Multiple sequence alignment - TraesCS7A01G024600

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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 TraesCS7A01G024600 chr7A 100.000 2516 0 0 1 2516 9721314 9718799 0.000000e+00 4647.0
1 TraesCS7A01G024600 chr7A 99.640 278 1 0 1 278 67732607 67732330 2.230000e-140 508.0
2 TraesCS7A01G024600 chr7A 82.916 439 50 16 1025 1461 10017105 10017520 3.060000e-99 372.0
3 TraesCS7A01G024600 chr7A 81.757 444 55 18 1025 1461 9997237 9997661 5.150000e-92 348.0
4 TraesCS7A01G024600 chr7A 94.595 37 1 1 2013 2049 9719360 9719325 3.500000e-04 56.5
5 TraesCS7A01G024600 chr4A 86.468 1574 107 59 465 1964 728128884 728130425 0.000000e+00 1629.0
6 TraesCS7A01G024600 chr4A 81.124 445 56 19 1025 1461 727842119 727841695 5.190000e-87 331.0
7 TraesCS7A01G024600 chr4A 82.879 257 30 9 1215 1461 730498491 730498743 4.210000e-53 219.0
8 TraesCS7A01G024600 chr4A 76.389 432 82 11 1031 1461 731075969 731075557 5.450000e-52 215.0
9 TraesCS7A01G024600 chr4A 81.304 230 34 5 2282 2502 728130896 728131125 7.150000e-41 178.0
10 TraesCS7A01G024600 chr4A 83.000 200 27 5 1722 1919 728720648 728720842 9.250000e-40 174.0
11 TraesCS7A01G024600 chr4A 74.715 439 85 11 1024 1461 729308217 729307804 3.330000e-39 172.0
12 TraesCS7A01G024600 chr7D 84.520 1770 133 86 279 1990 10595809 10594123 0.000000e+00 1620.0
13 TraesCS7A01G024600 chr7D 86.384 896 82 20 1028 1919 10568737 10567878 0.000000e+00 942.0
14 TraesCS7A01G024600 chr7D 87.402 508 52 8 2013 2515 10594159 10593659 7.810000e-160 573.0
15 TraesCS7A01G024600 chr7D 89.894 376 28 7 1363 1736 10587029 10586662 2.260000e-130 475.0
16 TraesCS7A01G024600 chr7D 83.410 434 47 16 1030 1461 10804543 10804953 1.830000e-101 379.0
17 TraesCS7A01G024600 chr7D 79.612 515 66 18 2010 2515 10570946 10570462 1.440000e-87 333.0
18 TraesCS7A01G024600 chr7D 81.023 469 45 29 1000 1461 10810419 10810850 1.440000e-87 333.0
19 TraesCS7A01G024600 chr7D 80.044 451 64 19 1025 1468 22477510 22477079 6.760000e-81 311.0
20 TraesCS7A01G024600 chr7D 89.787 235 19 5 1734 1964 10571156 10570923 1.890000e-76 296.0
21 TraesCS7A01G024600 chr7D 85.714 84 6 3 655 737 10810033 10810111 1.600000e-12 84.2
22 TraesCS7A01G024600 chr5B 99.640 278 1 0 2 279 533757139 533756862 2.230000e-140 508.0
23 TraesCS7A01G024600 chr2B 98.944 284 1 1 1 282 114725322 114725039 8.030000e-140 507.0
24 TraesCS7A01G024600 chr1A 98.601 286 4 0 1 286 153593265 153593550 8.030000e-140 507.0
25 TraesCS7A01G024600 chr1B 98.936 282 3 0 1 282 38553556 38553275 2.890000e-139 505.0
26 TraesCS7A01G024600 chr7B 98.258 287 5 0 1 287 709790874 709791160 1.040000e-138 503.0
27 TraesCS7A01G024600 chr6B 98.932 281 3 0 4 284 87514524 87514244 1.040000e-138 503.0
28 TraesCS7A01G024600 chr4B 98.252 286 5 0 1 286 69581469 69581184 3.740000e-138 501.0
29 TraesCS7A01G024600 chr3A 97.917 288 4 2 1 288 119382699 119382414 4.830000e-137 497.0


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 TraesCS7A01G024600 chr7A 9718799 9721314 2515 True 2351.750000 4647 97.2975 1 2516 2 chr7A.!!$R2 2515
1 TraesCS7A01G024600 chr4A 728128884 728131125 2241 False 903.500000 1629 83.8860 465 2502 2 chr4A.!!$F3 2037
2 TraesCS7A01G024600 chr7D 10593659 10595809 2150 True 1096.500000 1620 85.9610 279 2515 2 chr7D.!!$R4 2236
3 TraesCS7A01G024600 chr7D 10567878 10571156 3278 True 523.666667 942 85.2610 1028 2515 3 chr7D.!!$R3 1487
4 TraesCS7A01G024600 chr7D 10810033 10810850 817 False 208.600000 333 83.3685 655 1461 2 chr7D.!!$F2 806

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
345 350 0.179032 TCCATGTTTGTGCGGACTGT 60.179 50.0 8.99 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 3444 1.065926 AGCGATGTTGCTCTGGAATGA 60.066 47.619 0.0 0.0 42.95 2.57 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
20 21 1.683917 ACGTGTCTCTCAGAAGCAACT 59.316 47.619 0.00 0.00 0.00 3.16
21 22 2.885266 ACGTGTCTCTCAGAAGCAACTA 59.115 45.455 0.00 0.00 0.00 2.24
22 23 3.238441 CGTGTCTCTCAGAAGCAACTAC 58.762 50.000 0.00 0.00 0.00 2.73
23 24 3.304726 CGTGTCTCTCAGAAGCAACTACA 60.305 47.826 0.00 0.00 0.00 2.74
24 25 4.233789 GTGTCTCTCAGAAGCAACTACAG 58.766 47.826 0.00 0.00 0.00 2.74
26 27 4.769488 TGTCTCTCAGAAGCAACTACAGAT 59.231 41.667 0.00 0.00 0.00 2.90
27 28 5.105957 TGTCTCTCAGAAGCAACTACAGATC 60.106 44.000 0.00 0.00 0.00 2.75
28 29 5.012893 TCTCTCAGAAGCAACTACAGATCA 58.987 41.667 0.00 0.00 0.00 2.92
29 30 5.478332 TCTCTCAGAAGCAACTACAGATCAA 59.522 40.000 0.00 0.00 0.00 2.57
30 31 5.718146 TCTCAGAAGCAACTACAGATCAAG 58.282 41.667 0.00 0.00 0.00 3.02
33 34 6.291377 TCAGAAGCAACTACAGATCAAGTTT 58.709 36.000 0.00 0.00 33.72 2.66
34 35 7.441836 TCAGAAGCAACTACAGATCAAGTTTA 58.558 34.615 0.00 0.00 33.72 2.01
37 38 9.289782 AGAAGCAACTACAGATCAAGTTTATTT 57.710 29.630 0.00 0.00 33.72 1.40
40 41 9.289782 AGCAACTACAGATCAAGTTTATTTCTT 57.710 29.630 0.00 0.00 33.72 2.52
41 42 9.548208 GCAACTACAGATCAAGTTTATTTCTTC 57.452 33.333 0.00 0.00 33.72 2.87
43 44 9.793259 AACTACAGATCAAGTTTATTTCTTCCA 57.207 29.630 0.00 0.00 32.00 3.53
44 45 9.793259 ACTACAGATCAAGTTTATTTCTTCCAA 57.207 29.630 0.00 0.00 0.00 3.53
46 47 8.115490 ACAGATCAAGTTTATTTCTTCCAAGG 57.885 34.615 0.00 0.00 0.00 3.61
47 48 7.944554 ACAGATCAAGTTTATTTCTTCCAAGGA 59.055 33.333 0.00 0.00 0.00 3.36
