Multiple sequence alignment - TraesCS4A01G052500

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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 TraesCS4A01G052500 chr4A 100.000 3236 0 0 1 3236 43370199 43366964 0.000000e+00 5976.0
1 TraesCS4A01G052500 chr4A 74.074 432 55 24 1442 1855 43368692 43368300 1.220000e-24 124.0
2 TraesCS4A01G052500 chr4A 74.074 432 55 24 1508 1900 43368758 43368345 1.220000e-24 124.0
3 TraesCS4A01G052500 chr4A 73.413 504 61 42 1349 1815 43368752 43368285 1.580000e-23 121.0
4 TraesCS4A01G052500 chr4A 73.413 504 61 42 1448 1915 43368851 43368385 1.580000e-23 121.0
5 TraesCS4A01G052500 chr4B 94.001 1567 70 12 343 1900 517953928 517955479 0.000000e+00 2351.0
6 TraesCS4A01G052500 chr4B 89.615 1820 120 40 1438 3234 517955083 517956856 0.000000e+00 2250.0
7 TraesCS4A01G052500 chr4B 75.059 425 54 30 1439 1855 517955144 517955524 2.010000e-32 150.0
8 TraesCS4A01G052500 chr4B 73.633 512 72 31 1442 1920 517954919 517955400 4.350000e-29 139.0
9 TraesCS4A01G052500 chr4B 82.812 128 17 3 375 502 617400981 617401103 3.410000e-20 110.0
10 TraesCS4A01G052500 chr4D 91.066 1567 82 17 339 1900 420146766 420145253 0.000000e+00 2065.0
11 TraesCS4A01G052500 chr4D 84.952 1761 142 66 1349 3055 420145738 420144047 0.000000e+00 1670.0
12 TraesCS4A01G052500 chr4D 81.176 340 58 6 19 354 286103049 286102712 5.320000e-68 268.0
13 TraesCS4A01G052500 chr4D 80.588 340 60 6 19 354 286059091 286058754 1.150000e-64 257.0
14 TraesCS4A01G052500 chr4D 95.098 102 4 1 3135 3236 420143879 420143779 3.340000e-35 159.0
15 TraesCS4A01G052500 chr4D 73.780 492 76 35 1448 1920 420145789 420145332 9.360000e-31 145.0
16 TraesCS4A01G052500 chr4D 74.451 364 47 24 1494 1855 420145527 420145208 7.340000e-22 115.0
17 TraesCS4A01G052500 chr5A 82.303 356 52 9 12 363 627779970 627780318 6.790000e-77 298.0
18 TraesCS4A01G052500 chr5A 81.972 355 55 7 12 363 626443465 626443813 3.160000e-75 292.0
19 TraesCS4A01G052500 chr5A 81.972 355 54 8 12 363 627660709 627661056 3.160000e-75 292.0
20 TraesCS4A01G052500 chr5A 81.538 195 28 6 543 735 338221461 338221649 1.550000e-33 154.0
21 TraesCS4A01G052500 chr5A 79.703 202 30 7 538 734 659886408 659886603 5.630000e-28 135.0
22 TraesCS4A01G052500 chr1A 81.579 342 49 10 20 357 583885191 583884860 1.480000e-68 270.0
23 TraesCS4A01G052500 chr1A 88.000 100 10 2 548 645 34176396 34176297 2.040000e-22 117.0
24 TraesCS4A01G052500 chr3D 81.050 343 60 5 16 354 27062764 27063105 5.320000e-68 268.0
25 TraesCS4A01G052500 chr3D 80.294 340 63 4 20 356 24200008 24200346 1.490000e-63 254.0
26 TraesCS4A01G052500 chr2D 80.531 339 63 3 18 354 216045479 216045816 1.150000e-64 257.0
27 TraesCS4A01G052500 chr2D 85.542 83 6 4 3053 3133 416856717 416856639 7.440000e-12 82.4
28 TraesCS4A01G052500 chr2D 85.185 81 8 3 3054 3133 558112156 558112079 2.680000e-11 80.5
29 TraesCS4A01G052500 chr6B 82.857 175 27 3 353 526 17804557 17804385 1.550000e-33 154.0
30 TraesCS4A01G052500 chr6D 87.200 125 14 2 536 659 460882219 460882096 1.210000e-29 141.0
31 TraesCS4A01G052500 chr6D 80.319 188 29 4 548 733 434464284 434464465 5.630000e-28 135.0
32 TraesCS4A01G052500 chr6D 82.581 155 22 3 365 518 127485531 127485681 7.280000e-27 132.0
33 TraesCS4A01G052500 chr3B 92.857 84 6 0 567 650 29483372 29483289 4.380000e-24 122.0
34 TraesCS4A01G052500 chr3B 86.047 86 6 4 3049 3130 707431400 707431483 1.600000e-13 87.9
35 TraesCS4A01G052500 chr3B 86.747 83 5 4 3052 3130 707431484 707431404 1.600000e-13 87.9
36 TraesCS4A01G052500 chr3B 76.250 160 24 8 365 514 111860618 111860463 4.480000e-09 73.1
37 TraesCS4A01G052500 chr3B 91.892 37 3 0 376 412 452682361 452682397 6.000000e-03 52.8
38 TraesCS4A01G052500 chr3A 84.348 115 16 2 536 649 38602466 38602353 9.490000e-21 111.0
39 TraesCS4A01G052500 chr3A 83.486 109 15 2 548 654 716381117 716381010 7.390000e-17 99.0
40 TraesCS4A01G052500 chr3A 86.747 83 6 4 3052 3131 238688625 238688705 1.600000e-13 87.9
41 TraesCS4A01G052500 chr3A 84.091 88 6 4 3047 3129 469414721 469414637 9.630000e-11 78.7
42 TraesCS4A01G052500 chr2B 86.747 83 8 3 3048 3129 656942020 656941940 4.450000e-14 89.8
43 TraesCS4A01G052500 chr5B 87.179 78 5 3 3053 3130 331215415 331215343 2.070000e-12 84.2
44 TraesCS4A01G052500 chr6A 94.444 36 2 0 377 412 155576984 155576949 4.510000e-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 TraesCS4A01G052500 chr4A 43366964 43370199 3235 True 1293.2 5976 78.9948 1 3236 5 chr4A.!!$R1 3235
1 TraesCS4A01G052500 chr4B 517953928 517956856 2928 False 1222.5 2351 83.0770 343 3234 4 chr4B.!!$F2 2891
2 TraesCS4A01G052500 chr4D 420143779 420146766 2987 True 830.8 2065 83.8694 339 3236 5 chr4D.!!$R3 2897

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
