Multiple sequence alignment - TraesCS5D01G047200

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 TraesCS5D01G047200 chr5D 100.000 2846 0 0 1 2846 45484076 45486921 0.000000e+00 5256.0
1 TraesCS5D01G047200 chr5D 82.475 1301 182 20 742 1999 45492029 45493326 0.000000e+00 1098.0
2 TraesCS5D01G047200 chr5D 81.030 854 126 26 1536 2374 45499462 45500294 0.000000e+00 647.0
3 TraesCS5D01G047200 chr5A 91.765 2380 127 21 423 2761 36362406 36364757 0.000000e+00 3245.0
4 TraesCS5D01G047200 chr5A 87.241 290 33 3 742 1030 36368181 36368467 7.600000e-86 327.0
5 TraesCS5D01G047200 chr5A 89.764 254 23 1 1654 1904 36368468 36368721 3.540000e-84 322.0
6 TraesCS5D01G047200 chr5A 93.506 77 4 1 2761 2836 36364798 36364874 2.320000e-21 113.0
7 TraesCS5D01G047200 chr5A 93.617 47 1 2 232 276 605241770 605241816 5.090000e-08 69.4
8 TraesCS5D01G047200 chr5B 92.199 1346 76 12 325 1651 45534281 45535616 0.000000e+00 1877.0
9 TraesCS5D01G047200 chr5B 92.472 890 50 6 1645 2525 45536361 45537242 0.000000e+00 1256.0
10 TraesCS5D01G047200 chr5B 82.507 1069 139 16 741 1769 45540969 45542029 0.000000e+00 894.0
11 TraesCS5D01G047200 chr5B 77.741 602 95 28 1793 2376 45555554 45556134 1.630000e-87 333.0
12 TraesCS5D01G047200 chr5B 87.097 279 26 7 2566 2834 45537239 45537517 9.900000e-80 307.0
13 TraesCS5D01G047200 chr3D 97.561 41 0 1 237 276 377201863 377201903 5.090000e-08 69.4
14 TraesCS5D01G047200 chr3A 93.478 46 2 1 232 276 112940992 112940947 1.830000e-07 67.6
15 TraesCS5D01G047200 chr7A 97.436 39 0 1 239 276 187432441 187432479 6.580000e-07 65.8
16 TraesCS5D01G047200 chr6D 97.436 39 0 1 239 276 82969862 82969900 6.580000e-07 65.8
17 TraesCS5D01G047200 chr6D 97.436 39 0 1 239 276 410152903 410152941 6.580000e-07 65.8
18 TraesCS5D01G047200 chr6A 97.436 39 0 1 239 276 99787439 99787477 6.580000e-07 65.8
19 TraesCS5D01G047200 chr1D 97.436 39 0 1 239 276 303314694 303314732 6.580000e-07 65.8
20 TraesCS5D01G047200 chr1D 91.489 47 3 1 230 275 238320621 238320667 2.370000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G047200 chr5D 45484076 45486921 2845 False 5256.00 5256 100.00000 1 2846 1 chr5D.!!$F1 2845
1 TraesCS5D01G047200 chr5D 45492029 45493326 1297 False 1098.00 1098 82.47500 742 1999 1 chr5D.!!$F2 1257
2 TraesCS5D01G047200 chr5D 45499462 45500294 832 False 647.00 647 81.03000 1536 2374 1 chr5D.!!$F3 838
3 TraesCS5D01G047200 chr5A 36362406 36368721 6315 False 1001.75 3245 90.56900 423 2836 4 chr5A.!!$F2 2413
4 TraesCS5D01G047200 chr5B 45534281 45542029 7748 False 1083.50 1877 88.56875 325 2834 4 chr5B.!!$F2 2509
5 TraesCS5D01G047200 chr5B 45555554 45556134 580 False 333.00 333 77.74100 1793 2376 1 chr5B.!!$F1 583

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
252 253 0.106116 ACTGATACTCCCTCCGTCCC 60.106 60.0 0.0 0.0 0.0 4.46 F
253 254 0.106167 CTGATACTCCCTCCGTCCCA 60.106 60.0 0.0 0.0 0.0 4.37 F
258 259 0.328258 ACTCCCTCCGTCCCAAAATG 59.672 55.0 0.0 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1489 1518 0.033781 TTGCTGAATGGTGCTTTGCC 59.966 50.0 0.00 0.0 0.0 4.52 R
1569 1634 0.179018 GTTGGCTCTCCTGTTGTGGT 60.179 55.0 0.00 0.0 0.0 4.16 R
2000 2831 0.730840 CGGACCGACAATAAAAGCCC 59.269 55.0 8.64 0.0 0.0 5.19 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
22 23 3.810896 GGCGCGGCTAGGGTTTTG 61.811 66.667 27.05 0.00 34.93 2.44
23 24 2.744709 GCGCGGCTAGGGTTTTGA 60.745 61.111 8.83 0.00 34.93 2.69
24 25 3.035576 GCGCGGCTAGGGTTTTGAC 62.036 63.158 8.83 0.00 34.93 3.18
25 26 1.375523 CGCGGCTAGGGTTTTGACT 60.376 57.895 0.00 0.00 0.00 3.41
26 27 0.953960 CGCGGCTAGGGTTTTGACTT 60.954 55.000 0.00 0.00 0.00 3.01
27 28 0.521735 GCGGCTAGGGTTTTGACTTG 59.478 55.000 0.00 0.00 0.00 3.16
28 29 1.165270 CGGCTAGGGTTTTGACTTGG 58.835 55.000 0.00 0.00 0.00 3.61
29 30 1.545841 GGCTAGGGTTTTGACTTGGG 58.454 55.000 0.00 0.00 0.00 4.12
30 31 1.545841 GCTAGGGTTTTGACTTGGGG 58.454 55.000 0.00 0.00 0.00 4.96
31 32 1.545841 CTAGGGTTTTGACTTGGGGC 58.454 55.000 0.00 0.00 0.00 5.80
32 33 1.075536 CTAGGGTTTTGACTTGGGGCT 59.924 52.381 0.00 0.00 0.00 5.19
33 34 0.469892 AGGGTTTTGACTTGGGGCTG 60.470 55.000 0.00 0.00 0.00 4.85
34 35 1.471829 GGGTTTTGACTTGGGGCTGG 61.472 60.000 0.00 0.00 0.00 4.85
35 36 0.759060 GGTTTTGACTTGGGGCTGGT 60.759 55.000 0.00 0.00 0.00 4.00
36 37 1.119684 GTTTTGACTTGGGGCTGGTT 58.880 50.000 0.00 0.00 0.00 3.67
37 38 1.484653 GTTTTGACTTGGGGCTGGTTT 59.515 47.619 0.00 0.00 0.00 3.27
38 39 1.408969 TTTGACTTGGGGCTGGTTTC 58.591 50.000 0.00 0.00 0.00 2.78
39 40 0.555769 TTGACTTGGGGCTGGTTTCT 59.444 50.000 0.00 0.00 0.00 2.52
40 41 0.555769 TGACTTGGGGCTGGTTTCTT 59.444 50.000 0.00 0.00 0.00 2.52
41 42 1.063266 TGACTTGGGGCTGGTTTCTTT 60.063 47.619 0.00 0.00 0.00 2.52
42 43 2.175931 TGACTTGGGGCTGGTTTCTTTA 59.824 45.455 0.00 0.00 0.00 1.85
43 44 3.181423 TGACTTGGGGCTGGTTTCTTTAT 60.181 43.478 0.00 0.00 0.00 1.40
44 45 3.832490 GACTTGGGGCTGGTTTCTTTATT 59.168 43.478 0.00 0.00 0.00 1.40
45 46 3.832490 ACTTGGGGCTGGTTTCTTTATTC 59.168 43.478 0.00 0.00 0.00 1.75
46 47 2.442413 TGGGGCTGGTTTCTTTATTCG 58.558 47.619 0.00 0.00 0.00 3.34
47 48 1.749063 GGGGCTGGTTTCTTTATTCGG 59.251 52.381 0.00 0.00 0.00 4.30
48 49 1.749063 GGGCTGGTTTCTTTATTCGGG 59.251 52.381 0.00 0.00 0.00 5.14
