Multiple sequence alignment - TraesCS2A01G341300

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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 TraesCS2A01G341300 chr2A 100.000 3287 0 0 1 3287 577214625 577211339 0.000000e+00 6071.0
1 TraesCS2A01G341300 chr2A 91.031 223 14 3 216 435 16064437 16064218 2.480000e-76 296.0
2 TraesCS2A01G341300 chr2A 90.667 225 13 5 213 437 519404004 519403788 3.210000e-75 292.0
3 TraesCS2A01G341300 chr2A 89.177 231 16 5 213 442 35678509 35678287 2.500000e-71 279.0
4 TraesCS2A01G341300 chr2A 85.821 134 17 2 554 686 135473364 135473232 1.230000e-29 141.0
5 TraesCS2A01G341300 chr2A 88.136 59 4 3 2420 2475 757995686 757995628 2.120000e-07 67.6
6 TraesCS2A01G341300 chr2B 95.656 2302 82 9 969 3258 484490637 484492932 0.000000e+00 3681.0
7 TraesCS2A01G341300 chr2B 92.105 532 32 5 437 967 484490050 484490572 0.000000e+00 741.0
8 TraesCS2A01G341300 chr2B 86.364 132 17 1 556 686 608226860 608226729 3.420000e-30 143.0
9 TraesCS2A01G341300 chr2D 95.855 2099 73 4 969 3056 409284629 409282534 0.000000e+00 3382.0
10 TraesCS2A01G341300 chr2D 93.494 538 33 2 437 973 409285224 409284688 0.000000e+00 798.0
11 TraesCS2A01G341300 chr2D 91.364 220 12 3 216 435 449513513 449513301 8.920000e-76 294.0
12 TraesCS2A01G341300 chr2D 94.211 190 10 1 3097 3286 409282537 409282349 4.150000e-74 289.0
13 TraesCS2A01G341300 chr2D 87.264 212 25 2 1 211 8146453 8146243 1.180000e-59 241.0
14 TraesCS2A01G341300 chr2D 86.364 132 16 2 556 686 373883461 373883591 3.420000e-30 143.0
15 TraesCS2A01G341300 chr6D 91.441 222 15 2 217 435 472448997 472448777 5.330000e-78 302.0
16 TraesCS2A01G341300 chr6D 86.070 201 26 2 2 201 38134076 38133877 7.140000e-52 215.0
17 TraesCS2A01G341300 chr6D 89.091 55 3 2 2426 2478 84476211 84476158 7.610000e-07 65.8
18 TraesCS2A01G341300 chr6A 91.071 224 16 4 212 435 141298548 141298329 1.920000e-77 300.0
19 TraesCS2A01G341300 chr6A 86.893 206 25 2 1 205 596907366 596907162 2.550000e-56 230.0
20 TraesCS2A01G341300 chr3A 91.324 219 8 6 217 435 184272625 184272418 4.150000e-74 289.0
21 TraesCS2A01G341300 chr3A 85.990 207 28 1 1 206 59534493 59534699 1.540000e-53 220.0
22 TraesCS2A01G341300 chr3A 93.617 47 0 3 2420 2463 691505942 691505896 2.120000e-07 67.6
23 TraesCS2A01G341300 chr3A 90.000 50 3 1 2426 2473 712702494 712702445 2.740000e-06 63.9
24 TraesCS2A01G341300 chr5A 90.498 221 16 4 217 437 693065144 693065359 1.490000e-73 287.0
25 TraesCS2A01G341300 chr5A 89.270 233 10 10 217 448 414976532 414976314 8.980000e-71 278.0
26 TraesCS2A01G341300 chr5A 85.922 206 27 2 2 206 440673197 440672993 5.520000e-53 219.0
27 TraesCS2A01G341300 chr5B 86.408 206 27 1 2 206 219821816 219821611 1.190000e-54 224.0
28 TraesCS2A01G341300 chr5B 86.466 133 14 4 557 686 129721809 129721940 3.420000e-30 143.0
29 TraesCS2A01G341300 chr7A 85.990 207 26 3 1 205 448120052 448120257 5.520000e-53 219.0
30 TraesCS2A01G341300 chr1D 85.922 206 27 2 2 205 45511672 45511877 5.520000e-53 219.0
31 TraesCS2A01G341300 chr1D 90.566 53 3 2 2424 2474 270036791 270036843 5.890000e-08 69.4
32 TraesCS2A01G341300 chr1D 93.023 43 1 2 2423 2463 431797899 431797941 9.850000e-06 62.1
33 TraesCS2A01G341300 chr1B 86.341 205 21 5 7 205 421088831 421088628 1.990000e-52 217.0
34 TraesCS2A01G341300 chr1B 86.667 135 10 7 2345 2475 49864499 49864629 3.420000e-30 143.0
35 TraesCS2A01G341300 chr1B 100.000 31 0 0 2426 2456 593053163 593053193 1.270000e-04 58.4
36 TraesCS2A01G341300 chr3D 86.567 134 16 2 554 686 128214143 128214011 2.640000e-31 147.0
37 TraesCS2A01G341300 chr3B 86.923 130 16 1 558 686 552226540 552226411 9.510000e-31 145.0
38 TraesCS2A01G341300 chr5D 86.364 132 17 1 556 686 291881901 291881770 3.420000e-30 143.0
39 TraesCS2A01G341300 chr7D 90.385 52 2 3 2424 2473 563516535 563516485 7.610000e-07 65.8
40 TraesCS2A01G341300 chr1A 90.000 50 4 1 2426 2474 375466733 375466782 2.740000e-06 63.9


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 TraesCS2A01G341300 chr2A 577211339 577214625 3286 True 6071.000000 6071 100.0000 1 3287 1 chr2A.!!$R5 3286
1 TraesCS2A01G341300 chr2B 484490050 484492932 2882 False 2211.000000 3681 93.8805 437 3258 2 chr2B.!!$F1 2821
2 TraesCS2A01G341300 chr2D 409282349 409285224 2875 True 1489.666667 3382 94.5200 437 3286 3 chr2D.!!$R3 2849

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
290 291 0.036022 TGGATGACACGTGGCATTCA 59.964 50.0 36.64 36.64 46.54 2.57 F
321 322 0.037447 GCATCTAATCTGCCCCTCCC 59.963 60.0 0.00 0.00 33.44 4.30 F
418 419 0.393132 TCTCGCGTGAGACCTGATCT 60.393 55.0 24.28 0.00 46.25 2.75 F
1813 1878 0.462789 ACAGGACGTTCGACTTGGTT 59.537 50.0 10.50 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1143 1208 0.100682 GAAGTCGCCGCACTCTATGA 59.899 55.0 0.00 0.0 0.00 2.15 R
1530 1595 0.393077 CTGGTTCTTCCACTGGTCGT 59.607 55.0 0.00 0.0 41.93 4.34 R
2131 2199 0.976073 TTGAGTCGTCCCATCCCTCC 60.976 60.0 0.00 0.0 0.00 4.30 R
3207 3288 0.318360 TCACGATGAAACTGTCGCGT 60.318 50.0 5.77 0.0 41.31 6.01 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
90 91 9.667500 GAAACTACATTTCGTAACGAATCTAAC 57.332 33.333 0.00 0.00 45.28 2.34
91 92 8.746922 AACTACATTTCGTAACGAATCTAACA 57.253 30.769 0.00 0.00 45.28 2.41
92 93 8.746922 ACTACATTTCGTAACGAATCTAACAA 57.253 30.769 0.00 0.00 45.28 2.83
93 94 9.362539 ACTACATTTCGTAACGAATCTAACAAT 57.637 29.630 0.00 0.00 45.28 2.71
