Multiple sequence alignment - TraesCS7D01G415300

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G415300 chr7D 100.000 3117 0 0 1 3117 533903350 533906466 0.000000e+00 5757.0
1 TraesCS7D01G415300 chr7D 79.730 148 22 8 2853 2996 66603478 66603621 1.980000e-17 100.0
2 TraesCS7D01G415300 chr7A 95.407 2569 66 22 582 3117 613631339 613633888 0.000000e+00 4043.0
3 TraesCS7D01G415300 chr7A 78.284 746 127 27 1982 2708 615328186 615328915 6.130000e-122 448.0
4 TraesCS7D01G415300 chr7A 100.000 36 0 0 631 666 657524215 657524180 2.010000e-07 67.6
5 TraesCS7D01G415300 chr7B 92.507 2589 141 21 547 3117 574468756 574471309 0.000000e+00 3657.0
6 TraesCS7D01G415300 chr7B 88.333 60 7 0 1855 1914 575367339 575367398 4.310000e-09 73.1
7 TraesCS7D01G415300 chr7B 86.667 60 6 2 629 687 527855519 527855577 7.220000e-07 65.8
8 TraesCS7D01G415300 chr3A 78.092 283 55 6 53 331 213781082 213780803 4.130000e-39 172.0
9 TraesCS7D01G415300 chr1D 92.793 111 7 1 553 662 436328441 436328551 3.220000e-35 159.0
10 TraesCS7D01G415300 chr1D 81.548 168 27 4 166 331 452691155 452691320 5.420000e-28 135.0
11 TraesCS7D01G415300 chr5D 82.840 169 26 3 165 331 327117902 327117735 6.960000e-32 148.0
12 TraesCS7D01G415300 chr5D 83.333 150 23 2 184 331 388047327 388047178 1.510000e-28 137.0
13 TraesCS7D01G415300 chr5D 91.304 92 6 2 582 671 227731780 227731689 1.170000e-24 124.0
14 TraesCS7D01G415300 chr2B 80.240 167 31 2 167 331 184560572 184560738 1.170000e-24 124.0
15 TraesCS7D01G415300 chr2B 80.473 169 27 6 168 331 556222550 556222383 1.170000e-24 124.0
16 TraesCS7D01G415300 chr2B 76.623 231 31 13 20 236 380302221 380302000 4.250000e-19 106.0
17 TraesCS7D01G415300 chr3D 81.879 149 24 2 184 331 479114277 479114423 4.220000e-24 122.0
18 TraesCS7D01G415300 chrUn 81.046 153 28 1 165 316 150955092 150955244 1.520000e-23 121.0
19 TraesCS7D01G415300 chrUn 81.046 153 28 1 165 316 306634316 306634164 1.520000e-23 121.0
20 TraesCS7D01G415300 chrUn 100.000 30 0 0 2809 2838 202163553 202163524 4.340000e-04 56.5
21 TraesCS7D01G415300 chrUn 100.000 30 0 0 2809 2838 202180654 202180625 4.340000e-04 56.5
22 TraesCS7D01G415300 chrUn 100.000 30 0 0 2809 2838 202184737 202184708 4.340000e-04 56.5
23 TraesCS7D01G415300 chrUn 92.500 40 1 2 2800 2838 210163095 210163133 4.340000e-04 56.5
24 TraesCS7D01G415300 chrUn 92.500 40 1 2 2800 2838 210630980 210631018 4.340000e-04 56.5
25 TraesCS7D01G415300 chr4B 87.736 106 9 3 553 657 72658205 72658103 1.520000e-23 121.0
26 TraesCS7D01G415300 chr5A 82.407 108 17 2 582 687 535354403 535354510 3.310000e-15 93.5
27 TraesCS7D01G415300 chr4A 95.455 44 1 1 400 442 36280226 36280183 5.580000e-08 69.4
28 TraesCS7D01G415300 chr4A 85.000 60 7 2 2809 2867 681792788 681792846 3.360000e-05 60.2
29 TraesCS7D01G415300 chr6B 93.023 43 3 0 629 671 693067735 693067693 2.600000e-06 63.9
30 TraesCS7D01G415300 chr6B 100.000 32 0 0 2808 2839 579212908 579212939 3.360000e-05 60.2
31 TraesCS7D01G415300 chr5B 97.297 37 1 0 635 671 569765946 569765982 2.600000e-06 63.9


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 TraesCS7D01G415300 chr7D 533903350 533906466 3116 False 5757 5757 100.000 1 3117 1 chr7D.!!$F2 3116
1 TraesCS7D01G415300 chr7A 613631339 613633888 2549 False 4043 4043 95.407 582 3117 1 chr7A.!!$F1 2535
2 TraesCS7D01G415300 chr7A 615328186 615328915 729 False 448 448 78.284 1982 2708 1 chr7A.!!$F2 726
3 TraesCS7D01G415300 chr7B 574468756 574471309 2553 False 3657 3657 92.507 547 3117 1 chr7B.!!$F2 2570

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
67 68 0.034670 GCCATCAAGGAGGAGTTGCT 60.035 55.0 0.00 0.00 41.22 3.91 F
396 397 0.108424 CAGAGGACTGGGCTTCGAAG 60.108 60.0 21.02 21.02 40.14 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1422 1474 1.450312 GCACAAGGGATGGACCTCG 60.450 63.158 0.0 0.0 40.87 4.63 R
2365 2425 1.525077 GGCGACTCCCAACACAACA 60.525 57.895 0.0 0.0 0.00 3.33 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
34 35 3.630148 GCCATCATCGCCGACGTG 61.630 66.667 0.00 0.00 41.18 4.49
35 36 3.630148 CCATCATCGCCGACGTGC 61.630 66.667 0.00 0.00 41.18 5.34
36 37 2.583319 CATCATCGCCGACGTGCT 60.583 61.111 0.00 0.00 41.18 4.40
37 38 2.583319 ATCATCGCCGACGTGCTG 60.583 61.111 0.00 0.00 41.18 4.41
52 53 4.790962 CTGCCACAGCCTCGCCAT 62.791 66.667 0.00 0.00 38.69 4.40
53 54 4.783621 TGCCACAGCCTCGCCATC 62.784 66.667 0.00 0.00 38.69 3.51
54 55 4.783621 GCCACAGCCTCGCCATCA 62.784 66.667 0.00 0.00 0.00 3.07
55 56 2.046023 CCACAGCCTCGCCATCAA 60.046 61.111 0.00 0.00 0.00 2.57
56 57 2.110967 CCACAGCCTCGCCATCAAG 61.111 63.158 0.00 0.00 0.00 3.02
57 58 2.110967 CACAGCCTCGCCATCAAGG 61.111 63.158 0.00 0.00 41.84 3.61
