Multiple sequence alignment - TraesCS3D01G384800

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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 TraesCS3D01G384800 chr3D 100.000 2928 0 0 1 2928 500089625 500092552 0.000000e+00 5408.0
1 TraesCS3D01G384800 chr3D 93.949 1289 42 12 657 1938 500018402 500019661 0.000000e+00 1916.0
2 TraesCS3D01G384800 chr3D 91.667 720 32 6 656 1372 500127206 500127900 0.000000e+00 972.0
3 TraesCS3D01G384800 chr3D 86.272 743 58 19 1080 1788 520245890 520246622 0.000000e+00 767.0
4 TraesCS3D01G384800 chr3D 86.771 703 45 16 1297 1973 520281343 520282023 0.000000e+00 739.0
5 TraesCS3D01G384800 chr3D 94.235 451 13 5 1499 1938 500127898 500128346 0.000000e+00 676.0
6 TraesCS3D01G384800 chr3D 95.238 126 6 0 2803 2928 8966441 8966566 1.780000e-47 200.0
7 TraesCS3D01G384800 chr4D 91.914 1212 53 12 657 1857 499214365 499213188 0.000000e+00 1653.0
8 TraesCS3D01G384800 chr4D 79.876 323 44 11 230 547 6748596 6748290 1.770000e-52 217.0
9 TraesCS3D01G384800 chr3A 91.431 1132 53 10 657 1780 639662384 639663479 0.000000e+00 1513.0
10 TraesCS3D01G384800 chr3A 91.254 1132 54 11 657 1780 639655587 639656681 0.000000e+00 1500.0
11 TraesCS3D01G384800 chr3A 92.315 1002 64 7 1938 2928 639579039 639580038 0.000000e+00 1411.0
12 TraesCS3D01G384800 chr3A 86.220 762 63 12 1080 1805 655786409 655787164 0.000000e+00 787.0
13 TraesCS3D01G384800 chr3A 86.013 765 62 19 1080 1805 655668768 655669526 0.000000e+00 778.0
14 TraesCS3D01G384800 chr3A 85.061 656 77 14 18 657 551702343 551701693 0.000000e+00 649.0
15 TraesCS3D01G384800 chr3A 92.330 339 13 2 657 995 639566759 639567084 1.230000e-128 470.0
16 TraesCS3D01G384800 chr3A 92.330 339 13 2 657 995 639576494 639576819 1.230000e-128 470.0
17 TraesCS3D01G384800 chr3A 95.050 101 5 0 1838 1938 639554384 639554484 3.020000e-35 159.0
18 TraesCS3D01G384800 chr3A 95.050 101 5 0 1838 1938 639557631 639557731 3.020000e-35 159.0
19 TraesCS3D01G384800 chr3A 95.050 101 5 0 1838 1938 639560874 639560974 3.020000e-35 159.0
20 TraesCS3D01G384800 chr3B 88.240 1301 91 25 657 1948 661756927 661758174 0.000000e+00 1498.0
21 TraesCS3D01G384800 chr3B 88.163 1301 89 28 657 1948 661785456 661786700 0.000000e+00 1489.0
22 TraesCS3D01G384800 chr3B 92.088 910 57 10 1472 2371 661568408 661569312 0.000000e+00 1267.0
23 TraesCS3D01G384800 chr3B 91.492 905 64 6 1477 2371 661570103 661571004 0.000000e+00 1232.0
24 TraesCS3D01G384800 chr3B 83.667 949 87 42 1080 1973 685066943 685067878 0.000000e+00 832.0
25 TraesCS3D01G384800 chr3B 91.631 466 21 11 1907 2369 661567122 661567572 1.920000e-176 628.0
26 TraesCS3D01G384800 chr3B 92.822 404 28 1 1037 1439 661568015 661568418 4.200000e-163 584.0
27 TraesCS3D01G384800 chr3B 87.648 421 37 4 657 1077 661571151 661571556 2.640000e-130 475.0
28 TraesCS3D01G384800 chr3B 94.650 243 12 1 1037 1278 661569756 661569998 2.750000e-100 375.0
29 TraesCS3D01G384800 chr3B 88.291 316 22 2 657 972 661569461 661569761 5.960000e-97 364.0
30 TraesCS3D01G384800 chr3B 90.909 220 16 4 1936 2154 661787955 661788171 2.850000e-75 292.0
31 TraesCS3D01G384800 chr3B 91.121 214 13 3 1936 2147 661759458 661759667 4.780000e-73 285.0
32 TraesCS3D01G384800 chr4A 93.846 520 30 2 107 625 11985451 11984933 0.000000e+00 782.0
33 TraesCS3D01G384800 chr4A 91.106 461 38 3 2329 2788 313704129 313704587 3.200000e-174 621.0
34 TraesCS3D01G384800 chr4A 100.000 62 0 0 48 109 11985750 11985689 6.630000e-22 115.0
35 TraesCS3D01G384800 chr7D 91.702 470 31 3 2329 2791 37952488 37952020 0.000000e+00 645.0
36 TraesCS3D01G384800 chr7D 84.310 478 50 18 52 508 60130725 60131198 7.450000e-121 444.0
37 TraesCS3D01G384800 chr7D 81.495 281 29 10 2650 2928 37952096 37951837 2.960000e-50 209.0
38 TraesCS3D01G384800 chr5A 91.957 460 33 4 2330 2788 311630722 311631178 2.460000e-180 641.0
39 TraesCS3D01G384800 chr5A 89.979 469 38 4 2330 2791 396518306 396517840 5.400000e-167 597.0
40 TraesCS3D01G384800 chr5A 95.122 123 6 0 2806 2928 320489103 320488981 8.280000e-46 195.0
41 TraesCS3D01G384800 chr5A 93.651 126 8 0 2803 2928 311631239 311631364 3.850000e-44 189.0
42 TraesCS3D01G384800 chr6A 91.757 461 36 2 2329 2788 18040745 18041204 8.850000e-180 640.0
43 TraesCS3D01G384800 chr6A 90.405 469 36 4 2330 2791 11519225 11518759 2.500000e-170 608.0
44 TraesCS3D01G384800 chr6A 94.309 123 7 0 2806 2928 396391573 396391451 3.850000e-44 189.0
45 TraesCS3D01G384800 chr6A 100.000 29 0 0 31 59 522635047 522635075 1.000000e-03 54.7
46 TraesCS3D01G384800 chr1A 91.379 464 38 2 2329 2791 90117338 90116876 4.120000e-178 634.0
47 TraesCS3D01G384800 chr1A 81.004 279 34 8 2650 2928 90116952 90116693 1.380000e-48 204.0
48 TraesCS3D01G384800 chr7A 90.213 470 38 3 2330 2791 572346438 572345969 8.970000e-170 606.0
49 TraesCS3D01G384800 chr7A 85.833 360 45 6 229 585 584103106 584103462 7.660000e-101 377.0
50 TraesCS3D01G384800 chr7A 94.309 123 7 0 2806 2928 309555352 309555230 3.850000e-44 189.0
51 TraesCS3D01G384800 chr7A 86.709 158 16 5 230 384 575317360 575317205 1.400000e-38 171.0
52 TraesCS3D01G384800 chr2A 84.060 596 67 19 48 619 758096037 758095446 1.530000e-152 549.0
53 TraesCS3D01G384800 chr2A 85.577 104 14 1 554 657 393011646 393011748 1.110000e-19 108.0
54 TraesCS3D01G384800 chr1D 85.885 503 52 14 133 619 89233054 89233553 4.330000e-143 518.0
