Multiple sequence alignment - TraesCS3B01G600400

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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 TraesCS3B01G600400 chr3B 100.000 3870 0 0 1 3870 821084379 821080510 0.000000e+00 7147.0
1 TraesCS3B01G600400 chr3B 96.926 488 12 1 420 904 454482955 454483442 0.000000e+00 815.0
2 TraesCS3B01G600400 chr3B 100.000 75 0 0 2777 2851 821081538 821081464 5.210000e-29 139.0
3 TraesCS3B01G600400 chr3B 100.000 75 0 0 2842 2916 821081603 821081529 5.210000e-29 139.0
4 TraesCS3B01G600400 chr3B 82.474 97 13 4 1075 1170 700995443 700995350 8.910000e-12 82.4
5 TraesCS3B01G600400 chr3B 81.443 97 14 4 1075 1170 816270858 816270765 4.150000e-10 76.8
6 TraesCS3B01G600400 chr5B 98.470 2419 33 2 433 2851 283028821 283026407 0.000000e+00 4259.0
7 TraesCS3B01G600400 chr5B 99.223 1030 6 2 2842 3870 283026481 283025453 0.000000e+00 1857.0
8 TraesCS3B01G600400 chr5B 80.841 214 37 3 2039 2252 533483843 533484052 8.600000e-37 165.0
9 TraesCS3B01G600400 chr7B 92.028 1129 64 7 1745 2851 340508338 340509462 0.000000e+00 1563.0
10 TraesCS3B01G600400 chr7B 91.878 985 66 7 421 1403 340506815 340507787 0.000000e+00 1363.0
11 TraesCS3B01G600400 chr7B 87.250 400 25 4 3058 3433 340509909 340510306 2.140000e-117 433.0
12 TraesCS3B01G600400 chr7B 85.144 451 31 13 3456 3870 340516953 340517403 2.760000e-116 429.0
13 TraesCS3B01G600400 chr7B 95.580 181 6 2 1485 1665 340508163 340508341 4.890000e-74 289.0
14 TraesCS3B01G600400 chr7B 91.163 215 15 3 2842 3056 340509388 340509598 4.890000e-74 289.0
15 TraesCS3B01G600400 chr7B 91.089 101 7 2 1664 1764 412820928 412820830 6.740000e-28 135.0
16 TraesCS3B01G600400 chr3D 92.289 415 28 4 7 418 609924671 609924258 1.550000e-163 586.0
17 TraesCS3B01G600400 chr3D 92.857 56 4 0 1111 1166 565399464 565399519 8.910000e-12 82.4
18 TraesCS3B01G600400 chr1B 81.717 361 57 9 2010 2367 625423538 625423184 3.780000e-75 292.0
19 TraesCS3B01G600400 chr1B 90.291 103 10 0 1649 1751 634510176 634510074 6.740000e-28 135.0
20 TraesCS3B01G600400 chr7D 79.795 292 56 3 1952 2242 579358226 579357937 3.920000e-50 209.0
21 TraesCS3B01G600400 chr7D 78.912 294 60 2 1952 2244 599395770 599396062 8.480000e-47 198.0
22 TraesCS3B01G600400 chr7D 93.750 96 6 0 1655 1750 596643514 596643419 1.120000e-30 145.0
23 TraesCS3B01G600400 chr7D 81.884 138 25 0 2088 2225 318823999 318823862 2.440000e-22 117.0
24 TraesCS3B01G600400 chr7D 77.305 141 31 1 2088 2227 111363722 111363862 8.910000e-12 82.4
25 TraesCS3B01G600400 chr7D 80.612 98 15 3 1075 1170 32338022 32337927 5.360000e-09 73.1
26 TraesCS3B01G600400 chr2D 79.110 292 59 2 1952 2242 481681900 481681610 2.360000e-47 200.0
27 TraesCS3B01G600400 chr2D 79.675 123 23 2 1055 1176 534121783 534121662 1.920000e-13 87.9
28 TraesCS3B01G600400 chr1D 78.893 289 59 2 1952 2239 413793688 413793975 1.100000e-45 195.0
29 TraesCS3B01G600400 chr5A 95.604 91 4 0 1660 1750 324692656 324692566 3.120000e-31 147.0
30 TraesCS3B01G600400 chr5A 92.929 99 5 2 1654 1751 660190744 660190647 4.030000e-30 143.0
31 TraesCS3B01G600400 chr5D 93.617 94 6 0 1657 1750 343797657 343797564 1.450000e-29 141.0
32 TraesCS3B01G600400 chr2A 91.176 102 7 2 1657 1757 127212324 127212224 1.880000e-28 137.0
33 TraesCS3B01G600400 chr1A 91.176 102 7 2 1664 1763 95061124 95061225 1.880000e-28 137.0
34 TraesCS3B01G600400 chr4D 81.905 105 15 4 1075 1176 307493427 307493324 6.890000e-13 86.1
35 TraesCS3B01G600400 chrUn 77.536 138 30 1 2091 2227 112300896 112300759 8.910000e-12 82.4
36 TraesCS3B01G600400 chr4B 82.474 97 13 4 1075 1170 104446856 104446763 8.910000e-12 82.4


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 TraesCS3B01G600400 chr3B 821080510 821084379 3869 True 2475.0 7147 100.0000 1 3870 3 chr3B.!!$R3 3869
1 TraesCS3B01G600400 chr5B 283025453 283028821 3368 True 3058.0 4259 98.8465 433 3870 2 chr5B.!!$R1 3437
2 TraesCS3B01G600400 chr7B 340506815 340510306 3491 False 787.4 1563 91.5798 421 3433 5 chr7B.!!$F2 3012

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
838 840 0.543410 TTCCCCGCACTACCTCTTCA 60.543 55.0 0.0 0.0 0.00 3.02 F
