Multiple sequence alignment - TraesCS3A01G153300

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 TraesCS3A01G153300 chr3A 100.000 4191 0 0 1 4191 144148661 144152851 0.000000e+00 7740
1 TraesCS3A01G153300 chr3B 91.967 3946 180 64 276 4184 187800122 187803967 0.000000e+00 5404
2 TraesCS3A01G153300 chr3D 91.593 2724 101 46 727 3368 131349058 131351735 0.000000e+00 3644
3 TraesCS3A01G153300 chr3D 89.562 776 46 16 3412 4184 131351738 131352481 0.000000e+00 952
4 TraesCS3A01G153300 chr3D 90.039 512 26 14 249 742 131347961 131348465 1.270000e-179 640
5 TraesCS3A01G153300 chr7A 91.026 78 7 0 129 206 418112416 418112493 5.730000e-19 106


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 TraesCS3A01G153300 chr3A 144148661 144152851 4190 False 7740.000000 7740 100.000 1 4191 1 chr3A.!!$F1 4190
1 TraesCS3A01G153300 chr3B 187800122 187803967 3845 False 5404.000000 5404 91.967 276 4184 1 chr3B.!!$F1 3908
2 TraesCS3A01G153300 chr3D 131347961 131352481 4520 False 1745.333333 3644 90.398 249 4184 3 chr3D.!!$F1 3935

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
134 135 0.093026 CCGAAACTAAAGTGCTCGCG 59.907 55.000 0.00 0.0 34.67 5.87 F
135 136 0.093026 CGAAACTAAAGTGCTCGCGG 59.907 55.000 6.13 0.0 30.87 6.46 F
1206 1870 0.104409 AGGGCGGGGGAAAGATAGAT 60.104 55.000 0.00 0.0 0.00 1.98 F
1278 1943 2.912624 GCCCATATTGCGCCTGCTC 61.913 63.158 4.18 0.0 43.34 4.26 F
2345 3053 1.493950 GATGGAGCAGTTCGGCATCG 61.494 60.000 0.00 0.0 35.83 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1187 1851 0.104409 ATCTATCTTTCCCCCGCCCT 60.104 55.000 0.0 0.0 0.00 5.19 R
1302 1967 0.401738 TCCTGGAGCACCCAAAGAAG 59.598 55.000 0.0 0.0 46.07 2.85 R
2087 2767 0.959553 AGTATCCGCCGACGATGATT 59.040 50.000 0.0 0.0 43.93 2.57 R
2410 3118 1.279840 GTCGAACACCTTGCTGCAC 59.720 57.895 0.0 0.0 0.00 4.57 R
3910 4645 0.039256 GCACGCCAAAAAGCATCAGA 60.039 50.000 0.0 0.0 0.00 3.27 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.767255 CCCTCGCTCCGCTGCTTT 62.767 66.667 0.00 0.00 0.00 3.51
26 27 2.184322 CCTCGCTCCGCTGCTTTA 59.816 61.111 0.00 0.00 0.00 1.85
27 28 1.447838 CCTCGCTCCGCTGCTTTAA 60.448 57.895 0.00 0.00 0.00 1.52
28 29 1.696832 CCTCGCTCCGCTGCTTTAAC 61.697 60.000 0.00 0.00 0.00 2.01
29 30 0.737715 CTCGCTCCGCTGCTTTAACT 60.738 55.000 0.00 0.00 0.00 2.24
30 31 0.736325 TCGCTCCGCTGCTTTAACTC 60.736 55.000 0.00 0.00 0.00 3.01
31 32 0.737715 CGCTCCGCTGCTTTAACTCT 60.738 55.000 0.00 0.00 0.00 3.24
32 33 1.003108 GCTCCGCTGCTTTAACTCTC 58.997 55.000 0.00 0.00 0.00 3.20
33 34 1.404851 GCTCCGCTGCTTTAACTCTCT 60.405 52.381 0.00 0.00 0.00 3.10
34 35 2.535331 CTCCGCTGCTTTAACTCTCTC 58.465 52.381 0.00 0.00 0.00 3.20
35 36 1.204941 TCCGCTGCTTTAACTCTCTCC 59.795 52.381 0.00 0.00 0.00 3.71
36 37 1.066858 CCGCTGCTTTAACTCTCTCCA 60.067 52.381 0.00 0.00 0.00 3.86
37 38 2.612972 CCGCTGCTTTAACTCTCTCCAA 60.613 50.000 0.00 0.00 0.00 3.53
38 39 2.670414 CGCTGCTTTAACTCTCTCCAAG 59.330 50.000 0.00 0.00 0.00 3.61
39 40 3.615110 CGCTGCTTTAACTCTCTCCAAGA 60.615 47.826 0.00 0.00 0.00 3.02
40 41 4.319177 GCTGCTTTAACTCTCTCCAAGAA 58.681 43.478 0.00 0.00 32.23 2.52
41 42 4.757149 GCTGCTTTAACTCTCTCCAAGAAA 59.243 41.667 0.00 0.00 32.23 2.52
42 43 5.414144 GCTGCTTTAACTCTCTCCAAGAAAT 59.586 40.000 0.00 0.00 32.23 2.17
43 44 6.622462 GCTGCTTTAACTCTCTCCAAGAAATG 60.622 42.308 0.00 0.00 32.23 2.32
44 45 6.533730 TGCTTTAACTCTCTCCAAGAAATGA 58.466 36.000 0.00 0.00 32.23 2.57
45 46 6.652481 TGCTTTAACTCTCTCCAAGAAATGAG 59.348 38.462 0.00 0.00 32.23 2.90
46 47 6.876257 GCTTTAACTCTCTCCAAGAAATGAGA 59.124 38.462 0.00 0.00 32.23 3.27
47 48 7.389053 GCTTTAACTCTCTCCAAGAAATGAGAA 59.611 37.037 0.00 0.00 35.50 2.87
48 49 9.277783 CTTTAACTCTCTCCAAGAAATGAGAAA 57.722 33.333 0.00 0.00 35.50 2.52
49 50 8.839310 TTAACTCTCTCCAAGAAATGAGAAAG 57.161 34.615 0.00 0.00 35.50 2.62
50 51 5.803552 ACTCTCTCCAAGAAATGAGAAAGG 58.196 41.667 0.00 0.00 35.50 3.11
51 52 5.545723 ACTCTCTCCAAGAAATGAGAAAGGA 59.454 40.000 0.00 0.00 35.50 3.36
52 53 6.215227 ACTCTCTCCAAGAAATGAGAAAGGAT 59.785 38.462 0.00 0.00 35.50 3.24
53 54 7.401493 ACTCTCTCCAAGAAATGAGAAAGGATA 59.599 37.037 0.00 0.00 35.50 2.59
54 55 7.790027 TCTCTCCAAGAAATGAGAAAGGATAG 58.210 38.462 0.00 0.00 33.30 2.08
55 56 7.621285 TCTCTCCAAGAAATGAGAAAGGATAGA 59.379 37.037 0.00 0.00 33.30 1.98
56 57 8.150827 TCTCCAAGAAATGAGAAAGGATAGAA 57.849 34.615 0.00 0.00 0.00 2.10
57 58 8.605947 TCTCCAAGAAATGAGAAAGGATAGAAA 58.394 33.333 0.00 0.00 0.00 2.52
58 59 9.406113 CTCCAAGAAATGAGAAAGGATAGAAAT 57.594 33.333 0.00 0.00 0.00 2.17
59 60 9.182214 TCCAAGAAATGAGAAAGGATAGAAATG 57.818 33.333 0.00 0.00 0.00 2.32
60 61 9.182214 CCAAGAAATGAGAAAGGATAGAAATGA 57.818 33.333 0.00 0.00 0.00 2.57
83 84 8.499403 TGAAAATAAACAAAAAGGACAAAGGG 57.501 30.769 0.00 0.00 0.00 3.95
84 85 8.322091 TGAAAATAAACAAAAAGGACAAAGGGA 58.678 29.630 0.00 0.00 0.00 4.20
85 86 8.731275 AAAATAAACAAAAAGGACAAAGGGAG 57.269 30.769 0.00 0.00 0.00 4.30
86 87 4.753516 AAACAAAAAGGACAAAGGGAGG 57.246 40.909 0.00 0.00 0.00 4.30