55 TraesCS3D01G384800 chr4B 80.864 324 47 12 230 547 12094123 12093809 1.050000e-59 241.0
56 TraesCS3D01G384800 chr5D 95.238 126 6 0 2803 2928 366006176 366006301 1.780000e-47 200.0
57 TraesCS3D01G384800 chr5B 83.951 81 11 2 18 97 678867594 678867515 3.130000e-10 76.8


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 TraesCS3D01G384800 chr3D 500089625 500092552 2927 False 5408.000000 5408 100.000000 1 2928 1 chr3D.!!$F3 2927
1 TraesCS3D01G384800 chr3D 500018402 500019661 1259 False 1916.000000 1916 93.949000 657 1938 1 chr3D.!!$F2 1281
2 TraesCS3D01G384800 chr3D 500127206 500128346 1140 False 824.000000 972 92.951000 656 1938 2 chr3D.!!$F6 1282
3 TraesCS3D01G384800 chr3D 520245890 520246622 732 False 767.000000 767 86.272000 1080 1788 1 chr3D.!!$F4 708
4 TraesCS3D01G384800 chr3D 520281343 520282023 680 False 739.000000 739 86.771000 1297 1973 1 chr3D.!!$F5 676
5 TraesCS3D01G384800 chr4D 499213188 499214365 1177 True 1653.000000 1653 91.914000 657 1857 1 chr4D.!!$R2 1200
6 TraesCS3D01G384800 chr3A 639662384 639663479 1095 False 1513.000000 1513 91.431000 657 1780 1 chr3A.!!$F3 1123
7 TraesCS3D01G384800 chr3A 639655587 639656681 1094 False 1500.000000 1500 91.254000 657 1780 1 chr3A.!!$F2 1123
8 TraesCS3D01G384800 chr3A 639576494 639580038 3544 False 940.500000 1411 92.322500 657 2928 2 chr3A.!!$F7 2271
9 TraesCS3D01G384800 chr3A 655786409 655787164 755 False 787.000000 787 86.220000 1080 1805 1 chr3A.!!$F5 725
10 TraesCS3D01G384800 chr3A 655668768 655669526 758 False 778.000000 778 86.013000 1080 1805 1 chr3A.!!$F4 725
11 TraesCS3D01G384800 chr3A 551701693 551702343 650 True 649.000000 649 85.061000 18 657 1 chr3A.!!$R1 639
12 TraesCS3D01G384800 chr3B 661756927 661759667 2740 False 891.500000 1498 89.680500 657 2147 2 chr3B.!!$F3 1490
13 TraesCS3D01G384800 chr3B 661785456 661788171 2715 False 890.500000 1489 89.536000 657 2154 2 chr3B.!!$F4 1497
14 TraesCS3D01G384800 chr3B 685066943 685067878 935 False 832.000000 832 83.667000 1080 1973 1 chr3B.!!$F1 893
15 TraesCS3D01G384800 chr3B 661567122 661571556 4434 False 703.571429 1267 91.231714 657 2371 7 chr3B.!!$F2 1714
16 TraesCS3D01G384800 chr4A 11984933 11985750 817 True 448.500000 782 96.923000 48 625 2 chr4A.!!$R1 577
17 TraesCS3D01G384800 chr7D 37951837 37952488 651 True 427.000000 645 86.598500 2329 2928 2 chr7D.!!$R1 599
18 TraesCS3D01G384800 chr5A 311630722 311631364 642 False 415.000000 641 92.804000 2330 2928 2 chr5A.!!$F1 598
19 TraesCS3D01G384800 chr1A 90116693 90117338 645 True 419.000000 634 86.191500 2329 2928 2 chr1A.!!$R1 599
20 TraesCS3D01G384800 chr2A 758095446 758096037 591 True 549.000000 549 84.060000 48 619 1 chr2A.!!$R1 571

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
46 47 0.108186 CTTCTAGCATGCACGGGACA 60.108 55.0 21.98 0.0 0.00 4.02 F
610 612 0.253610 TGACGAAACAAGGGTGTGGT 59.746 50.0 0.00 0.0 38.27 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 1921 2.487762 ACTACCGTTAAATGGTCGACGA 59.512 45.455 9.92 5.99 38.67 4.20 R
2269 4603 0.178891 AGAGGAGGGGCTCAGAACAA 60.179 55.000 0.00 0.00 31.08 2.83 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
33 34 3.654414 ACCACGAGAAAAGCACTTCTAG 58.346 45.455 0.00 3.88 35.76 2.43
46 47 0.108186 CTTCTAGCATGCACGGGACA 60.108 55.000 21.98 0.00 0.00 4.02
131 133 9.988815 AGTAGTATTTGCTATTCCAGAGTAATG 57.011 33.333 0.00 0.00 0.00 1.90
132 134 9.765795 GTAGTATTTGCTATTCCAGAGTAATGT 57.234 33.333 0.00 0.00 0.00 2.71
137 139 8.677148 TTTGCTATTCCAGAGTAATGTAATCC 57.323 34.615 0.00 0.00 0.00 3.01
138 140 7.618019 TGCTATTCCAGAGTAATGTAATCCT 57.382 36.000 0.00 0.00 0.00 3.24
139 141 8.721133 TGCTATTCCAGAGTAATGTAATCCTA 57.279 34.615 0.00 0.00 0.00 2.94
178 180 9.814899 TCATCAATCAACTTTATCTCTTCTCTC 57.185 33.333 0.00 0.00 0.00 3.20
179 181 9.820725 CATCAATCAACTTTATCTCTTCTCTCT 57.179 33.333 0.00 0.00 0.00 3.10
181 183 8.474025 TCAATCAACTTTATCTCTTCTCTCTCC 58.526 37.037 0.00 0.00 0.00 3.71
183 185 7.639113 TCAACTTTATCTCTTCTCTCTCCTC 57.361 40.000 0.00 0.00 0.00 3.71
184 186 7.178573 TCAACTTTATCTCTTCTCTCTCCTCA 58.821 38.462 0.00 0.00 0.00 3.86
185 187 7.838696 TCAACTTTATCTCTTCTCTCTCCTCAT 59.161 37.037 0.00 0.00 0.00 2.90
186 188 8.477256 CAACTTTATCTCTTCTCTCTCCTCATT 58.523 37.037 0.00 0.00 0.00 2.57
187 189 8.608185 ACTTTATCTCTTCTCTCTCCTCATTT 57.392 34.615 0.00 0.00 0.00 2.32
188 190 9.045745 ACTTTATCTCTTCTCTCTCCTCATTTT 57.954 33.333 0.00 0.00 0.00 1.82
189 191 9.533253 CTTTATCTCTTCTCTCTCCTCATTTTC 57.467 37.037 0.00 0.00 0.00 2.29
190 192 5.930837 TCTCTTCTCTCTCCTCATTTTCC 57.069 43.478 0.00 0.00 0.00 3.13
191 193 4.714308 TCTCTTCTCTCTCCTCATTTTCCC 59.286 45.833 0.00 0.00 0.00 3.97
192 194 3.777522 TCTTCTCTCTCCTCATTTTCCCC 59.222 47.826 0.00 0.00 0.00 4.81
193 195 3.498614 TCTCTCTCCTCATTTTCCCCT 57.501 47.619 0.00 0.00 0.00 4.79
194 196 3.379452 TCTCTCTCCTCATTTTCCCCTC 58.621 50.000 0.00 0.00 0.00 4.30
196 198 2.840651 TCTCTCCTCATTTTCCCCTCAC 59.159 50.000 0.00 0.00 0.00 3.51
198 200 2.305927 TCTCCTCATTTTCCCCTCACAC 59.694 50.000 0.00 0.00 0.00 3.82
199 201 1.354368 TCCTCATTTTCCCCTCACACC 59.646 52.381 0.00 0.00 0.00 4.16
202 204 1.496857 TCATTTTCCCCTCACACCACA 59.503 47.619 0.00 0.00 0.00 4.17
203 205 1.613437 CATTTTCCCCTCACACCACAC 59.387 52.381 0.00 0.00 0.00 3.82
