Multiple sequence alignment - TraesCS2D01G180100

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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 TraesCS2D01G180100 chr2D 100.000 2362 0 0 386 2747 124798929 124796568 0.000000e+00 4362.0
1 TraesCS2D01G180100 chr2D 82.195 820 97 32 977 1764 124476666 124475864 0.000000e+00 660.0
2 TraesCS2D01G180100 chr2D 100.000 193 0 0 1 193 124799314 124799122 9.350000e-95 357.0
3 TraesCS2D01G180100 chr2A 93.285 1385 52 20 392 1765 130715484 130714130 0.000000e+00 2004.0
4 TraesCS2D01G180100 chr2A 89.879 247 17 5 1995 2239 130714129 130713889 7.390000e-81 311.0
5 TraesCS2D01G180100 chr2A 76.423 246 46 10 2476 2711 706531716 706531473 3.710000e-24 122.0
6 TraesCS2D01G180100 chr2B 93.225 797 36 10 983 1764 177545835 177545042 0.000000e+00 1157.0
7 TraesCS2D01G180100 chr2B 90.748 789 48 16 1969 2747 177217883 177217110 0.000000e+00 1029.0
8 TraesCS2D01G180100 chr2B 90.248 605 35 6 406 986 177547890 177547286 0.000000e+00 769.0
9 TraesCS2D01G180100 chr2B 80.218 824 106 33 977 1764 177119535 177118733 1.430000e-157 566.0
10 TraesCS2D01G180100 chr2B 84.837 521 49 14 1263 1761 177218537 177218025 5.280000e-137 497.0
11 TraesCS2D01G180100 chr2B 88.785 107 7 4 2038 2141 177118706 177118602 2.870000e-25 126.0
12 TraesCS2D01G180100 chr2B 86.364 66 5 4 1866 1929 52463175 52463238 4.910000e-08 69.4
13 TraesCS2D01G180100 chr1B 90.724 539 40 4 1237 1765 15375905 15375367 0.000000e+00 710.0
14 TraesCS2D01G180100 chr1B 89.394 396 33 3 1264 1653 15370053 15369661 8.840000e-135 490.0
15 TraesCS2D01G180100 chr1B 91.727 278 22 1 1488 1764 15369659 15369382 4.290000e-103 385.0
16 TraesCS2D01G180100 chr1B 94.444 90 4 1 1909 1998 456268085 456268173 1.330000e-28 137.0
17 TraesCS2D01G180100 chr1B 100.000 29 0 0 2679 2707 176140916 176140944 1.000000e-03 54.7
18 TraesCS2D01G180100 chr7B 86.290 248 28 5 2129 2374 385026980 385027223 5.830000e-67 265.0
19 TraesCS2D01G180100 chr7B 93.750 48 2 1 2636 2682 159509370 159509417 1.360000e-08 71.3
20 TraesCS2D01G180100 chr1D 87.568 185 21 2 2425 2608 43200534 43200717 2.140000e-51 213.0
21 TraesCS2D01G180100 chr4A 84.656 189 18 8 2534 2714 98551980 98551795 7.820000e-41 178.0
22 TraesCS2D01G180100 chr7D 96.739 92 3 0 1909 2000 169823455 169823364 1.320000e-33 154.0
23 TraesCS2D01G180100 chr7D 96.739 92 2 1 1909 2000 51998853 51998763 4.740000e-33 152.0
24 TraesCS2D01G180100 chr7D 96.703 91 1 2 1907 1996 51998767 51998856 1.700000e-32 150.0
25 TraesCS2D01G180100 chr7D 95.506 89 4 0 1909 1997 177106944 177106856 2.850000e-30 143.0
26 TraesCS2D01G180100 chr7D 96.471 85 3 0 1909 1993 49381982 49381898 1.030000e-29 141.0
27 TraesCS2D01G180100 chr7D 95.402 87 4 0 1908 1994 187082005 187081919 3.690000e-29 139.0
28 TraesCS2D01G180100 chr6D 96.512 86 3 0 1909 1994 17316627 17316712 2.850000e-30 143.0
29 TraesCS2D01G180100 chr3B 78.008 241 39 11 2476 2711 158699126 158699357 3.690000e-29 139.0
30 TraesCS2D01G180100 chr4D 94.382 89 5 0 1909 1997 3719282 3719370 1.330000e-28 137.0
31 TraesCS2D01G180100 chr3D 77.130 223 38 10 2494 2711 107662491 107662705 1.730000e-22 117.0


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 TraesCS2D01G180100 chr2D 124796568 124799314 2746 True 2359.5 4362 100.0000 1 2747 2 chr2D.!!$R2 2746
1 TraesCS2D01G180100 chr2D 124475864 124476666 802 True 660.0 660 82.1950 977 1764 1 chr2D.!!$R1 787
2 TraesCS2D01G180100 chr2A 130713889 130715484 1595 True 1157.5 2004 91.5820 392 2239 2 chr2A.!!$R2 1847
3 TraesCS2D01G180100 chr2B 177545042 177547890 2848 True 963.0 1157 91.7365 406 1764 2 chr2B.!!$R3 1358
4 TraesCS2D01G180100 chr2B 177217110 177218537 1427 True 763.0 1029 87.7925 1263 2747 2 chr2B.!!$R2 1484
5 TraesCS2D01G180100 chr2B 177118602 177119535 933 True 346.0 566 84.5015 977 2141 2 chr2B.!!$R1 1164
6 TraesCS2D01G180100 chr1B 15375367 15375905 538 True 710.0 710 90.7240 1237 1765 1 chr1B.!!$R1 528
7 TraesCS2D01G180100 chr1B 15369382 15370053 671 True 437.5 490 90.5605 1264 1764 2 chr1B.!!$R2 500

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
65 66 0.029167 GTCGCTCGGTCTAGCTAACC 59.971 60.0 12.51 12.51 40.49 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 3614 0.042131 ATTGTGGGACGGAGGGAGTA 59.958 55.0 0.0 0.0 0.0 2.59 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
17 18 4.004348 AGAGTCCACGACATCGCT 57.996 55.556 0.14 0.00 44.43 4.93
18 19 1.508545 AGAGTCCACGACATCGCTG 59.491 57.895 0.14 0.00 44.43 5.18
19 20 2.125912 AGTCCACGACATCGCTGC 60.126 61.111 0.14 0.00 44.43 5.25
20 21 2.432456 GTCCACGACATCGCTGCA 60.432 61.111 0.14 0.00 44.43 4.41
21 22 2.027073 GTCCACGACATCGCTGCAA 61.027 57.895 0.14 0.00 44.43 4.08
22 23 1.301322 TCCACGACATCGCTGCAAA 60.301 52.632 0.14 0.00 44.43 3.68
23 24 0.673333 TCCACGACATCGCTGCAAAT 60.673 50.000 0.14 0.00 44.43 2.32
24 25 1.006086 CCACGACATCGCTGCAAATA 58.994 50.000 0.14 0.00 44.43 1.40
25 26 1.599071 CCACGACATCGCTGCAAATAT 59.401 47.619 0.14 0.00 44.43 1.28
26 27 2.799978 CCACGACATCGCTGCAAATATA 59.200 45.455 0.14 0.00 44.43 0.86
27 28 3.247411 CCACGACATCGCTGCAAATATAA 59.753 43.478 0.14 0.00 44.43 0.98
28 29 4.448891 CACGACATCGCTGCAAATATAAG 58.551 43.478 0.14 0.00 44.43 1.73
29 30 3.059597 ACGACATCGCTGCAAATATAAGC 60.060 43.478 0.14 0.00 44.43 3.09
30 31 3.665323 CGACATCGCTGCAAATATAAGCC 60.665 47.826 0.00 0.00 33.24 4.35
31 32 3.213506 ACATCGCTGCAAATATAAGCCA 58.786 40.909 0.00 0.00 33.24 4.75
