Multiple sequence alignment - TraesCS2B01G351000

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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 TraesCS2B01G351000 chr2B 100.000 3548 0 0 1 3548 498312157 498308610 0.000000e+00 6553.0
1 TraesCS2B01G351000 chr2D 92.777 2312 99 30 245 2533 424016418 424014152 0.000000e+00 3282.0
2 TraesCS2B01G351000 chr2D 81.206 995 89 45 744 1713 624297970 624297049 0.000000e+00 712.0
3 TraesCS2B01G351000 chr2D 87.712 236 29 0 3 238 373935930 373935695 3.490000e-70 276.0
4 TraesCS2B01G351000 chr2A 92.631 2144 86 24 415 2533 564217666 564219762 0.000000e+00 3018.0
5 TraesCS2B01G351000 chr2A 96.857 1018 7 1 2531 3548 704756462 704757454 0.000000e+00 1679.0
6 TraesCS2B01G351000 chr2A 90.854 164 13 2 1141 1303 755700288 755700126 5.960000e-53 219.0
7 TraesCS2B01G351000 chr2A 86.325 117 14 2 920 1036 755700456 755700342 3.720000e-25 126.0
8 TraesCS2B01G351000 chrUn 84.987 373 27 15 1359 1711 232286346 232285983 5.640000e-93 351.0
9 TraesCS2B01G351000 chrUn 92.994 157 11 0 1134 1290 232287795 232287639 2.750000e-56 230.0
10 TraesCS2B01G351000 chr6D 88.983 236 26 0 3 238 301498435 301498200 3.460000e-75 292.0
11 TraesCS2B01G351000 chr6D 91.954 87 7 0 1603 1689 432709198 432709112 4.810000e-24 122.0
12 TraesCS2B01G351000 chr7D 88.889 234 26 0 5 238 263829852 263829619 4.480000e-74 289.0
13 TraesCS2B01G351000 chr7D 87.712 236 29 0 3 238 139983458 139983223 3.490000e-70 276.0
14 TraesCS2B01G351000 chr3A 88.034 234 28 0 5 238 463275381 463275614 9.700000e-71 278.0
15 TraesCS2B01G351000 chr3A 93.976 83 5 0 1603 1685 514611935 514611853 3.720000e-25 126.0
16 TraesCS2B01G351000 chr7A 87.712 236 29 0 3 238 536117857 536117622 3.490000e-70 276.0
17 TraesCS2B01G351000 chr6B 87.712 236 29 0 3 238 227211733 227211498 3.490000e-70 276.0
18 TraesCS2B01G351000 chr1D 87.712 236 29 0 3 238 300812982 300813217 3.490000e-70 276.0
19 TraesCS2B01G351000 chr4D 87.448 239 28 2 3 240 340013019 340013256 1.250000e-69 274.0
20 TraesCS2B01G351000 chr4D 85.366 123 18 0 1598 1720 335349327 335349449 1.030000e-25 128.0
21 TraesCS2B01G351000 chr4B 86.400 125 13 3 1598 1720 413500301 413500423 2.220000e-27 134.0
22 TraesCS2B01G351000 chr4A 85.950 121 13 3 1601 1719 137523974 137523856 3.720000e-25 126.0
23 TraesCS2B01G351000 chr1B 90.196 51 3 2 2534 2583 562887469 562887518 8.220000e-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 TraesCS2B01G351000 chr2B 498308610 498312157 3547 True 6553.0 6553 100.0000 1 3548 1 chr2B.!!$R1 3547
1 TraesCS2B01G351000 chr2D 424014152 424016418 2266 True 3282.0 3282 92.7770 245 2533 1 chr2D.!!$R2 2288
2 TraesCS2B01G351000 chr2D 624297049 624297970 921 True 712.0 712 81.2060 744 1713 1 chr2D.!!$R3 969
3 TraesCS2B01G351000 chr2A 564217666 564219762 2096 False 3018.0 3018 92.6310 415 2533 1 chr2A.!!$F1 2118
4 TraesCS2B01G351000 chr2A 704756462 704757454 992 False 1679.0 1679 96.8570 2531 3548 1 chr2A.!!$F2 1017
5 TraesCS2B01G351000 chrUn 232285983 232287795 1812 True 290.5 351 88.9905 1134 1711 2 chrUn.!!$R1 577

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
143 144 0.037605 CCCAAAGCGGAGAAGTACGT 60.038 55.000 0.00 0.00 36.56 3.57 F
145 146 1.067776 CCAAAGCGGAGAAGTACGTCT 60.068 52.381 11.33 11.33 36.56 4.18 F
1581 2914 0.636733 GCGTTTTGCTGATCAATGCG 59.363 50.000 0.00 0.00 41.73 4.73 F
2247 3580 0.035176 GGCCAGCATTGCAGGAAAAA 59.965 50.000 22.88 0.00 37.40 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1558 2878 0.039256 TTGATCAGCAAAACGCCAGC 60.039 50.000 0.00 0.0 44.04 4.85 R
1925 3258 0.955428 GTTGAAGCAGGGCGTGATGA 60.955 55.000 12.03 0.0 0.00 2.92 R
2404 3737 0.661552 CTAGCTAAGCTCGCCGTGTA 59.338 55.000 4.50 0.0 40.44 2.90 R
3136 4469 3.749064 GAGTGGACCGCTGCTCGA 61.749 66.667 13.57 0.0 41.67 4.04 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
26 27 4.501071 TCTAAAGCCGTTTAGATGACACC 58.499 43.478 4.49 0.00 46.12 4.16
27 28 1.722011 AAGCCGTTTAGATGACACCG 58.278 50.000 0.00 0.00 0.00 4.94
28 29 0.606604 AGCCGTTTAGATGACACCGT 59.393 50.000 0.00 0.00 0.00 4.83
29 30 1.820519 AGCCGTTTAGATGACACCGTA 59.179 47.619 0.00 0.00 0.00 4.02
30 31 2.429610 AGCCGTTTAGATGACACCGTAT 59.570 45.455 0.00 0.00 0.00 3.06
31 32 2.538449 GCCGTTTAGATGACACCGTATG 59.462 50.000 0.00 0.00 0.00 2.39
32 33 3.735820 GCCGTTTAGATGACACCGTATGA 60.736 47.826 0.00 0.00 0.00 2.15
