Multiple sequence alignment - TraesCS6A01G383100

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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 TraesCS6A01G383100 chr6A 100.000 2466 0 0 1 2466 602161008 602158543 0.000000e+00 4554.0
1 TraesCS6A01G383100 chr6A 90.236 297 23 1 988 1278 602168764 602169060 1.380000e-102 383.0
2 TraesCS6A01G383100 chr6A 90.236 297 23 1 988 1278 602340524 602340820 1.380000e-102 383.0
3 TraesCS6A01G383100 chr6B 89.136 1123 94 17 1368 2466 692714970 692713852 0.000000e+00 1373.0
4 TraesCS6A01G383100 chr6B 86.475 1146 100 24 1368 2466 692612371 692611234 0.000000e+00 1206.0
5 TraesCS6A01G383100 chr6B 93.111 450 30 1 852 1300 692715831 692715382 0.000000e+00 658.0
6 TraesCS6A01G383100 chr6B 92.222 450 34 1 852 1300 692613426 692612977 9.620000e-179 636.0
7 TraesCS6A01G383100 chr6B 88.442 398 39 7 2074 2466 692583282 692582887 7.980000e-130 473.0
8 TraesCS6A01G383100 chr6B 92.903 310 20 1 986 1295 692597322 692597015 1.350000e-122 449.0
9 TraesCS6A01G383100 chr6B 87.733 375 37 5 987 1361 692586126 692585761 1.750000e-116 429.0
10 TraesCS6A01G383100 chr6B 88.418 354 31 3 1744 2089 692583649 692583298 3.790000e-113 418.0
11 TraesCS6A01G383100 chr6B 87.293 362 45 1 1377 1737 692585216 692584855 1.760000e-111 412.0
12 TraesCS6A01G383100 chr6B 88.462 286 27 1 997 1276 692733047 692733332 8.450000e-90 340.0
13 TraesCS6A01G383100 chr6B 91.429 245 20 1 1377 1620 692596388 692596144 3.930000e-88 335.0
14 TraesCS6A01G383100 chr6B 90.845 142 12 1 852 992 692602632 692602491 3.240000e-44 189.0
15 TraesCS6A01G383100 chr6B 84.932 146 15 6 85 225 234684327 234684184 9.190000e-30 141.0
16 TraesCS6A01G383100 chr3B 88.599 614 57 10 229 840 775308958 775308356 0.000000e+00 734.0
17 TraesCS6A01G383100 chr3B 83.840 625 86 7 229 840 616234022 616233400 4.570000e-162 580.0
18 TraesCS6A01G383100 chr3B 86.538 52 6 1 790 840 737881238 737881187 3.430000e-04 56.5
19 TraesCS6A01G383100 chr6D 87.599 629 56 6 1396 2014 455453944 455453328 0.000000e+00 710.0
20 TraesCS6A01G383100 chr6D 88.793 464 45 6 2007 2466 455450472 455450012 1.660000e-156 562.0
21 TraesCS6A01G383100 chr6D 90.028 361 27 5 1002 1362 455454855 455454504 2.230000e-125 459.0
22 TraesCS6A01G383100 chr6D 89.899 297 24 1 988 1278 455501345 455501641 6.440000e-101 377.0
23 TraesCS6A01G383100 chr2A 84.175 594 79 9 229 810 700377872 700377282 1.660000e-156 562.0
24 TraesCS6A01G383100 chr7D 81.467 518 68 17 229 723 3164576 3165088 1.370000e-107 399.0
25 TraesCS6A01G383100 chr7D 81.041 538 68 18 229 738 3099190 3098659 4.940000e-107 398.0
26 TraesCS6A01G383100 chr2B 83.418 392 58 6 229 618 8335080 8334694 8.390000e-95 357.0
27 TraesCS6A01G383100 chr2B 82.487 394 55 13 229 614 517741633 517742020 1.410000e-87 333.0
28 TraesCS6A01G383100 chr3A 83.505 388 56 7 229 612 355277913 355277530 3.020000e-94 355.0
29 TraesCS6A01G383100 chr7A 82.519 389 59 7 229 612 518689093 518689477 1.410000e-87 333.0
30 TraesCS6A01G383100 chr2D 89.151 212 17 5 19 225 545739296 545739086 2.430000e-65 259.0
31 TraesCS6A01G383100 chr2D 90.741 162 13 2 66 225 94714010 94713849 5.340000e-52 215.0
32 TraesCS6A01G383100 chr7B 86.607 224 17 7 2 225 44228277 44228487 4.100000e-58 235.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G383100 chr6A 602158543 602161008 2465 True 4554.0 4554 100.000000 1 2466 1 chr6A.!!$R1 2465
1 TraesCS6A01G383100 chr6B 692713852 692715831 1979 True 1015.5 1373 91.123500 852 2466 2 chr6B.!!$R6 1614
2 TraesCS6A01G383100 chr6B 692611234 692613426 2192 True 921.0 1206 89.348500 852 2466 2 chr6B.!!$R5 1614
3 TraesCS6A01G383100 chr6B 692582887 692586126 3239 True 433.0 473 87.971500 987 2466 4 chr6B.!!$R3 1479
4 TraesCS6A01G383100 chr6B 692596144 692597322 1178 True 392.0 449 92.166000 986 1620 2 chr6B.!!$R4 634
5 TraesCS6A01G383100 chr3B 775308356 775308958 602 True 734.0 734 88.599000 229 840 1 chr3B.!!$R3 611
6 TraesCS6A01G383100 chr3B 616233400 616234022 622 True 580.0 580 83.840000 229 840 1 chr3B.!!$R1 611
7 TraesCS6A01G383100 chr6D 455450012 455454855 4843 True 577.0 710 88.806667 1002 2466 3 chr6D.!!$R1 1464
8 TraesCS6A01G383100 chr2A 700377282 700377872 590 True 562.0 562 84.175000 229 810 1 chr2A.!!$R1 581
9 TraesCS6A01G383100 chr7D 3164576 3165088 512 False 399.0 399 81.467000 229 723 1 chr7D.!!$F1 494
10 TraesCS6A01G383100 chr7D 3098659 3099190 531 True 398.0 398 81.041000 229 738 1 chr7D.!!$R1 509

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
754 756 0.175073 ATGCGGGGTTAGAAGACGAC 59.825 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 3763 0.321741 TTTTGTTCCCGCGGATGCTA 60.322 50.0 30.73 9.78 39.65 3.49 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
61 62 4.400529 AAAAAGCTTCAACCGGTGATTT 57.599 36.364 8.52 3.53 35.70 2.17
62 63 5.523438 AAAAAGCTTCAACCGGTGATTTA 57.477 34.783 8.52 0.00 35.70 1.40
63 64 5.523438 AAAAGCTTCAACCGGTGATTTAA 57.477 34.783 8.52 0.00 35.70 1.52
