Multiple sequence alignment - TraesCS2B01G441300

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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 TraesCS2B01G441300 chr2B 100.000 3254 0 0 1 3254 632987203 632990456 0.000000e+00 6010.0
1 TraesCS2B01G441300 chr2B 83.551 1453 197 23 959 2387 633575330 633576764 0.000000e+00 1321.0
2 TraesCS2B01G441300 chr2B 79.119 1408 246 26 1066 2445 633584892 633586279 0.000000e+00 928.0
3 TraesCS2B01G441300 chr2B 95.703 256 9 2 393 647 632927076 632927330 8.400000e-111 411.0
4 TraesCS2B01G441300 chr2D 93.878 2924 93 32 392 3254 533164652 533167550 0.000000e+00 4329.0
5 TraesCS2B01G441300 chr2D 90.097 1747 107 24 836 2543 533251573 533253292 0.000000e+00 2207.0
6 TraesCS2B01G441300 chr2D 84.319 1505 178 23 899 2387 533658221 533659683 0.000000e+00 1419.0
7 TraesCS2B01G441300 chr2D 78.763 1601 253 52 974 2528 533668446 533670005 0.000000e+00 992.0
8 TraesCS2B01G441300 chr2D 79.010 1334 221 38 959 2255 534135134 534136445 0.000000e+00 857.0
9 TraesCS2B01G441300 chr2D 77.972 1430 242 39 1066 2445 533662507 533663913 0.000000e+00 828.0
10 TraesCS2B01G441300 chr2D 88.770 187 16 5 457 641 533206726 533206909 1.170000e-54 224.0
11 TraesCS2B01G441300 chr2D 96.000 50 2 0 737 786 533251427 533251476 7.480000e-12 82.4
12 TraesCS2B01G441300 chr2A 89.946 2228 109 49 393 2534 677545499 677547697 0.000000e+00 2767.0
13 TraesCS2B01G441300 chrUn 83.709 1332 179 18 1075 2388 26138820 26140131 0.000000e+00 1223.0
14 TraesCS2B01G441300 chr7B 92.910 409 12 5 3 394 184982133 184981725 2.180000e-161 579.0
15 TraesCS2B01G441300 chr7B 85.227 88 13 0 1150 1237 657663197 657663110 1.240000e-14 91.6
16 TraesCS2B01G441300 chr3B 91.463 410 17 6 3 394 770761815 770761406 6.140000e-152 547.0
17 TraesCS2B01G441300 chr1B 94.461 343 13 1 3 345 15889368 15889032 1.030000e-144 523.0
18 TraesCS2B01G441300 chr1B 81.707 82 14 1 2973 3054 522830850 522830770 2.100000e-07 67.6
19 TraesCS2B01G441300 chr7A 78.087 826 127 40 1457 2260 81916748 81915955 1.060000e-129 473.0
20 TraesCS2B01G441300 chr7A 76.866 134 31 0 1108 1241 677825376 677825509 3.480000e-10 76.8
21 TraesCS2B01G441300 chr7A 87.692 65 6 2 2977 3040 49640358 49640295 1.250000e-09 75.0
22 TraesCS2B01G441300 chr4A 84.892 139 21 0 1100 1238 729677854 729677992 1.220000e-29 141.0
23 TraesCS2B01G441300 chr6D 80.769 182 26 6 66 241 36252290 36252112 2.040000e-27 134.0
24 TraesCS2B01G441300 chr5D 78.440 218 33 8 11 222 323846792 323846583 2.630000e-26 130.0
25 TraesCS2B01G441300 chr6B 80.220 182 27 7 66 241 75941096 75940918 9.480000e-26 128.0
26 TraesCS2B01G441300 chr7D 81.061 132 25 0 1100 1231 581039903 581040034 4.440000e-19 106.0
27 TraesCS2B01G441300 chr1A 90.000 80 8 0 2980 3059 495704656 495704735 1.600000e-18 104.0
28 TraesCS2B01G441300 chr1A 81.176 85 15 1 2973 3057 488202702 488202619 2.100000e-07 67.6
29 TraesCS2B01G441300 chr3A 79.389 131 22 4 1109 1235 691837697 691837568 1.610000e-13 87.9
30 TraesCS2B01G441300 chr3A 93.478 46 3 0 2977 3022 509887463 509887418 5.830000e-08 69.4
31 TraesCS2B01G441300 chr5B 87.879 66 7 1 2976 3041 686209499 686209563 3.480000e-10 76.8


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 TraesCS2B01G441300 chr2B 632987203 632990456 3253 False 6010.0 6010 100.0000 1 3254 1 chr2B.!!$F2 3253
1 TraesCS2B01G441300 chr2B 633575330 633576764 1434 False 1321.0 1321 83.5510 959 2387 1 chr2B.!!$F3 1428
2 TraesCS2B01G441300 chr2B 633584892 633586279 1387 False 928.0 928 79.1190 1066 2445 1 chr2B.!!$F4 1379
3 TraesCS2B01G441300 chr2D 533164652 533167550 2898 False 4329.0 4329 93.8780 392 3254 1 chr2D.!!$F1 2862
4 TraesCS2B01G441300 chr2D 533251427 533253292 1865 False 1144.7 2207 93.0485 737 2543 2 chr2D.!!$F5 1806
5 TraesCS2B01G441300 chr2D 533658221 533663913 5692 False 1123.5 1419 81.1455 899 2445 2 chr2D.!!$F6 1546
6 TraesCS2B01G441300 chr2D 533668446 533670005 1559 False 992.0 992 78.7630 974 2528 1 chr2D.!!$F3 1554
7 TraesCS2B01G441300 chr2D 534135134 534136445 1311 False 857.0 857 79.0100 959 2255 1 chr2D.!!$F4 1296
8 TraesCS2B01G441300 chr2A 677545499 677547697 2198 False 2767.0 2767 89.9460 393 2534 1 chr2A.!!$F1 2141
9 TraesCS2B01G441300 chrUn 26138820 26140131 1311 False 1223.0 1223 83.7090 1075 2388 1 chrUn.!!$F1 1313
10 TraesCS2B01G441300 chr7A 81915955 81916748 793 True 473.0 473 78.0870 1457 2260 1 chr7A.!!$R2 803

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
870 931 1.077501 CCTCATGGACAATGGCGGT 60.078 57.895 0.0 0.0 36.86 5.68 F
1437 1569 0.036306 TCCCTTCCACTCTTTTCGGC 59.964 55.000 0.0 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2150 2311 3.386726 ACTACGGATCCGATGGAATTTCA 59.613 43.478 39.55 10.12 42.83 2.69 R
