Multiple sequence alignment - TraesCS5D01G227100

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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 TraesCS5D01G227100 chr5D 100.000 2270 0 0 1 2270 335050696 335048427 0.000000e+00 4193.0
1 TraesCS5D01G227100 chr5D 93.050 518 36 0 1753 2270 292957928 292957411 0.000000e+00 758.0
2 TraesCS5D01G227100 chr5D 91.288 528 45 1 1744 2270 390634067 390633540 0.000000e+00 719.0
3 TraesCS5D01G227100 chr5D 86.667 300 28 10 1137 1430 334974383 334974090 2.810000e-84 322.0
4 TraesCS5D01G227100 chr5B 88.499 1426 87 38 359 1753 391828374 391826995 0.000000e+00 1653.0
5 TraesCS5D01G227100 chr5A 89.897 1168 65 24 236 1381 436331013 436329877 0.000000e+00 1454.0
6 TraesCS5D01G227100 chr5A 83.256 215 15 9 1556 1753 436329867 436329657 6.440000e-41 178.0
7 TraesCS5D01G227100 chr1D 93.103 522 30 2 1754 2270 18443013 18442493 0.000000e+00 760.0
8 TraesCS5D01G227100 chr1D 93.064 519 33 2 1754 2270 433383426 433383943 0.000000e+00 756.0
9 TraesCS5D01G227100 chr1D 91.876 517 41 1 1754 2270 8128674 8128159 0.000000e+00 721.0
10 TraesCS5D01G227100 chr3D 93.204 515 35 0 1756 2270 484438211 484438725 0.000000e+00 758.0
11 TraesCS5D01G227100 chr3D 100.000 29 0 0 130 158 132232300 132232328 1.000000e-03 54.7
12 TraesCS5D01G227100 chr4D 92.678 519 37 1 1753 2270 445329319 445328801 0.000000e+00 747.0
13 TraesCS5D01G227100 chr4B 91.939 521 41 1 1750 2270 59854521 59855040 0.000000e+00 728.0
14 TraesCS5D01G227100 chr7D 91.699 518 42 1 1754 2270 396579971 396579454 0.000000e+00 717.0
15 TraesCS5D01G227100 chr4A 88.462 52 3 3 125 176 631960098 631960050 2.440000e-05 60.2
16 TraesCS5D01G227100 chr4A 97.143 35 1 0 120 154 713467042 713467008 2.440000e-05 60.2
17 TraesCS5D01G227100 chr2A 100.000 28 0 0 131 158 54693904 54693931 4.000000e-03 52.8


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 TraesCS5D01G227100 chr5D 335048427 335050696 2269 True 4193 4193 100.0000 1 2270 1 chr5D.!!$R3 2269
1 TraesCS5D01G227100 chr5D 292957411 292957928 517 True 758 758 93.0500 1753 2270 1 chr5D.!!$R1 517
2 TraesCS5D01G227100 chr5D 390633540 390634067 527 True 719 719 91.2880 1744 2270 1 chr5D.!!$R4 526
3 TraesCS5D01G227100 chr5B 391826995 391828374 1379 True 1653 1653 88.4990 359 1753 1 chr5B.!!$R1 1394
4 TraesCS5D01G227100 chr5A 436329657 436331013 1356 True 816 1454 86.5765 236 1753 2 chr5A.!!$R1 1517
5 TraesCS5D01G227100 chr1D 18442493 18443013 520 True 760 760 93.1030 1754 2270 1 chr1D.!!$R2 516
6 TraesCS5D01G227100 chr1D 433383426 433383943 517 False 756 756 93.0640 1754 2270 1 chr1D.!!$F1 516
7 TraesCS5D01G227100 chr1D 8128159 8128674 515 True 721 721 91.8760 1754 2270 1 chr1D.!!$R1 516
8 TraesCS5D01G227100 chr3D 484438211 484438725 514 False 758 758 93.2040 1756 2270 1 chr3D.!!$F2 514
9 TraesCS5D01G227100 chr4D 445328801 445329319 518 True 747 747 92.6780 1753 2270 1 chr4D.!!$R1 517
10 TraesCS5D01G227100 chr4B 59854521 59855040 519 False 728 728 91.9390 1750 2270 1 chr4B.!!$F1 520
11 TraesCS5D01G227100 chr7D 396579454 396579971 517 True 717 717 91.6990 1754 2270 1 chr7D.!!$R1 516

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
74 75 0.032952 AAACAGCGAGGCAACGTAGA 59.967 50.0 0.0 0.0 46.39 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1503 1536 0.389426 CGGGGTCATCTTTCGTCGTT 60.389 55.0 0.0 0.0 0.0 3.85 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
38 39 6.862944 GCTAAATTATCTAGCTCGCTACAG 57.137 41.667 0.00 0.00 38.99 2.74
39 40 6.613233 GCTAAATTATCTAGCTCGCTACAGA 58.387 40.000 0.00 0.00 38.99 3.41
40 41 6.525280 GCTAAATTATCTAGCTCGCTACAGAC 59.475 42.308 0.00 0.00 38.99 3.51
41 42 6.392625 AAATTATCTAGCTCGCTACAGACA 57.607 37.500 0.00 0.00 0.00 3.41
42 43 6.582677 AATTATCTAGCTCGCTACAGACAT 57.417 37.500 0.00 0.00 0.00 3.06
43 44 6.582677 ATTATCTAGCTCGCTACAGACATT 57.417 37.500 0.00 0.00 0.00 2.71
44 45 7.689446 ATTATCTAGCTCGCTACAGACATTA 57.311 36.000 0.00 0.00 0.00 1.90
45 46 7.506328 TTATCTAGCTCGCTACAGACATTAA 57.494 36.000 0.00 0.00 0.00 1.40
46 47 5.425577 TCTAGCTCGCTACAGACATTAAG 57.574 43.478 0.00 0.00 0.00 1.85
47 48 2.815478 AGCTCGCTACAGACATTAAGC 58.185 47.619 0.00 0.00 0.00 3.09
48 49 1.861575 GCTCGCTACAGACATTAAGCC 59.138 52.381 0.00 0.00 0.00 4.35
49 50 2.474816 CTCGCTACAGACATTAAGCCC 58.525 52.381 0.00 0.00 0.00 5.19
50 51 2.101582 CTCGCTACAGACATTAAGCCCT 59.898 50.000 0.00 0.00 0.00 5.19
51 52 2.159099 TCGCTACAGACATTAAGCCCTG 60.159 50.000 0.00 0.00 0.00 4.45
52 53 2.565841 GCTACAGACATTAAGCCCTGG 58.434 52.381 0.00 0.00 0.00 4.45
53 54 2.565841 CTACAGACATTAAGCCCTGGC 58.434 52.381 0.00 0.00 42.33 4.85