48 49 8.964772 CAGATCAAGTTTATTTCTTCCAAGGAT 58.035 33.333 0.00 0.00 0.00 3.24
49 50 9.183368 AGATCAAGTTTATTTCTTCCAAGGATC 57.817 33.333 0.00 0.00 0.00 3.36
50 51 8.884124 ATCAAGTTTATTTCTTCCAAGGATCA 57.116 30.769 0.00 0.00 0.00 2.92
51 52 8.704849 TCAAGTTTATTTCTTCCAAGGATCAA 57.295 30.769 0.00 0.00 0.00 2.57
52 53 8.576442 TCAAGTTTATTTCTTCCAAGGATCAAC 58.424 33.333 0.00 0.00 0.00 3.18
53 54 8.579863 CAAGTTTATTTCTTCCAAGGATCAACT 58.420 33.333 0.00 0.00 0.00 3.16
55 56 8.579863 AGTTTATTTCTTCCAAGGATCAACTTG 58.420 33.333 5.08 5.08 45.71 3.16
56 57 4.853924 TTTCTTCCAAGGATCAACTTGC 57.146 40.909 6.27 0.00 44.98 4.01
57 58 3.795688 TCTTCCAAGGATCAACTTGCT 57.204 42.857 6.27 0.00 44.98 3.91
58 59 3.415212 TCTTCCAAGGATCAACTTGCTG 58.585 45.455 6.27 0.70 44.98 4.41
59 60 3.072915 TCTTCCAAGGATCAACTTGCTGA 59.927 43.478 6.27 2.53 44.98 4.26
60 61 2.783135 TCCAAGGATCAACTTGCTGAC 58.217 47.619 6.27 0.00 44.98 3.51
61 62 2.106338 TCCAAGGATCAACTTGCTGACA 59.894 45.455 6.27 0.00 44.98 3.58
62 63 3.087031 CCAAGGATCAACTTGCTGACAT 58.913 45.455 6.27 0.00 44.98 3.06
63 64 3.128242 CCAAGGATCAACTTGCTGACATC 59.872 47.826 6.27 0.00 44.98 3.06
66 67 4.260170 AGGATCAACTTGCTGACATCTTC 58.740 43.478 0.00 0.00 0.00 2.87
67 68 4.005650 GGATCAACTTGCTGACATCTTCA 58.994 43.478 0.00 0.00 0.00 3.02
68 69 4.142730 GGATCAACTTGCTGACATCTTCAC 60.143 45.833 0.00 0.00 0.00 3.18
69 70 3.141398 TCAACTTGCTGACATCTTCACC 58.859 45.455 0.00 0.00 0.00 4.02
70 71 2.880268 CAACTTGCTGACATCTTCACCA 59.120 45.455 0.00 0.00 0.00 4.17
71 72 3.213206 ACTTGCTGACATCTTCACCAA 57.787 42.857 0.00 0.00 30.51 3.67
72 73 3.144506 ACTTGCTGACATCTTCACCAAG 58.855 45.455 7.48 7.48 46.91 3.61
74 75 0.807496 GCTGACATCTTCACCAAGCC 59.193 55.000 0.00 0.00 0.00 4.35
77 78 3.087031 CTGACATCTTCACCAAGCCATT 58.913 45.455 0.00 0.00 0.00 3.16
79 80 1.547372 ACATCTTCACCAAGCCATTGC 59.453 47.619 0.00 0.00 34.91 3.56
80 81 1.134907 CATCTTCACCAAGCCATTGCC 60.135 52.381 0.00 0.00 38.69 4.52
83 84 1.345415 CTTCACCAAGCCATTGCCTTT 59.655 47.619 0.00 0.00 38.69 3.11
84 85 0.680618 TCACCAAGCCATTGCCTTTG 59.319 50.000 0.00 0.00 38.69 2.77
85 86 0.952010 CACCAAGCCATTGCCTTTGC 60.952 55.000 0.00 0.00 38.69 3.68
87 88 1.371932 CAAGCCATTGCCTTTGCCA 59.628 52.632 0.00 0.00 38.69 4.92
89 90 1.409251 AAGCCATTGCCTTTGCCACA 61.409 50.000 0.00 0.00 38.69 4.17
90 91 1.375013 GCCATTGCCTTTGCCACAG 60.375 57.895 0.00 0.00 36.33 3.66
91 92 2.051941 CCATTGCCTTTGCCACAGT 58.948 52.632 0.00 0.00 36.33 3.55
92 93 0.393820 CCATTGCCTTTGCCACAGTT 59.606 50.000 0.00 0.00 36.33 3.16
93 94 1.202675 CCATTGCCTTTGCCACAGTTT 60.203 47.619 0.00 0.00 36.33 2.66
94 95 1.868498 CATTGCCTTTGCCACAGTTTG 59.132 47.619 0.00 0.00 36.33 2.93
96 97 0.746063 TGCCTTTGCCACAGTTTGAG 59.254 50.000 0.00 0.00 36.33 3.02
98 99 1.269257 GCCTTTGCCACAGTTTGAGAC 60.269 52.381 0.00 0.00 0.00 3.36
100 101 2.689983 CCTTTGCCACAGTTTGAGACTT 59.310 45.455 0.00 0.00 36.10 3.01
101 102 3.489738 CCTTTGCCACAGTTTGAGACTTG 60.490 47.826 0.00 0.00 36.10 3.16
102 103 1.024271 TGCCACAGTTTGAGACTTGC 58.976 50.000 0.00 0.00 36.10 4.01
103 104 1.024271 GCCACAGTTTGAGACTTGCA 58.976 50.000 0.00 0.00 36.10 4.08
104 105 1.002033 GCCACAGTTTGAGACTTGCAG 60.002 52.381 0.00 0.00 36.10 4.41
105 106 1.605710 CCACAGTTTGAGACTTGCAGG 59.394 52.381 0.00 0.00 36.10 4.85
106 107 1.002033 CACAGTTTGAGACTTGCAGGC 60.002 52.381 0.00 0.00 36.10 4.85
107 108 0.236711 CAGTTTGAGACTTGCAGGCG 59.763 55.000 0.00 0.00 36.10 5.52
118 119 3.111038 GCAGGCGCAATCTTACCC 58.889 61.111 10.83 0.00 38.36 3.69
119 120 1.452108 GCAGGCGCAATCTTACCCT 60.452 57.895 10.83 0.00 38.36 4.34
120 121 1.032114 GCAGGCGCAATCTTACCCTT 61.032 55.000 10.83 0.00 38.36 3.95
121 122 1.017387 CAGGCGCAATCTTACCCTTC 58.983 55.000 10.83 0.00 0.00 3.46
122 123 0.912486 AGGCGCAATCTTACCCTTCT 59.088 50.000 10.83 0.00 0.00 2.85
123 124 2.116238 AGGCGCAATCTTACCCTTCTA 58.884 47.619 10.83 0.00 0.00 2.10
126 127 3.244249 GGCGCAATCTTACCCTTCTAGAT 60.244 47.826 10.83 0.00 0.00 1.98
127 128 4.381411 GCGCAATCTTACCCTTCTAGATT 58.619 43.478 0.30 0.00 38.74 2.40
128 129 4.449405 GCGCAATCTTACCCTTCTAGATTC 59.551 45.833 0.30 0.00 36.70 2.52
129 130 5.601662 CGCAATCTTACCCTTCTAGATTCA 58.398 41.667 0.00 0.00 36.70 2.57
130 131 6.226787 CGCAATCTTACCCTTCTAGATTCAT 58.773 40.000 0.00 0.00 36.70 2.57
133 134 9.213799 GCAATCTTACCCTTCTAGATTCATTAG 57.786 37.037 0.00 0.00 36.70 1.73
140 141 7.569240 ACCCTTCTAGATTCATTAGAAAGTGG 58.431 38.462 0.00 0.00 36.87 4.00
142 143 7.278875 CCTTCTAGATTCATTAGAAAGTGGCT 58.721 38.462 0.00 0.00 36.87 4.75
143 144 8.424918 CCTTCTAGATTCATTAGAAAGTGGCTA 58.575 37.037 0.00 0.00 36.87 3.93
144 145 9.823647 CTTCTAGATTCATTAGAAAGTGGCTAA 57.176 33.333 0.00 0.00 36.87 3.09
145 146 9.823647 TTCTAGATTCATTAGAAAGTGGCTAAG 57.176 33.333 0.00 0.00 37.29 2.18
146 147 9.201989 TCTAGATTCATTAGAAAGTGGCTAAGA 57.798 33.333 0.00 0.00 37.29 2.10
147 148 9.995003 CTAGATTCATTAGAAAGTGGCTAAGAT 57.005 33.333 0.00 0.00 37.29 2.40
149 150 9.118300 AGATTCATTAGAAAGTGGCTAAGATTG 57.882 33.333 0.00 0.00 37.29 2.67
150 151 9.113838 GATTCATTAGAAAGTGGCTAAGATTGA 57.886 33.333 0.00 0.00 37.29 2.57
151 152 8.498054 TTCATTAGAAAGTGGCTAAGATTGAG 57.502 34.615 0.00 0.00 31.94 3.02
153 154 4.227864 AGAAAGTGGCTAAGATTGAGGG 57.772 45.455 0.00 0.00 0.00 4.30
