Multiple sequence alignment - TraesCS2B01G157400

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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 TraesCS2B01G157400 chr2B 100.000 2634 0 0 442 3075 131307166 131309799 0.000000e+00 4865.0
1 TraesCS2B01G157400 chr2B 100.000 205 0 0 1 205 131306725 131306929 2.240000e-101 379.0
2 TraesCS2B01G157400 chr2D 89.463 1547 110 31 586 2120 79927027 79928532 0.000000e+00 1905.0
3 TraesCS2B01G157400 chr2D 88.010 1226 108 16 802 2010 79915041 79916244 0.000000e+00 1413.0
4 TraesCS2B01G157400 chr2D 89.051 959 66 24 2116 3063 79941069 79941999 0.000000e+00 1153.0
5 TraesCS2B01G157400 chr2D 92.118 203 15 1 482 683 79914779 79914981 5.020000e-73 285.0
6 TraesCS2B01G157400 chr2A 88.660 776 54 21 2309 3075 80536546 80537296 0.000000e+00 915.0
7 TraesCS2B01G157400 chr2A 87.345 806 80 9 1202 2000 80532552 80533342 0.000000e+00 904.0
8 TraesCS2B01G157400 chr2A 82.463 479 58 19 484 953 80531863 80532324 2.220000e-106 396.0
9 TraesCS2B01G157400 chr3B 75.956 915 161 43 1091 1962 187519742 187520640 1.710000e-112 416.0
10 TraesCS2B01G157400 chr4D 95.337 193 7 1 1 191 298274186 298274378 3.850000e-79 305.0
11 TraesCS2B01G157400 chr7D 95.312 192 7 1 1 190 544559341 544559150 1.390000e-78 303.0
12 TraesCS2B01G157400 chr7D 93.750 192 10 1 1 190 599238637 599238446 1.400000e-73 287.0
13 TraesCS2B01G157400 chr4A 93.229 192 10 2 1 190 686556209 686556019 2.330000e-71 279.0
14 TraesCS2B01G157400 chr3D 93.194 191 11 1 1 189 31889847 31889657 2.330000e-71 279.0
15 TraesCS2B01G157400 chr3D 76.744 301 50 14 1087 1372 131011516 131011811 1.910000e-32 150.0
16 TraesCS2B01G157400 chr6B 92.670 191 12 1 1 189 173437355 173437165 1.090000e-69 274.0
17 TraesCS2B01G157400 chr1A 91.710 193 14 1 1 191 65651091 65650899 1.820000e-67 267.0
18 TraesCS2B01G157400 chr1A 88.235 51 4 2 1342 1391 553477524 553477573 3.310000e-05 60.2
19 TraesCS2B01G157400 chr4B 91.667 192 13 2 1 190 172449814 172450004 2.350000e-66 263.0
20 TraesCS2B01G157400 chr7B 90.576 191 16 1 1 189 706501401 706501591 5.090000e-63 252.0
21 TraesCS2B01G157400 chr1B 88.235 51 4 2 1342 1391 635153479 635153528 3.310000e-05 60.2


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 TraesCS2B01G157400 chr2B 131306725 131309799 3074 False 2622.000000 4865 100.000 1 3075 2 chr2B.!!$F1 3074
1 TraesCS2B01G157400 chr2D 79927027 79928532 1505 False 1905.000000 1905 89.463 586 2120 1 chr2D.!!$F1 1534
2 TraesCS2B01G157400 chr2D 79941069 79941999 930 False 1153.000000 1153 89.051 2116 3063 1 chr2D.!!$F2 947
3 TraesCS2B01G157400 chr2D 79914779 79916244 1465 False 849.000000 1413 90.064 482 2010 2 chr2D.!!$F3 1528
4 TraesCS2B01G157400 chr2A 80531863 80537296 5433 False 738.333333 915 86.156 484 3075 3 chr2A.!!$F1 2591
5 TraesCS2B01G157400 chr3B 187519742 187520640 898 False 416.000000 416 75.956 1091 1962 1 chr3B.!!$F1 871

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
115 116 0.033405 CTCTACTCCCCCGTTCCTGA 60.033 60.0 0.00 0.00 0.0 3.86 F
513 514 0.107312 CCTCCCACAATCTCCAGCTG 60.107 60.0 6.78 6.78 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1045 1063 0.539438 GGGTGCTTGATGGTGTGGAA 60.539 55.0 0.0 0.0 0.0 3.53 R
2220 5337 0.458025 GACCCCGACGTGCTAAGAAG 60.458 60.0 0.0 0.0 0.0 2.85 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
36 37 4.574674 TGTAATGAGATCAGCAAAGGGT 57.425 40.909 0.00 0.00 0.00 4.34
37 38 4.517285 TGTAATGAGATCAGCAAAGGGTC 58.483 43.478 0.00 0.00 0.00 4.46
38 39 2.725221 ATGAGATCAGCAAAGGGTCC 57.275 50.000 0.00 0.00 0.00 4.46
39 40 1.361204 TGAGATCAGCAAAGGGTCCA 58.639 50.000 0.00 0.00 0.00 4.02
40 41 1.280133 TGAGATCAGCAAAGGGTCCAG 59.720 52.381 0.00 0.00 0.00 3.86
41 42 0.034670 AGATCAGCAAAGGGTCCAGC 60.035 55.000 0.00 0.00 0.00 4.85
42 43 0.322816 GATCAGCAAAGGGTCCAGCA 60.323 55.000 0.00 0.00 0.00 4.41
43 44 0.333993 ATCAGCAAAGGGTCCAGCAT 59.666 50.000 0.00 0.00 0.00 3.79
44 45 0.991146 TCAGCAAAGGGTCCAGCATA 59.009 50.000 0.00 0.00 0.00 3.14
45 46 1.565759 TCAGCAAAGGGTCCAGCATAT 59.434 47.619 0.00 0.00 0.00 1.78
46 47 2.025037 TCAGCAAAGGGTCCAGCATATT 60.025 45.455 0.00 0.00 0.00 1.28
47 48 2.762327 CAGCAAAGGGTCCAGCATATTT 59.238 45.455 0.00 0.00 0.00 1.40
48 49 2.762327 AGCAAAGGGTCCAGCATATTTG 59.238 45.455 0.00 0.00 0.00 2.32
49 50 2.497273 GCAAAGGGTCCAGCATATTTGT 59.503 45.455 0.00 0.00 31.84 2.83
50 51 3.676873 GCAAAGGGTCCAGCATATTTGTG 60.677 47.826 0.00 0.00 31.84 3.33
51 52 3.456380 AAGGGTCCAGCATATTTGTGT 57.544 42.857 0.00 0.00 0.00 3.72
52 53 2.726821 AGGGTCCAGCATATTTGTGTG 58.273 47.619 0.00 0.00 0.00 3.82
53 54 1.134946 GGGTCCAGCATATTTGTGTGC 59.865 52.381 0.00 0.00 41.57 4.57
54 55 1.202177 GGTCCAGCATATTTGTGTGCG 60.202 52.381 0.00 0.00 45.69 5.34
55 56 1.737236 GTCCAGCATATTTGTGTGCGA 59.263 47.619 0.00 0.00 45.69 5.10
56 57 2.161410 GTCCAGCATATTTGTGTGCGAA 59.839 45.455 0.00 0.00 45.69 4.70
57 58 2.419673 TCCAGCATATTTGTGTGCGAAG 59.580 45.455 0.00 0.00 45.69 3.79
76 77 3.639222 CGTGCTTGTACGCTTTCTG 57.361 52.632 0.00 0.00 37.24 3.02
77 78 0.859232 CGTGCTTGTACGCTTTCTGT 59.141 50.000 0.00 0.00 37.24 3.41
