Multiple sequence alignment - TraesCS2D01G529200

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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 TraesCS2D01G529200 chr2D 100.000 3929 0 0 1 3929 616576149 616580077 0.000000e+00 7256
1 TraesCS2D01G529200 chr2D 95.918 147 6 0 1898 2044 362930820 362930966 5.070000e-59 239
2 TraesCS2D01G529200 chr2B 91.272 1501 60 22 2043 3525 751540490 751541937 0.000000e+00 1980
3 TraesCS2D01G529200 chr2B 84.677 1997 122 74 1 1897 751538564 751540476 0.000000e+00 1823
4 TraesCS2D01G529200 chr2A 96.285 996 29 7 2388 3378 746763700 746764692 0.000000e+00 1628
5 TraesCS2D01G529200 chr2A 84.174 1567 106 78 1 1514 746761363 746762840 0.000000e+00 1389
6 TraesCS2D01G529200 chr2A 90.000 550 29 8 3381 3927 746764772 746765298 0.000000e+00 688
7 TraesCS2D01G529200 chr2A 91.667 348 20 3 1547 1885 746762959 746763306 1.280000e-129 473
8 TraesCS2D01G529200 chr2A 84.416 154 14 1 2043 2196 746763341 746763484 4.090000e-30 143
9 TraesCS2D01G529200 chr6D 96.599 147 5 0 1898 2044 15516939 15517085 1.090000e-60 244
10 TraesCS2D01G529200 chr6D 94.156 154 8 1 1891 2044 426106885 426106733 2.360000e-57 233
11 TraesCS2D01G529200 chr6D 93.038 158 9 2 1894 2051 93213749 93213904 3.050000e-56 230
12 TraesCS2D01G529200 chr4A 96.599 147 5 0 1898 2044 517406483 517406629 1.090000e-60 244
13 TraesCS2D01G529200 chr6B 95.918 147 6 0 1898 2044 720912205 720912059 5.070000e-59 239
14 TraesCS2D01G529200 chr1A 95.918 147 6 0 1898 2044 566481020 566481166 5.070000e-59 239
15 TraesCS2D01G529200 chr5B 93.671 158 9 1 1898 2055 490757561 490757405 6.560000e-58 235
16 TraesCS2D01G529200 chr4D 92.638 163 10 2 1898 2059 3590486 3590647 2.360000e-57 233


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 TraesCS2D01G529200 chr2D 616576149 616580077 3928 False 7256.0 7256 100.0000 1 3929 1 chr2D.!!$F2 3928
1 TraesCS2D01G529200 chr2B 751538564 751541937 3373 False 1901.5 1980 87.9745 1 3525 2 chr2B.!!$F1 3524
2 TraesCS2D01G529200 chr2A 746761363 746765298 3935 False 864.2 1628 89.3084 1 3927 5 chr2A.!!$F1 3926

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
572 610 0.034059 ACCTGCAGAGTCTGAAACCG 59.966 55.0 24.55 6.18 32.44 4.44 F
1094 1176 0.035739 GACACCGAGGTAAAGCCCAA 59.964 55.0 0.00 0.00 38.26 4.12 F
2348 2580 0.179163 GCTTCCATGCCGCTTGTTAC 60.179 55.0 5.61 0.00 0.00 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 2564 0.323302 TCAGTAACAAGCGGCATGGA 59.677 50.0 10.21 0.0 0.00 3.41 R
2808 3092 0.457509 CATCGTCTTCAGCAGCGACT 60.458 55.0 0.00 0.0 35.01 4.18 R
3800 4172 0.107410 CACATAGCGCCCCTACCAAA 60.107 55.0 2.29 0.0 0.00 3.28 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
102 116 1.135315 CCAGCGGCACAAAATCTCG 59.865 57.895 1.45 0.00 0.00 4.04
103 117 1.135315 CAGCGGCACAAAATCTCGG 59.865 57.895 1.45 0.00 0.00 4.63
105 119 1.134694 GCGGCACAAAATCTCGGTC 59.865 57.895 0.00 0.00 0.00 4.79
106 120 1.419922 CGGCACAAAATCTCGGTCG 59.580 57.895 0.00 0.00 0.00 4.79
212 226 3.584848 GCTCCTCTATCCTCTCTCTCTCT 59.415 52.174 0.00 0.00 0.00 3.10
213 227 4.323104 GCTCCTCTATCCTCTCTCTCTCTC 60.323 54.167 0.00 0.00 0.00 3.20
214 228 5.090139 CTCCTCTATCCTCTCTCTCTCTCT 58.910 50.000 0.00 0.00 0.00 3.10
215 229 5.087323 TCCTCTATCCTCTCTCTCTCTCTC 58.913 50.000 0.00 0.00 0.00 3.20
291 316 2.680339 TGAGAGCGCTCATATATCCTCG 59.320 50.000 36.87 0.00 45.88 4.63
317 347 1.002430 TCCAGATCTGTGGTCTGTTGC 59.998 52.381 21.11 0.00 41.13 4.17
371 403 1.405821 ACCTCTCCTGTTTATCTCGCG 59.594 52.381 0.00 0.00 0.00 5.87
401 433 3.428870 ACGCATCTCAACTACTTTTCACG 59.571 43.478 0.00 0.00 0.00 4.35
402 434 3.673338 CGCATCTCAACTACTTTTCACGA 59.327 43.478 0.00 0.00 0.00 4.35
409 441 4.980434 TCAACTACTTTTCACGACTGCTAC 59.020 41.667 0.00 0.00 0.00 3.58
411 443 5.954296 ACTACTTTTCACGACTGCTACTA 57.046 39.130 0.00 0.00 0.00 1.82
421 453 4.272748 CACGACTGCTACTAGTAGTATGCA 59.727 45.833 26.76 22.27 41.29 3.96
422 454 5.049336 CACGACTGCTACTAGTAGTATGCAT 60.049 44.000 26.76 3.79 41.29 3.96
423 455 6.147328 CACGACTGCTACTAGTAGTATGCATA 59.853 42.308 26.76 1.16 41.29 3.14
424 456 6.879993 ACGACTGCTACTAGTAGTATGCATAT 59.120 38.462 26.76 17.84 41.29 1.78
425 457 7.390996 ACGACTGCTACTAGTAGTATGCATATT 59.609 37.037 26.76 8.42 41.29 1.28
426 458 7.694367 CGACTGCTACTAGTAGTATGCATATTG 59.306 40.741 26.76 17.40 41.29 1.90
427 459 7.316640 ACTGCTACTAGTAGTATGCATATTGC 58.683 38.462 26.76 9.46 39.42 3.56
