Multiple sequence alignment - TraesCS3D01G258900

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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 TraesCS3D01G258900 chr3D 100.000 5711 0 0 1 5711 360872751 360867041 0.000000e+00 10547
1 TraesCS3D01G258900 chr3D 86.032 315 40 4 1 311 551001940 551001626 9.170000e-88 335
2 TraesCS3D01G258900 chr3D 85.987 314 37 7 1 309 121211567 121211878 4.270000e-86 329
3 TraesCS3D01G258900 chr3A 92.217 4561 198 73 534 5020 481022571 481018094 0.000000e+00 6311
4 TraesCS3D01G258900 chr3A 91.704 663 40 9 3937 4593 480970797 480970144 0.000000e+00 905
5 TraesCS3D01G258900 chr3A 86.788 386 39 6 4578 4962 480970128 480969754 2.460000e-113 420
6 TraesCS3D01G258900 chr3A 84.375 192 14 4 353 536 481023028 481022845 2.120000e-39 174
7 TraesCS3D01G258900 chr3B 92.530 3119 180 32 804 3902 469770876 469767791 0.000000e+00 4420
8 TraesCS3D01G258900 chr3B 92.118 1015 65 9 3953 4962 469767701 469766697 0.000000e+00 1417
9 TraesCS3D01G258900 chr3B 82.735 724 78 33 5026 5711 131081349 131082063 8.190000e-168 601
10 TraesCS3D01G258900 chr3B 89.976 409 23 8 321 716 469771477 469771074 3.950000e-141 512
11 TraesCS3D01G258900 chr3B 84.921 378 40 13 5171 5542 820379992 820379626 3.250000e-97 366
12 TraesCS3D01G258900 chr3B 86.408 103 14 0 5017 5119 820381556 820381454 4.680000e-21 113
13 TraesCS3D01G258900 chr7D 96.751 708 11 1 5016 5711 104097565 104096858 0.000000e+00 1170
14 TraesCS3D01G258900 chr7D 87.580 314 34 5 3 311 585427150 585426837 5.440000e-95 359
15 TraesCS3D01G258900 chr5D 96.624 711 12 2 5012 5711 9940373 9939664 0.000000e+00 1170
16 TraesCS3D01G258900 chrUn 96.871 703 10 1 5021 5711 94191472 94190770 0.000000e+00 1166
17 TraesCS3D01G258900 chr1A 95.615 707 18 6 5017 5711 519964055 519964760 0.000000e+00 1122
18 TraesCS3D01G258900 chr6D 95.231 713 21 2 5012 5711 436842440 436843152 0.000000e+00 1116
19 TraesCS3D01G258900 chr6D 86.262 313 38 5 1 309 146943448 146943759 9.170000e-88 335
20 TraesCS3D01G258900 chr4A 93.503 708 32 4 5017 5711 369309443 369310149 0.000000e+00 1040
21 TraesCS3D01G258900 chr4A 82.810 733 80 35 5016 5711 89943612 89942889 1.050000e-171 614
22 TraesCS3D01G258900 chr7B 82.597 724 79 33 5026 5711 541698250 541698964 3.810000e-166 595
23 TraesCS3D01G258900 chr4D 86.262 313 39 4 1 309 319684919 319685231 2.550000e-88 337
24 TraesCS3D01G258900 chr5B 86.076 316 39 5 1 311 486286385 486286700 9.170000e-88 335
25 TraesCS3D01G258900 chr6B 85.443 316 40 5 1 312 702278325 702278012 1.980000e-84 324
26 TraesCS3D01G258900 chr4B 85.390 308 41 4 1 304 401886122 401885815 3.320000e-82 316
27 TraesCS3D01G258900 chr4B 84.451 328 43 7 2 324 598415556 598415880 3.320000e-82 316


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 TraesCS3D01G258900 chr3D 360867041 360872751 5710 True 10547.000000 10547 100.000000 1 5711 1 chr3D.!!$R1 5710
1 TraesCS3D01G258900 chr3A 481018094 481023028 4934 True 3242.500000 6311 88.296000 353 5020 2 chr3A.!!$R2 4667
2 TraesCS3D01G258900 chr3A 480969754 480970797 1043 True 662.500000 905 89.246000 3937 4962 2 chr3A.!!$R1 1025
3 TraesCS3D01G258900 chr3B 469766697 469771477 4780 True 2116.333333 4420 91.541333 321 4962 3 chr3B.!!$R1 4641
4 TraesCS3D01G258900 chr3B 131081349 131082063 714 False 601.000000 601 82.735000 5026 5711 1 chr3B.!!$F1 685
5 TraesCS3D01G258900 chr3B 820379626 820381556 1930 True 239.500000 366 85.664500 5017 5542 2 chr3B.!!$R2 525
6 TraesCS3D01G258900 chr7D 104096858 104097565 707 True 1170.000000 1170 96.751000 5016 5711 1 chr7D.!!$R1 695
7 TraesCS3D01G258900 chr5D 9939664 9940373 709 True 1170.000000 1170 96.624000 5012 5711 1 chr5D.!!$R1 699
8 TraesCS3D01G258900 chrUn 94190770 94191472 702 True 1166.000000 1166 96.871000 5021 5711 1 chrUn.!!$R1 690
9 TraesCS3D01G258900 chr1A 519964055 519964760 705 False 1122.000000 1122 95.615000 5017 5711 1 chr1A.!!$F1 694
10 TraesCS3D01G258900 chr6D 436842440 436843152 712 False 1116.000000 1116 95.231000 5012 5711 1 chr6D.!!$F2 699
11 TraesCS3D01G258900 chr4A 369309443 369310149 706 False 1040.000000 1040 93.503000 5017 5711 1 chr4A.!!$F1 694
12 TraesCS3D01G258900 chr4A 89942889 89943612 723 True 614.000000 614 82.810000 5016 5711 1 chr4A.!!$R1 695
13 TraesCS3D01G258900 chr7B 541698250 541698964 714 False 595.000000 595 82.597000 5026 5711 1 chr7B.!!$F1 685

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
175 176 0.025770 CGAAATTTACGCGCGGACAT 59.974 50.000 35.22 22.77 0.00 3.06 F
538 830 0.040942 TGCTACCACCCCCGTAACTA 59.959 55.000 0.00 0.00 0.00 2.24 F
811 1223 0.179097 GTCGTTGCTCATCCTCCTCC 60.179 60.000 0.00 0.00 0.00 4.30 F
1337 1766 0.320697 GAGCGCCCCGAGGTAATAAT 59.679 55.000 2.29 0.00 34.57 1.28 F
2422 2856 1.480954 GGATGCGGAGGTAAGAGAACA 59.519 52.381 0.00 0.00 0.00 3.18 F
3417 3863 0.883833 CACTGGTGGAATTGGTGAGC 59.116 55.000 0.00 0.00 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1130 1559 0.455633 GCAAACAGAGAAGCCATGCG 60.456 55.000 0.00 0.0 0.00 4.73 R
2405 2839 1.000506 GTGTGTTCTCTTACCTCCGCA 59.999 52.381 0.00 0.0 0.00 5.69 R
2746 3183 1.931172 GGTTCACGATAATGTGTCGGG 59.069 52.381 0.00 0.0 43.57 5.14 R
