Multiple sequence alignment - TraesCS4B01G140400

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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 TraesCS4B01G140400 chr4B 100.000 3736 0 0 1 3736 184860735 184864470 0.000000e+00 6900.0
1 TraesCS4B01G140400 chr4A 92.875 3551 118 53 236 3736 449121632 449118167 0.000000e+00 5031.0
2 TraesCS4B01G140400 chr4D 93.583 1839 65 19 1908 3729 121968556 121970358 0.000000e+00 2693.0
3 TraesCS4B01G140400 chr4D 92.062 1096 33 14 236 1307 121966889 121967954 0.000000e+00 1493.0
4 TraesCS4B01G140400 chr4D 83.982 437 38 16 1428 1855 121968127 121968540 1.260000e-104 390.0
5 TraesCS4B01G140400 chr4D 94.444 54 1 2 1 54 134547034 134547085 8.600000e-12 82.4
6 TraesCS4B01G140400 chr5B 82.468 154 15 6 66 208 6571097 6570945 1.410000e-24 124.0
7 TraesCS4B01G140400 chrUn 98.148 54 1 0 1 54 81639527 81639474 1.100000e-15 95.3
8 TraesCS4B01G140400 chrUn 93.617 47 3 0 2174 2220 153391836 153391882 1.860000e-08 71.3
9 TraesCS4B01G140400 chr3D 96.364 55 1 1 1 55 568438888 568438835 5.140000e-14 89.8
10 TraesCS4B01G140400 chr3A 96.226 53 2 0 1 53 619847767 619847819 1.850000e-13 87.9
11 TraesCS4B01G140400 chr7B 94.643 56 2 1 1 56 180048387 180048333 6.650000e-13 86.1
12 TraesCS4B01G140400 chr7B 90.000 50 5 0 2171 2220 524244352 524244303 8.660000e-07 65.8
13 TraesCS4B01G140400 chr6D 94.545 55 2 1 1 55 262194025 262193972 2.390000e-12 84.2
14 TraesCS4B01G140400 chr6D 91.837 49 3 1 2172 2220 443269338 443269385 2.410000e-07 67.6
15 TraesCS4B01G140400 chr2B 94.231 52 3 0 1 52 110418714 110418765 3.090000e-11 80.5
16 TraesCS4B01G140400 chr6A 93.617 47 3 0 2174 2220 48088979 48089025 1.860000e-08 71.3
17 TraesCS4B01G140400 chr1A 97.561 41 1 0 2180 2220 14600397 14600357 1.860000e-08 71.3
18 TraesCS4B01G140400 chr5D 97.500 40 1 0 2181 2220 342698211 342698172 6.700000e-08 69.4
19 TraesCS4B01G140400 chr5A 91.837 49 3 1 2172 2220 335267150 335267197 2.410000e-07 67.6
20 TraesCS4B01G140400 chr7D 90.000 50 5 0 2171 2220 495871972 495871923 8.660000e-07 65.8


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 TraesCS4B01G140400 chr4B 184860735 184864470 3735 False 6900.000000 6900 100.000000 1 3736 1 chr4B.!!$F1 3735
1 TraesCS4B01G140400 chr4A 449118167 449121632 3465 True 5031.000000 5031 92.875000 236 3736 1 chr4A.!!$R1 3500
2 TraesCS4B01G140400 chr4D 121966889 121970358 3469 False 1525.333333 2693 89.875667 236 3729 3 chr4D.!!$F2 3493

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
404 416 0.324275 GAAGGGCTTGGGGTGCATTA 60.324 55.0 0.00 0.00 0.00 1.90 F
1166 1207 0.251297 CAGGTGGTTGATCTGGCCAA 60.251 55.0 7.01 0.00 33.66 4.52 F
2156 2300 0.776176 ATCCCTCTCCGGTACCGTAT 59.224 55.0 31.24 10.87 37.81 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1901 2045 0.188342 AATTTATCAGGCCGGCCCAT 59.812 50.0 41.72 33.16 36.58 4.00 R
2523 2668 0.107361 TCGTCAGACTCATCGCCCTA 60.107 55.0 0.00 0.00 0.00 3.53 R
3158 3320 0.888619 TTCGAGCCGATCTCACTGTT 59.111 50.0 0.00 0.00 41.98 3.16 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
27 28 4.744795 GAGAAGCCTCCTTGAGTTATGA 57.255 45.455 0.00 0.00 33.30 2.15
28 29 4.692228 GAGAAGCCTCCTTGAGTTATGAG 58.308 47.826 0.00 0.00 33.30 2.90
29 30 4.357325 AGAAGCCTCCTTGAGTTATGAGA 58.643 43.478 0.00 0.00 0.00 3.27
30 31 4.968080 AGAAGCCTCCTTGAGTTATGAGAT 59.032 41.667 0.00 0.00 0.00 2.75
31 32 6.139671 AGAAGCCTCCTTGAGTTATGAGATA 58.860 40.000 0.00 0.00 0.00 1.98
32 33 6.786959 AGAAGCCTCCTTGAGTTATGAGATAT 59.213 38.462 0.00 0.00 0.00 1.63
33 34 7.292120 AGAAGCCTCCTTGAGTTATGAGATATT 59.708 37.037 0.00 0.00 0.00 1.28
34 35 7.003402 AGCCTCCTTGAGTTATGAGATATTC 57.997 40.000 0.00 0.00 0.00 1.75
35 36 6.786959 AGCCTCCTTGAGTTATGAGATATTCT 59.213 38.462 0.00 0.00 0.00 2.40
36 37 7.292120 AGCCTCCTTGAGTTATGAGATATTCTT 59.708 37.037 0.00 0.00 0.00 2.52
37 38 7.936301 GCCTCCTTGAGTTATGAGATATTCTTT 59.064 37.037 0.00 0.00 0.00 2.52
38 39 9.844257 CCTCCTTGAGTTATGAGATATTCTTTT 57.156 33.333 0.00 0.00 0.00 2.27
43 44 8.980481 TGAGTTATGAGATATTCTTTTTCCCC 57.020 34.615 0.00 0.00 0.00 4.81
44 45 7.715249 TGAGTTATGAGATATTCTTTTTCCCCG 59.285 37.037 0.00 0.00 0.00 5.73
45 46 6.486993 AGTTATGAGATATTCTTTTTCCCCGC 59.513 38.462 0.00 0.00 0.00 6.13
46 47 4.229304 TGAGATATTCTTTTTCCCCGCA 57.771 40.909 0.00 0.00 0.00 5.69
47 48 4.594970 TGAGATATTCTTTTTCCCCGCAA 58.405 39.130 0.00 0.00 0.00 4.85
48 49 5.013547 TGAGATATTCTTTTTCCCCGCAAA 58.986 37.500 0.00 0.00 0.00 3.68
