Multiple sequence alignment - TraesCS1D01G364900

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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 TraesCS1D01G364900 chr1D 100.000 3939 0 0 973 4911 445545423 445541485 0.000000e+00 7275.0
1 TraesCS1D01G364900 chr1D 100.000 662 0 0 1 662 445546395 445545734 0.000000e+00 1223.0
2 TraesCS1D01G364900 chr1D 83.255 424 41 13 973 1373 318518812 318519228 3.610000e-96 363.0
3 TraesCS1D01G364900 chr1A 93.281 3676 159 46 995 4634 541635888 541632265 0.000000e+00 5339.0
4 TraesCS1D01G364900 chr1A 96.364 275 8 2 231 504 541636502 541636229 7.500000e-123 451.0
5 TraesCS1D01G364900 chr1A 87.055 309 7 11 4626 4911 541632223 541631925 7.930000e-83 318.0
6 TraesCS1D01G364900 chr1A 95.506 89 3 1 506 594 541636198 541636111 1.840000e-29 141.0
7 TraesCS1D01G364900 chr1B 89.424 3423 230 68 973 4351 608536430 608533096 0.000000e+00 4194.0
8 TraesCS1D01G364900 chr1B 86.877 381 20 14 231 609 608536976 608536624 2.750000e-107 399.0
9 TraesCS1D01G364900 chr1B 80.777 489 63 11 973 1439 588395187 588394708 2.170000e-93 353.0
10 TraesCS1D01G364900 chr1B 85.757 337 33 7 1481 1816 588394710 588394388 4.710000e-90 342.0
11 TraesCS1D01G364900 chr1B 81.527 406 67 8 3028 3429 610974355 610974756 1.320000e-85 327.0
12 TraesCS1D01G364900 chr1B 80.707 368 49 13 2472 2829 611133341 611133696 2.910000e-67 267.0
13 TraesCS1D01G364900 chr1B 85.446 213 6 8 4708 4898 608532660 608532451 1.080000e-46 198.0
14 TraesCS1D01G364900 chr1B 98.000 50 0 1 613 662 608536596 608536548 8.760000e-13 86.1
15 TraesCS1D01G364900 chr3B 82.041 490 55 13 973 1439 12172033 12172512 2.140000e-103 387.0
16 TraesCS1D01G364900 chr3B 89.706 136 11 1 1305 1440 632428527 632428659 2.350000e-38 171.0
17 TraesCS1D01G364900 chr3B 81.871 171 25 3 1478 1647 12172508 12172673 6.630000e-29 139.0
18 TraesCS1D01G364900 chr4A 81.800 489 57 14 973 1439 654456890 654456412 9.980000e-102 381.0
19 TraesCS1D01G364900 chr4A 81.800 489 57 14 973 1439 654485687 654485209 9.980000e-102 381.0
20 TraesCS1D01G364900 chr4A 86.014 286 36 1 1493 1778 654456401 654456120 2.220000e-78 303.0
21 TraesCS1D01G364900 chr4A 85.284 299 39 2 1481 1778 654485211 654484917 2.220000e-78 303.0
22 TraesCS1D01G364900 chr7D 82.506 423 44 14 974 1373 172775582 172775167 1.310000e-90 344.0
23 TraesCS1D01G364900 chr7D 82.075 424 46 14 973 1373 176463411 176462995 7.880000e-88 335.0
24 TraesCS1D01G364900 chr5D 82.311 424 45 14 973 1373 309193478 309193062 1.690000e-89 340.0
25 TraesCS1D01G364900 chr5D 82.075 424 45 15 973 1373 429180432 429180017 2.830000e-87 333.0
26 TraesCS1D01G364900 chr3D 81.132 424 50 14 973 1373 119680162 119680578 3.690000e-81 313.0
27 TraesCS1D01G364900 chrUn 86.014 286 36 1 1487 1772 387519066 387519347 2.220000e-78 303.0
28 TraesCS1D01G364900 chr2B 81.847 314 47 8 3150 3460 736392030 736392336 6.310000e-64 255.0
29 TraesCS1D01G364900 chr5B 89.706 136 11 1 1305 1440 522630209 522630341 2.350000e-38 171.0
30 TraesCS1D01G364900 chr5A 85.093 161 20 1 1487 1647 116202515 116202671 1.410000e-35 161.0
31 TraesCS1D01G364900 chr4B 94.186 86 5 0 973 1058 639306161 639306246 1.110000e-26 132.0


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 TraesCS1D01G364900 chr1D 445541485 445546395 4910 True 4249.000 7275 100.00000 1 4911 2 chr1D.!!$R1 4910
1 TraesCS1D01G364900 chr1A 541631925 541636502 4577 True 1562.250 5339 93.05150 231 4911 4 chr1A.!!$R1 4680
2 TraesCS1D01G364900 chr1B 608532451 608536976 4525 True 1219.275 4194 89.93675 231 4898 4 chr1B.!!$R2 4667
3 TraesCS1D01G364900 chr1B 588394388 588395187 799 True 347.500 353 83.26700 973 1816 2 chr1B.!!$R1 843
4 TraesCS1D01G364900 chr3B 12172033 12172673 640 False 263.000 387 81.95600 973 1647 2 chr3B.!!$F2 674
5 TraesCS1D01G364900 chr4A 654456120 654456890 770 True 342.000 381 83.90700 973 1778 2 chr4A.!!$R1 805
6 TraesCS1D01G364900 chr4A 654484917 654485687 770 True 342.000 381 83.54200 973 1778 2 chr4A.!!$R2 805

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
504 505 0.179018 AATATTCCGGCAGGCAGGAC 60.179 55.000 12.75 0.00 39.88 3.85 F
1253 1345 0.094730 CGTCGTTCGCCTTTCATTCC 59.905 55.000 0.00 0.00 0.00 3.01 F
1636 1732 0.250166 AGTACAGGTTGGTTCGTGGC 60.250 55.000 0.00 0.00 0.00 5.01 F
2998 3106 2.158971 GCCAAAGGGTTTCAAGCTTGAA 60.159 45.455 32.86 32.86 39.60 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1418 1510 0.395312 CGTAGTGGAACCCCTGTTGT 59.605 55.0 0.00 0.00 37.80 3.32 R
2728 2835 1.583556 TTCCTCTGCAGGGAAGCATA 58.416 50.0 24.49 9.52 44.68 3.14 R
3362 3470 5.010012 CACAAGAGCAAACATAAAGGAGGTT 59.990 40.0 0.00 0.00 32.12 3.50 R
4391 4541 0.249322 CGTCGGACAGTGTTCCAGTT 60.249 55.0 9.10 0.00 35.04 3.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.608948 TTTTGTTGTGTTTCTGGGTTGT 57.391 36.364 0.00 0.00 0.00 3.32
27 28 4.608948 TTTGTTGTGTTTCTGGGTTGTT 57.391 36.364 0.00 0.00 0.00 2.83