3121 3851 1.005037 TGCATCACCACTGACGACC 60.005 57.895 0.00 0.00 0.00 4.79 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 4.511617 TTCATCTCCATCTCGCATACTC 57.488 45.455 0.00 0.00 0.00 2.59
22 23 3.760738 TCATCTCCATCTCGCATACTCT 58.239 45.455 0.00 0.00 0.00 3.24
23 24 3.505293 TCATCTCCATCTCGCATACTCTG 59.495 47.826 0.00 0.00 0.00 3.35
40 41 8.385789 CATACTCTGCAAACATATCAAAACAC 57.614 34.615 0.00 0.00 0.00 3.32
41 42 6.389830 ACTCTGCAAACATATCAAAACACA 57.610 33.333 0.00 0.00 0.00 3.72
42 43 6.208644 ACTCTGCAAACATATCAAAACACAC 58.791 36.000 0.00 0.00 0.00 3.82
43 44 5.527951 TCTGCAAACATATCAAAACACACC 58.472 37.500 0.00 0.00 0.00 4.16
44 45 5.301551 TCTGCAAACATATCAAAACACACCT 59.698 36.000 0.00 0.00 0.00 4.00
45 46 5.911752 TGCAAACATATCAAAACACACCTT 58.088 33.333 0.00 0.00 0.00 3.50
46 47 6.344500 TGCAAACATATCAAAACACACCTTT 58.656 32.000 0.00 0.00 0.00 3.11
47 48 6.820656 TGCAAACATATCAAAACACACCTTTT 59.179 30.769 0.00 0.00 0.00 2.27
48 49 7.125113 GCAAACATATCAAAACACACCTTTTG 58.875 34.615 0.00 0.00 40.90 2.44
49 50 7.201600 GCAAACATATCAAAACACACCTTTTGT 60.202 33.333 4.73 0.00 40.55 2.83
50 51 9.307121 CAAACATATCAAAACACACCTTTTGTA 57.693 29.630 4.73 0.00 40.55 2.41
58 59 9.689976 TCAAAACACACCTTTTGTATTATCATG 57.310 29.630 4.73 0.00 40.55 3.07
59 60 8.434661 CAAAACACACCTTTTGTATTATCATGC 58.565 33.333 0.00 0.00 35.67 4.06
60 61 5.879237 ACACACCTTTTGTATTATCATGCG 58.121 37.500 0.00 0.00 35.67 4.73
61 62 4.734854 CACACCTTTTGTATTATCATGCGC 59.265 41.667 0.00 0.00 35.67 6.09
62 63 4.397730 ACACCTTTTGTATTATCATGCGCA 59.602 37.500 14.96 14.96 36.32 6.09
63 64 5.105957 ACACCTTTTGTATTATCATGCGCAA 60.106 36.000 17.11 0.00 36.32 4.85
64 65 5.229887 CACCTTTTGTATTATCATGCGCAAC 59.770 40.000 17.11 6.69 0.00 4.17
65 66 5.105957 ACCTTTTGTATTATCATGCGCAACA 60.106 36.000 17.11 9.86 0.00 3.33
66 67 5.804473 CCTTTTGTATTATCATGCGCAACAA 59.196 36.000 17.11 16.08 0.00 2.83
67 68 6.309980 CCTTTTGTATTATCATGCGCAACAAA 59.690 34.615 23.25 23.25 34.55 2.83
68 69 7.010367 CCTTTTGTATTATCATGCGCAACAAAT 59.990 33.333 25.97 19.54 35.85 2.32
69 70 8.917415 TTTTGTATTATCATGCGCAACAAATA 57.083 26.923 25.97 18.75 35.85 1.40
70 71 9.526713 TTTTGTATTATCATGCGCAACAAATAT 57.473 25.926 25.97 14.36 35.85 1.28
114 115 7.698836 ATGCAACACTTCTGATTGTTAAAAC 57.301 32.000 0.00 0.00 34.12 2.43
115 116 6.862209 TGCAACACTTCTGATTGTTAAAACT 58.138 32.000 5.21 0.00 34.12 2.66
116 117 6.972328 TGCAACACTTCTGATTGTTAAAACTC 59.028 34.615 5.21 0.00 34.12 3.01
117 118 6.140737 GCAACACTTCTGATTGTTAAAACTCG 59.859 38.462 5.21 0.00 34.12 4.18
118 119 7.406553 CAACACTTCTGATTGTTAAAACTCGA 58.593 34.615 5.21 0.00 34.12 4.04
119 120 7.730364 ACACTTCTGATTGTTAAAACTCGAT 57.270 32.000 0.00 0.00 0.00 3.59
120 121 7.576236 ACACTTCTGATTGTTAAAACTCGATG 58.424 34.615 0.00 0.00 0.00 3.84
121 122 7.441157 ACACTTCTGATTGTTAAAACTCGATGA 59.559 33.333 0.00 0.00 0.00 2.92
122 123 7.954248 CACTTCTGATTGTTAAAACTCGATGAG 59.046 37.037 0.00 0.00 35.52 2.90
123 124 7.657761 ACTTCTGATTGTTAAAACTCGATGAGT 59.342 33.333 0.00 0.00 45.64 3.41
137 138 7.321745 ACTCGATGAGTTTTTAATCCAATCC 57.678 36.000 0.00 0.00 40.28 3.01
138 139 6.884295 ACTCGATGAGTTTTTAATCCAATCCA 59.116 34.615 0.00 0.00 40.28 3.41
139 140 7.557719 ACTCGATGAGTTTTTAATCCAATCCAT 59.442 33.333 0.00 0.00 40.28 3.41
140 141 7.930217 TCGATGAGTTTTTAATCCAATCCATC 58.070 34.615 0.00 0.00 0.00 3.51
141 142 7.555914 TCGATGAGTTTTTAATCCAATCCATCA 59.444 33.333 0.00 0.00 0.00 3.07
142 143 8.355169 CGATGAGTTTTTAATCCAATCCATCAT 58.645 33.333 0.00 0.00 0.00 2.45
147 148 9.822185 AGTTTTTAATCCAATCCATCATAAAGC 57.178 29.630 0.00 0.00 0.00 3.51
148 149 9.822185 GTTTTTAATCCAATCCATCATAAAGCT 57.178 29.630 0.00 0.00 0.00 3.74
151 152 9.820725 TTTAATCCAATCCATCATAAAGCTTTG 57.179 29.630 22.02 6.89 0.00 2.77
152 153 7.427989 AATCCAATCCATCATAAAGCTTTGT 57.572 32.000 22.02 12.64 0.00 2.83
153 154 6.455360 TCCAATCCATCATAAAGCTTTGTC 57.545 37.500 22.02 0.00 0.00 3.18
154 155 5.951148 TCCAATCCATCATAAAGCTTTGTCA 59.049 36.000 22.02 1.07 0.00 3.58
155 156 6.436847 TCCAATCCATCATAAAGCTTTGTCAA 59.563 34.615 22.02 6.02 0.00 3.18
156 157 7.124599 TCCAATCCATCATAAAGCTTTGTCAAT 59.875 33.333 22.02 8.07 0.00 2.57
157 158 7.437267 CCAATCCATCATAAAGCTTTGTCAATC 59.563 37.037 22.02 0.00 0.00 2.67
158 159 7.649533 ATCCATCATAAAGCTTTGTCAATCA 57.350 32.000 22.02 0.00 0.00 2.57
159 160 7.465353 TCCATCATAAAGCTTTGTCAATCAA 57.535 32.000 22.02 0.00 0.00 2.57
160 161 7.894708 TCCATCATAAAGCTTTGTCAATCAAA 58.105 30.769 22.02 0.00 42.79 2.69
161 162 8.366401 TCCATCATAAAGCTTTGTCAATCAAAA 58.634 29.630 22.02 0.00 44.08 2.44
162 163 9.158233 CCATCATAAAGCTTTGTCAATCAAAAT 57.842 29.630 22.02 0.00 44.08 1.82