456 488 6.644347 TCATATCTCTTTTGTTCCTCCTGTC 58.356 40.000 0.00 0.00 0.00 3.51
473 505 2.945668 CTGTCAATTAACCCTAGCTGCC 59.054 50.000 0.00 0.00 0.00 4.85
474 506 1.940613 GTCAATTAACCCTAGCTGCCG 59.059 52.381 0.00 0.00 0.00 5.69
476 508 2.158957 TCAATTAACCCTAGCTGCCGAG 60.159 50.000 0.00 0.00 0.00 4.63
513 551 1.136695 CTGTTCTAGGCTCTGCTCTGG 59.863 57.143 0.00 0.00 0.00 3.86
572 610 0.034059 ACCTGCAGAGTCTGAAACCG 59.966 55.000 24.55 6.18 32.44 4.44
622 660 4.022762 TCGCTGAGAGAAATATACTCCTGC 60.023 45.833 6.32 10.51 35.27 4.85
623 661 4.022416 CGCTGAGAGAAATATACTCCTGCT 60.022 45.833 16.76 0.00 35.27 4.24
626 664 6.239289 GCTGAGAGAAATATACTCCTGCTCTT 60.239 42.308 0.00 0.00 35.27 2.85
627 665 7.283625 TGAGAGAAATATACTCCTGCTCTTC 57.716 40.000 0.00 0.00 35.27 2.87
628 666 7.066142 TGAGAGAAATATACTCCTGCTCTTCT 58.934 38.462 0.00 0.00 35.27 2.85
629 667 7.563188 TGAGAGAAATATACTCCTGCTCTTCTT 59.437 37.037 0.00 0.00 35.27 2.52
630 668 7.951591 AGAGAAATATACTCCTGCTCTTCTTC 58.048 38.462 6.32 0.00 35.27 2.87
691 732 1.478510 GGCACTTCTGTGAGCTAGCTA 59.521 52.381 19.38 0.47 46.55 3.32
692 733 2.481104 GGCACTTCTGTGAGCTAGCTAG 60.481 54.545 19.38 16.84 46.55 3.42
694 735 3.768406 CACTTCTGTGAGCTAGCTAGTG 58.232 50.000 22.25 22.25 46.55 2.74
696 737 1.107114 TCTGTGAGCTAGCTAGTGGC 58.893 55.000 19.38 8.93 42.19 5.01
700 741 2.025155 GTGAGCTAGCTAGTGGCAGTA 58.975 52.381 19.38 1.44 44.79 2.74
704 745 3.215975 AGCTAGCTAGTGGCAGTAGTAC 58.784 50.000 25.87 13.37 44.79 2.73
723 765 8.598041 AGTAGTACCATCTGTTCAGAAGAAAAT 58.402 33.333 6.60 0.00 35.08 1.82
754 796 1.265236 CCTCTGTTCTCTGACCTGCT 58.735 55.000 0.00 0.00 0.00 4.24
757 799 1.821753 TCTGTTCTCTGACCTGCTAGC 59.178 52.381 8.10 8.10 0.00 3.42
776 821 0.833834 CAGCGGAGGATAGGGTGGAT 60.834 60.000 0.00 0.00 0.00 3.41
802 847 5.371115 TTGCTAGAATTAGGTGCAACAAC 57.629 39.130 3.64 0.00 39.98 3.32
803 848 4.651778 TGCTAGAATTAGGTGCAACAACT 58.348 39.130 3.64 0.00 39.98 3.16
812 857 0.954452 GTGCAACAACTTCTCTGGGG 59.046 55.000 0.00 0.00 36.32 4.96
903 951 1.168407 TTCCTGCTGCTTGTGTGCTC 61.168 55.000 0.00 0.00 0.00 4.26
908 956 2.595463 TGCTTGTGTGCTCCTGCC 60.595 61.111 0.00 0.00 38.71 4.85
909 957 2.282040 GCTTGTGTGCTCCTGCCT 60.282 61.111 0.00 0.00 38.71 4.75
911 959 1.374190 CTTGTGTGCTCCTGCCTCT 59.626 57.895 0.00 0.00 38.71 3.69
912 960 0.954449 CTTGTGTGCTCCTGCCTCTG 60.954 60.000 0.00 0.00 38.71 3.35
913 961 2.046507 GTGTGCTCCTGCCTCTGG 60.047 66.667 0.00 0.00 38.71 3.86
941 990 5.947228 AACTAACGGTAAAAGTAAAGCCC 57.053 39.130 0.00 0.00 0.00 5.19
942 991 4.326826 ACTAACGGTAAAAGTAAAGCCCC 58.673 43.478 0.00 0.00 0.00 5.80
943 992 1.812235 ACGGTAAAAGTAAAGCCCCG 58.188 50.000 0.00 0.00 39.75 5.73
950 999 1.349067 AAGTAAAGCCCCGTCTCTGT 58.651 50.000 0.00 0.00 0.00 3.41
1063 1145 4.778415 CCGACCTGCTCACCGTCG 62.778 72.222 2.01 2.01 46.79 5.12
1064 1146 4.778415 CGACCTGCTCACCGTCGG 62.778 72.222 10.48 10.48 44.26 4.79
1094 1176 0.035739 GACACCGAGGTAAAGCCCAA 59.964 55.000 0.00 0.00 38.26 4.12
1103 1185 2.823747 AGGTAAAGCCCAAACGAAATCC 59.176 45.455 0.00 0.00 38.26 3.01
1104 1186 2.414957 GGTAAAGCCCAAACGAAATCCG 60.415 50.000 0.00 0.00 45.44 4.18
1128 1210 3.730061 GCGGCAAAAATCACATCTCTCTG 60.730 47.826 0.00 0.00 0.00 3.35
1130 1212 4.436584 CGGCAAAAATCACATCTCTCTGTC 60.437 45.833 0.00 0.00 0.00 3.51
1131 1213 4.436584 GGCAAAAATCACATCTCTCTGTCG 60.437 45.833 0.00 0.00 0.00 4.35
1132 1214 4.153117 GCAAAAATCACATCTCTCTGTCGT 59.847 41.667 0.00 0.00 0.00 4.34
1133 1215 5.334414 GCAAAAATCACATCTCTCTGTCGTT 60.334 40.000 0.00 0.00 0.00 3.85
1276 1384 0.948678 TCCAGCTTTTGTACCGTTGC 59.051 50.000 0.00 0.00 0.00 4.17
1398 1507 4.399395 CTCAGCCCGCTCCTTGCA 62.399 66.667 0.00 0.00 43.06 4.08
1429 1542 2.710096 TATTACAGCTCCTTGCCACC 57.290 50.000 0.00 0.00 44.23 4.61
1860 2074 3.054434 AGCATACAAGGTATGGAACTGCA 60.054 43.478 15.81 0.00 0.00 4.41
1897 2122 5.487488 TGGTTATGGAGGTAGATCTTTGTGT 59.513 40.000 0.00 0.00 0.00 3.72
1898 2123 6.049790 GGTTATGGAGGTAGATCTTTGTGTC 58.950 44.000 0.00 0.00 0.00 3.67
1899 2124 4.762289 ATGGAGGTAGATCTTTGTGTCC 57.238 45.455 0.00 1.55 0.00 4.02
1900 2125 3.791320 TGGAGGTAGATCTTTGTGTCCT 58.209 45.455 0.00 0.00 0.00 3.85
1901 2126 4.942944 TGGAGGTAGATCTTTGTGTCCTA 58.057 43.478 0.00 0.00 0.00 2.94
1902 2127 5.338632 TGGAGGTAGATCTTTGTGTCCTAA 58.661 41.667 0.00 0.00 0.00 2.69