54 55 0.698238 ACAGACATTAAGCCCTGGCA 59.302 50.000 11.38 0.00 44.88 4.92
55 56 1.075374 ACAGACATTAAGCCCTGGCAA 59.925 47.619 11.38 0.00 44.88 4.52
56 57 2.170166 CAGACATTAAGCCCTGGCAAA 58.830 47.619 11.38 4.72 44.88 3.68
57 58 2.562298 CAGACATTAAGCCCTGGCAAAA 59.438 45.455 11.38 4.35 44.88 2.44
58 59 2.562738 AGACATTAAGCCCTGGCAAAAC 59.437 45.455 11.38 1.83 44.88 2.43
59 60 2.298729 GACATTAAGCCCTGGCAAAACA 59.701 45.455 11.38 0.00 44.88 2.83
60 61 2.299867 ACATTAAGCCCTGGCAAAACAG 59.700 45.455 11.38 3.68 44.88 3.16
61 62 0.678950 TTAAGCCCTGGCAAAACAGC 59.321 50.000 11.38 0.00 44.88 4.40
62 63 1.523154 TAAGCCCTGGCAAAACAGCG 61.523 55.000 11.38 0.00 44.88 5.18
63 64 3.294493 GCCCTGGCAAAACAGCGA 61.294 61.111 2.58 0.00 41.49 4.93
64 65 2.956987 CCCTGGCAAAACAGCGAG 59.043 61.111 0.00 0.00 39.68 5.03
66 67 2.256461 CTGGCAAAACAGCGAGGC 59.744 61.111 0.00 0.00 36.80 4.70
67 68 2.518112 TGGCAAAACAGCGAGGCA 60.518 55.556 0.00 0.00 34.64 4.75
68 69 2.074230 CTGGCAAAACAGCGAGGCAA 62.074 55.000 0.00 0.00 36.80 4.52
69 70 1.661509 GGCAAAACAGCGAGGCAAC 60.662 57.895 0.00 0.00 34.64 4.17
70 71 2.010817 GCAAAACAGCGAGGCAACG 61.011 57.895 0.00 0.08 46.39 4.10
71 72 1.355210 CAAAACAGCGAGGCAACGT 59.645 52.632 6.06 0.00 46.39 3.99
72 73 0.584396 CAAAACAGCGAGGCAACGTA 59.416 50.000 0.00 0.00 46.39 3.57
73 74 0.865769 AAAACAGCGAGGCAACGTAG 59.134 50.000 0.00 2.38 46.39 3.51
74 75 0.032952 AAACAGCGAGGCAACGTAGA 59.967 50.000 0.00 0.00 46.39 2.59
75 76 0.666577 AACAGCGAGGCAACGTAGAC 60.667 55.000 0.00 0.00 46.39 2.59
76 77 1.080772 CAGCGAGGCAACGTAGACA 60.081 57.895 0.00 0.00 46.39 3.41
77 78 1.073216 CAGCGAGGCAACGTAGACAG 61.073 60.000 0.00 0.00 46.39 3.51
78 79 1.211969 GCGAGGCAACGTAGACAGA 59.788 57.895 0.00 0.00 46.39 3.41
79 80 1.071567 GCGAGGCAACGTAGACAGAC 61.072 60.000 0.00 0.00 46.39 3.51
80 81 0.240145 CGAGGCAACGTAGACAGACA 59.760 55.000 0.00 0.00 46.39 3.41
81 82 1.135373 CGAGGCAACGTAGACAGACAT 60.135 52.381 0.00 0.00 46.39 3.06
82 83 2.531206 GAGGCAACGTAGACAGACATC 58.469 52.381 0.00 0.00 46.39 3.06
83 84 1.893137 AGGCAACGTAGACAGACATCA 59.107 47.619 0.00 0.00 46.39 3.07
84 85 2.497675 AGGCAACGTAGACAGACATCAT 59.502 45.455 0.00 0.00 46.39 2.45
85 86 2.604914 GGCAACGTAGACAGACATCATG 59.395 50.000 0.00 0.00 0.00 3.07
86 87 3.254060 GCAACGTAGACAGACATCATGT 58.746 45.455 0.00 0.00 0.00 3.21
87 88 4.421058 GCAACGTAGACAGACATCATGTA 58.579 43.478 0.00 0.00 0.00 2.29
88 89 4.862574 GCAACGTAGACAGACATCATGTAA 59.137 41.667 0.00 0.00 0.00 2.41
89 90 5.520288 GCAACGTAGACAGACATCATGTAAT 59.480 40.000 0.00 0.00 0.00 1.89
91 92 5.592054 ACGTAGACAGACATCATGTAATGG 58.408 41.667 7.26 0.00 46.73 3.16
92 93 4.984785 CGTAGACAGACATCATGTAATGGG 59.015 45.833 7.26 0.00 46.73 4.00
93 94 5.221244 CGTAGACAGACATCATGTAATGGGA 60.221 44.000 7.26 0.00 46.73 4.37
94 95 5.901413 AGACAGACATCATGTAATGGGAT 57.099 39.130 7.26 0.00 46.73 3.85
95 96 7.309194 CGTAGACAGACATCATGTAATGGGATA 60.309 40.741 7.26 0.00 46.73 2.59
96 97 7.565190 AGACAGACATCATGTAATGGGATAT 57.435 36.000 7.26 0.00 46.73 1.63
97 98 7.982252 AGACAGACATCATGTAATGGGATATT 58.018 34.615 7.26 0.00 46.73 1.28
98 99 8.443176 AGACAGACATCATGTAATGGGATATTT 58.557 33.333 7.26 0.00 46.73 1.40
99 100 9.071276 GACAGACATCATGTAATGGGATATTTT 57.929 33.333 7.26 0.00 46.73 1.82
100 101 9.425248 ACAGACATCATGTAATGGGATATTTTT 57.575 29.630 7.26 0.00 46.73 1.94
114 115 8.584063 TGGGATATTTTTAACAAGTTACTCCC 57.416 34.615 0.00 0.00 38.32 4.30
115 116 8.395605 TGGGATATTTTTAACAAGTTACTCCCT 58.604 33.333 0.00 0.00 38.58 4.20
116 117 8.900781 GGGATATTTTTAACAAGTTACTCCCTC 58.099 37.037 0.00 0.00 35.59 4.30
117 118 9.682465 GGATATTTTTAACAAGTTACTCCCTCT 57.318 33.333 0.00 0.00 0.00 3.69
121 122 8.617290 TTTTTAACAAGTTACTCCCTCTGATC 57.383 34.615 0.00 0.00 0.00 2.92
122 123 4.828072 AACAAGTTACTCCCTCTGATCC 57.172 45.455 0.00 0.00 0.00 3.36
123 124 3.791320 ACAAGTTACTCCCTCTGATCCA 58.209 45.455 0.00 0.00 0.00 3.41
124 125 4.366267 ACAAGTTACTCCCTCTGATCCAT 58.634 43.478 0.00 0.00 0.00 3.41
125 126 5.529289 ACAAGTTACTCCCTCTGATCCATA 58.471 41.667 0.00 0.00 0.00 2.74
126 127 5.364157 ACAAGTTACTCCCTCTGATCCATAC 59.636 44.000 0.00 0.00 0.00 2.39
127 128 5.144159 AGTTACTCCCTCTGATCCATACA 57.856 43.478 0.00 0.00 0.00 2.29
128 129 5.529289 AGTTACTCCCTCTGATCCATACAA 58.471 41.667 0.00 0.00 0.00 2.41
129 130 5.964477 AGTTACTCCCTCTGATCCATACAAA 59.036 40.000 0.00 0.00 0.00 2.83
130 131 6.098982 AGTTACTCCCTCTGATCCATACAAAG 59.901 42.308 0.00 0.00 0.00 2.77
131 132 4.366267 ACTCCCTCTGATCCATACAAAGT 58.634 43.478 0.00 0.00 0.00 2.66
132 133 4.785376 ACTCCCTCTGATCCATACAAAGTT 59.215 41.667 0.00 0.00 0.00 2.66
