060 2.367567 GAGTACGATGATTAAGGGGGCA 59.632 50.000 0.00 0.00 0.00 5.36
1037 1062 4.589374 AGAAGAGTACGATGATTAAGGGGG 59.411 45.833 0.00 0.00 0.00 5.40
1131 1156 2.037367 TGGAGGCTGCCTACGAGT 59.963 61.111 25.27 0.23 37.26 4.18
1196 1221 2.202864 GCTTGCGAGAGAGCTCCC 60.203 66.667 10.93 0.00 37.91 4.30
1495 1528 1.135257 GCACTCGTCTGTGATGTAGCT 60.135 52.381 9.37 0.00 40.12 3.32
1650 1689 3.365265 CCACCGGCAAGCTTCACC 61.365 66.667 0.00 0.00 0.00 4.02
1822 1861 2.249413 CTCAGCAGCACCCCGAGAAT 62.249 60.000 0.00 0.00 0.00 2.40
1870 1909 1.606601 CGGTGGTGAGGTCCAGAGA 60.607 63.158 0.00 0.00 38.23 3.10
1911 1950 0.899720 TCCCGGCTACGAACATTTCT 59.100 50.000 0.00 0.00 44.60 2.52
1947 1986 2.053865 CATGGCCCATTCCAGCGTT 61.054 57.895 0.00 0.00 39.89 4.84
1992 2031 3.650950 GCCTGGGCCTTGTGGAGA 61.651 66.667 4.53 0.00 34.57 3.71
2130 2173 1.218316 GGACCGTGGTAGCAGGAAG 59.782 63.158 15.79 3.07 0.00 3.46
2213 2256 2.597217 CAAGGCCCAGGCGTTCAA 60.597 61.111 13.44 0.00 45.69 2.69
2297 2340 4.778143 GAAGTCCATGGCGGCGGT 62.778 66.667 9.78 0.00 33.14 5.68
2459 4812 0.813821 TCAGACATGTCGAGCTCCTG 59.186 55.000 19.85 10.96 34.09 3.86
2541 5430 8.118607 CGTCCTAAACCTATTAATTTTCGAACC 58.881 37.037 0.00 0.00 0.00 3.62
2542 5431 7.637519 GCGTCCTAAACCTATTAATTTTCGAAC 59.362 37.037 0.00 0.00 0.00 3.95
2619 5510 1.072159 GTTGCCTCCTGCTCACACT 59.928 57.895 0.00 0.00 42.00 3.55
2639 5530 0.533491 GTCCACACACTGCCCGTATA 59.467 55.000 0.00 0.00 0.00 1.47
2648 5539 4.330944 TTCTAATGTTCGTCCACACACT 57.669 40.909 0.00 0.00 0.00 3.55
2682 5573 1.865865 CACGAAATAGCTACGCCCAT 58.134 50.000 0.00 0.00 0.00 4.00
2703 5594 2.892852 AGTAGTACTTGTTGGGCGTGTA 59.107 45.455 0.00 0.00 0.00 2.90
2746 5637 0.033228 TGGGCATTTTTGCTTCGTGG 59.967 50.000 0.00 0.00 34.73 4.94
2799 5693 3.012560 GGCAGCTAAATCGCCATCT 57.987 52.632 7.12 0.00 45.52 2.90
2813 5707 3.723172 CGTCATTCCGGATGGCAG 58.277 61.111 4.15 0.96 40.47 4.85
2830 5724 3.244422 TGCCATCCCGAATAACTACATCC 60.244 47.826 0.00 0.00 0.00 3.51
2842 5736 2.364632 CAACTACATTTGCCATCCCGA 58.635 47.619 0.00 0.00 0.00 5.14
2927 5823 5.694816 CAACTATGGTTTGTTTACATGCGA 58.305 37.500 0.00 0.00 32.73 5.10
2931 5827 4.521256 ACGGCAACTATGGTTTGTTTACAT 59.479 37.500 0.00 0.00 32.73 2.29
2937 5833 1.606668 CACACGGCAACTATGGTTTGT 59.393 47.619 0.00 0.00 32.73 2.83
2997 5893 7.396055 ACATGGCAACTAGGTAAAATACACAAT 59.604 33.333 0.00 0.00 37.61 2.71
2998 5894 6.717540 ACATGGCAACTAGGTAAAATACACAA 59.282 34.615 0.00 0.00 37.61 3.33
3004 5900 5.538433 ACAACACATGGCAACTAGGTAAAAT 59.462 36.000 0.00 0.00 37.61 1.82
3008 5904 3.558321 GGACAACACATGGCAACTAGGTA 60.558 47.826 0.00 0.00 39.66 3.08
3021 5917 6.890979 TGACAATTATGATTGGACAACACA 57.109 33.333 14.10 1.53 45.56 3.72
3026 5922 7.779326 ACCATACATGACAATTATGATTGGACA 59.221 33.333 14.10 12.97 45.56 4.02
3033 5929 8.503196 GCGATTAACCATACATGACAATTATGA 58.497 33.333 0.00 0.00 0.00 2.15
3038 5934 5.822519 ACTGCGATTAACCATACATGACAAT 59.177 36.000 0.00 0.00 0.00 2.71
3090 5986 3.013921 CGGTAACTGCAATTGTGGGTAT 58.986 45.455 7.40 0.00 0.00 2.73
3094 5990 2.151202 AGACGGTAACTGCAATTGTGG 58.849 47.619 7.40 2.94 0.00 4.17
3096 5992 3.000727 GCTAGACGGTAACTGCAATTGT 58.999 45.455 7.40 0.00 0.00 2.71
3100 5996 2.409975 GTTGCTAGACGGTAACTGCAA 58.590 47.619 0.00 0.00 37.96 4.08
3247 6143 1.072331 ACTAGTTTCTGCCCACACAGG 59.928 52.381 0.00 0.00 38.26 4.00
3314 6211 2.048127 GGCGTTGGAGAGTTCGCT 60.048 61.111 8.18 0.00 46.37 4.93
3374 6271 3.921119 TTGCATGAATCTTGACACACC 57.079 42.857 0.00 0.00 0.00 4.16
3389 6286 5.895636 TCATCGTCCAGTTAAATTTGCAT 57.104 34.783 0.00 0.00 0.00 3.96
3419 6316 6.015772 GTGGTAATTTTACAACTCACCCACAT 60.016 38.462 0.00 0.00 35.23 3.21
3421 6318 5.299782 TGTGGTAATTTTACAACTCACCCAC 59.700 40.000 8.93 0.00 38.21 4.61
3422 6319 5.299782 GTGTGGTAATTTTACAACTCACCCA 59.700 40.000 8.93 0.00 38.21 4.51
3423 6320 5.299782 TGTGTGGTAATTTTACAACTCACCC 59.700 40.000 8.93 0.00 36.62 4.61
3424 6321 6.380095 TGTGTGGTAATTTTACAACTCACC 57.620 37.500 8.93 0.00 36.62 4.02
3469 6371 5.437060 TCAAGCAGGTGAGATAATAAACCC 58.563 41.667 0.00 0.00 32.85 4.11


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

AutoCloner maintained by Alex Coulton.