105 106 8.902540 ACGAATCTAACAATAATGATTAGGCA 57.097 30.769 0.00 0.00 30.41 4.75
106 107 8.774586 ACGAATCTAACAATAATGATTAGGCAC 58.225 33.333 0.00 0.00 30.41 5.01
107 108 8.993121 CGAATCTAACAATAATGATTAGGCACT 58.007 33.333 0.00 0.00 46.37 4.40
109 110 9.632638 AATCTAACAATAATGATTAGGCACTGT 57.367 29.630 0.00 0.00 41.52 3.55
110 111 8.437360 TCTAACAATAATGATTAGGCACTGTG 57.563 34.615 2.76 2.76 41.52 3.66
111 112 8.264347 TCTAACAATAATGATTAGGCACTGTGA 58.736 33.333 12.86 0.00 41.52 3.58
112 113 7.701539 AACAATAATGATTAGGCACTGTGAA 57.298 32.000 12.86 0.00 41.52 3.18
113 114 7.886629 ACAATAATGATTAGGCACTGTGAAT 57.113 32.000 12.86 2.28 41.52 2.57
114 115 7.709947 ACAATAATGATTAGGCACTGTGAATG 58.290 34.615 12.86 0.00 41.52 2.67
115 116 7.340232 ACAATAATGATTAGGCACTGTGAATGT 59.660 33.333 12.86 0.00 41.52 2.71
116 117 7.886629 ATAATGATTAGGCACTGTGAATGTT 57.113 32.000 12.86 3.35 41.52 2.71
117 118 5.571784 ATGATTAGGCACTGTGAATGTTG 57.428 39.130 12.86 0.00 41.52 3.33
118 119 4.650734 TGATTAGGCACTGTGAATGTTGA 58.349 39.130 12.86 0.00 41.52 3.18
119 120 5.255687 TGATTAGGCACTGTGAATGTTGAT 58.744 37.500 12.86 0.00 41.52 2.57
120 121 6.413892 TGATTAGGCACTGTGAATGTTGATA 58.586 36.000 12.86 0.00 41.52 2.15
121 122 6.539826 TGATTAGGCACTGTGAATGTTGATAG 59.460 38.462 12.86 0.00 41.52 2.08
122 123 4.292186 AGGCACTGTGAATGTTGATAGT 57.708 40.909 12.86 0.00 37.18 2.12
123 124 4.655963 AGGCACTGTGAATGTTGATAGTT 58.344 39.130 12.86 0.00 37.18 2.24
124 125 5.072741 AGGCACTGTGAATGTTGATAGTTT 58.927 37.500 12.86 0.00 37.18 2.66
125 126 5.536161 AGGCACTGTGAATGTTGATAGTTTT 59.464 36.000 12.86 0.00 37.18 2.43
126 127 6.040842 AGGCACTGTGAATGTTGATAGTTTTT 59.959 34.615 12.86 0.00 37.18 1.94
127 128 6.363357 GGCACTGTGAATGTTGATAGTTTTTC 59.637 38.462 12.86 0.00 0.00 2.29
128 129 7.141363 GCACTGTGAATGTTGATAGTTTTTCT 58.859 34.615 12.86 0.00 0.00 2.52
129 130 8.289618 GCACTGTGAATGTTGATAGTTTTTCTA 58.710 33.333 12.86 0.00 0.00 2.10
167 168 7.120923 AGTAGAGGTACTTTGACTTTGAACA 57.879 36.000 0.00 0.00 41.55 3.18
168 169 7.562135 AGTAGAGGTACTTTGACTTTGAACAA 58.438 34.615 0.00 0.00 41.55 2.83
169 170 8.044908 AGTAGAGGTACTTTGACTTTGAACAAA 58.955 33.333 0.00 0.17 41.55 2.83
170 171 7.696992 AGAGGTACTTTGACTTTGAACAAAA 57.303 32.000 1.76 0.00 41.55 2.44
171 172 7.535997 AGAGGTACTTTGACTTTGAACAAAAC 58.464 34.615 1.76 0.00 41.55 2.43
172 173 7.393515 AGAGGTACTTTGACTTTGAACAAAACT 59.606 33.333 1.76 0.00 41.55 2.66
173 174 7.892609 AGGTACTTTGACTTTGAACAAAACTT 58.107 30.769 1.76 0.00 35.95 2.66
174 175 9.016438 AGGTACTTTGACTTTGAACAAAACTTA 57.984 29.630 1.76 0.00 35.95 2.24
175 176 9.797556 GGTACTTTGACTTTGAACAAAACTTAT 57.202 29.630 1.76 0.00 35.95 1.73
180 181 9.809096 TTTGACTTTGAACAAAACTTATATGCA 57.191 25.926 0.00 0.00 33.90 3.96
181 182 9.462174 TTGACTTTGAACAAAACTTATATGCAG 57.538 29.630 0.00 0.00 0.00 4.41
182 183 8.845227 TGACTTTGAACAAAACTTATATGCAGA 58.155 29.630 0.00 0.00 0.00 4.26
183 184 9.118236 GACTTTGAACAAAACTTATATGCAGAC 57.882 33.333 0.00 0.00 0.00 3.51
184 185 8.850156 ACTTTGAACAAAACTTATATGCAGACT 58.150 29.630 0.00 0.00 0.00 3.24
195 196 8.142994 ACTTATATGCAGACTAAAAATGACCG 57.857 34.615 0.00 0.00 0.00 4.79
196 197 7.226720 ACTTATATGCAGACTAAAAATGACCGG 59.773 37.037 0.00 0.00 0.00 5.28
197 198 3.410631 TGCAGACTAAAAATGACCGGA 57.589 42.857 9.46 0.00 0.00 5.14
198 199 3.334691 TGCAGACTAAAAATGACCGGAG 58.665 45.455 9.46 0.00 0.00 4.63
215 216 3.654414 CGGAGGGAGTATGTTATGAAGC 58.346 50.000 0.00 0.00 0.00 3.86
216 217 3.654414 GGAGGGAGTATGTTATGAAGCG 58.346 50.000 0.00 0.00 0.00 4.68
217 218 3.555168 GGAGGGAGTATGTTATGAAGCGG 60.555 52.174 0.00 0.00 0.00 5.52
218 219 3.305720 AGGGAGTATGTTATGAAGCGGA 58.694 45.455 0.00 0.00 0.00 5.54
219 220 3.709653 AGGGAGTATGTTATGAAGCGGAA 59.290 43.478 0.00 0.00 0.00 4.30
220 221 4.163458 AGGGAGTATGTTATGAAGCGGAAA 59.837 41.667 0.00 0.00 0.00 3.13
221 222 4.879545 GGGAGTATGTTATGAAGCGGAAAA 59.120 41.667 0.00 0.00 0.00 2.29
222 223 5.355910 GGGAGTATGTTATGAAGCGGAAAAA 59.644 40.000 0.00 0.00 0.00 1.94
252 253 2.367486 AGACTAGGTCTCACGGTTAGC 58.633 52.381 0.00 0.00 38.71 3.09
253 254 2.089980 GACTAGGTCTCACGGTTAGCA 58.910 52.381 0.00 0.00 0.00 3.49
254 255 2.093106 ACTAGGTCTCACGGTTAGCAG 58.907 52.381 0.00 0.00 0.00 4.24
255 256 1.405821 CTAGGTCTCACGGTTAGCAGG 59.594 57.143 0.00 0.00 0.00 4.85
256 257 0.542232 AGGTCTCACGGTTAGCAGGT 60.542 55.000 0.00 0.00 0.00 4.00
257 258 0.389948 GGTCTCACGGTTAGCAGGTG 60.390 60.000 0.00 0.00 0.00 4.00
258 259 0.601558 GTCTCACGGTTAGCAGGTGA 59.398 55.000 3.41 3.41 38.29 4.02
260 261 3.045518 TCACGGTTAGCAGGTGAGA 57.954 52.632 0.00 0.00 35.89 3.27
261 262 0.601558 TCACGGTTAGCAGGTGAGAC 59.398 55.000 0.00 0.00 35.89 3.36
262 263 0.389948 CACGGTTAGCAGGTGAGACC 60.390 60.000 0.00 0.00 38.99 3.85
263 264 1.218316 CGGTTAGCAGGTGAGACCC 59.782 63.158 0.00 0.00 39.75 4.46
264 265 1.218316 GGTTAGCAGGTGAGACCCG 59.782 63.158 0.00 0.00 39.75 5.28
265 266 1.448013 GTTAGCAGGTGAGACCCGC 60.448 63.158 0.00 0.00 41.94 6.13
266 267 2.656069 TTAGCAGGTGAGACCCGCC 61.656 63.158 0.00 0.00 42.60 6.13
269 270 4.087892 CAGGTGAGACCCGCCCTG 62.088 72.222 0.00 0.00 46.65 4.45
270 271 4.316823 AGGTGAGACCCGCCCTGA 62.317 66.667 0.00 0.00 46.65 3.86
271 272 3.083997 GGTGAGACCCGCCCTGAT 61.084 66.667 0.00 0.00 39.55 2.90
272 273 2.187946 GTGAGACCCGCCCTGATG 59.812 66.667 0.00 0.00 0.00 3.07
