Multiple sequence alignment - TraesCS5D01G071500

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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 TraesCS5D01G071500 chr5D 100.000 5104 0 0 1 5104 69410078 69415181 0.000000e+00 9426.0
1 TraesCS5D01G071500 chr5D 89.242 2045 142 42 341 2349 69423709 69425711 0.000000e+00 2486.0
2 TraesCS5D01G071500 chr5D 95.426 962 42 2 3108 4069 69426599 69427558 0.000000e+00 1531.0
3 TraesCS5D01G071500 chr5D 95.271 867 39 2 4239 5104 8402792 8403657 0.000000e+00 1373.0
4 TraesCS5D01G071500 chr5D 97.627 295 7 0 2606 2900 69426009 69426303 1.640000e-139 507.0
5 TraesCS5D01G071500 chr5D 92.486 346 22 2 1 344 489733251 489732908 4.590000e-135 492.0
6 TraesCS5D01G071500 chr5D 81.352 429 48 17 907 1315 69432042 69432458 2.290000e-83 320.0
7 TraesCS5D01G071500 chr5D 98.750 160 1 1 2348 2507 69425805 69425963 3.010000e-72 283.0
8 TraesCS5D01G071500 chr5D 88.940 217 17 4 2884 3096 69426318 69426531 1.410000e-65 261.0
9 TraesCS5D01G071500 chr5D 84.133 271 29 8 3108 3370 69469251 69469515 3.050000e-62 250.0
10 TraesCS5D01G071500 chr5D 82.407 108 12 3 2271 2376 69468478 69468580 2.530000e-13 87.9
11 TraesCS5D01G071500 chr5D 93.220 59 3 1 2534 2591 69425967 69426025 9.110000e-13 86.1
12 TraesCS5D01G071500 chr5B 91.949 1503 68 19 639 2106 75235575 75237059 0.000000e+00 2056.0
13 TraesCS5D01G071500 chr5B 92.500 1200 66 15 3032 4222 75250441 75251625 0.000000e+00 1696.0
14 TraesCS5D01G071500 chr5B 91.425 863 43 14 2108 2964 75249602 75250439 0.000000e+00 1155.0
15 TraesCS5D01G071500 chr5B 87.689 926 99 12 3126 4044 75319203 75320120 0.000000e+00 1064.0
16 TraesCS5D01G071500 chr5B 88.323 668 65 10 3126 3787 75685882 75686542 0.000000e+00 789.0
17 TraesCS5D01G071500 chr5B 82.368 380 34 13 913 1271 75681337 75681704 2.990000e-77 300.0
18 TraesCS5D01G071500 chr5B 89.121 239 22 3 404 641 75222042 75222277 1.390000e-75 294.0
19 TraesCS5D01G071500 chr5B 80.707 368 46 19 2736 3090 75318772 75319127 3.920000e-66 263.0
20 TraesCS5D01G071500 chr5B 78.571 252 18 19 2271 2497 75318377 75318617 3.210000e-27 134.0
21 TraesCS5D01G071500 chr5B 78.571 252 18 19 2271 2497 75682305 75682545 3.210000e-27 134.0
22 TraesCS5D01G071500 chr5B 81.013 79 9 5 1266 1340 75317732 75317808 1.980000e-04 58.4
23 TraesCS5D01G071500 chr5A 95.964 991 39 1 3123 4112 60131462 60132452 0.000000e+00 1607.0
24 TraesCS5D01G071500 chr5A 87.585 1176 74 28 532 1675 60125428 60126563 0.000000e+00 1297.0
25 TraesCS5D01G071500 chr5A 88.078 562 57 6 3515 4076 60246309 60246860 0.000000e+00 658.0
26 TraesCS5D01G071500 chr5A 94.444 306 17 0 2603 2908 60130739 60131044 5.980000e-129 472.0
27 TraesCS5D01G071500 chr5A 91.570 344 26 2 1 341 665886832 665887175 5.980000e-129 472.0
28 TraesCS5D01G071500 chr5A 79.846 521 65 20 1773 2262 60128873 60129384 1.360000e-90 344.0
29 TraesCS5D01G071500 chr5A 91.903 247 11 6 2259 2505 60129464 60129701 2.280000e-88 337.0
30 TraesCS5D01G071500 chr5A 82.075 424 43 13 913 1315 60201594 60202005 1.060000e-86 331.0
31 TraesCS5D01G071500 chr5A 90.187 214 12 4 2891 3096 60131057 60131269 2.340000e-68 270.0
32 TraesCS5D01G071500 chr5A 95.506 89 3 1 452 539 60124052 60124140 1.920000e-29 141.0
33 TraesCS5D01G071500 chr6A 94.681 1034 52 2 3092 4122 555487310 555488343 0.000000e+00 1602.0
34 TraesCS5D01G071500 chr6A 82.110 654 75 19 1773 2397 555485855 555486495 5.860000e-144 521.0
35 TraesCS5D01G071500 chr6A 93.485 307 17 2 2603 2908 555486618 555486922 2.170000e-123 453.0
36 TraesCS5D01G071500 chr6A 86.293 321 20 6 1421 1723 555485430 555485744 1.370000e-85 327.0
37 TraesCS5D01G071500 chr6A 92.925 212 9 3 2891 3096 555486935 555487146 2.310000e-78 303.0
38 TraesCS5D01G071500 chr6A 87.755 98 8 3 2486 2583 555486533 555486626 1.500000e-20 111.0
39 TraesCS5D01G071500 chr2A 94.919 866 40 3 4242 5104 555844219 555843355 0.000000e+00 1352.0
40 TraesCS5D01G071500 chr2A 93.894 868 49 4 4237 5101 79464347 79465213 0.000000e+00 1306.0
41 TraesCS5D01G071500 chr2A 96.875 32 1 0 679 710 604128139 604128108 3.000000e-03 54.7
42 TraesCS5D01G071500 chr7D 94.780 862 43 2 4244 5104 610250531 610249671 0.000000e+00 1341.0
43 TraesCS5D01G071500 chr7D 84.703 876 113 14 3192 4051 568698143 568699013 0.000000e+00 856.0
44 TraesCS5D01G071500 chr7D 92.174 345 23 3 1 343 136876573 136876915 7.680000e-133 484.0
