Multiple sequence alignment - TraesCS4D01G101800

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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 TraesCS4D01G101800 chr4D 100.000 6045 0 0 1 6045 80140040 80146084 0.000000e+00 11164
1 TraesCS4D01G101800 chr4B 95.607 5713 150 34 384 6042 112350870 112356535 0.000000e+00 9066
2 TraesCS4D01G101800 chr4A 95.137 5737 156 45 384 6045 505795306 505789618 0.000000e+00 8935
3 TraesCS4D01G101800 chr4A 93.671 395 23 1 1 393 477304785 477304391 1.880000e-164 590
4 TraesCS4D01G101800 chr2A 85.880 2408 235 42 1953 4321 779205905 779203564 0.000000e+00 2466
5 TraesCS4D01G101800 chr2A 84.141 227 31 1 3758 3984 779203325 779203546 1.320000e-51 215
6 TraesCS4D01G101800 chr2A 81.250 160 11 3 4617 4770 779202990 779202844 1.780000e-20 111
7 TraesCS4D01G101800 chr2B 85.963 1204 133 14 1953 3132 777334778 777335969 0.000000e+00 1254
8 TraesCS4D01G101800 chr2B 83.970 811 79 24 3103 3892 777335979 777336759 0.000000e+00 730
9 TraesCS4D01G101800 chr2B 89.835 423 40 2 3901 4321 777336930 777337351 1.920000e-149 540
10 TraesCS4D01G101800 chr6D 94.987 399 17 2 1 397 428663049 428663446 1.850000e-174 623
11 TraesCS4D01G101800 chr6D 92.965 398 25 2 1 395 45623113 45622716 1.460000e-160 577
12 TraesCS4D01G101800 chr6D 93.350 391 24 1 1 389 344157406 344157796 1.460000e-160 577
13 TraesCS4D01G101800 chr2D 94.430 395 20 1 1 393 368975297 368975691 1.860000e-169 606
14 TraesCS4D01G101800 chr2D 93.655 394 22 2 1 392 567015448 567015840 2.430000e-163 586
15 TraesCS4D01G101800 chr5D 94.162 394 21 1 1 392 519543644 519543251 3.120000e-167 599
16 TraesCS4D01G101800 chr7A 93.367 392 24 1 1 390 82174647 82175038 4.060000e-161 579
17 TraesCS4D01G101800 chr5A 92.965 398 25 2 1 395 387237602 387237205 1.460000e-160 577
18 TraesCS4D01G101800 chr5A 85.946 185 16 4 1211 1395 563769678 563769852 8.000000e-44 189
19 TraesCS4D01G101800 chr5A 92.157 102 8 0 1438 1539 563769863 563769964 1.760000e-30 145


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 TraesCS4D01G101800 chr4D 80140040 80146084 6044 False 11164.000000 11164 100.000000 1 6045 1 chr4D.!!$F1 6044
1 TraesCS4D01G101800 chr4B 112350870 112356535 5665 False 9066.000000 9066 95.607000 384 6042 1 chr4B.!!$F1 5658
2 TraesCS4D01G101800 chr4A 505789618 505795306 5688 True 8935.000000 8935 95.137000 384 6045 1 chr4A.!!$R2 5661
3 TraesCS4D01G101800 chr2A 779202844 779205905 3061 True 1288.500000 2466 83.565000 1953 4770 2 chr2A.!!$R1 2817
4 TraesCS4D01G101800 chr2B 777334778 777337351 2573 False 841.333333 1254 86.589333 1953 4321 3 chr2B.!!$F1 2368

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
328 329 0.107361 CACGACCCCAAATCCCTACC 60.107 60.000 0.00 0.0 0.00 3.18 F
936 962 0.178891 TCCCCCACAGCTCTTCTCTT 60.179 55.000 0.00 0.0 0.00 2.85 F
1594 1642 1.212751 GGCAAATTCGAGGTGGTGC 59.787 57.895 0.00 0.0 0.00 5.01 F
2430 2508 2.158813 TGTGAACCCTCAGTTTCTCCAC 60.159 50.000 0.00 0.0 39.40 4.02 F
2835 2925 4.130118 TCTTCTTCAGCAACTGAACCTTC 58.870 43.478 5.94 0.0 44.27 3.46 F
2878 2968 4.621068 TGCACTCTAAATGTAATGCAGC 57.379 40.909 0.00 0.0 38.11 5.25 F
3065 3155 5.477984 TGCTCTTTATTGACAGGAAATGCTT 59.522 36.000 0.00 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1397 1428 0.383949 CAACCAACCACCCAAACTCG 59.616 55.000 0.00 0.00 0.00 4.18 R
2878 2968 0.039256 CACACATTTGGCCACCTTCG 60.039 55.000 3.88 0.00 0.00 3.79 R
3215 3357 2.936919 AGTGACTGTGATTGCTTGGA 57.063 45.000 0.00 0.00 0.00 3.53 R
4306 4633 0.398318 ACCTGACTGAAGCTTGGTCC 59.602 55.000 19.90 2.06 0.00 4.46 R
4837 5598 1.808390 CCGTAACGGGCTAGTGCAC 60.808 63.158 9.40 9.40 44.15 4.57 R
5014 5775 7.587037 TCTTCTTGGAGAATCAAATGTTTGT 57.413 32.000 5.48 0.00 33.13 2.83 R
5129 5895 4.405680 AGGGCTAAACAGAAAGCAAAAAGT 59.594 37.500 0.00 0.00 40.61 2.66 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
25 26 5.320549 GATTGGCACAGTCATTTGAATCT 57.679 39.130 0.00 0.00 44.84 2.40
26 27 5.717119 GATTGGCACAGTCATTTGAATCTT 58.283 37.500 0.00 0.00 44.84 2.40
27 28 4.771590 TGGCACAGTCATTTGAATCTTC 57.228 40.909 0.00 0.00 0.00 2.87
28 29 4.143543 TGGCACAGTCATTTGAATCTTCA 58.856 39.130 0.00 0.00 34.92 3.02
29 30 4.583907 TGGCACAGTCATTTGAATCTTCAA 59.416 37.500 1.28 1.28 44.78 2.69
43 44 7.345422 TGAATCTTCAAAATGACTTGGTTGA 57.655 32.000 0.00 0.00 33.55 3.18
44 45 7.428020 TGAATCTTCAAAATGACTTGGTTGAG 58.572 34.615 0.00 0.00 33.55 3.02
45 46 5.186996 TCTTCAAAATGACTTGGTTGAGC 57.813 39.130 0.00 0.00 31.98 4.26
46 47 4.644234 TCTTCAAAATGACTTGGTTGAGCA 59.356 37.500 0.00 0.00 31.98 4.26
47 48 4.305989 TCAAAATGACTTGGTTGAGCAC 57.694 40.909 0.00 0.00 0.00 4.40
48 49 3.044986 CAAAATGACTTGGTTGAGCACG 58.955 45.455 0.00 0.00 0.00 5.34
49 50 1.967319 AATGACTTGGTTGAGCACGT 58.033 45.000 0.00 0.00 0.00 4.49
