Multiple sequence alignment - TraesCS5D01G291100

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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 TraesCS5D01G291100 chr5D 100.000 2791 0 0 1 2791 388832166 388829376 0.000000e+00 5155.0
1 TraesCS5D01G291100 chr5B 92.295 1207 49 19 774 1953 467228047 467226858 0.000000e+00 1674.0
2 TraesCS5D01G291100 chr5B 89.799 745 39 13 1 713 467228881 467228142 0.000000e+00 920.0
3 TraesCS5D01G291100 chr5B 88.950 181 12 2 2039 2215 467226847 467226671 1.680000e-52 217.0
4 TraesCS5D01G291100 chr5B 91.597 119 6 3 2556 2672 467226089 467225973 8.000000e-36 161.0
5 TraesCS5D01G291100 chr5B 91.071 112 7 2 2562 2671 467178347 467178237 6.230000e-32 148.0
6 TraesCS5D01G291100 chr5A 88.111 1371 88 28 770 2093 491949793 491948451 0.000000e+00 1559.0
7 TraesCS5D01G291100 chr5A 100.000 47 0 0 2276 2322 491948364 491948318 1.380000e-13 87.9
8 TraesCS5D01G291100 chr5A 97.959 49 0 1 2624 2671 491947500 491947452 1.780000e-12 84.2
9 TraesCS5D01G291100 chr5A 90.476 63 4 2 1915 1976 620406360 620406421 6.410000e-12 82.4
10 TraesCS5D01G291100 chr5A 94.737 38 2 0 2211 2248 458968005 458967968 3.000000e-05 60.2
11 TraesCS5D01G291100 chr6A 91.096 146 13 0 177 322 609034187 609034332 6.100000e-47 198.0
12 TraesCS5D01G291100 chr7D 87.097 155 19 1 161 314 575360437 575360591 1.030000e-39 174.0
13 TraesCS5D01G291100 chr6D 86.061 165 18 3 163 326 462199799 462199959 3.700000e-39 172.0
14 TraesCS5D01G291100 chr3A 88.496 113 13 0 201 313 586084416 586084304 1.350000e-28 137.0
15 TraesCS5D01G291100 chr1A 80.952 168 27 5 163 326 20921955 20921789 8.110000e-26 128.0
16 TraesCS5D01G291100 chr4A 93.023 43 2 1 1935 1976 623337197 623337155 8.350000e-06 62.1
17 TraesCS5D01G291100 chr4A 97.143 35 1 0 2215 2249 662113768 662113734 3.000000e-05 60.2
18 TraesCS5D01G291100 chr4A 92.500 40 1 2 2215 2252 7144347 7144308 3.880000e-04 56.5
19 TraesCS5D01G291100 chr7B 97.143 35 1 0 2215 2249 681618860 681618894 3.000000e-05 60.2
20 TraesCS5D01G291100 chr7A 97.143 35 1 0 2215 2249 21259941 21259975 3.000000e-05 60.2
21 TraesCS5D01G291100 chr4B 97.143 35 1 0 2215 2249 568667441 568667475 3.000000e-05 60.2
22 TraesCS5D01G291100 chr3B 97.143 35 1 0 2215 2249 186752876 186752842 3.000000e-05 60.2
23 TraesCS5D01G291100 chr1B 97.059 34 1 0 2216 2249 669921258 669921225 1.080000e-04 58.4
24 TraesCS5D01G291100 chr2A 90.476 42 3 1 2201 2242 747330447 747330487 1.000000e-03 54.7
25 TraesCS5D01G291100 chr4D 96.774 31 1 0 1687 1717 446440400 446440370 5.000000e-03 52.8


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 TraesCS5D01G291100 chr5D 388829376 388832166 2790 True 5155.000000 5155 100.000000 1 2791 1 chr5D.!!$R1 2790
1 TraesCS5D01G291100 chr5B 467225973 467228881 2908 True 743.000000 1674 90.660250 1 2672 4 chr5B.!!$R2 2671
2 TraesCS5D01G291100 chr5A 491947452 491949793 2341 True 577.033333 1559 95.356667 770 2671 3 chr5A.!!$R2 1901

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
301 308 0.242017 GGCACACAACCATGCTCTTC 59.758 55.0 0.0 0.0 41.74 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2260 2398 0.17904 GTTGTCCCTCCGTTCCACAA 60.179 55.0 0.0 0.0 0.0 3.33 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
46 53 7.600375 TGTTCAGCAAACATGAAACAAGTTTAA 59.400 29.630 0.00 0.00 42.95 1.52
211 218 6.149474 CCCGTGGCATTATAATTAAGAAGGAG 59.851 42.308 0.00 0.00 0.00 3.69
238 245 5.008217 TGTGAGACACCAAGTTTTAAATCCG 59.992 40.000 0.00 0.00 32.73 4.18
301 308 0.242017 GGCACACAACCATGCTCTTC 59.758 55.000 0.00 0.00 41.74 2.87
304 311 0.773644 ACACAACCATGCTCTTCCCT 59.226 50.000 0.00 0.00 0.00 4.20
307 314 1.004044 ACAACCATGCTCTTCCCTCTG 59.996 52.381 0.00 0.00 0.00 3.35
332 339 5.044846 GGCTAGGTTCCCATCCACAATATAT 60.045 44.000 0.00 0.00 0.00 0.86
342 349 7.006509 CCCATCCACAATATATTTTCTGGAGT 58.993 38.462 16.24 1.23 31.40 3.85
344 351 9.745018 CCATCCACAATATATTTTCTGGAGTAT 57.255 33.333 16.24 3.87 31.40 2.12
394 422 5.630680 GTCACCAACAACATAAAGATGCAAG 59.369 40.000 0.00 0.00 36.43 4.01
421 449 8.420189 CAGATCTTAAATTTCACTTTGTTTCGC 58.580 33.333 0.00 0.00 0.00 4.70
463 491 5.460646 ACATGAAACTAATGTGAAAAGGCG 58.539 37.500 0.00 0.00 36.89 5.52
474 502 3.546714 AAAAGGCGTCGGAGGGTGG 62.547 63.158 0.00 0.00 0.00 4.61
485 513 2.832129 TCGGAGGGTGGAGCATATTATC 59.168 50.000 0.00 0.00 0.00 1.75
509 537 0.398318 AGTGGGTGGAGCAAGTCTTC 59.602 55.000 0.00 0.00 0.00 2.87
525 553 3.067106 GTCTTCGTGAAATCTCTGCCAA 58.933 45.455 0.00 0.00 0.00 4.52
549 577 2.097110 ACACTGTGTGGAGTCCCTAA 57.903 50.000 13.50 0.00 37.94 2.69
627 658 8.934023 TGACAGAATACAGGGAAATAAACTTT 57.066 30.769 0.00 0.00 0.00 2.66
689 726 7.166691 ACTACTCCTACACGTGAAATATTGT 57.833 36.000 25.01 13.37 0.00 2.71
690 727 7.033791 ACTACTCCTACACGTGAAATATTGTG 58.966 38.462 25.01 7.55 38.28 3.33
707 744 1.306911 TGGAGCCCAGGACTGCATA 60.307 57.895 0.00 0.00 29.77 3.14
713 750 1.875576 GCCCAGGACTGCATAGATTCG 60.876 57.143 0.00 0.00 0.00 3.34
714 751 1.688735 CCCAGGACTGCATAGATTCGA 59.311 52.381 0.00 0.00 0.00 3.71
715 752 2.103094 CCCAGGACTGCATAGATTCGAA 59.897 50.000 0.00 0.00 0.00 3.71