133 134 5.102953 TCCCTCTGATCCATACAAAGTTG 57.897 43.478 0.00 0.00 0.00 3.16
134 135 4.536090 TCCCTCTGATCCATACAAAGTTGT 59.464 41.667 1.75 1.75 44.86 3.32
135 136 5.724370 TCCCTCTGATCCATACAAAGTTGTA 59.276 40.000 6.37 6.37 46.55 2.41
136 137 5.817816 CCCTCTGATCCATACAAAGTTGTAC 59.182 44.000 6.05 0.00 45.47 2.90
137 138 6.352222 CCCTCTGATCCATACAAAGTTGTACT 60.352 42.308 6.05 0.00 45.47 2.73
138 139 7.147724 CCCTCTGATCCATACAAAGTTGTACTA 60.148 40.741 6.05 0.00 45.47 1.82
139 140 8.258007 CCTCTGATCCATACAAAGTTGTACTAA 58.742 37.037 6.05 0.00 45.47 2.24
140 141 9.653287 CTCTGATCCATACAAAGTTGTACTAAA 57.347 33.333 6.05 0.00 45.47 1.85
143 144 9.952030 TGATCCATACAAAGTTGTACTAAATCA 57.048 29.630 6.05 9.87 45.47 2.57
146 147 8.714179 TCCATACAAAGTTGTACTAAATCAACG 58.286 33.333 6.05 0.00 45.47 4.10
147 148 8.714179 CCATACAAAGTTGTACTAAATCAACGA 58.286 33.333 6.05 0.00 45.47 3.85
148 149 9.525007 CATACAAAGTTGTACTAAATCAACGAC 57.475 33.333 6.05 0.00 45.47 4.34
149 150 7.542534 ACAAAGTTGTACTAAATCAACGACA 57.457 32.000 0.00 0.00 45.56 4.35
150 151 7.627340 ACAAAGTTGTACTAAATCAACGACAG 58.373 34.615 0.00 0.00 45.56 3.51
151 152 7.279313 ACAAAGTTGTACTAAATCAACGACAGT 59.721 33.333 0.00 0.00 45.56 3.55
152 153 7.781548 AAGTTGTACTAAATCAACGACAGTT 57.218 32.000 0.00 0.00 45.56 3.16
153 154 8.876275 AAGTTGTACTAAATCAACGACAGTTA 57.124 30.769 0.00 0.00 45.56 2.24
154 155 8.876275 AGTTGTACTAAATCAACGACAGTTAA 57.124 30.769 0.00 0.00 45.56 2.01
155 156 9.485206 AGTTGTACTAAATCAACGACAGTTAAT 57.515 29.630 0.00 0.00 45.56 1.40
163 164 8.706492 AAATCAACGACAGTTAATATTACGGA 57.294 30.769 0.00 0.00 38.79 4.69
164 165 8.882415 AATCAACGACAGTTAATATTACGGAT 57.118 30.769 0.00 0.00 38.79 4.18
165 166 7.919313 TCAACGACAGTTAATATTACGGATC 57.081 36.000 0.00 0.00 38.79 3.36
166 167 6.634035 TCAACGACAGTTAATATTACGGATCG 59.366 38.462 13.06 13.06 38.79 3.69
167 168 5.455392 ACGACAGTTAATATTACGGATCGG 58.545 41.667 16.55 0.00 0.00 4.18
168 169 5.239306 ACGACAGTTAATATTACGGATCGGA 59.761 40.000 7.35 0.00 0.00 4.55
169 170 5.793952 CGACAGTTAATATTACGGATCGGAG 59.206 44.000 7.35 0.00 0.00 4.63
170 171 6.022163 ACAGTTAATATTACGGATCGGAGG 57.978 41.667 7.35 0.00 0.00 4.30
171 172 5.047519 ACAGTTAATATTACGGATCGGAGGG 60.048 44.000 7.35 0.00 0.00 4.30
172 173 5.184479 CAGTTAATATTACGGATCGGAGGGA 59.816 44.000 7.35 0.00 0.00 4.20
173 174 5.418209 AGTTAATATTACGGATCGGAGGGAG 59.582 44.000 7.35 0.00 0.00 4.30
174 175 2.965671 TATTACGGATCGGAGGGAGT 57.034 50.000 7.35 0.00 0.00 3.85
175 176 2.965671 ATTACGGATCGGAGGGAGTA 57.034 50.000 7.35 0.00 0.00 2.59
176 177 2.734755 TTACGGATCGGAGGGAGTAA 57.265 50.000 7.35 0.00 0.00 2.24
177 178 2.965671 TACGGATCGGAGGGAGTAAT 57.034 50.000 7.35 0.00 0.00 1.89
178 179 2.083628 ACGGATCGGAGGGAGTAATT 57.916 50.000 7.35 0.00 0.00 1.40
179 180 2.395619 ACGGATCGGAGGGAGTAATTT 58.604 47.619 7.35 0.00 0.00 1.82
180 181 2.102588 ACGGATCGGAGGGAGTAATTTG 59.897 50.000 7.35 0.00 0.00 2.32
181 182 2.102588 CGGATCGGAGGGAGTAATTTGT 59.897 50.000 0.00 0.00 0.00 2.83
182 183 3.431766 CGGATCGGAGGGAGTAATTTGTT 60.432 47.826 0.00 0.00 0.00 2.83
183 184 4.202182 CGGATCGGAGGGAGTAATTTGTTA 60.202 45.833 0.00 0.00 0.00 2.41
184 185 5.510861 CGGATCGGAGGGAGTAATTTGTTAT 60.511 44.000 0.00 0.00 0.00 1.89
185 186 5.932883 GGATCGGAGGGAGTAATTTGTTATC 59.067 44.000 0.00 0.00 0.00 1.75
186 187 6.239629 GGATCGGAGGGAGTAATTTGTTATCT 60.240 42.308 0.00 0.00 0.00 1.98
187 188 7.039223 GGATCGGAGGGAGTAATTTGTTATCTA 60.039 40.741 0.00 0.00 0.00 1.98
188 189 7.047460 TCGGAGGGAGTAATTTGTTATCTAC 57.953 40.000 0.00 0.00 0.00 2.59
189 190 6.837568 TCGGAGGGAGTAATTTGTTATCTACT 59.162 38.462 0.00 0.00 0.00 2.57
190 191 7.014038 TCGGAGGGAGTAATTTGTTATCTACTC 59.986 40.741 0.00 0.00 39.60 2.59
217 218 3.502191 TTTTGGAAACACAGTGCAGAC 57.498 42.857 0.00 0.00 42.67 3.51
218 219 1.388547 TTGGAAACACAGTGCAGACC 58.611 50.000 0.00 0.23 42.67 3.85
219 220 0.465460 TGGAAACACAGTGCAGACCC 60.465 55.000 0.00 0.00 33.40 4.46
220 221 0.465460 GGAAACACAGTGCAGACCCA 60.465 55.000 0.00 0.00 0.00 4.51
221 222 1.609208 GAAACACAGTGCAGACCCAT 58.391 50.000 0.00 0.00 0.00 4.00
222 223 1.267806 GAAACACAGTGCAGACCCATG 59.732 52.381 0.00 0.00 0.00 3.66
223 224 1.174712 AACACAGTGCAGACCCATGC 61.175 55.000 0.00 0.00 46.68 4.06
229 230 3.583383 GCAGACCCATGCACTCAC 58.417 61.111 0.00 0.00 45.77 3.51
230 231 1.302752 GCAGACCCATGCACTCACA 60.303 57.895 0.00 0.00 45.77 3.58
231 232 0.679002 GCAGACCCATGCACTCACAT 60.679 55.000 0.00 0.00 45.77 3.21
232 233 1.407299 GCAGACCCATGCACTCACATA 60.407 52.381 0.00 0.00 45.77 2.29
233 234 2.283298 CAGACCCATGCACTCACATAC 58.717 52.381 0.00 0.00 0.00 2.39
