Multiple sequence alignment - TraesCS7A01G072700

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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 TraesCS7A01G072700 chr7A 100.000 2240 0 0 1 2240 38139469 38137230 0.000000e+00 4137.0
1 TraesCS7A01G072700 chr7A 90.756 238 22 0 12 249 30259707 30259470 3.590000e-83 318.0
2 TraesCS7A01G072700 chr7D 86.298 1248 121 30 381 1585 38472780 38471540 0.000000e+00 1312.0
3 TraesCS7A01G072700 chr7D 93.257 608 36 1 1633 2240 134196942 134197544 0.000000e+00 891.0
4 TraesCS7A01G072700 chr7D 90.713 463 35 8 822 1281 38509531 38509074 5.290000e-171 610.0
5 TraesCS7A01G072700 chr7D 80.780 359 39 15 386 738 38509888 38509554 1.030000e-63 254.0
6 TraesCS7A01G072700 chr7D 82.857 140 13 7 463 592 38662996 38662858 5.060000e-22 115.0
7 TraesCS7A01G072700 chr6D 94.371 604 30 1 1637 2240 14615524 14616123 0.000000e+00 924.0
8 TraesCS7A01G072700 chr6D 93.421 608 35 3 1633 2240 87385640 87386242 0.000000e+00 896.0
9 TraesCS7A01G072700 chr6D 93.761 593 33 1 1648 2240 464465369 464465957 0.000000e+00 887.0
10 TraesCS7A01G072700 chrUn 93.543 604 34 3 1637 2240 83929054 83928456 0.000000e+00 894.0
11 TraesCS7A01G072700 chr5B 93.377 604 36 1 1637 2240 680927232 680927831 0.000000e+00 891.0
12 TraesCS7A01G072700 chr1D 93.212 604 36 2 1637 2240 472002108 472001510 0.000000e+00 883.0
13 TraesCS7A01G072700 chr5D 93.046 604 38 1 1637 2240 383301558 383300959 0.000000e+00 880.0
14 TraesCS7A01G072700 chr4D 93.178 601 35 5 1640 2240 47729346 47728752 0.000000e+00 878.0
15 TraesCS7A01G072700 chr6A 91.968 249 20 0 1 249 615954340 615954588 1.270000e-92 350.0
16 TraesCS7A01G072700 chr5A 90.763 249 23 0 1 249 395879206 395879454 1.280000e-87 333.0
17 TraesCS7A01G072700 chr1B 90.763 249 23 0 1 249 608840319 608840071 1.280000e-87 333.0
18 TraesCS7A01G072700 chr1B 90.336 238 22 1 12 249 682337726 682337962 6.010000e-81 311.0
19 TraesCS7A01G072700 chr4A 89.960 249 25 0 1 249 611934744 611934992 2.780000e-84 322.0
20 TraesCS7A01G072700 chr7B 90.336 238 23 0 12 249 402828135 402827898 1.670000e-81 313.0
21 TraesCS7A01G072700 chr7B 100.000 36 0 0 1312 1347 648697880 648697845 1.440000e-07 67.6
22 TraesCS7A01G072700 chr6B 90.336 238 22 1 12 249 49412459 49412223 6.010000e-81 311.0
23 TraesCS7A01G072700 chr3A 88.755 249 28 0 1 249 47490650 47490402 2.790000e-79 305.0


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 TraesCS7A01G072700 chr7A 38137230 38139469 2239 True 4137 4137 100.0000 1 2240 1 chr7A.!!$R2 2239
1 TraesCS7A01G072700 chr7D 38471540 38472780 1240 True 1312 1312 86.2980 381 1585 1 chr7D.!!$R1 1204
2 TraesCS7A01G072700 chr7D 134196942 134197544 602 False 891 891 93.2570 1633 2240 1 chr7D.!!$F1 607
3 TraesCS7A01G072700 chr7D 38509074 38509888 814 True 432 610 85.7465 386 1281 2 chr7D.!!$R3 895
4 TraesCS7A01G072700 chr6D 14615524 14616123 599 False 924 924 94.3710 1637 2240 1 chr6D.!!$F1 603
5 TraesCS7A01G072700 chr6D 87385640 87386242 602 False 896 896 93.4210 1633 2240 1 chr6D.!!$F2 607
6 TraesCS7A01G072700 chr6D 464465369 464465957 588 False 887 887 93.7610 1648 2240 1 chr6D.!!$F3 592
7 TraesCS7A01G072700 chrUn 83928456 83929054 598 True 894 894 93.5430 1637 2240 1 chrUn.!!$R1 603
8 TraesCS7A01G072700 chr5B 680927232 680927831 599 False 891 891 93.3770 1637 2240 1 chr5B.!!$F1 603
9 TraesCS7A01G072700 chr1D 472001510 472002108 598 True 883 883 93.2120 1637 2240 1 chr1D.!!$R1 603
10 TraesCS7A01G072700 chr5D 383300959 383301558 599 True 880 880 93.0460 1637 2240 1 chr5D.!!$R1 603
11 TraesCS7A01G072700 chr4D 47728752 47729346 594 True 878 878 93.1780 1640 2240 1 chr4D.!!$R1 600

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
311 312 0.036765 GGCTTCACATGACCCGTGTA 60.037 55.0 0.0 0.0 35.79 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2123 2173 0.394352 GCCGTCATCACCCTTCCATT 60.394 55.0 0.0 0.0 0.0 3.16 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.217743 GTCCTAGGTCGAGCCCGG 61.218 72.222 11.73 12.01 38.26 5.73
18 19 4.517934 TCCTAGGTCGAGCCCGGG 62.518 72.222 19.09 19.09 38.26 5.73
19 20 4.517934 CCTAGGTCGAGCCCGGGA 62.518 72.222 29.31 0.00 38.26 5.14
20 21 2.203509 CTAGGTCGAGCCCGGGAT 60.204 66.667 29.31 22.30 38.26 3.85
21 22 2.520982 TAGGTCGAGCCCGGGATG 60.521 66.667 29.31 13.71 38.26 3.51
51 52 4.569023 CGCTGCCGCCATCTCGTA 62.569 66.667 0.00 0.00 0.00 3.43
52 53 2.962253 GCTGCCGCCATCTCGTAC 60.962 66.667 0.00 0.00 0.00 3.67
53 54 2.808315 CTGCCGCCATCTCGTACT 59.192 61.111 0.00 0.00 0.00 2.73
54 55 2.030551 CTGCCGCCATCTCGTACTA 58.969 57.895 0.00 0.00 0.00 1.82
55 56 0.317938 CTGCCGCCATCTCGTACTAC 60.318 60.000 0.00 0.00 0.00 2.73
56 57 0.750546 TGCCGCCATCTCGTACTACT 60.751 55.000 0.00 0.00 0.00 2.57
57 58 0.040246 GCCGCCATCTCGTACTACTC 60.040 60.000 0.00 0.00 0.00 2.59
58 59 0.592148 CCGCCATCTCGTACTACTCC 59.408 60.000 0.00 0.00 0.00 3.85
59 60 0.592148 CGCCATCTCGTACTACTCCC 59.408 60.000 0.00 0.00 0.00 4.30
60 61 0.592148 GCCATCTCGTACTACTCCCG 59.408 60.000 0.00 0.00 0.00 5.14
61 62 0.592148 CCATCTCGTACTACTCCCGC 59.408 60.000 0.00 0.00 0.00 6.13
62 63 0.592148 CATCTCGTACTACTCCCGCC 59.408 60.000 0.00 0.00 0.00 6.13
63 64 0.182061 ATCTCGTACTACTCCCGCCA 59.818 55.000 0.00 0.00 0.00 5.69