2231 2528 0.973632 TGGTTGCTCGGTGAGTATGT 59.026 50.0 0.0 0.0 31.39 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2832 3152 0.179150 CTCTAGCACACGAGGCTGTC 60.179 60.000 0.00 0.0 42.62 3.51 R
3160 3789 3.709987 GCAACATGGCCATCATTTCTAC 58.290 45.455 17.61 0.0 32.92 2.59 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
74 75 9.766277 TTTCACATTTTTACAGAATTTGTTTGC 57.234 25.926 0.00 0.00 41.29 3.68
75 76 8.484641 TCACATTTTTACAGAATTTGTTTGCA 57.515 26.923 0.00 0.00 41.29 4.08
76 77 9.107177 TCACATTTTTACAGAATTTGTTTGCAT 57.893 25.926 0.00 0.00 41.29 3.96
85 86 8.436046 ACAGAATTTGTTTGCATACATTTTGT 57.564 26.923 10.90 11.23 36.31 2.83
86 87 8.336806 ACAGAATTTGTTTGCATACATTTTGTG 58.663 29.630 10.90 15.96 36.31 3.33
87 88 8.549548 CAGAATTTGTTTGCATACATTTTGTGA 58.450 29.630 10.90 0.00 0.00 3.58
88 89 9.275398 AGAATTTGTTTGCATACATTTTGTGAT 57.725 25.926 10.90 0.00 0.00 3.06
89 90 9.881529 GAATTTGTTTGCATACATTTTGTGATT 57.118 25.926 10.90 3.94 0.00 2.57
91 92 9.881529 ATTTGTTTGCATACATTTTGTGATTTC 57.118 25.926 10.90 0.00 0.00 2.17
92 93 8.429493 TTGTTTGCATACATTTTGTGATTTCA 57.571 26.923 10.90 0.00 0.00 2.69
93 94 8.604640 TGTTTGCATACATTTTGTGATTTCAT 57.395 26.923 5.83 0.00 0.00 2.57
94 95 8.496751 TGTTTGCATACATTTTGTGATTTCATG 58.503 29.630 5.83 0.00 0.00 3.07
95 96 7.598189 TTGCATACATTTTGTGATTTCATGG 57.402 32.000 0.00 0.00 0.00 3.66
96 97 6.932947 TGCATACATTTTGTGATTTCATGGA 58.067 32.000 0.00 0.00 0.00 3.41
97 98 6.812656 TGCATACATTTTGTGATTTCATGGAC 59.187 34.615 0.00 0.00 0.00 4.02
98 99 6.812656 GCATACATTTTGTGATTTCATGGACA 59.187 34.615 0.00 0.00 0.00 4.02
99 100 7.493320 GCATACATTTTGTGATTTCATGGACAT 59.507 33.333 0.00 0.00 0.00 3.06
100 101 9.373603 CATACATTTTGTGATTTCATGGACATT 57.626 29.630 0.00 0.00 0.00 2.71
101 102 9.947433 ATACATTTTGTGATTTCATGGACATTT 57.053 25.926 0.00 0.00 0.00 2.32
102 103 8.680039 ACATTTTGTGATTTCATGGACATTTT 57.320 26.923 0.00 0.00 0.00 1.82
103 104 9.122779 ACATTTTGTGATTTCATGGACATTTTT 57.877 25.926 0.00 0.00 0.00 1.94
104 105 9.601971 CATTTTGTGATTTCATGGACATTTTTC 57.398 29.630 0.00 0.00 0.00 2.29
105 106 8.728337 TTTTGTGATTTCATGGACATTTTTCA 57.272 26.923 0.00 0.00 0.00 2.69
106 107 8.905660 TTTGTGATTTCATGGACATTTTTCAT 57.094 26.923 0.00 0.00 0.00 2.57
107 108 9.993454 TTTGTGATTTCATGGACATTTTTCATA 57.007 25.926 0.00 0.00 0.00 2.15
109 110 9.806203 TGTGATTTCATGGACATTTTTCATATC 57.194 29.630 0.00 0.00 0.00 1.63
110 111 9.252962 GTGATTTCATGGACATTTTTCATATCC 57.747 33.333 0.00 0.00 0.00 2.59
111 112 8.979534 TGATTTCATGGACATTTTTCATATCCA 58.020 29.630 0.00 0.00 43.42 3.41
112 113 9.252962 GATTTCATGGACATTTTTCATATCCAC 57.747 33.333 0.00 0.00 42.12 4.02
113 114 6.375945 TCATGGACATTTTTCATATCCACG 57.624 37.500 0.00 0.00 42.12 4.94
114 115 5.299028 TCATGGACATTTTTCATATCCACGG 59.701 40.000 0.00 0.00 42.12 4.94
115 116 4.849518 TGGACATTTTTCATATCCACGGA 58.150 39.130 0.00 0.00 34.50 4.69
116 117 4.638421 TGGACATTTTTCATATCCACGGAC 59.362 41.667 0.00 0.00 34.50 4.79
117 118 4.638421 GGACATTTTTCATATCCACGGACA 59.362 41.667 0.00 0.00 0.00 4.02
118 119 5.299279 GGACATTTTTCATATCCACGGACAT 59.701 40.000 0.00 0.00 0.00 3.06
119 120 6.183360 GGACATTTTTCATATCCACGGACATT 60.183 38.462 0.00 0.00 0.00 2.71
120 121 7.169158 ACATTTTTCATATCCACGGACATTT 57.831 32.000 0.00 0.00 0.00 2.32
121 122 7.610865 ACATTTTTCATATCCACGGACATTTT 58.389 30.769 0.00 0.00 0.00 1.82
122 123 8.093927 ACATTTTTCATATCCACGGACATTTTT 58.906 29.630 0.00 0.00 0.00 1.94
143 144 6.430962 TTTTGGATCCATGAACATTTTCCA 57.569 33.333 17.06 0.00 0.00 3.53
144 145 6.430962 TTTGGATCCATGAACATTTTCCAA 57.569 33.333 17.06 13.81 39.36 3.53
145 146 6.430962 TTGGATCCATGAACATTTTCCAAA 57.569 33.333 17.06 0.00 38.47 3.28
146 147 6.623979 TGGATCCATGAACATTTTCCAAAT 57.376 33.333 11.44 0.00 0.00 2.32
147 148 7.018487 TGGATCCATGAACATTTTCCAAATT 57.982 32.000 11.44 0.00 0.00 1.82
148 149 7.460071 TGGATCCATGAACATTTTCCAAATTT 58.540 30.769 11.44 0.00 0.00 1.82
149 150 7.607223 TGGATCCATGAACATTTTCCAAATTTC 59.393 33.333 11.44 0.00 0.00 2.17
150 151 7.825761 GGATCCATGAACATTTTCCAAATTTCT 59.174 33.333 6.95 0.00 0.00 2.52
151 152 7.966246 TCCATGAACATTTTCCAAATTTCTG 57.034 32.000 0.00 0.00 0.00 3.02
152 153 7.733969 TCCATGAACATTTTCCAAATTTCTGA 58.266 30.769 0.00 0.00 0.00 3.27
153 154 8.377034 TCCATGAACATTTTCCAAATTTCTGAT 58.623 29.630 0.00 0.00 0.00 2.90