28 29 3.859411 TGTTGTGTTTCTGGGTTGTTC 57.141 42.857 0.00 0.00 0.00 3.18
29 30 3.426615 TGTTGTGTTTCTGGGTTGTTCT 58.573 40.909 0.00 0.00 0.00 3.01
30 31 3.829601 TGTTGTGTTTCTGGGTTGTTCTT 59.170 39.130 0.00 0.00 0.00 2.52
31 32 4.173256 GTTGTGTTTCTGGGTTGTTCTTG 58.827 43.478 0.00 0.00 0.00 3.02
32 33 3.691575 TGTGTTTCTGGGTTGTTCTTGA 58.308 40.909 0.00 0.00 0.00 3.02
33 34 3.694072 TGTGTTTCTGGGTTGTTCTTGAG 59.306 43.478 0.00 0.00 0.00 3.02
34 35 3.066760 GTGTTTCTGGGTTGTTCTTGAGG 59.933 47.826 0.00 0.00 0.00 3.86
35 36 3.288092 GTTTCTGGGTTGTTCTTGAGGT 58.712 45.455 0.00 0.00 0.00 3.85
36 37 2.638480 TCTGGGTTGTTCTTGAGGTG 57.362 50.000 0.00 0.00 0.00 4.00
37 38 1.142870 TCTGGGTTGTTCTTGAGGTGG 59.857 52.381 0.00 0.00 0.00 4.61
38 39 1.142870 CTGGGTTGTTCTTGAGGTGGA 59.857 52.381 0.00 0.00 0.00 4.02
39 40 1.780309 TGGGTTGTTCTTGAGGTGGAT 59.220 47.619 0.00 0.00 0.00 3.41
40 41 2.162681 GGGTTGTTCTTGAGGTGGATG 58.837 52.381 0.00 0.00 0.00 3.51
41 42 2.489073 GGGTTGTTCTTGAGGTGGATGT 60.489 50.000 0.00 0.00 0.00 3.06
42 43 3.222603 GGTTGTTCTTGAGGTGGATGTT 58.777 45.455 0.00 0.00 0.00 2.71
43 44 3.636764 GGTTGTTCTTGAGGTGGATGTTT 59.363 43.478 0.00 0.00 0.00 2.83
44 45 4.099419 GGTTGTTCTTGAGGTGGATGTTTT 59.901 41.667 0.00 0.00 0.00 2.43
45 46 4.916983 TGTTCTTGAGGTGGATGTTTTG 57.083 40.909 0.00 0.00 0.00 2.44
46 47 4.277476 TGTTCTTGAGGTGGATGTTTTGT 58.723 39.130 0.00 0.00 0.00 2.83
47 48 4.709397 TGTTCTTGAGGTGGATGTTTTGTT 59.291 37.500 0.00 0.00 0.00 2.83
48 49 5.888724 TGTTCTTGAGGTGGATGTTTTGTTA 59.111 36.000 0.00 0.00 0.00 2.41
49 50 6.549364 TGTTCTTGAGGTGGATGTTTTGTTAT 59.451 34.615 0.00 0.00 0.00 1.89
50 51 7.069331 TGTTCTTGAGGTGGATGTTTTGTTATT 59.931 33.333 0.00 0.00 0.00 1.40
51 52 7.595819 TCTTGAGGTGGATGTTTTGTTATTT 57.404 32.000 0.00 0.00 0.00 1.40
52 53 8.017418 TCTTGAGGTGGATGTTTTGTTATTTT 57.983 30.769 0.00 0.00 0.00 1.82
53 54 7.925483 TCTTGAGGTGGATGTTTTGTTATTTTG 59.075 33.333 0.00 0.00 0.00 2.44
54 55 7.118496 TGAGGTGGATGTTTTGTTATTTTGT 57.882 32.000 0.00 0.00 0.00 2.83
55 56 7.560368 TGAGGTGGATGTTTTGTTATTTTGTT 58.440 30.769 0.00 0.00 0.00 2.83
56 57 7.493971 TGAGGTGGATGTTTTGTTATTTTGTTG 59.506 33.333 0.00 0.00 0.00 3.33
57 58 7.334858 AGGTGGATGTTTTGTTATTTTGTTGT 58.665 30.769 0.00 0.00 0.00 3.32
58 59 8.478877 AGGTGGATGTTTTGTTATTTTGTTGTA 58.521 29.630 0.00 0.00 0.00 2.41
59 60 8.544597 GGTGGATGTTTTGTTATTTTGTTGTAC 58.455 33.333 0.00 0.00 0.00 2.90
60 61 8.544597 GTGGATGTTTTGTTATTTTGTTGTACC 58.455 33.333 0.00 0.00 0.00 3.34
61 62 7.435488 TGGATGTTTTGTTATTTTGTTGTACCG 59.565 33.333 0.00 0.00 0.00 4.02
62 63 7.648510 GGATGTTTTGTTATTTTGTTGTACCGA 59.351 33.333 0.00 0.00 0.00 4.69
63 64 7.972623 TGTTTTGTTATTTTGTTGTACCGAG 57.027 32.000 0.00 0.00 0.00 4.63
64 65 7.536855 TGTTTTGTTATTTTGTTGTACCGAGT 58.463 30.769 0.00 0.00 0.00 4.18
65 66 8.671921 TGTTTTGTTATTTTGTTGTACCGAGTA 58.328 29.630 0.00 0.00 0.00 2.59
66 67 9.500864 GTTTTGTTATTTTGTTGTACCGAGTAA 57.499 29.630 0.00 0.00 0.00 2.24
69 70 9.881529 TTGTTATTTTGTTGTACCGAGTAATTC 57.118 29.630 0.00 0.00 0.00 2.17
70 71 9.275398 TGTTATTTTGTTGTACCGAGTAATTCT 57.725 29.630 0.00 0.00 0.00 2.40
71 72 9.750882 GTTATTTTGTTGTACCGAGTAATTCTC 57.249 33.333 0.00 0.00 39.62 2.87
87 88 9.535878 GAGTAATTCTCGAACAGGAATCTAATT 57.464 33.333 0.00 0.00 31.87 1.40
88 89 9.892130 AGTAATTCTCGAACAGGAATCTAATTT 57.108 29.630 0.00 0.00 31.87 1.82
91 92 9.454859 AATTCTCGAACAGGAATCTAATTTTCT 57.545 29.630 0.00 0.00 31.87 2.52
92 93 8.848474 TTCTCGAACAGGAATCTAATTTTCTT 57.152 30.769 0.00 0.00 0.00 2.52
93 94 8.848474 TCTCGAACAGGAATCTAATTTTCTTT 57.152 30.769 0.00 0.00 0.00 2.52
94 95 9.938280 TCTCGAACAGGAATCTAATTTTCTTTA 57.062 29.630 0.00 0.00 0.00 1.85
96 97 9.938280 TCGAACAGGAATCTAATTTTCTTTAGA 57.062 29.630 0.00 0.00 41.23 2.10
100 101 9.720769 ACAGGAATCTAATTTTCTTTAGAACGA 57.279 29.630 0.00 0.00 40.57 3.85
107 108 9.886132 TCTAATTTTCTTTAGAACGATAAGCCT 57.114 29.630 0.00 0.00 35.73 4.58
114 115 9.886132 TTCTTTAGAACGATAAGCCTATTTTCT 57.114 29.630 0.00 5.79 30.71 2.52
120 121 9.110502 AGAACGATAAGCCTATTTTCTAAAAGG 57.889 33.333 0.00 0.00 0.00 3.11
121 122 9.106070 GAACGATAAGCCTATTTTCTAAAAGGA 57.894 33.333 0.00 0.00 0.00 3.36
122 123 8.434733 ACGATAAGCCTATTTTCTAAAAGGAC 57.565 34.615 0.00 0.00 0.00 3.85
123 124 8.044908 ACGATAAGCCTATTTTCTAAAAGGACA 58.955 33.333 0.00 0.00 0.00 4.02
124 125 9.057089 CGATAAGCCTATTTTCTAAAAGGACAT 57.943 33.333 0.00 0.00 0.00 3.06
128 129 9.700831 AAGCCTATTTTCTAAAAGGACATACAT 57.299 29.630 0.00 0.00 0.00 2.29
189 190 9.747898 TCAATTATATAAACCCTTGTTGTCTGT 57.252 29.630 0.00 0.00 34.13 3.41
191 192 8.747538 ATTATATAAACCCTTGTTGTCTGTCC 57.252 34.615 0.00 0.00 34.13 4.02
192 193 4.724279 ATAAACCCTTGTTGTCTGTCCT 57.276 40.909 0.00 0.00 34.13 3.85
193 194 5.836024 ATAAACCCTTGTTGTCTGTCCTA 57.164 39.130 0.00 0.00 34.13 2.94
194 195 4.724279 AAACCCTTGTTGTCTGTCCTAT 57.276 40.909 0.00 0.00 34.13 2.57
195 196 5.836024 AAACCCTTGTTGTCTGTCCTATA 57.164 39.130 0.00 0.00 34.13 1.31
