Multiple sequence alignment - TraesCS2B01G297800

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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 TraesCS2B01G297800 chr2B 100.000 3844 0 0 1 3844 416877859 416874016 0.000000e+00 7099
1 TraesCS2B01G297800 chr2A 94.702 3624 146 21 244 3841 468501068 468497465 0.000000e+00 5587
2 TraesCS2B01G297800 chr2A 92.784 194 12 2 2 193 51641311 51641504 2.920000e-71 279
3 TraesCS2B01G297800 chr2D 94.813 3547 122 28 329 3844 350799540 350796025 0.000000e+00 5474
4 TraesCS2B01G297800 chr2D 91.667 192 15 1 2 192 571525041 571525232 8.190000e-67 265
5 TraesCS2B01G297800 chr6A 90.821 207 14 4 2 203 522223935 522223729 4.890000e-69 272
6 TraesCS2B01G297800 chr7B 90.686 204 14 4 6 204 383602639 383602842 2.280000e-67 267
7 TraesCS2B01G297800 chr5B 89.904 208 15 5 2 203 618269915 618270122 2.950000e-66 263
8 TraesCS2B01G297800 chr1D 91.192 193 16 1 2 193 489327229 489327421 1.060000e-65 261
9 TraesCS2B01G297800 chr1D 91.192 193 16 1 2 193 489434953 489435145 1.060000e-65 261
10 TraesCS2B01G297800 chr6D 89.372 207 18 3 2 204 11913255 11913461 1.370000e-64 257
11 TraesCS2B01G297800 chr3D 89.372 207 17 4 2 203 13161669 13161463 4.930000e-64 255
12 TraesCS2B01G297800 chr4B 100.000 40 0 0 2466 2505 649248316 649248277 1.480000e-09 75


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 TraesCS2B01G297800 chr2B 416874016 416877859 3843 True 7099 7099 100.000 1 3844 1 chr2B.!!$R1 3843
1 TraesCS2B01G297800 chr2A 468497465 468501068 3603 True 5587 5587 94.702 244 3841 1 chr2A.!!$R1 3597
2 TraesCS2B01G297800 chr2D 350796025 350799540 3515 True 5474 5474 94.813 329 3844 1 chr2D.!!$R1 3515

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
196 197 0.034089 GGGACTTGAACCCTGGGATG 60.034 60.0 22.23 6.69 43.65 3.51 F
197 198 0.034089 GGACTTGAACCCTGGGATGG 60.034 60.0 22.23 7.04 0.00 3.51 F
656 660 0.314935 TTCGTACTTTCTCGGGCGTT 59.685 50.0 0.00 0.00 0.00 4.84 F
2274 2302 0.035458 CCTCCCCAACACACTCTGAC 59.965 60.0 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1057 1069 1.229529 ACCCAGGACCGTGGAGAAT 60.230 57.895 10.06 0.00 40.44 2.40 R
1447 1468 1.552792 GCAGAAGGGACTAGCAGAACT 59.447 52.381 0.00 0.00 38.49 3.01 R
2305 2333 1.342174 AGCCAACAAATGTTCAGCTGG 59.658 47.619 15.13 7.84 40.85 4.85 R
3635 3677 1.063469 CGTGAGCAGTTTTCCGTGTTT 59.937 47.619 0.00 0.00 0.00 2.83 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.580729 TTATAAACGCACACACGCAC 57.419 45.000 0.00 0.00 36.19 5.34
20 21 1.499049 TATAAACGCACACACGCACA 58.501 45.000 0.00 0.00 36.19 4.57
21 22 0.041663 ATAAACGCACACACGCACAC 60.042 50.000 0.00 0.00 36.19 3.82
22 23 2.037913 TAAACGCACACACGCACACC 62.038 55.000 0.00 0.00 36.19 4.16
25 26 2.280524 GCACACACGCACACCCTA 60.281 61.111 0.00 0.00 0.00 3.53
26 27 2.604174 GCACACACGCACACCCTAC 61.604 63.158 0.00 0.00 0.00 3.18
27 28 1.959226 CACACACGCACACCCTACC 60.959 63.158 0.00 0.00 0.00 3.18
28 29 2.138179 ACACACGCACACCCTACCT 61.138 57.895 0.00 0.00 0.00 3.08
29 30 1.374252 CACACGCACACCCTACCTC 60.374 63.158 0.00 0.00 0.00 3.85
30 31 1.533273 ACACGCACACCCTACCTCT 60.533 57.895 0.00 0.00 0.00 3.69
31 32 0.251474 ACACGCACACCCTACCTCTA 60.251 55.000 0.00 0.00 0.00 2.43
32 33 1.112113 CACGCACACCCTACCTCTAT 58.888 55.000 0.00 0.00 0.00 1.98
33 34 1.112113 ACGCACACCCTACCTCTATG 58.888 55.000 0.00 0.00 0.00 2.23
34 35 1.341679 ACGCACACCCTACCTCTATGA 60.342 52.381 0.00 0.00 0.00 2.15
35 36 1.338337 CGCACACCCTACCTCTATGAG 59.662 57.143 0.00 0.00 0.00 2.90
36 37 1.069358 GCACACCCTACCTCTATGAGC 59.931 57.143 0.00 0.00 0.00 4.26
37 38 2.388735 CACACCCTACCTCTATGAGCA 58.611 52.381 0.00 0.00 0.00 4.26
38 39 2.101582 CACACCCTACCTCTATGAGCAC 59.898 54.545 0.00 0.00 0.00 4.40
39 40 1.689273 CACCCTACCTCTATGAGCACC 59.311 57.143 0.00 0.00 0.00 5.01
40 41 1.576272 ACCCTACCTCTATGAGCACCT 59.424 52.381 0.00 0.00 0.00 4.00
41 42 2.243810 CCCTACCTCTATGAGCACCTC 58.756 57.143 0.00 0.00 0.00 3.85
42 43 2.243810 CCTACCTCTATGAGCACCTCC 58.756 57.143 0.00 0.00 0.00 4.30
43 44 2.424957 CCTACCTCTATGAGCACCTCCA 60.425 54.545 0.00 0.00 0.00 3.86
44 45 2.254152 ACCTCTATGAGCACCTCCAA 57.746 50.000 0.00 0.00 0.00 3.53
45 46 2.551270 ACCTCTATGAGCACCTCCAAA 58.449 47.619 0.00 0.00 0.00 3.28
46 47 2.912956 ACCTCTATGAGCACCTCCAAAA 59.087 45.455 0.00 0.00 0.00 2.44
47 48 3.054802 ACCTCTATGAGCACCTCCAAAAG 60.055 47.826 0.00 0.00 0.00 2.27
48 49 3.198635 CCTCTATGAGCACCTCCAAAAGA 59.801 47.826 0.00 0.00 0.00 2.52
49 50 4.187694 CTCTATGAGCACCTCCAAAAGAC 58.812 47.826 0.00 0.00 0.00 3.01
50 51 3.840666 TCTATGAGCACCTCCAAAAGACT 59.159 43.478 0.00 0.00 0.00 3.24
51 52 2.260844 TGAGCACCTCCAAAAGACTG 57.739 50.000 0.00 0.00 0.00 3.51
