Multiple sequence alignment - TraesCS3D01G474800

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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 TraesCS3D01G474800 chr3D 100.000 3038 0 0 1 3038 575724839 575727876 0.000000e+00 5611.0
1 TraesCS3D01G474800 chr3D 85.864 1047 98 35 1020 2039 577255859 577254836 0.000000e+00 1068.0
2 TraesCS3D01G474800 chr3D 95.706 326 14 0 1504 1829 577264186 577263861 2.680000e-145 525.0
3 TraesCS3D01G474800 chr3D 87.957 465 24 8 636 1099 577264842 577264409 1.250000e-143 520.0
4 TraesCS3D01G474800 chr3D 85.882 170 18 2 1938 2101 577263863 577263694 3.110000e-40 176.0
5 TraesCS3D01G474800 chr3D 82.258 124 14 7 2051 2172 577254316 577254199 1.930000e-17 100.0
6 TraesCS3D01G474800 chr3A 91.504 1636 64 33 636 2239 711217428 711219020 0.000000e+00 2182.0
7 TraesCS3D01G474800 chr3A 83.540 1531 135 62 662 2144 711202600 711204061 0.000000e+00 1323.0
8 TraesCS3D01G474800 chr3A 89.606 635 47 10 1494 2110 712571794 712571161 0.000000e+00 789.0
9 TraesCS3D01G474800 chr3A 78.571 322 40 15 217 525 711202107 711202412 5.170000e-43 185.0
10 TraesCS3D01G474800 chr3A 82.822 163 15 9 368 525 711216968 711217122 1.900000e-27 134.0
11 TraesCS3D01G474800 chr3A 83.594 128 15 4 246 371 711216819 711216942 6.880000e-22 115.0
12 TraesCS3D01G474800 chr3A 97.059 34 1 0 2227 2260 711219035 711219068 1.180000e-04 58.4
13 TraesCS3D01G474800 chr3B 92.000 1250 68 13 900 2135 766631126 766632357 0.000000e+00 1725.0
14 TraesCS3D01G474800 chr3B 85.232 1334 107 35 877 2179 769056501 769055227 0.000000e+00 1290.0
15 TraesCS3D01G474800 chr3B 85.224 1225 133 24 903 2088 768904998 768903783 0.000000e+00 1216.0
16 TraesCS3D01G474800 chr3B 85.729 967 101 18 903 1844 768929706 768928752 0.000000e+00 987.0
17 TraesCS3D01G474800 chr3B 93.088 217 10 2 628 840 766630903 766631118 2.270000e-81 313.0
18 TraesCS3D01G474800 chr3B 93.902 82 4 1 2181 2261 766632363 766632444 4.110000e-24 122.0
19 TraesCS3D01G474800 chr3B 87.500 72 6 2 778 849 769056575 769056507 2.510000e-11 80.5
20 TraesCS3D01G474800 chr3B 94.118 51 3 0 321 371 766630478 766630528 9.030000e-11 78.7
21 TraesCS3D01G474800 chr3B 93.023 43 3 0 568 610 766630802 766630844 2.530000e-06 63.9
22 TraesCS3D01G474800 chr5D 95.785 783 23 5 2264 3038 420787566 420788346 0.000000e+00 1254.0
23 TraesCS3D01G474800 chr5D 95.147 783 28 5 2264 3038 420779475 420780255 0.000000e+00 1227.0
24 TraesCS3D01G474800 chr5D 95.147 783 28 5 2264 3038 433154808 433154028 0.000000e+00 1227.0
25 TraesCS3D01G474800 chr2D 95.652 782 25 4 2264 3038 63144584 63145363 0.000000e+00 1247.0
26 TraesCS3D01G474800 chr6D 95.641 780 27 3 2264 3038 72670084 72670861 0.000000e+00 1245.0
27 TraesCS3D01G474800 chr6D 95.519 781 27 3 2264 3038 23691917 23691139 0.000000e+00 1242.0
28 TraesCS3D01G474800 chr6D 95.396 782 28 3 2264 3038 36948197 36948977 0.000000e+00 1238.0
29 TraesCS3D01G474800 chr6D 95.391 781 28 3 2264 3038 72678275 72679053 0.000000e+00 1236.0
30 TraesCS3D01G474800 chr6D 95.063 790 29 5 2257 3038 23723822 23723035 0.000000e+00 1234.0
31 TraesCS3D01G474800 chr6D 86.054 925 83 23 1193 2080 276456743 276455828 0.000000e+00 952.0
32 TraesCS3D01G474800 chr6B 84.861 1004 97 29 1175 2144 438386790 438385808 0.000000e+00 961.0
33 TraesCS3D01G474800 chr6A 86.489 903 79 19 1164 2032 399722103 399722996 0.000000e+00 952.0


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 TraesCS3D01G474800 chr3D 575724839 575727876 3037 False 5611.00 5611 100.000000 1 3038 1 chr3D.!!$F1 3037
1 TraesCS3D01G474800 chr3D 577254199 577255859 1660 True 584.00 1068 84.061000 1020 2172 2 chr3D.!!$R1 1152
2 TraesCS3D01G474800 chr3D 577263694 577264842 1148 True 407.00 525 89.848333 636 2101 3 chr3D.!!$R2 1465
3 TraesCS3D01G474800 chr3A 712571161 712571794 633 True 789.00 789 89.606000 1494 2110 1 chr3A.!!$R1 616
4 TraesCS3D01G474800 chr3A 711202107 711204061 1954 False 754.00 1323 81.055500 217 2144 2 chr3A.!!$F1 1927
5 TraesCS3D01G474800 chr3A 711216819 711219068 2249 False 622.35 2182 88.744750 246 2260 4 chr3A.!!$F2 2014
6 TraesCS3D01G474800 chr3B 768903783 768904998 1215 True 1216.00 1216 85.224000 903 2088 1 chr3B.!!$R1 1185
7 TraesCS3D01G474800 chr3B 768928752 768929706 954 True 987.00 987 85.729000 903 1844 1 chr3B.!!$R2 941
8 TraesCS3D01G474800 chr3B 769055227 769056575 1348 True 685.25 1290 86.366000 778 2179 2 chr3B.!!$R3 1401
9 TraesCS3D01G474800 chr3B 766630478 766632444 1966 False 460.52 1725 93.226200 321 2261 5 chr3B.!!$F1 1940
10 TraesCS3D01G474800 chr5D 420787566 420788346 780 False 1254.00 1254 95.785000 2264 3038 1 chr5D.!!$F2 774
11 TraesCS3D01G474800 chr5D 420779475 420780255 780 False 1227.00 1227 95.147000 2264 3038 1 chr5D.!!$F1 774
12 TraesCS3D01G474800 chr5D 433154028 433154808 780 True 1227.00 1227 95.147000 2264 3038 1 chr5D.!!$R1 774
13 TraesCS3D01G474800 chr2D 63144584 63145363 779 False 1247.00 1247 95.652000 2264 3038 1 chr2D.!!$F1 774
14 TraesCS3D01G474800 chr6D 72670084 72670861 777 False 1245.00 1245 95.641000 2264 3038 1 chr6D.!!$F2 774
15 TraesCS3D01G474800 chr6D 23691139 23691917 778 True 1242.00 1242 95.519000 2264 3038 1 chr6D.!!$R1 774