33 34 4.617959 CCGTTTAGATGACACCGTATGAT 58.382 43.478 0.00 0.00 0.00 2.45
34 35 5.047847 CCGTTTAGATGACACCGTATGATT 58.952 41.667 0.00 0.00 0.00 2.57
35 36 5.522460 CCGTTTAGATGACACCGTATGATTT 59.478 40.000 0.00 0.00 0.00 2.17
36 37 6.698329 CCGTTTAGATGACACCGTATGATTTA 59.302 38.462 0.00 0.00 0.00 1.40
37 38 7.384115 CCGTTTAGATGACACCGTATGATTTAT 59.616 37.037 0.00 0.00 0.00 1.40
38 39 8.214472 CGTTTAGATGACACCGTATGATTTATG 58.786 37.037 0.00 0.00 0.00 1.90
39 40 8.495949 GTTTAGATGACACCGTATGATTTATGG 58.504 37.037 0.00 0.00 0.00 2.74
40 41 6.174720 AGATGACACCGTATGATTTATGGT 57.825 37.500 0.00 0.00 37.30 3.55
41 42 6.591935 AGATGACACCGTATGATTTATGGTT 58.408 36.000 0.00 0.00 34.78 3.67
42 43 7.054124 AGATGACACCGTATGATTTATGGTTT 58.946 34.615 0.00 0.00 34.78 3.27
43 44 6.429791 TGACACCGTATGATTTATGGTTTG 57.570 37.500 0.00 0.00 34.78 2.93
44 45 5.355630 TGACACCGTATGATTTATGGTTTGG 59.644 40.000 0.00 0.00 34.78 3.28
45 46 4.097286 ACACCGTATGATTTATGGTTTGGC 59.903 41.667 0.00 0.00 34.78 4.52
46 47 4.097135 CACCGTATGATTTATGGTTTGGCA 59.903 41.667 0.00 0.00 34.78 4.92
47 48 4.707448 ACCGTATGATTTATGGTTTGGCAA 59.293 37.500 0.00 0.00 33.26 4.52
48 49 5.186021 ACCGTATGATTTATGGTTTGGCAAA 59.814 36.000 8.93 8.93 33.26 3.68
49 50 6.102663 CCGTATGATTTATGGTTTGGCAAAA 58.897 36.000 15.29 0.00 0.00 2.44
50 51 6.591834 CCGTATGATTTATGGTTTGGCAAAAA 59.408 34.615 15.29 6.65 0.00 1.94
77 78 9.511144 ACCTAAGTTGTCGTTTCTTAAATTTTG 57.489 29.630 0.00 0.00 0.00 2.44
78 79 9.724839 CCTAAGTTGTCGTTTCTTAAATTTTGA 57.275 29.630 0.00 0.00 0.00 2.69
80 81 8.628882 AAGTTGTCGTTTCTTAAATTTTGAGG 57.371 30.769 0.00 0.00 0.00 3.86
81 82 7.992008 AGTTGTCGTTTCTTAAATTTTGAGGA 58.008 30.769 0.00 0.00 0.00 3.71
82 83 8.463607 AGTTGTCGTTTCTTAAATTTTGAGGAA 58.536 29.630 0.00 0.00 0.00 3.36
83 84 9.078753 GTTGTCGTTTCTTAAATTTTGAGGAAA 57.921 29.630 0.00 0.00 0.00 3.13
84 85 9.810545 TTGTCGTTTCTTAAATTTTGAGGAAAT 57.189 25.926 0.00 0.00 39.63 2.17
85 86 9.243637 TGTCGTTTCTTAAATTTTGAGGAAATG 57.756 29.630 0.00 4.00 37.98 2.32
86 87 9.458374 GTCGTTTCTTAAATTTTGAGGAAATGA 57.542 29.630 12.79 12.79 37.98 2.57
87 88 9.458374 TCGTTTCTTAAATTTTGAGGAAATGAC 57.542 29.630 12.79 0.00 37.98 3.06
88 89 8.417176 CGTTTCTTAAATTTTGAGGAAATGACG 58.583 33.333 10.21 4.19 37.98 4.35
89 90 7.867445 TTCTTAAATTTTGAGGAAATGACGC 57.133 32.000 0.00 0.00 37.98 5.19
90 91 7.214467 TCTTAAATTTTGAGGAAATGACGCT 57.786 32.000 0.00 0.00 37.98 5.07
91 92 7.657336 TCTTAAATTTTGAGGAAATGACGCTT 58.343 30.769 0.00 0.00 37.98 4.68
92 93 8.788806 TCTTAAATTTTGAGGAAATGACGCTTA 58.211 29.630 0.00 0.00 37.98 3.09
93 94 9.573133 CTTAAATTTTGAGGAAATGACGCTTAT 57.427 29.630 0.00 0.00 37.98 1.73
94 95 7.816945 AAATTTTGAGGAAATGACGCTTATG 57.183 32.000 0.00 0.00 37.98 1.90
95 96 5.957842 TTTTGAGGAAATGACGCTTATGT 57.042 34.783 0.00 0.00 0.00 2.29
96 97 5.545658 TTTGAGGAAATGACGCTTATGTC 57.454 39.130 0.00 0.00 39.37 3.06
103 104 2.010145 TGACGCTTATGTCAAGAGGC 57.990 50.000 0.00 0.00 45.40 4.70
104 105 1.550524 TGACGCTTATGTCAAGAGGCT 59.449 47.619 0.00 0.00 45.40 4.58
105 106 2.028112 TGACGCTTATGTCAAGAGGCTT 60.028 45.455 0.00 0.00 45.40 4.35
106 107 2.605366 GACGCTTATGTCAAGAGGCTTC 59.395 50.000 0.00 0.00 38.75 3.86
107 108 2.028112 ACGCTTATGTCAAGAGGCTTCA 60.028 45.455 0.00 0.00 0.00 3.02
108 109 2.606725 CGCTTATGTCAAGAGGCTTCAG 59.393 50.000 0.00 0.00 0.00 3.02
109 110 2.354199 GCTTATGTCAAGAGGCTTCAGC 59.646 50.000 0.00 0.00 41.14 4.26
121 122 1.216122 GCTTCAGCCTGATAAGCTCG 58.784 55.000 10.48 0.00 41.85 5.03
122 123 1.202463 GCTTCAGCCTGATAAGCTCGA 60.202 52.381 10.48 0.00 41.85 4.04
123 124 2.547642 GCTTCAGCCTGATAAGCTCGAT 60.548 50.000 10.48 0.00 41.85 3.59
124 125 3.316283 CTTCAGCCTGATAAGCTCGATC 58.684 50.000 0.00 0.00 38.95 3.69
125 126 1.615883 TCAGCCTGATAAGCTCGATCC 59.384 52.381 0.00 0.00 38.95 3.36
126 127 0.972883 AGCCTGATAAGCTCGATCCC 59.027 55.000 6.20 0.00 34.91 3.85
127 128 0.681733 GCCTGATAAGCTCGATCCCA 59.318 55.000 6.20 0.00 0.00 4.37
128 129 1.070758 GCCTGATAAGCTCGATCCCAA 59.929 52.381 6.20 0.00 0.00 4.12
129 130 2.485479 GCCTGATAAGCTCGATCCCAAA 60.485 50.000 6.20 0.00 0.00 3.28
130 131 3.397482 CCTGATAAGCTCGATCCCAAAG 58.603 50.000 6.20 0.00 0.00 2.77
131 132 2.805099 CTGATAAGCTCGATCCCAAAGC 59.195 50.000 6.20 0.00 36.27 3.51
132 133 1.795286 GATAAGCTCGATCCCAAAGCG 59.205 52.381 0.00 0.00 40.95 4.68
133 134 0.179084 TAAGCTCGATCCCAAAGCGG 60.179 55.000 0.00 0.00 40.95 5.52