234 235 1.134699 AGACCCATGCACTCACATACG 60.135 52.381 0.00 0.00 0.00 3.06
238 239 1.935873 CCATGCACTCACATACGAAGG 59.064 52.381 0.00 0.00 0.00 3.46
255 256 5.831997 ACGAAGGCAATTAGATTTAATGCC 58.168 37.500 15.56 15.56 40.24 4.40
260 261 6.809869 AGGCAATTAGATTTAATGCCAGTTC 58.190 36.000 20.95 4.97 41.20 3.01
263 264 6.183360 GCAATTAGATTTAATGCCAGTTCCCT 60.183 38.462 0.00 0.00 30.00 4.20
264 265 7.428826 CAATTAGATTTAATGCCAGTTCCCTC 58.571 38.462 0.00 0.00 30.00 4.30
265 266 4.870021 AGATTTAATGCCAGTTCCCTCT 57.130 40.909 0.00 0.00 0.00 3.69
268 269 6.731467 AGATTTAATGCCAGTTCCCTCTTTA 58.269 36.000 0.00 0.00 0.00 1.85
270 271 6.584185 TTTAATGCCAGTTCCCTCTTTAAC 57.416 37.500 0.00 0.00 0.00 2.01
283 288 6.610830 TCCCTCTTTAACCTCAACAAAGAAT 58.389 36.000 0.00 0.00 37.72 2.40
310 315 2.230508 AGATGTGCTGCATGGAAAAGTG 59.769 45.455 5.27 0.00 38.06 3.16
311 316 1.401761 TGTGCTGCATGGAAAAGTGT 58.598 45.000 5.27 0.00 0.00 3.55
348 353 9.777843 CTTGTAAAGTTGCATTTCGATTTTTAC 57.222 29.630 0.00 0.00 39.70 2.01
349 354 7.987486 TGTAAAGTTGCATTTCGATTTTTACG 58.013 30.769 0.00 0.00 0.00 3.18
350 355 7.644551 TGTAAAGTTGCATTTCGATTTTTACGT 59.355 29.630 0.00 0.00 0.00 3.57
351 356 6.669485 AAGTTGCATTTCGATTTTTACGTC 57.331 33.333 0.00 0.00 0.00 4.34
352 357 5.753744 AGTTGCATTTCGATTTTTACGTCA 58.246 33.333 0.00 0.00 0.00 4.35
353 358 6.202937 AGTTGCATTTCGATTTTTACGTCAA 58.797 32.000 0.00 0.00 0.00 3.18
354 359 6.693545 AGTTGCATTTCGATTTTTACGTCAAA 59.306 30.769 0.00 0.00 0.00 2.69
355 360 7.221067 AGTTGCATTTCGATTTTTACGTCAAAA 59.779 29.630 9.87 9.87 34.26 2.44
388 398 5.062558 GCATTTCGATTTAAAGCATGCAACT 59.937 36.000 21.98 5.92 33.25 3.16
435 445 7.222224 GTCCGAACTAGTTGACCTTTACATATG 59.778 40.741 14.14 0.00 0.00 1.78
436 446 7.039882 CCGAACTAGTTGACCTTTACATATGT 58.960 38.462 14.14 13.93 0.00 2.29
521 537 6.633325 TCCTCATCTTTTCTCCTTTGATCT 57.367 37.500 0.00 0.00 0.00 2.75
548 564 3.181472 CCTTTTTCACTTTTGCTCCTGCT 60.181 43.478 0.00 0.00 40.48 4.24
625 641 3.054139 TCTTGCTAATCATGCCCTTCAGT 60.054 43.478 0.00 0.00 0.00 3.41
663 679 0.104855 AGCTTGCGCTAATGGATCGA 59.895 50.000 9.73 0.00 46.79 3.59
705 723 0.472471 TTTCCCGTGCAACTTCCTCT 59.528 50.000 0.00 0.00 31.75 3.69
730 748 2.047844 CTCCCGTGCACTGACTGG 60.048 66.667 16.19 8.04 0.00 4.00
740 758 1.598130 ACTGACTGGCCGTTTCAGC 60.598 57.895 21.95 3.14 40.46 4.26
752 774 3.002791 CCGTTTCAGCAGCATCTCTTTA 58.997 45.455 0.00 0.00 0.00 1.85
790 812 8.677148 TTGCAACTAGTATCTTTTTCTGTTCT 57.323 30.769 0.00 0.00 0.00 3.01
864 886 2.932167 GATCCGTTATCGCTTGAAGC 57.068 50.000 7.20 7.20 38.02 3.86
903 925 3.190079 CTGGTAGAGTAGTGCGTACGTA 58.810 50.000 17.90 10.06 36.66 3.57
906 928 3.370978 GGTAGAGTAGTGCGTACGTACAA 59.629 47.826 32.81 10.04 36.66 2.41
946 970 5.007626 TCACATCCGTTCTTTGTTCTTTGAG 59.992 40.000 0.00 0.00 0.00 3.02
964 995 6.535150 TCTTTGAGTTGAGTTGACACTTGTAG 59.465 38.462 0.00 0.00 31.22 2.74
980 1011 6.151144 ACACTTGTAGCTCTGTTTGTTTTTCT 59.849 34.615 0.00 0.00 0.00 2.52
1018 1050 1.821136 GCATGGGTTTTCAGAGGAAGG 59.179 52.381 0.00 0.00 33.82 3.46
1285 1317 1.002792 GTTGACGAGCCACCTTGTTTC 60.003 52.381 0.00 0.00 35.80 2.78
1327 1360 7.817910 TTAGTTACAGAAGAGGGGGATTTTA 57.182 36.000 0.00 0.00 0.00 1.52
1457 1490 8.754080 ACAGTAATTATCACTGAAACTAGAGCT 58.246 33.333 12.70 0.00 45.10 4.09
1471 1504 1.896220 AGAGCTGTTCAAATCGGCAA 58.104 45.000 0.00 0.00 39.38 4.52
1479 1512 1.909700 TCAAATCGGCAAAGGCTCTT 58.090 45.000 0.00 0.00 40.87 2.85
1516 1549 4.904724 CGTATCTCCTAACGACGAAAGATG 59.095 45.833 0.00 0.00 41.55 2.90
1559 1592 2.270047 GAGCTGATCTGCACTCTGAAC 58.730 52.381 24.33 4.08 34.99 3.18
1564 1597 2.038164 TGATCTGCACTCTGAACAGCTT 59.962 45.455 0.00 0.00 0.00 3.74
1568 1601 0.039708 GCACTCTGAACAGCTTTGCC 60.040 55.000 9.39 0.00 0.00 4.52
1609 1642 0.867746 CAACAGTCACCCGTGTCATG 59.132 55.000 0.00 0.00 0.00 3.07
1610 1643 0.468226 AACAGTCACCCGTGTCATGT 59.532 50.000 0.00 0.00 0.00 3.21
1615 1652 0.250124 TCACCCGTGTCATGTCCAAC 60.250 55.000 0.00 0.00 0.00 3.77
1645 1682 2.638719 GCATGCAGTGCGTCAACA 59.361 55.556 14.21 0.00 45.23 3.33
1646 1683 1.441515 GCATGCAGTGCGTCAACAG 60.442 57.895 14.21 0.00 45.23 3.16
1648 1685 1.893335 ATGCAGTGCGTCAACAGCA 60.893 52.632 11.20 7.35 45.12 4.41
1736 1786 7.973944 GGTAAGGTCTTAATTTGTAAGGCATTG 59.026 37.037 7.62 0.00 34.63 2.82
1760 1810 5.749109 GGATCAAGAAACGTATGTGTAGAGG 59.251 44.000 0.00 0.00 0.00 3.69
1768 1818 8.692710 AGAAACGTATGTGTAGAGGATGATTTA 58.307 33.333 0.00 0.00 0.00 1.40
1796 1846 6.540205 CATCGATAATTGATTGATCGTGCAT 58.460 36.000 0.00 0.00 42.37 3.96
1830 1881 0.251922 TAGGTACAAGGGGTGCGACT 60.252 55.000 0.00 0.00 32.16 4.18