16 TraesCS3D01G474800 chr6D 36948197 36948977 780 False 1238.00 1238 95.396000 2264 3038 1 chr6D.!!$F1 774
17 TraesCS3D01G474800 chr6D 72678275 72679053 778 False 1236.00 1236 95.391000 2264 3038 1 chr6D.!!$F3 774
18 TraesCS3D01G474800 chr6D 23723035 23723822 787 True 1234.00 1234 95.063000 2257 3038 1 chr6D.!!$R2 781
19 TraesCS3D01G474800 chr6D 276455828 276456743 915 True 952.00 952 86.054000 1193 2080 1 chr6D.!!$R3 887
20 TraesCS3D01G474800 chr6B 438385808 438386790 982 True 961.00 961 84.861000 1175 2144 1 chr6B.!!$R1 969
21 TraesCS3D01G474800 chr6A 399722103 399722996 893 False 952.00 952 86.489000 1164 2032 1 chr6A.!!$F1 868

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
143 144 0.041663 GCAACGCACGAGCTTTTGTA 60.042 50.0 14.36 0.0 39.1 2.41 F
822 1110 0.106669 TCTCCACCCGTCGATCATCT 60.107 55.0 0.00 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1124 1476 0.321653 GGCAGGTGGAGGTGTAAGTG 60.322 60.0 0.0 0.0 0.0 3.16 R
2510 3618 0.251922 AGGTGCCTTAGGTCGTGGTA 60.252 55.0 0.0 0.0 0.0 3.25 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
23 24 3.034924 TGCAAAAAGGAGCATCGGT 57.965 47.368 0.00 0.00 35.51 4.69
24 25 2.192664 TGCAAAAAGGAGCATCGGTA 57.807 45.000 0.00 0.00 35.51 4.02
25 26 2.722094 TGCAAAAAGGAGCATCGGTAT 58.278 42.857 0.00 0.00 35.51 2.73
26 27 2.423185 TGCAAAAAGGAGCATCGGTATG 59.577 45.455 0.00 0.00 35.51 2.39
27 28 2.223572 GCAAAAAGGAGCATCGGTATGG 60.224 50.000 0.00 0.00 34.37 2.74
28 29 3.016736 CAAAAAGGAGCATCGGTATGGT 58.983 45.455 0.00 0.00 46.32 3.55
29 30 2.332063 AAAGGAGCATCGGTATGGTG 57.668 50.000 0.00 0.00 43.75 4.17
30 31 1.204146 AAGGAGCATCGGTATGGTGT 58.796 50.000 0.00 0.00 43.75 4.16
31 32 0.465705 AGGAGCATCGGTATGGTGTG 59.534 55.000 0.00 0.00 43.75 3.82
32 33 0.532862 GGAGCATCGGTATGGTGTGG 60.533 60.000 0.00 0.00 43.75 4.17
33 34 0.464036 GAGCATCGGTATGGTGTGGA 59.536 55.000 0.00 0.00 43.75 4.02
34 35 1.070758 GAGCATCGGTATGGTGTGGAT 59.929 52.381 0.00 0.00 43.75 3.41
35 36 1.202687 AGCATCGGTATGGTGTGGATG 60.203 52.381 0.00 0.00 42.17 3.51
36 37 1.202639 GCATCGGTATGGTGTGGATGA 60.203 52.381 3.70 0.00 37.31 2.92
37 38 2.744823 GCATCGGTATGGTGTGGATGAA 60.745 50.000 3.70 0.00 37.31 2.57
38 39 2.684001 TCGGTATGGTGTGGATGAAC 57.316 50.000 0.00 0.00 0.00 3.18
39 40 1.134936 TCGGTATGGTGTGGATGAACG 60.135 52.381 0.00 0.00 0.00 3.95
40 41 1.134936 CGGTATGGTGTGGATGAACGA 60.135 52.381 0.00 0.00 0.00 3.85
41 42 2.277084 GGTATGGTGTGGATGAACGAC 58.723 52.381 0.00 0.00 0.00 4.34
42 43 2.093658 GGTATGGTGTGGATGAACGACT 60.094 50.000 0.00 0.00 0.00 4.18
43 44 3.131577 GGTATGGTGTGGATGAACGACTA 59.868 47.826 0.00 0.00 0.00 2.59
44 45 4.202223 GGTATGGTGTGGATGAACGACTAT 60.202 45.833 0.00 0.00 0.00 2.12
45 46 3.245518 TGGTGTGGATGAACGACTATG 57.754 47.619 0.00 0.00 0.00 2.23
46 47 2.829120 TGGTGTGGATGAACGACTATGA 59.171 45.455 0.00 0.00 0.00 2.15
47 48 3.259625 TGGTGTGGATGAACGACTATGAA 59.740 43.478 0.00 0.00 0.00 2.57
48 49 4.250464 GGTGTGGATGAACGACTATGAAA 58.750 43.478 0.00 0.00 0.00 2.69
49 50 4.693566 GGTGTGGATGAACGACTATGAAAA 59.306 41.667 0.00 0.00 0.00 2.29
50 51 5.354234 GGTGTGGATGAACGACTATGAAAAT 59.646 40.000 0.00 0.00 0.00 1.82
51 52 6.250819 GTGTGGATGAACGACTATGAAAATG 58.749 40.000 0.00 0.00 0.00 2.32
52 53 5.937540 TGTGGATGAACGACTATGAAAATGT 59.062 36.000 0.00 0.00 0.00 2.71
53 54 6.092122 TGTGGATGAACGACTATGAAAATGTC 59.908 38.462 0.00 0.00 0.00 3.06
54 55 6.092122 GTGGATGAACGACTATGAAAATGTCA 59.908 38.462 0.00 0.00 41.67 3.58
55 56 6.652900 TGGATGAACGACTATGAAAATGTCAA 59.347 34.615 0.00 0.00 40.50 3.18
56 57 7.336679 TGGATGAACGACTATGAAAATGTCAAT 59.663 33.333 0.00 0.00 40.50 2.57
57 58 8.826710 GGATGAACGACTATGAAAATGTCAATA 58.173 33.333 0.00 0.00 40.50 1.90
58 59 9.855361 GATGAACGACTATGAAAATGTCAATAG 57.145 33.333 0.00 0.00 40.50 1.73
59 60 7.684670 TGAACGACTATGAAAATGTCAATAGC 58.315 34.615 0.00 0.00 40.50 2.97
60 61 6.274001 ACGACTATGAAAATGTCAATAGCG 57.726 37.500 0.00 0.00 40.50 4.26
61 62 6.040247 ACGACTATGAAAATGTCAATAGCGA 58.960 36.000 0.00 0.00 40.50 4.93
62 63 6.533723 ACGACTATGAAAATGTCAATAGCGAA 59.466 34.615 0.00 0.00 40.50 4.70
63 64 7.059817 CGACTATGAAAATGTCAATAGCGAAG 58.940 38.462 0.00 0.00 40.50 3.79
64 65 7.251704 ACTATGAAAATGTCAATAGCGAAGG 57.748 36.000 0.00 0.00 40.50 3.46
65 66 7.047891 ACTATGAAAATGTCAATAGCGAAGGA 58.952 34.615 0.00 0.00 40.50 3.36
66 67 5.801350 TGAAAATGTCAATAGCGAAGGAG 57.199 39.130 0.00 0.00 31.51 3.69
67 68 5.487433 TGAAAATGTCAATAGCGAAGGAGA 58.513 37.500 0.00 0.00 31.51 3.71
68 69 5.351465 TGAAAATGTCAATAGCGAAGGAGAC 59.649 40.000 0.00 0.00 31.51 3.36
69 70 2.561733 TGTCAATAGCGAAGGAGACG 57.438 50.000 0.00 0.00 0.00 4.18
76 77 2.578178 CGAAGGAGACGCGCAGAG 60.578 66.667 5.73 0.00 0.00 3.35
85 86 2.986311 ACGCGCAGAGTCTTTTTCA 58.014 47.368 5.73 0.00 33.29 2.69
86 87 1.295792 ACGCGCAGAGTCTTTTTCAA 58.704 45.000 5.73 0.00 33.29 2.69
87 88 1.003866 ACGCGCAGAGTCTTTTTCAAC 60.004 47.619 5.73 0.00 33.29 3.18
88 89 1.663494 GCGCAGAGTCTTTTTCAACG 58.337 50.000 0.30 0.00 0.00 4.10
89 90 1.260561 GCGCAGAGTCTTTTTCAACGA 59.739 47.619 0.30 0.00 0.00 3.85
90 91 2.096218 GCGCAGAGTCTTTTTCAACGAT 60.096 45.455 0.30 0.00 0.00 3.73
