Multiple sequence alignment - TraesCS3A01G240100

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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 TraesCS3A01G240100 chr3A 100.000 2708 0 0 1 2708 450305310 450302603 0.000000e+00 5001
1 TraesCS3A01G240100 chr3D 92.051 2189 82 29 570 2708 332804822 332802676 0.000000e+00 2994
2 TraesCS3A01G240100 chr3B 92.367 1297 70 15 888 2174 431990306 431989029 0.000000e+00 1820
3 TraesCS3A01G240100 chr3B 93.846 325 15 3 573 892 431991819 431991495 4.050000e-133 484
4 TraesCS3A01G240100 chr3B 90.602 266 8 7 2171 2423 431988764 431988503 1.200000e-88 337
5 TraesCS3A01G240100 chr3B 86.282 277 18 9 2434 2692 431988205 431987931 1.590000e-72 283
6 TraesCS3A01G240100 chr1D 75.439 285 44 19 1208 1473 474725924 474726201 6.130000e-22 115
7 TraesCS3A01G240100 chr1B 83.607 122 11 4 1364 1485 659997734 659997846 3.690000e-19 106
8 TraesCS3A01G240100 chr1B 77.957 186 23 9 1300 1473 659975229 659975408 1.720000e-17 100
9 TraesCS3A01G240100 chr1A 82.576 132 11 6 1359 1487 570265513 570265635 3.690000e-19 106


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 TraesCS3A01G240100 chr3A 450302603 450305310 2707 True 5001 5001 100.00000 1 2708 1 chr3A.!!$R1 2707
1 TraesCS3A01G240100 chr3D 332802676 332804822 2146 True 2994 2994 92.05100 570 2708 1 chr3D.!!$R1 2138
2 TraesCS3A01G240100 chr3B 431987931 431991819 3888 True 731 1820 90.77425 573 2692 4 chr3B.!!$R1 2119

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
175 176 0.249911 GGTAGGTGGCTGGCGATTAG 60.25 60.0 0.0 0.0 0.0 1.73 F
176 177 0.249911 GTAGGTGGCTGGCGATTAGG 60.25 60.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1476 2673 1.452145 GCCCTGAAGTGGCGTTCAAA 61.452 55.0 3.97 0.0 39.48 2.69 R
2129 3340 2.319136 TCAACTAATAACGCCGCCAT 57.681 45.0 0.00 0.0 0.00 4.40 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
17 18 2.903855 GGGTCCGACGGCGATAGA 60.904 66.667 15.16 0.00 40.82 1.98
18 19 2.638154 GGTCCGACGGCGATAGAG 59.362 66.667 15.16 0.00 40.82 2.43
19 20 2.638154 GTCCGACGGCGATAGAGG 59.362 66.667 15.16 9.19 40.82 3.69
20 21 2.593725 TCCGACGGCGATAGAGGG 60.594 66.667 15.16 5.09 40.82 4.30
21 22 3.671411 CCGACGGCGATAGAGGGG 61.671 72.222 15.16 0.00 40.82 4.79
22 23 4.344474 CGACGGCGATAGAGGGGC 62.344 72.222 16.62 0.00 40.82 5.80
23 24 3.224324 GACGGCGATAGAGGGGCA 61.224 66.667 16.62 0.00 39.76 5.36
24 25 3.214250 GACGGCGATAGAGGGGCAG 62.214 68.421 16.62 0.00 39.76 4.85
25 26 4.671569 CGGCGATAGAGGGGCAGC 62.672 72.222 0.00 0.00 39.76 5.25
26 27 4.671569 GGCGATAGAGGGGCAGCG 62.672 72.222 0.00 0.00 39.76 5.18
27 28 4.671569 GCGATAGAGGGGCAGCGG 62.672 72.222 0.00 0.00 39.76 5.52
28 29 3.227276 CGATAGAGGGGCAGCGGT 61.227 66.667 0.00 0.00 39.76 5.68
29 30 1.901948 CGATAGAGGGGCAGCGGTA 60.902 63.158 0.00 0.00 39.76 4.02
30 31 1.867919 CGATAGAGGGGCAGCGGTAG 61.868 65.000 0.00 0.00 39.76 3.18
31 32 1.534235 ATAGAGGGGCAGCGGTAGG 60.534 63.158 0.00 0.00 0.00 3.18
103 104 3.081133 CGAATGACGCGGGAGTTG 58.919 61.111 12.47 0.00 34.51 3.16
104 105 2.452813 CGAATGACGCGGGAGTTGG 61.453 63.158 12.47 0.00 34.51 3.77
105 106 1.375523 GAATGACGCGGGAGTTGGT 60.376 57.895 12.47 0.00 0.00 3.67
106 107 1.635663 GAATGACGCGGGAGTTGGTG 61.636 60.000 12.47 0.00 0.00 4.17
107 108 3.605749 ATGACGCGGGAGTTGGTGG 62.606 63.158 12.47 0.00 0.00 4.61
108 109 3.998672 GACGCGGGAGTTGGTGGA 61.999 66.667 12.47 0.00 0.00 4.02
109 110 4.309950 ACGCGGGAGTTGGTGGAC 62.310 66.667 12.47 0.00 0.00 4.02
110 111 4.308458 CGCGGGAGTTGGTGGACA 62.308 66.667 0.00 0.00 0.00 4.02
111 112 2.668550 GCGGGAGTTGGTGGACAC 60.669 66.667 0.00 0.00 0.00 3.67
112 113 2.357034 CGGGAGTTGGTGGACACG 60.357 66.667 0.00 0.00 0.00 4.49
113 114 2.032071 GGGAGTTGGTGGACACGG 59.968 66.667 0.00 0.00 0.00 4.94
114 115 2.668550 GGAGTTGGTGGACACGGC 60.669 66.667 0.00 0.00 0.00 5.68
115 116 2.426023 GAGTTGGTGGACACGGCT 59.574 61.111 0.00 0.00 0.00 5.52