134 135 1.899437 AAGCTCGATCCCAAAGCGGA 61.899 55.000 0.00 0.00 40.95 5.54
135 136 1.884926 GCTCGATCCCAAAGCGGAG 60.885 63.158 0.00 0.00 36.56 4.63
136 137 1.816537 CTCGATCCCAAAGCGGAGA 59.183 57.895 0.00 0.00 36.56 3.71
137 138 0.175760 CTCGATCCCAAAGCGGAGAA 59.824 55.000 0.00 0.00 36.56 2.87
138 139 0.175760 TCGATCCCAAAGCGGAGAAG 59.824 55.000 0.00 0.00 36.56 2.85
139 140 0.108138 CGATCCCAAAGCGGAGAAGT 60.108 55.000 0.00 0.00 36.56 3.01
140 141 1.136305 CGATCCCAAAGCGGAGAAGTA 59.864 52.381 0.00 0.00 36.56 2.24
141 142 2.552031 GATCCCAAAGCGGAGAAGTAC 58.448 52.381 0.00 0.00 36.56 2.73
142 143 0.245539 TCCCAAAGCGGAGAAGTACG 59.754 55.000 0.00 0.00 36.56 3.67
143 144 0.037605 CCCAAAGCGGAGAAGTACGT 60.038 55.000 0.00 0.00 36.56 3.57
144 145 1.347320 CCAAAGCGGAGAAGTACGTC 58.653 55.000 0.00 0.00 36.56 4.34
145 146 1.067776 CCAAAGCGGAGAAGTACGTCT 60.068 52.381 11.33 11.33 36.56 4.18
146 147 2.609737 CCAAAGCGGAGAAGTACGTCTT 60.610 50.000 12.74 0.00 36.46 3.01
174 175 6.614657 AGGATATCCTAAAGAAACCATTGGG 58.385 40.000 23.34 0.00 46.48 4.12
176 177 7.352522 AGGATATCCTAAAGAAACCATTGGGTA 59.647 37.037 23.34 0.00 46.55 3.69
191 192 7.510549 CCATTGGGTATACCTTTTATCACAG 57.489 40.000 21.25 5.05 41.11 3.66
192 193 7.287061 CCATTGGGTATACCTTTTATCACAGA 58.713 38.462 21.25 0.00 41.11 3.41
193 194 7.944554 CCATTGGGTATACCTTTTATCACAGAT 59.055 37.037 21.25 0.00 41.11 2.90
194 195 9.003658 CATTGGGTATACCTTTTATCACAGATC 57.996 37.037 21.25 0.33 41.11 2.75
195 196 7.931015 TGGGTATACCTTTTATCACAGATCT 57.069 36.000 21.25 0.00 41.11 2.75
196 197 9.442062 TTGGGTATACCTTTTATCACAGATCTA 57.558 33.333 21.25 0.00 41.11 1.98
197 198 9.442062 TGGGTATACCTTTTATCACAGATCTAA 57.558 33.333 21.25 0.00 41.11 2.10
198 199 9.930693 GGGTATACCTTTTATCACAGATCTAAG 57.069 37.037 21.25 0.00 35.85 2.18
199 200 9.930693 GGTATACCTTTTATCACAGATCTAAGG 57.069 37.037 15.09 14.15 37.33 2.69
200 201 9.930693 GTATACCTTTTATCACAGATCTAAGGG 57.069 37.037 18.21 10.48 35.99 3.95
201 202 5.685728 ACCTTTTATCACAGATCTAAGGGC 58.314 41.667 18.21 0.00 35.99 5.19
202 203 5.191722 ACCTTTTATCACAGATCTAAGGGCA 59.808 40.000 18.21 0.00 35.99 5.36
203 204 6.126361 ACCTTTTATCACAGATCTAAGGGCAT 60.126 38.462 18.21 0.37 35.99 4.40
204 205 6.206243 CCTTTTATCACAGATCTAAGGGCATG 59.794 42.308 9.49 0.00 0.00 4.06
205 206 6.499106 TTTATCACAGATCTAAGGGCATGA 57.501 37.500 0.00 0.00 0.00 3.07
206 207 6.692849 TTATCACAGATCTAAGGGCATGAT 57.307 37.500 0.00 0.00 0.00 2.45
207 208 4.613925 TCACAGATCTAAGGGCATGATC 57.386 45.455 0.00 0.00 37.46 2.92
208 209 4.229639 TCACAGATCTAAGGGCATGATCT 58.770 43.478 0.00 0.00 45.21 2.75
209 210 4.657504 TCACAGATCTAAGGGCATGATCTT 59.342 41.667 0.00 1.29 42.75 2.40
210 211 5.131642 TCACAGATCTAAGGGCATGATCTTT 59.868 40.000 0.00 0.00 42.75 2.52
211 212 6.327365 TCACAGATCTAAGGGCATGATCTTTA 59.673 38.462 0.00 0.00 42.75 1.85
212 213 7.016957 TCACAGATCTAAGGGCATGATCTTTAT 59.983 37.037 0.00 0.00 42.75 1.40
213 214 7.664731 CACAGATCTAAGGGCATGATCTTTATT 59.335 37.037 0.00 0.00 42.75 1.40
214 215 7.664731 ACAGATCTAAGGGCATGATCTTTATTG 59.335 37.037 0.00 0.00 42.75 1.90
215 216 7.664731 CAGATCTAAGGGCATGATCTTTATTGT 59.335 37.037 0.00 0.00 42.75 2.71
216 217 7.882271 AGATCTAAGGGCATGATCTTTATTGTC 59.118 37.037 0.00 0.00 42.75 3.18
217 218 6.899089 TCTAAGGGCATGATCTTTATTGTCA 58.101 36.000 0.00 0.00 0.00 3.58
218 219 7.345691 TCTAAGGGCATGATCTTTATTGTCAA 58.654 34.615 0.00 0.00 0.00 3.18
219 220 6.461110 AAGGGCATGATCTTTATTGTCAAG 57.539 37.500 0.00 0.00 0.00 3.02
220 221 5.759059 AGGGCATGATCTTTATTGTCAAGA 58.241 37.500 0.00 0.00 34.74 3.02
221 222 6.189859 AGGGCATGATCTTTATTGTCAAGAA 58.810 36.000 0.00 0.00 33.94 2.52
222 223 6.096001 AGGGCATGATCTTTATTGTCAAGAAC 59.904 38.462 0.00 0.00 33.94 3.01
223 224 5.967674 GGCATGATCTTTATTGTCAAGAACG 59.032 40.000 0.00 0.00 33.94 3.95
224 225 5.967674 GCATGATCTTTATTGTCAAGAACGG 59.032 40.000 0.00 0.00 33.94 4.44
225 226 6.489675 CATGATCTTTATTGTCAAGAACGGG 58.510 40.000 0.00 0.00 33.94 5.28
226 227 5.556915 TGATCTTTATTGTCAAGAACGGGT 58.443 37.500 0.00 0.00 33.94 5.28
227 228 5.642063 TGATCTTTATTGTCAAGAACGGGTC 59.358 40.000 0.00 0.00 33.94 4.46
228 229 4.320870 TCTTTATTGTCAAGAACGGGTCC 58.679 43.478 0.00 0.00 0.00 4.46
229 230 4.041198 TCTTTATTGTCAAGAACGGGTCCT 59.959 41.667 0.00 0.00 0.00 3.85
230 231 2.951229 ATTGTCAAGAACGGGTCCTT 57.049 45.000 0.00 0.00 0.00 3.36
