Multiple sequence alignment - TraesCS7B01G286400

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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 TraesCS7B01G286400 chr7B 100.000 4085 0 0 1 4085 521611696 521615780 0.000000e+00 7544
1 TraesCS7B01G286400 chr7D 93.555 3910 158 31 233 4085 492215944 492219816 0.000000e+00 5738
2 TraesCS7B01G286400 chr7A 94.365 3141 140 21 342 3457 558751192 558754320 0.000000e+00 4785
3 TraesCS7B01G286400 chr7A 91.725 568 31 6 3532 4085 558754334 558754899 0.000000e+00 774
4 TraesCS7B01G286400 chr7A 92.308 117 8 1 233 348 558746856 558746972 9.080000e-37 165
5 TraesCS7B01G286400 chr1B 94.273 227 12 1 1 226 596115885 596116111 3.020000e-91 346
6 TraesCS7B01G286400 chr3D 89.083 229 11 3 1 229 612533833 612533619 5.200000e-69 272
7 TraesCS7B01G286400 chr6A 88.312 231 12 10 1 231 47533517 47533732 3.130000e-66 263
8 TraesCS7B01G286400 chrUn 87.665 227 13 4 1 227 95706381 95706592 2.440000e-62 250


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 TraesCS7B01G286400 chr7B 521611696 521615780 4084 False 7544.0 7544 100.000 1 4085 1 chr7B.!!$F1 4084
1 TraesCS7B01G286400 chr7D 492215944 492219816 3872 False 5738.0 5738 93.555 233 4085 1 chr7D.!!$F1 3852
2 TraesCS7B01G286400 chr7A 558751192 558754899 3707 False 2779.5 4785 93.045 342 4085 2 chr7A.!!$F2 3743

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
27 28 0.028770 CAGTTTCGAAAACTGCGCCA 59.971 50.0 13.1 0.0 40.80 5.69 F
77 78 0.033109 GCCCTTCCAGGTTTATGGCT 60.033 55.0 0.0 0.0 40.41 4.75 F
119 120 0.108804 GGCGAACCATCTCGTCTCAA 60.109 55.0 0.0 0.0 40.28 3.02 F
211 212 0.108945 GAGCAAACCAGCATCCAAGC 60.109 55.0 0.0 0.0 36.85 4.01 F
2203 2259 0.035534 TGCGGTGCCATTATGTCTGT 60.036 50.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1832 1885 1.000843 ACATAGTCGCAGTGTGCTTCA 59.999 47.619 0.00 0.00 42.25 3.02 R
1907 1960 7.441836 TGCAGATAAGTGACTAAAGAGAACAA 58.558 34.615 0.00 0.00 0.00 2.83 R
2108 2163 5.857268 AGTGCTTTGAAACATTTGCCTAAT 58.143 33.333 0.00 0.00 0.00 1.73 R
2583 2640 1.019673 CTTTGATGGCATCCCAGTCG 58.980 55.000 23.92 3.84 46.24 4.18 R
3201 3269 0.033601 TGCCTCCCACAAAGTGTGTT 60.034 50.000 7.55 0.00 46.45 3.32 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
17 18 2.423874 TCGCCAGGCAGTTTCGAA 59.576 55.556 13.30 0.00 0.00 3.71
18 19 1.227704 TCGCCAGGCAGTTTCGAAA 60.228 52.632 13.30 6.47 0.00 3.46
19 20 0.816018 TCGCCAGGCAGTTTCGAAAA 60.816 50.000 13.10 0.00 0.00 2.29
20 21 0.660300 CGCCAGGCAGTTTCGAAAAC 60.660 55.000 13.10 7.23 0.00 2.43
21 22 0.668535 GCCAGGCAGTTTCGAAAACT 59.331 50.000 13.10 9.44 0.00 2.66
26 27 2.783440 CAGTTTCGAAAACTGCGCC 58.217 52.632 13.10 0.00 40.80 6.53
27 28 0.028770 CAGTTTCGAAAACTGCGCCA 59.971 50.000 13.10 0.00 40.80 5.69
28 29 0.736053 AGTTTCGAAAACTGCGCCAA 59.264 45.000 13.10 0.00 0.00 4.52
29 30 0.843872 GTTTCGAAAACTGCGCCAAC 59.156 50.000 13.10 0.00 0.00 3.77
30 31 0.590230 TTTCGAAAACTGCGCCAACG 60.590 50.000 8.44 2.45 44.07 4.10
31 32 1.707239 TTCGAAAACTGCGCCAACGT 61.707 50.000 4.18 0.00 42.83 3.99
32 33 1.721133 CGAAAACTGCGCCAACGTC 60.721 57.895 4.18 0.00 42.83 4.34
33 34 1.353804 GAAAACTGCGCCAACGTCA 59.646 52.632 4.18 0.00 42.83 4.35
34 35 0.928451 GAAAACTGCGCCAACGTCAC 60.928 55.000 4.18 0.00 42.83 3.67
35 36 2.331019 AAAACTGCGCCAACGTCACC 62.331 55.000 4.18 0.00 42.83 4.02
38 39 4.893601 TGCGCCAACGTCACCGAA 62.894 61.111 4.18 0.00 42.83 4.30
39 40 4.072088 GCGCCAACGTCACCGAAG 62.072 66.667 0.00 0.00 42.83 3.79
40 41 4.072088 CGCCAACGTCACCGAAGC 62.072 66.667 0.00 0.00 37.88 3.86
41 42 4.072088 GCCAACGTCACCGAAGCG 62.072 66.667 0.00 0.00 37.88 4.68
42 43 2.660552 CCAACGTCACCGAAGCGT 60.661 61.111 0.00 0.00 40.81 5.07
43 44 2.544359 CAACGTCACCGAAGCGTG 59.456 61.111 0.00 0.00 38.92 5.34
44 45 2.660552 AACGTCACCGAAGCGTGG 60.661 61.111 0.00 0.00 38.92 4.94
45 46 4.657824 ACGTCACCGAAGCGTGGG 62.658 66.667 0.00 0.00 37.47 4.61
57 58 4.752879 CGTGGGCGGTAGTGGTGG 62.753 72.222 0.00 0.00 0.00 4.61
58 59 4.404098 GTGGGCGGTAGTGGTGGG 62.404 72.222 0.00 0.00 0.00 4.61
63 64 3.327404 CGGTAGTGGTGGGCCCTT 61.327 66.667 25.70 5.94 0.00 3.95
64 65 2.675371 GGTAGTGGTGGGCCCTTC 59.325 66.667 25.70 16.05 0.00 3.46
65 66 2.675371 GTAGTGGTGGGCCCTTCC 59.325 66.667 25.70 24.49 0.00 3.46