974 989 0.039472 TGTCTCCTCTGCTCAGCTCT 59.961 55.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 2334 0.389025 CCAAACACAAAGCCCCTCAC 59.611 55.0 0.0 0.0 0.0 3.51 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 8.798975 TCCATATTGAAAGACTTATACTCCCT 57.201 34.615 0.00 0.00 0.00 4.20
27 28 8.871125 TCCATATTGAAAGACTTATACTCCCTC 58.129 37.037 0.00 0.00 0.00 4.30
28 29 7.815068 CCATATTGAAAGACTTATACTCCCTCG 59.185 40.741 0.00 0.00 0.00 4.63
29 30 5.593679 TTGAAAGACTTATACTCCCTCGG 57.406 43.478 0.00 0.00 0.00 4.63
30 31 4.607239 TGAAAGACTTATACTCCCTCGGT 58.393 43.478 0.00 0.00 0.00 4.69
31 32 5.021458 TGAAAGACTTATACTCCCTCGGTT 58.979 41.667 0.00 0.00 0.00 4.44
32 33 5.126707 TGAAAGACTTATACTCCCTCGGTTC 59.873 44.000 0.00 0.00 0.00 3.62
33 34 3.564264 AGACTTATACTCCCTCGGTTCC 58.436 50.000 0.00 0.00 0.00 3.62
34 35 3.204831 AGACTTATACTCCCTCGGTTCCT 59.795 47.826 0.00 0.00 0.00 3.36
35 36 3.959449 GACTTATACTCCCTCGGTTCCTT 59.041 47.826 0.00 0.00 0.00 3.36
36 37 4.359996 ACTTATACTCCCTCGGTTCCTTT 58.640 43.478 0.00 0.00 0.00 3.11
37 38 5.522641 ACTTATACTCCCTCGGTTCCTTTA 58.477 41.667 0.00 0.00 0.00 1.85
38 39 6.141790 ACTTATACTCCCTCGGTTCCTTTAT 58.858 40.000 0.00 0.00 0.00 1.40
39 40 7.300658 ACTTATACTCCCTCGGTTCCTTTATA 58.699 38.462 0.00 0.00 0.00 0.98
40 41 7.954620 ACTTATACTCCCTCGGTTCCTTTATAT 59.045 37.037 0.00 0.00 0.00 0.86
41 42 9.471702 CTTATACTCCCTCGGTTCCTTTATATA 57.528 37.037 0.00 0.00 0.00 0.86
42 43 7.715266 ATACTCCCTCGGTTCCTTTATATAC 57.285 40.000 0.00 0.00 0.00 1.47
43 44 4.522022 ACTCCCTCGGTTCCTTTATATACG 59.478 45.833 0.00 0.00 0.00 3.06
44 45 3.828451 TCCCTCGGTTCCTTTATATACGG 59.172 47.826 0.00 0.00 0.00 4.02
45 46 3.575687 CCCTCGGTTCCTTTATATACGGT 59.424 47.826 0.00 0.00 0.00 4.83
46 47 4.553323 CCTCGGTTCCTTTATATACGGTG 58.447 47.826 0.00 0.00 0.00 4.94
47 48 4.038402 CCTCGGTTCCTTTATATACGGTGT 59.962 45.833 0.00 0.00 0.00 4.16
48 49 5.241506 CCTCGGTTCCTTTATATACGGTGTA 59.758 44.000 0.00 0.00 0.00 2.90
49 50 6.071728 CCTCGGTTCCTTTATATACGGTGTAT 60.072 42.308 2.90 2.90 0.00 2.29
50 51 7.288810 TCGGTTCCTTTATATACGGTGTATT 57.711 36.000 2.65 0.00 0.00 1.89
51 52 7.725251 TCGGTTCCTTTATATACGGTGTATTT 58.275 34.615 2.65 0.00 0.00 1.40
52 53 7.652909 TCGGTTCCTTTATATACGGTGTATTTG 59.347 37.037 2.65 0.00 0.00 2.32
53 54 7.439056 CGGTTCCTTTATATACGGTGTATTTGT 59.561 37.037 2.65 0.00 0.00 2.83
54 55 9.112725 GGTTCCTTTATATACGGTGTATTTGTT 57.887 33.333 2.65 0.00 0.00 2.83
83 84 7.701539 ATAAAATCTCACAATGTAAGGTGCA 57.298 32.000 0.00 0.00 35.04 4.57
84 85 6.594788 AAAATCTCACAATGTAAGGTGCAT 57.405 33.333 0.00 0.00 35.04 3.96
85 86 6.594788 AAATCTCACAATGTAAGGTGCATT 57.405 33.333 0.00 0.00 37.06 3.56
86 87 6.594788 AATCTCACAATGTAAGGTGCATTT 57.405 33.333 0.00 0.00 34.68 2.32
87 88 5.375417 TCTCACAATGTAAGGTGCATTTG 57.625 39.130 0.00 0.00 34.68 2.32
88 89 4.826733 TCTCACAATGTAAGGTGCATTTGT 59.173 37.500 0.00 0.00 34.68 2.83
89 90 5.301551 TCTCACAATGTAAGGTGCATTTGTT 59.698 36.000 0.00 0.00 34.68 2.83
90 91 5.527951 TCACAATGTAAGGTGCATTTGTTC 58.472 37.500 0.00 0.00 34.68 3.18
91 92 5.301551 TCACAATGTAAGGTGCATTTGTTCT 59.698 36.000 0.00 0.00 34.68 3.01
92 93 6.488344 TCACAATGTAAGGTGCATTTGTTCTA 59.512 34.615 0.00 0.00 34.68 2.10
93 94 7.013750 TCACAATGTAAGGTGCATTTGTTCTAA 59.986 33.333 0.00 0.00 34.68 2.10
94 95 7.814107 CACAATGTAAGGTGCATTTGTTCTAAT 59.186 33.333 0.00 0.00 34.68 1.73
95 96 8.367156 ACAATGTAAGGTGCATTTGTTCTAATT 58.633 29.630 0.00 0.00 34.68 1.40
96 97 8.863049 CAATGTAAGGTGCATTTGTTCTAATTC 58.137 33.333 0.00 0.00 34.68 2.17
97 98 6.919721 TGTAAGGTGCATTTGTTCTAATTCC 58.080 36.000 0.00 0.00 0.00 3.01
98 99 6.719370 TGTAAGGTGCATTTGTTCTAATTCCT 59.281 34.615 0.00 0.00 0.00 3.36
99 100 5.904362 AGGTGCATTTGTTCTAATTCCTC 57.096 39.130 0.00 0.00 0.00 3.71
100 101 5.324409 AGGTGCATTTGTTCTAATTCCTCA 58.676 37.500 0.00 0.00 0.00 3.86
101 102 5.954150 AGGTGCATTTGTTCTAATTCCTCAT 59.046 36.000 0.00 0.00 0.00 2.90
102 103 7.118723 AGGTGCATTTGTTCTAATTCCTCATA 58.881 34.615 0.00 0.00 0.00 2.15
103 104 7.615365 AGGTGCATTTGTTCTAATTCCTCATAA 59.385 33.333 0.00 0.00 0.00 1.90
104 105 8.416329 GGTGCATTTGTTCTAATTCCTCATAAT 58.584 33.333 0.00 0.00 0.00 1.28
105 106 9.807649 GTGCATTTGTTCTAATTCCTCATAATT 57.192 29.630 0.00 0.00 33.69 1.40
164 165 9.487790 CTCTTTCCTGATTATCTGTATCTTTCC 57.512 37.037 0.00 0.00 0.00 3.13
165 166 9.218525 TCTTTCCTGATTATCTGTATCTTTCCT 57.781 33.333 0.00 0.00 0.00 3.36
166 167 9.844257 CTTTCCTGATTATCTGTATCTTTCCTT 57.156 33.333 0.00 0.00 0.00 3.36
167 168 9.618890 TTTCCTGATTATCTGTATCTTTCCTTG 57.381 33.333 0.00 0.00 0.00 3.61
168 169 8.324191 TCCTGATTATCTGTATCTTTCCTTGT 57.676 34.615 0.00 0.00 0.00 3.16
169 170 9.434275 TCCTGATTATCTGTATCTTTCCTTGTA 57.566 33.333 0.00 0.00 0.00 2.41
