Multiple sequence alignment - TraesCS1D01G386200

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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 TraesCS1D01G386200 chr1D 100.000 4717 0 0 1 4717 459031806 459027090 0.000000e+00 8711.0
1 TraesCS1D01G386200 chr1D 85.738 4130 532 41 198 4300 459042393 459038294 0.000000e+00 4311.0
2 TraesCS1D01G386200 chr1B 86.053 4223 511 38 108 4300 631203975 631199801 0.000000e+00 4464.0
3 TraesCS1D01G386200 chr1B 84.898 4443 580 65 1 4392 631222282 631217880 0.000000e+00 4403.0
4 TraesCS1D01G386200 chr1A 87.285 3311 368 33 235 3508 551463775 551460481 0.000000e+00 3733.0
5 TraesCS1D01G386200 chr1A 80.824 1700 268 37 2975 4658 551443294 551441637 0.000000e+00 1280.0
6 TraesCS1D01G386200 chr1A 83.705 718 109 4 3492 4208 551458803 551458093 0.000000e+00 671.0
7 TraesCS1D01G386200 chr1A 86.607 112 14 1 85 195 551463774 551463663 6.410000e-24 122.0
8 TraesCS1D01G386200 chr3D 78.573 3953 735 72 355 4245 428251410 428255312 0.000000e+00 2505.0
9 TraesCS1D01G386200 chr3D 78.166 3980 738 95 282 4187 428245383 428249305 0.000000e+00 2414.0
10 TraesCS1D01G386200 chr3D 89.655 58 4 1 1 58 428245239 428245294 6.550000e-09 73.1
11 TraesCS1D01G386200 chr3A 78.270 3953 748 70 355 4245 557413361 557409458 0.000000e+00 2438.0
12 TraesCS1D01G386200 chr3A 77.199 3991 765 93 360 4268 557419092 557415165 0.000000e+00 2194.0
13 TraesCS1D01G386200 chr3B 77.613 4114 766 106 282 4319 559880868 559884902 0.000000e+00 2351.0
14 TraesCS1D01G386200 chr3B 79.643 2019 336 48 355 2329 559886830 559888817 0.000000e+00 1382.0
15 TraesCS1D01G386200 chr3B 89.474 57 4 1 2 58 559880726 559880780 2.350000e-08 71.3
16 TraesCS1D01G386200 chr6D 77.018 3951 788 93 358 4259 469800194 469804073 0.000000e+00 2156.0
17 TraesCS1D01G386200 chrUn 76.577 3962 805 94 358 4270 62079784 62075897 0.000000e+00 2061.0
18 TraesCS1D01G386200 chr4A 75.172 3923 843 86 391 4238 734385227 734389093 0.000000e+00 1727.0
19 TraesCS1D01G386200 chr4A 74.828 3790 808 99 385 4091 736896812 736900538 0.000000e+00 1580.0
20 TraesCS1D01G386200 chr7B 75.872 3067 648 74 1140 4175 746528352 746525347 0.000000e+00 1480.0
21 TraesCS1D01G386200 chr7B 76.977 1985 399 39 380 2330 744260778 744258818 0.000000e+00 1081.0
22 TraesCS1D01G386200 chr7B 76.542 1978 404 38 380 2322 743738228 743740180 0.000000e+00 1027.0
23 TraesCS1D01G386200 chr2D 73.194 1052 253 21 3142 4182 633216738 633217771 2.090000e-93 353.0
24 TraesCS1D01G386200 chr2B 78.796 382 78 2 358 739 776410740 776411118 2.180000e-63 254.0


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 TraesCS1D01G386200 chr1D 459027090 459031806 4716 True 8711.000000 8711 100.000000 1 4717 1 chr1D.!!$R1 4716
1 TraesCS1D01G386200 chr1D 459038294 459042393 4099 True 4311.000000 4311 85.738000 198 4300 1 chr1D.!!$R2 4102
2 TraesCS1D01G386200 chr1B 631199801 631203975 4174 True 4464.000000 4464 86.053000 108 4300 1 chr1B.!!$R1 4192
3 TraesCS1D01G386200 chr1B 631217880 631222282 4402 True 4403.000000 4403 84.898000 1 4392 1 chr1B.!!$R2 4391
4 TraesCS1D01G386200 chr1A 551458093 551463775 5682 True 1508.666667 3733 85.865667 85 4208 3 chr1A.!!$R2 4123
5 TraesCS1D01G386200 chr1A 551441637 551443294 1657 True 1280.000000 1280 80.824000 2975 4658 1 chr1A.!!$R1 1683
6 TraesCS1D01G386200 chr3D 428245239 428255312 10073 False 1664.033333 2505 82.131333 1 4245 3 chr3D.!!$F1 4244
7 TraesCS1D01G386200 chr3A 557409458 557419092 9634 True 2316.000000 2438 77.734500 355 4268 2 chr3A.!!$R1 3913
8 TraesCS1D01G386200 chr3B 559880726 559888817 8091 False 1268.100000 2351 82.243333 2 4319 3 chr3B.!!$F1 4317
9 TraesCS1D01G386200 chr6D 469800194 469804073 3879 False 2156.000000 2156 77.018000 358 4259 1 chr6D.!!$F1 3901
10 TraesCS1D01G386200 chrUn 62075897 62079784 3887 True 2061.000000 2061 76.577000 358 4270 1 chrUn.!!$R1 3912
11 TraesCS1D01G386200 chr4A 734385227 734389093 3866 False 1727.000000 1727 75.172000 391 4238 1 chr4A.!!$F1 3847
12 TraesCS1D01G386200 chr4A 736896812 736900538 3726 False 1580.000000 1580 74.828000 385 4091 1 chr4A.!!$F2 3706
13 TraesCS1D01G386200 chr7B 746525347 746528352 3005 True 1480.000000 1480 75.872000 1140 4175 1 chr7B.!!$R2 3035
14 TraesCS1D01G386200 chr7B 744258818 744260778 1960 True 1081.000000 1081 76.977000 380 2330 1 chr7B.!!$R1 1950
15 TraesCS1D01G386200 chr7B 743738228 743740180 1952 False 1027.000000 1027 76.542000 380 2322 1 chr7B.!!$F1 1942
16 TraesCS1D01G386200 chr2D 633216738 633217771 1033 False 353.000000 353 73.194000 3142 4182 1 chr2D.!!$F1 1040

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
438 608 0.031857 CTCCTCGCTGATGCTTCGAT 59.968 55.0 0.00 0.00 36.97 3.59 F
1468 7416 0.952280 CAGAGATCTTAGCCGGCGTA 59.048 55.0 23.20 12.37 0.00 4.42 F
3085 15044 0.657312 GCAATTGATGGCATCGACGA 59.343 50.0 19.47 0.00 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 7909 0.238289 GCATGGTATTTCCGCCATCG 59.762 55.0 0.0 0.0 43.05 3.84 R
3360 15334 0.036294 GGACCTCTTTGGACGGAAGG 60.036 60.0 0.0 0.0 39.71 3.46 R