49 50 5.478679 TGAGATATTCTTTTTCCCCGCAAAA 59.521 36.000 0.00 0.00 0.00 2.44
50 51 6.015010 TGAGATATTCTTTTTCCCCGCAAAAA 60.015 34.615 0.00 0.00 34.72 1.94
76 77 7.934855 AAAAAGAGATCACTCATGCTATTGT 57.065 32.000 0.00 0.00 44.79 2.71
78 79 9.453572 AAAAAGAGATCACTCATGCTATTGTAA 57.546 29.630 0.00 0.00 44.79 2.41
79 80 9.624373 AAAAGAGATCACTCATGCTATTGTAAT 57.376 29.630 0.00 0.00 44.79 1.89
80 81 8.604640 AAGAGATCACTCATGCTATTGTAATG 57.395 34.615 0.00 0.00 44.79 1.90
81 82 7.733969 AGAGATCACTCATGCTATTGTAATGT 58.266 34.615 0.00 0.00 44.79 2.71
82 83 8.864087 AGAGATCACTCATGCTATTGTAATGTA 58.136 33.333 0.00 0.00 44.79 2.29
83 84 9.481340 GAGATCACTCATGCTATTGTAATGTAA 57.519 33.333 0.00 0.00 42.21 2.41
84 85 9.836864 AGATCACTCATGCTATTGTAATGTAAA 57.163 29.630 0.00 0.00 0.00 2.01
118 119 8.067751 ACTACTATTGCACAACTATTCTCTCA 57.932 34.615 0.00 0.00 0.00 3.27
119 120 7.976734 ACTACTATTGCACAACTATTCTCTCAC 59.023 37.037 0.00 0.00 0.00 3.51
120 121 6.701340 ACTATTGCACAACTATTCTCTCACA 58.299 36.000 0.00 0.00 0.00 3.58
121 122 5.869753 ATTGCACAACTATTCTCTCACAC 57.130 39.130 0.00 0.00 0.00 3.82
122 123 4.335400 TGCACAACTATTCTCTCACACA 57.665 40.909 0.00 0.00 0.00 3.72
123 124 4.058124 TGCACAACTATTCTCTCACACAC 58.942 43.478 0.00 0.00 0.00 3.82
124 125 4.202253 TGCACAACTATTCTCTCACACACT 60.202 41.667 0.00 0.00 0.00 3.55
125 126 5.010617 TGCACAACTATTCTCTCACACACTA 59.989 40.000 0.00 0.00 0.00 2.74
126 127 5.346281 GCACAACTATTCTCTCACACACTAC 59.654 44.000 0.00 0.00 0.00 2.73
127 128 6.447162 CACAACTATTCTCTCACACACTACA 58.553 40.000 0.00 0.00 0.00 2.74
128 129 6.923508 CACAACTATTCTCTCACACACTACAA 59.076 38.462 0.00 0.00 0.00 2.41
129 130 7.438160 CACAACTATTCTCTCACACACTACAAA 59.562 37.037 0.00 0.00 0.00 2.83
130 131 7.653713 ACAACTATTCTCTCACACACTACAAAG 59.346 37.037 0.00 0.00 0.00 2.77
131 132 7.526142 ACTATTCTCTCACACACTACAAAGA 57.474 36.000 0.00 0.00 0.00 2.52
132 133 8.128322 ACTATTCTCTCACACACTACAAAGAT 57.872 34.615 0.00 0.00 0.00 2.40
133 134 9.244292 ACTATTCTCTCACACACTACAAAGATA 57.756 33.333 0.00 0.00 0.00 1.98
134 135 9.509855 CTATTCTCTCACACACTACAAAGATAC 57.490 37.037 0.00 0.00 0.00 2.24
135 136 6.894339 TCTCTCACACACTACAAAGATACA 57.106 37.500 0.00 0.00 0.00 2.29
136 137 7.284919 TCTCTCACACACTACAAAGATACAA 57.715 36.000 0.00 0.00 0.00 2.41
137 138 7.722363 TCTCTCACACACTACAAAGATACAAA 58.278 34.615 0.00 0.00 0.00 2.83
138 139 7.652105 TCTCTCACACACTACAAAGATACAAAC 59.348 37.037 0.00 0.00 0.00 2.93
139 140 7.269316 TCTCACACACTACAAAGATACAAACA 58.731 34.615 0.00 0.00 0.00 2.83
140 141 7.931407 TCTCACACACTACAAAGATACAAACAT 59.069 33.333 0.00 0.00 0.00 2.71
141 142 7.860613 TCACACACTACAAAGATACAAACATG 58.139 34.615 0.00 0.00 0.00 3.21
142 143 6.578545 CACACACTACAAAGATACAAACATGC 59.421 38.462 0.00 0.00 0.00 4.06
143 144 6.262049 ACACACTACAAAGATACAAACATGCA 59.738 34.615 0.00 0.00 0.00 3.96
144 145 6.798476 CACACTACAAAGATACAAACATGCAG 59.202 38.462 0.00 0.00 0.00 4.41
145 146 6.710295 ACACTACAAAGATACAAACATGCAGA 59.290 34.615 0.00 0.00 0.00 4.26
146 147 7.228507 ACACTACAAAGATACAAACATGCAGAA 59.771 33.333 0.00 0.00 0.00 3.02
147 148 7.535258 CACTACAAAGATACAAACATGCAGAAC 59.465 37.037 0.00 0.00 0.00 3.01
148 149 5.451908 ACAAAGATACAAACATGCAGAACG 58.548 37.500 0.00 0.00 0.00 3.95
149 150 5.008613 ACAAAGATACAAACATGCAGAACGT 59.991 36.000 0.00 0.00 0.00 3.99
150 151 6.203915 ACAAAGATACAAACATGCAGAACGTA 59.796 34.615 0.00 0.00 0.00 3.57
151 152 5.779806 AGATACAAACATGCAGAACGTAC 57.220 39.130 0.00 0.00 0.00 3.67
152 153 5.234752 AGATACAAACATGCAGAACGTACA 58.765 37.500 0.00 0.00 0.00 2.90
153 154 5.699001 AGATACAAACATGCAGAACGTACAA 59.301 36.000 0.00 0.00 0.00 2.41
154 155 3.947626 ACAAACATGCAGAACGTACAAC 58.052 40.909 0.00 0.00 0.00 3.32
156 157 2.143008 ACATGCAGAACGTACAACGA 57.857 45.000 6.44 0.00 46.05 3.85
157 158 2.475818 ACATGCAGAACGTACAACGAA 58.524 42.857 6.44 0.00 46.05 3.85
158 159 3.064207 ACATGCAGAACGTACAACGAAT 58.936 40.909 6.44 0.00 46.05 3.34
159 160 3.496884 ACATGCAGAACGTACAACGAATT 59.503 39.130 6.44 0.00 46.05 2.17
160 161 4.687018 ACATGCAGAACGTACAACGAATTA 59.313 37.500 6.44 0.00 46.05 1.40
161 162 5.350365 ACATGCAGAACGTACAACGAATTAT 59.650 36.000 6.44 0.00 46.05 1.28
162 163 5.444586 TGCAGAACGTACAACGAATTATC 57.555 39.130 6.44 0.00 46.05 1.75
163 164 4.924462 TGCAGAACGTACAACGAATTATCA 59.076 37.500 6.44 0.00 46.05 2.15
164 165 5.579119 TGCAGAACGTACAACGAATTATCAT 59.421 36.000 6.44 0.00 46.05 2.45
165 166 6.752815 TGCAGAACGTACAACGAATTATCATA 59.247 34.615 6.44 0.00 46.05 2.15