273 274 3.083349 TGAGACCCGCCCTGATGG 61.083 66.667 0.00 0.00 37.09 3.51
274 275 2.764128 GAGACCCGCCCTGATGGA 60.764 66.667 0.00 0.00 35.39 3.41
275 276 2.040464 AGACCCGCCCTGATGGAT 60.040 61.111 0.00 0.00 35.39 3.41
276 277 2.111878 GACCCGCCCTGATGGATG 59.888 66.667 0.00 0.00 35.39 3.51
277 278 2.366837 ACCCGCCCTGATGGATGA 60.367 61.111 0.00 0.00 35.39 2.92
278 279 2.111878 CCCGCCCTGATGGATGAC 59.888 66.667 0.00 0.00 35.39 3.06
279 280 2.745308 CCCGCCCTGATGGATGACA 61.745 63.158 0.00 0.00 35.39 3.58
280 281 1.524621 CCGCCCTGATGGATGACAC 60.525 63.158 0.00 0.00 35.39 3.67
281 282 1.884464 CGCCCTGATGGATGACACG 60.884 63.158 0.00 0.00 35.39 4.49
282 283 1.221840 GCCCTGATGGATGACACGT 59.778 57.895 0.00 0.00 35.39 4.49
283 284 1.091771 GCCCTGATGGATGACACGTG 61.092 60.000 15.48 15.48 35.39 4.49
284 285 0.462581 CCCTGATGGATGACACGTGG 60.463 60.000 21.57 1.66 35.39 4.94
285 286 1.091771 CCTGATGGATGACACGTGGC 61.092 60.000 21.57 19.24 34.57 5.01
286 287 0.391528 CTGATGGATGACACGTGGCA 60.392 55.000 29.28 29.28 37.54 4.92
288 289 1.339920 TGATGGATGACACGTGGCATT 60.340 47.619 36.07 22.11 45.42 3.56
289 290 1.331756 GATGGATGACACGTGGCATTC 59.668 52.381 36.07 34.16 45.42 2.67
290 291 0.036022 TGGATGACACGTGGCATTCA 59.964 50.000 36.64 36.64 46.54 2.57
291 292 0.447801 GGATGACACGTGGCATTCAC 59.552 55.000 36.07 24.74 45.42 3.18
292 293 1.155889 GATGACACGTGGCATTCACA 58.844 50.000 36.07 9.07 45.42 3.58
293 294 1.535028 GATGACACGTGGCATTCACAA 59.465 47.619 36.07 8.22 45.42 3.33
294 295 1.383523 TGACACGTGGCATTCACAAA 58.616 45.000 23.03 0.00 46.36 2.83
295 296 1.952990 TGACACGTGGCATTCACAAAT 59.047 42.857 23.03 0.00 46.36 2.32
296 297 2.360483 TGACACGTGGCATTCACAAATT 59.640 40.909 23.03 0.00 46.36 1.82
297 298 3.565902 TGACACGTGGCATTCACAAATTA 59.434 39.130 23.03 0.00 46.36 1.40
298 299 3.896122 ACACGTGGCATTCACAAATTAC 58.104 40.909 21.57 0.00 46.36 1.89
299 300 3.316588 ACACGTGGCATTCACAAATTACA 59.683 39.130 21.57 0.00 46.36 2.41
300 301 4.202060 ACACGTGGCATTCACAAATTACAA 60.202 37.500 21.57 0.00 46.36 2.41
301 302 4.742167 CACGTGGCATTCACAAATTACAAA 59.258 37.500 7.95 0.00 46.36 2.83
302 303 4.981674 ACGTGGCATTCACAAATTACAAAG 59.018 37.500 0.00 0.00 46.36 2.77
303 304 4.143347 CGTGGCATTCACAAATTACAAAGC 60.143 41.667 0.00 0.00 46.36 3.51
304 305 4.749099 GTGGCATTCACAAATTACAAAGCA 59.251 37.500 0.00 0.00 45.39 3.91
305 306 5.409214 GTGGCATTCACAAATTACAAAGCAT 59.591 36.000 0.00 0.00 45.39 3.79
306 307 5.638657 TGGCATTCACAAATTACAAAGCATC 59.361 36.000 0.00 0.00 0.00 3.91
307 308 5.870978 GGCATTCACAAATTACAAAGCATCT 59.129 36.000 0.00 0.00 0.00 2.90
308 309 7.035004 GGCATTCACAAATTACAAAGCATCTA 58.965 34.615 0.00 0.00 0.00 1.98
309 310 7.545265 GGCATTCACAAATTACAAAGCATCTAA 59.455 33.333 0.00 0.00 0.00 2.10
310 311 9.090692 GCATTCACAAATTACAAAGCATCTAAT 57.909 29.630 0.00 0.00 0.00 1.73
313 314 9.844790 TTCACAAATTACAAAGCATCTAATCTG 57.155 29.630 0.00 0.00 0.00 2.90
314 315 7.970061 TCACAAATTACAAAGCATCTAATCTGC 59.030 33.333 0.00 0.00 39.97 4.26
315 316 7.221452 CACAAATTACAAAGCATCTAATCTGCC 59.779 37.037 0.00 0.00 40.56 4.85
316 317 6.396829 AATTACAAAGCATCTAATCTGCCC 57.603 37.500 0.00 0.00 40.56 5.36
317 318 2.659428 ACAAAGCATCTAATCTGCCCC 58.341 47.619 0.00 0.00 40.56 5.80
318 319 2.243221 ACAAAGCATCTAATCTGCCCCT 59.757 45.455 0.00 0.00 40.56 4.79
319 320 2.883386 CAAAGCATCTAATCTGCCCCTC 59.117 50.000 0.00 0.00 40.56 4.30
320 321 1.063183 AGCATCTAATCTGCCCCTCC 58.937 55.000 0.00 0.00 40.56 4.30
321 322 0.037447 GCATCTAATCTGCCCCTCCC 59.963 60.000 0.00 0.00 33.44 4.30
322 323 0.695347 CATCTAATCTGCCCCTCCCC 59.305 60.000 0.00 0.00 0.00 4.81
323 324 0.476611 ATCTAATCTGCCCCTCCCCC 60.477 60.000 0.00 0.00 0.00 5.40
340 341 3.018423 CCCCCTCCCTGATTTTAAGTG 57.982 52.381 0.00 0.00 0.00 3.16
341 342 2.358195 CCCCCTCCCTGATTTTAAGTGG 60.358 54.545 0.00 0.00 0.00 4.00
342 343 2.358195 CCCCTCCCTGATTTTAAGTGGG 60.358 54.545 0.00 0.00 39.22 4.61
343 344 2.358195 CCCTCCCTGATTTTAAGTGGGG 60.358 54.545 0.00 0.00 38.43 4.96
344 345 2.358195 CCTCCCTGATTTTAAGTGGGGG 60.358 54.545 0.00 0.00 38.15 5.40
345 346 2.580783 CTCCCTGATTTTAAGTGGGGGA 59.419 50.000 0.00 0.00 40.81 4.81
346 347 3.205282 CTCCCTGATTTTAAGTGGGGGAT 59.795 47.826 0.00 0.00 40.81 3.85
347 348 3.052944 TCCCTGATTTTAAGTGGGGGATG 60.053 47.826 0.00 0.00 36.72 3.51
348 349 3.309848 CCCTGATTTTAAGTGGGGGATGT 60.310 47.826 0.00 0.00 34.71 3.06
349 350 3.701040 CCTGATTTTAAGTGGGGGATGTG 59.299 47.826 0.00 0.00 0.00 3.21
350 351 4.569653 CCTGATTTTAAGTGGGGGATGTGA 60.570 45.833 0.00 0.00 0.00 3.58
351 352 5.203528 CTGATTTTAAGTGGGGGATGTGAT 58.796 41.667 0.00 0.00 0.00 3.06
352 353 6.334378 TGATTTTAAGTGGGGGATGTGATA 57.666 37.500 0.00 0.00 0.00 2.15
353 354 6.364701 TGATTTTAAGTGGGGGATGTGATAG 58.635 40.000 0.00 0.00 0.00 2.08
354 355 6.159575 TGATTTTAAGTGGGGGATGTGATAGA 59.840 38.462 0.00 0.00 0.00 1.98
355 356 6.590656 TTTTAAGTGGGGGATGTGATAGAT 57.409 37.500 0.00 0.00 0.00 1.98
356 357 5.567037 TTAAGTGGGGGATGTGATAGATG 57.433 43.478 0.00 0.00 0.00 2.90
357 358 1.701847 AGTGGGGGATGTGATAGATGC 59.298 52.381 0.00 0.00 0.00 3.91
358 359 1.701847 GTGGGGGATGTGATAGATGCT 59.298 52.381 0.00 0.00 0.00 3.79
359 360 2.107204 GTGGGGGATGTGATAGATGCTT 59.893 50.000 0.00 0.00 0.00 3.91
360 361 2.785269 TGGGGGATGTGATAGATGCTTT 59.215 45.455 0.00 0.00 0.00 3.51
361 362 3.152341 GGGGGATGTGATAGATGCTTTG 58.848 50.000 0.00 0.00 0.00 2.77