52 53 1.768275 TGAGCACCTCCAAAAGACTGA 59.232 47.619 0.00 0.00 0.00 3.41
53 54 2.224378 TGAGCACCTCCAAAAGACTGAG 60.224 50.000 0.00 0.00 0.00 3.35
54 55 0.877743 GCACCTCCAAAAGACTGAGC 59.122 55.000 0.00 0.00 0.00 4.26
55 56 1.528129 CACCTCCAAAAGACTGAGCC 58.472 55.000 0.00 0.00 0.00 4.70
56 57 0.035458 ACCTCCAAAAGACTGAGCCG 59.965 55.000 0.00 0.00 0.00 5.52
57 58 0.035458 CCTCCAAAAGACTGAGCCGT 59.965 55.000 0.00 0.00 0.00 5.68
58 59 1.433534 CTCCAAAAGACTGAGCCGTC 58.566 55.000 0.00 0.00 0.00 4.79
59 60 0.756294 TCCAAAAGACTGAGCCGTCA 59.244 50.000 1.91 0.00 36.38 4.35
60 61 1.347707 TCCAAAAGACTGAGCCGTCAT 59.652 47.619 1.91 0.00 36.38 3.06
61 62 2.565391 TCCAAAAGACTGAGCCGTCATA 59.435 45.455 1.91 0.00 36.38 2.15
62 63 3.197766 TCCAAAAGACTGAGCCGTCATAT 59.802 43.478 1.91 0.00 36.38 1.78
63 64 3.557595 CCAAAAGACTGAGCCGTCATATC 59.442 47.826 1.91 0.00 36.38 1.63
64 65 4.183865 CAAAAGACTGAGCCGTCATATCA 58.816 43.478 1.91 0.00 36.38 2.15
65 66 4.679373 AAAGACTGAGCCGTCATATCAT 57.321 40.909 1.91 0.00 36.38 2.45
66 67 3.932545 AGACTGAGCCGTCATATCATC 57.067 47.619 1.91 0.00 36.38 2.92
67 68 3.495331 AGACTGAGCCGTCATATCATCT 58.505 45.455 1.91 0.00 36.38 2.90
68 69 3.894427 AGACTGAGCCGTCATATCATCTT 59.106 43.478 1.91 0.00 36.38 2.40
69 70 3.986572 GACTGAGCCGTCATATCATCTTG 59.013 47.826 0.00 0.00 34.11 3.02
70 71 3.638627 ACTGAGCCGTCATATCATCTTGA 59.361 43.478 0.00 0.00 30.18 3.02
71 72 4.100035 ACTGAGCCGTCATATCATCTTGAA 59.900 41.667 0.00 0.00 30.18 2.69
72 73 5.022282 TGAGCCGTCATATCATCTTGAAA 57.978 39.130 0.00 0.00 0.00 2.69
73 74 5.614308 TGAGCCGTCATATCATCTTGAAAT 58.386 37.500 0.00 0.00 0.00 2.17
74 75 6.057533 TGAGCCGTCATATCATCTTGAAATT 58.942 36.000 0.00 0.00 0.00 1.82
75 76 6.543465 TGAGCCGTCATATCATCTTGAAATTT 59.457 34.615 0.00 0.00 0.00 1.82
76 77 7.714813 TGAGCCGTCATATCATCTTGAAATTTA 59.285 33.333 0.00 0.00 0.00 1.40
77 78 7.865707 AGCCGTCATATCATCTTGAAATTTAC 58.134 34.615 0.00 0.00 0.00 2.01
78 79 6.792250 GCCGTCATATCATCTTGAAATTTACG 59.208 38.462 0.00 0.00 0.00 3.18
79 80 7.307160 GCCGTCATATCATCTTGAAATTTACGA 60.307 37.037 0.00 0.00 0.00 3.43
80 81 8.547894 CCGTCATATCATCTTGAAATTTACGAA 58.452 33.333 0.00 0.00 0.00 3.85
81 82 9.573102 CGTCATATCATCTTGAAATTTACGAAG 57.427 33.333 0.00 0.00 0.00 3.79
82 83 9.374960 GTCATATCATCTTGAAATTTACGAAGC 57.625 33.333 0.00 0.00 0.00 3.86
83 84 8.559536 TCATATCATCTTGAAATTTACGAAGCC 58.440 33.333 0.00 0.00 0.00 4.35
84 85 5.216566 TCATCTTGAAATTTACGAAGCCG 57.783 39.130 0.00 0.00 42.50 5.52
85 86 3.465122 TCTTGAAATTTACGAAGCCGC 57.535 42.857 0.00 0.00 39.95 6.53
86 87 2.160813 TCTTGAAATTTACGAAGCCGCC 59.839 45.455 0.00 0.00 39.95 6.13
87 88 0.444651 TGAAATTTACGAAGCCGCCG 59.555 50.000 0.00 0.00 39.95 6.46
88 89 0.445043 GAAATTTACGAAGCCGCCGT 59.555 50.000 0.00 0.41 43.26 5.68
89 90 1.660104 GAAATTTACGAAGCCGCCGTA 59.340 47.619 0.00 0.00 40.95 4.02
90 91 1.283736 AATTTACGAAGCCGCCGTAG 58.716 50.000 0.00 0.00 42.42 3.51
104 105 2.051879 CCGTAGGCACATCATCGTAG 57.948 55.000 0.00 0.00 46.14 3.51
105 106 1.607148 CCGTAGGCACATCATCGTAGA 59.393 52.381 0.00 0.00 46.14 2.59
106 107 2.604855 CCGTAGGCACATCATCGTAGAC 60.605 54.545 0.00 0.00 46.14 2.59
107 108 2.651701 GTAGGCACATCATCGTAGACG 58.348 52.381 0.00 0.00 42.51 4.18
108 109 0.385751 AGGCACATCATCGTAGACGG 59.614 55.000 1.67 0.00 42.51 4.79
109 110 0.597637 GGCACATCATCGTAGACGGG 60.598 60.000 1.67 0.00 42.51 5.28
110 111 0.384309 GCACATCATCGTAGACGGGA 59.616 55.000 1.67 1.30 42.51 5.14
111 112 1.202371 GCACATCATCGTAGACGGGAA 60.202 52.381 1.67 0.00 42.51 3.97
112 113 2.460918 CACATCATCGTAGACGGGAAC 58.539 52.381 1.67 0.00 42.51 3.62
125 126 4.115270 GGAACGTCTCCTCCCACT 57.885 61.111 8.87 0.00 41.61 4.00
126 127 3.277962 GGAACGTCTCCTCCCACTA 57.722 57.895 8.87 0.00 41.61 2.74
127 128 1.553706 GGAACGTCTCCTCCCACTAA 58.446 55.000 8.87 0.00 41.61 2.24
128 129 1.897802 GGAACGTCTCCTCCCACTAAA 59.102 52.381 8.87 0.00 41.61 1.85
129 130 2.500504 GGAACGTCTCCTCCCACTAAAT 59.499 50.000 8.87 0.00 41.61 1.40
130 131 3.522553 GAACGTCTCCTCCCACTAAATG 58.477 50.000 0.00 0.00 0.00 2.32
131 132 1.207329 ACGTCTCCTCCCACTAAATGC 59.793 52.381 0.00 0.00 0.00 3.56
132 133 1.802880 CGTCTCCTCCCACTAAATGCG 60.803 57.143 0.00 0.00 0.00 4.73
133 134 0.178068 TCTCCTCCCACTAAATGCGC 59.822 55.000 0.00 0.00 0.00 6.09
134 135 0.107703 CTCCTCCCACTAAATGCGCA 60.108 55.000 14.96 14.96 0.00 6.09
135 136 0.546122 TCCTCCCACTAAATGCGCAT 59.454 50.000 19.28 19.28 0.00 4.73
136 137 0.947244 CCTCCCACTAAATGCGCATC 59.053 55.000 25.53 0.00 0.00 3.91
137 138 0.583438 CTCCCACTAAATGCGCATCG 59.417 55.000 25.53 17.09 0.00 3.84
149 150 3.521534 CGCATCGCTGGAAATCTTG 57.478 52.632 0.00 0.00 0.00 3.02
150 151 1.009078 CGCATCGCTGGAAATCTTGA 58.991 50.000 0.00 0.00 0.00 3.02
