Multiple sequence alignment - TraesCS2D01G371600

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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 TraesCS2D01G371600 chr2D 100.000 3176 0 0 1 3176 475983724 475986899 0.000000e+00 5866.0
1 TraesCS2D01G371600 chr2D 95.442 1470 42 15 478 1935 475876248 475877704 0.000000e+00 2320.0
2 TraesCS2D01G371600 chr2D 86.364 1232 81 41 730 1935 475498830 475500000 0.000000e+00 1264.0
3 TraesCS2D01G371600 chr2B 90.939 3035 182 30 158 3137 556675247 556678243 0.000000e+00 3995.0
4 TraesCS2D01G371600 chr2B 83.219 1162 88 40 809 1935 556595451 556596540 0.000000e+00 966.0
5 TraesCS2D01G371600 chr2B 87.291 779 60 18 1165 1934 556517293 556518041 0.000000e+00 854.0
6 TraesCS2D01G371600 chr2B 92.308 195 10 4 918 1108 556517088 556517281 4.040000e-69 272.0
7 TraesCS2D01G371600 chr2B 92.063 63 4 1 722 784 556595395 556595456 1.570000e-13 87.9
8 TraesCS2D01G371600 chr2A 91.261 1888 97 39 695 2547 617812444 617814298 0.000000e+00 2510.0
9 TraesCS2D01G371600 chr2A 85.131 1029 78 35 924 1935 617730579 617731549 0.000000e+00 983.0
10 TraesCS2D01G371600 chr2A 89.936 626 29 20 2535 3137 617814687 617815301 0.000000e+00 776.0
11 TraesCS2D01G371600 chr2A 90.083 484 38 3 1458 1931 617762324 617762807 1.250000e-173 619.0
12 TraesCS2D01G371600 chr6B 81.573 445 80 2 1493 1936 473541094 473540651 1.800000e-97 366.0
13 TraesCS2D01G371600 chr4D 97.674 43 1 0 3134 3176 13208174 13208132 1.220000e-09 75.0
14 TraesCS2D01G371600 chr4D 91.837 49 3 1 3129 3176 413764367 413764415 2.040000e-07 67.6
15 TraesCS2D01G371600 chr7A 97.561 41 1 0 3136 3176 649126534 649126494 1.580000e-08 71.3
16 TraesCS2D01G371600 chr3A 97.561 41 1 0 3136 3176 706510627 706510587 1.580000e-08 71.3
17 TraesCS2D01G371600 chr1A 97.561 41 1 0 3136 3176 22932003 22932043 1.580000e-08 71.3
18 TraesCS2D01G371600 chr1D 97.500 40 1 0 3137 3176 487219327 487219288 5.680000e-08 69.4
19 TraesCS2D01G371600 chr7D 93.478 46 2 1 3131 3176 589370057 589370013 2.040000e-07 67.6
20 TraesCS2D01G371600 chr7D 91.837 49 2 2 3128 3176 613769559 613769605 2.040000e-07 67.6
21 TraesCS2D01G371600 chr6D 97.436 39 1 0 3138 3176 62227146 62227108 2.040000e-07 67.6


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G371600 chr2D 475983724 475986899 3175 False 5866.00 5866 100.0000 1 3176 1 chr2D.!!$F3 3175
1 TraesCS2D01G371600 chr2D 475876248 475877704 1456 False 2320.00 2320 95.4420 478 1935 1 chr2D.!!$F2 1457
2 TraesCS2D01G371600 chr2D 475498830 475500000 1170 False 1264.00 1264 86.3640 730 1935 1 chr2D.!!$F1 1205
3 TraesCS2D01G371600 chr2B 556675247 556678243 2996 False 3995.00 3995 90.9390 158 3137 1 chr2B.!!$F1 2979
4 TraesCS2D01G371600 chr2B 556517088 556518041 953 False 563.00 854 89.7995 918 1934 2 chr2B.!!$F2 1016
5 TraesCS2D01G371600 chr2B 556595395 556596540 1145 False 526.95 966 87.6410 722 1935 2 chr2B.!!$F3 1213
6 TraesCS2D01G371600 chr2A 617812444 617815301 2857 False 1643.00 2510 90.5985 695 3137 2 chr2A.!!$F3 2442
7 TraesCS2D01G371600 chr2A 617730579 617731549 970 False 983.00 983 85.1310 924 1935 1 chr2A.!!$F1 1011

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
107 108 0.037447 TTTGGGTCGGCACATGATGA 59.963 50.0 0.0 0.0 0.00 2.92 F
153 154 0.108585 GCTTCTGGGTGTCCTGTTGA 59.891 55.0 0.0 0.0 34.13 3.18 F
554 573 0.261696 AAACACCTGCAAACCTCCCT 59.738 50.0 0.0 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 2039 0.543174 GGGGTCAGAGGTGTGACTCT 60.543 60.0 7.05 0.00 45.85 3.24 R
1942 2045 1.673767 ATTGATGGGGTCAGAGGTGT 58.326 50.0 0.00 0.00 38.29 4.16 R
2523 2650 0.616891 ATCCGGTGTCCTTTGGTACC 59.383 55.0 4.43 4.43 0.00 3.34 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
25 26 7.091443 CCTAAAATGGATCGATACTAGTGACC 58.909 42.308 9.52 0.00 0.00 4.02
26 27 6.479972 AAAATGGATCGATACTAGTGACCA 57.520 37.500 9.52 4.91 0.00 4.02
27 28 6.479972 AAATGGATCGATACTAGTGACCAA 57.520 37.500 9.52 0.00 0.00 3.67
28 29 6.672266 AATGGATCGATACTAGTGACCAAT 57.328 37.500 9.52 0.00 0.00 3.16
29 30 5.707242 TGGATCGATACTAGTGACCAATC 57.293 43.478 9.52 0.00 0.00 2.67
30 31 5.137551 TGGATCGATACTAGTGACCAATCA 58.862 41.667 9.52 0.00 0.00 2.57
31 32 5.775195 TGGATCGATACTAGTGACCAATCAT 59.225 40.000 9.52 0.00 37.14 2.45
32 33 6.096036 GGATCGATACTAGTGACCAATCATG 58.904 44.000 5.39 0.00 37.14 3.07
33 34 4.871513 TCGATACTAGTGACCAATCATGC 58.128 43.478 5.39 0.00 37.14 4.06
34 35 3.990469 CGATACTAGTGACCAATCATGCC 59.010 47.826 5.39 0.00 37.14 4.40
35 36 4.262207 CGATACTAGTGACCAATCATGCCT 60.262 45.833 5.39 0.00 37.14 4.75
36 37 5.048013 CGATACTAGTGACCAATCATGCCTA 60.048 44.000 5.39 0.00 37.14 3.93
37 38 6.516693 CGATACTAGTGACCAATCATGCCTAA 60.517 42.308 5.39 0.00 37.14 2.69
38 39 4.770795 ACTAGTGACCAATCATGCCTAAC 58.229 43.478 0.00 0.00 37.14 2.34
