Multiple sequence alignment - TraesCS5B01G335800

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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 TraesCS5B01G335800 chr5B 100.000 4257 0 0 1 4257 518963363 518959107 0.000000e+00 7862.0
1 TraesCS5B01G335800 chr5B 100.000 30 0 0 3735 3764 518959537 518959508 5.950000e-04 56.5
2 TraesCS5B01G335800 chr5B 100.000 30 0 0 3827 3856 518959629 518959600 5.950000e-04 56.5
3 TraesCS5B01G335800 chr5D 91.414 3331 117 57 139 3411 429717554 429714335 0.000000e+00 4410.0
4 TraesCS5B01G335800 chr5D 90.842 404 22 7 3862 4257 429713910 429713514 1.050000e-145 527.0
5 TraesCS5B01G335800 chr5D 80.098 407 36 23 3411 3806 429714283 429713911 1.170000e-65 261.0
6 TraesCS5B01G335800 chr5D 100.000 30 0 0 3827 3856 429713982 429713953 5.950000e-04 56.5
7 TraesCS5B01G335800 chr5A 93.773 1381 40 13 763 2132 545567415 545566070 0.000000e+00 2032.0
8 TraesCS5B01G335800 chr5A 86.042 1655 118 63 2190 3806 545566057 545564478 0.000000e+00 1672.0
9 TraesCS5B01G335800 chr5A 94.444 396 16 3 3862 4257 545564477 545564088 4.710000e-169 604.0
10 TraesCS5B01G335800 chr5A 82.317 328 28 17 373 677 545567825 545567505 1.520000e-64 257.0
11 TraesCS5B01G335800 chr5A 88.235 170 13 3 133 295 545586989 545586820 3.360000e-46 196.0
12 TraesCS5B01G335800 chr5A 91.228 57 0 1 679 730 545567474 545567418 5.900000e-09 73.1
13 TraesCS5B01G335800 chr5A 97.297 37 1 0 298 334 545567869 545567833 3.550000e-06 63.9
14 TraesCS5B01G335800 chr2B 85.577 208 23 2 1055 1261 158360082 158360283 1.200000e-50 211.0
15 TraesCS5B01G335800 chr2B 82.143 140 23 2 1 139 18108236 18108374 7.480000e-23 119.0
16 TraesCS5B01G335800 chr2D 86.154 195 20 2 1055 1248 190368425 190368237 2.010000e-48 204.0
17 TraesCS5B01G335800 chr2D 82.955 176 17 5 1073 1248 625162257 625162419 3.430000e-31 147.0
18 TraesCS5B01G335800 chr6D 85.641 195 21 2 1055 1248 86025541 86025353 9.340000e-47 198.0
19 TraesCS5B01G335800 chr1A 85.128 195 22 2 1055 1248 528933785 528933597 4.340000e-45 193.0


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 TraesCS5B01G335800 chr5B 518959107 518963363 4256 True 2658.333333 7862 100.000000 1 4257 3 chr5B.!!$R1 4256
1 TraesCS5B01G335800 chr5D 429713514 429717554 4040 True 1313.625000 4410 90.588500 139 4257 4 chr5D.!!$R1 4118
2 TraesCS5B01G335800 chr5A 545564088 545567869 3781 True 783.666667 2032 90.850167 298 4257 6 chr5A.!!$R2 3959

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
26 27 0.033699 ACCTACTACCCGGTCACCTC 60.034 60.0 0.00 0.0 0.0 3.85 F
162 163 0.036388 TACAGGCCGAAAAGGAGCAG 60.036 55.0 0.00 0.0 45.0 4.24 F
879 952 0.322906 CCTTCCTTGAGTTGGGCCTC 60.323 60.0 4.53 0.0 0.0 4.70 F
2129 2220 0.179094 CCGCTTAATCACCACCGCTA 60.179 55.0 0.00 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 1762 3.204827 ATGGAGCGGCGCATGAAC 61.205 61.111 35.02 18.27 0.0 3.18 R
2118 2209 0.108992 GATTGACGTAGCGGTGGTGA 60.109 55.000 0.00 0.00 0.0 4.02 R
2408 2534 0.107165 AGCCTCTTTACCAATCGCCC 60.107 55.000 0.00 0.00 0.0 6.13 R
3399 3554 0.319555 ATATGCAGTATTCGCCGCGT 60.320 50.000 13.39 0.00 0.0 6.01 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
18 19 1.895238 CACCCACACCTACTACCCG 59.105 63.158 0.00 0.00 0.00 5.28
19 20 1.305549 ACCCACACCTACTACCCGG 60.306 63.158 0.00 0.00 0.00 5.73
20 21 1.305549 CCCACACCTACTACCCGGT 60.306 63.158 0.00 0.00 0.00 5.28
21 22 1.325476 CCCACACCTACTACCCGGTC 61.325 65.000 0.00 0.00 0.00 4.79
22 23 0.612732 CCACACCTACTACCCGGTCA 60.613 60.000 0.00 0.00 0.00 4.02
23 24 0.529378 CACACCTACTACCCGGTCAC 59.471 60.000 0.00 0.00 0.00 3.67
24 25 0.613012 ACACCTACTACCCGGTCACC 60.613 60.000 0.00 0.00 0.00 4.02
25 26 0.324091 CACCTACTACCCGGTCACCT 60.324 60.000 0.00 0.00 0.00 4.00
26 27 0.033699 ACCTACTACCCGGTCACCTC 60.034 60.000 0.00 0.00 0.00 3.85
27 28 1.099879 CCTACTACCCGGTCACCTCG 61.100 65.000 0.00 0.00 0.00 4.63
28 29 1.077501 TACTACCCGGTCACCTCGG 60.078 63.158 0.00 0.00 46.43 4.63
35 36 4.176752 GGTCACCTCGGGCCCATC 62.177 72.222 24.92 0.00 0.00 3.51
36 37 3.083997 GTCACCTCGGGCCCATCT 61.084 66.667 24.92 0.00 0.00 2.90
37 38 3.083349 TCACCTCGGGCCCATCTG 61.083 66.667 24.92 11.02 0.00 2.90
38 39 4.864334 CACCTCGGGCCCATCTGC 62.864 72.222 24.92 0.00 0.00 4.26
72 73 4.516195 GGCTTCGCCCTCGTCCTC 62.516 72.222 0.00 0.00 44.06 3.71
73 74 4.516195 GCTTCGCCCTCGTCCTCC 62.516 72.222 0.00 0.00 36.96 4.30
74 75 2.756283 CTTCGCCCTCGTCCTCCT 60.756 66.667 0.00 0.00 36.96 3.69
75 76 3.068691 TTCGCCCTCGTCCTCCTG 61.069 66.667 0.00 0.00 36.96 3.86
76 77 3.881019 TTCGCCCTCGTCCTCCTGT 62.881 63.158 0.00 0.00 36.96 4.00
77 78 3.827898 CGCCCTCGTCCTCCTGTC 61.828 72.222 0.00 0.00 0.00 3.51
78 79 2.363147 GCCCTCGTCCTCCTGTCT 60.363 66.667 0.00 0.00 0.00 3.41
79 80 1.985116 GCCCTCGTCCTCCTGTCTT 60.985 63.158 0.00 0.00 0.00 3.01
80 81 1.893786 CCCTCGTCCTCCTGTCTTG 59.106 63.158 0.00 0.00 0.00 3.02
81 82 0.900647 CCCTCGTCCTCCTGTCTTGT 60.901 60.000 0.00 0.00 0.00 3.16