151 152 1.398041 CGCATCGCTGGAAATCTTGAA 59.602 47.619 0.00 0.00 0.00 2.69
152 153 2.159531 CGCATCGCTGGAAATCTTGAAA 60.160 45.455 0.00 0.00 0.00 2.69
153 154 3.488047 CGCATCGCTGGAAATCTTGAAAT 60.488 43.478 0.00 0.00 0.00 2.17
154 155 4.260743 CGCATCGCTGGAAATCTTGAAATA 60.261 41.667 0.00 0.00 0.00 1.40
155 156 5.581605 GCATCGCTGGAAATCTTGAAATAA 58.418 37.500 0.00 0.00 0.00 1.40
156 157 6.211515 GCATCGCTGGAAATCTTGAAATAAT 58.788 36.000 0.00 0.00 0.00 1.28
157 158 6.361748 GCATCGCTGGAAATCTTGAAATAATC 59.638 38.462 0.00 0.00 0.00 1.75
158 159 6.377327 TCGCTGGAAATCTTGAAATAATCC 57.623 37.500 0.00 0.00 0.00 3.01
159 160 5.885352 TCGCTGGAAATCTTGAAATAATCCA 59.115 36.000 0.00 0.00 34.52 3.41
170 171 9.903682 ATCTTGAAATAATCCAGAATAAATGCG 57.096 29.630 0.00 0.00 33.86 4.73
171 172 9.119418 TCTTGAAATAATCCAGAATAAATGCGA 57.881 29.630 0.00 0.00 27.43 5.10
172 173 9.390795 CTTGAAATAATCCAGAATAAATGCGAG 57.609 33.333 0.00 0.00 0.00 5.03
173 174 7.362662 TGAAATAATCCAGAATAAATGCGAGC 58.637 34.615 0.00 0.00 0.00 5.03
174 175 6.882610 AATAATCCAGAATAAATGCGAGCA 57.117 33.333 0.00 0.00 0.00 4.26
175 176 4.558538 AATCCAGAATAAATGCGAGCAC 57.441 40.909 0.00 0.00 0.00 4.40
176 177 2.288666 TCCAGAATAAATGCGAGCACC 58.711 47.619 0.00 0.00 0.00 5.01
177 178 1.003545 CCAGAATAAATGCGAGCACCG 60.004 52.381 0.00 0.00 42.21 4.94
178 179 1.003545 CAGAATAAATGCGAGCACCGG 60.004 52.381 0.00 0.00 39.04 5.28
179 180 0.307760 GAATAAATGCGAGCACCGGG 59.692 55.000 6.32 0.00 39.04 5.73
180 181 0.107410 AATAAATGCGAGCACCGGGA 60.107 50.000 6.32 0.00 39.04 5.14
181 182 0.814010 ATAAATGCGAGCACCGGGAC 60.814 55.000 6.32 0.00 39.04 4.46
182 183 1.895020 TAAATGCGAGCACCGGGACT 61.895 55.000 6.32 1.15 39.04 3.85
183 184 2.748058 AAATGCGAGCACCGGGACTT 62.748 55.000 6.32 0.00 39.04 3.01
184 185 3.958147 ATGCGAGCACCGGGACTTG 62.958 63.158 6.32 7.69 39.04 3.16
185 186 4.373116 GCGAGCACCGGGACTTGA 62.373 66.667 15.50 0.00 39.04 3.02
186 187 2.342279 CGAGCACCGGGACTTGAA 59.658 61.111 6.32 0.00 33.91 2.69
187 188 2.027625 CGAGCACCGGGACTTGAAC 61.028 63.158 6.32 0.00 33.91 3.18
188 189 1.671379 GAGCACCGGGACTTGAACC 60.671 63.158 6.32 0.00 0.00 3.62
189 190 2.671963 GCACCGGGACTTGAACCC 60.672 66.667 6.32 0.00 43.57 4.11
190 191 3.157680 CACCGGGACTTGAACCCT 58.842 61.111 6.32 0.00 44.72 4.34
191 192 1.302511 CACCGGGACTTGAACCCTG 60.303 63.158 6.32 0.00 44.72 4.45
192 193 2.351276 CCGGGACTTGAACCCTGG 59.649 66.667 0.00 0.00 44.72 4.45
193 194 2.351276 CGGGACTTGAACCCTGGG 59.649 66.667 12.28 12.28 44.72 4.45
194 195 2.221299 CGGGACTTGAACCCTGGGA 61.221 63.158 22.23 0.00 44.72 4.37
195 196 1.562672 CGGGACTTGAACCCTGGGAT 61.563 60.000 22.23 7.74 44.72 3.85
196 197 0.034089 GGGACTTGAACCCTGGGATG 60.034 60.000 22.23 6.69 43.65 3.51
197 198 0.034089 GGACTTGAACCCTGGGATGG 60.034 60.000 22.23 7.04 0.00 3.51
206 207 2.668850 CCCTGGGATGGGGATATAGT 57.331 55.000 7.01 0.00 46.50 2.12
207 208 2.934722 CCCTGGGATGGGGATATAGTT 58.065 52.381 7.01 0.00 46.50 2.24
208 209 3.269034 CCCTGGGATGGGGATATAGTTT 58.731 50.000 7.01 0.00 46.50 2.66
209 210 3.010584 CCCTGGGATGGGGATATAGTTTG 59.989 52.174 7.01 0.00 46.50 2.93
210 211 3.657727 CCTGGGATGGGGATATAGTTTGT 59.342 47.826 0.00 0.00 0.00 2.83
211 212 4.106341 CCTGGGATGGGGATATAGTTTGTT 59.894 45.833 0.00 0.00 0.00 2.83
212 213 5.060427 TGGGATGGGGATATAGTTTGTTG 57.940 43.478 0.00 0.00 0.00 3.33
213 214 4.480537 TGGGATGGGGATATAGTTTGTTGT 59.519 41.667 0.00 0.00 0.00 3.32
214 215 5.043732 TGGGATGGGGATATAGTTTGTTGTT 60.044 40.000 0.00 0.00 0.00 2.83
215 216 6.160636 TGGGATGGGGATATAGTTTGTTGTTA 59.839 38.462 0.00 0.00 0.00 2.41
216 217 7.147033 TGGGATGGGGATATAGTTTGTTGTTAT 60.147 37.037 0.00 0.00 0.00 1.89
217 218 8.387813 GGGATGGGGATATAGTTTGTTGTTATA 58.612 37.037 0.00 0.00 0.00 0.98
218 219 9.802039 GGATGGGGATATAGTTTGTTGTTATAA 57.198 33.333 0.00 0.00 0.00 0.98
227 228 8.746922 ATAGTTTGTTGTTATAACTTCGACGA 57.253 30.769 16.33 0.00 34.26 4.20
228 229 7.647907 AGTTTGTTGTTATAACTTCGACGAT 57.352 32.000 16.33 0.00 0.00 3.73
229 230 8.746922 AGTTTGTTGTTATAACTTCGACGATA 57.253 30.769 16.33 0.00 0.00 2.92
230 231 8.857216 AGTTTGTTGTTATAACTTCGACGATAG 58.143 33.333 16.33 1.97 46.19 2.08
231 232 8.853345 GTTTGTTGTTATAACTTCGACGATAGA 58.147 33.333 16.33 0.00 41.38 1.98
232 233 7.959718 TGTTGTTATAACTTCGACGATAGAC 57.040 36.000 16.33 0.00 41.38 2.59
233 234 7.755591 TGTTGTTATAACTTCGACGATAGACT 58.244 34.615 16.33 0.00 41.38 3.24
234 235 8.882736 TGTTGTTATAACTTCGACGATAGACTA 58.117 33.333 16.33 0.00 41.38 2.59
235 236 9.367717 GTTGTTATAACTTCGACGATAGACTAG 57.632 37.037 16.33 0.00 41.38 2.57
236 237 8.081208 TGTTATAACTTCGACGATAGACTAGG 57.919 38.462 16.33 0.00 41.38 3.02
