Multiple sequence alignment - TraesCS6A01G306800

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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 TraesCS6A01G306800 chr6A 100.000 3753 0 0 1 3753 540619064 540615312 0.000000e+00 6931.0
1 TraesCS6A01G306800 chr6A 98.857 175 2 0 1669 1843 168007031 168007205 2.810000e-81 313.0
2 TraesCS6A01G306800 chr6A 84.783 184 13 3 186 355 537876446 537876264 1.790000e-38 171.0
3 TraesCS6A01G306800 chr6A 86.076 158 7 3 185 328 1672293 1672137 5.020000e-34 156.0
4 TraesCS6A01G306800 chr6B 93.778 1768 77 13 1839 3605 590667935 590666200 0.000000e+00 2625.0
5 TraesCS6A01G306800 chr6B 89.135 1353 57 40 356 1669 590669224 590667923 0.000000e+00 1602.0
6 TraesCS6A01G306800 chr6B 89.103 156 15 2 3599 3752 590666169 590666014 3.830000e-45 193.0
7 TraesCS6A01G306800 chr6B 92.473 93 5 1 3191 3283 590666545 590666455 8.460000e-27 132.0
8 TraesCS6A01G306800 chr6D 95.169 1511 58 7 1839 3346 394618685 394617187 0.000000e+00 2372.0
9 TraesCS6A01G306800 chr6D 92.131 1347 44 25 356 1669 394619990 394618673 0.000000e+00 1844.0
10 TraesCS6A01G306800 chr6D 81.151 504 52 20 3237 3705 394617343 394616848 7.660000e-97 364.0
11 TraesCS6A01G306800 chr6D 95.181 166 7 1 22 186 394620147 394619982 1.030000e-65 261.0
12 TraesCS6A01G306800 chr7B 81.852 540 94 4 2188 2725 105559527 105558990 5.720000e-123 451.0
13 TraesCS6A01G306800 chr7B 98.333 180 3 0 1669 1848 672656371 672656192 2.180000e-82 316.0
14 TraesCS6A01G306800 chr7D 82.306 503 89 0 2223 2725 140327718 140327216 1.600000e-118 436.0
15 TraesCS6A01G306800 chr7A 82.306 503 89 0 2223 2725 142158555 142158053 1.600000e-118 436.0
16 TraesCS6A01G306800 chr7A 97.802 182 3 1 1662 1843 605175715 605175535 2.810000e-81 313.0
17 TraesCS6A01G306800 chr7A 95.385 195 8 1 1668 1862 157005684 157005491 3.640000e-80 309.0
18 TraesCS6A01G306800 chr7A 84.783 184 12 3 187 355 509467305 509467123 1.790000e-38 171.0
19 TraesCS6A01G306800 chr7A 85.795 176 8 3 185 344 660549871 660550045 1.790000e-38 171.0
20 TraesCS6A01G306800 chr1A 96.875 192 5 1 1661 1851 259053012 259052821 1.680000e-83 320.0
21 TraesCS6A01G306800 chr1A 85.526 152 8 4 183 320 492563786 492563635 3.020000e-31 147.0
22 TraesCS6A01G306800 chr5A 98.857 175 2 0 1670 1844 177619245 177619419 2.810000e-81 313.0
23 TraesCS6A01G306800 chr5A 88.043 184 8 4 185 355 535243692 535243510 4.910000e-49 206.0
24 TraesCS6A01G306800 chr5A 86.170 188 10 3 183 355 29678146 29678332 4.950000e-44 189.0
25 TraesCS6A01G306800 chr5A 85.792 183 11 3 187 355 71460386 71460205 2.980000e-41 180.0
26 TraesCS6A01G306800 chr5A 84.324 185 14 8 185 355 397506069 397505886 2.320000e-37 167.0
27 TraesCS6A01G306800 chr5A 100.000 33 0 0 22 54 666591124 666591156 1.130000e-05 62.1
28 TraesCS6A01G306800 chr5B 98.315 178 2 1 1670 1846 291789293 291789116 1.010000e-80 311.0
29 TraesCS6A01G306800 chr2B 97.778 180 2 2 1666 1843 309492654 309492833 3.640000e-80 309.0
30 TraesCS6A01G306800 chr2A 96.685 181 4 2 1670 1849 419198353 419198174 2.190000e-77 300.0
31 TraesCS6A01G306800 chr2A 94.737 95 5 0 187 281 59640682 59640776 8.400000e-32 148.0
32 TraesCS6A01G306800 chr2A 81.868 182 18 5 185 353 729192345 729192166 5.050000e-29 139.0
33 TraesCS6A01G306800 chr3A 85.635 181 12 3 186 353 12118438 12118259 1.070000e-40 178.0
34 TraesCS6A01G306800 chr3A 84.530 181 14 3 187 354 702962422 702962601 2.320000e-37 167.0
35 TraesCS6A01G306800 chr3A 95.588 68 1 2 271 338 724707668 724707603 1.430000e-19 108.0
36 TraesCS6A01G306800 chr4A 84.615 182 13 7 188 355 594365099 594364919 2.320000e-37 167.0
37 TraesCS6A01G306800 chr3D 82.119 151 16 6 184 324 17671029 17671178 6.590000e-23 119.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G306800 chr6A 540615312 540619064 3752 True 6931.00 6931 100.00000 1 3753 1 chr6A.!!$R3 3752
1 TraesCS6A01G306800 chr6B 590666014 590669224 3210 True 1138.00 2625 91.12225 356 3752 4 chr6B.!!$R1 3396
2 TraesCS6A01G306800 chr6D 394616848 394620147 3299 True 1210.25 2372 90.90800 22 3705 4 chr6D.!!$R1 3683
3 TraesCS6A01G306800 chr7B 105558990 105559527 537 True 451.00 451 81.85200 2188 2725 1 chr7B.!!$R1 537
4 TraesCS6A01G306800 chr7D 140327216 140327718 502 True 436.00 436 82.30600 2223 2725 1 chr7D.!!$R1 502
5 TraesCS6A01G306800 chr7A 142158053 142158555 502 True 436.00 436 82.30600 2223 2725 1 chr7A.!!$R1 502

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
435 438 0.466555 AGGAGGCTACCGCTCTACTG 60.467 60.0 0.00 0.0 36.09 2.74 F
1243 1294 0.032267 CTTCGCGGTAATCCTCCTCC 59.968 60.0 6.13 0.0 0.00 4.30 F
1749 1808 0.170339 GGAAAATCGACCGCTTTGGG 59.830 55.0 0.00 0.0 44.64 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 1789 0.170339 CCCAAAGCGGTCGATTTTCC 59.830 55.0 3.79 0.0 30.80 3.13 R
2197 2260 1.491670 CAATACCACTCTCATCGCCG 58.508 55.0 0.00 0.0 0.00 6.46 R
3730 3863 0.181824 ACACTGGCGTTAACCAAGGT 59.818 50.0 0.00 0.0 39.86 3.50 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
61 62 4.540359 ACATTAGTTTACAGCGGTGGTA 57.460 40.909 20.20 6.21 0.00 3.25
130 131 2.640316 AAGTGGTTCCTGGTCAAGTC 57.360 50.000 0.00 0.00 0.00 3.01
150 151 2.304831 GGCAGGAAGGAAGGAGCCT 61.305 63.158 0.00 0.00 40.93 4.58
175 176 1.019278 TTCCGTCGCAATCTTCTGGC 61.019 55.000 0.00 0.00 0.00 4.85
