Multiple sequence alignment - TraesCS3A01G368500

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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 TraesCS3A01G368500 chr3A 100.000 2549 0 0 1 2549 617400451 617402999 0.000 4708.0
1 TraesCS3A01G368500 chr3A 97.034 1989 53 5 564 2549 735555332 735557317 0.000 3341.0
2 TraesCS3A01G368500 chr3A 96.910 1974 55 5 567 2537 54951912 54953882 0.000 3302.0
3 TraesCS3A01G368500 chr6B 96.979 1986 55 5 567 2549 660437749 660435766 0.000 3330.0
4 TraesCS3A01G368500 chr7A 96.977 1985 54 6 570 2549 701581937 701583920 0.000 3328.0
5 TraesCS3A01G368500 chr7A 93.840 487 28 1 91 575 109221037 109220551 0.000 732.0
6 TraesCS3A01G368500 chr7B 96.872 1982 56 6 573 2549 552932143 552930163 0.000 3312.0
7 TraesCS3A01G368500 chr6A 97.054 1969 54 4 572 2537 617222870 617220903 0.000 3312.0
8 TraesCS3A01G368500 chr1A 96.818 1980 61 2 571 2549 22791527 22793505 0.000 3306.0
9 TraesCS3A01G368500 chr3B 96.541 1995 62 7 558 2549 379294080 379296070 0.000 3295.0
10 TraesCS3A01G368500 chr3B 94.262 488 23 4 91 575 101920852 101920367 0.000 741.0
11 TraesCS3A01G368500 chr2B 96.588 1993 58 8 549 2537 776222941 776224927 0.000 3295.0
12 TraesCS3A01G368500 chr2B 100.000 28 0 0 59 86 3411984 3411957 0.005 52.8
13 TraesCS3A01G368500 chr5D 93.890 491 26 3 85 572 503285488 503285977 0.000 737.0
14 TraesCS3A01G368500 chr5D 93.333 495 29 2 85 575 6182758 6182264 0.000 728.0
15 TraesCS3A01G368500 chr5D 94.008 484 24 4 92 572 120798066 120798547 0.000 728.0
16 TraesCS3A01G368500 chr5D 92.525 495 32 3 85 575 513641509 513641016 0.000 704.0
17 TraesCS3A01G368500 chr1D 93.522 494 28 3 85 575 51879885 51879393 0.000 732.0
18 TraesCS3A01G368500 chr6D 93.634 487 28 2 91 575 45513369 45512884 0.000 725.0
19 TraesCS3A01G368500 chr2A 92.540 496 32 3 85 575 335832443 335831948 0.000 706.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G368500 chr3A 617400451 617402999 2548 False 4708 4708 100.000 1 2549 1 chr3A.!!$F2 2548
1 TraesCS3A01G368500 chr3A 735555332 735557317 1985 False 3341 3341 97.034 564 2549 1 chr3A.!!$F3 1985
2 TraesCS3A01G368500 chr3A 54951912 54953882 1970 False 3302 3302 96.910 567 2537 1 chr3A.!!$F1 1970
3 TraesCS3A01G368500 chr6B 660435766 660437749 1983 True 3330 3330 96.979 567 2549 1 chr6B.!!$R1 1982
4 TraesCS3A01G368500 chr7A 701581937 701583920 1983 False 3328 3328 96.977 570 2549 1 chr7A.!!$F1 1979
5 TraesCS3A01G368500 chr7B 552930163 552932143 1980 True 3312 3312 96.872 573 2549 1 chr7B.!!$R1 1976
6 TraesCS3A01G368500 chr6A 617220903 617222870 1967 True 3312 3312 97.054 572 2537 1 chr6A.!!$R1 1965
7 TraesCS3A01G368500 chr1A 22791527 22793505 1978 False 3306 3306 96.818 571 2549 1 chr1A.!!$F1 1978
8 TraesCS3A01G368500 chr3B 379294080 379296070 1990 False 3295 3295 96.541 558 2549 1 chr3B.!!$F1 1991
9 TraesCS3A01G368500 chr2B 776222941 776224927 1986 False 3295 3295 96.588 549 2537 1 chr2B.!!$F1 1988

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
267 268 0.238553 GCCTGACAAACTTCGAAGCC 59.761 55.0 24.86 9.62 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2219 2227 0.17668 CTTGCCATCTGTCCTAGCGT 59.823 55.0 0.0 0.0 0.0 5.07 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
26 27 9.137459 TGTTATTGGGTTTGTATTTGAAAGAGA 57.863 29.630 0.00 0.00 0.00 3.10
32 33 9.527157 TGGGTTTGTATTTGAAAGAGATATTCA 57.473 29.630 0.00 0.00 35.11 2.57
70 71 8.397215 TCATGACATTGAATTAGAAAAATGCG 57.603 30.769 0.00 0.00 34.13 4.73
71 72 8.242739 TCATGACATTGAATTAGAAAAATGCGA 58.757 29.630 0.00 0.00 34.13 5.10
72 73 8.529102 CATGACATTGAATTAGAAAAATGCGAG 58.471 33.333 0.00 0.00 34.13 5.03
73 74 6.527722 TGACATTGAATTAGAAAAATGCGAGC 59.472 34.615 0.00 0.00 34.13 5.03
74 75 6.389091 ACATTGAATTAGAAAAATGCGAGCA 58.611 32.000 0.00 0.00 34.13 4.26
75 76 6.308766 ACATTGAATTAGAAAAATGCGAGCAC 59.691 34.615 0.00 0.00 34.13 4.40
76 77 4.732784 TGAATTAGAAAAATGCGAGCACC 58.267 39.130 0.00 0.00 0.00 5.01
77 78 4.217334 TGAATTAGAAAAATGCGAGCACCA 59.783 37.500 0.00 0.00 0.00 4.17
78 79 4.782019 ATTAGAAAAATGCGAGCACCAA 57.218 36.364 0.00 0.00 0.00 3.67
79 80 4.782019 TTAGAAAAATGCGAGCACCAAT 57.218 36.364 0.00 0.00 0.00 3.16
80 81 2.950433 AGAAAAATGCGAGCACCAATG 58.050 42.857 0.00 0.00 0.00 2.82
81 82 2.297033 AGAAAAATGCGAGCACCAATGT 59.703 40.909 0.00 0.00 0.00 2.71
82 83 2.352503 AAAATGCGAGCACCAATGTC 57.647 45.000 0.00 0.00 0.00 3.06
83 84 1.246649 AAATGCGAGCACCAATGTCA 58.753 45.000 0.00 0.00 0.00 3.58
84 85 1.246649 AATGCGAGCACCAATGTCAA 58.753 45.000 0.00 0.00 0.00 3.18
85 86 1.246649 ATGCGAGCACCAATGTCAAA 58.753 45.000 0.00 0.00 0.00 2.69
86 87 1.028130 TGCGAGCACCAATGTCAAAA 58.972 45.000 0.00 0.00 0.00 2.44
87 88 1.268999 TGCGAGCACCAATGTCAAAAC 60.269 47.619 0.00 0.00 0.00 2.43
88 89 1.268999 GCGAGCACCAATGTCAAAACA 60.269 47.619 0.00 0.00 40.38 2.83