4522 18204 0.108615 AAGAGTGGAAGGACGATGCG 60.109 55.0 0.0 0.0 0.00 4.73 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
82 98 1.886861 CTGCGTCCGGTGTTCTTTCG 61.887 60.000 0.00 0.00 0.00 3.46
83 99 1.662446 GCGTCCGGTGTTCTTTCGA 60.662 57.895 0.00 0.00 0.00 3.71
93 109 2.940410 GTGTTCTTTCGACTGTTTCCCA 59.060 45.455 0.00 0.00 0.00 4.37
95 111 4.753107 GTGTTCTTTCGACTGTTTCCCATA 59.247 41.667 0.00 0.00 0.00 2.74
96 112 4.994852 TGTTCTTTCGACTGTTTCCCATAG 59.005 41.667 0.00 0.00 0.00 2.23
98 114 5.988310 TCTTTCGACTGTTTCCCATAGTA 57.012 39.130 0.00 0.00 0.00 1.82
136 301 4.975631 TCCAAAGTTTCCTCCATTTCGTA 58.024 39.130 0.00 0.00 0.00 3.43
142 307 8.726988 CAAAGTTTCCTCCATTTCGTATCTTTA 58.273 33.333 0.00 0.00 0.00 1.85
143 308 7.845066 AGTTTCCTCCATTTCGTATCTTTAC 57.155 36.000 0.00 0.00 0.00 2.01
144 309 7.391620 AGTTTCCTCCATTTCGTATCTTTACA 58.608 34.615 0.00 0.00 0.00 2.41
145 310 7.333672 AGTTTCCTCCATTTCGTATCTTTACAC 59.666 37.037 0.00 0.00 0.00 2.90
146 311 6.540438 TCCTCCATTTCGTATCTTTACACT 57.460 37.500 0.00 0.00 0.00 3.55
147 312 7.649533 TCCTCCATTTCGTATCTTTACACTA 57.350 36.000 0.00 0.00 0.00 2.74
148 313 7.486647 TCCTCCATTTCGTATCTTTACACTAC 58.513 38.462 0.00 0.00 0.00 2.73
149 314 7.123098 TCCTCCATTTCGTATCTTTACACTACA 59.877 37.037 0.00 0.00 0.00 2.74
150 315 7.222224 CCTCCATTTCGTATCTTTACACTACAC 59.778 40.741 0.00 0.00 0.00 2.90
151 316 7.037438 TCCATTTCGTATCTTTACACTACACC 58.963 38.462 0.00 0.00 0.00 4.16
152 317 7.039882 CCATTTCGTATCTTTACACTACACCT 58.960 38.462 0.00 0.00 0.00 4.00
153 318 8.192774 CCATTTCGTATCTTTACACTACACCTA 58.807 37.037 0.00 0.00 0.00 3.08
154 319 9.577110 CATTTCGTATCTTTACACTACACCTAA 57.423 33.333 0.00 0.00 0.00 2.69
155 320 9.798994 ATTTCGTATCTTTACACTACACCTAAG 57.201 33.333 0.00 0.00 0.00 2.18
156 321 8.565896 TTCGTATCTTTACACTACACCTAAGA 57.434 34.615 0.00 0.00 0.00 2.10
157 322 8.743085 TCGTATCTTTACACTACACCTAAGAT 57.257 34.615 0.00 0.00 36.58 2.40
158 323 9.182214 TCGTATCTTTACACTACACCTAAGATT 57.818 33.333 0.00 0.00 34.95 2.40
159 324 9.448294 CGTATCTTTACACTACACCTAAGATTC 57.552 37.037 0.00 0.00 34.95 2.52
160 325 9.747293 GTATCTTTACACTACACCTAAGATTCC 57.253 37.037 0.00 0.00 34.95 3.01
161 326 8.611051 ATCTTTACACTACACCTAAGATTCCT 57.389 34.615 0.00 0.00 30.44 3.36
162 327 7.837863 TCTTTACACTACACCTAAGATTCCTG 58.162 38.462 0.00 0.00 0.00 3.86
163 328 4.473477 ACACTACACCTAAGATTCCTGC 57.527 45.455 0.00 0.00 0.00 4.85
164 329 3.838317 ACACTACACCTAAGATTCCTGCA 59.162 43.478 0.00 0.00 0.00 4.41
165 330 4.471386 ACACTACACCTAAGATTCCTGCAT 59.529 41.667 0.00 0.00 0.00 3.96
166 331 5.053145 CACTACACCTAAGATTCCTGCATC 58.947 45.833 0.00 0.00 0.00 3.91
167 332 3.567478 ACACCTAAGATTCCTGCATCC 57.433 47.619 0.00 0.00 0.00 3.51
168 333 3.118531 ACACCTAAGATTCCTGCATCCT 58.881 45.455 0.00 0.00 0.00 3.24
169 334 3.135530 ACACCTAAGATTCCTGCATCCTC 59.864 47.826 0.00 0.00 0.00 3.71
170 335 3.135348 CACCTAAGATTCCTGCATCCTCA 59.865 47.826 0.00 0.00 0.00 3.86
171 336 3.782523 ACCTAAGATTCCTGCATCCTCAA 59.217 43.478 0.00 0.00 0.00 3.02
172 337 4.228210 ACCTAAGATTCCTGCATCCTCAAA 59.772 41.667 0.00 0.00 0.00 2.69
173 338 5.195940 CCTAAGATTCCTGCATCCTCAAAA 58.804 41.667 0.00 0.00 0.00 2.44
174 339 5.832060 CCTAAGATTCCTGCATCCTCAAAAT 59.168 40.000 0.00 0.00 0.00 1.82
175 340 6.323225 CCTAAGATTCCTGCATCCTCAAAATT 59.677 38.462 0.00 0.00 0.00 1.82
176 341 7.503566 CCTAAGATTCCTGCATCCTCAAAATTA 59.496 37.037 0.00 0.00 0.00 1.40
177 342 7.909485 AAGATTCCTGCATCCTCAAAATTAT 57.091 32.000 0.00 0.00 0.00 1.28
178 343 7.521871 AGATTCCTGCATCCTCAAAATTATC 57.478 36.000 0.00 0.00 0.00 1.75
179 344 7.296098 AGATTCCTGCATCCTCAAAATTATCT 58.704 34.615 0.00 0.00 0.00 1.98
180 345 6.704289 TTCCTGCATCCTCAAAATTATCTG 57.296 37.500 0.00 0.00 0.00 2.90
181 346 6.005066 TCCTGCATCCTCAAAATTATCTGA 57.995 37.500 0.00 0.00 0.00 3.27
182 347 6.425735 TCCTGCATCCTCAAAATTATCTGAA 58.574 36.000 0.00 0.00 0.00 3.02
183 348 6.891361 TCCTGCATCCTCAAAATTATCTGAAA 59.109 34.615 0.00 0.00 0.00 2.69
184 349 7.396907 TCCTGCATCCTCAAAATTATCTGAAAA 59.603 33.333 0.00 0.00 0.00 2.29
185 350 7.705325 CCTGCATCCTCAAAATTATCTGAAAAG 59.295 37.037 0.00 0.00 0.00 2.27
186 351 7.037438 TGCATCCTCAAAATTATCTGAAAAGC 58.963 34.615 0.00 0.00 0.00 3.51
187 352 7.037438 GCATCCTCAAAATTATCTGAAAAGCA 58.963 34.615 0.00 0.00 0.00 3.91
188 353 7.709613 GCATCCTCAAAATTATCTGAAAAGCAT 59.290 33.333 0.00 0.00 0.00 3.79
189 354 9.245962 CATCCTCAAAATTATCTGAAAAGCATC 57.754 33.333 0.00 0.00 0.00 3.91
190 355 7.775120 TCCTCAAAATTATCTGAAAAGCATCC 58.225 34.615 0.00 0.00 0.00 3.51
191 356 6.982724 CCTCAAAATTATCTGAAAAGCATCCC 59.017 38.462 0.00 0.00 0.00 3.85
192 357 7.364056 CCTCAAAATTATCTGAAAAGCATCCCA 60.364 37.037 0.00 0.00 0.00 4.37
193 358 7.905265 TCAAAATTATCTGAAAAGCATCCCAA 58.095 30.769 0.00 0.00 0.00 4.12
194 359 8.373981 TCAAAATTATCTGAAAAGCATCCCAAA 58.626 29.630 0.00 0.00 0.00 3.28
195 360 9.001542 CAAAATTATCTGAAAAGCATCCCAAAA 57.998 29.630 0.00 0.00 0.00 2.44
196 361 9.571816 AAAATTATCTGAAAAGCATCCCAAAAA 57.428 25.926 0.00 0.00 0.00 1.94
244 409 7.610305 GTCTGGAATTCTATTACCTGTTTCCAA 59.390 37.037 5.23 0.00 40.25 3.53