50 51 1.229428 ATGACTTGGTTGAGCACGTG 58.771 50.000 12.28 12.28 0.00 4.49
51 52 0.107897 TGACTTGGTTGAGCACGTGT 60.108 50.000 18.38 3.69 0.00 4.49
52 53 0.304705 GACTTGGTTGAGCACGTGTG 59.695 55.000 18.38 0.00 0.00 3.82
53 54 1.095228 ACTTGGTTGAGCACGTGTGG 61.095 55.000 18.38 0.00 0.00 4.17
54 55 1.785041 CTTGGTTGAGCACGTGTGGG 61.785 60.000 18.38 0.00 0.00 4.61
55 56 2.110213 GGTTGAGCACGTGTGGGA 59.890 61.111 18.38 0.00 0.00 4.37
56 57 1.302511 GGTTGAGCACGTGTGGGAT 60.303 57.895 18.38 0.00 0.00 3.85
57 58 0.889186 GGTTGAGCACGTGTGGGATT 60.889 55.000 18.38 0.00 0.00 3.01
58 59 1.609580 GGTTGAGCACGTGTGGGATTA 60.610 52.381 18.38 0.00 0.00 1.75
59 60 1.463444 GTTGAGCACGTGTGGGATTAC 59.537 52.381 18.38 3.27 0.00 1.89
60 61 0.682292 TGAGCACGTGTGGGATTACA 59.318 50.000 18.38 3.61 0.00 2.41
61 62 1.277842 TGAGCACGTGTGGGATTACAT 59.722 47.619 18.38 0.00 32.43 2.29
62 63 2.290008 TGAGCACGTGTGGGATTACATT 60.290 45.455 18.38 0.00 32.43 2.71
63 64 2.083774 AGCACGTGTGGGATTACATTG 58.916 47.619 18.38 0.00 32.43 2.82
64 65 1.132262 GCACGTGTGGGATTACATTGG 59.868 52.381 18.38 0.00 32.43 3.16
65 66 1.132262 CACGTGTGGGATTACATTGGC 59.868 52.381 7.58 0.00 32.43 4.52
66 67 1.271652 ACGTGTGGGATTACATTGGCA 60.272 47.619 0.00 0.00 32.43 4.92
67 68 1.815613 CGTGTGGGATTACATTGGCAA 59.184 47.619 0.68 0.68 32.43 4.52
68 69 2.415357 CGTGTGGGATTACATTGGCAAC 60.415 50.000 0.00 0.00 32.43 4.17
69 70 2.094234 GTGTGGGATTACATTGGCAACC 60.094 50.000 0.00 0.00 32.43 3.77
70 71 2.175202 GTGGGATTACATTGGCAACCA 58.825 47.619 0.00 0.00 0.00 3.67
82 83 4.955925 TTGGCAACCAATAGACGTATTG 57.044 40.909 0.00 4.37 43.67 1.90
98 99 8.330466 AGACGTATTGGTTCATTTTATGTTCA 57.670 30.769 0.00 0.00 0.00 3.18
99 100 8.788806 AGACGTATTGGTTCATTTTATGTTCAA 58.211 29.630 0.00 0.00 0.00 2.69
100 101 8.736751 ACGTATTGGTTCATTTTATGTTCAAC 57.263 30.769 0.00 0.00 0.00 3.18
101 102 8.573035 ACGTATTGGTTCATTTTATGTTCAACT 58.427 29.630 0.00 0.00 0.00 3.16
106 107 9.959749 TTGGTTCATTTTATGTTCAACTAAGAC 57.040 29.630 0.00 0.00 0.00 3.01
107 108 9.126151 TGGTTCATTTTATGTTCAACTAAGACA 57.874 29.630 0.00 0.00 0.00 3.41
108 109 9.959749 GGTTCATTTTATGTTCAACTAAGACAA 57.040 29.630 0.00 0.00 0.00 3.18
118 119 8.781067 TGTTCAACTAAGACAATTTCGATTTG 57.219 30.769 6.98 6.98 0.00 2.32
119 120 7.860373 TGTTCAACTAAGACAATTTCGATTTGG 59.140 33.333 11.83 0.00 0.00 3.28
120 121 7.504924 TCAACTAAGACAATTTCGATTTGGT 57.495 32.000 11.83 0.00 0.00 3.67
121 122 7.936584 TCAACTAAGACAATTTCGATTTGGTT 58.063 30.769 11.83 7.99 0.00 3.67
122 123 9.058174 TCAACTAAGACAATTTCGATTTGGTTA 57.942 29.630 11.83 8.52 0.00 2.85
123 124 9.840427 CAACTAAGACAATTTCGATTTGGTTAT 57.160 29.630 11.83 0.99 0.00 1.89
197 198 8.519492 AATTTTCAGACAAATATTTGGACGTG 57.481 30.769 27.43 18.84 42.34 4.49
198 199 4.678509 TCAGACAAATATTTGGACGTGC 57.321 40.909 27.43 0.00 42.34 5.34
199 200 4.068599 TCAGACAAATATTTGGACGTGCA 58.931 39.130 27.43 5.33 42.34 4.57
200 201 4.517075 TCAGACAAATATTTGGACGTGCAA 59.483 37.500 27.43 19.24 42.34 4.08
201 202 5.009110 TCAGACAAATATTTGGACGTGCAAA 59.991 36.000 32.70 32.70 42.34 3.68
202 203 5.116983 CAGACAAATATTTGGACGTGCAAAC 59.883 40.000 33.15 19.97 42.34 2.93
203 204 5.009610 AGACAAATATTTGGACGTGCAAACT 59.990 36.000 33.15 23.69 42.34 2.66
204 205 6.205853 AGACAAATATTTGGACGTGCAAACTA 59.794 34.615 33.15 24.77 42.34 2.24
205 206 6.378582 ACAAATATTTGGACGTGCAAACTAG 58.621 36.000 33.15 22.85 42.34 2.57
206 207 6.016610 ACAAATATTTGGACGTGCAAACTAGT 60.017 34.615 33.15 23.39 42.34 2.57
207 208 6.569179 AATATTTGGACGTGCAAACTAGTT 57.431 33.333 33.15 20.98 0.00 2.24
208 209 4.911514 ATTTGGACGTGCAAACTAGTTT 57.088 36.364 33.15 16.48 0.00 2.66
209 210 4.705337 TTTGGACGTGCAAACTAGTTTT 57.295 36.364 28.37 3.60 0.00 2.43
210 211 3.684103 TGGACGTGCAAACTAGTTTTG 57.316 42.857 18.25 14.09 46.57 2.44
211 212 3.271729 TGGACGTGCAAACTAGTTTTGA 58.728 40.909 18.25 5.12 46.76 2.69
212 213 3.880490 TGGACGTGCAAACTAGTTTTGAT 59.120 39.130 18.25 2.92 46.76 2.57
213 214 5.057819 TGGACGTGCAAACTAGTTTTGATA 58.942 37.500 18.25 2.72 46.76 2.15
214 215 5.527951 TGGACGTGCAAACTAGTTTTGATAA 59.472 36.000 18.25 0.19 46.76 1.75
215 216 6.077838 GGACGTGCAAACTAGTTTTGATAAG 58.922 40.000 18.25 7.36 46.76 1.73
216 217 6.073440 GGACGTGCAAACTAGTTTTGATAAGA 60.073 38.462 18.25 0.00 46.76 2.10
217 218 7.254227 ACGTGCAAACTAGTTTTGATAAGAA 57.746 32.000 18.25 0.00 46.76 2.52
218 219 7.871853 ACGTGCAAACTAGTTTTGATAAGAAT 58.128 30.769 18.25 0.00 46.76 2.40
219 220 8.995220 ACGTGCAAACTAGTTTTGATAAGAATA 58.005 29.630 18.25 0.00 46.76 1.75
220 221 9.988350 CGTGCAAACTAGTTTTGATAAGAATAT 57.012 29.630 18.25 0.00 46.76 1.28
233 234 9.598517 TTTGATAAGAATATGGACATTTTTGGC 57.401 29.630 0.00 0.00 0.00 4.52
234 235 7.725251 TGATAAGAATATGGACATTTTTGGCC 58.275 34.615 0.00 0.00 37.53 5.36
