Multiple sequence alignment - TraesCS5B01G088100

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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 TraesCS5B01G088100 chr5B 100.000 2495 0 0 1 2495 113088020 113085526 0.000000e+00 4608
1 TraesCS5B01G088100 chr5B 81.910 398 72 0 1101 1498 113327888 113327491 1.110000e-88 337
2 TraesCS5B01G088100 chr5D 94.044 1679 57 19 837 2495 103985788 103984133 0.000000e+00 2507
3 TraesCS5B01G088100 chr5D 93.345 571 26 10 243 805 103986345 103985779 0.000000e+00 833
4 TraesCS5B01G088100 chr5D 79.641 501 85 7 999 1498 104113148 104112664 6.610000e-91 344
5 TraesCS5B01G088100 chr5D 79.084 502 89 6 996 1497 104142959 104142474 5.140000e-87 331
6 TraesCS5B01G088100 chr5D 80.845 355 47 16 314 652 549767757 549767408 2.460000e-65 259
7 TraesCS5B01G088100 chr5A 91.184 1123 56 20 791 1895 94689808 94690905 0.000000e+00 1485
8 TraesCS5B01G088100 chr5A 84.268 553 64 20 246 784 94688942 94689485 3.680000e-143 518
9 TraesCS5B01G088100 chr5A 88.480 408 40 7 2092 2495 94691291 94691695 1.040000e-133 486
10 TraesCS5B01G088100 chr5A 79.482 502 84 8 999 1498 94310799 94311283 3.070000e-89 339
11 TraesCS5B01G088100 chr5A 89.140 221 22 2 17 235 57140098 57140318 8.790000e-70 274
12 TraesCS5B01G088100 chr6D 79.167 504 82 15 999 1495 9147176 9147663 6.650000e-86 327
13 TraesCS5B01G088100 chr6B 78.770 504 87 13 1001 1500 16970593 16971080 1.110000e-83 320
14 TraesCS5B01G088100 chr6A 80.918 414 70 7 1090 1500 10138034 10137627 4.000000e-83 318
15 TraesCS5B01G088100 chr3D 84.290 331 30 19 333 652 126385801 126385482 1.120000e-78 303
16 TraesCS5B01G088100 chr3D 90.950 221 18 2 17 235 541408398 541408618 1.880000e-76 296
17 TraesCS5B01G088100 chr7A 83.235 340 39 12 378 704 156321346 156321012 1.880000e-76 296
18 TraesCS5B01G088100 chr1D 90.950 221 18 2 17 235 246951331 246951551 1.880000e-76 296
19 TraesCS5B01G088100 chr1D 84.564 298 28 16 372 660 462387478 462387766 1.890000e-71 279
20 TraesCS5B01G088100 chr4D 90.179 224 20 2 17 238 31017816 31017593 8.730000e-75 291
21 TraesCS5B01G088100 chr4D 88.789 223 19 5 17 235 484629653 484629873 4.090000e-68 268
22 TraesCS5B01G088100 chrUn 90.045 221 20 2 17 235 40653777 40653997 4.060000e-73 285
23 TraesCS5B01G088100 chrUn 89.286 224 22 2 17 238 287444295 287444072 1.890000e-71 279
24 TraesCS5B01G088100 chr3B 89.732 224 21 2 17 238 98994163 98993940 4.060000e-73 285
25 TraesCS5B01G088100 chr3B 80.247 405 55 22 313 704 680220069 680220461 5.250000e-72 281
26 TraesCS5B01G088100 chr3B 90.233 215 19 2 17 229 736885183 736885397 1.890000e-71 279
27 TraesCS5B01G088100 chr3A 81.429 350 48 14 313 652 652833218 652833560 1.140000e-68 270
28 TraesCS5B01G088100 chr7B 81.180 356 42 18 319 657 621455738 621456085 1.900000e-66 263


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 TraesCS5B01G088100 chr5B 113085526 113088020 2494 True 4608.000000 4608 100.000000 1 2495 1 chr5B.!!$R1 2494