32 33 3.251729 ACATCGCTGCAAATATAAGCCAG 59.748 43.478 0.00 0.00 33.24 4.85
33 34 3.192541 TCGCTGCAAATATAAGCCAGA 57.807 42.857 0.00 0.00 33.24 3.86
34 35 3.540617 TCGCTGCAAATATAAGCCAGAA 58.459 40.909 0.00 0.00 33.24 3.02
35 36 4.136796 TCGCTGCAAATATAAGCCAGAAT 58.863 39.130 0.00 0.00 33.24 2.40
36 37 5.304778 TCGCTGCAAATATAAGCCAGAATA 58.695 37.500 0.00 0.00 33.24 1.75
37 38 5.409520 TCGCTGCAAATATAAGCCAGAATAG 59.590 40.000 0.00 0.00 33.24 1.73
38 39 5.391310 CGCTGCAAATATAAGCCAGAATAGG 60.391 44.000 0.00 0.00 33.24 2.57
47 48 1.668419 GCCAGAATAGGCGATGTTGT 58.332 50.000 0.00 0.00 46.12 3.32
48 49 1.599542 GCCAGAATAGGCGATGTTGTC 59.400 52.381 0.00 0.00 46.12 3.18
56 57 3.374330 CGATGTTGTCGCTCGGTC 58.626 61.111 0.00 0.00 44.33 4.79
57 58 1.154016 CGATGTTGTCGCTCGGTCT 60.154 57.895 0.00 0.00 44.33 3.85
58 59 0.098200 CGATGTTGTCGCTCGGTCTA 59.902 55.000 0.00 0.00 44.33 2.59
59 60 1.828832 GATGTTGTCGCTCGGTCTAG 58.171 55.000 0.00 0.00 0.00 2.43
60 61 0.179134 ATGTTGTCGCTCGGTCTAGC 60.179 55.000 0.00 0.00 39.21 3.42
61 62 1.241990 TGTTGTCGCTCGGTCTAGCT 61.242 55.000 0.00 0.00 40.49 3.32
62 63 0.731417 GTTGTCGCTCGGTCTAGCTA 59.269 55.000 0.00 0.00 40.49 3.32
63 64 1.131883 GTTGTCGCTCGGTCTAGCTAA 59.868 52.381 0.00 0.00 40.49 3.09
64 65 0.731417 TGTCGCTCGGTCTAGCTAAC 59.269 55.000 0.00 0.00 40.49 2.34
65 66 0.029167 GTCGCTCGGTCTAGCTAACC 59.971 60.000 12.51 12.51 40.49 2.85
66 67 0.393402 TCGCTCGGTCTAGCTAACCA 60.393 55.000 18.93 9.61 40.49 3.67
67 68 0.669077 CGCTCGGTCTAGCTAACCAT 59.331 55.000 18.93 0.00 40.49 3.55
68 69 1.600663 CGCTCGGTCTAGCTAACCATG 60.601 57.143 18.93 13.46 40.49 3.66
69 70 1.269831 GCTCGGTCTAGCTAACCATGG 60.270 57.143 11.19 11.19 39.50 3.66
70 71 2.032620 CTCGGTCTAGCTAACCATGGT 58.967 52.381 13.00 13.00 36.53 3.55
71 72 2.431057 CTCGGTCTAGCTAACCATGGTT 59.569 50.000 31.85 31.85 41.65 3.67
72 73 2.835764 TCGGTCTAGCTAACCATGGTTT 59.164 45.455 34.04 19.44 39.31 3.27
73 74 3.118884 TCGGTCTAGCTAACCATGGTTTC 60.119 47.826 34.04 24.40 39.31 2.78
74 75 3.118738 CGGTCTAGCTAACCATGGTTTCT 60.119 47.826 34.04 28.95 39.31 2.52
75 76 4.098960 CGGTCTAGCTAACCATGGTTTCTA 59.901 45.833 34.04 28.59 39.31 2.10
76 77 5.602628 GGTCTAGCTAACCATGGTTTCTAG 58.397 45.833 33.92 33.92 39.11 2.43
77 78 5.453480 GGTCTAGCTAACCATGGTTTCTAGG 60.453 48.000 35.82 26.75 38.75 3.02
78 79 5.363005 GTCTAGCTAACCATGGTTTCTAGGA 59.637 44.000 35.82 27.73 38.75 2.94
79 80 5.962031 TCTAGCTAACCATGGTTTCTAGGAA 59.038 40.000 35.82 26.47 38.75 3.36
80 81 4.844884 AGCTAACCATGGTTTCTAGGAAC 58.155 43.478 34.04 11.42 39.31 3.62
81 82 4.536489 AGCTAACCATGGTTTCTAGGAACT 59.464 41.667 34.04 13.53 40.14 3.01
82 83 4.876679 GCTAACCATGGTTTCTAGGAACTC 59.123 45.833 34.04 9.57 38.61 3.01
83 84 3.611766 ACCATGGTTTCTAGGAACTCG 57.388 47.619 13.00 2.83 41.75 4.18
84 85 3.170717 ACCATGGTTTCTAGGAACTCGA 58.829 45.455 13.00 0.00 41.75 4.04
85 86 3.056035 ACCATGGTTTCTAGGAACTCGAC 60.056 47.826 13.00 0.00 41.75 4.20
86 87 3.056107 CCATGGTTTCTAGGAACTCGACA 60.056 47.826 13.68 3.64 41.75 4.35
87 88 4.562757 CCATGGTTTCTAGGAACTCGACAA 60.563 45.833 13.68 0.00 41.75 3.18
88 89 4.252971 TGGTTTCTAGGAACTCGACAAG 57.747 45.455 13.68 0.00 41.75 3.16
89 90 3.006537 TGGTTTCTAGGAACTCGACAAGG 59.993 47.826 13.68 0.00 41.75 3.61
90 91 3.006644 GGTTTCTAGGAACTCGACAAGGT 59.993 47.826 13.68 0.00 41.75 3.50
91 92 4.236147 GTTTCTAGGAACTCGACAAGGTC 58.764 47.826 6.66 0.00 41.38 3.85
92 93 3.436577 TCTAGGAACTCGACAAGGTCT 57.563 47.619 0.00 0.00 41.84 3.85
93 94 4.564782 TCTAGGAACTCGACAAGGTCTA 57.435 45.455 0.00 0.00 41.84 2.59
94 95 4.515361 TCTAGGAACTCGACAAGGTCTAG 58.485 47.826 0.00 0.00 41.84 2.43
95 96 2.448453 AGGAACTCGACAAGGTCTAGG 58.552 52.381 3.44 0.00 41.84 3.02
96 97 2.041350 AGGAACTCGACAAGGTCTAGGA 59.959 50.000 3.44 0.00 41.84 2.94
97 98 2.164017 GGAACTCGACAAGGTCTAGGAC 59.836 54.545 3.44 0.00 41.84 3.85
98 99 7.839662 TAGGAACTCGACAAGGTCTAGGACC 62.840 52.000 8.52 8.52 46.68 4.46
110 111 4.940905 GTCTAGGACCTCCAATTAGGAC 57.059 50.000 0.00 0.00 43.07 3.85
113 114 1.591768 GGACCTCCAATTAGGACCCA 58.408 55.000 1.07 0.00 43.30 4.51
114 115 1.920351 GGACCTCCAATTAGGACCCAA 59.080 52.381 1.07 0.00 43.30 4.12
115 116 2.356844 GGACCTCCAATTAGGACCCAAC 60.357 54.545 1.07 0.00 43.30 3.77
116 117 2.576648 GACCTCCAATTAGGACCCAACT 59.423 50.000 1.07 0.00 43.07 3.16
117 118 2.576648 ACCTCCAATTAGGACCCAACTC 59.423 50.000 1.07 0.00 43.07 3.01
118 119 2.092375 CCTCCAATTAGGACCCAACTCC 60.092 54.545 0.00 0.00 43.07 3.85
119 120 2.846827 CTCCAATTAGGACCCAACTCCT 59.153 50.000 0.00 0.00 43.07 3.69
120 121 2.844348 TCCAATTAGGACCCAACTCCTC 59.156 50.000 0.00 0.00 43.07 3.71
121 122 2.420129 CCAATTAGGACCCAACTCCTCG 60.420 54.545 0.00 0.00 40.12 4.63
122 123 2.236395 CAATTAGGACCCAACTCCTCGT 59.764 50.000 0.00 0.00 40.12 4.18
123 124 1.263356 TTAGGACCCAACTCCTCGTG 58.737 55.000 0.00 0.00 40.12 4.35
124 125 0.613853 TAGGACCCAACTCCTCGTGG 60.614 60.000 0.00 0.00 40.12 4.94
125 126 2.663196 GACCCAACTCCTCGTGGG 59.337 66.667 7.19 7.19 46.64 4.61
126 127 3.607370 GACCCAACTCCTCGTGGGC 62.607 68.421 8.67 0.00 45.19 5.36
127 128 4.760047 CCCAACTCCTCGTGGGCG 62.760 72.222 3.23 0.00 35.14 6.13
128 129 3.691342 CCAACTCCTCGTGGGCGA 61.691 66.667 3.23 0.00 45.79 5.54
138 139 2.074547 TCGTGGGCGAAACTCTAAAG 57.925 50.000 0.00 0.00 44.92 1.85
139 140 1.076332 CGTGGGCGAAACTCTAAAGG 58.924 55.000 0.00 0.00 41.33 3.11
140 141 1.450025 GTGGGCGAAACTCTAAAGGG 58.550 55.000 0.00 0.00 0.00 3.95
