Multiple sequence alignment - TraesCS4A01G346900

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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 TraesCS4A01G346900 chr4A 100.000 2858 0 0 1 2858 625266203 625263346 0.000000e+00 5278.0
1 TraesCS4A01G346900 chr4A 83.559 1180 176 11 987 2155 625368120 625366948 0.000000e+00 1088.0
2 TraesCS4A01G346900 chr4A 84.302 860 130 5 990 1845 625282144 625281286 0.000000e+00 835.0
3 TraesCS4A01G346900 chr4A 83.182 880 139 6 990 1861 625372737 625371859 0.000000e+00 797.0
4 TraesCS4A01G346900 chr4A 84.017 463 72 2 990 1451 625322262 625321801 7.270000e-121 444.0
5 TraesCS4A01G346900 chr4A 76.954 742 119 33 1288 2011 624351233 624351940 2.690000e-100 375.0
6 TraesCS4A01G346900 chr4A 81.915 282 37 8 705 982 625373047 625372776 2.870000e-55 226.0
7 TraesCS4A01G346900 chr4A 86.667 210 18 7 783 982 625282392 625282183 1.030000e-54 224.0
8 TraesCS4A01G346900 chr4A 82.014 278 27 12 718 982 625322568 625322301 6.200000e-52 215.0
9 TraesCS4A01G346900 chr4A 83.420 193 27 3 1918 2110 625281258 625281071 1.050000e-39 174.0
10 TraesCS4A01G346900 chr5D 94.616 1263 60 5 932 2192 543830546 543831802 0.000000e+00 1949.0
11 TraesCS4A01G346900 chr5D 97.256 656 16 2 2204 2858 243093453 243094107 0.000000e+00 1110.0
12 TraesCS4A01G346900 chr5D 83.252 1224 183 13 987 2199 543776595 543777807 0.000000e+00 1105.0
13 TraesCS4A01G346900 chr5D 93.665 663 38 4 2197 2858 374292251 374292910 0.000000e+00 989.0
14 TraesCS4A01G346900 chr5D 84.149 858 129 7 990 1842 543817173 543818028 0.000000e+00 824.0
15 TraesCS4A01G346900 chr5D 92.647 544 29 9 440 974 543830003 543830544 0.000000e+00 773.0
16 TraesCS4A01G346900 chr5D 85.745 463 64 2 990 1451 543803608 543804069 3.310000e-134 488.0
17 TraesCS4A01G346900 chr5D 81.071 560 95 7 1288 1840 544149690 544150245 1.220000e-118 436.0
18 TraesCS4A01G346900 chr5D 83.986 281 30 7 706 982 543803300 543803569 3.650000e-64 255.0
19 TraesCS4A01G346900 chr5D 81.786 280 41 7 705 982 543771621 543771892 2.870000e-55 226.0
20 TraesCS4A01G346900 chr5D 87.562 201 13 4 1 201 543829818 543830006 3.710000e-54 222.0
21 TraesCS4A01G346900 chr5D 85.714 210 20 7 783 982 543816925 543817134 2.230000e-51 213.0
22 TraesCS4A01G346900 chr5D 82.775 209 29 5 1902 2110 543818045 543818246 2.260000e-41 180.0
23 TraesCS4A01G346900 chr5D 82.564 195 29 3 1916 2110 543778000 543778189 1.760000e-37 167.0
24 TraesCS4A01G346900 chr5B 92.740 1281 85 5 932 2210 685657834 685656560 0.000000e+00 1844.0
25 TraesCS4A01G346900 chr5B 94.665 656 31 2 2204 2858 440264676 440264024 0.000000e+00 1014.0
26 TraesCS4A01G346900 chr5B 89.818 550 35 13 443 974 685658382 685657836 0.000000e+00 686.0
27 TraesCS4A01G346900 chr5B 86.538 208 19 8 783 982 685692052 685691846 1.330000e-53 220.0
28 TraesCS4A01G346900 chr5B 83.333 192 27 3 1919 2110 685690920 685690734 3.790000e-39 172.0
29 TraesCS4A01G346900 chr7D 96.970 660 17 3 2200 2858 540241729 540241072 0.000000e+00 1105.0
30 TraesCS4A01G346900 chr7D 92.946 241 17 0 198 438 31062082 31061842 4.530000e-93 351.0
31 TraesCS4A01G346900 chr7D 91.498 247 20 1 198 444 88202914 88202669 3.530000e-89 339.0
32 TraesCS4A01G346900 chr1B 95.579 656 28 1 2204 2858 466944117 466943462 0.000000e+00 1050.0
33 TraesCS4A01G346900 chr6B 95.303 660 26 2 2202 2856 708040681 708040022 0.000000e+00 1042.0
34 TraesCS4A01G346900 chr6B 92.339 248 19 0 198 445 523343637 523343884 1.260000e-93 353.0
35 TraesCS4A01G346900 chr6A 94.046 655 37 2 2205 2858 3382225 3381572 0.000000e+00 992.0
36 TraesCS4A01G346900 chr6A 100.000 28 0 0 85 112 510884275 510884248 5.000000e-03 52.8
37 TraesCS4A01G346900 chr3B 92.632 665 44 4 2199 2858 380510343 380511007 0.000000e+00 952.0
38 TraesCS4A01G346900 chr1A 91.768 656 49 2 2204 2858 365502405 365501754 0.000000e+00 907.0
39 TraesCS4A01G346900 chr2A 93.388 242 15 1 198 438 362446136 362445895 9.740000e-95 357.0
40 TraesCS4A01G346900 chr2B 92.946 241 16 1 198 438 399350443 399350682 1.630000e-92 350.0
41 TraesCS4A01G346900 chr2B 91.498 247 21 0 198 444 151649506 151649260 9.810000e-90 340.0
42 TraesCS4A01G346900 chr1D 92.245 245 18 1 198 442 27881649 27881892 2.110000e-91 346.0
43 TraesCS4A01G346900 chr1D 100.000 28 0 0 85 112 452753055 452753082 5.000000e-03 52.8
44 TraesCS4A01G346900 chr4D 91.770 243 19 1 200 442 26896015 26895774 1.270000e-88 337.0
45 TraesCS4A01G346900 chr2D 91.701 241 20 0 198 438 295166643 295166403 4.560000e-88 335.0
