Multiple sequence alignment - TraesCS2B01G081300

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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 TraesCS2B01G081300 chr2B 100.000 5288 0 0 1 5288 45549029 45554316 0.000000e+00 9766.0
1 TraesCS2B01G081300 chr2B 87.392 4069 415 48 714 4754 45672307 45676305 0.000000e+00 4582.0
2 TraesCS2B01G081300 chr2B 87.055 4102 435 48 806 4854 44746113 44742055 0.000000e+00 4545.0
3 TraesCS2B01G081300 chr2B 86.858 1986 226 19 2327 4302 45679788 45681748 0.000000e+00 2189.0
4 TraesCS2B01G081300 chr2B 86.017 236 21 2 266 489 45671638 45671873 5.290000e-60 243.0
5 TraesCS2B01G081300 chr2B 84.937 239 13 7 266 487 44746893 44746661 2.480000e-53 220.0
6 TraesCS2B01G081300 chr2B 84.848 231 18 4 266 479 45033932 45033702 3.210000e-52 217.0
7 TraesCS2B01G081300 chr2B 84.052 232 15 9 1 230 45671319 45671530 2.500000e-48 204.0
8 TraesCS2B01G081300 chr2B 85.714 182 10 7 82 252 44747141 44746965 1.510000e-40 178.0
9 TraesCS2B01G081300 chr2B 90.909 55 5 0 1 55 44747189 44747135 2.040000e-09 75.0
10 TraesCS2B01G081300 chr2D 92.408 3899 263 17 882 4773 27995592 27991720 0.000000e+00 5529.0
11 TraesCS2B01G081300 chr2D 87.647 4007 432 28 329 4300 27953970 27949992 0.000000e+00 4599.0
12 TraesCS2B01G081300 chr2D 86.402 3530 437 34 906 4414 27982279 27978772 0.000000e+00 3819.0
13 TraesCS2B01G081300 chr2D 88.007 3227 348 27 626 3837 27935855 27932653 0.000000e+00 3779.0
14 TraesCS2B01G081300 chr2D 93.304 2240 109 17 340 2564 27968074 27965861 0.000000e+00 3267.0
15 TraesCS2B01G081300 chr2D 90.498 1726 139 15 2698 4419 27965864 27964160 0.000000e+00 2255.0
16 TraesCS2B01G081300 chr2D 87.105 411 52 1 3903 4312 27932612 27932202 1.040000e-126 464.0
17 TraesCS2B01G081300 chr2D 85.283 265 21 8 1 252 27996751 27996492 1.890000e-64 257.0
18 TraesCS2B01G081300 chr2D 84.733 262 17 10 1 252 27968522 27968274 1.900000e-59 241.0
19 TraesCS2B01G081300 chr2D 84.898 245 25 1 266 498 27996392 27996148 2.460000e-58 237.0
20 TraesCS2B01G081300 chr2D 90.789 76 7 0 771 846 27995671 27995596 9.370000e-18 102.0
21 TraesCS2B01G081300 chr2D 94.118 51 0 2 266 313 27968180 27968130 2.040000e-09 75.0
22 TraesCS2B01G081300 chr2D 92.157 51 4 0 4851 4901 27960905 27960955 7.350000e-09 73.1
23 TraesCS2B01G081300 chr2A 88.664 4093 415 28 335 4394 30179736 30175660 0.000000e+00 4942.0
24 TraesCS2B01G081300 chr2A 84.738 3774 502 46 669 4416 30171126 30167401 0.000000e+00 3711.0
25 TraesCS2B01G081300 chr2A 88.149 2177 252 6 1400 3573 30157762 30155589 0.000000e+00 2586.0
26 TraesCS2B01G081300 chr2A 83.437 1292 183 24 588 1870 30159134 30157865 0.000000e+00 1171.0
27 TraesCS2B01G081300 chr2A 87.317 410 52 0 3903 4312 30155141 30154732 2.230000e-128 470.0
28 TraesCS2B01G081300 chr2A 82.890 263 31 7 4515 4770 30175247 30174992 1.920000e-54 224.0
29 TraesCS2B01G081300 chr2A 91.772 158 13 0 5083 5240 758368995 758368838 2.480000e-53 220.0
30 TraesCS2B01G081300 chr3B 96.078 153 6 0 5085 5237 454615570 454615722 3.160000e-62 250.0
31 TraesCS2B01G081300 chr5B 94.194 155 7 2 5083 5236 544531908 544532061 8.850000e-58 235.0
32 TraesCS2B01G081300 chr3A 93.671 158 9 1 5082 5238 535325145 535324988 8.850000e-58 235.0
33 TraesCS2B01G081300 chr3A 93.631 157 9 1 5083 5238 18826410 18826566 3.180000e-57 233.0
34 TraesCS2B01G081300 chr5D 92.949 156 10 1 5082 5236 434755137 434754982 5.330000e-55 226.0
35 TraesCS2B01G081300 chr6D 90.964 166 13 2 5072 5237 414120428 414120591 6.890000e-54 222.0
36 TraesCS2B01G081300 chr6A 90.476 168 14 2 5071 5237 609824719 609824553 2.480000e-53 220.0
37 TraesCS2B01G081300 chr1A 90.361 166 14 2 5073 5237 219381995 219382159 3.210000e-52 217.0


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 TraesCS2B01G081300 chr2B 45549029 45554316 5287 False 9766.00 9766 100.000000 1 5288 1 chr2B.!!$F1 5287
1 TraesCS2B01G081300 chr2B 45671319 45681748 10429 False 1804.50 4582 86.079750 1 4754 4 chr2B.!!$F2 4753
2 TraesCS2B01G081300 chr2B 44742055 44747189 5134 True 1254.50 4545 87.153750 1 4854 4 chr2B.!!$R2 4853
3 TraesCS2B01G081300 chr2D 27949992 27953970 3978 True 4599.00 4599 87.647000 329 4300 1 chr2D.!!$R1 3971
4 TraesCS2B01G081300 chr2D 27978772 27982279 3507 True 3819.00 3819 86.402000 906 4414 1 chr2D.!!$R2 3508
5 TraesCS2B01G081300 chr2D 27932202 27935855 3653 True 2121.50 3779 87.556000 626 4312 2 chr2D.!!$R3 3686
6 TraesCS2B01G081300 chr2D 27991720 27996751 5031 True 1531.25 5529 88.344500 1 4773 4 chr2D.!!$R5 4772
7 TraesCS2B01G081300 chr2D 27964160 27968522 4362 True 1459.50 3267 90.663250 1 4419 4 chr2D.!!$R4 4418
8 TraesCS2B01G081300 chr2A 30167401 30179736 12335 True 2959.00 4942 85.430667 335 4770 3 chr2A.!!$R3 4435
9 TraesCS2B01G081300 chr2A 30154732 30159134 4402 True 1409.00 2586 86.301000 588 4312 3 chr2A.!!$R2 3724

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
178 187 0.602638 TTGATTGCGACTCTGCGGTT 60.603 50.0 0.0 0.0 37.81 4.44 F
1052 1611 0.605319 GTTCCTCCGTTGCACCATGA 60.605 55.0 0.0 0.0 0.00 3.07 F
2109 3241 1.153353 GCAACTTGCTTACTGGCGTA 58.847 50.0 6.5 0.0 40.96 4.42 F
3696 4996 0.036732 TCCACTGCGATTTGAAGCCT 59.963 50.0 0.0 0.0 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1770 2902 1.066573 AGGAGTGAACGCAAGGATGAG 60.067 52.381 0.00 0.00 46.39 2.90 R