1 TraesCS5B01G088100 chr5D 103984133 103986345 2212 True 1670.000000 2507 93.694500 243 2495 2 chr5D.!!$R4 2252
2 TraesCS5B01G088100 chr5A 94688942 94691695 2753 False 829.666667 1485 87.977333 246 2495 3 chr5A.!!$F3 2249

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
175 176 0.034574 TGTCGCATATGGGGCTGTTT 60.035 50.0 22.96 0.0 33.42 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1604 1947 0.586319 ACAGCAAATCCGACACAACG 59.414 50.0 0.0 0.0 0.0 4.1 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
21 22 1.292546 CTCCCCCTTCCTCTTCTAGGT 59.707 57.143 0.00 0.00 46.62 3.08
22 23 1.291335 TCCCCCTTCCTCTTCTAGGTC 59.709 57.143 0.00 0.00 46.62 3.85
23 24 1.292546 CCCCCTTCCTCTTCTAGGTCT 59.707 57.143 0.00 0.00 46.62 3.85
24 25 2.293251 CCCCCTTCCTCTTCTAGGTCTT 60.293 54.545 0.00 0.00 46.62 3.01
25 26 3.052033 CCCCCTTCCTCTTCTAGGTCTTA 60.052 52.174 0.00 0.00 46.62 2.10
26 27 4.574390 CCCCCTTCCTCTTCTAGGTCTTAA 60.574 50.000 0.00 0.00 46.62 1.85
27 28 5.220521 CCCCTTCCTCTTCTAGGTCTTAAT 58.779 45.833 0.00 0.00 46.62 1.40
28 29 5.305902 CCCCTTCCTCTTCTAGGTCTTAATC 59.694 48.000 0.00 0.00 46.62 1.75
29 30 5.900123 CCCTTCCTCTTCTAGGTCTTAATCA 59.100 44.000 0.00 0.00 46.62 2.57
30 31 6.556874 CCCTTCCTCTTCTAGGTCTTAATCAT 59.443 42.308 0.00 0.00 46.62 2.45
31 32 7.730784 CCCTTCCTCTTCTAGGTCTTAATCATA 59.269 40.741 0.00 0.00 46.62 2.15
32 33 8.581578 CCTTCCTCTTCTAGGTCTTAATCATAC 58.418 40.741 0.00 0.00 46.62 2.39
33 34 8.480133 TTCCTCTTCTAGGTCTTAATCATACC 57.520 38.462 0.00 0.00 46.62 2.73
34 35 7.011382 TCCTCTTCTAGGTCTTAATCATACCC 58.989 42.308 0.00 0.00 46.62 3.69
35 36 6.782988 CCTCTTCTAGGTCTTAATCATACCCA 59.217 42.308 0.00 0.00 40.94 4.51
36 37 7.456269 CCTCTTCTAGGTCTTAATCATACCCAT 59.544 40.741 0.00 0.00 40.94 4.00
37 38 8.195165 TCTTCTAGGTCTTAATCATACCCATG 57.805 38.462 0.00 0.00 33.53 3.66
38 39 6.360370 TCTAGGTCTTAATCATACCCATGC 57.640 41.667 0.00 0.00 33.53 4.06
39 40 4.008074 AGGTCTTAATCATACCCATGCG 57.992 45.455 0.00 0.00 33.53 4.73
40 41 3.074412 GGTCTTAATCATACCCATGCGG 58.926 50.000 0.00 0.00 37.81 5.69
60 61 3.726291 GGCAACCAAACAACATGTAGT 57.274 42.857 0.00 0.00 0.00 2.73
61 62 4.053469 GGCAACCAAACAACATGTAGTT 57.947 40.909 0.00 0.00 42.42 2.24
71 72 1.286501 ACATGTAGTTGTATGCGCCG 58.713 50.000 4.18 0.00 0.00 6.46
72 73 1.286501 CATGTAGTTGTATGCGCCGT 58.713 50.000 4.18 0.00 0.00 5.68
73 74 1.005032 CATGTAGTTGTATGCGCCGTG 60.005 52.381 4.18 0.00 0.00 4.94
74 75 0.244178 TGTAGTTGTATGCGCCGTGA 59.756 50.000 4.18 0.00 0.00 4.35
75 76 0.643820 GTAGTTGTATGCGCCGTGAC 59.356 55.000 4.18 0.00 0.00 3.67
76 77 0.244178 TAGTTGTATGCGCCGTGACA 59.756 50.000 4.18 0.09 0.00 3.58
77 78 0.601576 AGTTGTATGCGCCGTGACAA 60.602 50.000 4.18 7.18 0.00 3.18
78 79 0.446222 GTTGTATGCGCCGTGACAAT 59.554 50.000 4.18 0.00 34.54 2.71
79 80 0.445829 TTGTATGCGCCGTGACAATG 59.554 50.000 4.18 0.00 0.00 2.82
80 81 1.297598 GTATGCGCCGTGACAATGC 60.298 57.895 4.18 0.00 0.00 3.56
81 82 1.743252 TATGCGCCGTGACAATGCA 60.743 52.632 4.18 0.00 40.23 3.96