91 92 3.726436 CGCAGAGTCTTTTTCAACGATC 58.274 45.455 0.00 0.00 0.00 3.69
92 93 3.184379 CGCAGAGTCTTTTTCAACGATCA 59.816 43.478 0.00 0.00 0.00 2.92
93 94 4.665142 CGCAGAGTCTTTTTCAACGATCAG 60.665 45.833 0.00 0.00 0.00 2.90
94 95 4.706527 CAGAGTCTTTTTCAACGATCAGC 58.293 43.478 0.00 0.00 0.00 4.26
95 96 4.212004 CAGAGTCTTTTTCAACGATCAGCA 59.788 41.667 0.00 0.00 0.00 4.41
96 97 4.816385 AGAGTCTTTTTCAACGATCAGCAA 59.184 37.500 0.00 0.00 0.00 3.91
97 98 5.471456 AGAGTCTTTTTCAACGATCAGCAAT 59.529 36.000 0.00 0.00 0.00 3.56
98 99 5.693814 AGTCTTTTTCAACGATCAGCAATC 58.306 37.500 0.00 0.00 0.00 2.67
99 100 4.853743 GTCTTTTTCAACGATCAGCAATCC 59.146 41.667 0.00 0.00 0.00 3.01
100 101 3.469899 TTTTCAACGATCAGCAATCCG 57.530 42.857 0.00 0.00 0.00 4.18
101 102 2.378445 TTCAACGATCAGCAATCCGA 57.622 45.000 0.00 0.00 0.00 4.55
102 103 2.378445 TCAACGATCAGCAATCCGAA 57.622 45.000 0.00 0.00 0.00 4.30
103 104 2.270923 TCAACGATCAGCAATCCGAAG 58.729 47.619 0.00 0.00 0.00 3.79
104 105 1.009829 AACGATCAGCAATCCGAAGC 58.990 50.000 0.00 0.00 0.00 3.86
105 106 0.108186 ACGATCAGCAATCCGAAGCA 60.108 50.000 0.00 0.00 0.00 3.91
106 107 0.302890 CGATCAGCAATCCGAAGCAC 59.697 55.000 0.00 0.00 0.00 4.40
107 108 1.661341 GATCAGCAATCCGAAGCACT 58.339 50.000 0.00 0.00 0.00 4.40
108 109 1.596727 GATCAGCAATCCGAAGCACTC 59.403 52.381 0.00 0.00 0.00 3.51
109 110 0.391661 TCAGCAATCCGAAGCACTCC 60.392 55.000 0.00 0.00 0.00 3.85
110 111 1.448540 AGCAATCCGAAGCACTCCG 60.449 57.895 0.00 0.00 0.00 4.63
111 112 2.464459 GCAATCCGAAGCACTCCGG 61.464 63.158 0.00 0.00 46.57 5.14
116 117 4.719997 CGAAGCACTCCGGATCTC 57.280 61.111 3.57 0.00 0.00 2.75
117 118 1.066587 CGAAGCACTCCGGATCTCC 59.933 63.158 3.57 0.00 0.00 3.71
118 119 1.667154 CGAAGCACTCCGGATCTCCA 61.667 60.000 3.57 0.00 35.14 3.86
119 120 0.755686 GAAGCACTCCGGATCTCCAT 59.244 55.000 3.57 0.00 35.14 3.41
120 121 0.755686 AAGCACTCCGGATCTCCATC 59.244 55.000 3.57 0.00 35.14 3.51
121 122 1.118356 AGCACTCCGGATCTCCATCC 61.118 60.000 3.57 0.00 45.04 3.51
122 123 2.053618 CACTCCGGATCTCCATCCC 58.946 63.158 3.57 0.00 45.67 3.85
123 124 0.470833 CACTCCGGATCTCCATCCCT 60.471 60.000 3.57 0.00 45.67 4.20
124 125 0.470833 ACTCCGGATCTCCATCCCTG 60.471 60.000 3.57 0.00 45.67 4.45
125 126 1.825281 CTCCGGATCTCCATCCCTGC 61.825 65.000 3.57 0.00 45.67 4.85
126 127 2.142761 CCGGATCTCCATCCCTGCA 61.143 63.158 0.00 0.00 45.67 4.41
127 128 1.699054 CCGGATCTCCATCCCTGCAA 61.699 60.000 0.00 0.00 45.67 4.08
128 129 0.533755 CGGATCTCCATCCCTGCAAC 60.534 60.000 0.00 0.00 45.67 4.17
129 130 0.533755 GGATCTCCATCCCTGCAACG 60.534 60.000 0.00 0.00 42.91 4.10
130 131 1.153086 ATCTCCATCCCTGCAACGC 60.153 57.895 0.00 0.00 0.00 4.84
131 132 1.913951 ATCTCCATCCCTGCAACGCA 61.914 55.000 0.00 0.00 36.92 5.24
132 133 2.359850 TCCATCCCTGCAACGCAC 60.360 61.111 0.00 0.00 33.79 5.34
133 134 3.803082 CCATCCCTGCAACGCACG 61.803 66.667 0.00 0.00 33.79 5.34
134 135 2.741985 CATCCCTGCAACGCACGA 60.742 61.111 0.00 0.00 33.79 4.35
135 136 2.434884 ATCCCTGCAACGCACGAG 60.435 61.111 0.00 0.00 33.79 4.18
138 139 3.349006 CCTGCAACGCACGAGCTT 61.349 61.111 2.73 0.00 39.10 3.74
139 140 2.633657 CTGCAACGCACGAGCTTT 59.366 55.556 2.73 0.00 39.10 3.51
140 141 1.009675 CTGCAACGCACGAGCTTTT 60.010 52.632 2.73 0.00 39.10 2.27
141 142 1.264141 CTGCAACGCACGAGCTTTTG 61.264 55.000 2.73 7.39 39.10 2.44
142 143 1.298339 GCAACGCACGAGCTTTTGT 60.298 52.632 14.36 0.00 39.10 2.83
143 144 0.041663 GCAACGCACGAGCTTTTGTA 60.042 50.000 14.36 0.00 39.10 2.41
144 145 1.937359 CAACGCACGAGCTTTTGTAG 58.063 50.000 2.73 0.00 39.10 2.74
152 153 3.288484 GCTTTTGTAGCCCCCTGC 58.712 61.111 0.00 0.00 44.48 4.85
153 154 1.606313 GCTTTTGTAGCCCCCTGCA 60.606 57.895 0.00 0.00 44.48 4.41
154 155 0.972471 GCTTTTGTAGCCCCCTGCAT 60.972 55.000 0.00 0.00 44.48 3.96
155 156 1.106285 CTTTTGTAGCCCCCTGCATC 58.894 55.000 0.00 0.00 44.83 3.91
156 157 0.324275 TTTTGTAGCCCCCTGCATCC 60.324 55.000 0.00 0.00 44.83 3.51
157 158 1.505151 TTTGTAGCCCCCTGCATCCA 61.505 55.000 0.00 0.00 44.83 3.41
158 159 1.925285 TTGTAGCCCCCTGCATCCAG 61.925 60.000 0.00 0.00 44.83 3.86
159 160 3.492353 TAGCCCCCTGCATCCAGC 61.492 66.667 0.00 0.00 44.83 4.85
172 173 2.225963 GCATCCAGCATGACTTATCTGC 59.774 50.000 0.00 0.00 44.79 4.26
173 174 3.741249 CATCCAGCATGACTTATCTGCT 58.259 45.455 0.00 0.00 46.72 4.24
178 179 3.139850 AGCATGACTTATCTGCTGATGC 58.860 45.455 15.71 10.13 44.21 3.91
179 180 3.139850 GCATGACTTATCTGCTGATGCT 58.860 45.455 15.71 0.00 40.48 3.79
180 181 3.186817 GCATGACTTATCTGCTGATGCTC 59.813 47.826 15.71 7.86 40.48 4.26
181 182 4.377897 CATGACTTATCTGCTGATGCTCA 58.622 43.478 15.71 12.45 40.48 4.26
182 183 4.476628 TGACTTATCTGCTGATGCTCAA 57.523 40.909 15.71 1.87 40.48 3.02
183 184 4.439968 TGACTTATCTGCTGATGCTCAAG 58.560 43.478 15.71 12.78 40.48 3.02
184 185 4.081254 TGACTTATCTGCTGATGCTCAAGT 60.081 41.667 15.71 15.52 40.48 3.16
185 186 5.127682 TGACTTATCTGCTGATGCTCAAGTA 59.872 40.000 15.71 4.87 40.48 2.24
186 187 5.599732 ACTTATCTGCTGATGCTCAAGTAG 58.400 41.667 15.71 3.78 40.48 2.57
187 188 5.128499 ACTTATCTGCTGATGCTCAAGTAGT 59.872 40.000 15.71 4.28 40.48 2.73
188 189 6.322456 ACTTATCTGCTGATGCTCAAGTAGTA 59.678 38.462 15.71 0.00 40.48 1.82