49 50 1.749063 GGCTGGTTTCTTTATTCGGGG 59.251 52.381 0.00 0.00 0.00 5.73
50 51 2.619590 GGCTGGTTTCTTTATTCGGGGA 60.620 50.000 0.00 0.00 0.00 4.81
51 52 2.683362 GCTGGTTTCTTTATTCGGGGAG 59.317 50.000 0.00 0.00 0.00 4.30
52 53 3.621461 GCTGGTTTCTTTATTCGGGGAGA 60.621 47.826 0.00 0.00 0.00 3.71
53 54 4.192317 CTGGTTTCTTTATTCGGGGAGAG 58.808 47.826 0.00 0.00 0.00 3.20
54 55 3.054655 TGGTTTCTTTATTCGGGGAGAGG 60.055 47.826 0.00 0.00 0.00 3.69
55 56 3.199289 GGTTTCTTTATTCGGGGAGAGGA 59.801 47.826 0.00 0.00 0.00 3.71
56 57 4.443621 GTTTCTTTATTCGGGGAGAGGAG 58.556 47.826 0.00 0.00 0.00 3.69
57 58 3.682592 TCTTTATTCGGGGAGAGGAGA 57.317 47.619 0.00 0.00 0.00 3.71
58 59 3.297736 TCTTTATTCGGGGAGAGGAGAC 58.702 50.000 0.00 0.00 0.00 3.36
59 60 1.688772 TTATTCGGGGAGAGGAGACG 58.311 55.000 0.00 0.00 0.00 4.18
60 61 0.549950 TATTCGGGGAGAGGAGACGT 59.450 55.000 0.00 0.00 0.00 4.34
61 62 0.549950 ATTCGGGGAGAGGAGACGTA 59.450 55.000 0.00 0.00 0.00 3.57
62 63 0.393537 TTCGGGGAGAGGAGACGTAC 60.394 60.000 0.00 0.00 0.00 3.67
63 64 1.077930 CGGGGAGAGGAGACGTACA 60.078 63.158 0.00 0.00 0.00 2.90
64 65 0.465824 CGGGGAGAGGAGACGTACAT 60.466 60.000 0.00 0.00 0.00 2.29
65 66 1.202734 CGGGGAGAGGAGACGTACATA 60.203 57.143 0.00 0.00 0.00 2.29
66 67 2.228925 GGGGAGAGGAGACGTACATAC 58.771 57.143 0.00 0.00 0.00 2.39
67 68 2.422519 GGGGAGAGGAGACGTACATACA 60.423 54.545 0.00 0.00 0.00 2.29
68 69 3.488363 GGGAGAGGAGACGTACATACAT 58.512 50.000 0.00 0.00 0.00 2.29
69 70 4.506271 GGGGAGAGGAGACGTACATACATA 60.506 50.000 0.00 0.00 0.00 2.29
70 71 5.254901 GGGAGAGGAGACGTACATACATAT 58.745 45.833 0.00 0.00 0.00 1.78
71 72 5.711036 GGGAGAGGAGACGTACATACATATT 59.289 44.000 0.00 0.00 0.00 1.28
72 73 6.127952 GGGAGAGGAGACGTACATACATATTC 60.128 46.154 0.00 0.00 0.00 1.75
73 74 6.402334 GGAGAGGAGACGTACATACATATTCG 60.402 46.154 0.00 0.00 0.00 3.34
74 75 5.411977 AGAGGAGACGTACATACATATTCGG 59.588 44.000 0.00 0.00 0.00 4.30
75 76 4.458295 AGGAGACGTACATACATATTCGGG 59.542 45.833 0.00 0.00 0.00 5.14
76 77 4.456911 GGAGACGTACATACATATTCGGGA 59.543 45.833 0.00 0.00 0.00 5.14
77 78 5.048504 GGAGACGTACATACATATTCGGGAA 60.049 44.000 0.00 0.00 0.00 3.97
78 79 6.349944 GGAGACGTACATACATATTCGGGAAT 60.350 42.308 0.00 0.00 34.93 3.01
79 80 6.989659 AGACGTACATACATATTCGGGAATT 58.010 36.000 0.00 0.00 32.50 2.17
80 81 7.439381 AGACGTACATACATATTCGGGAATTT 58.561 34.615 0.00 0.00 32.50 1.82
81 82 8.579006 AGACGTACATACATATTCGGGAATTTA 58.421 33.333 0.00 0.00 32.50 1.40
82 83 8.752766 ACGTACATACATATTCGGGAATTTAG 57.247 34.615 0.00 0.00 32.50 1.85
83 84 8.362639 ACGTACATACATATTCGGGAATTTAGT 58.637 33.333 0.00 0.00 32.50 2.24
84 85 8.644619 CGTACATACATATTCGGGAATTTAGTG 58.355 37.037 0.00 0.00 32.50 2.74
85 86 9.701098 GTACATACATATTCGGGAATTTAGTGA 57.299 33.333 0.00 0.00 32.50 3.41
86 87 8.603242 ACATACATATTCGGGAATTTAGTGAC 57.397 34.615 0.00 0.00 32.50 3.67
87 88 8.429641 ACATACATATTCGGGAATTTAGTGACT 58.570 33.333 0.00 0.00 32.50 3.41
88 89 9.923143 CATACATATTCGGGAATTTAGTGACTA 57.077 33.333 0.00 0.00 32.50 2.59
90 91 7.442656 ACATATTCGGGAATTTAGTGACTAGG 58.557 38.462 0.00 0.00 32.50 3.02
91 92 7.289317 ACATATTCGGGAATTTAGTGACTAGGA 59.711 37.037 0.00 0.00 32.50 2.94
92 93 6.555463 ATTCGGGAATTTAGTGACTAGGAA 57.445 37.500 0.00 0.00 0.00 3.36
93 94 5.334724 TCGGGAATTTAGTGACTAGGAAC 57.665 43.478 0.00 0.00 0.00 3.62
94 95 4.773674 TCGGGAATTTAGTGACTAGGAACA 59.226 41.667 0.00 0.00 0.00 3.18
95 96 5.246656 TCGGGAATTTAGTGACTAGGAACAA 59.753 40.000 0.00 0.00 0.00 2.83
96 97 5.935789 CGGGAATTTAGTGACTAGGAACAAA 59.064 40.000 0.00 0.00 0.00 2.83
97 98 6.598064 CGGGAATTTAGTGACTAGGAACAAAT 59.402 38.462 0.00 0.00 0.00 2.32
98 99 7.767198 CGGGAATTTAGTGACTAGGAACAAATA 59.233 37.037 0.00 0.00 0.00 1.40
99 100 9.457436 GGGAATTTAGTGACTAGGAACAAATAA 57.543 33.333 0.00 0.00 0.00 1.40
105 106 9.595823 TTAGTGACTAGGAACAAATAACTATGC 57.404 33.333 0.00 0.00 0.00 3.14
106 107 7.620880 AGTGACTAGGAACAAATAACTATGCA 58.379 34.615 0.00 0.00 0.00 3.96
107 108 7.766278 AGTGACTAGGAACAAATAACTATGCAG 59.234 37.037 0.00 0.00 0.00 4.41
108 109 7.764443 GTGACTAGGAACAAATAACTATGCAGA 59.236 37.037 0.00 0.00 0.00 4.26
109 110 8.486210 TGACTAGGAACAAATAACTATGCAGAT 58.514 33.333 0.00 0.00 0.00 2.90
110 111 9.982651 GACTAGGAACAAATAACTATGCAGATA 57.017 33.333 0.00 0.00 0.00 1.98
111 112 9.988815 ACTAGGAACAAATAACTATGCAGATAG 57.011 33.333 0.00 0.00 38.06 2.08
117 118 8.103948 ACAAATAACTATGCAGATAGAATGGC 57.896 34.615 1.33 0.00 35.90 4.40
118 119 7.175641 ACAAATAACTATGCAGATAGAATGGCC 59.824 37.037 0.00 0.00 35.90 5.36
119 120 4.989875 AACTATGCAGATAGAATGGCCT 57.010 40.909 3.32 0.00 35.90 5.19
120 121 4.989875 ACTATGCAGATAGAATGGCCTT 57.010 40.909 3.32 0.00 35.90 4.35
121 122 4.904241 ACTATGCAGATAGAATGGCCTTC 58.096 43.478 3.32 5.53 35.90 3.46
122 123 2.645838 TGCAGATAGAATGGCCTTCC 57.354 50.000 3.32 0.00 34.11 3.46
123 124 1.143684 TGCAGATAGAATGGCCTTCCC 59.856 52.381 3.32 0.00 34.11 3.97
124 125 1.423161 GCAGATAGAATGGCCTTCCCT 59.577 52.381 3.32 1.42 34.11 4.20
125 126 2.551938 GCAGATAGAATGGCCTTCCCTC 60.552 54.545 3.32 5.46 34.11 4.30
126 127 2.707791 CAGATAGAATGGCCTTCCCTCA 59.292 50.000 3.32 0.00 34.11 3.86
127 128 2.708325 AGATAGAATGGCCTTCCCTCAC 59.292 50.000 3.32 0.00 34.11 3.51
128 129 1.965414 TAGAATGGCCTTCCCTCACA 58.035 50.000 3.32 0.00 34.11 3.58
