Multiple sequence alignment - TraesCS6B01G383000

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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 TraesCS6B01G383000 chr6B 100.000 2615 0 0 1 2615 658118382 658120996 0.000000e+00 4830.0
1 TraesCS6B01G383000 chr6A 92.366 1847 59 30 1 1821 581964318 581966108 0.000000e+00 2555.0
2 TraesCS6B01G383000 chr6A 94.118 187 10 1 2224 2409 581966101 581966287 1.530000e-72 283.0
3 TraesCS6B01G383000 chr6D 93.096 1767 73 20 1 1748 434603462 434605198 0.000000e+00 2542.0
4 TraesCS6B01G383000 chr6D 85.919 419 43 9 1819 2223 437338253 437338669 1.440000e-117 433.0
5 TraesCS6B01G383000 chr6D 88.043 368 37 2 2231 2598 434605485 434605845 1.860000e-116 429.0
6 TraesCS6B01G383000 chr6D 87.131 373 42 6 1853 2222 11743800 11744169 4.030000e-113 418.0
7 TraesCS6B01G383000 chr7D 80.763 629 96 18 999 1616 549318819 549318205 3.940000e-128 468.0
8 TraesCS6B01G383000 chr7D 79.937 633 98 21 999 1620 549368929 549368315 3.090000e-119 438.0
9 TraesCS6B01G383000 chr7D 80.117 171 19 12 229 394 549370024 549369864 2.130000e-21 113.0
10 TraesCS6B01G383000 chr7D 93.617 47 1 1 636 680 549319192 549319146 4.670000e-08 69.4
11 TraesCS6B01G383000 chr7D 93.617 47 1 1 636 680 549369670 549369624 4.670000e-08 69.4
12 TraesCS6B01G383000 chr7A 86.375 411 48 7 1817 2222 30863492 30863899 2.390000e-120 442.0
13 TraesCS6B01G383000 chr3B 86.216 399 49 6 1824 2220 157659527 157659921 6.690000e-116 427.0
14 TraesCS6B01G383000 chr3A 87.234 376 42 6 1824 2195 638744626 638744999 8.650000e-115 424.0
15 TraesCS6B01G383000 chr3A 86.400 375 45 6 1824 2195 26213680 26214051 3.130000e-109 405.0
16 TraesCS6B01G383000 chr2D 87.263 369 42 5 1855 2221 536231747 536231382 1.450000e-112 416.0
17 TraesCS6B01G383000 chr5D 85.086 409 53 7 1820 2223 43215905 43216310 6.740000e-111 411.0
18 TraesCS6B01G383000 chr5D 78.626 131 20 6 280 407 125781416 125781291 2.160000e-11 80.5
19 TraesCS6B01G383000 chr1A 86.508 378 43 8 1824 2196 4043540 4043166 2.420000e-110 409.0


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 TraesCS6B01G383000 chr6B 658118382 658120996 2614 False 4830.0 4830 100.0000 1 2615 1 chr6B.!!$F1 2614
1 TraesCS6B01G383000 chr6A 581964318 581966287 1969 False 1419.0 2555 93.2420 1 2409 2 chr6A.!!$F1 2408
2 TraesCS6B01G383000 chr6D 434603462 434605845 2383 False 1485.5 2542 90.5695 1 2598 2 chr6D.!!$F3 2597
3 TraesCS6B01G383000 chr7D 549318205 549319192 987 True 268.7 468 87.1900 636 1616 2 chr7D.!!$R1 980
4 TraesCS6B01G383000 chr7D 549368315 549370024 1709 True 206.8 438 84.5570 229 1620 3 chr7D.!!$R2 1391

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
504 513 0.405973 AGGTTGCTTTCCTTCTCCCC 59.594 55.0 0.0 0.0 30.18 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 2863 0.036875 GGAAAGTAGTGGCTGCACCT 59.963 55.0 0.5 0.0 40.22 4.0 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
35 36 7.725844 AGTCCTCTACCTTCAATTTGTGAAATT 59.274 33.333 0.00 0.00 45.67 1.82
92 93 3.885297 GGTGCTAGTTATGATGTTGCCAT 59.115 43.478 0.00 0.00 0.00 4.40
170 171 9.799106 AATTTCCCCACATCTTAGTTGATATAG 57.201 33.333 0.00 0.00 0.00 1.31
231 232 8.247562 AGTAAGCTGAGAGTTACTATTCACTTG 58.752 37.037 6.03 3.89 37.64 3.16
288 297 1.997311 TGGGGCTGAGGATGAGTGG 60.997 63.158 0.00 0.00 0.00 4.00
290 299 1.690633 GGGCTGAGGATGAGTGGGA 60.691 63.158 0.00 0.00 0.00 4.37
334 343 7.519008 CGAGAATCCACTTTGGTATATCTTTGC 60.519 40.741 0.00 0.00 39.03 3.68
504 513 0.405973 AGGTTGCTTTCCTTCTCCCC 59.594 55.000 0.00 0.00 30.18 4.81
505 514 0.612174 GGTTGCTTTCCTTCTCCCCC 60.612 60.000 0.00 0.00 0.00 5.40
506 515 0.960861 GTTGCTTTCCTTCTCCCCCG 60.961 60.000 0.00 0.00 0.00 5.73
507 516 2.137177 TTGCTTTCCTTCTCCCCCGG 62.137 60.000 0.00 0.00 0.00 5.73
508 517 2.272471 CTTTCCTTCTCCCCCGGC 59.728 66.667 0.00 0.00 0.00 6.13
509 518 3.335729 TTTCCTTCTCCCCCGGCC 61.336 66.667 0.00 0.00 0.00 6.13
588 607 3.677424 GCTCGCTCTTGTCTGGTCTTAAT 60.677 47.826 0.00 0.00 0.00 1.40
605 624 8.537016 TGGTCTTAATTCTTAACTGCTAGCTAA 58.463 33.333 17.23 5.53 0.00 3.09
606 625 9.549078 GGTCTTAATTCTTAACTGCTAGCTAAT 57.451 33.333 17.23 4.14 0.00 1.73
932 1292 8.808092 ACTCCAGAGAAAATATATACTGGTAGC 58.192 37.037 12.25 0.00 43.39 3.58
1412 1848 4.086178 CTCGTCGTCGTCTGCGGT 62.086 66.667 1.33 0.00 38.89 5.68
1714 2163 7.609760 TGCACTATTGTTCTTGTACTTATGG 57.390 36.000 0.00 0.00 0.00 2.74
1738 2189 5.888105 GACATACTACGTCCTCTGCTTAAA 58.112 41.667 0.00 0.00 0.00 1.52
1803 2465 1.790481 GCCGCGTTTGCTAAATCTCAC 60.790 52.381 4.92 0.00 39.65 3.51
1806 2468 2.495939 GCGTTTGCTAAATCTCACGTG 58.504 47.619 9.94 9.94 38.39 4.49
1838 2500 8.485578 AAAATTATGGGAGTGGTTTTTCTACA 57.514 30.769 0.00 0.00 0.00 2.74
1839 2501 7.462571 AATTATGGGAGTGGTTTTTCTACAC 57.537 36.000 0.00 0.00 35.43 2.90
1840 2502 3.217681 TGGGAGTGGTTTTTCTACACC 57.782 47.619 0.00 0.00 37.50 4.16
1841 2503 2.511659 GGGAGTGGTTTTTCTACACCC 58.488 52.381 0.00 0.00 46.61 4.61
1842 2504 2.511659 GGAGTGGTTTTTCTACACCCC 58.488 52.381 0.00 0.00 33.61 4.95
1843 2505 2.158579 GGAGTGGTTTTTCTACACCCCA 60.159 50.000 0.00 0.00 33.61 4.96