58 59 2.293318 ACAGCCTCGCCATCAAGGA 61.293 57.895 0.00 0.00 41.22 3.36
59 60 1.523258 CAGCCTCGCCATCAAGGAG 60.523 63.158 0.00 0.00 41.22 3.69
63 64 2.206635 CTCGCCATCAAGGAGGAGT 58.793 57.895 0.00 0.00 41.22 3.85
64 65 0.539051 CTCGCCATCAAGGAGGAGTT 59.461 55.000 0.00 0.00 41.22 3.01
65 66 0.250234 TCGCCATCAAGGAGGAGTTG 59.750 55.000 0.00 0.00 41.22 3.16
66 67 1.372087 CGCCATCAAGGAGGAGTTGC 61.372 60.000 0.00 0.00 41.22 4.17
67 68 0.034670 GCCATCAAGGAGGAGTTGCT 60.035 55.000 0.00 0.00 41.22 3.91
68 69 1.747709 CCATCAAGGAGGAGTTGCTG 58.252 55.000 0.00 0.00 41.22 4.41
69 70 1.093159 CATCAAGGAGGAGTTGCTGC 58.907 55.000 0.00 0.00 0.00 5.25
70 71 0.034670 ATCAAGGAGGAGTTGCTGCC 60.035 55.000 0.00 0.00 0.00 4.85
71 72 1.676967 CAAGGAGGAGTTGCTGCCC 60.677 63.158 0.00 0.00 0.00 5.36
72 73 3.259633 AAGGAGGAGTTGCTGCCCG 62.260 63.158 0.00 0.00 0.00 6.13
77 78 3.567797 GAGTTGCTGCCCGCGATC 61.568 66.667 8.23 0.00 43.27 3.69
78 79 4.393155 AGTTGCTGCCCGCGATCA 62.393 61.111 8.23 3.52 43.27 2.92
79 80 3.430862 GTTGCTGCCCGCGATCAA 61.431 61.111 8.23 0.73 43.27 2.57
80 81 3.126879 TTGCTGCCCGCGATCAAG 61.127 61.111 8.23 0.00 43.27 3.02
81 82 3.604129 TTGCTGCCCGCGATCAAGA 62.604 57.895 8.23 0.00 43.27 3.02
82 83 2.819595 GCTGCCCGCGATCAAGAA 60.820 61.111 8.23 0.00 0.00 2.52
83 84 2.817423 GCTGCCCGCGATCAAGAAG 61.817 63.158 8.23 0.00 0.00 2.85
84 85 2.125147 TGCCCGCGATCAAGAAGG 60.125 61.111 8.23 0.00 0.00 3.46
85 86 3.577313 GCCCGCGATCAAGAAGGC 61.577 66.667 8.23 5.10 0.00 4.35
87 88 3.929948 CCGCGATCAAGAAGGCGC 61.930 66.667 8.23 0.00 46.67 6.53
88 89 3.929948 CGCGATCAAGAAGGCGCC 61.930 66.667 21.89 21.89 46.04 6.53
89 90 3.929948 GCGATCAAGAAGGCGCCG 61.930 66.667 23.20 6.32 43.33 6.46
90 91 3.264897 CGATCAAGAAGGCGCCGG 61.265 66.667 23.20 9.77 0.00 6.13
91 92 2.897350 GATCAAGAAGGCGCCGGG 60.897 66.667 23.20 10.16 0.00 5.73
110 111 3.148279 CGCCTCCTCCGCTACCTT 61.148 66.667 0.00 0.00 0.00 3.50
111 112 2.501610 GCCTCCTCCGCTACCTTG 59.498 66.667 0.00 0.00 0.00 3.61
112 113 3.095347 GCCTCCTCCGCTACCTTGG 62.095 68.421 0.00 0.00 0.00 3.61
113 114 1.381327 CCTCCTCCGCTACCTTGGA 60.381 63.158 0.00 0.00 0.00 3.53
116 117 4.356979 CTCCGCTACCTTGGAGGA 57.643 61.111 0.07 0.00 46.55 3.71
117 118 2.119886 CTCCGCTACCTTGGAGGAG 58.880 63.158 0.07 0.00 46.55 3.69
118 119 1.381327 TCCGCTACCTTGGAGGAGG 60.381 63.158 0.07 0.00 37.67 4.30
119 120 2.501610 CGCTACCTTGGAGGAGGC 59.498 66.667 0.07 3.85 40.65 4.70
120 121 2.501610 GCTACCTTGGAGGAGGCG 59.498 66.667 0.07 0.00 40.65 5.52
121 122 3.095347 GCTACCTTGGAGGAGGCGG 62.095 68.421 0.07 0.00 40.65 6.13
122 123 1.686110 CTACCTTGGAGGAGGCGGT 60.686 63.158 0.07 0.00 40.65 5.68
123 124 1.961180 CTACCTTGGAGGAGGCGGTG 61.961 65.000 0.07 0.00 40.65 4.94
124 125 4.785453 CCTTGGAGGAGGCGGTGC 62.785 72.222 0.00 0.00 37.67 5.01
146 147 3.056328 GGCTTGAGGGCCGTTGTC 61.056 66.667 0.00 0.00 42.82 3.18
147 148 2.032681 GCTTGAGGGCCGTTGTCT 59.967 61.111 0.00 0.00 0.00 3.41
148 149 2.035442 GCTTGAGGGCCGTTGTCTC 61.035 63.158 0.00 0.00 0.00 3.36
149 150 1.376037 CTTGAGGGCCGTTGTCTCC 60.376 63.158 0.00 0.00 0.00 3.71
150 151 3.234630 TTGAGGGCCGTTGTCTCCG 62.235 63.158 0.00 0.00 0.00 4.63
151 152 3.379445 GAGGGCCGTTGTCTCCGA 61.379 66.667 0.00 0.00 0.00 4.55
152 153 3.358076 GAGGGCCGTTGTCTCCGAG 62.358 68.421 0.00 0.00 0.00 4.63
153 154 4.452733 GGGCCGTTGTCTCCGAGG 62.453 72.222 0.00 0.00 0.00 4.63
172 173 3.755628 GGAGTGCGTGGCGAGGTA 61.756 66.667 0.00 0.00 0.00 3.08
173 174 2.506438 GAGTGCGTGGCGAGGTAC 60.506 66.667 1.58 1.58 0.00 3.34
174 175 3.277211 GAGTGCGTGGCGAGGTACA 62.277 63.158 11.67 0.00 0.00 2.90
175 176 2.356553 GTGCGTGGCGAGGTACAA 60.357 61.111 4.88 0.00 0.00 2.41
176 177 2.356553 TGCGTGGCGAGGTACAAC 60.357 61.111 0.00 0.00 0.00 3.32
177 178 3.116531 GCGTGGCGAGGTACAACC 61.117 66.667 0.00 0.00 38.99 3.77
178 179 2.340809 CGTGGCGAGGTACAACCA 59.659 61.111 0.00 0.00 41.95 3.67
179 180 1.736645 CGTGGCGAGGTACAACCAG 60.737 63.158 0.00 0.00 41.95 4.00
180 181 2.033194 GTGGCGAGGTACAACCAGC 61.033 63.158 7.70 7.70 41.95 4.85
181 182 2.813908 GGCGAGGTACAACCAGCG 60.814 66.667 0.00 8.20 42.46 5.18
182 183 2.048503 GCGAGGTACAACCAGCGT 60.049 61.111 11.29 0.00 41.95 5.07
183 184 1.213537 GCGAGGTACAACCAGCGTA 59.786 57.895 11.29 0.00 41.95 4.42
184 185 0.388907 GCGAGGTACAACCAGCGTAA 60.389 55.000 11.29 0.00 41.95 3.18
185 186 1.738030 GCGAGGTACAACCAGCGTAAT 60.738 52.381 11.29 0.00 41.95 1.89
186 187 1.924524 CGAGGTACAACCAGCGTAATG 59.075 52.381 0.00 0.00 41.95 1.90
187 188 1.664151 GAGGTACAACCAGCGTAATGC 59.336 52.381 0.00 0.00 41.95 3.56
188 189 1.677820 AGGTACAACCAGCGTAATGCC 60.678 52.381 0.00 0.00 41.95 4.40
196 197 2.052237 GCGTAATGCCGATTGCCG 60.052 61.111 0.00 0.00 40.16 5.69
