Multiple sequence alignment - TraesCS4D01G283900

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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 TraesCS4D01G283900 chr4D 100.000 3726 0 0 1 3726 455529159 455532884 0.000000e+00 6881
1 TraesCS4D01G283900 chr4D 81.088 1158 197 16 1049 2193 455652557 455653705 0.000000e+00 905
2 TraesCS4D01G283900 chr4D 83.224 918 142 9 927 1834 455599864 455600779 0.000000e+00 832
3 TraesCS4D01G283900 chr4D 93.586 343 21 1 370 712 419418607 419418948 9.230000e-141 510
4 TraesCS4D01G283900 chr4D 72.635 888 177 43 1331 2195 452557461 452556617 2.240000e-57 233
5 TraesCS4D01G283900 chr4D 83.482 224 37 0 1011 1234 455618661 455618884 3.770000e-50 209
6 TraesCS4D01G283900 chr4D 73.037 675 141 29 1544 2196 455648708 455649363 2.270000e-47 200
7 TraesCS4D01G283900 chr4D 89.928 139 12 2 239 375 419418244 419418382 1.060000e-40 178
8 TraesCS4D01G283900 chr4D 73.000 400 78 15 1064 1460 455648312 455648684 3.040000e-21 113
9 TraesCS4D01G283900 chr4B 92.724 2845 148 27 753 3549 568600077 568602910 0.000000e+00 4052
10 TraesCS4D01G283900 chr4B 80.730 1261 218 15 945 2196 568714549 568715793 0.000000e+00 959
11 TraesCS4D01G283900 chr4B 73.973 657 129 29 1557 2195 565743150 565742518 1.040000e-55 228
12 TraesCS4D01G283900 chr4B 72.370 865 190 33 1282 2114 568634662 568635509 1.040000e-55 228
13 TraesCS4D01G283900 chr4B 79.070 258 45 4 1871 2119 568665975 568666232 6.400000e-38 169
14 TraesCS4D01G283900 chr4B 77.049 305 60 6 1895 2196 568605431 568605728 2.300000e-37 167
15 TraesCS4D01G283900 chr4B 85.714 147 15 5 230 375 425293240 425293381 2.320000e-32 150
16 TraesCS4D01G283900 chr4A 95.818 1626 59 4 791 2415 12400215 12401832 0.000000e+00 2617
17 TraesCS4D01G283900 chr4A 90.793 1173 62 24 2415 3565 12401994 12403142 0.000000e+00 1526
18 TraesCS4D01G283900 chr4A 79.511 1269 205 37 946 2194 12163098 12161865 0.000000e+00 852
19 TraesCS4D01G283900 chr4A 83.315 893 142 7 943 1830 12211080 12210190 0.000000e+00 817
20 TraesCS4D01G283900 chr4A 94.079 152 9 0 3573 3724 12387055 12386904 8.050000e-57 231
21 TraesCS4D01G283900 chr4A 78.125 320 54 12 1888 2196 12210159 12209845 4.910000e-44 189
22 TraesCS4D01G283900 chr4A 73.815 401 76 15 1064 1460 12169776 12169401 8.400000e-27 132
23 TraesCS4D01G283900 chr2D 95.252 337 15 1 370 706 644013532 644013197 1.970000e-147 532
24 TraesCS4D01G283900 chr2D 94.152 342 19 1 370 711 56634196 56634536 1.530000e-143 520
25 TraesCS4D01G283900 chr2D 93.660 347 20 2 370 716 346438034 346438378 5.520000e-143 518
26 TraesCS4D01G283900 chr2D 93.605 344 20 2 370 713 236137018 236137359 2.570000e-141 512
27 TraesCS4D01G283900 chr2D 96.047 253 10 0 2 254 596267033 596266781 2.680000e-111 412
28 TraesCS4D01G283900 chr2D 95.257 253 12 0 2 254 603143684 603143936 5.800000e-108 401
29 TraesCS4D01G283900 chr2D 95.257 253 12 0 2 254 627748575 627748323 5.800000e-108 401
30 TraesCS4D01G283900 chr2D 91.367 139 10 2 239 375 7033099 7033237 4.910000e-44 189
31 TraesCS4D01G283900 chr2D 89.928 139 12 2 239 375 165437252 165437114 1.060000e-40 178
32 TraesCS4D01G283900 chr2D 87.755 147 12 5 230 375 130721837 130721696 2.300000e-37 167
33 TraesCS4D01G283900 chr7A 94.721 341 14 3 370 709 215116882 215116545 9.170000e-146 527
34 TraesCS4D01G283900 chr6B 94.955 337 15 2 370 706 636476164 636476498 9.170000e-146 527
35 TraesCS4D01G283900 chr6B 96.552 87 3 0 2258 2344 551951958 551951872 1.080000e-30 145
36 TraesCS4D01G283900 chr6B 95.294 85 4 0 2260 2344 48874037 48874121 6.490000e-28 135
37 TraesCS4D01G283900 chr1D 94.362 337 18 1 370 706 250225352 250225687 1.980000e-142 516
38 TraesCS4D01G283900 chr1D 95.652 253 11 0 2 254 250224654 250224906 1.250000e-109 407
39 TraesCS4D01G283900 chr1D 89.209 139 13 2 239 375 424636504 424636642 4.950000e-39 172
40 TraesCS4D01G283900 chr1D 89.209 139 13 2 239 375 426390298 426390160 4.950000e-39 172
41 TraesCS4D01G283900 chr3D 94.100 339 19 1 370 708 515976018 515975681 7.140000e-142 514
42 TraesCS4D01G283900 chr3D 95.257 253 12 0 2 254 382521812 382521560 5.800000e-108 401
43 TraesCS4D01G283900 chr3D 95.257 253 12 0 2 254 553936065 553935813 5.800000e-108 401
44 TraesCS4D01G283900 chr3D 89.928 139 12 2 239 375 45867091 45867229 1.060000e-40 178
45 TraesCS4D01G283900 chr3D 95.294 85 4 0 2260 2344 22679146 22679062 6.490000e-28 135
46 TraesCS4D01G283900 chr3D 95.294 85 4 0 2260 2344 22767812 22767896 6.490000e-28 135
47 TraesCS4D01G283900 chr3D 91.089 101 8 1 2254 2354 66523470 66523371 6.490000e-28 135
48 TraesCS4D01G283900 chr5D 95.968 248 10 0 2 249 179971690 179971443 1.610000e-108 403
49 TraesCS4D01G283900 chr5D 85.567 194 28 0 1048 1241 431609846 431609653 1.750000e-48 204
50 TraesCS4D01G283900 chr5D 86.022 186 26 0 1049 1234 431617926 431617741 2.270000e-47 200
51 TraesCS4D01G283900 chr5D 87.075 147 13 5 230 375 544616836 544616977 1.070000e-35 161
52 TraesCS4D01G283900 chr5A 95.257 253 12 0 2 254 17723902 17724154 5.800000e-108 401
53 TraesCS4D01G283900 chr5A 85.484 186 27 0 1049 1234 546703517 546703332 1.060000e-45 195
54 TraesCS4D01G283900 chr6D 95.257 253 11 1 2 254 232376474 232376223 2.080000e-107 399
55 TraesCS4D01G283900 chr6D 92.222 90 7 0 2261 2350 299191348 299191259 1.090000e-25 128
56 TraesCS4D01G283900 chr5B 87.629 194 24 0 1048 1241 521154649 521154456 3.740000e-55 226