717 754 3.993081 CCAGGACTGCATAGATTCGAATC 59.007 47.826 27.16 27.16 35.64 2.52
718 755 4.262377 CCAGGACTGCATAGATTCGAATCT 60.262 45.833 35.72 35.72 46.85 2.40
719 756 4.922692 CAGGACTGCATAGATTCGAATCTC 59.077 45.833 37.12 25.42 44.30 2.75
720 757 4.021544 AGGACTGCATAGATTCGAATCTCC 60.022 45.833 37.12 29.26 44.30 3.71
721 758 4.262207 GGACTGCATAGATTCGAATCTCCA 60.262 45.833 37.12 29.00 44.30 3.86
722 759 5.282055 ACTGCATAGATTCGAATCTCCAA 57.718 39.130 37.12 23.93 44.30 3.53
723 760 5.862845 ACTGCATAGATTCGAATCTCCAAT 58.137 37.500 37.12 24.92 44.30 3.16
724 761 6.997655 ACTGCATAGATTCGAATCTCCAATA 58.002 36.000 37.12 23.26 44.30 1.90
725 762 7.095910 ACTGCATAGATTCGAATCTCCAATAG 58.904 38.462 37.12 28.85 44.30 1.73
726 763 7.039434 ACTGCATAGATTCGAATCTCCAATAGA 60.039 37.037 37.12 21.95 44.30 1.98
728 765 7.978414 TGCATAGATTCGAATCTCCAATAGATC 59.022 37.037 37.12 19.08 44.56 2.75
729 766 7.978414 GCATAGATTCGAATCTCCAATAGATCA 59.022 37.037 37.12 19.99 44.56 2.92
730 767 9.866798 CATAGATTCGAATCTCCAATAGATCAA 57.133 33.333 37.12 19.53 44.56 2.57
732 769 7.385267 AGATTCGAATCTCCAATAGATCAAGG 58.615 38.462 30.53 0.00 44.56 3.61
734 771 3.999663 CGAATCTCCAATAGATCAAGGGC 59.000 47.826 0.00 0.00 44.56 5.19
735 772 3.692257 ATCTCCAATAGATCAAGGGCG 57.308 47.619 0.00 0.00 41.32 6.13
737 774 2.630098 TCTCCAATAGATCAAGGGCGAG 59.370 50.000 0.00 0.00 0.00 5.03
738 775 1.070758 TCCAATAGATCAAGGGCGAGC 59.929 52.381 0.00 0.00 0.00 5.03
739 776 1.517242 CAATAGATCAAGGGCGAGCC 58.483 55.000 5.37 5.37 0.00 4.70
760 797 2.569059 CAGGACTGCATGGATTCGAAT 58.431 47.619 11.20 11.20 0.00 3.34
767 804 3.819337 CTGCATGGATTCGAATCTCCAAT 59.181 43.478 31.32 19.21 44.41 3.16
769 806 4.756642 TGCATGGATTCGAATCTCCAATAC 59.243 41.667 31.32 19.21 44.41 1.89
770 807 4.756642 GCATGGATTCGAATCTCCAATACA 59.243 41.667 31.32 21.13 44.41 2.29
771 808 5.413833 GCATGGATTCGAATCTCCAATACAT 59.586 40.000 31.32 22.17 44.41 2.29
772 809 6.622245 GCATGGATTCGAATCTCCAATACATG 60.622 42.308 31.32 29.56 45.83 3.21
800 873 3.498927 TTACTTTTCTCGGAGGCGTAG 57.501 47.619 4.96 1.14 0.00 3.51
880 958 9.893634 TCCGTTCAAAATATAAATCCTCTTACA 57.106 29.630 0.00 0.00 0.00 2.41
897 975 2.094762 ACATTGACGCCTCTACCAAC 57.905 50.000 0.00 0.00 0.00 3.77
898 976 1.338769 ACATTGACGCCTCTACCAACC 60.339 52.381 0.00 0.00 0.00 3.77
975 1055 3.360533 TCAATCGCGATCTAGAAACGAC 58.639 45.455 23.92 13.39 35.33 4.34
993 1073 0.537188 ACCAACTCGCCGATCAATCT 59.463 50.000 0.00 0.00 0.00 2.40
994 1074 1.212616 CCAACTCGCCGATCAATCTC 58.787 55.000 0.00 0.00 0.00 2.75
995 1075 0.848942 CAACTCGCCGATCAATCTCG 59.151 55.000 0.00 0.00 38.37 4.04
996 1076 0.872021 AACTCGCCGATCAATCTCGC 60.872 55.000 0.00 0.00 37.33 5.03
997 1077 1.299392 CTCGCCGATCAATCTCGCA 60.299 57.895 0.00 0.00 37.33 5.10
998 1078 1.274126 CTCGCCGATCAATCTCGCAG 61.274 60.000 0.00 0.00 37.33 5.18
1035 1118 0.620700 GGTTTGCTCCCCTCCTCCTA 60.621 60.000 0.00 0.00 0.00 2.94
1242 1328 1.447838 CTGCTACATCGCCAACGGT 60.448 57.895 0.00 0.00 40.63 4.83
1360 1446 3.490419 CGACAGTAAGTAGCCACCATACC 60.490 52.174 0.00 0.00 0.00 2.73
1368 1454 1.819632 GCCACCATACCAAGCCTCG 60.820 63.158 0.00 0.00 0.00 4.63
1385 1471 2.095718 CCTCGCATGATCGATCGAACTA 60.096 50.000 23.50 11.64 37.87 2.24
1386 1472 2.905546 CTCGCATGATCGATCGAACTAC 59.094 50.000 23.50 13.84 37.87 2.73
1387 1473 1.639475 CGCATGATCGATCGAACTACG 59.361 52.381 23.50 18.76 44.09 3.51
1388 1474 2.651701 GCATGATCGATCGAACTACGT 58.348 47.619 23.50 12.05 43.13 3.57
1389 1475 3.663493 CGCATGATCGATCGAACTACGTA 60.663 47.826 23.50 3.21 43.13 3.57
1390 1476 4.404324 GCATGATCGATCGAACTACGTAT 58.596 43.478 23.50 5.63 43.13 3.06
1391 1477 5.557388 GCATGATCGATCGAACTACGTATA 58.443 41.667 23.50 1.65 43.13 1.47
1398 1484 6.903419 TCGATCGAACTACGTATACTCTCTA 58.097 40.000 16.99 0.00 43.13 2.43
1403 1489 8.116651 TCGAACTACGTATACTCTCTACCTAT 57.883 38.462 0.00 0.00 43.13 2.57
1549 1642 5.517322 CCTTCAGGTATGTACTGGTAGTC 57.483 47.826 0.00 0.00 36.62 2.59
1550 1643 4.036498 CCTTCAGGTATGTACTGGTAGTCG 59.964 50.000 0.00 0.00 36.62 4.18
1551 1644 2.947652 TCAGGTATGTACTGGTAGTCGC 59.052 50.000 0.00 0.00 36.62 5.19
1569 1662 1.203928 GCTTGACACCGAGATCGATG 58.796 55.000 0.54 0.00 43.02 3.84
1573 1666 0.744874 GACACCGAGATCGATGGGAA 59.255 55.000 0.54 0.00 37.14 3.97
1575 1668 1.134788 ACACCGAGATCGATGGGAAAC 60.135 52.381 0.54 0.00 37.14 2.78
1727 1824 0.467384 CCTCCGGCAGTGATCAATCT 59.533 55.000 0.00 0.00 0.00 2.40
1808 1905 0.383231 GAAGATGGGAATTGCAGCCG 59.617 55.000 0.00 0.00 0.00 5.52
1838 1935 5.306419 AGCTATGATATCAGGACTTGCAGAA 59.694 40.000 11.78 0.00 0.00 3.02
1841 1938 7.986320 GCTATGATATCAGGACTTGCAGAATAT 59.014 37.037 11.78 0.00 0.00 1.28
1868 1982 9.604626 GAATATTAGCTGCAGATTGAAACATAC 57.395 33.333 20.43 0.00 0.00 2.39
1956 2085 7.841282 TCAAATAGGTAGGAGTTAGATGAGG 57.159 40.000 0.00 0.00 0.00 3.86
1960 2089 4.625963 AGGTAGGAGTTAGATGAGGCTTT 58.374 43.478 0.00 0.00 0.00 3.51
1961 2090 4.407296 AGGTAGGAGTTAGATGAGGCTTTG 59.593 45.833 0.00 0.00 0.00 2.77
1965 2094 6.374417 AGGAGTTAGATGAGGCTTTGTTAA 57.626 37.500 0.00 0.00 0.00 2.01
