Multiple sequence alignment - TraesCS4A01G204600

Loading Multiple Alignment...

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 TraesCS4A01G204600 chr4A 100.000 2685 0 0 433 3117 496115613 496112929 0.000000e+00 4959.0
1 TraesCS4A01G204600 chr4A 82.632 380 66 0 2702 3081 603032863 603033242 1.380000e-88 337.0
2 TraesCS4A01G204600 chr4A 100.000 88 0 0 1 88 496116045 496115958 2.490000e-36 163.0
3 TraesCS4A01G204600 chr4D 93.723 1593 61 11 433 2004 84174463 84172889 0.000000e+00 2351.0
4 TraesCS4A01G204600 chr4D 81.243 901 147 16 2083 2970 216536865 216537756 0.000000e+00 708.0
5 TraesCS4A01G204600 chr4D 95.402 87 3 1 1996 2082 84009075 84008990 1.510000e-28 137.0
6 TraesCS4A01G204600 chr4B 98.778 900 8 2 1052 1950 119109688 119108791 0.000000e+00 1598.0
7 TraesCS4A01G204600 chr4B 88.854 646 46 15 433 1065 119110479 119109847 0.000000e+00 771.0
8 TraesCS4A01G204600 chr4B 85.449 323 43 4 2777 3096 245635114 245634793 1.790000e-87 333.0
9 TraesCS4A01G204600 chr4B 82.114 369 63 2 2371 2739 245635478 245635113 2.330000e-81 313.0
10 TraesCS4A01G204600 chr6D 89.062 448 49 0 2483 2930 24019868 24020315 9.770000e-155 556.0
11 TraesCS4A01G204600 chr6D 85.099 302 40 3 2190 2490 24016475 24016772 1.400000e-78 303.0
12 TraesCS4A01G204600 chr6D 91.011 178 16 0 2940 3117 24021711 24021888 1.120000e-59 241.0
13 TraesCS4A01G204600 chr6D 86.047 86 12 0 3 88 187276847 187276932 3.310000e-15 93.5
14 TraesCS4A01G204600 chr2B 81.270 630 114 4 2470 3097 57140747 57140120 9.970000e-140 507.0
15 TraesCS4A01G204600 chr6A 90.988 344 31 0 2774 3117 22546090 22546433 6.090000e-127 464.0
16 TraesCS4A01G204600 chr3B 75.510 686 143 21 2411 3080 685387904 685387228 2.330000e-81 313.0
17 TraesCS4A01G204600 chr5D 87.719 228 28 0 743 970 504794709 504794482 1.840000e-67 267.0
18 TraesCS4A01G204600 chr5D 97.674 43 1 0 690 732 279193434 279193476 1.200000e-09 75.0
19 TraesCS4A01G204600 chr3A 72.899 690 157 28 2380 3054 131040859 131041533 8.760000e-51 211.0
20 TraesCS4A01G204600 chr7D 72.144 639 160 17 2395 3023 384022493 384021863 8.880000e-41 178.0
21 TraesCS4A01G204600 chr3D 73.488 430 99 14 2395 2817 248635267 248635688 6.960000e-32 148.0
22 TraesCS4A01G204600 chr1B 85.849 106 15 0 2404 2509 562034001 562034106 2.540000e-21 113.0
23 TraesCS4A01G204600 chr1D 91.667 48 4 0 2457 2504 122902381 122902428 2.010000e-07 67.6


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 TraesCS4A01G204600 chr4A 496112929 496116045 3116 True 2561.000000 4959 100.000000 1 3117 2 chr4A.!!$R1 3116
1 TraesCS4A01G204600 chr4D 84172889 84174463 1574 True 2351.000000 2351 93.723000 433 2004 1 chr4D.!!$R2 1571
2 TraesCS4A01G204600 chr4D 216536865 216537756 891 False 708.000000 708 81.243000 2083 2970 1 chr4D.!!$F1 887
3 TraesCS4A01G204600 chr4B 119108791 119110479 1688 True 1184.500000 1598 93.816000 433 1950 2 chr4B.!!$R1 1517
4 TraesCS4A01G204600 chr4B 245634793 245635478 685 True 323.000000 333 83.781500 2371 3096 2 chr4B.!!$R2 725
5 TraesCS4A01G204600 chr6D 24016475 24021888 5413 False 366.666667 556 88.390667 2190 3117 3 chr6D.!!$F2 927
6 TraesCS4A01G204600 chr2B 57140120 57140747 627 True 507.000000 507 81.270000 2470 3097 1 chr2B.!!$R1 627
7 TraesCS4A01G204600 chr3B 685387228 685387904 676 True 313.000000 313 75.510000 2411 3080 1 chr3B.!!$R1 669
8 TraesCS4A01G204600 chr3A 131040859 131041533 674 False 211.000000 211 72.899000 2380 3054 1 chr3A.!!$F1 674

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
845 858 0.032615 AAATATTTGGCTCGCCCCCA 60.033 50.0 5.33 0.0 34.56 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2259 2454 0.036875 CTGGTTCGGCTTCCTTCCTT 59.963 55.0 0.0 0.0 0.0 3.36 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
19 20 1.318576 GAAACAGAGGGTTGTGGTGG 58.681 55.000 0.00 0.00 40.35 4.61
20 21 0.755327 AAACAGAGGGTTGTGGTGGC 60.755 55.000 0.00 0.00 40.35 5.01
21 22 2.669569 CAGAGGGTTGTGGTGGCG 60.670 66.667 0.00 0.00 0.00 5.69
22 23 2.847234 AGAGGGTTGTGGTGGCGA 60.847 61.111 0.00 0.00 0.00 5.54
23 24 2.224159 AGAGGGTTGTGGTGGCGAT 61.224 57.895 0.00 0.00 0.00 4.58
24 25 0.907704 AGAGGGTTGTGGTGGCGATA 60.908 55.000 0.00 0.00 0.00 2.92
25 26 0.035820 GAGGGTTGTGGTGGCGATAA 60.036 55.000 0.00 0.00 0.00 1.75
26 27 0.623723 AGGGTTGTGGTGGCGATAAT 59.376 50.000 0.00 0.00 0.00 1.28