2387 3519 0.615331 TGGTCCTGAGAGCATGTTCC 59.385 55.000 5.87 0.00 45.34 3.62 R
3798 5098 0.102481 ATCCAATCGTTCCTCCGACG 59.898 55.000 0.00 0.00 40.08 5.12 R
5255 14986 0.179092 GGCATCAAAGATGCTTGGGC 60.179 55.000 25.61 9.81 44.02 5.36 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
56 58 1.511305 GACATCGGCGTCTCCAAGA 59.489 57.895 6.85 0.00 32.92 3.02
124 133 3.106054 ACCTGCATCTGTCATTCTCTCT 58.894 45.455 0.00 0.00 0.00 3.10
125 134 3.132646 ACCTGCATCTGTCATTCTCTCTC 59.867 47.826 0.00 0.00 0.00 3.20
126 135 3.385433 CCTGCATCTGTCATTCTCTCTCT 59.615 47.826 0.00 0.00 0.00 3.10
127 136 4.500205 CCTGCATCTGTCATTCTCTCTCTC 60.500 50.000 0.00 0.00 0.00 3.20
176 185 1.016130 AGTTGATTGCGACTCTGCGG 61.016 55.000 0.00 0.00 33.31 5.69
177 186 1.005037 TTGATTGCGACTCTGCGGT 60.005 52.632 0.00 0.00 37.81 5.68
178 187 0.602638 TTGATTGCGACTCTGCGGTT 60.603 50.000 0.00 0.00 37.81 4.44
179 188 1.014044 TGATTGCGACTCTGCGGTTC 61.014 55.000 0.00 0.00 37.81 3.62
180 189 0.737715 GATTGCGACTCTGCGGTTCT 60.738 55.000 0.00 0.00 37.81 3.01
197 216 1.019673 TCTCGGGTACGTGATACTGC 58.980 55.000 0.00 0.00 41.85 4.40
206 225 3.829886 ACGTGATACTGCAATTTGTGG 57.170 42.857 0.00 0.00 0.00 4.17
252 272 2.161855 GGAGATGGTGCACACAATTCA 58.838 47.619 20.43 6.42 0.00 2.57
255 275 4.002982 GAGATGGTGCACACAATTCAGTA 58.997 43.478 20.43 0.00 0.00 2.74
256 276 4.592942 AGATGGTGCACACAATTCAGTAT 58.407 39.130 20.43 0.00 0.00 2.12
257 277 5.744171 AGATGGTGCACACAATTCAGTATA 58.256 37.500 20.43 0.00 0.00 1.47
258 278 5.586243 AGATGGTGCACACAATTCAGTATAC 59.414 40.000 20.43 0.00 0.00 1.47
259 279 4.905429 TGGTGCACACAATTCAGTATACT 58.095 39.130 20.43 0.00 0.00 2.12
260 280 5.312895 TGGTGCACACAATTCAGTATACTT 58.687 37.500 20.43 0.00 0.00 2.24
261 281 5.411361 TGGTGCACACAATTCAGTATACTTC 59.589 40.000 20.43 0.00 0.00 3.01
262 282 5.411361 GGTGCACACAATTCAGTATACTTCA 59.589 40.000 20.43 0.00 0.00 3.02
263 283 6.402550 GGTGCACACAATTCAGTATACTTCAG 60.403 42.308 20.43 0.00 0.00 3.02
264 284 6.147821 GTGCACACAATTCAGTATACTTCAGT 59.852 38.462 13.17 0.00 0.00 3.41
265 285 7.330946 GTGCACACAATTCAGTATACTTCAGTA 59.669 37.037 13.17 0.00 34.67 2.74
266 286 8.040727 TGCACACAATTCAGTATACTTCAGTAT 58.959 33.333 1.56 4.87 43.15 2.12
267 287 8.883731 GCACACAATTCAGTATACTTCAGTATT 58.116 33.333 1.56 0.00 41.18 1.89
356 497 1.201647 TCGTGTGGAGGAAGTTCGATC 59.798 52.381 0.00 0.00 0.00 3.69
380 521 3.243724 GGGGATAGCTGGATACTGACTT 58.756 50.000 0.00 0.00 37.83 3.01
381 522 3.648545 GGGGATAGCTGGATACTGACTTT 59.351 47.826 0.00 0.00 37.83 2.66
472 616 2.089980 CCTGCTTCTTGTCCTTGATGG 58.910 52.381 0.00 0.00 37.10 3.51
662 834 1.341080 AGCCAACATGTCCCCTTTTG 58.659 50.000 0.00 0.00 0.00 2.44
768 947 6.159293 TGTACTTGCACTTTGATAGACTCAG 58.841 40.000 0.00 0.00 34.68 3.35
791 970 5.472137 AGTGGTATATGCACACGTTTTCTTT 59.528 36.000 0.00 0.00 39.95 2.52
793 972 6.739550 GTGGTATATGCACACGTTTTCTTTAC 59.260 38.462 0.00 0.00 0.00 2.01
812 991 5.772393 TTACCCACATAAACCTCTCACAT 57.228 39.130 0.00 0.00 0.00 3.21
813 992 6.877668 TTACCCACATAAACCTCTCACATA 57.122 37.500 0.00 0.00 0.00 2.29
846 1369 4.141892 TGCCCAGGCTATTTTTCAATCATG 60.142 41.667 10.58 0.00 42.51 3.07
909 1432 6.313905 ACTGAAGTCAAAGTCAAGTACAAGTG 59.686 38.462 0.00 0.00 0.00 3.16
949 1472 7.542477 CCTTACTTCCACATATATCTAAGCACG 59.458 40.741 0.00 0.00 0.00 5.34
1043 1602 1.279271 CCAATCTCTGGTTCCTCCGTT 59.721 52.381 0.00 0.00 40.78 4.44
1044 1603 2.350522 CAATCTCTGGTTCCTCCGTTG 58.649 52.381 0.00 0.00 39.52 4.10
1052 1611 0.605319 GTTCCTCCGTTGCACCATGA 60.605 55.000 0.00 0.00 0.00 3.07
1322 1881 2.005451 GCTGCTCACAGGAACACTATG 58.995 52.381 0.00 0.00 44.63 2.23
1499 2058 4.280677 AGGTACAGCTGCATCTCTTAGATC 59.719 45.833 15.27 0.00 31.32 2.75
1566 2698 5.790593 TCCTTAGCAAATAGTTCGTCACTT 58.209 37.500 0.00 0.00 36.88 3.16
1604 2736 5.303589 TCTCACGTAATAACTTATCTGGGGG 59.696 44.000 0.00 0.00 0.00 5.40
1640 2772 4.305989 TGTTCAACTCATCCAAACTTGC 57.694 40.909 0.00 0.00 0.00 4.01
1697 2829 4.142160 GGCTATCCCACATTTCCAAAAGAC 60.142 45.833 0.00 0.00 0.00 3.01
1743 2875 2.519013 ACAGGGAATTCACTTTCTGGC 58.481 47.619 7.72 0.00 0.00 4.85
1770 2902 3.026694 ACCAGCATCTTTAGGAAATGCC 58.973 45.455 3.13 0.00 45.42 4.40
1800 2932 1.719600 GTTCACTCCTGCTAGCACAG 58.280 55.000 14.93 14.88 37.42 3.66
1970 3102 6.775708 ACAAATTTACTGGACAGCTACCTTA 58.224 36.000 9.92 0.60 0.00 2.69
2043 3175 2.024176 AATTTCGTGGATCAGTCCCG 57.976 50.000 0.00 0.00 44.41 5.14
2109 3241 1.153353 GCAACTTGCTTACTGGCGTA 58.847 50.000 6.50 0.00 40.96 4.42
2387 3519 2.046023 TCTGCTTGACATGGGCCG 60.046 61.111 0.00 0.00 0.00 6.13
2493 3625 3.688185 CAGGTCAGATTCCATCAACAGTG 59.312 47.826 0.00 0.00 0.00 3.66
2614 3746 6.428771 GCTAAACATGTCAGTTAACCACCTTA 59.571 38.462 0.00 0.00 0.00 2.69
2733 3865 7.259088 AGTTAGTAACCTGATCAATCTTGGT 57.741 36.000 9.46 0.00 36.47 3.67
2756 3888 4.580167 TCTCCTTGATGTTTCCAACAACAG 59.420 41.667 0.67 0.00 45.86 3.16
2819 3951 4.100653 TCAACTGCTATCCCTTCAGATCAG 59.899 45.833 0.00 0.00 0.00 2.90
3166 4322 3.055021 TCCACCAATTACTATTGCCGTGA 60.055 43.478 0.00 0.00 39.87 4.35
3420 4576 7.588497 AGGTTCAAGAAATAGCTTTTTCACT 57.412 32.000 25.27 13.12 37.93 3.41
3457 4613 2.281484 ACACTCGCCACCGCAATT 60.281 55.556 0.00 0.00 34.03 2.32
3510 4666 6.821665 CGGTAGATTTTGAGGGTGAAGAATTA 59.178 38.462 0.00 0.00 0.00 1.40
