Multiple sequence alignment - TraesCS2B01G212400

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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 TraesCS2B01G212400 chr2B 100.000 2832 0 0 1 2832 196542643 196539812 0.000000e+00 5230
1 TraesCS2B01G212400 chr2B 98.404 376 5 1 1 376 7933561 7933935 0.000000e+00 660
2 TraesCS2B01G212400 chr2B 92.857 168 10 2 2652 2817 763452774 763452941 2.820000e-60 243
3 TraesCS2B01G212400 chr2B 92.353 170 12 1 2653 2821 278161810 278161979 1.010000e-59 241
4 TraesCS2B01G212400 chr2D 95.554 2294 70 11 386 2658 138517313 138515031 0.000000e+00 3642
5 TraesCS2B01G212400 chr2D 94.410 161 9 0 2657 2817 73737370 73737210 6.060000e-62 248
6 TraesCS2B01G212400 chr2A 93.095 2317 89 27 376 2653 163097036 163099320 0.000000e+00 3326
7 TraesCS2B01G212400 chr4B 98.925 372 4 0 1 372 462585356 462584985 0.000000e+00 665
8 TraesCS2B01G212400 chr4B 98.123 373 6 1 1 372 52657193 52657565 0.000000e+00 649
9 TraesCS2B01G212400 chr4B 94.512 164 9 0 2655 2818 181685989 181685826 1.300000e-63 254
10 TraesCS2B01G212400 chr4B 82.990 194 31 2 1045 1237 75779729 75779537 1.040000e-39 174
11 TraesCS2B01G212400 chr7A 97.900 381 8 0 1 381 717563811 717563431 0.000000e+00 660
12 TraesCS2B01G212400 chr7A 98.387 372 6 0 1 372 258689322 258689693 0.000000e+00 654
13 TraesCS2B01G212400 chr6A 98.400 375 5 1 1 375 153687282 153687655 0.000000e+00 658
14 TraesCS2B01G212400 chr1A 97.403 385 9 1 1 384 519250891 519251275 0.000000e+00 654
15 TraesCS2B01G212400 chr7B 98.118 372 7 0 1 372 356738355 356737984 0.000000e+00 649
16 TraesCS2B01G212400 chr1B 97.143 385 10 1 1 384 198532758 198532374 0.000000e+00 649
17 TraesCS2B01G212400 chr5A 94.410 161 9 0 2657 2817 470679254 470679414 6.060000e-62 248
18 TraesCS2B01G212400 chr6B 93.865 163 10 0 2657 2819 86407219 86407057 2.180000e-61 246
19 TraesCS2B01G212400 chrUn 92.857 168 12 0 2654 2821 34149716 34149883 7.840000e-61 244
20 TraesCS2B01G212400 chrUn 92.857 168 12 0 2654 2821 282034022 282034189 7.840000e-61 244
21 TraesCS2B01G212400 chr5B 91.813 171 14 0 2654 2824 405526326 405526496 3.650000e-59 239
22 TraesCS2B01G212400 chr4D 83.085 201 31 3 1038 1237 51616881 51616683 2.240000e-41 180
23 TraesCS2B01G212400 chr4A 83.085 201 31 3 1038 1237 544953077 544953275 2.240000e-41 180


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 TraesCS2B01G212400 chr2B 196539812 196542643 2831 True 5230 5230 100.000 1 2832 1 chr2B.!!$R1 2831
1 TraesCS2B01G212400 chr2D 138515031 138517313 2282 True 3642 3642 95.554 386 2658 1 chr2D.!!$R2 2272
2 TraesCS2B01G212400 chr2A 163097036 163099320 2284 False 3326 3326 93.095 376 2653 1 chr2A.!!$F1 2277

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
353 354 0.105039 AAGTATAGTGAGCAGCCGGC 59.895 55.0 21.89 21.89 45.3 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2302 2342 0.039527 GGTGGCGTGAAACATTGACC 60.04 55.0 0.0 0.0 35.74 4.02 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
24 25 7.813852 GTACTATAGTTGCACCATATAGCAC 57.186 40.000 11.40 10.58 41.05 4.40
25 26 5.794894 ACTATAGTTGCACCATATAGCACC 58.205 41.667 14.57 0.00 41.05 5.01
26 27 4.705110 ATAGTTGCACCATATAGCACCA 57.295 40.909 0.00 0.00 41.05 4.17
27 28 3.364460 AGTTGCACCATATAGCACCAA 57.636 42.857 0.00 0.00 41.05 3.67
28 29 3.696045 AGTTGCACCATATAGCACCAAA 58.304 40.909 0.00 0.00 41.05 3.28
29 30 3.696051 AGTTGCACCATATAGCACCAAAG 59.304 43.478 0.00 0.00 41.05 2.77
30 31 3.364460 TGCACCATATAGCACCAAAGT 57.636 42.857 0.00 0.00 35.51 2.66
31 32 3.696045 TGCACCATATAGCACCAAAGTT 58.304 40.909 0.00 0.00 35.51 2.66
32 33 4.849518 TGCACCATATAGCACCAAAGTTA 58.150 39.130 0.00 0.00 35.51 2.24
33 34 4.881273 TGCACCATATAGCACCAAAGTTAG 59.119 41.667 0.00 0.00 35.51 2.34
34 35 4.261197 GCACCATATAGCACCAAAGTTAGC 60.261 45.833 0.00 0.00 0.00 3.09
35 36 4.881273 CACCATATAGCACCAAAGTTAGCA 59.119 41.667 0.00 0.00 0.00 3.49
36 37 5.532406 CACCATATAGCACCAAAGTTAGCAT 59.468 40.000 0.00 0.00 0.00 3.79
37 38 5.765182 ACCATATAGCACCAAAGTTAGCATC 59.235 40.000 0.00 0.00 0.00 3.91
38 39 5.764686 CCATATAGCACCAAAGTTAGCATCA 59.235 40.000 0.00 0.00 0.00 3.07
39 40 6.262944 CCATATAGCACCAAAGTTAGCATCAA 59.737 38.462 0.00 0.00 0.00 2.57
40 41 7.201812 CCATATAGCACCAAAGTTAGCATCAAA 60.202 37.037 0.00 0.00 0.00 2.69
41 42 4.935352 AGCACCAAAGTTAGCATCAAAA 57.065 36.364 0.00 0.00 0.00 2.44
42 43 5.275067 AGCACCAAAGTTAGCATCAAAAA 57.725 34.783 0.00 0.00 0.00 1.94
63 64 5.692613 AAAAATTCGTCGAAACATACCCA 57.307 34.783 12.40 0.00 0.00 4.51
64 65 5.890424 AAAATTCGTCGAAACATACCCAT 57.110 34.783 12.40 0.00 0.00 4.00
65 66 6.988622 AAAATTCGTCGAAACATACCCATA 57.011 33.333 12.40 0.00 0.00 2.74
66 67 7.562454 AAAATTCGTCGAAACATACCCATAT 57.438 32.000 12.40 0.00 0.00 1.78
67 68 6.539649 AATTCGTCGAAACATACCCATATG 57.460 37.500 12.40 0.00 43.46 1.78
68 69 3.985008 TCGTCGAAACATACCCATATGG 58.015 45.455 15.41 15.41 42.32 2.74
84 85 6.346477 CCATATGGGATCTAGTTTCGAAGA 57.654 41.667 14.52 0.00 40.01 2.87
85 86 6.940739 CCATATGGGATCTAGTTTCGAAGAT 58.059 40.000 14.52 0.00 40.01 2.40