1903 2128 5.783360 TGGAGGTAGATCTTTGTGTCCTAAA 59.217 40.000 0.00 0.00 0.00 1.85
1904 2129 6.443849 TGGAGGTAGATCTTTGTGTCCTAAAT 59.556 38.462 0.00 0.00 0.00 1.40
1905 2130 7.622081 TGGAGGTAGATCTTTGTGTCCTAAATA 59.378 37.037 0.00 0.00 0.00 1.40
1906 2131 8.652290 GGAGGTAGATCTTTGTGTCCTAAATAT 58.348 37.037 0.00 0.00 0.00 1.28
1933 2158 9.853177 AAGTCTTTTTAGATATTCCACTATGGG 57.147 33.333 0.00 0.00 38.32 4.00
1934 2159 7.939588 AGTCTTTTTAGATATTCCACTATGGGC 59.060 37.037 0.00 0.00 38.32 5.36
1935 2160 7.939588 GTCTTTTTAGATATTCCACTATGGGCT 59.060 37.037 0.00 0.00 38.32 5.19
1936 2161 9.166222 TCTTTTTAGATATTCCACTATGGGCTA 57.834 33.333 0.00 0.00 38.32 3.93
1937 2162 9.220767 CTTTTTAGATATTCCACTATGGGCTAC 57.779 37.037 0.00 0.00 38.32 3.58
1938 2163 7.865530 TTTAGATATTCCACTATGGGCTACA 57.134 36.000 0.00 0.00 38.32 2.74
1939 2164 8.449423 TTTAGATATTCCACTATGGGCTACAT 57.551 34.615 0.00 0.46 43.68 2.29
1940 2165 9.555411 TTTAGATATTCCACTATGGGCTACATA 57.445 33.333 0.00 2.52 41.03 2.29
1941 2166 7.425224 AGATATTCCACTATGGGCTACATAC 57.575 40.000 0.00 0.00 41.03 2.39
1942 2167 4.537135 ATTCCACTATGGGCTACATACG 57.463 45.455 0.00 0.00 41.03 3.06
1943 2168 2.244695 TCCACTATGGGCTACATACGG 58.755 52.381 0.00 3.24 41.03 4.02
1944 2169 2.158430 TCCACTATGGGCTACATACGGA 60.158 50.000 0.00 9.40 41.03 4.69
1945 2170 2.231478 CCACTATGGGCTACATACGGAG 59.769 54.545 0.00 0.00 41.03 4.63
1946 2171 4.317166 CCACTATGGGCTACATACGGAGT 61.317 52.174 0.00 0.00 41.03 3.85
1947 2172 5.050403 CCACTATGGGCTACATACGGAGTA 61.050 50.000 0.00 0.00 40.09 2.59
1948 2173 6.501062 CCACTATGGGCTACATACGGAGTAA 61.501 48.000 0.00 0.00 39.49 2.24
1949 2174 7.917141 CCACTATGGGCTACATACGGAGTAAA 61.917 46.154 0.00 0.00 39.49 2.01
1950 2175 9.302474 CCACTATGGGCTACATACGGAGTAAAA 62.302 44.444 0.00 0.00 39.49 1.52
2010 2235 9.866655 ACATCCATATGTAATTTGTAGTGGAAT 57.133 29.630 1.24 0.00 44.66 3.01
2013 2238 9.778741 TCCATATGTAATTTGTAGTGGAATCTC 57.221 33.333 1.24 0.00 32.02 2.75
2014 2239 9.784531 CCATATGTAATTTGTAGTGGAATCTCT 57.215 33.333 1.24 0.00 0.00 3.10
2024 2249 9.847224 TTTGTAGTGGAATCTCTAAAAAGACTT 57.153 29.630 0.00 0.00 28.58 3.01
2041 2266 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
2083 2308 2.079925 GAAGGTAAACTGGCTGAGCTG 58.920 52.381 3.72 0.00 0.00 4.24
2091 2318 3.533606 ACTGGCTGAGCTGTGTATAAG 57.466 47.619 3.72 0.00 0.00 1.73
2093 2320 3.193263 CTGGCTGAGCTGTGTATAAGTG 58.807 50.000 3.72 0.00 0.00 3.16
2200 2427 2.371841 TGCTCCTTTCCTGCTAAAGTGA 59.628 45.455 0.00 0.00 35.16 3.41
2202 2429 4.225042 TGCTCCTTTCCTGCTAAAGTGATA 59.775 41.667 0.00 0.00 35.16 2.15
2205 2432 5.186198 TCCTTTCCTGCTAAAGTGATAAGC 58.814 41.667 0.00 0.00 35.16 3.09
2206 2433 4.034510 CCTTTCCTGCTAAAGTGATAAGCG 59.965 45.833 0.00 0.00 39.14 4.68
2209 2436 2.286294 CCTGCTAAAGTGATAAGCGCTG 59.714 50.000 12.58 0.00 39.14 5.18
2246 2473 3.583806 CAGCCGATTCTAGGATAGCAAG 58.416 50.000 7.98 0.00 38.99 4.01
2269 2496 4.798574 CAGGGTTGTTGTTTATTGAGCTC 58.201 43.478 6.82 6.82 0.00 4.09
2294 2521 7.065085 TCTGCTCTTTTTGCTCACTAATATGAC 59.935 37.037 0.00 0.00 0.00 3.06
2295 2522 6.881065 TGCTCTTTTTGCTCACTAATATGACT 59.119 34.615 0.00 0.00 0.00 3.41
2319 2547 8.135529 ACTTGCTGAGTTTACCATAAGAAAAAC 58.864 33.333 0.00 0.00 33.92 2.43
2321 2553 5.567915 GCTGAGTTTACCATAAGAAAAACGC 59.432 40.000 0.00 0.00 37.02 4.84
2340 2572 0.591659 CATGATCTGCTTCCATGCCG 59.408 55.000 0.00 0.00 32.47 5.69
2348 2580 0.179163 GCTTCCATGCCGCTTGTTAC 60.179 55.000 5.61 0.00 0.00 2.50
2370 2602 5.193679 ACTGACTAGCTTTTGGTCACTTTT 58.806 37.500 0.00 0.00 41.72 2.27
2371 2603 6.354130 ACTGACTAGCTTTTGGTCACTTTTA 58.646 36.000 0.00 0.00 41.72 1.52
2372 2604 6.998673 ACTGACTAGCTTTTGGTCACTTTTAT 59.001 34.615 0.00 0.00 41.72 1.40
2396 2628 5.659440 AATCCTTTGTTCTTGTGTTGTGT 57.341 34.783 0.00 0.00 0.00 3.72
2409 2641 4.058817 TGTGTTGTGTTTGTGGGTTTTTC 58.941 39.130 0.00 0.00 0.00 2.29
2412 2644 3.601443 TGTGTTTGTGGGTTTTTCAGG 57.399 42.857 0.00 0.00 0.00 3.86
2416 2648 4.757657 GTGTTTGTGGGTTTTTCAGGTTTT 59.242 37.500 0.00 0.00 0.00 2.43
2417 2649 4.757149 TGTTTGTGGGTTTTTCAGGTTTTG 59.243 37.500 0.00 0.00 0.00 2.44
2472 2753 6.714810 TGTGACTTAACTATGTTTGCCTGATT 59.285 34.615 0.00 0.00 0.00 2.57
2586 2867 0.876342 GCGAAGATGATGACGGGGAC 60.876 60.000 0.00 0.00 0.00 4.46
2733 3014 2.039084 GGAAGAACAAGAGGAGCAGGAA 59.961 50.000 0.00 0.00 0.00 3.36
2790 3074 2.541794 CGACGATGACAATGAGGACGAT 60.542 50.000 0.00 0.00 0.00 3.73