169 170 9.777575 AAAGCTTTGTCAATCAAAATTTTCAAG 57.222 25.926 11.80 0.00 44.08 3.02
170 171 7.922837 AGCTTTGTCAATCAAAATTTTCAAGG 58.077 30.769 0.00 3.42 44.08 3.61
171 172 6.634035 GCTTTGTCAATCAAAATTTTCAAGGC 59.366 34.615 14.63 14.63 44.08 4.35
172 173 5.903764 TGTCAATCAAAATTTTCAAGGCG 57.096 34.783 0.00 0.00 0.00 5.52
173 174 5.355596 TGTCAATCAAAATTTTCAAGGCGT 58.644 33.333 0.00 0.00 0.00 5.68
174 175 5.461737 TGTCAATCAAAATTTTCAAGGCGTC 59.538 36.000 0.00 0.00 0.00 5.19
175 176 5.461737 GTCAATCAAAATTTTCAAGGCGTCA 59.538 36.000 0.00 0.00 0.00 4.35
176 177 6.146021 GTCAATCAAAATTTTCAAGGCGTCAT 59.854 34.615 0.00 0.00 0.00 3.06
177 178 6.365789 TCAATCAAAATTTTCAAGGCGTCATC 59.634 34.615 0.00 0.00 0.00 2.92
178 179 5.193663 TCAAAATTTTCAAGGCGTCATCA 57.806 34.783 0.00 0.00 0.00 3.07
179 180 5.595885 TCAAAATTTTCAAGGCGTCATCAA 58.404 33.333 0.00 0.00 0.00 2.57
180 181 6.045318 TCAAAATTTTCAAGGCGTCATCAAA 58.955 32.000 0.00 0.00 0.00 2.69
181 182 6.536582 TCAAAATTTTCAAGGCGTCATCAAAA 59.463 30.769 0.00 0.00 0.00 2.44
182 183 6.529463 AAATTTTCAAGGCGTCATCAAAAG 57.471 33.333 0.00 0.00 0.00 2.27
183 184 2.704725 TTCAAGGCGTCATCAAAAGC 57.295 45.000 0.00 0.00 0.00 3.51
189 190 2.184385 GCGTCATCAAAAGCCATCAG 57.816 50.000 0.00 0.00 0.00 2.90
190 191 1.470098 GCGTCATCAAAAGCCATCAGT 59.530 47.619 0.00 0.00 0.00 3.41
191 192 2.476854 GCGTCATCAAAAGCCATCAGTC 60.477 50.000 0.00 0.00 0.00 3.51
192 193 3.005554 CGTCATCAAAAGCCATCAGTCT 58.994 45.455 0.00 0.00 0.00 3.24
193 194 3.438087 CGTCATCAAAAGCCATCAGTCTT 59.562 43.478 0.00 0.00 0.00 3.01
194 195 4.631377 CGTCATCAAAAGCCATCAGTCTTA 59.369 41.667 0.00 0.00 0.00 2.10
195 196 5.295292 CGTCATCAAAAGCCATCAGTCTTAT 59.705 40.000 0.00 0.00 0.00 1.73
196 197 6.510799 CGTCATCAAAAGCCATCAGTCTTATC 60.511 42.308 0.00 0.00 0.00 1.75
197 198 6.541641 GTCATCAAAAGCCATCAGTCTTATCT 59.458 38.462 0.00 0.00 0.00 1.98
198 199 7.712639 GTCATCAAAAGCCATCAGTCTTATCTA 59.287 37.037 0.00 0.00 0.00 1.98
199 200 8.435187 TCATCAAAAGCCATCAGTCTTATCTAT 58.565 33.333 0.00 0.00 0.00 1.98
200 201 8.504815 CATCAAAAGCCATCAGTCTTATCTATG 58.495 37.037 0.00 0.00 0.00 2.23
201 202 7.795047 TCAAAAGCCATCAGTCTTATCTATGA 58.205 34.615 0.00 0.00 0.00 2.15
202 203 8.435187 TCAAAAGCCATCAGTCTTATCTATGAT 58.565 33.333 0.00 0.00 32.70 2.45
203 204 8.719648 CAAAAGCCATCAGTCTTATCTATGATC 58.280 37.037 0.00 0.00 30.09 2.92
204 205 7.795534 AAGCCATCAGTCTTATCTATGATCT 57.204 36.000 0.00 0.00 30.09 2.75
205 206 8.891985 AAGCCATCAGTCTTATCTATGATCTA 57.108 34.615 0.00 0.00 30.09 1.98
206 207 9.491406 AAGCCATCAGTCTTATCTATGATCTAT 57.509 33.333 0.00 0.00 30.09 1.98
207 208 8.916062 AGCCATCAGTCTTATCTATGATCTATG 58.084 37.037 0.00 0.00 30.09 2.23
208 209 8.911965 GCCATCAGTCTTATCTATGATCTATGA 58.088 37.037 0.00 0.00 30.09 2.15
275 276 8.846943 ATCATATGCAATTTATACTTCGACCA 57.153 30.769 0.00 0.00 0.00 4.02
276 277 8.310406 TCATATGCAATTTATACTTCGACCAG 57.690 34.615 0.00 0.00 0.00 4.00
277 278 8.147704 TCATATGCAATTTATACTTCGACCAGA 58.852 33.333 0.00 0.00 0.00 3.86
278 279 8.939929 CATATGCAATTTATACTTCGACCAGAT 58.060 33.333 0.00 0.00 0.00 2.90
280 281 8.902540 ATGCAATTTATACTTCGACCAGATAA 57.097 30.769 0.00 0.00 0.00 1.75
281 282 8.902540 TGCAATTTATACTTCGACCAGATAAT 57.097 30.769 0.00 0.00 0.00 1.28
282 283 9.990360 TGCAATTTATACTTCGACCAGATAATA 57.010 29.630 0.00 0.00 0.00 0.98
290 291 7.468141 ACTTCGACCAGATAATATGATAGCA 57.532 36.000 0.00 0.00 0.00 3.49
291 292 8.072321 ACTTCGACCAGATAATATGATAGCAT 57.928 34.615 0.00 0.00 38.54 3.79
292 293 9.190317 ACTTCGACCAGATAATATGATAGCATA 57.810 33.333 2.64 2.64 41.00 3.14
341 342 8.840833 TTAAAGATGCACTTAGTGTAATGACA 57.159 30.769 14.23 2.55 37.93 3.58
342 343 7.744087 AAAGATGCACTTAGTGTAATGACAA 57.256 32.000 14.23 0.00 36.04 3.18
343 344 7.744087 AAGATGCACTTAGTGTAATGACAAA 57.256 32.000 14.23 0.00 35.59 2.83
344 345 7.928307 AGATGCACTTAGTGTAATGACAAAT 57.072 32.000 14.23 0.00 37.31 2.32
345 346 9.448438 AAGATGCACTTAGTGTAATGACAAATA 57.552 29.630 14.23 0.00 35.59 1.40
346 347 9.448438 AGATGCACTTAGTGTAATGACAAATAA 57.552 29.630 14.23 0.00 37.31 1.40
370 371 6.539649 TTAAAGATGACAGTTTTGAGACCG 57.460 37.500 0.00 0.00 0.00 4.79
371 372 2.417719 AGATGACAGTTTTGAGACCGC 58.582 47.619 0.00 0.00 0.00 5.68
372 373 2.143122 GATGACAGTTTTGAGACCGCA 58.857 47.619 0.00 0.00 0.00 5.69
373 374 2.031258 TGACAGTTTTGAGACCGCAA 57.969 45.000 0.00 0.00 0.00 4.85
374 375 1.939934 TGACAGTTTTGAGACCGCAAG 59.060 47.619 0.00 0.00 0.00 4.01
375 376 2.210116 GACAGTTTTGAGACCGCAAGA 58.790 47.619 0.00 0.00 43.02 3.02
376 377 2.612212 GACAGTTTTGAGACCGCAAGAA 59.388 45.455 0.00 0.00 43.02 2.52
377 378 3.013921 ACAGTTTTGAGACCGCAAGAAA 58.986 40.909 0.00 0.00 43.02 2.52
378 379 3.181500 ACAGTTTTGAGACCGCAAGAAAC 60.181 43.478 0.00 0.00 43.02 2.78