189 190 5.804944 ATCTGCTGATGCTCAAGTAGTAT 57.195 39.130 5.15 0.00 40.48 2.12
190 191 6.907853 ATCTGCTGATGCTCAAGTAGTATA 57.092 37.500 5.15 0.00 40.48 1.47
191 192 6.907853 TCTGCTGATGCTCAAGTAGTATAT 57.092 37.500 0.00 0.00 40.48 0.86
192 193 6.685657 TCTGCTGATGCTCAAGTAGTATATG 58.314 40.000 0.00 0.00 40.48 1.78
193 194 6.266330 TCTGCTGATGCTCAAGTAGTATATGT 59.734 38.462 0.00 0.00 40.48 2.29
194 195 6.820335 TGCTGATGCTCAAGTAGTATATGTT 58.180 36.000 0.00 0.00 40.48 2.71
195 196 7.275183 TGCTGATGCTCAAGTAGTATATGTTT 58.725 34.615 0.00 0.00 40.48 2.83
196 197 7.770433 TGCTGATGCTCAAGTAGTATATGTTTT 59.230 33.333 0.00 0.00 40.48 2.43
197 198 8.616076 GCTGATGCTCAAGTAGTATATGTTTTT 58.384 33.333 0.00 0.00 36.03 1.94
220 221 5.667539 TGGTTGAACATTTTCCACTTTCA 57.332 34.783 0.00 0.00 29.87 2.69
221 222 6.042638 TGGTTGAACATTTTCCACTTTCAA 57.957 33.333 0.00 0.00 34.58 2.69
228 229 8.087750 TGAACATTTTCCACTTTCAATATGGAC 58.912 33.333 0.00 0.00 42.26 4.02
232 233 9.439500 CATTTTCCACTTTCAATATGGACAAAT 57.561 29.630 0.00 0.00 42.26 2.32
234 235 5.964758 TCCACTTTCAATATGGACAAATGC 58.035 37.500 0.00 0.00 37.60 3.56
242 243 7.092137 TCAATATGGACAAATGCTCTGAAAG 57.908 36.000 0.00 0.00 0.00 2.62
248 249 4.321527 GGACAAATGCTCTGAAAGGGAAAG 60.322 45.833 0.00 0.00 35.24 2.62
250 251 4.895297 ACAAATGCTCTGAAAGGGAAAGAA 59.105 37.500 0.00 0.00 35.24 2.52
251 252 5.363580 ACAAATGCTCTGAAAGGGAAAGAAA 59.636 36.000 0.00 0.00 35.24 2.52
252 253 6.127083 ACAAATGCTCTGAAAGGGAAAGAAAA 60.127 34.615 0.00 0.00 35.24 2.29
253 254 6.676990 AATGCTCTGAAAGGGAAAGAAAAT 57.323 33.333 0.00 0.00 35.24 1.82
257 258 6.155136 GCTCTGAAAGGGAAAGAAAATCTTG 58.845 40.000 0.00 0.00 35.24 3.02
262 263 5.876651 AAGGGAAAGAAAATCTTGCTGTT 57.123 34.783 0.00 0.00 36.71 3.16
271 272 1.800805 ATCTTGCTGTTCCGTGTGAG 58.199 50.000 0.00 0.00 0.00 3.51
272 273 0.464036 TCTTGCTGTTCCGTGTGAGT 59.536 50.000 0.00 0.00 0.00 3.41
289 291 7.340699 CGTGTGAGTTTTAGCTAATCATGATC 58.659 38.462 9.06 0.00 0.00 2.92
316 318 2.831685 ACCGTTCTACTGATTGCACA 57.168 45.000 0.00 0.00 0.00 4.57
317 319 2.413837 ACCGTTCTACTGATTGCACAC 58.586 47.619 0.00 0.00 0.00 3.82
318 320 1.390123 CCGTTCTACTGATTGCACACG 59.610 52.381 0.00 0.00 0.00 4.49
319 321 2.058798 CGTTCTACTGATTGCACACGT 58.941 47.619 0.00 0.00 0.00 4.49
372 403 2.746362 AGAGAAGTGTACTACCGTTCCG 59.254 50.000 0.00 0.00 0.00 4.30
428 475 6.153851 TCGTTATTATGTCACCGGATGGATAT 59.846 38.462 9.46 9.13 39.21 1.63
429 476 7.339976 TCGTTATTATGTCACCGGATGGATATA 59.660 37.037 9.46 8.10 39.21 0.86
433 480 8.783660 ATTATGTCACCGGATGGATATATACT 57.216 34.615 9.46 0.00 39.21 2.12
434 481 6.716934 ATGTCACCGGATGGATATATACTC 57.283 41.667 9.46 0.00 39.21 2.59
435 482 4.638865 TGTCACCGGATGGATATATACTCG 59.361 45.833 9.46 0.00 39.21 4.18
436 483 4.036498 GTCACCGGATGGATATATACTCGG 59.964 50.000 9.46 17.40 41.65 4.63
437 484 3.318275 CACCGGATGGATATATACTCGGG 59.682 52.174 9.46 17.47 40.40 5.14
438 485 2.296471 CCGGATGGATATATACTCGGGC 59.704 54.545 0.00 0.00 37.49 6.13
439 486 3.223435 CGGATGGATATATACTCGGGCT 58.777 50.000 0.00 0.00 0.00 5.19
440 487 3.637229 CGGATGGATATATACTCGGGCTT 59.363 47.826 0.00 0.00 0.00 4.35
441 488 4.261656 CGGATGGATATATACTCGGGCTTC 60.262 50.000 0.00 0.00 0.00 3.86
443 490 3.021695 TGGATATATACTCGGGCTTCGG 58.978 50.000 0.00 0.00 39.77 4.30
444 491 3.022406 GGATATATACTCGGGCTTCGGT 58.978 50.000 0.00 1.35 39.77 4.69
445 492 3.446516 GGATATATACTCGGGCTTCGGTT 59.553 47.826 0.00 0.00 39.77 4.44
446 493 4.081807 GGATATATACTCGGGCTTCGGTTT 60.082 45.833 0.00 0.00 39.77 3.27
447 494 2.877043 TATACTCGGGCTTCGGTTTC 57.123 50.000 0.00 0.00 39.77 2.78
448 495 0.899720 ATACTCGGGCTTCGGTTTCA 59.100 50.000 0.00 0.00 39.77 2.69
473 536 2.452813 CGTGTCACGGGTAGCATGC 61.453 63.158 17.75 10.51 38.08 4.06
528 619 0.389817 TCTGCTGATGCACACGGTAC 60.390 55.000 0.00 0.00 45.31 3.34
554 653 5.321102 TGGCAGTACATAAAGACACCATTT 58.679 37.500 0.00 0.00 0.00 2.32
556 655 5.393027 GGCAGTACATAAAGACACCATTTGG 60.393 44.000 0.00 0.00 42.17 3.28
574 677 5.838531 TTTGGTGGTTACAACTTACAAGG 57.161 39.130 0.00 0.00 34.61 3.61
720 1002 1.002990 CCACGGGGAAGGGTGTAAC 60.003 63.158 0.00 0.00 35.59 2.50
821 1109 0.744874 TTCTCCACCCGTCGATCATC 59.255 55.000 0.00 0.00 0.00 2.92
822 1110 0.106669 TCTCCACCCGTCGATCATCT 60.107 55.000 0.00 0.00 0.00 2.90
823 1111 0.312416 CTCCACCCGTCGATCATCTC 59.688 60.000 0.00 0.00 0.00 2.75
825 1113 1.391933 CCACCCGTCGATCATCTCCA 61.392 60.000 0.00 0.00 0.00 3.86
826 1114 0.676184 CACCCGTCGATCATCTCCAT 59.324 55.000 0.00 0.00 0.00 3.41
827 1115 1.069204 CACCCGTCGATCATCTCCATT 59.931 52.381 0.00 0.00 0.00 3.16
828 1116 1.341531 ACCCGTCGATCATCTCCATTC 59.658 52.381 0.00 0.00 0.00 2.67
831 1119 2.036475 CCGTCGATCATCTCCATTCCTT 59.964 50.000 0.00 0.00 0.00 3.36
837 1125 4.650734 GATCATCTCCATTCCTTCCTTCC 58.349 47.826 0.00 0.00 0.00 3.46
891 1187 2.248487 CACCAAGAAGACGCTACGTAC 58.752 52.381 0.00 0.00 41.37 3.67
906 1202 3.227810 ACGTACTGTAGCACTTAAGCC 57.772 47.619 1.29 0.00 34.23 4.35
995 1317 2.684843 CGAGACCAGCAAGCAAGCC 61.685 63.158 0.00 0.00 34.23 4.35
1035 1357 1.753463 CTCCTCCTCCTACGCCGTT 60.753 63.158 0.00 0.00 0.00 4.44