154 155 3.846588 AGAAAGTGGCTAAGATTGAGGGA 59.153 43.478 0.00 0.00 0.00 4.20
155 156 3.922171 AAGTGGCTAAGATTGAGGGAG 57.078 47.619 0.00 0.00 0.00 4.30
156 157 2.122768 AGTGGCTAAGATTGAGGGAGG 58.877 52.381 0.00 0.00 0.00 4.30
160 161 1.840635 GCTAAGATTGAGGGAGGGTGT 59.159 52.381 0.00 0.00 0.00 4.16
161 162 2.239907 GCTAAGATTGAGGGAGGGTGTT 59.760 50.000 0.00 0.00 0.00 3.32
162 163 3.454812 GCTAAGATTGAGGGAGGGTGTTA 59.545 47.826 0.00 0.00 0.00 2.41
164 165 3.491766 AGATTGAGGGAGGGTGTTAGA 57.508 47.619 0.00 0.00 0.00 2.10
165 166 3.108376 AGATTGAGGGAGGGTGTTAGAC 58.892 50.000 0.00 0.00 0.00 2.59
166 167 2.715763 TTGAGGGAGGGTGTTAGACT 57.284 50.000 0.00 0.00 0.00 3.24
167 168 1.938585 TGAGGGAGGGTGTTAGACTG 58.061 55.000 0.00 0.00 0.00 3.51
170 171 3.012502 TGAGGGAGGGTGTTAGACTGTAT 59.987 47.826 0.00 0.00 0.00 2.29
171 172 4.031611 GAGGGAGGGTGTTAGACTGTATT 58.968 47.826 0.00 0.00 0.00 1.89
172 173 4.436079 AGGGAGGGTGTTAGACTGTATTT 58.564 43.478 0.00 0.00 0.00 1.40
173 174 5.596763 AGGGAGGGTGTTAGACTGTATTTA 58.403 41.667 0.00 0.00 0.00 1.40
174 175 5.424573 AGGGAGGGTGTTAGACTGTATTTAC 59.575 44.000 0.00 0.00 0.00 2.01
175 176 5.188359 GGGAGGGTGTTAGACTGTATTTACA 59.812 44.000 0.00 0.00 34.56 2.41
176 177 6.126854 GGGAGGGTGTTAGACTGTATTTACAT 60.127 42.308 0.00 0.00 35.36 2.29
177 178 6.761714 GGAGGGTGTTAGACTGTATTTACATG 59.238 42.308 0.00 0.00 35.36 3.21
178 179 7.253905 AGGGTGTTAGACTGTATTTACATGT 57.746 36.000 2.69 2.69 35.36 3.21
179 180 7.103641 AGGGTGTTAGACTGTATTTACATGTG 58.896 38.462 9.11 0.00 35.36 3.21
180 181 6.877322 GGGTGTTAGACTGTATTTACATGTGT 59.123 38.462 9.11 0.00 35.36 3.72
181 182 8.036575 GGGTGTTAGACTGTATTTACATGTGTA 58.963 37.037 9.11 0.00 35.36 2.90
182 183 9.595823 GGTGTTAGACTGTATTTACATGTGTAT 57.404 33.333 9.11 4.21 35.36 2.29
202 203 9.299963 TGTGTATATTGTAACGTTGTATACCAC 57.700 33.333 11.99 14.15 30.78 4.16
203 204 8.755018 GTGTATATTGTAACGTTGTATACCACC 58.245 37.037 11.99 6.07 30.78 4.61
204 205 8.694540 TGTATATTGTAACGTTGTATACCACCT 58.305 33.333 11.99 0.00 30.78 4.00
205 206 9.185192 GTATATTGTAACGTTGTATACCACCTC 57.815 37.037 11.99 0.00 0.00 3.85
206 207 5.465532 TTGTAACGTTGTATACCACCTCA 57.534 39.130 11.99 0.00 0.00 3.86
208 209 6.040209 TGTAACGTTGTATACCACCTCATT 57.960 37.500 11.99 0.00 0.00 2.57
209 210 7.167924 TGTAACGTTGTATACCACCTCATTA 57.832 36.000 11.99 0.00 0.00 1.90
211 212 8.911965 TGTAACGTTGTATACCACCTCATTATA 58.088 33.333 11.99 0.00 0.00 0.98
212 213 9.918630 GTAACGTTGTATACCACCTCATTATAT 57.081 33.333 11.99 0.00 0.00 0.86
228 229 9.935241 CCTCATTATATATATGTGTGATAGGCC 57.065 37.037 5.44 0.00 0.00 5.19
231 232 9.494271 CATTATATATATGTGTGATAGGCCACC 57.506 37.037 5.01 0.00 36.26 4.61
232 233 4.844349 ATATATGTGTGATAGGCCACCC 57.156 45.455 5.01 0.00 36.26 4.61
249 250 2.584608 CCTAGAGGGTTGTGCCGG 59.415 66.667 0.00 0.00 38.44 6.13
250 251 2.291043 CCTAGAGGGTTGTGCCGGT 61.291 63.158 1.90 0.00 38.44 5.28
251 252 1.677552 CTAGAGGGTTGTGCCGGTT 59.322 57.895 1.90 0.00 38.44 4.44
252 253 0.391263 CTAGAGGGTTGTGCCGGTTC 60.391 60.000 1.90 0.00 38.44 3.62
253 254 1.833787 TAGAGGGTTGTGCCGGTTCC 61.834 60.000 1.90 0.00 38.44 3.62
275 276 3.308832 CCCCCAAAGCCTATTGTCTTACA 60.309 47.826 0.00 0.00 0.00 2.41
276 277 3.947834 CCCCAAAGCCTATTGTCTTACAG 59.052 47.826 0.00 0.00 0.00 2.74
281 282 3.813443 AGCCTATTGTCTTACAGCCATG 58.187 45.455 0.00 0.00 0.00 3.66
289 290 2.096496 GTCTTACAGCCATGCACACATC 59.904 50.000 0.00 0.00 32.87 3.06
340 345 0.321564 TCTCCTCCATGTTTGTGCGG 60.322 55.000 0.00 0.00 0.00 5.69
345 350 0.179032 TCCATGTTTGTGCGGACTGT 60.179 50.000 8.99 0.00 0.00 3.55
368 373 0.759346 GTGCCGGTGATATCCCTTCT 59.241 55.000 1.90 0.00 0.00 2.85
371 376 1.717032 CCGGTGATATCCCTTCTCCA 58.283 55.000 0.00 0.00 0.00 3.86
372 377 1.344763 CCGGTGATATCCCTTCTCCAC 59.655 57.143 0.00 0.00 0.00 4.02
373 378 1.000163 CGGTGATATCCCTTCTCCACG 60.000 57.143 0.00 0.00 0.00 4.94
374 379 1.270358 GGTGATATCCCTTCTCCACGC 60.270 57.143 0.00 0.00 0.00 5.34
377 382 1.128188 ATATCCCTTCTCCACGCCCC 61.128 60.000 0.00 0.00 0.00 5.80
416 433 1.208535 CTGTCCGCCCCATAACACTAA 59.791 52.381 0.00 0.00 0.00 2.24
424 441 1.405797 CCCATAACACTAACCGCCGAA 60.406 52.381 0.00 0.00 0.00 4.30
427 444 1.008361 TAACACTAACCGCCGAACGC 61.008 55.000 0.00 0.00 41.76 4.84
450 467 0.684805 CTCCCTAGCTCCACCGAGTT 60.685 60.000 0.00 0.00 38.49 3.01
451 468 0.970937 TCCCTAGCTCCACCGAGTTG 60.971 60.000 0.00 0.00 38.49 3.16
627 648 3.753434 ACGCAGCTAGCACGCTCT 61.753 61.111 24.66 9.44 46.13 4.09
629 650 2.584694 GCAGCTAGCACGCTCTCC 60.585 66.667 18.83 0.00 44.79 3.71
630 651 3.074999 GCAGCTAGCACGCTCTCCT 62.075 63.158 18.83 0.00 44.79 3.69
709 742 1.139816 CCATCCATCGTCGACACACG 61.140 60.000 17.16 1.66 41.36 4.49
720 753 0.248907 CGACACACGACCTTGTCACT 60.249 55.000 0.00 0.00 45.77 3.41
722 755 0.248907 ACACACGACCTTGTCACTCG 60.249 55.000 0.00 0.00 32.09 4.18
754 801 2.684001 TAATTGGGAGTGCACCTACG 57.316 50.000 14.63 0.00 0.00 3.51
762 809 1.807573 GTGCACCTACGCTCTCTGC 60.808 63.158 5.22 0.00 38.57 4.26
784 858 0.680280 ACTGTACATCTCCGTCGCCT 60.680 55.000 0.00 0.00 0.00 5.52
796 870 3.565214 TCGCCTTCCTGCAACCCA 61.565 61.111 0.00 0.00 0.00 4.51
808 882 1.303317 CAACCCACACCCTGTAGCC 60.303 63.158 0.00 0.00 0.00 3.93
848 954 1.096416 GTGTCACTCTCCTACCTCCG 58.904 60.000 0.00 0.00 0.00 4.63