235 236 5.357742 AAGAATATGGACATTTTTGGCCC 57.642 39.130 0.00 0.00 35.66 5.80
236 237 4.623863 AGAATATGGACATTTTTGGCCCT 58.376 39.130 0.00 0.00 35.66 5.19
237 238 4.406649 AGAATATGGACATTTTTGGCCCTG 59.593 41.667 0.00 0.00 35.66 4.45
238 239 2.323999 ATGGACATTTTTGGCCCTGA 57.676 45.000 0.00 0.00 35.66 3.86
239 240 1.337118 TGGACATTTTTGGCCCTGAC 58.663 50.000 0.00 0.00 35.66 3.51
240 241 0.243636 GGACATTTTTGGCCCTGACG 59.756 55.000 0.00 0.00 0.00 4.35
241 242 0.243636 GACATTTTTGGCCCTGACGG 59.756 55.000 0.00 0.00 0.00 4.79
242 243 0.178975 ACATTTTTGGCCCTGACGGA 60.179 50.000 0.00 0.00 0.00 4.69
243 244 1.185315 CATTTTTGGCCCTGACGGAT 58.815 50.000 0.00 0.00 0.00 4.18
244 245 2.291282 ACATTTTTGGCCCTGACGGATA 60.291 45.455 0.00 0.00 0.00 2.59
245 246 2.122783 TTTTTGGCCCTGACGGATAG 57.877 50.000 0.00 0.00 0.00 2.08
246 247 0.254747 TTTTGGCCCTGACGGATAGG 59.745 55.000 0.00 0.00 35.01 2.57
247 248 0.619255 TTTGGCCCTGACGGATAGGA 60.619 55.000 0.00 0.00 37.52 2.94
248 249 0.399949 TTGGCCCTGACGGATAGGAT 60.400 55.000 0.00 0.00 37.52 3.24
249 250 1.121407 TGGCCCTGACGGATAGGATG 61.121 60.000 0.00 0.00 37.52 3.51
250 251 1.674057 GCCCTGACGGATAGGATGG 59.326 63.158 3.73 0.00 37.52 3.51
251 252 1.831652 GCCCTGACGGATAGGATGGG 61.832 65.000 3.73 0.00 37.52 4.00
252 253 1.194781 CCCTGACGGATAGGATGGGG 61.195 65.000 3.73 0.00 37.52 4.96
253 254 1.674057 CTGACGGATAGGATGGGGC 59.326 63.158 0.00 0.00 0.00 5.80
254 255 1.074850 TGACGGATAGGATGGGGCA 60.075 57.895 0.00 0.00 0.00 5.36
255 256 0.692756 TGACGGATAGGATGGGGCAA 60.693 55.000 0.00 0.00 0.00 4.52
256 257 0.472471 GACGGATAGGATGGGGCAAA 59.528 55.000 0.00 0.00 0.00 3.68
257 258 1.073923 GACGGATAGGATGGGGCAAAT 59.926 52.381 0.00 0.00 0.00 2.32
258 259 1.202927 ACGGATAGGATGGGGCAAATG 60.203 52.381 0.00 0.00 0.00 2.32
259 260 1.887956 CGGATAGGATGGGGCAAATGG 60.888 57.143 0.00 0.00 0.00 3.16
260 261 1.428912 GGATAGGATGGGGCAAATGGA 59.571 52.381 0.00 0.00 0.00 3.41
261 262 2.043526 GGATAGGATGGGGCAAATGGAT 59.956 50.000 0.00 0.00 0.00 3.41
262 263 2.681319 TAGGATGGGGCAAATGGATG 57.319 50.000 0.00 0.00 0.00 3.51
263 264 0.761702 AGGATGGGGCAAATGGATGC 60.762 55.000 0.00 0.00 45.67 3.91
273 274 2.910479 ATGGATGCGGCCATGCTG 60.910 61.111 2.24 0.00 46.62 4.41
297 298 4.609018 CGGCTACCGCATCCCAGG 62.609 72.222 0.00 0.00 41.17 4.45
298 299 3.161450 GGCTACCGCATCCCAGGA 61.161 66.667 0.00 0.00 38.10 3.86
299 300 2.109181 GCTACCGCATCCCAGGAC 59.891 66.667 0.00 0.00 35.78 3.85
300 301 2.731571 GCTACCGCATCCCAGGACA 61.732 63.158 0.00 0.00 35.78 4.02
301 302 1.144057 CTACCGCATCCCAGGACAC 59.856 63.158 0.00 0.00 0.00 3.67
302 303 2.629050 CTACCGCATCCCAGGACACG 62.629 65.000 3.74 3.74 0.00 4.49
306 307 4.838152 CATCCCAGGACACGCCCG 62.838 72.222 0.00 0.00 37.37 6.13
320 321 3.943691 CCCGGACACGACCCCAAA 61.944 66.667 0.73 0.00 44.60 3.28
321 322 2.349755 CCGGACACGACCCCAAAT 59.650 61.111 0.00 0.00 44.60 2.32
322 323 1.743995 CCGGACACGACCCCAAATC 60.744 63.158 0.00 0.00 44.60 2.17
323 324 1.743995 CGGACACGACCCCAAATCC 60.744 63.158 0.00 0.00 44.60 3.01
324 325 1.378119 GGACACGACCCCAAATCCC 60.378 63.158 0.00 0.00 0.00 3.85
325 326 1.683441 GACACGACCCCAAATCCCT 59.317 57.895 0.00 0.00 0.00 4.20
326 327 0.906775 GACACGACCCCAAATCCCTA 59.093 55.000 0.00 0.00 0.00 3.53
327 328 0.616891 ACACGACCCCAAATCCCTAC 59.383 55.000 0.00 0.00 0.00 3.18
328 329 0.107361 CACGACCCCAAATCCCTACC 60.107 60.000 0.00 0.00 0.00 3.18
329 330 1.276859 ACGACCCCAAATCCCTACCC 61.277 60.000 0.00 0.00 0.00 3.69
330 331 1.276140 CGACCCCAAATCCCTACCCA 61.276 60.000 0.00 0.00 0.00 4.51
331 332 1.004436 GACCCCAAATCCCTACCCAA 58.996 55.000 0.00 0.00 0.00 4.12
332 333 1.359818 GACCCCAAATCCCTACCCAAA 59.640 52.381 0.00 0.00 0.00 3.28
333 334 1.078159 ACCCCAAATCCCTACCCAAAC 59.922 52.381 0.00 0.00 0.00 2.93
334 335 1.470051 CCCAAATCCCTACCCAAACG 58.530 55.000 0.00 0.00 0.00 3.60
335 336 1.470051 CCAAATCCCTACCCAAACGG 58.530 55.000 0.00 0.00 37.81 4.44
336 337 1.004979 CCAAATCCCTACCCAAACGGA 59.995 52.381 0.00 0.00 34.64 4.69
337 338 2.089201 CAAATCCCTACCCAAACGGAC 58.911 52.381 0.00 0.00 34.64 4.79
338 339 1.364269 AATCCCTACCCAAACGGACA 58.636 50.000 0.00 0.00 34.64 4.02
339 340 0.909623 ATCCCTACCCAAACGGACAG 59.090 55.000 0.00 0.00 34.64 3.51
340 341 0.178926 TCCCTACCCAAACGGACAGA 60.179 55.000 0.00 0.00 34.64 3.41
341 342 0.688487 CCCTACCCAAACGGACAGAA 59.312 55.000 0.00 0.00 34.64 3.02
342 343 1.280998 CCCTACCCAAACGGACAGAAT 59.719 52.381 0.00 0.00 34.64 2.40
343 344 2.290705 CCCTACCCAAACGGACAGAATT 60.291 50.000 0.00 0.00 34.64 2.17
344 345 3.007635 CCTACCCAAACGGACAGAATTC 58.992 50.000 0.00 0.00 34.64 2.17
345 346 1.519408 ACCCAAACGGACAGAATTCG 58.481 50.000 0.00 0.00 34.64 3.34
346 347 0.802494 CCCAAACGGACAGAATTCGG 59.198 55.000 3.87 3.87 0.00 4.30