170 171 9.703892 CCTGATTATCTGTATCTTTCCTTGTAG 57.296 37.037 0.00 0.00 0.00 2.74
171 172 9.202273 CTGATTATCTGTATCTTTCCTTGTAGC 57.798 37.037 0.00 0.00 0.00 3.58
172 173 8.704668 TGATTATCTGTATCTTTCCTTGTAGCA 58.295 33.333 0.00 0.00 0.00 3.49
173 174 9.547753 GATTATCTGTATCTTTCCTTGTAGCAA 57.452 33.333 0.00 0.00 0.00 3.91
174 175 9.905713 ATTATCTGTATCTTTCCTTGTAGCAAA 57.094 29.630 0.00 0.00 0.00 3.68
175 176 9.733556 TTATCTGTATCTTTCCTTGTAGCAAAA 57.266 29.630 0.00 0.00 0.00 2.44
176 177 7.672983 TCTGTATCTTTCCTTGTAGCAAAAG 57.327 36.000 0.00 0.00 0.00 2.27
177 178 7.450074 TCTGTATCTTTCCTTGTAGCAAAAGA 58.550 34.615 0.00 0.00 40.78 2.52
178 179 7.936847 TCTGTATCTTTCCTTGTAGCAAAAGAA 59.063 33.333 0.00 0.00 40.14 2.52
179 180 8.635765 TGTATCTTTCCTTGTAGCAAAAGAAT 57.364 30.769 0.00 0.00 40.14 2.40
180 181 8.514594 TGTATCTTTCCTTGTAGCAAAAGAATG 58.485 33.333 0.00 0.00 40.14 2.67
181 182 7.765695 ATCTTTCCTTGTAGCAAAAGAATGA 57.234 32.000 0.00 9.85 40.14 2.57
182 183 7.581213 TCTTTCCTTGTAGCAAAAGAATGAA 57.419 32.000 0.00 0.00 35.43 2.57
183 184 8.006298 TCTTTCCTTGTAGCAAAAGAATGAAA 57.994 30.769 0.00 0.00 35.43 2.69
184 185 8.474025 TCTTTCCTTGTAGCAAAAGAATGAAAA 58.526 29.630 0.00 0.00 35.43 2.29
185 186 9.264719 CTTTCCTTGTAGCAAAAGAATGAAAAT 57.735 29.630 0.00 0.00 31.81 1.82
221 222 8.776680 TTTTTGCACGTATCTCTTACTTTTTC 57.223 30.769 0.00 0.00 0.00 2.29
222 223 7.724305 TTTGCACGTATCTCTTACTTTTTCT 57.276 32.000 0.00 0.00 0.00 2.52
223 224 6.706055 TGCACGTATCTCTTACTTTTTCTG 57.294 37.500 0.00 0.00 0.00 3.02
224 225 5.637810 TGCACGTATCTCTTACTTTTTCTGG 59.362 40.000 0.00 0.00 0.00 3.86
225 226 5.867716 GCACGTATCTCTTACTTTTTCTGGA 59.132 40.000 0.00 0.00 0.00 3.86
226 227 6.183360 GCACGTATCTCTTACTTTTTCTGGAC 60.183 42.308 0.00 0.00 0.00 4.02
227 228 7.091443 CACGTATCTCTTACTTTTTCTGGACT 58.909 38.462 0.00 0.00 0.00 3.85
228 229 8.242053 CACGTATCTCTTACTTTTTCTGGACTA 58.758 37.037 0.00 0.00 0.00 2.59
229 230 8.800332 ACGTATCTCTTACTTTTTCTGGACTAA 58.200 33.333 0.00 0.00 0.00 2.24
230 231 9.804758 CGTATCTCTTACTTTTTCTGGACTAAT 57.195 33.333 0.00 0.00 0.00 1.73
241 242 9.760660 CTTTTTCTGGACTAATTGATTTACTCG 57.239 33.333 0.00 0.00 0.00 4.18
242 243 6.903883 TTCTGGACTAATTGATTTACTCGC 57.096 37.500 0.00 0.00 0.00 5.03
243 244 5.357257 TCTGGACTAATTGATTTACTCGCC 58.643 41.667 0.00 0.00 0.00 5.54
244 245 5.092554 TGGACTAATTGATTTACTCGCCA 57.907 39.130 0.00 0.00 0.00 5.69
245 246 4.873827 TGGACTAATTGATTTACTCGCCAC 59.126 41.667 0.00 0.00 0.00 5.01
246 247 5.116882 GGACTAATTGATTTACTCGCCACT 58.883 41.667 0.00 0.00 0.00 4.00
247 248 5.006746 GGACTAATTGATTTACTCGCCACTG 59.993 44.000 0.00 0.00 0.00 3.66
248 249 5.730550 ACTAATTGATTTACTCGCCACTGA 58.269 37.500 0.00 0.00 0.00 3.41
249 250 4.946784 AATTGATTTACTCGCCACTGAC 57.053 40.909 0.00 0.00 0.00 3.51
250 251 2.380084 TGATTTACTCGCCACTGACC 57.620 50.000 0.00 0.00 0.00 4.02
251 252 1.621317 TGATTTACTCGCCACTGACCA 59.379 47.619 0.00 0.00 0.00 4.02
252 253 2.037902 TGATTTACTCGCCACTGACCAA 59.962 45.455 0.00 0.00 0.00 3.67
253 254 1.873698 TTTACTCGCCACTGACCAAC 58.126 50.000 0.00 0.00 0.00 3.77
254 255 0.753867 TTACTCGCCACTGACCAACA 59.246 50.000 0.00 0.00 0.00 3.33
267 268 4.935352 TGACCAACAGATTTTTCAAGGG 57.065 40.909 0.00 0.00 0.00 3.95
268 269 4.285863 TGACCAACAGATTTTTCAAGGGT 58.714 39.130 0.00 0.00 0.00 4.34
269 270 5.450453 TGACCAACAGATTTTTCAAGGGTA 58.550 37.500 0.00 0.00 0.00 3.69
270 271 5.894393 TGACCAACAGATTTTTCAAGGGTAA 59.106 36.000 0.00 0.00 0.00 2.85
271 272 6.553100 TGACCAACAGATTTTTCAAGGGTAAT 59.447 34.615 0.00 0.00 0.00 1.89
272 273 7.070571 TGACCAACAGATTTTTCAAGGGTAATT 59.929 33.333 0.00 0.00 0.00 1.40
273 274 7.801104 ACCAACAGATTTTTCAAGGGTAATTT 58.199 30.769 0.00 0.00 0.00 1.82
274 275 7.931407 ACCAACAGATTTTTCAAGGGTAATTTC 59.069 33.333 0.00 0.00 0.00 2.17
275 276 7.116233 CCAACAGATTTTTCAAGGGTAATTTCG 59.884 37.037 0.00 0.00 0.00 3.46
276 277 7.284919 ACAGATTTTTCAAGGGTAATTTCGT 57.715 32.000 0.00 0.00 0.00 3.85
277 278 7.368059 ACAGATTTTTCAAGGGTAATTTCGTC 58.632 34.615 0.00 0.00 0.00 4.20
278 279 6.806739 CAGATTTTTCAAGGGTAATTTCGTCC 59.193 38.462 0.00 0.00 0.00 4.79
279 280 6.719829 AGATTTTTCAAGGGTAATTTCGTCCT 59.280 34.615 0.00 0.00 0.00 3.85
280 281 7.886446 AGATTTTTCAAGGGTAATTTCGTCCTA 59.114 33.333 0.00 0.00 0.00 2.94
281 282 7.820578 TTTTTCAAGGGTAATTTCGTCCTAA 57.179 32.000 0.00 0.00 0.00 2.69
282 283 6.806388 TTTCAAGGGTAATTTCGTCCTAAC 57.194 37.500 0.00 0.00 0.00 2.34
283 284 5.750352 TCAAGGGTAATTTCGTCCTAACT 57.250 39.130 0.00 0.00 0.00 2.24
284 285 6.117975 TCAAGGGTAATTTCGTCCTAACTT 57.882 37.500 0.00 0.00 0.00 2.66
285 286 6.168389 TCAAGGGTAATTTCGTCCTAACTTC 58.832 40.000 0.00 0.00 0.00 3.01
286 287 6.013984 TCAAGGGTAATTTCGTCCTAACTTCT 60.014 38.462 0.00 0.00 0.00 2.85
287 288 5.975282 AGGGTAATTTCGTCCTAACTTCTC 58.025 41.667 0.00 0.00 0.00 2.87