1920 1971 3.635373 ACCCAGACCTACATACATGTACG 59.365 47.826 7.96 1.73 41.97 3.67
1921 1972 3.005472 CCCAGACCTACATACATGTACGG 59.995 52.174 7.96 8.96 41.97 4.02
2119 2177 2.799562 CGAGCTCAATATGCTTCGTCCA 60.800 50.000 15.40 0.00 41.30 4.02
2122 2180 3.133691 GCTCAATATGCTTCGTCCATCA 58.866 45.455 0.00 0.00 0.00 3.07
2147 2206 3.240134 GACAGGGTTGGCAGCGAGA 62.240 63.158 0.00 0.00 30.39 4.04
2153 2212 0.108138 GGTTGGCAGCGAGATACACT 60.108 55.000 0.00 0.00 0.00 3.55
2200 2259 1.740296 CCGCCTTGGTAACCTCACG 60.740 63.158 0.00 0.00 0.00 4.35
2201 2260 1.740296 CGCCTTGGTAACCTCACGG 60.740 63.158 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.525280 GTCTGTAGCGAGCTAGATAATTTAGC 59.475 42.308 4.89 0.17 42.99 3.09
16 17 7.585867 TGTCTGTAGCGAGCTAGATAATTTAG 58.414 38.462 4.89 0.00 0.00 1.85
17 18 7.506328 TGTCTGTAGCGAGCTAGATAATTTA 57.494 36.000 4.89 0.00 0.00 1.40
18 19 6.392625 TGTCTGTAGCGAGCTAGATAATTT 57.607 37.500 4.89 0.00 0.00 1.82
19 20 6.582677 ATGTCTGTAGCGAGCTAGATAATT 57.417 37.500 4.89 0.00 0.00 1.40
20 21 6.582677 AATGTCTGTAGCGAGCTAGATAAT 57.417 37.500 4.89 0.00 0.00 1.28
21 22 7.506328 TTAATGTCTGTAGCGAGCTAGATAA 57.494 36.000 4.89 0.00 0.00 1.75
22 23 6.348622 GCTTAATGTCTGTAGCGAGCTAGATA 60.349 42.308 4.89 1.19 0.00 1.98
23 24 5.563867 GCTTAATGTCTGTAGCGAGCTAGAT 60.564 44.000 4.89 0.00 0.00 1.98
24 25 4.261238 GCTTAATGTCTGTAGCGAGCTAGA 60.261 45.833 4.89 3.34 0.00 2.43
25 26 3.978217 GCTTAATGTCTGTAGCGAGCTAG 59.022 47.826 4.89 0.00 0.00 3.42
26 27 3.243434 GGCTTAATGTCTGTAGCGAGCTA 60.243 47.826 0.00 0.00 34.50 3.32
27 28 2.482142 GGCTTAATGTCTGTAGCGAGCT 60.482 50.000 2.25 2.25 34.50 4.09
28 29 1.861575 GGCTTAATGTCTGTAGCGAGC 59.138 52.381 0.00 0.00 34.50 5.03
29 30 2.101582 AGGGCTTAATGTCTGTAGCGAG 59.898 50.000 0.00 0.00 34.50 5.03
30 31 2.108168 AGGGCTTAATGTCTGTAGCGA 58.892 47.619 0.00 0.00 34.50 4.93
31 32 2.205074 CAGGGCTTAATGTCTGTAGCG 58.795 52.381 0.00 0.00 34.50 4.26
32 33 2.565841 CCAGGGCTTAATGTCTGTAGC 58.434 52.381 0.00 0.00 0.00 3.58
33 34 2.092968 TGCCAGGGCTTAATGTCTGTAG 60.093 50.000 12.19 0.00 42.51 2.74
34 35 1.912731 TGCCAGGGCTTAATGTCTGTA 59.087 47.619 12.19 0.00 42.51 2.74
35 36 0.698238 TGCCAGGGCTTAATGTCTGT 59.302 50.000 12.19 0.00 42.51 3.41
36 37 1.838112 TTGCCAGGGCTTAATGTCTG 58.162 50.000 12.19 0.00 42.51 3.51
37 38 2.562738 GTTTTGCCAGGGCTTAATGTCT 59.437 45.455 12.19 0.00 42.51 3.41
38 39 2.298729 TGTTTTGCCAGGGCTTAATGTC 59.701 45.455 12.19 1.96 42.51 3.06
39 40 2.299867 CTGTTTTGCCAGGGCTTAATGT 59.700 45.455 12.19 0.00 42.51 2.71
40 41 2.932187 GCTGTTTTGCCAGGGCTTAATG 60.932 50.000 12.19 4.77 42.51 1.90
41 42 1.276138 GCTGTTTTGCCAGGGCTTAAT 59.724 47.619 12.19 0.00 42.51 1.40
42 43 0.678950 GCTGTTTTGCCAGGGCTTAA 59.321 50.000 12.19 3.26 42.51 1.85
43 44 1.523154 CGCTGTTTTGCCAGGGCTTA 61.523 55.000 12.19 0.00 42.51 3.09
44 45 2.859981 CGCTGTTTTGCCAGGGCTT 61.860 57.895 12.19 0.00 42.51 4.35
45 46 3.297620 CGCTGTTTTGCCAGGGCT 61.298 61.111 12.19 0.00 42.51 5.19
46 47 3.273080 CTCGCTGTTTTGCCAGGGC 62.273 63.158 2.62 2.62 43.10 5.19
47 48 2.629656 CCTCGCTGTTTTGCCAGGG 61.630 63.158 0.00 0.00 44.34 4.45
48 49 2.956987 CCTCGCTGTTTTGCCAGG 59.043 61.111 0.00 0.00 35.20 4.45
49 50 2.074230 TTGCCTCGCTGTTTTGCCAG 62.074 55.000 0.00 0.00 35.49 4.85
50 51 2.124060 TTGCCTCGCTGTTTTGCCA 61.124 52.632 0.00 0.00 0.00 4.92
51 52 1.661509 GTTGCCTCGCTGTTTTGCC 60.662 57.895 0.00 0.00 0.00 4.52
52 53 2.010817 CGTTGCCTCGCTGTTTTGC 61.011 57.895 0.00 0.00 0.00 3.68
53 54 0.584396 TACGTTGCCTCGCTGTTTTG 59.416 50.000 0.00 0.00 0.00 2.44
54 55 0.865769 CTACGTTGCCTCGCTGTTTT 59.134 50.000 0.00 0.00 0.00 2.43
55 56 0.032952 TCTACGTTGCCTCGCTGTTT 59.967 50.000 0.00 0.00 0.00 2.83
56 57 0.666577 GTCTACGTTGCCTCGCTGTT 60.667 55.000 0.00 0.00 0.00 3.16
57 58 1.080705 GTCTACGTTGCCTCGCTGT 60.081 57.895 0.00 0.00 0.00 4.40
58 59 1.073216 CTGTCTACGTTGCCTCGCTG 61.073 60.000 0.00 0.00 0.00 5.18
59 60 1.213013 CTGTCTACGTTGCCTCGCT 59.787 57.895 0.00 0.00 0.00 4.93
60 61 1.071567 GTCTGTCTACGTTGCCTCGC 61.072 60.000 0.00 0.00 0.00 5.03
61 62 0.240145 TGTCTGTCTACGTTGCCTCG 59.760 55.000 0.00 0.00 0.00 4.63
62 63 2.094700 TGATGTCTGTCTACGTTGCCTC 60.095 50.000 0.00 0.00 0.00 4.70
63 64 1.893137 TGATGTCTGTCTACGTTGCCT 59.107 47.619 0.00 0.00 0.00 4.75
64 65 2.363788 TGATGTCTGTCTACGTTGCC 57.636 50.000 0.00 0.00 0.00 4.52
65 66 3.254060 ACATGATGTCTGTCTACGTTGC 58.746 45.455 0.00 0.00 0.00 4.17
66 67 6.019559 CCATTACATGATGTCTGTCTACGTTG 60.020 42.308 0.00 0.00 0.00 4.10
67 68 6.042777 CCATTACATGATGTCTGTCTACGTT 58.957 40.000 0.00 0.00 0.00 3.99
68 69 5.451937 CCCATTACATGATGTCTGTCTACGT 60.452 44.000 0.00 0.00 0.00 3.57
