Multiple sequence alignment - TraesCS5B01G100200

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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 TraesCS5B01G100200 chr5B 100.000 5106 0 0 1 5106 133019845 133014740 0.000000e+00 9430.0
1 TraesCS5B01G100200 chr5B 90.431 209 13 7 3 209 552683437 552683640 8.430000e-68 268.0
2 TraesCS5B01G100200 chr5B 88.942 208 15 6 3 207 48588239 48588037 3.050000e-62 250.0
3 TraesCS5B01G100200 chr5B 90.769 65 5 1 2018 2082 65524633 65524570 9.110000e-13 86.1
4 TraesCS5B01G100200 chr5D 92.222 2507 122 24 231 2667 119817658 119815155 0.000000e+00 3482.0
5 TraesCS5B01G100200 chr5D 92.090 1593 59 19 2797 4365 119814972 119813423 0.000000e+00 2182.0
6 TraesCS5B01G100200 chr5D 85.258 658 49 12 4467 5106 119771944 119771317 7.210000e-178 634.0
7 TraesCS5B01G100200 chr5D 77.662 385 69 13 1905 2280 529158138 529158514 8.610000e-53 219.0
8 TraesCS5B01G100200 chr5A 91.798 1268 61 20 3231 4458 130143318 130142054 0.000000e+00 1725.0
9 TraesCS5B01G100200 chr5A 95.391 933 29 3 853 1772 130146991 130146060 0.000000e+00 1472.0
10 TraesCS5B01G100200 chr5A 90.111 900 78 5 1761 2649 130145084 130144185 0.000000e+00 1158.0
11 TraesCS5B01G100200 chr5A 89.740 653 19 18 4462 5106 130141534 130140922 0.000000e+00 791.0
12 TraesCS5B01G100200 chr5A 87.912 637 63 10 209 835 130150009 130149377 0.000000e+00 737.0
13 TraesCS5B01G100200 chr5A 94.958 357 17 1 2806 3161 130143693 130143337 4.470000e-155 558.0
14 TraesCS5B01G100200 chr5A 88.312 77 9 0 2484 2560 530784386 530784310 5.440000e-15 93.5
15 TraesCS5B01G100200 chr5A 92.857 42 3 0 786 827 132961871 132961912 1.540000e-05 62.1
16 TraesCS5B01G100200 chr7A 84.078 716 59 26 1160 1828 35526027 35525320 1.550000e-179 640.0
17 TraesCS5B01G100200 chr7A 84.585 253 18 5 971 1206 35526661 35526413 1.110000e-56 231.0
18 TraesCS5B01G100200 chr7A 83.122 237 19 5 971 1190 86821030 86820798 4.030000e-46 196.0
19 TraesCS5B01G100200 chrUn 83.894 714 62 25 1160 1828 351776745 351776040 2.590000e-177 632.0
20 TraesCS5B01G100200 chrUn 82.276 536 42 25 1160 1650 346351394 346351921 1.020000e-111 414.0
21 TraesCS5B01G100200 chr2A 83.894 714 62 25 1160 1828 137149575 137148870 2.590000e-177 632.0
22 TraesCS5B01G100200 chr2A 82.276 536 42 25 1160 1650 137151956 137151429 1.020000e-111 414.0
23 TraesCS5B01G100200 chr2A 85.141 249 20 4 971 1206 137152586 137152342 6.610000e-59 239.0
24 TraesCS5B01G100200 chr2A 84.739 249 21 4 971 1206 137150205 137149961 3.070000e-57 233.0
25 TraesCS5B01G100200 chr2A 73.593 231 54 6 2443 2670 371725246 371725020 1.180000e-11 82.4
26 TraesCS5B01G100200 chr7B 94.712 208 9 2 1 208 387788467 387788672 6.380000e-84 322.0
27 TraesCS5B01G100200 chr7B 77.739 283 36 19 1932 2201 110315223 110314955 1.150000e-31 148.0
28 TraesCS5B01G100200 chr4B 94.313 211 7 3 3 210 283540014 283539806 8.250000e-83 318.0
29 TraesCS5B01G100200 chr4B 88.517 209 13 7 1 209 528260284 528260087 5.110000e-60 243.0
30 TraesCS5B01G100200 chr6B 94.634 205 8 1 4 208 382633104 382632903 1.070000e-81 315.0
31 TraesCS5B01G100200 chr7D 79.582 431 72 8 1827 2254 568617995 568618412 1.390000e-75 294.0
32 TraesCS5B01G100200 chr7D 75.060 417 82 17 1888 2291 43868964 43869371 1.890000e-39 174.0
33 TraesCS5B01G100200 chr7D 89.189 74 5 3 2475 2546 209795923 209795995 7.040000e-14 89.8
34 TraesCS5B01G100200 chr1B 90.952 210 11 7 9 216 271068509 271068306 5.040000e-70 276.0
35 TraesCS5B01G100200 chr2B 91.327 196 9 6 14 209 759134973 759135160 1.410000e-65 261.0
36 TraesCS5B01G100200 chr2B 89.756 205 11 9 9 207 615863677 615863477 2.360000e-63 254.0
37 TraesCS5B01G100200 chr2B 78.571 112 23 1 2448 2559 363763479 363763589 7.090000e-09 73.1
38 TraesCS5B01G100200 chr4D 98.039 51 1 0 780 830 5546790 5546840 7.040000e-14 89.8
39 TraesCS5B01G100200 chr4D 94.118 51 2 1 777 827 60117283 60117234 5.480000e-10 76.8
40 TraesCS5B01G100200 chr2D 80.208 96 18 1 2443 2538 298457820 298457726 2.550000e-08 71.3
41 TraesCS5B01G100200 chr2D 97.297 37 0 1 786 822 477067695 477067730 1.540000e-05 62.1
42 TraesCS5B01G100200 chr6A 94.737 38 2 0 2629 2666 484612815 484612778 5.520000e-05 60.2
43 TraesCS5B01G100200 chr3D 81.818 66 11 1 2460 2525 111903028 111903092 3.000000e-03 54.7
44 TraesCS5B01G100200 chr3D 92.308 39 1 1 2481 2519 535509661 535509625 3.000000e-03 54.7


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 TraesCS5B01G100200 chr5B 133014740 133019845 5105 True 9430.0 9430 100.000000 1 5106 1 chr5B.!!$R3 5105
1 TraesCS5B01G100200 chr5D 119813423 119817658 4235 True 2832.0 3482 92.156000 231 4365 2 chr5D.!!$R2 4134
2 TraesCS5B01G100200 chr5D 119771317 119771944 627 True 634.0 634 85.258000 4467 5106 1 chr5D.!!$R1 639
3 TraesCS5B01G100200 chr5A 130140922 130150009 9087 True 1073.5 1725 91.651667 209 5106 6 chr5A.!!$R2 4897
4 TraesCS5B01G100200 chr7A 35525320 35526661 1341 True 435.5 640 84.331500 971 1828 2 chr7A.!!$R2 857
5 TraesCS5B01G100200 chrUn 351776040 351776745 705 True 632.0 632 83.894000 1160 1828 1 chrUn.!!$R1 668
6 TraesCS5B01G100200 chrUn 346351394 346351921 527 False 414.0 414 82.276000 1160 1650 1 chrUn.!!$F1 490
7 TraesCS5B01G100200 chr2A 137148870 137152586 3716 True 379.5 632 84.012500 971 1828 4 chr2A.!!$R2 857

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
185 186 0.671796 GTTGCAGTGGGGTGTTTACC 59.328 55.000 0.0 0.0 46.76 2.85 F