66 67 2.208640 TAGTGGTGGGCCCTTCCA 59.791 61.111 27.46 27.46 36.21 3.53
67 68 1.923395 TAGTGGTGGGCCCTTCCAG 60.923 63.158 30.33 0.00 37.50 3.86
68 69 4.366684 GTGGTGGGCCCTTCCAGG 62.367 72.222 30.33 0.00 37.50 4.45
69 70 4.938756 TGGTGGGCCCTTCCAGGT 62.939 66.667 27.46 0.00 37.50 4.00
70 71 3.590574 GGTGGGCCCTTCCAGGTT 61.591 66.667 25.70 0.00 37.50 3.50
71 72 2.526110 GTGGGCCCTTCCAGGTTT 59.474 61.111 25.70 0.00 37.50 3.27
72 73 1.771646 GTGGGCCCTTCCAGGTTTA 59.228 57.895 25.70 0.00 37.50 2.01
73 74 0.335019 GTGGGCCCTTCCAGGTTTAT 59.665 55.000 25.70 0.00 37.50 1.40
74 75 0.334676 TGGGCCCTTCCAGGTTTATG 59.665 55.000 25.70 0.00 36.21 1.90
75 76 0.397114 GGGCCCTTCCAGGTTTATGG 60.397 60.000 17.04 0.00 42.11 2.74
76 77 1.043116 GGCCCTTCCAGGTTTATGGC 61.043 60.000 0.00 0.00 40.41 4.40
77 78 0.033109 GCCCTTCCAGGTTTATGGCT 60.033 55.000 0.00 0.00 40.41 4.75
78 79 1.767759 CCCTTCCAGGTTTATGGCTG 58.232 55.000 0.00 0.00 40.41 4.85
79 80 1.005924 CCCTTCCAGGTTTATGGCTGT 59.994 52.381 0.00 0.00 40.41 4.40
80 81 2.369394 CCTTCCAGGTTTATGGCTGTC 58.631 52.381 0.00 0.00 40.41 3.51
81 82 2.009774 CTTCCAGGTTTATGGCTGTCG 58.990 52.381 0.00 0.00 40.41 4.35
82 83 0.981183 TCCAGGTTTATGGCTGTCGT 59.019 50.000 0.00 0.00 40.41 4.34
83 84 1.086696 CCAGGTTTATGGCTGTCGTG 58.913 55.000 0.00 0.00 32.48 4.35
84 85 1.338674 CCAGGTTTATGGCTGTCGTGA 60.339 52.381 0.00 0.00 32.48 4.35
85 86 2.422597 CAGGTTTATGGCTGTCGTGAA 58.577 47.619 0.00 0.00 0.00 3.18
86 87 2.416547 CAGGTTTATGGCTGTCGTGAAG 59.583 50.000 0.00 0.00 0.00 3.02
87 88 2.038557 AGGTTTATGGCTGTCGTGAAGT 59.961 45.455 0.00 0.00 0.00 3.01
88 89 2.159627 GGTTTATGGCTGTCGTGAAGTG 59.840 50.000 0.00 0.00 0.00 3.16
89 90 1.438651 TTATGGCTGTCGTGAAGTGC 58.561 50.000 0.00 0.00 0.00 4.40
90 91 0.391130 TATGGCTGTCGTGAAGTGCC 60.391 55.000 0.00 0.00 43.49 5.01
91 92 3.414700 GGCTGTCGTGAAGTGCCG 61.415 66.667 0.00 0.00 33.96 5.69
92 93 4.077188 GCTGTCGTGAAGTGCCGC 62.077 66.667 0.00 0.00 0.00 6.53
93 94 3.767230 CTGTCGTGAAGTGCCGCG 61.767 66.667 0.00 0.00 40.97 6.46
111 112 4.514577 CGAGCCGGCGAACCATCT 62.515 66.667 23.20 0.00 34.57 2.90
112 113 2.586357 GAGCCGGCGAACCATCTC 60.586 66.667 23.20 6.54 34.57 2.75
113 114 4.514577 AGCCGGCGAACCATCTCG 62.515 66.667 23.20 0.00 41.84 4.04
114 115 4.814294 GCCGGCGAACCATCTCGT 62.814 66.667 12.58 0.00 40.99 4.18
115 116 2.582498 CCGGCGAACCATCTCGTC 60.582 66.667 9.30 0.00 40.99 4.20
116 117 2.490217 CGGCGAACCATCTCGTCT 59.510 61.111 0.00 0.00 41.26 4.18
117 118 1.586564 CGGCGAACCATCTCGTCTC 60.587 63.158 0.00 0.00 41.26 3.36
118 119 1.511305 GGCGAACCATCTCGTCTCA 59.489 57.895 0.00 0.00 40.28 3.27
119 120 0.108804 GGCGAACCATCTCGTCTCAA 60.109 55.000 0.00 0.00 40.28 3.02
120 121 1.671850 GGCGAACCATCTCGTCTCAAA 60.672 52.381 0.00 0.00 40.28 2.69
121 122 1.390463 GCGAACCATCTCGTCTCAAAC 59.610 52.381 0.00 0.00 40.99 2.93
122 123 2.672714 CGAACCATCTCGTCTCAAACA 58.327 47.619 0.00 0.00 34.08 2.83
123 124 3.057019 CGAACCATCTCGTCTCAAACAA 58.943 45.455 0.00 0.00 34.08 2.83
124 125 3.493129 CGAACCATCTCGTCTCAAACAAA 59.507 43.478 0.00 0.00 34.08 2.83
125 126 4.025229 CGAACCATCTCGTCTCAAACAAAA 60.025 41.667 0.00 0.00 34.08 2.44
126 127 5.503357 CGAACCATCTCGTCTCAAACAAAAA 60.503 40.000 0.00 0.00 34.08 1.94
143 144 2.774439 AAAAACACCTGTGCACGATC 57.226 45.000 13.13 0.00 0.00 3.69
144 145 0.586319 AAAACACCTGTGCACGATCG 59.414 50.000 14.88 14.88 0.00 3.69
145 146 1.841663 AAACACCTGTGCACGATCGC 61.842 55.000 16.60 0.00 0.00 4.58
146 147 3.490759 CACCTGTGCACGATCGCC 61.491 66.667 16.60 7.25 0.00 5.54
147 148 4.760047 ACCTGTGCACGATCGCCC 62.760 66.667 16.60 6.85 0.00 6.13
161 162 4.415332 GCCCGTGCGACTTCGAGA 62.415 66.667 2.02 0.00 43.02 4.04
162 163 2.490217 CCCGTGCGACTTCGAGAT 59.510 61.111 2.02 0.00 43.02 2.75
163 164 1.586564 CCCGTGCGACTTCGAGATC 60.587 63.158 2.02 0.00 43.02 2.75
164 165 1.934956 CCGTGCGACTTCGAGATCG 60.935 63.158 14.16 14.16 43.02 3.69
165 166 1.934956 CGTGCGACTTCGAGATCGG 60.935 63.158 18.47 2.73 43.02 4.18
166 167 1.428219 GTGCGACTTCGAGATCGGA 59.572 57.895 18.47 14.47 43.02 4.55
167 168 1.428219 TGCGACTTCGAGATCGGAC 59.572 57.895 18.47 6.75 43.02 4.79
168 169 1.651730 GCGACTTCGAGATCGGACG 60.652 63.158 18.47 1.28 43.02 4.79