204 206 0.464735 TTTTCCCCTCACACCACACG 60.465 55.000 0.00 0.00 0.00 4.49
205 207 2.951475 TTTCCCCTCACACCACACGC 62.951 60.000 0.00 0.00 0.00 5.34
206 208 4.248842 CCCCTCACACCACACGCA 62.249 66.667 0.00 0.00 0.00 5.24
207 209 2.972505 CCCTCACACCACACGCAC 60.973 66.667 0.00 0.00 0.00 5.34
208 210 2.203001 CCTCACACCACACGCACA 60.203 61.111 0.00 0.00 0.00 4.57
209 211 2.534019 CCTCACACCACACGCACAC 61.534 63.158 0.00 0.00 0.00 3.82
210 212 1.813337 CTCACACCACACGCACACA 60.813 57.895 0.00 0.00 0.00 3.72
211 213 1.765161 CTCACACCACACGCACACAG 61.765 60.000 0.00 0.00 0.00 3.66
213 215 1.521457 ACACCACACGCACACAGAG 60.521 57.895 0.00 0.00 0.00 3.35
214 216 1.521457 CACCACACGCACACAGAGT 60.521 57.895 0.00 0.00 0.00 3.24
215 217 1.089481 CACCACACGCACACAGAGTT 61.089 55.000 0.00 0.00 0.00 3.01
216 218 0.810031 ACCACACGCACACAGAGTTC 60.810 55.000 0.00 0.00 0.00 3.01
217 219 0.530650 CCACACGCACACAGAGTTCT 60.531 55.000 0.00 0.00 0.00 3.01
218 220 0.855349 CACACGCACACAGAGTTCTC 59.145 55.000 0.00 0.00 0.00 2.87
219 221 0.747255 ACACGCACACAGAGTTCTCT 59.253 50.000 0.00 0.00 0.00 3.10
222 224 1.268352 ACGCACACAGAGTTCTCTCTC 59.732 52.381 0.00 0.00 46.84 3.20
223 225 1.402194 CGCACACAGAGTTCTCTCTCC 60.402 57.143 0.00 0.00 46.84 3.71
224 226 1.892474 GCACACAGAGTTCTCTCTCCT 59.108 52.381 0.00 0.00 46.84 3.69
225 227 3.085533 GCACACAGAGTTCTCTCTCCTA 58.914 50.000 0.00 0.00 46.84 2.94
228 230 4.394920 CACACAGAGTTCTCTCTCCTACTC 59.605 50.000 0.00 0.00 46.84 2.59
229 231 4.042311 ACACAGAGTTCTCTCTCCTACTCA 59.958 45.833 0.00 0.00 46.84 3.41
231 233 4.042311 ACAGAGTTCTCTCTCCTACTCACA 59.958 45.833 0.00 0.00 46.84 3.58
232 234 5.192927 CAGAGTTCTCTCTCCTACTCACAT 58.807 45.833 0.00 0.00 46.84 3.21
235 237 3.372440 TCTCTCTCCTACTCACATGCA 57.628 47.619 0.00 0.00 0.00 3.96
236 238 3.908476 TCTCTCTCCTACTCACATGCAT 58.092 45.455 0.00 0.00 0.00 3.96
237 239 4.285020 TCTCTCTCCTACTCACATGCATT 58.715 43.478 0.00 0.00 0.00 3.56
238 240 4.713814 TCTCTCTCCTACTCACATGCATTT 59.286 41.667 0.00 0.00 0.00 2.32
240 242 6.552725 TCTCTCTCCTACTCACATGCATTTAT 59.447 38.462 0.00 0.00 0.00 1.40
241 243 7.070447 TCTCTCTCCTACTCACATGCATTTATT 59.930 37.037 0.00 0.00 0.00 1.40
242 244 7.568349 TCTCTCCTACTCACATGCATTTATTT 58.432 34.615 0.00 0.00 0.00 1.40
243 245 8.049117 TCTCTCCTACTCACATGCATTTATTTT 58.951 33.333 0.00 0.00 0.00 1.82
244 246 8.579850 TCTCCTACTCACATGCATTTATTTTT 57.420 30.769 0.00 0.00 0.00 1.94
245 247 8.677300 TCTCCTACTCACATGCATTTATTTTTC 58.323 33.333 0.00 0.00 0.00 2.29
246 248 8.347004 TCCTACTCACATGCATTTATTTTTCA 57.653 30.769 0.00 0.00 0.00 2.69
247 249 8.801299 TCCTACTCACATGCATTTATTTTTCAA 58.199 29.630 0.00 0.00 0.00 2.69
248 250 9.590451 CCTACTCACATGCATTTATTTTTCAAT 57.410 29.630 0.00 0.00 0.00 2.57
251 253 9.715121 ACTCACATGCATTTATTTTTCAATCTT 57.285 25.926 0.00 0.00 0.00 2.40
321 323 8.776376 ATTCTGTTTGAACATGTGTTTTTCTT 57.224 26.923 0.00 0.00 38.56 2.52
324 326 8.494347 TCTGTTTGAACATGTGTTTTTCTTTTG 58.506 29.630 0.00 0.00 38.56 2.44
325 327 8.370493 TGTTTGAACATGTGTTTTTCTTTTGA 57.630 26.923 0.00 0.00 38.56 2.69
326 328 8.997323 TGTTTGAACATGTGTTTTTCTTTTGAT 58.003 25.926 0.00 0.00 38.56 2.57
365 367 9.435688 ACAAGCTAAATATCATATATGCGTTGA 57.564 29.630 7.92 0.00 0.00 3.18
367 369 9.435688 AAGCTAAATATCATATATGCGTTGACA 57.564 29.630 7.92 0.00 0.00 3.58
368 370 9.435688 AGCTAAATATCATATATGCGTTGACAA 57.564 29.630 7.92 0.00 0.00 3.18
374 376 6.976636 TCATATATGCGTTGACAAAGTTCA 57.023 33.333 7.92 0.00 0.00 3.18
375 377 7.371126 TCATATATGCGTTGACAAAGTTCAA 57.629 32.000 7.92 0.00 32.94 2.69
376 378 7.811653 TCATATATGCGTTGACAAAGTTCAAA 58.188 30.769 7.92 0.00 37.24 2.69
377 379 8.458052 TCATATATGCGTTGACAAAGTTCAAAT 58.542 29.630 7.92 0.00 37.24 2.32
378 380 9.075519 CATATATGCGTTGACAAAGTTCAAATT 57.924 29.630 0.00 0.00 37.24 1.82
379 381 7.945033 ATATGCGTTGACAAAGTTCAAATTT 57.055 28.000 3.06 0.00 37.24 1.82
380 382 5.694674 TGCGTTGACAAAGTTCAAATTTC 57.305 34.783 3.06 0.00 37.24 2.17
381 383 5.164233 TGCGTTGACAAAGTTCAAATTTCA 58.836 33.333 3.06 0.00 37.24 2.69
382 384 5.635280 TGCGTTGACAAAGTTCAAATTTCAA 59.365 32.000 3.06 0.00 37.24 2.69
383 385 6.146184 TGCGTTGACAAAGTTCAAATTTCAAA 59.854 30.769 3.06 0.00 37.24 2.69
384 386 7.148507 TGCGTTGACAAAGTTCAAATTTCAAAT 60.149 29.630 3.06 0.00 37.24 2.32
385 387 7.691877 GCGTTGACAAAGTTCAAATTTCAAATT 59.308 29.630 3.06 0.00 37.24 1.82
422 424 6.088016 TGACAAAAATCATGAAACTGAGGG 57.912 37.500 0.00 0.00 0.00 4.30
423 425 5.832595 TGACAAAAATCATGAAACTGAGGGA 59.167 36.000 0.00 0.00 0.00 4.20
425 427 5.835280 ACAAAAATCATGAAACTGAGGGAGT 59.165 36.000 0.00 0.00 35.94 3.85
426 428 7.004086 ACAAAAATCATGAAACTGAGGGAGTA 58.996 34.615 0.00 0.00 33.09 2.59
427 429 7.671398 ACAAAAATCATGAAACTGAGGGAGTAT 59.329 33.333 0.00 0.00 33.09 2.12
428 430 9.177608 CAAAAATCATGAAACTGAGGGAGTATA 57.822 33.333 0.00 0.00 33.09 1.47
430 432 9.927081 AAAATCATGAAACTGAGGGAGTATAAT 57.073 29.630 0.00 0.00 33.09 1.28
431 433 9.927081 AAATCATGAAACTGAGGGAGTATAATT 57.073 29.630 0.00 0.00 33.09 1.40
432 434 9.927081 AATCATGAAACTGAGGGAGTATAATTT 57.073 29.630 0.00 0.00 33.09 1.82
433 435 9.927081 ATCATGAAACTGAGGGAGTATAATTTT 57.073 29.630 0.00 0.00 33.09 1.82
435 437 8.960591 CATGAAACTGAGGGAGTATAATTTTGT 58.039 33.333 0.00 0.00 33.09 2.83
436 438 8.335532 TGAAACTGAGGGAGTATAATTTTGTG 57.664 34.615 0.00 0.00 33.09 3.33