27 28 1.841277 AGGGTTGTGGTGGCGATAATA 59.159 47.619 0.00 0.00 0.00 0.98
28 29 2.441750 AGGGTTGTGGTGGCGATAATAT 59.558 45.455 0.00 0.00 0.00 1.28
29 30 3.117663 AGGGTTGTGGTGGCGATAATATT 60.118 43.478 0.00 0.00 0.00 1.28
30 31 3.252458 GGGTTGTGGTGGCGATAATATTC 59.748 47.826 0.00 0.00 0.00 1.75
31 32 4.134563 GGTTGTGGTGGCGATAATATTCT 58.865 43.478 0.00 0.00 0.00 2.40
32 33 4.578928 GGTTGTGGTGGCGATAATATTCTT 59.421 41.667 0.00 0.00 0.00 2.52
33 34 5.067283 GGTTGTGGTGGCGATAATATTCTTT 59.933 40.000 0.00 0.00 0.00 2.52
34 35 6.199393 GTTGTGGTGGCGATAATATTCTTTC 58.801 40.000 0.00 0.00 0.00 2.62
35 36 4.509970 TGTGGTGGCGATAATATTCTTTCG 59.490 41.667 9.71 9.71 34.83 3.46
36 37 4.062293 TGGTGGCGATAATATTCTTTCGG 58.938 43.478 13.80 1.59 32.45 4.30
37 38 3.435671 GGTGGCGATAATATTCTTTCGGG 59.564 47.826 13.80 0.00 32.45 5.14
38 39 4.062991 GTGGCGATAATATTCTTTCGGGT 58.937 43.478 13.80 0.00 32.45 5.28
39 40 4.514066 GTGGCGATAATATTCTTTCGGGTT 59.486 41.667 13.80 0.00 32.45 4.11
40 41 4.753107 TGGCGATAATATTCTTTCGGGTTC 59.247 41.667 13.80 2.10 32.45 3.62
41 42 4.753107 GGCGATAATATTCTTTCGGGTTCA 59.247 41.667 13.80 0.00 32.45 3.18
42 43 5.333875 GGCGATAATATTCTTTCGGGTTCAC 60.334 44.000 13.80 1.34 32.45 3.18
43 44 5.465724 GCGATAATATTCTTTCGGGTTCACT 59.534 40.000 13.80 0.00 32.45 3.41
44 45 6.018180 GCGATAATATTCTTTCGGGTTCACTT 60.018 38.462 13.80 0.00 32.45 3.16
45 46 7.466860 GCGATAATATTCTTTCGGGTTCACTTT 60.467 37.037 13.80 0.00 32.45 2.66
46 47 8.395633 CGATAATATTCTTTCGGGTTCACTTTT 58.604 33.333 0.00 0.00 0.00 2.27
47 48 9.503427 GATAATATTCTTTCGGGTTCACTTTTG 57.497 33.333 0.00 0.00 0.00 2.44
48 49 7.519032 AATATTCTTTCGGGTTCACTTTTGA 57.481 32.000 0.00 0.00 0.00 2.69
49 50 4.893424 TTCTTTCGGGTTCACTTTTGAG 57.107 40.909 0.00 0.00 31.71 3.02
50 51 3.211045 TCTTTCGGGTTCACTTTTGAGG 58.789 45.455 0.00 0.00 31.71 3.86
51 52 1.975660 TTCGGGTTCACTTTTGAGGG 58.024 50.000 0.00 0.00 31.71 4.30
52 53 0.841289 TCGGGTTCACTTTTGAGGGT 59.159 50.000 0.00 0.00 31.71 4.34
53 54 1.213430 TCGGGTTCACTTTTGAGGGTT 59.787 47.619 0.00 0.00 31.71 4.11
54 55 1.607148 CGGGTTCACTTTTGAGGGTTC 59.393 52.381 0.00 0.00 31.71 3.62
55 56 1.961394 GGGTTCACTTTTGAGGGTTCC 59.039 52.381 0.00 0.00 31.71 3.62
56 57 1.607148 GGTTCACTTTTGAGGGTTCCG 59.393 52.381 0.00 0.00 31.71 4.30
57 58 1.607148 GTTCACTTTTGAGGGTTCCGG 59.393 52.381 0.00 0.00 31.71 5.14
58 59 0.109723 TCACTTTTGAGGGTTCCGGG 59.890 55.000 0.00 0.00 0.00 5.73
59 60 0.109723 CACTTTTGAGGGTTCCGGGA 59.890 55.000 0.00 0.00 0.00 5.14
60 61 0.848053 ACTTTTGAGGGTTCCGGGAA 59.152 50.000 5.09 5.09 0.00 3.97
61 62 1.427753 ACTTTTGAGGGTTCCGGGAAT 59.572 47.619 13.48 0.00 0.00 3.01
62 63 2.158370 ACTTTTGAGGGTTCCGGGAATT 60.158 45.455 13.48 1.91 0.00 2.17
63 64 3.074836 ACTTTTGAGGGTTCCGGGAATTA 59.925 43.478 13.48 0.00 0.00 1.40
64 65 4.264217 ACTTTTGAGGGTTCCGGGAATTAT 60.264 41.667 13.48 1.45 0.00 1.28
65 66 5.044698 ACTTTTGAGGGTTCCGGGAATTATA 60.045 40.000 13.48 0.00 0.00 0.98
66 67 4.699925 TTGAGGGTTCCGGGAATTATAG 57.300 45.455 13.48 0.00 0.00 1.31
67 68 2.976882 TGAGGGTTCCGGGAATTATAGG 59.023 50.000 13.48 0.00 0.00 2.57
68 69 3.245441 GAGGGTTCCGGGAATTATAGGA 58.755 50.000 13.48 0.00 0.00 2.94
69 70 3.844804 GAGGGTTCCGGGAATTATAGGAT 59.155 47.826 13.48 0.00 32.19 3.24
70 71 4.248652 AGGGTTCCGGGAATTATAGGATT 58.751 43.478 13.48 0.00 32.19 3.01
71 72 4.668335 AGGGTTCCGGGAATTATAGGATTT 59.332 41.667 13.48 0.00 32.19 2.17
72 73 5.853364 AGGGTTCCGGGAATTATAGGATTTA 59.147 40.000 13.48 0.00 32.19 1.40
73 74 6.507843 AGGGTTCCGGGAATTATAGGATTTAT 59.492 38.462 13.48 0.00 32.19 1.40
74 75 7.685486 AGGGTTCCGGGAATTATAGGATTTATA 59.315 37.037 13.48 0.00 32.19 0.98
75 76 7.991460 GGGTTCCGGGAATTATAGGATTTATAG 59.009 40.741 13.48 0.00 32.19 1.31
76 77 8.546322 GGTTCCGGGAATTATAGGATTTATAGT 58.454 37.037 13.48 0.00 32.19 2.12
77 78 9.955102 GTTCCGGGAATTATAGGATTTATAGTT 57.045 33.333 13.48 0.00 32.19 2.24
78 79 9.953565 TTCCGGGAATTATAGGATTTATAGTTG 57.046 33.333 5.09 0.00 32.19 3.16
79 80 8.545472 TCCGGGAATTATAGGATTTATAGTTGG 58.455 37.037 0.00 0.00 0.00 3.77
80 81 8.545472 CCGGGAATTATAGGATTTATAGTTGGA 58.455 37.037 0.00 0.00 0.00 3.53
81 82 9.953565 CGGGAATTATAGGATTTATAGTTGGAA 57.046 33.333 0.00 0.00 0.00 3.53
629 642 3.119101 ACGTATCAACCACCTCTAGCTTG 60.119 47.826 0.00 0.00 0.00 4.01
635 648 1.517257 CACCTCTAGCTTGCGACGG 60.517 63.158 0.00 0.00 0.00 4.79