3696 4996 0.036732 TCCACTGCGATTTGAAGCCT 59.963 50.000 0.00 0.00 0.00 4.58
3751 5051 1.608336 ATCGGTGACTTCGGGTCCA 60.608 57.895 6.91 0.00 43.89 4.02
3798 5098 0.813821 GACCAGAAGGCTTGATTGGC 59.186 55.000 3.46 3.08 39.06 4.52
3838 5138 7.807198 TGGATATATTGCACCTGGTAAGTTAA 58.193 34.615 0.00 0.00 0.00 2.01
3840 5140 9.127277 GGATATATTGCACCTGGTAAGTTAAAA 57.873 33.333 0.00 0.00 0.00 1.52
3877 5183 4.179926 TGACTTTCGATCTCAACTCTGG 57.820 45.455 0.00 0.00 0.00 3.86
3882 5188 3.073274 TCGATCTCAACTCTGGTCTCA 57.927 47.619 0.00 0.00 0.00 3.27
3892 5198 5.710099 TCAACTCTGGTCTCACTTTGTTTTT 59.290 36.000 0.00 0.00 0.00 1.94
3893 5199 6.882140 TCAACTCTGGTCTCACTTTGTTTTTA 59.118 34.615 0.00 0.00 0.00 1.52
3925 5231 4.060038 AGTATTTATGTCCACTGCTCCG 57.940 45.455 0.00 0.00 0.00 4.63
3960 5267 2.669781 GGGATGGGATGCAAAATCTCA 58.330 47.619 0.00 0.00 32.41 3.27
3965 5272 2.231964 TGGGATGCAAAATCTCAACAGC 59.768 45.455 0.00 0.00 0.00 4.40
4092 5399 2.092914 CCTAGCTTTCCCCGACAGAATT 60.093 50.000 0.00 0.00 0.00 2.17
4122 5429 4.358868 TCTAGATCCCCATATGCCATCT 57.641 45.455 11.75 11.75 0.00 2.90
4153 5460 2.233654 GCGGCTGCATCTCTACGTG 61.234 63.158 14.08 0.00 42.15 4.49
4155 5462 0.458543 CGGCTGCATCTCTACGTGTT 60.459 55.000 0.00 0.00 0.00 3.32
4427 14009 8.414778 AGTAGCTGTACCACTTATAGAACAATC 58.585 37.037 0.00 0.00 0.00 2.67
4431 14013 7.446106 TGTACCACTTATAGAACAATCCCAT 57.554 36.000 0.00 0.00 0.00 4.00
4470 14053 8.435931 TGTATCTGCCTATCTGGTAAATATGT 57.564 34.615 0.00 0.00 38.35 2.29
4471 14054 8.314021 TGTATCTGCCTATCTGGTAAATATGTG 58.686 37.037 0.00 0.00 38.35 3.21
4481 14064 4.141287 TGGTAAATATGTGCCACTATGCC 58.859 43.478 0.00 0.00 0.00 4.40
4566 14151 2.608970 TAGCATTTGGGAGGGAGCGC 62.609 60.000 0.00 0.00 0.00 5.92
4580 14165 2.755929 AGCGCCGAAGCTCTTTTAG 58.244 52.632 2.29 0.00 45.67 1.85
4614 14199 6.764379 TCACTGAAACAACATAGGTGTGATA 58.236 36.000 0.00 0.00 38.92 2.15
4627 14212 9.407380 ACATAGGTGTGATATTTTGAAATGCTA 57.593 29.630 0.00 0.00 37.14 3.49
4660 14245 8.247562 ACTGTACATATTTCTGAGAGAAGTGTC 58.752 37.037 0.00 0.00 35.37 3.67
4663 14248 6.692486 ACATATTTCTGAGAGAAGTGTCGTT 58.308 36.000 0.00 0.00 35.37 3.85
4674 14259 5.409826 AGAGAAGTGTCGTTGATTTGATTCC 59.590 40.000 0.00 0.00 0.00 3.01
4730 14317 7.201785 GGACACTCAACTTTCAAACCAGATAAA 60.202 37.037 0.00 0.00 0.00 1.40
4741 14328 3.490060 ACCAGATAAATTTGGCCCCTT 57.510 42.857 0.00 0.00 38.03 3.95
4742 14329 3.106827 ACCAGATAAATTTGGCCCCTTG 58.893 45.455 0.00 0.00 38.03 3.61
4754 14341 0.827507 GCCCCTTGCCTGACTCAAAA 60.828 55.000 0.00 0.00 0.00 2.44
4756 14343 1.691196 CCCTTGCCTGACTCAAAACA 58.309 50.000 0.00 0.00 0.00 2.83
4757 14344 2.031120 CCCTTGCCTGACTCAAAACAA 58.969 47.619 0.00 0.00 0.00 2.83
4779 14386 8.712285 ACAATTTGATGGATGAAGCAATAAAG 57.288 30.769 2.79 0.00 0.00 1.85
4783 14390 8.936070 TTTGATGGATGAAGCAATAAAGAATG 57.064 30.769 0.00 0.00 0.00 2.67
4796 14403 9.987272 AGCAATAAAGAATGGATAAAATTAGGC 57.013 29.630 0.00 0.00 0.00 3.93
4803 14410 6.377146 AGAATGGATAAAATTAGGCAACACGT 59.623 34.615 0.00 0.00 41.41 4.49
4805 14412 7.633193 ATGGATAAAATTAGGCAACACGTAA 57.367 32.000 0.00 0.00 41.41 3.18
4808 14415 8.024285 TGGATAAAATTAGGCAACACGTAAAAG 58.976 33.333 0.00 0.00 41.41 2.27
4809 14416 7.486870 GGATAAAATTAGGCAACACGTAAAAGG 59.513 37.037 0.00 0.00 41.41 3.11
4825 14432 6.754675 ACGTAAAAGGGAAATGTGTTCAAAAG 59.245 34.615 0.00 0.00 0.00 2.27
4829 14436 4.492646 AGGGAAATGTGTTCAAAAGGGAT 58.507 39.130 0.00 0.00 0.00 3.85
4835 14442 9.936759 GGAAATGTGTTCAAAAGGGATTATTTA 57.063 29.630 0.00 0.00 0.00 1.40
4858 14465 9.796120 TTTATCTCAAAGAACAATGAAACGTTT 57.204 25.926 14.57 14.57 0.00 3.60
4862 14469 8.402472 TCTCAAAGAACAATGAAACGTTTATGT 58.598 29.630 14.65 15.77 0.00 2.29
4863 14470 9.658475 CTCAAAGAACAATGAAACGTTTATGTA 57.342 29.630 14.65 1.40 0.00 2.29
4864 14471 9.658475 TCAAAGAACAATGAAACGTTTATGTAG 57.342 29.630 14.65 6.02 0.00 2.74
4867 14474 9.659830 AAGAACAATGAAACGTTTATGTAGAAC 57.340 29.630 14.65 11.10 0.00 3.01
4919 14637 6.968131 TCATACAAGATTTCTGAAGTTCCG 57.032 37.500 0.00 0.00 0.00 4.30
4920 14638 6.464222 TCATACAAGATTTCTGAAGTTCCGT 58.536 36.000 0.00 0.00 0.00 4.69
4925 14643 7.639945 ACAAGATTTCTGAAGTTCCGTAAAAG 58.360 34.615 0.00 0.00 0.00 2.27
4927 14645 6.296803 AGATTTCTGAAGTTCCGTAAAAGGT 58.703 36.000 0.00 0.00 0.00 3.50
4928 14646 6.771267 AGATTTCTGAAGTTCCGTAAAAGGTT 59.229 34.615 0.00 0.00 0.00 3.50
4929 14647 5.744666 TTCTGAAGTTCCGTAAAAGGTTG 57.255 39.130 0.00 0.00 0.00 3.77
4930 14648 5.026038 TCTGAAGTTCCGTAAAAGGTTGA 57.974 39.130 0.00 0.00 0.00 3.18
4972 14694 9.330063 AGAAAATCAGGAAATTTCAAGGAAAAC 57.670 29.630 19.49 5.69 35.11 2.43
4974 14696 9.631257 AAAATCAGGAAATTTCAAGGAAAACAT 57.369 25.926 19.49 0.00 35.11 2.71
4975 14697 8.611654 AATCAGGAAATTTCAAGGAAAACATG 57.388 30.769 19.49 0.00 35.11 3.21
4976 14698 7.123355 TCAGGAAATTTCAAGGAAAACATGT 57.877 32.000 19.49 0.00 35.11 3.21
5018 14749 9.703892 ATTATATCAGCTCTGTTAGAACATGTC 57.296 33.333 0.00 0.00 38.41 3.06
5022 14753 5.357032 TCAGCTCTGTTAGAACATGTCGATA 59.643 40.000 0.00 0.00 38.41 2.92
5030 14761 6.914215 TGTTAGAACATGTCGATACGGTATTC 59.086 38.462 0.00 0.00 33.17 1.75
5034 14765 5.258456 ACATGTCGATACGGTATTCAAGT 57.742 39.130 1.57 3.77 0.00 3.16
5039 14770 8.597227 CATGTCGATACGGTATTCAAGTAAAAA 58.403 33.333 1.57 0.00 0.00 1.94