2808 3092 3.243068 ACGATGACGATGATGACGATGAA 60.243 43.478 0.00 0.00 42.66 2.57
2869 3153 1.361271 GACGACCAGGACAACGACA 59.639 57.895 0.00 0.00 0.00 4.35
2874 3158 1.798813 GACCAGGACAACGACAATGAC 59.201 52.381 0.00 0.00 0.00 3.06
3077 3362 5.643777 CGATTAGAGGGAACTTTGTTGTCAT 59.356 40.000 0.00 0.00 44.43 3.06
3083 3368 3.066203 GGGAACTTTGTTGTCATCGTTGT 59.934 43.478 0.00 0.00 0.00 3.32
3135 3420 6.425577 TGTTTCGCTAACATAATTGTACCC 57.574 37.500 0.00 0.00 41.73 3.69
3335 3627 6.123045 TCTGCTGATGATGGTGATGATTAT 57.877 37.500 0.00 0.00 0.00 1.28
3372 3664 9.148879 AGATATATGGCTTGTTAGTGTAGTTCT 57.851 33.333 0.00 0.00 0.00 3.01
3378 3670 4.021368 GCTTGTTAGTGTAGTTCTCCCTCA 60.021 45.833 0.00 0.00 0.00 3.86
3379 3671 5.337652 GCTTGTTAGTGTAGTTCTCCCTCAT 60.338 44.000 0.00 0.00 0.00 2.90
3386 3755 2.166907 AGTTCTCCCTCATGACGGAT 57.833 50.000 13.09 0.00 0.00 4.18
3476 3847 0.740149 CTTTGCACACTGTCCAAGCA 59.260 50.000 0.00 0.00 0.00 3.91
3529 3900 0.687354 CTAGGAAGGTGCCACAGTGT 59.313 55.000 0.00 0.00 0.00 3.55
3556 3928 1.902508 TGCCACCCTTCAGAGAAGTAG 59.097 52.381 6.08 0.44 0.00 2.57
3557 3929 1.406205 GCCACCCTTCAGAGAAGTAGC 60.406 57.143 6.08 0.43 0.00 3.58
3558 3930 2.183679 CCACCCTTCAGAGAAGTAGCT 58.816 52.381 6.08 0.00 0.00 3.32
3559 3931 2.167487 CCACCCTTCAGAGAAGTAGCTC 59.833 54.545 0.00 0.00 35.11 4.09
3560 3932 2.828520 CACCCTTCAGAGAAGTAGCTCA 59.171 50.000 0.00 0.00 37.37 4.26
3561 3933 3.450457 CACCCTTCAGAGAAGTAGCTCAT 59.550 47.826 0.00 0.00 37.37 2.90
3562 3934 4.646945 CACCCTTCAGAGAAGTAGCTCATA 59.353 45.833 0.00 0.00 37.37 2.15
3563 3935 5.304101 CACCCTTCAGAGAAGTAGCTCATAT 59.696 44.000 0.00 0.00 37.37 1.78
3564 3936 5.538433 ACCCTTCAGAGAAGTAGCTCATATC 59.462 44.000 0.00 0.00 37.37 1.63
3565 3937 5.538053 CCCTTCAGAGAAGTAGCTCATATCA 59.462 44.000 0.00 0.00 37.37 2.15
3566 3938 6.041409 CCCTTCAGAGAAGTAGCTCATATCAA 59.959 42.308 0.00 0.00 37.37 2.57
3567 3939 7.418368 CCCTTCAGAGAAGTAGCTCATATCAAA 60.418 40.741 0.00 0.00 37.37 2.69
3568 3940 7.984050 CCTTCAGAGAAGTAGCTCATATCAAAA 59.016 37.037 0.00 0.00 37.37 2.44
3569 3941 9.376075 CTTCAGAGAAGTAGCTCATATCAAAAA 57.624 33.333 0.00 0.00 37.37 1.94
3570 3942 8.939201 TCAGAGAAGTAGCTCATATCAAAAAG 57.061 34.615 0.00 0.00 37.37 2.27
3571 3943 7.984050 TCAGAGAAGTAGCTCATATCAAAAAGG 59.016 37.037 0.00 0.00 37.37 3.11
3572 3944 7.984050 CAGAGAAGTAGCTCATATCAAAAAGGA 59.016 37.037 0.00 0.00 37.37 3.36
3575 3947 9.692325 AGAAGTAGCTCATATCAAAAAGGAAAT 57.308 29.630 0.00 0.00 0.00 2.17
3582 3954 7.644157 GCTCATATCAAAAAGGAAATCGTTACC 59.356 37.037 0.00 0.00 0.00 2.85
3589 3961 2.547990 AGGAAATCGTTACCTCCCTGT 58.452 47.619 0.00 0.00 0.00 4.00
3612 3984 6.322969 TGTTAGGAGGTTTCTTTTTCCCTTTC 59.677 38.462 0.00 0.00 0.00 2.62
3631 4003 1.448893 GCGGTTGCGATTGGTAGGA 60.449 57.895 0.00 0.00 0.00 2.94
3653 4025 2.871022 CAATCATCCTCTCCAAGCTTCG 59.129 50.000 0.00 0.00 0.00 3.79
3695 4067 2.103601 CCAATGGCATGAAAAGGATCCC 59.896 50.000 8.55 0.00 0.00 3.85
3696 4068 2.767394 CAATGGCATGAAAAGGATCCCA 59.233 45.455 8.55 0.00 0.00 4.37
3697 4069 2.148446 TGGCATGAAAAGGATCCCAG 57.852 50.000 8.55 0.00 0.00 4.45
3698 4070 1.358787 TGGCATGAAAAGGATCCCAGT 59.641 47.619 8.55 0.00 0.00 4.00
3713 4085 3.386237 AGTCAGTGCCTCGGCTCC 61.386 66.667 9.65 0.00 42.51 4.70
3733 4105 5.010415 GCTCCGGCTAATAGTTTAGGTTAGA 59.990 44.000 0.00 0.00 36.18 2.10
3745 4117 0.907704 AGGTTAGATGACCGGTGGCA 60.908 55.000 14.63 4.70 44.62 4.92
3817 4189 1.757682 TTTTTGGTAGGGGCGCTATG 58.242 50.000 14.77 0.00 0.00 2.23
3829 4201 1.893808 CGCTATGTGGGTGGATGGC 60.894 63.158 0.00 0.00 0.00 4.40
3857 4229 6.794158 CGTTTCATCTTTGAGCTAGTCTTTTG 59.206 38.462 0.00 0.00 32.27 2.44
3874 4246 1.361204 TTGGGCTCTGATTCACCTCA 58.639 50.000 0.00 0.00 0.00 3.86
3879 4251 3.006247 GGCTCTGATTCACCTCAAGTTC 58.994 50.000 0.00 0.00 0.00 3.01
3927 4299 0.458669 TGGCCTAGATTTCCGTCGTC 59.541 55.000 3.32 0.00 0.00 4.20
3928 4300 0.745468 GGCCTAGATTTCCGTCGTCT 59.255 55.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 116 2.362889 TAACCCGAGGACCCGACC 60.363 66.667 4.18 0.00 0.00 4.79
103 117 3.073742 GCTAACCCGAGGACCCGAC 62.074 68.421 4.18 0.00 0.00 4.79
105 119 4.203076 CGCTAACCCGAGGACCCG 62.203 72.222 0.00 0.00 0.00 5.28
106 120 3.846430 CCGCTAACCCGAGGACCC 61.846 72.222 0.00 0.00 0.00 4.46
212 226 3.030291 GAGAAAGAGGATGCTGGAGAGA 58.970 50.000 0.00 0.00 0.00 3.10