89 90 2.797792 GCGAGCACCAATGTCAAAACAA 60.798 45.455 0.00 0.00 39.30 2.83
90 91 2.788786 CGAGCACCAATGTCAAAACAAC 59.211 45.455 0.00 0.00 39.30 3.32
91 92 3.123050 GAGCACCAATGTCAAAACAACC 58.877 45.455 0.00 0.00 39.30 3.77
92 93 2.158971 AGCACCAATGTCAAAACAACCC 60.159 45.455 0.00 0.00 39.30 4.11
93 94 2.832563 CACCAATGTCAAAACAACCCC 58.167 47.619 0.00 0.00 39.30 4.95
94 95 1.765904 ACCAATGTCAAAACAACCCCC 59.234 47.619 0.00 0.00 39.30 5.40
116 117 5.363562 CCTAGAAACGTATAGGGGGTTTT 57.636 43.478 11.71 0.00 35.39 2.43
117 118 5.363101 CCTAGAAACGTATAGGGGGTTTTC 58.637 45.833 11.71 0.00 35.39 2.29
118 119 5.129980 CCTAGAAACGTATAGGGGGTTTTCT 59.870 44.000 11.71 11.29 35.39 2.52
119 120 5.095145 AGAAACGTATAGGGGGTTTTCTC 57.905 43.478 0.00 0.00 34.29 2.87
120 121 3.920231 AACGTATAGGGGGTTTTCTCC 57.080 47.619 0.00 0.00 40.44 3.71
121 122 3.126323 ACGTATAGGGGGTTTTCTCCT 57.874 47.619 0.00 0.00 41.08 3.69
122 123 3.036819 ACGTATAGGGGGTTTTCTCCTC 58.963 50.000 0.00 0.00 41.08 3.71
123 124 3.036091 CGTATAGGGGGTTTTCTCCTCA 58.964 50.000 0.00 0.00 41.08 3.86
124 125 3.646637 CGTATAGGGGGTTTTCTCCTCAT 59.353 47.826 0.00 0.00 41.08 2.90
125 126 4.836736 CGTATAGGGGGTTTTCTCCTCATA 59.163 45.833 0.00 0.00 41.08 2.15
126 127 5.279356 CGTATAGGGGGTTTTCTCCTCATAC 60.279 48.000 0.00 0.00 41.08 2.39
127 128 2.929301 AGGGGGTTTTCTCCTCATACA 58.071 47.619 0.00 0.00 41.08 2.29
128 129 2.846827 AGGGGGTTTTCTCCTCATACAG 59.153 50.000 0.00 0.00 41.08 2.74
129 130 2.644676 GGGGTTTTCTCCTCATACAGC 58.355 52.381 0.00 0.00 37.51 4.40
130 131 2.239907 GGGGTTTTCTCCTCATACAGCT 59.760 50.000 0.00 0.00 37.51 4.24
131 132 3.536570 GGGTTTTCTCCTCATACAGCTC 58.463 50.000 0.00 0.00 0.00 4.09
132 133 3.190874 GGTTTTCTCCTCATACAGCTCG 58.809 50.000 0.00 0.00 0.00 5.03
133 134 3.119101 GGTTTTCTCCTCATACAGCTCGA 60.119 47.826 0.00 0.00 0.00 4.04
134 135 4.109050 GTTTTCTCCTCATACAGCTCGAG 58.891 47.826 8.45 8.45 0.00 4.04
135 136 3.283259 TTCTCCTCATACAGCTCGAGA 57.717 47.619 18.75 0.00 0.00 4.04
136 137 3.283259 TCTCCTCATACAGCTCGAGAA 57.717 47.619 18.75 0.00 0.00 2.87
137 138 3.621558 TCTCCTCATACAGCTCGAGAAA 58.378 45.455 18.75 0.00 0.00 2.52
138 139 4.017126 TCTCCTCATACAGCTCGAGAAAA 58.983 43.478 18.75 0.00 0.00 2.29
139 140 4.646945 TCTCCTCATACAGCTCGAGAAAAT 59.353 41.667 18.75 0.08 0.00 1.82
140 141 4.686972 TCCTCATACAGCTCGAGAAAATG 58.313 43.478 18.75 13.06 0.00 2.32
141 142 4.402474 TCCTCATACAGCTCGAGAAAATGA 59.598 41.667 18.75 16.34 0.00 2.57
142 143 5.069648 TCCTCATACAGCTCGAGAAAATGAT 59.930 40.000 18.75 0.00 0.00 2.45
143 144 5.757320 CCTCATACAGCTCGAGAAAATGATT 59.243 40.000 18.75 0.00 0.00 2.57
144 145 6.073873 CCTCATACAGCTCGAGAAAATGATTC 60.074 42.308 18.75 0.00 0.00 2.52
145 146 5.460091 TCATACAGCTCGAGAAAATGATTCG 59.540 40.000 18.75 1.67 35.76 3.34
146 147 3.849911 ACAGCTCGAGAAAATGATTCGA 58.150 40.909 18.75 0.00 40.64 3.71
147 148 4.245660 ACAGCTCGAGAAAATGATTCGAA 58.754 39.130 18.75 0.00 42.09 3.71
148 149 4.872691 ACAGCTCGAGAAAATGATTCGAAT 59.127 37.500 18.75 11.20 42.09 3.34
149 150 5.352569 ACAGCTCGAGAAAATGATTCGAATT 59.647 36.000 18.75 0.00 42.09 2.17
150 151 6.128172 ACAGCTCGAGAAAATGATTCGAATTT 60.128 34.615 18.75 2.93 42.09 1.82
151 152 6.410337 CAGCTCGAGAAAATGATTCGAATTTC 59.590 38.462 18.75 12.37 42.09 2.17
152 153 5.390859 GCTCGAGAAAATGATTCGAATTTCG 59.609 40.000 18.75 12.54 42.09 3.46
153 154 5.795766 TCGAGAAAATGATTCGAATTTCGG 58.204 37.500 18.02 10.01 40.05 4.30
154 155 5.350365 TCGAGAAAATGATTCGAATTTCGGT 59.650 36.000 18.02 7.97 40.05 4.69
155 156 5.672856 CGAGAAAATGATTCGAATTTCGGTC 59.327 40.000 18.02 15.79 40.88 4.79
156 157 5.560148 AGAAAATGATTCGAATTTCGGTCG 58.440 37.500 18.02 0.00 40.88 4.79
157 158 5.350365 AGAAAATGATTCGAATTTCGGTCGA 59.650 36.000 18.02 8.56 45.30 4.20
158 159 5.734855 AAATGATTCGAATTTCGGTCGAT 57.265 34.783 18.02 7.96 46.15 3.59
159 160 6.838198 AAATGATTCGAATTTCGGTCGATA 57.162 33.333 18.02 3.37 46.15 2.92
160 161 6.838198 AATGATTCGAATTTCGGTCGATAA 57.162 33.333 18.02 5.06 46.15 1.75
161 162 7.421530 AATGATTCGAATTTCGGTCGATAAT 57.578 32.000 18.02 9.42 46.15 1.28
162 163 8.528917 AATGATTCGAATTTCGGTCGATAATA 57.471 30.769 18.02 2.18 46.15 0.98
163 164 7.933728 TGATTCGAATTTCGGTCGATAATAA 57.066 32.000 18.02 3.03 46.15 1.40
164 165 8.528917 TGATTCGAATTTCGGTCGATAATAAT 57.471 30.769 18.02 7.47 46.15 1.28
165 166 9.628746 TGATTCGAATTTCGGTCGATAATAATA 57.371 29.630 18.02 0.00 46.15 0.98
167 168 9.850628 ATTCGAATTTCGGTCGATAATAATAGA 57.149 29.630 18.02 0.00 46.15 1.98
168 169 9.681692 TTCGAATTTCGGTCGATAATAATAGAA 57.318 29.630 18.02 0.00 46.15 2.10
169 170 9.681692 TCGAATTTCGGTCGATAATAATAGAAA 57.318 29.630 18.02 0.00 42.31 2.52
188 189 9.547753 AATAGAAATTAGACTATGACGTGCATT 57.452 29.630 0.00 0.00 38.44 3.56
190 191 8.942338 AGAAATTAGACTATGACGTGCATTAA 57.058 30.769 0.00 0.00 38.44 1.40
