Multiple sequence alignment - TraesCS2D01G326400

Loading Multiple Alignment...

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 TraesCS2D01G326400 chr2D 100.000 4693 0 0 1 4693 419788067 419783375 0.000000e+00 8667.0
1 TraesCS2D01G326400 chr2B 92.269 3557 169 53 567 4096 492152288 492148811 0.000000e+00 4948.0
2 TraesCS2D01G326400 chr2B 92.934 467 7 6 4234 4692 492148480 492148032 0.000000e+00 656.0
3 TraesCS2D01G326400 chr2B 91.111 315 14 8 217 520 492153028 492152717 9.400000e-112 414.0
4 TraesCS2D01G326400 chr2B 95.833 48 2 0 4111 4158 492148825 492148778 1.400000e-10 78.7
5 TraesCS2D01G326400 chr2A 93.851 1854 81 19 2118 3966 570190640 570192465 0.000000e+00 2761.0
6 TraesCS2D01G326400 chr2A 87.664 1524 105 27 632 2122 570189008 570190481 0.000000e+00 1696.0
7 TraesCS2D01G326400 chr2A 95.856 555 7 4 4140 4693 570192644 570193183 0.000000e+00 883.0
8 TraesCS2D01G326400 chr2A 86.179 369 20 7 225 592 570188669 570189007 2.060000e-98 370.0
9 TraesCS2D01G326400 chr3B 82.513 1727 202 50 2253 3953 21404149 21405801 0.000000e+00 1424.0
10 TraesCS2D01G326400 chr3B 74.442 403 74 13 1166 1561 21402835 21403215 3.780000e-31 147.0
11 TraesCS2D01G326400 chr3A 83.551 1453 156 45 2253 3680 22230236 22228842 0.000000e+00 1282.0
12 TraesCS2D01G326400 chr3A 89.595 173 18 0 3556 3728 22147920 22147748 2.200000e-53 220.0
13 TraesCS2D01G326400 chr3A 91.892 74 6 0 1476 1549 22231265 22231192 2.310000e-18 104.0
14 TraesCS2D01G326400 chr3D 84.457 1261 139 30 2253 3492 14448095 14449319 0.000000e+00 1190.0
15 TraesCS2D01G326400 chr3D 76.960 421 62 22 1149 1561 14446792 14447185 1.710000e-49 207.0
16 TraesCS2D01G326400 chr3D 98.291 117 2 0 3564 3680 14449377 14449493 6.160000e-49 206.0
17 TraesCS2D01G326400 chr7D 89.583 192 20 0 4475 4666 531553840 531554031 1.300000e-60 244.0
18 TraesCS2D01G326400 chr7A 84.524 252 33 5 4418 4666 611969535 611969783 1.300000e-60 244.0
19 TraesCS2D01G326400 chr7A 83.539 243 34 5 4414 4653 611776746 611776985 6.110000e-54 222.0
20 TraesCS2D01G326400 chr5D 86.802 197 25 1 4470 4666 318059886 318060081 7.910000e-53 219.0
21 TraesCS2D01G326400 chr5A 86.802 197 25 1 4470 4666 412913483 412913678 7.910000e-53 219.0


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 TraesCS2D01G326400 chr2D 419783375 419788067 4692 True 8667.000000 8667 100.000000 1 4693 1 chr2D.!!$R1 4692
1 TraesCS2D01G326400 chr2B 492148032 492153028 4996 True 1524.175000 4948 93.036750 217 4692 4 chr2B.!!$R1 4475
2 TraesCS2D01G326400 chr2A 570188669 570193183 4514 False 1427.500000 2761 90.887500 225 4693 4 chr2A.!!$F1 4468
3 TraesCS2D01G326400 chr3B 21402835 21405801 2966 False 785.500000 1424 78.477500 1166 3953 2 chr3B.!!$F1 2787
4 TraesCS2D01G326400 chr3A 22228842 22231265 2423 True 693.000000 1282 87.721500 1476 3680 2 chr3A.!!$R2 2204
5 TraesCS2D01G326400 chr3D 14446792 14449493 2701 False 534.333333 1190 86.569333 1149 3680 3 chr3D.!!$F1 2531

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
793 1224 0.174389 CTAGTGCGAGACCATGTGCT 59.826 55.000 0.00 0.0 0.00 4.40 F
1572 2055 0.610232 GTTTCACATGCTCCTGGCCT 60.610 55.000 3.32 0.0 40.92 5.19 F
1655 2138 0.960364 CACTTGGTGGGTTGATCCGG 60.960 60.000 0.00 0.0 37.00 5.14 F
3116 4409 1.474478 CAGGAGTGCTTTCGAGCTCTA 59.526 52.381 12.85 0.0 38.54 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 2193 0.106149 ACTTCCGCTCGAACCAGTTT 59.894 50.000 0.0 0.0 0.00 2.66 R
3545 4850 0.450583 TACCAGTTAGCACTCTCGCG 59.549 55.000 0.0 0.0 36.85 5.87 R
3567 4873 1.555533 GACCCCCTGGAAGAGTTACAG 59.444 57.143 0.0 0.0 34.07 2.74 R
4158 5540 1.094785 GCCTTCGCTCATTGGCTTAA 58.905 50.000 0.0 0.0 41.92 1.85 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
17 18 2.503546 TTGGTCACTGCACGCTCA 59.496 55.556 0.00 0.00 0.00 4.26
18 19 1.595109 TTGGTCACTGCACGCTCAG 60.595 57.895 3.30 3.30 39.86 3.35
31 32 4.057730 CACGCTCAGTGTACATTTCAAG 57.942 45.455 0.00 0.00 45.51 3.02
32 33 2.480419 ACGCTCAGTGTACATTTCAAGC 59.520 45.455 0.00 3.14 0.00 4.01
33 34 2.738846 CGCTCAGTGTACATTTCAAGCT 59.261 45.455 0.00 0.00 0.00 3.74
34 35 3.187227 CGCTCAGTGTACATTTCAAGCTT 59.813 43.478 0.00 0.00 0.00 3.74
35 36 4.667668 CGCTCAGTGTACATTTCAAGCTTC 60.668 45.833 0.00 0.00 0.00 3.86
36 37 4.667668 GCTCAGTGTACATTTCAAGCTTCG 60.668 45.833 0.00 0.00 0.00 3.79
37 38 4.627058 TCAGTGTACATTTCAAGCTTCGA 58.373 39.130 0.00 0.00 0.00 3.71
38 39 4.447724 TCAGTGTACATTTCAAGCTTCGAC 59.552 41.667 0.00 0.00 0.00 4.20
39 40 3.428870 AGTGTACATTTCAAGCTTCGACG 59.571 43.478 0.00 0.00 0.00 5.12
40 41 3.427528 GTGTACATTTCAAGCTTCGACGA 59.572 43.478 0.00 0.00 0.00 4.20
41 42 3.673338 TGTACATTTCAAGCTTCGACGAG 59.327 43.478 0.00 0.00 0.00 4.18
42 43 1.461127 ACATTTCAAGCTTCGACGAGC 59.539 47.619 0.00 0.62 43.02 5.03
43 44 1.460743 CATTTCAAGCTTCGACGAGCA 59.539 47.619 11.49 0.00 45.12 4.26
44 45 1.577468 TTTCAAGCTTCGACGAGCAA 58.423 45.000 11.49 0.00 45.12 3.91
45 46 0.859232 TTCAAGCTTCGACGAGCAAC 59.141 50.000 11.49 2.26 45.12 4.17
46 47 1.128611 CAAGCTTCGACGAGCAACG 59.871 57.895 11.49 1.99 45.12 4.10
58 59 3.169207 CGAGCAACGTAAAAGTGAAGG 57.831 47.619 0.00 0.00 37.22 3.46
59 60 2.798283 CGAGCAACGTAAAAGTGAAGGA 59.202 45.455 0.00 0.00 37.22 3.36