82 83 1.094650 TATGCGCCGTGACAATGCAT 61.095 50.000 4.18 9.72 46.94 3.96
83 84 2.577644 GCGCCGTGACAATGCATG 60.578 61.111 0.00 0.00 0.00 4.06
84 85 2.577644 CGCCGTGACAATGCATGC 60.578 61.111 11.82 11.82 0.00 4.06
85 86 2.567569 GCCGTGACAATGCATGCA 59.432 55.556 25.04 25.04 0.00 3.96
86 87 1.080637 GCCGTGACAATGCATGCAA 60.081 52.632 26.68 4.34 0.00 4.08
87 88 1.346378 GCCGTGACAATGCATGCAAC 61.346 55.000 26.68 16.73 0.00 4.17
88 89 0.241749 CCGTGACAATGCATGCAACT 59.758 50.000 26.68 12.42 0.00 3.16
89 90 1.468127 CCGTGACAATGCATGCAACTA 59.532 47.619 26.68 6.93 0.00 2.24
90 91 2.095314 CCGTGACAATGCATGCAACTAA 60.095 45.455 26.68 6.92 0.00 2.24
91 92 3.563508 CGTGACAATGCATGCAACTAAA 58.436 40.909 26.68 8.09 0.00 1.85
92 93 3.361644 CGTGACAATGCATGCAACTAAAC 59.638 43.478 26.68 18.42 0.00 2.01
93 94 4.297510 GTGACAATGCATGCAACTAAACA 58.702 39.130 26.68 16.45 0.00 2.83
94 95 4.744137 GTGACAATGCATGCAACTAAACAA 59.256 37.500 26.68 3.00 0.00 2.83
95 96 5.406175 GTGACAATGCATGCAACTAAACAAT 59.594 36.000 26.68 0.80 0.00 2.71
96 97 5.405873 TGACAATGCATGCAACTAAACAATG 59.594 36.000 26.68 13.77 0.00 2.82
97 98 4.152759 ACAATGCATGCAACTAAACAATGC 59.847 37.500 26.68 0.00 40.45 3.56
98 99 2.326664 TGCATGCAACTAAACAATGCG 58.673 42.857 20.30 0.00 42.91 4.73
99 100 2.288091 TGCATGCAACTAAACAATGCGT 60.288 40.909 20.30 0.00 42.91 5.24
100 101 2.342354 GCATGCAACTAAACAATGCGTC 59.658 45.455 14.21 0.00 42.91 5.19
101 102 3.563508 CATGCAACTAAACAATGCGTCA 58.436 40.909 0.00 0.00 42.91 4.35
102 103 3.699779 TGCAACTAAACAATGCGTCAA 57.300 38.095 0.00 0.00 42.91 3.18
103 104 4.033990 TGCAACTAAACAATGCGTCAAA 57.966 36.364 0.00 0.00 42.91 2.69
104 105 4.041049 TGCAACTAAACAATGCGTCAAAG 58.959 39.130 0.00 0.00 42.91 2.77
105 106 4.041723 GCAACTAAACAATGCGTCAAAGT 58.958 39.130 0.00 0.00 0.00 2.66
106 107 4.502645 GCAACTAAACAATGCGTCAAAGTT 59.497 37.500 0.00 0.00 0.00 2.66
107 108 5.554324 GCAACTAAACAATGCGTCAAAGTTG 60.554 40.000 7.35 7.35 40.72 3.16
108 109 5.493133 ACTAAACAATGCGTCAAAGTTGA 57.507 34.783 0.00 0.00 34.20 3.18
109 110 6.072112 ACTAAACAATGCGTCAAAGTTGAT 57.928 33.333 0.00 0.00 39.73 2.57
110 111 6.142817 ACTAAACAATGCGTCAAAGTTGATC 58.857 36.000 0.00 0.00 39.73 2.92
111 112 3.559238 ACAATGCGTCAAAGTTGATCC 57.441 42.857 0.00 0.00 39.73 3.36
112 113 2.228822 ACAATGCGTCAAAGTTGATCCC 59.771 45.455 0.00 0.00 39.73 3.85
113 114 1.463674 ATGCGTCAAAGTTGATCCCC 58.536 50.000 0.00 0.00 39.73 4.81
114 115 0.400213 TGCGTCAAAGTTGATCCCCT 59.600 50.000 0.00 0.00 39.73 4.79
115 116 1.626321 TGCGTCAAAGTTGATCCCCTA 59.374 47.619 0.00 0.00 39.73 3.53
116 117 2.039216 TGCGTCAAAGTTGATCCCCTAA 59.961 45.455 0.00 0.00 39.73 2.69
117 118 3.279434 GCGTCAAAGTTGATCCCCTAAT 58.721 45.455 0.00 0.00 39.73 1.73
118 119 3.065371 GCGTCAAAGTTGATCCCCTAATG 59.935 47.826 0.00 0.00 39.73 1.90
119 120 3.065371 CGTCAAAGTTGATCCCCTAATGC 59.935 47.826 0.00 0.00 39.73 3.56
120 121 4.016444 GTCAAAGTTGATCCCCTAATGCA 58.984 43.478 0.00 0.00 39.73 3.96
121 122 4.096984 GTCAAAGTTGATCCCCTAATGCAG 59.903 45.833 0.00 0.00 39.73 4.41