169 170 1.011019 CGACTTCGAGATCGGACGG 60.011 63.158 11.42 0.00 43.02 4.79
170 171 1.298488 GACTTCGAGATCGGACGGC 60.298 63.158 1.91 0.00 40.29 5.68
171 172 1.716826 GACTTCGAGATCGGACGGCT 61.717 60.000 1.91 0.00 40.29 5.52
172 173 1.009449 CTTCGAGATCGGACGGCTC 60.009 63.158 1.91 0.00 40.29 4.70
173 174 1.440938 CTTCGAGATCGGACGGCTCT 61.441 60.000 1.91 5.92 40.29 4.09
174 175 1.715862 TTCGAGATCGGACGGCTCTG 61.716 60.000 1.91 7.15 40.29 3.35
175 176 2.180862 CGAGATCGGACGGCTCTGA 61.181 63.158 11.51 0.00 36.18 3.27
176 177 1.652012 GAGATCGGACGGCTCTGAG 59.348 63.158 0.00 0.00 35.13 3.35
177 178 0.816018 GAGATCGGACGGCTCTGAGA 60.816 60.000 9.28 0.00 35.13 3.27
178 179 0.817634 AGATCGGACGGCTCTGAGAG 60.818 60.000 9.28 4.80 35.13 3.20
206 207 2.099062 CGCGAGCAAACCAGCATC 59.901 61.111 0.00 0.00 36.85 3.91
207 208 2.486966 GCGAGCAAACCAGCATCC 59.513 61.111 0.00 0.00 36.85 3.51
208 209 2.334946 GCGAGCAAACCAGCATCCA 61.335 57.895 0.00 0.00 36.85 3.41
209 210 1.865788 GCGAGCAAACCAGCATCCAA 61.866 55.000 0.00 0.00 36.85 3.53
210 211 0.169672 CGAGCAAACCAGCATCCAAG 59.830 55.000 0.00 0.00 36.85 3.61
211 212 0.108945 GAGCAAACCAGCATCCAAGC 60.109 55.000 0.00 0.00 36.85 4.01
212 213 0.828762 AGCAAACCAGCATCCAAGCA 60.829 50.000 0.00 0.00 36.85 3.91
213 214 0.668401 GCAAACCAGCATCCAAGCAC 60.668 55.000 0.00 0.00 36.85 4.40
214 215 0.963962 CAAACCAGCATCCAAGCACT 59.036 50.000 0.00 0.00 36.85 4.40
215 216 1.342174 CAAACCAGCATCCAAGCACTT 59.658 47.619 0.00 0.00 36.85 3.16
216 217 1.708341 AACCAGCATCCAAGCACTTT 58.292 45.000 0.00 0.00 36.85 2.66
217 218 1.708341 ACCAGCATCCAAGCACTTTT 58.292 45.000 0.00 0.00 36.85 2.27
218 219 2.041701 ACCAGCATCCAAGCACTTTTT 58.958 42.857 0.00 0.00 36.85 1.94
219 220 3.230134 ACCAGCATCCAAGCACTTTTTA 58.770 40.909 0.00 0.00 36.85 1.52
220 221 3.256631 ACCAGCATCCAAGCACTTTTTAG 59.743 43.478 0.00 0.00 36.85 1.85
221 222 3.248266 CAGCATCCAAGCACTTTTTAGC 58.752 45.455 0.00 0.00 36.85 3.09
222 223 2.892852 AGCATCCAAGCACTTTTTAGCA 59.107 40.909 0.00 0.00 36.85 3.49
223 224 3.512724 AGCATCCAAGCACTTTTTAGCAT 59.487 39.130 0.00 0.00 36.85 3.79
224 225 4.020839 AGCATCCAAGCACTTTTTAGCATT 60.021 37.500 0.00 0.00 36.85 3.56
225 226 4.692155 GCATCCAAGCACTTTTTAGCATTT 59.308 37.500 0.00 0.00 0.00 2.32
226 227 5.390145 GCATCCAAGCACTTTTTAGCATTTG 60.390 40.000 0.00 0.00 0.00 2.32
227 228 4.630111 TCCAAGCACTTTTTAGCATTTGG 58.370 39.130 0.00 0.00 37.39 3.28
228 229 3.747529 CCAAGCACTTTTTAGCATTTGGG 59.252 43.478 0.00 0.00 34.33 4.12
229 230 4.379652 CAAGCACTTTTTAGCATTTGGGT 58.620 39.130 0.00 0.00 0.00 4.51
230 231 4.687901 AGCACTTTTTAGCATTTGGGTT 57.312 36.364 0.00 0.00 0.00 4.11
231 232 4.379652 AGCACTTTTTAGCATTTGGGTTG 58.620 39.130 0.00 0.00 0.00 3.77
241 242 8.738645 TTTAGCATTTGGGTTGTATTTTTGTT 57.261 26.923 0.00 0.00 0.00 2.83
394 395 8.531146 CCAAACAACTCAAACAATATCCCTAAT 58.469 33.333 0.00 0.00 0.00 1.73
432 433 7.745620 AACCGATTTCTTCATGAGTTTAAGT 57.254 32.000 0.00 0.00 0.00 2.24
492 493 4.478699 GTGTTCATGTTGTGATCCATGTG 58.521 43.478 8.83 0.00 39.53 3.21
495 496 3.753815 TCATGTTGTGATCCATGTGTGT 58.246 40.909 8.83 0.00 39.53 3.72
520 521 3.704800 AAGCTAGGTTGTTCTTCCTCC 57.295 47.619 6.33 0.00 35.51 4.30
560 561 5.775195 TGACCACTATACGATCATCATCCTT 59.225 40.000 0.00 0.00 0.00 3.36
578 579 3.025978 CCTTTCATGGCTAATGGCTCAA 58.974 45.455 0.00 0.00 41.46 3.02
594 595 3.936453 GGCTCAACGTACCATACATTCAA 59.064 43.478 0.00 0.00 0.00 2.69
599 600 5.640357 TCAACGTACCATACATTCAACTTCC 59.360 40.000 0.00 0.00 0.00 3.46
625 626 5.062528 TGCATGTGTCAAAGTCAATAGTCA 58.937 37.500 0.00 0.00 0.00 3.41
631 632 6.597672 TGTGTCAAAGTCAATAGTCACACTTT 59.402 34.615 0.00 0.00 39.20 2.66
639 649 6.428159 AGTCAATAGTCACACTTTTCCACATC 59.572 38.462 0.00 0.00 0.00 3.06
640 650 5.408299 TCAATAGTCACACTTTTCCACATCG 59.592 40.000 0.00 0.00 0.00 3.84
641 651 3.194005 AGTCACACTTTTCCACATCGT 57.806 42.857 0.00 0.00 0.00 3.73
642 652 3.131396 AGTCACACTTTTCCACATCGTC 58.869 45.455 0.00 0.00 0.00 4.20
643 653 2.096909 GTCACACTTTTCCACATCGTCG 60.097 50.000 0.00 0.00 0.00 5.12
644 654 1.194547 CACACTTTTCCACATCGTCGG 59.805 52.381 0.00 0.00 0.00 4.79
645 655 1.202604 ACACTTTTCCACATCGTCGGT 60.203 47.619 0.00 0.00 0.00 4.69
646 656 1.459592 CACTTTTCCACATCGTCGGTC 59.540 52.381 0.00 0.00 0.00 4.79
