Multiple sequence alignment - TraesCS3B01G571200

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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 TraesCS3B01G571200 chr3B 100.000 2748 0 0 1 2748 802922550 802919803 0.000000e+00 5075.0
1 TraesCS3B01G571200 chr3B 91.857 1228 59 22 932 2128 802902696 802901479 0.000000e+00 1676.0
2 TraesCS3B01G571200 chr3B 90.672 536 38 7 1602 2128 802993269 802992737 0.000000e+00 702.0
3 TraesCS3B01G571200 chr3B 88.587 552 45 10 1603 2139 802965263 802965811 0.000000e+00 654.0
4 TraesCS3B01G571200 chr3B 88.868 530 49 9 654 1174 802994244 802993716 0.000000e+00 643.0
5 TraesCS3B01G571200 chr3B 89.899 396 33 3 1187 1577 802993654 802993261 1.140000e-138 503.0
6 TraesCS3B01G571200 chr3B 80.727 550 78 15 291 824 803002400 803002937 1.190000e-108 403.0
7 TraesCS3B01G571200 chr3B 87.831 189 21 2 965 1152 802996530 802996343 1.280000e-53 220.0
8 TraesCS3B01G571200 chr3B 80.586 273 50 2 1047 1319 775562788 775562519 9.970000e-50 207.0
9 TraesCS3B01G571200 chr3B 80.176 227 35 7 1045 1266 779303188 779303409 7.880000e-36 161.0
10 TraesCS3B01G571200 chr3B 81.443 194 35 1 2555 2748 802966433 802966625 1.020000e-34 158.0
11 TraesCS3B01G571200 chr3B 81.152 191 31 3 1048 1237 779307802 779307616 6.130000e-32 148.0
12 TraesCS3B01G571200 chr3B 92.857 70 5 0 1 70 498454325 498454394 4.840000e-18 102.0
13 TraesCS3B01G571200 chr3D 90.476 462 39 2 1345 1806 596886069 596885613 3.030000e-169 604.0
14 TraesCS3B01G571200 chr3D 89.831 413 39 3 936 1345 596886611 596886199 6.740000e-146 527.0
15 TraesCS3B01G571200 chr3D 82.306 373 58 7 938 1306 596896345 596896713 1.590000e-82 316.0
16 TraesCS3B01G571200 chr3A 80.952 273 49 2 1047 1319 715594814 715594545 2.140000e-51 213.0
17 TraesCS3B01G571200 chr4A 82.645 121 21 0 1117 1237 659460305 659460425 1.040000e-19 108.0
18 TraesCS3B01G571200 chr4D 90.769 65 6 0 6 70 292907346 292907282 1.360000e-13 87.9


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 TraesCS3B01G571200 chr3B 802919803 802922550 2747 True 5075.0 5075 100.0000 1 2748 1 chr3B.!!$R4 2747
1 TraesCS3B01G571200 chr3B 802901479 802902696 1217 True 1676.0 1676 91.8570 932 2128 1 chr3B.!!$R3 1196
2 TraesCS3B01G571200 chr3B 802992737 802996530 3793 True 517.0 702 89.3175 654 2128 4 chr3B.!!$R5 1474
3 TraesCS3B01G571200 chr3B 802965263 802966625 1362 False 406.0 654 85.0150 1603 2748 2 chr3B.!!$F4 1145
4 TraesCS3B01G571200 chr3B 803002400 803002937 537 False 403.0 403 80.7270 291 824 1 chr3B.!!$F3 533
5 TraesCS3B01G571200 chr3D 596885613 596886611 998 True 565.5 604 90.1535 936 1806 2 chr3D.!!$R1 870

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
221 222 0.039618 ACATGGGGTAGGCCAAAGTG 59.96 55.0 5.01 0.0 36.17 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1971 3829 0.035056 AGTAATGGTGGCTGCACTCC 60.035 55.0 0.5 2.28 0.0 3.85 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
23 24 4.005032 GAGCCGAGACTCGAATGC 57.995 61.111 26.11 19.63 43.74 3.56
25 26 0.869454 GAGCCGAGACTCGAATGCTG 60.869 60.000 25.31 11.03 43.74 4.41
26 27 1.880340 GCCGAGACTCGAATGCTGG 60.880 63.158 26.11 8.44 43.74 4.85
27 28 1.513158 CCGAGACTCGAATGCTGGT 59.487 57.895 26.11 0.00 43.74 4.00
28 29 0.803768 CCGAGACTCGAATGCTGGTG 60.804 60.000 26.11 2.03 43.74 4.17
29 30 0.803768 CGAGACTCGAATGCTGGTGG 60.804 60.000 20.25 0.00 43.74 4.61
31 32 1.194781 AGACTCGAATGCTGGTGGGT 61.195 55.000 0.00 0.00 0.00 4.51
32 33 0.321653 GACTCGAATGCTGGTGGGTT 60.322 55.000 0.00 0.00 0.00 4.11
33 34 0.606401 ACTCGAATGCTGGTGGGTTG 60.606 55.000 0.00 0.00 0.00 3.77
34 35 1.303236 TCGAATGCTGGTGGGTTGG 60.303 57.895 0.00 0.00 0.00 3.77
35 36 1.603455 CGAATGCTGGTGGGTTGGT 60.603 57.895 0.00 0.00 0.00 3.67
37 38 0.318120 GAATGCTGGTGGGTTGGTTG 59.682 55.000 0.00 0.00 0.00 3.77
38 39 0.398381 AATGCTGGTGGGTTGGTTGT 60.398 50.000 0.00 0.00 0.00 3.32
39 40 1.114722 ATGCTGGTGGGTTGGTTGTG 61.115 55.000 0.00 0.00 0.00 3.33
40 41 1.454847 GCTGGTGGGTTGGTTGTGA 60.455 57.895 0.00 0.00 0.00 3.58
41 42 1.040339 GCTGGTGGGTTGGTTGTGAA 61.040 55.000 0.00 0.00 0.00 3.18
42 43 0.744281 CTGGTGGGTTGGTTGTGAAC 59.256 55.000 0.00 0.00 0.00 3.18
43 44 0.333312 TGGTGGGTTGGTTGTGAACT 59.667 50.000 0.00 0.00 0.00 3.01
44 45 1.029681 GGTGGGTTGGTTGTGAACTC 58.970 55.000 0.00 0.00 0.00 3.01
45 46 1.029681 GTGGGTTGGTTGTGAACTCC 58.970 55.000 0.00 0.00 0.00 3.85
48 49 1.652563 GTTGGTTGTGAACTCCCGC 59.347 57.895 0.00 0.00 0.00 6.13
49 50 1.890041 TTGGTTGTGAACTCCCGCG 60.890 57.895 0.00 0.00 0.00 6.46
50 51 3.723348 GGTTGTGAACTCCCGCGC 61.723 66.667 0.00 0.00 0.00 6.86
51 52 3.723348 GTTGTGAACTCCCGCGCC 61.723 66.667 0.00 0.00 0.00 6.53
52 53 3.936203 TTGTGAACTCCCGCGCCT 61.936 61.111 0.00 0.00 0.00 5.52
53 54 3.469863 TTGTGAACTCCCGCGCCTT 62.470 57.895 0.00 0.00 0.00 4.35
57 58 3.876589 GAACTCCCGCGCCTTGTCA 62.877 63.158 0.00 0.00 0.00 3.58
58 59 3.469863 AACTCCCGCGCCTTGTCAA 62.470 57.895 0.00 0.00 0.00 3.18
59 60 3.423154 CTCCCGCGCCTTGTCAAC 61.423 66.667 0.00 0.00 0.00 3.18
60 61 3.883744 CTCCCGCGCCTTGTCAACT 62.884 63.158 0.00 0.00 0.00 3.16
62 63 2.664851 CCGCGCCTTGTCAACTGA 60.665 61.111 0.00 0.00 0.00 3.41
64 65 2.558313 GCGCCTTGTCAACTGAGC 59.442 61.111 0.00 0.00 0.00 4.26