78 79 1.397190 CGTGCTTGTACGCTTTCTGTG 60.397 52.381 0.00 0.00 37.24 3.66
79 80 1.864711 GTGCTTGTACGCTTTCTGTGA 59.135 47.619 0.00 0.00 0.00 3.58
80 81 1.864711 TGCTTGTACGCTTTCTGTGAC 59.135 47.619 0.00 0.00 0.00 3.67
81 82 2.135933 GCTTGTACGCTTTCTGTGACT 58.864 47.619 0.00 0.00 0.00 3.41
82 83 2.096713 GCTTGTACGCTTTCTGTGACTG 60.097 50.000 0.00 0.00 0.00 3.51
83 84 3.381045 CTTGTACGCTTTCTGTGACTGA 58.619 45.455 0.00 0.00 0.00 3.41
84 85 3.013276 TGTACGCTTTCTGTGACTGAG 57.987 47.619 0.00 0.00 0.00 3.35
85 86 2.621526 TGTACGCTTTCTGTGACTGAGA 59.378 45.455 0.00 0.00 0.00 3.27
86 87 2.430546 ACGCTTTCTGTGACTGAGAG 57.569 50.000 5.78 5.78 0.00 3.20
87 88 1.066914 CGCTTTCTGTGACTGAGAGC 58.933 55.000 20.16 20.16 36.64 4.09
88 89 1.336702 CGCTTTCTGTGACTGAGAGCT 60.337 52.381 24.75 0.00 37.39 4.09
89 90 2.067766 GCTTTCTGTGACTGAGAGCTG 58.932 52.381 21.95 2.67 36.89 4.24
90 91 2.686235 CTTTCTGTGACTGAGAGCTGG 58.314 52.381 0.00 0.00 0.00 4.85
91 92 1.709578 TTCTGTGACTGAGAGCTGGT 58.290 50.000 0.00 0.00 0.00 4.00
92 93 1.709578 TCTGTGACTGAGAGCTGGTT 58.290 50.000 0.00 0.00 0.00 3.67
93 94 2.876581 TCTGTGACTGAGAGCTGGTTA 58.123 47.619 0.00 0.00 0.00 2.85
94 95 3.435275 TCTGTGACTGAGAGCTGGTTAT 58.565 45.455 0.00 0.00 0.00 1.89
95 96 4.600062 TCTGTGACTGAGAGCTGGTTATA 58.400 43.478 0.00 0.00 0.00 0.98
96 97 4.399618 TCTGTGACTGAGAGCTGGTTATAC 59.600 45.833 0.00 0.00 0.00 1.47
97 98 4.344978 TGTGACTGAGAGCTGGTTATACT 58.655 43.478 0.00 0.00 0.00 2.12
98 99 4.399618 TGTGACTGAGAGCTGGTTATACTC 59.600 45.833 0.00 0.00 0.00 2.59
99 100 4.642885 GTGACTGAGAGCTGGTTATACTCT 59.357 45.833 0.00 0.00 43.35 3.24
100 101 5.823570 GTGACTGAGAGCTGGTTATACTCTA 59.176 44.000 0.00 0.00 40.80 2.43
101 102 5.823570 TGACTGAGAGCTGGTTATACTCTAC 59.176 44.000 0.00 0.00 40.80 2.59
102 103 6.008696 ACTGAGAGCTGGTTATACTCTACT 57.991 41.667 0.00 0.00 40.80 2.57
103 104 6.059484 ACTGAGAGCTGGTTATACTCTACTC 58.941 44.000 0.00 0.00 40.80 2.59
104 105 5.378332 TGAGAGCTGGTTATACTCTACTCC 58.622 45.833 0.00 0.00 40.80 3.85
105 106 4.732065 AGAGCTGGTTATACTCTACTCCC 58.268 47.826 0.00 0.00 38.98 4.30
106 107 3.827876 GAGCTGGTTATACTCTACTCCCC 59.172 52.174 0.00 0.00 0.00 4.81
107 108 2.898612 GCTGGTTATACTCTACTCCCCC 59.101 54.545 0.00 0.00 0.00 5.40
108 109 3.155501 CTGGTTATACTCTACTCCCCCG 58.844 54.545 0.00 0.00 0.00 5.73
109 110 2.515429 TGGTTATACTCTACTCCCCCGT 59.485 50.000 0.00 0.00 0.00 5.28
110 111 3.052642 TGGTTATACTCTACTCCCCCGTT 60.053 47.826 0.00 0.00 0.00 4.44
111 112 3.571828 GGTTATACTCTACTCCCCCGTTC 59.428 52.174 0.00 0.00 0.00 3.95
112 113 2.378378 ATACTCTACTCCCCCGTTCC 57.622 55.000 0.00 0.00 0.00 3.62
113 114 1.302907 TACTCTACTCCCCCGTTCCT 58.697 55.000 0.00 0.00 0.00 3.36
114 115 0.324460 ACTCTACTCCCCCGTTCCTG 60.324 60.000 0.00 0.00 0.00 3.86
115 116 0.033405 CTCTACTCCCCCGTTCCTGA 60.033 60.000 0.00 0.00 0.00 3.86
116 117 0.635009 TCTACTCCCCCGTTCCTGAT 59.365 55.000 0.00 0.00 0.00 2.90
117 118 1.041437 CTACTCCCCCGTTCCTGATC 58.959 60.000 0.00 0.00 0.00 2.92
118 119 0.337082 TACTCCCCCGTTCCTGATCA 59.663 55.000 0.00 0.00 0.00 2.92
119 120 0.978146 ACTCCCCCGTTCCTGATCAG 60.978 60.000 16.24 16.24 0.00 2.90
120 121 2.190578 CCCCCGTTCCTGATCAGC 59.809 66.667 17.76 2.95 0.00 4.26
121 122 2.669133 CCCCCGTTCCTGATCAGCA 61.669 63.158 17.76 0.00 0.00 4.41
122 123 1.153289 CCCCGTTCCTGATCAGCAG 60.153 63.158 17.76 4.89 44.49 4.24
123 124 1.817099 CCCGTTCCTGATCAGCAGC 60.817 63.158 17.76 3.48 43.50 5.25
124 125 1.817099 CCGTTCCTGATCAGCAGCC 60.817 63.158 17.76 3.78 43.50 4.85
125 126 1.220206 CGTTCCTGATCAGCAGCCT 59.780 57.895 17.76 0.00 43.50 4.58
126 127 0.461548 CGTTCCTGATCAGCAGCCTA 59.538 55.000 17.76 0.00 43.50 3.93
127 128 1.069823 CGTTCCTGATCAGCAGCCTAT 59.930 52.381 17.76 0.00 43.50 2.57
128 129 2.484417 CGTTCCTGATCAGCAGCCTATT 60.484 50.000 17.76 0.00 43.50 1.73
129 130 2.877168 GTTCCTGATCAGCAGCCTATTG 59.123 50.000 17.76 0.35 43.50 1.90
130 131 1.419012 TCCTGATCAGCAGCCTATTGG 59.581 52.381 17.76 0.39 43.50 3.16
140 141 4.445699 CCTATTGGCCGACTGCTC 57.554 61.111 0.00 0.00 40.92 4.26
141 142 1.522092 CCTATTGGCCGACTGCTCA 59.478 57.895 0.00 0.00 40.92 4.26
142 143 0.531532 CCTATTGGCCGACTGCTCAG 60.532 60.000 0.00 0.00 40.92 3.35
143 144 1.153369 TATTGGCCGACTGCTCAGC 60.153 57.895 0.00 0.00 40.92 4.26
144 145 2.906182 TATTGGCCGACTGCTCAGCG 62.906 60.000 0.00 2.33 40.92 5.18
156 157 2.904664 CTCAGCGAGCACTTGTTGA 58.095 52.632 4.60 4.60 33.90 3.18
157 158 1.220529 CTCAGCGAGCACTTGTTGAA 58.779 50.000 6.00 0.00 34.49 2.69
158 159 1.802960 CTCAGCGAGCACTTGTTGAAT 59.197 47.619 6.00 0.00 34.49 2.57
159 160 2.995939 CTCAGCGAGCACTTGTTGAATA 59.004 45.455 6.00 0.00 34.49 1.75
160 161 3.398406 TCAGCGAGCACTTGTTGAATAA 58.602 40.909 2.26 0.00 32.36 1.40
161 162 3.812609 TCAGCGAGCACTTGTTGAATAAA 59.187 39.130 2.26 0.00 32.36 1.40
162 163 4.083855 TCAGCGAGCACTTGTTGAATAAAG 60.084 41.667 2.26 0.00 32.36 1.85
163 164 2.911102 GCGAGCACTTGTTGAATAAAGC 59.089 45.455 0.00 0.00 0.00 3.51
164 165 3.365364 GCGAGCACTTGTTGAATAAAGCT 60.365 43.478 1.94 1.94 0.00 3.74