60 61 3.246699 CGAGCAACGTAAAAGTGAAGGAA 59.753 43.478 0.00 0.00 37.22 3.36
61 62 4.260456 CGAGCAACGTAAAAGTGAAGGAAA 60.260 41.667 0.00 0.00 37.22 3.13
62 63 5.570234 AGCAACGTAAAAGTGAAGGAAAA 57.430 34.783 0.00 0.00 0.00 2.29
63 64 5.337554 AGCAACGTAAAAGTGAAGGAAAAC 58.662 37.500 0.00 0.00 0.00 2.43
64 65 4.501559 GCAACGTAAAAGTGAAGGAAAACC 59.498 41.667 0.00 0.00 0.00 3.27
65 66 5.677852 GCAACGTAAAAGTGAAGGAAAACCT 60.678 40.000 0.00 0.00 0.00 3.50
66 67 5.494632 ACGTAAAAGTGAAGGAAAACCTG 57.505 39.130 0.00 0.00 0.00 4.00
67 68 4.201980 ACGTAAAAGTGAAGGAAAACCTGC 60.202 41.667 0.00 0.00 0.00 4.85
68 69 4.036380 CGTAAAAGTGAAGGAAAACCTGCT 59.964 41.667 0.00 0.00 0.00 4.24
69 70 5.237779 CGTAAAAGTGAAGGAAAACCTGCTA 59.762 40.000 0.00 0.00 0.00 3.49
70 71 6.238538 CGTAAAAGTGAAGGAAAACCTGCTAA 60.239 38.462 0.00 0.00 0.00 3.09
71 72 6.731292 AAAAGTGAAGGAAAACCTGCTAAT 57.269 33.333 0.00 0.00 0.00 1.73
72 73 7.833285 AAAAGTGAAGGAAAACCTGCTAATA 57.167 32.000 0.00 0.00 0.00 0.98
73 74 8.422577 AAAAGTGAAGGAAAACCTGCTAATAT 57.577 30.769 0.00 0.00 0.00 1.28
74 75 9.528489 AAAAGTGAAGGAAAACCTGCTAATATA 57.472 29.630 0.00 0.00 0.00 0.86
75 76 8.738645 AAGTGAAGGAAAACCTGCTAATATAG 57.261 34.615 0.00 0.00 0.00 1.31
76 77 7.862675 AGTGAAGGAAAACCTGCTAATATAGT 58.137 34.615 0.00 0.00 0.00 2.12
77 78 8.329502 AGTGAAGGAAAACCTGCTAATATAGTT 58.670 33.333 0.00 0.00 0.00 2.24
78 79 8.957466 GTGAAGGAAAACCTGCTAATATAGTTT 58.043 33.333 0.00 0.00 32.26 2.66
79 80 9.528489 TGAAGGAAAACCTGCTAATATAGTTTT 57.472 29.630 0.00 0.00 41.84 2.43
82 83 9.528489 AGGAAAACCTGCTAATATAGTTTTTGA 57.472 29.630 0.00 0.00 39.89 2.69
107 108 7.536895 TGTAGTTGTACATTTTACACGTTGT 57.463 32.000 0.00 0.00 34.02 3.32
108 109 7.620215 TGTAGTTGTACATTTTACACGTTGTC 58.380 34.615 0.00 0.00 34.02 3.18
109 110 6.913873 AGTTGTACATTTTACACGTTGTCT 57.086 33.333 0.00 0.00 0.00 3.41
110 111 7.311364 AGTTGTACATTTTACACGTTGTCTT 57.689 32.000 0.00 0.00 0.00 3.01
111 112 7.404203 AGTTGTACATTTTACACGTTGTCTTC 58.596 34.615 0.00 0.00 0.00 2.87
112 113 7.279313 AGTTGTACATTTTACACGTTGTCTTCT 59.721 33.333 0.00 0.00 0.00 2.85
113 114 6.939627 TGTACATTTTACACGTTGTCTTCTG 58.060 36.000 0.00 0.00 0.00 3.02
114 115 6.535865 TGTACATTTTACACGTTGTCTTCTGT 59.464 34.615 0.00 0.00 0.00 3.41
115 116 6.431198 ACATTTTACACGTTGTCTTCTGTT 57.569 33.333 0.00 0.00 0.00 3.16
116 117 6.255215 ACATTTTACACGTTGTCTTCTGTTG 58.745 36.000 0.00 0.00 0.00 3.33
117 118 5.866335 TTTTACACGTTGTCTTCTGTTGT 57.134 34.783 0.00 0.00 0.00 3.32
118 119 5.459110 TTTACACGTTGTCTTCTGTTGTC 57.541 39.130 0.00 0.00 0.00 3.18
119 120 1.924524 ACACGTTGTCTTCTGTTGTCG 59.075 47.619 0.00 0.00 0.00 4.35
120 121 1.924524 CACGTTGTCTTCTGTTGTCGT 59.075 47.619 0.00 0.00 0.00 4.34
121 122 2.034842 CACGTTGTCTTCTGTTGTCGTC 60.035 50.000 0.00 0.00 0.00 4.20
122 123 1.521423 CGTTGTCTTCTGTTGTCGTCC 59.479 52.381 0.00 0.00 0.00 4.79
123 124 2.798499 CGTTGTCTTCTGTTGTCGTCCT 60.798 50.000 0.00 0.00 0.00 3.85
124 125 3.195661 GTTGTCTTCTGTTGTCGTCCTT 58.804 45.455 0.00 0.00 0.00 3.36
125 126 2.821546 TGTCTTCTGTTGTCGTCCTTG 58.178 47.619 0.00 0.00 0.00 3.61
126 127 2.135933 GTCTTCTGTTGTCGTCCTTGG 58.864 52.381 0.00 0.00 0.00 3.61
127 128 1.760613 TCTTCTGTTGTCGTCCTTGGT 59.239 47.619 0.00 0.00 0.00 3.67
128 129 2.169769 TCTTCTGTTGTCGTCCTTGGTT 59.830 45.455 0.00 0.00 0.00 3.67
129 130 2.702592 TCTGTTGTCGTCCTTGGTTT 57.297 45.000 0.00 0.00 0.00 3.27
130 131 3.823281 TCTGTTGTCGTCCTTGGTTTA 57.177 42.857 0.00 0.00 0.00 2.01
131 132 4.345859 TCTGTTGTCGTCCTTGGTTTAT 57.654 40.909 0.00 0.00 0.00 1.40
132 133 4.062293 TCTGTTGTCGTCCTTGGTTTATG 58.938 43.478 0.00 0.00 0.00 1.90
133 134 3.811083 TGTTGTCGTCCTTGGTTTATGT 58.189 40.909 0.00 0.00 0.00 2.29
134 135 4.200874 TGTTGTCGTCCTTGGTTTATGTT 58.799 39.130 0.00 0.00 0.00 2.71
135 136 4.035792 TGTTGTCGTCCTTGGTTTATGTTG 59.964 41.667 0.00 0.00 0.00 3.33
136 137 2.550606 TGTCGTCCTTGGTTTATGTTGC 59.449 45.455 0.00 0.00 0.00 4.17
137 138 2.812011 GTCGTCCTTGGTTTATGTTGCT 59.188 45.455 0.00 0.00 0.00 3.91
138 139 3.071479 TCGTCCTTGGTTTATGTTGCTC 58.929 45.455 0.00 0.00 0.00 4.26
139 140 2.159707 CGTCCTTGGTTTATGTTGCTCG 60.160 50.000 0.00 0.00 0.00 5.03
140 141 1.810151 TCCTTGGTTTATGTTGCTCGC 59.190 47.619 0.00 0.00 0.00 5.03
141 142 1.812571 CCTTGGTTTATGTTGCTCGCT 59.187 47.619 0.00 0.00 0.00 4.93
142 143 2.414559 CCTTGGTTTATGTTGCTCGCTG 60.415 50.000 0.00 0.00 0.00 5.18
143 144 2.177394 TGGTTTATGTTGCTCGCTGA 57.823 45.000 0.00 0.00 0.00 4.26
144 145 2.710377 TGGTTTATGTTGCTCGCTGAT 58.290 42.857 0.00 0.00 0.00 2.90
145 146 3.081061 TGGTTTATGTTGCTCGCTGATT 58.919 40.909 0.00 0.00 0.00 2.57
146 147 3.505680 TGGTTTATGTTGCTCGCTGATTT 59.494 39.130 0.00 0.00 0.00 2.17
147 148 4.022416 TGGTTTATGTTGCTCGCTGATTTT 60.022 37.500 0.00 0.00 0.00 1.82
148 149 4.558860 GGTTTATGTTGCTCGCTGATTTTC 59.441 41.667 0.00 0.00 0.00 2.29
149 150 5.393962 GTTTATGTTGCTCGCTGATTTTCT 58.606 37.500 0.00 0.00 0.00 2.52
150 151 5.627499 TTATGTTGCTCGCTGATTTTCTT 57.373 34.783 0.00 0.00 0.00 2.52
151 152 3.272439 TGTTGCTCGCTGATTTTCTTG 57.728 42.857 0.00 0.00 0.00 3.02
152 153 2.877786 TGTTGCTCGCTGATTTTCTTGA 59.122 40.909 0.00 0.00 0.00 3.02
153 154 3.503363 TGTTGCTCGCTGATTTTCTTGAT 59.497 39.130 0.00 0.00 0.00 2.57