122 123 3.303351 AAGTTGATCCCCTAATGCAGG 57.697 47.619 0.00 0.00 45.07 4.85
123 124 7.054868 TCAAAGTTGATCCCCTAATGCAGGA 62.055 44.000 0.00 0.00 38.35 3.86
124 125 8.455959 TCAAAGTTGATCCCCTAATGCAGGAA 62.456 42.308 0.00 0.00 38.35 3.36
137 138 4.630644 ATGCAGGAAGTCCATATGTAGG 57.369 45.455 1.24 0.00 38.89 3.18
138 139 2.104792 TGCAGGAAGTCCATATGTAGGC 59.895 50.000 1.24 0.00 38.89 3.93
139 140 2.104792 GCAGGAAGTCCATATGTAGGCA 59.895 50.000 1.24 0.00 38.89 4.75
140 141 3.433598 GCAGGAAGTCCATATGTAGGCAA 60.434 47.826 1.24 0.00 38.89 4.52
141 142 4.130118 CAGGAAGTCCATATGTAGGCAAC 58.870 47.826 1.24 0.00 38.89 4.17
142 143 3.136626 AGGAAGTCCATATGTAGGCAACC 59.863 47.826 1.24 0.00 38.89 3.77
143 144 3.118038 GGAAGTCCATATGTAGGCAACCA 60.118 47.826 1.24 0.00 35.64 3.67
144 145 4.523083 GAAGTCCATATGTAGGCAACCAA 58.477 43.478 1.24 0.00 37.17 3.67
145 146 4.584638 AGTCCATATGTAGGCAACCAAA 57.415 40.909 1.24 0.00 37.17 3.28
146 147 4.270008 AGTCCATATGTAGGCAACCAAAC 58.730 43.478 1.24 0.00 37.17 2.93
147 148 4.013728 GTCCATATGTAGGCAACCAAACA 58.986 43.478 1.24 0.00 37.17 2.83
148 149 4.461081 GTCCATATGTAGGCAACCAAACAA 59.539 41.667 1.24 0.00 37.17 2.83
149 150 4.461081 TCCATATGTAGGCAACCAAACAAC 59.539 41.667 1.24 0.00 37.17 3.32
150 151 4.462483 CCATATGTAGGCAACCAAACAACT 59.538 41.667 1.24 0.00 37.17 3.16
151 152 5.047377 CCATATGTAGGCAACCAAACAACTT 60.047 40.000 1.24 0.00 37.17 2.66
152 153 3.791973 TGTAGGCAACCAAACAACTTG 57.208 42.857 0.00 0.00 34.52 3.16
153 154 3.357203 TGTAGGCAACCAAACAACTTGA 58.643 40.909 0.00 0.00 37.17 3.02
154 155 3.380004 TGTAGGCAACCAAACAACTTGAG 59.620 43.478 0.00 0.00 37.17 3.02
155 156 2.733956 AGGCAACCAAACAACTTGAGA 58.266 42.857 0.00 0.00 37.17 3.27
156 157 3.299503 AGGCAACCAAACAACTTGAGAT 58.700 40.909 0.00 0.00 37.17 2.75
157 158 3.068590 AGGCAACCAAACAACTTGAGATG 59.931 43.478 0.00 0.00 37.17 2.90
158 159 3.181476 GGCAACCAAACAACTTGAGATGT 60.181 43.478 0.00 0.00 37.17 3.06
159 160 4.044426 GCAACCAAACAACTTGAGATGTC 58.956 43.478 0.00 0.00 37.17 3.06
160 161 4.282068 CAACCAAACAACTTGAGATGTCG 58.718 43.478 0.00 0.00 37.17 4.35
161 162 2.290641 ACCAAACAACTTGAGATGTCGC 59.709 45.455 0.00 0.00 37.17 5.19
162 163 2.290367 CCAAACAACTTGAGATGTCGCA 59.710 45.455 0.00 0.00 37.17 5.10
163 164 3.058016 CCAAACAACTTGAGATGTCGCAT 60.058 43.478 0.00 0.00 37.17 4.73
164 165 4.154015 CCAAACAACTTGAGATGTCGCATA 59.846 41.667 0.00 0.00 37.17 3.14
165 166 5.163723 CCAAACAACTTGAGATGTCGCATAT 60.164 40.000 0.00 0.00 37.17 1.78
166 167 5.475273 AACAACTTGAGATGTCGCATATG 57.525 39.130 0.00 0.00 30.44 1.78
167 168 3.873361 ACAACTTGAGATGTCGCATATGG 59.127 43.478 4.56 0.00 0.00 2.74
168 169 3.117491 ACTTGAGATGTCGCATATGGG 57.883 47.619 13.38 13.38 0.00 4.00
169 170 2.224378 ACTTGAGATGTCGCATATGGGG 60.224 50.000 18.68 3.12 0.00 4.96
170 171 0.035317 TGAGATGTCGCATATGGGGC 59.965 55.000 16.86 16.86 0.00 5.80
171 172 0.322975 GAGATGTCGCATATGGGGCT 59.677 55.000 22.96 13.44 33.42 5.19