245 410 8.336235 TCTGGAATTCTATTACCTGTTTCCAAT 58.664 33.333 5.23 0.00 40.25 3.16
246 411 8.519799 TGGAATTCTATTACCTGTTTCCAATC 57.480 34.615 5.23 0.00 38.47 2.67
247 412 7.282224 TGGAATTCTATTACCTGTTTCCAATCG 59.718 37.037 5.23 0.00 38.47 3.34
248 413 6.619801 ATTCTATTACCTGTTTCCAATCGC 57.380 37.500 0.00 0.00 0.00 4.58
250 415 5.741011 TCTATTACCTGTTTCCAATCGCTT 58.259 37.500 0.00 0.00 0.00 4.68
260 425 4.782019 TTCCAATCGCTTGCAGTTAAAT 57.218 36.364 0.00 0.00 0.00 1.40
271 436 6.215845 GCTTGCAGTTAAATTCTTCCAAAGA 58.784 36.000 0.00 0.00 35.26 2.52
277 442 7.543520 GCAGTTAAATTCTTCCAAAGATTCCTG 59.456 37.037 0.00 0.00 37.38 3.86
278 443 7.543520 CAGTTAAATTCTTCCAAAGATTCCTGC 59.456 37.037 0.00 0.00 37.38 4.85
283 448 6.423776 TTCTTCCAAAGATTCCTGCATTTT 57.576 33.333 0.00 0.00 37.38 1.82
309 474 7.253905 TGTCTTTTACACTAGGCCTAAGATT 57.746 36.000 14.85 1.05 31.43 2.40
311 476 6.762187 GTCTTTTACACTAGGCCTAAGATTCC 59.238 42.308 14.85 0.00 0.00 3.01
330 500 6.606395 AGATTCCTGCATTCTCAAAATTAGCT 59.394 34.615 0.00 0.00 0.00 3.32
336 506 7.063074 CCTGCATTCTCAAAATTAGCTGAAAAG 59.937 37.037 0.00 0.00 0.00 2.27
369 539 1.451927 GCAGTGATTCCATGGCGGA 60.452 57.895 6.96 0.00 44.40 5.54
438 608 0.031857 CTCCTCGCTGATGCTTCGAT 59.968 55.000 0.00 0.00 36.97 3.59
459 629 1.353022 GTACCTTGGGGTTGACATGGA 59.647 52.381 0.00 0.00 44.73 3.41
502 672 1.259609 CCACCATCATGCCACAGTTT 58.740 50.000 0.00 0.00 0.00 2.66
588 758 2.620585 AGCTCAAACAAGCCTTCTTCAC 59.379 45.455 0.00 0.00 43.56 3.18
649 819 3.442441 CGCAAAGCAAAGGGTGGA 58.558 55.556 0.00 0.00 0.00 4.02
834 6762 1.849692 TGGTAATAATGCAGAGGGCCA 59.150 47.619 6.18 0.00 43.89 5.36
1245 7178 5.577945 GCTTGTATTGGATGATGTTTGGTTG 59.422 40.000 0.00 0.00 0.00 3.77
1267 7203 4.080186 TGGAAGAATCTGGCAATGAGATGA 60.080 41.667 0.00 0.00 30.30 2.92
1463 7411 5.841810 AGAAGAAATCAGAGATCTTAGCCG 58.158 41.667 0.00 0.00 33.73 5.52
1468 7416 0.952280 CAGAGATCTTAGCCGGCGTA 59.048 55.000 23.20 12.37 0.00 4.42
1473 7421 2.429610 AGATCTTAGCCGGCGTAAGAAA 59.570 45.455 32.84 21.30 39.40 2.52
1532 7480 1.340405 ACGATCTCCTTTGGCAGCAAT 60.340 47.619 0.00 0.00 0.00 3.56
1540 7488 2.331194 CTTTGGCAGCAATAACTGTGC 58.669 47.619 0.00 0.00 42.55 4.57
1554 7502 1.490693 CTGTGCGTTCGCAGTTGAGT 61.491 55.000 19.93 0.00 43.83 3.41
1573 7521 8.261522 AGTTGAGTAGGAAAAAGGATATCACTC 58.738 37.037 4.83 6.14 0.00 3.51
1594 7560 4.785301 TCCATGGAAAGATGCTCTAAAGG 58.215 43.478 13.46 0.00 0.00 3.11
1650 7616 7.086376 TGTTGTGGAGTTACGATAAGTTAGAC 58.914 38.462 0.00 0.00 0.00 2.59
1698 7664 4.953940 TTGCAGCTTATTTCCAAAAGGT 57.046 36.364 0.00 0.00 33.90 3.50
1759 7725 2.098117 GCAGAGGGATTTGTTGATTCGG 59.902 50.000 0.00 0.00 0.00 4.30
1787 7753 6.522054 ACGAGAACAAAAGAGTGGAAGATAA 58.478 36.000 0.00 0.00 0.00 1.75
1796 7762 3.718956 AGAGTGGAAGATAATGGAAGGGG 59.281 47.826 0.00 0.00 0.00 4.79
1840 7806 6.795399 TCAGTTTCATTCTTTCAACCAGTTC 58.205 36.000 0.00 0.00 0.00 3.01
1937 7909 7.095691 GCACTGCTTCAGATTAGAAGATGATAC 60.096 40.741 7.81 0.00 46.18 2.24
1944 7916 5.514559 CAGATTAGAAGATGATACGATGGCG 59.485 44.000 0.00 0.00 44.79 5.69
1974 7948 5.049828 CCATGCACTATTCGACACTTATCA 58.950 41.667 0.00 0.00 0.00 2.15
1985 7959 3.121279 CGACACTTATCAGTTCGTGTTGG 59.879 47.826 0.00 0.00 40.37 3.77
2070 8044 6.488006 GCATTGACCCAGTTATAGATGATGTT 59.512 38.462 0.00 0.00 0.00 2.71
2141 8118 2.178912 TTGGCAGCCTACAACAGTAC 57.821 50.000 14.15 0.00 0.00 2.73
2169 8154 3.282021 GCCAGAATCAATTGGTGAGCTA 58.718 45.455 5.42 0.00 40.43 3.32
2223 8208 3.674138 CGTGGATTTCTGAATTGCCAAGG 60.674 47.826 7.63 0.00 0.00 3.61
2232 8217 2.288948 TGAATTGCCAAGGTCATTGTGC 60.289 45.455 0.00 0.72 37.17 4.57
2256 8241 5.696724 CACTCTTTACCACTTACAGTTCCTG 59.303 44.000 0.00 0.00 37.52 3.86
2266 8251 5.817816 CACTTACAGTTCCTGAAGTTCAGTT 59.182 40.000 27.07 10.42 42.80 3.16
2288 8273 2.689983 ACAAAGTTGAGAGTTTGCCTGG 59.310 45.455 6.62 0.00 45.81 4.45
2335 8326 1.383523 GTATCTGGAAGGGCACAAGC 58.616 55.000 0.00 0.00 41.10 4.01
2339 8330 1.856265 CTGGAAGGGCACAAGCGTTC 61.856 60.000 0.00 0.00 43.41 3.95
2458 14406 2.200081 AGGGATATGAGTTGTGGCAGT 58.800 47.619 0.00 0.00 0.00 4.40
2487 14435 2.032681 AACGAGCTTGGTGGCCTC 59.967 61.111 3.32 0.00 0.00 4.70
2513 14461 6.695292 AAATGTCACGAATCTTGAAAATGC 57.305 33.333 0.00 0.00 0.00 3.56
2559 14507 1.658114 GAACCTGCACCGGAAAACC 59.342 57.895 9.46 0.00 0.00 3.27
2622 14570 5.769662 TGGCATAAATATAGAGGGCAGTTTG 59.230 40.000 0.00 0.00 0.00 2.93
2778 14726 5.625311 GCTTGTTAATTGCACTGTGTTAGAC 59.375 40.000 9.86 2.60 0.00 2.59
2860 14808 4.398319 ACCAAACCTGAAGACATTACCTG 58.602 43.478 0.00 0.00 0.00 4.00
2895 14843 7.500559 GCAGGTCTTAAGGAGTTATCAATTGAT 59.499 37.037 23.75 23.75 38.51 2.57
2949 14897 3.753815 TGAACCAGAACAGCATGATCAA 58.246 40.909 0.00 0.00 40.79 2.57
2950 14898 3.754850 TGAACCAGAACAGCATGATCAAG 59.245 43.478 0.00 0.00 40.79 3.02
2953 14901 2.089201 CAGAACAGCATGATCAAGGCA 58.911 47.619 20.66 0.00 40.79 4.75
3003 14951 7.142306 GGTATCAAACCTTTCTTTGGTAGTC 57.858 40.000 0.00 0.00 45.75 2.59
3007 14955 6.601332 TCAAACCTTTCTTTGGTAGTCTCAT 58.399 36.000 0.00 0.00 36.69 2.90
3008 14956 7.060421 TCAAACCTTTCTTTGGTAGTCTCATT 58.940 34.615 0.00 0.00 36.69 2.57