696 709 8.035394 TCTCTCAAGTATTCTGATACAAACACC 58.965 37.037 0.07 0.00 40.51 4.16
699 712 9.653287 CTCAAGTATTCTGATACAAACACCTTA 57.347 33.333 0.07 0.00 40.51 2.69
736 749 1.631405 TTTGACCATGGCTTTGAGGG 58.369 50.000 13.04 0.00 0.00 4.30
738 751 0.776810 TGACCATGGCTTTGAGGGAA 59.223 50.000 13.04 0.00 0.00 3.97
804 817 0.180642 TGGCCTTGACCAACGTGTTA 59.819 50.000 3.32 0.00 36.55 2.41
845 858 0.032615 AAATATTTGGCTCGCCCCCA 60.033 50.000 5.33 0.00 34.56 4.96
848 861 1.858739 TATTTGGCTCGCCCCCAACT 61.859 55.000 5.33 0.29 41.77 3.16
861 874 0.179936 CCCAACTCATCTGCTCTCCC 59.820 60.000 0.00 0.00 0.00 4.30
862 875 0.179936 CCAACTCATCTGCTCTCCCC 59.820 60.000 0.00 0.00 0.00 4.81
883 896 4.414852 CCGTTGATTCTGTAGCCAAAATG 58.585 43.478 0.00 0.00 0.00 2.32
973 986 2.555547 GCAGCAACCAAACGGCTCT 61.556 57.895 0.00 0.00 35.27 4.09
986 1001 1.893137 ACGGCTCTGTGTTCAGACATA 59.107 47.619 0.00 0.00 44.58 2.29
995 1010 7.482169 TCTGTGTTCAGACATAAGAAGGTAT 57.518 36.000 0.00 0.00 44.58 2.73
1003 1018 6.323996 TCAGACATAAGAAGGTATTCGTCCAT 59.676 38.462 0.00 0.00 40.58 3.41
1027 1043 9.903682 CATAAATCTAAGGCATACTTTCATTGG 57.096 33.333 0.00 0.00 40.64 3.16
1118 1306 0.671251 TGTGCCCACGAAAATTCACC 59.329 50.000 0.00 0.00 0.00 4.02
1231 1420 4.147449 CAGGGTGGCGATCGCTCA 62.147 66.667 36.25 28.56 41.60 4.26
1933 2122 5.477291 TGTACTAGCTCAGTTTGCTTAGAGT 59.523 40.000 0.00 0.00 41.46 3.24
1945 2134 5.450818 TTGCTTAGAGTTATGGGTGGATT 57.549 39.130 0.00 0.00 0.00 3.01
1955 2144 8.945193 AGAGTTATGGGTGGATTATTAAGCTAA 58.055 33.333 0.00 0.00 0.00 3.09
1974 2163 4.572795 GCTAACCAGTAAAAGAGGATGCTC 59.427 45.833 6.03 6.03 0.00 4.26
1989 2183 1.048601 TGCTCTCTTTGTCCCGTTCT 58.951 50.000 0.00 0.00 0.00 3.01
2004 2198 4.461081 TCCCGTTCTTCCAAATGTTAATGG 59.539 41.667 0.00 0.00 38.09 3.16
2005 2199 4.381505 CCCGTTCTTCCAAATGTTAATGGG 60.382 45.833 0.00 0.00 36.95 4.00
2006 2200 4.461081 CCGTTCTTCCAAATGTTAATGGGA 59.539 41.667 0.00 0.00 37.31 4.37
2007 2201 5.047660 CCGTTCTTCCAAATGTTAATGGGAA 60.048 40.000 0.00 0.00 37.31 3.97
2008 2202 6.350949 CCGTTCTTCCAAATGTTAATGGGAAT 60.351 38.462 0.00 0.00 37.05 3.01
2009 2203 6.751888 CGTTCTTCCAAATGTTAATGGGAATC 59.248 38.462 0.00 0.00 37.05 2.52
2010 2204 6.790232 TCTTCCAAATGTTAATGGGAATCC 57.210 37.500 0.00 0.00 37.05 3.01
2011 2205 6.502138 TCTTCCAAATGTTAATGGGAATCCT 58.498 36.000 0.00 0.00 37.05 3.24
2012 2206 7.647827 TCTTCCAAATGTTAATGGGAATCCTA 58.352 34.615 0.00 0.00 37.05 2.94
2013 2207 8.119246 TCTTCCAAATGTTAATGGGAATCCTAA 58.881 33.333 0.00 0.00 37.05 2.69
2014 2208 8.671987 TTCCAAATGTTAATGGGAATCCTAAA 57.328 30.769 0.00 0.00 37.31 1.85
2015 2209 8.671987 TCCAAATGTTAATGGGAATCCTAAAA 57.328 30.769 0.00 0.00 37.31 1.52
2016 2210 8.757877 TCCAAATGTTAATGGGAATCCTAAAAG 58.242 33.333 0.00 0.00 37.31 2.27
2017 2211 7.986889 CCAAATGTTAATGGGAATCCTAAAAGG 59.013 37.037 0.00 0.00 32.88 3.11
2018 2212 6.731292 ATGTTAATGGGAATCCTAAAAGGC 57.269 37.500 0.00 0.00 34.61 4.35
2019 2213 5.584913 TGTTAATGGGAATCCTAAAAGGCA 58.415 37.500 0.00 0.00 34.61 4.75
2020 2214 6.201591 TGTTAATGGGAATCCTAAAAGGCAT 58.798 36.000 0.00 0.00 34.61 4.40
2021 2215 6.098124 TGTTAATGGGAATCCTAAAAGGCATG 59.902 38.462 0.00 0.00 34.61 4.06
2022 2216 3.756082 TGGGAATCCTAAAAGGCATGT 57.244 42.857 0.00 0.00 34.61 3.21
2023 2217 4.871871 TGGGAATCCTAAAAGGCATGTA 57.128 40.909 0.00 0.00 34.61 2.29
2024 2218 5.199982 TGGGAATCCTAAAAGGCATGTAA 57.800 39.130 0.00 0.00 34.61 2.41
2025 2219 5.584913 TGGGAATCCTAAAAGGCATGTAAA 58.415 37.500 0.00 0.00 34.61 2.01
2026 2220 6.201591 TGGGAATCCTAAAAGGCATGTAAAT 58.798 36.000 0.00 0.00 34.61 1.40
2027 2221 6.671779 TGGGAATCCTAAAAGGCATGTAAATT 59.328 34.615 0.00 0.00 34.61 1.82
2028 2222 7.147742 TGGGAATCCTAAAAGGCATGTAAATTC 60.148 37.037 0.00 0.00 34.61 2.17
2029 2223 6.918022 GGAATCCTAAAAGGCATGTAAATTCG 59.082 38.462 0.00 0.00 34.61 3.34
2030 2224 7.404671 AATCCTAAAAGGCATGTAAATTCGT 57.595 32.000 0.00 0.00 34.61 3.85
2031 2225 6.431198 TCCTAAAAGGCATGTAAATTCGTC 57.569 37.500 0.00 0.00 34.61 4.20
2032 2226 5.941058 TCCTAAAAGGCATGTAAATTCGTCA 59.059 36.000 0.00 0.00 34.61 4.35
2033 2227 6.601613 TCCTAAAAGGCATGTAAATTCGTCAT 59.398 34.615 0.00 0.00 34.61 3.06
2034 2228 7.122055 TCCTAAAAGGCATGTAAATTCGTCATT 59.878 33.333 0.00 0.00 34.61 2.57
2035 2229 6.949578 AAAAGGCATGTAAATTCGTCATTG 57.050 33.333 0.00 0.00 0.00 2.82