141 142 0.322187 TGGGCGAAACTCTAAAGGGC 60.322 55.000 0.00 0.00 0.00 5.19
142 143 0.322187 GGGCGAAACTCTAAAGGGCA 60.322 55.000 0.00 0.00 0.00 5.36
143 144 0.803117 GGCGAAACTCTAAAGGGCAC 59.197 55.000 0.00 0.00 0.00 5.01
144 145 0.442699 GCGAAACTCTAAAGGGCACG 59.557 55.000 0.00 0.00 0.00 5.34
145 146 1.792006 CGAAACTCTAAAGGGCACGT 58.208 50.000 0.00 0.00 0.00 4.49
146 147 1.459592 CGAAACTCTAAAGGGCACGTG 59.540 52.381 12.28 12.28 0.00 4.49
147 148 1.197036 GAAACTCTAAAGGGCACGTGC 59.803 52.381 32.15 32.15 41.14 5.34
148 149 0.396811 AACTCTAAAGGGCACGTGCT 59.603 50.000 36.84 21.61 41.70 4.40
149 150 0.320771 ACTCTAAAGGGCACGTGCTG 60.321 55.000 36.84 20.18 41.70 4.41
150 151 1.639298 CTCTAAAGGGCACGTGCTGC 61.639 60.000 36.84 22.76 46.31 5.25
162 163 3.658075 TGCTGCATTGCACGCGAA 61.658 55.556 15.93 0.00 38.12 4.70
163 164 3.167945 GCTGCATTGCACGCGAAC 61.168 61.111 15.93 4.29 33.79 3.95
164 165 2.251963 CTGCATTGCACGCGAACA 59.748 55.556 15.93 7.56 33.79 3.18
165 166 2.051435 TGCATTGCACGCGAACAC 60.051 55.556 15.93 0.00 31.71 3.32
166 167 2.051435 GCATTGCACGCGAACACA 60.051 55.556 15.93 1.42 0.00 3.72
167 168 1.656875 GCATTGCACGCGAACACAA 60.657 52.632 15.93 11.70 0.00 3.33
168 169 1.003262 GCATTGCACGCGAACACAAT 61.003 50.000 15.93 13.55 33.12 2.71
169 170 0.704008 CATTGCACGCGAACACAATG 59.296 50.000 15.93 20.76 42.23 2.82
170 171 0.310543 ATTGCACGCGAACACAATGT 59.689 45.000 15.93 0.00 31.76 2.71
171 172 0.590984 TTGCACGCGAACACAATGTG 60.591 50.000 15.93 12.40 39.75 3.21
172 173 1.725625 GCACGCGAACACAATGTGG 60.726 57.895 15.93 1.67 37.94 4.17
173 174 1.082169 CACGCGAACACAATGTGGG 60.082 57.895 15.93 7.58 37.94 4.61
174 175 2.126888 CGCGAACACAATGTGGGC 60.127 61.111 18.37 15.65 37.94 5.36
175 176 2.258286 GCGAACACAATGTGGGCC 59.742 61.111 18.37 0.00 37.94 5.80
176 177 2.268076 GCGAACACAATGTGGGCCT 61.268 57.895 18.37 0.00 37.94 5.19
177 178 1.805428 GCGAACACAATGTGGGCCTT 61.805 55.000 18.37 2.36 37.94 4.35
178 179 0.240945 CGAACACAATGTGGGCCTTC 59.759 55.000 18.37 10.78 37.94 3.46
179 180 0.240945 GAACACAATGTGGGCCTTCG 59.759 55.000 18.37 0.00 37.94 3.79
180 181 0.467290 AACACAATGTGGGCCTTCGT 60.467 50.000 18.37 0.00 37.94 3.85
181 182 0.889186 ACACAATGTGGGCCTTCGTC 60.889 55.000 18.37 0.00 37.94 4.20
182 183 0.606401 CACAATGTGGGCCTTCGTCT 60.606 55.000 5.29 0.00 0.00 4.18
183 184 0.321653 ACAATGTGGGCCTTCGTCTC 60.322 55.000 4.53 0.00 0.00 3.36
184 185 1.026718 CAATGTGGGCCTTCGTCTCC 61.027 60.000 4.53 0.00 0.00 3.71
185 186 2.521958 AATGTGGGCCTTCGTCTCCG 62.522 60.000 4.53 0.00 0.00 4.63
186 187 4.452733 GTGGGCCTTCGTCTCCGG 62.453 72.222 4.53 0.00 33.95 5.14
189 190 4.144703 GGCCTTCGTCTCCGGGAC 62.145 72.222 0.00 7.35 41.28 4.46
190 191 3.379445 GCCTTCGTCTCCGGGACA 61.379 66.667 19.10 7.25 44.70 4.02
191 192 2.722201 GCCTTCGTCTCCGGGACAT 61.722 63.158 19.10 0.00 44.70 3.06
192 193 1.437986 CCTTCGTCTCCGGGACATC 59.562 63.158 19.10 0.00 44.70 3.06
437 438 6.584942 GCAAATTTGTAACCTTGGTTAGCTAC 59.415 38.462 19.03 4.66 0.00 3.58
533 534 5.221263 ACCGTGTATTCTTGGCTATGTAGAG 60.221 44.000 0.00 0.00 0.00 2.43
535 536 5.009710 CGTGTATTCTTGGCTATGTAGAGGA 59.990 44.000 0.00 0.00 0.00 3.71
544 549 6.902771 TGGCTATGTAGAGGAAGATAAGTC 57.097 41.667 0.00 0.00 0.00 3.01
572 577 2.027745 TGAGACTTGAGAGATGCCCAAC 60.028 50.000 0.00 0.00 0.00 3.77
600 625 6.537566 CCTCAAATCACTAATGTCGAACTTG 58.462 40.000 0.00 0.00 0.00 3.16
623 648 1.032014 TTTCCTTCAACCTGCACAGC 58.968 50.000 0.00 0.00 0.00 4.40
677 702 4.517075 GCATATCAAGAAGGTTAGAAGGGC 59.483 45.833 0.00 0.00 0.00 5.19
715 740 4.367023 TCCACGTACGGTGCAGGC 62.367 66.667 21.06 0.00 45.62 4.85
820 849 2.202878 TGGCGCGTCCTTATCTGC 60.203 61.111 8.89 0.00 35.26 4.26
847 876 6.074142 GCAATTTCCCGCTTGAAATGATTATC 60.074 38.462 10.06 0.00 42.58 1.75
894 923 2.205022 TTCTGGCCACTTGATCAAGG 57.795 50.000 33.11 21.55 42.53 3.61
926 955 2.745281 GCCCTATAAACAGTTGACGCAA 59.255 45.455 0.00 0.00 0.00 4.85
935 964 1.135603 CAGTTGACGCAATGGTCATGG 60.136 52.381 5.62 0.00 45.62 3.66
1152 2637 2.135933 GATACCACCAGCTTATCGTGC 58.864 52.381 0.00 0.00 0.00 5.34
1177 2662 0.700564 ACTGCTGGTTCCCACATCAT 59.299 50.000 0.00 0.00 0.00 2.45
1178 2663 1.340405 ACTGCTGGTTCCCACATCATC 60.340 52.381 0.00 0.00 0.00 2.92
1179 2664 0.392863 TGCTGGTTCCCACATCATCG 60.393 55.000 0.00 0.00 0.00 3.84
1188 2673 1.097547 CCACATCATCGTCCTTGGCC 61.098 60.000 0.00 0.00 0.00 5.36
1191 2676 1.271871 ACATCATCGTCCTTGGCCAAA 60.272 47.619 20.91 4.13 0.00 3.28
1386 2899 1.043116 CCTCCATCACCTACGCCTCA 61.043 60.000 0.00 0.00 0.00 3.86
1495 3196 2.626743 ACCTTCTACTACTGCAACACGT 59.373 45.455 0.00 0.00 0.00 4.49
1557 3258 4.154347 CAGGACCTGCGGAGGCTC 62.154 72.222 24.53 18.41 44.33 4.70
1714 3415 1.154282 GTCGTCATGTCGTCTCGCA 60.154 57.895 11.96 0.00 0.00 5.10
1761 3467 8.245701 ACGAACTCTGATTTCTGATAAGAAAC 57.754 34.615 7.45 3.34 40.12 2.78
1766 3472 9.646427 ACTCTGATTTCTGATAAGAAACTACAC 57.354 33.333 7.45 0.00 40.12 2.90
1767 3473 9.092876 CTCTGATTTCTGATAAGAAACTACACC 57.907 37.037 7.45 0.00 40.12 4.16
1768 3474 8.593679 TCTGATTTCTGATAAGAAACTACACCA 58.406 33.333 7.45 0.00 40.12 4.17
1769 3475 9.219603 CTGATTTCTGATAAGAAACTACACCAA 57.780 33.333 7.45 0.00 40.12 3.67
1770 3476 9.739276 TGATTTCTGATAAGAAACTACACCAAT 57.261 29.630 7.45 0.00 40.12 3.16
1773 3479 9.793259 TTTCTGATAAGAAACTACACCAATTCT 57.207 29.630 0.61 0.00 33.40 2.40
1774 3480 9.793259 TTCTGATAAGAAACTACACCAATTCTT 57.207 29.630 5.14 5.14 42.82 2.52