64 65 0.463295 TCTCGTACTACTCCCGCCAG 60.463 60.000 0.00 0.00 0.00 4.85
65 66 1.445716 CTCGTACTACTCCCGCCAGG 61.446 65.000 0.00 0.00 37.24 4.45
66 67 1.751927 CGTACTACTCCCGCCAGGT 60.752 63.158 0.00 0.00 36.75 4.00
67 68 1.814527 GTACTACTCCCGCCAGGTG 59.185 63.158 0.00 0.00 36.75 4.00
68 69 2.056223 TACTACTCCCGCCAGGTGC 61.056 63.158 0.00 0.00 36.75 5.01
69 70 2.791613 TACTACTCCCGCCAGGTGCA 62.792 60.000 0.00 0.00 41.33 4.57
70 71 3.376935 CTACTCCCGCCAGGTGCAG 62.377 68.421 0.00 0.00 41.33 4.41
116 117 4.521062 GCTGCTCGCCATCCTCGT 62.521 66.667 0.00 0.00 0.00 4.18
117 118 2.279120 CTGCTCGCCATCCTCGTC 60.279 66.667 0.00 0.00 0.00 4.20
118 119 4.193334 TGCTCGCCATCCTCGTCG 62.193 66.667 0.00 0.00 0.00 5.12
119 120 4.933064 GCTCGCCATCCTCGTCGG 62.933 72.222 0.00 0.00 0.00 4.79
124 125 2.815308 CCATCCTCGTCGGAAGGG 59.185 66.667 9.07 6.56 45.11 3.95
125 126 1.756950 CCATCCTCGTCGGAAGGGA 60.757 63.158 9.07 0.00 45.11 4.20
126 127 1.739338 CCATCCTCGTCGGAAGGGAG 61.739 65.000 9.07 0.00 45.11 4.30
127 128 3.084304 TCCTCGTCGGAAGGGAGA 58.916 61.111 0.50 0.00 39.40 3.71
128 129 1.613610 TCCTCGTCGGAAGGGAGAT 59.386 57.895 0.50 0.00 39.40 2.75
129 130 0.465824 TCCTCGTCGGAAGGGAGATC 60.466 60.000 0.50 0.00 39.40 2.75
130 131 1.457009 CCTCGTCGGAAGGGAGATCC 61.457 65.000 0.00 0.00 35.15 3.36
131 132 0.752009 CTCGTCGGAAGGGAGATCCA 60.752 60.000 0.47 0.00 36.74 3.41
132 133 0.323999 TCGTCGGAAGGGAGATCCAA 60.324 55.000 0.47 0.00 36.74 3.53
133 134 0.535335 CGTCGGAAGGGAGATCCAAA 59.465 55.000 0.47 0.00 36.74 3.28
134 135 1.139058 CGTCGGAAGGGAGATCCAAAT 59.861 52.381 0.47 0.00 36.74 2.32
135 136 2.803492 CGTCGGAAGGGAGATCCAAATC 60.803 54.545 0.47 0.00 36.74 2.17
136 137 2.170607 GTCGGAAGGGAGATCCAAATCA 59.829 50.000 0.47 0.00 36.74 2.57
137 138 2.435805 TCGGAAGGGAGATCCAAATCAG 59.564 50.000 0.47 0.00 36.74 2.90
138 139 2.486191 CGGAAGGGAGATCCAAATCAGG 60.486 54.545 0.47 0.00 36.74 3.86
139 140 2.158549 GGAAGGGAGATCCAAATCAGGG 60.159 54.545 0.47 0.00 36.92 4.45
140 141 0.849417 AGGGAGATCCAAATCAGGGC 59.151 55.000 0.47 0.00 38.24 5.19
141 142 0.536006 GGGAGATCCAAATCAGGGCG 60.536 60.000 0.47 0.00 37.91 6.13
142 143 1.169034 GGAGATCCAAATCAGGGCGC 61.169 60.000 0.00 0.00 34.07 6.53
143 144 1.152881 AGATCCAAATCAGGGCGCC 60.153 57.895 21.18 21.18 34.07 6.53
144 145 2.516930 ATCCAAATCAGGGCGCCG 60.517 61.111 22.54 7.85 0.00 6.46
163 164 2.986413 CGCCTCGGATCTCGGGAT 60.986 66.667 0.00 0.00 43.26 3.85
164 165 2.653702 GCCTCGGATCTCGGGATG 59.346 66.667 0.20 0.00 43.26 3.51
165 166 2.653702 CCTCGGATCTCGGGATGC 59.346 66.667 0.20 3.96 43.26 3.91
166 167 2.653702 CTCGGATCTCGGGATGCC 59.346 66.667 11.58 7.39 43.26 4.40
167 168 2.123468 TCGGATCTCGGGATGCCA 60.123 61.111 11.58 0.00 37.05 4.92
168 169 2.152297 CTCGGATCTCGGGATGCCAG 62.152 65.000 11.58 3.84 43.26 4.85
169 170 2.203082 CGGATCTCGGGATGCCAGA 61.203 63.158 11.58 5.98 37.05 3.86
170 171 1.670590 GGATCTCGGGATGCCAGAG 59.329 63.158 0.20 15.52 45.01 3.35
171 172 1.670590 GATCTCGGGATGCCAGAGG 59.329 63.158 19.39 0.00 44.07 3.69
172 173 0.829602 GATCTCGGGATGCCAGAGGA 60.830 60.000 19.39 10.48 44.07 3.71
173 174 0.831288 ATCTCGGGATGCCAGAGGAG 60.831 60.000 19.39 11.12 44.07 3.69
174 175 2.444706 TCGGGATGCCAGAGGAGG 60.445 66.667 3.39 0.00 0.00 4.30
175 176 2.765807 CGGGATGCCAGAGGAGGT 60.766 66.667 3.39 0.00 0.00 3.85
176 177 2.801631 CGGGATGCCAGAGGAGGTC 61.802 68.421 3.39 0.00 0.00 3.85
177 178 2.447714 GGGATGCCAGAGGAGGTCC 61.448 68.421 0.00 0.00 0.00 4.46
178 179 2.801631 GGATGCCAGAGGAGGTCCG 61.802 68.421 0.00 0.00 42.08 4.79
179 180 3.453070 GATGCCAGAGGAGGTCCGC 62.453 68.421 0.00 0.00 42.08 5.54
212 213 4.858680 GGGCCTTGGCCTAGCGAC 62.859 72.222 27.45 8.45 45.39 5.19
213 214 4.096003 GGCCTTGGCCTAGCGACA 62.096 66.667 22.47 0.00 0.00 4.35
214 215 2.190578 GCCTTGGCCTAGCGACAT 59.809 61.111 8.91 0.00 0.00 3.06
215 216 1.452108 GCCTTGGCCTAGCGACATT 60.452 57.895 8.91 0.00 0.00 2.71
216 217 1.718757 GCCTTGGCCTAGCGACATTG 61.719 60.000 8.91 0.00 0.00 2.82
217 218 1.718757 CCTTGGCCTAGCGACATTGC 61.719 60.000 8.91 0.00 0.00 3.56
218 219 1.718757 CTTGGCCTAGCGACATTGCC 61.719 60.000 3.32 0.00 42.49 4.52
219 220 3.272334 GGCCTAGCGACATTGCCG 61.272 66.667 0.00 0.00 34.65 5.69
220 221 2.202878 GCCTAGCGACATTGCCGA 60.203 61.111 0.00 0.00 34.65 5.54
221 222 1.595382 GCCTAGCGACATTGCCGAT 60.595 57.895 0.00 0.00 34.65 4.18
222 223 1.835483 GCCTAGCGACATTGCCGATG 61.835 60.000 0.00 0.00 41.71 3.84
223 224 1.224069 CCTAGCGACATTGCCGATGG 61.224 60.000 0.00 0.00 40.21 3.51
245 246 3.493303 GGAGGGAGGGGGATGCAC 61.493 72.222 0.00 0.00 0.00 4.57
246 247 3.866582 GAGGGAGGGGGATGCACG 61.867 72.222 0.00 0.00 0.00 5.34
250 251 3.728373 GAGGGGGATGCACGGGTT 61.728 66.667 0.00 0.00 0.00 4.11
251 252 3.995506 GAGGGGGATGCACGGGTTG 62.996 68.421 0.00 0.00 0.00 3.77
254 255 4.041762 GGGATGCACGGGTTGGGA 62.042 66.667 0.00 0.00 0.00 4.37
255 256 2.438434 GGATGCACGGGTTGGGAG 60.438 66.667 0.00 0.00 0.00 4.30
256 257 2.438434 GATGCACGGGTTGGGAGG 60.438 66.667 0.00 0.00 0.00 4.30
257 258 2.933287 ATGCACGGGTTGGGAGGA 60.933 61.111 0.00 0.00 0.00 3.71
258 259 2.876368 GATGCACGGGTTGGGAGGAG 62.876 65.000 0.00 0.00 0.00 3.69
259 260 4.410400 GCACGGGTTGGGAGGAGG 62.410 72.222 0.00 0.00 0.00 4.30