46 TraesCS4A01G346900 chr7A 100.000 30 0 0 84 113 268866732 268866761 3.980000e-04 56.5


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 TraesCS4A01G346900 chr4A 625263346 625266203 2857 True 5278.000000 5278 100.000000 1 2858 1 chr4A.!!$R1 2857
1 TraesCS4A01G346900 chr4A 625366948 625373047 6099 True 703.666667 1088 82.885333 705 2155 3 chr4A.!!$R4 1450
2 TraesCS4A01G346900 chr4A 625281071 625282392 1321 True 411.000000 835 84.796333 783 2110 3 chr4A.!!$R2 1327
3 TraesCS4A01G346900 chr4A 624351233 624351940 707 False 375.000000 375 76.954000 1288 2011 1 chr4A.!!$F1 723
4 TraesCS4A01G346900 chr4A 625321801 625322568 767 True 329.500000 444 83.015500 718 1451 2 chr4A.!!$R3 733
5 TraesCS4A01G346900 chr5D 243093453 243094107 654 False 1110.000000 1110 97.256000 2204 2858 1 chr5D.!!$F1 654
6 TraesCS4A01G346900 chr5D 374292251 374292910 659 False 989.000000 989 93.665000 2197 2858 1 chr5D.!!$F2 661
7 TraesCS4A01G346900 chr5D 543829818 543831802 1984 False 981.333333 1949 91.608333 1 2192 3 chr5D.!!$F8 2191
8 TraesCS4A01G346900 chr5D 543776595 543778189 1594 False 636.000000 1105 82.908000 987 2199 2 chr5D.!!$F5 1212
9 TraesCS4A01G346900 chr5D 544149690 544150245 555 False 436.000000 436 81.071000 1288 1840 1 chr5D.!!$F4 552
10 TraesCS4A01G346900 chr5D 543816925 543818246 1321 False 405.666667 824 84.212667 783 2110 3 chr5D.!!$F7 1327
11 TraesCS4A01G346900 chr5D 543803300 543804069 769 False 371.500000 488 84.865500 706 1451 2 chr5D.!!$F6 745
12 TraesCS4A01G346900 chr5B 685656560 685658382 1822 True 1265.000000 1844 91.279000 443 2210 2 chr5B.!!$R2 1767
13 TraesCS4A01G346900 chr5B 440264024 440264676 652 True 1014.000000 1014 94.665000 2204 2858 1 chr5B.!!$R1 654
14 TraesCS4A01G346900 chr7D 540241072 540241729 657 True 1105.000000 1105 96.970000 2200 2858 1 chr7D.!!$R3 658
15 TraesCS4A01G346900 chr1B 466943462 466944117 655 True 1050.000000 1050 95.579000 2204 2858 1 chr1B.!!$R1 654
16 TraesCS4A01G346900 chr6B 708040022 708040681 659 True 1042.000000 1042 95.303000 2202 2856 1 chr6B.!!$R1 654
17 TraesCS4A01G346900 chr6A 3381572 3382225 653 True 992.000000 992 94.046000 2205 2858 1 chr6A.!!$R1 653
18 TraesCS4A01G346900 chr3B 380510343 380511007 664 False 952.000000 952 92.632000 2199 2858 1 chr3B.!!$F1 659
19 TraesCS4A01G346900 chr1A 365501754 365502405 651 True 907.000000 907 91.768000 2204 2858 1 chr1A.!!$R1 654

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
555 556 0.106719 ATTAGGCCGGTCACAATGGG 60.107 55.0 9.71 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2491 7696 0.394488 TTCGATCTCTCGGCCTGTCT 60.394 55.0 0.0 0.0 45.1 3.41 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
26 27 3.286353 TGTTGCAATGGACAAGTCTTCA 58.714 40.909 0.59 0.00 0.00 3.02
40 41 6.773638 ACAAGTCTTCAATGACATCTACCTT 58.226 36.000 0.00 0.00 39.27 3.50
41 42 7.907389 ACAAGTCTTCAATGACATCTACCTTA 58.093 34.615 0.00 0.00 39.27 2.69
42 43 7.819900 ACAAGTCTTCAATGACATCTACCTTAC 59.180 37.037 0.00 0.00 39.27 2.34
43 44 6.879400 AGTCTTCAATGACATCTACCTTACC 58.121 40.000 0.00 0.00 39.27 2.85
44 45 6.049790 GTCTTCAATGACATCTACCTTACCC 58.950 44.000 0.00 0.00 36.97 3.69
82 83 2.400399 TCGGTTGAGTGCTAGAAAACG 58.600 47.619 0.00 0.00 34.12 3.60
88 89 2.301870 TGAGTGCTAGAAAACGGACCAT 59.698 45.455 0.00 0.00 0.00 3.55
111 112 3.261643 TCGGCATGAATGGTGAGCTATAT 59.738 43.478 0.00 0.00 0.00 0.86
112 113 4.466015 TCGGCATGAATGGTGAGCTATATA 59.534 41.667 0.00 0.00 0.00 0.86
113 114 5.129320 TCGGCATGAATGGTGAGCTATATAT 59.871 40.000 0.00 0.00 0.00 0.86
114 115 6.323739 TCGGCATGAATGGTGAGCTATATATA 59.676 38.462 0.00 0.00 0.00 0.86
115 116 7.015584 TCGGCATGAATGGTGAGCTATATATAT 59.984 37.037 0.00 0.00 0.00 0.86
116 117 8.306761 CGGCATGAATGGTGAGCTATATATATA 58.693 37.037 0.00 2.49 0.00 0.86
117 118 9.429359 GGCATGAATGGTGAGCTATATATATAC 57.571 37.037 0.00 0.00 0.00 1.47
118 119 9.429359 GCATGAATGGTGAGCTATATATATACC 57.571 37.037 0.00 2.02 0.00 2.73
179 180 7.190871 TGTTTCTAAATTCTTGTTTCACGTCC 58.809 34.615 0.00 0.00 0.00 4.79
187 188 0.736053 TGTTTCACGTCCAGCCAAAC 59.264 50.000 0.00 0.00 0.00 2.93
190 191 0.107410 TTCACGTCCAGCCAAACACT 60.107 50.000 0.00 0.00 0.00 3.55
195 196 2.300723 ACGTCCAGCCAAACACTACATA 59.699 45.455 0.00 0.00 0.00 2.29
200 201 6.113411 GTCCAGCCAAACACTACATATTACT 58.887 40.000 0.00 0.00 0.00 2.24
201 202 6.258068 GTCCAGCCAAACACTACATATTACTC 59.742 42.308 0.00 0.00 0.00 2.59
202 203 5.527582 CCAGCCAAACACTACATATTACTCC 59.472 44.000 0.00 0.00 0.00 3.85
203 204 5.527582 CAGCCAAACACTACATATTACTCCC 59.472 44.000 0.00 0.00 0.00 4.30