237 238 3.967203 AACTTCGACGATAGACTAGGC 57.033 47.619 0.00 0.00 41.38 3.93
238 239 3.196939 ACTTCGACGATAGACTAGGCT 57.803 47.619 2.16 2.16 41.38 4.58
239 240 3.132925 ACTTCGACGATAGACTAGGCTC 58.867 50.000 0.00 0.00 41.38 4.70
240 241 3.181463 ACTTCGACGATAGACTAGGCTCT 60.181 47.826 0.00 0.00 41.38 4.09
241 242 2.756829 TCGACGATAGACTAGGCTCTG 58.243 52.381 0.00 0.00 41.38 3.35
242 243 2.102757 TCGACGATAGACTAGGCTCTGT 59.897 50.000 0.00 0.00 41.38 3.41
249 250 2.114616 AGACTAGGCTCTGTTCCCATG 58.885 52.381 0.00 0.00 0.00 3.66
260 261 5.310409 TCTGTTCCCATGTTCTTTCTCTT 57.690 39.130 0.00 0.00 0.00 2.85
286 287 5.742453 CAGTATATGATACCCACGCGTATTC 59.258 44.000 13.44 5.27 0.00 1.75
289 290 1.404748 TGATACCCACGCGTATTCGAA 59.595 47.619 13.44 0.00 39.71 3.71
336 337 1.757118 GTTCTCCCAGTGGATCGATCA 59.243 52.381 25.93 10.23 40.80 2.92
363 364 4.680237 TGACAGACCCGCTTGCGG 62.680 66.667 25.17 25.17 0.00 5.69
388 389 4.779733 ATCGGAGCTCCACCCGGT 62.780 66.667 31.67 12.80 45.36 5.28
640 644 1.135431 TCTTGCCATTTCCGCATTTCG 60.135 47.619 0.00 0.00 35.83 3.46
650 654 2.256174 TCCGCATTTCGTACTTTCTCG 58.744 47.619 0.00 0.00 36.19 4.04
656 660 0.314935 TTCGTACTTTCTCGGGCGTT 59.685 50.000 0.00 0.00 0.00 4.84
690 698 2.753055 TCGATTGACCGTGGATTTCA 57.247 45.000 0.00 0.00 0.00 2.69
738 746 5.880332 GTGTGGATAAGTGCTTGATTCCTTA 59.120 40.000 9.91 0.00 0.00 2.69
743 751 2.898705 AGTGCTTGATTCCTTAGCTCG 58.101 47.619 0.00 0.00 35.93 5.03
774 782 3.058224 CGACTGAGTTGGGGATGTTTTTC 60.058 47.826 0.00 0.00 0.00 2.29
780 788 4.803452 AGTTGGGGATGTTTTTCTCTTCA 58.197 39.130 0.00 0.00 0.00 3.02
782 790 5.478332 AGTTGGGGATGTTTTTCTCTTCATC 59.522 40.000 0.00 0.00 36.81 2.92
793 801 8.796475 TGTTTTTCTCTTCATCCTATTTTCTGG 58.204 33.333 0.00 0.00 0.00 3.86
881 893 5.115480 GGAACAGATGAAGGATCTTGTCTC 58.885 45.833 0.00 0.00 39.64 3.36
891 903 4.841422 AGGATCTTGTCTCCAGAATTGTG 58.159 43.478 0.00 0.00 35.08 3.33
916 928 6.417191 TTTTATGTTTCACTATCGTCCAGC 57.583 37.500 0.00 0.00 0.00 4.85
952 964 4.485163 GTTCTTTGCAGTGTGTTTTCTGT 58.515 39.130 0.00 0.00 34.57 3.41
964 976 7.865707 AGTGTGTTTTCTGTCATACTGAAATC 58.134 34.615 11.33 11.07 42.70 2.17
1057 1069 1.992277 GAAGGCTCCTCCTCCAGCA 60.992 63.158 0.00 0.00 46.94 4.41
1071 1083 1.599047 CAGCATTCTCCACGGTCCT 59.401 57.895 0.00 0.00 0.00 3.85
1074 1086 1.221840 CATTCTCCACGGTCCTGGG 59.778 63.158 7.32 0.00 31.41 4.45
1088 1100 2.930019 TGGGTCCAGAGGTGCAGG 60.930 66.667 0.00 0.00 0.00 4.85
1195 1207 0.661552 TCGATCGTCCGAGGTGATTC 59.338 55.000 15.94 0.00 34.19 2.52
1230 1247 4.265904 TCTGGATAACAAGTTCGCTTCA 57.734 40.909 0.00 0.00 34.74 3.02
1243 1260 5.057149 AGTTCGCTTCACTTCTTGTTATGT 58.943 37.500 0.00 0.00 0.00 2.29
1408 1429 1.339824 ACCATCAAGAGCTGGAGCAAG 60.340 52.381 0.00 0.00 45.16 4.01
1447 1468 4.794648 GGGCTGGCGGCATGTGTA 62.795 66.667 21.68 0.00 44.01 2.90
1738 1759 4.026640 GCAAATGTGGCATGCTTAAATACG 60.027 41.667 18.92 1.82 37.12 3.06
1816 1837 3.473647 CCAGCTCCATGCCTCGGA 61.474 66.667 0.00 0.00 44.23 4.55
1984 2005 2.429058 CCCGATCCATCTGCCCTG 59.571 66.667 0.00 0.00 0.00 4.45
2263 2291 0.120377 ACTGGTATGTCCCTCCCCAA 59.880 55.000 0.00 0.00 34.77 4.12
2274 2302 0.035458 CCTCCCCAACACACTCTGAC 59.965 60.000 0.00 0.00 0.00 3.51
2305 2333 6.037098 CCATTGCTGTAGTACTTGAGTCTAC 58.963 44.000 0.00 10.91 35.86 2.59
2322 2350 4.516698 AGTCTACCAGCTGAACATTTGTTG 59.483 41.667 17.39 3.73 38.56 3.33
2561 2590 2.511145 GCTGAGCCTCCTCTTGCG 60.511 66.667 0.00 0.00 38.93 4.85
2798 2827 2.920912 TTGGAGGCGACCGAGGTT 60.921 61.111 0.00 0.00 0.00 3.50
2840 2869 2.548920 CCTGCCGATAAGGAAGCTAAGG 60.549 54.545 0.00 0.00 45.00 2.69
3005 3034 4.667573 TGATAATGTTTTACCCACTGGCA 58.332 39.130 0.00 0.00 33.59 4.92
3011 3040 1.394618 TTTACCCACTGGCACAACAC 58.605 50.000 0.00 0.00 38.70 3.32
3150 3181 6.552008 TGTTTCTGGGGATAGTTCAAATTCT 58.448 36.000 0.00 0.00 0.00 2.40
3161 3192 8.841300 GGATAGTTCAAATTCTGTTATTCTCCC 58.159 37.037 0.00 0.00 0.00 4.30
3324 3360 3.969287 AATCACTCTTCAGCAGTAGCA 57.031 42.857 0.00 0.00 45.49 3.49
3325 3361 3.969287 ATCACTCTTCAGCAGTAGCAA 57.031 42.857 0.00 0.00 45.49 3.91
3426 3468 0.331278 ATCCATTTGGCGAGGGAACA 59.669 50.000 1.80 0.00 32.25 3.18
3495 3537 7.672351 TTTTGTACTTGATTTTAGTGCAACG 57.328 32.000 6.11 0.00 44.26 4.10
3504 3546 7.151999 TGATTTTAGTGCAACGGTAATGAAT 57.848 32.000 0.00 0.00 45.86 2.57
3544 3586 8.089115 TCAGATATACATATAATCTCGCTCCG 57.911 38.462 0.00 0.00 0.00 4.63
3599 3641 6.764085 CGTTATCATTGTGGTAATGGAACCTA 59.236 38.462 0.00 0.00 40.44 3.08
3609 3651 1.972588 ATGGAACCTAACTCCCAGCT 58.027 50.000 0.00 0.00 31.32 4.24
3627 3669 2.089350 AGCTAGGGAGGGGTATGGAAAT 60.089 50.000 0.00 0.00 0.00 2.17
3698 3740 5.335661 CCACACATCTCAATGGCATCATATG 60.336 44.000 0.00 5.56 37.19 1.78