166 167 7.275999 TGCAGAACGTACAACGAATTATCATAA 59.724 33.333 6.44 0.00 46.05 1.90
167 168 8.111836 GCAGAACGTACAACGAATTATCATAAA 58.888 33.333 6.44 0.00 46.05 1.40
168 169 9.405083 CAGAACGTACAACGAATTATCATAAAC 57.595 33.333 6.44 0.00 46.05 2.01
169 170 9.362539 AGAACGTACAACGAATTATCATAAACT 57.637 29.630 6.44 0.00 46.05 2.66
170 171 9.962759 GAACGTACAACGAATTATCATAAACTT 57.037 29.630 6.44 0.00 46.05 2.66
171 172 9.962759 AACGTACAACGAATTATCATAAACTTC 57.037 29.630 6.44 0.00 46.05 3.01
172 173 8.316046 ACGTACAACGAATTATCATAAACTTCG 58.684 33.333 10.35 10.35 46.05 3.79
185 186 8.806177 ATCATAAACTTCGTAAAAACAAACCC 57.194 30.769 0.00 0.00 0.00 4.11
186 187 7.201835 TCATAAACTTCGTAAAAACAAACCCC 58.798 34.615 0.00 0.00 0.00 4.95
187 188 5.402997 AAACTTCGTAAAAACAAACCCCA 57.597 34.783 0.00 0.00 0.00 4.96
188 189 5.402997 AACTTCGTAAAAACAAACCCCAA 57.597 34.783 0.00 0.00 0.00 4.12
189 190 4.746729 ACTTCGTAAAAACAAACCCCAAC 58.253 39.130 0.00 0.00 0.00 3.77
190 191 3.417690 TCGTAAAAACAAACCCCAACG 57.582 42.857 0.00 0.00 0.00 4.10
191 192 3.012518 TCGTAAAAACAAACCCCAACGA 58.987 40.909 0.00 0.00 35.94 3.85
192 193 3.441572 TCGTAAAAACAAACCCCAACGAA 59.558 39.130 0.00 0.00 35.43 3.85
193 194 4.097589 TCGTAAAAACAAACCCCAACGAAT 59.902 37.500 0.00 0.00 35.43 3.34
194 195 4.441744 CGTAAAAACAAACCCCAACGAATC 59.558 41.667 0.00 0.00 0.00 2.52
195 196 4.473477 AAAAACAAACCCCAACGAATCA 57.527 36.364 0.00 0.00 0.00 2.57
196 197 3.446310 AAACAAACCCCAACGAATCAC 57.554 42.857 0.00 0.00 0.00 3.06
197 198 2.358322 ACAAACCCCAACGAATCACT 57.642 45.000 0.00 0.00 0.00 3.41
198 199 3.495434 ACAAACCCCAACGAATCACTA 57.505 42.857 0.00 0.00 0.00 2.74
199 200 3.408634 ACAAACCCCAACGAATCACTAG 58.591 45.455 0.00 0.00 0.00 2.57
200 201 3.071892 ACAAACCCCAACGAATCACTAGA 59.928 43.478 0.00 0.00 0.00 2.43
201 202 3.611766 AACCCCAACGAATCACTAGAG 57.388 47.619 0.00 0.00 0.00 2.43
202 203 1.207329 ACCCCAACGAATCACTAGAGC 59.793 52.381 0.00 0.00 0.00 4.09
203 204 1.560923 CCCAACGAATCACTAGAGCG 58.439 55.000 0.00 0.00 0.00 5.03
204 205 0.924090 CCAACGAATCACTAGAGCGC 59.076 55.000 0.00 0.00 0.00 5.92
205 206 0.567968 CAACGAATCACTAGAGCGCG 59.432 55.000 0.00 0.00 0.00 6.86
206 207 0.525668 AACGAATCACTAGAGCGCGG 60.526 55.000 8.83 0.00 0.00 6.46
207 208 2.296480 CGAATCACTAGAGCGCGGC 61.296 63.158 8.83 0.00 0.00 6.53
208 209 1.951631 GAATCACTAGAGCGCGGCC 60.952 63.158 8.83 0.00 0.00 6.13
209 210 3.774959 AATCACTAGAGCGCGGCCG 62.775 63.158 24.05 24.05 37.57 6.13
227 228 2.785921 CGCACTACTCGCTCGTCT 59.214 61.111 0.00 0.00 0.00 4.18
228 229 2.004445 CGCACTACTCGCTCGTCTA 58.996 57.895 0.00 0.00 0.00 2.59
229 230 0.372679 CGCACTACTCGCTCGTCTAA 59.627 55.000 0.00 0.00 0.00 2.10
230 231 1.201998 CGCACTACTCGCTCGTCTAAA 60.202 52.381 0.00 0.00 0.00 1.85
231 232 2.539142 CGCACTACTCGCTCGTCTAAAT 60.539 50.000 0.00 0.00 0.00 1.40
232 233 2.784380 GCACTACTCGCTCGTCTAAATG 59.216 50.000 0.00 0.00 0.00 2.32
233 234 3.487042 GCACTACTCGCTCGTCTAAATGA 60.487 47.826 0.00 0.00 0.00 2.57
234 235 4.659088 CACTACTCGCTCGTCTAAATGAA 58.341 43.478 0.00 0.00 0.00 2.57
285 286 3.377485 TGATTCAGCTGTACCTACTCGAC 59.623 47.826 14.67 0.00 0.00 4.20
290 294 3.440872 CAGCTGTACCTACTCGACTCTTT 59.559 47.826 5.25 0.00 0.00 2.52
356 368 4.526262 AGATACTGACAAGCTGACTGACTT 59.474 41.667 0.00 0.00 0.00 3.01
386 398 2.651071 TGCACCGCATTGAAATGGA 58.349 47.368 5.25 0.00 36.90 3.41
401 413 4.299796 GGAAGGGCTTGGGGTGCA 62.300 66.667 0.00 0.00 0.00 4.57
402 414 2.037847 GAAGGGCTTGGGGTGCAT 59.962 61.111 0.00 0.00 0.00 3.96
403 415 1.610379 GAAGGGCTTGGGGTGCATT 60.610 57.895 0.00 0.00 0.00 3.56
404 416 0.324275 GAAGGGCTTGGGGTGCATTA 60.324 55.000 0.00 0.00 0.00 1.90
537 552 1.886037 TGTACGTACGCTTGATCGTG 58.114 50.000 20.18 0.00 43.21 4.35
623 638 3.718815 GCGCTATATATCTTGCCTACCC 58.281 50.000 0.00 0.00 0.00 3.69
628 643 5.452636 GCTATATATCTTGCCTACCCTGCTC 60.453 48.000 0.00 0.00 0.00 4.26
629 644 1.424638 TATCTTGCCTACCCTGCTCC 58.575 55.000 0.00 0.00 0.00 4.70
642 657 1.409064 CCTGCTCCATGCTAAGTACGA 59.591 52.381 0.00 0.00 43.37 3.43
643 658 2.544694 CCTGCTCCATGCTAAGTACGAG 60.545 54.545 0.00 0.00 43.37 4.18
644 659 2.099921 CTGCTCCATGCTAAGTACGAGT 59.900 50.000 0.00 0.00 43.37 4.18
645 660 3.284617 TGCTCCATGCTAAGTACGAGTA 58.715 45.455 0.00 0.00 43.37 2.59
646 661 3.066342 TGCTCCATGCTAAGTACGAGTAC 59.934 47.826 5.32 5.32 43.37 2.73
647 662 3.066342 GCTCCATGCTAAGTACGAGTACA 59.934 47.826 14.83 0.00 37.32 2.90
648 663 4.790123 GCTCCATGCTAAGTACGAGTACAG 60.790 50.000 14.83 6.33 37.32 2.74