87 88 2.677914 ACAAAAAGGACAAAGGGAGGG 58.322 47.619 0.00 0.00 0.00 4.30
88 89 1.344438 CAAAAAGGACAAAGGGAGGGC 59.656 52.381 0.00 0.00 0.00 5.19
89 90 0.560688 AAAAGGACAAAGGGAGGGCA 59.439 50.000 0.00 0.00 0.00 5.36
90 91 0.113190 AAAGGACAAAGGGAGGGCAG 59.887 55.000 0.00 0.00 0.00 4.85
91 92 1.793820 AAGGACAAAGGGAGGGCAGG 61.794 60.000 0.00 0.00 0.00 4.85
92 93 2.356667 GACAAAGGGAGGGCAGGG 59.643 66.667 0.00 0.00 0.00 4.45
93 94 3.268032 ACAAAGGGAGGGCAGGGG 61.268 66.667 0.00 0.00 0.00 4.79
94 95 2.941025 CAAAGGGAGGGCAGGGGA 60.941 66.667 0.00 0.00 0.00 4.81
95 96 2.941583 AAAGGGAGGGCAGGGGAC 60.942 66.667 0.00 0.00 0.00 4.46
103 104 3.384532 GGCAGGGGACGGACGTTA 61.385 66.667 0.00 0.00 0.00 3.18
104 105 2.658422 GCAGGGGACGGACGTTAA 59.342 61.111 0.00 0.00 0.00 2.01
105 106 1.739196 GCAGGGGACGGACGTTAAC 60.739 63.158 0.00 0.00 0.00 2.01
106 107 1.444895 CAGGGGACGGACGTTAACG 60.445 63.158 25.68 25.68 46.33 3.18
107 108 2.125952 GGGGACGGACGTTAACGG 60.126 66.667 29.81 15.85 44.95 4.44
108 109 2.125952 GGGACGGACGTTAACGGG 60.126 66.667 29.81 20.42 44.95 5.28
109 110 2.810887 GGACGGACGTTAACGGGC 60.811 66.667 29.81 20.82 44.95 6.13
110 111 2.259511 GACGGACGTTAACGGGCT 59.740 61.111 29.81 11.09 44.95 5.19
111 112 2.048877 ACGGACGTTAACGGGCTG 60.049 61.111 29.81 25.60 44.95 4.85
112 113 2.812178 CGGACGTTAACGGGCTGG 60.812 66.667 29.81 14.15 44.95 4.85
113 114 3.122971 GGACGTTAACGGGCTGGC 61.123 66.667 29.81 12.41 44.95 4.85
114 115 3.122971 GACGTTAACGGGCTGGCC 61.123 66.667 29.81 10.75 44.95 5.36
124 125 2.353573 GGCTGGCCCCGAAACTAA 59.646 61.111 0.00 0.00 0.00 2.24
125 126 1.303806 GGCTGGCCCCGAAACTAAA 60.304 57.895 0.00 0.00 0.00 1.85
126 127 1.313091 GGCTGGCCCCGAAACTAAAG 61.313 60.000 0.00 0.00 0.00 1.85
127 128 0.608308 GCTGGCCCCGAAACTAAAGT 60.608 55.000 0.00 0.00 0.00 2.66
128 129 1.165270 CTGGCCCCGAAACTAAAGTG 58.835 55.000 0.00 0.00 0.00 3.16
129 130 0.891904 TGGCCCCGAAACTAAAGTGC 60.892 55.000 0.00 0.00 0.00 4.40
130 131 0.608308 GGCCCCGAAACTAAAGTGCT 60.608 55.000 0.00 0.00 0.00 4.40
131 132 0.803117 GCCCCGAAACTAAAGTGCTC 59.197 55.000 0.00 0.00 0.00 4.26
132 133 1.076332 CCCCGAAACTAAAGTGCTCG 58.924 55.000 7.54 7.54 35.33 5.03
133 134 0.442699 CCCGAAACTAAAGTGCTCGC 59.557 55.000 8.59 0.00 34.67 5.03
134 135 0.093026 CCGAAACTAAAGTGCTCGCG 59.907 55.000 0.00 0.00 34.67 5.87
135 136 0.093026 CGAAACTAAAGTGCTCGCGG 59.907 55.000 6.13 0.00 30.87 6.46
136 137 1.145803 GAAACTAAAGTGCTCGCGGT 58.854 50.000 6.13 0.00 0.00 5.68
137 138 0.865769 AAACTAAAGTGCTCGCGGTG 59.134 50.000 6.13 0.07 0.00 4.94
138 139 1.566018 AACTAAAGTGCTCGCGGTGC 61.566 55.000 6.13 12.35 0.00 5.01
139 140 2.027073 CTAAAGTGCTCGCGGTGCA 61.027 57.895 20.20 20.20 38.19 4.57
140 141 1.959899 CTAAAGTGCTCGCGGTGCAG 61.960 60.000 23.44 7.98 41.41 4.41
141 142 2.428960 TAAAGTGCTCGCGGTGCAGA 62.429 55.000 23.44 10.10 41.41 4.26
142 143 3.596066 AAGTGCTCGCGGTGCAGAT 62.596 57.895 23.44 14.64 41.41 2.90
143 144 3.558411 GTGCTCGCGGTGCAGATC 61.558 66.667 23.44 11.62 41.41 2.75
144 145 3.763356 TGCTCGCGGTGCAGATCT 61.763 61.111 20.20 0.00 35.31 2.75
145 146 2.959071 GCTCGCGGTGCAGATCTC 60.959 66.667 17.43 0.00 0.00 2.75
146 147 2.653448 CTCGCGGTGCAGATCTCG 60.653 66.667 6.13 0.00 0.00 4.04
147 148 4.193334 TCGCGGTGCAGATCTCGG 62.193 66.667 6.13 0.00 0.00 4.63
149 150 4.819761 GCGGTGCAGATCTCGGCA 62.820 66.667 3.70 3.70 44.34 5.69
153 154 4.842292 TGCAGATCTCGGCATGAC 57.158 55.556 3.70 0.00 41.86 3.06
154 155 1.899617 TGCAGATCTCGGCATGACA 59.100 52.632 0.00 0.00 41.86 3.58
155 156 0.466963 TGCAGATCTCGGCATGACAT 59.533 50.000 0.00 0.00 41.86 3.06
156 157 1.146637 GCAGATCTCGGCATGACATC 58.853 55.000 0.00 0.00 37.03 3.06
157 158 1.416373 CAGATCTCGGCATGACATCG 58.584 55.000 0.00 0.00 28.28 3.84
158 159 1.000938 CAGATCTCGGCATGACATCGA 60.001 52.381 0.00 0.06 28.28 3.59
159 160 1.683385 AGATCTCGGCATGACATCGAA 59.317 47.619 0.00 0.00 32.35 3.71
160 161 1.789464 GATCTCGGCATGACATCGAAC 59.211 52.381 0.00 0.00 32.35 3.95
161 162 0.525455 TCTCGGCATGACATCGAACG 60.525 55.000 0.00 0.00 32.35 3.95
162 163 1.482621 CTCGGCATGACATCGAACGG 61.483 60.000 0.00 0.00 32.35 4.44
163 164 2.709475 GGCATGACATCGAACGGC 59.291 61.111 0.00 0.00 0.00 5.68
164 165 2.709475 GCATGACATCGAACGGCC 59.291 61.111 0.00 0.00 0.00 6.13
165 166 2.106074 GCATGACATCGAACGGCCA 61.106 57.895 2.24 0.00 0.00 5.36
166 167 1.643868 GCATGACATCGAACGGCCAA 61.644 55.000 2.24 0.00 0.00 4.52
167 168 0.801872 CATGACATCGAACGGCCAAA 59.198 50.000 2.24 0.00 0.00 3.28
168 169 1.198867 CATGACATCGAACGGCCAAAA 59.801 47.619 2.24 0.00 0.00 2.44
169 170 1.309950 TGACATCGAACGGCCAAAAA 58.690 45.000 2.24 0.00 0.00 1.94
192 193 8.688747 AAAAATGATTGAAGGCCAATTGTAAA 57.311 26.923 5.01 0.00 45.00 2.01
193 194 8.866970 AAAATGATTGAAGGCCAATTGTAAAT 57.133 26.923 5.01 0.00 45.00 1.40
194 195 8.496707 AAATGATTGAAGGCCAATTGTAAATC 57.503 30.769 5.01 5.05 45.00 2.17
195 196 6.602410 TGATTGAAGGCCAATTGTAAATCA 57.398 33.333 5.01 7.63 45.00 2.57
196 197 6.632909 TGATTGAAGGCCAATTGTAAATCAG 58.367 36.000 5.01 0.00 45.00 2.90