1844 2506 3.146847 GAGTGGTTTTTCTACACCCCAG 58.853 50.000 0.00 0.00 35.79 4.45
1845 2507 2.512476 AGTGGTTTTTCTACACCCCAGT 59.488 45.455 0.00 0.00 35.79 4.00
1846 2508 2.882761 GTGGTTTTTCTACACCCCAGTC 59.117 50.000 0.00 0.00 31.24 3.51
1847 2509 2.158579 TGGTTTTTCTACACCCCAGTCC 60.159 50.000 0.00 0.00 31.24 3.85
1848 2510 2.148768 GTTTTTCTACACCCCAGTCCG 58.851 52.381 0.00 0.00 0.00 4.79
1849 2511 0.688487 TTTTCTACACCCCAGTCCGG 59.312 55.000 0.00 0.00 0.00 5.14
1850 2512 0.472352 TTTCTACACCCCAGTCCGGT 60.472 55.000 0.00 0.00 0.00 5.28
1851 2513 0.472352 TTCTACACCCCAGTCCGGTT 60.472 55.000 0.00 0.00 0.00 4.44
1852 2514 0.901580 TCTACACCCCAGTCCGGTTC 60.902 60.000 0.00 0.00 0.00 3.62
1853 2515 1.152290 TACACCCCAGTCCGGTTCA 60.152 57.895 0.00 0.00 0.00 3.18
1854 2516 1.474332 TACACCCCAGTCCGGTTCAC 61.474 60.000 0.00 0.00 0.00 3.18
1855 2517 3.246880 ACCCCAGTCCGGTTCACC 61.247 66.667 0.00 0.00 0.00 4.02
1856 2518 4.029809 CCCCAGTCCGGTTCACCC 62.030 72.222 0.00 0.00 0.00 4.61
1857 2519 3.246112 CCCAGTCCGGTTCACCCA 61.246 66.667 0.00 0.00 0.00 4.51
1858 2520 2.032071 CCAGTCCGGTTCACCCAC 59.968 66.667 0.00 0.00 0.00 4.61
1859 2521 2.357034 CAGTCCGGTTCACCCACG 60.357 66.667 0.00 0.00 0.00 4.94
1870 2532 2.045045 ACCCACGGTGCATCCATG 60.045 61.111 1.68 0.00 32.98 3.66
1944 2606 7.700505 TGATCATCAACAAATGTTATGAGAGC 58.299 34.615 16.25 9.54 36.32 4.09
1945 2607 7.555195 TGATCATCAACAAATGTTATGAGAGCT 59.445 33.333 16.25 0.00 36.32 4.09
1946 2608 7.692460 TCATCAACAAATGTTATGAGAGCTT 57.308 32.000 0.00 0.00 36.32 3.74
1947 2609 7.532571 TCATCAACAAATGTTATGAGAGCTTG 58.467 34.615 0.00 0.00 36.32 4.01
1948 2610 5.702865 TCAACAAATGTTATGAGAGCTTGC 58.297 37.500 0.00 0.00 36.32 4.01
1949 2611 5.241285 TCAACAAATGTTATGAGAGCTTGCA 59.759 36.000 0.00 0.00 36.32 4.08
1950 2612 5.710513 ACAAATGTTATGAGAGCTTGCAA 57.289 34.783 0.00 0.00 0.00 4.08
1951 2613 6.088016 ACAAATGTTATGAGAGCTTGCAAA 57.912 33.333 0.00 0.00 0.00 3.68
1952 2614 6.643770 AACAAATGTTATGAGAGCTTGCAAAG 59.356 34.615 0.00 0.00 41.17 2.77
1962 2624 3.575399 CTTGCAAAGCTTGGTGGTC 57.425 52.632 0.00 0.00 36.98 4.02
1963 2625 0.746063 CTTGCAAAGCTTGGTGGTCA 59.254 50.000 0.00 0.00 36.98 4.02
1964 2626 1.136695 CTTGCAAAGCTTGGTGGTCAA 59.863 47.619 0.00 0.00 36.98 3.18
1965 2627 1.189752 TGCAAAGCTTGGTGGTCAAA 58.810 45.000 0.00 0.00 34.56 2.69
1966 2628 1.761784 TGCAAAGCTTGGTGGTCAAAT 59.238 42.857 0.00 0.00 34.56 2.32
1967 2629 2.961741 TGCAAAGCTTGGTGGTCAAATA 59.038 40.909 0.00 0.00 34.56 1.40
1968 2630 3.386078 TGCAAAGCTTGGTGGTCAAATAA 59.614 39.130 0.00 0.00 34.56 1.40
1969 2631 3.740832 GCAAAGCTTGGTGGTCAAATAAC 59.259 43.478 0.00 0.00 34.56 1.89
1970 2632 4.739137 GCAAAGCTTGGTGGTCAAATAACA 60.739 41.667 0.00 0.00 34.56 2.41
1971 2633 5.540911 CAAAGCTTGGTGGTCAAATAACAT 58.459 37.500 0.00 0.00 34.56 2.71
1972 2634 5.806654 AAGCTTGGTGGTCAAATAACATT 57.193 34.783 0.00 0.00 34.56 2.71
1973 2635 5.391312 AGCTTGGTGGTCAAATAACATTC 57.609 39.130 0.00 0.00 34.56 2.67
1974 2636 4.082787 AGCTTGGTGGTCAAATAACATTCG 60.083 41.667 0.00 0.00 34.56 3.34
1975 2637 4.083003 GCTTGGTGGTCAAATAACATTCGA 60.083 41.667 0.00 0.00 34.56 3.71
1976 2638 5.621197 TTGGTGGTCAAATAACATTCGAG 57.379 39.130 0.00 0.00 31.46 4.04
1977 2639 4.006989 TGGTGGTCAAATAACATTCGAGG 58.993 43.478 0.00 0.00 0.00 4.63
1978 2640 4.258543 GGTGGTCAAATAACATTCGAGGA 58.741 43.478 0.00 0.00 0.00 3.71
1979 2641 4.332819 GGTGGTCAAATAACATTCGAGGAG 59.667 45.833 0.00 0.00 0.00 3.69
1980 2642 3.938963 TGGTCAAATAACATTCGAGGAGC 59.061 43.478 0.00 0.00 0.00 4.70
1981 2643 4.192317 GGTCAAATAACATTCGAGGAGCT 58.808 43.478 0.00 0.00 0.00 4.09
1982 2644 4.636206 GGTCAAATAACATTCGAGGAGCTT 59.364 41.667 0.00 0.00 0.00 3.74
1983 2645 5.123979 GGTCAAATAACATTCGAGGAGCTTT 59.876 40.000 0.00 0.00 0.00 3.51
1984 2646 6.024049 GTCAAATAACATTCGAGGAGCTTTG 58.976 40.000 0.00 0.00 0.00 2.77
1985 2647 5.705441 TCAAATAACATTCGAGGAGCTTTGT 59.295 36.000 0.00 0.00 0.00 2.83
1986 2648 6.876789 TCAAATAACATTCGAGGAGCTTTGTA 59.123 34.615 0.00 0.00 0.00 2.41
1987 2649 6.663944 AATAACATTCGAGGAGCTTTGTAC 57.336 37.500 0.00 0.00 0.00 2.90
1988 2650 3.678056 ACATTCGAGGAGCTTTGTACA 57.322 42.857 0.00 0.00 0.00 2.90
1989 2651 4.002906 ACATTCGAGGAGCTTTGTACAA 57.997 40.909 3.59 3.59 0.00 2.41
1990 2652 4.385825 ACATTCGAGGAGCTTTGTACAAA 58.614 39.130 19.53 19.53 0.00 2.83
1991 2653 4.819630 ACATTCGAGGAGCTTTGTACAAAA 59.180 37.500 20.89 4.44 0.00 2.44
1992 2654 5.298276 ACATTCGAGGAGCTTTGTACAAAAA 59.702 36.000 20.89 10.66 0.00 1.94
2016 2678 9.736023 AAAAGACAACATCAGTGAAAATTAGTC 57.264 29.630 0.00 1.58 0.00 2.59
2017 2679 8.450578 AAGACAACATCAGTGAAAATTAGTCA 57.549 30.769 0.00 0.00 0.00 3.41
2018 2680 8.450578 AGACAACATCAGTGAAAATTAGTCAA 57.549 30.769 0.00 0.00 0.00 3.18
2019 2681 8.902806 AGACAACATCAGTGAAAATTAGTCAAA 58.097 29.630 0.00 0.00 0.00 2.69
2020 2682 9.515020 GACAACATCAGTGAAAATTAGTCAAAA 57.485 29.630 0.00 0.00 0.00 2.44
2029 2691 9.463443 AGTGAAAATTAGTCAAAATGTAAGTGC 57.537 29.630 0.00 0.00 0.00 4.40
2030 2692 9.243637 GTGAAAATTAGTCAAAATGTAAGTGCA 57.756 29.630 0.00 0.00 0.00 4.57