116 117 1.668151 GAGTTGGTGGACACGGCTC 60.668 63.158 0.00 1.02 0.00 4.70
117 118 3.041940 GTTGGTGGACACGGCTCG 61.042 66.667 0.00 0.00 0.00 5.03
118 119 4.308458 TTGGTGGACACGGCTCGG 62.308 66.667 0.00 0.00 0.00 4.63
135 136 2.427410 GCGGCAGCAACAACTTCG 60.427 61.111 3.18 0.00 44.35 3.79
136 137 2.252260 CGGCAGCAACAACTTCGG 59.748 61.111 0.00 0.00 0.00 4.30
137 138 2.644992 GGCAGCAACAACTTCGGG 59.355 61.111 0.00 0.00 0.00 5.14
138 139 2.193536 GGCAGCAACAACTTCGGGT 61.194 57.895 0.00 0.00 0.00 5.28
139 140 1.008538 GCAGCAACAACTTCGGGTG 60.009 57.895 0.00 0.00 38.88 4.61
140 141 1.444119 GCAGCAACAACTTCGGGTGA 61.444 55.000 0.00 0.00 35.92 4.02
141 142 1.238439 CAGCAACAACTTCGGGTGAT 58.762 50.000 0.00 0.00 35.92 3.06
142 143 1.197721 CAGCAACAACTTCGGGTGATC 59.802 52.381 0.00 0.00 35.92 2.92
143 144 0.521735 GCAACAACTTCGGGTGATCC 59.478 55.000 0.00 0.00 35.92 3.36
160 161 3.962421 CGACGGCGGGCTAGGTAG 61.962 72.222 13.24 0.00 0.00 3.18
161 162 3.603671 GACGGCGGGCTAGGTAGG 61.604 72.222 13.24 0.00 0.00 3.18
162 163 4.453892 ACGGCGGGCTAGGTAGGT 62.454 66.667 13.24 0.00 0.00 3.08
163 164 3.912907 CGGCGGGCTAGGTAGGTG 61.913 72.222 0.00 0.00 0.00 4.00
164 165 3.547513 GGCGGGCTAGGTAGGTGG 61.548 72.222 0.00 0.00 0.00 4.61
165 166 4.237207 GCGGGCTAGGTAGGTGGC 62.237 72.222 0.00 0.00 0.00 5.01
166 167 2.444140 CGGGCTAGGTAGGTGGCT 60.444 66.667 0.00 0.00 0.00 4.75
167 168 2.797278 CGGGCTAGGTAGGTGGCTG 61.797 68.421 0.00 0.00 0.00 4.85
168 169 2.444256 GGGCTAGGTAGGTGGCTGG 61.444 68.421 0.00 0.00 0.00 4.85
169 170 2.506472 GCTAGGTAGGTGGCTGGC 59.494 66.667 0.00 0.00 0.00 4.85
170 171 2.815308 CTAGGTAGGTGGCTGGCG 59.185 66.667 0.00 0.00 0.00 5.69
171 172 1.756950 CTAGGTAGGTGGCTGGCGA 60.757 63.158 0.00 0.00 0.00 5.54
172 173 1.075525 TAGGTAGGTGGCTGGCGAT 60.076 57.895 0.00 0.00 0.00 4.58
173 174 0.689745 TAGGTAGGTGGCTGGCGATT 60.690 55.000 0.00 0.00 0.00 3.34
174 175 0.689745 AGGTAGGTGGCTGGCGATTA 60.690 55.000 0.00 0.00 0.00 1.75
175 176 0.249911 GGTAGGTGGCTGGCGATTAG 60.250 60.000 0.00 0.00 0.00 1.73
176 177 0.249911 GTAGGTGGCTGGCGATTAGG 60.250 60.000 0.00 0.00 0.00 2.69
177 178 0.689745 TAGGTGGCTGGCGATTAGGT 60.690 55.000 0.00 0.00 0.00 3.08
178 179 1.819632 GGTGGCTGGCGATTAGGTG 60.820 63.158 0.00 0.00 0.00 4.00
179 180 2.124736 TGGCTGGCGATTAGGTGC 60.125 61.111 0.00 0.00 0.00 5.01
180 181 3.272334 GGCTGGCGATTAGGTGCG 61.272 66.667 0.00 0.00 0.00 5.34
181 182 3.272334 GCTGGCGATTAGGTGCGG 61.272 66.667 0.00 0.00 0.00 5.69
182 183 2.499205 CTGGCGATTAGGTGCGGA 59.501 61.111 0.00 0.00 0.00 5.54
183 184 1.883084 CTGGCGATTAGGTGCGGAC 60.883 63.158 0.00 0.00 0.00 4.79
184 185 2.960129 GGCGATTAGGTGCGGACG 60.960 66.667 0.00 0.00 0.00 4.79
185 186 2.202703 GCGATTAGGTGCGGACGT 60.203 61.111 7.57 7.57 0.00 4.34
186 187 2.514013 GCGATTAGGTGCGGACGTG 61.514 63.158 12.79 0.00 0.00 4.49
187 188 2.514013 CGATTAGGTGCGGACGTGC 61.514 63.158 12.79 0.00 0.00 5.34
188 189 1.447140 GATTAGGTGCGGACGTGCA 60.447 57.895 12.79 1.42 43.95 4.57
194 195 3.984749 TGCGGACGTGCAGCTGTA 61.985 61.111 16.64 8.31 40.62 2.74
195 196 3.181967 GCGGACGTGCAGCTGTAG 61.182 66.667 16.64 9.49 34.66 2.74
196 197 2.566529 CGGACGTGCAGCTGTAGA 59.433 61.111 16.64 0.00 0.00 2.59
197 198 1.080772 CGGACGTGCAGCTGTAGAA 60.081 57.895 16.64 0.00 0.00 2.10
198 199 1.073216 CGGACGTGCAGCTGTAGAAG 61.073 60.000 16.64 7.88 0.00 2.85
228 229 4.813526 CGAGAGACGCGTGGACGG 62.814 72.222 20.70 0.00 40.23 4.79
229 230 3.735029 GAGAGACGCGTGGACGGT 61.735 66.667 20.70 0.00 40.23 4.83
230 231 3.948086 GAGAGACGCGTGGACGGTG 62.948 68.421 20.70 0.00 40.23 4.94
231 232 4.034258 GAGACGCGTGGACGGTGA 62.034 66.667 20.70 0.00 40.23 4.02
232 233 4.338539 AGACGCGTGGACGGTGAC 62.339 66.667 20.70 0.00 40.23 3.67
282 283 4.530857 CGGCGGTGTGGGAGGATC 62.531 72.222 0.00 0.00 0.00 3.36
283 284 4.530857 GGCGGTGTGGGAGGATCG 62.531 72.222 0.00 0.00 34.37 3.69