57 TraesCS4D01G283900 chr7D 91.367 139 10 2 239 375 64047077 64047215 4.910000e-44 189
58 TraesCS4D01G283900 chr7D 90.647 139 11 2 239 375 175931769 175931631 2.290000e-42 183
59 TraesCS4D01G283900 chr2A 90.647 139 11 2 239 375 661434121 661433983 2.290000e-42 183
60 TraesCS4D01G283900 chr1B 85.315 143 16 4 230 372 37060055 37059918 3.880000e-30 143
61 TraesCS4D01G283900 chr7B 89.720 107 11 0 2244 2350 639796301 639796195 1.800000e-28 137


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 TraesCS4D01G283900 chr4D 455529159 455532884 3725 False 6881.0 6881 100.000000 1 3726 1 chr4D.!!$F1 3725
1 TraesCS4D01G283900 chr4D 455599864 455600779 915 False 832.0 832 83.224000 927 1834 1 chr4D.!!$F2 907
2 TraesCS4D01G283900 chr4D 455648312 455653705 5393 False 406.0 905 75.708333 1049 2196 3 chr4D.!!$F5 1147
3 TraesCS4D01G283900 chr4D 419418244 419418948 704 False 344.0 510 91.757000 239 712 2 chr4D.!!$F4 473
4 TraesCS4D01G283900 chr4D 452556617 452557461 844 True 233.0 233 72.635000 1331 2195 1 chr4D.!!$R1 864
5 TraesCS4D01G283900 chr4B 568600077 568605728 5651 False 2109.5 4052 84.886500 753 3549 2 chr4B.!!$F5 2796
6 TraesCS4D01G283900 chr4B 568714549 568715793 1244 False 959.0 959 80.730000 945 2196 1 chr4B.!!$F4 1251
7 TraesCS4D01G283900 chr4B 565742518 565743150 632 True 228.0 228 73.973000 1557 2195 1 chr4B.!!$R1 638
8 TraesCS4D01G283900 chr4B 568634662 568635509 847 False 228.0 228 72.370000 1282 2114 1 chr4B.!!$F2 832
9 TraesCS4D01G283900 chr4A 12400215 12403142 2927 False 2071.5 2617 93.305500 791 3565 2 chr4A.!!$F1 2774
10 TraesCS4D01G283900 chr4A 12161865 12163098 1233 True 852.0 852 79.511000 946 2194 1 chr4A.!!$R1 1248
11 TraesCS4D01G283900 chr4A 12209845 12211080 1235 True 503.0 817 80.720000 943 2196 2 chr4A.!!$R4 1253
12 TraesCS4D01G283900 chr1D 250224654 250225687 1033 False 461.5 516 95.007000 2 706 2 chr1D.!!$F2 704


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
255 346 0.461961 GACTGCATAGGAGCCGTTCT 59.538 55.0 0.0 0.0 31.92 3.01 F
1309 4515 0.109226 GGTCTCCAACTTCGTCTCCG 60.109 60.0 0.0 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 5094 0.107508 CAATGGTCGGCATGTCCTCT 60.108 55.000 0.0 0.0 0.00 3.69 R
3190 6648 1.202348 GCTAGTCTTGCTCGCATCTCA 60.202 52.381 0.0 0.0 36.11 3.27 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
42 43 6.426980 TTGATCTGAAGTTCACATATGTGC 57.573 37.500 27.71 16.38 45.25 4.57
44 45 6.877236 TGATCTGAAGTTCACATATGTGCTA 58.123 36.000 27.71 16.56 45.25 3.49
50 51 3.198635 AGTTCACATATGTGCTAGCTGGT 59.801 43.478 27.71 3.96 45.25 4.00
127 128 1.820581 GGATCAACATCCCCGACGA 59.179 57.895 0.00 0.00 42.91 4.20
163 164 4.129757 TGCTGGCTATGCATGTCG 57.870 55.556 10.16 0.00 35.31 4.35
251 342 0.600557 CTAGGACTGCATAGGAGCCG 59.399 60.000 0.00 0.00 0.00 5.52
255 346 0.461961 GACTGCATAGGAGCCGTTCT 59.538 55.000 0.00 0.00 31.92 3.01
263 354 2.170012 AGGAGCCGTTCTACCCATAA 57.830 50.000 0.00 0.00 0.00 1.90
278 369 5.789574 ACCCATAATCCACTCAGGTTAAA 57.210 39.130 0.00 0.00 39.02 1.52
317 408 3.812053 GCATTCTGCATAACTCGATCCTT 59.188 43.478 0.00 0.00 44.26 3.36
335 426 2.089980 CTTCAGTGGGGCTTTGATGAG 58.910 52.381 0.00 0.00 0.00 2.90
391 722 7.809331 TGACAATTTGAACTGTCATTTGATAGC 59.191 33.333 4.11 0.00 45.31 2.97
444 775 3.441572 GCTGGCACTACATGTTCAGATTT 59.558 43.478 2.30 0.00 35.24 2.17
476 807 4.408276 AGCTCACCACTAGTTAGAAGTGA 58.592 43.478 4.84 12.19 45.89 3.41
569 900 2.946785 ACGTGGGGTCAAAAATGGTTA 58.053 42.857 0.00 0.00 0.00 2.85
625 956 1.843368 ATGTGCATCTGGGGTCTTTG 58.157 50.000 0.00 0.00 0.00 2.77
706 1037 1.338337 CAATGTAACCAAACACGCCCA 59.662 47.619 0.00 0.00 30.75 5.36
714 1045 2.159382 CCAAACACGCCCATAGTTCTT 58.841 47.619 0.00 0.00 0.00 2.52
715 1046 2.556622 CCAAACACGCCCATAGTTCTTT 59.443 45.455 0.00 0.00 0.00 2.52
716 1047 3.005367 CCAAACACGCCCATAGTTCTTTT 59.995 43.478 0.00 0.00 0.00 2.27
717 1048 4.216687 CCAAACACGCCCATAGTTCTTTTA 59.783 41.667 0.00 0.00 0.00 1.52
719 1050 3.606687 ACACGCCCATAGTTCTTTTAGG 58.393 45.455 0.00 0.00 0.00 2.69
720 1051 2.943033 CACGCCCATAGTTCTTTTAGGG 59.057 50.000 0.00 0.00 39.33 3.53
721 1052 2.092592 ACGCCCATAGTTCTTTTAGGGG 60.093 50.000 0.00 0.00 43.39 4.79
722 1053 2.092592 CGCCCATAGTTCTTTTAGGGGT 60.093 50.000 4.19 0.00 42.68 4.95
723 1054 3.552875 GCCCATAGTTCTTTTAGGGGTC 58.447 50.000 4.19 0.00 42.68 4.46
724 1055 3.687551 GCCCATAGTTCTTTTAGGGGTCC 60.688 52.174 4.19 0.00 42.68 4.46
726 1057 4.229812 CCCATAGTTCTTTTAGGGGTCCTT 59.770 45.833 0.00 0.00 37.35 3.36
728 1059 6.102762 CCCATAGTTCTTTTAGGGGTCCTTAT 59.897 42.308 0.00 0.00 37.35 1.73
729 1060 6.998673 CCATAGTTCTTTTAGGGGTCCTTATG 59.001 42.308 0.00 0.00 34.61 1.90
732 1063 4.855298 TCTTTTAGGGGTCCTTATGGTG 57.145 45.455 0.00 0.00 34.61 4.17
733 1064 3.526019 TCTTTTAGGGGTCCTTATGGTGG 59.474 47.826 0.00 0.00 34.61 4.61
734 1065 2.672703 TTAGGGGTCCTTATGGTGGT 57.327 50.000 0.00 0.00 34.61 4.16
735 1066 3.799590 TTAGGGGTCCTTATGGTGGTA 57.200 47.619 0.00 0.00 34.61 3.25
736 1067 2.910360 AGGGGTCCTTATGGTGGTAT 57.090 50.000 0.00 0.00 34.23 2.73
740 1071 3.248888 GGGTCCTTATGGTGGTATAGCT 58.751 50.000 3.20 0.00 34.23 3.32
742 1073 4.104261 GGGTCCTTATGGTGGTATAGCTTT 59.896 45.833 3.20 0.00 34.23 3.51
743 1074 5.398695 GGGTCCTTATGGTGGTATAGCTTTT 60.399 44.000 3.20 0.00 34.23 2.27
744 1075 6.127101 GGTCCTTATGGTGGTATAGCTTTTT 58.873 40.000 3.20 0.00 34.23 1.94