197 198 6.211184 TGATTGAAGGCCAATTGTAAATCAGT 59.789 34.615 5.01 1.08 45.00 3.41
198 199 6.418057 TTGAAGGCCAATTGTAAATCAGTT 57.582 33.333 5.01 0.00 0.00 3.16
199 200 5.782047 TGAAGGCCAATTGTAAATCAGTTG 58.218 37.500 5.01 0.00 41.42 3.16
200 201 5.538053 TGAAGGCCAATTGTAAATCAGTTGA 59.462 36.000 5.01 0.00 43.42 3.18
201 202 5.391312 AGGCCAATTGTAAATCAGTTGAC 57.609 39.130 5.01 0.00 43.42 3.18
202 203 5.079643 AGGCCAATTGTAAATCAGTTGACT 58.920 37.500 5.01 0.00 43.42 3.41
203 204 5.047802 AGGCCAATTGTAAATCAGTTGACTG 60.048 40.000 5.01 4.77 43.42 3.51
217 218 6.753897 CAGTTGACTGAAAAATAGCCAAAC 57.246 37.500 5.19 0.00 46.59 2.93
218 219 5.691754 CAGTTGACTGAAAAATAGCCAAACC 59.308 40.000 5.19 0.00 46.59 3.27
219 220 4.497473 TGACTGAAAAATAGCCAAACCG 57.503 40.909 0.00 0.00 0.00 4.44
220 221 3.886505 TGACTGAAAAATAGCCAAACCGT 59.113 39.130 0.00 0.00 0.00 4.83
221 222 5.064558 TGACTGAAAAATAGCCAAACCGTA 58.935 37.500 0.00 0.00 0.00 4.02
222 223 5.531659 TGACTGAAAAATAGCCAAACCGTAA 59.468 36.000 0.00 0.00 0.00 3.18
223 224 6.039493 TGACTGAAAAATAGCCAAACCGTAAA 59.961 34.615 0.00 0.00 0.00 2.01
224 225 6.807789 ACTGAAAAATAGCCAAACCGTAAAA 58.192 32.000 0.00 0.00 0.00 1.52
225 226 7.266400 ACTGAAAAATAGCCAAACCGTAAAAA 58.734 30.769 0.00 0.00 0.00 1.94
263 264 2.607750 GGTCCCACCTCAGGCTCA 60.608 66.667 0.00 0.00 34.73 4.26
322 323 1.101635 GCCCTTGCCTATCGTTTCCC 61.102 60.000 0.00 0.00 0.00 3.97
326 327 0.393808 TTGCCTATCGTTTCCCAGCC 60.394 55.000 0.00 0.00 0.00 4.85
327 328 1.526225 GCCTATCGTTTCCCAGCCC 60.526 63.158 0.00 0.00 0.00 5.19
397 402 2.039137 GGTCCGTCTCTCCCCCTT 59.961 66.667 0.00 0.00 0.00 3.95
398 403 2.359967 GGTCCGTCTCTCCCCCTTG 61.360 68.421 0.00 0.00 0.00 3.61
400 405 2.685380 CCGTCTCTCCCCCTTGCT 60.685 66.667 0.00 0.00 0.00 3.91
402 407 1.684049 CGTCTCTCCCCCTTGCTCT 60.684 63.158 0.00 0.00 0.00 4.09
403 408 1.261238 CGTCTCTCCCCCTTGCTCTT 61.261 60.000 0.00 0.00 0.00 2.85
405 410 0.618968 TCTCTCCCCCTTGCTCTTCC 60.619 60.000 0.00 0.00 0.00 3.46
406 411 0.620121 CTCTCCCCCTTGCTCTTCCT 60.620 60.000 0.00 0.00 0.00 3.36
410 415 1.631071 CCCCCTTGCTCTTCCTCCTC 61.631 65.000 0.00 0.00 0.00 3.71
429 434 2.122989 TCCTCCTCCGGCCATACC 60.123 66.667 2.24 0.00 0.00 2.73
474 483 4.966787 GTGGGGGCACGCTTGGAA 62.967 66.667 4.05 0.00 42.66 3.53
485 494 1.233285 CGCTTGGAAACTCTGCTGCT 61.233 55.000 0.00 0.00 0.00 4.24
523 532 0.107459 CTAACCAGGCTGGCTCCTTC 60.107 60.000 33.04 0.00 42.67 3.46
524 533 0.840288 TAACCAGGCTGGCTCCTTCA 60.840 55.000 33.04 2.45 42.67 3.02
570 579 0.111446 AGAGGATGGCGCTAGCTAGA 59.889 55.000 25.15 3.42 44.37 2.43
571 580 0.962489 GAGGATGGCGCTAGCTAGAA 59.038 55.000 25.15 6.63 44.37 2.10
572 581 1.548269 GAGGATGGCGCTAGCTAGAAT 59.452 52.381 25.15 11.11 44.37 2.40
691 714 3.202706 GGGCGCCGAAGAATGGAC 61.203 66.667 22.54 0.00 0.00 4.02
692 715 3.564027 GGCGCCGAAGAATGGACG 61.564 66.667 12.58 0.00 0.00 4.79
842 1494 7.012894 TCCAACCCGCATTACTTCAATATTAAG 59.987 37.037 0.00 0.00 0.00 1.85
843 1495 7.201785 CCAACCCGCATTACTTCAATATTAAGT 60.202 37.037 12.12 12.12 40.25 2.24
845 1497 8.374327 ACCCGCATTACTTCAATATTAAGTAC 57.626 34.615 12.91 0.00 38.74 2.73
846 1498 7.988599 ACCCGCATTACTTCAATATTAAGTACA 59.011 33.333 12.91 8.24 38.74 2.90
875 1527 2.995466 TAGCAAGCAACACTGAATGC 57.005 45.000 0.00 4.13 42.87 3.56
920 1572 1.052287 GTGCGCTTCATTTGGTTTCG 58.948 50.000 9.73 0.00 0.00 3.46
925 1581 2.405025 CGCTTCATTTGGTTTCGAAAGC 59.595 45.455 28.47 28.47 36.95 3.51
938 1594 5.741040 GGTTTCGAAAGCATCATTCAGAATC 59.259 40.000 29.74 5.49 36.47 2.52
1006 1662 2.218953 TAGCGGTGCTACAATGCTAC 57.781 50.000 0.00 0.00 40.44 3.58
1009 1665 1.062587 GCGGTGCTACAATGCTACAAG 59.937 52.381 0.00 0.00 0.00 3.16
1068 1724 1.676006 ACGGGCAAGACAAGAAACAAG 59.324 47.619 0.00 0.00 0.00 3.16
1117 1773 1.654023 GGTAAGCACCGGATTGCACC 61.654 60.000 18.29 13.76 45.62 5.01
1142 1806 6.858993 CGGAGTACTAGATAAGAATGACAAGC 59.141 42.308 0.00 0.00 0.00 4.01
1143 1807 7.468768 CGGAGTACTAGATAAGAATGACAAGCA 60.469 40.741 0.00 0.00 0.00 3.91
1144 1808 7.865385 GGAGTACTAGATAAGAATGACAAGCAG 59.135 40.741 0.00 0.00 0.00 4.24
1154 1818 0.815213 TGACAAGCAGCTGTGACCAC 60.815 55.000 16.64 3.99 0.00 4.16
1187 1851 4.335400 TGCCTGCACATTTCGAGATATA 57.665 40.909 0.00 0.00 0.00 0.86
1206 1870 0.104409 AGGGCGGGGGAAAGATAGAT 60.104 55.000 0.00 0.00 0.00 1.98
1238 1903 6.074005 GTGAATTTTGTGTGATCGACTTCTC 58.926 40.000 0.00 0.00 0.00 2.87
1240 1905 7.116376 GTGAATTTTGTGTGATCGACTTCTCTA 59.884 37.037 0.00 0.00 0.00 2.43
1241 1906 6.952935 ATTTTGTGTGATCGACTTCTCTAC 57.047 37.500 0.00 0.00 0.00 2.59
1242 1907 5.707242 TTTGTGTGATCGACTTCTCTACT 57.293 39.130 0.00 0.00 0.00 2.57
1243 1908 4.948608 TGTGTGATCGACTTCTCTACTC 57.051 45.455 0.00 0.00 0.00 2.59
1261 1926 3.964909 ACTCTTTCCGTGATTTTTGTGC 58.035 40.909 0.00 0.00 0.00 4.57
1276 1941 3.218470 TGCCCATATTGCGCCTGC 61.218 61.111 4.18 0.00 43.20 4.85
1278 1943 2.912624 GCCCATATTGCGCCTGCTC 61.913 63.158 4.18 0.00 43.34 4.26
