Multiple sequence alignment - TraesCS2A01G538700

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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 TraesCS2A01G538700 chr2A 100.000 3315 0 0 1 3315 751495335 751492021 0.000000e+00 6122.0
1 TraesCS2A01G538700 chr2A 90.909 77 6 1 178 253 768045147 768045223 5.850000e-18 102.0
2 TraesCS2A01G538700 chr2D 90.858 1772 109 21 987 2740 619870694 619868958 0.000000e+00 2326.0
3 TraesCS2A01G538700 chr2D 87.943 987 74 23 2106 3077 619832809 619831853 0.000000e+00 1122.0
4 TraesCS2A01G538700 chr2D 90.417 720 39 3 1391 2110 619848625 619847936 0.000000e+00 920.0
5 TraesCS2A01G538700 chr2D 89.904 416 27 9 987 1393 619850403 619849994 3.790000e-144 521.0
6 TraesCS2A01G538700 chr2D 88.980 245 19 5 703 945 619871013 619870775 2.500000e-76 296.0
7 TraesCS2A01G538700 chr2D 93.525 139 7 1 3095 3231 619831726 619831588 4.330000e-49 206.0
8 TraesCS2A01G538700 chr2D 89.091 165 14 4 679 843 619850701 619850541 5.610000e-48 202.0
9 TraesCS2A01G538700 chr2D 79.336 271 23 18 2993 3256 619868599 619868355 3.420000e-35 159.0
10 TraesCS2A01G538700 chr2D 84.375 160 18 5 1 155 619871905 619871748 2.060000e-32 150.0
11 TraesCS2A01G538700 chr2D 82.222 180 12 7 491 670 619871236 619871077 1.600000e-28 137.0
12 TraesCS2A01G538700 chr2D 92.308 91 5 2 353 443 619871633 619871545 9.650000e-26 128.0
13 TraesCS2A01G538700 chr2D 88.889 90 10 0 3217 3306 619808500 619808411 9.720000e-21 111.0
14 TraesCS2A01G538700 chr2D 89.412 85 9 0 180 264 29185923 29186007 1.260000e-19 108.0
15 TraesCS2A01G538700 chr2D 89.024 82 9 0 177 258 604700838 604700919 5.850000e-18 102.0
16 TraesCS2A01G538700 chr2D 90.244 41 4 0 862 902 619850537 619850497 2.000000e-03 54.7
17 TraesCS2A01G538700 chr2B 86.841 1801 144 57 987 2740 759524721 759522967 0.000000e+00 1927.0
18 TraesCS2A01G538700 chr2B 79.146 609 71 33 381 962 759525369 759524790 1.450000e-98 370.0
19 TraesCS2A01G538700 chr7D 90.244 82 8 0 177 258 41857154 41857073 1.260000e-19 108.0
20 TraesCS2A01G538700 chr6A 90.244 82 8 0 177 258 107689968 107690049 1.260000e-19 108.0
21 TraesCS2A01G538700 chr5D 92.000 75 6 0 177 251 138466119 138466045 4.520000e-19 106.0
22 TraesCS2A01G538700 chr1A 90.123 81 8 0 178 258 297875971 297876051 4.520000e-19 106.0
23 TraesCS2A01G538700 chr5A 87.778 90 7 1 178 267 38187579 38187664 5.850000e-18 102.0
24 TraesCS2A01G538700 chr4D 88.889 81 9 0 178 258 4098819 4098899 2.100000e-17 100.0


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 TraesCS2A01G538700 chr2A 751492021 751495335 3314 True 6122.000000 6122 100.0000 1 3315 1 chr2A.!!$R1 3314
1 TraesCS2A01G538700 chr2D 619831588 619832809 1221 True 664.000000 1122 90.7340 2106 3231 2 chr2D.!!$R2 1125
2 TraesCS2A01G538700 chr2D 619868355 619871905 3550 True 532.666667 2326 86.3465 1 3256 6 chr2D.!!$R4 3255
3 TraesCS2A01G538700 chr2D 619847936 619850701 2765 True 424.425000 920 89.9140 679 2110 4 chr2D.!!$R3 1431
4 TraesCS2A01G538700 chr2B 759522967 759525369 2402 True 1148.500000 1927 82.9935 381 2740 2 chr2B.!!$R1 2359

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
768 1100 0.030195 TGCAGGGGATCTGGTATCCA 60.030 55.0 6.38 0.0 43.54 3.41 F
917 1259 0.107066 TCCAGATGGAATGCACGCAT 60.107 50.0 0.00 0.0 42.18 4.73 F
1716 3592 0.174845 TCCCAGCTTATGACCGAACG 59.825 55.0 0.00 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 3803 0.107703 TGGTGATGAAGCCGATGTCC 60.108 55.000 0.00 0.0 0.00 4.02 R
2202 4078 0.902531 CCTGTACATCCTCGGGTGTT 59.097 55.000 7.23 0.0 0.00 3.32 R
2847 4783 2.066262 TCGAACAACTTCATCGAAGGC 58.934 47.619 8.49 0.0 43.25 4.35 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
40 41 9.632807 TCAATTATCTTTGACCCGTTTTATTTG 57.367 29.630 0.00 0.00 30.82 2.32
41 42 9.632807 CAATTATCTTTGACCCGTTTTATTTGA 57.367 29.630 0.00 0.00 0.00 2.69
45 46 5.472137 TCTTTGACCCGTTTTATTTGAGAGG 59.528 40.000 0.00 0.00 0.00 3.69
46 47 4.627284 TGACCCGTTTTATTTGAGAGGA 57.373 40.909 0.00 0.00 0.00 3.71
81 87 5.804639 TCTTGTACTATCATTTGGCAGTGT 58.195 37.500 0.00 0.00 0.00 3.55
89 95 7.739825 ACTATCATTTGGCAGTGTATATGACT 58.260 34.615 0.00 0.00 0.00 3.41
94 100 7.992608 TCATTTGGCAGTGTATATGACTATTGT 59.007 33.333 0.00 0.00 0.00 2.71
115 121 5.676552 TGTTTTATAGATAAAGCAGGGCGA 58.323 37.500 7.28 0.00 38.14 5.54
117 123 6.600032 TGTTTTATAGATAAAGCAGGGCGAAA 59.400 34.615 7.28 0.00 38.14 3.46
118 124 7.121463 TGTTTTATAGATAAAGCAGGGCGAAAA 59.879 33.333 7.28 0.00 38.14 2.29
119 125 7.633193 TTTATAGATAAAGCAGGGCGAAAAA 57.367 32.000 0.00 0.00 0.00 1.94
123 129 5.410924 AGATAAAGCAGGGCGAAAAATTTC 58.589 37.500 0.00 0.00 0.00 2.17