39 40 3.719268 AGTGACCAATCATGCCTAACA 57.281 42.857 0.00 0.00 37.14 2.41
40 41 3.347216 AGTGACCAATCATGCCTAACAC 58.653 45.455 0.00 0.00 37.14 3.32
41 42 3.081061 GTGACCAATCATGCCTAACACA 58.919 45.455 0.00 0.00 37.14 3.72
42 43 3.505680 GTGACCAATCATGCCTAACACAA 59.494 43.478 0.00 0.00 37.14 3.33
43 44 3.505680 TGACCAATCATGCCTAACACAAC 59.494 43.478 0.00 0.00 0.00 3.32
44 45 3.495331 ACCAATCATGCCTAACACAACA 58.505 40.909 0.00 0.00 0.00 3.33
45 46 4.088634 ACCAATCATGCCTAACACAACAT 58.911 39.130 0.00 0.00 0.00 2.71
46 47 4.527816 ACCAATCATGCCTAACACAACATT 59.472 37.500 0.00 0.00 0.00 2.71
47 48 5.104374 CCAATCATGCCTAACACAACATTC 58.896 41.667 0.00 0.00 0.00 2.67
48 49 5.336610 CCAATCATGCCTAACACAACATTCA 60.337 40.000 0.00 0.00 0.00 2.57
49 50 6.334989 CAATCATGCCTAACACAACATTCAT 58.665 36.000 0.00 0.00 0.00 2.57
50 51 5.565592 TCATGCCTAACACAACATTCATC 57.434 39.130 0.00 0.00 0.00 2.92
51 52 4.398988 TCATGCCTAACACAACATTCATCC 59.601 41.667 0.00 0.00 0.00 3.51
52 53 4.032960 TGCCTAACACAACATTCATCCT 57.967 40.909 0.00 0.00 0.00 3.24
53 54 4.406456 TGCCTAACACAACATTCATCCTT 58.594 39.130 0.00 0.00 0.00 3.36
54 55 4.458989 TGCCTAACACAACATTCATCCTTC 59.541 41.667 0.00 0.00 0.00 3.46
55 56 4.702131 GCCTAACACAACATTCATCCTTCT 59.298 41.667 0.00 0.00 0.00 2.85
56 57 5.183904 GCCTAACACAACATTCATCCTTCTT 59.816 40.000 0.00 0.00 0.00 2.52
57 58 6.294731 GCCTAACACAACATTCATCCTTCTTT 60.295 38.462 0.00 0.00 0.00 2.52
58 59 7.661040 CCTAACACAACATTCATCCTTCTTTT 58.339 34.615 0.00 0.00 0.00 2.27
59 60 7.596248 CCTAACACAACATTCATCCTTCTTTTG 59.404 37.037 0.00 0.00 0.00 2.44
60 61 5.846203 ACACAACATTCATCCTTCTTTTGG 58.154 37.500 0.00 0.00 0.00 3.28
61 62 5.598005 ACACAACATTCATCCTTCTTTTGGA 59.402 36.000 0.00 0.00 38.06 3.53
62 63 6.098124 ACACAACATTCATCCTTCTTTTGGAA 59.902 34.615 0.00 0.00 37.13 3.53
63 64 6.985645 CACAACATTCATCCTTCTTTTGGAAA 59.014 34.615 0.00 0.00 37.13 3.13
64 65 7.495279 CACAACATTCATCCTTCTTTTGGAAAA 59.505 33.333 0.00 0.00 37.13 2.29
65 66 8.046107 ACAACATTCATCCTTCTTTTGGAAAAA 58.954 29.630 0.00 0.00 37.13 1.94
83 84 3.560357 AAAAATTAGCCCCCTCCACTT 57.440 42.857 0.00 0.00 0.00 3.16
84 85 2.828661 AAATTAGCCCCCTCCACTTC 57.171 50.000 0.00 0.00 0.00 3.01
85 86 1.987080 AATTAGCCCCCTCCACTTCT 58.013 50.000 0.00 0.00 0.00 2.85
86 87 1.987080 ATTAGCCCCCTCCACTTCTT 58.013 50.000 0.00 0.00 0.00 2.52
87 88 1.286248 TTAGCCCCCTCCACTTCTTC 58.714 55.000 0.00 0.00 0.00 2.87
88 89 0.417841 TAGCCCCCTCCACTTCTTCT 59.582 55.000 0.00 0.00 0.00 2.85
89 90 0.476611 AGCCCCCTCCACTTCTTCTT 60.477 55.000 0.00 0.00 0.00 2.52
90 91 0.405973 GCCCCCTCCACTTCTTCTTT 59.594 55.000 0.00 0.00 0.00 2.52
91 92 1.888391 GCCCCCTCCACTTCTTCTTTG 60.888 57.143 0.00 0.00 0.00 2.77
92 93 1.272147 CCCCCTCCACTTCTTCTTTGG 60.272 57.143 0.00 0.00 0.00 3.28
93 94 1.272147 CCCCTCCACTTCTTCTTTGGG 60.272 57.143 0.00 0.00 0.00 4.12
94 95 1.425448 CCCTCCACTTCTTCTTTGGGT 59.575 52.381 0.00 0.00 0.00 4.51
95 96 2.553247 CCCTCCACTTCTTCTTTGGGTC 60.553 54.545 0.00 0.00 0.00 4.46
96 97 2.417719 CTCCACTTCTTCTTTGGGTCG 58.582 52.381 0.00 0.00 0.00 4.79
97 98 1.071699 TCCACTTCTTCTTTGGGTCGG 59.928 52.381 0.00 0.00 0.00 4.79
98 99 0.875059 CACTTCTTCTTTGGGTCGGC 59.125 55.000 0.00 0.00 0.00 5.54
99 100 0.472471 ACTTCTTCTTTGGGTCGGCA 59.528 50.000 0.00 0.00 0.00 5.69
100 101 0.875059 CTTCTTCTTTGGGTCGGCAC 59.125 55.000 0.00 0.00 0.00 5.01
101 102 0.181587 TTCTTCTTTGGGTCGGCACA 59.818 50.000 0.00 0.00 0.00 4.57
102 103 0.400213 TCTTCTTTGGGTCGGCACAT 59.600 50.000 0.00 0.00 0.00 3.21
103 104 0.523072 CTTCTTTGGGTCGGCACATG 59.477 55.000 0.00 0.00 0.00 3.21
104 105 0.109532 TTCTTTGGGTCGGCACATGA 59.890 50.000 0.00 0.00 0.00 3.07
105 106 0.327924 TCTTTGGGTCGGCACATGAT 59.672 50.000 0.00 0.00 0.00 2.45
106 107 0.452987 CTTTGGGTCGGCACATGATG 59.547 55.000 0.00 0.00 0.00 3.07
107 108 0.037447 TTTGGGTCGGCACATGATGA 59.963 50.000 0.00 0.00 0.00 2.92
108 109 0.255604 TTGGGTCGGCACATGATGAT 59.744 50.000 0.00 0.00 0.00 2.45
109 110 0.179048 TGGGTCGGCACATGATGATC 60.179 55.000 0.00 0.00 0.00 2.92
110 111 0.179048 GGGTCGGCACATGATGATCA 60.179 55.000 0.00 0.00 0.00 2.92
111 112 0.940126 GGTCGGCACATGATGATCAC 59.060 55.000 0.00 0.00 0.00 3.06
112 113 1.473965 GGTCGGCACATGATGATCACT 60.474 52.381 0.00 0.00 0.00 3.41
113 114 1.596260 GTCGGCACATGATGATCACTG 59.404 52.381 0.00 0.43 0.00 3.66
114 115 0.306840 CGGCACATGATGATCACTGC 59.693 55.000 15.26 15.26 34.37 4.40
115 116 1.676746 GGCACATGATGATCACTGCT 58.323 50.000 20.24 0.00 35.09 4.24
116 117 1.602851 GGCACATGATGATCACTGCTC 59.397 52.381 20.24 10.99 35.09 4.26
117 118 2.285977 GCACATGATGATCACTGCTCA 58.714 47.619 15.97 0.00 33.10 4.26
118 119 2.031807 GCACATGATGATCACTGCTCAC 59.968 50.000 15.97 0.00 33.10 3.51
119 120 3.532542 CACATGATGATCACTGCTCACT 58.467 45.455 0.00 0.00 0.00 3.41