1982 2111 7.225734 GCTTTGTTAATTCTCATCTACTCCCTC 59.774 40.741 0.00 0.00 0.00 4.30
1985 2114 9.661954 TTGTTAATTCTCATCTACTCCCTCTAT 57.338 33.333 0.00 0.00 0.00 1.98
2065 2199 8.443176 AGGAATAGATGAGAATTAGCAAATCCA 58.557 33.333 0.00 0.00 0.00 3.41
2079 2217 8.627487 TTAGCAAATCCATTGTTTTATTAGCG 57.373 30.769 0.00 0.00 41.32 4.26
2087 2225 8.909708 TCCATTGTTTTATTAGCGAAATTCTG 57.090 30.769 0.00 0.00 0.00 3.02
2128 2266 2.806244 GGTGTTTCTTGCGTGTATGACT 59.194 45.455 0.00 0.00 0.00 3.41
2170 2308 6.127535 GCCTATATCCAAGTGCATGCATTAAT 60.128 38.462 25.64 15.64 0.00 1.40
2171 2309 7.578189 GCCTATATCCAAGTGCATGCATTAATT 60.578 37.037 25.64 13.52 0.00 1.40
2172 2310 8.959548 CCTATATCCAAGTGCATGCATTAATTA 58.040 33.333 25.64 11.99 0.00 1.40
2179 2317 7.096353 CCAAGTGCATGCATTAATTAAATCGAG 60.096 37.037 25.64 4.76 0.00 4.04
2187 2325 5.693814 CATTAATTAAATCGAGCAGGAGGC 58.306 41.667 1.21 0.00 45.30 4.70
2221 2359 4.838904 ACTTTAACCATGTACTCCCTCC 57.161 45.455 0.00 0.00 0.00 4.30
2222 2360 3.522343 ACTTTAACCATGTACTCCCTCCC 59.478 47.826 0.00 0.00 0.00 4.30
2223 2361 2.953093 TAACCATGTACTCCCTCCCA 57.047 50.000 0.00 0.00 0.00 4.37
2224 2362 2.286935 AACCATGTACTCCCTCCCAT 57.713 50.000 0.00 0.00 0.00 4.00
2225 2363 3.431411 AACCATGTACTCCCTCCCATA 57.569 47.619 0.00 0.00 0.00 2.74
2226 2364 3.431411 ACCATGTACTCCCTCCCATAA 57.569 47.619 0.00 0.00 0.00 1.90
2227 2365 3.954662 ACCATGTACTCCCTCCCATAAT 58.045 45.455 0.00 0.00 0.00 1.28
2228 2366 5.101254 ACCATGTACTCCCTCCCATAATA 57.899 43.478 0.00 0.00 0.00 0.98
2229 2367 5.676125 ACCATGTACTCCCTCCCATAATAT 58.324 41.667 0.00 0.00 0.00 1.28
2230 2368 6.822374 ACCATGTACTCCCTCCCATAATATA 58.178 40.000 0.00 0.00 0.00 0.86
2231 2369 7.260891 ACCATGTACTCCCTCCCATAATATAA 58.739 38.462 0.00 0.00 0.00 0.98
2232 2370 7.403231 ACCATGTACTCCCTCCCATAATATAAG 59.597 40.741 0.00 0.00 0.00 1.73
2233 2371 7.623677 CCATGTACTCCCTCCCATAATATAAGA 59.376 40.741 0.00 0.00 0.00 2.10
2234 2372 8.700051 CATGTACTCCCTCCCATAATATAAGAG 58.300 40.741 0.00 0.00 0.00 2.85
2235 2373 7.776745 TGTACTCCCTCCCATAATATAAGAGT 58.223 38.462 0.00 0.00 36.18 3.24
2236 2374 7.674348 TGTACTCCCTCCCATAATATAAGAGTG 59.326 40.741 0.00 0.00 34.19 3.51
2237 2375 6.635021 ACTCCCTCCCATAATATAAGAGTGT 58.365 40.000 0.00 0.00 31.21 3.55
2238 2376 7.082972 ACTCCCTCCCATAATATAAGAGTGTT 58.917 38.462 0.00 0.00 31.21 3.32
2239 2377 7.572861 ACTCCCTCCCATAATATAAGAGTGTTT 59.427 37.037 0.00 0.00 31.21 2.83
2240 2378 8.344939 TCCCTCCCATAATATAAGAGTGTTTT 57.655 34.615 0.00 0.00 0.00 2.43
2241 2379 8.787818 TCCCTCCCATAATATAAGAGTGTTTTT 58.212 33.333 0.00 0.00 0.00 1.94
2242 2380 8.850156 CCCTCCCATAATATAAGAGTGTTTTTG 58.150 37.037 0.00 0.00 0.00 2.44
2243 2381 9.627123 CCTCCCATAATATAAGAGTGTTTTTGA 57.373 33.333 0.00 0.00 0.00 2.69
2245 2383 9.967451 TCCCATAATATAAGAGTGTTTTTGACA 57.033 29.630 0.00 0.00 35.42 3.58
2272 2410 9.976511 TTATAGTTCTTATATTGTGGAACGGAG 57.023 33.333 0.00 0.00 42.39 4.63
2273 2411 5.671493 AGTTCTTATATTGTGGAACGGAGG 58.329 41.667 0.00 0.00 42.39 4.30
2274 2412 4.682778 TCTTATATTGTGGAACGGAGGG 57.317 45.455 0.00 0.00 42.39 4.30
2275 2413 4.291792 TCTTATATTGTGGAACGGAGGGA 58.708 43.478 0.00 0.00 42.39 4.20
2276 2414 4.100498 TCTTATATTGTGGAACGGAGGGAC 59.900 45.833 0.00 0.00 42.39 4.46
2277 2415 1.646912 TATTGTGGAACGGAGGGACA 58.353 50.000 0.00 0.00 42.39 4.02
2278 2416 0.768622 ATTGTGGAACGGAGGGACAA 59.231 50.000 0.00 0.00 42.39 3.18
2279 2417 0.179040 TTGTGGAACGGAGGGACAAC 60.179 55.000 0.00 0.00 42.39 3.32
2280 2418 1.338890 TGTGGAACGGAGGGACAACA 61.339 55.000 0.00 0.00 42.39 3.33
2281 2419 0.179040 GTGGAACGGAGGGACAACAA 60.179 55.000 0.00 0.00 0.00 2.83
2282 2420 0.768622 TGGAACGGAGGGACAACAAT 59.231 50.000 0.00 0.00 0.00 2.71
2283 2421 1.165270 GGAACGGAGGGACAACAATG 58.835 55.000 0.00 0.00 0.00 2.82
2284 2422 1.544759 GGAACGGAGGGACAACAATGT 60.545 52.381 0.00 0.00 44.25 2.71
2285 2423 2.289819 GGAACGGAGGGACAACAATGTA 60.290 50.000 0.00 0.00 40.74 2.29
2286 2424 3.404899 GAACGGAGGGACAACAATGTAA 58.595 45.455 0.00 0.00 40.74 2.41
2287 2425 3.713826 ACGGAGGGACAACAATGTAAT 57.286 42.857 0.00 0.00 40.74 1.89
2288 2426 4.028993 ACGGAGGGACAACAATGTAATT 57.971 40.909 0.00 0.00 40.74 1.40
2289 2427 4.403734 ACGGAGGGACAACAATGTAATTT 58.596 39.130 0.00 0.00 40.74 1.82
2346 2504 5.990668 ACCCATATTACTGAGTTTCTCCAC 58.009 41.667 0.00 0.00 0.00 4.02
2352 2510 6.672266 ATTACTGAGTTTCTCCACTCTCAA 57.328 37.500 0.00 0.00 43.32 3.02
2353 2511 4.329462 ACTGAGTTTCTCCACTCTCAAC 57.671 45.455 2.70 0.00 43.32 3.18
2359 2517 4.276926 AGTTTCTCCACTCTCAACATTTGC 59.723 41.667 0.00 0.00 0.00 3.68
2360 2518 2.416747 TCTCCACTCTCAACATTTGCG 58.583 47.619 0.00 0.00 0.00 4.85
2391 2549 2.019249 TGGTTCCTACGATACTCACCG 58.981 52.381 0.00 0.00 0.00 4.94
2396 2554 0.663688 CTACGATACTCACCGCTGCT 59.336 55.000 0.00 0.00 0.00 4.24
2397 2555 0.380733 TACGATACTCACCGCTGCTG 59.619 55.000 0.00 0.00 0.00 4.41
2430 2590 5.458041 AAGCAATGCTTCTTTCTTAGCAA 57.542 34.783 15.60 0.00 46.77 3.91
2431 2591 5.846203 AAGCAATGCTTCTTTCTTAGCAAA 58.154 33.333 15.60 0.00 46.77 3.68