191 192 9.547753 AGAAATTAGACTATGACGTGCATTAAT 57.452 29.630 0.00 0.00 38.44 1.40
195 196 6.604735 AGACTATGACGTGCATTAATTTCC 57.395 37.500 0.00 0.00 38.44 3.13
196 197 6.349300 AGACTATGACGTGCATTAATTTCCT 58.651 36.000 0.00 0.00 38.44 3.36
197 198 6.823689 AGACTATGACGTGCATTAATTTCCTT 59.176 34.615 0.00 0.00 38.44 3.36
198 199 7.985184 AGACTATGACGTGCATTAATTTCCTTA 59.015 33.333 0.00 0.00 38.44 2.69
199 200 7.916552 ACTATGACGTGCATTAATTTCCTTAC 58.083 34.615 0.00 0.00 38.44 2.34
200 201 6.751514 ATGACGTGCATTAATTTCCTTACA 57.248 33.333 0.00 0.00 31.73 2.41
201 202 6.176975 TGACGTGCATTAATTTCCTTACAG 57.823 37.500 0.00 0.00 0.00 2.74
202 203 5.935206 TGACGTGCATTAATTTCCTTACAGA 59.065 36.000 0.00 0.00 0.00 3.41
203 204 6.428465 TGACGTGCATTAATTTCCTTACAGAA 59.572 34.615 0.00 0.00 0.00 3.02
204 205 7.041030 TGACGTGCATTAATTTCCTTACAGAAA 60.041 33.333 0.00 0.00 39.92 2.52
205 206 7.653647 ACGTGCATTAATTTCCTTACAGAAAA 58.346 30.769 0.00 0.00 39.11 2.29
206 207 8.138712 ACGTGCATTAATTTCCTTACAGAAAAA 58.861 29.630 0.00 0.00 39.11 1.94
238 239 8.722480 TCAATTTATACTCATGACTCAAGTGG 57.278 34.615 0.00 0.00 0.00 4.00
239 240 7.770433 TCAATTTATACTCATGACTCAAGTGGG 59.230 37.037 0.00 0.00 0.00 4.61
240 241 3.550437 ATACTCATGACTCAAGTGGGC 57.450 47.619 0.00 0.00 0.00 5.36
241 242 1.356124 ACTCATGACTCAAGTGGGCT 58.644 50.000 0.00 0.00 0.00 5.19
242 243 2.540383 ACTCATGACTCAAGTGGGCTA 58.460 47.619 0.00 0.00 0.00 3.93
243 244 2.906389 ACTCATGACTCAAGTGGGCTAA 59.094 45.455 0.00 0.00 0.00 3.09
244 245 3.521126 ACTCATGACTCAAGTGGGCTAAT 59.479 43.478 0.00 0.00 0.00 1.73
245 246 4.018960 ACTCATGACTCAAGTGGGCTAATT 60.019 41.667 0.00 0.00 0.00 1.40
246 247 4.922206 TCATGACTCAAGTGGGCTAATTT 58.078 39.130 0.00 0.00 0.00 1.82
247 248 5.324409 TCATGACTCAAGTGGGCTAATTTT 58.676 37.500 0.00 0.00 0.00 1.82
248 249 5.183713 TCATGACTCAAGTGGGCTAATTTTG 59.816 40.000 0.00 0.00 0.00 2.44
249 250 3.255642 TGACTCAAGTGGGCTAATTTTGC 59.744 43.478 0.00 0.00 0.00 3.68
265 266 3.691049 TTTGCCTGACAAACTTCGAAG 57.309 42.857 23.43 23.43 43.35 3.79
266 267 0.944386 TGCCTGACAAACTTCGAAGC 59.056 50.000 24.86 9.08 0.00 3.86
267 268 0.238553 GCCTGACAAACTTCGAAGCC 59.761 55.000 24.86 9.62 0.00 4.35
268 269 1.593196 CCTGACAAACTTCGAAGCCA 58.407 50.000 24.86 13.30 0.00 4.75
269 270 1.946768 CCTGACAAACTTCGAAGCCAA 59.053 47.619 24.86 4.46 0.00 4.52
270 271 2.357637 CCTGACAAACTTCGAAGCCAAA 59.642 45.455 24.86 5.49 0.00 3.28
271 272 3.181491 CCTGACAAACTTCGAAGCCAAAA 60.181 43.478 24.86 6.03 0.00 2.44
272 273 4.499696 CCTGACAAACTTCGAAGCCAAAAT 60.500 41.667 24.86 6.04 0.00 1.82
273 274 4.606961 TGACAAACTTCGAAGCCAAAATC 58.393 39.130 24.86 14.67 0.00 2.17
274 275 3.977427 ACAAACTTCGAAGCCAAAATCC 58.023 40.909 24.86 0.00 0.00 3.01
275 276 3.636764 ACAAACTTCGAAGCCAAAATCCT 59.363 39.130 24.86 0.00 0.00 3.24
276 277 4.099419 ACAAACTTCGAAGCCAAAATCCTT 59.901 37.500 24.86 5.60 0.00 3.36
277 278 4.937201 AACTTCGAAGCCAAAATCCTTT 57.063 36.364 24.86 4.86 0.00 3.11
278 279 6.183360 ACAAACTTCGAAGCCAAAATCCTTTA 60.183 34.615 24.86 0.00 0.00 1.85
279 280 6.399639 AACTTCGAAGCCAAAATCCTTTAA 57.600 33.333 24.86 0.00 0.00 1.52
280 281 6.399639 ACTTCGAAGCCAAAATCCTTTAAA 57.600 33.333 24.86 0.00 0.00 1.52
281 282 6.811954 ACTTCGAAGCCAAAATCCTTTAAAA 58.188 32.000 24.86 0.00 0.00 1.52
282 283 7.269316 ACTTCGAAGCCAAAATCCTTTAAAAA 58.731 30.769 24.86 0.00 0.00 1.94
283 284 7.931407 ACTTCGAAGCCAAAATCCTTTAAAAAT 59.069 29.630 24.86 0.00 0.00 1.82
284 285 9.418045 CTTCGAAGCCAAAATCCTTTAAAAATA 57.582 29.630 13.09 0.00 0.00 1.40
285 286 9.765795 TTCGAAGCCAAAATCCTTTAAAAATAA 57.234 25.926 0.00 0.00 0.00 1.40
286 287 9.936759 TCGAAGCCAAAATCCTTTAAAAATAAT 57.063 25.926 0.00 0.00 0.00 1.28
308 309 9.930693 ATAATTGAGTCGTCTTTAAACTCTTCT 57.069 29.630 5.97 0.00 40.07 2.85
309 310 8.664211 AATTGAGTCGTCTTTAAACTCTTCTT 57.336 30.769 5.97 0.00 40.07 2.52
310 311 8.664211 ATTGAGTCGTCTTTAAACTCTTCTTT 57.336 30.769 5.97 0.00 40.07 2.52
311 312 7.464830 TGAGTCGTCTTTAAACTCTTCTTTG 57.535 36.000 5.97 0.00 40.07 2.77
312 313 7.039882 TGAGTCGTCTTTAAACTCTTCTTTGT 58.960 34.615 5.97 0.00 40.07 2.83
313 314 7.222224 TGAGTCGTCTTTAAACTCTTCTTTGTC 59.778 37.037 5.97 0.00 40.07 3.18
314 315 7.266400 AGTCGTCTTTAAACTCTTCTTTGTCT 58.734 34.615 0.00 0.00 0.00 3.41
315 316 7.435784 AGTCGTCTTTAAACTCTTCTTTGTCTC 59.564 37.037 0.00 0.00 0.00 3.36
316 317 7.222224 GTCGTCTTTAAACTCTTCTTTGTCTCA 59.778 37.037 0.00 0.00 0.00 3.27
317 318 7.926555 TCGTCTTTAAACTCTTCTTTGTCTCAT 59.073 33.333 0.00 0.00 0.00 2.90
318 319 8.552034 CGTCTTTAAACTCTTCTTTGTCTCATT 58.448 33.333 0.00 0.00 0.00 2.57
325 326 9.525409 AAACTCTTCTTTGTCTCATTTCAAATG 57.475 29.630 3.46 3.46 33.93 2.32
326 327 8.455903 ACTCTTCTTTGTCTCATTTCAAATGA 57.544 30.769 12.35 12.35 33.93 2.57
327 328 8.906867 ACTCTTCTTTGTCTCATTTCAAATGAA 58.093 29.630 13.84 3.12 33.93 2.57