150 156 4.589374 AGTAGTAGGTAGTGGATTGATGCC 59.411 45.833 0.00 0.00 0.00 4.40
155 161 4.298626 AGGTAGTGGATTGATGCCTCTTA 58.701 43.478 0.00 0.00 32.09 2.10
156 162 4.910304 AGGTAGTGGATTGATGCCTCTTAT 59.090 41.667 0.00 0.00 32.09 1.73
157 163 4.999950 GGTAGTGGATTGATGCCTCTTATG 59.000 45.833 0.00 0.00 32.09 1.90
158 164 4.096190 AGTGGATTGATGCCTCTTATGG 57.904 45.455 0.00 0.00 0.00 2.74
159 165 3.461085 AGTGGATTGATGCCTCTTATGGT 59.539 43.478 0.00 0.00 0.00 3.55
160 166 3.567164 GTGGATTGATGCCTCTTATGGTG 59.433 47.826 0.00 0.00 0.00 4.17
161 167 2.555757 GGATTGATGCCTCTTATGGTGC 59.444 50.000 0.00 0.00 0.00 5.01
162 168 2.057137 TTGATGCCTCTTATGGTGCC 57.943 50.000 0.00 0.00 0.00 5.01
163 169 1.216064 TGATGCCTCTTATGGTGCCT 58.784 50.000 0.00 0.00 0.00 4.75
164 170 2.407562 TGATGCCTCTTATGGTGCCTA 58.592 47.619 0.00 0.00 0.00 3.93
165 171 2.104792 TGATGCCTCTTATGGTGCCTAC 59.895 50.000 0.00 0.00 0.00 3.18
166 172 1.879575 TGCCTCTTATGGTGCCTACT 58.120 50.000 0.00 0.00 0.00 2.57
167 173 1.762957 TGCCTCTTATGGTGCCTACTC 59.237 52.381 0.00 0.00 0.00 2.59
168 174 1.070914 GCCTCTTATGGTGCCTACTCC 59.929 57.143 0.00 0.00 0.00 3.85
169 175 1.694696 CCTCTTATGGTGCCTACTCCC 59.305 57.143 0.00 0.00 0.00 4.30
170 176 2.683768 CTCTTATGGTGCCTACTCCCT 58.316 52.381 0.00 0.00 0.00 4.20
171 177 2.630580 CTCTTATGGTGCCTACTCCCTC 59.369 54.545 0.00 0.00 0.00 4.30
172 178 1.694696 CTTATGGTGCCTACTCCCTCC 59.305 57.143 0.00 0.00 0.00 4.30
173 179 0.469331 TATGGTGCCTACTCCCTCCG 60.469 60.000 0.00 0.00 0.00 4.63
174 180 3.851128 GGTGCCTACTCCCTCCGC 61.851 72.222 0.00 0.00 0.00 5.54
175 181 3.851128 GTGCCTACTCCCTCCGCC 61.851 72.222 0.00 0.00 0.00 6.13
177 183 4.862823 GCCTACTCCCTCCGCCCT 62.863 72.222 0.00 0.00 0.00 5.19
178 184 2.041819 CCTACTCCCTCCGCCCTT 60.042 66.667 0.00 0.00 0.00 3.95
179 185 1.689582 CCTACTCCCTCCGCCCTTT 60.690 63.158 0.00 0.00 0.00 3.11
180 186 1.272554 CCTACTCCCTCCGCCCTTTT 61.273 60.000 0.00 0.00 0.00 2.27
181 187 0.178301 CTACTCCCTCCGCCCTTTTC 59.822 60.000 0.00 0.00 0.00 2.29
182 188 0.252558 TACTCCCTCCGCCCTTTTCT 60.253 55.000 0.00 0.00 0.00 2.52
183 189 0.252558 ACTCCCTCCGCCCTTTTCTA 60.253 55.000 0.00 0.00 0.00 2.10
184 190 1.132500 CTCCCTCCGCCCTTTTCTAT 58.868 55.000 0.00 0.00 0.00 1.98
185 191 2.326428 CTCCCTCCGCCCTTTTCTATA 58.674 52.381 0.00 0.00 0.00 1.31
186 192 2.704065 CTCCCTCCGCCCTTTTCTATAA 59.296 50.000 0.00 0.00 0.00 0.98
187 193 3.116959 TCCCTCCGCCCTTTTCTATAAA 58.883 45.455 0.00 0.00 0.00 1.40
188 194 3.135895 TCCCTCCGCCCTTTTCTATAAAG 59.864 47.826 0.00 0.00 0.00 1.85
189 195 3.118000 CCCTCCGCCCTTTTCTATAAAGT 60.118 47.826 0.00 0.00 0.00 2.66
190 196 4.524053 CCTCCGCCCTTTTCTATAAAGTT 58.476 43.478 0.00 0.00 0.00 2.66
191 197 4.335594 CCTCCGCCCTTTTCTATAAAGTTG 59.664 45.833 0.00 0.00 0.00 3.16
192 198 4.266714 TCCGCCCTTTTCTATAAAGTTGG 58.733 43.478 0.00 0.00 0.00 3.77
193 199 4.014406 CCGCCCTTTTCTATAAAGTTGGT 58.986 43.478 0.00 0.00 0.00 3.67
194 200 4.095932 CCGCCCTTTTCTATAAAGTTGGTC 59.904 45.833 0.00 0.00 0.00 4.02
195 201 4.698304 CGCCCTTTTCTATAAAGTTGGTCA 59.302 41.667 0.00 0.00 0.00 4.02
196 202 5.182380 CGCCCTTTTCTATAAAGTTGGTCAA 59.818 40.000 0.00 0.00 0.00 3.18
197 203 6.294286 CGCCCTTTTCTATAAAGTTGGTCAAA 60.294 38.462 0.00 0.00 0.00 2.69
198 204 7.438564 GCCCTTTTCTATAAAGTTGGTCAAAA 58.561 34.615 0.00 0.00 0.00 2.44
199 205 8.094548 GCCCTTTTCTATAAAGTTGGTCAAAAT 58.905 33.333 0.00 0.00 0.00 1.82
200 206 9.996554 CCCTTTTCTATAAAGTTGGTCAAAATT 57.003 29.630 0.00 0.00 0.00 1.82
233 239 8.690203 TTTGACTTAAGACAAAATCTGGATGA 57.310 30.769 24.34 4.50 37.88 2.92
234 240 8.690203 TTGACTTAAGACAAAATCTGGATGAA 57.310 30.769 16.33 0.00 37.88 2.57
235 241 8.099364 TGACTTAAGACAAAATCTGGATGAAC 57.901 34.615 10.09 0.00 37.88 3.18
236 242 7.719193 TGACTTAAGACAAAATCTGGATGAACA 59.281 33.333 10.09 0.00 37.88 3.18
237 243 8.463930 ACTTAAGACAAAATCTGGATGAACAA 57.536 30.769 10.09 0.00 37.88 2.83
238 244 9.082313 ACTTAAGACAAAATCTGGATGAACAAT 57.918 29.630 10.09 0.00 37.88 2.71
239 245 9.918630 CTTAAGACAAAATCTGGATGAACAATT 57.081 29.630 0.00 0.00 37.88 2.32
244 250 9.859427 GACAAAATCTGGATGAACAATTATTCA 57.141 29.630 0.84 0.84 42.62 2.57
245 251 9.643693 ACAAAATCTGGATGAACAATTATTCAC 57.356 29.630 0.25 0.00 41.29 3.18
246 252 8.800972 CAAAATCTGGATGAACAATTATTCACG 58.199 33.333 0.25 0.00 41.29 4.35
247 253 6.624352 ATCTGGATGAACAATTATTCACGG 57.376 37.500 0.25 0.00 41.29 4.94
248 254 5.739959 TCTGGATGAACAATTATTCACGGA 58.260 37.500 0.25 0.00 41.29 4.69
249 255 6.356556 TCTGGATGAACAATTATTCACGGAT 58.643 36.000 0.25 0.00 41.29 4.18