647 657 1.076332 CTTTTCCACATCGTCGGTCC 58.924 55.000 0.00 0.00 0.00 4.46
765 782 0.388649 GCACTTGTCCTCATCGTCGT 60.389 55.000 0.00 0.00 0.00 4.34
806 826 3.795688 AGGTTCATGTGGGCCATATAG 57.204 47.619 15.95 10.35 30.71 1.31
814 834 1.710809 GTGGGCCATATAGGGTGGATT 59.289 52.381 10.70 0.00 39.12 3.01
937 957 1.985116 GGCCTCGTTCCTCAGACCT 60.985 63.158 0.00 0.00 0.00 3.85
959 979 0.770499 TGGATCAGAGCCCACAACAA 59.230 50.000 1.14 0.00 0.00 2.83
960 980 1.168714 GGATCAGAGCCCACAACAAC 58.831 55.000 0.00 0.00 0.00 3.32
961 981 1.545428 GGATCAGAGCCCACAACAACA 60.545 52.381 0.00 0.00 0.00 3.33
962 982 1.537202 GATCAGAGCCCACAACAACAC 59.463 52.381 0.00 0.00 0.00 3.32
1035 1056 2.272471 GCCCCTTTCCTCCCGAAG 59.728 66.667 0.00 0.00 0.00 3.79
1084 1105 4.148825 GCCTCGCCATGTCTCCGT 62.149 66.667 0.00 0.00 0.00 4.69
1086 1107 2.278206 CTCGCCATGTCTCCGTCG 60.278 66.667 0.00 0.00 0.00 5.12
1308 1353 0.541063 TGGTGGACAACTCGGAGCTA 60.541 55.000 4.58 0.00 0.00 3.32
1445 1491 1.405121 GGTAACCCACACTTAGGAGCG 60.405 57.143 0.00 0.00 0.00 5.03
1459 1505 1.347907 GAGCGTCTAGGTCGTCGTC 59.652 63.158 9.23 0.00 37.64 4.20
1463 1509 0.369589 CGTCTAGGTCGTCGTCTCAC 59.630 60.000 0.00 0.00 0.00 3.51
1482 1528 4.903054 TCACTACGACTCAACTCTAGGAA 58.097 43.478 0.00 0.00 0.00 3.36
1484 1530 5.180868 TCACTACGACTCAACTCTAGGAAAC 59.819 44.000 0.00 0.00 0.00 2.78
1499 1545 2.755103 AGGAAACCCGAATTTGAGCATC 59.245 45.455 0.00 0.00 0.00 3.91
1666 1716 4.601406 ATGGGTAGGCAGTTATTTCCAA 57.399 40.909 0.00 0.00 0.00 3.53
1793 1846 4.450419 CCACTTTTTGTTCAGTTTTGTGCA 59.550 37.500 0.00 0.00 0.00 4.57
1796 1849 7.076983 CACTTTTTGTTCAGTTTTGTGCAAAT 58.923 30.769 0.00 0.00 33.15 2.32
1832 1885 1.691196 TACAAGCTGCAAAGCTGGTT 58.309 45.000 12.77 6.81 46.11 3.67
1887 1940 5.652994 TGGGTAATGTGCCAATTCTTTAC 57.347 39.130 0.00 0.00 0.00 2.01
1951 2004 2.928731 GCAGACTTCTGTAGTGGCTCAC 60.929 54.545 8.04 0.00 45.45 3.51
1956 2009 5.423610 AGACTTCTGTAGTGGCTCACATATT 59.576 40.000 7.86 0.00 37.17 1.28
2108 2163 9.968870 AAGCAACCGAACTATTTTGTTTTATTA 57.031 25.926 0.00 0.00 0.00 0.98
2203 2259 0.035534 TGCGGTGCCATTATGTCTGT 60.036 50.000 0.00 0.00 0.00 3.41
2481 2538 1.295792 GCATATTTCCGCGACTGGAA 58.704 50.000 8.23 0.00 46.12 3.53
2583 2640 3.282885 AGATGGGAAGAAATTTCGAGCC 58.717 45.455 12.42 13.77 0.00 4.70
2987 3044 4.892934 GGGGTTGCATGATATGGTAAAGAA 59.107 41.667 0.00 0.00 0.00 2.52
3053 3110 4.315803 ACCTCTTTACAGTCACAAATCGG 58.684 43.478 0.00 0.00 0.00 4.18
3148 3205 3.939592 GGAGGGAAACTAAAGATGAACCG 59.060 47.826 0.00 0.00 0.00 4.44
3201 3269 7.230849 AGATTGTATCAGCATTTTTGTTGGA 57.769 32.000 0.00 0.00 0.00 3.53
3202 3270 7.669427 AGATTGTATCAGCATTTTTGTTGGAA 58.331 30.769 0.00 0.00 0.00 3.53
3203 3271 7.599998 AGATTGTATCAGCATTTTTGTTGGAAC 59.400 33.333 0.00 0.00 0.00 3.62
3204 3272 6.154203 TGTATCAGCATTTTTGTTGGAACA 57.846 33.333 0.00 0.00 37.08 3.18
3205 3273 5.982516 TGTATCAGCATTTTTGTTGGAACAC 59.017 36.000 0.00 0.00 39.29 3.32
3206 3274 4.462508 TCAGCATTTTTGTTGGAACACA 57.537 36.364 0.00 0.00 39.29 3.72
3207 3275 4.180057 TCAGCATTTTTGTTGGAACACAC 58.820 39.130 0.00 0.00 39.29 3.82
3208 3276 4.081752 TCAGCATTTTTGTTGGAACACACT 60.082 37.500 0.00 0.00 39.29 3.55
3209 3277 4.630940 CAGCATTTTTGTTGGAACACACTT 59.369 37.500 0.00 0.00 39.29 3.16
3252 3320 6.362820 GTCGTGGTTCTGTAAAAGAGAACTAG 59.637 42.308 14.32 8.03 45.82 2.57
3358 3428 4.615949 TGTTGTAACAATTGATGTGCACC 58.384 39.130 15.69 0.00 42.99 5.01
3382 3452 6.391227 TCTGCAGACATTATTACGATCTGA 57.609 37.500 13.74 0.00 39.33 3.27
3387 3457 9.710900 TGCAGACATTATTACGATCTGATATTT 57.289 29.630 3.80 0.00 39.33 1.40
3436 3506 8.177119 TGGACTCAACATTGCTTTAACTTTAT 57.823 30.769 0.00 0.00 0.00 1.40
3496 3568 4.021016 AGTGCTCCCTCCGATTCATAATAC 60.021 45.833 0.00 0.00 0.00 1.89
3499 3571 4.157289 GCTCCCTCCGATTCATAATACGTA 59.843 45.833 0.00 0.00 0.00 3.57
3502 3574 5.065602 TCCCTCCGATTCATAATACGTATCG 59.934 44.000 8.86 8.05 38.19 2.92
3504 3576 4.665212 TCCGATTCATAATACGTATCGCC 58.335 43.478 8.86 0.00 37.39 5.54
3505 3577 3.795101 CCGATTCATAATACGTATCGCCC 59.205 47.826 8.86 0.00 37.39 6.13
3514 3586 1.073177 ACGTATCGCCCGTTTTGAAG 58.927 50.000 0.00 0.00 34.28 3.02
3523 3595 2.287970 GCCCGTTTTGAAGTAAGGTTGG 60.288 50.000 0.00 0.00 0.00 3.77