45 TraesCS5D01G071500 chr7D 85.657 251 30 5 1066 1314 568695323 568695569 5.070000e-65 259.0
46 TraesCS5D01G071500 chr7D 89.041 73 6 2 2800 2871 568697174 568697245 7.040000e-14 89.8
47 TraesCS5D01G071500 chr1A 94.579 867 44 3 4240 5104 405641878 405642743 0.000000e+00 1338.0
48 TraesCS5D01G071500 chr1A 93.671 869 50 5 4236 5101 552496178 552497044 0.000000e+00 1295.0
49 TraesCS5D01G071500 chr1D 94.374 871 39 5 4240 5104 12486421 12487287 0.000000e+00 1328.0
50 TraesCS5D01G071500 chr1D 93.064 346 21 2 1 344 349189544 349189200 2.120000e-138 503.0
51 TraesCS5D01G071500 chr1D 92.169 332 17 4 10 341 259769767 259769445 1.290000e-125 460.0
52 TraesCS5D01G071500 chr7A 94.009 868 45 6 4240 5104 93918532 93919395 0.000000e+00 1308.0
53 TraesCS5D01G071500 chr7A 84.760 853 114 11 3210 4051 657431886 657431039 0.000000e+00 841.0
54 TraesCS5D01G071500 chr7A 84.247 146 14 7 1064 1202 657441358 657441215 3.210000e-27 134.0
55 TraesCS5D01G071500 chr7A 89.041 73 6 2 2800 2871 657434891 657434820 7.040000e-14 89.8
56 TraesCS5D01G071500 chr4A 93.981 864 48 4 4240 5101 95596367 95597228 0.000000e+00 1304.0
57 TraesCS5D01G071500 chr4A 90.988 344 28 2 1 341 620424969 620424626 1.290000e-125 460.0
58 TraesCS5D01G071500 chr7B 83.853 737 99 14 3331 4051 624792045 624791313 0.000000e+00 684.0
59 TraesCS5D01G071500 chr7B 88.372 215 20 3 1105 1314 624797621 624797407 2.360000e-63 254.0
60 TraesCS5D01G071500 chr7B 86.614 127 17 0 3210 3336 624792409 624792283 1.920000e-29 141.0
61 TraesCS5D01G071500 chr7B 89.041 73 6 2 2800 2871 624793193 624793122 7.040000e-14 89.8
62 TraesCS5D01G071500 chr4D 92.373 354 13 5 1 343 23234766 23235116 4.590000e-135 492.0
63 TraesCS5D01G071500 chr4D 91.066 347 26 3 1 343 66507572 66507917 1.000000e-126 464.0
64 TraesCS5D01G071500 chr3A 91.860 344 25 2 1 341 642030059 642030402 1.290000e-130 477.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G071500 chr5D 69410078 69415181 5103 False 9426.000000 9426 100.000000 1 5104 1 chr5D.!!$F2 5103
1 TraesCS5D01G071500 chr5D 8402792 8403657 865 False 1373.000000 1373 95.271000 4239 5104 1 chr5D.!!$F1 865
2 TraesCS5D01G071500 chr5D 69423709 69427558 3849 False 859.016667 2486 93.867500 341 4069 6 chr5D.!!$F4 3728
3 TraesCS5D01G071500 chr5B 75235575 75237059 1484 False 2056.000000 2056 91.949000 639 2106 1 chr5B.!!$F2 1467
4 TraesCS5D01G071500 chr5B 75249602 75251625 2023 False 1425.500000 1696 91.962500 2108 4222 2 chr5B.!!$F3 2114
5 TraesCS5D01G071500 chr5B 75681337 75686542 5205 False 407.666667 789 83.087333 913 3787 3 chr5B.!!$F5 2874
6 TraesCS5D01G071500 chr5B 75317732 75320120 2388 False 379.850000 1064 81.995000 1266 4044 4 chr5B.!!$F4 2778
7 TraesCS5D01G071500 chr5A 60246309 60246860 551 False 658.000000 658 88.078000 3515 4076 1 chr5A.!!$F2 561
8 TraesCS5D01G071500 chr5A 60124052 60132452 8400 False 638.285714 1607 90.776429 452 4112 7 chr5A.!!$F4 3660
9 TraesCS5D01G071500 chr6A 555485430 555488343 2913 False 552.833333 1602 89.541500 1421 4122 6 chr6A.!!$F1 2701
10 TraesCS5D01G071500 chr2A 555843355 555844219 864 True 1352.000000 1352 94.919000 4242 5104 1 chr2A.!!$R1 862
11 TraesCS5D01G071500 chr2A 79464347 79465213 866 False 1306.000000 1306 93.894000 4237 5101 1 chr2A.!!$F1 864
12 TraesCS5D01G071500 chr7D 610249671 610250531 860 True 1341.000000 1341 94.780000 4244 5104 1 chr7D.!!$R1 860
13 TraesCS5D01G071500 chr7D 568695323 568699013 3690 False 401.600000 856 86.467000 1066 4051 3 chr7D.!!$F2 2985
14 TraesCS5D01G071500 chr1A 405641878 405642743 865 False 1338.000000 1338 94.579000 4240 5104 1 chr1A.!!$F1 864
15 TraesCS5D01G071500 chr1A 552496178 552497044 866 False 1295.000000 1295 93.671000 4236 5101 1 chr1A.!!$F2 865
16 TraesCS5D01G071500 chr1D 12486421 12487287 866 False 1328.000000 1328 94.374000 4240 5104 1 chr1D.!!$F1 864
17 TraesCS5D01G071500 chr7A 93918532 93919395 863 False 1308.000000 1308 94.009000 4240 5104 1 chr7A.!!$F1 864
18 TraesCS5D01G071500 chr7A 657431039 657434891 3852 True 465.400000 841 86.900500 2800 4051 2 chr7A.!!$R2 1251
19 TraesCS5D01G071500 chr4A 95596367 95597228 861 False 1304.000000 1304 93.981000 4240 5101 1 chr4A.!!$F1 861
20 TraesCS5D01G071500 chr7B 624791313 624793193 1880 True 304.933333 684 86.502667 2800 4051 3 chr7B.!!$R2 1251

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
