Multiple sequence alignment - TraesCS2A01G277900

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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 TraesCS2A01G277900 chr2A 100.000 4356 0 0 1 4356 460898731 460903086 0.000000e+00 8045
1 TraesCS2A01G277900 chr2B 92.156 2078 76 33 1709 3748 412400418 412402446 0.000000e+00 2854
2 TraesCS2A01G277900 chr2B 87.910 1373 79 39 374 1708 412399069 412400392 0.000000e+00 1535
3 TraesCS2A01G277900 chr2B 96.078 204 8 0 4153 4356 412402726 412402929 2.510000e-87 333
4 TraesCS2A01G277900 chr2D 90.743 2031 76 33 405 2361 346574230 346576222 0.000000e+00 2606
5 TraesCS2A01G277900 chr2D 94.258 1550 50 26 2343 3871 346576242 346577773 0.000000e+00 2333
6 TraesCS2A01G277900 chr2D 90.192 520 13 14 3873 4356 346578013 346578530 1.020000e-180 643
7 TraesCS2A01G277900 chr2D 89.231 260 26 2 1 259 25848682 25848940 1.510000e-84 324
8 TraesCS2A01G277900 chr7D 89.507 1096 101 8 2367 3456 91679601 91678514 0.000000e+00 1375
9 TraesCS2A01G277900 chr7D 90.060 332 31 1 1925 2256 91681370 91681041 3.110000e-116 429
10 TraesCS2A01G277900 chr7D 88.636 264 28 2 1 262 364627025 364627288 1.950000e-83 320
11 TraesCS2A01G277900 chr7D 81.385 231 27 12 1710 1936 91687732 91687514 1.610000e-39 174
12 TraesCS2A01G277900 chr7A 86.996 1215 125 30 2254 3458 93252478 93251287 0.000000e+00 1338
13 TraesCS2A01G277900 chr7A 84.112 321 36 8 1721 2036 93253161 93252851 3.290000e-76 296
14 TraesCS2A01G277900 chr7B 88.493 1095 112 9 2368 3456 43249060 43250146 0.000000e+00 1312
15 TraesCS2A01G277900 chr7B 85.625 480 57 8 1710 2186 43247528 43247998 1.090000e-135 494
16 TraesCS2A01G277900 chr7B 88.593 263 28 2 1 262 378921818 378922079 7.030000e-83 318
17 TraesCS2A01G277900 chr5D 85.013 754 97 8 2644 3381 543586797 543586044 0.000000e+00 752
18 TraesCS2A01G277900 chr5D 88.679 265 26 4 1 262 411105011 411104748 1.950000e-83 320
19 TraesCS2A01G277900 chr5D 92.105 152 12 0 1963 2114 543587234 543587083 9.490000e-52 215
20 TraesCS2A01G277900 chr5A 88.560 507 54 4 2574 3080 9593706 9593204 2.880000e-171 612
21 TraesCS2A01G277900 chr5A 88.083 386 42 4 1875 2256 9595523 9595138 5.140000e-124 455
22 TraesCS2A01G277900 chr5A 85.677 384 44 7 3084 3456 9590239 9589856 1.140000e-105 394
23 TraesCS2A01G277900 chr5A 85.000 340 36 9 2254 2588 9594544 9594215 9.030000e-87 331
24 TraesCS2A01G277900 chr4D 89.773 264 23 4 1 263 322076447 322076187 6.980000e-88 335
25 TraesCS2A01G277900 chr4D 88.679 265 27 3 1 263 380345731 380345468 1.950000e-83 320
26 TraesCS2A01G277900 chr6D 89.015 264 26 3 1 262 347168326 347168064 1.510000e-84 324
27 TraesCS2A01G277900 chr6D 88.679 265 25 5 1 263 352834344 352834083 7.030000e-83 318
28 TraesCS2A01G277900 chr6B 88.973 263 26 3 1 261 523507778 523508039 5.430000e-84 322


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 TraesCS2A01G277900 chr2A 460898731 460903086 4355 False 8045.000000 8045 100.0000 1 4356 1 chr2A.!!$F1 4355
1 TraesCS2A01G277900 chr2B 412399069 412402929 3860 False 1574.000000 2854 92.0480 374 4356 3 chr2B.!!$F1 3982
2 TraesCS2A01G277900 chr2D 346574230 346578530 4300 False 1860.666667 2606 91.7310 405 4356 3 chr2D.!!$F2 3951
3 TraesCS2A01G277900 chr7D 91678514 91681370 2856 True 902.000000 1375 89.7835 1925 3456 2 chr7D.!!$R2 1531
4 TraesCS2A01G277900 chr7A 93251287 93253161 1874 True 817.000000 1338 85.5540 1721 3458 2 chr7A.!!$R1 1737
5 TraesCS2A01G277900 chr7B 43247528 43250146 2618 False 903.000000 1312 87.0590 1710 3456 2 chr7B.!!$F2 1746
6 TraesCS2A01G277900 chr5D 543586044 543587234 1190 True 483.500000 752 88.5590 1963 3381 2 chr5D.!!$R2 1418
7 TraesCS2A01G277900 chr5A 9589856 9595523 5667 True 448.000000 612 86.8300 1875 3456 4 chr5A.!!$R1 1581

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
963 999 0.029567 CCACGATACTCACGAGGCTC 59.970 60.000 3.87 3.87 35.20 4.70 F
1993 2103 0.708802 TAGAAGTCCCCGTCCCTTCT 59.291 55.000 6.41 6.41 45.11 2.85 F
2363 3443 2.287849 TGTGTGTGTTTGTGTGTGTTGG 60.288 45.455 0.00 0.00 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2788 5127 0.188342 ACTTGGCACCAATGGACCTT 59.812 50.000 6.16 0.0 35.20 3.50 R
3257 8572 0.039708 AACGGGAACTTCGAGTCGAC 60.040 55.000 16.28 7.7 34.89 4.20 R
3725 9069 1.630369 TGCTTTGGGCTCTCAGTATGT 59.370 47.619 0.00 0.0 42.39 2.29 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
78 79 4.293694 CGAAGATCTCGTCGCAGG 57.706 61.111 3.99 0.00 42.89 4.85
79 80 1.298713 CGAAGATCTCGTCGCAGGG 60.299 63.158 3.99 0.00 42.89 4.45
80 81 1.715862 CGAAGATCTCGTCGCAGGGA 61.716 60.000 3.99 0.00 42.89 4.20
81 82 0.456221 GAAGATCTCGTCGCAGGGAA 59.544 55.000 0.00 0.00 0.00 3.97
82 83 1.067821 GAAGATCTCGTCGCAGGGAAT 59.932 52.381 0.00 0.00 0.00 3.01
83 84 1.115467 AGATCTCGTCGCAGGGAATT 58.885 50.000 0.00 0.00 0.00 2.17