3524 3596 2.953648 CCCGTTTTGAAGTAAGGTTGGT 59.046 45.455 0.00 0.00 0.00 3.67
3525 3597 3.382227 CCCGTTTTGAAGTAAGGTTGGTT 59.618 43.478 0.00 0.00 0.00 3.67
3526 3598 4.498513 CCCGTTTTGAAGTAAGGTTGGTTC 60.499 45.833 0.00 0.00 0.00 3.62
3527 3599 4.096682 CCGTTTTGAAGTAAGGTTGGTTCA 59.903 41.667 0.00 0.00 0.00 3.18
3528 3600 5.393243 CCGTTTTGAAGTAAGGTTGGTTCAA 60.393 40.000 0.00 0.00 37.18 2.69
3529 3601 5.513849 CGTTTTGAAGTAAGGTTGGTTCAAC 59.486 40.000 2.46 2.46 42.89 3.18
3550 3635 3.942748 ACCTTCAAAACTGCGACACTTAA 59.057 39.130 0.00 0.00 0.00 1.85
3561 3646 3.069016 TGCGACACTTAATATGGATCGGT 59.931 43.478 0.00 0.00 0.00 4.69
3563 3648 4.794981 GCGACACTTAATATGGATCGGTGA 60.795 45.833 0.00 0.00 0.00 4.02
3624 3709 5.512753 TCTCAGTTCTATGCATGAGTCTC 57.487 43.478 10.16 0.00 40.07 3.36
3701 3798 7.147976 ACATCAATGCTAACCAAAGAAAGAAC 58.852 34.615 0.00 0.00 0.00 3.01
3763 3861 3.991773 CTGGGTGAAAATTGCTTGTGATG 59.008 43.478 0.00 0.00 0.00 3.07
3867 3965 2.814280 TGTCGTTCTTGGAGAAGGTC 57.186 50.000 9.40 5.77 40.08 3.85
3885 3983 3.314331 AGCCTCACGTCCCAGTGG 61.314 66.667 0.63 0.63 42.10 4.00
4063 4161 4.708177 GCCATGGCTGAAGTAGAATAGAA 58.292 43.478 29.98 0.00 38.26 2.10
4065 4163 5.686124 GCCATGGCTGAAGTAGAATAGAACT 60.686 44.000 29.98 0.00 38.26 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.660300 GTTTTCGAAACTGCCTGGCG 60.660 55.000 14.98 11.36 0.00 5.69
3 4 2.405892 CAGTTTTCGAAACTGCCTGG 57.594 50.000 20.00 0.00 40.80 4.45
9 10 0.736053 TTGGCGCAGTTTTCGAAACT 59.264 45.000 10.79 8.50 0.00 2.66
10 11 0.843872 GTTGGCGCAGTTTTCGAAAC 59.156 50.000 10.79 6.25 0.00 2.78
11 12 0.590230 CGTTGGCGCAGTTTTCGAAA 60.590 50.000 10.83 6.47 0.00 3.46
12 13 1.010574 CGTTGGCGCAGTTTTCGAA 60.011 52.632 10.83 0.00 0.00 3.71
13 14 2.096481 GACGTTGGCGCAGTTTTCGA 62.096 55.000 10.83 0.00 42.83 3.71
14 15 1.721133 GACGTTGGCGCAGTTTTCG 60.721 57.895 10.83 7.40 42.83 3.46
15 16 0.928451 GTGACGTTGGCGCAGTTTTC 60.928 55.000 10.83 0.00 42.83 2.29
16 17 1.063488 GTGACGTTGGCGCAGTTTT 59.937 52.632 10.83 0.00 42.83 2.43
17 18 2.713154 GTGACGTTGGCGCAGTTT 59.287 55.556 10.83 0.00 42.83 2.66
18 19 3.276846 GGTGACGTTGGCGCAGTT 61.277 61.111 10.83 0.00 42.83 3.16
35 36 4.430765 ACTACCGCCCACGCTTCG 62.431 66.667 0.00 0.00 38.22 3.79
36 37 2.813908 CACTACCGCCCACGCTTC 60.814 66.667 0.00 0.00 38.22 3.86
37 38 4.388499 CCACTACCGCCCACGCTT 62.388 66.667 0.00 0.00 38.22 4.68
40 41 4.752879 CCACCACTACCGCCCACG 62.753 72.222 0.00 0.00 39.67 4.94
41 42 4.404098 CCCACCACTACCGCCCAC 62.404 72.222 0.00 0.00 0.00 4.61
46 47 3.325201 GAAGGGCCCACCACTACCG 62.325 68.421 27.56 0.00 43.89 4.02
47 48 2.675371 GAAGGGCCCACCACTACC 59.325 66.667 27.56 0.00 43.89 3.18
48 49 2.198304 CTGGAAGGGCCCACCACTAC 62.198 65.000 29.20 11.98 43.89 2.73
49 50 1.923395 CTGGAAGGGCCCACCACTA 60.923 63.158 29.20 14.21 43.89 2.74
50 51 3.260100 CTGGAAGGGCCCACCACT 61.260 66.667 29.20 5.61 43.89 4.00
61 62 2.009774 CGACAGCCATAAACCTGGAAG 58.990 52.381 0.00 0.00 38.69 3.46
62 63 1.349688 ACGACAGCCATAAACCTGGAA 59.650 47.619 0.00 0.00 38.69 3.53
63 64 0.981183 ACGACAGCCATAAACCTGGA 59.019 50.000 0.00 0.00 38.69 3.86
64 65 1.086696 CACGACAGCCATAAACCTGG 58.913 55.000 0.00 0.00 39.45 4.45
65 66 2.093306 TCACGACAGCCATAAACCTG 57.907 50.000 0.00 0.00 35.26 4.00
66 67 2.038557 ACTTCACGACAGCCATAAACCT 59.961 45.455 0.00 0.00 0.00 3.50
67 68 2.159627 CACTTCACGACAGCCATAAACC 59.840 50.000 0.00 0.00 0.00 3.27
68 69 2.412847 GCACTTCACGACAGCCATAAAC 60.413 50.000 0.00 0.00 0.00 2.01
69 70 1.804151 GCACTTCACGACAGCCATAAA 59.196 47.619 0.00 0.00 0.00 1.40
70 71 1.438651 GCACTTCACGACAGCCATAA 58.561 50.000 0.00 0.00 0.00 1.90
71 72 0.391130 GGCACTTCACGACAGCCATA 60.391 55.000 0.00 0.00 44.59 2.74
72 73 1.672356 GGCACTTCACGACAGCCAT 60.672 57.895 0.00 0.00 44.59 4.40
73 74 2.280797 GGCACTTCACGACAGCCA 60.281 61.111 0.00 0.00 44.59 4.75
74 75 3.414700 CGGCACTTCACGACAGCC 61.415 66.667 0.00 0.00 41.86 4.85
75 76 4.077188 GCGGCACTTCACGACAGC 62.077 66.667 0.00 0.00 0.00 4.40
76 77 3.767230 CGCGGCACTTCACGACAG 61.767 66.667 0.00 0.00 0.00 3.51
94 95 4.514577 AGATGGTTCGCCGGCTCG 62.515 66.667 26.68 10.37 41.18 5.03
95 96 2.586357 GAGATGGTTCGCCGGCTC 60.586 66.667 26.68 14.27 41.18 4.70