64 65 5.722021 AAAGCTTCAACCGGTGATTTAAT 57.278 34.783 8.52 0.00 35.70 1.40
65 66 5.722021 AAGCTTCAACCGGTGATTTAATT 57.278 34.783 8.52 0.00 35.70 1.40
66 67 5.722021 AGCTTCAACCGGTGATTTAATTT 57.278 34.783 8.52 0.00 35.70 1.82
67 68 5.469479 AGCTTCAACCGGTGATTTAATTTG 58.531 37.500 8.52 0.00 35.70 2.32
68 69 4.091365 GCTTCAACCGGTGATTTAATTTGC 59.909 41.667 8.52 0.00 35.70 3.68
69 70 5.461032 TTCAACCGGTGATTTAATTTGCT 57.539 34.783 8.52 0.00 35.70 3.91
70 71 4.804108 TCAACCGGTGATTTAATTTGCTG 58.196 39.130 8.52 0.00 0.00 4.41
71 72 3.866883 ACCGGTGATTTAATTTGCTGG 57.133 42.857 6.12 0.00 0.00 4.85
72 73 3.426615 ACCGGTGATTTAATTTGCTGGA 58.573 40.909 6.12 0.00 0.00 3.86
73 74 3.829601 ACCGGTGATTTAATTTGCTGGAA 59.170 39.130 6.12 0.00 0.00 3.53
74 75 4.173256 CCGGTGATTTAATTTGCTGGAAC 58.827 43.478 0.00 0.00 0.00 3.62
75 76 4.173256 CGGTGATTTAATTTGCTGGAACC 58.827 43.478 0.00 0.00 0.00 3.62
76 77 4.321601 CGGTGATTTAATTTGCTGGAACCA 60.322 41.667 0.00 0.00 0.00 3.67
77 78 5.546526 GGTGATTTAATTTGCTGGAACCAA 58.453 37.500 0.00 0.00 0.00 3.67
78 79 6.172630 GGTGATTTAATTTGCTGGAACCAAT 58.827 36.000 0.00 0.00 0.00 3.16
79 80 6.654582 GGTGATTTAATTTGCTGGAACCAATT 59.345 34.615 0.00 0.00 0.00 2.32
80 81 7.361116 GGTGATTTAATTTGCTGGAACCAATTG 60.361 37.037 0.00 0.00 0.00 2.32
81 82 7.387397 GTGATTTAATTTGCTGGAACCAATTGA 59.613 33.333 7.12 0.00 0.00 2.57
82 83 8.102047 TGATTTAATTTGCTGGAACCAATTGAT 58.898 29.630 7.12 0.00 0.00 2.57
83 84 7.670009 TTTAATTTGCTGGAACCAATTGATG 57.330 32.000 7.12 0.00 0.00 3.07
84 85 4.895668 ATTTGCTGGAACCAATTGATGT 57.104 36.364 7.12 0.00 0.00 3.06
85 86 4.686191 TTTGCTGGAACCAATTGATGTT 57.314 36.364 7.12 3.21 0.00 2.71
86 87 4.686191 TTGCTGGAACCAATTGATGTTT 57.314 36.364 7.12 0.00 0.00 2.83
87 88 4.686191 TGCTGGAACCAATTGATGTTTT 57.314 36.364 7.12 0.00 0.00 2.43
88 89 5.033589 TGCTGGAACCAATTGATGTTTTT 57.966 34.783 7.12 0.00 0.00 1.94
89 90 4.815308 TGCTGGAACCAATTGATGTTTTTG 59.185 37.500 7.12 0.00 0.00 2.44
90 91 4.815846 GCTGGAACCAATTGATGTTTTTGT 59.184 37.500 7.12 0.00 0.00 2.83
91 92 5.296531 GCTGGAACCAATTGATGTTTTTGTT 59.703 36.000 7.12 0.00 0.00 2.83
92 93 6.674694 TGGAACCAATTGATGTTTTTGTTG 57.325 33.333 7.12 0.00 0.00 3.33
93 94 5.587844 TGGAACCAATTGATGTTTTTGTTGG 59.412 36.000 7.12 0.00 41.33 3.77
94 95 5.819901 GGAACCAATTGATGTTTTTGTTGGA 59.180 36.000 7.12 0.00 38.65 3.53
95 96 6.317391 GGAACCAATTGATGTTTTTGTTGGAA 59.683 34.615 7.12 0.00 38.65 3.53
96 97 6.676237 ACCAATTGATGTTTTTGTTGGAAC 57.324 33.333 7.12 0.00 38.65 3.62
97 98 5.588246 ACCAATTGATGTTTTTGTTGGAACC 59.412 36.000 7.12 0.00 38.65 3.62
98 99 5.587844 CCAATTGATGTTTTTGTTGGAACCA 59.412 36.000 7.12 0.00 38.65 3.67
99 100 6.094603 CCAATTGATGTTTTTGTTGGAACCAA 59.905 34.615 7.12 1.83 38.65 3.67
100 101 7.201803 CCAATTGATGTTTTTGTTGGAACCAAT 60.202 33.333 7.12 0.00 38.65 3.16
101 102 7.878547 ATTGATGTTTTTGTTGGAACCAATT 57.121 28.000 9.53 0.00 38.28 2.32
102 103 7.693969 TTGATGTTTTTGTTGGAACCAATTT 57.306 28.000 9.53 0.00 38.28 1.82
103 104 7.693969 TGATGTTTTTGTTGGAACCAATTTT 57.306 28.000 9.53 0.00 38.28 1.82
104 105 7.756558 TGATGTTTTTGTTGGAACCAATTTTC 58.243 30.769 9.53 0.00 38.28 2.29
105 106 7.609532 TGATGTTTTTGTTGGAACCAATTTTCT 59.390 29.630 9.53 0.00 38.28 2.52
106 107 7.751768 TGTTTTTGTTGGAACCAATTTTCTT 57.248 28.000 9.53 0.00 38.28 2.52
107 108 7.811653 TGTTTTTGTTGGAACCAATTTTCTTC 58.188 30.769 9.53 0.00 38.28 2.87
108 109 7.445402 TGTTTTTGTTGGAACCAATTTTCTTCA 59.555 29.630 9.53 0.00 38.28 3.02
109 110 8.458052 GTTTTTGTTGGAACCAATTTTCTTCAT 58.542 29.630 9.53 0.00 38.28 2.57
110 111 7.551035 TTTGTTGGAACCAATTTTCTTCATG 57.449 32.000 9.53 0.00 38.28 3.07
111 112 6.477053 TGTTGGAACCAATTTTCTTCATGA 57.523 33.333 9.53 0.00 38.28 3.07
112 113 6.514947 TGTTGGAACCAATTTTCTTCATGAG 58.485 36.000 9.53 0.00 38.28 2.90
113 114 5.726980 TGGAACCAATTTTCTTCATGAGG 57.273 39.130 0.00 0.00 0.00 3.86
114 115 5.147032 TGGAACCAATTTTCTTCATGAGGT 58.853 37.500 4.57 0.00 0.00 3.85
115 116 5.010922 TGGAACCAATTTTCTTCATGAGGTG 59.989 40.000 4.57 0.00 0.00 4.00
116 117 4.525912 ACCAATTTTCTTCATGAGGTGC 57.474 40.909 4.57 0.00 0.00 5.01
117 118 3.057315 ACCAATTTTCTTCATGAGGTGCG 60.057 43.478 4.57 0.00 0.00 5.34
118 119 3.504863 CAATTTTCTTCATGAGGTGCGG 58.495 45.455 4.57 0.00 0.00 5.69
119 120 0.881118 TTTTCTTCATGAGGTGCGGC 59.119 50.000 4.57 0.00 0.00 6.53
120 121 1.298157 TTTCTTCATGAGGTGCGGCG 61.298 55.000 0.51 0.51 0.00 6.46
121 122 3.197790 CTTCATGAGGTGCGGCGG 61.198 66.667 9.78 0.00 0.00 6.13
132 133 3.799755 GCGGCGGCGAGACATTTT 61.800 61.111 36.87 0.00 0.00 1.82
133 134 2.867472 CGGCGGCGAGACATTTTT 59.133 55.556 29.19 0.00 0.00 1.94
159 160 9.928236 TTATTTTTGCTGTATTTGTGCTTTTTC 57.072 25.926 0.00 0.00 0.00 2.29
160 161 5.982465 TTTGCTGTATTTGTGCTTTTTCC 57.018 34.783 0.00 0.00 0.00 3.13
161 162 4.935352 TGCTGTATTTGTGCTTTTTCCT 57.065 36.364 0.00 0.00 0.00 3.36
162 163 4.619973 TGCTGTATTTGTGCTTTTTCCTG 58.380 39.130 0.00 0.00 0.00 3.86
163 164 3.989817 GCTGTATTTGTGCTTTTTCCTGG 59.010 43.478 0.00 0.00 0.00 4.45