196 197 6.388619 AAACCCTTGTTGTCTGTCCTATAT 57.611 37.500 0.00 0.00 34.13 0.86
197 198 6.388619 AACCCTTGTTGTCTGTCCTATATT 57.611 37.500 0.00 0.00 32.13 1.28
198 199 5.990668 ACCCTTGTTGTCTGTCCTATATTC 58.009 41.667 0.00 0.00 0.00 1.75
199 200 5.487488 ACCCTTGTTGTCTGTCCTATATTCA 59.513 40.000 0.00 0.00 0.00 2.57
200 201 6.012858 ACCCTTGTTGTCTGTCCTATATTCAA 60.013 38.462 0.00 0.00 0.00 2.69
201 202 6.540189 CCCTTGTTGTCTGTCCTATATTCAAG 59.460 42.308 0.00 0.00 0.00 3.02
202 203 7.106239 CCTTGTTGTCTGTCCTATATTCAAGT 58.894 38.462 0.00 0.00 0.00 3.16
203 204 7.065085 CCTTGTTGTCTGTCCTATATTCAAGTG 59.935 40.741 0.00 0.00 0.00 3.16
204 205 5.874810 TGTTGTCTGTCCTATATTCAAGTGC 59.125 40.000 0.00 0.00 0.00 4.40
205 206 5.939764 TGTCTGTCCTATATTCAAGTGCT 57.060 39.130 0.00 0.00 0.00 4.40
206 207 6.299805 TGTCTGTCCTATATTCAAGTGCTT 57.700 37.500 0.00 0.00 0.00 3.91
207 208 7.418337 TGTCTGTCCTATATTCAAGTGCTTA 57.582 36.000 0.00 0.00 0.00 3.09
208 209 7.265673 TGTCTGTCCTATATTCAAGTGCTTAC 58.734 38.462 0.00 0.00 0.00 2.34
209 210 6.702282 GTCTGTCCTATATTCAAGTGCTTACC 59.298 42.308 0.00 0.00 0.00 2.85
210 211 6.611642 TCTGTCCTATATTCAAGTGCTTACCT 59.388 38.462 0.00 0.00 0.00 3.08
211 212 7.783119 TCTGTCCTATATTCAAGTGCTTACCTA 59.217 37.037 0.00 0.00 0.00 3.08
212 213 7.723324 TGTCCTATATTCAAGTGCTTACCTAC 58.277 38.462 0.00 0.00 0.00 3.18
213 214 7.563924 TGTCCTATATTCAAGTGCTTACCTACT 59.436 37.037 0.00 0.00 0.00 2.57
214 215 7.868415 GTCCTATATTCAAGTGCTTACCTACTG 59.132 40.741 0.00 0.00 0.00 2.74
215 216 6.647067 CCTATATTCAAGTGCTTACCTACTGC 59.353 42.308 0.00 0.00 0.00 4.40
216 217 2.762535 TCAAGTGCTTACCTACTGCC 57.237 50.000 0.00 0.00 0.00 4.85
217 218 2.257207 TCAAGTGCTTACCTACTGCCT 58.743 47.619 0.00 0.00 0.00 4.75
218 219 3.437213 TCAAGTGCTTACCTACTGCCTA 58.563 45.455 0.00 0.00 0.00 3.93
219 220 3.447586 TCAAGTGCTTACCTACTGCCTAG 59.552 47.826 0.00 0.00 0.00 3.02
220 221 1.757699 AGTGCTTACCTACTGCCTAGC 59.242 52.381 0.00 0.00 0.00 3.42
221 222 1.480954 GTGCTTACCTACTGCCTAGCA 59.519 52.381 0.00 0.00 36.38 3.49
222 223 2.103263 GTGCTTACCTACTGCCTAGCAT 59.897 50.000 0.00 0.00 40.32 3.79
223 224 3.321111 GTGCTTACCTACTGCCTAGCATA 59.679 47.826 0.00 0.00 40.32 3.14
224 225 3.964688 TGCTTACCTACTGCCTAGCATAA 59.035 43.478 0.00 0.00 38.13 1.90
225 226 4.407621 TGCTTACCTACTGCCTAGCATAAA 59.592 41.667 0.00 0.00 38.13 1.40
226 227 5.071788 TGCTTACCTACTGCCTAGCATAAAT 59.928 40.000 0.00 0.00 38.13 1.40
227 228 5.998363 GCTTACCTACTGCCTAGCATAAATT 59.002 40.000 0.00 0.00 38.13 1.82
228 229 6.486993 GCTTACCTACTGCCTAGCATAAATTT 59.513 38.462 0.00 0.00 38.13 1.82
229 230 7.013369 GCTTACCTACTGCCTAGCATAAATTTT 59.987 37.037 0.00 0.00 38.13 1.82
230 231 6.944234 ACCTACTGCCTAGCATAAATTTTC 57.056 37.500 0.00 0.00 38.13 2.29
231 232 5.828328 ACCTACTGCCTAGCATAAATTTTCC 59.172 40.000 0.00 0.00 38.13 3.13
232 233 4.900635 ACTGCCTAGCATAAATTTTCCG 57.099 40.909 0.00 0.00 38.13 4.30
233 234 3.066760 ACTGCCTAGCATAAATTTTCCGC 59.933 43.478 0.00 0.00 38.13 5.54
234 235 3.020274 TGCCTAGCATAAATTTTCCGCA 58.980 40.909 0.00 0.00 31.71 5.69
348 349 2.420129 CGATGAGGATCTCCCCGTTTTT 60.420 50.000 0.00 0.00 36.42 1.94
362 363 5.593502 TCCCCGTTTTTATTGCCGTATAAAT 59.406 36.000 0.00 0.00 31.88 1.40
390 391 3.192422 TCAAATCCGTCCAATCGCAATTT 59.808 39.130 0.00 0.00 0.00 1.82
398 399 4.271687 GTCCAATCGCAATTTATGTCGAC 58.728 43.478 9.11 9.11 39.27 4.20
504 505 0.179018 AATATTCCGGCAGGCAGGAC 60.179 55.000 12.75 0.00 39.88 3.85
1143 1213 0.651031 GGTCTTATCGGTTTCGCTGC 59.349 55.000 0.00 0.00 36.13 5.25
1245 1337 2.126189 GCCTTACGTCGTTCGCCT 60.126 61.111 1.78 0.00 44.19 5.52
1252 1344 0.788391 ACGTCGTTCGCCTTTCATTC 59.212 50.000 0.00 0.00 44.19 2.67
1253 1345 0.094730 CGTCGTTCGCCTTTCATTCC 59.905 55.000 0.00 0.00 0.00 3.01
1282 1374 2.900546 TCTGGGTTGTTTTTGTGGTGTT 59.099 40.909 0.00 0.00 0.00 3.32
1283 1375 3.056465 TCTGGGTTGTTTTTGTGGTGTTC 60.056 43.478 0.00 0.00 0.00 3.18
1416 1508 4.704540 CGCTCAGAGAGATCCAGGTATAAT 59.295 45.833 0.00 0.00 0.00 1.28
1417 1509 5.883115 CGCTCAGAGAGATCCAGGTATAATA 59.117 44.000 0.00 0.00 0.00 0.98
1418 1510 6.375736 CGCTCAGAGAGATCCAGGTATAATAA 59.624 42.308 0.00 0.00 0.00 1.40
1419 1511 7.543756 GCTCAGAGAGATCCAGGTATAATAAC 58.456 42.308 0.00 0.00 0.00 1.89
1420 1512 7.177568 GCTCAGAGAGATCCAGGTATAATAACA 59.822 40.741 0.00 0.00 0.00 2.41
1484 1578 3.056607 GTGGCATGAATTTGGTACTGCTT 60.057 43.478 0.00 0.00 0.00 3.91
1545 1639 1.009829 AGTGCGATTTCTGCGATTCC 58.990 50.000 0.00 0.00 34.24 3.01
1561 1655 3.818787 CCCTGATGCCACTTGCGC 61.819 66.667 0.00 0.00 45.60 6.09
1608 1703 0.947244 CTGCCATTGATAAGACGGCC 59.053 55.000 0.00 0.00 42.27 6.13
1634 1730 2.234300 ACAGTACAGGTTGGTTCGTG 57.766 50.000 0.00 0.00 0.00 4.35
1636 1732 0.250166 AGTACAGGTTGGTTCGTGGC 60.250 55.000 0.00 0.00 0.00 5.01
1637 1733 0.250166 GTACAGGTTGGTTCGTGGCT 60.250 55.000 0.00 0.00 0.00 4.75
1690 1786 6.070538 ACTGAGCAAGGACTGTTGAATATAGT 60.071 38.462 0.00 0.00 0.00 2.12