129 130 1.075601 AGAATGGCCTTCCCTCACAA 58.924 50.000 3.32 0.00 34.11 3.33
130 131 1.428912 AGAATGGCCTTCCCTCACAAA 59.571 47.619 3.32 0.00 34.11 2.83
131 132 2.158325 AGAATGGCCTTCCCTCACAAAA 60.158 45.455 3.32 0.00 34.11 2.44
132 133 2.397044 ATGGCCTTCCCTCACAAAAA 57.603 45.000 3.32 0.00 0.00 1.94
162 163 9.825109 ACTATGTAGAGAGAAATTTTAGCTTCC 57.175 33.333 0.00 0.00 0.00 3.46
163 164 9.267084 CTATGTAGAGAGAAATTTTAGCTTCCC 57.733 37.037 0.00 0.00 0.00 3.97
164 165 7.016153 TGTAGAGAGAAATTTTAGCTTCCCA 57.984 36.000 0.00 0.00 0.00 4.37
165 166 7.458397 TGTAGAGAGAAATTTTAGCTTCCCAA 58.542 34.615 0.00 0.00 0.00 4.12
166 167 7.942341 TGTAGAGAGAAATTTTAGCTTCCCAAA 59.058 33.333 0.00 0.00 0.00 3.28
167 168 7.220741 AGAGAGAAATTTTAGCTTCCCAAAC 57.779 36.000 0.00 0.00 0.00 2.93
168 169 6.777580 AGAGAGAAATTTTAGCTTCCCAAACA 59.222 34.615 0.00 0.00 0.00 2.83
169 170 7.452813 AGAGAGAAATTTTAGCTTCCCAAACAT 59.547 33.333 0.00 0.00 0.00 2.71
170 171 7.966812 AGAGAAATTTTAGCTTCCCAAACATT 58.033 30.769 0.00 0.00 0.00 2.71
171 172 7.874528 AGAGAAATTTTAGCTTCCCAAACATTG 59.125 33.333 0.00 0.00 0.00 2.82
172 173 7.508687 AGAAATTTTAGCTTCCCAAACATTGT 58.491 30.769 0.00 0.00 0.00 2.71
173 174 8.646900 AGAAATTTTAGCTTCCCAAACATTGTA 58.353 29.630 0.00 0.00 0.00 2.41
174 175 8.831715 AAATTTTAGCTTCCCAAACATTGTAG 57.168 30.769 0.00 0.00 0.00 2.74
175 176 6.969993 TTTTAGCTTCCCAAACATTGTAGT 57.030 33.333 0.00 0.00 0.00 2.73
176 177 6.569179 TTTAGCTTCCCAAACATTGTAGTC 57.431 37.500 0.00 0.00 0.00 2.59
177 178 3.421844 AGCTTCCCAAACATTGTAGTCC 58.578 45.455 0.00 0.00 0.00 3.85
178 179 3.153919 GCTTCCCAAACATTGTAGTCCA 58.846 45.455 0.00 0.00 0.00 4.02
179 180 3.763897 GCTTCCCAAACATTGTAGTCCAT 59.236 43.478 0.00 0.00 0.00 3.41
180 181 4.220602 GCTTCCCAAACATTGTAGTCCATT 59.779 41.667 0.00 0.00 0.00 3.16
181 182 5.279456 GCTTCCCAAACATTGTAGTCCATTT 60.279 40.000 0.00 0.00 0.00 2.32
182 183 6.739331 TTCCCAAACATTGTAGTCCATTTT 57.261 33.333 0.00 0.00 0.00 1.82
183 184 6.739331 TCCCAAACATTGTAGTCCATTTTT 57.261 33.333 0.00 0.00 0.00 1.94
184 185 6.754193 TCCCAAACATTGTAGTCCATTTTTC 58.246 36.000 0.00 0.00 0.00 2.29
185 186 6.325028 TCCCAAACATTGTAGTCCATTTTTCA 59.675 34.615 0.00 0.00 0.00 2.69
186 187 6.989169 CCCAAACATTGTAGTCCATTTTTCAA 59.011 34.615 0.00 0.00 0.00 2.69
187 188 7.042119 CCCAAACATTGTAGTCCATTTTTCAAC 60.042 37.037 0.00 0.00 0.00 3.18
188 189 7.493971 CCAAACATTGTAGTCCATTTTTCAACA 59.506 33.333 0.00 0.00 0.00 3.33
189 190 9.044150 CAAACATTGTAGTCCATTTTTCAACAT 57.956 29.630 0.00 0.00 0.00 2.71
190 191 8.816640 AACATTGTAGTCCATTTTTCAACATC 57.183 30.769 0.00 0.00 0.00 3.06
191 192 7.378181 ACATTGTAGTCCATTTTTCAACATCC 58.622 34.615 0.00 0.00 0.00 3.51
192 193 6.968263 TTGTAGTCCATTTTTCAACATCCA 57.032 33.333 0.00 0.00 0.00 3.41
193 194 6.968263 TGTAGTCCATTTTTCAACATCCAA 57.032 33.333 0.00 0.00 0.00 3.53
194 195 7.353414 TGTAGTCCATTTTTCAACATCCAAA 57.647 32.000 0.00 0.00 0.00 3.28
195 196 7.432869 TGTAGTCCATTTTTCAACATCCAAAG 58.567 34.615 0.00 0.00 0.00 2.77
196 197 6.484364 AGTCCATTTTTCAACATCCAAAGT 57.516 33.333 0.00 0.00 0.00 2.66
197 198 6.888105 AGTCCATTTTTCAACATCCAAAGTT 58.112 32.000 0.00 0.00 0.00 2.66
198 199 7.337938 AGTCCATTTTTCAACATCCAAAGTTT 58.662 30.769 0.00 0.00 0.00 2.66
199 200 7.828717 AGTCCATTTTTCAACATCCAAAGTTTT 59.171 29.630 0.00 0.00 0.00 2.43
200 201 8.458052 GTCCATTTTTCAACATCCAAAGTTTTT 58.542 29.630 0.00 0.00 0.00 1.94
230 231 9.613428 AAACATACAATCTTTATTCCATCGAGA 57.387 29.630 0.00 0.00 0.00 4.04
231 232 9.784531 AACATACAATCTTTATTCCATCGAGAT 57.215 29.630 0.00 0.00 0.00 2.75
236 237 9.265901 ACAATCTTTATTCCATCGAGATAACTG 57.734 33.333 0.00 0.00 0.00 3.16
237 238 9.481340 CAATCTTTATTCCATCGAGATAACTGA 57.519 33.333 0.00 0.00 0.00 3.41
243 244 6.576662 TTCCATCGAGATAACTGATACTCC 57.423 41.667 0.00 0.00 0.00 3.85
244 245 5.010933 TCCATCGAGATAACTGATACTCCC 58.989 45.833 0.00 0.00 0.00 4.30
245 246 5.013547 CCATCGAGATAACTGATACTCCCT 58.986 45.833 0.00 0.00 0.00 4.20
246 247 5.124776 CCATCGAGATAACTGATACTCCCTC 59.875 48.000 0.00 0.00 0.00 4.30
247 248 4.653868 TCGAGATAACTGATACTCCCTCC 58.346 47.826 0.00 0.00 0.00 4.30
248 249 3.437395 CGAGATAACTGATACTCCCTCCG 59.563 52.174 0.00 0.00 0.00 4.63
249 250 4.400120 GAGATAACTGATACTCCCTCCGT 58.600 47.826 0.00 0.00 0.00 4.69
250 251 4.400120 AGATAACTGATACTCCCTCCGTC 58.600 47.826 0.00 0.00 0.00 4.79
251 252 1.777941 AACTGATACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
252 253 0.106116 ACTGATACTCCCTCCGTCCC 60.106 60.000 0.00 0.00 0.00 4.46
253 254 0.106167 CTGATACTCCCTCCGTCCCA 60.106 60.000 0.00 0.00 0.00 4.37
254 255 0.337082 TGATACTCCCTCCGTCCCAA 59.663 55.000 0.00 0.00 0.00 4.12
255 256 1.273381 TGATACTCCCTCCGTCCCAAA 60.273 52.381 0.00 0.00 0.00 3.28
256 257 1.835531 GATACTCCCTCCGTCCCAAAA 59.164 52.381 0.00 0.00 0.00 2.44
257 258 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
258 259 0.328258 ACTCCCTCCGTCCCAAAATG 59.672 55.000 0.00 0.00 0.00 2.32
259 260 0.328258 CTCCCTCCGTCCCAAAATGT 59.672 55.000 0.00 0.00 0.00 2.71
260 261 1.557832 CTCCCTCCGTCCCAAAATGTA 59.442 52.381 0.00 0.00 0.00 2.29
261 262 1.986631 TCCCTCCGTCCCAAAATGTAA 59.013 47.619 0.00 0.00 0.00 2.41
262 263 2.026636 TCCCTCCGTCCCAAAATGTAAG 60.027 50.000 0.00 0.00 0.00 2.34