260 261 3.717294 CACGGGTTGGGAGGAGGG 61.717 72.222 0.00 0.00 0.00 4.30
261 262 4.265507 ACGGGTTGGGAGGAGGGT 62.266 66.667 0.00 0.00 0.00 4.34
262 263 2.933834 CGGGTTGGGAGGAGGGTT 60.934 66.667 0.00 0.00 0.00 4.11
263 264 2.763902 GGGTTGGGAGGAGGGTTG 59.236 66.667 0.00 0.00 0.00 3.77
264 265 2.763902 GGTTGGGAGGAGGGTTGG 59.236 66.667 0.00 0.00 0.00 3.77
265 266 2.763902 GTTGGGAGGAGGGTTGGG 59.236 66.667 0.00 0.00 0.00 4.12
266 267 2.534272 TTGGGAGGAGGGTTGGGG 60.534 66.667 0.00 0.00 0.00 4.96
267 268 3.135716 TTGGGAGGAGGGTTGGGGA 62.136 63.158 0.00 0.00 0.00 4.81
268 269 2.692741 GGGAGGAGGGTTGGGGAG 60.693 72.222 0.00 0.00 0.00 4.30
269 270 2.692741 GGAGGAGGGTTGGGGAGG 60.693 72.222 0.00 0.00 0.00 4.30
270 271 2.454941 GAGGAGGGTTGGGGAGGA 59.545 66.667 0.00 0.00 0.00 3.71
271 272 1.690985 GAGGAGGGTTGGGGAGGAG 60.691 68.421 0.00 0.00 0.00 3.69
272 273 2.692741 GGAGGGTTGGGGAGGAGG 60.693 72.222 0.00 0.00 0.00 4.30
273 274 2.454941 GAGGGTTGGGGAGGAGGA 59.545 66.667 0.00 0.00 0.00 3.71
274 275 1.690985 GAGGGTTGGGGAGGAGGAG 60.691 68.421 0.00 0.00 0.00 3.69
275 276 2.125225 GGGTTGGGGAGGAGGAGT 59.875 66.667 0.00 0.00 0.00 3.85
276 277 1.160289 AGGGTTGGGGAGGAGGAGTA 61.160 60.000 0.00 0.00 0.00 2.59
277 278 0.691413 GGGTTGGGGAGGAGGAGTAG 60.691 65.000 0.00 0.00 0.00 2.57
278 279 0.691413 GGTTGGGGAGGAGGAGTAGG 60.691 65.000 0.00 0.00 0.00 3.18
279 280 0.691413 GTTGGGGAGGAGGAGTAGGG 60.691 65.000 0.00 0.00 0.00 3.53
280 281 0.858598 TTGGGGAGGAGGAGTAGGGA 60.859 60.000 0.00 0.00 0.00 4.20
281 282 0.633835 TGGGGAGGAGGAGTAGGGAT 60.634 60.000 0.00 0.00 0.00 3.85
282 283 1.348267 TGGGGAGGAGGAGTAGGGATA 60.348 57.143 0.00 0.00 0.00 2.59
283 284 2.012236 GGGGAGGAGGAGTAGGGATAT 58.988 57.143 0.00 0.00 0.00 1.63
284 285 2.387510 GGGGAGGAGGAGTAGGGATATT 59.612 54.545 0.00 0.00 0.00 1.28
285 286 3.445987 GGGAGGAGGAGTAGGGATATTG 58.554 54.545 0.00 0.00 0.00 1.90
286 287 3.181405 GGGAGGAGGAGTAGGGATATTGT 60.181 52.174 0.00 0.00 0.00 2.71
287 288 3.835395 GGAGGAGGAGTAGGGATATTGTG 59.165 52.174 0.00 0.00 0.00 3.33
288 289 3.243724 AGGAGGAGTAGGGATATTGTGC 58.756 50.000 0.00 0.00 0.00 4.57
289 290 2.303311 GGAGGAGTAGGGATATTGTGCC 59.697 54.545 0.00 0.00 38.92 5.01
296 297 2.959465 GGGATATTGTGCCTAGGCTT 57.041 50.000 33.07 17.74 42.51 4.35
297 298 2.784347 GGGATATTGTGCCTAGGCTTC 58.216 52.381 33.07 24.72 42.51 3.86
298 299 2.106511 GGGATATTGTGCCTAGGCTTCA 59.893 50.000 33.07 26.78 42.51 3.02
299 300 3.142174 GGATATTGTGCCTAGGCTTCAC 58.858 50.000 33.07 23.29 42.51 3.18
300 301 3.433598 GGATATTGTGCCTAGGCTTCACA 60.434 47.826 33.07 25.55 42.51 3.58
301 302 2.814805 ATTGTGCCTAGGCTTCACAT 57.185 45.000 33.07 21.24 40.00 3.21
302 303 1.825090 TTGTGCCTAGGCTTCACATG 58.175 50.000 33.07 0.00 40.00 3.21
303 304 0.983467 TGTGCCTAGGCTTCACATGA 59.017 50.000 33.07 8.77 42.51 3.07
304 305 1.339055 TGTGCCTAGGCTTCACATGAC 60.339 52.381 33.07 20.46 42.51 3.06
305 306 0.253044 TGCCTAGGCTTCACATGACC 59.747 55.000 33.07 1.38 42.51 4.02
306 307 0.464554 GCCTAGGCTTCACATGACCC 60.465 60.000 27.17 0.00 38.26 4.46
307 308 0.179073 CCTAGGCTTCACATGACCCG 60.179 60.000 0.00 0.00 0.00 5.28
308 309 0.537188 CTAGGCTTCACATGACCCGT 59.463 55.000 0.00 0.00 0.00 5.28
309 310 0.249120 TAGGCTTCACATGACCCGTG 59.751 55.000 0.00 0.00 35.63 4.94
310 311 1.302511 GGCTTCACATGACCCGTGT 60.303 57.895 0.00 0.00 35.79 4.49
311 312 0.036765 GGCTTCACATGACCCGTGTA 60.037 55.000 0.00 0.00 35.79 2.90
312 313 1.076332 GCTTCACATGACCCGTGTAC 58.924 55.000 0.00 0.00 35.79 2.90
313 314 1.346365 CTTCACATGACCCGTGTACG 58.654 55.000 0.00 0.00 35.79 3.67
328 329 3.066190 ACGGAAGTGGATCGCCGA 61.066 61.111 7.16 0.00 46.29 5.54
329 330 2.582498 CGGAAGTGGATCGCCGAC 60.582 66.667 0.00 0.00 46.29 4.79
330 331 2.202892 GGAAGTGGATCGCCGACC 60.203 66.667 0.00 0.00 36.79 4.79
331 332 2.577059 GAAGTGGATCGCCGACCA 59.423 61.111 4.62 4.62 36.79 4.02
332 333 1.144057 GAAGTGGATCGCCGACCAT 59.856 57.895 10.73 0.00 38.48 3.55
333 334 0.876342 GAAGTGGATCGCCGACCATC 60.876 60.000 10.73 3.56 38.48 3.51
334 335 1.613317 AAGTGGATCGCCGACCATCA 61.613 55.000 10.73 0.00 38.48 3.07
335 336 1.069765 GTGGATCGCCGACCATCAT 59.930 57.895 10.73 0.00 38.48 2.45
336 337 1.069596 TGGATCGCCGACCATCATG 59.930 57.895 4.62 0.00 36.79 3.07
337 338 1.669115 GGATCGCCGACCATCATGG 60.669 63.158 0.54 0.54 45.02 3.66
338 339 2.281070 ATCGCCGACCATCATGGC 60.281 61.111 2.52 0.00 42.67 4.40
339 340 3.832237 ATCGCCGACCATCATGGCC 62.832 63.158 2.52 0.00 46.12 5.36
377 378 3.120385 CATGCGCGCCTGTCTGAA 61.120 61.111 30.77 7.41 0.00 3.02
378 379 2.358615 ATGCGCGCCTGTCTGAAA 60.359 55.556 30.77 6.52 0.00 2.69
379 380 1.965930 ATGCGCGCCTGTCTGAAAA 60.966 52.632 30.77 5.62 0.00 2.29
384 385 2.708514 CGCGCCTGTCTGAAAATTATG 58.291 47.619 0.00 0.00 0.00 1.90
396 397 0.534873 AAATTATGCAACACCGGGCC 59.465 50.000 6.32 0.00 0.00 5.80
502 508 2.674380 GCCTCACCCAGCCAGTTG 60.674 66.667 0.00 0.00 0.00 3.16
515 521 3.118112 CAGCCAGTTGATATCCTTCCACT 60.118 47.826 0.00 0.00 0.00 4.00
535 541 6.072397 TCCACTATAAACAAATCCCAAACACG 60.072 38.462 0.00 0.00 0.00 4.49
543 549 3.417069 AATCCCAAACACGACTCATCA 57.583 42.857 0.00 0.00 0.00 3.07
550 556 2.152699 CACGACTCATCACCGACGC 61.153 63.158 0.00 0.00 0.00 5.19
589 603 1.520787 GGAACGATCGCGACCCATT 60.521 57.895 12.93 3.29 41.64 3.16