86 87 7.038659 CCATATGGGATCTAGTTTCGAAGATC 58.961 42.308 14.52 14.01 44.88 2.75
87 88 7.093552 CCATATGGGATCTAGTTTCGAAGATCT 60.094 40.741 19.29 12.50 44.94 2.75
88 89 5.776173 TGGGATCTAGTTTCGAAGATCTC 57.224 43.478 19.29 17.27 45.96 2.75
96 97 3.877145 CGAAGATCTCGTCGCGAC 58.123 61.111 28.96 28.96 42.89 5.19
106 107 2.851104 GTCGCGACGAACCCAAAG 59.149 61.111 25.19 0.00 37.72 2.77
107 108 2.356553 TCGCGACGAACCCAAAGG 60.357 61.111 3.71 0.00 40.04 3.11
120 121 2.514803 CCCAAAGGTGAAAACGGATCT 58.485 47.619 0.00 0.00 0.00 2.75
121 122 2.228822 CCCAAAGGTGAAAACGGATCTG 59.771 50.000 0.00 0.00 0.00 2.90
122 123 3.146066 CCAAAGGTGAAAACGGATCTGA 58.854 45.455 9.00 0.00 0.00 3.27
123 124 3.568007 CCAAAGGTGAAAACGGATCTGAA 59.432 43.478 9.00 0.00 0.00 3.02
124 125 4.218417 CCAAAGGTGAAAACGGATCTGAAT 59.782 41.667 9.00 0.00 0.00 2.57
125 126 5.278957 CCAAAGGTGAAAACGGATCTGAATT 60.279 40.000 9.00 2.31 0.00 2.17
126 127 5.629079 AAGGTGAAAACGGATCTGAATTC 57.371 39.130 9.00 12.00 0.00 2.17
127 128 4.010349 AGGTGAAAACGGATCTGAATTCC 58.990 43.478 9.00 6.35 0.00 3.01
128 129 3.756434 GGTGAAAACGGATCTGAATTCCA 59.244 43.478 9.00 0.00 32.45 3.53
129 130 4.217550 GGTGAAAACGGATCTGAATTCCAA 59.782 41.667 9.00 0.00 32.45 3.53
130 131 5.154222 GTGAAAACGGATCTGAATTCCAAC 58.846 41.667 9.00 4.17 32.45 3.77
131 132 4.824537 TGAAAACGGATCTGAATTCCAACA 59.175 37.500 9.00 0.75 32.45 3.33
132 133 5.476599 TGAAAACGGATCTGAATTCCAACAT 59.523 36.000 9.00 0.00 32.45 2.71
133 134 4.970662 AACGGATCTGAATTCCAACATG 57.029 40.909 9.00 0.00 32.45 3.21
134 135 3.955471 ACGGATCTGAATTCCAACATGT 58.045 40.909 9.00 0.00 32.45 3.21
135 136 3.691118 ACGGATCTGAATTCCAACATGTG 59.309 43.478 9.00 0.00 32.45 3.21
151 152 8.687824 CCAACATGTGGTTTAAAAGATATGAC 57.312 34.615 0.00 0.00 43.20 3.06
152 153 8.522830 CCAACATGTGGTTTAAAAGATATGACT 58.477 33.333 0.00 0.00 43.20 3.41
153 154 9.912634 CAACATGTGGTTTAAAAGATATGACTT 57.087 29.630 0.00 0.00 37.72 3.01
190 191 8.782533 AAGAGACGAAAATAAATGTGTTTCAC 57.217 30.769 0.00 0.00 32.00 3.18
191 192 7.069569 AGAGACGAAAATAAATGTGTTTCACG 58.930 34.615 0.00 0.00 37.14 4.35
192 193 6.140110 AGACGAAAATAAATGTGTTTCACGG 58.860 36.000 0.00 0.00 37.14 4.94
193 194 6.017770 AGACGAAAATAAATGTGTTTCACGGA 60.018 34.615 0.00 0.00 37.14 4.69
194 195 5.910723 ACGAAAATAAATGTGTTTCACGGAC 59.089 36.000 0.00 0.00 37.14 4.79
195 196 5.341196 CGAAAATAAATGTGTTTCACGGACC 59.659 40.000 0.00 0.00 37.14 4.46
196 197 5.776173 AAATAAATGTGTTTCACGGACCA 57.224 34.783 0.00 0.00 37.14 4.02
197 198 5.371115 AATAAATGTGTTTCACGGACCAG 57.629 39.130 0.00 0.00 37.14 4.00
198 199 2.341846 AATGTGTTTCACGGACCAGT 57.658 45.000 0.00 0.00 37.14 4.00
199 200 1.878953 ATGTGTTTCACGGACCAGTC 58.121 50.000 0.00 0.00 37.14 3.51
200 201 0.828022 TGTGTTTCACGGACCAGTCT 59.172 50.000 0.00 0.00 37.14 3.24
201 202 1.217882 GTGTTTCACGGACCAGTCTG 58.782 55.000 5.06 5.06 41.63 3.51
203 204 2.033372 TGTTTCACGGACCAGTCTGTA 58.967 47.619 11.80 0.00 46.70 2.74
204 205 2.223876 TGTTTCACGGACCAGTCTGTAC 60.224 50.000 11.80 7.86 46.70 2.90
205 206 0.594602 TTCACGGACCAGTCTGTACG 59.405 55.000 11.80 2.63 46.70 3.67
206 207 1.443872 CACGGACCAGTCTGTACGC 60.444 63.158 11.80 0.00 46.59 4.42
207 208 1.900016 ACGGACCAGTCTGTACGCA 60.900 57.895 10.53 0.00 46.59 5.24
208 209 1.248785 ACGGACCAGTCTGTACGCAT 61.249 55.000 10.53 0.00 46.59 4.73
209 210 0.108804 CGGACCAGTCTGTACGCATT 60.109 55.000 0.00 0.00 35.50 3.56
210 211 1.671850 CGGACCAGTCTGTACGCATTT 60.672 52.381 0.00 0.00 35.50 2.32
211 212 1.732259 GGACCAGTCTGTACGCATTTG 59.268 52.381 0.00 0.00 0.00 2.32
212 213 1.128692 GACCAGTCTGTACGCATTTGC 59.871 52.381 0.00 0.00 37.78 3.68
213 214 1.270839 ACCAGTCTGTACGCATTTGCT 60.271 47.619 0.00 0.00 39.32 3.91
214 215 2.028476 ACCAGTCTGTACGCATTTGCTA 60.028 45.455 0.00 0.00 39.32 3.49
215 216 3.198068 CCAGTCTGTACGCATTTGCTAT 58.802 45.455 0.00 0.00 39.32 2.97
216 217 4.142026 ACCAGTCTGTACGCATTTGCTATA 60.142 41.667 0.00 0.00 39.32 1.31
217 218 4.209288 CCAGTCTGTACGCATTTGCTATAC 59.791 45.833 0.00 4.32 39.32 1.47
218 219 4.042398 AGTCTGTACGCATTTGCTATACG 58.958 43.478 0.51 0.00 39.32 3.06
219 220 2.792674 TCTGTACGCATTTGCTATACGC 59.207 45.455 0.51 0.00 39.32 4.42
263 264 9.349713 ACATCCATTAACTAACAGAAAAAGACA 57.650 29.630 0.00 0.00 0.00 3.41
264 265 9.612620 CATCCATTAACTAACAGAAAAAGACAC 57.387 33.333 0.00 0.00 0.00 3.67
265 266 8.740123 TCCATTAACTAACAGAAAAAGACACA 57.260 30.769 0.00 0.00 0.00 3.72
266 267 8.617809 TCCATTAACTAACAGAAAAAGACACAC 58.382 33.333 0.00 0.00 0.00 3.82
267 268 8.402472 CCATTAACTAACAGAAAAAGACACACA 58.598 33.333 0.00 0.00 0.00 3.72
268 269 9.781834 CATTAACTAACAGAAAAAGACACACAA 57.218 29.630 0.00 0.00 0.00 3.33
272 273 8.958119 ACTAACAGAAAAAGACACACAATAGA 57.042 30.769 0.00 0.00 0.00 1.98
273 274 9.561069 ACTAACAGAAAAAGACACACAATAGAT 57.439 29.630 0.00 0.00 0.00 1.98
318 319 9.981114 ATTAGAGGACCAAAACTTGTAATTTTG 57.019 29.630 0.00 3.72 43.59 2.44
323 324 4.723879 CAAAACTTGTAATTTTGGGCCG 57.276 40.909 0.00 0.00 41.37 6.13
324 325 3.394674 AAACTTGTAATTTTGGGCCGG 57.605 42.857 0.00 0.00 0.00 6.13
325 326 0.606096 ACTTGTAATTTTGGGCCGGC 59.394 50.000 21.18 21.18 0.00 6.13