263 264 2.026636 CCCTCCGTCCCAAAATGTAAGA 60.027 50.000 0.00 0.00 0.00 2.10
264 265 3.371595 CCCTCCGTCCCAAAATGTAAGAT 60.372 47.826 0.00 0.00 0.00 2.40
265 266 3.877508 CCTCCGTCCCAAAATGTAAGATC 59.122 47.826 0.00 0.00 0.00 2.75
266 267 4.513442 CTCCGTCCCAAAATGTAAGATCA 58.487 43.478 0.00 0.00 0.00 2.92
267 268 5.110814 TCCGTCCCAAAATGTAAGATCAT 57.889 39.130 0.00 0.00 0.00 2.45
268 269 5.505780 TCCGTCCCAAAATGTAAGATCATT 58.494 37.500 0.00 0.00 39.35 2.57
269 270 5.949354 TCCGTCCCAAAATGTAAGATCATTT 59.051 36.000 0.00 0.00 45.94 2.32
278 279 5.818136 ATGTAAGATCATTTTGACACCGG 57.182 39.130 0.00 0.00 0.00 5.28
279 280 4.900684 TGTAAGATCATTTTGACACCGGA 58.099 39.130 9.46 0.00 0.00 5.14
280 281 4.935205 TGTAAGATCATTTTGACACCGGAG 59.065 41.667 9.46 1.26 0.00 4.63
281 282 8.757495 AATGTAAGATCATTTTGACACCGGAGG 61.757 40.741 9.46 1.46 44.07 4.30
298 299 5.821516 CGGAGGGAGTACATCATAGTATC 57.178 47.826 0.00 0.00 0.00 2.24
299 300 5.502079 CGGAGGGAGTACATCATAGTATCT 58.498 45.833 0.00 0.00 0.00 1.98
300 301 6.651086 CGGAGGGAGTACATCATAGTATCTA 58.349 44.000 0.00 0.00 0.00 1.98
301 302 7.284074 CGGAGGGAGTACATCATAGTATCTAT 58.716 42.308 0.00 0.00 0.00 1.98
302 303 7.442969 CGGAGGGAGTACATCATAGTATCTATC 59.557 44.444 0.00 0.00 0.00 2.08
303 304 8.499406 GGAGGGAGTACATCATAGTATCTATCT 58.501 40.741 0.00 0.00 0.00 1.98
430 431 6.975197 TGATATGAGACTAGAGCAAAAGTTCG 59.025 38.462 0.00 0.00 0.00 3.95
522 523 3.643763 AGACATCTCGTGAATATTCGGC 58.356 45.455 10.80 5.53 0.00 5.54
615 618 7.233962 TGCATGAATGGATGGCTTAGATTAAAT 59.766 33.333 0.00 0.00 0.00 1.40
663 666 9.483916 GTAAGAGAGGATAATCTTAAAAGAGCC 57.516 37.037 0.00 0.00 39.17 4.70
666 669 7.127955 AGAGAGGATAATCTTAAAAGAGCCCAA 59.872 37.037 0.00 0.00 38.66 4.12
683 686 6.441604 AGAGCCCAAATTGAAAATCTACCATT 59.558 34.615 0.00 0.00 0.00 3.16
808 812 2.135933 GCTTATCGCTACCATGTGTCC 58.864 52.381 0.00 0.00 35.14 4.02
850 854 7.648112 GCGTTACTAGTTCATAGATGATGACAA 59.352 37.037 0.00 0.00 44.53 3.18
929 935 1.062488 AGCACACCAGTCCCCTTTCT 61.062 55.000 0.00 0.00 0.00 2.52
1010 1021 0.749091 CAAGATCTCATGGCCGCCAA 60.749 55.000 18.00 0.00 36.95 4.52
1231 1248 2.421314 CTCTGCCACCACACGTGA 59.579 61.111 25.01 0.00 46.20 4.35
1350 1379 0.813610 CACAAGTGCCTTCACCGTCA 60.814 55.000 0.00 0.00 44.16 4.35
1415 1444 4.379243 ACCGAGCCAAGCGACAGG 62.379 66.667 0.00 0.00 0.00 4.00
1424 1453 3.537206 AAGCGACAGGCCTGGTGAC 62.537 63.158 35.42 21.27 45.17 3.67
1461 1490 0.681887 CTGGTCTGGCATTGGCATCA 60.682 55.000 13.83 11.14 43.71 3.07
1472 1501 0.758310 TTGGCATCAACCCAAGTGCA 60.758 50.000 0.00 0.00 37.43 4.57
1473 1502 0.542467 TGGCATCAACCCAAGTGCAT 60.542 50.000 0.00 0.00 39.27 3.96
1489 1518 2.278596 ATCCGATTGTCGCGACGG 60.279 61.111 31.88 28.22 45.61 4.79
1490 1519 3.768185 ATCCGATTGTCGCGACGGG 62.768 63.158 31.88 27.36 44.57 5.28
1789 2613 2.032528 CGAGAAGGCTTGCACCCA 59.967 61.111 3.46 0.00 0.00 4.51
1844 2668 1.402968 CCTGAACATGCCGGAGATTTG 59.597 52.381 5.05 0.00 0.00 2.32
1850 2674 4.156455 ACATGCCGGAGATTTGATTAGT 57.844 40.909 5.05 0.00 0.00 2.24
1957 2788 2.693267 ATTAGAGTCCGGCAGTTTCC 57.307 50.000 0.00 0.00 0.00 3.13
2000 2831 7.547227 AGTATTTAATTTTGGTGGCTAGCTTG 58.453 34.615 15.72 0.00 0.00 4.01
2071 2902 3.758554 CACCATGGTCCGATCTTTCTTTT 59.241 43.478 16.53 0.00 0.00 2.27
2104 2937 5.278907 CCTTTGTCTTGGTCATGTATTTGCA 60.279 40.000 0.00 0.00 0.00 4.08
2156 2991 6.292757 GCTTTACTAATTCTTAGCCGCCTAAC 60.293 42.308 0.00 0.00 36.71 2.34
2258 3095 8.281212 ACCCATGTTAGATCAAGTTTCAATAC 57.719 34.615 0.00 0.00 0.00 1.89
2259 3096 8.109634 ACCCATGTTAGATCAAGTTTCAATACT 58.890 33.333 0.00 0.00 0.00 2.12
2260 3097 9.613428 CCCATGTTAGATCAAGTTTCAATACTA 57.387 33.333 0.00 0.00 0.00 1.82
2343 3181 8.970859 AACATAGGGAAAAGACTTGAGATATG 57.029 34.615 0.00 0.00 0.00 1.78
2449 3287 1.181786 CAGACTGAGGTGGAGGACTC 58.818 60.000 0.00 0.00 0.00 3.36
2464 3302 5.422331 TGGAGGACTCGATGAAATTTAGAGT 59.578 40.000 14.11 14.11 43.88 3.24
2467 3305 4.271291 GGACTCGATGAAATTTAGAGTGGC 59.729 45.833 17.25 8.29 41.61 5.01
2471 3309 3.941483 CGATGAAATTTAGAGTGGCAGGT 59.059 43.478 0.00 0.00 0.00 4.00
2518 3364 1.144708 TCCTTGTTTGGATGGCAGACA 59.855 47.619 0.00 0.00 0.00 3.41
2543 3389 3.509967 ACTTGCCTTACCAAATTGTAGGC 59.490 43.478 18.20 18.20 36.44 3.93
2557 3403 3.799432 TGTAGGCATTAACCAACAGGT 57.201 42.857 0.00 0.00 37.19 4.00
2567 3413 0.405585 ACCAACAGGTAAGGCATGCT 59.594 50.000 18.92 0.24 32.67 3.79
2573 3419 1.205417 CAGGTAAGGCATGCTTTTGGG 59.795 52.381 20.95 4.76 0.00 4.12
2630 3476 1.930371 GCCACCGCTTTTGATTGTGTC 60.930 52.381 0.00 0.00 0.00 3.67
2635 3481 3.244422 ACCGCTTTTGATTGTGTCTCCTA 60.244 43.478 0.00 0.00 0.00 2.94
2649 3495 2.148611 TCCTACGCGGGAGATCCTA 58.851 57.895 12.47 0.00 35.95 2.94
2653 3499 2.160205 CTACGCGGGAGATCCTAATGA 58.840 52.381 12.47 0.00 35.95 2.57
2654 3500 1.633774 ACGCGGGAGATCCTAATGAT 58.366 50.000 12.47 0.00 36.01 2.45
2692 3543 1.309499 TTAATTGACGCCCCGCTTGG 61.309 55.000 0.00 0.00 0.00 3.61
2765 3616 5.462034 CACGTCTTGGATTCAGATTTCTC 57.538 43.478 0.00 0.00 0.00 2.87
2766 3617 4.931601 CACGTCTTGGATTCAGATTTCTCA 59.068 41.667 0.00 0.00 0.00 3.27
2768 3619 5.814705 ACGTCTTGGATTCAGATTTCTCATC 59.185 40.000 0.00 0.00 0.00 2.92
2769 3620 5.814188 CGTCTTGGATTCAGATTTCTCATCA 59.186 40.000 0.00 0.00 0.00 3.07