82 83 0.244994 CCTCGTCCTCCTGTCTTGTG 59.755 60.000 0.00 0.00 0.00 3.33
83 84 0.244994 CTCGTCCTCCTGTCTTGTGG 59.755 60.000 0.00 0.00 0.00 4.17
84 85 1.185618 TCGTCCTCCTGTCTTGTGGG 61.186 60.000 0.00 0.00 0.00 4.61
85 86 1.472662 CGTCCTCCTGTCTTGTGGGT 61.473 60.000 0.00 0.00 0.00 4.51
86 87 0.321996 GTCCTCCTGTCTTGTGGGTC 59.678 60.000 0.00 0.00 0.00 4.46
87 88 0.191064 TCCTCCTGTCTTGTGGGTCT 59.809 55.000 0.00 0.00 0.00 3.85
88 89 1.431633 TCCTCCTGTCTTGTGGGTCTA 59.568 52.381 0.00 0.00 0.00 2.59
89 90 1.827969 CCTCCTGTCTTGTGGGTCTAG 59.172 57.143 0.00 0.00 0.00 2.43
90 91 1.205893 CTCCTGTCTTGTGGGTCTAGC 59.794 57.143 0.00 0.00 0.00 3.42
91 92 1.203187 TCCTGTCTTGTGGGTCTAGCT 60.203 52.381 0.00 0.00 0.00 3.32
92 93 1.205893 CCTGTCTTGTGGGTCTAGCTC 59.794 57.143 0.00 0.00 0.00 4.09
93 94 0.888619 TGTCTTGTGGGTCTAGCTCG 59.111 55.000 0.00 0.00 0.00 5.03
94 95 0.889306 GTCTTGTGGGTCTAGCTCGT 59.111 55.000 0.00 0.00 0.00 4.18
95 96 1.135344 GTCTTGTGGGTCTAGCTCGTC 60.135 57.143 0.00 0.00 0.00 4.20
96 97 0.888619 CTTGTGGGTCTAGCTCGTCA 59.111 55.000 0.00 0.00 0.00 4.35
97 98 0.888619 TTGTGGGTCTAGCTCGTCAG 59.111 55.000 0.00 0.00 0.00 3.51
116 117 2.499685 GCCTAGCGGTGGTAGTGG 59.500 66.667 0.00 0.00 32.45 4.00
117 118 3.090219 GCCTAGCGGTGGTAGTGGG 62.090 68.421 0.00 0.00 32.45 4.61
118 119 2.432300 CCTAGCGGTGGTAGTGGGG 61.432 68.421 0.00 0.00 32.45 4.96
119 120 1.684734 CTAGCGGTGGTAGTGGGGT 60.685 63.158 0.00 0.00 0.00 4.95
120 121 1.956629 CTAGCGGTGGTAGTGGGGTG 61.957 65.000 0.00 0.00 0.00 4.61
121 122 4.404098 GCGGTGGTAGTGGGGTGG 62.404 72.222 0.00 0.00 0.00 4.61
122 123 2.926242 CGGTGGTAGTGGGGTGGT 60.926 66.667 0.00 0.00 0.00 4.16
123 124 2.754375 GGTGGTAGTGGGGTGGTG 59.246 66.667 0.00 0.00 0.00 4.17
124 125 2.754375 GTGGTAGTGGGGTGGTGG 59.246 66.667 0.00 0.00 0.00 4.61
125 126 3.253838 TGGTAGTGGGGTGGTGGC 61.254 66.667 0.00 0.00 0.00 5.01
126 127 4.404098 GGTAGTGGGGTGGTGGCG 62.404 72.222 0.00 0.00 0.00 5.69
127 128 3.633116 GTAGTGGGGTGGTGGCGT 61.633 66.667 0.00 0.00 0.00 5.68
128 129 3.315949 TAGTGGGGTGGTGGCGTC 61.316 66.667 0.00 0.00 0.00 5.19
132 133 4.699522 GGGGTGGTGGCGTCAGTC 62.700 72.222 0.00 0.00 0.00 3.51
134 135 4.295119 GGTGGTGGCGTCAGTCGT 62.295 66.667 0.00 0.00 42.13 4.34
135 136 3.036084 GTGGTGGCGTCAGTCGTG 61.036 66.667 0.00 0.00 42.13 4.35
136 137 3.220658 TGGTGGCGTCAGTCGTGA 61.221 61.111 0.00 0.00 42.13 4.35
150 151 3.555956 CAGTCGTGACATTATTACAGGCC 59.444 47.826 0.00 0.00 0.00 5.19
151 152 2.538449 GTCGTGACATTATTACAGGCCG 59.462 50.000 0.00 0.00 0.00 6.13
157 158 4.638421 TGACATTATTACAGGCCGAAAAGG 59.362 41.667 0.00 0.00 44.97 3.11
159 160 4.881850 ACATTATTACAGGCCGAAAAGGAG 59.118 41.667 0.00 0.00 45.00 3.69
162 163 0.036388 TACAGGCCGAAAAGGAGCAG 60.036 55.000 0.00 0.00 45.00 4.24
163 164 1.302832 CAGGCCGAAAAGGAGCAGT 60.303 57.895 0.00 0.00 45.00 4.40
165 166 0.690762 AGGCCGAAAAGGAGCAGTAA 59.309 50.000 0.00 0.00 45.00 2.24
166 167 0.803117 GGCCGAAAAGGAGCAGTAAC 59.197 55.000 0.00 0.00 45.00 2.50
167 168 0.442699 GCCGAAAAGGAGCAGTAACG 59.557 55.000 0.00 0.00 45.00 3.18
201 202 2.027460 CACGGCCACCAAAAGCAC 59.973 61.111 2.24 0.00 0.00 4.40
228 229 2.375766 CCTGCTCGTGTCAACTCGC 61.376 63.158 0.03 0.00 33.44 5.03
229 230 2.355837 TGCTCGTGTCAACTCGCC 60.356 61.111 0.03 0.00 33.44 5.54
230 231 2.355837 GCTCGTGTCAACTCGCCA 60.356 61.111 0.03 0.00 33.44 5.69
231 232 2.375766 GCTCGTGTCAACTCGCCAG 61.376 63.158 0.03 0.00 33.44 4.85
232 233 1.007271 CTCGTGTCAACTCGCCAGT 60.007 57.895 0.03 0.00 33.44 4.00
233 234 0.597637 CTCGTGTCAACTCGCCAGTT 60.598 55.000 0.00 0.00 44.26 3.16
234 235 0.669619 TCGTGTCAACTCGCCAGTTA 59.330 50.000 0.00 0.00 41.24 2.24
327 328 0.596083 TTGGATTTGCCGTTTGCGTG 60.596 50.000 0.00 0.00 45.60 5.34
334 335 4.368808 CCGTTTGCGTGGTGCTCG 62.369 66.667 0.00 0.00 46.63 5.03
335 336 3.334751 CGTTTGCGTGGTGCTCGA 61.335 61.111 0.00 0.00 46.63 4.04
336 337 2.248431 GTTTGCGTGGTGCTCGAC 59.752 61.111 0.00 0.00 46.63 4.20
337 338 2.108157 TTTGCGTGGTGCTCGACT 59.892 55.556 0.00 0.00 46.63 4.18
338 339 2.243957 TTTGCGTGGTGCTCGACTG 61.244 57.895 0.00 0.00 46.63 3.51
341 342 2.807045 CGTGGTGCTCGACTGCTC 60.807 66.667 0.00 0.00 0.00 4.26
342 343 2.807045 GTGGTGCTCGACTGCTCG 60.807 66.667 0.00 0.00 41.65 5.03
358 359 1.138636 CTCGTGCATGCTCTGTCTCG 61.139 60.000 20.33 11.48 0.00 4.04
364 365 0.813821 CATGCTCTGTCTCGGTCTCA 59.186 55.000 0.00 0.00 0.00 3.27
443 447 1.362717 CATGCCCAGCAATAGCAGC 59.637 57.895 0.00 0.00 43.62 5.25
444 448 1.076559 ATGCCCAGCAATAGCAGCA 60.077 52.632 0.00 0.00 43.62 4.41
445 449 1.389609 ATGCCCAGCAATAGCAGCAC 61.390 55.000 0.00 0.00 43.62 4.40
446 450 2.779033 GCCCAGCAATAGCAGCACC 61.779 63.158 0.00 0.00 45.49 5.01
447 451 1.378911 CCCAGCAATAGCAGCACCA 60.379 57.895 0.00 0.00 45.49 4.17
448 452 1.381928 CCCAGCAATAGCAGCACCAG 61.382 60.000 0.00 0.00 45.49 4.00
449 453 1.381928 CCAGCAATAGCAGCACCAGG 61.382 60.000 0.00 0.00 45.49 4.45