379 380 3.013921 AGTTTTGAGACCGCAAGAAACA 58.986 40.909 0.00 0.00 43.02 2.83
380 381 3.442273 AGTTTTGAGACCGCAAGAAACAA 59.558 39.130 0.00 0.00 43.02 2.83
381 382 4.082463 AGTTTTGAGACCGCAAGAAACAAA 60.082 37.500 0.00 0.00 43.02 2.83
382 383 3.691049 TTGAGACCGCAAGAAACAAAG 57.309 42.857 0.00 0.00 43.02 2.77
383 384 2.912771 TGAGACCGCAAGAAACAAAGA 58.087 42.857 0.00 0.00 43.02 2.52
384 385 3.275143 TGAGACCGCAAGAAACAAAGAA 58.725 40.909 0.00 0.00 43.02 2.52
385 386 3.692101 TGAGACCGCAAGAAACAAAGAAA 59.308 39.130 0.00 0.00 43.02 2.52
386 387 4.156922 TGAGACCGCAAGAAACAAAGAAAA 59.843 37.500 0.00 0.00 43.02 2.29
387 388 5.066968 AGACCGCAAGAAACAAAGAAAAA 57.933 34.783 0.00 0.00 43.02 1.94
388 389 4.862574 AGACCGCAAGAAACAAAGAAAAAC 59.137 37.500 0.00 0.00 43.02 2.43
389 390 4.561105 ACCGCAAGAAACAAAGAAAAACA 58.439 34.783 0.00 0.00 43.02 2.83
390 391 4.991687 ACCGCAAGAAACAAAGAAAAACAA 59.008 33.333 0.00 0.00 43.02 2.83
407 408 4.954118 ACTGACGGCACCCCTCCA 62.954 66.667 0.00 0.00 0.00 3.86
408 409 3.402681 CTGACGGCACCCCTCCAT 61.403 66.667 0.00 0.00 0.00 3.41
414 415 2.668632 GCACCCCTCCATTGACGA 59.331 61.111 0.00 0.00 0.00 4.20
433 434 2.074729 ACCTCTCGGTCCTTGATAGG 57.925 55.000 0.00 0.00 40.27 2.57
444 445 1.759459 CTTGATAGGGAGGGGGTCGC 61.759 65.000 0.00 0.00 38.43 5.19
499 500 1.673168 GCTGTTGAGCATCTTAGGGG 58.327 55.000 0.00 0.00 45.46 4.79
507 508 3.780294 TGAGCATCTTAGGGGCTTTTCTA 59.220 43.478 0.69 0.00 38.15 2.10
519 520 6.512120 AGGGGCTTTTCTATAATTTTTCCCT 58.488 36.000 0.00 0.00 35.29 4.20
545 546 6.000840 TCATGTGAGGTGCTTTGTATTGTTA 58.999 36.000 0.00 0.00 0.00 2.41
571 573 5.575053 ATCCTCTATAATGGATCTGGGGA 57.425 43.478 0.00 0.00 38.60 4.81
576 578 6.155393 CCTCTATAATGGATCTGGGGACTTAC 59.845 46.154 0.00 0.00 0.00 2.34
579 581 2.940514 TGGATCTGGGGACTTACTCA 57.059 50.000 0.00 0.00 0.00 3.41
585 587 4.891992 TCTGGGGACTTACTCAGAAAAG 57.108 45.455 0.00 0.00 33.87 2.27
589 591 6.044404 TCTGGGGACTTACTCAGAAAAGAAAT 59.956 38.462 0.00 0.00 33.87 2.17
590 592 6.003950 TGGGGACTTACTCAGAAAAGAAATG 58.996 40.000 0.00 0.00 0.00 2.32
591 593 6.183361 TGGGGACTTACTCAGAAAAGAAATGA 60.183 38.462 0.00 0.00 0.00 2.57
592 594 6.149640 GGGGACTTACTCAGAAAAGAAATGAC 59.850 42.308 0.00 0.00 0.00 3.06
593 595 6.710744 GGGACTTACTCAGAAAAGAAATGACA 59.289 38.462 0.00 0.00 0.00 3.58
594 596 7.095017 GGGACTTACTCAGAAAAGAAATGACAG 60.095 40.741 0.00 0.00 0.00 3.51
596 598 7.283329 ACTTACTCAGAAAAGAAATGACAGGT 58.717 34.615 0.00 0.00 0.00 4.00
611 615 9.383519 GAAATGACAGGTAATCACTTTAGATGA 57.616 33.333 0.00 0.00 0.00 2.92
630 634 5.824624 AGATGAACAGGTAAATCGCATTGAT 59.175 36.000 0.00 0.00 39.67 2.57
772 786 1.638467 CCGCTAATCTCGTTGCTGC 59.362 57.895 0.00 0.00 0.00 5.25
786 800 2.537560 GCTGCCGAACATCATCCCG 61.538 63.158 0.00 0.00 0.00 5.14
870 931 1.077501 CCTCATGGACAATGGCGGT 60.078 57.895 0.00 0.00 36.86 5.68
895 956 3.741476 GCCGCTGCCTCAAACCAG 61.741 66.667 0.00 0.00 0.00 4.00
897 958 2.281761 CGCTGCCTCAAACCAGGT 60.282 61.111 0.00 0.00 35.72 4.00
898 959 2.328099 CGCTGCCTCAAACCAGGTC 61.328 63.158 0.00 0.00 35.72 3.85
899 960 1.973812 GCTGCCTCAAACCAGGTCC 60.974 63.158 0.00 0.00 35.72 4.46
900 961 1.672356 CTGCCTCAAACCAGGTCCG 60.672 63.158 0.00 0.00 35.72 4.79
901 962 3.056328 GCCTCAAACCAGGTCCGC 61.056 66.667 0.00 0.00 35.72 5.54
902 963 2.742372 CCTCAAACCAGGTCCGCG 60.742 66.667 0.00 0.00 0.00 6.46
903 964 2.342279 CTCAAACCAGGTCCGCGA 59.658 61.111 8.23 0.00 0.00 5.87
904 965 1.738099 CTCAAACCAGGTCCGCGAG 60.738 63.158 8.23 0.00 0.00 5.03
905 966 3.423154 CAAACCAGGTCCGCGAGC 61.423 66.667 8.23 3.31 0.00 5.03
906 967 3.626924 AAACCAGGTCCGCGAGCT 61.627 61.111 8.23 6.01 41.33 4.09
907 968 2.280552 AAACCAGGTCCGCGAGCTA 61.281 57.895 8.23 0.00 38.40 3.32
908 969 2.227089 AAACCAGGTCCGCGAGCTAG 62.227 60.000 8.23 4.64 38.40 3.42
909 970 3.141488 CCAGGTCCGCGAGCTAGT 61.141 66.667 8.23 0.00 38.40 2.57
910 971 2.711922 CCAGGTCCGCGAGCTAGTT 61.712 63.158 8.23 0.00 38.40 2.24
911 972 1.226717 CAGGTCCGCGAGCTAGTTC 60.227 63.158 8.23 0.00 38.40 3.01
939 1034 2.646175 TTCGTCCTTCTCGCCCAGG 61.646 63.158 0.00 0.00 0.00 4.45
955 1050 1.747355 CCAGGTTGATGAATCCACTGC 59.253 52.381 0.00 0.00 0.00 4.40
957 1052 3.021695 CAGGTTGATGAATCCACTGCAT 58.978 45.455 0.00 0.00 0.00 3.96
975 1070 9.458727 CCACTGCATAGATTGATTTATCCTAAT 57.541 33.333 0.00 0.00 0.00 1.73
979 1074 7.770433 TGCATAGATTGATTTATCCTAATCCCG 59.230 37.037 0.00 0.00 34.34 5.14
1162 1285 4.361253 GCTTCAAGTGCGTCTCCA 57.639 55.556 0.00 0.00 0.00 3.86
1293 1416 0.181587 TTCACTTCGCCAAAGTCCCA 59.818 50.000 0.00 0.00 45.28 4.37
1296 1419 1.675641 CTTCGCCAAAGTCCCAGGG 60.676 63.158 0.00 0.00 0.00 4.45