2036 2230 5.643379 AAGGCATGTAAATTCGTCATTGT 57.357 34.783 0.00 0.00 0.00 2.71
2037 2231 5.643379 AGGCATGTAAATTCGTCATTGTT 57.357 34.783 0.00 0.00 0.00 2.83
2038 2232 6.024552 AGGCATGTAAATTCGTCATTGTTT 57.975 33.333 0.00 0.00 0.00 2.83
2039 2233 6.092748 AGGCATGTAAATTCGTCATTGTTTC 58.907 36.000 0.00 0.00 0.00 2.78
2040 2234 5.288472 GGCATGTAAATTCGTCATTGTTTCC 59.712 40.000 0.00 0.00 0.00 3.13
2041 2235 5.861251 GCATGTAAATTCGTCATTGTTTCCA 59.139 36.000 0.00 0.00 0.00 3.53
2042 2236 6.531240 GCATGTAAATTCGTCATTGTTTCCAT 59.469 34.615 0.00 0.00 0.00 3.41
2043 2237 7.063308 GCATGTAAATTCGTCATTGTTTCCATT 59.937 33.333 0.00 0.00 0.00 3.16
2044 2238 8.586273 CATGTAAATTCGTCATTGTTTCCATTC 58.414 33.333 0.00 0.00 0.00 2.67
2045 2239 7.652727 TGTAAATTCGTCATTGTTTCCATTCA 58.347 30.769 0.00 0.00 0.00 2.57
2046 2240 8.303156 TGTAAATTCGTCATTGTTTCCATTCAT 58.697 29.630 0.00 0.00 0.00 2.57
2047 2241 9.139174 GTAAATTCGTCATTGTTTCCATTCATT 57.861 29.630 0.00 0.00 0.00 2.57
2048 2242 7.816945 AATTCGTCATTGTTTCCATTCATTC 57.183 32.000 0.00 0.00 0.00 2.67
2049 2243 5.956068 TCGTCATTGTTTCCATTCATTCA 57.044 34.783 0.00 0.00 0.00 2.57
2050 2244 6.324561 TCGTCATTGTTTCCATTCATTCAA 57.675 33.333 0.00 0.00 0.00 2.69
2051 2245 6.380995 TCGTCATTGTTTCCATTCATTCAAG 58.619 36.000 0.00 0.00 0.00 3.02
2052 2246 6.016360 TCGTCATTGTTTCCATTCATTCAAGT 60.016 34.615 0.00 0.00 0.00 3.16
2053 2247 6.088483 CGTCATTGTTTCCATTCATTCAAGTG 59.912 38.462 0.00 0.00 0.00 3.16
2054 2248 6.366877 GTCATTGTTTCCATTCATTCAAGTGG 59.633 38.462 0.00 0.00 0.00 4.00
2055 2249 5.867903 TTGTTTCCATTCATTCAAGTGGT 57.132 34.783 0.00 0.00 33.47 4.16
2056 2250 5.867903 TGTTTCCATTCATTCAAGTGGTT 57.132 34.783 0.00 0.00 33.47 3.67
2057 2251 6.232581 TGTTTCCATTCATTCAAGTGGTTT 57.767 33.333 0.00 0.00 33.47 3.27
2058 2252 7.353414 TGTTTCCATTCATTCAAGTGGTTTA 57.647 32.000 0.00 0.00 33.47 2.01
2059 2253 7.432869 TGTTTCCATTCATTCAAGTGGTTTAG 58.567 34.615 0.00 0.00 33.47 1.85
2060 2254 6.588719 TTCCATTCATTCAAGTGGTTTAGG 57.411 37.500 0.00 0.00 33.47 2.69
2061 2255 4.462483 TCCATTCATTCAAGTGGTTTAGGC 59.538 41.667 0.00 0.00 33.47 3.93
2062 2256 4.463891 CCATTCATTCAAGTGGTTTAGGCT 59.536 41.667 0.00 0.00 0.00 4.58
2063 2257 5.404946 CATTCATTCAAGTGGTTTAGGCTG 58.595 41.667 0.00 0.00 0.00 4.85
2064 2258 4.365514 TCATTCAAGTGGTTTAGGCTGA 57.634 40.909 0.00 0.00 0.00 4.26
2065 2259 4.922206 TCATTCAAGTGGTTTAGGCTGAT 58.078 39.130 0.00 0.00 0.00 2.90
2066 2260 4.701651 TCATTCAAGTGGTTTAGGCTGATG 59.298 41.667 0.00 0.00 0.00 3.07
2067 2261 3.071874 TCAAGTGGTTTAGGCTGATGG 57.928 47.619 0.00 0.00 0.00 3.51
2068 2262 2.642311 TCAAGTGGTTTAGGCTGATGGA 59.358 45.455 0.00 0.00 0.00 3.41
2069 2263 3.012518 CAAGTGGTTTAGGCTGATGGAG 58.987 50.000 0.00 0.00 0.00 3.86
2070 2264 2.269940 AGTGGTTTAGGCTGATGGAGT 58.730 47.619 0.00 0.00 0.00 3.85
2071 2265 3.450904 AGTGGTTTAGGCTGATGGAGTA 58.549 45.455 0.00 0.00 0.00 2.59
2072 2266 3.844211 AGTGGTTTAGGCTGATGGAGTAA 59.156 43.478 0.00 0.00 0.00 2.24
2073 2267 4.080863 AGTGGTTTAGGCTGATGGAGTAAG 60.081 45.833 0.00 0.00 0.00 2.34
2074 2268 3.199946 TGGTTTAGGCTGATGGAGTAAGG 59.800 47.826 0.00 0.00 0.00 2.69
2075 2269 3.433740 GGTTTAGGCTGATGGAGTAAGGG 60.434 52.174 0.00 0.00 0.00 3.95
2076 2270 1.424638 TAGGCTGATGGAGTAAGGGC 58.575 55.000 0.00 0.00 0.00 5.19
2077 2271 0.621571 AGGCTGATGGAGTAAGGGCA 60.622 55.000 0.00 0.00 0.00 5.36
2078 2272 0.475906 GGCTGATGGAGTAAGGGCAT 59.524 55.000 0.00 0.00 0.00 4.40
2079 2273 1.602311 GCTGATGGAGTAAGGGCATG 58.398 55.000 0.00 0.00 0.00 4.06
2080 2274 1.133976 GCTGATGGAGTAAGGGCATGT 60.134 52.381 0.00 0.00 0.00 3.21
2081 2275 2.104792 GCTGATGGAGTAAGGGCATGTA 59.895 50.000 0.00 0.00 0.00 2.29
2082 2276 3.244700 GCTGATGGAGTAAGGGCATGTAT 60.245 47.826 0.00 0.00 0.00 2.29
2083 2277 4.747931 GCTGATGGAGTAAGGGCATGTATT 60.748 45.833 0.00 0.00 0.00 1.89
2084 2278 5.380043 CTGATGGAGTAAGGGCATGTATTT 58.620 41.667 0.00 0.00 0.00 1.40
2085 2279 5.765510 TGATGGAGTAAGGGCATGTATTTT 58.234 37.500 0.00 0.00 0.00 1.82
2086 2280 6.194235 TGATGGAGTAAGGGCATGTATTTTT 58.806 36.000 0.00 0.00 0.00 1.94
2140 2334 3.267974 CCTTCAGGCAGGTTTCGC 58.732 61.111 0.00 0.00 0.00 4.70
2146 2340 4.700365 GGCAGGTTTCGCCGCAAC 62.700 66.667 0.00 0.00 43.70 4.17
2152 2346 1.226717 GTTTCGCCGCAACCAAACA 60.227 52.632 0.00 0.00 0.00 2.83