197 198 2.052237 CGTAATGCCGATTGCCGC 60.052 61.111 0.00 0.00 40.16 6.53
198 199 2.534019 CGTAATGCCGATTGCCGCT 61.534 57.895 0.00 0.00 40.16 5.52
199 200 1.279840 GTAATGCCGATTGCCGCTC 59.720 57.895 0.00 0.00 40.16 5.03
200 201 1.891919 TAATGCCGATTGCCGCTCC 60.892 57.895 0.00 0.00 40.16 4.70
213 214 2.261671 GCTCCGCGTTCTCCAAGA 59.738 61.111 4.92 0.00 0.00 3.02
214 215 1.807573 GCTCCGCGTTCTCCAAGAG 60.808 63.158 4.92 2.60 0.00 2.85
215 216 1.807573 CTCCGCGTTCTCCAAGAGC 60.808 63.158 4.92 0.00 0.00 4.09
220 221 4.968197 GTTCTCCAAGAGCGACGT 57.032 55.556 0.00 0.00 0.00 4.34
222 223 1.897641 GTTCTCCAAGAGCGACGTAG 58.102 55.000 0.00 0.00 0.00 3.51
223 224 0.170561 TTCTCCAAGAGCGACGTAGC 59.829 55.000 13.21 13.21 37.41 3.58
224 225 1.583967 CTCCAAGAGCGACGTAGCG 60.584 63.158 15.11 3.42 43.00 4.26
232 233 3.320078 CGACGTAGCGCCGGATTG 61.320 66.667 5.05 0.00 0.00 2.67
233 234 2.960129 GACGTAGCGCCGGATTGG 60.960 66.667 5.05 0.00 42.50 3.16
234 235 4.524318 ACGTAGCGCCGGATTGGG 62.524 66.667 5.05 0.00 38.63 4.12
235 236 4.524318 CGTAGCGCCGGATTGGGT 62.524 66.667 5.05 0.00 38.63 4.51
236 237 2.588034 GTAGCGCCGGATTGGGTC 60.588 66.667 5.05 0.00 38.63 4.46
237 238 3.857038 TAGCGCCGGATTGGGTCC 61.857 66.667 5.05 0.00 44.10 4.46
244 245 2.046700 GGATTGGGTCCGCAACGA 60.047 61.111 0.00 0.00 37.23 3.85
245 246 1.451387 GGATTGGGTCCGCAACGAT 60.451 57.895 0.00 0.00 37.23 3.73
246 247 1.436983 GGATTGGGTCCGCAACGATC 61.437 60.000 0.00 0.00 37.23 3.69
247 248 1.436983 GATTGGGTCCGCAACGATCC 61.437 60.000 0.00 0.00 0.00 3.36
248 249 1.910580 ATTGGGTCCGCAACGATCCT 61.911 55.000 0.00 0.00 0.00 3.24
249 250 2.511600 GGGTCCGCAACGATCCTG 60.512 66.667 0.00 0.00 0.00 3.86
250 251 2.577059 GGTCCGCAACGATCCTGA 59.423 61.111 0.00 0.00 0.00 3.86
251 252 1.810030 GGTCCGCAACGATCCTGAC 60.810 63.158 0.00 0.00 0.00 3.51
252 253 1.810030 GTCCGCAACGATCCTGACC 60.810 63.158 0.00 0.00 0.00 4.02
253 254 1.982395 TCCGCAACGATCCTGACCT 60.982 57.895 0.00 0.00 0.00 3.85
254 255 1.519455 CCGCAACGATCCTGACCTC 60.519 63.158 0.00 0.00 0.00 3.85
255 256 1.874019 CGCAACGATCCTGACCTCG 60.874 63.158 0.00 0.00 40.62 4.63
256 257 2.167861 GCAACGATCCTGACCTCGC 61.168 63.158 0.00 0.00 38.42 5.03
257 258 1.874019 CAACGATCCTGACCTCGCG 60.874 63.158 0.00 0.00 38.42 5.87
258 259 3.701604 AACGATCCTGACCTCGCGC 62.702 63.158 0.00 0.00 38.42 6.86
259 260 4.933064 CGATCCTGACCTCGCGCC 62.933 72.222 0.00 0.00 0.00 6.53
260 261 3.838271 GATCCTGACCTCGCGCCA 61.838 66.667 0.00 0.00 0.00 5.69
261 262 4.148825 ATCCTGACCTCGCGCCAC 62.149 66.667 0.00 0.00 0.00 5.01
282 283 2.262915 GGTGCTCGACCACTCCAG 59.737 66.667 10.55 0.00 45.34 3.86
283 284 2.262915 GTGCTCGACCACTCCAGG 59.737 66.667 3.54 0.00 33.02 4.45
284 285 2.117423 TGCTCGACCACTCCAGGA 59.883 61.111 0.00 0.00 0.00 3.86
285 286 2.276116 TGCTCGACCACTCCAGGAC 61.276 63.158 0.00 0.00 0.00 3.85
286 287 3.007973 GCTCGACCACTCCAGGACC 62.008 68.421 0.00 0.00 0.00 4.46
287 288 1.606601 CTCGACCACTCCAGGACCA 60.607 63.158 0.00 0.00 0.00 4.02
288 289 1.878656 CTCGACCACTCCAGGACCAC 61.879 65.000 0.00 0.00 0.00 4.16
289 290 2.943978 CGACCACTCCAGGACCACC 61.944 68.421 0.00 0.00 0.00 4.61
290 291 2.923035 ACCACTCCAGGACCACCG 60.923 66.667 0.00 0.00 41.83 4.94
291 292 4.394712 CCACTCCAGGACCACCGC 62.395 72.222 0.00 0.00 41.83 5.68
292 293 4.742201 CACTCCAGGACCACCGCG 62.742 72.222 0.00 0.00 41.83 6.46
297 298 4.436998 CAGGACCACCGCGGAGAC 62.437 72.222 35.90 21.70 41.83 3.36
335 336 2.811317 GCTTGACGGCGAGGAGTG 60.811 66.667 16.62 0.00 0.00 3.51
336 337 2.125912 CTTGACGGCGAGGAGTGG 60.126 66.667 16.62 0.00 0.00 4.00
337 338 4.373116 TTGACGGCGAGGAGTGGC 62.373 66.667 16.62 0.00 0.00 5.01
343 344 4.143333 GCGAGGAGTGGCCGCTTA 62.143 66.667 22.22 0.00 44.83 3.09
344 345 2.105128 CGAGGAGTGGCCGCTTAG 59.895 66.667 22.22 8.49 43.43 2.18
345 346 2.202946 GAGGAGTGGCCGCTTAGC 60.203 66.667 22.22 7.69 43.43 3.09
346 347 3.003173 AGGAGTGGCCGCTTAGCA 61.003 61.111 22.22 0.00 43.43 3.49
347 348 2.046314 GGAGTGGCCGCTTAGCAA 60.046 61.111 22.22 0.00 0.00 3.91
348 349 2.399356 GGAGTGGCCGCTTAGCAAC 61.399 63.158 22.22 6.04 36.91 4.17
349 350 2.750350 AGTGGCCGCTTAGCAACT 59.250 55.556 14.67 0.00 42.42 3.16
350 351 1.672356 AGTGGCCGCTTAGCAACTG 60.672 57.895 14.67 0.00 45.55 3.16
351 352 3.055719 TGGCCGCTTAGCAACTGC 61.056 61.111 4.70 0.69 42.49 4.40
385 386 4.400961 GCGGCAAGGCAGAGGACT 62.401 66.667 0.00 0.00 0.00 3.85
386 387 2.435586 CGGCAAGGCAGAGGACTG 60.436 66.667 0.00 0.00 45.91 3.51
387 388 2.045536 GGCAAGGCAGAGGACTGG 60.046 66.667 0.00 0.00 43.62 4.00
388 389 2.045536 GCAAGGCAGAGGACTGGG 60.046 66.667 0.00 0.00 43.62 4.45
389 390 2.045536 CAAGGCAGAGGACTGGGC 60.046 66.667 0.00 0.00 43.62 5.36