326 327 0.108377 CTTGTAATTTTGGGCCGGCC 60.108 55.000 38.57 38.57 0.00 6.13
327 328 1.878656 TTGTAATTTTGGGCCGGCCG 61.879 55.000 38.22 21.04 36.85 6.13
328 329 3.453679 TAATTTTGGGCCGGCCGC 61.454 61.111 38.22 29.79 36.85 6.53
329 330 3.948004 TAATTTTGGGCCGGCCGCT 62.948 57.895 38.22 20.15 37.74 5.52
339 340 2.890474 CGGCCGCTCGCAAAGTAT 60.890 61.111 14.67 0.00 40.31 2.12
340 341 1.590525 CGGCCGCTCGCAAAGTATA 60.591 57.895 14.67 0.00 40.31 1.47
341 342 1.548973 CGGCCGCTCGCAAAGTATAG 61.549 60.000 14.67 0.00 40.31 1.31
342 343 0.529992 GGCCGCTCGCAAAGTATAGT 60.530 55.000 0.00 0.00 40.31 2.12
343 344 0.577269 GCCGCTCGCAAAGTATAGTG 59.423 55.000 0.00 0.00 37.47 2.74
344 345 1.801395 GCCGCTCGCAAAGTATAGTGA 60.801 52.381 0.00 0.00 37.47 3.41
345 346 2.120232 CCGCTCGCAAAGTATAGTGAG 58.880 52.381 0.00 0.00 43.40 3.51
349 350 2.537625 CTCGCAAAGTATAGTGAGCAGC 59.462 50.000 5.62 0.00 35.83 5.25
350 351 1.594862 CGCAAAGTATAGTGAGCAGCC 59.405 52.381 0.00 0.00 0.00 4.85
351 352 1.594862 GCAAAGTATAGTGAGCAGCCG 59.405 52.381 0.00 0.00 0.00 5.52
352 353 2.205074 CAAAGTATAGTGAGCAGCCGG 58.795 52.381 0.00 0.00 0.00 6.13
353 354 0.105039 AAGTATAGTGAGCAGCCGGC 59.895 55.000 21.89 21.89 45.30 6.13
354 355 1.301009 GTATAGTGAGCAGCCGGCC 60.301 63.158 26.15 9.10 46.50 6.13
355 356 2.856628 TATAGTGAGCAGCCGGCCG 61.857 63.158 26.15 21.04 46.50 6.13
370 371 4.253257 CCGCTCGCTAGACCGGTC 62.253 72.222 27.67 27.67 39.96 4.79
371 372 4.253257 CGCTCGCTAGACCGGTCC 62.253 72.222 30.82 14.89 0.00 4.46
372 373 3.138798 GCTCGCTAGACCGGTCCA 61.139 66.667 30.82 17.53 0.00 4.02
373 374 2.707849 GCTCGCTAGACCGGTCCAA 61.708 63.158 30.82 18.31 0.00 3.53
374 375 1.888018 CTCGCTAGACCGGTCCAAA 59.112 57.895 30.82 15.70 0.00 3.28
375 376 0.245539 CTCGCTAGACCGGTCCAAAA 59.754 55.000 30.82 13.15 0.00 2.44
376 377 0.899720 TCGCTAGACCGGTCCAAAAT 59.100 50.000 30.82 14.70 0.00 1.82
377 378 2.100252 CTCGCTAGACCGGTCCAAAATA 59.900 50.000 30.82 15.06 0.00 1.40
378 379 2.696707 TCGCTAGACCGGTCCAAAATAT 59.303 45.455 30.82 13.15 0.00 1.28
379 380 3.890756 TCGCTAGACCGGTCCAAAATATA 59.109 43.478 30.82 13.61 0.00 0.86
380 381 4.525487 TCGCTAGACCGGTCCAAAATATAT 59.475 41.667 30.82 11.62 0.00 0.86
381 382 5.711506 TCGCTAGACCGGTCCAAAATATATA 59.288 40.000 30.82 12.16 0.00 0.86
382 383 6.379133 TCGCTAGACCGGTCCAAAATATATAT 59.621 38.462 30.82 10.31 0.00 0.86
383 384 6.475727 CGCTAGACCGGTCCAAAATATATATG 59.524 42.308 30.82 2.58 0.00 1.78
402 403 8.825667 ATATATGCACACATAATCGTACAACA 57.174 30.769 0.00 0.00 41.99 3.33
940 961 3.162666 CCTCCTCGCCTGGTTATATACA 58.837 50.000 0.00 0.00 0.00 2.29
949 970 1.695242 TGGTTATATACACCGCCCCTG 59.305 52.381 8.59 0.00 37.07 4.45
989 1010 1.657751 GCTTCTTGATCGGGGTTGGC 61.658 60.000 0.00 0.00 0.00 4.52
993 1014 3.936772 TTGATCGGGGTTGGCTGGC 62.937 63.158 0.00 0.00 0.00 4.85
1059 1080 2.825836 GGGATGAGCTGCAACGGG 60.826 66.667 1.02 0.00 0.00 5.28
1128 1149 2.429767 CCTGCTCTGGATCGAGGCA 61.430 63.158 16.05 16.05 0.00 4.75
1273 1297 0.687354 ATGGTCTTCTTGGCACGACT 59.313 50.000 0.00 0.00 0.00 4.18
1283 1307 2.931386 GCACGACTATGCATCGGC 59.069 61.111 0.19 0.00 45.39 5.54
1534 1558 3.379445 GAAGGCGGAGTCGGTGGA 61.379 66.667 0.00 0.00 36.95 4.02
1621 1645 2.649034 GTGACGCCGAGGAAGACA 59.351 61.111 0.00 0.00 0.00 3.41
1669 1693 4.803426 GAGCCCTCGTGCGACCTG 62.803 72.222 0.00 0.00 36.02 4.00
1863 1893 6.119144 AGTTATTAATCTGCGCGTTCATTT 57.881 33.333 8.43 0.00 0.00 2.32
1888 1918 1.206072 GTAGTACCGCGCGATCGAT 59.794 57.895 34.63 15.32 38.10 3.59
1890 1920 1.223417 TAGTACCGCGCGATCGATCA 61.223 55.000 34.63 6.89 38.10 2.92
1891 1921 2.075489 GTACCGCGCGATCGATCAG 61.075 63.158 34.63 17.82 38.10 2.90
1950 1984 4.072131 CAGCTGAACTTTTTGGTAGCCTA 58.928 43.478 8.42 0.00 31.82 3.93
2093 2127 4.982916 CGATAATAGTACCGCTGCTTTCTT 59.017 41.667 0.00 0.00 0.00 2.52
2165 2201 2.524306 AGCTCTCTGATCTTATCCGGG 58.476 52.381 0.00 0.00 0.00 5.73
2179 2215 2.510691 CGGGGCGTGATTAGCGTT 60.511 61.111 0.00 0.00 35.00 4.84
2203 2243 2.772189 GCGAGTGCGTGTGCTAAG 59.228 61.111 0.00 0.00 43.34 2.18
2218 2258 1.293924 CTAAGACGCCATTGCTCCTG 58.706 55.000 0.00 0.00 34.43 3.86
2291 2331 2.159626 CGTGTTTTTGTGAACTGGTCGT 60.160 45.455 0.00 0.00 0.00 4.34
2302 2342 4.207224 GTGAACTGGTCGTATGATTGATCG 59.793 45.833 0.00 0.00 0.00 3.69
2358 2402 1.159285 GTACAGCTTGTGATGCAGCA 58.841 50.000 0.00 0.00 31.91 4.41
2665 2718 3.258971 GCATCAGCATATACTCCCTCC 57.741 52.381 0.00 0.00 41.58 4.30
2666 2719 2.417924 GCATCAGCATATACTCCCTCCG 60.418 54.545 0.00 0.00 41.58 4.63
2667 2720 2.677542 TCAGCATATACTCCCTCCGT 57.322 50.000 0.00 0.00 0.00 4.69
2668 2721 2.958818 TCAGCATATACTCCCTCCGTT 58.041 47.619 0.00 0.00 0.00 4.44
2669 2722 2.891580 TCAGCATATACTCCCTCCGTTC 59.108 50.000 0.00 0.00 0.00 3.95
2670 2723 2.028930 CAGCATATACTCCCTCCGTTCC 60.029 54.545 0.00 0.00 0.00 3.62
2671 2724 2.158295 AGCATATACTCCCTCCGTTCCT 60.158 50.000 0.00 0.00 0.00 3.36
2672 2725 3.075582 AGCATATACTCCCTCCGTTCCTA 59.924 47.826 0.00 0.00 0.00 2.94
2673 2726 3.830755 GCATATACTCCCTCCGTTCCTAA 59.169 47.826 0.00 0.00 0.00 2.69