250 256 6.260714 TCTGGATGAACAATTATTCACGGATG 59.739 38.462 0.25 0.00 41.29 3.51
251 257 5.299028 TGGATGAACAATTATTCACGGATGG 59.701 40.000 0.25 0.00 41.29 3.51
252 258 5.530915 GGATGAACAATTATTCACGGATGGA 59.469 40.000 0.25 0.00 41.29 3.41
253 259 5.811399 TGAACAATTATTCACGGATGGAC 57.189 39.130 0.00 0.00 33.62 4.02
254 260 4.331443 TGAACAATTATTCACGGATGGACG 59.669 41.667 0.00 0.00 33.62 4.79
255 261 3.202906 ACAATTATTCACGGATGGACGG 58.797 45.455 0.00 0.00 38.39 4.79
256 262 3.118555 ACAATTATTCACGGATGGACGGA 60.119 43.478 0.00 0.00 38.39 4.69
257 263 2.882927 TTATTCACGGATGGACGGAG 57.117 50.000 0.00 0.00 38.39 4.63
258 264 1.037493 TATTCACGGATGGACGGAGG 58.963 55.000 0.00 0.00 38.39 4.30
259 265 1.686325 ATTCACGGATGGACGGAGGG 61.686 60.000 0.00 0.00 38.39 4.30
260 266 2.758327 CACGGATGGACGGAGGGA 60.758 66.667 0.00 0.00 38.39 4.20
261 267 2.442272 ACGGATGGACGGAGGGAG 60.442 66.667 0.00 0.00 38.39 4.30
262 268 2.442272 CGGATGGACGGAGGGAGT 60.442 66.667 0.00 0.00 0.00 3.85
263 269 1.152819 CGGATGGACGGAGGGAGTA 60.153 63.158 0.00 0.00 0.00 2.59
264 270 1.453762 CGGATGGACGGAGGGAGTAC 61.454 65.000 0.00 0.00 0.00 2.73
265 271 0.396695 GGATGGACGGAGGGAGTACA 60.397 60.000 0.00 0.00 36.79 2.90
266 272 1.705873 GATGGACGGAGGGAGTACAT 58.294 55.000 0.00 0.00 45.16 2.29
267 273 1.341531 GATGGACGGAGGGAGTACATG 59.658 57.143 0.00 0.00 42.75 3.21
268 274 1.327690 TGGACGGAGGGAGTACATGC 61.328 60.000 0.00 0.00 0.00 4.06
269 275 1.043673 GGACGGAGGGAGTACATGCT 61.044 60.000 0.00 0.00 0.00 3.79
270 276 0.386113 GACGGAGGGAGTACATGCTC 59.614 60.000 0.00 0.00 34.89 4.26
271 277 0.033011 ACGGAGGGAGTACATGCTCT 60.033 55.000 0.00 0.00 35.89 4.09
274 280 2.739932 CGGAGGGAGTACATGCTCTTTG 60.740 54.545 0.00 0.00 35.89 2.77
280 286 5.001232 GGGAGTACATGCTCTTTGTTGTAA 58.999 41.667 0.00 0.00 35.89 2.41
321 327 9.660544 AGGCTATCCATTACCATTTTCTTTATT 57.339 29.630 0.00 0.00 33.74 1.40
345 369 9.986157 ATTAATGATGGAGCCACATAAGATAAT 57.014 29.630 0.00 0.00 0.00 1.28
349 373 7.168219 TGATGGAGCCACATAAGATAATAACC 58.832 38.462 0.00 0.00 0.00 2.85
350 374 6.763715 TGGAGCCACATAAGATAATAACCT 57.236 37.500 0.00 0.00 0.00 3.50
351 375 7.865530 TGGAGCCACATAAGATAATAACCTA 57.134 36.000 0.00 0.00 0.00 3.08
401 429 0.798776 ACAGAAAATCGCTGCTTCGG 59.201 50.000 0.00 0.00 36.86 4.30
443 709 2.511600 GAATCCCTCGTGCACCGG 60.512 66.667 12.15 11.97 37.11 5.28
466 732 3.368501 CCTCCCTCCCTCCCTCCA 61.369 72.222 0.00 0.00 0.00 3.86
469 735 2.122189 CCCTCCCTCCCTCCATCC 60.122 72.222 0.00 0.00 0.00 3.51
470 736 2.122189 CCTCCCTCCCTCCATCCC 60.122 72.222 0.00 0.00 0.00 3.85
471 737 2.731461 CCTCCCTCCCTCCATCCCT 61.731 68.421 0.00 0.00 0.00 4.20
473 739 1.630333 TCCCTCCCTCCATCCCTCT 60.630 63.158 0.00 0.00 0.00 3.69
515 804 4.923281 AGAAAAACAAGCATTATCCAACGC 59.077 37.500 0.00 0.00 0.00 4.84
545 834 1.172812 AACTTGGGCAGAGCGAAACC 61.173 55.000 0.00 0.00 0.00 3.27
567 856 2.337749 ATCGCGAGCCTACTTGGTCG 62.338 60.000 16.66 8.13 40.09 4.79
569 858 2.579787 CGAGCCTACTTGGTCGCG 60.580 66.667 0.00 0.00 38.35 5.87
598 897 4.621087 AAACCCACAGCTGGCCCC 62.621 66.667 19.93 0.00 36.00 5.80
603 902 4.659172 CACAGCTGGCCCCGGAAA 62.659 66.667 19.93 0.00 0.00 3.13
604 903 4.351054 ACAGCTGGCCCCGGAAAG 62.351 66.667 19.93 0.00 0.00 2.62
646 948 1.884464 CATCACCTGGACGCCGATG 60.884 63.158 0.00 0.91 0.00 3.84
670 972 2.103736 GGCGTGCGTACTCCTACC 59.896 66.667 5.32 0.00 0.00 3.18
671 973 2.103736 GCGTGCGTACTCCTACCC 59.896 66.667 1.24 0.00 0.00 3.69
674 976 3.142838 TGCGTACTCCTACCCCGC 61.143 66.667 0.00 0.00 44.27 6.13
677 979 4.261781 GTACTCCTACCCCGCGCG 62.262 72.222 25.67 25.67 0.00 6.86
681 990 4.488136 TCCTACCCCGCGCGACTA 62.488 66.667 34.63 15.63 0.00 2.59
768 1100 0.030195 TGCAGGGGATCTGGTATCCA 60.030 55.000 6.38 0.00 43.54 3.41
779 1111 0.334335 TGGTATCCATTGCTTGCCCA 59.666 50.000 0.00 0.00 0.00 5.36
801 1143 4.899239 CATCGCGTCTGCCTCCCC 62.899 72.222 5.77 0.00 38.08 4.81
815 1157 2.757099 CCCCATGCCCTCTTGTGC 60.757 66.667 0.00 0.00 0.00 4.57
818 1160 3.818787 CATGCCCTCTTGTGCGCC 61.819 66.667 4.18 0.00 0.00 6.53
890 1232 2.354805 CGCCCTATAAATCCCACTAGCC 60.355 54.545 0.00 0.00 0.00 3.93
891 1233 2.642807 GCCCTATAAATCCCACTAGCCA 59.357 50.000 0.00 0.00 0.00 4.75
917 1259 0.107066 TCCAGATGGAATGCACGCAT 60.107 50.000 0.00 0.00 42.18 4.73
919 1261 0.309922 CAGATGGAATGCACGCATCC 59.690 55.000 4.73 8.89 35.31 3.51
930 1272 0.652592 CACGCATCCGAACCATCTTC 59.347 55.000 0.00 0.00 38.29 2.87
931 1273 0.537188 ACGCATCCGAACCATCTTCT 59.463 50.000 0.00 0.00 38.29 2.85
932 1274 1.066143 ACGCATCCGAACCATCTTCTT 60.066 47.619 0.00 0.00 38.29 2.52