172 173 0.035881 AGATGTCGCATATGGGGCTG 59.964 55.000 22.96 0.00 33.42 4.85
173 174 0.250467 GATGTCGCATATGGGGCTGT 60.250 55.000 22.96 12.97 33.42 4.40
174 175 0.183492 ATGTCGCATATGGGGCTGTT 59.817 50.000 22.96 7.42 33.42 3.16
175 176 0.034574 TGTCGCATATGGGGCTGTTT 60.035 50.000 22.96 0.00 33.42 2.83
176 177 1.102978 GTCGCATATGGGGCTGTTTT 58.897 50.000 16.48 0.00 0.00 2.43
177 178 1.476488 GTCGCATATGGGGCTGTTTTT 59.524 47.619 16.48 0.00 0.00 1.94
178 179 1.748493 TCGCATATGGGGCTGTTTTTC 59.252 47.619 18.68 0.00 0.00 2.29
179 180 1.202405 CGCATATGGGGCTGTTTTTCC 60.202 52.381 11.82 0.00 0.00 3.13
180 181 1.830477 GCATATGGGGCTGTTTTTCCA 59.170 47.619 4.56 0.00 0.00 3.53
181 182 2.159057 GCATATGGGGCTGTTTTTCCAG 60.159 50.000 4.56 0.00 35.49 3.86
182 183 3.364549 CATATGGGGCTGTTTTTCCAGA 58.635 45.455 0.00 0.00 34.23 3.86
183 184 1.928868 ATGGGGCTGTTTTTCCAGAG 58.071 50.000 0.00 0.00 34.23 3.35
184 185 0.827507 TGGGGCTGTTTTTCCAGAGC 60.828 55.000 0.00 0.00 34.23 4.09
188 189 0.600057 GCTGTTTTTCCAGAGCCAGG 59.400 55.000 0.00 0.00 34.23 4.45
189 190 0.600057 CTGTTTTTCCAGAGCCAGGC 59.400 55.000 1.84 1.84 34.23 4.85
190 191 0.185901 TGTTTTTCCAGAGCCAGGCT 59.814 50.000 16.12 16.12 43.88 4.58
191 192 1.423541 TGTTTTTCCAGAGCCAGGCTA 59.576 47.619 16.16 0.00 39.88 3.93
192 193 2.158534 TGTTTTTCCAGAGCCAGGCTAA 60.159 45.455 16.16 1.20 39.88 3.09
193 194 2.489722 GTTTTTCCAGAGCCAGGCTAAG 59.510 50.000 16.16 9.96 39.88 2.18
194 195 1.362224 TTTCCAGAGCCAGGCTAAGT 58.638 50.000 16.16 0.00 39.88 2.24
195 196 0.615331 TTCCAGAGCCAGGCTAAGTG 59.385 55.000 16.16 12.34 39.88 3.16
196 197 1.222936 CCAGAGCCAGGCTAAGTGG 59.777 63.158 16.16 17.68 39.88 4.00
197 198 1.267574 CCAGAGCCAGGCTAAGTGGA 61.268 60.000 24.51 0.00 39.88 4.02
198 199 0.177604 CAGAGCCAGGCTAAGTGGAG 59.822 60.000 16.16 0.00 39.88 3.86
199 200 0.041833 AGAGCCAGGCTAAGTGGAGA 59.958 55.000 16.16 0.00 39.88 3.71
200 201 0.905357 GAGCCAGGCTAAGTGGAGAA 59.095 55.000 16.16 0.00 39.88 2.87
201 202 1.279271 GAGCCAGGCTAAGTGGAGAAA 59.721 52.381 16.16 0.00 39.88 2.52
202 203 1.280421 AGCCAGGCTAAGTGGAGAAAG 59.720 52.381 14.18 0.00 36.99 2.62
203 204 1.680249 GCCAGGCTAAGTGGAGAAAGG 60.680 57.143 3.29 0.00 37.23 3.11
204 205 1.630878 CCAGGCTAAGTGGAGAAAGGT 59.369 52.381 0.00 0.00 37.23 3.50
205 206 2.838202 CCAGGCTAAGTGGAGAAAGGTA 59.162 50.000 0.00 0.00 37.23 3.08
206 207 3.456277 CCAGGCTAAGTGGAGAAAGGTAT 59.544 47.826 0.00 0.00 37.23 2.73
207 208 4.446371 CAGGCTAAGTGGAGAAAGGTATG 58.554 47.826 0.00 0.00 0.00 2.39
208 209 3.118223 AGGCTAAGTGGAGAAAGGTATGC 60.118 47.826 0.00 0.00 0.00 3.14
209 210 3.370527 GGCTAAGTGGAGAAAGGTATGCA 60.371 47.826 0.00 0.00 0.00 3.96
210 211 4.261801 GCTAAGTGGAGAAAGGTATGCAA 58.738 43.478 0.00 0.00 0.00 4.08
211 212 4.095036 GCTAAGTGGAGAAAGGTATGCAAC 59.905 45.833 0.00 0.00 0.00 4.17
212 213 2.699954 AGTGGAGAAAGGTATGCAACG 58.300 47.619 0.00 0.00 0.00 4.10
213 214 1.130561 GTGGAGAAAGGTATGCAACGC 59.869 52.381 0.00 0.00 0.00 4.84
214 215 1.271108 TGGAGAAAGGTATGCAACGCA 60.271 47.619 0.00 0.00 44.86 5.24