390 391 2.204059 AAGGCAGAGGACTGGGCT 60.204 61.111 0.00 0.00 43.62 5.19
391 392 1.849823 AAGGCAGAGGACTGGGCTT 60.850 57.895 0.00 0.00 43.62 4.35
392 393 1.846712 AAGGCAGAGGACTGGGCTTC 61.847 60.000 0.00 0.00 42.92 3.86
393 394 2.125350 GCAGAGGACTGGGCTTCG 60.125 66.667 0.00 0.00 43.62 3.79
394 395 2.650116 GCAGAGGACTGGGCTTCGA 61.650 63.158 0.00 0.00 43.62 3.71
395 396 1.975327 CAGAGGACTGGGCTTCGAA 59.025 57.895 0.00 0.00 40.14 3.71
396 397 0.108424 CAGAGGACTGGGCTTCGAAG 60.108 60.000 21.02 21.02 40.14 3.79
397 398 1.219393 GAGGACTGGGCTTCGAAGG 59.781 63.158 25.77 11.96 0.00 3.46
405 406 4.090057 GCTTCGAAGGCCACACGC 62.090 66.667 25.77 6.65 0.00 5.34
406 407 2.664851 CTTCGAAGGCCACACGCA 60.665 61.111 17.70 0.00 40.31 5.24
407 408 2.664851 TTCGAAGGCCACACGCAG 60.665 61.111 5.01 0.00 40.31 5.18
410 411 3.730761 GAAGGCCACACGCAGCAG 61.731 66.667 5.01 0.00 40.31 4.24
451 452 4.699522 GACCCTCCAGCGCCGTTT 62.700 66.667 2.29 0.00 0.00 3.60
452 453 4.699522 ACCCTCCAGCGCCGTTTC 62.700 66.667 2.29 0.00 0.00 2.78
453 454 4.697756 CCCTCCAGCGCCGTTTCA 62.698 66.667 2.29 0.00 0.00 2.69
454 455 3.423154 CCTCCAGCGCCGTTTCAC 61.423 66.667 2.29 0.00 0.00 3.18
455 456 3.423154 CTCCAGCGCCGTTTCACC 61.423 66.667 2.29 0.00 0.00 4.02
456 457 4.243008 TCCAGCGCCGTTTCACCA 62.243 61.111 2.29 0.00 0.00 4.17
457 458 4.025401 CCAGCGCCGTTTCACCAC 62.025 66.667 2.29 0.00 0.00 4.16
458 459 4.368808 CAGCGCCGTTTCACCACG 62.369 66.667 2.29 0.00 40.02 4.94
459 460 4.595538 AGCGCCGTTTCACCACGA 62.596 61.111 2.29 0.00 43.15 4.35
460 461 4.364409 GCGCCGTTTCACCACGAC 62.364 66.667 0.00 0.00 43.15 4.34
461 462 4.054455 CGCCGTTTCACCACGACG 62.054 66.667 0.00 0.00 43.15 5.12
462 463 2.659244 GCCGTTTCACCACGACGA 60.659 61.111 0.00 0.00 43.15 4.20
463 464 2.025418 GCCGTTTCACCACGACGAT 61.025 57.895 0.00 0.00 43.15 3.73
464 465 1.779061 CCGTTTCACCACGACGATG 59.221 57.895 0.00 0.00 43.15 3.84
465 466 0.665068 CCGTTTCACCACGACGATGA 60.665 55.000 0.00 0.00 43.15 2.92
466 467 0.433492 CGTTTCACCACGACGATGAC 59.567 55.000 0.00 0.00 43.15 3.06
467 468 1.493772 GTTTCACCACGACGATGACA 58.506 50.000 0.00 0.00 0.00 3.58
468 469 1.862201 GTTTCACCACGACGATGACAA 59.138 47.619 0.00 0.00 0.00 3.18
469 470 1.493772 TTCACCACGACGATGACAAC 58.506 50.000 0.00 0.00 0.00 3.32
470 471 0.662077 TCACCACGACGATGACAACG 60.662 55.000 0.00 3.29 0.00 4.10
471 472 0.662077 CACCACGACGATGACAACGA 60.662 55.000 12.41 0.00 34.70 3.85
472 473 0.662374 ACCACGACGATGACAACGAC 60.662 55.000 12.41 4.81 34.70 4.34
474 475 0.723459 CACGACGATGACAACGACGA 60.723 55.000 28.99 0.00 46.85 4.20
475 476 0.723790 ACGACGATGACAACGACGAC 60.724 55.000 28.99 10.60 46.85 4.34
476 477 1.708375 CGACGATGACAACGACGACG 61.708 60.000 21.07 5.58 46.85 5.12
477 478 0.451628 GACGATGACAACGACGACGA 60.452 55.000 15.32 0.00 42.66 4.20
478 479 0.452287 ACGATGACAACGACGACGAG 60.452 55.000 15.32 8.51 42.66 4.18
479 480 1.126421 CGATGACAACGACGACGAGG 61.126 60.000 15.32 7.78 42.66 4.63
480 481 0.109873 GATGACAACGACGACGAGGT 60.110 55.000 15.32 11.05 42.66 3.85
481 482 1.129251 GATGACAACGACGACGAGGTA 59.871 52.381 15.32 0.63 42.66 3.08
482 483 0.514255 TGACAACGACGACGAGGTAG 59.486 55.000 15.32 1.40 42.66 3.18
483 484 0.179205 GACAACGACGACGAGGTAGG 60.179 60.000 15.32 0.00 42.66 3.18
484 485 1.136147 CAACGACGACGAGGTAGGG 59.864 63.158 15.32 0.00 42.66 3.53
485 486 2.694760 AACGACGACGAGGTAGGGC 61.695 63.158 15.32 0.00 42.66 5.19
486 487 4.233635 CGACGACGAGGTAGGGCG 62.234 72.222 0.00 0.00 42.66 6.13
487 488 3.885521 GACGACGAGGTAGGGCGG 61.886 72.222 0.00 0.00 0.00 6.13
493 494 4.468689 GAGGTAGGGCGGCCACAC 62.469 72.222 31.59 25.26 0.00 3.82
496 497 3.762247 GTAGGGCGGCCACACGTA 61.762 66.667 31.59 10.55 35.98 3.57
497 498 3.762247 TAGGGCGGCCACACGTAC 61.762 66.667 31.59 0.67 35.98 3.67
505 506 3.618750 CCACACGTACGGGGTGGT 61.619 66.667 34.68 18.23 45.48 4.16
506 507 2.048877 CACACGTACGGGGTGGTC 60.049 66.667 23.48 0.00 39.69 4.02
507 508 3.673484 ACACGTACGGGGTGGTCG 61.673 66.667 23.48 0.93 39.69 4.79
508 509 3.673484 CACGTACGGGGTGGTCGT 61.673 66.667 21.06 0.00 43.64 4.34
509 510 3.673484 ACGTACGGGGTGGTCGTG 61.673 66.667 21.06 0.00 41.24 4.35
515 516 3.777910 GGGGTGGTCGTGCGGTAT 61.778 66.667 0.00 0.00 0.00 2.73
516 517 2.425569 GGGGTGGTCGTGCGGTATA 61.426 63.158 0.00 0.00 0.00 1.47
517 518 1.066918 GGGTGGTCGTGCGGTATAG 59.933 63.158 0.00 0.00 0.00 1.31
518 519 1.066918 GGTGGTCGTGCGGTATAGG 59.933 63.158 0.00 0.00 0.00 2.57
519 520 1.386525 GGTGGTCGTGCGGTATAGGA 61.387 60.000 0.00 0.00 0.00 2.94
520 521 0.672342 GTGGTCGTGCGGTATAGGAT 59.328 55.000 0.00 0.00 0.00 3.24
521 522 1.068127 GTGGTCGTGCGGTATAGGATT 59.932 52.381 0.00 0.00 0.00 3.01