154 155 4.694982 TGTTGCTCGCTGATTTTCTTGATA 59.305 37.500 0.00 0.00 0.00 2.15
155 156 5.181056 TGTTGCTCGCTGATTTTCTTGATAA 59.819 36.000 0.00 0.00 0.00 1.75
156 157 5.878332 TGCTCGCTGATTTTCTTGATAAA 57.122 34.783 0.00 0.00 0.00 1.40
157 158 5.631026 TGCTCGCTGATTTTCTTGATAAAC 58.369 37.500 0.00 0.00 0.00 2.01
158 159 4.725754 GCTCGCTGATTTTCTTGATAAACG 59.274 41.667 0.00 0.00 0.00 3.60
159 160 5.671329 GCTCGCTGATTTTCTTGATAAACGT 60.671 40.000 0.00 0.00 0.00 3.99
160 161 6.236017 TCGCTGATTTTCTTGATAAACGTT 57.764 33.333 0.00 0.00 0.00 3.99
161 162 7.354025 TCGCTGATTTTCTTGATAAACGTTA 57.646 32.000 0.00 0.00 0.00 3.18
162 163 7.453034 TCGCTGATTTTCTTGATAAACGTTAG 58.547 34.615 0.00 0.00 0.00 2.34
163 164 7.329962 TCGCTGATTTTCTTGATAAACGTTAGA 59.670 33.333 0.00 0.00 0.00 2.10
164 165 8.116753 CGCTGATTTTCTTGATAAACGTTAGAT 58.883 33.333 0.00 0.00 0.00 1.98
165 166 9.214953 GCTGATTTTCTTGATAAACGTTAGATG 57.785 33.333 0.00 0.00 0.00 2.90
173 174 9.982291 TCTTGATAAACGTTAGATGTAAAATGC 57.018 29.630 0.00 0.00 0.00 3.56
174 175 9.221775 CTTGATAAACGTTAGATGTAAAATGCC 57.778 33.333 0.00 0.00 0.00 4.40
175 176 7.699566 TGATAAACGTTAGATGTAAAATGCCC 58.300 34.615 0.00 0.00 0.00 5.36
176 177 7.554835 TGATAAACGTTAGATGTAAAATGCCCT 59.445 33.333 0.00 0.00 0.00 5.19
177 178 6.584185 AAACGTTAGATGTAAAATGCCCTT 57.416 33.333 0.00 0.00 0.00 3.95
178 179 6.584185 AACGTTAGATGTAAAATGCCCTTT 57.416 33.333 0.00 0.00 0.00 3.11
179 180 5.949735 ACGTTAGATGTAAAATGCCCTTTG 58.050 37.500 0.00 0.00 0.00 2.77
180 181 5.475564 ACGTTAGATGTAAAATGCCCTTTGT 59.524 36.000 0.00 0.00 0.00 2.83
181 182 6.027749 CGTTAGATGTAAAATGCCCTTTGTC 58.972 40.000 0.00 0.00 0.00 3.18
182 183 6.128007 CGTTAGATGTAAAATGCCCTTTGTCT 60.128 38.462 0.00 0.00 0.00 3.41
183 184 7.065324 CGTTAGATGTAAAATGCCCTTTGTCTA 59.935 37.037 0.00 0.00 0.00 2.59
184 185 8.903820 GTTAGATGTAAAATGCCCTTTGTCTAT 58.096 33.333 0.00 0.00 0.00 1.98
185 186 7.338800 AGATGTAAAATGCCCTTTGTCTATG 57.661 36.000 0.00 0.00 0.00 2.23
186 187 6.891908 AGATGTAAAATGCCCTTTGTCTATGT 59.108 34.615 0.00 0.00 0.00 2.29
187 188 6.909550 TGTAAAATGCCCTTTGTCTATGTT 57.090 33.333 0.00 0.00 0.00 2.71
188 189 7.296628 TGTAAAATGCCCTTTGTCTATGTTT 57.703 32.000 0.00 0.00 0.00 2.83
189 190 8.410673 TGTAAAATGCCCTTTGTCTATGTTTA 57.589 30.769 0.00 0.00 0.00 2.01
190 191 8.301002 TGTAAAATGCCCTTTGTCTATGTTTAC 58.699 33.333 0.00 0.00 0.00 2.01
191 192 7.539034 AAAATGCCCTTTGTCTATGTTTACT 57.461 32.000 0.00 0.00 0.00 2.24
192 193 8.644374 AAAATGCCCTTTGTCTATGTTTACTA 57.356 30.769 0.00 0.00 0.00 1.82
193 194 8.644374 AAATGCCCTTTGTCTATGTTTACTAA 57.356 30.769 0.00 0.00 0.00 2.24
194 195 8.644374 AATGCCCTTTGTCTATGTTTACTAAA 57.356 30.769 0.00 0.00 0.00 1.85
195 196 8.644374 ATGCCCTTTGTCTATGTTTACTAAAA 57.356 30.769 0.00 0.00 0.00 1.52
196 197 8.644374 TGCCCTTTGTCTATGTTTACTAAAAT 57.356 30.769 0.00 0.00 0.00 1.82
197 198 9.742144 TGCCCTTTGTCTATGTTTACTAAAATA 57.258 29.630 0.00 0.00 0.00 1.40
238 239 4.485024 AGTAACTATACTGATGCGACGG 57.515 45.455 0.00 0.00 40.88 4.79
243 244 1.681538 ATACTGATGCGACGGAGACT 58.318 50.000 0.00 0.00 0.00 3.24
360 362 2.483876 CCACATGTAGATCGGCGATTT 58.516 47.619 24.81 20.84 0.00 2.17
408 410 0.752054 GAGGGAGAGATGCCTCACTG 59.248 60.000 10.55 0.00 46.25 3.66
438 450 1.340248 CCGGCGATAATAGACACAGGT 59.660 52.381 9.30 0.00 0.00 4.00
439 451 2.555325 CCGGCGATAATAGACACAGGTA 59.445 50.000 9.30 0.00 0.00 3.08
440 452 3.366070 CCGGCGATAATAGACACAGGTAG 60.366 52.174 9.30 0.00 0.00 3.18
551 969 2.541762 GCCTAGCATCTGATGTTCGTTC 59.458 50.000 18.19 1.52 0.00 3.95
574 992 3.118408 TGGTTCCTGTATACATGTGAGCC 60.118 47.826 9.11 18.26 0.00 4.70
577 995 1.768275 CCTGTATACATGTGAGCCCCA 59.232 52.381 9.11 0.00 0.00 4.96
586 1004 1.489481 TGTGAGCCCCACTAGAGATG 58.511 55.000 0.00 0.00 45.86 2.90
596 1015 4.103785 CCCCACTAGAGATGGATGAAATGT 59.896 45.833 0.00 0.00 39.87 2.71
610 1029 6.430925 TGGATGAAATGTAAGGAACAACTGAG 59.569 38.462 0.00 0.00 42.70 3.35
698 1123 3.712907 CACCTACCCACCCACCCG 61.713 72.222 0.00 0.00 0.00 5.28
747 1178 3.717294 CCTCCACCCCGGTTGAGG 61.717 72.222 17.17 17.17 46.74 3.86
748 1179 4.410400 CTCCACCCCGGTTGAGGC 62.410 72.222 0.00 0.00 35.17 4.70
793 1224 0.174389 CTAGTGCGAGACCATGTGCT 59.826 55.000 0.00 0.00 0.00 4.40
820 1251 4.317291 CGTGCGTTCAGTGCTTTTTATTAC 59.683 41.667 0.00 0.00 0.00 1.89
855 1286 4.090057 GCAACGCCTTCCTCGTGC 62.090 66.667 0.00 0.00 40.36 5.34
856 1287 3.423154 CAACGCCTTCCTCGTGCC 61.423 66.667 0.00 0.00 40.36 5.01
857 1288 3.936203 AACGCCTTCCTCGTGCCA 61.936 61.111 0.00 0.00 40.36 4.92
858 1289 3.254024 AACGCCTTCCTCGTGCCAT 62.254 57.895 0.00 0.00 40.36 4.40
859 1290 3.197790 CGCCTTCCTCGTGCCATG 61.198 66.667 0.00 0.00 0.00 3.66
1041 1497 2.395619 TCCGAAATCCCTCCCTTCTAC 58.604 52.381 0.00 0.00 0.00 2.59
1042 1498 2.023307 TCCGAAATCCCTCCCTTCTACT 60.023 50.000 0.00 0.00 0.00 2.57
1043 1499 2.103263 CCGAAATCCCTCCCTTCTACTG 59.897 54.545 0.00 0.00 0.00 2.74
1044 1500 2.766828 CGAAATCCCTCCCTTCTACTGT 59.233 50.000 0.00 0.00 0.00 3.55
1045 1501 3.958798 CGAAATCCCTCCCTTCTACTGTA 59.041 47.826 0.00 0.00 0.00 2.74
1046 1502 4.589374 CGAAATCCCTCCCTTCTACTGTAT 59.411 45.833 0.00 0.00 0.00 2.29