96 97 4.514577 CGAGATGGTTCGCCGGCT 62.515 66.667 26.68 3.45 41.18 5.52
97 98 4.814294 ACGAGATGGTTCGCCGGC 62.814 66.667 19.07 19.07 44.15 6.13
98 99 2.582498 GACGAGATGGTTCGCCGG 60.582 66.667 0.00 0.00 44.15 6.13
99 100 1.586564 GAGACGAGATGGTTCGCCG 60.587 63.158 0.00 0.00 44.15 6.46
100 101 0.108804 TTGAGACGAGATGGTTCGCC 60.109 55.000 0.00 0.00 44.15 5.54
101 102 1.390463 GTTTGAGACGAGATGGTTCGC 59.610 52.381 0.00 0.00 44.15 4.70
102 103 2.672714 TGTTTGAGACGAGATGGTTCG 58.327 47.619 0.00 0.00 45.70 3.95
103 104 5.418310 TTTTGTTTGAGACGAGATGGTTC 57.582 39.130 0.00 0.00 0.00 3.62
104 105 5.828299 TTTTTGTTTGAGACGAGATGGTT 57.172 34.783 0.00 0.00 0.00 3.67
124 125 1.002900 CGATCGTGCACAGGTGTTTTT 60.003 47.619 18.64 0.00 0.00 1.94
125 126 0.586319 CGATCGTGCACAGGTGTTTT 59.414 50.000 18.64 0.00 0.00 2.43
126 127 1.841663 GCGATCGTGCACAGGTGTTT 61.842 55.000 18.64 0.00 34.15 2.83
127 128 2.317609 GCGATCGTGCACAGGTGTT 61.318 57.895 18.64 0.00 34.15 3.32
128 129 2.738521 GCGATCGTGCACAGGTGT 60.739 61.111 18.64 0.00 34.15 4.16
129 130 3.490759 GGCGATCGTGCACAGGTG 61.491 66.667 18.64 4.69 36.28 4.00
130 131 4.760047 GGGCGATCGTGCACAGGT 62.760 66.667 18.64 5.86 38.45 4.00
144 145 3.701604 ATCTCGAAGTCGCACGGGC 62.702 63.158 0.00 0.00 39.60 6.13
145 146 1.586564 GATCTCGAAGTCGCACGGG 60.587 63.158 0.00 0.00 39.60 5.28
146 147 1.934956 CGATCTCGAAGTCGCACGG 60.935 63.158 6.23 0.00 43.02 4.94
147 148 1.934956 CCGATCTCGAAGTCGCACG 60.935 63.158 12.22 0.00 43.02 5.34
148 149 0.862283 GTCCGATCTCGAAGTCGCAC 60.862 60.000 12.22 5.68 43.02 5.34
149 150 1.428219 GTCCGATCTCGAAGTCGCA 59.572 57.895 12.22 0.00 43.02 5.10
150 151 1.651730 CGTCCGATCTCGAAGTCGC 60.652 63.158 12.22 1.56 43.02 5.19
151 152 1.011019 CCGTCCGATCTCGAAGTCG 60.011 63.158 11.05 11.05 43.02 4.18
152 153 1.298488 GCCGTCCGATCTCGAAGTC 60.298 63.158 0.22 0.00 43.02 3.01
153 154 1.716826 GAGCCGTCCGATCTCGAAGT 61.717 60.000 0.22 0.00 43.02 3.01
154 155 1.009449 GAGCCGTCCGATCTCGAAG 60.009 63.158 0.22 0.00 43.02 3.79
155 156 1.451567 AGAGCCGTCCGATCTCGAA 60.452 57.895 0.22 0.00 43.02 3.71
156 157 2.180862 CAGAGCCGTCCGATCTCGA 61.181 63.158 0.22 0.00 43.02 4.04
157 158 2.111932 CTCAGAGCCGTCCGATCTCG 62.112 65.000 0.00 0.00 39.44 4.04
158 159 0.816018 TCTCAGAGCCGTCCGATCTC 60.816 60.000 0.00 0.00 0.00 2.75
159 160 0.817634 CTCTCAGAGCCGTCCGATCT 60.818 60.000 0.00 0.00 0.00 2.75
160 161 1.652012 CTCTCAGAGCCGTCCGATC 59.348 63.158 0.00 0.00 0.00 3.69
161 162 3.834726 CTCTCAGAGCCGTCCGAT 58.165 61.111 0.00 0.00 0.00 4.18
185 186 4.139420 CTGGTTTGCTCGCGCGAG 62.139 66.667 46.00 46.00 44.56 5.03
188 189 4.107051 ATGCTGGTTTGCTCGCGC 62.107 61.111 0.00 0.00 0.00 6.86
189 190 2.099062 GATGCTGGTTTGCTCGCG 59.901 61.111 0.00 0.00 0.00 5.87
190 191 1.865788 TTGGATGCTGGTTTGCTCGC 61.866 55.000 0.00 0.00 0.00 5.03
191 192 0.169672 CTTGGATGCTGGTTTGCTCG 59.830 55.000 0.00 0.00 0.00 5.03
192 193 0.108945 GCTTGGATGCTGGTTTGCTC 60.109 55.000 0.00 0.00 0.00 4.26
193 194 0.828762 TGCTTGGATGCTGGTTTGCT 60.829 50.000 0.00 0.00 0.00 3.91
194 195 0.668401 GTGCTTGGATGCTGGTTTGC 60.668 55.000 0.00 0.00 0.00 3.68
195 196 0.963962 AGTGCTTGGATGCTGGTTTG 59.036 50.000 0.00 0.00 0.00 2.93
196 197 1.708341 AAGTGCTTGGATGCTGGTTT 58.292 45.000 0.00 0.00 0.00 3.27
197 198 1.708341 AAAGTGCTTGGATGCTGGTT 58.292 45.000 0.00 0.00 0.00 3.67
198 199 1.708341 AAAAGTGCTTGGATGCTGGT 58.292 45.000 0.00 0.00 0.00 4.00
199 200 2.825861 AAAAAGTGCTTGGATGCTGG 57.174 45.000 0.00 0.00 0.00 4.85
200 201 3.248266 GCTAAAAAGTGCTTGGATGCTG 58.752 45.455 0.00 0.00 0.00 4.41
201 202 2.892852 TGCTAAAAAGTGCTTGGATGCT 59.107 40.909 0.00 0.00 0.00 3.79
202 203 3.302365 TGCTAAAAAGTGCTTGGATGC 57.698 42.857 0.00 0.00 0.00 3.91
203 204 5.121142 CCAAATGCTAAAAAGTGCTTGGATG 59.879 40.000 0.00 0.00 36.94 3.51
204 205 5.240121 CCAAATGCTAAAAAGTGCTTGGAT 58.760 37.500 0.00 0.00 36.94 3.41
205 206 4.502950 CCCAAATGCTAAAAAGTGCTTGGA 60.503 41.667 0.00 0.00 36.94 3.53
206 207 3.747529 CCCAAATGCTAAAAAGTGCTTGG 59.252 43.478 0.00 0.00 35.55 3.61
207 208 4.379652 ACCCAAATGCTAAAAAGTGCTTG 58.620 39.130 0.00 0.00 0.00 4.01
208 209 4.687901 ACCCAAATGCTAAAAAGTGCTT 57.312 36.364 0.00 0.00 0.00 3.91
209 210 4.141733 ACAACCCAAATGCTAAAAAGTGCT 60.142 37.500 0.00 0.00 0.00 4.40