919 1061 0.933791 ACCCCTCCTCCTCCTCATCT 60.934 60.000 0.00 0.00 0.00 2.90
925 1067 1.219213 TCCTCCTCCTCATCTTCCTCC 59.781 57.143 0.00 0.00 0.00 4.30
929 1071 1.220236 CCTCCTCATCTTCCTCCTCCT 59.780 57.143 0.00 0.00 0.00 3.69
930 1072 2.360209 CCTCCTCATCTTCCTCCTCCTT 60.360 54.545 0.00 0.00 0.00 3.36
939 1081 5.060427 TCTTCCTCCTCCTTCTATCTCTG 57.940 47.826 0.00 0.00 0.00 3.35
954 1096 1.398739 TCTCTGTAGCTTTCGAGCTCG 59.601 52.381 30.03 30.03 45.00 5.03
976 1153 1.227089 CGTCCTCCTGATTCGGCTG 60.227 63.158 0.00 0.00 0.00 4.85
977 1154 1.901085 GTCCTCCTGATTCGGCTGT 59.099 57.895 0.00 0.00 0.00 4.40
978 1155 0.179097 GTCCTCCTGATTCGGCTGTC 60.179 60.000 0.00 0.00 0.00 3.51
979 1156 1.144936 CCTCCTGATTCGGCTGTCC 59.855 63.158 0.00 0.00 0.00 4.02
997 1174 4.445699 GGCAGCCCGTAGATCAAG 57.554 61.111 0.00 0.00 0.00 3.02
998 1175 1.823295 GGCAGCCCGTAGATCAAGA 59.177 57.895 0.00 0.00 0.00 3.02
1039 2432 4.559063 CGGAGATGCCCAGGCTGG 62.559 72.222 27.04 27.04 42.51 4.85
1059 2452 1.066502 GTGCTCAACCTCCTCTTCCTC 60.067 57.143 0.00 0.00 0.00 3.71
1150 2549 0.803117 CAGCTTCGACTACTCGGACA 59.197 55.000 0.00 0.00 40.58 4.02
1184 2583 4.003788 CTTCGCCGACCACCACCT 62.004 66.667 0.00 0.00 0.00 4.00
1188 2587 4.699522 GCCGACCACCACCTCCAC 62.700 72.222 0.00 0.00 0.00 4.02
1189 2588 3.238497 CCGACCACCACCTCCACA 61.238 66.667 0.00 0.00 0.00 4.17
1190 2589 2.030562 CGACCACCACCTCCACAC 59.969 66.667 0.00 0.00 0.00 3.82
1191 2590 2.030562 GACCACCACCTCCACACG 59.969 66.667 0.00 0.00 0.00 4.49
1197 2614 3.349006 CACCTCCACACGCAGCAC 61.349 66.667 0.00 0.00 0.00 4.40
1526 2952 1.667830 CGTCGTGATTGGCACTGGT 60.668 57.895 0.00 0.00 45.49 4.00
1528 2954 1.374125 TCGTGATTGGCACTGGTCG 60.374 57.895 0.00 0.00 45.49 4.79
1596 3025 0.471022 GGGATCCTGAGGAGAGGGTC 60.471 65.000 12.58 0.00 41.98 4.46
1714 3149 2.155155 GGCGTCGACATATTTTCCGATC 59.845 50.000 17.16 0.00 33.47 3.69
1715 3150 2.160143 GCGTCGACATATTTTCCGATCG 60.160 50.000 17.16 8.51 33.47 3.69
1806 3244 2.299013 GGTTGATTTGGGTTTGGACTCC 59.701 50.000 0.00 0.00 0.00 3.85
1863 3302 7.089770 ACAAGAAAGAAGAAAAGGAGAACAC 57.910 36.000 0.00 0.00 0.00 3.32
1864 3303 6.659242 ACAAGAAAGAAGAAAAGGAGAACACA 59.341 34.615 0.00 0.00 0.00 3.72
1865 3304 7.340487 ACAAGAAAGAAGAAAAGGAGAACACAT 59.660 33.333 0.00 0.00 0.00 3.21
1866 3305 7.269477 AGAAAGAAGAAAAGGAGAACACATG 57.731 36.000 0.00 0.00 0.00 3.21
1919 3370 1.492764 TAGAGGGGGTGAATCCGAAC 58.507 55.000 0.00 0.00 37.00 3.95
1920 3371 0.252742 AGAGGGGGTGAATCCGAACT 60.253 55.000 0.00 0.00 37.00 3.01
1921 3372 1.007963 AGAGGGGGTGAATCCGAACTA 59.992 52.381 0.00 0.00 37.00 2.24
1923 3374 2.237893 GAGGGGGTGAATCCGAACTAAA 59.762 50.000 0.00 0.00 37.00 1.85
1924 3375 2.850568 AGGGGGTGAATCCGAACTAAAT 59.149 45.455 0.00 0.00 37.00 1.40
1926 3377 3.211865 GGGGTGAATCCGAACTAAATCC 58.788 50.000 0.00 0.00 37.00 3.01
1927 3378 2.870411 GGGTGAATCCGAACTAAATCCG 59.130 50.000 0.00 0.00 37.00 4.18
1928 3379 3.528532 GGTGAATCCGAACTAAATCCGT 58.471 45.455 0.00 0.00 0.00 4.69
1929 3380 3.937079 GGTGAATCCGAACTAAATCCGTT 59.063 43.478 0.00 0.00 0.00 4.44
1930 3381 4.201783 GGTGAATCCGAACTAAATCCGTTG 60.202 45.833 0.00 0.00 0.00 4.10
1933 3384 6.091169 GTGAATCCGAACTAAATCCGTTGTTA 59.909 38.462 0.00 0.00 0.00 2.41
1935 3386 7.980662 TGAATCCGAACTAAATCCGTTGTTATA 59.019 33.333 0.00 0.00 0.00 0.98
1936 3387 8.721019 AATCCGAACTAAATCCGTTGTTATAA 57.279 30.769 0.00 0.00 0.00 0.98
1937 3388 7.760131 TCCGAACTAAATCCGTTGTTATAAG 57.240 36.000 0.00 0.00 0.00 1.73
1938 3389 6.757947 TCCGAACTAAATCCGTTGTTATAAGG 59.242 38.462 0.00 0.00 0.00 2.69
1940 3391 7.064966 CCGAACTAAATCCGTTGTTATAAGGTT 59.935 37.037 0.00 0.00 0.00 3.50
1944 3395 9.511272 ACTAAATCCGTTGTTATAAGGTTTTCT 57.489 29.630 2.45 0.00 30.88 2.52
1948 3399 9.687210 AATCCGTTGTTATAAGGTTTTCTTTTC 57.313 29.630 0.00 0.00 36.93 2.29
1949 3400 8.454570 TCCGTTGTTATAAGGTTTTCTTTTCT 57.545 30.769 0.00 0.00 36.93 2.52
1950 3401 8.905850 TCCGTTGTTATAAGGTTTTCTTTTCTT 58.094 29.630 0.00 0.00 36.93 2.52
1951 3402 9.524106 CCGTTGTTATAAGGTTTTCTTTTCTTT 57.476 29.630 0.00 0.00 36.93 2.52
1961 3412 9.739276 AAGGTTTTCTTTTCTTTTCCTTTTCAT 57.261 25.926 0.00 0.00 31.17 2.57
1962 3413 9.739276 AGGTTTTCTTTTCTTTTCCTTTTCATT 57.261 25.926 0.00 0.00 0.00 2.57
1963 3414 9.988350 GGTTTTCTTTTCTTTTCCTTTTCATTC 57.012 29.630 0.00 0.00 0.00 2.67
1964 3415 9.988350 GTTTTCTTTTCTTTTCCTTTTCATTCC 57.012 29.630 0.00 0.00 0.00 3.01
1965 3416 9.958180 TTTTCTTTTCTTTTCCTTTTCATTCCT 57.042 25.926 0.00 0.00 0.00 3.36
1966 3417 9.958180 TTTCTTTTCTTTTCCTTTTCATTCCTT 57.042 25.926 0.00 0.00 0.00 3.36
1967 3418 9.958180 TTCTTTTCTTTTCCTTTTCATTCCTTT 57.042 25.926 0.00 0.00 0.00 3.11
1968 3419 9.958180 TCTTTTCTTTTCCTTTTCATTCCTTTT 57.042 25.926 0.00 0.00 0.00 2.27
1970 3421 9.732130 TTTTCTTTTCCTTTTCATTCCTTTTCA 57.268 25.926 0.00 0.00 0.00 2.69
1971 3422 9.904198 TTTCTTTTCCTTTTCATTCCTTTTCAT 57.096 25.926 0.00 0.00 0.00 2.57
1972 3423 9.904198 TTCTTTTCCTTTTCATTCCTTTTCATT 57.096 25.926 0.00 0.00 0.00 2.57
1973 3424 9.546428 TCTTTTCCTTTTCATTCCTTTTCATTC 57.454 29.630 0.00 0.00 0.00 2.67
1974 3425 9.551734 CTTTTCCTTTTCATTCCTTTTCATTCT 57.448 29.630 0.00 0.00 0.00 2.40
1975 3426 9.904198 TTTTCCTTTTCATTCCTTTTCATTCTT 57.096 25.926 0.00 0.00 0.00 2.52
1976 3427 8.891671 TTCCTTTTCATTCCTTTTCATTCTTG 57.108 30.769 0.00 0.00 0.00 3.02