393 394 0.036765 TGGTAGGGCGACAATGTCAC 60.037 55.0 14.24 3.27 32.09 3.67 F
952 2255 0.250234 ATCCCACCATCATATCGCCG 59.750 55.0 0.00 0.00 0.00 6.46 F
1819 5467 0.667184 GCCACAACTGCCAAATTCGG 60.667 55.0 0.00 0.00 0.00 4.30 F
1976 5648 0.524862 AGTAGTAGGAACACGCCGTG 59.475 55.0 16.94 16.94 39.75 4.94 F
1977 5649 1.074872 GTAGTAGGAACACGCCGTGC 61.075 60.0 18.59 1.16 36.98 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1316 2668 0.319040 ATCGATCGATTGGTCAGGCG 60.319 55.000 24.60 2.77 0.00 5.52 R
1885 5542 1.151668 GAGAGAGTTGCACGCATGTT 58.848 50.000 0.00 0.00 0.00 2.71 R
3219 14710 0.840617 TAATACAGCCCCATCGCCAA 59.159 50.000 0.00 0.00 0.00 4.52 R
3884 15652 1.576421 GTACACGTCGGTTCCGAGT 59.424 57.895 14.40 11.27 39.22 4.18 R
4135 15917 1.094785 GTCCCGGACACATTGGAATG 58.905 55.000 13.05 0.00 42.10 2.67 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
85 86 3.249961 GGGGATAGGCCGGGGAAG 61.250 72.222 2.18 0.00 37.63 3.46
86 87 3.955044 GGGATAGGCCGGGGAAGC 61.955 72.222 2.18 0.00 37.63 3.86
87 88 4.315941 GGATAGGCCGGGGAAGCG 62.316 72.222 2.18 0.00 0.00 4.68
88 89 4.990553 GATAGGCCGGGGAAGCGC 62.991 72.222 2.18 0.00 0.00 5.92
155 156 4.410400 GGGGGTGGGAGTTGCGAG 62.410 72.222 0.00 0.00 0.00 5.03
158 159 4.373116 GGTGGGAGTTGCGAGCGA 62.373 66.667 0.00 0.00 0.00 4.93
159 160 2.811317 GTGGGAGTTGCGAGCGAG 60.811 66.667 0.00 0.00 0.00 5.03
160 161 4.742201 TGGGAGTTGCGAGCGAGC 62.742 66.667 0.00 0.00 37.71 5.03
205 206 3.174788 GGCACGTGATCCCGTTTC 58.825 61.111 22.23 0.00 39.45 2.78
206 207 2.736682 GGCACGTGATCCCGTTTCG 61.737 63.158 22.23 0.00 39.45 3.46
208 209 2.433664 ACGTGATCCCGTTTCGGC 60.434 61.111 0.00 0.00 46.86 5.54
209 210 3.192922 CGTGATCCCGTTTCGGCC 61.193 66.667 2.41 0.00 46.86 6.13
210 211 2.822701 GTGATCCCGTTTCGGCCC 60.823 66.667 0.00 0.00 46.86 5.80
211 212 4.460683 TGATCCCGTTTCGGCCCG 62.461 66.667 0.00 0.00 46.86 6.13
226 227 4.271816 CCGCGCGCTGACCTAGAT 62.272 66.667 30.48 0.00 0.00 1.98
227 228 2.637589 CGCGCGCTGACCTAGATA 59.362 61.111 30.48 0.00 0.00 1.98
228 229 1.210413 CGCGCGCTGACCTAGATAT 59.790 57.895 30.48 0.00 0.00 1.63
229 230 1.067743 CGCGCGCTGACCTAGATATG 61.068 60.000 30.48 4.24 0.00 1.78
230 231 1.347817 GCGCGCTGACCTAGATATGC 61.348 60.000 26.67 0.00 0.00 3.14
231 232 0.734253 CGCGCTGACCTAGATATGCC 60.734 60.000 5.56 0.00 0.00 4.40
232 233 0.734253 GCGCTGACCTAGATATGCCG 60.734 60.000 0.00 0.00 0.00 5.69
233 234 0.734253 CGCTGACCTAGATATGCCGC 60.734 60.000 0.00 0.00 0.00 6.53
234 235 0.734253 GCTGACCTAGATATGCCGCG 60.734 60.000 0.00 0.00 0.00 6.46
235 236 0.734253 CTGACCTAGATATGCCGCGC 60.734 60.000 0.00 0.00 0.00 6.86
236 237 1.801913 GACCTAGATATGCCGCGCG 60.802 63.158 25.67 25.67 0.00 6.86
237 238 3.181967 CCTAGATATGCCGCGCGC 61.182 66.667 27.36 23.91 38.31 6.86
238 239 3.536394 CTAGATATGCCGCGCGCG 61.536 66.667 43.73 43.73 42.08 6.86
268 269 3.866582 GCCCGCTGGAGCCACTAT 61.867 66.667 0.00 0.00 37.91 2.12
269 270 2.507854 GCCCGCTGGAGCCACTATA 61.508 63.158 0.00 0.00 37.91 1.31
270 271 1.367840 CCCGCTGGAGCCACTATAC 59.632 63.158 0.00 0.00 37.91 1.47
271 272 1.367840 CCGCTGGAGCCACTATACC 59.632 63.158 0.00 0.00 37.91 2.73
272 273 1.007271 CGCTGGAGCCACTATACCG 60.007 63.158 0.00 0.00 37.91 4.02
273 274 1.367840 GCTGGAGCCACTATACCGG 59.632 63.158 0.00 0.00 34.31 5.28
274 275 1.400530 GCTGGAGCCACTATACCGGT 61.401 60.000 13.98 13.98 34.31 5.28
275 276 1.120530 CTGGAGCCACTATACCGGTT 58.879 55.000 15.04 3.05 0.00 4.44
276 277 0.828022 TGGAGCCACTATACCGGTTG 59.172 55.000 15.04 4.29 0.00 3.77
277 278 0.828677 GGAGCCACTATACCGGTTGT 59.171 55.000 15.04 7.13 0.00 3.32
278 279 1.472728 GGAGCCACTATACCGGTTGTG 60.473 57.143 15.04 19.06 0.00 3.33
279 280 0.107848 AGCCACTATACCGGTTGTGC 60.108 55.000 15.04 14.87 0.00 4.57
280 281 1.426041 GCCACTATACCGGTTGTGCG 61.426 60.000 15.04 14.00 0.00 5.34
281 282 1.426041 CCACTATACCGGTTGTGCGC 61.426 60.000 15.04 0.00 0.00 6.09
282 283 1.517694 ACTATACCGGTTGTGCGCG 60.518 57.895 15.04 0.00 0.00 6.86
283 284 2.867091 CTATACCGGTTGTGCGCGC 61.867 63.158 27.26 27.26 0.00 6.86
284 285 3.359515 TATACCGGTTGTGCGCGCT 62.360 57.895 33.29 11.88 0.00 5.92
285 286 2.002509 TATACCGGTTGTGCGCGCTA 62.003 55.000 33.29 18.69 0.00 4.26
286 287 2.839043 ATACCGGTTGTGCGCGCTAA 62.839 55.000 33.29 23.46 0.00 3.09
287 288 3.718097 CCGGTTGTGCGCGCTAAA 61.718 61.111 33.29 22.67 0.00 1.85