3212 3658 2.809446 CTCATGGAAAGTGCATGCATG 58.191 47.619 25.64 22.7 44.48 4.06 R
3537 3983 2.647299 TCTGCCCAGGTTTAAGATCCAA 59.353 45.455 0.00 0.0 0.00 3.53 R
5013 5561 0.828022 TCCGAACACGCCCATAATCT 59.172 50.000 0.00 0.0 0.00 2.40 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
44 45 2.253452 GCAAGTGCGCCAACTGAG 59.747 61.111 4.18 0.46 0.00 3.35
45 46 2.253452 CAAGTGCGCCAACTGAGC 59.747 61.111 4.18 0.00 0.00 4.26
46 47 2.111878 AAGTGCGCCAACTGAGCT 59.888 55.556 4.18 0.00 0.00 4.09
47 48 2.256591 AAGTGCGCCAACTGAGCTG 61.257 57.895 4.18 0.00 0.00 4.24
48 49 2.947938 AAGTGCGCCAACTGAGCTGT 62.948 55.000 4.18 0.00 0.00 4.40
49 50 2.974148 TGCGCCAACTGAGCTGTG 60.974 61.111 4.18 0.00 0.00 3.66
50 51 2.974698 GCGCCAACTGAGCTGTGT 60.975 61.111 0.00 0.00 0.00 3.72
51 52 2.941333 CGCCAACTGAGCTGTGTG 59.059 61.111 0.00 0.00 0.00 3.82
52 53 2.610694 CGCCAACTGAGCTGTGTGG 61.611 63.158 0.00 0.00 0.00 4.17
53 54 1.526917 GCCAACTGAGCTGTGTGGT 60.527 57.895 0.00 0.00 0.00 4.16
54 55 1.789078 GCCAACTGAGCTGTGTGGTG 61.789 60.000 0.00 0.00 0.00 4.17
55 56 0.464373 CCAACTGAGCTGTGTGGTGT 60.464 55.000 0.00 0.00 0.00 4.16
56 57 1.382522 CAACTGAGCTGTGTGGTGTT 58.617 50.000 0.00 0.00 0.00 3.32
57 58 1.745087 CAACTGAGCTGTGTGGTGTTT 59.255 47.619 0.00 0.00 0.00 2.83
58 59 2.128771 ACTGAGCTGTGTGGTGTTTT 57.871 45.000 0.00 0.00 0.00 2.43
59 60 2.446435 ACTGAGCTGTGTGGTGTTTTT 58.554 42.857 0.00 0.00 0.00 1.94
80 81 4.614555 TTTAAGCTGACATTGTATGCCG 57.385 40.909 9.10 0.00 0.00 5.69
81 82 1.382522 AAGCTGACATTGTATGCCGG 58.617 50.000 0.00 0.00 0.00 6.13
82 83 1.097547 AGCTGACATTGTATGCCGGC 61.098 55.000 22.73 22.73 44.22 6.13
83 84 1.643292 CTGACATTGTATGCCGGCG 59.357 57.895 23.90 7.94 0.00 6.46
84 85 2.327940 GACATTGTATGCCGGCGC 59.672 61.111 23.90 15.15 0.00 6.53
85 86 2.124736 ACATTGTATGCCGGCGCT 60.125 55.556 23.90 14.61 35.36 5.92
86 87 2.328989 CATTGTATGCCGGCGCTG 59.671 61.111 23.90 9.96 35.36 5.18
87 88 2.901840 ATTGTATGCCGGCGCTGG 60.902 61.111 31.57 31.57 35.36 4.85
104 105 3.121934 GCATGATGCCGGCATGAA 58.878 55.556 44.96 31.72 44.49 2.57
105 106 1.299620 GCATGATGCCGGCATGAAC 60.300 57.895 44.96 30.19 44.49 3.18
106 107 1.731433 GCATGATGCCGGCATGAACT 61.731 55.000 44.96 24.17 44.49 3.01
107 108 0.742505 CATGATGCCGGCATGAACTT 59.257 50.000 44.96 25.08 44.49 2.66
108 109 1.027357 ATGATGCCGGCATGAACTTC 58.973 50.000 44.96 30.02 36.70 3.01
109 110 1.353103 GATGCCGGCATGAACTTCG 59.647 57.895 44.96 0.00 36.70 3.79
110 111 2.051804 GATGCCGGCATGAACTTCGG 62.052 60.000 44.96 2.19 44.70 4.30
111 112 3.508840 GCCGGCATGAACTTCGGG 61.509 66.667 24.80 0.00 42.43 5.14
112 113 3.508840 CCGGCATGAACTTCGGGC 61.509 66.667 0.00 0.00 38.93 6.13
113 114 3.864686 CGGCATGAACTTCGGGCG 61.865 66.667 12.59 12.59 42.72 6.13
114 115 2.435938 GGCATGAACTTCGGGCGA 60.436 61.111 0.00 0.00 0.00 5.54
115 116 2.750888 GGCATGAACTTCGGGCGAC 61.751 63.158 0.00 0.00 0.00 5.19
116 117 3.081133 CATGAACTTCGGGCGACG 58.919 61.111 0.00 0.00 46.11 5.12
128 129 3.857854 GCGACGACATGGCAGCTG 61.858 66.667 10.11 10.11 31.07 4.24
129 130 3.190849 CGACGACATGGCAGCTGG 61.191 66.667 17.12 0.31 0.00 4.85
130 131 3.503363 GACGACATGGCAGCTGGC 61.503 66.667 31.92 31.92 43.74 4.85
137 138 2.437449 TGGCAGCTGGCATGAACT 59.563 55.556 36.53 0.00 46.12 3.01
138 139 1.684629 TGGCAGCTGGCATGAACTA 59.315 52.632 36.53 14.47 46.12 2.24
139 140 0.256752 TGGCAGCTGGCATGAACTAT 59.743 50.000 36.53 0.00 46.12 2.12
140 141 2.020181 TGGCAGCTGGCATGAACTATG 61.020 52.381 36.53 0.00 46.12 2.23
141 142 0.666913 GCAGCTGGCATGAACTATGG 59.333 55.000 17.12 0.00 43.97 2.74
146 147 2.633657 GCATGAACTATGGCCGCG 59.366 61.111 0.00 0.00 37.26 6.46
147 148 2.896801 GCATGAACTATGGCCGCGG 61.897 63.158 24.05 24.05 37.26 6.46
148 149 2.111043 ATGAACTATGGCCGCGGG 59.889 61.111 29.38 12.50 0.00 6.13
171 172 1.593426 TTTTCGAAATTTACGCGCGG 58.407 45.000 35.22 16.31 0.00 6.46
172 173 0.788995 TTTCGAAATTTACGCGCGGA 59.211 45.000 35.22 26.20 0.00 5.54
173 174 0.093365 TTCGAAATTTACGCGCGGAC 59.907 50.000 35.22 12.61 0.00 4.79
174 175 1.007848 TCGAAATTTACGCGCGGACA 61.008 50.000 35.22 21.20 0.00 4.02
175 176 0.025770 CGAAATTTACGCGCGGACAT 59.974 50.000 35.22 22.77 0.00 3.06
176 177 1.452717 GAAATTTACGCGCGGACATG 58.547 50.000 35.22 5.29 0.00 3.21
177 178 1.061421 GAAATTTACGCGCGGACATGA 59.939 47.619 35.22 7.58 0.00 3.07
178 179 1.080298 AATTTACGCGCGGACATGAA 58.920 45.000 35.22 17.73 0.00 2.57
179 180 1.080298 ATTTACGCGCGGACATGAAA 58.920 45.000 35.22 17.30 0.00 2.69
180 181 1.080298 TTTACGCGCGGACATGAAAT 58.920 45.000 35.22 12.16 0.00 2.17
190 191 3.903783 CATGAAATGGGTCGCGGT 58.096 55.556 6.13 0.00 41.79 5.68
191 192 1.721487 CATGAAATGGGTCGCGGTC 59.279 57.895 6.13 0.00 41.79 4.79
192 193 1.813753 ATGAAATGGGTCGCGGTCG 60.814 57.895 6.13 0.00 0.00 4.79
193 194 2.433664 GAAATGGGTCGCGGTCGT 60.434 61.111 6.13 0.00 36.96 4.34
194 195 2.030958 GAAATGGGTCGCGGTCGTT 61.031 57.895 6.13 0.88 36.96 3.85
195 196 0.737019 GAAATGGGTCGCGGTCGTTA 60.737 55.000 6.13 0.00 36.96 3.18
196 197 0.738412 AAATGGGTCGCGGTCGTTAG 60.738 55.000 6.13 0.00 36.96 2.34
197 198 2.567564 AATGGGTCGCGGTCGTTAGG 62.568 60.000 6.13 0.00 36.96 2.69