2433 2593 6.423001 AAGCAATGCTTCTTTCTTAGCAAAAG 59.577 34.615 15.60 0.00 46.77 2.27
2434 2594 7.899747 AAGCAATGCTTCTTTCTTAGCAAAAGT 60.900 33.333 15.60 0.00 46.77 2.66
2438 2598 7.190920 TGCTTCTTTCTTAGCAAAAGTAGTC 57.809 36.000 0.00 0.00 43.88 2.59
2439 2599 6.992715 TGCTTCTTTCTTAGCAAAAGTAGTCT 59.007 34.615 0.00 0.00 43.88 3.24
2441 2601 8.436970 GCTTCTTTCTTAGCAAAAGTAGTCTAC 58.563 37.037 1.39 1.39 35.07 2.59
2443 2603 9.477484 TTCTTTCTTAGCAAAAGTAGTCTACAG 57.523 33.333 12.54 0.00 35.64 2.74
2444 2604 7.599245 TCTTTCTTAGCAAAAGTAGTCTACAGC 59.401 37.037 12.54 9.93 35.64 4.40
2455 2899 0.172803 GTCTACAGCCACCTACACCG 59.827 60.000 0.00 0.00 0.00 4.94
2473 2917 1.679139 CGCCTCTCTGAGATGACTCT 58.321 55.000 13.26 0.00 42.99 3.24
2489 2966 7.046652 AGATGACTCTTTTGGTCAGACATATG 58.953 38.462 2.17 0.00 45.14 1.78
2506 2983 0.258774 ATGGATCCTCCCAAAACCCG 59.741 55.000 14.23 0.00 40.04 5.28
2507 2984 1.137594 TGGATCCTCCCAAAACCCGT 61.138 55.000 14.23 0.00 35.03 5.28
2508 2985 0.913924 GGATCCTCCCAAAACCCGTA 59.086 55.000 3.84 0.00 0.00 4.02
2509 2986 1.134189 GGATCCTCCCAAAACCCGTAG 60.134 57.143 3.84 0.00 0.00 3.51
2510 2987 0.255033 ATCCTCCCAAAACCCGTAGC 59.745 55.000 0.00 0.00 0.00 3.58
2511 2988 1.378119 CCTCCCAAAACCCGTAGCC 60.378 63.158 0.00 0.00 0.00 3.93
2512 2989 1.377229 CTCCCAAAACCCGTAGCCA 59.623 57.895 0.00 0.00 0.00 4.75
2513 2990 0.250989 CTCCCAAAACCCGTAGCCAA 60.251 55.000 0.00 0.00 0.00 4.52
2514 2991 0.185416 TCCCAAAACCCGTAGCCAAA 59.815 50.000 0.00 0.00 0.00 3.28
2515 2992 1.041437 CCCAAAACCCGTAGCCAAAA 58.959 50.000 0.00 0.00 0.00 2.44
2516 2993 1.413077 CCCAAAACCCGTAGCCAAAAA 59.587 47.619 0.00 0.00 0.00 1.94
2517 2994 2.037902 CCCAAAACCCGTAGCCAAAAAT 59.962 45.455 0.00 0.00 0.00 1.82
2518 2995 3.495276 CCCAAAACCCGTAGCCAAAAATT 60.495 43.478 0.00 0.00 0.00 1.82
2519 2996 3.743911 CCAAAACCCGTAGCCAAAAATTC 59.256 43.478 0.00 0.00 0.00 2.17
2520 2997 4.372656 CAAAACCCGTAGCCAAAAATTCA 58.627 39.130 0.00 0.00 0.00 2.57
2521 2998 4.674281 AAACCCGTAGCCAAAAATTCAA 57.326 36.364 0.00 0.00 0.00 2.69
2522 2999 4.674281 AACCCGTAGCCAAAAATTCAAA 57.326 36.364 0.00 0.00 0.00 2.69
2523 3000 4.674281 ACCCGTAGCCAAAAATTCAAAA 57.326 36.364 0.00 0.00 0.00 2.44
2524 3001 5.024785 ACCCGTAGCCAAAAATTCAAAAA 57.975 34.783 0.00 0.00 0.00 1.94
2607 3132 1.084289 GACTAACCAATGCCACGACC 58.916 55.000 0.00 0.00 0.00 4.79
2622 3147 1.449601 GACCCGCGATGACCATTGT 60.450 57.895 8.23 0.00 0.00 2.71
2672 3417 1.263752 TGTTGTGCACATGATGACGTG 59.736 47.619 22.39 0.00 38.80 4.49
2676 3421 3.501396 CACATGATGACGTGCCCC 58.499 61.111 0.00 0.00 36.58 5.80
2677 3422 2.125147 ACATGATGACGTGCCCCG 60.125 61.111 0.00 0.00 44.03 5.73
2678 3423 3.576356 CATGATGACGTGCCCCGC 61.576 66.667 0.00 0.00 41.42 6.13
2679 3424 3.785859 ATGATGACGTGCCCCGCT 61.786 61.111 0.00 0.00 41.42 5.52
2680 3425 4.758251 TGATGACGTGCCCCGCTG 62.758 66.667 0.00 0.00 41.42 5.18
2687 3432 4.715523 GTGCCCCGCTGCTACCAA 62.716 66.667 0.00 0.00 0.00 3.67
2688 3433 4.715523 TGCCCCGCTGCTACCAAC 62.716 66.667 0.00 0.00 0.00 3.77
2689 3434 4.715523 GCCCCGCTGCTACCAACA 62.716 66.667 0.00 0.00 0.00 3.33
2690 3435 2.272146 CCCCGCTGCTACCAACAT 59.728 61.111 0.00 0.00 0.00 2.71
2691 3436 1.819632 CCCCGCTGCTACCAACATC 60.820 63.158 0.00 0.00 0.00 3.06
2692 3437 1.221840 CCCGCTGCTACCAACATCT 59.778 57.895 0.00 0.00 0.00 2.90
2693 3438 1.091771 CCCGCTGCTACCAACATCTG 61.092 60.000 0.00 0.00 0.00 2.90
2710 3455 7.819644 CAACATCTGGATAAAAGTTGACATCA 58.180 34.615 0.00 0.00 38.80 3.07
2711 3456 8.298854 CAACATCTGGATAAAAGTTGACATCAA 58.701 33.333 0.00 0.00 38.80 2.57
2712 3457 8.408043 ACATCTGGATAAAAGTTGACATCAAA 57.592 30.769 0.00 0.00 37.63 2.69
2713 3458 8.299570 ACATCTGGATAAAAGTTGACATCAAAC 58.700 33.333 0.00 0.00 37.63 2.93
2714 3459 7.214467 TCTGGATAAAAGTTGACATCAAACC 57.786 36.000 0.00 0.00 37.63 3.27
2715 3460 6.007936 TGGATAAAAGTTGACATCAAACCG 57.992 37.500 0.00 0.00 37.63 4.44
2716 3461 5.765677 TGGATAAAAGTTGACATCAAACCGA 59.234 36.000 0.00 0.00 37.63 4.69
2717 3462 6.432783 TGGATAAAAGTTGACATCAAACCGAT 59.567 34.615 0.00 0.00 37.63 4.18
2718 3463 7.608376 TGGATAAAAGTTGACATCAAACCGATA 59.392 33.333 0.00 0.00 37.63 2.92
2719 3464 8.122952 GGATAAAAGTTGACATCAAACCGATAG 58.877 37.037 0.00 0.00 37.63 2.08
2720 3465 4.946784 AAGTTGACATCAAACCGATAGC 57.053 40.909 0.00 0.00 37.63 2.97
2721 3466 3.937814 AGTTGACATCAAACCGATAGCA 58.062 40.909 0.00 0.00 37.63 3.49
2722 3467 4.517285 AGTTGACATCAAACCGATAGCAT 58.483 39.130 0.00 0.00 37.63 3.79
2723 3468 4.333649 AGTTGACATCAAACCGATAGCATG 59.666 41.667 0.00 0.00 37.63 4.06
2724 3469 3.872696 TGACATCAAACCGATAGCATGT 58.127 40.909 0.00 0.00 31.20 3.21
2725 3470 4.260985 TGACATCAAACCGATAGCATGTT 58.739 39.130 0.00 0.00 31.20 2.71
2726 3471 4.094739 TGACATCAAACCGATAGCATGTTG 59.905 41.667 0.00 0.00 31.20 3.33
2727 3472 4.260985 ACATCAAACCGATAGCATGTTGA 58.739 39.130 0.00 0.00 31.20 3.18
2728 3473 4.883585 ACATCAAACCGATAGCATGTTGAT 59.116 37.500 0.00 0.00 31.20 2.57
2729 3474 4.880886 TCAAACCGATAGCATGTTGATG 57.119 40.909 0.00 0.00 0.00 3.07
2730 3475 3.627123 TCAAACCGATAGCATGTTGATGG 59.373 43.478 0.00 0.00 0.00 3.51