84 85 1.482593 AGATCTCGTCGCAGGGAATTT 59.517 47.619 0.00 0.00 0.00 1.82
85 86 2.693591 AGATCTCGTCGCAGGGAATTTA 59.306 45.455 0.00 0.00 0.00 1.40
86 87 2.579207 TCTCGTCGCAGGGAATTTAG 57.421 50.000 0.00 0.00 0.00 1.85
87 88 1.822990 TCTCGTCGCAGGGAATTTAGT 59.177 47.619 0.00 0.00 0.00 2.24
88 89 1.927174 CTCGTCGCAGGGAATTTAGTG 59.073 52.381 0.00 0.00 0.00 2.74
89 90 1.006832 CGTCGCAGGGAATTTAGTGG 58.993 55.000 0.00 0.00 0.00 4.00
90 91 1.674817 CGTCGCAGGGAATTTAGTGGT 60.675 52.381 0.00 0.00 0.00 4.16
91 92 1.737793 GTCGCAGGGAATTTAGTGGTG 59.262 52.381 0.00 0.00 0.00 4.17
92 93 0.451783 CGCAGGGAATTTAGTGGTGC 59.548 55.000 0.00 0.00 0.00 5.01
93 94 1.544724 GCAGGGAATTTAGTGGTGCA 58.455 50.000 0.00 0.00 0.00 4.57
94 95 1.892474 GCAGGGAATTTAGTGGTGCAA 59.108 47.619 0.00 0.00 0.00 4.08
95 96 2.298729 GCAGGGAATTTAGTGGTGCAAA 59.701 45.455 0.00 0.00 0.00 3.68
96 97 3.860754 GCAGGGAATTTAGTGGTGCAAAC 60.861 47.826 0.00 0.00 0.00 2.93
97 98 2.556622 AGGGAATTTAGTGGTGCAAACG 59.443 45.455 0.00 0.00 0.00 3.60
98 99 2.352323 GGGAATTTAGTGGTGCAAACGG 60.352 50.000 0.00 0.00 0.00 4.44
99 100 2.554893 GGAATTTAGTGGTGCAAACGGA 59.445 45.455 0.00 0.00 0.00 4.69
100 101 3.192633 GGAATTTAGTGGTGCAAACGGAT 59.807 43.478 0.00 0.00 0.00 4.18
101 102 4.321675 GGAATTTAGTGGTGCAAACGGATT 60.322 41.667 0.00 0.00 0.00 3.01
102 103 4.864704 ATTTAGTGGTGCAAACGGATTT 57.135 36.364 0.00 0.00 0.00 2.17
103 104 4.657436 TTTAGTGGTGCAAACGGATTTT 57.343 36.364 0.00 0.00 0.00 1.82
104 105 2.793278 AGTGGTGCAAACGGATTTTC 57.207 45.000 0.00 0.00 0.00 2.29
105 106 2.028130 AGTGGTGCAAACGGATTTTCA 58.972 42.857 0.00 0.00 0.00 2.69
106 107 2.428890 AGTGGTGCAAACGGATTTTCAA 59.571 40.909 0.00 0.00 0.00 2.69
107 108 3.069443 AGTGGTGCAAACGGATTTTCAAT 59.931 39.130 0.00 0.00 0.00 2.57
108 109 3.428534 GTGGTGCAAACGGATTTTCAATC 59.571 43.478 0.00 0.00 0.00 2.67
109 110 2.661195 GGTGCAAACGGATTTTCAATCG 59.339 45.455 0.00 0.00 0.00 3.34
110 111 2.661195 GTGCAAACGGATTTTCAATCGG 59.339 45.455 0.00 3.25 0.00 4.18
111 112 2.554462 TGCAAACGGATTTTCAATCGGA 59.446 40.909 10.13 0.00 0.00 4.55
112 113 3.192422 TGCAAACGGATTTTCAATCGGAT 59.808 39.130 10.13 0.00 0.00 4.18
113 114 4.173256 GCAAACGGATTTTCAATCGGATT 58.827 39.130 10.13 0.00 0.00 3.01
114 115 5.106118 TGCAAACGGATTTTCAATCGGATTA 60.106 36.000 2.35 0.00 0.00 1.75
115 116 5.977129 GCAAACGGATTTTCAATCGGATTAT 59.023 36.000 2.35 0.00 0.00 1.28
116 117 6.475402 GCAAACGGATTTTCAATCGGATTATT 59.525 34.615 2.35 0.00 0.00 1.40
117 118 7.305993 GCAAACGGATTTTCAATCGGATTATTC 60.306 37.037 2.35 0.00 0.00 1.75
118 119 6.935741 ACGGATTTTCAATCGGATTATTCA 57.064 33.333 2.35 0.00 0.00 2.57
119 120 7.510549 ACGGATTTTCAATCGGATTATTCAT 57.489 32.000 2.35 0.00 0.00 2.57
120 121 7.940850 ACGGATTTTCAATCGGATTATTCATT 58.059 30.769 2.35 0.00 0.00 2.57
121 122 8.413229 ACGGATTTTCAATCGGATTATTCATTT 58.587 29.630 2.35 0.00 0.00 2.32
122 123 9.891828 CGGATTTTCAATCGGATTATTCATTTA 57.108 29.630 2.35 0.00 0.00 1.40
172 173 9.985730 AAAAATCTAAAAAGATTCTCACATGCA 57.014 25.926 1.35 0.00 37.52 3.96
174 175 9.582431 AAATCTAAAAAGATTCTCACATGCATG 57.418 29.630 25.09 25.09 37.52 4.06
175 176 6.558009 TCTAAAAAGATTCTCACATGCATGC 58.442 36.000 26.53 11.82 0.00 4.06
176 177 4.794278 AAAAGATTCTCACATGCATGCA 57.206 36.364 26.53 25.04 0.00 3.96
177 178 5.339008 AAAAGATTCTCACATGCATGCAT 57.661 34.783 27.46 27.46 37.08 3.96
187 188 2.802792 GCATGCATGCGGTGACAT 59.197 55.556 33.99 3.77 44.67 3.06
189 190 1.065109 CATGCATGCGGTGACATGG 59.935 57.895 14.93 0.00 46.14 3.66
190 191 2.777972 ATGCATGCGGTGACATGGC 61.778 57.895 14.09 0.00 46.14 4.40
191 192 4.541482 GCATGCGGTGACATGGCG 62.541 66.667 0.00 0.00 46.14 5.69
192 193 4.541482 CATGCGGTGACATGGCGC 62.541 66.667 2.56 2.56 43.05 6.53
196 197 3.490759 CGGTGACATGGCGCAGTC 61.491 66.667 15.38 14.65 35.37 3.51
197 198 2.046892 GGTGACATGGCGCAGTCT 60.047 61.111 15.38 0.00 35.81 3.24
198 199 1.218047 GGTGACATGGCGCAGTCTA 59.782 57.895 15.38 10.14 35.81 2.59
199 200 0.179073 GGTGACATGGCGCAGTCTAT 60.179 55.000 15.38 2.31 35.81 1.98
200 201 0.933097 GTGACATGGCGCAGTCTATG 59.067 55.000 21.84 14.31 35.81 2.23
201 202 0.536724 TGACATGGCGCAGTCTATGT 59.463 50.000 21.84 16.76 38.08 2.29
202 203 0.933097 GACATGGCGCAGTCTATGTG 59.067 55.000 10.83 0.00 42.62 3.21
203 204 0.250234 ACATGGCGCAGTCTATGTGT 59.750 50.000 10.83 0.00 41.71 3.72
204 205 1.339055 ACATGGCGCAGTCTATGTGTT 60.339 47.619 10.83 0.00 41.71 3.32
205 206 2.093711 ACATGGCGCAGTCTATGTGTTA 60.094 45.455 10.83 0.00 41.71 2.41
206 207 2.979814 TGGCGCAGTCTATGTGTTAT 57.020 45.000 10.83 0.00 41.71 1.89
207 208 4.202212 ACATGGCGCAGTCTATGTGTTATA 60.202 41.667 10.83 0.00 41.71 0.98
208 209 3.977427 TGGCGCAGTCTATGTGTTATAG 58.023 45.455 10.83 0.00 41.71 1.31
209 210 3.243737 TGGCGCAGTCTATGTGTTATAGG 60.244 47.826 10.83 0.00 41.71 2.57