288 289 5.720520 AGGGTAATTTCGTCCTAACTTCTCT 59.279 40.000 0.00 0.00 0.00 3.10
289 290 6.894103 AGGGTAATTTCGTCCTAACTTCTCTA 59.106 38.462 0.00 0.00 0.00 2.43
290 291 7.564292 AGGGTAATTTCGTCCTAACTTCTCTAT 59.436 37.037 0.00 0.00 0.00 1.98
291 292 8.854117 GGGTAATTTCGTCCTAACTTCTCTATA 58.146 37.037 0.00 0.00 0.00 1.31
315 316 9.944376 ATAATTATATGCCTTAGTCATCGTGTT 57.056 29.630 0.00 0.00 0.00 3.32
317 318 9.772973 AATTATATGCCTTAGTCATCGTGTTAA 57.227 29.630 0.00 0.00 0.00 2.01
318 319 9.772973 ATTATATGCCTTAGTCATCGTGTTAAA 57.227 29.630 0.00 0.00 0.00 1.52
319 320 9.602568 TTATATGCCTTAGTCATCGTGTTAAAA 57.397 29.630 0.00 0.00 0.00 1.52
320 321 6.811253 ATGCCTTAGTCATCGTGTTAAAAA 57.189 33.333 0.00 0.00 0.00 1.94
321 322 6.811253 TGCCTTAGTCATCGTGTTAAAAAT 57.189 33.333 0.00 0.00 0.00 1.82
322 323 7.908827 TGCCTTAGTCATCGTGTTAAAAATA 57.091 32.000 0.00 0.00 0.00 1.40
323 324 8.325421 TGCCTTAGTCATCGTGTTAAAAATAA 57.675 30.769 0.00 0.00 0.00 1.40
324 325 8.952278 TGCCTTAGTCATCGTGTTAAAAATAAT 58.048 29.630 0.00 0.00 0.00 1.28
359 360 1.409427 GGAACGGAGGGAGTACATCAG 59.591 57.143 0.00 0.00 0.00 2.90
379 380 4.997395 TCAGATGTTGGAGCACTAGTTTTC 59.003 41.667 0.00 0.00 0.00 2.29
484 495 9.740239 TTATACAACGTCTATGTTTACATCTCC 57.260 33.333 0.00 0.00 37.76 3.71
485 496 6.032956 ACAACGTCTATGTTTACATCTCCA 57.967 37.500 0.00 0.00 37.76 3.86
486 497 6.460781 ACAACGTCTATGTTTACATCTCCAA 58.539 36.000 0.00 0.00 37.76 3.53
487 498 6.932400 ACAACGTCTATGTTTACATCTCCAAA 59.068 34.615 0.00 0.00 37.76 3.28
488 499 7.606456 ACAACGTCTATGTTTACATCTCCAAAT 59.394 33.333 0.00 0.00 37.76 2.32
489 500 9.093970 CAACGTCTATGTTTACATCTCCAAATA 57.906 33.333 0.00 0.00 37.76 1.40
490 501 9.832445 AACGTCTATGTTTACATCTCCAAATAT 57.168 29.630 0.00 0.00 37.76 1.28
593 605 2.031560 GCACGAACACATGACAACTTCA 59.968 45.455 0.00 0.00 39.11 3.02
801 814 3.803082 CGTGTGCCCGGAATGCAG 61.803 66.667 0.73 0.00 39.87 4.41
872 885 1.743772 CGAGGGAGGTTCGCATCAAAT 60.744 52.381 0.00 0.00 0.00 2.32
902 915 1.517694 CACGACCACGAATACCCCG 60.518 63.158 0.00 0.00 42.66 5.73
903 916 1.978617 ACGACCACGAATACCCCGT 60.979 57.895 0.00 0.00 42.66 5.28
939 952 2.586357 GTCTGATCGAAGCCCCGC 60.586 66.667 0.00 0.00 0.00 6.13
974 989 0.039472 TGTCTCCTCTGCTCAGCTCT 59.961 55.000 0.00 0.00 0.00 4.09
1284 1299 1.617357 GACTACCTCCACAAGTTCGGT 59.383 52.381 0.00 0.00 0.00 4.69
1326 1341 3.885521 GGCAAGCATCAGCCGAGC 61.886 66.667 0.00 0.00 41.70 5.03
1419 1437 3.322254 GGAGGTACGAACAGGATGATGAT 59.678 47.826 0.00 0.00 39.69 2.45
1420 1438 4.302455 GAGGTACGAACAGGATGATGATG 58.698 47.826 0.00 0.00 39.69 3.07
1422 1440 4.038522 AGGTACGAACAGGATGATGATGAG 59.961 45.833 0.00 0.00 39.69 2.90
1423 1441 4.202161 GGTACGAACAGGATGATGATGAGT 60.202 45.833 0.00 0.00 39.69 3.41
1425 1443 4.938080 ACGAACAGGATGATGATGAGTAC 58.062 43.478 0.00 0.00 39.69 2.73
1461 1479 1.763545 GGTGGGAGGTATGAAGAGGAC 59.236 57.143 0.00 0.00 0.00 3.85
1503 1521 1.204146 CTAGTGGTGGTGGTGGCTAT 58.796 55.000 0.00 0.00 0.00 2.97
1538 1556 6.549364 AGGTATGAGGAAGAAGATGAGTACAG 59.451 42.308 0.00 0.00 0.00 2.74
1623 1641 2.185310 CTCCTAGTGGTGGTGGTGGC 62.185 65.000 0.00 0.00 34.23 5.01
1624 1642 2.525124 CCTAGTGGTGGTGGTGGCA 61.525 63.158 0.00 0.00 0.00 4.92
1625 1643 1.003355 CTAGTGGTGGTGGTGGCAG 60.003 63.158 0.00 0.00 0.00 4.85
1629 1647 4.204028 GGTGGTGGTGGCAGTGGT 62.204 66.667 0.00 0.00 0.00 4.16
1653 1671 1.522900 ATGGTGGGGGAAGGTATGAG 58.477 55.000 0.00 0.00 0.00 2.90
1664 1682 4.263243 GGGAAGGTATGAGGAAGATGATGG 60.263 50.000 0.00 0.00 0.00 3.51
1796 1817 1.825474 TGAGTACAAGAGGCCTAGTGC 59.175 52.381 4.42 8.94 40.16 4.40
1815 1836 0.914644 CTGGAAGCCATGGAGGAAGA 59.085 55.000 18.40 0.00 41.22 2.87
1827 1848 6.522114 GCCATGGAGGAAGATATGAAGAAGAT 60.522 42.308 18.40 0.00 41.22 2.40
1932 1998 1.522580 GGATGAGTCAGAAGGCGGC 60.523 63.158 0.00 0.00 0.00 6.53
1951 2017 1.331756 GCGGCATTGGAGACTACATTG 59.668 52.381 5.36 5.36 0.00 2.82
2098 2164 0.955919 CCGCCCTGAGAGTGGAAAAC 60.956 60.000 0.00 0.00 37.02 2.43
2100 2166 1.611673 CGCCCTGAGAGTGGAAAACAT 60.612 52.381 0.00 0.00 0.00 2.71
2142 2208 3.084786 GGCAGATTACCTGAAACTTGCT 58.915 45.455 0.00 0.00 45.78 3.91
2169 2235 4.397417 GGTTTCATGAAGAAGGATGGTGAG 59.603 45.833 8.41 0.00 37.57 3.51
2238 2304 4.406943 GGTTCATGAAGAAGCGTTGATTC 58.593 43.478 8.80 0.00 43.93 2.52
2252 2318 6.108687 AGCGTTGATTCATAACTGATCTTCA 58.891 36.000 0.00 0.00 0.00 3.02
2261 2328 9.896645 ATTCATAACTGATCTTCACTACATTGT 57.103 29.630 0.00 0.00 0.00 2.71
2267 2334 6.596888 ACTGATCTTCACTACATTGTGATTGG 59.403 38.462 0.00 0.00 45.03 3.16
2271 2338 5.934043 TCTTCACTACATTGTGATTGGTGAG 59.066 40.000 0.00 0.00 45.03 3.51
2274 2341 2.220653 ACATTGTGATTGGTGAGGGG 57.779 50.000 0.00 0.00 0.00 4.79