347 348 1.609580 CCCAAACGGACAGAATTCGGA 60.610 52.381 12.79 0.00 0.00 4.55
348 349 1.463444 CCAAACGGACAGAATTCGGAC 59.537 52.381 12.79 6.06 0.00 4.79
349 350 2.139917 CAAACGGACAGAATTCGGACA 58.860 47.619 12.79 0.00 0.00 4.02
350 351 2.536761 AACGGACAGAATTCGGACAA 57.463 45.000 12.79 0.00 0.00 3.18
351 352 2.536761 ACGGACAGAATTCGGACAAA 57.463 45.000 12.79 0.00 0.00 2.83
352 353 2.841215 ACGGACAGAATTCGGACAAAA 58.159 42.857 12.79 0.00 0.00 2.44
353 354 2.546789 ACGGACAGAATTCGGACAAAAC 59.453 45.455 12.79 0.00 0.00 2.43
354 355 2.411031 CGGACAGAATTCGGACAAAACG 60.411 50.000 12.79 1.93 0.00 3.60
355 356 2.095919 GGACAGAATTCGGACAAAACGG 60.096 50.000 12.79 0.00 0.00 4.44
356 357 2.803956 GACAGAATTCGGACAAAACGGA 59.196 45.455 12.79 0.00 0.00 4.69
357 358 2.546789 ACAGAATTCGGACAAAACGGAC 59.453 45.455 12.79 0.00 0.00 4.79
358 359 1.796459 AGAATTCGGACAAAACGGACG 59.204 47.619 0.00 0.00 0.00 4.79
359 360 1.528161 GAATTCGGACAAAACGGACGT 59.472 47.619 0.00 0.00 0.00 4.34
360 361 1.142474 ATTCGGACAAAACGGACGTC 58.858 50.000 7.13 7.13 0.00 4.34
361 362 0.875474 TTCGGACAAAACGGACGTCC 60.875 55.000 25.28 25.28 44.79 4.79
362 363 4.442018 GGACAAAACGGACGTCCA 57.558 55.556 32.80 0.00 46.98 4.02
363 364 2.922779 GGACAAAACGGACGTCCAT 58.077 52.632 32.80 17.77 46.98 3.41
364 365 1.232119 GGACAAAACGGACGTCCATT 58.768 50.000 32.80 23.21 46.98 3.16
365 366 1.605232 GGACAAAACGGACGTCCATTT 59.395 47.619 32.80 27.66 46.98 2.32
366 367 2.603652 GGACAAAACGGACGTCCATTTG 60.604 50.000 36.89 36.89 46.98 2.32
367 368 1.335496 ACAAAACGGACGTCCATTTGG 59.665 47.619 38.79 33.51 42.26 3.28
368 369 0.955905 AAAACGGACGTCCATTTGGG 59.044 50.000 32.80 18.20 31.08 4.12
369 370 0.891904 AAACGGACGTCCATTTGGGG 60.892 55.000 32.80 17.49 37.22 4.96
370 371 2.059345 AACGGACGTCCATTTGGGGT 62.059 55.000 32.80 18.15 37.22 4.95
371 372 1.743995 CGGACGTCCATTTGGGGTC 60.744 63.158 32.80 3.24 37.90 4.46
372 373 1.743995 GGACGTCCATTTGGGGTCG 60.744 63.158 29.75 10.13 38.82 4.79
373 374 2.359478 ACGTCCATTTGGGGTCGC 60.359 61.111 0.00 0.00 37.71 5.19
374 375 3.496131 CGTCCATTTGGGGTCGCG 61.496 66.667 0.00 0.00 37.22 5.87
375 376 3.131478 GTCCATTTGGGGTCGCGG 61.131 66.667 6.13 0.00 37.22 6.46
400 401 3.201930 TGGAGTTGGCCTAATAGCATCAA 59.798 43.478 3.32 0.00 0.00 2.57
438 439 1.517361 CGGCAGCCAGTGAGTGATA 59.483 57.895 13.30 0.00 0.00 2.15
446 447 4.946157 CAGCCAGTGAGTGATAAAGGAAAT 59.054 41.667 0.00 0.00 0.00 2.17
451 453 7.201652 GCCAGTGAGTGATAAAGGAAATAAGAC 60.202 40.741 0.00 0.00 0.00 3.01
549 552 3.249189 ACATCCACGCCACCACCT 61.249 61.111 0.00 0.00 0.00 4.00
553 556 2.748058 ATCCACGCCACCACCTTGTC 62.748 60.000 0.00 0.00 0.00 3.18
702 728 3.314331 ACGCACAGGGTGAGGGAG 61.314 66.667 0.00 0.00 37.65 4.30
720 746 1.006571 GCTCGAGACAACCAACGGA 60.007 57.895 18.75 0.00 0.00 4.69
797 823 0.455633 CCGGTCGTTACAAGAGTCCG 60.456 60.000 0.00 0.00 36.85 4.79
819 845 2.124487 CCCTCTCGCTCCTCGTCT 60.124 66.667 0.00 0.00 39.67 4.18
821 847 2.530497 CCTCTCGCTCCTCGTCTCG 61.530 68.421 0.00 0.00 39.67 4.04
901 927 1.517276 CGACGACGATAGCCATTTCAC 59.483 52.381 0.00 0.00 42.66 3.18
902 928 1.859080 GACGACGATAGCCATTTCACC 59.141 52.381 0.00 0.00 42.67 4.02
926 952 0.628522 TCTCTCTCTCTCCCCCACAG 59.371 60.000 0.00 0.00 0.00 3.66
936 962 0.178891 TCCCCCACAGCTCTTCTCTT 60.179 55.000 0.00 0.00 0.00 2.85
944 970 3.249559 CACAGCTCTTCTCTTTGTGGAAC 59.750 47.826 0.00 0.00 36.41 3.62
1397 1428 1.483415 TGGTCCGGTAGTTAATCTGCC 59.517 52.381 0.00 3.28 43.94 4.85
1548 1580 9.657121 GCTGTTCTGCTGAATTATTATTCTTAC 57.343 33.333 9.40 0.00 40.68 2.34
1575 1610 6.561737 TTTTTGTTGAATATGCCGTCAGTA 57.438 33.333 0.00 0.00 0.00 2.74
1594 1642 1.212751 GGCAAATTCGAGGTGGTGC 59.787 57.895 0.00 0.00 0.00 5.01
1803 1862 8.496916 TGGATCTCCTTGAATCTTTGATTCATA 58.503 33.333 19.47 11.75 37.79 2.15
1806 1865 8.915057 TCTCCTTGAATCTTTGATTCATATCC 57.085 34.615 19.47 0.00 37.79 2.59
1861 1926 2.761208 TGTTCGATGGGTTTGGTTTTGT 59.239 40.909 0.00 0.00 0.00 2.83
1981 2047 3.112580 CGGTGATTTTTCGTTGCTGTTT 58.887 40.909 0.00 0.00 0.00 2.83
2058 2128 8.585471 ATCTCATCTGGAATTTGTTATTGTGT 57.415 30.769 0.00 0.00 0.00 3.72
2282 2360 4.437820 GTGCGTTTCAACTGACTTGATTTC 59.562 41.667 0.00 0.00 38.74 2.17
2430 2508 2.158813 TGTGAACCCTCAGTTTCTCCAC 60.159 50.000 0.00 0.00 39.40 4.02
2835 2925 4.130118 TCTTCTTCAGCAACTGAACCTTC 58.870 43.478 5.94 0.00 44.27 3.46
2878 2968 4.621068 TGCACTCTAAATGTAATGCAGC 57.379 40.909 0.00 0.00 38.11 5.25
3065 3155 5.477984 TGCTCTTTATTGACAGGAAATGCTT 59.522 36.000 0.00 0.00 0.00 3.91
3151 3280 5.679734 AAACATATGACGATCTTCCATGC 57.320 39.130 10.38 0.00 0.00 4.06
3350 3498 5.820423 ACTGTAGTGCAAACAATGAAGTGTA 59.180 36.000 4.83 0.00 0.00 2.90
3930 4254 7.013834 TCCCATGTATTTTCCCTTGTTAGTTT 58.986 34.615 0.00 0.00 0.00 2.66
3932 4256 8.466798 CCCATGTATTTTCCCTTGTTAGTTTAG 58.533 37.037 0.00 0.00 0.00 1.85