164 165 4.261994 GCTGTATTTGTGCTTTTTCCTGGA 60.262 41.667 0.00 0.00 0.00 3.86
165 166 5.738783 GCTGTATTTGTGCTTTTTCCTGGAA 60.739 40.000 4.68 4.68 0.00 3.53
166 167 5.596845 TGTATTTGTGCTTTTTCCTGGAAC 58.403 37.500 9.04 0.00 0.00 3.62
167 168 3.535280 TTTGTGCTTTTTCCTGGAACC 57.465 42.857 9.04 0.00 0.00 3.62
168 169 2.151502 TGTGCTTTTTCCTGGAACCA 57.848 45.000 9.04 1.63 0.00 3.67
169 170 2.676748 TGTGCTTTTTCCTGGAACCAT 58.323 42.857 9.04 0.00 0.00 3.55
170 171 2.627699 TGTGCTTTTTCCTGGAACCATC 59.372 45.455 9.04 0.10 0.00 3.51
171 172 2.627699 GTGCTTTTTCCTGGAACCATCA 59.372 45.455 9.04 2.80 0.00 3.07
172 173 3.069443 GTGCTTTTTCCTGGAACCATCAA 59.931 43.478 9.04 0.00 0.00 2.57
173 174 3.708631 TGCTTTTTCCTGGAACCATCAAA 59.291 39.130 9.04 5.89 0.00 2.69
174 175 4.347583 TGCTTTTTCCTGGAACCATCAAAT 59.652 37.500 9.04 0.00 0.00 2.32
175 176 4.692155 GCTTTTTCCTGGAACCATCAAATG 59.308 41.667 9.04 3.58 0.00 2.32
176 177 5.511202 GCTTTTTCCTGGAACCATCAAATGA 60.511 40.000 9.04 0.00 0.00 2.57
177 178 6.684897 TTTTTCCTGGAACCATCAAATGAT 57.315 33.333 9.04 0.00 34.56 2.45
178 179 6.684897 TTTTCCTGGAACCATCAAATGATT 57.315 33.333 9.04 0.00 31.21 2.57
179 180 6.684897 TTTCCTGGAACCATCAAATGATTT 57.315 33.333 9.04 0.00 31.21 2.17
180 181 6.684897 TTCCTGGAACCATCAAATGATTTT 57.315 33.333 4.68 0.00 31.21 1.82
181 182 6.040209 TCCTGGAACCATCAAATGATTTTG 57.960 37.500 0.00 0.00 42.98 2.44
182 183 4.632688 CCTGGAACCATCAAATGATTTTGC 59.367 41.667 0.00 0.00 41.66 3.68
183 184 5.484715 CTGGAACCATCAAATGATTTTGCT 58.515 37.500 0.00 0.00 41.66 3.91
184 185 6.351202 CCTGGAACCATCAAATGATTTTGCTA 60.351 38.462 0.00 0.00 41.66 3.49
185 186 6.397272 TGGAACCATCAAATGATTTTGCTAC 58.603 36.000 0.00 0.00 41.66 3.58
186 187 6.014755 TGGAACCATCAAATGATTTTGCTACA 60.015 34.615 0.00 0.00 41.66 2.74
187 188 6.873076 GGAACCATCAAATGATTTTGCTACAA 59.127 34.615 0.00 0.00 41.66 2.41
188 189 7.063780 GGAACCATCAAATGATTTTGCTACAAG 59.936 37.037 0.00 0.00 41.66 3.16
189 190 6.400568 ACCATCAAATGATTTTGCTACAAGG 58.599 36.000 0.00 0.00 41.66 3.61
190 191 6.211184 ACCATCAAATGATTTTGCTACAAGGA 59.789 34.615 0.00 0.00 41.66 3.36
191 192 6.755141 CCATCAAATGATTTTGCTACAAGGAG 59.245 38.462 0.00 0.00 41.66 3.69
192 193 5.713025 TCAAATGATTTTGCTACAAGGAGC 58.287 37.500 0.00 0.00 41.66 4.70
193 194 5.477984 TCAAATGATTTTGCTACAAGGAGCT 59.522 36.000 5.79 0.00 43.27 4.09
194 195 5.990120 AATGATTTTGCTACAAGGAGCTT 57.010 34.783 5.79 0.00 43.27 3.74
195 196 5.990120 ATGATTTTGCTACAAGGAGCTTT 57.010 34.783 5.79 0.00 43.27 3.51
196 197 5.125100 TGATTTTGCTACAAGGAGCTTTG 57.875 39.130 5.79 0.00 43.27 2.77
197 198 4.826733 TGATTTTGCTACAAGGAGCTTTGA 59.173 37.500 5.79 0.00 43.27 2.69
198 199 5.477984 TGATTTTGCTACAAGGAGCTTTGAT 59.522 36.000 5.79 0.00 43.27 2.57
199 200 5.789643 TTTTGCTACAAGGAGCTTTGATT 57.210 34.783 5.79 0.00 43.27 2.57
200 201 5.789643 TTTGCTACAAGGAGCTTTGATTT 57.210 34.783 5.79 0.00 43.27 2.17
201 202 5.789643 TTGCTACAAGGAGCTTTGATTTT 57.210 34.783 5.79 0.00 43.27 1.82
202 203 5.789643 TGCTACAAGGAGCTTTGATTTTT 57.210 34.783 5.79 0.00 43.27 1.94
203 204 5.531634 TGCTACAAGGAGCTTTGATTTTTG 58.468 37.500 5.79 0.00 43.27 2.44
204 205 4.386954 GCTACAAGGAGCTTTGATTTTTGC 59.613 41.667 5.15 0.00 39.50 3.68
205 206 4.677673 ACAAGGAGCTTTGATTTTTGCT 57.322 36.364 5.15 0.00 38.59 3.91
206 207 4.374399 ACAAGGAGCTTTGATTTTTGCTG 58.626 39.130 5.15 0.00 35.76 4.41
207 208 3.672767 AGGAGCTTTGATTTTTGCTGG 57.327 42.857 0.00 0.00 35.76 4.85
208 209 3.233507 AGGAGCTTTGATTTTTGCTGGA 58.766 40.909 0.00 0.00 35.76 3.86
209 210 3.642848 AGGAGCTTTGATTTTTGCTGGAA 59.357 39.130 0.00 0.00 35.76 3.53
210 211 3.742882 GGAGCTTTGATTTTTGCTGGAAC 59.257 43.478 0.00 0.00 35.76 3.62
211 212 3.732212 AGCTTTGATTTTTGCTGGAACC 58.268 40.909 0.00 0.00 34.19 3.62
212 213 2.476241 GCTTTGATTTTTGCTGGAACCG 59.524 45.455 0.00 0.00 0.00 4.44
213 214 2.147436 TTGATTTTTGCTGGAACCGC 57.853 45.000 0.00 0.00 0.00 5.68
214 215 0.316841 TGATTTTTGCTGGAACCGCC 59.683 50.000 0.00 0.00 37.10 6.13
215 216 0.603065 GATTTTTGCTGGAACCGCCT 59.397 50.000 0.00 0.00 37.63 5.52
216 217 0.318120 ATTTTTGCTGGAACCGCCTG 59.682 50.000 0.00 0.00 37.63 4.85
217 218 0.753479 TTTTTGCTGGAACCGCCTGA 60.753 50.000 0.00 0.00 37.79 3.86
218 219 0.753479 TTTTGCTGGAACCGCCTGAA 60.753 50.000 0.00 0.00 37.79 3.02
219 220 1.172180 TTTGCTGGAACCGCCTGAAG 61.172 55.000 0.00 0.00 37.79 3.02
220 221 3.435186 GCTGGAACCGCCTGAAGC 61.435 66.667 0.00 0.00 37.79 3.86
256 257 8.498358 CATTTAATTTTTGCTGGAACCTCTTTC 58.502 33.333 0.00 0.00 0.00 2.62
272 274 7.112452 ACCTCTTTCAATTTTTGCTACAACT 57.888 32.000 0.00 0.00 0.00 3.16
352 354 0.246635 ACGGACGAGCTATGTTTGCT 59.753 50.000 0.00 0.00 44.24 3.91
404 406 2.482864 GGTCAAATTTGTTGCCACCAG 58.517 47.619 17.47 0.00 0.00 4.00
443 445 1.850640 TTTTTCGTGAGCTCGTCGC 59.149 52.632 20.96 6.76 39.57 5.19
445 447 2.686956 TTTTCGTGAGCTCGTCGCCA 62.687 55.000 20.96 10.83 40.39 5.69
459 461 4.947147 GCCAGGGTGTTGCGACCA 62.947 66.667 0.45 0.00 37.80 4.02
490 492 1.452953 TACTGGAGCTATGGCCGTCG 61.453 60.000 0.00 0.00 39.73 5.12
