Multiple sequence alignment - TraesCS3D01G062100

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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 TraesCS3D01G062100 chr3D 100.000 2474 0 0 1 2474 27173098 27170625 0.000000e+00 4569.0
1 TraesCS3D01G062100 chr3D 85.028 895 78 31 723 1580 26809442 26810317 0.000000e+00 859.0
2 TraesCS3D01G062100 chr3D 81.441 916 89 40 728 1580 27053867 27054764 0.000000e+00 675.0
3 TraesCS3D01G062100 chr3D 80.538 930 95 43 728 1585 26687507 26686592 9.650000e-179 636.0
4 TraesCS3D01G062100 chr3D 86.792 106 5 6 628 727 26809316 26809418 2.600000e-20 110.0
5 TraesCS3D01G062100 chr3B 93.134 1369 51 13 628 1981 45367520 45366180 0.000000e+00 1967.0
6 TraesCS3D01G062100 chr3B 84.641 918 84 31 723 1594 45304498 45303592 0.000000e+00 861.0
7 TraesCS3D01G062100 chr3B 94.000 250 14 1 222 471 45372954 45372706 6.460000e-101 377.0
8 TraesCS3D01G062100 chr3B 90.541 222 20 1 1 222 45373358 45373138 2.410000e-75 292.0
9 TraesCS3D01G062100 chr3B 90.244 164 7 5 471 633 45367802 45367647 3.230000e-49 206.0
10 TraesCS3D01G062100 chr3B 85.849 106 6 6 628 727 45304624 45304522 1.210000e-18 104.0
11 TraesCS3D01G062100 chr3A 94.530 914 41 7 723 1628 37316924 37316012 0.000000e+00 1402.0
12 TraesCS3D01G062100 chr3A 82.346 878 98 35 728 1585 37308702 37307862 0.000000e+00 710.0
13 TraesCS3D01G062100 chr3A 81.025 917 105 38 728 1585 37305691 37304785 0.000000e+00 665.0
14 TraesCS3D01G062100 chr3A 79.253 1017 119 54 628 1585 37242929 37241946 2.090000e-175 625.0
15 TraesCS3D01G062100 chr3A 91.743 109 7 1 1620 1728 37311087 37310981 1.530000e-32 150.0
16 TraesCS3D01G062100 chr3A 91.111 45 3 1 628 671 37309004 37308960 2.660000e-05 60.2
17 TraesCS3D01G062100 chr4D 83.654 416 52 15 1988 2395 248828085 248828492 6.460000e-101 377.0
18 TraesCS3D01G062100 chr4D 82.410 415 62 10 1988 2395 407759491 407759081 3.910000e-93 351.0
19 TraesCS3D01G062100 chr4D 93.478 46 3 0 369 414 496872406 496872361 4.410000e-08 69.4
20 TraesCS3D01G062100 chr7D 83.415 410 53 12 1988 2387 40121309 40120905 1.400000e-97 366.0
21 TraesCS3D01G062100 chr7D 92.982 57 3 1 672 727 139937963 139937907 5.670000e-12 82.4
22 TraesCS3D01G062100 chr5D 82.850 414 60 9 1988 2395 419267460 419267868 6.500000e-96 361.0
23 TraesCS3D01G062100 chr5D 89.005 191 10 2 225 415 374314552 374314731 2.480000e-55 226.0
24 TraesCS3D01G062100 chr5D 95.833 48 2 0 369 416 374313826 374313779 7.340000e-11 78.7
25 TraesCS3D01G062100 chr2D 82.567 413 59 11 1988 2395 534127584 534127988 3.910000e-93 351.0
26 TraesCS3D01G062100 chr2D 80.930 430 65 11 1973 2395 603126111 603125692 8.530000e-85 324.0
27 TraesCS3D01G062100 chr1A 82.169 415 63 10 1988 2396 582605379 582605788 1.820000e-91 346.0
28 TraesCS3D01G062100 chr6A 81.446 415 66 10 1988 2395 595708877 595708467 1.830000e-86 329.0
29 TraesCS3D01G062100 chr6D 80.660 424 68 13 1978 2395 49640411 49640826 1.430000e-82 316.0
30 TraesCS3D01G062100 chrUn 91.441 222 19 0 1 222 30101932 30101711 3.090000e-79 305.0
31 TraesCS3D01G062100 chrUn 92.268 194 13 2 221 413 30101529 30101337 8.720000e-70 274.0
32 TraesCS3D01G062100 chrUn 91.489 47 3 1 367 413 229503159 229503114 2.050000e-06 63.9
33 TraesCS3D01G062100 chr1D 91.489 47 3 1 367 413 463602509 463602464 2.050000e-06 63.9
34 TraesCS3D01G062100 chr1D 91.489 47 3 1 367 413 463649530 463649485 2.050000e-06 63.9


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 TraesCS3D01G062100 chr3D 27170625 27173098 2473 True 4569.0 4569 100.00000 1 2474 1 chr3D.!!$R2 2473
1 TraesCS3D01G062100 chr3D 27053867 27054764 897 False 675.0 675 81.44100 728 1580 1 chr3D.!!$F1 852
2 TraesCS3D01G062100 chr3D 26686592 26687507 915 True 636.0 636 80.53800 728 1585 1 chr3D.!!$R1 857
3 TraesCS3D01G062100 chr3D 26809316 26810317 1001 False 484.5 859 85.91000 628 1580 2 chr3D.!!$F2 952
4 TraesCS3D01G062100 chr3B 45366180 45367802 1622 True 1086.5 1967 91.68900 471 1981 2 chr3B.!!$R2 1510
5 TraesCS3D01G062100 chr3B 45303592 45304624 1032 True 482.5 861 85.24500 628 1594 2 chr3B.!!$R1 966
6 TraesCS3D01G062100 chr3B 45372706 45373358 652 True 334.5 377 92.27050 1 471 2 chr3B.!!$R3 470
7 TraesCS3D01G062100 chr3A 37316012 37316924 912 True 1402.0 1402 94.53000 723 1628 1 chr3A.!!$R2 905
8 TraesCS3D01G062100 chr3A 37241946 37242929 983 True 625.0 625 79.25300 628 1585 1 chr3A.!!$R1 957
9 TraesCS3D01G062100 chr3A 37304785 37311087 6302 True 396.3 710 86.55625 628 1728 4 chr3A.!!$R3 1100
10 TraesCS3D01G062100 chrUn 30101337 30101932 595 True 289.5 305 91.85450 1 413 2 chrUn.!!$R2 412

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
124 125 0.527817 CCAGCATCGACGTAAGGACC 60.528 60.0 0.0 0.0 46.39 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 6475 0.100325 TTTGTGTGTTCAAGCAGCCG 59.9 50.0 0.0 0.0 0.0 5.52 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
107 108 0.895530 GACAGTCGGATTCACCTCCA 59.104 55.000 0.00 0.00 34.78 3.86
124 125 0.527817 CCAGCATCGACGTAAGGACC 60.528 60.000 0.00 0.00 46.39 4.46
156 157 1.076332 GTTATGTCAGACACGCCACC 58.924 55.000 5.05 0.00 0.00 4.61
434 620 3.962530 ATGGAAGGGGGAAGCCCGA 62.963 63.158 0.00 0.00 46.66 5.14
543 729 9.995003 TGCAAATTACCTAAATCAAGACAATTT 57.005 25.926 0.00 0.00 0.00 1.82