65 66 1.963338 GCGCCTTGTCAACTGAGCT 60.963 57.895 0.00 0.00 0.00 4.09
66 67 0.670546 GCGCCTTGTCAACTGAGCTA 60.671 55.000 0.00 0.00 0.00 3.32
67 68 1.071605 CGCCTTGTCAACTGAGCTAC 58.928 55.000 0.00 0.00 0.00 3.58
68 69 1.071605 GCCTTGTCAACTGAGCTACG 58.928 55.000 0.00 0.00 0.00 3.51
69 70 1.071605 CCTTGTCAACTGAGCTACGC 58.928 55.000 0.00 0.00 0.00 4.42
70 71 1.605457 CCTTGTCAACTGAGCTACGCA 60.605 52.381 0.00 0.00 0.00 5.24
71 72 2.135139 CTTGTCAACTGAGCTACGCAA 58.865 47.619 0.00 0.00 0.00 4.85
72 73 2.455674 TGTCAACTGAGCTACGCAAT 57.544 45.000 0.00 0.00 0.00 3.56
74 75 2.069273 GTCAACTGAGCTACGCAATGT 58.931 47.619 0.00 0.00 0.00 2.71
75 76 2.480419 GTCAACTGAGCTACGCAATGTT 59.520 45.455 0.00 0.00 0.00 2.71
76 77 2.736721 TCAACTGAGCTACGCAATGTTC 59.263 45.455 0.00 0.00 0.00 3.18
77 78 2.738846 CAACTGAGCTACGCAATGTTCT 59.261 45.455 0.00 0.00 0.00 3.01
78 79 2.611518 ACTGAGCTACGCAATGTTCTC 58.388 47.619 0.00 0.00 32.68 2.87
79 80 1.929836 CTGAGCTACGCAATGTTCTCC 59.070 52.381 0.00 0.00 31.68 3.71
80 81 1.550524 TGAGCTACGCAATGTTCTCCT 59.449 47.619 0.00 0.00 31.68 3.69
82 83 0.375106 GCTACGCAATGTTCTCCTGC 59.625 55.000 0.00 0.00 0.00 4.85
83 84 1.725641 CTACGCAATGTTCTCCTGCA 58.274 50.000 0.00 0.00 35.78 4.41
84 85 2.283298 CTACGCAATGTTCTCCTGCAT 58.717 47.619 0.00 0.00 35.78 3.96
85 86 1.538047 ACGCAATGTTCTCCTGCATT 58.462 45.000 0.00 0.00 35.78 3.56
86 87 2.710377 ACGCAATGTTCTCCTGCATTA 58.290 42.857 0.00 0.00 35.78 1.90
87 88 2.679837 ACGCAATGTTCTCCTGCATTAG 59.320 45.455 0.00 0.00 35.78 1.73
102 103 7.062749 CCTGCATTAGGTTTAGGTATACAGA 57.937 40.000 5.01 0.00 42.00 3.41
139 140 8.130671 TGTTGACTATACTATATACCCCTTGC 57.869 38.462 0.00 0.00 0.00 4.01
140 141 7.954056 TGTTGACTATACTATATACCCCTTGCT 59.046 37.037 0.00 0.00 0.00 3.91
141 142 8.813951 GTTGACTATACTATATACCCCTTGCTT 58.186 37.037 0.00 0.00 0.00 3.91
219 220 2.348411 CTACATGGGGTAGGCCAAAG 57.652 55.000 5.01 0.00 44.77 2.77
220 221 1.564348 CTACATGGGGTAGGCCAAAGT 59.436 52.381 5.01 0.00 44.77 2.66
221 222 0.039618 ACATGGGGTAGGCCAAAGTG 59.960 55.000 5.01 0.00 36.17 3.16
222 223 0.039618 CATGGGGTAGGCCAAAGTGT 59.960 55.000 5.01 0.00 36.17 3.55
224 225 0.178975 TGGGGTAGGCCAAAGTGTTG 60.179 55.000 5.01 0.00 36.17 3.33
225 226 0.111639 GGGGTAGGCCAAAGTGTTGA 59.888 55.000 5.01 0.00 36.83 3.18
226 227 1.534729 GGGTAGGCCAAAGTGTTGAG 58.465 55.000 5.01 0.00 36.83 3.02
229 230 1.537202 GTAGGCCAAAGTGTTGAGCAG 59.463 52.381 5.01 0.00 36.83 4.24
230 231 0.106519 AGGCCAAAGTGTTGAGCAGT 60.107 50.000 5.01 0.00 36.83 4.40
231 232 0.312102 GGCCAAAGTGTTGAGCAGTC 59.688 55.000 0.00 0.00 36.83 3.51
232 233 0.312102 GCCAAAGTGTTGAGCAGTCC 59.688 55.000 0.00 0.00 36.83 3.85
233 234 1.679139 CCAAAGTGTTGAGCAGTCCA 58.321 50.000 0.00 0.00 36.83 4.02
234 235 2.233271 CCAAAGTGTTGAGCAGTCCAT 58.767 47.619 0.00 0.00 36.83 3.41
235 236 2.624838 CCAAAGTGTTGAGCAGTCCATT 59.375 45.455 0.00 0.00 36.83 3.16
236 237 3.068590 CCAAAGTGTTGAGCAGTCCATTT 59.931 43.478 0.00 0.00 36.83 2.32
237 238 4.293415 CAAAGTGTTGAGCAGTCCATTTC 58.707 43.478 0.00 0.00 36.83 2.17
239 240 2.143122 GTGTTGAGCAGTCCATTTCGA 58.857 47.619 0.00 0.00 0.00 3.71
240 241 2.158449 GTGTTGAGCAGTCCATTTCGAG 59.842 50.000 0.00 0.00 0.00 4.04
241 242 2.037121 TGTTGAGCAGTCCATTTCGAGA 59.963 45.455 0.00 0.00 0.00 4.04
243 244 1.895798 TGAGCAGTCCATTTCGAGACT 59.104 47.619 0.00 0.00 44.12 3.24
246 247 2.300152 AGCAGTCCATTTCGAGACTTGA 59.700 45.455 2.51 0.00 41.38 3.02
247 248 2.413453 GCAGTCCATTTCGAGACTTGAC 59.587 50.000 2.51 0.16 41.38 3.18
248 249 2.663602 CAGTCCATTTCGAGACTTGACG 59.336 50.000 2.51 0.00 41.38 4.35
249 250 1.993370 GTCCATTTCGAGACTTGACGG 59.007 52.381 0.00 0.00 0.00 4.79
252 253 2.604914 CCATTTCGAGACTTGACGGATG 59.395 50.000 0.00 0.00 0.00 3.51
253 254 3.511699 CATTTCGAGACTTGACGGATGA 58.488 45.455 0.00 0.00 0.00 2.92
255 256 3.653539 TTCGAGACTTGACGGATGAAA 57.346 42.857 0.00 0.00 0.00 2.69
256 257 3.653539 TCGAGACTTGACGGATGAAAA 57.346 42.857 0.00 0.00 0.00 2.29
259 260 5.716094 TCGAGACTTGACGGATGAAAAATA 58.284 37.500 0.00 0.00 0.00 1.40
260 261 5.805486 TCGAGACTTGACGGATGAAAAATAG 59.195 40.000 0.00 0.00 0.00 1.73
263 264 6.464222 AGACTTGACGGATGAAAAATAGTGA 58.536 36.000 0.00 0.00 0.00 3.41
264 265 6.934645 AGACTTGACGGATGAAAAATAGTGAA 59.065 34.615 0.00 0.00 0.00 3.18
265 266 7.607991 AGACTTGACGGATGAAAAATAGTGAAT 59.392 33.333 0.00 0.00 0.00 2.57
266 267 7.752695 ACTTGACGGATGAAAAATAGTGAATC 58.247 34.615 0.00 0.00 0.00 2.52
267 268 6.677781 TGACGGATGAAAAATAGTGAATCC 57.322 37.500 0.00 0.00 0.00 3.01
268 269 5.588648 TGACGGATGAAAAATAGTGAATCCC 59.411 40.000 0.00 0.00 31.71 3.85
269 270 5.505780 ACGGATGAAAAATAGTGAATCCCA 58.494 37.500 0.00 0.00 31.71 4.37
270 271 5.357032 ACGGATGAAAAATAGTGAATCCCAC 59.643 40.000 0.00 0.00 46.03 4.61
278 279 2.927004 GTGAATCCCACTTGTCGCA 58.073 52.632 0.00 0.00 42.44 5.10
279 280 0.517316 GTGAATCCCACTTGTCGCAC 59.483 55.000 0.00 0.00 42.44 5.34
280 281 0.396435 TGAATCCCACTTGTCGCACT 59.604 50.000 0.00 0.00 0.00 4.40
283 284 1.238439 ATCCCACTTGTCGCACTTTG 58.762 50.000 0.00 0.00 0.00 2.77
284 285 1.008538 CCCACTTGTCGCACTTTGC 60.009 57.895 0.00 0.00 40.69 3.68
305 306 2.028112 CGATAGGCTAGCCCAAATAGCA 60.028 50.000 30.42 5.81 46.07 3.49