154 155 9.005777 CCATGAACATTTTCCAAATTTCTGATT 57.994 29.630 0.00 0.00 0.00 2.57
157 158 9.206870 TGAACATTTTCCAAATTTCTGATTAGC 57.793 29.630 0.00 0.00 0.00 3.09
158 159 9.428097 GAACATTTTCCAAATTTCTGATTAGCT 57.572 29.630 0.00 0.00 0.00 3.32
159 160 9.783081 AACATTTTCCAAATTTCTGATTAGCTT 57.217 25.926 0.00 0.00 0.00 3.74
160 161 9.783081 ACATTTTCCAAATTTCTGATTAGCTTT 57.217 25.926 0.00 0.00 0.00 3.51
204 205 7.712264 TTTGAAATCTGCACACATTTTTAGG 57.288 32.000 0.00 0.00 0.00 2.69
205 206 6.403866 TGAAATCTGCACACATTTTTAGGT 57.596 33.333 0.00 0.00 0.00 3.08
206 207 6.815089 TGAAATCTGCACACATTTTTAGGTT 58.185 32.000 0.00 0.00 0.00 3.50
207 208 7.271511 TGAAATCTGCACACATTTTTAGGTTT 58.728 30.769 0.00 0.00 0.00 3.27
208 209 7.768120 TGAAATCTGCACACATTTTTAGGTTTT 59.232 29.630 0.00 0.00 0.00 2.43
209 210 8.504812 AAATCTGCACACATTTTTAGGTTTTT 57.495 26.923 0.00 0.00 0.00 1.94
252 253 8.075593 ACATGAACATTTTCTTTTCAAATCCG 57.924 30.769 0.00 0.00 33.13 4.18
253 254 6.523676 TGAACATTTTCTTTTCAAATCCGC 57.476 33.333 0.00 0.00 32.36 5.54
254 255 5.174761 TGAACATTTTCTTTTCAAATCCGCG 59.825 36.000 0.00 0.00 32.36 6.46
255 256 4.865776 ACATTTTCTTTTCAAATCCGCGA 58.134 34.783 8.23 0.00 0.00 5.87
256 257 5.469479 ACATTTTCTTTTCAAATCCGCGAT 58.531 33.333 8.23 0.00 0.00 4.58
257 258 5.572896 ACATTTTCTTTTCAAATCCGCGATC 59.427 36.000 8.23 0.00 0.00 3.69
258 259 4.757799 TTTCTTTTCAAATCCGCGATCA 57.242 36.364 8.23 0.00 0.00 2.92
259 260 4.757799 TTCTTTTCAAATCCGCGATCAA 57.242 36.364 8.23 0.00 0.00 2.57
260 261 4.963276 TCTTTTCAAATCCGCGATCAAT 57.037 36.364 8.23 0.00 0.00 2.57
261 262 4.661125 TCTTTTCAAATCCGCGATCAATG 58.339 39.130 8.23 0.00 0.00 2.82
262 263 2.473530 TTCAAATCCGCGATCAATGC 57.526 45.000 8.23 0.00 0.00 3.56
263 264 1.667236 TCAAATCCGCGATCAATGCT 58.333 45.000 8.23 0.00 0.00 3.79
264 265 2.016318 TCAAATCCGCGATCAATGCTT 58.984 42.857 8.23 0.00 0.00 3.91
265 266 2.114056 CAAATCCGCGATCAATGCTTG 58.886 47.619 8.23 0.00 0.00 4.01
266 267 1.667236 AATCCGCGATCAATGCTTGA 58.333 45.000 8.23 0.00 45.01 3.02
267 268 1.667236 ATCCGCGATCAATGCTTGAA 58.333 45.000 8.23 0.00 43.95 2.69
268 269 1.667236 TCCGCGATCAATGCTTGAAT 58.333 45.000 8.23 0.00 43.95 2.57
269 270 2.016318 TCCGCGATCAATGCTTGAATT 58.984 42.857 8.23 0.00 43.95 2.17
270 271 2.032054 TCCGCGATCAATGCTTGAATTC 59.968 45.455 8.23 0.00 43.95 2.17
271 272 2.223317 CCGCGATCAATGCTTGAATTCA 60.223 45.455 8.23 3.38 43.95 2.57
272 273 3.549423 CCGCGATCAATGCTTGAATTCAT 60.549 43.478 8.23 0.00 43.95 2.57
273 274 3.420904 CGCGATCAATGCTTGAATTCATG 59.579 43.478 9.40 12.82 43.95 3.07
274 275 4.603985 GCGATCAATGCTTGAATTCATGA 58.396 39.130 21.92 16.13 43.95 3.07
275 276 5.220381 GCGATCAATGCTTGAATTCATGAT 58.780 37.500 21.92 19.53 43.95 2.45
276 277 5.690409 GCGATCAATGCTTGAATTCATGATT 59.310 36.000 21.92 15.29 43.95 2.57
277 278 6.200286 GCGATCAATGCTTGAATTCATGATTT 59.800 34.615 21.92 12.40 43.95 2.17
278 279 7.254319 GCGATCAATGCTTGAATTCATGATTTT 60.254 33.333 21.92 10.40 43.95 1.82
279 280 8.600625 CGATCAATGCTTGAATTCATGATTTTT 58.399 29.630 21.92 8.42 43.95 1.94
306 307 9.144747 TCAAGTTCTCAGAAGAAATAGAATTCG 57.855 33.333 0.00 0.00 43.04 3.34
307 308 8.930760 CAAGTTCTCAGAAGAAATAGAATTCGT 58.069 33.333 0.00 0.00 43.04 3.85
308 309 8.472683 AGTTCTCAGAAGAAATAGAATTCGTG 57.527 34.615 0.00 0.00 43.04 4.35
309 310 8.307483 AGTTCTCAGAAGAAATAGAATTCGTGA 58.693 33.333 0.00 0.00 43.04 4.35
310 311 8.591312 GTTCTCAGAAGAAATAGAATTCGTGAG 58.409 37.037 0.00 3.44 43.04 3.51
311 312 6.754209 TCTCAGAAGAAATAGAATTCGTGAGC 59.246 38.462 0.00 0.00 36.95 4.26
312 313 5.516696 TCAGAAGAAATAGAATTCGTGAGCG 59.483 40.000 0.00 0.00 39.92 5.03
313 314 5.516696 CAGAAGAAATAGAATTCGTGAGCGA 59.483 40.000 0.00 0.00 46.36 4.93
326 327 5.065791 TCGTGAGCGATATTTTGAATTCG 57.934 39.130 0.04 0.00 42.81 3.34
327 328 4.565166 TCGTGAGCGATATTTTGAATTCGT 59.435 37.500 0.04 0.00 42.81 3.85
328 329 4.661776 CGTGAGCGATATTTTGAATTCGTG 59.338 41.667 0.04 0.00 41.33 4.35
329 330 5.560148 GTGAGCGATATTTTGAATTCGTGT 58.440 37.500 0.04 0.00 34.24 4.49
330 331 5.449113 GTGAGCGATATTTTGAATTCGTGTG 59.551 40.000 0.04 0.00 34.24 3.82
331 332 4.342772 AGCGATATTTTGAATTCGTGTGC 58.657 39.130 0.04 0.00 34.24 4.57