933 1275 2.167693 ACGCATCCGAACCATCTTCTTA 59.832 45.455 0.00 0.00 38.29 2.10
934 1276 2.797156 CGCATCCGAACCATCTTCTTAG 59.203 50.000 0.00 0.00 36.29 2.18
935 1277 3.490933 CGCATCCGAACCATCTTCTTAGA 60.491 47.826 0.00 0.00 36.29 2.10
936 1278 4.442706 GCATCCGAACCATCTTCTTAGAA 58.557 43.478 0.00 0.00 33.20 2.10
937 1279 4.509600 GCATCCGAACCATCTTCTTAGAAG 59.490 45.833 15.30 15.30 33.20 2.85
938 1280 5.682471 GCATCCGAACCATCTTCTTAGAAGA 60.682 44.000 24.50 24.50 33.20 2.87
939 1281 5.995565 TCCGAACCATCTTCTTAGAAGAA 57.004 39.130 25.77 8.99 42.41 2.52
974 1316 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
975 1317 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
976 1318 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
979 1321 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
981 1323 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
982 1324 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
983 1325 8.887036 AAGAAGAAGAAGAAGAAGAAGAAGAC 57.113 34.615 0.00 0.00 0.00 3.01
985 1327 8.482128 AGAAGAAGAAGAAGAAGAAGAAGACAA 58.518 33.333 0.00 0.00 0.00 3.18
993 1403 7.675062 AGAAGAAGAAGAAGACAATCTTAGCA 58.325 34.615 0.00 0.00 39.70 3.49
995 1405 8.682936 AAGAAGAAGAAGACAATCTTAGCAAA 57.317 30.769 0.00 0.00 39.70 3.68
1166 1582 2.617274 GGTGCTTCCAGGTTCGTGC 61.617 63.158 0.00 0.00 35.97 5.34
1168 1584 3.056328 GCTTCCAGGTTCGTGCCC 61.056 66.667 0.00 0.00 0.00 5.36
1196 1616 2.159234 GCTCTGCTTCTGCTTGTTACTG 59.841 50.000 0.00 0.00 40.48 2.74
1197 1617 2.146342 TCTGCTTCTGCTTGTTACTGC 58.854 47.619 0.00 0.00 40.48 4.40
1198 1618 2.149578 CTGCTTCTGCTTGTTACTGCT 58.850 47.619 3.26 0.00 40.48 4.24
1199 1619 2.146342 TGCTTCTGCTTGTTACTGCTC 58.854 47.619 3.26 0.00 40.48 4.26
1265 1723 1.261619 CTGCACGGTCAGTTCAGAAAC 59.738 52.381 0.00 0.00 45.07 2.78
1288 1746 4.142403 CGGATAGGGTTACAAGTTACACGA 60.142 45.833 0.00 0.00 0.00 4.35
1343 1815 3.072211 GTGACCTGGCACTAAGTTAACC 58.928 50.000 0.88 0.00 35.91 2.85
1405 3252 0.982673 GACATGCTGACACGTACGTC 59.017 55.000 19.94 9.19 36.40 4.34
1575 3451 4.115199 ACGGGATCAGCAAGGCCC 62.115 66.667 0.00 0.00 37.21 5.80
1608 3484 1.146263 CACTACGCCAATCCCCTCC 59.854 63.158 0.00 0.00 0.00 4.30
1655 3531 2.006888 CAACCGGCAACATACAGGTAG 58.993 52.381 0.00 0.00 34.35 3.18
1656 3532 1.563924 ACCGGCAACATACAGGTAGA 58.436 50.000 0.00 0.00 32.76 2.59
1716 3592 0.174845 TCCCAGCTTATGACCGAACG 59.825 55.000 0.00 0.00 0.00 3.95
1774 3650 1.227205 GGAGATGCAGAGGCTGTCG 60.227 63.158 0.00 0.00 41.91 4.35
1775 3651 1.227205 GAGATGCAGAGGCTGTCGG 60.227 63.158 0.00 0.00 41.91 4.79
1786 3662 4.291047 CTGTCGGTGCAGCTCATT 57.709 55.556 14.92 0.00 0.00 2.57
1864 3740 3.512516 GGGCTGCAGTTCATCGCC 61.513 66.667 16.64 9.08 39.98 5.54
1867 3743 2.758089 GCTGCAGTTCATCGCCCTG 61.758 63.158 16.64 0.00 0.00 4.45
2122 3998 1.678728 GCCATCCTCAACACCGATGAA 60.679 52.381 0.00 0.00 36.33 2.57
2326 4205 5.596845 GACAGTGCTTAAATGGGAAACAAA 58.403 37.500 0.00 0.00 0.00 2.83
2327 4206 5.983540 ACAGTGCTTAAATGGGAAACAAAA 58.016 33.333 0.00 0.00 0.00 2.44
2328 4207 6.591001 ACAGTGCTTAAATGGGAAACAAAAT 58.409 32.000 0.00 0.00 0.00 1.82
2329 4208 7.731054 ACAGTGCTTAAATGGGAAACAAAATA 58.269 30.769 0.00 0.00 0.00 1.40
2358 4240 4.530553 TGGTTCAGCTCCACTAAGACATAA 59.469 41.667 0.00 0.00 0.00 1.90
2359 4241 5.012664 TGGTTCAGCTCCACTAAGACATAAA 59.987 40.000 0.00 0.00 0.00 1.40
2360 4242 5.938125 GGTTCAGCTCCACTAAGACATAAAA 59.062 40.000 0.00 0.00 0.00 1.52
2404 4286 6.149308 TGCAGATAAGTGTCCATTTAGTTGTG 59.851 38.462 0.00 0.00 0.00 3.33
2405 4287 6.149474 GCAGATAAGTGTCCATTTAGTTGTGT 59.851 38.462 0.00 0.00 0.00 3.72
2406 4288 7.624344 GCAGATAAGTGTCCATTTAGTTGTGTC 60.624 40.741 0.00 0.00 0.00 3.67
2407 4289 6.879458 AGATAAGTGTCCATTTAGTTGTGTCC 59.121 38.462 0.00 0.00 0.00 4.02
2470 4352 8.685838 TTAATTATGCCTCCATTACCAAGTAC 57.314 34.615 0.00 0.00 32.85 2.73
2478 4360 6.739008 GCCTCCATTACCAAGTACTATCTCAC 60.739 46.154 0.00 0.00 0.00 3.51
2515 4397 3.758755 TGGTATTAGCAGAGCTGGATG 57.241 47.619 0.00 0.00 40.10 3.51
2768 4669 6.843069 ACAATTTACTGTTTGACATTTGCC 57.157 33.333 0.00 0.00 0.00 4.52
2781 4717 3.012518 ACATTTGCCTGACATACTGAGC 58.987 45.455 0.00 0.00 0.00 4.26
2803 4739 7.123397 TGAGCAAGATAACTCTAGTGTTCTGAT 59.877 37.037 13.20 6.49 33.92 2.90
2805 4741 7.978975 AGCAAGATAACTCTAGTGTTCTGATTC 59.021 37.037 13.20 5.33 0.00 2.52
2806 4742 7.978975 GCAAGATAACTCTAGTGTTCTGATTCT 59.021 37.037 13.20 7.14 0.00 2.40
2807 4743 9.299963 CAAGATAACTCTAGTGTTCTGATTCTG 57.700 37.037 13.20 0.00 0.00 3.02
2808 4744 8.006298 AGATAACTCTAGTGTTCTGATTCTGG 57.994 38.462 13.20 0.00 0.00 3.86