3765 3807 3.509967 TCATAGGTACACACTCACACCAG 59.490 47.826 0.00 0.00 33.27 4.00
3766 3808 1.789523 AGGTACACACTCACACCAGT 58.210 50.000 0.00 0.00 33.27 4.00
3767 3809 2.953453 AGGTACACACTCACACCAGTA 58.047 47.619 0.00 0.00 33.27 2.74
3768 3810 2.891580 AGGTACACACTCACACCAGTAG 59.108 50.000 0.00 0.00 33.27 2.57
3769 3811 2.626743 GGTACACACTCACACCAGTAGT 59.373 50.000 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.865340 TGTGCGTGTGTGCGTTTATAA 59.135 42.857 0.00 0.00 37.81 0.98
1 2 1.192757 GTGTGCGTGTGTGCGTTTATA 59.807 47.619 0.00 0.00 37.81 0.98
2 3 0.041663 GTGTGCGTGTGTGCGTTTAT 60.042 50.000 0.00 0.00 37.81 1.40
3 4 1.348938 GTGTGCGTGTGTGCGTTTA 59.651 52.632 0.00 0.00 37.81 2.01
4 5 2.099446 GTGTGCGTGTGTGCGTTT 59.901 55.556 0.00 0.00 37.81 3.60
8 9 2.280524 TAGGGTGTGCGTGTGTGC 60.281 61.111 0.00 0.00 0.00 4.57
9 10 1.959226 GGTAGGGTGTGCGTGTGTG 60.959 63.158 0.00 0.00 0.00 3.82
10 11 2.095978 GAGGTAGGGTGTGCGTGTGT 62.096 60.000 0.00 0.00 0.00 3.72
11 12 1.374252 GAGGTAGGGTGTGCGTGTG 60.374 63.158 0.00 0.00 0.00 3.82
12 13 0.251474 TAGAGGTAGGGTGTGCGTGT 60.251 55.000 0.00 0.00 0.00 4.49
13 14 1.112113 ATAGAGGTAGGGTGTGCGTG 58.888 55.000 0.00 0.00 0.00 5.34
14 15 1.112113 CATAGAGGTAGGGTGTGCGT 58.888 55.000 0.00 0.00 0.00 5.24
15 16 1.338337 CTCATAGAGGTAGGGTGTGCG 59.662 57.143 0.00 0.00 0.00 5.34
16 17 1.069358 GCTCATAGAGGTAGGGTGTGC 59.931 57.143 0.00 0.00 0.00 4.57
17 18 2.101582 GTGCTCATAGAGGTAGGGTGTG 59.898 54.545 0.00 0.00 0.00 3.82
18 19 2.389715 GTGCTCATAGAGGTAGGGTGT 58.610 52.381 0.00 0.00 0.00 4.16
19 20 1.689273 GGTGCTCATAGAGGTAGGGTG 59.311 57.143 0.00 0.00 0.00 4.61
20 21 1.576272 AGGTGCTCATAGAGGTAGGGT 59.424 52.381 0.00 0.00 0.00 4.34
21 22 2.243810 GAGGTGCTCATAGAGGTAGGG 58.756 57.143 0.00 0.00 0.00 3.53
22 23 2.243810 GGAGGTGCTCATAGAGGTAGG 58.756 57.143 0.00 0.00 31.08 3.18
23 24 2.950781 TGGAGGTGCTCATAGAGGTAG 58.049 52.381 0.00 0.00 31.08 3.18
24 25 3.398318 TTGGAGGTGCTCATAGAGGTA 57.602 47.619 0.00 0.00 31.08 3.08
25 26 2.254152 TTGGAGGTGCTCATAGAGGT 57.746 50.000 0.00 0.00 31.08 3.85
26 27 3.198635 TCTTTTGGAGGTGCTCATAGAGG 59.801 47.826 0.00 0.00 31.08 3.69
27 28 4.081198 AGTCTTTTGGAGGTGCTCATAGAG 60.081 45.833 0.00 0.00 31.08 2.43
28 29 3.840666 AGTCTTTTGGAGGTGCTCATAGA 59.159 43.478 0.00 0.00 31.08 1.98
29 30 3.937706 CAGTCTTTTGGAGGTGCTCATAG 59.062 47.826 0.00 0.00 31.08 2.23
30 31 3.582647 TCAGTCTTTTGGAGGTGCTCATA 59.417 43.478 0.00 0.00 31.08 2.15
31 32 2.373169 TCAGTCTTTTGGAGGTGCTCAT 59.627 45.455 0.00 0.00 31.08 2.90
32 33 1.768275 TCAGTCTTTTGGAGGTGCTCA 59.232 47.619 0.00 0.00 31.08 4.26
33 34 2.421619 CTCAGTCTTTTGGAGGTGCTC 58.578 52.381 0.00 0.00 0.00 4.26
34 35 1.544314 GCTCAGTCTTTTGGAGGTGCT 60.544 52.381 0.00 0.00 0.00 4.40
35 36 0.877743 GCTCAGTCTTTTGGAGGTGC 59.122 55.000 0.00 0.00 0.00 5.01
36 37 1.528129 GGCTCAGTCTTTTGGAGGTG 58.472 55.000 0.00 0.00 0.00 4.00
37 38 0.035458 CGGCTCAGTCTTTTGGAGGT 59.965 55.000 0.00 0.00 0.00 3.85
38 39 0.035458 ACGGCTCAGTCTTTTGGAGG 59.965 55.000 0.00 0.00 0.00 4.30
39 40 1.270305 TGACGGCTCAGTCTTTTGGAG 60.270 52.381 0.00 0.00 41.47 3.86
40 41 0.756294 TGACGGCTCAGTCTTTTGGA 59.244 50.000 0.00 0.00 41.47 3.53
41 42 1.813513 ATGACGGCTCAGTCTTTTGG 58.186 50.000 0.00 0.00 41.47 3.28
42 43 4.183865 TGATATGACGGCTCAGTCTTTTG 58.816 43.478 0.00 0.00 41.47 2.44
43 44 4.471904 TGATATGACGGCTCAGTCTTTT 57.528 40.909 0.00 0.00 41.47 2.27
44 45 4.343526 AGATGATATGACGGCTCAGTCTTT 59.656 41.667 0.00 1.16 41.47 2.52
45 46 3.894427 AGATGATATGACGGCTCAGTCTT 59.106 43.478 0.00 5.52 41.47 3.01
46 47 3.495331 AGATGATATGACGGCTCAGTCT 58.505 45.455 0.00 0.00 41.47 3.24
47 48 3.932545 AGATGATATGACGGCTCAGTC 57.067 47.619 0.00 1.58 41.30 3.51
48 49 3.638627 TCAAGATGATATGACGGCTCAGT 59.361 43.478 0.00 0.00 0.00 3.41
49 50 4.248691 TCAAGATGATATGACGGCTCAG 57.751 45.455 0.00 0.00 0.00 3.35
50 51 4.670896 TTCAAGATGATATGACGGCTCA 57.329 40.909 0.00 0.00 0.00 4.26
51 52 6.551385 AATTTCAAGATGATATGACGGCTC 57.449 37.500 0.00 0.00 0.00 4.70
52 53 6.949352 AAATTTCAAGATGATATGACGGCT 57.051 33.333 0.00 0.00 0.00 5.52
53 54 6.792250 CGTAAATTTCAAGATGATATGACGGC 59.208 38.462 0.00 0.00 31.19 5.68
54 55 8.072238 TCGTAAATTTCAAGATGATATGACGG 57.928 34.615 0.00 0.00 33.32 4.79
55 56 9.573102 CTTCGTAAATTTCAAGATGATATGACG 57.427 33.333 0.00 0.00 33.53 4.35
56 57 9.374960 GCTTCGTAAATTTCAAGATGATATGAC 57.625 33.333 0.00 0.00 0.00 3.06
57 58 8.559536 GGCTTCGTAAATTTCAAGATGATATGA 58.440 33.333 0.00 0.00 0.00 2.15
58 59 7.531871 CGGCTTCGTAAATTTCAAGATGATATG 59.468 37.037 0.00 0.00 0.00 1.78
59 60 7.576236 CGGCTTCGTAAATTTCAAGATGATAT 58.424 34.615 0.00 0.00 0.00 1.63