332 333 4.094911 GCGATATTTTGAATTCGTGTGCA 58.905 39.130 0.04 0.00 34.24 4.57
333 334 4.556912 GCGATATTTTGAATTCGTGTGCAA 59.443 37.500 0.04 0.00 34.24 4.08
334 335 5.229887 GCGATATTTTGAATTCGTGTGCAAT 59.770 36.000 0.04 0.00 34.24 3.56
335 336 6.237542 GCGATATTTTGAATTCGTGTGCAATT 60.238 34.615 0.04 0.00 34.24 2.32
336 337 7.665471 CGATATTTTGAATTCGTGTGCAATTT 58.335 30.769 0.04 0.00 0.00 1.82
337 338 8.161610 CGATATTTTGAATTCGTGTGCAATTTT 58.838 29.630 0.04 0.00 0.00 1.82
338 339 9.810231 GATATTTTGAATTCGTGTGCAATTTTT 57.190 25.926 0.04 0.00 0.00 1.94
397 398 9.887406 ATTTTTAAATAGAAGAAAGCGAAACGA 57.113 25.926 0.00 0.00 0.00 3.85
398 399 8.703823 TTTTAAATAGAAGAAAGCGAAACGAC 57.296 30.769 0.00 0.00 0.00 4.34
399 400 7.647907 TTAAATAGAAGAAAGCGAAACGACT 57.352 32.000 0.00 0.00 0.00 4.18
400 401 5.765072 AATAGAAGAAAGCGAAACGACTC 57.235 39.130 0.00 0.00 0.00 3.36
401 402 2.052157 AGAAGAAAGCGAAACGACTCG 58.948 47.619 0.00 0.00 41.84 4.18
402 403 2.049228 GAAGAAAGCGAAACGACTCGA 58.951 47.619 5.20 0.00 41.44 4.04
403 404 2.129823 AGAAAGCGAAACGACTCGAA 57.870 45.000 5.20 0.00 41.44 3.71
404 405 2.466846 AGAAAGCGAAACGACTCGAAA 58.533 42.857 5.20 0.00 41.44 3.46
405 406 2.861935 AGAAAGCGAAACGACTCGAAAA 59.138 40.909 5.20 0.00 41.44 2.29
406 407 3.307782 AGAAAGCGAAACGACTCGAAAAA 59.692 39.130 5.20 0.00 41.44 1.94
424 425 0.981183 AAAGGCTGATGTACGGGACA 59.019 50.000 0.00 0.00 43.97 4.02
716 717 1.388547 TGAGCGGTAATTGAATGGGC 58.611 50.000 0.00 0.00 0.00 5.36
830 832 0.748450 CGTAATCCTTCCCCGCACTA 59.252 55.000 0.00 0.00 0.00 2.74
838 840 0.543410 TTCCCCGCACTACCTCTTCA 60.543 55.000 0.00 0.00 0.00 3.02
1672 1969 6.885376 TCATCGAGATAAATAGTACTCCCTCC 59.115 42.308 0.00 0.00 0.00 4.30
1673 1970 5.243981 TCGAGATAAATAGTACTCCCTCCG 58.756 45.833 0.00 0.00 0.00 4.63
1674 1971 5.002516 CGAGATAAATAGTACTCCCTCCGT 58.997 45.833 0.00 0.00 0.00 4.69
1690 1987 7.930325 ACTCCCTCCGTAAACTAATATAAAAGC 59.070 37.037 0.00 0.00 0.00 3.51
1874 2171 2.479566 CAGAATGTACAGTGGTGGCT 57.520 50.000 0.00 0.00 0.00 4.75
2086 2383 1.302431 CCCAACTGTCGGCACATCA 60.302 57.895 0.00 0.00 0.00 3.07
2159 2456 4.497291 AAGGGCTTTGGTATTCGATACA 57.503 40.909 0.00 0.00 37.48 2.29
2231 2528 0.973632 TGGTTGCTCGGTGAGTATGT 59.026 50.000 0.00 0.00 31.39 2.29
2242 2539 6.036735 GCTCGGTGAGTATGTAATTTTTGCTA 59.963 38.462 0.00 0.00 31.39 3.49
2828 3148 6.436738 AACATGAGAATGATGAGGATAGCT 57.563 37.500 0.00 0.00 31.68 3.32
2829 3149 5.795972 ACATGAGAATGATGAGGATAGCTG 58.204 41.667 0.00 0.00 31.68 4.24
2830 3150 5.307456 ACATGAGAATGATGAGGATAGCTGT 59.693 40.000 0.00 0.00 31.68 4.40
2831 3151 6.496218 ACATGAGAATGATGAGGATAGCTGTA 59.504 38.462 0.00 0.00 31.68 2.74
2832 3152 6.587206 TGAGAATGATGAGGATAGCTGTAG 57.413 41.667 0.00 0.00 0.00 2.74
2833 3153 6.310149 TGAGAATGATGAGGATAGCTGTAGA 58.690 40.000 0.00 0.00 0.00 2.59
2834 3154 6.208402 TGAGAATGATGAGGATAGCTGTAGAC 59.792 42.308 0.00 0.00 0.00 2.59
2835 3155 6.073981 AGAATGATGAGGATAGCTGTAGACA 58.926 40.000 0.00 0.00 0.00 3.41
2836 3156 5.981088 ATGATGAGGATAGCTGTAGACAG 57.019 43.478 5.26 5.26 46.40 3.51
2845 3165 3.408389 CTGTAGACAGCCTCGTGTG 57.592 57.895 0.00 0.00 37.15 3.82
2846 3166 0.734253 CTGTAGACAGCCTCGTGTGC 60.734 60.000 0.00 0.00 37.15 4.57
2847 3167 1.179174 TGTAGACAGCCTCGTGTGCT 61.179 55.000 0.00 0.00 40.41 4.40
2848 3168 0.809385 GTAGACAGCCTCGTGTGCTA 59.191 55.000 1.12 0.00 36.81 3.49
2849 3169 1.095600 TAGACAGCCTCGTGTGCTAG 58.904 55.000 1.12 0.00 36.81 3.42
2850 3170 0.609406 AGACAGCCTCGTGTGCTAGA 60.609 55.000 0.00 0.00 36.81 2.43
2851 3171 0.179150 GACAGCCTCGTGTGCTAGAG 60.179 60.000 0.00 0.00 36.81 2.43
2852 3172 1.518133 CAGCCTCGTGTGCTAGAGC 60.518 63.158 0.00 0.00 36.81 4.09
2853 3173 2.202810 GCCTCGTGTGCTAGAGCC 60.203 66.667 0.00 0.00 41.18 4.70
2854 3174 3.006756 GCCTCGTGTGCTAGAGCCA 62.007 63.158 0.00 0.00 41.18 4.75
2855 3175 1.140589 CCTCGTGTGCTAGAGCCAG 59.859 63.158 0.00 0.00 41.18 4.85
2856 3176 1.140589 CTCGTGTGCTAGAGCCAGG 59.859 63.158 0.00 3.22 41.18 4.45
2857 3177 1.304134 TCGTGTGCTAGAGCCAGGA 60.304 57.895 0.00 5.39 41.18 3.86
2858 3178 0.898326 TCGTGTGCTAGAGCCAGGAA 60.898 55.000 10.80 0.33 41.18 3.36
2859 3179 0.176680 CGTGTGCTAGAGCCAGGAAT 59.823 55.000 0.00 0.00 41.18 3.01