2674 2727 4.282703 GCATATACTCCCTCCGTTCCTAAA 59.717 45.833 0.00 0.00 0.00 1.85
2675 2728 5.046520 GCATATACTCCCTCCGTTCCTAAAT 60.047 44.000 0.00 0.00 0.00 1.40
2676 2729 6.154021 GCATATACTCCCTCCGTTCCTAAATA 59.846 42.308 0.00 0.00 0.00 1.40
2677 2730 7.147707 GCATATACTCCCTCCGTTCCTAAATAT 60.148 40.741 0.00 0.00 0.00 1.28
2678 2731 9.417561 CATATACTCCCTCCGTTCCTAAATATA 57.582 37.037 0.00 0.00 0.00 0.86
2680 2733 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2681 2734 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2682 2735 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2683 2736 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2684 2737 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2685 2738 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2686 2739 8.645110 CCCTCCGTTCCTAAATATAAGTCTTTA 58.355 37.037 0.00 0.00 0.00 1.85
2705 2758 8.371699 AGTCTTTATAGAGATTTCACTATGGGC 58.628 37.037 7.52 1.65 33.08 5.36
2706 2759 7.604545 GTCTTTATAGAGATTTCACTATGGGCC 59.395 40.741 0.00 0.00 33.08 5.80
2707 2760 7.292356 TCTTTATAGAGATTTCACTATGGGCCA 59.708 37.037 9.61 9.61 33.08 5.36
2708 2761 3.567478 AGAGATTTCACTATGGGCCAC 57.433 47.619 9.28 0.00 0.00 5.01
2709 2762 2.158900 AGAGATTTCACTATGGGCCACG 60.159 50.000 9.28 5.60 0.00 4.94
2710 2763 1.559682 AGATTTCACTATGGGCCACGT 59.440 47.619 9.28 6.39 0.00 4.49
2711 2764 2.769663 AGATTTCACTATGGGCCACGTA 59.230 45.455 9.28 0.00 0.00 3.57
2712 2765 2.389962 TTTCACTATGGGCCACGTAC 57.610 50.000 9.28 0.00 0.00 3.67
2713 2766 1.268066 TTCACTATGGGCCACGTACA 58.732 50.000 9.28 0.00 0.00 2.90
2714 2767 1.268066 TCACTATGGGCCACGTACAA 58.732 50.000 9.28 0.00 0.00 2.41
2715 2768 1.624312 TCACTATGGGCCACGTACAAA 59.376 47.619 9.28 0.00 0.00 2.83
2716 2769 2.237643 TCACTATGGGCCACGTACAAAT 59.762 45.455 9.28 0.00 0.00 2.32
2717 2770 2.354510 CACTATGGGCCACGTACAAATG 59.645 50.000 9.28 0.00 0.00 2.32
2718 2771 2.026636 ACTATGGGCCACGTACAAATGT 60.027 45.455 9.28 0.00 0.00 2.71
2719 2772 2.791347 ATGGGCCACGTACAAATGTA 57.209 45.000 9.28 0.00 0.00 2.29
2720 2773 2.791347 TGGGCCACGTACAAATGTAT 57.209 45.000 0.00 0.00 32.54 2.29
2721 2774 3.908643 TGGGCCACGTACAAATGTATA 57.091 42.857 0.00 0.00 32.54 1.47
2722 2775 4.425180 TGGGCCACGTACAAATGTATAT 57.575 40.909 0.00 0.00 32.54 0.86
2723 2776 5.548181 TGGGCCACGTACAAATGTATATA 57.452 39.130 0.00 0.00 32.54 0.86
2724 2777 5.543714 TGGGCCACGTACAAATGTATATAG 58.456 41.667 0.00 0.00 32.54 1.31
2725 2778 5.304871 TGGGCCACGTACAAATGTATATAGA 59.695 40.000 0.00 0.00 32.54 1.98
2726 2779 6.014070 TGGGCCACGTACAAATGTATATAGAT 60.014 38.462 0.00 0.00 32.54 1.98
2727 2780 6.312918 GGGCCACGTACAAATGTATATAGATG 59.687 42.308 4.39 0.00 32.54 2.90
2728 2781 6.183360 GGCCACGTACAAATGTATATAGATGC 60.183 42.308 0.00 0.00 32.54 3.91
2729 2782 6.367695 GCCACGTACAAATGTATATAGATGCA 59.632 38.462 0.00 0.00 32.54 3.96
2730 2783 7.064609 GCCACGTACAAATGTATATAGATGCAT 59.935 37.037 0.00 0.00 39.80 3.96
2731 2784 8.935844 CCACGTACAAATGTATATAGATGCATT 58.064 33.333 7.72 7.72 46.62 3.56
2748 2801 8.798859 AGATGCATTTTAGAGTGTAGTTCATT 57.201 30.769 0.00 0.00 0.00 2.57
2749 2802 8.887717 AGATGCATTTTAGAGTGTAGTTCATTC 58.112 33.333 0.00 0.00 33.75 2.67
2750 2803 7.977789 TGCATTTTAGAGTGTAGTTCATTCA 57.022 32.000 0.00 0.00 35.62 2.57
2751 2804 7.806690 TGCATTTTAGAGTGTAGTTCATTCAC 58.193 34.615 0.00 0.00 35.62 3.18
2752 2805 7.661437 TGCATTTTAGAGTGTAGTTCATTCACT 59.339 33.333 0.00 0.00 43.72 3.41
2753 2806 8.507249 GCATTTTAGAGTGTAGTTCATTCACTT 58.493 33.333 0.00 0.00 41.58 3.16
2759 2812 8.819643 AGAGTGTAGTTCATTCACTTTACTTC 57.180 34.615 0.00 0.00 41.58 3.01
2760 2813 7.595502 AGAGTGTAGTTCATTCACTTTACTTCG 59.404 37.037 0.00 0.00 41.58 3.79
2761 2814 7.208080 AGTGTAGTTCATTCACTTTACTTCGT 58.792 34.615 0.00 0.00 39.00 3.85
2762 2815 8.355169 AGTGTAGTTCATTCACTTTACTTCGTA 58.645 33.333 0.00 0.00 39.00 3.43
2763 2816 9.136952 GTGTAGTTCATTCACTTTACTTCGTAT 57.863 33.333 0.00 0.00 0.00 3.06
2764 2817 9.135843 TGTAGTTCATTCACTTTACTTCGTATG 57.864 33.333 0.00 0.00 0.00 2.39
2765 2818 9.136952 GTAGTTCATTCACTTTACTTCGTATGT 57.863 33.333 0.00 0.00 0.00 2.29
2766 2819 8.018677 AGTTCATTCACTTTACTTCGTATGTG 57.981 34.615 0.00 0.00 0.00 3.21
2767 2820 6.961359 TCATTCACTTTACTTCGTATGTGG 57.039 37.500 0.00 0.00 0.00 4.17
2768 2821 6.460781 TCATTCACTTTACTTCGTATGTGGT 58.539 36.000 0.00 0.00 0.00 4.16
2769 2822 6.588756 TCATTCACTTTACTTCGTATGTGGTC 59.411 38.462 0.00 0.00 0.00 4.02
2770 2823 4.813027 TCACTTTACTTCGTATGTGGTCC 58.187 43.478 0.00 0.00 0.00 4.46
2771 2824 4.281435 TCACTTTACTTCGTATGTGGTCCA 59.719 41.667 0.00 0.00 0.00 4.02
2772 2825 5.046878 TCACTTTACTTCGTATGTGGTCCAT 60.047 40.000 0.00 0.00 37.58 3.41
2773 2826 6.153170 TCACTTTACTTCGTATGTGGTCCATA 59.847 38.462 0.00 0.00 34.86 2.74
2774 2827 6.475727 CACTTTACTTCGTATGTGGTCCATAG 59.524 42.308 0.00 0.00 36.71 2.23
2775 2828 6.154021 ACTTTACTTCGTATGTGGTCCATAGT 59.846 38.462 0.00 0.00 36.71 2.12
2776 2829 4.386867 ACTTCGTATGTGGTCCATAGTG 57.613 45.455 0.00 0.00 36.71 2.74
2777 2830 4.021229 ACTTCGTATGTGGTCCATAGTGA 58.979 43.478 0.00 0.00 36.71 3.41