491 493 2.758327 TGGAGCTATGGCCGTCGT 60.758 61.111 0.00 0.00 39.73 4.34
542 544 3.812865 AACCGCGGCCGTAAGTTGT 62.813 57.895 28.58 11.93 0.00 3.32
546 548 2.899044 GCGGCCGTAAGTTGTTGCA 61.899 57.895 28.70 0.00 0.00 4.08
552 554 2.916111 CCGTAAGTTGTTGCATGTGTC 58.084 47.619 0.00 0.00 0.00 3.67
564 566 2.119029 ATGTGTCGATCCGGCGAGA 61.119 57.895 9.30 4.16 41.49 4.04
572 574 1.212616 GATCCGGCGAGAAAGACATG 58.787 55.000 9.30 0.00 0.00 3.21
576 578 1.272781 CGGCGAGAAAGACATGAGAC 58.727 55.000 0.00 0.00 0.00 3.36
583 585 1.905687 GAAAGACATGAGACGACGACG 59.094 52.381 5.58 5.58 45.75 5.12
713 715 3.394836 GCAGGGGAGGAAGACGCT 61.395 66.667 0.00 0.00 0.00 5.07
714 716 2.058595 GCAGGGGAGGAAGACGCTA 61.059 63.158 0.00 0.00 0.00 4.26
724 726 2.169352 AGGAAGACGCTATGCTTGTCAT 59.831 45.455 0.00 0.00 39.17 3.06
740 742 1.802960 GTCATGGCATCTAAGATGCGG 59.197 52.381 2.63 0.00 45.41 5.69
743 745 1.344953 TGGCATCTAAGATGCGGGGT 61.345 55.000 2.63 0.00 45.41 4.95
744 746 0.179018 GGCATCTAAGATGCGGGGTT 60.179 55.000 2.63 0.00 45.41 4.11
748 750 3.494398 GCATCTAAGATGCGGGGTTAGAA 60.494 47.826 0.00 0.00 36.59 2.10
751 753 2.693267 AAGATGCGGGGTTAGAAGAC 57.307 50.000 0.00 0.00 0.00 3.01
754 756 0.175073 ATGCGGGGTTAGAAGACGAC 59.825 55.000 0.00 0.00 0.00 4.34
755 757 1.153686 GCGGGGTTAGAAGACGACC 60.154 63.158 0.00 0.00 0.00 4.79
756 758 1.602327 GCGGGGTTAGAAGACGACCT 61.602 60.000 0.00 0.00 33.90 3.85
757 759 1.755179 CGGGGTTAGAAGACGACCTA 58.245 55.000 0.00 0.00 33.90 3.08
758 760 1.403323 CGGGGTTAGAAGACGACCTAC 59.597 57.143 0.00 0.00 33.90 3.18
759 761 2.732763 GGGGTTAGAAGACGACCTACT 58.267 52.381 0.00 0.00 33.90 2.57
776 778 2.360225 TGTCACGGGATCGGACGA 60.360 61.111 9.58 0.00 41.39 4.20
780 782 1.591594 CACGGGATCGGACGATTGG 60.592 63.158 8.75 4.24 41.39 3.16
789 791 4.502604 GGATCGGACGATTGGAATTAGGAA 60.503 45.833 8.75 0.00 34.60 3.36
800 802 3.054948 TGGAATTAGGAAAATCGGACGGT 60.055 43.478 0.00 0.00 0.00 4.83
803 805 1.729284 TAGGAAAATCGGACGGTTGC 58.271 50.000 0.00 0.00 0.00 4.17
804 806 1.133869 GGAAAATCGGACGGTTGCG 59.866 57.895 0.00 0.00 38.05 4.85
805 807 1.133869 GAAAATCGGACGGTTGCGG 59.866 57.895 0.00 0.00 37.14 5.69
806 808 2.248274 GAAAATCGGACGGTTGCGGG 62.248 60.000 0.00 0.00 37.14 6.13
807 809 3.540367 AAATCGGACGGTTGCGGGT 62.540 57.895 0.00 0.00 37.14 5.28
808 810 3.540367 AATCGGACGGTTGCGGGTT 62.540 57.895 0.00 0.00 37.14 4.11
809 811 4.973055 TCGGACGGTTGCGGGTTG 62.973 66.667 0.00 0.00 37.14 3.77
810 812 4.973055 CGGACGGTTGCGGGTTGA 62.973 66.667 0.00 0.00 31.88 3.18
811 813 3.351416 GGACGGTTGCGGGTTGAC 61.351 66.667 0.00 0.00 0.00 3.18
812 814 3.351416 GACGGTTGCGGGTTGACC 61.351 66.667 0.00 0.00 0.00 4.02
821 823 2.283604 GGGTTGACCGGCCCAAAT 60.284 61.111 9.83 0.00 44.23 2.32
822 824 1.911269 GGGTTGACCGGCCCAAATT 60.911 57.895 9.83 0.00 44.23 1.82
823 825 1.476845 GGGTTGACCGGCCCAAATTT 61.477 55.000 9.83 0.00 44.23 1.82
824 826 0.320334 GGTTGACCGGCCCAAATTTG 60.320 55.000 11.40 11.40 0.00 2.32
825 827 0.676736 GTTGACCGGCCCAAATTTGA 59.323 50.000 19.86 0.00 0.00 2.69
826 828 0.965439 TTGACCGGCCCAAATTTGAG 59.035 50.000 19.86 7.62 0.00 3.02
827 829 1.215382 GACCGGCCCAAATTTGAGC 59.785 57.895 19.86 17.73 0.00 4.26
828 830 2.181525 CCGGCCCAAATTTGAGCG 59.818 61.111 19.86 13.31 32.11 5.03
829 831 2.181525 CGGCCCAAATTTGAGCGG 59.818 61.111 19.86 17.63 32.11 5.52
830 832 2.635443 CGGCCCAAATTTGAGCGGT 61.635 57.895 19.86 0.00 32.11 5.68
831 833 1.079888 GGCCCAAATTTGAGCGGTG 60.080 57.895 19.86 1.45 32.11 4.94
832 834 1.737735 GCCCAAATTTGAGCGGTGC 60.738 57.895 19.86 8.08 0.00 5.01
833 835 1.444212 CCCAAATTTGAGCGGTGCG 60.444 57.895 19.86 0.00 0.00 5.34
983 985 3.509442 TCCATCCAACAGGAAGCAATTT 58.491 40.909 0.00 0.00 34.49 1.82
1278 1380 1.400990 GCAAGCTCGTGGTACGTACG 61.401 60.000 18.98 15.01 43.14 3.67
1279 1381 0.110056 CAAGCTCGTGGTACGTACGT 60.110 55.000 25.98 25.98 43.14 3.57
1308 1411 4.537688 AGATCCCATGTATATCACCCCAAG 59.462 45.833 0.00 0.00 0.00 3.61
1309 1412 3.675613 TCCCATGTATATCACCCCAAGT 58.324 45.455 0.00 0.00 0.00 3.16
1335 1438 3.350219 ACCCAACCAGTACTGCTTATG 57.650 47.619 17.86 11.84 0.00 1.90
1347 1453 6.257849 CAGTACTGCTTATGAAAATCGGCTAA 59.742 38.462 10.54 0.00 0.00 3.09
1350 1456 5.239525 ACTGCTTATGAAAATCGGCTAATCC 59.760 40.000 0.00 0.00 0.00 3.01
1358 1474 2.969628 ATCGGCTAATCCATCGATCC 57.030 50.000 0.00 0.00 37.77 3.36
1363 1479 0.608130 CTAATCCATCGATCCGCCCA 59.392 55.000 0.00 0.00 0.00 5.36
1366 2028 3.550431 CCATCGATCCGCCCAGGT 61.550 66.667 0.00 0.00 41.99 4.00
1482 2160 1.471684 CTAGGCGAGTTCTACAACGGT 59.528 52.381 0.00 0.00 37.61 4.83
1486 2164 2.129607 GCGAGTTCTACAACGGTGAAA 58.870 47.619 7.88 0.00 37.61 2.69
1719 2401 4.272504 CAGTTCGTTGGTGAAAGTACATGT 59.727 41.667 2.69 2.69 0.00 3.21
1731 2413 7.237173 GTGAAAGTACATGTCTGTTGCTATTC 58.763 38.462 0.00 0.09 36.79 1.75
1736 2418 5.779806 ACATGTCTGTTGCTATTCGTAAC 57.220 39.130 0.00 0.00 38.52 2.50
1737 2419 5.479306 ACATGTCTGTTGCTATTCGTAACT 58.521 37.500 0.00 0.00 38.79 2.24
