Multiple sequence alignment - TraesCS4A01G145500

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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 TraesCS4A01G145500 chr4A 100.000 3824 0 0 1 3824 248836928 248833105 0.000000e+00 7062
1 TraesCS4A01G145500 chr4B 95.672 2611 101 6 666 3266 150734969 150737577 0.000000e+00 4185
2 TraesCS4A01G145500 chr4B 96.484 455 16 0 3370 3824 150737574 150738028 0.000000e+00 752
3 TraesCS4A01G145500 chr4B 88.710 248 13 9 443 682 150732526 150732766 4.830000e-74 289
4 TraesCS4A01G145500 chr4D 96.463 2290 79 2 703 2991 195022589 195020301 0.000000e+00 3779
5 TraesCS4A01G145500 chr4D 97.802 455 10 0 3370 3824 195019515 195019061 0.000000e+00 785
6 TraesCS4A01G145500 chr4D 84.387 538 24 13 209 709 195023653 195023139 1.240000e-129 473
7 TraesCS4A01G145500 chr4D 97.744 266 4 1 3003 3266 195019777 195019512 1.250000e-124 457
8 TraesCS4A01G145500 chr4D 94.709 189 10 0 15 203 314486620 314486432 1.040000e-75 294
9 TraesCS4A01G145500 chr7B 91.586 309 25 1 1742 2050 279842828 279843135 3.530000e-115 425
10 TraesCS4A01G145500 chr7B 95.699 186 8 0 15 200 70302247 70302062 2.230000e-77 300
11 TraesCS4A01G145500 chr5B 95.699 186 8 0 15 200 420054629 420054444 2.230000e-77 300
12 TraesCS4A01G145500 chr2B 95.699 186 8 0 15 200 74429841 74429656 2.230000e-77 300
13 TraesCS4A01G145500 chr2A 95.676 185 8 0 15 199 525895475 525895659 8.030000e-77 298
14 TraesCS4A01G145500 chrUn 93.069 202 12 1 1 200 77839618 77839819 1.040000e-75 294
15 TraesCS4A01G145500 chr6B 94.737 190 9 1 15 203 696813670 696813859 1.040000e-75 294
16 TraesCS4A01G145500 chr6A 94.709 189 10 0 15 203 103854133 103854321 1.040000e-75 294
17 TraesCS4A01G145500 chr2D 95.628 183 8 0 15 197 486471768 486471950 1.040000e-75 294


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 TraesCS4A01G145500 chr4A 248833105 248836928 3823 True 7062.0 7062 100.000 1 3824 1 chr4A.!!$R1 3823
1 TraesCS4A01G145500 chr4B 150732526 150738028 5502 False 1742.0 4185 93.622 443 3824 3 chr4B.!!$F1 3381
2 TraesCS4A01G145500 chr4D 195019061 195023653 4592 True 1373.5 3779 94.099 209 3824 4 chr4D.!!$R2 3615

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
132 133 0.178990 GTCAGGGGTGCTTGGAACTT 60.179 55.0 0.0 0.0 0.00 2.66 F
1069 3889 0.249120 CTCCCATGTAGCGGTCAACA 59.751 55.0 0.0 0.0 0.00 3.33 F
1871 4691 0.319728 AGTACTGAGCTGTGTGCAGG 59.680 55.0 0.0 0.0 45.94 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 4645 0.108585 GCCAGTTCACCAACAGAGGA 59.891 55.0 0.0 0.0 34.6 3.71 R
2466 5286 0.033504 AGTGAACACGTTGATCCGCT 59.966 50.0 0.0 0.0 36.2 5.52 R
3268 6602 0.037326 TGTGCTTGCGGTCTAAGGAG 60.037 55.0 0.0 0.0 0.0 3.69 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
19 20 3.289128 TCGCAAGTGTTGTGAGGAG 57.711 52.632 0.00 0.00 44.54 3.69
20 21 0.464036 TCGCAAGTGTTGTGAGGAGT 59.536 50.000 0.00 0.00 44.54 3.85
21 22 1.134521 TCGCAAGTGTTGTGAGGAGTT 60.135 47.619 0.00 0.00 44.54 3.01
22 23 2.101750 TCGCAAGTGTTGTGAGGAGTTA 59.898 45.455 0.00 0.00 44.54 2.24
23 24 2.869801 CGCAAGTGTTGTGAGGAGTTAA 59.130 45.455 0.00 0.00 43.66 2.01
24 25 3.311322 CGCAAGTGTTGTGAGGAGTTAAA 59.689 43.478 0.00 0.00 43.66 1.52
25 26 4.024048 CGCAAGTGTTGTGAGGAGTTAAAT 60.024 41.667 0.00 0.00 43.66 1.40
26 27 5.215160 GCAAGTGTTGTGAGGAGTTAAATG 58.785 41.667 0.00 0.00 0.00 2.32
27 28 5.008613 GCAAGTGTTGTGAGGAGTTAAATGA 59.991 40.000 0.00 0.00 0.00 2.57
28 29 6.662616 CAAGTGTTGTGAGGAGTTAAATGAG 58.337 40.000 0.00 0.00 0.00 2.90
29 30 5.308825 AGTGTTGTGAGGAGTTAAATGAGG 58.691 41.667 0.00 0.00 0.00 3.86
30 31 5.071788 AGTGTTGTGAGGAGTTAAATGAGGA 59.928 40.000 0.00 0.00 0.00 3.71
31 32 5.409826 GTGTTGTGAGGAGTTAAATGAGGAG 59.590 44.000 0.00 0.00 0.00 3.69
32 33 5.306937 TGTTGTGAGGAGTTAAATGAGGAGA 59.693 40.000 0.00 0.00 0.00 3.71
33 34 5.667539 TGTGAGGAGTTAAATGAGGAGAG 57.332 43.478 0.00 0.00 0.00 3.20
34 35 5.333581 TGTGAGGAGTTAAATGAGGAGAGA 58.666 41.667 0.00 0.00 0.00 3.10
35 36 5.420421 TGTGAGGAGTTAAATGAGGAGAGAG 59.580 44.000 0.00 0.00 0.00 3.20
36 37 5.654650 GTGAGGAGTTAAATGAGGAGAGAGA 59.345 44.000 0.00 0.00 0.00 3.10
37 38 5.890985 TGAGGAGTTAAATGAGGAGAGAGAG 59.109 44.000 0.00 0.00 0.00 3.20
38 39 5.208121 AGGAGTTAAATGAGGAGAGAGAGG 58.792 45.833 0.00 0.00 0.00 3.69
39 40 5.043732 AGGAGTTAAATGAGGAGAGAGAGGA 60.044 44.000 0.00 0.00 0.00 3.71
40 41 5.068591 GGAGTTAAATGAGGAGAGAGAGGAC 59.931 48.000 0.00 0.00 0.00 3.85
41 42 5.837829 AGTTAAATGAGGAGAGAGAGGACT 58.162 41.667 0.00 0.00 0.00 3.85
42 43 6.975949 AGTTAAATGAGGAGAGAGAGGACTA 58.024 40.000 0.00 0.00 0.00 2.59
43 44 7.415086 AGTTAAATGAGGAGAGAGAGGACTAA 58.585 38.462 0.00 0.00 0.00 2.24
44 45 8.065007 AGTTAAATGAGGAGAGAGAGGACTAAT 58.935 37.037 0.00 0.00 0.00 1.73
45 46 6.976934 AAATGAGGAGAGAGAGGACTAATC 57.023 41.667 0.00 0.00 0.00 1.75
46 47 4.447138 TGAGGAGAGAGAGGACTAATCC 57.553 50.000 0.00 0.00 46.69 3.01
61 62 6.296803 GGACTAATCCACATTTTAGTAGGGG 58.703 44.000 0.00 0.00 45.47 4.79
62 63 6.126565 GGACTAATCCACATTTTAGTAGGGGT 60.127 42.308 0.00 0.00 45.47 4.95
63 64 7.071572 GGACTAATCCACATTTTAGTAGGGGTA 59.928 40.741 0.00 0.00 45.47 3.69