210 211 3.005472 GGCGCAGTCTATGTGTTATAGGA 59.995 47.826 10.83 0.00 41.71 2.94
211 212 3.982058 GCGCAGTCTATGTGTTATAGGAC 59.018 47.826 0.30 0.00 41.71 3.85
212 213 4.219802 CGCAGTCTATGTGTTATAGGACG 58.780 47.826 0.00 0.00 34.56 4.79
213 214 4.261072 CGCAGTCTATGTGTTATAGGACGT 60.261 45.833 0.00 0.00 34.56 4.34
214 215 4.976731 GCAGTCTATGTGTTATAGGACGTG 59.023 45.833 0.00 0.00 0.00 4.49
215 216 5.450137 GCAGTCTATGTGTTATAGGACGTGT 60.450 44.000 0.00 0.00 0.00 4.49
216 217 5.971792 CAGTCTATGTGTTATAGGACGTGTG 59.028 44.000 0.00 0.00 0.00 3.82
217 218 5.067413 AGTCTATGTGTTATAGGACGTGTGG 59.933 44.000 0.00 0.00 0.00 4.17
218 219 5.066893 GTCTATGTGTTATAGGACGTGTGGA 59.933 44.000 0.00 0.00 0.00 4.02
219 220 3.581024 TGTGTTATAGGACGTGTGGAC 57.419 47.619 0.00 0.00 0.00 4.02
228 229 3.326109 CGTGTGGACGGGTTTGAC 58.674 61.111 0.00 0.00 42.18 3.18
229 230 1.227438 CGTGTGGACGGGTTTGACT 60.227 57.895 0.00 0.00 42.18 3.41
230 231 1.219522 CGTGTGGACGGGTTTGACTC 61.220 60.000 0.00 0.00 42.18 3.36
231 232 0.883370 GTGTGGACGGGTTTGACTCC 60.883 60.000 0.00 0.00 0.00 3.85
232 233 1.302271 GTGGACGGGTTTGACTCCC 60.302 63.158 0.00 0.00 41.41 4.30
233 234 1.766864 TGGACGGGTTTGACTCCCA 60.767 57.895 1.91 0.00 44.81 4.37
234 235 1.131303 TGGACGGGTTTGACTCCCAT 61.131 55.000 1.91 0.00 44.81 4.00
235 236 0.392595 GGACGGGTTTGACTCCCATC 60.393 60.000 1.91 0.00 44.81 3.51
236 237 0.323629 GACGGGTTTGACTCCCATCA 59.676 55.000 1.91 0.00 44.81 3.07
237 238 0.036306 ACGGGTTTGACTCCCATCAC 59.964 55.000 1.91 0.00 44.81 3.06
238 239 0.036164 CGGGTTTGACTCCCATCACA 59.964 55.000 1.91 0.00 44.81 3.58
239 240 1.534729 GGGTTTGACTCCCATCACAC 58.465 55.000 0.00 0.00 44.05 3.82
240 241 1.156736 GGTTTGACTCCCATCACACG 58.843 55.000 0.00 0.00 31.30 4.49
241 242 1.542547 GGTTTGACTCCCATCACACGT 60.543 52.381 0.00 0.00 31.30 4.49
242 243 2.289195 GGTTTGACTCCCATCACACGTA 60.289 50.000 0.00 0.00 31.30 3.57
243 244 3.596214 GTTTGACTCCCATCACACGTAT 58.404 45.455 0.00 0.00 0.00 3.06
244 245 2.959507 TGACTCCCATCACACGTATG 57.040 50.000 0.00 0.00 0.00 2.39
245 246 1.480545 TGACTCCCATCACACGTATGG 59.519 52.381 8.61 8.61 43.06 2.74
246 247 1.754803 GACTCCCATCACACGTATGGA 59.245 52.381 15.96 1.67 45.77 3.41
247 248 1.480954 ACTCCCATCACACGTATGGAC 59.519 52.381 15.96 0.00 45.77 4.02
267 268 3.103793 CGTTAGCGTTGTCCTTGATTG 57.896 47.619 0.00 0.00 0.00 2.67
268 269 2.734606 CGTTAGCGTTGTCCTTGATTGA 59.265 45.455 0.00 0.00 0.00 2.57
269 270 3.185594 CGTTAGCGTTGTCCTTGATTGAA 59.814 43.478 0.00 0.00 0.00 2.69
270 271 4.319190 CGTTAGCGTTGTCCTTGATTGAAA 60.319 41.667 0.00 0.00 0.00 2.69
271 272 3.626028 AGCGTTGTCCTTGATTGAAAC 57.374 42.857 0.00 0.00 0.00 2.78
272 273 2.948979 AGCGTTGTCCTTGATTGAAACA 59.051 40.909 0.00 0.00 0.00 2.83
273 274 3.569701 AGCGTTGTCCTTGATTGAAACAT 59.430 39.130 0.00 0.00 0.00 2.71
274 275 4.037923 AGCGTTGTCCTTGATTGAAACATT 59.962 37.500 0.00 0.00 0.00 2.71
275 276 4.744631 GCGTTGTCCTTGATTGAAACATTT 59.255 37.500 0.00 0.00 0.00 2.32
276 277 5.332506 GCGTTGTCCTTGATTGAAACATTTG 60.333 40.000 0.00 0.00 0.00 2.32
277 278 5.976534 CGTTGTCCTTGATTGAAACATTTGA 59.023 36.000 0.00 0.00 0.00 2.69
278 279 6.475076 CGTTGTCCTTGATTGAAACATTTGAA 59.525 34.615 0.00 0.00 0.00 2.69
279 280 7.306167 CGTTGTCCTTGATTGAAACATTTGAAG 60.306 37.037 0.00 0.00 0.00 3.02
280 281 7.111247 TGTCCTTGATTGAAACATTTGAAGT 57.889 32.000 0.00 0.00 0.00 3.01
281 282 8.231692 TGTCCTTGATTGAAACATTTGAAGTA 57.768 30.769 0.00 0.00 0.00 2.24
282 283 8.352201 TGTCCTTGATTGAAACATTTGAAGTAG 58.648 33.333 0.00 0.00 0.00 2.57
283 284 8.567948 GTCCTTGATTGAAACATTTGAAGTAGA 58.432 33.333 0.00 0.00 0.00 2.59
284 285 9.130661 TCCTTGATTGAAACATTTGAAGTAGAA 57.869 29.630 0.00 0.00 0.00 2.10
285 286 9.918630 CCTTGATTGAAACATTTGAAGTAGAAT 57.081 29.630 0.00 0.00 0.00 2.40
294 295 9.778993 AAACATTTGAAGTAGAATCAATGATCG 57.221 29.630 0.00 0.00 36.72 3.69
295 296 8.498054 ACATTTGAAGTAGAATCAATGATCGT 57.502 30.769 0.00 0.00 36.72 3.73
296 297 8.950210 ACATTTGAAGTAGAATCAATGATCGTT 58.050 29.630 0.00 0.00 36.72 3.85
297 298 9.778993 CATTTGAAGTAGAATCAATGATCGTTT 57.221 29.630 0.00 0.00 36.72 3.60
306 307 8.722480 AGAATCAATGATCGTTTAATCAGACA 57.278 30.769 0.00 0.00 38.96 3.41
307 308 8.607459 AGAATCAATGATCGTTTAATCAGACAC 58.393 33.333 0.00 0.00 38.96 3.67
308 309 8.498054 AATCAATGATCGTTTAATCAGACACT 57.502 30.769 0.00 0.00 38.96 3.55
309 310 7.525688 TCAATGATCGTTTAATCAGACACTC 57.474 36.000 0.00 0.00 38.96 3.51
310 311 7.323420 TCAATGATCGTTTAATCAGACACTCT 58.677 34.615 0.00 0.00 38.96 3.24
311 312 7.819415 TCAATGATCGTTTAATCAGACACTCTT 59.181 33.333 0.00 0.00 38.96 2.85
312 313 8.446273 CAATGATCGTTTAATCAGACACTCTTT 58.554 33.333 0.00 0.00 38.96 2.52
313 314 9.653287 AATGATCGTTTAATCAGACACTCTTTA 57.347 29.630 0.00 0.00 38.96 1.85