1048 1370 2.355363 CCGTTGCGGTCGTTCTCA 60.355 61.111 0.00 0.00 42.73 3.27
1116 1468 0.694444 CTGCCCCCACACCTATACCT 60.694 60.000 0.00 0.00 0.00 3.08
1117 1469 0.986019 TGCCCCCACACCTATACCTG 60.986 60.000 0.00 0.00 0.00 4.00
1118 1470 1.837090 CCCCCACACCTATACCTGC 59.163 63.158 0.00 0.00 0.00 4.85
1123 1475 0.986019 CACACCTATACCTGCCCCCA 60.986 60.000 0.00 0.00 0.00 4.96
1124 1476 0.986550 ACACCTATACCTGCCCCCAC 60.987 60.000 0.00 0.00 0.00 4.61
1125 1477 0.986019 CACCTATACCTGCCCCCACA 60.986 60.000 0.00 0.00 0.00 4.17
1427 1908 4.019983 CTGCTACCAGGTCCGAGT 57.980 61.111 0.00 0.00 35.38 4.18
1429 1910 0.965866 CTGCTACCAGGTCCGAGTCA 60.966 60.000 0.00 0.00 35.38 3.41
1431 1912 1.064240 TGCTACCAGGTCCGAGTCATA 60.064 52.381 0.00 0.00 0.00 2.15
1490 2006 0.109412 GACGGGTCTTTGATCGTCGT 60.109 55.000 0.00 0.00 41.60 4.34
2136 3216 3.468063 GTCCCTTGTGACGTCCCT 58.532 61.111 14.12 0.00 0.00 4.20
2137 3217 1.752833 GTCCCTTGTGACGTCCCTT 59.247 57.895 14.12 0.00 0.00 3.95
2138 3218 0.602905 GTCCCTTGTGACGTCCCTTG 60.603 60.000 14.12 0.93 0.00 3.61
2139 3219 1.052124 TCCCTTGTGACGTCCCTTGT 61.052 55.000 14.12 0.00 0.00 3.16
2140 3220 0.884704 CCCTTGTGACGTCCCTTGTG 60.885 60.000 14.12 0.00 0.00 3.33
2141 3221 1.507141 CCTTGTGACGTCCCTTGTGC 61.507 60.000 14.12 0.00 0.00 4.57
2142 3222 1.831389 CTTGTGACGTCCCTTGTGCG 61.831 60.000 14.12 0.00 0.00 5.34
2143 3223 2.279918 GTGACGTCCCTTGTGCGT 60.280 61.111 14.12 0.00 41.81 5.24
2179 3259 3.364062 GTCGTGTGCTAGCTATGTACTG 58.636 50.000 17.23 2.86 0.00 2.74
2180 3260 3.014623 TCGTGTGCTAGCTATGTACTGT 58.985 45.455 17.23 0.00 0.00 3.55
2181 3261 4.034858 GTCGTGTGCTAGCTATGTACTGTA 59.965 45.833 17.23 0.00 0.00 2.74
2182 3262 4.034858 TCGTGTGCTAGCTATGTACTGTAC 59.965 45.833 17.23 10.98 0.00 2.90
2204 3284 4.807304 ACGTGTTATCATTTATCGTGTCCC 59.193 41.667 0.00 0.00 0.00 4.46
2254 3361 6.378564 TGACAACTTTAGTTTGTGGGATTTGA 59.621 34.615 0.00 0.00 35.83 2.69
2261 3368 3.140144 AGTTTGTGGGATTTGAAGGAGGA 59.860 43.478 0.00 0.00 0.00 3.71
2262 3369 3.439857 TTGTGGGATTTGAAGGAGGAG 57.560 47.619 0.00 0.00 0.00 3.69
2268 3375 3.519913 GGGATTTGAAGGAGGAGTGTAGT 59.480 47.826 0.00 0.00 0.00 2.73
2283 3390 3.322254 AGTGTAGTGACCAGACCTCAAAG 59.678 47.826 0.00 0.00 0.00 2.77
2349 3456 2.799978 CTGACACGCACAGTACAAATGA 59.200 45.455 0.00 0.00 0.00 2.57
2510 3618 4.100963 TCCAACGGCATCACTGAGTATAAT 59.899 41.667 0.00 0.00 0.00 1.28
2537 3645 2.233186 GACCTAAGGCACCTTACTCGTT 59.767 50.000 5.00 0.00 37.47 3.85
2781 3901 3.285484 GTTGACAGCATCTCAATCCCAT 58.715 45.455 0.00 0.00 30.46 4.00
2845 3966 9.317936 GTAACATAGTGATGAGATTCACATGAA 57.682 33.333 0.00 0.00 46.81 2.57
2954 4075 1.639722 TTCCCCACAAGACTCGATCA 58.360 50.000 0.00 0.00 0.00 2.92
2969 4090 1.587547 GATCACCTCCGCTTGATTCC 58.412 55.000 0.00 0.00 32.43 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.192664 TACCGATGCTCCTTTTTGCA 57.807 45.000 0.00 0.00 43.67 4.08
6 7 2.223572 CCATACCGATGCTCCTTTTTGC 60.224 50.000 0.00 0.00 0.00 3.68
7 8 3.016736 ACCATACCGATGCTCCTTTTTG 58.983 45.455 0.00 0.00 0.00 2.44
10 11 1.559682 ACACCATACCGATGCTCCTTT 59.440 47.619 0.00 0.00 0.00 3.11
11 12 1.134401 CACACCATACCGATGCTCCTT 60.134 52.381 0.00 0.00 0.00 3.36
12 13 0.465705 CACACCATACCGATGCTCCT 59.534 55.000 0.00 0.00 0.00 3.69
13 14 0.532862 CCACACCATACCGATGCTCC 60.533 60.000 0.00 0.00 0.00 4.70
14 15 0.464036 TCCACACCATACCGATGCTC 59.536 55.000 0.00 0.00 0.00 4.26
15 16 1.131638 ATCCACACCATACCGATGCT 58.868 50.000 0.00 0.00 0.00 3.79
16 17 1.202639 TCATCCACACCATACCGATGC 60.203 52.381 0.00 0.00 32.23 3.91
17 18 2.872245 GTTCATCCACACCATACCGATG 59.128 50.000 0.00 0.00 33.22 3.84
18 19 2.483013 CGTTCATCCACACCATACCGAT 60.483 50.000 0.00 0.00 0.00 4.18
19 20 1.134936 CGTTCATCCACACCATACCGA 60.135 52.381 0.00 0.00 0.00 4.69
20 21 1.134936 TCGTTCATCCACACCATACCG 60.135 52.381 0.00 0.00 0.00 4.02
21 22 2.093658 AGTCGTTCATCCACACCATACC 60.094 50.000 0.00 0.00 0.00 2.73
22 23 3.247006 AGTCGTTCATCCACACCATAC 57.753 47.619 0.00 0.00 0.00 2.39
23 24 4.647399 TCATAGTCGTTCATCCACACCATA 59.353 41.667 0.00 0.00 0.00 2.74
24 25 3.450817 TCATAGTCGTTCATCCACACCAT 59.549 43.478 0.00 0.00 0.00 3.55
25 26 2.829120 TCATAGTCGTTCATCCACACCA 59.171 45.455 0.00 0.00 0.00 4.17
26 27 3.520290 TCATAGTCGTTCATCCACACC 57.480 47.619 0.00 0.00 0.00 4.16
27 28 5.856126 TTTTCATAGTCGTTCATCCACAC 57.144 39.130 0.00 0.00 0.00 3.82
28 29 5.937540 ACATTTTCATAGTCGTTCATCCACA 59.062 36.000 0.00 0.00 0.00 4.17
29 30 6.092122 TGACATTTTCATAGTCGTTCATCCAC 59.908 38.462 0.00 0.00 35.09 4.02
30 31 6.169800 TGACATTTTCATAGTCGTTCATCCA 58.830 36.000 0.00 0.00 35.09 3.41
31 32 6.662414 TGACATTTTCATAGTCGTTCATCC 57.338 37.500 0.00 0.00 35.09 3.51
32 33 9.855361 CTATTGACATTTTCATAGTCGTTCATC 57.145 33.333 0.00 0.00 35.09 2.92
33 34 8.338259 GCTATTGACATTTTCATAGTCGTTCAT 58.662 33.333 0.00 0.00 35.09 2.57
34 35 7.464045 CGCTATTGACATTTTCATAGTCGTTCA 60.464 37.037 0.00 0.00 35.09 3.18
35 36 6.841286 CGCTATTGACATTTTCATAGTCGTTC 59.159 38.462 0.00 0.00 35.09 3.95
36 37 6.533723 TCGCTATTGACATTTTCATAGTCGTT 59.466 34.615 0.00 0.00 35.09 3.85
37 38 6.040247 TCGCTATTGACATTTTCATAGTCGT 58.960 36.000 0.00 0.00 35.09 4.34