592 606 1.956629 AACGATCGCGACCCATTCCT 61.957 55.000 12.93 0.00 41.64 3.36
593 607 1.661821 CGATCGCGACCCATTCCTC 60.662 63.158 12.93 0.55 40.82 3.71
672 687 1.700739 TCCCACTCCGTAAACAATGGT 59.299 47.619 0.00 0.00 35.53 3.55
785 800 2.125512 GCGTCACGGCTCCTTCAT 60.126 61.111 0.00 0.00 0.00 2.57
789 804 0.526524 GTCACGGCTCCTTCATCGAG 60.527 60.000 0.00 0.00 0.00 4.04
848 865 3.504906 ACGTGTATATATCACCAGTCGGG 59.495 47.826 0.00 0.00 44.81 5.14
860 878 2.357881 GTCGGGGGTGTCGGAAAC 60.358 66.667 0.00 0.00 0.00 2.78
888 906 3.065655 CAAAGGCAGAGTTCAGAGACAG 58.934 50.000 0.00 0.00 0.00 3.51
915 933 2.139118 GACAGAGGAACAGAGCAACAC 58.861 52.381 0.00 0.00 0.00 3.32
930 948 2.143925 CAACACCCGAAAGAAGAGTCC 58.856 52.381 0.00 0.00 0.00 3.85
934 952 3.067833 CACCCGAAAGAAGAGTCCTTTC 58.932 50.000 10.31 10.31 43.53 2.62
943 961 4.484912 AGAAGAGTCCTTTCCTACACAGT 58.515 43.478 0.00 0.00 31.62 3.55
959 977 1.027357 CAGTGCAGACCAACTTTGCT 58.973 50.000 0.00 0.00 38.60 3.91
968 986 4.580580 CAGACCAACTTTGCTAGGAAACTT 59.419 41.667 5.16 0.73 43.67 2.66
970 988 5.656859 AGACCAACTTTGCTAGGAAACTTTT 59.343 36.000 5.16 0.00 43.67 2.27
1109 1130 3.854669 CGGAGGGAAGCAGGCGAT 61.855 66.667 0.00 0.00 0.00 4.58
1122 1143 0.177604 AGGCGATGGAGAAGAAGCAG 59.822 55.000 0.00 0.00 0.00 4.24
1243 1264 7.720074 TCGAGTACATAATATCCTCTTGAGTGT 59.280 37.037 0.00 0.00 0.00 3.55
1295 1316 5.515106 TCTTCTTTCTTTTTCACTTCCCCA 58.485 37.500 0.00 0.00 0.00 4.96
1304 1325 1.751927 CACTTCCCCATCTGCTGCC 60.752 63.158 0.00 0.00 0.00 4.85
1305 1326 2.515523 CTTCCCCATCTGCTGCCG 60.516 66.667 0.00 0.00 0.00 5.69
1307 1328 3.626996 TTCCCCATCTGCTGCCGTG 62.627 63.158 0.00 0.00 0.00 4.94
1320 1341 0.681564 TGCCGTGTGAGGTTTGGTTT 60.682 50.000 0.00 0.00 0.00 3.27
1324 1345 2.425668 CCGTGTGAGGTTTGGTTTCTTT 59.574 45.455 0.00 0.00 0.00 2.52
1326 1347 4.490743 CGTGTGAGGTTTGGTTTCTTTTT 58.509 39.130 0.00 0.00 0.00 1.94
1341 1370 7.148137 TGGTTTCTTTTTGACCAAGAGACTTAC 60.148 37.037 4.05 0.00 40.31 2.34
1345 1374 7.741785 TCTTTTTGACCAAGAGACTTACCATA 58.258 34.615 0.00 0.00 0.00 2.74
1353 1382 5.986135 CCAAGAGACTTACCATATACACAGC 59.014 44.000 0.00 0.00 0.00 4.40
1354 1383 5.440234 AGAGACTTACCATATACACAGCG 57.560 43.478 0.00 0.00 0.00 5.18
1361 1390 4.308899 ACCATATACACAGCGAGAGAAC 57.691 45.455 0.00 0.00 0.00 3.01
1363 1392 3.243101 CCATATACACAGCGAGAGAACGT 60.243 47.826 0.00 0.00 35.59 3.99
1364 1393 4.024302 CCATATACACAGCGAGAGAACGTA 60.024 45.833 0.00 0.00 35.59 3.57
1376 1405 4.907010 CGAGAGAACGTATGAGCTGATAAC 59.093 45.833 0.00 0.00 0.00 1.89
1387 1416 4.245660 TGAGCTGATAACTACACAGTTGC 58.754 43.478 0.00 0.00 44.81 4.17
1407 1444 3.119388 TGCTTGATTTACTGATGCCTTGC 60.119 43.478 0.00 0.00 0.00 4.01
1424 1461 3.429085 CTTGCATATGTTTCGGTTGCTC 58.571 45.455 4.29 0.00 34.47 4.26
1429 1466 6.052360 TGCATATGTTTCGGTTGCTCTATAA 58.948 36.000 4.29 0.00 34.47 0.98
1430 1467 6.202762 TGCATATGTTTCGGTTGCTCTATAAG 59.797 38.462 4.29 0.00 34.47 1.73
1431 1468 6.202954 GCATATGTTTCGGTTGCTCTATAAGT 59.797 38.462 4.29 0.00 0.00 2.24
1432 1469 7.569591 GCATATGTTTCGGTTGCTCTATAAGTC 60.570 40.741 4.29 0.00 0.00 3.01
1433 1470 5.401531 TGTTTCGGTTGCTCTATAAGTCT 57.598 39.130 0.00 0.00 0.00 3.24
1436 1473 8.229253 TGTTTCGGTTGCTCTATAAGTCTATA 57.771 34.615 0.00 0.00 0.00 1.31
1437 1474 8.133627 TGTTTCGGTTGCTCTATAAGTCTATAC 58.866 37.037 0.00 0.00 0.00 1.47
1438 1475 8.351461 GTTTCGGTTGCTCTATAAGTCTATACT 58.649 37.037 0.00 0.00 37.65 2.12
1439 1476 7.436430 TCGGTTGCTCTATAAGTCTATACTG 57.564 40.000 0.00 0.00 35.62 2.74
1440 1477 7.222161 TCGGTTGCTCTATAAGTCTATACTGA 58.778 38.462 0.00 0.00 35.62 3.41
1441 1478 7.718314 TCGGTTGCTCTATAAGTCTATACTGAA 59.282 37.037 0.00 0.00 35.62 3.02
1442 1479 8.350722 CGGTTGCTCTATAAGTCTATACTGAAA 58.649 37.037 0.00 0.00 35.62 2.69
1444 1481 9.187455 GTTGCTCTATAAGTCTATACTGAAAGC 57.813 37.037 0.00 0.00 37.60 3.51
1445 1482 8.465273 TGCTCTATAAGTCTATACTGAAAGCA 57.535 34.615 0.00 0.00 37.60 3.91
1446 1483 8.914011 TGCTCTATAAGTCTATACTGAAAGCAA 58.086 33.333 0.00 0.00 37.60 3.91
1447 1484 9.921637 GCTCTATAAGTCTATACTGAAAGCAAT 57.078 33.333 0.00 0.00 37.60 3.56
1460 1507 3.181447 TGAAAGCAATTTTGATGGGGCAA 60.181 39.130 0.00 0.00 0.00 4.52
1467 1514 5.415389 GCAATTTTGATGGGGCAACTATTTT 59.585 36.000 0.00 0.00 0.00 1.82
1469 1516 7.282901 GCAATTTTGATGGGGCAACTATTTTAT 59.717 33.333 0.00 0.00 0.00 1.40
1514 1563 9.366216 GGCAAAACCAGTAGAAAAATATTAAGG 57.634 33.333 0.00 0.00 38.86 2.69
1593 1643 9.769093 AAACTATTCAGAAATTTATGCACGTAC 57.231 29.630 7.96 0.00 0.00 3.67
1594 1644 7.916552 ACTATTCAGAAATTTATGCACGTACC 58.083 34.615 7.96 0.00 0.00 3.34
1595 1645 7.769044 ACTATTCAGAAATTTATGCACGTACCT 59.231 33.333 7.96 0.00 0.00 3.08
1596 1646 9.256477 CTATTCAGAAATTTATGCACGTACCTA 57.744 33.333 7.96 0.00 0.00 3.08
1597 1647 7.534085 TTCAGAAATTTATGCACGTACCTAG 57.466 36.000 7.96 0.00 0.00 3.02
1598 1648 6.636705 TCAGAAATTTATGCACGTACCTAGT 58.363 36.000 7.96 0.00 0.00 2.57
1599 1649 6.755141 TCAGAAATTTATGCACGTACCTAGTC 59.245 38.462 7.96 0.00 0.00 2.59
1600 1650 6.533723 CAGAAATTTATGCACGTACCTAGTCA 59.466 38.462 0.00 0.00 0.00 3.41
1601 1651 7.224753 CAGAAATTTATGCACGTACCTAGTCAT 59.775 37.037 0.00 0.00 0.00 3.06