308 309 4.109675 GCGGCAGGGTGGTGGTAT 62.110 66.667 0.00 0.00 0.00 2.73
309 310 2.124736 CGGCAGGGTGGTGGTATG 60.125 66.667 0.00 0.00 0.00 2.39
310 311 2.275418 GGCAGGGTGGTGGTATGG 59.725 66.667 0.00 0.00 0.00 2.74
311 312 2.275418 GCAGGGTGGTGGTATGGG 59.725 66.667 0.00 0.00 0.00 4.00
312 313 2.305607 GCAGGGTGGTGGTATGGGA 61.306 63.158 0.00 0.00 0.00 4.37
313 314 1.915228 CAGGGTGGTGGTATGGGAG 59.085 63.158 0.00 0.00 0.00 4.30
314 315 1.307866 AGGGTGGTGGTATGGGAGG 60.308 63.158 0.00 0.00 0.00 4.30
315 316 1.307517 GGGTGGTGGTATGGGAGGA 60.308 63.158 0.00 0.00 0.00 3.71
316 317 1.345715 GGGTGGTGGTATGGGAGGAG 61.346 65.000 0.00 0.00 0.00 3.69
317 318 1.527370 GTGGTGGTATGGGAGGAGC 59.473 63.158 0.00 0.00 0.00 4.70
318 319 2.063979 TGGTGGTATGGGAGGAGCG 61.064 63.158 0.00 0.00 0.00 5.03
319 320 2.109181 GTGGTATGGGAGGAGCGC 59.891 66.667 0.00 0.00 0.00 5.92
320 321 3.536917 TGGTATGGGAGGAGCGCG 61.537 66.667 0.00 0.00 0.00 6.86
321 322 4.301027 GGTATGGGAGGAGCGCGG 62.301 72.222 8.83 0.00 0.00 6.46
322 323 4.971125 GTATGGGAGGAGCGCGGC 62.971 72.222 8.83 0.00 0.00 6.53
397 398 4.440127 GCGACGGCGGGGAGTAAA 62.440 66.667 15.06 0.00 38.16 2.01
398 399 2.262292 CGACGGCGGGGAGTAAAA 59.738 61.111 13.24 0.00 0.00 1.52
399 400 2.096442 CGACGGCGGGGAGTAAAAC 61.096 63.158 13.24 0.00 0.00 2.43
400 401 1.742880 GACGGCGGGGAGTAAAACC 60.743 63.158 13.24 0.00 0.00 3.27
401 402 2.176314 GACGGCGGGGAGTAAAACCT 62.176 60.000 13.24 0.00 0.00 3.50
402 403 0.904394 ACGGCGGGGAGTAAAACCTA 60.904 55.000 13.24 0.00 0.00 3.08
403 404 0.249955 CGGCGGGGAGTAAAACCTAA 59.750 55.000 0.00 0.00 0.00 2.69
404 405 1.338960 CGGCGGGGAGTAAAACCTAAA 60.339 52.381 0.00 0.00 0.00 1.85
405 406 2.794103 GGCGGGGAGTAAAACCTAAAA 58.206 47.619 0.00 0.00 0.00 1.52
406 407 3.156293 GGCGGGGAGTAAAACCTAAAAA 58.844 45.455 0.00 0.00 0.00 1.94
429 430 9.965902 AAAAACTGACCATGTAGAGAGATATTT 57.034 29.630 0.00 0.00 0.00 1.40
430 431 9.965902 AAAACTGACCATGTAGAGAGATATTTT 57.034 29.630 0.00 0.00 0.00 1.82
431 432 8.954950 AACTGACCATGTAGAGAGATATTTTG 57.045 34.615 0.00 0.00 0.00 2.44
432 433 6.989169 ACTGACCATGTAGAGAGATATTTTGC 59.011 38.462 0.00 0.00 0.00 3.68
433 434 6.888105 TGACCATGTAGAGAGATATTTTGCA 58.112 36.000 0.00 0.00 0.00 4.08
434 435 7.337938 TGACCATGTAGAGAGATATTTTGCAA 58.662 34.615 0.00 0.00 0.00 4.08
435 436 7.994911 TGACCATGTAGAGAGATATTTTGCAAT 59.005 33.333 0.00 0.00 0.00 3.56
436 437 9.494271 GACCATGTAGAGAGATATTTTGCAATA 57.506 33.333 0.00 0.00 0.00 1.90
463 464 8.467963 AATAATCATTGTATTGATGGTGCAGA 57.532 30.769 0.00 0.00 36.48 4.26
464 465 6.971726 AATCATTGTATTGATGGTGCAGAT 57.028 33.333 0.00 0.00 36.48 2.90
465 466 5.761165 TCATTGTATTGATGGTGCAGATG 57.239 39.130 0.00 0.00 0.00 2.90
466 467 4.037089 TCATTGTATTGATGGTGCAGATGC 59.963 41.667 0.00 0.00 42.50 3.91
467 468 7.639943 ATCATTGTATTGATGGTGCAGATGCA 61.640 38.462 2.75 2.75 40.71 3.96
527 528 8.941995 ACTATACATAACTAGAAGATGAGCCA 57.058 34.615 0.00 0.00 0.00 4.75
528 529 8.798402 ACTATACATAACTAGAAGATGAGCCAC 58.202 37.037 0.00 0.00 0.00 5.01
529 530 5.939764 ACATAACTAGAAGATGAGCCACA 57.060 39.130 0.00 0.00 0.00 4.17
530 531 6.299805 ACATAACTAGAAGATGAGCCACAA 57.700 37.500 0.00 0.00 0.00 3.33
531 532 6.109359 ACATAACTAGAAGATGAGCCACAAC 58.891 40.000 0.00 0.00 0.00 3.32
532 533 4.623932 AACTAGAAGATGAGCCACAACA 57.376 40.909 0.00 0.00 0.00 3.33
533 534 3.931578 ACTAGAAGATGAGCCACAACAC 58.068 45.455 0.00 0.00 0.00 3.32
534 535 1.800805 AGAAGATGAGCCACAACACG 58.199 50.000 0.00 0.00 0.00 4.49
535 536 1.070758 AGAAGATGAGCCACAACACGT 59.929 47.619 0.00 0.00 0.00 4.49
536 537 2.299013 AGAAGATGAGCCACAACACGTA 59.701 45.455 0.00 0.00 0.00 3.57
537 538 2.831685 AGATGAGCCACAACACGTAA 57.168 45.000 0.00 0.00 0.00 3.18
538 539 3.334583 AGATGAGCCACAACACGTAAT 57.665 42.857 0.00 0.00 0.00 1.89
539 540 4.465632 AGATGAGCCACAACACGTAATA 57.534 40.909 0.00 0.00 0.00 0.98