120 121 3.556365 CACATGATGATCACTGCTCACTC 59.444 47.826 0.00 0.00 0.00 3.51
121 122 2.573941 TGATGATCACTGCTCACTCG 57.426 50.000 0.00 0.00 0.00 4.18
122 123 1.135721 TGATGATCACTGCTCACTCGG 59.864 52.381 0.00 0.00 0.00 4.63
123 124 1.406898 GATGATCACTGCTCACTCGGA 59.593 52.381 0.00 0.00 0.00 4.55
124 125 1.478631 TGATCACTGCTCACTCGGAT 58.521 50.000 0.00 0.00 0.00 4.18
125 126 1.406898 TGATCACTGCTCACTCGGATC 59.593 52.381 0.00 0.00 33.52 3.36
126 127 0.749649 ATCACTGCTCACTCGGATCC 59.250 55.000 0.00 0.00 0.00 3.36
127 128 0.611896 TCACTGCTCACTCGGATCCA 60.612 55.000 13.41 0.00 0.00 3.41
128 129 0.463204 CACTGCTCACTCGGATCCAT 59.537 55.000 13.41 0.00 0.00 3.41
129 130 0.463204 ACTGCTCACTCGGATCCATG 59.537 55.000 13.41 6.94 0.00 3.66
130 131 0.463204 CTGCTCACTCGGATCCATGT 59.537 55.000 13.41 6.68 0.00 3.21
131 132 0.461548 TGCTCACTCGGATCCATGTC 59.538 55.000 13.41 4.57 0.00 3.06
132 133 0.749649 GCTCACTCGGATCCATGTCT 59.250 55.000 13.41 0.00 0.00 3.41
133 134 1.957177 GCTCACTCGGATCCATGTCTA 59.043 52.381 13.41 0.00 0.00 2.59
134 135 2.030363 GCTCACTCGGATCCATGTCTAG 60.030 54.545 13.41 9.84 0.00 2.43
135 136 1.957177 TCACTCGGATCCATGTCTAGC 59.043 52.381 13.41 0.00 0.00 3.42
136 137 1.959985 CACTCGGATCCATGTCTAGCT 59.040 52.381 13.41 0.00 0.00 3.32
137 138 2.363680 CACTCGGATCCATGTCTAGCTT 59.636 50.000 13.41 0.00 0.00 3.74
138 139 2.625790 ACTCGGATCCATGTCTAGCTTC 59.374 50.000 13.41 0.00 0.00 3.86
139 140 2.890311 CTCGGATCCATGTCTAGCTTCT 59.110 50.000 13.41 0.00 0.00 2.85
140 141 2.625314 TCGGATCCATGTCTAGCTTCTG 59.375 50.000 13.41 0.00 0.00 3.02
141 142 2.288702 CGGATCCATGTCTAGCTTCTGG 60.289 54.545 13.41 0.00 0.00 3.86
142 143 2.038295 GGATCCATGTCTAGCTTCTGGG 59.962 54.545 6.95 0.00 0.00 4.45
143 144 2.254152 TCCATGTCTAGCTTCTGGGT 57.746 50.000 0.00 0.00 0.00 4.51
144 145 1.833630 TCCATGTCTAGCTTCTGGGTG 59.166 52.381 0.00 0.00 0.00 4.61
145 146 1.556911 CCATGTCTAGCTTCTGGGTGT 59.443 52.381 0.00 0.00 0.00 4.16
146 147 2.419297 CCATGTCTAGCTTCTGGGTGTC 60.419 54.545 0.00 0.00 0.00 3.67
147 148 1.267121 TGTCTAGCTTCTGGGTGTCC 58.733 55.000 0.00 0.00 0.00 4.02
148 149 1.203187 TGTCTAGCTTCTGGGTGTCCT 60.203 52.381 0.00 0.00 0.00 3.85
149 150 1.205893 GTCTAGCTTCTGGGTGTCCTG 59.794 57.143 0.00 0.00 0.00 3.86
150 151 1.203187 TCTAGCTTCTGGGTGTCCTGT 60.203 52.381 0.00 0.00 34.13 4.00
151 152 1.625818 CTAGCTTCTGGGTGTCCTGTT 59.374 52.381 0.00 0.00 34.13 3.16
152 153 0.109342 AGCTTCTGGGTGTCCTGTTG 59.891 55.000 0.00 0.00 34.13 3.33
153 154 0.108585 GCTTCTGGGTGTCCTGTTGA 59.891 55.000 0.00 0.00 34.13 3.18
154 155 1.879796 GCTTCTGGGTGTCCTGTTGAG 60.880 57.143 0.00 0.00 34.13 3.02
155 156 1.417890 CTTCTGGGTGTCCTGTTGAGT 59.582 52.381 0.00 0.00 34.13 3.41
156 157 0.758734 TCTGGGTGTCCTGTTGAGTG 59.241 55.000 0.00 0.00 34.13 3.51
165 166 1.571460 CTGTTGAGTGTTCGGCTGC 59.429 57.895 0.00 0.00 0.00 5.25
169 170 2.355837 GAGTGTTCGGCTGCGACA 60.356 61.111 0.00 0.00 0.00 4.35
171 172 2.159272 GAGTGTTCGGCTGCGACAAC 62.159 60.000 3.53 2.70 0.00 3.32
186 187 1.729131 CAACCACGCCGTTGATTGC 60.729 57.895 9.06 0.00 44.88 3.56
193 194 3.055719 CCGTTGATTGCGTGGGCT 61.056 61.111 0.00 0.00 40.82 5.19
229 230 0.739561 GAGCTATGTCGGACGAGGTT 59.260 55.000 13.61 0.88 0.00 3.50
231 232 0.591741 GCTATGTCGGACGAGGTTCG 60.592 60.000 3.34 0.00 46.93 3.95
232 233 0.591741 CTATGTCGGACGAGGTTCGC 60.592 60.000 3.34 0.00 45.12 4.70
236 237 2.202492 CGGACGAGGTTCGCTCTG 60.202 66.667 0.00 0.00 45.12 3.35
241 242 2.182030 GAGGTTCGCTCTGACCGG 59.818 66.667 0.00 0.00 0.00 5.28
242 243 3.991536 GAGGTTCGCTCTGACCGGC 62.992 68.421 0.00 0.00 0.00 6.13
244 245 4.070552 GTTCGCTCTGACCGGCCT 62.071 66.667 0.00 0.00 0.00 5.19
248 249 4.154347 GCTCTGACCGGCCTCCTG 62.154 72.222 0.00 0.00 0.00 3.86
267 268 3.119096 GCACCGCCCGACTTCTTC 61.119 66.667 0.00 0.00 0.00 2.87
292 293 3.683966 TTGTGGCGACGGGTGTTGT 62.684 57.895 0.00 0.00 0.00 3.32
301 302 1.227438 CGGGTGTTGTCTTCCACGT 60.227 57.895 0.00 0.00 32.30 4.49
303 304 0.883370 GGGTGTTGTCTTCCACGTCC 60.883 60.000 0.00 0.00 32.30 4.79
307 308 3.851845 TTGTCTTCCACGTCCGCGG 62.852 63.158 22.12 22.12 43.45 6.46
370 371 1.068474 GACGACAATCAACGGTCCTG 58.932 55.000 0.00 0.00 0.00 3.86
372 373 1.787847 GACAATCAACGGTCCTGCG 59.212 57.895 0.00 0.00 0.00 5.18
388 407 4.752879 CGGCGGTGGACCACGAAT 62.753 66.667 18.40 0.00 37.99 3.34
413 432 1.872197 GAGGGAGGCGATGATCGAGG 61.872 65.000 20.25 0.00 43.74 4.63
416 435 1.068083 GAGGCGATGATCGAGGCAA 59.932 57.895 20.25 0.00 43.74 4.52
421 440 0.848942 CGATGATCGAGGCAAAGACG 59.151 55.000 9.62 0.00 43.74 4.18
422 441 1.212616 GATGATCGAGGCAAAGACGG 58.787 55.000 0.00 0.00 0.00 4.79
443 462 1.548986 GAAAATGGATGGCTTTCGCG 58.451 50.000 0.00 0.00 36.88 5.87
447 466 0.676466 ATGGATGGCTTTCGCGTGAA 60.676 50.000 7.45 7.45 36.88 3.18
463 482 4.438065 CGCGTGAAAACATTGATGGGAATA 60.438 41.667 0.00 0.00 0.00 1.75