328 329 9.909644 CTCTTCTTTGTCTCATTTCAAATGAAT 57.090 29.630 13.84 0.00 33.93 2.57
360 361 9.618890 TTTATTCCTAAATCTGATCCAACTCTG 57.381 33.333 0.00 0.00 0.00 3.35
361 362 6.627087 TTCCTAAATCTGATCCAACTCTGT 57.373 37.500 0.00 0.00 0.00 3.41
362 363 6.627087 TCCTAAATCTGATCCAACTCTGTT 57.373 37.500 0.00 0.00 0.00 3.16
363 364 6.409704 TCCTAAATCTGATCCAACTCTGTTG 58.590 40.000 3.69 3.69 0.00 3.33
364 365 6.013379 TCCTAAATCTGATCCAACTCTGTTGT 60.013 38.462 9.20 0.00 0.00 3.32
365 366 6.656693 CCTAAATCTGATCCAACTCTGTTGTT 59.343 38.462 9.20 0.00 0.00 2.83
366 367 5.954296 AATCTGATCCAACTCTGTTGTTG 57.046 39.130 9.20 0.00 44.81 3.33
385 386 9.814899 TGTTGTTGAGATAATTGAAAATTGTGT 57.185 25.926 0.00 0.00 0.00 3.72
404 405 9.574516 AATTGTGTTTACTTGTTCTAGAATCCT 57.425 29.630 8.75 0.00 0.00 3.24
405 406 8.974060 TTGTGTTTACTTGTTCTAGAATCCTT 57.026 30.769 8.75 0.00 0.00 3.36
406 407 8.974060 TGTGTTTACTTGTTCTAGAATCCTTT 57.026 30.769 8.75 0.00 0.00 3.11
427 428 9.312904 TCCTTTATCTTTGATTTGTGAAATCCT 57.687 29.630 6.59 0.00 45.23 3.24
428 429 9.933723 CCTTTATCTTTGATTTGTGAAATCCTT 57.066 29.630 6.59 0.00 45.23 3.36
430 431 9.709495 TTTATCTTTGATTTGTGAAATCCTTGG 57.291 29.630 6.59 0.00 45.23 3.61
431 432 6.100404 TCTTTGATTTGTGAAATCCTTGGG 57.900 37.500 6.59 0.00 45.23 4.12
432 433 5.602145 TCTTTGATTTGTGAAATCCTTGGGT 59.398 36.000 6.59 0.00 45.23 4.51
433 434 5.885449 TTGATTTGTGAAATCCTTGGGTT 57.115 34.783 6.59 0.00 45.23 4.11
434 435 5.885449 TGATTTGTGAAATCCTTGGGTTT 57.115 34.783 0.00 0.00 45.23 3.27
435 436 6.985653 TGATTTGTGAAATCCTTGGGTTTA 57.014 33.333 0.00 0.00 45.23 2.01
436 437 6.991938 TGATTTGTGAAATCCTTGGGTTTAG 58.008 36.000 0.00 0.00 45.23 1.85
437 438 6.780031 TGATTTGTGAAATCCTTGGGTTTAGA 59.220 34.615 0.00 0.00 45.23 2.10
438 439 6.399639 TTTGTGAAATCCTTGGGTTTAGAC 57.600 37.500 0.00 0.00 0.00 2.59
439 440 5.055265 TGTGAAATCCTTGGGTTTAGACA 57.945 39.130 0.00 2.43 0.00 3.41
440 441 5.640147 TGTGAAATCCTTGGGTTTAGACAT 58.360 37.500 0.00 0.00 0.00 3.06
441 442 6.074648 TGTGAAATCCTTGGGTTTAGACATT 58.925 36.000 0.00 0.00 0.00 2.71
442 443 7.235079 TGTGAAATCCTTGGGTTTAGACATTA 58.765 34.615 0.00 0.00 0.00 1.90
443 444 7.175990 TGTGAAATCCTTGGGTTTAGACATTAC 59.824 37.037 0.00 0.00 0.00 1.89
444 445 7.393515 GTGAAATCCTTGGGTTTAGACATTACT 59.606 37.037 0.00 0.00 0.00 2.24
445 446 7.393234 TGAAATCCTTGGGTTTAGACATTACTG 59.607 37.037 0.00 0.00 0.00 2.74
446 447 5.836024 TCCTTGGGTTTAGACATTACTGT 57.164 39.130 0.00 0.00 38.67 3.55
447 448 6.938698 TCCTTGGGTTTAGACATTACTGTA 57.061 37.500 0.00 0.00 35.14 2.74
448 449 6.942976 TCCTTGGGTTTAGACATTACTGTAG 58.057 40.000 0.00 0.00 35.14 2.74
449 450 6.070424 TCCTTGGGTTTAGACATTACTGTAGG 60.070 42.308 0.00 0.00 35.14 3.18
450 451 6.070424 CCTTGGGTTTAGACATTACTGTAGGA 60.070 42.308 0.00 0.00 35.14 2.94
451 452 6.938698 TGGGTTTAGACATTACTGTAGGAA 57.061 37.500 0.00 0.00 35.14 3.36
452 453 7.504926 TGGGTTTAGACATTACTGTAGGAAT 57.495 36.000 0.00 0.00 35.14 3.01
453 454 7.924541 TGGGTTTAGACATTACTGTAGGAATT 58.075 34.615 0.00 0.00 35.14 2.17
454 455 8.044908 TGGGTTTAGACATTACTGTAGGAATTC 58.955 37.037 0.00 0.00 35.14 2.17
455 456 7.498239 GGGTTTAGACATTACTGTAGGAATTCC 59.502 40.741 17.31 17.31 35.14 3.01
488 489 9.730420 TTTTCTTTCAAAAGAGTAGCAACATAC 57.270 29.630 5.42 0.00 45.01 2.39
489 490 7.435068 TCTTTCAAAAGAGTAGCAACATACC 57.565 36.000 1.06 0.00 39.95 2.73
490 491 7.224297 TCTTTCAAAAGAGTAGCAACATACCT 58.776 34.615 1.06 0.00 39.95 3.08
491 492 7.719633 TCTTTCAAAAGAGTAGCAACATACCTT 59.280 33.333 1.06 0.00 39.95 3.50
492 493 7.817418 TTCAAAAGAGTAGCAACATACCTTT 57.183 32.000 0.00 0.00 32.39 3.11
493 494 7.817418 TCAAAAGAGTAGCAACATACCTTTT 57.183 32.000 0.00 0.00 37.03 2.27
494 495 8.232913 TCAAAAGAGTAGCAACATACCTTTTT 57.767 30.769 0.00 2.52 35.86 1.94
550 551 9.898576 TCTTCTATTGAAATCTAATAGGAGGGA 57.101 33.333 11.26 0.00 41.22 4.20
557 558 9.799106 TTGAAATCTAATAGGAGGGATTGATTC 57.201 33.333 0.00 0.00 0.00 2.52
558 559 9.175577 TGAAATCTAATAGGAGGGATTGATTCT 57.824 33.333 0.00 0.00 0.00 2.40
559 560 9.447157 GAAATCTAATAGGAGGGATTGATTCTG 57.553 37.037 0.00 0.00 0.00 3.02
560 561 8.748179 AATCTAATAGGAGGGATTGATTCTGA 57.252 34.615 0.00 0.00 0.00 3.27
561 562 8.930287 ATCTAATAGGAGGGATTGATTCTGAT 57.070 34.615 0.00 0.00 0.00 2.90
566 567 9.796242 AATAGGAGGGATTGATTCTGATATACT 57.204 33.333 0.00 0.00 0.00 2.12
567 568 9.796242 ATAGGAGGGATTGATTCTGATATACTT 57.204 33.333 0.00 0.00 0.00 2.24
568 569 8.517323 AGGAGGGATTGATTCTGATATACTTT 57.483 34.615 0.00 0.00 0.00 2.66
569 570 8.953665 AGGAGGGATTGATTCTGATATACTTTT 58.046 33.333 0.00 0.00 0.00 2.27
619 620 4.578928 GTGGTGTCCATGTACTCAGTTTTT 59.421 41.667 0.00 0.00 35.28 1.94
656 657 1.064003 TGCTCAGTTTTGCCCCTAGA 58.936 50.000 0.00 0.00 0.00 2.43
662 663 0.250597 GTTTTGCCCCTAGACCGTGT 60.251 55.000 0.00 0.00 0.00 4.49