2031 2693 9.979578 TGAAAATTAGTCAAAATGTAAGTGCAT 57.020 25.926 0.00 0.00 0.00 3.96
2034 2696 9.762933 AAATTAGTCAAAATGTAAGTGCATTGT 57.237 25.926 0.00 0.00 38.87 2.71
2035 2697 9.762933 AATTAGTCAAAATGTAAGTGCATTGTT 57.237 25.926 0.00 0.00 38.87 2.83
2036 2698 9.762933 ATTAGTCAAAATGTAAGTGCATTGTTT 57.237 25.926 0.00 0.00 38.87 2.83
2037 2699 7.467557 AGTCAAAATGTAAGTGCATTGTTTG 57.532 32.000 0.00 0.00 38.87 2.93
2038 2700 7.264221 AGTCAAAATGTAAGTGCATTGTTTGA 58.736 30.769 0.00 5.60 38.87 2.69
2039 2701 7.436080 AGTCAAAATGTAAGTGCATTGTTTGAG 59.564 33.333 8.56 0.00 36.80 3.02
2040 2702 6.200665 TCAAAATGTAAGTGCATTGTTTGAGC 59.799 34.615 0.00 0.00 38.87 4.26
2041 2703 4.852134 ATGTAAGTGCATTGTTTGAGCA 57.148 36.364 0.00 0.00 35.63 4.26
2042 2704 4.227512 TGTAAGTGCATTGTTTGAGCAG 57.772 40.909 0.00 0.00 39.21 4.24
2043 2705 3.882288 TGTAAGTGCATTGTTTGAGCAGA 59.118 39.130 0.00 0.00 39.21 4.26
2044 2706 4.520111 TGTAAGTGCATTGTTTGAGCAGAT 59.480 37.500 0.00 0.00 39.21 2.90
2045 2707 4.595762 AAGTGCATTGTTTGAGCAGATT 57.404 36.364 0.00 0.00 39.21 2.40
2046 2708 4.595762 AGTGCATTGTTTGAGCAGATTT 57.404 36.364 0.00 0.00 39.21 2.17
2047 2709 4.952460 AGTGCATTGTTTGAGCAGATTTT 58.048 34.783 0.00 0.00 39.21 1.82
2048 2710 4.748102 AGTGCATTGTTTGAGCAGATTTTG 59.252 37.500 0.00 0.00 39.21 2.44
2049 2711 4.508861 GTGCATTGTTTGAGCAGATTTTGT 59.491 37.500 0.00 0.00 39.21 2.83
2050 2712 5.691305 GTGCATTGTTTGAGCAGATTTTGTA 59.309 36.000 0.00 0.00 39.21 2.41
2051 2713 6.200665 GTGCATTGTTTGAGCAGATTTTGTAA 59.799 34.615 0.00 0.00 39.21 2.41
2052 2714 6.930164 TGCATTGTTTGAGCAGATTTTGTAAT 59.070 30.769 0.00 0.00 33.75 1.89
2053 2715 7.441760 TGCATTGTTTGAGCAGATTTTGTAATT 59.558 29.630 0.00 0.00 33.75 1.40
2054 2716 8.284693 GCATTGTTTGAGCAGATTTTGTAATTT 58.715 29.630 0.00 0.00 0.00 1.82
2077 2739 6.575162 TTTTTCTTTTCTGTATGGAGCTCC 57.425 37.500 26.78 26.78 0.00 4.70
2078 2740 5.505181 TTTCTTTTCTGTATGGAGCTCCT 57.495 39.130 32.28 20.00 36.82 3.69
2079 2741 4.744795 TCTTTTCTGTATGGAGCTCCTC 57.255 45.455 32.28 21.69 36.82 3.71
2080 2742 3.131223 TCTTTTCTGTATGGAGCTCCTCG 59.869 47.826 32.28 15.83 36.82 4.63
2081 2743 2.437085 TTCTGTATGGAGCTCCTCGA 57.563 50.000 32.28 14.20 36.82 4.04
2082 2744 2.437085 TCTGTATGGAGCTCCTCGAA 57.563 50.000 32.28 13.81 36.82 3.71
2083 2745 2.950781 TCTGTATGGAGCTCCTCGAAT 58.049 47.619 32.28 19.85 36.82 3.34
2084 2746 2.625314 TCTGTATGGAGCTCCTCGAATG 59.375 50.000 32.28 17.65 36.82 2.67
2085 2747 2.363680 CTGTATGGAGCTCCTCGAATGT 59.636 50.000 32.28 12.30 36.82 2.71
2086 2748 2.766263 TGTATGGAGCTCCTCGAATGTT 59.234 45.455 32.28 10.07 36.82 2.71
2087 2749 3.958147 TGTATGGAGCTCCTCGAATGTTA 59.042 43.478 32.28 10.24 36.82 2.41
2088 2750 4.588951 TGTATGGAGCTCCTCGAATGTTAT 59.411 41.667 32.28 16.67 36.82 1.89
2089 2751 4.696479 ATGGAGCTCCTCGAATGTTATT 57.304 40.909 32.28 0.00 36.82 1.40
2090 2752 4.487714 TGGAGCTCCTCGAATGTTATTT 57.512 40.909 32.28 0.00 36.82 1.40
2091 2753 4.191544 TGGAGCTCCTCGAATGTTATTTG 58.808 43.478 32.28 0.00 36.82 2.32
2092 2754 4.081142 TGGAGCTCCTCGAATGTTATTTGA 60.081 41.667 32.28 4.17 36.82 2.69
2093 2755 4.271291 GGAGCTCCTCGAATGTTATTTGAC 59.729 45.833 26.25 0.00 0.00 3.18
2094 2756 4.192317 AGCTCCTCGAATGTTATTTGACC 58.808 43.478 0.00 0.00 0.00 4.02
2095 2757 3.938963 GCTCCTCGAATGTTATTTGACCA 59.061 43.478 0.00 0.00 0.00 4.02
2096 2758 4.201822 GCTCCTCGAATGTTATTTGACCAC 60.202 45.833 0.00 0.00 0.00 4.16
2097 2759 4.258543 TCCTCGAATGTTATTTGACCACC 58.741 43.478 0.00 0.00 0.00 4.61
2098 2760 4.006989 CCTCGAATGTTATTTGACCACCA 58.993 43.478 0.00 0.00 0.00 4.17
2099 2761 4.457603 CCTCGAATGTTATTTGACCACCAA 59.542 41.667 0.00 0.00 0.00 3.67
2101 2763 5.764131 TCGAATGTTATTTGACCACCAAAC 58.236 37.500 0.00 0.00 46.41 2.93
2102 2764 5.533154 TCGAATGTTATTTGACCACCAAACT 59.467 36.000 0.00 0.00 46.41 2.66
2103 2765 6.039941 TCGAATGTTATTTGACCACCAAACTT 59.960 34.615 0.00 0.00 46.41 2.66
2104 2766 6.699642 CGAATGTTATTTGACCACCAAACTTT 59.300 34.615 0.00 0.00 46.41 2.66
2105 2767 7.306515 CGAATGTTATTTGACCACCAAACTTTG 60.307 37.037 0.00 0.00 46.41 2.77
2106 2768 5.112686 TGTTATTTGACCACCAAACTTTGC 58.887 37.500 0.00 0.00 46.41 3.68
2107 2769 3.902881 ATTTGACCACCAAACTTTGCA 57.097 38.095 0.00 0.00 46.41 4.08
2108 2770 2.957491 TTGACCACCAAACTTTGCAG 57.043 45.000 0.00 0.00 0.00 4.41
2109 2771 0.459489 TGACCACCAAACTTTGCAGC 59.541 50.000 0.00 0.00 0.00 5.25
2110 2772 0.459489 GACCACCAAACTTTGCAGCA 59.541 50.000 0.00 0.00 0.00 4.41
2111 2773 0.175531 ACCACCAAACTTTGCAGCAC 59.824 50.000 0.00 0.00 0.00 4.40
2112 2774 0.461135 CCACCAAACTTTGCAGCACT 59.539 50.000 0.00 0.00 0.00 4.40
2113 2775 1.536709 CCACCAAACTTTGCAGCACTC 60.537 52.381 0.00 0.00 0.00 3.51
2114 2776 1.134753 CACCAAACTTTGCAGCACTCA 59.865 47.619 0.00 0.00 0.00 3.41
2115 2777 2.034124 ACCAAACTTTGCAGCACTCAT 58.966 42.857 0.00 0.00 0.00 2.90
2116 2778 3.004629 CACCAAACTTTGCAGCACTCATA 59.995 43.478 0.00 0.00 0.00 2.15
2117 2779 3.636300 ACCAAACTTTGCAGCACTCATAA 59.364 39.130 0.00 0.00 0.00 1.90
2118 2780 3.983344 CCAAACTTTGCAGCACTCATAAC 59.017 43.478 0.00 0.00 0.00 1.89