649 664 4.267536 TCCATGCTAAGTACGAGTACAGT 58.732 43.478 14.83 5.70 38.48 3.55
650 665 4.095932 TCCATGCTAAGTACGAGTACAGTG 59.904 45.833 14.83 5.88 38.48 3.66
693 708 9.883142 TGTCTCCTGTTTTTGTTTAATTTGATT 57.117 25.926 0.00 0.00 0.00 2.57
753 772 3.844090 GGAGAGAGTCCGGCAGGC 61.844 72.222 0.00 0.00 34.84 4.85
754 773 3.071206 GAGAGAGTCCGGCAGGCA 61.071 66.667 0.00 0.00 37.47 4.75
906 925 1.210967 CATTAACTTCGCCCCACCCTA 59.789 52.381 0.00 0.00 0.00 3.53
936 959 1.696884 GCCTTCTTCCTCCATCCCTAG 59.303 57.143 0.00 0.00 0.00 3.02
1127 1165 3.785859 ACCGGCAGCATCATCCGT 61.786 61.111 0.00 0.00 41.46 4.69
1166 1207 0.251297 CAGGTGGTTGATCTGGCCAA 60.251 55.000 7.01 0.00 33.66 4.52
1188 1229 3.399181 TACAAGGCCAGGGAGCGG 61.399 66.667 5.01 0.00 0.00 5.52
1223 1264 1.065928 GGTCGTCTGCCTACATCCG 59.934 63.158 0.00 0.00 0.00 4.18
1343 1446 8.252964 AGTATTACAGTTCATTCGTTTTCCTC 57.747 34.615 0.00 0.00 0.00 3.71
1467 1586 3.814268 CGGTTGGGATTGGCAGCG 61.814 66.667 0.00 0.00 0.00 5.18
1547 1666 4.019411 TCTGGTCAGTCCTGCAATTATCAA 60.019 41.667 0.00 0.00 37.07 2.57
1548 1667 4.858850 TGGTCAGTCCTGCAATTATCAAT 58.141 39.130 0.00 0.00 37.07 2.57
1549 1668 6.000246 TGGTCAGTCCTGCAATTATCAATA 58.000 37.500 0.00 0.00 37.07 1.90
1550 1669 6.604171 TGGTCAGTCCTGCAATTATCAATAT 58.396 36.000 0.00 0.00 37.07 1.28
1551 1670 6.712095 TGGTCAGTCCTGCAATTATCAATATC 59.288 38.462 0.00 0.00 37.07 1.63
1552 1671 6.712095 GGTCAGTCCTGCAATTATCAATATCA 59.288 38.462 0.00 0.00 0.00 2.15
1614 1739 6.024563 TCTGGGGGATTATTTTTGCTCATA 57.975 37.500 0.00 0.00 0.00 2.15
1638 1763 4.320667 TCGATGTCACTAAAATGTTGCG 57.679 40.909 0.00 0.00 0.00 4.85
1724 1849 1.443194 CTGTCGGTTGCATGCAAGC 60.443 57.895 39.67 39.67 46.99 4.01
1772 1897 2.604914 CACGATCTACAGGTACGTACGT 59.395 50.000 25.98 25.98 35.78 3.57
1773 1898 3.796717 CACGATCTACAGGTACGTACGTA 59.203 47.826 23.60 23.60 35.78 3.57
1804 1943 3.725305 CGTGCACTACTATCCGATCGATC 60.725 52.174 18.66 15.68 31.92 3.69
1874 2018 3.191669 CAACCATGCATGCAAATTCGAT 58.808 40.909 26.68 2.56 0.00 3.59
1923 2067 1.886542 GGGCCGGCCTGATAAATTAAG 59.113 52.381 42.70 0.00 36.10 1.85
2080 2224 1.613610 CTACCTCGACCTCCTCCCA 59.386 63.158 0.00 0.00 0.00 4.37
2085 2229 1.305046 TCGACCTCCTCCCACTTCC 60.305 63.158 0.00 0.00 0.00 3.46
2086 2230 2.359967 CGACCTCCTCCCACTTCCC 61.360 68.421 0.00 0.00 0.00 3.97
2087 2231 1.229529 GACCTCCTCCCACTTCCCA 60.230 63.158 0.00 0.00 0.00 4.37
2098 2242 3.953775 CTTCCCACCACCACCGCT 61.954 66.667 0.00 0.00 0.00 5.52
2152 2296 1.902432 CCGATCCCTCTCCGGTACC 60.902 68.421 0.16 0.16 38.55 3.34
2156 2300 0.776176 ATCCCTCTCCGGTACCGTAT 59.224 55.000 31.24 10.87 37.81 3.06
2178 2322 7.008719 CGTATTACCTGCAGATCGATTAATCAG 59.991 40.741 17.39 8.31 0.00 2.90
2447 2592 3.982576 AATTCACAACAACGTCCCTTC 57.017 42.857 0.00 0.00 0.00 3.46
2520 2665 2.412770 GACCCCGTACGTGTTAACATTG 59.587 50.000 12.26 10.17 0.00 2.82
2523 2668 4.183101 CCCCGTACGTGTTAACATTGTAT 58.817 43.478 20.01 6.24 0.00 2.29
2577 2722 2.796304 TGAAAGCACTTGAAACAAGCG 58.204 42.857 10.78 3.69 0.00 4.68
2581 2726 0.594796 GCACTTGAAACAAGCGTGGG 60.595 55.000 4.26 0.00 0.00 4.61
2588 2736 1.812571 GAAACAAGCGTGGGTCATCAT 59.187 47.619 4.26 0.00 0.00 2.45
2589 2737 1.453155 AACAAGCGTGGGTCATCATC 58.547 50.000 4.26 0.00 0.00 2.92
2609 2757 4.188247 TCATCACAAGTACAGTACTGCC 57.812 45.455 22.90 13.39 39.39 4.85
2627 2775 4.792804 GACCAGCTGCAGGGGAGC 62.793 72.222 17.12 0.36 36.65 4.70
2949 3108 3.338818 AGCACGCACATATGTATTTGC 57.661 42.857 19.71 19.71 36.35 3.68
2976 3135 2.217620 GCGCGCTTATTTGTTGTTGTTT 59.782 40.909 26.67 0.00 0.00 2.83
3071 3233 5.063880 ACAATTGGTCTGGTAGAACTGAAC 58.936 41.667 10.83 0.00 31.84 3.18
3077 3239 2.632996 TCTGGTAGAACTGAACTGGGTG 59.367 50.000 0.00 0.00 0.00 4.61
3158 3320 3.245016 ACAAAAGGGACTCATCATCAGCA 60.245 43.478 0.00 0.00 38.49 4.41
3171 3333 1.931841 CATCAGCAACAGTGAGATCGG 59.068 52.381 0.00 0.00 0.00 4.18
3174 3336 0.108424 AGCAACAGTGAGATCGGCTC 60.108 55.000 0.00 0.00 44.21 4.70
3359 3521 1.620822 ACCGCTGGCTCATTCTTTTT 58.379 45.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.404073 TCTCATAACTCAAGGAGGCTTCTC 59.596 45.833 0.00 0.00 33.35 2.87
7 8 4.357325 TCTCATAACTCAAGGAGGCTTCT 58.643 43.478 0.00 0.00 33.35 2.85
8 9 4.744795 TCTCATAACTCAAGGAGGCTTC 57.255 45.455 0.00 0.00 33.35 3.86
9 10 7.292120 AGAATATCTCATAACTCAAGGAGGCTT 59.708 37.037 0.00 0.00 33.35 4.35
10 11 6.786959 AGAATATCTCATAACTCAAGGAGGCT 59.213 38.462 0.00 0.00 33.35 4.58