3036 14995 9.525826 GAGGATTCCATATATGAAACAAAGGAT 57.474 33.333 14.54 0.00 0.00 3.24
3083 15042 2.097954 TCAAGCAATTGATGGCATCGAC 59.902 45.455 19.47 7.56 0.00 4.20
3085 15044 0.657312 GCAATTGATGGCATCGACGA 59.343 50.000 19.47 0.00 0.00 4.20
3102 15061 2.201732 ACGAATGCGGATATGTCACAC 58.798 47.619 0.00 0.00 43.17 3.82
3170 15144 6.196918 AGAGGATAGAATCAATGCATGGAA 57.803 37.500 8.12 0.00 0.00 3.53
3186 15160 1.243902 GGAAATGTTGCCACGAGGAA 58.756 50.000 1.86 0.00 36.89 3.36
3247 15221 2.862541 TGGTTCCACCATCAGAACTTG 58.137 47.619 3.22 0.00 44.79 3.16
3248 15222 2.174639 TGGTTCCACCATCAGAACTTGT 59.825 45.455 3.22 0.00 44.79 3.16
3264 15238 5.237344 AGAACTTGTCCAACTTCATCTTTCG 59.763 40.000 3.40 0.00 0.00 3.46
3341 15315 6.474427 TCACTGACACGTTTGTTCTTAACTAG 59.526 38.462 0.00 0.00 35.47 2.57
3360 15334 6.472686 ACTAGGATCATGACTTTGACTACC 57.527 41.667 0.00 0.00 0.00 3.18
3369 15343 1.622312 ACTTTGACTACCCTTCCGTCC 59.378 52.381 0.00 0.00 0.00 4.79
3370 15344 1.621814 CTTTGACTACCCTTCCGTCCA 59.378 52.381 0.00 0.00 0.00 4.02
3488 17156 7.016296 TCCCTTTTGGAGGTTAGATTGATTTT 58.984 34.615 0.00 0.00 44.71 1.82
3508 17176 3.176924 TCTGCCCTTCTCTAGACTTGT 57.823 47.619 0.00 0.00 0.00 3.16
3521 17189 0.801251 GACTTGTCACATGGAGCAGC 59.199 55.000 0.00 0.00 0.00 5.25
3598 17266 8.037758 CAGATAATTTCTTCAGTACTGACCTGT 58.962 37.037 25.13 10.88 39.66 4.00
3656 17324 1.329906 CTCTGCATCCTTGTCGATTGC 59.670 52.381 0.00 0.00 0.00 3.56
3680 17348 4.262808 CCATCTGACCTCCCTTGTATCATC 60.263 50.000 0.00 0.00 0.00 2.92
3753 17421 6.032094 CCTGCAACTTCATGATGTATGTTTC 58.968 40.000 14.07 2.77 38.01 2.78
3849 17517 1.135489 GTGATGCTCAACCACATGCTG 60.135 52.381 0.00 0.00 0.00 4.41
3866 17534 3.478509 TGCTGTCGGCTAAAGGTTTTAA 58.521 40.909 5.01 0.00 42.39 1.52
3873 17541 5.240183 GTCGGCTAAAGGTTTTAAAGTTCCT 59.760 40.000 3.78 3.78 0.00 3.36
3916 17584 1.401539 GCAAGGAGCAATCCGTTTCAC 60.402 52.381 0.00 0.00 44.79 3.18
3961 17629 0.108186 TGTGCGGTGCCTGAGATTAG 60.108 55.000 0.00 0.00 0.00 1.73
3985 17653 0.036010 CTGCGAAATGAGGTCCCTGT 60.036 55.000 0.00 0.00 0.00 4.00
3986 17654 0.036388 TGCGAAATGAGGTCCCTGTC 60.036 55.000 0.00 0.00 0.00 3.51
3987 17655 0.036388 GCGAAATGAGGTCCCTGTCA 60.036 55.000 0.00 0.00 0.00 3.58
3988 17656 1.726853 CGAAATGAGGTCCCTGTCAC 58.273 55.000 0.00 0.00 0.00 3.67
3989 17657 1.276421 CGAAATGAGGTCCCTGTCACT 59.724 52.381 0.00 0.00 0.00 3.41
3990 17658 2.704572 GAAATGAGGTCCCTGTCACTG 58.295 52.381 0.00 0.00 0.00 3.66
3999 17667 1.071699 TCCCTGTCACTGCCAGTAAAC 59.928 52.381 0.00 0.00 0.00 2.01
4004 17672 2.371841 TGTCACTGCCAGTAAACCTGAT 59.628 45.455 0.00 0.00 44.49 2.90
4015 17683 1.901591 AAACCTGATGTGCCTGTCTG 58.098 50.000 0.00 0.00 0.00 3.51
4032 17700 0.730834 CTGGTCTGACGCGACTTGAG 60.731 60.000 15.93 0.00 34.38 3.02
4033 17701 1.286260 GGTCTGACGCGACTTGAGT 59.714 57.895 15.93 0.00 34.38 3.41
4136 17807 0.037877 AAGGAGAGCTGCAATGCACT 59.962 50.000 2.72 6.94 36.63 4.40
4182 17853 1.801765 GCGAGTATCCGTTGGAAGGAC 60.802 57.143 0.00 0.00 41.10 3.85
4247 17925 8.664669 AATAGAAAGGTAAATGTTCCACCAAT 57.335 30.769 0.00 0.00 34.62 3.16
4270 17948 5.410067 TGCTCTCAAAGAAAACCTTTTGTG 58.590 37.500 0.00 0.00 42.13 3.33
4276 17954 6.337356 TCAAAGAAAACCTTTTGTGGACATC 58.663 36.000 0.00 0.00 42.13 3.06
4384 18063 4.202111 ACGAAGTTTCATTTTCCAACAGGG 60.202 41.667 0.00 0.00 37.78 4.45
4409 18088 5.405935 AAAAAGTGGTTCCTATCCAATGC 57.594 39.130 0.00 0.00 36.68 3.56
4411 18090 1.134098 AGTGGTTCCTATCCAATGCCG 60.134 52.381 0.00 0.00 36.68 5.69
4413 18092 0.472471 GGTTCCTATCCAATGCCGGA 59.528 55.000 5.05 0.00 40.07 5.14
4417 18099 0.758734 CCTATCCAATGCCGGACAGA 59.241 55.000 5.05 0.00 38.07 3.41
4421 18103 0.400213 TCCAATGCCGGACAGAAGTT 59.600 50.000 5.05 0.00 0.00 2.66
4422 18104 1.202879 TCCAATGCCGGACAGAAGTTT 60.203 47.619 5.05 0.00 0.00 2.66
4437 18119 1.878953 AGTTTAGTGTTGGACTGCCG 58.121 50.000 0.00 0.00 35.96 5.69
4439 18121 1.225376 TTTAGTGTTGGACTGCCGCG 61.225 55.000 0.00 0.00 35.96 6.46
4464 18146 7.905493 CGAAGCTCATTTACAATTTAACTCTCC 59.095 37.037 0.00 0.00 0.00 3.71
4465 18147 7.308782 AGCTCATTTACAATTTAACTCTCCG 57.691 36.000 0.00 0.00 0.00 4.63
4468 18150 5.640357 TCATTTACAATTTAACTCTCCGCGT 59.360 36.000 4.92 0.00 0.00 6.01
4474 18156 0.388134 TTAACTCTCCGCGTGCTGTC 60.388 55.000 4.92 0.00 0.00 3.51
4475 18157 1.241990 TAACTCTCCGCGTGCTGTCT 61.242 55.000 4.92 0.00 0.00 3.41
4479 18161 3.558099 CTCCGCGTGCTGTCTGTCA 62.558 63.158 4.92 0.00 0.00 3.58
4480 18162 3.108289 CCGCGTGCTGTCTGTCAG 61.108 66.667 4.92 0.00 46.12 3.51
4487 18169 1.070445 GCTGTCTGTCAGTGGTGCT 59.930 57.895 0.00 0.00 45.23 4.40
4507 18189 2.039613 CTGACCTCTTGGCTCCTTTCTT 59.960 50.000 0.00 0.00 36.63 2.52
4509 18191 2.304470 GACCTCTTGGCTCCTTTCTTCT 59.696 50.000 0.00 0.00 36.63 2.85
4511 18193 3.139211 ACCTCTTGGCTCCTTTCTTCTTT 59.861 43.478 0.00 0.00 36.63 2.52
4516 18198 5.835280 TCTTGGCTCCTTTCTTCTTTGATTT 59.165 36.000 0.00 0.00 0.00 2.17
4520 18202 5.242615 GGCTCCTTTCTTCTTTGATTTCTGT 59.757 40.000 0.00 0.00 0.00 3.41
4521 18203 6.148264 GCTCCTTTCTTCTTTGATTTCTGTG 58.852 40.000 0.00 0.00 0.00 3.66