2119 2781 4.499526 CCAAACTTTGCAGCACTCATAACA 60.500 41.667 0.00 0.00 0.00 2.41
2120 2782 5.224888 CAAACTTTGCAGCACTCATAACAT 58.775 37.500 0.00 0.00 0.00 2.71
2121 2783 5.458041 AACTTTGCAGCACTCATAACATT 57.542 34.783 0.00 0.00 0.00 2.71
2122 2784 5.458041 ACTTTGCAGCACTCATAACATTT 57.542 34.783 0.00 0.00 0.00 2.32
2123 2785 5.224888 ACTTTGCAGCACTCATAACATTTG 58.775 37.500 0.00 0.00 0.00 2.32
2124 2786 4.852134 TTGCAGCACTCATAACATTTGT 57.148 36.364 0.00 0.00 0.00 2.83
2125 2787 4.852134 TGCAGCACTCATAACATTTGTT 57.148 36.364 0.00 1.08 41.73 2.83
2126 2788 4.548494 TGCAGCACTCATAACATTTGTTG 58.452 39.130 6.21 0.00 38.90 3.33
2127 2789 4.277921 TGCAGCACTCATAACATTTGTTGA 59.722 37.500 6.21 0.00 38.90 3.18
2128 2790 5.047872 TGCAGCACTCATAACATTTGTTGAT 60.048 36.000 6.21 0.00 38.90 2.57
2129 2791 6.150809 TGCAGCACTCATAACATTTGTTGATA 59.849 34.615 6.21 0.00 38.90 2.15
2130 2792 7.028962 GCAGCACTCATAACATTTGTTGATAA 58.971 34.615 6.21 0.00 38.90 1.75
2131 2793 7.703621 GCAGCACTCATAACATTTGTTGATAAT 59.296 33.333 6.21 0.00 38.90 1.28
2132 2794 9.229784 CAGCACTCATAACATTTGTTGATAATC 57.770 33.333 6.21 0.00 38.90 1.75
2133 2795 8.959548 AGCACTCATAACATTTGTTGATAATCA 58.040 29.630 6.21 0.00 38.90 2.57
2134 2796 9.740239 GCACTCATAACATTTGTTGATAATCAT 57.260 29.630 6.21 0.00 38.90 2.45
2203 2865 4.415783 GGGTGCACCAAAGGTAGG 57.584 61.111 35.78 0.00 39.85 3.18
2204 2866 1.458927 GGGTGCACCAAAGGTAGGT 59.541 57.895 35.78 0.00 40.85 3.08
2209 2871 4.821935 ACCAAAGGTAGGTGCAGC 57.178 55.556 8.11 8.11 38.13 5.25
2210 2872 1.074951 ACCAAAGGTAGGTGCAGCC 59.925 57.895 13.29 4.65 38.13 4.85
2211 2873 1.074775 CCAAAGGTAGGTGCAGCCA 59.925 57.895 13.29 0.00 40.61 4.75
2212 2874 1.244019 CCAAAGGTAGGTGCAGCCAC 61.244 60.000 13.29 9.41 40.61 5.01
2213 2875 0.250901 CAAAGGTAGGTGCAGCCACT 60.251 55.000 13.29 5.50 41.75 4.00
2214 2876 1.003118 CAAAGGTAGGTGCAGCCACTA 59.997 52.381 13.29 0.00 41.75 2.74
2215 2877 0.613777 AAGGTAGGTGCAGCCACTAC 59.386 55.000 13.29 8.71 41.75 2.73
2216 2878 0.252284 AGGTAGGTGCAGCCACTACT 60.252 55.000 13.29 0.00 41.75 2.57
2217 2879 0.613777 GGTAGGTGCAGCCACTACTT 59.386 55.000 13.29 0.00 41.75 2.24
2218 2880 1.003233 GGTAGGTGCAGCCACTACTTT 59.997 52.381 13.29 0.00 41.75 2.66
2219 2881 2.347731 GTAGGTGCAGCCACTACTTTC 58.652 52.381 13.29 0.00 41.75 2.62
2220 2882 0.036875 AGGTGCAGCCACTACTTTCC 59.963 55.000 13.29 0.00 41.75 3.13
2221 2883 0.960861 GGTGCAGCCACTACTTTCCC 60.961 60.000 4.03 0.00 41.75 3.97
2222 2884 0.250727 GTGCAGCCACTACTTTCCCA 60.251 55.000 0.00 0.00 38.93 4.37
2223 2885 0.476338 TGCAGCCACTACTTTCCCAA 59.524 50.000 0.00 0.00 0.00 4.12
2224 2886 1.133637 TGCAGCCACTACTTTCCCAAA 60.134 47.619 0.00 0.00 0.00 3.28
2225 2887 1.960689 GCAGCCACTACTTTCCCAAAA 59.039 47.619 0.00 0.00 0.00 2.44
2226 2888 2.364002 GCAGCCACTACTTTCCCAAAAA 59.636 45.455 0.00 0.00 0.00 1.94
2290 2953 1.939769 GAGGAGGTGAGGAGCGACAC 61.940 65.000 0.00 0.00 36.44 3.67
2297 2960 1.137825 GAGGAGCGACACGAAGGAG 59.862 63.158 0.00 0.00 0.00 3.69
2301 2964 2.733593 GCGACACGAAGGAGCGTT 60.734 61.111 0.00 0.00 43.59 4.84
2331 2994 3.987404 GCCAAGCCATGAACGAGT 58.013 55.556 0.00 0.00 0.00 4.18
2404 3067 2.313427 GGGGATGCAGGGGTTACCA 61.313 63.158 2.98 0.00 43.89 3.25
2411 3074 0.400594 GCAGGGGTTACCAGAGTTGT 59.599 55.000 2.98 0.00 43.89 3.32
2417 3080 3.325716 GGGGTTACCAGAGTTGTTGTAGA 59.674 47.826 2.98 0.00 39.85 2.59
2420 3083 6.002082 GGGTTACCAGAGTTGTTGTAGATTT 58.998 40.000 2.98 0.00 36.50 2.17
2423 3086 4.398319 ACCAGAGTTGTTGTAGATTTGGG 58.602 43.478 0.00 0.00 0.00 4.12
2425 3088 3.758554 CAGAGTTGTTGTAGATTTGGGGG 59.241 47.826 0.00 0.00 0.00 5.40
2460 3123 2.586079 CTGGCGGTGGCTATCACG 60.586 66.667 0.00 0.00 46.96 4.35
2468 3131 2.189521 GGCTATCACGGTGGGGTG 59.810 66.667 8.50 0.00 39.29 4.61
2469 3132 2.189521 GCTATCACGGTGGGGTGG 59.810 66.667 8.50 0.00 38.46 4.61
2470 3133 2.908015 CTATCACGGTGGGGTGGG 59.092 66.667 8.50 0.00 38.46 4.61
2471 3134 2.689402 TATCACGGTGGGGTGGGG 60.689 66.667 8.50 0.00 38.46 4.96
2472 3135 3.566016 TATCACGGTGGGGTGGGGT 62.566 63.158 8.50 0.00 38.46 4.95
2495 3158 2.204090 GGGGGTGGGGAGTTGAGA 60.204 66.667 0.00 0.00 0.00 3.27
2500 3163 1.645710 GGTGGGGAGTTGAGAGAAGA 58.354 55.000 0.00 0.00 0.00 2.87
2503 3166 1.132849 TGGGGAGTTGAGAGAAGACCA 60.133 52.381 0.00 0.00 0.00 4.02
2507 3170 2.635427 GGAGTTGAGAGAAGACCAAGGT 59.365 50.000 0.00 0.00 0.00 3.50
2515 3178 1.527433 GAAGACCAAGGTGGCAAGGC 61.527 60.000 0.00 0.00 42.67 4.35
2516 3179 2.203480 GACCAAGGTGGCAAGGCA 60.203 61.111 0.00 0.00 42.67 4.75
2520 3183 1.474332 CCAAGGTGGCAAGGCAATGT 61.474 55.000 0.00 0.00 0.00 2.71
2529 3192 0.168788 CAAGGCAATGTGTGGTAGCG 59.831 55.000 0.00 0.00 0.00 4.26
2532 3195 3.051392 GCAATGTGTGGTAGCGCCC 62.051 63.158 2.29 0.00 36.04 6.13
2569 3232 3.344137 ATGCCGGTGGTTAGGGCTG 62.344 63.158 1.90 0.00 46.97 4.85
2599 3262 4.357947 GGCGTCTGCGTGAGGACA 62.358 66.667 3.86 0.00 44.10 4.02
2600 3263 2.355837 GCGTCTGCGTGAGGACAA 60.356 61.111 3.86 0.00 40.81 3.18
2601 3264 2.375766 GCGTCTGCGTGAGGACAAG 61.376 63.158 3.86 0.00 40.81 3.16