1977 3428 8.021898 TCCTTTTCATTCCTTTTCATTCTTGT 57.978 30.769 0.00 0.00 0.00 3.16
1978 3429 8.485392 TCCTTTTCATTCCTTTTCATTCTTGTT 58.515 29.630 0.00 0.00 0.00 2.83
1979 3430 9.762933 CCTTTTCATTCCTTTTCATTCTTGTTA 57.237 29.630 0.00 0.00 0.00 2.41
2004 3455 5.397142 AGGTTTCATTTTCATTCCAGAGC 57.603 39.130 0.00 0.00 0.00 4.09
2005 3456 4.834496 AGGTTTCATTTTCATTCCAGAGCA 59.166 37.500 0.00 0.00 0.00 4.26
2006 3457 5.305128 AGGTTTCATTTTCATTCCAGAGCAA 59.695 36.000 0.00 0.00 0.00 3.91
2007 3458 5.406477 GGTTTCATTTTCATTCCAGAGCAAC 59.594 40.000 0.00 0.00 0.00 4.17
2008 3459 5.787953 TTCATTTTCATTCCAGAGCAACA 57.212 34.783 0.00 0.00 0.00 3.33
2009 3460 5.988310 TCATTTTCATTCCAGAGCAACAT 57.012 34.783 0.00 0.00 0.00 2.71
2010 3461 5.957798 TCATTTTCATTCCAGAGCAACATC 58.042 37.500 0.00 0.00 0.00 3.06
2208 3669 5.300752 CCCTGTGGTAGCATACATAGAAAG 58.699 45.833 0.00 0.00 45.43 2.62
2215 3676 7.928706 GTGGTAGCATACATAGAAAGTCTGAAT 59.071 37.037 0.00 0.00 45.43 2.57
2225 3686 9.831737 ACATAGAAAGTCTGAATTTTGAATTCG 57.168 29.630 4.47 4.69 0.00 3.34
2244 3705 2.887889 TTGTACGGTTGCTGCGTGC 61.888 57.895 0.00 0.00 43.25 5.34
2246 3707 4.308458 TACGGTTGCTGCGTGCCT 62.308 61.111 0.00 0.00 42.00 4.75
2303 3992 6.856757 ACAGAATTCCCTGGCAAATATCTAT 58.143 36.000 0.65 0.00 38.44 1.98
2309 3998 3.120199 CCCTGGCAAATATCTATTTCGCG 60.120 47.826 0.00 0.00 33.88 5.87
2336 4025 2.535934 TAATCCGTTTGCGATGTTGC 57.464 45.000 0.00 0.00 41.33 4.17
2342 4040 1.791555 CGTTTGCGATGTTGCTCCATC 60.792 52.381 6.21 6.21 41.33 3.51
2368 4066 4.859304 AGCCGTTACATCATCGGTTATA 57.141 40.909 0.00 0.00 45.11 0.98
2456 4156 7.501559 AGATGTCATATAAAGCTGAATGCAACT 59.498 33.333 0.00 0.00 45.94 3.16
2505 4205 7.768120 GCCATCTCAGATCAATAGTATAAAGGG 59.232 40.741 0.00 0.00 0.00 3.95
2509 4209 9.883293 TCTCAGATCAATAGTATAAAGGGAAGA 57.117 33.333 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.430546 AGTTGCTTCTGAGAGACACG 57.569 50.000 0.00 0.00 0.00 4.49
2 3 4.022762 TCTGTAGTTGCTTCTGAGAGACAC 60.023 45.833 0.00 0.00 0.00 3.67
3 4 4.145052 TCTGTAGTTGCTTCTGAGAGACA 58.855 43.478 0.00 0.00 0.00 3.41
4 5 4.775058 TCTGTAGTTGCTTCTGAGAGAC 57.225 45.455 0.00 0.00 0.00 3.36
5 6 5.012893 TGATCTGTAGTTGCTTCTGAGAGA 58.987 41.667 0.00 0.00 0.00 3.10
6 7 5.321959 TGATCTGTAGTTGCTTCTGAGAG 57.678 43.478 0.00 0.00 0.00 3.20
7 8 5.244851 ACTTGATCTGTAGTTGCTTCTGAGA 59.755 40.000 0.00 0.00 0.00 3.27
8 9 5.477510 ACTTGATCTGTAGTTGCTTCTGAG 58.522 41.667 0.00 0.00 0.00 3.35
9 10 5.474578 ACTTGATCTGTAGTTGCTTCTGA 57.525 39.130 0.00 0.00 0.00 3.27
10 11 6.551385 AAACTTGATCTGTAGTTGCTTCTG 57.449 37.500 8.52 0.00 34.95 3.02
12 13 9.548208 GAAATAAACTTGATCTGTAGTTGCTTC 57.452 33.333 8.52 8.16 34.95 3.86
13 14 9.289782 AGAAATAAACTTGATCTGTAGTTGCTT 57.710 29.630 8.52 4.47 34.95 3.91
15 16 9.548208 GAAGAAATAAACTTGATCTGTAGTTGC 57.452 33.333 8.52 0.00 34.95 4.17
17 18 9.793259 TGGAAGAAATAAACTTGATCTGTAGTT 57.207 29.630 0.00 0.00 36.20 2.24
18 19 9.793259 TTGGAAGAAATAAACTTGATCTGTAGT 57.207 29.630 0.00 0.00 0.00 2.73
20 21 9.231297 CCTTGGAAGAAATAAACTTGATCTGTA 57.769 33.333 0.00 0.00 0.00 2.74
21 22 7.944554 TCCTTGGAAGAAATAAACTTGATCTGT 59.055 33.333 0.00 0.00 0.00 3.41
22 23 8.340618 TCCTTGGAAGAAATAAACTTGATCTG 57.659 34.615 0.00 0.00 0.00 2.90
23 24 9.183368 GATCCTTGGAAGAAATAAACTTGATCT 57.817 33.333 0.00 0.00 0.00 2.75
24 25 8.960591 TGATCCTTGGAAGAAATAAACTTGATC 58.039 33.333 0.00 0.00 0.00 2.92
26 27 8.576442 GTTGATCCTTGGAAGAAATAAACTTGA 58.424 33.333 0.00 0.00 0.00 3.02
27 28 8.579863 AGTTGATCCTTGGAAGAAATAAACTTG 58.420 33.333 0.00 0.00 27.30 3.16
28 29 8.712228 AGTTGATCCTTGGAAGAAATAAACTT 57.288 30.769 0.00 0.00 27.30 2.66
29 30 8.579863 CAAGTTGATCCTTGGAAGAAATAAACT 58.420 33.333 0.00 0.00 38.51 2.66
30 31 7.329471 GCAAGTTGATCCTTGGAAGAAATAAAC 59.671 37.037 7.16 0.00 41.70 2.01
33 34 6.151648 CAGCAAGTTGATCCTTGGAAGAAATA 59.848 38.462 7.16 0.00 41.70 1.40
34 35 5.047519 CAGCAAGTTGATCCTTGGAAGAAAT 60.048 40.000 7.16 0.00 41.70 2.17
37 38 3.072915 TCAGCAAGTTGATCCTTGGAAGA 59.927 43.478 7.16 0.00 41.70 2.87
40 41 2.106338 TGTCAGCAAGTTGATCCTTGGA 59.894 45.455 7.16 0.00 41.70 3.53
41 42 2.507484 TGTCAGCAAGTTGATCCTTGG 58.493 47.619 7.16 0.00 41.70 3.61
42 43 4.008330 AGATGTCAGCAAGTTGATCCTTG 58.992 43.478 7.16 7.21 43.76 3.61
43 44 4.298103 AGATGTCAGCAAGTTGATCCTT 57.702 40.909 7.16 0.00 0.00 3.36
44 45 3.996921 AGATGTCAGCAAGTTGATCCT 57.003 42.857 7.16 0.00 0.00 3.24
46 47 4.967437 GTGAAGATGTCAGCAAGTTGATC 58.033 43.478 7.16 0.06 36.74 2.92
56 57 2.189594 TGGCTTGGTGAAGATGTCAG 57.810 50.000 0.00 0.00 36.74 3.51
57 58 2.821378 CAATGGCTTGGTGAAGATGTCA 59.179 45.455 0.00 0.00 0.00 3.58
58 59 2.416431 GCAATGGCTTGGTGAAGATGTC 60.416 50.000 0.00 0.00 36.96 3.06
59 60 1.547372 GCAATGGCTTGGTGAAGATGT 59.453 47.619 0.00 0.00 36.96 3.06
60 61 1.134907 GGCAATGGCTTGGTGAAGATG 60.135 52.381 0.00 0.00 40.87 2.90
61 62 1.188863 GGCAATGGCTTGGTGAAGAT 58.811 50.000 0.00 0.00 40.87 2.40
62 63 0.112995 AGGCAATGGCTTGGTGAAGA 59.887 50.000 2.53 0.00 40.87 2.87
63 64 0.971386 AAGGCAATGGCTTGGTGAAG 59.029 50.000 21.46 0.00 46.51 3.02
71 72 1.823169 CTGTGGCAAAGGCAATGGCT 61.823 55.000 2.53 2.53 43.24 4.75
72 73 1.375013 CTGTGGCAAAGGCAATGGC 60.375 57.895 0.00 0.00 43.71 4.40
74 75 1.868498 CAAACTGTGGCAAAGGCAATG 59.132 47.619 9.97 0.00 43.71 2.82