198 199 4.503314 GGGTCGCGGTCGTTAGGG 62.503 72.222 6.13 0.00 36.96 3.53
199 200 4.503314 GGTCGCGGTCGTTAGGGG 62.503 72.222 6.13 0.00 36.96 4.79
203 204 4.078516 GCGGTCGTTAGGGGCACT 62.079 66.667 0.00 0.00 0.00 4.40
204 205 2.125673 CGGTCGTTAGGGGCACTG 60.126 66.667 0.00 0.00 0.00 3.66
205 206 2.436115 GGTCGTTAGGGGCACTGC 60.436 66.667 0.00 0.00 0.00 4.40
216 217 4.994744 GCACTGCCAACCCAAATC 57.005 55.556 0.00 0.00 0.00 2.17
217 218 2.354902 GCACTGCCAACCCAAATCT 58.645 52.632 0.00 0.00 0.00 2.40
218 219 0.681175 GCACTGCCAACCCAAATCTT 59.319 50.000 0.00 0.00 0.00 2.40
219 220 1.892474 GCACTGCCAACCCAAATCTTA 59.108 47.619 0.00 0.00 0.00 2.10
220 221 2.298729 GCACTGCCAACCCAAATCTTAA 59.701 45.455 0.00 0.00 0.00 1.85
221 222 3.244044 GCACTGCCAACCCAAATCTTAAA 60.244 43.478 0.00 0.00 0.00 1.52
222 223 4.742138 GCACTGCCAACCCAAATCTTAAAA 60.742 41.667 0.00 0.00 0.00 1.52
223 224 5.363939 CACTGCCAACCCAAATCTTAAAAA 58.636 37.500 0.00 0.00 0.00 1.94
224 225 5.466393 CACTGCCAACCCAAATCTTAAAAAG 59.534 40.000 0.00 0.00 0.00 2.27
225 226 4.967036 TGCCAACCCAAATCTTAAAAAGG 58.033 39.130 0.00 0.00 0.00 3.11
226 227 3.751175 GCCAACCCAAATCTTAAAAAGGC 59.249 43.478 0.00 0.00 0.00 4.35
227 228 3.993736 CCAACCCAAATCTTAAAAAGGCG 59.006 43.478 0.00 0.00 0.00 5.52
228 229 3.953712 ACCCAAATCTTAAAAAGGCGG 57.046 42.857 0.00 0.00 0.00 6.13
229 230 3.502356 ACCCAAATCTTAAAAAGGCGGA 58.498 40.909 0.00 0.00 0.00 5.54
230 231 3.257375 ACCCAAATCTTAAAAAGGCGGAC 59.743 43.478 0.00 0.00 0.00 4.79
231 232 3.498082 CCAAATCTTAAAAAGGCGGACG 58.502 45.455 0.00 0.00 0.00 4.79
232 233 2.913777 AATCTTAAAAAGGCGGACGC 57.086 45.000 8.39 8.39 41.06 5.19
258 259 4.939368 CGCCCACCCAAACGGACA 62.939 66.667 0.00 0.00 34.64 4.02
259 260 2.519780 GCCCACCCAAACGGACAA 60.520 61.111 0.00 0.00 34.64 3.18
260 261 2.128507 GCCCACCCAAACGGACAAA 61.129 57.895 0.00 0.00 34.64 2.83
261 262 1.677637 GCCCACCCAAACGGACAAAA 61.678 55.000 0.00 0.00 34.64 2.44
262 263 0.824759 CCCACCCAAACGGACAAAAA 59.175 50.000 0.00 0.00 34.64 1.94
281 282 3.982127 AAAAGACAAAAACGCCGTTTG 57.018 38.095 16.86 8.08 40.95 2.93
283 284 2.640346 AGACAAAAACGCCGTTTGTT 57.360 40.000 16.86 9.72 46.50 2.83
284 285 2.949142 AGACAAAAACGCCGTTTGTTT 58.051 38.095 16.86 3.20 46.50 2.83
285 286 2.664085 AGACAAAAACGCCGTTTGTTTG 59.336 40.909 16.86 18.71 46.50 2.93
286 287 1.727335 ACAAAAACGCCGTTTGTTTGG 59.273 42.857 23.33 8.43 44.73 3.28
287 288 1.061276 CAAAAACGCCGTTTGTTTGGG 59.939 47.619 16.86 0.00 39.36 4.12
288 289 0.246910 AAAACGCCGTTTGTTTGGGT 59.753 45.000 16.86 0.00 39.36 4.51
289 290 0.179132 AAACGCCGTTTGTTTGGGTC 60.179 50.000 15.33 0.00 38.08 4.46
290 291 2.051703 CGCCGTTTGTTTGGGTCG 60.052 61.111 0.00 0.00 0.00 4.79
291 292 2.333581 GCCGTTTGTTTGGGTCGG 59.666 61.111 0.00 0.00 43.37 4.79
292 293 2.333581 CCGTTTGTTTGGGTCGGC 59.666 61.111 0.00 0.00 35.01 5.54
293 294 2.051703 CGTTTGTTTGGGTCGGCG 60.052 61.111 0.00 0.00 0.00 6.46
294 295 2.354188 GTTTGTTTGGGTCGGCGC 60.354 61.111 0.00 0.00 0.00 6.53
295 296 3.955101 TTTGTTTGGGTCGGCGCG 61.955 61.111 0.00 0.00 0.00 6.86
309 310 2.740055 CGCGCTGGAGTTGCTCTT 60.740 61.111 5.56 0.00 0.00 2.85
310 311 1.446099 CGCGCTGGAGTTGCTCTTA 60.446 57.895 5.56 0.00 0.00 2.10
311 312 1.687494 CGCGCTGGAGTTGCTCTTAC 61.687 60.000 5.56 0.00 0.00 2.34
312 313 0.390472 GCGCTGGAGTTGCTCTTACT 60.390 55.000 0.00 0.00 0.00 2.24
313 314 1.941668 GCGCTGGAGTTGCTCTTACTT 60.942 52.381 0.00 0.00 0.00 2.24
314 315 1.996191 CGCTGGAGTTGCTCTTACTTC 59.004 52.381 0.00 0.00 0.00 3.01
315 316 2.351455 GCTGGAGTTGCTCTTACTTCC 58.649 52.381 0.00 0.00 0.00 3.46
316 317 2.289694 GCTGGAGTTGCTCTTACTTCCA 60.290 50.000 0.00 0.00 0.00 3.53
317 318 3.807209 GCTGGAGTTGCTCTTACTTCCAA 60.807 47.826 0.00 0.00 0.00 3.53
318 319 4.389374 CTGGAGTTGCTCTTACTTCCAAA 58.611 43.478 0.00 0.00 0.00 3.28
319 320 4.787551 TGGAGTTGCTCTTACTTCCAAAA 58.212 39.130 0.00 0.00 0.00 2.44
361 368 0.248539 GTGCCACGACGAGATAGGAC 60.249 60.000 0.00 0.00 0.00 3.85
423 438 1.471676 GGTGTGGCGAGAAATCGAGAT 60.472 52.381 1.17 0.00 34.64 2.75
434 449 6.546395 CGAGAAATCGAGATGGAAATTTGTT 58.454 36.000 0.00 0.00 34.64 2.83
442 457 3.129287 AGATGGAAATTTGTTAGCCAGCG 59.871 43.478 0.00 0.00 39.81 5.18
468 483 0.608640 ACCACGTCCTCCAGATTCAC 59.391 55.000 0.00 0.00 0.00 3.18
474 489 1.135333 GTCCTCCAGATTCACTCGTCC 59.865 57.143 0.00 0.00 0.00 4.79
483 498 2.536761 TTCACTCGTCCCATTTCGTT 57.463 45.000 0.00 0.00 0.00 3.85
484 499 2.074547 TCACTCGTCCCATTTCGTTC 57.925 50.000 0.00 0.00 0.00 3.95
485 500 1.341852 TCACTCGTCCCATTTCGTTCA 59.658 47.619 0.00 0.00 0.00 3.18
486 501 2.028476 TCACTCGTCCCATTTCGTTCAT 60.028 45.455 0.00 0.00 0.00 2.57
487 502 2.348666 CACTCGTCCCATTTCGTTCATC 59.651 50.000 0.00 0.00 0.00 2.92
496 511 3.426695 CCATTTCGTTCATCTGGCAGTTC 60.427 47.826 15.27 1.30 0.00 3.01
538 830 0.040942 TGCTACCACCCCCGTAACTA 59.959 55.000 0.00 0.00 0.00 2.24
552 844 3.383761 CGTAACTAAACCCAACGTCAGT 58.616 45.455 0.00 0.00 0.00 3.41
608 905 1.758783 CTCAGCCAAAGCGACAAAAC 58.241 50.000 0.00 0.00 46.67 2.43
618 917 2.994849 AGCGACAAAACCGAAATCAAC 58.005 42.857 0.00 0.00 0.00 3.18
697 996 3.331319 ATCGGTCGACTCGATCCG 58.669 61.111 26.04 24.51 42.82 4.18
736 1035 2.708051 GCCCGCCTATATAACCCTTTC 58.292 52.381 0.00 0.00 0.00 2.62