573 759 2.496679 AGAGAAATGGGCCCTAGCTA 57.503 50.000 25.70 1.02 39.73 3.32
580 766 7.407328 AGAGAAATGGGCCCTAGCTAATTATAT 59.593 37.037 25.70 0.00 39.73 0.86
581 767 7.349598 AGAAATGGGCCCTAGCTAATTATATG 58.650 38.462 25.70 0.00 39.73 1.78
582 768 6.658555 AATGGGCCCTAGCTAATTATATGT 57.341 37.500 25.70 0.00 39.73 2.29
583 769 5.693769 TGGGCCCTAGCTAATTATATGTC 57.306 43.478 25.70 0.00 39.73 3.06
587 773 6.058183 GGCCCTAGCTAATTATATGTCCATG 58.942 44.000 0.00 0.00 39.73 3.66
588 774 5.529060 GCCCTAGCTAATTATATGTCCATGC 59.471 44.000 0.00 0.00 35.50 4.06
589 775 6.058183 CCCTAGCTAATTATATGTCCATGCC 58.942 44.000 0.00 0.00 0.00 4.40
590 776 6.352996 CCCTAGCTAATTATATGTCCATGCCA 60.353 42.308 0.00 0.00 0.00 4.92
591 777 7.112122 CCTAGCTAATTATATGTCCATGCCAA 58.888 38.462 0.00 0.00 0.00 4.52
592 778 7.611467 CCTAGCTAATTATATGTCCATGCCAAA 59.389 37.037 0.00 0.00 0.00 3.28
593 779 7.838079 AGCTAATTATATGTCCATGCCAAAA 57.162 32.000 0.00 0.00 0.00 2.44
611 797 7.322664 TGCCAAAATAAATTGATGAGGAGTTC 58.677 34.615 0.00 0.00 31.84 3.01
620 806 2.909006 TGATGAGGAGTTCTCCTTGCTT 59.091 45.455 20.48 8.70 40.86 3.91
785 2448 8.477419 AATTATTGTATGGAAACCAATCGGAT 57.523 30.769 0.00 0.00 36.95 4.18
898 2593 6.600032 TGGTAAATATGGCGTAATCAACACTT 59.400 34.615 0.00 0.00 0.00 3.16
931 2638 1.318576 GCCTACAAATAGCCGGCAAT 58.681 50.000 31.54 12.06 40.41 3.56
963 2674 5.392380 GCAGAATAGCATTACAACAAGCACT 60.392 40.000 0.00 0.00 0.00 4.40
987 2698 2.282290 ACACACGTACGTACAGCAAAAC 59.718 45.455 22.34 0.00 0.00 2.43
1139 2867 5.464389 GCTGATTTTGATCAACAACTGCTTT 59.536 36.000 19.54 0.00 38.29 3.51
1193 2938 4.020218 CACCATATCGGACCTCCATGTTAT 60.020 45.833 0.00 0.00 38.63 1.89
1216 2961 2.032071 CCGCCACGGGAAAGAACT 59.968 61.111 0.00 0.00 44.15 3.01
1485 6308 2.115427 TGCTCGTGATTGGGAGGATTA 58.885 47.619 0.00 0.00 0.00 1.75
1667 6510 3.250040 ACACAAAATGTACACGAGCTTCC 59.750 43.478 0.00 0.00 40.88 3.46
1668 6511 2.478894 ACAAAATGTACACGAGCTTCCG 59.521 45.455 0.00 0.00 0.00 4.30
1669 6512 2.734606 CAAAATGTACACGAGCTTCCGA 59.265 45.455 0.00 0.00 0.00 4.55
1708 6551 0.035056 ACTTGTATGCACTGGGCTCC 60.035 55.000 2.50 0.00 45.15 4.70
1714 6557 0.333993 ATGCACTGGGCTCCTTTGAT 59.666 50.000 2.50 0.00 45.15 2.57
1736 6579 0.323629 TCACGGCTTAGGTTTGGAGG 59.676 55.000 0.00 0.00 0.00 4.30
1746 6589 7.468220 CGGCTTAGGTTTGGAGGAAAAATATAC 60.468 40.741 0.00 0.00 0.00 1.47
1747 6590 7.560262 GGCTTAGGTTTGGAGGAAAAATATACT 59.440 37.037 0.00 0.00 0.00 2.12
1748 6591 9.623000 GCTTAGGTTTGGAGGAAAAATATACTA 57.377 33.333 0.00 0.00 0.00 1.82
1791 6634 5.124645 AGATCATTCATCCTGCAAAGAGAC 58.875 41.667 0.00 0.00 30.71 3.36
1794 6637 3.616956 TTCATCCTGCAAAGAGACGAT 57.383 42.857 0.00 0.00 0.00 3.73
1795 6638 4.736126 TTCATCCTGCAAAGAGACGATA 57.264 40.909 0.00 0.00 0.00 2.92
1796 6639 4.046938 TCATCCTGCAAAGAGACGATAC 57.953 45.455 0.00 0.00 0.00 2.24
1797 6640 3.447229 TCATCCTGCAAAGAGACGATACA 59.553 43.478 0.00 0.00 0.00 2.29
1798 6641 3.510388 TCCTGCAAAGAGACGATACAG 57.490 47.619 0.00 0.00 0.00 2.74
1799 6642 2.166459 TCCTGCAAAGAGACGATACAGG 59.834 50.000 0.00 0.00 43.65 4.00
1800 6643 1.929836 CTGCAAAGAGACGATACAGGC 59.070 52.381 0.00 0.00 0.00 4.85
1801 6644 1.275010 TGCAAAGAGACGATACAGGCA 59.725 47.619 0.00 0.00 0.00 4.75
1802 6645 2.289382 TGCAAAGAGACGATACAGGCAA 60.289 45.455 0.00 0.00 0.00 4.52
1803 6646 2.742053 GCAAAGAGACGATACAGGCAAA 59.258 45.455 0.00 0.00 0.00 3.68
1804 6647 3.375299 GCAAAGAGACGATACAGGCAAAT 59.625 43.478 0.00 0.00 0.00 2.32
1805 6648 4.142600 GCAAAGAGACGATACAGGCAAATT 60.143 41.667 0.00 0.00 0.00 1.82
1806 6649 5.064707 GCAAAGAGACGATACAGGCAAATTA 59.935 40.000 0.00 0.00 0.00 1.40
1807 6650 6.403200 GCAAAGAGACGATACAGGCAAATTAA 60.403 38.462 0.00 0.00 0.00 1.40
1808 6651 7.526608 CAAAGAGACGATACAGGCAAATTAAA 58.473 34.615 0.00 0.00 0.00 1.52
1809 6652 6.663944 AGAGACGATACAGGCAAATTAAAC 57.336 37.500 0.00 0.00 0.00 2.01
1810 6653 6.407202 AGAGACGATACAGGCAAATTAAACT 58.593 36.000 0.00 0.00 0.00 2.66
1811 6654 7.553334 AGAGACGATACAGGCAAATTAAACTA 58.447 34.615 0.00 0.00 0.00 2.24
1812 6655 8.204836 AGAGACGATACAGGCAAATTAAACTAT 58.795 33.333 0.00 0.00 0.00 2.12
1813 6656 8.366671 AGACGATACAGGCAAATTAAACTATC 57.633 34.615 0.00 0.00 0.00 2.08
1814 6657 7.441458 AGACGATACAGGCAAATTAAACTATCC 59.559 37.037 0.00 0.00 0.00 2.59
1815 6658 7.280356 ACGATACAGGCAAATTAAACTATCCT 58.720 34.615 0.00 0.00 0.00 3.24
1850 6693 2.753043 CCTTGCCCGCTTGCTGAT 60.753 61.111 0.00 0.00 0.00 2.90
1929 6772 8.560576 TGAAGCTCTTTCAAGAAAATTAAACG 57.439 30.769 0.00 0.00 42.69 3.60
1951 6794 0.243365 GCATCCAATTGTTGACCGCA 59.757 50.000 4.43 0.00 0.00 5.69
1952 6795 1.981254 CATCCAATTGTTGACCGCAC 58.019 50.000 4.43 0.00 0.00 5.34
1981 6824 9.370126 GTAATGCACGAATACAGATTACAAATC 57.630 33.333 0.00 0.00 0.00 2.17
1982 6825 6.976636 TGCACGAATACAGATTACAAATCA 57.023 33.333 0.00 0.00 0.00 2.57
1983 6826 7.552458 TGCACGAATACAGATTACAAATCAT 57.448 32.000 0.00 0.00 0.00 2.45
1984 6827 7.984391 TGCACGAATACAGATTACAAATCATT 58.016 30.769 0.00 0.00 0.00 2.57
1985 6828 8.122330 TGCACGAATACAGATTACAAATCATTC 58.878 33.333 0.00 2.94 0.00 2.67
1986 6829 8.338259 GCACGAATACAGATTACAAATCATTCT 58.662 33.333 0.00 0.00 0.00 2.40