2156 2350 2.227568 CGCCGCAACCAAACAACAC 61.228 57.895 0.00 0.00 0.00 3.32
2158 2352 1.513158 CCGCAACCAAACAACACCA 59.487 52.632 0.00 0.00 0.00 4.17
2162 2356 2.417719 GCAACCAAACAACACCAAACA 58.582 42.857 0.00 0.00 0.00 2.83
2165 2359 4.261197 GCAACCAAACAACACCAAACAAAA 60.261 37.500 0.00 0.00 0.00 2.44
2168 2362 4.881850 ACCAAACAACACCAAACAAAACAA 59.118 33.333 0.00 0.00 0.00 2.83
2170 2364 6.039829 ACCAAACAACACCAAACAAAACAAAT 59.960 30.769 0.00 0.00 0.00 2.32
2174 2368 9.617975 AAACAACACCAAACAAAACAAATAATG 57.382 25.926 0.00 0.00 0.00 1.90
2192 2386 1.006813 TGGGCCACAACCATAAGGAT 58.993 50.000 0.00 0.00 38.69 3.24
2201 2395 6.414732 CCACAACCATAAGGATTAAGACAGA 58.585 40.000 0.00 0.00 38.69 3.41
2204 2398 7.390440 CACAACCATAAGGATTAAGACAGAACA 59.610 37.037 0.00 0.00 38.69 3.18
2208 2402 7.400339 ACCATAAGGATTAAGACAGAACAGAGA 59.600 37.037 0.00 0.00 38.69 3.10
2219 2413 3.201290 CAGAACAGAGATACATGGCACC 58.799 50.000 0.00 0.00 0.00 5.01
2233 2428 2.275380 GCACCCAGGCCAAAACGAT 61.275 57.895 5.01 0.00 0.00 3.73
2244 2439 1.896660 AAAACGATGGCACGCAGGT 60.897 52.632 8.93 0.00 36.70 4.00
2259 2454 2.416836 CGCAGGTCGAAACTATGAAGGA 60.417 50.000 0.00 0.00 41.67 3.36
2261 2456 3.619038 GCAGGTCGAAACTATGAAGGAAG 59.381 47.826 0.00 0.00 0.00 3.46
2266 2473 4.870991 GTCGAAACTATGAAGGAAGGAAGG 59.129 45.833 0.00 0.00 0.00 3.46
2267 2474 4.775780 TCGAAACTATGAAGGAAGGAAGGA 59.224 41.667 0.00 0.00 0.00 3.36
2268 2475 5.247564 TCGAAACTATGAAGGAAGGAAGGAA 59.752 40.000 0.00 0.00 0.00 3.36
2269 2476 5.582665 CGAAACTATGAAGGAAGGAAGGAAG 59.417 44.000 0.00 0.00 0.00 3.46
2276 2483 0.677098 GGAAGGAAGGAAGCCGAACC 60.677 60.000 0.00 0.00 0.00 3.62
2289 2496 2.971598 CGAACCAGGCCACCCTCAT 61.972 63.158 5.01 0.00 40.33 2.90
2300 2508 1.478105 CCACCCTCATAAGCCAAAAGC 59.522 52.381 0.00 0.00 44.25 3.51
2309 2517 2.034221 GCCAAAAGCGACCTCCCT 59.966 61.111 0.00 0.00 0.00 4.20
2310 2518 2.041115 GCCAAAAGCGACCTCCCTC 61.041 63.158 0.00 0.00 0.00 4.30
2314 2522 1.469335 AAAAGCGACCTCCCTCGACA 61.469 55.000 0.00 0.00 35.58 4.35
2324 2532 1.218316 CCCTCGACAACTAGCCACC 59.782 63.158 0.00 0.00 0.00 4.61
2354 2562 3.056536 TGCTGCGAGATAGAAGAAGTTGT 60.057 43.478 0.00 0.00 0.00 3.32
2366 2574 4.455877 AGAAGAAGTTGTAGCCCGAATTTG 59.544 41.667 0.00 0.00 0.00 2.32
2367 2575 3.081804 AGAAGTTGTAGCCCGAATTTGG 58.918 45.455 4.52 4.52 0.00 3.28
2402 2611 0.038251 AAAGCATCGCAGTCGTCAGA 60.038 50.000 0.00 0.00 36.96 3.27
2504 5816 7.906160 TGCTCGATAGTAAATTTGTTTCTAGC 58.094 34.615 0.00 6.66 37.40 3.42
2509 5821 5.526010 AGTAAATTTGTTTCTAGCCGTCG 57.474 39.130 0.00 0.00 0.00 5.12
2527 5839 0.034477 CGATAGGGCCCAACAAACCT 60.034 55.000 27.56 2.06 37.13 3.50
2614 5933 2.112691 TCAGAGAAAGAGGAGGGGTTCT 59.887 50.000 0.00 0.00 33.07 3.01
2635 5954 2.600769 AGACCCGAAGCCACGACT 60.601 61.111 0.00 0.00 35.09 4.18
2678 5997 1.963515 GGCCAAGACACAGTGGAAAAT 59.036 47.619 5.31 0.00 37.03 1.82
2688 6007 8.585471 AGACACAGTGGAAAATGATATGATTT 57.415 30.769 5.31 0.00 0.00 2.17
2915 6236 2.203640 ACCAGACGCAGAGTGGGA 60.204 61.111 0.00 0.00 38.03 4.37
3004 7711 3.674528 CTCTTCAGGAGACAAAGAGCA 57.325 47.619 0.00 0.00 44.45 4.26
3005 7712 4.205065 CTCTTCAGGAGACAAAGAGCAT 57.795 45.455 0.00 0.00 44.45 3.79
3054 7762 5.247337 TCGGAGAGCTTAGAGATAGAGATCA 59.753 44.000 0.00 0.00 34.17 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.318576 CCACCACAACCCTCTGTTTC 58.681 55.000 0.00 0.00 34.00 2.78
1 2 0.755327 GCCACCACAACCCTCTGTTT 60.755 55.000 0.00 0.00 34.00 2.83
3 4 2.515901 GCCACCACAACCCTCTGT 59.484 61.111 0.00 0.00 0.00 3.41
4 5 2.469465 ATCGCCACCACAACCCTCTG 62.469 60.000 0.00 0.00 0.00 3.35
5 6 0.907704 TATCGCCACCACAACCCTCT 60.908 55.000 0.00 0.00 0.00 3.69
6 7 0.035820 TTATCGCCACCACAACCCTC 60.036 55.000 0.00 0.00 0.00 4.30
8 9 2.335316 TATTATCGCCACCACAACCC 57.665 50.000 0.00 0.00 0.00 4.11
9 10 4.134563 AGAATATTATCGCCACCACAACC 58.865 43.478 0.00 0.00 0.00 3.77
10 11 5.751243 AAGAATATTATCGCCACCACAAC 57.249 39.130 0.00 0.00 0.00 3.32
11 12 5.007234 CGAAAGAATATTATCGCCACCACAA 59.993 40.000 5.25 0.00 0.00 3.33
12 13 4.509970 CGAAAGAATATTATCGCCACCACA 59.490 41.667 5.25 0.00 0.00 4.17
13 14 4.084013 CCGAAAGAATATTATCGCCACCAC 60.084 45.833 10.62 0.00 34.13 4.16
14 15 4.062293 CCGAAAGAATATTATCGCCACCA 58.938 43.478 10.62 0.00 34.13 4.17
15 16 3.435671 CCCGAAAGAATATTATCGCCACC 59.564 47.826 10.62 0.00 34.13 4.61