802 803 1.915769 GTGGGACCCAGCAGAGAGT 60.916 63.158 15.52 0.00 32.34 3.24
913 914 3.444805 GAGAGAGAGCACGGCGGT 61.445 66.667 13.24 0.00 0.00 5.68
1078 1079 1.957562 CCTGTCTTCGTCTGTCCGT 59.042 57.895 0.00 0.00 0.00 4.69
1118 1119 0.969894 CGGAGGGTTTCTCAGACACT 59.030 55.000 0.00 0.00 44.19 3.55
1251 1252 1.170442 TCATGCAGGTGACATGCTTG 58.830 50.000 25.65 25.65 45.33 4.01
1294 1295 4.012374 GGCCAAGACTCTGATGAATGAAA 58.988 43.478 0.00 0.00 0.00 2.69
1431 1432 5.470098 TGTTGAGCTTAGGATGTTGAAGAAC 59.530 40.000 0.00 0.00 0.00 3.01
1490 1491 4.349342 ACCCATTTGCAAATACTTTTGGGA 59.651 37.500 36.19 7.30 42.09 4.37
1533 1534 6.017026 TCGCACTGGTTGTAATGTTGAAAATA 60.017 34.615 0.00 0.00 0.00 1.40
1835 1840 1.270550 GCATCCAATTAGGCCCATTCG 59.729 52.381 0.00 0.00 37.29 3.34
1934 1939 7.346751 TGTGGAAGCTAATTGAATTATTCCC 57.653 36.000 19.79 14.30 34.91 3.97
2001 2006 4.695455 AGTCCAATTCAAATACACCGTGAG 59.305 41.667 5.28 0.00 0.00 3.51
2186 2194 3.691342 CTCGAACCCAGGACCGCA 61.691 66.667 0.00 0.00 0.00 5.69
2219 2227 0.037017 TTTAGGGCTGCGCTGGTAAA 59.963 50.000 27.01 17.14 0.00 2.01
2318 2329 4.946784 AAAATAGTGAGACCGTGAATGC 57.053 40.909 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 8.862074 CGCATTTTTCTAATTCAATGTCATGAA 58.138 29.630 0.00 0.00 43.03 2.57
45 46 8.242739 TCGCATTTTTCTAATTCAATGTCATGA 58.757 29.630 0.00 0.00 0.00 3.07
46 47 8.397215 TCGCATTTTTCTAATTCAATGTCATG 57.603 30.769 0.00 0.00 0.00 3.07
47 48 7.221452 GCTCGCATTTTTCTAATTCAATGTCAT 59.779 33.333 0.00 0.00 0.00 3.06
48 49 6.527722 GCTCGCATTTTTCTAATTCAATGTCA 59.472 34.615 0.00 0.00 0.00 3.58
49 50 6.527722 TGCTCGCATTTTTCTAATTCAATGTC 59.472 34.615 0.00 0.00 0.00 3.06
50 51 6.308766 GTGCTCGCATTTTTCTAATTCAATGT 59.691 34.615 0.00 0.00 0.00 2.71
51 52 6.237648 GGTGCTCGCATTTTTCTAATTCAATG 60.238 38.462 0.00 0.00 0.00 2.82
52 53 5.807011 GGTGCTCGCATTTTTCTAATTCAAT 59.193 36.000 0.00 0.00 0.00 2.57
53 54 5.160641 GGTGCTCGCATTTTTCTAATTCAA 58.839 37.500 0.00 0.00 0.00 2.69
54 55 4.217334 TGGTGCTCGCATTTTTCTAATTCA 59.783 37.500 0.00 0.00 0.00 2.57
55 56 4.732784 TGGTGCTCGCATTTTTCTAATTC 58.267 39.130 0.00 0.00 0.00 2.17
56 57 4.782019 TGGTGCTCGCATTTTTCTAATT 57.218 36.364 0.00 0.00 0.00 1.40
57 58 4.782019 TTGGTGCTCGCATTTTTCTAAT 57.218 36.364 0.00 0.00 0.00 1.73
58 59 4.022416 ACATTGGTGCTCGCATTTTTCTAA 60.022 37.500 0.00 0.00 0.00 2.10
59 60 3.505680 ACATTGGTGCTCGCATTTTTCTA 59.494 39.130 0.00 0.00 0.00 2.10
60 61 2.297033 ACATTGGTGCTCGCATTTTTCT 59.703 40.909 0.00 0.00 0.00 2.52
61 62 2.663119 GACATTGGTGCTCGCATTTTTC 59.337 45.455 0.00 0.00 0.00 2.29
62 63 2.035704 TGACATTGGTGCTCGCATTTTT 59.964 40.909 0.00 0.00 0.00 1.94
63 64 1.612950 TGACATTGGTGCTCGCATTTT 59.387 42.857 0.00 0.00 0.00 1.82
64 65 1.246649 TGACATTGGTGCTCGCATTT 58.753 45.000 0.00 0.00 0.00 2.32
65 66 1.246649 TTGACATTGGTGCTCGCATT 58.753 45.000 0.00 0.00 0.00 3.56
66 67 1.246649 TTTGACATTGGTGCTCGCAT 58.753 45.000 0.00 0.00 0.00 4.73
67 68 1.028130 TTTTGACATTGGTGCTCGCA 58.972 45.000 0.00 0.00 0.00 5.10
68 69 1.268999 TGTTTTGACATTGGTGCTCGC 60.269 47.619 0.00 0.00 0.00 5.03
69 70 2.772568 TGTTTTGACATTGGTGCTCG 57.227 45.000 0.00 0.00 0.00 5.03
70 71 3.123050 GGTTGTTTTGACATTGGTGCTC 58.877 45.455 0.00 0.00 0.00 4.26
71 72 2.158971 GGGTTGTTTTGACATTGGTGCT 60.159 45.455 0.00 0.00 0.00 4.40
72 73 2.209273 GGGTTGTTTTGACATTGGTGC 58.791 47.619 0.00 0.00 0.00 5.01
73 74 2.484594 GGGGGTTGTTTTGACATTGGTG 60.485 50.000 0.00 0.00 0.00 4.17
74 75 1.765904 GGGGGTTGTTTTGACATTGGT 59.234 47.619 0.00 0.00 0.00 3.67
75 76 2.542020 GGGGGTTGTTTTGACATTGG 57.458 50.000 0.00 0.00 0.00 3.16
94 95 5.129980 AGAAAACCCCCTATACGTTTCTAGG 59.870 44.000 0.00 2.26 35.29 3.02
95 96 6.231258 AGAAAACCCCCTATACGTTTCTAG 57.769 41.667 0.00 0.00 0.00 2.43
96 97 5.129320 GGAGAAAACCCCCTATACGTTTCTA 59.871 44.000 0.00 0.00 0.00 2.10
97 98 4.080695 GGAGAAAACCCCCTATACGTTTCT 60.081 45.833 0.00 0.00 0.00 2.52
98 99 4.080695 AGGAGAAAACCCCCTATACGTTTC 60.081 45.833 0.00 0.00 0.00 2.78
99 100 3.848377 AGGAGAAAACCCCCTATACGTTT 59.152 43.478 0.00 0.00 0.00 3.60
100 101 3.453717 GAGGAGAAAACCCCCTATACGTT 59.546 47.826 0.00 0.00 0.00 3.99
101 102 3.036819 GAGGAGAAAACCCCCTATACGT 58.963 50.000 0.00 0.00 0.00 3.57
102 103 3.036091 TGAGGAGAAAACCCCCTATACG 58.964 50.000 0.00 0.00 0.00 3.06
103 104 5.605488 TGTATGAGGAGAAAACCCCCTATAC 59.395 44.000 0.00 0.00 0.00 1.47
104 105 5.795079 TGTATGAGGAGAAAACCCCCTATA 58.205 41.667 0.00 0.00 0.00 1.31
105 106 4.641868 TGTATGAGGAGAAAACCCCCTAT 58.358 43.478 0.00 0.00 0.00 2.57
106 107 4.037927 CTGTATGAGGAGAAAACCCCCTA 58.962 47.826 0.00 0.00 0.00 3.53
107 108 2.846827 CTGTATGAGGAGAAAACCCCCT 59.153 50.000 0.00 0.00 0.00 4.79
108 109 2.684038 GCTGTATGAGGAGAAAACCCCC 60.684 54.545 0.00 0.00 0.00 5.40
109 110 2.239907 AGCTGTATGAGGAGAAAACCCC 59.760 50.000 0.00 0.00 0.00 4.95