2809 4745 7.836685 AGATAACTCTAGTGTTCTGATTCTGGA 59.163 37.037 13.20 0.00 0.00 3.86
2810 4746 5.913137 ACTCTAGTGTTCTGATTCTGGAG 57.087 43.478 12.32 12.32 39.96 3.86
2811 4747 5.575157 ACTCTAGTGTTCTGATTCTGGAGA 58.425 41.667 17.26 2.07 38.36 3.71
2812 4748 6.013379 ACTCTAGTGTTCTGATTCTGGAGAA 58.987 40.000 17.26 0.00 38.36 2.87
2847 4783 8.657074 ATGCTTCACATTGAAATTTATCATGG 57.343 30.769 0.00 0.00 35.73 3.66
2891 4827 1.492599 TGGTGGTTCCACAACATCTGA 59.507 47.619 21.25 0.00 41.93 3.27
2900 4850 3.068024 TCCACAACATCTGAAAAACCAGC 59.932 43.478 0.00 0.00 34.28 4.85
2997 4965 9.793259 AGTAAATGTTATTTCTCTCAAGAACCA 57.207 29.630 0.00 0.00 41.23 3.67
3000 4968 8.868522 AATGTTATTTCTCTCAAGAACCATGA 57.131 30.769 0.00 0.00 41.23 3.07
3003 4971 9.300681 TGTTATTTCTCTCAAGAACCATGAAAT 57.699 29.630 0.00 0.00 41.23 2.17
3049 5072 4.035558 ACACATAAACTGTTCACTGTGCTG 59.964 41.667 20.56 0.00 37.98 4.41
3060 5083 2.300152 TCACTGTGCTGGGTAGAAAGAG 59.700 50.000 2.12 0.00 0.00 2.85
3077 5100 9.274206 GTAGAAAGAGGTACAAGAAGAAAACAT 57.726 33.333 0.00 0.00 0.00 2.71
3136 5274 4.928615 CAGCTGTTCCTCAAAACAAAAACA 59.071 37.500 5.25 0.00 38.60 2.83
3184 5328 5.282055 TCTATTGCCTCTGTGGTATCAAG 57.718 43.478 0.00 0.00 38.35 3.02
3237 5381 0.179116 CTGGAGCTGAGATGTCGTGG 60.179 60.000 0.00 0.00 0.00 4.94
3260 5404 2.286365 TGGCCGACCAAGAGATTTTT 57.714 45.000 0.00 0.00 45.37 1.94
3297 5441 9.995003 ATTAAACAAAATCTTTGCCTAATCACA 57.005 25.926 0.00 0.00 0.00 3.58
3298 5442 9.995003 TTAAACAAAATCTTTGCCTAATCACAT 57.005 25.926 0.00 0.00 0.00 3.21
3299 5443 8.907222 AAACAAAATCTTTGCCTAATCACATT 57.093 26.923 0.00 0.00 0.00 2.71
3300 5444 9.995003 AAACAAAATCTTTGCCTAATCACATTA 57.005 25.926 0.00 0.00 0.00 1.90
3301 5445 9.995003 AACAAAATCTTTGCCTAATCACATTAA 57.005 25.926 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 7.564793 ACACTGCCAAATGATAGTACAAGATA 58.435 34.615 0.00 0.00 0.00 1.98
59 60 7.792374 ATACACTGCCAAATGATAGTACAAG 57.208 36.000 0.00 0.00 0.00 3.16
65 66 9.881649 ATAGTCATATACACTGCCAAATGATAG 57.118 33.333 0.00 0.00 0.00 2.08
69 70 8.158169 ACAATAGTCATATACACTGCCAAATG 57.842 34.615 0.00 0.00 0.00 2.32
70 71 8.752005 AACAATAGTCATATACACTGCCAAAT 57.248 30.769 0.00 0.00 0.00 2.32
89 95 7.934665 TCGCCCTGCTTTATCTATAAAACAATA 59.065 33.333 1.50 0.00 30.64 1.90
94 100 7.633193 TTTTCGCCCTGCTTTATCTATAAAA 57.367 32.000 0.00 0.00 32.39 1.52
115 121 8.033626 CCACTACCTACTACTCTCGAAATTTTT 58.966 37.037 0.00 0.00 0.00 1.94
117 123 6.888632 TCCACTACCTACTACTCTCGAAATTT 59.111 38.462 0.00 0.00 0.00 1.82
118 124 6.421485 TCCACTACCTACTACTCTCGAAATT 58.579 40.000 0.00 0.00 0.00 1.82
119 125 5.999044 TCCACTACCTACTACTCTCGAAAT 58.001 41.667 0.00 0.00 0.00 2.17
123 129 5.366460 TCAATCCACTACCTACTACTCTCG 58.634 45.833 0.00 0.00 0.00 4.04
130 136 3.643792 GAGGCATCAATCCACTACCTACT 59.356 47.826 0.00 0.00 0.00 2.57
133 139 2.769209 AGAGGCATCAATCCACTACCT 58.231 47.619 0.00 0.00 0.00 3.08
134 140 3.567478 AAGAGGCATCAATCCACTACC 57.433 47.619 0.00 0.00 0.00 3.18
150 156 2.630580 GAGGGAGTAGGCACCATAAGAG 59.369 54.545 0.00 0.00 0.00 2.85
155 161 1.762460 CGGAGGGAGTAGGCACCAT 60.762 63.158 0.00 0.00 0.00 3.55
156 162 2.363795 CGGAGGGAGTAGGCACCA 60.364 66.667 0.00 0.00 0.00 4.17
157 163 3.851128 GCGGAGGGAGTAGGCACC 61.851 72.222 0.00 0.00 0.00 5.01
158 164 3.851128 GGCGGAGGGAGTAGGCAC 61.851 72.222 0.00 0.00 0.00 5.01
160 166 4.862823 AGGGCGGAGGGAGTAGGC 62.863 72.222 0.00 0.00 0.00 3.93
161 167 1.272554 AAAAGGGCGGAGGGAGTAGG 61.273 60.000 0.00 0.00 0.00 3.18
162 168 0.178301 GAAAAGGGCGGAGGGAGTAG 59.822 60.000 0.00 0.00 0.00 2.57
163 169 0.252558 AGAAAAGGGCGGAGGGAGTA 60.253 55.000 0.00 0.00 0.00 2.59
164 170 0.252558 TAGAAAAGGGCGGAGGGAGT 60.253 55.000 0.00 0.00 0.00 3.85
165 171 1.132500 ATAGAAAAGGGCGGAGGGAG 58.868 55.000 0.00 0.00 0.00 4.30
166 172 2.482414 TATAGAAAAGGGCGGAGGGA 57.518 50.000 0.00 0.00 0.00 4.20
167 173 3.118000 ACTTTATAGAAAAGGGCGGAGGG 60.118 47.826 2.86 0.00 0.00 4.30
168 174 4.152284 ACTTTATAGAAAAGGGCGGAGG 57.848 45.455 2.86 0.00 0.00 4.30
169 175 4.335594 CCAACTTTATAGAAAAGGGCGGAG 59.664 45.833 2.86 0.00 0.00 4.63
170 176 4.263594 ACCAACTTTATAGAAAAGGGCGGA 60.264 41.667 2.86 0.00 0.00 5.54
171 177 4.014406 ACCAACTTTATAGAAAAGGGCGG 58.986 43.478 2.86 2.63 0.00 6.13
172 178 4.698304 TGACCAACTTTATAGAAAAGGGCG 59.302 41.667 2.86 0.00 0.00 6.13
173 179 6.584185 TTGACCAACTTTATAGAAAAGGGC 57.416 37.500 2.86 1.22 0.00 5.19
174 180 9.996554 AATTTTGACCAACTTTATAGAAAAGGG 57.003 29.630 2.86 0.51 0.00 3.95
207 213 9.130661 TCATCCAGATTTTGTCTTAAGTCAAAA 57.869 29.630 29.68 29.68 43.27 2.44