466 485 6.460123 GCGTGAAAACATTGATGGGAATATCT 60.460 38.462 0.00 0.00 0.00 1.98
472 491 9.768662 AAAACATTGATGGGAATATCTAAATGC 57.231 29.630 0.00 0.00 29.96 3.56
474 493 5.627499 TTGATGGGAATATCTAAATGCGC 57.373 39.130 0.00 0.00 0.00 6.09
526 545 3.360340 GTCCGAGTCCGACGTGGT 61.360 66.667 0.00 0.00 39.52 4.16
539 558 1.521906 CGTGGTGGTCGTCCAAACA 60.522 57.895 2.02 3.07 46.15 2.83
542 561 4.870190 GTGGTCGTCCAAACACCT 57.130 55.556 2.02 0.00 46.15 4.00
554 573 0.261696 AAACACCTGCAAACCTCCCT 59.738 50.000 0.00 0.00 0.00 4.20
559 578 1.710809 ACCTGCAAACCTCCCTTATGT 59.289 47.619 0.00 0.00 0.00 2.29
568 587 6.295292 GCAAACCTCCCTTATGTTTTGATTCT 60.295 38.462 0.00 0.00 30.19 2.40
582 601 9.635520 ATGTTTTGATTCTGATTTGTGAGATTC 57.364 29.630 0.00 0.00 0.00 2.52
617 636 6.238484 GGATCGGTCCAGACAAATTTAATGAG 60.238 42.308 10.69 0.00 44.42 2.90
618 637 5.556915 TCGGTCCAGACAAATTTAATGAGT 58.443 37.500 0.00 0.00 0.00 3.41
619 638 5.411361 TCGGTCCAGACAAATTTAATGAGTG 59.589 40.000 0.00 0.00 0.00 3.51
634 653 0.668535 GAGTGTTGTTGGAGGGCAAC 59.331 55.000 0.00 0.00 43.60 4.17
661 680 6.906157 ATGTCTGAACTGTTTGATCCAAAT 57.094 33.333 0.00 0.00 35.74 2.32
671 690 7.189087 ACTGTTTGATCCAAATATTTAGGGGT 58.811 34.615 0.00 0.00 35.74 4.95
672 691 7.124147 ACTGTTTGATCCAAATATTTAGGGGTG 59.876 37.037 0.00 0.00 35.74 4.61
673 692 7.185565 TGTTTGATCCAAATATTTAGGGGTGA 58.814 34.615 0.00 0.00 35.74 4.02
678 697 8.064389 TGATCCAAATATTTAGGGGTGATTTGA 58.936 33.333 0.00 0.00 38.99 2.69
689 708 3.571401 GGGGTGATTTGATGATCCATGTC 59.429 47.826 0.00 0.00 0.00 3.06
693 720 3.811497 TGATTTGATGATCCATGTCGCTC 59.189 43.478 0.00 0.00 0.00 5.03
751 778 1.528076 TGCATGTGACAGCCGGTTT 60.528 52.632 1.90 0.00 0.00 3.27
1936 2039 4.519437 CTCGAGCAGGCCATCGCA 62.519 66.667 17.33 8.03 38.79 5.10
1942 2045 2.580815 CAGGCCATCGCAGAGTCA 59.419 61.111 5.01 0.00 43.63 3.41
1995 2098 1.270110 CGTACGCGCTGTGTGTGTTA 61.270 55.000 16.96 0.00 42.47 2.41
2482 2609 9.279904 CGTTATTTGTTGAACTGAAAAGTACAA 57.720 29.630 0.00 0.00 0.00 2.41
2507 2634 2.262423 AAGAAACAGCACTGGGAGAC 57.738 50.000 2.21 0.00 34.19 3.36
2523 2650 3.638484 GGAGACCAAAATTTGTGGAACG 58.362 45.455 12.75 0.00 42.39 3.95
2524 2651 3.552068 GGAGACCAAAATTTGTGGAACGG 60.552 47.826 12.75 4.74 42.39 4.44
2596 3139 1.734465 GTGGTGACAACTAGCTGCATC 59.266 52.381 1.02 0.00 46.06 3.91
2597 3140 1.347378 TGGTGACAACTAGCTGCATCA 59.653 47.619 1.02 0.00 37.44 3.07
2598 3141 2.026915 TGGTGACAACTAGCTGCATCAT 60.027 45.455 1.02 0.00 37.44 2.45
2599 3142 2.353889 GGTGACAACTAGCTGCATCATG 59.646 50.000 1.02 0.00 0.00 3.07
2600 3143 3.264947 GTGACAACTAGCTGCATCATGA 58.735 45.455 1.02 0.00 0.00 3.07
2601 3144 3.686241 GTGACAACTAGCTGCATCATGAA 59.314 43.478 0.00 0.00 0.00 2.57
2602 3145 4.154737 GTGACAACTAGCTGCATCATGAAA 59.845 41.667 0.00 0.00 0.00 2.69
2603 3146 4.761227 TGACAACTAGCTGCATCATGAAAA 59.239 37.500 0.00 0.00 0.00 2.29
2604 3147 5.106436 TGACAACTAGCTGCATCATGAAAAG 60.106 40.000 0.00 0.00 0.00 2.27
2605 3148 4.103357 CAACTAGCTGCATCATGAAAAGC 58.897 43.478 15.99 15.99 0.00 3.51
2606 3149 3.618351 ACTAGCTGCATCATGAAAAGCT 58.382 40.909 24.74 24.74 45.72 3.74
2607 3150 2.941453 AGCTGCATCATGAAAAGCTG 57.059 45.000 22.32 18.93 42.44 4.24
2608 3151 1.278238 GCTGCATCATGAAAAGCTGC 58.722 50.000 23.54 23.54 42.90 5.25
2609 3152 1.403647 GCTGCATCATGAAAAGCTGCA 60.404 47.619 28.34 23.77 46.72 4.41
2610 3153 2.738643 GCTGCATCATGAAAAGCTGCAT 60.739 45.455 28.34 0.62 46.72 3.96
2697 3240 4.868450 TCCCAACGAAATTAATACAGCG 57.132 40.909 0.00 0.00 0.00 5.18
2751 3295 8.071967 CGAATATTCTGATAACACATGCATGTT 58.928 33.333 29.48 19.29 44.87 2.71
2761 3305 9.467258 GATAACACATGCATGTTGCTATTTTAT 57.533 29.630 29.48 19.49 45.31 1.40
2968 3538 3.436700 AAAAGGTCAAACCGAAAGCAG 57.563 42.857 0.00 0.00 44.90 4.24
3012 3582 1.473258 ATTGCTTTGCTTCGGCCATA 58.527 45.000 2.24 0.00 40.91 2.74
3058 3628 4.252878 CCAAACACTTTTGAAGGCTTGTT 58.747 39.130 3.46 0.00 44.38 2.83
3137 3708 2.067013 GTCGAGGCAACCTTCAACTAC 58.933 52.381 0.00 0.00 31.76 2.73
3138 3709 1.689813 TCGAGGCAACCTTCAACTACA 59.310 47.619 0.00 0.00 31.76 2.74
3139 3710 1.798813 CGAGGCAACCTTCAACTACAC 59.201 52.381 0.00 0.00 31.76 2.90
3140 3711 2.548067 CGAGGCAACCTTCAACTACACT 60.548 50.000 0.00 0.00 31.76 3.55
3141 3712 3.305813 CGAGGCAACCTTCAACTACACTA 60.306 47.826 0.00 0.00 31.76 2.74
3142 3713 4.246458 GAGGCAACCTTCAACTACACTAG 58.754 47.826 0.00 0.00 31.76 2.57
3143 3714 3.646637 AGGCAACCTTCAACTACACTAGT 59.353 43.478 0.00 0.00 37.91 2.57
3144 3715 4.836736 AGGCAACCTTCAACTACACTAGTA 59.163 41.667 0.00 0.00 35.60 1.82
3145 3716 5.047235 AGGCAACCTTCAACTACACTAGTAG 60.047 44.000 0.00 0.00 45.91 2.57
3146 3717 7.200655 AGGCAACCTTCAACTACACTAGTAGA 61.201 42.308 3.59 0.00 44.26 2.59
3147 3718 8.616628 AGGCAACCTTCAACTACACTAGTAGAA 61.617 40.741 3.59 0.00 44.26 2.10