4522 18204 6.076981 TCCTTTCTTCTTTGATTTCTGTGC 57.923 37.500 0.00 0.00 0.00 4.57
4529 18211 1.155889 TTGATTTCTGTGCGCATCGT 58.844 45.000 15.91 0.00 0.00 3.73
4530 18212 0.721154 TGATTTCTGTGCGCATCGTC 59.279 50.000 15.91 0.00 0.00 4.20
4548 18230 0.832135 TCCTTCCACTCTTGACGGCT 60.832 55.000 0.00 0.00 0.00 5.52
4552 18234 0.904865 TCCACTCTTGACGGCTCCAT 60.905 55.000 0.00 0.00 0.00 3.41
4556 18238 1.207329 ACTCTTGACGGCTCCATTACC 59.793 52.381 0.00 0.00 0.00 2.85
4568 18250 1.831106 TCCATTACCGTGCTGAGACAT 59.169 47.619 0.00 0.00 0.00 3.06
4572 18254 0.389817 TACCGTGCTGAGACATGTGC 60.390 55.000 1.15 0.00 0.00 4.57
4579 18261 2.288763 TGCTGAGACATGTGCGTCTAAA 60.289 45.455 1.15 0.00 46.26 1.85
4588 18270 3.899835 TGTGCGTCTAAATTCGAATCG 57.100 42.857 11.83 11.20 0.00 3.34
4591 18273 2.028763 TGCGTCTAAATTCGAATCGTGC 59.971 45.455 11.83 10.31 0.00 5.34
4598 18280 4.458951 AAATTCGAATCGTGCTCTATGC 57.541 40.909 11.83 0.00 43.25 3.14
4603 18285 2.034254 CGAATCGTGCTCTATGCTGTTG 60.034 50.000 0.00 0.00 43.37 3.33
4614 18319 5.625311 GCTCTATGCTGTTGTGTTTTGTTAC 59.375 40.000 0.00 0.00 38.95 2.50
4620 18325 4.420168 CTGTTGTGTTTTGTTACCCTGTG 58.580 43.478 0.00 0.00 0.00 3.66
4648 18355 6.200854 GGAGTGTTACTTTTGATTTTGCTTGG 59.799 38.462 0.00 0.00 0.00 3.61
4659 18366 0.746063 TTTGCTTGGTGCTGGACTTG 59.254 50.000 0.00 0.00 43.37 3.16
4660 18367 1.108727 TTGCTTGGTGCTGGACTTGG 61.109 55.000 0.00 0.00 43.37 3.61
4661 18368 2.270986 GCTTGGTGCTGGACTTGGG 61.271 63.158 0.00 0.00 38.95 4.12
4662 18369 1.604593 CTTGGTGCTGGACTTGGGG 60.605 63.158 0.00 0.00 0.00 4.96
4663 18370 2.357593 CTTGGTGCTGGACTTGGGGT 62.358 60.000 0.00 0.00 0.00 4.95
4664 18371 1.943730 TTGGTGCTGGACTTGGGGTT 61.944 55.000 0.00 0.00 0.00 4.11
4665 18372 1.903404 GGTGCTGGACTTGGGGTTG 60.903 63.158 0.00 0.00 0.00 3.77
4668 18375 1.150536 GCTGGACTTGGGGTTGTGA 59.849 57.895 0.00 0.00 0.00 3.58
4669 18376 0.251341 GCTGGACTTGGGGTTGTGAT 60.251 55.000 0.00 0.00 0.00 3.06
4670 18377 1.538047 CTGGACTTGGGGTTGTGATG 58.462 55.000 0.00 0.00 0.00 3.07
4671 18378 0.850100 TGGACTTGGGGTTGTGATGT 59.150 50.000 0.00 0.00 0.00 3.06
4672 18379 2.039746 CTGGACTTGGGGTTGTGATGTA 59.960 50.000 0.00 0.00 0.00 2.29
4673 18380 2.224670 TGGACTTGGGGTTGTGATGTAC 60.225 50.000 0.00 0.00 0.00 2.90
4674 18381 2.039879 GGACTTGGGGTTGTGATGTACT 59.960 50.000 0.00 0.00 0.00 2.73
4675 18382 3.497942 GGACTTGGGGTTGTGATGTACTT 60.498 47.826 0.00 0.00 0.00 2.24
4676 18383 3.751518 ACTTGGGGTTGTGATGTACTTC 58.248 45.455 1.85 1.85 0.00 3.01
4678 18385 3.866703 TGGGGTTGTGATGTACTTCAA 57.133 42.857 12.62 2.17 0.00 2.69
4679 18386 4.380843 TGGGGTTGTGATGTACTTCAAT 57.619 40.909 12.62 0.00 0.00 2.57
4680 18387 5.506730 TGGGGTTGTGATGTACTTCAATA 57.493 39.130 12.62 3.46 0.00 1.90
4681 18388 6.073447 TGGGGTTGTGATGTACTTCAATAT 57.927 37.500 12.62 0.00 0.00 1.28
4684 18391 6.483640 GGGGTTGTGATGTACTTCAATATCTC 59.516 42.308 12.62 1.73 0.00 2.75
4685 18392 7.047891 GGGTTGTGATGTACTTCAATATCTCA 58.952 38.462 12.62 3.70 0.00 3.27
4688 18395 8.935844 GTTGTGATGTACTTCAATATCTCACAA 58.064 33.333 12.62 9.89 45.13 3.33
4692 18693 9.371136 TGATGTACTTCAATATCTCACAACTTC 57.629 33.333 8.89 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 83 1.137513 CAGTCGAAAGAACACCGGAC 58.862 55.000 9.46 0.00 45.01 4.79
73 89 3.269538 TGGGAAACAGTCGAAAGAACA 57.730 42.857 0.00 0.00 45.01 3.18
82 98 4.130118 CTGGCATACTATGGGAAACAGTC 58.870 47.826 0.00 0.00 0.00 3.51
83 99 3.523564 ACTGGCATACTATGGGAAACAGT 59.476 43.478 0.00 0.00 32.37 3.55
93 109 9.474313 TTTGGAAGATTTTAACTGGCATACTAT 57.526 29.630 0.00 0.00 0.00 2.12
95 111 7.451566 ACTTTGGAAGATTTTAACTGGCATACT 59.548 33.333 0.00 0.00 0.00 2.12
96 112 7.602753 ACTTTGGAAGATTTTAACTGGCATAC 58.397 34.615 0.00 0.00 0.00 2.39
98 114 6.670695 ACTTTGGAAGATTTTAACTGGCAT 57.329 33.333 0.00 0.00 0.00 4.40
136 301 8.478877 CAGGAATCTTAGGTGTAGTGTAAAGAT 58.521 37.037 0.00 0.00 35.71 2.40
142 307 3.838317 TGCAGGAATCTTAGGTGTAGTGT 59.162 43.478 0.00 0.00 0.00 3.55
143 308 4.471904 TGCAGGAATCTTAGGTGTAGTG 57.528 45.455 0.00 0.00 0.00 2.74
144 309 4.101741 GGATGCAGGAATCTTAGGTGTAGT 59.898 45.833 0.00 0.00 0.00 2.73
145 310 4.346418 AGGATGCAGGAATCTTAGGTGTAG 59.654 45.833 0.00 0.00 0.00 2.74
146 311 4.298626 AGGATGCAGGAATCTTAGGTGTA 58.701 43.478 0.00 0.00 0.00 2.90
147 312 3.118531 AGGATGCAGGAATCTTAGGTGT 58.881 45.455 0.00 0.00 0.00 4.16
148 313 3.135348 TGAGGATGCAGGAATCTTAGGTG 59.865 47.826 0.00 0.00 0.00 4.00
149 314 3.387962 TGAGGATGCAGGAATCTTAGGT 58.612 45.455 0.00 0.00 0.00 3.08
150 315 4.428294 TTGAGGATGCAGGAATCTTAGG 57.572 45.455 0.00 0.00 0.00 2.69
151 316 6.956202 ATTTTGAGGATGCAGGAATCTTAG 57.044 37.500 0.00 0.00 0.00 2.18
152 317 9.071276 GATAATTTTGAGGATGCAGGAATCTTA 57.929 33.333 0.00 0.00 0.00 2.10
153 318 7.783596 AGATAATTTTGAGGATGCAGGAATCTT 59.216 33.333 0.00 0.00 0.00 2.40
154 319 7.230913 CAGATAATTTTGAGGATGCAGGAATCT 59.769 37.037 0.00 0.00 0.00 2.40
155 320 7.230108 TCAGATAATTTTGAGGATGCAGGAATC 59.770 37.037 0.00 0.00 0.00 2.52
156 321 7.064866 TCAGATAATTTTGAGGATGCAGGAAT 58.935 34.615 0.00 0.00 0.00 3.01