204 205 5.428783 AGCCAAACACTACATATTACTCCCT 59.571 40.000 0.00 0.00 0.00 4.20
205 206 5.758784 GCCAAACACTACATATTACTCCCTC 59.241 44.000 0.00 0.00 0.00 4.30
206 207 6.408206 GCCAAACACTACATATTACTCCCTCT 60.408 42.308 0.00 0.00 0.00 3.69
207 208 7.201974 GCCAAACACTACATATTACTCCCTCTA 60.202 40.741 0.00 0.00 0.00 2.43
208 209 8.871125 CCAAACACTACATATTACTCCCTCTAT 58.129 37.037 0.00 0.00 0.00 1.98
212 213 9.656323 ACACTACATATTACTCCCTCTATTTCA 57.344 33.333 0.00 0.00 0.00 2.69
225 226 9.213799 CTCCCTCTATTTCAAAATATAGTGAGC 57.786 37.037 7.13 0.00 29.81 4.26
226 227 8.157476 TCCCTCTATTTCAAAATATAGTGAGCC 58.843 37.037 6.96 0.00 31.03 4.70
227 228 7.391833 CCCTCTATTTCAAAATATAGTGAGCCC 59.608 40.741 6.96 0.00 31.03 5.19
228 229 7.118390 CCTCTATTTCAAAATATAGTGAGCCCG 59.882 40.741 6.96 0.00 31.03 6.13
229 230 4.893424 TTTCAAAATATAGTGAGCCCGC 57.107 40.909 0.00 0.00 0.00 6.13
230 231 2.479837 TCAAAATATAGTGAGCCCGCG 58.520 47.619 0.00 0.00 0.00 6.46
231 232 1.069906 CAAAATATAGTGAGCCCGCGC 60.070 52.381 0.00 0.00 0.00 6.86
244 245 3.515286 CGCGCTTCCCGAGGTCTA 61.515 66.667 5.56 0.00 40.02 2.59
245 246 2.890371 GCGCTTCCCGAGGTCTAA 59.110 61.111 0.00 0.00 40.02 2.10
246 247 1.518792 GCGCTTCCCGAGGTCTAAC 60.519 63.158 0.00 0.00 40.02 2.34
247 248 1.946475 GCGCTTCCCGAGGTCTAACT 61.946 60.000 0.00 0.00 40.02 2.24
248 249 0.531200 CGCTTCCCGAGGTCTAACTT 59.469 55.000 0.00 0.00 40.02 2.66
249 250 1.067071 CGCTTCCCGAGGTCTAACTTT 60.067 52.381 0.00 0.00 40.02 2.66
250 251 2.347731 GCTTCCCGAGGTCTAACTTTG 58.652 52.381 0.00 0.00 0.00 2.77
251 252 2.028385 GCTTCCCGAGGTCTAACTTTGA 60.028 50.000 0.00 0.00 0.00 2.69
252 253 3.369576 GCTTCCCGAGGTCTAACTTTGAT 60.370 47.826 0.00 0.00 0.00 2.57
253 254 4.434520 CTTCCCGAGGTCTAACTTTGATC 58.565 47.826 0.00 0.00 0.00 2.92
254 255 3.437213 TCCCGAGGTCTAACTTTGATCA 58.563 45.455 0.00 0.00 0.00 2.92
255 256 4.030913 TCCCGAGGTCTAACTTTGATCAT 58.969 43.478 0.00 0.00 0.00 2.45
256 257 5.205821 TCCCGAGGTCTAACTTTGATCATA 58.794 41.667 0.00 0.00 0.00 2.15
257 258 5.659525 TCCCGAGGTCTAACTTTGATCATAA 59.340 40.000 0.00 0.00 0.00 1.90
258 259 6.155565 TCCCGAGGTCTAACTTTGATCATAAA 59.844 38.462 0.00 0.00 0.00 1.40
259 260 6.992715 CCCGAGGTCTAACTTTGATCATAAAT 59.007 38.462 0.00 0.00 0.00 1.40
260 261 7.499232 CCCGAGGTCTAACTTTGATCATAAATT 59.501 37.037 0.00 0.00 0.00 1.82
261 262 8.893727 CCGAGGTCTAACTTTGATCATAAATTT 58.106 33.333 0.00 0.00 0.00 1.82
269 270 8.980143 AACTTTGATCATAAATTTAACCACCG 57.020 30.769 1.21 0.00 0.00 4.94
270 271 8.343168 ACTTTGATCATAAATTTAACCACCGA 57.657 30.769 1.21 0.00 0.00 4.69
271 272 8.458843 ACTTTGATCATAAATTTAACCACCGAG 58.541 33.333 1.21 0.01 0.00 4.63
272 273 8.568676 TTTGATCATAAATTTAACCACCGAGA 57.431 30.769 1.21 0.00 0.00 4.04
273 274 7.548196 TGATCATAAATTTAACCACCGAGAC 57.452 36.000 1.21 0.00 0.00 3.36
274 275 6.540914 TGATCATAAATTTAACCACCGAGACC 59.459 38.462 1.21 0.00 0.00 3.85
275 276 4.871557 TCATAAATTTAACCACCGAGACCG 59.128 41.667 1.21 0.00 0.00 4.79
276 277 3.405823 AAATTTAACCACCGAGACCGA 57.594 42.857 0.00 0.00 38.22 4.69
277 278 2.375173 ATTTAACCACCGAGACCGAC 57.625 50.000 0.00 0.00 38.22 4.79
278 279 1.331214 TTTAACCACCGAGACCGACT 58.669 50.000 0.00 0.00 38.22 4.18
279 280 0.599558 TTAACCACCGAGACCGACTG 59.400 55.000 0.00 0.00 38.22 3.51
280 281 1.870055 TAACCACCGAGACCGACTGC 61.870 60.000 0.00 0.00 38.22 4.40
281 282 4.778415 CCACCGAGACCGACTGCG 62.778 72.222 0.00 0.00 38.22 5.18
291 292 2.048222 CGACTGCGGCAGGAGAAA 60.048 61.111 31.38 0.00 39.30 2.52
292 293 1.667830 CGACTGCGGCAGGAGAAAA 60.668 57.895 31.38 0.00 39.30 2.29
293 294 1.227999 CGACTGCGGCAGGAGAAAAA 61.228 55.000 31.38 0.00 39.30 1.94
327 328 9.981114 AATTGGAAACTTCTTTTGAATACGAAT 57.019 25.926 0.00 0.00 37.85 3.34
328 329 9.981114 ATTGGAAACTTCTTTTGAATACGAATT 57.019 25.926 0.00 0.00 37.85 2.17
329 330 9.458374 TTGGAAACTTCTTTTGAATACGAATTC 57.542 29.630 0.00 0.00 41.69 2.17
343 344 9.661563 TGAATACGAATTCACTGGTATAACTTT 57.338 29.630 6.22 0.00 45.17 2.66
346 347 6.608610 ACGAATTCACTGGTATAACTTTTGC 58.391 36.000 6.22 0.00 0.00 3.68
347 348 6.430000 ACGAATTCACTGGTATAACTTTTGCT 59.570 34.615 6.22 0.00 0.00 3.91
348 349 6.961554 CGAATTCACTGGTATAACTTTTGCTC 59.038 38.462 6.22 0.00 0.00 4.26
349 350 6.759497 ATTCACTGGTATAACTTTTGCTCC 57.241 37.500 0.00 0.00 0.00 4.70
350 351 4.585879 TCACTGGTATAACTTTTGCTCCC 58.414 43.478 0.00 0.00 0.00 4.30
351 352 3.374058 CACTGGTATAACTTTTGCTCCCG 59.626 47.826 0.00 0.00 0.00 5.14
352 353 2.354821 CTGGTATAACTTTTGCTCCCGC 59.645 50.000 0.00 0.00 0.00 6.13