756 786 1.079888 GCCTCAAAATGGCGGTTGG 60.080 57.895 0.0 0.0 41.03 3.77 F
2111 8836 0.538977 TCCGGTGTCTCCTCTTCGTT 60.539 55.000 0.0 0.0 0.00 3.85 F
2677 9403 0.031212 AATATGGGCTGGGTTTGGGG 60.031 55.000 0.0 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1222 6901 0.535102 AAGAACCAACAGCCAGGTCG 60.535 55.0 0.00 0.0 37.07 4.79 R
2676 9402 0.040692 GCCAAAACGTTCGGAACTCC 60.041 55.0 18.31 0.0 0.00 3.85 R
3220 10310 0.542805 GGTATAACAGTCCCCCGCAA 59.457 55.0 0.00 0.0 0.00 4.85 R
4578 12227 0.179073 ATCAAAGATCGGGGTCGCAG 60.179 55.0 0.00 0.0 36.13 5.18 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 9.996554 TCTTTTTGTTCCTTTCTTTCTTTTCTT 57.003 25.926 0.00 0.00 0.00 2.52
31 32 9.996554 TTGTTCCTTTCTTTCTTTTCTTTTTCT 57.003 25.926 0.00 0.00 0.00 2.52
32 33 9.996554 TGTTCCTTTCTTTCTTTTCTTTTTCTT 57.003 25.926 0.00 0.00 0.00 2.52
114 115 9.730420 TTTTCTTTTCTTTATTTCTGTTCGAGG 57.270 29.630 0.00 0.00 0.00 4.63
115 116 7.435068 TCTTTTCTTTATTTCTGTTCGAGGG 57.565 36.000 0.00 0.00 0.00 4.30
116 117 5.622770 TTTCTTTATTTCTGTTCGAGGGC 57.377 39.130 0.00 0.00 0.00 5.19
117 118 4.553330 TCTTTATTTCTGTTCGAGGGCT 57.447 40.909 0.00 0.00 0.00 5.19
118 119 4.906618 TCTTTATTTCTGTTCGAGGGCTT 58.093 39.130 0.00 0.00 0.00 4.35
119 120 6.045072 TCTTTATTTCTGTTCGAGGGCTTA 57.955 37.500 0.00 0.00 0.00 3.09
120 121 5.873164 TCTTTATTTCTGTTCGAGGGCTTAC 59.127 40.000 0.00 0.00 0.00 2.34
121 122 2.467566 TTTCTGTTCGAGGGCTTACC 57.532 50.000 0.00 0.00 40.67 2.85
137 138 4.828072 CTTACCTCAAGCCCTTAAGACT 57.172 45.455 3.36 0.00 0.00 3.24
138 139 5.934402 CTTACCTCAAGCCCTTAAGACTA 57.066 43.478 3.36 0.00 0.00 2.59
139 140 5.662456 CTTACCTCAAGCCCTTAAGACTAC 58.338 45.833 3.36 0.00 0.00 2.73
140 141 3.792515 ACCTCAAGCCCTTAAGACTACT 58.207 45.455 3.36 0.00 0.00 2.57
141 142 4.168883 ACCTCAAGCCCTTAAGACTACTT 58.831 43.478 3.36 0.00 39.81 2.24
142 143 4.597940 ACCTCAAGCCCTTAAGACTACTTT 59.402 41.667 3.36 0.00 37.53 2.66
143 144 5.783875 ACCTCAAGCCCTTAAGACTACTTTA 59.216 40.000 3.36 0.00 37.53 1.85
144 145 6.107343 CCTCAAGCCCTTAAGACTACTTTAC 58.893 44.000 3.36 0.00 37.53 2.01
145 146 6.070710 CCTCAAGCCCTTAAGACTACTTTACT 60.071 42.308 3.36 0.00 37.53 2.24
146 147 7.312415 TCAAGCCCTTAAGACTACTTTACTT 57.688 36.000 3.36 0.00 37.53 2.24
147 148 8.426569 TCAAGCCCTTAAGACTACTTTACTTA 57.573 34.615 3.36 0.00 37.53 2.24
148 149 8.529476 TCAAGCCCTTAAGACTACTTTACTTAG 58.471 37.037 3.36 0.00 37.53 2.18
149 150 7.421087 AGCCCTTAAGACTACTTTACTTAGG 57.579 40.000 3.36 0.00 37.53 2.69
150 151 6.958778 AGCCCTTAAGACTACTTTACTTAGGT 59.041 38.462 3.36 0.00 37.53 3.08
151 152 7.457218 AGCCCTTAAGACTACTTTACTTAGGTT 59.543 37.037 3.36 0.00 37.53 3.50
152 153 8.753133 GCCCTTAAGACTACTTTACTTAGGTTA 58.247 37.037 3.36 0.00 37.53 2.85
178 179 6.680148 AATTAATAAAAGTTGCAGTGGGGT 57.320 33.333 0.00 0.00 0.00 4.95
179 180 5.461032 TTAATAAAAGTTGCAGTGGGGTG 57.539 39.130 0.00 0.00 0.00 4.61
180 181 2.445682 TAAAAGTTGCAGTGGGGTGT 57.554 45.000 0.00 0.00 0.00 4.16
181 182 1.567357 AAAAGTTGCAGTGGGGTGTT 58.433 45.000 0.00 0.00 0.00 3.32
182 183 1.567357 AAAGTTGCAGTGGGGTGTTT 58.433 45.000 0.00 0.00 0.00 2.83
183 184 2.445682 AAGTTGCAGTGGGGTGTTTA 57.554 45.000 0.00 0.00 0.00 2.01
184 185 1.687563 AGTTGCAGTGGGGTGTTTAC 58.312 50.000 0.00 0.00 0.00 2.01
185 186 0.671796 GTTGCAGTGGGGTGTTTACC 59.328 55.000 0.00 0.00 46.76 2.85
201 202 7.614494 GGTGTTTACCCTACTGTTTATAGTCA 58.386 38.462 0.00 0.00 41.36 3.41
202 203 8.096414 GGTGTTTACCCTACTGTTTATAGTCAA 58.904 37.037 0.00 0.00 41.36 3.18
203 204 9.492973 GTGTTTACCCTACTGTTTATAGTCAAA 57.507 33.333 0.00 0.00 32.19 2.69
250 251 1.268899 CAGAAGTCTACCGTCGTTGGT 59.731 52.381 6.57 6.57 46.26 3.67
288 289 1.700955 ATTCTACCGCCGGAGTGTAT 58.299 50.000 11.71 0.00 0.00 2.29
335 336 7.487484 TCTGAAAAACTTGCAAACATGTATCA 58.513 30.769 0.00 0.00 33.33 2.15
448 450 4.430007 TGACGCTAAATGTCATGGAGTAC 58.570 43.478 0.00 0.00 41.20 2.73
538 541 5.238006 TGGTTTGTTCTGTAAGTTTTCGG 57.762 39.130 0.00 0.00 33.76 4.30
756 786 1.079888 GCCTCAAAATGGCGGTTGG 60.080 57.895 0.00 0.00 41.03 3.77
1137 3576 3.327404 GGCGGAAGTCCTCCCCAA 61.327 66.667 0.00 0.00 41.87 4.12
1206 4073 4.937201 TCTTGGATCTCGCTTAGCATTA 57.063 40.909 4.70 0.00 0.00 1.90
1222 6901 2.805845 CATTAGCTTGCTGTGCCATTC 58.194 47.619 5.26 0.00 0.00 2.67
1258 6937 2.778299 TCTTGATGCCACCACAACTAC 58.222 47.619 0.00 0.00 0.00 2.73
1593 7314 8.448615 GTTAAGTCAGCCAATTCGTATAGTTTT 58.551 33.333 0.00 0.00 0.00 2.43
1747 7475 6.578545 CGTGAACAGTCTATCCAAAATTGTTG 59.421 38.462 0.00 0.00 0.00 3.33
1774 8489 8.795513 TCACAGTTTGTTCATGACATTATTGAT 58.204 29.630 0.00 0.00 38.26 2.57
1813 8528 6.103997 AGCTGTTGCATTTGATGGATTTAAG 58.896 36.000 0.00 0.00 42.74 1.85
1824 8539 6.817765 TGATGGATTTAAGTGTGAAGAACC 57.182 37.500 0.00 0.00 0.00 3.62
1867 8582 5.641155 ACTAACAAAAGTGAGCCCCTAAAT 58.359 37.500 0.00 0.00 0.00 1.40
1877 8592 0.751643 GCCCCTAAATGTGCACGGAT 60.752 55.000 13.13 2.71 0.00 4.18
1912 8637 0.893727 GCCCGGTGACACCTCATTTT 60.894 55.000 22.14 0.00 35.66 1.82
1923 8648 5.593909 TGACACCTCATTTTTCACTCATTGT 59.406 36.000 0.00 0.00 0.00 2.71
1925 8650 7.041167 TGACACCTCATTTTTCACTCATTGTAG 60.041 37.037 0.00 0.00 0.00 2.74
1926 8651 6.772716 ACACCTCATTTTTCACTCATTGTAGT 59.227 34.615 0.00 0.00 0.00 2.73
2028 8753 6.323266 ACTACAAACTAGCTACTTGTCATCG 58.677 40.000 16.23 8.96 35.09 3.84
2037 8762 4.584743 AGCTACTTGTCATCGGATATGTCA 59.415 41.667 0.00 0.00 0.00 3.58