314 315 9.653287 ATGATCGTTTAATCAGACACTCTTTAA 57.347 29.630 0.00 0.00 38.96 1.52
315 316 9.483916 TGATCGTTTAATCAGACACTCTTTAAA 57.516 29.630 0.00 0.00 32.03 1.52
324 325 7.566760 TCAGACACTCTTTAAAAATTGAGCA 57.433 32.000 2.90 0.00 0.00 4.26
325 326 7.995289 TCAGACACTCTTTAAAAATTGAGCAA 58.005 30.769 2.90 0.00 0.00 3.91
326 327 8.632679 TCAGACACTCTTTAAAAATTGAGCAAT 58.367 29.630 2.90 0.00 0.00 3.56
327 328 8.909671 CAGACACTCTTTAAAAATTGAGCAATC 58.090 33.333 0.00 0.03 0.00 2.67
328 329 8.854117 AGACACTCTTTAAAAATTGAGCAATCT 58.146 29.630 0.00 1.82 0.00 2.40
359 360 6.934561 ATTTTTCTCTCTTTATTGCAACGC 57.065 33.333 0.00 0.00 0.00 4.84
360 361 5.431420 TTTTCTCTCTTTATTGCAACGCA 57.569 34.783 0.00 0.00 36.47 5.24
361 362 4.404507 TTCTCTCTTTATTGCAACGCAC 57.595 40.909 0.00 0.00 38.71 5.34
362 363 2.411748 TCTCTCTTTATTGCAACGCACG 59.588 45.455 0.00 0.00 38.71 5.34
363 364 2.409012 TCTCTTTATTGCAACGCACGA 58.591 42.857 0.00 0.00 38.71 4.35
364 365 2.411748 TCTCTTTATTGCAACGCACGAG 59.588 45.455 0.00 4.83 38.71 4.18
365 366 1.136085 TCTTTATTGCAACGCACGAGC 60.136 47.619 0.00 0.00 38.71 5.03
366 367 0.588737 TTTATTGCAACGCACGAGCA 59.411 45.000 0.00 9.96 38.71 4.26
367 368 0.801872 TTATTGCAACGCACGAGCAT 59.198 45.000 0.00 0.00 38.71 3.79
368 369 0.096802 TATTGCAACGCACGAGCATG 59.903 50.000 0.00 4.49 38.71 4.06
369 370 1.855213 ATTGCAACGCACGAGCATGT 61.855 50.000 0.00 0.00 38.71 3.21
370 371 2.057654 TTGCAACGCACGAGCATGTT 62.058 50.000 13.57 0.00 38.71 2.71
371 372 1.370414 GCAACGCACGAGCATGTTT 60.370 52.632 5.50 0.00 42.27 2.83
372 373 0.110419 GCAACGCACGAGCATGTTTA 60.110 50.000 5.50 0.00 42.27 2.01
384 385 6.032775 CACGAGCATGTTTAAGCAAAATACAG 59.967 38.462 0.00 0.00 0.00 2.74
402 403 3.056313 GAAGCTTGCGCATGTCCCC 62.056 63.158 22.50 7.68 39.10 4.81
427 428 0.896940 AAGGTTGGCTGGTGCAGATG 60.897 55.000 0.00 0.00 41.91 2.90
446 447 2.656069 GCGGAAGTACCTGGGCTGA 61.656 63.158 0.00 0.00 36.31 4.26
645 679 0.165944 GACCAAACGAGCCAACATCG 59.834 55.000 0.00 0.00 45.54 3.84
685 719 1.293498 GTGTCAGCCCAGTCACGAT 59.707 57.895 0.00 0.00 0.00 3.73
744 780 0.034380 GGCCTTCTAGAACCAACCCC 60.034 60.000 0.00 0.00 0.00 4.95
751 787 4.682778 TCTAGAACCAACCCCGATATTG 57.317 45.455 0.00 0.00 0.00 1.90
918 954 4.592192 ATCTCCGGCCACGCATCG 62.592 66.667 2.24 0.00 39.22 3.84
963 999 0.029567 CCACGATACTCACGAGGCTC 59.970 60.000 3.87 3.87 35.20 4.70
1099 1138 6.476053 CCTCAAGGTAAAGAGTTACTATTCGC 59.524 42.308 0.00 0.00 39.73 4.70
1118 1157 1.079336 GGTAGCGGGTCGAAGCTTT 60.079 57.895 14.97 0.00 44.15 3.51
1124 1163 2.028748 AGCGGGTCGAAGCTTTTTAGTA 60.029 45.455 0.00 0.00 41.52 1.82
1159 1198 3.627218 GGCGCGCGAGATTGGTAC 61.627 66.667 37.18 12.28 0.00 3.34
1215 1255 7.177921 ACTGGCTAATTGACTACAGTTAGTACA 59.822 37.037 11.79 10.49 43.48 2.90
1343 1397 5.474825 GACAAGTAGTCAAGAAGCTAGCTT 58.525 41.667 29.71 29.71 46.77 3.74
1442 1517 5.221945 TGGTTTCTATGGTGGTGATGTGTTA 60.222 40.000 0.00 0.00 0.00 2.41
1453 1528 5.014202 TGGTGATGTGTTACACTAGCTAGA 58.986 41.667 27.45 1.72 37.22 2.43
1454 1529 5.656859 TGGTGATGTGTTACACTAGCTAGAT 59.343 40.000 27.45 16.25 37.22 1.98
1455 1530 6.154534 TGGTGATGTGTTACACTAGCTAGATT 59.845 38.462 27.45 14.82 37.22 2.40
1456 1531 6.477033 GGTGATGTGTTACACTAGCTAGATTG 59.523 42.308 27.45 17.58 37.22 2.67
1537 1612 6.537301 CAGTGGAATTAGTTAAATAGGTCGCA 59.463 38.462 0.00 0.00 0.00 5.10
1550 1625 1.361668 GGTCGCACATACCTGCTGTG 61.362 60.000 0.00 0.00 45.39 3.66
1660 1735 8.753498 CGAGTCAGTCGGAAATTTATTATTTG 57.247 34.615 0.00 0.00 45.58 2.32
1795 1896 9.635404 TTCTTTTCACAAGAACCCTATTTTAGA 57.365 29.630 0.00 0.00 32.39 2.10
1803 1904 9.495382 ACAAGAACCCTATTTTAGACTAGAGAT 57.505 33.333 0.00 0.00 0.00 2.75
1804 1905 9.974980 CAAGAACCCTATTTTAGACTAGAGATC 57.025 37.037 0.00 0.00 0.00 2.75
1954 2062 7.331791 AGAACCTATAAACCTGTGATTCTGAC 58.668 38.462 0.00 0.00 0.00 3.51
1993 2103 0.708802 TAGAAGTCCCCGTCCCTTCT 59.291 55.000 6.41 6.41 45.11 2.85
2075 2185 7.989739 CTGGAAGATACAGAAAGGGGACTTGA 61.990 46.154 0.00 0.00 45.05 3.02
2196 2611 4.101114 TCTGTTTGGAGGCTTCCTATGTA 58.899 43.478 16.82 0.00 44.36 2.29
2197 2612 4.721776 TCTGTTTGGAGGCTTCCTATGTAT 59.278 41.667 16.82 0.00 44.36 2.29
2363 3443 2.287849 TGTGTGTGTTTGTGTGTGTTGG 60.288 45.455 0.00 0.00 0.00 3.77
2415 4222 3.004734 GCATCTCTTCTCTACTGCTCCTC 59.995 52.174 0.00 0.00 0.00 3.71
2788 5127 2.997315 ACTGCGCTCCAGGCACTA 60.997 61.111 9.73 0.00 46.14 2.74
3095 8407 4.783621 TGCTCAGTGATGCCGGGC 62.784 66.667 13.32 13.32 0.00 6.13
3152 8464 2.435410 CATCTGCGCTGCACAGGA 60.435 61.111 16.79 5.27 35.78 3.86
3257 8572 2.328099 GGCAAGCTGAAGACGGTGG 61.328 63.158 0.00 0.00 0.00 4.61
3283 8598 1.344942 CGAAGTTCCCGTTGAGCGAG 61.345 60.000 0.00 0.00 44.77 5.03
3288 8603 4.069232 CCCGTTGAGCGAGGCAGA 62.069 66.667 0.00 0.00 44.77 4.26