353 354 1.674441 GGTATAACTTTTGCTCCCGCC 59.326 52.381 0.00 0.00 34.43 6.13
354 355 1.329599 GTATAACTTTTGCTCCCGCCG 59.670 52.381 0.00 0.00 34.43 6.46
355 356 1.654023 ATAACTTTTGCTCCCGCCGC 61.654 55.000 0.00 0.00 34.43 6.53
356 357 4.887932 TATAACTTTTGCTCCCGCCGCA 62.888 50.000 0.00 0.00 35.22 5.69
357 358 3.669344 CTTTTGCTCCCGCCGCAA 61.669 61.111 0.00 0.00 44.83 4.85
358 359 2.988684 TTTTGCTCCCGCCGCAAT 60.989 55.556 5.33 0.00 45.67 3.56
359 360 2.872337 CTTTTGCTCCCGCCGCAATC 62.872 60.000 5.33 0.00 45.67 2.67
370 371 3.081133 CGCAATCGGTCTCGTTGG 58.919 61.111 0.00 0.00 37.69 3.77
371 372 1.736645 CGCAATCGGTCTCGTTGGT 60.737 57.895 0.00 0.00 37.69 3.67
372 373 1.289109 CGCAATCGGTCTCGTTGGTT 61.289 55.000 0.00 0.00 37.69 3.67
373 374 1.717194 GCAATCGGTCTCGTTGGTTA 58.283 50.000 0.00 0.00 37.69 2.85
374 375 2.070783 GCAATCGGTCTCGTTGGTTAA 58.929 47.619 0.00 0.00 37.69 2.01
375 376 2.481185 GCAATCGGTCTCGTTGGTTAAA 59.519 45.455 0.00 0.00 37.69 1.52
376 377 3.126343 GCAATCGGTCTCGTTGGTTAAAT 59.874 43.478 0.00 0.00 37.69 1.40
377 378 4.379082 GCAATCGGTCTCGTTGGTTAAATT 60.379 41.667 0.00 0.00 37.69 1.82
378 379 5.695818 CAATCGGTCTCGTTGGTTAAATTT 58.304 37.500 0.00 0.00 37.69 1.82
379 380 6.621164 GCAATCGGTCTCGTTGGTTAAATTTA 60.621 38.462 0.00 0.00 37.69 1.40
380 381 7.469260 CAATCGGTCTCGTTGGTTAAATTTAT 58.531 34.615 0.00 0.00 37.69 1.40
381 382 8.605746 CAATCGGTCTCGTTGGTTAAATTTATA 58.394 33.333 0.00 0.00 37.69 0.98
382 383 8.721019 ATCGGTCTCGTTGGTTAAATTTATAA 57.279 30.769 0.00 0.00 37.69 0.98
383 384 8.721019 TCGGTCTCGTTGGTTAAATTTATAAT 57.279 30.769 0.00 0.00 37.69 1.28
384 385 8.819974 TCGGTCTCGTTGGTTAAATTTATAATC 58.180 33.333 0.00 0.00 37.69 1.75
385 386 8.605746 CGGTCTCGTTGGTTAAATTTATAATCA 58.394 33.333 0.00 0.00 0.00 2.57
399 400 8.687824 AATTTATAATCAAAGTTGAAGCACGG 57.312 30.769 0.00 0.00 41.13 4.94
400 401 4.701956 ATAATCAAAGTTGAAGCACGGG 57.298 40.909 0.00 0.00 41.13 5.28
401 402 2.270352 ATCAAAGTTGAAGCACGGGA 57.730 45.000 0.00 0.00 41.13 5.14
402 403 2.045561 TCAAAGTTGAAGCACGGGAA 57.954 45.000 0.00 0.00 33.55 3.97
403 404 2.582052 TCAAAGTTGAAGCACGGGAAT 58.418 42.857 0.00 0.00 33.55 3.01
404 405 3.745799 TCAAAGTTGAAGCACGGGAATA 58.254 40.909 0.00 0.00 33.55 1.75
405 406 3.751175 TCAAAGTTGAAGCACGGGAATAG 59.249 43.478 0.00 0.00 33.55 1.73
406 407 3.695830 AAGTTGAAGCACGGGAATAGA 57.304 42.857 0.00 0.00 0.00 1.98
407 408 3.252974 AGTTGAAGCACGGGAATAGAG 57.747 47.619 0.00 0.00 0.00 2.43
408 409 2.832129 AGTTGAAGCACGGGAATAGAGA 59.168 45.455 0.00 0.00 0.00 3.10
409 410 3.260884 AGTTGAAGCACGGGAATAGAGAA 59.739 43.478 0.00 0.00 0.00 2.87
410 411 3.973206 TGAAGCACGGGAATAGAGAAA 57.027 42.857 0.00 0.00 0.00 2.52
411 412 3.861840 TGAAGCACGGGAATAGAGAAAG 58.138 45.455 0.00 0.00 0.00 2.62
412 413 2.317530 AGCACGGGAATAGAGAAAGC 57.682 50.000 0.00 0.00 0.00 3.51
413 414 1.555075 AGCACGGGAATAGAGAAAGCA 59.445 47.619 0.00 0.00 0.00 3.91
414 415 1.666189 GCACGGGAATAGAGAAAGCAC 59.334 52.381 0.00 0.00 0.00 4.40
415 416 2.678190 GCACGGGAATAGAGAAAGCACT 60.678 50.000 0.00 0.00 0.00 4.40
416 417 3.430374 GCACGGGAATAGAGAAAGCACTA 60.430 47.826 0.00 0.00 0.00 2.74
417 418 4.740934 GCACGGGAATAGAGAAAGCACTAT 60.741 45.833 0.00 0.00 30.52 2.12
418 419 5.509163 GCACGGGAATAGAGAAAGCACTATA 60.509 44.000 0.00 0.00 29.39 1.31
419 420 6.692486 CACGGGAATAGAGAAAGCACTATAT 58.308 40.000 0.00 0.00 29.39 0.86
420 421 7.155328 CACGGGAATAGAGAAAGCACTATATT 58.845 38.462 0.00 0.00 37.12 1.28
421 422 7.657761 CACGGGAATAGAGAAAGCACTATATTT 59.342 37.037 0.00 0.00 35.39 1.40
422 423 8.211629 ACGGGAATAGAGAAAGCACTATATTTT 58.788 33.333 0.00 0.00 35.39 1.82
423 424 9.057089 CGGGAATAGAGAAAGCACTATATTTTT 57.943 33.333 0.00 0.00 35.39 1.94
429 430 7.752695 AGAGAAAGCACTATATTTTTGAACGG 58.247 34.615 0.00 0.00 0.00 4.44
430 431 7.606456 AGAGAAAGCACTATATTTTTGAACGGA 59.394 33.333 0.00 0.00 0.00 4.69
431 432 8.106247 AGAAAGCACTATATTTTTGAACGGAA 57.894 30.769 0.00 0.00 0.00 4.30
432 433 8.237267 AGAAAGCACTATATTTTTGAACGGAAG 58.763 33.333 0.00 0.00 0.00 3.46
433 434 6.436843 AGCACTATATTTTTGAACGGAAGG 57.563 37.500 0.00 0.00 0.00 3.46
434 435 6.177610 AGCACTATATTTTTGAACGGAAGGA 58.822 36.000 0.00 0.00 0.00 3.36
435 436 6.316390 AGCACTATATTTTTGAACGGAAGGAG 59.684 38.462 0.00 0.00 0.00 3.69
436 437 6.093633 GCACTATATTTTTGAACGGAAGGAGT 59.906 38.462 0.00 0.00 0.00 3.85
437 438 7.279313 GCACTATATTTTTGAACGGAAGGAGTA 59.721 37.037 0.00 0.00 0.00 2.59
438 439 8.818057 CACTATATTTTTGAACGGAAGGAGTAG 58.182 37.037 0.00 0.00 0.00 2.57