208 214 8.690203 TCATCCAGATTTTGTCTTAAGTCAAA 57.310 30.769 19.60 19.60 34.00 2.69
209 215 8.567948 GTTCATCCAGATTTTGTCTTAAGTCAA 58.432 33.333 10.54 10.54 34.00 3.18
210 216 7.719193 TGTTCATCCAGATTTTGTCTTAAGTCA 59.281 33.333 1.63 0.00 34.00 3.41
211 217 8.099364 TGTTCATCCAGATTTTGTCTTAAGTC 57.901 34.615 1.63 0.00 34.00 3.01
212 218 8.463930 TTGTTCATCCAGATTTTGTCTTAAGT 57.536 30.769 1.63 0.00 34.00 2.24
213 219 9.918630 AATTGTTCATCCAGATTTTGTCTTAAG 57.081 29.630 0.00 0.00 34.00 1.85
218 224 9.859427 TGAATAATTGTTCATCCAGATTTTGTC 57.141 29.630 13.03 0.00 33.41 3.18
219 225 9.643693 GTGAATAATTGTTCATCCAGATTTTGT 57.356 29.630 18.96 0.00 39.99 2.83
220 226 8.800972 CGTGAATAATTGTTCATCCAGATTTTG 58.199 33.333 18.96 0.00 39.99 2.44
221 227 7.975616 CCGTGAATAATTGTTCATCCAGATTTT 59.024 33.333 18.96 0.00 39.99 1.82
222 228 7.339212 TCCGTGAATAATTGTTCATCCAGATTT 59.661 33.333 18.96 0.00 39.99 2.17
223 229 6.828273 TCCGTGAATAATTGTTCATCCAGATT 59.172 34.615 18.96 0.00 39.99 2.40
224 230 6.356556 TCCGTGAATAATTGTTCATCCAGAT 58.643 36.000 18.96 0.00 39.99 2.90
225 231 5.739959 TCCGTGAATAATTGTTCATCCAGA 58.260 37.500 18.96 11.33 39.99 3.86
226 232 6.432936 CATCCGTGAATAATTGTTCATCCAG 58.567 40.000 18.96 11.47 39.99 3.86
227 233 5.299028 CCATCCGTGAATAATTGTTCATCCA 59.701 40.000 18.96 7.72 39.99 3.41
228 234 5.530915 TCCATCCGTGAATAATTGTTCATCC 59.469 40.000 18.96 7.91 39.99 3.51
229 235 6.430451 GTCCATCCGTGAATAATTGTTCATC 58.570 40.000 18.96 12.21 39.99 2.92
230 236 5.007626 CGTCCATCCGTGAATAATTGTTCAT 59.992 40.000 18.96 2.37 39.99 2.57
231 237 4.331443 CGTCCATCCGTGAATAATTGTTCA 59.669 41.667 13.03 13.03 35.84 3.18
232 238 4.260620 CCGTCCATCCGTGAATAATTGTTC 60.261 45.833 7.91 7.91 0.00 3.18
233 239 3.625764 CCGTCCATCCGTGAATAATTGTT 59.374 43.478 0.00 0.00 0.00 2.83
234 240 3.118555 TCCGTCCATCCGTGAATAATTGT 60.119 43.478 0.00 0.00 0.00 2.71
235 241 3.462982 TCCGTCCATCCGTGAATAATTG 58.537 45.455 0.00 0.00 0.00 2.32
236 242 3.494398 CCTCCGTCCATCCGTGAATAATT 60.494 47.826 0.00 0.00 0.00 1.40
237 243 2.037251 CCTCCGTCCATCCGTGAATAAT 59.963 50.000 0.00 0.00 0.00 1.28
238 244 1.411246 CCTCCGTCCATCCGTGAATAA 59.589 52.381 0.00 0.00 0.00 1.40
239 245 1.037493 CCTCCGTCCATCCGTGAATA 58.963 55.000 0.00 0.00 0.00 1.75
240 246 1.686325 CCCTCCGTCCATCCGTGAAT 61.686 60.000 0.00 0.00 0.00 2.57
241 247 2.355986 CCCTCCGTCCATCCGTGAA 61.356 63.158 0.00 0.00 0.00 3.18
242 248 2.758327 CCCTCCGTCCATCCGTGA 60.758 66.667 0.00 0.00 0.00 4.35
243 249 2.758327 TCCCTCCGTCCATCCGTG 60.758 66.667 0.00 0.00 0.00 4.94
244 250 1.929860 TACTCCCTCCGTCCATCCGT 61.930 60.000 0.00 0.00 0.00 4.69
245 251 1.152819 TACTCCCTCCGTCCATCCG 60.153 63.158 0.00 0.00 0.00 4.18
246 252 0.396695 TGTACTCCCTCCGTCCATCC 60.397 60.000 0.00 0.00 0.00 3.51
247 253 1.341531 CATGTACTCCCTCCGTCCATC 59.658 57.143 0.00 0.00 0.00 3.51
248 254 1.414158 CATGTACTCCCTCCGTCCAT 58.586 55.000 0.00 0.00 0.00 3.41
249 255 1.327690 GCATGTACTCCCTCCGTCCA 61.328 60.000 0.00 0.00 0.00 4.02
250 256 1.043673 AGCATGTACTCCCTCCGTCC 61.044 60.000 0.00 0.00 0.00 4.79
251 257 0.386113 GAGCATGTACTCCCTCCGTC 59.614 60.000 0.00 0.00 0.00 4.79
252 258 0.033011 AGAGCATGTACTCCCTCCGT 60.033 55.000 0.00 0.00 37.39 4.69
253 259 1.115467 AAGAGCATGTACTCCCTCCG 58.885 55.000 0.00 0.00 37.39 4.63
254 260 2.237392 ACAAAGAGCATGTACTCCCTCC 59.763 50.000 0.00 0.00 37.39 4.30
255 261 3.618690 ACAAAGAGCATGTACTCCCTC 57.381 47.619 0.00 0.00 37.39 4.30
256 262 3.073062 ACAACAAAGAGCATGTACTCCCT 59.927 43.478 0.00 0.00 37.39 4.20
257 263 3.412386 ACAACAAAGAGCATGTACTCCC 58.588 45.455 0.00 0.00 37.39 4.30
258 264 5.468746 TGTTACAACAAAGAGCATGTACTCC 59.531 40.000 0.00 0.00 35.05 3.85
259 265 6.539649 TGTTACAACAAAGAGCATGTACTC 57.460 37.500 0.00 0.00 35.67 2.59
260 266 6.935741 TTGTTACAACAAAGAGCATGTACT 57.064 33.333 5.08 0.00 45.17 2.73
274 280 4.455877 CCTCCATCCAGAGTTTGTTACAAC 59.544 45.833 0.00 0.00 31.53 3.32
280 286 1.366319 AGCCTCCATCCAGAGTTTGT 58.634 50.000 0.00 0.00 31.53 2.83
331 337 9.515226 TTTCCATAGGTTATTATCTTATGTGGC 57.485 33.333 0.00 0.00 0.00 5.01
345 369 3.620488 CCTGCTGCTTTTCCATAGGTTA 58.380 45.455 0.00 0.00 0.00 2.85
347 371 1.957113 GCCTGCTGCTTTTCCATAGGT 60.957 52.381 0.00 0.00 36.87 3.08
349 373 0.379669 CGCCTGCTGCTTTTCCATAG 59.620 55.000 0.00 0.00 38.05 2.23
350 374 1.031571 CCGCCTGCTGCTTTTCCATA 61.032 55.000 0.00 0.00 38.05 2.74
351 375 2.345760 CCGCCTGCTGCTTTTCCAT 61.346 57.895 0.00 0.00 38.05 3.41
372 400 2.159693 GCGATTTTCTGTTTCGGGAGAC 60.160 50.000 0.00 0.00 39.59 3.36
373 401 2.073816 GCGATTTTCTGTTTCGGGAGA 58.926 47.619 0.00 0.00 33.62 3.71