2784 3677 3.769300 TCTCATCAGGACTTCAAATCGGA 59.231 43.478 0.00 0.00 0.00 4.55
2789 3682 5.102953 TCAGGACTTCAAATCGGATGATT 57.897 39.130 0.00 0.00 46.75 2.57
2838 3731 2.542597 CATTTTCCAATGCATCCACGG 58.457 47.619 0.00 0.00 33.57 4.94
2839 3732 0.246086 TTTTCCAATGCATCCACGGC 59.754 50.000 0.00 0.00 0.00 5.68
2841 3734 3.891400 CCAATGCATCCACGGCCG 61.891 66.667 26.86 26.86 0.00 6.13
2842 3735 2.823593 CAATGCATCCACGGCCGA 60.824 61.111 35.90 10.61 0.00 5.54
2843 3736 2.188829 CAATGCATCCACGGCCGAT 61.189 57.895 35.90 12.97 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.810896 CAAAACCCTAGCCGCGCC 61.811 66.667 0.00 0.00 0.00 6.53
6 7 2.744709 TCAAAACCCTAGCCGCGC 60.745 61.111 0.00 0.00 0.00 6.86
7 8 0.953960 AAGTCAAAACCCTAGCCGCG 60.954 55.000 0.00 0.00 0.00 6.46
8 9 0.521735 CAAGTCAAAACCCTAGCCGC 59.478 55.000 0.00 0.00 0.00 6.53
9 10 1.165270 CCAAGTCAAAACCCTAGCCG 58.835 55.000 0.00 0.00 0.00 5.52
10 11 1.545841 CCCAAGTCAAAACCCTAGCC 58.454 55.000 0.00 0.00 0.00 3.93
11 12 1.545841 CCCCAAGTCAAAACCCTAGC 58.454 55.000 0.00 0.00 0.00 3.42
12 13 1.075536 AGCCCCAAGTCAAAACCCTAG 59.924 52.381 0.00 0.00 0.00 3.02
13 14 1.154430 AGCCCCAAGTCAAAACCCTA 58.846 50.000 0.00 0.00 0.00 3.53
14 15 0.469892 CAGCCCCAAGTCAAAACCCT 60.470 55.000 0.00 0.00 0.00 4.34
15 16 1.471829 CCAGCCCCAAGTCAAAACCC 61.472 60.000 0.00 0.00 0.00 4.11
16 17 0.759060 ACCAGCCCCAAGTCAAAACC 60.759 55.000 0.00 0.00 0.00 3.27
17 18 1.119684 AACCAGCCCCAAGTCAAAAC 58.880 50.000 0.00 0.00 0.00 2.43
18 19 1.760029 GAAACCAGCCCCAAGTCAAAA 59.240 47.619 0.00 0.00 0.00 2.44
19 20 1.063266 AGAAACCAGCCCCAAGTCAAA 60.063 47.619 0.00 0.00 0.00 2.69
20 21 0.555769 AGAAACCAGCCCCAAGTCAA 59.444 50.000 0.00 0.00 0.00 3.18
21 22 0.555769 AAGAAACCAGCCCCAAGTCA 59.444 50.000 0.00 0.00 0.00 3.41
22 23 1.704641 AAAGAAACCAGCCCCAAGTC 58.295 50.000 0.00 0.00 0.00 3.01
23 24 3.542969 ATAAAGAAACCAGCCCCAAGT 57.457 42.857 0.00 0.00 0.00 3.16
24 25 3.119495 CGAATAAAGAAACCAGCCCCAAG 60.119 47.826 0.00 0.00 0.00 3.61
25 26 2.823154 CGAATAAAGAAACCAGCCCCAA 59.177 45.455 0.00 0.00 0.00 4.12
26 27 2.442413 CGAATAAAGAAACCAGCCCCA 58.558 47.619 0.00 0.00 0.00 4.96
27 28 1.749063 CCGAATAAAGAAACCAGCCCC 59.251 52.381 0.00 0.00 0.00 5.80
28 29 1.749063 CCCGAATAAAGAAACCAGCCC 59.251 52.381 0.00 0.00 0.00 5.19
29 30 1.749063 CCCCGAATAAAGAAACCAGCC 59.251 52.381 0.00 0.00 0.00 4.85
30 31 2.683362 CTCCCCGAATAAAGAAACCAGC 59.317 50.000 0.00 0.00 0.00 4.85
31 32 4.192317 CTCTCCCCGAATAAAGAAACCAG 58.808 47.826 0.00 0.00 0.00 4.00
32 33 3.054655 CCTCTCCCCGAATAAAGAAACCA 60.055 47.826 0.00 0.00 0.00 3.67
33 34 3.199289 TCCTCTCCCCGAATAAAGAAACC 59.801 47.826 0.00 0.00 0.00 3.27
34 35 4.161754 TCTCCTCTCCCCGAATAAAGAAAC 59.838 45.833 0.00 0.00 0.00 2.78
35 36 4.161754 GTCTCCTCTCCCCGAATAAAGAAA 59.838 45.833 0.00 0.00 0.00 2.52
36 37 3.705072 GTCTCCTCTCCCCGAATAAAGAA 59.295 47.826 0.00 0.00 0.00 2.52
37 38 3.297736 GTCTCCTCTCCCCGAATAAAGA 58.702 50.000 0.00 0.00 0.00 2.52
38 39 2.034812 CGTCTCCTCTCCCCGAATAAAG 59.965 54.545 0.00 0.00 0.00 1.85
39 40 2.029623 CGTCTCCTCTCCCCGAATAAA 58.970 52.381 0.00 0.00 0.00 1.40
40 41 1.064166 ACGTCTCCTCTCCCCGAATAA 60.064 52.381 0.00 0.00 0.00 1.40
41 42 0.549950 ACGTCTCCTCTCCCCGAATA 59.450 55.000 0.00 0.00 0.00 1.75
42 43 0.549950 TACGTCTCCTCTCCCCGAAT 59.450 55.000 0.00 0.00 0.00 3.34
43 44 0.393537 GTACGTCTCCTCTCCCCGAA 60.394 60.000 0.00 0.00 0.00 4.30
44 45 1.222936 GTACGTCTCCTCTCCCCGA 59.777 63.158 0.00 0.00 0.00 5.14
45 46 0.465824 ATGTACGTCTCCTCTCCCCG 60.466 60.000 0.00 0.00 0.00 5.73
46 47 2.228925 GTATGTACGTCTCCTCTCCCC 58.771 57.143 0.00 0.00 0.00 4.81
47 48 2.928334 TGTATGTACGTCTCCTCTCCC 58.072 52.381 0.00 0.00 0.00 4.30
48 49 6.402334 CGAATATGTATGTACGTCTCCTCTCC 60.402 46.154 0.00 0.00 0.00 3.71
49 50 6.402334 CCGAATATGTATGTACGTCTCCTCTC 60.402 46.154 0.00 0.00 0.00 3.20
50 51 5.411977 CCGAATATGTATGTACGTCTCCTCT 59.588 44.000 0.00 0.00 0.00 3.69
51 52 5.391736 CCCGAATATGTATGTACGTCTCCTC 60.392 48.000 0.00 0.00 0.00 3.71
52 53 4.458295 CCCGAATATGTATGTACGTCTCCT 59.542 45.833 0.00 0.00 0.00 3.69
53 54 4.456911 TCCCGAATATGTATGTACGTCTCC 59.543 45.833 0.00 0.00 0.00 3.71
54 55 5.618056 TCCCGAATATGTATGTACGTCTC 57.382 43.478 0.00 0.00 0.00 3.36
55 56 6.585695 ATTCCCGAATATGTATGTACGTCT 57.414 37.500 0.00 0.00 0.00 4.18
56 57 7.647907 AAATTCCCGAATATGTATGTACGTC 57.352 36.000 0.00 0.00 0.00 4.34
57 58 8.362639 ACTAAATTCCCGAATATGTATGTACGT 58.637 33.333 0.00 0.00 0.00 3.57
58 59 8.644619 CACTAAATTCCCGAATATGTATGTACG 58.355 37.037 0.00 0.00 0.00 3.67
59 60 9.701098 TCACTAAATTCCCGAATATGTATGTAC 57.299 33.333 0.00 0.00 0.00 2.90
60 61 9.701098 GTCACTAAATTCCCGAATATGTATGTA 57.299 33.333 0.00 0.00 0.00 2.29
61 62 8.429641 AGTCACTAAATTCCCGAATATGTATGT 58.570 33.333 0.00 0.00 0.00 2.29
62 63 8.833231 AGTCACTAAATTCCCGAATATGTATG 57.167 34.615 0.00 0.00 0.00 2.39
64 65 8.582437 CCTAGTCACTAAATTCCCGAATATGTA 58.418 37.037 0.00 0.00 0.00 2.29
65 66 7.289317 TCCTAGTCACTAAATTCCCGAATATGT 59.711 37.037 0.00 0.00 0.00 2.29
66 67 7.667557 TCCTAGTCACTAAATTCCCGAATATG 58.332 38.462 0.00 0.00 0.00 1.78
67 68 7.850935 TCCTAGTCACTAAATTCCCGAATAT 57.149 36.000 0.00 0.00 0.00 1.28
68 69 7.124599 TGTTCCTAGTCACTAAATTCCCGAATA 59.875 37.037 0.00 0.00 0.00 1.75