110 111 3.536570 GAGCTGTATGAGGAGAAAACCC 58.463 50.000 0.00 0.00 0.00 4.11
111 112 3.119101 TCGAGCTGTATGAGGAGAAAACC 60.119 47.826 0.00 0.00 0.00 3.27
112 113 4.109050 CTCGAGCTGTATGAGGAGAAAAC 58.891 47.826 0.00 0.00 0.00 2.43
113 114 4.017126 TCTCGAGCTGTATGAGGAGAAAA 58.983 43.478 7.81 0.00 0.00 2.29
114 115 3.621558 TCTCGAGCTGTATGAGGAGAAA 58.378 45.455 7.81 0.00 0.00 2.52
115 116 3.283259 TCTCGAGCTGTATGAGGAGAA 57.717 47.619 7.81 0.00 0.00 2.87
116 117 3.283259 TTCTCGAGCTGTATGAGGAGA 57.717 47.619 7.81 0.00 0.00 3.71
117 118 4.377839 TTTTCTCGAGCTGTATGAGGAG 57.622 45.455 7.81 0.00 0.00 3.69
118 119 4.402474 TCATTTTCTCGAGCTGTATGAGGA 59.598 41.667 7.81 0.00 0.00 3.71
119 120 4.686972 TCATTTTCTCGAGCTGTATGAGG 58.313 43.478 7.81 0.00 0.00 3.86
120 121 6.345644 CGAATCATTTTCTCGAGCTGTATGAG 60.346 42.308 7.81 0.00 34.52 2.90
121 122 5.460091 CGAATCATTTTCTCGAGCTGTATGA 59.540 40.000 7.81 13.43 34.52 2.15
122 123 5.460091 TCGAATCATTTTCTCGAGCTGTATG 59.540 40.000 7.81 8.67 36.72 2.39
123 124 5.592054 TCGAATCATTTTCTCGAGCTGTAT 58.408 37.500 7.81 0.00 36.72 2.29
124 125 4.993905 TCGAATCATTTTCTCGAGCTGTA 58.006 39.130 7.81 0.00 36.72 2.74
125 126 3.849911 TCGAATCATTTTCTCGAGCTGT 58.150 40.909 7.81 0.00 36.72 4.40
126 127 4.847365 TTCGAATCATTTTCTCGAGCTG 57.153 40.909 7.81 2.78 42.09 4.24
127 128 6.428385 AAATTCGAATCATTTTCTCGAGCT 57.572 33.333 11.83 0.00 42.09 4.09
128 129 5.390859 CGAAATTCGAATCATTTTCTCGAGC 59.609 40.000 11.83 0.00 43.74 5.03
129 130 5.898606 CCGAAATTCGAATCATTTTCTCGAG 59.101 40.000 17.75 5.93 43.74 4.04
130 131 5.350365 ACCGAAATTCGAATCATTTTCTCGA 59.650 36.000 17.75 0.00 43.74 4.04
131 132 5.560148 ACCGAAATTCGAATCATTTTCTCG 58.440 37.500 17.75 10.47 43.74 4.04
132 133 5.672856 CGACCGAAATTCGAATCATTTTCTC 59.327 40.000 17.75 6.21 43.74 2.87
133 134 5.350365 TCGACCGAAATTCGAATCATTTTCT 59.650 36.000 17.75 0.00 43.74 2.52
134 135 5.556470 TCGACCGAAATTCGAATCATTTTC 58.444 37.500 17.75 11.05 43.74 2.29
135 136 5.539582 TCGACCGAAATTCGAATCATTTT 57.460 34.783 17.75 2.35 43.74 1.82
162 163 9.547753 AATGCACGTCATAGTCTAATTTCTATT 57.452 29.630 0.00 0.00 34.33 1.73
165 166 8.942338 TTAATGCACGTCATAGTCTAATTTCT 57.058 30.769 0.00 0.00 34.33 2.52
169 170 8.774586 GGAAATTAATGCACGTCATAGTCTAAT 58.225 33.333 0.00 0.00 34.33 1.73
170 171 7.985184 AGGAAATTAATGCACGTCATAGTCTAA 59.015 33.333 0.00 0.00 34.33 2.10
171 172 7.497595 AGGAAATTAATGCACGTCATAGTCTA 58.502 34.615 0.00 0.00 34.33 2.59
172 173 6.349300 AGGAAATTAATGCACGTCATAGTCT 58.651 36.000 0.00 0.00 34.33 3.24
173 174 6.604735 AGGAAATTAATGCACGTCATAGTC 57.395 37.500 0.00 0.00 34.33 2.59
174 175 7.551262 TGTAAGGAAATTAATGCACGTCATAGT 59.449 33.333 0.00 0.00 34.33 2.12
175 176 7.915508 TGTAAGGAAATTAATGCACGTCATAG 58.084 34.615 0.00 0.00 34.33 2.23
176 177 7.766738 TCTGTAAGGAAATTAATGCACGTCATA 59.233 33.333 0.00 0.00 34.33 2.15
177 178 6.597672 TCTGTAAGGAAATTAATGCACGTCAT 59.402 34.615 0.00 0.00 36.87 3.06
178 179 5.935206 TCTGTAAGGAAATTAATGCACGTCA 59.065 36.000 0.00 0.00 0.00 4.35
179 180 6.417191 TCTGTAAGGAAATTAATGCACGTC 57.583 37.500 0.00 0.00 0.00 4.34
180 181 6.811253 TTCTGTAAGGAAATTAATGCACGT 57.189 33.333 0.00 0.00 0.00 4.49
181 182 8.514136 TTTTTCTGTAAGGAAATTAATGCACG 57.486 30.769 0.00 0.00 42.05 5.34
212 213 9.166173 CCACTTGAGTCATGAGTATAAATTGAA 57.834 33.333 12.65 0.00 0.00 2.69
213 214 7.770433 CCCACTTGAGTCATGAGTATAAATTGA 59.230 37.037 12.65 0.00 0.00 2.57
214 215 7.467811 GCCCACTTGAGTCATGAGTATAAATTG 60.468 40.741 12.65 3.80 0.00 2.32
215 216 6.543831 GCCCACTTGAGTCATGAGTATAAATT 59.456 38.462 12.65 0.00 0.00 1.82
216 217 6.058183 GCCCACTTGAGTCATGAGTATAAAT 58.942 40.000 12.65 0.00 0.00 1.40
217 218 5.189736 AGCCCACTTGAGTCATGAGTATAAA 59.810 40.000 12.65 0.00 0.00 1.40
218 219 4.716784 AGCCCACTTGAGTCATGAGTATAA 59.283 41.667 12.65 1.56 0.00 0.98
219 220 4.290093 AGCCCACTTGAGTCATGAGTATA 58.710 43.478 12.65 0.00 0.00 1.47
220 221 3.110705 AGCCCACTTGAGTCATGAGTAT 58.889 45.455 12.65 0.00 0.00 2.12
221 222 2.540383 AGCCCACTTGAGTCATGAGTA 58.460 47.619 12.65 0.00 0.00 2.59
222 223 1.356124 AGCCCACTTGAGTCATGAGT 58.644 50.000 12.65 1.67 0.00 3.41
223 224 3.616956 TTAGCCCACTTGAGTCATGAG 57.383 47.619 12.65 4.90 0.00 2.90
224 225 4.574674 AATTAGCCCACTTGAGTCATGA 57.425 40.909 12.65 0.00 0.00 3.07
225 226 5.404946 CAAAATTAGCCCACTTGAGTCATG 58.595 41.667 4.53 4.53 0.00 3.07
226 227 4.082026 GCAAAATTAGCCCACTTGAGTCAT 60.082 41.667 0.00 0.00 0.00 3.06
227 228 3.255642 GCAAAATTAGCCCACTTGAGTCA 59.744 43.478 0.00 0.00 0.00 3.41
228 229 3.367395 GGCAAAATTAGCCCACTTGAGTC 60.367 47.826 10.04 0.00 46.50 3.36
229 230 2.562738 GGCAAAATTAGCCCACTTGAGT 59.437 45.455 10.04 0.00 46.50 3.41
230 231 3.236632 GGCAAAATTAGCCCACTTGAG 57.763 47.619 10.04 0.00 46.50 3.02
245 246 2.223479 GCTTCGAAGTTTGTCAGGCAAA 60.223 45.455 25.24 0.00 44.05 3.68
246 247 1.333619 GCTTCGAAGTTTGTCAGGCAA 59.666 47.619 25.24 0.00 34.87 4.52