2099 8824 0.878961 GCGTGAAGAAACTCCGGTGT 60.879 55.000 2.61 2.61 0.00 4.16
2111 8836 0.538977 TCCGGTGTCTCCTCTTCGTT 60.539 55.000 0.00 0.00 0.00 3.85
2121 8846 2.757868 CTCCTCTTCGTTGTCCTCATCT 59.242 50.000 0.00 0.00 0.00 2.90
2123 8848 2.232452 CCTCTTCGTTGTCCTCATCTGT 59.768 50.000 0.00 0.00 0.00 3.41
2171 8897 2.435938 TGGATGAAGCGGCGGTTC 60.436 61.111 36.64 36.64 40.03 3.62
2224 8950 1.908340 GAGGATGGCCACTGCTCTGT 61.908 60.000 21.28 0.67 37.74 3.41
2225 8951 1.001641 GGATGGCCACTGCTCTGTT 60.002 57.895 8.16 0.00 37.74 3.16
2282 9008 1.381599 GCCCTCCATGCCAAATCCA 60.382 57.895 0.00 0.00 0.00 3.41
2321 9047 2.969238 CGATGCGCATCTCCACCC 60.969 66.667 38.93 18.80 35.72 4.61
2322 9048 2.190313 GATGCGCATCTCCACCCA 59.810 61.111 36.92 0.51 35.04 4.51
2336 9062 2.835431 CCCAGGTCTCCGCTCGAT 60.835 66.667 0.00 0.00 0.00 3.59
2364 9090 3.442625 GGGGTCAACATTTTGTAGTAGGC 59.557 47.826 0.00 0.00 34.02 3.93
2429 9155 1.625565 AGAGAGGGAGAGGGAGGCT 60.626 63.158 0.00 0.00 0.00 4.58
2464 9190 1.388531 GTGGACTGGAGGGAGAGGA 59.611 63.158 0.00 0.00 0.00 3.71
2565 9291 2.106074 GTGCGATGAATGCGGACCA 61.106 57.895 0.00 0.00 43.01 4.02
2674 9400 2.985957 CCAAATATGGGCTGGGTTTG 57.014 50.000 0.00 0.00 43.51 2.93
2675 9401 1.485895 CCAAATATGGGCTGGGTTTGG 59.514 52.381 9.37 9.37 43.51 3.28
2676 9402 1.485895 CAAATATGGGCTGGGTTTGGG 59.514 52.381 0.00 0.00 0.00 4.12
2677 9403 0.031212 AATATGGGCTGGGTTTGGGG 60.031 55.000 0.00 0.00 0.00 4.96
2678 9404 0.928726 ATATGGGCTGGGTTTGGGGA 60.929 55.000 0.00 0.00 0.00 4.81
2679 9405 1.580066 TATGGGCTGGGTTTGGGGAG 61.580 60.000 0.00 0.00 0.00 4.30
2680 9406 3.590574 GGGCTGGGTTTGGGGAGT 61.591 66.667 0.00 0.00 0.00 3.85
2681 9407 2.526110 GGCTGGGTTTGGGGAGTT 59.474 61.111 0.00 0.00 0.00 3.01
2682 9408 1.606601 GGCTGGGTTTGGGGAGTTC 60.607 63.158 0.00 0.00 0.00 3.01
2683 9409 1.606601 GCTGGGTTTGGGGAGTTCC 60.607 63.158 0.00 0.00 0.00 3.62
2684 9410 1.303317 CTGGGTTTGGGGAGTTCCG 60.303 63.158 0.00 0.00 36.71 4.30
2685 9411 1.770927 TGGGTTTGGGGAGTTCCGA 60.771 57.895 0.00 0.00 36.71 4.55
2686 9412 1.354168 TGGGTTTGGGGAGTTCCGAA 61.354 55.000 0.00 0.00 36.71 4.30
2687 9413 0.892358 GGGTTTGGGGAGTTCCGAAC 60.892 60.000 2.81 2.81 45.88 3.95
2688 9414 1.232621 GGTTTGGGGAGTTCCGAACG 61.233 60.000 5.62 0.00 46.97 3.95
2689 9415 0.533531 GTTTGGGGAGTTCCGAACGT 60.534 55.000 5.62 0.00 40.26 3.99
2690 9416 0.180878 TTTGGGGAGTTCCGAACGTT 59.819 50.000 0.00 0.00 32.80 3.99
2691 9417 0.180878 TTGGGGAGTTCCGAACGTTT 59.819 50.000 0.46 0.00 36.71 3.60
2692 9418 0.180878 TGGGGAGTTCCGAACGTTTT 59.819 50.000 0.46 0.00 36.71 2.43
2693 9419 0.589708 GGGGAGTTCCGAACGTTTTG 59.410 55.000 0.46 0.00 36.71 2.44
2694 9420 0.589708 GGGAGTTCCGAACGTTTTGG 59.410 55.000 12.86 12.86 36.71 3.28
2695 9421 0.040692 GGAGTTCCGAACGTTTTGGC 60.041 55.000 13.93 3.62 36.23 4.52
2696 9422 0.942252 GAGTTCCGAACGTTTTGGCT 59.058 50.000 13.93 7.69 36.23 4.75
2697 9423 0.661020 AGTTCCGAACGTTTTGGCTG 59.339 50.000 13.93 0.00 36.23 4.85
2698 9424 0.317519 GTTCCGAACGTTTTGGCTGG 60.318 55.000 13.93 5.30 33.95 4.85
2699 9425 1.448922 TTCCGAACGTTTTGGCTGGG 61.449 55.000 13.93 0.00 33.95 4.45
2700 9426 2.190841 CCGAACGTTTTGGCTGGGT 61.191 57.895 0.46 0.00 0.00 4.51
2701 9427 0.885596 CCGAACGTTTTGGCTGGGTA 60.886 55.000 0.46 0.00 0.00 3.69
2702 9428 1.161843 CGAACGTTTTGGCTGGGTAT 58.838 50.000 0.46 0.00 0.00 2.73
2703 9429 2.348660 CGAACGTTTTGGCTGGGTATA 58.651 47.619 0.46 0.00 0.00 1.47
2704 9430 2.350498 CGAACGTTTTGGCTGGGTATAG 59.650 50.000 0.46 0.00 0.00 1.31
2705 9431 2.413310 ACGTTTTGGCTGGGTATAGG 57.587 50.000 0.00 0.00 0.00 2.57
2706 9432 1.064979 ACGTTTTGGCTGGGTATAGGG 60.065 52.381 0.00 0.00 0.00 3.53
2707 9433 1.749286 CGTTTTGGCTGGGTATAGGGG 60.749 57.143 0.00 0.00 0.00 4.79
2708 9434 1.286849 GTTTTGGCTGGGTATAGGGGT 59.713 52.381 0.00 0.00 0.00 4.95
2709 9435 1.688750 TTTGGCTGGGTATAGGGGTT 58.311 50.000 0.00 0.00 0.00 4.11
2710 9436 1.218844 TTGGCTGGGTATAGGGGTTC 58.781 55.000 0.00 0.00 0.00 3.62
2711 9437 0.345502 TGGCTGGGTATAGGGGTTCT 59.654 55.000 0.00 0.00 0.00 3.01
2712 9438 0.765510 GGCTGGGTATAGGGGTTCTG 59.234 60.000 0.00 0.00 0.00 3.02
2713 9439 0.765510 GCTGGGTATAGGGGTTCTGG 59.234 60.000 0.00 0.00 0.00 3.86
2714 9440 1.975196 GCTGGGTATAGGGGTTCTGGT 60.975 57.143 0.00 0.00 0.00 4.00
2715 9441 2.488836 CTGGGTATAGGGGTTCTGGTT 58.511 52.381 0.00 0.00 0.00 3.67
2716 9442 2.172717 CTGGGTATAGGGGTTCTGGTTG 59.827 54.545 0.00 0.00 0.00 3.77
2717 9443 1.493446 GGGTATAGGGGTTCTGGTTGG 59.507 57.143 0.00 0.00 0.00 3.77
2718 9444 1.493446 GGTATAGGGGTTCTGGTTGGG 59.507 57.143 0.00 0.00 0.00 4.12
2719 9445 2.202707 GTATAGGGGTTCTGGTTGGGT 58.797 52.381 0.00 0.00 0.00 4.51
2720 9446 0.999712 ATAGGGGTTCTGGTTGGGTG 59.000 55.000 0.00 0.00 0.00 4.61
2721 9447 1.785353 TAGGGGTTCTGGTTGGGTGC 61.785 60.000 0.00 0.00 0.00 5.01
2722 9448 2.600470 GGGTTCTGGTTGGGTGCC 60.600 66.667 0.00 0.00 0.00 5.01
2723 9449 2.197324 GGTTCTGGTTGGGTGCCA 59.803 61.111 0.00 0.00 34.42 4.92
2724 9450 1.456705 GGTTCTGGTTGGGTGCCAA 60.457 57.895 0.00 0.00 41.69 4.52
2725 9451 0.831711 GGTTCTGGTTGGGTGCCAAT 60.832 55.000 0.00 0.00 45.80 3.16
2726 9452 1.047801 GTTCTGGTTGGGTGCCAATT 58.952 50.000 0.00 0.00 45.80 2.32
2727 9453 1.416030 GTTCTGGTTGGGTGCCAATTT 59.584 47.619 0.00 0.00 45.80 1.82
2728 9454 1.337118 TCTGGTTGGGTGCCAATTTC 58.663 50.000 0.00 0.00 45.80 2.17