877 1208 0.684535 TTCACACGAGCCCATTCAGA 59.315 50.000 0.00 0.00 0.00 3.27
882 1213 2.464459 CGAGCCCATTCAGAACGCC 61.464 63.158 0.00 0.00 0.00 5.68
1309 4515 0.109226 GGTCTCCAACTTCGTCTCCG 60.109 60.000 0.00 0.00 0.00 4.63
1497 4704 3.871006 CGGAAATCATCTGGAATCGTCAA 59.129 43.478 0.00 0.00 0.00 3.18
1645 4879 2.182030 CCGACGAGGAACAGGAGC 59.818 66.667 0.00 0.00 45.00 4.70
1709 4949 3.136077 AGTGACATGATCTCCATTGAGGG 59.864 47.826 0.00 0.00 39.23 4.30
1825 5065 1.480954 TGGGTGAGGAAGAACTATCGC 59.519 52.381 0.00 0.00 0.00 4.58
1848 5088 6.238842 CGCTGATTGGTCCAATATTTGAAGAT 60.239 38.462 17.33 0.00 33.90 2.40
1867 5107 2.364972 TGATAGAGAGGACATGCCGA 57.635 50.000 0.00 0.00 43.43 5.54
1950 5208 5.529289 AGACTCTACCTATGGTCAATGGAA 58.471 41.667 0.00 0.00 37.09 3.53
2020 5292 1.291877 CGAACCGTTGCTCCCTTCTG 61.292 60.000 0.00 0.00 0.00 3.02
2039 5320 0.251341 GGTGCCCTCTTGGATGTGTT 60.251 55.000 0.00 0.00 35.39 3.32
2040 5321 1.168714 GTGCCCTCTTGGATGTGTTC 58.831 55.000 0.00 0.00 35.39 3.18
2146 5427 1.409427 GCAAGGAGGTACATAGAGCGT 59.591 52.381 0.00 0.00 0.00 5.07
2229 5510 8.023128 GCACATTTAGTCATGAACACTAAACAT 58.977 33.333 16.28 8.19 44.97 2.71
2488 5932 0.958382 GTGTGGGTGTGTGTGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
2490 5934 0.958382 GTGGGTGTGTGTGTGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
2491 5935 0.957888 TGGGTGTGTGTGTGTGTGTG 60.958 55.000 0.00 0.00 0.00 3.82
2492 5936 0.958382 GGGTGTGTGTGTGTGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
2493 5937 0.167908 GGTGTGTGTGTGTGTGTGTG 59.832 55.000 0.00 0.00 0.00 3.82
2494 5938 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2625 6080 3.995199 TGGACAGCTAGAGTTGAAGTTG 58.005 45.455 0.00 0.00 0.00 3.16
2660 6117 0.978907 TGCTCCTCTTGTGCTCATCA 59.021 50.000 0.00 0.00 34.56 3.07
2777 6234 4.624882 GCATAATCAAATGGCGTCAAAACA 59.375 37.500 0.00 0.00 0.00 2.83
2863 6320 2.557924 GCTGGATGTGTTGGATTGTTCA 59.442 45.455 0.00 0.00 0.00 3.18
2877 6334 4.565652 GGATTGTTCAGTCAGGGTGTATGT 60.566 45.833 0.00 0.00 0.00 2.29
2910 6367 2.292103 TTGTGCTTGTGCCAAAACTC 57.708 45.000 0.00 0.00 38.71 3.01
2916 6373 1.939934 CTTGTGCCAAAACTCGAGTCA 59.060 47.619 20.33 9.28 0.00 3.41
2961 6418 4.487948 CAGCAGGGTATTGATGTGTTTTG 58.512 43.478 0.00 0.00 30.17 2.44
3065 6522 8.707796 TTTTAAGGAGACGGAGATATCTATGT 57.292 34.615 4.89 7.13 0.00 2.29
3067 6524 8.789825 TTAAGGAGACGGAGATATCTATGTAC 57.210 38.462 4.89 5.37 0.00 2.90
3068 6525 6.630203 AGGAGACGGAGATATCTATGTACT 57.370 41.667 4.89 6.81 0.00 2.73
3069 6526 7.736881 AGGAGACGGAGATATCTATGTACTA 57.263 40.000 4.89 0.00 0.00 1.82
3070 6527 8.148437 AGGAGACGGAGATATCTATGTACTAA 57.852 38.462 4.89 0.00 0.00 2.24
3157 6614 2.849942 AGGCAAGCCCATTTTTGTTTC 58.150 42.857 7.62 0.00 36.58 2.78
3190 6648 9.775854 TGTGGTTTCATAAATTTGATCAACATT 57.224 25.926 7.89 8.73 0.00 2.71
3201 6659 2.610833 TGATCAACATTGAGATGCGAGC 59.389 45.455 0.00 0.00 41.08 5.03
3216 6674 1.914634 CGAGCAAGACTAGCGATTGT 58.085 50.000 0.00 0.00 37.01 2.71
3230 6688 3.941483 AGCGATTGTTTATTGGTGGAGAG 59.059 43.478 0.00 0.00 0.00 3.20
3231 6689 3.487544 GCGATTGTTTATTGGTGGAGAGC 60.488 47.826 0.00 0.00 0.00 4.09
3232 6690 3.242413 CGATTGTTTATTGGTGGAGAGCG 60.242 47.826 0.00 0.00 0.00 5.03
3233 6691 3.410631 TTGTTTATTGGTGGAGAGCGA 57.589 42.857 0.00 0.00 0.00 4.93
3234 6692 2.695359 TGTTTATTGGTGGAGAGCGAC 58.305 47.619 0.00 0.00 0.00 5.19
3235 6693 1.659098 GTTTATTGGTGGAGAGCGACG 59.341 52.381 0.00 0.00 0.00 5.12
3236 6694 0.174845 TTATTGGTGGAGAGCGACGG 59.825 55.000 0.00 0.00 0.00 4.79
3237 6695 0.681887 TATTGGTGGAGAGCGACGGA 60.682 55.000 0.00 0.00 0.00 4.69
3240 6698 2.179517 GTGGAGAGCGACGGACAG 59.820 66.667 0.00 0.00 0.00 3.51
3241 6699 3.749064 TGGAGAGCGACGGACAGC 61.749 66.667 0.00 0.00 0.00 4.40
3242 6700 4.500116 GGAGAGCGACGGACAGCC 62.500 72.222 0.00 0.00 0.00 4.85
3243 6701 3.444805 GAGAGCGACGGACAGCCT 61.445 66.667 0.00 0.00 0.00 4.58
3256 6721 2.424956 GGACAGCCTCCAATGACATTTC 59.575 50.000 0.00 0.00 39.21 2.17
3336 6804 6.633500 TCCTCAACAAATCTTTTGTACCAG 57.367 37.500 6.09 3.46 31.50 4.00
3360 6828 1.896220 ATCAATTGGAGTGTGTGCGT 58.104 45.000 5.42 0.00 0.00 5.24
3387 6862 5.714047 CACTGCATGTGTTAGAGTTAGAGA 58.286 41.667 7.80 0.00 41.53 3.10
3388 6863 6.336566 CACTGCATGTGTTAGAGTTAGAGAT 58.663 40.000 7.80 0.00 41.53 2.75
3389 6864 7.484140 CACTGCATGTGTTAGAGTTAGAGATA 58.516 38.462 7.80 0.00 41.53 1.98
3390 6865 7.433719 CACTGCATGTGTTAGAGTTAGAGATAC 59.566 40.741 7.80 0.00 41.53 2.24
3432 6907 3.744660 AGATCGAATCAAACATAGGGGC 58.255 45.455 0.00 0.00 0.00 5.80
3485 6973 1.304134 GAAAGGGGACGCCAACCAT 60.304 57.895 11.67 0.00 0.00 3.55
3507 6995 9.613428 ACCATCGAAAATTCACTATATCAAGAA 57.387 29.630 0.00 0.00 0.00 2.52
3533 7023 7.175104 AGATTACAAATGCCGGGATATACAAT 58.825 34.615 9.63 7.16 0.00 2.71
3555 7045 5.670792 TTGATCAACTTATCCCGTGTAGT 57.329 39.130 3.38 0.00 0.00 2.73
3565 7055 1.693062 TCCCGTGTAGTGGCTTACAAA 59.307 47.619 4.42 0.00 35.47 2.83
3566 7056 2.073816 CCCGTGTAGTGGCTTACAAAG 58.926 52.381 4.42 3.11 35.47 2.77
3567 7057 2.073816 CCGTGTAGTGGCTTACAAAGG 58.926 52.381 4.42 7.28 35.47 3.11
3568 7058 2.289195 CCGTGTAGTGGCTTACAAAGGA 60.289 50.000 14.34 0.00 36.50 3.36
3569 7059 3.596214 CGTGTAGTGGCTTACAAAGGAT 58.404 45.455 4.42 0.00 35.47 3.24
3570 7060 4.382254 CCGTGTAGTGGCTTACAAAGGATA 60.382 45.833 14.34 0.00 36.50 2.59
3571 7061 5.357257 CGTGTAGTGGCTTACAAAGGATAT 58.643 41.667 4.42 0.00 35.47 1.63