306 307 2.930826 TAGGCTAGCCCAAATAGCAC 57.069 50.000 30.42 0.76 46.07 4.40
310 311 1.583054 CTAGCCCAAATAGCACCGAC 58.417 55.000 0.00 0.00 0.00 4.79
322 323 1.019805 GCACCGACAGAAGTTAGGCC 61.020 60.000 0.00 0.00 31.52 5.19
330 331 2.035155 AAGTTAGGCCGGCCCAAC 59.965 61.111 39.65 39.65 36.58 3.77
332 333 2.044352 GTTAGGCCGGCCCAACAT 60.044 61.111 40.71 27.22 36.58 2.71
333 334 1.680989 GTTAGGCCGGCCCAACATT 60.681 57.895 40.71 26.53 36.58 2.71
346 347 4.388485 GCCCAACATTCATTTCCTGTTTT 58.612 39.130 0.00 0.00 30.99 2.43
349 350 5.466393 CCCAACATTCATTTCCTGTTTTCAC 59.534 40.000 0.00 0.00 30.99 3.18
355 356 4.927422 TCATTTCCTGTTTTCACGGTTTC 58.073 39.130 0.00 0.00 0.00 2.78
357 358 0.658897 TCCTGTTTTCACGGTTTCGC 59.341 50.000 0.00 0.00 40.63 4.70
367 368 1.154469 CGGTTTCGCGAAGGCTTTC 60.154 57.895 22.21 9.17 36.88 2.62
388 389 3.563808 TCTGGATGGTTTGTCGAGTTTTG 59.436 43.478 0.00 0.00 0.00 2.44
389 390 2.034053 TGGATGGTTTGTCGAGTTTTGC 59.966 45.455 0.00 0.00 0.00 3.68
392 393 3.577649 TGGTTTGTCGAGTTTTGCAAA 57.422 38.095 8.05 8.05 0.00 3.68
397 398 3.859411 TGTCGAGTTTTGCAAAGGTTT 57.141 38.095 12.41 0.00 0.00 3.27
599 604 3.669251 TTTTTAAATGGTTGGCTCCCG 57.331 42.857 0.00 0.00 0.00 5.14
601 606 2.122783 TTAAATGGTTGGCTCCCGAG 57.877 50.000 0.00 0.00 0.00 4.63
615 620 1.270550 TCCCGAGTAACTCCGTTGAAC 59.729 52.381 0.00 0.00 0.00 3.18
620 625 2.728318 GAGTAACTCCGTTGAACCGAAC 59.272 50.000 0.00 0.00 0.00 3.95
630 635 6.819284 TCCGTTGAACCGAACCTTTATATAT 58.181 36.000 0.00 0.00 0.00 0.86
633 638 9.211485 CCGTTGAACCGAACCTTTATATATAAT 57.789 33.333 6.01 0.00 0.00 1.28
679 2313 1.476891 TCATCTCGAGGCGCTTACTTT 59.523 47.619 13.56 0.00 0.00 2.66
711 2351 0.537188 ATGTGTGGCTCCCGAGTAAG 59.463 55.000 0.00 0.00 0.00 2.34
717 2357 0.389757 GGCTCCCGAGTAAGTCCATC 59.610 60.000 0.00 0.00 0.00 3.51
771 2414 5.982890 ACAAGTTTATTGGGTTGAGGATG 57.017 39.130 0.00 0.00 0.00 3.51
847 2490 4.308458 CCCGCACCGTGACTCCAA 62.308 66.667 1.65 0.00 0.00 3.53
877 2520 4.100808 AGTGAAGAGCTCAGTCTTTCAAGT 59.899 41.667 17.77 4.94 36.89 3.16
878 2521 4.210955 GTGAAGAGCTCAGTCTTTCAAGTG 59.789 45.833 17.77 0.00 36.89 3.16
888 2531 5.812642 TCAGTCTTTCAAGTGTCAAGAGAAC 59.187 40.000 0.00 0.00 0.00 3.01
902 2545 5.007626 GTCAAGAGAACATACAGCAACACAA 59.992 40.000 0.00 0.00 0.00 3.33
912 2555 6.429692 ACATACAGCAACACAACAATAGCTAA 59.570 34.615 0.00 0.00 0.00 3.09
947 2591 3.711863 TCACTATAGGTACCACCCGTTT 58.288 45.455 15.94 0.00 39.75 3.60
948 2592 3.701040 TCACTATAGGTACCACCCGTTTC 59.299 47.826 15.94 0.00 39.75 2.78
949 2593 3.448301 CACTATAGGTACCACCCGTTTCA 59.552 47.826 15.94 0.00 39.75 2.69
950 2594 4.100498 CACTATAGGTACCACCCGTTTCAT 59.900 45.833 15.94 0.00 39.75 2.57
951 2595 5.302568 CACTATAGGTACCACCCGTTTCATA 59.697 44.000 15.94 0.00 39.75 2.15
1183 2831 2.825836 CCGTGCTCCTTCATGGCC 60.826 66.667 0.00 0.00 36.44 5.36
1408 3240 3.195610 TCTGGATGTCGATATGTATGGCC 59.804 47.826 0.00 0.00 0.00 5.36
1446 3281 2.158081 AGGAGGAGGACTTCTTGAAGGT 60.158 50.000 13.97 1.28 27.05 3.50
1477 3312 0.685785 ATCTGCTGCTTCTCGAGGGA 60.686 55.000 13.56 0.63 0.00 4.20
1483 3318 1.188219 TGCTTCTCGAGGGACAGCTT 61.188 55.000 13.56 0.00 0.00 3.74
1498 3334 2.716969 ACAGCTTAAGGGGAAGAGGTTT 59.283 45.455 4.29 0.00 0.00 3.27
1543 3379 0.909133 TGGACATAGCTGCCAGTGGA 60.909 55.000 15.20 0.00 0.00 4.02
1740 3579 0.529378 CAAGCAATGGCAGAGGTTCC 59.471 55.000 0.00 0.00 44.61 3.62
1753 3592 0.250513 AGGTTCCGAAGTGATCCAGC 59.749 55.000 0.00 0.00 0.00 4.85
1764 3603 2.893637 GTGATCCAGCGTTATCACTGT 58.106 47.619 16.35 0.00 45.52 3.55
1776 3615 5.347093 GCGTTATCACTGTGAGGATATCATG 59.653 44.000 16.46 0.00 40.92 3.07
1777 3616 5.866092 CGTTATCACTGTGAGGATATCATGG 59.134 44.000 16.46 0.00 40.92 3.66
1784 3625 6.213397 CACTGTGAGGATATCATGGGGTTATA 59.787 42.308 0.32 0.00 40.92 0.98
1851 3700 5.690997 AAAGGAACAAGCTACTTAAGTGC 57.309 39.130 18.56 17.75 0.00 4.40
1860 3709 0.036765 TACTTAAGTGCTGTGCCGGG 60.037 55.000 18.56 0.00 0.00 5.73
1971 3829 6.237648 GCAGATTGTATTTCTTTTCCAATGCG 60.238 38.462 0.00 0.00 0.00 4.73
1972 3830 6.254157 CAGATTGTATTTCTTTTCCAATGCGG 59.746 38.462 0.00 0.00 0.00 5.69
1973 3831 5.713792 TTGTATTTCTTTTCCAATGCGGA 57.286 34.783 0.00 0.00 44.40 5.54
1993 3857 1.017387 GTGCAGCCACCATTACTAGC 58.983 55.000 0.00 0.00 35.92 3.42
2022 3902 6.240894 TGAAACTGATGCTCTGGTTTTAGAT 58.759 36.000 0.00 0.00 32.95 1.98
2055 3935 8.089597 TCACTTATTTATGACCACGAGTTTGTA 58.910 33.333 0.00 0.00 0.00 2.41
2183 4105 9.823647 CTAAATGTATGGTCCATCTATATGACC 57.176 37.037 7.92 0.00 34.84 4.02
2184 4106 6.814954 ATGTATGGTCCATCTATATGACCC 57.185 41.667 7.92 0.00 34.75 4.46
2188 4110 4.425772 TGGTCCATCTATATGACCCGATT 58.574 43.478 5.53 0.00 34.75 3.34
2197 4119 2.113860 ATGACCCGATTCACTGGTTG 57.886 50.000 0.00 0.00 36.26 3.77
2207 4129 5.007626 CCGATTCACTGGTTGGTGTTATATG 59.992 44.000 0.00 0.00 38.28 1.78
2211 4133 5.736813 TCACTGGTTGGTGTTATATGGTAC 58.263 41.667 0.00 0.00 38.28 3.34
2212 4134 5.486063 TCACTGGTTGGTGTTATATGGTACT 59.514 40.000 0.00 0.00 38.28 2.73
2229 4151 6.428083 TGGTACTCTGTTATGTTTTGAGGA 57.572 37.500 0.00 0.00 0.00 3.71
2265 4187 8.053026 TGAGGGATTAGTAATATAGAAGACGC 57.947 38.462 0.00 0.00 0.00 5.19