2778 2831 4.464951 ACTTCGTATGTGGTCCATAGTGAA 59.535 41.667 0.00 0.00 36.71 3.18
2779 2832 5.046878 ACTTCGTATGTGGTCCATAGTGAAA 60.047 40.000 0.00 0.00 36.71 2.69
2780 2833 5.607939 TCGTATGTGGTCCATAGTGAAAT 57.392 39.130 0.00 0.00 36.71 2.17
2781 2834 5.356426 TCGTATGTGGTCCATAGTGAAATG 58.644 41.667 0.00 0.00 36.71 2.32
2782 2835 5.105106 TCGTATGTGGTCCATAGTGAAATGT 60.105 40.000 0.00 0.00 36.71 2.71
2783 2836 5.234329 CGTATGTGGTCCATAGTGAAATGTC 59.766 44.000 0.00 0.00 36.71 3.06
2784 2837 4.908601 TGTGGTCCATAGTGAAATGTCT 57.091 40.909 0.00 0.00 0.00 3.41
2785 2838 5.241403 TGTGGTCCATAGTGAAATGTCTT 57.759 39.130 0.00 0.00 0.00 3.01
2786 2839 5.245531 TGTGGTCCATAGTGAAATGTCTTC 58.754 41.667 0.00 0.00 0.00 2.87
2787 2840 5.221823 TGTGGTCCATAGTGAAATGTCTTCA 60.222 40.000 0.00 0.00 0.00 3.02
2788 2841 5.705441 GTGGTCCATAGTGAAATGTCTTCAA 59.295 40.000 0.00 0.00 0.00 2.69
2789 2842 6.206634 GTGGTCCATAGTGAAATGTCTTCAAA 59.793 38.462 0.00 0.00 0.00 2.69
2790 2843 6.430925 TGGTCCATAGTGAAATGTCTTCAAAG 59.569 38.462 0.00 0.00 0.00 2.77
2791 2844 6.655003 GGTCCATAGTGAAATGTCTTCAAAGA 59.345 38.462 0.00 0.00 0.00 2.52
2808 2861 9.595823 TCTTCAAAGACTTATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2809 2862 9.595823 CTTCAAAGACTTATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2810 2863 9.595823 TTCAAAGACTTATATTTAGGAACGGAG 57.404 33.333 0.00 0.00 0.00 4.63
2811 2864 8.202137 TCAAAGACTTATATTTAGGAACGGAGG 58.798 37.037 0.00 0.00 0.00 4.30
2812 2865 7.909485 AAGACTTATATTTAGGAACGGAGGA 57.091 36.000 0.00 0.00 0.00 3.71
2813 2866 7.909485 AGACTTATATTTAGGAACGGAGGAA 57.091 36.000 0.00 0.00 0.00 3.36
2814 2867 7.953752 AGACTTATATTTAGGAACGGAGGAAG 58.046 38.462 0.00 0.00 0.00 3.46
2815 2868 7.564292 AGACTTATATTTAGGAACGGAGGAAGT 59.436 37.037 0.00 0.00 0.00 3.01
2816 2869 8.773033 ACTTATATTTAGGAACGGAGGAAGTA 57.227 34.615 0.00 0.00 0.00 2.24
2817 2870 9.377238 ACTTATATTTAGGAACGGAGGAAGTAT 57.623 33.333 0.00 0.00 0.00 2.12
2823 2876 9.916360 ATTTAGGAACGGAGGAAGTATATTTTT 57.084 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.812160 GGTGCTATATGGTGCAACTATAGTAC 59.188 42.308 24.49 24.49 43.72 2.73
3 4 5.793817 TGGTGCTATATGGTGCAACTATAG 58.206 41.667 17.24 17.24 43.72 1.31
4 5 5.816955 TGGTGCTATATGGTGCAACTATA 57.183 39.130 2.04 0.00 46.08 1.31
5 6 4.705110 TGGTGCTATATGGTGCAACTAT 57.295 40.909 2.04 1.05 46.08 2.12
6 7 4.495690 TTGGTGCTATATGGTGCAACTA 57.504 40.909 2.04 6.18 46.08 2.24
7 8 3.364460 TTGGTGCTATATGGTGCAACT 57.636 42.857 2.04 0.00 46.08 3.16
8 9 3.443681 ACTTTGGTGCTATATGGTGCAAC 59.556 43.478 0.00 0.00 46.10 4.17
9 10 3.696045 ACTTTGGTGCTATATGGTGCAA 58.304 40.909 0.00 0.00 41.10 4.08
10 11 3.364460 ACTTTGGTGCTATATGGTGCA 57.636 42.857 0.00 0.00 36.79 4.57
11 12 4.261197 GCTAACTTTGGTGCTATATGGTGC 60.261 45.833 0.00 0.00 0.00 5.01
12 13 4.881273 TGCTAACTTTGGTGCTATATGGTG 59.119 41.667 0.00 0.00 0.00 4.17
13 14 5.110814 TGCTAACTTTGGTGCTATATGGT 57.889 39.130 0.00 0.00 0.00 3.55
14 15 5.764686 TGATGCTAACTTTGGTGCTATATGG 59.235 40.000 0.00 0.00 0.00 2.74
15 16 6.866010 TGATGCTAACTTTGGTGCTATATG 57.134 37.500 0.00 0.00 0.00 1.78
16 17 7.880160 TTTGATGCTAACTTTGGTGCTATAT 57.120 32.000 0.00 0.00 0.00 0.86
17 18 7.695480 TTTTGATGCTAACTTTGGTGCTATA 57.305 32.000 0.00 0.00 0.00 1.31
18 19 6.588719 TTTTGATGCTAACTTTGGTGCTAT 57.411 33.333 0.00 0.00 0.00 2.97
19 20 6.398234 TTTTTGATGCTAACTTTGGTGCTA 57.602 33.333 0.00 0.00 0.00 3.49
20 21 4.935352 TTTTGATGCTAACTTTGGTGCT 57.065 36.364 0.00 0.00 0.00 4.40
41 42 5.692613 TGGGTATGTTTCGACGAATTTTT 57.307 34.783 11.71 0.03 0.00 1.94
42 43 5.890424 ATGGGTATGTTTCGACGAATTTT 57.110 34.783 11.71 1.80 0.00 1.82
43 44 6.017440 CCATATGGGTATGTTTCGACGAATTT 60.017 38.462 14.52 2.15 36.72 1.82
44 45 5.468746 CCATATGGGTATGTTTCGACGAATT 59.531 40.000 14.52 2.51 36.72 2.17
45 46 4.994852 CCATATGGGTATGTTTCGACGAAT 59.005 41.667 14.52 0.00 36.72 3.34
46 47 4.373527 CCATATGGGTATGTTTCGACGAA 58.626 43.478 14.52 6.10 36.72 3.85
47 48 3.985008 CCATATGGGTATGTTTCGACGA 58.015 45.455 14.52 0.00 36.72 4.20
61 62 6.346477 TCTTCGAAACTAGATCCCATATGG 57.654 41.667 15.41 15.41 0.00 2.74
62 63 7.835822 AGATCTTCGAAACTAGATCCCATATG 58.164 38.462 17.33 0.00 45.05 1.78
63 64 8.062065 GAGATCTTCGAAACTAGATCCCATAT 57.938 38.462 17.33 3.20 45.05 1.78
64 65 7.455641 GAGATCTTCGAAACTAGATCCCATA 57.544 40.000 17.33 0.00 45.05 2.74
65 66 6.339587 GAGATCTTCGAAACTAGATCCCAT 57.660 41.667 17.33 3.79 45.05 4.00
66 67 5.776173 GAGATCTTCGAAACTAGATCCCA 57.224 43.478 17.33 0.00 45.05 4.37
89 90 2.664436 CCTTTGGGTTCGTCGCGAC 61.664 63.158 28.96 28.96 34.89 5.19
90 91 2.356553 CCTTTGGGTTCGTCGCGA 60.357 61.111 3.71 3.71 0.00 5.87
91 92 2.663852 ACCTTTGGGTTCGTCGCG 60.664 61.111 0.00 0.00 44.73 5.87
92 93 1.161563 TTCACCTTTGGGTTCGTCGC 61.162 55.000 0.00 0.00 44.73 5.19
93 94 1.301423 TTTCACCTTTGGGTTCGTCG 58.699 50.000 0.00 0.00 44.73 5.12
94 95 2.540157 CGTTTTCACCTTTGGGTTCGTC 60.540 50.000 0.00 0.00 44.73 4.20
95 96 1.402613 CGTTTTCACCTTTGGGTTCGT 59.597 47.619 0.00 0.00 44.73 3.85
96 97 1.268845 CCGTTTTCACCTTTGGGTTCG 60.269 52.381 0.00 0.00 44.73 3.95