213 227 3.033184 AGAGAAAGAGGATGCTGGAGAG 58.967 50.000 0.00 0.00 0.00 3.20
214 228 3.030291 GAGAGAAAGAGGATGCTGGAGA 58.970 50.000 0.00 0.00 0.00 3.71
215 229 2.102925 GGAGAGAAAGAGGATGCTGGAG 59.897 54.545 0.00 0.00 0.00 3.86
256 270 1.737363 GCTCTCAACGGGCAGAACTAG 60.737 57.143 0.00 0.00 0.00 2.57
286 311 1.133945 CAGATCTGGAGGTCTCGAGGA 60.134 57.143 15.38 0.00 36.30 3.71
291 316 1.754226 GACCACAGATCTGGAGGTCTC 59.246 57.143 37.23 25.04 46.78 3.36
317 347 0.972134 TTGTGAGGAGGCAGAGACTG 59.028 55.000 0.00 0.00 34.12 3.51
371 403 9.821662 AAAAGTAGTTGAGATGCGTTAATAAAC 57.178 29.630 0.00 0.00 0.00 2.01
392 424 4.850347 ACTAGTAGCAGTCGTGAAAAGT 57.150 40.909 0.00 0.00 0.00 2.66
398 430 4.272748 TGCATACTACTAGTAGCAGTCGTG 59.727 45.833 26.54 16.94 33.66 4.35
401 433 7.486551 GCAATATGCATACTACTAGTAGCAGTC 59.513 40.741 26.54 15.22 44.26 3.51
402 434 7.316640 GCAATATGCATACTACTAGTAGCAGT 58.683 38.462 26.54 14.79 44.26 4.40
424 456 9.412460 AGGAACAAAAGAGATATGATTATGCAA 57.588 29.630 0.00 0.00 0.00 4.08
425 457 8.985315 AGGAACAAAAGAGATATGATTATGCA 57.015 30.769 0.00 0.00 0.00 3.96
426 458 8.510505 GGAGGAACAAAAGAGATATGATTATGC 58.489 37.037 0.00 0.00 0.00 3.14
427 459 9.790344 AGGAGGAACAAAAGAGATATGATTATG 57.210 33.333 0.00 0.00 0.00 1.90
442 474 4.830600 GGGTTAATTGACAGGAGGAACAAA 59.169 41.667 2.50 0.00 0.00 2.83
456 488 2.158957 TCTCGGCAGCTAGGGTTAATTG 60.159 50.000 0.00 0.00 0.00 2.32
473 505 0.721718 GTGCGAAATCCAACCTCTCG 59.278 55.000 0.00 0.00 0.00 4.04
474 506 1.087501 GGTGCGAAATCCAACCTCTC 58.912 55.000 0.00 0.00 0.00 3.20
476 508 0.804989 CAGGTGCGAAATCCAACCTC 59.195 55.000 0.00 0.00 0.00 3.85
482 514 2.280628 CCTAGAACAGGTGCGAAATCC 58.719 52.381 0.00 0.00 39.91 3.01
513 551 1.022451 CACAATTTGCCATGGCCTGC 61.022 55.000 33.44 9.62 41.09 4.85
540 578 1.009675 GCAGGTGCACACAAACGAG 60.010 57.895 20.43 0.55 41.59 4.18
572 610 1.818642 AATCTGTGCTGAAGCCTGAC 58.181 50.000 0.00 0.00 41.18 3.51
614 652 2.291024 ACGAGGAAGAAGAGCAGGAGTA 60.291 50.000 0.00 0.00 0.00 2.59
616 654 1.181786 ACGAGGAAGAAGAGCAGGAG 58.818 55.000 0.00 0.00 0.00 3.69
617 655 1.633774 AACGAGGAAGAAGAGCAGGA 58.366 50.000 0.00 0.00 0.00 3.86
619 657 3.431572 CAGAAAACGAGGAAGAAGAGCAG 59.568 47.826 0.00 0.00 0.00 4.24
620 658 3.181465 ACAGAAAACGAGGAAGAAGAGCA 60.181 43.478 0.00 0.00 0.00 4.26
622 660 7.540299 AGTATACAGAAAACGAGGAAGAAGAG 58.460 38.462 5.50 0.00 0.00 2.85
623 661 7.463961 AGTATACAGAAAACGAGGAAGAAGA 57.536 36.000 5.50 0.00 0.00 2.87
626 664 5.413833 ACGAGTATACAGAAAACGAGGAAGA 59.586 40.000 5.50 0.00 0.00 2.87
627 665 5.638783 ACGAGTATACAGAAAACGAGGAAG 58.361 41.667 5.50 0.00 0.00 3.46
628 666 5.633830 ACGAGTATACAGAAAACGAGGAA 57.366 39.130 5.50 0.00 0.00 3.36
629 667 5.633830 AACGAGTATACAGAAAACGAGGA 57.366 39.130 5.50 0.00 0.00 3.71
630 668 6.585322 AGAAAACGAGTATACAGAAAACGAGG 59.415 38.462 5.50 0.00 0.00 4.63
691 732 2.821437 ACAGATGGTACTACTGCCACT 58.179 47.619 11.93 0.00 37.62 4.00
692 733 3.056107 TGAACAGATGGTACTACTGCCAC 60.056 47.826 11.93 6.73 37.62 5.01
694 735 3.447586 TCTGAACAGATGGTACTACTGCC 59.552 47.826 0.00 7.15 36.21 4.85
696 737 6.516739 TCTTCTGAACAGATGGTACTACTG 57.483 41.667 14.57 10.94 37.29 2.74
700 741 9.388506 CATATTTTCTTCTGAACAGATGGTACT 57.611 33.333 14.57 4.54 37.29 2.73
704 745 8.048534 ACACATATTTTCTTCTGAACAGATGG 57.951 34.615 14.57 7.90 36.47 3.51
723 765 3.994392 GAGAACAGAGGCGAAAACACATA 59.006 43.478 0.00 0.00 0.00 2.29
754 796 0.827925 CACCCTATCCTCCGCTGCTA 60.828 60.000 0.00 0.00 0.00 3.49
757 799 0.833834 ATCCACCCTATCCTCCGCTG 60.834 60.000 0.00 0.00 0.00 5.18
908 956 5.824904 TTACCGTTAGTTAGTAGCCAGAG 57.175 43.478 0.00 0.00 0.00 3.35
909 957 6.209391 ACTTTTACCGTTAGTTAGTAGCCAGA 59.791 38.462 0.00 0.00 0.00 3.86
911 959 6.345096 ACTTTTACCGTTAGTTAGTAGCCA 57.655 37.500 0.00 0.00 0.00 4.75
912 960 8.757164 TTTACTTTTACCGTTAGTTAGTAGCC 57.243 34.615 0.00 0.00 0.00 3.93
913 961 8.376203 GCTTTACTTTTACCGTTAGTTAGTAGC 58.624 37.037 0.00 0.00 0.00 3.58
914 962 8.864024 GGCTTTACTTTTACCGTTAGTTAGTAG 58.136 37.037 0.00 0.00 0.00 2.57
916 964 6.650807 GGGCTTTACTTTTACCGTTAGTTAGT 59.349 38.462 0.00 0.00 0.00 2.24
950 999 3.069586 AGGAGAAATCAACACGTCAGTCA 59.930 43.478 0.00 0.00 0.00 3.41
1036 1118 4.477975 CAGGTCGGCGAGGACGTC 62.478 72.222 11.20 7.13 41.98 4.34
1039 1121 4.500116 GAGCAGGTCGGCGAGGAC 62.500 72.222 11.20 3.60 39.27 3.85
1041 1123 4.803426 GTGAGCAGGTCGGCGAGG 62.803 72.222 11.20 4.03 39.27 4.63