215 216 1.398390 GGAGAAAGGTATGCAACGCAG 59.602 52.381 0.00 0.00 43.65 5.18
216 217 1.398390 GAGAAAGGTATGCAACGCAGG 59.602 52.381 0.00 0.00 43.65 4.85
217 218 1.165270 GAAAGGTATGCAACGCAGGT 58.835 50.000 0.00 0.00 43.65 4.00
218 219 2.027561 AGAAAGGTATGCAACGCAGGTA 60.028 45.455 0.00 0.00 43.65 3.08
219 220 1.734163 AAGGTATGCAACGCAGGTAC 58.266 50.000 0.00 0.00 43.65 3.34
220 221 0.459585 AGGTATGCAACGCAGGTACG 60.460 55.000 0.00 0.00 43.65 3.67
221 222 1.426041 GGTATGCAACGCAGGTACGG 61.426 60.000 0.00 0.00 43.65 4.02
222 223 0.738412 GTATGCAACGCAGGTACGGT 60.738 55.000 0.00 0.00 43.65 4.83
223 224 0.816373 TATGCAACGCAGGTACGGTA 59.184 50.000 0.00 0.00 43.65 4.02
224 225 0.459585 ATGCAACGCAGGTACGGTAG 60.460 55.000 0.00 0.00 43.65 3.18
225 226 2.450345 GCAACGCAGGTACGGTAGC 61.450 63.158 9.26 9.26 37.37 3.58
226 227 1.808390 CAACGCAGGTACGGTAGCC 60.808 63.158 13.34 6.26 37.37 3.93
292 293 2.342279 CCCGCTCTCCGACACAAA 59.658 61.111 0.00 0.00 40.02 2.83
431 439 7.931578 TTGACCTTTCATTGTATCGGTAAAT 57.068 32.000 0.00 0.00 0.00 1.40
543 552 9.830975 AGCAAATAGTTTTTGTATTCTTTTGGT 57.169 25.926 7.71 0.00 0.00 3.67
698 710 8.340757 ACTATATACACCCAAAAATCAAGGGAA 58.659 33.333 3.32 0.00 45.80 3.97
870 1200 0.962855 GCCAAGCCTTCCCTGAGTTC 60.963 60.000 0.00 0.00 0.00 3.01
941 1274 3.126001 TCACAGTGAGCCTTAAACCTG 57.874 47.619 0.00 0.00 0.00 4.00
942 1275 2.154462 CACAGTGAGCCTTAAACCTGG 58.846 52.381 0.00 0.00 0.00 4.45
1192 1534 3.397613 CTGCTCTACAGCCCTGGCC 62.398 68.421 4.13 0.00 46.26 5.36
1527 1869 5.508994 GCTGGGTGTGTTTAATAAGTTTGCT 60.509 40.000 0.00 0.00 0.00 3.91
1548 1890 2.353889 TGCTCGGTGATCTTAGTCGTAC 59.646 50.000 0.00 0.00 0.00 3.67
1581 1924 6.644592 GCTAGTTAGTTATCATCTGCTCCAAG 59.355 42.308 0.00 0.00 0.00 3.61
1604 1947 1.582502 GCTATTGTACTGTCGTGTCGC 59.417 52.381 0.00 0.00 0.00 5.19
1607 1950 0.248580 TTGTACTGTCGTGTCGCGTT 60.249 50.000 5.77 0.00 42.13 4.84
1608 1951 0.931202 TGTACTGTCGTGTCGCGTTG 60.931 55.000 5.77 0.00 42.13 4.10
1609 1952 0.931662 GTACTGTCGTGTCGCGTTGT 60.932 55.000 5.77 6.09 42.13 3.32
1610 1953 0.931202 TACTGTCGTGTCGCGTTGTG 60.931 55.000 5.77 0.00 42.13 3.33
1611 1954 2.202636 TGTCGTGTCGCGTTGTGT 60.203 55.556 5.77 0.00 42.13 3.72
1612 1955 2.130554 CTGTCGTGTCGCGTTGTGTC 62.131 60.000 5.77 0.00 42.13 3.67
1613 1956 3.020105 TCGTGTCGCGTTGTGTCG 61.020 61.111 5.77 4.38 42.13 4.35
1650 1993 0.168128 GTAGTTGCGGTGGTGAATGC 59.832 55.000 0.00 0.00 0.00 3.56
1670 2013 2.286294 GCGTGGCTAGAGATGTTTCATG 59.714 50.000 0.00 0.00 0.00 3.07
1895 2246 3.511540 TCCTCGCGATGGATGAATCTAAT 59.488 43.478 19.22 0.00 0.00 1.73
2021 2373 0.317479 AACCCGAGAGAGAACCAACG 59.683 55.000 0.00 0.00 0.00 4.10
2036 2440 1.804151 CCAACGACAATGTGGAACGAT 59.196 47.619 1.61 0.00 42.39 3.73
2050 2454 5.588648 TGTGGAACGATGATTAATTTCTCCC 59.411 40.000 0.00 0.00 42.39 4.30
2055 2459 3.809832 CGATGATTAATTTCTCCCGCAGT 59.190 43.478 0.00 0.00 0.00 4.40
2098 2694 5.590259 AGAATCACAGCCGCTGTATTTTTAT 59.410 36.000 25.29 10.97 43.43 1.40