157 322 6.425735 TCAGATAATTTTGAGGATGCAGGAA 58.574 36.000 0.00 0.00 0.00 3.36
158 323 6.005066 TCAGATAATTTTGAGGATGCAGGA 57.995 37.500 0.00 0.00 0.00 3.86
159 324 6.704289 TTCAGATAATTTTGAGGATGCAGG 57.296 37.500 0.00 0.00 0.00 4.85
160 325 7.222224 GCTTTTCAGATAATTTTGAGGATGCAG 59.778 37.037 0.00 0.00 0.00 4.41
161 326 7.037438 GCTTTTCAGATAATTTTGAGGATGCA 58.963 34.615 0.00 0.00 0.00 3.96
162 327 7.037438 TGCTTTTCAGATAATTTTGAGGATGC 58.963 34.615 0.00 0.00 0.00 3.91
163 328 9.245962 GATGCTTTTCAGATAATTTTGAGGATG 57.754 33.333 0.00 0.00 0.00 3.51
164 329 8.419442 GGATGCTTTTCAGATAATTTTGAGGAT 58.581 33.333 0.00 0.00 0.00 3.24
165 330 7.147846 GGGATGCTTTTCAGATAATTTTGAGGA 60.148 37.037 0.00 0.00 0.00 3.71
166 331 6.982724 GGGATGCTTTTCAGATAATTTTGAGG 59.017 38.462 0.00 0.00 0.00 3.86
167 332 7.549839 TGGGATGCTTTTCAGATAATTTTGAG 58.450 34.615 0.00 0.00 0.00 3.02
168 333 7.479352 TGGGATGCTTTTCAGATAATTTTGA 57.521 32.000 0.00 0.00 0.00 2.69
169 334 8.550710 TTTGGGATGCTTTTCAGATAATTTTG 57.449 30.769 0.00 0.00 0.00 2.44
170 335 9.571816 TTTTTGGGATGCTTTTCAGATAATTTT 57.428 25.926 0.00 0.00 0.00 1.82
213 378 6.051717 CAGGTAATAGAATTCCAGACACAGG 58.948 44.000 0.65 0.00 0.00 4.00
218 383 7.110155 TGGAAACAGGTAATAGAATTCCAGAC 58.890 38.462 0.65 0.00 39.75 3.51
221 386 7.282224 CGATTGGAAACAGGTAATAGAATTCCA 59.718 37.037 0.65 0.00 44.54 3.53
225 390 6.357367 AGCGATTGGAAACAGGTAATAGAAT 58.643 36.000 0.00 0.00 44.54 2.40
230 395 3.119495 GCAAGCGATTGGAAACAGGTAAT 60.119 43.478 16.16 0.00 44.54 1.89
244 409 4.458989 TGGAAGAATTTAACTGCAAGCGAT 59.541 37.500 0.00 0.00 37.60 4.58
245 410 3.818210 TGGAAGAATTTAACTGCAAGCGA 59.182 39.130 0.00 0.00 37.60 4.93
246 411 4.159377 TGGAAGAATTTAACTGCAAGCG 57.841 40.909 0.00 0.00 37.60 4.68
247 412 6.215845 TCTTTGGAAGAATTTAACTGCAAGC 58.784 36.000 0.00 0.00 33.01 4.01
248 413 8.822652 AATCTTTGGAAGAATTTAACTGCAAG 57.177 30.769 0.00 0.00 41.63 4.01
250 415 7.233348 AGGAATCTTTGGAAGAATTTAACTGCA 59.767 33.333 0.00 0.00 41.63 4.41
260 425 6.183360 ACAAAATGCAGGAATCTTTGGAAGAA 60.183 34.615 0.00 0.00 41.63 2.52
271 436 6.815089 TGTAAAAGACACAAAATGCAGGAAT 58.185 32.000 0.00 0.00 31.20 3.01
299 464 3.145286 GAGAATGCAGGAATCTTAGGCC 58.855 50.000 0.00 0.00 0.00 5.19
309 474 5.255687 TCAGCTAATTTTGAGAATGCAGGA 58.744 37.500 0.00 0.00 0.00 3.86
311 476 7.411588 GCTTTTCAGCTAATTTTGAGAATGCAG 60.412 37.037 0.00 0.00 43.51 4.41
350 520 1.452651 CCGCCATGGAATCACTGCT 60.453 57.895 18.40 0.00 42.00 4.24
351 521 1.451927 TCCGCCATGGAATCACTGC 60.452 57.895 18.40 0.00 46.38 4.40
352 522 4.961637 TCCGCCATGGAATCACTG 57.038 55.556 18.40 0.00 46.38 3.66
502 672 2.014857 GCTGCTTCAATCATCAGCTCA 58.985 47.619 5.89 0.00 46.00 4.26
781 967 3.878160 AGAAGATCACGGAACTCCTTC 57.122 47.619 0.00 0.00 0.00 3.46
834 6762 1.266718 CAACGGCTGCTTGTACAACAT 59.733 47.619 3.59 0.00 0.00 2.71
1245 7178 4.458397 TCATCTCATTGCCAGATTCTTCC 58.542 43.478 0.00 0.00 0.00 3.46
1463 7411 5.005875 GCAATCTCTTCTAGTTTCTTACGCC 59.994 44.000 0.00 0.00 0.00 5.68
1468 7416 7.238486 TCTCTGCAATCTCTTCTAGTTTCTT 57.762 36.000 0.00 0.00 0.00 2.52
1473 7421 4.711355 AGCTTCTCTGCAATCTCTTCTAGT 59.289 41.667 0.00 0.00 34.99 2.57
1532 7480 4.742274 ACTGCGAACGCACAGTTA 57.258 50.000 17.70 0.00 44.59 2.24
1540 7488 2.060326 TTCCTACTCAACTGCGAACG 57.940 50.000 0.00 0.00 0.00 3.95
1554 7502 6.619437 TCCATGGAGTGATATCCTTTTTCCTA 59.381 38.462 11.44 0.00 40.29 2.94
1594 7560 3.751698 GTGGGATCACTTAAGTTGTCCAC 59.248 47.826 26.01 23.59 40.58 4.02
1650 7616 4.509756 CATCTCTGCAGACGTGGG 57.490 61.111 13.74 2.51 0.00 4.61
1698 7664 6.014242 CCAACTCCCTGATGTTATAGCTATGA 60.014 42.308 16.77 5.16 0.00 2.15
1759 7725 2.287009 CCACTCTTTTGTTCTCGTTGCC 60.287 50.000 0.00 0.00 0.00 4.52
1787 7753 0.779997 ACTGAAGCAACCCCTTCCAT 59.220 50.000 0.00 0.00 40.34 3.41
1796 7762 2.999355 GAGACCATCTCACTGAAGCAAC 59.001 50.000 0.87 0.00 42.90 4.17
1937 7909 0.238289 GCATGGTATTTCCGCCATCG 59.762 55.000 0.00 0.00 43.05 3.84
1944 7916 4.814234 TGTCGAATAGTGCATGGTATTTCC 59.186 41.667 0.00 0.00 0.00 3.13
1974 7948 4.464951 TGTATCATACTCCCAACACGAACT 59.535 41.667 0.00 0.00 0.00 3.01
1985 7959 7.388776 TGCTTTGCTTATGATGTATCATACTCC 59.611 37.037 12.78 6.43 46.28 3.85
2070 8044 9.665719 TGCAGTATCAGATTAAAAACATCACTA 57.334 29.630 0.00 0.00 0.00 2.74
2087 8061 5.617529 CGCAACTTTGAATTCTGCAGTATCA 60.618 40.000 14.67 13.38 33.19 2.15
2103 8080 5.413213 TGCCAAATATAGTACACGCAACTTT 59.587 36.000 0.00 0.00 0.00 2.66
2141 8118 3.007182 ACCAATTGATTCTGGCAACTTGG 59.993 43.478 7.12 0.70 38.46 3.61
2223 8208 3.815401 AGTGGTAAAGAGTGCACAATGAC 59.185 43.478 21.04 9.77 0.00 3.06
2256 8241 7.541122 ACTCTCAACTTTGTAACTGAACTTC 57.459 36.000 0.00 0.00 0.00 3.01
2266 8251 3.882888 CCAGGCAAACTCTCAACTTTGTA 59.117 43.478 0.00 0.00 31.20 2.41
2301 8286 7.549488 CCTTCCAGATACCACAACTTACTTAAG 59.451 40.741 0.00 0.00 39.18 1.85
2322 8307 0.321298 TAGAACGCTTGTGCCCTTCC 60.321 55.000 0.00 0.00 35.36 3.46
2335 8326 7.713764 TGTTGTATGGATCATGAATAGAACG 57.286 36.000 15.61 0.00 34.47 3.95
2339 8330 8.107399 AGCATTGTTGTATGGATCATGAATAG 57.893 34.615 0.00 0.00 0.00 1.73