450 454 1.751927 AGCAATAGCAGCACCAGGC 60.752 57.895 0.00 0.00 45.49 4.85
874 947 3.416156 CCTTCTTCCTTCCTTGAGTTGG 58.584 50.000 0.00 0.00 0.00 3.77
876 949 1.073923 TCTTCCTTCCTTGAGTTGGGC 59.926 52.381 0.00 0.00 0.00 5.36
878 951 0.772124 TCCTTCCTTGAGTTGGGCCT 60.772 55.000 4.53 0.00 0.00 5.19
879 952 0.322906 CCTTCCTTGAGTTGGGCCTC 60.323 60.000 4.53 0.00 0.00 4.70
880 953 0.695347 CTTCCTTGAGTTGGGCCTCT 59.305 55.000 4.53 2.90 32.50 3.69
896 973 1.407025 CCTCTTTTAAGTCTCCCGCCC 60.407 57.143 0.00 0.00 0.00 6.13
899 976 2.808181 TTTTAAGTCTCCCGCCCCGC 62.808 60.000 0.00 0.00 0.00 6.13
948 1025 4.891727 CCCTTGATAGCGCGCGGT 62.892 66.667 37.43 37.43 0.00 5.68
949 1026 3.630148 CCTTGATAGCGCGCGGTG 61.630 66.667 41.12 25.06 0.00 4.94
950 1027 4.285149 CTTGATAGCGCGCGGTGC 62.285 66.667 41.12 31.41 39.59 5.01
1024 1103 2.361357 CCGAGGTGGAGGTCGTCT 60.361 66.667 0.00 0.00 42.00 4.18
1026 1105 2.751913 CGAGGTGGAGGTCGTCTCG 61.752 68.421 0.00 0.00 43.34 4.04
1065 1144 3.068881 CCGGGCAAGAAGAGGACA 58.931 61.111 0.00 0.00 0.00 4.02
1910 2001 4.988598 CGTGCACAAGGAGCCGGT 62.989 66.667 18.64 0.00 0.00 5.28
2067 2158 3.983494 ATCTGCTCCCGGATCGCG 61.983 66.667 0.73 0.00 31.31 5.87
2120 2211 4.695217 AAAAATCGCTTCCGCTTAATCA 57.305 36.364 0.00 0.00 0.00 2.57
2121 2212 3.675467 AAATCGCTTCCGCTTAATCAC 57.325 42.857 0.00 0.00 0.00 3.06
2122 2213 1.583054 ATCGCTTCCGCTTAATCACC 58.417 50.000 0.00 0.00 0.00 4.02
2123 2214 0.248012 TCGCTTCCGCTTAATCACCA 59.752 50.000 0.00 0.00 0.00 4.17
2124 2215 0.373716 CGCTTCCGCTTAATCACCAC 59.626 55.000 0.00 0.00 0.00 4.16
2125 2216 0.733150 GCTTCCGCTTAATCACCACC 59.267 55.000 0.00 0.00 0.00 4.61
2126 2217 1.006832 CTTCCGCTTAATCACCACCG 58.993 55.000 0.00 0.00 0.00 4.94
2127 2218 1.022451 TTCCGCTTAATCACCACCGC 61.022 55.000 0.00 0.00 0.00 5.68
2128 2219 1.449601 CCGCTTAATCACCACCGCT 60.450 57.895 0.00 0.00 0.00 5.52
2129 2220 0.179094 CCGCTTAATCACCACCGCTA 60.179 55.000 0.00 0.00 0.00 4.26
2130 2221 0.928229 CGCTTAATCACCACCGCTAC 59.072 55.000 0.00 0.00 0.00 3.58
2131 2222 0.928229 GCTTAATCACCACCGCTACG 59.072 55.000 0.00 0.00 0.00 3.51
2132 2223 1.738030 GCTTAATCACCACCGCTACGT 60.738 52.381 0.00 0.00 0.00 3.57
2133 2224 2.190981 CTTAATCACCACCGCTACGTC 58.809 52.381 0.00 0.00 0.00 4.34
2139 2230 0.319083 ACCACCGCTACGTCAATCAA 59.681 50.000 0.00 0.00 0.00 2.57
2149 2259 2.683968 ACGTCAATCAATACTGCACGT 58.316 42.857 0.00 0.00 34.34 4.49
2157 2267 2.159393 TCAATACTGCACGTACGTACCC 60.159 50.000 22.34 12.76 0.00 3.69
2162 2272 1.372872 GCACGTACGTACCCGGTTT 60.373 57.895 22.34 0.00 38.78 3.27
2165 2275 2.223386 GCACGTACGTACCCGGTTTATA 60.223 50.000 22.34 0.00 38.78 0.98
2166 2276 3.550030 GCACGTACGTACCCGGTTTATAT 60.550 47.826 22.34 0.00 38.78 0.86
2167 2277 4.319911 GCACGTACGTACCCGGTTTATATA 60.320 45.833 22.34 0.00 38.78 0.86
2213 2323 8.786826 ATCAAGTGGTAATTTAGAATGTCGAA 57.213 30.769 0.00 0.00 0.00 3.71
2294 2412 5.555069 CGTTAGAACACGTCGCTTTAGTTTT 60.555 40.000 0.00 0.00 35.34 2.43
2295 2413 6.344936 CGTTAGAACACGTCGCTTTAGTTTTA 60.345 38.462 0.00 0.00 35.34 1.52
2296 2414 5.971895 AGAACACGTCGCTTTAGTTTTAA 57.028 34.783 0.00 0.00 0.00 1.52
2297 2415 5.731278 AGAACACGTCGCTTTAGTTTTAAC 58.269 37.500 0.00 0.00 0.00 2.01
2316 2434 7.900782 TTTAACTAACTTTTGAGGAGATCCG 57.099 36.000 0.00 0.00 42.08 4.18
2318 2436 5.074584 ACTAACTTTTGAGGAGATCCGTC 57.925 43.478 0.00 0.00 42.08 4.79
2322 2443 4.030913 ACTTTTGAGGAGATCCGTCCATA 58.969 43.478 3.98 0.00 39.34 2.74
2325 2446 3.026707 TGAGGAGATCCGTCCATACAA 57.973 47.619 3.98 0.00 39.34 2.41
2330 2451 1.139058 AGATCCGTCCATACAACAGCC 59.861 52.381 0.00 0.00 0.00 4.85
2408 2534 6.846283 GTGAACAGTAGTTGATCGAAAGTTTG 59.154 38.462 0.00 0.00 38.30 2.93
2480 2606 0.989890 GTCGACTTCATGCACGTACC 59.010 55.000 8.70 0.00 0.00 3.34
2481 2607 0.599060 TCGACTTCATGCACGTACCA 59.401 50.000 0.00 0.00 0.00 3.25
2482 2608 0.713883 CGACTTCATGCACGTACCAC 59.286 55.000 0.00 0.00 0.00 4.16
2614 2740 3.131478 CCCGAACGGAACATGGCC 61.131 66.667 15.07 0.00 37.50 5.36
2672 2798 0.692476 CACAGTGGAGGGAATGTGGA 59.308 55.000 0.00 0.00 39.45 4.02
2673 2799 0.987294 ACAGTGGAGGGAATGTGGAG 59.013 55.000 0.00 0.00 0.00 3.86
2674 2800 0.393537 CAGTGGAGGGAATGTGGAGC 60.394 60.000 0.00 0.00 0.00 4.70
2701 2827 2.034879 CCTGCCTGCCACGTACAAG 61.035 63.158 0.00 0.00 0.00 3.16
2702 2828 1.301716 CTGCCTGCCACGTACAAGT 60.302 57.895 0.00 0.00 0.00 3.16
2703 2829 1.568612 CTGCCTGCCACGTACAAGTG 61.569 60.000 0.00 0.00 41.53 3.16
2704 2830 1.597027 GCCTGCCACGTACAAGTGT 60.597 57.895 0.00 0.00 40.33 3.55
2705 2831 0.320073 GCCTGCCACGTACAAGTGTA 60.320 55.000 0.00 0.00 40.33 2.90
2706 2832 1.425412 CCTGCCACGTACAAGTGTAC 58.575 55.000 10.92 10.92 45.47 2.90
2730 2867 4.462133 CCTCCAGCTGAATCATTCTGAAT 58.538 43.478 17.39 0.00 0.00 2.57
2748 2888 7.843490 TCTGAATTGCATTAGTACCAACTAC 57.157 36.000 0.00 0.00 37.94 2.73
2749 2889 7.620880 TCTGAATTGCATTAGTACCAACTACT 58.379 34.615 0.00 0.00 37.94 2.57