1695 1791 6.250819 CAAGGACTGTTGAATATAGTTTGCG 58.749 40.000 0.00 0.00 0.00 4.85
1731 1827 3.429141 CGCTTCAGGCTGTGCTGG 61.429 66.667 23.96 12.06 39.13 4.85
1757 1853 4.428294 TCCTGCCATGATTCTAGGAAAG 57.572 45.455 0.00 0.00 34.77 2.62
1973 2075 5.920840 GGATTTTCCTGTTTCTACACTTTGC 59.079 40.000 0.00 0.00 32.53 3.68
1974 2076 4.911514 TTTCCTGTTTCTACACTTTGCC 57.088 40.909 0.00 0.00 0.00 4.52
2091 2193 6.879458 AGAAGGATGGTATCATATAAAACGGC 59.121 38.462 0.00 0.00 32.98 5.68
2133 2236 8.967664 AAACACAACTAGTATGTTTGGACTTA 57.032 30.769 25.97 0.00 43.19 2.24
2164 2267 5.401531 TCTAGTTGTATCTGTTGGTGGAC 57.598 43.478 0.00 0.00 0.00 4.02
2323 2426 3.138304 TGATACCAATATCGGTGCTTGC 58.862 45.455 0.00 0.00 40.26 4.01
2336 2440 3.365868 CGGTGCTTGCTATTTGCTGTTTA 60.366 43.478 0.00 0.00 43.37 2.01
2337 2441 4.675146 CGGTGCTTGCTATTTGCTGTTTAT 60.675 41.667 0.00 0.00 43.37 1.40
2415 2519 5.643348 TGTACCATGACAATAACTGCTCAAG 59.357 40.000 0.00 0.00 0.00 3.02
2652 2759 4.006319 ACCTGTGCTAAGATCTTTTGAGC 58.994 43.478 14.36 16.60 34.56 4.26
2858 2966 4.944962 TGTCTTTAGATCCATTTGCACG 57.055 40.909 0.00 0.00 0.00 5.34
2998 3106 2.158971 GCCAAAGGGTTTCAAGCTTGAA 60.159 45.455 32.86 32.86 39.60 2.69
3061 3169 5.676532 TTTCGAAAACGTACCACATGATT 57.323 34.783 8.44 0.00 0.00 2.57
3329 3437 2.303022 TCCACCTCAAGTTCCTGATGAC 59.697 50.000 0.00 0.00 0.00 3.06
3402 3512 5.391950 GCTCTTGTGTTTGAAACTTCTGTGA 60.392 40.000 9.69 0.47 0.00 3.58
3416 3526 4.694509 ACTTCTGTGAGAGCATGATTTGAC 59.305 41.667 0.00 0.00 0.00 3.18
3487 3597 8.758829 AGCAAGATTATGATATCGGGTATGTAA 58.241 33.333 0.00 0.00 0.00 2.41
3498 3608 8.948631 ATATCGGGTATGTAAAATATGCTCTG 57.051 34.615 0.00 0.00 0.00 3.35
3529 3639 5.939883 ACTGCAGTTCTATGCTTCAATGTTA 59.060 36.000 15.25 0.00 46.63 2.41
3544 3654 8.940952 GCTTCAATGTTAGTTCTCTGTTCTAAT 58.059 33.333 0.00 0.00 0.00 1.73
3643 3757 2.670414 CGCTCAAGATGAGGACTTTGAC 59.330 50.000 9.25 0.00 44.43 3.18
3682 3796 6.756221 TGATGAAGATGATGACGAAGATGAT 58.244 36.000 0.00 0.00 0.00 2.45
3709 3823 4.765629 AGGATGAAGATGAGGATGAGGAT 58.234 43.478 0.00 0.00 0.00 3.24
3727 3841 4.222336 AGGATGACGAGGAAGATGAAGAT 58.778 43.478 0.00 0.00 0.00 2.40
3787 3901 5.376625 AGAGTTGTTTCATGCTCCTGTTAA 58.623 37.500 0.00 0.00 0.00 2.01
3789 3903 7.168219 AGAGTTGTTTCATGCTCCTGTTAATA 58.832 34.615 0.00 0.00 0.00 0.98
3790 3904 7.335422 AGAGTTGTTTCATGCTCCTGTTAATAG 59.665 37.037 0.00 0.00 0.00 1.73
3802 3923 4.081087 TCCTGTTAATAGGTTCAGTCCAGC 60.081 45.833 16.95 0.00 38.99 4.85
3803 3924 3.857052 TGTTAATAGGTTCAGTCCAGCG 58.143 45.455 0.00 0.00 0.00 5.18
3804 3925 3.259876 TGTTAATAGGTTCAGTCCAGCGT 59.740 43.478 0.00 0.00 0.00 5.07
3805 3926 2.674796 AATAGGTTCAGTCCAGCGTC 57.325 50.000 0.00 0.00 0.00 5.19
3809 3930 2.111384 AGGTTCAGTCCAGCGTCATAT 58.889 47.619 0.00 0.00 0.00 1.78
3814 3935 5.324697 GTTCAGTCCAGCGTCATATTTTTC 58.675 41.667 0.00 0.00 0.00 2.29
3817 3938 2.031683 GTCCAGCGTCATATTTTTCCCG 59.968 50.000 0.00 0.00 0.00 5.14
3847 3968 5.163416 CCTTTGTTGATTTGAACAGAAGGGT 60.163 40.000 0.42 0.00 38.62 4.34
3971 4092 1.340889 TGTTTGGTTCTGCTTGATGCC 59.659 47.619 0.00 0.00 42.00 4.40
4012 4133 2.276740 GAGCCAGTGGGGGATTGG 59.723 66.667 12.15 0.00 37.04 3.16
4015 4136 1.229177 GCCAGTGGGGGATTGGTTT 60.229 57.895 12.15 0.00 33.84 3.27
4016 4137 0.835971 GCCAGTGGGGGATTGGTTTT 60.836 55.000 12.15 0.00 33.84 2.43
4019 4140 1.344114 CAGTGGGGGATTGGTTTTGTG 59.656 52.381 0.00 0.00 0.00 3.33
4100 4234 8.865090 TCAATTGTTGTATTGGGTTGAAATACT 58.135 29.630 5.13 0.00 39.94 2.12
4135 4269 2.195922 CGAGTGATCATCGATGTTGCA 58.804 47.619 24.09 16.96 42.76 4.08
4162 4296 3.136809 TGGTAGTCCTACTTGTTTTGCCA 59.863 43.478 4.58 0.00 36.36 4.92
4251 4386 1.143183 GGCTATTTCTCGGGTCGCA 59.857 57.895 0.00 0.00 0.00 5.10
4287 4422 0.179032 TGTCGAAAGGCCTGAGCAAA 60.179 50.000 5.69 0.00 42.56 3.68
4288 4423 0.519077 GTCGAAAGGCCTGAGCAAAG 59.481 55.000 5.69 0.00 42.56 2.77
4349 4499 1.619654 CAGTGTGGAGGCCAAAATCA 58.380 50.000 5.01 0.00 34.18 2.57
4393 4543 8.888332 CCTTTTGGTTTCAATGTTTACAAAAC 57.112 30.769 0.00 0.00 34.08 2.43
4394 4544 8.726068 CCTTTTGGTTTCAATGTTTACAAAACT 58.274 29.630 4.35 0.00 34.08 2.66
4395 4545 9.540431 CTTTTGGTTTCAATGTTTACAAAACTG 57.460 29.630 4.35 0.00 34.08 3.16
4396 4546 7.602517 TTGGTTTCAATGTTTACAAAACTGG 57.397 32.000 4.35 0.00 31.99 4.00
4397 4547 6.936279 TGGTTTCAATGTTTACAAAACTGGA 58.064 32.000 4.35 0.00 31.99 3.86
4398 4548 7.386851 TGGTTTCAATGTTTACAAAACTGGAA 58.613 30.769 4.35 3.19 31.99 3.53
4399 4549 7.332182 TGGTTTCAATGTTTACAAAACTGGAAC 59.668 33.333 4.35 5.95 31.99 3.62
4403 4553 7.032580 TCAATGTTTACAAAACTGGAACACTG 58.967 34.615 4.35 0.00 33.58 3.66
4405 4555 5.945155 TGTTTACAAAACTGGAACACTGTC 58.055 37.500 4.35 0.00 0.00 3.51
4407 4557 2.014128 ACAAAACTGGAACACTGTCCG 58.986 47.619 0.00 0.00 40.96 4.79
4408 4558 2.285083 CAAAACTGGAACACTGTCCGA 58.715 47.619 0.00 0.00 40.96 4.55
4490 4640 4.628333 CAGGAAAAGTTAGTAATCCGCGAA 59.372 41.667 8.23 0.00 35.31 4.70