2143 2739 3.431415 ACTGGGTAAATTTGGCCTCTTC 58.569 45.455 3.32 0.00 0.00 2.87
2154 2750 2.762745 TGGCCTCTTCTTTGTTCGTAC 58.237 47.619 3.32 0.00 0.00 3.67
2191 2787 2.510664 GAAGGCCTCGACTGGAGAT 58.489 57.895 5.23 0.00 46.23 2.75
2193 2789 0.616111 AAGGCCTCGACTGGAGATGT 60.616 55.000 5.23 0.00 46.23 3.06
2285 2889 1.298788 CCACCGCCGTTTGTTGTTC 60.299 57.895 0.00 0.00 0.00 3.18
2335 2941 3.525199 GGGTAGATTCCATGGCATATCCT 59.475 47.826 6.96 0.00 35.26 3.24
2362 2968 2.042843 CGGGCCCCTACTCAGTCT 60.043 66.667 18.66 0.00 0.00 3.24
2465 3071 0.710567 GCGCATCGATCGATTACTGG 59.289 55.000 27.45 16.71 31.62 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.841282 TGGGTATGATTAAGACCTAGAAGAG 57.159 40.000 0.00 0.00 33.48 2.85
12 13 7.256332 GCATGGGTATGATTAAGACCTAGAAGA 60.256 40.741 0.00 0.00 36.36 2.87
13 14 6.876257 GCATGGGTATGATTAAGACCTAGAAG 59.124 42.308 0.00 0.00 36.36 2.85
14 15 6.518369 CGCATGGGTATGATTAAGACCTAGAA 60.518 42.308 0.68 0.00 36.36 2.10
15 16 5.047306 CGCATGGGTATGATTAAGACCTAGA 60.047 44.000 0.68 0.00 36.36 2.43
16 17 5.171476 CGCATGGGTATGATTAAGACCTAG 58.829 45.833 0.68 0.00 36.36 3.02
17 18 4.020573 CCGCATGGGTATGATTAAGACCTA 60.021 45.833 9.14 0.00 36.36 3.08
18 19 3.244561 CCGCATGGGTATGATTAAGACCT 60.245 47.826 9.14 0.00 36.36 3.85
19 20 3.074412 CCGCATGGGTATGATTAAGACC 58.926 50.000 9.14 0.00 36.36 3.85
33 34 2.048316 GTTTGGTTGCCCGCATGG 60.048 61.111 0.00 0.00 37.09 3.66
34 35 1.068753 TTGTTTGGTTGCCCGCATG 59.931 52.632 0.00 0.00 0.00 4.06
35 36 1.068921 GTTGTTTGGTTGCCCGCAT 59.931 52.632 0.00 0.00 0.00 4.73
36 37 1.680522 ATGTTGTTTGGTTGCCCGCA 61.681 50.000 0.00 0.00 0.00 5.69
37 38 1.068921 ATGTTGTTTGGTTGCCCGC 59.931 52.632 0.00 0.00 0.00 6.13
38 39 0.103937 ACATGTTGTTTGGTTGCCCG 59.896 50.000 0.00 0.00 0.00 6.13
39 40 2.364002 ACTACATGTTGTTTGGTTGCCC 59.636 45.455 2.30 0.00 0.00 5.36
40 41 3.726291 ACTACATGTTGTTTGGTTGCC 57.274 42.857 2.30 0.00 0.00 4.52
51 52 1.663643 CGGCGCATACAACTACATGTT 59.336 47.619 10.83 0.00 39.92 2.71
52 53 1.286501 CGGCGCATACAACTACATGT 58.713 50.000 10.83 2.69 37.32 3.21
53 54 1.005032 CACGGCGCATACAACTACATG 60.005 52.381 10.83 0.00 0.00 3.21
54 55 1.134936 TCACGGCGCATACAACTACAT 60.135 47.619 10.83 0.00 0.00 2.29
55 56 0.244178 TCACGGCGCATACAACTACA 59.756 50.000 10.83 0.00 0.00 2.74
56 57 0.643820 GTCACGGCGCATACAACTAC 59.356 55.000 10.83 0.00 0.00 2.73
57 58 0.244178 TGTCACGGCGCATACAACTA 59.756 50.000 10.83 0.00 0.00 2.24
58 59 0.601576 TTGTCACGGCGCATACAACT 60.602 50.000 10.83 0.00 0.00 3.16
59 60 0.446222 ATTGTCACGGCGCATACAAC 59.554 50.000 19.84 0.52 34.89 3.32
60 61 0.445829 CATTGTCACGGCGCATACAA 59.554 50.000 19.76 19.76 36.37 2.41
61 62 1.976478 GCATTGTCACGGCGCATACA 61.976 55.000 10.83 6.09 0.00 2.29
62 63 1.297598 GCATTGTCACGGCGCATAC 60.298 57.895 10.83 2.99 0.00 2.39
63 64 1.094650 ATGCATTGTCACGGCGCATA 61.095 50.000 10.83 0.00 41.32 3.14
64 65 2.409055 ATGCATTGTCACGGCGCAT 61.409 52.632 10.83 0.00 38.44 4.73