1769 3653 9.884636 TTCTTTATCTATTTTCATCTCGACCAA 57.115 29.630 0.00 0.00 0.00 3.67
1780 3664 6.709018 TCATCTCGACCAATACATTGACTA 57.291 37.500 3.48 0.00 40.14 2.59
1786 3670 7.284716 TCTCGACCAATACATTGACTAGTATGT 59.715 37.037 14.23 14.23 40.14 2.29
1879 3763 7.770897 GTACAACATGTATCAGGAGATTTTCCT 59.229 37.037 0.00 0.00 45.21 3.36
1896 3780 1.153449 CTAGCATCCGCGGGAACAA 60.153 57.895 27.83 5.39 45.49 2.83
1933 3817 6.367969 GCAAAGTAAGGAAAGAACATCTACGA 59.632 38.462 0.00 0.00 0.00 3.43
1957 3841 7.748683 CGATCGTTCTTCATTTGGTTCATTTAA 59.251 33.333 7.03 0.00 0.00 1.52
2001 3892 6.808212 CCAACACCTGCAAACTAATCTATTTG 59.192 38.462 0.00 0.00 38.57 2.32
2063 6836 2.634815 ATGAGCTGAATTGCCTCGAT 57.365 45.000 0.00 0.00 0.00 3.59
2067 6840 1.009829 GCTGAATTGCCTCGATTCGT 58.990 50.000 5.89 0.00 37.13 3.85
2092 6894 2.487762 CCACACGGTTTAGTGATTGCAT 59.512 45.455 4.00 0.00 44.43 3.96
2108 6910 7.329226 AGTGATTGCATAAAAGAAATTGGAACG 59.671 33.333 0.00 0.00 0.00 3.95
2113 6915 5.743872 GCATAAAAGAAATTGGAACGCTAGG 59.256 40.000 0.00 0.00 0.00 3.02
2167 6973 2.005971 AACGAAGCGGAATGTCTACC 57.994 50.000 0.00 0.00 0.00 3.18
2196 7003 3.102052 AGGCAACAGAGTGCAAAAATG 57.898 42.857 0.00 0.00 46.81 2.32
2279 7088 3.394606 AGTTATCCACTCCACAACCACTT 59.605 43.478 0.00 0.00 0.00 3.16
2283 7092 3.547746 TCCACTCCACAACCACTTAAAC 58.452 45.455 0.00 0.00 0.00 2.01
2293 7102 7.444183 TCCACAACCACTTAAACTGAATTCTAG 59.556 37.037 7.05 5.30 0.00 2.43
2349 7159 7.753580 GGAAACAAGGTAATAATAGTTGTGTGC 59.246 37.037 0.00 0.00 31.80 4.57
2351 7161 7.611213 ACAAGGTAATAATAGTTGTGTGCTC 57.389 36.000 0.00 0.00 30.25 4.26
2370 7193 4.761227 TGCTCTATGATTCACAACTGCAAA 59.239 37.500 0.00 0.00 0.00 3.68
2372 7195 5.627499 TCTATGATTCACAACTGCAAACC 57.373 39.130 0.00 0.00 0.00 3.27
2377 7200 4.402155 TGATTCACAACTGCAAACCTCTTT 59.598 37.500 0.00 0.00 0.00 2.52
2442 7270 8.462016 AGTTATGTTACTCAATTGCTTCATTCC 58.538 33.333 0.00 0.00 0.00 3.01
2457 7285 8.816640 TGCTTCATTCCACTTTCTTTTATTTC 57.183 30.769 0.00 0.00 0.00 2.17
2458 7286 8.420222 TGCTTCATTCCACTTTCTTTTATTTCA 58.580 29.630 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.810755 CCTACGGTGGAAGCTTTTTCC 59.189 52.381 0.00 0.00 39.03 3.13
1 2 2.774687 TCCTACGGTGGAAGCTTTTTC 58.225 47.619 0.00 0.00 32.39 2.29
2 3 2.943036 TCCTACGGTGGAAGCTTTTT 57.057 45.000 0.00 0.00 32.39 1.94
3 4 2.943036 TTCCTACGGTGGAAGCTTTT 57.057 45.000 0.00 0.00 40.80 2.27
4 5 2.943036 TTTCCTACGGTGGAAGCTTT 57.057 45.000 0.00 0.00 45.58 3.51
5 6 2.943036 TTTTCCTACGGTGGAAGCTT 57.057 45.000 0.00 0.00 45.58 3.74
6 7 2.943036 TTTTTCCTACGGTGGAAGCT 57.057 45.000 10.49 0.00 45.58 3.74
40 41 4.400529 AAATCACCGGTTGAAGCTTTTT 57.599 36.364 2.97 0.81 37.92 1.94
41 42 5.523438 TTAAATCACCGGTTGAAGCTTTT 57.477 34.783 2.97 6.49 37.92 2.27
42 43 5.722021 ATTAAATCACCGGTTGAAGCTTT 57.278 34.783 2.97 6.82 37.92 3.51
43 44 5.722021 AATTAAATCACCGGTTGAAGCTT 57.278 34.783 2.97 0.00 37.92 3.74
44 45 5.469479 CAAATTAAATCACCGGTTGAAGCT 58.531 37.500 2.97 0.00 37.92 3.74
45 46 4.091365 GCAAATTAAATCACCGGTTGAAGC 59.909 41.667 2.97 0.00 37.92 3.86
46 47 5.345741 CAGCAAATTAAATCACCGGTTGAAG 59.654 40.000 2.97 0.00 37.92 3.02
47 48 5.226396 CAGCAAATTAAATCACCGGTTGAA 58.774 37.500 2.97 0.00 37.92 2.69
48 49 4.321601 CCAGCAAATTAAATCACCGGTTGA 60.322 41.667 2.97 6.80 39.11 3.18
49 50 3.925913 CCAGCAAATTAAATCACCGGTTG 59.074 43.478 2.97 0.00 0.00 3.77
50 51 3.829601 TCCAGCAAATTAAATCACCGGTT 59.170 39.130 2.97 0.00 0.00 4.44
51 52 3.426615 TCCAGCAAATTAAATCACCGGT 58.573 40.909 0.00 0.00 0.00 5.28
52 53 4.173256 GTTCCAGCAAATTAAATCACCGG 58.827 43.478 0.00 0.00 0.00 5.28
53 54 4.173256 GGTTCCAGCAAATTAAATCACCG 58.827 43.478 0.00 0.00 0.00 4.94
54 55 5.146010 TGGTTCCAGCAAATTAAATCACC 57.854 39.130 0.00 0.00 0.00 4.02
55 56 7.387397 TCAATTGGTTCCAGCAAATTAAATCAC 59.613 33.333 5.42 0.00 39.20 3.06
56 57 7.448420 TCAATTGGTTCCAGCAAATTAAATCA 58.552 30.769 5.42 0.00 39.20 2.57
57 58 7.903995 TCAATTGGTTCCAGCAAATTAAATC 57.096 32.000 5.42 0.00 39.20 2.17
58 59 7.884354 ACATCAATTGGTTCCAGCAAATTAAAT 59.116 29.630 5.42 0.00 39.20 1.40
59 60 7.222872 ACATCAATTGGTTCCAGCAAATTAAA 58.777 30.769 5.42 0.00 39.20 1.52
60 61 6.767456 ACATCAATTGGTTCCAGCAAATTAA 58.233 32.000 5.42 0.00 39.20 1.40
61 62 6.357579 ACATCAATTGGTTCCAGCAAATTA 57.642 33.333 5.42 0.00 39.20 1.40
62 63 5.231702 ACATCAATTGGTTCCAGCAAATT 57.768 34.783 5.42 0.00 39.20 1.82
63 64 4.895668 ACATCAATTGGTTCCAGCAAAT 57.104 36.364 5.42 0.00 39.20 2.32
64 65 4.686191 AACATCAATTGGTTCCAGCAAA 57.314 36.364 5.42 0.00 39.20 3.68
65 66 4.686191 AAACATCAATTGGTTCCAGCAA 57.314 36.364 5.42 0.00 40.12 3.91
66 67 4.686191 AAAACATCAATTGGTTCCAGCA 57.314 36.364 5.42 0.00 32.76 4.41
67 68 4.815846 ACAAAAACATCAATTGGTTCCAGC 59.184 37.500 5.42 0.00 32.76 4.85
68 69 6.238429 CCAACAAAAACATCAATTGGTTCCAG 60.238 38.462 5.42 0.00 32.76 3.86
69 70 5.587844 CCAACAAAAACATCAATTGGTTCCA 59.412 36.000 5.42 0.00 32.76 3.53
70 71 5.819901 TCCAACAAAAACATCAATTGGTTCC 59.180 36.000 5.42 0.00 32.76 3.62