4500 4675 2.403252 AATCCGCGAAGACTTTGGAT 57.597 45.000 8.23 10.26 41.09 3.41
4509 4684 4.631813 GCGAAGACTTTGGATATCACTTGT 59.368 41.667 4.83 0.00 0.00 3.16
4546 4721 4.083110 GCATCAGAAAGCAGCTGTCTTTTA 60.083 41.667 26.18 18.69 34.24 1.52
4602 4777 4.360951 AAGGAATGTTCGTTTGGAGGTA 57.639 40.909 0.00 0.00 31.89 3.08
4649 4894 7.875327 AAACACTACTTGTCATGGTTTTAGT 57.125 32.000 0.00 0.00 37.51 2.24
4653 4898 8.863086 ACACTACTTGTCATGGTTTTAGTAGTA 58.137 33.333 18.02 0.00 43.69 1.82
4654 4899 9.355215 CACTACTTGTCATGGTTTTAGTAGTAG 57.645 37.037 18.02 0.00 43.69 2.57
4655 4900 9.086758 ACTACTTGTCATGGTTTTAGTAGTAGT 57.913 33.333 17.45 0.00 43.69 2.73
4768 5170 6.586344 CCTGATTATGAACTCCTTGAGCTAA 58.414 40.000 0.00 0.00 32.04 3.09
4769 5171 7.050377 CCTGATTATGAACTCCTTGAGCTAAA 58.950 38.462 0.00 0.00 32.04 1.85
4770 5172 7.718753 CCTGATTATGAACTCCTTGAGCTAAAT 59.281 37.037 0.00 0.00 32.04 1.40
4771 5173 8.442632 TGATTATGAACTCCTTGAGCTAAATG 57.557 34.615 0.00 0.00 32.04 2.32
4772 5174 6.683974 TTATGAACTCCTTGAGCTAAATGC 57.316 37.500 0.00 0.00 43.29 3.56
4773 5175 4.019792 TGAACTCCTTGAGCTAAATGCA 57.980 40.909 0.00 0.00 45.94 3.96
4774 5176 4.592942 TGAACTCCTTGAGCTAAATGCAT 58.407 39.130 0.00 0.00 45.94 3.96
4775 5177 4.397103 TGAACTCCTTGAGCTAAATGCATG 59.603 41.667 0.00 0.00 45.94 4.06
4776 5178 4.226427 ACTCCTTGAGCTAAATGCATGA 57.774 40.909 0.00 0.00 45.94 3.07
4783 5185 4.081406 TGAGCTAAATGCATGACAAAGGT 58.919 39.130 0.00 0.00 45.94 3.50
4872 5290 4.511826 CACTCTTTCAGTGTAGTTCCAACC 59.488 45.833 0.00 0.00 46.81 3.77
4879 5297 2.104281 AGTGTAGTTCCAACCTCACCAC 59.896 50.000 9.52 0.00 35.27 4.16
4881 5299 1.418637 GTAGTTCCAACCTCACCACCA 59.581 52.381 0.00 0.00 0.00 4.17
4882 5300 0.474184 AGTTCCAACCTCACCACCAG 59.526 55.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.962155 ACAACCCAGAAACACAACAAAAA 58.038 34.783 0.00 0.00 0.00 1.94
5 6 4.608948 ACAACCCAGAAACACAACAAAA 57.391 36.364 0.00 0.00 0.00 2.44
6 7 4.282195 AGAACAACCCAGAAACACAACAAA 59.718 37.500 0.00 0.00 0.00 2.83
7 8 3.829601 AGAACAACCCAGAAACACAACAA 59.170 39.130 0.00 0.00 0.00 2.83
8 9 3.426615 AGAACAACCCAGAAACACAACA 58.573 40.909 0.00 0.00 0.00 3.33
9 10 4.082463 TCAAGAACAACCCAGAAACACAAC 60.082 41.667 0.00 0.00 0.00 3.32
10 11 4.082845 TCAAGAACAACCCAGAAACACAA 58.917 39.130 0.00 0.00 0.00 3.33
11 12 3.691575 TCAAGAACAACCCAGAAACACA 58.308 40.909 0.00 0.00 0.00 3.72
12 13 3.066760 CCTCAAGAACAACCCAGAAACAC 59.933 47.826 0.00 0.00 0.00 3.32
13 14 3.287222 CCTCAAGAACAACCCAGAAACA 58.713 45.455 0.00 0.00 0.00 2.83
14 15 3.066760 CACCTCAAGAACAACCCAGAAAC 59.933 47.826 0.00 0.00 0.00 2.78
15 16 3.287222 CACCTCAAGAACAACCCAGAAA 58.713 45.455 0.00 0.00 0.00 2.52
16 17 2.422803 CCACCTCAAGAACAACCCAGAA 60.423 50.000 0.00 0.00 0.00 3.02
17 18 1.142870 CCACCTCAAGAACAACCCAGA 59.857 52.381 0.00 0.00 0.00 3.86
18 19 1.142870 TCCACCTCAAGAACAACCCAG 59.857 52.381 0.00 0.00 0.00 4.45
19 20 1.217916 TCCACCTCAAGAACAACCCA 58.782 50.000 0.00 0.00 0.00 4.51
20 21 2.162681 CATCCACCTCAAGAACAACCC 58.837 52.381 0.00 0.00 0.00 4.11
21 22 2.863809 ACATCCACCTCAAGAACAACC 58.136 47.619 0.00 0.00 0.00 3.77
22 23 4.918810 AAACATCCACCTCAAGAACAAC 57.081 40.909 0.00 0.00 0.00 3.32
23 24 4.709397 ACAAAACATCCACCTCAAGAACAA 59.291 37.500 0.00 0.00 0.00 2.83
24 25 4.277476 ACAAAACATCCACCTCAAGAACA 58.723 39.130 0.00 0.00 0.00 3.18
25 26 4.918810 ACAAAACATCCACCTCAAGAAC 57.081 40.909 0.00 0.00 0.00 3.01
26 27 7.595819 AATAACAAAACATCCACCTCAAGAA 57.404 32.000 0.00 0.00 0.00 2.52
27 28 7.595819 AAATAACAAAACATCCACCTCAAGA 57.404 32.000 0.00 0.00 0.00 3.02
28 29 7.710475 ACAAAATAACAAAACATCCACCTCAAG 59.290 33.333 0.00 0.00 0.00 3.02
29 30 7.560368 ACAAAATAACAAAACATCCACCTCAA 58.440 30.769 0.00 0.00 0.00 3.02
30 31 7.118496 ACAAAATAACAAAACATCCACCTCA 57.882 32.000 0.00 0.00 0.00 3.86
31 32 7.494298 ACAACAAAATAACAAAACATCCACCTC 59.506 33.333 0.00 0.00 0.00 3.85
32 33 7.334858 ACAACAAAATAACAAAACATCCACCT 58.665 30.769 0.00 0.00 0.00 4.00
33 34 7.546778 ACAACAAAATAACAAAACATCCACC 57.453 32.000 0.00 0.00 0.00 4.61
34 35 8.544597 GGTACAACAAAATAACAAAACATCCAC 58.455 33.333 0.00 0.00 0.00 4.02
35 36 7.435488 CGGTACAACAAAATAACAAAACATCCA 59.565 33.333 0.00 0.00 0.00 3.41
36 37 7.648510 TCGGTACAACAAAATAACAAAACATCC 59.351 33.333 0.00 0.00 0.00 3.51
37 38 8.563289 TCGGTACAACAAAATAACAAAACATC 57.437 30.769 0.00 0.00 0.00 3.06
38 39 8.192110 ACTCGGTACAACAAAATAACAAAACAT 58.808 29.630 0.00 0.00 0.00 2.71
39 40 7.536855 ACTCGGTACAACAAAATAACAAAACA 58.463 30.769 0.00 0.00 0.00 2.83
40 41 7.974243 ACTCGGTACAACAAAATAACAAAAC 57.026 32.000 0.00 0.00 0.00 2.43
43 44 9.881529 GAATTACTCGGTACAACAAAATAACAA 57.118 29.630 0.00 0.00 0.00 2.83
44 45 9.275398 AGAATTACTCGGTACAACAAAATAACA 57.725 29.630 0.00 0.00 0.00 2.41
45 46 9.750882 GAGAATTACTCGGTACAACAAAATAAC 57.249 33.333 0.00 0.00 35.84 1.89
61 62 9.535878 AATTAGATTCCTGTTCGAGAATTACTC 57.464 33.333 0.00 0.00 41.79 2.59