437 439 8.160765 TGAAACTGAGGGAGTATAATTTTGTGA 58.839 33.333 0.00 0.00 33.09 3.58
490 492 8.779354 ATAAAACTCAACTAGATGGAACTGAC 57.221 34.615 0.00 0.00 0.00 3.51
491 493 6.426646 AAACTCAACTAGATGGAACTGACT 57.573 37.500 0.00 0.00 0.00 3.41
493 495 7.726033 AACTCAACTAGATGGAACTGACTAT 57.274 36.000 0.00 0.00 0.00 2.12
494 496 7.106439 ACTCAACTAGATGGAACTGACTATG 57.894 40.000 0.00 0.00 0.00 2.23
498 500 8.762645 TCAACTAGATGGAACTGACTATGAAAT 58.237 33.333 0.00 0.00 0.00 2.17
504 506 7.869937 AGATGGAACTGACTATGAAATATCACG 59.130 37.037 0.00 0.00 38.69 4.35
505 507 6.873997 TGGAACTGACTATGAAATATCACGT 58.126 36.000 0.00 0.00 38.69 4.49
506 508 7.327975 TGGAACTGACTATGAAATATCACGTT 58.672 34.615 0.00 0.00 38.69 3.99
508 510 8.753175 GGAACTGACTATGAAATATCACGTTAC 58.247 37.037 0.00 0.00 38.69 2.50
509 511 8.644318 AACTGACTATGAAATATCACGTTACC 57.356 34.615 0.00 0.00 38.69 2.85
510 512 7.778083 ACTGACTATGAAATATCACGTTACCA 58.222 34.615 0.00 0.00 38.69 3.25
511 513 7.705325 ACTGACTATGAAATATCACGTTACCAC 59.295 37.037 0.00 0.00 38.69 4.16
513 515 8.201464 TGACTATGAAATATCACGTTACCACAT 58.799 33.333 0.00 0.00 38.69 3.21
519 521 9.483916 TGAAATATCACGTTACCACATATTAGG 57.516 33.333 0.00 0.00 0.00 2.69
520 522 9.485206 GAAATATCACGTTACCACATATTAGGT 57.515 33.333 0.00 1.73 41.89 3.08
522 524 5.918426 TCACGTTACCACATATTAGGTGA 57.082 39.130 9.93 0.00 38.87 4.02
523 525 5.898174 TCACGTTACCACATATTAGGTGAG 58.102 41.667 9.93 3.32 38.87 3.51
524 526 5.653330 TCACGTTACCACATATTAGGTGAGA 59.347 40.000 9.93 0.00 38.87 3.27
525 527 5.977725 CACGTTACCACATATTAGGTGAGAG 59.022 44.000 9.93 0.00 38.87 3.20
526 528 5.889853 ACGTTACCACATATTAGGTGAGAGA 59.110 40.000 9.93 0.00 38.87 3.10
528 530 7.093640 ACGTTACCACATATTAGGTGAGAGAAA 60.094 37.037 9.93 0.00 38.87 2.52
530 532 8.880750 GTTACCACATATTAGGTGAGAGAAAAC 58.119 37.037 9.93 2.34 38.87 2.43
531 533 7.016153 ACCACATATTAGGTGAGAGAAAACA 57.984 36.000 9.93 0.00 38.54 2.83
532 534 7.633789 ACCACATATTAGGTGAGAGAAAACAT 58.366 34.615 9.93 0.00 38.54 2.71
533 535 8.109634 ACCACATATTAGGTGAGAGAAAACATT 58.890 33.333 9.93 0.00 38.54 2.71
534 536 8.400947 CCACATATTAGGTGAGAGAAAACATTG 58.599 37.037 9.93 0.00 38.54 2.82
535 537 8.950210 CACATATTAGGTGAGAGAAAACATTGT 58.050 33.333 2.33 0.00 38.54 2.71
536 538 8.950210 ACATATTAGGTGAGAGAAAACATTGTG 58.050 33.333 0.00 0.00 0.00 3.33
537 539 8.950210 CATATTAGGTGAGAGAAAACATTGTGT 58.050 33.333 0.00 0.00 0.00 3.72
538 540 6.618287 TTAGGTGAGAGAAAACATTGTGTG 57.382 37.500 0.00 0.00 0.00 3.82
539 541 4.780815 AGGTGAGAGAAAACATTGTGTGA 58.219 39.130 0.00 0.00 0.00 3.58
540 542 5.380043 AGGTGAGAGAAAACATTGTGTGAT 58.620 37.500 0.00 0.00 0.00 3.06
541 543 5.240183 AGGTGAGAGAAAACATTGTGTGATG 59.760 40.000 0.00 0.00 0.00 3.07
542 544 5.009010 GGTGAGAGAAAACATTGTGTGATGT 59.991 40.000 0.00 0.00 41.83 3.06
543 545 6.138761 GTGAGAGAAAACATTGTGTGATGTC 58.861 40.000 0.00 0.00 39.25 3.06
545 547 6.017687 TGAGAGAAAACATTGTGTGATGTCAG 60.018 38.462 0.00 0.00 39.25 3.51
546 548 5.240183 AGAGAAAACATTGTGTGATGTCAGG 59.760 40.000 0.00 0.00 39.25 3.86
547 549 4.279169 AGAAAACATTGTGTGATGTCAGGG 59.721 41.667 0.00 0.00 39.25 4.45
549 551 3.726557 ACATTGTGTGATGTCAGGGAT 57.273 42.857 0.00 0.00 35.39 3.85
550 552 4.842531 ACATTGTGTGATGTCAGGGATA 57.157 40.909 0.00 0.00 35.39 2.59
551 553 4.517285 ACATTGTGTGATGTCAGGGATAC 58.483 43.478 0.00 0.00 35.39 2.24
552 554 4.019411 ACATTGTGTGATGTCAGGGATACA 60.019 41.667 0.00 0.00 35.39 2.29
553 555 4.632327 TTGTGTGATGTCAGGGATACAA 57.368 40.909 0.00 0.00 39.74 2.41
554 556 4.842531 TGTGTGATGTCAGGGATACAAT 57.157 40.909 0.00 0.00 39.74 2.71
556 558 6.499106 TGTGTGATGTCAGGGATACAATAT 57.501 37.500 0.00 0.00 39.74 1.28
557 559 6.899089 TGTGTGATGTCAGGGATACAATATT 58.101 36.000 0.00 0.00 39.74 1.28
558 560 7.345691 TGTGTGATGTCAGGGATACAATATTT 58.654 34.615 0.00 0.00 39.74 1.40
559 561 8.490311 TGTGTGATGTCAGGGATACAATATTTA 58.510 33.333 0.00 0.00 39.74 1.40
566 568 8.723365 TGTCAGGGATACAATATTTAATCACCT 58.277 33.333 5.71 7.64 39.74 4.00
581 583 8.731275 TTTAATCACCTTACATACTGTGATGG 57.269 34.615 4.90 0.00 45.14 3.51
583 585 3.517500 TCACCTTACATACTGTGATGGCA 59.482 43.478 0.00 0.00 33.09 4.92
584 586 3.623060 CACCTTACATACTGTGATGGCAC 59.377 47.826 0.00 0.00 45.35 5.01
599 601 2.627945 TGGCACATATCCTGACGAAAC 58.372 47.619 0.00 0.00 0.00 2.78
600 602 2.027653 TGGCACATATCCTGACGAAACA 60.028 45.455 0.00 0.00 0.00 2.83
601 603 3.006940 GGCACATATCCTGACGAAACAA 58.993 45.455 0.00 0.00 0.00 2.83
602 604 3.063997 GGCACATATCCTGACGAAACAAG 59.936 47.826 0.00 0.00 0.00 3.16
603 605 3.063997 GCACATATCCTGACGAAACAAGG 59.936 47.826 0.00 0.00 0.00 3.61
604 606 3.623060 CACATATCCTGACGAAACAAGGG 59.377 47.826 0.00 0.00 0.00 3.95
605 607 3.263425 ACATATCCTGACGAAACAAGGGT 59.737 43.478 0.00 0.00 0.00 4.34
606 608 2.185004 ATCCTGACGAAACAAGGGTG 57.815 50.000 0.00 0.00 0.00 4.61
607 609 0.834612 TCCTGACGAAACAAGGGTGT 59.165 50.000 0.00 0.00 40.75 4.16
608 610 0.944386 CCTGACGAAACAAGGGTGTG 59.056 55.000 0.00 0.00 38.27 3.82
609 611 0.944386 CTGACGAAACAAGGGTGTGG 59.056 55.000 0.00 0.00 38.27 4.17
610 612 0.253610 TGACGAAACAAGGGTGTGGT 59.746 50.000 0.00 0.00 38.27 4.16
611 613 0.661020 GACGAAACAAGGGTGTGGTG 59.339 55.000 0.00 0.00 38.27 4.17
612 614 0.750182 ACGAAACAAGGGTGTGGTGG 60.750 55.000 0.00 0.00 38.27 4.61