165 166 4.398247 CGAGCACTTGTTGAATAAAGCTC 58.602 43.478 14.44 14.44 42.67 4.09
166 167 4.153117 CGAGCACTTGTTGAATAAAGCTCT 59.847 41.667 18.94 6.24 43.61 4.09
167 168 5.334414 CGAGCACTTGTTGAATAAAGCTCTT 60.334 40.000 18.94 0.00 43.61 2.85
168 169 6.396829 AGCACTTGTTGAATAAAGCTCTTT 57.603 33.333 0.00 0.27 36.63 2.52
169 170 7.510549 AGCACTTGTTGAATAAAGCTCTTTA 57.489 32.000 4.74 4.74 39.12 1.85
170 171 7.940850 AGCACTTGTTGAATAAAGCTCTTTAA 58.059 30.769 6.22 0.00 38.38 1.52
171 172 8.078596 AGCACTTGTTGAATAAAGCTCTTTAAG 58.921 33.333 6.22 2.75 38.38 1.85
172 173 7.327032 GCACTTGTTGAATAAAGCTCTTTAAGG 59.673 37.037 6.22 0.00 38.38 2.69
173 174 8.352942 CACTTGTTGAATAAAGCTCTTTAAGGT 58.647 33.333 6.22 0.00 38.38 3.50
181 182 2.796557 AGCTCTTTAAGGTTTCCCTGC 58.203 47.619 0.00 0.00 41.56 4.85
182 183 2.108250 AGCTCTTTAAGGTTTCCCTGCA 59.892 45.455 0.00 0.00 41.56 4.41
183 184 2.890945 GCTCTTTAAGGTTTCCCTGCAA 59.109 45.455 0.00 0.00 41.56 4.08
184 185 3.320826 GCTCTTTAAGGTTTCCCTGCAAA 59.679 43.478 0.00 0.00 41.56 3.68
185 186 4.202212 GCTCTTTAAGGTTTCCCTGCAAAA 60.202 41.667 0.00 0.00 41.56 2.44
186 187 5.683770 GCTCTTTAAGGTTTCCCTGCAAAAA 60.684 40.000 0.00 0.00 41.56 1.94
459 460 3.123674 CGCTTCTGGAGTGTACACC 57.876 57.895 22.28 13.34 0.00 4.16
460 461 0.317160 CGCTTCTGGAGTGTACACCA 59.683 55.000 22.28 13.30 35.35 4.17
461 462 1.797025 GCTTCTGGAGTGTACACCAC 58.203 55.000 22.28 15.45 44.89 4.16
470 471 2.165319 GTGTACACCACTCCCTTGAC 57.835 55.000 15.42 0.00 41.11 3.18
471 472 1.053424 TGTACACCACTCCCTTGACC 58.947 55.000 0.00 0.00 0.00 4.02
472 473 1.053424 GTACACCACTCCCTTGACCA 58.947 55.000 0.00 0.00 0.00 4.02
473 474 1.002087 GTACACCACTCCCTTGACCAG 59.998 57.143 0.00 0.00 0.00 4.00
474 475 1.302832 CACCACTCCCTTGACCAGC 60.303 63.158 0.00 0.00 0.00 4.85
475 476 1.462238 ACCACTCCCTTGACCAGCT 60.462 57.895 0.00 0.00 0.00 4.24
476 477 1.298014 CCACTCCCTTGACCAGCTC 59.702 63.158 0.00 0.00 0.00 4.09
477 478 1.298014 CACTCCCTTGACCAGCTCC 59.702 63.158 0.00 0.00 0.00 4.70
478 479 1.152030 ACTCCCTTGACCAGCTCCA 60.152 57.895 0.00 0.00 0.00 3.86
479 480 1.197430 ACTCCCTTGACCAGCTCCAG 61.197 60.000 0.00 0.00 0.00 3.86
480 481 2.045536 CCCTTGACCAGCTCCAGC 60.046 66.667 0.00 0.00 42.49 4.85
502 503 1.435563 TCCTACTCCTTTCCTCCCACA 59.564 52.381 0.00 0.00 0.00 4.17
513 514 0.107312 CCTCCCACAATCTCCAGCTG 60.107 60.000 6.78 6.78 0.00 4.24
539 540 1.345715 CCCTCCGCCATTACTCCCTT 61.346 60.000 0.00 0.00 0.00 3.95
551 552 0.539438 ACTCCCTTGCGGCAATTTGA 60.539 50.000 16.80 11.56 0.00 2.69
620 621 2.043115 TCTAGGAGACTGGAAGGAGCAA 59.957 50.000 0.00 0.00 45.89 3.91
633 634 4.450419 GGAAGGAGCAAAGATGACGATATG 59.550 45.833 0.00 0.00 0.00 1.78
740 751 3.065371 GGAGATTCGTGCAAAAATCCGAT 59.935 43.478 15.27 1.94 33.29 4.18
773 787 4.657824 CCGCGGGAGTCGTTGTGT 62.658 66.667 20.10 0.00 41.72 3.72
779 793 0.320771 GGGAGTCGTTGTGTGCTGAT 60.321 55.000 0.00 0.00 0.00 2.90
800 814 4.333913 TGTTTGCACATTAGCATTTGGT 57.666 36.364 0.00 0.00 45.19 3.67
830 844 1.671054 GGAAAGTGCGCTACTGGCA 60.671 57.895 9.73 0.00 40.26 4.92
898 912 7.567048 GCGATCATTGGTAGAAACAGTATAACG 60.567 40.741 0.00 0.00 0.00 3.18
932 946 2.652079 CCATCTATCGCGCGCTGTG 61.652 63.158 30.48 17.80 0.00 3.66
949 963 2.335011 GGGCGCACCAAACTGTTC 59.665 61.111 10.83 0.00 39.85 3.18
952 966 0.179124 GGCGCACCAAACTGTTCAAA 60.179 50.000 10.83 0.00 35.26 2.69
953 967 0.920664 GCGCACCAAACTGTTCAAAC 59.079 50.000 0.30 0.00 0.00 2.93
954 968 1.469079 GCGCACCAAACTGTTCAAACT 60.469 47.619 0.30 0.00 0.00 2.66
997 1014 3.746949 CTGGATCTCAGCCCCGCAC 62.747 68.421 0.00 0.00 36.60 5.34
1045 1063 4.585070 CCGGACATGGCATCCAAT 57.415 55.556 0.00 0.00 36.95 3.16
1046 1064 2.811307 CCGGACATGGCATCCAATT 58.189 52.632 0.00 0.00 36.95 2.32
1047 1065 0.670162 CCGGACATGGCATCCAATTC 59.330 55.000 0.00 0.00 36.95 2.17
1048 1066 0.670162 CGGACATGGCATCCAATTCC 59.330 55.000 0.00 3.84 36.95 3.01
1066 1084 1.978617 CACACCATCAAGCACCCCC 60.979 63.158 0.00 0.00 0.00 5.40
1070 1088 4.776322 CATCAAGCACCCCCGCGA 62.776 66.667 8.23 0.00 36.85 5.87
1071 1089 4.473520 ATCAAGCACCCCCGCGAG 62.474 66.667 8.23 0.00 36.85 5.03
1136 1154 1.734477 GTCGGCGATGGATCATCCG 60.734 63.158 14.79 9.75 40.17 4.18
1141 1159 2.743928 GATGGATCATCCGCCGCC 60.744 66.667 0.00 0.00 40.17 6.13
1199 1256 3.814005 ATGATCTGCATTTGCCTTTCC 57.186 42.857 0.00 0.00 41.18 3.13
1211 1268 4.664150 TTGCCTTTCCGTTTCATTCTTT 57.336 36.364 0.00 0.00 0.00 2.52
1704 1785 4.749310 CGCTGCTGTCCGGCTTCT 62.749 66.667 0.00 0.00 43.91 2.85
1776 1857 1.725665 CTGACCTACGATTCCGCGA 59.274 57.895 8.23 0.00 39.95 5.87
1787 1868 2.061773 GATTCCGCGATCGTGATCAAT 58.938 47.619 29.21 21.33 37.69 2.57
2019 5124 1.589716 GCCTGGCCTAGTTGCACTTG 61.590 60.000 7.66 0.00 0.00 3.16
2020 5125 0.962356 CCTGGCCTAGTTGCACTTGG 60.962 60.000 3.32 10.71 42.76 3.61
2053 5158 9.999009 AAACTTTGTTGTTTTTAGAGTAGCTAC 57.001 29.630 16.43 16.43 36.86 3.58
2054 5159 8.959705 ACTTTGTTGTTTTTAGAGTAGCTACT 57.040 30.769 26.35 26.35 39.71 2.57
2066 5171 6.394025 AGAGTAGCTACTAATAACTGGCAC 57.606 41.667 26.11 9.27 36.50 5.01
2095 5200 2.053627 CAGCAATTCGGCACAAACTTC 58.946 47.619 0.00 0.00 35.83 3.01