1602 1652 7.438459 AGAAATTTATGCACGTACCTAGTCATC 59.562 37.037 0.00 0.00 0.00 2.92
1603 1653 5.585820 TTTATGCACGTACCTAGTCATCA 57.414 39.130 0.00 0.00 0.00 3.07
1604 1654 5.585820 TTATGCACGTACCTAGTCATCAA 57.414 39.130 0.00 0.00 0.00 2.57
1605 1655 4.672587 ATGCACGTACCTAGTCATCAAT 57.327 40.909 0.00 0.00 0.00 2.57
1606 1656 4.041740 TGCACGTACCTAGTCATCAATC 57.958 45.455 0.00 0.00 0.00 2.67
1607 1657 3.445805 TGCACGTACCTAGTCATCAATCA 59.554 43.478 0.00 0.00 0.00 2.57
1608 1658 4.081917 TGCACGTACCTAGTCATCAATCAA 60.082 41.667 0.00 0.00 0.00 2.57
1609 1659 4.868171 GCACGTACCTAGTCATCAATCAAA 59.132 41.667 0.00 0.00 0.00 2.69
1610 1660 5.350365 GCACGTACCTAGTCATCAATCAAAA 59.650 40.000 0.00 0.00 0.00 2.44
1611 1661 6.128391 GCACGTACCTAGTCATCAATCAAAAA 60.128 38.462 0.00 0.00 0.00 1.94
1631 1681 5.717038 AAAAGAAAACCACGCAAAATCTG 57.283 34.783 0.00 0.00 0.00 2.90
1722 1772 1.668101 CTCGTCTCCAGTGGCCCTAC 61.668 65.000 3.51 0.00 0.00 3.18
1810 1860 3.951680 CCTGTCTTGTTAGGGTTTGTGTT 59.048 43.478 0.00 0.00 0.00 3.32
1816 1866 3.626930 TGTTAGGGTTTGTGTTCTGCTT 58.373 40.909 0.00 0.00 0.00 3.91
1867 1917 3.747852 AGATGGAATAAAGGTCTCCCCA 58.252 45.455 0.00 0.00 34.66 4.96
1928 1978 1.739667 CGTGTGGAGGTGTGTCTCA 59.260 57.895 0.00 0.00 35.58 3.27
1930 1980 1.040646 GTGTGGAGGTGTGTCTCAGA 58.959 55.000 0.00 0.00 35.58 3.27
1931 1981 1.620819 GTGTGGAGGTGTGTCTCAGAT 59.379 52.381 0.00 0.00 35.58 2.90
1932 1982 2.826128 GTGTGGAGGTGTGTCTCAGATA 59.174 50.000 0.00 0.00 35.58 1.98
2068 2118 4.609018 CGCTGGTCCTATGGGGCG 62.609 72.222 2.38 2.38 38.30 6.13
2105 2155 3.890756 TCCCGACTGTCTACTACAACAAA 59.109 43.478 6.21 0.00 37.74 2.83
2144 2194 2.577059 GAAGGGTGATGACGGCGA 59.423 61.111 16.62 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.217743 CCGGGCTCGACCTAGGAC 61.218 72.222 17.98 8.80 38.10 3.85
1 2 4.517934 CCCGGGCTCGACCTAGGA 62.518 72.222 17.98 0.00 38.10 2.94
2 3 3.811807 ATCCCGGGCTCGACCTAGG 62.812 68.421 18.49 7.41 39.10 3.02
3 4 2.203509 ATCCCGGGCTCGACCTAG 60.204 66.667 18.49 0.00 39.10 3.02
4 5 2.520982 CATCCCGGGCTCGACCTA 60.521 66.667 18.49 0.00 39.10 3.08
34 35 4.569023 TACGAGATGGCGGCAGCG 62.569 66.667 21.99 22.74 46.35 5.18
35 36 2.071844 TAGTACGAGATGGCGGCAGC 62.072 60.000 20.74 20.74 44.18 5.25
36 37 0.317938 GTAGTACGAGATGGCGGCAG 60.318 60.000 19.29 6.06 35.12 4.85
37 38 0.750546 AGTAGTACGAGATGGCGGCA 60.751 55.000 16.34 16.34 35.12 5.69
38 39 0.040246 GAGTAGTACGAGATGGCGGC 60.040 60.000 0.00 0.00 35.12 6.53
39 40 0.592148 GGAGTAGTACGAGATGGCGG 59.408 60.000 0.00 0.00 35.12 6.13
40 41 0.592148 GGGAGTAGTACGAGATGGCG 59.408 60.000 0.00 0.00 37.29 5.69
41 42 0.592148 CGGGAGTAGTACGAGATGGC 59.408 60.000 0.00 0.00 0.00 4.40
42 43 0.592148 GCGGGAGTAGTACGAGATGG 59.408 60.000 0.00 0.00 0.00 3.51
43 44 0.592148 GGCGGGAGTAGTACGAGATG 59.408 60.000 0.00 0.00 0.00 2.90
44 45 0.182061 TGGCGGGAGTAGTACGAGAT 59.818 55.000 0.00 0.00 0.00 2.75
45 46 0.463295 CTGGCGGGAGTAGTACGAGA 60.463 60.000 0.00 0.00 0.00 4.04
46 47 1.445716 CCTGGCGGGAGTAGTACGAG 61.446 65.000 6.48 0.00 37.23 4.18
47 48 1.452651 CCTGGCGGGAGTAGTACGA 60.453 63.158 6.48 0.00 37.23 3.43
48 49 1.751927 ACCTGGCGGGAGTAGTACG 60.752 63.158 21.81 0.00 38.76 3.67
49 50 1.814527 CACCTGGCGGGAGTAGTAC 59.185 63.158 21.81 0.00 38.76 2.73
50 51 2.056223 GCACCTGGCGGGAGTAGTA 61.056 63.158 21.81 0.00 38.76 1.82
51 52 3.391382 GCACCTGGCGGGAGTAGT 61.391 66.667 21.81 0.00 38.76 2.73
100 101 2.279120 GACGAGGATGGCGAGCAG 60.279 66.667 0.00 0.00 0.00 4.24
101 102 4.193334 CGACGAGGATGGCGAGCA 62.193 66.667 0.00 0.00 0.00 4.26
102 103 4.933064 CCGACGAGGATGGCGAGC 62.933 72.222 0.00 0.00 45.00 5.03
103 104 3.209812 TCCGACGAGGATGGCGAG 61.210 66.667 0.00 0.00 45.98 5.03
111 112 1.457009 GGATCTCCCTTCCGACGAGG 61.457 65.000 0.00 0.00 42.97 4.63
112 113 0.752009 TGGATCTCCCTTCCGACGAG 60.752 60.000 0.00 0.00 35.94 4.18
113 114 0.323999 TTGGATCTCCCTTCCGACGA 60.324 55.000 0.00 0.00 35.94 4.20
114 115 0.535335 TTTGGATCTCCCTTCCGACG 59.465 55.000 0.00 0.00 35.94 5.12
115 116 2.170607 TGATTTGGATCTCCCTTCCGAC 59.829 50.000 0.00 0.00 35.94 4.79
116 117 2.435805 CTGATTTGGATCTCCCTTCCGA 59.564 50.000 0.00 0.00 35.94 4.55
117 118 2.486191 CCTGATTTGGATCTCCCTTCCG 60.486 54.545 0.00 0.00 35.94 4.30
118 119 2.158549 CCCTGATTTGGATCTCCCTTCC 60.159 54.545 0.00 0.00 35.38 3.46
119 120 2.751143 GCCCTGATTTGGATCTCCCTTC 60.751 54.545 0.00 0.00 35.38 3.46
120 121 1.216427 GCCCTGATTTGGATCTCCCTT 59.784 52.381 0.00 0.00 35.38 3.95
121 122 0.849417 GCCCTGATTTGGATCTCCCT 59.151 55.000 0.00 0.00 35.38 4.20
122 123 0.536006 CGCCCTGATTTGGATCTCCC 60.536 60.000 0.00 0.00 33.28 4.30
123 124 1.169034 GCGCCCTGATTTGGATCTCC 61.169 60.000 0.00 0.00 33.28 3.71
124 125 1.169034 GGCGCCCTGATTTGGATCTC 61.169 60.000 18.11 0.00 33.28 2.75
125 126 1.152881 GGCGCCCTGATTTGGATCT 60.153 57.895 18.11 0.00 33.28 2.75
126 127 2.546494 CGGCGCCCTGATTTGGATC 61.546 63.158 23.46 0.00 0.00 3.36
127 128 2.516930 CGGCGCCCTGATTTGGAT 60.517 61.111 23.46 0.00 0.00 3.41
146 147 2.986413 ATCCCGAGATCCGAGGCG 60.986 66.667 5.32 0.00 41.76 5.52
147 148 2.653702 CATCCCGAGATCCGAGGC 59.346 66.667 5.32 0.00 41.76 4.70
148 149 2.653702 GCATCCCGAGATCCGAGG 59.346 66.667 5.32 5.37 41.76 4.63
149 150 2.152297 CTGGCATCCCGAGATCCGAG 62.152 65.000 5.32 0.00 41.76 4.63