1047 1503 5.773680 CGAAATCCCTCCCTTCTACTGTATA 59.226 44.000 0.00 0.00 0.00 1.47
1054 1510 7.409397 TCCCTCCCTTCTACTGTATATATAGCT 59.591 40.741 6.42 0.00 0.00 3.32
1090 1546 1.005867 TTTCTCCCGTTCCGTTCCG 60.006 57.895 0.00 0.00 0.00 4.30
1091 1547 3.578515 TTCTCCCGTTCCGTTCCGC 62.579 63.158 0.00 0.00 0.00 5.54
1095 1551 3.770424 CCGTTCCGTTCCGCGTTC 61.770 66.667 4.92 0.00 39.32 3.95
1096 1552 3.770424 CGTTCCGTTCCGCGTTCC 61.770 66.667 4.92 0.00 39.32 3.62
1097 1553 2.356673 GTTCCGTTCCGCGTTCCT 60.357 61.111 4.92 0.00 39.32 3.36
1105 1561 3.072468 CCGCGTTCCTGACCCCTA 61.072 66.667 4.92 0.00 0.00 3.53
1130 1586 1.388065 CCACGGACAAAAACCCAGCA 61.388 55.000 0.00 0.00 0.00 4.41
1281 1747 2.125793 GCCACCCTCCGTACGAAC 60.126 66.667 18.76 0.00 0.00 3.95
1287 1753 2.693762 CCTCCGTACGAACCGCTCA 61.694 63.158 18.76 0.00 0.00 4.26
1290 1757 2.514013 CCGTACGAACCGCTCATGC 61.514 63.158 18.76 0.00 0.00 4.06
1303 1770 1.699634 GCTCATGCCCCTGGTTCTATA 59.300 52.381 0.00 0.00 0.00 1.31
1305 1772 2.705658 CTCATGCCCCTGGTTCTATACA 59.294 50.000 0.00 0.00 0.00 2.29
1307 1774 3.072915 TCATGCCCCTGGTTCTATACATG 59.927 47.826 0.00 0.00 35.99 3.21
1311 1778 2.039084 CCCCTGGTTCTATACATGCCTC 59.961 54.545 0.00 0.00 0.00 4.70
1313 1780 3.244353 CCCTGGTTCTATACATGCCTCTG 60.244 52.174 0.00 0.00 0.00 3.35
1314 1781 3.389329 CCTGGTTCTATACATGCCTCTGT 59.611 47.826 0.00 0.00 0.00 3.41
1316 1783 4.769688 TGGTTCTATACATGCCTCTGTTG 58.230 43.478 0.00 0.00 0.00 3.33
1317 1784 4.225042 TGGTTCTATACATGCCTCTGTTGT 59.775 41.667 0.00 0.00 0.00 3.32
1318 1785 5.186198 GGTTCTATACATGCCTCTGTTGTT 58.814 41.667 0.00 0.00 0.00 2.83
1319 1786 5.648092 GGTTCTATACATGCCTCTGTTGTTT 59.352 40.000 0.00 0.00 0.00 2.83
1320 1787 6.151144 GGTTCTATACATGCCTCTGTTGTTTT 59.849 38.462 0.00 0.00 0.00 2.43
1321 1788 6.985188 TCTATACATGCCTCTGTTGTTTTC 57.015 37.500 0.00 0.00 0.00 2.29
1322 1789 6.711277 TCTATACATGCCTCTGTTGTTTTCT 58.289 36.000 0.00 0.00 0.00 2.52
1323 1790 3.996150 ACATGCCTCTGTTGTTTTCTG 57.004 42.857 0.00 0.00 0.00 3.02
1324 1791 2.035066 ACATGCCTCTGTTGTTTTCTGC 59.965 45.455 0.00 0.00 0.00 4.26
1353 1824 2.064762 CCGAATCTCAGATCGATTGGC 58.935 52.381 0.00 0.00 41.43 4.52
1358 1829 2.910199 TCTCAGATCGATTGGCCTTTG 58.090 47.619 3.32 0.00 0.00 2.77
1572 2055 0.610232 GTTTCACATGCTCCTGGCCT 60.610 55.000 3.32 0.00 40.92 5.19
1576 2059 1.565759 TCACATGCTCCTGGCCTATTT 59.434 47.619 3.32 0.00 40.92 1.40
1626 2109 3.840437 GCCATATCTTTGCCGGCA 58.160 55.556 29.03 29.03 42.50 5.69
1631 2114 3.614092 CCATATCTTTGCCGGCATAGAT 58.386 45.455 43.44 43.44 43.53 1.98
1655 2138 0.960364 CACTTGGTGGGTTGATCCGG 60.960 60.000 0.00 0.00 37.00 5.14
1682 2165 7.860872 ACGTTTCAATGTTCATAGAGTTTTTCC 59.139 33.333 0.00 0.00 0.00 3.13
1694 2177 7.508977 TCATAGAGTTTTTCCTCCCATGTTTTT 59.491 33.333 0.00 0.00 31.32 1.94
1695 2178 6.161855 AGAGTTTTTCCTCCCATGTTTTTC 57.838 37.500 0.00 0.00 31.53 2.29
1797 2280 8.208718 AGTTTTTCCATTTAAAAAGGCAGAAC 57.791 30.769 5.42 6.59 38.60 3.01
1801 2284 6.478512 TCCATTTAAAAAGGCAGAACAAGT 57.521 33.333 5.42 0.00 0.00 3.16
1824 2307 3.450904 TCCACTGCCCTCAAGTATACTT 58.549 45.455 12.50 12.50 36.45 2.24
2458 3728 3.954904 GAGGTATAGTTCTCTGAGCACCA 59.045 47.826 3.80 0.00 0.00 4.17
3047 4329 4.060900 AGTTGACTGACACTGCTATTGTG 58.939 43.478 0.00 0.00 40.87 3.33
3116 4409 1.474478 CAGGAGTGCTTTCGAGCTCTA 59.526 52.381 12.85 0.00 38.54 2.43
3118 4411 2.763448 AGGAGTGCTTTCGAGCTCTATT 59.237 45.455 12.85 0.00 38.54 1.73
3119 4412 2.863137 GGAGTGCTTTCGAGCTCTATTG 59.137 50.000 12.85 0.83 38.54 1.90
3121 4414 4.440250 GGAGTGCTTTCGAGCTCTATTGTA 60.440 45.833 12.85 0.00 38.54 2.41
3122 4415 4.425520 AGTGCTTTCGAGCTCTATTGTAC 58.574 43.478 12.85 9.07 36.95 2.90
3449 4748 2.435805 GGCATGGACTGAAGATGGACTA 59.564 50.000 0.00 0.00 0.00 2.59
3536 4841 3.003480 GTCGCTTAGGCACAATTCTCTT 58.997 45.455 0.00 0.00 38.60 2.85
3539 4844 5.050490 TCGCTTAGGCACAATTCTCTTATC 58.950 41.667 0.00 0.00 38.60 1.75
3543 4848 3.462021 AGGCACAATTCTCTTATCGCTC 58.538 45.455 0.00 0.00 0.00 5.03
3544 4849 3.133721 AGGCACAATTCTCTTATCGCTCT 59.866 43.478 0.00 0.00 0.00 4.09
3545 4850 3.492756 GGCACAATTCTCTTATCGCTCTC 59.507 47.826 0.00 0.00 0.00 3.20
3546 4851 3.181377 GCACAATTCTCTTATCGCTCTCG 59.819 47.826 0.00 0.00 0.00 4.04
3547 4852 3.181377 CACAATTCTCTTATCGCTCTCGC 59.819 47.826 0.00 0.00 35.26 5.03
3562 4867 1.506718 TCGCGAGAGTGCTAACTGG 59.493 57.895 3.71 0.00 42.50 4.00
3567 4873 2.464865 CGAGAGTGCTAACTGGTATGC 58.535 52.381 0.00 0.00 36.52 3.14
3695 5007 1.110518 CCTCCGAGGGGAAGTAGAGC 61.111 65.000 6.53 0.00 43.27 4.09
3746 5062 8.815565 AAGTAGAGACTATTGTTGAGAGATCA 57.184 34.615 0.00 0.00 33.58 2.92
3747 5063 8.450578 AGTAGAGACTATTGTTGAGAGATCAG 57.549 38.462 0.00 0.00 32.65 2.90
3748 5064 8.271458 AGTAGAGACTATTGTTGAGAGATCAGA 58.729 37.037 0.00 0.00 32.65 3.27
3750 5066 8.169977 AGAGACTATTGTTGAGAGATCAGATC 57.830 38.462 1.64 1.64 0.00 2.75
3751 5067 7.779326 AGAGACTATTGTTGAGAGATCAGATCA 59.221 37.037 13.14 0.00 0.00 2.92
3752 5068 7.944061 AGACTATTGTTGAGAGATCAGATCAG 58.056 38.462 13.14 0.00 0.00 2.90
3753 5069 7.014518 AGACTATTGTTGAGAGATCAGATCAGG 59.985 40.741 13.14 0.00 0.00 3.86
3754 5070 3.815856 TGTTGAGAGATCAGATCAGGC 57.184 47.619 13.14 1.92 0.00 4.85