2750 2890 8.755028 TCTGAATTGCATTAGTACCAACTACTA 58.245 33.333 0.00 0.00 37.94 1.82
2751 2891 8.942338 TGAATTGCATTAGTACCAACTACTAG 57.058 34.615 0.00 0.00 38.85 2.57
2752 2892 7.494625 TGAATTGCATTAGTACCAACTACTAGC 59.505 37.037 0.00 0.00 38.85 3.42
2753 2893 6.540438 TTGCATTAGTACCAACTACTAGCT 57.460 37.500 0.00 0.00 38.85 3.32
2754 2894 6.540438 TGCATTAGTACCAACTACTAGCTT 57.460 37.500 0.00 0.00 38.85 3.74
2755 2895 6.942976 TGCATTAGTACCAACTACTAGCTTT 58.057 36.000 0.00 0.00 38.85 3.51
2756 2896 6.816640 TGCATTAGTACCAACTACTAGCTTTG 59.183 38.462 0.00 0.00 38.85 2.77
2757 2897 6.238130 GCATTAGTACCAACTACTAGCTTTGC 60.238 42.308 0.00 0.00 38.85 3.68
2760 2900 5.617252 AGTACCAACTACTAGCTTTGCAAA 58.383 37.500 12.14 12.14 33.53 3.68
2858 2998 7.839705 CCTACCCTATCCTTAGCACTAATCATA 59.160 40.741 0.00 0.00 0.00 2.15
2867 3007 9.596308 TCCTTAGCACTAATCATAATACTACCA 57.404 33.333 0.00 0.00 0.00 3.25
2908 3048 2.358737 GTGGTGGGCTGAACGAGG 60.359 66.667 0.00 0.00 0.00 4.63
3143 3289 2.361357 ACCTCTACGACCGCTGCT 60.361 61.111 0.00 0.00 0.00 4.24
3396 3551 0.393132 TGTTGGTTTCAGCCACGACA 60.393 50.000 0.00 0.00 38.42 4.35
3399 3554 1.593209 GGTTTCAGCCACGACACGA 60.593 57.895 0.00 0.00 0.00 4.35
3452 3666 6.866248 ACAATGAAAAGTTTGTCACGTTTTCT 59.134 30.769 11.80 0.87 37.22 2.52
3453 3667 7.383843 ACAATGAAAAGTTTGTCACGTTTTCTT 59.616 29.630 11.80 5.94 37.22 2.52
3458 3672 4.773013 AGTTTGTCACGTTTTCTTCCCTA 58.227 39.130 0.00 0.00 0.00 3.53
3459 3673 5.374071 AGTTTGTCACGTTTTCTTCCCTAT 58.626 37.500 0.00 0.00 0.00 2.57
3465 3679 7.669427 TGTCACGTTTTCTTCCCTATAGTTTA 58.331 34.615 0.00 0.00 0.00 2.01
3467 3681 6.808212 TCACGTTTTCTTCCCTATAGTTTACG 59.192 38.462 0.00 0.00 0.00 3.18
3562 3779 1.066605 GCATGATGCGAGGCTCAAAAT 59.933 47.619 15.95 4.27 31.71 1.82
3583 3800 7.573968 AAATTGAACTCCCTAGCATGATTAC 57.426 36.000 0.00 0.00 0.00 1.89
3584 3801 4.322080 TGAACTCCCTAGCATGATTACG 57.678 45.455 0.00 0.00 0.00 3.18
3587 3805 2.297597 ACTCCCTAGCATGATTACGCTC 59.702 50.000 0.00 0.00 39.70 5.03
3601 3823 2.033141 GCTCTGACAGGCCAAGCA 59.967 61.111 5.01 0.00 33.21 3.91
3609 3831 2.297033 TGACAGGCCAAGCAAATTTCTC 59.703 45.455 5.01 0.00 0.00 2.87
3664 3888 3.067833 GACCAACAGGTGAGAAGCTAAC 58.932 50.000 0.00 0.00 35.25 2.34
3677 3904 4.626042 AGAAGCTAACGATCTGCCATAAG 58.374 43.478 0.00 0.00 0.00 1.73
3709 3936 5.357742 ACAACAGATAGTGCATCCATACA 57.642 39.130 0.00 0.00 33.75 2.29
3711 3938 5.819379 ACAACAGATAGTGCATCCATACAAG 59.181 40.000 0.00 0.00 33.75 3.16
3729 3956 8.919661 CCATACAAGAAAAGAAAAATGAAGAGC 58.080 33.333 0.00 0.00 0.00 4.09
3773 4001 2.033801 CCTAGGCAGCAAATGTACATGC 59.966 50.000 9.63 11.33 42.87 4.06
3803 4031 2.221981 CGTGAAAGCACTGAAGGAGAAC 59.778 50.000 0.00 0.00 42.93 3.01
3806 4034 4.276926 GTGAAAGCACTGAAGGAGAACAAT 59.723 41.667 0.00 0.00 41.84 2.71
3807 4035 4.516698 TGAAAGCACTGAAGGAGAACAATC 59.483 41.667 0.00 0.00 0.00 2.67
3808 4036 2.693069 AGCACTGAAGGAGAACAATCG 58.307 47.619 0.00 0.00 0.00 3.34
3809 4037 1.129437 GCACTGAAGGAGAACAATCGC 59.871 52.381 0.00 0.00 0.00 4.58
3810 4038 1.391485 CACTGAAGGAGAACAATCGCG 59.609 52.381 0.00 0.00 0.00 5.87
3811 4039 0.371645 CTGAAGGAGAACAATCGCGC 59.628 55.000 0.00 0.00 0.00 6.86
3812 4040 1.019278 TGAAGGAGAACAATCGCGCC 61.019 55.000 0.00 0.00 0.00 6.53
3813 4041 1.003839 AAGGAGAACAATCGCGCCA 60.004 52.632 0.00 0.00 0.00 5.69
3814 4042 1.298859 AAGGAGAACAATCGCGCCAC 61.299 55.000 0.00 0.00 0.00 5.01
3815 4043 2.750888 GGAGAACAATCGCGCCACC 61.751 63.158 0.00 0.00 0.00 4.61
3816 4044 2.031919 AGAACAATCGCGCCACCA 59.968 55.556 0.00 0.00 0.00 4.17
3817 4045 1.369091 GAGAACAATCGCGCCACCAT 61.369 55.000 0.00 0.00 0.00 3.55
3818 4046 1.226379 GAACAATCGCGCCACCATG 60.226 57.895 0.00 0.00 0.00 3.66
3819 4047 3.340953 AACAATCGCGCCACCATGC 62.341 57.895 0.00 0.00 0.00 4.06
3829 4057 1.877637 GCCACCATGCGTATCATACA 58.122 50.000 0.00 0.00 33.19 2.29
3830 4058 2.217750 GCCACCATGCGTATCATACAA 58.782 47.619 0.00 0.00 33.19 2.41
3831 4059 2.616376 GCCACCATGCGTATCATACAAA 59.384 45.455 0.00 0.00 33.19 2.83
3832 4060 3.066064 GCCACCATGCGTATCATACAAAA 59.934 43.478 0.00 0.00 33.19 2.44
3833 4061 4.439426 GCCACCATGCGTATCATACAAAAA 60.439 41.667 0.00 0.00 33.19 1.94
3834 4062 5.034152 CCACCATGCGTATCATACAAAAAC 58.966 41.667 0.00 0.00 33.19 2.43
3835 4063 5.392487 CCACCATGCGTATCATACAAAAACA 60.392 40.000 0.00 0.00 33.19 2.83
3836 4064 6.089476 CACCATGCGTATCATACAAAAACAA 58.911 36.000 0.00 0.00 33.19 2.83
3837 4065 6.033407 CACCATGCGTATCATACAAAAACAAC 59.967 38.462 0.00 0.00 33.19 3.32
3838 4066 6.072175 ACCATGCGTATCATACAAAAACAACT 60.072 34.615 0.00 0.00 33.19 3.16
3839 4067 6.806249 CCATGCGTATCATACAAAAACAACTT 59.194 34.615 0.00 0.00 33.19 2.66
3840 4068 7.965655 CCATGCGTATCATACAAAAACAACTTA 59.034 33.333 0.00 0.00 33.19 2.24
3841 4069 8.998989 CATGCGTATCATACAAAAACAACTTAG 58.001 33.333 0.00 0.00 33.19 2.18
3842 4070 8.090250 TGCGTATCATACAAAAACAACTTAGT 57.910 30.769 0.00 0.00 0.00 2.24