64 65 7.799081 ACTAATCCACATTTTAGTAGGGGTAC 58.201 38.462 0.00 0.00 36.99 3.34
65 66 7.147426 ACTAATCCACATTTTAGTAGGGGTACC 60.147 40.741 2.17 2.17 41.38 3.34
109 110 7.905265 GTCTTAAGACTAGTTTTAACCCCTCT 58.095 38.462 25.30 0.00 41.65 3.69
110 111 8.373981 GTCTTAAGACTAGTTTTAACCCCTCTT 58.626 37.037 25.30 3.56 41.65 2.85
111 112 8.942033 TCTTAAGACTAGTTTTAACCCCTCTTT 58.058 33.333 13.15 0.00 0.00 2.52
114 115 7.868792 AGACTAGTTTTAACCCCTCTTTAGT 57.131 36.000 0.00 0.00 0.00 2.24
115 116 7.905265 AGACTAGTTTTAACCCCTCTTTAGTC 58.095 38.462 0.00 0.00 36.42 2.59
116 117 7.511714 AGACTAGTTTTAACCCCTCTTTAGTCA 59.488 37.037 0.00 0.00 37.83 3.41
117 118 7.677892 ACTAGTTTTAACCCCTCTTTAGTCAG 58.322 38.462 0.00 0.00 0.00 3.51
118 119 5.877491 AGTTTTAACCCCTCTTTAGTCAGG 58.123 41.667 0.00 0.00 0.00 3.86
123 124 0.253327 CCCTCTTTAGTCAGGGGTGC 59.747 60.000 0.00 0.00 45.39 5.01
124 125 1.280457 CCTCTTTAGTCAGGGGTGCT 58.720 55.000 0.00 0.00 28.24 4.40
125 126 1.630878 CCTCTTTAGTCAGGGGTGCTT 59.369 52.381 0.00 0.00 28.24 3.91
126 127 2.616510 CCTCTTTAGTCAGGGGTGCTTG 60.617 54.545 0.00 0.00 28.24 4.01
127 128 1.351017 TCTTTAGTCAGGGGTGCTTGG 59.649 52.381 0.00 0.00 0.00 3.61
128 129 1.351017 CTTTAGTCAGGGGTGCTTGGA 59.649 52.381 0.00 0.00 0.00 3.53
129 130 1.440618 TTAGTCAGGGGTGCTTGGAA 58.559 50.000 0.00 0.00 0.00 3.53
130 131 0.690762 TAGTCAGGGGTGCTTGGAAC 59.309 55.000 0.00 0.00 0.00 3.62
131 132 1.062488 AGTCAGGGGTGCTTGGAACT 61.062 55.000 0.00 0.00 0.00 3.01
132 133 0.178990 GTCAGGGGTGCTTGGAACTT 60.179 55.000 0.00 0.00 0.00 2.66
133 134 0.555769 TCAGGGGTGCTTGGAACTTT 59.444 50.000 0.00 0.00 0.00 2.66
134 135 1.777878 TCAGGGGTGCTTGGAACTTTA 59.222 47.619 0.00 0.00 0.00 1.85
135 136 2.162681 CAGGGGTGCTTGGAACTTTAG 58.837 52.381 0.00 0.00 0.00 1.85
136 137 0.888619 GGGGTGCTTGGAACTTTAGC 59.111 55.000 0.00 0.00 35.50 3.09
137 138 0.888619 GGGTGCTTGGAACTTTAGCC 59.111 55.000 0.00 0.00 34.03 3.93
138 139 1.547901 GGGTGCTTGGAACTTTAGCCT 60.548 52.381 0.00 0.00 34.03 4.58
139 140 1.813178 GGTGCTTGGAACTTTAGCCTC 59.187 52.381 0.00 0.00 34.03 4.70
140 141 2.553247 GGTGCTTGGAACTTTAGCCTCT 60.553 50.000 0.00 0.00 34.03 3.69
141 142 3.149981 GTGCTTGGAACTTTAGCCTCTT 58.850 45.455 0.00 0.00 34.03 2.85
142 143 4.324267 GTGCTTGGAACTTTAGCCTCTTA 58.676 43.478 0.00 0.00 34.03 2.10
143 144 4.760204 GTGCTTGGAACTTTAGCCTCTTAA 59.240 41.667 0.00 0.00 34.03 1.85
144 145 5.240844 GTGCTTGGAACTTTAGCCTCTTAAA 59.759 40.000 0.00 0.00 34.03 1.52
145 146 5.830991 TGCTTGGAACTTTAGCCTCTTAAAA 59.169 36.000 0.00 0.00 34.03 1.52
146 147 6.322712 TGCTTGGAACTTTAGCCTCTTAAAAA 59.677 34.615 0.00 0.00 34.03 1.94
180 181 9.595823 TTTAATCAGACTAAAATAAGTCCCTCG 57.404 33.333 0.54 0.00 45.86 4.63
181 182 5.593679 TCAGACTAAAATAAGTCCCTCGG 57.406 43.478 0.54 0.00 45.86 4.63
182 183 5.266788 TCAGACTAAAATAAGTCCCTCGGA 58.733 41.667 0.54 0.00 45.86 4.55
183 184 5.897824 TCAGACTAAAATAAGTCCCTCGGAT 59.102 40.000 0.54 0.00 45.86 4.18
184 185 6.040616 TCAGACTAAAATAAGTCCCTCGGATC 59.959 42.308 0.54 0.00 45.86 3.36
185 186 5.304871 AGACTAAAATAAGTCCCTCGGATCC 59.695 44.000 0.00 0.00 45.86 3.36
186 187 4.966805 ACTAAAATAAGTCCCTCGGATCCA 59.033 41.667 13.41 0.00 32.73 3.41
187 188 4.855298 AAAATAAGTCCCTCGGATCCAA 57.145 40.909 13.41 0.00 32.73 3.53
188 189 4.855298 AAATAAGTCCCTCGGATCCAAA 57.145 40.909 13.41 0.00 32.73 3.28
189 190 5.388599 AAATAAGTCCCTCGGATCCAAAT 57.611 39.130 13.41 0.00 32.73 2.32
190 191 6.509523 AAATAAGTCCCTCGGATCCAAATA 57.490 37.500 13.41 0.00 32.73 1.40
191 192 3.840124 AAGTCCCTCGGATCCAAATAC 57.160 47.619 13.41 2.92 32.73 1.89
192 193 2.047830 AGTCCCTCGGATCCAAATACC 58.952 52.381 13.41 0.00 32.73 2.73
193 194 1.071857 GTCCCTCGGATCCAAATACCC 59.928 57.143 13.41 0.00 32.73 3.69
194 195 1.061657 TCCCTCGGATCCAAATACCCT 60.062 52.381 13.41 0.00 0.00 4.34
195 196 1.348036 CCCTCGGATCCAAATACCCTC 59.652 57.143 13.41 0.00 0.00 4.30
196 197 2.330216 CCTCGGATCCAAATACCCTCT 58.670 52.381 13.41 0.00 0.00 3.69
197 198 2.706190 CCTCGGATCCAAATACCCTCTT 59.294 50.000 13.41 0.00 0.00 2.85
198 199 3.901844 CCTCGGATCCAAATACCCTCTTA 59.098 47.826 13.41 0.00 0.00 2.10
199 200 4.021016 CCTCGGATCCAAATACCCTCTTAG 60.021 50.000 13.41 0.00 0.00 2.18
200 201 4.811498 TCGGATCCAAATACCCTCTTAGA 58.189 43.478 13.41 0.00 0.00 2.10
201 202 5.213519 TCGGATCCAAATACCCTCTTAGAA 58.786 41.667 13.41 0.00 0.00 2.10
202 203 5.844516 TCGGATCCAAATACCCTCTTAGAAT 59.155 40.000 13.41 0.00 0.00 2.40
203 204 5.934625 CGGATCCAAATACCCTCTTAGAATG 59.065 44.000 13.41 0.00 0.00 2.67
204 205 6.464465 CGGATCCAAATACCCTCTTAGAATGT 60.464 42.308 13.41 0.00 0.00 2.71
205 206 7.256190 CGGATCCAAATACCCTCTTAGAATGTA 60.256 40.741 13.41 0.00 0.00 2.29
206 207 8.437575 GGATCCAAATACCCTCTTAGAATGTAA 58.562 37.037 6.95 0.00 0.00 2.41
207 208 9.847224 GATCCAAATACCCTCTTAGAATGTAAA 57.153 33.333 0.00 0.00 0.00 2.01
234 235 1.813513 AAATTGAGTCCGACTGCCTG 58.186 50.000 5.57 0.00 0.00 4.85
246 247 1.970114 CTGCCTGCTGTGGGTTCAG 60.970 63.158 0.00 0.00 38.35 3.02
249 250 0.955919 GCCTGCTGTGGGTTCAGTAC 60.956 60.000 0.00 0.00 37.70 2.73
256 257 6.056090 TGCTGTGGGTTCAGTACATTTATA 57.944 37.500 0.00 0.00 37.70 0.98