4306 4633 8.408601 CAATTAATAGAACATCCTTGGGTGAAG 58.591 37.037 6.95 0.00 0.00 3.02
5014 5775 0.106419 AAACCCCTCGCCAGAAAACA 60.106 50.000 0.00 0.00 0.00 2.83
5044 5805 9.300681 ACATTTGATTCTCCAAGAAGATTGTAA 57.699 29.630 0.00 0.00 37.69 2.41
5129 5895 5.152934 AGAACTTAGGAGGACAAAGGTGTA 58.847 41.667 0.00 0.00 38.41 2.90
5130 5896 4.886496 ACTTAGGAGGACAAAGGTGTAC 57.114 45.455 0.00 0.00 38.41 2.90
5370 6136 7.172868 TCGGTGATTTACAGATAAGGTGTTA 57.827 36.000 0.00 0.00 0.00 2.41
5756 6522 2.262915 GCAGCAGCGTGTAGAGGT 59.737 61.111 0.00 0.00 0.00 3.85
6042 6808 4.899239 CATCCAGGACGGCGAGGC 62.899 72.222 16.62 1.71 33.14 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.921119 TCAAATGACTGTGCCAATCAC 57.079 42.857 0.00 0.00 45.82 3.06
2 3 4.768448 AGATTCAAATGACTGTGCCAATCA 59.232 37.500 0.00 0.00 0.00 2.57
5 6 4.583907 TGAAGATTCAAATGACTGTGCCAA 59.416 37.500 0.00 0.00 33.55 4.52
18 19 7.780064 TCAACCAAGTCATTTTGAAGATTCAA 58.220 30.769 3.91 3.91 44.78 2.69
19 20 7.345422 TCAACCAAGTCATTTTGAAGATTCA 57.655 32.000 0.00 0.00 34.92 2.57
20 21 6.364435 GCTCAACCAAGTCATTTTGAAGATTC 59.636 38.462 0.00 0.00 0.00 2.52
21 22 6.183360 TGCTCAACCAAGTCATTTTGAAGATT 60.183 34.615 0.00 0.00 0.00 2.40
22 23 5.302568 TGCTCAACCAAGTCATTTTGAAGAT 59.697 36.000 0.00 0.00 0.00 2.40
23 24 4.644234 TGCTCAACCAAGTCATTTTGAAGA 59.356 37.500 0.00 0.00 0.00 2.87
24 25 4.741676 GTGCTCAACCAAGTCATTTTGAAG 59.258 41.667 0.00 0.00 0.00 3.02
25 26 4.681744 GTGCTCAACCAAGTCATTTTGAA 58.318 39.130 0.00 0.00 0.00 2.69
26 27 3.243035 CGTGCTCAACCAAGTCATTTTGA 60.243 43.478 0.00 0.00 0.00 2.69
27 28 3.044986 CGTGCTCAACCAAGTCATTTTG 58.955 45.455 0.00 0.00 0.00 2.44
28 29 2.687935 ACGTGCTCAACCAAGTCATTTT 59.312 40.909 0.00 0.00 0.00 1.82
29 30 2.033299 CACGTGCTCAACCAAGTCATTT 59.967 45.455 0.82 0.00 0.00 2.32
30 31 1.603802 CACGTGCTCAACCAAGTCATT 59.396 47.619 0.82 0.00 0.00 2.57
31 32 1.229428 CACGTGCTCAACCAAGTCAT 58.771 50.000 0.82 0.00 0.00 3.06
32 33 0.107897 ACACGTGCTCAACCAAGTCA 60.108 50.000 17.22 0.00 0.00 3.41
33 34 0.304705 CACACGTGCTCAACCAAGTC 59.695 55.000 17.22 0.00 0.00 3.01
34 35 1.095228 CCACACGTGCTCAACCAAGT 61.095 55.000 17.22 0.00 0.00 3.16
35 36 1.648720 CCACACGTGCTCAACCAAG 59.351 57.895 17.22 0.00 0.00 3.61
36 37 1.821759 CCCACACGTGCTCAACCAA 60.822 57.895 17.22 0.00 0.00 3.67
37 38 2.050836 ATCCCACACGTGCTCAACCA 62.051 55.000 17.22 0.00 0.00 3.67
38 39 0.889186 AATCCCACACGTGCTCAACC 60.889 55.000 17.22 0.00 0.00 3.77
39 40 1.463444 GTAATCCCACACGTGCTCAAC 59.537 52.381 17.22 1.33 0.00 3.18
40 41 1.070914 TGTAATCCCACACGTGCTCAA 59.929 47.619 17.22 0.00 0.00 3.02
41 42 0.682292 TGTAATCCCACACGTGCTCA 59.318 50.000 17.22 0.00 0.00 4.26
42 43 2.024176 ATGTAATCCCACACGTGCTC 57.976 50.000 17.22 0.00 0.00 4.26
43 44 2.083774 CAATGTAATCCCACACGTGCT 58.916 47.619 17.22 0.00 0.00 4.40
44 45 1.132262 CCAATGTAATCCCACACGTGC 59.868 52.381 17.22 0.00 0.00 5.34
45 46 1.132262 GCCAATGTAATCCCACACGTG 59.868 52.381 15.48 15.48 0.00 4.49
46 47 1.271652 TGCCAATGTAATCCCACACGT 60.272 47.619 0.00 0.00 0.00 4.49
47 48 1.458398 TGCCAATGTAATCCCACACG 58.542 50.000 0.00 0.00 0.00 4.49
48 49 2.094234 GGTTGCCAATGTAATCCCACAC 60.094 50.000 0.00 0.00 0.00 3.82
49 50 2.175202 GGTTGCCAATGTAATCCCACA 58.825 47.619 0.00 0.00 0.00 4.17
50 51 2.175202 TGGTTGCCAATGTAATCCCAC 58.825 47.619 0.00 0.00 0.00 4.61
51 52 2.612285 TGGTTGCCAATGTAATCCCA 57.388 45.000 0.00 0.00 0.00 4.37
72 73 9.438228 TGAACATAAAATGAACCAATACGTCTA 57.562 29.630 0.00 0.00 0.00 2.59
73 74 8.330466 TGAACATAAAATGAACCAATACGTCT 57.670 30.769 0.00 0.00 0.00 4.18
74 75 8.846607 GTTGAACATAAAATGAACCAATACGTC 58.153 33.333 0.00 0.00 0.00 4.34
75 76 8.573035 AGTTGAACATAAAATGAACCAATACGT 58.427 29.630 0.00 0.00 0.00 3.57
76 77 8.964420 AGTTGAACATAAAATGAACCAATACG 57.036 30.769 0.00 0.00 0.00 3.06
80 81 9.959749 GTCTTAGTTGAACATAAAATGAACCAA 57.040 29.630 0.00 0.00 0.00 3.67
81 82 9.126151 TGTCTTAGTTGAACATAAAATGAACCA 57.874 29.630 0.00 0.00 0.00 3.67
82 83 9.959749 TTGTCTTAGTTGAACATAAAATGAACC 57.040 29.630 0.00 0.00 0.00 3.62
92 93 9.398170 CAAATCGAAATTGTCTTAGTTGAACAT 57.602 29.630 0.00 0.00 0.00 2.71
93 94 7.860373 CCAAATCGAAATTGTCTTAGTTGAACA 59.140 33.333 11.83 0.00 0.00 3.18
94 95 7.860872 ACCAAATCGAAATTGTCTTAGTTGAAC 59.139 33.333 11.83 0.00 0.00 3.18
95 96 7.936584 ACCAAATCGAAATTGTCTTAGTTGAA 58.063 30.769 11.83 0.00 0.00 2.69
96 97 7.504924 ACCAAATCGAAATTGTCTTAGTTGA 57.495 32.000 11.83 0.00 0.00 3.18
97 98 9.840427 ATAACCAAATCGAAATTGTCTTAGTTG 57.160 29.630 11.83 0.00 0.00 3.16
133 134 9.717942 CAACCCAATTGAAATTGTCCTTAATAA 57.282 29.630 7.12 0.00 43.24 1.40
134 135 8.875168 ACAACCCAATTGAAATTGTCCTTAATA 58.125 29.630 7.12 0.00 43.24 0.98
135 136 7.744733 ACAACCCAATTGAAATTGTCCTTAAT 58.255 30.769 7.12 0.00 43.24 1.40