179 180 3.880846 CGCAATCTTCTGGCGGCC 61.881 66.667 13.32 13.32 46.46 6.13
180 181 3.880846 GCAATCTTCTGGCGGCCG 61.881 66.667 24.05 24.05 0.00 6.13
181 182 3.204827 CAATCTTCTGGCGGCCGG 61.205 66.667 29.38 22.11 0.00 6.13
185 186 4.467084 CTTCTGGCGGCCGGCTAA 62.467 66.667 45.12 35.97 42.94 3.09
186 187 4.770874 TTCTGGCGGCCGGCTAAC 62.771 66.667 45.12 21.51 42.94 2.34
191 192 3.053896 GCGGCCGGCTAACAGTTT 61.054 61.111 29.38 0.00 39.11 2.66
192 193 2.867472 CGGCCGGCTAACAGTTTG 59.133 61.111 28.56 1.16 0.00 2.93
193 194 1.964373 CGGCCGGCTAACAGTTTGT 60.964 57.895 28.56 0.00 0.00 2.83
194 195 1.873863 GGCCGGCTAACAGTTTGTC 59.126 57.895 28.56 0.00 0.00 3.18
195 196 0.605589 GGCCGGCTAACAGTTTGTCT 60.606 55.000 28.56 0.00 0.00 3.41
196 197 1.338389 GGCCGGCTAACAGTTTGTCTA 60.338 52.381 28.56 0.00 0.00 2.59
197 198 2.419667 GCCGGCTAACAGTTTGTCTAA 58.580 47.619 22.15 0.00 0.00 2.10
198 199 3.007635 GCCGGCTAACAGTTTGTCTAAT 58.992 45.455 22.15 0.00 0.00 1.73
199 200 3.439129 GCCGGCTAACAGTTTGTCTAATT 59.561 43.478 22.15 0.00 0.00 1.40
200 201 4.436986 GCCGGCTAACAGTTTGTCTAATTC 60.437 45.833 22.15 0.00 0.00 2.17
201 202 4.693566 CCGGCTAACAGTTTGTCTAATTCA 59.306 41.667 0.00 0.00 0.00 2.57
202 203 5.354234 CCGGCTAACAGTTTGTCTAATTCAT 59.646 40.000 0.00 0.00 0.00 2.57
203 204 6.537301 CCGGCTAACAGTTTGTCTAATTCATA 59.463 38.462 0.00 0.00 0.00 2.15
204 205 7.226720 CCGGCTAACAGTTTGTCTAATTCATAT 59.773 37.037 0.00 0.00 0.00 1.78
205 206 8.276325 CGGCTAACAGTTTGTCTAATTCATATC 58.724 37.037 0.00 0.00 0.00 1.63
206 207 9.331282 GGCTAACAGTTTGTCTAATTCATATCT 57.669 33.333 0.00 0.00 0.00 1.98
228 229 7.849804 TCTAGATGCTTTTTAAGGATGTCAC 57.150 36.000 0.00 0.00 39.87 3.67
229 230 7.394016 TCTAGATGCTTTTTAAGGATGTCACA 58.606 34.615 0.00 0.00 39.87 3.58
230 231 8.049117 TCTAGATGCTTTTTAAGGATGTCACAT 58.951 33.333 0.00 0.00 39.87 3.21
231 232 7.472334 AGATGCTTTTTAAGGATGTCACATT 57.528 32.000 0.00 0.00 39.87 2.71
232 233 7.899973 AGATGCTTTTTAAGGATGTCACATTT 58.100 30.769 0.00 0.00 39.87 2.32
233 234 9.023962 AGATGCTTTTTAAGGATGTCACATTTA 57.976 29.630 0.00 0.00 39.87 1.40
234 235 9.638239 GATGCTTTTTAAGGATGTCACATTTAA 57.362 29.630 0.00 0.00 39.87 1.52
235 236 9.643693 ATGCTTTTTAAGGATGTCACATTTAAG 57.356 29.630 0.00 0.00 38.22 1.85
236 237 7.598493 TGCTTTTTAAGGATGTCACATTTAAGC 59.402 33.333 0.00 0.00 0.00 3.09
237 238 7.814587 GCTTTTTAAGGATGTCACATTTAAGCT 59.185 33.333 0.00 0.00 0.00 3.74
238 239 9.346725 CTTTTTAAGGATGTCACATTTAAGCTC 57.653 33.333 0.00 0.00 0.00 4.09
239 240 8.635765 TTTTAAGGATGTCACATTTAAGCTCT 57.364 30.769 0.00 0.00 0.00 4.09
240 241 7.849804 TTAAGGATGTCACATTTAAGCTCTC 57.150 36.000 0.00 0.00 0.00 3.20
241 242 5.426689 AGGATGTCACATTTAAGCTCTCA 57.573 39.130 0.00 0.00 0.00 3.27
242 243 5.181748 AGGATGTCACATTTAAGCTCTCAC 58.818 41.667 0.00 0.00 0.00 3.51
243 244 4.937620 GGATGTCACATTTAAGCTCTCACA 59.062 41.667 0.00 0.00 0.00 3.58
244 245 5.412594 GGATGTCACATTTAAGCTCTCACAA 59.587 40.000 0.00 0.00 0.00 3.33
245 246 5.929697 TGTCACATTTAAGCTCTCACAAG 57.070 39.130 0.00 0.00 0.00 3.16
246 247 5.368145 TGTCACATTTAAGCTCTCACAAGT 58.632 37.500 0.00 0.00 0.00 3.16
247 248 6.521162 TGTCACATTTAAGCTCTCACAAGTA 58.479 36.000 0.00 0.00 0.00 2.24
248 249 7.161404 TGTCACATTTAAGCTCTCACAAGTAT 58.839 34.615 0.00 0.00 0.00 2.12
249 250 8.311109 TGTCACATTTAAGCTCTCACAAGTATA 58.689 33.333 0.00 0.00 0.00 1.47
250 251 9.319143 GTCACATTTAAGCTCTCACAAGTATAT 57.681 33.333 0.00 0.00 0.00 0.86
256 257 9.830975 TTTAAGCTCTCACAAGTATATAATGCA 57.169 29.630 0.00 0.00 0.00 3.96
258 259 8.545229 AAGCTCTCACAAGTATATAATGCATC 57.455 34.615 0.00 0.00 0.00 3.91
259 260 7.674120 AGCTCTCACAAGTATATAATGCATCA 58.326 34.615 0.00 0.00 0.00 3.07
260 261 8.152898 AGCTCTCACAAGTATATAATGCATCAA 58.847 33.333 0.00 0.00 0.00 2.57
261 262 8.226448 GCTCTCACAAGTATATAATGCATCAAC 58.774 37.037 0.00 0.00 0.00 3.18
262 263 9.264719 CTCTCACAAGTATATAATGCATCAACA 57.735 33.333 0.00 0.00 0.00 3.33
263 264 9.612066 TCTCACAAGTATATAATGCATCAACAA 57.388 29.630 0.00 0.00 0.00 2.83
264 265 9.874215 CTCACAAGTATATAATGCATCAACAAG 57.126 33.333 0.00 0.00 0.00 3.16
265 266 9.612066 TCACAAGTATATAATGCATCAACAAGA 57.388 29.630 0.00 0.00 0.00 3.02
298 299 9.495572 AAAAATTAGACCACAAACAAAGTGAAA 57.504 25.926 0.00 0.00 39.30 2.69
299 300 9.495572 AAAATTAGACCACAAACAAAGTGAAAA 57.504 25.926 0.00 0.00 39.30 2.29
300 301 9.665719 AAATTAGACCACAAACAAAGTGAAAAT 57.334 25.926 0.00 0.00 39.30 1.82
301 302 8.871686 ATTAGACCACAAACAAAGTGAAAATC 57.128 30.769 0.00 0.00 39.30 2.17
302 303 6.279513 AGACCACAAACAAAGTGAAAATCA 57.720 33.333 0.00 0.00 39.30 2.57
303 304 6.332630 AGACCACAAACAAAGTGAAAATCAG 58.667 36.000 0.00 0.00 39.30 2.90
304 305 4.869861 ACCACAAACAAAGTGAAAATCAGC 59.130 37.500 0.00 0.00 39.30 4.26
305 306 5.111293 CCACAAACAAAGTGAAAATCAGCT 58.889 37.500 0.00 0.00 39.30 4.24
306 307 5.581874 CCACAAACAAAGTGAAAATCAGCTT 59.418 36.000 0.00 0.00 39.30 3.74
307 308 6.756074 CCACAAACAAAGTGAAAATCAGCTTA 59.244 34.615 0.00 0.00 39.30 3.09
308 309 7.043192 CCACAAACAAAGTGAAAATCAGCTTAG 60.043 37.037 0.00 0.00 39.30 2.18
309 310 7.701924 CACAAACAAAGTGAAAATCAGCTTAGA 59.298 33.333 0.00 0.00 39.30 2.10
310 311 8.416329 ACAAACAAAGTGAAAATCAGCTTAGAT 58.584 29.630 0.00 0.00 0.00 1.98
311 312 8.697067 CAAACAAAGTGAAAATCAGCTTAGATG 58.303 33.333 0.00 0.00 0.00 2.90