2400 2469 2.309136 ATGCCCAAGGTGCTACTTTT 57.691 45.000 0.00 0.00 0.00 2.27
2401 2470 2.961531 TGCCCAAGGTGCTACTTTTA 57.038 45.000 0.00 0.00 0.00 1.52
2559 2628 4.843220 ATTTGAATGTAGCTATGCTGGC 57.157 40.909 0.00 0.00 40.10 4.85
2563 2632 3.258123 TGAATGTAGCTATGCTGGCGATA 59.742 43.478 0.00 0.00 40.10 2.92
2568 2637 3.742433 AGCTATGCTGGCGATATATCC 57.258 47.619 7.15 0.48 37.57 2.59
2607 2676 4.406456 TGAACTGAACCCTAATGCAATGT 58.594 39.130 0.00 0.00 0.00 2.71
2820 2892 5.227569 TCTGCATCTTACTTTCCTGTTCA 57.772 39.130 0.00 0.00 0.00 3.18
2902 2974 3.821033 ACACCTTTTCAACTGATGGTAGC 59.179 43.478 0.00 0.00 0.00 3.58
2914 2986 8.271458 TCAACTGATGGTAGCTTTGGATATTTA 58.729 33.333 0.00 0.00 0.00 1.40
2937 3025 3.438781 TGTCAAATGATGGTAGTTTCCGC 59.561 43.478 0.00 0.00 0.00 5.54
2971 3059 4.967575 CAGTTAAGTGGCAAACTAACGTTG 59.032 41.667 11.99 3.57 38.56 4.10
3043 3132 5.880332 TCATGTTATCAGCTTGAACTAACCC 59.120 40.000 0.00 0.00 0.00 4.11
3080 3176 3.558321 CCTCCGTCCCAAAATAAGTGTCA 60.558 47.826 0.00 0.00 0.00 3.58
3098 3194 7.948278 AGTGTCACTGATTTAGTACAAAGTC 57.052 36.000 4.21 0.00 37.60 3.01
3100 3196 5.924254 TGTCACTGATTTAGTACAAAGTCGG 59.076 40.000 0.00 0.00 37.60 4.79
3106 3202 6.457355 TGATTTAGTACAAAGTCGGCACTTA 58.543 36.000 0.00 0.00 42.45 2.24
3107 3203 6.366877 TGATTTAGTACAAAGTCGGCACTTAC 59.633 38.462 0.00 0.03 42.45 2.34
3167 3351 3.902218 CACATTTCCCAGATACCATGGT 58.098 45.455 23.55 23.55 35.96 3.55
3226 3410 1.801178 CGTGAGCTGTTCTTTCTTCCC 59.199 52.381 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.875168 AGGGAGTATAAGTCTTTCAATATGGAG 58.125 37.037 0.00 0.00 0.00 3.86
1 2 8.798975 AGGGAGTATAAGTCTTTCAATATGGA 57.201 34.615 0.00 0.00 0.00 3.41
2 3 7.815068 CGAGGGAGTATAAGTCTTTCAATATGG 59.185 40.741 0.00 0.00 0.00 2.74
3 4 7.815068 CCGAGGGAGTATAAGTCTTTCAATATG 59.185 40.741 0.00 0.00 0.00 1.78
4 5 7.509659 ACCGAGGGAGTATAAGTCTTTCAATAT 59.490 37.037 0.00 0.00 0.00 1.28
5 6 6.837568 ACCGAGGGAGTATAAGTCTTTCAATA 59.162 38.462 0.00 0.00 0.00 1.90
6 7 5.661759 ACCGAGGGAGTATAAGTCTTTCAAT 59.338 40.000 0.00 0.00 0.00 2.57
7 8 5.021458 ACCGAGGGAGTATAAGTCTTTCAA 58.979 41.667 0.00 0.00 0.00 2.69
8 9 4.607239 ACCGAGGGAGTATAAGTCTTTCA 58.393 43.478 0.00 0.00 0.00 2.69
9 10 5.451659 GGAACCGAGGGAGTATAAGTCTTTC 60.452 48.000 0.00 0.00 0.00 2.62
10 11 4.405036 GGAACCGAGGGAGTATAAGTCTTT 59.595 45.833 0.00 0.00 0.00 2.52
11 12 3.959449 GGAACCGAGGGAGTATAAGTCTT 59.041 47.826 0.00 0.00 0.00 3.01
12 13 3.204831 AGGAACCGAGGGAGTATAAGTCT 59.795 47.826 0.00 0.00 0.00 3.24
13 14 3.564264 AGGAACCGAGGGAGTATAAGTC 58.436 50.000 0.00 0.00 0.00 3.01
14 15 3.684408 AGGAACCGAGGGAGTATAAGT 57.316 47.619 0.00 0.00 0.00 2.24
15 16 6.667558 ATAAAGGAACCGAGGGAGTATAAG 57.332 41.667 0.00 0.00 0.00 1.73
16 17 9.247861 GTATATAAAGGAACCGAGGGAGTATAA 57.752 37.037 0.00 0.00 0.00 0.98
17 18 7.554118 CGTATATAAAGGAACCGAGGGAGTATA 59.446 40.741 0.00 0.00 0.00 1.47
18 19 6.376581 CGTATATAAAGGAACCGAGGGAGTAT 59.623 42.308 0.00 0.00 0.00 2.12
19 20 5.707298 CGTATATAAAGGAACCGAGGGAGTA 59.293 44.000 0.00 0.00 0.00 2.59
20 21 4.522022 CGTATATAAAGGAACCGAGGGAGT 59.478 45.833 0.00 0.00 0.00 3.85
21 22 4.082354 CCGTATATAAAGGAACCGAGGGAG 60.082 50.000 0.37 0.00 0.00 4.30
22 23 3.828451 CCGTATATAAAGGAACCGAGGGA 59.172 47.826 0.37 0.00 0.00 4.20
23 24 3.575687 ACCGTATATAAAGGAACCGAGGG 59.424 47.826 11.31 0.00 0.00 4.30
24 25 4.038402 ACACCGTATATAAAGGAACCGAGG 59.962 45.833 11.31 0.00 0.00 4.63
25 26 5.192327 ACACCGTATATAAAGGAACCGAG 57.808 43.478 11.31 0.00 0.00 4.63
26 27 6.899393 ATACACCGTATATAAAGGAACCGA 57.101 37.500 11.31 0.00 0.00 4.69
27 28 7.439056 ACAAATACACCGTATATAAAGGAACCG 59.561 37.037 11.31 0.00 0.00 4.44
28 29 8.667076 ACAAATACACCGTATATAAAGGAACC 57.333 34.615 11.31 0.00 0.00 3.62
57 58 9.237187 TGCACCTTACATTGTGAGATTTTATAA 57.763 29.630 9.98 0.00 34.37 0.98
58 59 8.800370 TGCACCTTACATTGTGAGATTTTATA 57.200 30.769 9.98 0.00 34.37 0.98
59 60 7.701539 TGCACCTTACATTGTGAGATTTTAT 57.298 32.000 9.98 0.00 34.37 1.40
60 61 7.701539 ATGCACCTTACATTGTGAGATTTTA 57.298 32.000 9.98 0.00 34.37 1.52
61 62 6.594788 ATGCACCTTACATTGTGAGATTTT 57.405 33.333 9.98 0.00 34.37 1.82
62 63 6.594788 AATGCACCTTACATTGTGAGATTT 57.405 33.333 9.98 0.00 36.41 2.17
63 64 6.015180 ACAAATGCACCTTACATTGTGAGATT 60.015 34.615 9.98 0.00 37.78 2.40
64 65 5.477984 ACAAATGCACCTTACATTGTGAGAT 59.522 36.000 9.98 0.00 37.78 2.75
65 66 4.826733 ACAAATGCACCTTACATTGTGAGA 59.173 37.500 9.98 0.00 37.78 3.27
66 67 5.125100 ACAAATGCACCTTACATTGTGAG 57.875 39.130 0.00 0.01 37.78 3.51
67 68 5.301551 AGAACAAATGCACCTTACATTGTGA 59.698 36.000 0.00 0.00 37.78 3.58
68 69 5.531634 AGAACAAATGCACCTTACATTGTG 58.468 37.500 0.00 0.00 37.78 3.33
69 70 5.789643 AGAACAAATGCACCTTACATTGT 57.210 34.783 0.00 0.00 37.78 2.71