1775 3481 9.793259 TCTGATAAGAAACTACACCAATTCTTT 57.207 29.630 5.10 0.00 41.15 2.52
1796 3502 9.545611 TTCTTTTAAAATATAAGACGTTTCGGC 57.454 29.630 0.09 0.00 33.59 5.54
1797 3503 8.719648 TCTTTTAAAATATAAGACGTTTCGGCA 58.280 29.630 0.09 0.00 37.34 5.69
1798 3504 8.883789 TTTTAAAATATAAGACGTTTCGGCAG 57.116 30.769 0.00 0.00 37.34 4.85
1799 3505 7.599630 TTAAAATATAAGACGTTTCGGCAGT 57.400 32.000 0.00 0.00 37.34 4.40
1800 3506 6.490566 AAAATATAAGACGTTTCGGCAGTT 57.509 33.333 0.00 0.00 37.34 3.16
1801 3507 6.490566 AAATATAAGACGTTTCGGCAGTTT 57.509 33.333 0.00 0.00 37.34 2.66
1802 3508 7.599630 AAATATAAGACGTTTCGGCAGTTTA 57.400 32.000 0.00 0.00 37.34 2.01
1803 3509 6.823678 ATATAAGACGTTTCGGCAGTTTAG 57.176 37.500 0.00 0.00 37.34 1.85
1804 3510 2.521105 AGACGTTTCGGCAGTTTAGT 57.479 45.000 0.00 0.00 37.34 2.24
1805 3511 2.132762 AGACGTTTCGGCAGTTTAGTG 58.867 47.619 0.00 0.00 37.34 2.74
1806 3512 1.862827 GACGTTTCGGCAGTTTAGTGT 59.137 47.619 0.00 0.00 33.63 3.55
1807 3513 2.282407 ACGTTTCGGCAGTTTAGTGTT 58.718 42.857 0.00 0.00 0.00 3.32
1808 3514 2.679336 ACGTTTCGGCAGTTTAGTGTTT 59.321 40.909 0.00 0.00 0.00 2.83
1809 3515 3.242511 ACGTTTCGGCAGTTTAGTGTTTC 60.243 43.478 0.00 0.00 0.00 2.78
1810 3516 3.001939 CGTTTCGGCAGTTTAGTGTTTCT 59.998 43.478 0.00 0.00 0.00 2.52
1811 3517 4.209703 CGTTTCGGCAGTTTAGTGTTTCTA 59.790 41.667 0.00 0.00 0.00 2.10
1812 3518 5.276963 CGTTTCGGCAGTTTAGTGTTTCTAA 60.277 40.000 0.00 0.00 36.91 2.10
1813 3519 6.488817 GTTTCGGCAGTTTAGTGTTTCTAAA 58.511 36.000 0.00 0.00 43.65 1.85
1814 3520 6.870971 TTCGGCAGTTTAGTGTTTCTAAAT 57.129 33.333 3.88 0.00 46.16 1.40
1815 3521 7.966246 TTCGGCAGTTTAGTGTTTCTAAATA 57.034 32.000 3.88 0.00 46.16 1.40
1816 3522 8.556213 TTCGGCAGTTTAGTGTTTCTAAATAT 57.444 30.769 3.88 0.00 46.16 1.28
1817 3523 9.656040 TTCGGCAGTTTAGTGTTTCTAAATATA 57.344 29.630 3.88 0.00 46.16 0.86
1818 3524 9.656040 TCGGCAGTTTAGTGTTTCTAAATATAA 57.344 29.630 3.88 0.00 46.16 0.98
1819 3525 9.916397 CGGCAGTTTAGTGTTTCTAAATATAAG 57.084 33.333 3.88 0.00 46.16 1.73
1862 3568 3.742433 TTTTTGCATGGATTTGACGGT 57.258 38.095 0.00 0.00 0.00 4.83
1863 3569 4.855715 TTTTTGCATGGATTTGACGGTA 57.144 36.364 0.00 0.00 0.00 4.02
1864 3570 5.398603 TTTTTGCATGGATTTGACGGTAT 57.601 34.783 0.00 0.00 0.00 2.73
1865 3571 6.516739 TTTTTGCATGGATTTGACGGTATA 57.483 33.333 0.00 0.00 0.00 1.47
1866 3572 6.516739 TTTTGCATGGATTTGACGGTATAA 57.483 33.333 0.00 0.00 0.00 0.98
1867 3573 6.707440 TTTGCATGGATTTGACGGTATAAT 57.293 33.333 0.00 0.00 0.00 1.28
1868 3574 6.707440 TTGCATGGATTTGACGGTATAATT 57.293 33.333 0.00 0.00 0.00 1.40
1869 3575 6.707440 TGCATGGATTTGACGGTATAATTT 57.293 33.333 0.00 0.00 0.00 1.82
1870 3576 7.809546 TGCATGGATTTGACGGTATAATTTA 57.190 32.000 0.00 0.00 0.00 1.40
1871 3577 8.226819 TGCATGGATTTGACGGTATAATTTAA 57.773 30.769 0.00 0.00 0.00 1.52
1872 3578 8.687242 TGCATGGATTTGACGGTATAATTTAAA 58.313 29.630 0.00 0.00 0.00 1.52
1873 3579 8.964150 GCATGGATTTGACGGTATAATTTAAAC 58.036 33.333 0.00 0.00 0.00 2.01
1877 3583 8.964150 GGATTTGACGGTATAATTTAAACATGC 58.036 33.333 0.00 0.00 0.00 4.06
1878 3584 8.865590 ATTTGACGGTATAATTTAAACATGCC 57.134 30.769 8.07 8.07 0.00 4.40
1879 3585 7.392494 TTGACGGTATAATTTAAACATGCCA 57.608 32.000 14.92 0.00 0.00 4.92
1880 3586 7.392494 TGACGGTATAATTTAAACATGCCAA 57.608 32.000 14.92 2.67 0.00 4.52
1881 3587 7.827701 TGACGGTATAATTTAAACATGCCAAA 58.172 30.769 14.92 0.00 0.00 3.28
1882 3588 8.304596 TGACGGTATAATTTAAACATGCCAAAA 58.695 29.630 14.92 0.00 0.00 2.44
1883 3589 8.468720 ACGGTATAATTTAAACATGCCAAAAC 57.531 30.769 14.92 0.00 0.00 2.43
1884 3590 7.273815 ACGGTATAATTTAAACATGCCAAAACG 59.726 33.333 14.92 4.42 0.00 3.60
1885 3591 7.273815 CGGTATAATTTAAACATGCCAAAACGT 59.726 33.333 14.92 0.00 0.00 3.99
1886 3592 8.927721 GGTATAATTTAAACATGCCAAAACGTT 58.072 29.630 11.59 0.00 0.00 3.99
1905 3611 5.895216 CGTTTTACGTTAGAAACAGAGGT 57.105 39.130 16.70 0.00 36.74 3.85
1906 3612 6.991485 CGTTTTACGTTAGAAACAGAGGTA 57.009 37.500 16.70 0.00 36.74 3.08
1907 3613 7.031046 CGTTTTACGTTAGAAACAGAGGTAG 57.969 40.000 16.70 1.95 36.74 3.18
1908 3614 6.638468 CGTTTTACGTTAGAAACAGAGGTAGT 59.362 38.462 16.70 0.00 36.74 2.73
1909 3615 7.803189 CGTTTTACGTTAGAAACAGAGGTAGTA 59.197 37.037 16.70 0.00 36.74 1.82
1910 3616 8.906693 GTTTTACGTTAGAAACAGAGGTAGTAC 58.093 37.037 13.58 0.00 36.15 2.73
1920 3626 1.965935 GAGGTAGTACTCCCTCCGTC 58.034 60.000 21.08 0.00 41.22 4.79
1923 3629 0.257039 GTAGTACTCCCTCCGTCCCA 59.743 60.000 0.00 0.00 0.00 4.37
1924 3630 0.257039 TAGTACTCCCTCCGTCCCAC 59.743 60.000 0.00 0.00 0.00 4.61
1931 3637 2.969950 CTCCCTCCGTCCCACAATATAA 59.030 50.000 0.00 0.00 0.00 0.98
1933 3639 2.969950 CCCTCCGTCCCACAATATAAGA 59.030 50.000 0.00 0.00 0.00 2.10
1934 3640 3.006967 CCCTCCGTCCCACAATATAAGAG 59.993 52.174 0.00 0.00 0.00 2.85
1935 3641 3.555168 CCTCCGTCCCACAATATAAGAGC 60.555 52.174 0.00 0.00 0.00 4.09
1936 3642 2.035449 TCCGTCCCACAATATAAGAGCG 59.965 50.000 0.00 0.00 0.00 5.03
1937 3643 2.223971 CCGTCCCACAATATAAGAGCGT 60.224 50.000 0.00 0.00 0.00 5.07
1938 3644 3.454375 CGTCCCACAATATAAGAGCGTT 58.546 45.455 0.00 0.00 0.00 4.84
1940 3646 4.331717 CGTCCCACAATATAAGAGCGTTTT 59.668 41.667 0.00 0.00 0.00 2.43
1941 3647 5.163794 CGTCCCACAATATAAGAGCGTTTTT 60.164 40.000 0.00 0.00 0.00 1.94
1942 3648 6.027749 GTCCCACAATATAAGAGCGTTTTTG 58.972 40.000 0.00 0.00 0.00 2.44
1943 3649 5.941058 TCCCACAATATAAGAGCGTTTTTGA 59.059 36.000 0.00 0.00 0.00 2.69