3780 5096 0.756815 GCAGGATGGGGCCTAAAAGG 60.757 60.000 0.84 0.00 36.22 3.11
3799 5115 3.683802 AGGCAAACAGATTCAGAGGAAG 58.316 45.455 0.00 0.00 36.25 3.46
3833 5151 2.489938 AGAGCTTTCCGTTGCCATTA 57.510 45.000 0.00 0.00 0.00 1.90
3888 5208 5.050490 CGAGATCCCGTATGAACTTCATTT 58.950 41.667 9.57 0.00 38.26 2.32
3952 5272 3.349022 TCGGTGGAAACTGAAGTTGTTT 58.651 40.909 0.00 0.00 39.92 2.83
3995 5315 1.614903 CCTTCTGGCACAATGCTTCAA 59.385 47.619 0.13 0.00 44.28 2.69
4011 5332 5.185454 TGCTTCAAACTTCAGAGTTCAGAA 58.815 37.500 0.00 1.00 45.18 3.02
4058 5379 3.444034 GGTTTATGCCTTTCCCAACTCTC 59.556 47.826 0.00 0.00 0.00 3.20
4066 5448 4.141937 GCCTTTCCCAACTCTCTTTTTGTT 60.142 41.667 0.00 0.00 0.00 2.83
4069 5451 6.535150 CCTTTCCCAACTCTCTTTTTGTTTTC 59.465 38.462 0.00 0.00 0.00 2.29
4070 5452 5.243426 TCCCAACTCTCTTTTTGTTTTCG 57.757 39.130 0.00 0.00 0.00 3.46
4071 5453 4.944930 TCCCAACTCTCTTTTTGTTTTCGA 59.055 37.500 0.00 0.00 0.00 3.71
4072 5454 5.065988 TCCCAACTCTCTTTTTGTTTTCGAG 59.934 40.000 0.00 0.00 0.00 4.04
4076 5458 7.540745 CCAACTCTCTTTTTGTTTTCGAGAAAA 59.459 33.333 6.89 6.89 37.90 2.29
4077 5459 8.578769 CAACTCTCTTTTTGTTTTCGAGAAAAG 58.421 33.333 10.85 2.57 40.53 2.27
4079 5461 6.033966 TCTCTTTTTGTTTTCGAGAAAAGCC 58.966 36.000 10.85 2.40 40.53 4.35
4082 5464 6.871492 TCTTTTTGTTTTCGAGAAAAGCCTTT 59.129 30.769 10.85 0.00 40.53 3.11
4093 5475 4.657013 AGAAAAGCCTTTCCAACTCCTAG 58.343 43.478 4.13 0.00 41.72 3.02
4098 5480 3.157881 GCCTTTCCAACTCCTAGCTTTT 58.842 45.455 0.00 0.00 0.00 2.27
4127 5509 5.721960 TGAGAAGTTCCAACTCCTAGCTAAT 59.278 40.000 0.00 0.00 38.57 1.73
4158 5540 0.107456 CTGACAGCTCGGCCCATTAT 59.893 55.000 0.00 0.00 0.00 1.28
4206 5588 1.673665 CAAGAGCCCAGACCACAGC 60.674 63.158 0.00 0.00 0.00 4.40
4354 5966 1.481056 CCGTTCCCTTCCACCTGTCT 61.481 60.000 0.00 0.00 0.00 3.41
4680 6292 0.757512 GGTAACTTCCGATCCCTCCC 59.242 60.000 0.00 0.00 0.00 4.30
4686 6298 2.913060 CCGATCCCTCCCGTCCTC 60.913 72.222 0.00 0.00 0.00 3.71
4687 6299 2.196229 CGATCCCTCCCGTCCTCT 59.804 66.667 0.00 0.00 0.00 3.69
4688 6300 2.196925 CGATCCCTCCCGTCCTCTG 61.197 68.421 0.00 0.00 0.00 3.35
4689 6301 2.444895 ATCCCTCCCGTCCTCTGC 60.445 66.667 0.00 0.00 0.00 4.26
4690 6302 2.937959 GATCCCTCCCGTCCTCTGCT 62.938 65.000 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.595109 CTGAGCGTGCAGTGACCAA 60.595 57.895 0.00 0.00 0.00 3.67
1 2 2.029518 CTGAGCGTGCAGTGACCA 59.970 61.111 0.00 0.00 0.00 4.02
2 3 2.029666 ACTGAGCGTGCAGTGACC 59.970 61.111 10.76 0.00 46.72 4.02
11 12 2.480419 GCTTGAAATGTACACTGAGCGT 59.520 45.455 0.00 0.00 0.00 5.07
12 13 2.738846 AGCTTGAAATGTACACTGAGCG 59.261 45.455 0.00 0.00 34.29 5.03
13 14 4.667668 CGAAGCTTGAAATGTACACTGAGC 60.668 45.833 2.10 4.13 0.00 4.26
14 15 4.686091 TCGAAGCTTGAAATGTACACTGAG 59.314 41.667 2.10 0.00 0.00 3.35
15 16 4.447724 GTCGAAGCTTGAAATGTACACTGA 59.552 41.667 2.10 0.00 0.00 3.41
16 17 4.664139 CGTCGAAGCTTGAAATGTACACTG 60.664 45.833 2.10 0.00 0.00 3.66
17 18 3.428870 CGTCGAAGCTTGAAATGTACACT 59.571 43.478 2.10 0.00 0.00 3.55
18 19 3.427528 TCGTCGAAGCTTGAAATGTACAC 59.572 43.478 2.10 0.00 0.00 2.90
19 20 3.644823 TCGTCGAAGCTTGAAATGTACA 58.355 40.909 2.10 0.00 0.00 2.90
20 21 3.482112 GCTCGTCGAAGCTTGAAATGTAC 60.482 47.826 2.10 0.00 39.27 2.90
21 22 2.666508 GCTCGTCGAAGCTTGAAATGTA 59.333 45.455 2.10 0.00 39.27 2.29
22 23 1.461127 GCTCGTCGAAGCTTGAAATGT 59.539 47.619 2.10 0.00 39.27 2.71
23 24 1.460743 TGCTCGTCGAAGCTTGAAATG 59.539 47.619 2.10 0.00 42.94 2.32
24 25 1.795768 TGCTCGTCGAAGCTTGAAAT 58.204 45.000 2.10 0.00 42.94 2.17
25 26 1.260561 GTTGCTCGTCGAAGCTTGAAA 59.739 47.619 2.10 0.00 42.94 2.69
26 27 0.859232 GTTGCTCGTCGAAGCTTGAA 59.141 50.000 2.10 0.00 42.94 2.69
27 28 1.275471 CGTTGCTCGTCGAAGCTTGA 61.275 55.000 2.10 0.00 42.94 3.02
28 29 1.128611 CGTTGCTCGTCGAAGCTTG 59.871 57.895 2.10 0.00 42.94 4.01
29 30 3.538841 CGTTGCTCGTCGAAGCTT 58.461 55.556 10.30 0.00 42.94 3.74
38 39 2.798283 TCCTTCACTTTTACGTTGCTCG 59.202 45.455 0.00 0.84 46.00 5.03
39 40 4.806342 TTCCTTCACTTTTACGTTGCTC 57.194 40.909 0.00 0.00 0.00 4.26
40 41 5.337554 GTTTTCCTTCACTTTTACGTTGCT 58.662 37.500 0.00 0.00 0.00 3.91
41 42 4.501559 GGTTTTCCTTCACTTTTACGTTGC 59.498 41.667 0.00 0.00 36.94 4.17
77 78 9.653067 CGTGTAAAATGTACAACTACATCAAAA 57.347 29.630 14.49 0.00 41.92 2.44
78 79 8.828644 ACGTGTAAAATGTACAACTACATCAAA 58.171 29.630 14.49 0.00 41.92 2.69
79 80 8.367943 ACGTGTAAAATGTACAACTACATCAA 57.632 30.769 14.49 0.00 41.92 2.57
80 81 7.949903 ACGTGTAAAATGTACAACTACATCA 57.050 32.000 14.49 2.00 41.92 3.07
81 82 8.277713 ACAACGTGTAAAATGTACAACTACATC 58.722 33.333 14.49 9.58 41.92 3.06
82 83 8.145316 ACAACGTGTAAAATGTACAACTACAT 57.855 30.769 14.49 2.34 44.22 2.29
83 84 7.492020 AGACAACGTGTAAAATGTACAACTACA 59.508 33.333 0.00 5.36 37.28 2.74
84 85 7.844482 AGACAACGTGTAAAATGTACAACTAC 58.156 34.615 0.00 2.66 0.00 2.73
85 86 8.422973 AAGACAACGTGTAAAATGTACAACTA 57.577 30.769 0.00 0.00 0.00 2.24
86 87 6.913873 AGACAACGTGTAAAATGTACAACT 57.086 33.333 0.00 0.00 0.00 3.16
87 88 7.372396 CAGAAGACAACGTGTAAAATGTACAAC 59.628 37.037 0.00 0.00 0.00 3.32
88 89 7.064847 ACAGAAGACAACGTGTAAAATGTACAA 59.935 33.333 0.00 0.00 0.00 2.41