3371 8686 1.005557 GCTGATCGTCGTCAATGCTTC 60.006 52.381 0.00 0.00 0.00 3.86
3398 8723 6.273825 AGTATTAAGGACTTGCATACAGACG 58.726 40.000 13.95 0.00 0.00 4.18
3460 8792 3.131400 ACTTGTGCGTTTGTTTATTGGGT 59.869 39.130 0.00 0.00 0.00 4.51
3461 8793 3.085443 TGTGCGTTTGTTTATTGGGTG 57.915 42.857 0.00 0.00 0.00 4.61
3462 8794 2.688446 TGTGCGTTTGTTTATTGGGTGA 59.312 40.909 0.00 0.00 0.00 4.02
3463 8795 3.319405 TGTGCGTTTGTTTATTGGGTGAT 59.681 39.130 0.00 0.00 0.00 3.06
3464 8796 3.672867 GTGCGTTTGTTTATTGGGTGATG 59.327 43.478 0.00 0.00 0.00 3.07
3479 8811 4.007659 GGGTGATGGTTCGTTTATTCAGT 58.992 43.478 0.00 0.00 0.00 3.41
3484 8816 8.885722 GGTGATGGTTCGTTTATTCAGTTTATA 58.114 33.333 0.00 0.00 0.00 0.98
3725 9069 4.090761 ACCTCTGCAGAAGAACAAATCA 57.909 40.909 19.22 0.00 33.37 2.57
3726 9070 3.817647 ACCTCTGCAGAAGAACAAATCAC 59.182 43.478 19.22 0.00 33.37 3.06
3764 9108 0.686769 AGAACAGTAGGGGCGTAGGG 60.687 60.000 0.00 0.00 0.00 3.53
3809 9153 9.841880 GACCAAATTAGGAAGTTCAATTCTAAC 57.158 33.333 5.01 0.00 0.00 2.34
3837 9181 3.559171 GGGACTGTGATGCCTTTTAGTCA 60.559 47.826 0.00 0.00 37.01 3.41
3844 9188 4.646492 GTGATGCCTTTTAGTCATTCCCAT 59.354 41.667 0.00 0.00 0.00 4.00
3851 9195 7.453126 TGCCTTTTAGTCATTCCCATAAAAAGA 59.547 33.333 0.00 0.00 35.50 2.52
3861 9205 4.810345 TCCCATAAAAAGAGGTTTGGTGT 58.190 39.130 0.00 0.00 0.00 4.16
3871 9215 9.594478 AAAAAGAGGTTTGGTGTACTAATTTTG 57.406 29.630 0.00 0.00 0.00 2.44
3944 9527 1.802960 ACAGCAAATCAAGCTCGTGAG 59.197 47.619 0.00 0.00 41.14 3.51
3952 9535 0.738975 CAAGCTCGTGAGGATACGGA 59.261 55.000 0.00 0.00 43.85 4.69
3998 9582 3.512329 TGCGAATCAGGTGACCTAGTTTA 59.488 43.478 2.59 0.00 29.64 2.01
3999 9583 4.161565 TGCGAATCAGGTGACCTAGTTTAT 59.838 41.667 2.59 0.00 29.64 1.40
4088 9678 4.487714 AGTTATGTCGTGGGATGACAAT 57.512 40.909 2.87 0.00 46.03 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 0.456221 TTCCCTGCGACGAGATCTTC 59.544 55.000 0.00 0.00 0.00 2.87
63 64 1.115467 ATTCCCTGCGACGAGATCTT 58.885 50.000 0.00 0.00 0.00 2.40
64 65 1.115467 AATTCCCTGCGACGAGATCT 58.885 50.000 0.00 0.00 0.00 2.75
65 66 1.941325 AAATTCCCTGCGACGAGATC 58.059 50.000 0.00 0.00 0.00 2.75
66 67 2.431057 ACTAAATTCCCTGCGACGAGAT 59.569 45.455 0.00 0.00 0.00 2.75
67 68 1.822990 ACTAAATTCCCTGCGACGAGA 59.177 47.619 0.00 0.00 0.00 4.04
68 69 1.927174 CACTAAATTCCCTGCGACGAG 59.073 52.381 0.00 0.00 0.00 4.18
69 70 1.404986 CCACTAAATTCCCTGCGACGA 60.405 52.381 0.00 0.00 0.00 4.20
70 71 1.006832 CCACTAAATTCCCTGCGACG 58.993 55.000 0.00 0.00 0.00 5.12
71 72 1.737793 CACCACTAAATTCCCTGCGAC 59.262 52.381 0.00 0.00 0.00 5.19
72 73 1.948611 GCACCACTAAATTCCCTGCGA 60.949 52.381 0.00 0.00 0.00 5.10
73 74 0.451783 GCACCACTAAATTCCCTGCG 59.548 55.000 0.00 0.00 0.00 5.18
74 75 1.544724 TGCACCACTAAATTCCCTGC 58.455 50.000 0.00 0.00 0.00 4.85
75 76 3.611530 CGTTTGCACCACTAAATTCCCTG 60.612 47.826 0.00 0.00 0.00 4.45
76 77 2.556622 CGTTTGCACCACTAAATTCCCT 59.443 45.455 0.00 0.00 0.00 4.20
77 78 2.352323 CCGTTTGCACCACTAAATTCCC 60.352 50.000 0.00 0.00 0.00 3.97
78 79 2.554893 TCCGTTTGCACCACTAAATTCC 59.445 45.455 0.00 0.00 0.00 3.01
79 80 3.907894 TCCGTTTGCACCACTAAATTC 57.092 42.857 0.00 0.00 0.00 2.17
80 81 4.864704 AATCCGTTTGCACCACTAAATT 57.135 36.364 0.00 0.00 0.00 1.82
81 82 4.864704 AAATCCGTTTGCACCACTAAAT 57.135 36.364 0.00 0.00 0.00 1.40
82 83 4.098044 TGAAAATCCGTTTGCACCACTAAA 59.902 37.500 0.00 0.00 27.59 1.85
83 84 3.632604 TGAAAATCCGTTTGCACCACTAA 59.367 39.130 0.00 0.00 27.59 2.24
84 85 3.215151 TGAAAATCCGTTTGCACCACTA 58.785 40.909 0.00 0.00 27.59 2.74
85 86 2.028130 TGAAAATCCGTTTGCACCACT 58.972 42.857 0.00 0.00 27.59 4.00
86 87 2.500509 TGAAAATCCGTTTGCACCAC 57.499 45.000 0.00 0.00 27.59 4.16
87 88 3.648009 GATTGAAAATCCGTTTGCACCA 58.352 40.909 0.00 0.00 32.52 4.17
88 89 2.661195 CGATTGAAAATCCGTTTGCACC 59.339 45.455 0.00 0.00 32.52 5.01
89 90 2.661195 CCGATTGAAAATCCGTTTGCAC 59.339 45.455 0.00 0.00 32.52 4.57
90 91 2.554462 TCCGATTGAAAATCCGTTTGCA 59.446 40.909 0.00 0.00 30.84 4.08
91 92 3.210358 TCCGATTGAAAATCCGTTTGC 57.790 42.857 0.00 0.00 0.00 3.68
92 93 7.700234 TGAATAATCCGATTGAAAATCCGTTTG 59.300 33.333 3.73 0.00 0.00 2.93
93 94 7.767261 TGAATAATCCGATTGAAAATCCGTTT 58.233 30.769 3.73 0.00 0.00 3.60
94 95 7.328277 TGAATAATCCGATTGAAAATCCGTT 57.672 32.000 3.73 0.00 0.00 4.44
95 96 6.935741 TGAATAATCCGATTGAAAATCCGT 57.064 33.333 3.73 0.00 0.00 4.69
96 97 8.801715 AAATGAATAATCCGATTGAAAATCCG 57.198 30.769 3.73 0.00 0.00 4.18
146 147 9.985730 TGCATGTGAGAATCTTTTTAGATTTTT 57.014 25.926 2.26 0.00 38.50 1.94
148 149 9.582431 CATGCATGTGAGAATCTTTTTAGATTT 57.418 29.630 18.91 0.00 38.50 2.17
149 150 7.705325 GCATGCATGTGAGAATCTTTTTAGATT 59.295 33.333 26.79 0.26 40.81 2.40
150 151 7.147966 TGCATGCATGTGAGAATCTTTTTAGAT 60.148 33.333 26.79 0.00 34.92 1.98