5067 14798 9.726438 AAAATTTGTAACTAGTAGAGTGCATCT 57.274 29.630 3.59 0.00 38.87 2.90
5106 14837 7.149973 TGGGATAAGTATATTTTTCGTCCTCG 58.850 38.462 0.00 0.00 38.55 4.63
5131 14862 5.688348 CTCTTCCGAGAGTTTACAAATCG 57.312 43.478 0.00 0.00 43.66 3.34
5133 14864 5.159209 TCTTCCGAGAGTTTACAAATCGTC 58.841 41.667 0.00 0.00 0.00 4.20
5134 14865 3.841643 TCCGAGAGTTTACAAATCGTCC 58.158 45.455 0.00 0.00 0.00 4.79
5135 14866 2.928116 CCGAGAGTTTACAAATCGTCCC 59.072 50.000 0.00 0.00 0.00 4.46
5136 14867 3.368116 CCGAGAGTTTACAAATCGTCCCT 60.368 47.826 0.00 0.00 0.00 4.20
5137 14868 3.858238 CGAGAGTTTACAAATCGTCCCTC 59.142 47.826 0.00 0.00 0.00 4.30
5139 14870 5.223449 AGAGTTTACAAATCGTCCCTCAA 57.777 39.130 0.00 0.00 0.00 3.02
5140 14871 4.995487 AGAGTTTACAAATCGTCCCTCAAC 59.005 41.667 0.00 0.00 0.00 3.18
5141 14872 4.969484 AGTTTACAAATCGTCCCTCAACT 58.031 39.130 0.00 0.00 0.00 3.16
5142 14873 4.995487 AGTTTACAAATCGTCCCTCAACTC 59.005 41.667 0.00 0.00 0.00 3.01
5144 14875 3.485463 ACAAATCGTCCCTCAACTCAA 57.515 42.857 0.00 0.00 0.00 3.02
5145 14876 3.815809 ACAAATCGTCCCTCAACTCAAA 58.184 40.909 0.00 0.00 0.00 2.69
5146 14877 4.204012 ACAAATCGTCCCTCAACTCAAAA 58.796 39.130 0.00 0.00 0.00 2.44
5147 14878 4.036380 ACAAATCGTCCCTCAACTCAAAAC 59.964 41.667 0.00 0.00 0.00 2.43
5149 14880 1.487142 TCGTCCCTCAACTCAAAACCA 59.513 47.619 0.00 0.00 0.00 3.67
5150 14881 1.873591 CGTCCCTCAACTCAAAACCAG 59.126 52.381 0.00 0.00 0.00 4.00
5152 14883 3.756117 GTCCCTCAACTCAAAACCAGAT 58.244 45.455 0.00 0.00 0.00 2.90
5155 14886 4.597507 TCCCTCAACTCAAAACCAGATAGT 59.402 41.667 0.00 0.00 0.00 2.12
5156 14887 5.073144 TCCCTCAACTCAAAACCAGATAGTT 59.927 40.000 0.00 0.00 0.00 2.24
5157 14888 5.770162 CCCTCAACTCAAAACCAGATAGTTT 59.230 40.000 0.00 0.00 41.67 2.66
5159 14890 7.363431 CCTCAACTCAAAACCAGATAGTTTTC 58.637 38.462 0.00 0.00 45.73 2.29
5161 14892 8.463930 TCAACTCAAAACCAGATAGTTTTCAT 57.536 30.769 0.00 0.00 45.73 2.57
5162 14893 8.567948 TCAACTCAAAACCAGATAGTTTTCATC 58.432 33.333 0.00 0.00 45.73 2.92
5164 14895 6.434340 ACTCAAAACCAGATAGTTTTCATCCC 59.566 38.462 0.00 0.00 45.73 3.85
5165 14896 6.552008 TCAAAACCAGATAGTTTTCATCCCT 58.448 36.000 0.00 0.00 45.73 4.20
5166 14897 6.659242 TCAAAACCAGATAGTTTTCATCCCTC 59.341 38.462 0.00 0.00 45.73 4.30
5167 14898 5.779241 AACCAGATAGTTTTCATCCCTCA 57.221 39.130 0.00 0.00 0.00 3.86
5168 14899 5.779241 ACCAGATAGTTTTCATCCCTCAA 57.221 39.130 0.00 0.00 0.00 3.02
5169 14900 5.501156 ACCAGATAGTTTTCATCCCTCAAC 58.499 41.667 0.00 0.00 0.00 3.18
5171 14902 6.443849 ACCAGATAGTTTTCATCCCTCAACTA 59.556 38.462 0.00 0.00 36.43 2.24
5177 14908 9.753674 ATAGTTTTCATCCCTCAACTATCAAAA 57.246 29.630 0.00 0.00 37.75 2.44
5178 14909 7.886338 AGTTTTCATCCCTCAACTATCAAAAC 58.114 34.615 0.00 0.00 33.40 2.43
5179 14910 6.834168 TTTCATCCCTCAACTATCAAAACC 57.166 37.500 0.00 0.00 0.00 3.27
5180 14911 5.512942 TCATCCCTCAACTATCAAAACCA 57.487 39.130 0.00 0.00 0.00 3.67
5184 14915 6.884472 TCCCTCAACTATCAAAACCAGATA 57.116 37.500 0.00 0.00 0.00 1.98
5185 14916 7.265599 TCCCTCAACTATCAAAACCAGATAA 57.734 36.000 0.00 0.00 0.00 1.75
5188 14919 8.971073 CCCTCAACTATCAAAACCAGATAATTT 58.029 33.333 0.00 0.00 0.00 1.82
5192 14923 9.840427 CAACTATCAAAACCAGATAATTTTCGT 57.160 29.630 0.00 0.00 0.00 3.85
5194 14925 8.674607 ACTATCAAAACCAGATAATTTTCGTCC 58.325 33.333 0.00 0.00 0.00 4.79
5196 14927 6.007703 TCAAAACCAGATAATTTTCGTCCCT 58.992 36.000 0.00 0.00 0.00 4.20
5197 14928 6.150474 TCAAAACCAGATAATTTTCGTCCCTC 59.850 38.462 0.00 0.00 0.00 4.30
5198 14929 4.837093 ACCAGATAATTTTCGTCCCTCA 57.163 40.909 0.00 0.00 0.00 3.86
5199 14930 4.514401 ACCAGATAATTTTCGTCCCTCAC 58.486 43.478 0.00 0.00 0.00 3.51
5207 14938 2.811317 CGTCCCTCACGCTGCTTC 60.811 66.667 0.00 0.00 42.87 3.86
5208 14939 2.811317 GTCCCTCACGCTGCTTCG 60.811 66.667 0.00 0.00 0.00 3.79
5209 14940 4.069232 TCCCTCACGCTGCTTCGG 62.069 66.667 0.00 0.00 0.00 4.30
5218 14949 2.561373 CTGCTTCGGGCGGTTTTC 59.439 61.111 2.69 0.00 45.43 2.29
5219 14950 3.308878 CTGCTTCGGGCGGTTTTCG 62.309 63.158 2.69 0.00 45.43 3.46
5220 14951 3.351416 GCTTCGGGCGGTTTTCGT 61.351 61.111 0.00 0.00 41.72 3.85
5221 14952 2.858158 CTTCGGGCGGTTTTCGTC 59.142 61.111 0.00 0.00 43.79 4.20
5224 14955 4.084888 CGGGCGGTTTTCGTCTGC 62.085 66.667 0.00 0.00 43.24 4.26
5225 14956 2.975799 GGGCGGTTTTCGTCTGCA 60.976 61.111 0.00 0.00 44.01 4.41
5227 14958 1.154225 GGCGGTTTTCGTCTGCATG 60.154 57.895 0.00 0.00 40.86 4.06
5228 14959 1.573829 GGCGGTTTTCGTCTGCATGA 61.574 55.000 0.00 0.00 40.86 3.07
5230 14961 1.950472 CGGTTTTCGTCTGCATGAAC 58.050 50.000 0.00 0.00 0.00 3.18
5233 14964 2.290641 GGTTTTCGTCTGCATGAACAGT 59.709 45.455 0.00 0.00 38.84 3.55
5234 14965 3.496884 GGTTTTCGTCTGCATGAACAGTA 59.503 43.478 0.00 0.00 38.84 2.74
5237 14968 5.940192 TTTCGTCTGCATGAACAGTAAAT 57.060 34.783 0.00 0.00 38.84 1.40
5238 14969 7.295201 GTTTTCGTCTGCATGAACAGTAAATA 58.705 34.615 0.00 0.00 38.84 1.40
5239 14970 7.609760 TTTCGTCTGCATGAACAGTAAATAT 57.390 32.000 0.00 0.00 38.84 1.28
5240 14971 6.588348 TCGTCTGCATGAACAGTAAATATG 57.412 37.500 0.00 0.00 38.84 1.78
5241 14972 5.006649 TCGTCTGCATGAACAGTAAATATGC 59.993 40.000 0.00 0.00 43.21 3.14
5243 14974 5.967674 GTCTGCATGAACAGTAAATATGCAC 59.032 40.000 6.14 0.00 46.31 4.57