1345 1468 1.073923 TCTCTTTCTTGCCTTCCCACC 59.926 52.381 0.00 0.00 0.00 4.61
1382 1514 3.359002 GCTGGACACCTGCAAAGG 58.641 61.111 13.25 0.00 45.75 3.11
1383 1515 2.924105 GCTGGACACCTGCAAAGGC 61.924 63.158 13.25 0.00 45.75 4.35
1384 1516 1.228367 CTGGACACCTGCAAAGGCT 60.228 57.895 0.00 0.00 41.91 4.58
1385 1517 1.521450 CTGGACACCTGCAAAGGCTG 61.521 60.000 0.00 0.00 41.91 4.85
1425 1557 2.954611 GCGCACAAGTTCCCTTCC 59.045 61.111 0.30 0.00 0.00 3.46
1430 1562 1.202818 GCACAAGTTCCCTTCCACTCT 60.203 52.381 0.00 0.00 0.00 3.24
1437 1569 0.036306 TCCCTTCCACTCTTTTCGGC 59.964 55.000 0.00 0.00 0.00 5.54
1455 1587 2.652496 GACGACGATGAGCCGCTC 60.652 66.667 13.81 13.81 0.00 5.03
2150 2311 3.869832 GCATCATACGATATGCAGCATCT 59.130 43.478 12.38 0.94 46.19 2.90
2362 2538 9.251792 TGAATTTTCTTCAGTCATGTCATTTTG 57.748 29.630 0.00 0.00 0.00 2.44
2519 2737 7.409697 TGTCGCTAAATTATTCTGAAATCTGC 58.590 34.615 0.00 0.00 0.00 4.26
2551 3105 8.078060 TGTCAATGACCTATGAATTCAGTCTA 57.922 34.615 20.63 11.63 0.00 2.59
2755 3468 9.403110 CTTTCTTATTTGTCTGTTGATTTCTGG 57.597 33.333 0.00 0.00 0.00 3.86
2852 3565 3.973973 CCTGGTATCCCCACAGATTAAGA 59.026 47.826 0.00 0.00 38.72 2.10
2885 3598 7.488150 TGATTACTATCGTTGTTTGTCTAGCTG 59.512 37.037 0.00 0.00 33.23 4.24
2941 3654 7.040823 GCTAAATTATGCTTCTGTAATCTGGCT 60.041 37.037 0.00 0.00 0.00 4.75
3102 3815 4.010349 GCCTGTAATGTACTGAAAGCCTT 58.990 43.478 0.00 0.00 37.60 4.35
3121 3851 9.606631 AAAGCCTTAGTAGTCTATTTGATCTTG 57.393 33.333 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.505293 CAGAGTATGCGAGATGGAGATGA 59.495 47.826 0.00 0.00 0.00 2.92
3 4 2.230992 GCAGAGTATGCGAGATGGAGAT 59.769 50.000 0.00 0.00 46.99 2.75
4 5 1.611006 GCAGAGTATGCGAGATGGAGA 59.389 52.381 0.00 0.00 46.99 3.71
5 6 2.063156 GCAGAGTATGCGAGATGGAG 57.937 55.000 0.00 0.00 46.99 3.86
15 16 8.022550 TGTGTTTTGATATGTTTGCAGAGTATG 58.977 33.333 0.00 0.00 0.00 2.39
16 17 8.023128 GTGTGTTTTGATATGTTTGCAGAGTAT 58.977 33.333 0.00 0.00 0.00 2.12
17 18 7.359595 GTGTGTTTTGATATGTTTGCAGAGTA 58.640 34.615 0.00 0.00 0.00 2.59
18 19 6.208644 GTGTGTTTTGATATGTTTGCAGAGT 58.791 36.000 0.00 0.00 0.00 3.24
19 20 5.630680 GGTGTGTTTTGATATGTTTGCAGAG 59.369 40.000 0.00 0.00 0.00 3.35
20 21 5.301551 AGGTGTGTTTTGATATGTTTGCAGA 59.698 36.000 0.00 0.00 0.00 4.26
21 22 5.531634 AGGTGTGTTTTGATATGTTTGCAG 58.468 37.500 0.00 0.00 0.00 4.41
22 23 5.528043 AGGTGTGTTTTGATATGTTTGCA 57.472 34.783 0.00 0.00 0.00 4.08
23 24 6.843069 AAAGGTGTGTTTTGATATGTTTGC 57.157 33.333 0.00 0.00 0.00 3.68
24 25 8.195617 ACAAAAGGTGTGTTTTGATATGTTTG 57.804 30.769 14.33 0.00 46.19 2.93
32 33 9.689976 CATGATAATACAAAAGGTGTGTTTTGA 57.310 29.630 14.33 1.39 46.19 2.69
34 35 7.328249 CGCATGATAATACAAAAGGTGTGTTTT 59.672 33.333 0.00 0.00 38.29 2.43
35 36 6.806249 CGCATGATAATACAAAAGGTGTGTTT 59.194 34.615 0.00 0.00 38.29 2.83
36 37 6.321717 CGCATGATAATACAAAAGGTGTGTT 58.678 36.000 0.00 0.00 43.31 3.32
37 38 5.676079 GCGCATGATAATACAAAAGGTGTGT 60.676 40.000 0.30 0.00 41.89 3.72
38 39 4.734854 GCGCATGATAATACAAAAGGTGTG 59.265 41.667 0.30 0.00 41.89 3.82
39 40 4.397730 TGCGCATGATAATACAAAAGGTGT 59.602 37.500 5.66 0.00 44.82 4.16
40 41 4.919206 TGCGCATGATAATACAAAAGGTG 58.081 39.130 5.66 0.00 0.00 4.00
41 42 5.105957 TGTTGCGCATGATAATACAAAAGGT 60.106 36.000 12.75 0.00 0.00 3.50
42 43 5.339177 TGTTGCGCATGATAATACAAAAGG 58.661 37.500 12.75 0.00 0.00 3.11
43 44 6.867799 TTGTTGCGCATGATAATACAAAAG 57.132 33.333 12.75 0.00 0.00 2.27
44 45 7.824704 ATTTGTTGCGCATGATAATACAAAA 57.175 28.000 27.91 16.78 37.50 2.44
88 89 9.410556 GTTTTAACAATCAGAAGTGTTGCATAT 57.589 29.630 11.45 0.00 43.10 1.78
89 90 8.629158 AGTTTTAACAATCAGAAGTGTTGCATA 58.371 29.630 11.45 0.00 43.10 3.14
90 91 7.491682 AGTTTTAACAATCAGAAGTGTTGCAT 58.508 30.769 11.45 0.00 43.10 3.96
91 92 6.862209 AGTTTTAACAATCAGAAGTGTTGCA 58.138 32.000 11.45 0.00 43.10 4.08
92 93 6.140737 CGAGTTTTAACAATCAGAAGTGTTGC 59.859 38.462 11.45 2.54 43.10 4.17
93 94 7.406553 TCGAGTTTTAACAATCAGAAGTGTTG 58.593 34.615 11.45 0.00 43.10 3.33
94 95 7.548196 TCGAGTTTTAACAATCAGAAGTGTT 57.452 32.000 7.73 7.73 45.06 3.32
95 96 7.441157 TCATCGAGTTTTAACAATCAGAAGTGT 59.559 33.333 0.00 0.00 34.61 3.55
96 97 7.796838 TCATCGAGTTTTAACAATCAGAAGTG 58.203 34.615 0.00 0.00 0.00 3.16
97 98 7.657761 ACTCATCGAGTTTTAACAATCAGAAGT 59.342 33.333 0.00 0.00 40.28 3.01
98 99 8.023050 ACTCATCGAGTTTTAACAATCAGAAG 57.977 34.615 0.00 0.00 40.28 2.85
99 100 7.962964 ACTCATCGAGTTTTAACAATCAGAA 57.037 32.000 0.00 0.00 40.28 3.02
113 114 6.884295 TGGATTGGATTAAAAACTCATCGAGT 59.116 34.615 0.00 0.00 45.64 4.18
114 115 7.320443 TGGATTGGATTAAAAACTCATCGAG 57.680 36.000 0.00 0.00 35.52 4.04
115 116 7.555914 TGATGGATTGGATTAAAAACTCATCGA 59.444 33.333 0.00 0.00 32.50 3.59