71 72 6.917217 TCCAACAAAAACATCAATTGGTTC 57.083 33.333 5.42 0.00 32.76 3.62
72 73 6.094742 GGTTCCAACAAAAACATCAATTGGTT 59.905 34.615 5.42 0.00 36.59 3.67
73 74 5.588246 GGTTCCAACAAAAACATCAATTGGT 59.412 36.000 5.42 0.00 38.20 3.67
74 75 5.587844 TGGTTCCAACAAAAACATCAATTGG 59.412 36.000 5.42 0.00 38.35 3.16
75 76 6.674694 TGGTTCCAACAAAAACATCAATTG 57.325 33.333 0.00 0.00 0.00 2.32
76 77 7.878547 ATTGGTTCCAACAAAAACATCAATT 57.121 28.000 6.41 0.00 0.00 2.32
77 78 7.878547 AATTGGTTCCAACAAAAACATCAAT 57.121 28.000 6.41 0.00 0.00 2.57
78 79 7.693969 AAATTGGTTCCAACAAAAACATCAA 57.306 28.000 6.41 0.00 0.00 2.57
79 80 7.609532 AGAAAATTGGTTCCAACAAAAACATCA 59.390 29.630 6.41 0.00 0.00 3.07
80 81 7.984391 AGAAAATTGGTTCCAACAAAAACATC 58.016 30.769 6.41 0.00 0.00 3.06
81 82 7.936496 AGAAAATTGGTTCCAACAAAAACAT 57.064 28.000 6.41 0.00 0.00 2.71
82 83 7.445402 TGAAGAAAATTGGTTCCAACAAAAACA 59.555 29.630 6.41 0.96 0.00 2.83
83 84 7.811653 TGAAGAAAATTGGTTCCAACAAAAAC 58.188 30.769 6.41 0.00 0.00 2.43
84 85 7.986085 TGAAGAAAATTGGTTCCAACAAAAA 57.014 28.000 6.41 0.00 0.00 1.94
85 86 7.826252 TCATGAAGAAAATTGGTTCCAACAAAA 59.174 29.630 6.41 0.00 0.00 2.44
86 87 7.334090 TCATGAAGAAAATTGGTTCCAACAAA 58.666 30.769 6.41 0.00 0.00 2.83
87 88 6.882656 TCATGAAGAAAATTGGTTCCAACAA 58.117 32.000 6.41 0.00 0.00 2.83
88 89 6.462768 CCTCATGAAGAAAATTGGTTCCAACA 60.463 38.462 6.41 0.00 0.00 3.33
89 90 5.928264 CCTCATGAAGAAAATTGGTTCCAAC 59.072 40.000 6.41 0.00 0.00 3.77
90 91 5.602145 ACCTCATGAAGAAAATTGGTTCCAA 59.398 36.000 6.74 6.74 0.00 3.53
91 92 5.010922 CACCTCATGAAGAAAATTGGTTCCA 59.989 40.000 0.00 0.00 0.00 3.53
92 93 5.473039 CACCTCATGAAGAAAATTGGTTCC 58.527 41.667 0.00 0.00 0.00 3.62
93 94 4.925646 GCACCTCATGAAGAAAATTGGTTC 59.074 41.667 0.00 0.00 0.00 3.62
94 95 4.559300 CGCACCTCATGAAGAAAATTGGTT 60.559 41.667 0.00 0.00 0.00 3.67
95 96 3.057315 CGCACCTCATGAAGAAAATTGGT 60.057 43.478 0.00 0.00 0.00 3.67
96 97 3.504863 CGCACCTCATGAAGAAAATTGG 58.495 45.455 0.00 0.00 0.00 3.16
97 98 3.504863 CCGCACCTCATGAAGAAAATTG 58.495 45.455 0.00 0.00 0.00 2.32
98 99 2.094545 GCCGCACCTCATGAAGAAAATT 60.095 45.455 0.00 0.00 0.00 1.82
99 100 1.474077 GCCGCACCTCATGAAGAAAAT 59.526 47.619 0.00 0.00 0.00 1.82
100 101 0.881118 GCCGCACCTCATGAAGAAAA 59.119 50.000 0.00 0.00 0.00 2.29
101 102 1.298157 CGCCGCACCTCATGAAGAAA 61.298 55.000 0.00 0.00 0.00 2.52
102 103 1.741401 CGCCGCACCTCATGAAGAA 60.741 57.895 0.00 0.00 0.00 2.52
103 104 2.125552 CGCCGCACCTCATGAAGA 60.126 61.111 0.00 0.00 0.00 2.87
104 105 3.197790 CCGCCGCACCTCATGAAG 61.198 66.667 0.00 0.00 0.00 3.02
115 116 3.322706 AAAAATGTCTCGCCGCCGC 62.323 57.895 0.00 0.00 0.00 6.53
116 117 2.867472 AAAAATGTCTCGCCGCCG 59.133 55.556 0.00 0.00 0.00 6.46
133 134 9.928236 GAAAAAGCACAAATACAGCAAAAATAA 57.072 25.926 0.00 0.00 0.00 1.40
134 135 8.555361 GGAAAAAGCACAAATACAGCAAAAATA 58.445 29.630 0.00 0.00 0.00 1.40
135 136 7.282901 AGGAAAAAGCACAAATACAGCAAAAAT 59.717 29.630 0.00 0.00 0.00 1.82
136 137 6.597280 AGGAAAAAGCACAAATACAGCAAAAA 59.403 30.769 0.00 0.00 0.00 1.94
137 138 6.036953 CAGGAAAAAGCACAAATACAGCAAAA 59.963 34.615 0.00 0.00 0.00 2.44
138 139 5.523188 CAGGAAAAAGCACAAATACAGCAAA 59.477 36.000 0.00 0.00 0.00 3.68
139 140 5.049167 CAGGAAAAAGCACAAATACAGCAA 58.951 37.500 0.00 0.00 0.00 3.91
140 141 4.501229 CCAGGAAAAAGCACAAATACAGCA 60.501 41.667 0.00 0.00 0.00 4.41
141 142 3.989817 CCAGGAAAAAGCACAAATACAGC 59.010 43.478 0.00 0.00 0.00 4.40
142 143 5.452078 TCCAGGAAAAAGCACAAATACAG 57.548 39.130 0.00 0.00 0.00 2.74
143 144 5.452636 GGTTCCAGGAAAAAGCACAAATACA 60.453 40.000 2.45 0.00 0.00 2.29
144 145 4.988540 GGTTCCAGGAAAAAGCACAAATAC 59.011 41.667 2.45 0.00 0.00 1.89
145 146 4.651503 TGGTTCCAGGAAAAAGCACAAATA 59.348 37.500 2.45 0.00 0.00 1.40
146 147 3.454082 TGGTTCCAGGAAAAAGCACAAAT 59.546 39.130 2.45 0.00 0.00 2.32
147 148 2.834549 TGGTTCCAGGAAAAAGCACAAA 59.165 40.909 2.45 0.00 0.00 2.83
148 149 2.461695 TGGTTCCAGGAAAAAGCACAA 58.538 42.857 2.45 0.00 0.00 3.33
149 150 2.151502 TGGTTCCAGGAAAAAGCACA 57.848 45.000 2.45 0.00 0.00 4.57
150 151 2.627699 TGATGGTTCCAGGAAAAAGCAC 59.372 45.455 2.45 0.00 35.89 4.40
151 152 2.956132 TGATGGTTCCAGGAAAAAGCA 58.044 42.857 2.45 1.06 37.30 3.91
152 153 4.335400 TTTGATGGTTCCAGGAAAAAGC 57.665 40.909 2.45 0.00 0.00 3.51
153 154 6.100404 TCATTTGATGGTTCCAGGAAAAAG 57.900 37.500 2.45 0.00 0.00 2.27
154 155 6.684897 ATCATTTGATGGTTCCAGGAAAAA 57.315 33.333 2.45 0.68 32.68 1.94
155 156 6.684897 AATCATTTGATGGTTCCAGGAAAA 57.315 33.333 2.45 0.00 34.49 2.29
156 157 6.684897 AAATCATTTGATGGTTCCAGGAAA 57.315 33.333 2.45 0.00 31.01 3.13
157 158 6.684897 AAAATCATTTGATGGTTCCAGGAA 57.315 33.333 0.00 0.00 31.01 3.36
171 172 5.990120 AGCTCCTTGTAGCAAAATCATTT 57.010 34.783 0.00 0.00 45.30 2.32
172 173 5.990120 AAGCTCCTTGTAGCAAAATCATT 57.010 34.783 0.00 0.00 45.30 2.57
173 174 5.477984 TCAAAGCTCCTTGTAGCAAAATCAT 59.522 36.000 0.00 0.00 45.30 2.45
174 175 4.826733 TCAAAGCTCCTTGTAGCAAAATCA 59.173 37.500 0.00 0.00 45.30 2.57