374 402 2.076863 AGCGATTTTCTGTTTCGGGAG 58.923 47.619 0.00 0.00 33.62 4.30
385 413 1.501741 TGCCGAAGCAGCGATTTTC 59.498 52.632 0.00 0.00 46.52 2.29
443 709 2.122769 GAGGGAGGGAGGGGCTAC 60.123 72.222 0.00 0.00 0.00 3.58
484 756 1.873591 TGCTTGTTTTTCTCGAGCTCC 59.126 47.619 7.81 0.00 41.40 4.70
491 763 5.060940 GCGTTGGATAATGCTTGTTTTTCTC 59.939 40.000 0.00 0.00 43.81 2.87
492 764 4.923281 GCGTTGGATAATGCTTGTTTTTCT 59.077 37.500 0.00 0.00 43.81 2.52
493 765 4.683781 TGCGTTGGATAATGCTTGTTTTTC 59.316 37.500 5.89 0.00 46.58 2.29
494 766 4.447389 GTGCGTTGGATAATGCTTGTTTTT 59.553 37.500 5.89 0.00 46.58 1.94
540 829 0.526954 TAGGCTCGCGATTCGGTTTC 60.527 55.000 10.36 0.00 39.05 2.78
545 834 1.209275 CCAAGTAGGCTCGCGATTCG 61.209 60.000 10.36 0.62 40.15 3.34
575 864 2.594592 AGCTGTGGGTTTCGGCAC 60.595 61.111 0.00 0.00 39.38 5.01
576 865 2.594303 CAGCTGTGGGTTTCGGCA 60.594 61.111 5.25 0.00 39.38 5.69
577 866 3.365265 CCAGCTGTGGGTTTCGGC 61.365 66.667 13.81 0.00 40.67 5.54
598 897 3.440415 GCCCCTTTCCGCTTTCCG 61.440 66.667 0.00 0.00 0.00 4.30
599 898 3.068691 GGCCCCTTTCCGCTTTCC 61.069 66.667 0.00 0.00 0.00 3.13
600 899 3.440415 CGGCCCCTTTCCGCTTTC 61.440 66.667 0.00 0.00 40.46 2.62
658 960 4.261781 CGCGGGGTAGGAGTACGC 62.262 72.222 0.00 0.00 46.04 4.42
701 1010 0.517316 CCGCTTGGACTTCCTTTTCG 59.483 55.000 0.00 0.00 36.82 3.46
702 1011 1.605753 ACCGCTTGGACTTCCTTTTC 58.394 50.000 0.00 0.00 36.82 2.29
784 1116 4.899239 GGGGAGGCAGACGCGATG 62.899 72.222 15.93 12.80 39.92 3.84
890 1232 2.486982 GCATTCCATCTGGATTCCGATG 59.513 50.000 21.02 21.02 44.98 3.84
891 1233 2.107031 TGCATTCCATCTGGATTCCGAT 59.893 45.455 0.00 1.58 44.98 4.18
917 1259 5.995565 TTCTTCTAAGAAGATGGTTCGGA 57.004 39.130 5.52 0.00 39.95 4.55
974 1316 6.371271 GCTCTTTGCTAAGATTGTCTTCTTCT 59.629 38.462 11.05 0.00 39.58 2.85
975 1317 6.148480 TGCTCTTTGCTAAGATTGTCTTCTTC 59.852 38.462 11.05 0.00 39.58 2.87
976 1318 6.000219 TGCTCTTTGCTAAGATTGTCTTCTT 59.000 36.000 11.05 0.00 39.58 2.52
979 1321 5.125097 CCATGCTCTTTGCTAAGATTGTCTT 59.875 40.000 11.05 0.00 39.58 3.01
981 1323 4.732938 GCCATGCTCTTTGCTAAGATTGTC 60.733 45.833 11.05 2.70 39.58 3.18
982 1324 3.129988 GCCATGCTCTTTGCTAAGATTGT 59.870 43.478 11.05 0.00 39.58 2.71
983 1325 3.703420 GCCATGCTCTTTGCTAAGATTG 58.297 45.455 11.05 9.17 39.58 2.67
985 1327 1.945394 CGCCATGCTCTTTGCTAAGAT 59.055 47.619 11.05 0.00 39.58 2.40
990 1400 3.807538 CGCGCCATGCTCTTTGCT 61.808 61.111 0.00 0.00 43.27 3.91
1006 1416 3.286751 CTGGTGGTTGTGGTGGCG 61.287 66.667 0.00 0.00 0.00 5.69
1054 1470 0.887247 CCAATGTTGATCACCGGCAA 59.113 50.000 0.00 0.00 0.00 4.52
1146 1562 2.742372 CGAACCTGGAAGCACCCG 60.742 66.667 0.00 0.00 38.00 5.28
1166 1582 2.354259 CAGAAGCAGAGCAACTAAGGG 58.646 52.381 0.00 0.00 0.00 3.95
1168 1584 2.697654 AGCAGAAGCAGAGCAACTAAG 58.302 47.619 0.00 0.00 45.49 2.18
1196 1616 4.527583 CGCAGAGCAGGAGGGAGC 62.528 72.222 0.00 0.00 0.00 4.70
1197 1617 3.073735 ACGCAGAGCAGGAGGGAG 61.074 66.667 0.00 0.00 0.00 4.30
1198 1618 3.071206 GACGCAGAGCAGGAGGGA 61.071 66.667 0.00 0.00 0.00 4.20
1199 1619 4.154347 GGACGCAGAGCAGGAGGG 62.154 72.222 0.00 0.00 0.00 4.30
1265 1723 4.107622 CGTGTAACTTGTAACCCTATCCG 58.892 47.826 0.00 0.00 31.75 4.18
1288 1746 4.664677 GGTGCGTCCACGTCAGCT 62.665 66.667 14.32 0.00 43.00 4.24
1343 1815 3.529634 TTGTCGCTTGTTTTGGATACG 57.470 42.857 0.00 0.00 42.51 3.06
1575 3451 4.285851 GTGCTTGAGGAAGGACCG 57.714 61.111 0.00 0.00 43.02 4.79
1623 3499 2.551912 CCGGTTGTGTTGGCCAGTC 61.552 63.158 5.11 4.10 0.00 3.51
1624 3500 2.518349 CCGGTTGTGTTGGCCAGT 60.518 61.111 5.11 0.00 0.00 4.00
1655 3531 8.999431 TCTTGTAAAAGTTGATGTCCAAGTATC 58.001 33.333 0.00 0.00 37.44 2.24
1656 3532 8.918202 TCTTGTAAAAGTTGATGTCCAAGTAT 57.082 30.769 0.00 0.00 37.44 2.12
1716 3592 2.632377 TCTTCCTGCCGATCAACATTC 58.368 47.619 0.00 0.00 0.00 2.67
1762 3638 4.687215 TGCACCGACAGCCTCTGC 62.687 66.667 0.00 0.00 34.37 4.26
1774 3650 3.455469 GCCCCAATGAGCTGCACC 61.455 66.667 1.02 0.00 0.00 5.01
1775 3651 3.455469 GGCCCCAATGAGCTGCAC 61.455 66.667 1.02 0.00 0.00 4.57
1814 3690 0.618458 TCCTGCAGGTACATTGGGTC 59.382 55.000 31.58 0.00 36.34 4.46
1815 3691 0.620556 CTCCTGCAGGTACATTGGGT 59.379 55.000 31.58 0.00 36.34 4.51
1861 3737 1.740296 CGGGTAGTTGTTCAGGGCG 60.740 63.158 0.00 0.00 0.00 6.13
1864 3740 0.673644 CCTGCGGGTAGTTGTTCAGG 60.674 60.000 2.29 0.00 35.68 3.86
1867 3743 1.376812 CCCCTGCGGGTAGTTGTTC 60.377 63.158 11.58 0.00 45.50 3.18
1927 3803 0.107703 TGGTGATGAAGCCGATGTCC 60.108 55.000 0.00 0.00 0.00 4.02
2202 4078 0.902531 CCTGTACATCCTCGGGTGTT 59.097 55.000 7.23 0.00 0.00 3.32