3160 3731 7.745620 ACACTAGTAGAAAAAGGGTCATTTG 57.254 36.000 3.59 0.00 0.00 2.32
3161 3732 7.287810 ACACTAGTAGAAAAAGGGTCATTTGT 58.712 34.615 3.59 0.00 0.00 2.83
3162 3733 7.444487 ACACTAGTAGAAAAAGGGTCATTTGTC 59.556 37.037 3.59 0.00 0.00 3.18
3163 3734 6.940867 ACTAGTAGAAAAAGGGTCATTTGTCC 59.059 38.462 3.59 0.00 28.13 4.02
3164 3735 5.077564 AGTAGAAAAAGGGTCATTTGTCCC 58.922 41.667 4.88 4.88 42.66 4.46
3165 3736 2.890945 AGAAAAAGGGTCATTTGTCCCG 59.109 45.455 7.15 0.00 46.13 5.14
3166 3737 2.668144 AAAAGGGTCATTTGTCCCGA 57.332 45.000 7.15 0.00 46.13 5.14
3167 3738 2.899303 AAAGGGTCATTTGTCCCGAT 57.101 45.000 7.15 0.00 46.13 4.18
3168 3739 2.899303 AAGGGTCATTTGTCCCGATT 57.101 45.000 7.15 0.00 46.13 3.34
3169 3740 2.420058 AGGGTCATTTGTCCCGATTC 57.580 50.000 7.15 0.00 46.13 2.52
3170 3741 1.633432 AGGGTCATTTGTCCCGATTCA 59.367 47.619 7.15 0.00 46.13 2.57
3171 3742 2.242196 AGGGTCATTTGTCCCGATTCAT 59.758 45.455 7.15 0.00 46.13 2.57
3172 3743 3.458118 AGGGTCATTTGTCCCGATTCATA 59.542 43.478 7.15 0.00 46.13 2.15
3173 3744 4.080015 AGGGTCATTTGTCCCGATTCATAA 60.080 41.667 7.15 0.00 46.13 1.90
3174 3745 4.275936 GGGTCATTTGTCCCGATTCATAAG 59.724 45.833 0.00 0.00 33.91 1.73
3175 3746 4.275936 GGTCATTTGTCCCGATTCATAAGG 59.724 45.833 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.091443 GGTCACTAGTATCGATCCATTTTAGG 58.909 42.308 0.00 0.00 0.00 2.69
1 2 7.658261 TGGTCACTAGTATCGATCCATTTTAG 58.342 38.462 0.00 0.00 0.00 1.85
2 3 7.591421 TGGTCACTAGTATCGATCCATTTTA 57.409 36.000 0.00 0.00 0.00 1.52
3 4 6.479972 TGGTCACTAGTATCGATCCATTTT 57.520 37.500 0.00 0.00 0.00 1.82
4 5 6.479972 TTGGTCACTAGTATCGATCCATTT 57.520 37.500 0.00 0.00 0.00 2.32
5 6 6.267699 TGATTGGTCACTAGTATCGATCCATT 59.732 38.462 0.00 0.00 0.00 3.16
6 7 5.775195 TGATTGGTCACTAGTATCGATCCAT 59.225 40.000 0.00 0.00 0.00 3.41
7 8 5.137551 TGATTGGTCACTAGTATCGATCCA 58.862 41.667 0.00 0.00 0.00 3.41
8 9 5.707242 TGATTGGTCACTAGTATCGATCC 57.293 43.478 0.00 0.00 0.00 3.36
9 10 5.574830 GCATGATTGGTCACTAGTATCGATC 59.425 44.000 0.00 4.11 37.14 3.69
10 11 5.473931 GCATGATTGGTCACTAGTATCGAT 58.526 41.667 2.16 2.16 37.14 3.59
11 12 4.262036 GGCATGATTGGTCACTAGTATCGA 60.262 45.833 0.00 0.00 37.14 3.59
12 13 3.990469 GGCATGATTGGTCACTAGTATCG 59.010 47.826 0.00 0.00 37.14 2.92
13 14 5.220710 AGGCATGATTGGTCACTAGTATC 57.779 43.478 0.00 0.00 37.14 2.24
14 15 6.099701 TGTTAGGCATGATTGGTCACTAGTAT 59.900 38.462 0.00 0.00 37.14 2.12
15 16 5.423931 TGTTAGGCATGATTGGTCACTAGTA 59.576 40.000 0.00 0.00 37.14 1.82
16 17 4.225042 TGTTAGGCATGATTGGTCACTAGT 59.775 41.667 0.00 0.00 37.14 2.57
17 18 4.572389 GTGTTAGGCATGATTGGTCACTAG 59.428 45.833 0.00 0.00 37.14 2.57
18 19 4.019771 TGTGTTAGGCATGATTGGTCACTA 60.020 41.667 0.00 0.00 37.14 2.74
19 20 3.244875 TGTGTTAGGCATGATTGGTCACT 60.245 43.478 0.00 0.00 37.14 3.41
20 21 3.081061 TGTGTTAGGCATGATTGGTCAC 58.919 45.455 0.00 0.00 37.14 3.67
21 22 3.431673 TGTGTTAGGCATGATTGGTCA 57.568 42.857 0.00 0.00 39.04 4.02
22 23 3.505680 TGTTGTGTTAGGCATGATTGGTC 59.494 43.478 0.00 0.00 0.00 4.02
23 24 3.495331 TGTTGTGTTAGGCATGATTGGT 58.505 40.909 0.00 0.00 0.00 3.67
24 25 4.724074 ATGTTGTGTTAGGCATGATTGG 57.276 40.909 0.00 0.00 0.00 3.16
25 26 5.712004 TGAATGTTGTGTTAGGCATGATTG 58.288 37.500 0.00 0.00 0.00 2.67
26 27 5.981088 TGAATGTTGTGTTAGGCATGATT 57.019 34.783 0.00 0.00 0.00 2.57
27 28 5.068198 GGATGAATGTTGTGTTAGGCATGAT 59.932 40.000 0.00 0.00 0.00 2.45
28 29 4.398988 GGATGAATGTTGTGTTAGGCATGA 59.601 41.667 0.00 0.00 0.00 3.07
29 30 4.400251 AGGATGAATGTTGTGTTAGGCATG 59.600 41.667 0.00 0.00 0.00 4.06
30 31 4.603131 AGGATGAATGTTGTGTTAGGCAT 58.397 39.130 0.00 0.00 0.00 4.40
31 32 4.032960 AGGATGAATGTTGTGTTAGGCA 57.967 40.909 0.00 0.00 0.00 4.75
32 33 4.702131 AGAAGGATGAATGTTGTGTTAGGC 59.298 41.667 0.00 0.00 0.00 3.93
33 34 6.824305 AAGAAGGATGAATGTTGTGTTAGG 57.176 37.500 0.00 0.00 0.00 2.69
34 35 7.596248 CCAAAAGAAGGATGAATGTTGTGTTAG 59.404 37.037 0.00 0.00 0.00 2.34
35 36 7.286546 TCCAAAAGAAGGATGAATGTTGTGTTA 59.713 33.333 0.00 0.00 0.00 2.41
36 37 6.098124 TCCAAAAGAAGGATGAATGTTGTGTT 59.902 34.615 0.00 0.00 0.00 3.32
37 38 5.598005 TCCAAAAGAAGGATGAATGTTGTGT 59.402 36.000 0.00 0.00 0.00 3.72
38 39 6.088016 TCCAAAAGAAGGATGAATGTTGTG 57.912 37.500 0.00 0.00 0.00 3.33
39 40 6.729690 TTCCAAAAGAAGGATGAATGTTGT 57.270 33.333 0.00 0.00 34.56 3.32
40 41 8.436046 TTTTTCCAAAAGAAGGATGAATGTTG 57.564 30.769 0.00 0.00 35.40 3.33
63 64 3.077543 AGAAGTGGAGGGGGCTAATTTTT 59.922 43.478 0.00 0.00 0.00 1.94
64 65 2.654896 AGAAGTGGAGGGGGCTAATTTT 59.345 45.455 0.00 0.00 0.00 1.82
65 66 2.288525 AGAAGTGGAGGGGGCTAATTT 58.711 47.619 0.00 0.00 0.00 1.82
66 67 1.987080 AGAAGTGGAGGGGGCTAATT 58.013 50.000 0.00 0.00 0.00 1.40
67 68 1.847088 GAAGAAGTGGAGGGGGCTAAT 59.153 52.381 0.00 0.00 0.00 1.73