116 117 7.706159 TGATGGATTGGATTAAAAACTCATCG 58.294 34.615 0.00 0.00 32.50 3.84
121 122 9.822185 GCTTTATGATGGATTGGATTAAAAACT 57.178 29.630 0.00 0.00 0.00 2.66
122 123 9.822185 AGCTTTATGATGGATTGGATTAAAAAC 57.178 29.630 0.00 0.00 0.00 2.43
125 126 9.820725 CAAAGCTTTATGATGGATTGGATTAAA 57.179 29.630 12.25 0.00 0.00 1.52
126 127 8.980596 ACAAAGCTTTATGATGGATTGGATTAA 58.019 29.630 12.25 0.00 0.00 1.40
127 128 8.537728 ACAAAGCTTTATGATGGATTGGATTA 57.462 30.769 12.25 0.00 0.00 1.75
128 129 7.124599 TGACAAAGCTTTATGATGGATTGGATT 59.875 33.333 12.25 0.00 0.00 3.01
129 130 6.608405 TGACAAAGCTTTATGATGGATTGGAT 59.392 34.615 12.25 0.00 0.00 3.41
130 131 5.951148 TGACAAAGCTTTATGATGGATTGGA 59.049 36.000 12.25 0.00 0.00 3.53
131 132 6.211587 TGACAAAGCTTTATGATGGATTGG 57.788 37.500 12.25 0.00 0.00 3.16
132 133 7.977293 TGATTGACAAAGCTTTATGATGGATTG 59.023 33.333 12.25 0.00 0.00 2.67
133 134 8.070034 TGATTGACAAAGCTTTATGATGGATT 57.930 30.769 12.25 0.00 0.00 3.01
134 135 7.649533 TGATTGACAAAGCTTTATGATGGAT 57.350 32.000 12.25 0.25 0.00 3.41
135 136 7.465353 TTGATTGACAAAGCTTTATGATGGA 57.535 32.000 12.25 0.00 35.39 3.41
136 137 8.537049 TTTTGATTGACAAAGCTTTATGATGG 57.463 30.769 12.25 0.56 46.93 3.51
143 144 9.777575 CTTGAAAATTTTGATTGACAAAGCTTT 57.222 25.926 8.47 5.69 46.93 3.51
144 145 8.400186 CCTTGAAAATTTTGATTGACAAAGCTT 58.600 29.630 8.47 0.00 46.93 3.74
145 146 7.467675 GCCTTGAAAATTTTGATTGACAAAGCT 60.468 33.333 8.47 0.00 46.93 3.74
146 147 6.634035 GCCTTGAAAATTTTGATTGACAAAGC 59.366 34.615 8.47 6.85 46.93 3.51
147 148 6.847289 CGCCTTGAAAATTTTGATTGACAAAG 59.153 34.615 8.47 0.70 46.93 2.77
148 149 6.314896 ACGCCTTGAAAATTTTGATTGACAAA 59.685 30.769 8.47 0.00 45.22 2.83
149 150 5.814705 ACGCCTTGAAAATTTTGATTGACAA 59.185 32.000 8.47 4.41 36.65 3.18
150 151 5.355596 ACGCCTTGAAAATTTTGATTGACA 58.644 33.333 8.47 0.00 0.00 3.58
151 152 5.461737 TGACGCCTTGAAAATTTTGATTGAC 59.538 36.000 8.47 0.00 0.00 3.18
152 153 5.595885 TGACGCCTTGAAAATTTTGATTGA 58.404 33.333 8.47 0.00 0.00 2.57
153 154 5.903764 TGACGCCTTGAAAATTTTGATTG 57.096 34.783 8.47 0.00 0.00 2.67
154 155 6.222389 TGATGACGCCTTGAAAATTTTGATT 58.778 32.000 8.47 0.00 0.00 2.57
155 156 5.782047 TGATGACGCCTTGAAAATTTTGAT 58.218 33.333 8.47 0.00 0.00 2.57
156 157 5.193663 TGATGACGCCTTGAAAATTTTGA 57.806 34.783 8.47 0.00 0.00 2.69
157 158 5.903764 TTGATGACGCCTTGAAAATTTTG 57.096 34.783 8.47 0.00 0.00 2.44
158 159 6.511605 GCTTTTGATGACGCCTTGAAAATTTT 60.512 34.615 2.28 2.28 0.00 1.82
159 160 5.050159 GCTTTTGATGACGCCTTGAAAATTT 60.050 36.000 0.00 0.00 0.00 1.82
160 161 4.448732 GCTTTTGATGACGCCTTGAAAATT 59.551 37.500 0.00 0.00 0.00 1.82
161 162 3.989817 GCTTTTGATGACGCCTTGAAAAT 59.010 39.130 0.00 0.00 0.00 1.82
162 163 3.380142 GCTTTTGATGACGCCTTGAAAA 58.620 40.909 0.00 0.00 0.00 2.29
163 164 2.288152 GGCTTTTGATGACGCCTTGAAA 60.288 45.455 0.00 0.00 39.42 2.69
164 165 1.269448 GGCTTTTGATGACGCCTTGAA 59.731 47.619 0.00 0.00 39.42 2.69
165 166 0.881118 GGCTTTTGATGACGCCTTGA 59.119 50.000 0.00 0.00 39.42 3.02
166 167 0.597568 TGGCTTTTGATGACGCCTTG 59.402 50.000 0.00 0.00 42.90 3.61
167 168 1.474077 GATGGCTTTTGATGACGCCTT 59.526 47.619 0.00 0.00 42.90 4.35
168 169 1.098050 GATGGCTTTTGATGACGCCT 58.902 50.000 0.00 0.00 42.90 5.52
169 170 0.810648 TGATGGCTTTTGATGACGCC 59.189 50.000 0.00 0.00 42.78 5.68
170 171 1.470098 ACTGATGGCTTTTGATGACGC 59.530 47.619 0.00 0.00 0.00 5.19
171 172 3.005554 AGACTGATGGCTTTTGATGACG 58.994 45.455 0.00 0.00 0.00 4.35
172 173 6.541641 AGATAAGACTGATGGCTTTTGATGAC 59.458 38.462 0.00 0.00 0.00 3.06
173 174 6.656902 AGATAAGACTGATGGCTTTTGATGA 58.343 36.000 0.00 0.00 0.00 2.92
174 175 6.939132 AGATAAGACTGATGGCTTTTGATG 57.061 37.500 0.00 0.00 0.00 3.07
175 176 8.435187 TCATAGATAAGACTGATGGCTTTTGAT 58.565 33.333 0.00 0.00 0.00 2.57
176 177 7.795047 TCATAGATAAGACTGATGGCTTTTGA 58.205 34.615 0.00 0.00 0.00 2.69
177 178 8.618702 ATCATAGATAAGACTGATGGCTTTTG 57.381 34.615 0.00 0.00 0.00 2.44
178 179 8.658619 AGATCATAGATAAGACTGATGGCTTTT 58.341 33.333 0.00 0.00 0.00 2.27
179 180 8.204903 AGATCATAGATAAGACTGATGGCTTT 57.795 34.615 0.00 0.00 0.00 3.51
180 181 7.795534 AGATCATAGATAAGACTGATGGCTT 57.204 36.000 0.00 0.00 0.00 4.35
181 182 8.916062 CATAGATCATAGATAAGACTGATGGCT 58.084 37.037 0.00 0.00 0.00 4.75
182 183 8.911965 TCATAGATCATAGATAAGACTGATGGC 58.088 37.037 0.00 0.00 0.00 4.40
249 250 9.936759 TGGTCGAAGTATAAATTGCATATGATA 57.063 29.630 6.97 0.00 0.00 2.15
250 251 8.846943 TGGTCGAAGTATAAATTGCATATGAT 57.153 30.769 6.97 0.00 0.00 2.45
251 252 8.147704 TCTGGTCGAAGTATAAATTGCATATGA 58.852 33.333 6.97 0.00 0.00 2.15
252 253 8.310406 TCTGGTCGAAGTATAAATTGCATATG 57.690 34.615 0.00 0.00 0.00 1.78
254 255 9.990360 TTATCTGGTCGAAGTATAAATTGCATA 57.010 29.630 0.00 0.00 0.00 3.14