231 232 2.721425 TTGTCAAGAACGGGTCCTTT 57.279 45.000 0.00 0.00 0.00 3.11
232 233 2.249844 TGTCAAGAACGGGTCCTTTC 57.750 50.000 0.00 0.00 0.00 2.62
233 234 1.766496 TGTCAAGAACGGGTCCTTTCT 59.234 47.619 3.28 3.28 36.32 2.52
234 235 2.967201 TGTCAAGAACGGGTCCTTTCTA 59.033 45.455 8.82 0.00 34.16 2.10
235 236 3.006537 TGTCAAGAACGGGTCCTTTCTAG 59.993 47.826 8.82 0.00 34.16 2.43
236 237 3.257624 GTCAAGAACGGGTCCTTTCTAGA 59.742 47.826 8.82 0.00 34.16 2.43
237 238 3.510360 TCAAGAACGGGTCCTTTCTAGAG 59.490 47.826 8.82 3.96 34.16 2.43
238 239 2.458620 AGAACGGGTCCTTTCTAGAGG 58.541 52.381 6.93 0.00 33.63 3.69
239 240 2.042706 AGAACGGGTCCTTTCTAGAGGA 59.957 50.000 6.93 0.00 43.47 3.71
280 281 3.090952 CAACTTTGCATCCGGTTTTCA 57.909 42.857 0.00 0.00 0.00 2.69
312 313 3.382832 CGGACGAGCCCCAGAACT 61.383 66.667 0.00 0.00 0.00 3.01
314 315 1.601419 CGGACGAGCCCCAGAACTTA 61.601 60.000 0.00 0.00 0.00 2.24
320 321 1.070289 GAGCCCCAGAACTTATACGGG 59.930 57.143 0.00 0.00 36.59 5.28
326 327 2.224209 CCAGAACTTATACGGGGCGATT 60.224 50.000 0.00 0.00 0.00 3.34
327 328 3.006110 CCAGAACTTATACGGGGCGATTA 59.994 47.826 0.00 0.00 0.00 1.75
331 332 3.167485 ACTTATACGGGGCGATTATGGA 58.833 45.455 0.00 0.00 0.00 3.41
345 346 4.201812 CGATTATGGATGACAAACTGCGTT 60.202 41.667 0.00 0.00 0.00 4.84
349 350 2.143122 GGATGACAAACTGCGTTCAGA 58.857 47.619 0.00 0.00 42.95 3.27
351 352 2.595124 TGACAAACTGCGTTCAGAGA 57.405 45.000 0.00 0.00 42.95 3.10
481 483 9.482627 GCAATAGAATGTAGCACTAGATTAACT 57.517 33.333 0.00 0.00 30.42 2.24
542 545 5.046591 ACGATCCATTCACCTCTCAAAGTAA 60.047 40.000 0.00 0.00 0.00 2.24
548 551 7.505585 TCCATTCACCTCTCAAAGTAATTTTGT 59.494 33.333 0.22 0.00 45.17 2.83
549 552 7.596248 CCATTCACCTCTCAAAGTAATTTTGTG 59.404 37.037 0.22 0.00 45.17 3.33
553 556 6.259550 CCTCTCAAAGTAATTTTGTGGAGG 57.740 41.667 18.95 18.95 46.81 4.30
568 571 3.261897 TGTGGAGGAAAATCTGGAGTCTC 59.738 47.826 0.00 0.00 0.00 3.36
844 885 3.637273 GCAACCTGTCCCGTCCCT 61.637 66.667 0.00 0.00 0.00 4.20
845 886 2.288025 GCAACCTGTCCCGTCCCTA 61.288 63.158 0.00 0.00 0.00 3.53
1091 1158 2.266689 GCCTACCGGAAAGCGGAA 59.733 61.111 9.46 0.00 0.00 4.30
1327 2626 3.002965 GGTTAAGTGGAAGGAACGTGTTG 59.997 47.826 0.00 0.00 0.00 3.33
1396 2709 4.749310 CAGCGCTGCGGGAAGAGT 62.749 66.667 26.68 0.00 0.00 3.24
1558 2878 0.667453 TCTGAGCTAGCTGCATCTCG 59.333 55.000 24.99 8.15 45.94 4.04
1579 2912 2.256174 CTGGCGTTTTGCTGATCAATG 58.744 47.619 0.00 0.00 45.43 2.82
1580 2913 0.994263 GGCGTTTTGCTGATCAATGC 59.006 50.000 0.00 0.00 45.43 3.56
1581 2914 0.636733 GCGTTTTGCTGATCAATGCG 59.363 50.000 0.00 0.00 41.73 4.73
1582 2915 1.967762 CGTTTTGCTGATCAATGCGT 58.032 45.000 0.00 0.00 34.12 5.24
1583 2916 2.318578 CGTTTTGCTGATCAATGCGTT 58.681 42.857 0.00 0.00 34.12 4.84
1584 2917 2.089427 CGTTTTGCTGATCAATGCGTTG 59.911 45.455 12.66 12.66 34.12 4.10
1725 3058 2.029073 CCCGTCACGCACAAGTCT 59.971 61.111 0.00 0.00 0.00 3.24
1942 3275 1.078918 CTCATCACGCCCTGCTTCA 60.079 57.895 0.00 0.00 0.00 3.02
1943 3276 0.674581 CTCATCACGCCCTGCTTCAA 60.675 55.000 0.00 0.00 0.00 2.69
2097 3430 1.743995 GTACGCCGCATTCAACCCT 60.744 57.895 0.00 0.00 0.00 4.34
2103 3436 2.126346 GCATTCAACCCTGCGCAC 60.126 61.111 5.66 0.00 0.00 5.34
2247 3580 0.035176 GGCCAGCATTGCAGGAAAAA 59.965 50.000 22.88 0.00 37.40 1.94
2386 3719 1.725665 CCCGACGAGCTGACGAATA 59.274 57.895 1.33 0.00 37.99 1.75
2404 3737 8.779303 TGACGAATAACATGTGTGACTAAATTT 58.221 29.630 0.00 0.00 0.00 1.82
2443 3776 1.070975 GCATCATCGATGAACGTCAGC 60.071 52.381 30.41 21.39 42.09 4.26
2454 3787 4.544689 CGTCAGCTCGCCGGAGAG 62.545 72.222 28.81 28.81 43.27 3.20
2461 3794 0.179097 GCTCGCCGGAGAGAAGAAAT 60.179 55.000 35.76 0.00 43.27 2.17
2463 3796 0.460311 TCGCCGGAGAGAAGAAATCC 59.540 55.000 5.05 0.00 0.00 3.01
2464 3797 0.461961 CGCCGGAGAGAAGAAATCCT 59.538 55.000 5.05 0.00 0.00 3.24
2465 3798 1.681793 CGCCGGAGAGAAGAAATCCTA 59.318 52.381 5.05 0.00 0.00 2.94
2466 3799 2.287909 CGCCGGAGAGAAGAAATCCTAG 60.288 54.545 5.05 0.00 0.00 3.02
2467 3800 2.959707 GCCGGAGAGAAGAAATCCTAGA 59.040 50.000 5.05 0.00 0.00 2.43
2468 3801 3.005367 GCCGGAGAGAAGAAATCCTAGAG 59.995 52.174 5.05 0.00 0.00 2.43
2469 3802 3.572255 CCGGAGAGAAGAAATCCTAGAGG 59.428 52.174 0.00 0.00 0.00 3.69
2505 3838 7.920738 ACGATTCTAGAAGCACATAAATTTCC 58.079 34.615 19.99 0.00 0.00 3.13
2535 3868 6.754675 GTGCCTGAGAAGAGTTAGAATAAGAC 59.245 42.308 0.00 0.00 0.00 3.01