2388 8382 2.846193 TGTTGGAGCGAAGTTAGCTTT 58.154 42.857 12.01 0.00 46.13 3.51
2427 14375 5.441718 ACTCATATCCCTTCTGCTTTTGA 57.558 39.130 0.00 0.00 0.00 2.69
2458 14406 0.976641 AGCTCGTTCATGTCCCTCAA 59.023 50.000 0.00 0.00 0.00 3.02
2487 14435 8.368126 GCATTTTCAAGATTCGTGACATTTAAG 58.632 33.333 1.54 0.00 0.00 1.85
2513 14461 0.825010 AGCTTCACCCTTTGCAGTGG 60.825 55.000 4.21 2.41 34.67 4.00
2525 14473 3.675698 CAGGTTCGACTCTAAAGCTTCAC 59.324 47.826 0.00 0.00 31.20 3.18
2559 14507 1.891150 AGGTGCAAGCTTTCAAGATGG 59.109 47.619 0.00 0.00 46.63 3.51
2615 14563 2.555757 AGAATCTCCAAGTGCAAACTGC 59.444 45.455 0.00 0.00 45.29 4.40
2622 14570 2.363683 CCTTCCAGAATCTCCAAGTGC 58.636 52.381 0.00 0.00 0.00 4.40
2655 14603 0.118346 TGAGGCCCCTAAGTTGAGGA 59.882 55.000 0.00 0.00 39.15 3.71
2748 14696 4.022329 ACAGTGCAATTAACAAGCCTAACC 60.022 41.667 0.00 0.00 0.00 2.85
2749 14697 4.917415 CACAGTGCAATTAACAAGCCTAAC 59.083 41.667 0.00 0.00 0.00 2.34
2778 14726 2.414785 GGCATTGGTTGGTAGGCCG 61.415 63.158 0.00 0.00 37.67 6.13
2827 14775 6.262273 GTCTTCAGGTTTGGTACATTCTTGAA 59.738 38.462 0.00 0.41 39.30 2.69
2838 14786 4.398319 CAGGTAATGTCTTCAGGTTTGGT 58.602 43.478 0.00 0.00 0.00 3.67
2949 14897 2.306805 TGTCCTCATGATGTTCTTGCCT 59.693 45.455 0.00 0.00 0.00 4.75
2950 14898 2.681848 CTGTCCTCATGATGTTCTTGCC 59.318 50.000 0.00 0.00 0.00 4.52
2953 14901 3.584406 TGGTCTGTCCTCATGATGTTCTT 59.416 43.478 0.00 0.00 37.07 2.52
3008 14956 9.135189 CCTTTGTTTCATATATGGAATCCTCAA 57.865 33.333 9.70 6.57 0.00 3.02
3055 15014 3.380637 GCCATCAATTGCTTGAGAGATGT 59.619 43.478 0.00 0.00 44.32 3.06
3063 15022 2.456989 GTCGATGCCATCAATTGCTTG 58.543 47.619 5.40 0.92 0.00 4.01
3083 15042 1.190103 CGTGTGACATATCCGCATTCG 59.810 52.381 0.00 0.00 0.00 3.34
3085 15044 2.309528 ACGTGTGACATATCCGCATT 57.690 45.000 0.00 0.00 0.00 3.56
3102 15061 4.511826 AGAGCACTTCTAAGGTTTTCAACG 59.488 41.667 0.00 0.00 33.23 4.10
3186 15160 4.471904 TGCGTAAATGAGTCTCATCCTT 57.528 40.909 15.75 9.93 35.76 3.36
3247 15221 4.670221 GCATGACGAAAGATGAAGTTGGAC 60.670 45.833 0.00 0.00 0.00 4.02
3248 15222 3.436704 GCATGACGAAAGATGAAGTTGGA 59.563 43.478 0.00 0.00 0.00 3.53
3264 15238 4.450419 GCCTCATCTGTAATACTGCATGAC 59.550 45.833 0.00 0.00 0.00 3.06
3341 15315 4.762289 AGGGTAGTCAAAGTCATGATCC 57.238 45.455 0.00 0.00 0.00 3.36
3360 15334 0.036294 GGACCTCTTTGGACGGAAGG 60.036 60.000 0.00 0.00 39.71 3.46
3369 15343 4.022849 GTCAAATGTTGGAGGACCTCTTTG 60.023 45.833 20.97 20.28 37.04 2.77
3370 15344 4.145052 GTCAAATGTTGGAGGACCTCTTT 58.855 43.478 20.97 10.26 37.04 2.52
3433 15407 1.487558 TCGTAAGCCCCCTAATGAACC 59.512 52.381 0.00 0.00 37.18 3.62
3435 15409 1.140252 GCTCGTAAGCCCCCTAATGAA 59.860 52.381 0.00 0.00 43.10 2.57
3488 17156 3.093057 GACAAGTCTAGAGAAGGGCAGA 58.907 50.000 0.00 0.00 0.00 4.26
3508 17176 2.089201 CATTTCAGCTGCTCCATGTGA 58.911 47.619 9.47 0.00 0.00 3.58
3521 17189 6.688637 TCTCAACAGATAATGGCATTTCAG 57.311 37.500 19.21 13.81 0.00 3.02
3560 17228 3.829886 AATTATCTGCAACCACACACG 57.170 42.857 0.00 0.00 0.00 4.49
3598 17266 1.480954 GGAAAGGTCTATCAGGTGCGA 59.519 52.381 0.00 0.00 0.00 5.10
3656 17324 1.879575 TACAAGGGAGGTCAGATGGG 58.120 55.000 0.00 0.00 0.00 4.00
3680 17348 5.946972 AGATCCGGGAGATGTAGTAGTATTG 59.053 44.000 0.00 0.00 34.42 1.90
3753 17421 3.256383 TGTTGAGCTTTGGGACATCAATG 59.744 43.478 0.00 0.00 39.30 2.82
3849 17517 5.240183 AGGAACTTTAAAACCTTTAGCCGAC 59.760 40.000 3.40 0.00 27.25 4.79
3873 17541 2.628178 TCCTTCAAGAGCGAGAGTTTCA 59.372 45.455 0.00 0.00 0.00 2.69
3905 17573 4.627467 CAGATTCTTCGAGTGAAACGGATT 59.373 41.667 6.95 0.00 45.86 3.01
3916 17584 6.174451 TGAGAAATTTGCAGATTCTTCGAG 57.826 37.500 2.51 0.00 33.73 4.04
3961 17629 1.079503 GACCTCATTTCGCAGTCACC 58.920 55.000 0.00 0.00 0.00 4.02
3999 17667 0.392193 GACCAGACAGGCACATCAGG 60.392 60.000 0.00 0.00 43.14 3.86
4004 17672 1.748403 GTCAGACCAGACAGGCACA 59.252 57.895 0.00 0.00 43.14 4.57
4015 17683 0.318784 AACTCAAGTCGCGTCAGACC 60.319 55.000 5.77 0.00 41.83 3.85
4032 17700 1.363807 GTTGGGGCAGTTGCAGAAC 59.636 57.895 6.43 2.04 44.36 3.01
4033 17701 0.469705 ATGTTGGGGCAGTTGCAGAA 60.470 50.000 6.43 0.00 44.36 3.02
4136 17807 0.405198 TGGCCAGCTTTCTCCATCAA 59.595 50.000 0.00 0.00 0.00 2.57
4182 17853 7.612668 ATCTGAAATCACAGTTCATCTGAAG 57.387 36.000 1.79 0.00 46.27 3.02
4247 17925 5.410067 CACAAAAGGTTTTCTTTGAGAGCA 58.590 37.500 1.80 0.00 44.30 4.26
4334 18012 1.098050 AGCCTGCATCCGAATTGAAC 58.902 50.000 0.00 0.00 0.00 3.18
4337 18015 1.731433 CCCAGCCTGCATCCGAATTG 61.731 60.000 0.00 0.00 0.00 2.32
4392 18071 1.308998 CGGCATTGGATAGGAACCAC 58.691 55.000 0.00 0.00 37.13 4.16
4393 18072 0.182537 CCGGCATTGGATAGGAACCA 59.817 55.000 0.00 0.00 35.47 3.67
4397 18076 0.758734 CTGTCCGGCATTGGATAGGA 59.241 55.000 0.00 0.00 41.95 2.94
4398 18077 0.758734 TCTGTCCGGCATTGGATAGG 59.241 55.000 13.21 1.18 44.76 2.57
4400 18079 1.837439 ACTTCTGTCCGGCATTGGATA 59.163 47.619 0.00 0.00 40.91 2.59
4401 18080 0.620556 ACTTCTGTCCGGCATTGGAT 59.379 50.000 0.00 0.00 40.91 3.41
4402 18081 0.400213 AACTTCTGTCCGGCATTGGA 59.600 50.000 0.00 0.00 35.04 3.53