2602 3265 1.285950 CGTCTGCGTGAGGACAAGA 59.714 57.895 0.00 0.00 32.72 3.02
2603 3266 0.730834 CGTCTGCGTGAGGACAAGAG 60.731 60.000 0.00 0.00 32.72 2.85
2604 3267 0.598562 GTCTGCGTGAGGACAAGAGA 59.401 55.000 0.00 0.00 33.19 3.10
2605 3268 1.000163 GTCTGCGTGAGGACAAGAGAA 60.000 52.381 0.00 0.00 33.19 2.87
2606 3269 1.270826 TCTGCGTGAGGACAAGAGAAG 59.729 52.381 0.00 0.00 0.00 2.85
2607 3270 0.319900 TGCGTGAGGACAAGAGAAGC 60.320 55.000 0.00 0.00 0.00 3.86
2608 3271 0.319900 GCGTGAGGACAAGAGAAGCA 60.320 55.000 0.00 0.00 0.00 3.91
2609 3272 1.873903 GCGTGAGGACAAGAGAAGCAA 60.874 52.381 0.00 0.00 0.00 3.91
2610 3273 2.693069 CGTGAGGACAAGAGAAGCAAT 58.307 47.619 0.00 0.00 0.00 3.56
2611 3274 2.670414 CGTGAGGACAAGAGAAGCAATC 59.330 50.000 0.00 0.00 0.00 2.67
2612 3275 2.670414 GTGAGGACAAGAGAAGCAATCG 59.330 50.000 0.00 0.00 0.00 3.34
2613 3276 2.275318 GAGGACAAGAGAAGCAATCGG 58.725 52.381 0.00 0.00 0.00 4.18
2614 3277 1.902508 AGGACAAGAGAAGCAATCGGA 59.097 47.619 0.00 0.00 0.00 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 4.332819 CCAAACGAGTTACAGATCATTCCC 59.667 45.833 0.00 0.00 0.00 3.97
101 102 5.454329 GGGATGTGAGGGTAGGTGTTATTAC 60.454 48.000 0.00 0.00 0.00 1.89
169 170 9.830975 AAAATGCCTTTTACTCAACAAAATACT 57.169 25.926 0.00 0.00 32.81 2.12
170 171 9.862585 CAAAATGCCTTTTACTCAACAAAATAC 57.137 29.630 0.00 0.00 32.81 1.89
231 232 9.552114 CTCTTGTCACAATAATCAATTCTTCAC 57.448 33.333 0.00 0.00 0.00 3.18
288 297 4.433615 TCGAACATTCAAGTCTGCTATCC 58.566 43.478 0.00 0.00 0.00 2.59
290 299 5.330455 TCTCGAACATTCAAGTCTGCTAT 57.670 39.130 0.00 0.00 0.00 2.97
334 343 3.321682 TGCCATGAGGAACAAGAAAAAGG 59.678 43.478 0.00 0.00 36.89 3.11
504 513 1.353394 AATCTAGGAAAGGGGGCCGG 61.353 60.000 0.00 0.00 0.00 6.13
505 514 1.430992 TAATCTAGGAAAGGGGGCCG 58.569 55.000 0.00 0.00 0.00 6.13
506 515 4.788617 TCATATAATCTAGGAAAGGGGGCC 59.211 45.833 0.00 0.00 0.00 5.80
507 516 6.360618 CATCATATAATCTAGGAAAGGGGGC 58.639 44.000 0.00 0.00 0.00 5.80
508 517 6.448387 ACCATCATATAATCTAGGAAAGGGGG 59.552 42.308 0.00 0.00 0.00 5.40
509 518 7.182749 TGACCATCATATAATCTAGGAAAGGGG 59.817 40.741 0.00 0.00 0.00 4.79
510 519 8.150827 TGACCATCATATAATCTAGGAAAGGG 57.849 38.462 0.00 0.00 0.00 3.95
511 520 9.610705 CATGACCATCATATAATCTAGGAAAGG 57.389 37.037 0.00 0.00 34.28 3.11
605 624 7.394359 GTGTATATCCATGGCTGGTGAATTAAT 59.606 37.037 6.96 0.00 43.61 1.40
606 625 6.714810 GTGTATATCCATGGCTGGTGAATTAA 59.285 38.462 6.96 0.00 43.61 1.40
607 626 6.183361 TGTGTATATCCATGGCTGGTGAATTA 60.183 38.462 6.96 0.00 43.61 1.40
608 627 5.072741 GTGTATATCCATGGCTGGTGAATT 58.927 41.667 6.96 0.00 43.61 2.17
892 1016 7.450124 TTCTCTGGAGTAGTTAGTGTAGTTG 57.550 40.000 0.00 0.00 0.00 3.16
894 1018 8.653036 ATTTTCTCTGGAGTAGTTAGTGTAGT 57.347 34.615 0.00 0.00 0.00 2.73
907 1031 7.971168 CGCTACCAGTATATATTTTCTCTGGAG 59.029 40.741 17.39 12.31 43.28 3.86
908 1032 7.577046 GCGCTACCAGTATATATTTTCTCTGGA 60.577 40.741 17.39 5.07 43.28 3.86
977 1357 0.248843 GGTGCACAAGAGGAGAGAGG 59.751 60.000 20.43 0.00 0.00 3.69
1087 1514 2.745884 CAACGCCCCGATCAGCAA 60.746 61.111 0.00 0.00 0.00 3.91
1422 1858 3.435186 GCCTCTGCAGTTTCGGCC 61.435 66.667 14.67 0.00 37.47 6.13
1533 1969 3.874141 GACGACAGCGACGCACTCA 62.874 63.158 23.70 0.00 41.64 3.41
1637 2076 8.950961 CAAAAGTAATTTATCGACTGATGCATG 58.049 33.333 2.46 0.00 35.99 4.06
1817 2479 5.318630 GGTGTAGAAAAACCACTCCCATAA 58.681 41.667 0.00 0.00 36.41 1.90
1818 2480 4.263594 GGGTGTAGAAAAACCACTCCCATA 60.264 45.833 6.28 0.00 42.82 2.74
1820 2482 2.158579 GGGTGTAGAAAAACCACTCCCA 60.159 50.000 6.28 0.00 42.82 4.37
1821 2483 2.511659 GGGTGTAGAAAAACCACTCCC 58.488 52.381 0.00 0.00 38.44 4.30
1822 2484 2.511659 GGGGTGTAGAAAAACCACTCC 58.488 52.381 0.00 0.00 42.17 3.85
1823 2485 3.146847 CTGGGGTGTAGAAAAACCACTC 58.853 50.000 0.00 0.00 40.77 3.51
1824 2486 2.512476 ACTGGGGTGTAGAAAAACCACT 59.488 45.455 0.00 0.00 40.77 4.00
1825 2487 2.882761 GACTGGGGTGTAGAAAAACCAC 59.117 50.000 0.00 0.00 40.53 4.16
1826 2488 2.158579 GGACTGGGGTGTAGAAAAACCA 60.159 50.000 0.00 0.00 38.27 3.67
1827 2489 2.511659 GGACTGGGGTGTAGAAAAACC 58.488 52.381 0.00 0.00 35.59 3.27
1828 2490 2.148768 CGGACTGGGGTGTAGAAAAAC 58.851 52.381 0.00 0.00 0.00 2.43
1829 2491 1.072648 CCGGACTGGGGTGTAGAAAAA 59.927 52.381 0.00 0.00 0.00 1.94
1830 2492 0.688487 CCGGACTGGGGTGTAGAAAA 59.312 55.000 0.00 0.00 0.00 2.29
1831 2493 0.472352 ACCGGACTGGGGTGTAGAAA 60.472 55.000 9.46 0.00 44.64 2.52
1832 2494 0.472352 AACCGGACTGGGGTGTAGAA 60.472 55.000 9.46 0.00 44.64 2.10
1833 2495 0.901580 GAACCGGACTGGGGTGTAGA 60.902 60.000 9.46 0.00 44.64 2.59
1834 2496 1.189524 TGAACCGGACTGGGGTGTAG 61.190 60.000 9.46 0.00 44.64 2.74
1835 2497 1.152290 TGAACCGGACTGGGGTGTA 60.152 57.895 9.46 0.00 44.64 2.90
1836 2498 2.446994 TGAACCGGACTGGGGTGT 60.447 61.111 9.46 0.00 44.64 4.16
1837 2499 2.032071 GTGAACCGGACTGGGGTG 59.968 66.667 9.46 0.00 44.64 4.61
1838 2500 3.246880 GGTGAACCGGACTGGGGT 61.247 66.667 9.46 0.00 44.64 4.95
1839 2501 4.029809 GGGTGAACCGGACTGGGG 62.030 72.222 9.46 0.00 44.64 4.96