2650 3983 3.826236 TCTACGCAACACTAGACTCAC 57.174 47.619 0.00 0.00 0.00 3.51
3042 4375 3.817787 CCGCCATGGTGTCATCTG 58.182 61.111 23.44 3.59 0.00 2.90
3043 4376 1.820906 CCGCCATGGTGTCATCTGG 60.821 63.158 23.44 2.85 0.00 3.86
3044 4377 2.475466 CGCCATGGTGTCATCTGGC 61.475 63.158 17.59 13.59 38.42 4.85
3045 4378 2.123428 GCCATGGTGTCATCTGGCC 61.123 63.158 14.67 0.00 36.81 5.36
3046 4379 1.820906 CCATGGTGTCATCTGGCCG 60.821 63.158 2.57 0.00 0.00 6.13
3047 4380 1.820906 CATGGTGTCATCTGGCCGG 60.821 63.158 4.71 4.71 0.00 6.13
3048 4381 3.047807 ATGGTGTCATCTGGCCGGG 62.048 63.158 12.87 0.00 0.00 5.73
3049 4382 3.399181 GGTGTCATCTGGCCGGGA 61.399 66.667 12.87 6.17 0.00 5.14
3050 4383 2.125106 GTGTCATCTGGCCGGGAC 60.125 66.667 12.87 12.76 0.00 4.46
3136 4469 1.153369 CGGTTCGGAGGTCATGCAT 60.153 57.895 0.00 0.00 0.00 3.96
3137 4470 1.154205 CGGTTCGGAGGTCATGCATC 61.154 60.000 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.329256 GGTGTCATCTAAACGGCTTTAGAC 59.671 45.833 16.20 9.21 46.93 2.59
5 6 3.306166 CGGTGTCATCTAAACGGCTTTAG 59.694 47.826 9.02 9.02 40.20 1.85
6 7 3.255725 CGGTGTCATCTAAACGGCTTTA 58.744 45.455 0.00 0.00 0.00 1.85
7 8 2.073816 CGGTGTCATCTAAACGGCTTT 58.926 47.619 0.00 0.00 0.00 3.51
8 9 1.001633 ACGGTGTCATCTAAACGGCTT 59.998 47.619 0.00 0.00 0.00 4.35
9 10 0.606604 ACGGTGTCATCTAAACGGCT 59.393 50.000 0.00 0.00 0.00 5.52
10 11 2.282701 TACGGTGTCATCTAAACGGC 57.717 50.000 0.00 0.00 0.00 5.68
11 12 4.036567 TCATACGGTGTCATCTAAACGG 57.963 45.455 0.00 0.00 0.00 4.44
12 13 6.583912 AAATCATACGGTGTCATCTAAACG 57.416 37.500 0.00 0.00 0.00 3.60
13 14 8.495949 CCATAAATCATACGGTGTCATCTAAAC 58.504 37.037 0.00 0.00 0.00 2.01
14 15 8.208224 ACCATAAATCATACGGTGTCATCTAAA 58.792 33.333 0.00 0.00 0.00 1.85
15 16 7.732025 ACCATAAATCATACGGTGTCATCTAA 58.268 34.615 0.00 0.00 0.00 2.10
16 17 7.297936 ACCATAAATCATACGGTGTCATCTA 57.702 36.000 0.00 0.00 0.00 1.98
17 18 6.174720 ACCATAAATCATACGGTGTCATCT 57.825 37.500 0.00 0.00 0.00 2.90
18 19 6.861065 AACCATAAATCATACGGTGTCATC 57.139 37.500 0.00 0.00 0.00 2.92
19 20 6.039270 CCAAACCATAAATCATACGGTGTCAT 59.961 38.462 0.00 0.00 0.00 3.06
20 21 5.355630 CCAAACCATAAATCATACGGTGTCA 59.644 40.000 0.00 0.00 0.00 3.58
21 22 5.732247 GCCAAACCATAAATCATACGGTGTC 60.732 44.000 0.00 0.00 0.00 3.67
22 23 4.097286 GCCAAACCATAAATCATACGGTGT 59.903 41.667 0.00 0.00 0.00 4.16
23 24 4.097135 TGCCAAACCATAAATCATACGGTG 59.903 41.667 0.00 0.00 0.00 4.94
24 25 4.274147 TGCCAAACCATAAATCATACGGT 58.726 39.130 0.00 0.00 0.00 4.83
25 26 4.909696 TGCCAAACCATAAATCATACGG 57.090 40.909 0.00 0.00 0.00 4.02
26 27 7.588143 TTTTTGCCAAACCATAAATCATACG 57.412 32.000 0.00 0.00 0.00 3.06
51 52 9.511144 CAAAATTTAAGAAACGACAACTTAGGT 57.489 29.630 0.00 0.00 0.00 3.08
52 53 9.724839 TCAAAATTTAAGAAACGACAACTTAGG 57.275 29.630 0.00 0.00 0.00 2.69
54 55 9.724839 CCTCAAAATTTAAGAAACGACAACTTA 57.275 29.630 0.00 0.00 0.00 2.24
55 56 8.463607 TCCTCAAAATTTAAGAAACGACAACTT 58.536 29.630 0.00 0.00 0.00 2.66
56 57 7.992008 TCCTCAAAATTTAAGAAACGACAACT 58.008 30.769 0.00 0.00 0.00 3.16
57 58 8.623310 TTCCTCAAAATTTAAGAAACGACAAC 57.377 30.769 0.00 0.00 0.00 3.32
58 59 9.810545 ATTTCCTCAAAATTTAAGAAACGACAA 57.189 25.926 0.00 0.00 33.69 3.18
59 60 9.243637 CATTTCCTCAAAATTTAAGAAACGACA 57.756 29.630 0.00 0.00 35.32 4.35
60 61 9.458374 TCATTTCCTCAAAATTTAAGAAACGAC 57.542 29.630 0.00 0.00 35.32 4.34
61 62 9.458374 GTCATTTCCTCAAAATTTAAGAAACGA 57.542 29.630 0.00 0.00 35.32 3.85
62 63 8.417176 CGTCATTTCCTCAAAATTTAAGAAACG 58.583 33.333 0.00 0.00 35.32 3.60
63 64 8.214472 GCGTCATTTCCTCAAAATTTAAGAAAC 58.786 33.333 0.00 0.00 35.32 2.78
64 65 8.141268 AGCGTCATTTCCTCAAAATTTAAGAAA 58.859 29.630 0.00 0.00 35.32 2.52
65 66 7.657336 AGCGTCATTTCCTCAAAATTTAAGAA 58.343 30.769 0.00 0.00 35.32 2.52
66 67 7.214467 AGCGTCATTTCCTCAAAATTTAAGA 57.786 32.000 0.00 0.00 35.32 2.10
67 68 7.873739 AAGCGTCATTTCCTCAAAATTTAAG 57.126 32.000 0.00 0.00 35.32 1.85
68 69 9.352784 CATAAGCGTCATTTCCTCAAAATTTAA 57.647 29.630 0.00 0.00 35.32 1.52
69 70 8.519526 ACATAAGCGTCATTTCCTCAAAATTTA 58.480 29.630 0.00 0.00 35.32 1.40
70 71 7.378181 ACATAAGCGTCATTTCCTCAAAATTT 58.622 30.769 0.00 0.00 35.32 1.82
71 72 6.924111 ACATAAGCGTCATTTCCTCAAAATT 58.076 32.000 0.00 0.00 35.32 1.82
72 73 6.150976 TGACATAAGCGTCATTTCCTCAAAAT 59.849 34.615 0.00 0.00 40.94 1.82
73 74 5.471797 TGACATAAGCGTCATTTCCTCAAAA 59.528 36.000 0.00 0.00 40.94 2.44