77 78 0.746063 CTCAAACTGTGGCAAAGGCA 59.254 50.000 9.97 0.00 43.71 4.75
79 80 2.301346 AGTCTCAAACTGTGGCAAAGG 58.699 47.619 9.97 0.00 36.65 3.11
80 81 3.699067 CAAGTCTCAAACTGTGGCAAAG 58.301 45.455 2.28 2.28 38.58 2.77
83 84 1.024271 GCAAGTCTCAAACTGTGGCA 58.976 50.000 0.00 0.00 38.58 4.92
84 85 1.002033 CTGCAAGTCTCAAACTGTGGC 60.002 52.381 0.00 0.00 38.58 5.01
85 86 1.605710 CCTGCAAGTCTCAAACTGTGG 59.394 52.381 0.00 0.00 38.58 4.17
87 88 1.312815 GCCTGCAAGTCTCAAACTGT 58.687 50.000 0.00 0.00 38.58 3.55
89 90 1.510480 GCGCCTGCAAGTCTCAAACT 61.510 55.000 0.00 0.00 42.15 2.66
90 91 1.081840 GCGCCTGCAAGTCTCAAAC 60.082 57.895 0.00 0.00 42.15 2.93
91 92 3.343972 GCGCCTGCAAGTCTCAAA 58.656 55.556 0.00 0.00 42.15 2.69
101 102 1.032114 AAGGGTAAGATTGCGCCTGC 61.032 55.000 4.18 0.00 43.20 4.85
102 103 1.017387 GAAGGGTAAGATTGCGCCTG 58.983 55.000 4.18 0.00 0.00 4.85
103 104 0.912486 AGAAGGGTAAGATTGCGCCT 59.088 50.000 4.18 0.00 0.00 5.52
104 105 2.102588 TCTAGAAGGGTAAGATTGCGCC 59.897 50.000 4.18 0.00 0.00 6.53
105 106 3.454371 TCTAGAAGGGTAAGATTGCGC 57.546 47.619 0.00 0.00 0.00 6.09
106 107 5.601662 TGAATCTAGAAGGGTAAGATTGCG 58.398 41.667 0.00 0.00 39.46 4.85
107 108 9.213799 CTAATGAATCTAGAAGGGTAAGATTGC 57.786 37.037 0.00 0.00 39.46 3.56
114 115 8.705594 CCACTTTCTAATGAATCTAGAAGGGTA 58.294 37.037 0.00 0.00 37.00 3.69
115 116 7.569240 CCACTTTCTAATGAATCTAGAAGGGT 58.431 38.462 0.00 2.45 37.00 4.34
116 117 6.484977 GCCACTTTCTAATGAATCTAGAAGGG 59.515 42.308 0.00 5.17 37.00 3.95
117 118 7.278875 AGCCACTTTCTAATGAATCTAGAAGG 58.721 38.462 0.00 1.61 36.87 3.46
118 119 9.823647 TTAGCCACTTTCTAATGAATCTAGAAG 57.176 33.333 0.00 0.00 36.87 2.85
119 120 9.823647 CTTAGCCACTTTCTAATGAATCTAGAA 57.176 33.333 0.00 0.00 34.35 2.10
120 121 9.201989 TCTTAGCCACTTTCTAATGAATCTAGA 57.798 33.333 0.00 0.00 31.56 2.43
121 122 9.995003 ATCTTAGCCACTTTCTAATGAATCTAG 57.005 33.333 0.00 0.00 31.56 2.43
123 124 9.118300 CAATCTTAGCCACTTTCTAATGAATCT 57.882 33.333 0.00 0.00 31.56 2.40
126 127 7.554118 CCTCAATCTTAGCCACTTTCTAATGAA 59.446 37.037 0.00 0.00 0.00 2.57
127 128 7.050377 CCTCAATCTTAGCCACTTTCTAATGA 58.950 38.462 0.00 0.00 0.00 2.57
128 129 6.261826 CCCTCAATCTTAGCCACTTTCTAATG 59.738 42.308 0.00 0.00 0.00 1.90
129 130 6.158695 TCCCTCAATCTTAGCCACTTTCTAAT 59.841 38.462 0.00 0.00 0.00 1.73
130 131 5.487488 TCCCTCAATCTTAGCCACTTTCTAA 59.513 40.000 0.00 0.00 0.00 2.10
133 134 4.195416 CTCCCTCAATCTTAGCCACTTTC 58.805 47.826 0.00 0.00 0.00 2.62
134 135 3.054065 CCTCCCTCAATCTTAGCCACTTT 60.054 47.826 0.00 0.00 0.00 2.66
135 136 2.507471 CCTCCCTCAATCTTAGCCACTT 59.493 50.000 0.00 0.00 0.00 3.16
137 138 1.141858 CCCTCCCTCAATCTTAGCCAC 59.858 57.143 0.00 0.00 0.00 5.01
138 139 1.274416 ACCCTCCCTCAATCTTAGCCA 60.274 52.381 0.00 0.00 0.00 4.75
139 140 1.141858 CACCCTCCCTCAATCTTAGCC 59.858 57.143 0.00 0.00 0.00 3.93
140 141 1.840635 ACACCCTCCCTCAATCTTAGC 59.159 52.381 0.00 0.00 0.00 3.09
142 143 4.715297 GTCTAACACCCTCCCTCAATCTTA 59.285 45.833 0.00 0.00 0.00 2.10
143 144 3.519913 GTCTAACACCCTCCCTCAATCTT 59.480 47.826 0.00 0.00 0.00 2.40
144 145 3.108376 GTCTAACACCCTCCCTCAATCT 58.892 50.000 0.00 0.00 0.00 2.40
145 146 3.108376 AGTCTAACACCCTCCCTCAATC 58.892 50.000 0.00 0.00 0.00 2.67
146 147 2.840651 CAGTCTAACACCCTCCCTCAAT 59.159 50.000 0.00 0.00 0.00 2.57
147 148 2.257207 CAGTCTAACACCCTCCCTCAA 58.743 52.381 0.00 0.00 0.00 3.02
148 149 1.149288 ACAGTCTAACACCCTCCCTCA 59.851 52.381 0.00 0.00 0.00 3.86
149 150 1.939980 ACAGTCTAACACCCTCCCTC 58.060 55.000 0.00 0.00 0.00 4.30
150 151 3.778622 ATACAGTCTAACACCCTCCCT 57.221 47.619 0.00 0.00 0.00 4.20
151 152 4.838904 AAATACAGTCTAACACCCTCCC 57.161 45.455 0.00 0.00 0.00 4.30
153 154 7.277981 CACATGTAAATACAGTCTAACACCCTC 59.722 40.741 0.00 0.00 39.92 4.30
154 155 7.103641 CACATGTAAATACAGTCTAACACCCT 58.896 38.462 0.00 0.00 39.92 4.34
155 156 6.877322 ACACATGTAAATACAGTCTAACACCC 59.123 38.462 0.00 0.00 39.92 4.61
156 157 7.900782 ACACATGTAAATACAGTCTAACACC 57.099 36.000 0.00 0.00 39.92 4.16
176 177 9.299963 GTGGTATACAACGTTACAATATACACA 57.700 33.333 20.89 16.35 32.62 3.72
177 178 8.755018 GGTGGTATACAACGTTACAATATACAC 58.245 37.037 20.89 18.40 32.62 2.90
178 179 8.694540 AGGTGGTATACAACGTTACAATATACA 58.305 33.333 20.89 12.28 43.31 2.29
179 180 9.185192 GAGGTGGTATACAACGTTACAATATAC 57.815 37.037 7.03 10.70 43.31 1.47
180 181 8.911965 TGAGGTGGTATACAACGTTACAATATA 58.088 33.333 7.03 0.00 43.31 0.86
181 182 7.784037 TGAGGTGGTATACAACGTTACAATAT 58.216 34.615 7.03 0.00 43.31 1.28
182 183 7.167924 TGAGGTGGTATACAACGTTACAATA 57.832 36.000 7.03 0.00 43.31 1.90
183 184 6.040209 TGAGGTGGTATACAACGTTACAAT 57.960 37.500 7.03 0.00 43.31 2.71
184 185 5.465532 TGAGGTGGTATACAACGTTACAA 57.534 39.130 7.03 0.00 43.31 2.41
185 186 5.664294 ATGAGGTGGTATACAACGTTACA 57.336 39.130 7.03 2.59 43.31 2.41
186 187 9.918630 ATATAATGAGGTGGTATACAACGTTAC 57.081 33.333 7.03 0.00 43.31 2.50
202 203 9.935241 GGCCTATCACACATATATATAATGAGG 57.065 37.037 12.18 9.70 0.00 3.86
205 206 9.494271 GGTGGCCTATCACACATATATATAATG 57.506 37.037 3.32 1.65 39.31 1.90
206 207 8.660435 GGGTGGCCTATCACACATATATATAAT 58.340 37.037 3.32 0.00 40.56 1.28
208 209 6.557253 GGGGTGGCCTATCACACATATATATA 59.443 42.308 3.32 0.00 42.50 0.86
209 210 5.369699 GGGGTGGCCTATCACACATATATAT 59.630 44.000 3.32 0.00 42.50 0.86