1076 1158 0.475044 TTTGGGCTTTACCTCGGTGT 59.525 50.000 0.00 0.00 39.10 4.16
1103 1185 0.984109 GATGTGATTTTTGCCGCACG 59.016 50.000 0.00 0.00 34.12 5.34
1104 1186 2.095059 AGAGATGTGATTTTTGCCGCAC 60.095 45.455 0.00 0.00 0.00 5.34
1108 1190 4.436584 CGACAGAGAGATGTGATTTTTGCC 60.437 45.833 0.00 0.00 32.25 4.52
1109 1191 4.153117 ACGACAGAGAGATGTGATTTTTGC 59.847 41.667 0.00 0.00 32.25 3.68
1128 1210 7.222654 CCACACGAAAATAGTAGTAAAACGAC 58.777 38.462 0.00 0.00 0.00 4.34
1130 1212 6.146021 ACCCACACGAAAATAGTAGTAAAACG 59.854 38.462 0.00 0.00 0.00 3.60
1131 1213 7.425577 ACCCACACGAAAATAGTAGTAAAAC 57.574 36.000 0.00 0.00 0.00 2.43
1132 1214 8.987890 GTAACCCACACGAAAATAGTAGTAAAA 58.012 33.333 0.00 0.00 0.00 1.52
1133 1215 8.367156 AGTAACCCACACGAAAATAGTAGTAAA 58.633 33.333 0.00 0.00 0.00 2.01
1178 1278 1.313091 ACACGCATGCTACTCGAGGA 61.313 55.000 18.41 7.44 0.00 3.71
1233 1334 4.641094 TGGAACGGCCGTGATATTATTTTT 59.359 37.500 34.95 11.65 40.66 1.94
1238 1339 2.289195 GGATGGAACGGCCGTGATATTA 60.289 50.000 34.95 15.62 40.66 0.98
1276 1384 4.098654 AGTCCAAACCATATCTCACTCTCG 59.901 45.833 0.00 0.00 0.00 4.04
1397 1506 5.448360 GGAGCTGTAATAAAGAAGCAAGCTG 60.448 44.000 0.00 0.00 38.14 4.24
1398 1507 4.637977 GGAGCTGTAATAAAGAAGCAAGCT 59.362 41.667 0.00 0.00 38.14 3.74
1522 1649 5.165911 CGTATACCGTCACTTGACTACAT 57.834 43.478 7.74 1.00 42.66 2.29
1543 1700 1.762419 ACCGTAGCATAATACGCACG 58.238 50.000 0.91 0.00 45.56 5.34
1544 1701 5.403166 TGATTAACCGTAGCATAATACGCAC 59.597 40.000 0.91 0.00 45.56 5.34
1545 1702 5.403166 GTGATTAACCGTAGCATAATACGCA 59.597 40.000 0.91 0.00 45.56 5.24
1585 1786 2.671177 CGCGTCAAAGACAGCCTGG 61.671 63.158 0.00 0.00 32.00 4.45
1860 2074 3.025978 CCATAACCACAAGCATGTCCAT 58.974 45.455 0.00 0.00 37.82 3.41
1907 2132 9.853177 CCCATAGTGGAATATCTAAAAAGACTT 57.147 33.333 0.00 0.00 40.96 3.01
1908 2133 7.939588 GCCCATAGTGGAATATCTAAAAAGACT 59.060 37.037 0.00 0.00 40.96 3.24
1909 2134 7.939588 AGCCCATAGTGGAATATCTAAAAAGAC 59.060 37.037 0.00 0.00 40.96 3.01
1910 2135 8.045720 AGCCCATAGTGGAATATCTAAAAAGA 57.954 34.615 0.00 0.00 40.96 2.52
1911 2136 9.220767 GTAGCCCATAGTGGAATATCTAAAAAG 57.779 37.037 0.00 0.00 40.96 2.27
1912 2137 8.719596 TGTAGCCCATAGTGGAATATCTAAAAA 58.280 33.333 0.00 0.00 40.96 1.94
1913 2138 8.270137 TGTAGCCCATAGTGGAATATCTAAAA 57.730 34.615 0.00 0.00 40.96 1.52
1914 2139 7.865530 TGTAGCCCATAGTGGAATATCTAAA 57.134 36.000 0.00 0.00 40.96 1.85
1915 2140 8.978472 GTATGTAGCCCATAGTGGAATATCTAA 58.022 37.037 0.00 0.00 40.96 2.10
1916 2141 7.284716 CGTATGTAGCCCATAGTGGAATATCTA 59.715 40.741 0.00 0.00 40.96 1.98
1917 2142 6.096987 CGTATGTAGCCCATAGTGGAATATCT 59.903 42.308 0.00 0.00 40.96 1.98
1918 2143 6.273825 CGTATGTAGCCCATAGTGGAATATC 58.726 44.000 0.00 0.00 40.96 1.63
1919 2144 5.128827 CCGTATGTAGCCCATAGTGGAATAT 59.871 44.000 0.00 0.00 40.96 1.28
1920 2145 4.464951 CCGTATGTAGCCCATAGTGGAATA 59.535 45.833 0.00 0.00 40.96 1.75
1921 2146 3.260884 CCGTATGTAGCCCATAGTGGAAT 59.739 47.826 0.00 0.00 40.96 3.01
1922 2147 2.631062 CCGTATGTAGCCCATAGTGGAA 59.369 50.000 0.00 0.00 40.96 3.53
1923 2148 2.158430 TCCGTATGTAGCCCATAGTGGA 60.158 50.000 0.00 9.28 40.96 4.02
1924 2149 2.231478 CTCCGTATGTAGCCCATAGTGG 59.769 54.545 6.12 6.12 36.71 4.00
1925 2150 2.891580 ACTCCGTATGTAGCCCATAGTG 59.108 50.000 0.00 0.00 36.71 2.74
1926 2151 3.240310 ACTCCGTATGTAGCCCATAGT 57.760 47.619 0.00 0.00 36.71 2.12
1927 2152 5.717078 TTTACTCCGTATGTAGCCCATAG 57.283 43.478 0.00 0.00 36.71 2.23
1928 2153 6.268158 TCATTTTACTCCGTATGTAGCCCATA 59.732 38.462 0.00 0.00 34.86 2.74
1929 2154 5.071250 TCATTTTACTCCGTATGTAGCCCAT 59.929 40.000 0.00 0.00 37.58 4.00
1930 2155 4.406326 TCATTTTACTCCGTATGTAGCCCA 59.594 41.667 0.00 0.00 0.00 5.36
1931 2156 4.952460 TCATTTTACTCCGTATGTAGCCC 58.048 43.478 0.00 0.00 0.00 5.19
1932 2157 5.462398 CACTCATTTTACTCCGTATGTAGCC 59.538 44.000 0.00 0.00 0.00 3.93
1933 2158 6.270815 TCACTCATTTTACTCCGTATGTAGC 58.729 40.000 0.00 0.00 0.00 3.58
1934 2159 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
1935 2160 8.692710 AGATTCACTCATTTTACTCCGTATGTA 58.307 33.333 0.00 0.00 0.00 2.29
1936 2161 7.556844 AGATTCACTCATTTTACTCCGTATGT 58.443 34.615 0.00 0.00 0.00 2.29
1937 2162 8.969267 GTAGATTCACTCATTTTACTCCGTATG 58.031 37.037 0.00 0.00 0.00 2.39
1938 2163 8.692710 TGTAGATTCACTCATTTTACTCCGTAT 58.307 33.333 0.00 0.00 0.00 3.06