738 1037 2.640826 CCCGCCTATATAACCCTTTCCA 59.359 50.000 0.00 0.00 0.00 3.53
739 1038 3.558533 CCCGCCTATATAACCCTTTCCAC 60.559 52.174 0.00 0.00 0.00 4.02
741 1040 4.445162 CCGCCTATATAACCCTTTCCACAA 60.445 45.833 0.00 0.00 0.00 3.33
743 1042 4.825634 GCCTATATAACCCTTTCCACAACC 59.174 45.833 0.00 0.00 0.00 3.77
744 1043 5.398695 GCCTATATAACCCTTTCCACAACCT 60.399 44.000 0.00 0.00 0.00 3.50
745 1044 6.296803 CCTATATAACCCTTTCCACAACCTC 58.703 44.000 0.00 0.00 0.00 3.85
746 1045 5.789574 ATATAACCCTTTCCACAACCTCA 57.210 39.130 0.00 0.00 0.00 3.86
786 1092 1.145377 AGTTCGTTCACACCCGCTT 59.855 52.632 0.00 0.00 0.00 4.68
795 1207 2.805353 CACCCGCTTCACTCGTCG 60.805 66.667 0.00 0.00 0.00 5.12
796 1208 3.292936 ACCCGCTTCACTCGTCGT 61.293 61.111 0.00 0.00 0.00 4.34
802 1214 0.939577 GCTTCACTCGTCGTTGCTCA 60.940 55.000 0.00 0.00 0.00 4.26
809 1221 0.965866 TCGTCGTTGCTCATCCTCCT 60.966 55.000 0.00 0.00 0.00 3.69
811 1223 0.179097 GTCGTTGCTCATCCTCCTCC 60.179 60.000 0.00 0.00 0.00 4.30
813 1225 1.333636 CGTTGCTCATCCTCCTCCCT 61.334 60.000 0.00 0.00 0.00 4.20
815 1227 1.630126 TTGCTCATCCTCCTCCCTGC 61.630 60.000 0.00 0.00 0.00 4.85
816 1228 2.068821 GCTCATCCTCCTCCCTGCA 61.069 63.158 0.00 0.00 0.00 4.41
817 1229 1.828768 CTCATCCTCCTCCCTGCAC 59.171 63.158 0.00 0.00 0.00 4.57
942 1354 2.507769 CGCCTCCCGTAACGAACC 60.508 66.667 0.00 0.00 0.00 3.62
943 1355 2.658422 GCCTCCCGTAACGAACCA 59.342 61.111 0.00 0.00 0.00 3.67
944 1356 1.219935 GCCTCCCGTAACGAACCAT 59.780 57.895 0.00 0.00 0.00 3.55
973 1385 1.134694 GAATTCACGCGGAACAGCC 59.865 57.895 12.47 0.00 38.60 4.85
1036 1460 2.740826 TCGCTGCCAACGGTAAGC 60.741 61.111 0.00 0.00 33.35 3.09
1041 1465 1.003839 TGCCAACGGTAAGCAGGAG 60.004 57.895 1.26 0.00 31.65 3.69
1042 1466 1.745489 GCCAACGGTAAGCAGGAGG 60.745 63.158 0.00 0.00 0.00 4.30
1043 1467 1.078426 CCAACGGTAAGCAGGAGGG 60.078 63.158 0.00 0.00 0.00 4.30
1044 1468 1.078426 CAACGGTAAGCAGGAGGGG 60.078 63.158 0.00 0.00 0.00 4.79
1045 1469 2.967946 AACGGTAAGCAGGAGGGGC 61.968 63.158 0.00 0.00 0.00 5.80
1046 1470 3.083997 CGGTAAGCAGGAGGGGCT 61.084 66.667 0.00 0.00 45.15 5.19
1047 1471 2.911928 GGTAAGCAGGAGGGGCTC 59.088 66.667 0.00 0.00 41.66 4.70
1092 1521 3.581687 GATCGGGCCGGATCTCTGC 62.582 68.421 34.46 16.82 39.75 4.26
1337 1766 0.320697 GAGCGCCCCGAGGTAATAAT 59.679 55.000 2.29 0.00 34.57 1.28
1479 1909 5.107760 GCATGTGTGTTGATTTACTGCTTTG 60.108 40.000 0.00 0.00 0.00 2.77
1500 1931 2.037208 CCCACCCGGCTCCAAATT 59.963 61.111 0.00 0.00 0.00 1.82
1508 1939 3.194755 ACCCGGCTCCAAATTTAATCAAC 59.805 43.478 0.00 0.00 0.00 3.18
1692 2125 8.122472 AGTCCTGGTTTGGTTAAGAAAATATG 57.878 34.615 0.00 0.00 0.00 1.78
1722 2155 4.021719 ACTTGAGATGATGCCAAAAACCTG 60.022 41.667 0.00 0.00 0.00 4.00
1837 2270 9.699410 TTCATCCTCCTGTATTTTACATTCAAT 57.301 29.630 0.00 0.00 38.15 2.57
1882 2315 8.405418 TCAGTTATCATATACGAAGCCTTACT 57.595 34.615 0.00 0.00 0.00 2.24
1978 2411 9.490379 ACTTTATAACATGTTTCTCTCGACTTT 57.510 29.630 17.78 0.00 0.00 2.66
2008 2441 7.540474 TCACCATTCTCATATAGTTCTACCC 57.460 40.000 0.00 0.00 0.00 3.69
2405 2839 6.098409 ACTGGTTACTGATGTATCTTTCGGAT 59.902 38.462 0.00 0.00 38.38 4.18
2422 2856 1.480954 GGATGCGGAGGTAAGAGAACA 59.519 52.381 0.00 0.00 0.00 3.18
2436 2870 7.453752 AGGTAAGAGAACACACTTATGAACCTA 59.546 37.037 0.00 0.00 32.83 3.08
2441 2875 9.036980 AGAGAACACACTTATGAACCTAGTTAT 57.963 33.333 0.00 0.00 0.00 1.89
2746 3183 5.357032 TGGAGACTCAAAAAGGAAAGTGAAC 59.643 40.000 4.53 0.00 0.00 3.18
2871 3316 9.414295 TGTTTTCTGCTCTATTTGAAATTGATG 57.586 29.630 2.73 0.18 0.00 3.07
2983 3428 8.837099 ATTTTATGTAGGATTGAATGGTTCCA 57.163 30.769 0.00 0.00 31.65 3.53
3212 3658 6.688578 TCTCAGTCCATTGTACACTTTAGAC 58.311 40.000 0.00 0.00 0.00 2.59
3260 3706 8.991783 AGTGAAATTGATGAATATGACTCCAT 57.008 30.769 0.00 0.00 36.81 3.41
3296 3742 3.940209 TGGCTATGGCAAAAAGTCAAG 57.060 42.857 2.58 0.00 40.87 3.02
3417 3863 0.883833 CACTGGTGGAATTGGTGAGC 59.116 55.000 0.00 0.00 0.00 4.26
3489 3935 6.603224 AGTTTGTAATGTACCCTTACAACCA 58.397 36.000 21.35 11.52 44.47 3.67
3906 4362 8.306038 TCATGCTTAGTTTTGCATCTACAAATT 58.694 29.630 0.00 0.00 46.65 1.82
3907 4363 8.928733 CATGCTTAGTTTTGCATCTACAAATTT 58.071 29.630 0.00 0.00 46.65 1.82
3908 4364 8.885494 TGCTTAGTTTTGCATCTACAAATTTT 57.115 26.923 0.00 0.00 39.18 1.82
3931 4387 4.403015 TGACGTGTTTGCATCTACAATG 57.597 40.909 0.00 0.00 0.00 2.82
3964 4459 4.943705 TCTCTGTGTCATTCCTTATTTGGC 59.056 41.667 0.00 0.00 0.00 4.52
3965 4460 4.661222 TCTGTGTCATTCCTTATTTGGCA 58.339 39.130 0.00 0.00 0.00 4.92
3971 4466 4.096984 GTCATTCCTTATTTGGCACCAGAG 59.903 45.833 0.00 0.00 0.00 3.35
4177 4673 1.453928 GGCTTATGGACAGGTGCCC 60.454 63.158 0.00 0.00 34.81 5.36
4178 4674 1.302949 GCTTATGGACAGGTGCCCA 59.697 57.895 0.00 0.00 36.79 5.36
4214 4710 8.651391 TGATATATTGTTAGTACCGTTTGTGG 57.349 34.615 0.00 0.00 0.00 4.17
4215 4711 8.476447 TGATATATTGTTAGTACCGTTTGTGGA 58.524 33.333 0.00 0.00 0.00 4.02
4227 4725 3.801594 CCGTTTGTGGAAGAAAATGTTGG 59.198 43.478 0.00 0.00 27.72 3.77
4228 4726 3.245048 CGTTTGTGGAAGAAAATGTTGGC 59.755 43.478 0.00 0.00 27.72 4.52
4510 5016 0.239347 CGACTTCGGTCAGGTAACGT 59.761 55.000 0.00 0.00 44.65 3.99