62 63 9.892130 AAATTAGATTCCTGTTCGAGAATTACT 57.108 29.630 0.00 0.00 32.91 2.24
65 66 9.454859 AGAAAATTAGATTCCTGTTCGAGAATT 57.545 29.630 0.00 0.00 32.91 2.17
66 67 9.454859 AAGAAAATTAGATTCCTGTTCGAGAAT 57.545 29.630 0.00 0.00 35.43 2.40
67 68 8.848474 AAGAAAATTAGATTCCTGTTCGAGAA 57.152 30.769 0.00 0.00 0.00 2.87
68 69 8.848474 AAAGAAAATTAGATTCCTGTTCGAGA 57.152 30.769 0.00 0.00 0.00 4.04
70 71 9.938280 TCTAAAGAAAATTAGATTCCTGTTCGA 57.062 29.630 0.00 0.00 37.07 3.71
74 75 9.720769 TCGTTCTAAAGAAAATTAGATTCCTGT 57.279 29.630 0.00 0.00 40.57 4.00
81 82 9.886132 AGGCTTATCGTTCTAAAGAAAATTAGA 57.114 29.630 0.00 0.00 39.51 2.10
88 89 9.886132 AGAAAATAGGCTTATCGTTCTAAAGAA 57.114 29.630 11.04 0.00 28.91 2.52
94 95 9.110502 CCTTTTAGAAAATAGGCTTATCGTTCT 57.889 33.333 14.99 14.99 32.53 3.01
95 96 9.106070 TCCTTTTAGAAAATAGGCTTATCGTTC 57.894 33.333 0.00 4.81 34.70 3.95
96 97 8.890718 GTCCTTTTAGAAAATAGGCTTATCGTT 58.109 33.333 0.00 0.00 34.70 3.85
97 98 8.044908 TGTCCTTTTAGAAAATAGGCTTATCGT 58.955 33.333 0.00 0.00 34.70 3.73
98 99 8.433421 TGTCCTTTTAGAAAATAGGCTTATCG 57.567 34.615 0.00 0.00 34.70 2.92
102 103 9.700831 ATGTATGTCCTTTTAGAAAATAGGCTT 57.299 29.630 0.00 0.00 34.70 4.35
163 164 9.747898 ACAGACAACAAGGGTTTATATAATTGA 57.252 29.630 11.65 0.00 34.21 2.57
165 166 9.185680 GGACAGACAACAAGGGTTTATATAATT 57.814 33.333 0.00 0.00 34.21 1.40
166 167 8.557450 AGGACAGACAACAAGGGTTTATATAAT 58.443 33.333 0.00 0.00 34.21 1.28
167 168 7.924541 AGGACAGACAACAAGGGTTTATATAA 58.075 34.615 0.00 0.00 34.21 0.98
168 169 7.504926 AGGACAGACAACAAGGGTTTATATA 57.495 36.000 0.00 0.00 34.21 0.86
169 170 6.388619 AGGACAGACAACAAGGGTTTATAT 57.611 37.500 0.00 0.00 34.21 0.86
170 171 5.836024 AGGACAGACAACAAGGGTTTATA 57.164 39.130 0.00 0.00 34.21 0.98
171 172 4.724279 AGGACAGACAACAAGGGTTTAT 57.276 40.909 0.00 0.00 34.21 1.40
172 173 5.836024 ATAGGACAGACAACAAGGGTTTA 57.164 39.130 0.00 0.00 34.21 2.01
173 174 4.724279 ATAGGACAGACAACAAGGGTTT 57.276 40.909 0.00 0.00 34.21 3.27
174 175 6.012858 TGAATATAGGACAGACAACAAGGGTT 60.013 38.462 0.00 0.00 37.87 4.11
175 176 5.487488 TGAATATAGGACAGACAACAAGGGT 59.513 40.000 0.00 0.00 0.00 4.34
176 177 5.989477 TGAATATAGGACAGACAACAAGGG 58.011 41.667 0.00 0.00 0.00 3.95
177 178 7.065085 CACTTGAATATAGGACAGACAACAAGG 59.935 40.741 0.00 0.00 36.41 3.61
178 179 7.413438 GCACTTGAATATAGGACAGACAACAAG 60.413 40.741 0.00 0.00 37.56 3.16
179 180 6.371548 GCACTTGAATATAGGACAGACAACAA 59.628 38.462 0.00 0.00 0.00 2.83
180 181 5.874810 GCACTTGAATATAGGACAGACAACA 59.125 40.000 0.00 0.00 0.00 3.33
181 182 6.109359 AGCACTTGAATATAGGACAGACAAC 58.891 40.000 0.00 0.00 0.00 3.32
182 183 6.299805 AGCACTTGAATATAGGACAGACAA 57.700 37.500 0.00 0.00 0.00 3.18
183 184 5.939764 AGCACTTGAATATAGGACAGACA 57.060 39.130 0.00 0.00 0.00 3.41
184 185 6.702282 GGTAAGCACTTGAATATAGGACAGAC 59.298 42.308 0.00 0.00 0.00 3.51
185 186 6.611642 AGGTAAGCACTTGAATATAGGACAGA 59.388 38.462 0.00 0.00 0.00 3.41
186 187 6.821388 AGGTAAGCACTTGAATATAGGACAG 58.179 40.000 0.00 0.00 0.00 3.51
187 188 6.808321 AGGTAAGCACTTGAATATAGGACA 57.192 37.500 0.00 0.00 0.00 4.02
188 189 7.868415 CAGTAGGTAAGCACTTGAATATAGGAC 59.132 40.741 0.00 0.00 0.00 3.85
189 190 7.471539 GCAGTAGGTAAGCACTTGAATATAGGA 60.472 40.741 0.00 0.00 0.00 2.94
190 191 6.647067 GCAGTAGGTAAGCACTTGAATATAGG 59.353 42.308 0.00 0.00 0.00 2.57
191 192 6.647067 GGCAGTAGGTAAGCACTTGAATATAG 59.353 42.308 0.00 0.00 0.00 1.31
192 193 6.326583 AGGCAGTAGGTAAGCACTTGAATATA 59.673 38.462 0.00 0.00 0.00 0.86
193 194 5.131142 AGGCAGTAGGTAAGCACTTGAATAT 59.869 40.000 0.00 0.00 0.00 1.28
194 195 4.469945 AGGCAGTAGGTAAGCACTTGAATA 59.530 41.667 0.00 0.00 0.00 1.75
195 196 3.264450 AGGCAGTAGGTAAGCACTTGAAT 59.736 43.478 0.00 0.00 0.00 2.57
196 197 2.637872 AGGCAGTAGGTAAGCACTTGAA 59.362 45.455 0.00 0.00 0.00 2.69
197 198 2.257207 AGGCAGTAGGTAAGCACTTGA 58.743 47.619 0.00 0.00 0.00 3.02
198 199 2.770164 AGGCAGTAGGTAAGCACTTG 57.230 50.000 0.00 0.00 0.00 3.16
199 200 2.168728 GCTAGGCAGTAGGTAAGCACTT 59.831 50.000 0.00 0.00 0.00 3.16
200 201 1.757699 GCTAGGCAGTAGGTAAGCACT 59.242 52.381 0.00 0.00 0.00 4.40
201 202 1.480954 TGCTAGGCAGTAGGTAAGCAC 59.519 52.381 0.00 0.00 35.20 4.40
202 203 1.860641 TGCTAGGCAGTAGGTAAGCA 58.139 50.000 0.00 0.00 37.62 3.91
203 204 4.602340 TTATGCTAGGCAGTAGGTAAGC 57.398 45.455 0.00 0.00 43.65 3.09
204 205 8.451908 AAAATTTATGCTAGGCAGTAGGTAAG 57.548 34.615 0.00 0.00 43.65 2.34
205 206 7.501225 GGAAAATTTATGCTAGGCAGTAGGTAA 59.499 37.037 0.00 0.00 43.65 2.85
206 207 6.996282 GGAAAATTTATGCTAGGCAGTAGGTA 59.004 38.462 0.00 0.00 43.65 3.08
207 208 5.828328 GGAAAATTTATGCTAGGCAGTAGGT 59.172 40.000 0.00 0.00 43.65 3.08
208 209 5.049405 CGGAAAATTTATGCTAGGCAGTAGG 60.049 44.000 0.00 0.00 43.65 3.18
209 210 5.560953 GCGGAAAATTTATGCTAGGCAGTAG 60.561 44.000 0.00 0.00 43.65 2.57
210 211 4.274950 GCGGAAAATTTATGCTAGGCAGTA 59.725 41.667 0.00 0.00 43.65 2.74