38 39 6.510746 TCGCTATTGACATTTTCATAGTCG 57.489 37.500 0.00 0.00 35.09 4.18
39 40 7.224753 TCCTTCGCTATTGACATTTTCATAGTC 59.775 37.037 0.00 0.00 32.84 2.59
40 41 7.047891 TCCTTCGCTATTGACATTTTCATAGT 58.952 34.615 0.00 0.00 32.84 2.12
41 42 7.439356 TCTCCTTCGCTATTGACATTTTCATAG 59.561 37.037 0.00 0.00 32.84 2.23
42 43 7.224753 GTCTCCTTCGCTATTGACATTTTCATA 59.775 37.037 0.00 0.00 32.84 2.15
43 44 6.037610 GTCTCCTTCGCTATTGACATTTTCAT 59.962 38.462 0.00 0.00 32.84 2.57
44 45 5.351465 GTCTCCTTCGCTATTGACATTTTCA 59.649 40.000 0.00 0.00 0.00 2.69
45 46 5.500931 CGTCTCCTTCGCTATTGACATTTTC 60.501 44.000 0.00 0.00 0.00 2.29
46 47 4.330074 CGTCTCCTTCGCTATTGACATTTT 59.670 41.667 0.00 0.00 0.00 1.82
47 48 3.865745 CGTCTCCTTCGCTATTGACATTT 59.134 43.478 0.00 0.00 0.00 2.32
48 49 3.448686 CGTCTCCTTCGCTATTGACATT 58.551 45.455 0.00 0.00 0.00 2.71
49 50 3.085443 CGTCTCCTTCGCTATTGACAT 57.915 47.619 0.00 0.00 0.00 3.06
50 51 2.561733 CGTCTCCTTCGCTATTGACA 57.438 50.000 0.00 0.00 0.00 3.58
59 60 2.578178 CTCTGCGCGTCTCCTTCG 60.578 66.667 8.43 0.00 0.00 3.79
60 61 1.515304 GACTCTGCGCGTCTCCTTC 60.515 63.158 8.43 0.00 0.00 3.46
61 62 1.528292 AAGACTCTGCGCGTCTCCTT 61.528 55.000 15.39 7.48 40.65 3.36
62 63 1.528292 AAAGACTCTGCGCGTCTCCT 61.528 55.000 15.39 5.13 40.65 3.69
63 64 0.667792 AAAAGACTCTGCGCGTCTCC 60.668 55.000 15.39 0.00 40.65 3.71
64 65 1.125202 GAAAAAGACTCTGCGCGTCTC 59.875 52.381 15.39 1.90 40.65 3.36
65 66 1.140816 GAAAAAGACTCTGCGCGTCT 58.859 50.000 8.43 10.21 43.20 4.18
66 67 0.859232 TGAAAAAGACTCTGCGCGTC 59.141 50.000 8.43 4.09 0.00 5.19
67 68 1.003866 GTTGAAAAAGACTCTGCGCGT 60.004 47.619 8.43 0.00 0.00 6.01
68 69 1.663494 GTTGAAAAAGACTCTGCGCG 58.337 50.000 0.00 0.00 0.00 6.86
69 70 1.260561 TCGTTGAAAAAGACTCTGCGC 59.739 47.619 0.00 0.00 26.63 6.09
70 71 3.184379 TGATCGTTGAAAAAGACTCTGCG 59.816 43.478 0.00 0.00 37.09 5.18
71 72 4.706527 CTGATCGTTGAAAAAGACTCTGC 58.293 43.478 0.00 0.00 37.09 4.26
72 73 4.212004 TGCTGATCGTTGAAAAAGACTCTG 59.788 41.667 0.00 0.00 37.09 3.35
73 74 4.380531 TGCTGATCGTTGAAAAAGACTCT 58.619 39.130 0.00 0.00 37.09 3.24
74 75 4.732285 TGCTGATCGTTGAAAAAGACTC 57.268 40.909 0.00 0.00 37.09 3.36
75 76 5.335191 GGATTGCTGATCGTTGAAAAAGACT 60.335 40.000 0.00 0.00 37.09 3.24
76 77 4.853743 GGATTGCTGATCGTTGAAAAAGAC 59.146 41.667 0.00 0.00 37.09 3.01
77 78 4.378356 CGGATTGCTGATCGTTGAAAAAGA 60.378 41.667 0.00 0.00 39.01 2.52
78 79 3.848019 CGGATTGCTGATCGTTGAAAAAG 59.152 43.478 0.00 0.00 35.49 2.27
79 80 3.500299 TCGGATTGCTGATCGTTGAAAAA 59.500 39.130 0.00 0.00 35.49 1.94
80 81 3.070748 TCGGATTGCTGATCGTTGAAAA 58.929 40.909 0.00 0.00 35.49 2.29
81 82 2.694213 TCGGATTGCTGATCGTTGAAA 58.306 42.857 0.00 0.00 35.49 2.69
82 83 2.378445 TCGGATTGCTGATCGTTGAA 57.622 45.000 0.00 0.00 35.49 2.69
83 84 2.270923 CTTCGGATTGCTGATCGTTGA 58.729 47.619 0.00 0.00 35.49 3.18
84 85 1.267732 GCTTCGGATTGCTGATCGTTG 60.268 52.381 0.00 0.00 35.49 4.10
85 86 1.009829 GCTTCGGATTGCTGATCGTT 58.990 50.000 0.00 0.00 35.49 3.85
86 87 0.108186 TGCTTCGGATTGCTGATCGT 60.108 50.000 5.38 0.00 35.49 3.73
87 88 0.302890 GTGCTTCGGATTGCTGATCG 59.697 55.000 5.38 0.00 35.49 3.69
88 89 1.596727 GAGTGCTTCGGATTGCTGATC 59.403 52.381 5.38 0.00 0.00 2.92
89 90 1.661341 GAGTGCTTCGGATTGCTGAT 58.339 50.000 5.38 0.00 0.00 2.90
90 91 0.391661 GGAGTGCTTCGGATTGCTGA 60.392 55.000 5.38 0.00 0.00 4.26
91 92 1.699656 CGGAGTGCTTCGGATTGCTG 61.700 60.000 5.38 0.00 0.00 4.41
92 93 1.448540 CGGAGTGCTTCGGATTGCT 60.449 57.895 5.38 0.00 0.00 3.91
93 94 3.093278 CGGAGTGCTTCGGATTGC 58.907 61.111 0.00 0.00 0.00 3.56
98 99 1.066587 GAGATCCGGAGTGCTTCGG 59.933 63.158 11.34 12.50 46.89 4.30
99 100 1.066587 GGAGATCCGGAGTGCTTCG 59.933 63.158 11.34 0.00 0.00 3.79
100 101 0.755686 ATGGAGATCCGGAGTGCTTC 59.244 55.000 11.34 6.70 39.43 3.86
101 102 0.755686 GATGGAGATCCGGAGTGCTT 59.244 55.000 11.34 3.09 39.43 3.91
102 103 1.118356 GGATGGAGATCCGGAGTGCT 61.118 60.000 11.34 7.18 39.04 4.40
103 104 1.369321 GGATGGAGATCCGGAGTGC 59.631 63.158 11.34 5.65 39.04 4.40
110 111 0.533755 CGTTGCAGGGATGGAGATCC 60.534 60.000 0.00 0.00 46.99 3.36
111 112 1.162800 GCGTTGCAGGGATGGAGATC 61.163 60.000 0.00 0.00 0.00 2.75
112 113 1.153086 GCGTTGCAGGGATGGAGAT 60.153 57.895 0.00 0.00 0.00 2.75
113 114 2.268920 GCGTTGCAGGGATGGAGA 59.731 61.111 0.00 0.00 0.00 3.71
114 115 2.046023 TGCGTTGCAGGGATGGAG 60.046 61.111 0.00 0.00 33.32 3.86
115 116 2.359850 GTGCGTTGCAGGGATGGA 60.360 61.111 0.00 0.00 40.08 3.41
116 117 3.803082 CGTGCGTTGCAGGGATGG 61.803 66.667 3.70 0.00 40.08 3.51
117 118 2.741985 TCGTGCGTTGCAGGGATG 60.742 61.111 11.06 0.00 43.44 3.51
118 119 2.434884 CTCGTGCGTTGCAGGGAT 60.435 61.111 11.06 0.00 43.44 3.85
121 122 2.392613 AAAAGCTCGTGCGTTGCAGG 62.393 55.000 11.22 5.19 44.42 4.85
122 123 1.009675 AAAAGCTCGTGCGTTGCAG 60.010 52.632 11.22 0.00 45.42 4.41
123 124 1.298264 CAAAAGCTCGTGCGTTGCA 60.298 52.632 11.22 0.00 45.42 4.08
124 125 0.041663 TACAAAAGCTCGTGCGTTGC 60.042 50.000 21.18 4.81 45.42 4.17
125 126 1.937359 CTACAAAAGCTCGTGCGTTG 58.063 50.000 20.23 20.23 45.42 4.10
136 137 1.106285 GATGCAGGGGGCTACAAAAG 58.894 55.000 0.00 0.00 45.15 2.27
137 138 0.324275 GGATGCAGGGGGCTACAAAA 60.324 55.000 0.00 0.00 45.15 2.44