3572 7062 6.461927 CCGTGTAGTGGCTTACAAAGGATATA 60.462 42.308 14.34 0.00 36.50 0.86
3573 7063 7.152645 CGTGTAGTGGCTTACAAAGGATATAT 58.847 38.462 4.42 0.00 35.47 0.86
3574 7064 7.328737 CGTGTAGTGGCTTACAAAGGATATATC 59.671 40.741 3.96 3.96 35.47 1.63
3575 7065 7.603024 GTGTAGTGGCTTACAAAGGATATATCC 59.397 40.741 22.33 22.33 39.88 2.59
3592 7082 2.125773 TCCTACTGGGAGACTTCGAC 57.874 55.000 0.00 0.00 39.58 4.20
3593 7083 1.353358 TCCTACTGGGAGACTTCGACA 59.647 52.381 0.00 0.00 39.58 4.35
3594 7084 2.025226 TCCTACTGGGAGACTTCGACAT 60.025 50.000 0.00 0.00 39.58 3.06
3595 7085 2.099921 CCTACTGGGAGACTTCGACATG 59.900 54.545 0.00 0.00 37.23 3.21
3596 7086 1.633774 ACTGGGAGACTTCGACATGT 58.366 50.000 0.00 0.00 0.00 3.21
3597 7087 2.803956 ACTGGGAGACTTCGACATGTA 58.196 47.619 0.00 0.00 0.00 2.29
3598 7088 2.492484 ACTGGGAGACTTCGACATGTAC 59.508 50.000 0.00 0.00 0.00 2.90
3599 7089 2.492088 CTGGGAGACTTCGACATGTACA 59.508 50.000 0.00 0.00 0.00 2.90
3600 7090 2.492088 TGGGAGACTTCGACATGTACAG 59.508 50.000 0.00 0.00 0.00 2.74
3601 7091 2.753452 GGGAGACTTCGACATGTACAGA 59.247 50.000 0.00 0.00 0.00 3.41
3602 7092 3.381908 GGGAGACTTCGACATGTACAGAT 59.618 47.826 0.00 0.00 0.00 2.90
3603 7093 4.142138 GGGAGACTTCGACATGTACAGATT 60.142 45.833 0.00 0.00 0.00 2.40
3604 7094 5.411781 GGAGACTTCGACATGTACAGATTT 58.588 41.667 0.00 0.00 0.00 2.17
3605 7095 5.289675 GGAGACTTCGACATGTACAGATTTG 59.710 44.000 0.00 0.00 0.00 2.32
3606 7096 5.171476 AGACTTCGACATGTACAGATTTGG 58.829 41.667 0.00 0.00 0.00 3.28
3607 7097 4.894784 ACTTCGACATGTACAGATTTGGT 58.105 39.130 0.00 0.00 0.00 3.67
3608 7098 4.929808 ACTTCGACATGTACAGATTTGGTC 59.070 41.667 0.00 1.69 0.00 4.02
3609 7099 4.529109 TCGACATGTACAGATTTGGTCA 57.471 40.909 0.00 0.00 0.00 4.02
3610 7100 4.242475 TCGACATGTACAGATTTGGTCAC 58.758 43.478 0.00 0.00 0.00 3.67
3611 7101 3.060761 CGACATGTACAGATTTGGTCACG 59.939 47.826 0.00 0.00 0.00 4.35
3612 7102 4.242475 GACATGTACAGATTTGGTCACGA 58.758 43.478 0.00 0.00 0.00 4.35
3613 7103 4.245660 ACATGTACAGATTTGGTCACGAG 58.754 43.478 0.00 0.00 0.00 4.18
3614 7104 4.021456 ACATGTACAGATTTGGTCACGAGA 60.021 41.667 0.00 0.00 0.00 4.04
3615 7105 4.594123 TGTACAGATTTGGTCACGAGAA 57.406 40.909 0.00 0.00 0.00 2.87
3616 7106 4.951254 TGTACAGATTTGGTCACGAGAAA 58.049 39.130 0.00 0.00 0.00 2.52
3617 7107 5.547465 TGTACAGATTTGGTCACGAGAAAT 58.453 37.500 0.00 0.00 0.00 2.17
3618 7108 5.637810 TGTACAGATTTGGTCACGAGAAATC 59.362 40.000 0.00 0.00 36.67 2.17
3619 7109 4.641396 ACAGATTTGGTCACGAGAAATCA 58.359 39.130 0.00 0.00 38.17 2.57
3620 7110 5.063204 ACAGATTTGGTCACGAGAAATCAA 58.937 37.500 0.00 1.16 38.17 2.57
3621 7111 5.180117 ACAGATTTGGTCACGAGAAATCAAG 59.820 40.000 0.00 0.00 38.17 3.02
3622 7112 4.697352 AGATTTGGTCACGAGAAATCAAGG 59.303 41.667 0.00 0.00 38.17 3.61
3623 7113 2.472695 TGGTCACGAGAAATCAAGGG 57.527 50.000 0.00 0.00 0.00 3.95
3624 7114 1.003118 TGGTCACGAGAAATCAAGGGG 59.997 52.381 0.00 0.00 0.00 4.79
3625 7115 1.278127 GGTCACGAGAAATCAAGGGGA 59.722 52.381 0.00 0.00 0.00 4.81
3626 7116 2.347731 GTCACGAGAAATCAAGGGGAC 58.652 52.381 0.00 0.00 0.00 4.46
3627 7117 1.974957 TCACGAGAAATCAAGGGGACA 59.025 47.619 0.00 0.00 0.00 4.02
3628 7118 2.076863 CACGAGAAATCAAGGGGACAC 58.923 52.381 0.00 0.00 0.00 3.67
3629 7119 1.697432 ACGAGAAATCAAGGGGACACA 59.303 47.619 0.00 0.00 0.00 3.72
3630 7120 2.105821 ACGAGAAATCAAGGGGACACAA 59.894 45.455 0.00 0.00 0.00 3.33
3631 7121 2.744202 CGAGAAATCAAGGGGACACAAG 59.256 50.000 0.00 0.00 0.00 3.16
3632 7122 3.557054 CGAGAAATCAAGGGGACACAAGA 60.557 47.826 0.00 0.00 0.00 3.02
3633 7123 4.398319 GAGAAATCAAGGGGACACAAGAA 58.602 43.478 0.00 0.00 0.00 2.52
3634 7124 4.145052 AGAAATCAAGGGGACACAAGAAC 58.855 43.478 0.00 0.00 0.00 3.01
3635 7125 3.884037 AATCAAGGGGACACAAGAACT 57.116 42.857 0.00 0.00 0.00 3.01
3636 7126 2.638480 TCAAGGGGACACAAGAACTG 57.362 50.000 0.00 0.00 0.00 3.16
3637 7127 1.142870 TCAAGGGGACACAAGAACTGG 59.857 52.381 0.00 0.00 0.00 4.00
3638 7128 0.478507 AAGGGGACACAAGAACTGGG 59.521 55.000 0.00 0.00 0.00 4.45
3640 7130 0.185175 GGGGACACAAGAACTGGGTT 59.815 55.000 0.00 0.00 43.76 4.11
3641 7131 1.318576 GGGACACAAGAACTGGGTTG 58.681 55.000 0.00 0.00 43.76 3.77
3642 7132 1.409661 GGGACACAAGAACTGGGTTGT 60.410 52.381 0.00 0.00 43.76 3.32
3647 7137 2.586425 ACAAGAACTGGGTTGTGATGG 58.414 47.619 0.00 0.00 35.55 3.51
3648 7138 2.174639 ACAAGAACTGGGTTGTGATGGA 59.825 45.455 0.00 0.00 35.55 3.41
3649 7139 3.221771 CAAGAACTGGGTTGTGATGGAA 58.778 45.455 0.00 0.00 0.00 3.53
3650 7140 3.593442 AGAACTGGGTTGTGATGGAAA 57.407 42.857 0.00 0.00 0.00 3.13
3651 7141 3.490348 AGAACTGGGTTGTGATGGAAAG 58.510 45.455 0.00 0.00 0.00 2.62
3652 7142 3.117512 AGAACTGGGTTGTGATGGAAAGT 60.118 43.478 0.00 0.00 0.00 2.66
3653 7143 3.312736 ACTGGGTTGTGATGGAAAGTT 57.687 42.857 0.00 0.00 0.00 2.66
3654 7144 3.642141 ACTGGGTTGTGATGGAAAGTTT 58.358 40.909 0.00 0.00 0.00 2.66
3655 7145 4.030216 ACTGGGTTGTGATGGAAAGTTTT 58.970 39.130 0.00 0.00 0.00 2.43
3656 7146 5.205056 ACTGGGTTGTGATGGAAAGTTTTA 58.795 37.500 0.00 0.00 0.00 1.52
3657 7147 5.659079 ACTGGGTTGTGATGGAAAGTTTTAA 59.341 36.000 0.00 0.00 0.00 1.52
3658 7148 6.326323 ACTGGGTTGTGATGGAAAGTTTTAAT 59.674 34.615 0.00 0.00 0.00 1.40
3659 7149 7.507616 ACTGGGTTGTGATGGAAAGTTTTAATA 59.492 33.333 0.00 0.00 0.00 0.98
3660 7150 8.251383 TGGGTTGTGATGGAAAGTTTTAATAA 57.749 30.769 0.00 0.00 0.00 1.40