211 212 3.066760 GCGGAAAATTTATGCTAGGCAGT 59.933 43.478 0.00 0.00 43.65 4.40
212 213 3.066621 TGCGGAAAATTTATGCTAGGCAG 59.933 43.478 9.66 0.00 43.65 4.85
213 214 3.020274 TGCGGAAAATTTATGCTAGGCA 58.980 40.909 9.66 0.00 44.86 4.75
214 215 3.708563 TGCGGAAAATTTATGCTAGGC 57.291 42.857 9.66 0.00 0.00 3.93
215 216 6.312399 TGTATGCGGAAAATTTATGCTAGG 57.688 37.500 9.66 0.00 0.00 3.02
216 217 9.891828 TTATTGTATGCGGAAAATTTATGCTAG 57.108 29.630 9.66 0.00 0.00 3.42
218 219 9.410556 GATTATTGTATGCGGAAAATTTATGCT 57.589 29.630 9.66 1.05 0.00 3.79
219 220 9.410556 AGATTATTGTATGCGGAAAATTTATGC 57.589 29.630 0.00 0.00 0.00 3.14
222 223 9.743057 CCAAGATTATTGTATGCGGAAAATTTA 57.257 29.630 0.00 0.00 0.00 1.40
223 224 7.224557 GCCAAGATTATTGTATGCGGAAAATTT 59.775 33.333 0.00 0.00 0.00 1.82
224 225 6.701400 GCCAAGATTATTGTATGCGGAAAATT 59.299 34.615 0.00 0.00 0.00 1.82
225 226 6.183360 TGCCAAGATTATTGTATGCGGAAAAT 60.183 34.615 0.00 0.00 0.00 1.82
226 227 5.126222 TGCCAAGATTATTGTATGCGGAAAA 59.874 36.000 0.00 0.00 0.00 2.29
227 228 4.642437 TGCCAAGATTATTGTATGCGGAAA 59.358 37.500 0.00 0.00 0.00 3.13
228 229 4.036262 GTGCCAAGATTATTGTATGCGGAA 59.964 41.667 0.00 0.00 0.00 4.30
229 230 3.563808 GTGCCAAGATTATTGTATGCGGA 59.436 43.478 0.00 0.00 0.00 5.54
230 231 3.606846 CGTGCCAAGATTATTGTATGCGG 60.607 47.826 0.00 0.00 0.00 5.69
231 232 3.544651 CGTGCCAAGATTATTGTATGCG 58.455 45.455 0.00 0.00 0.00 4.73
232 233 3.563808 TCCGTGCCAAGATTATTGTATGC 59.436 43.478 0.00 0.00 0.00 3.14
233 234 5.702670 AGATCCGTGCCAAGATTATTGTATG 59.297 40.000 0.00 0.00 0.00 2.39
234 235 5.869579 AGATCCGTGCCAAGATTATTGTAT 58.130 37.500 0.00 0.00 0.00 2.29
348 349 7.867305 TTTGAGGTGAATTTATACGGCAATA 57.133 32.000 0.00 0.00 0.00 1.90
362 363 2.940994 TTGGACGGATTTGAGGTGAA 57.059 45.000 0.00 0.00 0.00 3.18
390 391 2.355986 AAGCCAGCCCGTCGACATA 61.356 57.895 17.16 0.00 0.00 2.29
504 505 3.343788 GAGACGGACGGTGCTCCTG 62.344 68.421 2.85 0.00 0.00 3.86
609 644 3.574780 GGCCGCGATTTATAGCCC 58.425 61.111 8.23 0.00 37.66 5.19
611 646 1.866925 GTGGGCCGCGATTTATAGC 59.133 57.895 8.23 0.00 0.00 2.97
1087 1155 3.215587 AACAGCAGCAAGGAGGGGG 62.216 63.158 0.00 0.00 0.00 5.40
1088 1156 1.975407 CAACAGCAGCAAGGAGGGG 60.975 63.158 0.00 0.00 0.00 4.79
1092 1160 2.979676 CGGCAACAGCAGCAAGGA 60.980 61.111 0.00 0.00 0.00 3.36
1143 1213 1.081892 CTCTGCATCGAAACCACCAG 58.918 55.000 0.00 0.00 0.00 4.00
1245 1337 0.332632 CAGAGCCCCCTGGAATGAAA 59.667 55.000 0.00 0.00 0.00 2.69
1253 1345 2.371897 AAACAACCCAGAGCCCCCTG 62.372 60.000 0.00 0.00 0.00 4.45
1282 1374 1.375908 GCACCGAATCAGCACAGGA 60.376 57.895 0.00 0.00 0.00 3.86
1283 1375 1.376424 AGCACCGAATCAGCACAGG 60.376 57.895 0.00 0.00 0.00 4.00
1416 1508 2.037511 CGTAGTGGAACCCCTGTTGTTA 59.962 50.000 0.00 0.00 37.80 2.41
1417 1509 1.202722 CGTAGTGGAACCCCTGTTGTT 60.203 52.381 0.00 0.00 37.80 2.83
1418 1510 0.395312 CGTAGTGGAACCCCTGTTGT 59.605 55.000 0.00 0.00 37.80 3.32
1419 1511 0.953960 GCGTAGTGGAACCCCTGTTG 60.954 60.000 0.00 0.00 37.80 3.33
1420 1512 1.373812 GCGTAGTGGAACCCCTGTT 59.626 57.895 0.00 0.00 37.80 3.16
1484 1578 2.016393 CTGCCGCGAATCACCTAGGA 62.016 60.000 17.98 0.00 0.00 2.94
1545 1639 1.434622 CTAGCGCAAGTGGCATCAGG 61.435 60.000 11.47 0.00 45.17 3.86
1561 1655 5.320549 ACCAAGTTGTATGTACCGTCTAG 57.679 43.478 1.45 0.00 0.00 2.43
1624 1720 0.865769 CAGTACAGCCACGAACCAAC 59.134 55.000 0.00 0.00 0.00 3.77
1653 1749 2.680312 TGCTCAGTCAGGATAGCAAC 57.320 50.000 0.00 0.00 41.74 4.17
1690 1786 1.807742 ACTAATAAGCAACCGCGCAAA 59.192 42.857 8.75 0.00 45.49 3.68
1695 1791 1.326548 CGTCCACTAATAAGCAACCGC 59.673 52.381 0.00 0.00 38.99 5.68
1731 1827 4.070716 CCTAGAATCATGGCAGGAATCAC 58.929 47.826 18.29 5.31 0.00 3.06
1757 1853 7.206687 ACTAAAATCTAGACAGCTGCTATCAC 58.793 38.462 15.27 0.00 0.00 3.06
1973 2075 2.093783 GTCGCCTTGTTCGAAATACTGG 59.906 50.000 0.00 0.00 37.73 4.00
1974 2076 2.734606 TGTCGCCTTGTTCGAAATACTG 59.265 45.455 0.00 0.00 37.73 2.74
2091 2193 5.355596 TGTGTTTTCCAAAAATAGCCAGTG 58.644 37.500 0.00 0.00 0.00 3.66
2138 2241 8.204836 GTCCACCAACAGATACAACTAGATTAT 58.795 37.037 0.00 0.00 0.00 1.28
2156 2259 6.460953 GCAAACAAAGATAAGAAGTCCACCAA 60.461 38.462 0.00 0.00 0.00 3.67
2164 2267 5.632347 CCAAGCAGCAAACAAAGATAAGAAG 59.368 40.000 0.00 0.00 0.00 2.85
2323 2426 5.807011 GGCAACAGGAATAAACAGCAAATAG 59.193 40.000 0.00 0.00 0.00 1.73
2449 2553 7.977789 TCAAGACAGCTTGTATTGTATGAAA 57.022 32.000 17.31 2.10 46.33 2.69
2652 2759 6.489022 TGATCTCCATCCAGCATAGAAAATTG 59.511 38.462 0.00 0.00 0.00 2.32
2719 2826 6.600388 TCTGCAGGGAAGCATAATATACAAA 58.400 36.000 15.13 0.00 44.68 2.83
2728 2835 1.583556 TTCCTCTGCAGGGAAGCATA 58.416 50.000 24.49 9.52 44.68 3.14
2998 3106 9.927081 AAGAATGGATTAGTATTGAAGTGGAAT 57.073 29.630 0.00 0.00 0.00 3.01
3061 3169 6.612863 TCTCTAGGATTGGTTCATCTTCATCA 59.387 38.462 0.00 0.00 0.00 3.07
3329 3437 6.226052 TGTATCCTCATCAATTTCCTCATCG 58.774 40.000 0.00 0.00 0.00 3.84
3362 3470 5.010012 CACAAGAGCAAACATAAAGGAGGTT 59.990 40.000 0.00 0.00 32.12 3.50