4557 5066 4.695455 GTGAACTGGCAGTTTAGAAGCATA 59.305 41.667 31.60 9.10 38.80 3.14
4659 5198 0.658897 GGTGGAACGCGAAACTTCAA 59.341 50.000 15.93 0.00 41.51 2.69
4754 5293 6.783892 TTGCAAATAAAGTGGCTTCATTTC 57.216 33.333 0.00 0.00 0.00 2.17
4760 5299 7.716799 AATAAAGTGGCTTCATTTCCATGTA 57.283 32.000 0.00 0.00 34.47 2.29
4801 5340 9.646427 TTGGTTTTGCAATTGATATTTACCTAC 57.354 29.630 10.34 0.00 0.00 3.18
4836 5375 5.220416 GGTGATTCGAGAAAACTGGTTATCG 60.220 44.000 6.63 6.63 0.00 2.92
4842 5381 2.028385 AGAAAACTGGTTATCGCGGTCT 60.028 45.455 6.13 0.00 0.00 3.85
4910 5449 9.227777 ACCTATGTTTGAAGTATAAAACCACTC 57.772 33.333 0.00 0.00 35.80 3.51
4914 5453 6.543100 TGTTTGAAGTATAAAACCACTCCGTT 59.457 34.615 0.00 0.00 35.80 4.44
4930 5469 1.439679 CGTTGCTTTCCTACCAGACC 58.560 55.000 0.00 0.00 0.00 3.85
4954 5502 4.804108 TGACCTGTGAAGTTTGTGTTTTG 58.196 39.130 0.00 0.00 0.00 2.44
4959 5507 2.983803 GTGAAGTTTGTGTTTTGTGCGT 59.016 40.909 0.00 0.00 0.00 5.24
4962 5510 0.368567 GTTTGTGTTTTGTGCGTGCC 59.631 50.000 0.00 0.00 0.00 5.01
4963 5511 0.038251 TTTGTGTTTTGTGCGTGCCA 60.038 45.000 0.00 0.00 0.00 4.92
4980 5528 5.677091 GCGTGCCATTTTCATCTACTGAATT 60.677 40.000 0.00 0.00 43.30 2.17
4981 5529 6.324819 CGTGCCATTTTCATCTACTGAATTT 58.675 36.000 0.00 0.00 43.30 1.82
4982 5530 6.808212 CGTGCCATTTTCATCTACTGAATTTT 59.192 34.615 0.00 0.00 43.30 1.82
4983 5531 7.201376 CGTGCCATTTTCATCTACTGAATTTTG 60.201 37.037 0.00 0.00 43.30 2.44
4984 5532 7.063780 GTGCCATTTTCATCTACTGAATTTTGG 59.936 37.037 0.00 0.00 43.30 3.28
4991 5539 7.452880 TCATCTACTGAATTTTGGTTTGGAG 57.547 36.000 0.00 0.00 0.00 3.86
5011 5559 3.339547 TCCTTGAGGAAAAAGCCCG 57.660 52.632 0.00 0.00 42.18 6.13
5013 5561 0.251165 CCTTGAGGAAAAAGCCCGGA 60.251 55.000 0.73 0.00 37.39 5.14
5014 5562 1.168714 CTTGAGGAAAAAGCCCGGAG 58.831 55.000 0.73 0.00 0.00 4.63
5019 5567 3.202151 TGAGGAAAAAGCCCGGAGATTAT 59.798 43.478 0.73 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.253452 CTCAGTTGGCGCACTTGC 59.747 61.111 10.83 0.00 37.78 4.01
28 29 2.253452 GCTCAGTTGGCGCACTTG 59.747 61.111 10.83 1.48 0.00 3.16
29 30 2.111878 AGCTCAGTTGGCGCACTT 59.888 55.556 10.83 0.00 34.52 3.16
30 31 2.667536 CAGCTCAGTTGGCGCACT 60.668 61.111 10.83 1.02 34.52 4.40
31 32 2.974698 ACAGCTCAGTTGGCGCAC 60.975 61.111 10.83 0.00 34.52 5.34
32 33 2.974148 CACAGCTCAGTTGGCGCA 60.974 61.111 10.83 0.00 34.52 6.09
33 34 2.974698 ACACAGCTCAGTTGGCGC 60.975 61.111 0.00 0.00 34.52 6.53
34 35 2.610694 CCACACAGCTCAGTTGGCG 61.611 63.158 0.00 0.00 34.52 5.69
35 36 1.526917 ACCACACAGCTCAGTTGGC 60.527 57.895 0.00 0.00 0.00 4.52
36 37 0.464373 ACACCACACAGCTCAGTTGG 60.464 55.000 0.00 0.00 0.00 3.77
37 38 1.382522 AACACCACACAGCTCAGTTG 58.617 50.000 0.00 0.00 0.00 3.16
38 39 2.128771 AAACACCACACAGCTCAGTT 57.871 45.000 0.00 0.00 0.00 3.16
39 40 2.128771 AAAACACCACACAGCTCAGT 57.871 45.000 0.00 0.00 0.00 3.41
57 58 5.398169 CGGCATACAATGTCAGCTTAAAAA 58.602 37.500 9.29 0.00 33.60 1.94
58 59 4.142491 CCGGCATACAATGTCAGCTTAAAA 60.142 41.667 9.29 0.00 33.60 1.52
59 60 3.376859 CCGGCATACAATGTCAGCTTAAA 59.623 43.478 9.29 0.00 33.60 1.52
60 61 2.942376 CCGGCATACAATGTCAGCTTAA 59.058 45.455 9.29 0.00 33.60 1.85
61 62 2.560504 CCGGCATACAATGTCAGCTTA 58.439 47.619 9.29 0.00 33.60 3.09
62 63 1.382522 CCGGCATACAATGTCAGCTT 58.617 50.000 9.29 0.00 33.60 3.74
63 64 1.097547 GCCGGCATACAATGTCAGCT 61.098 55.000 24.80 0.00 33.60 4.24
64 65 1.356624 GCCGGCATACAATGTCAGC 59.643 57.895 24.80 0.00 33.60 4.26
65 66 1.643292 CGCCGGCATACAATGTCAG 59.357 57.895 28.98 0.37 33.60 3.51
66 67 2.468670 GCGCCGGCATACAATGTCA 61.469 57.895 28.98 0.00 39.62 3.58
67 68 2.180204 AGCGCCGGCATACAATGTC 61.180 57.895 28.98 4.53 43.41 3.06
68 69 2.124736 AGCGCCGGCATACAATGT 60.125 55.556 28.98 0.00 43.41 2.71
69 70 2.328989 CAGCGCCGGCATACAATG 59.671 61.111 28.98 9.29 43.41 2.82
70 71 2.901840 CCAGCGCCGGCATACAAT 60.902 61.111 28.98 1.24 43.41 2.71
87 88 1.299620 GTTCATGCCGGCATCATGC 60.300 57.895 38.60 23.49 44.08 4.06
88 89 0.742505 AAGTTCATGCCGGCATCATG 59.257 50.000 38.60 28.85 41.87 3.07
89 90 1.027357 GAAGTTCATGCCGGCATCAT 58.973 50.000 38.60 20.90 33.90 2.45
90 91 1.368345 CGAAGTTCATGCCGGCATCA 61.368 55.000 38.60 26.53 33.90 3.07
91 92 1.353103 CGAAGTTCATGCCGGCATC 59.647 57.895 38.60 26.84 33.90 3.91
92 93 2.114670 CCGAAGTTCATGCCGGCAT 61.115 57.895 36.10 36.10 35.29 4.40
93 94 2.745884 CCGAAGTTCATGCCGGCA 60.746 61.111 34.80 34.80 35.29 5.69
94 95 3.508840 CCCGAAGTTCATGCCGGC 61.509 66.667 22.73 22.73 40.56 6.13
95 96 3.508840 GCCCGAAGTTCATGCCGG 61.509 66.667 0.00 0.00 41.47 6.13
96 97 3.864686 CGCCCGAAGTTCATGCCG 61.865 66.667 3.32 0.00 0.00 5.69
97 98 2.435938 TCGCCCGAAGTTCATGCC 60.436 61.111 3.32 0.00 0.00 4.40
98 99 2.785258 GTCGCCCGAAGTTCATGC 59.215 61.111 3.32 3.72 0.00 4.06
99 100 1.445410 TCGTCGCCCGAAGTTCATG 60.445 57.895 3.32 0.00 44.03 3.07
100 101 2.967397 TCGTCGCCCGAAGTTCAT 59.033 55.556 3.32 0.00 44.03 2.57
111 112 3.857854 CAGCTGCCATGTCGTCGC 61.858 66.667 0.00 0.00 0.00 5.19
112 113 3.190849 CCAGCTGCCATGTCGTCG 61.191 66.667 8.66 0.00 0.00 5.12
113 114 3.503363 GCCAGCTGCCATGTCGTC 61.503 66.667 8.66 0.00 0.00 4.20