74 75 5.000591 TGACATAAGCGTCATTTCCTCAAA 58.999 37.500 0.00 0.00 40.94 2.69
75 76 4.574892 TGACATAAGCGTCATTTCCTCAA 58.425 39.130 0.00 0.00 40.94 3.02
76 77 4.200838 TGACATAAGCGTCATTTCCTCA 57.799 40.909 0.00 0.00 40.94 3.86
77 78 4.870426 TCTTGACATAAGCGTCATTTCCTC 59.130 41.667 0.00 0.00 45.03 3.71
78 79 4.832248 TCTTGACATAAGCGTCATTTCCT 58.168 39.130 0.00 0.00 45.03 3.36
79 80 4.034510 CCTCTTGACATAAGCGTCATTTCC 59.965 45.833 0.00 0.00 45.03 3.13
80 81 4.494855 GCCTCTTGACATAAGCGTCATTTC 60.495 45.833 0.00 0.00 45.03 2.17
81 82 3.375299 GCCTCTTGACATAAGCGTCATTT 59.625 43.478 0.00 0.00 45.03 2.32
82 83 2.939103 GCCTCTTGACATAAGCGTCATT 59.061 45.455 0.00 0.00 45.03 2.57
83 84 2.169352 AGCCTCTTGACATAAGCGTCAT 59.831 45.455 0.00 0.00 45.03 3.06
84 85 1.550524 AGCCTCTTGACATAAGCGTCA 59.449 47.619 0.00 0.00 44.05 4.35
85 86 2.301577 AGCCTCTTGACATAAGCGTC 57.698 50.000 0.00 0.00 36.40 5.19
86 87 2.028112 TGAAGCCTCTTGACATAAGCGT 60.028 45.455 0.00 0.00 0.00 5.07
87 88 2.606725 CTGAAGCCTCTTGACATAAGCG 59.393 50.000 0.00 0.00 0.00 4.68
88 89 2.354199 GCTGAAGCCTCTTGACATAAGC 59.646 50.000 0.00 0.00 34.31 3.09
102 103 1.202463 TCGAGCTTATCAGGCTGAAGC 60.202 52.381 26.39 26.39 44.79 3.86
103 104 2.879002 TCGAGCTTATCAGGCTGAAG 57.121 50.000 22.84 16.26 40.40 3.02
104 105 2.036475 GGATCGAGCTTATCAGGCTGAA 59.964 50.000 22.84 4.84 40.40 3.02
105 106 1.615883 GGATCGAGCTTATCAGGCTGA 59.384 52.381 21.19 21.19 40.40 4.26
106 107 1.337635 GGGATCGAGCTTATCAGGCTG 60.338 57.143 8.58 8.58 40.40 4.85
107 108 0.972883 GGGATCGAGCTTATCAGGCT 59.027 55.000 0.00 0.00 43.26 4.58
108 109 0.681733 TGGGATCGAGCTTATCAGGC 59.318 55.000 0.00 0.00 0.00 4.85
109 110 3.397482 CTTTGGGATCGAGCTTATCAGG 58.603 50.000 0.00 0.00 0.00 3.86
110 111 2.805099 GCTTTGGGATCGAGCTTATCAG 59.195 50.000 0.00 2.87 33.72 2.90
111 112 2.803133 CGCTTTGGGATCGAGCTTATCA 60.803 50.000 0.00 0.00 34.33 2.15
112 113 1.795286 CGCTTTGGGATCGAGCTTATC 59.205 52.381 0.00 0.00 34.33 1.75
113 114 1.541233 CCGCTTTGGGATCGAGCTTAT 60.541 52.381 0.00 0.00 34.33 1.73
114 115 0.179084 CCGCTTTGGGATCGAGCTTA 60.179 55.000 0.00 0.00 34.33 3.09
115 116 1.450312 CCGCTTTGGGATCGAGCTT 60.450 57.895 0.00 0.00 34.33 3.74
116 117 2.187946 CCGCTTTGGGATCGAGCT 59.812 61.111 0.00 0.00 34.33 4.09
117 118 1.884926 CTCCGCTTTGGGATCGAGC 60.885 63.158 0.00 0.00 38.76 5.03
118 119 0.175760 TTCTCCGCTTTGGGATCGAG 59.824 55.000 0.00 0.00 38.76 4.04
119 120 0.175760 CTTCTCCGCTTTGGGATCGA 59.824 55.000 0.00 0.00 38.76 3.59
120 121 0.108138 ACTTCTCCGCTTTGGGATCG 60.108 55.000 0.00 0.00 38.76 3.69
121 122 2.552031 GTACTTCTCCGCTTTGGGATC 58.448 52.381 0.00 0.00 38.76 3.36
122 123 1.134788 CGTACTTCTCCGCTTTGGGAT 60.135 52.381 0.00 0.00 38.76 3.85
123 124 0.245539 CGTACTTCTCCGCTTTGGGA 59.754 55.000 0.00 0.00 38.76 4.37
124 125 0.037605 ACGTACTTCTCCGCTTTGGG 60.038 55.000 0.00 0.00 38.76 4.12
125 126 1.067776 AGACGTACTTCTCCGCTTTGG 60.068 52.381 0.00 0.00 40.09 3.28
126 127 2.349297 AGACGTACTTCTCCGCTTTG 57.651 50.000 0.00 0.00 0.00 2.77
149 150 7.352522 ACCCAATGGTTTCTTTAGGATATCCTA 59.647 37.037 25.03 25.03 44.75 2.94
150 151 6.162241 ACCCAATGGTTTCTTTAGGATATCCT 59.838 38.462 27.21 27.21 44.75 3.24
151 152 6.373759 ACCCAATGGTTTCTTTAGGATATCC 58.626 40.000 14.41 14.41 44.75 2.59
154 155 8.442374 GGTATACCCAATGGTTTCTTTAGGATA 58.558 37.037 11.17 0.00 44.75 2.59
155 156 7.130442 AGGTATACCCAATGGTTTCTTTAGGAT 59.870 37.037 18.65 0.00 44.75 3.24
156 157 6.449041 AGGTATACCCAATGGTTTCTTTAGGA 59.551 38.462 18.65 0.00 44.75 2.94
157 158 6.669631 AGGTATACCCAATGGTTTCTTTAGG 58.330 40.000 18.65 0.00 44.75 2.69
158 159 8.589701 AAAGGTATACCCAATGGTTTCTTTAG 57.410 34.615 18.65 0.00 44.75 1.85
159 160 8.959676 AAAAGGTATACCCAATGGTTTCTTTA 57.040 30.769 18.65 0.00 44.75 1.85
160 161 7.865530 AAAAGGTATACCCAATGGTTTCTTT 57.134 32.000 18.65 5.56 44.75 2.52
161 162 9.197306 GATAAAAGGTATACCCAATGGTTTCTT 57.803 33.333 18.65 0.00 44.75 2.52
162 163 8.340757 TGATAAAAGGTATACCCAATGGTTTCT 58.659 33.333 18.65 3.21 44.75 2.52
163 164 8.410912 GTGATAAAAGGTATACCCAATGGTTTC 58.589 37.037 18.65 6.52 44.75 2.78
164 165 7.896496 TGTGATAAAAGGTATACCCAATGGTTT 59.104 33.333 18.65 8.37 44.75 3.27
165 166 7.415086 TGTGATAAAAGGTATACCCAATGGTT 58.585 34.615 18.65 2.08 44.75 3.67
167 168 7.287061 TCTGTGATAAAAGGTATACCCAATGG 58.713 38.462 18.65 0.00 36.42 3.16