210 211 4.126437 ACAACCCAAATGCTAAAAAGTGC 58.874 39.130 0.00 0.00 0.00 4.40
211 212 7.961325 AATACAACCCAAATGCTAAAAAGTG 57.039 32.000 0.00 0.00 0.00 3.16
212 213 8.972458 AAAATACAACCCAAATGCTAAAAAGT 57.028 26.923 0.00 0.00 0.00 2.66
213 214 9.662545 CAAAAATACAACCCAAATGCTAAAAAG 57.337 29.630 0.00 0.00 0.00 2.27
214 215 9.178758 ACAAAAATACAACCCAAATGCTAAAAA 57.821 25.926 0.00 0.00 0.00 1.94
215 216 8.738645 ACAAAAATACAACCCAAATGCTAAAA 57.261 26.923 0.00 0.00 0.00 1.52
216 217 8.616076 CAACAAAAATACAACCCAAATGCTAAA 58.384 29.630 0.00 0.00 0.00 1.85
217 218 7.770897 ACAACAAAAATACAACCCAAATGCTAA 59.229 29.630 0.00 0.00 0.00 3.09
218 219 7.275920 ACAACAAAAATACAACCCAAATGCTA 58.724 30.769 0.00 0.00 0.00 3.49
219 220 6.118852 ACAACAAAAATACAACCCAAATGCT 58.881 32.000 0.00 0.00 0.00 3.79
220 221 6.370433 ACAACAAAAATACAACCCAAATGC 57.630 33.333 0.00 0.00 0.00 3.56
221 222 9.631452 AAAAACAACAAAAATACAACCCAAATG 57.369 25.926 0.00 0.00 0.00 2.32
368 369 6.345096 AGGGATATTGTTTGAGTTGTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
420 421 7.061094 GCCAATTCTTTTCGACTTAAACTCATG 59.939 37.037 0.00 0.00 0.00 3.07
432 433 6.648725 CCAAAAATAAGGCCAATTCTTTTCGA 59.351 34.615 5.01 0.00 0.00 3.71
492 493 4.884247 AGAACAACCTAGCTTAGTCACAC 58.116 43.478 0.00 0.00 0.00 3.82
495 496 4.838986 AGGAAGAACAACCTAGCTTAGTCA 59.161 41.667 0.00 0.00 34.47 3.41
520 521 1.952133 TCACGAGCAAAACCCGTCG 60.952 57.895 0.00 0.00 38.40 5.12
535 536 5.184096 AGGATGATGATCGTATAGTGGTCAC 59.816 44.000 0.00 0.00 0.00 3.67
560 561 2.016318 CGTTGAGCCATTAGCCATGAA 58.984 47.619 0.00 0.00 45.47 2.57
578 579 4.224370 AGGGAAGTTGAATGTATGGTACGT 59.776 41.667 0.00 0.00 0.00 3.57
594 595 2.363306 TTGACACATGCAAGGGAAGT 57.637 45.000 0.00 0.00 0.00 3.01
599 600 3.713858 TTGACTTTGACACATGCAAGG 57.286 42.857 0.00 0.00 0.00 3.61
625 626 1.202604 ACCGACGATGTGGAAAAGTGT 60.203 47.619 0.00 0.00 0.00 3.55
631 632 2.975536 GGGACCGACGATGTGGAA 59.024 61.111 0.00 0.00 0.00 3.53
639 649 0.731855 GAAAGAGAACGGGACCGACG 60.732 60.000 18.80 3.19 42.83 5.12
640 650 0.731855 CGAAAGAGAACGGGACCGAC 60.732 60.000 18.80 10.73 42.83 4.79
641 651 1.582968 CGAAAGAGAACGGGACCGA 59.417 57.895 18.80 0.00 42.83 4.69
642 652 2.092882 GCGAAAGAGAACGGGACCG 61.093 63.158 9.56 9.56 46.03 4.79
643 653 1.740664 GGCGAAAGAGAACGGGACC 60.741 63.158 0.00 0.00 0.00 4.46
644 654 0.736672 GAGGCGAAAGAGAACGGGAC 60.737 60.000 0.00 0.00 0.00 4.46
645 655 1.590147 GAGGCGAAAGAGAACGGGA 59.410 57.895 0.00 0.00 0.00 5.14
646 656 1.448013 GGAGGCGAAAGAGAACGGG 60.448 63.158 0.00 0.00 0.00 5.28
647 657 0.037232 AAGGAGGCGAAAGAGAACGG 60.037 55.000 0.00 0.00 0.00 4.44
765 782 4.161189 CCTAGCTGAGATTTGTTGAGAGGA 59.839 45.833 0.00 0.00 0.00 3.71
806 826 0.107214 TTCGATGAGCCAATCCACCC 60.107 55.000 0.00 0.00 0.00 4.61
814 834 0.796312 GTCGCTTTTTCGATGAGCCA 59.204 50.000 8.90 0.00 40.84 4.75
937 957 1.555075 GTTGTGGGCTCTGATCCAGTA 59.445 52.381 0.00 0.00 33.13 2.74
1035 1056 4.856607 CGGAAGAGGAGGCGCGAC 62.857 72.222 12.10 7.34 0.00 5.19
1308 1353 2.360350 CACAGCATGCGGAAGGGT 60.360 61.111 24.99 8.42 42.53 4.34
1431 1477 1.405821 CCTAGACGCTCCTAAGTGTGG 59.594 57.143 0.00 0.00 46.11 4.17
1445 1491 1.724429 AGTGAGACGACGACCTAGAC 58.276 55.000 0.00 0.00 0.00 2.59
1459 1505 4.505808 TCCTAGAGTTGAGTCGTAGTGAG 58.494 47.826 0.00 0.00 0.00 3.51
1463 1509 4.142425 GGGTTTCCTAGAGTTGAGTCGTAG 60.142 50.000 0.00 0.00 0.00 3.51
1469 1515 3.955650 TTCGGGTTTCCTAGAGTTGAG 57.044 47.619 0.00 0.00 0.00 3.02
1471 1517 5.001232 TCAAATTCGGGTTTCCTAGAGTTG 58.999 41.667 0.00 0.00 0.00 3.16
1482 1528 1.468520 CACGATGCTCAAATTCGGGTT 59.531 47.619 0.00 0.00 37.20 4.11
1484 1530 1.368641 TCACGATGCTCAAATTCGGG 58.631 50.000 0.00 0.00 37.62 5.14
1499 1545 2.607187 GTGGTCTACAGGTGAATCACG 58.393 52.381 7.35 0.00 34.83 4.35
1641 1689 6.678547 TGGAAATAACTGCCTACCCATTATT 58.321 36.000 0.00 0.00 0.00 1.40
1718 1771 9.146984 CAATGTCATATTCTGCACAAGATTTTT 57.853 29.630 0.00 0.00 33.93 1.94
1728 1781 8.459911 AGATTTGATCAATGTCATATTCTGCA 57.540 30.769 9.40 0.00 0.00 4.41
1757 1810 4.640690 AGTGGGCGGTCCTCCTGT 62.641 66.667 0.00 0.00 36.20 4.00
1793 1846 7.599998 GCTTGTAACAAAATGTCAGGATCATTT 59.400 33.333 0.00 0.00 44.14 2.32