138 139 1.306296 GGATGCAGGGGGCTACAAA 59.694 57.895 0.00 0.00 45.15 2.83
139 140 1.925285 CTGGATGCAGGGGGCTACAA 61.925 60.000 6.28 0.00 45.15 2.41
140 141 2.286045 TGGATGCAGGGGGCTACA 60.286 61.111 0.00 0.00 45.15 2.74
141 142 2.512896 CTGGATGCAGGGGGCTAC 59.487 66.667 6.28 0.00 45.15 3.58
142 143 3.492353 GCTGGATGCAGGGGGCTA 61.492 66.667 16.65 0.00 45.15 3.93
151 152 2.225963 GCAGATAAGTCATGCTGGATGC 59.774 50.000 4.06 0.26 43.25 3.91
158 159 3.139850 AGCATCAGCAGATAAGTCATGC 58.860 45.455 0.00 0.00 45.49 4.06
159 160 4.377897 TGAGCATCAGCAGATAAGTCATG 58.622 43.478 0.00 0.00 42.56 3.07
160 161 4.684484 TGAGCATCAGCAGATAAGTCAT 57.316 40.909 0.00 0.00 42.56 3.06
194 195 7.445402 TGAAAGTGGAAAATGTTCAACCAAAAA 59.555 29.630 0.00 0.00 38.32 1.94
195 196 6.936900 TGAAAGTGGAAAATGTTCAACCAAAA 59.063 30.769 0.00 0.00 38.32 2.44
196 197 6.467677 TGAAAGTGGAAAATGTTCAACCAAA 58.532 32.000 0.00 0.00 38.32 3.28
197 198 6.042638 TGAAAGTGGAAAATGTTCAACCAA 57.957 33.333 0.00 0.00 38.32 3.67
198 199 5.667539 TGAAAGTGGAAAATGTTCAACCA 57.332 34.783 0.00 0.00 38.32 3.67
199 200 8.711457 CATATTGAAAGTGGAAAATGTTCAACC 58.289 33.333 0.00 0.00 38.32 3.77
200 201 8.711457 CCATATTGAAAGTGGAAAATGTTCAAC 58.289 33.333 0.00 0.00 40.06 3.18
201 202 8.646004 TCCATATTGAAAGTGGAAAATGTTCAA 58.354 29.630 0.00 0.00 41.12 2.69
202 203 8.087750 GTCCATATTGAAAGTGGAAAATGTTCA 58.912 33.333 3.86 0.00 43.19 3.18
203 204 8.087750 TGTCCATATTGAAAGTGGAAAATGTTC 58.912 33.333 3.86 0.00 43.19 3.18
204 205 7.961351 TGTCCATATTGAAAGTGGAAAATGTT 58.039 30.769 3.86 0.00 43.19 2.71
205 206 7.537596 TGTCCATATTGAAAGTGGAAAATGT 57.462 32.000 3.86 0.00 43.19 2.71
206 207 8.830201 TTTGTCCATATTGAAAGTGGAAAATG 57.170 30.769 5.88 0.00 43.19 2.32
207 208 9.439500 CATTTGTCCATATTGAAAGTGGAAAAT 57.561 29.630 5.88 9.34 43.19 1.82
208 209 7.387397 GCATTTGTCCATATTGAAAGTGGAAAA 59.613 33.333 3.86 2.84 43.19 2.29
209 210 6.873076 GCATTTGTCCATATTGAAAGTGGAAA 59.127 34.615 3.86 0.00 43.19 3.13
210 211 6.211184 AGCATTTGTCCATATTGAAAGTGGAA 59.789 34.615 3.86 0.00 43.19 3.53
211 212 5.716228 AGCATTTGTCCATATTGAAAGTGGA 59.284 36.000 0.00 0.00 39.61 4.02
212 213 5.969423 AGCATTTGTCCATATTGAAAGTGG 58.031 37.500 0.00 0.00 0.00 4.00
213 214 6.750501 CAGAGCATTTGTCCATATTGAAAGTG 59.249 38.462 0.00 0.00 0.00 3.16
214 215 6.660521 TCAGAGCATTTGTCCATATTGAAAGT 59.339 34.615 0.00 0.00 0.00 2.66
215 216 7.092137 TCAGAGCATTTGTCCATATTGAAAG 57.908 36.000 0.00 0.00 0.00 2.62
220 221 5.361857 CCCTTTCAGAGCATTTGTCCATATT 59.638 40.000 0.00 0.00 0.00 1.28
221 222 4.891756 CCCTTTCAGAGCATTTGTCCATAT 59.108 41.667 0.00 0.00 0.00 1.78
228 229 5.458041 TTCTTTCCCTTTCAGAGCATTTG 57.542 39.130 0.00 0.00 0.00 2.32
232 233 5.388654 AGATTTTCTTTCCCTTTCAGAGCA 58.611 37.500 0.00 0.00 0.00 4.26
234 235 6.015603 AGCAAGATTTTCTTTCCCTTTCAGAG 60.016 38.462 0.00 0.00 33.78 3.35
242 243 4.560128 GGAACAGCAAGATTTTCTTTCCC 58.440 43.478 0.00 0.00 33.78 3.97
248 249 3.003275 TCACACGGAACAGCAAGATTTTC 59.997 43.478 0.00 0.00 0.00 2.29
250 251 2.549754 CTCACACGGAACAGCAAGATTT 59.450 45.455 0.00 0.00 0.00 2.17
251 252 2.146342 CTCACACGGAACAGCAAGATT 58.854 47.619 0.00 0.00 0.00 2.40
252 253 1.070758 ACTCACACGGAACAGCAAGAT 59.929 47.619 0.00 0.00 0.00 2.40
253 254 0.464036 ACTCACACGGAACAGCAAGA 59.536 50.000 0.00 0.00 0.00 3.02
257 258 2.349532 GCTAAAACTCACACGGAACAGC 60.350 50.000 0.00 0.00 0.00 4.40
262 263 5.142061 TGATTAGCTAAAACTCACACGGA 57.858 39.130 10.85 0.00 0.00 4.69
271 272 5.673337 TGCGGATCATGATTAGCTAAAAC 57.327 39.130 26.02 8.50 0.00 2.43
272 273 5.822519 AGTTGCGGATCATGATTAGCTAAAA 59.177 36.000 26.02 15.56 0.00 1.52
289 291 1.200716 TCAGTAGAACGGTAGTTGCGG 59.799 52.381 0.00 0.00 41.34 5.69
316 318 0.321919 TCTGCCTCGGTGTAGTACGT 60.322 55.000 0.00 0.00 0.00 3.57
317 319 1.022735 ATCTGCCTCGGTGTAGTACG 58.977 55.000 0.00 0.00 0.00 3.67
318 320 4.277672 TCATAATCTGCCTCGGTGTAGTAC 59.722 45.833 0.00 0.00 0.00 2.73
319 321 4.277672 GTCATAATCTGCCTCGGTGTAGTA 59.722 45.833 0.00 0.00 0.00 1.82
428 475 2.101783 TGAAACCGAAGCCCGAGTATA 58.898 47.619 0.00 0.00 41.76 1.47
429 476 0.899720 TGAAACCGAAGCCCGAGTAT 59.100 50.000 0.00 0.00 41.76 2.12
431 478 0.391263 GATGAAACCGAAGCCCGAGT 60.391 55.000 0.00 0.00 41.76 4.18
432 479 0.391130 TGATGAAACCGAAGCCCGAG 60.391 55.000 0.00 0.00 41.76 4.63
433 480 0.251916 ATGATGAAACCGAAGCCCGA 59.748 50.000 0.00 0.00 41.76 5.14
434 481 0.378257 CATGATGAAACCGAAGCCCG 59.622 55.000 0.00 0.00 38.18 6.13
435 482 0.101219 GCATGATGAAACCGAAGCCC 59.899 55.000 0.00 0.00 0.00 5.19
436 483 0.101219 GGCATGATGAAACCGAAGCC 59.899 55.000 0.00 0.00 0.00 4.35
437 484 3.629858 GGCATGATGAAACCGAAGC 57.370 52.632 0.00 0.00 0.00 3.86
443 490 1.464023 CGTGACACGGCATGATGAAAC 60.464 52.381 20.26 0.00 38.08 2.78
444 491 0.795698 CGTGACACGGCATGATGAAA 59.204 50.000 20.26 0.00 38.08 2.69
445 492 2.454921 CGTGACACGGCATGATGAA 58.545 52.632 20.26 0.00 38.08 2.57
446 493 4.183771 CGTGACACGGCATGATGA 57.816 55.556 20.26 0.00 38.08 2.92
470 533 7.166851 CCAAGATAATCAGATAGAGGTTGCAT 58.833 38.462 0.00 0.00 0.00 3.96
473 536 6.528321 TGCCAAGATAATCAGATAGAGGTTG 58.472 40.000 0.00 0.00 0.00 3.77
528 619 4.759693 TGGTGTCTTTATGTACTGCCAAAG 59.240 41.667 0.00 0.00 0.00 2.77