1987 6830 9.855361 CACGAATACAGATTACAAATCATTCTC 57.145 33.333 0.00 0.00 0.00 2.87
1988 6831 9.823647 ACGAATACAGATTACAAATCATTCTCT 57.176 29.630 0.00 0.00 0.00 3.10
2006 6849 9.658799 TCATTCTCTAATAATATAGCAAGGTGC 57.341 33.333 0.00 0.00 45.46 5.01
2016 6859 3.936585 GCAAGGTGCGTTTCTTCAA 57.063 47.368 0.00 0.00 31.71 2.69
2017 6860 2.422276 GCAAGGTGCGTTTCTTCAAT 57.578 45.000 0.00 0.00 31.71 2.57
2018 6861 2.742774 GCAAGGTGCGTTTCTTCAATT 58.257 42.857 0.00 0.00 31.71 2.32
2019 6862 3.123050 GCAAGGTGCGTTTCTTCAATTT 58.877 40.909 0.00 0.00 31.71 1.82
2020 6863 3.555547 GCAAGGTGCGTTTCTTCAATTTT 59.444 39.130 0.00 0.00 31.71 1.82
2021 6864 4.033932 GCAAGGTGCGTTTCTTCAATTTTT 59.966 37.500 0.00 0.00 31.71 1.94
2043 6886 8.885494 TTTTTCATCCTTTCATCGTTGAATTT 57.115 26.923 9.61 0.00 41.38 1.82
2044 6887 8.885494 TTTTCATCCTTTCATCGTTGAATTTT 57.115 26.923 9.61 0.00 41.38 1.82
2045 6888 8.885494 TTTCATCCTTTCATCGTTGAATTTTT 57.115 26.923 9.61 0.00 41.38 1.94
2074 6917 6.753107 ATCCGAGGTGGTACTAAATTTTTG 57.247 37.500 0.00 0.00 39.52 2.44
2075 6918 5.623169 TCCGAGGTGGTACTAAATTTTTGT 58.377 37.500 0.00 2.00 39.52 2.83
2076 6919 5.470777 TCCGAGGTGGTACTAAATTTTTGTG 59.529 40.000 0.00 0.00 39.52 3.33
2077 6920 5.335348 CCGAGGTGGTACTAAATTTTTGTGG 60.335 44.000 0.00 0.00 0.00 4.17
2078 6921 5.239963 CGAGGTGGTACTAAATTTTTGTGGT 59.760 40.000 0.00 0.00 0.00 4.16
2079 6922 6.567132 CGAGGTGGTACTAAATTTTTGTGGTC 60.567 42.308 0.00 0.00 0.00 4.02
2080 6923 5.537295 AGGTGGTACTAAATTTTTGTGGTCC 59.463 40.000 0.00 6.87 0.00 4.46
2081 6924 5.302313 GGTGGTACTAAATTTTTGTGGTCCA 59.698 40.000 0.00 8.81 0.00 4.02
2082 6925 6.014925 GGTGGTACTAAATTTTTGTGGTCCAT 60.015 38.462 0.00 0.00 0.00 3.41
2083 6926 7.088272 GTGGTACTAAATTTTTGTGGTCCATC 58.912 38.462 0.00 0.00 0.00 3.51
2084 6927 7.007723 TGGTACTAAATTTTTGTGGTCCATCT 58.992 34.615 0.00 0.00 0.00 2.90
2085 6928 7.040062 TGGTACTAAATTTTTGTGGTCCATCTG 60.040 37.037 0.00 0.00 0.00 2.90
2086 6929 5.783111 ACTAAATTTTTGTGGTCCATCTGC 58.217 37.500 0.00 0.00 0.00 4.26
2087 6930 4.961438 AAATTTTTGTGGTCCATCTGCT 57.039 36.364 0.00 0.00 0.00 4.24
2088 6931 6.719370 ACTAAATTTTTGTGGTCCATCTGCTA 59.281 34.615 0.00 0.00 0.00 3.49
2089 6932 5.649782 AATTTTTGTGGTCCATCTGCTAG 57.350 39.130 0.00 0.00 0.00 3.42
2090 6933 4.365514 TTTTTGTGGTCCATCTGCTAGA 57.634 40.909 0.00 0.00 0.00 2.43
2091 6934 4.365514 TTTTGTGGTCCATCTGCTAGAA 57.634 40.909 0.00 0.00 0.00 2.10
2092 6935 4.365514 TTTGTGGTCCATCTGCTAGAAA 57.634 40.909 0.00 0.00 0.00 2.52
2093 6936 4.365514 TTGTGGTCCATCTGCTAGAAAA 57.634 40.909 0.00 0.00 0.00 2.29
2094 6937 4.574674 TGTGGTCCATCTGCTAGAAAAT 57.425 40.909 0.00 0.00 0.00 1.82
2095 6938 5.692115 TGTGGTCCATCTGCTAGAAAATA 57.308 39.130 0.00 0.00 0.00 1.40
2096 6939 6.061022 TGTGGTCCATCTGCTAGAAAATAA 57.939 37.500 0.00 0.00 0.00 1.40
2097 6940 6.480763 TGTGGTCCATCTGCTAGAAAATAAA 58.519 36.000 0.00 0.00 0.00 1.40
2098 6941 6.945435 TGTGGTCCATCTGCTAGAAAATAAAA 59.055 34.615 0.00 0.00 0.00 1.52
2099 6942 7.615365 TGTGGTCCATCTGCTAGAAAATAAAAT 59.385 33.333 0.00 0.00 0.00 1.82
2100 6943 9.120538 GTGGTCCATCTGCTAGAAAATAAAATA 57.879 33.333 0.00 0.00 0.00 1.40
2101 6944 9.693739 TGGTCCATCTGCTAGAAAATAAAATAA 57.306 29.630 0.00 0.00 0.00 1.40
2122 6965 9.463443 AAATAAAGAGTTTCGTCCAGAATTTTG 57.537 29.630 0.00 0.00 38.86 2.44
2123 6966 6.451064 AAAGAGTTTCGTCCAGAATTTTGT 57.549 33.333 0.00 0.00 38.86 2.83
2124 6967 7.562454 AAAGAGTTTCGTCCAGAATTTTGTA 57.438 32.000 0.00 0.00 38.86 2.41
2125 6968 6.541111 AGAGTTTCGTCCAGAATTTTGTAC 57.459 37.500 0.00 0.00 38.86 2.90
2126 6969 5.176958 AGAGTTTCGTCCAGAATTTTGTACG 59.823 40.000 7.64 7.64 38.86 3.67
2127 6970 4.812626 AGTTTCGTCCAGAATTTTGTACGT 59.187 37.500 12.65 0.00 38.86 3.57
2128 6971 4.718858 TTCGTCCAGAATTTTGTACGTG 57.281 40.909 12.65 0.00 33.14 4.49
2129 6972 3.061322 TCGTCCAGAATTTTGTACGTGG 58.939 45.455 12.65 0.00 0.00 4.94
2130 6973 2.158841 CGTCCAGAATTTTGTACGTGGG 59.841 50.000 6.01 0.00 0.00 4.61
2131 6974 3.404899 GTCCAGAATTTTGTACGTGGGA 58.595 45.455 0.00 0.00 0.00 4.37
2132 6975 3.187842 GTCCAGAATTTTGTACGTGGGAC 59.812 47.826 0.00 0.00 35.96 4.46
2142 6985 4.345962 CGTGGGACGCACGTGGTA 62.346 66.667 30.39 0.00 40.71 3.25
2143 6986 2.029369 GTGGGACGCACGTGGTAA 59.971 61.111 18.88 0.78 39.55 2.85
2144 6987 2.025418 GTGGGACGCACGTGGTAAG 61.025 63.158 18.88 0.00 39.55 2.34
2145 6988 2.433664 GGGACGCACGTGGTAAGG 60.434 66.667 18.88 0.00 0.00 2.69
2146 6989 3.116531 GGACGCACGTGGTAAGGC 61.117 66.667 18.88 0.00 0.00 4.35
2147 6990 3.116531 GACGCACGTGGTAAGGCC 61.117 66.667 18.88 0.00 37.90 5.19
2148 6991 4.692475 ACGCACGTGGTAAGGCCC 62.692 66.667 18.88 0.00 36.04 5.80
2149 6992 4.690719 CGCACGTGGTAAGGCCCA 62.691 66.667 18.88 0.00 36.04 5.36
2150 6993 2.746277 GCACGTGGTAAGGCCCAG 60.746 66.667 18.88 0.00 34.43 4.45
2151 6994 3.065306 CACGTGGTAAGGCCCAGA 58.935 61.111 7.95 0.00 34.43 3.86
2152 6995 1.373435 CACGTGGTAAGGCCCAGAA 59.627 57.895 7.95 0.00 34.43 3.02
2153 6996 0.250553 CACGTGGTAAGGCCCAGAAA 60.251 55.000 7.95 0.00 34.43 2.52
2154 6997 0.475044 ACGTGGTAAGGCCCAGAAAA 59.525 50.000 0.00 0.00 34.43 2.29
2155 6998 1.165270 CGTGGTAAGGCCCAGAAAAG 58.835 55.000 0.00 0.00 34.43 2.27
2156 6999 1.271163 CGTGGTAAGGCCCAGAAAAGA 60.271 52.381 0.00 0.00 34.43 2.52