613 615 0.464735 CGAAACAAGGGTGTGGTGGA 60.465 55.000 0.00 0.00 38.27 4.02
614 616 1.817740 CGAAACAAGGGTGTGGTGGAT 60.818 52.381 0.00 0.00 38.27 3.41
615 617 1.613437 GAAACAAGGGTGTGGTGGATG 59.387 52.381 0.00 0.00 38.27 3.51
616 618 0.827507 AACAAGGGTGTGGTGGATGC 60.828 55.000 0.00 0.00 38.27 3.91
617 619 1.228521 CAAGGGTGTGGTGGATGCA 60.229 57.895 0.00 0.00 0.00 3.96
618 620 0.612732 CAAGGGTGTGGTGGATGCAT 60.613 55.000 0.00 0.00 0.00 3.96
619 621 0.612732 AAGGGTGTGGTGGATGCATG 60.613 55.000 2.46 0.00 0.00 4.06
620 622 2.713967 GGGTGTGGTGGATGCATGC 61.714 63.158 11.82 11.82 0.00 4.06
621 623 1.978080 GGTGTGGTGGATGCATGCA 60.978 57.895 25.04 25.04 0.00 3.96
622 624 1.213537 GTGTGGTGGATGCATGCAC 59.786 57.895 35.44 35.44 46.73 4.57
626 628 4.217035 GTGGATGCATGCACGGTA 57.783 55.556 31.53 7.12 39.29 4.02
627 629 2.706636 GTGGATGCATGCACGGTAT 58.293 52.632 31.53 6.46 39.29 2.73
628 630 0.588252 GTGGATGCATGCACGGTATC 59.412 55.000 31.53 16.16 39.29 2.24
629 631 0.469494 TGGATGCATGCACGGTATCT 59.531 50.000 25.37 4.65 0.00 1.98
630 632 1.691434 TGGATGCATGCACGGTATCTA 59.309 47.619 25.37 11.55 0.00 1.98
631 633 2.069273 GGATGCATGCACGGTATCTAC 58.931 52.381 25.37 1.26 0.00 2.59
632 634 2.069273 GATGCATGCACGGTATCTACC 58.931 52.381 25.37 0.00 42.98 3.18
650 652 3.740384 CGTGCACGGTAGAAAAACC 57.260 52.632 31.15 0.00 36.08 3.27
651 653 0.938713 CGTGCACGGTAGAAAAACCA 59.061 50.000 31.15 0.00 39.71 3.67
652 654 1.070175 CGTGCACGGTAGAAAAACCAG 60.070 52.381 31.15 0.00 39.71 4.00
653 655 1.944709 GTGCACGGTAGAAAAACCAGT 59.055 47.619 0.00 0.00 39.71 4.00
654 656 2.032290 GTGCACGGTAGAAAAACCAGTC 60.032 50.000 0.00 0.00 39.71 3.51
708 710 6.128035 GGTGCAGTATGTGTTGTATGAATTGA 60.128 38.462 0.00 0.00 39.31 2.57
711 713 7.121020 TGCAGTATGTGTTGTATGAATTGATGT 59.879 33.333 0.00 0.00 39.31 3.06
760 762 2.089980 ACTGCTCATCCAAATCTGCAC 58.910 47.619 0.00 0.00 0.00 4.57
1039 1056 3.268595 CCTGTGACCCCCTATTACCTTTT 59.731 47.826 0.00 0.00 0.00 2.27
1168 1188 4.424566 GCCAACGTCGACGGCCTA 62.425 66.667 37.89 0.00 44.95 3.93
1238 1258 1.831652 CGCCTGGGAGTTCAACCTCT 61.832 60.000 0.00 0.00 0.00 3.69
1363 1416 2.514592 CTCATTGGCGCCGGACAT 60.515 61.111 23.90 8.25 0.00 3.06
1790 1874 0.442310 ATTCGAATGTGCAACGGACG 59.558 50.000 10.50 0.00 42.39 4.79
1827 1921 1.336795 GCTTAATTGGGCACTTGCGTT 60.337 47.619 0.00 0.00 43.26 4.84
1834 1928 2.167918 GCACTTGCGTTCGTCGAC 59.832 61.111 5.18 5.18 42.86 4.20
1842 1936 1.456544 TGCGTTCGTCGACCATTTAAC 59.543 47.619 10.58 6.20 42.86 2.01
1965 4291 3.821748 ACTTCCAGTCAAGGGTTCTTTC 58.178 45.455 0.00 0.00 0.00 2.62
2012 4340 8.898761 AGGTTTTAATGATGCGTGATGTATTTA 58.101 29.630 0.00 0.00 0.00 1.40
2079 4407 4.674904 CGATCGCTCGCGCTAGCT 62.675 66.667 28.37 13.46 40.49 3.32
2094 4422 4.553547 GCGCTAGCTACCTCATCATTTTTG 60.554 45.833 13.93 0.00 41.01 2.44
2095 4423 4.811024 CGCTAGCTACCTCATCATTTTTGA 59.189 41.667 13.93 0.00 0.00 2.69
2105 4433 5.252969 TCATCATTTTTGATGTGCTAGCC 57.747 39.130 13.29 4.15 44.33 3.93
2114 4442 3.603532 TGATGTGCTAGCCAGAGAAAAG 58.396 45.455 13.29 0.00 0.00 2.27
2174 4503 1.066929 GGAGACGCAATTGGGCAAAAT 60.067 47.619 21.34 2.33 0.00 1.82
2272 4606 4.908687 TCACGCTGCCGCACTTGT 62.909 61.111 0.00 0.00 38.22 3.16
2311 4645 3.007323 GTACCACCGGCCTCCCTT 61.007 66.667 0.00 0.00 0.00 3.95
2327 4661 2.117865 CCCTTCTCTGCATCTCTCCTT 58.882 52.381 0.00 0.00 0.00 3.36
2500 5671 3.788227 ACACAGCCCAGAAGATTACAA 57.212 42.857 0.00 0.00 0.00 2.41
2679 5850 7.750229 AGAGATTACATGTTTCAAAGAGCAA 57.250 32.000 2.30 0.00 0.00 3.91
2720 5893 5.989477 TCCAATAGATTCGGACAAGAACAT 58.011 37.500 0.00 0.00 32.39 2.71
2730 5903 7.827819 TTCGGACAAGAACATAAGATTACAG 57.172 36.000 0.00 0.00 0.00 2.74
2756 5929 7.255625 GGTTTCAAAGAAGGTCAAGCTAAAGAT 60.256 37.037 0.00 0.00 0.00 2.40
2767 6544 6.545298 GGTCAAGCTAAAGATCTCAATCCAAT 59.455 38.462 0.00 0.00 31.78 3.16
2772 6549 8.027524 AGCTAAAGATCTCAATCCAATAGACA 57.972 34.615 0.00 0.00 31.78 3.41
2775 6552 7.856145 AAAGATCTCAATCCAATAGACACAC 57.144 36.000 0.00 0.00 31.78 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.622456 CGTGGTTGGTTGGCACGC 62.622 66.667 0.00 0.00 32.60 5.34
1 2 2.892334 CTCGTGGTTGGTTGGCACG 61.892 63.158 0.00 0.00 40.17 5.34
2 3 1.098712 TTCTCGTGGTTGGTTGGCAC 61.099 55.000 0.00 0.00 0.00 5.01
3 4 0.394488 TTTCTCGTGGTTGGTTGGCA 60.394 50.000 0.00 0.00 0.00 4.92
4 5 0.741915 TTTTCTCGTGGTTGGTTGGC 59.258 50.000 0.00 0.00 0.00 4.52
5 6 1.269051 GCTTTTCTCGTGGTTGGTTGG 60.269 52.381 0.00 0.00 0.00 3.77
6 7 1.403679 TGCTTTTCTCGTGGTTGGTTG 59.596 47.619 0.00 0.00 0.00 3.77
10 11 2.614057 AGAAGTGCTTTTCTCGTGGTTG 59.386 45.455 0.00 0.00 31.97 3.77
11 12 2.919228 AGAAGTGCTTTTCTCGTGGTT 58.081 42.857 0.00 0.00 31.97 3.67
12 13 2.622064 AGAAGTGCTTTTCTCGTGGT 57.378 45.000 0.00 0.00 31.97 4.16
13 14 2.413453 GCTAGAAGTGCTTTTCTCGTGG 59.587 50.000 6.56 0.17 38.35 4.94
14 15 3.059884 TGCTAGAAGTGCTTTTCTCGTG 58.940 45.455 6.56 2.03 38.35 4.35
16 17 3.484886 GCATGCTAGAAGTGCTTTTCTCG 60.485 47.826 11.37 3.13 38.35 4.04
46 47 1.750399 GTTGAGCCATGCACGGGAT 60.750 57.895 10.34 3.37 0.00 3.85
152 154 9.814899 GAGAGAAGAGATAAAGTTGATTGATGA 57.185 33.333 0.00 0.00 0.00 2.92
153 155 9.820725 AGAGAGAAGAGATAAAGTTGATTGATG 57.179 33.333 0.00 0.00 0.00 3.07
155 157 8.474025 GGAGAGAGAAGAGATAAAGTTGATTGA 58.526 37.037 0.00 0.00 0.00 2.57