2108 5213 5.030936 GCACAAACTTCAAACTTCAGAGAC 58.969 41.667 0.00 0.00 0.00 3.36
2169 5278 5.242393 TCCTTCCTACACTGTTACAGTACAC 59.758 44.000 18.19 0.00 43.43 2.90
2176 5285 5.054477 ACACTGTTACAGTACACATGTTCC 58.946 41.667 18.19 0.00 43.43 3.62
2186 5295 0.388520 CACATGTTCCTCGTGCTCGA 60.389 55.000 10.80 10.80 44.12 4.04
2208 5317 2.203015 CGATCCCCAACCGCGAAT 60.203 61.111 8.23 0.00 0.00 3.34
2209 5318 2.244651 CGATCCCCAACCGCGAATC 61.245 63.158 8.23 0.00 0.00 2.52
2210 5319 2.203015 ATCCCCAACCGCGAATCG 60.203 61.111 8.23 0.00 38.08 3.34
2211 5320 2.638330 GATCCCCAACCGCGAATCGA 62.638 60.000 8.23 0.00 41.67 3.59
2212 5321 2.040009 ATCCCCAACCGCGAATCGAT 62.040 55.000 8.23 0.00 41.67 3.59
2213 5322 1.817941 CCCCAACCGCGAATCGATT 60.818 57.895 11.20 11.20 41.67 3.34
2231 5348 3.238570 CGATTCGTTCTCTTCTTAGCACG 59.761 47.826 0.00 0.00 0.00 5.34
2292 5409 2.159156 TGTACATGTACATCACGAGGCC 60.159 50.000 30.31 0.00 40.77 5.19
2565 5682 1.743252 CTTCGGCCTCTCCTGCAAC 60.743 63.158 0.00 0.00 0.00 4.17
2642 5766 6.407475 ACAAAACTTGTTGAATGCTTTGAC 57.593 33.333 0.00 0.00 42.22 3.18
2661 5785 1.762957 ACTGGGATCGGTATCACCTTG 59.237 52.381 0.00 0.00 34.31 3.61
2757 5881 0.824109 TGATGAACAGCCCGTAGAGG 59.176 55.000 0.00 0.00 40.63 3.69
2807 5931 3.181503 CCAGCAAGATACACATCTGCAAC 60.182 47.826 0.00 0.00 40.81 4.17
2808 5932 3.437741 CAGCAAGATACACATCTGCAACA 59.562 43.478 0.00 0.00 40.81 3.33
2809 5933 3.688185 AGCAAGATACACATCTGCAACAG 59.312 43.478 0.00 0.00 40.81 3.16
2810 5934 3.730061 GCAAGATACACATCTGCAACAGC 60.730 47.826 0.00 0.00 40.81 4.40
2811 5935 3.339253 AGATACACATCTGCAACAGCA 57.661 42.857 0.00 0.00 40.15 4.41
2812 5936 3.678289 AGATACACATCTGCAACAGCAA 58.322 40.909 0.00 0.00 40.15 3.91
2813 5937 4.074259 AGATACACATCTGCAACAGCAAA 58.926 39.130 0.00 0.00 40.15 3.68
2814 5938 2.787601 ACACATCTGCAACAGCAAAG 57.212 45.000 0.00 0.00 37.91 2.77
2815 5939 2.026641 ACACATCTGCAACAGCAAAGT 58.973 42.857 0.00 0.00 37.91 2.66
2816 5940 2.223641 ACACATCTGCAACAGCAAAGTG 60.224 45.455 12.11 12.11 37.91 3.16
2817 5941 2.033675 CACATCTGCAACAGCAAAGTGA 59.966 45.455 9.52 0.00 37.91 3.41
2818 5942 2.689471 ACATCTGCAACAGCAAAGTGAA 59.311 40.909 0.00 0.00 37.91 3.18
2819 5943 3.130869 ACATCTGCAACAGCAAAGTGAAA 59.869 39.130 0.00 0.00 37.91 2.69
2820 5944 3.865011 TCTGCAACAGCAAAGTGAAAA 57.135 38.095 0.00 0.00 37.91 2.29
2821 5945 4.185467 TCTGCAACAGCAAAGTGAAAAA 57.815 36.364 0.00 0.00 37.91 1.94
2855 5979 4.041075 TCAGTAGCAGTTGGTGTAAATCCA 59.959 41.667 0.00 0.00 0.00 3.41
2856 5980 4.393062 CAGTAGCAGTTGGTGTAAATCCAG 59.607 45.833 0.00 0.00 36.28 3.86
2857 5981 3.508845 AGCAGTTGGTGTAAATCCAGT 57.491 42.857 0.00 0.00 36.28 4.00
2858 5982 3.412386 AGCAGTTGGTGTAAATCCAGTC 58.588 45.455 0.00 0.00 36.28 3.51
2859 5983 3.146066 GCAGTTGGTGTAAATCCAGTCA 58.854 45.455 0.00 0.00 36.28 3.41
2860 5984 3.758554 GCAGTTGGTGTAAATCCAGTCAT 59.241 43.478 0.00 0.00 36.28 3.06
2861 5985 4.142600 GCAGTTGGTGTAAATCCAGTCATC 60.143 45.833 0.00 0.00 36.28 2.92
2862 5986 5.003160 CAGTTGGTGTAAATCCAGTCATCA 58.997 41.667 0.00 0.00 36.28 3.07
2863 5987 5.649395 CAGTTGGTGTAAATCCAGTCATCAT 59.351 40.000 0.00 0.00 36.28 2.45
2864 5988 5.649395 AGTTGGTGTAAATCCAGTCATCATG 59.351 40.000 0.00 0.00 36.28 3.07
2865 5989 5.178096 TGGTGTAAATCCAGTCATCATGT 57.822 39.130 0.00 0.00 0.00 3.21
2866 5990 4.943093 TGGTGTAAATCCAGTCATCATGTG 59.057 41.667 0.00 0.00 0.00 3.21
2867 5991 4.943705 GGTGTAAATCCAGTCATCATGTGT 59.056 41.667 0.00 0.00 0.00 3.72
2868 5992 6.112734 GGTGTAAATCCAGTCATCATGTGTA 58.887 40.000 0.00 0.00 0.00 2.90
2872 6002 8.046107 TGTAAATCCAGTCATCATGTGTATCAA 58.954 33.333 0.00 0.00 0.00 2.57
2881 6011 6.476706 GTCATCATGTGTATCAATTCGACAGA 59.523 38.462 0.00 0.00 0.00 3.41
2883 6013 6.207691 TCATGTGTATCAATTCGACAGAGA 57.792 37.500 0.00 0.00 0.00 3.10
2885 6015 7.267857 TCATGTGTATCAATTCGACAGAGAAT 58.732 34.615 0.00 0.00 42.13 2.40
2886 6016 8.413229 TCATGTGTATCAATTCGACAGAGAATA 58.587 33.333 0.00 0.00 39.69 1.75
2887 6017 9.201127 CATGTGTATCAATTCGACAGAGAATAT 57.799 33.333 0.00 0.00 39.69 1.28
2889 6019 9.599866 TGTGTATCAATTCGACAGAGAATATTT 57.400 29.630 0.00 0.00 39.69 1.40
2891 6021 9.816354 TGTATCAATTCGACAGAGAATATTTCA 57.184 29.630 0.00 0.00 39.69 2.69
2893 6023 8.954950 ATCAATTCGACAGAGAATATTTCAGT 57.045 30.769 0.00 0.00 39.69 3.41
2937 6068 0.839946 GGACCATCTGCCCTGTATGT 59.160 55.000 0.00 0.00 0.00 2.29
3009 6140 1.004745 ACACATCCCTGATCACCAACC 59.995 52.381 0.00 0.00 0.00 3.77
3020 6151 5.097742 TGATCACCAACCGATACAAGATT 57.902 39.130 0.00 0.00 0.00 2.40
3029 6160 9.106070 ACCAACCGATACAAGATTCTTAATTAC 57.894 33.333 0.00 0.00 0.00 1.89
3048 6179 9.825109 TTAATTACATCCATCTGAACGATGTTA 57.175 29.630 20.97 15.41 46.56 2.41
3063 6194 9.478768 TGAACGATGTTACTCACTAATAACAAA 57.521 29.630 1.33 0.00 42.81 2.83
3064 6195 9.953825 GAACGATGTTACTCACTAATAACAAAG 57.046 33.333 1.33 2.11 42.81 2.77
3065 6196 9.485206 AACGATGTTACTCACTAATAACAAAGT 57.515 29.630 1.33 2.62 42.81 2.66
3066 6197 9.136952 ACGATGTTACTCACTAATAACAAAGTC 57.863 33.333 1.33 0.00 42.81 3.01