1939 2164 7.972277 GTGTAGATTCACTCATTTTACTCCGTA 59.028 37.037 0.00 0.00 35.68 4.02
1940 2165 6.812160 GTGTAGATTCACTCATTTTACTCCGT 59.188 38.462 0.00 0.00 35.68 4.69
1941 2166 7.036220 AGTGTAGATTCACTCATTTTACTCCG 58.964 38.462 0.00 0.00 44.07 4.63
1987 2212 9.778741 GAGATTCCACTACAAATTACATATGGA 57.221 33.333 7.80 0.00 33.21 3.41
1988 2213 9.784531 AGAGATTCCACTACAAATTACATATGG 57.215 33.333 7.80 0.00 0.00 2.74
1998 2223 9.847224 AAGTCTTTTTAGAGATTCCACTACAAA 57.153 29.630 0.00 0.00 0.00 2.83
2015 2240 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
2016 2241 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
2017 2242 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2018 2243 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2019 2244 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2020 2245 6.661304 TCCCTCCGTTCCTAAATATAAGTC 57.339 41.667 0.00 0.00 0.00 3.01
2021 2246 7.291651 TGAATCCCTCCGTTCCTAAATATAAGT 59.708 37.037 0.00 0.00 0.00 2.24
2022 2247 7.676947 TGAATCCCTCCGTTCCTAAATATAAG 58.323 38.462 0.00 0.00 0.00 1.73
2023 2248 7.511371 TCTGAATCCCTCCGTTCCTAAATATAA 59.489 37.037 0.00 0.00 0.00 0.98
2024 2249 7.014449 TCTGAATCCCTCCGTTCCTAAATATA 58.986 38.462 0.00 0.00 0.00 0.86
2025 2250 5.844516 TCTGAATCCCTCCGTTCCTAAATAT 59.155 40.000 0.00 0.00 0.00 1.28
2026 2251 5.213519 TCTGAATCCCTCCGTTCCTAAATA 58.786 41.667 0.00 0.00 0.00 1.40
2027 2252 4.037927 TCTGAATCCCTCCGTTCCTAAAT 58.962 43.478 0.00 0.00 0.00 1.40
2028 2253 3.446968 TCTGAATCCCTCCGTTCCTAAA 58.553 45.455 0.00 0.00 0.00 1.85
2029 2254 3.110293 TCTGAATCCCTCCGTTCCTAA 57.890 47.619 0.00 0.00 0.00 2.69
2030 2255 2.840640 TCTGAATCCCTCCGTTCCTA 57.159 50.000 0.00 0.00 0.00 2.94
2031 2256 1.834263 CTTCTGAATCCCTCCGTTCCT 59.166 52.381 0.00 0.00 0.00 3.36
2032 2257 1.831736 TCTTCTGAATCCCTCCGTTCC 59.168 52.381 0.00 0.00 0.00 3.62
2033 2258 3.828875 ATCTTCTGAATCCCTCCGTTC 57.171 47.619 0.00 0.00 0.00 3.95
2034 2259 6.070538 CCATATATCTTCTGAATCCCTCCGTT 60.071 42.308 0.00 0.00 0.00 4.44
2035 2260 5.423610 CCATATATCTTCTGAATCCCTCCGT 59.576 44.000 0.00 0.00 0.00 4.69
2036 2261 5.163364 CCCATATATCTTCTGAATCCCTCCG 60.163 48.000 0.00 0.00 0.00 4.63
2037 2262 5.728741 ACCCATATATCTTCTGAATCCCTCC 59.271 44.000 0.00 0.00 0.00 4.30
2038 2263 6.882768 ACCCATATATCTTCTGAATCCCTC 57.117 41.667 0.00 0.00 0.00 4.30
2039 2264 6.794493 TCAACCCATATATCTTCTGAATCCCT 59.206 38.462 0.00 0.00 0.00 4.20
2040 2265 7.020827 TCAACCCATATATCTTCTGAATCCC 57.979 40.000 0.00 0.00 0.00 3.85
2041 2266 7.609532 CCTTCAACCCATATATCTTCTGAATCC 59.390 40.741 0.00 0.00 0.00 3.01
2083 2308 9.216117 ACAACCTCAGTTTTATCACTTATACAC 57.784 33.333 0.00 0.00 32.45 2.90
2091 2318 5.452777 GCTGAACAACCTCAGTTTTATCAC 58.547 41.667 2.81 0.00 44.04 3.06
2093 2320 4.762251 AGGCTGAACAACCTCAGTTTTATC 59.238 41.667 2.81 0.00 44.04 1.75
2200 2427 1.197721 GCACTGTTTGTCAGCGCTTAT 59.802 47.619 7.50 0.00 45.45 1.73
2202 2429 1.356624 GCACTGTTTGTCAGCGCTT 59.643 52.632 7.50 0.00 45.45 4.68
2209 2436 0.593263 GCTGCTGTGCACTGTTTGTC 60.593 55.000 22.70 8.20 33.79 3.18
2219 2446 1.156645 CCTAGAATCGGCTGCTGTGC 61.157 60.000 8.55 0.00 0.00 4.57
2246 2473 3.005791 AGCTCAATAAACAACAACCCTGC 59.994 43.478 0.00 0.00 0.00 4.85
2269 2496 7.065563 AGTCATATTAGTGAGCAAAAAGAGCAG 59.934 37.037 0.00 0.00 0.00 4.24
2277 2504 6.172630 TCAGCAAGTCATATTAGTGAGCAAA 58.827 36.000 0.00 0.00 0.00 3.68
2294 2521 7.323656 CGTTTTTCTTATGGTAAACTCAGCAAG 59.676 37.037 0.00 0.00 0.00 4.01
2295 2522 7.136119 CGTTTTTCTTATGGTAAACTCAGCAA 58.864 34.615 0.00 0.00 0.00 3.91
2321 2553 0.591659 CGGCATGGAAGCAGATCATG 59.408 55.000 0.00 0.00 40.66 3.07
2332 2564 0.323302 TCAGTAACAAGCGGCATGGA 59.677 50.000 10.21 0.00 0.00 3.41
2340 2572 4.515567 ACCAAAAGCTAGTCAGTAACAAGC 59.484 41.667 0.00 0.00 0.00 4.01
2348 2580 5.757850 AAAAGTGACCAAAAGCTAGTCAG 57.242 39.130 8.55 0.00 40.98 3.51
2370 2602 8.908903 ACACAACACAAGAACAAAGGATTAATA 58.091 29.630 0.00 0.00 0.00 0.98
2371 2603 7.781056 ACACAACACAAGAACAAAGGATTAAT 58.219 30.769 0.00 0.00 0.00 1.40
2372 2604 7.164230 ACACAACACAAGAACAAAGGATTAA 57.836 32.000 0.00 0.00 0.00 1.40
2396 2628 4.974399 ACAAAACCTGAAAAACCCACAAA 58.026 34.783 0.00 0.00 0.00 2.83
2409 2641 4.694982 ACCAAAGCTTGAAAACAAAACCTG 59.305 37.500 0.00 0.00 0.00 4.00
2412 2644 5.163864 CCAGACCAAAGCTTGAAAACAAAAC 60.164 40.000 0.00 0.00 0.00 2.43
2416 2648 3.360867 TCCAGACCAAAGCTTGAAAACA 58.639 40.909 0.00 0.00 0.00 2.83