11 12 7.003402 AGAATATCTCATAACTCAAGGAGGC 57.997 40.000 0.00 0.00 33.35 4.70
12 13 9.844257 AAAAGAATATCTCATAACTCAAGGAGG 57.156 33.333 0.00 0.00 33.35 4.30
17 18 9.408648 GGGGAAAAAGAATATCTCATAACTCAA 57.591 33.333 0.00 0.00 0.00 3.02
18 19 7.715249 CGGGGAAAAAGAATATCTCATAACTCA 59.285 37.037 0.00 0.00 0.00 3.41
19 20 7.308049 GCGGGGAAAAAGAATATCTCATAACTC 60.308 40.741 0.00 0.00 0.00 3.01
20 21 6.486993 GCGGGGAAAAAGAATATCTCATAACT 59.513 38.462 0.00 0.00 0.00 2.24
21 22 6.262273 TGCGGGGAAAAAGAATATCTCATAAC 59.738 38.462 0.00 0.00 0.00 1.89
22 23 6.361433 TGCGGGGAAAAAGAATATCTCATAA 58.639 36.000 0.00 0.00 0.00 1.90
23 24 5.935945 TGCGGGGAAAAAGAATATCTCATA 58.064 37.500 0.00 0.00 0.00 2.15
24 25 4.792068 TGCGGGGAAAAAGAATATCTCAT 58.208 39.130 0.00 0.00 0.00 2.90
25 26 4.229304 TGCGGGGAAAAAGAATATCTCA 57.771 40.909 0.00 0.00 0.00 3.27
26 27 5.576447 TTTGCGGGGAAAAAGAATATCTC 57.424 39.130 0.00 0.00 0.00 2.75
27 28 5.993748 TTTTGCGGGGAAAAAGAATATCT 57.006 34.783 0.00 0.00 0.00 1.98
52 53 7.934855 ACAATAGCATGAGTGATCTCTTTTT 57.065 32.000 0.00 0.00 40.98 1.94
53 54 9.624373 ATTACAATAGCATGAGTGATCTCTTTT 57.376 29.630 0.00 0.00 40.98 2.27
54 55 9.053840 CATTACAATAGCATGAGTGATCTCTTT 57.946 33.333 0.00 0.00 40.98 2.52
55 56 8.209584 ACATTACAATAGCATGAGTGATCTCTT 58.790 33.333 0.00 0.00 40.98 2.85
56 57 7.733969 ACATTACAATAGCATGAGTGATCTCT 58.266 34.615 0.00 0.00 40.98 3.10
57 58 7.959689 ACATTACAATAGCATGAGTGATCTC 57.040 36.000 0.00 0.00 40.79 2.75
58 59 9.836864 TTTACATTACAATAGCATGAGTGATCT 57.163 29.630 0.00 0.00 0.00 2.75
92 93 9.185680 TGAGAGAATAGTTGTGCAATAGTAGTA 57.814 33.333 0.00 0.00 0.00 1.82
93 94 7.976734 GTGAGAGAATAGTTGTGCAATAGTAGT 59.023 37.037 0.00 0.00 0.00 2.73
94 95 7.976175 TGTGAGAGAATAGTTGTGCAATAGTAG 59.024 37.037 0.00 0.00 0.00 2.57
95 96 7.759886 GTGTGAGAGAATAGTTGTGCAATAGTA 59.240 37.037 0.00 0.00 0.00 1.82
96 97 6.591834 GTGTGAGAGAATAGTTGTGCAATAGT 59.408 38.462 0.00 0.00 0.00 2.12
97 98 6.591448 TGTGTGAGAGAATAGTTGTGCAATAG 59.409 38.462 0.00 0.00 0.00 1.73
98 99 6.368791 GTGTGTGAGAGAATAGTTGTGCAATA 59.631 38.462 0.00 0.00 0.00 1.90
99 100 5.180117 GTGTGTGAGAGAATAGTTGTGCAAT 59.820 40.000 0.00 0.00 0.00 3.56
100 101 4.511454 GTGTGTGAGAGAATAGTTGTGCAA 59.489 41.667 0.00 0.00 0.00 4.08
101 102 4.058124 GTGTGTGAGAGAATAGTTGTGCA 58.942 43.478 0.00 0.00 0.00 4.57
102 103 4.310769 AGTGTGTGAGAGAATAGTTGTGC 58.689 43.478 0.00 0.00 0.00 4.57
103 104 6.447162 TGTAGTGTGTGAGAGAATAGTTGTG 58.553 40.000 0.00 0.00 0.00 3.33
104 105 6.650427 TGTAGTGTGTGAGAGAATAGTTGT 57.350 37.500 0.00 0.00 0.00 3.32
105 106 7.867909 TCTTTGTAGTGTGTGAGAGAATAGTTG 59.132 37.037 0.00 0.00 0.00 3.16
106 107 7.952671 TCTTTGTAGTGTGTGAGAGAATAGTT 58.047 34.615 0.00 0.00 0.00 2.24
107 108 7.526142 TCTTTGTAGTGTGTGAGAGAATAGT 57.474 36.000 0.00 0.00 0.00 2.12
108 109 9.509855 GTATCTTTGTAGTGTGTGAGAGAATAG 57.490 37.037 0.00 0.00 0.00 1.73
109 110 9.020731 TGTATCTTTGTAGTGTGTGAGAGAATA 57.979 33.333 0.00 0.00 0.00 1.75
110 111 7.896811 TGTATCTTTGTAGTGTGTGAGAGAAT 58.103 34.615 0.00 0.00 0.00 2.40
111 112 7.284919 TGTATCTTTGTAGTGTGTGAGAGAA 57.715 36.000 0.00 0.00 0.00 2.87
112 113 6.894339 TGTATCTTTGTAGTGTGTGAGAGA 57.106 37.500 0.00 0.00 0.00 3.10
113 114 7.438160 TGTTTGTATCTTTGTAGTGTGTGAGAG 59.562 37.037 0.00 0.00 0.00 3.20
114 115 7.269316 TGTTTGTATCTTTGTAGTGTGTGAGA 58.731 34.615 0.00 0.00 0.00 3.27
115 116 7.477144 TGTTTGTATCTTTGTAGTGTGTGAG 57.523 36.000 0.00 0.00 0.00 3.51
116 117 7.519809 GCATGTTTGTATCTTTGTAGTGTGTGA 60.520 37.037 0.00 0.00 0.00 3.58
117 118 6.578545 GCATGTTTGTATCTTTGTAGTGTGTG 59.421 38.462 0.00 0.00 0.00 3.82
118 119 6.262049 TGCATGTTTGTATCTTTGTAGTGTGT 59.738 34.615 0.00 0.00 0.00 3.72
119 120 6.667370 TGCATGTTTGTATCTTTGTAGTGTG 58.333 36.000 0.00 0.00 0.00 3.82
120 121 6.710295 TCTGCATGTTTGTATCTTTGTAGTGT 59.290 34.615 0.00 0.00 0.00 3.55
121 122 7.132694 TCTGCATGTTTGTATCTTTGTAGTG 57.867 36.000 0.00 0.00 0.00 2.74
122 123 7.571244 CGTTCTGCATGTTTGTATCTTTGTAGT 60.571 37.037 0.00 0.00 0.00 2.73
123 124 6.738200 CGTTCTGCATGTTTGTATCTTTGTAG 59.262 38.462 0.00 0.00 0.00 2.74
124 125 6.203915 ACGTTCTGCATGTTTGTATCTTTGTA 59.796 34.615 0.00 0.00 0.00 2.41
125 126 5.008613 ACGTTCTGCATGTTTGTATCTTTGT 59.991 36.000 0.00 0.00 0.00 2.83
126 127 5.451908 ACGTTCTGCATGTTTGTATCTTTG 58.548 37.500 0.00 0.00 0.00 2.77
127 128 5.689383 ACGTTCTGCATGTTTGTATCTTT 57.311 34.783 0.00 0.00 0.00 2.52
128 129 5.699001 TGTACGTTCTGCATGTTTGTATCTT 59.301 36.000 0.00 0.00 0.00 2.40