16 17 4.062991 ACCCGAAAGAATATTATCGCCAC 58.937 43.478 10.62 0.00 34.13 5.01
17 18 4.345859 ACCCGAAAGAATATTATCGCCA 57.654 40.909 10.62 0.00 34.13 5.69
18 19 4.753107 TGAACCCGAAAGAATATTATCGCC 59.247 41.667 10.62 3.39 34.13 5.54
19 20 5.465724 AGTGAACCCGAAAGAATATTATCGC 59.534 40.000 10.62 0.00 34.13 4.58
20 21 7.478520 AAGTGAACCCGAAAGAATATTATCG 57.521 36.000 9.59 9.59 35.19 2.92
21 22 9.503427 CAAAAGTGAACCCGAAAGAATATTATC 57.497 33.333 0.00 0.00 0.00 1.75
22 23 9.238368 TCAAAAGTGAACCCGAAAGAATATTAT 57.762 29.630 0.00 0.00 0.00 1.28
23 24 8.624367 TCAAAAGTGAACCCGAAAGAATATTA 57.376 30.769 0.00 0.00 0.00 0.98
24 25 7.309194 CCTCAAAAGTGAACCCGAAAGAATATT 60.309 37.037 0.00 0.00 31.88 1.28
25 26 6.151144 CCTCAAAAGTGAACCCGAAAGAATAT 59.849 38.462 0.00 0.00 31.88 1.28
26 27 5.472137 CCTCAAAAGTGAACCCGAAAGAATA 59.528 40.000 0.00 0.00 31.88 1.75
27 28 4.278419 CCTCAAAAGTGAACCCGAAAGAAT 59.722 41.667 0.00 0.00 31.88 2.40
28 29 3.630312 CCTCAAAAGTGAACCCGAAAGAA 59.370 43.478 0.00 0.00 31.88 2.52
29 30 3.211045 CCTCAAAAGTGAACCCGAAAGA 58.789 45.455 0.00 0.00 31.88 2.52
30 31 2.293399 CCCTCAAAAGTGAACCCGAAAG 59.707 50.000 0.00 0.00 31.88 2.62
31 32 2.303175 CCCTCAAAAGTGAACCCGAAA 58.697 47.619 0.00 0.00 31.88 3.46
32 33 1.213430 ACCCTCAAAAGTGAACCCGAA 59.787 47.619 0.00 0.00 31.88 4.30
33 34 0.841289 ACCCTCAAAAGTGAACCCGA 59.159 50.000 0.00 0.00 31.88 5.14
34 35 1.607148 GAACCCTCAAAAGTGAACCCG 59.393 52.381 0.00 0.00 31.88 5.28
35 36 1.961394 GGAACCCTCAAAAGTGAACCC 59.039 52.381 0.00 0.00 31.88 4.11
36 37 1.607148 CGGAACCCTCAAAAGTGAACC 59.393 52.381 0.00 0.00 31.88 3.62
37 38 1.607148 CCGGAACCCTCAAAAGTGAAC 59.393 52.381 0.00 0.00 31.88 3.18
38 39 1.477923 CCCGGAACCCTCAAAAGTGAA 60.478 52.381 0.73 0.00 31.88 3.18
39 40 0.109723 CCCGGAACCCTCAAAAGTGA 59.890 55.000 0.73 0.00 0.00 3.41
40 41 0.109723 TCCCGGAACCCTCAAAAGTG 59.890 55.000 0.73 0.00 0.00 3.16
41 42 0.848053 TTCCCGGAACCCTCAAAAGT 59.152 50.000 0.73 0.00 0.00 2.66
42 43 2.215942 ATTCCCGGAACCCTCAAAAG 57.784 50.000 0.73 0.00 0.00 2.27
43 44 2.687003 AATTCCCGGAACCCTCAAAA 57.313 45.000 0.73 0.00 0.00 2.44
44 45 4.141344 CCTATAATTCCCGGAACCCTCAAA 60.141 45.833 0.73 0.00 0.00 2.69
45 46 3.393278 CCTATAATTCCCGGAACCCTCAA 59.607 47.826 0.73 0.00 0.00 3.02
46 47 2.976882 CCTATAATTCCCGGAACCCTCA 59.023 50.000 0.73 0.00 0.00 3.86
47 48 3.245441 TCCTATAATTCCCGGAACCCTC 58.755 50.000 0.73 0.00 0.00 4.30
48 49 3.355857 TCCTATAATTCCCGGAACCCT 57.644 47.619 0.73 0.00 0.00 4.34
49 50 4.652679 AATCCTATAATTCCCGGAACCC 57.347 45.455 0.73 0.00 0.00 4.11
50 51 8.546322 ACTATAAATCCTATAATTCCCGGAACC 58.454 37.037 0.73 0.00 0.00 3.62
51 52 9.955102 AACTATAAATCCTATAATTCCCGGAAC 57.045 33.333 0.73 0.00 0.00 3.62
52 53 9.953565 CAACTATAAATCCTATAATTCCCGGAA 57.046 33.333 0.73 1.31 0.00 4.30
53 54 8.545472 CCAACTATAAATCCTATAATTCCCGGA 58.455 37.037 0.73 0.00 0.00 5.14
54 55 8.545472 TCCAACTATAAATCCTATAATTCCCGG 58.455 37.037 0.00 0.00 0.00 5.73
55 56 9.953565 TTCCAACTATAAATCCTATAATTCCCG 57.046 33.333 0.00 0.00 0.00 5.14
615 628 1.592223 GTCGCAAGCTAGAGGTGGT 59.408 57.895 0.00 0.00 37.18 4.16
629 642 0.600255 ATAGCTAATGGCACCGTCGC 60.600 55.000 0.00 0.00 44.79 5.19
635 648 6.260936 AGAATACACAACATAGCTAATGGCAC 59.739 38.462 0.00 0.00 44.79 5.01
681 694 5.766174 GGTGGTTAAGGTGTTTGTATCAGAA 59.234 40.000 0.00 0.00 0.00 3.02
696 709 5.622770 AATTTTCTACTGCGGTGGTTAAG 57.377 39.130 8.92 0.00 0.00 1.85
699 712 3.886505 TCAAATTTTCTACTGCGGTGGTT 59.113 39.130 8.92 0.00 0.00 3.67
736 749 3.373565 CCAAACAGCCCCCGCTTC 61.374 66.667 0.00 0.00 45.55 3.86
740 753 1.750399 CTGATCCAAACAGCCCCCG 60.750 63.158 0.00 0.00 0.00 5.73
789 802 0.110823 GCGCTAACACGTTGGTCAAG 60.111 55.000 0.00 0.00 34.88 3.02
804 817 0.679002 AGCTGATCCAAATGTGCGCT 60.679 50.000 9.73 0.00 0.00 5.92
845 858 0.616111 ACGGGGAGAGCAGATGAGTT 60.616 55.000 0.00 0.00 0.00 3.01
848 861 0.614697 TCAACGGGGAGAGCAGATGA 60.615 55.000 0.00 0.00 0.00 2.92
861 874 4.082787 ACATTTTGGCTACAGAATCAACGG 60.083 41.667 0.00 0.00 29.76 4.44
862 875 5.046910 ACATTTTGGCTACAGAATCAACG 57.953 39.130 0.00 0.00 29.76 4.10
973 986 6.811665 CGAATACCTTCTTATGTCTGAACACA 59.188 38.462 0.00 0.00 38.48 3.72
986 1001 9.765795 CTTAGATTTATGGACGAATACCTTCTT 57.234 33.333 0.00 0.00 0.00 2.52
995 1010 7.062749 AGTATGCCTTAGATTTATGGACGAA 57.937 36.000 0.00 0.00 0.00 3.85