2729 9455 1.133199 TCTGGTTGGGTGCCAATTTCT 60.133 47.619 0.00 0.00 45.80 2.52
2730 9456 1.693606 CTGGTTGGGTGCCAATTTCTT 59.306 47.619 0.00 0.00 45.80 2.52
2731 9457 1.415659 TGGTTGGGTGCCAATTTCTTG 59.584 47.619 0.00 0.00 45.80 3.02
2732 9458 1.691434 GGTTGGGTGCCAATTTCTTGA 59.309 47.619 0.00 0.00 45.80 3.02
2733 9459 2.547855 GGTTGGGTGCCAATTTCTTGAC 60.548 50.000 0.00 0.00 45.80 3.18
2734 9460 1.337118 TGGGTGCCAATTTCTTGACC 58.663 50.000 0.00 0.00 34.04 4.02
2735 9461 0.243636 GGGTGCCAATTTCTTGACCG 59.756 55.000 0.00 0.00 32.53 4.79
2736 9462 0.243636 GGTGCCAATTTCTTGACCGG 59.756 55.000 0.00 0.00 34.04 5.28
2737 9463 0.243636 GTGCCAATTTCTTGACCGGG 59.756 55.000 6.32 0.00 34.04 5.73
2738 9464 0.178975 TGCCAATTTCTTGACCGGGT 60.179 50.000 6.32 0.00 34.04 5.28
2739 9465 0.526211 GCCAATTTCTTGACCGGGTC 59.474 55.000 20.36 20.36 34.04 4.46
2740 9466 0.802494 CCAATTTCTTGACCGGGTCG 59.198 55.000 21.52 9.05 34.95 4.79
2741 9467 0.168128 CAATTTCTTGACCGGGTCGC 59.832 55.000 21.52 0.50 34.95 5.19
2742 9468 0.958876 AATTTCTTGACCGGGTCGCC 60.959 55.000 21.52 0.00 34.95 5.54
2743 9469 2.814913 ATTTCTTGACCGGGTCGCCC 62.815 60.000 21.52 4.96 41.09 6.13
2779 9864 1.751437 GGGGGTCAAGTTGTAGATGC 58.249 55.000 2.11 0.00 0.00 3.91
2780 9865 1.282157 GGGGGTCAAGTTGTAGATGCT 59.718 52.381 2.11 0.00 0.00 3.79
2781 9866 2.633488 GGGGTCAAGTTGTAGATGCTC 58.367 52.381 2.11 0.00 0.00 4.26
2782 9867 2.237392 GGGGTCAAGTTGTAGATGCTCT 59.763 50.000 2.11 0.00 0.00 4.09
2783 9868 3.526534 GGGTCAAGTTGTAGATGCTCTC 58.473 50.000 2.11 0.00 0.00 3.20
2784 9869 3.055819 GGGTCAAGTTGTAGATGCTCTCA 60.056 47.826 2.11 0.00 0.00 3.27
2785 9870 3.929610 GGTCAAGTTGTAGATGCTCTCAC 59.070 47.826 2.11 0.00 0.00 3.51
2786 9871 4.322349 GGTCAAGTTGTAGATGCTCTCACT 60.322 45.833 2.11 0.00 0.00 3.41
2787 9872 5.105716 GGTCAAGTTGTAGATGCTCTCACTA 60.106 44.000 2.11 0.00 0.00 2.74
2788 9873 6.406400 GGTCAAGTTGTAGATGCTCTCACTAT 60.406 42.308 2.11 0.00 0.00 2.12
2789 9874 6.695278 GTCAAGTTGTAGATGCTCTCACTATC 59.305 42.308 2.11 0.00 0.00 2.08
2790 9875 5.782893 AGTTGTAGATGCTCTCACTATCC 57.217 43.478 0.00 0.00 0.00 2.59
2791 9876 5.204292 AGTTGTAGATGCTCTCACTATCCA 58.796 41.667 0.00 0.00 0.00 3.41
2792 9877 5.301551 AGTTGTAGATGCTCTCACTATCCAG 59.698 44.000 0.00 0.00 0.00 3.86
2793 9878 4.797743 TGTAGATGCTCTCACTATCCAGT 58.202 43.478 0.00 0.00 34.42 4.00
2794 9879 4.824537 TGTAGATGCTCTCACTATCCAGTC 59.175 45.833 0.00 0.00 30.46 3.51
2795 9880 3.908476 AGATGCTCTCACTATCCAGTCA 58.092 45.455 0.00 0.00 30.46 3.41
2983 10073 2.383298 ATGCGACACGTTTCTTTGTG 57.617 45.000 0.00 0.00 41.81 3.33
3003 10093 7.493499 TTGTGATGGGGTAATGATTTCAATT 57.507 32.000 0.00 0.00 0.00 2.32
3213 10303 5.897377 AAGTTTGATGTGCTGTTATACCC 57.103 39.130 0.00 0.00 0.00 3.69
3214 10304 4.270008 AGTTTGATGTGCTGTTATACCCC 58.730 43.478 0.00 0.00 0.00 4.95
3215 10305 4.018415 AGTTTGATGTGCTGTTATACCCCT 60.018 41.667 0.00 0.00 0.00 4.79
3216 10306 4.584638 TTGATGTGCTGTTATACCCCTT 57.415 40.909 0.00 0.00 0.00 3.95
3217 10307 4.584638 TGATGTGCTGTTATACCCCTTT 57.415 40.909 0.00 0.00 0.00 3.11
3218 10308 4.929479 TGATGTGCTGTTATACCCCTTTT 58.071 39.130 0.00 0.00 0.00 2.27
3219 10309 5.329399 TGATGTGCTGTTATACCCCTTTTT 58.671 37.500 0.00 0.00 0.00 1.94
3234 10324 4.688770 TTTTTGCGGGGGACTGTT 57.311 50.000 0.00 0.00 39.64 3.16
3314 10404 5.391312 AAAGTTGTGTCTTCTTTGCTTGT 57.609 34.783 0.00 0.00 31.47 3.16
3386 10478 7.235935 ACATCACCATCTTGATTTTGACATT 57.764 32.000 0.00 0.00 33.74 2.71
3647 10739 2.738846 CAGAAATGGGTGAAGTGAGTCG 59.261 50.000 0.00 0.00 0.00 4.18
3690 10782 4.078454 TCCCTGGGCTAAAGTACCATAGTA 60.078 45.833 8.22 0.00 33.07 1.82
3691 10783 4.844655 CCCTGGGCTAAAGTACCATAGTAT 59.155 45.833 0.00 0.00 33.07 2.12
3737 10829 8.972458 TGCACTGCATATAAACCTATAAAGAA 57.028 30.769 0.00 0.00 31.71 2.52
3776 10868 9.956640 AATCATTCTATTGAGTCTGAACTTTCT 57.043 29.630 0.00 0.00 35.28 2.52
3791 10883 7.397761 TCTGAACTTTCTTTAGTTTTTGGGGAA 59.602 33.333 0.00 0.00 38.43 3.97
3796 10888 9.038072 ACTTTCTTTAGTTTTTGGGGAAAAGTA 57.962 29.630 0.00 0.00 40.47 2.24
3798 10890 9.656040 TTTCTTTAGTTTTTGGGGAAAAGTAAC 57.344 29.630 9.73 0.00 45.73 2.50
3872 10969 3.447586 TCCTAAGGTGAGAACATCCGAAG 59.552 47.826 0.00 0.00 0.00 3.79
3880 10977 0.391263 GAACATCCGAAGCCGAACCT 60.391 55.000 0.00 0.00 38.22 3.50
4002 11099 2.579201 CGTGGACCAGATCGCCTT 59.421 61.111 0.00 0.00 0.00 4.35
4186 11283 4.396166 ACAACTGGACAGACAAGTTTCTTG 59.604 41.667 6.29 7.78 0.00 3.02
4206 11303 7.647907 TCTTGATAGTGTTTTCGTAGGTTTC 57.352 36.000 0.00 0.00 0.00 2.78
4308 11411 4.941263 TGTTGCCTAAATAAAGATGAGCGT 59.059 37.500 0.00 0.00 0.00 5.07
4309 11412 5.064707 TGTTGCCTAAATAAAGATGAGCGTC 59.935 40.000 0.00 0.00 0.00 5.19
4413 11546 7.877612 TCATGCACAGAGATTGTAGTTAGAAAA 59.122 33.333 0.00 0.00 38.16 2.29
4444 11577 9.482627 TTGTTGTTCAGTTTACAAATTTGTCTT 57.517 25.926 26.46 6.06 42.35 3.01
4509 12158 3.248029 GTGAGCTTCACTGCACGG 58.752 61.111 8.50 0.00 43.73 4.94
4573 12222 0.953471 TCGCAATCAAACGGTCCCTG 60.953 55.000 0.00 0.00 0.00 4.45
4574 12223 1.212751 GCAATCAAACGGTCCCTGC 59.787 57.895 0.00 0.00 0.00 4.85
4575 12224 1.501741 CAATCAAACGGTCCCTGCG 59.498 57.895 0.00 0.00 0.00 5.18
4576 12225 0.953471 CAATCAAACGGTCCCTGCGA 60.953 55.000 0.00 0.00 0.00 5.10
4577 12226 0.673644 AATCAAACGGTCCCTGCGAG 60.674 55.000 0.00 0.00 0.00 5.03
4578 12227 3.423154 CAAACGGTCCCTGCGAGC 61.423 66.667 0.00 0.00 35.53 5.03