2157 7000 2.160205 GTGGTAAGGCCCAGAAAAGAC 58.840 52.381 0.00 0.00 34.43 3.01
2158 7001 1.777878 TGGTAAGGCCCAGAAAAGACA 59.222 47.619 0.00 0.00 36.04 3.41
2159 7002 2.160205 GGTAAGGCCCAGAAAAGACAC 58.840 52.381 0.00 0.00 0.00 3.67
2160 7003 2.160205 GTAAGGCCCAGAAAAGACACC 58.840 52.381 0.00 0.00 0.00 4.16
2161 7004 0.178961 AAGGCCCAGAAAAGACACCC 60.179 55.000 0.00 0.00 0.00 4.61
2162 7005 1.152830 GGCCCAGAAAAGACACCCA 59.847 57.895 0.00 0.00 0.00 4.51
2163 7006 0.251787 GGCCCAGAAAAGACACCCAT 60.252 55.000 0.00 0.00 0.00 4.00
2164 7007 1.632589 GCCCAGAAAAGACACCCATT 58.367 50.000 0.00 0.00 0.00 3.16
2165 7008 1.970640 GCCCAGAAAAGACACCCATTT 59.029 47.619 0.00 0.00 0.00 2.32
2166 7009 3.161866 GCCCAGAAAAGACACCCATTTA 58.838 45.455 0.00 0.00 0.00 1.40
2167 7010 3.576550 GCCCAGAAAAGACACCCATTTAA 59.423 43.478 0.00 0.00 0.00 1.52
2168 7011 4.321974 GCCCAGAAAAGACACCCATTTAAG 60.322 45.833 0.00 0.00 0.00 1.85
2169 7012 4.832823 CCCAGAAAAGACACCCATTTAAGT 59.167 41.667 0.00 0.00 0.00 2.24
2170 7013 5.048013 CCCAGAAAAGACACCCATTTAAGTC 60.048 44.000 0.00 0.00 0.00 3.01
2171 7014 5.048013 CCAGAAAAGACACCCATTTAAGTCC 60.048 44.000 0.00 0.00 0.00 3.85
2172 7015 5.770162 CAGAAAAGACACCCATTTAAGTCCT 59.230 40.000 0.00 0.00 0.00 3.85
2173 7016 5.770162 AGAAAAGACACCCATTTAAGTCCTG 59.230 40.000 0.00 0.00 0.00 3.86
2174 7017 3.073274 AGACACCCATTTAAGTCCTGC 57.927 47.619 0.00 0.00 0.00 4.85
2175 7018 1.737793 GACACCCATTTAAGTCCTGCG 59.262 52.381 0.00 0.00 0.00 5.18
2176 7019 0.451783 CACCCATTTAAGTCCTGCGC 59.548 55.000 0.00 0.00 0.00 6.09
2177 7020 0.037590 ACCCATTTAAGTCCTGCGCA 59.962 50.000 10.98 10.98 0.00 6.09
2178 7021 0.451783 CCCATTTAAGTCCTGCGCAC 59.548 55.000 5.66 0.00 0.00 5.34
2179 7022 1.164411 CCATTTAAGTCCTGCGCACA 58.836 50.000 5.66 0.00 0.00 4.57
2180 7023 1.539388 CCATTTAAGTCCTGCGCACAA 59.461 47.619 5.66 0.00 0.00 3.33
2181 7024 2.030363 CCATTTAAGTCCTGCGCACAAA 60.030 45.455 5.66 0.41 0.00 2.83
2182 7025 3.236816 CATTTAAGTCCTGCGCACAAAG 58.763 45.455 5.66 0.00 0.00 2.77
2183 7026 0.591170 TTAAGTCCTGCGCACAAAGC 59.409 50.000 5.66 0.00 40.87 3.51
2184 7027 0.250295 TAAGTCCTGCGCACAAAGCT 60.250 50.000 5.66 0.00 42.61 3.74
2185 7028 1.789078 AAGTCCTGCGCACAAAGCTG 61.789 55.000 5.66 0.00 42.61 4.24
2187 7030 3.289834 CCTGCGCACAAAGCTGGT 61.290 61.111 5.66 0.00 45.09 4.00
2188 7031 1.965930 CCTGCGCACAAAGCTGGTA 60.966 57.895 5.66 0.00 45.09 3.25
2189 7032 1.514678 CCTGCGCACAAAGCTGGTAA 61.515 55.000 5.66 0.00 45.09 2.85
2190 7033 0.523072 CTGCGCACAAAGCTGGTAAT 59.477 50.000 5.66 0.00 42.61 1.89
2191 7034 0.521291 TGCGCACAAAGCTGGTAATC 59.479 50.000 5.66 0.00 42.61 1.75
2192 7035 0.804989 GCGCACAAAGCTGGTAATCT 59.195 50.000 0.30 0.00 42.61 2.40
2193 7036 1.200020 GCGCACAAAGCTGGTAATCTT 59.800 47.619 0.30 0.00 42.61 2.40
2194 7037 2.351738 GCGCACAAAGCTGGTAATCTTT 60.352 45.455 0.30 0.00 42.61 2.52
2195 7038 3.119990 GCGCACAAAGCTGGTAATCTTTA 60.120 43.478 0.30 0.00 42.61 1.85
2196 7039 4.438744 GCGCACAAAGCTGGTAATCTTTAT 60.439 41.667 0.30 0.00 42.61 1.40
2197 7040 5.640732 CGCACAAAGCTGGTAATCTTTATT 58.359 37.500 0.00 0.00 42.61 1.40
2198 7041 6.092748 CGCACAAAGCTGGTAATCTTTATTT 58.907 36.000 0.00 0.00 42.61 1.40
2199 7042 6.033831 CGCACAAAGCTGGTAATCTTTATTTG 59.966 38.462 0.00 0.00 42.61 2.32
2200 7043 6.868339 GCACAAAGCTGGTAATCTTTATTTGT 59.132 34.615 0.00 0.00 39.48 2.83
2201 7044 7.062255 GCACAAAGCTGGTAATCTTTATTTGTC 59.938 37.037 0.00 0.00 37.48 3.18
2202 7045 7.271223 CACAAAGCTGGTAATCTTTATTTGTCG 59.729 37.037 0.00 0.00 37.48 4.35
2203 7046 5.485662 AGCTGGTAATCTTTATTTGTCGC 57.514 39.130 0.00 0.00 0.00 5.19
2204 7047 4.941263 AGCTGGTAATCTTTATTTGTCGCA 59.059 37.500 0.00 0.00 0.00 5.10
2205 7048 5.028375 GCTGGTAATCTTTATTTGTCGCAC 58.972 41.667 0.00 0.00 0.00 5.34
2206 7049 5.391523 GCTGGTAATCTTTATTTGTCGCACA 60.392 40.000 0.00 0.00 0.00 4.57
2207 7050 6.561737 TGGTAATCTTTATTTGTCGCACAA 57.438 33.333 0.00 0.00 36.11 3.33
2223 7066 4.395581 GCACAAAGCGACATATAGATGG 57.604 45.455 1.85 0.00 37.39 3.51
2224 7067 4.058124 GCACAAAGCGACATATAGATGGA 58.942 43.478 1.85 0.00 37.39 3.41
2225 7068 4.151335 GCACAAAGCGACATATAGATGGAG 59.849 45.833 1.85 0.00 37.39 3.86
2226 7069 4.151335 CACAAAGCGACATATAGATGGAGC 59.849 45.833 10.15 10.15 38.84 4.70
2227 7070 4.039730 ACAAAGCGACATATAGATGGAGCT 59.960 41.667 13.64 13.64 45.67 4.09
2228 7071 4.881019 AAGCGACATATAGATGGAGCTT 57.119 40.909 21.08 21.08 46.14 3.74
2229 7072 4.448537 AGCGACATATAGATGGAGCTTC 57.551 45.455 13.64 0.00 43.11 3.86
2230 7073 3.194542 AGCGACATATAGATGGAGCTTCC 59.805 47.826 13.64 0.00 43.11 3.46
2231 7074 3.677424 GCGACATATAGATGGAGCTTCCC 60.677 52.174 10.68 0.00 37.39 3.97
2232 7075 3.511540 CGACATATAGATGGAGCTTCCCA 59.488 47.826 1.85 0.00 41.05 4.37
2239 7082 0.319728 ATGGAGCTTCCCATCGATCG 59.680 55.000 9.36 9.36 43.07 3.69
2240 7083 1.666234 GGAGCTTCCCATCGATCGC 60.666 63.158 11.09 0.00 0.00 4.58
2241 7084 1.666234 GAGCTTCCCATCGATCGCC 60.666 63.158 11.09 0.00 0.00 5.54
2242 7085 2.666526 GCTTCCCATCGATCGCCC 60.667 66.667 11.09 0.00 0.00 6.13
2243 7086 2.821685 CTTCCCATCGATCGCCCA 59.178 61.111 11.09 0.00 0.00 5.36
2244 7087 1.372683 CTTCCCATCGATCGCCCAT 59.627 57.895 11.09 0.00 0.00 4.00
2245 7088 0.250467 CTTCCCATCGATCGCCCATT 60.250 55.000 11.09 0.00 0.00 3.16