68 69 1.203440 AGAAGAAGTGGAGGGGGCTAA 60.203 52.381 0.00 0.00 0.00 3.09
69 70 0.417841 AGAAGAAGTGGAGGGGGCTA 59.582 55.000 0.00 0.00 0.00 3.93
70 71 0.476611 AAGAAGAAGTGGAGGGGGCT 60.477 55.000 0.00 0.00 0.00 5.19
71 72 0.405973 AAAGAAGAAGTGGAGGGGGC 59.594 55.000 0.00 0.00 0.00 5.80
72 73 1.272147 CCAAAGAAGAAGTGGAGGGGG 60.272 57.143 0.00 0.00 34.05 5.40
73 74 1.272147 CCCAAAGAAGAAGTGGAGGGG 60.272 57.143 0.00 0.00 34.05 4.79
74 75 1.425448 ACCCAAAGAAGAAGTGGAGGG 59.575 52.381 0.00 0.00 40.88 4.30
75 76 2.784347 GACCCAAAGAAGAAGTGGAGG 58.216 52.381 0.00 0.00 34.05 4.30
76 77 2.417719 CGACCCAAAGAAGAAGTGGAG 58.582 52.381 0.00 0.00 34.05 3.86
77 78 1.071699 CCGACCCAAAGAAGAAGTGGA 59.928 52.381 0.00 0.00 34.05 4.02
78 79 1.523758 CCGACCCAAAGAAGAAGTGG 58.476 55.000 0.00 0.00 0.00 4.00
79 80 0.875059 GCCGACCCAAAGAAGAAGTG 59.125 55.000 0.00 0.00 0.00 3.16
80 81 0.472471 TGCCGACCCAAAGAAGAAGT 59.528 50.000 0.00 0.00 0.00 3.01
81 82 0.875059 GTGCCGACCCAAAGAAGAAG 59.125 55.000 0.00 0.00 0.00 2.85
82 83 0.181587 TGTGCCGACCCAAAGAAGAA 59.818 50.000 0.00 0.00 0.00 2.52
83 84 0.400213 ATGTGCCGACCCAAAGAAGA 59.600 50.000 0.00 0.00 0.00 2.87
84 85 0.523072 CATGTGCCGACCCAAAGAAG 59.477 55.000 0.00 0.00 0.00 2.85
85 86 0.109532 TCATGTGCCGACCCAAAGAA 59.890 50.000 0.00 0.00 0.00 2.52
86 87 0.327924 ATCATGTGCCGACCCAAAGA 59.672 50.000 0.00 0.00 0.00 2.52
87 88 0.452987 CATCATGTGCCGACCCAAAG 59.547 55.000 0.00 0.00 0.00 2.77
88 89 0.037447 TCATCATGTGCCGACCCAAA 59.963 50.000 0.00 0.00 0.00 3.28
89 90 0.255604 ATCATCATGTGCCGACCCAA 59.744 50.000 0.00 0.00 0.00 4.12
90 91 0.179048 GATCATCATGTGCCGACCCA 60.179 55.000 0.00 0.00 0.00 4.51
91 92 0.179048 TGATCATCATGTGCCGACCC 60.179 55.000 0.00 0.00 0.00 4.46
92 93 0.940126 GTGATCATCATGTGCCGACC 59.060 55.000 0.00 0.00 0.00 4.79
93 94 1.596260 CAGTGATCATCATGTGCCGAC 59.404 52.381 0.00 0.00 0.00 4.79
94 95 1.944032 CAGTGATCATCATGTGCCGA 58.056 50.000 0.00 0.00 0.00 5.54
95 96 0.306840 GCAGTGATCATCATGTGCCG 59.693 55.000 12.12 0.00 34.81 5.69
96 97 1.602851 GAGCAGTGATCATCATGTGCC 59.397 52.381 17.37 8.62 38.95 5.01
97 98 2.031807 GTGAGCAGTGATCATCATGTGC 59.968 50.000 15.17 14.45 38.64 4.57
98 99 3.532542 AGTGAGCAGTGATCATCATGTG 58.467 45.455 15.17 0.00 28.52 3.21
99 100 3.737355 CGAGTGAGCAGTGATCATCATGT 60.737 47.826 15.17 0.00 28.52 3.21
100 101 2.795470 CGAGTGAGCAGTGATCATCATG 59.205 50.000 15.17 1.63 28.52 3.07
101 102 2.223994 CCGAGTGAGCAGTGATCATCAT 60.224 50.000 15.17 3.88 28.52 2.45
102 103 1.135721 CCGAGTGAGCAGTGATCATCA 59.864 52.381 15.17 0.00 28.52 3.07
103 104 1.406898 TCCGAGTGAGCAGTGATCATC 59.593 52.381 15.17 11.62 28.52 2.92
104 105 1.478631 TCCGAGTGAGCAGTGATCAT 58.521 50.000 15.17 3.74 28.52 2.45
105 106 1.406898 GATCCGAGTGAGCAGTGATCA 59.593 52.381 7.06 7.06 31.27 2.92
106 107 1.269517 GGATCCGAGTGAGCAGTGATC 60.270 57.143 0.17 0.17 0.00 2.92
107 108 0.749649 GGATCCGAGTGAGCAGTGAT 59.250 55.000 0.00 0.00 0.00 3.06
108 109 0.611896 TGGATCCGAGTGAGCAGTGA 60.612 55.000 7.39 0.00 0.00 3.41
109 110 0.463204 ATGGATCCGAGTGAGCAGTG 59.537 55.000 7.39 0.00 0.00 3.66
110 111 0.463204 CATGGATCCGAGTGAGCAGT 59.537 55.000 7.39 0.00 0.00 4.40
111 112 0.463204 ACATGGATCCGAGTGAGCAG 59.537 55.000 15.93 0.00 0.00 4.24
112 113 0.461548 GACATGGATCCGAGTGAGCA 59.538 55.000 13.06 0.00 0.00 4.26
113 114 0.749649 AGACATGGATCCGAGTGAGC 59.250 55.000 13.06 7.18 0.00 4.26
114 115 2.030363 GCTAGACATGGATCCGAGTGAG 60.030 54.545 13.06 10.73 0.00 3.51
115 116 1.957177 GCTAGACATGGATCCGAGTGA 59.043 52.381 13.06 1.54 0.00 3.41
116 117 1.959985 AGCTAGACATGGATCCGAGTG 59.040 52.381 13.06 11.08 0.00 3.51
117 118 2.373335 AGCTAGACATGGATCCGAGT 57.627 50.000 7.39 8.00 0.00 4.18
118 119 2.890311 AGAAGCTAGACATGGATCCGAG 59.110 50.000 7.39 4.36 0.00 4.63
119 120 2.625314 CAGAAGCTAGACATGGATCCGA 59.375 50.000 7.39 0.00 0.00 4.55
120 121 2.288702 CCAGAAGCTAGACATGGATCCG 60.289 54.545 7.39 0.00 32.55 4.18
121 122 2.038295 CCCAGAAGCTAGACATGGATCC 59.962 54.545 4.20 4.20 32.55 3.36
122 123 2.703007 ACCCAGAAGCTAGACATGGATC 59.297 50.000 0.00 0.00 32.55 3.36
123 124 2.437281 CACCCAGAAGCTAGACATGGAT 59.563 50.000 0.00 0.00 32.55 3.41
124 125 1.833630 CACCCAGAAGCTAGACATGGA 59.166 52.381 0.00 0.00 32.55 3.41
125 126 1.556911 ACACCCAGAAGCTAGACATGG 59.443 52.381 0.00 0.00 0.00 3.66
126 127 2.419297 GGACACCCAGAAGCTAGACATG 60.419 54.545 0.00 0.00 0.00 3.21
127 128 1.834263 GGACACCCAGAAGCTAGACAT 59.166 52.381 0.00 0.00 0.00 3.06
128 129 1.203187 AGGACACCCAGAAGCTAGACA 60.203 52.381 0.00 0.00 33.88 3.41
129 130 1.205893 CAGGACACCCAGAAGCTAGAC 59.794 57.143 0.00 0.00 33.88 2.59
130 131 1.203187 ACAGGACACCCAGAAGCTAGA 60.203 52.381 0.00 0.00 33.88 2.43
131 132 1.270907 ACAGGACACCCAGAAGCTAG 58.729 55.000 0.00 0.00 33.88 3.42
132 133 1.347707 CAACAGGACACCCAGAAGCTA 59.652 52.381 0.00 0.00 33.88 3.32