1944 3650 6.027749 CCCACAATATAAGAGCGTTTTTGAC 58.972 40.000 0.00 0.00 0.00 3.18
1945 3651 6.348950 CCCACAATATAAGAGCGTTTTTGACA 60.349 38.462 0.00 0.00 0.00 3.58
1946 3652 6.523201 CCACAATATAAGAGCGTTTTTGACAC 59.477 38.462 0.00 0.00 0.00 3.67
1948 3654 8.440059 CACAATATAAGAGCGTTTTTGACACTA 58.560 33.333 0.00 0.00 0.00 2.74
1949 3655 8.440833 ACAATATAAGAGCGTTTTTGACACTAC 58.559 33.333 0.00 0.00 0.00 2.73
1951 3657 8.718102 ATATAAGAGCGTTTTTGACACTACAT 57.282 30.769 0.00 0.00 0.00 2.29
1952 3658 5.751243 AAGAGCGTTTTTGACACTACATT 57.249 34.783 0.00 0.00 0.00 2.71
1954 3660 6.854496 AGAGCGTTTTTGACACTACATTAA 57.146 33.333 0.00 0.00 0.00 1.40
1956 3662 7.298122 AGAGCGTTTTTGACACTACATTAATG 58.702 34.615 14.01 14.01 0.00 1.90
1957 3663 6.966021 AGCGTTTTTGACACTACATTAATGT 58.034 32.000 23.80 23.80 44.48 2.71
1966 3672 7.248381 GACACTACATTAATGTCAAAAACGC 57.752 36.000 24.00 4.91 41.94 4.84
1967 3673 6.966021 ACACTACATTAATGTCAAAAACGCT 58.034 32.000 24.00 0.00 41.97 5.07
1978 3764 8.673626 AATGTCAAAAACGCTCTTATATTGTG 57.326 30.769 0.00 0.00 0.00 3.33
1980 3766 6.027749 GTCAAAAACGCTCTTATATTGTGGG 58.972 40.000 0.00 0.00 0.00 4.61
1997 3783 1.572415 TGGGACGGAGGGAGTAGTATT 59.428 52.381 0.00 0.00 0.00 1.89
2012 3800 5.539048 AGTAGTATTTACGGCCATTAGCAG 58.461 41.667 2.24 0.00 46.50 4.24
2013 3801 3.139077 AGTATTTACGGCCATTAGCAGC 58.861 45.455 2.24 0.00 46.50 5.25
2017 3805 3.485463 TTACGGCCATTAGCAGCTAAT 57.515 42.857 20.31 20.31 46.50 1.73
2033 3821 7.000472 AGCAGCTAATTTCCATATGTATGTGT 59.000 34.615 0.00 0.00 31.82 3.72
2069 3857 5.598005 AGATCTGCTTCTAGTACATTGCTCT 59.402 40.000 0.00 0.00 0.00 4.09
2070 3858 5.255710 TCTGCTTCTAGTACATTGCTCTC 57.744 43.478 0.00 0.00 0.00 3.20
2111 3902 7.184862 ACCTTCATCCTTTATTCTTGGACAAT 58.815 34.615 0.00 0.00 32.16 2.71
2170 3961 5.010012 AGTTTCAAATGAACTTCGCAGGATT 59.990 36.000 0.00 0.00 33.13 3.01
2192 3983 4.460263 TGCAGTCCTTACACAACATTTCT 58.540 39.130 0.00 0.00 0.00 2.52
2216 4010 7.545265 TCTTATATTGCTTGTTTGATTTGTGGC 59.455 33.333 0.00 0.00 0.00 5.01
2217 4011 1.850377 TGCTTGTTTGATTTGTGGCG 58.150 45.000 0.00 0.00 0.00 5.69
2219 4013 2.159184 TGCTTGTTTGATTTGTGGCGAA 60.159 40.909 0.00 0.00 0.00 4.70
2233 4027 3.936453 TGTGGCGAACATTCCATAGTAAC 59.064 43.478 0.00 0.00 34.47 2.50
2240 4034 6.199531 GCGAACATTCCATAGTAACGATGTAA 59.800 38.462 0.00 0.00 0.00 2.41
2244 4038 7.553334 ACATTCCATAGTAACGATGTAACAGT 58.447 34.615 0.00 0.00 0.00 3.55
2245 4039 8.689061 ACATTCCATAGTAACGATGTAACAGTA 58.311 33.333 0.00 0.00 0.00 2.74
2326 4121 6.015940 ACAAATCAGTTCATTTCTTCTGTCCC 60.016 38.462 0.00 0.00 0.00 4.46
2331 4126 3.053831 TCATTTCTTCTGTCCCGGTTC 57.946 47.619 0.00 0.00 0.00 3.62
2333 4128 3.072476 TCATTTCTTCTGTCCCGGTTCTT 59.928 43.478 0.00 0.00 0.00 2.52
2408 4204 9.817809 CCTAAATAGTTGATTGCTACTGACTTA 57.182 33.333 0.00 0.00 32.42 2.24
2418 4214 8.314021 TGATTGCTACTGACTTAAATCTTCTCA 58.686 33.333 0.00 0.00 0.00 3.27
2428 4224 8.579006 TGACTTAAATCTTCTCAACATGCAAAT 58.421 29.630 0.00 0.00 0.00 2.32
2451 4247 1.065998 GCAAATCCAACATGCCACCAT 60.066 47.619 0.00 0.00 34.03 3.55
2558 4355 6.968904 CACCATGTATGCTACTCAAATTCAAC 59.031 38.462 0.00 0.00 0.00 3.18
2681 4478 8.266392 TCATTGAAATAATTGCAACCAATTCC 57.734 30.769 0.00 0.00 45.99 3.01
2711 4508 1.334243 ACGCGAGGTAACATCTCTAGC 59.666 52.381 15.93 0.00 41.41 3.42
2723 4520 9.849166 GGTAACATCTCTAGCTTATGTAGAATC 57.151 37.037 0.00 0.00 33.59 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.508545 CAGCGATGTCGTGGACTCT 59.491 57.895 4.20 0.00 42.22 3.24
1 2 2.161486 GCAGCGATGTCGTGGACTC 61.161 63.158 1.22 0.00 42.22 3.36
2 3 2.125912 GCAGCGATGTCGTGGACT 60.126 61.111 1.22 0.00 42.22 3.85
3 4 1.565156 TTTGCAGCGATGTCGTGGAC 61.565 55.000 1.22 0.00 42.22 4.02
4 5 0.673333 ATTTGCAGCGATGTCGTGGA 60.673 50.000 1.22 0.49 42.22 4.02
5 6 1.006086 TATTTGCAGCGATGTCGTGG 58.994 50.000 1.22 0.00 42.22 4.94
6 7 4.448891 CTTATATTTGCAGCGATGTCGTG 58.551 43.478 1.22 3.04 42.22 4.35
7 8 3.059597 GCTTATATTTGCAGCGATGTCGT 60.060 43.478 1.22 0.00 42.22 4.34
8 9 3.473367 GCTTATATTTGCAGCGATGTCG 58.527 45.455 1.22 0.00 43.27 4.35
9 10 3.250762 TGGCTTATATTTGCAGCGATGTC 59.749 43.478 1.22 0.00 34.09 3.06
10 11 3.213506 TGGCTTATATTTGCAGCGATGT 58.786 40.909 1.22 0.00 34.09 3.06
11 12 3.499537 TCTGGCTTATATTTGCAGCGATG 59.500 43.478 0.00 0.00 34.09 3.84
12 13 3.743521 TCTGGCTTATATTTGCAGCGAT 58.256 40.909 0.00 0.00 34.09 4.58
13 14 3.192541 TCTGGCTTATATTTGCAGCGA 57.807 42.857 0.00 0.00 34.09 4.93
14 15 3.969117 TTCTGGCTTATATTTGCAGCG 57.031 42.857 0.00 0.00 34.09 5.18
15 16 5.947443 CCTATTCTGGCTTATATTTGCAGC 58.053 41.667 0.00 0.00 0.00 5.25
28 29 3.931630 CGACAACATCGCCTATTCTGGC 61.932 54.545 0.00 0.00 45.52 4.85
29 30 1.860950 CGACAACATCGCCTATTCTGG 59.139 52.381 0.00 0.00 45.52 3.86
40 41 1.828832 CTAGACCGAGCGACAACATC 58.171 55.000 0.00 0.00 0.00 3.06
41 42 0.179134 GCTAGACCGAGCGACAACAT 60.179 55.000 0.00 0.00 31.57 2.71
42 43 1.211969 GCTAGACCGAGCGACAACA 59.788 57.895 0.00 0.00 31.57 3.33
43 44 4.074454 GCTAGACCGAGCGACAAC 57.926 61.111 0.00 0.00 31.57 3.32
49 50 1.269831 CCATGGTTAGCTAGACCGAGC 60.270 57.143 2.57 3.41 43.19 5.03
50 51 2.032620 ACCATGGTTAGCTAGACCGAG 58.967 52.381 13.00 11.87 40.13 4.63
51 52 2.154567 ACCATGGTTAGCTAGACCGA 57.845 50.000 13.00 8.85 40.13 4.69
52 53 2.981859 AACCATGGTTAGCTAGACCG 57.018 50.000 28.86 8.01 40.13 4.79
53 54 4.489306 AGAAACCATGGTTAGCTAGACC 57.511 45.455 30.01 14.61 37.35 3.85