3843 4071 8.012809 TGCGTATCATACAAAAACAACTTAGTG 58.987 33.333 0.00 0.00 0.00 2.74
3844 4072 7.007099 GCGTATCATACAAAAACAACTTAGTGC 59.993 37.037 0.00 0.00 0.00 4.40
3845 4073 7.480542 CGTATCATACAAAAACAACTTAGTGCC 59.519 37.037 0.00 0.00 0.00 5.01
3846 4074 6.952773 TCATACAAAAACAACTTAGTGCCT 57.047 33.333 0.00 0.00 0.00 4.75
3847 4075 8.630054 ATCATACAAAAACAACTTAGTGCCTA 57.370 30.769 0.00 0.00 0.00 3.93
3848 4076 8.094798 TCATACAAAAACAACTTAGTGCCTAG 57.905 34.615 0.00 0.00 0.00 3.02
3849 4077 5.767816 ACAAAAACAACTTAGTGCCTAGG 57.232 39.130 3.67 3.67 0.00 3.02
3850 4078 4.037565 ACAAAAACAACTTAGTGCCTAGGC 59.962 41.667 27.71 27.71 42.35 3.93
3882 4110 1.738099 CCAAGAACGGTCAGGCTCG 60.738 63.158 1.87 0.00 0.00 5.03
3892 4120 1.205893 GGTCAGGCTCGTCTTCAGATT 59.794 52.381 0.00 0.00 0.00 2.40
3909 4137 1.392853 GATTGAGCGTTCTGACTGCAG 59.607 52.381 13.48 13.48 43.67 4.41
3939 4167 8.839343 TGCAAGACCATTACATAACTTATCATG 58.161 33.333 0.00 0.00 0.00 3.07
3976 4204 6.270927 CCAGGATTCAAAGGATATACTGGAGA 59.729 42.308 6.73 0.00 44.26 3.71
3996 4232 2.257409 CTCCCCCTCAATGGACACCG 62.257 65.000 0.00 0.00 38.35 4.94
3998 4234 1.635817 CCCCCTCAATGGACACCGAT 61.636 60.000 0.00 0.00 38.35 4.18
4007 4243 0.758734 TGGACACCGATCCATGATCC 59.241 55.000 0.00 2.89 44.14 3.36
4014 4250 3.321968 CACCGATCCATGATCCTCTGTAA 59.678 47.826 0.00 0.00 35.83 2.41
4027 4263 8.985315 TGATCCTCTGTAAAATTCATTATGCT 57.015 30.769 0.00 0.00 0.00 3.79
4170 4406 5.107133 AGCTTTGCTGCATCACATAAATTC 58.893 37.500 1.84 0.00 37.57 2.17
4175 4411 5.827666 TGCTGCATCACATAAATTCAGATG 58.172 37.500 0.00 0.00 39.17 2.90
4211 4447 9.932207 TGAGCAAAGAATAAATCAATCAAATGT 57.068 25.926 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.610554 CCGGGTAGTAGGTGTGGGTG 61.611 65.000 0.00 0.00 0.00 4.61
1 2 1.305549 CCGGGTAGTAGGTGTGGGT 60.306 63.158 0.00 0.00 0.00 4.51
2 3 1.305549 ACCGGGTAGTAGGTGTGGG 60.306 63.158 6.32 0.00 39.66 4.61
3 4 0.612732 TGACCGGGTAGTAGGTGTGG 60.613 60.000 6.32 0.00 41.51 4.17
4 5 0.529378 GTGACCGGGTAGTAGGTGTG 59.471 60.000 6.32 0.00 41.51 3.82
5 6 0.613012 GGTGACCGGGTAGTAGGTGT 60.613 60.000 6.32 0.00 41.51 4.16
6 7 0.324091 AGGTGACCGGGTAGTAGGTG 60.324 60.000 6.32 0.00 41.51 4.00
7 8 0.033699 GAGGTGACCGGGTAGTAGGT 60.034 60.000 6.32 0.00 44.64 3.08
8 9 1.099879 CGAGGTGACCGGGTAGTAGG 61.100 65.000 6.32 0.00 0.00 3.18
9 10 1.099879 CCGAGGTGACCGGGTAGTAG 61.100 65.000 6.32 0.00 43.05 2.57
10 11 1.077501 CCGAGGTGACCGGGTAGTA 60.078 63.158 6.32 0.00 43.05 1.82
11 12 2.362120 CCGAGGTGACCGGGTAGT 60.362 66.667 6.32 0.00 43.05 2.73
18 19 4.176752 GATGGGCCCGAGGTGACC 62.177 72.222 19.37 0.00 0.00 4.02
19 20 3.083997 AGATGGGCCCGAGGTGAC 61.084 66.667 19.37 2.91 0.00 3.67
20 21 3.083349 CAGATGGGCCCGAGGTGA 61.083 66.667 19.37 0.00 0.00 4.02
21 22 4.864334 GCAGATGGGCCCGAGGTG 62.864 72.222 19.37 13.02 0.00 4.00
57 58 2.756283 AGGAGGACGAGGGCGAAG 60.756 66.667 0.00 0.00 41.64 3.79
58 59 3.068691 CAGGAGGACGAGGGCGAA 61.069 66.667 0.00 0.00 41.64 4.70
59 60 4.361971 ACAGGAGGACGAGGGCGA 62.362 66.667 0.00 0.00 41.64 5.54
60 61 3.827898 GACAGGAGGACGAGGGCG 61.828 72.222 0.00 0.00 44.79 6.13
61 62 1.985116 AAGACAGGAGGACGAGGGC 60.985 63.158 0.00 0.00 0.00 5.19
62 63 0.900647 ACAAGACAGGAGGACGAGGG 60.901 60.000 0.00 0.00 0.00 4.30
63 64 0.244994 CACAAGACAGGAGGACGAGG 59.755 60.000 0.00 0.00 0.00 4.63
64 65 0.244994 CCACAAGACAGGAGGACGAG 59.755 60.000 0.00 0.00 0.00 4.18
65 66 1.185618 CCCACAAGACAGGAGGACGA 61.186 60.000 0.00 0.00 0.00 4.20
66 67 1.293498 CCCACAAGACAGGAGGACG 59.707 63.158 0.00 0.00 0.00 4.79
67 68 0.321996 GACCCACAAGACAGGAGGAC 59.678 60.000 0.00 0.00 0.00 3.85
68 69 0.191064 AGACCCACAAGACAGGAGGA 59.809 55.000 0.00 0.00 0.00 3.71
69 70 1.827969 CTAGACCCACAAGACAGGAGG 59.172 57.143 0.00 0.00 0.00 4.30
70 71 1.205893 GCTAGACCCACAAGACAGGAG 59.794 57.143 0.00 0.00 0.00 3.69
71 72 1.203187 AGCTAGACCCACAAGACAGGA 60.203 52.381 0.00 0.00 0.00 3.86
72 73 1.205893 GAGCTAGACCCACAAGACAGG 59.794 57.143 0.00 0.00 0.00 4.00
73 74 1.135257 CGAGCTAGACCCACAAGACAG 60.135 57.143 0.00 0.00 0.00 3.51
74 75 0.888619 CGAGCTAGACCCACAAGACA 59.111 55.000 0.00 0.00 0.00 3.41
75 76 0.889306 ACGAGCTAGACCCACAAGAC 59.111 55.000 0.00 0.00 0.00 3.01
76 77 1.174783 GACGAGCTAGACCCACAAGA 58.825 55.000 0.00 0.00 0.00 3.02
77 78 0.888619 TGACGAGCTAGACCCACAAG 59.111 55.000 0.00 0.00 0.00 3.16
78 79 0.888619 CTGACGAGCTAGACCCACAA 59.111 55.000 0.00 0.00 0.00 3.33
79 80 1.595993 GCTGACGAGCTAGACCCACA 61.596 60.000 0.00 0.00 42.52 4.17
80 81 1.139947 GCTGACGAGCTAGACCCAC 59.860 63.158 0.00 0.00 42.52 4.61
81 82 2.407428 CGCTGACGAGCTAGACCCA 61.407 63.158 0.00 0.00 43.77 4.51
82 83 2.409651 CGCTGACGAGCTAGACCC 59.590 66.667 0.00 0.00 43.77 4.46
83 84 2.278271 GCGCTGACGAGCTAGACC 60.278 66.667 0.00 0.00 43.77 3.85
84 85 1.437772 TAGGCGCTGACGAGCTAGAC 61.438 60.000 7.64 0.00 43.77 2.59
85 86 1.153229 TAGGCGCTGACGAGCTAGA 60.153 57.895 7.64 0.00 43.77 2.43
86 87 1.281353 CTAGGCGCTGACGAGCTAG 59.719 63.158 7.64 3.63 43.77 3.42