2860 3180 1.661341 GTGTGCTAGAGCCAGGAATG 58.339 55.000 0.00 0.00 41.18 2.67
2861 3181 1.065854 GTGTGCTAGAGCCAGGAATGT 60.066 52.381 0.00 0.00 41.18 2.71
2862 3182 1.208052 TGTGCTAGAGCCAGGAATGTC 59.792 52.381 0.00 0.00 41.18 3.06
2863 3183 1.208052 GTGCTAGAGCCAGGAATGTCA 59.792 52.381 0.00 0.00 41.18 3.58
2864 3184 1.208052 TGCTAGAGCCAGGAATGTCAC 59.792 52.381 0.00 0.00 41.18 3.67
2865 3185 1.484240 GCTAGAGCCAGGAATGTCACT 59.516 52.381 0.00 0.00 34.31 3.41
2866 3186 2.741228 GCTAGAGCCAGGAATGTCACTG 60.741 54.545 0.00 0.00 34.31 3.66
2867 3187 1.356124 AGAGCCAGGAATGTCACTGT 58.644 50.000 0.00 0.00 32.90 3.55
2868 3188 1.002888 AGAGCCAGGAATGTCACTGTG 59.997 52.381 0.17 0.17 32.90 3.66
2869 3189 1.002430 GAGCCAGGAATGTCACTGTGA 59.998 52.381 6.36 6.36 32.90 3.58
2870 3190 1.421268 AGCCAGGAATGTCACTGTGAA 59.579 47.619 12.81 3.73 32.90 3.18
2871 3191 2.158623 AGCCAGGAATGTCACTGTGAAA 60.159 45.455 12.81 7.74 32.90 2.69
2872 3192 2.030805 GCCAGGAATGTCACTGTGAAAC 60.031 50.000 12.81 2.21 32.90 2.78
2888 3208 5.807909 TGTGAAACATGAGAATGATGAGGA 58.192 37.500 0.00 0.00 45.67 3.71
3111 3740 6.369005 GTTGCATGTATGTATCAGAAGATGC 58.631 40.000 0.00 0.00 37.38 3.91
3496 4150 4.202441 AGCATATGACTGGCTAAACAAGG 58.798 43.478 6.97 0.00 35.82 3.61
3614 4268 6.454318 CGAGGTTCTCAAATATTGTTCAGACG 60.454 42.308 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 9.766277 GCAAACAAATTCTGTAAAAATGTGAAA 57.234 25.926 0.00 0.00 37.23 2.69
49 50 8.939929 TGCAAACAAATTCTGTAAAAATGTGAA 58.060 25.926 0.00 0.00 37.23 3.18
50 51 8.484641 TGCAAACAAATTCTGTAAAAATGTGA 57.515 26.923 0.00 0.00 37.23 3.58
59 60 9.539825 ACAAAATGTATGCAAACAAATTCTGTA 57.460 25.926 0.00 0.00 37.23 2.74
60 61 8.336806 CACAAAATGTATGCAAACAAATTCTGT 58.663 29.630 0.00 0.00 41.27 3.41
61 62 8.549548 TCACAAAATGTATGCAAACAAATTCTG 58.450 29.630 0.00 0.00 32.02 3.02
62 63 8.659925 TCACAAAATGTATGCAAACAAATTCT 57.340 26.923 0.00 0.00 32.02 2.40
63 64 9.881529 AATCACAAAATGTATGCAAACAAATTC 57.118 25.926 0.00 0.00 32.02 2.17
65 66 9.881529 GAAATCACAAAATGTATGCAAACAAAT 57.118 25.926 0.00 0.00 32.02 2.32
66 67 8.886719 TGAAATCACAAAATGTATGCAAACAAA 58.113 25.926 0.00 0.00 32.02 2.83
67 68 8.429493 TGAAATCACAAAATGTATGCAAACAA 57.571 26.923 0.00 0.00 32.02 2.83
68 69 8.496751 CATGAAATCACAAAATGTATGCAAACA 58.503 29.630 0.00 0.00 0.00 2.83
69 70 7.958567 CCATGAAATCACAAAATGTATGCAAAC 59.041 33.333 0.00 0.00 0.00 2.93
70 71 7.876582 TCCATGAAATCACAAAATGTATGCAAA 59.123 29.630 0.00 0.00 0.00 3.68
71 72 7.331440 GTCCATGAAATCACAAAATGTATGCAA 59.669 33.333 0.00 0.00 0.00 4.08
72 73 6.812656 GTCCATGAAATCACAAAATGTATGCA 59.187 34.615 0.00 0.00 0.00 3.96
73 74 6.812656 TGTCCATGAAATCACAAAATGTATGC 59.187 34.615 0.00 0.00 0.00 3.14
74 75 8.936070 ATGTCCATGAAATCACAAAATGTATG 57.064 30.769 0.00 0.00 0.00 2.39
75 76 9.947433 AAATGTCCATGAAATCACAAAATGTAT 57.053 25.926 0.00 0.00 0.00 2.29
76 77 9.775854 AAAATGTCCATGAAATCACAAAATGTA 57.224 25.926 0.00 0.00 0.00 2.29
77 78 8.680039 AAAATGTCCATGAAATCACAAAATGT 57.320 26.923 0.00 0.00 0.00 2.71
78 79 9.601971 GAAAAATGTCCATGAAATCACAAAATG 57.398 29.630 0.00 0.00 0.00 2.32
79 80 9.339850 TGAAAAATGTCCATGAAATCACAAAAT 57.660 25.926 0.00 0.00 0.00 1.82
80 81 8.728337 TGAAAAATGTCCATGAAATCACAAAA 57.272 26.923 0.00 0.00 0.00 2.44
81 82 8.905660 ATGAAAAATGTCCATGAAATCACAAA 57.094 26.923 0.00 0.00 0.00 2.83
83 84 9.806203 GATATGAAAAATGTCCATGAAATCACA 57.194 29.630 0.00 0.00 0.00 3.58
84 85 9.252962 GGATATGAAAAATGTCCATGAAATCAC 57.747 33.333 0.00 0.00 30.73 3.06
85 86 8.979534 TGGATATGAAAAATGTCCATGAAATCA 58.020 29.630 0.00 0.00 34.93 2.57
86 87 9.252962 GTGGATATGAAAAATGTCCATGAAATC 57.747 33.333 7.02 0.00 40.57 2.17
87 88 7.922278 CGTGGATATGAAAAATGTCCATGAAAT 59.078 33.333 14.73 0.00 44.27 2.17
88 89 7.257003 CGTGGATATGAAAAATGTCCATGAAA 58.743 34.615 14.73 0.00 44.27 2.69
89 90 6.183360 CCGTGGATATGAAAAATGTCCATGAA 60.183 38.462 19.26 0.00 44.27 2.57
90 91 5.299028 CCGTGGATATGAAAAATGTCCATGA 59.701 40.000 19.26 0.00 44.27 3.07
91 92 5.299028 TCCGTGGATATGAAAAATGTCCATG 59.701 40.000 13.50 13.50 42.44 3.66
92 93 5.299279 GTCCGTGGATATGAAAAATGTCCAT 59.701 40.000 7.02 0.00 40.57 3.41
93 94 4.638421 GTCCGTGGATATGAAAAATGTCCA 59.362 41.667 0.18 0.18 37.04 4.02
94 95 4.638421 TGTCCGTGGATATGAAAAATGTCC 59.362 41.667 0.00 0.00 0.00 4.02