1840 2502 3.246112 TGGGTGAACCGGACTGGG 61.246 66.667 9.46 0.00 44.64 4.45
1841 2503 2.032071 GTGGGTGAACCGGACTGG 59.968 66.667 9.46 0.00 44.64 4.00
1842 2504 2.357034 CGTGGGTGAACCGGACTG 60.357 66.667 9.46 0.00 44.64 3.51
1843 2505 3.622826 CCGTGGGTGAACCGGACT 61.623 66.667 9.46 0.00 44.41 3.85
1844 2506 3.932483 ACCGTGGGTGAACCGGAC 61.932 66.667 9.46 1.77 44.41 4.79
1918 2580 8.350722 GCTCTCATAACATTTGTTGATGATCAT 58.649 33.333 8.25 8.25 38.90 2.45
1919 2581 7.555195 AGCTCTCATAACATTTGTTGATGATCA 59.445 33.333 0.00 0.00 38.90 2.92
1920 2582 7.928103 AGCTCTCATAACATTTGTTGATGATC 58.072 34.615 6.21 0.00 38.90 2.92
1921 2583 7.876936 AGCTCTCATAACATTTGTTGATGAT 57.123 32.000 6.21 0.00 38.90 2.45
1922 2584 7.532571 CAAGCTCTCATAACATTTGTTGATGA 58.467 34.615 6.21 9.61 38.90 2.92
1923 2585 6.252869 GCAAGCTCTCATAACATTTGTTGATG 59.747 38.462 6.21 6.43 38.90 3.07
1924 2586 6.071784 TGCAAGCTCTCATAACATTTGTTGAT 60.072 34.615 6.21 0.00 38.90 2.57
1925 2587 5.241285 TGCAAGCTCTCATAACATTTGTTGA 59.759 36.000 6.21 0.00 38.90 3.18
1926 2588 5.463286 TGCAAGCTCTCATAACATTTGTTG 58.537 37.500 6.21 0.00 38.90 3.33
1927 2589 5.710513 TGCAAGCTCTCATAACATTTGTT 57.289 34.783 1.08 1.08 41.73 2.83
1928 2590 5.710513 TTGCAAGCTCTCATAACATTTGT 57.289 34.783 0.00 0.00 0.00 2.83
1929 2591 6.627690 CTTTGCAAGCTCTCATAACATTTG 57.372 37.500 0.00 0.00 0.00 2.32
1944 2606 0.746063 TGACCACCAAGCTTTGCAAG 59.254 50.000 0.00 0.00 0.00 4.01
1945 2607 1.189752 TTGACCACCAAGCTTTGCAA 58.810 45.000 0.00 0.00 0.00 4.08
1946 2608 1.189752 TTTGACCACCAAGCTTTGCA 58.810 45.000 0.00 0.00 35.94 4.08
1947 2609 2.531522 ATTTGACCACCAAGCTTTGC 57.468 45.000 0.00 0.00 35.94 3.68
1948 2610 4.942852 TGTTATTTGACCACCAAGCTTTG 58.057 39.130 0.00 0.00 35.94 2.77
1949 2611 5.806654 ATGTTATTTGACCACCAAGCTTT 57.193 34.783 0.00 0.00 35.94 3.51
1950 2612 5.564651 CGAATGTTATTTGACCACCAAGCTT 60.565 40.000 0.00 0.00 35.94 3.74
1951 2613 4.082787 CGAATGTTATTTGACCACCAAGCT 60.083 41.667 0.00 0.00 35.94 3.74
1952 2614 4.083003 TCGAATGTTATTTGACCACCAAGC 60.083 41.667 0.00 0.00 35.94 4.01
1953 2615 5.391950 CCTCGAATGTTATTTGACCACCAAG 60.392 44.000 0.00 0.00 35.94 3.61
1954 2616 4.457603 CCTCGAATGTTATTTGACCACCAA 59.542 41.667 0.00 0.00 0.00 3.67
1955 2617 4.006989 CCTCGAATGTTATTTGACCACCA 58.993 43.478 0.00 0.00 0.00 4.17
1956 2618 4.258543 TCCTCGAATGTTATTTGACCACC 58.741 43.478 0.00 0.00 0.00 4.61
1957 2619 4.201822 GCTCCTCGAATGTTATTTGACCAC 60.202 45.833 0.00 0.00 0.00 4.16
1958 2620 3.938963 GCTCCTCGAATGTTATTTGACCA 59.061 43.478 0.00 0.00 0.00 4.02
1959 2621 4.192317 AGCTCCTCGAATGTTATTTGACC 58.808 43.478 0.00 0.00 0.00 4.02
1960 2622 5.803020 AAGCTCCTCGAATGTTATTTGAC 57.197 39.130 0.00 0.00 0.00 3.18
1961 2623 5.705441 ACAAAGCTCCTCGAATGTTATTTGA 59.295 36.000 12.70 0.00 0.00 2.69
1962 2624 5.942872 ACAAAGCTCCTCGAATGTTATTTG 58.057 37.500 0.00 6.96 0.00 2.32
1963 2625 6.653320 TGTACAAAGCTCCTCGAATGTTATTT 59.347 34.615 0.00 0.00 0.00 1.40
1964 2626 6.170506 TGTACAAAGCTCCTCGAATGTTATT 58.829 36.000 0.00 0.00 0.00 1.40
1965 2627 5.730550 TGTACAAAGCTCCTCGAATGTTAT 58.269 37.500 0.00 0.00 0.00 1.89
1966 2628 5.142061 TGTACAAAGCTCCTCGAATGTTA 57.858 39.130 0.00 0.00 0.00 2.41
1967 2629 4.002906 TGTACAAAGCTCCTCGAATGTT 57.997 40.909 0.00 0.00 0.00 2.71
1968 2630 3.678056 TGTACAAAGCTCCTCGAATGT 57.322 42.857 0.00 0.00 0.00 2.71
1969 2631 5.356882 TTTTGTACAAAGCTCCTCGAATG 57.643 39.130 19.72 0.00 0.00 2.67
1990 2652 9.736023 GACTAATTTTCACTGATGTTGTCTTTT 57.264 29.630 0.00 0.00 0.00 2.27
1991 2653 8.902806 TGACTAATTTTCACTGATGTTGTCTTT 58.097 29.630 0.00 0.00 0.00 2.52
1992 2654 8.450578 TGACTAATTTTCACTGATGTTGTCTT 57.549 30.769 0.00 0.00 0.00 3.01
1993 2655 8.450578 TTGACTAATTTTCACTGATGTTGTCT 57.549 30.769 0.00 0.00 0.00 3.41
1994 2656 9.515020 TTTTGACTAATTTTCACTGATGTTGTC 57.485 29.630 0.00 0.00 0.00 3.18
2003 2665 9.463443 GCACTTACATTTTGACTAATTTTCACT 57.537 29.630 0.00 0.00 0.00 3.41
2004 2666 9.243637 TGCACTTACATTTTGACTAATTTTCAC 57.756 29.630 0.00 0.00 0.00 3.18
2005 2667 9.979578 ATGCACTTACATTTTGACTAATTTTCA 57.020 25.926 0.00 0.00 0.00 2.69
2008 2670 9.762933 ACAATGCACTTACATTTTGACTAATTT 57.237 25.926 0.00 0.00 38.19 1.82
2009 2671 9.762933 AACAATGCACTTACATTTTGACTAATT 57.237 25.926 0.00 0.00 38.19 1.40
2010 2672 9.762933 AAACAATGCACTTACATTTTGACTAAT 57.237 25.926 0.00 0.00 38.19 1.73
2011 2673 9.029243 CAAACAATGCACTTACATTTTGACTAA 57.971 29.630 0.00 0.00 38.19 2.24
2012 2674 8.409371 TCAAACAATGCACTTACATTTTGACTA 58.591 29.630 0.00 0.00 38.19 2.59
2013 2675 7.264221 TCAAACAATGCACTTACATTTTGACT 58.736 30.769 0.00 0.00 38.19 3.41
2014 2676 7.462109 TCAAACAATGCACTTACATTTTGAC 57.538 32.000 0.00 0.00 38.19 3.18
2015 2677 6.200665 GCTCAAACAATGCACTTACATTTTGA 59.799 34.615 0.00 0.00 38.19 2.69
2016 2678 6.018913 TGCTCAAACAATGCACTTACATTTTG 60.019 34.615 0.00 0.00 38.19 2.44
2017 2679 6.047870 TGCTCAAACAATGCACTTACATTTT 58.952 32.000 0.00 0.00 38.19 1.82
2018 2680 5.599732 TGCTCAAACAATGCACTTACATTT 58.400 33.333 0.00 0.00 38.19 2.32
2019 2681 5.009911 TCTGCTCAAACAATGCACTTACATT 59.990 36.000 0.00 0.00 40.90 2.71