150 151 2.123468 TGGCATCCCGAGATCCGA 60.123 61.111 5.32 0.00 41.76 4.55
151 152 2.152297 CTCTGGCATCCCGAGATCCG 62.152 65.000 0.00 0.00 35.28 4.18
152 153 1.670590 CTCTGGCATCCCGAGATCC 59.329 63.158 0.00 0.00 35.28 3.36
153 154 0.829602 TCCTCTGGCATCCCGAGATC 60.830 60.000 5.95 0.00 35.28 2.75
154 155 0.831288 CTCCTCTGGCATCCCGAGAT 60.831 60.000 5.95 0.00 35.28 2.75
155 156 1.456518 CTCCTCTGGCATCCCGAGA 60.457 63.158 5.95 0.00 35.28 4.04
156 157 2.506061 CCTCCTCTGGCATCCCGAG 61.506 68.421 0.00 0.00 34.01 4.63
157 158 2.444706 CCTCCTCTGGCATCCCGA 60.445 66.667 0.00 0.00 0.00 5.14
158 159 2.765807 ACCTCCTCTGGCATCCCG 60.766 66.667 0.00 0.00 0.00 5.14
159 160 2.447714 GGACCTCCTCTGGCATCCC 61.448 68.421 0.00 0.00 0.00 3.85
160 161 2.801631 CGGACCTCCTCTGGCATCC 61.802 68.421 0.00 0.00 0.00 3.51
161 162 2.818132 CGGACCTCCTCTGGCATC 59.182 66.667 0.00 0.00 0.00 3.91
162 163 3.474570 GCGGACCTCCTCTGGCAT 61.475 66.667 0.00 0.00 0.00 4.40
197 198 1.452108 AATGTCGCTAGGCCAAGGC 60.452 57.895 5.01 1.52 41.06 4.35
198 199 1.718757 GCAATGTCGCTAGGCCAAGG 61.719 60.000 5.01 0.00 0.00 3.61
199 200 1.718757 GGCAATGTCGCTAGGCCAAG 61.719 60.000 5.01 0.00 44.01 3.61
200 201 1.748879 GGCAATGTCGCTAGGCCAA 60.749 57.895 5.01 0.00 44.01 4.52
201 202 2.124736 GGCAATGTCGCTAGGCCA 60.125 61.111 5.01 0.00 44.01 5.36
202 203 2.996168 ATCGGCAATGTCGCTAGGCC 62.996 60.000 0.85 0.00 41.20 5.19
203 204 1.595382 ATCGGCAATGTCGCTAGGC 60.595 57.895 0.85 0.00 0.00 3.93
204 205 1.224069 CCATCGGCAATGTCGCTAGG 61.224 60.000 0.85 0.00 33.13 3.02
205 206 2.229039 CCATCGGCAATGTCGCTAG 58.771 57.895 0.85 0.00 33.13 3.42
206 207 4.436515 CCATCGGCAATGTCGCTA 57.563 55.556 0.85 0.00 33.13 4.26
228 229 3.493303 GTGCATCCCCCTCCCTCC 61.493 72.222 0.00 0.00 0.00 4.30
229 230 3.866582 CGTGCATCCCCCTCCCTC 61.867 72.222 0.00 0.00 0.00 4.30
233 234 3.728373 AACCCGTGCATCCCCCTC 61.728 66.667 0.00 0.00 0.00 4.30
234 235 4.047125 CAACCCGTGCATCCCCCT 62.047 66.667 0.00 0.00 0.00 4.79
237 238 3.995506 CTCCCAACCCGTGCATCCC 62.996 68.421 0.00 0.00 0.00 3.85
238 239 2.438434 CTCCCAACCCGTGCATCC 60.438 66.667 0.00 0.00 0.00 3.51
239 240 2.438434 CCTCCCAACCCGTGCATC 60.438 66.667 0.00 0.00 0.00 3.91
240 241 2.933287 TCCTCCCAACCCGTGCAT 60.933 61.111 0.00 0.00 0.00 3.96
241 242 3.636231 CTCCTCCCAACCCGTGCA 61.636 66.667 0.00 0.00 0.00 4.57
242 243 4.410400 CCTCCTCCCAACCCGTGC 62.410 72.222 0.00 0.00 0.00 5.34
243 244 3.717294 CCCTCCTCCCAACCCGTG 61.717 72.222 0.00 0.00 0.00 4.94
244 245 3.805151 AACCCTCCTCCCAACCCGT 62.805 63.158 0.00 0.00 0.00 5.28
245 246 2.933834 AACCCTCCTCCCAACCCG 60.934 66.667 0.00 0.00 0.00 5.28
246 247 2.763902 CAACCCTCCTCCCAACCC 59.236 66.667 0.00 0.00 0.00 4.11
247 248 2.763902 CCAACCCTCCTCCCAACC 59.236 66.667 0.00 0.00 0.00 3.77
248 249 2.763902 CCCAACCCTCCTCCCAAC 59.236 66.667 0.00 0.00 0.00 3.77
249 250 2.534272 CCCCAACCCTCCTCCCAA 60.534 66.667 0.00 0.00 0.00 4.12
250 251 3.547737 TCCCCAACCCTCCTCCCA 61.548 66.667 0.00 0.00 0.00 4.37
251 252 2.692741 CTCCCCAACCCTCCTCCC 60.693 72.222 0.00 0.00 0.00 4.30
252 253 2.692741 CCTCCCCAACCCTCCTCC 60.693 72.222 0.00 0.00 0.00 4.30
253 254 1.690985 CTCCTCCCCAACCCTCCTC 60.691 68.421 0.00 0.00 0.00 3.71
254 255 2.456840 CTCCTCCCCAACCCTCCT 59.543 66.667 0.00 0.00 0.00 3.69
255 256 2.692741 CCTCCTCCCCAACCCTCC 60.693 72.222 0.00 0.00 0.00 4.30
256 257 1.690985 CTCCTCCTCCCCAACCCTC 60.691 68.421 0.00 0.00 0.00 4.30
257 258 1.160289 TACTCCTCCTCCCCAACCCT 61.160 60.000 0.00 0.00 0.00 4.34
258 259 0.691413 CTACTCCTCCTCCCCAACCC 60.691 65.000 0.00 0.00 0.00 4.11
259 260 0.691413 CCTACTCCTCCTCCCCAACC 60.691 65.000 0.00 0.00 0.00 3.77
260 261 0.691413 CCCTACTCCTCCTCCCCAAC 60.691 65.000 0.00 0.00 0.00 3.77
261 262 0.858598 TCCCTACTCCTCCTCCCCAA 60.859 60.000 0.00 0.00 0.00 4.12
262 263 0.633835 ATCCCTACTCCTCCTCCCCA 60.634 60.000 0.00 0.00 0.00 4.96
263 264 1.469082 TATCCCTACTCCTCCTCCCC 58.531 60.000 0.00 0.00 0.00 4.81
264 265 3.181405 ACAATATCCCTACTCCTCCTCCC 60.181 52.174 0.00 0.00 0.00 4.30
265 266 3.835395 CACAATATCCCTACTCCTCCTCC 59.165 52.174 0.00 0.00 0.00 4.30
266 267 3.259625 GCACAATATCCCTACTCCTCCTC 59.740 52.174 0.00 0.00 0.00 3.71
267 268 3.243724 GCACAATATCCCTACTCCTCCT 58.756 50.000 0.00 0.00 0.00 3.69
268 269 2.303311 GGCACAATATCCCTACTCCTCC 59.697 54.545 0.00 0.00 0.00 4.30
269 270 3.243724 AGGCACAATATCCCTACTCCTC 58.756 50.000 0.00 0.00 0.00 3.71
270 271 3.352611 AGGCACAATATCCCTACTCCT 57.647 47.619 0.00 0.00 0.00 3.69
271 272 3.515901 CCTAGGCACAATATCCCTACTCC 59.484 52.174 0.00 0.00 0.00 3.85
272 273 3.055747 GCCTAGGCACAATATCCCTACTC 60.056 52.174 29.33 0.00 41.49 2.59
273 274 2.907042 GCCTAGGCACAATATCCCTACT 59.093 50.000 29.33 0.00 41.49 2.57
274 275 2.907042 AGCCTAGGCACAATATCCCTAC 59.093 50.000 34.70 0.57 44.88 3.18
275 276 3.275848 AGCCTAGGCACAATATCCCTA 57.724 47.619 34.70 0.00 44.88 3.53
276 277 2.124560 AGCCTAGGCACAATATCCCT 57.875 50.000 34.70 7.82 44.88 4.20
277 278 2.106511 TGAAGCCTAGGCACAATATCCC 59.893 50.000 34.70 12.65 44.88 3.85
278 279 3.142174 GTGAAGCCTAGGCACAATATCC 58.858 50.000 34.70 16.94 44.88 2.59
279 280 3.808728 TGTGAAGCCTAGGCACAATATC 58.191 45.455 34.70 20.77 44.88 1.63
280 281 3.931907 TGTGAAGCCTAGGCACAATAT 57.068 42.857 34.70 11.07 44.88 1.28