382 410 4.286813 AGATCCTCTGGTTCTTGGGATA 57.713 45.455 0.00 0.00 36.98 2.59
385 413 4.778213 TCCTCTGGTTCTTGGGATATTG 57.222 45.455 0.00 0.00 0.00 1.90
389 417 5.398353 CCTCTGGTTCTTGGGATATTGTGAT 60.398 44.000 0.00 0.00 0.00 3.06
414 442 6.821665 TCCCGGACTTTATTTCTCATTACTTG 59.178 38.462 0.73 0.00 0.00 3.16
415 443 6.598064 CCCGGACTTTATTTCTCATTACTTGT 59.402 38.462 0.73 0.00 0.00 3.16
416 444 7.767198 CCCGGACTTTATTTCTCATTACTTGTA 59.233 37.037 0.73 0.00 0.00 2.41
417 445 9.158233 CCGGACTTTATTTCTCATTACTTGTAA 57.842 33.333 0.00 0.00 0.00 2.41
426 454 8.771920 TTTCTCATTACTTGTAATCGACATGT 57.228 30.769 0.00 0.00 45.63 3.21
427 455 7.987268 TCTCATTACTTGTAATCGACATGTC 57.013 36.000 16.21 16.21 43.43 3.06
428 456 7.772166 TCTCATTACTTGTAATCGACATGTCT 58.228 34.615 22.95 7.76 43.43 3.41
429 457 8.899771 TCTCATTACTTGTAATCGACATGTCTA 58.100 33.333 22.95 13.43 43.43 2.59
430 458 9.684448 CTCATTACTTGTAATCGACATGTCTAT 57.316 33.333 22.95 15.20 43.43 1.98
517 547 9.750783 ATACTCCAGTATAATATACTTGGACGT 57.249 33.333 18.81 19.72 39.29 4.34
1069 3889 0.249120 CTCCCATGTAGCGGTCAACA 59.751 55.000 0.00 0.00 0.00 3.33
1099 3919 3.706373 AGCAGGTGGATTCGGCGT 61.706 61.111 6.85 0.00 0.00 5.68
1389 4209 1.070786 GTCAGCAAAGACGGGGTCA 59.929 57.895 0.00 0.00 34.60 4.02
1443 4263 2.503061 CCGGAGCATGAGGTGGAG 59.497 66.667 0.00 0.00 0.00 3.86
1444 4264 2.060383 CCGGAGCATGAGGTGGAGA 61.060 63.158 0.00 0.00 0.00 3.71
1446 4266 0.467384 CGGAGCATGAGGTGGAGAAT 59.533 55.000 0.00 0.00 0.00 2.40
1453 4273 3.370315 GCATGAGGTGGAGAATCTCAAGT 60.370 47.826 12.79 0.00 40.37 3.16
1489 4309 1.909302 TCCTTAAGGAGGCAGTTGAGG 59.091 52.381 20.72 0.00 45.87 3.86
1539 4359 2.433318 GTCGACCAGTGCTCTGCC 60.433 66.667 10.32 3.69 40.09 4.85
1546 4366 2.125229 AGTGCTCTGCCGATGCTG 60.125 61.111 0.00 0.00 38.71 4.41
1547 4367 3.873883 GTGCTCTGCCGATGCTGC 61.874 66.667 0.00 0.00 38.71 5.25
1548 4368 4.091939 TGCTCTGCCGATGCTGCT 62.092 61.111 0.00 0.00 38.71 4.24
1568 4388 2.755876 ACTCGCCGATCTGGAGCA 60.756 61.111 7.64 0.00 42.00 4.26
1746 4566 2.066999 GGAGGAGGCCGAAGTGGAT 61.067 63.158 0.00 0.00 42.00 3.41
1753 4573 3.118519 GGAGGCCGAAGTGGATAAACTTA 60.119 47.826 0.00 0.00 40.48 2.24
1756 4576 4.941873 AGGCCGAAGTGGATAAACTTAAAG 59.058 41.667 0.00 0.00 40.48 1.85
1765 4585 6.210984 AGTGGATAAACTTAAAGTCGAGGAGT 59.789 38.462 0.00 0.00 0.00 3.85
1788 4608 2.435586 CGCAGGAAGCAGGTGGAG 60.436 66.667 0.00 0.00 46.13 3.86
1825 4645 4.322650 CCGAAAATGTCACCCAATTGGAAT 60.323 41.667 26.60 10.73 37.39 3.01
1871 4691 0.319728 AGTACTGAGCTGTGTGCAGG 59.680 55.000 0.00 0.00 45.94 4.85
1928 4748 1.665916 CCACGGCTCACAGTGTCAG 60.666 63.158 0.00 0.00 36.69 3.51
2025 4845 4.779696 AGGAGAAGCTTGATGAGAAATCC 58.220 43.478 2.10 0.00 0.00 3.01
2152 4972 2.392662 TGGAGATGGAGACTAGCAAGG 58.607 52.381 0.00 0.00 0.00 3.61
2187 5007 0.539051 CGCAGAAGGAGGTGGAGAAT 59.461 55.000 0.00 0.00 0.00 2.40
2406 5226 2.439156 GCCATGGCCTCTGTCCAC 60.439 66.667 27.24 0.00 36.26 4.02
2451 5271 0.614812 TGATGGCTAAGCTGACTGCA 59.385 50.000 7.11 0.00 45.94 4.41
2466 5286 1.897133 ACTGCACTGAACGGTACCATA 59.103 47.619 13.54 0.00 0.00 2.74
2502 5322 5.698089 TGTTCACTGTGATGATCTCAAGAAC 59.302 40.000 22.19 22.19 36.55 3.01
2531 5351 0.033991 TCGCTCCTAGCTGAGAAGGT 60.034 55.000 5.28 0.00 39.60 3.50
2534 5354 1.552792 GCTCCTAGCTGAGAAGGTTGT 59.447 52.381 5.28 0.00 38.45 3.32
2668 5488 3.317993 GGCAGAAGCACTAAACAAGGAAA 59.682 43.478 0.00 0.00 44.61 3.13
2782 5602 0.669625 GTGCCCTACCACGACTGTTC 60.670 60.000 0.00 0.00 0.00 3.18
2845 5665 4.857509 ACAGAGAACTCTTTTACTCGCT 57.142 40.909 1.24 0.00 37.98 4.93
2898 5718 3.690460 AGAATAACCAGGCTTCCACTTG 58.310 45.455 0.00 0.00 0.00 3.16
2991 5811 5.050159 GTGTTTGCATGTTTTCCTGGAATTC 60.050 40.000 10.45 7.14 0.00 2.17
3180 6514 7.954788 AAACAGATGAAGAGAGAACACTTAC 57.045 36.000 0.00 0.00 0.00 2.34
3265 6599 7.486407 AAAGGATTTGGATTATGCACTTCTT 57.514 32.000 0.00 0.00 36.60 2.52
3266 6600 7.486407 AAGGATTTGGATTATGCACTTCTTT 57.514 32.000 0.00 0.00 0.00 2.52
3267 6601 7.105241 AGGATTTGGATTATGCACTTCTTTC 57.895 36.000 0.00 0.00 0.00 2.62
3268 6602 6.097412 AGGATTTGGATTATGCACTTCTTTCC 59.903 38.462 0.00 0.00 0.00 3.13
3269 6603 6.097412 GGATTTGGATTATGCACTTCTTTCCT 59.903 38.462 0.00 0.00 0.00 3.36
3270 6604 6.515272 TTTGGATTATGCACTTCTTTCCTC 57.485 37.500 0.00 0.00 0.00 3.71
3271 6605 4.526970 TGGATTATGCACTTCTTTCCTCC 58.473 43.478 0.00 0.00 0.00 4.30
3272 6606 4.228210 TGGATTATGCACTTCTTTCCTCCT 59.772 41.667 0.00 0.00 0.00 3.69
3273 6607 5.196695 GGATTATGCACTTCTTTCCTCCTT 58.803 41.667 0.00 0.00 0.00 3.36
3274 6608 6.069673 TGGATTATGCACTTCTTTCCTCCTTA 60.070 38.462 0.00 0.00 0.00 2.69
3275 6609 6.484977 GGATTATGCACTTCTTTCCTCCTTAG 59.515 42.308 0.00 0.00 0.00 2.18
3276 6610 6.620877 TTATGCACTTCTTTCCTCCTTAGA 57.379 37.500 0.00 0.00 0.00 2.10
3277 6611 4.273148 TGCACTTCTTTCCTCCTTAGAC 57.727 45.455 0.00 0.00 0.00 2.59
3278 6612 3.008049 TGCACTTCTTTCCTCCTTAGACC 59.992 47.826 0.00 0.00 0.00 3.85
3279 6613 3.851098 CACTTCTTTCCTCCTTAGACCG 58.149 50.000 0.00 0.00 0.00 4.79