3067 6198 9.135843 CGATGTTACTCACTAATAACAAAGTCA 57.864 33.333 1.33 0.00 42.81 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.154847 CTGATCTCATTACATGTTGAACAGTAA 57.845 33.333 2.30 16.68 34.20 2.24
4 5 6.093219 GCTGATCTCATTACATGTTGAACAGT 59.907 38.462 2.30 5.05 37.23 3.55
5 6 6.093082 TGCTGATCTCATTACATGTTGAACAG 59.907 38.462 2.30 12.55 37.54 3.16
6 7 5.939296 TGCTGATCTCATTACATGTTGAACA 59.061 36.000 2.30 0.00 0.00 3.18
7 8 6.426980 TGCTGATCTCATTACATGTTGAAC 57.573 37.500 2.30 0.00 0.00 3.18
8 9 7.362315 CCTTTGCTGATCTCATTACATGTTGAA 60.362 37.037 2.30 0.00 0.00 2.69
9 10 6.094464 CCTTTGCTGATCTCATTACATGTTGA 59.906 38.462 2.30 1.20 0.00 3.18
10 11 6.263344 CCTTTGCTGATCTCATTACATGTTG 58.737 40.000 2.30 0.00 0.00 3.33
11 12 5.359009 CCCTTTGCTGATCTCATTACATGTT 59.641 40.000 2.30 0.00 0.00 2.71
12 13 4.885907 CCCTTTGCTGATCTCATTACATGT 59.114 41.667 2.69 2.69 0.00 3.21
13 14 4.885907 ACCCTTTGCTGATCTCATTACATG 59.114 41.667 0.00 0.00 0.00 3.21
14 15 5.121380 ACCCTTTGCTGATCTCATTACAT 57.879 39.130 0.00 0.00 0.00 2.29
15 16 4.517285 GACCCTTTGCTGATCTCATTACA 58.483 43.478 0.00 0.00 0.00 2.41
16 17 3.879892 GGACCCTTTGCTGATCTCATTAC 59.120 47.826 0.00 0.00 0.00 1.89
17 18 3.523157 TGGACCCTTTGCTGATCTCATTA 59.477 43.478 0.00 0.00 0.00 1.90
18 19 2.309755 TGGACCCTTTGCTGATCTCATT 59.690 45.455 0.00 0.00 0.00 2.57
19 20 1.918262 TGGACCCTTTGCTGATCTCAT 59.082 47.619 0.00 0.00 0.00 2.90
20 21 1.280133 CTGGACCCTTTGCTGATCTCA 59.720 52.381 0.00 0.00 0.00 3.27
21 22 2.016096 GCTGGACCCTTTGCTGATCTC 61.016 57.143 0.00 0.00 0.00 2.75
22 23 0.034670 GCTGGACCCTTTGCTGATCT 60.035 55.000 0.00 0.00 0.00 2.75
23 24 0.322816 TGCTGGACCCTTTGCTGATC 60.323 55.000 0.00 0.00 0.00 2.92
24 25 0.333993 ATGCTGGACCCTTTGCTGAT 59.666 50.000 0.00 0.00 0.00 2.90
25 26 0.991146 TATGCTGGACCCTTTGCTGA 59.009 50.000 0.00 0.00 0.00 4.26
26 27 2.062971 ATATGCTGGACCCTTTGCTG 57.937 50.000 0.00 0.00 0.00 4.41
27 28 2.762327 CAAATATGCTGGACCCTTTGCT 59.238 45.455 0.00 0.00 0.00 3.91
28 29 2.497273 ACAAATATGCTGGACCCTTTGC 59.503 45.455 0.00 0.00 0.00 3.68
29 30 3.511146 ACACAAATATGCTGGACCCTTTG 59.489 43.478 0.00 0.00 0.00 2.77
30 31 3.511146 CACACAAATATGCTGGACCCTTT 59.489 43.478 0.00 0.00 0.00 3.11
31 32 3.091545 CACACAAATATGCTGGACCCTT 58.908 45.455 0.00 0.00 0.00 3.95
32 33 2.726821 CACACAAATATGCTGGACCCT 58.273 47.619 0.00 0.00 0.00 4.34
33 34 1.134946 GCACACAAATATGCTGGACCC 59.865 52.381 0.00 0.00 38.84 4.46
34 35 1.202177 CGCACACAAATATGCTGGACC 60.202 52.381 0.00 0.00 39.79 4.46
35 36 1.737236 TCGCACACAAATATGCTGGAC 59.263 47.619 0.00 0.00 39.79 4.02
36 37 2.106477 TCGCACACAAATATGCTGGA 57.894 45.000 0.00 0.00 39.79 3.86
37 38 2.789208 CTTCGCACACAAATATGCTGG 58.211 47.619 0.00 0.00 39.79 4.85
38 39 2.179589 GCTTCGCACACAAATATGCTG 58.820 47.619 0.00 0.00 39.79 4.41
39 40 1.202065 CGCTTCGCACACAAATATGCT 60.202 47.619 0.00 0.00 39.79 3.79
40 41 1.182673 CGCTTCGCACACAAATATGC 58.817 50.000 0.00 0.00 38.52 3.14
41 42 2.168384 CACGCTTCGCACACAAATATG 58.832 47.619 0.00 0.00 0.00 1.78
42 43 1.465689 GCACGCTTCGCACACAAATAT 60.466 47.619 0.00 0.00 0.00 1.28
43 44 0.110419 GCACGCTTCGCACACAAATA 60.110 50.000 0.00 0.00 0.00 1.40
44 45 1.370414 GCACGCTTCGCACACAAAT 60.370 52.632 0.00 0.00 0.00 2.32
45 46 1.987704 AAGCACGCTTCGCACACAAA 61.988 50.000 0.00 0.00 0.00 2.83
46 47 2.468670 AAGCACGCTTCGCACACAA 61.469 52.632 0.00 0.00 0.00 3.33
47 48 2.894879 AAGCACGCTTCGCACACA 60.895 55.556 0.00 0.00 0.00 3.72
48 49 1.827315 TACAAGCACGCTTCGCACAC 61.827 55.000 0.16 0.00 33.42 3.82
49 50 1.592939 TACAAGCACGCTTCGCACA 60.593 52.632 0.16 0.00 33.42 4.57
50 51 1.154654 GTACAAGCACGCTTCGCAC 60.155 57.895 0.16 0.00 33.42 5.34
51 52 2.653967 CGTACAAGCACGCTTCGCA 61.654 57.895 0.16 0.00 34.78 5.10
52 53 2.093983 CGTACAAGCACGCTTCGC 59.906 61.111 0.16 0.00 34.78 4.70
58 59 0.859232 ACAGAAAGCGTACAAGCACG 59.141 50.000 0.00 0.00 44.71 5.34
59 60 1.864711 TCACAGAAAGCGTACAAGCAC 59.135 47.619 0.00 0.00 40.15 4.40
60 61 1.864711 GTCACAGAAAGCGTACAAGCA 59.135 47.619 0.00 0.00 40.15 3.91
61 62 2.096713 CAGTCACAGAAAGCGTACAAGC 60.097 50.000 0.00 0.00 37.41 4.01
62 63 3.381045 TCAGTCACAGAAAGCGTACAAG 58.619 45.455 0.00 0.00 0.00 3.16
63 64 3.067601 TCTCAGTCACAGAAAGCGTACAA 59.932 43.478 0.00 0.00 0.00 2.41
64 65 2.621526 TCTCAGTCACAGAAAGCGTACA 59.378 45.455 0.00 0.00 0.00 2.90
65 66 3.238441 CTCTCAGTCACAGAAAGCGTAC 58.762 50.000 0.00 0.00 0.00 3.67
66 67 2.351835 GCTCTCAGTCACAGAAAGCGTA 60.352 50.000 0.00 0.00 0.00 4.42
67 68 1.604185 GCTCTCAGTCACAGAAAGCGT 60.604 52.381 0.00 0.00 0.00 5.07
68 69 1.066914 GCTCTCAGTCACAGAAAGCG 58.933 55.000 0.00 0.00 0.00 4.68
69 70 2.067766 CAGCTCTCAGTCACAGAAAGC 58.932 52.381 0.00 0.00 0.00 3.51
70 71 2.036992 ACCAGCTCTCAGTCACAGAAAG 59.963 50.000 0.00 0.00 0.00 2.62
71 72 2.042464 ACCAGCTCTCAGTCACAGAAA 58.958 47.619 0.00 0.00 0.00 2.52
72 73 1.709578 ACCAGCTCTCAGTCACAGAA 58.290 50.000 0.00 0.00 0.00 3.02
73 74 1.709578 AACCAGCTCTCAGTCACAGA 58.290 50.000 0.00 0.00 0.00 3.41
74 75 3.883830 ATAACCAGCTCTCAGTCACAG 57.116 47.619 0.00 0.00 0.00 3.66
75 76 4.344978 AGTATAACCAGCTCTCAGTCACA 58.655 43.478 0.00 0.00 0.00 3.58