540 541 5.023533 AGATGAGCCACAACACGTAATAT 57.976 39.130 0.00 0.00 0.00 1.28
541 542 6.156748 AGATGAGCCACAACACGTAATATA 57.843 37.500 0.00 0.00 0.00 0.86
542 543 6.759272 AGATGAGCCACAACACGTAATATAT 58.241 36.000 0.00 0.00 0.00 0.86
543 544 7.892609 AGATGAGCCACAACACGTAATATATA 58.107 34.615 0.00 0.00 0.00 0.86
544 545 8.531982 AGATGAGCCACAACACGTAATATATAT 58.468 33.333 0.00 0.00 0.00 0.86
545 546 9.797556 GATGAGCCACAACACGTAATATATATA 57.202 33.333 0.00 0.00 0.00 0.86
547 548 9.414295 TGAGCCACAACACGTAATATATATAAC 57.586 33.333 0.00 0.00 0.00 1.89
548 549 9.414295 GAGCCACAACACGTAATATATATAACA 57.586 33.333 0.00 0.00 0.00 2.41
549 550 9.199982 AGCCACAACACGTAATATATATAACAC 57.800 33.333 0.00 0.00 0.00 3.32
550 551 8.980610 GCCACAACACGTAATATATATAACACA 58.019 33.333 0.00 0.00 0.00 3.72
574 575 9.449719 ACAAAGTACAACTCAATAATAAGAGGG 57.550 33.333 0.00 0.00 36.20 4.30
575 576 8.893727 CAAAGTACAACTCAATAATAAGAGGGG 58.106 37.037 0.00 0.00 36.20 4.79
576 577 6.592870 AGTACAACTCAATAATAAGAGGGGC 58.407 40.000 0.00 0.00 36.20 5.80
577 578 4.793201 ACAACTCAATAATAAGAGGGGCC 58.207 43.478 0.00 0.00 36.20 5.80
667 668 5.917541 TGTCCTCATTTAGTTCGTGTTTC 57.082 39.130 0.00 0.00 0.00 2.78
755 759 4.690719 ACCAAACGCGCCGGATCA 62.691 61.111 5.05 0.00 0.00 2.92
767 771 1.154205 CCGGATCAAAGCTACGCCTG 61.154 60.000 0.00 0.00 0.00 4.85
790 794 0.747283 CATCACTTCAGCTCCTGGGC 60.747 60.000 0.00 0.00 31.51 5.36
1476 2673 2.495084 GGCAAGGAGAAGTTCGTCTTT 58.505 47.619 9.88 3.50 36.40 2.52
1488 2685 1.658994 TCGTCTTTTTGAACGCCACT 58.341 45.000 0.00 0.00 0.00 4.00
1701 2901 0.687098 TACGGCGAAGTTATCCCCCA 60.687 55.000 16.62 0.00 0.00 4.96
1721 2921 3.438360 CATTCTAATGCGTTTCTTGGCC 58.562 45.455 0.00 0.00 0.00 5.36
1894 3096 6.122964 TCTCAACAATAGAGATCGGAGAAGA 58.877 40.000 0.00 0.00 37.22 2.87
1895 3097 6.775142 TCTCAACAATAGAGATCGGAGAAGAT 59.225 38.462 0.00 0.00 37.22 2.40
1896 3098 7.939588 TCTCAACAATAGAGATCGGAGAAGATA 59.060 37.037 0.00 0.00 37.22 1.98
1899 3101 9.781834 CAACAATAGAGATCGGAGAAGATATAC 57.218 37.037 0.00 0.00 43.58 1.47
1900 3102 8.203937 ACAATAGAGATCGGAGAAGATATACG 57.796 38.462 0.00 0.00 43.58 3.06
1901 3103 7.825270 ACAATAGAGATCGGAGAAGATATACGT 59.175 37.037 0.00 0.00 43.58 3.57
2129 3340 1.331214 CTTTTGGGCAAAGCTCTGGA 58.669 50.000 0.00 0.00 35.66 3.86
2213 3692 4.277174 ACGTACAAAACAATTCATGCCTCA 59.723 37.500 0.00 0.00 0.00 3.86
2220 3700 4.978083 ACAATTCATGCCTCATTGTCTC 57.022 40.909 6.58 0.00 36.60 3.36
2283 3780 9.909644 TCAGTACAGAGACTGTTCTATTTTTAC 57.090 33.333 9.63 0.00 42.59 2.01
2350 3847 6.140265 CACGTAGAGTACAATATACTTGTGCG 59.860 42.308 0.00 0.00 39.48 5.34
2370 3867 3.607078 GCGGAACAGTCAAACAGTTCATC 60.607 47.826 14.60 4.79 43.62 2.92
2376 3873 1.126846 GTCAAACAGTTCATCCTCGCG 59.873 52.381 0.00 0.00 0.00 5.87
2423 3920 9.521841 AGGATTCTGATTCTGTCGATTATACTA 57.478 33.333 0.00 0.00 0.00 1.82
2428 3925 9.121658 TCTGATTCTGTCGATTATACTACAACT 57.878 33.333 0.00 0.00 0.00 3.16
2475 4263 4.606457 AGCAAGAATTTCGCTGATGTAC 57.394 40.909 5.91 0.00 33.91 2.90
2562 4363 4.756084 GCATCTACAATTATGCAGGTCC 57.244 45.455 6.12 0.00 46.19 4.46
2564 4365 4.453819 GCATCTACAATTATGCAGGTCCTC 59.546 45.833 6.12 0.00 46.19 3.71
2570 4371 3.956199 CAATTATGCAGGTCCTCACCAAT 59.044 43.478 0.00 0.00 46.68 3.16
2676 4481 1.381463 CGCCCATCCATCCATCCAT 59.619 57.895 0.00 0.00 0.00 3.41
2677 4482 0.679002 CGCCCATCCATCCATCCATC 60.679 60.000 0.00 0.00 0.00 3.51
2678 4483 0.406750 GCCCATCCATCCATCCATCA 59.593 55.000 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.903855 TCTATCGCCGTCGGACCC 60.904 66.667 17.49 0.00 36.13 4.46
2 3 2.638154 CCTCTATCGCCGTCGGAC 59.362 66.667 17.49 5.49 36.13 4.79
3 4 2.593725 CCCTCTATCGCCGTCGGA 60.594 66.667 17.49 0.00 36.13 4.55
4 5 3.671411 CCCCTCTATCGCCGTCGG 61.671 72.222 6.99 6.99 36.13 4.79
5 6 4.344474 GCCCCTCTATCGCCGTCG 62.344 72.222 0.00 0.00 0.00 5.12