3280 6614 2.234168 ACTTCTTTCCTCCTTAGACCGC 59.766 50.000 0.00 0.00 0.00 5.68
3281 6615 1.933021 TCTTTCCTCCTTAGACCGCA 58.067 50.000 0.00 0.00 0.00 5.69
3282 6616 2.253610 TCTTTCCTCCTTAGACCGCAA 58.746 47.619 0.00 0.00 0.00 4.85
3283 6617 2.233922 TCTTTCCTCCTTAGACCGCAAG 59.766 50.000 0.00 0.00 0.00 4.01
3284 6618 0.249398 TTCCTCCTTAGACCGCAAGC 59.751 55.000 0.00 0.00 0.00 4.01
3285 6619 0.902984 TCCTCCTTAGACCGCAAGCA 60.903 55.000 0.00 0.00 0.00 3.91
3286 6620 0.741221 CCTCCTTAGACCGCAAGCAC 60.741 60.000 0.00 0.00 0.00 4.40
3287 6621 0.037326 CTCCTTAGACCGCAAGCACA 60.037 55.000 0.00 0.00 0.00 4.57
3288 6622 0.037326 TCCTTAGACCGCAAGCACAG 60.037 55.000 0.00 0.00 0.00 3.66
3289 6623 0.320771 CCTTAGACCGCAAGCACAGT 60.321 55.000 0.00 0.00 0.00 3.55
3290 6624 1.512926 CTTAGACCGCAAGCACAGTT 58.487 50.000 0.00 0.00 0.00 3.16
3291 6625 1.195448 CTTAGACCGCAAGCACAGTTG 59.805 52.381 0.00 0.00 0.00 3.16
3292 6626 0.105964 TAGACCGCAAGCACAGTTGT 59.894 50.000 0.00 0.00 0.00 3.32
3293 6627 1.160329 AGACCGCAAGCACAGTTGTC 61.160 55.000 0.00 0.00 0.00 3.18
3294 6628 1.153168 ACCGCAAGCACAGTTGTCT 60.153 52.632 0.00 0.00 0.00 3.41
3295 6629 0.105964 ACCGCAAGCACAGTTGTCTA 59.894 50.000 0.00 0.00 0.00 2.59
3296 6630 1.225855 CCGCAAGCACAGTTGTCTAA 58.774 50.000 0.00 0.00 0.00 2.10
3297 6631 1.069906 CCGCAAGCACAGTTGTCTAAC 60.070 52.381 0.00 0.00 37.06 2.34
3299 6633 2.287915 CGCAAGCACAGTTGTCTAACTT 59.712 45.455 0.00 0.00 44.57 2.66
3300 6634 3.242739 CGCAAGCACAGTTGTCTAACTTT 60.243 43.478 0.00 0.00 44.57 2.66
3301 6635 4.025229 CGCAAGCACAGTTGTCTAACTTTA 60.025 41.667 0.00 0.00 44.57 1.85
3302 6636 5.334105 CGCAAGCACAGTTGTCTAACTTTAT 60.334 40.000 0.00 0.00 44.57 1.40
3303 6637 6.128661 CGCAAGCACAGTTGTCTAACTTTATA 60.129 38.462 0.00 0.00 44.57 0.98
3304 6638 7.015877 GCAAGCACAGTTGTCTAACTTTATAC 58.984 38.462 0.00 0.00 44.57 1.47
3305 6639 7.519002 CAAGCACAGTTGTCTAACTTTATACC 58.481 38.462 0.00 0.00 44.57 2.73
3306 6640 6.171213 AGCACAGTTGTCTAACTTTATACCC 58.829 40.000 0.00 0.00 44.57 3.69
3307 6641 6.013639 AGCACAGTTGTCTAACTTTATACCCT 60.014 38.462 0.00 0.00 44.57 4.34
3308 6642 6.313164 GCACAGTTGTCTAACTTTATACCCTC 59.687 42.308 0.00 0.00 44.57 4.30
3309 6643 6.817140 CACAGTTGTCTAACTTTATACCCTCC 59.183 42.308 0.00 0.00 44.57 4.30
3310 6644 6.729569 ACAGTTGTCTAACTTTATACCCTCCT 59.270 38.462 0.00 0.00 44.57 3.69
3311 6645 7.897565 ACAGTTGTCTAACTTTATACCCTCCTA 59.102 37.037 0.00 0.00 44.57 2.94
3312 6646 8.196103 CAGTTGTCTAACTTTATACCCTCCTAC 58.804 40.741 0.00 0.00 44.57 3.18
3313 6647 8.121185 AGTTGTCTAACTTTATACCCTCCTACT 58.879 37.037 0.00 0.00 44.57 2.57
3314 6648 9.413734 GTTGTCTAACTTTATACCCTCCTACTA 57.586 37.037 0.00 0.00 33.94 1.82
3315 6649 8.986929 TGTCTAACTTTATACCCTCCTACTAC 57.013 38.462 0.00 0.00 0.00 2.73
3316 6650 8.001292 TGTCTAACTTTATACCCTCCTACTACC 58.999 40.741 0.00 0.00 0.00 3.18
3317 6651 8.001292 GTCTAACTTTATACCCTCCTACTACCA 58.999 40.741 0.00 0.00 0.00 3.25
3318 6652 8.568723 TCTAACTTTATACCCTCCTACTACCAA 58.431 37.037 0.00 0.00 0.00 3.67
3319 6653 7.429374 AACTTTATACCCTCCTACTACCAAC 57.571 40.000 0.00 0.00 0.00 3.77
3320 6654 6.505754 ACTTTATACCCTCCTACTACCAACA 58.494 40.000 0.00 0.00 0.00 3.33
3321 6655 6.961721 ACTTTATACCCTCCTACTACCAACAA 59.038 38.462 0.00 0.00 0.00 2.83
3322 6656 7.626487 ACTTTATACCCTCCTACTACCAACAAT 59.374 37.037 0.00 0.00 0.00 2.71
3323 6657 8.396619 TTTATACCCTCCTACTACCAACAATT 57.603 34.615 0.00 0.00 0.00 2.32
3324 6658 9.504705 TTTATACCCTCCTACTACCAACAATTA 57.495 33.333 0.00 0.00 0.00 1.40
3325 6659 9.678981 TTATACCCTCCTACTACCAACAATTAT 57.321 33.333 0.00 0.00 0.00 1.28
3326 6660 6.496144 ACCCTCCTACTACCAACAATTATC 57.504 41.667 0.00 0.00 0.00 1.75
3327 6661 5.968167 ACCCTCCTACTACCAACAATTATCA 59.032 40.000 0.00 0.00 0.00 2.15
3328 6662 6.445786 ACCCTCCTACTACCAACAATTATCAA 59.554 38.462 0.00 0.00 0.00 2.57
3329 6663 7.128883 ACCCTCCTACTACCAACAATTATCAAT 59.871 37.037 0.00 0.00 0.00 2.57
3330 6664 8.656806 CCCTCCTACTACCAACAATTATCAATA 58.343 37.037 0.00 0.00 0.00 1.90
3341 6675 9.248291 CCAACAATTATCAATATTGTACTTGGC 57.752 33.333 14.97 0.00 37.52 4.52
3342 6676 8.957028 CAACAATTATCAATATTGTACTTGGCG 58.043 33.333 14.97 8.82 37.52 5.69
3343 6677 8.220755 ACAATTATCAATATTGTACTTGGCGT 57.779 30.769 14.97 2.67 36.83 5.68
3344 6678 8.682710 ACAATTATCAATATTGTACTTGGCGTT 58.317 29.630 14.97 1.35 36.83 4.84
3345 6679 9.515020 CAATTATCAATATTGTACTTGGCGTTT 57.485 29.630 14.97 0.00 0.00 3.60
3348 6682 9.602568 TTATCAATATTGTACTTGGCGTTTAGA 57.397 29.630 14.97 0.00 0.00 2.10
3349 6683 7.908827 TCAATATTGTACTTGGCGTTTAGAA 57.091 32.000 14.97 0.00 0.00 2.10
3350 6684 7.745015 TCAATATTGTACTTGGCGTTTAGAAC 58.255 34.615 14.97 0.00 0.00 3.01
3351 6685 7.388224 TCAATATTGTACTTGGCGTTTAGAACA 59.612 33.333 14.97 0.00 0.00 3.18
3352 6686 7.859325 ATATTGTACTTGGCGTTTAGAACAT 57.141 32.000 0.00 0.00 0.00 2.71
3353 6687 6.569179 ATTGTACTTGGCGTTTAGAACATT 57.431 33.333 0.00 0.00 0.00 2.71
3354 6688 5.600908 TGTACTTGGCGTTTAGAACATTC 57.399 39.130 0.00 0.00 0.00 2.67
3355 6689 5.057819 TGTACTTGGCGTTTAGAACATTCA 58.942 37.500 0.00 0.00 0.00 2.57
3356 6690 4.749245 ACTTGGCGTTTAGAACATTCAG 57.251 40.909 0.00 0.00 0.00 3.02