522 523 2.294233 GTGGTCGTGCGGTATAGGATTA 59.706 50.000 0.00 0.00 0.00 1.75
523 524 2.957680 TGGTCGTGCGGTATAGGATTAA 59.042 45.455 0.00 0.00 0.00 1.40
524 525 3.005050 TGGTCGTGCGGTATAGGATTAAG 59.995 47.826 0.00 0.00 0.00 1.85
525 526 3.005155 GGTCGTGCGGTATAGGATTAAGT 59.995 47.826 0.00 0.00 0.00 2.24
526 527 4.500375 GGTCGTGCGGTATAGGATTAAGTT 60.500 45.833 0.00 0.00 0.00 2.66
527 528 5.045872 GTCGTGCGGTATAGGATTAAGTTT 58.954 41.667 0.00 0.00 0.00 2.66
528 529 5.521372 GTCGTGCGGTATAGGATTAAGTTTT 59.479 40.000 0.00 0.00 0.00 2.43
529 530 6.036408 GTCGTGCGGTATAGGATTAAGTTTTT 59.964 38.462 0.00 0.00 0.00 1.94
624 627 8.093063 CGAATTTCGTCCAATTAGTTTGAATC 57.907 34.615 10.61 0.00 34.60 2.52
664 667 3.195698 GCGTTGGATGACGGCCTC 61.196 66.667 0.00 0.00 42.98 4.70
671 674 1.890979 GATGACGGCCTCCTGCATG 60.891 63.158 0.00 0.00 43.89 4.06
933 968 3.550030 CCACACCGAAAACAGATCCAAAC 60.550 47.826 0.00 0.00 0.00 2.93
990 1025 4.941309 TCGCCCGATCCGATCCGA 62.941 66.667 2.69 3.80 0.00 4.55
1422 1474 1.542492 TCGACTCTGTAACCCCTGAC 58.458 55.000 0.00 0.00 0.00 3.51
1439 1491 1.983224 ACGAGGTCCATCCCTTGTG 59.017 57.895 0.00 0.00 45.73 3.33
1448 1500 0.809385 CATCCCTTGTGCTCTGCAAG 59.191 55.000 0.00 0.00 41.47 4.01
1464 1516 1.881498 GCAAGCTGTCTTCTCTGCCTT 60.881 52.381 0.00 0.00 33.76 4.35
1650 1702 2.563179 CTGTATCCCCTGATAAGGTCCG 59.437 54.545 0.00 0.00 35.28 4.79
1904 1960 0.037975 GGTCCGTCTCTTGCCGTTTA 60.038 55.000 0.00 0.00 0.00 2.01
1980 2036 9.276590 CTTGAATGATATTGCAAGGTGATAGTA 57.723 33.333 4.94 0.00 35.34 1.82
2226 2285 6.725364 TGAGATTTAGGGAGAAGCTGAAAAT 58.275 36.000 0.00 0.00 0.00 1.82
2346 2405 5.602145 TCTGAAATGTTGTCTGGGGAAAATT 59.398 36.000 0.00 0.00 0.00 1.82
2578 2639 0.391130 ACATCACCGTTATGCTGCGT 60.391 50.000 0.00 0.00 0.00 5.24
2604 2674 8.552083 TTCTCGTCAGTTGTAATACTAGTGTA 57.448 34.615 5.39 0.00 0.00 2.90
3024 3099 7.828717 TGAACATTGATAAATTGCCTCTAGTCA 59.171 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.630148 CACGTCGGCGATGATGGC 61.630 66.667 33.51 9.51 42.00 4.40
18 19 3.630148 GCACGTCGGCGATGATGG 61.630 66.667 33.51 21.93 42.00 3.51
19 20 2.583319 AGCACGTCGGCGATGATG 60.583 61.111 33.51 25.65 42.00 3.07
20 21 2.583319 CAGCACGTCGGCGATGAT 60.583 61.111 33.51 15.86 42.00 2.45
35 36 4.790962 ATGGCGAGGCTGTGGCAG 62.791 66.667 16.04 0.00 44.30 4.85
36 37 4.783621 GATGGCGAGGCTGTGGCA 62.784 66.667 13.79 13.79 45.22 4.92
37 38 4.783621 TGATGGCGAGGCTGTGGC 62.784 66.667 0.00 0.00 37.82 5.01
38 39 2.046023 TTGATGGCGAGGCTGTGG 60.046 61.111 0.00 0.00 0.00 4.17
39 40 2.110967 CCTTGATGGCGAGGCTGTG 61.111 63.158 0.00 0.00 38.83 3.66
40 41 2.249413 CTCCTTGATGGCGAGGCTGT 62.249 60.000 0.00 0.00 44.25 4.40
41 42 1.523258 CTCCTTGATGGCGAGGCTG 60.523 63.158 0.00 0.00 44.25 4.85
42 43 2.739996 CCTCCTTGATGGCGAGGCT 61.740 63.158 0.00 0.00 44.25 4.58
43 44 2.203126 CCTCCTTGATGGCGAGGC 60.203 66.667 0.00 0.00 44.25 4.70
44 45 1.333636 ACTCCTCCTTGATGGCGAGG 61.334 60.000 0.00 0.00 45.73 4.63
45 46 0.539051 AACTCCTCCTTGATGGCGAG 59.461 55.000 0.00 0.00 37.71 5.03
46 47 0.250234 CAACTCCTCCTTGATGGCGA 59.750 55.000 0.00 0.00 35.26 5.54
47 48 1.372087 GCAACTCCTCCTTGATGGCG 61.372 60.000 0.00 0.00 35.26 5.69
48 49 0.034670 AGCAACTCCTCCTTGATGGC 60.035 55.000 0.00 0.00 35.26 4.40
49 50 1.747709 CAGCAACTCCTCCTTGATGG 58.252 55.000 0.00 0.00 32.51 3.51
50 51 1.093159 GCAGCAACTCCTCCTTGATG 58.907 55.000 0.00 0.00 37.94 3.07
51 52 0.034670 GGCAGCAACTCCTCCTTGAT 60.035 55.000 0.00 0.00 0.00 2.57
52 53 1.376466 GGCAGCAACTCCTCCTTGA 59.624 57.895 0.00 0.00 0.00 3.02
53 54 1.676967 GGGCAGCAACTCCTCCTTG 60.677 63.158 0.00 0.00 0.00 3.61
54 55 2.759795 GGGCAGCAACTCCTCCTT 59.240 61.111 0.00 0.00 0.00 3.36
55 56 3.710722 CGGGCAGCAACTCCTCCT 61.711 66.667 0.00 0.00 0.00 3.69
65 66 2.817423 CTTCTTGATCGCGGGCAGC 61.817 63.158 6.13 0.00 43.95 5.25
66 67 2.176273 CCTTCTTGATCGCGGGCAG 61.176 63.158 6.13 0.00 0.00 4.85
67 68 2.125147 CCTTCTTGATCGCGGGCA 60.125 61.111 6.13 1.18 0.00 5.36
68 69 3.577313 GCCTTCTTGATCGCGGGC 61.577 66.667 6.13 4.32 0.00 6.13
69 70 3.264897 CGCCTTCTTGATCGCGGG 61.265 66.667 6.13 0.00 40.91 6.13
70 71 3.929948 GCGCCTTCTTGATCGCGG 61.930 66.667 6.13 0.00 44.60 6.46
72 73 3.929948 CGGCGCCTTCTTGATCGC 61.930 66.667 26.68 0.00 45.99 4.58
73 74 3.264897 CCGGCGCCTTCTTGATCG 61.265 66.667 26.68 7.45 0.00 3.69
74 75 2.897350 CCCGGCGCCTTCTTGATC 60.897 66.667 26.68 0.00 0.00 2.92
93 94 3.148279 AAGGTAGCGGAGGAGGCG 61.148 66.667 0.00 0.00 35.00 5.52
94 95 2.501610 CAAGGTAGCGGAGGAGGC 59.498 66.667 0.00 0.00 0.00 4.70
95 96 1.381327 TCCAAGGTAGCGGAGGAGG 60.381 63.158 0.00 0.00 0.00 4.30
96 97 2.119886 CTCCAAGGTAGCGGAGGAG 58.880 63.158 13.35 13.35 44.37 3.69