247 248 0.944386 GCTTCGAAGTTTGTCAGGCA 59.056 50.000 25.24 0.00 0.00 4.75
248 249 0.238553 GGCTTCGAAGTTTGTCAGGC 59.761 55.000 25.24 9.18 0.00 4.85
249 250 1.593196 TGGCTTCGAAGTTTGTCAGG 58.407 50.000 25.24 0.00 0.00 3.86
250 251 3.691049 TTTGGCTTCGAAGTTTGTCAG 57.309 42.857 25.24 0.00 0.00 3.51
251 252 4.499019 GGATTTTGGCTTCGAAGTTTGTCA 60.499 41.667 25.24 13.33 0.00 3.58
252 253 3.981416 GGATTTTGGCTTCGAAGTTTGTC 59.019 43.478 25.24 15.26 0.00 3.18
253 254 3.636764 AGGATTTTGGCTTCGAAGTTTGT 59.363 39.130 25.24 8.11 0.00 2.83
254 255 4.243007 AGGATTTTGGCTTCGAAGTTTG 57.757 40.909 25.24 2.25 0.00 2.93
255 256 4.937201 AAGGATTTTGGCTTCGAAGTTT 57.063 36.364 25.24 5.36 0.00 2.66
256 257 4.937201 AAAGGATTTTGGCTTCGAAGTT 57.063 36.364 25.24 6.54 31.62 2.66
257 258 6.399639 TTTAAAGGATTTTGGCTTCGAAGT 57.600 33.333 25.24 5.20 40.09 3.01
258 259 7.707774 TTTTTAAAGGATTTTGGCTTCGAAG 57.292 32.000 21.02 21.02 40.09 3.79
259 260 9.765795 TTATTTTTAAAGGATTTTGGCTTCGAA 57.234 25.926 0.00 0.00 40.09 3.71
260 261 9.936759 ATTATTTTTAAAGGATTTTGGCTTCGA 57.063 25.926 0.00 0.00 40.09 3.71
282 283 9.930693 AGAAGAGTTTAAAGACGACTCAATTAT 57.069 29.630 6.94 0.00 41.67 1.28
283 284 9.760077 AAGAAGAGTTTAAAGACGACTCAATTA 57.240 29.630 6.94 0.00 41.67 1.40
284 285 8.664211 AAGAAGAGTTTAAAGACGACTCAATT 57.336 30.769 6.94 0.00 41.67 2.32
285 286 8.552034 CAAAGAAGAGTTTAAAGACGACTCAAT 58.448 33.333 6.94 0.00 41.67 2.57
286 287 7.548075 ACAAAGAAGAGTTTAAAGACGACTCAA 59.452 33.333 6.94 0.00 41.67 3.02
287 288 7.039882 ACAAAGAAGAGTTTAAAGACGACTCA 58.960 34.615 6.94 0.00 41.67 3.41
288 289 7.435784 AGACAAAGAAGAGTTTAAAGACGACTC 59.564 37.037 0.00 0.00 39.99 3.36
289 290 7.266400 AGACAAAGAAGAGTTTAAAGACGACT 58.734 34.615 0.00 0.00 0.00 4.18
290 291 7.222224 TGAGACAAAGAAGAGTTTAAAGACGAC 59.778 37.037 0.00 0.00 0.00 4.34
291 292 7.262772 TGAGACAAAGAAGAGTTTAAAGACGA 58.737 34.615 0.00 0.00 0.00 4.20
292 293 7.464830 TGAGACAAAGAAGAGTTTAAAGACG 57.535 36.000 0.00 0.00 0.00 4.18
299 300 9.525409 CATTTGAAATGAGACAAAGAAGAGTTT 57.475 29.630 12.37 0.00 38.94 2.66
300 301 8.906867 TCATTTGAAATGAGACAAAGAAGAGTT 58.093 29.630 16.04 0.00 38.94 3.01
301 302 8.455903 TCATTTGAAATGAGACAAAGAAGAGT 57.544 30.769 16.04 0.00 38.94 3.24
302 303 9.909644 ATTCATTTGAAATGAGACAAAGAAGAG 57.090 29.630 18.72 0.00 38.94 2.85
334 335 9.618890 CAGAGTTGGATCAGATTTAGGAATAAA 57.381 33.333 0.00 0.00 0.00 1.40
335 336 8.772250 ACAGAGTTGGATCAGATTTAGGAATAA 58.228 33.333 0.00 0.00 0.00 1.40
336 337 8.324191 ACAGAGTTGGATCAGATTTAGGAATA 57.676 34.615 0.00 0.00 0.00 1.75
337 338 7.205515 ACAGAGTTGGATCAGATTTAGGAAT 57.794 36.000 0.00 0.00 0.00 3.01
338 339 6.627087 ACAGAGTTGGATCAGATTTAGGAA 57.373 37.500 0.00 0.00 0.00 3.36
339 340 6.013379 ACAACAGAGTTGGATCAGATTTAGGA 60.013 38.462 13.71 0.00 0.00 2.94
340 341 6.176183 ACAACAGAGTTGGATCAGATTTAGG 58.824 40.000 13.71 0.00 0.00 2.69
341 342 7.388776 TCAACAACAGAGTTGGATCAGATTTAG 59.611 37.037 13.71 0.00 46.74 1.85
342 343 7.223584 TCAACAACAGAGTTGGATCAGATTTA 58.776 34.615 13.71 0.00 46.74 1.40
343 344 6.064060 TCAACAACAGAGTTGGATCAGATTT 58.936 36.000 13.71 0.00 46.74 2.17
344 345 5.624159 TCAACAACAGAGTTGGATCAGATT 58.376 37.500 13.71 0.00 46.74 2.40
345 346 5.012458 TCTCAACAACAGAGTTGGATCAGAT 59.988 40.000 13.71 0.00 46.74 2.90
346 347 4.344968 TCTCAACAACAGAGTTGGATCAGA 59.655 41.667 13.71 6.84 46.74 3.27
347 348 4.635223 TCTCAACAACAGAGTTGGATCAG 58.365 43.478 13.71 4.94 46.74 2.90
348 349 4.687901 TCTCAACAACAGAGTTGGATCA 57.312 40.909 13.71 0.00 46.74 2.92
349 350 7.856145 ATTATCTCAACAACAGAGTTGGATC 57.144 36.000 13.71 0.00 46.74 3.36
350 351 7.884877 TCAATTATCTCAACAACAGAGTTGGAT 59.115 33.333 13.71 8.95 46.74 3.41
351 352 7.223584 TCAATTATCTCAACAACAGAGTTGGA 58.776 34.615 13.71 2.66 46.74 3.53
352 353 7.439157 TCAATTATCTCAACAACAGAGTTGG 57.561 36.000 13.71 0.00 46.74 3.77
359 360 9.814899 ACACAATTTTCAATTATCTCAACAACA 57.185 25.926 0.00 0.00 0.00 3.33
378 379 9.574516 AGGATTCTAGAACAAGTAAACACAATT 57.425 29.630 7.48 0.00 0.00 2.32
379 380 9.574516 AAGGATTCTAGAACAAGTAAACACAAT 57.425 29.630 7.48 0.00 0.00 2.71
380 381 8.974060 AAGGATTCTAGAACAAGTAAACACAA 57.026 30.769 7.48 0.00 0.00 3.33
381 382 8.974060 AAAGGATTCTAGAACAAGTAAACACA 57.026 30.769 7.48 0.00 0.00 3.72
413 414 7.090808 GTCTAAACCCAAGGATTTCACAAATC 58.909 38.462 1.01 1.01 45.12 2.17
414 415 6.553100 TGTCTAAACCCAAGGATTTCACAAAT 59.447 34.615 0.00 0.00 0.00 2.32
415 416 5.894393 TGTCTAAACCCAAGGATTTCACAAA 59.106 36.000 0.00 0.00 0.00 2.83
416 417 5.450453 TGTCTAAACCCAAGGATTTCACAA 58.550 37.500 0.00 0.00 0.00 3.33
417 418 5.055265 TGTCTAAACCCAAGGATTTCACA 57.945 39.130 0.00 0.00 0.00 3.58
418 419 6.590234 AATGTCTAAACCCAAGGATTTCAC 57.410 37.500 0.00 0.00 0.00 3.18
419 420 7.393234 CAGTAATGTCTAAACCCAAGGATTTCA 59.607 37.037 0.00 0.00 0.00 2.69