3376 3484 5.048083 ACAGAAGTTTCAAACACAAGAGCAA 60.048 36.000 2.41 0.00 0.00 3.91
3402 3512 5.128991 TGAGAGAGATGTCAAATCATGCTCT 59.871 40.000 0.00 0.00 38.10 4.09
3416 3526 6.522946 TCAGCCTATTGAAATGAGAGAGATG 58.477 40.000 0.00 0.00 0.00 2.90
3544 3654 6.973642 AGATCTGGGAAACAAGAATGGATAA 58.026 36.000 0.00 0.00 0.00 1.75
3670 3784 3.018423 TCCTCCTCATCATCTTCGTCA 57.982 47.619 0.00 0.00 0.00 4.35
3682 3796 3.695357 TCCTCATCTTCATCCTCCTCA 57.305 47.619 0.00 0.00 0.00 3.86
3709 3823 4.646492 TCATCATCTTCATCTTCCTCGTCA 59.354 41.667 0.00 0.00 0.00 4.35
3727 3841 4.405680 ACCTTCTTATCACCATCGTCATCA 59.594 41.667 0.00 0.00 0.00 3.07
3787 3901 1.557099 TGACGCTGGACTGAACCTAT 58.443 50.000 0.00 0.00 0.00 2.57
3789 3903 1.557099 TATGACGCTGGACTGAACCT 58.443 50.000 0.00 0.00 0.00 3.50
3790 3904 2.604046 ATATGACGCTGGACTGAACC 57.396 50.000 0.00 0.00 0.00 3.62
3802 3923 5.705902 AGGAAAAACGGGAAAAATATGACG 58.294 37.500 0.00 0.00 0.00 4.35
3803 3924 7.439955 ACAAAGGAAAAACGGGAAAAATATGAC 59.560 33.333 0.00 0.00 0.00 3.06
3804 3925 7.501844 ACAAAGGAAAAACGGGAAAAATATGA 58.498 30.769 0.00 0.00 0.00 2.15
3805 3926 7.722795 ACAAAGGAAAAACGGGAAAAATATG 57.277 32.000 0.00 0.00 0.00 1.78
3809 3930 5.548406 TCAACAAAGGAAAAACGGGAAAAA 58.452 33.333 0.00 0.00 0.00 1.94
3814 3935 5.112686 TCAAATCAACAAAGGAAAAACGGG 58.887 37.500 0.00 0.00 0.00 5.28
3817 3938 8.250538 TCTGTTCAAATCAACAAAGGAAAAAC 57.749 30.769 0.00 0.00 35.83 2.43
3847 3968 4.020617 CCTGCAGGAACTCGCCCA 62.021 66.667 29.88 0.00 34.60 5.36
3971 4092 2.349438 CGGAACCAAACTCAACGACATG 60.349 50.000 0.00 0.00 0.00 3.21
4012 4133 1.737201 CCCACCGGTTCCACAAAAC 59.263 57.895 2.97 0.00 0.00 2.43
4015 4136 3.892162 CCCCCACCGGTTCCACAA 61.892 66.667 2.97 0.00 0.00 3.33
4135 4269 6.183360 GCAAAACAAGTAGGACTACCAAACTT 60.183 38.462 5.90 0.00 41.81 2.66
4251 4386 4.439057 TCGACACAAGTTTAGTTTCAGCT 58.561 39.130 0.00 0.00 0.00 4.24
4287 4422 3.513515 TGAAACCAGTGAAACCAAAAGCT 59.486 39.130 0.00 0.00 37.80 3.74
4288 4423 3.855858 TGAAACCAGTGAAACCAAAAGC 58.144 40.909 0.00 0.00 37.80 3.51
4341 4491 4.508461 TCACAGCAGACATTGATTTTGG 57.492 40.909 0.00 0.00 0.00 3.28
4349 4499 6.655078 AAAGGTTTAATCACAGCAGACATT 57.345 33.333 0.00 0.00 0.00 2.71
4381 4531 6.405397 GGACAGTGTTCCAGTTTTGTAAACAT 60.405 38.462 0.00 0.00 35.49 2.71
4388 4538 2.031683 GTCGGACAGTGTTCCAGTTTTG 59.968 50.000 2.62 0.00 35.04 2.44
4389 4539 2.285977 GTCGGACAGTGTTCCAGTTTT 58.714 47.619 2.62 0.00 35.04 2.43
4391 4541 0.249322 CGTCGGACAGTGTTCCAGTT 60.249 55.000 9.10 0.00 35.04 3.16
4392 4542 1.362717 CGTCGGACAGTGTTCCAGT 59.637 57.895 9.10 0.00 35.04 4.00
4393 4543 0.939577 CACGTCGGACAGTGTTCCAG 60.940 60.000 18.45 0.00 35.04 3.86
4394 4544 1.066752 CACGTCGGACAGTGTTCCA 59.933 57.895 18.45 0.00 35.04 3.53
4395 4545 1.663702 CCACGTCGGACAGTGTTCC 60.664 63.158 22.17 0.00 36.69 3.62
4396 4546 0.663568 CTCCACGTCGGACAGTGTTC 60.664 60.000 22.17 0.00 39.64 3.18
4397 4547 1.362717 CTCCACGTCGGACAGTGTT 59.637 57.895 22.17 0.00 39.64 3.32
4398 4548 2.561956 CCTCCACGTCGGACAGTGT 61.562 63.158 22.17 0.00 39.64 3.55
4399 4549 2.258591 CCTCCACGTCGGACAGTG 59.741 66.667 19.25 19.25 39.64 3.66
4403 4553 2.091102 TTTCACCCTCCACGTCGGAC 62.091 60.000 0.00 0.00 39.64 4.79
4405 4555 0.739813 GATTTCACCCTCCACGTCGG 60.740 60.000 0.00 0.00 0.00 4.79
4407 4557 0.739813 CCGATTTCACCCTCCACGTC 60.740 60.000 0.00 0.00 0.00 4.34
4408 4558 1.189524 TCCGATTTCACCCTCCACGT 61.190 55.000 0.00 0.00 0.00 4.49
4419 4569 1.063764 ACGCGTAGAGTCTCCGATTTC 59.936 52.381 11.67 0.00 33.29 2.17
4490 4640 6.344500 CAGCTACAAGTGATATCCAAAGTCT 58.656 40.000 0.00 0.00 0.00 3.24
4500 4675 6.426980 CAGAAAATGCAGCTACAAGTGATA 57.573 37.500 0.00 0.00 0.00 2.15
4529 4704 7.339953 CACAAAAATAAAAGACAGCTGCTTTC 58.660 34.615 25.85 13.74 34.68 2.62
4536 4711 8.693542 AGATATGCACAAAAATAAAAGACAGC 57.306 30.769 0.00 0.00 0.00 4.40
4546 4721 5.507817 CCGTGCCATAGATATGCACAAAAAT 60.508 40.000 13.47 0.00 38.96 1.82
4602 4777 0.266152 ATCCGTTCCTCCCTCTCCAT 59.734 55.000 0.00 0.00 0.00 3.41
4653 4898 8.264347 ACCATGGTTTTTGTTCTCATTTAAACT 58.736 29.630 13.00 0.00 0.00 2.66
4654 4899 8.432110 ACCATGGTTTTTGTTCTCATTTAAAC 57.568 30.769 13.00 0.00 0.00 2.01
4655 4900 9.454859 AAACCATGGTTTTTGTTCTCATTTAAA 57.545 25.926 32.77 0.00 44.84 1.52
4773 5175 3.346426 GGTGCAGGACCTTTGTCAT 57.654 52.632 3.25 0.00 43.65 3.06
4774 5176 4.898607 GGTGCAGGACCTTTGTCA 57.101 55.556 3.25 0.00 43.65 3.58
4858 5276 2.104281 GTGGTGAGGTTGGAACTACACT 59.896 50.000 14.21 0.00 36.27 3.55
4872 5290 0.947244 GTGTGCTTTCTGGTGGTGAG 59.053 55.000 0.00 0.00 0.00 3.51
4879 5297 0.535780 TCTGCCTGTGTGCTTTCTGG 60.536 55.000 0.00 0.00 0.00 3.86
4881 5299 0.761187 TCTCTGCCTGTGTGCTTTCT 59.239 50.000 0.00 0.00 0.00 2.52
4882 5300 1.155042 CTCTCTGCCTGTGTGCTTTC 58.845 55.000 0.00 0.00 0.00 2.62


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

AutoCloner maintained by Alex Coulton.