89 90 6.535865 ACAGAAGACAACGTGTAAAATGTACA 59.464 34.615 0.00 0.00 0.00 2.90
90 91 6.940714 ACAGAAGACAACGTGTAAAATGTAC 58.059 36.000 0.00 0.00 0.00 2.90
91 92 7.064847 ACAACAGAAGACAACGTGTAAAATGTA 59.935 33.333 0.00 0.00 0.00 2.29
92 93 6.128117 ACAACAGAAGACAACGTGTAAAATGT 60.128 34.615 0.00 0.00 0.00 2.71
93 94 6.255215 ACAACAGAAGACAACGTGTAAAATG 58.745 36.000 0.00 0.00 0.00 2.32
94 95 6.431198 ACAACAGAAGACAACGTGTAAAAT 57.569 33.333 0.00 0.00 0.00 1.82
95 96 5.444877 CGACAACAGAAGACAACGTGTAAAA 60.445 40.000 0.00 0.00 0.00 1.52
96 97 4.031991 CGACAACAGAAGACAACGTGTAAA 59.968 41.667 0.00 0.00 0.00 2.01
97 98 3.548668 CGACAACAGAAGACAACGTGTAA 59.451 43.478 0.00 0.00 0.00 2.41
98 99 3.110358 CGACAACAGAAGACAACGTGTA 58.890 45.455 0.00 0.00 0.00 2.90
99 100 1.924524 CGACAACAGAAGACAACGTGT 59.075 47.619 0.00 0.00 0.00 4.49
100 101 1.924524 ACGACAACAGAAGACAACGTG 59.075 47.619 0.00 0.00 0.00 4.49
101 102 2.190981 GACGACAACAGAAGACAACGT 58.809 47.619 0.00 0.00 35.53 3.99
102 103 1.521423 GGACGACAACAGAAGACAACG 59.479 52.381 0.00 0.00 0.00 4.10
103 104 2.822764 AGGACGACAACAGAAGACAAC 58.177 47.619 0.00 0.00 0.00 3.32
104 105 3.194861 CAAGGACGACAACAGAAGACAA 58.805 45.455 0.00 0.00 0.00 3.18
105 106 2.483013 CCAAGGACGACAACAGAAGACA 60.483 50.000 0.00 0.00 0.00 3.41
106 107 2.135933 CCAAGGACGACAACAGAAGAC 58.864 52.381 0.00 0.00 0.00 3.01
107 108 1.760613 ACCAAGGACGACAACAGAAGA 59.239 47.619 0.00 0.00 0.00 2.87
108 109 2.240493 ACCAAGGACGACAACAGAAG 57.760 50.000 0.00 0.00 0.00 2.85
109 110 2.702592 AACCAAGGACGACAACAGAA 57.297 45.000 0.00 0.00 0.00 3.02
110 111 2.702592 AAACCAAGGACGACAACAGA 57.297 45.000 0.00 0.00 0.00 3.41
111 112 3.813166 ACATAAACCAAGGACGACAACAG 59.187 43.478 0.00 0.00 0.00 3.16
112 113 3.811083 ACATAAACCAAGGACGACAACA 58.189 40.909 0.00 0.00 0.00 3.33
113 114 4.533222 CAACATAAACCAAGGACGACAAC 58.467 43.478 0.00 0.00 0.00 3.32
114 115 3.003897 GCAACATAAACCAAGGACGACAA 59.996 43.478 0.00 0.00 0.00 3.18
115 116 2.550606 GCAACATAAACCAAGGACGACA 59.449 45.455 0.00 0.00 0.00 4.35
116 117 2.812011 AGCAACATAAACCAAGGACGAC 59.188 45.455 0.00 0.00 0.00 4.34
117 118 3.071479 GAGCAACATAAACCAAGGACGA 58.929 45.455 0.00 0.00 0.00 4.20
118 119 2.159707 CGAGCAACATAAACCAAGGACG 60.160 50.000 0.00 0.00 0.00 4.79
119 120 2.414161 GCGAGCAACATAAACCAAGGAC 60.414 50.000 0.00 0.00 0.00 3.85
120 121 1.810151 GCGAGCAACATAAACCAAGGA 59.190 47.619 0.00 0.00 0.00 3.36
121 122 1.812571 AGCGAGCAACATAAACCAAGG 59.187 47.619 0.00 0.00 0.00 3.61
122 123 2.483877 TCAGCGAGCAACATAAACCAAG 59.516 45.455 0.00 0.00 0.00 3.61
123 124 2.499197 TCAGCGAGCAACATAAACCAA 58.501 42.857 0.00 0.00 0.00 3.67
124 125 2.177394 TCAGCGAGCAACATAAACCA 57.823 45.000 0.00 0.00 0.00 3.67
125 126 3.764885 AATCAGCGAGCAACATAAACC 57.235 42.857 0.00 0.00 0.00 3.27
126 127 5.393962 AGAAAATCAGCGAGCAACATAAAC 58.606 37.500 0.00 0.00 0.00 2.01
127 128 5.627499 AGAAAATCAGCGAGCAACATAAA 57.373 34.783 0.00 0.00 0.00 1.40
128 129 5.181056 TCAAGAAAATCAGCGAGCAACATAA 59.819 36.000 0.00 0.00 0.00 1.90
129 130 4.694982 TCAAGAAAATCAGCGAGCAACATA 59.305 37.500 0.00 0.00 0.00 2.29
130 131 3.503363 TCAAGAAAATCAGCGAGCAACAT 59.497 39.130 0.00 0.00 0.00 2.71
131 132 2.877786 TCAAGAAAATCAGCGAGCAACA 59.122 40.909 0.00 0.00 0.00 3.33
132 133 3.542712 TCAAGAAAATCAGCGAGCAAC 57.457 42.857 0.00 0.00 0.00 4.17
133 134 5.878332 TTATCAAGAAAATCAGCGAGCAA 57.122 34.783 0.00 0.00 0.00 3.91
134 135 5.631026 GTTTATCAAGAAAATCAGCGAGCA 58.369 37.500 0.00 0.00 0.00 4.26
135 136 4.725754 CGTTTATCAAGAAAATCAGCGAGC 59.274 41.667 0.00 0.00 0.00 5.03
136 137 5.858475 ACGTTTATCAAGAAAATCAGCGAG 58.142 37.500 0.00 0.00 0.00 5.03
137 138 5.856126 ACGTTTATCAAGAAAATCAGCGA 57.144 34.783 0.00 0.00 0.00 4.93
138 139 7.453034 TCTAACGTTTATCAAGAAAATCAGCG 58.547 34.615 5.91 0.00 0.00 5.18
139 140 9.214953 CATCTAACGTTTATCAAGAAAATCAGC 57.785 33.333 5.91 0.00 0.00 4.26
147 148 9.982291 GCATTTTACATCTAACGTTTATCAAGA 57.018 29.630 5.91 2.66 0.00 3.02
148 149 9.221775 GGCATTTTACATCTAACGTTTATCAAG 57.778 33.333 5.91 0.00 0.00 3.02
149 150 8.185505 GGGCATTTTACATCTAACGTTTATCAA 58.814 33.333 5.91 0.00 0.00 2.57
150 151 7.554835 AGGGCATTTTACATCTAACGTTTATCA 59.445 33.333 5.91 0.00 0.00 2.15
151 152 7.927048 AGGGCATTTTACATCTAACGTTTATC 58.073 34.615 5.91 0.00 0.00 1.75
152 153 7.875327 AGGGCATTTTACATCTAACGTTTAT 57.125 32.000 5.91 0.00 0.00 1.40
153 154 7.690952 AAGGGCATTTTACATCTAACGTTTA 57.309 32.000 5.91 0.00 0.00 2.01
154 155 6.584185 AAGGGCATTTTACATCTAACGTTT 57.416 33.333 5.91 0.00 0.00 3.60
155 156 6.015772 ACAAAGGGCATTTTACATCTAACGTT 60.016 34.615 5.88 5.88 0.00 3.99
156 157 5.475564 ACAAAGGGCATTTTACATCTAACGT 59.524 36.000 0.00 0.00 0.00 3.99
157 158 5.949735 ACAAAGGGCATTTTACATCTAACG 58.050 37.500 0.00 0.00 0.00 3.18
158 159 7.158099 AGACAAAGGGCATTTTACATCTAAC 57.842 36.000 0.00 0.00 0.00 2.34
159 160 8.902806 CATAGACAAAGGGCATTTTACATCTAA 58.097 33.333 0.00 0.00 0.00 2.10
160 161 8.052748 ACATAGACAAAGGGCATTTTACATCTA 58.947 33.333 0.00 1.29 0.00 1.98
161 162 6.891908 ACATAGACAAAGGGCATTTTACATCT 59.108 34.615 0.00 0.00 0.00 2.90
162 163 7.100458 ACATAGACAAAGGGCATTTTACATC 57.900 36.000 0.00 0.00 0.00 3.06
163 164 7.480760 AACATAGACAAAGGGCATTTTACAT 57.519 32.000 0.00 0.00 0.00 2.29