95 96 5.811399 TGTCCGTGGATATGAAAAATGTC 57.189 39.130 0.00 0.00 0.00 3.06
96 97 6.773976 AATGTCCGTGGATATGAAAAATGT 57.226 33.333 0.00 0.00 0.00 2.71
97 98 8.477984 AAAAATGTCCGTGGATATGAAAAATG 57.522 30.769 0.00 0.00 0.00 2.32
119 120 6.835174 TGGAAAATGTTCATGGATCCAAAAA 58.165 32.000 20.67 13.15 35.25 1.94
120 121 6.430962 TGGAAAATGTTCATGGATCCAAAA 57.569 33.333 20.67 13.54 35.25 2.44
121 122 6.430962 TTGGAAAATGTTCATGGATCCAAA 57.569 33.333 20.67 6.66 41.19 3.28
122 123 6.430962 TTTGGAAAATGTTCATGGATCCAA 57.569 33.333 20.67 16.17 42.11 3.53
123 124 6.623979 ATTTGGAAAATGTTCATGGATCCA 57.376 33.333 18.88 18.88 35.25 3.41
124 125 7.825761 AGAAATTTGGAAAATGTTCATGGATCC 59.174 33.333 4.20 4.20 35.25 3.36
125 126 8.662141 CAGAAATTTGGAAAATGTTCATGGATC 58.338 33.333 0.00 0.00 35.25 3.36
126 127 8.377034 TCAGAAATTTGGAAAATGTTCATGGAT 58.623 29.630 0.00 0.00 35.25 3.41
127 128 7.733969 TCAGAAATTTGGAAAATGTTCATGGA 58.266 30.769 0.00 0.00 35.25 3.41
128 129 7.966246 TCAGAAATTTGGAAAATGTTCATGG 57.034 32.000 0.00 0.00 35.25 3.66
131 132 9.206870 GCTAATCAGAAATTTGGAAAATGTTCA 57.793 29.630 0.00 0.00 35.25 3.18
132 133 9.428097 AGCTAATCAGAAATTTGGAAAATGTTC 57.572 29.630 0.00 0.00 0.00 3.18
133 134 9.783081 AAGCTAATCAGAAATTTGGAAAATGTT 57.217 25.926 0.00 0.00 0.00 2.71
134 135 9.783081 AAAGCTAATCAGAAATTTGGAAAATGT 57.217 25.926 0.00 0.00 0.00 2.71
178 179 8.610896 CCTAAAAATGTGTGCAGATTTCAAAAA 58.389 29.630 7.58 0.00 33.81 1.94
179 180 7.768120 ACCTAAAAATGTGTGCAGATTTCAAAA 59.232 29.630 7.58 0.00 33.81 2.44
180 181 7.271511 ACCTAAAAATGTGTGCAGATTTCAAA 58.728 30.769 7.58 0.00 33.81 2.69
181 182 6.815089 ACCTAAAAATGTGTGCAGATTTCAA 58.185 32.000 7.58 0.32 33.81 2.69
182 183 6.403866 ACCTAAAAATGTGTGCAGATTTCA 57.596 33.333 7.58 0.31 33.81 2.69
183 184 7.713764 AAACCTAAAAATGTGTGCAGATTTC 57.286 32.000 7.58 0.00 33.81 2.17
184 185 8.504812 AAAAACCTAAAAATGTGTGCAGATTT 57.495 26.923 2.05 2.05 36.06 2.17
226 227 9.190858 CGGATTTGAAAAGAAAATGTTCATGTA 57.809 29.630 0.00 0.00 36.09 2.29
227 228 7.307337 GCGGATTTGAAAAGAAAATGTTCATGT 60.307 33.333 0.00 0.00 36.09 3.21
228 229 7.011189 GCGGATTTGAAAAGAAAATGTTCATG 58.989 34.615 0.00 0.00 36.09 3.07
229 230 6.128849 CGCGGATTTGAAAAGAAAATGTTCAT 60.129 34.615 0.00 0.00 36.09 2.57
230 231 5.174761 CGCGGATTTGAAAAGAAAATGTTCA 59.825 36.000 0.00 0.00 36.09 3.18
231 232 5.401079 TCGCGGATTTGAAAAGAAAATGTTC 59.599 36.000 6.13 0.00 0.00 3.18
232 233 5.285651 TCGCGGATTTGAAAAGAAAATGTT 58.714 33.333 6.13 0.00 0.00 2.71
233 234 4.865776 TCGCGGATTTGAAAAGAAAATGT 58.134 34.783 6.13 0.00 0.00 2.71
234 235 5.572511 TGATCGCGGATTTGAAAAGAAAATG 59.427 36.000 6.13 0.00 0.00 2.32
235 236 5.708948 TGATCGCGGATTTGAAAAGAAAAT 58.291 33.333 6.13 0.00 0.00 1.82
236 237 5.114785 TGATCGCGGATTTGAAAAGAAAA 57.885 34.783 6.13 0.00 0.00 2.29
237 238 4.757799 TGATCGCGGATTTGAAAAGAAA 57.242 36.364 6.13 0.00 0.00 2.52
238 239 4.757799 TTGATCGCGGATTTGAAAAGAA 57.242 36.364 6.13 0.00 0.00 2.52
239 240 4.661125 CATTGATCGCGGATTTGAAAAGA 58.339 39.130 6.13 0.00 0.00 2.52
240 241 3.241322 GCATTGATCGCGGATTTGAAAAG 59.759 43.478 6.13 0.00 0.00 2.27
241 242 3.119531 AGCATTGATCGCGGATTTGAAAA 60.120 39.130 6.13 0.00 0.00 2.29
242 243 2.423185 AGCATTGATCGCGGATTTGAAA 59.577 40.909 6.13 0.00 0.00 2.69
243 244 2.016318 AGCATTGATCGCGGATTTGAA 58.984 42.857 6.13 0.00 0.00 2.69
244 245 1.667236 AGCATTGATCGCGGATTTGA 58.333 45.000 6.13 0.00 0.00 2.69
245 246 2.480224 AAGCATTGATCGCGGATTTG 57.520 45.000 6.13 0.00 0.00 2.32
280 281 9.144747 CGAATTCTATTTCTTCTGAGAACTTGA 57.855 33.333 3.52 0.00 41.46 3.02
281 282 8.930760 ACGAATTCTATTTCTTCTGAGAACTTG 58.069 33.333 3.52 0.00 41.46 3.16
282 283 8.930760 CACGAATTCTATTTCTTCTGAGAACTT 58.069 33.333 3.52 0.00 41.46 2.66
283 284 8.307483 TCACGAATTCTATTTCTTCTGAGAACT 58.693 33.333 3.52 0.00 41.46 3.01
284 285 8.467402 TCACGAATTCTATTTCTTCTGAGAAC 57.533 34.615 3.52 0.00 41.46 3.01
285 286 7.276658 GCTCACGAATTCTATTTCTTCTGAGAA 59.723 37.037 3.52 0.00 40.07 2.87
286 287 6.754209 GCTCACGAATTCTATTTCTTCTGAGA 59.246 38.462 3.52 0.00 32.26 3.27
287 288 6.291532 CGCTCACGAATTCTATTTCTTCTGAG 60.292 42.308 3.52 0.00 43.93 3.35
288 289 5.516696 CGCTCACGAATTCTATTTCTTCTGA 59.483 40.000 3.52 0.00 43.93 3.27