3661 7151 8.875168 TGGGTTGTGATGGAAAGTTTTAATAAT 58.125 29.630 0.00 0.00 0.00 1.28
3662 7152 9.719355 GGGTTGTGATGGAAAGTTTTAATAATT 57.281 29.630 0.00 0.00 0.00 1.40
3669 7159 9.463443 GATGGAAAGTTTTAATAATTGGATCCG 57.537 33.333 7.39 0.00 0.00 4.18
3670 7160 7.777095 TGGAAAGTTTTAATAATTGGATCCGG 58.223 34.615 7.39 0.00 0.00 5.14
3671 7161 7.147811 TGGAAAGTTTTAATAATTGGATCCGGG 60.148 37.037 7.39 0.00 0.00 5.73
3672 7162 7.068962 GGAAAGTTTTAATAATTGGATCCGGGA 59.931 37.037 7.39 0.00 0.00 5.14
3673 7163 6.954487 AGTTTTAATAATTGGATCCGGGAC 57.046 37.500 7.39 0.00 0.00 4.46
3674 7164 6.428295 AGTTTTAATAATTGGATCCGGGACA 58.572 36.000 7.39 0.00 0.00 4.02
3675 7165 6.893005 AGTTTTAATAATTGGATCCGGGACAA 59.107 34.615 7.39 5.14 0.00 3.18
3676 7166 7.563556 AGTTTTAATAATTGGATCCGGGACAAT 59.436 33.333 7.39 7.49 36.46 2.71
3677 7167 6.892658 TTAATAATTGGATCCGGGACAATG 57.107 37.500 16.24 0.00 35.22 2.82
3678 7168 1.402787 AATTGGATCCGGGACAATGC 58.597 50.000 16.24 3.18 35.22 3.56
3679 7169 0.552848 ATTGGATCCGGGACAATGCT 59.447 50.000 15.22 0.00 33.87 3.79
3680 7170 1.208706 TTGGATCCGGGACAATGCTA 58.791 50.000 7.39 0.00 0.00 3.49
3681 7171 1.434188 TGGATCCGGGACAATGCTAT 58.566 50.000 7.39 0.00 0.00 2.97
3682 7172 1.072173 TGGATCCGGGACAATGCTATG 59.928 52.381 7.39 0.00 0.00 2.23
3683 7173 1.611673 GGATCCGGGACAATGCTATGG 60.612 57.143 0.00 0.00 0.00 2.74
3684 7174 1.347707 GATCCGGGACAATGCTATGGA 59.652 52.381 0.00 0.00 0.00 3.41
3685 7175 1.434188 TCCGGGACAATGCTATGGAT 58.566 50.000 0.00 0.00 0.00 3.41
3686 7176 1.072173 TCCGGGACAATGCTATGGATG 59.928 52.381 0.00 0.00 0.00 3.51
3687 7177 1.072173 CCGGGACAATGCTATGGATGA 59.928 52.381 0.00 0.00 0.00 2.92
3688 7178 2.146342 CGGGACAATGCTATGGATGAC 58.854 52.381 0.00 0.00 0.00 3.06
3689 7179 2.485302 CGGGACAATGCTATGGATGACA 60.485 50.000 0.00 0.00 0.00 3.58
3690 7180 3.759581 GGGACAATGCTATGGATGACAT 58.240 45.455 0.00 0.00 43.68 3.06
3691 7181 3.755378 GGGACAATGCTATGGATGACATC 59.245 47.826 6.91 6.91 41.03 3.06
3692 7182 3.434641 GGACAATGCTATGGATGACATCG 59.565 47.826 9.31 0.00 41.03 3.84
3693 7183 4.309933 GACAATGCTATGGATGACATCGA 58.690 43.478 9.31 5.97 41.03 3.59
3694 7184 4.903054 ACAATGCTATGGATGACATCGAT 58.097 39.130 16.03 16.03 41.03 3.59
3695 7185 4.694037 ACAATGCTATGGATGACATCGATG 59.306 41.667 23.68 23.68 41.03 3.84
3696 7186 4.548451 ATGCTATGGATGACATCGATGT 57.452 40.909 30.37 30.37 45.16 3.06
3707 7197 2.699954 ACATCGATGTCTCCAACCAAC 58.300 47.619 25.18 0.00 35.87 3.77
3708 7198 2.038426 ACATCGATGTCTCCAACCAACA 59.962 45.455 25.18 0.00 35.87 3.33
3709 7199 2.455674 TCGATGTCTCCAACCAACAG 57.544 50.000 0.00 0.00 0.00 3.16
3710 7200 1.691976 TCGATGTCTCCAACCAACAGT 59.308 47.619 0.00 0.00 0.00 3.55
3711 7201 2.104111 TCGATGTCTCCAACCAACAGTT 59.896 45.455 0.00 0.00 40.16 3.16
3712 7202 2.480419 CGATGTCTCCAACCAACAGTTC 59.520 50.000 0.00 0.00 36.18 3.01
3713 7203 3.476552 GATGTCTCCAACCAACAGTTCA 58.523 45.455 0.00 0.00 36.18 3.18
3714 7204 2.639065 TGTCTCCAACCAACAGTTCAC 58.361 47.619 0.00 0.00 36.18 3.18
3715 7205 2.238646 TGTCTCCAACCAACAGTTCACT 59.761 45.455 0.00 0.00 36.18 3.41
3716 7206 3.279434 GTCTCCAACCAACAGTTCACTT 58.721 45.455 0.00 0.00 36.18 3.16
3717 7207 3.065371 GTCTCCAACCAACAGTTCACTTG 59.935 47.826 0.00 0.00 36.18 3.16
3718 7208 2.358898 CTCCAACCAACAGTTCACTTGG 59.641 50.000 6.75 6.75 42.45 3.61
3721 7211 1.663695 ACCAACAGTTCACTTGGTCG 58.336 50.000 0.00 0.00 45.94 4.79
3722 7212 0.944386 CCAACAGTTCACTTGGTCGG 59.056 55.000 0.00 0.00 33.46 4.79
3723 7213 1.474320 CCAACAGTTCACTTGGTCGGA 60.474 52.381 0.00 0.00 33.46 4.55
3724 7214 1.597663 CAACAGTTCACTTGGTCGGAC 59.402 52.381 0.00 0.00 0.00 4.79
3725 7215 0.828022 ACAGTTCACTTGGTCGGACA 59.172 50.000 10.76 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 8.627208 ACATATGTGAACTTCAGATCAAAGTT 57.373 30.769 20.11 20.11 46.74 2.66
42 43 1.616628 ACCCCTCCCAACCAGCTAG 60.617 63.158 0.00 0.00 0.00 3.42
44 45 2.936032 GACCCCTCCCAACCAGCT 60.936 66.667 0.00 0.00 0.00 4.24
127 128 3.584848 AGCATCTCCAAGGTAGAACTTGT 59.415 43.478 6.57 0.00 44.89 3.16
163 164 0.179702 GGGTGGAAGAATACCCGACC 59.820 60.000 0.00 0.00 46.42 4.79
243 244 3.317455 TTATGGGTAGAACGGCTCCTA 57.683 47.619 0.00 0.00 0.00 2.94
251 342 4.409247 ACCTGAGTGGATTATGGGTAGAAC 59.591 45.833 0.00 0.00 39.71 3.01
255 346 6.445786 AGTTTAACCTGAGTGGATTATGGGTA 59.554 38.462 0.00 0.00 39.71 3.69
263 354 5.941788 AGAACAAGTTTAACCTGAGTGGAT 58.058 37.500 0.26 0.00 39.71 3.41
278 369 6.498304 CAGAATGCAACAAGTAAGAACAAGT 58.502 36.000 0.00 0.00 0.00 3.16
310 401 0.035056 AAAGCCCCACTGAAGGATCG 60.035 55.000 0.00 0.00 0.00 3.69
317 408 0.322816 GCTCATCAAAGCCCCACTGA 60.323 55.000 0.00 0.00 36.22 3.41
335 426 0.747283 CTTCCTCCTCAGGCATGTGC 60.747 60.000 0.00 0.00 40.12 4.57
339 430 0.043940 ACCTCTTCCTCCTCAGGCAT 59.956 55.000 0.00 0.00 40.12 4.40
391 722 4.940046 ACAAATGACAGCTCATCCTAACTG 59.060 41.667 0.00 0.00 35.96 3.16
499 830 6.571344 GCACATATGACATTGGTGTTTGGTTA 60.571 38.462 10.38 0.00 39.09 2.85
511 842 3.058016 GCATTAGGCGCACATATGACATT 60.058 43.478 10.83 0.00 0.00 2.71
552 883 5.004361 TGAGATAACCATTTTTGACCCCA 57.996 39.130 0.00 0.00 0.00 4.96
553 884 5.682212 GCATGAGATAACCATTTTTGACCCC 60.682 44.000 0.00 0.00 0.00 4.95
569 900 4.818546 GCATGTACCTTAGTTGCATGAGAT 59.181 41.667 11.46 0.00 38.96 2.75
625 956 1.304381 TTTGAGGGGATGCAGGCAC 60.304 57.895 0.00 0.00 0.00 5.01
706 1037 6.681541 ACCATAAGGACCCCTAAAAGAACTAT 59.318 38.462 0.00 0.00 38.69 2.12