1296 1961 4.707105 TGCTCATCTCAAACAAGTCAAGA 58.293 39.130 0.00 0.00 0.00 3.02
1302 1967 6.260936 TCATCTCAAACAAGTCAAGAGTTTCC 59.739 38.462 0.00 0.00 33.54 3.13
2345 3053 1.493950 GATGGAGCAGTTCGGCATCG 61.494 60.000 0.00 0.00 35.83 3.84
2410 3118 3.136123 CTGGGGCACATGGCGAAG 61.136 66.667 0.00 0.00 46.16 3.79
2479 3187 1.086067 CGCAGGTGTACAGCATCCTG 61.086 60.000 25.75 22.93 43.23 3.86
2637 3345 4.690719 CGCCGCCAGGGTGTACAA 62.691 66.667 0.00 0.00 41.61 2.41
3046 3760 1.372087 GGGCTGGAGACTTTGCATCG 61.372 60.000 0.00 0.00 0.00 3.84
3103 3817 2.279120 CAGCTCCGACTGCGATCC 60.279 66.667 0.00 0.00 40.82 3.36
3119 3833 2.499303 ATCCTCGGGGTTTTGCAGGG 62.499 60.000 0.00 0.00 0.00 4.45
3121 3835 1.675641 CTCGGGGTTTTGCAGGGAG 60.676 63.158 0.00 0.00 0.00 4.30
3256 3971 4.969359 TGTAAAACCCAATTCTTCCCCAAA 59.031 37.500 0.00 0.00 0.00 3.28
3257 3972 5.428783 TGTAAAACCCAATTCTTCCCCAAAA 59.571 36.000 0.00 0.00 0.00 2.44
3258 3973 5.661503 AAAACCCAATTCTTCCCCAAAAT 57.338 34.783 0.00 0.00 0.00 1.82
3259 3974 5.661503 AAACCCAATTCTTCCCCAAAATT 57.338 34.783 0.00 0.00 0.00 1.82
3260 3975 5.661503 AACCCAATTCTTCCCCAAAATTT 57.338 34.783 0.00 0.00 0.00 1.82
3261 3976 6.771934 AACCCAATTCTTCCCCAAAATTTA 57.228 33.333 0.00 0.00 0.00 1.40
3329 4061 4.633126 CACATTGGTCTTCGATTCAGATGT 59.367 41.667 0.00 0.00 0.00 3.06
3330 4062 4.872691 ACATTGGTCTTCGATTCAGATGTC 59.127 41.667 0.00 0.00 0.00 3.06
3331 4063 4.808414 TTGGTCTTCGATTCAGATGTCT 57.192 40.909 0.00 0.00 0.00 3.41
3332 4064 4.377839 TGGTCTTCGATTCAGATGTCTC 57.622 45.455 0.00 0.00 0.00 3.36
3333 4065 3.763897 TGGTCTTCGATTCAGATGTCTCA 59.236 43.478 0.00 0.00 0.00 3.27
3334 4066 4.109050 GGTCTTCGATTCAGATGTCTCAC 58.891 47.826 0.00 0.00 0.00 3.51
3352 4084 3.176411 TCACTCTCACCATTCCACAGAT 58.824 45.455 0.00 0.00 0.00 2.90
3428 4160 3.754850 TCTCAATCAAACACTGATGCTGG 59.245 43.478 0.00 0.00 44.43 4.85
3440 4172 7.559590 ACACTGATGCTGGAGAATTATTAAC 57.440 36.000 0.00 0.00 0.00 2.01
3464 4196 0.887247 TGGTTCCAATGCCATGAACG 59.113 50.000 0.00 0.00 39.36 3.95
3465 4197 1.173043 GGTTCCAATGCCATGAACGA 58.827 50.000 0.00 0.00 39.36 3.85
3466 4198 1.135402 GGTTCCAATGCCATGAACGAC 60.135 52.381 0.00 0.00 39.36 4.34
3500 4232 9.856488 ATATCTACACGATCACAACCATTATAC 57.144 33.333 0.00 0.00 33.48 1.47
3501 4233 6.203647 TCTACACGATCACAACCATTATACG 58.796 40.000 0.00 0.00 0.00 3.06
3502 4234 3.554324 ACACGATCACAACCATTATACGC 59.446 43.478 0.00 0.00 0.00 4.42
3503 4235 3.802139 CACGATCACAACCATTATACGCT 59.198 43.478 0.00 0.00 0.00 5.07
3504 4236 4.049186 ACGATCACAACCATTATACGCTC 58.951 43.478 0.00 0.00 0.00 5.03
3505 4237 4.202121 ACGATCACAACCATTATACGCTCT 60.202 41.667 0.00 0.00 0.00 4.09
3506 4238 4.745125 CGATCACAACCATTATACGCTCTT 59.255 41.667 0.00 0.00 0.00 2.85
3507 4239 5.918576 CGATCACAACCATTATACGCTCTTA 59.081 40.000 0.00 0.00 0.00 2.10
3513 4245 8.487970 CACAACCATTATACGCTCTTATACTTG 58.512 37.037 0.00 0.00 0.00 3.16
3515 4250 8.700644 CAACCATTATACGCTCTTATACTTGTC 58.299 37.037 0.00 0.00 0.00 3.18
3599 4334 0.392863 TCATGATGGGCTTGTCGGTG 60.393 55.000 0.00 0.00 0.00 4.94
3704 4439 2.358737 GCCAAGTCCACGGTGAGG 60.359 66.667 10.28 4.64 0.00 3.86
3826 4561 1.673033 CGGCTGGTAGAACTTGTCCAG 60.673 57.143 5.79 5.79 46.96 3.86
3852 4587 3.487417 CAGCAGCAGCAGCAGTAG 58.513 61.111 12.92 0.00 45.49 2.57
3869 4604 0.966920 TAGGAGGCGGCATTAGCTAC 59.033 55.000 13.08 0.00 41.70 3.58
3896 4631 2.594131 TCTGACGGAGGAACTTCAGAA 58.406 47.619 0.00 0.00 41.16 3.02
3899 4634 2.070028 GACGGAGGAACTTCAGAAAGC 58.930 52.381 0.00 0.00 41.55 3.51
3900 4635 1.071605 CGGAGGAACTTCAGAAAGCG 58.928 55.000 0.00 0.00 41.55 4.68
3902 4637 1.002087 GGAGGAACTTCAGAAAGCGGA 59.998 52.381 0.00 0.00 41.55 5.54
3903 4638 2.342179 GAGGAACTTCAGAAAGCGGAG 58.658 52.381 0.00 0.00 41.55 4.63
3904 4639 1.694696 AGGAACTTCAGAAAGCGGAGT 59.305 47.619 0.00 0.00 35.81 3.85
3905 4640 2.104963 AGGAACTTCAGAAAGCGGAGTT 59.895 45.455 0.00 0.00 35.81 3.01
3906 4641 2.480802 GGAACTTCAGAAAGCGGAGTTC 59.519 50.000 3.21 3.21 35.81 3.01
3907 4642 2.171341 ACTTCAGAAAGCGGAGTTCC 57.829 50.000 0.00 0.00 35.81 3.62
3908 4643 1.694696 ACTTCAGAAAGCGGAGTTCCT 59.305 47.619 0.00 0.00 35.81 3.36
3909 4644 2.289133 ACTTCAGAAAGCGGAGTTCCTC 60.289 50.000 0.00 0.00 35.81 3.71
3910 4645 1.633774 TCAGAAAGCGGAGTTCCTCT 58.366 50.000 0.00 0.00 31.21 3.69
3921 4656 3.949132 GGAGTTCCTCTCTGATGCTTTT 58.051 45.455 0.00 0.00 42.40 2.27
3925 4660 2.440409 TCCTCTCTGATGCTTTTTGGC 58.560 47.619 0.00 0.00 0.00 4.52
3961 4702 1.302033 GCTGGCGATGGGTATCTGG 60.302 63.158 0.00 0.00 0.00 3.86
3991 4732 0.179936 GCTGGATGGAGGTGGAAGAG 59.820 60.000 0.00 0.00 0.00 2.85
4030 4771 2.513259 GGAGGGGTTGTGGACGTCA 61.513 63.158 18.91 0.27 0.00 4.35
4036 4777 1.068474 GGTTGTGGACGTCAATCTCG 58.932 55.000 18.91 0.00 0.00 4.04
4137 4878 1.677576 CAAGCTCTGCACAGAACCAAA 59.322 47.619 1.42 0.00 36.94 3.28
4151 4892 7.264947 CACAGAACCAAACAAATTCTAAGGTT 58.735 34.615 0.00 0.00 40.31 3.50
4152 4893 7.222611 CACAGAACCAAACAAATTCTAAGGTTG 59.777 37.037 0.00 0.00 37.95 3.77