114 115 3.633609 ATGCCAGCTGCCATGTCGT 62.634 57.895 9.80 0.00 40.16 4.34
115 116 2.827190 ATGCCAGCTGCCATGTCG 60.827 61.111 9.80 0.00 40.16 4.35
116 117 1.317431 TTCATGCCAGCTGCCATGTC 61.317 55.000 30.46 7.31 40.16 3.06
117 118 1.304630 TTCATGCCAGCTGCCATGT 60.305 52.632 30.46 1.06 40.16 3.21
118 119 1.141019 GTTCATGCCAGCTGCCATG 59.859 57.895 27.44 27.44 40.16 3.66
119 120 0.256752 TAGTTCATGCCAGCTGCCAT 59.743 50.000 8.66 6.20 40.16 4.40
120 121 0.256752 ATAGTTCATGCCAGCTGCCA 59.743 50.000 8.66 3.15 40.16 4.92
121 122 0.666913 CATAGTTCATGCCAGCTGCC 59.333 55.000 8.66 0.00 40.16 4.85
122 123 0.666913 CCATAGTTCATGCCAGCTGC 59.333 55.000 8.66 4.57 41.77 5.25
123 124 0.666913 GCCATAGTTCATGCCAGCTG 59.333 55.000 6.78 6.78 32.84 4.24
124 125 0.466922 GGCCATAGTTCATGCCAGCT 60.467 55.000 0.00 0.00 33.48 4.24
125 126 1.789078 CGGCCATAGTTCATGCCAGC 61.789 60.000 2.24 0.00 33.09 4.85
126 127 1.789078 GCGGCCATAGTTCATGCCAG 61.789 60.000 2.24 0.00 33.09 4.85
127 128 1.823470 GCGGCCATAGTTCATGCCA 60.823 57.895 2.24 0.00 33.09 4.92
128 129 2.896801 CGCGGCCATAGTTCATGCC 61.897 63.158 2.24 0.00 32.84 4.40
129 130 2.633657 CGCGGCCATAGTTCATGC 59.366 61.111 2.24 0.00 32.84 4.06
130 131 2.253758 CCCGCGGCCATAGTTCATG 61.254 63.158 22.85 0.00 0.00 3.07
131 132 2.111043 CCCGCGGCCATAGTTCAT 59.889 61.111 22.85 0.00 0.00 2.57
132 133 4.849310 GCCCGCGGCCATAGTTCA 62.849 66.667 22.85 0.00 44.06 3.18
151 152 1.970608 CCGCGCGTAAATTTCGAAAAA 59.029 42.857 29.95 0.62 0.00 1.94
152 153 1.194098 TCCGCGCGTAAATTTCGAAAA 59.806 42.857 29.95 0.00 0.00 2.29
153 154 0.788995 TCCGCGCGTAAATTTCGAAA 59.211 45.000 29.95 13.91 0.00 3.46
154 155 0.093365 GTCCGCGCGTAAATTTCGAA 59.907 50.000 29.95 0.00 0.00 3.71
155 156 1.007848 TGTCCGCGCGTAAATTTCGA 61.008 50.000 29.95 13.19 0.00 3.71
156 157 0.025770 ATGTCCGCGCGTAAATTTCG 59.974 50.000 29.95 10.76 0.00 3.46
157 158 1.061421 TCATGTCCGCGCGTAAATTTC 59.939 47.619 29.95 10.59 0.00 2.17
158 159 1.080298 TCATGTCCGCGCGTAAATTT 58.920 45.000 29.95 5.17 0.00 1.82
159 160 1.080298 TTCATGTCCGCGCGTAAATT 58.920 45.000 29.95 6.36 0.00 1.82
160 161 1.080298 TTTCATGTCCGCGCGTAAAT 58.920 45.000 29.95 11.43 0.00 1.40
161 162 1.080298 ATTTCATGTCCGCGCGTAAA 58.920 45.000 29.95 8.88 0.00 2.01
162 163 0.371989 CATTTCATGTCCGCGCGTAA 59.628 50.000 29.95 14.01 0.00 3.18
163 164 1.425267 CCATTTCATGTCCGCGCGTA 61.425 55.000 29.95 11.05 0.00 4.42
164 165 2.749865 CCATTTCATGTCCGCGCGT 61.750 57.895 29.95 7.00 0.00 6.01
165 166 2.023181 CCATTTCATGTCCGCGCG 59.977 61.111 25.67 25.67 0.00 6.86
166 167 2.322999 GACCCATTTCATGTCCGCGC 62.323 60.000 0.00 0.00 0.00 6.86
167 168 1.721487 GACCCATTTCATGTCCGCG 59.279 57.895 0.00 0.00 0.00 6.46
168 169 1.721487 CGACCCATTTCATGTCCGC 59.279 57.895 0.00 0.00 0.00 5.54
169 170 1.721487 GCGACCCATTTCATGTCCG 59.279 57.895 0.00 0.00 0.00 4.79
170 171 1.714899 CCGCGACCCATTTCATGTCC 61.715 60.000 8.23 0.00 0.00 4.02
171 172 1.024579 ACCGCGACCCATTTCATGTC 61.025 55.000 8.23 0.00 0.00 3.06
172 173 1.002624 ACCGCGACCCATTTCATGT 60.003 52.632 8.23 0.00 0.00 3.21
173 174 1.721487 GACCGCGACCCATTTCATG 59.279 57.895 8.23 0.00 0.00 3.07
174 175 1.813753 CGACCGCGACCCATTTCAT 60.814 57.895 8.23 0.00 40.82 2.57
175 176 2.433491 CGACCGCGACCCATTTCA 60.433 61.111 8.23 0.00 40.82 2.69
176 177 0.737019 TAACGACCGCGACCCATTTC 60.737 55.000 8.23 0.00 41.64 2.17
177 178 0.738412 CTAACGACCGCGACCCATTT 60.738 55.000 8.23 0.00 41.64 2.32
178 179 1.153706 CTAACGACCGCGACCCATT 60.154 57.895 8.23 0.00 41.64 3.16
179 180 2.493030 CTAACGACCGCGACCCAT 59.507 61.111 8.23 0.00 41.64 4.00
180 181 3.751246 CCTAACGACCGCGACCCA 61.751 66.667 8.23 0.00 41.64 4.51
181 182 4.503314 CCCTAACGACCGCGACCC 62.503 72.222 8.23 0.00 41.64 4.46
182 183 4.503314 CCCCTAACGACCGCGACC 62.503 72.222 8.23 0.00 41.64 4.79
186 187 4.078516 AGTGCCCCTAACGACCGC 62.079 66.667 0.00 0.00 0.00 5.68
187 188 2.125673 CAGTGCCCCTAACGACCG 60.126 66.667 0.00 0.00 0.00 4.79
188 189 2.436115 GCAGTGCCCCTAACGACC 60.436 66.667 2.85 0.00 0.00 4.79
189 190 2.436115 GGCAGTGCCCCTAACGAC 60.436 66.667 24.53 0.00 44.06 4.34
199 200 0.681175 AAGATTTGGGTTGGCAGTGC 59.319 50.000 6.55 6.55 0.00 4.40
200 201 4.599047 TTTAAGATTTGGGTTGGCAGTG 57.401 40.909 0.00 0.00 0.00 3.66
201 202 5.454613 CCTTTTTAAGATTTGGGTTGGCAGT 60.455 40.000 0.00 0.00 0.00 4.40
202 203 4.996758 CCTTTTTAAGATTTGGGTTGGCAG 59.003 41.667 0.00 0.00 0.00 4.85
203 204 4.745172 GCCTTTTTAAGATTTGGGTTGGCA 60.745 41.667 0.00 0.00 35.94 4.92
204 205 3.751175 GCCTTTTTAAGATTTGGGTTGGC 59.249 43.478 0.00 0.00 0.00 4.52
205 206 3.993736 CGCCTTTTTAAGATTTGGGTTGG 59.006 43.478 0.00 0.00 0.00 3.77
206 207 3.993736 CCGCCTTTTTAAGATTTGGGTTG 59.006 43.478 0.00 0.00 0.00 3.77
207 208 3.898741 TCCGCCTTTTTAAGATTTGGGTT 59.101 39.130 0.00 0.00 0.00 4.11
208 209 3.257375 GTCCGCCTTTTTAAGATTTGGGT 59.743 43.478 0.00 0.00 0.00 4.51
209 210 3.672241 CGTCCGCCTTTTTAAGATTTGGG 60.672 47.826 0.00 0.00 0.00 4.12
210 211 3.498082 CGTCCGCCTTTTTAAGATTTGG 58.502 45.455 0.00 0.00 0.00 3.28
211 212 2.914838 GCGTCCGCCTTTTTAAGATTTG 59.085 45.455 0.00 0.00 34.56 2.32
212 213 3.211803 GCGTCCGCCTTTTTAAGATTT 57.788 42.857 0.00 0.00 34.56 2.17