2731 3476 3.281727 AACCGATAGCATGTTGATGGT 57.718 42.857 0.00 0.00 42.93 3.55
2732 3477 4.415881 AACCGATAGCATGTTGATGGTA 57.584 40.909 0.00 0.00 44.59 3.25
2739 3484 6.931790 ATAGCATGTTGATGGTATCTCTCT 57.068 37.500 0.00 0.00 45.95 3.10
2740 3485 5.212532 AGCATGTTGATGGTATCTCTCTC 57.787 43.478 0.00 0.00 38.56 3.20
2741 3486 4.652881 AGCATGTTGATGGTATCTCTCTCA 59.347 41.667 0.00 0.00 38.56 3.27
2742 3487 4.749099 GCATGTTGATGGTATCTCTCTCAC 59.251 45.833 0.00 0.00 0.00 3.51
2743 3488 5.295950 CATGTTGATGGTATCTCTCTCACC 58.704 45.833 0.00 0.00 0.00 4.02
2744 3489 4.614475 TGTTGATGGTATCTCTCTCACCT 58.386 43.478 0.00 0.00 33.28 4.00
2745 3490 5.766590 TGTTGATGGTATCTCTCTCACCTA 58.233 41.667 0.00 0.00 33.28 3.08
2746 3491 5.594725 TGTTGATGGTATCTCTCTCACCTAC 59.405 44.000 0.00 0.00 33.28 3.18
2747 3492 4.390264 TGATGGTATCTCTCTCACCTACG 58.610 47.826 0.00 0.00 33.28 3.51
2748 3493 4.102681 TGATGGTATCTCTCTCACCTACGA 59.897 45.833 0.00 0.00 33.28 3.43
2749 3494 4.498894 TGGTATCTCTCTCACCTACGAA 57.501 45.455 0.00 0.00 33.28 3.85
2750 3495 4.197750 TGGTATCTCTCTCACCTACGAAC 58.802 47.826 0.00 0.00 33.28 3.95
2751 3496 3.565063 GGTATCTCTCTCACCTACGAACC 59.435 52.174 0.00 0.00 0.00 3.62
2752 3497 2.873094 TCTCTCTCACCTACGAACCA 57.127 50.000 0.00 0.00 0.00 3.67
2753 3498 3.367646 TCTCTCTCACCTACGAACCAT 57.632 47.619 0.00 0.00 0.00 3.55
2754 3499 3.280295 TCTCTCTCACCTACGAACCATC 58.720 50.000 0.00 0.00 0.00 3.51
2755 3500 3.017442 CTCTCTCACCTACGAACCATCA 58.983 50.000 0.00 0.00 0.00 3.07
2756 3501 3.017442 TCTCTCACCTACGAACCATCAG 58.983 50.000 0.00 0.00 0.00 2.90
2757 3502 2.755655 CTCTCACCTACGAACCATCAGT 59.244 50.000 0.00 0.00 0.00 3.41
2758 3503 3.162666 TCTCACCTACGAACCATCAGTT 58.837 45.455 0.00 0.00 43.07 3.16
2783 3528 7.391148 CAGTTATTACTGTATTTTGGGCACT 57.609 36.000 3.66 0.00 45.46 4.40
2784 3529 7.826690 CAGTTATTACTGTATTTTGGGCACTT 58.173 34.615 3.66 0.00 45.46 3.16
2785 3530 7.968405 CAGTTATTACTGTATTTTGGGCACTTC 59.032 37.037 3.66 0.00 45.46 3.01
2786 3531 7.888546 AGTTATTACTGTATTTTGGGCACTTCT 59.111 33.333 0.00 0.00 31.99 2.85
2787 3532 5.957842 TTACTGTATTTTGGGCACTTCTG 57.042 39.130 0.00 0.00 0.00 3.02
2788 3533 2.558359 ACTGTATTTTGGGCACTTCTGC 59.442 45.455 0.00 0.00 43.41 4.26
2789 3534 2.821969 CTGTATTTTGGGCACTTCTGCT 59.178 45.455 0.00 0.00 43.66 4.24
2790 3535 3.230134 TGTATTTTGGGCACTTCTGCTT 58.770 40.909 0.00 0.00 43.66 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 7.093354 TGTTAAACTTGTTTCATGTTTGCTGA 58.907 30.769 17.67 2.55 40.31 4.26
46 53 8.691661 AACATGGTAAAACTCTATGAAACTGT 57.308 30.769 0.00 0.00 0.00 3.55
93 100 7.010830 GTGGAACTCTACGAAACTGTTAAACTT 59.989 37.037 0.00 0.00 0.00 2.66
332 339 9.801873 CTTTTGAAACAAGAATACTCCAGAAAA 57.198 29.630 0.00 0.00 0.00 2.29
342 349 8.536175 AGGGTTTTGACTTTTGAAACAAGAATA 58.464 29.630 0.00 0.00 35.53 1.75
344 351 6.764379 AGGGTTTTGACTTTTGAAACAAGAA 58.236 32.000 0.00 0.00 35.53 2.52
345 352 6.353404 AGGGTTTTGACTTTTGAAACAAGA 57.647 33.333 0.00 0.00 35.53 3.02
346 353 5.288472 CGAGGGTTTTGACTTTTGAAACAAG 59.712 40.000 0.00 0.00 35.53 3.16
347 354 5.164954 CGAGGGTTTTGACTTTTGAAACAA 58.835 37.500 0.00 0.00 35.53 2.83
348 355 4.218852 ACGAGGGTTTTGACTTTTGAAACA 59.781 37.500 0.00 0.00 35.53 2.83
350 357 4.459685 TGACGAGGGTTTTGACTTTTGAAA 59.540 37.500 0.00 0.00 0.00 2.69
351 358 4.011023 TGACGAGGGTTTTGACTTTTGAA 58.989 39.130 0.00 0.00 0.00 2.69
352 359 3.375922 GTGACGAGGGTTTTGACTTTTGA 59.624 43.478 0.00 0.00 0.00 2.69
353 360 3.488553 GGTGACGAGGGTTTTGACTTTTG 60.489 47.826 0.00 0.00 0.00 2.44
354 361 2.686405 GGTGACGAGGGTTTTGACTTTT 59.314 45.455 0.00 0.00 0.00 2.27
394 422 8.420189 CGAAACAAAGTGAAATTTAAGATCTGC 58.580 33.333 0.00 0.00 0.00 4.26
463 491 0.759346 AATATGCTCCACCCTCCGAC 59.241 55.000 0.00 0.00 0.00 4.79
474 502 4.923871 CACCCACTGTACGATAATATGCTC 59.076 45.833 0.00 0.00 0.00 4.26
485 513 0.670546 CTTGCTCCACCCACTGTACG 60.671 60.000 0.00 0.00 0.00 3.67
509 537 3.904136 ACTTTTGGCAGAGATTTCACG 57.096 42.857 6.92 0.00 0.00 4.35
525 553 2.104281 GGGACTCCACACAGTGTACTTT 59.896 50.000 5.69 0.00 0.00 2.66
560 588 4.080129 AGCCAGTCATTATTCTCCACACAT 60.080 41.667 0.00 0.00 0.00 3.21
575 603 5.205759 CAGTATGTCATATCAGCCAGTCA 57.794 43.478 0.00 0.00 0.00 3.41
666 703 6.475727 CCACAATATTTCACGTGTAGGAGTAG 59.524 42.308 16.51 3.75 0.00 2.57
667 704 6.153170 TCCACAATATTTCACGTGTAGGAGTA 59.847 38.462 16.51 2.55 0.00 2.59
668 705 5.046878 TCCACAATATTTCACGTGTAGGAGT 60.047 40.000 16.51 4.39 0.00 3.85
669 706 5.416083 TCCACAATATTTCACGTGTAGGAG 58.584 41.667 16.51 3.77 0.00 3.69
670 707 5.408880 TCCACAATATTTCACGTGTAGGA 57.591 39.130 16.51 4.24 0.00 2.94
671 708 4.034048 GCTCCACAATATTTCACGTGTAGG 59.966 45.833 16.51 1.70 0.00 3.18
672 709 4.034048 GGCTCCACAATATTTCACGTGTAG 59.966 45.833 16.51 0.00 0.00 2.74
673 710 3.936453 GGCTCCACAATATTTCACGTGTA 59.064 43.478 16.51 2.27 0.00 2.90
674 711 2.747446 GGCTCCACAATATTTCACGTGT 59.253 45.455 16.51 0.00 0.00 4.49
689 726 1.306911 TATGCAGTCCTGGGCTCCA 60.307 57.895 0.00 0.00 0.00 3.86
690 727 1.050988 TCTATGCAGTCCTGGGCTCC 61.051 60.000 0.00 0.00 0.00 4.70