2266 4188 7.086230 AGGGATTAGTAATATAGAAGACGCG 57.914 40.000 3.53 3.53 0.00 6.01
2267 4189 6.883217 AGGGATTAGTAATATAGAAGACGCGA 59.117 38.462 15.93 0.00 0.00 5.87
2268 4190 7.556996 AGGGATTAGTAATATAGAAGACGCGAT 59.443 37.037 15.93 0.00 0.00 4.58
2269 4191 7.644551 GGGATTAGTAATATAGAAGACGCGATG 59.355 40.741 15.93 0.00 0.00 3.84
2270 4192 7.644551 GGATTAGTAATATAGAAGACGCGATGG 59.355 40.741 15.93 0.00 0.00 3.51
2271 4193 5.961396 AGTAATATAGAAGACGCGATGGT 57.039 39.130 15.93 0.00 0.00 3.55
2272 4194 5.700846 AGTAATATAGAAGACGCGATGGTG 58.299 41.667 15.93 0.00 0.00 4.17
2273 4195 3.577649 ATATAGAAGACGCGATGGTGG 57.422 47.619 15.93 0.00 0.00 4.61
2274 4196 0.249489 ATAGAAGACGCGATGGTGGC 60.249 55.000 15.93 0.00 0.00 5.01
2275 4197 2.292794 TAGAAGACGCGATGGTGGCC 62.293 60.000 15.93 0.00 29.39 5.36
2276 4198 3.665675 GAAGACGCGATGGTGGCCT 62.666 63.158 15.93 0.00 29.39 5.19
2277 4199 3.254024 AAGACGCGATGGTGGCCTT 62.254 57.895 15.93 0.00 29.39 4.35
2278 4200 3.195698 GACGCGATGGTGGCCTTC 61.196 66.667 15.93 0.00 0.00 3.46
2279 4201 4.778143 ACGCGATGGTGGCCTTCC 62.778 66.667 15.93 7.51 0.00 3.46
2281 4203 4.115199 GCGATGGTGGCCTTCCCT 62.115 66.667 3.32 0.00 0.00 4.20
2282 4204 2.190578 CGATGGTGGCCTTCCCTC 59.809 66.667 3.32 8.40 0.00 4.30
2283 4205 2.669133 CGATGGTGGCCTTCCCTCA 61.669 63.158 3.32 0.00 0.00 3.86
2284 4206 1.691219 GATGGTGGCCTTCCCTCAA 59.309 57.895 3.32 0.00 0.00 3.02
2285 4207 0.039618 GATGGTGGCCTTCCCTCAAA 59.960 55.000 3.32 0.00 0.00 2.69
2286 4208 0.486879 ATGGTGGCCTTCCCTCAAAA 59.513 50.000 3.32 0.00 0.00 2.44
2287 4209 0.263172 TGGTGGCCTTCCCTCAAAAA 59.737 50.000 3.32 0.00 0.00 1.94
2332 4256 7.333423 CGAGTTGAATGATTCCTAGTGGTAAAA 59.667 37.037 2.26 0.00 34.23 1.52
2333 4257 9.178758 GAGTTGAATGATTCCTAGTGGTAAAAT 57.821 33.333 2.26 0.00 34.23 1.82
2341 4265 9.173021 TGATTCCTAGTGGTAAAATTGTACATG 57.827 33.333 8.06 0.00 34.23 3.21
2346 4270 9.010029 CCTAGTGGTAAAATTGTACATGTCTTT 57.990 33.333 0.00 0.00 0.00 2.52
2398 4322 9.793259 TTTTTAGAAAATCATGACTGGAGTACT 57.207 29.630 0.00 0.00 0.00 2.73
2399 4323 8.777865 TTTAGAAAATCATGACTGGAGTACTG 57.222 34.615 0.00 0.00 0.00 2.74
2400 4324 6.611613 AGAAAATCATGACTGGAGTACTGA 57.388 37.500 0.00 0.00 0.00 3.41
2402 4326 6.876257 AGAAAATCATGACTGGAGTACTGAAC 59.124 38.462 0.00 0.00 0.00 3.18
2410 4334 4.426704 ACTGGAGTACTGAACCATAACCT 58.573 43.478 0.00 0.00 33.08 3.50
2416 4340 5.721232 AGTACTGAACCATAACCTCTTTCG 58.279 41.667 0.00 0.00 0.00 3.46
2425 4349 5.773176 ACCATAACCTCTTTCGAAAATGGTT 59.227 36.000 31.63 31.63 42.35 3.67
2428 4352 2.812011 ACCTCTTTCGAAAATGGTTCCG 59.188 45.455 21.62 6.05 0.00 4.30
2429 4353 3.071479 CCTCTTTCGAAAATGGTTCCGA 58.929 45.455 12.41 2.29 0.00 4.55
2436 4360 7.713507 TCTTTCGAAAATGGTTCCGATATATGT 59.286 33.333 12.41 0.00 0.00 2.29
2437 4361 6.779115 TCGAAAATGGTTCCGATATATGTG 57.221 37.500 0.00 0.00 0.00 3.21
2438 4362 6.517605 TCGAAAATGGTTCCGATATATGTGA 58.482 36.000 0.00 0.00 0.00 3.58
2443 4402 4.883083 TGGTTCCGATATATGTGAAGCTC 58.117 43.478 17.32 4.52 36.47 4.09
2445 4404 3.850122 TCCGATATATGTGAAGCTCCG 57.150 47.619 0.00 0.00 0.00 4.63
2453 4412 9.516314 CGATATATGTGAAGCTCCGATATTTTA 57.484 33.333 0.00 0.00 0.00 1.52
2464 4423 5.753438 GCTCCGATATTTTACATGTCACAGA 59.247 40.000 0.00 0.00 0.00 3.41
2468 4427 7.277760 TCCGATATTTTACATGTCACAGAACAG 59.722 37.037 0.00 0.00 31.50 3.16
2470 4429 8.655970 CGATATTTTACATGTCACAGAACAGAA 58.344 33.333 0.00 0.00 31.50 3.02
2474 4433 7.566760 TTTACATGTCACAGAACAGAAATGT 57.433 32.000 0.00 0.00 43.31 2.71
2475 4434 7.566760 TTACATGTCACAGAACAGAAATGTT 57.433 32.000 0.00 0.00 39.12 2.71
2485 4444 7.167968 CACAGAACAGAAATGTTAATGTGGTTG 59.832 37.037 20.49 5.87 41.20 3.77
2494 4453 5.895636 TGTTAATGTGGTTGATGGCTTAG 57.104 39.130 0.00 0.00 0.00 2.18
2500 4459 3.820467 TGTGGTTGATGGCTTAGACTTTG 59.180 43.478 0.00 0.00 0.00 2.77
2504 4463 3.350219 TGATGGCTTAGACTTTGACCC 57.650 47.619 0.00 0.00 0.00 4.46
2505 4464 2.026262 TGATGGCTTAGACTTTGACCCC 60.026 50.000 0.00 0.00 0.00 4.95
2506 4465 1.440618 TGGCTTAGACTTTGACCCCA 58.559 50.000 0.00 0.00 0.00 4.96
2515 4474 2.627699 GACTTTGACCCCATTTGCAAGA 59.372 45.455 0.00 0.00 0.00 3.02
2522 4481 7.487822 TTGACCCCATTTGCAAGAAATTATA 57.512 32.000 0.00 0.00 0.00 0.98
2525 4484 6.201591 ACCCCATTTGCAAGAAATTATAGGA 58.798 36.000 0.00 0.00 0.00 2.94
2558 4517 5.578336 AGCAAAAGCTTGTTTCTTTGAACTC 59.422 36.000 0.00 0.00 34.34 3.01
2559 4518 5.499176 GCAAAAGCTTGTTTCTTTGAACTCG 60.499 40.000 0.00 0.00 34.34 4.18
2564 4706 4.495828 GCTTGTTTCTTTGAACTCGTCAAC 59.504 41.667 0.00 0.00 46.09 3.18
2571 4713 7.490962 TTCTTTGAACTCGTCAACATACAAT 57.509 32.000 0.00 0.00 46.09 2.71
2572 4714 6.887368 TCTTTGAACTCGTCAACATACAATG 58.113 36.000 0.00 0.00 46.09 2.82
2577 4719 3.673338 ACTCGTCAACATACAATGACACG 59.327 43.478 6.70 0.01 44.84 4.49
2580 4722 4.618067 TCGTCAACATACAATGACACGTAC 59.382 41.667 6.70 0.00 44.84 3.67
2587 4729 1.262151 ACAATGACACGTACGCCAAAC 59.738 47.619 16.72 3.49 0.00 2.93
2602 4744 3.270877 GCCAAACAGAGTTACCATCGAT 58.729 45.455 0.00 0.00 0.00 3.59
2605 4747 5.353123 GCCAAACAGAGTTACCATCGATTAA 59.647 40.000 0.00 0.00 0.00 1.40
2608 4750 9.104965 CCAAACAGAGTTACCATCGATTAATAA 57.895 33.333 0.00 0.00 0.00 1.40