133 134 0.109342 CAACAGGACACCCAGAAGCT 59.891 55.000 0.00 0.00 33.88 3.74
134 135 0.108585 TCAACAGGACACCCAGAAGC 59.891 55.000 0.00 0.00 33.88 3.86
135 136 1.417890 ACTCAACAGGACACCCAGAAG 59.582 52.381 0.00 0.00 33.88 2.85
136 137 1.140852 CACTCAACAGGACACCCAGAA 59.859 52.381 0.00 0.00 33.88 3.02
137 138 0.758734 CACTCAACAGGACACCCAGA 59.241 55.000 0.00 0.00 33.88 3.86
138 139 0.469917 ACACTCAACAGGACACCCAG 59.530 55.000 0.00 0.00 33.88 4.45
139 140 0.916086 AACACTCAACAGGACACCCA 59.084 50.000 0.00 0.00 33.88 4.51
140 141 1.594331 GAACACTCAACAGGACACCC 58.406 55.000 0.00 0.00 0.00 4.61
141 142 1.217882 CGAACACTCAACAGGACACC 58.782 55.000 0.00 0.00 0.00 4.16
142 143 1.217882 CCGAACACTCAACAGGACAC 58.782 55.000 0.00 0.00 0.00 3.67
143 144 0.531974 GCCGAACACTCAACAGGACA 60.532 55.000 0.00 0.00 0.00 4.02
144 145 0.249911 AGCCGAACACTCAACAGGAC 60.250 55.000 0.00 0.00 0.00 3.85
145 146 0.249868 CAGCCGAACACTCAACAGGA 60.250 55.000 0.00 0.00 0.00 3.86
146 147 1.845809 GCAGCCGAACACTCAACAGG 61.846 60.000 0.00 0.00 0.00 4.00
147 148 1.571460 GCAGCCGAACACTCAACAG 59.429 57.895 0.00 0.00 0.00 3.16
148 149 2.243957 CGCAGCCGAACACTCAACA 61.244 57.895 0.00 0.00 36.29 3.33
149 150 1.954146 TCGCAGCCGAACACTCAAC 60.954 57.895 0.00 0.00 41.17 3.18
150 151 1.954146 GTCGCAGCCGAACACTCAA 60.954 57.895 0.00 0.00 46.34 3.02
151 152 2.355837 GTCGCAGCCGAACACTCA 60.356 61.111 0.00 0.00 46.34 3.41
152 153 1.954146 TTGTCGCAGCCGAACACTC 60.954 57.895 0.00 0.00 46.34 3.51
153 154 2.108157 TTGTCGCAGCCGAACACT 59.892 55.556 0.00 0.00 46.34 3.55
154 155 2.248431 GTTGTCGCAGCCGAACAC 59.752 61.111 0.00 0.00 46.34 3.32
155 156 2.970324 GGTTGTCGCAGCCGAACA 60.970 61.111 0.00 0.00 46.34 3.18
156 157 2.970324 TGGTTGTCGCAGCCGAAC 60.970 61.111 7.87 0.00 46.34 3.95
165 166 1.837538 AATCAACGGCGTGGTTGTCG 61.838 55.000 15.70 0.00 45.75 4.35
169 170 2.642700 GCAATCAACGGCGTGGTT 59.357 55.556 15.70 7.78 0.00 3.67
175 176 4.776647 GCCCACGCAATCAACGGC 62.777 66.667 0.00 0.00 34.03 5.68
180 181 1.376683 GGTGTAGCCCACGCAATCA 60.377 57.895 2.45 0.00 45.52 2.57
186 187 3.319198 ACCCTGGTGTAGCCCACG 61.319 66.667 0.00 0.00 45.52 4.94
188 189 2.933287 CCACCCTGGTGTAGCCCA 60.933 66.667 14.89 0.00 44.02 5.36
189 190 4.426313 GCCACCCTGGTGTAGCCC 62.426 72.222 14.89 0.00 44.02 5.19
198 199 2.786495 ATAGCTCGTCGCCACCCTG 61.786 63.158 0.00 0.00 40.39 4.45
210 211 0.739561 AACCTCGTCCGACATAGCTC 59.260 55.000 0.00 0.00 0.00 4.09
223 224 2.202492 CGGTCAGAGCGAACCTCG 60.202 66.667 17.25 0.00 45.54 4.63
231 232 4.154347 CAGGAGGCCGGTCAGAGC 62.154 72.222 9.71 0.00 0.00 4.09
232 233 4.154347 GCAGGAGGCCGGTCAGAG 62.154 72.222 9.71 0.00 36.11 3.35
254 255 2.202623 CGAGGAAGAAGTCGGGCG 60.203 66.667 0.00 0.00 32.40 6.13
258 259 0.038159 ACAAGGCGAGGAAGAAGTCG 60.038 55.000 0.00 0.00 39.25 4.18
284 285 0.883370 GGACGTGGAAGACAACACCC 60.883 60.000 0.00 0.00 34.18 4.61
286 287 1.828331 GCGGACGTGGAAGACAACAC 61.828 60.000 0.00 0.00 0.00 3.32
287 288 1.593209 GCGGACGTGGAAGACAACA 60.593 57.895 0.00 0.00 0.00 3.33
326 327 1.376037 GAGCCAAAGGACCCGAGTG 60.376 63.158 0.00 0.00 0.00 3.51
327 328 2.593956 GGAGCCAAAGGACCCGAGT 61.594 63.158 0.00 0.00 0.00 4.18
349 350 1.017701 GGACCGTTGATTGTCGTCCC 61.018 60.000 0.00 0.00 32.19 4.46
352 353 0.949105 GCAGGACCGTTGATTGTCGT 60.949 55.000 0.00 0.00 32.19 4.34
372 373 3.124921 CATTCGTGGTCCACCGCC 61.125 66.667 16.60 0.00 43.41 6.13
378 379 0.464452 CCTCCTACCATTCGTGGTCC 59.536 60.000 2.92 0.00 42.99 4.46
379 380 0.464452 CCCTCCTACCATTCGTGGTC 59.536 60.000 2.92 0.00 42.99 4.02
380 381 0.042131 TCCCTCCTACCATTCGTGGT 59.958 55.000 5.34 5.34 45.46 4.16
381 382 0.753262 CTCCCTCCTACCATTCGTGG 59.247 60.000 0.00 0.00 0.00 4.94
383 384 1.049289 GCCTCCCTCCTACCATTCGT 61.049 60.000 0.00 0.00 0.00 3.85
384 385 1.749033 GCCTCCCTCCTACCATTCG 59.251 63.158 0.00 0.00 0.00 3.34
385 386 0.759436 TCGCCTCCCTCCTACCATTC 60.759 60.000 0.00 0.00 0.00 2.67
388 407 1.457643 CATCGCCTCCCTCCTACCA 60.458 63.158 0.00 0.00 0.00 3.25
413 432 1.253100 TCCATTTTCCCCGTCTTTGC 58.747 50.000 0.00 0.00 0.00 3.68
416 435 1.959989 GCCATCCATTTTCCCCGTCTT 60.960 52.381 0.00 0.00 0.00 3.01
421 440 1.136891 CGAAAGCCATCCATTTTCCCC 59.863 52.381 0.00 0.00 0.00 4.81
422 441 2.584492 CGAAAGCCATCCATTTTCCC 57.416 50.000 0.00 0.00 0.00 3.97
447 466 8.084073 CGCATTTAGATATTCCCATCAATGTTT 58.916 33.333 0.00 0.00 0.00 2.83
463 482 0.941463 CGGAGCTCGCGCATTTAGAT 60.941 55.000 8.75 0.00 39.10 1.98
466 485 2.584970 CCGGAGCTCGCGCATTTA 60.585 61.111 8.75 0.00 39.10 1.40
494 513 2.756400 GACATGCCCAGTCCACCA 59.244 61.111 0.00 0.00 0.00 4.17
512 531 3.606065 GACCACCACGTCGGACTCG 62.606 68.421 6.57 0.00 38.63 4.18
526 545 1.525077 GCAGGTGTTTGGACGACCA 60.525 57.895 1.37 1.37 45.34 4.02
535 554 0.261696 AGGGAGGTTTGCAGGTGTTT 59.738 50.000 0.00 0.00 0.00 2.83