211 212 3.523564 GGGGTGGCCTATCACACATATAT 59.476 47.826 3.32 0.00 42.50 0.86
212 213 2.910319 GGGGTGGCCTATCACACATATA 59.090 50.000 3.32 0.00 42.50 0.86
213 214 1.705186 GGGGTGGCCTATCACACATAT 59.295 52.381 3.32 0.00 42.50 1.78
215 216 0.624500 AGGGGTGGCCTATCACACAT 60.625 55.000 3.32 0.00 42.50 3.21
217 218 0.759346 CTAGGGGTGGCCTATCACAC 59.241 60.000 3.32 0.00 40.15 3.82
218 219 0.639943 TCTAGGGGTGGCCTATCACA 59.360 55.000 3.32 0.00 39.27 3.58
219 220 1.343069 CTCTAGGGGTGGCCTATCAC 58.657 60.000 3.32 0.00 36.95 3.06
221 222 3.074788 CCTCTAGGGGTGGCCTATC 57.925 63.158 3.32 0.00 0.00 2.08
232 233 1.838073 AACCGGCACAACCCTCTAGG 61.838 60.000 0.00 0.00 43.78 3.02
235 236 2.430367 GAACCGGCACAACCCTCT 59.570 61.111 0.00 0.00 33.26 3.69
237 238 4.280019 GGGAACCGGCACAACCCT 62.280 66.667 0.00 0.00 40.86 4.34
253 254 2.532250 AAGACAATAGGCTTTGGGGG 57.468 50.000 0.00 0.00 0.00 5.40
255 256 3.378427 GCTGTAAGACAATAGGCTTTGGG 59.622 47.826 0.00 0.00 34.07 4.12
256 257 3.378427 GGCTGTAAGACAATAGGCTTTGG 59.622 47.826 0.00 0.00 46.27 3.28
257 258 4.622701 GGCTGTAAGACAATAGGCTTTG 57.377 45.455 0.00 0.00 46.27 2.77
270 271 1.063027 CGATGTGTGCATGGCTGTAAG 59.937 52.381 0.00 0.00 35.07 2.34
271 272 1.085893 CGATGTGTGCATGGCTGTAA 58.914 50.000 0.00 0.00 35.07 2.41
275 276 0.742281 GTCTCGATGTGTGCATGGCT 60.742 55.000 0.00 0.00 35.07 4.75
276 277 1.020861 TGTCTCGATGTGTGCATGGC 61.021 55.000 0.00 0.00 35.07 4.40
281 282 1.790387 GGCTTGTCTCGATGTGTGC 59.210 57.895 0.00 0.00 0.00 4.57
289 290 3.197790 CATGGGCGGCTTGTCTCG 61.198 66.667 9.56 0.00 0.00 4.04
312 317 3.728305 ATGGAGGAGAGGGCCCTGG 62.728 68.421 34.59 0.00 33.36 4.45
314 319 2.040043 CATGGAGGAGAGGGCCCT 60.040 66.667 29.18 29.18 36.57 5.19
320 325 1.081892 CGCACAAACATGGAGGAGAG 58.918 55.000 0.00 0.00 0.00 3.20
345 350 2.108157 GATATCACCGGCACCGCA 59.892 61.111 0.00 0.00 38.24 5.69
355 360 1.270358 GGCGTGGAGAAGGGATATCAC 60.270 57.143 4.83 0.00 0.00 3.06
381 386 2.987149 CGGACAGAATATACACGGATGC 59.013 50.000 0.00 0.00 0.00 3.91
383 388 2.029290 GGCGGACAGAATATACACGGAT 60.029 50.000 0.00 0.00 0.00 4.18
386 391 1.604693 GGGGCGGACAGAATATACACG 60.605 57.143 0.00 0.00 0.00 4.49
387 392 1.414919 TGGGGCGGACAGAATATACAC 59.585 52.381 0.00 0.00 0.00 2.90
389 394 4.251268 GTTATGGGGCGGACAGAATATAC 58.749 47.826 0.00 0.00 0.00 1.47
392 397 2.120312 TGTTATGGGGCGGACAGAATA 58.880 47.619 0.00 0.00 0.00 1.75
433 450 1.517832 CAACTCGGTGGAGCTAGGG 59.482 63.158 0.00 0.00 44.48 3.53
434 451 1.153549 GCAACTCGGTGGAGCTAGG 60.154 63.158 0.00 0.00 44.48 3.02
435 452 0.459237 CTGCAACTCGGTGGAGCTAG 60.459 60.000 0.00 0.00 44.48 3.42
450 467 1.824760 ACATGTGCACAGTGCTGCA 60.825 52.632 25.84 22.67 45.31 4.41
451 468 1.371267 CACATGTGCACAGTGCTGC 60.371 57.895 25.84 18.18 45.31 5.25
627 648 0.182775 TCGTCGATGGATGGAGAGGA 59.817 55.000 4.48 0.00 0.00 3.71
629 650 2.344504 CATCGTCGATGGATGGAGAG 57.655 55.000 24.59 0.00 38.07 3.20
709 742 2.355837 TGCGCGAGTGACAAGGTC 60.356 61.111 12.10 0.00 0.00 3.85
720 753 3.181505 CCCAATTAATTAACTGTGCGCGA 60.182 43.478 12.10 0.00 0.00 5.87
722 755 4.142469 ACTCCCAATTAATTAACTGTGCGC 60.142 41.667 0.00 0.00 0.00 6.09
754 801 0.539051 ATGTACAGTGGGCAGAGAGC 59.461 55.000 0.33 0.00 44.65 4.09
762 809 0.100682 CGACGGAGATGTACAGTGGG 59.899 60.000 0.33 0.00 0.00 4.61
784 858 2.197324 GGGTGTGGGTTGCAGGAA 59.803 61.111 0.00 0.00 0.00 3.36
796 870 2.237392 GAGAAATGAGGCTACAGGGTGT 59.763 50.000 0.00 0.00 0.00 4.16
808 882 3.133721 ACAAGGAGGGATCGAGAAATGAG 59.866 47.826 0.00 0.00 0.00 2.90
848 954 3.588210 AGCTAGAGGTAGAAGGAGGAC 57.412 52.381 0.00 0.00 0.00 3.85
919 1061 4.890499 ACAGAGATAGAAGGAGGAGGAA 57.110 45.455 0.00 0.00 0.00 3.36
925 1067 5.529430 TCGAAAGCTACAGAGATAGAAGGAG 59.471 44.000 0.00 0.00 0.00 3.69
929 1071 5.176407 GCTCGAAAGCTACAGAGATAGAA 57.824 43.478 14.13 0.00 45.55 2.10
930 1072 4.822036 GCTCGAAAGCTACAGAGATAGA 57.178 45.455 14.13 0.00 45.55 1.98
954 1096 0.179108 CCGAATCAGGAGGACGAACC 60.179 60.000 0.00 0.00 39.35 3.62
976 1153 3.501458 GATCTACGGGCTGCCGGAC 62.501 68.421 29.90 8.27 37.53 4.79
977 1154 3.224324 GATCTACGGGCTGCCGGA 61.224 66.667 29.90 16.83 37.53 5.14
978 1155 2.978452 CTTGATCTACGGGCTGCCGG 62.978 65.000 22.90 22.90 37.53 6.13
979 1156 1.592669 CTTGATCTACGGGCTGCCG 60.593 63.158 13.40 10.64 39.31 5.69
980 1157 0.178068 TTCTTGATCTACGGGCTGCC 59.822 55.000 11.05 11.05 0.00 4.85
981 1158 2.024176 TTTCTTGATCTACGGGCTGC 57.976 50.000 0.00 0.00 0.00 5.25
982 1159 2.874701 CCATTTCTTGATCTACGGGCTG 59.125 50.000 0.00 0.00 0.00 4.85
985 1162 2.172717 ACCCCATTTCTTGATCTACGGG 59.827 50.000 0.00 0.00 0.00 5.28
986 1163 3.560636 ACCCCATTTCTTGATCTACGG 57.439 47.619 0.00 0.00 0.00 4.02
987 1164 3.877508 GGAACCCCATTTCTTGATCTACG 59.122 47.826 0.00 0.00 0.00 3.51
1039 2432 0.980423 AGGAAGAGGAGGTTGAGCAC 59.020 55.000 0.00 0.00 0.00 4.40
1154 2553 2.278013 CGAAGTAGGCGTCGGAGC 60.278 66.667 0.00 0.00 41.61 4.70
1156 2555 3.818787 GGCGAAGTAGGCGTCGGA 61.819 66.667 5.28 0.00 44.55 4.55
1184 2583 4.927782 GGTGGTGCTGCGTGTGGA 62.928 66.667 0.00 0.00 0.00 4.02
1191 2590 4.927782 TGGTCGTGGTGGTGCTGC 62.928 66.667 0.00 0.00 0.00 5.25
1526 2952 3.744719 CACCCCGAACGAGCTCGA 61.745 66.667 40.58 0.00 41.44 4.04
1528 2954 4.070552 AGCACCCCGAACGAGCTC 62.071 66.667 2.73 2.73 0.00 4.09