87 88 2.835705 GCTAGGCGCTGACGAGCTA 61.836 63.158 7.64 0.00 43.77 3.32
88 89 4.200283 GCTAGGCGCTGACGAGCT 62.200 66.667 7.64 0.00 43.77 4.09
99 100 2.499685 CCACTACCACCGCTAGGC 59.500 66.667 0.00 0.00 42.76 3.93
100 101 2.432300 CCCCACTACCACCGCTAGG 61.432 68.421 0.00 0.00 45.13 3.02
101 102 1.684734 ACCCCACTACCACCGCTAG 60.685 63.158 0.00 0.00 0.00 3.42
102 103 1.985662 CACCCCACTACCACCGCTA 60.986 63.158 0.00 0.00 0.00 4.26
103 104 3.319198 CACCCCACTACCACCGCT 61.319 66.667 0.00 0.00 0.00 5.52
104 105 4.404098 CCACCCCACTACCACCGC 62.404 72.222 0.00 0.00 0.00 5.68
105 106 2.926242 ACCACCCCACTACCACCG 60.926 66.667 0.00 0.00 0.00 4.94
106 107 2.754375 CACCACCCCACTACCACC 59.246 66.667 0.00 0.00 0.00 4.61
107 108 2.754375 CCACCACCCCACTACCAC 59.246 66.667 0.00 0.00 0.00 4.16
108 109 3.253838 GCCACCACCCCACTACCA 61.254 66.667 0.00 0.00 0.00 3.25
109 110 4.404098 CGCCACCACCCCACTACC 62.404 72.222 0.00 0.00 0.00 3.18
110 111 3.600898 GACGCCACCACCCCACTAC 62.601 68.421 0.00 0.00 0.00 2.73
111 112 3.315949 GACGCCACCACCCCACTA 61.316 66.667 0.00 0.00 0.00 2.74
115 116 4.699522 GACTGACGCCACCACCCC 62.700 72.222 0.00 0.00 0.00 4.95
117 118 4.295119 ACGACTGACGCCACCACC 62.295 66.667 0.00 0.00 46.94 4.61
118 119 3.036084 CACGACTGACGCCACCAC 61.036 66.667 0.00 0.00 46.94 4.16
119 120 3.220658 TCACGACTGACGCCACCA 61.221 61.111 0.00 0.00 46.94 4.17
120 121 2.733593 GTCACGACTGACGCCACC 60.734 66.667 0.00 0.00 46.94 4.61
126 127 4.267928 GCCTGTAATAATGTCACGACTGAC 59.732 45.833 0.00 0.00 46.34 3.51
127 128 4.430007 GCCTGTAATAATGTCACGACTGA 58.570 43.478 0.00 0.00 0.00 3.41
128 129 3.555956 GGCCTGTAATAATGTCACGACTG 59.444 47.826 0.00 0.00 0.00 3.51
129 130 3.737047 CGGCCTGTAATAATGTCACGACT 60.737 47.826 0.00 0.00 0.00 4.18
130 131 2.538449 CGGCCTGTAATAATGTCACGAC 59.462 50.000 0.00 0.00 0.00 4.34
131 132 2.427812 TCGGCCTGTAATAATGTCACGA 59.572 45.455 0.00 0.00 0.00 4.35
132 133 2.816689 TCGGCCTGTAATAATGTCACG 58.183 47.619 0.00 0.00 0.00 4.35
133 134 5.448632 CCTTTTCGGCCTGTAATAATGTCAC 60.449 44.000 0.00 0.00 0.00 3.67
134 135 4.638421 CCTTTTCGGCCTGTAATAATGTCA 59.362 41.667 0.00 0.00 0.00 3.58
135 136 4.879545 TCCTTTTCGGCCTGTAATAATGTC 59.120 41.667 0.00 0.00 0.00 3.06
136 137 4.850680 TCCTTTTCGGCCTGTAATAATGT 58.149 39.130 0.00 0.00 0.00 2.71
137 138 4.261197 GCTCCTTTTCGGCCTGTAATAATG 60.261 45.833 0.00 0.00 0.00 1.90
150 151 0.442699 GCCGTTACTGCTCCTTTTCG 59.557 55.000 0.00 0.00 0.00 3.46
151 152 0.803117 GGCCGTTACTGCTCCTTTTC 59.197 55.000 0.00 0.00 0.00 2.29
157 158 2.886124 GCTCGGCCGTTACTGCTC 60.886 66.667 27.15 2.64 0.00 4.26
159 160 3.188786 CTGCTCGGCCGTTACTGC 61.189 66.667 27.15 21.06 0.00 4.40
162 163 2.508663 GACCTGCTCGGCCGTTAC 60.509 66.667 27.15 16.11 35.61 2.50
163 164 4.124351 CGACCTGCTCGGCCGTTA 62.124 66.667 27.15 11.72 38.87 3.18
201 202 2.281070 ACGAGCAGGCAACAGTGG 60.281 61.111 0.00 0.00 41.41 4.00
228 229 1.935300 GCTCACGGTCACAGTAACTGG 60.935 57.143 0.00 0.00 35.51 4.00
229 230 1.419374 GCTCACGGTCACAGTAACTG 58.581 55.000 0.00 0.00 37.52 3.16
230 231 0.039437 CGCTCACGGTCACAGTAACT 60.039 55.000 0.00 0.00 34.97 2.24
231 232 2.431539 CGCTCACGGTCACAGTAAC 58.568 57.895 0.00 0.00 34.97 2.50
232 233 4.957266 CGCTCACGGTCACAGTAA 57.043 55.556 0.00 0.00 34.97 2.24
338 339 1.419874 GAGACAGAGCATGCACGAGC 61.420 60.000 21.98 8.15 42.57 5.03
339 340 1.138636 CGAGACAGAGCATGCACGAG 61.139 60.000 21.98 14.13 0.00 4.18
340 341 1.153958 CGAGACAGAGCATGCACGA 60.154 57.895 21.98 0.00 0.00 4.35
341 342 2.163390 CCGAGACAGAGCATGCACG 61.163 63.158 21.98 12.39 0.00 5.34
342 343 1.079543 ACCGAGACAGAGCATGCAC 60.080 57.895 21.98 14.59 0.00 4.57
358 359 1.545706 GGTGAGGGGTGAGTGAGACC 61.546 65.000 0.00 0.00 0.00 3.85
364 365 1.915769 GCTGAGGTGAGGGGTGAGT 60.916 63.158 0.00 0.00 0.00 3.41
478 487 3.583086 GCGGTGGATTTAGCCGGC 61.583 66.667 21.89 21.89 45.02 6.13
656 690 0.515564 GAGATAGAGAGGTCGCGAGC 59.484 60.000 29.78 29.78 0.00 5.03
874 947 2.012554 GCGGGAGACTTAAAAGAGGCC 61.013 57.143 0.00 0.00 0.00 5.19
876 949 1.407025 GGGCGGGAGACTTAAAAGAGG 60.407 57.143 0.00 0.00 38.60 3.69
878 951 0.616891 GGGGCGGGAGACTTAAAAGA 59.383 55.000 0.00 0.00 38.60 2.52
879 952 0.743345 CGGGGCGGGAGACTTAAAAG 60.743 60.000 0.00 0.00 38.60 2.27
880 953 1.297364 CGGGGCGGGAGACTTAAAA 59.703 57.895 0.00 0.00 38.60 1.52
1065 1144 4.334118 TGCAGCAGCGTGGTGGAT 62.334 61.111 15.50 0.00 45.26 3.41
1671 1762 3.204827 ATGGAGCGGCGCATGAAC 61.205 61.111 35.02 18.27 0.00 3.18
2107 2198 1.006832 CGGTGGTGATTAAGCGGAAG 58.993 55.000 0.00 0.00 33.85 3.46
2109 2200 1.448893 GCGGTGGTGATTAAGCGGA 60.449 57.895 0.00 0.00 37.74 5.54
2111 2202 0.928229 GTAGCGGTGGTGATTAAGCG 59.072 55.000 0.00 0.00 40.12 4.68
2112 2203 0.928229 CGTAGCGGTGGTGATTAAGC 59.072 55.000 0.00 0.00 0.00 3.09
2115 2206 1.175654 TGACGTAGCGGTGGTGATTA 58.824 50.000 0.00 0.00 0.00 1.75
2116 2207 0.319083 TTGACGTAGCGGTGGTGATT 59.681 50.000 0.00 0.00 0.00 2.57