289 290 5.722237 CGCTCACGAATTCTATTTCTTCTG 58.278 41.667 3.52 0.00 43.93 3.02
290 291 5.957910 CGCTCACGAATTCTATTTCTTCT 57.042 39.130 3.52 0.00 43.93 2.85
305 306 4.661776 CACGAATTCAAAATATCGCTCACG 59.338 41.667 6.22 0.00 38.80 4.35
306 307 5.449113 CACACGAATTCAAAATATCGCTCAC 59.551 40.000 6.22 0.00 38.80 3.51
307 308 5.559227 CACACGAATTCAAAATATCGCTCA 58.441 37.500 6.22 0.00 38.80 4.26
308 309 4.434588 GCACACGAATTCAAAATATCGCTC 59.565 41.667 6.22 0.00 38.80 5.03
309 310 4.142708 TGCACACGAATTCAAAATATCGCT 60.143 37.500 6.22 0.00 38.80 4.93
310 311 4.094911 TGCACACGAATTCAAAATATCGC 58.905 39.130 6.22 0.00 38.80 4.58
311 312 6.795053 ATTGCACACGAATTCAAAATATCG 57.205 33.333 6.22 0.00 40.90 2.92
312 313 9.810231 AAAAATTGCACACGAATTCAAAATATC 57.190 25.926 6.22 0.00 0.00 1.63
371 372 9.887406 TCGTTTCGCTTTCTTCTATTTAAAAAT 57.113 25.926 0.00 0.00 0.00 1.82
372 373 9.161684 GTCGTTTCGCTTTCTTCTATTTAAAAA 57.838 29.630 0.00 0.00 0.00 1.94
373 374 8.553696 AGTCGTTTCGCTTTCTTCTATTTAAAA 58.446 29.630 0.00 0.00 0.00 1.52
374 375 8.080083 AGTCGTTTCGCTTTCTTCTATTTAAA 57.920 30.769 0.00 0.00 0.00 1.52
375 376 7.410087 CGAGTCGTTTCGCTTTCTTCTATTTAA 60.410 37.037 3.82 0.00 33.39 1.52
376 377 6.033196 CGAGTCGTTTCGCTTTCTTCTATTTA 59.967 38.462 3.82 0.00 33.39 1.40
377 378 5.164080 CGAGTCGTTTCGCTTTCTTCTATTT 60.164 40.000 3.82 0.00 33.39 1.40
378 379 4.323868 CGAGTCGTTTCGCTTTCTTCTATT 59.676 41.667 3.82 0.00 33.39 1.73
379 380 3.852536 CGAGTCGTTTCGCTTTCTTCTAT 59.147 43.478 3.82 0.00 33.39 1.98
380 381 3.058708 TCGAGTCGTTTCGCTTTCTTCTA 60.059 43.478 13.12 0.00 40.29 2.10
381 382 2.052157 CGAGTCGTTTCGCTTTCTTCT 58.948 47.619 3.82 0.00 33.39 2.85
382 383 2.049228 TCGAGTCGTTTCGCTTTCTTC 58.951 47.619 13.12 0.00 40.29 2.87
383 384 2.129823 TCGAGTCGTTTCGCTTTCTT 57.870 45.000 13.12 0.00 40.29 2.52
384 385 2.129823 TTCGAGTCGTTTCGCTTTCT 57.870 45.000 13.12 0.00 40.29 2.52
385 386 2.916735 TTTCGAGTCGTTTCGCTTTC 57.083 45.000 13.12 0.00 40.29 2.62
386 387 3.661758 TTTTTCGAGTCGTTTCGCTTT 57.338 38.095 13.12 0.00 40.29 3.51
403 404 2.224670 TGTCCCGTACATCAGCCTTTTT 60.225 45.455 0.00 0.00 31.43 1.94
404 405 1.349688 TGTCCCGTACATCAGCCTTTT 59.650 47.619 0.00 0.00 31.43 2.27
405 406 0.981183 TGTCCCGTACATCAGCCTTT 59.019 50.000 0.00 0.00 31.43 3.11
406 407 1.134401 CATGTCCCGTACATCAGCCTT 60.134 52.381 0.00 0.00 46.15 4.35
407 408 0.465705 CATGTCCCGTACATCAGCCT 59.534 55.000 0.00 0.00 46.15 4.58
408 409 0.532862 CCATGTCCCGTACATCAGCC 60.533 60.000 0.00 0.00 46.15 4.85
409 410 0.464036 TCCATGTCCCGTACATCAGC 59.536 55.000 0.00 0.00 46.15 4.26
410 411 1.757118 ACTCCATGTCCCGTACATCAG 59.243 52.381 0.00 1.38 46.15 2.90
411 412 1.860641 ACTCCATGTCCCGTACATCA 58.139 50.000 0.00 0.00 46.15 3.07
412 413 4.602340 ATTACTCCATGTCCCGTACATC 57.398 45.455 0.00 0.00 46.15 3.06
414 415 3.770388 TCAATTACTCCATGTCCCGTACA 59.230 43.478 0.00 0.00 43.86 2.90
415 416 4.369182 CTCAATTACTCCATGTCCCGTAC 58.631 47.826 0.00 0.00 0.00 3.67
416 417 3.181469 GCTCAATTACTCCATGTCCCGTA 60.181 47.826 0.00 0.00 0.00 4.02
417 418 2.420129 GCTCAATTACTCCATGTCCCGT 60.420 50.000 0.00 0.00 0.00 5.28
418 419 2.158900 AGCTCAATTACTCCATGTCCCG 60.159 50.000 0.00 0.00 0.00 5.14
419 420 3.471680 GAGCTCAATTACTCCATGTCCC 58.528 50.000 9.40 0.00 0.00 4.46
424 425 1.202698 GCCCGAGCTCAATTACTCCAT 60.203 52.381 15.40 0.00 35.50 3.41
716 717 2.262471 CTGTCGAAGGTACCGGACGG 62.262 65.000 20.70 20.70 42.03 4.79
1040 1042 0.593128 GATTTGTGCCTTCGCTGTGT 59.407 50.000 0.00 0.00 35.36 3.72
1717 2014 6.581542 CCTCCGTAAACTAATATAAGAGCGTG 59.418 42.308 0.00 0.00 0.00 5.34
1901 2198 3.382865 TGCAACATTAAGGAAACACAGCA 59.617 39.130 0.00 0.00 0.00 4.41
2086 2383 1.614241 CCTCCCCAACCGAGTCGAAT 61.614 60.000 15.64 0.00 0.00 3.34
2159 2456 3.258372 TCAACATTCAGTCGGCTCTTACT 59.742 43.478 0.00 0.00 0.00 2.24
2231 2528 4.940654 GCCCCAGCAAAATAGCAAAAATTA 59.059 37.500 0.00 0.00 39.53 1.40
2242 2539 1.075374 TGTCAGTAGCCCCAGCAAAAT 59.925 47.619 0.00 0.00 43.56 1.82
2828 3148 1.179174 AGCACACGAGGCTGTCTACA 61.179 55.000 0.00 0.00 40.80 2.74
2829 3149 0.809385 TAGCACACGAGGCTGTCTAC 59.191 55.000 0.00 0.00 42.62 2.59
2830 3150 1.095600 CTAGCACACGAGGCTGTCTA 58.904 55.000 0.00 0.00 42.62 2.59