4157 4901 8.068892 ACCAAACAAATTCTAAGGTTGTGTAA 57.931 30.769 0.00 0.00 35.70 2.41
4158 4902 8.700973 ACCAAACAAATTCTAAGGTTGTGTAAT 58.299 29.630 0.00 0.00 35.70 1.89
4163 4907 9.449719 ACAAATTCTAAGGTTGTGTAATAGAGG 57.550 33.333 0.00 0.00 34.28 3.69
4165 4909 7.989947 ATTCTAAGGTTGTGTAATAGAGGGA 57.010 36.000 0.00 0.00 0.00 4.20
4184 4928 6.100424 AGAGGGAGATACTGAATTTAAGGTGG 59.900 42.308 0.00 0.00 0.00 4.61
4185 4929 4.822350 GGGAGATACTGAATTTAAGGTGGC 59.178 45.833 0.00 0.00 0.00 5.01
4186 4930 5.437060 GGAGATACTGAATTTAAGGTGGCA 58.563 41.667 0.00 0.00 0.00 4.92
4187 4931 5.529060 GGAGATACTGAATTTAAGGTGGCAG 59.471 44.000 0.00 0.00 0.00 4.85
4188 4932 6.313519 AGATACTGAATTTAAGGTGGCAGA 57.686 37.500 0.00 0.00 0.00 4.26
4189 4933 6.352516 AGATACTGAATTTAAGGTGGCAGAG 58.647 40.000 0.00 0.00 0.00 3.35
4190 4934 4.640771 ACTGAATTTAAGGTGGCAGAGA 57.359 40.909 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.535331 GAGAGAGTTAAAGCAGCGGAG 58.465 52.381 0.00 0.00 0.00 4.63
15 16 1.204941 GGAGAGAGTTAAAGCAGCGGA 59.795 52.381 0.00 0.00 0.00 5.54
16 17 1.066858 TGGAGAGAGTTAAAGCAGCGG 60.067 52.381 0.00 0.00 0.00 5.52
17 18 2.370281 TGGAGAGAGTTAAAGCAGCG 57.630 50.000 0.00 0.00 0.00 5.18
18 19 3.931578 TCTTGGAGAGAGTTAAAGCAGC 58.068 45.455 0.00 0.00 0.00 5.25
19 20 6.652481 TCATTTCTTGGAGAGAGTTAAAGCAG 59.348 38.462 0.00 0.00 35.37 4.24
20 21 6.533730 TCATTTCTTGGAGAGAGTTAAAGCA 58.466 36.000 0.00 0.00 35.37 3.91
21 22 6.876257 TCTCATTTCTTGGAGAGAGTTAAAGC 59.124 38.462 0.00 0.00 35.34 3.51
22 23 8.839310 TTCTCATTTCTTGGAGAGAGTTAAAG 57.161 34.615 0.00 0.00 40.91 1.85
23 24 9.277783 CTTTCTCATTTCTTGGAGAGAGTTAAA 57.722 33.333 0.00 0.00 40.91 1.52
24 25 7.880195 CCTTTCTCATTTCTTGGAGAGAGTTAA 59.120 37.037 0.00 0.00 39.48 2.01
25 26 7.235606 TCCTTTCTCATTTCTTGGAGAGAGTTA 59.764 37.037 0.00 0.00 39.48 2.24
26 27 6.043706 TCCTTTCTCATTTCTTGGAGAGAGTT 59.956 38.462 0.00 0.00 39.48 3.01
27 28 5.545723 TCCTTTCTCATTTCTTGGAGAGAGT 59.454 40.000 0.00 0.00 39.48 3.24
28 29 6.047511 TCCTTTCTCATTTCTTGGAGAGAG 57.952 41.667 0.00 0.00 40.91 3.20
29 30 6.633325 ATCCTTTCTCATTTCTTGGAGAGA 57.367 37.500 0.00 0.00 40.91 3.10
30 31 7.790027 TCTATCCTTTCTCATTTCTTGGAGAG 58.210 38.462 0.00 0.00 40.91 3.20
31 32 7.739995 TCTATCCTTTCTCATTTCTTGGAGA 57.260 36.000 0.00 0.00 38.34 3.71
32 33 8.798859 TTTCTATCCTTTCTCATTTCTTGGAG 57.201 34.615 0.00 0.00 0.00 3.86
33 34 9.182214 CATTTCTATCCTTTCTCATTTCTTGGA 57.818 33.333 0.00 0.00 0.00 3.53
34 35 9.182214 TCATTTCTATCCTTTCTCATTTCTTGG 57.818 33.333 0.00 0.00 0.00 3.61
57 58 9.119418 CCCTTTGTCCTTTTTGTTTATTTTCAT 57.881 29.630 0.00 0.00 0.00 2.57
58 59 8.322091 TCCCTTTGTCCTTTTTGTTTATTTTCA 58.678 29.630 0.00 0.00 0.00 2.69
59 60 8.725405 TCCCTTTGTCCTTTTTGTTTATTTTC 57.275 30.769 0.00 0.00 0.00 2.29
60 61 7.773224 CCTCCCTTTGTCCTTTTTGTTTATTTT 59.227 33.333 0.00 0.00 0.00 1.82
61 62 7.279615 CCTCCCTTTGTCCTTTTTGTTTATTT 58.720 34.615 0.00 0.00 0.00 1.40
62 63 6.183361 CCCTCCCTTTGTCCTTTTTGTTTATT 60.183 38.462 0.00 0.00 0.00 1.40
63 64 5.306937 CCCTCCCTTTGTCCTTTTTGTTTAT 59.693 40.000 0.00 0.00 0.00 1.40
64 65 4.651962 CCCTCCCTTTGTCCTTTTTGTTTA 59.348 41.667 0.00 0.00 0.00 2.01
65 66 3.454447 CCCTCCCTTTGTCCTTTTTGTTT 59.546 43.478 0.00 0.00 0.00 2.83
66 67 3.038280 CCCTCCCTTTGTCCTTTTTGTT 58.962 45.455 0.00 0.00 0.00 2.83
67 68 2.677914 CCCTCCCTTTGTCCTTTTTGT 58.322 47.619 0.00 0.00 0.00 2.83
68 69 1.344438 GCCCTCCCTTTGTCCTTTTTG 59.656 52.381 0.00 0.00 0.00 2.44
69 70 1.062505 TGCCCTCCCTTTGTCCTTTTT 60.063 47.619 0.00 0.00 0.00 1.94
70 71 0.560688 TGCCCTCCCTTTGTCCTTTT 59.439 50.000 0.00 0.00 0.00 2.27
71 72 0.113190 CTGCCCTCCCTTTGTCCTTT 59.887 55.000 0.00 0.00 0.00 3.11
72 73 1.770324 CTGCCCTCCCTTTGTCCTT 59.230 57.895 0.00 0.00 0.00 3.36
73 74 2.234296 CCTGCCCTCCCTTTGTCCT 61.234 63.158 0.00 0.00 0.00 3.85
74 75 2.356667 CCTGCCCTCCCTTTGTCC 59.643 66.667 0.00 0.00 0.00 4.02
75 76 2.356667 CCCTGCCCTCCCTTTGTC 59.643 66.667 0.00 0.00 0.00 3.18
76 77 3.268032 CCCCTGCCCTCCCTTTGT 61.268 66.667 0.00 0.00 0.00 2.83
77 78 2.941025 TCCCCTGCCCTCCCTTTG 60.941 66.667 0.00 0.00 0.00 2.77
78 79 2.941583 GTCCCCTGCCCTCCCTTT 60.942 66.667 0.00 0.00 0.00 3.11
86 87 2.946346 TTAACGTCCGTCCCCTGCC 61.946 63.158 0.00 0.00 0.00 4.85
87 88 1.739196 GTTAACGTCCGTCCCCTGC 60.739 63.158 0.00 0.00 0.00 4.85
88 89 1.444895 CGTTAACGTCCGTCCCCTG 60.445 63.158 19.75 0.00 34.11 4.45
89 90 2.639327 CCGTTAACGTCCGTCCCCT 61.639 63.158 25.15 0.00 37.74 4.79
90 91 2.125952 CCGTTAACGTCCGTCCCC 60.126 66.667 25.15 0.00 37.74 4.81
91 92 2.125952 CCCGTTAACGTCCGTCCC 60.126 66.667 25.15 0.00 37.74 4.46
92 93 2.810887 GCCCGTTAACGTCCGTCC 60.811 66.667 25.15 4.50 37.74 4.79
93 94 2.090524 CAGCCCGTTAACGTCCGTC 61.091 63.158 25.15 9.96 37.74 4.79
94 95 2.048877 CAGCCCGTTAACGTCCGT 60.049 61.111 25.15 5.51 37.74 4.69
95 96 2.812178 CCAGCCCGTTAACGTCCG 60.812 66.667 25.15 13.67 37.74 4.79
96 97 3.122971 GCCAGCCCGTTAACGTCC 61.123 66.667 25.15 15.56 37.74 4.79
97 98 3.122971 GGCCAGCCCGTTAACGTC 61.123 66.667 25.15 16.47 37.74 4.34