554 653 3.215975 GCCTTGTAAGTTGTAACCACCA 58.784 45.455 0.00 0.00 0.00 4.17
556 655 4.096682 TGTTGCCTTGTAAGTTGTAACCAC 59.903 41.667 0.00 0.00 0.00 4.16
574 677 1.537348 CCATATGCAGCCACATGTTGC 60.537 52.381 13.84 13.84 38.30 4.17
660 942 9.741647 CTCTATGCTTTTAAAAATCATCTTCCC 57.258 33.333 14.82 0.00 0.00 3.97
709 991 1.376812 CCGGCTGGTTACACCCTTC 60.377 63.158 2.29 0.00 37.50 3.46
821 1109 2.849318 AGGAAGGAAGGAAGGAATGGAG 59.151 50.000 0.00 0.00 0.00 3.86
822 1110 2.934722 AGGAAGGAAGGAAGGAATGGA 58.065 47.619 0.00 0.00 0.00 3.41
823 1111 3.625853 GAAGGAAGGAAGGAAGGAATGG 58.374 50.000 0.00 0.00 0.00 3.16
825 1113 3.546840 AGGAAGGAAGGAAGGAAGGAAT 58.453 45.455 0.00 0.00 0.00 3.01
826 1114 3.005529 AGGAAGGAAGGAAGGAAGGAA 57.994 47.619 0.00 0.00 0.00 3.36
827 1115 2.743131 AGGAAGGAAGGAAGGAAGGA 57.257 50.000 0.00 0.00 0.00 3.36
828 1116 2.916269 AGAAGGAAGGAAGGAAGGAAGG 59.084 50.000 0.00 0.00 0.00 3.46
831 1119 2.913617 GGAAGAAGGAAGGAAGGAAGGA 59.086 50.000 0.00 0.00 0.00 3.36
837 1125 6.244654 AGATCAAAAGGAAGAAGGAAGGAAG 58.755 40.000 0.00 0.00 0.00 3.46
891 1187 1.002366 CAGCGGCTTAAGTGCTACAG 58.998 55.000 19.53 8.10 37.15 2.74
906 1202 1.225855 TGCGAATTTATAGGCCAGCG 58.774 50.000 5.01 0.00 0.00 5.18
995 1317 4.790962 AGGTCGCTGCCATGGCTG 62.791 66.667 35.53 34.11 42.51 4.85
1035 1357 1.446099 GCAGATGAGAACGACCGCA 60.446 57.895 0.00 0.00 0.00 5.69
1043 1365 1.153489 GCGAGCAGGCAGATGAGAA 60.153 57.895 0.00 0.00 0.00 2.87
1116 1468 1.772567 AGGTGTAAGTGTGGGGGCA 60.773 57.895 0.00 0.00 0.00 5.36
1117 1469 1.002502 GAGGTGTAAGTGTGGGGGC 60.003 63.158 0.00 0.00 0.00 5.80
1118 1470 1.131303 TGGAGGTGTAAGTGTGGGGG 61.131 60.000 0.00 0.00 0.00 5.40
1123 1475 0.396811 GCAGGTGGAGGTGTAAGTGT 59.603 55.000 0.00 0.00 0.00 3.55
1124 1476 0.321653 GGCAGGTGGAGGTGTAAGTG 60.322 60.000 0.00 0.00 0.00 3.16
1125 1477 1.489560 GGGCAGGTGGAGGTGTAAGT 61.490 60.000 0.00 0.00 0.00 2.24
1423 1904 1.835483 GCAATGCCGGCTATGACTCG 61.835 60.000 29.70 8.30 0.00 4.18
1426 1907 1.097547 ACTGCAATGCCGGCTATGAC 61.098 55.000 29.70 20.02 0.00 3.06
1427 1908 0.394216 AACTGCAATGCCGGCTATGA 60.394 50.000 29.70 7.47 0.00 2.15
1429 1910 2.008268 GCAACTGCAATGCCGGCTAT 62.008 55.000 29.70 16.59 41.59 2.97
1431 1912 4.060038 GCAACTGCAATGCCGGCT 62.060 61.111 29.70 10.60 41.59 5.52
1473 1989 0.388134 ACACGACGATCAAAGACCCG 60.388 55.000 0.00 0.00 0.00 5.28
1490 2006 1.275505 CACGCAAACACAATGCAACA 58.724 45.000 0.00 0.00 44.01 3.33
1575 2098 3.022406 GACGGGGTAGTAGTTCATGTCT 58.978 50.000 0.00 0.00 0.00 3.41
2045 3096 2.871453 CATGCCTTCCATGGATCATCA 58.129 47.619 17.06 11.67 46.09 3.07
2088 3162 5.916883 GCTATATAGCTTGGCACAACAAATG 59.083 40.000 24.63 0.00 45.62 2.32
2122 3202 1.507141 GCACAAGGGACGTCACAAGG 61.507 60.000 22.01 11.14 0.00 3.61
2135 3215 2.246397 CACGCACTGACGCACAAG 59.754 61.111 0.00 0.00 36.19 3.16
2136 3216 2.510464 ACACGCACTGACGCACAA 60.510 55.556 0.00 0.00 36.19 3.33
2137 3217 2.959599 GACACGCACTGACGCACA 60.960 61.111 0.00 0.00 36.19 4.57
2138 3218 3.702555 GGACACGCACTGACGCAC 61.703 66.667 0.00 0.00 36.19 5.34
2139 3219 3.841379 GAGGACACGCACTGACGCA 62.841 63.158 0.00 0.00 36.19 5.24
2140 3220 3.106407 GAGGACACGCACTGACGC 61.106 66.667 0.00 0.00 36.19 5.19
2141 3221 2.801162 CGAGGACACGCACTGACG 60.801 66.667 0.00 0.00 39.50 4.35
2142 3222 1.729838 GACGAGGACACGCACTGAC 60.730 63.158 0.00 0.00 36.70 3.51
2143 3223 2.643272 GACGAGGACACGCACTGA 59.357 61.111 0.00 0.00 36.70 3.41
2144 3224 2.801162 CGACGAGGACACGCACTG 60.801 66.667 0.00 0.00 36.70 3.66
2145 3225 3.285215 ACGACGAGGACACGCACT 61.285 61.111 0.00 0.00 36.70 4.40
2179 3259 6.074676 GGGACACGATAAATGATAACACGTAC 60.075 42.308 0.00 0.00 0.00 3.67
2180 3260 5.978919 GGGACACGATAAATGATAACACGTA 59.021 40.000 0.00 0.00 0.00 3.57
2181 3261 4.807304 GGGACACGATAAATGATAACACGT 59.193 41.667 0.00 0.00 0.00 4.49
2182 3262 4.806775 TGGGACACGATAAATGATAACACG 59.193 41.667 0.00 0.00 0.00 4.49
2204 3284 9.556030 CACGTATGTATATGTACAAGGATAGTG 57.444 37.037 6.39 7.67 43.60 2.74
2254 3361 2.110188 TCTGGTCACTACACTCCTCCTT 59.890 50.000 0.00 0.00 0.00 3.36
2261 3368 2.677542 TGAGGTCTGGTCACTACACT 57.322 50.000 0.00 0.00 0.00 3.55
2262 3369 3.321111 TCTTTGAGGTCTGGTCACTACAC 59.679 47.826 0.00 0.00 0.00 2.90
2268 3375 2.964209 AGACTCTTTGAGGTCTGGTCA 58.036 47.619 0.00 0.00 40.71 4.02
2283 3390 3.295734 TGCACAGAAGCACAGACTC 57.704 52.632 0.00 0.00 40.11 3.36
2368 3476 6.704493 ACTCGTTGTAATAAGTGTGTGATTGT 59.296 34.615 0.00 0.00 0.00 2.71
2446 3554 3.695830 TCCAAGTCTTCCGCTGTTATT 57.304 42.857 0.00 0.00 0.00 1.40
2510 3618 0.251922 AGGTGCCTTAGGTCGTGGTA 60.252 55.000 0.00 0.00 0.00 3.25
2537 3645 4.198530 TCATGTTGCAGACTTTTCAGACA 58.801 39.130 0.00 0.00 0.00 3.41
2628 3740 6.996509 TGCATGTAGTGATAGCATCATTCTA 58.003 36.000 0.00 0.00 42.04 2.10
2744 3858 5.738783 GCTGTCAACCATGTTTAACAACCAT 60.739 40.000 0.66 0.00 31.02 3.55
2845 3966 9.751542 CGTTTTGAGTATCTAGTATCTGGATTT 57.248 33.333 1.39 0.00 33.80 2.17
2954 4075 2.584608 CGGGAATCAAGCGGAGGT 59.415 61.111 0.00 0.00 44.60 3.85
2969 4090 3.261580 TCTCAAACATCATGTAGTGCGG 58.738 45.455 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.