69 70 6.070424 TGTTCCTAGTCACTAAATTCCCGAAT 60.070 38.462 0.00 0.00 0.00 3.34
70 71 5.246656 TGTTCCTAGTCACTAAATTCCCGAA 59.753 40.000 0.00 0.00 0.00 4.30
71 72 4.773674 TGTTCCTAGTCACTAAATTCCCGA 59.226 41.667 0.00 0.00 0.00 5.14
72 73 5.080969 TGTTCCTAGTCACTAAATTCCCG 57.919 43.478 0.00 0.00 0.00 5.14
73 74 7.939784 ATTTGTTCCTAGTCACTAAATTCCC 57.060 36.000 0.00 0.00 0.00 3.97
79 80 9.595823 GCATAGTTATTTGTTCCTAGTCACTAA 57.404 33.333 0.00 0.00 0.00 2.24
80 81 8.755028 TGCATAGTTATTTGTTCCTAGTCACTA 58.245 33.333 0.00 0.00 0.00 2.74
81 82 7.620880 TGCATAGTTATTTGTTCCTAGTCACT 58.379 34.615 0.00 0.00 0.00 3.41
82 83 7.764443 TCTGCATAGTTATTTGTTCCTAGTCAC 59.236 37.037 0.00 0.00 0.00 3.67
83 84 7.847096 TCTGCATAGTTATTTGTTCCTAGTCA 58.153 34.615 0.00 0.00 0.00 3.41
84 85 8.894768 ATCTGCATAGTTATTTGTTCCTAGTC 57.105 34.615 0.00 0.00 0.00 2.59
85 86 9.988815 CTATCTGCATAGTTATTTGTTCCTAGT 57.011 33.333 0.00 0.00 0.00 2.57
91 92 8.571336 GCCATTCTATCTGCATAGTTATTTGTT 58.429 33.333 0.00 0.00 34.54 2.83
92 93 7.175641 GGCCATTCTATCTGCATAGTTATTTGT 59.824 37.037 0.00 0.00 34.54 2.83
93 94 7.392673 AGGCCATTCTATCTGCATAGTTATTTG 59.607 37.037 5.01 0.00 34.54 2.32
94 95 7.465116 AGGCCATTCTATCTGCATAGTTATTT 58.535 34.615 5.01 0.00 34.54 1.40
95 96 7.025520 AGGCCATTCTATCTGCATAGTTATT 57.974 36.000 5.01 0.00 34.54 1.40
96 97 6.633325 AGGCCATTCTATCTGCATAGTTAT 57.367 37.500 5.01 0.00 34.54 1.89
97 98 6.439636 AAGGCCATTCTATCTGCATAGTTA 57.560 37.500 5.01 0.00 34.54 2.24
98 99 4.989875 AGGCCATTCTATCTGCATAGTT 57.010 40.909 5.01 0.00 34.54 2.24
99 100 4.263243 GGAAGGCCATTCTATCTGCATAGT 60.263 45.833 5.01 0.00 38.07 2.12
100 101 4.260170 GGAAGGCCATTCTATCTGCATAG 58.740 47.826 5.01 0.00 38.07 2.23
101 102 3.009473 GGGAAGGCCATTCTATCTGCATA 59.991 47.826 5.01 0.00 38.07 3.14
102 103 2.224967 GGGAAGGCCATTCTATCTGCAT 60.225 50.000 5.01 0.00 38.07 3.96
103 104 1.143684 GGGAAGGCCATTCTATCTGCA 59.856 52.381 5.01 0.00 38.07 4.41
104 105 1.423161 AGGGAAGGCCATTCTATCTGC 59.577 52.381 5.01 0.00 38.07 4.26
105 106 2.707791 TGAGGGAAGGCCATTCTATCTG 59.292 50.000 5.01 0.00 38.07 2.90
106 107 2.708325 GTGAGGGAAGGCCATTCTATCT 59.292 50.000 5.01 5.77 38.07 1.98
107 108 2.439507 TGTGAGGGAAGGCCATTCTATC 59.560 50.000 5.01 8.77 38.07 2.08
108 109 2.492025 TGTGAGGGAAGGCCATTCTAT 58.508 47.619 5.01 0.00 38.07 1.98
109 110 1.965414 TGTGAGGGAAGGCCATTCTA 58.035 50.000 5.01 0.00 38.07 2.10
110 111 1.075601 TTGTGAGGGAAGGCCATTCT 58.924 50.000 5.01 0.00 38.07 2.40
111 112 1.923356 TTTGTGAGGGAAGGCCATTC 58.077 50.000 5.01 5.92 37.17 2.67
112 113 2.397044 TTTTGTGAGGGAAGGCCATT 57.603 45.000 5.01 0.00 35.15 3.16
113 114 2.397044 TTTTTGTGAGGGAAGGCCAT 57.603 45.000 5.01 0.00 35.15 4.40
114 115 3.935371 TTTTTGTGAGGGAAGGCCA 57.065 47.368 5.01 0.00 35.15 5.36
136 137 9.825109 GGAAGCTAAAATTTCTCTCTACATAGT 57.175 33.333 0.00 0.00 0.00 2.12
137 138 9.267084 GGGAAGCTAAAATTTCTCTCTACATAG 57.733 37.037 0.00 0.00 0.00 2.23
138 139 8.768397 TGGGAAGCTAAAATTTCTCTCTACATA 58.232 33.333 0.00 0.00 0.00 2.29
139 140 7.633789 TGGGAAGCTAAAATTTCTCTCTACAT 58.366 34.615 0.00 0.00 0.00 2.29
140 141 7.016153 TGGGAAGCTAAAATTTCTCTCTACA 57.984 36.000 0.00 0.00 0.00 2.74
141 142 7.923414 TTGGGAAGCTAAAATTTCTCTCTAC 57.077 36.000 0.00 0.00 0.00 2.59
142 143 7.942341 TGTTTGGGAAGCTAAAATTTCTCTCTA 59.058 33.333 0.00 0.00 0.00 2.43
143 144 6.777580 TGTTTGGGAAGCTAAAATTTCTCTCT 59.222 34.615 0.00 0.00 0.00 3.10
144 145 6.981722 TGTTTGGGAAGCTAAAATTTCTCTC 58.018 36.000 0.00 0.00 0.00 3.20
145 146 6.976934 TGTTTGGGAAGCTAAAATTTCTCT 57.023 33.333 0.00 0.00 0.00 3.10
146 147 7.657354 ACAATGTTTGGGAAGCTAAAATTTCTC 59.343 33.333 0.00 0.00 34.12 2.87
147 148 7.508687 ACAATGTTTGGGAAGCTAAAATTTCT 58.491 30.769 0.00 0.00 34.12 2.52
148 149 7.728847 ACAATGTTTGGGAAGCTAAAATTTC 57.271 32.000 0.00 0.00 34.12 2.17
149 150 8.428852 ACTACAATGTTTGGGAAGCTAAAATTT 58.571 29.630 0.00 0.00 34.12 1.82
150 151 7.962441 ACTACAATGTTTGGGAAGCTAAAATT 58.038 30.769 0.00 0.00 34.12 1.82
151 152 7.309805 GGACTACAATGTTTGGGAAGCTAAAAT 60.310 37.037 0.00 0.00 34.12 1.82
152 153 6.015772 GGACTACAATGTTTGGGAAGCTAAAA 60.016 38.462 0.00 0.00 34.12 1.52
153 154 5.475564 GGACTACAATGTTTGGGAAGCTAAA 59.524 40.000 0.00 0.00 34.12 1.85
154 155 5.007682 GGACTACAATGTTTGGGAAGCTAA 58.992 41.667 0.00 0.00 34.12 3.09
155 156 4.042311 TGGACTACAATGTTTGGGAAGCTA 59.958 41.667 0.00 0.00 34.12 3.32
156 157 3.181434 TGGACTACAATGTTTGGGAAGCT 60.181 43.478 0.00 0.00 34.12 3.74
157 158 3.153919 TGGACTACAATGTTTGGGAAGC 58.846 45.455 0.00 0.00 34.12 3.86
158 159 5.982890 AATGGACTACAATGTTTGGGAAG 57.017 39.130 0.00 0.00 34.12 3.46
159 160 6.739331 AAAATGGACTACAATGTTTGGGAA 57.261 33.333 0.00 0.00 34.12 3.97
160 161 6.325028 TGAAAAATGGACTACAATGTTTGGGA 59.675 34.615 0.00 0.00 34.12 4.37
161 162 6.520272 TGAAAAATGGACTACAATGTTTGGG 58.480 36.000 0.00 0.00 34.12 4.12
162 163 7.493971 TGTTGAAAAATGGACTACAATGTTTGG 59.506 33.333 0.00 0.00 34.12 3.28
163 164 8.417780 TGTTGAAAAATGGACTACAATGTTTG 57.582 30.769 0.00 0.00 0.00 2.93
164 165 9.260002 GATGTTGAAAAATGGACTACAATGTTT 57.740 29.630 0.00 0.00 0.00 2.83
165 166 7.872483 GGATGTTGAAAAATGGACTACAATGTT 59.128 33.333 0.00 0.00 0.00 2.71
166 167 7.015098 TGGATGTTGAAAAATGGACTACAATGT 59.985 33.333 0.00 0.00 0.00 2.71
167 168 7.377398 TGGATGTTGAAAAATGGACTACAATG 58.623 34.615 0.00 0.00 0.00 2.82