107 108 1.303806 TTTAGTTTCGGGGCCAGCC 60.304 57.895 4.39 0.00 0.00 4.85
108 109 0.608308 ACTTTAGTTTCGGGGCCAGC 60.608 55.000 4.39 0.00 0.00 4.85
109 110 1.165270 CACTTTAGTTTCGGGGCCAG 58.835 55.000 4.39 0.00 0.00 4.85
110 111 0.891904 GCACTTTAGTTTCGGGGCCA 60.892 55.000 4.39 0.00 0.00 5.36
111 112 0.608308 AGCACTTTAGTTTCGGGGCC 60.608 55.000 0.00 0.00 0.00 5.80
112 113 0.803117 GAGCACTTTAGTTTCGGGGC 59.197 55.000 0.00 0.00 0.00 5.80
113 114 1.076332 CGAGCACTTTAGTTTCGGGG 58.924 55.000 5.93 0.00 32.32 5.73
114 115 0.442699 GCGAGCACTTTAGTTTCGGG 59.557 55.000 12.61 0.00 34.83 5.14
115 116 0.093026 CGCGAGCACTTTAGTTTCGG 59.907 55.000 0.00 3.41 34.83 4.30
116 117 0.093026 CCGCGAGCACTTTAGTTTCG 59.907 55.000 8.23 8.43 36.34 3.46
117 118 1.136336 CACCGCGAGCACTTTAGTTTC 60.136 52.381 8.23 0.00 0.00 2.78
118 119 0.865769 CACCGCGAGCACTTTAGTTT 59.134 50.000 8.23 0.00 0.00 2.66
119 120 1.566018 GCACCGCGAGCACTTTAGTT 61.566 55.000 8.23 0.00 0.00 2.24
120 121 2.027625 GCACCGCGAGCACTTTAGT 61.028 57.895 8.23 0.00 0.00 2.24
121 122 1.959899 CTGCACCGCGAGCACTTTAG 61.960 60.000 19.74 8.31 37.02 1.85
122 123 2.027073 CTGCACCGCGAGCACTTTA 61.027 57.895 19.74 1.93 37.02 1.85
123 124 3.349006 CTGCACCGCGAGCACTTT 61.349 61.111 19.74 0.00 37.02 2.66
124 125 3.596066 ATCTGCACCGCGAGCACTT 62.596 57.895 19.74 9.18 37.02 3.16
125 126 3.997064 GATCTGCACCGCGAGCACT 62.997 63.158 19.74 11.51 37.02 4.40
126 127 3.558411 GATCTGCACCGCGAGCAC 61.558 66.667 19.74 8.95 37.02 4.40
127 128 3.706563 GAGATCTGCACCGCGAGCA 62.707 63.158 21.66 21.66 40.19 4.26
128 129 2.959071 GAGATCTGCACCGCGAGC 60.959 66.667 8.23 12.67 0.00 5.03
129 130 2.653448 CGAGATCTGCACCGCGAG 60.653 66.667 8.23 0.00 0.00 5.03
130 131 4.193334 CCGAGATCTGCACCGCGA 62.193 66.667 8.23 0.00 0.00 5.87
132 133 4.819761 TGCCGAGATCTGCACCGC 62.820 66.667 0.00 0.00 31.18 5.68
133 134 2.107750 ATGCCGAGATCTGCACCG 59.892 61.111 9.71 2.38 38.84 4.94
134 135 1.144716 TCATGCCGAGATCTGCACC 59.855 57.895 9.71 0.00 38.84 5.01
135 136 0.460811 TGTCATGCCGAGATCTGCAC 60.461 55.000 9.71 0.00 38.84 4.57
136 137 0.466963 ATGTCATGCCGAGATCTGCA 59.533 50.000 9.91 9.91 40.24 4.41
137 138 1.146637 GATGTCATGCCGAGATCTGC 58.853 55.000 0.00 0.00 40.47 4.26
138 139 1.000938 TCGATGTCATGCCGAGATCTG 60.001 52.381 0.00 0.00 41.27 2.90
139 140 1.322442 TCGATGTCATGCCGAGATCT 58.678 50.000 0.00 0.00 41.27 2.75
140 141 1.789464 GTTCGATGTCATGCCGAGATC 59.211 52.381 0.00 1.46 40.29 2.75
141 142 1.858091 GTTCGATGTCATGCCGAGAT 58.142 50.000 0.00 0.00 33.66 2.75
142 143 0.525455 CGTTCGATGTCATGCCGAGA 60.525 55.000 0.00 0.00 33.66 4.04
143 144 1.482621 CCGTTCGATGTCATGCCGAG 61.483 60.000 0.00 0.00 33.66 4.63
144 145 1.518352 CCGTTCGATGTCATGCCGA 60.518 57.895 0.00 0.00 0.00 5.54
145 146 3.005898 CCGTTCGATGTCATGCCG 58.994 61.111 0.00 0.00 0.00 5.69
146 147 2.709475 GCCGTTCGATGTCATGCC 59.291 61.111 0.00 0.00 0.00 4.40
147 148 1.643868 TTGGCCGTTCGATGTCATGC 61.644 55.000 0.00 0.00 0.00 4.06
148 149 0.801872 TTTGGCCGTTCGATGTCATG 59.198 50.000 0.00 0.00 0.00 3.07
149 150 1.529226 TTTTGGCCGTTCGATGTCAT 58.471 45.000 0.00 0.00 0.00 3.06
150 151 1.309950 TTTTTGGCCGTTCGATGTCA 58.690 45.000 0.00 0.00 0.00 3.58
167 168 8.688747 TTTACAATTGGCCTTCAATCATTTTT 57.311 26.923 10.83 0.00 44.68 1.94
168 169 8.866970 ATTTACAATTGGCCTTCAATCATTTT 57.133 26.923 10.83 0.00 44.68 1.82
169 170 8.102047 TGATTTACAATTGGCCTTCAATCATTT 58.898 29.630 10.83 0.00 44.68 2.32
170 171 7.622713 TGATTTACAATTGGCCTTCAATCATT 58.377 30.769 10.83 0.00 44.68 2.57
171 172 7.093201 ACTGATTTACAATTGGCCTTCAATCAT 60.093 33.333 10.83 3.00 44.68 2.45
172 173 6.211184 ACTGATTTACAATTGGCCTTCAATCA 59.789 34.615 10.83 11.60 44.68 2.57
173 174 6.633856 ACTGATTTACAATTGGCCTTCAATC 58.366 36.000 10.83 8.10 44.68 2.67
175 176 6.041409 TCAACTGATTTACAATTGGCCTTCAA 59.959 34.615 10.83 0.00 36.53 2.69
176 177 5.538053 TCAACTGATTTACAATTGGCCTTCA 59.462 36.000 10.83 6.79 36.53 3.02
177 178 5.863935 GTCAACTGATTTACAATTGGCCTTC 59.136 40.000 10.83 2.41 34.81 3.46
178 179 5.539955 AGTCAACTGATTTACAATTGGCCTT 59.460 36.000 10.83 0.00 40.53 4.35
179 180 5.047802 CAGTCAACTGATTTACAATTGGCCT 60.048 40.000 10.83 0.00 46.59 5.19
180 181 5.163513 CAGTCAACTGATTTACAATTGGCC 58.836 41.667 10.83 0.00 46.59 5.36
194 195 5.691754 GGTTTGGCTATTTTTCAGTCAACTG 59.308 40.000 3.69 3.69 45.08 3.16
195 196 5.507315 CGGTTTGGCTATTTTTCAGTCAACT 60.507 40.000 0.00 0.00 37.35 3.16
196 197 4.679654 CGGTTTGGCTATTTTTCAGTCAAC 59.320 41.667 0.00 0.00 37.35 3.18
197 198 4.339814 ACGGTTTGGCTATTTTTCAGTCAA 59.660 37.500 0.00 0.00 35.89 3.18
198 199 3.886505 ACGGTTTGGCTATTTTTCAGTCA 59.113 39.130 0.00 0.00 0.00 3.41
199 200 4.499037 ACGGTTTGGCTATTTTTCAGTC 57.501 40.909 0.00 0.00 0.00 3.51
200 201 6.394025 TTTACGGTTTGGCTATTTTTCAGT 57.606 33.333 0.00 0.00 0.00 3.41
201 202 7.701809 TTTTTACGGTTTGGCTATTTTTCAG 57.298 32.000 0.00 0.00 0.00 3.02
236 237 4.447342 GTGGGACCCATGCCCTGG 62.447 72.222 18.51 0.00 46.19 4.45
237 238 4.447342 GGTGGGACCCATGCCCTG 62.447 72.222 18.51 0.00 46.19 4.45