255 256 8.902540 TTATCTGGTCGAAGTATAAATTGCAT 57.097 30.769 0.00 0.00 0.00 3.96
256 257 8.902540 ATTATCTGGTCGAAGTATAAATTGCA 57.097 30.769 0.00 0.00 0.00 4.08
264 265 9.190317 TGCTATCATATTATCTGGTCGAAGTAT 57.810 33.333 0.00 0.00 0.00 2.12
265 266 8.575649 TGCTATCATATTATCTGGTCGAAGTA 57.424 34.615 0.00 0.00 0.00 2.24
266 267 7.468141 TGCTATCATATTATCTGGTCGAAGT 57.532 36.000 0.00 0.00 0.00 3.01
315 316 9.448438 TGTCATTACACTAAGTGCATCTTTAAT 57.552 29.630 6.82 3.61 36.98 1.40
316 317 8.840833 TGTCATTACACTAAGTGCATCTTTAA 57.159 30.769 6.82 1.82 36.98 1.52
317 318 8.840833 TTGTCATTACACTAAGTGCATCTTTA 57.159 30.769 6.82 0.00 36.98 1.85
318 319 7.744087 TTGTCATTACACTAAGTGCATCTTT 57.256 32.000 6.82 0.00 36.98 2.52
319 320 7.744087 TTTGTCATTACACTAAGTGCATCTT 57.256 32.000 0.00 0.00 36.98 2.40
320 321 7.928307 ATTTGTCATTACACTAAGTGCATCT 57.072 32.000 0.00 0.00 36.98 2.90
344 345 8.717821 CGGTCTCAAAACTGTCATCTTTAATTA 58.282 33.333 0.00 0.00 0.00 1.40
345 346 7.584987 CGGTCTCAAAACTGTCATCTTTAATT 58.415 34.615 0.00 0.00 0.00 1.40
346 347 6.348540 GCGGTCTCAAAACTGTCATCTTTAAT 60.349 38.462 0.00 0.00 0.00 1.40
347 348 5.049680 GCGGTCTCAAAACTGTCATCTTTAA 60.050 40.000 0.00 0.00 0.00 1.52
348 349 4.451096 GCGGTCTCAAAACTGTCATCTTTA 59.549 41.667 0.00 0.00 0.00 1.85
349 350 3.251004 GCGGTCTCAAAACTGTCATCTTT 59.749 43.478 0.00 0.00 0.00 2.52
350 351 2.808543 GCGGTCTCAAAACTGTCATCTT 59.191 45.455 0.00 0.00 0.00 2.40
351 352 2.224281 TGCGGTCTCAAAACTGTCATCT 60.224 45.455 0.00 0.00 0.00 2.90
352 353 2.143122 TGCGGTCTCAAAACTGTCATC 58.857 47.619 0.00 0.00 0.00 2.92
353 354 2.254546 TGCGGTCTCAAAACTGTCAT 57.745 45.000 0.00 0.00 0.00 3.06
354 355 1.939934 CTTGCGGTCTCAAAACTGTCA 59.060 47.619 0.00 0.00 0.00 3.58
355 356 2.210116 TCTTGCGGTCTCAAAACTGTC 58.790 47.619 0.00 0.00 0.00 3.51
356 357 2.325583 TCTTGCGGTCTCAAAACTGT 57.674 45.000 0.00 0.00 0.00 3.55
357 358 3.181501 TGTTTCTTGCGGTCTCAAAACTG 60.182 43.478 0.00 0.00 0.00 3.16
358 359 3.013921 TGTTTCTTGCGGTCTCAAAACT 58.986 40.909 0.00 0.00 0.00 2.66
359 360 3.414549 TGTTTCTTGCGGTCTCAAAAC 57.585 42.857 0.00 0.00 0.00 2.43
360 361 4.156922 TCTTTGTTTCTTGCGGTCTCAAAA 59.843 37.500 0.00 0.00 0.00 2.44
361 362 3.692101 TCTTTGTTTCTTGCGGTCTCAAA 59.308 39.130 0.00 0.00 0.00 2.69
362 363 3.275143 TCTTTGTTTCTTGCGGTCTCAA 58.725 40.909 0.00 0.00 0.00 3.02
363 364 2.912771 TCTTTGTTTCTTGCGGTCTCA 58.087 42.857 0.00 0.00 0.00 3.27
364 365 3.963383 TTCTTTGTTTCTTGCGGTCTC 57.037 42.857 0.00 0.00 0.00 3.36
365 366 4.712122 TTTTCTTTGTTTCTTGCGGTCT 57.288 36.364 0.00 0.00 0.00 3.85
366 367 4.623595 TGTTTTTCTTTGTTTCTTGCGGTC 59.376 37.500 0.00 0.00 0.00 4.79
367 368 4.561105 TGTTTTTCTTTGTTTCTTGCGGT 58.439 34.783 0.00 0.00 0.00 5.68
368 369 5.120053 AGTTGTTTTTCTTTGTTTCTTGCGG 59.880 36.000 0.00 0.00 0.00 5.69
369 370 6.008875 CAGTTGTTTTTCTTTGTTTCTTGCG 58.991 36.000 0.00 0.00 0.00 4.85
370 371 7.009440 GTCAGTTGTTTTTCTTTGTTTCTTGC 58.991 34.615 0.00 0.00 0.00 4.01
371 372 7.219922 CGTCAGTTGTTTTTCTTTGTTTCTTG 58.780 34.615 0.00 0.00 0.00 3.02
372 373 6.364976 CCGTCAGTTGTTTTTCTTTGTTTCTT 59.635 34.615 0.00 0.00 0.00 2.52
373 374 5.861787 CCGTCAGTTGTTTTTCTTTGTTTCT 59.138 36.000 0.00 0.00 0.00 2.52
374 375 5.444087 GCCGTCAGTTGTTTTTCTTTGTTTC 60.444 40.000 0.00 0.00 0.00 2.78
375 376 4.387559 GCCGTCAGTTGTTTTTCTTTGTTT 59.612 37.500 0.00 0.00 0.00 2.83
376 377 3.924073 GCCGTCAGTTGTTTTTCTTTGTT 59.076 39.130 0.00 0.00 0.00 2.83
377 378 3.057174 TGCCGTCAGTTGTTTTTCTTTGT 60.057 39.130 0.00 0.00 0.00 2.83
378 379 3.303229 GTGCCGTCAGTTGTTTTTCTTTG 59.697 43.478 0.00 0.00 0.00 2.77
379 380 3.507786 GTGCCGTCAGTTGTTTTTCTTT 58.492 40.909 0.00 0.00 0.00 2.52
380 381 2.159296 GGTGCCGTCAGTTGTTTTTCTT 60.159 45.455 0.00 0.00 0.00 2.52
381 382 1.404035 GGTGCCGTCAGTTGTTTTTCT 59.596 47.619 0.00 0.00 0.00 2.52
382 383 1.535226 GGGTGCCGTCAGTTGTTTTTC 60.535 52.381 0.00 0.00 0.00 2.29
383 384 0.458260 GGGTGCCGTCAGTTGTTTTT 59.542 50.000 0.00 0.00 0.00 1.94
384 385 1.388837 GGGGTGCCGTCAGTTGTTTT 61.389 55.000 0.00 0.00 0.00 2.43
385 386 1.826487 GGGGTGCCGTCAGTTGTTT 60.826 57.895 0.00 0.00 0.00 2.83
386 387 2.203294 GGGGTGCCGTCAGTTGTT 60.203 61.111 0.00 0.00 0.00 2.83
387 388 3.168528 AGGGGTGCCGTCAGTTGT 61.169 61.111 0.00 0.00 0.00 3.32
388 389 2.358737 GAGGGGTGCCGTCAGTTG 60.359 66.667 0.00 0.00 38.20 3.16
389 390 3.637273 GGAGGGGTGCCGTCAGTT 61.637 66.667 0.00 0.00 39.85 3.16
390 391 4.954118 TGGAGGGGTGCCGTCAGT 62.954 66.667 0.00 0.00 39.85 3.41
498 499 9.890629 ATGAAAGGGAAAAATTATAGAAAAGCC 57.109 29.630 0.00 0.00 0.00 4.35
507 508 7.614494 CACCTCACATGAAAGGGAAAAATTAT 58.386 34.615 18.25 0.00 36.95 1.28