2635 4777 6.829229 ATTGATTGAAACTGATGCTCTGAA 57.171 33.333 0.00 0.00 0.00 3.02
2667 4809 7.123547 AGTTTTTGGTCACTTGGTTATGAAGAA 59.876 33.333 0.00 0.00 0.00 2.52
2691 4833 7.190920 AGAGTTTATGTGTTTCTGCTTGTAC 57.809 36.000 0.00 0.00 0.00 2.90
2694 4836 7.996385 AGTTTATGTGTTTCTGCTTGTACTTT 58.004 30.769 0.00 0.00 0.00 2.66
2695 4837 7.915397 AGTTTATGTGTTTCTGCTTGTACTTTG 59.085 33.333 0.00 0.00 0.00 2.77
2696 4838 5.835113 ATGTGTTTCTGCTTGTACTTTGT 57.165 34.783 0.00 0.00 0.00 2.83
2705 4847 2.357637 GCTTGTACTTTGTGAAGCACCA 59.642 45.455 8.12 0.00 40.47 4.17
2706 4848 3.792124 GCTTGTACTTTGTGAAGCACCAC 60.792 47.826 8.12 2.03 40.47 4.16
2707 4849 2.294074 TGTACTTTGTGAAGCACCACC 58.706 47.619 6.12 0.00 36.29 4.61
2712 4854 0.467844 TTGTGAAGCACCACCAGCAT 60.468 50.000 6.12 0.00 36.26 3.79
2713 4855 0.890542 TGTGAAGCACCACCAGCATC 60.891 55.000 6.12 0.00 36.26 3.91
2714 4856 0.890542 GTGAAGCACCACCAGCATCA 60.891 55.000 0.00 0.00 37.37 3.07
2718 4860 2.048444 AGCACCACCAGCATCATTAG 57.952 50.000 0.00 0.00 0.00 1.73
2721 4863 2.954318 GCACCACCAGCATCATTAGAAT 59.046 45.455 0.00 0.00 0.00 2.40
2722 4864 3.004106 GCACCACCAGCATCATTAGAATC 59.996 47.826 0.00 0.00 0.00 2.52
2727 4869 5.359009 CCACCAGCATCATTAGAATCTGTTT 59.641 40.000 0.00 0.00 0.00 2.83
2728 4870 6.127535 CCACCAGCATCATTAGAATCTGTTTT 60.128 38.462 0.00 0.00 0.00 2.43
2730 4872 8.627403 CACCAGCATCATTAGAATCTGTTTTAT 58.373 33.333 0.00 0.00 0.00 1.40
2731 4873 9.851686 ACCAGCATCATTAGAATCTGTTTTATA 57.148 29.630 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.803768 CACCAGCATTCGAGTCTCGG 60.804 60.000 21.63 7.47 40.88 4.63
10 11 0.803768 CCACCAGCATTCGAGTCTCG 60.804 60.000 16.33 16.33 42.10 4.04
11 12 0.460987 CCCACCAGCATTCGAGTCTC 60.461 60.000 0.00 0.00 0.00 3.36
13 14 0.321653 AACCCACCAGCATTCGAGTC 60.322 55.000 0.00 0.00 0.00 3.36
14 15 0.606401 CAACCCACCAGCATTCGAGT 60.606 55.000 0.00 0.00 0.00 4.18
15 16 1.308069 CCAACCCACCAGCATTCGAG 61.308 60.000 0.00 0.00 0.00 4.04
18 19 0.318120 CAACCAACCCACCAGCATTC 59.682 55.000 0.00 0.00 0.00 2.67
20 21 1.114722 CACAACCAACCCACCAGCAT 61.115 55.000 0.00 0.00 0.00 3.79
21 22 1.756172 CACAACCAACCCACCAGCA 60.756 57.895 0.00 0.00 0.00 4.41
22 23 1.040339 TTCACAACCAACCCACCAGC 61.040 55.000 0.00 0.00 0.00 4.85
23 24 0.744281 GTTCACAACCAACCCACCAG 59.256 55.000 0.00 0.00 0.00 4.00
25 26 1.029681 GAGTTCACAACCAACCCACC 58.970 55.000 0.00 0.00 0.00 4.61
26 27 1.029681 GGAGTTCACAACCAACCCAC 58.970 55.000 0.00 0.00 0.00 4.61
27 28 0.106419 GGGAGTTCACAACCAACCCA 60.106 55.000 0.00 0.00 38.64 4.51
28 29 1.170290 CGGGAGTTCACAACCAACCC 61.170 60.000 0.00 0.00 36.82 4.11
29 30 1.792118 GCGGGAGTTCACAACCAACC 61.792 60.000 0.00 0.00 0.00 3.77
31 32 1.890041 CGCGGGAGTTCACAACCAA 60.890 57.895 0.00 0.00 0.00 3.67
32 33 2.280524 CGCGGGAGTTCACAACCA 60.281 61.111 0.00 0.00 0.00 3.67
33 34 3.723348 GCGCGGGAGTTCACAACC 61.723 66.667 8.83 0.00 0.00 3.77
34 35 3.723348 GGCGCGGGAGTTCACAAC 61.723 66.667 8.83 0.00 0.00 3.32
35 36 3.469863 AAGGCGCGGGAGTTCACAA 62.470 57.895 8.83 0.00 0.00 3.33
37 38 3.423154 CAAGGCGCGGGAGTTCAC 61.423 66.667 8.83 0.00 0.00 3.18
38 39 3.876589 GACAAGGCGCGGGAGTTCA 62.877 63.158 8.83 0.00 0.00 3.18
39 40 3.119096 GACAAGGCGCGGGAGTTC 61.119 66.667 8.83 0.00 0.00 3.01
40 41 3.469863 TTGACAAGGCGCGGGAGTT 62.470 57.895 8.83 0.00 0.00 3.01
41 42 3.936203 TTGACAAGGCGCGGGAGT 61.936 61.111 8.83 0.00 0.00 3.85
42 43 3.423154 GTTGACAAGGCGCGGGAG 61.423 66.667 8.83 0.00 0.00 4.30
43 44 3.936203 AGTTGACAAGGCGCGGGA 61.936 61.111 8.83 0.00 0.00 5.14
44 45 3.726517 CAGTTGACAAGGCGCGGG 61.727 66.667 8.83 0.00 0.00 6.13
45 46 2.664851 TCAGTTGACAAGGCGCGG 60.665 61.111 8.83 0.00 0.00 6.46
48 49 1.071605 GTAGCTCAGTTGACAAGGCG 58.928 55.000 0.00 0.00 0.00 5.52
49 50 1.071605 CGTAGCTCAGTTGACAAGGC 58.928 55.000 0.00 0.00 0.00 4.35
64 65 1.725641 TGCAGGAGAACATTGCGTAG 58.274 50.000 0.00 0.00 40.62 3.51
65 66 2.401583 ATGCAGGAGAACATTGCGTA 57.598 45.000 0.00 0.00 40.62 4.42
66 67 1.538047 AATGCAGGAGAACATTGCGT 58.462 45.000 0.00 0.00 40.62 5.24
67 68 3.329743 CTAATGCAGGAGAACATTGCG 57.670 47.619 0.00 0.00 40.62 4.85
113 114 8.759782 GCAAGGGGTATATAGTATAGTCAACAT 58.240 37.037 0.00 0.00 0.00 2.71
114 115 7.954056 AGCAAGGGGTATATAGTATAGTCAACA 59.046 37.037 0.00 0.00 0.00 3.33
116 117 8.967779 AAGCAAGGGGTATATAGTATAGTCAA 57.032 34.615 0.00 0.00 0.00 3.18
201 202 1.283613 CACTTTGGCCTACCCCATGTA 59.716 52.381 3.32 0.00 34.21 2.29
207 208 1.534729 CTCAACACTTTGGCCTACCC 58.465 55.000 3.32 0.00 33.06 3.69
208 209 0.881796 GCTCAACACTTTGGCCTACC 59.118 55.000 3.32 0.00 33.06 3.18
209 210 1.537202 CTGCTCAACACTTTGGCCTAC 59.463 52.381 3.32 0.00 33.06 3.18
210 211 1.142870 ACTGCTCAACACTTTGGCCTA 59.857 47.619 3.32 0.00 33.06 3.93
211 212 0.106519 ACTGCTCAACACTTTGGCCT 60.107 50.000 3.32 0.00 33.06 5.19
212 213 0.312102 GACTGCTCAACACTTTGGCC 59.688 55.000 0.00 0.00 33.06 5.36
213 214 0.312102 GGACTGCTCAACACTTTGGC 59.688 55.000 0.00 0.00 33.06 4.52
214 215 1.679139 TGGACTGCTCAACACTTTGG 58.321 50.000 0.00 0.00 33.06 3.28
216 217 3.003689 CGAAATGGACTGCTCAACACTTT 59.996 43.478 0.00 0.00 0.00 2.66
218 219 2.146342 CGAAATGGACTGCTCAACACT 58.854 47.619 0.00 0.00 0.00 3.55