2020 2682 4.520111 TCTGCTCAAACAATGCACTTACAT 59.480 37.500 0.00 0.00 32.91 2.29
2021 2683 3.882288 TCTGCTCAAACAATGCACTTACA 59.118 39.130 0.00 0.00 32.91 2.41
2022 2684 4.488126 TCTGCTCAAACAATGCACTTAC 57.512 40.909 0.00 0.00 32.91 2.34
2023 2685 5.710513 AATCTGCTCAAACAATGCACTTA 57.289 34.783 0.00 0.00 32.91 2.24
2024 2686 4.595762 AATCTGCTCAAACAATGCACTT 57.404 36.364 0.00 0.00 32.91 3.16
2025 2687 4.595762 AAATCTGCTCAAACAATGCACT 57.404 36.364 0.00 0.00 32.91 4.40
2026 2688 4.508861 ACAAAATCTGCTCAAACAATGCAC 59.491 37.500 0.00 0.00 32.91 4.57
2027 2689 4.695396 ACAAAATCTGCTCAAACAATGCA 58.305 34.783 0.00 0.00 35.30 3.96
2028 2690 6.768029 TTACAAAATCTGCTCAAACAATGC 57.232 33.333 0.00 0.00 0.00 3.56
2054 2716 6.306987 AGGAGCTCCATACAGAAAAGAAAAA 58.693 36.000 33.90 0.00 38.89 1.94
2055 2717 5.880901 AGGAGCTCCATACAGAAAAGAAAA 58.119 37.500 33.90 0.00 38.89 2.29
2056 2718 5.491982 GAGGAGCTCCATACAGAAAAGAAA 58.508 41.667 33.90 0.00 38.89 2.52
2057 2719 4.382040 CGAGGAGCTCCATACAGAAAAGAA 60.382 45.833 33.90 0.00 38.89 2.52
2058 2720 3.131223 CGAGGAGCTCCATACAGAAAAGA 59.869 47.826 33.90 0.00 38.89 2.52
2059 2721 3.131223 TCGAGGAGCTCCATACAGAAAAG 59.869 47.826 33.90 11.93 38.89 2.27
2060 2722 3.096852 TCGAGGAGCTCCATACAGAAAA 58.903 45.455 33.90 6.30 38.89 2.29
2061 2723 2.735151 TCGAGGAGCTCCATACAGAAA 58.265 47.619 33.90 7.90 38.89 2.52
2062 2724 2.437085 TCGAGGAGCTCCATACAGAA 57.563 50.000 33.90 9.48 38.89 3.02
2063 2725 2.437085 TTCGAGGAGCTCCATACAGA 57.563 50.000 33.90 20.67 38.89 3.41
2064 2726 2.363680 ACATTCGAGGAGCTCCATACAG 59.636 50.000 33.90 20.05 38.89 2.74
2065 2727 2.388735 ACATTCGAGGAGCTCCATACA 58.611 47.619 33.90 15.73 38.89 2.29
2066 2728 3.460857 AACATTCGAGGAGCTCCATAC 57.539 47.619 33.90 21.98 38.89 2.39
2067 2729 5.808366 AATAACATTCGAGGAGCTCCATA 57.192 39.130 33.90 16.08 38.89 2.74
2068 2730 4.696479 AATAACATTCGAGGAGCTCCAT 57.304 40.909 33.90 19.09 38.89 3.41
2069 2731 4.081142 TCAAATAACATTCGAGGAGCTCCA 60.081 41.667 33.90 14.51 38.89 3.86
2070 2732 4.271291 GTCAAATAACATTCGAGGAGCTCC 59.729 45.833 26.22 26.22 0.00 4.70
2071 2733 4.271291 GGTCAAATAACATTCGAGGAGCTC 59.729 45.833 4.71 4.71 0.00 4.09
2072 2734 4.192317 GGTCAAATAACATTCGAGGAGCT 58.808 43.478 0.00 0.00 0.00 4.09
2073 2735 3.938963 TGGTCAAATAACATTCGAGGAGC 59.061 43.478 0.00 0.00 0.00 4.70
2074 2736 4.332819 GGTGGTCAAATAACATTCGAGGAG 59.667 45.833 0.00 0.00 0.00 3.69
2075 2737 4.258543 GGTGGTCAAATAACATTCGAGGA 58.741 43.478 0.00 0.00 0.00 3.71
2076 2738 4.006989 TGGTGGTCAAATAACATTCGAGG 58.993 43.478 0.00 0.00 0.00 4.63
2077 2739 5.621197 TTGGTGGTCAAATAACATTCGAG 57.379 39.130 0.00 0.00 31.46 4.04
2078 2740 5.533154 AGTTTGGTGGTCAAATAACATTCGA 59.467 36.000 0.00 0.00 45.79 3.71
2079 2741 5.768317 AGTTTGGTGGTCAAATAACATTCG 58.232 37.500 0.00 0.00 45.79 3.34
2080 2742 7.518211 GCAAAGTTTGGTGGTCAAATAACATTC 60.518 37.037 17.11 0.00 45.79 2.67
2081 2743 6.259829 GCAAAGTTTGGTGGTCAAATAACATT 59.740 34.615 17.11 0.00 45.79 2.71
2082 2744 5.757808 GCAAAGTTTGGTGGTCAAATAACAT 59.242 36.000 17.11 0.00 45.79 2.71
2083 2745 5.112686 GCAAAGTTTGGTGGTCAAATAACA 58.887 37.500 17.11 0.00 45.79 2.41
2084 2746 5.112686 TGCAAAGTTTGGTGGTCAAATAAC 58.887 37.500 17.11 0.00 45.79 1.89
2085 2747 5.344743 TGCAAAGTTTGGTGGTCAAATAA 57.655 34.783 17.11 0.00 45.79 1.40
2086 2748 4.739137 GCTGCAAAGTTTGGTGGTCAAATA 60.739 41.667 17.11 0.00 45.79 1.40
2087 2749 3.795877 CTGCAAAGTTTGGTGGTCAAAT 58.204 40.909 17.11 0.00 45.79 2.32
2088 2750 2.676463 GCTGCAAAGTTTGGTGGTCAAA 60.676 45.455 17.11 0.00 42.50 2.69
2089 2751 1.134848 GCTGCAAAGTTTGGTGGTCAA 60.135 47.619 17.11 0.00 0.00 3.18
2090 2752 0.459489 GCTGCAAAGTTTGGTGGTCA 59.541 50.000 17.11 5.37 0.00 4.02
2091 2753 0.459489 TGCTGCAAAGTTTGGTGGTC 59.541 50.000 17.11 0.82 0.00 4.02
2092 2754 0.175531 GTGCTGCAAAGTTTGGTGGT 59.824 50.000 17.11 0.00 0.00 4.16
2093 2755 0.461135 AGTGCTGCAAAGTTTGGTGG 59.539 50.000 17.11 0.00 0.00 4.61
2094 2756 1.134753 TGAGTGCTGCAAAGTTTGGTG 59.865 47.619 17.11 0.00 0.00 4.17
2095 2757 1.473258 TGAGTGCTGCAAAGTTTGGT 58.527 45.000 17.11 0.00 0.00 3.67
2096 2758 2.806608 ATGAGTGCTGCAAAGTTTGG 57.193 45.000 17.11 2.82 0.00 3.28
2097 2759 4.609947 TGTTATGAGTGCTGCAAAGTTTG 58.390 39.130 11.41 11.41 0.00 2.93
2098 2760 4.916983 TGTTATGAGTGCTGCAAAGTTT 57.083 36.364 2.77 0.00 0.00 2.66
2099 2761 5.458041 AATGTTATGAGTGCTGCAAAGTT 57.542 34.783 2.77 0.00 0.00 2.66
2100 2762 5.221303 ACAAATGTTATGAGTGCTGCAAAGT 60.221 36.000 2.77 0.00 0.00 2.66
2101 2763 5.224888 ACAAATGTTATGAGTGCTGCAAAG 58.775 37.500 2.77 0.00 0.00 2.77
2102 2764 5.199024 ACAAATGTTATGAGTGCTGCAAA 57.801 34.783 2.77 0.00 0.00 3.68
2103 2765 4.852134 ACAAATGTTATGAGTGCTGCAA 57.148 36.364 2.77 0.00 0.00 4.08
2104 2766 4.277921 TCAACAAATGTTATGAGTGCTGCA 59.722 37.500 0.00 0.00 36.32 4.41
2105 2767 4.797471 TCAACAAATGTTATGAGTGCTGC 58.203 39.130 0.00 0.00 36.32 5.25
2106 2768 9.229784 GATTATCAACAAATGTTATGAGTGCTG 57.770 33.333 0.00 0.00 36.32 4.41
2107 2769 8.959548 TGATTATCAACAAATGTTATGAGTGCT 58.040 29.630 0.00 0.00 36.32 4.40
2108 2770 9.740239 ATGATTATCAACAAATGTTATGAGTGC 57.260 29.630 0.00 0.00 36.32 4.40