7 8 3.227276 CTGCCCCTCTATCGCCGT 61.227 66.667 0.00 0.00 0.00 5.68
9 10 4.671569 CGCTGCCCCTCTATCGCC 62.672 72.222 0.00 0.00 0.00 5.54
10 11 4.671569 CCGCTGCCCCTCTATCGC 62.672 72.222 0.00 0.00 0.00 4.58
11 12 1.867919 CTACCGCTGCCCCTCTATCG 61.868 65.000 0.00 0.00 0.00 2.92
12 13 1.536943 CCTACCGCTGCCCCTCTATC 61.537 65.000 0.00 0.00 0.00 2.08
13 14 1.534235 CCTACCGCTGCCCCTCTAT 60.534 63.158 0.00 0.00 0.00 1.98
14 15 2.123425 CCTACCGCTGCCCCTCTA 60.123 66.667 0.00 0.00 0.00 2.43
41 42 4.175489 ACCCGATCGCTCGTGTCG 62.175 66.667 10.32 10.84 43.49 4.35
42 43 2.278013 GACCCGATCGCTCGTGTC 60.278 66.667 10.32 8.42 43.26 3.67
43 44 4.175489 CGACCCGATCGCTCGTGT 62.175 66.667 19.63 1.64 45.52 4.49
86 87 2.452813 CCAACTCCCGCGTCATTCG 61.453 63.158 4.92 0.00 43.12 3.34
87 88 1.375523 ACCAACTCCCGCGTCATTC 60.376 57.895 4.92 0.00 0.00 2.67
88 89 1.671054 CACCAACTCCCGCGTCATT 60.671 57.895 4.92 0.00 0.00 2.57
89 90 2.047274 CACCAACTCCCGCGTCAT 60.047 61.111 4.92 0.00 0.00 3.06
90 91 4.308458 CCACCAACTCCCGCGTCA 62.308 66.667 4.92 0.00 0.00 4.35
91 92 3.998672 TCCACCAACTCCCGCGTC 61.999 66.667 4.92 0.00 0.00 5.19
92 93 4.309950 GTCCACCAACTCCCGCGT 62.310 66.667 4.92 0.00 0.00 6.01
93 94 4.308458 TGTCCACCAACTCCCGCG 62.308 66.667 0.00 0.00 0.00 6.46
94 95 2.668550 GTGTCCACCAACTCCCGC 60.669 66.667 0.00 0.00 0.00 6.13
95 96 2.357034 CGTGTCCACCAACTCCCG 60.357 66.667 0.00 0.00 0.00 5.14
96 97 2.032071 CCGTGTCCACCAACTCCC 59.968 66.667 0.00 0.00 0.00 4.30
97 98 2.668550 GCCGTGTCCACCAACTCC 60.669 66.667 0.00 0.00 0.00 3.85
98 99 1.668151 GAGCCGTGTCCACCAACTC 60.668 63.158 0.00 0.00 0.00 3.01
99 100 2.426023 GAGCCGTGTCCACCAACT 59.574 61.111 0.00 0.00 0.00 3.16
100 101 3.041940 CGAGCCGTGTCCACCAAC 61.042 66.667 0.00 0.00 0.00 3.77
101 102 4.308458 CCGAGCCGTGTCCACCAA 62.308 66.667 0.00 0.00 0.00 3.67
114 115 4.389576 GTTGTTGCTGCCGCCGAG 62.390 66.667 0.00 0.00 34.43 4.63
115 116 4.927782 AGTTGTTGCTGCCGCCGA 62.928 61.111 0.00 0.00 34.43 5.54
116 117 3.879351 GAAGTTGTTGCTGCCGCCG 62.879 63.158 0.00 0.00 34.43 6.46
117 118 2.050077 GAAGTTGTTGCTGCCGCC 60.050 61.111 0.00 0.00 34.43 6.13
118 119 2.427410 CGAAGTTGTTGCTGCCGC 60.427 61.111 0.00 0.00 0.00 6.53
119 120 2.252260 CCGAAGTTGTTGCTGCCG 59.748 61.111 0.00 0.00 0.00 5.69
120 121 2.193536 ACCCGAAGTTGTTGCTGCC 61.194 57.895 0.00 0.00 0.00 4.85
121 122 1.008538 CACCCGAAGTTGTTGCTGC 60.009 57.895 0.00 0.00 0.00 5.25
122 123 1.197721 GATCACCCGAAGTTGTTGCTG 59.802 52.381 0.00 0.00 0.00 4.41
123 124 1.523758 GATCACCCGAAGTTGTTGCT 58.476 50.000 0.00 0.00 0.00 3.91
124 125 0.521735 GGATCACCCGAAGTTGTTGC 59.478 55.000 0.00 0.00 0.00 4.17
143 144 3.962421 CTACCTAGCCCGCCGTCG 61.962 72.222 0.00 0.00 0.00 5.12
144 145 3.603671 CCTACCTAGCCCGCCGTC 61.604 72.222 0.00 0.00 0.00 4.79
145 146 4.453892 ACCTACCTAGCCCGCCGT 62.454 66.667 0.00 0.00 0.00 5.68
146 147 3.912907 CACCTACCTAGCCCGCCG 61.913 72.222 0.00 0.00 0.00 6.46
147 148 3.547513 CCACCTACCTAGCCCGCC 61.548 72.222 0.00 0.00 0.00 6.13
148 149 4.237207 GCCACCTACCTAGCCCGC 62.237 72.222 0.00 0.00 0.00 6.13
149 150 2.444140 AGCCACCTACCTAGCCCG 60.444 66.667 0.00 0.00 0.00 6.13
150 151 2.444256 CCAGCCACCTACCTAGCCC 61.444 68.421 0.00 0.00 0.00 5.19
151 152 3.108288 GCCAGCCACCTACCTAGCC 62.108 68.421 0.00 0.00 0.00 3.93
152 153 2.506472 GCCAGCCACCTACCTAGC 59.494 66.667 0.00 0.00 0.00 3.42
153 154 1.115930 ATCGCCAGCCACCTACCTAG 61.116 60.000 0.00 0.00 0.00 3.02
154 155 0.689745 AATCGCCAGCCACCTACCTA 60.690 55.000 0.00 0.00 0.00 3.08
155 156 0.689745 TAATCGCCAGCCACCTACCT 60.690 55.000 0.00 0.00 0.00 3.08
156 157 0.249911 CTAATCGCCAGCCACCTACC 60.250 60.000 0.00 0.00 0.00 3.18
157 158 0.249911 CCTAATCGCCAGCCACCTAC 60.250 60.000 0.00 0.00 0.00 3.18
158 159 0.689745 ACCTAATCGCCAGCCACCTA 60.690 55.000 0.00 0.00 0.00 3.08
159 160 1.995626 ACCTAATCGCCAGCCACCT 60.996 57.895 0.00 0.00 0.00 4.00