129 130 5.234752 TGTACGTTCTGCATGTTTGTATCT 58.765 37.500 0.00 0.00 0.00 1.98
130 131 5.524511 TGTACGTTCTGCATGTTTGTATC 57.475 39.130 0.00 0.00 0.00 2.24
131 132 5.613795 CGTTGTACGTTCTGCATGTTTGTAT 60.614 40.000 0.00 0.00 36.74 2.29
132 133 4.318192 CGTTGTACGTTCTGCATGTTTGTA 60.318 41.667 0.00 0.00 36.74 2.41
133 134 3.545228 CGTTGTACGTTCTGCATGTTTGT 60.545 43.478 0.00 0.00 36.74 2.83
134 135 2.964123 CGTTGTACGTTCTGCATGTTTG 59.036 45.455 0.00 0.00 36.74 2.93
135 136 2.867368 TCGTTGTACGTTCTGCATGTTT 59.133 40.909 0.00 0.00 43.14 2.83
136 137 2.475818 TCGTTGTACGTTCTGCATGTT 58.524 42.857 0.00 0.00 43.14 2.71
137 138 2.143008 TCGTTGTACGTTCTGCATGT 57.857 45.000 0.00 0.00 43.14 3.21
138 139 3.722555 ATTCGTTGTACGTTCTGCATG 57.277 42.857 0.00 0.00 43.14 4.06
139 140 5.579119 TGATAATTCGTTGTACGTTCTGCAT 59.421 36.000 0.00 0.00 43.14 3.96
140 141 4.924462 TGATAATTCGTTGTACGTTCTGCA 59.076 37.500 0.00 0.00 43.14 4.41
141 142 5.444586 TGATAATTCGTTGTACGTTCTGC 57.555 39.130 0.00 0.00 43.14 4.26
142 143 9.405083 GTTTATGATAATTCGTTGTACGTTCTG 57.595 33.333 0.00 0.00 43.14 3.02
143 144 9.362539 AGTTTATGATAATTCGTTGTACGTTCT 57.637 29.630 0.00 0.00 43.14 3.01
144 145 9.962759 AAGTTTATGATAATTCGTTGTACGTTC 57.037 29.630 0.00 0.00 43.14 3.95
145 146 9.962759 GAAGTTTATGATAATTCGTTGTACGTT 57.037 29.630 0.00 0.00 43.14 3.99
146 147 8.316046 CGAAGTTTATGATAATTCGTTGTACGT 58.684 33.333 10.98 0.00 43.14 3.57
147 148 8.661973 CGAAGTTTATGATAATTCGTTGTACG 57.338 34.615 10.98 0.00 44.19 3.67
159 160 9.896263 GGGTTTGTTTTTACGAAGTTTATGATA 57.104 29.630 0.00 0.00 37.78 2.15
160 161 7.868922 GGGGTTTGTTTTTACGAAGTTTATGAT 59.131 33.333 0.00 0.00 37.78 2.45
161 162 7.147949 TGGGGTTTGTTTTTACGAAGTTTATGA 60.148 33.333 0.00 0.00 37.78 2.15
162 163 6.979238 TGGGGTTTGTTTTTACGAAGTTTATG 59.021 34.615 0.00 0.00 37.78 1.90
163 164 7.110043 TGGGGTTTGTTTTTACGAAGTTTAT 57.890 32.000 0.00 0.00 37.78 1.40
164 165 6.521151 TGGGGTTTGTTTTTACGAAGTTTA 57.479 33.333 0.00 0.00 37.78 2.01
165 166 5.402997 TGGGGTTTGTTTTTACGAAGTTT 57.597 34.783 0.00 0.00 37.78 2.66
166 167 5.170021 GTTGGGGTTTGTTTTTACGAAGTT 58.830 37.500 0.00 0.00 37.78 2.66
167 168 9.446507 ATTCGTTGGGGTTTGTTTTTACGAAGT 62.447 37.037 0.00 0.00 45.85 3.01
168 169 3.792421 CGTTGGGGTTTGTTTTTACGAAG 59.208 43.478 0.00 0.00 0.00 3.79
169 170 3.441572 TCGTTGGGGTTTGTTTTTACGAA 59.558 39.130 0.00 0.00 34.34 3.85
170 171 3.012518 TCGTTGGGGTTTGTTTTTACGA 58.987 40.909 0.00 0.00 34.81 3.43
171 172 3.417690 TCGTTGGGGTTTGTTTTTACG 57.582 42.857 0.00 0.00 0.00 3.18
172 173 5.232626 GTGATTCGTTGGGGTTTGTTTTTAC 59.767 40.000 0.00 0.00 0.00 2.01
173 174 5.127356 AGTGATTCGTTGGGGTTTGTTTTTA 59.873 36.000 0.00 0.00 0.00 1.52
174 175 4.081365 AGTGATTCGTTGGGGTTTGTTTTT 60.081 37.500 0.00 0.00 0.00 1.94
175 176 3.449377 AGTGATTCGTTGGGGTTTGTTTT 59.551 39.130 0.00 0.00 0.00 2.43
176 177 3.028130 AGTGATTCGTTGGGGTTTGTTT 58.972 40.909 0.00 0.00 0.00 2.83
177 178 2.661718 AGTGATTCGTTGGGGTTTGTT 58.338 42.857 0.00 0.00 0.00 2.83
178 179 2.358322 AGTGATTCGTTGGGGTTTGT 57.642 45.000 0.00 0.00 0.00 2.83
179 180 3.670625 TCTAGTGATTCGTTGGGGTTTG 58.329 45.455 0.00 0.00 0.00 2.93
180 181 3.868754 GCTCTAGTGATTCGTTGGGGTTT 60.869 47.826 0.00 0.00 0.00 3.27
181 182 2.354805 GCTCTAGTGATTCGTTGGGGTT 60.355 50.000 0.00 0.00 0.00 4.11
182 183 1.207329 GCTCTAGTGATTCGTTGGGGT 59.793 52.381 0.00 0.00 0.00 4.95
183 184 1.802880 CGCTCTAGTGATTCGTTGGGG 60.803 57.143 0.00 0.00 0.00 4.96
184 185 1.560923 CGCTCTAGTGATTCGTTGGG 58.439 55.000 0.00 0.00 0.00 4.12
185 186 0.924090 GCGCTCTAGTGATTCGTTGG 59.076 55.000 0.00 0.00 0.00 3.77
186 187 0.567968 CGCGCTCTAGTGATTCGTTG 59.432 55.000 5.56 0.00 0.00 4.10
187 188 0.525668 CCGCGCTCTAGTGATTCGTT 60.526 55.000 5.56 0.00 0.00 3.85
188 189 1.064296 CCGCGCTCTAGTGATTCGT 59.936 57.895 5.56 0.00 0.00 3.85
189 190 2.296480 GCCGCGCTCTAGTGATTCG 61.296 63.158 5.56 0.00 0.00 3.34
190 191 1.951631 GGCCGCGCTCTAGTGATTC 60.952 63.158 5.56 0.00 0.00 2.52
191 192 2.107141 GGCCGCGCTCTAGTGATT 59.893 61.111 5.56 0.00 0.00 2.57
192 193 4.271816 CGGCCGCGCTCTAGTGAT 62.272 66.667 14.67 0.00 0.00 3.06
210 211 0.372679 TTAGACGAGCGAGTAGTGCG 59.627 55.000 0.00 0.00 37.44 5.34
211 212 2.539346 TTTAGACGAGCGAGTAGTGC 57.461 50.000 0.00 0.00 0.00 4.40
212 213 4.274421 TCATTTAGACGAGCGAGTAGTG 57.726 45.455 0.00 0.00 0.00 2.74
213 214 4.634883 TCTTCATTTAGACGAGCGAGTAGT 59.365 41.667 0.00 0.00 0.00 2.73
214 215 5.158101 TCTTCATTTAGACGAGCGAGTAG 57.842 43.478 0.00 0.00 0.00 2.57