362 363 3.435601 GGGGGATGTGATAGATGCTTTGT 60.436 47.826 0.00 0.00 0.00 2.83
363 364 3.567164 GGGGATGTGATAGATGCTTTGTG 59.433 47.826 0.00 0.00 0.00 3.33
364 365 4.454678 GGGATGTGATAGATGCTTTGTGA 58.545 43.478 0.00 0.00 0.00 3.58
365 366 5.068636 GGGATGTGATAGATGCTTTGTGAT 58.931 41.667 0.00 0.00 0.00 3.06
366 367 5.533903 GGGATGTGATAGATGCTTTGTGATT 59.466 40.000 0.00 0.00 0.00 2.57
367 368 6.040166 GGGATGTGATAGATGCTTTGTGATTT 59.960 38.462 0.00 0.00 0.00 2.17
368 369 6.916387 GGATGTGATAGATGCTTTGTGATTTG 59.084 38.462 0.00 0.00 0.00 2.32
369 370 6.822667 TGTGATAGATGCTTTGTGATTTGT 57.177 33.333 0.00 0.00 0.00 2.83
370 371 6.614160 TGTGATAGATGCTTTGTGATTTGTG 58.386 36.000 0.00 0.00 0.00 3.33
371 372 6.430616 TGTGATAGATGCTTTGTGATTTGTGA 59.569 34.615 0.00 0.00 0.00 3.58
372 373 7.040548 TGTGATAGATGCTTTGTGATTTGTGAA 60.041 33.333 0.00 0.00 0.00 3.18
373 374 7.972277 GTGATAGATGCTTTGTGATTTGTGAAT 59.028 33.333 0.00 0.00 0.00 2.57
374 375 7.971722 TGATAGATGCTTTGTGATTTGTGAATG 59.028 33.333 0.00 0.00 0.00 2.67
375 376 6.092955 AGATGCTTTGTGATTTGTGAATGT 57.907 33.333 0.00 0.00 0.00 2.71
376 377 6.154445 AGATGCTTTGTGATTTGTGAATGTC 58.846 36.000 0.00 0.00 0.00 3.06
377 378 5.259832 TGCTTTGTGATTTGTGAATGTCA 57.740 34.783 0.00 0.00 0.00 3.58
378 379 5.845103 TGCTTTGTGATTTGTGAATGTCAT 58.155 33.333 0.00 0.00 0.00 3.06
379 380 5.692654 TGCTTTGTGATTTGTGAATGTCATG 59.307 36.000 0.00 0.00 0.00 3.07
380 381 5.693104 GCTTTGTGATTTGTGAATGTCATGT 59.307 36.000 0.00 0.00 0.00 3.21
381 382 6.346279 GCTTTGTGATTTGTGAATGTCATGTG 60.346 38.462 0.00 0.00 0.00 3.21
382 383 5.771153 TGTGATTTGTGAATGTCATGTGT 57.229 34.783 0.00 0.00 0.00 3.72
383 384 5.761003 TGTGATTTGTGAATGTCATGTGTC 58.239 37.500 0.00 0.00 0.00 3.67
384 385 5.298777 TGTGATTTGTGAATGTCATGTGTCA 59.701 36.000 0.00 0.00 0.00 3.58
385 386 6.016108 TGTGATTTGTGAATGTCATGTGTCAT 60.016 34.615 0.00 0.00 0.00 3.06
386 387 6.525628 GTGATTTGTGAATGTCATGTGTCATC 59.474 38.462 0.00 0.00 0.00 2.92
387 388 5.375417 TTTGTGAATGTCATGTGTCATCC 57.625 39.130 0.00 0.00 0.00 3.51
388 389 4.018484 TGTGAATGTCATGTGTCATCCA 57.982 40.909 0.00 0.00 0.00 3.41
389 390 4.591929 TGTGAATGTCATGTGTCATCCAT 58.408 39.130 0.00 0.00 0.00 3.41
390 391 4.637091 TGTGAATGTCATGTGTCATCCATC 59.363 41.667 0.00 0.00 0.00 3.51
391 392 4.637091 GTGAATGTCATGTGTCATCCATCA 59.363 41.667 0.00 0.00 0.00 3.07
392 393 4.879545 TGAATGTCATGTGTCATCCATCAG 59.120 41.667 0.00 0.00 0.00 2.90
393 394 3.271055 TGTCATGTGTCATCCATCAGG 57.729 47.619 0.00 0.00 0.00 3.86
404 405 4.766970 CATCAGGATGGGTCTCGC 57.233 61.111 1.25 0.00 36.16 5.03
405 406 1.300465 CATCAGGATGGGTCTCGCG 60.300 63.158 0.00 0.00 36.16 5.87
406 407 1.758514 ATCAGGATGGGTCTCGCGT 60.759 57.895 5.77 0.00 36.16 6.01
407 408 2.021068 ATCAGGATGGGTCTCGCGTG 62.021 60.000 5.77 3.13 36.16 5.34
408 409 2.362503 AGGATGGGTCTCGCGTGA 60.363 61.111 5.77 6.33 0.00 4.35
409 410 2.105128 GGATGGGTCTCGCGTGAG 59.895 66.667 19.99 19.99 43.99 3.51
416 417 4.320910 TCTCGCGTGAGACCTGAT 57.679 55.556 24.28 0.00 46.25 2.90
417 418 2.099143 TCTCGCGTGAGACCTGATC 58.901 57.895 24.28 0.00 46.25 2.92
418 419 0.393132 TCTCGCGTGAGACCTGATCT 60.393 55.000 24.28 0.00 46.25 2.75
434 435 8.210265 AGACCTGATCTCATAGAATTCTTTTCC 58.790 37.037 14.36 0.00 28.16 3.13
435 436 7.865820 ACCTGATCTCATAGAATTCTTTTCCA 58.134 34.615 14.36 0.00 0.00 3.53
549 550 1.611977 CTTACAGGAGACACGGTGACA 59.388 52.381 16.29 0.00 0.00 3.58
562 563 4.035909 ACACGGTGACATGTTCCTTTTTAC 59.964 41.667 16.29 0.00 0.00 2.01
565 566 4.320202 CGGTGACATGTTCCTTTTTACAGG 60.320 45.833 15.61 0.00 34.86 4.00
644 645 6.127338 TGTCTATATACATCTGTATGCAGCCC 60.127 42.308 5.85 5.12 41.03 5.19
645 646 6.097554 GTCTATATACATCTGTATGCAGCCCT 59.902 42.308 5.85 0.00 41.03 5.19
667 668 9.185680 GCCCTTATTAAAATCTCTAAAAGGACA 57.814 33.333 0.00 0.00 35.34 4.02
823 825 9.525409 GATGAGCAAGATAACAAGCAAAATTAT 57.475 29.630 0.00 0.00 0.00 1.28
995 1060 8.409371 TCTATATATACTCCGTAGTCCGTACTG 58.591 40.741 0.00 0.00 36.36 2.74
1005 1070 1.080772 TCCGTACTGCTTCAGCACG 60.081 57.895 11.43 11.43 46.80 5.34
1015 1080 1.795768 CTTCAGCACGCCTACTCAAA 58.204 50.000 0.00 0.00 0.00 2.69
1055 1120 2.122729 CTCTGGTCACCCTCCCCA 59.877 66.667 0.00 0.00 0.00 4.96
1109 1174 2.331893 CCCGTGAAATGCCTTGCGA 61.332 57.895 0.00 0.00 0.00 5.10
1130 1195 0.962356 CTGCAAATTCGTCAGCCCCT 60.962 55.000 0.00 0.00 0.00 4.79
1151 1216 3.917760 GGCGCGCCCTCATAGAGT 61.918 66.667 39.89 0.00 0.00 3.24
1180 1245 3.660111 GTCAGCCACCACCGCAAC 61.660 66.667 0.00 0.00 0.00 4.17
1186 1251 4.007940 CACCACCGCAACCGTTCG 62.008 66.667 0.00 0.00 0.00 3.95
1189 1254 2.355363 CACCGCAACCGTTCGAGA 60.355 61.111 5.14 0.00 0.00 4.04
1210 1275 1.227002 GAGTCGGCCGTCCATTCTC 60.227 63.158 27.15 18.32 0.00 2.87
1226 1291 2.682136 TCGTCATCCCCCGCAAGA 60.682 61.111 0.00 0.00 43.02 3.02
1281 1346 2.356818 ATCAGCTTCTACCGCCTCGC 62.357 60.000 0.00 0.00 0.00 5.03
1813 1878 0.462789 ACAGGACGTTCGACTTGGTT 59.537 50.000 10.50 0.00 0.00 3.67
1904 1969 1.787847 GTCAACATTGCGACCTCGG 59.212 57.895 0.00 0.00 40.23 4.63
1995 2063 3.557595 CCAGATGATGTTAGTTTCGGCTC 59.442 47.826 0.00 0.00 0.00 4.70
1996 2064 3.557595 CAGATGATGTTAGTTTCGGCTCC 59.442 47.826 0.00 0.00 0.00 4.70
2011 2079 1.078214 CTCCGATGCCTTCTTGCCA 60.078 57.895 0.00 0.00 0.00 4.92
2104 2172 2.675348 GAGGAGCGGAGATGTTGAAAAG 59.325 50.000 0.00 0.00 0.00 2.27