2290 4166 2.001812 CACTGTCGATCTTGAGGGTG 57.998 55.000 0.00 0.00 0.00 4.61
2326 4205 6.006275 AGTGGAGCTGAACCAATGTATATT 57.994 37.500 0.00 0.00 39.22 1.28
2327 4206 5.636903 AGTGGAGCTGAACCAATGTATAT 57.363 39.130 0.00 0.00 39.22 0.86
2328 4207 6.382859 TCTTAGTGGAGCTGAACCAATGTATA 59.617 38.462 3.33 0.00 39.22 1.47
2329 4208 5.189736 TCTTAGTGGAGCTGAACCAATGTAT 59.810 40.000 3.33 0.00 39.22 2.29
2358 4240 4.874966 GCAGAGTCTCATTCAGCTATGTTT 59.125 41.667 1.94 0.00 0.00 2.83
2359 4241 4.081254 TGCAGAGTCTCATTCAGCTATGTT 60.081 41.667 1.94 0.00 0.00 2.71
2360 4242 3.450096 TGCAGAGTCTCATTCAGCTATGT 59.550 43.478 1.94 0.00 0.00 2.29
2470 4352 8.670135 CATACTCCCTTATTCGTAGTGAGATAG 58.330 40.741 0.00 0.00 0.00 2.08
2478 4360 8.189460 GCTAATACCATACTCCCTTATTCGTAG 58.811 40.741 0.00 0.00 0.00 3.51
2515 4397 1.819632 CCCTGCTAATCACACGCCC 60.820 63.158 0.00 0.00 0.00 6.13
2546 4428 3.074538 CCAAAGAAAGGAAGGGAGAGGAA 59.925 47.826 0.00 0.00 0.00 3.36
2547 4429 2.644798 CCAAAGAAAGGAAGGGAGAGGA 59.355 50.000 0.00 0.00 0.00 3.71
2548 4430 2.291217 CCCAAAGAAAGGAAGGGAGAGG 60.291 54.545 0.00 0.00 42.25 3.69
2555 4437 3.324556 TGCATTTCCCCAAAGAAAGGAAG 59.675 43.478 3.13 0.00 39.31 3.46
2558 4440 2.613725 GCTGCATTTCCCCAAAGAAAGG 60.614 50.000 0.00 0.00 39.04 3.11
2679 4564 3.230976 ACTGACACACACATAGGACTGA 58.769 45.455 0.00 0.00 0.00 3.41
2760 4661 3.012518 GCTCAGTATGTCAGGCAAATGT 58.987 45.455 0.00 0.00 37.40 2.71
2768 4669 6.804677 AGAGTTATCTTGCTCAGTATGTCAG 58.195 40.000 0.00 0.00 31.03 3.51
2781 4717 9.299963 CAGAATCAGAACACTAGAGTTATCTTG 57.700 37.037 5.48 3.48 36.96 3.02
2803 4739 5.869579 AGCATAAGAAACAGTTCTCCAGAA 58.130 37.500 0.00 0.00 43.59 3.02
2805 4741 5.702670 TGAAGCATAAGAAACAGTTCTCCAG 59.297 40.000 0.00 0.00 43.59 3.86
2806 4742 5.470098 GTGAAGCATAAGAAACAGTTCTCCA 59.530 40.000 0.00 0.00 43.59 3.86
2807 4743 5.470098 TGTGAAGCATAAGAAACAGTTCTCC 59.530 40.000 0.00 0.00 43.59 3.71
2808 4744 6.545504 TGTGAAGCATAAGAAACAGTTCTC 57.454 37.500 0.00 0.00 43.59 2.87
2809 4745 7.229306 TCAATGTGAAGCATAAGAAACAGTTCT 59.771 33.333 0.00 0.00 40.44 3.01
2810 4746 7.362662 TCAATGTGAAGCATAAGAAACAGTTC 58.637 34.615 0.00 0.00 36.67 3.01
2811 4747 7.275888 TCAATGTGAAGCATAAGAAACAGTT 57.724 32.000 0.00 0.00 36.67 3.16
2812 4748 6.882610 TCAATGTGAAGCATAAGAAACAGT 57.117 33.333 0.00 0.00 36.67 3.55
2847 4783 2.066262 TCGAACAACTTCATCGAAGGC 58.934 47.619 8.49 0.00 43.25 4.35
2882 4818 3.354089 ACGCTGGTTTTTCAGATGTTG 57.646 42.857 0.00 0.00 36.93 3.33
2891 4827 4.134563 ACAGAAGATGTACGCTGGTTTTT 58.865 39.130 0.00 0.00 41.60 1.94
2932 4882 6.897259 TGCGAGGACATTTACATTTACTAC 57.103 37.500 0.00 0.00 0.00 2.73
2934 4884 6.811253 TTTGCGAGGACATTTACATTTACT 57.189 33.333 0.00 0.00 0.00 2.24
2935 4885 7.861176 TTTTTGCGAGGACATTTACATTTAC 57.139 32.000 0.00 0.00 0.00 2.01
3006 4974 7.069852 TGTGTGAAAAATGTTTTTGGTCATG 57.930 32.000 8.09 0.00 40.21 3.07
3007 4975 7.862512 ATGTGTGAAAAATGTTTTTGGTCAT 57.137 28.000 8.09 5.42 40.21 3.06
3008 4976 8.777865 TTATGTGTGAAAAATGTTTTTGGTCA 57.222 26.923 8.09 0.00 40.21 4.02
3009 4977 9.484326 GTTTATGTGTGAAAAATGTTTTTGGTC 57.516 29.630 8.09 0.00 40.21 4.02
3010 4978 9.225436 AGTTTATGTGTGAAAAATGTTTTTGGT 57.775 25.926 8.09 0.00 40.21 3.67
3011 4979 9.488124 CAGTTTATGTGTGAAAAATGTTTTTGG 57.512 29.630 8.09 0.00 40.21 3.28
3018 5041 8.533965 CAGTGAACAGTTTATGTGTGAAAAATG 58.466 33.333 0.00 0.00 43.00 2.32
3049 5072 5.997384 TCTTCTTGTACCTCTTTCTACCC 57.003 43.478 0.00 0.00 0.00 3.69
3088 5226 6.681729 TTTTCTTGTCCATGTACTCCTACT 57.318 37.500 0.00 0.00 0.00 2.57
3089 5227 7.103641 TGATTTTCTTGTCCATGTACTCCTAC 58.896 38.462 0.00 0.00 0.00 3.18
3090 5228 7.252612 TGATTTTCTTGTCCATGTACTCCTA 57.747 36.000 0.00 0.00 0.00 2.94
3091 5229 6.126863 TGATTTTCTTGTCCATGTACTCCT 57.873 37.500 0.00 0.00 0.00 3.69
3092 5230 5.163713 GCTGATTTTCTTGTCCATGTACTCC 60.164 44.000 0.00 0.00 0.00 3.85
3093 5231 5.645497 AGCTGATTTTCTTGTCCATGTACTC 59.355 40.000 0.00 0.00 0.00 2.59
3146 5284 6.987992 AGGCAATAGATAATTTGGCATGTTTG 59.012 34.615 11.08 0.00 0.00 2.93
3184 5328 4.498009 CCAACAAACTTGTCTCATGTGGAC 60.498 45.833 12.30 12.30 41.31 4.02
3271 5415 9.995003 TGTGATTAGGCAAAGATTTTGTTTAAT 57.005 25.926 3.77 7.51 0.00 1.40
3272 5416 9.995003 ATGTGATTAGGCAAAGATTTTGTTTAA 57.005 25.926 3.77 3.87 0.00 1.52
3273 5417 9.995003 AATGTGATTAGGCAAAGATTTTGTTTA 57.005 25.926 3.77 0.00 0.00 2.01
3274 5418 8.907222 AATGTGATTAGGCAAAGATTTTGTTT 57.093 26.923 3.77 0.00 0.00 2.83
3275 5419 9.995003 TTAATGTGATTAGGCAAAGATTTTGTT 57.005 25.926 3.77 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.