157 159 8.608185 AGGAGAGAGAAGAGATAAAGTTGATT 57.392 34.615 0.00 0.00 0.00 2.57
158 160 7.838696 TGAGGAGAGAGAAGAGATAAAGTTGAT 59.161 37.037 0.00 0.00 0.00 2.57
160 162 7.403312 TGAGGAGAGAGAAGAGATAAAGTTG 57.597 40.000 0.00 0.00 0.00 3.16
161 163 8.608185 AATGAGGAGAGAGAAGAGATAAAGTT 57.392 34.615 0.00 0.00 0.00 2.66
162 164 8.608185 AAATGAGGAGAGAGAAGAGATAAAGT 57.392 34.615 0.00 0.00 0.00 2.66
164 166 8.482128 GGAAAATGAGGAGAGAGAAGAGATAAA 58.518 37.037 0.00 0.00 0.00 1.40
165 167 7.070571 GGGAAAATGAGGAGAGAGAAGAGATAA 59.929 40.741 0.00 0.00 0.00 1.75
166 168 6.553100 GGGAAAATGAGGAGAGAGAAGAGATA 59.447 42.308 0.00 0.00 0.00 1.98
167 169 5.366477 GGGAAAATGAGGAGAGAGAAGAGAT 59.634 44.000 0.00 0.00 0.00 2.75
168 170 4.714308 GGGAAAATGAGGAGAGAGAAGAGA 59.286 45.833 0.00 0.00 0.00 3.10
169 171 4.141733 GGGGAAAATGAGGAGAGAGAAGAG 60.142 50.000 0.00 0.00 0.00 2.85
172 174 3.777522 GAGGGGAAAATGAGGAGAGAGAA 59.222 47.826 0.00 0.00 0.00 2.87
174 176 3.110705 TGAGGGGAAAATGAGGAGAGAG 58.889 50.000 0.00 0.00 0.00 3.20
176 178 2.573462 TGTGAGGGGAAAATGAGGAGAG 59.427 50.000 0.00 0.00 0.00 3.20
178 180 2.619074 GGTGTGAGGGGAAAATGAGGAG 60.619 54.545 0.00 0.00 0.00 3.69
179 181 1.354368 GGTGTGAGGGGAAAATGAGGA 59.646 52.381 0.00 0.00 0.00 3.71
180 182 1.075374 TGGTGTGAGGGGAAAATGAGG 59.925 52.381 0.00 0.00 0.00 3.86
181 183 2.162681 GTGGTGTGAGGGGAAAATGAG 58.837 52.381 0.00 0.00 0.00 2.90
183 185 1.613437 GTGTGGTGTGAGGGGAAAATG 59.387 52.381 0.00 0.00 0.00 2.32
184 186 1.817740 CGTGTGGTGTGAGGGGAAAAT 60.818 52.381 0.00 0.00 0.00 1.82
185 187 0.464735 CGTGTGGTGTGAGGGGAAAA 60.465 55.000 0.00 0.00 0.00 2.29
186 188 1.147376 CGTGTGGTGTGAGGGGAAA 59.853 57.895 0.00 0.00 0.00 3.13
187 189 2.825982 CGTGTGGTGTGAGGGGAA 59.174 61.111 0.00 0.00 0.00 3.97
188 190 3.936203 GCGTGTGGTGTGAGGGGA 61.936 66.667 0.00 0.00 0.00 4.81
189 191 4.248842 TGCGTGTGGTGTGAGGGG 62.249 66.667 0.00 0.00 0.00 4.79
190 192 2.972505 GTGCGTGTGGTGTGAGGG 60.973 66.667 0.00 0.00 0.00 4.30
191 193 2.203001 TGTGCGTGTGGTGTGAGG 60.203 61.111 0.00 0.00 0.00 3.86
192 194 1.765161 CTGTGTGCGTGTGGTGTGAG 61.765 60.000 0.00 0.00 0.00 3.51
193 195 1.813337 CTGTGTGCGTGTGGTGTGA 60.813 57.895 0.00 0.00 0.00 3.58
194 196 1.765161 CTCTGTGTGCGTGTGGTGTG 61.765 60.000 0.00 0.00 0.00 3.82
196 198 1.089481 AACTCTGTGTGCGTGTGGTG 61.089 55.000 0.00 0.00 0.00 4.17
198 200 0.530650 AGAACTCTGTGTGCGTGTGG 60.531 55.000 0.00 0.00 0.00 4.17
199 201 0.855349 GAGAACTCTGTGTGCGTGTG 59.145 55.000 0.00 0.00 0.00 3.82
202 204 3.875838 GAGAGAACTCTGTGTGCGT 57.124 52.632 9.16 0.00 40.61 5.24
211 213 4.202010 GCATGTGAGTAGGAGAGAGAACTC 60.202 50.000 0.00 0.00 42.90 3.01
213 215 3.445450 TGCATGTGAGTAGGAGAGAGAAC 59.555 47.826 0.00 0.00 0.00 3.01
214 216 3.701664 TGCATGTGAGTAGGAGAGAGAA 58.298 45.455 0.00 0.00 0.00 2.87
215 217 3.372440 TGCATGTGAGTAGGAGAGAGA 57.628 47.619 0.00 0.00 0.00 3.10
216 218 4.669206 AATGCATGTGAGTAGGAGAGAG 57.331 45.455 0.00 0.00 0.00 3.20
217 219 6.737720 ATAAATGCATGTGAGTAGGAGAGA 57.262 37.500 0.00 0.00 0.00 3.10
218 220 7.798596 AAATAAATGCATGTGAGTAGGAGAG 57.201 36.000 0.00 0.00 0.00 3.20
219 221 8.579850 AAAAATAAATGCATGTGAGTAGGAGA 57.420 30.769 0.00 0.00 0.00 3.71
221 223 8.347004 TGAAAAATAAATGCATGTGAGTAGGA 57.653 30.769 0.00 0.00 0.00 2.94
222 224 8.984891 TTGAAAAATAAATGCATGTGAGTAGG 57.015 30.769 0.00 0.00 0.00 3.18
225 227 9.715121 AAGATTGAAAAATAAATGCATGTGAGT 57.285 25.926 0.00 0.00 0.00 3.41
240 242 9.936759 AGTTGTTCCAAGTTTAAGATTGAAAAA 57.063 25.926 3.90 0.00 0.00 1.94
295 297 9.868277 AAGAAAAACACATGTTCAAACAGAATA 57.132 25.926 0.00 0.00 43.04 1.75
296 298 8.776376 AAGAAAAACACATGTTCAAACAGAAT 57.224 26.923 0.00 0.00 43.04 2.40
297 299 8.600449 AAAGAAAAACACATGTTCAAACAGAA 57.400 26.923 0.00 0.00 43.04 3.02
299 301 8.494347 TCAAAAGAAAAACACATGTTCAAACAG 58.506 29.630 0.00 0.00 43.04 3.16
300 302 8.370493 TCAAAAGAAAAACACATGTTCAAACA 57.630 26.923 0.00 0.00 44.06 2.83
301 303 9.824534 AATCAAAAGAAAAACACATGTTCAAAC 57.175 25.926 0.00 0.00 37.25 2.93
339 341 9.435688 TCAACGCATATATGATATTTAGCTTGT 57.564 29.630 17.10 0.00 0.00 3.16
340 342 9.694520 GTCAACGCATATATGATATTTAGCTTG 57.305 33.333 17.10 5.46 0.00 4.01
341 343 9.435688 TGTCAACGCATATATGATATTTAGCTT 57.564 29.630 17.10 0.00 0.00 3.74
350 352 7.552458 TGAACTTTGTCAACGCATATATGAT 57.448 32.000 17.10 0.44 0.00 2.45
353 355 9.638239 AAATTTGAACTTTGTCAACGCATATAT 57.362 25.926 0.00 0.00 37.24 0.86
355 357 7.651304 TGAAATTTGAACTTTGTCAACGCATAT 59.349 29.630 0.00 0.00 37.24 1.78
358 360 5.164233 TGAAATTTGAACTTTGTCAACGCA 58.836 33.333 0.00 0.00 37.24 5.24
398 400 6.494491 TCCCTCAGTTTCATGATTTTTGTCAT 59.506 34.615 0.00 0.00 39.34 3.06
399 401 5.832595 TCCCTCAGTTTCATGATTTTTGTCA 59.167 36.000 0.00 0.00 0.00 3.58
400 402 6.015940 ACTCCCTCAGTTTCATGATTTTTGTC 60.016 38.462 0.00 0.00 26.56 3.18
401 403 5.835280 ACTCCCTCAGTTTCATGATTTTTGT 59.165 36.000 0.00 0.00 26.56 2.83
402 404 6.336842 ACTCCCTCAGTTTCATGATTTTTG 57.663 37.500 0.00 0.00 26.56 2.44
403 405 9.753674 TTATACTCCCTCAGTTTCATGATTTTT 57.246 29.630 0.00 0.00 36.43 1.94
404 406 9.927081 ATTATACTCCCTCAGTTTCATGATTTT 57.073 29.630 0.00 0.00 36.43 1.82
405 407 9.927081 AATTATACTCCCTCAGTTTCATGATTT 57.073 29.630 0.00 0.00 36.43 2.17
406 408 9.927081 AAATTATACTCCCTCAGTTTCATGATT 57.073 29.630 0.00 0.00 36.43 2.57