2246 7089 0.534877 TTCCCATCGATCGCCCATTG 60.535 55.000 11.09 2.81 0.00 2.82
2247 7090 1.227943 CCCATCGATCGCCCATTGT 60.228 57.895 11.09 0.00 0.00 2.71
2248 7091 0.819259 CCCATCGATCGCCCATTGTT 60.819 55.000 11.09 0.00 0.00 2.83
2249 7092 0.308684 CCATCGATCGCCCATTGTTG 59.691 55.000 11.09 0.00 0.00 3.33
2250 7093 0.308684 CATCGATCGCCCATTGTTGG 59.691 55.000 11.09 0.00 43.23 3.77
2258 7101 4.850193 CCATTGTTGGGTCAGCCT 57.150 55.556 0.00 0.00 39.56 4.58
2259 7102 3.976704 CCATTGTTGGGTCAGCCTA 57.023 52.632 0.00 0.00 39.56 3.93
2260 7103 2.442236 CCATTGTTGGGTCAGCCTAT 57.558 50.000 0.00 0.00 39.56 2.57
2261 7104 2.738743 CCATTGTTGGGTCAGCCTATT 58.261 47.619 0.00 0.00 39.56 1.73
2262 7105 3.099141 CCATTGTTGGGTCAGCCTATTT 58.901 45.455 0.00 0.00 39.56 1.40
2263 7106 3.515104 CCATTGTTGGGTCAGCCTATTTT 59.485 43.478 0.00 0.00 39.56 1.82
2264 7107 4.381932 CCATTGTTGGGTCAGCCTATTTTC 60.382 45.833 0.00 0.00 39.56 2.29
2265 7108 3.517296 TGTTGGGTCAGCCTATTTTCA 57.483 42.857 0.00 0.00 34.45 2.69
2266 7109 4.046286 TGTTGGGTCAGCCTATTTTCAT 57.954 40.909 0.00 0.00 34.45 2.57
2267 7110 4.415596 TGTTGGGTCAGCCTATTTTCATT 58.584 39.130 0.00 0.00 34.45 2.57
2268 7111 4.837860 TGTTGGGTCAGCCTATTTTCATTT 59.162 37.500 0.00 0.00 34.45 2.32
2269 7112 5.306678 TGTTGGGTCAGCCTATTTTCATTTT 59.693 36.000 0.00 0.00 34.45 1.82
2270 7113 6.183361 TGTTGGGTCAGCCTATTTTCATTTTT 60.183 34.615 0.00 0.00 34.45 1.94
2307 7150 8.776061 TTTCTATTTTTCTTCTTTCCCTTCCA 57.224 30.769 0.00 0.00 0.00 3.53
2308 7151 8.776061 TTCTATTTTTCTTCTTTCCCTTCCAA 57.224 30.769 0.00 0.00 0.00 3.53
2309 7152 8.409358 TCTATTTTTCTTCTTTCCCTTCCAAG 57.591 34.615 0.00 0.00 0.00 3.61
2310 7153 8.004801 TCTATTTTTCTTCTTTCCCTTCCAAGT 58.995 33.333 0.00 0.00 0.00 3.16
2311 7154 6.867519 TTTTTCTTCTTTCCCTTCCAAGTT 57.132 33.333 0.00 0.00 0.00 2.66
2312 7155 7.964666 TTTTTCTTCTTTCCCTTCCAAGTTA 57.035 32.000 0.00 0.00 0.00 2.24
2313 7156 8.547481 TTTTTCTTCTTTCCCTTCCAAGTTAT 57.453 30.769 0.00 0.00 0.00 1.89
2314 7157 8.547481 TTTTCTTCTTTCCCTTCCAAGTTATT 57.453 30.769 0.00 0.00 0.00 1.40
2315 7158 8.547481 TTTCTTCTTTCCCTTCCAAGTTATTT 57.453 30.769 0.00 0.00 0.00 1.40
2316 7159 8.547481 TTCTTCTTTCCCTTCCAAGTTATTTT 57.453 30.769 0.00 0.00 0.00 1.82
2317 7160 8.547481 TCTTCTTTCCCTTCCAAGTTATTTTT 57.453 30.769 0.00 0.00 0.00 1.94
2361 7204 9.780413 TTTTCTTTGAATTTTCCAAAATTTCGG 57.220 25.926 10.59 0.00 45.70 4.30
2362 7205 8.499403 TTCTTTGAATTTTCCAAAATTTCGGT 57.501 26.923 10.59 0.00 45.70 4.69
2363 7206 8.499403 TCTTTGAATTTTCCAAAATTTCGGTT 57.501 26.923 10.59 0.00 45.70 4.44
2364 7207 8.951243 TCTTTGAATTTTCCAAAATTTCGGTTT 58.049 25.926 10.59 0.00 45.70 3.27
2365 7208 9.566530 CTTTGAATTTTCCAAAATTTCGGTTTT 57.433 25.926 10.59 0.00 45.70 2.43
2366 7209 8.902040 TTGAATTTTCCAAAATTTCGGTTTTG 57.098 26.923 10.59 11.88 45.70 2.44
2367 7210 8.045176 TGAATTTTCCAAAATTTCGGTTTTGT 57.955 26.923 10.59 2.47 45.70 2.83
2368 7211 8.178313 TGAATTTTCCAAAATTTCGGTTTTGTC 58.822 29.630 10.59 9.05 45.70 3.18
2369 7212 6.424176 TTTTCCAAAATTTCGGTTTTGTCC 57.576 33.333 15.35 0.00 43.93 4.02
2370 7213 5.346181 TTCCAAAATTTCGGTTTTGTCCT 57.654 34.783 15.35 0.00 43.93 3.85
2371 7214 6.466885 TTCCAAAATTTCGGTTTTGTCCTA 57.533 33.333 15.35 2.50 43.93 2.94
2372 7215 6.466885 TCCAAAATTTCGGTTTTGTCCTAA 57.533 33.333 15.35 0.00 43.93 2.69
2373 7216 7.056844 TCCAAAATTTCGGTTTTGTCCTAAT 57.943 32.000 15.35 0.00 43.93 1.73
2374 7217 7.501844 TCCAAAATTTCGGTTTTGTCCTAATT 58.498 30.769 15.35 0.00 43.93 1.40
2375 7218 7.988028 TCCAAAATTTCGGTTTTGTCCTAATTT 59.012 29.630 15.35 0.00 43.93 1.82
2376 7219 8.616942 CCAAAATTTCGGTTTTGTCCTAATTTT 58.383 29.630 15.35 0.00 43.93 1.82
2377 7220 9.644993 CAAAATTTCGGTTTTGTCCTAATTTTC 57.355 29.630 11.09 0.00 41.72 2.29
2378 7221 7.631915 AATTTCGGTTTTGTCCTAATTTTCG 57.368 32.000 0.00 0.00 0.00 3.46
2379 7222 5.754543 TTCGGTTTTGTCCTAATTTTCGT 57.245 34.783 0.00 0.00 0.00 3.85
2380 7223 5.754543 TCGGTTTTGTCCTAATTTTCGTT 57.245 34.783 0.00 0.00 0.00 3.85
2381 7224 6.857777 TCGGTTTTGTCCTAATTTTCGTTA 57.142 33.333 0.00 0.00 0.00 3.18
2382 7225 7.256756 TCGGTTTTGTCCTAATTTTCGTTAA 57.743 32.000 0.00 0.00 0.00 2.01
2383 7226 7.701445 TCGGTTTTGTCCTAATTTTCGTTAAA 58.299 30.769 0.00 0.00 0.00 1.52
2384 7227 8.351461 TCGGTTTTGTCCTAATTTTCGTTAAAT 58.649 29.630 0.00 0.00 38.08 1.40
2385 7228 8.632551 CGGTTTTGTCCTAATTTTCGTTAAATC 58.367 33.333 0.00 0.00 35.39 2.17
2386 7229 9.687210 GGTTTTGTCCTAATTTTCGTTAAATCT 57.313 29.630 0.00 0.00 35.39 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.176851 GAGGACCGCGACTCCGAC 62.177 72.222 8.23 7.40 38.22 4.79
107 108 1.028330 TCGGTCCTTACGTCGATGCT 61.028 55.000 4.06 0.00 0.00 3.79
124 125 2.508439 ATAACAGCGGCACCGTCG 60.508 61.111 11.27 4.70 42.09 5.12
156 157 1.800315 GATGACCACGACGTCCACG 60.800 63.158 10.58 1.10 46.33 4.94
164 165 2.229302 TCGTATGTGTTGATGACCACGA 59.771 45.455 0.00 0.00 0.00 4.35
543 729 4.566488 GGCCCATTTCTCTTTCTCTTCTCA 60.566 45.833 0.00 0.00 0.00 3.27
580 766 6.944096 TCATCAATTTATTTTGGCATGGACA 58.056 32.000 0.00 0.00 0.00 4.02
581 767 6.480981 CCTCATCAATTTATTTTGGCATGGAC 59.519 38.462 0.00 0.00 0.00 4.02
582 768 6.383436 TCCTCATCAATTTATTTTGGCATGGA 59.617 34.615 0.00 0.00 0.00 3.41