281 282 3.199727 TCATGTGAAGCCTAGGCACAATA 59.800 43.478 34.70 23.14 44.62 1.90
282 283 2.025981 TCATGTGAAGCCTAGGCACAAT 60.026 45.455 34.70 22.47 44.62 2.71
283 284 1.350684 TCATGTGAAGCCTAGGCACAA 59.649 47.619 34.70 21.50 44.62 3.33
284 285 0.983467 TCATGTGAAGCCTAGGCACA 59.017 50.000 34.70 28.51 45.40 4.57
285 286 1.373570 GTCATGTGAAGCCTAGGCAC 58.626 55.000 34.70 26.29 44.88 5.01
286 287 0.253044 GGTCATGTGAAGCCTAGGCA 59.747 55.000 34.70 15.08 44.88 4.75
287 288 0.464554 GGGTCATGTGAAGCCTAGGC 60.465 60.000 27.19 27.19 42.33 3.93
288 289 0.179073 CGGGTCATGTGAAGCCTAGG 60.179 60.000 3.67 3.67 31.98 3.02
289 290 0.537188 ACGGGTCATGTGAAGCCTAG 59.463 55.000 0.00 0.00 31.98 3.02
290 291 0.249120 CACGGGTCATGTGAAGCCTA 59.751 55.000 0.00 0.00 39.73 3.93
291 292 1.003355 CACGGGTCATGTGAAGCCT 60.003 57.895 0.00 0.00 39.73 4.58
292 293 0.036765 TACACGGGTCATGTGAAGCC 60.037 55.000 0.00 0.00 39.73 4.35
293 294 1.076332 GTACACGGGTCATGTGAAGC 58.924 55.000 0.00 0.00 39.73 3.86
294 295 1.346365 CGTACACGGGTCATGTGAAG 58.654 55.000 0.00 0.00 39.73 3.02
295 296 3.500455 CGTACACGGGTCATGTGAA 57.500 52.632 0.00 0.00 39.73 3.18
306 307 1.138047 GCGATCCACTTCCGTACACG 61.138 60.000 0.00 0.00 39.44 4.49
307 308 0.804933 GGCGATCCACTTCCGTACAC 60.805 60.000 0.00 0.00 0.00 2.90
308 309 1.514087 GGCGATCCACTTCCGTACA 59.486 57.895 0.00 0.00 0.00 2.90
309 310 1.588139 CGGCGATCCACTTCCGTAC 60.588 63.158 0.00 0.00 37.33 3.67
310 311 1.750018 TCGGCGATCCACTTCCGTA 60.750 57.895 4.99 0.00 42.28 4.02
311 312 3.066190 TCGGCGATCCACTTCCGT 61.066 61.111 4.99 0.00 42.28 4.69
312 313 2.582498 GTCGGCGATCCACTTCCG 60.582 66.667 14.79 0.00 42.96 4.30
313 314 2.202892 GGTCGGCGATCCACTTCC 60.203 66.667 14.79 3.35 0.00 3.46
314 315 0.876342 GATGGTCGGCGATCCACTTC 60.876 60.000 25.79 18.87 36.50 3.01
315 316 1.144057 GATGGTCGGCGATCCACTT 59.856 57.895 25.79 15.54 36.50 3.16
316 317 1.402896 ATGATGGTCGGCGATCCACT 61.403 55.000 25.79 17.50 36.50 4.00
317 318 1.069765 ATGATGGTCGGCGATCCAC 59.930 57.895 25.79 20.29 36.50 4.02
318 319 1.069596 CATGATGGTCGGCGATCCA 59.930 57.895 25.58 25.58 38.14 3.41
319 320 1.669115 CCATGATGGTCGGCGATCC 60.669 63.158 18.78 18.18 31.35 3.36
320 321 2.320587 GCCATGATGGTCGGCGATC 61.321 63.158 14.79 14.58 40.46 3.69
321 322 2.281070 GCCATGATGGTCGGCGAT 60.281 61.111 14.79 0.00 40.46 4.58
360 361 2.186350 TTTTCAGACAGGCGCGCATG 62.186 55.000 40.19 40.19 0.00 4.06
361 362 1.308069 ATTTTCAGACAGGCGCGCAT 61.308 50.000 34.42 26.01 0.00 4.73
362 363 1.514678 AATTTTCAGACAGGCGCGCA 61.515 50.000 34.42 7.29 0.00 6.09
363 364 0.446222 TAATTTTCAGACAGGCGCGC 59.554 50.000 25.94 25.94 0.00 6.86
364 365 2.708514 CATAATTTTCAGACAGGCGCG 58.291 47.619 0.00 0.00 0.00 6.86
365 366 2.159393 TGCATAATTTTCAGACAGGCGC 60.159 45.455 0.00 0.00 0.00 6.53
366 367 3.763097 TGCATAATTTTCAGACAGGCG 57.237 42.857 0.00 0.00 0.00 5.52
367 368 4.622740 GTGTTGCATAATTTTCAGACAGGC 59.377 41.667 0.00 0.00 0.00 4.85
368 369 5.163513 GGTGTTGCATAATTTTCAGACAGG 58.836 41.667 0.00 0.00 0.00 4.00
369 370 4.853196 CGGTGTTGCATAATTTTCAGACAG 59.147 41.667 0.00 0.00 0.00 3.51
370 371 4.320861 CCGGTGTTGCATAATTTTCAGACA 60.321 41.667 0.00 0.00 0.00 3.41
371 372 4.165779 CCGGTGTTGCATAATTTTCAGAC 58.834 43.478 0.00 0.00 0.00 3.51
372 373 3.192422 CCCGGTGTTGCATAATTTTCAGA 59.808 43.478 0.00 0.00 0.00 3.27
373 374 3.510719 CCCGGTGTTGCATAATTTTCAG 58.489 45.455 0.00 0.00 0.00 3.02
374 375 2.353208 GCCCGGTGTTGCATAATTTTCA 60.353 45.455 0.00 0.00 0.00 2.69
375 376 2.267426 GCCCGGTGTTGCATAATTTTC 58.733 47.619 0.00 0.00 0.00 2.29
376 377 1.066502 GGCCCGGTGTTGCATAATTTT 60.067 47.619 0.00 0.00 0.00 1.82
377 378 0.534873 GGCCCGGTGTTGCATAATTT 59.465 50.000 0.00 0.00 0.00 1.82
378 379 1.662438 CGGCCCGGTGTTGCATAATT 61.662 55.000 0.00 0.00 0.00 1.40
379 380 2.118404 CGGCCCGGTGTTGCATAAT 61.118 57.895 0.00 0.00 0.00 1.28
458 459 2.551270 TGGAACTCAGCTAGGGAACAT 58.449 47.619 0.00 0.00 0.00 2.71
466 472 1.336887 GCGACACTTGGAACTCAGCTA 60.337 52.381 0.00 0.00 0.00 3.32
502 508 9.232473 GGGATTTGTTTATAGTGGAAGGATATC 57.768 37.037 0.00 0.00 0.00 1.63
515 521 6.711194 TGAGTCGTGTTTGGGATTTGTTTATA 59.289 34.615 0.00 0.00 0.00 0.98
535 541 2.161486 GCTGCGTCGGTGATGAGTC 61.161 63.158 0.00 0.00 0.00 3.36
543 549 3.596066 AATGAGCTGCTGCGTCGGT 62.596 57.895 7.01 0.00 45.42 4.69
550 556 3.739300 CCAACAAAAGAAATGAGCTGCTG 59.261 43.478 7.01 0.00 0.00 4.41
672 687 2.632996 ACATGAGAGAGTTTGACCGGAA 59.367 45.455 9.46 0.00 0.00 4.30
785 800 4.329545 AGGCAAAAGCGGGCTCGA 62.330 61.111 12.03 0.00 36.23 4.04
812 827 1.039233 ACACGTACGGGGGATAGGTG 61.039 60.000 23.48 8.78 41.81 4.00
848 865 2.359478 ATGCCGTTTCCGACACCC 60.359 61.111 0.00 0.00 35.63 4.61
854 872 1.506262 CCTTTGGATGCCGTTTCCG 59.494 57.895 0.00 0.00 35.94 4.30
860 878 0.962356 AACTCTGCCTTTGGATGCCG 60.962 55.000 0.00 0.00 0.00 5.69
862 880 1.471684 CTGAACTCTGCCTTTGGATGC 59.528 52.381 0.00 0.00 0.00 3.91
871 889 1.892474 ACTCTGTCTCTGAACTCTGCC 59.108 52.381 0.00 0.00 0.00 4.85
872 890 2.556189 TGACTCTGTCTCTGAACTCTGC 59.444 50.000 0.00 0.00 33.15 4.26
888 906 3.613910 GCTCTGTTCCTCTGTCTTGACTC 60.614 52.174 2.35 0.00 0.00 3.36
915 933 2.303311 AGGAAAGGACTCTTCTTTCGGG 59.697 50.000 9.51 0.00 46.50 5.14