407 409 9.927081 AAAATTATACTCCCTCAGTTTCATGAT 57.073 29.630 0.00 0.00 36.43 2.45
409 411 8.960591 ACAAAATTATACTCCCTCAGTTTCATG 58.039 33.333 0.00 0.00 36.43 3.07
410 412 8.960591 CACAAAATTATACTCCCTCAGTTTCAT 58.039 33.333 0.00 0.00 36.43 2.57
411 413 8.160765 TCACAAAATTATACTCCCTCAGTTTCA 58.839 33.333 0.00 0.00 36.43 2.69
412 414 8.561738 TCACAAAATTATACTCCCTCAGTTTC 57.438 34.615 0.00 0.00 36.43 2.78
464 466 9.220767 GTCAGTTCCATCTAGTTGAGTTTTATT 57.779 33.333 2.20 0.00 0.00 1.40
466 468 7.963532 AGTCAGTTCCATCTAGTTGAGTTTTA 58.036 34.615 2.20 0.00 0.00 1.52
467 469 6.831976 AGTCAGTTCCATCTAGTTGAGTTTT 58.168 36.000 2.20 0.00 0.00 2.43
469 471 7.397476 TCATAGTCAGTTCCATCTAGTTGAGTT 59.603 37.037 2.20 0.00 0.00 3.01
470 472 6.892456 TCATAGTCAGTTCCATCTAGTTGAGT 59.108 38.462 2.20 0.00 0.00 3.41
471 473 7.340122 TCATAGTCAGTTCCATCTAGTTGAG 57.660 40.000 2.20 0.00 0.00 3.02
472 474 7.718334 TTCATAGTCAGTTCCATCTAGTTGA 57.282 36.000 2.20 0.00 0.00 3.18
473 475 8.954950 ATTTCATAGTCAGTTCCATCTAGTTG 57.045 34.615 0.00 0.00 0.00 3.16
478 480 7.869937 CGTGATATTTCATAGTCAGTTCCATCT 59.130 37.037 0.00 0.00 33.56 2.90
479 481 7.653713 ACGTGATATTTCATAGTCAGTTCCATC 59.346 37.037 0.00 0.00 33.56 3.51
480 482 7.500992 ACGTGATATTTCATAGTCAGTTCCAT 58.499 34.615 0.00 0.00 33.56 3.41
482 484 7.772332 AACGTGATATTTCATAGTCAGTTCC 57.228 36.000 0.00 0.00 33.56 3.62
483 485 8.753175 GGTAACGTGATATTTCATAGTCAGTTC 58.247 37.037 0.00 0.00 33.56 3.01
485 487 7.705325 GTGGTAACGTGATATTTCATAGTCAGT 59.295 37.037 0.00 0.00 42.51 3.41
488 490 7.997107 TGTGGTAACGTGATATTTCATAGTC 57.003 36.000 0.00 0.00 42.51 2.59
493 495 9.483916 CCTAATATGTGGTAACGTGATATTTCA 57.516 33.333 0.00 0.00 42.51 2.69
494 496 9.485206 ACCTAATATGTGGTAACGTGATATTTC 57.515 33.333 0.00 0.00 42.51 2.17
498 500 7.503230 TCTCACCTAATATGTGGTAACGTGATA 59.497 37.037 0.00 0.00 42.51 2.15
500 502 5.653330 TCTCACCTAATATGTGGTAACGTGA 59.347 40.000 0.00 0.00 42.51 4.35
501 503 5.898174 TCTCACCTAATATGTGGTAACGTG 58.102 41.667 0.00 0.00 42.51 4.49
503 505 6.387041 TCTCTCACCTAATATGTGGTAACG 57.613 41.667 0.25 0.00 42.51 3.18
504 506 8.880750 GTTTTCTCTCACCTAATATGTGGTAAC 58.119 37.037 0.25 0.00 34.79 2.50
505 507 8.598916 TGTTTTCTCTCACCTAATATGTGGTAA 58.401 33.333 0.25 0.00 34.79 2.85
506 508 8.141298 TGTTTTCTCTCACCTAATATGTGGTA 57.859 34.615 0.25 0.00 34.79 3.25
508 510 8.400947 CAATGTTTTCTCTCACCTAATATGTGG 58.599 37.037 0.00 0.00 34.46 4.17
509 511 8.950210 ACAATGTTTTCTCTCACCTAATATGTG 58.050 33.333 0.00 0.00 35.01 3.21
510 512 8.950210 CACAATGTTTTCTCTCACCTAATATGT 58.050 33.333 0.00 0.00 0.00 2.29
511 513 8.950210 ACACAATGTTTTCTCTCACCTAATATG 58.050 33.333 0.00 0.00 0.00 1.78
513 515 8.154203 TCACACAATGTTTTCTCTCACCTAATA 58.846 33.333 0.00 0.00 0.00 0.98
515 517 6.353323 TCACACAATGTTTTCTCTCACCTAA 58.647 36.000 0.00 0.00 0.00 2.69
516 518 5.924356 TCACACAATGTTTTCTCTCACCTA 58.076 37.500 0.00 0.00 0.00 3.08
517 519 4.780815 TCACACAATGTTTTCTCTCACCT 58.219 39.130 0.00 0.00 0.00 4.00
519 521 6.064846 ACATCACACAATGTTTTCTCTCAC 57.935 37.500 0.00 0.00 36.47 3.51
520 522 5.821995 TGACATCACACAATGTTTTCTCTCA 59.178 36.000 0.00 0.00 39.93 3.27
522 524 5.240183 CCTGACATCACACAATGTTTTCTCT 59.760 40.000 0.00 0.00 39.93 3.10
523 525 5.455392 CCTGACATCACACAATGTTTTCTC 58.545 41.667 0.00 0.00 39.93 2.87
524 526 4.279169 CCCTGACATCACACAATGTTTTCT 59.721 41.667 0.00 0.00 39.93 2.52
525 527 4.278170 TCCCTGACATCACACAATGTTTTC 59.722 41.667 0.00 0.00 39.93 2.29
526 528 4.214310 TCCCTGACATCACACAATGTTTT 58.786 39.130 0.00 0.00 39.93 2.43
528 530 3.507162 TCCCTGACATCACACAATGTT 57.493 42.857 0.00 0.00 39.93 2.71
530 532 4.516323 TGTATCCCTGACATCACACAATG 58.484 43.478 0.00 0.00 0.00 2.82
531 533 4.842531 TGTATCCCTGACATCACACAAT 57.157 40.909 0.00 0.00 0.00 2.71
532 534 4.632327 TTGTATCCCTGACATCACACAA 57.368 40.909 0.00 0.00 0.00 3.33
533 535 4.842531 ATTGTATCCCTGACATCACACA 57.157 40.909 0.00 0.00 0.00 3.72
534 536 7.807977 AAATATTGTATCCCTGACATCACAC 57.192 36.000 0.00 0.00 0.00 3.82
539 541 9.520515 GGTGATTAAATATTGTATCCCTGACAT 57.479 33.333 7.30 0.00 0.00 3.06
540 542 8.723365 AGGTGATTAAATATTGTATCCCTGACA 58.277 33.333 13.44 0.00 0.00 3.58
541 543 9.574516 AAGGTGATTAAATATTGTATCCCTGAC 57.425 33.333 14.20 5.84 0.00 3.51
575 577 2.138320 CGTCAGGATATGTGCCATCAC 58.862 52.381 0.00 0.00 43.40 3.06
576 578 2.038659 TCGTCAGGATATGTGCCATCA 58.961 47.619 0.00 0.00 0.00 3.07
577 579 2.820059 TCGTCAGGATATGTGCCATC 57.180 50.000 0.00 0.00 0.00 3.51
578 580 3.206150 GTTTCGTCAGGATATGTGCCAT 58.794 45.455 0.00 0.00 0.00 4.40
579 581 2.027653 TGTTTCGTCAGGATATGTGCCA 60.028 45.455 0.00 0.00 0.00 4.92
580 582 2.627945 TGTTTCGTCAGGATATGTGCC 58.372 47.619 0.00 0.00 0.00 5.01
581 583 3.063997 CCTTGTTTCGTCAGGATATGTGC 59.936 47.826 0.00 0.00 0.00 4.57
583 585 3.263425 ACCCTTGTTTCGTCAGGATATGT 59.737 43.478 0.00 0.00 0.00 2.29
584 586 3.623060 CACCCTTGTTTCGTCAGGATATG 59.377 47.826 0.00 0.00 0.00 1.78
586 588 2.635915 ACACCCTTGTTTCGTCAGGATA 59.364 45.455 0.00 0.00 28.43 2.59
589 591 0.944386 CACACCCTTGTTTCGTCAGG 59.056 55.000 0.00 0.00 31.66 3.86
591 593 0.253610 ACCACACCCTTGTTTCGTCA 59.746 50.000 0.00 0.00 31.66 4.35
592 594 0.661020 CACCACACCCTTGTTTCGTC 59.339 55.000 0.00 0.00 31.66 4.20
593 595 0.750182 CCACCACACCCTTGTTTCGT 60.750 55.000 0.00 0.00 31.66 3.85