2417 2649 4.202151 ACATCCAGACCAAAGCTTGAAAAC 60.202 41.667 0.00 0.00 0.00 2.43
2472 2753 4.219507 CCACAAATAATGCCCTGTACAACA 59.780 41.667 0.00 0.00 0.00 3.33
2733 3014 1.606889 GTCGTCACCTCCTCCACCT 60.607 63.158 0.00 0.00 0.00 4.00
2790 3074 3.695816 GACTTCATCGTCATCATCGTCA 58.304 45.455 0.00 0.00 34.11 4.35
2808 3092 0.457509 CATCGTCTTCAGCAGCGACT 60.458 55.000 0.00 0.00 35.01 4.18
2869 3153 0.675837 TCGTCGTCCTCCTCGTCATT 60.676 55.000 0.00 0.00 0.00 2.57
2874 3158 2.800581 CTCGTCGTCGTCCTCCTCG 61.801 68.421 1.33 0.00 38.33 4.63
3077 3362 2.354510 CTCCACAGAAGCAAAACAACGA 59.645 45.455 0.00 0.00 0.00 3.85
3083 3368 3.250762 CGATCAACTCCACAGAAGCAAAA 59.749 43.478 0.00 0.00 0.00 2.44
3335 3627 8.435931 ACAAGCCATATATCTAGACATTACCA 57.564 34.615 0.00 0.00 0.00 3.25
3370 3662 0.261696 TCCATCCGTCATGAGGGAGA 59.738 55.000 33.60 25.56 46.97 3.71
3378 3670 6.978674 TCTAGAAAATACTCCATCCGTCAT 57.021 37.500 0.00 0.00 0.00 3.06
3379 3671 6.978674 ATCTAGAAAATACTCCATCCGTCA 57.021 37.500 0.00 0.00 0.00 4.35
3476 3847 0.616891 TGTGACATCTGAGCCATGCT 59.383 50.000 0.00 0.00 43.88 3.79
3529 3900 0.325933 CTGAAGGGTGGCATCAGTGA 59.674 55.000 0.00 0.00 36.64 3.41
3556 3928 7.644157 GGTAACGATTTCCTTTTTGATATGAGC 59.356 37.037 0.00 0.00 0.00 4.26
3557 3929 8.893727 AGGTAACGATTTCCTTTTTGATATGAG 58.106 33.333 0.00 0.00 46.39 2.90
3558 3930 8.801882 AGGTAACGATTTCCTTTTTGATATGA 57.198 30.769 0.00 0.00 46.39 2.15
3559 3931 8.129211 GGAGGTAACGATTTCCTTTTTGATATG 58.871 37.037 0.00 0.00 46.39 1.78
3560 3932 7.284716 GGGAGGTAACGATTTCCTTTTTGATAT 59.715 37.037 0.00 0.00 46.39 1.63
3561 3933 6.600427 GGGAGGTAACGATTTCCTTTTTGATA 59.400 38.462 0.00 0.00 46.39 2.15
3562 3934 5.417894 GGGAGGTAACGATTTCCTTTTTGAT 59.582 40.000 0.00 0.00 46.39 2.57
3563 3935 4.763279 GGGAGGTAACGATTTCCTTTTTGA 59.237 41.667 0.00 0.00 46.39 2.69
3564 3936 4.765339 AGGGAGGTAACGATTTCCTTTTTG 59.235 41.667 0.00 0.00 46.39 2.44
3565 3937 4.765339 CAGGGAGGTAACGATTTCCTTTTT 59.235 41.667 0.00 0.00 46.39 1.94
3566 3938 4.202535 ACAGGGAGGTAACGATTTCCTTTT 60.203 41.667 0.00 0.00 46.39 2.27
3567 3939 3.329814 ACAGGGAGGTAACGATTTCCTTT 59.670 43.478 0.00 0.00 46.39 3.11
3568 3940 2.910977 ACAGGGAGGTAACGATTTCCTT 59.089 45.455 0.00 0.00 46.39 3.36
3569 3941 2.547990 ACAGGGAGGTAACGATTTCCT 58.452 47.619 0.00 0.00 46.39 3.36
3570 3942 3.345508 AACAGGGAGGTAACGATTTCC 57.654 47.619 0.00 0.00 46.39 3.13
3571 3943 4.161001 TCCTAACAGGGAGGTAACGATTTC 59.839 45.833 0.00 0.00 37.63 2.17
3572 3944 4.098894 TCCTAACAGGGAGGTAACGATTT 58.901 43.478 0.00 0.00 37.63 2.17
3575 3947 2.731572 CTCCTAACAGGGAGGTAACGA 58.268 52.381 2.84 0.00 46.63 3.85
3589 3961 5.533528 CGAAAGGGAAAAAGAAACCTCCTAA 59.466 40.000 0.00 0.00 31.69 2.69
3629 4001 2.172293 AGCTTGGAGAGGATGATTGTCC 59.828 50.000 0.00 0.00 38.62 4.02
3631 4003 3.681034 CGAAGCTTGGAGAGGATGATTGT 60.681 47.826 2.10 0.00 0.00 2.71
3653 4025 1.026718 CGCTCCATGGGTTCCTTGAC 61.027 60.000 13.02 0.00 31.33 3.18
3683 4055 2.553028 GCACTGACTGGGATCCTTTTCA 60.553 50.000 12.58 10.21 0.00 2.69
3695 4067 2.125753 GAGCCGAGGCACTGACTG 60.126 66.667 17.18 0.00 41.55 3.51
3696 4068 3.386237 GGAGCCGAGGCACTGACT 61.386 66.667 17.18 0.00 41.55 3.41
3697 4069 4.803426 CGGAGCCGAGGCACTGAC 62.803 72.222 17.18 2.34 41.55 3.51
3713 4085 6.867293 GGTCATCTAACCTAAACTATTAGCCG 59.133 42.308 0.00 0.00 37.74 5.52
3715 4087 6.867293 CCGGTCATCTAACCTAAACTATTAGC 59.133 42.308 0.00 0.00 37.74 3.09
3733 4105 2.284625 TCTCCTGCCACCGGTCAT 60.285 61.111 2.59 0.00 0.00 3.06
3745 4117 2.444895 GCACCGGGATCCTCTCCT 60.445 66.667 12.58 0.00 44.28 3.69
3767 4139 2.030371 ACCTAAACTACTAGCCGGAGC 58.970 52.381 5.05 0.00 40.32 4.70
3798 4170 1.004979 ACATAGCGCCCCTACCAAAAA 59.995 47.619 2.29 0.00 0.00 1.94
3800 4172 0.107410 CACATAGCGCCCCTACCAAA 60.107 55.000 2.29 0.00 0.00 3.28
3801 4173 1.524961 CACATAGCGCCCCTACCAA 59.475 57.895 2.29 0.00 0.00 3.67
3802 4174 2.439960 CCACATAGCGCCCCTACCA 61.440 63.158 2.29 0.00 0.00 3.25
3803 4175 2.426023 CCACATAGCGCCCCTACC 59.574 66.667 2.29 0.00 0.00 3.18
3829 4201 0.798776 AGCTCAAAGATGAAACGCCG 59.201 50.000 0.00 0.00 34.49 6.46
3857 4229 1.280421 ACTTGAGGTGAATCAGAGCCC 59.720 52.381 0.00 0.00 0.00 5.19
3901 4273 2.564947 CGGAAATCTAGGCCATAGCTCT 59.435 50.000 5.01 0.00 39.73 4.09


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

AutoCloner maintained by Alex Coulton.