151 152 6.151480 TGCATGCATGTGAGAATCTTTTTAGA 59.849 34.615 26.79 0.00 34.92 2.10
152 153 6.327154 TGCATGCATGTGAGAATCTTTTTAG 58.673 36.000 26.79 0.00 34.92 1.85
153 154 6.270156 TGCATGCATGTGAGAATCTTTTTA 57.730 33.333 26.79 0.00 34.92 1.52
154 155 5.142061 TGCATGCATGTGAGAATCTTTTT 57.858 34.783 26.79 0.00 34.92 1.94
155 156 4.794278 TGCATGCATGTGAGAATCTTTT 57.206 36.364 26.79 0.00 34.92 2.27
156 157 4.682787 CATGCATGCATGTGAGAATCTTT 58.317 39.130 40.30 13.48 46.20 2.52
157 158 4.307443 CATGCATGCATGTGAGAATCTT 57.693 40.909 40.30 13.68 46.20 2.40
158 159 3.990318 CATGCATGCATGTGAGAATCT 57.010 42.857 40.30 14.19 46.20 2.40
171 172 1.065109 CCATGTCACCGCATGCATG 59.935 57.895 22.70 22.70 43.46 4.06
172 173 2.777972 GCCATGTCACCGCATGCAT 61.778 57.895 19.57 1.32 43.46 3.96
173 174 3.442167 GCCATGTCACCGCATGCA 61.442 61.111 19.57 0.00 43.46 3.96
174 175 4.541482 CGCCATGTCACCGCATGC 62.541 66.667 7.91 7.91 43.46 4.06
175 176 4.541482 GCGCCATGTCACCGCATG 62.541 66.667 0.00 0.00 46.32 4.06
179 180 2.557059 TAGACTGCGCCATGTCACCG 62.557 60.000 21.38 0.00 35.81 4.94
180 181 0.179073 ATAGACTGCGCCATGTCACC 60.179 55.000 21.38 2.47 35.81 4.02
181 182 0.933097 CATAGACTGCGCCATGTCAC 59.067 55.000 21.38 3.04 35.81 3.67
182 183 0.536724 ACATAGACTGCGCCATGTCA 59.463 50.000 21.38 11.53 35.81 3.58
183 184 0.933097 CACATAGACTGCGCCATGTC 59.067 55.000 4.18 11.06 29.31 3.06
184 185 0.250234 ACACATAGACTGCGCCATGT 59.750 50.000 4.18 0.19 31.91 3.21
185 186 1.372582 AACACATAGACTGCGCCATG 58.627 50.000 4.18 3.20 0.00 3.66
186 187 2.979814 TAACACATAGACTGCGCCAT 57.020 45.000 4.18 0.00 0.00 4.40
187 188 2.979814 ATAACACATAGACTGCGCCA 57.020 45.000 4.18 0.00 0.00 5.69
188 189 3.005472 TCCTATAACACATAGACTGCGCC 59.995 47.826 4.18 0.00 0.00 6.53
189 190 3.982058 GTCCTATAACACATAGACTGCGC 59.018 47.826 0.00 0.00 0.00 6.09
190 191 4.219802 CGTCCTATAACACATAGACTGCG 58.780 47.826 0.00 0.00 0.00 5.18
191 192 4.976731 CACGTCCTATAACACATAGACTGC 59.023 45.833 0.00 0.00 0.00 4.40
192 193 5.971792 CACACGTCCTATAACACATAGACTG 59.028 44.000 0.00 0.00 0.00 3.51
193 194 5.067413 CCACACGTCCTATAACACATAGACT 59.933 44.000 0.00 0.00 0.00 3.24
194 195 5.066893 TCCACACGTCCTATAACACATAGAC 59.933 44.000 0.00 0.00 0.00 2.59
195 196 5.066893 GTCCACACGTCCTATAACACATAGA 59.933 44.000 0.00 0.00 0.00 1.98
196 197 5.279384 GTCCACACGTCCTATAACACATAG 58.721 45.833 0.00 0.00 0.00 2.23
197 198 4.201940 CGTCCACACGTCCTATAACACATA 60.202 45.833 0.00 0.00 41.42 2.29
198 199 3.428452 CGTCCACACGTCCTATAACACAT 60.428 47.826 0.00 0.00 41.42 3.21
199 200 2.095110 CGTCCACACGTCCTATAACACA 60.095 50.000 0.00 0.00 41.42 3.72
200 201 2.523015 CGTCCACACGTCCTATAACAC 58.477 52.381 0.00 0.00 41.42 3.32
201 202 1.473677 CCGTCCACACGTCCTATAACA 59.526 52.381 0.00 0.00 45.17 2.41
202 203 1.202336 CCCGTCCACACGTCCTATAAC 60.202 57.143 0.00 0.00 45.17 1.89
203 204 1.105457 CCCGTCCACACGTCCTATAA 58.895 55.000 0.00 0.00 45.17 0.98
204 205 0.034186 ACCCGTCCACACGTCCTATA 60.034 55.000 0.00 0.00 45.17 1.31
205 206 0.901580 AACCCGTCCACACGTCCTAT 60.902 55.000 0.00 0.00 45.17 2.57
206 207 1.114722 AAACCCGTCCACACGTCCTA 61.115 55.000 0.00 0.00 45.17 2.94
207 208 2.437396 AAACCCGTCCACACGTCCT 61.437 57.895 0.00 0.00 45.17 3.85
208 209 2.109593 AAACCCGTCCACACGTCC 59.890 61.111 0.00 0.00 45.17 4.79
209 210 1.227321 TCAAACCCGTCCACACGTC 60.227 57.895 0.00 0.00 45.17 4.34
210 211 1.522130 GTCAAACCCGTCCACACGT 60.522 57.895 0.00 0.00 45.17 4.49
211 212 1.219522 GAGTCAAACCCGTCCACACG 61.220 60.000 0.00 0.00 46.29 4.49
212 213 0.883370 GGAGTCAAACCCGTCCACAC 60.883 60.000 0.00 0.00 0.00 3.82
213 214 1.448497 GGAGTCAAACCCGTCCACA 59.552 57.895 0.00 0.00 0.00 4.17
214 215 1.302271 GGGAGTCAAACCCGTCCAC 60.302 63.158 0.00 0.00 37.85 4.02
215 216 3.153825 GGGAGTCAAACCCGTCCA 58.846 61.111 0.00 0.00 37.85 4.02
220 221 1.534729 GTGTGATGGGAGTCAAACCC 58.465 55.000 0.00 0.00 46.87 4.11
221 222 1.156736 CGTGTGATGGGAGTCAAACC 58.843 55.000 0.00 0.00 33.62 3.27
222 223 1.878953 ACGTGTGATGGGAGTCAAAC 58.121 50.000 0.00 0.00 33.80 2.93
223 224 3.595173 CATACGTGTGATGGGAGTCAAA 58.405 45.455 6.42 0.00 0.00 2.69
224 225 2.093711 CCATACGTGTGATGGGAGTCAA 60.094 50.000 14.51 0.00 40.29 3.18
225 226 1.480545 CCATACGTGTGATGGGAGTCA 59.519 52.381 14.51 0.00 40.29 3.41
226 227 1.754803 TCCATACGTGTGATGGGAGTC 59.245 52.381 14.51 0.00 43.58 3.36
227 228 1.480954 GTCCATACGTGTGATGGGAGT 59.519 52.381 14.51 0.00 43.58 3.85
228 229 1.536072 CGTCCATACGTGTGATGGGAG 60.536 57.143 14.51 5.62 43.58 4.30
229 230 0.458260 CGTCCATACGTGTGATGGGA 59.542 55.000 14.51 0.00 43.58 4.37
230 231 2.971997 CGTCCATACGTGTGATGGG 58.028 57.895 14.51 0.00 43.58 4.00
248 249 4.742438 TTCAATCAAGGACAACGCTAAC 57.258 40.909 0.00 0.00 0.00 2.34
249 250 4.576873 TGTTTCAATCAAGGACAACGCTAA 59.423 37.500 0.00 0.00 0.00 3.09