97 98 4.356979 CTCCAAGGTAGCGGAGGA 57.643 61.111 7.73 5.65 44.37 3.71
100 101 1.381327 CCTCCTCCAAGGTAGCGGA 60.381 63.158 0.00 0.00 36.53 5.54
101 102 3.095347 GCCTCCTCCAAGGTAGCGG 62.095 68.421 0.00 0.00 38.79 5.52
102 103 2.501610 GCCTCCTCCAAGGTAGCG 59.498 66.667 0.00 0.00 38.79 4.26
103 104 2.501610 CGCCTCCTCCAAGGTAGC 59.498 66.667 0.00 0.00 38.79 3.58
104 105 1.686110 ACCGCCTCCTCCAAGGTAG 60.686 63.158 0.00 0.00 38.79 3.18
105 106 1.987855 CACCGCCTCCTCCAAGGTA 60.988 63.158 0.00 0.00 38.79 3.08
106 107 3.322466 CACCGCCTCCTCCAAGGT 61.322 66.667 0.00 0.00 38.79 3.50
107 108 4.785453 GCACCGCCTCCTCCAAGG 62.785 72.222 0.00 0.00 39.62 3.61
108 109 4.785453 GGCACCGCCTCCTCCAAG 62.785 72.222 0.00 0.00 46.69 3.61
130 131 2.032681 AGACAACGGCCCTCAAGC 59.967 61.111 0.00 0.00 0.00 4.01
131 132 1.376037 GGAGACAACGGCCCTCAAG 60.376 63.158 0.00 0.00 0.00 3.02
132 133 2.747686 GGAGACAACGGCCCTCAA 59.252 61.111 0.00 0.00 0.00 3.02
133 134 3.691342 CGGAGACAACGGCCCTCA 61.691 66.667 0.00 0.00 0.00 3.86
134 135 3.358076 CTCGGAGACAACGGCCCTC 62.358 68.421 0.00 0.00 0.00 4.30
135 136 3.382832 CTCGGAGACAACGGCCCT 61.383 66.667 0.00 0.00 0.00 5.19
136 137 4.452733 CCTCGGAGACAACGGCCC 62.453 72.222 6.58 0.00 0.00 5.80
155 156 3.755628 TACCTCGCCACGCACTCC 61.756 66.667 0.00 0.00 0.00 3.85
156 157 2.506438 GTACCTCGCCACGCACTC 60.506 66.667 0.00 0.00 0.00 3.51
157 158 2.863346 TTGTACCTCGCCACGCACT 61.863 57.895 0.00 0.00 0.00 4.40
158 159 2.356553 TTGTACCTCGCCACGCAC 60.357 61.111 0.00 0.00 0.00 5.34
159 160 2.356553 GTTGTACCTCGCCACGCA 60.357 61.111 0.00 0.00 0.00 5.24
160 161 3.116531 GGTTGTACCTCGCCACGC 61.117 66.667 0.00 0.00 34.73 5.34
161 162 1.736645 CTGGTTGTACCTCGCCACG 60.737 63.158 0.00 0.00 39.58 4.94
162 163 2.033194 GCTGGTTGTACCTCGCCAC 61.033 63.158 0.00 0.00 39.58 5.01
163 164 2.345991 GCTGGTTGTACCTCGCCA 59.654 61.111 0.00 0.00 39.58 5.69
164 165 2.216750 TACGCTGGTTGTACCTCGCC 62.217 60.000 9.69 0.00 39.58 5.54
165 166 0.388907 TTACGCTGGTTGTACCTCGC 60.389 55.000 9.69 6.04 39.58 5.03
166 167 1.924524 CATTACGCTGGTTGTACCTCG 59.075 52.381 8.67 8.67 39.58 4.63
167 168 1.664151 GCATTACGCTGGTTGTACCTC 59.336 52.381 0.00 0.00 39.58 3.85
168 169 1.677820 GGCATTACGCTGGTTGTACCT 60.678 52.381 0.00 0.00 41.91 3.08
169 170 0.730840 GGCATTACGCTGGTTGTACC 59.269 55.000 0.00 0.00 41.91 3.34
170 171 0.372334 CGGCATTACGCTGGTTGTAC 59.628 55.000 0.00 0.00 43.91 2.90
171 172 2.757212 CGGCATTACGCTGGTTGTA 58.243 52.632 0.00 0.00 43.91 2.41
172 173 3.573558 CGGCATTACGCTGGTTGT 58.426 55.556 0.00 0.00 43.91 3.32
174 175 3.168773 AATCGGCATTACGCTGGTT 57.831 47.368 0.00 0.00 45.96 3.67
197 198 1.807573 GCTCTTGGAGAACGCGGAG 60.808 63.158 12.47 5.67 0.00 4.63
198 199 2.261671 GCTCTTGGAGAACGCGGA 59.738 61.111 12.47 0.00 0.00 5.54
199 200 3.181967 CGCTCTTGGAGAACGCGG 61.182 66.667 12.47 0.00 35.91 6.46
200 201 2.126463 TCGCTCTTGGAGAACGCG 60.126 61.111 3.53 3.53 39.37 6.01
201 202 2.437343 CGTCGCTCTTGGAGAACGC 61.437 63.158 8.91 0.00 34.14 4.84
202 203 0.167470 TACGTCGCTCTTGGAGAACG 59.833 55.000 15.79 15.79 42.08 3.95
203 204 1.897641 CTACGTCGCTCTTGGAGAAC 58.102 55.000 0.00 0.00 0.00 3.01
204 205 0.170561 GCTACGTCGCTCTTGGAGAA 59.829 55.000 4.57 0.00 0.00 2.87
205 206 1.801332 GCTACGTCGCTCTTGGAGA 59.199 57.895 4.57 0.00 0.00 3.71
206 207 1.583967 CGCTACGTCGCTCTTGGAG 60.584 63.158 10.57 0.00 0.00 3.86
207 208 2.483745 CGCTACGTCGCTCTTGGA 59.516 61.111 10.57 0.00 0.00 3.53
216 217 2.960129 CCAATCCGGCGCTACGTC 60.960 66.667 7.64 0.00 0.00 4.34
217 218 4.524318 CCCAATCCGGCGCTACGT 62.524 66.667 7.64 0.00 0.00 3.57
218 219 4.524318 ACCCAATCCGGCGCTACG 62.524 66.667 7.64 2.53 0.00 3.51
219 220 2.588034 GACCCAATCCGGCGCTAC 60.588 66.667 7.64 0.00 0.00 3.58
220 221 3.857038 GGACCCAATCCGGCGCTA 61.857 66.667 7.64 0.00 37.88 4.26
227 228 1.436983 GATCGTTGCGGACCCAATCC 61.437 60.000 0.00 0.00 45.20 3.01
228 229 1.436983 GGATCGTTGCGGACCCAATC 61.437 60.000 0.00 0.00 0.00 2.67
229 230 1.451387 GGATCGTTGCGGACCCAAT 60.451 57.895 0.00 0.00 0.00 3.16
230 231 2.046700 GGATCGTTGCGGACCCAA 60.047 61.111 0.00 0.00 0.00 4.12
231 232 3.000819 AGGATCGTTGCGGACCCA 61.001 61.111 0.00 0.00 0.00 4.51
232 233 2.511600 CAGGATCGTTGCGGACCC 60.512 66.667 0.00 0.00 0.00 4.46
233 234 1.810030 GTCAGGATCGTTGCGGACC 60.810 63.158 6.95 0.00 33.41 4.46
234 235 1.810030 GGTCAGGATCGTTGCGGAC 60.810 63.158 9.23 9.23 37.60 4.79
235 236 1.945354 GAGGTCAGGATCGTTGCGGA 61.945 60.000 0.00 0.00 0.00 5.54
236 237 1.519455 GAGGTCAGGATCGTTGCGG 60.519 63.158 0.00 0.00 0.00 5.69
237 238 1.874019 CGAGGTCAGGATCGTTGCG 60.874 63.158 0.00 0.00 34.30 4.85
238 239 2.167861 GCGAGGTCAGGATCGTTGC 61.168 63.158 0.00 0.00 40.97 4.17