160 161 1.819632 CACCTAATCGCCAGCCACC 60.820 63.158 0.00 0.00 0.00 4.61
161 162 2.472909 GCACCTAATCGCCAGCCAC 61.473 63.158 0.00 0.00 0.00 5.01
162 163 2.124736 GCACCTAATCGCCAGCCA 60.125 61.111 0.00 0.00 0.00 4.75
163 164 3.272334 CGCACCTAATCGCCAGCC 61.272 66.667 0.00 0.00 0.00 4.85
164 165 3.272334 CCGCACCTAATCGCCAGC 61.272 66.667 0.00 0.00 0.00 4.85
165 166 1.883084 GTCCGCACCTAATCGCCAG 60.883 63.158 0.00 0.00 0.00 4.85
166 167 2.185867 GTCCGCACCTAATCGCCA 59.814 61.111 0.00 0.00 0.00 5.69
167 168 2.960129 CGTCCGCACCTAATCGCC 60.960 66.667 0.00 0.00 0.00 5.54
168 169 2.202703 ACGTCCGCACCTAATCGC 60.203 61.111 0.00 0.00 0.00 4.58
169 170 2.514013 GCACGTCCGCACCTAATCG 61.514 63.158 0.00 0.00 0.00 3.34
170 171 1.421410 CTGCACGTCCGCACCTAATC 61.421 60.000 0.00 0.00 36.86 1.75
171 172 1.447838 CTGCACGTCCGCACCTAAT 60.448 57.895 0.00 0.00 36.86 1.73
172 173 2.048597 CTGCACGTCCGCACCTAA 60.049 61.111 0.00 0.00 36.86 2.69
173 174 4.735132 GCTGCACGTCCGCACCTA 62.735 66.667 0.00 0.00 36.86 3.08
177 178 3.914605 CTACAGCTGCACGTCCGCA 62.915 63.158 15.27 0.26 40.32 5.69
178 179 3.181967 CTACAGCTGCACGTCCGC 61.182 66.667 15.27 0.00 0.00 5.54
179 180 1.073216 CTTCTACAGCTGCACGTCCG 61.073 60.000 15.27 0.00 0.00 4.79
180 181 1.355066 GCTTCTACAGCTGCACGTCC 61.355 60.000 15.27 0.00 46.27 4.79
181 182 2.074124 GCTTCTACAGCTGCACGTC 58.926 57.895 15.27 0.00 46.27 4.34
182 183 4.268687 GCTTCTACAGCTGCACGT 57.731 55.556 15.27 0.67 46.27 4.49
189 190 4.821589 AGCCGCCGCTTCTACAGC 62.822 66.667 0.00 0.00 45.55 4.40
190 191 2.887568 CAGCCGCCGCTTCTACAG 60.888 66.667 0.00 0.00 45.55 2.74
191 192 4.451150 CCAGCCGCCGCTTCTACA 62.451 66.667 0.00 0.00 45.55 2.74
211 212 4.813526 CCGTCCACGCGTCTCTCG 62.814 72.222 9.86 12.07 43.12 4.04
212 213 3.735029 ACCGTCCACGCGTCTCTC 61.735 66.667 9.86 0.00 38.18 3.20
213 214 4.039357 CACCGTCCACGCGTCTCT 62.039 66.667 9.86 0.00 38.18 3.10
214 215 4.034258 TCACCGTCCACGCGTCTC 62.034 66.667 9.86 1.23 38.18 3.36
215 216 4.338539 GTCACCGTCCACGCGTCT 62.339 66.667 9.86 0.00 38.18 4.18
265 266 4.530857 GATCCTCCCACACCGCCG 62.531 72.222 0.00 0.00 0.00 6.46
266 267 4.530857 CGATCCTCCCACACCGCC 62.531 72.222 0.00 0.00 0.00 6.13
268 269 4.873129 CGCGATCCTCCCACACCG 62.873 72.222 0.00 0.00 0.00 4.94
291 292 4.109675 ATACCACCACCCTGCCGC 62.110 66.667 0.00 0.00 0.00 6.53
292 293 2.124736 CATACCACCACCCTGCCG 60.125 66.667 0.00 0.00 0.00 5.69
293 294 2.275418 CCATACCACCACCCTGCC 59.725 66.667 0.00 0.00 0.00 4.85
294 295 2.270874 CTCCCATACCACCACCCTGC 62.271 65.000 0.00 0.00 0.00 4.85
295 296 1.635817 CCTCCCATACCACCACCCTG 61.636 65.000 0.00 0.00 0.00 4.45
296 297 1.307866 CCTCCCATACCACCACCCT 60.308 63.158 0.00 0.00 0.00 4.34
297 298 1.307517 TCCTCCCATACCACCACCC 60.308 63.158 0.00 0.00 0.00 4.61
298 299 1.984288 GCTCCTCCCATACCACCACC 61.984 65.000 0.00 0.00 0.00 4.61
299 300 1.527370 GCTCCTCCCATACCACCAC 59.473 63.158 0.00 0.00 0.00 4.16
300 301 2.063979 CGCTCCTCCCATACCACCA 61.064 63.158 0.00 0.00 0.00 4.17
301 302 2.822399 CGCTCCTCCCATACCACC 59.178 66.667 0.00 0.00 0.00 4.61
302 303 2.109181 GCGCTCCTCCCATACCAC 59.891 66.667 0.00 0.00 0.00 4.16
303 304 3.536917 CGCGCTCCTCCCATACCA 61.537 66.667 5.56 0.00 0.00 3.25
304 305 4.301027 CCGCGCTCCTCCCATACC 62.301 72.222 5.56 0.00 0.00 2.73
305 306 4.971125 GCCGCGCTCCTCCCATAC 62.971 72.222 5.56 0.00 0.00 2.39
346 347 4.651008 TCCCGTGCCGTCGTTGTC 62.651 66.667 0.00 0.00 0.00 3.18
347 348 4.657824 CTCCCGTGCCGTCGTTGT 62.658 66.667 0.00 0.00 0.00 3.32
380 381 3.938019 TTTTACTCCCCGCCGTCGC 62.938 63.158 0.00 0.00 0.00 5.19
381 382 2.096442 GTTTTACTCCCCGCCGTCG 61.096 63.158 0.00 0.00 0.00 5.12
382 383 1.742880 GGTTTTACTCCCCGCCGTC 60.743 63.158 0.00 0.00 0.00 4.79
383 384 0.904394 TAGGTTTTACTCCCCGCCGT 60.904 55.000 0.00 0.00 0.00 5.68
384 385 0.249955 TTAGGTTTTACTCCCCGCCG 59.750 55.000 0.00 0.00 0.00 6.46
385 386 2.495155 TTTAGGTTTTACTCCCCGCC 57.505 50.000 0.00 0.00 0.00 6.13