2111 2179 3.127548 CGGAGATGTTGAAAAGGTGATGG 59.872 47.826 0.00 0.00 0.00 3.51
2131 2199 4.960938 TGGACCTGGAAGATATCGATTTG 58.039 43.478 1.71 0.00 34.07 2.32
2275 2344 8.443937 GTTTTGTTCATTAGTAGCTAGGTTCAG 58.556 37.037 0.00 0.00 0.00 3.02
2393 2462 0.249398 GCTACTTCTCTTTCCCCGCA 59.751 55.000 0.00 0.00 0.00 5.69
2408 2477 0.250234 CCGCATCCTGTTCTTCCAGA 59.750 55.000 0.00 0.00 34.23 3.86
2707 2780 4.437682 TTTGTTCACCCAGTCAAGAGAT 57.562 40.909 0.00 0.00 0.00 2.75
2794 2867 0.173481 TCTCAATTGACTCGCCTCCG 59.827 55.000 3.38 0.00 0.00 4.63
2850 2931 1.087501 GAGCAAATTCCCTCACGTCC 58.912 55.000 0.00 0.00 0.00 4.79
2851 2932 0.673644 AGCAAATTCCCTCACGTCCG 60.674 55.000 0.00 0.00 0.00 4.79
3045 3126 1.134995 TGGCTTGACTGTGAGCTATCG 60.135 52.381 11.19 0.00 38.89 2.92
3056 3137 7.061752 ACTGTGAGCTATCGTTTTGAATTAC 57.938 36.000 0.00 0.00 0.00 1.89
3063 3144 1.460359 TCGTTTTGAATTACCGGACGC 59.540 47.619 9.46 0.00 0.00 5.19
3134 3215 4.774726 AGACAACATGTGTACTCTCTCCAT 59.225 41.667 0.00 0.00 41.96 3.41
3220 3301 3.372822 AGAAGAAAAACGCGACAGTTTCA 59.627 39.130 15.93 0.00 42.81 2.69
3227 3308 3.929095 GCGACAGTTTCATCGTGAC 57.071 52.632 0.00 0.00 40.49 3.67
3234 3315 4.631131 ACAGTTTCATCGTGACTCATCAA 58.369 39.130 0.00 0.00 36.31 2.57
3286 3367 4.864704 AATTGGCAGACAAATTACGGTT 57.135 36.364 0.00 0.00 43.46 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 9.337396 TGCCTAATCATTATTGTTAGATTCGTT 57.663 29.630 0.00 0.00 33.22 3.85
80 81 8.774586 GTGCCTAATCATTATTGTTAGATTCGT 58.225 33.333 0.00 0.00 33.22 3.85
81 82 8.993121 AGTGCCTAATCATTATTGTTAGATTCG 58.007 33.333 0.00 0.00 33.22 3.34
83 84 9.632638 ACAGTGCCTAATCATTATTGTTAGATT 57.367 29.630 0.00 0.00 35.17 2.40
84 85 9.060347 CACAGTGCCTAATCATTATTGTTAGAT 57.940 33.333 0.00 0.00 0.00 1.98
85 86 8.264347 TCACAGTGCCTAATCATTATTGTTAGA 58.736 33.333 0.00 0.00 0.00 2.10
86 87 8.437360 TCACAGTGCCTAATCATTATTGTTAG 57.563 34.615 0.00 0.00 0.00 2.34
87 88 8.800370 TTCACAGTGCCTAATCATTATTGTTA 57.200 30.769 0.00 0.00 0.00 2.41
88 89 7.701539 TTCACAGTGCCTAATCATTATTGTT 57.298 32.000 0.00 0.00 0.00 2.83
89 90 7.340232 ACATTCACAGTGCCTAATCATTATTGT 59.660 33.333 0.00 0.00 0.00 2.71
90 91 7.709947 ACATTCACAGTGCCTAATCATTATTG 58.290 34.615 0.00 0.00 0.00 1.90
91 92 7.886629 ACATTCACAGTGCCTAATCATTATT 57.113 32.000 0.00 0.00 0.00 1.40
92 93 7.557358 TCAACATTCACAGTGCCTAATCATTAT 59.443 33.333 0.00 0.00 0.00 1.28
93 94 6.883756 TCAACATTCACAGTGCCTAATCATTA 59.116 34.615 0.00 0.00 0.00 1.90
94 95 5.711506 TCAACATTCACAGTGCCTAATCATT 59.288 36.000 0.00 0.00 0.00 2.57
95 96 5.255687 TCAACATTCACAGTGCCTAATCAT 58.744 37.500 0.00 0.00 0.00 2.45
96 97 4.650734 TCAACATTCACAGTGCCTAATCA 58.349 39.130 0.00 0.00 0.00 2.57
97 98 5.824904 ATCAACATTCACAGTGCCTAATC 57.175 39.130 0.00 0.00 0.00 1.75
98 99 6.418101 ACTATCAACATTCACAGTGCCTAAT 58.582 36.000 0.00 0.00 0.00 1.73
99 100 5.804639 ACTATCAACATTCACAGTGCCTAA 58.195 37.500 0.00 0.00 0.00 2.69
100 101 5.420725 ACTATCAACATTCACAGTGCCTA 57.579 39.130 0.00 0.00 0.00 3.93
101 102 4.292186 ACTATCAACATTCACAGTGCCT 57.708 40.909 0.00 0.00 0.00 4.75
102 103 5.376854 AAACTATCAACATTCACAGTGCC 57.623 39.130 0.00 0.00 0.00 5.01
103 104 7.141363 AGAAAAACTATCAACATTCACAGTGC 58.859 34.615 0.00 0.00 0.00 4.40
134 135 9.317827 AGTCAAAGTACCTCTACTTTTACCATA 57.682 33.333 11.45 0.00 46.75 2.74
135 136 8.203681 AGTCAAAGTACCTCTACTTTTACCAT 57.796 34.615 11.45 0.00 46.75 3.55
136 137 7.607615 AGTCAAAGTACCTCTACTTTTACCA 57.392 36.000 11.45 0.00 46.75 3.25
137 138 8.771766 CAAAGTCAAAGTACCTCTACTTTTACC 58.228 37.037 11.45 2.12 46.75 2.85
138 139 9.538508 TCAAAGTCAAAGTACCTCTACTTTTAC 57.461 33.333 9.88 8.62 46.75 2.01
140 141 8.890718 GTTCAAAGTCAAAGTACCTCTACTTTT 58.109 33.333 9.88 0.00 46.75 2.27
142 143 7.562135 TGTTCAAAGTCAAAGTACCTCTACTT 58.438 34.615 0.00 0.00 43.87 2.24
143 144 7.120923 TGTTCAAAGTCAAAGTACCTCTACT 57.879 36.000 0.00 0.00 34.38 2.57
144 145 7.781548 TTGTTCAAAGTCAAAGTACCTCTAC 57.218 36.000 0.00 0.00 0.00 2.59
145 146 8.671028 GTTTTGTTCAAAGTCAAAGTACCTCTA 58.329 33.333 0.00 0.00 35.47 2.43
146 147 7.393515 AGTTTTGTTCAAAGTCAAAGTACCTCT 59.606 33.333 0.00 0.00 35.47 3.69
147 148 7.535997 AGTTTTGTTCAAAGTCAAAGTACCTC 58.464 34.615 0.00 0.00 35.47 3.85
148 149 7.462571 AGTTTTGTTCAAAGTCAAAGTACCT 57.537 32.000 0.00 0.00 35.47 3.08
149 150 9.797556 ATAAGTTTTGTTCAAAGTCAAAGTACC 57.202 29.630 0.00 0.00 35.47 3.34
154 155 9.809096 TGCATATAAGTTTTGTTCAAAGTCAAA 57.191 25.926 0.00 0.00 32.75 2.69
155 156 9.462174 CTGCATATAAGTTTTGTTCAAAGTCAA 57.538 29.630 0.00 0.00 0.00 3.18
156 157 8.845227 TCTGCATATAAGTTTTGTTCAAAGTCA 58.155 29.630 0.00 0.00 0.00 3.41
157 158 9.118236 GTCTGCATATAAGTTTTGTTCAAAGTC 57.882 33.333 0.00 0.00 0.00 3.01
158 159 8.850156 AGTCTGCATATAAGTTTTGTTCAAAGT 58.150 29.630 0.00 0.00 0.00 2.66
169 170 8.612619 CGGTCATTTTTAGTCTGCATATAAGTT 58.387 33.333 0.00 0.00 0.00 2.66
170 171 7.226720 CCGGTCATTTTTAGTCTGCATATAAGT 59.773 37.037 0.00 0.00 0.00 2.24
171 172 7.441157 TCCGGTCATTTTTAGTCTGCATATAAG 59.559 37.037 0.00 0.00 0.00 1.73
172 173 7.276658 TCCGGTCATTTTTAGTCTGCATATAA 58.723 34.615 0.00 0.00 0.00 0.98
173 174 6.822442 TCCGGTCATTTTTAGTCTGCATATA 58.178 36.000 0.00 0.00 0.00 0.86
174 175 5.680619 TCCGGTCATTTTTAGTCTGCATAT 58.319 37.500 0.00 0.00 0.00 1.78
175 176 5.092554 TCCGGTCATTTTTAGTCTGCATA 57.907 39.130 0.00 0.00 0.00 3.14
176 177 3.941483 CTCCGGTCATTTTTAGTCTGCAT 59.059 43.478 0.00 0.00 0.00 3.96