2831 3151 0.609406 TCTAGCACACGAGGCTGTCT 60.609 55.000 0.00 0.00 42.62 3.41
2832 3152 0.179150 CTCTAGCACACGAGGCTGTC 60.179 60.000 0.00 0.00 42.62 3.51
2833 3153 1.886585 CTCTAGCACACGAGGCTGT 59.113 57.895 0.00 0.00 42.62 4.40
2834 3154 1.518133 GCTCTAGCACACGAGGCTG 60.518 63.158 0.00 0.00 42.62 4.85
2835 3155 2.716017 GGCTCTAGCACACGAGGCT 61.716 63.158 4.07 0.00 45.97 4.58
2836 3156 2.202810 GGCTCTAGCACACGAGGC 60.203 66.667 4.07 0.00 43.97 4.70
2837 3157 1.140589 CTGGCTCTAGCACACGAGG 59.859 63.158 4.07 0.00 44.36 4.63
2838 3158 1.140589 CCTGGCTCTAGCACACGAG 59.859 63.158 4.07 0.00 44.36 4.18
2839 3159 0.898326 TTCCTGGCTCTAGCACACGA 60.898 55.000 4.07 0.00 44.36 4.35
2840 3160 0.176680 ATTCCTGGCTCTAGCACACG 59.823 55.000 4.07 0.00 44.36 4.49
2841 3161 1.065854 ACATTCCTGGCTCTAGCACAC 60.066 52.381 4.07 0.00 44.36 3.82
2842 3162 1.208052 GACATTCCTGGCTCTAGCACA 59.792 52.381 4.07 0.00 44.36 4.57
2843 3163 1.208052 TGACATTCCTGGCTCTAGCAC 59.792 52.381 4.07 0.00 44.36 4.40
2844 3164 1.208052 GTGACATTCCTGGCTCTAGCA 59.792 52.381 4.07 0.00 44.36 3.49
2845 3165 1.484240 AGTGACATTCCTGGCTCTAGC 59.516 52.381 0.00 0.00 32.45 3.42
2846 3166 2.499289 ACAGTGACATTCCTGGCTCTAG 59.501 50.000 0.00 0.00 32.45 2.43
2847 3167 2.234661 CACAGTGACATTCCTGGCTCTA 59.765 50.000 0.00 0.00 32.45 2.43
2848 3168 1.002888 CACAGTGACATTCCTGGCTCT 59.997 52.381 0.00 0.00 34.53 4.09
2849 3169 1.002430 TCACAGTGACATTCCTGGCTC 59.998 52.381 0.00 0.00 32.90 4.70
2850 3170 1.059098 TCACAGTGACATTCCTGGCT 58.941 50.000 0.00 0.00 32.90 4.75
2851 3171 1.896220 TTCACAGTGACATTCCTGGC 58.104 50.000 1.52 0.00 32.90 4.85
2852 3172 3.213506 TGTTTCACAGTGACATTCCTGG 58.786 45.455 1.52 0.00 32.90 4.45
2853 3173 4.516321 TCATGTTTCACAGTGACATTCCTG 59.484 41.667 1.52 0.00 32.01 3.86
2854 3174 4.717877 TCATGTTTCACAGTGACATTCCT 58.282 39.130 1.52 0.00 32.01 3.36
2855 3175 4.756642 TCTCATGTTTCACAGTGACATTCC 59.243 41.667 1.52 0.00 32.01 3.01
2856 3176 5.929697 TCTCATGTTTCACAGTGACATTC 57.070 39.130 1.52 0.00 32.01 2.67
2857 3177 6.487668 TCATTCTCATGTTTCACAGTGACATT 59.512 34.615 1.52 0.00 32.01 2.71
2858 3178 5.999600 TCATTCTCATGTTTCACAGTGACAT 59.000 36.000 1.52 2.20 34.52 3.06
2859 3179 5.367302 TCATTCTCATGTTTCACAGTGACA 58.633 37.500 1.52 0.00 0.00 3.58
2860 3180 5.929697 TCATTCTCATGTTTCACAGTGAC 57.070 39.130 1.52 0.00 0.00 3.67
2861 3181 6.232692 TCATCATTCTCATGTTTCACAGTGA 58.767 36.000 0.00 0.00 0.00 3.41
2862 3182 6.403309 CCTCATCATTCTCATGTTTCACAGTG 60.403 42.308 0.00 0.00 0.00 3.66
2863 3183 5.646793 CCTCATCATTCTCATGTTTCACAGT 59.353 40.000 0.00 0.00 0.00 3.55
2864 3184 5.878669 TCCTCATCATTCTCATGTTTCACAG 59.121 40.000 0.00 0.00 0.00 3.66
2865 3185 5.807909 TCCTCATCATTCTCATGTTTCACA 58.192 37.500 0.00 0.00 0.00 3.58
2866 3186 6.939132 ATCCTCATCATTCTCATGTTTCAC 57.061 37.500 0.00 0.00 0.00 3.18
2867 3187 6.709397 GCTATCCTCATCATTCTCATGTTTCA 59.291 38.462 0.00 0.00 0.00 2.69
2868 3188 6.935771 AGCTATCCTCATCATTCTCATGTTTC 59.064 38.462 0.00 0.00 0.00 2.78
2869 3189 6.711194 CAGCTATCCTCATCATTCTCATGTTT 59.289 38.462 0.00 0.00 0.00 2.83
2870 3190 6.183361 ACAGCTATCCTCATCATTCTCATGTT 60.183 38.462 0.00 0.00 0.00 2.71
2871 3191 5.307456 ACAGCTATCCTCATCATTCTCATGT 59.693 40.000 0.00 0.00 0.00 3.21
2872 3192 5.795972 ACAGCTATCCTCATCATTCTCATG 58.204 41.667 0.00 0.00 0.00 3.07
2873 3193 6.952938 TCTACAGCTATCCTCATCATTCTCAT 59.047 38.462 0.00 0.00 0.00 2.90
2874 3194 6.208402 GTCTACAGCTATCCTCATCATTCTCA 59.792 42.308 0.00 0.00 0.00 3.27
2875 3195 6.208402 TGTCTACAGCTATCCTCATCATTCTC 59.792 42.308 0.00 0.00 0.00 2.87
2876 3196 6.073981 TGTCTACAGCTATCCTCATCATTCT 58.926 40.000 0.00 0.00 0.00 2.40
2877 3197 6.338214 TGTCTACAGCTATCCTCATCATTC 57.662 41.667 0.00 0.00 0.00 2.67
2878 3198 6.343716 CTGTCTACAGCTATCCTCATCATT 57.656 41.667 0.00 0.00 37.15 2.57
2879 3199 5.981088 CTGTCTACAGCTATCCTCATCAT 57.019 43.478 0.00 0.00 37.15 2.45
3160 3789 3.709987 GCAACATGGCCATCATTTCTAC 58.290 45.455 17.61 0.00 32.92 2.59
3496 4150 6.183360 CCTGCAAATCAAACATGTTTAGCATC 60.183 38.462 22.87 11.37 35.19 3.91
3736 4390 5.981088 TCCAATGCTTTATTGTCACACAT 57.019 34.783 0.00 0.00 43.78 3.21


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

AutoCloner maintained by Alex Coulton.