4579 12228 3.626924 AAACGGTCCCTGCGAGCT 61.627 61.111 0.00 0.00 36.81 4.09
4580 12229 3.883744 AAACGGTCCCTGCGAGCTG 62.884 63.158 0.00 0.00 36.81 4.24
4695 12365 3.003173 CCAGCGGTCCTCTTCCCA 61.003 66.667 0.00 0.00 0.00 4.37
4696 12366 2.266055 CAGCGGTCCTCTTCCCAC 59.734 66.667 0.00 0.00 0.00 4.61
4697 12367 2.120718 AGCGGTCCTCTTCCCACT 59.879 61.111 0.00 0.00 0.00 4.00
4698 12368 1.985116 AGCGGTCCTCTTCCCACTC 60.985 63.158 0.00 0.00 0.00 3.51
4699 12369 1.985116 GCGGTCCTCTTCCCACTCT 60.985 63.158 0.00 0.00 0.00 3.24
4700 12370 1.950973 GCGGTCCTCTTCCCACTCTC 61.951 65.000 0.00 0.00 0.00 3.20
4701 12371 1.324005 CGGTCCTCTTCCCACTCTCC 61.324 65.000 0.00 0.00 0.00 3.71
4702 12372 1.324005 GGTCCTCTTCCCACTCTCCG 61.324 65.000 0.00 0.00 0.00 4.63
4703 12373 1.682684 TCCTCTTCCCACTCTCCGC 60.683 63.158 0.00 0.00 0.00 5.54
4754 12424 0.317479 AAGCTTCTGCCGACGTTAGT 59.683 50.000 0.00 0.00 40.80 2.24
4758 12428 0.942410 TTCTGCCGACGTTAGTGTGC 60.942 55.000 0.00 0.00 0.00 4.57
4863 12545 1.374252 CCACGGGACCTTCGACTTG 60.374 63.158 0.00 0.00 0.00 3.16
4902 12584 2.664851 CCGGTGAGTTGCTCGCAA 60.665 61.111 11.14 0.00 42.14 4.85
4904 12586 1.577328 CCGGTGAGTTGCTCGCAATT 61.577 55.000 7.67 3.30 42.14 2.32
4908 12590 2.420022 GGTGAGTTGCTCGCAATTGTAT 59.580 45.455 7.67 0.00 42.14 2.29
4909 12591 3.485877 GGTGAGTTGCTCGCAATTGTATC 60.486 47.826 7.67 3.04 42.14 2.24
4910 12592 3.125146 GTGAGTTGCTCGCAATTGTATCA 59.875 43.478 7.67 5.30 40.33 2.15
4911 12593 3.125146 TGAGTTGCTCGCAATTGTATCAC 59.875 43.478 7.67 0.00 38.28 3.06
5045 12727 2.393271 AGCGCTTGTGCTAATCTTCT 57.607 45.000 2.64 0.00 45.14 2.85
5046 12728 2.704572 AGCGCTTGTGCTAATCTTCTT 58.295 42.857 2.64 0.00 45.14 2.52
5047 12729 2.675348 AGCGCTTGTGCTAATCTTCTTC 59.325 45.455 2.64 0.00 45.14 2.87
5048 12730 2.535732 GCGCTTGTGCTAATCTTCTTCG 60.536 50.000 0.00 0.00 36.97 3.79
5049 12731 2.923655 CGCTTGTGCTAATCTTCTTCGA 59.076 45.455 0.00 0.00 36.97 3.71
5052 12734 5.103000 GCTTGTGCTAATCTTCTTCGAGTA 58.897 41.667 0.00 0.00 36.03 2.59
5064 12746 7.776933 TCTTCTTCGAGTAAATTGATCATGG 57.223 36.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.996554 AAGAAAAGAAAGAAAGGAACAAAAAGA 57.003 25.926 0.00 0.00 0.00 2.52
5 6 9.996554 AGAAAAAGAAAAGAAAGAAAGGAACAA 57.003 25.926 0.00 0.00 0.00 2.83
6 7 9.996554 AAGAAAAAGAAAAGAAAGAAAGGAACA 57.003 25.926 0.00 0.00 0.00 3.18
88 89 9.730420 CCTCGAACAGAAATAAAGAAAAGAAAA 57.270 29.630 0.00 0.00 0.00 2.29
89 90 8.349983 CCCTCGAACAGAAATAAAGAAAAGAAA 58.650 33.333 0.00 0.00 0.00 2.52
90 91 7.521585 GCCCTCGAACAGAAATAAAGAAAAGAA 60.522 37.037 0.00 0.00 0.00 2.52
91 92 6.072673 GCCCTCGAACAGAAATAAAGAAAAGA 60.073 38.462 0.00 0.00 0.00 2.52
92 93 6.072452 AGCCCTCGAACAGAAATAAAGAAAAG 60.072 38.462 0.00 0.00 0.00 2.27
93 94 5.768164 AGCCCTCGAACAGAAATAAAGAAAA 59.232 36.000 0.00 0.00 0.00 2.29
94 95 5.313712 AGCCCTCGAACAGAAATAAAGAAA 58.686 37.500 0.00 0.00 0.00 2.52
95 96 4.906618 AGCCCTCGAACAGAAATAAAGAA 58.093 39.130 0.00 0.00 0.00 2.52
96 97 4.553330 AGCCCTCGAACAGAAATAAAGA 57.447 40.909 0.00 0.00 0.00 2.52
97 98 5.064834 GGTAAGCCCTCGAACAGAAATAAAG 59.935 44.000 0.00 0.00 0.00 1.85
98 99 4.939439 GGTAAGCCCTCGAACAGAAATAAA 59.061 41.667 0.00 0.00 0.00 1.40
99 100 4.224370 AGGTAAGCCCTCGAACAGAAATAA 59.776 41.667 0.00 0.00 40.71 1.40
100 101 3.773119 AGGTAAGCCCTCGAACAGAAATA 59.227 43.478 0.00 0.00 40.71 1.40
101 102 2.572104 AGGTAAGCCCTCGAACAGAAAT 59.428 45.455 0.00 0.00 40.71 2.17
102 103 1.975680 AGGTAAGCCCTCGAACAGAAA 59.024 47.619 0.00 0.00 40.71 2.52
103 104 1.640917 AGGTAAGCCCTCGAACAGAA 58.359 50.000 0.00 0.00 40.71 3.02
104 105 3.376082 AGGTAAGCCCTCGAACAGA 57.624 52.632 0.00 0.00 40.71 3.41
115 116 9.417418 AAGTAGTCTTAAGGGCTTGAGGTAAGC 62.417 44.444 1.85 3.16 45.02 3.09
116 117 4.828072 AGTCTTAAGGGCTTGAGGTAAG 57.172 45.455 1.85 0.00 39.49 2.34
117 118 5.339477 AGTAGTCTTAAGGGCTTGAGGTAA 58.661 41.667 1.85 0.00 0.00 2.85
118 119 4.944177 AGTAGTCTTAAGGGCTTGAGGTA 58.056 43.478 1.85 0.00 0.00 3.08
119 120 3.792515 AGTAGTCTTAAGGGCTTGAGGT 58.207 45.455 1.85 0.00 0.00 3.85
120 121 4.828072 AAGTAGTCTTAAGGGCTTGAGG 57.172 45.455 1.85 0.00 31.46 3.86
121 122 6.937392 AGTAAAGTAGTCTTAAGGGCTTGAG 58.063 40.000 1.85 0.00 33.09 3.02
122 123 6.930068 AGTAAAGTAGTCTTAAGGGCTTGA 57.070 37.500 1.85 0.00 33.09 3.02
123 124 7.764901 CCTAAGTAAAGTAGTCTTAAGGGCTTG 59.235 40.741 1.85 0.00 33.09 4.01
124 125 7.457218 ACCTAAGTAAAGTAGTCTTAAGGGCTT 59.543 37.037 1.85 0.00 33.09 4.35
125 126 6.958778 ACCTAAGTAAAGTAGTCTTAAGGGCT 59.041 38.462 1.85 4.34 33.09 5.19
126 127 7.180322 ACCTAAGTAAAGTAGTCTTAAGGGC 57.820 40.000 1.85 0.00 33.09 5.19
152 153 8.821817 ACCCCACTGCAACTTTTATTAATTAAT 58.178 29.630 14.86 14.86 0.00 1.40
153 154 8.091449 CACCCCACTGCAACTTTTATTAATTAA 58.909 33.333 0.00 0.00 0.00 1.40
154 155 7.233757 ACACCCCACTGCAACTTTTATTAATTA 59.766 33.333 0.00 0.00 0.00 1.40
155 156 6.042666 ACACCCCACTGCAACTTTTATTAATT 59.957 34.615 0.00 0.00 0.00 1.40
156 157 5.542251 ACACCCCACTGCAACTTTTATTAAT 59.458 36.000 0.00 0.00 0.00 1.40
157 158 4.896482 ACACCCCACTGCAACTTTTATTAA 59.104 37.500 0.00 0.00 0.00 1.40
158 159 4.475345 ACACCCCACTGCAACTTTTATTA 58.525 39.130 0.00 0.00 0.00 0.98
159 160 3.304829 ACACCCCACTGCAACTTTTATT 58.695 40.909 0.00 0.00 0.00 1.40
160 161 2.957474 ACACCCCACTGCAACTTTTAT 58.043 42.857 0.00 0.00 0.00 1.40
161 162 2.445682 ACACCCCACTGCAACTTTTA 57.554 45.000 0.00 0.00 0.00 1.52