215 216 5.353400 TCTTCTTCATTTAGACGAGCGAGTA 59.647 40.000 0.00 0.00 0.00 2.59
216 217 4.156190 TCTTCTTCATTTAGACGAGCGAGT 59.844 41.667 0.00 0.00 0.00 4.18
217 218 4.497608 GTCTTCTTCATTTAGACGAGCGAG 59.502 45.833 0.00 0.00 0.00 5.03
218 219 4.413087 GTCTTCTTCATTTAGACGAGCGA 58.587 43.478 0.00 0.00 0.00 4.93
219 220 3.548268 GGTCTTCTTCATTTAGACGAGCG 59.452 47.826 0.00 0.00 39.30 5.03
220 221 4.564769 CAGGTCTTCTTCATTTAGACGAGC 59.435 45.833 0.00 0.00 39.70 5.03
221 222 5.955488 TCAGGTCTTCTTCATTTAGACGAG 58.045 41.667 0.00 0.00 39.30 4.18
222 223 5.977489 TCAGGTCTTCTTCATTTAGACGA 57.023 39.130 0.00 0.00 39.30 4.20
223 224 5.457148 CGATCAGGTCTTCTTCATTTAGACG 59.543 44.000 0.00 0.00 39.30 4.18
224 225 6.565234 TCGATCAGGTCTTCTTCATTTAGAC 58.435 40.000 0.00 0.00 38.02 2.59
225 226 6.775594 TCGATCAGGTCTTCTTCATTTAGA 57.224 37.500 0.00 0.00 0.00 2.10
226 227 7.205992 TGATCGATCAGGTCTTCTTCATTTAG 58.794 38.462 23.99 0.00 32.11 1.85
227 228 7.112452 TGATCGATCAGGTCTTCTTCATTTA 57.888 36.000 23.99 0.00 32.11 1.40
228 229 5.982356 TGATCGATCAGGTCTTCTTCATTT 58.018 37.500 23.99 0.00 32.11 2.32
229 230 5.604758 TGATCGATCAGGTCTTCTTCATT 57.395 39.130 23.99 0.00 32.11 2.57
230 231 5.511031 CCATGATCGATCAGGTCTTCTTCAT 60.511 44.000 31.35 10.90 40.64 2.57
231 232 4.202192 CCATGATCGATCAGGTCTTCTTCA 60.202 45.833 31.35 9.08 40.64 3.02
232 233 4.202202 ACCATGATCGATCAGGTCTTCTTC 60.202 45.833 31.35 3.51 40.64 2.87
233 234 3.708631 ACCATGATCGATCAGGTCTTCTT 59.291 43.478 31.35 12.72 40.64 2.52
234 235 3.303938 ACCATGATCGATCAGGTCTTCT 58.696 45.455 31.35 13.40 40.64 2.85
356 368 2.662596 GGTGCATCCTGACACGGA 59.337 61.111 0.00 0.00 37.68 4.69
386 398 0.116143 TTAATGCACCCCAAGCCCTT 59.884 50.000 0.00 0.00 0.00 3.95
401 413 7.255451 CCTGGATGTACGCACCAATAAATTAAT 60.255 37.037 6.87 0.00 33.14 1.40
402 414 6.038825 CCTGGATGTACGCACCAATAAATTAA 59.961 38.462 6.87 0.00 33.14 1.40
403 415 5.529430 CCTGGATGTACGCACCAATAAATTA 59.471 40.000 6.87 0.00 33.14 1.40
404 416 4.338118 CCTGGATGTACGCACCAATAAATT 59.662 41.667 6.87 0.00 33.14 1.82
444 456 2.091122 CGTACAGCTATACGCATGCATG 59.909 50.000 22.70 22.70 41.28 4.06
537 552 2.615240 GCCCAAAATGTTTGGTGGATCC 60.615 50.000 16.49 4.20 37.88 3.36
623 638 4.790123 GTACTCGTACTTAGCATGGAGCAG 60.790 50.000 0.00 0.00 38.18 4.24
628 643 4.142447 ACACTGTACTCGTACTTAGCATGG 60.142 45.833 8.51 0.00 37.00 3.66
629 644 4.982999 ACACTGTACTCGTACTTAGCATG 58.017 43.478 8.51 0.00 37.00 4.06
642 657 6.912951 ATGGAAACTACTGTACACTGTACT 57.087 37.500 18.16 4.07 0.00 2.73
643 658 7.440255 ACAAATGGAAACTACTGTACACTGTAC 59.560 37.037 11.82 11.82 0.00 2.90
644 659 7.502696 ACAAATGGAAACTACTGTACACTGTA 58.497 34.615 0.00 0.00 0.00 2.74
645 660 6.354130 ACAAATGGAAACTACTGTACACTGT 58.646 36.000 0.00 0.00 0.00 3.55
646 661 6.706270 AGACAAATGGAAACTACTGTACACTG 59.294 38.462 0.00 0.00 0.00 3.66
647 662 6.827727 AGACAAATGGAAACTACTGTACACT 58.172 36.000 0.00 0.00 0.00 3.55
648 663 6.147328 GGAGACAAATGGAAACTACTGTACAC 59.853 42.308 0.00 0.00 0.00 2.90
649 664 6.042781 AGGAGACAAATGGAAACTACTGTACA 59.957 38.462 0.00 0.00 0.00 2.90
650 665 6.369065 CAGGAGACAAATGGAAACTACTGTAC 59.631 42.308 0.00 0.00 35.54 2.90
693 708 5.009510 TCGCTTTTTCAGGTTGATTCATCAA 59.990 36.000 0.00 0.00 43.94 2.57
694 709 4.518590 TCGCTTTTTCAGGTTGATTCATCA 59.481 37.500 0.00 0.00 34.44 3.07
695 710 5.046910 TCGCTTTTTCAGGTTGATTCATC 57.953 39.130 0.00 0.00 0.00 2.92
696 711 5.649782 ATCGCTTTTTCAGGTTGATTCAT 57.350 34.783 0.00 0.00 0.00 2.57
697 712 5.009510 TGAATCGCTTTTTCAGGTTGATTCA 59.990 36.000 9.85 9.85 44.50 2.57
761 780 1.185315 GGGTGGTTACTGCATGCATT 58.815 50.000 22.97 18.85 0.00 3.56
862 881 4.530857 GACTCATGGACCGGGCGG 62.531 72.222 6.32 0.00 42.03 6.13
863 882 4.530857 GGACTCATGGACCGGGCG 62.531 72.222 6.32 0.00 0.00 6.13
864 883 2.966732 TTGGACTCATGGACCGGGC 61.967 63.158 6.32 0.21 0.00 6.13
865 884 1.078426 GTTGGACTCATGGACCGGG 60.078 63.158 6.32 0.00 0.00 5.73
906 925 1.006162 AGGAAGAAGGCGACTAGGAGT 59.994 52.381 0.00 0.00 42.68 3.85
1127 1165 1.001745 CTGCACATCGTCAACGTCGA 61.002 55.000 0.00 0.02 41.45 4.20
1166 1207 0.618968 CTCCCTGGCCTTGTACTCCT 60.619 60.000 3.32 0.00 0.00 3.69
1206 1247 1.589196 GCGGATGTAGGCAGACGAC 60.589 63.158 0.00 0.00 32.00 4.34
1223 1264 1.664321 ATGGTCGTGTAGGAGACGGC 61.664 60.000 0.00 0.00 40.71 5.68
1343 1446 4.424061 TCGAAATGCAAAACCTCATCAG 57.576 40.909 0.00 0.00 0.00 2.90
1485 1604 1.853963 AGCGGTCCAGATAGTTGACT 58.146 50.000 0.00 0.00 0.00 3.41
1548 1667 9.481340 GAGATAATCAACACTAGCAACATGATA 57.519 33.333 0.00 0.00 0.00 2.15