238 239 4.701437 AGGTGGGACCCATGCCCT 62.701 66.667 18.51 16.05 46.19 5.19
239 240 4.129148 GAGGTGGGACCCATGCCC 62.129 72.222 18.51 13.76 46.22 5.36
240 241 3.338250 TGAGGTGGGACCCATGCC 61.338 66.667 18.51 14.57 39.75 4.40
241 242 2.273449 CTGAGGTGGGACCCATGC 59.727 66.667 18.51 9.80 39.75 4.06
242 243 3.001514 CCTGAGGTGGGACCCATG 58.998 66.667 18.51 5.07 39.75 3.66
243 244 3.017581 GCCTGAGGTGGGACCCAT 61.018 66.667 18.51 0.00 39.75 4.00
244 245 4.270153 AGCCTGAGGTGGGACCCA 62.270 66.667 9.95 9.95 39.75 4.51
245 246 3.403558 GAGCCTGAGGTGGGACCC 61.404 72.222 2.45 2.45 39.75 4.46
246 247 2.607750 TGAGCCTGAGGTGGGACC 60.608 66.667 0.00 0.00 38.99 4.46
247 248 2.664081 CCTGAGCCTGAGGTGGGAC 61.664 68.421 0.00 0.00 0.00 4.46
308 309 1.223487 GGCTGGGAAACGATAGGCA 59.777 57.895 0.00 0.00 43.77 4.75
397 402 0.032615 GAGGAGGAGGAGGAAGAGCA 60.033 60.000 0.00 0.00 0.00 4.26
398 403 0.759060 GGAGGAGGAGGAGGAAGAGC 60.759 65.000 0.00 0.00 0.00 4.09
400 405 0.930726 GAGGAGGAGGAGGAGGAAGA 59.069 60.000 0.00 0.00 0.00 2.87
402 407 1.939082 CGGAGGAGGAGGAGGAGGAA 61.939 65.000 0.00 0.00 0.00 3.36
403 408 2.387772 CGGAGGAGGAGGAGGAGGA 61.388 68.421 0.00 0.00 0.00 3.71
474 483 0.321034 TCATTCGCAGCAGCAGAGTT 60.321 50.000 0.82 0.00 42.27 3.01
485 494 2.309528 GGTACATCACCTCATTCGCA 57.690 50.000 0.00 0.00 44.79 5.10
523 532 1.008538 GGCGGCAGAAACACAAGTG 60.009 57.895 3.07 0.00 0.00 3.16
524 533 2.542907 CGGCGGCAGAAACACAAGT 61.543 57.895 10.53 0.00 0.00 3.16
657 680 3.307445 CAGCAGACTGGAGGAGGG 58.693 66.667 4.26 0.00 40.48 4.30
676 699 4.223964 GCGTCCATTCTTCGGCGC 62.224 66.667 0.00 0.00 40.15 6.53
677 700 3.564027 GGCGTCCATTCTTCGGCG 61.564 66.667 0.00 0.00 39.90 6.46
691 714 1.339610 TCCCTGAATTTGTTGTTGGCG 59.660 47.619 0.00 0.00 0.00 5.69
692 715 3.328505 CATCCCTGAATTTGTTGTTGGC 58.671 45.455 0.00 0.00 0.00 4.52
776 1406 7.611467 ACACATATCTATCTCACTTGGCAAAAA 59.389 33.333 0.00 0.00 0.00 1.94
842 1494 6.588756 TGTTGCTTGCTATACTTGTACTGTAC 59.411 38.462 10.98 10.98 0.00 2.90
843 1495 6.588756 GTGTTGCTTGCTATACTTGTACTGTA 59.411 38.462 0.00 0.00 0.00 2.74
845 1497 5.639506 AGTGTTGCTTGCTATACTTGTACTG 59.360 40.000 0.00 0.00 0.00 2.74
846 1498 5.639506 CAGTGTTGCTTGCTATACTTGTACT 59.360 40.000 4.12 0.00 0.00 2.73
859 1511 2.292569 ACTCTGCATTCAGTGTTGCTTG 59.707 45.455 17.49 12.10 42.45 4.01
875 1527 3.466836 TGCAGAACACAAACCTACTCTG 58.533 45.455 0.00 0.00 34.69 3.35
911 1563 5.009510 TCTGAATGATGCTTTCGAAACCAAA 59.990 36.000 6.47 0.69 0.00 3.28
920 1572 4.982916 GCCATGATTCTGAATGATGCTTTC 59.017 41.667 20.13 8.35 32.07 2.62
925 1581 5.473504 TCAGATGCCATGATTCTGAATGATG 59.526 40.000 19.03 19.03 42.06 3.07
938 1594 5.533528 TGTCAGGATTTATTCAGATGCCATG 59.466 40.000 0.00 0.00 0.00 3.66
952 1608 1.985159 TGGCCAGTAGTGTCAGGATTT 59.015 47.619 0.00 0.00 0.00 2.17
993 1649 2.616960 CCGTCTTGTAGCATTGTAGCA 58.383 47.619 0.00 0.00 36.85 3.49
994 1650 1.327764 GCCGTCTTGTAGCATTGTAGC 59.672 52.381 0.00 0.00 0.00 3.58
996 1652 2.753055 TGCCGTCTTGTAGCATTGTA 57.247 45.000 0.00 0.00 0.00 2.41
1006 1662 1.390123 CGTCAGTTGTATGCCGTCTTG 59.610 52.381 0.00 0.00 0.00 3.02
1009 1665 1.693083 GGCGTCAGTTGTATGCCGTC 61.693 60.000 0.00 0.00 35.77 4.79
1068 1724 0.253327 ATCCGTTGAGCTCTTTCCCC 59.747 55.000 16.19 0.00 0.00 4.81
1117 1773 6.858993 GCTTGTCATTCTTATCTAGTACTCCG 59.141 42.308 0.00 0.00 0.00 4.63
1118 1774 7.717568 TGCTTGTCATTCTTATCTAGTACTCC 58.282 38.462 0.00 0.00 0.00 3.85
1119 1775 7.381139 GCTGCTTGTCATTCTTATCTAGTACTC 59.619 40.741 0.00 0.00 0.00 2.59
1120 1776 7.069331 AGCTGCTTGTCATTCTTATCTAGTACT 59.931 37.037 0.00 0.00 0.00 2.73
1121 1777 7.168972 CAGCTGCTTGTCATTCTTATCTAGTAC 59.831 40.741 0.00 0.00 0.00 2.73
1122 1778 7.147828 ACAGCTGCTTGTCATTCTTATCTAGTA 60.148 37.037 15.27 0.00 0.00 1.82
1124 1780 6.018913 CACAGCTGCTTGTCATTCTTATCTAG 60.019 42.308 15.27 0.00 0.00 2.43
1144 1808 2.072298 GAACTGAGATGTGGTCACAGC 58.928 52.381 10.93 10.93 45.89 4.40
1154 1818 1.467734 GTGCAGGCAAGAACTGAGATG 59.532 52.381 0.00 0.00 38.20 2.90
1187 1851 0.104409 ATCTATCTTTCCCCCGCCCT 60.104 55.000 0.00 0.00 0.00 5.19
1206 1870 6.128035 CGATCACACAAAATTCACCAAGGATA 60.128 38.462 0.00 0.00 0.00 2.59
1238 1903 5.147162 GCACAAAAATCACGGAAAGAGTAG 58.853 41.667 0.00 0.00 0.00 2.57
1240 1905 3.243401 GGCACAAAAATCACGGAAAGAGT 60.243 43.478 0.00 0.00 0.00 3.24
1241 1906 3.308530 GGCACAAAAATCACGGAAAGAG 58.691 45.455 0.00 0.00 0.00 2.85
1242 1907 2.035321 GGGCACAAAAATCACGGAAAGA 59.965 45.455 0.00 0.00 0.00 2.52
1243 1908 2.223923 TGGGCACAAAAATCACGGAAAG 60.224 45.455 0.00 0.00 0.00 2.62
1261 1926 0.892358 ATGAGCAGGCGCAATATGGG 60.892 55.000 10.83 0.00 42.27 4.00
1276 1941 6.857777 AACTCTTGACTTGTTTGAGATGAG 57.142 37.500 0.00 0.00 0.00 2.90
1278 1943 6.261826 AGGAAACTCTTGACTTGTTTGAGATG 59.738 38.462 0.00 0.00 32.90 2.90
1296 1961 2.753168 GGAGCACCCAAAGAAGGAAACT 60.753 50.000 0.00 0.00 37.24 2.66
1302 1967 0.401738 TCCTGGAGCACCCAAAGAAG 59.598 55.000 0.00 0.00 46.07 2.85