168 169 7.537596 TGGATGTTGAAAAATGGACTACAAT 57.462 32.000 0.00 0.00 0.00 2.71
169 170 6.968263 TGGATGTTGAAAAATGGACTACAA 57.032 33.333 0.00 0.00 0.00 2.41
170 171 6.968263 TTGGATGTTGAAAAATGGACTACA 57.032 33.333 0.00 0.00 0.00 2.74
171 172 7.433680 ACTTTGGATGTTGAAAAATGGACTAC 58.566 34.615 0.00 0.00 0.00 2.73
172 173 7.595819 ACTTTGGATGTTGAAAAATGGACTA 57.404 32.000 0.00 0.00 0.00 2.59
173 174 6.484364 ACTTTGGATGTTGAAAAATGGACT 57.516 33.333 0.00 0.00 0.00 3.85
174 175 7.552458 AAACTTTGGATGTTGAAAAATGGAC 57.448 32.000 0.00 0.00 0.00 4.02
175 176 8.572855 AAAAACTTTGGATGTTGAAAAATGGA 57.427 26.923 0.00 0.00 0.00 3.41
204 205 9.613428 TCTCGATGGAATAAAGATTGTATGTTT 57.387 29.630 0.00 0.00 0.00 2.83
205 206 9.784531 ATCTCGATGGAATAAAGATTGTATGTT 57.215 29.630 0.00 0.00 26.72 2.71
210 211 9.265901 CAGTTATCTCGATGGAATAAAGATTGT 57.734 33.333 0.00 0.00 32.06 2.71
211 212 9.481340 TCAGTTATCTCGATGGAATAAAGATTG 57.519 33.333 0.00 0.00 32.06 2.67
217 218 8.740906 GGAGTATCAGTTATCTCGATGGAATAA 58.259 37.037 0.00 0.00 36.25 1.40
218 219 7.339721 GGGAGTATCAGTTATCTCGATGGAATA 59.660 40.741 0.00 0.00 36.25 1.75
219 220 6.153680 GGGAGTATCAGTTATCTCGATGGAAT 59.846 42.308 0.00 0.00 36.25 3.01
220 221 5.477291 GGGAGTATCAGTTATCTCGATGGAA 59.523 44.000 0.00 0.00 36.25 3.53
221 222 5.010933 GGGAGTATCAGTTATCTCGATGGA 58.989 45.833 0.00 0.00 36.25 3.41
222 223 5.013547 AGGGAGTATCAGTTATCTCGATGG 58.986 45.833 0.00 0.00 36.25 3.51
223 224 5.124776 GGAGGGAGTATCAGTTATCTCGATG 59.875 48.000 0.00 0.00 36.25 3.84
224 225 5.258051 GGAGGGAGTATCAGTTATCTCGAT 58.742 45.833 0.00 0.00 36.25 3.59
225 226 4.653868 GGAGGGAGTATCAGTTATCTCGA 58.346 47.826 0.00 0.00 36.25 4.04
226 227 3.437395 CGGAGGGAGTATCAGTTATCTCG 59.563 52.174 0.00 0.00 36.25 4.04
227 228 4.400120 ACGGAGGGAGTATCAGTTATCTC 58.600 47.826 0.00 0.00 36.25 2.75
228 229 4.400120 GACGGAGGGAGTATCAGTTATCT 58.600 47.826 0.00 0.00 36.25 1.98
229 230 3.506844 GGACGGAGGGAGTATCAGTTATC 59.493 52.174 0.00 0.00 36.25 1.75
230 231 3.498334 GGACGGAGGGAGTATCAGTTAT 58.502 50.000 0.00 0.00 36.25 1.89
231 232 2.423947 GGGACGGAGGGAGTATCAGTTA 60.424 54.545 0.00 0.00 36.25 2.24
232 233 1.688627 GGGACGGAGGGAGTATCAGTT 60.689 57.143 0.00 0.00 36.25 3.16
233 234 0.106116 GGGACGGAGGGAGTATCAGT 60.106 60.000 0.00 0.00 36.25 3.41
234 235 0.106167 TGGGACGGAGGGAGTATCAG 60.106 60.000 0.00 0.00 36.25 2.90
235 236 0.337082 TTGGGACGGAGGGAGTATCA 59.663 55.000 0.00 0.00 36.25 2.15
236 237 1.492764 TTTGGGACGGAGGGAGTATC 58.507 55.000 0.00 0.00 0.00 2.24
237 238 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
238 239 1.557832 CATTTTGGGACGGAGGGAGTA 59.442 52.381 0.00 0.00 0.00 2.59
239 240 0.328258 CATTTTGGGACGGAGGGAGT 59.672 55.000 0.00 0.00 0.00 3.85
240 241 0.328258 ACATTTTGGGACGGAGGGAG 59.672 55.000 0.00 0.00 0.00 4.30
241 242 1.659022 TACATTTTGGGACGGAGGGA 58.341 50.000 0.00 0.00 0.00 4.20
242 243 2.026636 TCTTACATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
243 244 3.343941 TCTTACATTTTGGGACGGAGG 57.656 47.619 0.00 0.00 0.00 4.30
244 245 4.513442 TGATCTTACATTTTGGGACGGAG 58.487 43.478 0.00 0.00 0.00 4.63
245 246 4.561500 TGATCTTACATTTTGGGACGGA 57.438 40.909 0.00 0.00 0.00 4.69
246 247 5.835113 AATGATCTTACATTTTGGGACGG 57.165 39.130 0.00 0.00 37.20 4.79
255 256 5.943416 TCCGGTGTCAAAATGATCTTACATT 59.057 36.000 0.00 0.00 41.43 2.71
256 257 5.496556 TCCGGTGTCAAAATGATCTTACAT 58.503 37.500 0.00 0.00 0.00 2.29
257 258 4.900684 TCCGGTGTCAAAATGATCTTACA 58.099 39.130 0.00 0.00 0.00 2.41
258 259 4.332819 CCTCCGGTGTCAAAATGATCTTAC 59.667 45.833 0.00 0.00 0.00 2.34
259 260 4.513442 CCTCCGGTGTCAAAATGATCTTA 58.487 43.478 0.00 0.00 0.00 2.10
260 261 3.347216 CCTCCGGTGTCAAAATGATCTT 58.653 45.455 0.00 0.00 0.00 2.40
261 262 2.356125 CCCTCCGGTGTCAAAATGATCT 60.356 50.000 0.00 0.00 0.00 2.75
262 263 2.017049 CCCTCCGGTGTCAAAATGATC 58.983 52.381 0.00 0.00 0.00 2.92
263 264 1.633432 TCCCTCCGGTGTCAAAATGAT 59.367 47.619 0.00 0.00 0.00 2.45
264 265 1.003118 CTCCCTCCGGTGTCAAAATGA 59.997 52.381 0.00 0.00 0.00 2.57
265 266 1.271379 ACTCCCTCCGGTGTCAAAATG 60.271 52.381 0.00 0.00 29.65 2.32
266 267 1.064825 ACTCCCTCCGGTGTCAAAAT 58.935 50.000 0.00 0.00 29.65 1.82
267 268 1.345415 GTACTCCCTCCGGTGTCAAAA 59.655 52.381 0.00 0.00 37.13 2.44
268 269 0.971386 GTACTCCCTCCGGTGTCAAA 59.029 55.000 0.00 0.00 37.13 2.69
269 270 0.178955 TGTACTCCCTCCGGTGTCAA 60.179 55.000 0.00 0.00 37.13 3.18
270 271 0.040646 ATGTACTCCCTCCGGTGTCA 59.959 55.000 0.00 0.00 37.13 3.58
271 272 0.745468 GATGTACTCCCTCCGGTGTC 59.255 60.000 0.00 0.00 37.13 3.67
272 273 0.040646 TGATGTACTCCCTCCGGTGT 59.959 55.000 0.00 0.00 39.25 4.16
273 274 1.414158 ATGATGTACTCCCTCCGGTG 58.586 55.000 0.00 0.00 0.00 4.94
274 275 2.177233 ACTATGATGTACTCCCTCCGGT 59.823 50.000 0.00 0.00 0.00 5.28
275 276 2.877866 ACTATGATGTACTCCCTCCGG 58.122 52.381 0.00 0.00 0.00 5.14
276 277 5.502079 AGATACTATGATGTACTCCCTCCG 58.498 45.833 0.00 0.00 0.00 4.63
277 278 8.499406 AGATAGATACTATGATGTACTCCCTCC 58.501 40.741 0.00 0.00 0.00 4.30
297 298 9.890629 AGTTGCACTATGAAACAAATAGATAGA 57.109 29.630 2.59 0.00 32.85 1.98
301 302 9.502091 ACTAAGTTGCACTATGAAACAAATAGA 57.498 29.630 2.59 0.00 32.85 1.98
304 305 9.816354 AAAACTAAGTTGCACTATGAAACAAAT 57.184 25.926 2.59 0.00 0.00 2.32