439 440 8.537858 ACTATATTTTTGAACGGAAGGAGTAGT 58.462 33.333 0.00 0.00 0.00 2.73
465 466 4.203226 TGGTAATTAATGATGGCGCTTCA 58.797 39.130 7.64 11.84 0.00 3.02
480 481 2.680577 GCTTCAGCATTTTCCCACAAG 58.319 47.619 0.00 0.00 41.59 3.16
492 493 9.435688 GCATTTTCCCACAAGTTTTCTATAATT 57.564 29.630 0.00 0.00 0.00 1.40
522 523 7.685594 AGAATTATTCGGCTTAAGAAAAGTCG 58.314 34.615 6.67 5.45 45.74 4.18
554 555 1.762708 AATTAGGCCGGTCACAATGG 58.237 50.000 9.71 0.00 0.00 3.16
555 556 0.106719 ATTAGGCCGGTCACAATGGG 60.107 55.000 9.71 0.00 0.00 4.00
591 596 5.798125 ACCATGTCATCCACACTATCTAG 57.202 43.478 0.00 0.00 38.04 2.43
594 599 6.556495 ACCATGTCATCCACACTATCTAGATT 59.444 38.462 11.25 0.00 38.04 2.40
655 660 3.363787 GGATTTGCCTGTGTCCCTT 57.636 52.632 0.00 0.00 0.00 3.95
664 678 2.487265 GCCTGTGTCCCTTTTTCTCTCA 60.487 50.000 0.00 0.00 0.00 3.27
675 689 3.558931 TTTTCTCTCAGTGCACTGGAA 57.441 42.857 39.04 31.11 43.91 3.53
698 712 1.337384 TAGCCGCATGGGATCACTGT 61.337 55.000 12.02 0.00 38.47 3.55
733 747 1.956477 GGCGACAAGGCAATAATGGAT 59.044 47.619 0.00 0.00 45.92 3.41
775 794 0.877743 GAAGTTGCCAGCTTGAGTCC 59.122 55.000 0.00 0.00 0.00 3.85
849 869 2.757099 GGCAGTCATGGGCCTTGG 60.757 66.667 18.35 4.88 46.74 3.61
899 928 4.456280 TGCAACACATGGTTACAAACAA 57.544 36.364 0.00 0.00 37.72 2.83
930 959 2.446435 AGATAACATGCACCACCCAAC 58.554 47.619 0.00 0.00 0.00 3.77
931 960 2.166829 GATAACATGCACCACCCAACA 58.833 47.619 0.00 0.00 0.00 3.33
932 961 1.614996 TAACATGCACCACCCAACAG 58.385 50.000 0.00 0.00 0.00 3.16
1005 1081 0.681887 CCACAGCTGAATCCATGGCA 60.682 55.000 23.35 0.00 0.00 4.92
1021 1097 2.652530 CAAAATGCGGGCTGCTGT 59.347 55.556 20.66 5.35 46.63 4.40
1317 6013 1.099689 CCAACAACAAACTGGTCGGT 58.900 50.000 0.00 0.00 0.00 4.69
1433 6132 0.811915 CTCAAGGGTCTCGTCATCGT 59.188 55.000 0.00 0.00 38.33 3.73
1461 6160 5.863397 TCGTTCACTAGGTATGGTTTTTACG 59.137 40.000 0.00 0.00 0.00 3.18
1617 6322 3.258123 GGAATAACAACAATGTGGCTGGT 59.742 43.478 0.00 0.00 40.46 4.00
1743 6452 6.433847 TCCGGGAATGACAATAATGTATCT 57.566 37.500 0.00 0.00 40.74 1.98
1806 6515 2.224670 TGGGACCAACAACACTGTATCC 60.225 50.000 0.00 0.00 33.45 2.59
1852 6564 3.851098 AGCAACAAAGTCGTAGGAGATC 58.149 45.455 0.00 0.00 0.00 2.75
1860 6572 7.106239 ACAAAGTCGTAGGAGATCAATGATTT 58.894 34.615 0.00 0.00 0.00 2.17
1871 6583 9.300681 AGGAGATCAATGATTTTGTAAGTGAAA 57.699 29.630 0.00 0.00 0.00 2.69
1886 6598 3.701664 AGTGAAATGGTTCCATCTTCCC 58.298 45.455 4.72 3.83 32.28 3.97
1892 6604 0.902531 GGTTCCATCTTCCCTGACGA 59.097 55.000 0.00 0.00 0.00 4.20
1898 6614 1.480137 CATCTTCCCTGACGAAGCTCT 59.520 52.381 0.00 0.00 39.33 4.09
1968 7157 6.458206 CCAATCGTGTTATGTAACTTCATGGG 60.458 42.308 4.71 0.00 37.12 4.00
2049 7245 4.001618 TGATGAACTGAATGTCAACGGA 57.998 40.909 0.00 0.00 0.00 4.69
2183 7380 1.066605 CTTATGCTGATTGGGCTGTGC 59.933 52.381 0.00 0.00 0.00 4.57
2192 7389 0.251253 TTGGGCTGTGCATCACATGA 60.251 50.000 0.00 0.00 43.71 3.07
2442 7647 0.108615 CCCGACAAGAACAGCTCGAT 60.109 55.000 0.00 0.00 0.00 3.59
2467 7672 1.379916 CATCAGGCACCTCCCAACA 59.620 57.895 0.00 0.00 34.51 3.33
2491 7696 1.686355 ACGACAACCCAATCAAAGCA 58.314 45.000 0.00 0.00 0.00 3.91
2528 7733 2.679059 CGAAGGTCATCCATCAAGCAGT 60.679 50.000 0.00 0.00 35.89 4.40
2541 7750 1.067565 CAAGCAGTGAGAGACGCCTTA 60.068 52.381 0.00 0.00 0.00 2.69
2822 8031 1.351076 TGCTCCATGACACCAAGAGA 58.649 50.000 0.00 0.00 31.86 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.569111 AGAACATAGGGTAAGGTAGATGTCATT 59.431 37.037 0.00 0.00 0.00 2.57
40 41 4.368067 AGGCTACCAAAGAACATAGGGTA 58.632 43.478 0.00 0.00 33.14 3.69
41 42 3.190439 AGGCTACCAAAGAACATAGGGT 58.810 45.455 0.00 0.00 35.66 4.34
42 43 3.741388 CGAGGCTACCAAAGAACATAGGG 60.741 52.174 0.00 0.00 0.00 3.53
43 44 3.458189 CGAGGCTACCAAAGAACATAGG 58.542 50.000 0.00 0.00 0.00 2.57
44 45 3.118738 ACCGAGGCTACCAAAGAACATAG 60.119 47.826 0.00 0.00 0.00 2.23
88 89 0.035152 AGCTCACCATTCATGCCGAA 60.035 50.000 0.00 0.00 38.22 4.30
165 166 0.179234 TGGCTGGACGTGAAACAAGA 59.821 50.000 0.00 0.00 35.74 3.02
169 170 0.736053 TGTTTGGCTGGACGTGAAAC 59.264 50.000 0.00 0.00 0.00 2.78
176 177 6.113411 AGTAATATGTAGTGTTTGGCTGGAC 58.887 40.000 0.00 0.00 0.00 4.02
177 178 6.308015 AGTAATATGTAGTGTTTGGCTGGA 57.692 37.500 0.00 0.00 0.00 3.86
179 180 5.527582 GGGAGTAATATGTAGTGTTTGGCTG 59.472 44.000 0.00 0.00 0.00 4.85
200 201 8.157476 GGCTCACTATATTTTGAAATAGAGGGA 58.843 37.037 17.39 17.39 45.34 4.20
201 202 7.391833 GGGCTCACTATATTTTGAAATAGAGGG 59.608 40.741 17.53 14.95 42.24 4.30