2087 2767 0.959553 AGTATCCGCCGACGATGATT 59.040 50.000 0.00 0.00 43.93 2.57
2249 2929 1.513800 CTCGCTCTGAGCTCACGTG 60.514 63.158 25.59 9.94 39.60 4.49
2345 3053 1.985447 TACGTCACGATGTCCGGCTC 61.985 60.000 2.91 0.00 43.93 4.70
2410 3118 1.279840 GTCGAACACCTTGCTGCAC 59.720 57.895 0.00 0.00 0.00 4.57
2430 3138 1.878656 GATCCCGGCCTCTACCATCG 61.879 65.000 0.00 0.00 0.00 3.84
2914 3622 2.128017 TTGTCGTCGTCGTCGTCG 60.128 61.111 14.18 14.18 46.06 5.12
2915 3623 2.415997 GCTTGTCGTCGTCGTCGTC 61.416 63.158 11.41 6.94 38.33 4.20
2916 3624 2.426425 GCTTGTCGTCGTCGTCGT 60.426 61.111 11.41 0.00 38.33 4.34
2917 3625 2.127345 AGCTTGTCGTCGTCGTCG 60.127 61.111 5.50 5.50 38.33 5.12
2918 3626 2.708059 GCAGCTTGTCGTCGTCGTC 61.708 63.158 1.33 0.00 38.33 4.20
2919 3627 2.729862 GCAGCTTGTCGTCGTCGT 60.730 61.111 1.33 0.00 38.33 4.34
2985 3699 2.186826 ACCTGCACGAAACTGGCAC 61.187 57.895 0.00 0.00 33.34 5.01
3103 3817 1.675641 CTCCCTGCAAAACCCCGAG 60.676 63.158 0.00 0.00 0.00 4.63
3119 3833 2.105466 CCTGCTTCTGCCTTCGCTC 61.105 63.158 0.00 0.00 38.71 5.03
3121 3835 3.130160 CCCTGCTTCTGCCTTCGC 61.130 66.667 0.00 0.00 38.71 4.70
3123 3837 1.676967 CCACCCTGCTTCTGCCTTC 60.677 63.158 0.00 0.00 38.71 3.46
3329 4061 2.564504 CTGTGGAATGGTGAGAGTGAGA 59.435 50.000 0.00 0.00 0.00 3.27
3330 4062 2.564504 TCTGTGGAATGGTGAGAGTGAG 59.435 50.000 0.00 0.00 0.00 3.51
3331 4063 2.608623 TCTGTGGAATGGTGAGAGTGA 58.391 47.619 0.00 0.00 0.00 3.41
3332 4064 3.055602 TGATCTGTGGAATGGTGAGAGTG 60.056 47.826 0.00 0.00 0.00 3.51
3333 4065 3.176411 TGATCTGTGGAATGGTGAGAGT 58.824 45.455 0.00 0.00 0.00 3.24
3334 4066 3.450096 TCTGATCTGTGGAATGGTGAGAG 59.550 47.826 0.00 0.00 0.00 3.20
3352 4084 0.687354 GCTGTTTGAGGGGAGTCTGA 59.313 55.000 0.00 0.00 0.00 3.27
3440 4172 1.411246 CATGGCATTGGAACCATCTGG 59.589 52.381 0.00 0.00 44.97 3.86
3452 4184 1.269448 GTTGTGGTCGTTCATGGCATT 59.731 47.619 0.00 0.00 0.00 3.56
3456 4188 4.635765 AGATATTGTTGTGGTCGTTCATGG 59.364 41.667 0.00 0.00 0.00 3.66
3464 4196 6.019801 GTGATCGTGTAGATATTGTTGTGGTC 60.020 42.308 0.00 0.00 40.26 4.02
3465 4197 5.810587 GTGATCGTGTAGATATTGTTGTGGT 59.189 40.000 0.00 0.00 40.26 4.16
3466 4198 5.810074 TGTGATCGTGTAGATATTGTTGTGG 59.190 40.000 0.00 0.00 40.26 4.17
3500 4232 9.820229 TTGTTAATTTTGACAAGTATAAGAGCG 57.180 29.630 0.00 0.00 32.62 5.03
3513 4245 7.928908 TGCTTGAGATGTTGTTAATTTTGAC 57.071 32.000 0.00 0.00 0.00 3.18
3540 4275 5.819901 GCAGCTACTCTTGATTTGGTAATCT 59.180 40.000 0.00 0.00 40.68 2.40
3544 4279 4.551702 TGCAGCTACTCTTGATTTGGTA 57.448 40.909 0.00 0.00 0.00 3.25
3577 4312 1.475571 CCGACAAGCCCATCATGATCA 60.476 52.381 4.86 0.00 0.00 2.92
3599 4334 1.403514 CCGGTTCTTGTGAGCTCTCTC 60.404 57.143 16.19 6.25 39.78 3.20
3844 4579 2.599645 AATGCCGCCTCCTACTGCTG 62.600 60.000 0.00 0.00 0.00 4.41
3847 4582 0.601311 GCTAATGCCGCCTCCTACTG 60.601 60.000 0.00 0.00 0.00 2.74
3848 4583 0.760945 AGCTAATGCCGCCTCCTACT 60.761 55.000 0.00 0.00 40.80 2.57
3849 4584 0.966920 TAGCTAATGCCGCCTCCTAC 59.033 55.000 0.00 0.00 40.80 3.18
3850 4585 0.966920 GTAGCTAATGCCGCCTCCTA 59.033 55.000 0.00 0.00 40.80 2.94
3851 4586 1.749033 GTAGCTAATGCCGCCTCCT 59.251 57.895 0.00 0.00 40.80 3.69
3852 4587 1.301795 GGTAGCTAATGCCGCCTCC 60.302 63.158 0.00 0.00 40.80 4.30
3869 4604 0.535335 TTCCTCCGTCAGAATTCCGG 59.465 55.000 13.57 13.57 43.03 5.14
3886 4621 2.480802 GGAACTCCGCTTTCTGAAGTTC 59.519 50.000 8.46 8.46 35.25 3.01
3903 4638 3.366781 GCCAAAAAGCATCAGAGAGGAAC 60.367 47.826 0.00 0.00 0.00 3.62
3904 4639 2.821969 GCCAAAAAGCATCAGAGAGGAA 59.178 45.455 0.00 0.00 0.00 3.36
3905 4640 2.440409 GCCAAAAAGCATCAGAGAGGA 58.560 47.619 0.00 0.00 0.00 3.71
3906 4641 1.131883 CGCCAAAAAGCATCAGAGAGG 59.868 52.381 0.00 0.00 0.00 3.69
3907 4642 1.808945 ACGCCAAAAAGCATCAGAGAG 59.191 47.619 0.00 0.00 0.00 3.20
3908 4643 1.536766 CACGCCAAAAAGCATCAGAGA 59.463 47.619 0.00 0.00 0.00 3.10
3909 4644 1.973138 CACGCCAAAAAGCATCAGAG 58.027 50.000 0.00 0.00 0.00 3.35
3910 4645 0.039256 GCACGCCAAAAAGCATCAGA 60.039 50.000 0.00 0.00 0.00 3.27
3921 4656 2.352388 GTCAGGTAATTAGCACGCCAA 58.648 47.619 16.53 0.00 0.00 4.52
3925 4660 0.928229 GCGGTCAGGTAATTAGCACG 59.072 55.000 16.53 14.54 0.00 5.34
3961 4702 3.513515 CCTCCATCCAGCTCTACTATTCC 59.486 52.174 0.00 0.00 0.00 3.01
3991 4732 0.664761 CCATGTTCGGCATCCATGTC 59.335 55.000 0.00 0.00 35.19 3.06
4030 4771 0.528017 TGAACTGCTCGCTCGAGATT 59.472 50.000 18.75 12.23 44.53 2.40
4036 4777 0.456824 TCACGATGAACTGCTCGCTC 60.457 55.000 0.00 0.00 38.42 5.03
4137 4878 9.449719 CCTCTATTACACAACCTTAGAATTTGT 57.550 33.333 0.00 0.00 33.69 2.83
4151 4892 8.783660 AATTCAGTATCTCCCTCTATTACACA 57.216 34.615 0.00 0.00 0.00 3.72
4157 4901 8.875168 CACCTTAAATTCAGTATCTCCCTCTAT 58.125 37.037 0.00 0.00 0.00 1.98
4158 4902 7.290248 CCACCTTAAATTCAGTATCTCCCTCTA 59.710 40.741 0.00 0.00 0.00 2.43
4163 4907 5.437060 TGCCACCTTAAATTCAGTATCTCC 58.563 41.667 0.00 0.00 0.00 3.71
4165 4909 6.156949 TCTCTGCCACCTTAAATTCAGTATCT 59.843 38.462 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.