177 178 3.334691 CTCCGGTCATTTTTAGTCTGCA 58.665 45.455 0.00 0.00 0.00 4.41
178 179 2.678336 CCTCCGGTCATTTTTAGTCTGC 59.322 50.000 0.00 0.00 0.00 4.26
179 180 3.055385 TCCCTCCGGTCATTTTTAGTCTG 60.055 47.826 0.00 0.00 0.00 3.51
180 181 3.178865 TCCCTCCGGTCATTTTTAGTCT 58.821 45.455 0.00 0.00 0.00 3.24
181 182 3.055312 ACTCCCTCCGGTCATTTTTAGTC 60.055 47.826 0.00 0.00 0.00 2.59
182 183 2.910977 ACTCCCTCCGGTCATTTTTAGT 59.089 45.455 0.00 0.00 0.00 2.24
183 184 3.629142 ACTCCCTCCGGTCATTTTTAG 57.371 47.619 0.00 0.00 0.00 1.85
184 185 4.472108 ACATACTCCCTCCGGTCATTTTTA 59.528 41.667 0.00 0.00 0.00 1.52
185 186 3.265995 ACATACTCCCTCCGGTCATTTTT 59.734 43.478 0.00 0.00 0.00 1.94
186 187 2.844348 ACATACTCCCTCCGGTCATTTT 59.156 45.455 0.00 0.00 0.00 1.82
187 188 2.478292 ACATACTCCCTCCGGTCATTT 58.522 47.619 0.00 0.00 0.00 2.32
188 189 2.176247 ACATACTCCCTCCGGTCATT 57.824 50.000 0.00 0.00 0.00 2.57
189 190 2.176247 AACATACTCCCTCCGGTCAT 57.824 50.000 0.00 0.00 0.00 3.06
190 191 2.832643 TAACATACTCCCTCCGGTCA 57.167 50.000 0.00 0.00 0.00 4.02
191 192 3.228453 TCATAACATACTCCCTCCGGTC 58.772 50.000 0.00 0.00 0.00 4.79
192 193 3.323774 TCATAACATACTCCCTCCGGT 57.676 47.619 0.00 0.00 0.00 5.28
193 194 3.555168 GCTTCATAACATACTCCCTCCGG 60.555 52.174 0.00 0.00 0.00 5.14
194 195 3.654414 GCTTCATAACATACTCCCTCCG 58.346 50.000 0.00 0.00 0.00 4.63
195 196 3.555168 CCGCTTCATAACATACTCCCTCC 60.555 52.174 0.00 0.00 0.00 4.30
196 197 3.321111 TCCGCTTCATAACATACTCCCTC 59.679 47.826 0.00 0.00 0.00 4.30
197 198 3.305720 TCCGCTTCATAACATACTCCCT 58.694 45.455 0.00 0.00 0.00 4.20
198 199 3.746045 TCCGCTTCATAACATACTCCC 57.254 47.619 0.00 0.00 0.00 4.30
199 200 6.431198 TTTTTCCGCTTCATAACATACTCC 57.569 37.500 0.00 0.00 0.00 3.85
232 233 2.290768 TGCTAACCGTGAGACCTAGTCT 60.291 50.000 0.00 0.00 46.42 3.24
233 234 2.089980 TGCTAACCGTGAGACCTAGTC 58.910 52.381 0.00 0.00 0.00 2.59
234 235 2.093106 CTGCTAACCGTGAGACCTAGT 58.907 52.381 0.00 0.00 0.00 2.57
235 236 1.405821 CCTGCTAACCGTGAGACCTAG 59.594 57.143 0.00 0.00 0.00 3.02
236 237 1.272313 ACCTGCTAACCGTGAGACCTA 60.272 52.381 0.00 0.00 0.00 3.08
237 238 0.542232 ACCTGCTAACCGTGAGACCT 60.542 55.000 0.00 0.00 0.00 3.85
238 239 0.389948 CACCTGCTAACCGTGAGACC 60.390 60.000 0.00 0.00 0.00 3.85
239 240 0.601558 TCACCTGCTAACCGTGAGAC 59.398 55.000 0.00 0.00 32.85 3.36
240 241 3.045518 TCACCTGCTAACCGTGAGA 57.954 52.632 0.00 0.00 32.85 3.27
241 242 3.425578 CTCACCTGCTAACCGTGAG 57.574 57.895 2.35 2.35 45.33 3.51
242 243 0.601558 GTCTCACCTGCTAACCGTGA 59.398 55.000 0.00 0.00 35.34 4.35
243 244 0.389948 GGTCTCACCTGCTAACCGTG 60.390 60.000 0.00 0.00 34.73 4.94
244 245 1.542187 GGGTCTCACCTGCTAACCGT 61.542 60.000 0.00 0.00 38.64 4.83
245 246 1.218316 GGGTCTCACCTGCTAACCG 59.782 63.158 0.00 0.00 38.64 4.44
246 247 1.218316 CGGGTCTCACCTGCTAACC 59.782 63.158 0.00 0.00 37.90 2.85
247 248 4.913126 CGGGTCTCACCTGCTAAC 57.087 61.111 0.00 0.00 37.90 2.34
253 254 3.625632 ATCAGGGCGGGTCTCACCT 62.626 63.158 0.00 0.00 38.64 4.00
254 255 3.083997 ATCAGGGCGGGTCTCACC 61.084 66.667 0.00 0.00 37.60 4.02
255 256 2.187946 CATCAGGGCGGGTCTCAC 59.812 66.667 0.00 0.00 0.00 3.51
256 257 2.896677 ATCCATCAGGGCGGGTCTCA 62.897 60.000 0.00 0.00 36.21 3.27
257 258 2.143419 ATCCATCAGGGCGGGTCTC 61.143 63.158 0.00 0.00 36.21 3.36
258 259 2.040464 ATCCATCAGGGCGGGTCT 60.040 61.111 0.00 0.00 36.21 3.85
259 260 2.111878 CATCCATCAGGGCGGGTC 59.888 66.667 0.00 0.00 36.21 4.46
260 261 2.366837 TCATCCATCAGGGCGGGT 60.367 61.111 0.00 0.00 36.21 5.28
261 262 2.111878 GTCATCCATCAGGGCGGG 59.888 66.667 0.00 0.00 36.21 6.13
262 263 1.524621 GTGTCATCCATCAGGGCGG 60.525 63.158 0.00 0.00 36.21 6.13
263 264 1.884464 CGTGTCATCCATCAGGGCG 60.884 63.158 0.00 0.00 36.21 6.13
264 265 1.091771 CACGTGTCATCCATCAGGGC 61.092 60.000 7.58 0.00 36.21 5.19
265 266 0.462581 CCACGTGTCATCCATCAGGG 60.463 60.000 15.65 0.00 34.83 4.45
266 267 1.091771 GCCACGTGTCATCCATCAGG 61.092 60.000 15.65 0.00 0.00 3.86
267 268 0.391528 TGCCACGTGTCATCCATCAG 60.392 55.000 15.65 0.00 0.00 2.90
268 269 0.252761 ATGCCACGTGTCATCCATCA 59.747 50.000 15.65 0.00 0.00 3.07
269 270 1.331756 GAATGCCACGTGTCATCCATC 59.668 52.381 13.12 3.25 0.00 3.51
270 271 1.339920 TGAATGCCACGTGTCATCCAT 60.340 47.619 13.12 0.00 0.00 3.41
271 272 0.036022 TGAATGCCACGTGTCATCCA 59.964 50.000 13.12 2.86 0.00 3.41
272 273 0.447801 GTGAATGCCACGTGTCATCC 59.552 55.000 13.12 0.00 35.86 3.51
273 274 3.975992 GTGAATGCCACGTGTCATC 57.024 52.632 13.12 7.23 35.86 2.92
281 282 4.749099 TGCTTTGTAATTTGTGAATGCCAC 59.251 37.500 0.00 0.00 45.88 5.01
282 283 4.953667 TGCTTTGTAATTTGTGAATGCCA 58.046 34.783 0.00 0.00 0.00 4.92
283 284 5.870978 AGATGCTTTGTAATTTGTGAATGCC 59.129 36.000 0.00 0.00 0.00 4.40
284 285 6.956299 AGATGCTTTGTAATTTGTGAATGC 57.044 33.333 0.00 0.00 0.00 3.56
287 288 9.844790 CAGATTAGATGCTTTGTAATTTGTGAA 57.155 29.630 0.00 0.00 0.00 3.18
288 289 7.970061 GCAGATTAGATGCTTTGTAATTTGTGA 59.030 33.333 8.35 0.00 40.59 3.58
289 290 7.221452 GGCAGATTAGATGCTTTGTAATTTGTG 59.779 37.037 0.00 0.00 43.35 3.33
290 291 7.260603 GGCAGATTAGATGCTTTGTAATTTGT 58.739 34.615 0.00 0.00 43.35 2.83
291 292 6.698766 GGGCAGATTAGATGCTTTGTAATTTG 59.301 38.462 0.00 0.00 43.35 2.32
292 293 6.183360 GGGGCAGATTAGATGCTTTGTAATTT 60.183 38.462 0.00 0.00 43.35 1.82
293 294 5.302823 GGGGCAGATTAGATGCTTTGTAATT 59.697 40.000 0.00 0.00 43.35 1.40