594 596 0.464735 TCCACCACACCCTTGTTTCG 60.465 55.000 0.00 0.00 31.66 3.46
596 598 1.703411 CATCCACCACACCCTTGTTT 58.297 50.000 0.00 0.00 31.66 2.83
597 599 0.827507 GCATCCACCACACCCTTGTT 60.828 55.000 0.00 0.00 31.66 2.83
599 601 0.612732 ATGCATCCACCACACCCTTG 60.613 55.000 0.00 0.00 0.00 3.61
600 602 0.612732 CATGCATCCACCACACCCTT 60.613 55.000 0.00 0.00 0.00 3.95
601 603 1.000521 CATGCATCCACCACACCCT 60.001 57.895 0.00 0.00 0.00 4.34
602 604 2.713967 GCATGCATCCACCACACCC 61.714 63.158 14.21 0.00 0.00 4.61
603 605 1.978080 TGCATGCATCCACCACACC 60.978 57.895 18.46 0.00 0.00 4.16
604 606 1.213537 GTGCATGCATCCACCACAC 59.786 57.895 25.64 3.24 30.89 3.82
605 607 2.334181 CGTGCATGCATCCACCACA 61.334 57.895 25.64 0.00 30.89 4.17
606 608 2.486504 CGTGCATGCATCCACCAC 59.513 61.111 25.64 7.95 0.00 4.16
607 609 2.190488 TACCGTGCATGCATCCACCA 62.190 55.000 25.64 4.61 0.00 4.17
608 610 0.819259 ATACCGTGCATGCATCCACC 60.819 55.000 25.64 9.55 0.00 4.61
609 611 0.588252 GATACCGTGCATGCATCCAC 59.412 55.000 25.64 10.92 0.00 4.02
610 612 0.469494 AGATACCGTGCATGCATCCA 59.531 50.000 25.64 10.10 0.00 3.41
611 613 2.069273 GTAGATACCGTGCATGCATCC 58.931 52.381 25.64 11.18 0.00 3.51
612 614 2.069273 GGTAGATACCGTGCATGCATC 58.931 52.381 25.64 16.75 36.50 3.91
613 615 2.169832 GGTAGATACCGTGCATGCAT 57.830 50.000 25.64 10.90 36.50 3.96
614 616 3.678921 GGTAGATACCGTGCATGCA 57.321 52.632 18.46 18.46 36.50 3.96
632 634 0.938713 TGGTTTTTCTACCGTGCACG 59.061 50.000 31.77 31.77 41.28 5.34
633 635 1.944709 ACTGGTTTTTCTACCGTGCAC 59.055 47.619 6.82 6.82 41.28 4.57
634 636 2.158871 AGACTGGTTTTTCTACCGTGCA 60.159 45.455 0.00 0.00 41.28 4.57
635 637 2.479275 GAGACTGGTTTTTCTACCGTGC 59.521 50.000 0.00 0.00 41.28 5.34
636 638 3.724374 TGAGACTGGTTTTTCTACCGTG 58.276 45.455 0.00 0.00 41.28 4.94
637 639 4.124970 GTTGAGACTGGTTTTTCTACCGT 58.875 43.478 0.00 0.00 41.28 4.83
638 640 3.497262 GGTTGAGACTGGTTTTTCTACCG 59.503 47.826 0.00 0.00 41.28 4.02
639 641 4.457466 TGGTTGAGACTGGTTTTTCTACC 58.543 43.478 0.00 0.00 36.44 3.18
640 642 5.220989 GGTTGGTTGAGACTGGTTTTTCTAC 60.221 44.000 0.00 0.00 0.00 2.59
641 643 4.885325 GGTTGGTTGAGACTGGTTTTTCTA 59.115 41.667 0.00 0.00 0.00 2.10
642 644 3.699538 GGTTGGTTGAGACTGGTTTTTCT 59.300 43.478 0.00 0.00 0.00 2.52
643 645 3.445805 TGGTTGGTTGAGACTGGTTTTTC 59.554 43.478 0.00 0.00 0.00 2.29
644 646 3.194755 GTGGTTGGTTGAGACTGGTTTTT 59.805 43.478 0.00 0.00 0.00 1.94
645 647 2.758423 GTGGTTGGTTGAGACTGGTTTT 59.242 45.455 0.00 0.00 0.00 2.43
646 648 2.375146 GTGGTTGGTTGAGACTGGTTT 58.625 47.619 0.00 0.00 0.00 3.27
647 649 1.745827 CGTGGTTGGTTGAGACTGGTT 60.746 52.381 0.00 0.00 0.00 3.67
648 650 0.179056 CGTGGTTGGTTGAGACTGGT 60.179 55.000 0.00 0.00 0.00 4.00
649 651 0.179056 ACGTGGTTGGTTGAGACTGG 60.179 55.000 0.00 0.00 0.00 4.00
650 652 2.132762 GTACGTGGTTGGTTGAGACTG 58.867 52.381 0.00 0.00 0.00 3.51
651 653 2.037144 AGTACGTGGTTGGTTGAGACT 58.963 47.619 0.00 0.00 0.00 3.24
652 654 2.132762 CAGTACGTGGTTGGTTGAGAC 58.867 52.381 0.00 0.00 0.00 3.36
653 655 2.033372 TCAGTACGTGGTTGGTTGAGA 58.967 47.619 0.00 0.00 0.00 3.27
654 656 2.035449 TCTCAGTACGTGGTTGGTTGAG 59.965 50.000 0.00 1.22 33.63 3.02
708 710 0.918983 AACATGGGGACGATGGACAT 59.081 50.000 0.00 0.00 0.00 3.06
711 713 1.077787 GCAACATGGGGACGATGGA 60.078 57.895 0.00 0.00 0.00 3.41
760 762 1.889170 TGGATATCACAGCCTAGCTCG 59.111 52.381 4.83 0.00 36.40 5.03
921 938 5.559148 ATCTCAGTTCTCAAAGACCAAGT 57.441 39.130 0.00 0.00 0.00 3.16
984 1001 7.338196 CCAGCTTCTTCGAGGAGATATATCTTA 59.662 40.741 16.37 0.00 37.25 2.10
1168 1188 4.394712 CCGACCTGGAGCGGCTTT 62.395 66.667 16.89 0.00 41.17 3.51
1827 1921 2.487762 ACTACCGTTAAATGGTCGACGA 59.512 45.455 9.92 5.99 38.67 4.20
1834 1928 7.318141 TCTTCTGAACTACTACCGTTAAATGG 58.682 38.462 0.00 0.00 0.00 3.16
1842 1936 7.536855 ACTAACAATCTTCTGAACTACTACCG 58.463 38.462 0.00 0.00 0.00 4.02
1941 2723 8.980173 CTGAAAGAACCCTTGACTGGAAGTTTT 61.980 40.741 0.00 0.00 43.96 2.43
1994 4322 7.883229 TTACGATAAATACATCACGCATCAT 57.117 32.000 0.00 0.00 0.00 2.45
2026 4354 6.638873 CGCTATTGGAGATGTTAACTACTCAG 59.361 42.308 23.21 16.57 0.00 3.35
2079 4407 6.038603 GCTAGCACATCAAAAATGATGAGGTA 59.961 38.462 21.88 20.51 46.25 3.08
2094 4422 3.866651 TCTTTTCTCTGGCTAGCACATC 58.133 45.455 18.24 0.00 0.00 3.06
2095 4423 3.988976 TCTTTTCTCTGGCTAGCACAT 57.011 42.857 18.24 0.00 0.00 3.21
2105 4433 4.261614 CCCCTTCCGTTTTTCTTTTCTCTG 60.262 45.833 0.00 0.00 0.00 3.35
2114 4442 4.501915 CCCTTTTTACCCCTTCCGTTTTTC 60.502 45.833 0.00 0.00 0.00 2.29
2174 4503 2.279073 CGGAGACCCCAGGCTAGA 59.721 66.667 0.00 0.00 34.14 2.43
2269 4603 0.178891 AGAGGAGGGGCTCAGAACAA 60.179 55.000 0.00 0.00 31.08 2.83
2272 4606 1.280457 GAAAGAGGAGGGGCTCAGAA 58.720 55.000 0.00 0.00 31.08 3.02
2311 4645 2.812658 TGACAAGGAGAGATGCAGAGA 58.187 47.619 0.00 0.00 0.00 3.10
2327 4661 1.065491 CGACCCATTCCCATCTTGACA 60.065 52.381 0.00 0.00 0.00 3.58
2629 5800 5.811399 TCTCGCCAATTTACTAAATGTGG 57.189 39.130 13.28 13.28 34.75 4.17
2679 5850 4.640771 TGGATTGAGGTCTTTAGCTTGT 57.359 40.909 0.00 0.00 32.30 3.16
2720 5893 8.215050 TGACCTTCTTTGAAACCTGTAATCTTA 58.785 33.333 0.00 0.00 0.00 2.10
2730 5903 5.767816 TTAGCTTGACCTTCTTTGAAACC 57.232 39.130 0.00 0.00 0.00 3.27
2756 5929 5.482163 TGTGTGTGTCTATTGGATTGAGA 57.518 39.130 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.