3357 6691 3.058224 ACTTGGCGTTTAGAACATTCAGC 60.058 43.478 0.00 0.00 0.00 4.26
3358 6692 2.778299 TGGCGTTTAGAACATTCAGCT 58.222 42.857 0.00 0.00 0.00 4.24
3359 6693 2.483877 TGGCGTTTAGAACATTCAGCTG 59.516 45.455 7.63 7.63 0.00 4.24
3360 6694 2.484264 GGCGTTTAGAACATTCAGCTGT 59.516 45.455 14.67 0.00 0.00 4.40
3361 6695 3.058224 GGCGTTTAGAACATTCAGCTGTT 60.058 43.478 14.67 0.34 41.92 3.16
3362 6696 4.537015 GCGTTTAGAACATTCAGCTGTTT 58.463 39.130 14.67 3.00 39.40 2.83
3363 6697 4.976116 GCGTTTAGAACATTCAGCTGTTTT 59.024 37.500 14.67 2.63 39.40 2.43
3364 6698 5.458779 GCGTTTAGAACATTCAGCTGTTTTT 59.541 36.000 14.67 2.99 39.40 1.94
3395 6729 2.332063 ATGGTTGTAGCTCGATTGGG 57.668 50.000 0.00 0.00 0.00 4.12
3434 6768 3.382865 TGGCTCACTTGTTATTTGCAACA 59.617 39.130 0.00 0.00 36.65 3.33
3448 6782 9.991388 GTTATTTGCAACAAATAGACGGTAATA 57.009 29.630 0.00 0.00 0.00 0.98
3550 6884 4.401519 TCTGCTACACACTATCTGGTAACC 59.598 45.833 0.00 0.00 0.00 2.85
3673 7007 4.127171 CCCTATATGGTGGTTTCAGAACG 58.873 47.826 0.00 0.00 36.61 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.143305 CTCCTCACAACACTTGCGAG 58.857 55.000 0.00 0.00 39.06 5.03
2 3 1.299541 AACTCCTCACAACACTTGCG 58.700 50.000 0.00 0.00 0.00 4.85
3 4 4.893424 TTTAACTCCTCACAACACTTGC 57.107 40.909 0.00 0.00 0.00 4.01
4 5 6.293626 CCTCATTTAACTCCTCACAACACTTG 60.294 42.308 0.00 0.00 0.00 3.16
6 7 5.071788 TCCTCATTTAACTCCTCACAACACT 59.928 40.000 0.00 0.00 0.00 3.55
8 9 5.306937 TCTCCTCATTTAACTCCTCACAACA 59.693 40.000 0.00 0.00 0.00 3.33
9 10 5.794894 TCTCCTCATTTAACTCCTCACAAC 58.205 41.667 0.00 0.00 0.00 3.32
10 11 5.780282 TCTCTCCTCATTTAACTCCTCACAA 59.220 40.000 0.00 0.00 0.00 3.33
11 12 5.333581 TCTCTCCTCATTTAACTCCTCACA 58.666 41.667 0.00 0.00 0.00 3.58
12 13 5.654650 TCTCTCTCCTCATTTAACTCCTCAC 59.345 44.000 0.00 0.00 0.00 3.51
13 14 5.832221 TCTCTCTCCTCATTTAACTCCTCA 58.168 41.667 0.00 0.00 0.00 3.86
14 15 5.301805 CCTCTCTCTCCTCATTTAACTCCTC 59.698 48.000 0.00 0.00 0.00 3.71
15 16 5.043732 TCCTCTCTCTCCTCATTTAACTCCT 60.044 44.000 0.00 0.00 0.00 3.69
16 17 5.068591 GTCCTCTCTCTCCTCATTTAACTCC 59.931 48.000 0.00 0.00 0.00 3.85
17 18 5.891551 AGTCCTCTCTCTCCTCATTTAACTC 59.108 44.000 0.00 0.00 0.00 3.01
18 19 5.837829 AGTCCTCTCTCTCCTCATTTAACT 58.162 41.667 0.00 0.00 0.00 2.24
19 20 7.648039 TTAGTCCTCTCTCTCCTCATTTAAC 57.352 40.000 0.00 0.00 0.00 2.01
20 21 7.507616 GGATTAGTCCTCTCTCTCCTCATTTAA 59.492 40.741 0.00 0.00 41.60 1.52
21 22 7.007723 GGATTAGTCCTCTCTCTCCTCATTTA 58.992 42.308 0.00 0.00 41.60 1.40
22 23 5.838521 GGATTAGTCCTCTCTCTCCTCATTT 59.161 44.000 0.00 0.00 41.60 2.32
23 24 5.103301 TGGATTAGTCCTCTCTCTCCTCATT 60.103 44.000 5.79 0.00 45.32 2.57
24 25 4.418526 TGGATTAGTCCTCTCTCTCCTCAT 59.581 45.833 5.79 0.00 45.32 2.90
25 26 3.788708 TGGATTAGTCCTCTCTCTCCTCA 59.211 47.826 5.79 0.00 45.32 3.86
26 27 4.142038 GTGGATTAGTCCTCTCTCTCCTC 58.858 52.174 5.79 0.00 45.32 3.71
27 28 3.529734 TGTGGATTAGTCCTCTCTCTCCT 59.470 47.826 5.79 0.00 45.32 3.69
28 29 3.904717 TGTGGATTAGTCCTCTCTCTCC 58.095 50.000 5.79 0.00 45.32 3.71
29 30 6.478512 AAATGTGGATTAGTCCTCTCTCTC 57.521 41.667 5.79 0.00 45.32 3.20
30 31 6.882768 AAAATGTGGATTAGTCCTCTCTCT 57.117 37.500 5.79 0.00 45.32 3.10
31 32 7.787028 ACTAAAATGTGGATTAGTCCTCTCTC 58.213 38.462 5.79 0.00 45.32 3.20
32 33 7.741554 ACTAAAATGTGGATTAGTCCTCTCT 57.258 36.000 5.79 0.00 45.32 3.10
33 34 8.145122 CCTACTAAAATGTGGATTAGTCCTCTC 58.855 40.741 5.79 0.00 45.32 3.20
34 35 7.071321 CCCTACTAAAATGTGGATTAGTCCTCT 59.929 40.741 5.79 0.00 45.32 3.69
35 36 7.217906 CCCTACTAAAATGTGGATTAGTCCTC 58.782 42.308 5.79 2.58 45.32 3.71
36 37 6.101296 CCCCTACTAAAATGTGGATTAGTCCT 59.899 42.308 5.79 0.00 45.32 3.85
37 38 6.126565 ACCCCTACTAAAATGTGGATTAGTCC 60.127 42.308 0.00 0.00 40.53 3.85
38 39 6.896883 ACCCCTACTAAAATGTGGATTAGTC 58.103 40.000 1.78 0.00 40.53 2.59
39 40 6.903340 ACCCCTACTAAAATGTGGATTAGT 57.097 37.500 3.93 3.93 43.05 2.24
40 41 7.222161 GGTACCCCTACTAAAATGTGGATTAG 58.778 42.308 0.00 0.00 35.67 1.73
41 42 7.140522 GGTACCCCTACTAAAATGTGGATTA 57.859 40.000 0.00 0.00 0.00 1.75
42 43 6.009908 GGTACCCCTACTAAAATGTGGATT 57.990 41.667 0.00 0.00 0.00 3.01
43 44 5.641789 GGTACCCCTACTAAAATGTGGAT 57.358 43.478 0.00 0.00 0.00 3.41
84 85 7.905265 AGAGGGGTTAAAACTAGTCTTAAGAC 58.095 38.462 25.24 25.24 45.08 3.01
85 86 8.502047 AAGAGGGGTTAAAACTAGTCTTAAGA 57.498 34.615 0.00 0.00 0.00 2.10
88 89 9.384849 ACTAAAGAGGGGTTAAAACTAGTCTTA 57.615 33.333 0.00 0.00 0.00 2.10
89 90 8.272659 ACTAAAGAGGGGTTAAAACTAGTCTT 57.727 34.615 0.00 0.00 0.00 3.01
90 91 7.511714 TGACTAAAGAGGGGTTAAAACTAGTCT 59.488 37.037 0.00 0.00 32.68 3.24
91 92 7.674120 TGACTAAAGAGGGGTTAAAACTAGTC 58.326 38.462 0.00 8.25 0.00 2.59
92 93 7.256583 CCTGACTAAAGAGGGGTTAAAACTAGT 60.257 40.741 0.00 0.00 0.00 2.57
93 94 7.104290 CCTGACTAAAGAGGGGTTAAAACTAG 58.896 42.308 0.00 0.00 0.00 2.57
94 95 6.013119 CCCTGACTAAAGAGGGGTTAAAACTA 60.013 42.308 0.00 0.00 44.88 2.24
95 96 5.222068 CCCTGACTAAAGAGGGGTTAAAACT 60.222 44.000 0.00 0.00 44.88 2.66
96 97 5.008331 CCCTGACTAAAGAGGGGTTAAAAC 58.992 45.833 0.00 0.00 44.88 2.43