202 203 7.118390 CGGGCTCACTATATTTTGAAATAGAGG 59.882 40.741 17.53 9.82 41.91 3.69
203 204 7.360438 GCGGGCTCACTATATTTTGAAATAGAG 60.360 40.741 13.67 13.67 42.78 2.43
204 205 6.426937 GCGGGCTCACTATATTTTGAAATAGA 59.573 38.462 2.98 0.00 34.62 1.98
205 206 6.603095 GCGGGCTCACTATATTTTGAAATAG 58.397 40.000 2.98 0.00 34.62 1.73
206 207 5.178623 CGCGGGCTCACTATATTTTGAAATA 59.821 40.000 0.00 0.00 35.52 1.40
207 208 4.024048 CGCGGGCTCACTATATTTTGAAAT 60.024 41.667 0.00 0.00 0.00 2.17
208 209 3.311322 CGCGGGCTCACTATATTTTGAAA 59.689 43.478 0.00 0.00 0.00 2.69
209 210 2.869801 CGCGGGCTCACTATATTTTGAA 59.130 45.455 0.00 0.00 0.00 2.69
210 211 2.479837 CGCGGGCTCACTATATTTTGA 58.520 47.619 0.00 0.00 0.00 2.69
211 212 1.069906 GCGCGGGCTCACTATATTTTG 60.070 52.381 18.33 0.00 35.83 2.44
212 213 1.226746 GCGCGGGCTCACTATATTTT 58.773 50.000 18.33 0.00 35.83 1.82
213 214 2.914379 GCGCGGGCTCACTATATTT 58.086 52.632 18.33 0.00 35.83 1.40
214 215 4.675404 GCGCGGGCTCACTATATT 57.325 55.556 18.33 0.00 35.83 1.28
227 228 3.060020 TTAGACCTCGGGAAGCGCG 62.060 63.158 0.00 0.00 41.10 6.86
228 229 1.518792 GTTAGACCTCGGGAAGCGC 60.519 63.158 0.00 0.00 0.00 5.92
229 230 0.531200 AAGTTAGACCTCGGGAAGCG 59.469 55.000 0.00 0.00 0.00 4.68
230 231 2.028385 TCAAAGTTAGACCTCGGGAAGC 60.028 50.000 0.00 0.00 0.00 3.86
231 232 3.955650 TCAAAGTTAGACCTCGGGAAG 57.044 47.619 0.00 0.00 0.00 3.46
232 233 3.835978 TGATCAAAGTTAGACCTCGGGAA 59.164 43.478 0.00 0.00 0.00 3.97
233 234 3.437213 TGATCAAAGTTAGACCTCGGGA 58.563 45.455 0.00 0.00 0.00 5.14
234 235 3.887621 TGATCAAAGTTAGACCTCGGG 57.112 47.619 0.00 0.00 0.00 5.14
235 236 8.438676 AATTTATGATCAAAGTTAGACCTCGG 57.561 34.615 0.00 0.00 0.00 4.63
244 245 8.798402 TCGGTGGTTAAATTTATGATCAAAGTT 58.202 29.630 0.00 0.00 31.36 2.66
245 246 8.343168 TCGGTGGTTAAATTTATGATCAAAGT 57.657 30.769 0.00 0.00 0.00 2.66
246 247 8.673711 TCTCGGTGGTTAAATTTATGATCAAAG 58.326 33.333 0.00 0.00 0.00 2.77
247 248 8.455682 GTCTCGGTGGTTAAATTTATGATCAAA 58.544 33.333 0.00 0.00 0.00 2.69
248 249 7.066525 GGTCTCGGTGGTTAAATTTATGATCAA 59.933 37.037 0.00 0.00 0.00 2.57
249 250 6.540914 GGTCTCGGTGGTTAAATTTATGATCA 59.459 38.462 0.00 0.00 0.00 2.92
250 251 6.292703 CGGTCTCGGTGGTTAAATTTATGATC 60.293 42.308 0.00 0.00 0.00 2.92
251 252 5.526111 CGGTCTCGGTGGTTAAATTTATGAT 59.474 40.000 0.00 0.00 0.00 2.45
252 253 4.871557 CGGTCTCGGTGGTTAAATTTATGA 59.128 41.667 0.00 0.00 0.00 2.15
253 254 4.871557 TCGGTCTCGGTGGTTAAATTTATG 59.128 41.667 0.00 0.00 36.95 1.90
254 255 4.872124 GTCGGTCTCGGTGGTTAAATTTAT 59.128 41.667 0.00 0.00 36.95 1.40
255 256 4.021192 AGTCGGTCTCGGTGGTTAAATTTA 60.021 41.667 0.00 0.00 36.95 1.40
256 257 3.069289 GTCGGTCTCGGTGGTTAAATTT 58.931 45.455 0.00 0.00 36.95 1.82
257 258 2.301009 AGTCGGTCTCGGTGGTTAAATT 59.699 45.455 0.00 0.00 36.95 1.82
258 259 1.897802 AGTCGGTCTCGGTGGTTAAAT 59.102 47.619 0.00 0.00 36.95 1.40
259 260 1.000060 CAGTCGGTCTCGGTGGTTAAA 60.000 52.381 0.00 0.00 36.95 1.52
260 261 0.599558 CAGTCGGTCTCGGTGGTTAA 59.400 55.000 0.00 0.00 36.95 2.01
261 262 1.870055 GCAGTCGGTCTCGGTGGTTA 61.870 60.000 0.00 0.00 36.95 2.85
262 263 3.048602 CAGTCGGTCTCGGTGGTT 58.951 61.111 0.00 0.00 36.95 3.67
263 264 3.681835 GCAGTCGGTCTCGGTGGT 61.682 66.667 0.00 0.00 36.95 4.16
264 265 4.778415 CGCAGTCGGTCTCGGTGG 62.778 72.222 0.00 0.00 36.95 4.61
274 275 1.227999 TTTTTCTCCTGCCGCAGTCG 61.228 55.000 18.98 9.39 0.00 4.18
275 276 2.629002 TTTTTCTCCTGCCGCAGTC 58.371 52.632 18.98 0.00 0.00 3.51
276 277 4.898607 TTTTTCTCCTGCCGCAGT 57.101 50.000 18.98 0.00 0.00 4.40
301 302 9.981114 ATTCGTATTCAAAAGAAGTTTCCAATT 57.019 25.926 0.00 0.00 0.00 2.32
302 303 9.981114 AATTCGTATTCAAAAGAAGTTTCCAAT 57.019 25.926 0.00 0.00 0.00 3.16
303 304 9.458374 GAATTCGTATTCAAAAGAAGTTTCCAA 57.542 29.630 9.62 0.00 39.96 3.53
304 305 8.625651 TGAATTCGTATTCAAAAGAAGTTTCCA 58.374 29.630 14.23 0.00 45.38 3.53
317 318 9.661563 AAAGTTATACCAGTGAATTCGTATTCA 57.338 29.630 12.80 12.80 45.99 2.57
320 321 8.395633 GCAAAAGTTATACCAGTGAATTCGTAT 58.604 33.333 0.04 5.16 0.00 3.06
321 322 7.604927 AGCAAAAGTTATACCAGTGAATTCGTA 59.395 33.333 0.04 0.00 0.00 3.43
322 323 6.430000 AGCAAAAGTTATACCAGTGAATTCGT 59.570 34.615 0.04 0.00 0.00 3.85
323 324 6.842163 AGCAAAAGTTATACCAGTGAATTCG 58.158 36.000 0.04 0.00 0.00 3.34
324 325 7.251281 GGAGCAAAAGTTATACCAGTGAATTC 58.749 38.462 0.00 0.00 0.00 2.17
325 326 6.152831 GGGAGCAAAAGTTATACCAGTGAATT 59.847 38.462 0.00 0.00 0.00 2.17
326 327 5.652452 GGGAGCAAAAGTTATACCAGTGAAT 59.348 40.000 0.00 0.00 0.00 2.57
327 328 5.007682 GGGAGCAAAAGTTATACCAGTGAA 58.992 41.667 0.00 0.00 0.00 3.18