312 313 7.516198 ACAAAGTGAAAATCAGCTTAGATGT 57.484 32.000 0.00 0.00 0.00 3.06
313 314 7.365741 ACAAAGTGAAAATCAGCTTAGATGTG 58.634 34.615 0.00 0.00 0.00 3.21
314 315 7.229306 ACAAAGTGAAAATCAGCTTAGATGTGA 59.771 33.333 0.00 0.00 0.00 3.58
315 316 6.734104 AGTGAAAATCAGCTTAGATGTGAC 57.266 37.500 0.00 0.00 0.00 3.67
316 317 6.233434 AGTGAAAATCAGCTTAGATGTGACA 58.767 36.000 0.00 0.00 0.00 3.58
317 318 6.883217 AGTGAAAATCAGCTTAGATGTGACAT 59.117 34.615 0.00 0.00 0.00 3.06
318 319 8.043113 AGTGAAAATCAGCTTAGATGTGACATA 58.957 33.333 0.00 0.00 0.00 2.29
319 320 8.333908 GTGAAAATCAGCTTAGATGTGACATAG 58.666 37.037 0.00 0.00 0.00 2.23
320 321 8.260114 TGAAAATCAGCTTAGATGTGACATAGA 58.740 33.333 0.00 0.00 0.00 1.98
321 322 8.430801 AAAATCAGCTTAGATGTGACATAGAC 57.569 34.615 0.00 0.00 0.00 2.59
322 323 6.975196 ATCAGCTTAGATGTGACATAGACT 57.025 37.500 0.00 0.00 0.00 3.24
323 324 8.470657 AATCAGCTTAGATGTGACATAGACTA 57.529 34.615 0.00 0.00 0.00 2.59
324 325 8.648698 ATCAGCTTAGATGTGACATAGACTAT 57.351 34.615 0.00 0.00 0.00 2.12
325 326 7.880105 TCAGCTTAGATGTGACATAGACTATG 58.120 38.462 19.01 19.01 41.88 2.23
338 339 7.428282 ACATAGACTATGTCACGTCTAGATG 57.572 40.000 20.29 10.54 45.83 2.90
339 340 6.993308 ACATAGACTATGTCACGTCTAGATGT 59.007 38.462 20.29 11.99 45.83 3.06
340 341 5.743026 AGACTATGTCACGTCTAGATGTG 57.257 43.478 31.17 31.17 46.78 3.21
341 342 5.186942 AGACTATGTCACGTCTAGATGTGT 58.813 41.667 33.64 22.33 45.84 3.72
342 343 5.294799 AGACTATGTCACGTCTAGATGTGTC 59.705 44.000 33.64 29.76 45.84 3.67
343 344 3.784701 ATGTCACGTCTAGATGTGTCC 57.215 47.619 33.64 26.72 45.84 4.02
344 345 2.791655 TGTCACGTCTAGATGTGTCCT 58.208 47.619 33.64 5.69 45.84 3.85
345 346 3.946606 TGTCACGTCTAGATGTGTCCTA 58.053 45.455 33.64 18.81 45.84 2.94
346 347 4.524053 TGTCACGTCTAGATGTGTCCTAT 58.476 43.478 33.64 4.33 45.84 2.57
347 348 5.677567 TGTCACGTCTAGATGTGTCCTATA 58.322 41.667 33.64 17.90 45.84 1.31
348 349 5.526479 TGTCACGTCTAGATGTGTCCTATAC 59.474 44.000 33.64 25.72 45.84 1.47
349 350 5.526479 GTCACGTCTAGATGTGTCCTATACA 59.474 44.000 33.64 16.69 45.84 2.29
350 351 6.037940 GTCACGTCTAGATGTGTCCTATACAA 59.962 42.308 33.64 16.09 45.84 2.41
351 352 6.600427 TCACGTCTAGATGTGTCCTATACAAA 59.400 38.462 33.64 15.49 45.84 2.83
352 353 6.691818 CACGTCTAGATGTGTCCTATACAAAC 59.308 42.308 29.45 0.00 41.97 2.93
353 354 6.183360 ACGTCTAGATGTGTCCTATACAAACC 60.183 42.308 16.90 0.00 40.63 3.27
354 355 6.514063 GTCTAGATGTGTCCTATACAAACCC 58.486 44.000 0.00 0.00 40.63 4.11
419 422 0.759436 GGAATGGACTCGGGCTAGGA 60.759 60.000 0.00 0.00 0.00 2.94
435 438 0.466555 AGGAGGCTACCGCTCTACTG 60.467 60.000 0.00 0.00 36.09 2.74
753 775 0.976641 CGCCTATATTCCAGCCTCCA 59.023 55.000 0.00 0.00 0.00 3.86
757 779 1.276421 CTATATTCCAGCCTCCACCCG 59.724 57.143 0.00 0.00 0.00 5.28
807 845 1.144913 TGAAAAGTCCTCCAACCCCAG 59.855 52.381 0.00 0.00 0.00 4.45
811 849 2.610859 TCCTCCAACCCCAGAGCC 60.611 66.667 0.00 0.00 0.00 4.70
1164 1215 2.203596 AACGTCGTCTCCAGGGGT 60.204 61.111 0.00 0.00 0.00 4.95
1206 1257 2.437897 CAGCAGGCCTTCCAGGTT 59.562 61.111 0.00 0.00 37.80 3.50
1243 1294 0.032267 CTTCGCGGTAATCCTCCTCC 59.968 60.000 6.13 0.00 0.00 4.30
1244 1295 0.396695 TTCGCGGTAATCCTCCTCCT 60.397 55.000 6.13 0.00 0.00 3.69
1245 1296 0.822532 TCGCGGTAATCCTCCTCCTC 60.823 60.000 6.13 0.00 0.00 3.71
1264 1321 3.056465 CCTCGCCCTTTCCTGTCTATATC 60.056 52.174 0.00 0.00 0.00 1.63
1274 1331 4.742012 TCCTGTCTATATCCCTTCTGGTC 58.258 47.826 0.00 0.00 34.77 4.02
1354 1412 0.897621 AAGGCCTTTGCTGTATTGGC 59.102 50.000 13.78 0.00 42.56 4.52
1392 1450 4.499696 GCTGCAAAGTGCCTTTTCTCTTTA 60.500 41.667 0.00 0.00 44.23 1.85
1486 1545 1.544691 GAAGTGACTGGCTTAGGACGA 59.455 52.381 0.00 0.00 0.00 4.20
1539 1598 2.223340 CCGCATTCCACATAGAGCAAAC 60.223 50.000 0.00 0.00 0.00 2.93
1622 1681 5.119931 TGCTTATAACTGCAGTTTGGTTG 57.880 39.130 35.20 21.56 39.31 3.77
1663 1722 6.183359 GCCTTACGTTTTTGCGTTTATACTTG 60.183 38.462 0.00 0.00 43.04 3.16
1664 1723 6.183359 CCTTACGTTTTTGCGTTTATACTTGC 60.183 38.462 0.00 0.00 43.04 4.01
1665 1724 4.851010 ACGTTTTTGCGTTTATACTTGCT 58.149 34.783 0.00 0.00 43.04 3.91
1666 1725 5.988092 ACGTTTTTGCGTTTATACTTGCTA 58.012 33.333 0.00 0.00 43.04 3.49
1667 1726 6.604930 ACGTTTTTGCGTTTATACTTGCTAT 58.395 32.000 0.00 0.00 43.04 2.97
1668 1727 6.521821 ACGTTTTTGCGTTTATACTTGCTATG 59.478 34.615 0.00 0.00 43.04 2.23
1669 1728 6.504180 CGTTTTTGCGTTTATACTTGCTATGC 60.504 38.462 0.00 0.00 0.00 3.14
1670 1729 5.811399 TTTGCGTTTATACTTGCTATGCT 57.189 34.783 0.00 0.00 0.00 3.79
1671 1730 6.912203 TTTGCGTTTATACTTGCTATGCTA 57.088 33.333 0.00 0.00 0.00 3.49
1672 1731 7.490962 TTTGCGTTTATACTTGCTATGCTAT 57.509 32.000 0.00 0.00 0.00 2.97
1673 1732 6.466308 TGCGTTTATACTTGCTATGCTATG 57.534 37.500 0.00 0.00 0.00 2.23
1674 1733 5.989168 TGCGTTTATACTTGCTATGCTATGT 59.011 36.000 0.00 0.00 0.00 2.29
1675 1734 6.481976 TGCGTTTATACTTGCTATGCTATGTT 59.518 34.615 0.00 0.00 0.00 2.71
1676 1735 7.011950 TGCGTTTATACTTGCTATGCTATGTTT 59.988 33.333 0.00 0.00 0.00 2.83
1677 1736 7.855904 GCGTTTATACTTGCTATGCTATGTTTT 59.144 33.333 0.00 0.00 0.00 2.43
1678 1737 9.716507 CGTTTATACTTGCTATGCTATGTTTTT 57.283 29.630 0.00 0.00 0.00 1.94
1683 1742 9.736023 ATACTTGCTATGCTATGTTTTTAAAGC 57.264 29.630 0.00 0.00 35.51 3.51
1684 1743 6.747280 ACTTGCTATGCTATGTTTTTAAAGCG 59.253 34.615 0.00 0.00 37.80 4.68