5244 14975 4.907579 TGCATGAACAGTAAATATGCACG 58.092 39.130 6.14 0.00 46.31 5.34
5245 14976 3.725740 GCATGAACAGTAAATATGCACGC 59.274 43.478 0.00 0.00 42.63 5.34
5246 14977 4.730324 GCATGAACAGTAAATATGCACGCA 60.730 41.667 0.00 0.00 42.63 5.24
5247 14978 4.335082 TGAACAGTAAATATGCACGCAC 57.665 40.909 0.00 0.00 0.00 5.34
5248 14979 3.126171 TGAACAGTAAATATGCACGCACC 59.874 43.478 0.00 0.00 0.00 5.01
5249 14980 2.985896 ACAGTAAATATGCACGCACCT 58.014 42.857 0.00 0.00 0.00 4.00
5250 14981 3.343617 ACAGTAAATATGCACGCACCTT 58.656 40.909 0.00 0.00 0.00 3.50
5251 14982 3.126858 ACAGTAAATATGCACGCACCTTG 59.873 43.478 0.00 0.00 0.00 3.61
5252 14983 2.097466 AGTAAATATGCACGCACCTTGC 59.903 45.455 0.00 0.00 40.69 4.01
5261 14992 4.347453 GCACCTTGCACGCCCAAG 62.347 66.667 8.29 8.29 44.26 3.61
5262 14993 4.347453 CACCTTGCACGCCCAAGC 62.347 66.667 9.47 0.00 40.62 4.01
5263 14994 4.892965 ACCTTGCACGCCCAAGCA 62.893 61.111 9.47 0.00 40.62 3.91
5265 14996 2.180017 CTTGCACGCCCAAGCATC 59.820 61.111 3.15 0.00 40.94 3.91
5266 14997 2.282391 TTGCACGCCCAAGCATCT 60.282 55.556 0.00 0.00 40.94 2.90
5269 15000 1.444895 GCACGCCCAAGCATCTTTG 60.445 57.895 0.00 0.00 39.83 2.77
5271 15002 0.813184 CACGCCCAAGCATCTTTGAT 59.187 50.000 0.00 0.00 39.83 2.57
5272 15003 0.813184 ACGCCCAAGCATCTTTGATG 59.187 50.000 3.42 3.42 39.83 3.07
5273 15004 0.526954 CGCCCAAGCATCTTTGATGC 60.527 55.000 20.86 20.86 44.85 3.91
5274 15005 0.179092 GCCCAAGCATCTTTGATGCC 60.179 55.000 23.59 8.81 45.59 4.40
5275 15006 1.187974 CCCAAGCATCTTTGATGCCA 58.812 50.000 23.59 0.00 45.59 4.92
5276 15007 1.551430 CCCAAGCATCTTTGATGCCAA 59.449 47.619 23.59 0.00 45.59 4.52
5277 15008 2.027929 CCCAAGCATCTTTGATGCCAAA 60.028 45.455 23.59 0.00 45.59 3.28
5278 15009 3.557475 CCCAAGCATCTTTGATGCCAAAA 60.557 43.478 23.59 0.00 45.59 2.44
5279 15010 4.066490 CCAAGCATCTTTGATGCCAAAAA 58.934 39.130 23.59 0.00 45.59 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.379243 CGGGGCTCAAGACGCTGT 62.379 66.667 0.00 0.00 33.25 4.40
50 52 1.434513 ATGTGGCCCTTGGTCTTGGA 61.435 55.000 0.00 0.00 0.00 3.53
56 58 2.971598 CGAGGATGTGGCCCTTGGT 61.972 63.158 0.00 0.00 33.36 3.67
124 133 2.622942 GAGCACAAATTTGGTGTGGAGA 59.377 45.455 21.74 0.00 45.32 3.71
125 134 2.605338 CGAGCACAAATTTGGTGTGGAG 60.605 50.000 21.74 3.98 45.32 3.86
126 135 1.336440 CGAGCACAAATTTGGTGTGGA 59.664 47.619 21.74 0.00 45.32 4.02
127 136 1.336440 TCGAGCACAAATTTGGTGTGG 59.664 47.619 21.74 8.47 45.32 4.17
158 167 1.291877 ACCGCAGAGTCGCAATCAAC 61.292 55.000 7.54 0.00 0.00 3.18
176 185 2.793933 GCAGTATCACGTACCCGAGAAC 60.794 54.545 0.00 0.00 37.24 3.01
177 186 1.402968 GCAGTATCACGTACCCGAGAA 59.597 52.381 0.00 0.00 37.24 2.87
178 187 1.019673 GCAGTATCACGTACCCGAGA 58.980 55.000 0.00 0.00 38.05 4.04
179 188 0.736636 TGCAGTATCACGTACCCGAG 59.263 55.000 0.00 0.00 37.88 4.63
180 189 1.175654 TTGCAGTATCACGTACCCGA 58.824 50.000 0.00 0.00 37.88 5.14
197 216 3.813166 AGTAACAGGACGACCACAAATTG 59.187 43.478 6.71 0.00 38.94 2.32
206 225 4.421948 CATCCTAACAGTAACAGGACGAC 58.578 47.826 0.00 0.00 41.18 4.34
252 272 7.598759 ACCGGATTGAATACTGAAGTATACT 57.401 36.000 9.46 0.00 40.10 2.12
257 277 8.647796 TGATAATACCGGATTGAATACTGAAGT 58.352 33.333 9.46 0.00 0.00 3.01
258 278 9.658799 ATGATAATACCGGATTGAATACTGAAG 57.341 33.333 9.46 0.00 0.00 3.02
259 279 9.435688 CATGATAATACCGGATTGAATACTGAA 57.564 33.333 9.46 0.00 0.00 3.02
260 280 8.593679 ACATGATAATACCGGATTGAATACTGA 58.406 33.333 9.46 0.00 0.00 3.41
261 281 8.659491 CACATGATAATACCGGATTGAATACTG 58.341 37.037 9.46 0.00 0.00 2.74
262 282 7.824289 CCACATGATAATACCGGATTGAATACT 59.176 37.037 9.46 0.00 0.00 2.12
263 283 7.822334 TCCACATGATAATACCGGATTGAATAC 59.178 37.037 9.46 0.00 0.00 1.89
264 284 7.912719 TCCACATGATAATACCGGATTGAATA 58.087 34.615 9.46 0.00 0.00 1.75
265 285 6.778821 TCCACATGATAATACCGGATTGAAT 58.221 36.000 9.46 0.00 0.00 2.57
266 286 6.042666 TCTCCACATGATAATACCGGATTGAA 59.957 38.462 9.46 0.00 0.00 2.69
267 287 5.542251 TCTCCACATGATAATACCGGATTGA 59.458 40.000 9.46 0.00 0.00 2.57
268 288 5.793817 TCTCCACATGATAATACCGGATTG 58.206 41.667 9.46 0.00 0.00 2.67
269 289 5.046304 CCTCTCCACATGATAATACCGGATT 60.046 44.000 9.46 6.40 0.00 3.01
273 383 5.468540 TTCCTCTCCACATGATAATACCG 57.531 43.478 0.00 0.00 0.00 4.02
356 497 3.055530 GTCAGTATCCAGCTATCCCCATG 60.056 52.174 0.00 0.00 0.00 3.66
472 616 1.067354 CCTCCAAAGTGCCAATTCAGC 60.067 52.381 0.00 0.00 0.00 4.26
614 781 3.799281 ACCATCATTTATTTGCCACCG 57.201 42.857 0.00 0.00 0.00 4.94
748 927 4.391216 CCACTGAGTCTATCAAAGTGCAAG 59.609 45.833 0.00 0.00 37.52 4.01
768 947 4.939509 AGAAAACGTGTGCATATACCAC 57.060 40.909 0.00 0.00 0.00 4.16
791 970 7.419750 GGAATATGTGAGAGGTTTATGTGGGTA 60.420 40.741 0.00 0.00 0.00 3.69
793 972 5.765182 GGAATATGTGAGAGGTTTATGTGGG 59.235 44.000 0.00 0.00 0.00 4.61
812 991 1.077005 AGCCTGGGCACAAAAGGAATA 59.923 47.619 14.39 0.00 44.88 1.75
813 992 0.178924 AGCCTGGGCACAAAAGGAAT 60.179 50.000 14.39 0.00 44.88 3.01
909 1432 1.121378 GTAAGGGTAGGGGAGCTGAC 58.879 60.000 0.00 0.00 0.00 3.51
1043 1602 4.067896 GAGAAGAAAGAGTTCATGGTGCA 58.932 43.478 0.00 0.00 36.09 4.57
1044 1603 4.322567 AGAGAAGAAAGAGTTCATGGTGC 58.677 43.478 0.00 0.00 36.09 5.01
1052 1611 5.782845 AGGATGGTGTAGAGAAGAAAGAGTT 59.217 40.000 0.00 0.00 0.00 3.01
1322 1881 4.446413 GGGCTGCCATGCAACTGC 62.446 66.667 22.05 0.00 38.41 4.40