288 289 2.249896 CGGTTGTGCGCGCTAAAA 59.750 55.556 33.29 20.05 0.00 1.52
289 290 2.072654 CGGTTGTGCGCGCTAAAAC 61.073 57.895 33.29 28.56 0.00 2.43
290 291 2.072654 GGTTGTGCGCGCTAAAACG 61.073 57.895 33.29 0.00 0.00 3.60
291 292 2.072654 GTTGTGCGCGCTAAAACGG 61.073 57.895 33.29 0.00 0.00 4.44
296 297 2.483288 CGCGCTAAAACGGGCAAT 59.517 55.556 5.56 0.00 42.32 3.56
297 298 1.154112 CGCGCTAAAACGGGCAATT 60.154 52.632 5.56 0.00 42.32 2.32
298 299 0.731174 CGCGCTAAAACGGGCAATTT 60.731 50.000 5.56 0.00 42.32 1.82
299 300 1.424403 GCGCTAAAACGGGCAATTTT 58.576 45.000 0.00 3.81 41.86 1.82
300 301 2.597520 GCGCTAAAACGGGCAATTTTA 58.402 42.857 0.00 5.41 41.86 1.52
301 302 2.343246 GCGCTAAAACGGGCAATTTTAC 59.657 45.455 0.00 0.78 41.86 2.01
302 303 2.590712 CGCTAAAACGGGCAATTTTACG 59.409 45.455 2.14 6.90 31.79 3.18
303 304 2.918600 GCTAAAACGGGCAATTTTACGG 59.081 45.455 2.14 0.00 31.79 4.02
304 305 1.785768 AAAACGGGCAATTTTACGGC 58.214 45.000 0.00 0.00 0.00 5.68
305 306 0.387494 AAACGGGCAATTTTACGGCG 60.387 50.000 4.80 4.80 0.00 6.46
306 307 2.578445 CGGGCAATTTTACGGCGC 60.578 61.111 6.90 0.00 37.16 6.53
307 308 2.578445 GGGCAATTTTACGGCGCG 60.578 61.111 6.90 0.00 0.00 6.86
308 309 2.481464 GGCAATTTTACGGCGCGA 59.519 55.556 12.10 0.00 0.00 5.87
309 310 1.866059 GGCAATTTTACGGCGCGAC 60.866 57.895 12.10 5.80 0.00 5.19
310 311 2.205842 GCAATTTTACGGCGCGACG 61.206 57.895 36.13 36.13 40.31 5.12
327 328 4.166011 GCTAGTTTGGCGCGGCTG 62.166 66.667 33.23 16.16 0.00 4.85
328 329 2.742372 CTAGTTTGGCGCGGCTGT 60.742 61.111 33.23 16.80 0.00 4.40
329 330 2.281208 TAGTTTGGCGCGGCTGTT 60.281 55.556 33.23 17.83 0.00 3.16
330 331 2.513065 CTAGTTTGGCGCGGCTGTTG 62.513 60.000 33.23 14.34 0.00 3.33
331 332 4.999939 GTTTGGCGCGGCTGTTGG 63.000 66.667 33.23 0.00 0.00 3.77
336 337 3.869272 GCGCGGCTGTTGGAGATG 61.869 66.667 8.83 0.00 0.00 2.90
337 338 3.869272 CGCGGCTGTTGGAGATGC 61.869 66.667 0.00 0.00 0.00 3.91
338 339 2.437359 GCGGCTGTTGGAGATGCT 60.437 61.111 0.00 0.00 0.00 3.79
339 340 2.467826 GCGGCTGTTGGAGATGCTC 61.468 63.158 0.00 0.00 0.00 4.26
343 344 2.284190 GGCTGTTGGAGATGCTCTTAC 58.716 52.381 0.00 0.00 0.00 2.34
362 363 6.680810 TCTTACAGATGATTGCCAAAAGTTG 58.319 36.000 0.00 0.00 0.00 3.16
364 365 5.733620 ACAGATGATTGCCAAAAGTTGAT 57.266 34.783 0.00 0.00 0.00 2.57
393 394 0.036765 TGGTAGGGCGACAATGTCAC 60.037 55.000 14.24 3.27 32.09 3.67
411 412 3.057736 GTCACACTGTAAACGAGAGGCTA 60.058 47.826 0.00 0.00 0.00 3.93
595 1892 1.181098 GGCAAGCAAGGACATGTGGT 61.181 55.000 1.15 0.00 0.00 4.16
624 1921 5.424895 TCTTATTGGCCCAGCACAATAATTT 59.575 36.000 16.47 0.00 44.13 1.82
870 2170 6.873605 TCTTGAAACACTGTGTATGTATCCAG 59.126 38.462 14.69 8.93 0.00 3.86
952 2255 0.250234 ATCCCACCATCATATCGCCG 59.750 55.000 0.00 0.00 0.00 6.46
1316 2668 2.434134 CGAGAGGTACGCACGCAAC 61.434 63.158 0.00 0.00 35.09 4.17
1499 2873 3.889196 TGCATGAACCGTCTTTTGTAC 57.111 42.857 0.00 0.00 0.00 2.90
1716 5328 7.870826 TCATTTAATTGGCAATACGTATCCTG 58.129 34.615 14.05 5.71 0.00 3.86
1736 5348 2.758423 TGACGCACTGCCTCTCTAATTA 59.242 45.455 0.00 0.00 0.00 1.40
1819 5467 0.667184 GCCACAACTGCCAAATTCGG 60.667 55.000 0.00 0.00 0.00 4.30
1837 5485 8.930760 CAAATTCGGCAATCTTTGGTAATTTTA 58.069 29.630 0.00 0.00 0.00 1.52
1883 5540 1.387084 GTTTTCGTGACAGCGCTCTAG 59.613 52.381 7.13 0.00 0.00 2.43
1885 5542 0.879090 TTCGTGACAGCGCTCTAGAA 59.121 50.000 7.13 6.58 0.00 2.10
1921 5581 2.864946 CTCTCCATTTGTGCTGATCGAG 59.135 50.000 0.00 0.00 0.00 4.04
1971 5643 4.365899 TGCACATAGTAGTAGGAACACG 57.634 45.455 0.00 0.00 0.00 4.49
1972 5644 3.114065 GCACATAGTAGTAGGAACACGC 58.886 50.000 0.00 0.00 0.00 5.34
1973 5645 3.703420 CACATAGTAGTAGGAACACGCC 58.297 50.000 0.00 0.00 0.00 5.68
1975 5647 2.113860 TAGTAGTAGGAACACGCCGT 57.886 50.000 0.00 0.00 0.00 5.68
1976 5648 0.524862 AGTAGTAGGAACACGCCGTG 59.475 55.000 16.94 16.94 39.75 4.94
1977 5649 1.074872 GTAGTAGGAACACGCCGTGC 61.075 60.000 18.59 1.16 36.98 5.34
2056 5728 4.478317 TGATAGGGAGGATTGTGATTGGTT 59.522 41.667 0.00 0.00 0.00 3.67
2097 5771 3.689649 CCACCCGACTTAAAATCAAGAGG 59.310 47.826 0.00 0.00 0.00 3.69
2104 5778 6.039616 CGACTTAAAATCAAGAGGGAGAGAG 58.960 44.000 0.00 0.00 0.00 3.20
2230 5915 8.198109 CCTACTGCTTAATAGTGTCTGTACAAT 58.802 37.037 0.00 0.00 37.36 2.71
2246 6147 7.431084 GTCTGTACAATACAAACACCTGTTTTG 59.569 37.037 0.00 5.67 45.07 2.44