1549 1668 7.989170 TGAGATAATCAACACTAGCAACATGAT 59.011 33.333 0.00 0.00 34.02 2.45
1550 1669 7.330262 TGAGATAATCAACACTAGCAACATGA 58.670 34.615 0.00 0.00 34.02 3.07
1551 1670 7.543947 TGAGATAATCAACACTAGCAACATG 57.456 36.000 0.00 0.00 34.02 3.21
1552 1671 7.772292 ACATGAGATAATCAACACTAGCAACAT 59.228 33.333 0.00 0.00 42.53 2.71
1566 1685 7.566858 AAACAAACGCAAACATGAGATAATC 57.433 32.000 0.00 0.00 0.00 1.75
1614 1739 5.220472 CGCAACATTTTAGTGACATCGATCT 60.220 40.000 0.00 0.00 0.00 2.75
1638 1763 7.390440 TCTGCCATTAGGTTACAATATATGCAC 59.610 37.037 0.00 0.00 37.19 4.57
1724 1849 0.460311 GGTATGGTGACCTCGTCCAG 59.540 60.000 2.11 0.00 36.47 3.86
1775 1900 3.602491 CGGATAGTAGTGCACGTACGTAC 60.602 52.174 22.34 16.78 0.00 3.67
1776 1901 2.539688 CGGATAGTAGTGCACGTACGTA 59.460 50.000 22.34 3.16 0.00 3.57
1777 1902 1.328680 CGGATAGTAGTGCACGTACGT 59.671 52.381 16.72 16.72 0.00 3.57
1778 1903 1.594397 TCGGATAGTAGTGCACGTACG 59.406 52.381 15.01 15.01 0.00 3.67
1779 1904 3.663754 CGATCGGATAGTAGTGCACGTAC 60.664 52.174 12.01 13.75 0.00 3.67
1780 1905 2.477754 CGATCGGATAGTAGTGCACGTA 59.522 50.000 12.01 5.13 0.00 3.57
1781 1906 1.263484 CGATCGGATAGTAGTGCACGT 59.737 52.381 12.01 2.74 0.00 4.49
1782 1907 1.529865 TCGATCGGATAGTAGTGCACG 59.470 52.381 16.41 0.00 0.00 5.34
1783 1908 3.725305 CGATCGATCGGATAGTAGTGCAC 60.725 52.174 34.54 9.40 45.93 4.57
1804 1943 5.388890 GGAGCTTGTGATCGAATATAAAGCG 60.389 44.000 13.84 0.00 42.50 4.68
1899 2043 1.640593 TTTATCAGGCCGGCCCATGA 61.641 55.000 41.72 36.60 36.58 3.07
1900 2044 0.540365 ATTTATCAGGCCGGCCCATG 60.540 55.000 41.72 32.80 36.58 3.66
1901 2045 0.188342 AATTTATCAGGCCGGCCCAT 59.812 50.000 41.72 33.16 36.58 4.00
1923 2067 5.235831 CCATCACGCATATCATCCATCATAC 59.764 44.000 0.00 0.00 0.00 2.39
2080 2224 4.265056 GCGGTGGTGGTGGGAAGT 62.265 66.667 0.00 0.00 0.00 3.01
2098 2242 2.279451 CGAGATCGATTGGCGGCA 60.279 61.111 7.97 7.97 43.02 5.69
2152 2296 6.806739 TGATTAATCGATCTGCAGGTAATACG 59.193 38.462 15.13 6.67 0.00 3.06
2156 2300 6.161855 ACTGATTAATCGATCTGCAGGTAA 57.838 37.500 15.13 0.00 0.00 2.85
2447 2592 6.423604 AGGAAAAACAAACAAACAAGAGTGTG 59.576 34.615 0.00 0.00 38.27 3.82
2489 2634 4.081752 ACACGTACGGGGTCAATTATTGTA 60.082 41.667 23.48 0.00 0.00 2.41
2490 2635 3.264104 CACGTACGGGGTCAATTATTGT 58.736 45.455 21.06 0.00 0.00 2.71
2491 2636 3.264104 ACACGTACGGGGTCAATTATTG 58.736 45.455 23.48 7.49 0.00 1.90
2492 2637 3.615224 ACACGTACGGGGTCAATTATT 57.385 42.857 23.48 0.00 0.00 1.40
2520 2665 2.095668 CGTCAGACTCATCGCCCTATAC 60.096 54.545 0.00 0.00 0.00 1.47
2523 2668 0.107361 TCGTCAGACTCATCGCCCTA 60.107 55.000 0.00 0.00 0.00 3.53
2577 2722 3.614092 ACTTGTGATGATGATGACCCAC 58.386 45.455 0.00 0.00 0.00 4.61
2581 2726 7.221645 CAGTACTGTACTTGTGATGATGATGAC 59.778 40.741 17.46 0.00 36.76 3.06
2588 2736 3.366985 CGGCAGTACTGTACTTGTGATGA 60.367 47.826 23.44 0.00 36.76 2.92
2589 2737 2.923655 CGGCAGTACTGTACTTGTGATG 59.076 50.000 23.44 7.83 36.76 3.07
2609 2757 4.463879 CTCCCCTGCAGCTGGTCG 62.464 72.222 17.12 6.90 0.00 4.79
2627 2775 3.699067 GAATGCAATCACTGAAATCGGG 58.301 45.455 0.00 0.00 0.00 5.14
3071 3233 2.874701 CAACTGAACTCTGAACACCCAG 59.125 50.000 0.00 0.00 35.55 4.45
3077 3239 4.946784 ACACAACAACTGAACTCTGAAC 57.053 40.909 0.00 0.00 0.00 3.18
3158 3320 0.888619 TTCGAGCCGATCTCACTGTT 59.111 50.000 0.00 0.00 41.98 3.16
3171 3333 1.067213 AGAAAGGCAGACTCTTCGAGC 60.067 52.381 0.00 0.00 32.04 5.03
3174 3336 2.732412 TCAGAAAGGCAGACTCTTCG 57.268 50.000 0.00 0.00 0.00 3.79
3359 3521 7.390823 TGTGCTGTAGATTTGGATAACTAACA 58.609 34.615 0.00 0.00 0.00 2.41
3449 3611 4.202315 GCTATCTTCTTCTTCTTCTCCCCC 60.202 50.000 0.00 0.00 0.00 5.40
3452 3614 6.705825 GGATTGCTATCTTCTTCTTCTTCTCC 59.294 42.308 8.06 0.00 0.00 3.71
3453 3615 6.705825 GGGATTGCTATCTTCTTCTTCTTCTC 59.294 42.308 8.06 0.00 0.00 2.87
3454 3616 6.409120 GGGGATTGCTATCTTCTTCTTCTTCT 60.409 42.308 8.06 0.00 0.00 2.85
3659 3821 3.772932 CAAGCGTGCAATGGATGTTAAT 58.227 40.909 0.00 0.00 0.00 1.40
3684 3846 2.971598 GCTGGCTACTCCCCTGCAA 61.972 63.158 4.70 0.00 44.05 4.08
3685 3847 3.402681 GCTGGCTACTCCCCTGCA 61.403 66.667 4.70 0.00 44.05 4.41
3686 3848 2.601194 GAAGCTGGCTACTCCCCTGC 62.601 65.000 0.00 1.63 44.71 4.85
3687 3849 1.267574 TGAAGCTGGCTACTCCCCTG 61.268 60.000 0.00 0.00 0.00 4.45
3688 3850 0.980231 CTGAAGCTGGCTACTCCCCT 60.980 60.000 0.00 0.00 0.00 4.79
3689 3851 1.268283 ACTGAAGCTGGCTACTCCCC 61.268 60.000 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.