54 55 5.363005 TCCTAGAAACCATGGTTAGCTAGAC 59.637 44.000 38.29 23.33 41.04 2.59
55 56 5.525484 TCCTAGAAACCATGGTTAGCTAGA 58.475 41.667 38.29 29.18 41.04 2.43
56 57 5.871396 TCCTAGAAACCATGGTTAGCTAG 57.129 43.478 34.42 34.42 39.82 3.42
57 58 5.724854 AGTTCCTAGAAACCATGGTTAGCTA 59.275 40.000 30.01 27.67 37.35 3.32
58 59 4.536489 AGTTCCTAGAAACCATGGTTAGCT 59.464 41.667 30.01 28.00 37.35 3.32
59 60 4.844884 AGTTCCTAGAAACCATGGTTAGC 58.155 43.478 30.01 23.23 37.35 3.09
60 61 5.105473 TCGAGTTCCTAGAAACCATGGTTAG 60.105 44.000 30.01 22.27 37.35 2.34
61 62 4.773674 TCGAGTTCCTAGAAACCATGGTTA 59.226 41.667 30.01 14.19 37.35 2.85
62 63 3.581332 TCGAGTTCCTAGAAACCATGGTT 59.419 43.478 24.86 24.86 40.45 3.67
63 64 3.056035 GTCGAGTTCCTAGAAACCATGGT 60.056 47.826 13.00 13.00 0.00 3.55
64 65 3.056107 TGTCGAGTTCCTAGAAACCATGG 60.056 47.826 11.19 11.19 0.00 3.66
65 66 4.188247 TGTCGAGTTCCTAGAAACCATG 57.812 45.455 0.00 0.00 0.00 3.66
66 67 4.322801 CCTTGTCGAGTTCCTAGAAACCAT 60.323 45.833 0.00 0.00 0.00 3.55
67 68 3.006537 CCTTGTCGAGTTCCTAGAAACCA 59.993 47.826 0.00 0.00 0.00 3.67
68 69 3.006644 ACCTTGTCGAGTTCCTAGAAACC 59.993 47.826 0.00 0.00 0.00 3.27
69 70 4.022155 AGACCTTGTCGAGTTCCTAGAAAC 60.022 45.833 0.00 0.00 37.67 2.78
70 71 4.150359 AGACCTTGTCGAGTTCCTAGAAA 58.850 43.478 0.00 0.00 37.67 2.52
71 72 3.764218 AGACCTTGTCGAGTTCCTAGAA 58.236 45.455 0.00 0.00 37.67 2.10
72 73 3.436577 AGACCTTGTCGAGTTCCTAGA 57.563 47.619 0.00 0.00 37.67 2.43
73 74 3.628487 CCTAGACCTTGTCGAGTTCCTAG 59.372 52.174 0.00 0.00 37.67 3.02
74 75 3.265221 TCCTAGACCTTGTCGAGTTCCTA 59.735 47.826 0.00 0.00 37.67 2.94
75 76 2.041350 TCCTAGACCTTGTCGAGTTCCT 59.959 50.000 0.00 0.00 37.67 3.36
76 77 2.164017 GTCCTAGACCTTGTCGAGTTCC 59.836 54.545 0.00 0.00 37.67 3.62
77 78 3.490800 GTCCTAGACCTTGTCGAGTTC 57.509 52.381 0.00 0.00 37.67 3.01
88 89 3.924922 TCCTAATTGGAGGTCCTAGACC 58.075 50.000 5.60 5.60 41.98 3.85
96 97 6.886203 AGGAGTTGGGTCCTAATTGGAGGT 62.886 50.000 0.00 0.00 45.83 3.85
97 98 4.404061 AGGAGTTGGGTCCTAATTGGAGG 61.404 52.174 0.00 0.00 45.83 4.30
98 99 2.846827 AGGAGTTGGGTCCTAATTGGAG 59.153 50.000 0.00 0.00 45.83 3.86
99 100 2.929301 AGGAGTTGGGTCCTAATTGGA 58.071 47.619 0.00 0.00 45.83 3.53
107 108 2.663196 CCACGAGGAGTTGGGTCC 59.337 66.667 0.00 0.00 36.89 4.46
108 109 2.663196 CCCACGAGGAGTTGGGTC 59.337 66.667 0.00 0.00 38.24 4.46
109 110 3.637273 GCCCACGAGGAGTTGGGT 61.637 66.667 8.44 0.00 40.81 4.51
110 111 4.760047 CGCCCACGAGGAGTTGGG 62.760 72.222 0.00 0.51 43.93 4.12
111 112 3.691342 TCGCCCACGAGGAGTTGG 61.691 66.667 0.00 0.00 45.12 3.77
120 121 1.076332 CCTTTAGAGTTTCGCCCACG 58.924 55.000 0.00 0.00 42.01 4.94
121 122 1.450025 CCCTTTAGAGTTTCGCCCAC 58.550 55.000 0.00 0.00 0.00 4.61
122 123 0.322187 GCCCTTTAGAGTTTCGCCCA 60.322 55.000 0.00 0.00 0.00 5.36
123 124 0.322187 TGCCCTTTAGAGTTTCGCCC 60.322 55.000 0.00 0.00 0.00 6.13
124 125 0.803117 GTGCCCTTTAGAGTTTCGCC 59.197 55.000 0.00 0.00 0.00 5.54
125 126 0.442699 CGTGCCCTTTAGAGTTTCGC 59.557 55.000 0.00 0.00 0.00 4.70
126 127 1.459592 CACGTGCCCTTTAGAGTTTCG 59.540 52.381 0.82 0.00 0.00 3.46
127 128 1.197036 GCACGTGCCCTTTAGAGTTTC 59.803 52.381 30.12 0.00 34.31 2.78
128 129 1.202770 AGCACGTGCCCTTTAGAGTTT 60.203 47.619 35.51 10.89 43.38 2.66
129 130 0.396811 AGCACGTGCCCTTTAGAGTT 59.603 50.000 35.51 11.45 43.38 3.01
130 131 0.320771 CAGCACGTGCCCTTTAGAGT 60.321 55.000 35.51 12.26 43.38 3.24
131 132 2.460330 CAGCACGTGCCCTTTAGAG 58.540 57.895 35.51 12.35 43.38 2.43
132 133 4.693532 CAGCACGTGCCCTTTAGA 57.306 55.556 35.51 0.00 43.38 2.10
150 151 0.704008 CATTGTGTTCGCGTGCAATG 59.296 50.000 21.89 21.89 41.09 2.82
151 152 0.310543 ACATTGTGTTCGCGTGCAAT 59.689 45.000 5.77 9.84 32.48 3.56
152 153 0.590984 CACATTGTGTTCGCGTGCAA 60.591 50.000 5.77 7.87 0.00 4.08
153 154 1.010238 CACATTGTGTTCGCGTGCA 60.010 52.632 5.77 3.31 0.00 4.57
154 155 1.725625 CCACATTGTGTTCGCGTGC 60.726 57.895 15.34 0.15 0.00 5.34
155 156 1.082169 CCCACATTGTGTTCGCGTG 60.082 57.895 15.34 0.00 0.00 5.34
156 157 2.903547 GCCCACATTGTGTTCGCGT 61.904 57.895 15.34 0.00 0.00 6.01
157 158 2.126888 GCCCACATTGTGTTCGCG 60.127 61.111 15.34 0.00 0.00 5.87
158 159 1.805428 AAGGCCCACATTGTGTTCGC 61.805 55.000 15.34 12.67 0.00 4.70
159 160 0.240945 GAAGGCCCACATTGTGTTCG 59.759 55.000 15.34 4.09 0.00 3.95
160 161 0.240945 CGAAGGCCCACATTGTGTTC 59.759 55.000 15.34 10.92 0.00 3.18
161 162 0.467290 ACGAAGGCCCACATTGTGTT 60.467 50.000 15.34 3.27 0.00 3.32
162 163 0.889186 GACGAAGGCCCACATTGTGT 60.889 55.000 15.34 0.00 0.00 3.72
163 164 0.606401 AGACGAAGGCCCACATTGTG 60.606 55.000 9.92 9.92 0.00 3.33
164 165 0.321653 GAGACGAAGGCCCACATTGT 60.322 55.000 0.00 0.00 0.00 2.71
165 166 1.026718 GGAGACGAAGGCCCACATTG 61.027 60.000 0.00 0.00 0.00 2.82
166 167 1.299976 GGAGACGAAGGCCCACATT 59.700 57.895 0.00 0.00 0.00 2.71
167 168 2.990479 GGAGACGAAGGCCCACAT 59.010 61.111 0.00 0.00 0.00 3.21
385 386 4.349930 ACACACTATTATATCACCACCCCC 59.650 45.833 0.00 0.00 0.00 5.40
386 387 5.562298 ACACACTATTATATCACCACCCC 57.438 43.478 0.00 0.00 0.00 4.95
387 388 7.980099 GCTATACACACTATTATATCACCACCC 59.020 40.741 0.00 0.00 0.00 4.61
388 389 8.528643 TGCTATACACACTATTATATCACCACC 58.471 37.037 0.00 0.00 0.00 4.61
389 390 9.923143 TTGCTATACACACTATTATATCACCAC 57.077 33.333 0.00 0.00 0.00 4.16
533 534 3.118738 TCTCAAAGGCCGACTTATCTTCC 60.119 47.826 0.00 0.00 38.85 3.46
535 536 3.515901 AGTCTCAAAGGCCGACTTATCTT 59.484 43.478 4.56 0.00 38.85 2.40