539 558 1.710809 ACATAAGGGAGGTTTGCAGGT 59.289 47.619 0.00 0.00 0.00 4.00
542 561 4.219115 TCAAAACATAAGGGAGGTTTGCA 58.781 39.130 0.00 0.00 41.05 4.08
559 578 7.307694 CGGAATCTCACAAATCAGAATCAAAA 58.692 34.615 0.00 0.00 0.00 2.44
568 587 2.028476 ACGTCCGGAATCTCACAAATCA 60.028 45.455 5.23 0.00 0.00 2.57
634 653 6.506147 TGGATCAAACAGTTCAGACATTTTG 58.494 36.000 0.00 0.00 33.99 2.44
661 680 7.160457 TGGATCATCAAATCACCCCTAAATA 57.840 36.000 0.00 0.00 0.00 1.40
671 690 3.811497 GAGCGACATGGATCATCAAATCA 59.189 43.478 0.00 0.00 0.00 2.57
672 691 3.811497 TGAGCGACATGGATCATCAAATC 59.189 43.478 0.00 0.00 0.00 2.17
673 692 3.812262 TGAGCGACATGGATCATCAAAT 58.188 40.909 0.00 0.00 0.00 2.32
678 697 1.764723 TCCTTGAGCGACATGGATCAT 59.235 47.619 14.12 0.00 44.38 2.45
689 708 0.393537 AAATCTGCCCTCCTTGAGCG 60.394 55.000 0.00 0.00 0.00 5.03
693 720 2.494870 CCAGAAAAATCTGCCCTCCTTG 59.505 50.000 0.28 0.00 36.46 3.61
751 778 2.093021 TGATCGATGATGCCTTCAACCA 60.093 45.455 0.54 0.00 38.03 3.67
1936 2039 0.543174 GGGGTCAGAGGTGTGACTCT 60.543 60.000 7.05 0.00 45.85 3.24
1942 2045 1.673767 ATTGATGGGGTCAGAGGTGT 58.326 50.000 0.00 0.00 38.29 4.16
1995 2098 2.862541 ACCTATGCACACACACAACAT 58.137 42.857 0.00 0.00 0.00 2.71
2132 2258 5.402568 CGACTGTACCATTCATACATACAGC 59.597 44.000 9.11 3.06 44.26 4.40
2482 2609 4.023291 TCCCAGTGCTGTTTCTTTTCTTT 58.977 39.130 0.00 0.00 0.00 2.52
2507 2634 3.068307 TGGTACCGTTCCACAAATTTTGG 59.932 43.478 13.42 11.15 35.18 3.28
2523 2650 0.616891 ATCCGGTGTCCTTTGGTACC 59.383 55.000 4.43 4.43 0.00 3.34
2524 2651 1.002773 ACATCCGGTGTCCTTTGGTAC 59.997 52.381 0.00 0.00 35.77 3.34
2596 3139 4.500887 CCCCTGAATATGCAGCTTTTCATG 60.501 45.833 5.01 0.00 34.56 3.07
2597 3140 3.640029 CCCCTGAATATGCAGCTTTTCAT 59.360 43.478 5.01 0.00 34.56 2.57
2598 3141 3.025978 CCCCTGAATATGCAGCTTTTCA 58.974 45.455 5.01 0.00 34.56 2.69
2599 3142 3.026694 ACCCCTGAATATGCAGCTTTTC 58.973 45.455 5.01 0.00 34.56 2.29
2600 3143 3.105959 ACCCCTGAATATGCAGCTTTT 57.894 42.857 5.01 0.00 34.56 2.27
2601 3144 2.834638 ACCCCTGAATATGCAGCTTT 57.165 45.000 5.01 0.00 34.56 3.51
2602 3145 3.139025 ACATACCCCTGAATATGCAGCTT 59.861 43.478 5.01 0.00 34.56 3.74
2603 3146 2.713167 ACATACCCCTGAATATGCAGCT 59.287 45.455 5.01 0.00 34.56 4.24
2604 3147 3.077359 GACATACCCCTGAATATGCAGC 58.923 50.000 5.01 0.00 34.56 5.25
2605 3148 3.679389 GGACATACCCCTGAATATGCAG 58.321 50.000 3.37 3.37 32.92 4.41
2606 3149 3.788227 GGACATACCCCTGAATATGCA 57.212 47.619 0.00 0.00 32.92 3.96
2697 3240 2.005451 CAGCTGGCGAGGCAATATATC 58.995 52.381 5.57 0.00 0.00 1.63
2704 3247 2.124983 GAATCAGCTGGCGAGGCA 60.125 61.111 15.13 0.00 0.00 4.75
2920 3490 7.450014 TCTCTCTCTCTCTCTTTTGTACATGTT 59.550 37.037 2.30 0.00 0.00 2.71
2921 3491 6.945435 TCTCTCTCTCTCTCTTTTGTACATGT 59.055 38.462 2.69 2.69 0.00 3.21
2922 3492 7.389803 TCTCTCTCTCTCTCTTTTGTACATG 57.610 40.000 0.00 0.00 0.00 3.21
2923 3493 8.415950 TTTCTCTCTCTCTCTCTTTTGTACAT 57.584 34.615 0.00 0.00 0.00 2.29
2924 3494 7.825331 TTTCTCTCTCTCTCTCTTTTGTACA 57.175 36.000 0.00 0.00 0.00 2.90
2968 3538 6.478512 AGGAGAGTTGATATTGGAAGAGTC 57.521 41.667 0.00 0.00 0.00 3.36
3012 3582 6.923508 GGTTCTTGTTAGCAAAAGCTTGTATT 59.076 34.615 0.00 0.00 34.79 1.89
3026 3596 7.275560 CCTTCAAAAGTGTTTGGTTCTTGTTAG 59.724 37.037 0.00 0.00 43.70 2.34
3058 3628 8.735315 TCATAAATAATTTGGAACGAGCAGAAA 58.265 29.630 0.00 0.00 0.00 2.52
3137 3708 7.094762 GGACAAATGACCCTTTTTCTACTAGTG 60.095 40.741 5.39 0.00 0.00 2.74
3138 3709 6.940867 GGACAAATGACCCTTTTTCTACTAGT 59.059 38.462 0.00 0.00 0.00 2.57
3139 3710 6.374613 GGGACAAATGACCCTTTTTCTACTAG 59.625 42.308 12.83 0.00 44.84 2.57
3140 3711 6.243148 GGGACAAATGACCCTTTTTCTACTA 58.757 40.000 12.83 0.00 44.84 1.82
3141 3712 5.077564 GGGACAAATGACCCTTTTTCTACT 58.922 41.667 12.83 0.00 44.84 2.57
3142 3713 4.082949 CGGGACAAATGACCCTTTTTCTAC 60.083 45.833 16.90 0.00 45.84 2.59
3143 3714 4.076394 CGGGACAAATGACCCTTTTTCTA 58.924 43.478 16.90 0.00 45.84 2.10
3144 3715 2.890945 CGGGACAAATGACCCTTTTTCT 59.109 45.455 16.90 0.00 45.84 2.52
3145 3716 2.888414 TCGGGACAAATGACCCTTTTTC 59.112 45.455 16.90 0.00 45.84 2.29
3146 3717 2.952116 TCGGGACAAATGACCCTTTTT 58.048 42.857 16.90 0.00 45.84 1.94
3147 3718 2.668144 TCGGGACAAATGACCCTTTT 57.332 45.000 16.90 0.00 45.84 2.27
3148 3719 2.899303 ATCGGGACAAATGACCCTTT 57.101 45.000 16.90 3.69 45.84 3.11
3149 3720 2.041081 TGAATCGGGACAAATGACCCTT 59.959 45.455 16.90 7.15 45.84 3.95
3150 3721 1.633432 TGAATCGGGACAAATGACCCT 59.367 47.619 16.90 0.84 45.84 4.34
3151 3722 2.122783 TGAATCGGGACAAATGACCC 57.877 50.000 10.44 10.44 44.81 4.46
3152 3723 4.275936 CCTTATGAATCGGGACAAATGACC 59.724 45.833 0.00 0.00 0.00 4.02
3153 3724 5.424121 CCTTATGAATCGGGACAAATGAC 57.576 43.478 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.