420 421 7.393515 ACAGTAATGTCTAAACCCAAGGATTTC 59.606 37.037 0.00 0.00 0.00 2.17
421 422 7.238710 ACAGTAATGTCTAAACCCAAGGATTT 58.761 34.615 0.00 0.00 0.00 2.17
422 423 6.790319 ACAGTAATGTCTAAACCCAAGGATT 58.210 36.000 0.00 0.00 0.00 3.01
423 424 6.388619 ACAGTAATGTCTAAACCCAAGGAT 57.611 37.500 0.00 0.00 0.00 3.24
424 425 5.836024 ACAGTAATGTCTAAACCCAAGGA 57.164 39.130 0.00 0.00 0.00 3.36
425 426 6.070424 TCCTACAGTAATGTCTAAACCCAAGG 60.070 42.308 0.00 0.00 0.00 3.61
426 427 6.942976 TCCTACAGTAATGTCTAAACCCAAG 58.057 40.000 0.00 0.00 0.00 3.61
427 428 6.938698 TCCTACAGTAATGTCTAAACCCAA 57.061 37.500 0.00 0.00 0.00 4.12
428 429 6.938698 TTCCTACAGTAATGTCTAAACCCA 57.061 37.500 0.00 0.00 0.00 4.51
429 430 7.498239 GGAATTCCTACAGTAATGTCTAAACCC 59.502 40.741 17.73 0.00 0.00 4.11
430 431 8.265764 AGGAATTCCTACAGTAATGTCTAAACC 58.734 37.037 25.99 2.34 46.48 3.27
462 463 9.730420 GTATGTTGCTACTCTTTTGAAAGAAAA 57.270 29.630 7.51 0.00 43.84 2.29
463 464 8.349983 GGTATGTTGCTACTCTTTTGAAAGAAA 58.650 33.333 7.51 0.00 43.84 2.52
464 465 7.719633 AGGTATGTTGCTACTCTTTTGAAAGAA 59.280 33.333 7.51 0.00 43.84 2.52
465 466 7.224297 AGGTATGTTGCTACTCTTTTGAAAGA 58.776 34.615 6.07 6.07 42.41 2.52
466 467 7.440523 AGGTATGTTGCTACTCTTTTGAAAG 57.559 36.000 0.00 0.00 37.36 2.62
467 468 7.817418 AAGGTATGTTGCTACTCTTTTGAAA 57.183 32.000 0.00 0.00 0.00 2.69
468 469 7.817418 AAAGGTATGTTGCTACTCTTTTGAA 57.183 32.000 0.00 0.00 0.00 2.69
469 470 7.817418 AAAAGGTATGTTGCTACTCTTTTGA 57.183 32.000 14.92 0.00 34.48 2.69
524 525 9.898576 TCCCTCCTATTAGATTTCAATAGAAGA 57.101 33.333 4.13 0.00 37.93 2.87
531 532 9.799106 GAATCAATCCCTCCTATTAGATTTCAA 57.201 33.333 0.00 0.00 0.00 2.69
532 533 9.175577 AGAATCAATCCCTCCTATTAGATTTCA 57.824 33.333 0.00 0.00 0.00 2.69
533 534 9.447157 CAGAATCAATCCCTCCTATTAGATTTC 57.553 37.037 0.00 0.00 0.00 2.17
534 535 9.175577 TCAGAATCAATCCCTCCTATTAGATTT 57.824 33.333 0.00 0.00 0.00 2.17
535 536 8.748179 TCAGAATCAATCCCTCCTATTAGATT 57.252 34.615 0.00 0.00 0.00 2.40
536 537 8.930287 ATCAGAATCAATCCCTCCTATTAGAT 57.070 34.615 0.00 0.00 0.00 1.98
540 541 9.796242 AGTATATCAGAATCAATCCCTCCTATT 57.204 33.333 0.00 0.00 0.00 1.73
541 542 9.796242 AAGTATATCAGAATCAATCCCTCCTAT 57.204 33.333 0.00 0.00 0.00 2.57
542 543 9.621239 AAAGTATATCAGAATCAATCCCTCCTA 57.379 33.333 0.00 0.00 0.00 2.94
543 544 8.517323 AAAGTATATCAGAATCAATCCCTCCT 57.483 34.615 0.00 0.00 0.00 3.69
564 565 9.884636 GCAAAAGGATAATTAACCCATAAAAGT 57.115 29.630 8.09 0.00 0.00 2.66
565 566 9.325198 GGCAAAAGGATAATTAACCCATAAAAG 57.675 33.333 8.09 0.00 0.00 2.27
566 567 8.268605 GGGCAAAAGGATAATTAACCCATAAAA 58.731 33.333 8.09 0.00 34.82 1.52
567 568 7.625682 AGGGCAAAAGGATAATTAACCCATAAA 59.374 33.333 8.09 0.00 37.28 1.40
568 569 7.136203 AGGGCAAAAGGATAATTAACCCATAA 58.864 34.615 8.09 0.00 37.28 1.90
569 570 6.688554 AGGGCAAAAGGATAATTAACCCATA 58.311 36.000 8.09 0.00 37.28 2.74
619 620 2.013563 GCACAATTCGCATCTGAGGGA 61.014 52.381 0.00 0.00 0.00 4.20
656 657 4.640855 CGAGTCGGTGCACACGGT 62.641 66.667 20.43 10.57 33.91 4.83
802 803 1.806461 AACGGCTCTCTGCTCAACGA 61.806 55.000 0.00 0.00 42.39 3.85
913 914 1.267574 CCTCCACAGCTAGCTTCCCA 61.268 60.000 16.46 0.00 0.00 4.37
1118 1119 2.100197 ACGGACGATTCTGATTCCTCA 58.900 47.619 0.00 0.00 31.76 3.86
1125 1126 2.819422 CGTAGAACGGACGATTCTGA 57.181 50.000 14.97 0.00 42.98 3.27
1223 1224 2.297033 GTCACCTGCATGAACACCAAAT 59.703 45.455 0.00 0.00 0.00 2.32
1251 1252 2.160417 CAGAGCATCGACCCAAAGAAAC 59.840 50.000 0.00 0.00 42.67 2.78
1387 1388 0.529833 GCTAGCTCTCTGTCAGTGCA 59.470 55.000 7.70 0.00 43.07 4.57
1431 1432 5.248640 TGATCTTCAAGCTTCCTAACCTTG 58.751 41.667 0.00 0.00 37.80 3.61
1490 1491 6.260050 CAGTGCGATTACCATACCTACAAATT 59.740 38.462 0.00 0.00 0.00 1.82
1533 1534 6.666546 CCTCCATAATTCATGCCTTTCCATAT 59.333 38.462 0.00 0.00 32.84 1.78
1694 1698 9.414295 CTGCATTTCATTGATCAAAAGTTTCTA 57.586 29.630 13.09 0.00 0.00 2.10
1751 1756 0.398381 TTTGGCCCAAGAGCAACCTT 60.398 50.000 0.00 0.00 0.00 3.50
1752 1757 0.178924 ATTTGGCCCAAGAGCAACCT 60.179 50.000 0.00 0.00 0.00 3.50
1835 1840 2.124277 AAATACGCAAGAGAACCCCC 57.876 50.000 0.00 0.00 43.62 5.40
1934 1939 5.873179 TCTAACCTTAATTGTTTGGCTCG 57.127 39.130 0.00 0.00 0.00 5.03
1979 1984 4.454504 ACTCACGGTGTATTTGAATTGGAC 59.545 41.667 8.17 0.00 0.00 4.02
2001 2006 8.711457 CCATGACATTTTGGTCTTTGATTTAAC 58.289 33.333 0.00 0.00 38.61 2.01
2186 2194 2.604139 CCCTAAACACCACAAACCCAT 58.396 47.619 0.00 0.00 0.00 4.00
2219 2227 0.176680 CTTGCCATCTGTCCTAGCGT 59.823 55.000 0.00 0.00 0.00 5.07
2295 2305 5.122396 AGCATTCACGGTCTCACTATTTTTC 59.878 40.000 0.00 0.00 0.00 2.29
2318 2329 1.951130 ACTCTCACGCGTGTGCAAG 60.951 57.895 35.74 27.57 46.01 4.01
2345 2356 7.013178 CCCTCCAAAATTTAAGTGCAAAACAAT 59.987 33.333 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.