175 176 5.376854 TCAAAGCTCCTTGTAGCAAAATC 57.623 39.130 0.00 0.00 45.30 2.17
176 177 5.990120 ATCAAAGCTCCTTGTAGCAAAAT 57.010 34.783 0.00 0.00 45.30 1.82
177 178 5.789643 AATCAAAGCTCCTTGTAGCAAAA 57.210 34.783 0.00 0.00 45.30 2.44
178 179 5.789643 AAATCAAAGCTCCTTGTAGCAAA 57.210 34.783 0.00 0.00 45.30 3.68
179 180 5.789643 AAAATCAAAGCTCCTTGTAGCAA 57.210 34.783 0.00 0.00 45.30 3.91
180 181 5.531634 CAAAAATCAAAGCTCCTTGTAGCA 58.468 37.500 0.00 0.00 45.30 3.49
181 182 4.386954 GCAAAAATCAAAGCTCCTTGTAGC 59.613 41.667 0.00 0.00 43.11 3.58
182 183 5.632347 CAGCAAAAATCAAAGCTCCTTGTAG 59.368 40.000 0.00 0.00 34.61 2.74
183 184 5.509501 CCAGCAAAAATCAAAGCTCCTTGTA 60.510 40.000 0.00 0.00 34.61 2.41
184 185 4.374399 CAGCAAAAATCAAAGCTCCTTGT 58.626 39.130 0.00 0.00 34.61 3.16
185 186 3.744426 CCAGCAAAAATCAAAGCTCCTTG 59.256 43.478 0.00 0.00 34.61 3.61
186 187 3.642848 TCCAGCAAAAATCAAAGCTCCTT 59.357 39.130 0.00 0.00 34.61 3.36
187 188 3.233507 TCCAGCAAAAATCAAAGCTCCT 58.766 40.909 0.00 0.00 34.61 3.69
188 189 3.665745 TCCAGCAAAAATCAAAGCTCC 57.334 42.857 0.00 0.00 34.61 4.70
189 190 3.742882 GGTTCCAGCAAAAATCAAAGCTC 59.257 43.478 0.00 0.00 34.61 4.09
190 191 3.732212 GGTTCCAGCAAAAATCAAAGCT 58.268 40.909 0.00 0.00 37.95 3.74
191 192 2.476241 CGGTTCCAGCAAAAATCAAAGC 59.524 45.455 0.00 0.00 0.00 3.51
192 193 2.476241 GCGGTTCCAGCAAAAATCAAAG 59.524 45.455 0.00 0.00 34.19 2.77
193 194 2.478831 GCGGTTCCAGCAAAAATCAAA 58.521 42.857 0.00 0.00 34.19 2.69
194 195 1.270041 GGCGGTTCCAGCAAAAATCAA 60.270 47.619 7.63 0.00 36.08 2.57
195 196 0.316841 GGCGGTTCCAGCAAAAATCA 59.683 50.000 7.63 0.00 36.08 2.57
196 197 0.603065 AGGCGGTTCCAGCAAAAATC 59.397 50.000 7.63 0.00 37.29 2.17
197 198 0.318120 CAGGCGGTTCCAGCAAAAAT 59.682 50.000 7.63 0.00 37.29 1.82
198 199 0.753479 TCAGGCGGTTCCAGCAAAAA 60.753 50.000 7.63 0.00 37.29 1.94
199 200 0.753479 TTCAGGCGGTTCCAGCAAAA 60.753 50.000 7.63 0.00 37.29 2.44
200 201 1.152860 TTCAGGCGGTTCCAGCAAA 60.153 52.632 7.63 0.00 37.29 3.68
201 202 1.600636 CTTCAGGCGGTTCCAGCAA 60.601 57.895 7.63 0.00 37.29 3.91
202 203 2.032528 CTTCAGGCGGTTCCAGCA 59.967 61.111 7.63 0.00 37.29 4.41
203 204 3.435186 GCTTCAGGCGGTTCCAGC 61.435 66.667 0.00 0.00 37.29 4.85
212 213 0.178068 TGTATTCCTCCGCTTCAGGC 59.822 55.000 0.00 0.00 37.64 4.85
213 214 2.918712 ATGTATTCCTCCGCTTCAGG 57.081 50.000 0.00 0.00 0.00 3.86
214 215 6.867662 ATTAAATGTATTCCTCCGCTTCAG 57.132 37.500 0.00 0.00 0.00 3.02
215 216 7.639113 AAATTAAATGTATTCCTCCGCTTCA 57.361 32.000 0.00 0.00 0.00 3.02
216 217 8.807581 CAAAAATTAAATGTATTCCTCCGCTTC 58.192 33.333 0.00 0.00 0.00 3.86
217 218 7.277760 GCAAAAATTAAATGTATTCCTCCGCTT 59.722 33.333 0.00 0.00 0.00 4.68
218 219 6.756542 GCAAAAATTAAATGTATTCCTCCGCT 59.243 34.615 0.00 0.00 0.00 5.52
219 220 6.756542 AGCAAAAATTAAATGTATTCCTCCGC 59.243 34.615 0.00 0.00 0.00 5.54
220 221 7.222611 CCAGCAAAAATTAAATGTATTCCTCCG 59.777 37.037 0.00 0.00 0.00 4.63
221 222 8.257306 TCCAGCAAAAATTAAATGTATTCCTCC 58.743 33.333 0.00 0.00 0.00 4.30
222 223 9.651913 TTCCAGCAAAAATTAAATGTATTCCTC 57.348 29.630 0.00 0.00 0.00 3.71
223 224 9.435688 GTTCCAGCAAAAATTAAATGTATTCCT 57.564 29.630 0.00 0.00 0.00 3.36
224 225 8.664798 GGTTCCAGCAAAAATTAAATGTATTCC 58.335 33.333 0.00 0.00 0.00 3.01
225 226 9.435688 AGGTTCCAGCAAAAATTAAATGTATTC 57.564 29.630 0.00 0.00 0.00 1.75
226 227 9.435688 GAGGTTCCAGCAAAAATTAAATGTATT 57.564 29.630 0.00 0.00 0.00 1.89
227 228 8.815912 AGAGGTTCCAGCAAAAATTAAATGTAT 58.184 29.630 0.00 0.00 0.00 2.29
272 274 4.615682 CGATTGTAGCTTTTGTGATTGCCA 60.616 41.667 0.00 0.00 0.00 4.92
335 337 1.009829 CCAGCAAACATAGCTCGTCC 58.990 55.000 0.00 0.00 41.14 4.79
367 369 2.142319 GACCGCCGGTAGTAACAAAAA 58.858 47.619 9.73 0.00 35.25 1.94
368 370 1.069823 TGACCGCCGGTAGTAACAAAA 59.930 47.619 9.73 0.00 35.25 2.44
373 375 2.743126 CAAATTTGACCGCCGGTAGTAA 59.257 45.455 9.73 4.00 35.25 2.24
404 406 1.688735 AGGGCTTTCCTTTGAGTTTGC 59.311 47.619 0.00 0.00 45.47 3.68
443 445 2.669569 CTGGTCGCAACACCCTGG 60.670 66.667 0.00 0.00 35.26 4.45
445 447 4.988598 CGCTGGTCGCAACACCCT 62.989 66.667 0.00 0.00 39.08 4.34
474 476 1.452953 CTACGACGGCCATAGCTCCA 61.453 60.000 2.24 0.00 39.73 3.86
491 493 2.561956 GGCGATGGTAGCTCCGCTA 61.562 63.158 22.94 0.00 46.02 4.26
510 512 2.360475 GGTTGCAGCTCCCTCACC 60.360 66.667 0.00 0.00 0.00 4.02
542 544 2.106074 GCCGGATCGACACATGCAA 61.106 57.895 5.05 0.00 0.00 4.08
546 548 1.663379 TTCTCGCCGGATCGACACAT 61.663 55.000 5.05 0.00 34.46 3.21
552 554 0.249073 ATGTCTTTCTCGCCGGATCG 60.249 55.000 5.05 0.00 0.00 3.69
564 566 1.401148 CCGTCGTCGTCTCATGTCTTT 60.401 52.381 0.71 0.00 35.01 2.52
572 574 4.517703 CCTCGCCGTCGTCGTCTC 62.518 72.222 0.71 0.00 36.96 3.36
630 632 2.272146 GATGTGCACCCACCCGAT 59.728 61.111 15.69 0.00 41.35 4.18
643 645 4.722700 GTGGCTGCACGGGGATGT 62.723 66.667 0.50 0.00 0.00 3.06
724 726 1.344953 ACCCCGCATCTTAGATGCCA 61.345 55.000 33.08 0.00 41.71 4.92
727 729 4.039245 TCTTCTAACCCCGCATCTTAGATG 59.961 45.833 17.16 17.16 0.00 2.90