239 240 1.874019 CGCGAGGTCAGGATCGTTG 60.874 63.158 0.00 0.00 40.97 4.10
240 241 2.490217 CGCGAGGTCAGGATCGTT 59.510 61.111 0.00 0.00 40.97 3.85
241 242 4.194720 GCGCGAGGTCAGGATCGT 62.195 66.667 12.10 0.00 40.97 3.73
242 243 4.933064 GGCGCGAGGTCAGGATCG 62.933 72.222 12.10 0.00 41.79 3.69
243 244 3.838271 TGGCGCGAGGTCAGGATC 61.838 66.667 12.10 0.00 0.00 3.36
244 245 4.148825 GTGGCGCGAGGTCAGGAT 62.149 66.667 12.10 0.00 0.00 3.24
259 260 4.293648 TGGTCGAGCACCCACGTG 62.294 66.667 14.39 9.08 46.18 4.49
260 261 4.295119 GTGGTCGAGCACCCACGT 62.295 66.667 32.25 0.00 46.18 4.49
263 264 3.311110 GGAGTGGTCGAGCACCCA 61.311 66.667 36.62 15.85 46.18 4.51
264 265 3.302347 CTGGAGTGGTCGAGCACCC 62.302 68.421 36.62 33.67 46.18 4.61
266 267 2.262915 CCTGGAGTGGTCGAGCAC 59.737 66.667 34.43 34.43 0.00 4.40
267 268 2.117423 TCCTGGAGTGGTCGAGCA 59.883 61.111 14.39 14.39 0.00 4.26
268 269 2.574399 GTCCTGGAGTGGTCGAGC 59.426 66.667 7.89 7.89 0.00 5.03
269 270 1.606601 TGGTCCTGGAGTGGTCGAG 60.607 63.158 0.00 0.00 0.00 4.04
270 271 1.906824 GTGGTCCTGGAGTGGTCGA 60.907 63.158 0.00 0.00 0.00 4.20
271 272 2.657237 GTGGTCCTGGAGTGGTCG 59.343 66.667 0.00 0.00 0.00 4.79
272 273 2.943978 CGGTGGTCCTGGAGTGGTC 61.944 68.421 0.00 0.00 0.00 4.02
273 274 2.923035 CGGTGGTCCTGGAGTGGT 60.923 66.667 0.00 0.00 0.00 4.16
274 275 4.394712 GCGGTGGTCCTGGAGTGG 62.395 72.222 0.00 0.00 0.00 4.00
275 276 4.742201 CGCGGTGGTCCTGGAGTG 62.742 72.222 0.00 0.00 0.00 3.51
280 281 4.436998 GTCTCCGCGGTGGTCCTG 62.437 72.222 27.15 7.84 39.52 3.86
318 319 2.811317 CACTCCTCGCCGTCAAGC 60.811 66.667 0.00 0.00 0.00 4.01
319 320 2.125912 CCACTCCTCGCCGTCAAG 60.126 66.667 0.00 0.00 0.00 3.02
320 321 4.373116 GCCACTCCTCGCCGTCAA 62.373 66.667 0.00 0.00 0.00 3.18
327 328 2.105128 CTAAGCGGCCACTCCTCG 59.895 66.667 2.24 0.00 0.00 4.63
328 329 2.202946 GCTAAGCGGCCACTCCTC 60.203 66.667 2.24 0.00 0.00 3.71
329 330 2.592993 TTGCTAAGCGGCCACTCCT 61.593 57.895 2.24 0.00 0.00 3.69
330 331 2.046314 TTGCTAAGCGGCCACTCC 60.046 61.111 2.24 0.00 0.00 3.85
331 332 1.376037 AGTTGCTAAGCGGCCACTC 60.376 57.895 2.24 0.00 33.80 3.51
332 333 1.672356 CAGTTGCTAAGCGGCCACT 60.672 57.895 2.24 0.00 38.47 4.00
333 334 2.870372 CAGTTGCTAAGCGGCCAC 59.130 61.111 2.24 0.00 0.00 5.01
334 335 3.055719 GCAGTTGCTAAGCGGCCA 61.056 61.111 2.24 0.00 38.21 5.36
368 369 4.400961 AGTCCTCTGCCTTGCCGC 62.401 66.667 0.00 0.00 0.00 6.53
369 370 2.435586 CAGTCCTCTGCCTTGCCG 60.436 66.667 0.00 0.00 34.79 5.69
370 371 2.045536 CCAGTCCTCTGCCTTGCC 60.046 66.667 0.00 0.00 40.09 4.52
371 372 2.045536 CCCAGTCCTCTGCCTTGC 60.046 66.667 0.00 0.00 40.09 4.01
372 373 2.045536 GCCCAGTCCTCTGCCTTG 60.046 66.667 0.00 0.00 40.09 3.61
373 374 1.846712 GAAGCCCAGTCCTCTGCCTT 61.847 60.000 0.00 0.00 40.09 4.35
374 375 2.204059 AAGCCCAGTCCTCTGCCT 60.204 61.111 0.00 0.00 40.09 4.75
375 376 2.270527 GAAGCCCAGTCCTCTGCC 59.729 66.667 0.00 0.00 40.09 4.85
376 377 2.125350 CGAAGCCCAGTCCTCTGC 60.125 66.667 0.00 0.00 40.09 4.26
377 378 0.108424 CTTCGAAGCCCAGTCCTCTG 60.108 60.000 13.09 0.00 41.01 3.35
378 379 1.261238 CCTTCGAAGCCCAGTCCTCT 61.261 60.000 19.99 0.00 0.00 3.69
379 380 1.219393 CCTTCGAAGCCCAGTCCTC 59.781 63.158 19.99 0.00 0.00 3.71
380 381 2.960688 GCCTTCGAAGCCCAGTCCT 61.961 63.158 19.99 0.00 0.00 3.85
381 382 2.436824 GCCTTCGAAGCCCAGTCC 60.437 66.667 19.99 0.00 0.00 3.85
382 383 2.436824 GGCCTTCGAAGCCCAGTC 60.437 66.667 19.83 4.17 45.16 3.51
388 389 4.090057 GCGTGTGGCCTTCGAAGC 62.090 66.667 19.99 14.36 34.80 3.86
389 390 2.664851 TGCGTGTGGCCTTCGAAG 60.665 61.111 18.51 18.51 42.61 3.79
390 391 2.664851 CTGCGTGTGGCCTTCGAA 60.665 61.111 16.19 0.00 42.61 3.71
393 394 3.730761 CTGCTGCGTGTGGCCTTC 61.731 66.667 3.32 0.00 42.61 3.46
434 435 4.699522 AAACGGCGCTGGAGGGTC 62.700 66.667 22.44 0.00 0.00 4.46
435 436 4.699522 GAAACGGCGCTGGAGGGT 62.700 66.667 22.44 0.00 0.00 4.34
436 437 4.697756 TGAAACGGCGCTGGAGGG 62.698 66.667 22.44 0.00 0.00 4.30
437 438 3.423154 GTGAAACGGCGCTGGAGG 61.423 66.667 22.44 1.21 0.00 4.30
438 439 3.423154 GGTGAAACGGCGCTGGAG 61.423 66.667 22.44 6.18 38.12 3.86
439 440 4.243008 TGGTGAAACGGCGCTGGA 62.243 61.111 22.44 0.00 38.12 3.86
440 441 4.025401 GTGGTGAAACGGCGCTGG 62.025 66.667 22.44 9.44 38.12 4.85
441 442 4.368808 CGTGGTGAAACGGCGCTG 62.369 66.667 16.39 16.39 39.89 5.18
442 443 4.595538 TCGTGGTGAAACGGCGCT 62.596 61.111 6.90 0.00 43.73 5.92
443 444 4.364409 GTCGTGGTGAAACGGCGC 62.364 66.667 6.90 0.00 43.73 6.53
445 446 2.025418 ATCGTCGTGGTGAAACGGC 61.025 57.895 0.00 0.00 44.51 5.68
446 447 0.665068 TCATCGTCGTGGTGAAACGG 60.665 55.000 0.00 0.00 43.73 4.44
447 448 0.433492 GTCATCGTCGTGGTGAAACG 59.567 55.000 0.00 0.00 44.92 3.60