516 517 1.915141 AAGCACCTCACATGAAAGGG 58.085 50.000 18.25 9.25 36.95 3.95
519 520 5.301551 ACAATACAAAGCACCTCACATGAAA 59.698 36.000 0.00 0.00 0.00 2.69
561 562 3.033659 TCTGAGTAAGTCCCCAGATCC 57.966 52.381 0.00 0.00 31.45 3.36
571 573 7.283329 ACCTGTCATTTCTTTTCTGAGTAAGT 58.717 34.615 2.79 0.00 0.00 2.24
576 578 8.233190 GTGATTACCTGTCATTTCTTTTCTGAG 58.767 37.037 0.00 0.00 0.00 3.35
579 581 8.697507 AAGTGATTACCTGTCATTTCTTTTCT 57.302 30.769 0.00 0.00 0.00 2.52
585 587 9.383519 TCATCTAAAGTGATTACCTGTCATTTC 57.616 33.333 0.00 0.00 0.00 2.17
589 591 7.676004 TGTTCATCTAAAGTGATTACCTGTCA 58.324 34.615 0.00 0.00 0.00 3.58
590 592 7.278868 CCTGTTCATCTAAAGTGATTACCTGTC 59.721 40.741 0.00 0.00 0.00 3.51
591 593 7.106239 CCTGTTCATCTAAAGTGATTACCTGT 58.894 38.462 0.00 0.00 0.00 4.00
592 594 7.106239 ACCTGTTCATCTAAAGTGATTACCTG 58.894 38.462 0.00 0.00 0.00 4.00
593 595 7.259088 ACCTGTTCATCTAAAGTGATTACCT 57.741 36.000 0.00 0.00 0.00 3.08
594 596 9.444600 TTTACCTGTTCATCTAAAGTGATTACC 57.555 33.333 0.00 0.00 0.00 2.85
670 684 9.308318 TCGCGTATATATTACCGTATTACAGTA 57.692 33.333 5.77 0.00 0.00 2.74
672 686 9.489393 TTTCGCGTATATATTACCGTATTACAG 57.511 33.333 5.77 0.00 0.00 2.74
673 687 9.833182 TTTTCGCGTATATATTACCGTATTACA 57.167 29.630 5.77 0.00 0.00 2.41
681 695 9.789029 GTCTTTCTTTTTCGCGTATATATTACC 57.211 33.333 5.77 0.00 0.00 2.85
695 709 4.090498 GCCATGCAATCGTCTTTCTTTTTC 59.910 41.667 0.00 0.00 0.00 2.29
772 786 5.994887 TTTTTATACGGGATGATGTTCGG 57.005 39.130 0.00 0.00 0.00 4.30
883 944 2.429930 CGGACCTGGTTTGAGGCA 59.570 61.111 0.00 0.00 36.46 4.75
895 956 2.104530 GGAACTAGCTCGCGGACC 59.895 66.667 6.13 0.00 0.00 4.46
897 958 3.145551 GGGGAACTAGCTCGCGGA 61.146 66.667 6.13 0.00 0.00 5.54
898 959 4.222847 GGGGGAACTAGCTCGCGG 62.223 72.222 6.13 0.00 0.00 6.46
899 960 4.570663 CGGGGGAACTAGCTCGCG 62.571 72.222 0.00 0.00 38.34 5.87
900 961 3.427598 GACGGGGGAACTAGCTCGC 62.428 68.421 1.69 1.69 0.00 5.03
901 962 2.005960 CTGACGGGGGAACTAGCTCG 62.006 65.000 0.00 0.00 0.00 5.03
902 963 0.971447 ACTGACGGGGGAACTAGCTC 60.971 60.000 0.00 0.00 0.00 4.09
903 964 0.544595 AACTGACGGGGGAACTAGCT 60.545 55.000 0.00 0.00 0.00 3.32
904 965 0.108281 GAACTGACGGGGGAACTAGC 60.108 60.000 0.00 0.00 0.00 3.42
905 966 0.172803 CGAACTGACGGGGGAACTAG 59.827 60.000 0.00 0.00 0.00 2.57
906 967 0.540365 ACGAACTGACGGGGGAACTA 60.540 55.000 0.00 0.00 37.61 2.24
907 968 1.813728 GACGAACTGACGGGGGAACT 61.814 60.000 0.00 0.00 37.61 3.01
908 969 1.373873 GACGAACTGACGGGGGAAC 60.374 63.158 0.00 0.00 37.61 3.62
909 970 2.576832 GGACGAACTGACGGGGGAA 61.577 63.158 0.00 0.00 37.61 3.97
910 971 2.993264 GGACGAACTGACGGGGGA 60.993 66.667 0.00 0.00 37.61 4.81
911 972 2.502692 GAAGGACGAACTGACGGGGG 62.503 65.000 0.00 0.00 37.61 5.40
939 1034 6.261603 TCAATCTATGCAGTGGATTCATCAAC 59.738 38.462 1.20 0.00 36.04 3.18
955 1050 9.672673 AACGGGATTAGGATAAATCAATCTATG 57.327 33.333 0.00 0.00 37.56 2.23
957 1052 8.656806 ACAACGGGATTAGGATAAATCAATCTA 58.343 33.333 0.00 0.00 37.56 1.98
975 1070 0.882927 CGCTGAAAGGAACAACGGGA 60.883 55.000 0.00 0.00 0.00 5.14
979 1074 1.082104 CGCCGCTGAAAGGAACAAC 60.082 57.895 0.00 0.00 0.00 3.32
1345 1468 1.159285 TGGTCGACGTACCAGTACTG 58.841 55.000 16.34 16.34 44.68 2.74
1382 1514 2.832201 GGAGGAGGCCATTGCAGC 60.832 66.667 5.01 0.00 40.13 5.25
1383 1515 1.153005 GAGGAGGAGGCCATTGCAG 60.153 63.158 5.01 0.00 40.13 4.41
1384 1516 1.617536 AGAGGAGGAGGCCATTGCA 60.618 57.895 5.01 0.00 40.13 4.08
1385 1517 1.153005 CAGAGGAGGAGGCCATTGC 60.153 63.158 5.01 0.00 0.00 3.56
1386 1518 1.153005 GCAGAGGAGGAGGCCATTG 60.153 63.158 5.01 0.00 0.00 2.82
1387 1519 2.381941 GGCAGAGGAGGAGGCCATT 61.382 63.158 5.01 0.00 45.70 3.16
1388 1520 2.771762 GGCAGAGGAGGAGGCCAT 60.772 66.667 5.01 0.00 45.70 4.40
1425 1557 1.773496 GTCGTCGCCGAAAAGAGTG 59.227 57.895 0.00 0.00 46.26 3.51
1430 1562 1.068832 CTCATCGTCGTCGCCGAAAA 61.069 55.000 1.28 0.00 46.26 2.29
1437 1569 4.538283 AGCGGCTCATCGTCGTCG 62.538 66.667 0.00 0.00 44.09 5.12
1455 1587 5.150342 TGCAAACGATGTAATGGTATTCG 57.850 39.130 0.00 0.00 32.60 3.34
1662 1794 2.096013 GCGGCTTTCTCTGTAATTCCAC 59.904 50.000 0.00 0.00 0.00 4.02
2150 2311 3.386726 ACTACGGATCCGATGGAATTTCA 59.613 43.478 39.55 10.12 42.83 2.69
2362 2538 6.305693 ACAGAAAATCAAGCTACAGAACAC 57.694 37.500 0.00 0.00 0.00 3.32
2519 2737 7.636150 ATTCATAGGTCATTGACAAGAAAGG 57.364 36.000 18.09 1.28 33.68 3.11
2755 3468 3.686726 GGATGGCATCATTTAGGTCGATC 59.313 47.826 27.39 3.03 32.98 3.69
2885 3598 1.196808 CCCATTCGTGTGCAGTACAAC 59.803 52.381 0.00 0.00 41.89 3.32
3102 3815 7.555195 TGACGACCAAGATCAAATAGACTACTA 59.445 37.037 0.00 0.00 0.00 1.82
3121 3851 1.005037 TGCATCACCACTGACGACC 60.005 57.895 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.