714 1045 2.937442 ACCACCATAAGGACCCCTAAA 58.063 47.619 0.00 0.00 38.69 1.85
715 1046 2.672703 ACCACCATAAGGACCCCTAA 57.327 50.000 0.00 0.00 38.69 2.69
716 1047 4.758283 GCTATACCACCATAAGGACCCCTA 60.758 50.000 0.00 0.00 38.69 3.53
717 1048 2.910360 ATACCACCATAAGGACCCCT 57.090 50.000 0.00 0.00 38.69 4.79
719 1050 3.248888 AGCTATACCACCATAAGGACCC 58.751 50.000 0.00 0.00 38.69 4.46
720 1051 4.976540 AAGCTATACCACCATAAGGACC 57.023 45.455 0.00 0.00 38.69 4.46
742 1073 5.458508 GCTATACCCCATAAGCCCCTAAAAA 60.459 44.000 0.00 0.00 0.00 1.94
743 1074 4.043686 GCTATACCCCATAAGCCCCTAAAA 59.956 45.833 0.00 0.00 0.00 1.52
744 1075 3.590182 GCTATACCCCATAAGCCCCTAAA 59.410 47.826 0.00 0.00 0.00 1.85
745 1076 3.181388 AGCTATACCCCATAAGCCCCTAA 60.181 47.826 0.00 0.00 0.00 2.69
746 1077 2.389267 AGCTATACCCCATAAGCCCCTA 59.611 50.000 0.00 0.00 0.00 3.53
747 1078 1.154434 AGCTATACCCCATAAGCCCCT 59.846 52.381 0.00 0.00 0.00 4.79
748 1079 1.282157 CAGCTATACCCCATAAGCCCC 59.718 57.143 0.00 0.00 0.00 5.80
749 1080 1.985895 ACAGCTATACCCCATAAGCCC 59.014 52.381 0.00 0.00 0.00 5.19
750 1081 3.838903 AGTACAGCTATACCCCATAAGCC 59.161 47.826 0.00 0.00 0.00 4.35
752 1083 6.249951 AGAGAGTACAGCTATACCCCATAAG 58.750 44.000 0.00 0.00 0.00 1.73
753 1084 6.215515 AGAGAGTACAGCTATACCCCATAA 57.784 41.667 0.00 0.00 0.00 1.90
754 1085 5.281089 GGAGAGAGTACAGCTATACCCCATA 60.281 48.000 0.00 0.00 0.00 2.74
756 1087 3.181431 GGAGAGAGTACAGCTATACCCCA 60.181 52.174 0.00 0.00 0.00 4.96
757 1088 3.074836 AGGAGAGAGTACAGCTATACCCC 59.925 52.174 0.00 0.00 0.00 4.95
758 1089 4.376225 AGGAGAGAGTACAGCTATACCC 57.624 50.000 0.00 0.00 0.00 3.69
877 1208 2.589442 TTTCTGCGGTTCGGCGTT 60.589 55.556 6.85 0.00 35.06 4.84
882 1213 2.281208 TGGGGTTTCTGCGGTTCG 60.281 61.111 0.00 0.00 0.00 3.95
1422 4629 1.154073 GTAGGTGACGAGGTCGCAC 60.154 63.158 14.55 14.55 43.87 5.34
1470 4677 0.392327 TCCAGATGATTTCCGCGCAA 60.392 50.000 8.75 0.00 0.00 4.85
1497 4704 1.134068 TCCTCCTCATCGTCGTCATCT 60.134 52.381 0.00 0.00 0.00 2.90
1503 4713 1.644372 CTCGTCCTCCTCATCGTCG 59.356 63.158 0.00 0.00 0.00 5.12
1645 4879 4.051922 GAGTATACGGATGCAAAGGTGAG 58.948 47.826 0.00 0.00 0.00 3.51
1775 5015 8.208224 TGTACTCCACAATACTTTGGGTATATG 58.792 37.037 0.00 0.00 39.94 1.78
1825 5065 8.229253 TCATCTTCAAATATTGGACCAATCAG 57.771 34.615 23.11 11.46 35.54 2.90
1848 5088 1.957177 GTCGGCATGTCCTCTCTATCA 59.043 52.381 0.00 0.00 0.00 2.15
1853 5093 0.179000 AATGGTCGGCATGTCCTCTC 59.821 55.000 0.00 0.00 0.00 3.20
1854 5094 0.107508 CAATGGTCGGCATGTCCTCT 60.108 55.000 0.00 0.00 0.00 3.69
1863 5103 1.097547 CCATGAGGTCAATGGTCGGC 61.098 60.000 0.00 0.00 0.00 5.54
1867 5107 1.216175 CATCCCCATGAGGTCAATGGT 59.784 52.381 0.00 0.00 33.75 3.55
2039 5320 1.403679 CTTCTGCAAAACCAACCACGA 59.596 47.619 0.00 0.00 0.00 4.35
2040 5321 1.535860 CCTTCTGCAAAACCAACCACG 60.536 52.381 0.00 0.00 0.00 4.94
2146 5427 4.460382 GGGCATGACTCTTTTGAAAGATGA 59.540 41.667 0.00 0.00 43.52 2.92
2229 5510 4.868171 CGTAGTTAAAGCTAGTGAATGGCA 59.132 41.667 0.00 0.00 38.00 4.92
2331 5612 2.894126 CTCTACATGCTCCCTCCGTAAT 59.106 50.000 0.00 0.00 0.00 1.89
2492 5936 1.868498 GCGTAAGTGTTTAGTGGCACA 59.132 47.619 21.41 2.83 38.02 4.57
2493 5937 1.868498 TGCGTAAGTGTTTAGTGGCAC 59.132 47.619 10.29 10.29 41.68 5.01
2494 5938 2.242047 TGCGTAAGTGTTTAGTGGCA 57.758 45.000 0.00 0.00 41.68 4.92
2576 6020 2.549992 CCAAGAACATCCACAGAACGGA 60.550 50.000 0.00 0.00 36.84 4.69
2625 6080 2.552743 GGAGCACACTTTGTCCCTTAAC 59.447 50.000 0.00 0.00 0.00 2.01
2660 6117 9.240734 AGAAAACAAAGCTTCATAAGATGATCT 57.759 29.630 0.00 0.00 39.39 2.75
2755 6212 6.702972 TTGTTTTGACGCCATTTGATTATG 57.297 33.333 0.00 0.00 0.00 1.90
2777 6234 4.312443 CAGCAAAAGCAAACAGATCCATT 58.688 39.130 0.00 0.00 0.00 3.16
2863 6320 3.149196 CAAAAGCACATACACCCTGACT 58.851 45.455 0.00 0.00 0.00 3.41
2877 6334 3.591196 AGCACAAACAGAACAAAAGCA 57.409 38.095 0.00 0.00 0.00 3.91
2910 6367 1.723542 GACACAATGACTGCTGACTCG 59.276 52.381 0.00 0.00 0.00 4.18
2916 6373 2.224185 TGTTACGGACACAATGACTGCT 60.224 45.455 0.00 0.00 32.00 4.24
2951 6408 7.035612 CCTTAATTCCTTAGGCAAAACACATC 58.964 38.462 0.00 0.00 0.00 3.06
2961 6418 6.660800 ACTTCCTTACCTTAATTCCTTAGGC 58.339 40.000 0.00 0.00 0.00 3.93
3065 6522 6.350194 CGACATAGCCCAGCTGATTATTAGTA 60.350 42.308 17.39 0.00 40.10 1.82
3067 6524 4.867047 CGACATAGCCCAGCTGATTATTAG 59.133 45.833 17.39 1.79 40.10 1.73
3068 6525 4.526650 TCGACATAGCCCAGCTGATTATTA 59.473 41.667 17.39 0.58 40.10 0.98
3069 6526 3.324846 TCGACATAGCCCAGCTGATTATT 59.675 43.478 17.39 0.00 40.10 1.40
3070 6527 2.899900 TCGACATAGCCCAGCTGATTAT 59.100 45.455 17.39 7.01 40.10 1.28
3117 6574 2.162319 TCGAGCACTTGCACAATACA 57.838 45.000 3.62 0.00 45.16 2.29
3157 6614 9.734620 ATCAAATTTATGAAACCACATATCACG 57.265 29.630 0.00 0.00 33.60 4.35
3190 6648 1.202348 GCTAGTCTTGCTCGCATCTCA 60.202 52.381 0.00 0.00 36.11 3.27
3201 6659 6.250819 CACCAATAAACAATCGCTAGTCTTG 58.749 40.000 0.00 0.00 0.00 3.02
3216 6674 1.404986 CCGTCGCTCTCCACCAATAAA 60.405 52.381 0.00 0.00 0.00 1.40
3236 6694 2.096496 CGAAATGTCATTGGAGGCTGTC 59.904 50.000 0.00 0.00 0.00 3.51
3237 6695 2.086869 CGAAATGTCATTGGAGGCTGT 58.913 47.619 0.00 0.00 0.00 4.40
3240 6698 2.083774 TGTCGAAATGTCATTGGAGGC 58.916 47.619 0.00 0.00 0.00 4.70
3241 6699 6.624352 ATTATGTCGAAATGTCATTGGAGG 57.376 37.500 0.00 0.00 0.00 4.30
3242 6700 7.696755 TCAATTATGTCGAAATGTCATTGGAG 58.303 34.615 13.15 0.00 0.00 3.86