69 70 4.984785 CCCATTACATGATGTCTGTCTACG 59.015 45.833 0.00 0.00 0.00 3.51
70 71 6.161855 TCCCATTACATGATGTCTGTCTAC 57.838 41.667 0.00 0.00 0.00 2.59
71 72 8.670521 ATATCCCATTACATGATGTCTGTCTA 57.329 34.615 0.00 0.00 0.00 2.59
72 73 5.901413 ATCCCATTACATGATGTCTGTCT 57.099 39.130 0.00 0.00 0.00 3.41
73 74 8.627208 AAATATCCCATTACATGATGTCTGTC 57.373 34.615 0.00 0.00 0.00 3.51
74 75 9.425248 AAAAATATCCCATTACATGATGTCTGT 57.575 29.630 0.00 0.00 0.00 3.41
88 89 9.197306 GGGAGTAACTTGTTAAAAATATCCCAT 57.803 33.333 0.00 0.00 40.99 4.00
89 90 8.395605 AGGGAGTAACTTGTTAAAAATATCCCA 58.604 33.333 17.42 0.00 43.25 4.37
90 91 8.818622 AGGGAGTAACTTGTTAAAAATATCCC 57.181 34.615 0.00 0.00 41.51 3.85
91 92 9.682465 AGAGGGAGTAACTTGTTAAAAATATCC 57.318 33.333 0.00 0.00 0.00 2.59
95 96 9.232473 GATCAGAGGGAGTAACTTGTTAAAAAT 57.768 33.333 0.00 0.00 0.00 1.82
96 97 7.664318 GGATCAGAGGGAGTAACTTGTTAAAAA 59.336 37.037 0.00 0.00 0.00 1.94
97 98 7.166167 GGATCAGAGGGAGTAACTTGTTAAAA 58.834 38.462 0.00 0.00 0.00 1.52
98 99 6.271391 TGGATCAGAGGGAGTAACTTGTTAAA 59.729 38.462 0.00 0.00 0.00 1.52
99 100 5.783360 TGGATCAGAGGGAGTAACTTGTTAA 59.217 40.000 0.00 0.00 0.00 2.01
100 101 5.338632 TGGATCAGAGGGAGTAACTTGTTA 58.661 41.667 0.00 0.00 0.00 2.41
101 102 4.168101 TGGATCAGAGGGAGTAACTTGTT 58.832 43.478 0.00 0.00 0.00 2.83
102 103 3.791320 TGGATCAGAGGGAGTAACTTGT 58.209 45.455 0.00 0.00 0.00 3.16
103 104 5.363868 TGTATGGATCAGAGGGAGTAACTTG 59.636 44.000 0.00 0.00 0.00 3.16
104 105 5.529289 TGTATGGATCAGAGGGAGTAACTT 58.471 41.667 0.00 0.00 0.00 2.66
105 106 5.144159 TGTATGGATCAGAGGGAGTAACT 57.856 43.478 0.00 0.00 0.00 2.24
106 107 5.871396 TTGTATGGATCAGAGGGAGTAAC 57.129 43.478 0.00 0.00 0.00 2.50
107 108 5.964477 ACTTTGTATGGATCAGAGGGAGTAA 59.036 40.000 0.00 0.00 0.00 2.24
108 109 5.529289 ACTTTGTATGGATCAGAGGGAGTA 58.471 41.667 0.00 0.00 0.00 2.59
109 110 4.366267 ACTTTGTATGGATCAGAGGGAGT 58.634 43.478 0.00 0.00 0.00 3.85
110 111 5.121811 CAACTTTGTATGGATCAGAGGGAG 58.878 45.833 0.00 0.00 0.00 4.30
111 112 4.536090 ACAACTTTGTATGGATCAGAGGGA 59.464 41.667 0.00 0.00 40.16 4.20
112 113 4.848357 ACAACTTTGTATGGATCAGAGGG 58.152 43.478 0.00 0.00 40.16 4.30
113 114 6.644347 AGTACAACTTTGTATGGATCAGAGG 58.356 40.000 5.16 0.00 44.59 3.69
114 115 9.653287 TTTAGTACAACTTTGTATGGATCAGAG 57.347 33.333 5.16 0.00 44.59 3.35
117 118 9.952030 TGATTTAGTACAACTTTGTATGGATCA 57.048 29.630 5.16 9.47 44.59 2.92
120 121 8.714179 CGTTGATTTAGTACAACTTTGTATGGA 58.286 33.333 5.16 0.00 44.59 3.41
121 122 8.714179 TCGTTGATTTAGTACAACTTTGTATGG 58.286 33.333 5.16 0.00 44.59 2.74
122 123 9.525007 GTCGTTGATTTAGTACAACTTTGTATG 57.475 33.333 5.16 0.00 44.59 2.39
123 124 9.263538 TGTCGTTGATTTAGTACAACTTTGTAT 57.736 29.630 5.16 0.00 44.59 2.29
124 125 8.645730 TGTCGTTGATTTAGTACAACTTTGTA 57.354 30.769 0.00 0.00 42.53 2.41
125 126 7.279313 ACTGTCGTTGATTTAGTACAACTTTGT 59.721 33.333 0.00 0.00 42.53 2.83
126 127 7.627340 ACTGTCGTTGATTTAGTACAACTTTG 58.373 34.615 0.00 0.00 42.53 2.77
127 128 7.781548 ACTGTCGTTGATTTAGTACAACTTT 57.218 32.000 0.00 0.00 42.53 2.66
128 129 7.781548 AACTGTCGTTGATTTAGTACAACTT 57.218 32.000 0.00 0.00 42.53 2.66
129 130 8.876275 TTAACTGTCGTTGATTTAGTACAACT 57.124 30.769 0.00 0.00 42.53 3.16
137 138 9.800433 TCCGTAATATTAACTGTCGTTGATTTA 57.200 29.630 0.00 0.00 32.39 1.40
138 139 8.706492 TCCGTAATATTAACTGTCGTTGATTT 57.294 30.769 0.00 0.00 32.39 2.17
139 140 8.882415 ATCCGTAATATTAACTGTCGTTGATT 57.118 30.769 0.00 0.00 32.39 2.57
140 141 7.325338 CGATCCGTAATATTAACTGTCGTTGAT 59.675 37.037 0.00 0.00 34.25 2.57
141 142 6.634035 CGATCCGTAATATTAACTGTCGTTGA 59.366 38.462 0.00 0.00 34.59 3.18
142 143 6.129273 CCGATCCGTAATATTAACTGTCGTTG 60.129 42.308 14.83 3.93 34.59 4.10
143 144 5.916883 CCGATCCGTAATATTAACTGTCGTT 59.083 40.000 14.83 0.00 37.15 3.85
144 145 5.239306 TCCGATCCGTAATATTAACTGTCGT 59.761 40.000 14.83 0.00 0.00 4.34
145 146 5.692814 TCCGATCCGTAATATTAACTGTCG 58.307 41.667 0.00 5.84 0.00 4.35
146 147 6.091437 CCTCCGATCCGTAATATTAACTGTC 58.909 44.000 0.00 0.00 0.00 3.51
147 148 5.047519 CCCTCCGATCCGTAATATTAACTGT 60.048 44.000 0.00 0.00 0.00 3.55
148 149 5.184479 TCCCTCCGATCCGTAATATTAACTG 59.816 44.000 0.00 0.00 0.00 3.16
149 150 5.327732 TCCCTCCGATCCGTAATATTAACT 58.672 41.667 0.00 0.00 0.00 2.24
150 151 5.184671 ACTCCCTCCGATCCGTAATATTAAC 59.815 44.000 0.00 0.00 0.00 2.01
151 152 5.327732 ACTCCCTCCGATCCGTAATATTAA 58.672 41.667 0.00 0.00 0.00 1.40
152 153 4.927049 ACTCCCTCCGATCCGTAATATTA 58.073 43.478 0.00 0.00 0.00 0.98
153 154 3.775910 ACTCCCTCCGATCCGTAATATT 58.224 45.455 0.00 0.00 0.00 1.28
154 155 3.453059 ACTCCCTCCGATCCGTAATAT 57.547 47.619 0.00 0.00 0.00 1.28