2267 6250 3.880490 TGTTTTGCGAAATGTACCAGACT 59.120 39.130 1.61 0.00 0.00 3.24
2515 7609 7.031975 AGCACAAGAAATTAGTAGTACGTACC 58.968 38.462 21.80 7.94 31.06 3.34
2685 11162 1.345741 ACAGTATCTCCCATGCATCCG 59.654 52.381 0.00 0.00 0.00 4.18
2900 11384 5.104259 ACAACCACTCCCAATCTATTCTC 57.896 43.478 0.00 0.00 0.00 2.87
2998 13815 2.057137 ACTTCTGCAAAGGCACAAGA 57.943 45.000 10.86 0.00 45.53 3.02
2999 13816 2.378038 ACTTCTGCAAAGGCACAAGAA 58.622 42.857 10.86 1.68 45.53 2.52
3081 14265 9.548208 GAAAAAGCATAATCTTGTTCTGAGTAC 57.452 33.333 0.00 0.00 37.34 2.73
3098 14282 7.358066 TCTGAGTACAAGAAAAGTAGTACGTG 58.642 38.462 0.00 0.00 41.16 4.49
3104 14288 5.006358 ACAAGAAAAGTAGTACGTGCAACTG 59.994 40.000 6.38 0.00 31.75 3.16
3246 14737 1.146263 GGGCTGTATTACTGCGGCT 59.854 57.895 16.46 0.00 42.94 5.52
3341 15075 3.898509 CTCCGAGCCGAGAGCCTG 61.899 72.222 0.00 0.00 45.47 4.85
3467 15201 2.370445 CCTCCGGCAGTCCTTCCAT 61.370 63.158 0.00 0.00 0.00 3.41
3899 15667 1.510623 CGTACTCGGAACCGACGTG 60.511 63.158 12.04 5.72 44.01 4.49
4135 15917 1.391485 GTGATCACATCGCACACAGTC 59.609 52.381 21.07 0.00 39.52 3.51
4162 15944 1.933021 TGTGTCCGGGACATAAGACT 58.067 50.000 30.90 0.00 44.63 3.24
4174 15956 5.396884 GGGACATAAGACTGGCAGAGTTATT 60.397 44.000 23.66 5.05 33.83 1.40
4175 15957 6.116126 GGACATAAGACTGGCAGAGTTATTT 58.884 40.000 23.66 15.07 33.83 1.40
4176 15958 6.599638 GGACATAAGACTGGCAGAGTTATTTT 59.400 38.462 23.66 11.56 33.83 1.82
4177 15959 7.769044 GGACATAAGACTGGCAGAGTTATTTTA 59.231 37.037 23.66 4.54 33.83 1.52
4178 15960 9.331282 GACATAAGACTGGCAGAGTTATTTTAT 57.669 33.333 23.66 6.75 33.83 1.40
4183 15965 4.096984 ACTGGCAGAGTTATTTTATGCTGC 59.903 41.667 23.66 0.00 45.77 5.25
4187 15969 6.205464 TGGCAGAGTTATTTTATGCTGCTATC 59.795 38.462 0.00 0.00 45.77 2.08
4203 15985 3.109619 GCTATCTGTGCTAGTTCGTCAC 58.890 50.000 0.00 0.00 0.00 3.67
4204 15986 2.264109 ATCTGTGCTAGTTCGTCACG 57.736 50.000 0.00 0.00 33.69 4.35
4225 16007 0.586802 GCTCGGCGTGGATTAATTCC 59.413 55.000 6.85 0.00 45.69 3.01
4226 16008 1.810412 GCTCGGCGTGGATTAATTCCT 60.810 52.381 6.85 0.00 45.68 3.36
4227 16009 1.867233 CTCGGCGTGGATTAATTCCTG 59.133 52.381 6.85 0.00 45.68 3.86
4228 16010 1.208535 TCGGCGTGGATTAATTCCTGT 59.791 47.619 6.85 0.00 45.68 4.00
4229 16011 1.330521 CGGCGTGGATTAATTCCTGTG 59.669 52.381 0.00 0.00 45.68 3.66
4230 16012 1.065551 GGCGTGGATTAATTCCTGTGC 59.934 52.381 0.00 0.79 45.68 4.57
4231 16013 1.742831 GCGTGGATTAATTCCTGTGCA 59.257 47.619 0.00 0.00 45.68 4.57
4232 16014 2.477863 GCGTGGATTAATTCCTGTGCAC 60.478 50.000 10.75 10.75 45.68 4.57
4233 16015 3.009723 CGTGGATTAATTCCTGTGCACT 58.990 45.455 19.41 0.00 45.68 4.40
4234 16016 3.181507 CGTGGATTAATTCCTGTGCACTG 60.182 47.826 19.41 17.70 45.68 3.66
4238 16020 4.574013 GGATTAATTCCTGTGCACTGAGAG 59.426 45.833 23.75 9.96 41.78 3.20
4286 16074 1.670811 CAGGACGCATAAAAATCGCCT 59.329 47.619 0.00 0.00 32.79 5.52
4291 16079 3.006940 ACGCATAAAAATCGCCTTCTGA 58.993 40.909 0.00 0.00 0.00 3.27
4292 16080 3.438781 ACGCATAAAAATCGCCTTCTGAA 59.561 39.130 0.00 0.00 0.00 3.02
4353 16142 4.379243 CAGTCGTCGCCCCAGCTT 62.379 66.667 0.00 0.00 36.60 3.74
4403 16192 3.206374 GCCCCATTTCGGCGAATT 58.794 55.556 24.33 17.17 36.47 2.17
4431 16220 3.340814 CCATATGGGCGAGAATAAGCT 57.659 47.619 14.52 0.00 0.00 3.74
4661 16451 0.454600 CTGCAGTTGATGATGCACCC 59.545 55.000 5.25 0.00 46.97 4.61
4773 16563 6.530120 TGTAGTATGGTTCAGTGTCAAACAT 58.470 36.000 1.22 1.22 0.00 2.71
4783 16573 2.878406 AGTGTCAAACATTGGGTCTTCG 59.122 45.455 0.00 0.00 0.00 3.79
4793 16583 2.876645 GGTCTTCGTGCTCGCTCG 60.877 66.667 2.69 7.00 36.96 5.03
4890 16680 2.879646 GGTACCGGACAACAACAAATCA 59.120 45.455 9.46 0.00 0.00 2.57
4931 16721 1.513158 CGCTCGACATCCTTCCTGT 59.487 57.895 0.00 0.00 0.00 4.00
4939 16729 2.769095 GACATCCTTCCTGTAAGCCTCT 59.231 50.000 0.00 0.00 33.49 3.69
4948 16738 5.505181 TCCTGTAAGCCTCTTGAATCTTT 57.495 39.130 0.00 0.00 0.00 2.52
5087 16877 2.656002 TCTCGAAGTTCATCGGAGGAT 58.344 47.619 3.32 0.00 42.92 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 3.249961 CTTCCCCGGCCTATCCCC 61.250 72.222 0.00 0.00 0.00 4.81
69 70 3.955044 GCTTCCCCGGCCTATCCC 61.955 72.222 0.00 0.00 0.00 3.85
70 71 4.315941 CGCTTCCCCGGCCTATCC 62.316 72.222 0.00 0.00 0.00 2.59
71 72 4.990553 GCGCTTCCCCGGCCTATC 62.991 72.222 0.00 0.00 0.00 2.08