168 169 8.924511 ATCTGTGATAAAAGGTATACCCAATG 57.075 34.615 18.65 4.92 36.42 2.82
169 170 8.949421 AGATCTGTGATAAAAGGTATACCCAAT 58.051 33.333 18.65 6.92 36.42 3.16
170 171 8.331931 AGATCTGTGATAAAAGGTATACCCAA 57.668 34.615 18.65 2.02 36.42 4.12
171 172 7.931015 AGATCTGTGATAAAAGGTATACCCA 57.069 36.000 18.65 5.26 36.42 4.51
172 173 9.930693 CTTAGATCTGTGATAAAAGGTATACCC 57.069 37.037 18.65 2.49 36.42 3.69
173 174 9.930693 CCTTAGATCTGTGATAAAAGGTATACC 57.069 37.037 14.54 14.54 0.00 2.73
174 175 9.930693 CCCTTAGATCTGTGATAAAAGGTATAC 57.069 37.037 14.33 0.00 31.98 1.47
175 176 8.594550 GCCCTTAGATCTGTGATAAAAGGTATA 58.405 37.037 14.33 0.00 31.98 1.47
176 177 7.072454 TGCCCTTAGATCTGTGATAAAAGGTAT 59.928 37.037 14.33 0.00 31.98 2.73
177 178 6.385759 TGCCCTTAGATCTGTGATAAAAGGTA 59.614 38.462 14.33 3.92 31.98 3.08
178 179 5.191722 TGCCCTTAGATCTGTGATAAAAGGT 59.808 40.000 14.33 0.00 31.98 3.50
179 180 5.684704 TGCCCTTAGATCTGTGATAAAAGG 58.315 41.667 5.18 8.28 33.37 3.11
180 181 6.994496 TCATGCCCTTAGATCTGTGATAAAAG 59.006 38.462 5.18 0.00 0.00 2.27
181 182 6.899089 TCATGCCCTTAGATCTGTGATAAAA 58.101 36.000 5.18 0.00 0.00 1.52
182 183 6.499106 TCATGCCCTTAGATCTGTGATAAA 57.501 37.500 5.18 0.00 0.00 1.40
183 184 6.499699 AGATCATGCCCTTAGATCTGTGATAA 59.500 38.462 5.18 0.00 44.89 1.75
184 185 6.021672 AGATCATGCCCTTAGATCTGTGATA 58.978 40.000 5.18 0.00 44.89 2.15
185 186 4.845225 AGATCATGCCCTTAGATCTGTGAT 59.155 41.667 5.18 3.89 44.89 3.06
186 187 4.229639 AGATCATGCCCTTAGATCTGTGA 58.770 43.478 5.18 0.00 44.89 3.58
187 188 4.620589 AGATCATGCCCTTAGATCTGTG 57.379 45.455 5.18 0.00 44.89 3.66
188 189 5.643421 AAAGATCATGCCCTTAGATCTGT 57.357 39.130 5.18 0.00 45.62 3.41
189 190 7.664731 ACAATAAAGATCATGCCCTTAGATCTG 59.335 37.037 5.18 0.00 45.62 2.90
191 192 7.663081 TGACAATAAAGATCATGCCCTTAGATC 59.337 37.037 0.00 0.00 38.70 2.75
192 193 7.520798 TGACAATAAAGATCATGCCCTTAGAT 58.479 34.615 0.00 0.00 0.00 1.98
193 194 6.899089 TGACAATAAAGATCATGCCCTTAGA 58.101 36.000 0.00 0.00 0.00 2.10
194 195 7.500227 TCTTGACAATAAAGATCATGCCCTTAG 59.500 37.037 0.00 0.00 0.00 2.18
195 196 7.345691 TCTTGACAATAAAGATCATGCCCTTA 58.654 34.615 0.00 0.00 0.00 2.69
196 197 6.189859 TCTTGACAATAAAGATCATGCCCTT 58.810 36.000 0.00 0.00 0.00 3.95
197 198 5.759059 TCTTGACAATAAAGATCATGCCCT 58.241 37.500 0.00 0.00 0.00 5.19
198 199 6.268566 GTTCTTGACAATAAAGATCATGCCC 58.731 40.000 0.00 0.00 33.79 5.36
199 200 5.967674 CGTTCTTGACAATAAAGATCATGCC 59.032 40.000 0.00 0.00 33.79 4.40
200 201 5.967674 CCGTTCTTGACAATAAAGATCATGC 59.032 40.000 0.00 0.00 33.79 4.06
201 202 6.094048 ACCCGTTCTTGACAATAAAGATCATG 59.906 38.462 0.00 0.00 33.79 3.07
202 203 6.180472 ACCCGTTCTTGACAATAAAGATCAT 58.820 36.000 0.00 0.00 33.79 2.45
203 204 5.556915 ACCCGTTCTTGACAATAAAGATCA 58.443 37.500 0.00 0.00 33.79 2.92
204 205 5.064834 GGACCCGTTCTTGACAATAAAGATC 59.935 44.000 1.69 0.00 33.79 2.75
205 206 4.941873 GGACCCGTTCTTGACAATAAAGAT 59.058 41.667 1.69 0.00 33.79 2.40
206 207 4.041198 AGGACCCGTTCTTGACAATAAAGA 59.959 41.667 1.69 0.00 31.85 2.52
207 208 4.324267 AGGACCCGTTCTTGACAATAAAG 58.676 43.478 0.00 0.00 0.00 1.85
208 209 4.360951 AGGACCCGTTCTTGACAATAAA 57.639 40.909 0.00 0.00 0.00 1.40
209 210 4.360951 AAGGACCCGTTCTTGACAATAA 57.639 40.909 0.00 0.00 0.00 1.40
210 211 4.041198 AGAAAGGACCCGTTCTTGACAATA 59.959 41.667 10.72 0.00 40.76 1.90
211 212 2.951229 AAGGACCCGTTCTTGACAAT 57.049 45.000 0.00 0.00 0.00 2.71
212 213 2.171870 AGAAAGGACCCGTTCTTGACAA 59.828 45.455 10.72 0.00 40.76 3.18
213 214 1.766496 AGAAAGGACCCGTTCTTGACA 59.234 47.619 10.72 0.00 40.76 3.58
214 215 2.545537 AGAAAGGACCCGTTCTTGAC 57.454 50.000 10.72 0.00 40.76 3.18
215 216 3.503365 TCTAGAAAGGACCCGTTCTTGA 58.497 45.455 19.35 18.94 40.76 3.02
216 217 3.368531 CCTCTAGAAAGGACCCGTTCTTG 60.369 52.174 19.35 17.32 40.76 3.02
217 218 2.832733 CCTCTAGAAAGGACCCGTTCTT 59.167 50.000 19.35 0.00 40.76 2.52
218 219 2.042706 TCCTCTAGAAAGGACCCGTTCT 59.957 50.000 18.45 18.45 44.44 3.01
219 220 2.454538 TCCTCTAGAAAGGACCCGTTC 58.545 52.381 6.61 6.61 40.60 3.95
220 221 2.617840 TCCTCTAGAAAGGACCCGTT 57.382 50.000 0.00 0.00 40.60 4.44
226 227 0.686769 GGGCCGTCCTCTAGAAAGGA 60.687 60.000 0.00 0.00 43.30 3.36
227 228 1.687297 GGGGCCGTCCTCTAGAAAGG 61.687 65.000 0.00 0.00 37.81 3.11
228 229 0.688087 AGGGGCCGTCCTCTAGAAAG 60.688 60.000 0.00 0.00 42.85 2.62