213 214 2.913777 GCGTCCGCCTTTTTAAGATT 57.086 45.000 0.00 0.00 34.56 2.40
241 242 4.939368 TGTCCGTTTGGGTGGGCG 62.939 66.667 0.00 0.00 37.00 6.13
242 243 1.677637 TTTTGTCCGTTTGGGTGGGC 61.678 55.000 0.00 0.00 37.00 5.36
243 244 0.824759 TTTTTGTCCGTTTGGGTGGG 59.175 50.000 0.00 0.00 37.00 4.61
260 261 3.741856 ACAAACGGCGTTTTTGTCTTTTT 59.258 34.783 33.04 7.88 42.26 1.94
261 262 3.318886 ACAAACGGCGTTTTTGTCTTTT 58.681 36.364 33.04 8.67 42.26 2.27
262 263 2.949142 ACAAACGGCGTTTTTGTCTTT 58.051 38.095 33.04 9.45 42.26 2.52
263 264 2.640346 ACAAACGGCGTTTTTGTCTT 57.360 40.000 33.04 10.25 42.26 3.01
264 265 2.640346 AACAAACGGCGTTTTTGTCT 57.360 40.000 33.04 17.45 44.56 3.41
265 266 2.222618 CCAAACAAACGGCGTTTTTGTC 60.223 45.455 31.50 0.00 44.56 3.18
266 267 1.727335 CCAAACAAACGGCGTTTTTGT 59.273 42.857 31.50 27.01 46.73 2.83
267 268 1.061276 CCCAAACAAACGGCGTTTTTG 59.939 47.619 33.04 30.83 39.44 2.44
268 269 1.337917 ACCCAAACAAACGGCGTTTTT 60.338 42.857 33.04 25.34 34.40 1.94
269 270 0.246910 ACCCAAACAAACGGCGTTTT 59.753 45.000 33.04 21.40 34.40 2.43
270 271 0.179132 GACCCAAACAAACGGCGTTT 60.179 50.000 30.41 30.41 37.04 3.60
271 272 1.434287 GACCCAAACAAACGGCGTT 59.566 52.632 21.19 21.19 0.00 4.84
272 273 2.825975 CGACCCAAACAAACGGCGT 61.826 57.895 6.77 6.77 0.00 5.68
273 274 2.051703 CGACCCAAACAAACGGCG 60.052 61.111 4.80 4.80 0.00 6.46
274 275 2.333581 CCGACCCAAACAAACGGC 59.666 61.111 0.00 0.00 37.32 5.68
275 276 2.333581 GCCGACCCAAACAAACGG 59.666 61.111 0.00 0.00 45.26 4.44
276 277 2.051703 CGCCGACCCAAACAAACG 60.052 61.111 0.00 0.00 0.00 3.60
277 278 2.354188 GCGCCGACCCAAACAAAC 60.354 61.111 0.00 0.00 0.00 2.93
278 279 3.955101 CGCGCCGACCCAAACAAA 61.955 61.111 0.00 0.00 0.00 2.83
292 293 1.446099 TAAGAGCAACTCCAGCGCG 60.446 57.895 0.00 0.00 36.87 6.86
293 294 0.390472 AGTAAGAGCAACTCCAGCGC 60.390 55.000 0.00 0.00 37.01 5.92
294 295 1.996191 GAAGTAAGAGCAACTCCAGCG 59.004 52.381 0.00 0.00 37.01 5.18
295 296 2.289694 TGGAAGTAAGAGCAACTCCAGC 60.290 50.000 0.00 0.00 0.00 4.85
296 297 3.685139 TGGAAGTAAGAGCAACTCCAG 57.315 47.619 0.00 0.00 0.00 3.86
297 298 4.431416 TTTGGAAGTAAGAGCAACTCCA 57.569 40.909 0.00 0.00 0.00 3.86
298 299 5.767816 TTTTTGGAAGTAAGAGCAACTCC 57.232 39.130 0.00 0.00 0.00 3.85
324 325 2.159226 GCACTAGTAACGATGCCACTCT 60.159 50.000 0.00 0.00 31.71 3.24
326 327 2.295253 GCACTAGTAACGATGCCACT 57.705 50.000 0.00 0.00 31.71 4.00
330 331 0.921347 CGTGGCACTAGTAACGATGC 59.079 55.000 16.72 5.78 38.27 3.91
361 368 2.096713 GCTAGCCAAGTTGATATTCGCG 60.097 50.000 2.29 0.00 0.00 5.87
423 438 1.067915 GCGCTGGCTAACAAATTTCCA 60.068 47.619 0.00 0.00 35.83 3.53
468 483 2.604914 CAGATGAACGAAATGGGACGAG 59.395 50.000 0.00 0.00 0.00 4.18
474 489 2.086869 ACTGCCAGATGAACGAAATGG 58.913 47.619 0.00 0.00 0.00 3.16
496 511 3.202097 GGTGAATGGGTTTGTTTGTTGG 58.798 45.455 0.00 0.00 0.00 3.77
538 830 0.812412 CGGTGACTGACGTTGGGTTT 60.812 55.000 0.00 0.00 0.00 3.27
608 905 8.532977 AGGTTTGATTATTTTGTTGATTTCGG 57.467 30.769 0.00 0.00 0.00 4.30
618 917 6.449635 TGGATCGGAGGTTTGATTATTTTG 57.550 37.500 0.00 0.00 0.00 2.44
716 1015 2.617276 GGAAAGGGTTATATAGGCGGGC 60.617 54.545 0.00 0.00 0.00 6.13
727 1026 2.158579 GGTGAGGTTGTGGAAAGGGTTA 60.159 50.000 0.00 0.00 0.00 2.85
736 1035 2.115266 GGGTGGGTGAGGTTGTGG 59.885 66.667 0.00 0.00 0.00 4.17
738 1037 2.763645 GGTGGGTGGGTGAGGTTGT 61.764 63.158 0.00 0.00 0.00 3.32
739 1038 2.115266 GGTGGGTGGGTGAGGTTG 59.885 66.667 0.00 0.00 0.00 3.77
743 1042 3.976701 GATGCGGTGGGTGGGTGAG 62.977 68.421 0.00 0.00 0.00 3.51
744 1043 4.028490 GATGCGGTGGGTGGGTGA 62.028 66.667 0.00 0.00 0.00 4.02
759 1065 1.067974 TGTGAACGAACTGTGACGGAT 59.932 47.619 0.00 0.00 0.00 4.18
786 1092 0.109272 GGATGAGCAACGACGAGTGA 60.109 55.000 0.00 0.00 0.00 3.41
795 1207 0.179936 CAGGGAGGAGGATGAGCAAC 59.820 60.000 0.00 0.00 0.00 4.17
796 1208 1.630126 GCAGGGAGGAGGATGAGCAA 61.630 60.000 0.00 0.00 0.00 3.91
802 1214 2.367512 GGGTGCAGGGAGGAGGAT 60.368 66.667 0.00 0.00 0.00 3.24
809 1221 4.988716 ACGTCGAGGGTGCAGGGA 62.989 66.667 10.27 0.00 0.00 4.20
811 1223 2.890847 GATCACGTCGAGGGTGCAGG 62.891 65.000 10.27 0.00 35.39 4.85
813 1225 2.571757 GATCACGTCGAGGGTGCA 59.428 61.111 10.27 1.47 35.39 4.57
815 1227 2.494918 GGGATCACGTCGAGGGTG 59.505 66.667 10.27 9.94 36.74 4.61
816 1228 3.138798 CGGGATCACGTCGAGGGT 61.139 66.667 9.83 0.00 0.00 4.34
817 1229 3.138798 ACGGGATCACGTCGAGGG 61.139 66.667 19.33 0.00 45.08 4.30
854 1266 2.505337 CGGCGGTTGAACGATCGA 60.505 61.111 24.34 0.00 35.32 3.59
855 1267 4.204891 GCGGCGGTTGAACGATCG 62.205 66.667 14.88 14.88 35.47 3.69
942 1354 3.136763 CGTGAATTCAGAGGGGATGATG 58.863 50.000 8.80 0.00 0.00 3.07
943 1355 2.486191 GCGTGAATTCAGAGGGGATGAT 60.486 50.000 8.80 0.00 0.00 2.45
944 1356 1.134401 GCGTGAATTCAGAGGGGATGA 60.134 52.381 8.80 0.00 0.00 2.92
1016 1440 1.626654 CTTACCGTTGGCAGCGACTG 61.627 60.000 25.50 10.96 34.12 3.51
1018 1442 3.023591 GCTTACCGTTGGCAGCGAC 62.024 63.158 25.50 0.87 0.00 5.19
1080 1509 2.334653 CGAGAGCAGAGATCCGGC 59.665 66.667 0.00 0.00 36.16 6.13
1092 1521 1.078848 CTCCCCAACCAAGCGAGAG 60.079 63.158 0.00 0.00 0.00 3.20
1130 1559 0.455633 GCAAACAGAGAAGCCATGCG 60.456 55.000 0.00 0.00 0.00 4.73