60 61 6.511121 GCGGCTTCGTAAATTTCAAGATGATA 60.511 38.462 0.00 0.00 36.07 2.15
61 62 5.730568 GCGGCTTCGTAAATTTCAAGATGAT 60.731 40.000 0.00 0.00 36.07 2.45
62 63 4.436852 GCGGCTTCGTAAATTTCAAGATGA 60.437 41.667 0.00 0.00 36.07 2.92
63 64 3.786048 GCGGCTTCGTAAATTTCAAGATG 59.214 43.478 0.00 0.00 36.07 2.90
64 65 3.181500 GGCGGCTTCGTAAATTTCAAGAT 60.181 43.478 0.00 0.00 36.07 2.40
65 66 2.160813 GGCGGCTTCGTAAATTTCAAGA 59.839 45.455 0.00 0.00 36.07 3.02
66 67 2.515912 GGCGGCTTCGTAAATTTCAAG 58.484 47.619 0.00 0.00 36.07 3.02
67 68 1.135916 CGGCGGCTTCGTAAATTTCAA 60.136 47.619 7.61 0.00 36.07 2.69
68 69 0.444651 CGGCGGCTTCGTAAATTTCA 59.555 50.000 7.61 0.00 36.07 2.69
69 70 0.445043 ACGGCGGCTTCGTAAATTTC 59.555 50.000 13.24 0.00 39.22 2.17
70 71 1.662122 CTACGGCGGCTTCGTAAATTT 59.338 47.619 13.24 0.00 41.62 1.82
71 72 1.283736 CTACGGCGGCTTCGTAAATT 58.716 50.000 13.24 0.00 41.62 1.82
72 73 0.529119 CCTACGGCGGCTTCGTAAAT 60.529 55.000 13.24 0.00 41.62 1.40
73 74 1.153784 CCTACGGCGGCTTCGTAAA 60.154 57.895 13.24 0.00 41.62 2.01
74 75 2.491152 CCTACGGCGGCTTCGTAA 59.509 61.111 13.24 0.00 41.62 3.18
75 76 4.197498 GCCTACGGCGGCTTCGTA 62.197 66.667 13.24 10.30 46.63 3.43
85 86 1.607148 TCTACGATGATGTGCCTACGG 59.393 52.381 0.00 0.00 0.00 4.02
86 87 2.651701 GTCTACGATGATGTGCCTACG 58.348 52.381 0.00 0.00 0.00 3.51
87 88 2.604855 CCGTCTACGATGATGTGCCTAC 60.605 54.545 3.65 0.00 43.02 3.18
88 89 1.607148 CCGTCTACGATGATGTGCCTA 59.393 52.381 3.65 0.00 43.02 3.93
89 90 0.385751 CCGTCTACGATGATGTGCCT 59.614 55.000 3.65 0.00 43.02 4.75
90 91 0.597637 CCCGTCTACGATGATGTGCC 60.598 60.000 3.65 0.00 43.02 5.01
91 92 0.384309 TCCCGTCTACGATGATGTGC 59.616 55.000 3.65 0.00 43.02 4.57
92 93 2.460918 GTTCCCGTCTACGATGATGTG 58.539 52.381 3.65 0.00 43.02 3.21
93 94 1.065102 CGTTCCCGTCTACGATGATGT 59.935 52.381 3.65 0.00 43.02 3.06
94 95 1.065102 ACGTTCCCGTCTACGATGATG 59.935 52.381 3.65 0.00 46.28 3.07
95 96 1.386533 ACGTTCCCGTCTACGATGAT 58.613 50.000 3.65 0.00 46.28 2.45
96 97 2.858622 ACGTTCCCGTCTACGATGA 58.141 52.632 3.65 0.00 46.28 2.92
109 110 3.522553 CATTTAGTGGGAGGAGACGTTC 58.477 50.000 0.00 0.00 0.00 3.95
110 111 2.354805 GCATTTAGTGGGAGGAGACGTT 60.355 50.000 0.00 0.00 0.00 3.99
111 112 1.207329 GCATTTAGTGGGAGGAGACGT 59.793 52.381 0.00 0.00 0.00 4.34
112 113 1.802880 CGCATTTAGTGGGAGGAGACG 60.803 57.143 0.00 0.00 43.02 4.18
113 114 1.941325 CGCATTTAGTGGGAGGAGAC 58.059 55.000 0.00 0.00 43.02 3.36
114 115 0.178068 GCGCATTTAGTGGGAGGAGA 59.822 55.000 0.30 0.00 43.02 3.71
115 116 0.107703 TGCGCATTTAGTGGGAGGAG 60.108 55.000 5.66 0.00 43.02 3.69
116 117 0.546122 ATGCGCATTTAGTGGGAGGA 59.454 50.000 19.28 0.00 43.02 3.71
117 118 0.947244 GATGCGCATTTAGTGGGAGG 59.053 55.000 26.12 0.00 43.02 4.30
118 119 0.583438 CGATGCGCATTTAGTGGGAG 59.417 55.000 26.12 4.12 43.02 4.30
119 120 2.689083 CGATGCGCATTTAGTGGGA 58.311 52.632 26.12 0.00 43.02 4.37
131 132 1.009078 TCAAGATTTCCAGCGATGCG 58.991 50.000 0.00 0.00 0.00 4.73
132 133 3.492421 TTTCAAGATTTCCAGCGATGC 57.508 42.857 0.00 0.00 0.00 3.91
133 134 6.860023 GGATTATTTCAAGATTTCCAGCGATG 59.140 38.462 0.00 0.00 0.00 3.84
134 135 6.547141 TGGATTATTTCAAGATTTCCAGCGAT 59.453 34.615 0.00 0.00 0.00 4.58
135 136 5.885352 TGGATTATTTCAAGATTTCCAGCGA 59.115 36.000 0.00 0.00 0.00 4.93
136 137 6.038603 TCTGGATTATTTCAAGATTTCCAGCG 59.961 38.462 10.47 0.00 45.35 5.18
137 138 7.338800 TCTGGATTATTTCAAGATTTCCAGC 57.661 36.000 10.47 0.00 45.35 4.85
144 145 9.903682 CGCATTTATTCTGGATTATTTCAAGAT 57.096 29.630 0.00 0.00 34.24 2.40
145 146 9.119418 TCGCATTTATTCTGGATTATTTCAAGA 57.881 29.630 0.00 0.00 32.17 3.02
146 147 9.390795 CTCGCATTTATTCTGGATTATTTCAAG 57.609 33.333 0.00 0.00 0.00 3.02
147 148 7.862372 GCTCGCATTTATTCTGGATTATTTCAA 59.138 33.333 0.00 0.00 0.00 2.69
148 149 7.013178 TGCTCGCATTTATTCTGGATTATTTCA 59.987 33.333 0.00 0.00 0.00 2.69
149 150 7.324616 GTGCTCGCATTTATTCTGGATTATTTC 59.675 37.037 0.00 0.00 0.00 2.17
150 151 7.141363 GTGCTCGCATTTATTCTGGATTATTT 58.859 34.615 0.00 0.00 0.00 1.40
151 152 6.294176 GGTGCTCGCATTTATTCTGGATTATT 60.294 38.462 0.00 0.00 0.00 1.40
152 153 5.182001 GGTGCTCGCATTTATTCTGGATTAT 59.818 40.000 0.00 0.00 0.00 1.28
153 154 4.515191 GGTGCTCGCATTTATTCTGGATTA 59.485 41.667 0.00 0.00 0.00 1.75
154 155 3.316308 GGTGCTCGCATTTATTCTGGATT 59.684 43.478 0.00 0.00 0.00 3.01
155 156 2.880890 GGTGCTCGCATTTATTCTGGAT 59.119 45.455 0.00 0.00 0.00 3.41
156 157 2.288666 GGTGCTCGCATTTATTCTGGA 58.711 47.619 0.00 0.00 0.00 3.86
157 158 1.003545 CGGTGCTCGCATTTATTCTGG 60.004 52.381 0.00 0.00 0.00 3.86
158 159 1.003545 CCGGTGCTCGCATTTATTCTG 60.004 52.381 0.00 0.00 37.59 3.02
159 160 1.299541 CCGGTGCTCGCATTTATTCT 58.700 50.000 0.00 0.00 37.59 2.40