1685 1744 6.189677 TGCTATGCTATGTTTTTAAAGCGT 57.810 33.333 0.00 0.00 37.80 5.07
1686 1745 6.255215 TGCTATGCTATGTTTTTAAAGCGTC 58.745 36.000 0.00 0.00 37.80 5.19
1687 1746 5.681543 GCTATGCTATGTTTTTAAAGCGTCC 59.318 40.000 0.00 0.00 37.80 4.79
1688 1747 4.428615 TGCTATGTTTTTAAAGCGTCCC 57.571 40.909 0.00 0.00 37.80 4.46
1689 1748 4.076394 TGCTATGTTTTTAAAGCGTCCCT 58.924 39.130 0.00 0.00 37.80 4.20
1690 1749 5.247084 TGCTATGTTTTTAAAGCGTCCCTA 58.753 37.500 0.00 0.00 37.80 3.53
1691 1750 5.706369 TGCTATGTTTTTAAAGCGTCCCTAA 59.294 36.000 0.00 0.00 37.80 2.69
1692 1751 6.128117 TGCTATGTTTTTAAAGCGTCCCTAAG 60.128 38.462 0.00 0.00 37.80 2.18
1693 1752 5.638596 ATGTTTTTAAAGCGTCCCTAAGG 57.361 39.130 0.00 0.00 0.00 2.69
1694 1753 3.253921 TGTTTTTAAAGCGTCCCTAAGGC 59.746 43.478 0.00 0.00 39.09 4.35
1695 1754 1.729284 TTTAAAGCGTCCCTAAGGCG 58.271 50.000 0.00 0.00 43.57 5.52
1696 1755 0.896923 TTAAAGCGTCCCTAAGGCGA 59.103 50.000 0.00 0.00 43.57 5.54
1697 1756 0.174162 TAAAGCGTCCCTAAGGCGAC 59.826 55.000 0.00 0.00 43.57 5.19
1723 1782 4.516195 GTCGAAGCGCTCCCCCTC 62.516 72.222 12.06 2.47 0.00 4.30
1724 1783 4.761058 TCGAAGCGCTCCCCCTCT 62.761 66.667 12.06 0.00 0.00 3.69
1725 1784 4.521062 CGAAGCGCTCCCCCTCTG 62.521 72.222 12.06 0.00 0.00 3.35
1726 1785 4.847444 GAAGCGCTCCCCCTCTGC 62.847 72.222 12.06 0.00 0.00 4.26
1729 1788 4.416738 GCGCTCCCCCTCTGCTTT 62.417 66.667 0.00 0.00 0.00 3.51
1730 1789 2.437359 CGCTCCCCCTCTGCTTTG 60.437 66.667 0.00 0.00 0.00 2.77
1731 1790 2.044551 GCTCCCCCTCTGCTTTGG 60.045 66.667 0.00 0.00 0.00 3.28
1732 1791 2.606587 GCTCCCCCTCTGCTTTGGA 61.607 63.158 0.00 0.00 0.00 3.53
1733 1792 2.078452 CTCCCCCTCTGCTTTGGAA 58.922 57.895 0.00 0.00 0.00 3.53
1734 1793 0.405585 CTCCCCCTCTGCTTTGGAAA 59.594 55.000 0.00 0.00 0.00 3.13
1735 1794 0.856982 TCCCCCTCTGCTTTGGAAAA 59.143 50.000 0.00 0.00 0.00 2.29
1736 1795 1.432807 TCCCCCTCTGCTTTGGAAAAT 59.567 47.619 0.00 0.00 0.00 1.82
1737 1796 1.827344 CCCCCTCTGCTTTGGAAAATC 59.173 52.381 0.00 0.00 0.00 2.17
1738 1797 1.474077 CCCCTCTGCTTTGGAAAATCG 59.526 52.381 0.00 0.00 0.00 3.34
1739 1798 2.436417 CCCTCTGCTTTGGAAAATCGA 58.564 47.619 0.00 0.00 0.00 3.59
1740 1799 2.162408 CCCTCTGCTTTGGAAAATCGAC 59.838 50.000 0.00 0.00 0.00 4.20
1741 1800 2.162408 CCTCTGCTTTGGAAAATCGACC 59.838 50.000 0.00 0.00 0.00 4.79
1742 1801 1.804151 TCTGCTTTGGAAAATCGACCG 59.196 47.619 0.00 0.00 0.00 4.79
1743 1802 0.239879 TGCTTTGGAAAATCGACCGC 59.760 50.000 0.00 0.00 0.00 5.68
1744 1803 0.521735 GCTTTGGAAAATCGACCGCT 59.478 50.000 0.00 0.00 0.00 5.52
1745 1804 1.068541 GCTTTGGAAAATCGACCGCTT 60.069 47.619 0.00 0.00 0.00 4.68
1746 1805 2.607038 GCTTTGGAAAATCGACCGCTTT 60.607 45.455 0.00 0.00 0.00 3.51
1747 1806 2.697431 TTGGAAAATCGACCGCTTTG 57.303 45.000 0.00 0.00 0.00 2.77
1748 1807 0.878416 TGGAAAATCGACCGCTTTGG 59.122 50.000 0.00 0.00 46.41 3.28
1749 1808 0.170339 GGAAAATCGACCGCTTTGGG 59.830 55.000 0.00 0.00 44.64 4.12
1750 1809 0.456142 GAAAATCGACCGCTTTGGGC 60.456 55.000 0.00 0.00 45.45 5.36
1768 1827 3.195698 GCCTAGGCGTCCAAAGCG 61.196 66.667 20.16 0.00 35.00 4.68
1776 1835 4.770874 GTCCAAAGCGCCCGCCTA 62.771 66.667 2.29 0.00 43.17 3.93
1777 1836 4.467084 TCCAAAGCGCCCGCCTAG 62.467 66.667 2.29 0.00 43.17 3.02
1819 1878 4.817909 CCCCCTCCCTAAGGCGGT 62.818 72.222 0.00 0.00 44.71 5.68
1820 1879 2.284493 CCCCTCCCTAAGGCGGTA 59.716 66.667 0.00 0.00 44.71 4.02
1821 1880 1.383525 CCCCTCCCTAAGGCGGTAA 60.384 63.158 0.00 0.00 44.71 2.85
1822 1881 1.408453 CCCCTCCCTAAGGCGGTAAG 61.408 65.000 0.00 0.00 44.71 2.34
1823 1882 1.408453 CCCTCCCTAAGGCGGTAAGG 61.408 65.000 0.00 0.00 44.71 2.69
1844 1903 5.413969 GGCGTCGCCTTAAAAATATAGTT 57.586 39.130 28.98 0.00 46.69 2.24
1869 1928 5.453903 GCTATGGAAGATAAGAAGCTGACCA 60.454 44.000 0.00 0.00 34.49 4.02
1885 1944 5.244626 AGCTGACCATTGCTAACAAAGAAAT 59.755 36.000 0.00 0.00 39.77 2.17
1899 1958 5.885465 ACAAAGAAATCTGACCCTCTGAAT 58.115 37.500 0.00 0.00 0.00 2.57
1900 1959 6.310149 ACAAAGAAATCTGACCCTCTGAATT 58.690 36.000 0.00 0.00 0.00 2.17
1908 1967 9.440761 AAATCTGACCCTCTGAATTATAGTAGT 57.559 33.333 0.00 0.00 0.00 2.73
1983 2042 7.938140 ATAGCATACAACATGTTACAAACCT 57.062 32.000 11.53 6.44 0.00 3.50
2001 2064 4.669206 ACCTCAAAATTGATGCAACACA 57.331 36.364 0.00 0.00 36.46 3.72
2002 2065 5.021033 ACCTCAAAATTGATGCAACACAA 57.979 34.783 0.00 1.39 36.46 3.33
2003 2066 5.051816 ACCTCAAAATTGATGCAACACAAG 58.948 37.500 0.00 0.00 36.46 3.16
2004 2067 4.084223 CCTCAAAATTGATGCAACACAAGC 60.084 41.667 0.00 0.00 36.46 4.01
2023 2086 5.470098 ACAAGCTACACTTTATGTTGACTGG 59.530 40.000 0.00 0.00 43.19 4.00
2062 2125 6.197168 AGCTTCTCATGGGGAAAATTTGATA 58.803 36.000 0.00 0.00 0.00 2.15
2124 2187 8.554011 AGTAATACCAGGCCTTAACAATTCTTA 58.446 33.333 0.00 0.00 0.00 2.10
2130 2193 4.889995 AGGCCTTAACAATTCTTATGGAGC 59.110 41.667 0.00 0.00 0.00 4.70
2197 2260 5.841957 ATTTCCATGAACTGCAGGTTATC 57.158 39.130 19.93 11.00 38.41 1.75
2266 2329 2.033801 AGTGCTGCAATTTATCATCGCC 59.966 45.455 2.77 0.00 0.00 5.54
2611 2674 0.921896 ACCACCAGCTCTATGGCAAT 59.078 50.000 7.24 0.00 44.80 3.56
2657 2720 6.062258 TCTTCGTCCTTTGGGATAAGATTT 57.938 37.500 7.99 0.00 44.33 2.17
2765 2828 7.119116 CCAAGGCTGATTAATACGTGCATATTA 59.881 37.037 0.00 0.00 0.00 0.98
2891 2954 4.102649 GTGAGGGTTTTTCGTGTTTTCTG 58.897 43.478 0.00 0.00 0.00 3.02