305 306 9.646427 AAAAACTAAGTTGCACTATGAAACAAA 57.354 25.926 2.59 0.00 0.00 2.83
306 307 9.296400 GAAAAACTAAGTTGCACTATGAAACAA 57.704 29.630 2.59 0.00 0.00 2.83
307 308 7.642194 CGAAAAACTAAGTTGCACTATGAAACA 59.358 33.333 2.59 0.00 0.00 2.83
308 309 7.642586 ACGAAAAACTAAGTTGCACTATGAAAC 59.357 33.333 0.00 0.00 0.00 2.78
309 310 7.642194 CACGAAAAACTAAGTTGCACTATGAAA 59.358 33.333 0.00 0.00 0.00 2.69
310 311 7.011576 TCACGAAAAACTAAGTTGCACTATGAA 59.988 33.333 0.00 0.00 0.00 2.57
311 312 6.480651 TCACGAAAAACTAAGTTGCACTATGA 59.519 34.615 0.00 0.00 0.00 2.15
312 313 6.573725 GTCACGAAAAACTAAGTTGCACTATG 59.426 38.462 0.00 0.00 0.00 2.23
313 314 6.482308 AGTCACGAAAAACTAAGTTGCACTAT 59.518 34.615 0.00 0.00 0.00 2.12
314 315 5.813672 AGTCACGAAAAACTAAGTTGCACTA 59.186 36.000 0.00 0.00 0.00 2.74
315 316 4.634443 AGTCACGAAAAACTAAGTTGCACT 59.366 37.500 0.00 0.00 0.00 4.40
316 317 4.905269 AGTCACGAAAAACTAAGTTGCAC 58.095 39.130 0.00 0.00 0.00 4.57
317 318 6.665474 TTAGTCACGAAAAACTAAGTTGCA 57.335 33.333 0.00 0.00 34.03 4.08
323 324 8.598075 GTTTCACTCTTAGTCACGAAAAACTAA 58.402 33.333 0.00 0.00 36.71 2.24
366 367 9.611284 ATGTATTTAATTTGCACTGCATATACG 57.389 29.630 4.10 0.00 38.76 3.06
410 411 4.585955 ACGAACTTTTGCTCTAGTCTCA 57.414 40.909 0.00 0.00 0.00 3.27
495 496 6.744993 CGAATATTCACGAGATGTCTCCATAG 59.255 42.308 15.57 0.00 39.79 2.23
615 618 5.281314 ACCTTCTAGGAGGCAAGAGAAATA 58.719 41.667 17.89 0.00 40.65 1.40
663 666 7.599630 CCACAATGGTAGATTTTCAATTTGG 57.400 36.000 0.00 0.00 31.35 3.28
683 686 6.545666 AGAAAATCATGTGTTGAGTAACCACA 59.454 34.615 0.00 0.00 37.89 4.17
808 812 1.640428 ACGCTCGTGTTATGTGATGG 58.360 50.000 0.00 0.00 0.00 3.51
871 875 5.888724 CCTGCGAGAGATAGATATAAAGGGA 59.111 44.000 0.00 0.00 0.00 4.20
929 935 0.843309 TGTGGGAGCAAGGAACAAGA 59.157 50.000 0.00 0.00 0.00 3.02
1231 1248 1.003355 CACCCGCTGGAACATCTGT 60.003 57.895 0.00 0.00 38.20 3.41
1350 1379 2.182791 CTGACAGCGACTGCCGAT 59.817 61.111 6.74 0.00 44.31 4.18
1415 1444 2.048127 GAGTCACGGTCACCAGGC 60.048 66.667 0.00 0.00 0.00 4.85
1424 1453 2.358737 GGGCTGGTTGAGTCACGG 60.359 66.667 0.00 0.00 0.00 4.94
1461 1490 1.176527 CAATCGGATGCACTTGGGTT 58.823 50.000 0.00 0.00 0.00 4.11
1472 1501 2.278596 CCGTCGCGACAATCGGAT 60.279 61.111 35.71 0.00 44.86 4.18
1473 1502 4.485834 CCCGTCGCGACAATCGGA 62.486 66.667 35.71 0.00 44.86 4.55
1489 1518 0.033781 TTGCTGAATGGTGCTTTGCC 59.966 50.000 0.00 0.00 0.00 4.52
1490 1519 1.425412 CTTGCTGAATGGTGCTTTGC 58.575 50.000 0.00 0.00 0.00 3.68
1563 1628 1.688735 CTCTCCTGTTGTGGTGTCTGA 59.311 52.381 0.00 0.00 0.00 3.27
1569 1634 0.179018 GTTGGCTCTCCTGTTGTGGT 60.179 55.000 0.00 0.00 0.00 4.16
1844 2668 2.795175 TCTCCATCGCCGAACTAATC 57.205 50.000 0.00 0.00 0.00 1.75
1850 2674 1.676678 CCTCCTTCTCCATCGCCGAA 61.677 60.000 0.00 0.00 0.00 4.30
1957 2788 6.974932 AATACTACAGCTGTTCATCAACTG 57.025 37.500 27.06 6.79 43.49 3.16
2000 2831 0.730840 CGGACCGACAATAAAAGCCC 59.269 55.000 8.64 0.00 0.00 5.19
2014 2845 3.252458 AGCACAAGATAAAAACACGGACC 59.748 43.478 0.00 0.00 0.00 4.46
2071 2902 3.571590 ACCAAGACAAAGGGCATACAAA 58.428 40.909 0.00 0.00 0.00 2.83
2079 2910 5.713025 CAAATACATGACCAAGACAAAGGG 58.287 41.667 0.00 0.00 0.00 3.95
2156 2991 6.296803 ACCTTAACCAAGAGTTAGGAAACTG 58.703 40.000 0.00 0.00 46.09 3.16
2258 3095 9.494479 CACTTCATACATGTGCAAACTAAATAG 57.506 33.333 9.11 0.00 0.00 1.73
2259 3096 9.225436 TCACTTCATACATGTGCAAACTAAATA 57.775 29.630 9.11 0.00 31.48 1.40
2260 3097 8.109705 TCACTTCATACATGTGCAAACTAAAT 57.890 30.769 9.11 0.00 31.48 1.40
2272 3109 8.822652 TTAGCATATCACTCACTTCATACATG 57.177 34.615 0.00 0.00 0.00 3.21
2343 3181 9.807649 ATTCATAAGCTGTCCACAAAAATAATC 57.192 29.630 0.00 0.00 0.00 1.75
2449 3287 3.941483 ACCTGCCACTCTAAATTTCATCG 59.059 43.478 0.00 0.00 0.00 3.84
2464 3302 1.429930 TTTCACTCTACCACCTGCCA 58.570 50.000 0.00 0.00 0.00 4.92
2467 3305 5.152623 TCTGAATTTCACTCTACCACCTG 57.847 43.478 0.00 0.00 0.00 4.00
2471 3309 4.425772 TCCCTCTGAATTTCACTCTACCA 58.574 43.478 0.00 0.00 0.00 3.25
2540 3386 3.697166 CCTTACCTGTTGGTTAATGCCT 58.303 45.455 0.00 0.00 46.05 4.75
2543 3389 4.677779 GCATGCCTTACCTGTTGGTTAATG 60.678 45.833 6.36 0.00 46.05 1.90
2557 3403 2.099405 GCTACCCAAAAGCATGCCTTA 58.901 47.619 15.66 0.00 39.83 2.69
2573 3419 5.419760 GGATACGAAAATTTGGGAGCTAC 57.580 43.478 0.00 0.00 0.00 3.58
2616 3462 3.424962 GCGTAGGAGACACAATCAAAAGC 60.425 47.826 0.00 0.00 0.00 3.51
2620 3466 1.403647 CCGCGTAGGAGACACAATCAA 60.404 52.381 4.92 0.00 45.00 2.57
2635 3481 1.273606 CATCATTAGGATCTCCCGCGT 59.726 52.381 4.92 0.00 40.87 6.01
2692 3543 2.035442 GTGCCCTCACTCGCCTTTC 61.035 63.158 0.00 0.00 40.03 2.62
2719 3570 4.880120 GGGTATGTAGTTTGTAAGGGCTTC 59.120 45.833 0.00 0.00 0.00 3.86
2762 3613 3.769300 TCCGATTTGAAGTCCTGATGAGA 59.231 43.478 0.00 0.00 0.00 3.27
2763 3614 4.128925 TCCGATTTGAAGTCCTGATGAG 57.871 45.455 0.00 0.00 0.00 2.90
2764 3615 4.162131 TCATCCGATTTGAAGTCCTGATGA 59.838 41.667 11.11 11.11 36.09 2.92
2765 3616 4.445453 TCATCCGATTTGAAGTCCTGATG 58.555 43.478 7.90 7.90 0.00 3.07
2766 3617 4.760530 TCATCCGATTTGAAGTCCTGAT 57.239 40.909 0.00 0.00 0.00 2.90
2801 3694 8.529424 TGGAAAATGCATGAGATAATCTTTCT 57.471 30.769 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.