76 77 4.642885 AGAGTATAACCAGCTCTCAGTCAC 59.357 45.833 0.00 0.00 34.86 3.67
77 78 4.861196 AGAGTATAACCAGCTCTCAGTCA 58.139 43.478 0.00 0.00 34.86 3.41
78 79 6.059484 AGTAGAGTATAACCAGCTCTCAGTC 58.941 44.000 0.00 0.00 39.87 3.51
79 80 6.008696 AGTAGAGTATAACCAGCTCTCAGT 57.991 41.667 0.00 0.00 39.87 3.41
80 81 5.472137 GGAGTAGAGTATAACCAGCTCTCAG 59.528 48.000 0.00 0.00 39.87 3.35
81 82 5.378332 GGAGTAGAGTATAACCAGCTCTCA 58.622 45.833 0.00 0.00 39.87 3.27
82 83 4.763279 GGGAGTAGAGTATAACCAGCTCTC 59.237 50.000 0.00 0.00 39.87 3.20
83 84 4.448054 GGGGAGTAGAGTATAACCAGCTCT 60.448 50.000 0.00 0.00 41.78 4.09
84 85 3.827876 GGGGAGTAGAGTATAACCAGCTC 59.172 52.174 0.00 0.00 0.00 4.09
85 86 3.438225 GGGGGAGTAGAGTATAACCAGCT 60.438 52.174 0.00 0.00 0.00 4.24
86 87 2.898612 GGGGGAGTAGAGTATAACCAGC 59.101 54.545 0.00 0.00 0.00 4.85
87 88 3.155501 CGGGGGAGTAGAGTATAACCAG 58.844 54.545 0.00 0.00 0.00 4.00
88 89 2.515429 ACGGGGGAGTAGAGTATAACCA 59.485 50.000 0.00 0.00 0.00 3.67
89 90 3.235750 ACGGGGGAGTAGAGTATAACC 57.764 52.381 0.00 0.00 0.00 2.85
90 91 3.571828 GGAACGGGGGAGTAGAGTATAAC 59.428 52.174 0.00 0.00 0.00 1.89
91 92 3.464833 AGGAACGGGGGAGTAGAGTATAA 59.535 47.826 0.00 0.00 0.00 0.98
92 93 3.059097 AGGAACGGGGGAGTAGAGTATA 58.941 50.000 0.00 0.00 0.00 1.47
93 94 1.858246 AGGAACGGGGGAGTAGAGTAT 59.142 52.381 0.00 0.00 0.00 2.12
94 95 1.064166 CAGGAACGGGGGAGTAGAGTA 60.064 57.143 0.00 0.00 0.00 2.59
95 96 0.324460 CAGGAACGGGGGAGTAGAGT 60.324 60.000 0.00 0.00 0.00 3.24
96 97 0.033405 TCAGGAACGGGGGAGTAGAG 60.033 60.000 0.00 0.00 0.00 2.43
97 98 0.635009 ATCAGGAACGGGGGAGTAGA 59.365 55.000 0.00 0.00 0.00 2.59
98 99 1.041437 GATCAGGAACGGGGGAGTAG 58.959 60.000 0.00 0.00 0.00 2.57
99 100 0.337082 TGATCAGGAACGGGGGAGTA 59.663 55.000 0.00 0.00 0.00 2.59
100 101 0.978146 CTGATCAGGAACGGGGGAGT 60.978 60.000 15.38 0.00 0.00 3.85
101 102 1.826024 CTGATCAGGAACGGGGGAG 59.174 63.158 15.38 0.00 0.00 4.30
102 103 2.367202 GCTGATCAGGAACGGGGGA 61.367 63.158 23.89 0.00 0.00 4.81
103 104 2.190578 GCTGATCAGGAACGGGGG 59.809 66.667 23.89 0.00 0.00 5.40
104 105 1.153289 CTGCTGATCAGGAACGGGG 60.153 63.158 23.89 5.46 39.15 5.73
105 106 1.817099 GCTGCTGATCAGGAACGGG 60.817 63.158 23.89 10.53 43.06 5.28
106 107 1.817099 GGCTGCTGATCAGGAACGG 60.817 63.158 23.89 13.16 43.06 4.44
107 108 0.461548 TAGGCTGCTGATCAGGAACG 59.538 55.000 23.89 11.60 43.06 3.95
108 109 2.877168 CAATAGGCTGCTGATCAGGAAC 59.123 50.000 23.89 16.48 43.06 3.62
109 110 2.158711 CCAATAGGCTGCTGATCAGGAA 60.159 50.000 23.89 6.83 43.06 3.36
110 111 1.419012 CCAATAGGCTGCTGATCAGGA 59.581 52.381 23.89 20.40 43.06 3.86
111 112 1.893544 CCAATAGGCTGCTGATCAGG 58.106 55.000 23.89 9.58 43.06 3.86
123 124 0.531532 CTGAGCAGTCGGCCAATAGG 60.532 60.000 2.24 0.00 46.50 2.57
124 125 2.983433 CTGAGCAGTCGGCCAATAG 58.017 57.895 2.24 0.00 46.50 1.73
138 139 1.220529 TTCAACAAGTGCTCGCTGAG 58.779 50.000 1.80 1.80 0.00 3.35
139 140 1.882912 ATTCAACAAGTGCTCGCTGA 58.117 45.000 0.00 0.00 0.00 4.26
140 141 3.811722 TTATTCAACAAGTGCTCGCTG 57.188 42.857 0.00 0.00 0.00 5.18
141 142 3.365364 GCTTTATTCAACAAGTGCTCGCT 60.365 43.478 0.00 0.00 0.00 4.93
142 143 2.911102 GCTTTATTCAACAAGTGCTCGC 59.089 45.455 0.00 0.00 0.00 5.03
143 144 4.153117 AGAGCTTTATTCAACAAGTGCTCG 59.847 41.667 0.00 0.00 46.85 5.03
144 145 5.619625 AGAGCTTTATTCAACAAGTGCTC 57.380 39.130 0.00 0.00 43.94 4.26
145 146 6.396829 AAAGAGCTTTATTCAACAAGTGCT 57.603 33.333 0.00 0.00 0.00 4.40
146 147 7.327032 CCTTAAAGAGCTTTATTCAACAAGTGC 59.673 37.037 3.74 0.00 35.27 4.40
147 148 8.352942 ACCTTAAAGAGCTTTATTCAACAAGTG 58.647 33.333 3.74 0.00 35.27 3.16
148 149 8.465273 ACCTTAAAGAGCTTTATTCAACAAGT 57.535 30.769 3.74 0.00 35.27 3.16
149 150 9.750125 AAACCTTAAAGAGCTTTATTCAACAAG 57.250 29.630 3.74 0.00 35.27 3.16
150 151 9.744468 GAAACCTTAAAGAGCTTTATTCAACAA 57.256 29.630 3.74 0.00 35.27 2.83
151 152 8.357402 GGAAACCTTAAAGAGCTTTATTCAACA 58.643 33.333 3.74 0.00 35.27 3.33
152 153 8.744008 GGAAACCTTAAAGAGCTTTATTCAAC 57.256 34.615 3.74 0.00 35.27 3.18
441 442 0.317160 TGGTGTACACTCCAGAAGCG 59.683 55.000 24.55 0.00 34.88 4.68
442 443 1.797025 GTGGTGTACACTCCAGAAGC 58.203 55.000 24.55 6.80 46.72 3.86
452 453 1.053424 GGTCAAGGGAGTGGTGTACA 58.947 55.000 0.00 0.00 0.00 2.90
453 454 1.002087 CTGGTCAAGGGAGTGGTGTAC 59.998 57.143 0.00 0.00 0.00 2.90
454 455 1.348064 CTGGTCAAGGGAGTGGTGTA 58.652 55.000 0.00 0.00 0.00 2.90
455 456 2.056906 GCTGGTCAAGGGAGTGGTGT 62.057 60.000 0.00 0.00 0.00 4.16
456 457 1.302832 GCTGGTCAAGGGAGTGGTG 60.303 63.158 0.00 0.00 0.00 4.17
457 458 1.462238 AGCTGGTCAAGGGAGTGGT 60.462 57.895 0.00 0.00 0.00 4.16
458 459 1.298014 GAGCTGGTCAAGGGAGTGG 59.702 63.158 1.28 0.00 0.00 4.00
459 460 1.298014 GGAGCTGGTCAAGGGAGTG 59.702 63.158 9.30 0.00 0.00 3.51
460 461 1.152030 TGGAGCTGGTCAAGGGAGT 60.152 57.895 9.30 0.00 0.00 3.85
461 462 1.601171 CTGGAGCTGGTCAAGGGAG 59.399 63.158 9.30 0.00 0.00 4.30
462 463 2.596851 GCTGGAGCTGGTCAAGGGA 61.597 63.158 12.84 0.00 38.21 4.20
463 464 2.045536 GCTGGAGCTGGTCAAGGG 60.046 66.667 12.84 0.00 38.21 3.95