930 948 2.224281 TGGTCTGCACTGTGTAGGAAAG 60.224 50.000 22.78 1.33 30.69 2.62
934 952 1.070758 AGTTGGTCTGCACTGTGTAGG 59.929 52.381 22.78 7.37 30.69 3.18
943 961 1.419762 TCCTAGCAAAGTTGGTCTGCA 59.580 47.619 0.00 0.00 39.88 4.41
968 986 0.676782 GAGCTGCCGGCCTCTAAAAA 60.677 55.000 26.77 0.19 43.05 1.94
970 988 2.584608 GAGCTGCCGGCCTCTAAA 59.415 61.111 26.77 2.02 43.05 1.85
1044 1065 4.883354 CCGGCCCCAGCAATCTCC 62.883 72.222 0.00 0.00 42.56 3.71
1109 1130 0.612229 CTCCTGCTGCTTCTTCTCCA 59.388 55.000 0.00 0.00 0.00 3.86
1122 1143 1.216710 CTCGACCTTGTCCTCCTGC 59.783 63.158 0.00 0.00 0.00 4.85
1194 1215 1.179814 AGTTGAGCCCGTCGAACTCT 61.180 55.000 13.39 0.00 0.00 3.24
1276 1297 5.776744 CAGATGGGGAAGTGAAAAAGAAAG 58.223 41.667 0.00 0.00 0.00 2.62
1295 1316 2.116983 AACCTCACACGGCAGCAGAT 62.117 55.000 0.00 0.00 0.00 2.90
1304 1325 3.775661 AAAGAAACCAAACCTCACACG 57.224 42.857 0.00 0.00 0.00 4.49
1305 1326 5.347635 GTCAAAAAGAAACCAAACCTCACAC 59.652 40.000 0.00 0.00 0.00 3.82
1307 1328 4.868171 GGTCAAAAAGAAACCAAACCTCAC 59.132 41.667 0.00 0.00 33.11 3.51
1320 1341 5.996644 TGGTAAGTCTCTTGGTCAAAAAGA 58.003 37.500 0.00 0.00 32.80 2.52
1324 1345 8.038944 GTGTATATGGTAAGTCTCTTGGTCAAA 58.961 37.037 0.00 0.00 0.00 2.69
1326 1347 6.666113 TGTGTATATGGTAAGTCTCTTGGTCA 59.334 38.462 0.00 0.00 0.00 4.02
1341 1370 3.243101 ACGTTCTCTCGCTGTGTATATGG 60.243 47.826 0.00 0.00 0.00 2.74
1345 1374 3.626217 TCATACGTTCTCTCGCTGTGTAT 59.374 43.478 0.00 0.00 0.00 2.29
1353 1382 3.617540 ATCAGCTCATACGTTCTCTCG 57.382 47.619 0.00 0.00 0.00 4.04
1354 1383 6.067263 AGTTATCAGCTCATACGTTCTCTC 57.933 41.667 0.00 0.00 0.00 3.20
1361 1390 5.822278 ACTGTGTAGTTATCAGCTCATACG 58.178 41.667 0.00 0.00 31.66 3.06
1363 1392 6.042777 GCAACTGTGTAGTTATCAGCTCATA 58.957 40.000 0.00 0.00 45.12 2.15
1364 1393 4.872691 GCAACTGTGTAGTTATCAGCTCAT 59.127 41.667 0.00 0.00 45.12 2.90
1376 1405 6.785488 TCAGTAAATCAAGCAACTGTGTAG 57.215 37.500 0.00 0.00 40.18 2.74
1387 1416 4.707030 TGCAAGGCATCAGTAAATCAAG 57.293 40.909 0.00 0.00 31.71 3.02
1407 1444 7.653713 AGACTTATAGAGCAACCGAAACATATG 59.346 37.037 0.00 0.00 0.00 1.78
1416 1453 7.436430 TCAGTATAGACTTATAGAGCAACCG 57.564 40.000 0.00 0.00 31.73 4.44
1429 1466 8.680903 CCATCAAAATTGCTTTCAGTATAGACT 58.319 33.333 0.00 0.00 35.80 3.24
1430 1467 7.917505 CCCATCAAAATTGCTTTCAGTATAGAC 59.082 37.037 0.00 0.00 0.00 2.59
1431 1468 7.068593 CCCCATCAAAATTGCTTTCAGTATAGA 59.931 37.037 0.00 0.00 0.00 1.98
1432 1469 7.205297 CCCCATCAAAATTGCTTTCAGTATAG 58.795 38.462 0.00 0.00 0.00 1.31
1433 1470 6.406849 GCCCCATCAAAATTGCTTTCAGTATA 60.407 38.462 0.00 0.00 0.00 1.47
1436 1473 3.557686 GCCCCATCAAAATTGCTTTCAGT 60.558 43.478 0.00 0.00 0.00 3.41
1437 1474 3.004862 GCCCCATCAAAATTGCTTTCAG 58.995 45.455 0.00 0.00 0.00 3.02
1438 1475 2.371179 TGCCCCATCAAAATTGCTTTCA 59.629 40.909 0.00 0.00 0.00 2.69
1439 1476 3.056588 TGCCCCATCAAAATTGCTTTC 57.943 42.857 0.00 0.00 0.00 2.62
1440 1477 3.148412 GTTGCCCCATCAAAATTGCTTT 58.852 40.909 0.00 0.00 0.00 3.51
1441 1478 2.372837 AGTTGCCCCATCAAAATTGCTT 59.627 40.909 0.00 0.00 0.00 3.91
1442 1479 1.980036 AGTTGCCCCATCAAAATTGCT 59.020 42.857 0.00 0.00 0.00 3.91
1444 1481 8.735692 ATAAAATAGTTGCCCCATCAAAATTG 57.264 30.769 0.00 0.00 0.00 2.32
1447 1484 9.660180 GTTTATAAAATAGTTGCCCCATCAAAA 57.340 29.630 0.00 0.00 0.00 2.44
1449 1486 8.367660 TGTTTATAAAATAGTTGCCCCATCAA 57.632 30.769 0.00 0.00 0.00 2.57
1460 1507 7.040409 GCTAGGCTGCCATGTTTATAAAATAGT 60.040 37.037 22.65 0.00 0.00 2.12
1570 1620 8.142994 AGGTACGTGCATAAATTTCTGAATAG 57.857 34.615 5.86 0.00 0.00 1.73
1585 1635 3.445805 TGATTGATGACTAGGTACGTGCA 59.554 43.478 5.86 0.00 0.00 4.57
1586 1636 4.041740 TGATTGATGACTAGGTACGTGC 57.958 45.455 0.00 0.00 0.00 5.34
1587 1637 6.961359 TTTTGATTGATGACTAGGTACGTG 57.039 37.500 0.00 0.00 0.00 4.49
1608 1658 5.447144 GCAGATTTTGCGTGGTTTTCTTTTT 60.447 36.000 0.00 0.00 44.09 1.94
1609 1659 4.033932 GCAGATTTTGCGTGGTTTTCTTTT 59.966 37.500 0.00 0.00 44.09 2.27
1610 1660 3.555547 GCAGATTTTGCGTGGTTTTCTTT 59.444 39.130 0.00 0.00 44.09 2.52
1611 1661 3.123050 GCAGATTTTGCGTGGTTTTCTT 58.877 40.909 0.00 0.00 44.09 2.52
1612 1662 2.742774 GCAGATTTTGCGTGGTTTTCT 58.257 42.857 0.00 0.00 44.09 2.52
1810 1860 1.135373 CGTCTCGCCTTCTTAAGCAGA 60.135 52.381 3.47 0.00 0.00 4.26
1816 1866 2.488355 CGCCGTCTCGCCTTCTTA 59.512 61.111 0.00 0.00 0.00 2.10
1841 1891 6.240549 GGAGACCTTTATTCCATCTTCAGA 57.759 41.667 0.00 0.00 0.00 3.27
1930 1980 7.753630 AGCAAATCCACCAAAGATAGATCTAT 58.246 34.615 15.26 15.26 35.76 1.98
1931 1981 7.141758 AGCAAATCCACCAAAGATAGATCTA 57.858 36.000 4.57 4.57 35.76 1.98
1932 1982 6.011122 AGCAAATCCACCAAAGATAGATCT 57.989 37.500 0.00 0.00 39.22 2.75
2042 2092 1.264749 TAGGACCAGCGCACCAGAAT 61.265 55.000 11.47 0.00 0.00 2.40
2068 2118 0.458025 CGGGAAGTCCTCGTGCTAAC 60.458 60.000 0.00 0.00 35.95 2.34
2123 2173 0.394352 GCCGTCATCACCCTTCCATT 60.394 55.000 0.00 0.00 0.00 3.16
2129 2179 4.129737 CGTCGCCGTCATCACCCT 62.130 66.667 0.00 0.00 0.00 4.34
2144 2194 4.796231 AGCCGATCGAAAGCGCGT 62.796 61.111 18.66 0.00 37.46 6.01
2154 2204 2.520904 GCACTGAAGCGAGCCGATC 61.521 63.158 0.00 0.00 0.00 3.69
2155 2205 2.510238 GCACTGAAGCGAGCCGAT 60.510 61.111 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.