155 156 2.965671 ACTCCCTCCGATCCGTAATA 57.034 50.000 0.00 0.00 0.00 0.98
156 157 2.965671 TACTCCCTCCGATCCGTAAT 57.034 50.000 0.00 0.00 0.00 1.89
157 158 2.734755 TTACTCCCTCCGATCCGTAA 57.265 50.000 0.00 0.00 0.00 3.18
158 159 2.965671 ATTACTCCCTCCGATCCGTA 57.034 50.000 0.00 0.00 0.00 4.02
159 160 2.083628 AATTACTCCCTCCGATCCGT 57.916 50.000 0.00 0.00 0.00 4.69
160 161 2.102588 ACAAATTACTCCCTCCGATCCG 59.897 50.000 0.00 0.00 0.00 4.18
161 162 3.840124 ACAAATTACTCCCTCCGATCC 57.160 47.619 0.00 0.00 0.00 3.36
162 163 6.760291 AGATAACAAATTACTCCCTCCGATC 58.240 40.000 0.00 0.00 0.00 3.69
163 164 6.749036 AGATAACAAATTACTCCCTCCGAT 57.251 37.500 0.00 0.00 0.00 4.18
164 165 6.837568 AGTAGATAACAAATTACTCCCTCCGA 59.162 38.462 0.00 0.00 0.00 4.55
165 166 7.052142 AGTAGATAACAAATTACTCCCTCCG 57.948 40.000 0.00 0.00 0.00 4.63
196 197 3.367910 GGTCTGCACTGTGTTTCCAAAAA 60.368 43.478 9.86 0.00 0.00 1.94
197 198 2.165437 GGTCTGCACTGTGTTTCCAAAA 59.835 45.455 9.86 0.00 0.00 2.44
198 199 1.748493 GGTCTGCACTGTGTTTCCAAA 59.252 47.619 9.86 0.00 0.00 3.28
199 200 1.388547 GGTCTGCACTGTGTTTCCAA 58.611 50.000 9.86 0.00 0.00 3.53
200 201 0.465460 GGGTCTGCACTGTGTTTCCA 60.465 55.000 9.86 0.00 0.00 3.53
201 202 0.465460 TGGGTCTGCACTGTGTTTCC 60.465 55.000 9.86 7.17 0.00 3.13
202 203 1.267806 CATGGGTCTGCACTGTGTTTC 59.732 52.381 9.86 0.00 0.00 2.78
203 204 1.321474 CATGGGTCTGCACTGTGTTT 58.679 50.000 9.86 0.00 0.00 2.83
204 205 1.174712 GCATGGGTCTGCACTGTGTT 61.175 55.000 9.86 0.00 41.87 3.32
205 206 1.601759 GCATGGGTCTGCACTGTGT 60.602 57.895 9.86 0.00 41.87 3.72
206 207 1.601477 TGCATGGGTCTGCACTGTG 60.601 57.895 2.76 2.76 46.76 3.66
207 208 2.838360 TGCATGGGTCTGCACTGT 59.162 55.556 0.00 0.00 46.76 3.55
212 213 0.679002 ATGTGAGTGCATGGGTCTGC 60.679 55.000 0.00 0.00 42.62 4.26
213 214 2.283298 GTATGTGAGTGCATGGGTCTG 58.717 52.381 0.00 0.00 0.00 3.51
214 215 1.134699 CGTATGTGAGTGCATGGGTCT 60.135 52.381 0.00 0.00 0.00 3.85
215 216 1.134818 TCGTATGTGAGTGCATGGGTC 60.135 52.381 0.00 0.00 0.00 4.46
216 217 0.901827 TCGTATGTGAGTGCATGGGT 59.098 50.000 0.00 0.00 0.00 4.51
217 218 1.935873 CTTCGTATGTGAGTGCATGGG 59.064 52.381 0.00 0.00 0.00 4.00
218 219 1.935873 CCTTCGTATGTGAGTGCATGG 59.064 52.381 0.00 0.00 0.00 3.66
219 220 1.328680 GCCTTCGTATGTGAGTGCATG 59.671 52.381 0.00 0.00 0.00 4.06
220 221 1.066215 TGCCTTCGTATGTGAGTGCAT 60.066 47.619 0.00 0.00 0.00 3.96
221 222 0.320050 TGCCTTCGTATGTGAGTGCA 59.680 50.000 0.00 0.00 0.00 4.57
222 223 1.438651 TTGCCTTCGTATGTGAGTGC 58.561 50.000 0.00 0.00 0.00 4.40
223 224 5.109210 TCTAATTGCCTTCGTATGTGAGTG 58.891 41.667 0.00 0.00 0.00 3.51
224 225 5.339008 TCTAATTGCCTTCGTATGTGAGT 57.661 39.130 0.00 0.00 0.00 3.41
225 226 6.851222 AATCTAATTGCCTTCGTATGTGAG 57.149 37.500 0.00 0.00 0.00 3.51
226 227 8.725405 TTAAATCTAATTGCCTTCGTATGTGA 57.275 30.769 0.00 0.00 0.00 3.58
227 228 9.385902 CATTAAATCTAATTGCCTTCGTATGTG 57.614 33.333 0.00 0.00 0.00 3.21
228 229 8.076178 GCATTAAATCTAATTGCCTTCGTATGT 58.924 33.333 0.00 0.00 0.00 2.29
229 230 7.538678 GGCATTAAATCTAATTGCCTTCGTATG 59.461 37.037 6.72 0.00 37.97 2.39
230 231 7.230510 TGGCATTAAATCTAATTGCCTTCGTAT 59.769 33.333 13.58 0.00 39.69 3.06
231 232 6.544197 TGGCATTAAATCTAATTGCCTTCGTA 59.456 34.615 13.58 0.00 39.69 3.43
232 233 5.359576 TGGCATTAAATCTAATTGCCTTCGT 59.640 36.000 13.58 0.00 39.69 3.85
233 234 5.830912 TGGCATTAAATCTAATTGCCTTCG 58.169 37.500 13.58 0.00 39.69 3.79
234 235 6.809869 ACTGGCATTAAATCTAATTGCCTTC 58.190 36.000 13.58 0.00 39.69 3.46
238 239 5.985530 GGGAACTGGCATTAAATCTAATTGC 59.014 40.000 0.00 0.00 0.00 3.56
255 256 4.714632 TGTTGAGGTTAAAGAGGGAACTG 58.285 43.478 0.00 0.00 44.43 3.16
260 261 6.901081 ATTCTTTGTTGAGGTTAAAGAGGG 57.099 37.500 0.00 0.00 40.36 4.30
268 269 8.160106 ACATCTCTTCTATTCTTTGTTGAGGTT 58.840 33.333 0.00 0.00 0.00 3.50
270 271 7.413877 GCACATCTCTTCTATTCTTTGTTGAGG 60.414 40.741 0.00 0.00 0.00 3.86
283 288 2.767960 TCCATGCAGCACATCTCTTCTA 59.232 45.455 0.00 0.00 36.64 2.10
288 293 2.490903 ACTTTTCCATGCAGCACATCTC 59.509 45.455 0.00 0.00 36.64 2.75
310 315 2.949644 ACTTTACAAGCTGTTGGGTGAC 59.050 45.455 0.00 0.00 38.07 3.67
311 316 3.290948 ACTTTACAAGCTGTTGGGTGA 57.709 42.857 0.00 0.00 38.07 4.02
356 361 6.202570 TGCTTTAAATCGAAATGCAGCTTTTT 59.797 30.769 7.65 1.06 0.00 1.94
357 362 5.695816 TGCTTTAAATCGAAATGCAGCTTTT 59.304 32.000 5.98 5.98 0.00 2.27
362 367 4.563580 TGCATGCTTTAAATCGAAATGCAG 59.436 37.500 20.33 7.60 37.56 4.41
388 398 1.473258 CATTTTGGAGGGAATCGGCA 58.527 50.000 0.00 0.00 0.00 5.69
435 445 3.375782 AAAAGAGCACAAGGAATGCAC 57.624 42.857 0.00 0.00 45.92 4.57