70 71 8.761575 AATTAGAACAAATGCACCTTACATTG 57.238 30.769 0.00 0.00 37.78 2.82
71 72 8.034804 GGAATTAGAACAAATGCACCTTACATT 58.965 33.333 0.00 0.00 39.38 2.71
72 73 7.397192 AGGAATTAGAACAAATGCACCTTACAT 59.603 33.333 0.00 0.00 0.00 2.29
73 74 6.719370 AGGAATTAGAACAAATGCACCTTACA 59.281 34.615 0.00 0.00 0.00 2.41
74 75 7.094377 TGAGGAATTAGAACAAATGCACCTTAC 60.094 37.037 0.00 0.00 0.00 2.34
75 76 6.945435 TGAGGAATTAGAACAAATGCACCTTA 59.055 34.615 0.00 0.00 0.00 2.69
76 77 5.774690 TGAGGAATTAGAACAAATGCACCTT 59.225 36.000 0.00 0.00 0.00 3.50
77 78 5.324409 TGAGGAATTAGAACAAATGCACCT 58.676 37.500 0.00 0.00 0.00 4.00
78 79 5.643379 TGAGGAATTAGAACAAATGCACC 57.357 39.130 0.00 0.00 0.00 5.01
79 80 9.807649 AATTATGAGGAATTAGAACAAATGCAC 57.192 29.630 0.00 0.00 0.00 4.57
138 139 9.487790 GGAAAGATACAGATAATCAGGAAAGAG 57.512 37.037 0.00 0.00 0.00 2.85
139 140 9.218525 AGGAAAGATACAGATAATCAGGAAAGA 57.781 33.333 0.00 0.00 0.00 2.52
140 141 9.844257 AAGGAAAGATACAGATAATCAGGAAAG 57.156 33.333 0.00 0.00 0.00 2.62
141 142 9.618890 CAAGGAAAGATACAGATAATCAGGAAA 57.381 33.333 0.00 0.00 0.00 3.13
142 143 8.772250 ACAAGGAAAGATACAGATAATCAGGAA 58.228 33.333 0.00 0.00 0.00 3.36
143 144 8.324191 ACAAGGAAAGATACAGATAATCAGGA 57.676 34.615 0.00 0.00 0.00 3.86
144 145 9.703892 CTACAAGGAAAGATACAGATAATCAGG 57.296 37.037 0.00 0.00 0.00 3.86
145 146 9.202273 GCTACAAGGAAAGATACAGATAATCAG 57.798 37.037 0.00 0.00 0.00 2.90
146 147 8.704668 TGCTACAAGGAAAGATACAGATAATCA 58.295 33.333 0.00 0.00 0.00 2.57
147 148 9.547753 TTGCTACAAGGAAAGATACAGATAATC 57.452 33.333 0.00 0.00 0.00 1.75
148 149 9.905713 TTTGCTACAAGGAAAGATACAGATAAT 57.094 29.630 0.00 0.00 30.42 1.28
149 150 9.733556 TTTTGCTACAAGGAAAGATACAGATAA 57.266 29.630 0.00 0.00 36.88 1.75
150 151 9.383519 CTTTTGCTACAAGGAAAGATACAGATA 57.616 33.333 0.00 0.00 36.88 1.98
151 152 8.103305 TCTTTTGCTACAAGGAAAGATACAGAT 58.897 33.333 0.00 0.00 36.88 2.90
152 153 7.450074 TCTTTTGCTACAAGGAAAGATACAGA 58.550 34.615 0.00 0.00 36.88 3.41
153 154 7.672983 TCTTTTGCTACAAGGAAAGATACAG 57.327 36.000 0.00 0.00 36.88 2.74
154 155 8.514594 CATTCTTTTGCTACAAGGAAAGATACA 58.485 33.333 0.00 0.00 36.88 2.29
155 156 8.730680 TCATTCTTTTGCTACAAGGAAAGATAC 58.269 33.333 0.00 0.00 36.88 2.24
156 157 8.862325 TCATTCTTTTGCTACAAGGAAAGATA 57.138 30.769 0.00 0.00 36.88 1.98
157 158 7.765695 TCATTCTTTTGCTACAAGGAAAGAT 57.234 32.000 0.00 0.00 36.88 2.40
158 159 7.581213 TTCATTCTTTTGCTACAAGGAAAGA 57.419 32.000 0.00 0.00 36.88 2.52
159 160 8.647143 TTTTCATTCTTTTGCTACAAGGAAAG 57.353 30.769 0.00 0.00 36.88 2.62
196 197 8.617809 AGAAAAAGTAAGAGATACGTGCAAAAA 58.382 29.630 0.00 0.00 39.62 1.94
197 198 8.067784 CAGAAAAAGTAAGAGATACGTGCAAAA 58.932 33.333 0.00 0.00 39.62 2.44
198 199 7.307751 CCAGAAAAAGTAAGAGATACGTGCAAA 60.308 37.037 0.00 0.00 39.62 3.68
199 200 6.147164 CCAGAAAAAGTAAGAGATACGTGCAA 59.853 38.462 0.00 0.00 39.62 4.08
200 201 5.637810 CCAGAAAAAGTAAGAGATACGTGCA 59.362 40.000 0.00 0.00 39.62 4.57
201 202 5.867716 TCCAGAAAAAGTAAGAGATACGTGC 59.132 40.000 0.00 0.00 39.62 5.34
202 203 7.091443 AGTCCAGAAAAAGTAAGAGATACGTG 58.909 38.462 0.00 0.00 39.62 4.49
203 204 7.229581 AGTCCAGAAAAAGTAAGAGATACGT 57.770 36.000 0.00 0.00 39.62 3.57
204 205 9.804758 ATTAGTCCAGAAAAAGTAAGAGATACG 57.195 33.333 0.00 0.00 39.62 3.06
215 216 9.760660 CGAGTAAATCAATTAGTCCAGAAAAAG 57.239 33.333 0.00 0.00 39.74 2.27
216 217 8.234546 GCGAGTAAATCAATTAGTCCAGAAAAA 58.765 33.333 0.00 0.00 39.74 1.94
217 218 7.148306 GGCGAGTAAATCAATTAGTCCAGAAAA 60.148 37.037 0.00 0.00 39.74 2.29
218 219 6.315393 GGCGAGTAAATCAATTAGTCCAGAAA 59.685 38.462 0.00 0.00 39.74 2.52
219 220 5.815740 GGCGAGTAAATCAATTAGTCCAGAA 59.184 40.000 0.00 0.00 39.74 3.02
220 221 5.105106 TGGCGAGTAAATCAATTAGTCCAGA 60.105 40.000 0.00 0.00 39.74 3.86
221 222 5.006746 GTGGCGAGTAAATCAATTAGTCCAG 59.993 44.000 0.00 0.00 39.74 3.86
222 223 4.873827 GTGGCGAGTAAATCAATTAGTCCA 59.126 41.667 0.00 0.00 39.74 4.02
223 224 5.006746 CAGTGGCGAGTAAATCAATTAGTCC 59.993 44.000 0.00 0.00 39.74 3.85
224 225 5.810587 TCAGTGGCGAGTAAATCAATTAGTC 59.189 40.000 0.00 0.00 39.57 2.59
225 226 5.581085 GTCAGTGGCGAGTAAATCAATTAGT 59.419 40.000 0.00 0.00 0.00 2.24
226 227 5.006746 GGTCAGTGGCGAGTAAATCAATTAG 59.993 44.000 0.00 0.00 0.00 1.73
227 228 4.873827 GGTCAGTGGCGAGTAAATCAATTA 59.126 41.667 0.00 0.00 0.00 1.40
228 229 3.689649 GGTCAGTGGCGAGTAAATCAATT 59.310 43.478 0.00 0.00 0.00 2.32
229 230 3.270877 GGTCAGTGGCGAGTAAATCAAT 58.729 45.455 0.00 0.00 0.00 2.57
230 231 2.037902 TGGTCAGTGGCGAGTAAATCAA 59.962 45.455 0.00 0.00 0.00 2.57
231 232 1.621317 TGGTCAGTGGCGAGTAAATCA 59.379 47.619 0.00 0.00 0.00 2.57
232 233 2.380084 TGGTCAGTGGCGAGTAAATC 57.620 50.000 0.00 0.00 0.00 2.17
233 234 2.224426 TGTTGGTCAGTGGCGAGTAAAT 60.224 45.455 0.00 0.00 0.00 1.40