1177 1606 1.236616 CCTGCAACACATGAGCGGAA 61.237 55.000 0.00 0.00 36.79 4.30
1183 1612 1.902918 GCACCCCTGCAACACATGA 60.903 57.895 0.00 0.00 43.62 3.07
1184 1613 1.904865 AGCACCCCTGCAACACATG 60.905 57.895 0.00 0.00 46.97 3.21
1185 1614 1.904865 CAGCACCCCTGCAACACAT 60.905 57.895 0.00 0.00 46.97 3.21
1308 1737 4.821589 GGGCGCTCCTCCTTGTCG 62.822 72.222 7.64 0.00 0.00 4.35
1332 1761 4.392047 TGAAGCGATCTCATGGCATTATT 58.608 39.130 0.00 0.00 36.36 1.40
1337 1766 2.336945 AATGAAGCGATCTCATGGCA 57.663 45.000 0.00 0.00 36.36 4.92
1386 1815 9.416284 TGATGTATCCACAGATAGTACTTAACA 57.584 33.333 0.00 0.00 38.30 2.41
1500 1931 8.569641 GGTACCGCAAATATTATGGTTGATTAA 58.430 33.333 10.40 0.00 34.18 1.40
1508 1939 7.383687 TCTTCTAGGTACCGCAAATATTATGG 58.616 38.462 6.18 0.00 0.00 2.74
1518 1949 2.235155 TGCATTTCTTCTAGGTACCGCA 59.765 45.455 6.18 2.84 0.00 5.69
1655 2087 2.203182 AGGACTCGGGGGAACACA 59.797 61.111 0.00 0.00 0.00 3.72
1692 2125 1.293924 CATCATCTCAAGTGGACGCC 58.706 55.000 0.00 0.00 0.00 5.68
1722 2155 9.020731 TCCAAAGGGAAGAAAATATGTAAGTTC 57.979 33.333 0.00 0.00 41.32 3.01
1861 2294 8.967918 AGCATAGTAAGGCTTCGTATATGATAA 58.032 33.333 1.30 0.00 40.56 1.75
1912 2345 5.128205 TCATGTCTGCTTCATGGGAAATAG 58.872 41.667 13.24 0.00 41.79 1.73
2008 2441 9.442047 AGTAAAGACAGTATCTGAAAAGGAATG 57.558 33.333 3.70 0.00 37.88 2.67
2080 2513 1.414919 AGTTCACCAGTAAAGCGACCA 59.585 47.619 0.00 0.00 0.00 4.02
2405 2839 1.000506 GTGTGTTCTCTTACCTCCGCA 59.999 52.381 0.00 0.00 0.00 5.69
2422 2856 9.654663 GAGACAAATAACTAGGTTCATAAGTGT 57.345 33.333 0.00 0.00 0.00 3.55
2746 3183 1.931172 GGTTCACGATAATGTGTCGGG 59.069 52.381 0.00 0.00 43.57 5.14
2871 3316 8.148999 AGCTTATATGCAGTAAAGTAGGTAACC 58.851 37.037 12.65 0.00 34.99 2.85
2981 3426 4.097741 TCGGATAAGCAATGAAAATGGTGG 59.902 41.667 0.00 0.00 0.00 4.61
2983 3428 4.202050 GCTCGGATAAGCAATGAAAATGGT 60.202 41.667 0.00 0.00 42.05 3.55
3023 3468 9.855021 GCTCTTTAAAAGAAAATGCTACCATAA 57.145 29.630 0.00 0.00 37.02 1.90
3026 3471 7.524717 AGCTCTTTAAAAGAAAATGCTACCA 57.475 32.000 0.00 0.00 37.02 3.25
3065 3510 7.202001 GCATGGCCCTCTTTAAATACCTATTTT 60.202 37.037 0.00 0.00 37.16 1.82
3212 3658 2.809446 CTCATGGAAAGTGCATGCATG 58.191 47.619 25.64 22.70 44.48 4.06
3260 3706 6.239008 GCCATAGCCAACATATCTAAAAAGCA 60.239 38.462 0.00 0.00 0.00 3.91
3296 3742 2.990066 ATCCCCGATCTTCTGTTGAC 57.010 50.000 0.00 0.00 0.00 3.18
3442 3888 8.498054 ACTAGAATGTCACAGGTTTCATAATG 57.502 34.615 0.00 0.00 0.00 1.90
3489 3935 9.950496 AGTCTCTGTGAATGACAATAAATAAGT 57.050 29.630 0.00 0.00 32.80 2.24
3537 3983 2.647299 TCTGCCCAGGTTTAAGATCCAA 59.353 45.455 0.00 0.00 0.00 3.53
3906 4362 5.236655 TGTAGATGCAAACACGTCAAAAA 57.763 34.783 0.00 0.00 0.00 1.94
3907 4363 4.884458 TGTAGATGCAAACACGTCAAAA 57.116 36.364 0.00 0.00 0.00 2.44
3908 4364 4.884458 TTGTAGATGCAAACACGTCAAA 57.116 36.364 0.00 0.00 0.00 2.69
3931 4387 4.744795 ATGACACAGAGAGTAATCACCC 57.255 45.455 0.00 0.00 30.02 4.61
3964 4459 8.088981 ACTAGTCATAAAACTGTTACTCTGGTG 58.911 37.037 0.00 0.00 0.00 4.17
3965 4460 8.088981 CACTAGTCATAAAACTGTTACTCTGGT 58.911 37.037 0.00 0.00 0.00 4.00
3971 4466 6.369065 AGCAGCACTAGTCATAAAACTGTTAC 59.631 38.462 0.00 0.00 0.00 2.50
4206 4702 3.245048 GCCAACATTTTCTTCCACAAACG 59.755 43.478 0.00 0.00 0.00 3.60
4214 4710 4.541973 AATGGAGGCCAACATTTTCTTC 57.458 40.909 16.52 0.00 36.95 2.87
4215 4711 5.543790 AGTTAATGGAGGCCAACATTTTCTT 59.456 36.000 24.21 8.45 36.95 2.52
4227 4725 7.801716 TTGATGTATACAAGTTAATGGAGGC 57.198 36.000 10.14 0.00 0.00 4.70
4510 5016 2.265367 TGGCTCCCTCTGTAATGTTCA 58.735 47.619 0.00 0.00 0.00 3.18
4659 5198 1.981636 CTCACCAGCAGAGCTCCTT 59.018 57.895 10.93 0.00 36.40 3.36
4754 5293 7.386059 ACCAAATTAAGAAAAAGGCTACATGG 58.614 34.615 0.00 0.00 0.00 3.66
4760 5299 6.601217 TGCAAAACCAAATTAAGAAAAAGGCT 59.399 30.769 0.00 0.00 0.00 4.58
4801 5340 2.505405 TCGAATCACCGAGAGATAGGG 58.495 52.381 0.00 0.00 34.19 3.53
4836 5375 6.615839 GCATAATCGAATTAGTACAAGACCGC 60.616 42.308 0.00 0.00 0.00 5.68
4842 5381 7.758613 TTCACGCATAATCGAATTAGTACAA 57.241 32.000 0.00 0.00 0.00 2.41
4910 5449 1.439679 GTCTGGTAGGAAAGCAACGG 58.560 55.000 0.00 0.00 34.56 4.44
4914 5453 2.027192 GTCATGGTCTGGTAGGAAAGCA 60.027 50.000 0.00 0.00 0.00 3.91
4930 5469 4.637483 AACACAAACTTCACAGGTCATG 57.363 40.909 0.00 0.00 0.00 3.07
4954 5502 2.420022 AGTAGATGAAAATGGCACGCAC 59.580 45.455 0.00 0.00 0.00 5.34
4980 5528 3.053245 TCCTCAAGGAACTCCAAACCAAA 60.053 43.478 0.00 0.00 42.18 3.28
4981 5529 2.512056 TCCTCAAGGAACTCCAAACCAA 59.488 45.455 0.00 0.00 42.18 3.67
4982 5530 2.131854 TCCTCAAGGAACTCCAAACCA 58.868 47.619 0.00 0.00 42.18 3.67
4983 5531 2.951229 TCCTCAAGGAACTCCAAACC 57.049 50.000 0.00 0.00 42.18 3.27
5011 5559 1.217882 CGAACACGCCCATAATCTCC 58.782 55.000 0.00 0.00 0.00 3.71
5013 5561 0.828022 TCCGAACACGCCCATAATCT 59.172 50.000 0.00 0.00 0.00 2.40
5014 5562 1.878953 ATCCGAACACGCCCATAATC 58.121 50.000 0.00 0.00 0.00 1.75
5019 5567 1.669760 GTGAATCCGAACACGCCCA 60.670 57.895 0.00 0.00 0.00 5.36
5163 7133 4.250305 GTGTGGGGAGTGGCACGT 62.250 66.667 12.71 0.11 0.00 4.49
5177 7160 2.480845 GAGTGAAGCGGTAAGTTGTGT 58.519 47.619 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.