328 329 4.585879 GGGAGCAAAAGTTATACCAGTGA 58.414 43.478 0.00 0.00 0.00 3.41
329 330 3.374058 CGGGAGCAAAAGTTATACCAGTG 59.626 47.826 0.00 0.00 0.00 3.66
330 331 3.606687 CGGGAGCAAAAGTTATACCAGT 58.393 45.455 0.00 0.00 0.00 4.00
353 354 1.289109 AACCAACGAGACCGATTGCG 61.289 55.000 0.00 0.00 39.50 4.85
354 355 1.717194 TAACCAACGAGACCGATTGC 58.283 50.000 0.00 0.00 39.50 3.56
355 356 4.939509 ATTTAACCAACGAGACCGATTG 57.060 40.909 0.00 0.00 39.50 2.67
356 357 5.952526 AAATTTAACCAACGAGACCGATT 57.047 34.783 0.00 0.00 39.50 3.34
357 358 8.721019 TTATAAATTTAACCAACGAGACCGAT 57.279 30.769 1.21 0.00 39.50 4.18
358 359 8.721019 ATTATAAATTTAACCAACGAGACCGA 57.279 30.769 1.21 0.00 39.50 4.69
359 360 8.605746 TGATTATAAATTTAACCAACGAGACCG 58.394 33.333 1.21 0.00 42.50 4.79
373 374 9.139174 CCGTGCTTCAACTTTGATTATAAATTT 57.861 29.630 0.00 0.00 37.00 1.82
374 375 7.759433 CCCGTGCTTCAACTTTGATTATAAATT 59.241 33.333 0.00 0.00 37.00 1.82
375 376 7.122055 TCCCGTGCTTCAACTTTGATTATAAAT 59.878 33.333 0.00 0.00 37.00 1.40
376 377 6.431543 TCCCGTGCTTCAACTTTGATTATAAA 59.568 34.615 0.00 0.00 37.00 1.40
377 378 5.941058 TCCCGTGCTTCAACTTTGATTATAA 59.059 36.000 0.00 0.00 37.00 0.98
378 379 5.492895 TCCCGTGCTTCAACTTTGATTATA 58.507 37.500 0.00 0.00 37.00 0.98
379 380 4.331968 TCCCGTGCTTCAACTTTGATTAT 58.668 39.130 0.00 0.00 37.00 1.28
380 381 3.745799 TCCCGTGCTTCAACTTTGATTA 58.254 40.909 0.00 0.00 37.00 1.75
381 382 2.582052 TCCCGTGCTTCAACTTTGATT 58.418 42.857 0.00 0.00 37.00 2.57
382 383 2.270352 TCCCGTGCTTCAACTTTGAT 57.730 45.000 0.00 0.00 37.00 2.57
383 384 2.045561 TTCCCGTGCTTCAACTTTGA 57.954 45.000 0.00 0.00 34.92 2.69
384 385 3.751175 TCTATTCCCGTGCTTCAACTTTG 59.249 43.478 0.00 0.00 0.00 2.77
385 386 4.003648 CTCTATTCCCGTGCTTCAACTTT 58.996 43.478 0.00 0.00 0.00 2.66
386 387 3.260884 TCTCTATTCCCGTGCTTCAACTT 59.739 43.478 0.00 0.00 0.00 2.66
387 388 2.832129 TCTCTATTCCCGTGCTTCAACT 59.168 45.455 0.00 0.00 0.00 3.16
388 389 3.247006 TCTCTATTCCCGTGCTTCAAC 57.753 47.619 0.00 0.00 0.00 3.18
389 390 3.973206 TTCTCTATTCCCGTGCTTCAA 57.027 42.857 0.00 0.00 0.00 2.69
390 391 3.861840 CTTTCTCTATTCCCGTGCTTCA 58.138 45.455 0.00 0.00 0.00 3.02
391 392 2.609916 GCTTTCTCTATTCCCGTGCTTC 59.390 50.000 0.00 0.00 0.00 3.86
392 393 2.027192 TGCTTTCTCTATTCCCGTGCTT 60.027 45.455 0.00 0.00 0.00 3.91
393 394 1.555075 TGCTTTCTCTATTCCCGTGCT 59.445 47.619 0.00 0.00 0.00 4.40
394 395 1.666189 GTGCTTTCTCTATTCCCGTGC 59.334 52.381 0.00 0.00 0.00 5.34
395 396 3.252974 AGTGCTTTCTCTATTCCCGTG 57.747 47.619 0.00 0.00 0.00 4.94
396 397 6.919775 ATATAGTGCTTTCTCTATTCCCGT 57.080 37.500 0.00 0.00 32.87 5.28
397 398 8.608844 AAAATATAGTGCTTTCTCTATTCCCG 57.391 34.615 0.00 0.00 32.87 5.14
403 404 8.879759 CCGTTCAAAAATATAGTGCTTTCTCTA 58.120 33.333 0.00 0.00 0.00 2.43
404 405 7.606456 TCCGTTCAAAAATATAGTGCTTTCTCT 59.394 33.333 0.00 0.00 0.00 3.10
405 406 7.748847 TCCGTTCAAAAATATAGTGCTTTCTC 58.251 34.615 0.00 0.00 0.00 2.87
406 407 7.681939 TCCGTTCAAAAATATAGTGCTTTCT 57.318 32.000 0.00 0.00 0.00 2.52
407 408 7.484959 CCTTCCGTTCAAAAATATAGTGCTTTC 59.515 37.037 0.00 0.00 0.00 2.62
408 409 7.175990 TCCTTCCGTTCAAAAATATAGTGCTTT 59.824 33.333 0.00 0.00 0.00 3.51
409 410 6.657541 TCCTTCCGTTCAAAAATATAGTGCTT 59.342 34.615 0.00 0.00 0.00 3.91
410 411 6.177610 TCCTTCCGTTCAAAAATATAGTGCT 58.822 36.000 0.00 0.00 0.00 4.40
411 412 6.093633 ACTCCTTCCGTTCAAAAATATAGTGC 59.906 38.462 0.00 0.00 0.00 4.40
412 413 7.611213 ACTCCTTCCGTTCAAAAATATAGTG 57.389 36.000 0.00 0.00 0.00 2.74
413 414 8.537858 ACTACTCCTTCCGTTCAAAAATATAGT 58.462 33.333 0.00 0.00 0.00 2.12
414 415 8.943909 ACTACTCCTTCCGTTCAAAAATATAG 57.056 34.615 0.00 0.00 0.00 1.31
416 417 9.901172 AATACTACTCCTTCCGTTCAAAAATAT 57.099 29.630 0.00 0.00 0.00 1.28
417 418 9.729281 AAATACTACTCCTTCCGTTCAAAAATA 57.271 29.630 0.00 0.00 0.00 1.40
418 419 8.512138 CAAATACTACTCCTTCCGTTCAAAAAT 58.488 33.333 0.00 0.00 0.00 1.82
419 420 7.040961 CCAAATACTACTCCTTCCGTTCAAAAA 60.041 37.037 0.00 0.00 0.00 1.94
420 421 6.428771 CCAAATACTACTCCTTCCGTTCAAAA 59.571 38.462 0.00 0.00 0.00 2.44
421 422 5.935789 CCAAATACTACTCCTTCCGTTCAAA 59.064 40.000 0.00 0.00 0.00 2.69
422 423 5.012354 ACCAAATACTACTCCTTCCGTTCAA 59.988 40.000 0.00 0.00 0.00 2.69
423 424 4.529377 ACCAAATACTACTCCTTCCGTTCA 59.471 41.667 0.00 0.00 0.00 3.18
424 425 5.082251 ACCAAATACTACTCCTTCCGTTC 57.918 43.478 0.00 0.00 0.00 3.95
425 426 6.610075 TTACCAAATACTACTCCTTCCGTT 57.390 37.500 0.00 0.00 0.00 4.44