464 465 0.747283 GATGCTGGAGCTGGTCAAGG 60.747 60.000 12.84 1.71 42.66 3.61
465 466 0.747283 GGATGCTGGAGCTGGTCAAG 60.747 60.000 6.89 6.89 42.66 3.02
466 467 1.203441 AGGATGCTGGAGCTGGTCAA 61.203 55.000 9.30 0.00 42.66 3.18
467 468 0.325577 TAGGATGCTGGAGCTGGTCA 60.326 55.000 9.30 0.00 42.66 4.02
468 469 0.105778 GTAGGATGCTGGAGCTGGTC 59.894 60.000 0.00 0.00 42.66 4.02
469 470 0.326048 AGTAGGATGCTGGAGCTGGT 60.326 55.000 0.00 0.00 42.66 4.00
470 471 0.392336 GAGTAGGATGCTGGAGCTGG 59.608 60.000 0.00 0.00 42.66 4.85
471 472 0.392336 GGAGTAGGATGCTGGAGCTG 59.608 60.000 0.00 0.00 42.66 4.24
472 473 0.264359 AGGAGTAGGATGCTGGAGCT 59.736 55.000 0.00 0.00 42.66 4.09
473 474 1.127343 AAGGAGTAGGATGCTGGAGC 58.873 55.000 0.00 0.00 42.50 4.70
474 475 2.103941 GGAAAGGAGTAGGATGCTGGAG 59.896 54.545 0.00 0.00 0.00 3.86
475 476 2.119495 GGAAAGGAGTAGGATGCTGGA 58.881 52.381 0.00 0.00 0.00 3.86
476 477 2.103941 GAGGAAAGGAGTAGGATGCTGG 59.896 54.545 0.00 0.00 0.00 4.85
477 478 2.103941 GGAGGAAAGGAGTAGGATGCTG 59.896 54.545 0.00 0.00 0.00 4.41
478 479 2.403561 GGAGGAAAGGAGTAGGATGCT 58.596 52.381 0.00 0.00 0.00 3.79
479 480 1.418264 GGGAGGAAAGGAGTAGGATGC 59.582 57.143 0.00 0.00 0.00 3.91
480 481 2.436173 GTGGGAGGAAAGGAGTAGGATG 59.564 54.545 0.00 0.00 0.00 3.51
502 503 2.510238 GCGTCGCAGCTGGAGATT 60.510 61.111 17.12 0.00 0.00 2.40
539 540 0.881118 GGAGACTTCAAATTGCCGCA 59.119 50.000 0.00 0.00 0.00 5.69
633 634 2.054453 GCTTTGGAGCCATGGGGAC 61.054 63.158 15.13 0.00 43.29 4.46
773 787 2.557490 TGCTAATGTGCAAACATCAGCA 59.443 40.909 11.72 11.72 45.98 4.41
779 793 4.056740 CACCAAATGCTAATGTGCAAACA 58.943 39.130 0.00 0.00 46.61 2.83
800 814 2.223157 CGCACTTTCCGTTTTTCTCACA 60.223 45.455 0.00 0.00 0.00 3.58
837 851 1.741770 GCTGGATTATAGCCGCCCG 60.742 63.158 0.00 0.00 35.15 6.13
843 857 1.014564 GGTCGCCGCTGGATTATAGC 61.015 60.000 0.00 0.00 37.80 2.97
868 882 4.183865 TGTTTCTACCAATGATCGCTCAG 58.816 43.478 0.00 0.00 34.12 3.35
898 912 2.139118 GATGGTAGCGAATCTTCTGCC 58.861 52.381 0.00 1.03 35.91 4.85
932 946 2.010582 TTGAACAGTTTGGTGCGCCC 62.011 55.000 15.15 6.44 0.00 6.13
944 958 5.263185 CCGTAGTGTTTGAAGTTTGAACAG 58.737 41.667 5.53 0.00 34.29 3.16
945 959 4.437659 GCCGTAGTGTTTGAAGTTTGAACA 60.438 41.667 0.00 2.05 0.00 3.18
946 960 4.033019 GCCGTAGTGTTTGAAGTTTGAAC 58.967 43.478 0.00 0.00 0.00 3.18
947 961 3.942748 AGCCGTAGTGTTTGAAGTTTGAA 59.057 39.130 0.00 0.00 0.00 2.69
948 962 3.537580 AGCCGTAGTGTTTGAAGTTTGA 58.462 40.909 0.00 0.00 0.00 2.69
949 963 3.311322 TGAGCCGTAGTGTTTGAAGTTTG 59.689 43.478 0.00 0.00 0.00 2.93
952 966 2.902705 TGAGCCGTAGTGTTTGAAGT 57.097 45.000 0.00 0.00 0.00 3.01
953 967 7.715265 ATATATTGAGCCGTAGTGTTTGAAG 57.285 36.000 0.00 0.00 0.00 3.02
954 968 8.418662 AGTATATATTGAGCCGTAGTGTTTGAA 58.581 33.333 0.00 0.00 0.00 2.69
1043 1061 1.895131 GGTGCTTGATGGTGTGGAATT 59.105 47.619 0.00 0.00 0.00 2.17
1044 1062 1.549203 GGTGCTTGATGGTGTGGAAT 58.451 50.000 0.00 0.00 0.00 3.01
1045 1063 0.539438 GGGTGCTTGATGGTGTGGAA 60.539 55.000 0.00 0.00 0.00 3.53
1046 1064 1.074775 GGGTGCTTGATGGTGTGGA 59.925 57.895 0.00 0.00 0.00 4.02
1047 1065 1.978617 GGGGTGCTTGATGGTGTGG 60.979 63.158 0.00 0.00 0.00 4.17
1048 1066 1.978617 GGGGGTGCTTGATGGTGTG 60.979 63.158 0.00 0.00 0.00 3.82
1070 1088 2.564721 GGCTTTTCGGCACCTTGCT 61.565 57.895 0.00 0.00 44.28 3.91
1071 1089 2.049156 GGCTTTTCGGCACCTTGC 60.049 61.111 0.00 0.00 44.08 4.01
1141 1159 4.700365 TGCACCGTCGACTCTGCG 62.700 66.667 22.11 7.46 31.96 5.18
1169 1187 2.916702 TGCAGATCATACCATTCGCT 57.083 45.000 0.00 0.00 0.00 4.93
1199 1256 7.873739 AAGCTTTTGGATAAAGAATGAAACG 57.126 32.000 0.00 0.00 0.00 3.60
1211 1268 5.041287 CGACAGACGATAAGCTTTTGGATA 58.959 41.667 3.20 0.00 45.77 2.59
1704 1785 3.059386 GAAAACATCGGCCCGCCA 61.059 61.111 6.52 0.00 35.37 5.69
1859 1952 0.822532 ACGACAAGACTGGTCCGAGT 60.823 55.000 4.32 0.00 31.55 4.18
1956 2058 3.330198 AGGGATTATGATCAGCCTTGGA 58.670 45.455 0.09 0.00 33.77 3.53
2019 5124 4.418013 AAACAACAAAGTTTTTGCTGCC 57.582 36.364 0.00 0.00 38.49 4.85
2051 5156 6.937465 TGACATTTGTGTGCCAGTTATTAGTA 59.063 34.615 0.00 0.00 0.00 1.82
2052 5157 5.767665 TGACATTTGTGTGCCAGTTATTAGT 59.232 36.000 0.00 0.00 0.00 2.24
2053 5158 6.252967 TGACATTTGTGTGCCAGTTATTAG 57.747 37.500 0.00 0.00 0.00 1.73
2054 5159 5.335583 GCTGACATTTGTGTGCCAGTTATTA 60.336 40.000 0.00 0.00 0.00 0.98
2055 5160 4.559300 GCTGACATTTGTGTGCCAGTTATT 60.559 41.667 0.00 0.00 0.00 1.40
2056 5161 3.057315 GCTGACATTTGTGTGCCAGTTAT 60.057 43.478 0.00 0.00 0.00 1.89
2057 5162 2.293122 GCTGACATTTGTGTGCCAGTTA 59.707 45.455 0.00 0.00 0.00 2.24
2066 5171 1.987770 GCCGAATTGCTGACATTTGTG 59.012 47.619 0.00 0.00 0.00 3.33
2095 5200 5.470845 AAACACGAAGTCTCTGAAGTTTG 57.529 39.130 0.00 0.00 41.61 2.93
2136 5241 4.654262 ACAGTGTAGGAAGGAAGAACTTGA 59.346 41.667 0.00 0.00 0.00 3.02
2169 5278 4.889427 TCGAGCACGAGGAACATG 57.111 55.556 0.88 0.00 43.81 3.21
2190 5299 3.750373 ATTCGCGGTTGGGGATCGG 62.750 63.158 6.13 0.00 37.45 4.18
2191 5300 2.203015 ATTCGCGGTTGGGGATCG 60.203 61.111 6.13 0.00 37.45 3.69