2938 3002 4.078639 GGGAGTCCCATCTTGTATCAAG 57.921 50.000 24.35 3.44 44.65 3.02
2939 3003 3.181450 GGGAGTCCCATCTTGTATCAAGG 60.181 52.174 24.35 0.00 44.65 3.61
2940 3004 3.456277 GGAGTCCCATCTTGTATCAAGGT 59.544 47.826 0.00 0.00 0.00 3.50
2960 3024 6.106648 AGGTAAGGTATAGCGGGTAAAATC 57.893 41.667 0.00 0.00 0.00 2.17
3101 3165 0.952497 CAGCATCGTGTTGTCCTGCT 60.952 55.000 0.00 0.00 43.60 4.24
3126 3190 8.560576 TCATTTCGTTGTCTTCTTTTTCATTC 57.439 30.769 0.00 0.00 0.00 2.67
3286 3350 7.970614 GCTGAAATATAGTTTTGTTTCTGGAGG 59.029 37.037 0.00 0.00 33.12 4.30
3314 3378 2.038952 ACCAGTGAGCTGTGCTGAAATA 59.961 45.455 0.00 0.00 39.88 1.40
3315 3379 2.417933 CCAGTGAGCTGTGCTGAAATAC 59.582 50.000 0.00 0.00 39.88 1.89
3317 3381 3.124806 CAGTGAGCTGTGCTGAAATACAG 59.875 47.826 0.00 0.00 45.40 2.74
3346 3412 6.373186 TTGTTTCTGCTGATCATCATCATC 57.627 37.500 0.00 0.00 38.42 2.92
3347 3413 5.681639 TGTTTCTGCTGATCATCATCATCT 58.318 37.500 0.00 0.00 38.42 2.90
3351 3417 7.640597 TTCTGCTGATCATCATCATCTTTTT 57.359 32.000 0.00 0.00 38.42 1.94
3386 3452 1.019278 ACATCTGTAAAGCGTGCGGG 61.019 55.000 0.00 0.00 0.00 6.13
3388 3454 1.895020 ATCTGTAAAGCGTGCGGGGA 61.895 55.000 0.00 0.00 0.00 4.81
3415 3481 3.192541 TGCAGCTCTGTGTTTCAGTTA 57.807 42.857 0.00 0.00 43.97 2.24
3455 3521 2.435938 CGGGCTATGTTGTGGCGT 60.436 61.111 0.00 0.00 34.68 5.68
3473 3539 2.050350 TCGCCGGTCCAGGACTAAG 61.050 63.158 19.57 10.80 32.47 2.18
3613 3745 7.253905 AGTGGCAGGTTTACTAGAAGATTAA 57.746 36.000 0.00 0.00 0.00 1.40
3639 3771 2.016961 CAGCTGAAACGTGTGTGCT 58.983 52.632 8.42 0.00 0.00 4.40
3706 3839 5.551233 CCTAGAACATGAACCAGAAAGTCA 58.449 41.667 0.00 0.00 0.00 3.41
3707 3840 5.997746 CCTAGAACATGAACCAGAAAGTCAA 59.002 40.000 0.00 0.00 0.00 3.18
3708 3841 6.148480 CCTAGAACATGAACCAGAAAGTCAAG 59.852 42.308 0.00 0.00 0.00 3.02
3712 3845 4.402155 ACATGAACCAGAAAGTCAAGCAAA 59.598 37.500 0.00 0.00 0.00 3.68
3752 3885 1.531149 CTTGGTTAACGCCAGTGTGAG 59.469 52.381 0.00 0.00 40.01 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.630037 TCACTATATCTAAACTGCAGATTTCGA 58.370 33.333 23.35 17.20 34.58 3.71
1 2 8.803201 TCACTATATCTAAACTGCAGATTTCG 57.197 34.615 23.35 12.78 34.58 3.46
40 41 3.412237 ACCACCGCTGTAAACTAATGT 57.588 42.857 0.00 0.00 0.00 2.71
41 42 4.501071 AGTACCACCGCTGTAAACTAATG 58.499 43.478 0.00 0.00 0.00 1.90
52 53 3.449737 TCAGCTAAAATAGTACCACCGCT 59.550 43.478 0.00 0.00 0.00 5.52
130 131 2.586792 CTCCTTCCTTCCTGCCGG 59.413 66.667 0.00 0.00 0.00 6.13
150 151 2.163818 AGATTGCGACGGAACTTGAA 57.836 45.000 3.17 0.00 0.00 2.69
175 176 1.908066 GACAAACTGTTAGCCGGCCG 61.908 60.000 26.15 21.04 0.00 6.13
176 177 0.605589 AGACAAACTGTTAGCCGGCC 60.606 55.000 26.15 8.84 0.00 6.13
178 179 4.693566 TGAATTAGACAAACTGTTAGCCGG 59.306 41.667 0.00 0.00 0.00 6.13
179 180 5.856126 TGAATTAGACAAACTGTTAGCCG 57.144 39.130 0.00 0.00 0.00 5.52
180 181 9.331282 AGATATGAATTAGACAAACTGTTAGCC 57.669 33.333 0.00 0.00 0.00 3.93
202 203 9.547753 GTGACATCCTTAAAAAGCATCTAGATA 57.452 33.333 4.54 0.00 0.00 1.98
203 204 8.049117 TGTGACATCCTTAAAAAGCATCTAGAT 58.951 33.333 0.00 0.00 0.00 1.98
204 205 7.394016 TGTGACATCCTTAAAAAGCATCTAGA 58.606 34.615 0.00 0.00 0.00 2.43
205 206 7.615582 TGTGACATCCTTAAAAAGCATCTAG 57.384 36.000 0.00 0.00 0.00 2.43
206 207 8.579850 AATGTGACATCCTTAAAAAGCATCTA 57.420 30.769 0.00 0.00 0.00 1.98
207 208 7.472334 AATGTGACATCCTTAAAAAGCATCT 57.528 32.000 0.00 0.00 0.00 2.90
208 209 9.638239 TTAAATGTGACATCCTTAAAAAGCATC 57.362 29.630 0.00 0.00 0.00 3.91
209 210 9.643693 CTTAAATGTGACATCCTTAAAAAGCAT 57.356 29.630 0.00 0.00 0.00 3.79
210 211 7.598493 GCTTAAATGTGACATCCTTAAAAAGCA 59.402 33.333 0.00 0.00 34.68 3.91
211 212 7.814587 AGCTTAAATGTGACATCCTTAAAAAGC 59.185 33.333 0.00 3.59 34.73 3.51
212 213 9.346725 GAGCTTAAATGTGACATCCTTAAAAAG 57.653 33.333 0.00 0.00 0.00 2.27
213 214 9.077885 AGAGCTTAAATGTGACATCCTTAAAAA 57.922 29.630 0.00 0.00 0.00 1.94
214 215 8.635765 AGAGCTTAAATGTGACATCCTTAAAA 57.364 30.769 0.00 0.00 0.00 1.52
215 216 7.882791 TGAGAGCTTAAATGTGACATCCTTAAA 59.117 33.333 0.00 0.00 0.00 1.52
216 217 7.334421 GTGAGAGCTTAAATGTGACATCCTTAA 59.666 37.037 0.00 0.52 0.00 1.85
217 218 6.818644 GTGAGAGCTTAAATGTGACATCCTTA 59.181 38.462 0.00 0.00 0.00 2.69
218 219 5.645497 GTGAGAGCTTAAATGTGACATCCTT 59.355 40.000 0.00 0.00 0.00 3.36
219 220 5.181748 GTGAGAGCTTAAATGTGACATCCT 58.818 41.667 0.00 0.00 0.00 3.24
220 221 4.937620 TGTGAGAGCTTAAATGTGACATCC 59.062 41.667 0.00 0.00 0.00 3.51
221 222 6.148480 ACTTGTGAGAGCTTAAATGTGACATC 59.852 38.462 0.00 0.00 0.00 3.06
222 223 6.000219 ACTTGTGAGAGCTTAAATGTGACAT 59.000 36.000 0.00 0.00 0.00 3.06
223 224 5.368145 ACTTGTGAGAGCTTAAATGTGACA 58.632 37.500 0.00 0.00 0.00 3.58
224 225 5.931441 ACTTGTGAGAGCTTAAATGTGAC 57.069 39.130 0.00 0.00 0.00 3.67
230 231 9.830975 TGCATTATATACTTGTGAGAGCTTAAA 57.169 29.630 0.00 0.00 0.00 1.52
232 233 9.645059 GATGCATTATATACTTGTGAGAGCTTA 57.355 33.333 0.00 0.00 0.00 3.09
233 234 8.152898 TGATGCATTATATACTTGTGAGAGCTT 58.847 33.333 0.00 0.00 0.00 3.74
234 235 7.674120 TGATGCATTATATACTTGTGAGAGCT 58.326 34.615 0.00 0.00 0.00 4.09
235 236 7.895975 TGATGCATTATATACTTGTGAGAGC 57.104 36.000 0.00 0.00 0.00 4.09
236 237 9.264719 TGTTGATGCATTATATACTTGTGAGAG 57.735 33.333 0.00 0.00 0.00 3.20