4403 18082 1.247567 AAACTTCTGTCCGGCATTGG 58.752 50.000 0.00 0.00 0.00 3.16
4404 18083 3.074412 ACTAAACTTCTGTCCGGCATTG 58.926 45.455 0.00 0.00 0.00 2.82
4405 18084 3.074412 CACTAAACTTCTGTCCGGCATT 58.926 45.455 0.00 0.00 0.00 3.56
4406 18085 2.038557 ACACTAAACTTCTGTCCGGCAT 59.961 45.455 0.00 0.00 0.00 4.40
4407 18086 1.414919 ACACTAAACTTCTGTCCGGCA 59.585 47.619 0.00 0.00 0.00 5.69
4408 18087 2.165319 ACACTAAACTTCTGTCCGGC 57.835 50.000 0.00 0.00 0.00 6.13
4409 18088 2.806244 CCAACACTAAACTTCTGTCCGG 59.194 50.000 0.00 0.00 0.00 5.14
4411 18090 4.511826 CAGTCCAACACTAAACTTCTGTCC 59.488 45.833 0.00 0.00 32.21 4.02
4413 18092 3.877508 GCAGTCCAACACTAAACTTCTGT 59.122 43.478 0.00 0.00 32.21 3.41
4417 18099 2.218603 CGGCAGTCCAACACTAAACTT 58.781 47.619 0.00 0.00 32.21 2.66
4421 18103 1.666553 CGCGGCAGTCCAACACTAA 60.667 57.895 0.00 0.00 32.21 2.24
4422 18104 2.048597 CGCGGCAGTCCAACACTA 60.049 61.111 0.00 0.00 32.21 2.74
4437 18119 7.244192 AGAGTTAAATTGTAAATGAGCTTCGC 58.756 34.615 0.00 0.00 0.00 4.70
4439 18121 7.905493 CGGAGAGTTAAATTGTAAATGAGCTTC 59.095 37.037 0.00 0.00 0.00 3.86
4447 18129 4.377635 GCACGCGGAGAGTTAAATTGTAAA 60.378 41.667 12.47 0.00 39.58 2.01
4453 18135 1.337823 ACAGCACGCGGAGAGTTAAAT 60.338 47.619 12.47 0.00 39.58 1.40
4456 18138 1.211969 GACAGCACGCGGAGAGTTA 59.788 57.895 12.47 0.00 39.58 2.24
4479 18161 1.757306 CCAAGAGGTCAGCACCACT 59.243 57.895 0.00 0.00 46.68 4.00
4480 18162 1.968540 GCCAAGAGGTCAGCACCAC 60.969 63.158 0.00 0.00 46.68 4.16
4487 18169 1.734655 AGAAAGGAGCCAAGAGGTCA 58.265 50.000 0.00 0.00 45.21 4.02
4492 18174 4.437682 TCAAAGAAGAAAGGAGCCAAGA 57.562 40.909 0.00 0.00 0.00 3.02
4507 18189 2.159667 CGATGCGCACAGAAATCAAAGA 60.160 45.455 14.90 0.00 0.00 2.52
4509 18191 1.535028 ACGATGCGCACAGAAATCAAA 59.465 42.857 14.90 0.00 0.00 2.69
4511 18193 0.721154 GACGATGCGCACAGAAATCA 59.279 50.000 14.90 0.00 0.00 2.57
4516 18198 1.446099 GAAGGACGATGCGCACAGA 60.446 57.895 14.90 0.00 0.00 3.41
4520 18202 2.434185 GTGGAAGGACGATGCGCA 60.434 61.111 14.96 14.96 0.00 6.09
4521 18203 2.125512 AGTGGAAGGACGATGCGC 60.126 61.111 0.00 0.00 0.00 6.09
4522 18204 0.108615 AAGAGTGGAAGGACGATGCG 60.109 55.000 0.00 0.00 0.00 4.73
4529 18211 0.832135 AGCCGTCAAGAGTGGAAGGA 60.832 55.000 0.00 0.00 36.19 3.36
4530 18212 0.390472 GAGCCGTCAAGAGTGGAAGG 60.390 60.000 0.00 0.00 37.04 3.46
4548 18230 1.262417 TGTCTCAGCACGGTAATGGA 58.738 50.000 0.00 0.00 0.00 3.41
4552 18234 1.939381 GCACATGTCTCAGCACGGTAA 60.939 52.381 0.00 0.00 0.00 2.85
4556 18238 1.949015 GACGCACATGTCTCAGCACG 61.949 60.000 0.00 0.00 35.95 5.34
4568 18250 3.060230 CACGATTCGAATTTAGACGCACA 59.940 43.478 12.81 0.00 0.00 4.57
4572 18254 3.791887 AGAGCACGATTCGAATTTAGACG 59.208 43.478 12.81 12.85 0.00 4.18
4591 18273 6.142817 GGTAACAAAACACAACAGCATAGAG 58.857 40.000 0.00 0.00 0.00 2.43
4598 18280 4.082463 ACACAGGGTAACAAAACACAACAG 60.082 41.667 0.00 0.00 39.74 3.16
4603 18285 3.444388 TCCAACACAGGGTAACAAAACAC 59.556 43.478 0.00 0.00 39.74 3.32
4614 18319 2.930826 AGTAACACTCCAACACAGGG 57.069 50.000 0.00 0.00 0.00 4.45
4620 18325 6.756542 AGCAAAATCAAAAGTAACACTCCAAC 59.243 34.615 0.00 0.00 0.00 3.77
4648 18355 1.152756 ACAACCCCAAGTCCAGCAC 60.153 57.895 0.00 0.00 0.00 4.40
4659 18366 6.357367 AGATATTGAAGTACATCACAACCCC 58.643 40.000 0.00 0.00 0.00 4.95
4660 18367 7.011482 GTGAGATATTGAAGTACATCACAACCC 59.989 40.741 0.00 0.00 36.64 4.11
4661 18368 7.549134 TGTGAGATATTGAAGTACATCACAACC 59.451 37.037 0.00 0.00 41.86 3.77
4662 18369 8.479313 TGTGAGATATTGAAGTACATCACAAC 57.521 34.615 0.00 0.00 41.86 3.32
4664 18371 8.314021 AGTTGTGAGATATTGAAGTACATCACA 58.686 33.333 0.00 0.00 42.78 3.58
4665 18372 8.709386 AGTTGTGAGATATTGAAGTACATCAC 57.291 34.615 0.00 0.00 37.05 3.06
4668 18375 9.376075 CAGAAGTTGTGAGATATTGAAGTACAT 57.624 33.333 0.00 0.00 0.00 2.29
4669 18376 7.819415 CCAGAAGTTGTGAGATATTGAAGTACA 59.181 37.037 0.68 0.00 0.00 2.90
4670 18377 8.035394 TCCAGAAGTTGTGAGATATTGAAGTAC 58.965 37.037 0.68 0.00 0.00 2.73
4671 18378 8.134202 TCCAGAAGTTGTGAGATATTGAAGTA 57.866 34.615 0.68 0.00 0.00 2.24
4672 18379 7.009179 TCCAGAAGTTGTGAGATATTGAAGT 57.991 36.000 0.68 0.00 0.00 3.01
4673 18380 6.538021 CCTCCAGAAGTTGTGAGATATTGAAG 59.462 42.308 0.68 0.00 0.00 3.02
4674 18381 6.409704 CCTCCAGAAGTTGTGAGATATTGAA 58.590 40.000 0.68 0.00 0.00 2.69
4675 18382 5.104776 CCCTCCAGAAGTTGTGAGATATTGA 60.105 44.000 0.68 0.00 0.00 2.57
4676 18383 5.121811 CCCTCCAGAAGTTGTGAGATATTG 58.878 45.833 0.68 0.00 0.00 1.90
4678 18385 3.135530 GCCCTCCAGAAGTTGTGAGATAT 59.864 47.826 0.68 0.00 0.00 1.63
4679 18386 2.501723 GCCCTCCAGAAGTTGTGAGATA 59.498 50.000 0.68 0.00 0.00 1.98
4680 18387 1.280421 GCCCTCCAGAAGTTGTGAGAT 59.720 52.381 0.68 0.00 0.00 2.75
4681 18388 0.687354 GCCCTCCAGAAGTTGTGAGA 59.313 55.000 0.68 0.00 0.00 3.27
4684 18391 2.704572 CTTAGCCCTCCAGAAGTTGTG 58.295 52.381 0.00 0.00 0.00 3.33
4685 18392 1.003696 GCTTAGCCCTCCAGAAGTTGT 59.996 52.381 0.00 0.00 0.00 3.32
4688 18395 2.302019 GGCTTAGCCCTCCAGAAGT 58.698 57.895 13.12 0.00 44.06 3.01


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

AutoCloner maintained by Alex Coulton.