138 139 4.410400 CTCGCAACTCCCACCCCC 62.410 72.222 0.00 0.00 0.00 5.40
141 142 4.373116 TCGCTCGCAACTCCCACC 62.373 66.667 0.00 0.00 0.00 4.61
142 143 2.811317 CTCGCTCGCAACTCCCAC 60.811 66.667 0.00 0.00 0.00 4.61
143 144 4.742201 GCTCGCTCGCAACTCCCA 62.742 66.667 0.00 0.00 0.00 4.37
167 168 2.652893 CTTATTTGCTGCGCCCGCTC 62.653 60.000 17.83 6.41 42.51 5.03
168 169 2.749839 TTATTTGCTGCGCCCGCT 60.750 55.556 17.83 2.93 42.51 5.52
169 170 2.278142 CTTATTTGCTGCGCCCGC 60.278 61.111 4.18 8.60 42.35 6.13
170 171 2.278142 GCTTATTTGCTGCGCCCG 60.278 61.111 4.18 0.00 0.00 6.13
171 172 2.278142 CGCTTATTTGCTGCGCCC 60.278 61.111 4.18 0.00 43.08 6.13
174 175 1.869132 GTGCCGCTTATTTGCTGCG 60.869 57.895 0.00 0.00 44.26 5.18
175 176 1.869132 CGTGCCGCTTATTTGCTGC 60.869 57.895 0.00 0.00 42.22 5.25
176 177 0.794229 CACGTGCCGCTTATTTGCTG 60.794 55.000 0.82 0.00 0.00 4.41
177 178 0.953471 TCACGTGCCGCTTATTTGCT 60.953 50.000 11.67 0.00 0.00 3.91
178 179 0.098728 ATCACGTGCCGCTTATTTGC 59.901 50.000 11.67 0.00 0.00 3.68
179 180 1.268032 GGATCACGTGCCGCTTATTTG 60.268 52.381 11.67 0.00 0.00 2.32
180 181 1.014352 GGATCACGTGCCGCTTATTT 58.986 50.000 11.67 0.00 0.00 1.40
181 182 0.814010 GGGATCACGTGCCGCTTATT 60.814 55.000 11.67 0.00 0.00 1.40
182 183 1.227556 GGGATCACGTGCCGCTTAT 60.228 57.895 11.67 0.00 0.00 1.73
183 184 2.185867 GGGATCACGTGCCGCTTA 59.814 61.111 11.67 0.00 0.00 3.09
209 210 2.201436 ATATCTAGGTCAGCGCGCGG 62.201 60.000 33.06 26.50 0.00 6.46
210 211 1.067743 CATATCTAGGTCAGCGCGCG 61.068 60.000 28.44 28.44 0.00 6.86
211 212 1.347817 GCATATCTAGGTCAGCGCGC 61.348 60.000 26.66 26.66 0.00 6.86
212 213 0.734253 GGCATATCTAGGTCAGCGCG 60.734 60.000 0.00 0.00 0.00 6.86
213 214 0.734253 CGGCATATCTAGGTCAGCGC 60.734 60.000 0.00 0.00 0.00 5.92
214 215 0.734253 GCGGCATATCTAGGTCAGCG 60.734 60.000 0.00 0.00 0.00 5.18
215 216 0.734253 CGCGGCATATCTAGGTCAGC 60.734 60.000 0.00 0.00 0.00 4.26
216 217 0.734253 GCGCGGCATATCTAGGTCAG 60.734 60.000 8.83 0.00 0.00 3.51
217 218 1.289066 GCGCGGCATATCTAGGTCA 59.711 57.895 8.83 0.00 0.00 4.02
218 219 1.801913 CGCGCGGCATATCTAGGTC 60.802 63.158 24.84 0.00 0.00 3.85
219 220 2.258591 CGCGCGGCATATCTAGGT 59.741 61.111 24.84 0.00 0.00 3.08
220 221 3.181967 GCGCGCGGCATATCTAGG 61.182 66.667 33.06 0.00 42.87 3.02
221 222 3.536394 CGCGCGCGGCATATCTAG 61.536 66.667 43.28 13.53 43.84 2.43
251 252 2.507854 TATAGTGGCTCCAGCGGGC 61.508 63.158 0.00 0.00 43.26 6.13
252 253 1.367840 GTATAGTGGCTCCAGCGGG 59.632 63.158 0.00 0.00 43.26 6.13
253 254 1.367840 GGTATAGTGGCTCCAGCGG 59.632 63.158 0.00 0.00 43.26 5.52
254 255 1.007271 CGGTATAGTGGCTCCAGCG 60.007 63.158 0.00 0.00 43.26 5.18
255 256 1.367840 CCGGTATAGTGGCTCCAGC 59.632 63.158 0.00 0.00 41.14 4.85
256 257 1.120530 AACCGGTATAGTGGCTCCAG 58.879 55.000 8.00 0.00 0.00 3.86
257 258 0.828022 CAACCGGTATAGTGGCTCCA 59.172 55.000 8.00 0.00 0.00 3.86
258 259 0.828677 ACAACCGGTATAGTGGCTCC 59.171 55.000 8.00 0.00 0.00 4.70
259 260 1.935933 CACAACCGGTATAGTGGCTC 58.064 55.000 20.89 0.00 0.00 4.70
260 261 0.107848 GCACAACCGGTATAGTGGCT 60.108 55.000 26.31 1.46 32.80 4.75
261 262 1.426041 CGCACAACCGGTATAGTGGC 61.426 60.000 26.31 19.64 32.80 5.01
262 263 1.426041 GCGCACAACCGGTATAGTGG 61.426 60.000 26.31 19.65 32.80 4.00
263 264 1.748647 CGCGCACAACCGGTATAGTG 61.749 60.000 23.10 23.10 35.19 2.74
264 265 1.517694 CGCGCACAACCGGTATAGT 60.518 57.895 8.00 4.14 0.00 2.12
265 266 2.867091 GCGCGCACAACCGGTATAG 61.867 63.158 29.10 3.36 0.00 1.31
266 267 2.002509 TAGCGCGCACAACCGGTATA 62.003 55.000 35.10 9.76 36.51 1.47
267 268 2.839043 TTAGCGCGCACAACCGGTAT 62.839 55.000 35.10 10.92 37.29 2.73
268 269 3.570621 TTAGCGCGCACAACCGGTA 62.571 57.895 35.10 11.41 36.51 4.02
269 270 4.973055 TTAGCGCGCACAACCGGT 62.973 61.111 35.10 12.60 38.78 5.28
270 271 3.243274 TTTTAGCGCGCACAACCGG 62.243 57.895 35.10 0.00 0.00 5.28
271 272 2.072654 GTTTTAGCGCGCACAACCG 61.073 57.895 35.10 0.00 0.00 4.44
272 273 2.072654 CGTTTTAGCGCGCACAACC 61.073 57.895 35.10 16.42 0.00 3.77
273 274 2.072654 CCGTTTTAGCGCGCACAAC 61.073 57.895 35.10 27.68 0.00 3.32
274 275 2.249896 CCGTTTTAGCGCGCACAA 59.750 55.556 35.10 23.41 0.00 3.33
275 276 3.718097 CCCGTTTTAGCGCGCACA 61.718 61.111 35.10 18.34 0.00 4.57
278 279 3.677099 ATTGCCCGTTTTAGCGCGC 62.677 57.895 26.66 26.66 36.35 6.86
279 280 0.731174 AAATTGCCCGTTTTAGCGCG 60.731 50.000 0.00 0.00 0.00 6.86