2117 2208 0.535335 ATTGACGTAGCGGTGGTGAT 59.465 50.000 0.00 0.00 0.00 3.06
2118 2209 0.108992 GATTGACGTAGCGGTGGTGA 60.109 55.000 0.00 0.00 0.00 4.02
2119 2210 0.389296 TGATTGACGTAGCGGTGGTG 60.389 55.000 0.00 0.00 0.00 4.17
2120 2211 0.319083 TTGATTGACGTAGCGGTGGT 59.681 50.000 0.00 0.00 0.00 4.16
2121 2212 1.651987 ATTGATTGACGTAGCGGTGG 58.348 50.000 0.00 0.00 0.00 4.61
2122 2213 3.242944 CAGTATTGATTGACGTAGCGGTG 59.757 47.826 0.00 0.00 0.00 4.94
2123 2214 3.444916 CAGTATTGATTGACGTAGCGGT 58.555 45.455 0.00 0.00 0.00 5.68
2124 2215 2.218759 GCAGTATTGATTGACGTAGCGG 59.781 50.000 0.00 0.00 0.00 5.52
2125 2216 2.857748 TGCAGTATTGATTGACGTAGCG 59.142 45.455 0.00 0.00 0.00 4.26
2126 2217 3.301835 CGTGCAGTATTGATTGACGTAGC 60.302 47.826 0.00 0.00 0.00 3.58
2127 2218 3.857665 ACGTGCAGTATTGATTGACGTAG 59.142 43.478 0.00 0.00 36.85 3.51
2128 2219 3.840468 ACGTGCAGTATTGATTGACGTA 58.160 40.909 0.00 0.00 36.85 3.57
2129 2220 2.683968 ACGTGCAGTATTGATTGACGT 58.316 42.857 0.00 0.00 33.98 4.34
2130 2221 3.300944 CGTACGTGCAGTATTGATTGACG 60.301 47.826 7.22 0.00 37.69 4.35
2131 2222 3.611113 ACGTACGTGCAGTATTGATTGAC 59.389 43.478 22.14 0.00 37.69 3.18
2132 2223 3.840468 ACGTACGTGCAGTATTGATTGA 58.160 40.909 22.14 0.00 37.69 2.57
2133 2224 4.027132 GGTACGTACGTGCAGTATTGATTG 60.027 45.833 32.30 0.00 37.69 2.67
2139 2230 0.378257 CGGGTACGTACGTGCAGTAT 59.622 55.000 32.30 8.09 37.69 2.12
2149 2259 6.821160 TCGATCATATATAAACCGGGTACGTA 59.179 38.462 6.32 0.00 38.78 3.57
2294 2412 6.350780 GGACGGATCTCCTCAAAAGTTAGTTA 60.351 42.308 0.00 0.00 0.00 2.24
2295 2413 5.480205 GACGGATCTCCTCAAAAGTTAGTT 58.520 41.667 0.00 0.00 0.00 2.24
2296 2414 4.081586 GGACGGATCTCCTCAAAAGTTAGT 60.082 45.833 0.00 0.00 0.00 2.24
2297 2415 4.081642 TGGACGGATCTCCTCAAAAGTTAG 60.082 45.833 2.92 0.00 0.00 2.34
2316 2434 1.373570 GCAGAGGCTGTTGTATGGAC 58.626 55.000 0.00 0.00 36.96 4.02
2330 2451 2.989840 CAACTAACTGAACGGAGCAGAG 59.010 50.000 8.18 0.17 36.86 3.35
2336 2457 1.876416 GCAGCCAACTAACTGAACGGA 60.876 52.381 0.00 0.00 35.90 4.69
2339 2460 2.554032 ACATGCAGCCAACTAACTGAAC 59.446 45.455 0.00 0.00 35.90 3.18
2340 2461 2.553602 CACATGCAGCCAACTAACTGAA 59.446 45.455 0.00 0.00 35.90 3.02
2408 2534 0.107165 AGCCTCTTTACCAATCGCCC 60.107 55.000 0.00 0.00 0.00 6.13
2480 2606 4.647654 ACGAACCGTGCAGTAGTG 57.352 55.556 0.00 0.00 39.18 2.74
2504 2630 4.161565 AGAAAAGTGAGGTTTTTGAACCCC 59.838 41.667 4.77 0.00 43.87 4.95
2604 2730 1.802636 CATGTGACGGCCATGTTCC 59.197 57.895 2.24 0.00 35.94 3.62
2701 2827 0.912486 ATTCAGCTGGAGGGGTACAC 59.088 55.000 15.13 0.00 0.00 2.90
2702 2828 1.204146 GATTCAGCTGGAGGGGTACA 58.796 55.000 15.13 0.00 0.00 2.90
2703 2829 1.204146 TGATTCAGCTGGAGGGGTAC 58.796 55.000 15.13 0.00 0.00 3.34
2704 2830 2.196742 ATGATTCAGCTGGAGGGGTA 57.803 50.000 15.13 0.00 0.00 3.69
2705 2831 1.213926 GAATGATTCAGCTGGAGGGGT 59.786 52.381 15.13 0.00 0.00 4.95
2706 2832 1.493871 AGAATGATTCAGCTGGAGGGG 59.506 52.381 15.13 0.00 0.00 4.79
2730 2867 6.540438 AGCTAGTAGTTGGTACTAATGCAA 57.460 37.500 0.00 0.00 42.58 4.08
2748 2888 2.053627 CAAAGCCGTTTGCAAAGCTAG 58.946 47.619 21.96 15.30 44.83 3.42
2749 2889 2.132740 CAAAGCCGTTTGCAAAGCTA 57.867 45.000 21.96 0.00 44.83 3.32
2750 2890 2.976271 CAAAGCCGTTTGCAAAGCT 58.024 47.368 17.56 17.56 44.83 3.74
2757 2897 1.820233 CGCCTTTGCAAAGCCGTTTG 61.820 55.000 28.76 17.57 45.18 2.93
2760 2900 2.268076 ATCGCCTTTGCAAAGCCGT 61.268 52.632 33.22 21.61 37.98 5.68
2858 2998 5.683876 AGCAGTCAAGTGATGGTAGTATT 57.316 39.130 0.00 0.00 0.00 1.89
2862 3002 4.318332 TCAAAGCAGTCAAGTGATGGTAG 58.682 43.478 0.00 0.00 0.00 3.18
2863 3003 4.350368 TCAAAGCAGTCAAGTGATGGTA 57.650 40.909 0.00 0.00 0.00 3.25
2864 3004 3.213206 TCAAAGCAGTCAAGTGATGGT 57.787 42.857 0.00 0.00 0.00 3.55
2865 3005 3.754850 TCATCAAAGCAGTCAAGTGATGG 59.245 43.478 10.99 0.00 43.68 3.51
2866 3006 5.123344 TCATCATCAAAGCAGTCAAGTGATG 59.877 40.000 5.75 5.75 44.46 3.07
2867 3007 5.250982 TCATCATCAAAGCAGTCAAGTGAT 58.749 37.500 0.00 0.00 0.00 3.06
2868 3008 4.644498 TCATCATCAAAGCAGTCAAGTGA 58.356 39.130 0.00 0.00 0.00 3.41
2869 3009 4.454847 ACTCATCATCAAAGCAGTCAAGTG 59.545 41.667 0.00 0.00 0.00 3.16
2918 3064 3.731089 CCACCTGCAAATCAAAACACAT 58.269 40.909 0.00 0.00 0.00 3.21
3040 3186 2.125912 CGCTCCAGGTTGTCCTCG 60.126 66.667 0.00 0.00 43.07 4.63
3266 3421 3.512680 TGTACAAAGCCCAAACAAAACG 58.487 40.909 0.00 0.00 0.00 3.60
3268 3423 4.333926 GCAATGTACAAAGCCCAAACAAAA 59.666 37.500 0.00 0.00 0.00 2.44
3396 3551 2.578713 CAGTATTCGCCGCGTCGT 60.579 61.111 10.12 0.00 0.00 4.34
3399 3554 0.319555 ATATGCAGTATTCGCCGCGT 60.320 50.000 13.39 0.00 0.00 6.01
3452 3666 6.557110 GCAATTTTGCGTAAACTATAGGGAA 58.443 36.000 4.43 0.00 45.11 3.97
3453 3667 6.126568 GCAATTTTGCGTAAACTATAGGGA 57.873 37.500 4.43 0.00 45.11 4.20
3488 3705 1.468914 GGGTTTCGACTTCATGCCTTC 59.531 52.381 0.00 0.00 0.00 3.46
3489 3706 1.202879 TGGGTTTCGACTTCATGCCTT 60.203 47.619 0.00 0.00 0.00 4.35