164 165 6.909550 AACATAGACAAAGGGCATTTTACA 57.090 33.333 0.00 0.00 0.00 2.41
165 166 8.520351 AGTAAACATAGACAAAGGGCATTTTAC 58.480 33.333 0.00 0.00 0.00 2.01
166 167 8.644374 AGTAAACATAGACAAAGGGCATTTTA 57.356 30.769 0.00 0.00 0.00 1.52
167 168 7.539034 AGTAAACATAGACAAAGGGCATTTT 57.461 32.000 0.00 0.00 0.00 1.82
168 169 8.644374 TTAGTAAACATAGACAAAGGGCATTT 57.356 30.769 0.00 0.00 0.00 2.32
169 170 8.644374 TTTAGTAAACATAGACAAAGGGCATT 57.356 30.769 0.00 0.00 0.00 3.56
170 171 8.644374 TTTTAGTAAACATAGACAAAGGGCAT 57.356 30.769 0.00 0.00 0.00 4.40
171 172 8.644374 ATTTTAGTAAACATAGACAAAGGGCA 57.356 30.769 0.00 0.00 0.00 5.36
207 208 7.230108 GCATCAGTATAGTTACTGGTACTACCA 59.770 40.741 7.73 7.73 45.95 3.25
208 209 7.572724 CGCATCAGTATAGTTACTGGTACTACC 60.573 44.444 11.96 0.00 45.95 3.18
209 210 7.172190 TCGCATCAGTATAGTTACTGGTACTAC 59.828 40.741 11.96 0.00 45.95 2.73
210 211 7.172190 GTCGCATCAGTATAGTTACTGGTACTA 59.828 40.741 11.96 0.00 45.95 1.82
211 212 6.017275 GTCGCATCAGTATAGTTACTGGTACT 60.017 42.308 11.96 0.96 45.95 2.73
212 213 6.141462 GTCGCATCAGTATAGTTACTGGTAC 58.859 44.000 11.96 0.00 45.95 3.34
213 214 5.049886 CGTCGCATCAGTATAGTTACTGGTA 60.050 44.000 11.96 0.00 45.95 3.25
223 224 2.847441 AGTCTCCGTCGCATCAGTATA 58.153 47.619 0.00 0.00 0.00 1.47
269 270 1.889829 CTAGCGGGGAATCTCTCGAAT 59.110 52.381 0.00 0.00 0.00 3.34
345 347 4.380841 AACAGTAAATCGCCGATCTACA 57.619 40.909 12.66 0.00 0.00 2.74
360 362 9.569167 CTACTGATTGTCTCGAAATAAACAGTA 57.431 33.333 14.55 14.55 37.36 2.74
551 969 4.122776 GCTCACATGTATACAGGAACCAG 58.877 47.826 23.38 13.03 0.00 4.00
574 992 5.301835 ACATTTCATCCATCTCTAGTGGG 57.698 43.478 0.00 0.00 37.34 4.61
577 995 7.921041 TCCTTACATTTCATCCATCTCTAGT 57.079 36.000 0.00 0.00 0.00 2.57
586 1004 6.127897 CCTCAGTTGTTCCTTACATTTCATCC 60.128 42.308 0.00 0.00 36.44 3.51
596 1015 2.708861 TCTTGGCCTCAGTTGTTCCTTA 59.291 45.455 3.32 0.00 0.00 2.69
793 1224 3.935872 GCACTGAACGCACGCACA 61.936 61.111 0.00 0.00 0.00 4.57
820 1251 1.569493 CTTCTGCCGTTTCCGTGTG 59.431 57.895 0.00 0.00 0.00 3.82
1021 1475 2.023307 AGTAGAAGGGAGGGATTTCGGA 60.023 50.000 0.00 0.00 0.00 4.55
1041 1497 3.241553 CGCGCTTGCAGCTATATATACAG 59.758 47.826 5.56 0.00 39.60 2.74
1042 1498 3.179048 CGCGCTTGCAGCTATATATACA 58.821 45.455 5.56 0.00 39.60 2.29
1043 1499 2.034507 GCGCGCTTGCAGCTATATATAC 60.035 50.000 26.67 0.00 39.60 1.47
1044 1500 2.193447 GCGCGCTTGCAGCTATATATA 58.807 47.619 26.67 0.00 39.60 0.86
1045 1501 1.002366 GCGCGCTTGCAGCTATATAT 58.998 50.000 26.67 0.00 39.60 0.86
1046 1502 0.319469 TGCGCGCTTGCAGCTATATA 60.319 50.000 33.29 3.26 40.62 0.86
1047 1503 1.595109 TGCGCGCTTGCAGCTATAT 60.595 52.632 33.29 0.00 40.62 0.86
1090 1546 2.582978 GGTAGGGGTCAGGAACGC 59.417 66.667 0.00 0.00 40.01 4.84
1091 1547 2.364780 GGGGTAGGGGTCAGGAACG 61.365 68.421 0.00 0.00 0.00 3.95
1092 1548 2.364780 CGGGGTAGGGGTCAGGAAC 61.365 68.421 0.00 0.00 0.00 3.62
1093 1549 2.039951 CGGGGTAGGGGTCAGGAA 59.960 66.667 0.00 0.00 0.00 3.36
1094 1550 4.791069 GCGGGGTAGGGGTCAGGA 62.791 72.222 0.00 0.00 0.00 3.86
1204 1670 4.445545 GCGCAACGTAGTGCAGGC 62.446 66.667 12.40 4.92 45.00 4.85
1263 1729 3.384532 TTCGTACGGAGGGTGGCC 61.385 66.667 16.52 0.00 0.00 5.36
1281 1747 4.431131 AACCAGGGGCATGAGCGG 62.431 66.667 0.00 0.00 43.41 5.52
1287 1753 2.224867 GCATGTATAGAACCAGGGGCAT 60.225 50.000 0.00 0.00 0.00 4.40
1290 1757 2.039084 GAGGCATGTATAGAACCAGGGG 59.961 54.545 0.00 0.00 0.00 4.79
1303 1770 2.035066 GCAGAAAACAACAGAGGCATGT 59.965 45.455 0.00 0.00 33.96 3.21
1305 1772 1.615392 GGCAGAAAACAACAGAGGCAT 59.385 47.619 0.00 0.00 0.00 4.40
1307 1774 0.040067 CGGCAGAAAACAACAGAGGC 60.040 55.000 0.00 0.00 0.00 4.70
1311 1778 2.095567 CAGATCCGGCAGAAAACAACAG 60.096 50.000 0.00 0.00 0.00 3.16
1313 1780 1.401539 GCAGATCCGGCAGAAAACAAC 60.402 52.381 0.00 0.00 0.00 3.32
1314 1781 0.881118 GCAGATCCGGCAGAAAACAA 59.119 50.000 0.00 0.00 0.00 2.83
1316 1783 1.803289 GGCAGATCCGGCAGAAAAC 59.197 57.895 0.00 0.00 0.00 2.43
1317 1784 4.319133 GGCAGATCCGGCAGAAAA 57.681 55.556 0.00 0.00 0.00 2.29
1341 1808 3.932459 GCAAAGGCCAATCGATCTG 57.068 52.632 5.01 0.00 0.00 2.90
1358 1829 2.086251 CTCTCAGGATCTGCGAGGGC 62.086 65.000 6.94 0.00 39.00 5.19
1549 2028 1.475280 CCAGGAGCATGTGAAACCATG 59.525 52.381 0.00 0.00 44.07 3.66
1563 2046 1.959282 GGAATGCAAATAGGCCAGGAG 59.041 52.381 5.01 0.00 0.00 3.69
1572 2055 1.405105 GAAGCAGCCGGAATGCAAATA 59.595 47.619 27.53 0.00 46.31 1.40
1576 2059 2.042259 CAGAAGCAGCCGGAATGCA 61.042 57.895 27.53 0.00 46.31 3.96
1626 2109 3.454858 ACCCACCAAGTGACTCATCTAT 58.545 45.455 0.00 0.00 35.23 1.98
1631 2114 1.208706 TCAACCCACCAAGTGACTCA 58.791 50.000 0.00 0.00 35.23 3.41
1655 2138 8.782533 AAAAACTCTATGAACATTGAAACGTC 57.217 30.769 0.00 0.00 0.00 4.34
1710 2193 0.106149 ACTTCCGCTCGAACCAGTTT 59.894 50.000 0.00 0.00 0.00 2.66
1712 2195 1.289380 GACTTCCGCTCGAACCAGT 59.711 57.895 0.00 0.00 0.00 4.00
1792 2275 1.338020 GGGCAGTGGAAACTTGTTCTG 59.662 52.381 0.00 0.00 0.00 3.02
1797 2280 1.610522 CTTGAGGGCAGTGGAAACTTG 59.389 52.381 0.00 0.00 0.00 3.16
1801 2284 3.844211 AGTATACTTGAGGGCAGTGGAAA 59.156 43.478 0.00 0.00 0.00 3.13