234 235 1.139256 TGTTGGTCAGTGGCGAGTAAA 59.861 47.619 0.00 0.00 0.00 2.01
235 236 0.753867 TGTTGGTCAGTGGCGAGTAA 59.246 50.000 0.00 0.00 0.00 2.24
236 237 0.317160 CTGTTGGTCAGTGGCGAGTA 59.683 55.000 0.00 0.00 39.17 2.59
237 238 1.069765 CTGTTGGTCAGTGGCGAGT 59.930 57.895 0.00 0.00 39.17 4.18
238 239 0.036952 ATCTGTTGGTCAGTGGCGAG 60.037 55.000 0.00 0.00 43.97 5.03
239 240 0.396435 AATCTGTTGGTCAGTGGCGA 59.604 50.000 0.00 0.00 43.97 5.54
240 241 1.238439 AAATCTGTTGGTCAGTGGCG 58.762 50.000 0.00 0.00 43.97 5.69
241 242 3.068024 TGAAAAATCTGTTGGTCAGTGGC 59.932 43.478 0.00 0.00 43.97 5.01
242 243 4.916983 TGAAAAATCTGTTGGTCAGTGG 57.083 40.909 0.00 0.00 43.97 4.00
243 244 5.284079 CCTTGAAAAATCTGTTGGTCAGTG 58.716 41.667 0.00 0.00 43.97 3.66
244 245 4.342092 CCCTTGAAAAATCTGTTGGTCAGT 59.658 41.667 0.00 0.00 43.97 3.41
245 246 4.342092 ACCCTTGAAAAATCTGTTGGTCAG 59.658 41.667 0.00 0.00 44.85 3.51
246 247 4.285863 ACCCTTGAAAAATCTGTTGGTCA 58.714 39.130 0.00 0.00 0.00 4.02
247 248 4.937201 ACCCTTGAAAAATCTGTTGGTC 57.063 40.909 0.00 0.00 0.00 4.02
248 249 6.994421 ATTACCCTTGAAAAATCTGTTGGT 57.006 33.333 0.00 0.00 0.00 3.67
249 250 7.116233 CGAAATTACCCTTGAAAAATCTGTTGG 59.884 37.037 0.00 0.00 0.00 3.77
250 251 7.651704 ACGAAATTACCCTTGAAAAATCTGTTG 59.348 33.333 0.00 0.00 0.00 3.33
251 252 7.722363 ACGAAATTACCCTTGAAAAATCTGTT 58.278 30.769 0.00 0.00 0.00 3.16
252 253 7.284919 ACGAAATTACCCTTGAAAAATCTGT 57.715 32.000 0.00 0.00 0.00 3.41
253 254 6.806739 GGACGAAATTACCCTTGAAAAATCTG 59.193 38.462 0.00 0.00 0.00 2.90
254 255 6.719829 AGGACGAAATTACCCTTGAAAAATCT 59.280 34.615 0.00 0.00 0.00 2.40
255 256 6.920817 AGGACGAAATTACCCTTGAAAAATC 58.079 36.000 0.00 0.00 0.00 2.17
256 257 6.911250 AGGACGAAATTACCCTTGAAAAAT 57.089 33.333 0.00 0.00 0.00 1.82
257 258 7.503230 AGTTAGGACGAAATTACCCTTGAAAAA 59.497 33.333 0.00 0.00 0.00 1.94
258 259 6.999871 AGTTAGGACGAAATTACCCTTGAAAA 59.000 34.615 0.00 0.00 0.00 2.29
259 260 6.536447 AGTTAGGACGAAATTACCCTTGAAA 58.464 36.000 0.00 0.00 0.00 2.69
260 261 6.117975 AGTTAGGACGAAATTACCCTTGAA 57.882 37.500 0.00 0.00 0.00 2.69
261 262 5.750352 AGTTAGGACGAAATTACCCTTGA 57.250 39.130 0.00 0.00 0.00 3.02
262 263 6.171213 AGAAGTTAGGACGAAATTACCCTTG 58.829 40.000 0.00 0.00 0.00 3.61
263 264 6.212993 AGAGAAGTTAGGACGAAATTACCCTT 59.787 38.462 0.00 0.00 0.00 3.95
264 265 5.720520 AGAGAAGTTAGGACGAAATTACCCT 59.279 40.000 0.00 0.00 0.00 4.34
265 266 5.975282 AGAGAAGTTAGGACGAAATTACCC 58.025 41.667 0.00 0.00 0.00 3.69
289 290 9.944376 AACACGATGACTAAGGCATATAATTAT 57.056 29.630 2.97 2.97 0.00 1.28
291 292 9.772973 TTAACACGATGACTAAGGCATATAATT 57.227 29.630 0.00 0.00 0.00 1.40
292 293 9.772973 TTTAACACGATGACTAAGGCATATAAT 57.227 29.630 0.00 0.00 0.00 1.28
293 294 9.602568 TTTTAACACGATGACTAAGGCATATAA 57.397 29.630 0.00 0.00 0.00 0.98
294 295 9.602568 TTTTTAACACGATGACTAAGGCATATA 57.397 29.630 0.00 0.00 0.00 0.86
295 296 8.500753 TTTTTAACACGATGACTAAGGCATAT 57.499 30.769 0.00 0.00 0.00 1.78
296 297 7.908827 TTTTTAACACGATGACTAAGGCATA 57.091 32.000 0.00 0.00 0.00 3.14
297 298 6.811253 TTTTTAACACGATGACTAAGGCAT 57.189 33.333 0.00 0.00 0.00 4.40
298 299 6.811253 ATTTTTAACACGATGACTAAGGCA 57.189 33.333 0.00 0.00 0.00 4.75
319 320 8.819974 CCGTTCCTTTATGTAACGTGTATTATT 58.180 33.333 0.00 0.00 43.27 1.40
320 321 8.196771 TCCGTTCCTTTATGTAACGTGTATTAT 58.803 33.333 0.00 0.00 43.27 1.28
321 322 7.542890 TCCGTTCCTTTATGTAACGTGTATTA 58.457 34.615 0.00 0.00 43.27 0.98
322 323 6.397272 TCCGTTCCTTTATGTAACGTGTATT 58.603 36.000 0.00 0.00 43.27 1.89
323 324 5.964758 TCCGTTCCTTTATGTAACGTGTAT 58.035 37.500 0.00 0.00 43.27 2.29
324 325 5.384063 TCCGTTCCTTTATGTAACGTGTA 57.616 39.130 0.00 0.00 43.27 2.90
325 326 4.240096 CTCCGTTCCTTTATGTAACGTGT 58.760 43.478 0.00 0.00 43.27 4.49
326 327 3.615496 CCTCCGTTCCTTTATGTAACGTG 59.385 47.826 0.00 0.00 43.27 4.49
327 328 3.368739 CCCTCCGTTCCTTTATGTAACGT 60.369 47.826 0.00 0.00 43.27 3.99
328 329 3.119029 TCCCTCCGTTCCTTTATGTAACG 60.119 47.826 0.00 0.00 44.13 3.18
329 330 4.081254 ACTCCCTCCGTTCCTTTATGTAAC 60.081 45.833 0.00 0.00 0.00 2.50
330 331 4.098894 ACTCCCTCCGTTCCTTTATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
331 332 3.716431 ACTCCCTCCGTTCCTTTATGTA 58.284 45.455 0.00 0.00 0.00 2.29
332 333 2.547990 ACTCCCTCCGTTCCTTTATGT 58.452 47.619 0.00 0.00 0.00 2.29
333 334 3.449737 TGTACTCCCTCCGTTCCTTTATG 59.550 47.826 0.00 0.00 0.00 1.90
334 335 3.716431 TGTACTCCCTCCGTTCCTTTAT 58.284 45.455 0.00 0.00 0.00 1.40
335 336 3.173953 TGTACTCCCTCCGTTCCTTTA 57.826 47.619 0.00 0.00 0.00 1.85
336 337 2.019807 TGTACTCCCTCCGTTCCTTT 57.980 50.000 0.00 0.00 0.00 3.11
337 338 2.108970 GATGTACTCCCTCCGTTCCTT 58.891 52.381 0.00 0.00 0.00 3.36
359 360 4.072131 TGGAAAACTAGTGCTCCAACATC 58.928 43.478 19.26 0.10 35.02 3.06