219 220 2.143122 TCGAAATGGACTGCTCAACAC 58.857 47.619 0.00 0.00 0.00 3.32
220 221 2.037121 TCTCGAAATGGACTGCTCAACA 59.963 45.455 0.00 0.00 0.00 3.33
221 222 2.413453 GTCTCGAAATGGACTGCTCAAC 59.587 50.000 0.00 0.00 0.00 3.18
222 223 2.300152 AGTCTCGAAATGGACTGCTCAA 59.700 45.455 4.40 0.00 40.71 3.02
224 225 2.663826 AGTCTCGAAATGGACTGCTC 57.336 50.000 4.40 0.00 40.71 4.26
225 226 2.300152 TCAAGTCTCGAAATGGACTGCT 59.700 45.455 5.88 0.00 41.28 4.24
226 227 2.413453 GTCAAGTCTCGAAATGGACTGC 59.587 50.000 5.88 0.00 41.28 4.40
229 230 1.993370 CCGTCAAGTCTCGAAATGGAC 59.007 52.381 0.00 0.00 0.00 4.02
230 231 1.890489 TCCGTCAAGTCTCGAAATGGA 59.110 47.619 0.00 0.00 0.00 3.41
231 232 2.363788 TCCGTCAAGTCTCGAAATGG 57.636 50.000 0.00 0.00 0.00 3.16
232 233 3.511699 TCATCCGTCAAGTCTCGAAATG 58.488 45.455 0.00 0.00 0.00 2.32
233 234 3.868757 TCATCCGTCAAGTCTCGAAAT 57.131 42.857 0.00 0.00 0.00 2.17
234 235 3.653539 TTCATCCGTCAAGTCTCGAAA 57.346 42.857 0.00 0.00 0.00 3.46
235 236 3.653539 TTTCATCCGTCAAGTCTCGAA 57.346 42.857 0.00 0.00 0.00 3.71
236 237 3.653539 TTTTCATCCGTCAAGTCTCGA 57.346 42.857 0.00 0.00 0.00 4.04
237 238 4.928661 ATTTTTCATCCGTCAAGTCTCG 57.071 40.909 0.00 0.00 0.00 4.04
239 240 6.464222 TCACTATTTTTCATCCGTCAAGTCT 58.536 36.000 0.00 0.00 0.00 3.24
240 241 6.721571 TCACTATTTTTCATCCGTCAAGTC 57.278 37.500 0.00 0.00 0.00 3.01
241 242 7.148239 GGATTCACTATTTTTCATCCGTCAAGT 60.148 37.037 0.00 0.00 0.00 3.16
243 244 6.094881 GGGATTCACTATTTTTCATCCGTCAA 59.905 38.462 0.00 0.00 32.38 3.18
246 247 5.357032 GTGGGATTCACTATTTTTCATCCGT 59.643 40.000 0.00 0.00 42.86 4.69
247 248 5.821204 GTGGGATTCACTATTTTTCATCCG 58.179 41.667 0.00 0.00 42.86 4.18
260 261 0.517316 GTGCGACAAGTGGGATTCAC 59.483 55.000 0.00 0.00 46.39 3.18
263 264 1.608590 CAAAGTGCGACAAGTGGGATT 59.391 47.619 0.00 0.00 0.00 3.01
264 265 1.238439 CAAAGTGCGACAAGTGGGAT 58.762 50.000 0.00 0.00 0.00 3.85
265 266 1.444119 GCAAAGTGCGACAAGTGGGA 61.444 55.000 0.00 0.00 31.71 4.37
266 267 1.008538 GCAAAGTGCGACAAGTGGG 60.009 57.895 0.00 0.00 31.71 4.61
267 268 4.614673 GCAAAGTGCGACAAGTGG 57.385 55.556 0.00 0.00 31.71 4.00
276 277 0.583917 GCTAGCCTATCGCAAAGTGC 59.416 55.000 2.29 0.00 41.38 4.40
278 279 0.106894 GGGCTAGCCTATCGCAAAGT 59.893 55.000 32.18 0.00 41.38 2.66
279 280 0.106708 TGGGCTAGCCTATCGCAAAG 59.893 55.000 32.18 0.00 41.38 2.77
280 281 0.544223 TTGGGCTAGCCTATCGCAAA 59.456 50.000 32.18 8.35 41.38 3.68
283 284 2.622436 CTATTTGGGCTAGCCTATCGC 58.378 52.381 32.18 16.31 36.10 4.58
284 285 2.028112 TGCTATTTGGGCTAGCCTATCG 60.028 50.000 32.18 18.79 40.72 2.92
285 286 3.339141 GTGCTATTTGGGCTAGCCTATC 58.661 50.000 32.18 17.07 40.72 2.08
286 287 2.040412 GGTGCTATTTGGGCTAGCCTAT 59.960 50.000 32.18 23.23 40.72 2.57
287 288 1.420138 GGTGCTATTTGGGCTAGCCTA 59.580 52.381 32.18 25.37 40.72 3.93
288 289 0.183731 GGTGCTATTTGGGCTAGCCT 59.816 55.000 32.18 15.88 40.72 4.58
289 290 1.166531 CGGTGCTATTTGGGCTAGCC 61.167 60.000 26.55 26.55 40.72 3.93
305 306 1.590147 CGGCCTAACTTCTGTCGGT 59.410 57.895 0.00 0.00 0.00 4.69
306 307 1.153628 CCGGCCTAACTTCTGTCGG 60.154 63.158 0.00 0.00 0.00 4.79
310 311 2.124695 GGGCCGGCCTAACTTCTG 60.125 66.667 42.70 0.00 36.10 3.02
322 323 1.135024 CAGGAAATGAATGTTGGGCCG 60.135 52.381 0.00 0.00 0.00 6.13
330 331 4.870363 ACCGTGAAAACAGGAAATGAATG 58.130 39.130 0.00 0.00 0.00 2.67
332 333 4.993029 AACCGTGAAAACAGGAAATGAA 57.007 36.364 0.00 0.00 0.00 2.57
333 334 4.496673 CGAAACCGTGAAAACAGGAAATGA 60.497 41.667 0.00 0.00 0.00 2.57
346 347 2.981977 AAGCCTTCGCGAAACCGTGA 62.982 55.000 23.54 0.00 43.73 4.35
349 350 1.154469 GAAAGCCTTCGCGAAACCG 60.154 57.895 23.54 13.76 41.18 4.44
355 356 1.709147 CCATCCAGAAAGCCTTCGCG 61.709 60.000 0.00 0.00 41.18 5.87
357 358 1.826385 AACCATCCAGAAAGCCTTCG 58.174 50.000 0.00 0.00 36.61 3.79
367 368 3.853307 GCAAAACTCGACAAACCATCCAG 60.853 47.826 0.00 0.00 0.00 3.86
388 389 9.529325 AAACAAGAATTTACTAGAAACCTTTGC 57.471 29.630 0.00 0.00 0.00 3.68
392 393 7.783119 ACCCAAACAAGAATTTACTAGAAACCT 59.217 33.333 0.00 0.00 0.00 3.50
397 398 9.191479 TGAAAACCCAAACAAGAATTTACTAGA 57.809 29.630 0.00 0.00 0.00 2.43
502 503 9.474920 GTGATCACAAATTCCAGAAACATTTAA 57.525 29.630 21.07 0.00 0.00 1.52
503 504 8.859090 AGTGATCACAAATTCCAGAAACATTTA 58.141 29.630 27.02 0.00 0.00 1.40
580 585 2.823154 CTCGGGAGCCAACCATTTAAAA 59.177 45.455 0.00 0.00 0.00 1.52
582 587 1.353022 ACTCGGGAGCCAACCATTTAA 59.647 47.619 0.00 0.00 0.00 1.52
583 588 0.988832 ACTCGGGAGCCAACCATTTA 59.011 50.000 0.00 0.00 0.00 1.40
585 590 0.988832 TTACTCGGGAGCCAACCATT 59.011 50.000 0.00 0.00 0.00 3.16
588 593 0.108281 GAGTTACTCGGGAGCCAACC 60.108 60.000 0.00 0.00 31.01 3.77
590 595 1.601419 CGGAGTTACTCGGGAGCCAA 61.601 60.000 11.43 0.00 0.00 4.52
591 596 2.050350 CGGAGTTACTCGGGAGCCA 61.050 63.158 11.43 0.00 0.00 4.75
592 597 2.050934 ACGGAGTTACTCGGGAGCC 61.051 63.158 20.99 0.65 37.78 4.70
593 598 3.600843 ACGGAGTTACTCGGGAGC 58.399 61.111 20.99 0.86 37.78 4.70
615 620 7.827236 TCAAGCCCATTATATATAAAGGTTCGG 59.173 37.037 20.17 9.81 31.07 4.30
690 2330 0.902984 TACTCGGGAGCCACACATGT 60.903 55.000 0.00 0.00 0.00 3.21
717 2357 2.732366 CATCTGTACAGATTCGGTCCG 58.268 52.381 31.39 16.91 45.31 4.79