436 446 5.336690 GGAATAAAAGAGCACAAGGAATGCA 60.337 40.000 0.00 0.00 45.92 3.96
521 537 5.422012 AGGAGCAAAAGTGAAAAAGGAAAGA 59.578 36.000 0.00 0.00 0.00 2.52
548 564 2.902705 AGTTTTACTCAGGCGTGTGA 57.097 45.000 14.77 0.00 0.00 3.58
625 641 3.701040 AGCTTTGCCTTCTTTCAAGAACA 59.299 39.130 0.00 0.00 39.95 3.18
705 723 0.904865 AGTGCACGGGAGAGGAATCA 60.905 55.000 12.01 0.00 0.00 2.57
730 748 1.023513 AGAGATGCTGCTGAAACGGC 61.024 55.000 0.00 0.00 42.55 5.68
740 758 7.551035 AAGCATAGAAAGTAAAGAGATGCTG 57.449 36.000 7.19 0.00 45.76 4.41
752 774 6.884280 ACTAGTTGCAAAAGCATAGAAAGT 57.116 33.333 0.00 0.00 0.00 2.66
774 796 7.862873 CCAGTGGAAAAGAACAGAAAAAGATAC 59.137 37.037 1.68 0.00 0.00 2.24
790 812 5.242838 CCTGTGTTTATAAGCCAGTGGAAAA 59.757 40.000 15.20 1.79 0.00 2.29
794 816 2.423538 GCCTGTGTTTATAAGCCAGTGG 59.576 50.000 4.20 4.20 0.00 4.00
873 895 5.124645 GCACTACTCTACCAGTTAGCTAGA 58.875 45.833 0.00 0.00 36.43 2.43
903 925 4.164221 TGTGAAAGAAGAGAAGGGTCTTGT 59.836 41.667 0.00 0.00 36.89 3.16
906 928 4.019771 GGATGTGAAAGAAGAGAAGGGTCT 60.020 45.833 0.00 0.00 36.55 3.85
946 970 4.210120 CAGAGCTACAAGTGTCAACTCAAC 59.790 45.833 0.00 0.00 34.77 3.18
964 995 4.388469 TGCAAACAGAAAAACAAACAGAGC 59.612 37.500 0.00 0.00 0.00 4.09
980 1011 2.043551 TGCACCACCCTGCAAACA 60.044 55.556 0.00 0.00 44.28 2.83
1018 1050 0.459411 GCTCTCTCGGGCAGAAGAAC 60.459 60.000 0.00 0.00 0.00 3.01
1203 1235 4.980592 TCCAGGCTGCACCCCAGA 62.981 66.667 9.56 0.00 44.64 3.86
1310 1342 5.721480 ACCAAAATAAAATCCCCCTCTTCTG 59.279 40.000 0.00 0.00 0.00 3.02
1327 1360 5.486526 TGAAGAGCACAAAAACACCAAAAT 58.513 33.333 0.00 0.00 0.00 1.82
1452 1485 1.896220 TTGCCGATTTGAACAGCTCT 58.104 45.000 0.00 0.00 0.00 4.09
1457 1490 1.269448 GAGCCTTTGCCGATTTGAACA 59.731 47.619 0.00 0.00 38.69 3.18
1485 1518 6.146184 TCGTCGTTAGGAGATACGTATAAAGG 59.854 42.308 8.34 4.68 38.79 3.11
1486 1519 7.110179 TCGTCGTTAGGAGATACGTATAAAG 57.890 40.000 8.34 1.57 38.79 1.85
1487 1520 7.477144 TTCGTCGTTAGGAGATACGTATAAA 57.523 36.000 8.34 0.00 38.79 1.40
1490 1523 5.755375 TCTTTCGTCGTTAGGAGATACGTAT 59.245 40.000 8.05 8.05 38.79 3.06
1491 1524 5.109210 TCTTTCGTCGTTAGGAGATACGTA 58.891 41.667 0.00 0.00 38.79 3.57
1492 1525 3.935203 TCTTTCGTCGTTAGGAGATACGT 59.065 43.478 0.00 0.00 38.79 3.57
1493 1526 4.526970 TCTTTCGTCGTTAGGAGATACG 57.473 45.455 0.00 0.00 39.03 3.06
1494 1527 5.908499 GTCATCTTTCGTCGTTAGGAGATAC 59.092 44.000 0.00 0.00 0.00 2.24
1503 1536 0.389426 CGGGGTCATCTTTCGTCGTT 60.389 55.000 0.00 0.00 0.00 3.85
1540 1573 1.622312 TGTTCAGAGTGCAGATCAGCT 59.378 47.619 11.68 0.00 34.99 4.24
1550 1583 1.534595 GAGGCAAAGCTGTTCAGAGTG 59.465 52.381 3.84 0.00 0.00 3.51
1551 1584 1.141657 TGAGGCAAAGCTGTTCAGAGT 59.858 47.619 3.84 0.00 0.00 3.24
1553 1586 2.158769 TCTTGAGGCAAAGCTGTTCAGA 60.159 45.455 3.84 0.00 0.00 3.27
1554 1587 2.224606 TCTTGAGGCAAAGCTGTTCAG 58.775 47.619 0.00 0.00 0.00 3.02
1559 1592 0.956633 TTGCTCTTGAGGCAAAGCTG 59.043 50.000 0.00 0.00 45.05 4.24
1568 1601 2.322355 ACCGATCCATTGCTCTTGAG 57.678 50.000 0.00 0.00 0.00 3.02
1615 1652 2.353610 GCATGCTGAAACCCAGGGG 61.354 63.158 11.37 6.87 43.13 4.79
1642 1679 5.473039 GCTAAACTCAATTCCATTGCTGTT 58.527 37.500 0.00 0.00 40.05 3.16
1643 1680 4.082026 GGCTAAACTCAATTCCATTGCTGT 60.082 41.667 0.00 0.00 40.05 4.40
1644 1681 4.427312 GGCTAAACTCAATTCCATTGCTG 58.573 43.478 0.00 0.00 40.05 4.41
1645 1682 3.129287 CGGCTAAACTCAATTCCATTGCT 59.871 43.478 0.00 0.00 40.05 3.91
1646 1683 3.128589 TCGGCTAAACTCAATTCCATTGC 59.871 43.478 0.00 0.00 40.05 3.56
1648 1685 5.975693 TTTCGGCTAAACTCAATTCCATT 57.024 34.783 0.00 0.00 0.00 3.16
1694 1741 4.815846 ACCTTACCGTGTTCAAAAATACGT 59.184 37.500 0.00 0.00 45.28 3.57
1695 1742 5.178067 AGACCTTACCGTGTTCAAAAATACG 59.822 40.000 1.16 1.16 46.01 3.06
1696 1743 6.549912 AGACCTTACCGTGTTCAAAAATAC 57.450 37.500 0.00 0.00 0.00 1.89
1698 1745 7.571080 TTAAGACCTTACCGTGTTCAAAAAT 57.429 32.000 0.00 0.00 0.00 1.82
1736 1786 5.749109 CCTCTACACATACGTTTCTTGATCC 59.251 44.000 0.00 0.00 0.00 3.36
1768 1818 7.019418 CACGATCAATCAATTATCGATGCATT 58.981 34.615 8.54 3.49 43.96 3.56
1796 1846 9.209048 CCCTTGTACCTATATATATGTGCCTAA 57.791 37.037 5.44 1.73 0.00 2.69
2119 2177 1.283029 CCAACCCTGTCCATCACTGAT 59.717 52.381 0.00 0.00 0.00 2.90
2122 2180 1.380302 GCCAACCCTGTCCATCACT 59.620 57.895 0.00 0.00 0.00 3.41
2147 2206 0.601558 ACAACGTCTCCGCAGTGTAT 59.398 50.000 0.00 0.00 37.70 2.29
2153 2212 1.299850 CTGTGACAACGTCTCCGCA 60.300 57.895 0.00 0.00 37.70 5.69
2182 2241 1.740296 CGTGAGGTTACCAAGGCGG 60.740 63.158 3.51 0.00 42.50 6.13


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

AutoCloner maintained by Alex Coulton.