97 98 5.251182 CCCTGACTAAAGAGGGGTTAAAA 57.749 43.478 0.00 0.00 44.88 1.52
98 99 4.921644 CCCTGACTAAAGAGGGGTTAAA 57.078 45.455 0.00 0.00 44.88 1.52
105 106 1.280457 AGCACCCCTGACTAAAGAGG 58.720 55.000 0.00 0.00 0.00 3.69
106 107 2.616510 CCAAGCACCCCTGACTAAAGAG 60.617 54.545 0.00 0.00 0.00 2.85
107 108 1.351017 CCAAGCACCCCTGACTAAAGA 59.649 52.381 0.00 0.00 0.00 2.52
108 109 1.351017 TCCAAGCACCCCTGACTAAAG 59.649 52.381 0.00 0.00 0.00 1.85
109 110 1.440618 TCCAAGCACCCCTGACTAAA 58.559 50.000 0.00 0.00 0.00 1.85
110 111 1.073284 GTTCCAAGCACCCCTGACTAA 59.927 52.381 0.00 0.00 0.00 2.24
111 112 0.690762 GTTCCAAGCACCCCTGACTA 59.309 55.000 0.00 0.00 0.00 2.59
112 113 1.062488 AGTTCCAAGCACCCCTGACT 61.062 55.000 0.00 0.00 0.00 3.41
113 114 0.178990 AAGTTCCAAGCACCCCTGAC 60.179 55.000 0.00 0.00 0.00 3.51
114 115 0.555769 AAAGTTCCAAGCACCCCTGA 59.444 50.000 0.00 0.00 0.00 3.86
115 116 2.162681 CTAAAGTTCCAAGCACCCCTG 58.837 52.381 0.00 0.00 0.00 4.45
116 117 1.547901 GCTAAAGTTCCAAGCACCCCT 60.548 52.381 0.00 0.00 36.26 4.79
117 118 0.888619 GCTAAAGTTCCAAGCACCCC 59.111 55.000 0.00 0.00 36.26 4.95
118 119 0.888619 GGCTAAAGTTCCAAGCACCC 59.111 55.000 7.02 0.00 38.01 4.61
119 120 1.813178 GAGGCTAAAGTTCCAAGCACC 59.187 52.381 0.00 0.00 38.01 5.01
120 121 2.784347 AGAGGCTAAAGTTCCAAGCAC 58.216 47.619 0.00 2.09 38.01 4.40
121 122 3.508845 AAGAGGCTAAAGTTCCAAGCA 57.491 42.857 0.00 0.00 38.01 3.91
122 123 5.959618 TTTAAGAGGCTAAAGTTCCAAGC 57.040 39.130 0.00 0.00 35.47 4.01
154 155 9.595823 CGAGGGACTTATTTTAGTCTGATTAAA 57.404 33.333 1.71 1.71 41.55 1.52
155 156 8.202137 CCGAGGGACTTATTTTAGTCTGATTAA 58.798 37.037 0.00 0.00 41.55 1.40
156 157 7.562454 TCCGAGGGACTTATTTTAGTCTGATTA 59.438 37.037 0.00 0.00 41.55 1.75
157 158 6.383147 TCCGAGGGACTTATTTTAGTCTGATT 59.617 38.462 0.00 0.00 41.55 2.57
158 159 5.897824 TCCGAGGGACTTATTTTAGTCTGAT 59.102 40.000 0.00 0.00 41.55 2.90
159 160 5.266788 TCCGAGGGACTTATTTTAGTCTGA 58.733 41.667 0.00 0.00 41.55 3.27
160 161 5.593679 TCCGAGGGACTTATTTTAGTCTG 57.406 43.478 0.00 0.00 41.55 3.51
161 162 5.304871 GGATCCGAGGGACTTATTTTAGTCT 59.695 44.000 0.00 0.00 41.55 3.24
162 163 5.070047 TGGATCCGAGGGACTTATTTTAGTC 59.930 44.000 7.39 0.00 41.55 2.59
163 164 4.966805 TGGATCCGAGGGACTTATTTTAGT 59.033 41.667 7.39 0.00 41.55 2.24
164 165 5.546621 TGGATCCGAGGGACTTATTTTAG 57.453 43.478 7.39 0.00 41.55 1.85
165 166 5.961398 TTGGATCCGAGGGACTTATTTTA 57.039 39.130 7.39 0.00 41.55 1.52
166 167 4.855298 TTGGATCCGAGGGACTTATTTT 57.145 40.909 7.39 0.00 41.55 1.82
167 168 4.855298 TTTGGATCCGAGGGACTTATTT 57.145 40.909 7.39 0.00 41.55 1.40
168 169 5.221864 GGTATTTGGATCCGAGGGACTTATT 60.222 44.000 7.39 0.00 41.55 1.40
169 170 4.286291 GGTATTTGGATCCGAGGGACTTAT 59.714 45.833 7.39 0.00 41.55 1.73
170 171 3.644738 GGTATTTGGATCCGAGGGACTTA 59.355 47.826 7.39 0.00 41.55 2.24
171 172 2.438392 GGTATTTGGATCCGAGGGACTT 59.562 50.000 7.39 0.00 41.55 3.01
173 174 1.071857 GGGTATTTGGATCCGAGGGAC 59.928 57.143 7.39 4.51 32.98 4.46
174 175 1.061657 AGGGTATTTGGATCCGAGGGA 60.062 52.381 7.39 0.00 35.55 4.20
175 176 1.348036 GAGGGTATTTGGATCCGAGGG 59.652 57.143 7.39 0.00 0.00 4.30
176 177 2.330216 AGAGGGTATTTGGATCCGAGG 58.670 52.381 7.39 0.00 0.00 4.63
177 178 4.833380 TCTAAGAGGGTATTTGGATCCGAG 59.167 45.833 7.39 0.00 0.00 4.63
178 179 4.811498 TCTAAGAGGGTATTTGGATCCGA 58.189 43.478 7.39 1.27 0.00 4.55
179 180 5.546621 TTCTAAGAGGGTATTTGGATCCG 57.453 43.478 7.39 0.00 0.00 4.18
180 181 6.842676 ACATTCTAAGAGGGTATTTGGATCC 58.157 40.000 4.20 4.20 0.00 3.36
181 182 9.847224 TTTACATTCTAAGAGGGTATTTGGATC 57.153 33.333 0.00 0.00 0.00 3.36
183 184 9.457436 GTTTTACATTCTAAGAGGGTATTTGGA 57.543 33.333 0.00 0.00 0.00 3.53
184 185 8.683615 GGTTTTACATTCTAAGAGGGTATTTGG 58.316 37.037 0.00 0.00 0.00 3.28
185 186 8.395633 CGGTTTTACATTCTAAGAGGGTATTTG 58.604 37.037 0.00 0.00 0.00 2.32
186 187 8.105197 ACGGTTTTACATTCTAAGAGGGTATTT 58.895 33.333 0.00 0.00 0.00 1.40
187 188 7.551617 CACGGTTTTACATTCTAAGAGGGTATT 59.448 37.037 0.00 0.00 0.00 1.89
188 189 7.046033 CACGGTTTTACATTCTAAGAGGGTAT 58.954 38.462 0.00 0.00 0.00 2.73
189 190 6.211184 TCACGGTTTTACATTCTAAGAGGGTA 59.789 38.462 0.00 0.00 0.00 3.69
190 191 5.012354 TCACGGTTTTACATTCTAAGAGGGT 59.988 40.000 0.00 0.00 0.00 4.34
191 192 5.484715 TCACGGTTTTACATTCTAAGAGGG 58.515 41.667 0.00 0.00 0.00 4.30
192 193 7.429636 TTTCACGGTTTTACATTCTAAGAGG 57.570 36.000 0.00 0.00 0.00 3.69
193 194 9.893305 AATTTTCACGGTTTTACATTCTAAGAG 57.107 29.630 0.00 0.00 0.00 2.85
194 195 9.672086 CAATTTTCACGGTTTTACATTCTAAGA 57.328 29.630 0.00 0.00 0.00 2.10
195 196 9.672086 TCAATTTTCACGGTTTTACATTCTAAG 57.328 29.630 0.00 0.00 0.00 2.18
196 197 9.672086 CTCAATTTTCACGGTTTTACATTCTAA 57.328 29.630 0.00 0.00 0.00 2.10
197 198 8.842280 ACTCAATTTTCACGGTTTTACATTCTA 58.158 29.630 0.00 0.00 0.00 2.10
198 199 7.712797 ACTCAATTTTCACGGTTTTACATTCT 58.287 30.769 0.00 0.00 0.00 2.40
199 200 7.114388 GGACTCAATTTTCACGGTTTTACATTC 59.886 37.037 0.00 0.00 0.00 2.67
200 201 6.921307 GGACTCAATTTTCACGGTTTTACATT 59.079 34.615 0.00 0.00 0.00 2.71
201 202 6.443792 GGACTCAATTTTCACGGTTTTACAT 58.556 36.000 0.00 0.00 0.00 2.29