719 2359 3.444703 AGCATCTGTACAGATTCGGTC 57.555 47.619 31.39 18.62 45.31 4.79
771 2414 9.841880 GTTGGGATGTTTAAAGAAACTTATCTC 57.158 33.333 2.56 0.00 44.52 2.75
793 2436 6.656693 ACTGAGTTGATTCCTTCAATAGTTGG 59.343 38.462 0.00 0.00 45.77 3.77
799 2442 9.965902 ATAAACTACTGAGTTGATTCCTTCAAT 57.034 29.630 0.13 0.00 45.50 2.57
801 2444 8.816894 AGATAAACTACTGAGTTGATTCCTTCA 58.183 33.333 0.13 0.00 45.50 3.02
815 2458 1.760613 TGCGGGGGAGATAAACTACTG 59.239 52.381 0.00 0.00 0.00 2.74
847 2490 3.172339 ACTGAGCTCTTCACTCCTTGAT 58.828 45.455 16.19 0.00 32.84 2.57
877 2520 4.511454 GTGTTGCTGTATGTTCTCTTGACA 59.489 41.667 0.00 0.00 0.00 3.58
878 2521 4.511454 TGTGTTGCTGTATGTTCTCTTGAC 59.489 41.667 0.00 0.00 0.00 3.18
888 2531 5.300969 AGCTATTGTTGTGTTGCTGTATG 57.699 39.130 0.00 0.00 0.00 2.39
902 2545 2.356125 CCACTGGCCACTTAGCTATTGT 60.356 50.000 0.00 0.00 0.00 2.71
928 2571 3.711863 TGAAACGGGTGGTACCTATAGT 58.288 45.455 14.36 5.68 38.64 2.12
934 2577 1.740043 CGGTATGAAACGGGTGGTACC 60.740 57.143 4.43 4.43 37.60 3.34
947 2591 1.133823 AGCCAATGAATGCCGGTATGA 60.134 47.619 5.55 0.00 0.00 2.15
948 2592 1.321474 AGCCAATGAATGCCGGTATG 58.679 50.000 5.55 0.00 0.00 2.39
949 2593 2.071778 AAGCCAATGAATGCCGGTAT 57.928 45.000 1.90 0.00 0.00 2.73
950 2594 1.476085 CAAAGCCAATGAATGCCGGTA 59.524 47.619 1.90 0.00 0.00 4.02
951 2595 0.247185 CAAAGCCAATGAATGCCGGT 59.753 50.000 1.90 0.00 0.00 5.28
973 2620 2.961531 TCCAAATTCCGGACCTGAAA 57.038 45.000 1.83 0.00 0.00 2.69
1290 2987 1.002624 GTCGATGAACTGGGCCCAA 60.003 57.895 28.29 11.93 0.00 4.12
1408 3240 0.176680 CCTCCTCCTTGTCACCATCG 59.823 60.000 0.00 0.00 0.00 3.84
1446 3281 1.134280 GCAGCAGATTCTCCTTGGCTA 60.134 52.381 0.00 0.00 0.00 3.93
1477 3312 2.046280 ACCTCTTCCCCTTAAGCTGT 57.954 50.000 0.00 0.00 0.00 4.40
1507 3343 1.450312 CACGAGGCCAATGGAGTCC 60.450 63.158 5.01 0.73 0.00 3.85
1543 3379 0.249238 CTTCGAGCCAGCGAGCTAAT 60.249 55.000 3.33 0.00 45.15 1.73
1582 3418 0.463204 CATCGGTGAGCAGATCCACT 59.537 55.000 0.00 0.00 33.99 4.00
1740 3579 2.535984 GTGATAACGCTGGATCACTTCG 59.464 50.000 12.10 0.00 45.60 3.79
1753 3592 5.866092 CCATGATATCCTCACAGTGATAACG 59.134 44.000 2.97 0.00 36.48 3.18
1761 3600 5.768980 ATAACCCCATGATATCCTCACAG 57.231 43.478 0.00 0.00 36.48 3.66
1764 3603 7.829224 ATGTTATAACCCCATGATATCCTCA 57.171 36.000 13.01 0.00 38.53 3.86
1851 3700 0.251916 TCCATAGAAACCCGGCACAG 59.748 55.000 0.00 0.00 0.00 3.66
1860 3709 8.278729 ACACAGTAGTAGTACTCCATAGAAAC 57.721 38.462 5.96 0.00 37.40 2.78
1897 3746 5.880332 TGAGAAAGCAAGACAAGTTACAACT 59.120 36.000 0.00 0.00 42.04 3.16
1942 3791 7.953005 TGGAAAAGAAATACAATCTGCCATA 57.047 32.000 0.00 0.00 0.00 2.74
1948 3797 6.152661 TCCGCATTGGAAAAGAAATACAATCT 59.847 34.615 0.00 0.00 46.38 2.40
1971 3829 0.035056 AGTAATGGTGGCTGCACTCC 60.035 55.000 0.50 2.28 0.00 3.85
1972 3830 2.555199 CTAGTAATGGTGGCTGCACTC 58.445 52.381 0.50 0.00 0.00 3.51
1973 3831 1.407437 GCTAGTAATGGTGGCTGCACT 60.407 52.381 0.50 0.00 0.00 4.40
1993 3857 4.008330 ACCAGAGCATCAGTTTCAATCTG 58.992 43.478 0.00 0.00 37.82 2.90
2022 3902 7.226918 TCGTGGTCATAAATAAGTGAACAACAA 59.773 33.333 0.00 0.00 43.09 2.83
2149 4069 9.331466 AGATGGACCATACATTTAGAGTATCAT 57.669 33.333 7.05 0.00 37.82 2.45
2150 4070 8.727100 AGATGGACCATACATTTAGAGTATCA 57.273 34.615 7.05 0.00 37.82 2.15
2178 4100 1.340017 CCAACCAGTGAATCGGGTCAT 60.340 52.381 0.00 0.00 43.46 3.06
2183 4105 1.604604 AACACCAACCAGTGAATCGG 58.395 50.000 0.00 0.00 40.34 4.18
2184 4106 5.007626 CCATATAACACCAACCAGTGAATCG 59.992 44.000 0.00 0.00 40.34 3.34
2188 4110 4.919774 ACCATATAACACCAACCAGTGA 57.080 40.909 0.00 0.00 40.34 3.41
2197 4119 9.609346 AAACATAACAGAGTACCATATAACACC 57.391 33.333 0.00 0.00 0.00 4.16
2207 4129 6.935208 AGTTCCTCAAAACATAACAGAGTACC 59.065 38.462 0.00 0.00 0.00 3.34
2240 4162 7.148289 CGCGTCTTCTATATTACTAATCCCTCA 60.148 40.741 0.00 0.00 0.00 3.86
2247 4169 7.303261 CACCATCGCGTCTTCTATATTACTAA 58.697 38.462 5.77 0.00 0.00 2.24
2250 4172 4.857588 CCACCATCGCGTCTTCTATATTAC 59.142 45.833 5.77 0.00 0.00 1.89
2253 4175 2.352814 GCCACCATCGCGTCTTCTATAT 60.353 50.000 5.77 0.00 0.00 0.86
2254 4176 1.000607 GCCACCATCGCGTCTTCTATA 60.001 52.381 5.77 0.00 0.00 1.31
2255 4177 0.249489 GCCACCATCGCGTCTTCTAT 60.249 55.000 5.77 0.00 0.00 1.98
2256 4178 1.141019 GCCACCATCGCGTCTTCTA 59.859 57.895 5.77 0.00 0.00 2.10
2257 4179 2.125512 GCCACCATCGCGTCTTCT 60.126 61.111 5.77 0.00 0.00 2.85
2258 4180 3.195698 GGCCACCATCGCGTCTTC 61.196 66.667 5.77 0.00 0.00 2.87
2259 4181 3.254024 AAGGCCACCATCGCGTCTT 62.254 57.895 5.01 0.00 0.00 3.01
2260 4182 3.665675 GAAGGCCACCATCGCGTCT 62.666 63.158 5.01 0.00 0.00 4.18
2261 4183 3.195698 GAAGGCCACCATCGCGTC 61.196 66.667 5.01 0.00 0.00 5.19
2262 4184 4.778143 GGAAGGCCACCATCGCGT 62.778 66.667 5.01 0.00 0.00 6.01
2264 4186 4.115199 AGGGAAGGCCACCATCGC 62.115 66.667 18.41 12.46 35.00 4.58
2265 4187 2.190578 GAGGGAAGGCCACCATCG 59.809 66.667 18.41 0.00 35.15 3.84
2266 4188 0.039618 TTTGAGGGAAGGCCACCATC 59.960 55.000 21.28 21.28 38.48 3.51
2267 4189 0.486879 TTTTGAGGGAAGGCCACCAT 59.513 50.000 18.41 12.79 35.15 3.55
2268 4190 0.263172 TTTTTGAGGGAAGGCCACCA 59.737 50.000 18.41 0.00 35.15 4.17
2269 4191 3.141409 TTTTTGAGGGAAGGCCACC 57.859 52.632 5.01 8.14 35.15 4.61