1499 2058 4.685924 AGAATTGTTTGCAAGGTTGACAG 58.314 39.130 0.00 0.00 38.10 3.51
1536 2668 6.049149 CGAACTATTTGCTAAGGAATCAGGA 58.951 40.000 0.00 0.00 0.00 3.86
1604 2736 2.178580 TGAACAAATTGGCTGGGATCC 58.821 47.619 1.92 1.92 0.00 3.36
1614 2746 7.623770 CAAGTTTGGATGAGTTGAACAAATTG 58.376 34.615 0.00 0.00 34.11 2.32
1697 2829 1.066914 GAGAAACTGCAGAGCTGACG 58.933 55.000 23.35 0.00 0.00 4.35
1743 2875 4.422073 TCCTAAAGATGCTGGTATGGTG 57.578 45.455 0.00 0.00 0.00 4.17
1770 2902 1.066573 AGGAGTGAACGCAAGGATGAG 60.067 52.381 0.00 0.00 46.39 2.90
1800 2932 5.447818 CGGAATTGATCCTGCTAACTTGTTC 60.448 44.000 0.00 0.00 46.98 3.18
1831 2963 8.034804 CCTTTTTAGATTTGGAATTTGACCGAT 58.965 33.333 0.00 0.00 0.00 4.18
1970 3102 2.440409 GAAGTGAGTGGCCAATGTCAT 58.560 47.619 12.17 0.00 0.00 3.06
2043 3175 2.290896 TGACATGTTGGTCAGGGAATCC 60.291 50.000 0.00 0.00 42.56 3.01
2109 3241 2.971330 CAAGGATCCTAGAGATGGCACT 59.029 50.000 16.55 0.00 34.42 4.40
2387 3519 0.615331 TGGTCCTGAGAGCATGTTCC 59.385 55.000 5.87 0.00 45.34 3.62
2493 3625 3.440522 GGCTGAGTTGAACAAGATTACCC 59.559 47.826 0.00 0.00 0.00 3.69
2558 3690 7.043565 CAGCCTTTTGCATTGTCCTATATTTT 58.956 34.615 0.00 0.00 44.83 1.82
2614 3746 5.669447 AGAGTTCTCTTGGTATGGATCCATT 59.331 40.000 31.70 15.99 37.82 3.16
2756 3888 5.305644 TCAGAAGGAAGGCTACCAGATAATC 59.694 44.000 0.00 0.00 0.00 1.75
3166 4322 9.453572 AGTGACAACAACACATAATAATGAGAT 57.546 29.630 0.00 0.00 40.25 2.75
3197 4353 2.742589 GGTTGAGCTTTAGTTCCCTTCG 59.257 50.000 0.00 0.00 0.00 3.79
3288 4444 1.550524 CTGATCCGGTTGACCAGAGAA 59.449 52.381 0.00 0.00 35.14 2.87
3420 4576 2.286833 GTGTTTTAGCACTTCGCACTCA 59.713 45.455 0.00 0.00 46.13 3.41
3444 4600 2.136196 GAACCAAATTGCGGTGGCGA 62.136 55.000 0.70 0.00 44.10 5.54
3457 4613 4.318332 CACAGAGTGATAGCTTGAACCAA 58.682 43.478 0.00 0.00 35.23 3.67
3510 4666 7.170965 CCATGAACTCATATACTATGGCCTTT 58.829 38.462 3.32 0.00 34.26 3.11
3573 4729 1.524482 CAGCCTCCTTGAGCTACCC 59.476 63.158 0.00 0.00 37.18 3.69
3576 4738 0.615827 TCAGCAGCCTCCTTGAGCTA 60.616 55.000 0.00 0.00 37.18 3.32
3696 4996 0.111061 AGTCCAGCAGAACATTGCCA 59.889 50.000 0.00 0.00 45.18 4.92
3751 5051 6.284459 CACTACTTGAAGAGAGAAACTTGGT 58.716 40.000 0.00 0.00 0.00 3.67
3798 5098 0.102481 ATCCAATCGTTCCTCCGACG 59.898 55.000 0.00 0.00 40.08 5.12
3842 5142 9.971922 AGATCGAAAGTCATTTCAAAGATTTTT 57.028 25.926 0.00 0.00 44.27 1.94
3843 5143 9.617975 GAGATCGAAAGTCATTTCAAAGATTTT 57.382 29.630 0.00 0.00 44.27 1.82
3844 5144 8.786898 TGAGATCGAAAGTCATTTCAAAGATTT 58.213 29.630 0.00 0.00 44.27 2.17
3845 5145 8.327941 TGAGATCGAAAGTCATTTCAAAGATT 57.672 30.769 0.00 0.00 44.27 2.40
3846 5146 7.912056 TGAGATCGAAAGTCATTTCAAAGAT 57.088 32.000 0.00 0.00 44.27 2.40
3861 5166 3.191581 GTGAGACCAGAGTTGAGATCGAA 59.808 47.826 0.00 0.00 0.00 3.71
3866 5172 3.706594 ACAAAGTGAGACCAGAGTTGAGA 59.293 43.478 0.00 0.00 0.00 3.27
3899 5205 6.006275 AGCAGTGGACATAAATACTTGGAT 57.994 37.500 0.00 0.00 0.00 3.41
3900 5206 5.428253 GAGCAGTGGACATAAATACTTGGA 58.572 41.667 0.00 0.00 0.00 3.53
3925 5231 3.881089 CCCATCCCGTATTCTGTAAAACC 59.119 47.826 0.00 0.00 0.00 3.27
3960 5267 2.040278 ACCATACACATCACCAGCTGTT 59.960 45.455 13.81 0.00 0.00 3.16
3965 5272 2.677836 CCGAAACCATACACATCACCAG 59.322 50.000 0.00 0.00 0.00 4.00
4092 5399 1.008327 TGGGGATCTAGAACCTCAGCA 59.992 52.381 17.29 3.92 32.43 4.41
4143 5450 6.761099 ATGTACTTCTGAACACGTAGAGAT 57.239 37.500 0.00 0.00 0.00 2.75
4441 14024 7.849322 TTTACCAGATAGGCAGATACATACA 57.151 36.000 0.00 0.00 43.14 2.29
4444 14027 9.051259 ACATATTTACCAGATAGGCAGATACAT 57.949 33.333 0.00 0.00 43.14 2.29
4445 14028 8.314021 CACATATTTACCAGATAGGCAGATACA 58.686 37.037 0.00 0.00 43.14 2.29
4446 14029 7.278868 GCACATATTTACCAGATAGGCAGATAC 59.721 40.741 0.00 0.00 43.14 2.24
4447 14030 7.331026 GCACATATTTACCAGATAGGCAGATA 58.669 38.462 0.00 0.00 43.14 1.98
4448 14031 6.176183 GCACATATTTACCAGATAGGCAGAT 58.824 40.000 0.00 0.00 43.14 2.90
4449 14032 5.513094 GGCACATATTTACCAGATAGGCAGA 60.513 44.000 0.00 0.00 43.14 4.26
4450 14033 4.697352 GGCACATATTTACCAGATAGGCAG 59.303 45.833 0.00 0.00 43.14 4.85
4451 14034 4.103943 TGGCACATATTTACCAGATAGGCA 59.896 41.667 0.00 0.00 43.14 4.75
4452 14035 4.455877 GTGGCACATATTTACCAGATAGGC 59.544 45.833 13.86 0.00 44.52 3.93
4453 14036 5.869579 AGTGGCACATATTTACCAGATAGG 58.130 41.667 21.41 0.00 44.52 2.57
4454 14037 7.065085 GCATAGTGGCACATATTTACCAGATAG 59.935 40.741 21.41 1.19 44.52 2.08
4481 14064 1.938625 CTTATTTTTGCGGGCCCATG 58.061 50.000 24.92 7.60 0.00 3.66
4492 14075 6.617879 AGAAAGATTTACGCCGCTTATTTTT 58.382 32.000 0.00 0.00 0.00 1.94
4538 14123 6.306987 TCCCTCCCAAATGCTAGAAAATATC 58.693 40.000 0.00 0.00 0.00 1.63
4541 14126 4.540715 CTCCCTCCCAAATGCTAGAAAAT 58.459 43.478 0.00 0.00 0.00 1.82
4546 14131 0.533755 CGCTCCCTCCCAAATGCTAG 60.534 60.000 0.00 0.00 0.00 3.42
4566 14151 5.674933 ACAAAGTTCTAAAAGAGCTTCGG 57.325 39.130 6.50 5.44 43.54 4.30
4634 14219 8.128322 ACACTTCTCTCAGAAATATGTACAGT 57.872 34.615 0.33 0.00 33.19 3.55
4636 14221 7.094334 ACGACACTTCTCTCAGAAATATGTACA 60.094 37.037 0.00 0.00 33.19 2.90
4637 14222 7.251994 ACGACACTTCTCTCAGAAATATGTAC 58.748 38.462 0.00 0.00 33.19 2.90
4653 14238 5.613358 AGGAATCAAATCAACGACACTTC 57.387 39.130 0.00 0.00 0.00 3.01