136 137 7.130681 ACAACCCAATTGAAATTGTCCTTAA 57.869 32.000 7.12 0.00 43.24 1.85
137 138 6.739331 ACAACCCAATTGAAATTGTCCTTA 57.261 33.333 7.12 0.00 43.24 2.69
138 139 5.628797 ACAACCCAATTGAAATTGTCCTT 57.371 34.783 7.12 1.21 43.24 3.36
139 140 6.739331 TTACAACCCAATTGAAATTGTCCT 57.261 33.333 18.99 4.96 43.24 3.85
140 141 7.497579 AGTTTTACAACCCAATTGAAATTGTCC 59.502 33.333 18.99 10.23 43.24 4.02
141 142 8.432110 AGTTTTACAACCCAATTGAAATTGTC 57.568 30.769 18.99 9.71 43.24 3.18
171 172 9.619316 CACGTCCAAATATTTGTCTGAAAATTA 57.381 29.630 23.24 0.00 36.45 1.40
172 173 7.116233 GCACGTCCAAATATTTGTCTGAAAATT 59.884 33.333 23.24 0.00 36.45 1.82
173 174 6.586082 GCACGTCCAAATATTTGTCTGAAAAT 59.414 34.615 23.24 4.11 36.45 1.82
174 175 5.918011 GCACGTCCAAATATTTGTCTGAAAA 59.082 36.000 23.24 1.46 36.45 2.29
175 176 5.009110 TGCACGTCCAAATATTTGTCTGAAA 59.991 36.000 23.24 4.50 36.45 2.69
176 177 4.517075 TGCACGTCCAAATATTTGTCTGAA 59.483 37.500 23.24 7.55 36.45 3.02
177 178 4.068599 TGCACGTCCAAATATTTGTCTGA 58.931 39.130 23.24 12.88 36.45 3.27
178 179 4.418013 TGCACGTCCAAATATTTGTCTG 57.582 40.909 23.24 15.30 36.45 3.51
179 180 5.009610 AGTTTGCACGTCCAAATATTTGTCT 59.990 36.000 23.24 0.00 37.09 3.41
180 181 5.219633 AGTTTGCACGTCCAAATATTTGTC 58.780 37.500 23.24 15.67 37.09 3.18
181 182 5.195001 AGTTTGCACGTCCAAATATTTGT 57.805 34.783 23.24 5.47 37.09 2.83
182 183 6.378582 ACTAGTTTGCACGTCCAAATATTTG 58.621 36.000 19.40 19.40 37.09 2.32
183 184 6.569179 ACTAGTTTGCACGTCCAAATATTT 57.431 33.333 8.09 0.00 37.09 1.40
184 185 6.569179 AACTAGTTTGCACGTCCAAATATT 57.431 33.333 8.09 0.31 37.09 1.28
185 186 6.569179 AAACTAGTTTGCACGTCCAAATAT 57.431 33.333 19.94 3.07 37.09 1.28
186 187 6.038382 TCAAAACTAGTTTGCACGTCCAAATA 59.962 34.615 21.22 1.63 45.38 1.40
187 188 4.911514 AAACTAGTTTGCACGTCCAAAT 57.088 36.364 19.94 0.50 37.09 2.32
188 189 4.156190 TCAAAACTAGTTTGCACGTCCAAA 59.844 37.500 21.22 0.00 45.38 3.28
189 190 3.690139 TCAAAACTAGTTTGCACGTCCAA 59.310 39.130 21.22 0.00 45.38 3.53
190 191 3.271729 TCAAAACTAGTTTGCACGTCCA 58.728 40.909 21.22 0.00 45.38 4.02
191 192 3.955771 TCAAAACTAGTTTGCACGTCC 57.044 42.857 21.22 0.00 45.38 4.79
192 193 6.884187 TCTTATCAAAACTAGTTTGCACGTC 58.116 36.000 21.22 0.00 45.38 4.34
193 194 6.854496 TCTTATCAAAACTAGTTTGCACGT 57.146 33.333 21.22 2.61 45.38 4.49
194 195 9.988350 ATATTCTTATCAAAACTAGTTTGCACG 57.012 29.630 21.22 10.53 45.38 5.34
207 208 9.598517 GCCAAAAATGTCCATATTCTTATCAAA 57.401 29.630 0.00 0.00 0.00 2.69
208 209 8.203485 GGCCAAAAATGTCCATATTCTTATCAA 58.797 33.333 0.00 0.00 0.00 2.57
209 210 7.201992 GGGCCAAAAATGTCCATATTCTTATCA 60.202 37.037 4.39 0.00 0.00 2.15
210 211 7.015584 AGGGCCAAAAATGTCCATATTCTTATC 59.984 37.037 6.18 0.00 0.00 1.75
211 212 6.845975 AGGGCCAAAAATGTCCATATTCTTAT 59.154 34.615 6.18 0.00 0.00 1.73
212 213 6.098124 CAGGGCCAAAAATGTCCATATTCTTA 59.902 38.462 6.18 0.00 0.00 2.10
213 214 5.032170 AGGGCCAAAAATGTCCATATTCTT 58.968 37.500 6.18 0.00 0.00 2.52
214 215 4.406649 CAGGGCCAAAAATGTCCATATTCT 59.593 41.667 6.18 0.00 0.00 2.40
215 216 4.405358 TCAGGGCCAAAAATGTCCATATTC 59.595 41.667 6.18 0.00 0.00 1.75
216 217 4.162131 GTCAGGGCCAAAAATGTCCATATT 59.838 41.667 6.18 0.00 0.00 1.28
217 218 3.706086 GTCAGGGCCAAAAATGTCCATAT 59.294 43.478 6.18 0.00 0.00 1.78
218 219 3.096092 GTCAGGGCCAAAAATGTCCATA 58.904 45.455 6.18 0.00 0.00 2.74
219 220 1.901833 GTCAGGGCCAAAAATGTCCAT 59.098 47.619 6.18 0.00 0.00 3.41
220 221 1.337118 GTCAGGGCCAAAAATGTCCA 58.663 50.000 6.18 0.00 0.00 4.02
221 222 0.243636 CGTCAGGGCCAAAAATGTCC 59.756 55.000 6.18 0.00 0.00 4.02
222 223 0.243636 CCGTCAGGGCCAAAAATGTC 59.756 55.000 6.18 0.00 0.00 3.06
223 224 0.178975 TCCGTCAGGGCCAAAAATGT 60.179 50.000 6.18 0.00 38.33 2.71
224 225 1.185315 ATCCGTCAGGGCCAAAAATG 58.815 50.000 6.18 0.00 38.33 2.32
225 226 2.654863 CTATCCGTCAGGGCCAAAAAT 58.345 47.619 6.18 0.00 38.33 1.82
226 227 1.340600 CCTATCCGTCAGGGCCAAAAA 60.341 52.381 6.18 0.00 38.33 1.94
227 228 0.254747 CCTATCCGTCAGGGCCAAAA 59.745 55.000 6.18 0.00 38.33 2.44
228 229 0.619255 TCCTATCCGTCAGGGCCAAA 60.619 55.000 6.18 0.00 38.33 3.28
229 230 0.399949 ATCCTATCCGTCAGGGCCAA 60.400 55.000 6.18 0.00 38.33 4.52
230 231 1.121407 CATCCTATCCGTCAGGGCCA 61.121 60.000 6.18 0.00 38.33 5.36
231 232 1.674057 CATCCTATCCGTCAGGGCC 59.326 63.158 0.00 0.00 38.33 5.80
232 233 1.674057 CCATCCTATCCGTCAGGGC 59.326 63.158 0.00 0.00 38.33 5.19
233 234 1.194781 CCCCATCCTATCCGTCAGGG 61.195 65.000 0.00 0.00 38.33 4.45
234 235 1.831652 GCCCCATCCTATCCGTCAGG 61.832 65.000 0.00 0.00 39.46 3.86
235 236 1.121407 TGCCCCATCCTATCCGTCAG 61.121 60.000 0.00 0.00 0.00 3.51
236 237 0.692756 TTGCCCCATCCTATCCGTCA 60.693 55.000 0.00 0.00 0.00 4.35
237 238 0.472471 TTTGCCCCATCCTATCCGTC 59.528 55.000 0.00 0.00 0.00 4.79