544 549 1.273606 TCTCTCAAGTCTCAAAGGCCG 59.726 52.381 0.00 0.00 0.00 6.13
572 577 3.243877 CGACATTAGTGATTTGAGGCGAG 59.756 47.826 0.00 0.00 0.00 5.03
600 625 2.622942 TGTGCAGGTTGAAGGAAATGTC 59.377 45.455 0.00 0.00 0.00 3.06
623 648 3.133003 ACCTCCGATTCACATACTTCCTG 59.867 47.826 0.00 0.00 0.00 3.86
677 702 3.614092 ACAATAGGAATCCAGCACAGTG 58.386 45.455 0.61 0.00 0.00 3.66
820 849 2.437200 TTTCAAGCGGGAAATTGCTG 57.563 45.000 2.27 0.00 41.46 4.41
847 876 2.048503 AACGTCTTCTTCGGGGCG 60.049 61.111 0.00 0.00 0.00 6.13
894 923 6.122964 ACTGTTTATAGGGCAGAAATTCCTC 58.877 40.000 0.00 0.00 34.60 3.71
926 955 3.788227 ACTTACACACACCATGACCAT 57.212 42.857 0.00 0.00 0.00 3.55
935 964 4.416505 AGTCGTAGCTACTTACACACAC 57.583 45.455 21.20 5.44 0.00 3.82
1131 2616 2.755650 CACGATAAGCTGGTGGTATCC 58.244 52.381 0.00 0.00 30.52 2.59
1165 2650 2.009774 CAAGGACGATGATGTGGGAAC 58.990 52.381 0.00 0.00 0.00 3.62
1557 3258 1.651240 CCAGCACCTTGATCTTGGCG 61.651 60.000 0.00 0.00 0.00 5.69
1668 3369 2.821366 GGCACGATGAGCACCAGG 60.821 66.667 0.00 0.00 0.00 4.45
1714 3415 4.080299 GTCCCAGAAGTATTTCCCACAGAT 60.080 45.833 0.00 0.00 33.64 2.90
1770 3476 9.545611 GCCGAAACGTCTTATATTTTAAAAGAA 57.454 29.630 6.79 0.00 31.41 2.52
1771 3477 8.719648 TGCCGAAACGTCTTATATTTTAAAAGA 58.280 29.630 6.79 1.89 0.00 2.52
1772 3478 8.883789 TGCCGAAACGTCTTATATTTTAAAAG 57.116 30.769 6.79 0.00 0.00 2.27
1773 3479 8.505625 ACTGCCGAAACGTCTTATATTTTAAAA 58.494 29.630 2.51 2.51 0.00 1.52
1774 3480 8.031848 ACTGCCGAAACGTCTTATATTTTAAA 57.968 30.769 0.00 0.00 0.00 1.52
1775 3481 7.599630 ACTGCCGAAACGTCTTATATTTTAA 57.400 32.000 0.00 0.00 0.00 1.52
1776 3482 7.599630 AACTGCCGAAACGTCTTATATTTTA 57.400 32.000 0.00 0.00 0.00 1.52
1777 3483 6.490566 AACTGCCGAAACGTCTTATATTTT 57.509 33.333 0.00 0.00 0.00 1.82
1778 3484 6.490566 AAACTGCCGAAACGTCTTATATTT 57.509 33.333 0.00 0.00 0.00 1.40
1779 3485 6.815142 ACTAAACTGCCGAAACGTCTTATATT 59.185 34.615 0.00 0.00 0.00 1.28
1780 3486 6.255020 CACTAAACTGCCGAAACGTCTTATAT 59.745 38.462 0.00 0.00 0.00 0.86
1781 3487 5.574055 CACTAAACTGCCGAAACGTCTTATA 59.426 40.000 0.00 0.00 0.00 0.98
1782 3488 4.387862 CACTAAACTGCCGAAACGTCTTAT 59.612 41.667 0.00 0.00 0.00 1.73
1783 3489 3.737266 CACTAAACTGCCGAAACGTCTTA 59.263 43.478 0.00 0.00 0.00 2.10
1784 3490 2.542595 CACTAAACTGCCGAAACGTCTT 59.457 45.455 0.00 0.00 0.00 3.01
1785 3491 2.132762 CACTAAACTGCCGAAACGTCT 58.867 47.619 0.00 0.00 0.00 4.18
1786 3492 1.862827 ACACTAAACTGCCGAAACGTC 59.137 47.619 0.00 0.00 0.00 4.34
1787 3493 1.944032 ACACTAAACTGCCGAAACGT 58.056 45.000 0.00 0.00 0.00 3.99
1788 3494 3.001939 AGAAACACTAAACTGCCGAAACG 59.998 43.478 0.00 0.00 0.00 3.60
1789 3495 4.547406 AGAAACACTAAACTGCCGAAAC 57.453 40.909 0.00 0.00 0.00 2.78
1790 3496 6.680874 TTTAGAAACACTAAACTGCCGAAA 57.319 33.333 0.00 0.00 43.45 3.46
1842 3548 3.742433 ACCGTCAAATCCATGCAAAAA 57.258 38.095 0.00 0.00 0.00 1.94
1843 3549 6.516739 TTATACCGTCAAATCCATGCAAAA 57.483 33.333 0.00 0.00 0.00 2.44
1844 3550 6.707440 ATTATACCGTCAAATCCATGCAAA 57.293 33.333 0.00 0.00 0.00 3.68
1845 3551 6.707440 AATTATACCGTCAAATCCATGCAA 57.293 33.333 0.00 0.00 0.00 4.08
1846 3552 6.707440 AAATTATACCGTCAAATCCATGCA 57.293 33.333 0.00 0.00 0.00 3.96
1847 3553 8.964150 GTTTAAATTATACCGTCAAATCCATGC 58.036 33.333 0.00 0.00 0.00 4.06
1851 3557 8.964150 GCATGTTTAAATTATACCGTCAAATCC 58.036 33.333 0.00 0.00 0.00 3.01
1852 3558 8.964150 GGCATGTTTAAATTATACCGTCAAATC 58.036 33.333 0.00 0.00 0.00 2.17
1853 3559 8.470805 TGGCATGTTTAAATTATACCGTCAAAT 58.529 29.630 0.00 0.00 0.00 2.32
1854 3560 7.827701 TGGCATGTTTAAATTATACCGTCAAA 58.172 30.769 0.00 0.00 0.00 2.69
1855 3561 7.392494 TGGCATGTTTAAATTATACCGTCAA 57.608 32.000 0.00 0.00 0.00 3.18
1856 3562 7.392494 TTGGCATGTTTAAATTATACCGTCA 57.608 32.000 0.00 0.00 0.00 4.35
1857 3563 8.588789 GTTTTGGCATGTTTAAATTATACCGTC 58.411 33.333 0.00 0.00 0.00 4.79
1858 3564 7.273815 CGTTTTGGCATGTTTAAATTATACCGT 59.726 33.333 0.00 0.00 0.00 4.83
1859 3565 7.273815 ACGTTTTGGCATGTTTAAATTATACCG 59.726 33.333 0.00 0.00 0.00 4.02
1860 3566 8.468720 ACGTTTTGGCATGTTTAAATTATACC 57.531 30.769 0.00 0.00 0.00 2.73
1865 3571 7.846592 CGTAAAACGTTTTGGCATGTTTAAATT 59.153 29.630 31.26 6.28 35.27 1.82
1866 3572 7.338462 CGTAAAACGTTTTGGCATGTTTAAAT 58.662 30.769 31.26 6.90 35.27 1.40
1867 3573 6.693342 CGTAAAACGTTTTGGCATGTTTAAA 58.307 32.000 31.26 8.25 35.27 1.52
1868 3574 6.257169 CGTAAAACGTTTTGGCATGTTTAA 57.743 33.333 31.26 8.74 35.27 1.52
1869 3575 5.868177 CGTAAAACGTTTTGGCATGTTTA 57.132 34.783 31.26 9.44 35.27 2.01
1870 3576 4.763594 CGTAAAACGTTTTGGCATGTTT 57.236 36.364 31.26 8.70 37.46 2.83
1884 3590 7.936950 ACTACCTCTGTTTCTAACGTAAAAC 57.063 36.000 11.92 11.92 36.21 2.43
1885 3591 8.850156 AGTACTACCTCTGTTTCTAACGTAAAA 58.150 33.333 0.00 0.00 0.00 1.52
1886 3592 8.396272 AGTACTACCTCTGTTTCTAACGTAAA 57.604 34.615 0.00 0.00 0.00 2.01
1887 3593 7.119846 GGAGTACTACCTCTGTTTCTAACGTAA 59.880 40.741 0.00 0.00 0.00 3.18
1888 3594 6.595716 GGAGTACTACCTCTGTTTCTAACGTA 59.404 42.308 0.00 0.00 0.00 3.57
1889 3595 5.414144 GGAGTACTACCTCTGTTTCTAACGT 59.586 44.000 0.00 0.00 0.00 3.99
1890 3596 5.163673 GGGAGTACTACCTCTGTTTCTAACG 60.164 48.000 17.74 0.00 0.00 3.18
1891 3597 5.951148 AGGGAGTACTACCTCTGTTTCTAAC 59.049 44.000 22.04 0.00 40.91 2.34
1892 3598 6.150034 AGGGAGTACTACCTCTGTTTCTAA 57.850 41.667 22.04 0.00 40.91 2.10