97 98 2.025898 TCCGTTTTCACCTTTGGGTTC 58.974 47.619 0.00 0.00 44.73 3.62
98 99 2.146920 TCCGTTTTCACCTTTGGGTT 57.853 45.000 0.00 0.00 44.73 4.11
100 101 2.228822 CAGATCCGTTTTCACCTTTGGG 59.771 50.000 0.00 0.00 38.88 4.12
101 102 3.146066 TCAGATCCGTTTTCACCTTTGG 58.854 45.455 0.00 0.00 0.00 3.28
102 103 4.829064 TTCAGATCCGTTTTCACCTTTG 57.171 40.909 0.00 0.00 0.00 2.77
103 104 5.048013 GGAATTCAGATCCGTTTTCACCTTT 60.048 40.000 7.93 0.00 0.00 3.11
104 105 4.459337 GGAATTCAGATCCGTTTTCACCTT 59.541 41.667 7.93 0.00 0.00 3.50
105 106 4.010349 GGAATTCAGATCCGTTTTCACCT 58.990 43.478 7.93 0.00 0.00 4.00
106 107 3.756434 TGGAATTCAGATCCGTTTTCACC 59.244 43.478 7.93 0.00 39.98 4.02
107 108 5.154222 GTTGGAATTCAGATCCGTTTTCAC 58.846 41.667 7.93 0.00 39.98 3.18
108 109 4.824537 TGTTGGAATTCAGATCCGTTTTCA 59.175 37.500 7.93 0.00 39.98 2.69
109 110 5.371115 TGTTGGAATTCAGATCCGTTTTC 57.629 39.130 7.93 0.00 39.98 2.29
110 111 5.243730 ACATGTTGGAATTCAGATCCGTTTT 59.756 36.000 7.93 0.00 39.98 2.43
111 112 4.766891 ACATGTTGGAATTCAGATCCGTTT 59.233 37.500 7.93 0.00 39.98 3.60
112 113 4.156556 CACATGTTGGAATTCAGATCCGTT 59.843 41.667 7.93 0.00 39.98 4.44
113 114 3.691118 CACATGTTGGAATTCAGATCCGT 59.309 43.478 7.93 0.00 39.98 4.69
114 115 4.282950 CACATGTTGGAATTCAGATCCG 57.717 45.455 7.93 0.00 39.98 4.18
127 128 9.912634 AAGTCATATCTTTTAAACCACATGTTG 57.087 29.630 0.00 0.00 37.23 3.33
164 165 9.872757 GTGAAACACATTTATTTTCGTCTCTTA 57.127 29.630 0.00 0.00 36.32 2.10
165 166 7.586300 CGTGAAACACATTTATTTTCGTCTCTT 59.414 33.333 0.00 0.00 35.74 2.85
166 167 7.069569 CGTGAAACACATTTATTTTCGTCTCT 58.930 34.615 0.00 0.00 35.74 3.10
167 168 6.302313 CCGTGAAACACATTTATTTTCGTCTC 59.698 38.462 0.00 0.00 35.74 3.36
168 169 6.017770 TCCGTGAAACACATTTATTTTCGTCT 60.018 34.615 0.00 0.00 35.74 4.18
169 170 6.085849 GTCCGTGAAACACATTTATTTTCGTC 59.914 38.462 0.00 0.00 35.74 4.20
170 171 5.910723 GTCCGTGAAACACATTTATTTTCGT 59.089 36.000 0.00 0.00 35.74 3.85
171 172 5.341196 GGTCCGTGAAACACATTTATTTTCG 59.659 40.000 0.00 0.00 35.74 3.46
172 173 6.210078 TGGTCCGTGAAACACATTTATTTTC 58.790 36.000 0.00 0.00 35.74 2.29
173 174 6.150396 TGGTCCGTGAAACACATTTATTTT 57.850 33.333 0.00 0.00 35.74 1.82
174 175 5.300792 ACTGGTCCGTGAAACACATTTATTT 59.699 36.000 0.00 0.00 35.74 1.40
175 176 4.825085 ACTGGTCCGTGAAACACATTTATT 59.175 37.500 0.00 0.00 35.74 1.40
176 177 4.394729 ACTGGTCCGTGAAACACATTTAT 58.605 39.130 0.00 0.00 35.74 1.40
177 178 3.810941 GACTGGTCCGTGAAACACATTTA 59.189 43.478 0.00 0.00 35.74 1.40
178 179 2.616842 GACTGGTCCGTGAAACACATTT 59.383 45.455 0.00 0.00 35.74 2.32
179 180 2.158813 AGACTGGTCCGTGAAACACATT 60.159 45.455 0.00 0.00 35.74 2.71
180 181 1.416401 AGACTGGTCCGTGAAACACAT 59.584 47.619 0.00 0.00 35.74 3.21
181 182 0.828022 AGACTGGTCCGTGAAACACA 59.172 50.000 0.00 0.00 35.74 3.72
182 183 1.217882 CAGACTGGTCCGTGAAACAC 58.782 55.000 0.00 0.00 35.74 3.32
183 184 0.828022 ACAGACTGGTCCGTGAAACA 59.172 50.000 7.51 0.00 35.74 2.83
184 185 2.401351 GTACAGACTGGTCCGTGAAAC 58.599 52.381 7.51 0.00 0.00 2.78
185 186 1.001048 CGTACAGACTGGTCCGTGAAA 60.001 52.381 7.51 0.00 0.00 2.69
186 187 0.594602 CGTACAGACTGGTCCGTGAA 59.405 55.000 7.51 0.00 0.00 3.18
187 188 1.859427 GCGTACAGACTGGTCCGTGA 61.859 60.000 7.51 0.00 0.00 4.35
188 189 1.443872 GCGTACAGACTGGTCCGTG 60.444 63.158 7.51 0.00 0.00 4.94
189 190 1.248785 ATGCGTACAGACTGGTCCGT 61.249 55.000 7.51 0.00 0.00 4.69
190 191 0.108804 AATGCGTACAGACTGGTCCG 60.109 55.000 7.51 6.84 0.00 4.79
191 192 1.732259 CAAATGCGTACAGACTGGTCC 59.268 52.381 7.51 0.00 0.00 4.46
192 193 1.128692 GCAAATGCGTACAGACTGGTC 59.871 52.381 7.51 0.00 0.00 4.02
193 194 1.156736 GCAAATGCGTACAGACTGGT 58.843 50.000 7.51 0.00 0.00 4.00
194 195 3.975992 GCAAATGCGTACAGACTGG 57.024 52.632 7.51 0.00 0.00 4.00
237 238 9.349713 TGTCTTTTTCTGTTAGTTAATGGATGT 57.650 29.630 0.00 0.00 0.00 3.06
238 239 9.612620 GTGTCTTTTTCTGTTAGTTAATGGATG 57.387 33.333 0.00 0.00 0.00 3.51
239 240 9.349713 TGTGTCTTTTTCTGTTAGTTAATGGAT 57.650 29.630 0.00 0.00 0.00 3.41
240 241 8.617809 GTGTGTCTTTTTCTGTTAGTTAATGGA 58.382 33.333 0.00 0.00 0.00 3.41
241 242 8.402472 TGTGTGTCTTTTTCTGTTAGTTAATGG 58.598 33.333 0.00 0.00 0.00 3.16
242 243 9.781834 TTGTGTGTCTTTTTCTGTTAGTTAATG 57.218 29.630 0.00 0.00 0.00 1.90
246 247 9.391006 TCTATTGTGTGTCTTTTTCTGTTAGTT 57.609 29.630 0.00 0.00 0.00 2.24
247 248 8.958119 TCTATTGTGTGTCTTTTTCTGTTAGT 57.042 30.769 0.00 0.00 0.00 2.24
253 254 9.846248 GCAATTATCTATTGTGTGTCTTTTTCT 57.154 29.630 0.00 0.00 44.52 2.52
254 255 9.846248 AGCAATTATCTATTGTGTGTCTTTTTC 57.154 29.630 0.00 0.00 44.52 2.29
292 293 9.981114 CAAAATTACAAGTTTTGGTCCTCTAAT 57.019 29.630 3.98 0.00 40.88 1.73
302 303 3.496507 CCGGCCCAAAATTACAAGTTTTG 59.503 43.478 0.00 4.76 43.00 2.44
303 304 3.734463 CCGGCCCAAAATTACAAGTTTT 58.266 40.909 0.00 0.00 0.00 2.43
304 305 2.549134 GCCGGCCCAAAATTACAAGTTT 60.549 45.455 18.11 0.00 0.00 2.66
305 306 1.001520 GCCGGCCCAAAATTACAAGTT 59.998 47.619 18.11 0.00 0.00 2.66
306 307 0.606096 GCCGGCCCAAAATTACAAGT 59.394 50.000 18.11 0.00 0.00 3.16
307 308 0.108377 GGCCGGCCCAAAATTACAAG 60.108 55.000 36.64 0.00 0.00 3.16