707 744 7.385267 CCTTGATCTATTGGAGATTCGAATCT 58.615 38.462 34.89 34.89 45.48 2.40
713 750 3.999663 CGCCCTTGATCTATTGGAGATTC 59.000 47.826 0.00 0.00 45.48 2.52
714 751 3.648067 TCGCCCTTGATCTATTGGAGATT 59.352 43.478 0.00 0.00 45.48 2.40
717 754 2.869636 GCTCGCCCTTGATCTATTGGAG 60.870 54.545 0.00 0.00 0.00 3.86
718 755 1.070758 GCTCGCCCTTGATCTATTGGA 59.929 52.381 0.00 0.00 0.00 3.53
719 756 1.517242 GCTCGCCCTTGATCTATTGG 58.483 55.000 0.00 0.00 0.00 3.16
720 757 1.517242 GGCTCGCCCTTGATCTATTG 58.483 55.000 0.00 0.00 0.00 1.90
734 771 2.513204 CATGCAGTCCTGGGCTCG 60.513 66.667 0.00 0.00 0.00 5.03
735 772 1.992519 ATCCATGCAGTCCTGGGCTC 61.993 60.000 0.00 0.00 33.13 4.70
737 774 1.076485 AATCCATGCAGTCCTGGGC 60.076 57.895 4.27 0.00 33.13 5.36
738 775 0.816825 CGAATCCATGCAGTCCTGGG 60.817 60.000 4.27 0.00 33.13 4.45
739 776 0.178767 TCGAATCCATGCAGTCCTGG 59.821 55.000 0.00 0.00 0.00 4.45
740 777 2.028420 TTCGAATCCATGCAGTCCTG 57.972 50.000 0.00 0.00 0.00 3.86
767 804 7.124599 TCCGAGAAAAGTAATTCTACCCATGTA 59.875 37.037 0.00 0.00 39.70 2.29
769 806 6.346096 TCCGAGAAAAGTAATTCTACCCATG 58.654 40.000 0.00 0.00 39.70 3.66
770 807 6.408206 CCTCCGAGAAAAGTAATTCTACCCAT 60.408 42.308 0.00 0.00 39.70 4.00
771 808 5.105064 CCTCCGAGAAAAGTAATTCTACCCA 60.105 44.000 0.00 0.00 39.70 4.51
772 809 5.358090 CCTCCGAGAAAAGTAATTCTACCC 58.642 45.833 0.00 0.00 39.70 3.69
800 873 7.863375 AGTCAATACACAATACTCTCGCTATTC 59.137 37.037 0.00 0.00 0.00 1.75
880 958 0.252197 GGGTTGGTAGAGGCGTCAAT 59.748 55.000 9.41 0.00 0.00 2.57
886 964 1.821258 CGTAGGGGTTGGTAGAGGC 59.179 63.158 0.00 0.00 0.00 4.70
897 975 0.768622 TTATTGATGGGGCGTAGGGG 59.231 55.000 0.00 0.00 0.00 4.79
898 976 2.649531 TTTATTGATGGGGCGTAGGG 57.350 50.000 0.00 0.00 0.00 3.53
936 1016 0.852777 GAGGTGTACGTATGCATGCG 59.147 55.000 31.52 31.52 41.71 4.73
975 1055 1.212616 GAGATTGATCGGCGAGTTGG 58.787 55.000 17.22 0.00 0.00 3.77
995 1075 2.512286 TGCTAGACGCCATGCTGC 60.512 61.111 0.00 0.00 38.05 5.25
996 1076 3.403277 GTGCTAGACGCCATGCTG 58.597 61.111 0.00 0.00 38.05 4.41
1176 1262 2.882777 CTGTAGGCGTCGCAGCAG 60.883 66.667 20.50 18.02 39.27 4.24
1242 1328 3.755628 GTGGAGCGGCCGTAGACA 61.756 66.667 28.70 17.72 40.66 3.41
1360 1446 0.788995 GATCGATCATGCGAGGCTTG 59.211 55.000 20.52 0.00 44.26 4.01
1368 1454 2.651701 ACGTAGTTCGATCGATCATGC 58.348 47.619 24.40 12.96 37.78 4.06
1385 1471 4.689812 CGCACATAGGTAGAGAGTATACGT 59.310 45.833 0.00 0.00 0.00 3.57
1386 1472 4.435784 GCGCACATAGGTAGAGAGTATACG 60.436 50.000 0.30 0.00 0.00 3.06
1387 1473 4.435784 CGCGCACATAGGTAGAGAGTATAC 60.436 50.000 8.75 0.00 0.00 1.47
1388 1474 3.683340 CGCGCACATAGGTAGAGAGTATA 59.317 47.826 8.75 0.00 0.00 1.47
1389 1475 2.484651 CGCGCACATAGGTAGAGAGTAT 59.515 50.000 8.75 0.00 0.00 2.12
1390 1476 1.871676 CGCGCACATAGGTAGAGAGTA 59.128 52.381 8.75 0.00 0.00 2.59
1391 1477 0.663688 CGCGCACATAGGTAGAGAGT 59.336 55.000 8.75 0.00 0.00 3.24
1398 1484 0.736325 GTTCAGTCGCGCACATAGGT 60.736 55.000 8.75 0.00 0.00 3.08
1403 1489 1.661509 CAGAGTTCAGTCGCGCACA 60.662 57.895 8.75 0.00 0.00 4.57
1549 1642 2.444002 CATCGATCTCGGTGTCAAGCG 61.444 57.143 4.71 0.00 44.76 4.68
1550 1643 1.203928 CATCGATCTCGGTGTCAAGC 58.796 55.000 4.71 0.00 44.76 4.01
1569 1662 1.463444 CATCGACCGAAAGTGTTTCCC 59.537 52.381 0.00 0.00 36.30 3.97
1573 1666 2.035449 TCAGACATCGACCGAAAGTGTT 59.965 45.455 5.78 0.00 0.00 3.32
1575 1668 2.347697 TCAGACATCGACCGAAAGTG 57.652 50.000 5.78 0.00 0.00 3.16
1808 1905 7.277539 GCAAGTCCTGATATCATAGCTTATCAC 59.722 40.741 5.72 0.00 32.75 3.06
1841 1938 7.628769 TGTTTCAATCTGCAGCTAATATTCA 57.371 32.000 9.47 0.00 0.00 2.57
1940 2066 5.346181 ACAAAGCCTCATCTAACTCCTAC 57.654 43.478 0.00 0.00 0.00 3.18
1956 2085 7.051000 AGGGAGTAGATGAGAATTAACAAAGC 58.949 38.462 0.00 0.00 0.00 3.51
1965 2094 7.708624 AGCTTATAGAGGGAGTAGATGAGAAT 58.291 38.462 0.00 0.00 0.00 2.40
2016 2145 9.211485 TCCTCAACTTTTATAAGACGTTTTAGG 57.789 33.333 4.75 0.00 35.30 2.69
2065 2199 9.353999 GTTCCAGAATTTCGCTAATAAAACAAT 57.646 29.630 0.00 0.00 0.00 2.71
2087 2225 6.999950 ACACCCAAATAACCAATTTAGTTCC 58.000 36.000 0.00 0.00 35.54 3.62
2106 2244 2.095919 GTCATACACGCAAGAAACACCC 60.096 50.000 0.00 0.00 43.62 4.61
2179 2317 3.847671 AACCTTTATAGAGCCTCCTGC 57.152 47.619 0.00 0.00 41.71 4.85
2206 2344 3.431411 TTATGGGAGGGAGTACATGGT 57.569 47.619 0.00 0.00 0.00 3.55
2215 2353 7.947782 AAACACTCTTATATTATGGGAGGGA 57.052 36.000 13.34 0.00 32.45 4.20
2216 2354 8.850156 CAAAAACACTCTTATATTATGGGAGGG 58.150 37.037 7.82 7.82 34.07 4.30
2217 2355 9.627123 TCAAAAACACTCTTATATTATGGGAGG 57.373 33.333 10.39 4.88 0.00 4.30
2219 2357 9.967451 TGTCAAAAACACTCTTATATTATGGGA 57.033 29.630 0.00 0.00 31.20 4.37
2246 2384 9.976511 CTCCGTTCCACAATATAAGAACTATAA 57.023 33.333 0.00 0.00 37.15 0.98
2247 2385 8.582437 CCTCCGTTCCACAATATAAGAACTATA 58.418 37.037 0.00 0.00 37.15 1.31
2248 2386 7.442656 CCTCCGTTCCACAATATAAGAACTAT 58.557 38.462 0.00 0.00 37.15 2.12
2249 2387 6.183360 CCCTCCGTTCCACAATATAAGAACTA 60.183 42.308 0.00 0.00 37.15 2.24
2250 2388 5.396436 CCCTCCGTTCCACAATATAAGAACT 60.396 44.000 0.00 0.00 37.15 3.01