202 203 5.504337 CGGACTCAATTTTCACGGTTTTACA 60.504 40.000 0.00 0.00 0.00 2.41
203 204 4.907582 CGGACTCAATTTTCACGGTTTTAC 59.092 41.667 0.00 0.00 0.00 2.01
204 205 4.815308 TCGGACTCAATTTTCACGGTTTTA 59.185 37.500 0.00 0.00 0.00 1.52
205 206 3.628487 TCGGACTCAATTTTCACGGTTTT 59.372 39.130 0.00 0.00 0.00 2.43
206 207 3.002965 GTCGGACTCAATTTTCACGGTTT 59.997 43.478 0.00 0.00 0.00 3.27
207 208 2.546789 GTCGGACTCAATTTTCACGGTT 59.453 45.455 0.00 0.00 0.00 4.44
234 235 5.527582 CCTATAAATGTACTGAACCCACAGC 59.472 44.000 0.00 0.00 41.06 4.40
256 257 5.610132 ACATCCTGTCCAAGATAATCATCCT 59.390 40.000 0.00 0.00 0.00 3.24
267 268 4.422073 TTATAGCCACATCCTGTCCAAG 57.578 45.455 0.00 0.00 0.00 3.61
382 410 5.755849 AGAAATAAAGTCCGGGATCACAAT 58.244 37.500 0.00 0.00 0.00 2.71
385 413 4.766375 TGAGAAATAAAGTCCGGGATCAC 58.234 43.478 0.00 0.00 0.00 3.06
389 417 6.555463 AGTAATGAGAAATAAAGTCCGGGA 57.445 37.500 0.00 0.00 0.00 5.14
491 521 9.750783 ACGTCCAAGTATATTATACTGGAGTAT 57.249 33.333 22.22 4.74 43.15 2.12
513 543 5.282310 CACTCGCGGTAAACATATATACGTC 59.718 44.000 6.13 0.00 0.00 4.34
517 547 5.123805 TGCACTCGCGGTAAACATATATA 57.876 39.130 6.13 0.00 42.97 0.86
518 548 3.985008 TGCACTCGCGGTAAACATATAT 58.015 40.909 6.13 0.00 42.97 0.86
657 687 4.430765 TCGCCGTCGCTTCTTCCC 62.431 66.667 0.00 0.00 35.26 3.97
659 689 3.533691 CGTCGCCGTCGCTTCTTC 61.534 66.667 0.00 0.00 35.26 2.87
837 3650 0.843343 GGAGGGGTTTGGAGGTGGTA 60.843 60.000 0.00 0.00 0.00 3.25
915 3728 8.979574 GCGTGCTTATTAATACAGAGATTTAGT 58.020 33.333 0.00 0.00 0.00 2.24
1048 3868 0.616395 TTGACCGCTACATGGGAGGA 60.616 55.000 15.17 0.00 0.00 3.71
1333 4153 2.202743 CTCAATCGAAGGCGGCGA 60.203 61.111 12.98 7.16 42.48 5.54
1443 4263 1.656095 CCGTTGAGCGACTTGAGATTC 59.344 52.381 0.00 0.00 44.77 2.52
1444 4264 1.714794 CCGTTGAGCGACTTGAGATT 58.285 50.000 0.00 0.00 44.77 2.40
1446 4266 1.372997 GCCGTTGAGCGACTTGAGA 60.373 57.895 0.00 0.00 44.77 3.27
1471 4291 1.743996 GCCTCAACTGCCTCCTTAAG 58.256 55.000 0.00 0.00 0.00 1.85
1517 4337 2.029844 GAGCACTGGTCGACTTGCC 61.030 63.158 24.27 16.14 35.47 4.52
1546 4366 3.260483 CAGATCGGCGAGTGCAGC 61.260 66.667 17.22 0.00 45.35 5.25
1547 4367 2.584418 CCAGATCGGCGAGTGCAG 60.584 66.667 17.22 4.24 45.35 4.41
1548 4368 3.068064 TCCAGATCGGCGAGTGCA 61.068 61.111 17.22 0.00 45.35 4.57
1568 4388 2.671070 CAGCCCGGAAGACCACAT 59.329 61.111 0.73 0.00 35.59 3.21
1693 4513 2.990479 GACCCTGGCATCCGTCTT 59.010 61.111 0.00 0.00 0.00 3.01
1738 4558 7.095270 TCCTCGACTTTAAGTTTATCCACTTC 58.905 38.462 0.00 0.00 38.07 3.01
1746 4566 6.661304 AGGAACTCCTCGACTTTAAGTTTA 57.339 37.500 0.00 0.00 44.77 2.01
1774 4594 3.334054 GGCCTCCACCTGCTTCCT 61.334 66.667 0.00 0.00 0.00 3.36
1794 4614 1.126846 GTGACATTTTCGGACGCAGAG 59.873 52.381 0.00 0.00 0.00 3.35
1825 4645 0.108585 GCCAGTTCACCAACAGAGGA 59.891 55.000 0.00 0.00 34.60 3.71
1871 4691 1.733718 GCTTCTGCAATTCGCCTTTCC 60.734 52.381 0.00 0.00 41.33 3.13
1928 4748 1.155042 CACTTCTGCCTTGAGAGCAC 58.845 55.000 0.00 0.00 36.01 4.40
2025 4845 0.535780 TCAGGCTGTCCAACTGCTTG 60.536 55.000 15.27 12.69 46.33 4.01
2152 4972 2.875786 GCGCGGCATCTAACTCTGC 61.876 63.158 8.83 0.00 37.66 4.26
2187 5007 3.401033 TTTGCAACTTCGATCTGGAGA 57.599 42.857 0.00 0.00 0.00 3.71
2199 5019 1.368579 GCTGGTGGCATTTGCAACT 59.631 52.632 9.79 0.00 44.30 3.16
2228 5048 2.454832 ATCCACGTCAGCCACCACTG 62.455 60.000 0.00 0.00 39.12 3.66
2379 5199 2.792947 GGCCATGGCAGCATCCTTG 61.793 63.158 36.56 0.00 44.11 3.61
2406 5226 1.380524 CAGCCTCAGCATCTTTCTGG 58.619 55.000 0.00 0.00 43.56 3.86
2447 5267 2.540515 CTATGGTACCGTTCAGTGCAG 58.459 52.381 12.97 0.00 0.00 4.41
2451 5271 0.458669 CCGCTATGGTACCGTTCAGT 59.541 55.000 12.97 0.00 0.00 3.41
2466 5286 0.033504 AGTGAACACGTTGATCCGCT 59.966 50.000 0.00 0.00 36.20 5.52
2668 5488 2.145397 TTCAGGCTACCGATCTGTCT 57.855 50.000 0.00 0.00 0.00 3.41
2845 5665 2.192624 GCTCAAGCAAGCGAACAAAAA 58.807 42.857 0.00 0.00 41.59 1.94
2898 5718 9.169592 TCATATGGCAAAAGTAGGTAGTAAAAC 57.830 33.333 2.13 0.00 0.00 2.43
2991 5811 3.567164 AGACATTGAACAAAGACCAGCTG 59.433 43.478 6.78 6.78 0.00 4.24
3262 6596 1.933021 TGCGGTCTAAGGAGGAAAGA 58.067 50.000 0.00 0.00 0.00 2.52
3263 6597 2.622436 CTTGCGGTCTAAGGAGGAAAG 58.378 52.381 0.00 0.00 0.00 2.62
3264 6598 1.338769 GCTTGCGGTCTAAGGAGGAAA 60.339 52.381 0.00 0.00 0.00 3.13
3265 6599 0.249398 GCTTGCGGTCTAAGGAGGAA 59.751 55.000 0.00 0.00 0.00 3.36
3266 6600 0.902984 TGCTTGCGGTCTAAGGAGGA 60.903 55.000 0.00 0.00 0.00 3.71
3267 6601 0.741221 GTGCTTGCGGTCTAAGGAGG 60.741 60.000 0.00 0.00 0.00 4.30
3268 6602 0.037326 TGTGCTTGCGGTCTAAGGAG 60.037 55.000 0.00 0.00 0.00 3.69
3269 6603 0.037326 CTGTGCTTGCGGTCTAAGGA 60.037 55.000 0.00 0.00 0.00 3.36
3270 6604 0.320771 ACTGTGCTTGCGGTCTAAGG 60.321 55.000 0.00 0.00 0.00 2.69
3271 6605 1.195448 CAACTGTGCTTGCGGTCTAAG 59.805 52.381 0.00 0.00 0.00 2.18
3272 6606 1.225855 CAACTGTGCTTGCGGTCTAA 58.774 50.000 0.00 0.00 0.00 2.10
3273 6607 0.105964 ACAACTGTGCTTGCGGTCTA 59.894 50.000 0.00 0.00 0.00 2.59
3274 6608 1.153168 ACAACTGTGCTTGCGGTCT 60.153 52.632 0.00 0.00 0.00 3.85