4674 14259 7.820872 AGTATTTGAATTCATGGCTCCAAAAAG 59.179 33.333 9.40 0.00 0.00 2.27
4741 14328 4.998671 TCAAATTGTTTTGAGTCAGGCA 57.001 36.364 0.00 0.00 44.81 4.75
4754 14341 8.533657 TCTTTATTGCTTCATCCATCAAATTGT 58.466 29.630 0.00 0.00 0.00 2.71
4757 14344 9.542462 CATTCTTTATTGCTTCATCCATCAAAT 57.458 29.630 0.00 0.00 0.00 2.32
4776 14383 7.759433 CGTGTTGCCTAATTTTATCCATTCTTT 59.241 33.333 0.00 0.00 0.00 2.52
4779 14386 6.560711 ACGTGTTGCCTAATTTTATCCATTC 58.439 36.000 0.00 0.00 0.00 2.67
4782 14389 7.450124 TTTACGTGTTGCCTAATTTTATCCA 57.550 32.000 0.00 0.00 0.00 3.41
4783 14390 7.486870 CCTTTTACGTGTTGCCTAATTTTATCC 59.513 37.037 0.00 0.00 0.00 2.59
4790 14397 4.023726 TCCCTTTTACGTGTTGCCTAAT 57.976 40.909 0.00 0.00 0.00 1.73
4791 14398 3.488778 TCCCTTTTACGTGTTGCCTAA 57.511 42.857 0.00 0.00 0.00 2.69
4796 14403 4.927422 ACACATTTCCCTTTTACGTGTTG 58.073 39.130 0.00 0.00 32.49 3.33
4799 14406 5.176407 TGAACACATTTCCCTTTTACGTG 57.824 39.130 0.00 0.00 0.00 4.49
4800 14407 5.838531 TTGAACACATTTCCCTTTTACGT 57.161 34.783 0.00 0.00 0.00 3.57
4801 14408 6.200097 CCTTTTGAACACATTTCCCTTTTACG 59.800 38.462 0.00 0.00 0.00 3.18
4803 14410 6.384305 TCCCTTTTGAACACATTTCCCTTTTA 59.616 34.615 0.00 0.00 0.00 1.52
4805 14412 4.719273 TCCCTTTTGAACACATTTCCCTTT 59.281 37.500 0.00 0.00 0.00 3.11
4808 14415 4.890158 ATCCCTTTTGAACACATTTCCC 57.110 40.909 0.00 0.00 0.00 3.97
4809 14416 8.846943 AAATAATCCCTTTTGAACACATTTCC 57.153 30.769 0.00 0.00 0.00 3.13
4835 14442 9.398170 CATAAACGTTTCATTGTTCTTTGAGAT 57.602 29.630 18.42 0.00 0.00 2.75
4837 14444 8.560576 ACATAAACGTTTCATTGTTCTTTGAG 57.439 30.769 18.42 0.00 0.00 3.02
4843 14450 8.071368 TGGTTCTACATAAACGTTTCATTGTTC 58.929 33.333 18.42 10.43 0.00 3.18
4854 14461 7.802738 TCATGTTTCTTGGTTCTACATAAACG 58.197 34.615 0.00 0.00 33.12 3.60
4855 14462 9.559958 CATCATGTTTCTTGGTTCTACATAAAC 57.440 33.333 0.00 0.00 32.04 2.01
4856 14463 9.295825 ACATCATGTTTCTTGGTTCTACATAAA 57.704 29.630 0.00 0.00 0.00 1.40
4858 14465 8.862325 AACATCATGTTTCTTGGTTCTACATA 57.138 30.769 0.00 0.00 37.26 2.29
4859 14466 7.765695 AACATCATGTTTCTTGGTTCTACAT 57.234 32.000 0.00 0.00 37.26 2.29
4860 14467 7.581213 AAACATCATGTTTCTTGGTTCTACA 57.419 32.000 10.14 0.00 46.61 2.74
4895 14593 6.934645 ACGGAACTTCAGAAATCTTGTATGAA 59.065 34.615 0.00 0.00 0.00 2.57
4909 14627 5.744666 TTCAACCTTTTACGGAACTTCAG 57.255 39.130 0.00 0.00 0.00 3.02
4925 14643 9.691362 TTTTCTCTATGTTTATTGCTTTCAACC 57.309 29.630 0.00 0.00 34.60 3.77
4953 14675 7.790823 AACATGTTTTCCTTGAAATTTCCTG 57.209 32.000 15.48 7.94 31.34 3.86
4961 14683 8.783833 TCATTTCAAAACATGTTTTCCTTGAA 57.216 26.923 29.21 25.72 40.45 2.69
4963 14685 8.422973 TCTCATTTCAAAACATGTTTTCCTTG 57.577 30.769 29.21 22.59 40.45 3.61
4997 14728 4.158579 TCGACATGTTCTAACAGAGCTGAT 59.841 41.667 0.00 0.00 43.04 2.90
5001 14732 4.438145 CGTATCGACATGTTCTAACAGAGC 59.562 45.833 0.00 0.00 43.04 4.09
5002 14733 4.970611 CCGTATCGACATGTTCTAACAGAG 59.029 45.833 0.00 0.00 43.04 3.35
5009 14740 5.509716 TGAATACCGTATCGACATGTTCT 57.490 39.130 0.00 0.00 0.00 3.01
5010 14741 5.747197 ACTTGAATACCGTATCGACATGTTC 59.253 40.000 0.00 0.00 0.00 3.18
5012 14743 5.258456 ACTTGAATACCGTATCGACATGT 57.742 39.130 0.00 0.00 0.00 3.21
5042 14773 9.726438 AAGATGCACTCTACTAGTTACAAATTT 57.274 29.630 0.00 0.00 35.76 1.82
5044 14775 8.314751 ACAAGATGCACTCTACTAGTTACAAAT 58.685 33.333 0.00 0.00 35.76 2.32
5048 14779 9.804758 AAATACAAGATGCACTCTACTAGTTAC 57.195 33.333 0.00 0.00 35.76 2.50
5081 14812 7.014518 TCGAGGACGAAAAATATACTTATCCCA 59.985 37.037 0.00 0.00 45.74 4.37
5082 14813 7.373493 TCGAGGACGAAAAATATACTTATCCC 58.627 38.462 0.00 0.00 45.74 3.85
5097 14828 1.879372 TCGGAAGAGTTCGAGGACGAA 60.879 52.381 0.00 0.00 44.78 3.85
5098 14829 0.321034 TCGGAAGAGTTCGAGGACGA 60.321 55.000 0.00 0.00 40.38 4.20
5099 14830 2.168947 TCGGAAGAGTTCGAGGACG 58.831 57.895 0.00 0.00 36.84 4.79
5110 14841 5.130292 ACGATTTGTAAACTCTCGGAAGA 57.870 39.130 0.00 0.00 39.12 2.87
5111 14842 4.326548 GGACGATTTGTAAACTCTCGGAAG 59.673 45.833 0.00 0.00 33.82 3.46
5112 14843 4.240096 GGACGATTTGTAAACTCTCGGAA 58.760 43.478 0.00 0.00 33.82 4.30
5113 14844 3.367703 GGGACGATTTGTAAACTCTCGGA 60.368 47.826 0.00 0.00 33.82 4.55
5114 14845 2.928116 GGGACGATTTGTAAACTCTCGG 59.072 50.000 0.00 0.00 33.82 4.63
5118 14849 4.995487 AGTTGAGGGACGATTTGTAAACTC 59.005 41.667 0.00 0.00 0.00 3.01
5119 14850 4.969484 AGTTGAGGGACGATTTGTAAACT 58.031 39.130 0.00 0.00 0.00 2.66
5120 14851 4.753107 TGAGTTGAGGGACGATTTGTAAAC 59.247 41.667 0.00 0.00 0.00 2.01
5124 14855 3.485463 TTGAGTTGAGGGACGATTTGT 57.515 42.857 0.00 0.00 0.00 2.83
5125 14856 4.537015 GTTTTGAGTTGAGGGACGATTTG 58.463 43.478 0.00 0.00 0.00 2.32
5127 14858 3.146847 GGTTTTGAGTTGAGGGACGATT 58.853 45.455 0.00 0.00 0.00 3.34
5128 14859 2.105821 TGGTTTTGAGTTGAGGGACGAT 59.894 45.455 0.00 0.00 0.00 3.73
5129 14860 1.487142 TGGTTTTGAGTTGAGGGACGA 59.513 47.619 0.00 0.00 0.00 4.20
5131 14862 3.208747 TCTGGTTTTGAGTTGAGGGAC 57.791 47.619 0.00 0.00 0.00 4.46
5133 14864 4.911390 ACTATCTGGTTTTGAGTTGAGGG 58.089 43.478 0.00 0.00 0.00 4.30
5134 14865 6.884280 AAACTATCTGGTTTTGAGTTGAGG 57.116 37.500 0.00 0.00 36.16 3.86
5135 14866 7.930217 TGAAAACTATCTGGTTTTGAGTTGAG 58.070 34.615 8.84 0.00 45.62 3.02
5136 14867 7.873719 TGAAAACTATCTGGTTTTGAGTTGA 57.126 32.000 8.84 0.00 45.62 3.18