2251 2389 4.814771 CCCTCCGTTCCACAATATAAGAAC 59.185 45.833 0.00 0.00 36.19 3.01
2252 2390 4.717778 TCCCTCCGTTCCACAATATAAGAA 59.282 41.667 0.00 0.00 0.00 2.52
2253 2391 4.100498 GTCCCTCCGTTCCACAATATAAGA 59.900 45.833 0.00 0.00 0.00 2.10
2254 2392 4.141801 TGTCCCTCCGTTCCACAATATAAG 60.142 45.833 0.00 0.00 0.00 1.73
2255 2393 3.775866 TGTCCCTCCGTTCCACAATATAA 59.224 43.478 0.00 0.00 0.00 0.98
2256 2394 3.376636 TGTCCCTCCGTTCCACAATATA 58.623 45.455 0.00 0.00 0.00 0.86
2257 2395 2.193127 TGTCCCTCCGTTCCACAATAT 58.807 47.619 0.00 0.00 0.00 1.28
2258 2396 1.646912 TGTCCCTCCGTTCCACAATA 58.353 50.000 0.00 0.00 0.00 1.90
2259 2397 0.768622 TTGTCCCTCCGTTCCACAAT 59.231 50.000 0.00 0.00 0.00 2.71
2260 2398 0.179040 GTTGTCCCTCCGTTCCACAA 60.179 55.000 0.00 0.00 0.00 3.33
2261 2399 1.338890 TGTTGTCCCTCCGTTCCACA 61.339 55.000 0.00 0.00 0.00 4.17
2262 2400 0.179040 TTGTTGTCCCTCCGTTCCAC 60.179 55.000 0.00 0.00 0.00 4.02
2263 2401 0.768622 ATTGTTGTCCCTCCGTTCCA 59.231 50.000 0.00 0.00 0.00 3.53
2264 2402 1.165270 CATTGTTGTCCCTCCGTTCC 58.835 55.000 0.00 0.00 0.00 3.62
2265 2403 1.892209 ACATTGTTGTCCCTCCGTTC 58.108 50.000 0.00 0.00 0.00 3.95
2266 2404 3.495434 TTACATTGTTGTCCCTCCGTT 57.505 42.857 0.00 0.00 37.28 4.44
2267 2405 3.713826 ATTACATTGTTGTCCCTCCGT 57.286 42.857 0.00 0.00 37.28 4.69
2268 2406 5.385509 AAAATTACATTGTTGTCCCTCCG 57.614 39.130 0.00 0.00 37.28 4.63
2269 2407 7.039293 ACCTTAAAATTACATTGTTGTCCCTCC 60.039 37.037 0.00 0.00 37.28 4.30
2270 2408 7.812669 CACCTTAAAATTACATTGTTGTCCCTC 59.187 37.037 0.00 0.00 37.28 4.30
2271 2409 7.289084 ACACCTTAAAATTACATTGTTGTCCCT 59.711 33.333 0.00 0.00 37.28 4.20
2272 2410 7.438564 ACACCTTAAAATTACATTGTTGTCCC 58.561 34.615 0.00 0.00 37.28 4.46
2273 2411 8.138712 TGACACCTTAAAATTACATTGTTGTCC 58.861 33.333 0.00 0.00 37.28 4.02
2274 2412 9.522804 TTGACACCTTAAAATTACATTGTTGTC 57.477 29.630 0.00 0.00 37.28 3.18
2289 2427 9.653287 CTTGACTATGTTCTATTGACACCTTAA 57.347 33.333 0.00 0.00 0.00 1.85
2352 2510 2.029110 CCAATCCTTCCAACGCAAATGT 60.029 45.455 0.00 0.00 0.00 2.71
2353 2511 2.029110 ACCAATCCTTCCAACGCAAATG 60.029 45.455 0.00 0.00 0.00 2.32
2380 2538 2.233654 GCAGCAGCGGTGAGTATCG 61.234 63.158 20.69 0.00 38.61 2.92
2391 2549 2.872931 CTTCCCTGGAGAGCAGCAGC 62.873 65.000 0.00 0.00 42.56 5.25
2396 2554 0.034767 CATTGCTTCCCTGGAGAGCA 60.035 55.000 16.59 16.59 44.03 4.26
2397 2555 1.382692 GCATTGCTTCCCTGGAGAGC 61.383 60.000 12.52 12.52 36.95 4.09
2422 2582 5.245301 TGGCTGTAGACTACTTTTGCTAAGA 59.755 40.000 13.67 0.00 0.00 2.10
2426 2586 3.557264 GGTGGCTGTAGACTACTTTTGCT 60.557 47.826 13.67 0.00 0.00 3.91
2427 2587 2.742589 GGTGGCTGTAGACTACTTTTGC 59.257 50.000 13.67 11.51 0.00 3.68
2428 2588 4.273148 AGGTGGCTGTAGACTACTTTTG 57.727 45.455 13.67 3.38 0.00 2.44
2429 2589 4.836736 TGTAGGTGGCTGTAGACTACTTTT 59.163 41.667 13.67 0.00 36.04 2.27
2430 2590 4.220163 GTGTAGGTGGCTGTAGACTACTTT 59.780 45.833 13.67 0.00 36.04 2.66
2431 2591 3.762823 GTGTAGGTGGCTGTAGACTACTT 59.237 47.826 13.67 0.00 36.04 2.24
2433 2593 2.426381 GGTGTAGGTGGCTGTAGACTAC 59.574 54.545 5.62 5.62 35.71 2.73
2434 2594 2.731572 GGTGTAGGTGGCTGTAGACTA 58.268 52.381 0.00 0.00 0.00 2.59
2437 2597 1.601419 GCGGTGTAGGTGGCTGTAGA 61.601 60.000 0.00 0.00 0.00 2.59
2438 2598 1.153628 GCGGTGTAGGTGGCTGTAG 60.154 63.158 0.00 0.00 0.00 2.74
2439 2599 2.652095 GGCGGTGTAGGTGGCTGTA 61.652 63.158 0.00 0.00 0.00 2.74
2441 2601 3.665675 GAGGCGGTGTAGGTGGCTG 62.666 68.421 0.00 0.00 38.78 4.85
2443 2603 3.372554 GAGAGGCGGTGTAGGTGGC 62.373 68.421 0.00 0.00 0.00 5.01
2444 2604 1.682684 AGAGAGGCGGTGTAGGTGG 60.683 63.158 0.00 0.00 0.00 4.61
2455 2899 4.183101 CAAAAGAGTCATCTCAGAGAGGC 58.817 47.826 7.25 3.13 42.66 4.70
2473 2917 5.684704 GAGGATCCATATGTCTGACCAAAA 58.315 41.667 15.82 0.00 0.00 2.44
2531 3008 4.350245 GGGAAGGTATTGGCTAGGTTTTT 58.650 43.478 0.00 0.00 0.00 1.94
2532 3009 3.623954 CGGGAAGGTATTGGCTAGGTTTT 60.624 47.826 0.00 0.00 0.00 2.43
2533 3010 2.092592 CGGGAAGGTATTGGCTAGGTTT 60.093 50.000 0.00 0.00 0.00 3.27
2534 3011 1.489230 CGGGAAGGTATTGGCTAGGTT 59.511 52.381 0.00 0.00 0.00 3.50
2535 3012 1.129058 CGGGAAGGTATTGGCTAGGT 58.871 55.000 0.00 0.00 0.00 3.08
2536 3013 0.396811 CCGGGAAGGTATTGGCTAGG 59.603 60.000 0.00 0.00 34.51 3.02
2537 3014 0.250338 GCCGGGAAGGTATTGGCTAG 60.250 60.000 2.18 0.00 42.44 3.42
2607 3132 1.364721 TTACACAATGGTCATCGCGG 58.635 50.000 6.13 0.00 0.00 6.46
2610 3135 7.169308 GGTTAGTCTATTACACAATGGTCATCG 59.831 40.741 0.00 0.00 0.00 3.84
2622 3147 7.415095 GCACAATGCATTGGTTAGTCTATTACA 60.415 37.037 35.85 0.00 44.26 2.41
2672 3417 3.995506 ATGTTGGTAGCAGCGGGGC 62.996 63.158 4.27 0.00 0.00 5.80
2673 3418 1.819632 GATGTTGGTAGCAGCGGGG 60.820 63.158 4.27 0.00 0.00 5.73
2674 3419 1.091771 CAGATGTTGGTAGCAGCGGG 61.092 60.000 4.27 0.00 0.00 6.13
2675 3420 1.091771 CCAGATGTTGGTAGCAGCGG 61.092 60.000 4.27 0.00 42.41 5.52
2676 3421 2.387309 CCAGATGTTGGTAGCAGCG 58.613 57.895 4.27 0.00 42.41 5.18
2685 3430 7.819644 TGATGTCAACTTTTATCCAGATGTTG 58.180 34.615 0.00 0.00 36.93 3.33
2686 3431 8.408043 TTGATGTCAACTTTTATCCAGATGTT 57.592 30.769 0.00 0.00 0.00 2.71