448 449 1.493772 TGTCATCGTCGTGGTGAAAC 58.506 50.000 0.00 0.00 0.00 2.78
449 450 1.862201 GTTGTCATCGTCGTGGTGAAA 59.138 47.619 0.00 0.00 0.00 2.69
450 451 1.493772 GTTGTCATCGTCGTGGTGAA 58.506 50.000 0.00 0.00 0.00 3.18
451 452 0.662077 CGTTGTCATCGTCGTGGTGA 60.662 55.000 0.00 0.00 0.00 4.02
452 453 0.662077 TCGTTGTCATCGTCGTGGTG 60.662 55.000 3.38 0.00 0.00 4.17
453 454 0.662374 GTCGTTGTCATCGTCGTGGT 60.662 55.000 3.38 0.00 0.00 4.16
454 455 1.661948 CGTCGTTGTCATCGTCGTGG 61.662 60.000 12.67 0.00 35.85 4.94
455 456 0.723459 TCGTCGTTGTCATCGTCGTG 60.723 55.000 17.87 3.06 39.70 4.35
456 457 0.723790 GTCGTCGTTGTCATCGTCGT 60.724 55.000 17.87 0.00 39.70 4.34
457 458 1.708375 CGTCGTCGTTGTCATCGTCG 61.708 60.000 14.13 14.13 39.95 5.12
458 459 0.451628 TCGTCGTCGTTGTCATCGTC 60.452 55.000 1.33 0.00 38.33 4.20
459 460 0.452287 CTCGTCGTCGTTGTCATCGT 60.452 55.000 1.33 0.00 38.33 3.73
460 461 1.126421 CCTCGTCGTCGTTGTCATCG 61.126 60.000 1.33 0.00 38.33 3.84
461 462 0.109873 ACCTCGTCGTCGTTGTCATC 60.110 55.000 1.33 0.00 38.33 2.92
462 463 1.129998 CTACCTCGTCGTCGTTGTCAT 59.870 52.381 1.33 0.00 38.33 3.06
463 464 0.514255 CTACCTCGTCGTCGTTGTCA 59.486 55.000 1.33 0.00 38.33 3.58
464 465 0.179205 CCTACCTCGTCGTCGTTGTC 60.179 60.000 1.33 0.00 38.33 3.18
465 466 1.580845 CCCTACCTCGTCGTCGTTGT 61.581 60.000 1.33 3.54 38.33 3.32
466 467 1.136147 CCCTACCTCGTCGTCGTTG 59.864 63.158 1.33 0.00 38.33 4.10
467 468 2.694760 GCCCTACCTCGTCGTCGTT 61.695 63.158 1.33 0.00 38.33 3.85
468 469 3.130160 GCCCTACCTCGTCGTCGT 61.130 66.667 1.33 0.00 38.33 4.34
469 470 4.233635 CGCCCTACCTCGTCGTCG 62.234 72.222 0.00 0.00 38.55 5.12
470 471 3.885521 CCGCCCTACCTCGTCGTC 61.886 72.222 0.00 0.00 0.00 4.20
476 477 4.468689 GTGTGGCCGCCCTACCTC 62.469 72.222 15.15 0.00 0.00 3.85
479 480 3.762247 TACGTGTGGCCGCCCTAC 61.762 66.667 15.15 4.33 0.00 3.18
480 481 3.762247 GTACGTGTGGCCGCCCTA 61.762 66.667 15.15 0.00 0.00 3.53
489 490 2.048877 GACCACCCCGTACGTGTG 60.049 66.667 21.63 21.63 0.00 3.82
490 491 3.673484 CGACCACCCCGTACGTGT 61.673 66.667 15.21 8.19 0.00 4.49
491 492 3.673484 ACGACCACCCCGTACGTG 61.673 66.667 15.21 1.82 38.61 4.49
492 493 3.673484 CACGACCACCCCGTACGT 61.673 66.667 15.21 0.00 38.29 3.57
498 499 2.359570 CTATACCGCACGACCACCCC 62.360 65.000 0.00 0.00 0.00 4.95
499 500 1.066918 CTATACCGCACGACCACCC 59.933 63.158 0.00 0.00 0.00 4.61
500 501 1.066918 CCTATACCGCACGACCACC 59.933 63.158 0.00 0.00 0.00 4.61
501 502 0.672342 ATCCTATACCGCACGACCAC 59.328 55.000 0.00 0.00 0.00 4.16
502 503 1.405872 AATCCTATACCGCACGACCA 58.594 50.000 0.00 0.00 0.00 4.02
503 504 3.005155 ACTTAATCCTATACCGCACGACC 59.995 47.826 0.00 0.00 0.00 4.79
504 505 4.234530 ACTTAATCCTATACCGCACGAC 57.765 45.455 0.00 0.00 0.00 4.34
505 506 4.924305 AACTTAATCCTATACCGCACGA 57.076 40.909 0.00 0.00 0.00 4.35
506 507 5.978934 AAAACTTAATCCTATACCGCACG 57.021 39.130 0.00 0.00 0.00 5.34
580 581 0.879090 GTTCAAACCGGCGGATTTCT 59.121 50.000 35.78 6.54 0.00 2.52
624 627 2.881266 CGCATACATCCGGCCAACG 61.881 63.158 2.24 0.00 43.80 4.10
664 667 0.402887 TCCCAGGATATGCATGCAGG 59.597 55.000 26.69 19.27 0.00 4.85
671 674 0.036022 GGAGCAGTCCCAGGATATGC 59.964 60.000 15.44 15.44 38.87 3.14
827 862 1.307097 GTCTCTCATACGGGTAGCGT 58.693 55.000 0.00 0.00 0.00 5.07
828 863 0.235144 CGTCTCTCATACGGGTAGCG 59.765 60.000 0.00 0.00 36.71 4.26
878 913 1.681825 GGAAATGGAAACGTCAACGC 58.318 50.000 1.81 0.00 44.43 4.84
933 968 0.684153 GATGGATTGGTGTGGTGGGG 60.684 60.000 0.00 0.00 0.00 4.96
990 1025 4.195334 GGTGCCATGGCGAGGGAT 62.195 66.667 30.87 0.00 45.51 3.85
1044 1084 3.547249 GAGGTCGTCGAACACCGCA 62.547 63.158 13.74 0.00 37.79 5.69
1132 1184 3.873883 GCTGCCGTGCTCATGCTC 61.874 66.667 0.00 0.00 40.48 4.26
1422 1474 1.450312 GCACAAGGGATGGACCTCG 60.450 63.158 0.00 0.00 40.87 4.63
1650 1702 3.335579 ACAATTTGCTAACTCGAGGGAC 58.664 45.455 18.41 3.72 0.00 4.46
1732 1785 2.262572 GCGACGGCAATCAAAGAAAT 57.737 45.000 0.00 0.00 39.62 2.17
1975 2031 6.825213 TCTGCAACAGCAATCAAAGATACTAT 59.175 34.615 0.00 0.00 37.91 2.12
1980 2036 4.744570 CATCTGCAACAGCAATCAAAGAT 58.255 39.130 0.00 0.00 37.91 2.40
2226 2285 5.702670 CAGATCTTCTTAACAAAGTCCTGCA 59.297 40.000 0.00 0.00 0.00 4.41
2365 2425 1.525077 GGCGACTCCCAACACAACA 60.525 57.895 0.00 0.00 0.00 3.33
2578 2639 7.879070 ACACTAGTATTACAACTGACGAGAAA 58.121 34.615 0.00 0.00 0.00 2.52
2604 2674 5.625150 ACCATGTCTAAAGAAAGAAGTGCT 58.375 37.500 0.00 0.00 0.00 4.40
2669 2744 3.334691 TCATTTGGCTCTGGTAAGAACG 58.665 45.455 0.00 0.00 30.03 3.95
3024 3099 5.779922 TGCTTGACACGAGACTAATAAAGT 58.220 37.500 0.00 0.00 42.80 2.66


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

AutoCloner maintained by Alex Coulton.