5137 14868 7.809806 GGATGAAAACTATCTGGTTTTGAGTTG 59.190 37.037 8.84 0.00 45.62 3.16
5139 14870 6.434340 GGGATGAAAACTATCTGGTTTTGAGT 59.566 38.462 8.84 0.00 45.62 3.41
5140 14871 6.660949 AGGGATGAAAACTATCTGGTTTTGAG 59.339 38.462 8.84 0.00 45.62 3.02
5141 14872 6.552008 AGGGATGAAAACTATCTGGTTTTGA 58.448 36.000 8.84 1.87 45.62 2.69
5142 14873 6.434028 TGAGGGATGAAAACTATCTGGTTTTG 59.566 38.462 8.84 0.00 45.62 2.44
5144 14875 6.139679 TGAGGGATGAAAACTATCTGGTTT 57.860 37.500 0.00 0.00 40.59 3.27
5145 14876 5.779241 TGAGGGATGAAAACTATCTGGTT 57.221 39.130 0.00 0.00 0.00 3.67
5146 14877 5.251700 AGTTGAGGGATGAAAACTATCTGGT 59.748 40.000 0.00 0.00 31.26 4.00
5147 14878 5.749462 AGTTGAGGGATGAAAACTATCTGG 58.251 41.667 0.00 0.00 31.26 3.86
5152 14883 9.010029 GTTTTGATAGTTGAGGGATGAAAACTA 57.990 33.333 0.00 0.00 38.93 2.24
5155 14886 6.780031 TGGTTTTGATAGTTGAGGGATGAAAA 59.220 34.615 0.00 0.00 0.00 2.29
5156 14887 6.310941 TGGTTTTGATAGTTGAGGGATGAAA 58.689 36.000 0.00 0.00 0.00 2.69
5157 14888 5.886609 TGGTTTTGATAGTTGAGGGATGAA 58.113 37.500 0.00 0.00 0.00 2.57
5159 14890 5.500234 TCTGGTTTTGATAGTTGAGGGATG 58.500 41.667 0.00 0.00 0.00 3.51
5161 14892 5.779241 ATCTGGTTTTGATAGTTGAGGGA 57.221 39.130 0.00 0.00 0.00 4.20
5162 14893 8.525290 AATTATCTGGTTTTGATAGTTGAGGG 57.475 34.615 0.00 0.00 29.35 4.30
5166 14897 9.840427 ACGAAAATTATCTGGTTTTGATAGTTG 57.160 29.630 0.00 0.00 30.41 3.16
5168 14899 8.674607 GGACGAAAATTATCTGGTTTTGATAGT 58.325 33.333 0.00 0.00 0.00 2.12
5169 14900 8.129211 GGGACGAAAATTATCTGGTTTTGATAG 58.871 37.037 0.00 0.00 0.00 2.08
5171 14902 6.663523 AGGGACGAAAATTATCTGGTTTTGAT 59.336 34.615 0.00 0.00 0.00 2.57
5173 14904 6.072175 TGAGGGACGAAAATTATCTGGTTTTG 60.072 38.462 0.00 0.00 0.00 2.44
5176 14907 4.941873 GTGAGGGACGAAAATTATCTGGTT 59.058 41.667 0.00 0.00 0.00 3.67
5177 14908 4.514401 GTGAGGGACGAAAATTATCTGGT 58.486 43.478 0.00 0.00 0.00 4.00
5191 14922 2.811317 CGAAGCAGCGTGAGGGAC 60.811 66.667 0.00 0.00 0.00 4.46
5192 14923 4.069232 CCGAAGCAGCGTGAGGGA 62.069 66.667 0.00 0.00 0.00 4.20
5200 14931 3.610791 GAAAACCGCCCGAAGCAGC 62.611 63.158 0.00 0.00 44.04 5.25
5201 14932 2.561373 GAAAACCGCCCGAAGCAG 59.439 61.111 0.00 0.00 44.04 4.24
5202 14933 3.350612 CGAAAACCGCCCGAAGCA 61.351 61.111 0.00 0.00 44.04 3.91
5203 14934 3.304764 GACGAAAACCGCCCGAAGC 62.305 63.158 0.00 0.00 43.32 3.86
5204 14935 1.666872 AGACGAAAACCGCCCGAAG 60.667 57.895 0.00 0.00 43.32 3.79
5205 14936 1.957186 CAGACGAAAACCGCCCGAA 60.957 57.895 0.00 0.00 43.32 4.30
5206 14937 2.356553 CAGACGAAAACCGCCCGA 60.357 61.111 0.00 0.00 43.32 5.14
5207 14938 4.084888 GCAGACGAAAACCGCCCG 62.085 66.667 0.00 0.00 43.32 6.13
5208 14939 2.332654 ATGCAGACGAAAACCGCCC 61.333 57.895 0.00 0.00 43.32 6.13
5209 14940 1.154225 CATGCAGACGAAAACCGCC 60.154 57.895 0.00 0.00 43.32 6.13
5210 14941 0.237235 TTCATGCAGACGAAAACCGC 59.763 50.000 0.00 0.00 43.32 5.68
5211 14942 1.262950 TGTTCATGCAGACGAAAACCG 59.737 47.619 0.00 0.00 45.44 4.44
5212 14943 2.290641 ACTGTTCATGCAGACGAAAACC 59.709 45.455 7.27 0.00 39.62 3.27
5213 14944 3.609103 ACTGTTCATGCAGACGAAAAC 57.391 42.857 7.27 0.00 39.62 2.43
5214 14945 5.743026 TTTACTGTTCATGCAGACGAAAA 57.257 34.783 7.27 0.00 39.62 2.29
5215 14946 5.940192 ATTTACTGTTCATGCAGACGAAA 57.060 34.783 7.27 5.32 39.62 3.46
5217 14948 5.006649 GCATATTTACTGTTCATGCAGACGA 59.993 40.000 7.27 0.00 41.25 4.20
5218 14949 5.200454 GCATATTTACTGTTCATGCAGACG 58.800 41.667 7.27 0.00 41.25 4.18
5219 14950 6.122850 TGCATATTTACTGTTCATGCAGAC 57.877 37.500 7.27 0.00 45.09 3.51
5223 14954 3.725740 GCGTGCATATTTACTGTTCATGC 59.274 43.478 0.00 0.00 41.81 4.06
5224 14955 4.730042 GTGCGTGCATATTTACTGTTCATG 59.270 41.667 0.00 0.00 0.00 3.07
5225 14956 4.201910 GGTGCGTGCATATTTACTGTTCAT 60.202 41.667 0.00 0.00 0.00 2.57
5227 14958 3.374058 AGGTGCGTGCATATTTACTGTTC 59.626 43.478 0.00 0.00 0.00 3.18
5228 14959 3.343617 AGGTGCGTGCATATTTACTGTT 58.656 40.909 0.00 0.00 0.00 3.16
5230 14961 3.683989 CAAGGTGCGTGCATATTTACTG 58.316 45.455 0.00 0.00 0.00 2.74
5233 14964 2.842208 GCAAGGTGCGTGCATATTTA 57.158 45.000 0.00 0.00 41.80 1.40
5234 14965 3.719699 GCAAGGTGCGTGCATATTT 57.280 47.368 0.00 0.00 41.80 1.40
5244 14975 4.347453 CTTGGGCGTGCAAGGTGC 62.347 66.667 0.79 0.00 45.29 5.01
5245 14976 4.347453 GCTTGGGCGTGCAAGGTG 62.347 66.667 0.79 0.00 0.00 4.00
5246 14977 4.892965 TGCTTGGGCGTGCAAGGT 62.893 61.111 0.79 0.00 42.25 3.50
5247 14978 3.346631 GATGCTTGGGCGTGCAAGG 62.347 63.158 0.79 0.00 42.74 3.61
5248 14979 1.870055 AAGATGCTTGGGCGTGCAAG 61.870 55.000 0.00 0.00 42.74 4.01
5249 14980 1.462731 AAAGATGCTTGGGCGTGCAA 61.463 50.000 0.00 0.00 42.74 4.08
5250 14981 1.902918 AAAGATGCTTGGGCGTGCA 60.903 52.632 0.00 0.61 43.67 4.57
5251 14982 1.444895 CAAAGATGCTTGGGCGTGC 60.445 57.895 0.00 0.00 42.25 5.34
5252 14983 0.813184 ATCAAAGATGCTTGGGCGTG 59.187 50.000 0.00 0.00 42.25 5.34
5254 14985 0.526954 GCATCAAAGATGCTTGGGCG 60.527 55.000 21.22 0.00 41.52 6.13
5255 14986 0.179092 GGCATCAAAGATGCTTGGGC 60.179 55.000 25.61 9.81 44.02 5.36
5256 14987 1.187974 TGGCATCAAAGATGCTTGGG 58.812 50.000 25.61 0.00 44.02 4.12
5257 14988 3.322211 TTTGGCATCAAAGATGCTTGG 57.678 42.857 25.61 0.00 44.02 3.61


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

AutoCloner maintained by Alex Coulton.