426 427 6.803366 ATTACCAAATACTACTCCTTCCGT 57.197 37.500 0.00 0.00 0.00 4.69
427 428 9.774413 ATTAATTACCAAATACTACTCCTTCCG 57.226 33.333 0.00 0.00 0.00 4.30
434 435 8.999431 CGCCATCATTAATTACCAAATACTACT 58.001 33.333 0.00 0.00 0.00 2.57
435 436 7.749126 GCGCCATCATTAATTACCAAATACTAC 59.251 37.037 0.00 0.00 0.00 2.73
436 437 7.663905 AGCGCCATCATTAATTACCAAATACTA 59.336 33.333 2.29 0.00 0.00 1.82
437 438 6.490040 AGCGCCATCATTAATTACCAAATACT 59.510 34.615 2.29 0.00 0.00 2.12
438 439 6.677913 AGCGCCATCATTAATTACCAAATAC 58.322 36.000 2.29 0.00 0.00 1.89
439 440 6.892658 AGCGCCATCATTAATTACCAAATA 57.107 33.333 2.29 0.00 0.00 1.40
440 441 5.789643 AGCGCCATCATTAATTACCAAAT 57.210 34.783 2.29 0.00 0.00 2.32
441 442 5.126222 TGAAGCGCCATCATTAATTACCAAA 59.874 36.000 2.29 0.00 0.00 3.28
465 466 6.670695 ATAGAAAACTTGTGGGAAAATGCT 57.329 33.333 0.00 0.00 0.00 3.79
522 523 4.938226 CCGGCCTAATTTGAGGAATATCTC 59.062 45.833 0.00 0.00 39.15 2.75
554 555 2.292267 CATGGTATGGCTGAAGACACC 58.708 52.381 0.00 0.00 34.80 4.16
555 556 2.939103 GACATGGTATGGCTGAAGACAC 59.061 50.000 0.00 0.00 34.80 3.67
591 596 6.197655 GGACGTTAAAAGAAACAACACCAATC 59.802 38.462 0.00 0.00 0.00 2.67
594 599 4.437121 CGGACGTTAAAAGAAACAACACCA 60.437 41.667 0.00 0.00 0.00 4.17
610 615 7.159372 AGGAAAGATATTATTATGCGGACGTT 58.841 34.615 0.00 0.00 0.00 3.99
643 648 2.155279 GAGAGAAAAAGGGACACAGGC 58.845 52.381 0.00 0.00 0.00 4.85
644 649 3.181450 ACTGAGAGAAAAAGGGACACAGG 60.181 47.826 0.00 0.00 0.00 4.00
645 650 3.812053 CACTGAGAGAAAAAGGGACACAG 59.188 47.826 0.00 0.00 0.00 3.66
647 652 2.550180 GCACTGAGAGAAAAAGGGACAC 59.450 50.000 0.00 0.00 0.00 3.67
649 654 2.550180 GTGCACTGAGAGAAAAAGGGAC 59.450 50.000 10.32 0.00 0.00 4.46
651 656 2.551459 CAGTGCACTGAGAGAAAAAGGG 59.449 50.000 38.12 9.27 46.59 3.95
652 657 2.551459 CCAGTGCACTGAGAGAAAAAGG 59.449 50.000 41.50 21.12 46.59 3.11
653 658 3.470709 TCCAGTGCACTGAGAGAAAAAG 58.529 45.455 41.50 23.97 46.59 2.27
654 659 3.558931 TCCAGTGCACTGAGAGAAAAA 57.441 42.857 41.50 15.82 46.59 1.94
655 660 3.118261 AGTTCCAGTGCACTGAGAGAAAA 60.118 43.478 41.50 23.34 46.59 2.29
664 678 1.137086 CGGCTATAGTTCCAGTGCACT 59.863 52.381 15.25 15.25 0.00 4.40
675 689 1.276421 GTGATCCCATGCGGCTATAGT 59.724 52.381 0.00 0.00 0.00 2.12
698 712 0.539518 TCGCCAGCTGCCATAGTTAA 59.460 50.000 8.66 0.00 36.24 2.01
849 869 3.627577 TCGGTACTATTAGTCCGTGGTTC 59.372 47.826 22.58 1.38 38.83 3.62
899 928 7.065803 GTGGTGCATGTTATCTTATAGTGTGTT 59.934 37.037 0.00 0.00 0.00 3.32
1005 1081 1.290009 GAACAGCAGCCCGCATTTT 59.710 52.632 0.00 0.00 46.13 1.82
1021 1097 2.376518 AGAGGAATGCCAAGAACAGGAA 59.623 45.455 0.00 0.00 36.29 3.36
1065 1141 2.933287 AGGTCATCGGGGTGGCAA 60.933 61.111 0.00 0.00 0.00 4.52
1317 6013 1.419762 CCAATCCACGATGGGATGGTA 59.580 52.381 8.39 0.00 46.96 3.25
1433 6132 3.167485 ACCATACCTAGTGAACGACCAA 58.833 45.455 0.00 0.00 0.00 3.67
1461 6160 4.107622 GCTTCACATACAATGGCATGTTC 58.892 43.478 0.00 0.00 33.12 3.18
1617 6322 3.125316 GGTTACGACAGTGTTGTTGCTA 58.875 45.455 21.15 0.42 41.62 3.49
1672 6377 5.997746 CGATATGTTTGTCCCCAGATACAAT 59.002 40.000 0.00 0.00 35.64 2.71
1729 6438 5.703130 GGAAGCTCCCAGATACATTATTGTC 59.297 44.000 0.00 0.00 37.28 3.18
1743 6452 1.968493 GATACGGTATGGAAGCTCCCA 59.032 52.381 5.18 0.00 41.05 4.37
1806 6515 1.593006 GATACGACATGGTTGCTTCCG 59.407 52.381 0.00 0.00 0.00 4.30
1852 6564 8.711457 GGAACCATTTCACTTACAAAATCATTG 58.289 33.333 0.00 0.00 32.80 2.82
1860 6572 6.208599 GGAAGATGGAACCATTTCACTTACAA 59.791 38.462 19.54 0.00 36.70 2.41
1871 6583 1.210478 CGTCAGGGAAGATGGAACCAT 59.790 52.381 6.00 6.00 39.69 3.55
1886 6598 1.528586 CAACCACAAGAGCTTCGTCAG 59.471 52.381 0.00 0.00 0.00 3.51
1892 6604 2.301346 CTTGGACAACCACAAGAGCTT 58.699 47.619 0.00 0.00 46.80 3.74
1898 6614 1.340211 ACCGAACTTGGACAACCACAA 60.340 47.619 0.00 0.00 46.80 3.33
2030 7225 3.338249 CCTCCGTTGACATTCAGTTCAT 58.662 45.455 0.00 0.00 0.00 2.57
2034 7229 0.687354 AGCCTCCGTTGACATTCAGT 59.313 50.000 0.00 0.00 0.00 3.41
2041 7236 3.257933 CTGCAAGCCTCCGTTGAC 58.742 61.111 0.00 0.00 0.00 3.18
2442 7647 1.555075 GGAGGTGCCTGATGTCTTGTA 59.445 52.381 0.00 0.00 0.00 2.41
2467 7672 2.631160 TGATTGGGTTGTCGTTGAGT 57.369 45.000 0.00 0.00 0.00 3.41
2491 7696 0.394488 TTCGATCTCTCGGCCTGTCT 60.394 55.000 0.00 0.00 45.10 3.41
2528 7733 0.824109 CATGGGTAAGGCGTCTCTCA 59.176 55.000 0.00 0.00 0.00 3.27
2541 7750 3.210012 AAAGAGTGGCGCCATGGGT 62.210 57.895 35.23 17.99 0.00 4.51
2822 8031 1.204941 GTCAGGCGTCAACCAGTCTAT 59.795 52.381 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.