280 281 1.424403 AAAATTGCCCGTTTTAGCGC 58.576 45.000 0.00 0.00 0.00 5.92
281 282 2.590712 CGTAAAATTGCCCGTTTTAGCG 59.409 45.455 0.00 0.00 33.19 4.26
282 283 2.918600 CCGTAAAATTGCCCGTTTTAGC 59.081 45.455 0.00 0.00 33.19 3.09
283 284 2.918600 GCCGTAAAATTGCCCGTTTTAG 59.081 45.455 0.00 0.00 33.19 1.85
284 285 2.667724 CGCCGTAAAATTGCCCGTTTTA 60.668 45.455 0.00 0.00 31.71 1.52
285 286 1.785768 GCCGTAAAATTGCCCGTTTT 58.214 45.000 0.00 0.00 33.67 2.43
286 287 0.387494 CGCCGTAAAATTGCCCGTTT 60.387 50.000 0.00 0.00 0.00 3.60
287 288 1.210672 CGCCGTAAAATTGCCCGTT 59.789 52.632 0.00 0.00 0.00 4.44
288 289 2.871828 CGCCGTAAAATTGCCCGT 59.128 55.556 0.00 0.00 0.00 5.28
289 290 2.578445 GCGCCGTAAAATTGCCCG 60.578 61.111 0.00 0.00 0.00 6.13
290 291 2.578445 CGCGCCGTAAAATTGCCC 60.578 61.111 0.00 0.00 0.00 5.36
291 292 1.866059 GTCGCGCCGTAAAATTGCC 60.866 57.895 0.00 0.00 0.00 4.52
292 293 2.205842 CGTCGCGCCGTAAAATTGC 61.206 57.895 0.00 0.00 0.00 3.56
293 294 3.942407 CGTCGCGCCGTAAAATTG 58.058 55.556 0.00 0.00 0.00 2.32
310 311 4.166011 CAGCCGCGCCAAACTAGC 62.166 66.667 0.00 0.00 0.00 3.42
311 312 2.325082 AACAGCCGCGCCAAACTAG 61.325 57.895 0.00 0.00 0.00 2.57
312 313 2.281208 AACAGCCGCGCCAAACTA 60.281 55.556 0.00 0.00 0.00 2.24
313 314 3.964875 CAACAGCCGCGCCAAACT 61.965 61.111 0.00 0.00 0.00 2.66
314 315 4.999939 CCAACAGCCGCGCCAAAC 63.000 66.667 0.00 0.00 0.00 2.93
319 320 3.869272 CATCTCCAACAGCCGCGC 61.869 66.667 0.00 0.00 0.00 6.86
320 321 3.869272 GCATCTCCAACAGCCGCG 61.869 66.667 0.00 0.00 0.00 6.46
321 322 2.437359 AGCATCTCCAACAGCCGC 60.437 61.111 0.00 0.00 0.00 6.53
322 323 3.805267 GAGCATCTCCAACAGCCG 58.195 61.111 0.00 0.00 0.00 5.52
339 340 6.680810 TCAACTTTTGGCAATCATCTGTAAG 58.319 36.000 0.00 1.43 0.00 2.34
343 344 4.868171 CCATCAACTTTTGGCAATCATCTG 59.132 41.667 0.00 0.00 0.00 2.90
362 363 1.318576 CCCTACCAAATTCCGCCATC 58.681 55.000 0.00 0.00 0.00 3.51
364 365 1.379309 GCCCTACCAAATTCCGCCA 60.379 57.895 0.00 0.00 0.00 5.69
393 394 3.056749 AGGTTAGCCTCTCGTTTACAGTG 60.057 47.826 0.00 0.00 42.67 3.66
555 1852 9.853555 CTTGCCAACATCTTACATTAATTGTTA 57.146 29.630 1.65 0.00 39.87 2.41
558 1855 6.812656 TGCTTGCCAACATCTTACATTAATTG 59.187 34.615 0.00 0.00 0.00 2.32
559 1856 6.934056 TGCTTGCCAACATCTTACATTAATT 58.066 32.000 0.00 0.00 0.00 1.40
568 1865 1.615392 GTCCTTGCTTGCCAACATCTT 59.385 47.619 0.00 0.00 0.00 2.40
595 1892 0.255890 GCTGGGCCAATAAGAGACCA 59.744 55.000 8.04 0.00 0.00 4.02
624 1921 1.064611 TCAAACGGGTCCAAAACTCCA 60.065 47.619 0.00 0.00 0.00 3.86
673 1970 8.224720 TGAATAGATCGGAAATTTCCCCTATTT 58.775 33.333 30.30 22.35 44.67 1.40
675 1972 7.329746 TGAATAGATCGGAAATTTCCCCTAT 57.670 36.000 27.72 24.76 44.67 2.57
677 1974 5.646692 TGAATAGATCGGAAATTTCCCCT 57.353 39.130 27.72 22.81 44.67 4.79
718 2017 9.973450 TTTGCAAACAAATTAACAATAGCTAGA 57.027 25.926 8.05 0.00 40.84 2.43
819 2119 2.039624 ATGCACCTCTCCCTCCGT 59.960 61.111 0.00 0.00 0.00 4.69
870 2170 6.589139 GTGGTTAGTTGTTACATCTACTCCAC 59.411 42.308 24.04 24.04 35.91 4.02
908 2209 0.395586 TGGTCAGTGGCTTTGCACTT 60.396 50.000 0.00 0.00 0.00 3.16
952 2255 0.538287 AGCCAGGAAGGAACAAGCAC 60.538 55.000 0.00 0.00 41.22 4.40
1000 2305 2.758979 CAAGAGCAAGGAGGAATGCAAT 59.241 45.455 0.00 0.00 44.95 3.56
1316 2668 0.319040 ATCGATCGATTGGTCAGGCG 60.319 55.000 24.60 2.77 0.00 5.52
1546 2942 1.648720 GGCGTCGCATGCATAACAT 59.351 52.632 20.50 0.00 40.66 2.71
1549 2945 2.202810 TCGGCGTCGCATGCATAA 60.203 55.556 20.50 0.00 36.13 1.90
1716 5328 2.301577 AATTAGAGAGGCAGTGCGTC 57.698 50.000 26.43 26.43 42.77 5.19
1819 5467 4.803613 CGCCCTAAAATTACCAAAGATTGC 59.196 41.667 0.00 0.00 0.00 3.56
1837 5485 4.271776 GCTAATTTGTACGTTAATCGCCCT 59.728 41.667 0.00 0.00 44.19 5.19
1883 5540 1.532868 AGAGAGTTGCACGCATGTTTC 59.467 47.619 0.00 0.00 0.00 2.78
1885 5542 1.151668 GAGAGAGTTGCACGCATGTT 58.848 50.000 0.00 0.00 0.00 2.71
1971 5643 6.645415 AGATGTAGTATTAATTAGTGCACGGC 59.355 38.462 12.01 0.00 29.94 5.68
1972 5644 9.125906 GTAGATGTAGTATTAATTAGTGCACGG 57.874 37.037 12.01 0.00 29.94 4.94
1973 5645 9.673454 TGTAGATGTAGTATTAATTAGTGCACG 57.327 33.333 12.01 0.00 29.94 5.34
2022 5694 8.778059 ACAATCCTCCCTATCAGTTATTTGTAA 58.222 33.333 0.00 0.00 0.00 2.41
2037 5709 5.073691 CCTATAACCAATCACAATCCTCCCT 59.926 44.000 0.00 0.00 0.00 4.20
2056 5728 1.742308 GGCACCCTCATTCCCCTATA 58.258 55.000 0.00 0.00 0.00 1.31