3275 6609 1.160329 AGACAACTGTGCTTGCGGTC 61.160 55.000 0.00 0.00 0.00 4.79
3276 6610 0.105964 TAGACAACTGTGCTTGCGGT 59.894 50.000 0.00 0.00 0.00 5.68
3277 6611 1.069906 GTTAGACAACTGTGCTTGCGG 60.070 52.381 0.00 0.00 0.00 5.69
3278 6612 1.867233 AGTTAGACAACTGTGCTTGCG 59.133 47.619 0.00 0.00 43.50 4.85
3279 6613 3.971032 AAGTTAGACAACTGTGCTTGC 57.029 42.857 0.00 0.00 44.41 4.01
3280 6614 7.360946 GGGTATAAAGTTAGACAACTGTGCTTG 60.361 40.741 0.00 0.00 44.41 4.01
3281 6615 6.653740 GGGTATAAAGTTAGACAACTGTGCTT 59.346 38.462 0.00 0.00 44.41 3.91
3282 6616 6.013639 AGGGTATAAAGTTAGACAACTGTGCT 60.014 38.462 0.00 0.00 44.41 4.40
3283 6617 6.171213 AGGGTATAAAGTTAGACAACTGTGC 58.829 40.000 0.00 0.00 44.41 4.57
3284 6618 6.817140 GGAGGGTATAAAGTTAGACAACTGTG 59.183 42.308 0.00 0.00 44.41 3.66
3285 6619 6.729569 AGGAGGGTATAAAGTTAGACAACTGT 59.270 38.462 0.00 0.00 44.41 3.55
3286 6620 7.184067 AGGAGGGTATAAAGTTAGACAACTG 57.816 40.000 0.00 0.00 44.41 3.16
3288 6622 8.303780 AGTAGGAGGGTATAAAGTTAGACAAC 57.696 38.462 0.00 0.00 34.67 3.32
3289 6623 9.413734 GTAGTAGGAGGGTATAAAGTTAGACAA 57.586 37.037 0.00 0.00 0.00 3.18
3290 6624 8.001292 GGTAGTAGGAGGGTATAAAGTTAGACA 58.999 40.741 0.00 0.00 0.00 3.41
3291 6625 8.001292 TGGTAGTAGGAGGGTATAAAGTTAGAC 58.999 40.741 0.00 0.00 0.00 2.59
3292 6626 8.117870 TGGTAGTAGGAGGGTATAAAGTTAGA 57.882 38.462 0.00 0.00 0.00 2.10
3293 6627 8.637099 GTTGGTAGTAGGAGGGTATAAAGTTAG 58.363 40.741 0.00 0.00 0.00 2.34
3294 6628 8.121833 TGTTGGTAGTAGGAGGGTATAAAGTTA 58.878 37.037 0.00 0.00 0.00 2.24
3295 6629 6.961721 TGTTGGTAGTAGGAGGGTATAAAGTT 59.038 38.462 0.00 0.00 0.00 2.66
3296 6630 6.505754 TGTTGGTAGTAGGAGGGTATAAAGT 58.494 40.000 0.00 0.00 0.00 2.66
3297 6631 7.427989 TTGTTGGTAGTAGGAGGGTATAAAG 57.572 40.000 0.00 0.00 0.00 1.85
3298 6632 8.396619 AATTGTTGGTAGTAGGAGGGTATAAA 57.603 34.615 0.00 0.00 0.00 1.40
3299 6633 9.678981 ATAATTGTTGGTAGTAGGAGGGTATAA 57.321 33.333 0.00 0.00 0.00 0.98
3300 6634 9.317827 GATAATTGTTGGTAGTAGGAGGGTATA 57.682 37.037 0.00 0.00 0.00 1.47
3301 6635 7.792736 TGATAATTGTTGGTAGTAGGAGGGTAT 59.207 37.037 0.00 0.00 0.00 2.73
3302 6636 7.134162 TGATAATTGTTGGTAGTAGGAGGGTA 58.866 38.462 0.00 0.00 0.00 3.69
3303 6637 5.968167 TGATAATTGTTGGTAGTAGGAGGGT 59.032 40.000 0.00 0.00 0.00 4.34
3304 6638 6.494666 TGATAATTGTTGGTAGTAGGAGGG 57.505 41.667 0.00 0.00 0.00 4.30
3315 6649 9.248291 GCCAAGTACAATATTGATAATTGTTGG 57.752 33.333 22.16 20.06 39.08 3.77
3316 6650 8.957028 CGCCAAGTACAATATTGATAATTGTTG 58.043 33.333 22.16 13.80 39.08 3.33
3317 6651 8.682710 ACGCCAAGTACAATATTGATAATTGTT 58.317 29.630 22.16 9.22 39.08 2.83
3318 6652 8.220755 ACGCCAAGTACAATATTGATAATTGT 57.779 30.769 22.16 2.66 40.97 2.71
3319 6653 9.515020 AAACGCCAAGTACAATATTGATAATTG 57.485 29.630 22.16 20.61 0.00 2.32
3322 6656 9.602568 TCTAAACGCCAAGTACAATATTGATAA 57.397 29.630 22.16 4.32 0.00 1.75
3323 6657 9.602568 TTCTAAACGCCAAGTACAATATTGATA 57.397 29.630 22.16 7.87 0.00 2.15
3324 6658 8.395633 GTTCTAAACGCCAAGTACAATATTGAT 58.604 33.333 22.16 8.81 0.00 2.57
3325 6659 7.388224 TGTTCTAAACGCCAAGTACAATATTGA 59.612 33.333 22.16 3.15 0.00 2.57
3326 6660 7.523219 TGTTCTAAACGCCAAGTACAATATTG 58.477 34.615 14.01 14.01 0.00 1.90
3327 6661 7.675962 TGTTCTAAACGCCAAGTACAATATT 57.324 32.000 0.00 0.00 0.00 1.28
3328 6662 7.859325 ATGTTCTAAACGCCAAGTACAATAT 57.141 32.000 0.00 0.00 0.00 1.28
3329 6663 7.388224 TGAATGTTCTAAACGCCAAGTACAATA 59.612 33.333 0.00 0.00 0.00 1.90
3330 6664 6.205853 TGAATGTTCTAAACGCCAAGTACAAT 59.794 34.615 0.00 0.00 0.00 2.71
3331 6665 5.527951 TGAATGTTCTAAACGCCAAGTACAA 59.472 36.000 0.00 0.00 0.00 2.41
3332 6666 5.057819 TGAATGTTCTAAACGCCAAGTACA 58.942 37.500 0.00 0.00 0.00 2.90
3333 6667 5.600908 TGAATGTTCTAAACGCCAAGTAC 57.399 39.130 0.00 0.00 0.00 2.73
3334 6668 4.153475 GCTGAATGTTCTAAACGCCAAGTA 59.847 41.667 0.00 0.00 0.00 2.24
3335 6669 3.058224 GCTGAATGTTCTAAACGCCAAGT 60.058 43.478 0.00 0.00 0.00 3.16
3336 6670 3.189287 AGCTGAATGTTCTAAACGCCAAG 59.811 43.478 0.00 0.00 0.00 3.61
3337 6671 3.058293 CAGCTGAATGTTCTAAACGCCAA 60.058 43.478 8.42 0.00 0.00 4.52
3338 6672 2.483877 CAGCTGAATGTTCTAAACGCCA 59.516 45.455 8.42 0.00 0.00 5.69
3339 6673 2.484264 ACAGCTGAATGTTCTAAACGCC 59.516 45.455 23.35 0.00 0.00 5.68
3340 6674 3.813529 ACAGCTGAATGTTCTAAACGC 57.186 42.857 23.35 0.00 0.00 4.84
3363 6697 7.307751 CGAGCTACAACCATTGTAAGAGAAAAA 60.308 37.037 3.23 0.00 44.80 1.94
3364 6698 6.147164 CGAGCTACAACCATTGTAAGAGAAAA 59.853 38.462 3.23 0.00 44.80 2.29
3365 6699 5.637810 CGAGCTACAACCATTGTAAGAGAAA 59.362 40.000 3.23 0.00 44.80 2.52
3366 6700 5.047590 TCGAGCTACAACCATTGTAAGAGAA 60.048 40.000 3.23 0.00 44.80 2.87
3367 6701 4.461431 TCGAGCTACAACCATTGTAAGAGA 59.539 41.667 3.23 0.00 44.80 3.10
3368 6702 4.744570 TCGAGCTACAACCATTGTAAGAG 58.255 43.478 3.23 0.00 44.80 2.85
3395 6729 4.870426 TGAGCCACAAGATCGACTTTATTC 59.130 41.667 0.00 0.00 36.61 1.75
3434 6768 7.442656 AGCAGCAATACTATTACCGTCTATTT 58.557 34.615 0.00 0.00 0.00 1.40
3491 6825 9.606631 TGCAACAAATTTACAGAATAAAGGTTT 57.393 25.926 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.