3243 6701 7.552330 TCTCAATTATGTCGAAATGTCATTGGA 59.448 33.333 13.15 0.00 0.00 3.53
3280 6745 4.819105 TTCCACGGTAACTCAATGAGAT 57.181 40.909 18.20 7.86 33.32 2.75
3336 6804 3.612479 GCACACACTCCAATTGATTGTCC 60.612 47.826 7.12 0.00 34.90 4.02
3381 6856 5.654603 TTTCTTGCCTGTCGTATCTCTAA 57.345 39.130 0.00 0.00 0.00 2.10
3384 6859 3.060895 CGTTTTCTTGCCTGTCGTATCTC 59.939 47.826 0.00 0.00 0.00 2.75
3385 6860 2.993899 CGTTTTCTTGCCTGTCGTATCT 59.006 45.455 0.00 0.00 0.00 1.98
3386 6861 2.991190 TCGTTTTCTTGCCTGTCGTATC 59.009 45.455 0.00 0.00 0.00 2.24
3387 6862 2.993899 CTCGTTTTCTTGCCTGTCGTAT 59.006 45.455 0.00 0.00 0.00 3.06
3388 6863 2.400399 CTCGTTTTCTTGCCTGTCGTA 58.600 47.619 0.00 0.00 0.00 3.43
3389 6864 1.217882 CTCGTTTTCTTGCCTGTCGT 58.782 50.000 0.00 0.00 0.00 4.34
3390 6865 0.512952 CCTCGTTTTCTTGCCTGTCG 59.487 55.000 0.00 0.00 0.00 4.35
3432 6907 5.120053 GGTTTTCCATGTAAAAATCTTGCGG 59.880 40.000 0.00 0.00 40.31 5.69
3507 6995 6.539173 TGTATATCCCGGCATTTGTAATCTT 58.461 36.000 0.00 0.00 0.00 2.40
3533 7023 5.416083 CACTACACGGGATAAGTTGATCAA 58.584 41.667 3.38 3.38 0.00 2.57
3566 7056 5.591067 CGAAGTCTCCCAGTAGGATATATCC 59.409 48.000 22.33 22.33 46.33 2.59
3567 7057 6.316890 GTCGAAGTCTCCCAGTAGGATATATC 59.683 46.154 3.96 3.96 46.33 1.63
3568 7058 6.181908 GTCGAAGTCTCCCAGTAGGATATAT 58.818 44.000 0.00 0.00 46.33 0.86
3569 7059 5.072736 TGTCGAAGTCTCCCAGTAGGATATA 59.927 44.000 0.00 0.00 46.33 0.86
3570 7060 4.141228 TGTCGAAGTCTCCCAGTAGGATAT 60.141 45.833 0.00 0.00 46.33 1.63
3571 7061 3.201487 TGTCGAAGTCTCCCAGTAGGATA 59.799 47.826 0.00 0.00 46.33 2.59
3572 7062 2.025226 TGTCGAAGTCTCCCAGTAGGAT 60.025 50.000 0.00 0.00 46.33 3.24
3573 7063 1.353358 TGTCGAAGTCTCCCAGTAGGA 59.647 52.381 0.00 0.00 44.91 2.94
3574 7064 1.835494 TGTCGAAGTCTCCCAGTAGG 58.165 55.000 0.00 0.00 0.00 3.18
3575 7065 2.755655 ACATGTCGAAGTCTCCCAGTAG 59.244 50.000 0.00 0.00 0.00 2.57
3576 7066 2.803956 ACATGTCGAAGTCTCCCAGTA 58.196 47.619 0.00 0.00 0.00 2.74
3577 7067 1.633774 ACATGTCGAAGTCTCCCAGT 58.366 50.000 0.00 0.00 0.00 4.00
3578 7068 2.492088 TGTACATGTCGAAGTCTCCCAG 59.508 50.000 0.00 0.00 0.00 4.45
3579 7069 2.492088 CTGTACATGTCGAAGTCTCCCA 59.508 50.000 0.00 0.00 0.00 4.37
3580 7070 2.753452 TCTGTACATGTCGAAGTCTCCC 59.247 50.000 0.00 0.00 0.00 4.30
3581 7071 4.640789 ATCTGTACATGTCGAAGTCTCC 57.359 45.455 0.00 0.00 0.00 3.71
3582 7072 5.289675 CCAAATCTGTACATGTCGAAGTCTC 59.710 44.000 0.00 0.00 0.00 3.36
3583 7073 5.171476 CCAAATCTGTACATGTCGAAGTCT 58.829 41.667 0.00 0.00 0.00 3.24
3584 7074 4.929808 ACCAAATCTGTACATGTCGAAGTC 59.070 41.667 0.00 0.00 0.00 3.01
3585 7075 4.894784 ACCAAATCTGTACATGTCGAAGT 58.105 39.130 0.00 0.00 0.00 3.01
3586 7076 4.929211 TGACCAAATCTGTACATGTCGAAG 59.071 41.667 0.00 0.00 0.00 3.79
3587 7077 4.688879 GTGACCAAATCTGTACATGTCGAA 59.311 41.667 0.00 0.00 0.00 3.71
3588 7078 4.242475 GTGACCAAATCTGTACATGTCGA 58.758 43.478 0.00 0.00 0.00 4.20
3589 7079 3.060761 CGTGACCAAATCTGTACATGTCG 59.939 47.826 0.00 0.00 0.00 4.35
3590 7080 4.242475 TCGTGACCAAATCTGTACATGTC 58.758 43.478 0.00 0.00 0.00 3.06
3591 7081 4.021456 TCTCGTGACCAAATCTGTACATGT 60.021 41.667 2.69 2.69 0.00 3.21
3592 7082 4.494484 TCTCGTGACCAAATCTGTACATG 58.506 43.478 0.00 0.00 0.00 3.21
3593 7083 4.801330 TCTCGTGACCAAATCTGTACAT 57.199 40.909 0.00 0.00 0.00 2.29
3594 7084 4.594123 TTCTCGTGACCAAATCTGTACA 57.406 40.909 0.00 0.00 0.00 2.90
3595 7085 5.637810 TGATTTCTCGTGACCAAATCTGTAC 59.362 40.000 10.20 0.00 37.40 2.90
3596 7086 5.789521 TGATTTCTCGTGACCAAATCTGTA 58.210 37.500 10.20 0.00 37.40 2.74
3597 7087 4.641396 TGATTTCTCGTGACCAAATCTGT 58.359 39.130 10.20 0.00 37.40 3.41
3598 7088 5.391310 CCTTGATTTCTCGTGACCAAATCTG 60.391 44.000 10.20 5.27 37.40 2.90
3599 7089 4.697352 CCTTGATTTCTCGTGACCAAATCT 59.303 41.667 10.20 0.00 37.40 2.40
3600 7090 4.142600 CCCTTGATTTCTCGTGACCAAATC 60.143 45.833 4.27 4.27 37.14 2.17
3601 7091 3.758554 CCCTTGATTTCTCGTGACCAAAT 59.241 43.478 0.00 0.00 0.00 2.32
3602 7092 3.146066 CCCTTGATTTCTCGTGACCAAA 58.854 45.455 0.00 0.00 0.00 3.28
3603 7093 2.552155 CCCCTTGATTTCTCGTGACCAA 60.552 50.000 0.00 0.00 0.00 3.67
3604 7094 1.003118 CCCCTTGATTTCTCGTGACCA 59.997 52.381 0.00 0.00 0.00 4.02
3605 7095 1.278127 TCCCCTTGATTTCTCGTGACC 59.722 52.381 0.00 0.00 0.00 4.02
3606 7096 2.289444 TGTCCCCTTGATTTCTCGTGAC 60.289 50.000 0.00 0.00 0.00 3.67
3607 7097 1.974957 TGTCCCCTTGATTTCTCGTGA 59.025 47.619 0.00 0.00 0.00 4.35
3608 7098 2.076863 GTGTCCCCTTGATTTCTCGTG 58.923 52.381 0.00 0.00 0.00 4.35
3609 7099 1.697432 TGTGTCCCCTTGATTTCTCGT 59.303 47.619 0.00 0.00 0.00 4.18
3610 7100 2.472695 TGTGTCCCCTTGATTTCTCG 57.527 50.000 0.00 0.00 0.00 4.04
3611 7101 4.021102 TCTTGTGTCCCCTTGATTTCTC 57.979 45.455 0.00 0.00 0.00 2.87
3612 7102 4.141158 AGTTCTTGTGTCCCCTTGATTTCT 60.141 41.667 0.00 0.00 0.00 2.52
3613 7103 4.022849 CAGTTCTTGTGTCCCCTTGATTTC 60.023 45.833 0.00 0.00 0.00 2.17
3614 7104 3.891366 CAGTTCTTGTGTCCCCTTGATTT 59.109 43.478 0.00 0.00 0.00 2.17
3615 7105 3.490348 CAGTTCTTGTGTCCCCTTGATT 58.510 45.455 0.00 0.00 0.00 2.57
3616 7106 2.224867 CCAGTTCTTGTGTCCCCTTGAT 60.225 50.000 0.00 0.00 0.00 2.57
3617 7107 1.142870 CCAGTTCTTGTGTCCCCTTGA 59.857 52.381 0.00 0.00 0.00 3.02
3618 7108 1.609208 CCAGTTCTTGTGTCCCCTTG 58.391 55.000 0.00 0.00 0.00 3.61
3619 7109 0.478507 CCCAGTTCTTGTGTCCCCTT 59.521 55.000 0.00 0.00 0.00 3.95