403 404 9.965902 AAATATCTCTCTACATGGTCAGTTTTT 57.034 29.630 0.00 0.00 0.00 1.94
404 405 9.965902 AAAATATCTCTCTACATGGTCAGTTTT 57.034 29.630 0.00 0.00 0.00 2.43
405 406 9.388506 CAAAATATCTCTCTACATGGTCAGTTT 57.611 33.333 0.00 0.00 0.00 2.66
406 407 7.497249 GCAAAATATCTCTCTACATGGTCAGTT 59.503 37.037 0.00 0.00 0.00 3.16
407 408 6.989169 GCAAAATATCTCTCTACATGGTCAGT 59.011 38.462 0.00 0.00 0.00 3.41
408 409 6.988580 TGCAAAATATCTCTCTACATGGTCAG 59.011 38.462 0.00 0.00 0.00 3.51
409 410 6.888105 TGCAAAATATCTCTCTACATGGTCA 58.112 36.000 0.00 0.00 0.00 4.02
410 411 7.792374 TTGCAAAATATCTCTCTACATGGTC 57.208 36.000 0.00 0.00 0.00 4.02
437 438 9.571816 TCTGCACCATCAATACAATGATTATTA 57.428 29.630 0.00 0.00 37.96 0.98
438 439 8.467963 TCTGCACCATCAATACAATGATTATT 57.532 30.769 0.00 0.00 37.96 1.40
439 440 8.520351 CATCTGCACCATCAATACAATGATTAT 58.480 33.333 0.00 0.00 37.96 1.28
440 441 7.522562 GCATCTGCACCATCAATACAATGATTA 60.523 37.037 0.00 0.00 38.25 1.75
441 442 6.737622 GCATCTGCACCATCAATACAATGATT 60.738 38.462 0.00 0.00 38.25 2.57
442 443 5.278808 GCATCTGCACCATCAATACAATGAT 60.279 40.000 0.00 0.00 39.66 2.45
443 444 4.037089 GCATCTGCACCATCAATACAATGA 59.963 41.667 0.00 0.00 41.59 2.57
444 445 4.295870 GCATCTGCACCATCAATACAATG 58.704 43.478 0.00 0.00 41.59 2.82
445 446 4.579454 GCATCTGCACCATCAATACAAT 57.421 40.909 0.00 0.00 41.59 2.71
501 502 9.368416 TGGCTCATCTTCTAGTTATGTATAGTT 57.632 33.333 0.00 0.00 0.00 2.24
502 503 8.798402 GTGGCTCATCTTCTAGTTATGTATAGT 58.202 37.037 0.00 0.00 0.00 2.12
503 504 8.797438 TGTGGCTCATCTTCTAGTTATGTATAG 58.203 37.037 0.00 0.00 0.00 1.31
504 505 8.706322 TGTGGCTCATCTTCTAGTTATGTATA 57.294 34.615 0.00 0.00 0.00 1.47
505 506 7.603180 TGTGGCTCATCTTCTAGTTATGTAT 57.397 36.000 0.00 0.00 0.00 2.29
506 507 7.093509 TGTTGTGGCTCATCTTCTAGTTATGTA 60.094 37.037 0.00 0.00 0.00 2.29
507 508 5.939764 TGTGGCTCATCTTCTAGTTATGT 57.060 39.130 0.00 0.00 0.00 2.29
508 509 6.036517 GTGTTGTGGCTCATCTTCTAGTTATG 59.963 42.308 0.00 0.00 0.00 1.90
509 510 6.109359 GTGTTGTGGCTCATCTTCTAGTTAT 58.891 40.000 0.00 0.00 0.00 1.89
510 511 5.479306 GTGTTGTGGCTCATCTTCTAGTTA 58.521 41.667 0.00 0.00 0.00 2.24
511 512 4.319177 GTGTTGTGGCTCATCTTCTAGTT 58.681 43.478 0.00 0.00 0.00 2.24
512 513 3.615110 CGTGTTGTGGCTCATCTTCTAGT 60.615 47.826 0.00 0.00 0.00 2.57
513 514 2.926200 CGTGTTGTGGCTCATCTTCTAG 59.074 50.000 0.00 0.00 0.00 2.43
514 515 2.299013 ACGTGTTGTGGCTCATCTTCTA 59.701 45.455 0.00 0.00 0.00 2.10
515 516 1.070758 ACGTGTTGTGGCTCATCTTCT 59.929 47.619 0.00 0.00 0.00 2.85
516 517 1.512926 ACGTGTTGTGGCTCATCTTC 58.487 50.000 0.00 0.00 0.00 2.87
517 518 2.831685 TACGTGTTGTGGCTCATCTT 57.168 45.000 0.00 0.00 0.00 2.40
518 519 2.831685 TTACGTGTTGTGGCTCATCT 57.168 45.000 0.00 0.00 0.00 2.90
519 520 8.703604 ATATATATTACGTGTTGTGGCTCATC 57.296 34.615 0.00 0.00 0.00 2.92
521 522 9.414295 GTTATATATATTACGTGTTGTGGCTCA 57.586 33.333 0.00 0.00 0.00 4.26
522 523 9.414295 TGTTATATATATTACGTGTTGTGGCTC 57.586 33.333 0.00 0.00 0.00 4.70
523 524 9.199982 GTGTTATATATATTACGTGTTGTGGCT 57.800 33.333 0.00 0.00 0.00 4.75
524 525 8.980610 TGTGTTATATATATTACGTGTTGTGGC 58.019 33.333 0.00 0.00 0.00 5.01
548 549 9.449719 CCCTCTTATTATTGAGTTGTACTTTGT 57.550 33.333 0.00 0.00 0.00 2.83
549 550 8.893727 CCCCTCTTATTATTGAGTTGTACTTTG 58.106 37.037 0.00 0.00 0.00 2.77
550 551 7.556635 GCCCCTCTTATTATTGAGTTGTACTTT 59.443 37.037 0.00 0.00 0.00 2.66
551 552 7.054751 GCCCCTCTTATTATTGAGTTGTACTT 58.945 38.462 0.00 0.00 0.00 2.24
552 553 6.409349 GGCCCCTCTTATTATTGAGTTGTACT 60.409 42.308 0.00 0.00 0.00 2.73
553 554 5.763698 GGCCCCTCTTATTATTGAGTTGTAC 59.236 44.000 0.00 0.00 0.00 2.90
554 555 5.430417 TGGCCCCTCTTATTATTGAGTTGTA 59.570 40.000 0.00 0.00 0.00 2.41
555 556 4.229582 TGGCCCCTCTTATTATTGAGTTGT 59.770 41.667 0.00 0.00 0.00 3.32
556 557 4.792068 TGGCCCCTCTTATTATTGAGTTG 58.208 43.478 0.00 0.00 0.00 3.16