250 251 4.130857 TGTTTCAATCAAGGACAACGCTA 58.869 39.130 0.00 0.00 0.00 4.26
251 252 2.948979 TGTTTCAATCAAGGACAACGCT 59.051 40.909 0.00 0.00 0.00 5.07
252 253 3.347958 TGTTTCAATCAAGGACAACGC 57.652 42.857 0.00 0.00 0.00 4.84
253 254 5.976534 TCAAATGTTTCAATCAAGGACAACG 59.023 36.000 0.00 0.00 0.00 4.10
254 255 7.492344 ACTTCAAATGTTTCAATCAAGGACAAC 59.508 33.333 0.00 0.00 0.00 3.32
255 256 7.555087 ACTTCAAATGTTTCAATCAAGGACAA 58.445 30.769 0.00 0.00 0.00 3.18
256 257 7.111247 ACTTCAAATGTTTCAATCAAGGACA 57.889 32.000 0.00 0.00 0.00 4.02
257 258 8.567948 TCTACTTCAAATGTTTCAATCAAGGAC 58.432 33.333 0.00 0.00 0.00 3.85
258 259 8.690203 TCTACTTCAAATGTTTCAATCAAGGA 57.310 30.769 0.00 0.00 0.00 3.36
259 260 9.918630 ATTCTACTTCAAATGTTTCAATCAAGG 57.081 29.630 0.00 0.00 0.00 3.61
268 269 9.778993 CGATCATTGATTCTACTTCAAATGTTT 57.221 29.630 0.00 0.00 36.72 2.83
269 270 8.950210 ACGATCATTGATTCTACTTCAAATGTT 58.050 29.630 0.00 0.00 36.72 2.71
270 271 8.498054 ACGATCATTGATTCTACTTCAAATGT 57.502 30.769 0.00 0.00 36.72 2.71
271 272 9.778993 AAACGATCATTGATTCTACTTCAAATG 57.221 29.630 0.00 0.00 36.72 2.32
280 281 9.816354 TGTCTGATTAAACGATCATTGATTCTA 57.184 29.630 0.00 0.00 35.62 2.10
281 282 8.607459 GTGTCTGATTAAACGATCATTGATTCT 58.393 33.333 0.00 0.00 35.62 2.40
282 283 8.607459 AGTGTCTGATTAAACGATCATTGATTC 58.393 33.333 0.00 0.00 35.62 2.52
283 284 8.498054 AGTGTCTGATTAAACGATCATTGATT 57.502 30.769 0.00 0.00 35.62 2.57
284 285 7.984050 AGAGTGTCTGATTAAACGATCATTGAT 59.016 33.333 0.00 0.00 35.62 2.57
285 286 7.323420 AGAGTGTCTGATTAAACGATCATTGA 58.677 34.615 0.00 0.00 35.62 2.57
286 287 7.531280 AGAGTGTCTGATTAAACGATCATTG 57.469 36.000 0.00 0.00 35.62 2.82
287 288 8.553459 AAAGAGTGTCTGATTAAACGATCATT 57.447 30.769 0.00 0.00 35.62 2.57
288 289 9.653287 TTAAAGAGTGTCTGATTAAACGATCAT 57.347 29.630 0.00 0.00 35.62 2.45
289 290 9.483916 TTTAAAGAGTGTCTGATTAAACGATCA 57.516 29.630 0.00 0.00 34.96 2.92
298 299 8.632679 TGCTCAATTTTTAAAGAGTGTCTGATT 58.367 29.630 6.14 0.00 0.00 2.57
299 300 8.169977 TGCTCAATTTTTAAAGAGTGTCTGAT 57.830 30.769 6.14 0.00 0.00 2.90
300 301 7.566760 TGCTCAATTTTTAAAGAGTGTCTGA 57.433 32.000 6.14 0.00 0.00 3.27
301 302 8.807667 ATTGCTCAATTTTTAAAGAGTGTCTG 57.192 30.769 6.14 0.98 0.00 3.51
302 303 8.854117 AGATTGCTCAATTTTTAAAGAGTGTCT 58.146 29.630 6.14 0.00 0.00 3.41
333 334 9.716507 GCGTTGCAATAAAGAGAGAAAAATATA 57.283 29.630 0.59 0.00 0.00 0.86
334 335 8.243426 TGCGTTGCAATAAAGAGAGAAAAATAT 58.757 29.630 0.59 0.00 34.76 1.28
335 336 7.537306 GTGCGTTGCAATAAAGAGAGAAAAATA 59.463 33.333 0.59 0.00 41.47 1.40
336 337 6.363357 GTGCGTTGCAATAAAGAGAGAAAAAT 59.637 34.615 0.59 0.00 41.47 1.82
337 338 5.685511 GTGCGTTGCAATAAAGAGAGAAAAA 59.314 36.000 0.59 0.00 41.47 1.94
338 339 5.212194 GTGCGTTGCAATAAAGAGAGAAAA 58.788 37.500 0.59 0.00 41.47 2.29
339 340 4.610456 CGTGCGTTGCAATAAAGAGAGAAA 60.610 41.667 0.59 0.00 41.47 2.52
340 341 3.120683 CGTGCGTTGCAATAAAGAGAGAA 60.121 43.478 0.59 0.00 41.47 2.87
341 342 2.411748 CGTGCGTTGCAATAAAGAGAGA 59.588 45.455 0.59 0.00 41.47 3.10
342 343 2.411748 TCGTGCGTTGCAATAAAGAGAG 59.588 45.455 0.59 0.00 41.47 3.20
343 344 2.409012 TCGTGCGTTGCAATAAAGAGA 58.591 42.857 0.59 0.00 41.47 3.10
344 345 2.762472 CTCGTGCGTTGCAATAAAGAG 58.238 47.619 0.59 5.08 41.47 2.85
345 346 1.136085 GCTCGTGCGTTGCAATAAAGA 60.136 47.619 0.59 0.00 41.47 2.52
346 347 1.250476 GCTCGTGCGTTGCAATAAAG 58.750 50.000 0.59 0.00 41.47 1.85
347 348 0.588737 TGCTCGTGCGTTGCAATAAA 59.411 45.000 0.59 0.00 41.47 1.40
348 349 0.801872 ATGCTCGTGCGTTGCAATAA 59.198 45.000 0.59 0.00 41.47 1.40
349 350 0.096802 CATGCTCGTGCGTTGCAATA 59.903 50.000 0.59 0.00 41.47 1.90
350 351 1.154169 CATGCTCGTGCGTTGCAAT 60.154 52.632 0.59 0.00 41.47 3.56
351 352 2.057654 AACATGCTCGTGCGTTGCAA 62.058 50.000 15.23 0.00 41.47 4.08
352 353 2.057654 AAACATGCTCGTGCGTTGCA 62.058 50.000 0.50 14.15 43.34 4.08
353 354 0.110419 TAAACATGCTCGTGCGTTGC 60.110 50.000 0.50 5.71 43.34 4.17
354 355 2.233355 CTTAAACATGCTCGTGCGTTG 58.767 47.619 0.50 6.10 43.34 4.10
355 356 1.399727 GCTTAAACATGCTCGTGCGTT 60.400 47.619 0.50 0.00 43.34 4.84
356 357 0.165944 GCTTAAACATGCTCGTGCGT 59.834 50.000 4.84 0.99 43.34 5.24
357 358 0.165727 TGCTTAAACATGCTCGTGCG 59.834 50.000 4.84 0.00 43.34 5.34
358 359 2.330231 TTGCTTAAACATGCTCGTGC 57.670 45.000 1.71 1.71 40.20 5.34
359 360 5.855925 TGTATTTTGCTTAAACATGCTCGTG 59.144 36.000 0.00 0.00 0.00 4.35
360 361 6.007936 TGTATTTTGCTTAAACATGCTCGT 57.992 33.333 0.00 0.00 0.00 4.18
361 362 6.314018 TCTGTATTTTGCTTAAACATGCTCG 58.686 36.000 0.00 0.00 0.00 5.03
362 363 7.201384 GCTTCTGTATTTTGCTTAAACATGCTC 60.201 37.037 0.00 0.00 0.00 4.26
363 364 6.587608 GCTTCTGTATTTTGCTTAAACATGCT 59.412 34.615 0.00 0.00 0.00 3.79
364 365 6.587608 AGCTTCTGTATTTTGCTTAAACATGC 59.412 34.615 0.00 0.00 0.00 4.06