1003 1018 7.559533 TGCCAATGAAAGTATGCCTTAGATTTA 59.440 33.333 0.00 0.00 31.48 1.40
1027 1043 3.665675 ATCTCCAACGCGGACCTGC 62.666 63.158 12.47 0.00 39.64 4.85
1231 1420 0.318762 GACGAACCTTGCTCTGGTCT 59.681 55.000 0.00 0.00 36.69 3.85
1490 1679 2.269241 CCGAACCTGAAGGAGCCC 59.731 66.667 2.62 0.00 38.94 5.19
1933 2122 7.817440 TGGTTAGCTTAATAATCCACCCATAA 58.183 34.615 0.00 0.00 0.00 1.90
1945 2134 9.832445 CATCCTCTTTTACTGGTTAGCTTAATA 57.168 33.333 0.00 0.00 0.00 0.98
1974 2163 2.543777 TGGAAGAACGGGACAAAGAG 57.456 50.000 0.00 0.00 0.00 2.85
1989 2183 8.671987 TTTAGGATTCCCATTAACATTTGGAA 57.328 30.769 0.00 0.00 39.28 3.53
2004 2198 6.918022 CGAATTTACATGCCTTTTAGGATTCC 59.082 38.462 0.00 0.00 37.67 3.01
2005 2199 7.480810 ACGAATTTACATGCCTTTTAGGATTC 58.519 34.615 0.00 0.00 37.67 2.52
2006 2200 7.122055 TGACGAATTTACATGCCTTTTAGGATT 59.878 33.333 0.00 0.00 37.67 3.01
2007 2201 6.601613 TGACGAATTTACATGCCTTTTAGGAT 59.398 34.615 0.00 0.00 37.67 3.24
2008 2202 5.941058 TGACGAATTTACATGCCTTTTAGGA 59.059 36.000 0.00 0.00 37.67 2.94
2009 2203 6.189677 TGACGAATTTACATGCCTTTTAGG 57.810 37.500 0.00 0.00 38.80 2.69
2010 2204 7.754924 ACAATGACGAATTTACATGCCTTTTAG 59.245 33.333 0.00 0.00 0.00 1.85
2011 2205 7.598278 ACAATGACGAATTTACATGCCTTTTA 58.402 30.769 0.00 0.00 0.00 1.52
2012 2206 6.454795 ACAATGACGAATTTACATGCCTTTT 58.545 32.000 0.00 0.00 0.00 2.27
2013 2207 6.024552 ACAATGACGAATTTACATGCCTTT 57.975 33.333 0.00 0.00 0.00 3.11
2014 2208 5.643379 ACAATGACGAATTTACATGCCTT 57.357 34.783 0.00 0.00 0.00 4.35
2015 2209 5.643379 AACAATGACGAATTTACATGCCT 57.357 34.783 0.00 0.00 0.00 4.75
2016 2210 5.288472 GGAAACAATGACGAATTTACATGCC 59.712 40.000 0.00 0.00 0.00 4.40
2017 2211 5.861251 TGGAAACAATGACGAATTTACATGC 59.139 36.000 0.00 0.00 37.44 4.06
2035 2229 6.868339 CCTAAACCACTTGAATGAATGGAAAC 59.132 38.462 0.00 0.00 36.04 2.78
2036 2230 6.518200 GCCTAAACCACTTGAATGAATGGAAA 60.518 38.462 0.00 0.00 36.04 3.13
2037 2231 5.047377 GCCTAAACCACTTGAATGAATGGAA 60.047 40.000 0.00 0.00 36.04 3.53
2038 2232 4.462483 GCCTAAACCACTTGAATGAATGGA 59.538 41.667 0.00 0.00 36.04 3.41
2039 2233 4.463891 AGCCTAAACCACTTGAATGAATGG 59.536 41.667 0.00 0.00 38.26 3.16
2040 2234 5.183713 TCAGCCTAAACCACTTGAATGAATG 59.816 40.000 0.00 0.00 0.00 2.67
2041 2235 5.324409 TCAGCCTAAACCACTTGAATGAAT 58.676 37.500 0.00 0.00 0.00 2.57
2042 2236 4.724399 TCAGCCTAAACCACTTGAATGAA 58.276 39.130 0.00 0.00 0.00 2.57
2043 2237 4.365514 TCAGCCTAAACCACTTGAATGA 57.634 40.909 0.00 0.00 0.00 2.57
2044 2238 4.142315 CCATCAGCCTAAACCACTTGAATG 60.142 45.833 0.00 0.00 0.00 2.67
2045 2239 4.019174 CCATCAGCCTAAACCACTTGAAT 58.981 43.478 0.00 0.00 0.00 2.57
2046 2240 3.073798 TCCATCAGCCTAAACCACTTGAA 59.926 43.478 0.00 0.00 0.00 2.69
2047 2241 2.642311 TCCATCAGCCTAAACCACTTGA 59.358 45.455 0.00 0.00 0.00 3.02
2048 2242 3.012518 CTCCATCAGCCTAAACCACTTG 58.987 50.000 0.00 0.00 0.00 3.16
2049 2243 2.644798 ACTCCATCAGCCTAAACCACTT 59.355 45.455 0.00 0.00 0.00 3.16
2050 2244 2.269940 ACTCCATCAGCCTAAACCACT 58.730 47.619 0.00 0.00 0.00 4.00
2051 2245 2.789409 ACTCCATCAGCCTAAACCAC 57.211 50.000 0.00 0.00 0.00 4.16
2052 2246 3.199946 CCTTACTCCATCAGCCTAAACCA 59.800 47.826 0.00 0.00 0.00 3.67
2053 2247 3.433740 CCCTTACTCCATCAGCCTAAACC 60.434 52.174 0.00 0.00 0.00 3.27
2054 2248 3.809905 CCCTTACTCCATCAGCCTAAAC 58.190 50.000 0.00 0.00 0.00 2.01
2055 2249 2.172717 GCCCTTACTCCATCAGCCTAAA 59.827 50.000 0.00 0.00 0.00 1.85
2056 2250 1.768870 GCCCTTACTCCATCAGCCTAA 59.231 52.381 0.00 0.00 0.00 2.69
2057 2251 1.343985 TGCCCTTACTCCATCAGCCTA 60.344 52.381 0.00 0.00 0.00 3.93
2058 2252 0.621571 TGCCCTTACTCCATCAGCCT 60.622 55.000 0.00 0.00 0.00 4.58
2059 2253 0.475906 ATGCCCTTACTCCATCAGCC 59.524 55.000 0.00 0.00 0.00 4.85
2060 2254 1.133976 ACATGCCCTTACTCCATCAGC 60.134 52.381 0.00 0.00 0.00 4.26
2061 2255 4.630644 ATACATGCCCTTACTCCATCAG 57.369 45.455 0.00 0.00 0.00 2.90
2062 2256 5.387113 AAATACATGCCCTTACTCCATCA 57.613 39.130 0.00 0.00 0.00 3.07
2063 2257 6.715347 AAAAATACATGCCCTTACTCCATC 57.285 37.500 0.00 0.00 0.00 3.51
2083 2277 5.646360 CGGGCTGATACCTTTTCTCTAAAAA 59.354 40.000 0.00 0.00 34.26 1.94
2084 2278 5.046159 TCGGGCTGATACCTTTTCTCTAAAA 60.046 40.000 0.00 0.00 33.58 1.52
2085 2279 4.468510 TCGGGCTGATACCTTTTCTCTAAA 59.531 41.667 0.00 0.00 0.00 1.85