3620 7110 0.697854 ACCCAGTTCTTGTGTCCCCT 60.698 55.000 0.00 0.00 0.00 4.79
3621 7111 0.185175 AACCCAGTTCTTGTGTCCCC 59.815 55.000 0.00 0.00 0.00 4.81
3622 7112 1.318576 CAACCCAGTTCTTGTGTCCC 58.681 55.000 0.00 0.00 0.00 4.46
3623 7113 1.676006 CACAACCCAGTTCTTGTGTCC 59.324 52.381 2.94 0.00 41.53 4.02
3624 7114 2.639065 TCACAACCCAGTTCTTGTGTC 58.361 47.619 9.65 0.00 45.05 3.67
3625 7115 2.799126 TCACAACCCAGTTCTTGTGT 57.201 45.000 9.65 0.00 45.05 3.72
3626 7116 2.294233 CCATCACAACCCAGTTCTTGTG 59.706 50.000 4.48 4.48 45.81 3.33
3627 7117 2.174639 TCCATCACAACCCAGTTCTTGT 59.825 45.455 0.00 0.00 0.00 3.16
3628 7118 2.862541 TCCATCACAACCCAGTTCTTG 58.137 47.619 0.00 0.00 0.00 3.02
3629 7119 3.593442 TTCCATCACAACCCAGTTCTT 57.407 42.857 0.00 0.00 0.00 2.52
3630 7120 3.117512 ACTTTCCATCACAACCCAGTTCT 60.118 43.478 0.00 0.00 0.00 3.01
3631 7121 3.222603 ACTTTCCATCACAACCCAGTTC 58.777 45.455 0.00 0.00 0.00 3.01
3632 7122 3.312736 ACTTTCCATCACAACCCAGTT 57.687 42.857 0.00 0.00 0.00 3.16
3633 7123 3.312736 AACTTTCCATCACAACCCAGT 57.687 42.857 0.00 0.00 0.00 4.00
3634 7124 4.670896 AAAACTTTCCATCACAACCCAG 57.329 40.909 0.00 0.00 0.00 4.45
3635 7125 6.739331 ATTAAAACTTTCCATCACAACCCA 57.261 33.333 0.00 0.00 0.00 4.51
3636 7126 9.719355 AATTATTAAAACTTTCCATCACAACCC 57.281 29.630 0.00 0.00 0.00 4.11
3643 7133 9.463443 CGGATCCAATTATTAAAACTTTCCATC 57.537 33.333 13.41 0.00 0.00 3.51
3644 7134 8.421002 CCGGATCCAATTATTAAAACTTTCCAT 58.579 33.333 13.41 0.00 0.00 3.41
3645 7135 7.147811 CCCGGATCCAATTATTAAAACTTTCCA 60.148 37.037 13.41 0.00 0.00 3.53
3646 7136 7.068962 TCCCGGATCCAATTATTAAAACTTTCC 59.931 37.037 13.41 0.00 0.00 3.13
3647 7137 7.919091 GTCCCGGATCCAATTATTAAAACTTTC 59.081 37.037 13.41 0.00 0.00 2.62
3648 7138 7.397761 TGTCCCGGATCCAATTATTAAAACTTT 59.602 33.333 13.41 0.00 0.00 2.66
3649 7139 6.893005 TGTCCCGGATCCAATTATTAAAACTT 59.107 34.615 13.41 0.00 0.00 2.66
3650 7140 6.428295 TGTCCCGGATCCAATTATTAAAACT 58.572 36.000 13.41 0.00 0.00 2.66
3651 7141 6.702716 TGTCCCGGATCCAATTATTAAAAC 57.297 37.500 13.41 0.00 0.00 2.43
3652 7142 7.685641 GCATTGTCCCGGATCCAATTATTAAAA 60.686 37.037 13.41 0.00 0.00 1.52
3653 7143 6.239176 GCATTGTCCCGGATCCAATTATTAAA 60.239 38.462 13.41 0.00 0.00 1.52
3654 7144 5.242838 GCATTGTCCCGGATCCAATTATTAA 59.757 40.000 13.41 0.00 0.00 1.40
3655 7145 4.764823 GCATTGTCCCGGATCCAATTATTA 59.235 41.667 13.41 0.00 0.00 0.98
3656 7146 3.573967 GCATTGTCCCGGATCCAATTATT 59.426 43.478 13.41 0.00 0.00 1.40
3657 7147 3.157087 GCATTGTCCCGGATCCAATTAT 58.843 45.455 13.41 0.00 0.00 1.28
3658 7148 2.174639 AGCATTGTCCCGGATCCAATTA 59.825 45.455 13.41 0.00 0.00 1.40
3659 7149 1.063717 AGCATTGTCCCGGATCCAATT 60.064 47.619 13.41 0.00 0.00 2.32
3660 7150 0.552848 AGCATTGTCCCGGATCCAAT 59.447 50.000 13.41 5.13 0.00 3.16
3661 7151 1.208706 TAGCATTGTCCCGGATCCAA 58.791 50.000 13.41 2.50 0.00 3.53
3662 7152 1.072173 CATAGCATTGTCCCGGATCCA 59.928 52.381 13.41 0.00 0.00 3.41
3663 7153 1.611673 CCATAGCATTGTCCCGGATCC 60.612 57.143 0.73 0.00 0.00 3.36
3664 7154 1.347707 TCCATAGCATTGTCCCGGATC 59.652 52.381 0.73 0.00 0.00 3.36
3665 7155 1.434188 TCCATAGCATTGTCCCGGAT 58.566 50.000 0.73 0.00 0.00 4.18
3666 7156 1.072173 CATCCATAGCATTGTCCCGGA 59.928 52.381 0.73 0.00 0.00 5.14
3667 7157 1.072173 TCATCCATAGCATTGTCCCGG 59.928 52.381 0.00 0.00 0.00 5.73
3668 7158 2.146342 GTCATCCATAGCATTGTCCCG 58.854 52.381 0.00 0.00 0.00 5.14
3669 7159 3.213206 TGTCATCCATAGCATTGTCCC 57.787 47.619 0.00 0.00 0.00 4.46
3670 7160 3.434641 CGATGTCATCCATAGCATTGTCC 59.565 47.826 7.25 0.00 32.56 4.02
3671 7161 4.309933 TCGATGTCATCCATAGCATTGTC 58.690 43.478 7.25 0.00 32.56 3.18
3672 7162 4.341366 TCGATGTCATCCATAGCATTGT 57.659 40.909 7.25 0.00 32.56 2.71
3673 7163 4.694037 ACATCGATGTCATCCATAGCATTG 59.306 41.667 25.18 0.00 35.87 2.82
3674 7164 4.903054 ACATCGATGTCATCCATAGCATT 58.097 39.130 25.18 0.00 35.87 3.56
3675 7165 4.548451 ACATCGATGTCATCCATAGCAT 57.452 40.909 25.18 0.00 35.87 3.79
3687 7177 2.038426 TGTTGGTTGGAGACATCGATGT 59.962 45.455 30.37 30.37 45.16 3.06
3688 7178 2.674852 CTGTTGGTTGGAGACATCGATG 59.325 50.000 23.68 23.68 42.32 3.84
3689 7179 2.303022 ACTGTTGGTTGGAGACATCGAT 59.697 45.455 0.00 0.00 42.32 3.59
3690 7180 1.691976 ACTGTTGGTTGGAGACATCGA 59.308 47.619 0.00 0.00 42.32 3.59
3691 7181 2.169832 ACTGTTGGTTGGAGACATCG 57.830 50.000 0.00 0.00 42.32 3.84
3692 7182 3.251004 GTGAACTGTTGGTTGGAGACATC 59.749 47.826 0.00 0.00 42.32 3.06
3693 7183 3.117888 AGTGAACTGTTGGTTGGAGACAT 60.118 43.478 0.00 0.00 42.32 3.06
3694 7184 2.238646 AGTGAACTGTTGGTTGGAGACA 59.761 45.455 0.00 0.00 38.41 3.41
3695 7185 2.919228 AGTGAACTGTTGGTTGGAGAC 58.081 47.619 0.00 0.00 38.41 3.36
3696 7186 3.278574 CAAGTGAACTGTTGGTTGGAGA 58.721 45.455 0.00 0.00 38.41 3.71
3697 7187 2.358898 CCAAGTGAACTGTTGGTTGGAG 59.641 50.000 15.26 0.00 38.77 3.86
3698 7188 2.374184 CCAAGTGAACTGTTGGTTGGA 58.626 47.619 15.26 0.00 38.77 3.53
3699 7189 2.869233 CCAAGTGAACTGTTGGTTGG 57.131 50.000 0.00 4.39 38.77 3.77
3704 7194 1.597663 GTCCGACCAAGTGAACTGTTG 59.402 52.381 0.00 0.00 0.00 3.33
3705 7195 1.208535 TGTCCGACCAAGTGAACTGTT 59.791 47.619 0.00 0.00 0.00 3.16
3706 7196 0.828022 TGTCCGACCAAGTGAACTGT 59.172 50.000 0.00 0.00 0.00 3.55
3707 7197 3.678921 TGTCCGACCAAGTGAACTG 57.321 52.632 0.00 0.00 0.00 3.16



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

AutoCloner maintained by Alex Coulton.