308 309 1.878656 CGGCCGGCCCAAAATTACAA 61.879 55.000 39.24 0.00 0.00 2.41
309 310 2.344203 CGGCCGGCCCAAAATTACA 61.344 57.895 39.24 0.00 0.00 2.41
310 311 2.492560 CGGCCGGCCCAAAATTAC 59.507 61.111 39.24 11.89 0.00 1.89
311 312 3.453679 GCGGCCGGCCCAAAATTA 61.454 61.111 39.24 0.00 34.80 1.40
321 322 2.964438 TATACTTTGCGAGCGGCCGG 62.964 60.000 29.38 11.90 42.61 6.13
322 323 1.548973 CTATACTTTGCGAGCGGCCG 61.549 60.000 24.05 24.05 42.61 6.13
323 324 0.529992 ACTATACTTTGCGAGCGGCC 60.530 55.000 0.00 0.00 42.61 6.13
324 325 0.577269 CACTATACTTTGCGAGCGGC 59.423 55.000 0.00 0.00 43.96 6.53
325 326 2.120232 CTCACTATACTTTGCGAGCGG 58.880 52.381 0.00 0.00 0.00 5.52
326 327 1.518929 GCTCACTATACTTTGCGAGCG 59.481 52.381 0.00 0.00 36.84 5.03
327 328 2.537625 CTGCTCACTATACTTTGCGAGC 59.462 50.000 0.00 0.00 44.75 5.03
328 329 2.537625 GCTGCTCACTATACTTTGCGAG 59.462 50.000 0.00 0.00 0.00 5.03
329 330 2.540515 GCTGCTCACTATACTTTGCGA 58.459 47.619 0.00 0.00 0.00 5.10
330 331 1.594862 GGCTGCTCACTATACTTTGCG 59.405 52.381 0.00 0.00 0.00 4.85
331 332 1.594862 CGGCTGCTCACTATACTTTGC 59.405 52.381 0.00 0.00 0.00 3.68
332 333 2.205074 CCGGCTGCTCACTATACTTTG 58.795 52.381 0.00 0.00 0.00 2.77
333 334 1.473434 GCCGGCTGCTCACTATACTTT 60.473 52.381 22.15 0.00 36.87 2.66
334 335 0.105039 GCCGGCTGCTCACTATACTT 59.895 55.000 22.15 0.00 36.87 2.24
335 336 1.742768 GCCGGCTGCTCACTATACT 59.257 57.895 22.15 0.00 36.87 2.12
336 337 1.301009 GGCCGGCTGCTCACTATAC 60.301 63.158 28.56 0.00 40.92 1.47
337 338 2.856628 CGGCCGGCTGCTCACTATA 61.857 63.158 28.56 0.00 40.92 1.31
338 339 4.227134 CGGCCGGCTGCTCACTAT 62.227 66.667 28.56 0.00 40.92 2.12
355 356 2.221906 TTTGGACCGGTCTAGCGAGC 62.222 60.000 32.52 15.47 0.00 5.03
356 357 0.245539 TTTTGGACCGGTCTAGCGAG 59.754 55.000 32.52 0.00 0.00 5.03
357 358 0.899720 ATTTTGGACCGGTCTAGCGA 59.100 50.000 32.52 16.90 0.00 4.93
358 359 2.589798 TATTTTGGACCGGTCTAGCG 57.410 50.000 32.52 0.00 0.00 4.26
359 360 6.258068 GCATATATATTTTGGACCGGTCTAGC 59.742 42.308 32.52 18.37 0.00 3.42
360 361 7.277981 GTGCATATATATTTTGGACCGGTCTAG 59.722 40.741 32.52 12.71 0.00 2.43
361 362 7.101054 GTGCATATATATTTTGGACCGGTCTA 58.899 38.462 32.52 25.88 0.00 2.59
362 363 5.938125 GTGCATATATATTTTGGACCGGTCT 59.062 40.000 32.52 16.13 0.00 3.85
363 364 5.703592 TGTGCATATATATTTTGGACCGGTC 59.296 40.000 27.04 27.04 31.50 4.79
364 365 5.472137 GTGTGCATATATATTTTGGACCGGT 59.528 40.000 6.92 6.92 31.50 5.28
365 366 5.471797 TGTGTGCATATATATTTTGGACCGG 59.528 40.000 0.00 0.00 31.50 5.28
366 367 6.552859 TGTGTGCATATATATTTTGGACCG 57.447 37.500 13.68 0.00 31.50 4.79
376 377 9.915629 TGTTGTACGATTATGTGTGCATATATA 57.084 29.630 0.00 0.00 37.42 0.86
377 378 8.825667 TGTTGTACGATTATGTGTGCATATAT 57.174 30.769 0.00 0.00 37.42 0.86
378 379 8.649973 TTGTTGTACGATTATGTGTGCATATA 57.350 30.769 0.00 0.00 37.42 0.86
379 380 7.546778 TTGTTGTACGATTATGTGTGCATAT 57.453 32.000 0.00 0.00 37.42 1.78
380 381 6.969828 TTGTTGTACGATTATGTGTGCATA 57.030 33.333 0.00 0.00 36.58 3.14
381 382 5.871465 TTGTTGTACGATTATGTGTGCAT 57.129 34.783 0.00 0.00 39.03 3.96
382 383 5.674933 TTTGTTGTACGATTATGTGTGCA 57.325 34.783 0.00 0.00 0.00 4.57
383 384 6.310960 TCATTTGTTGTACGATTATGTGTGC 58.689 36.000 0.00 0.00 0.00 4.57
396 397 2.524306 CCAAGGGGCTCATTTGTTGTA 58.476 47.619 0.00 0.00 0.00 2.41
474 475 1.971695 GACCCTCCACCGCTTTTGG 60.972 63.158 0.00 0.00 35.18 3.28
501 510 4.510038 AAATAAATCGCTCCATGCATCC 57.490 40.909 0.00 0.00 43.06 3.51
503 512 5.521010 CACAAAAATAAATCGCTCCATGCAT 59.479 36.000 0.00 0.00 43.06 3.96
555 565 1.481056 AACCTTGTGACCTCCCTCGG 61.481 60.000 0.00 0.00 0.00 4.63
592 602 4.789075 CTGCCCACGTACGTCCGG 62.789 72.222 19.94 20.91 0.00 5.14
927 943 1.002773 GGGGCGGTGTATATAACCAGG 59.997 57.143 11.97 0.00 37.57 4.45
989 1010 1.833630 TCCCTCTCATACAACAGCCAG 59.166 52.381 0.00 0.00 0.00 4.85
993 1014 3.430098 GCTCACTCCCTCTCATACAACAG 60.430 52.174 0.00 0.00 0.00 3.16
1273 1297 5.279456 ACATATTCTGTACTGCCGATGCATA 60.279 40.000 0.00 0.00 41.13 3.14
1283 1307 7.672983 AAAGGTCAACACATATTCTGTACTG 57.327 36.000 0.00 0.00 35.91 2.74
1384 1408 1.375523 GCTCACCGGGTTGATCGTT 60.376 57.895 6.32 0.00 0.00 3.85
1525 1549 1.251527 ACAGATCGCTTCCACCGACT 61.252 55.000 0.00 0.00 37.56 4.18
1636 1660 4.954118 TCCTGGTGGTGGGACGCT 62.954 66.667 0.00 0.00 39.78 5.07
1863 1893 1.487452 CGCGCGGTACTACTACGGTA 61.487 60.000 24.84 0.00 0.00 4.02
1888 1918 3.497031 AGCGCGTCGATCGACTGA 61.497 61.111 37.12 8.42 42.54 3.41
2093 2127 4.305539 TGTAGTAGTAGTGGTGGTGCTA 57.694 45.455 0.00 0.00 0.00 3.49
2165 2201 1.226295 GGCAAACGCTAATCACGCC 60.226 57.895 0.00 0.00 0.00 5.68
2218 2258 0.747852 GGGAGAGTACTGTAGCCTGC 59.252 60.000 0.00 0.00 0.00 4.85
2254 2294 1.895798 ACACGGAAGAGCAGATCTCAA 59.104 47.619 0.00 0.00 44.35 3.02
2255 2295 1.550327 ACACGGAAGAGCAGATCTCA 58.450 50.000 0.00 0.00 44.35 3.27
2302 2342 0.039527 GGTGGCGTGAAACATTGACC 60.040 55.000 0.00 0.00 35.74 4.02
2358 2402 0.763652 CTATCTCAGCAGCCCCACAT 59.236 55.000 0.00 0.00 0.00 3.21