365 366 8.430063 CAAGCTTCTGTATTTTGCTTAAACATG 58.570 33.333 0.00 0.00 41.31 3.21
366 367 7.116805 GCAAGCTTCTGTATTTTGCTTAAACAT 59.883 33.333 0.00 0.00 41.31 2.71
367 368 6.420604 GCAAGCTTCTGTATTTTGCTTAAACA 59.579 34.615 0.00 0.00 41.31 2.83
368 369 6.398935 CGCAAGCTTCTGTATTTTGCTTAAAC 60.399 38.462 0.00 0.00 41.31 2.01
369 370 5.629020 CGCAAGCTTCTGTATTTTGCTTAAA 59.371 36.000 0.00 0.00 41.31 1.52
370 371 5.153513 CGCAAGCTTCTGTATTTTGCTTAA 58.846 37.500 0.00 0.00 41.31 1.85
371 372 4.722194 CGCAAGCTTCTGTATTTTGCTTA 58.278 39.130 0.00 0.00 41.31 3.09
372 373 3.568538 CGCAAGCTTCTGTATTTTGCTT 58.431 40.909 0.00 0.00 43.61 3.91
402 403 2.672996 CCAGCCAACCTTCCACGG 60.673 66.667 0.00 0.00 0.00 4.94
403 404 2.113139 ACCAGCCAACCTTCCACG 59.887 61.111 0.00 0.00 0.00 4.94
407 408 0.610232 ATCTGCACCAGCCAACCTTC 60.610 55.000 0.00 0.00 41.13 3.46
427 428 3.400054 AGCCCAGGTACTTCCGCC 61.400 66.667 0.00 0.00 41.99 6.13
432 433 1.853250 GCCCTTCAGCCCAGGTACTT 61.853 60.000 0.00 0.00 34.60 2.24
456 457 2.030457 GTGTATCTGTCGGCAAATTCGG 59.970 50.000 0.00 0.00 0.00 4.30
618 652 4.973055 TCGTTTGGTCCCGCACGG 62.973 66.667 1.02 1.02 33.39 4.94
645 679 2.672908 TTCATAGCGCCGTAGCCGAC 62.673 60.000 2.29 0.00 38.01 4.79
705 741 3.792047 CTGATGTGTGTGCGGCGG 61.792 66.667 9.78 0.00 0.00 6.13
706 742 4.450122 GCTGATGTGTGTGCGGCG 62.450 66.667 0.51 0.51 0.00 6.46
744 780 1.498865 GAGTGTGGGCCGCAATATCG 61.499 60.000 23.47 0.00 0.00 2.92
789 825 0.974010 ACGCGAGGAATCCTGGGTTA 60.974 55.000 15.93 0.00 31.76 2.85
918 954 0.385974 CTGTTTGCGTGTGCTTAGCC 60.386 55.000 0.29 0.00 43.34 3.93
1099 1138 2.830704 AAAGCTTCGACCCGCTACCG 62.831 60.000 0.00 0.00 34.96 4.02
1118 1157 5.178623 CGACCAGAACACAAAGCATACTAAA 59.821 40.000 0.00 0.00 0.00 1.85
1124 1163 1.238439 CCGACCAGAACACAAAGCAT 58.762 50.000 0.00 0.00 0.00 3.79
1159 1198 3.181497 CCAAATCATCCTTAGCACCAACG 60.181 47.826 0.00 0.00 0.00 4.10
1260 1314 0.459237 CTGACTGCGATCTCCACCAC 60.459 60.000 0.00 0.00 0.00 4.16
1261 1315 0.900182 ACTGACTGCGATCTCCACCA 60.900 55.000 0.00 0.00 0.00 4.17
1262 1316 0.247736 AACTGACTGCGATCTCCACC 59.752 55.000 0.00 0.00 0.00 4.61
1312 1366 4.318332 TCTTGACTACTTGTCTTGCCATG 58.682 43.478 0.00 0.00 45.54 3.66
1343 1397 7.878127 AGCAAAGTTCTATTACTTGAGTAAGCA 59.122 33.333 9.25 0.38 42.94 3.91
1453 1528 9.906660 GACACGAGAAAGAGAGAATATATCAAT 57.093 33.333 0.00 0.00 0.00 2.57
1454 1529 9.126151 AGACACGAGAAAGAGAGAATATATCAA 57.874 33.333 0.00 0.00 0.00 2.57
1455 1530 8.684386 AGACACGAGAAAGAGAGAATATATCA 57.316 34.615 0.00 0.00 0.00 2.15
1537 1612 0.107017 GCATCCCACAGCAGGTATGT 60.107 55.000 0.00 0.00 0.00 2.29
1660 1735 2.358898 ACACCAGACATGTGCAACTTTC 59.641 45.455 1.15 0.00 37.22 2.62
1760 1861 4.803452 TCTTGTGAAAAGAATCCCCTGTT 58.197 39.130 0.00 0.00 0.00 3.16
1795 1896 3.881314 AAGCTGTCAGGCAGATCTCTAGT 60.881 47.826 6.09 0.00 43.97 2.57
1954 2062 5.780984 TCTACATGCTGCATTAGAGAGATG 58.219 41.667 13.38 2.30 0.00 2.90
1993 2103 3.415212 CAGGACCTCATTCTTCTTTGCA 58.585 45.455 0.00 0.00 0.00 4.08
2196 2611 4.578105 GCTTGGTGCTATTTTGCTCTCTAT 59.422 41.667 0.00 0.00 38.95 1.98
2197 2612 3.941483 GCTTGGTGCTATTTTGCTCTCTA 59.059 43.478 0.00 0.00 38.95 2.43
2363 3443 5.978919 TCAGCAAGTTGTTTCATGAATTGAC 59.021 36.000 18.47 11.19 32.84 3.18
2415 4222 3.608707 GCAACATCAGTCACTGCAAGAAG 60.609 47.826 0.00 0.00 37.43 2.85
2788 5127 0.188342 ACTTGGCACCAATGGACCTT 59.812 50.000 6.16 0.00 35.20 3.50
3152 8464 2.094545 GGCGCTTCTTGGAAAATGTCAT 60.095 45.455 7.64 0.00 0.00 3.06
3217 8532 1.133199 TCCTTGAGCAACCCAACCAAT 60.133 47.619 0.00 0.00 0.00 3.16
3257 8572 0.039708 AACGGGAACTTCGAGTCGAC 60.040 55.000 16.28 7.70 34.89 4.20
3288 8603 4.254709 TGCTCTGCCACGCCTTGT 62.255 61.111 0.00 0.00 0.00 3.16
3371 8686 7.868415 GTCTGTATGCAAGTCCTTAATACTAGG 59.132 40.741 0.00 0.00 0.00 3.02
3398 8723 5.007385 ACATCTAAGTATTCACGTCCACC 57.993 43.478 0.00 0.00 0.00 4.61
3725 9069 1.630369 TGCTTTGGGCTCTCAGTATGT 59.370 47.619 0.00 0.00 42.39 2.29
3726 9070 2.093288 TCTGCTTTGGGCTCTCAGTATG 60.093 50.000 0.00 0.00 42.39 2.39
3764 9108 3.984633 GGTCTGCTATATTCAAGAGACGC 59.015 47.826 0.00 0.00 32.32 5.19
3829 9173 8.950007 ACCTCTTTTTATGGGAATGACTAAAA 57.050 30.769 0.00 0.00 0.00 1.52
3837 9181 5.843969 ACACCAAACCTCTTTTTATGGGAAT 59.156 36.000 0.00 0.00 32.21 3.01
3851 9195 5.830991 TGCTCAAAATTAGTACACCAAACCT 59.169 36.000 0.00 0.00 0.00 3.50
3871 9215 6.379386 GTTGGGTAATTGTTTAGAGTTGCTC 58.621 40.000 0.00 0.00 0.00 4.26
3944 9527 6.934048 AGTACAGTAGTTTACTCCGTATCC 57.066 41.667 0.00 0.00 36.76 2.59
4104 9694 2.366480 AAAGCAAGCATGGCACGCAA 62.366 50.000 8.75 0.00 37.68 4.85
4107 9697 2.063156 TTTAAAGCAAGCATGGCACG 57.937 45.000 0.00 0.00 37.68 5.34


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

AutoCloner maintained by Alex Coulton.