238 239 1.149101 ATTTGCCCCATCCTATCCGT 58.851 50.000 0.00 0.00 0.00 4.69
239 240 1.538047 CATTTGCCCCATCCTATCCG 58.462 55.000 0.00 0.00 0.00 4.18
240 241 1.428912 TCCATTTGCCCCATCCTATCC 59.571 52.381 0.00 0.00 0.00 2.59
241 242 2.978156 TCCATTTGCCCCATCCTATC 57.022 50.000 0.00 0.00 0.00 2.08
242 243 2.824303 GCATCCATTTGCCCCATCCTAT 60.824 50.000 0.00 0.00 36.60 2.57
243 244 1.481055 GCATCCATTTGCCCCATCCTA 60.481 52.381 0.00 0.00 36.60 2.94
244 245 0.761702 GCATCCATTTGCCCCATCCT 60.762 55.000 0.00 0.00 36.60 3.24
245 246 1.750297 GCATCCATTTGCCCCATCC 59.250 57.895 0.00 0.00 36.60 3.51
246 247 1.364901 CGCATCCATTTGCCCCATC 59.635 57.895 0.00 0.00 39.52 3.51
247 248 2.135581 CCGCATCCATTTGCCCCAT 61.136 57.895 0.00 0.00 39.52 4.00
248 249 2.759149 CCGCATCCATTTGCCCCA 60.759 61.111 0.00 0.00 39.52 4.96
249 250 4.225703 GCCGCATCCATTTGCCCC 62.226 66.667 0.00 0.00 39.52 5.80
250 251 4.225703 GGCCGCATCCATTTGCCC 62.226 66.667 0.00 0.00 39.52 5.36
251 252 2.799452 ATGGCCGCATCCATTTGCC 61.799 57.895 0.00 0.00 44.04 4.52
252 253 1.593209 CATGGCCGCATCCATTTGC 60.593 57.895 0.00 0.00 44.04 3.68
253 254 1.593209 GCATGGCCGCATCCATTTG 60.593 57.895 0.00 0.00 44.04 2.32
254 255 1.759299 AGCATGGCCGCATCCATTT 60.759 52.632 5.37 0.00 44.04 2.32
255 256 2.123597 AGCATGGCCGCATCCATT 60.124 55.556 5.37 0.00 44.04 3.16
281 282 3.161450 TCCTGGGATGCGGTAGCC 61.161 66.667 0.00 0.00 44.33 3.93
282 283 2.109181 GTCCTGGGATGCGGTAGC 59.891 66.667 0.00 0.00 45.41 3.58
283 284 1.144057 GTGTCCTGGGATGCGGTAG 59.856 63.158 0.00 0.00 0.00 3.18
284 285 2.717044 CGTGTCCTGGGATGCGGTA 61.717 63.158 0.00 0.00 0.00 4.02
285 286 4.082523 CGTGTCCTGGGATGCGGT 62.083 66.667 0.00 0.00 0.00 5.68
289 290 4.838152 CGGGCGTGTCCTGGGATG 62.838 72.222 0.00 0.00 37.58 3.51
303 304 3.262448 ATTTGGGGTCGTGTCCGGG 62.262 63.158 0.00 0.00 33.95 5.73
304 305 1.743995 GATTTGGGGTCGTGTCCGG 60.744 63.158 0.00 0.00 33.95 5.14
305 306 1.743995 GGATTTGGGGTCGTGTCCG 60.744 63.158 0.00 0.00 0.00 4.79
306 307 1.378119 GGGATTTGGGGTCGTGTCC 60.378 63.158 0.00 0.00 0.00 4.02
307 308 0.906775 TAGGGATTTGGGGTCGTGTC 59.093 55.000 0.00 0.00 0.00 3.67
308 309 0.616891 GTAGGGATTTGGGGTCGTGT 59.383 55.000 0.00 0.00 0.00 4.49
309 310 0.107361 GGTAGGGATTTGGGGTCGTG 60.107 60.000 0.00 0.00 0.00 4.35
310 311 1.276859 GGGTAGGGATTTGGGGTCGT 61.277 60.000 0.00 0.00 0.00 4.34
311 312 1.276140 TGGGTAGGGATTTGGGGTCG 61.276 60.000 0.00 0.00 0.00 4.79
312 313 1.004436 TTGGGTAGGGATTTGGGGTC 58.996 55.000 0.00 0.00 0.00 4.46
313 314 1.078159 GTTTGGGTAGGGATTTGGGGT 59.922 52.381 0.00 0.00 0.00 4.95
314 315 1.860641 GTTTGGGTAGGGATTTGGGG 58.139 55.000 0.00 0.00 0.00 4.96
315 316 1.470051 CGTTTGGGTAGGGATTTGGG 58.530 55.000 0.00 0.00 0.00 4.12
316 317 1.004979 TCCGTTTGGGTAGGGATTTGG 59.995 52.381 0.00 0.00 37.00 3.28
317 318 2.089201 GTCCGTTTGGGTAGGGATTTG 58.911 52.381 0.00 0.00 34.83 2.32
318 319 1.706305 TGTCCGTTTGGGTAGGGATTT 59.294 47.619 0.00 0.00 34.83 2.17
319 320 1.280998 CTGTCCGTTTGGGTAGGGATT 59.719 52.381 0.00 0.00 34.83 3.01
320 321 0.909623 CTGTCCGTTTGGGTAGGGAT 59.090 55.000 0.00 0.00 34.83 3.85
321 322 0.178926 TCTGTCCGTTTGGGTAGGGA 60.179 55.000 0.00 0.00 37.00 4.20
322 323 0.688487 TTCTGTCCGTTTGGGTAGGG 59.312 55.000 0.00 0.00 37.00 3.53
323 324 2.781681 ATTCTGTCCGTTTGGGTAGG 57.218 50.000 0.00 0.00 37.00 3.18
324 325 2.671396 CGAATTCTGTCCGTTTGGGTAG 59.329 50.000 3.52 0.00 37.00 3.18
325 326 2.613474 CCGAATTCTGTCCGTTTGGGTA 60.613 50.000 3.52 0.00 37.00 3.69
326 327 1.519408 CGAATTCTGTCCGTTTGGGT 58.481 50.000 3.52 0.00 37.00 4.51
327 328 0.802494 CCGAATTCTGTCCGTTTGGG 59.198 55.000 3.52 0.00 35.24 4.12
328 329 1.463444 GTCCGAATTCTGTCCGTTTGG 59.537 52.381 3.52 0.00 0.00 3.28
329 330 2.139917 TGTCCGAATTCTGTCCGTTTG 58.860 47.619 3.52 0.00 0.00 2.93
330 331 2.536761 TGTCCGAATTCTGTCCGTTT 57.463 45.000 3.52 0.00 0.00 3.60
331 332 2.536761 TTGTCCGAATTCTGTCCGTT 57.463 45.000 3.52 0.00 0.00 4.44
332 333 2.536761 TTTGTCCGAATTCTGTCCGT 57.463 45.000 3.52 0.00 0.00 4.69
333 334 2.411031 CGTTTTGTCCGAATTCTGTCCG 60.411 50.000 3.52 0.00 0.00 4.79
334 335 2.095919 CCGTTTTGTCCGAATTCTGTCC 60.096 50.000 3.52 0.00 0.00 4.02
335 336 2.803956 TCCGTTTTGTCCGAATTCTGTC 59.196 45.455 3.52 0.00 0.00 3.51
336 337 2.546789 GTCCGTTTTGTCCGAATTCTGT 59.453 45.455 3.52 0.00 0.00 3.41
337 338 2.411031 CGTCCGTTTTGTCCGAATTCTG 60.411 50.000 3.52 0.00 0.00 3.02
338 339 1.796459 CGTCCGTTTTGTCCGAATTCT 59.204 47.619 3.52 0.00 0.00 2.40
339 340 1.528161 ACGTCCGTTTTGTCCGAATTC 59.472 47.619 0.00 0.00 0.00 2.17
340 341 1.528161 GACGTCCGTTTTGTCCGAATT 59.472 47.619 3.51 0.00 0.00 2.17
341 342 1.142474 GACGTCCGTTTTGTCCGAAT 58.858 50.000 3.51 0.00 0.00 3.34
342 343 0.875474 GGACGTCCGTTTTGTCCGAA 60.875 55.000 20.85 0.00 42.42 4.30