2284 4206 6.259638 TCGCGTCTTCTATGTTTTTGTTTTT 58.740 32.000 5.77 0.00 0.00 1.94
2285 4207 5.812652 TCGCGTCTTCTATGTTTTTGTTTT 58.187 33.333 5.77 0.00 0.00 2.43
2286 4208 5.007332 ACTCGCGTCTTCTATGTTTTTGTTT 59.993 36.000 5.77 0.00 0.00 2.83
2287 4209 4.510340 ACTCGCGTCTTCTATGTTTTTGTT 59.490 37.500 5.77 0.00 0.00 2.83
2288 4210 4.056050 ACTCGCGTCTTCTATGTTTTTGT 58.944 39.130 5.77 0.00 0.00 2.83
2289 4211 4.647291 ACTCGCGTCTTCTATGTTTTTG 57.353 40.909 5.77 0.00 0.00 2.44
2290 4212 4.748102 TCAACTCGCGTCTTCTATGTTTTT 59.252 37.500 5.77 0.00 0.00 1.94
2291 4213 4.304110 TCAACTCGCGTCTTCTATGTTTT 58.696 39.130 5.77 0.00 0.00 2.43
2292 4214 3.909430 TCAACTCGCGTCTTCTATGTTT 58.091 40.909 5.77 0.00 0.00 2.83
2293 4215 3.570926 TCAACTCGCGTCTTCTATGTT 57.429 42.857 5.77 0.00 0.00 2.71
2303 4225 2.386661 AGGAATCATTCAACTCGCGT 57.613 45.000 5.77 0.00 0.00 6.01
2305 4227 3.557595 CCACTAGGAATCATTCAACTCGC 59.442 47.826 0.00 0.00 36.89 5.03
2306 4228 4.759782 ACCACTAGGAATCATTCAACTCG 58.240 43.478 0.00 0.00 38.69 4.18
2318 4242 8.380099 AGACATGTACAATTTTACCACTAGGAA 58.620 33.333 0.00 0.00 38.69 3.36
2320 4244 8.561738 AAGACATGTACAATTTTACCACTAGG 57.438 34.615 0.00 0.00 42.21 3.02
2346 4270 8.426489 AGACTACTGTAACATACCAAGACAAAA 58.574 33.333 0.00 0.00 0.00 2.44
2385 4309 5.104900 GGTTATGGTTCAGTACTCCAGTCAT 60.105 44.000 7.74 4.76 34.62 3.06
2398 4322 6.072175 CCATTTTCGAAAGAGGTTATGGTTCA 60.072 38.462 21.22 1.34 43.69 3.18
2399 4323 6.072119 ACCATTTTCGAAAGAGGTTATGGTTC 60.072 38.462 26.13 0.00 41.47 3.62
2400 4324 5.773176 ACCATTTTCGAAAGAGGTTATGGTT 59.227 36.000 26.13 15.94 41.47 3.67
2402 4326 5.897377 ACCATTTTCGAAAGAGGTTATGG 57.103 39.130 25.16 25.16 43.69 2.74
2410 4334 7.713507 ACATATATCGGAACCATTTTCGAAAGA 59.286 33.333 10.98 2.80 35.25 2.52
2416 4340 7.041098 AGCTTCACATATATCGGAACCATTTTC 60.041 37.037 0.00 0.00 0.00 2.29
2425 4349 3.418047 TCGGAGCTTCACATATATCGGA 58.582 45.455 0.00 0.00 0.00 4.55
2436 4360 6.257849 GTGACATGTAAAATATCGGAGCTTCA 59.742 38.462 0.00 0.00 0.00 3.02
2437 4361 6.257849 TGTGACATGTAAAATATCGGAGCTTC 59.742 38.462 0.00 0.00 0.00 3.86
2438 4362 6.112734 TGTGACATGTAAAATATCGGAGCTT 58.887 36.000 0.00 0.00 0.00 3.74
2443 4402 7.277760 TCTGTTCTGTGACATGTAAAATATCGG 59.722 37.037 0.00 0.00 0.00 4.18
2453 4412 7.566760 TTAACATTTCTGTTCTGTGACATGT 57.433 32.000 0.00 0.00 44.43 3.21
2468 4427 5.723295 AGCCATCAACCACATTAACATTTC 58.277 37.500 0.00 0.00 0.00 2.17
2470 4429 5.743636 AAGCCATCAACCACATTAACATT 57.256 34.783 0.00 0.00 0.00 2.71
2471 4430 6.095440 GTCTAAGCCATCAACCACATTAACAT 59.905 38.462 0.00 0.00 0.00 2.71
2472 4431 5.414454 GTCTAAGCCATCAACCACATTAACA 59.586 40.000 0.00 0.00 0.00 2.41
2473 4432 5.648092 AGTCTAAGCCATCAACCACATTAAC 59.352 40.000 0.00 0.00 0.00 2.01
2474 4433 5.815581 AGTCTAAGCCATCAACCACATTAA 58.184 37.500 0.00 0.00 0.00 1.40
2475 4434 5.435686 AGTCTAAGCCATCAACCACATTA 57.564 39.130 0.00 0.00 0.00 1.90
2485 4444 2.026262 TGGGGTCAAAGTCTAAGCCATC 60.026 50.000 0.00 0.00 32.14 3.51
2494 4453 2.627699 TCTTGCAAATGGGGTCAAAGTC 59.372 45.455 0.00 0.00 0.00 3.01
2500 4459 6.323739 TCCTATAATTTCTTGCAAATGGGGTC 59.676 38.462 0.00 0.00 0.00 4.46
2538 4497 5.106317 TGACGAGTTCAAAGAAACAAGCTTT 60.106 36.000 0.00 0.00 36.07 3.51
2544 4503 5.811399 ATGTTGACGAGTTCAAAGAAACA 57.189 34.783 0.00 0.00 46.09 2.83
2553 4512 5.609088 GTGTCATTGTATGTTGACGAGTTC 58.391 41.667 0.00 0.00 44.11 3.01
2558 4517 4.488101 CGTACGTGTCATTGTATGTTGACG 60.488 45.833 7.22 0.00 44.11 4.35
2559 4518 4.720110 GCGTACGTGTCATTGTATGTTGAC 60.720 45.833 17.90 0.00 42.05 3.18
2564 4706 2.263945 TGGCGTACGTGTCATTGTATG 58.736 47.619 17.90 4.03 0.00 2.39
2571 4713 0.102663 TCTGTTTGGCGTACGTGTCA 59.897 50.000 17.90 10.26 0.00 3.58
2572 4714 0.782384 CTCTGTTTGGCGTACGTGTC 59.218 55.000 17.90 7.71 0.00 3.67
2577 4719 2.758009 TGGTAACTCTGTTTGGCGTAC 58.242 47.619 0.00 0.00 37.61 3.67
2580 4722 1.393539 CGATGGTAACTCTGTTTGGCG 59.606 52.381 0.00 0.00 37.61 5.69
2608 4750 8.145767 TCAGAGCATCAGTTTCAATCAATTTTT 58.854 29.630 0.00 0.00 37.82 1.94
2609 4751 7.663827 TCAGAGCATCAGTTTCAATCAATTTT 58.336 30.769 0.00 0.00 37.82 1.82
2610 4752 7.223260 TCAGAGCATCAGTTTCAATCAATTT 57.777 32.000 0.00 0.00 37.82 1.82
2622 4764 7.992754 AAAACTCTAAATTCAGAGCATCAGT 57.007 32.000 5.45 0.00 45.03 3.41
2628 4770 6.858478 GTGACCAAAAACTCTAAATTCAGAGC 59.142 38.462 5.45 0.00 45.03 4.09
2630 4772 8.405531 CAAGTGACCAAAAACTCTAAATTCAGA 58.594 33.333 0.00 0.00 0.00 3.27
2631 4773 7.649306 CCAAGTGACCAAAAACTCTAAATTCAG 59.351 37.037 0.00 0.00 0.00 3.02
2635 4777 7.418337 AACCAAGTGACCAAAAACTCTAAAT 57.582 32.000 0.00 0.00 0.00 1.40
2667 4809 6.992715 AGTACAAGCAGAAACACATAAACTCT 59.007 34.615 0.00 0.00 0.00 3.24
2691 4833 0.031178 GCTGGTGGTGCTTCACAAAG 59.969 55.000 11.04 8.93 39.27 2.77
2694 4836 0.890542 GATGCTGGTGGTGCTTCACA 60.891 55.000 11.04 0.00 39.27 3.58
2695 4837 0.890542 TGATGCTGGTGGTGCTTCAC 60.891 55.000 0.00 2.13 38.88 3.18
2696 4838 0.038599 ATGATGCTGGTGGTGCTTCA 59.961 50.000 6.73 6.73 44.59 3.02
2705 4847 8.757982 ATAAAACAGATTCTAATGATGCTGGT 57.242 30.769 0.00 0.00 31.93 4.00


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

AutoCloner maintained by Alex Coulton.