583 769 6.584488 TCCTCATCAATTTATTTTGGCATGG 58.416 36.000 0.00 0.00 0.00 3.66
587 773 7.550712 AGAACTCCTCATCAATTTATTTTGGC 58.449 34.615 0.00 0.00 0.00 4.52
588 774 8.193438 GGAGAACTCCTCATCAATTTATTTTGG 58.807 37.037 12.98 0.00 46.16 3.28
611 797 1.072965 AGAAGGTGACCAAGCAAGGAG 59.927 52.381 3.63 0.00 0.00 3.69
620 806 3.516586 TCTACCATGAAGAAGGTGACCA 58.483 45.455 3.63 0.00 38.87 4.02
898 2593 2.505405 TGTAGGCGTTTTTATGGTGCA 58.495 42.857 0.00 0.00 0.00 4.57
931 2638 0.459899 ATGCTATTCTGCGTCGTCCA 59.540 50.000 0.00 0.00 35.36 4.02
938 2645 4.031028 GCTTGTTGTAATGCTATTCTGCG 58.969 43.478 0.00 0.00 35.36 5.18
963 2674 1.601430 TGCTGTACGTACGTGTGTGTA 59.399 47.619 30.25 13.84 0.00 2.90
987 2698 2.373224 GCCTCCATTTTTCTCTCCCAG 58.627 52.381 0.00 0.00 0.00 4.45
989 2700 1.005924 TGGCCTCCATTTTTCTCTCCC 59.994 52.381 3.32 0.00 0.00 4.30
990 2701 2.514458 TGGCCTCCATTTTTCTCTCC 57.486 50.000 3.32 0.00 0.00 3.71
995 2711 1.895131 TCAGCTTGGCCTCCATTTTTC 59.105 47.619 3.32 0.00 31.53 2.29
1146 2882 0.376852 GCGCATTGCCTATTCGAACA 59.623 50.000 0.30 0.00 37.76 3.18
1150 2886 0.316442 CACTGCGCATTGCCTATTCG 60.316 55.000 12.24 0.00 45.60 3.34
1398 6221 2.729360 CGCGTAGTTGAACTTGATGTGA 59.271 45.455 1.97 0.00 0.00 3.58
1485 6308 2.817844 GCCCAAACGATTCCAACTAACT 59.182 45.455 0.00 0.00 0.00 2.24
1632 6475 0.100325 TTTGTGTGTTCAAGCAGCCG 59.900 50.000 0.00 0.00 0.00 5.52
1714 6557 1.695242 TCCAAACCTAAGCCGTGAGAA 59.305 47.619 0.00 0.00 0.00 2.87
1762 6605 8.654094 TCTTTGCAGGATGAATGATCTATCTTA 58.346 33.333 0.00 0.00 39.69 2.10
1766 6609 6.935771 GTCTCTTTGCAGGATGAATGATCTAT 59.064 38.462 0.00 0.00 39.69 1.98
1791 6634 7.730364 AGGATAGTTTAATTTGCCTGTATCG 57.270 36.000 0.00 0.00 0.00 2.92
1812 6655 8.466798 GCAAGGCTTATTTTATCAAACTAAGGA 58.533 33.333 0.00 0.00 0.00 3.36
1813 6656 7.706607 GGCAAGGCTTATTTTATCAAACTAAGG 59.293 37.037 0.00 0.00 0.00 2.69
1814 6657 7.706607 GGGCAAGGCTTATTTTATCAAACTAAG 59.293 37.037 0.00 5.05 0.00 2.18
1815 6658 7.552459 GGGCAAGGCTTATTTTATCAAACTAA 58.448 34.615 0.00 0.00 0.00 2.24
1889 6732 3.466836 AGCTTCAACATTCTGTCGTGAA 58.533 40.909 0.00 0.00 29.59 3.18
1929 6772 1.133025 CGGTCAACAATTGGATGCCTC 59.867 52.381 10.83 3.36 0.00 4.70
1951 6794 6.985188 AATCTGTATTCGTGCATTACAAGT 57.015 33.333 0.00 0.00 0.00 3.16
1952 6795 7.905126 TGTAATCTGTATTCGTGCATTACAAG 58.095 34.615 0.00 0.00 35.04 3.16
1981 6824 8.598924 CGCACCTTGCTATATTATTAGAGAATG 58.401 37.037 0.00 0.00 42.25 2.67
1982 6825 8.314751 ACGCACCTTGCTATATTATTAGAGAAT 58.685 33.333 0.00 0.00 42.25 2.40
1983 6826 7.667557 ACGCACCTTGCTATATTATTAGAGAA 58.332 34.615 0.00 0.00 42.25 2.87
1984 6827 7.228314 ACGCACCTTGCTATATTATTAGAGA 57.772 36.000 0.00 0.00 42.25 3.10
1985 6828 7.891183 AACGCACCTTGCTATATTATTAGAG 57.109 36.000 0.00 0.00 42.25 2.43
1986 6829 8.148351 AGAAACGCACCTTGCTATATTATTAGA 58.852 33.333 0.00 0.00 42.25 2.10
1987 6830 8.311650 AGAAACGCACCTTGCTATATTATTAG 57.688 34.615 0.00 0.00 42.25 1.73
1988 6831 8.671384 AAGAAACGCACCTTGCTATATTATTA 57.329 30.769 0.00 0.00 42.25 0.98
1989 6832 7.282224 TGAAGAAACGCACCTTGCTATATTATT 59.718 33.333 0.00 0.00 42.25 1.40
1990 6833 6.765989 TGAAGAAACGCACCTTGCTATATTAT 59.234 34.615 0.00 0.00 42.25 1.28
1991 6834 6.110033 TGAAGAAACGCACCTTGCTATATTA 58.890 36.000 0.00 0.00 42.25 0.98
1992 6835 4.941263 TGAAGAAACGCACCTTGCTATATT 59.059 37.500 0.00 0.00 42.25 1.28
1993 6836 4.513442 TGAAGAAACGCACCTTGCTATAT 58.487 39.130 0.00 0.00 42.25 0.86
1994 6837 3.932822 TGAAGAAACGCACCTTGCTATA 58.067 40.909 0.00 0.00 42.25 1.31
1995 6838 2.778299 TGAAGAAACGCACCTTGCTAT 58.222 42.857 0.00 0.00 42.25 2.97
1996 6839 2.248280 TGAAGAAACGCACCTTGCTA 57.752 45.000 0.00 0.00 42.25 3.49
1997 6840 1.388547 TTGAAGAAACGCACCTTGCT 58.611 45.000 0.00 0.00 42.25 3.91
1998 6841 2.422276 ATTGAAGAAACGCACCTTGC 57.578 45.000 0.00 0.00 40.69 4.01
1999 6842 5.717038 AAAAATTGAAGAAACGCACCTTG 57.283 34.783 0.00 0.00 0.00 3.61
2048 6891 8.899771 CAAAAATTTAGTACCACCTCGGATATT 58.100 33.333 0.00 0.00 38.63 1.28
2049 6892 8.050930 ACAAAAATTTAGTACCACCTCGGATAT 58.949 33.333 0.00 0.00 38.63 1.63
2050 6893 7.334921 CACAAAAATTTAGTACCACCTCGGATA 59.665 37.037 0.00 0.00 38.63 2.59
2051 6894 6.150474 CACAAAAATTTAGTACCACCTCGGAT 59.850 38.462 0.00 0.00 38.63 4.18
2052 6895 5.470777 CACAAAAATTTAGTACCACCTCGGA 59.529 40.000 0.00 0.00 38.63 4.55
2053 6896 5.335348 CCACAAAAATTTAGTACCACCTCGG 60.335 44.000 0.00 0.00 42.50 4.63
2054 6897 5.239963 ACCACAAAAATTTAGTACCACCTCG 59.760 40.000 0.00 0.00 0.00 4.63
2055 6898 6.294342 GGACCACAAAAATTTAGTACCACCTC 60.294 42.308 0.00 0.00 0.00 3.85
2056 6899 5.537295 GGACCACAAAAATTTAGTACCACCT 59.463 40.000 0.00 0.00 0.00 4.00
2057 6900 5.302313 TGGACCACAAAAATTTAGTACCACC 59.698 40.000 0.00 0.00 0.00 4.61
2058 6901 6.394025 TGGACCACAAAAATTTAGTACCAC 57.606 37.500 0.00 0.00 0.00 4.16
2059 6902 7.007723 AGATGGACCACAAAAATTTAGTACCA 58.992 34.615 0.00 13.31 0.00 3.25
2060 6903 7.312899 CAGATGGACCACAAAAATTTAGTACC 58.687 38.462 0.00 0.22 0.00 3.34
2061 6904 6.806739 GCAGATGGACCACAAAAATTTAGTAC 59.193 38.462 0.00 0.00 0.00 2.73
2062 6905 6.719370 AGCAGATGGACCACAAAAATTTAGTA 59.281 34.615 0.00 0.00 0.00 1.82
2063 6906 5.539955 AGCAGATGGACCACAAAAATTTAGT 59.460 36.000 0.00 0.00 0.00 2.24
2064 6907 6.029346 AGCAGATGGACCACAAAAATTTAG 57.971 37.500 0.00 0.00 0.00 1.85