3496 3713 2.076863 CCAGTGATGGGTTTCGACTTC 58.923 52.381 0.00 0.00 0.00 3.01
3501 3718 0.744414 ATCGCCAGTGATGGGTTTCG 60.744 55.000 0.00 0.00 0.00 3.46
3551 3768 3.425659 AGGGAGTTCAATTTTGAGCCTC 58.574 45.455 3.86 8.03 38.94 4.70
3562 3779 4.693283 CGTAATCATGCTAGGGAGTTCAA 58.307 43.478 0.00 0.00 0.00 2.69
3583 3800 3.123620 GCTTGGCCTGTCAGAGCG 61.124 66.667 3.32 0.00 0.00 5.03
3584 3801 1.174712 TTTGCTTGGCCTGTCAGAGC 61.175 55.000 3.32 2.78 0.00 4.09
3587 3805 2.298163 AGAAATTTGCTTGGCCTGTCAG 59.702 45.455 3.32 0.00 0.00 3.51
3601 3823 4.767409 GCCCTACAAGGAACAGAGAAATTT 59.233 41.667 0.00 0.00 37.67 1.82
3609 3831 5.975693 TTTATTTGCCCTACAAGGAACAG 57.024 39.130 0.00 0.00 40.06 3.16
3664 3888 3.120752 CGAATTGCTCTTATGGCAGATCG 60.121 47.826 0.00 0.00 40.90 3.69
3677 3904 4.493220 GCACTATCTGTTGTCGAATTGCTC 60.493 45.833 0.00 0.00 0.00 4.26
3709 3936 6.149129 ACGGCTCTTCATTTTTCTTTTCTT 57.851 33.333 0.00 0.00 0.00 2.52
3711 3938 6.828502 AAACGGCTCTTCATTTTTCTTTTC 57.171 33.333 0.00 0.00 0.00 2.29
3729 3956 5.230516 GGCACTAAGTTGTTTTTGTAAACGG 59.769 40.000 0.00 0.00 45.29 4.44
3793 4021 1.019278 GGCGCGATTGTTCTCCTTCA 61.019 55.000 12.10 0.00 0.00 3.02
3810 4038 1.877637 TGTATGATACGCATGGTGGC 58.122 50.000 0.00 0.00 37.87 5.01
3811 4039 4.891627 TTTTGTATGATACGCATGGTGG 57.108 40.909 0.00 0.00 37.87 4.61
3812 4040 5.635866 TGTTTTTGTATGATACGCATGGTG 58.364 37.500 0.00 0.00 37.87 4.17
3813 4041 5.888691 TGTTTTTGTATGATACGCATGGT 57.111 34.783 0.00 0.00 37.87 3.55
3814 4042 6.321717 AGTTGTTTTTGTATGATACGCATGG 58.678 36.000 0.00 0.00 37.87 3.66
3815 4043 7.795431 AAGTTGTTTTTGTATGATACGCATG 57.205 32.000 0.00 0.00 37.87 4.06
3816 4044 8.726988 ACTAAGTTGTTTTTGTATGATACGCAT 58.273 29.630 0.00 0.00 41.08 4.73
3817 4045 8.012809 CACTAAGTTGTTTTTGTATGATACGCA 58.987 33.333 0.00 0.00 0.00 5.24
3818 4046 7.007099 GCACTAAGTTGTTTTTGTATGATACGC 59.993 37.037 0.00 0.00 0.00 4.42
3819 4047 7.480542 GGCACTAAGTTGTTTTTGTATGATACG 59.519 37.037 0.00 0.00 0.00 3.06
3820 4048 8.512138 AGGCACTAAGTTGTTTTTGTATGATAC 58.488 33.333 0.00 0.00 36.02 2.24
3821 4049 8.630054 AGGCACTAAGTTGTTTTTGTATGATA 57.370 30.769 0.00 0.00 36.02 2.15
3822 4050 7.524717 AGGCACTAAGTTGTTTTTGTATGAT 57.475 32.000 0.00 0.00 36.02 2.45
3823 4051 6.952773 AGGCACTAAGTTGTTTTTGTATGA 57.047 33.333 0.00 0.00 36.02 2.15
3824 4052 7.305474 CCTAGGCACTAAGTTGTTTTTGTATG 58.695 38.462 0.00 0.00 42.17 2.39
3825 4053 6.072119 GCCTAGGCACTAAGTTGTTTTTGTAT 60.072 38.462 29.33 0.00 42.17 2.29
3826 4054 5.239963 GCCTAGGCACTAAGTTGTTTTTGTA 59.760 40.000 29.33 0.00 42.17 2.41
3827 4055 4.037565 GCCTAGGCACTAAGTTGTTTTTGT 59.962 41.667 29.33 0.00 42.17 2.83
3828 4056 4.546570 GCCTAGGCACTAAGTTGTTTTTG 58.453 43.478 29.33 0.00 42.17 2.44
3829 4057 4.848562 GCCTAGGCACTAAGTTGTTTTT 57.151 40.909 29.33 0.00 42.17 1.94
3843 4071 2.356069 GACTATTTGTTGCTGCCTAGGC 59.644 50.000 27.71 27.71 42.35 3.93
3844 4072 2.945668 GGACTATTTGTTGCTGCCTAGG 59.054 50.000 3.67 3.67 0.00 3.02
3845 4073 3.609853 TGGACTATTTGTTGCTGCCTAG 58.390 45.455 0.00 0.00 0.00 3.02
3846 4074 3.712016 TGGACTATTTGTTGCTGCCTA 57.288 42.857 0.00 0.00 0.00 3.93
3847 4075 2.584835 TGGACTATTTGTTGCTGCCT 57.415 45.000 0.00 0.00 0.00 4.75
3848 4076 2.819608 TCTTGGACTATTTGTTGCTGCC 59.180 45.455 0.00 0.00 0.00 4.85
3849 4077 4.229876 GTTCTTGGACTATTTGTTGCTGC 58.770 43.478 0.00 0.00 0.00 5.25
3850 4078 4.466828 CGTTCTTGGACTATTTGTTGCTG 58.533 43.478 0.00 0.00 0.00 4.41
3851 4079 3.502211 CCGTTCTTGGACTATTTGTTGCT 59.498 43.478 0.00 0.00 0.00 3.91
3852 4080 3.252458 ACCGTTCTTGGACTATTTGTTGC 59.748 43.478 0.00 0.00 0.00 4.17
3853 4081 4.513692 TGACCGTTCTTGGACTATTTGTTG 59.486 41.667 0.00 0.00 0.00 3.33
3854 4082 4.710324 TGACCGTTCTTGGACTATTTGTT 58.290 39.130 0.00 0.00 0.00 2.83
3855 4083 4.315803 CTGACCGTTCTTGGACTATTTGT 58.684 43.478 0.00 0.00 0.00 2.83
3856 4084 3.684788 CCTGACCGTTCTTGGACTATTTG 59.315 47.826 0.00 0.00 0.00 2.32
3857 4085 3.868754 GCCTGACCGTTCTTGGACTATTT 60.869 47.826 0.00 0.00 0.00 1.40
3858 4086 2.354805 GCCTGACCGTTCTTGGACTATT 60.355 50.000 0.00 0.00 0.00 1.73
3859 4087 1.207329 GCCTGACCGTTCTTGGACTAT 59.793 52.381 0.00 0.00 0.00 2.12
3860 4088 0.606604 GCCTGACCGTTCTTGGACTA 59.393 55.000 0.00 0.00 0.00 2.59
3882 4110 3.579709 TCAGAACGCTCAATCTGAAGAC 58.420 45.455 3.16 0.00 46.67 3.01
3892 4120 1.005748 CCTGCAGTCAGAACGCTCA 60.006 57.895 13.81 0.00 42.95 4.26
3909 4137 5.186198 AGTTATGTAATGGTCTTGCACTCC 58.814 41.667 0.00 0.00 0.00 3.85
3939 4167 1.401905 GAATCCTGGTGGCGATTGTTC 59.598 52.381 0.00 0.00 0.00 3.18
3976 4204 1.208165 GGTGTCCATTGAGGGGGAGT 61.208 60.000 0.00 0.00 38.24 3.85
3996 4232 8.632906 ATGAATTTTACAGAGGATCATGGATC 57.367 34.615 0.00 0.00 37.82 3.36
4170 4406 2.449464 TGCTCATGTTTTCCCCATCTG 58.551 47.619 0.00 0.00 0.00 2.90
4175 4411 4.541973 ATTCTTTGCTCATGTTTTCCCC 57.458 40.909 0.00 0.00 0.00 4.81
4211 4447 0.108585 GCACCCTCAGACCTTGTGAA 59.891 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.