2192 5301 2.244651 CGATTCGCGGTTGGGGATC 61.245 63.158 6.13 0.00 39.18 3.36
2193 5302 2.040009 ATCGATTCGCGGTTGGGGAT 62.040 55.000 6.13 0.00 41.33 3.85
2194 5303 2.246761 AATCGATTCGCGGTTGGGGA 62.247 55.000 6.13 0.00 42.78 4.81
2195 5304 1.772063 GAATCGATTCGCGGTTGGGG 61.772 60.000 21.57 0.00 44.78 4.96
2196 5305 1.641677 GAATCGATTCGCGGTTGGG 59.358 57.895 21.57 0.00 44.78 4.12
2205 5314 5.744345 TGCTAAGAAGAGAACGAATCGATTC 59.256 40.000 25.18 25.18 0.00 2.52
2206 5315 5.517054 GTGCTAAGAAGAGAACGAATCGATT 59.483 40.000 11.20 11.20 0.00 3.34
2208 5317 4.413087 GTGCTAAGAAGAGAACGAATCGA 58.587 43.478 10.55 0.00 0.00 3.59
2209 5318 3.238570 CGTGCTAAGAAGAGAACGAATCG 59.761 47.826 0.00 0.00 33.03 3.34
2210 5319 4.167268 ACGTGCTAAGAAGAGAACGAATC 58.833 43.478 10.80 0.00 35.18 2.52
2211 5320 4.167268 GACGTGCTAAGAAGAGAACGAAT 58.833 43.478 10.80 0.00 35.18 3.34
2212 5321 3.562505 GACGTGCTAAGAAGAGAACGAA 58.437 45.455 10.80 0.00 35.18 3.85
2213 5322 2.412455 CGACGTGCTAAGAAGAGAACGA 60.412 50.000 10.80 0.00 35.18 3.85
2216 5325 1.201647 CCCGACGTGCTAAGAAGAGAA 59.798 52.381 0.00 0.00 0.00 2.87
2217 5326 0.809385 CCCGACGTGCTAAGAAGAGA 59.191 55.000 0.00 0.00 0.00 3.10
2220 5337 0.458025 GACCCCGACGTGCTAAGAAG 60.458 60.000 0.00 0.00 0.00 2.85
2247 5364 6.183309 TGTAGGTTGATATCTGATCGATCG 57.817 41.667 20.03 9.36 33.48 3.69
2251 5368 7.593825 TGTACATGTAGGTTGATATCTGATCG 58.406 38.462 5.62 0.00 0.00 3.69
2565 5682 3.458579 CGTCTCGTGCCGTCGTTG 61.459 66.667 0.00 0.00 0.00 4.10
2621 5742 5.581874 CCAGTCAAAGCATTCAACAAGTTTT 59.418 36.000 0.00 0.00 0.00 2.43
2642 5766 2.036475 CTCAAGGTGATACCGATCCCAG 59.964 54.545 0.00 0.00 44.90 4.45
2661 5785 1.734465 CTGTTTGGGATGTTCGCTCTC 59.266 52.381 0.00 0.00 0.00 3.20
2718 5842 0.164217 GCAACGCGTCCAACGATTTA 59.836 50.000 14.44 0.00 46.05 1.40
2720 5844 1.959226 AGCAACGCGTCCAACGATT 60.959 52.632 14.44 0.00 46.05 3.34
2757 5881 1.599240 GCTGATCTTCGGGATGGGC 60.599 63.158 0.00 0.00 34.33 5.36
2784 5908 2.236893 TGCAGATGTGTATCTTGCTGGA 59.763 45.455 0.00 0.00 41.71 3.86
2818 5942 7.568199 ACTGCTACTGACACTGTAAATTTTT 57.432 32.000 0.00 0.00 0.00 1.94
2819 5943 7.417612 CAACTGCTACTGACACTGTAAATTTT 58.582 34.615 0.00 0.00 0.00 1.82
2820 5944 6.017109 CCAACTGCTACTGACACTGTAAATTT 60.017 38.462 0.00 0.00 0.00 1.82
2821 5945 5.470098 CCAACTGCTACTGACACTGTAAATT 59.530 40.000 0.00 0.00 0.00 1.82
2822 5946 4.997395 CCAACTGCTACTGACACTGTAAAT 59.003 41.667 0.00 0.00 0.00 1.40
2823 5947 4.141801 ACCAACTGCTACTGACACTGTAAA 60.142 41.667 0.00 0.00 0.00 2.01
2824 5948 3.386726 ACCAACTGCTACTGACACTGTAA 59.613 43.478 0.00 0.00 0.00 2.41
2825 5949 2.963101 ACCAACTGCTACTGACACTGTA 59.037 45.455 0.00 0.00 0.00 2.74
2826 5950 1.762957 ACCAACTGCTACTGACACTGT 59.237 47.619 0.00 0.00 0.00 3.55
2827 5951 2.138320 CACCAACTGCTACTGACACTG 58.862 52.381 0.00 0.00 0.00 3.66
2828 5952 1.762957 ACACCAACTGCTACTGACACT 59.237 47.619 0.00 0.00 0.00 3.55
2829 5953 2.240493 ACACCAACTGCTACTGACAC 57.760 50.000 0.00 0.00 0.00 3.67
2830 5954 4.409718 TTTACACCAACTGCTACTGACA 57.590 40.909 0.00 0.00 0.00 3.58
2831 5955 4.392138 GGATTTACACCAACTGCTACTGAC 59.608 45.833 0.00 0.00 0.00 3.51
2832 5956 4.041075 TGGATTTACACCAACTGCTACTGA 59.959 41.667 0.00 0.00 34.25 3.41
2855 5979 6.340522 TGTCGAATTGATACACATGATGACT 58.659 36.000 0.00 0.00 0.00 3.41
2856 5980 6.476706 TCTGTCGAATTGATACACATGATGAC 59.523 38.462 0.00 0.00 0.00 3.06
2857 5981 6.572519 TCTGTCGAATTGATACACATGATGA 58.427 36.000 0.00 0.00 0.00 2.92
2858 5982 6.698766 TCTCTGTCGAATTGATACACATGATG 59.301 38.462 0.00 0.00 0.00 3.07
2859 5983 6.809869 TCTCTGTCGAATTGATACACATGAT 58.190 36.000 0.00 0.00 0.00 2.45
2860 5984 6.207691 TCTCTGTCGAATTGATACACATGA 57.792 37.500 0.00 0.00 0.00 3.07
2861 5985 6.892310 TTCTCTGTCGAATTGATACACATG 57.108 37.500 0.00 0.00 0.00 3.21
2862 5986 9.770097 AATATTCTCTGTCGAATTGATACACAT 57.230 29.630 0.00 0.00 35.40 3.21
2863 5987 9.599866 AAATATTCTCTGTCGAATTGATACACA 57.400 29.630 0.00 0.00 35.40 3.72
2865 5989 9.816354 TGAAATATTCTCTGTCGAATTGATACA 57.184 29.630 0.00 0.00 35.40 2.29
2868 5992 8.954950 ACTGAAATATTCTCTGTCGAATTGAT 57.045 30.769 0.00 0.00 35.40 2.57
2872 6002 8.258007 TGGTAACTGAAATATTCTCTGTCGAAT 58.742 33.333 0.00 0.00 36.01 3.34
2881 6011 6.435164 AGGCCATTGGTAACTGAAATATTCT 58.565 36.000 5.01 0.00 37.61 2.40
2883 6013 5.299279 CGAGGCCATTGGTAACTGAAATATT 59.701 40.000 5.01 0.00 37.61 1.28
2885 6015 4.080807 TCGAGGCCATTGGTAACTGAAATA 60.081 41.667 5.01 0.00 37.61 1.40
2886 6016 3.016736 CGAGGCCATTGGTAACTGAAAT 58.983 45.455 5.01 0.00 37.61 2.17
2887 6017 2.039216 TCGAGGCCATTGGTAACTGAAA 59.961 45.455 5.01 0.00 37.61 2.69
2889 6019 1.066430 GTCGAGGCCATTGGTAACTGA 60.066 52.381 5.01 0.00 37.61 3.41
2890 6020 1.369625 GTCGAGGCCATTGGTAACTG 58.630 55.000 5.01 0.00 37.61 3.16
2891 6021 0.108329 CGTCGAGGCCATTGGTAACT 60.108 55.000 5.01 0.51 37.61 2.24
2893 6023 0.108520 GTCGTCGAGGCCATTGGTAA 60.109 55.000 5.01 0.00 0.00 2.85
2937 6068 1.671054 GAGCTGCGCCAAAGGTGTA 60.671 57.895 4.18 0.00 35.34 2.90
2994 6125 1.760613 GTATCGGTTGGTGATCAGGGA 59.239 52.381 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.