162 163 1.567357 AACACCCCACTGCAACTTTT 58.433 45.000 0.00 0.00 0.00 2.27
163 164 1.567357 AAACACCCCACTGCAACTTT 58.433 45.000 0.00 0.00 0.00 2.66
164 165 2.028876 GTAAACACCCCACTGCAACTT 58.971 47.619 0.00 0.00 0.00 2.66
165 166 1.687563 GTAAACACCCCACTGCAACT 58.312 50.000 0.00 0.00 0.00 3.16
166 167 0.671796 GGTAAACACCCCACTGCAAC 59.328 55.000 0.00 0.00 0.00 4.17
167 168 0.468400 GGGTAAACACCCCACTGCAA 60.468 55.000 1.04 0.00 44.18 4.08
168 169 1.151908 GGGTAAACACCCCACTGCA 59.848 57.895 1.04 0.00 44.18 4.41
169 170 4.090723 GGGTAAACACCCCACTGC 57.909 61.111 1.04 0.00 44.18 4.40
176 177 7.614494 TGACTATAAACAGTAGGGTAAACACC 58.386 38.462 0.00 0.00 0.00 4.16
177 178 9.492973 TTTGACTATAAACAGTAGGGTAAACAC 57.507 33.333 0.00 0.00 0.00 3.32
204 205 7.653311 GGTCAATGTTAGCTGTCAAAGATTTTT 59.347 33.333 0.00 0.00 0.00 1.94
205 206 7.147976 GGTCAATGTTAGCTGTCAAAGATTTT 58.852 34.615 0.00 0.00 0.00 1.82
206 207 6.265196 TGGTCAATGTTAGCTGTCAAAGATTT 59.735 34.615 0.00 0.00 0.00 2.17
207 208 5.769662 TGGTCAATGTTAGCTGTCAAAGATT 59.230 36.000 0.00 0.00 0.00 2.40
220 221 4.525487 ACGGTAGACTTCTGGTCAATGTTA 59.475 41.667 0.00 0.00 46.72 2.41
222 223 2.897969 ACGGTAGACTTCTGGTCAATGT 59.102 45.455 0.00 0.00 46.72 2.71
288 289 1.302993 GACCCTTTTGCTACCGCCA 60.303 57.895 0.00 0.00 34.43 5.69
354 356 9.122779 ACAAAATCATTGTTTTGACCATTTGAT 57.877 25.926 20.96 0.00 46.78 2.57
448 450 5.177142 CGAGAACAATGCTTGATGAGGATAG 59.823 44.000 3.37 0.00 35.06 2.08
538 541 4.036852 CCTTGACAAAGAAAGAGTGGTTCC 59.963 45.833 0.00 0.00 35.19 3.62
679 689 8.066595 TGTGAAAACAAAATTTGACAGTGTTTG 58.933 29.630 13.19 0.00 40.53 2.93
756 786 2.368655 ATGCTTGGGATTTTCGTTGC 57.631 45.000 0.00 0.00 0.00 4.17
1137 3576 2.038837 TGACACGTCGAGCCGATCT 61.039 57.895 0.00 0.00 38.42 2.75
1222 6901 0.535102 AAGAACCAACAGCCAGGTCG 60.535 55.000 0.00 0.00 37.07 4.79
1258 6937 2.742372 AAAGCTACACGGCAGCGG 60.742 61.111 0.00 0.00 43.97 5.52
1341 7020 5.628797 TCATGAACTAGCCCAATATGACA 57.371 39.130 0.00 0.00 0.00 3.58
1384 7090 4.398358 CACATGATCTTTGTGAGCAGGATT 59.602 41.667 18.83 0.00 44.45 3.01
1593 7314 6.524734 AGTGTGATCATGCCGATAAATTCTA 58.475 36.000 0.00 0.00 33.17 2.10
1723 7444 7.425606 ACAACAATTTTGGATAGACTGTTCAC 58.574 34.615 0.00 0.00 0.00 3.18
1747 7475 8.075574 TCAATAATGTCATGAACAAACTGTGAC 58.924 33.333 0.00 0.00 42.37 3.67
1774 8489 5.709631 TGCAACAGCTTACCAAATTCTATGA 59.290 36.000 0.00 0.00 0.00 2.15
1813 8528 2.079925 GATGCTCTGGGTTCTTCACAC 58.920 52.381 0.00 0.00 0.00 3.82
1824 8539 3.055530 AGTTCCAGTTGTAGATGCTCTGG 60.056 47.826 0.00 0.00 44.69 3.86
1887 8612 2.665185 GTGTCACCGGGCACTGTC 60.665 66.667 6.32 0.00 33.22 3.51
1900 8625 6.076981 ACAATGAGTGAAAAATGAGGTGTC 57.923 37.500 0.00 0.00 0.00 3.67
1912 8637 4.588951 AGGAGTGTGACTACAATGAGTGAA 59.411 41.667 0.00 0.00 38.82 3.18
1923 8648 5.560722 TTTGGAAATGAGGAGTGTGACTA 57.439 39.130 0.00 0.00 0.00 2.59
1925 8650 4.156739 GGATTTGGAAATGAGGAGTGTGAC 59.843 45.833 0.00 0.00 0.00 3.67
1926 8651 4.043310 AGGATTTGGAAATGAGGAGTGTGA 59.957 41.667 0.00 0.00 0.00 3.58
2021 8746 4.344968 AGGTCATTGACATATCCGATGACA 59.655 41.667 23.44 1.79 42.98 3.58
2028 8753 3.817647 GCAAGGAGGTCATTGACATATCC 59.182 47.826 18.09 18.95 39.74 2.59
2037 8762 3.820425 TCCGGCAAGGAGGTCATT 58.180 55.556 0.00 0.00 45.98 2.57
2060 8785 2.484062 GCCAATGACCATGAGGCCG 61.484 63.158 12.87 0.00 37.04 6.13
2067 8792 3.133464 CACGCCGCCAATGACCAT 61.133 61.111 0.00 0.00 0.00 3.55
2099 8824 2.287977 TGAGGACAACGAAGAGGAGA 57.712 50.000 0.00 0.00 0.00 3.71
2111 8836 2.495270 GAGCTCTTCACAGATGAGGACA 59.505 50.000 6.43 0.00 36.11 4.02
2121 8846 2.301009 TGAAGCATGAGAGCTCTTCACA 59.699 45.455 19.36 12.01 45.89 3.58
2123 8848 2.673326 CGTGAAGCATGAGAGCTCTTCA 60.673 50.000 19.36 16.88 45.89 3.02
2224 8950 4.033776 CCCAAGCGGAGGAGGCAA 62.034 66.667 0.00 0.00 0.00 4.52
2276 9002 0.392193 CGTCAGAGCAGGCTGGATTT 60.392 55.000 17.64 0.00 36.55 2.17
2282 9008 1.905843 AGACACGTCAGAGCAGGCT 60.906 57.895 0.00 0.00 0.00 4.58
2321 9047 2.279120 GCATCGAGCGGAGACCTG 60.279 66.667 0.00 0.00 0.00 4.00
2336 9062 0.178975 AAAATGTTGACCCCGGAGCA 60.179 50.000 0.73 0.00 0.00 4.26
2444 9170 1.304547 CTCTCCCTCCAGTCCACGT 60.305 63.158 0.00 0.00 0.00 4.49
2464 9190 1.500736 CCTAGCCATCCCCATTTCCTT 59.499 52.381 0.00 0.00 0.00 3.36
2540 9266 1.371337 GCATTCATCGCACTGCTCCA 61.371 55.000 0.00 0.00 0.00 3.86
2546 9272 1.815421 GGTCCGCATTCATCGCACT 60.815 57.895 0.00 0.00 0.00 4.40
2550 9276 0.460109 TCACTGGTCCGCATTCATCG 60.460 55.000 0.00 0.00 0.00 3.84
2578 9304 1.002624 GCGGAAACCCATCAGTCCA 60.003 57.895 0.00 0.00 0.00 4.02
2667 9393 1.354168 TTCGGAACTCCCCAAACCCA 61.354 55.000 0.00 0.00 0.00 4.51
2668 9394 0.892358 GTTCGGAACTCCCCAAACCC 60.892 60.000 13.49 0.00 0.00 4.11
2669 9395 1.232621 CGTTCGGAACTCCCCAAACC 61.233 60.000 17.94 0.00 0.00 3.27
2670 9396 0.533531 ACGTTCGGAACTCCCCAAAC 60.534 55.000 17.94 0.00 0.00 2.93
2671 9397 0.180878 AACGTTCGGAACTCCCCAAA 59.819 50.000 17.94 0.00 0.00 3.28
2672 9398 0.180878 AAACGTTCGGAACTCCCCAA 59.819 50.000 17.94 0.00 0.00 4.12
2673 9399 0.180878 AAAACGTTCGGAACTCCCCA 59.819 50.000 17.94 0.00 0.00 4.96
2674 9400 0.589708 CAAAACGTTCGGAACTCCCC 59.410 55.000 17.94 0.00 0.00 4.81
2675 9401 0.589708 CCAAAACGTTCGGAACTCCC 59.410 55.000 17.94 0.00 0.00 4.30
2676 9402 0.040692 GCCAAAACGTTCGGAACTCC 60.041 55.000 18.31 0.00 0.00 3.85