2658 2711 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2659 2712 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2660 2713 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2679 2732 8.371699 GCCCATAGTGAAATCTCTATAAAGACT 58.628 37.037 5.06 0.00 33.04 3.24
2680 2733 7.604545 GGCCCATAGTGAAATCTCTATAAAGAC 59.395 40.741 0.00 0.00 33.04 3.01
2681 2734 7.292356 TGGCCCATAGTGAAATCTCTATAAAGA 59.708 37.037 0.00 0.00 33.04 2.52
2682 2735 7.389053 GTGGCCCATAGTGAAATCTCTATAAAG 59.611 40.741 0.00 0.50 33.04 1.85
2683 2736 7.224297 GTGGCCCATAGTGAAATCTCTATAAA 58.776 38.462 0.00 0.00 33.04 1.40
2684 2737 6.518369 CGTGGCCCATAGTGAAATCTCTATAA 60.518 42.308 0.00 0.00 33.04 0.98
2685 2738 5.047306 CGTGGCCCATAGTGAAATCTCTATA 60.047 44.000 0.00 0.00 33.04 1.31
2686 2739 4.262635 CGTGGCCCATAGTGAAATCTCTAT 60.263 45.833 0.00 0.37 34.17 1.98
2687 2740 3.069586 CGTGGCCCATAGTGAAATCTCTA 59.930 47.826 0.00 0.00 0.00 2.43
2688 2741 2.158900 CGTGGCCCATAGTGAAATCTCT 60.159 50.000 0.00 0.00 0.00 3.10
2689 2742 2.213499 CGTGGCCCATAGTGAAATCTC 58.787 52.381 0.00 0.00 0.00 2.75
2690 2743 1.559682 ACGTGGCCCATAGTGAAATCT 59.440 47.619 0.00 0.00 0.00 2.40
2691 2744 2.038387 ACGTGGCCCATAGTGAAATC 57.962 50.000 0.00 0.00 0.00 2.17
2692 2745 2.237643 TGTACGTGGCCCATAGTGAAAT 59.762 45.455 0.00 0.00 0.00 2.17
2693 2746 1.624312 TGTACGTGGCCCATAGTGAAA 59.376 47.619 0.00 0.00 0.00 2.69
2694 2747 1.268066 TGTACGTGGCCCATAGTGAA 58.732 50.000 0.00 0.00 0.00 3.18
2695 2748 1.268066 TTGTACGTGGCCCATAGTGA 58.732 50.000 0.00 0.00 0.00 3.41
2696 2749 2.102070 TTTGTACGTGGCCCATAGTG 57.898 50.000 0.00 0.00 0.00 2.74
2697 2750 2.026636 ACATTTGTACGTGGCCCATAGT 60.027 45.455 0.00 0.00 0.00 2.12
2698 2751 2.639065 ACATTTGTACGTGGCCCATAG 58.361 47.619 0.00 0.00 0.00 2.23
2699 2752 2.791347 ACATTTGTACGTGGCCCATA 57.209 45.000 0.00 0.00 0.00 2.74
2700 2753 2.791347 TACATTTGTACGTGGCCCAT 57.209 45.000 0.00 0.00 0.00 4.00
2701 2754 2.791347 ATACATTTGTACGTGGCCCA 57.209 45.000 0.00 0.00 32.72 5.36
2702 2755 5.786311 TCTATATACATTTGTACGTGGCCC 58.214 41.667 0.00 0.00 32.72 5.80
2703 2756 6.183360 GCATCTATATACATTTGTACGTGGCC 60.183 42.308 0.00 0.00 32.72 5.36
2704 2757 6.367695 TGCATCTATATACATTTGTACGTGGC 59.632 38.462 0.00 0.00 32.72 5.01
2705 2758 7.883229 TGCATCTATATACATTTGTACGTGG 57.117 36.000 0.00 0.00 32.72 4.94
2722 2775 9.890629 AATGAACTACACTCTAAAATGCATCTA 57.109 29.630 0.00 0.00 0.00 1.98
2723 2776 8.798859 AATGAACTACACTCTAAAATGCATCT 57.201 30.769 0.00 0.00 0.00 2.90
2724 2777 8.668353 TGAATGAACTACACTCTAAAATGCATC 58.332 33.333 0.00 0.00 0.00 3.91
2725 2778 8.454106 GTGAATGAACTACACTCTAAAATGCAT 58.546 33.333 0.00 0.00 0.00 3.96
2726 2779 7.661437 AGTGAATGAACTACACTCTAAAATGCA 59.339 33.333 0.00 0.00 40.19 3.96
2727 2780 8.034058 AGTGAATGAACTACACTCTAAAATGC 57.966 34.615 0.00 0.00 40.19 3.56
2733 2786 9.909644 GAAGTAAAGTGAATGAACTACACTCTA 57.090 33.333 0.00 0.00 42.81 2.43
2734 2787 7.595502 CGAAGTAAAGTGAATGAACTACACTCT 59.404 37.037 0.00 0.00 42.81 3.24
2735 2788 7.381678 ACGAAGTAAAGTGAATGAACTACACTC 59.618 37.037 0.00 0.00 41.94 3.51
2736 2789 7.208080 ACGAAGTAAAGTGAATGAACTACACT 58.792 34.615 0.00 0.00 41.94 3.55
2737 2790 7.404139 ACGAAGTAAAGTGAATGAACTACAC 57.596 36.000 0.00 0.00 41.94 2.90
2756 2809 4.649088 TCACTATGGACCACATACGAAG 57.351 45.455 0.00 0.00 41.03 3.79
2757 2810 5.408880 TTTCACTATGGACCACATACGAA 57.591 39.130 0.00 0.00 41.03 3.85
2758 2811 5.105106 ACATTTCACTATGGACCACATACGA 60.105 40.000 0.00 0.00 41.03 3.43
2759 2812 5.116180 ACATTTCACTATGGACCACATACG 58.884 41.667 0.00 0.00 41.03 3.06
2760 2813 6.349300 AGACATTTCACTATGGACCACATAC 58.651 40.000 0.00 0.00 41.03 2.39
2761 2814 6.560003 AGACATTTCACTATGGACCACATA 57.440 37.500 0.00 0.00 41.03 2.29
2762 2815 5.441718 AGACATTTCACTATGGACCACAT 57.558 39.130 0.00 0.00 43.68 3.21
2763 2816 4.908601 AGACATTTCACTATGGACCACA 57.091 40.909 0.00 0.00 0.00 4.17
2764 2817 5.245531 TGAAGACATTTCACTATGGACCAC 58.754 41.667 0.00 0.00 0.00 4.16
2765 2818 5.497464 TGAAGACATTTCACTATGGACCA 57.503 39.130 0.00 0.00 0.00 4.02
2766 2819 6.655003 TCTTTGAAGACATTTCACTATGGACC 59.345 38.462 0.00 0.00 0.00 4.46
2767 2820 7.672983 TCTTTGAAGACATTTCACTATGGAC 57.327 36.000 0.00 0.00 0.00 4.02
2782 2835 9.595823 CCGTTCCTAAATATAAGTCTTTGAAGA 57.404 33.333 0.00 0.00 0.00 2.87
2783 2836 9.595823 TCCGTTCCTAAATATAAGTCTTTGAAG 57.404 33.333 0.00 0.00 0.00 3.02
2784 2837 9.595823 CTCCGTTCCTAAATATAAGTCTTTGAA 57.404 33.333 0.00 0.00 0.00 2.69
2785 2838 8.202137 CCTCCGTTCCTAAATATAAGTCTTTGA 58.798 37.037 0.00 0.00 0.00 2.69
2786 2839 8.202137 TCCTCCGTTCCTAAATATAAGTCTTTG 58.798 37.037 0.00 0.00 0.00 2.77
2787 2840 8.315220 TCCTCCGTTCCTAAATATAAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
2788 2841 7.909485 TCCTCCGTTCCTAAATATAAGTCTT 57.091 36.000 0.00 0.00 0.00 3.01
2789 2842 7.564292 ACTTCCTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
2790 2843 7.724287 ACTTCCTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
2791 2844 7.672122 ACTTCCTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
2797 2850 9.916360 AAAAATATACTTCCTCCGTTCCTAAAT 57.084 29.630 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.