294 295 4.829492 GGGGCAGATTAGATGCTTTGTAAT 59.171 41.667 0.00 0.00 43.35 1.89
295 296 4.079787 AGGGGCAGATTAGATGCTTTGTAA 60.080 41.667 0.00 0.00 43.35 2.41
296 297 3.459598 AGGGGCAGATTAGATGCTTTGTA 59.540 43.478 0.00 0.00 43.35 2.41
297 298 2.243221 AGGGGCAGATTAGATGCTTTGT 59.757 45.455 0.00 0.00 43.35 2.83
298 299 2.883386 GAGGGGCAGATTAGATGCTTTG 59.117 50.000 0.00 0.00 43.35 2.77
299 300 2.158549 GGAGGGGCAGATTAGATGCTTT 60.159 50.000 0.00 0.00 43.35 3.51
300 301 1.423161 GGAGGGGCAGATTAGATGCTT 59.577 52.381 0.00 0.00 43.35 3.91
301 302 1.063183 GGAGGGGCAGATTAGATGCT 58.937 55.000 0.00 0.00 43.35 3.79
302 303 0.037447 GGGAGGGGCAGATTAGATGC 59.963 60.000 0.00 0.00 43.09 3.91
303 304 0.695347 GGGGAGGGGCAGATTAGATG 59.305 60.000 0.00 0.00 0.00 2.90
304 305 0.476611 GGGGGAGGGGCAGATTAGAT 60.477 60.000 0.00 0.00 0.00 1.98
305 306 1.073706 GGGGGAGGGGCAGATTAGA 60.074 63.158 0.00 0.00 0.00 2.10
306 307 3.581372 GGGGGAGGGGCAGATTAG 58.419 66.667 0.00 0.00 0.00 1.73
320 321 2.358195 CCACTTAAAATCAGGGAGGGGG 60.358 54.545 0.00 0.00 0.00 5.40
321 322 2.358195 CCCACTTAAAATCAGGGAGGGG 60.358 54.545 0.00 0.00 42.25 4.79
322 323 2.358195 CCCCACTTAAAATCAGGGAGGG 60.358 54.545 0.00 0.00 42.25 4.30
323 324 2.358195 CCCCCACTTAAAATCAGGGAGG 60.358 54.545 0.00 0.00 42.25 4.30
324 325 2.580783 TCCCCCACTTAAAATCAGGGAG 59.419 50.000 0.00 0.00 42.25 4.30
325 326 2.650013 TCCCCCACTTAAAATCAGGGA 58.350 47.619 0.00 0.00 42.25 4.20
326 327 3.299503 CATCCCCCACTTAAAATCAGGG 58.700 50.000 0.00 0.00 39.29 4.45
327 328 3.701040 CACATCCCCCACTTAAAATCAGG 59.299 47.826 0.00 0.00 0.00 3.86
328 329 4.599041 TCACATCCCCCACTTAAAATCAG 58.401 43.478 0.00 0.00 0.00 2.90
329 330 4.666412 TCACATCCCCCACTTAAAATCA 57.334 40.909 0.00 0.00 0.00 2.57
330 331 6.601332 TCTATCACATCCCCCACTTAAAATC 58.399 40.000 0.00 0.00 0.00 2.17
331 332 6.590656 TCTATCACATCCCCCACTTAAAAT 57.409 37.500 0.00 0.00 0.00 1.82
332 333 6.364701 CATCTATCACATCCCCCACTTAAAA 58.635 40.000 0.00 0.00 0.00 1.52
333 334 5.690097 GCATCTATCACATCCCCCACTTAAA 60.690 44.000 0.00 0.00 0.00 1.52
334 335 4.202461 GCATCTATCACATCCCCCACTTAA 60.202 45.833 0.00 0.00 0.00 1.85
335 336 3.327757 GCATCTATCACATCCCCCACTTA 59.672 47.826 0.00 0.00 0.00 2.24
336 337 2.107204 GCATCTATCACATCCCCCACTT 59.893 50.000 0.00 0.00 0.00 3.16
337 338 1.701847 GCATCTATCACATCCCCCACT 59.298 52.381 0.00 0.00 0.00 4.00
338 339 1.701847 AGCATCTATCACATCCCCCAC 59.298 52.381 0.00 0.00 0.00 4.61
339 340 2.123018 AGCATCTATCACATCCCCCA 57.877 50.000 0.00 0.00 0.00 4.96
340 341 3.152341 CAAAGCATCTATCACATCCCCC 58.848 50.000 0.00 0.00 0.00 5.40
341 342 3.567164 CACAAAGCATCTATCACATCCCC 59.433 47.826 0.00 0.00 0.00 4.81
342 343 4.454678 TCACAAAGCATCTATCACATCCC 58.545 43.478 0.00 0.00 0.00 3.85
343 344 6.630444 AATCACAAAGCATCTATCACATCC 57.370 37.500 0.00 0.00 0.00 3.51
344 345 7.431376 CACAAATCACAAAGCATCTATCACATC 59.569 37.037 0.00 0.00 0.00 3.06
345 346 7.121611 TCACAAATCACAAAGCATCTATCACAT 59.878 33.333 0.00 0.00 0.00 3.21
346 347 6.430616 TCACAAATCACAAAGCATCTATCACA 59.569 34.615 0.00 0.00 0.00 3.58
347 348 6.845302 TCACAAATCACAAAGCATCTATCAC 58.155 36.000 0.00 0.00 0.00 3.06
348 349 7.451501 TTCACAAATCACAAAGCATCTATCA 57.548 32.000 0.00 0.00 0.00 2.15
349 350 7.972277 ACATTCACAAATCACAAAGCATCTATC 59.028 33.333 0.00 0.00 0.00 2.08
350 351 7.833786 ACATTCACAAATCACAAAGCATCTAT 58.166 30.769 0.00 0.00 0.00 1.98
351 352 7.040548 TGACATTCACAAATCACAAAGCATCTA 60.041 33.333 0.00 0.00 0.00 1.98
352 353 6.092955 ACATTCACAAATCACAAAGCATCT 57.907 33.333 0.00 0.00 0.00 2.90
353 354 5.921976 TGACATTCACAAATCACAAAGCATC 59.078 36.000 0.00 0.00 0.00 3.91
354 355 5.845103 TGACATTCACAAATCACAAAGCAT 58.155 33.333 0.00 0.00 0.00 3.79
355 356 5.259832 TGACATTCACAAATCACAAAGCA 57.740 34.783 0.00 0.00 0.00 3.91
356 357 5.693104 ACATGACATTCACAAATCACAAAGC 59.307 36.000 0.00 0.00 0.00 3.51
357 358 6.698329 ACACATGACATTCACAAATCACAAAG 59.302 34.615 0.00 0.00 0.00 2.77
358 359 6.571605 ACACATGACATTCACAAATCACAAA 58.428 32.000 0.00 0.00 0.00 2.83
359 360 6.146601 ACACATGACATTCACAAATCACAA 57.853 33.333 0.00 0.00 0.00 3.33
360 361 5.298777 TGACACATGACATTCACAAATCACA 59.701 36.000 0.00 0.00 0.00 3.58
361 362 5.761003 TGACACATGACATTCACAAATCAC 58.239 37.500 0.00 0.00 0.00 3.06
362 363 6.349528 GGATGACACATGACATTCACAAATCA 60.350 38.462 0.00 0.00 31.08 2.57
363 364 6.032094 GGATGACACATGACATTCACAAATC 58.968 40.000 0.00 0.00 31.08 2.17
364 365 5.477637 TGGATGACACATGACATTCACAAAT 59.522 36.000 0.00 0.00 32.30 2.32
365 366 4.826183 TGGATGACACATGACATTCACAAA 59.174 37.500 0.00 0.00 32.30 2.83
366 367 4.396522 TGGATGACACATGACATTCACAA 58.603 39.130 0.00 0.00 32.30 3.33
367 368 4.018484 TGGATGACACATGACATTCACA 57.982 40.909 0.00 1.52 32.30 3.58
368 369 4.637091 TGATGGATGACACATGACATTCAC 59.363 41.667 7.35 3.86 38.23 3.18
369 370 4.846040 TGATGGATGACACATGACATTCA 58.154 39.130 7.60 7.60 39.34 2.57
370 371 4.275196 CCTGATGGATGACACATGACATTC 59.725 45.833 0.00 1.83 34.57 2.67
371 372 4.080186 TCCTGATGGATGACACATGACATT 60.080 41.667 0.00 0.00 37.46 2.71
372 373 3.457012 TCCTGATGGATGACACATGACAT 59.543 43.478 0.00 1.97 37.46 3.06
373 374 2.839425 TCCTGATGGATGACACATGACA 59.161 45.455 0.00 0.00 37.46 3.58
374 375 3.548745 TCCTGATGGATGACACATGAC 57.451 47.619 0.00 0.00 37.46 3.06
387 388 1.300465 CGCGAGACCCATCCTGATG 60.300 63.158 0.00 0.00 38.51 3.07