1824 2307 5.446143 AAACAACATTCCATGCTACGAAA 57.554 34.783 0.00 0.00 0.00 3.46
2598 3869 5.106078 ACTGTTCTGAGATTCGGTAAGAGAC 60.106 44.000 0.00 0.00 0.00 3.36
3047 4329 3.968649 ACATGTGTGCAGTTCAATGTTC 58.031 40.909 0.00 0.00 0.00 3.18
3116 4409 5.867716 CGTGCTCTAAACAGGTAAGTACAAT 59.132 40.000 0.00 0.00 0.00 2.71
3118 4411 4.801891 CGTGCTCTAAACAGGTAAGTACA 58.198 43.478 0.00 0.00 0.00 2.90
3119 4412 3.611549 GCGTGCTCTAAACAGGTAAGTAC 59.388 47.826 0.00 0.00 0.00 2.73
3121 4414 2.036733 TGCGTGCTCTAAACAGGTAAGT 59.963 45.455 0.00 0.00 0.00 2.24
3122 4415 2.412089 GTGCGTGCTCTAAACAGGTAAG 59.588 50.000 0.00 0.00 0.00 2.34
3543 4848 0.524392 CCAGTTAGCACTCTCGCGAG 60.524 60.000 30.03 30.03 43.10 5.03
3544 4849 1.241990 ACCAGTTAGCACTCTCGCGA 61.242 55.000 9.26 9.26 36.85 5.87
3545 4850 0.450583 TACCAGTTAGCACTCTCGCG 59.549 55.000 0.00 0.00 36.85 5.87
3546 4851 2.464865 CATACCAGTTAGCACTCTCGC 58.535 52.381 0.00 0.00 0.00 5.03
3547 4852 2.099921 AGCATACCAGTTAGCACTCTCG 59.900 50.000 0.00 0.00 0.00 4.04
3548 4853 3.118956 ACAGCATACCAGTTAGCACTCTC 60.119 47.826 0.00 0.00 0.00 3.20
3549 4854 2.834549 ACAGCATACCAGTTAGCACTCT 59.165 45.455 0.00 0.00 0.00 3.24
3550 4855 3.252974 ACAGCATACCAGTTAGCACTC 57.747 47.619 0.00 0.00 0.00 3.51
3551 4856 4.223032 AGTTACAGCATACCAGTTAGCACT 59.777 41.667 0.00 0.00 0.00 4.40
3552 4857 4.504858 AGTTACAGCATACCAGTTAGCAC 58.495 43.478 0.00 0.00 0.00 4.40
3553 4858 4.466370 AGAGTTACAGCATACCAGTTAGCA 59.534 41.667 0.00 0.00 0.00 3.49
3554 4859 5.012328 AGAGTTACAGCATACCAGTTAGC 57.988 43.478 0.00 0.00 0.00 3.09
3557 4862 4.286032 TGGAAGAGTTACAGCATACCAGTT 59.714 41.667 0.00 0.00 0.00 3.16
3562 4867 3.432326 CCCCTGGAAGAGTTACAGCATAC 60.432 52.174 0.00 0.00 34.07 2.39
3567 4873 1.555533 GACCCCCTGGAAGAGTTACAG 59.444 57.143 0.00 0.00 34.07 2.74
3695 5007 2.110901 ACTGCTCTGCTTCCTGAATG 57.889 50.000 0.00 0.00 0.00 2.67
3746 5062 3.013327 TGCCTGCCTGCCTGATCT 61.013 61.111 0.00 0.00 0.00 2.75
3747 5063 2.516460 CTGCCTGCCTGCCTGATC 60.516 66.667 0.00 0.00 0.00 2.92
3748 5064 4.124943 CCTGCCTGCCTGCCTGAT 62.125 66.667 0.00 0.00 0.00 2.90
3750 5066 4.124943 ATCCTGCCTGCCTGCCTG 62.125 66.667 0.00 0.00 0.00 4.85
3751 5067 4.124943 CATCCTGCCTGCCTGCCT 62.125 66.667 0.00 0.00 0.00 4.75
3754 5070 4.517934 CCCCATCCTGCCTGCCTG 62.518 72.222 0.00 0.00 0.00 4.85
3780 5096 2.751806 CCCTTCCTCTGAATCTGTTTGC 59.248 50.000 0.00 0.00 0.00 3.68
3799 5115 5.105310 GGAAAGCTCTTTTTCCCTTATTCCC 60.105 44.000 3.83 0.00 46.78 3.97
3888 5208 1.729517 CACGACGCACATAATTGACCA 59.270 47.619 0.00 0.00 0.00 4.02
3976 5296 3.054878 GTTTGAAGCATTGTGCCAGAAG 58.945 45.455 0.00 0.00 46.52 2.85
3987 5307 5.371526 TCTGAACTCTGAAGTTTGAAGCAT 58.628 37.500 0.00 0.00 45.80 3.79
4011 5332 5.122396 GGAACAGAGAACAAATAGCGAACAT 59.878 40.000 0.00 0.00 0.00 2.71
4058 5379 6.647212 AAGGCTTTTCTCGAAAACAAAAAG 57.353 33.333 0.00 0.00 40.18 2.27
4066 5448 3.951680 AGTTGGAAAGGCTTTTCTCGAAA 59.048 39.130 18.72 2.47 41.92 3.46
4069 5451 2.226674 GGAGTTGGAAAGGCTTTTCTCG 59.773 50.000 18.72 0.00 41.92 4.04
4070 5452 3.491342 AGGAGTTGGAAAGGCTTTTCTC 58.509 45.455 18.72 18.36 41.92 2.87
4071 5453 3.602205 AGGAGTTGGAAAGGCTTTTCT 57.398 42.857 18.72 12.27 41.92 2.52
4072 5454 3.191581 GCTAGGAGTTGGAAAGGCTTTTC 59.808 47.826 14.66 13.03 41.59 2.29
4076 5458 1.662686 AGCTAGGAGTTGGAAAGGCT 58.337 50.000 0.00 0.00 0.00 4.58
4077 5459 2.498644 AAGCTAGGAGTTGGAAAGGC 57.501 50.000 0.00 0.00 0.00 4.35
4100 5482 5.063880 GCTAGGAGTTGGAACTTCTCAAAA 58.936 41.667 3.46 0.00 40.97 2.44
4101 5483 4.348168 AGCTAGGAGTTGGAACTTCTCAAA 59.652 41.667 3.46 0.00 40.97 2.69
4102 5484 3.904339 AGCTAGGAGTTGGAACTTCTCAA 59.096 43.478 3.46 0.00 40.97 3.02
4103 5485 3.511477 AGCTAGGAGTTGGAACTTCTCA 58.489 45.455 3.46 0.00 40.97 3.27
4105 5487 6.898521 ACTATTAGCTAGGAGTTGGAACTTCT 59.101 38.462 5.65 5.65 46.48 2.85
4106 5488 6.981559 CACTATTAGCTAGGAGTTGGAACTTC 59.018 42.308 6.84 0.00 39.88 3.01
4107 5489 6.127026 CCACTATTAGCTAGGAGTTGGAACTT 60.127 42.308 6.84 0.00 39.88 2.66
4108 5490 5.364157 CCACTATTAGCTAGGAGTTGGAACT 59.636 44.000 6.84 0.00 43.16 3.01
4109 5491 5.363005 TCCACTATTAGCTAGGAGTTGGAAC 59.637 44.000 16.85 0.00 30.09 3.62
4110 5492 5.363005 GTCCACTATTAGCTAGGAGTTGGAA 59.637 44.000 18.82 9.26 33.18 3.53
4111 5493 4.894114 GTCCACTATTAGCTAGGAGTTGGA 59.106 45.833 16.03 16.03 30.37 3.53
4112 5494 4.039366 GGTCCACTATTAGCTAGGAGTTGG 59.961 50.000 6.84 10.88 0.00 3.77
4113 5495 4.261656 CGGTCCACTATTAGCTAGGAGTTG 60.262 50.000 6.84 4.87 0.00 3.16
4114 5496 3.890147 CGGTCCACTATTAGCTAGGAGTT 59.110 47.826 6.84 0.00 0.00 3.01
4115 5497 3.137913 TCGGTCCACTATTAGCTAGGAGT 59.862 47.826 0.00 1.85 0.00 3.85
4116 5498 3.502979 GTCGGTCCACTATTAGCTAGGAG 59.497 52.174 0.00 1.25 0.00 3.69
4117 5499 3.484407 GTCGGTCCACTATTAGCTAGGA 58.516 50.000 0.00 0.00 0.00 2.94
4127 5509 1.248785 GCTGTCAGGTCGGTCCACTA 61.249 60.000 1.14 0.00 39.02 2.74
4158 5540 1.094785 GCCTTCGCTCATTGGCTTAA 58.905 50.000 0.00 0.00 41.92 1.85
4354 5966 2.568612 CGACAAGCGAGAGAGGCA 59.431 61.111 0.00 0.00 44.57 4.75
4596 6208 4.194720 GCGGTGAGGACGAGCGAT 62.195 66.667 0.00 0.00 36.43 4.58


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

AutoCloner maintained by Alex Coulton.