237 238 9.612066 TTGTTGATGCATTATATACTTGTGAGA 57.388 29.630 0.00 0.00 0.00 3.27
238 239 9.874215 CTTGTTGATGCATTATATACTTGTGAG 57.126 33.333 0.00 0.00 0.00 3.51
239 240 9.612066 TCTTGTTGATGCATTATATACTTGTGA 57.388 29.630 0.00 0.00 0.00 3.58
272 273 9.495572 TTTCACTTTGTTTGTGGTCTAATTTTT 57.504 25.926 0.00 0.00 36.21 1.94
273 274 9.495572 TTTTCACTTTGTTTGTGGTCTAATTTT 57.504 25.926 0.00 0.00 36.21 1.82
274 275 9.665719 ATTTTCACTTTGTTTGTGGTCTAATTT 57.334 25.926 0.00 0.00 36.21 1.82
275 276 9.313118 GATTTTCACTTTGTTTGTGGTCTAATT 57.687 29.630 0.00 0.00 36.21 1.40
276 277 8.474025 TGATTTTCACTTTGTTTGTGGTCTAAT 58.526 29.630 0.00 0.00 36.21 1.73
277 278 7.831753 TGATTTTCACTTTGTTTGTGGTCTAA 58.168 30.769 0.00 0.00 36.21 2.10
278 279 7.397892 TGATTTTCACTTTGTTTGTGGTCTA 57.602 32.000 0.00 0.00 36.21 2.59
279 280 6.279513 TGATTTTCACTTTGTTTGTGGTCT 57.720 33.333 0.00 0.00 36.21 3.85
280 281 5.005682 GCTGATTTTCACTTTGTTTGTGGTC 59.994 40.000 0.00 0.00 36.21 4.02
281 282 4.869861 GCTGATTTTCACTTTGTTTGTGGT 59.130 37.500 0.00 0.00 36.21 4.16
282 283 5.111293 AGCTGATTTTCACTTTGTTTGTGG 58.889 37.500 0.00 0.00 36.21 4.17
283 284 6.651755 AAGCTGATTTTCACTTTGTTTGTG 57.348 33.333 0.00 0.00 36.82 3.33
284 285 7.771183 TCTAAGCTGATTTTCACTTTGTTTGT 58.229 30.769 0.00 0.00 0.00 2.83
285 286 8.697067 CATCTAAGCTGATTTTCACTTTGTTTG 58.303 33.333 0.00 0.00 0.00 2.93
286 287 8.416329 ACATCTAAGCTGATTTTCACTTTGTTT 58.584 29.630 0.00 0.00 0.00 2.83
287 288 7.864379 CACATCTAAGCTGATTTTCACTTTGTT 59.136 33.333 0.00 0.00 0.00 2.83
288 289 7.229306 TCACATCTAAGCTGATTTTCACTTTGT 59.771 33.333 0.00 0.00 0.00 2.83
289 290 7.536622 GTCACATCTAAGCTGATTTTCACTTTG 59.463 37.037 0.00 0.00 0.00 2.77
290 291 7.229306 TGTCACATCTAAGCTGATTTTCACTTT 59.771 33.333 0.00 0.00 0.00 2.66
291 292 6.712095 TGTCACATCTAAGCTGATTTTCACTT 59.288 34.615 0.00 0.00 0.00 3.16
292 293 6.233434 TGTCACATCTAAGCTGATTTTCACT 58.767 36.000 0.00 0.00 0.00 3.41
293 294 6.486253 TGTCACATCTAAGCTGATTTTCAC 57.514 37.500 0.00 0.00 0.00 3.18
294 295 8.260114 TCTATGTCACATCTAAGCTGATTTTCA 58.740 33.333 0.00 0.00 0.00 2.69
295 296 8.547069 GTCTATGTCACATCTAAGCTGATTTTC 58.453 37.037 0.00 0.00 0.00 2.29
296 297 8.263640 AGTCTATGTCACATCTAAGCTGATTTT 58.736 33.333 0.00 0.00 0.00 1.82
297 298 7.790027 AGTCTATGTCACATCTAAGCTGATTT 58.210 34.615 0.00 0.00 0.00 2.17
298 299 7.358770 AGTCTATGTCACATCTAAGCTGATT 57.641 36.000 0.00 0.00 0.00 2.57
299 300 6.975196 AGTCTATGTCACATCTAAGCTGAT 57.025 37.500 0.00 0.00 0.00 2.90
300 301 7.503902 ACATAGTCTATGTCACATCTAAGCTGA 59.496 37.037 18.13 0.00 45.83 4.26
301 302 7.656412 ACATAGTCTATGTCACATCTAAGCTG 58.344 38.462 18.13 0.00 45.83 4.24
302 303 7.831691 ACATAGTCTATGTCACATCTAAGCT 57.168 36.000 18.13 0.00 45.83 3.74
315 316 7.041712 ACACATCTAGACGTGACATAGTCTATG 60.042 40.741 24.69 16.85 45.47 2.23
316 317 6.993308 ACACATCTAGACGTGACATAGTCTAT 59.007 38.462 24.69 0.00 45.47 1.98
317 318 6.346896 ACACATCTAGACGTGACATAGTCTA 58.653 40.000 24.69 17.33 44.93 2.59
319 320 5.487153 ACACATCTAGACGTGACATAGTC 57.513 43.478 24.69 6.05 36.91 2.59
320 321 4.335874 GGACACATCTAGACGTGACATAGT 59.664 45.833 24.69 1.47 36.91 2.12
321 322 4.576873 AGGACACATCTAGACGTGACATAG 59.423 45.833 24.69 0.00 36.91 2.23
322 323 4.524053 AGGACACATCTAGACGTGACATA 58.476 43.478 24.69 0.00 36.91 2.29
323 324 3.357203 AGGACACATCTAGACGTGACAT 58.643 45.455 24.69 13.92 36.91 3.06
324 325 2.791655 AGGACACATCTAGACGTGACA 58.208 47.619 24.69 0.00 36.91 3.58
325 326 5.526479 TGTATAGGACACATCTAGACGTGAC 59.474 44.000 24.69 18.11 36.91 3.67
326 327 5.677567 TGTATAGGACACATCTAGACGTGA 58.322 41.667 24.69 3.24 36.91 4.35
327 328 6.373186 TTGTATAGGACACATCTAGACGTG 57.627 41.667 17.02 17.02 37.96 4.49
328 329 6.183360 GGTTTGTATAGGACACATCTAGACGT 60.183 42.308 0.00 0.00 37.96 4.34
329 330 6.207213 GGTTTGTATAGGACACATCTAGACG 58.793 44.000 0.00 0.00 37.96 4.18
330 331 6.514063 GGGTTTGTATAGGACACATCTAGAC 58.486 44.000 0.00 0.00 37.96 2.59
331 332 5.301045 CGGGTTTGTATAGGACACATCTAGA 59.699 44.000 0.00 0.00 37.96 2.43
332 333 5.529791 CGGGTTTGTATAGGACACATCTAG 58.470 45.833 0.00 0.00 37.96 2.43
333 334 4.202182 GCGGGTTTGTATAGGACACATCTA 60.202 45.833 0.00 0.00 37.96 1.98
334 335 3.431766 GCGGGTTTGTATAGGACACATCT 60.432 47.826 0.00 0.00 37.96 2.90
335 336 2.870411 GCGGGTTTGTATAGGACACATC 59.130 50.000 0.00 0.00 37.96 3.06
336 337 2.420967 GGCGGGTTTGTATAGGACACAT 60.421 50.000 0.00 0.00 37.96 3.21
337 338 1.065998 GGCGGGTTTGTATAGGACACA 60.066 52.381 0.00 0.00 37.96 3.72
338 339 1.660167 GGCGGGTTTGTATAGGACAC 58.340 55.000 0.00 0.00 37.96 3.67
339 340 0.176219 CGGCGGGTTTGTATAGGACA 59.824 55.000 0.00 0.00 35.78 4.02
340 341 0.531311 CCGGCGGGTTTGTATAGGAC 60.531 60.000 20.56 0.00 0.00 3.85
341 342 1.824658 CCGGCGGGTTTGTATAGGA 59.175 57.895 20.56 0.00 0.00 2.94
342 343 1.890510 GCCGGCGGGTTTGTATAGG 60.891 63.158 29.48 0.00 34.97 2.57
343 344 0.390124 TAGCCGGCGGGTTTGTATAG 59.610 55.000 36.94 1.40 34.28 1.31
344 345 0.829333 TTAGCCGGCGGGTTTGTATA 59.171 50.000 36.94 14.58 34.28 1.47
345 346 0.035247 TTTAGCCGGCGGGTTTGTAT 60.035 50.000 36.94 1.83 34.28 2.29
346 347 0.674269 CTTTAGCCGGCGGGTTTGTA 60.674 55.000 36.94 15.88 34.28 2.41
347 348 1.969589 CTTTAGCCGGCGGGTTTGT 60.970 57.895 36.94 3.61 34.28 2.83
348 349 2.874751 CTTTAGCCGGCGGGTTTG 59.125 61.111 36.94 21.27 34.28 2.93