160 161 0.307760 CCCGGTGCTCGCATTTATTC 59.692 55.000 0.00 0.00 37.59 1.75
161 162 0.107410 TCCCGGTGCTCGCATTTATT 60.107 50.000 0.00 0.00 37.59 1.40
162 163 0.814010 GTCCCGGTGCTCGCATTTAT 60.814 55.000 0.00 0.00 37.59 1.40
163 164 1.448893 GTCCCGGTGCTCGCATTTA 60.449 57.895 0.00 0.00 37.59 1.40
164 165 2.746277 GTCCCGGTGCTCGCATTT 60.746 61.111 0.00 0.00 37.59 2.32
165 166 3.254024 AAGTCCCGGTGCTCGCATT 62.254 57.895 0.00 0.00 37.59 3.56
166 167 3.706373 AAGTCCCGGTGCTCGCAT 61.706 61.111 0.00 0.00 37.59 4.73
167 168 4.680237 CAAGTCCCGGTGCTCGCA 62.680 66.667 0.00 0.00 37.59 5.10
168 169 3.876589 TTCAAGTCCCGGTGCTCGC 62.877 63.158 0.00 0.00 37.59 5.03
169 170 2.027625 GTTCAAGTCCCGGTGCTCG 61.028 63.158 0.00 0.00 38.88 5.03
170 171 1.671379 GGTTCAAGTCCCGGTGCTC 60.671 63.158 0.00 0.00 0.00 4.26
171 172 2.430367 GGTTCAAGTCCCGGTGCT 59.570 61.111 0.00 0.00 0.00 4.40
172 173 2.671963 GGGTTCAAGTCCCGGTGC 60.672 66.667 0.00 0.00 35.27 5.01
177 178 0.034089 CATCCCAGGGTTCAAGTCCC 60.034 60.000 5.01 0.00 44.90 4.46
178 179 0.034089 CCATCCCAGGGTTCAAGTCC 60.034 60.000 5.01 0.00 0.00 3.85
179 180 0.034089 CCCATCCCAGGGTTCAAGTC 60.034 60.000 5.01 0.00 44.24 3.01
180 181 2.087248 CCCATCCCAGGGTTCAAGT 58.913 57.895 5.01 0.00 44.24 3.16
188 189 3.657727 ACAAACTATATCCCCATCCCAGG 59.342 47.826 0.00 0.00 0.00 4.45
189 190 5.072741 CAACAAACTATATCCCCATCCCAG 58.927 45.833 0.00 0.00 0.00 4.45
190 191 4.480537 ACAACAAACTATATCCCCATCCCA 59.519 41.667 0.00 0.00 0.00 4.37
191 192 5.061721 ACAACAAACTATATCCCCATCCC 57.938 43.478 0.00 0.00 0.00 3.85
192 193 9.802039 TTATAACAACAAACTATATCCCCATCC 57.198 33.333 0.00 0.00 0.00 3.51
201 202 9.838975 TCGTCGAAGTTATAACAACAAACTATA 57.161 29.630 17.65 0.00 33.24 1.31
202 203 8.746922 TCGTCGAAGTTATAACAACAAACTAT 57.253 30.769 17.65 0.00 33.24 2.12
203 204 8.746922 ATCGTCGAAGTTATAACAACAAACTA 57.253 30.769 17.65 2.54 33.24 2.24
204 205 7.647907 ATCGTCGAAGTTATAACAACAAACT 57.352 32.000 17.65 0.00 35.01 2.66
205 206 8.853345 TCTATCGTCGAAGTTATAACAACAAAC 58.147 33.333 17.65 7.91 0.00 2.93
206 207 8.853345 GTCTATCGTCGAAGTTATAACAACAAA 58.147 33.333 17.65 2.83 0.00 2.83
207 208 8.239314 AGTCTATCGTCGAAGTTATAACAACAA 58.761 33.333 17.65 0.00 0.00 2.83
208 209 7.755591 AGTCTATCGTCGAAGTTATAACAACA 58.244 34.615 17.65 0.00 0.00 3.33
209 210 9.367717 CTAGTCTATCGTCGAAGTTATAACAAC 57.632 37.037 17.65 9.59 0.00 3.32
210 211 8.554528 CCTAGTCTATCGTCGAAGTTATAACAA 58.445 37.037 17.65 0.00 0.00 2.83
211 212 7.307632 GCCTAGTCTATCGTCGAAGTTATAACA 60.308 40.741 17.65 0.00 0.00 2.41
212 213 7.014702 GCCTAGTCTATCGTCGAAGTTATAAC 58.985 42.308 7.57 7.57 0.00 1.89
213 214 6.933521 AGCCTAGTCTATCGTCGAAGTTATAA 59.066 38.462 0.00 0.00 0.00 0.98
214 215 6.462500 AGCCTAGTCTATCGTCGAAGTTATA 58.538 40.000 0.00 0.00 0.00 0.98
215 216 5.307204 AGCCTAGTCTATCGTCGAAGTTAT 58.693 41.667 0.00 0.00 0.00 1.89
216 217 4.701765 AGCCTAGTCTATCGTCGAAGTTA 58.298 43.478 0.00 0.00 0.00 2.24
217 218 3.543665 AGCCTAGTCTATCGTCGAAGTT 58.456 45.455 0.00 0.00 0.00 2.66
218 219 3.132925 GAGCCTAGTCTATCGTCGAAGT 58.867 50.000 0.00 0.00 0.00 3.01
219 220 3.185594 CAGAGCCTAGTCTATCGTCGAAG 59.814 52.174 0.00 0.00 0.00 3.79
220 221 3.132160 CAGAGCCTAGTCTATCGTCGAA 58.868 50.000 0.00 0.00 0.00 3.71
221 222 2.102757 ACAGAGCCTAGTCTATCGTCGA 59.897 50.000 0.00 0.00 0.00 4.20
222 223 2.485903 ACAGAGCCTAGTCTATCGTCG 58.514 52.381 0.00 0.00 0.00 5.12
223 224 3.251487 GGAACAGAGCCTAGTCTATCGTC 59.749 52.174 0.00 0.00 0.00 4.20
224 225 3.215975 GGAACAGAGCCTAGTCTATCGT 58.784 50.000 0.00 0.00 0.00 3.73
225 226 2.554893 GGGAACAGAGCCTAGTCTATCG 59.445 54.545 0.00 0.00 0.00 2.92
226 227 3.567397 TGGGAACAGAGCCTAGTCTATC 58.433 50.000 0.00 0.00 35.01 2.08
227 228 3.689872 TGGGAACAGAGCCTAGTCTAT 57.310 47.619 0.00 0.00 35.01 1.98
238 239 7.956174 CTGTAAGAGAAAGAACATGGGAACAGA 60.956 40.741 0.00 0.00 40.11 3.41
239 240 6.148480 CTGTAAGAGAAAGAACATGGGAACAG 59.852 42.308 0.00 0.00 40.11 3.16
240 241 5.997746 CTGTAAGAGAAAGAACATGGGAACA 59.002 40.000 0.00 0.00 41.10 3.18
241 242 5.998363 ACTGTAAGAGAAAGAACATGGGAAC 59.002 40.000 0.00 0.00 37.43 3.62
242 243 6.187727 ACTGTAAGAGAAAGAACATGGGAA 57.812 37.500 0.00 0.00 37.43 3.97
260 261 4.074259 ACGCGTGGGTATCATATACTGTA 58.926 43.478 12.93 0.00 0.00 2.74
272 273 1.472082 TCTTTCGAATACGCGTGGGTA 59.528 47.619 24.59 0.62 39.58 3.69
274 275 1.352114 TTCTTTCGAATACGCGTGGG 58.648 50.000 24.59 8.19 39.58 4.61
299 300 5.126707 GGGAGAACTAAGAACAGGAACGATA 59.873 44.000 0.00 0.00 0.00 2.92
336 337 1.280457 GGGTCTGTCAGATCCCACTT 58.720 55.000 20.18 0.00 39.67 3.16
363 364 0.959553 TGGAGCTCCGATCCGATAAC 59.040 55.000 27.43 0.00 39.91 1.89
388 389 3.695606 GAGCACCAGAGGCACGGA 61.696 66.667 0.00 0.00 0.00 4.69