2065 6908 6.945435 TCTAGCAGATGGACCACAAAAATTTA 59.055 34.615 0.00 0.00 0.00 1.40
2066 6909 4.961438 AGCAGATGGACCACAAAAATTT 57.039 36.364 0.00 0.00 0.00 1.82
2067 6910 5.324409 TCTAGCAGATGGACCACAAAAATT 58.676 37.500 0.00 0.00 0.00 1.82
2068 6911 4.922206 TCTAGCAGATGGACCACAAAAAT 58.078 39.130 0.00 0.00 0.00 1.82
2069 6912 4.365514 TCTAGCAGATGGACCACAAAAA 57.634 40.909 0.00 0.00 0.00 1.94
2070 6913 4.365514 TTCTAGCAGATGGACCACAAAA 57.634 40.909 0.00 0.00 0.00 2.44
2071 6914 4.365514 TTTCTAGCAGATGGACCACAAA 57.634 40.909 0.00 0.00 0.00 2.83
2072 6915 4.365514 TTTTCTAGCAGATGGACCACAA 57.634 40.909 0.00 0.00 0.00 3.33
2073 6916 4.574674 ATTTTCTAGCAGATGGACCACA 57.425 40.909 0.00 0.00 0.00 4.17
2074 6917 7.391148 TTTTATTTTCTAGCAGATGGACCAC 57.609 36.000 0.00 0.00 0.00 4.16
2075 6918 9.693739 TTATTTTATTTTCTAGCAGATGGACCA 57.306 29.630 0.00 0.00 0.00 4.02
2096 6939 9.463443 CAAAATTCTGGACGAAACTCTTTATTT 57.537 29.630 0.00 0.00 34.79 1.40
2097 6940 8.630037 ACAAAATTCTGGACGAAACTCTTTATT 58.370 29.630 0.00 0.00 34.79 1.40
2098 6941 8.166422 ACAAAATTCTGGACGAAACTCTTTAT 57.834 30.769 0.00 0.00 34.79 1.40
2099 6942 7.562454 ACAAAATTCTGGACGAAACTCTTTA 57.438 32.000 0.00 0.00 34.79 1.85
2100 6943 6.451064 ACAAAATTCTGGACGAAACTCTTT 57.549 33.333 0.00 0.00 34.79 2.52
2101 6944 6.956047 GTACAAAATTCTGGACGAAACTCTT 58.044 36.000 0.00 0.00 34.79 2.85
2102 6945 6.541111 GTACAAAATTCTGGACGAAACTCT 57.459 37.500 0.00 0.00 34.79 3.24
2110 6953 3.187842 GTCCCACGTACAAAATTCTGGAC 59.812 47.826 0.00 0.00 33.69 4.02
2111 6954 3.404899 GTCCCACGTACAAAATTCTGGA 58.595 45.455 0.00 0.00 0.00 3.86
2112 6955 2.158841 CGTCCCACGTACAAAATTCTGG 59.841 50.000 0.00 0.00 36.74 3.86
2113 6956 2.412325 GCGTCCCACGTACAAAATTCTG 60.412 50.000 0.00 0.00 44.73 3.02
2114 6957 1.802365 GCGTCCCACGTACAAAATTCT 59.198 47.619 0.00 0.00 44.73 2.40
2115 6958 1.532007 TGCGTCCCACGTACAAAATTC 59.468 47.619 0.00 0.00 44.73 2.17
2116 6959 1.595466 TGCGTCCCACGTACAAAATT 58.405 45.000 0.00 0.00 44.73 1.82
2117 6960 3.309052 TGCGTCCCACGTACAAAAT 57.691 47.368 0.00 0.00 44.73 1.82
2118 6961 4.850822 TGCGTCCCACGTACAAAA 57.149 50.000 0.00 0.00 44.73 2.44
2126 6969 2.025418 CTTACCACGTGCGTCCCAC 61.025 63.158 10.91 0.00 41.15 4.61
2127 6970 2.340809 CTTACCACGTGCGTCCCA 59.659 61.111 10.91 0.00 0.00 4.37
2128 6971 2.433664 CCTTACCACGTGCGTCCC 60.434 66.667 10.91 0.00 0.00 4.46
2129 6972 3.116531 GCCTTACCACGTGCGTCC 61.117 66.667 10.91 0.00 0.00 4.79
2130 6973 3.116531 GGCCTTACCACGTGCGTC 61.117 66.667 10.91 0.00 38.86 5.19
2131 6974 4.692475 GGGCCTTACCACGTGCGT 62.692 66.667 10.91 12.26 42.05 5.24
2132 6975 4.690719 TGGGCCTTACCACGTGCG 62.691 66.667 10.91 6.24 42.05 5.34
2133 6976 2.741486 TTCTGGGCCTTACCACGTGC 62.741 60.000 10.91 0.00 42.05 5.34
2134 6977 0.250553 TTTCTGGGCCTTACCACGTG 60.251 55.000 9.08 9.08 42.05 4.49
2135 6978 0.475044 TTTTCTGGGCCTTACCACGT 59.525 50.000 4.53 0.00 42.05 4.49
2136 6979 1.165270 CTTTTCTGGGCCTTACCACG 58.835 55.000 4.53 0.00 42.05 4.94
2137 6980 2.160205 GTCTTTTCTGGGCCTTACCAC 58.840 52.381 4.53 0.00 42.05 4.16
2138 6981 1.777878 TGTCTTTTCTGGGCCTTACCA 59.222 47.619 4.53 0.00 42.05 3.25
2139 6982 2.160205 GTGTCTTTTCTGGGCCTTACC 58.840 52.381 4.53 0.00 37.93 2.85
2140 6983 2.160205 GGTGTCTTTTCTGGGCCTTAC 58.840 52.381 4.53 0.00 0.00 2.34
2141 6984 1.074889 GGGTGTCTTTTCTGGGCCTTA 59.925 52.381 4.53 0.00 0.00 2.69
2142 6985 0.178961 GGGTGTCTTTTCTGGGCCTT 60.179 55.000 4.53 0.00 0.00 4.35
2143 6986 1.360393 TGGGTGTCTTTTCTGGGCCT 61.360 55.000 4.53 0.00 0.00 5.19
2144 6987 0.251787 ATGGGTGTCTTTTCTGGGCC 60.252 55.000 0.00 0.00 0.00 5.80
2145 6988 1.632589 AATGGGTGTCTTTTCTGGGC 58.367 50.000 0.00 0.00 0.00 5.36
2146 6989 4.832823 ACTTAAATGGGTGTCTTTTCTGGG 59.167 41.667 0.00 0.00 0.00 4.45
2147 6990 5.048013 GGACTTAAATGGGTGTCTTTTCTGG 60.048 44.000 0.00 0.00 0.00 3.86
2148 6991 5.770162 AGGACTTAAATGGGTGTCTTTTCTG 59.230 40.000 0.00 0.00 0.00 3.02
2149 6992 5.770162 CAGGACTTAAATGGGTGTCTTTTCT 59.230 40.000 0.00 0.00 0.00 2.52
2150 6993 5.564848 GCAGGACTTAAATGGGTGTCTTTTC 60.565 44.000 0.00 0.00 0.00 2.29
2151 6994 4.280929 GCAGGACTTAAATGGGTGTCTTTT 59.719 41.667 0.00 0.00 0.00 2.27
2152 6995 3.826729 GCAGGACTTAAATGGGTGTCTTT 59.173 43.478 0.00 0.00 0.00 2.52
2153 6996 3.421844 GCAGGACTTAAATGGGTGTCTT 58.578 45.455 0.00 0.00 0.00 3.01
2154 6997 2.615493 CGCAGGACTTAAATGGGTGTCT 60.615 50.000 0.00 0.00 0.00 3.41
2155 6998 1.737793 CGCAGGACTTAAATGGGTGTC 59.262 52.381 0.00 0.00 0.00 3.67
2156 6999 1.821216 CGCAGGACTTAAATGGGTGT 58.179 50.000 0.00 0.00 0.00 4.16
2157 7000 0.451783 GCGCAGGACTTAAATGGGTG 59.548 55.000 0.30 0.00 0.00 4.61
2158 7001 0.037590 TGCGCAGGACTTAAATGGGT 59.962 50.000 5.66 0.00 0.00 4.51
2159 7002 2.866872 TGCGCAGGACTTAAATGGG 58.133 52.632 5.66 0.00 0.00 4.00
2175 7018 6.868339 ACAAATAAAGATTACCAGCTTTGTGC 59.132 34.615 0.00 0.00 43.29 4.57
2176 7019 7.271223 CGACAAATAAAGATTACCAGCTTTGTG 59.729 37.037 0.00 0.00 36.15 3.33
2177 7020 7.305474 CGACAAATAAAGATTACCAGCTTTGT 58.695 34.615 0.00 0.00 38.04 2.83
2178 7021 6.251376 GCGACAAATAAAGATTACCAGCTTTG 59.749 38.462 0.00 0.00 35.98 2.77
2179 7022 6.072175 TGCGACAAATAAAGATTACCAGCTTT 60.072 34.615 0.00 0.00 37.94 3.51