2086 2280 4.028131 TCGGGCTGATACCTTTTCTCTAA 58.972 43.478 0.00 0.00 0.00 2.10
2087 2281 3.383825 GTCGGGCTGATACCTTTTCTCTA 59.616 47.826 0.00 0.00 0.00 2.43
2088 2282 2.168728 GTCGGGCTGATACCTTTTCTCT 59.831 50.000 0.00 0.00 0.00 3.10
2089 2283 2.168728 AGTCGGGCTGATACCTTTTCTC 59.831 50.000 0.00 0.00 0.00 2.87
2090 2284 2.188817 AGTCGGGCTGATACCTTTTCT 58.811 47.619 0.00 0.00 0.00 2.52
2091 2285 2.693267 AGTCGGGCTGATACCTTTTC 57.307 50.000 0.00 0.00 0.00 2.29
2098 2292 7.389607 GGCTTTATTTATAAAGTCGGGCTGATA 59.610 37.037 18.51 0.00 46.78 2.15
2123 2317 3.267974 GCGAAACCTGCCTGAAGG 58.732 61.111 0.00 0.00 43.57 3.46
2134 2328 0.802607 TTGTTTGGTTGCGGCGAAAC 60.803 50.000 22.47 22.47 37.51 2.78
2135 2329 0.802607 GTTGTTTGGTTGCGGCGAAA 60.803 50.000 12.98 2.18 0.00 3.46
2139 2333 1.880796 GGTGTTGTTTGGTTGCGGC 60.881 57.895 0.00 0.00 0.00 6.53
2140 2334 0.108615 TTGGTGTTGTTTGGTTGCGG 60.109 50.000 0.00 0.00 0.00 5.69
2141 2335 1.391826 GTTTGGTGTTGTTTGGTTGCG 59.608 47.619 0.00 0.00 0.00 4.85
2142 2336 2.417719 TGTTTGGTGTTGTTTGGTTGC 58.582 42.857 0.00 0.00 0.00 4.17
2146 2340 5.424121 TTGTTTTGTTTGGTGTTGTTTGG 57.576 34.783 0.00 0.00 0.00 3.28
2152 2346 6.183360 GCCCATTATTTGTTTTGTTTGGTGTT 60.183 34.615 0.00 0.00 0.00 3.32
2156 2350 4.823989 TGGCCCATTATTTGTTTTGTTTGG 59.176 37.500 0.00 0.00 0.00 3.28
2158 2352 5.440610 TGTGGCCCATTATTTGTTTTGTTT 58.559 33.333 0.00 0.00 0.00 2.83
2162 2356 4.141390 TGGTTGTGGCCCATTATTTGTTTT 60.141 37.500 0.00 0.00 0.00 2.43
2165 2359 2.614259 TGGTTGTGGCCCATTATTTGT 58.386 42.857 0.00 0.00 0.00 2.83
2168 2362 3.966665 CCTTATGGTTGTGGCCCATTATT 59.033 43.478 0.00 0.00 42.63 1.40
2170 2364 2.583101 TCCTTATGGTTGTGGCCCATTA 59.417 45.455 0.00 0.00 42.63 1.90
2174 2368 2.159179 AATCCTTATGGTTGTGGCCC 57.841 50.000 0.00 0.00 34.23 5.80
2186 2380 9.475620 TGTATCTCTGTTCTGTCTTAATCCTTA 57.524 33.333 0.00 0.00 0.00 2.69
2192 2386 6.070824 TGCCATGTATCTCTGTTCTGTCTTAA 60.071 38.462 0.00 0.00 0.00 1.85
2201 2395 1.915489 TGGGTGCCATGTATCTCTGTT 59.085 47.619 0.00 0.00 0.00 3.16
2204 2398 1.135094 CCTGGGTGCCATGTATCTCT 58.865 55.000 0.00 0.00 30.82 3.10
2226 2420 1.852067 GACCTGCGTGCCATCGTTTT 61.852 55.000 0.00 0.00 0.00 2.43
2233 2428 2.089887 TAGTTTCGACCTGCGTGCCA 62.090 55.000 0.00 0.00 41.80 4.92
2244 2439 4.775780 TCCTTCCTTCCTTCATAGTTTCGA 59.224 41.667 0.00 0.00 0.00 3.71
2259 2454 0.036875 CTGGTTCGGCTTCCTTCCTT 59.963 55.000 0.00 0.00 0.00 3.36
2261 2456 1.377333 CCTGGTTCGGCTTCCTTCC 60.377 63.158 0.00 0.00 0.00 3.46
2276 2483 1.152881 GGCTTATGAGGGTGGCCTG 60.153 63.158 3.32 0.00 39.68 4.85
2285 2492 2.352960 GAGGTCGCTTTTGGCTTATGAG 59.647 50.000 0.00 0.00 39.13 2.90
2286 2493 2.356135 GAGGTCGCTTTTGGCTTATGA 58.644 47.619 0.00 0.00 39.13 2.15
2289 2496 0.322187 GGGAGGTCGCTTTTGGCTTA 60.322 55.000 0.00 0.00 39.13 3.09
2300 2508 0.733729 CTAGTTGTCGAGGGAGGTCG 59.266 60.000 0.00 0.00 41.51 4.79
2309 2517 1.972198 CCAGGTGGCTAGTTGTCGA 59.028 57.895 0.00 0.00 0.00 4.20
2310 2518 4.598257 CCAGGTGGCTAGTTGTCG 57.402 61.111 0.00 0.00 0.00 4.35
2324 2532 0.103755 TATCTCGCAGCAAGAGCCAG 59.896 55.000 0.00 0.00 43.56 4.85
2331 2539 3.876274 ACTTCTTCTATCTCGCAGCAA 57.124 42.857 0.00 0.00 0.00 3.91
2366 2574 0.539986 TTTCGACCTCCTATGTGCCC 59.460 55.000 0.00 0.00 0.00 5.36
2367 2575 1.941325 CTTTCGACCTCCTATGTGCC 58.059 55.000 0.00 0.00 0.00 5.01
2402 2611 6.406400 GCAGTAGTGGAGATCATTGACTAAGT 60.406 42.308 0.00 0.00 0.00 2.24
2504 5816 2.108362 GTTGGGCCCTATCGACGG 59.892 66.667 25.70 0.00 0.00 4.79
2509 5821 1.005450 TGAGGTTTGTTGGGCCCTATC 59.995 52.381 25.70 13.66 0.00 2.08
2527 5839 0.251121 TTTTGGCTCGGATTGGCTGA 60.251 50.000 0.00 0.00 0.00 4.26
2614 5933 2.050350 CGTGGCTTCGGGTCTCCTA 61.050 63.158 0.00 0.00 0.00 2.94
2638 5957 2.616842 CCAAGTTGGTCTGGTGTTGTAC 59.383 50.000 14.21 0.00 31.35 2.90
2678 5997 6.065976 ACTTGGAGGACACAAATCATATCA 57.934 37.500 0.00 0.00 0.00 2.15
2688 6007 1.816863 GCGGAGACTTGGAGGACACA 61.817 60.000 0.00 0.00 0.00 3.72
2915 6236 0.104304 GTGAGGACTCGGTTGTGTGT 59.896 55.000 0.00 0.00 0.00 3.72
3004 7711 1.073923 ACTGGGACTTGGCTTTTCGAT 59.926 47.619 0.00 0.00 0.00 3.59
3005 7712 0.472471 ACTGGGACTTGGCTTTTCGA 59.528 50.000 0.00 0.00 0.00 3.71
3054 7762 2.283388 TTACTGCTCGGACCCGGT 60.283 61.111 8.73 0.00 40.25 5.28


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

AutoCloner maintained by Alex Coulton.