2687 3432 8.299570 GTTTGATGTCAACTTTTATCCAGATGT 58.700 33.333 0.00 0.00 35.28 3.06
2688 3433 7.756722 GGTTTGATGTCAACTTTTATCCAGATG 59.243 37.037 0.00 0.00 35.28 2.90
2689 3434 7.362056 CGGTTTGATGTCAACTTTTATCCAGAT 60.362 37.037 0.00 0.00 35.28 2.90
2690 3435 6.072728 CGGTTTGATGTCAACTTTTATCCAGA 60.073 38.462 0.00 0.00 35.28 3.86
2691 3436 6.072728 TCGGTTTGATGTCAACTTTTATCCAG 60.073 38.462 0.00 0.00 35.28 3.86
2692 3437 5.765677 TCGGTTTGATGTCAACTTTTATCCA 59.234 36.000 0.00 0.00 35.28 3.41
2693 3438 6.249035 TCGGTTTGATGTCAACTTTTATCC 57.751 37.500 0.00 0.00 35.28 2.59
2694 3439 7.640240 GCTATCGGTTTGATGTCAACTTTTATC 59.360 37.037 0.00 0.00 37.99 1.75
2695 3440 7.120579 TGCTATCGGTTTGATGTCAACTTTTAT 59.879 33.333 0.00 0.00 37.99 1.40
2696 3441 6.428465 TGCTATCGGTTTGATGTCAACTTTTA 59.572 34.615 0.00 0.00 37.99 1.52
2697 3442 5.240623 TGCTATCGGTTTGATGTCAACTTTT 59.759 36.000 0.00 0.00 37.99 2.27
2698 3443 4.759693 TGCTATCGGTTTGATGTCAACTTT 59.240 37.500 0.00 0.00 37.99 2.66
2699 3444 4.323417 TGCTATCGGTTTGATGTCAACTT 58.677 39.130 0.00 0.00 37.99 2.66
2700 3445 3.937814 TGCTATCGGTTTGATGTCAACT 58.062 40.909 0.00 0.00 37.99 3.16
2701 3446 4.094887 ACATGCTATCGGTTTGATGTCAAC 59.905 41.667 0.00 0.00 37.99 3.18
2702 3447 4.260985 ACATGCTATCGGTTTGATGTCAA 58.739 39.130 0.00 0.00 37.99 3.18
2703 3448 3.872696 ACATGCTATCGGTTTGATGTCA 58.127 40.909 0.00 0.00 37.99 3.58
2704 3449 4.332543 TCAACATGCTATCGGTTTGATGTC 59.667 41.667 0.00 0.00 37.99 3.06
2705 3450 4.260985 TCAACATGCTATCGGTTTGATGT 58.739 39.130 0.00 0.00 37.99 3.06
2706 3451 4.880886 TCAACATGCTATCGGTTTGATG 57.119 40.909 0.00 0.00 37.99 3.07
2707 3452 4.276678 CCATCAACATGCTATCGGTTTGAT 59.723 41.667 0.00 0.00 41.30 2.57
2708 3453 3.627123 CCATCAACATGCTATCGGTTTGA 59.373 43.478 0.00 0.00 0.00 2.69
2709 3454 3.378112 ACCATCAACATGCTATCGGTTTG 59.622 43.478 0.00 0.00 0.00 2.93
2710 3455 3.620488 ACCATCAACATGCTATCGGTTT 58.380 40.909 0.00 0.00 0.00 3.27
2711 3456 3.281727 ACCATCAACATGCTATCGGTT 57.718 42.857 0.00 0.00 0.00 4.44
2712 3457 4.284490 AGATACCATCAACATGCTATCGGT 59.716 41.667 0.00 0.00 34.56 4.69
2713 3458 4.825422 AGATACCATCAACATGCTATCGG 58.175 43.478 0.00 0.00 34.56 4.18
2714 3459 5.718146 AGAGATACCATCAACATGCTATCG 58.282 41.667 0.00 0.00 34.56 2.92
2715 3460 6.934056 AGAGAGATACCATCAACATGCTATC 58.066 40.000 0.00 0.00 31.43 2.08
2716 3461 6.496218 TGAGAGAGATACCATCAACATGCTAT 59.504 38.462 0.00 0.00 0.00 2.97
2717 3462 5.835280 TGAGAGAGATACCATCAACATGCTA 59.165 40.000 0.00 0.00 0.00 3.49
2718 3463 4.652881 TGAGAGAGATACCATCAACATGCT 59.347 41.667 0.00 0.00 0.00 3.79
2719 3464 4.749099 GTGAGAGAGATACCATCAACATGC 59.251 45.833 0.00 0.00 0.00 4.06
2720 3465 5.070180 AGGTGAGAGAGATACCATCAACATG 59.930 44.000 0.00 0.00 36.94 3.21
2721 3466 5.215069 AGGTGAGAGAGATACCATCAACAT 58.785 41.667 0.00 0.00 36.94 2.71
2722 3467 4.614475 AGGTGAGAGAGATACCATCAACA 58.386 43.478 0.00 0.00 36.94 3.33
2723 3468 5.278071 CGTAGGTGAGAGAGATACCATCAAC 60.278 48.000 0.00 0.00 36.94 3.18
2724 3469 4.822350 CGTAGGTGAGAGAGATACCATCAA 59.178 45.833 0.00 0.00 36.94 2.57
2725 3470 4.102681 TCGTAGGTGAGAGAGATACCATCA 59.897 45.833 0.00 0.00 36.94 3.07
2726 3471 4.643463 TCGTAGGTGAGAGAGATACCATC 58.357 47.826 0.00 0.00 36.94 3.51
2727 3472 4.708576 TCGTAGGTGAGAGAGATACCAT 57.291 45.455 0.00 0.00 36.94 3.55
2728 3473 4.197750 GTTCGTAGGTGAGAGAGATACCA 58.802 47.826 0.00 0.00 36.94 3.25
2729 3474 3.565063 GGTTCGTAGGTGAGAGAGATACC 59.435 52.174 0.00 0.00 34.68 2.73
2730 3475 4.197750 TGGTTCGTAGGTGAGAGAGATAC 58.802 47.826 0.00 0.00 0.00 2.24
2731 3476 4.498894 TGGTTCGTAGGTGAGAGAGATA 57.501 45.455 0.00 0.00 0.00 1.98
2732 3477 3.367646 TGGTTCGTAGGTGAGAGAGAT 57.632 47.619 0.00 0.00 0.00 2.75
2733 3478 2.873094 TGGTTCGTAGGTGAGAGAGA 57.127 50.000 0.00 0.00 0.00 3.10
2734 3479 3.017442 TGATGGTTCGTAGGTGAGAGAG 58.983 50.000 0.00 0.00 0.00 3.20
2735 3480 3.017442 CTGATGGTTCGTAGGTGAGAGA 58.983 50.000 0.00 0.00 0.00 3.10
2736 3481 2.755655 ACTGATGGTTCGTAGGTGAGAG 59.244 50.000 0.00 0.00 0.00 3.20
2737 3482 2.803956 ACTGATGGTTCGTAGGTGAGA 58.196 47.619 0.00 0.00 0.00 3.27
2738 3483 3.512680 GAACTGATGGTTCGTAGGTGAG 58.487 50.000 0.00 0.00 43.75 3.51
2739 3484 3.587797 GAACTGATGGTTCGTAGGTGA 57.412 47.619 0.00 0.00 43.75 4.02
2760 3505 7.888546 AGAAGTGCCCAAAATACAGTAATAACT 59.111 33.333 0.00 0.00 35.91 2.24
2761 3506 7.968405 CAGAAGTGCCCAAAATACAGTAATAAC 59.032 37.037 0.00 0.00 0.00 1.89
2762 3507 7.362574 GCAGAAGTGCCCAAAATACAGTAATAA 60.363 37.037 0.00 0.00 44.72 1.40
2763 3508 6.094881 GCAGAAGTGCCCAAAATACAGTAATA 59.905 38.462 0.00 0.00 44.72 0.98
2764 3509 5.105756 GCAGAAGTGCCCAAAATACAGTAAT 60.106 40.000 0.00 0.00 44.72 1.89
2765 3510 4.217550 GCAGAAGTGCCCAAAATACAGTAA 59.782 41.667 0.00 0.00 44.72 2.24
2766 3511 3.756434 GCAGAAGTGCCCAAAATACAGTA 59.244 43.478 0.00 0.00 44.72 2.74
2767 3512 2.558359 GCAGAAGTGCCCAAAATACAGT 59.442 45.455 0.00 0.00 44.72 3.55
2768 3513 3.221964 GCAGAAGTGCCCAAAATACAG 57.778 47.619 0.00 0.00 44.72 2.74


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

AutoCloner maintained by Alex Coulton.