481 492 6.035005 CGCCGATACAAGATGTATATTTGGAG 59.965 42.308 3.15 2.74 43.08 3.86
482 493 5.867174 CGCCGATACAAGATGTATATTTGGA 59.133 40.000 3.15 0.00 43.08 3.53
483 494 5.867174 TCGCCGATACAAGATGTATATTTGG 59.133 40.000 3.15 5.09 43.08 3.28
484 495 6.944557 TCGCCGATACAAGATGTATATTTG 57.055 37.500 3.15 0.00 43.08 2.32
485 496 6.036083 GCATCGCCGATACAAGATGTATATTT 59.964 38.462 0.00 0.00 43.08 1.40
486 497 5.520288 GCATCGCCGATACAAGATGTATATT 59.480 40.000 0.00 0.00 43.08 1.28
487 498 5.043903 GCATCGCCGATACAAGATGTATAT 58.956 41.667 0.00 0.00 43.08 0.86
488 499 4.157840 AGCATCGCCGATACAAGATGTATA 59.842 41.667 0.00 0.00 43.08 1.47
489 500 3.056536 AGCATCGCCGATACAAGATGTAT 60.057 43.478 0.00 2.79 45.48 2.29
490 501 2.296190 AGCATCGCCGATACAAGATGTA 59.704 45.455 0.00 0.00 41.64 2.29
498 509 2.417339 TGTAAGAGCATCGCCGATAC 57.583 50.000 0.00 0.00 42.67 2.24
603 616 6.335471 TCCTCACGTCATTAAACTTGTCTA 57.665 37.500 0.00 0.00 0.00 2.59
604 617 5.209818 TCCTCACGTCATTAAACTTGTCT 57.790 39.130 0.00 0.00 0.00 3.41
769 782 0.463116 ACACGTTTTGCTCCCGTCTT 60.463 50.000 0.00 0.00 31.46 3.01
770 783 1.145377 ACACGTTTTGCTCCCGTCT 59.855 52.632 0.00 0.00 31.46 4.18
830 843 2.811317 CAGCTGCCGTCGGAGAAC 60.811 66.667 17.49 0.22 39.69 3.01
902 915 2.972505 CACGGCACAGGGACACAC 60.973 66.667 0.00 0.00 0.00 3.82
903 916 3.037686 AACACGGCACAGGGACACA 62.038 57.895 0.00 0.00 0.00 3.72
939 952 0.457035 GACAGAGCAGAGCAGAGAGG 59.543 60.000 0.00 0.00 0.00 3.69
974 989 1.308746 GGATCTGGGGAAAGGGGGA 60.309 63.158 0.00 0.00 0.00 4.81
1419 1437 0.037326 CGCTGGGCTTCTTGTACTCA 60.037 55.000 0.00 0.00 0.00 3.41
1420 1438 0.741221 CCGCTGGGCTTCTTGTACTC 60.741 60.000 0.00 0.00 0.00 2.59
1422 1440 1.003718 ACCGCTGGGCTTCTTGTAC 60.004 57.895 0.00 0.00 36.48 2.90
1423 1441 1.003839 CACCGCTGGGCTTCTTGTA 60.004 57.895 0.00 0.00 36.48 2.41
1425 1443 3.058160 CCACCGCTGGGCTTCTTG 61.058 66.667 0.00 0.00 36.48 3.02
1461 1479 2.428890 AGGCTTCTTCCTGTACTCATCG 59.571 50.000 0.00 0.00 34.56 3.84
1503 1521 1.364678 TCCTCATACCTTCCACCTCCA 59.635 52.381 0.00 0.00 0.00 3.86
1538 1556 0.615850 ACCACTGCTAGGCTTCTTCC 59.384 55.000 0.00 0.00 0.00 3.46
1623 1641 1.077501 CCCACCATAGCCACCACTG 60.078 63.158 0.00 0.00 0.00 3.66
1624 1642 2.308722 CCCCACCATAGCCACCACT 61.309 63.158 0.00 0.00 0.00 4.00
1625 1643 2.275418 CCCCACCATAGCCACCAC 59.725 66.667 0.00 0.00 0.00 4.16
1629 1647 2.006415 CCTTCCCCCACCATAGCCA 61.006 63.158 0.00 0.00 0.00 4.75
1653 1671 5.359194 TCTTCTTGTACCCATCATCTTCC 57.641 43.478 0.00 0.00 0.00 3.46
1664 1682 3.263261 GCACTAGGCTTCTTCTTGTACC 58.737 50.000 0.00 0.00 40.25 3.34
1796 1817 0.914644 TCTTCCTCCATGGCTTCCAG 59.085 55.000 6.96 0.00 36.75 3.86
1827 1848 4.220821 CCACTAGGCTTCTTCTTGTAGTCA 59.779 45.833 0.00 0.00 0.00 3.41
1932 1998 2.905075 TCAATGTAGTCTCCAATGCCG 58.095 47.619 0.00 0.00 0.00 5.69
1951 2017 2.622942 TCATGAAACCCTGTGCAAGTTC 59.377 45.455 0.00 0.00 0.00 3.01
2098 2164 1.153489 CACTGCCCTCCGACTCATG 60.153 63.158 0.00 0.00 0.00 3.07
2100 2166 2.997315 CCACTGCCCTCCGACTCA 60.997 66.667 0.00 0.00 0.00 3.41
2142 2208 4.568380 CCATCCTTCTTCATGAAACCCTGA 60.568 45.833 9.88 0.00 33.79 3.86
2178 2244 2.445845 TCCCCCATACCAGCTCCG 60.446 66.667 0.00 0.00 0.00 4.63
2238 2304 8.707938 TCACAATGTAGTGAAGATCAGTTATG 57.292 34.615 0.00 0.00 44.92 1.90
2252 2318 3.308402 CCCCTCACCAATCACAATGTAGT 60.308 47.826 0.00 0.00 0.00 2.73
2261 2328 0.482446 ACAAAGCCCCTCACCAATCA 59.518 50.000 0.00 0.00 0.00 2.57
2267 2334 0.389025 CCAAACACAAAGCCCCTCAC 59.611 55.000 0.00 0.00 0.00 3.51
2271 2338 2.035449 GACTAACCAAACACAAAGCCCC 59.965 50.000 0.00 0.00 0.00 5.80
2274 2341 2.956333 AGGGACTAACCAAACACAAAGC 59.044 45.455 0.00 0.00 41.20 3.51
2328 2397 4.155826 CAGCTTTGTCGGTGGAAATCATAA 59.844 41.667 0.00 0.00 0.00 1.90
2514 2583 9.474313 AATAATAGCCATTAGAAAACACCAAGA 57.526 29.630 0.00 0.00 30.22 3.02
2607 2676 3.754323 CCAAGGGTTTTAGATACGCACAA 59.246 43.478 0.00 0.00 0.00 3.33
2689 2758 8.044060 TCTTTAACTGAATCCAGCAAACATAG 57.956 34.615 0.00 0.00 44.16 2.23
2820 2892 5.358160 GCTACAAAATCAGAGCCAATAGGTT 59.642 40.000 0.00 0.00 37.19 3.50
2861 2933 4.142049 GGTGTCCTCAAAACAACCATGAAA 60.142 41.667 0.00 0.00 0.00 2.69
2914 2986 4.096382 GCGGAAACTACCATCATTTGACAT 59.904 41.667 0.00 0.00 0.00 3.06
2924 3012 1.559682 ACAGATGGCGGAAACTACCAT 59.440 47.619 0.00 0.00 44.75 3.55
2937 3025 3.684788 GCCACTTAACTGTACACAGATGG 59.315 47.826 16.05 13.91 46.59 3.51
2971 3059 6.801862 GCAGGTGTTGATGATGTTTACTTTAC 59.198 38.462 0.00 0.00 0.00 2.01
3043 3132 2.223971 ACGGAGGGAGTATATGTTTGCG 60.224 50.000 0.00 0.00 0.00 4.85
3080 3176 4.689345 GTGCCGACTTTGTACTAAATCAGT 59.311 41.667 0.00 0.00 41.62 3.41
3167 3351 1.832167 GTGGTGCTTTTCCTGCCCA 60.832 57.895 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.