1893 3599 5.793034 AGGGAGTACTACCTCTGTTTCTA 57.207 43.478 22.04 0.00 40.91 2.10
1894 3600 4.678538 AGGGAGTACTACCTCTGTTTCT 57.321 45.455 22.04 0.00 40.91 2.52
1903 3609 0.467106 GGGACGGAGGGAGTACTACC 60.467 65.000 17.30 17.30 0.00 3.18
1904 3610 0.257039 TGGGACGGAGGGAGTACTAC 59.743 60.000 0.00 0.00 0.00 2.73
1905 3611 0.257039 GTGGGACGGAGGGAGTACTA 59.743 60.000 0.00 0.00 0.00 1.82
1906 3612 1.000107 GTGGGACGGAGGGAGTACT 60.000 63.158 0.00 0.00 0.00 2.73
1907 3613 0.901580 TTGTGGGACGGAGGGAGTAC 60.902 60.000 0.00 0.00 0.00 2.73
1908 3614 0.042131 ATTGTGGGACGGAGGGAGTA 59.958 55.000 0.00 0.00 0.00 2.59
1909 3615 0.042131 TATTGTGGGACGGAGGGAGT 59.958 55.000 0.00 0.00 0.00 3.85
1910 3616 1.424638 ATATTGTGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
1920 3626 6.027749 GTCAAAAACGCTCTTATATTGTGGG 58.972 40.000 0.00 0.00 0.00 4.61
1923 3629 7.435068 AGTGTCAAAAACGCTCTTATATTGT 57.565 32.000 0.00 0.00 45.69 2.71
1924 3630 8.440059 TGTAGTGTCAAAAACGCTCTTATATTG 58.560 33.333 0.00 0.00 45.69 1.90
1931 3637 6.854496 TTAATGTAGTGTCAAAAACGCTCT 57.146 33.333 0.00 0.00 45.69 4.09
1934 3640 7.248381 GACATTAATGTAGTGTCAAAAACGC 57.752 36.000 20.83 0.15 42.77 4.84
1942 3648 7.075741 AGCGTTTTTGACATTAATGTAGTGTC 58.924 34.615 20.83 9.87 43.31 3.67
1943 3649 6.966021 AGCGTTTTTGACATTAATGTAGTGT 58.034 32.000 20.83 0.00 41.95 3.55
1944 3650 7.298122 AGAGCGTTTTTGACATTAATGTAGTG 58.702 34.615 20.83 8.21 41.95 2.74
1945 3651 7.435068 AGAGCGTTTTTGACATTAATGTAGT 57.565 32.000 20.83 0.00 41.95 2.73
1946 3652 9.988350 ATAAGAGCGTTTTTGACATTAATGTAG 57.012 29.630 20.83 7.93 41.95 2.74
1952 3658 9.767684 CACAATATAAGAGCGTTTTTGACATTA 57.232 29.630 0.00 0.00 0.00 1.90
1954 3660 7.250569 CCACAATATAAGAGCGTTTTTGACAT 58.749 34.615 0.00 0.00 0.00 3.06
1956 3662 6.027749 CCCACAATATAAGAGCGTTTTTGAC 58.972 40.000 0.00 0.00 0.00 3.18
1957 3663 5.941058 TCCCACAATATAAGAGCGTTTTTGA 59.059 36.000 0.00 0.00 0.00 2.69
1959 3665 5.163794 CGTCCCACAATATAAGAGCGTTTTT 60.164 40.000 0.00 0.00 0.00 1.94
1961 3667 3.869246 CGTCCCACAATATAAGAGCGTTT 59.131 43.478 0.00 0.00 0.00 3.60
1963 3669 2.223971 CCGTCCCACAATATAAGAGCGT 60.224 50.000 0.00 0.00 0.00 5.07
1964 3670 2.035449 TCCGTCCCACAATATAAGAGCG 59.965 50.000 0.00 0.00 0.00 5.03
1965 3671 3.555168 CCTCCGTCCCACAATATAAGAGC 60.555 52.174 0.00 0.00 0.00 4.09
1966 3672 3.006967 CCCTCCGTCCCACAATATAAGAG 59.993 52.174 0.00 0.00 0.00 2.85
1967 3673 2.969950 CCCTCCGTCCCACAATATAAGA 59.030 50.000 0.00 0.00 0.00 2.10
1976 3762 0.257039 TACTACTCCCTCCGTCCCAC 59.743 60.000 0.00 0.00 0.00 4.61
1977 3763 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
1978 3764 2.378378 AATACTACTCCCTCCGTCCC 57.622 55.000 0.00 0.00 0.00 4.46
1980 3766 3.251972 CCGTAAATACTACTCCCTCCGTC 59.748 52.174 0.00 0.00 0.00 4.79
1997 3783 2.992124 TTAGCTGCTAATGGCCGTAA 57.008 45.000 17.67 0.00 40.92 3.18
2033 3821 8.922237 ACTAGAAGCAGATCTCTCAATTAATCA 58.078 33.333 0.00 0.00 0.00 2.57
2069 3857 3.973206 AGGTACACAAATCATCCACGA 57.027 42.857 0.00 0.00 0.00 4.35
2070 3858 4.000325 TGAAGGTACACAAATCATCCACG 59.000 43.478 0.00 0.00 0.00 4.94
2095 3885 9.712305 ACCGATAGATATTGTCCAAGAATAAAG 57.288 33.333 0.00 0.00 39.76 1.85
2111 3902 1.632409 AGGCCCTACGACCGATAGATA 59.368 52.381 0.00 0.00 39.76 1.98
2115 3906 0.184451 AAGAGGCCCTACGACCGATA 59.816 55.000 0.00 0.00 0.00 2.92
2170 3961 4.460263 AGAAATGTTGTGTAAGGACTGCA 58.540 39.130 0.00 0.00 0.00 4.41
2192 3983 6.309980 CGCCACAAATCAAACAAGCAATATAA 59.690 34.615 0.00 0.00 0.00 0.98
2216 4010 7.221259 TGTTACATCGTTACTATGGAATGTTCG 59.779 37.037 0.00 0.00 30.08 3.95
2217 4011 8.415192 TGTTACATCGTTACTATGGAATGTTC 57.585 34.615 0.00 0.00 30.08 3.18
2219 4013 7.553334 ACTGTTACATCGTTACTATGGAATGT 58.447 34.615 0.00 0.00 30.08 2.71
2240 4034 9.673454 GTTTGGATTCTTACGAAATTTTACTGT 57.327 29.630 0.00 0.00 31.91 3.55
2244 4038 7.324135 GCGTGTTTGGATTCTTACGAAATTTTA 59.676 33.333 0.00 0.00 33.78 1.52
2245 4039 6.143278 GCGTGTTTGGATTCTTACGAAATTTT 59.857 34.615 0.00 0.00 33.78 1.82
2267 4061 1.375551 AAACAAAGTTCGTGGAGCGT 58.624 45.000 0.00 0.00 42.13 5.07
2268 4062 2.468532 AAAACAAAGTTCGTGGAGCG 57.531 45.000 0.00 0.00 43.01 5.03
2269 4063 4.281525 TGTAAAACAAAGTTCGTGGAGC 57.718 40.909 0.00 0.00 0.00 4.70
2271 4065 5.504337 CGGATTGTAAAACAAAGTTCGTGGA 60.504 40.000 0.00 0.00 41.96 4.02
2285 4080 7.484975 ACTGATTTGTTTCAACGGATTGTAAA 58.515 30.769 0.00 0.00 37.11 2.01
2326 4121 2.664916 CATGTGCAAAAGGAAGAACCG 58.335 47.619 0.00 0.00 44.74 4.44
2389 4185 8.854614 AAGATTTAAGTCAGTAGCAATCAACT 57.145 30.769 0.44 0.00 0.00 3.16
2428 4224 2.168106 GGTGGCATGTTGGATTTGCATA 59.832 45.455 0.00 0.00 38.12 3.14
2433 4229 1.065998 GCATGGTGGCATGTTGGATTT 60.066 47.619 0.00 0.00 35.16 2.17
2437 4233 3.378767 TGCATGGTGGCATGTTGG 58.621 55.556 0.00 0.00 39.25 3.77
2471 4267 3.628032 TGAGTTGACACGGTTGCATTAAA 59.372 39.130 0.00 0.00 0.00 1.52
2519 4315 6.534793 GCATACATGGTGAATTTTAAAGGTGG 59.465 38.462 0.00 0.00 0.00 4.61
2532 4329 6.413892 TGAATTTGAGTAGCATACATGGTGA 58.586 36.000 4.21 0.00 46.26 4.02
2603 4400 9.778741 AGATTAACATTGTGAGAGTTGAAACTA 57.221 29.630 0.00 0.00 39.88 2.24
2604 4401 8.682936 AGATTAACATTGTGAGAGTTGAAACT 57.317 30.769 0.00 0.00 43.16 2.66
2681 4478 4.081030 CCTCGCGTGTTGCTGCAG 62.081 66.667 10.11 10.11 43.27 4.41
2711 4508 5.896073 AAGGGGTGAGGATTCTACATAAG 57.104 43.478 0.00 0.00 0.00 1.73
2723 4520 0.251742 TGCCATGAAAAGGGGTGAGG 60.252 55.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.