1796 1849 5.769662 AGCTTGTAACAAAATGTCAGGATCA 59.230 36.000 0.00 0.00 0.00 2.92
1832 1885 1.000843 ACATAGTCGCAGTGTGCTTCA 59.999 47.619 0.00 0.00 42.25 3.02
1907 1960 7.441836 TGCAGATAAGTGACTAAAGAGAACAA 58.558 34.615 0.00 0.00 0.00 2.83
1976 2031 7.497595 AGGCAGATTATCTTTCGTAATGTACA 58.502 34.615 0.00 0.00 0.00 2.90
2108 2163 5.857268 AGTGCTTTGAAACATTTGCCTAAT 58.143 33.333 0.00 0.00 0.00 1.73
2583 2640 1.019673 CTTTGATGGCATCCCAGTCG 58.980 55.000 23.92 3.84 46.24 4.18
2752 2809 4.969484 TCTTCTTTCCACTCCTTTGTACC 58.031 43.478 0.00 0.00 0.00 3.34
2987 3044 1.374758 CCGCCGAGTTCTTTCAGCT 60.375 57.895 0.00 0.00 0.00 4.24
3015 3072 4.390129 AGAGGTCTGGTCTCTGTAAAGA 57.610 45.455 0.00 0.00 39.83 2.52
3053 3110 1.234615 TGCAGCTAGCCCGTTTGAAC 61.235 55.000 12.13 0.00 44.83 3.18
3148 3205 7.885399 ACTGATATTAGATATTTGGTGCCTTCC 59.115 37.037 0.78 0.00 0.00 3.46
3199 3267 1.318576 CCTCCCACAAAGTGTGTTCC 58.681 55.000 7.55 0.00 46.45 3.62
3200 3268 0.668535 GCCTCCCACAAAGTGTGTTC 59.331 55.000 7.55 0.00 46.45 3.18
3201 3269 0.033601 TGCCTCCCACAAAGTGTGTT 60.034 50.000 7.55 0.00 46.45 3.32
3202 3270 0.751643 GTGCCTCCCACAAAGTGTGT 60.752 55.000 7.55 0.00 46.45 3.72
3204 3272 1.152756 GGTGCCTCCCACAAAGTGT 60.153 57.895 0.00 0.00 46.50 3.55
3205 3273 0.540365 ATGGTGCCTCCCACAAAGTG 60.540 55.000 0.00 0.00 46.50 3.16
3206 3274 0.540365 CATGGTGCCTCCCACAAAGT 60.540 55.000 0.00 0.00 46.50 2.66
3207 3275 0.251297 TCATGGTGCCTCCCACAAAG 60.251 55.000 0.00 0.00 46.50 2.77
3208 3276 0.251297 CTCATGGTGCCTCCCACAAA 60.251 55.000 0.00 0.00 46.50 2.83
3209 3277 1.379916 CTCATGGTGCCTCCCACAA 59.620 57.895 0.00 0.00 46.50 3.33
3358 3428 6.442112 TCAGATCGTAATAATGTCTGCAGAG 58.558 40.000 18.89 1.64 36.97 3.35
3387 3457 8.900781 CCAGCTGTTACAAGATACTACTACTAA 58.099 37.037 13.81 0.00 0.00 2.24
3388 3458 8.270030 TCCAGCTGTTACAAGATACTACTACTA 58.730 37.037 13.81 0.00 0.00 1.82
3389 3459 7.067251 GTCCAGCTGTTACAAGATACTACTACT 59.933 40.741 13.81 0.00 0.00 2.57
3390 3460 7.067251 AGTCCAGCTGTTACAAGATACTACTAC 59.933 40.741 13.81 0.00 0.00 2.73
3391 3461 7.117397 AGTCCAGCTGTTACAAGATACTACTA 58.883 38.462 13.81 0.00 0.00 1.82
3403 3473 3.365364 GCAATGTTGAGTCCAGCTGTTAC 60.365 47.826 13.81 10.56 0.00 2.50
3476 3548 3.056749 ACGTATTATGAATCGGAGGGAGC 60.057 47.826 0.00 0.00 0.00 4.70
3484 3556 3.481028 CGGGCGATACGTATTATGAATCG 59.519 47.826 9.92 9.75 41.69 3.34
3496 3568 1.073177 ACTTCAAAACGGGCGATACG 58.927 50.000 0.00 0.00 37.36 3.06
3499 3571 2.081462 CCTTACTTCAAAACGGGCGAT 58.919 47.619 0.00 0.00 0.00 4.58
3502 3574 2.287970 CCAACCTTACTTCAAAACGGGC 60.288 50.000 0.00 0.00 0.00 6.13
3504 3576 4.096682 TGAACCAACCTTACTTCAAAACGG 59.903 41.667 0.00 0.00 0.00 4.44
3505 3577 5.238006 TGAACCAACCTTACTTCAAAACG 57.762 39.130 0.00 0.00 0.00 3.60
3523 3595 3.105937 GTCGCAGTTTTGAAGGTTGAAC 58.894 45.455 0.00 0.00 0.00 3.18
3524 3596 2.750166 TGTCGCAGTTTTGAAGGTTGAA 59.250 40.909 0.00 0.00 0.00 2.69
3525 3597 2.096819 GTGTCGCAGTTTTGAAGGTTGA 59.903 45.455 0.00 0.00 0.00 3.18
3526 3598 2.097466 AGTGTCGCAGTTTTGAAGGTTG 59.903 45.455 0.00 0.00 0.00 3.77
3527 3599 2.365582 AGTGTCGCAGTTTTGAAGGTT 58.634 42.857 0.00 0.00 0.00 3.50
3528 3600 2.038387 AGTGTCGCAGTTTTGAAGGT 57.962 45.000 0.00 0.00 0.00 3.50
3529 3601 4.545823 TTAAGTGTCGCAGTTTTGAAGG 57.454 40.909 5.46 0.00 0.00 3.46
3530 3602 6.742718 CCATATTAAGTGTCGCAGTTTTGAAG 59.257 38.462 5.46 0.00 0.00 3.02
3550 3635 2.968574 ACTTGCTCTCACCGATCCATAT 59.031 45.455 0.00 0.00 0.00 1.78
3561 3646 5.610398 TGTCAGTTCAAATACTTGCTCTCA 58.390 37.500 0.00 0.00 32.14 3.27
3563 3648 6.543831 AGTTTGTCAGTTCAAATACTTGCTCT 59.456 34.615 0.00 0.00 39.09 4.09
3763 3861 4.082665 TCAAGCCATCTCCATTCTCATC 57.917 45.455 0.00 0.00 0.00 2.92
3867 3965 2.047844 CACTGGGACGTGAGGCTG 60.048 66.667 0.00 0.00 40.87 4.85
3885 3983 0.530288 AGAAGCTCTTGAGGTCGCTC 59.470 55.000 2.69 0.00 31.30 5.03
4059 4157 2.558795 GGTCAGTCACTGCTCAGTTCTA 59.441 50.000 0.00 0.00 40.20 2.10
4060 4158 1.342819 GGTCAGTCACTGCTCAGTTCT 59.657 52.381 0.00 0.00 40.20 3.01
4063 4161 0.678395 CAGGTCAGTCACTGCTCAGT 59.322 55.000 0.00 0.00 43.61 3.41
4065 4163 0.676184 GACAGGTCAGTCACTGCTCA 59.324 55.000 0.00 0.00 38.25 4.26


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

AutoCloner maintained by Alex Coulton.