2677 9403 0.942252 AGCCAAAACGTTCGGAACTC 59.058 50.000 18.31 3.21 0.00 3.01
2678 9404 0.661020 CAGCCAAAACGTTCGGAACT 59.339 50.000 18.31 6.09 0.00 3.01
2679 9405 0.317519 CCAGCCAAAACGTTCGGAAC 60.318 55.000 18.31 10.83 0.00 3.62
2680 9406 1.448922 CCCAGCCAAAACGTTCGGAA 61.449 55.000 18.31 0.00 0.00 4.30
2681 9407 1.894756 CCCAGCCAAAACGTTCGGA 60.895 57.895 18.31 0.00 0.00 4.55
2682 9408 0.885596 TACCCAGCCAAAACGTTCGG 60.886 55.000 0.00 6.82 0.00 4.30
2683 9409 1.161843 ATACCCAGCCAAAACGTTCG 58.838 50.000 0.00 0.00 0.00 3.95
2684 9410 2.681344 CCTATACCCAGCCAAAACGTTC 59.319 50.000 0.00 0.00 0.00 3.95
2685 9411 2.619590 CCCTATACCCAGCCAAAACGTT 60.620 50.000 0.00 0.00 0.00 3.99
2686 9412 1.064979 CCCTATACCCAGCCAAAACGT 60.065 52.381 0.00 0.00 0.00 3.99
2687 9413 1.675552 CCCTATACCCAGCCAAAACG 58.324 55.000 0.00 0.00 0.00 3.60
2688 9414 1.286849 ACCCCTATACCCAGCCAAAAC 59.713 52.381 0.00 0.00 0.00 2.43
2689 9415 1.688750 ACCCCTATACCCAGCCAAAA 58.311 50.000 0.00 0.00 0.00 2.44
2690 9416 1.567175 GAACCCCTATACCCAGCCAAA 59.433 52.381 0.00 0.00 0.00 3.28
2691 9417 1.218844 GAACCCCTATACCCAGCCAA 58.781 55.000 0.00 0.00 0.00 4.52
2692 9418 0.345502 AGAACCCCTATACCCAGCCA 59.654 55.000 0.00 0.00 0.00 4.75
2693 9419 0.765510 CAGAACCCCTATACCCAGCC 59.234 60.000 0.00 0.00 0.00 4.85
2694 9420 0.765510 CCAGAACCCCTATACCCAGC 59.234 60.000 0.00 0.00 0.00 4.85
2695 9421 2.172717 CAACCAGAACCCCTATACCCAG 59.827 54.545 0.00 0.00 0.00 4.45
2696 9422 2.201830 CAACCAGAACCCCTATACCCA 58.798 52.381 0.00 0.00 0.00 4.51
2697 9423 1.493446 CCAACCAGAACCCCTATACCC 59.507 57.143 0.00 0.00 0.00 3.69
2698 9424 1.493446 CCCAACCAGAACCCCTATACC 59.507 57.143 0.00 0.00 0.00 2.73
2699 9425 2.092592 CACCCAACCAGAACCCCTATAC 60.093 54.545 0.00 0.00 0.00 1.47
2700 9426 2.201830 CACCCAACCAGAACCCCTATA 58.798 52.381 0.00 0.00 0.00 1.31
2701 9427 0.999712 CACCCAACCAGAACCCCTAT 59.000 55.000 0.00 0.00 0.00 2.57
2702 9428 1.785353 GCACCCAACCAGAACCCCTA 61.785 60.000 0.00 0.00 0.00 3.53
2703 9429 3.146828 GCACCCAACCAGAACCCCT 62.147 63.158 0.00 0.00 0.00 4.79
2704 9430 2.600470 GCACCCAACCAGAACCCC 60.600 66.667 0.00 0.00 0.00 4.95
2705 9431 2.600470 GGCACCCAACCAGAACCC 60.600 66.667 0.00 0.00 0.00 4.11
2706 9432 0.831711 ATTGGCACCCAACCAGAACC 60.832 55.000 0.00 0.00 46.95 3.62
2707 9433 1.047801 AATTGGCACCCAACCAGAAC 58.952 50.000 0.00 0.00 46.95 3.01
2708 9434 1.691434 GAAATTGGCACCCAACCAGAA 59.309 47.619 0.00 0.00 46.95 3.02
2709 9435 1.133199 AGAAATTGGCACCCAACCAGA 60.133 47.619 0.00 0.00 46.95 3.86
2710 9436 1.341080 AGAAATTGGCACCCAACCAG 58.659 50.000 0.00 0.00 46.95 4.00
2711 9437 1.415659 CAAGAAATTGGCACCCAACCA 59.584 47.619 0.00 0.00 46.95 3.67
2712 9438 1.691434 TCAAGAAATTGGCACCCAACC 59.309 47.619 0.00 0.00 46.95 3.77
2713 9439 2.547855 GGTCAAGAAATTGGCACCCAAC 60.548 50.000 0.00 0.00 46.95 3.77
2715 9441 1.337118 GGTCAAGAAATTGGCACCCA 58.663 50.000 0.00 0.00 0.00 4.51
2716 9442 0.243636 CGGTCAAGAAATTGGCACCC 59.756 55.000 0.00 0.00 0.00 4.61
2717 9443 0.243636 CCGGTCAAGAAATTGGCACC 59.756 55.000 0.00 0.00 0.00 5.01
2718 9444 0.243636 CCCGGTCAAGAAATTGGCAC 59.756 55.000 0.00 0.00 0.00 5.01
2719 9445 0.178975 ACCCGGTCAAGAAATTGGCA 60.179 50.000 0.00 0.00 0.00 4.92
2720 9446 0.526211 GACCCGGTCAAGAAATTGGC 59.474 55.000 13.05 0.00 32.09 4.52
2721 9447 0.802494 CGACCCGGTCAAGAAATTGG 59.198 55.000 17.87 0.00 32.09 3.16
2722 9448 0.168128 GCGACCCGGTCAAGAAATTG 59.832 55.000 17.87 0.00 32.09 2.32
2723 9449 0.958876 GGCGACCCGGTCAAGAAATT 60.959 55.000 17.87 0.00 32.09 1.82
2724 9450 1.376812 GGCGACCCGGTCAAGAAAT 60.377 57.895 17.87 0.00 32.09 2.17
2725 9451 2.031465 GGCGACCCGGTCAAGAAA 59.969 61.111 17.87 0.00 32.09 2.52
2760 9845 1.282157 AGCATCTACAACTTGACCCCC 59.718 52.381 0.00 0.00 0.00 5.40
2774 9859 3.908476 TGACTGGATAGTGAGAGCATCT 58.092 45.455 0.00 0.00 43.58 2.90
2779 9864 5.130145 AGGGAAATTGACTGGATAGTGAGAG 59.870 44.000 0.00 0.00 37.25 3.20
2780 9865 5.032846 AGGGAAATTGACTGGATAGTGAGA 58.967 41.667 0.00 0.00 37.25 3.27
2781 9866 5.121811 CAGGGAAATTGACTGGATAGTGAG 58.878 45.833 0.00 0.00 37.25 3.51
2782 9867 4.536090 ACAGGGAAATTGACTGGATAGTGA 59.464 41.667 8.56 0.00 37.25 3.41
2783 9868 4.848357 ACAGGGAAATTGACTGGATAGTG 58.152 43.478 8.56 0.00 37.25 2.74
2784 9869 6.215636 AGTTACAGGGAAATTGACTGGATAGT 59.784 38.462 8.56 0.00 40.66 2.12
2785 9870 6.653989 AGTTACAGGGAAATTGACTGGATAG 58.346 40.000 8.56 0.00 36.57 2.08
2786 9871 6.443849 AGAGTTACAGGGAAATTGACTGGATA 59.556 38.462 8.56 0.00 36.57 2.59
2787 9872 5.251700 AGAGTTACAGGGAAATTGACTGGAT 59.748 40.000 8.56 0.00 36.57 3.41
2788 9873 4.597507 AGAGTTACAGGGAAATTGACTGGA 59.402 41.667 8.56 0.00 36.57 3.86
2789 9874 4.911390 AGAGTTACAGGGAAATTGACTGG 58.089 43.478 8.56 0.00 36.57 4.00
2790 9875 4.627467 CGAGAGTTACAGGGAAATTGACTG 59.373 45.833 0.00 0.00 38.19 3.51
2791 9876 4.322801 CCGAGAGTTACAGGGAAATTGACT 60.323 45.833 0.00 0.00 0.00 3.41
2792 9877 3.933332 CCGAGAGTTACAGGGAAATTGAC 59.067 47.826 0.00 0.00 0.00 3.18
2793 9878 3.055385 CCCGAGAGTTACAGGGAAATTGA 60.055 47.826 0.00 0.00 46.64 2.57
2794 9879 3.270877 CCCGAGAGTTACAGGGAAATTG 58.729 50.000 0.00 0.00 46.64 2.32
2795 9880 3.629142 CCCGAGAGTTACAGGGAAATT 57.371 47.619 0.00 0.00 46.64 1.82
2934 10024 9.396022 CAAGTCATGTCACCCTTATAGTTAAAT 57.604 33.333 0.00 0.00 0.00 1.40
2936 10026 7.913789 ACAAGTCATGTCACCCTTATAGTTAA 58.086 34.615 0.00 0.00 37.96 2.01