388 389 1.758514 ACGCGAGACCCATCCTGAT 60.759 57.895 15.93 0.00 0.00 2.90
389 390 2.362503 ACGCGAGACCCATCCTGA 60.363 61.111 15.93 0.00 0.00 3.86
390 391 2.202797 CACGCGAGACCCATCCTG 60.203 66.667 15.93 0.00 0.00 3.86
391 392 2.362503 TCACGCGAGACCCATCCT 60.363 61.111 15.93 0.00 0.00 3.24
392 393 2.105128 CTCACGCGAGACCCATCC 59.895 66.667 15.93 0.00 42.34 3.51
393 394 3.197614 TCTCACGCGAGACCCATC 58.802 61.111 15.93 0.00 43.55 3.51
399 400 0.393132 AGATCAGGTCTCACGCGAGA 60.393 55.000 15.93 10.37 46.28 4.04
400 401 2.102554 AGATCAGGTCTCACGCGAG 58.897 57.895 15.93 4.59 40.98 5.03
401 402 4.320910 AGATCAGGTCTCACGCGA 57.679 55.556 15.93 0.00 28.45 5.87
408 409 8.210265 GGAAAAGAATTCTATGAGATCAGGTCT 58.790 37.037 8.75 0.00 40.81 3.85
409 410 7.989741 TGGAAAAGAATTCTATGAGATCAGGTC 59.010 37.037 8.75 0.00 0.00 3.85
410 411 7.865820 TGGAAAAGAATTCTATGAGATCAGGT 58.134 34.615 8.75 0.00 0.00 4.00
411 412 8.921353 ATGGAAAAGAATTCTATGAGATCAGG 57.079 34.615 8.75 0.00 0.00 3.86
425 426 9.193806 ACACATAGCTTCATAATGGAAAAGAAT 57.806 29.630 0.00 0.00 0.00 2.40
426 427 8.579850 ACACATAGCTTCATAATGGAAAAGAA 57.420 30.769 0.00 0.00 0.00 2.52
427 428 8.579850 AACACATAGCTTCATAATGGAAAAGA 57.420 30.769 0.00 0.00 0.00 2.52
428 429 9.722056 GTAACACATAGCTTCATAATGGAAAAG 57.278 33.333 0.00 0.00 0.00 2.27
429 430 9.237187 TGTAACACATAGCTTCATAATGGAAAA 57.763 29.630 0.00 0.00 0.00 2.29
430 431 8.800370 TGTAACACATAGCTTCATAATGGAAA 57.200 30.769 0.00 0.00 0.00 3.13
431 432 8.673711 GTTGTAACACATAGCTTCATAATGGAA 58.326 33.333 0.00 0.00 0.00 3.53
432 433 7.011016 CGTTGTAACACATAGCTTCATAATGGA 59.989 37.037 0.00 0.00 0.00 3.41
433 434 7.125755 CGTTGTAACACATAGCTTCATAATGG 58.874 38.462 0.00 0.00 0.00 3.16
434 435 7.125755 CCGTTGTAACACATAGCTTCATAATG 58.874 38.462 0.00 0.00 0.00 1.90
435 436 6.821665 ACCGTTGTAACACATAGCTTCATAAT 59.178 34.615 0.00 0.00 0.00 1.28
445 446 8.685427 ACACATATAGTACCGTTGTAACACATA 58.315 33.333 0.00 0.00 0.00 2.29
516 517 6.554982 TGTCTCCTGTAAGTCCTTATATGCAT 59.445 38.462 3.79 3.79 0.00 3.96
528 529 1.612463 GTCACCGTGTCTCCTGTAAGT 59.388 52.381 0.00 0.00 0.00 2.24
549 550 9.927668 CATATTTGAACCTGTAAAAAGGAACAT 57.072 29.630 0.00 0.00 40.02 2.71
562 563 7.226523 TCCGTATGTGATTCATATTTGAACCTG 59.773 37.037 0.33 0.00 44.36 4.00
565 566 7.072030 GCTCCGTATGTGATTCATATTTGAAC 58.928 38.462 0.33 0.00 44.36 3.18
579 580 3.684305 TCACTCATTTTGCTCCGTATGTG 59.316 43.478 0.00 0.00 0.00 3.21
583 584 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
633 634 7.290061 AGAGATTTTAATAAGGGCTGCATACA 58.710 34.615 0.50 0.00 0.00 2.29
639 640 9.408648 TCCTTTTAGAGATTTTAATAAGGGCTG 57.591 33.333 0.00 0.00 33.42 4.85
867 869 7.424227 TTGTTTTTATAACACACCTACCGAG 57.576 36.000 0.00 0.00 0.00 4.63
995 1060 0.670546 TTGAGTAGGCGTGCTGAAGC 60.671 55.000 0.47 0.00 42.50 3.86
1005 1070 1.000506 TGTCCGTCTGTTTGAGTAGGC 59.999 52.381 0.00 0.00 0.00 3.93
1015 1080 0.321671 CCATCTTGGTGTCCGTCTGT 59.678 55.000 0.00 0.00 31.35 3.41
1055 1120 6.238648 AGACTTCCATGAAAATTAGGTCGTT 58.761 36.000 0.00 0.00 0.00 3.85
1130 1195 2.835895 TATGAGGGCGCGCCAGTA 60.836 61.111 46.88 32.66 37.98 2.74
1143 1208 0.100682 GAAGTCGCCGCACTCTATGA 59.899 55.000 0.00 0.00 0.00 2.15
1180 1245 2.276743 CGACTCGCTCTCGAACGG 60.277 66.667 2.80 0.00 44.98 4.44
1183 1248 3.812019 GGCCGACTCGCTCTCGAA 61.812 66.667 0.00 0.00 44.98 3.71
1186 1251 4.539881 GACGGCCGACTCGCTCTC 62.540 72.222 35.90 12.84 0.00 3.20
1210 1275 1.153168 ATTCTTGCGGGGGATGACG 60.153 57.895 0.00 0.00 0.00 4.35
1226 1291 2.672961 TCTTCGTCTTCGATGCCATT 57.327 45.000 0.00 0.00 45.65 3.16
1530 1595 0.393077 CTGGTTCTTCCACTGGTCGT 59.607 55.000 0.00 0.00 41.93 4.34
1813 1878 1.602237 GAAACGAGGAGGGCATGGA 59.398 57.895 0.00 0.00 0.00 3.41
1904 1969 1.300697 ACACGTCAAAGGCCGTCTC 60.301 57.895 0.00 0.00 34.59 3.36
1977 2042 2.167693 TCGGAGCCGAAACTAACATCAT 59.832 45.455 9.50 0.00 46.01 2.45
2111 2179 5.215252 TCCAAATCGATATCTTCCAGGTC 57.785 43.478 0.00 0.00 0.00 3.85
2131 2199 0.976073 TTGAGTCGTCCCATCCCTCC 60.976 60.000 0.00 0.00 0.00 4.30
2275 2344 6.509418 TCACTCAAACCCTTTATTGTATGC 57.491 37.500 0.00 0.00 0.00 3.14
2618 2690 5.241728 ACCAAAGCACTTCTCTTTTATGGAC 59.758 40.000 0.00 0.00 31.94 4.02
2763 2836 7.275779 GCGAGTCAATTGAGAGTTAGAAATACA 59.724 37.037 8.80 0.00 0.00 2.29
2794 2867 1.706287 GCAAAATCTCGACGAGGGGC 61.706 60.000 23.92 15.79 0.00 5.80
2850 2931 4.944372 GGAGCGGCGGTATGGTCG 62.944 72.222 13.22 0.00 38.24 4.79
2851 2932 4.603946 GGGAGCGGCGGTATGGTC 62.604 72.222 13.22 0.00 0.00 4.02
3014 3095 4.278170 CACAGTCAAGCCATTTTCTTACCA 59.722 41.667 0.00 0.00 0.00 3.25
3045 3126 2.973419 TGCGTCCGGTAATTCAAAAC 57.027 45.000 0.00 0.00 0.00 2.43
3056 3137 1.209127 GGTCACAAAATGCGTCCGG 59.791 57.895 0.00 0.00 0.00 5.14
3063 3144 4.160252 CCAGAATAAGGGGGTCACAAAATG 59.840 45.833 0.00 0.00 0.00 2.32
3103 3184 6.040504 AGAGTACACATGTTGTCTTGTCACTA 59.959 38.462 0.00 0.00 39.91 2.74
3110 3191 4.588951 TGGAGAGAGTACACATGTTGTCTT 59.411 41.667 0.00 0.00 39.91 3.01
3134 3215 4.398044 GCCGACTTTAATTTTCCAGATGGA 59.602 41.667 0.00 0.00 43.73 3.41
3207 3288 0.318360 TCACGATGAAACTGTCGCGT 60.318 50.000 5.77 0.00 41.31 6.01
3220 3301 5.923114 CGGAATTCTATTGATGAGTCACGAT 59.077 40.000 5.23 0.00 33.11 3.73
3227 3308 6.030548 TCCTAGCGGAATTCTATTGATGAG 57.969 41.667 5.23 0.00 36.03 2.90


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

AutoCloner maintained by Alex Coulton.