229 230 0.976073 CAGGGGCCGTCCTCTAGAAA 60.976 60.000 0.00 0.00 42.77 2.52
230 231 1.381327 CAGGGGCCGTCCTCTAGAA 60.381 63.158 0.00 0.00 42.77 2.10
231 232 2.279073 CAGGGGCCGTCCTCTAGA 59.721 66.667 0.00 0.00 42.77 2.43
232 233 3.541713 GCAGGGGCCGTCCTCTAG 61.542 72.222 0.00 0.00 42.77 2.43
233 234 3.916438 TTGCAGGGGCCGTCCTCTA 62.916 63.158 0.00 0.00 42.77 2.43
235 236 3.860930 TTTTGCAGGGGCCGTCCTC 62.861 63.158 0.00 0.00 40.13 3.71
236 237 3.897122 TTTTGCAGGGGCCGTCCT 61.897 61.111 0.00 0.00 40.13 3.85
237 238 3.680786 GTTTTGCAGGGGCCGTCC 61.681 66.667 0.00 0.00 40.13 4.79
238 239 2.597510 AGTTTTGCAGGGGCCGTC 60.598 61.111 0.00 0.00 40.13 4.79
239 240 2.597510 GAGTTTTGCAGGGGCCGT 60.598 61.111 0.00 0.00 40.13 5.68
240 241 3.373565 GGAGTTTTGCAGGGGCCG 61.374 66.667 0.00 0.00 40.13 6.13
241 242 2.997315 GGGAGTTTTGCAGGGGCC 60.997 66.667 0.00 0.00 40.13 5.80
242 243 3.373565 CGGGAGTTTTGCAGGGGC 61.374 66.667 0.00 0.00 41.68 5.80
243 244 3.373565 GCGGGAGTTTTGCAGGGG 61.374 66.667 0.00 0.00 0.00 4.79
273 274 2.095212 GCTGTCCGAAATCCTGAAAACC 60.095 50.000 0.00 0.00 0.00 3.27
306 307 2.814280 ATCGCCCCGTATAAGTTCTG 57.186 50.000 0.00 0.00 0.00 3.02
312 313 3.770388 TCATCCATAATCGCCCCGTATAA 59.230 43.478 0.00 0.00 0.00 0.98
314 315 2.093658 GTCATCCATAATCGCCCCGTAT 60.094 50.000 0.00 0.00 0.00 3.06
320 321 3.548818 GCAGTTTGTCATCCATAATCGCC 60.549 47.826 0.00 0.00 0.00 5.54
321 322 3.621794 GCAGTTTGTCATCCATAATCGC 58.378 45.455 0.00 0.00 0.00 4.58
345 346 6.401394 CAAACATTCAGACCATACTCTCTGA 58.599 40.000 0.00 0.00 40.95 3.27
349 350 3.935203 CGCAAACATTCAGACCATACTCT 59.065 43.478 0.00 0.00 0.00 3.24
351 352 3.009723 CCGCAAACATTCAGACCATACT 58.990 45.455 0.00 0.00 0.00 2.12
451 452 4.655762 AGTGCTACATTCTATTGCTCGA 57.344 40.909 0.00 0.00 0.00 4.04
481 483 6.433716 TGACATGAGCAAGTCATATTTCCAAA 59.566 34.615 0.00 0.00 44.73 3.28
542 545 5.397360 ACTCCAGATTTTCCTCCACAAAAT 58.603 37.500 0.00 0.00 36.38 1.82
548 551 3.517100 CAGAGACTCCAGATTTTCCTCCA 59.483 47.826 0.00 0.00 0.00 3.86
549 552 3.517500 ACAGAGACTCCAGATTTTCCTCC 59.482 47.826 0.00 0.00 0.00 4.30
553 556 5.418840 AGAGAGACAGAGACTCCAGATTTTC 59.581 44.000 0.00 0.00 35.27 2.29
568 571 5.341872 AGGTCATTCATTCAGAGAGACAG 57.658 43.478 0.00 0.00 35.06 3.51
670 693 4.681978 AAGTCCGGTGCCGAGTGC 62.682 66.667 12.71 0.00 42.83 4.40
671 694 2.030562 AAAGTCCGGTGCCGAGTG 59.969 61.111 12.71 0.00 42.83 3.51
672 695 2.030562 CAAAGTCCGGTGCCGAGT 59.969 61.111 12.71 0.00 42.83 4.18
673 696 3.423154 GCAAAGTCCGGTGCCGAG 61.423 66.667 12.71 2.62 42.83 4.63
681 704 1.581934 TTCTGACAGTGCAAAGTCCG 58.418 50.000 14.97 10.10 33.89 4.79
742 765 3.815569 CTCGTCGATGCTCCGCTCC 62.816 68.421 0.00 0.00 0.00 4.70
1384 2697 3.121030 CGGCAACTCTTCCCGCAG 61.121 66.667 0.00 0.00 35.14 5.18
1538 2857 1.066757 CGAGATGCAGCTAGCTCAGAA 59.933 52.381 16.15 0.00 45.94 3.02
1558 2878 0.039256 TTGATCAGCAAAACGCCAGC 60.039 50.000 0.00 0.00 44.04 4.85
1580 2913 4.973360 CCAACGCCAACGCCAACG 62.973 66.667 0.00 0.00 45.53 4.10
1725 3058 1.377202 GGCCATGAGGTGCGAGAAA 60.377 57.895 0.00 0.00 37.19 2.52
1925 3258 0.955428 GTTGAAGCAGGGCGTGATGA 60.955 55.000 12.03 0.00 0.00 2.92
2088 3421 3.737172 GCGTGCGCAGGGTTGAAT 61.737 61.111 29.18 0.00 41.49 2.57
2165 3498 4.077184 TCCACATCGACGTGCCCC 62.077 66.667 6.01 0.00 35.47 5.80
2232 3565 1.050204 TGCCTTTTTCCTGCAATGCT 58.950 45.000 6.82 0.00 30.85 3.79
2283 3616 3.589654 CTTGCCGTCTTCCGCCTCA 62.590 63.158 0.00 0.00 34.38 3.86
2386 3719 6.664515 CCGTGTAAATTTAGTCACACATGTT 58.335 36.000 17.68 0.00 41.02 2.71
2404 3737 0.661552 CTAGCTAAGCTCGCCGTGTA 59.338 55.000 4.50 0.00 40.44 2.90
2443 3776 1.537135 GGATTTCTTCTCTCCGGCGAG 60.537 57.143 15.55 15.55 37.48 5.03
2454 3787 5.134202 GCTCTAGCCTCTAGGATTTCTTC 57.866 47.826 0.00 0.00 37.39 2.87
2469 3802 4.308899 TCTAGAATCGTTTGGCTCTAGC 57.691 45.455 0.00 0.00 38.07 3.42
2505 3838 1.153939 CTCTTCTCAGGCACCGTCG 60.154 63.158 0.00 0.00 0.00 5.12
2650 3983 1.134946 GGGCAAAACAGATCAATCGGG 59.865 52.381 0.00 0.00 0.00 5.14
2956 4289 4.439449 CGAGCGACATCTTGATTTCTAGTC 59.561 45.833 0.00 0.00 0.00 2.59
3034 4367 3.770040 CGTCCCGGCCAGATGACA 61.770 66.667 2.24 0.00 0.00 3.58
3035 4368 4.530857 CCGTCCCGGCCAGATGAC 62.531 72.222 12.56 7.12 41.17 3.06
3136 4469 3.749064 GAGTGGACCGCTGCTCGA 61.749 66.667 13.57 0.00 41.67 4.04


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

AutoCloner maintained by Alex Coulton.