2983 10073 6.729690 TCCAATTGAAATCATTACCCCATC 57.270 37.500 7.12 0.00 0.00 3.51
3003 10093 7.676683 AGTTATTACTCTATTCTTGGCTCCA 57.323 36.000 0.00 0.00 0.00 3.86
3217 10307 2.296073 ATAACAGTCCCCCGCAAAAA 57.704 45.000 0.00 0.00 0.00 1.94
3218 10308 2.618559 GGTATAACAGTCCCCCGCAAAA 60.619 50.000 0.00 0.00 0.00 2.44
3219 10309 1.065272 GGTATAACAGTCCCCCGCAAA 60.065 52.381 0.00 0.00 0.00 3.68
3220 10310 0.542805 GGTATAACAGTCCCCCGCAA 59.457 55.000 0.00 0.00 0.00 4.85
3221 10311 1.339644 GGGTATAACAGTCCCCCGCA 61.340 60.000 0.00 0.00 35.52 5.69
3222 10312 1.448924 GGGTATAACAGTCCCCCGC 59.551 63.158 0.00 0.00 35.52 6.13
3226 10316 4.857130 AAAGAAGGGGTATAACAGTCCC 57.143 45.455 0.00 0.00 40.41 4.46
3227 10317 6.383436 AGAGTAAAGAAGGGGTATAACAGTCC 59.617 42.308 0.00 0.00 0.00 3.85
3228 10318 7.266400 CAGAGTAAAGAAGGGGTATAACAGTC 58.734 42.308 0.00 0.00 0.00 3.51
3229 10319 6.351966 GCAGAGTAAAGAAGGGGTATAACAGT 60.352 42.308 0.00 0.00 0.00 3.55
3230 10320 6.049790 GCAGAGTAAAGAAGGGGTATAACAG 58.950 44.000 0.00 0.00 0.00 3.16
3231 10321 5.486063 TGCAGAGTAAAGAAGGGGTATAACA 59.514 40.000 0.00 0.00 0.00 2.41
3232 10322 5.985911 TGCAGAGTAAAGAAGGGGTATAAC 58.014 41.667 0.00 0.00 0.00 1.89
3233 10323 6.385759 TCATGCAGAGTAAAGAAGGGGTATAA 59.614 38.462 0.00 0.00 0.00 0.98
3234 10324 5.903010 TCATGCAGAGTAAAGAAGGGGTATA 59.097 40.000 0.00 0.00 0.00 1.47
3340 10431 9.959721 GATGTATCCCATAAGCTTATTTAGGAA 57.040 33.333 23.67 13.86 32.56 3.36
3342 10433 9.167311 GTGATGTATCCCATAAGCTTATTTAGG 57.833 37.037 16.46 16.25 32.56 2.69
3386 10478 4.214119 GTCAATAAAGCTTGCACTGAGACA 59.786 41.667 0.00 0.00 0.00 3.41
3491 10583 2.058798 CTGCAGTGCATTTTCAGCAAG 58.941 47.619 20.10 0.00 44.64 4.01
3494 10586 2.442084 GCTGCAGTGCATTTTCAGC 58.558 52.632 20.10 13.68 42.46 4.26
3647 10739 6.863126 CAGGGAGAACAATGTAAAAATCACAC 59.137 38.462 0.00 0.00 0.00 3.82
3690 10782 7.225931 GTGCAATGCAATAAAATCATCAAGGAT 59.774 33.333 10.44 0.00 41.47 3.24
3691 10783 6.535865 GTGCAATGCAATAAAATCATCAAGGA 59.464 34.615 10.44 0.00 41.47 3.36
3776 10868 7.399478 TCTGGTTACTTTTCCCCAAAAACTAAA 59.601 33.333 0.00 0.00 33.34 1.85
3791 10883 2.158608 AGCACAAGCCTCTGGTTACTTT 60.159 45.455 0.00 0.00 43.56 2.66
3796 10888 1.458639 GCAAGCACAAGCCTCTGGTT 61.459 55.000 0.00 0.00 43.56 3.67
3798 10890 1.863662 CTGCAAGCACAAGCCTCTGG 61.864 60.000 0.00 0.00 43.56 3.86
3942 11039 1.771854 TGGACTTTCCTTGGTACAGCA 59.228 47.619 0.00 0.00 37.46 4.41
4002 11099 0.603569 GGCTTCGACTCTGAACCTCA 59.396 55.000 0.00 0.00 0.00 3.86
4186 11283 8.771766 AGAAAAGAAACCTACGAAAACACTATC 58.228 33.333 0.00 0.00 0.00 2.08
4206 11303 6.527957 CAGCAACAACAACAAGAAAGAAAAG 58.472 36.000 0.00 0.00 0.00 2.27
4255 11358 3.154827 ACGGTTTCCAGTTTCCATCAT 57.845 42.857 0.00 0.00 0.00 2.45
4336 11469 0.250295 CCACGTCACAACTGACCCAT 60.250 55.000 0.00 0.00 43.64 4.00
4471 12120 7.095102 GCTCACAATTTCTTGCCAACAATATTT 60.095 33.333 0.00 0.00 35.69 1.40
4504 12153 2.997621 TTCAAATGCGTGCACCGTGC 62.998 55.000 16.93 16.93 45.29 5.34
4505 12154 0.998226 CTTCAAATGCGTGCACCGTG 60.998 55.000 12.15 0.00 39.32 4.94
4506 12155 1.282570 CTTCAAATGCGTGCACCGT 59.717 52.632 12.15 2.58 39.32 4.83
4507 12156 0.998226 CACTTCAAATGCGTGCACCG 60.998 55.000 12.15 7.80 40.40 4.94
4508 12157 0.310543 TCACTTCAAATGCGTGCACC 59.689 50.000 12.15 4.74 0.00 5.01
4509 12158 1.398595 GTCACTTCAAATGCGTGCAC 58.601 50.000 6.82 6.82 0.00 4.57
4574 12223 4.933064 GATCGGGGTCGCAGCTCG 62.933 72.222 1.87 1.87 40.15 5.03
4575 12224 2.579684 AAAGATCGGGGTCGCAGCTC 62.580 60.000 0.00 0.00 36.13 4.09
4576 12225 2.660064 AAAGATCGGGGTCGCAGCT 61.660 57.895 0.00 0.00 36.13 4.24
4577 12226 2.125106 AAAGATCGGGGTCGCAGC 60.125 61.111 0.00 0.00 36.13 5.25
4578 12227 0.179073 ATCAAAGATCGGGGTCGCAG 60.179 55.000 0.00 0.00 36.13 5.18
4579 12228 0.179084 GATCAAAGATCGGGGTCGCA 60.179 55.000 0.00 0.00 36.13 5.10
4580 12229 0.880718 GGATCAAAGATCGGGGTCGC 60.881 60.000 0.00 0.00 36.13 5.19
4583 12232 2.105477 CAGATGGATCAAAGATCGGGGT 59.895 50.000 0.00 0.00 0.00 4.95
4695 12365 4.467107 GGGGGAGAGGCGGAGAGT 62.467 72.222 0.00 0.00 0.00 3.24
4754 12424 1.067565 GTTCGAGATCTGGACAGCACA 60.068 52.381 6.97 0.00 0.00 4.57
4758 12428 2.757868 AGAAGGTTCGAGATCTGGACAG 59.242 50.000 6.97 0.00 0.00 3.51
4902 12584 6.782988 AGCCCATGTACTAGTAGTGATACAAT 59.217 38.462 13.29 0.00 31.65 2.71
4904 12586 5.702266 AGCCCATGTACTAGTAGTGATACA 58.298 41.667 13.29 9.70 32.38 2.29
4908 12590 4.207955 CTGAGCCCATGTACTAGTAGTGA 58.792 47.826 13.29 0.00 0.00 3.41
4909 12591 3.954904 ACTGAGCCCATGTACTAGTAGTG 59.045 47.826 13.29 5.61 0.00 2.74
4910 12592 3.954904 CACTGAGCCCATGTACTAGTAGT 59.045 47.826 8.14 8.14 0.00 2.73
4911 12593 4.207955 TCACTGAGCCCATGTACTAGTAG 58.792 47.826 1.87 0.00 0.00 2.57
4986 12668 4.500116 GGAGAGAGACGCCACGCC 62.500 72.222 0.00 0.00 38.35 5.68
5045 12727 5.427378 TCAGCCATGATCAATTTACTCGAA 58.573 37.500 0.00 0.00 0.00 3.71
5046 12728 5.022282 TCAGCCATGATCAATTTACTCGA 57.978 39.130 0.00 0.00 0.00 4.04
5047 12729 5.936686 ATCAGCCATGATCAATTTACTCG 57.063 39.130 0.00 0.00 42.76 4.18
5048 12730 7.486647 ACAAATCAGCCATGATCAATTTACTC 58.513 34.615 0.00 0.00 45.67 2.59
5049 12731 7.414222 ACAAATCAGCCATGATCAATTTACT 57.586 32.000 0.00 0.00 45.67 2.24
5052 12734 8.262227 ACATTACAAATCAGCCATGATCAATTT 58.738 29.630 0.00 0.00 45.67 1.82
5064 12746 5.627499 TGGTTGAGACATTACAAATCAGC 57.373 39.130 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.