1701 3136 1.165270 GGGGGCGATCGGAAAATATG 58.835 55.000 18.30 0.00 0.00 1.78
1715 3150 4.247380 CTCTCCATGCGAGGGGGC 62.247 72.222 10.23 0.00 39.30 5.80
1806 3244 2.430465 CTCTGGACACCAACTCCATTG 58.570 52.381 0.00 0.00 37.18 2.82
1813 3251 1.537202 GATGTTGCTCTGGACACCAAC 59.463 52.381 0.00 0.00 38.36 3.77
1823 3261 7.568349 TCTTTCTTGTATATGGATGTTGCTCT 58.432 34.615 0.00 0.00 0.00 4.09
1825 3263 8.049117 TCTTCTTTCTTGTATATGGATGTTGCT 58.951 33.333 0.00 0.00 0.00 3.91
1866 3305 9.900710 CCACTAATCTAAGTCTGATGTACATAC 57.099 37.037 8.71 3.62 0.00 2.39
1923 3374 9.074576 AGAAAAGAAAACCTTATAACAACGGAT 57.925 29.630 0.00 0.00 34.00 4.18
1924 3375 8.454570 AGAAAAGAAAACCTTATAACAACGGA 57.545 30.769 0.00 0.00 34.00 4.69
1935 3386 9.739276 ATGAAAAGGAAAAGAAAAGAAAACCTT 57.261 25.926 0.00 0.00 37.99 3.50
1936 3387 9.739276 AATGAAAAGGAAAAGAAAAGAAAACCT 57.261 25.926 0.00 0.00 0.00 3.50
1937 3388 9.988350 GAATGAAAAGGAAAAGAAAAGAAAACC 57.012 29.630 0.00 0.00 0.00 3.27
1938 3389 9.988350 GGAATGAAAAGGAAAAGAAAAGAAAAC 57.012 29.630 0.00 0.00 0.00 2.43
1940 3391 9.958180 AAGGAATGAAAAGGAAAAGAAAAGAAA 57.042 25.926 0.00 0.00 0.00 2.52
1944 3395 9.732130 TGAAAAGGAATGAAAAGGAAAAGAAAA 57.268 25.926 0.00 0.00 0.00 2.29
1945 3396 9.904198 ATGAAAAGGAATGAAAAGGAAAAGAAA 57.096 25.926 0.00 0.00 0.00 2.52
1946 3397 9.904198 AATGAAAAGGAATGAAAAGGAAAAGAA 57.096 25.926 0.00 0.00 0.00 2.52
1947 3398 9.546428 GAATGAAAAGGAATGAAAAGGAAAAGA 57.454 29.630 0.00 0.00 0.00 2.52
1948 3399 9.551734 AGAATGAAAAGGAATGAAAAGGAAAAG 57.448 29.630 0.00 0.00 0.00 2.27
1949 3400 9.904198 AAGAATGAAAAGGAATGAAAAGGAAAA 57.096 25.926 0.00 0.00 0.00 2.29
1950 3401 9.328845 CAAGAATGAAAAGGAATGAAAAGGAAA 57.671 29.630 0.00 0.00 0.00 3.13
1951 3402 8.485392 ACAAGAATGAAAAGGAATGAAAAGGAA 58.515 29.630 0.00 0.00 0.00 3.36
1952 3403 8.021898 ACAAGAATGAAAAGGAATGAAAAGGA 57.978 30.769 0.00 0.00 0.00 3.36
1953 3404 8.667076 AACAAGAATGAAAAGGAATGAAAAGG 57.333 30.769 0.00 0.00 0.00 3.11
1978 3429 8.686334 GCTCTGGAATGAAAATGAAACCTTATA 58.314 33.333 0.00 0.00 0.00 0.98
1979 3430 7.178983 TGCTCTGGAATGAAAATGAAACCTTAT 59.821 33.333 0.00 0.00 0.00 1.73
1980 3431 6.493115 TGCTCTGGAATGAAAATGAAACCTTA 59.507 34.615 0.00 0.00 0.00 2.69
1981 3432 5.305128 TGCTCTGGAATGAAAATGAAACCTT 59.695 36.000 0.00 0.00 0.00 3.50
1982 3433 4.834496 TGCTCTGGAATGAAAATGAAACCT 59.166 37.500 0.00 0.00 0.00 3.50
1983 3434 5.138125 TGCTCTGGAATGAAAATGAAACC 57.862 39.130 0.00 0.00 0.00 3.27
1984 3435 5.984926 TGTTGCTCTGGAATGAAAATGAAAC 59.015 36.000 0.00 0.00 0.00 2.78
1985 3436 6.159299 TGTTGCTCTGGAATGAAAATGAAA 57.841 33.333 0.00 0.00 0.00 2.69
1986 3437 5.787953 TGTTGCTCTGGAATGAAAATGAA 57.212 34.783 0.00 0.00 0.00 2.57
1987 3438 5.392272 CGATGTTGCTCTGGAATGAAAATGA 60.392 40.000 0.00 0.00 0.00 2.57
1988 3439 4.796830 CGATGTTGCTCTGGAATGAAAATG 59.203 41.667 0.00 0.00 0.00 2.32
1989 3440 4.676196 GCGATGTTGCTCTGGAATGAAAAT 60.676 41.667 0.00 0.00 0.00 1.82
1990 3441 3.366273 GCGATGTTGCTCTGGAATGAAAA 60.366 43.478 0.00 0.00 0.00 2.29
1991 3442 2.162208 GCGATGTTGCTCTGGAATGAAA 59.838 45.455 0.00 0.00 0.00 2.69
1992 3443 1.739466 GCGATGTTGCTCTGGAATGAA 59.261 47.619 0.00 0.00 0.00 2.57
1993 3444 1.065926 AGCGATGTTGCTCTGGAATGA 60.066 47.619 0.00 0.00 42.95 2.57
1994 3445 1.376543 AGCGATGTTGCTCTGGAATG 58.623 50.000 0.00 0.00 42.95 2.67
1995 3446 2.119801 AAGCGATGTTGCTCTGGAAT 57.880 45.000 0.00 0.00 46.60 3.01
1996 3447 1.896220 AAAGCGATGTTGCTCTGGAA 58.104 45.000 0.00 0.00 46.60 3.53
1997 3448 1.806542 GAAAAGCGATGTTGCTCTGGA 59.193 47.619 0.00 0.00 46.60 3.86
1998 3449 1.808945 AGAAAAGCGATGTTGCTCTGG 59.191 47.619 0.00 0.00 46.60 3.86
1999 3450 3.549299 AAGAAAAGCGATGTTGCTCTG 57.451 42.857 0.00 0.00 46.60 3.35
2000 3451 4.540824 GAAAAGAAAAGCGATGTTGCTCT 58.459 39.130 0.00 0.00 46.60 4.09
2001 3452 3.670523 GGAAAAGAAAAGCGATGTTGCTC 59.329 43.478 0.00 0.00 46.60 4.26
2003 3454 3.642705 AGGAAAAGAAAAGCGATGTTGC 58.357 40.909 0.00 0.00 0.00 4.17
2004 3455 6.255453 TGAAAAGGAAAAGAAAAGCGATGTTG 59.745 34.615 0.00 0.00 0.00 3.33
2005 3456 6.337356 TGAAAAGGAAAAGAAAAGCGATGTT 58.663 32.000 0.00 0.00 0.00 2.71
2006 3457 5.901552 TGAAAAGGAAAAGAAAAGCGATGT 58.098 33.333 0.00 0.00 0.00 3.06
2007 3458 7.383300 AGAATGAAAAGGAAAAGAAAAGCGATG 59.617 33.333 0.00 0.00 0.00 3.84
2008 3459 7.436933 AGAATGAAAAGGAAAAGAAAAGCGAT 58.563 30.769 0.00 0.00 0.00 4.58
2009 3460 6.805713 AGAATGAAAAGGAAAAGAAAAGCGA 58.194 32.000 0.00 0.00 0.00 4.93
2010 3461 7.010460 ACAAGAATGAAAAGGAAAAGAAAAGCG 59.990 33.333 0.00 0.00 0.00 4.68
2177 3638 3.576078 TGCTACCACAGGGGATAAATG 57.424 47.619 0.00 0.00 41.15 2.32
2208 3669 6.302313 CCGTACAACGAATTCAAAATTCAGAC 59.698 38.462 6.22 2.85 46.05 3.51
2215 3676 4.036352 GCAACCGTACAACGAATTCAAAA 58.964 39.130 6.22 0.00 46.05 2.44
2222 3683 1.823260 CGCAGCAACCGTACAACGAA 61.823 55.000 0.15 0.00 46.05 3.85
2225 3686 1.083015 CACGCAGCAACCGTACAAC 60.083 57.895 0.00 0.00 37.12 3.32
2251 3712 7.721402 TGTACAAGAACAAAATTTGCATAGGT 58.279 30.769 5.52 2.39 0.00 3.08
2309 3998 2.940410 TCGCAAACGGATTAATCCTTCC 59.060 45.455 27.86 9.59 44.93 3.46
2336 4025 3.452755 TGTAACGGCTACATGATGGAG 57.547 47.619 0.00 0.00 35.50 3.86
2456 4156 6.159293 GCAGGTGATGTCTCATCGATATTTA 58.841 40.000 0.00 0.00 37.60 1.40


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

AutoCloner maintained by Alex Coulton.