343 344 1.300080 GGACGTCCGTTTTGTCCGA 60.300 57.895 20.85 0.00 42.42 4.55
344 345 3.237290 GGACGTCCGTTTTGTCCG 58.763 61.111 20.85 0.00 42.42 4.79
351 352 1.302993 CCCCAAATGGACGTCCGTT 60.303 57.895 31.94 31.94 46.66 4.44
352 353 2.349755 CCCCAAATGGACGTCCGT 59.650 61.111 28.70 26.41 39.43 4.69
353 354 1.743995 GACCCCAAATGGACGTCCG 60.744 63.158 28.70 15.23 39.43 4.79
354 355 1.743995 CGACCCCAAATGGACGTCC 60.744 63.158 28.17 28.17 38.48 4.79
355 356 2.396157 GCGACCCCAAATGGACGTC 61.396 63.158 7.13 7.13 43.82 4.34
356 357 2.359478 GCGACCCCAAATGGACGT 60.359 61.111 0.00 0.00 43.82 4.34
357 358 3.496131 CGCGACCCCAAATGGACG 61.496 66.667 0.00 5.32 44.57 4.79
358 359 3.131478 CCGCGACCCCAAATGGAC 61.131 66.667 8.23 0.00 37.39 4.02
374 375 0.179468 TATTAGGCCAACTCCACGCC 59.821 55.000 5.01 0.00 43.35 5.68
375 376 1.583054 CTATTAGGCCAACTCCACGC 58.417 55.000 5.01 0.00 0.00 5.34
376 377 1.134521 TGCTATTAGGCCAACTCCACG 60.135 52.381 5.01 0.00 0.00 4.94
377 378 2.710096 TGCTATTAGGCCAACTCCAC 57.290 50.000 5.01 0.00 0.00 4.02
378 379 2.777114 TGATGCTATTAGGCCAACTCCA 59.223 45.455 5.01 0.00 0.00 3.86
379 380 3.492102 TGATGCTATTAGGCCAACTCC 57.508 47.619 5.01 0.00 0.00 3.85
380 381 5.368256 CATTGATGCTATTAGGCCAACTC 57.632 43.478 5.01 0.00 0.00 3.01
400 401 2.149578 GGCAGAGCGATTAATGAGCAT 58.850 47.619 13.10 1.47 0.00 3.79
407 408 1.521457 CTGCCGGCAGAGCGATTAA 60.521 57.895 46.72 13.46 46.30 1.40
438 439 5.222130 TGCAGGAAGAGGTCTTATTTCCTTT 60.222 40.000 2.03 0.00 45.35 3.11
446 447 0.905357 GGCTGCAGGAAGAGGTCTTA 59.095 55.000 17.12 0.00 36.11 2.10
573 598 2.033448 CAGTTGTTGGGGCGGCTA 59.967 61.111 9.56 0.00 0.00 3.93
699 725 1.009389 CGTTGGTTGTCTCGAGCTCC 61.009 60.000 7.81 7.71 0.00 4.70
700 726 1.009389 CCGTTGGTTGTCTCGAGCTC 61.009 60.000 7.81 2.73 0.00 4.09
701 727 1.006102 CCGTTGGTTGTCTCGAGCT 60.006 57.895 7.81 0.00 0.00 4.09
702 728 1.006571 TCCGTTGGTTGTCTCGAGC 60.007 57.895 7.81 3.58 0.00 5.03
819 845 0.834612 GAGGAGAGGAGAGGAGACGA 59.165 60.000 0.00 0.00 0.00 4.20
821 847 1.202651 CGAGAGGAGAGGAGAGGAGAC 60.203 61.905 0.00 0.00 0.00 3.36
901 927 0.478507 GGGAGAGAGAGAGAGAGGGG 59.521 65.000 0.00 0.00 0.00 4.79
902 928 0.478507 GGGGAGAGAGAGAGAGAGGG 59.521 65.000 0.00 0.00 0.00 4.30
936 962 2.250939 CGCGAAGGCTGTTCCACAA 61.251 57.895 0.00 0.00 37.29 3.33
1397 1428 0.383949 CAACCAACCACCCAAACTCG 59.616 55.000 0.00 0.00 0.00 4.18
1556 1588 3.792401 CCTACTGACGGCATATTCAACA 58.208 45.455 0.00 0.00 0.00 3.33
1557 1589 2.544267 GCCTACTGACGGCATATTCAAC 59.456 50.000 0.00 0.00 46.77 3.18
1559 1591 2.526304 GCCTACTGACGGCATATTCA 57.474 50.000 0.00 0.00 46.77 2.57
1575 1610 1.244019 GCACCACCTCGAATTTGCCT 61.244 55.000 0.00 0.00 0.00 4.75
1579 1614 1.813513 CTCAGCACCACCTCGAATTT 58.186 50.000 0.00 0.00 0.00 1.82
1584 1632 2.433838 CAGCTCAGCACCACCTCG 60.434 66.667 0.00 0.00 0.00 4.63
1673 1732 2.635915 TGGACACATAACTTTCGGGAGT 59.364 45.455 0.00 0.00 0.00 3.85
1861 1926 6.757897 ACAAGTTTTCATCTCTGTTGACAA 57.242 33.333 0.00 0.00 0.00 3.18
2058 2128 5.815740 GGCCACAGAGTTCGAGATTAATTTA 59.184 40.000 0.00 0.00 0.00 1.40
2224 2302 6.263842 CCAATCACTTGGCATCATTAGTACAT 59.736 38.462 0.00 0.00 45.28 2.29
2282 2360 9.676861 TCTGATATCCTATTGAATTAAGCATGG 57.323 33.333 0.00 0.00 0.00 3.66
2430 2508 4.314740 TGTTGGGTTGAAATTCTTTCCG 57.685 40.909 0.00 0.00 38.90 4.30
2835 2925 7.101054 TGCAGTTAAGTATACTGTACAAAGGG 58.899 38.462 6.06 0.00 43.81 3.95
2878 2968 0.039256 CACACATTTGGCCACCTTCG 60.039 55.000 3.88 0.00 0.00 3.79
3151 3280 8.115491 TGTTACATGTTCGATCGAGAATAAAG 57.885 34.615 18.54 8.38 32.25 1.85
3215 3357 2.936919 AGTGACTGTGATTGCTTGGA 57.063 45.000 0.00 0.00 0.00 3.53
3350 3498 7.494922 AGGGTAAATCTGCAAATAAAATGGT 57.505 32.000 0.00 0.00 0.00 3.55
3658 3820 3.118261 TGCTCCTTTGATATCCCTGTGAC 60.118 47.826 0.00 0.00 0.00 3.67
3930 4254 9.944376 GGAATAAATAGATATCAGTTGGTGCTA 57.056 33.333 5.32 0.00 0.00 3.49
3932 4256 7.121315 GGGGAATAAATAGATATCAGTTGGTGC 59.879 40.741 5.32 0.00 0.00 5.01
4279 4606 6.321181 TCACCCAAGGATGTTCTATTAATTGC 59.679 38.462 0.00 0.00 0.00 3.56
4306 4633 0.398318 ACCTGACTGAAGCTTGGTCC 59.602 55.000 19.90 2.06 0.00 4.46
4837 5598 1.808390 CCGTAACGGGCTAGTGCAC 60.808 63.158 9.40 9.40 44.15 4.57
5014 5775 7.587037 TCTTCTTGGAGAATCAAATGTTTGT 57.413 32.000 5.48 0.00 33.13 2.83
5129 5895 4.405680 AGGGCTAAACAGAAAGCAAAAAGT 59.594 37.500 0.00 0.00 40.61 2.66
5130 5896 4.948847 AGGGCTAAACAGAAAGCAAAAAG 58.051 39.130 0.00 0.00 40.61 2.27
5284 6050 1.262417 TCATACGAGGGACACAGCAA 58.738 50.000 0.00 0.00 0.00 3.91
5287 6053 2.690497 ACTGATCATACGAGGGACACAG 59.310 50.000 0.00 0.00 0.00 3.66
5370 6136 3.193479 GCCCTGATTTTCTCCAAATTCGT 59.807 43.478 0.00 0.00 35.02 3.85
5528 6294 4.081420 AGCAAATACTGACACTGGGACTAG 60.081 45.833 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.