2178 2840 0.895530 TTTGGTGCACCCACGAAAAA 59.104 45.000 32.62 21.21 45.19 1.94
2179 2841 0.457851 CTTTGGTGCACCCACGAAAA 59.542 50.000 32.62 22.87 45.05 2.29
2180 2842 1.388065 CCTTTGGTGCACCCACGAAA 61.388 55.000 32.62 23.22 45.19 3.46
2181 2843 1.826054 CCTTTGGTGCACCCACGAA 60.826 57.895 32.62 17.56 45.19 3.85
2182 2844 1.697082 TACCTTTGGTGCACCCACGA 61.697 55.000 32.62 11.85 45.19 4.35
2183 2845 1.228003 TACCTTTGGTGCACCCACG 60.228 57.895 32.62 19.42 45.19 4.94
2184 2846 0.893727 CCTACCTTTGGTGCACCCAC 60.894 60.000 32.62 9.14 45.19 4.61
2185 2847 1.357272 ACCTACCTTTGGTGCACCCA 61.357 55.000 32.62 20.45 43.27 4.51
2186 2848 0.893727 CACCTACCTTTGGTGCACCC 60.894 60.000 32.62 15.42 46.73 4.61
2187 2849 2.641197 CACCTACCTTTGGTGCACC 58.359 57.895 29.67 29.67 46.73 5.01
2192 2854 1.074951 GGCTGCACCTACCTTTGGT 59.925 57.895 0.50 0.00 40.16 3.67
2193 2855 1.074775 TGGCTGCACCTACCTTTGG 59.925 57.895 0.50 0.00 40.22 3.28
2194 2856 0.250901 AGTGGCTGCACCTACCTTTG 60.251 55.000 0.50 0.00 40.22 2.77
2195 2857 1.003233 GTAGTGGCTGCACCTACCTTT 59.997 52.381 13.78 0.00 40.22 3.11
2196 2858 0.613777 GTAGTGGCTGCACCTACCTT 59.386 55.000 13.78 0.00 40.22 3.50
2197 2859 0.252284 AGTAGTGGCTGCACCTACCT 60.252 55.000 18.51 8.31 40.22 3.08
2198 2860 0.613777 AAGTAGTGGCTGCACCTACC 59.386 55.000 18.51 6.75 40.22 3.18
2199 2861 2.347731 GAAAGTAGTGGCTGCACCTAC 58.652 52.381 15.88 15.88 40.22 3.18
2200 2862 1.278127 GGAAAGTAGTGGCTGCACCTA 59.722 52.381 0.50 0.00 40.22 3.08
2201 2863 0.036875 GGAAAGTAGTGGCTGCACCT 59.963 55.000 0.50 0.00 40.22 4.00
2202 2864 0.960861 GGGAAAGTAGTGGCTGCACC 60.961 60.000 0.50 0.00 39.84 5.01
2203 2865 0.250727 TGGGAAAGTAGTGGCTGCAC 60.251 55.000 0.50 0.00 0.00 4.57
2204 2866 0.476338 TTGGGAAAGTAGTGGCTGCA 59.524 50.000 0.50 0.00 0.00 4.41
2205 2867 1.616159 TTTGGGAAAGTAGTGGCTGC 58.384 50.000 0.00 0.00 0.00 5.25
2206 2868 4.871933 ATTTTTGGGAAAGTAGTGGCTG 57.128 40.909 0.00 0.00 0.00 4.85
2207 2869 7.147897 GCTATAATTTTTGGGAAAGTAGTGGCT 60.148 37.037 0.00 0.00 0.00 4.75
2208 2870 6.978659 GCTATAATTTTTGGGAAAGTAGTGGC 59.021 38.462 0.00 0.00 0.00 5.01
2209 2871 7.148137 ACGCTATAATTTTTGGGAAAGTAGTGG 60.148 37.037 2.16 0.00 0.00 4.00
2210 2872 7.758495 ACGCTATAATTTTTGGGAAAGTAGTG 58.242 34.615 2.16 0.00 0.00 2.74
2211 2873 7.608761 TGACGCTATAATTTTTGGGAAAGTAGT 59.391 33.333 2.16 0.00 0.00 2.73
2212 2874 7.981142 TGACGCTATAATTTTTGGGAAAGTAG 58.019 34.615 2.16 0.00 0.00 2.57
2213 2875 7.608761 ACTGACGCTATAATTTTTGGGAAAGTA 59.391 33.333 2.16 0.00 0.00 2.24
2214 2876 6.433093 ACTGACGCTATAATTTTTGGGAAAGT 59.567 34.615 2.16 2.75 0.00 2.66
2215 2877 6.852664 ACTGACGCTATAATTTTTGGGAAAG 58.147 36.000 2.16 2.28 0.00 2.62
2216 2878 6.431543 TGACTGACGCTATAATTTTTGGGAAA 59.568 34.615 2.16 0.00 0.00 3.13
2217 2879 5.941058 TGACTGACGCTATAATTTTTGGGAA 59.059 36.000 2.16 0.00 0.00 3.97
2218 2880 5.492895 TGACTGACGCTATAATTTTTGGGA 58.507 37.500 2.16 0.00 0.00 4.37
2219 2881 5.811399 TGACTGACGCTATAATTTTTGGG 57.189 39.130 0.00 0.00 0.00 4.12
2220 2882 7.754924 ACAAATGACTGACGCTATAATTTTTGG 59.245 33.333 0.00 0.00 0.00 3.28
2221 2883 8.577939 CACAAATGACTGACGCTATAATTTTTG 58.422 33.333 0.00 0.00 0.00 2.44
2222 2884 7.273381 GCACAAATGACTGACGCTATAATTTTT 59.727 33.333 0.00 0.00 0.00 1.94
2223 2885 6.747280 GCACAAATGACTGACGCTATAATTTT 59.253 34.615 0.00 0.00 0.00 1.82
2224 2886 6.094048 AGCACAAATGACTGACGCTATAATTT 59.906 34.615 0.00 0.00 30.41 1.82
2225 2887 5.586243 AGCACAAATGACTGACGCTATAATT 59.414 36.000 0.00 0.00 30.41 1.40
2226 2888 5.118990 AGCACAAATGACTGACGCTATAAT 58.881 37.500 0.00 0.00 30.41 1.28
2290 2953 3.423154 GTGGCCAACGCTCCTTCG 61.423 66.667 7.24 0.00 34.44 3.79
2331 2994 3.000819 CACACCCACCGGCTCCTA 61.001 66.667 0.00 0.00 0.00 2.94
2404 3067 4.034285 CCCCCAAATCTACAACAACTCT 57.966 45.455 0.00 0.00 0.00 3.24
2423 3086 0.106167 GGCCATCCCTCTAAAACCCC 60.106 60.000 0.00 0.00 0.00 4.95
2443 3106 2.586079 CGTGATAGCCACCGCCAG 60.586 66.667 0.00 0.00 42.76 4.85
2450 3113 2.285069 ACCCCACCGTGATAGCCA 60.285 61.111 0.00 0.00 0.00 4.75
2477 3140 2.531685 CTCAACTCCCCACCCCCA 60.532 66.667 0.00 0.00 0.00 4.96
2495 3158 0.111253 CCTTGCCACCTTGGTCTTCT 59.889 55.000 0.00 0.00 40.46 2.85
2500 3163 1.152269 ATTGCCTTGCCACCTTGGT 60.152 52.632 0.00 0.00 40.46 3.67
2503 3166 0.760189 ACACATTGCCTTGCCACCTT 60.760 50.000 0.00 0.00 0.00 3.50
2507 3170 0.178978 TACCACACATTGCCTTGCCA 60.179 50.000 0.00 0.00 0.00 4.92
2515 3178 2.749865 CGGGCGCTACCACACATTG 61.750 63.158 7.64 0.00 42.05 2.82
2516 3179 2.435938 CGGGCGCTACCACACATT 60.436 61.111 7.64 0.00 42.05 2.71
2538 3201 4.883354 GGCATCCCTCCCTTGCGG 62.883 72.222 0.00 0.00 37.25 5.69
2548 3211 2.192175 CCTAACCACCGGCATCCC 59.808 66.667 0.00 0.00 0.00 3.85
2579 3242 4.803426 CCTCACGCAGACGCCCTC 62.803 72.222 0.00 0.00 45.53 4.30
2586 3249 1.270826 CTTCTCTTGTCCTCACGCAGA 59.729 52.381 0.00 0.00 0.00 4.26
2589 3252 0.319900 TGCTTCTCTTGTCCTCACGC 60.320 55.000 0.00 0.00 0.00 5.34
2591 3254 2.670414 CGATTGCTTCTCTTGTCCTCAC 59.330 50.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.