557 558 5.466127 TTGGCCCCTCTTATTATTGAGTT 57.534 39.130 0.00 0.00 0.00 3.01
558 559 5.201243 GTTTGGCCCCTCTTATTATTGAGT 58.799 41.667 0.00 0.00 0.00 3.41
559 560 4.584743 GGTTTGGCCCCTCTTATTATTGAG 59.415 45.833 0.00 0.00 0.00 3.02
560 561 4.542697 GGTTTGGCCCCTCTTATTATTGA 58.457 43.478 0.00 0.00 0.00 2.57
561 562 4.937201 GGTTTGGCCCCTCTTATTATTG 57.063 45.455 0.00 0.00 0.00 1.90
574 575 1.077429 CTCAGGCTAGGGTTTGGCC 60.077 63.158 0.00 0.00 45.57 5.36
575 576 1.750780 GCTCAGGCTAGGGTTTGGC 60.751 63.158 0.00 0.00 35.22 4.52
576 577 1.450312 CGCTCAGGCTAGGGTTTGG 60.450 63.158 0.00 0.00 36.09 3.28
577 578 2.109126 GCGCTCAGGCTAGGGTTTG 61.109 63.158 0.00 0.00 36.09 2.93
667 668 1.134551 GCTCAGGCTAGAAGTCCCAAG 60.135 57.143 0.00 0.00 35.22 3.61
767 771 2.354259 CAGGAGCTGAAGTGATGGTTC 58.646 52.381 0.00 0.00 32.44 3.62
902 2099 3.920093 CTTGGCTGGGTCGGGTTCC 62.920 68.421 0.00 0.00 0.00 3.62
992 2189 0.337773 TCTGTCCTCCATGGCTCTCT 59.662 55.000 6.96 0.00 35.26 3.10
993 2190 0.752054 CTCTGTCCTCCATGGCTCTC 59.248 60.000 6.96 0.00 35.26 3.20
1064 2261 3.203412 CGTCTCCCTCCTCGTCGG 61.203 72.222 0.00 0.00 0.00 4.79
1347 2544 3.681835 GACGCCGGAGTGGACTGT 61.682 66.667 18.14 0.00 42.00 3.55
1476 2673 1.452145 GCCCTGAAGTGGCGTTCAAA 61.452 55.000 3.97 0.00 39.48 2.69
1488 2685 2.858476 TGCTTGGGAGGCCCTGAA 60.858 61.111 0.00 0.00 45.70 3.02
1572 2769 4.164221 CCTCCTCCTCCTTTGCTGTAATAA 59.836 45.833 0.00 0.00 0.00 1.40
1701 2901 3.356290 AGGCCAAGAAACGCATTAGAAT 58.644 40.909 5.01 0.00 0.00 2.40
1721 2921 2.421751 TTGACGGGGTAGAGAGAGAG 57.578 55.000 0.00 0.00 0.00 3.20
1820 3022 6.100424 AGCCAAGCAGATCCTAATTTAGTACT 59.900 38.462 0.00 0.00 0.00 2.73
1821 3023 6.292150 AGCCAAGCAGATCCTAATTTAGTAC 58.708 40.000 2.88 0.00 0.00 2.73
1822 3024 6.500589 AGCCAAGCAGATCCTAATTTAGTA 57.499 37.500 2.88 0.00 0.00 1.82
1823 3025 5.379706 AGCCAAGCAGATCCTAATTTAGT 57.620 39.130 2.88 0.00 0.00 2.24
1824 3026 6.429385 CCTTAGCCAAGCAGATCCTAATTTAG 59.571 42.308 0.00 0.00 0.00 1.85
1896 3098 8.964772 ACAGAGAACCTACAAAATAGTACGTAT 58.035 33.333 0.00 0.00 0.00 3.06
1899 3101 8.433126 CAAACAGAGAACCTACAAAATAGTACG 58.567 37.037 0.00 0.00 0.00 3.67
1900 3102 8.228464 GCAAACAGAGAACCTACAAAATAGTAC 58.772 37.037 0.00 0.00 0.00 2.73
1901 3103 8.154856 AGCAAACAGAGAACCTACAAAATAGTA 58.845 33.333 0.00 0.00 0.00 1.82
2062 3273 5.650266 GGTTACACCATACATGAATTCACCA 59.350 40.000 11.07 0.00 38.42 4.17
2129 3340 2.319136 TCAACTAATAACGCCGCCAT 57.681 45.000 0.00 0.00 0.00 4.40
2213 3692 4.406648 TGGCGACATCAATAGAGACAAT 57.593 40.909 0.00 0.00 33.40 2.71
2220 3700 3.763097 TTGCTTTGGCGACATCAATAG 57.237 42.857 0.00 0.00 42.32 1.73
2346 3843 1.014352 ACTGTTTGACTGTTCCGCAC 58.986 50.000 0.00 0.00 0.00 5.34
2370 3867 3.181515 TGCAATTTTGTATACACGCGAGG 60.182 43.478 15.93 7.12 0.00 4.63
2376 3873 6.375377 TCCTCGTTTGCAATTTTGTATACAC 58.625 36.000 4.68 0.00 0.00 2.90
2423 3920 8.722622 AGCCCACTACAATATAGTATAGTTGT 57.277 34.615 15.85 15.85 37.23 3.32
2425 3922 7.886970 TCGAGCCCACTACAATATAGTATAGTT 59.113 37.037 0.00 0.00 0.00 2.24
2426 3923 7.400439 TCGAGCCCACTACAATATAGTATAGT 58.600 38.462 0.00 0.00 0.00 2.12
2428 3925 9.910267 TTATCGAGCCCACTACAATATAGTATA 57.090 33.333 0.00 0.00 0.00 1.47
2431 3928 6.350277 GCTTATCGAGCCCACTACAATATAGT 60.350 42.308 0.00 0.00 46.01 2.12
2465 4253 1.078709 CAACTGGGTGTACATCAGCG 58.921 55.000 21.53 13.33 44.48 5.18
2475 4263 0.250124 TCGTAGTTGGCAACTGGGTG 60.250 55.000 36.40 23.79 42.84 4.61
2562 4363 4.695455 CCAGTAGTTGGTGTAATTGGTGAG 59.305 45.833 0.00 0.00 42.41 3.51
2651 4452 0.109342 GGATGGATGGGCGTCTTGAT 59.891 55.000 0.00 0.00 0.00 2.57
2676 4481 0.968901 ACCCGTCGCCTACTTGATGA 60.969 55.000 0.00 0.00 0.00 2.92
2677 4482 0.108329 AACCCGTCGCCTACTTGATG 60.108 55.000 0.00 0.00 0.00 3.07
2678 4483 0.175073 GAACCCGTCGCCTACTTGAT 59.825 55.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.