2081 5753 7.176589 TCTCTCTCCCTCTTGATTTTAAGTC 57.823 40.000 0.00 0.00 0.00 3.01
2097 5771 6.056090 ACCTTCCAAACTAATTCTCTCTCC 57.944 41.667 0.00 0.00 0.00 3.71
2104 5778 7.330946 GGTTTGCATAACCTTCCAAACTAATTC 59.669 37.037 18.09 0.00 43.82 2.17
2230 5915 4.386049 CGCAAAACAAAACAGGTGTTTGTA 59.614 37.500 8.82 0.00 45.97 2.41
2241 6142 5.517054 TCTGGTACATTTCGCAAAACAAAAC 59.483 36.000 0.00 0.00 38.20 2.43
2246 6147 4.483476 AGTCTGGTACATTTCGCAAAAC 57.517 40.909 0.00 0.00 38.20 2.43
2267 6250 5.741011 ACTTTCCACTTCTGTCAAGTGTTA 58.259 37.500 12.33 0.00 44.52 2.41
2515 7609 8.101654 AGCATCTCGGTTAATTAGTAGTAGAG 57.898 38.462 0.00 0.00 0.00 2.43
2685 11162 3.882888 TGACCAGGACACATCAGAAAAAC 59.117 43.478 0.00 0.00 0.00 2.43
2900 11384 9.204570 ACAAAATACAAGCTACTACTAGTTGTG 57.795 33.333 18.57 10.34 31.86 3.33
2947 11466 4.142773 GGGCAAATCACAAATGCATTTCTG 60.143 41.667 21.70 19.80 41.80 3.02
3081 14265 5.432157 CAGTTGCACGTACTACTTTTCTTG 58.568 41.667 0.00 0.00 0.00 3.02
3098 14282 5.899299 AGAATTAATCTGCATTCCAGTTGC 58.101 37.500 0.00 0.00 42.38 4.17
3166 14633 7.798596 AGCTTGTGAGAGGAATATTAATGTG 57.201 36.000 0.00 0.00 0.00 3.21
3219 14710 0.840617 TAATACAGCCCCATCGCCAA 59.159 50.000 0.00 0.00 0.00 4.52
3352 15086 1.918467 CTTCATCCTGCTGGCCCAGA 61.918 60.000 16.85 0.00 34.77 3.86
3884 15652 1.576421 GTACACGTCGGTTCCGAGT 59.424 57.895 14.40 11.27 39.22 4.18
4135 15917 1.094785 GTCCCGGACACATTGGAATG 58.905 55.000 13.05 0.00 42.10 2.67
4162 15944 4.272489 AGCAGCATAAAATAACTCTGCCA 58.728 39.130 8.22 0.00 45.63 4.92
4174 15956 5.282055 ACTAGCACAGATAGCAGCATAAA 57.718 39.130 0.00 0.00 0.00 1.40
4175 15957 4.944619 ACTAGCACAGATAGCAGCATAA 57.055 40.909 0.00 0.00 0.00 1.90
4176 15958 4.557496 CGAACTAGCACAGATAGCAGCATA 60.557 45.833 0.00 0.00 0.00 3.14
4177 15959 3.726607 GAACTAGCACAGATAGCAGCAT 58.273 45.455 0.00 0.00 0.00 3.79
4178 15960 2.480244 CGAACTAGCACAGATAGCAGCA 60.480 50.000 0.00 0.00 0.00 4.41
4183 15965 3.355270 CGTGACGAACTAGCACAGATAG 58.645 50.000 0.00 0.00 32.96 2.08
4187 15969 2.062779 GCGTGACGAACTAGCACAG 58.937 57.895 10.10 0.00 32.96 3.66
4222 16004 3.230976 TCTAACTCTCAGTGCACAGGAA 58.769 45.455 21.04 1.97 0.00 3.36
4223 16005 2.822561 CTCTAACTCTCAGTGCACAGGA 59.177 50.000 21.04 14.93 0.00 3.86
4224 16006 2.673610 GCTCTAACTCTCAGTGCACAGG 60.674 54.545 21.04 11.03 33.72 4.00
4225 16007 2.029560 TGCTCTAACTCTCAGTGCACAG 60.030 50.000 21.04 11.93 37.54 3.66
4226 16008 1.963515 TGCTCTAACTCTCAGTGCACA 59.036 47.619 21.04 0.00 37.54 4.57
4227 16009 2.732412 TGCTCTAACTCTCAGTGCAC 57.268 50.000 9.40 9.40 37.54 4.57
4228 16010 3.095332 AGATGCTCTAACTCTCAGTGCA 58.905 45.455 2.07 2.07 44.06 4.57
4229 16011 3.490761 GGAGATGCTCTAACTCTCAGTGC 60.491 52.174 0.00 0.00 37.70 4.40
4230 16012 3.698539 TGGAGATGCTCTAACTCTCAGTG 59.301 47.826 0.00 0.00 37.70 3.66
4231 16013 3.953612 CTGGAGATGCTCTAACTCTCAGT 59.046 47.826 0.00 0.00 37.70 3.41
4232 16014 3.243501 GCTGGAGATGCTCTAACTCTCAG 60.244 52.174 0.00 0.00 37.70 3.35
4233 16015 2.692557 GCTGGAGATGCTCTAACTCTCA 59.307 50.000 0.00 0.00 37.70 3.27
4234 16016 2.035832 GGCTGGAGATGCTCTAACTCTC 59.964 54.545 0.00 0.00 35.69 3.20
4238 16020 0.461961 ACGGCTGGAGATGCTCTAAC 59.538 55.000 0.00 0.00 0.00 2.34
4265 16053 1.668751 GGCGATTTTTATGCGTCCTGA 59.331 47.619 0.00 0.00 0.00 3.86
4286 16074 2.258013 CGCCGGTTTGCCTTCAGAA 61.258 57.895 1.90 0.00 0.00 3.02
4291 16079 0.606944 TTGTATCGCCGGTTTGCCTT 60.607 50.000 1.90 0.00 0.00 4.35
4292 16080 0.393808 ATTGTATCGCCGGTTTGCCT 60.394 50.000 1.90 0.00 0.00 4.75
4316 16104 2.978010 CGCAAAACCGCCTCCAGT 60.978 61.111 0.00 0.00 0.00 4.00
4428 16217 2.017049 GAACCACGCCAAATATGAGCT 58.983 47.619 0.00 0.00 0.00 4.09
4661 16451 1.454111 AGGAGATCCGAGACCCACG 60.454 63.158 0.00 0.00 42.08 4.94
4773 16563 2.357034 GCGAGCACGAAGACCCAA 60.357 61.111 8.01 0.00 42.66 4.12
4793 16583 2.096335 TCTTGCACAACATGATCATCGC 59.904 45.455 4.86 4.60 0.00 4.58
4890 16680 2.028748 GCATTTGGTGTGCTCCAATCTT 60.029 45.455 6.56 0.00 45.30 2.40
4931 16721 5.278957 GGTTTGCAAAGATTCAAGAGGCTTA 60.279 40.000 13.26 0.00 0.00 3.09
4939 16729 2.545532 CGCCTGGTTTGCAAAGATTCAA 60.546 45.455 13.26 0.00 0.00 2.69
4948 16738 1.732917 CAAGAACGCCTGGTTTGCA 59.267 52.632 0.00 0.00 39.50 4.08


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

AutoCloner maintained by Alex Coulton.