349 350 3.060000 GCTTTAGCCGGCGGGTTT 61.060 61.111 36.94 5.39 34.28 3.27
372 373 2.018544 CGTTGCTCGTTTGACCCAA 58.981 52.632 0.00 0.00 34.52 4.12
373 374 2.539338 GCGTTGCTCGTTTGACCCA 61.539 57.895 4.16 0.00 42.13 4.51
419 422 3.527641 GCAGTAGAGCGGTAGCCT 58.472 61.111 0.00 0.00 46.67 4.58
435 438 3.471680 AGATAGATTTTCCTTCCTGCGC 58.528 45.455 0.00 0.00 0.00 6.09
645 663 2.059190 GGGAGGAGACGAGGGGAAC 61.059 68.421 0.00 0.00 0.00 3.62
646 664 2.363361 GGGAGGAGACGAGGGGAA 59.637 66.667 0.00 0.00 0.00 3.97
726 748 2.032071 AATATAGGCGCGGTGGGC 59.968 61.111 8.83 0.00 40.84 5.36
727 749 1.375523 GGAATATAGGCGCGGTGGG 60.376 63.158 8.83 0.00 0.00 4.61
822 861 2.725008 GATCTCTCCGACGGGCAG 59.275 66.667 15.25 10.25 0.00 4.85
823 862 2.833582 GGATCTCTCCGACGGGCA 60.834 66.667 15.25 0.00 0.00 5.36
1110 1161 4.473520 CTGGGGTGCAGGCGGTAG 62.474 72.222 0.00 0.00 0.00 3.18
1144 1195 2.178521 CCTGGAGACGACGTTCCG 59.821 66.667 18.14 14.16 36.22 4.30
1243 1294 3.056465 GGATATAGACAGGAAAGGGCGAG 60.056 52.174 0.00 0.00 0.00 5.03
1244 1295 2.897969 GGATATAGACAGGAAAGGGCGA 59.102 50.000 0.00 0.00 0.00 5.54
1245 1296 2.028020 GGGATATAGACAGGAAAGGGCG 60.028 54.545 0.00 0.00 0.00 6.13
1274 1331 0.543277 TTCAGGTGGCCTATCTGCAG 59.457 55.000 7.63 7.63 37.44 4.41
1354 1412 3.306917 TGCAGCTCAAAATCATGGTTG 57.693 42.857 0.00 0.00 0.00 3.77
1420 1479 6.542852 GCTTATCAAGCGTCTCTCTATCTAG 58.457 44.000 0.00 0.00 45.74 2.43
1421 1480 6.489127 GCTTATCAAGCGTCTCTCTATCTA 57.511 41.667 0.00 0.00 45.74 1.98
1422 1481 5.371115 GCTTATCAAGCGTCTCTCTATCT 57.629 43.478 0.00 0.00 45.74 1.98
1486 1545 3.181466 GCCAAAACAATCCAAGACAAGGT 60.181 43.478 0.00 0.00 0.00 3.50
1539 1598 4.020218 TCACAGATAGTCAGGTCCCAAAAG 60.020 45.833 0.00 0.00 0.00 2.27
1580 1639 4.659111 CATGGCATGCTGATTTCCTTTA 57.341 40.909 18.92 0.00 0.00 1.85
1622 1681 1.744741 GGCTGAGCAACTCTCCAGC 60.745 63.158 6.82 0.00 41.18 4.85
1663 1722 5.681543 GGACGCTTTAAAAACATAGCATAGC 59.318 40.000 0.00 0.00 33.29 2.97
1664 1723 6.038271 AGGGACGCTTTAAAAACATAGCATAG 59.962 38.462 0.00 0.00 33.29 2.23
1665 1724 5.883673 AGGGACGCTTTAAAAACATAGCATA 59.116 36.000 0.00 0.00 33.29 3.14
1666 1725 4.705023 AGGGACGCTTTAAAAACATAGCAT 59.295 37.500 0.00 0.00 33.29 3.79
1667 1726 4.076394 AGGGACGCTTTAAAAACATAGCA 58.924 39.130 0.00 0.00 33.29 3.49
1668 1727 4.696899 AGGGACGCTTTAAAAACATAGC 57.303 40.909 0.00 0.00 0.00 2.97
1669 1728 6.677187 GCCTTAGGGACGCTTTAAAAACATAG 60.677 42.308 0.00 0.00 33.58 2.23
1670 1729 5.124297 GCCTTAGGGACGCTTTAAAAACATA 59.876 40.000 0.00 0.00 33.58 2.29
1671 1730 4.082408 GCCTTAGGGACGCTTTAAAAACAT 60.082 41.667 0.00 0.00 33.58 2.71
1672 1731 3.253921 GCCTTAGGGACGCTTTAAAAACA 59.746 43.478 0.00 0.00 33.58 2.83
1673 1732 3.668757 CGCCTTAGGGACGCTTTAAAAAC 60.669 47.826 0.00 0.00 33.58 2.43
1674 1733 2.485038 CGCCTTAGGGACGCTTTAAAAA 59.515 45.455 0.00 0.00 33.58 1.94
1675 1734 2.078392 CGCCTTAGGGACGCTTTAAAA 58.922 47.619 0.00 0.00 33.58 1.52
1676 1735 1.275856 TCGCCTTAGGGACGCTTTAAA 59.724 47.619 0.00 0.00 34.09 1.52
1677 1736 0.896923 TCGCCTTAGGGACGCTTTAA 59.103 50.000 0.00 0.00 34.09 1.52
1678 1737 0.174162 GTCGCCTTAGGGACGCTTTA 59.826 55.000 0.00 0.00 44.82 1.85
1679 1738 1.079336 GTCGCCTTAGGGACGCTTT 60.079 57.895 0.00 0.00 44.82 3.51
1680 1739 2.577593 GTCGCCTTAGGGACGCTT 59.422 61.111 0.00 0.00 44.82 4.68
1706 1765 4.516195 GAGGGGGAGCGCTTCGAC 62.516 72.222 13.26 5.82 0.00 4.20
1707 1766 4.761058 AGAGGGGGAGCGCTTCGA 62.761 66.667 13.26 0.00 0.00 3.71
1708 1767 4.521062 CAGAGGGGGAGCGCTTCG 62.521 72.222 13.26 0.00 0.00 3.79
1709 1768 4.847444 GCAGAGGGGGAGCGCTTC 62.847 72.222 13.26 10.24 0.00 3.86
1712 1771 4.416738 AAAGCAGAGGGGGAGCGC 62.417 66.667 0.00 0.00 0.00 5.92
1713 1772 2.437359 CAAAGCAGAGGGGGAGCG 60.437 66.667 0.00 0.00 0.00 5.03
1714 1773 2.044551 CCAAAGCAGAGGGGGAGC 60.045 66.667 0.00 0.00 0.00 4.70
1715 1774 0.405585 TTTCCAAAGCAGAGGGGGAG 59.594 55.000 0.00 0.00 0.00 4.30
1716 1775 0.856982 TTTTCCAAAGCAGAGGGGGA 59.143 50.000 0.00 0.00 0.00 4.81
1717 1776 1.827344 GATTTTCCAAAGCAGAGGGGG 59.173 52.381 0.00 0.00 0.00 5.40
1718 1777 1.474077 CGATTTTCCAAAGCAGAGGGG 59.526 52.381 0.00 0.00 0.00 4.79
1719 1778 2.162408 GTCGATTTTCCAAAGCAGAGGG 59.838 50.000 0.00 0.00 0.00 4.30
1720 1779 2.162408 GGTCGATTTTCCAAAGCAGAGG 59.838 50.000 0.00 0.00 0.00 3.69
1721 1780 2.159653 CGGTCGATTTTCCAAAGCAGAG 60.160 50.000 0.00 0.00 0.00 3.35
1722 1781 1.804151 CGGTCGATTTTCCAAAGCAGA 59.196 47.619 0.00 0.00 0.00 4.26
1723 1782 1.729149 GCGGTCGATTTTCCAAAGCAG 60.729 52.381 0.00 0.00 0.00 4.24
1724 1783 0.239879 GCGGTCGATTTTCCAAAGCA 59.760 50.000 0.00 0.00 0.00 3.91
1725 1784 0.521735 AGCGGTCGATTTTCCAAAGC 59.478 50.000 0.00 0.00 0.00 3.51
1726 1785 2.979813 CAAAGCGGTCGATTTTCCAAAG 59.020 45.455 3.79 0.00 30.80 2.77
1727 1786 2.287909 CCAAAGCGGTCGATTTTCCAAA 60.288 45.455 3.79 0.00 30.80 3.28
1728 1787 1.268352 CCAAAGCGGTCGATTTTCCAA 59.732 47.619 3.79 0.00 30.80 3.53
1729 1788 0.878416 CCAAAGCGGTCGATTTTCCA 59.122 50.000 3.79 0.00 30.80 3.53
1730 1789 0.170339 CCCAAAGCGGTCGATTTTCC 59.830 55.000 3.79 0.00 30.80 3.13
1731 1790 0.456142 GCCCAAAGCGGTCGATTTTC 60.456 55.000 3.79 0.00 30.80 2.29
1732 1791 1.584495 GCCCAAAGCGGTCGATTTT 59.416 52.632 3.79 0.00 30.80 1.82
1733 1792 3.274067 GCCCAAAGCGGTCGATTT 58.726 55.556 0.55 0.55 33.72 2.17