2180 7023 5.414454 TGCGACAAATAAAGATTACCAGCTT 59.586 36.000 0.00 0.00 0.00 3.74
2181 7024 4.941263 TGCGACAAATAAAGATTACCAGCT 59.059 37.500 0.00 0.00 0.00 4.24
2182 7025 5.028375 GTGCGACAAATAAAGATTACCAGC 58.972 41.667 0.00 0.00 0.00 4.85
2183 7026 6.176975 TGTGCGACAAATAAAGATTACCAG 57.823 37.500 0.00 0.00 0.00 4.00
2184 7027 6.561737 TTGTGCGACAAATAAAGATTACCA 57.438 33.333 0.00 0.00 34.76 3.25
2185 7028 6.033513 GCTTTGTGCGACAAATAAAGATTACC 59.966 38.462 12.68 0.00 45.79 2.85
2186 7029 6.967498 GCTTTGTGCGACAAATAAAGATTAC 58.033 36.000 12.68 0.00 45.79 1.89
2202 7045 4.058124 TCCATCTATATGTCGCTTTGTGC 58.942 43.478 0.00 0.00 38.57 4.57
2203 7046 4.151335 GCTCCATCTATATGTCGCTTTGTG 59.849 45.833 0.00 0.00 0.00 3.33
2204 7047 4.039730 AGCTCCATCTATATGTCGCTTTGT 59.960 41.667 0.00 0.00 34.77 2.83
2205 7048 4.564041 AGCTCCATCTATATGTCGCTTTG 58.436 43.478 0.00 0.00 34.77 2.77
2206 7049 4.881019 AGCTCCATCTATATGTCGCTTT 57.119 40.909 0.00 0.00 34.77 3.51
2207 7050 4.322349 GGAAGCTCCATCTATATGTCGCTT 60.322 45.833 11.40 11.40 43.53 4.68
2208 7051 3.194542 GGAAGCTCCATCTATATGTCGCT 59.805 47.826 0.00 0.00 37.94 4.93
2209 7052 3.516615 GGAAGCTCCATCTATATGTCGC 58.483 50.000 0.00 0.00 36.28 5.19
2210 7053 3.511540 TGGGAAGCTCCATCTATATGTCG 59.488 47.826 0.00 0.00 38.64 4.35
2211 7054 5.690464 ATGGGAAGCTCCATCTATATGTC 57.310 43.478 1.04 0.00 43.57 3.06
2221 7064 1.742146 CGATCGATGGGAAGCTCCA 59.258 57.895 10.26 0.00 38.64 3.86
2222 7065 1.666234 GCGATCGATGGGAAGCTCC 60.666 63.158 21.57 0.00 35.23 4.70
2223 7066 1.666234 GGCGATCGATGGGAAGCTC 60.666 63.158 21.57 0.00 34.19 4.09
2224 7067 2.423446 GGCGATCGATGGGAAGCT 59.577 61.111 21.57 0.00 34.19 3.74
2225 7068 2.666526 GGGCGATCGATGGGAAGC 60.667 66.667 21.57 0.05 0.00 3.86
2226 7069 0.250467 AATGGGCGATCGATGGGAAG 60.250 55.000 21.57 0.00 0.00 3.46
2227 7070 0.534877 CAATGGGCGATCGATGGGAA 60.535 55.000 21.57 0.00 0.00 3.97
2228 7071 1.071299 CAATGGGCGATCGATGGGA 59.929 57.895 21.57 0.00 0.00 4.37
2229 7072 0.819259 AACAATGGGCGATCGATGGG 60.819 55.000 21.57 4.86 0.00 4.00
2230 7073 0.308684 CAACAATGGGCGATCGATGG 59.691 55.000 21.57 1.74 0.00 3.51
2231 7074 0.308684 CCAACAATGGGCGATCGATG 59.691 55.000 21.57 11.06 43.51 3.84
2232 7075 2.706636 CCAACAATGGGCGATCGAT 58.293 52.632 21.57 0.00 43.51 3.59
2233 7076 4.217035 CCAACAATGGGCGATCGA 57.783 55.556 21.57 0.00 43.51 3.59
2242 7085 4.220382 TGAAAATAGGCTGACCCAACAATG 59.780 41.667 0.00 0.00 36.11 2.82
2243 7086 4.415596 TGAAAATAGGCTGACCCAACAAT 58.584 39.130 0.00 0.00 36.11 2.71
2244 7087 3.838565 TGAAAATAGGCTGACCCAACAA 58.161 40.909 0.00 0.00 36.11 2.83
2245 7088 3.517296 TGAAAATAGGCTGACCCAACA 57.483 42.857 0.00 0.00 36.11 3.33
2246 7089 5.405935 AAATGAAAATAGGCTGACCCAAC 57.594 39.130 0.00 0.00 36.11 3.77
2247 7090 6.432403 AAAAATGAAAATAGGCTGACCCAA 57.568 33.333 0.00 0.00 36.11 4.12
2281 7124 9.207868 TGGAAGGGAAAGAAGAAAAATAGAAAA 57.792 29.630 0.00 0.00 0.00 2.29
2282 7125 8.776061 TGGAAGGGAAAGAAGAAAAATAGAAA 57.224 30.769 0.00 0.00 0.00 2.52
2283 7126 8.776061 TTGGAAGGGAAAGAAGAAAAATAGAA 57.224 30.769 0.00 0.00 0.00 2.10
2284 7127 8.004801 ACTTGGAAGGGAAAGAAGAAAAATAGA 58.995 33.333 0.00 0.00 0.00 1.98
2285 7128 8.183104 ACTTGGAAGGGAAAGAAGAAAAATAG 57.817 34.615 0.00 0.00 0.00 1.73
2286 7129 8.547481 AACTTGGAAGGGAAAGAAGAAAAATA 57.453 30.769 0.00 0.00 0.00 1.40
2287 7130 7.437713 AACTTGGAAGGGAAAGAAGAAAAAT 57.562 32.000 0.00 0.00 0.00 1.82
2288 7131 6.867519 AACTTGGAAGGGAAAGAAGAAAAA 57.132 33.333 0.00 0.00 0.00 1.94
2289 7132 8.547481 AATAACTTGGAAGGGAAAGAAGAAAA 57.453 30.769 0.00 0.00 0.00 2.29
2290 7133 8.547481 AAATAACTTGGAAGGGAAAGAAGAAA 57.453 30.769 0.00 0.00 0.00 2.52
2291 7134 8.547481 AAAATAACTTGGAAGGGAAAGAAGAA 57.453 30.769 0.00 0.00 0.00 2.52
2292 7135 8.547481 AAAAATAACTTGGAAGGGAAAGAAGA 57.453 30.769 0.00 0.00 0.00 2.87
2335 7178 9.780413 CCGAAATTTTGGAAAATTCAAAGAAAA 57.220 25.926 18.49 0.00 45.16 2.29
2336 7179 8.951243 ACCGAAATTTTGGAAAATTCAAAGAAA 58.049 25.926 28.11 0.00 45.16 2.52
2337 7180 8.499403 ACCGAAATTTTGGAAAATTCAAAGAA 57.501 26.923 28.11 0.00 45.16 2.52
2338 7181 8.499403 AACCGAAATTTTGGAAAATTCAAAGA 57.501 26.923 28.11 0.00 45.16 2.52
2339 7182 9.566530 AAAACCGAAATTTTGGAAAATTCAAAG 57.433 25.926 28.11 0.61 45.16 2.77
2340 7183 9.346725 CAAAACCGAAATTTTGGAAAATTCAAA 57.653 25.926 28.11 0.00 45.16 2.69
2341 7184 8.902040 CAAAACCGAAATTTTGGAAAATTCAA 57.098 26.923 28.11 0.00 45.16 2.69
2352 7195 8.544597 CGAAAATTAGGACAAAACCGAAATTTT 58.455 29.630 17.47 17.47 43.77 1.82
2353 7196 7.707464 ACGAAAATTAGGACAAAACCGAAATTT 59.293 29.630 0.00 0.00 39.54 1.82
2354 7197 7.204604 ACGAAAATTAGGACAAAACCGAAATT 58.795 30.769 0.00 0.00 34.43 1.82
2355 7198 6.741109 ACGAAAATTAGGACAAAACCGAAAT 58.259 32.000 0.00 0.00 34.73 2.17
2356 7199 6.134040 ACGAAAATTAGGACAAAACCGAAA 57.866 33.333 0.00 0.00 34.73 3.46
2357 7200 5.754543 ACGAAAATTAGGACAAAACCGAA 57.245 34.783 0.00 0.00 34.73 4.30
2358 7201 5.754543 AACGAAAATTAGGACAAAACCGA 57.245 34.783 0.00 0.00 34.73 4.69
2359 7202 7.911362 TTTAACGAAAATTAGGACAAAACCG 57.089 32.000 0.00 0.00 34.73 4.44
2360 7203 9.687210 AGATTTAACGAAAATTAGGACAAAACC 57.313 29.630 0.00 0.00 37.93 3.27


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

AutoCloner maintained by Alex Coulton.