740 742 3.087781 ACAGTAGGTCGTCTTCTAACCC 58.912 50.000 0.00 0.00 33.33 4.11
754 756 0.750546 TCCGATCCCGTGACAGTAGG 60.751 60.000 0.00 0.00 0.00 3.18
755 757 0.381089 GTCCGATCCCGTGACAGTAG 59.619 60.000 0.00 0.00 36.59 2.57
756 758 1.371337 CGTCCGATCCCGTGACAGTA 61.371 60.000 0.00 0.00 36.47 2.74
757 759 2.697761 CGTCCGATCCCGTGACAGT 61.698 63.158 0.00 0.00 36.47 3.55
758 760 1.725557 ATCGTCCGATCCCGTGACAG 61.726 60.000 0.00 0.00 36.47 3.51
759 761 1.317431 AATCGTCCGATCCCGTGACA 61.317 55.000 2.23 0.00 36.47 3.58
776 778 4.578928 CCGTCCGATTTTCCTAATTCCAAT 59.421 41.667 0.00 0.00 0.00 3.16
780 782 4.729746 GCAACCGTCCGATTTTCCTAATTC 60.730 45.833 0.00 0.00 0.00 2.17
789 791 2.744709 CCCGCAACCGTCCGATTT 60.745 61.111 0.00 0.00 0.00 2.17
805 807 0.320334 CAAATTTGGGCCGGTCAACC 60.320 55.000 9.07 3.83 0.00 3.77
806 808 0.676736 TCAAATTTGGGCCGGTCAAC 59.323 50.000 17.90 0.00 0.00 3.18
807 809 0.965439 CTCAAATTTGGGCCGGTCAA 59.035 50.000 17.90 8.42 0.00 3.18
808 810 2.652313 CTCAAATTTGGGCCGGTCA 58.348 52.632 17.90 1.16 0.00 4.02
815 817 1.444212 CGCACCGCTCAAATTTGGG 60.444 57.895 17.90 16.04 0.00 4.12
816 818 4.151417 CGCACCGCTCAAATTTGG 57.849 55.556 17.90 9.84 0.00 3.28
838 840 2.606272 GACATTTTTACTAGGCGGGTCG 59.394 50.000 0.00 0.00 0.00 4.79
839 841 3.602483 TGACATTTTTACTAGGCGGGTC 58.398 45.455 0.00 0.00 0.00 4.46
840 842 3.706600 TGACATTTTTACTAGGCGGGT 57.293 42.857 0.00 0.00 0.00 5.28
841 843 3.315191 CCATGACATTTTTACTAGGCGGG 59.685 47.826 0.00 0.00 0.00 6.13
842 844 3.243068 GCCATGACATTTTTACTAGGCGG 60.243 47.826 0.00 0.00 0.00 6.13
843 845 3.627577 AGCCATGACATTTTTACTAGGCG 59.372 43.478 0.00 0.00 44.00 5.52
844 846 4.399303 ACAGCCATGACATTTTTACTAGGC 59.601 41.667 0.00 0.00 39.82 3.93
845 847 6.823689 AGTACAGCCATGACATTTTTACTAGG 59.176 38.462 0.00 0.00 0.00 3.02
846 848 7.677276 GCAGTACAGCCATGACATTTTTACTAG 60.677 40.741 0.00 0.00 0.00 2.57
847 849 6.093495 GCAGTACAGCCATGACATTTTTACTA 59.907 38.462 0.00 0.00 0.00 1.82
848 850 5.106157 GCAGTACAGCCATGACATTTTTACT 60.106 40.000 0.00 0.00 0.00 2.24
849 851 5.095490 GCAGTACAGCCATGACATTTTTAC 58.905 41.667 0.00 0.00 0.00 2.01
850 852 5.309323 GCAGTACAGCCATGACATTTTTA 57.691 39.130 0.00 0.00 0.00 1.52
929 931 1.205460 TCAGGGGGTTGGAGCCTTAC 61.205 60.000 0.00 0.00 35.71 2.34
983 985 1.074889 CCATGATGGGATGGATCTGCA 59.925 52.381 2.79 0.00 45.24 4.41
1128 1130 4.047059 GACCAGACGGCGTCGGAA 62.047 66.667 37.96 0.00 41.39 4.30
1278 1380 7.147880 GGGTGATATACATGGGATCTGTACTAC 60.148 44.444 0.00 0.00 32.24 2.73
1279 1381 6.895756 GGGTGATATACATGGGATCTGTACTA 59.104 42.308 0.00 0.00 32.24 1.82
1308 1411 0.251033 GTACTGGTTGGGTTGGGGAC 60.251 60.000 0.00 0.00 0.00 4.46
1309 1412 0.402272 AGTACTGGTTGGGTTGGGGA 60.402 55.000 0.00 0.00 0.00 4.81
1335 1438 4.093556 GGATCGATGGATTAGCCGATTTTC 59.906 45.833 0.54 0.00 41.17 2.29
1347 1453 2.587247 CCTGGGCGGATCGATGGAT 61.587 63.158 0.54 0.00 34.96 3.41
1350 1456 0.319900 CTTACCTGGGCGGATCGATG 60.320 60.000 0.54 0.00 36.31 3.84
1358 1474 1.878102 GCATATGGTCTTACCTGGGCG 60.878 57.143 4.56 0.00 39.58 6.13
1363 1479 4.220821 CGTATGAGGCATATGGTCTTACCT 59.779 45.833 4.56 0.70 39.58 3.08
1366 2028 4.082190 GCTCGTATGAGGCATATGGTCTTA 60.082 45.833 13.82 0.00 42.79 2.10
1439 2117 1.899437 GACCTCCATCCAGCCGTCAA 61.899 60.000 0.00 0.00 0.00 3.18
1650 2332 4.535526 AAGGTTTCACTTGCAACAACTT 57.464 36.364 0.00 0.00 0.00 2.66
1697 2379 4.448210 ACATGTACTTTCACCAACGAACT 58.552 39.130 0.00 0.00 0.00 3.01
1719 2401 5.183331 AGACAGAGTTACGAATAGCAACAGA 59.817 40.000 0.00 0.00 0.00 3.41
1879 3763 0.321741 TTTTGTTCCCGCGGATGCTA 60.322 50.000 30.73 9.78 39.65 3.49
1880 3764 1.602323 TTTTGTTCCCGCGGATGCT 60.602 52.632 30.73 0.00 39.65 3.79
1896 3780 6.043854 TCCTTACTTTGCTTTTGTTGGTTT 57.956 33.333 0.00 0.00 0.00 3.27
1933 3817 9.573133 GATTAAATGAACCAAATGAAGAACGAT 57.427 29.630 0.00 0.00 0.00 3.73
1957 3841 4.322080 TGGTATTTCGCTGAGAATCGAT 57.678 40.909 0.00 0.00 38.86 3.59
2044 6817 2.634815 ATCGAGGCAATTCAGCTCAT 57.365 45.000 0.00 0.00 34.17 2.90
2063 6836 2.622942 ACTAAACCGTGTGGAGTACGAA 59.377 45.455 0.00 0.00 43.82 3.85
2067 6840 4.562082 CAATCACTAAACCGTGTGGAGTA 58.438 43.478 0.00 0.00 39.21 2.59
2092 6894 5.318630 ACCCTAGCGTTCCAATTTCTTTTA 58.681 37.500 0.00 0.00 0.00 1.52
2108 6910 3.495806 CCATCAAAGGATCTGACCCTAGC 60.496 52.174 0.00 0.00 32.77 3.42
2113 6915 5.946377 AGTTTAACCATCAAAGGATCTGACC 59.054 40.000 0.00 0.00 0.00 4.02
2167 6973 1.000283 ACTCTGTTGCCTTGTCTCTCG 60.000 52.381 0.00 0.00 0.00 4.04
2196 7003 3.193267 TGCTGTAGTGAATTTTGGCATCC 59.807 43.478 0.00 0.00 0.00 3.51
2293 7102 7.964604 AGGAAGTACTGTAGTCATTGTTTTC 57.035 36.000 0.00 0.00 0.00 2.29
2349 7159 5.413833 AGGTTTGCAGTTGTGAATCATAGAG 59.586 40.000 0.00 0.00 0.00 2.43
2351 7161 5.413833 AGAGGTTTGCAGTTGTGAATCATAG 59.586 40.000 0.00 0.00 0.00 2.23
2417 7245 8.243426 TGGAATGAAGCAATTGAGTAACATAAC 58.757 33.333 10.34 4.67 0.00 1.89


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

AutoCloner maintained by Alex Coulton.