1751 1810 3.195698 CGCTTTGGACGCCTAGGC 61.196 66.667 24.75 24.75 37.85 3.93
1759 1818 4.770874 TAGGCGGGCGCTTTGGAC 62.771 66.667 7.64 0.00 41.60 4.02
1760 1819 4.467084 CTAGGCGGGCGCTTTGGA 62.467 66.667 7.64 0.00 41.60 3.53
1806 1865 1.446366 GCCTTACCGCCTTAGGGAG 59.554 63.158 0.00 0.00 35.02 4.30
1807 1866 2.428925 CGCCTTACCGCCTTAGGGA 61.429 63.158 0.00 0.00 35.02 4.20
1808 1867 2.108362 CGCCTTACCGCCTTAGGG 59.892 66.667 0.00 0.00 35.02 3.53
1809 1868 1.227176 GACGCCTTACCGCCTTAGG 60.227 63.158 0.00 0.00 37.30 2.69
1810 1869 1.588139 CGACGCCTTACCGCCTTAG 60.588 63.158 0.00 0.00 0.00 2.18
1811 1870 2.491152 CGACGCCTTACCGCCTTA 59.509 61.111 0.00 0.00 0.00 2.69
1823 1882 4.669283 GCAACTATATTTTTAAGGCGACGC 59.331 41.667 12.43 12.43 0.00 5.19
1824 1883 6.044512 AGCAACTATATTTTTAAGGCGACG 57.955 37.500 0.00 0.00 0.00 5.12
1825 1884 8.015658 CCATAGCAACTATATTTTTAAGGCGAC 58.984 37.037 0.00 0.00 0.00 5.19
1826 1885 7.934665 TCCATAGCAACTATATTTTTAAGGCGA 59.065 33.333 0.00 0.00 0.00 5.54
1827 1886 8.094798 TCCATAGCAACTATATTTTTAAGGCG 57.905 34.615 0.00 0.00 0.00 5.52
1828 1887 9.899226 CTTCCATAGCAACTATATTTTTAAGGC 57.101 33.333 0.00 0.00 0.00 4.35
1837 1896 9.883142 GCTTCTTATCTTCCATAGCAACTATAT 57.117 33.333 0.00 0.00 0.00 0.86
1838 1897 9.094578 AGCTTCTTATCTTCCATAGCAACTATA 57.905 33.333 0.00 0.00 0.00 1.31
1839 1898 7.877097 CAGCTTCTTATCTTCCATAGCAACTAT 59.123 37.037 0.00 0.00 0.00 2.12
1840 1899 7.069950 TCAGCTTCTTATCTTCCATAGCAACTA 59.930 37.037 0.00 0.00 0.00 2.24
1841 1900 6.054295 CAGCTTCTTATCTTCCATAGCAACT 58.946 40.000 0.00 0.00 0.00 3.16
1842 1901 6.018343 GTCAGCTTCTTATCTTCCATAGCAAC 60.018 42.308 0.00 0.00 0.00 4.17
1843 1902 6.051717 GTCAGCTTCTTATCTTCCATAGCAA 58.948 40.000 0.00 0.00 0.00 3.91
1844 1903 5.453903 GGTCAGCTTCTTATCTTCCATAGCA 60.454 44.000 0.00 0.00 0.00 3.49
1862 1921 4.503741 TTCTTTGTTAGCAATGGTCAGC 57.496 40.909 5.55 0.00 34.18 4.26
1869 1928 6.012745 AGGGTCAGATTTCTTTGTTAGCAAT 58.987 36.000 0.00 0.00 34.18 3.56
1885 1944 7.583625 TCACTACTATAATTCAGAGGGTCAGA 58.416 38.462 0.00 0.00 0.00 3.27
1899 1958 8.441572 ACTAGAATCAGCTCCTCACTACTATAA 58.558 37.037 0.00 0.00 0.00 0.98
1900 1959 7.980032 ACTAGAATCAGCTCCTCACTACTATA 58.020 38.462 0.00 0.00 0.00 1.31
1908 1967 4.898265 AGCAATACTAGAATCAGCTCCTCA 59.102 41.667 0.00 0.00 0.00 3.86
1983 2042 4.695396 AGCTTGTGTTGCATCAATTTTGA 58.305 34.783 0.00 0.00 42.14 2.69
2001 2064 5.865085 TCCAGTCAACATAAAGTGTAGCTT 58.135 37.500 0.00 0.00 41.14 3.74
2002 2065 5.483685 TCCAGTCAACATAAAGTGTAGCT 57.516 39.130 0.00 0.00 41.14 3.32
2003 2066 5.701290 ACTTCCAGTCAACATAAAGTGTAGC 59.299 40.000 0.00 0.00 41.14 3.58
2023 2086 8.768955 CCATGAGAAGCTATGTTGTTATACTTC 58.231 37.037 0.00 0.00 33.83 3.01
2124 2187 5.072872 AATGAAGCTATCAGGTAAGCTCCAT 59.927 40.000 0.00 0.00 44.56 3.41
2130 2193 9.764363 TGTGTATAAATGAAGCTATCAGGTAAG 57.236 33.333 0.00 0.00 42.53 2.34
2179 2242 1.942657 CCGATAACCTGCAGTTCATGG 59.057 52.381 13.81 3.38 40.05 3.66
2197 2260 1.491670 CAATACCACTCTCATCGCCG 58.508 55.000 0.00 0.00 0.00 6.46
2611 2674 7.708998 AGAAAGGTTGCGAAAAGTTGTATTTA 58.291 30.769 0.00 0.00 0.00 1.40
2765 2828 5.843673 TCTAAGCAGAACGAGAATCAGAT 57.156 39.130 0.00 0.00 33.17 2.90
2891 2954 8.382875 CAAACCAAATCAAAAGAAAGAAGTGTC 58.617 33.333 0.00 0.00 0.00 3.67
2936 3000 5.955961 TTTTACCCGCTATACCTTACCTT 57.044 39.130 0.00 0.00 0.00 3.50
2937 3001 5.842874 AGATTTTACCCGCTATACCTTACCT 59.157 40.000 0.00 0.00 0.00 3.08
2938 3002 6.106648 AGATTTTACCCGCTATACCTTACC 57.893 41.667 0.00 0.00 0.00 2.85
2939 3003 6.988580 ACAAGATTTTACCCGCTATACCTTAC 59.011 38.462 0.00 0.00 0.00 2.34
2940 3004 7.128234 ACAAGATTTTACCCGCTATACCTTA 57.872 36.000 0.00 0.00 0.00 2.69
2960 3024 7.514747 GCCGAGTATTCTTTCGTACAATACAAG 60.515 40.741 12.81 7.67 36.04 3.16
3101 3165 7.375808 CGAATGAAAAAGAAGACAACGAAATGA 59.624 33.333 0.00 0.00 0.00 2.57
3126 3190 3.243035 ACATTCATCCAACACAACACACG 60.243 43.478 0.00 0.00 0.00 4.49
3286 3350 3.149899 CAGCTCACTGGTGGATCAC 57.850 57.895 0.00 0.00 40.48 3.06
3314 3378 5.822519 TGATCAGCAGAAACAAAACTACTGT 59.177 36.000 0.00 0.00 31.68 3.55
3315 3379 6.304356 TGATCAGCAGAAACAAAACTACTG 57.696 37.500 0.00 0.00 0.00 2.74
3317 3381 6.902341 TGATGATCAGCAGAAACAAAACTAC 58.098 36.000 10.16 0.00 0.00 2.73
3415 3481 1.625315 TGCCTGACAGCAGAACTACAT 59.375 47.619 0.00 0.00 45.17 2.29
3455 3521 2.036098 TTAGTCCTGGACCGGCGA 59.964 61.111 22.81 2.44 32.18 5.54
3460 3526 3.636153 AATTCAGCTTAGTCCTGGACC 57.364 47.619 22.81 7.91 32.18 4.46
3473 3539 4.201666 TGCAACGAACAAACAAAATTCAGC 60.202 37.500 0.00 0.00 0.00 4.26
3613 3745 2.283298 CACGTTTCAGCTGCCATAGAT 58.717 47.619 9.47 0.00 0.00 1.98
3639 3771 4.697828 GGCTCAGATGATCGTAGTCATAGA 59.302 45.833 0.00 3.26 38.88 1.98
3708 3841 5.119743 GGTTTCAGAATTTCAGAGCATTTGC 59.880 40.000 0.00 0.00 42.49 3.68
3712 3845 5.047519 CCAAGGTTTCAGAATTTCAGAGCAT 60.048 40.000 0.00 0.00 0.00 3.79
3722 3855 3.254903 GGCGTTAACCAAGGTTTCAGAAT 59.745 43.478 10.13 0.00 39.31 2.40
3724 3857 2.223745 GGCGTTAACCAAGGTTTCAGA 58.776 47.619 10.13 0.00 39.31 3.27
3728 3861 1.679153 CACTGGCGTTAACCAAGGTTT 59.321 47.619 10.13 0.00 39.86 3.27
3730 3863 0.181824 ACACTGGCGTTAACCAAGGT 59.818 50.000 0.00 0.00 39.86 3.50


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

AutoCloner maintained by Alex Coulton.