564 568 2.358737 AAAGAACCTGAGCCGCCG 60.359 61.111 0.00 0.00 0.00 6.46
565 569 1.003233 AGAAAGAACCTGAGCCGCC 60.003 57.895 0.00 0.00 0.00 6.13
566 570 1.355066 CGAGAAAGAACCTGAGCCGC 61.355 60.000 0.00 0.00 0.00 6.53
567 571 0.737715 CCGAGAAAGAACCTGAGCCG 60.738 60.000 0.00 0.00 0.00 5.52
568 572 1.021920 GCCGAGAAAGAACCTGAGCC 61.022 60.000 0.00 0.00 0.00 4.70
569 573 1.021920 GGCCGAGAAAGAACCTGAGC 61.022 60.000 0.00 0.00 0.00 4.26
640 644 2.075979 AAGAACGCCCGAGAAAGTAC 57.924 50.000 0.00 0.00 0.00 2.73
650 654 0.536460 TCACTCCCAAAAGAACGCCC 60.536 55.000 0.00 0.00 0.00 6.13
656 660 4.695455 GTCAATCGAATCACTCCCAAAAGA 59.305 41.667 0.00 0.00 0.00 2.52
690 698 5.185828 CCAGATTTCTTTCCGGGAGAAAAAT 59.814 40.000 26.63 18.95 43.84 1.82
743 751 0.391263 CAACTCAGTCGGTAAGCCCC 60.391 60.000 0.00 0.00 0.00 5.80
754 762 4.141158 AGAGAAAAACATCCCCAACTCAGT 60.141 41.667 0.00 0.00 0.00 3.41
774 782 8.619546 GTCATTTCCAGAAAATAGGATGAAGAG 58.380 37.037 0.00 0.00 35.77 2.85
806 814 4.454678 AGATTGCACAAGAACAACTCTGA 58.545 39.130 0.00 0.00 33.37 3.27
807 815 4.320057 GGAGATTGCACAAGAACAACTCTG 60.320 45.833 0.00 0.00 33.37 3.35
916 928 2.386661 AAGAACCTACGTGCATCAGG 57.613 50.000 0.00 9.07 35.45 3.86
964 976 4.367450 TGCGTTTCCAGAGAAAATTTTGG 58.633 39.130 8.47 4.14 43.48 3.28
1006 1018 1.442017 GTTTAAAGCACTGCCGCGG 60.442 57.895 24.05 24.05 36.85 6.46
1057 1069 1.229529 ACCCAGGACCGTGGAGAAT 60.230 57.895 10.06 0.00 40.44 2.40
1071 1083 2.930019 CCTGCACCTCTGGACCCA 60.930 66.667 0.00 0.00 35.98 4.51
1074 1086 2.046507 CTGCCTGCACCTCTGGAC 60.047 66.667 0.00 0.00 35.98 4.02
1195 1207 2.099141 TCCAGAAACGAGCAATCAGG 57.901 50.000 0.00 0.00 0.00 3.86
1230 1247 5.368145 TGTCTCAGCAACATAACAAGAAGT 58.632 37.500 0.00 0.00 0.00 3.01
1243 1260 2.027469 AGCATCATGTCTGTCTCAGCAA 60.027 45.455 0.00 0.00 0.00 3.91
1286 1306 8.447053 GCTTTGTTTGTTGTTTCCTTAATCAAA 58.553 29.630 0.00 0.00 0.00 2.69
1287 1307 7.604164 TGCTTTGTTTGTTGTTTCCTTAATCAA 59.396 29.630 0.00 0.00 0.00 2.57
1288 1308 7.099764 TGCTTTGTTTGTTGTTTCCTTAATCA 58.900 30.769 0.00 0.00 0.00 2.57
1289 1309 7.532682 TGCTTTGTTTGTTGTTTCCTTAATC 57.467 32.000 0.00 0.00 0.00 1.75
1408 1429 2.591715 ACCGTGACCAGTTGCAGC 60.592 61.111 0.00 0.00 0.00 5.25
1447 1468 1.552792 GCAGAAGGGACTAGCAGAACT 59.447 52.381 0.00 0.00 38.49 3.01
1738 1759 2.915463 CTCGTCAGGTCGATTGTTACAC 59.085 50.000 0.00 0.00 39.12 2.90
1823 1844 8.891671 ATGACAAAGCACAAGAAAATGTTAAT 57.108 26.923 0.00 0.00 0.00 1.40
1963 1984 2.443394 GGCAGATGGATCGGGGACA 61.443 63.158 0.00 0.00 0.00 4.02
1984 2005 2.622942 TGCCATGTTGAAGTTCTTGACC 59.377 45.455 4.17 0.00 0.00 4.02
2263 2291 5.586243 GCAATGGTATAATGTCAGAGTGTGT 59.414 40.000 0.00 0.00 0.00 3.72
2274 2302 8.887036 TCAAGTACTACAGCAATGGTATAATG 57.113 34.615 0.00 0.00 0.00 1.90
2305 2333 1.342174 AGCCAACAAATGTTCAGCTGG 59.658 47.619 15.13 7.84 40.85 4.85
2322 2350 4.557695 CGATGAGAGAATGTACCTACAGCC 60.558 50.000 0.00 0.00 39.92 4.85
2561 2590 4.580995 TCAACAGTCCTCTCGATTCTATCC 59.419 45.833 0.00 0.00 0.00 2.59
2798 2827 3.011635 GCGGCTGAAGAGCTCCTCA 62.012 63.158 14.27 14.27 45.44 3.86
3005 3034 2.038557 AGCTAATCTGGGAACGTGTTGT 59.961 45.455 0.00 0.00 0.00 3.32
3011 3040 4.442706 ACACATAAGCTAATCTGGGAACG 58.557 43.478 0.00 0.00 0.00 3.95
3119 3150 5.216665 ACTATCCCCAGAAACAGGTAGTA 57.783 43.478 0.00 0.00 0.00 1.82
3120 3151 4.076175 ACTATCCCCAGAAACAGGTAGT 57.924 45.455 0.00 0.00 0.00 2.73
3121 3152 4.469945 TGAACTATCCCCAGAAACAGGTAG 59.530 45.833 0.00 0.00 0.00 3.18
3150 3181 7.732222 ATTGCCATAAAAAGGGAGAATAACA 57.268 32.000 0.00 0.00 0.00 2.41
3233 3267 8.621286 GGAGAAAAAGTTAACAAGATTGTGAGA 58.379 33.333 8.61 0.00 41.31 3.27
3234 3268 8.405531 TGGAGAAAAAGTTAACAAGATTGTGAG 58.594 33.333 8.61 0.00 41.31 3.51
3237 3271 8.062065 TGTGGAGAAAAAGTTAACAAGATTGT 57.938 30.769 8.61 0.00 44.72 2.71
3324 3360 4.763279 CCGTACCCCACTGTTTCTATTTTT 59.237 41.667 0.00 0.00 0.00 1.94
3325 3361 4.041938 TCCGTACCCCACTGTTTCTATTTT 59.958 41.667 0.00 0.00 0.00 1.82
3396 3438 2.735126 GCCAAATGGATACCGCTGTTTG 60.735 50.000 2.98 0.00 37.39 2.93
3426 3468 4.325816 CCCCTGAGTTAACCCCATATGTTT 60.326 45.833 0.88 0.00 0.00 2.83
3495 3537 2.477863 GGTTGCGCTGTGATTCATTACC 60.478 50.000 9.73 0.00 0.00 2.85
3504 3546 1.737735 CTGATCGGTTGCGCTGTGA 60.738 57.895 9.73 1.33 0.00 3.58
3544 3586 3.952535 ACGAGAAGTTTGCACATTGTTC 58.047 40.909 0.00 0.00 0.00 3.18
3609 3651 3.736227 TCATTTCCATACCCCTCCCTA 57.264 47.619 0.00 0.00 0.00 3.53
3635 3677 1.063469 CGTGAGCAGTTTTCCGTGTTT 59.937 47.619 0.00 0.00 0.00 2.83
3729 3771 7.992608 TGTGTACCTATGATTGCATTGTTCTAT 59.007 33.333 0.00 0.00 35.94 1.98


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

AutoCloner maintained by Alex Coulton.