65 66 3.055110 ATGCATTGTCACGGCGCA 61.055 55.556 10.83 0.00 36.95 6.09
66 67 2.577644 CATGCATTGTCACGGCGC 60.578 61.111 6.90 0.00 0.00 6.53
67 68 2.577644 GCATGCATTGTCACGGCG 60.578 61.111 14.21 4.80 0.00 6.46
68 69 1.080637 TTGCATGCATTGTCACGGC 60.081 52.632 23.37 0.00 0.00 5.68
69 70 0.241749 AGTTGCATGCATTGTCACGG 59.758 50.000 23.37 0.00 0.00 4.94
70 71 2.898181 TAGTTGCATGCATTGTCACG 57.102 45.000 23.37 0.00 0.00 4.35
71 72 4.297510 TGTTTAGTTGCATGCATTGTCAC 58.702 39.130 23.37 16.25 0.00 3.67
72 73 4.581077 TGTTTAGTTGCATGCATTGTCA 57.419 36.364 23.37 13.07 0.00 3.58
73 74 5.669357 GCATTGTTTAGTTGCATGCATTGTC 60.669 40.000 23.37 12.31 36.40 3.18
74 75 4.152759 GCATTGTTTAGTTGCATGCATTGT 59.847 37.500 23.37 11.57 36.40 2.71
75 76 4.643953 GCATTGTTTAGTTGCATGCATTG 58.356 39.130 23.37 9.02 36.40 2.82
76 77 3.368539 CGCATTGTTTAGTTGCATGCATT 59.631 39.130 23.37 15.45 36.15 3.56
77 78 2.924926 CGCATTGTTTAGTTGCATGCAT 59.075 40.909 23.37 10.46 36.15 3.96
78 79 2.288091 ACGCATTGTTTAGTTGCATGCA 60.288 40.909 18.46 18.46 36.15 3.96
79 80 2.327568 ACGCATTGTTTAGTTGCATGC 58.672 42.857 11.82 11.82 36.15 4.06
80 81 3.563508 TGACGCATTGTTTAGTTGCATG 58.436 40.909 0.00 0.00 36.15 4.06
81 82 3.913548 TGACGCATTGTTTAGTTGCAT 57.086 38.095 0.00 0.00 36.15 3.96
82 83 3.699779 TTGACGCATTGTTTAGTTGCA 57.300 38.095 0.00 0.00 36.15 4.08
83 84 4.041723 ACTTTGACGCATTGTTTAGTTGC 58.958 39.130 0.00 0.00 0.00 4.17
84 85 5.741510 TCAACTTTGACGCATTGTTTAGTTG 59.258 36.000 0.00 0.00 40.75 3.16
85 86 5.885881 TCAACTTTGACGCATTGTTTAGTT 58.114 33.333 0.00 0.00 31.01 2.24
86 87 5.493133 TCAACTTTGACGCATTGTTTAGT 57.507 34.783 0.00 0.00 31.01 2.24
87 88 5.569059 GGATCAACTTTGACGCATTGTTTAG 59.431 40.000 0.00 0.00 40.49 1.85
88 89 5.457140 GGATCAACTTTGACGCATTGTTTA 58.543 37.500 0.00 0.00 40.49 2.01
89 90 4.298332 GGATCAACTTTGACGCATTGTTT 58.702 39.130 0.00 0.00 40.49 2.83
90 91 3.305335 GGGATCAACTTTGACGCATTGTT 60.305 43.478 0.00 0.00 40.49 2.83
91 92 2.228822 GGGATCAACTTTGACGCATTGT 59.771 45.455 0.00 0.00 40.49 2.71
92 93 2.415893 GGGGATCAACTTTGACGCATTG 60.416 50.000 0.00 0.00 40.49 2.82
93 94 1.818674 GGGGATCAACTTTGACGCATT 59.181 47.619 0.00 0.00 40.49 3.56
94 95 1.004745 AGGGGATCAACTTTGACGCAT 59.995 47.619 0.00 0.00 40.49 4.73
95 96 0.400213 AGGGGATCAACTTTGACGCA 59.600 50.000 0.00 0.00 40.49 5.24
96 97 2.396590 TAGGGGATCAACTTTGACGC 57.603 50.000 0.00 0.00 40.49 5.19
97 98 3.065371 GCATTAGGGGATCAACTTTGACG 59.935 47.826 0.00 0.00 40.49 4.35
98 99 4.016444 TGCATTAGGGGATCAACTTTGAC 58.984 43.478 0.00 0.00 40.49 3.18
99 100 4.272489 CTGCATTAGGGGATCAACTTTGA 58.728 43.478 0.00 0.00 42.14 2.69
100 101 3.382546 CCTGCATTAGGGGATCAACTTTG 59.617 47.826 0.00 0.00 43.33 2.77
101 102 3.635591 CCTGCATTAGGGGATCAACTTT 58.364 45.455 0.00 0.00 43.33 2.66
102 103 3.303351 CCTGCATTAGGGGATCAACTT 57.697 47.619 0.00 0.00 43.33 2.66
113 114 6.169094 CCTACATATGGACTTCCTGCATTAG 58.831 44.000 7.80 0.00 36.82 1.73
114 115 5.513094 GCCTACATATGGACTTCCTGCATTA 60.513 44.000 7.80 0.00 36.82 1.90
115 116 4.747931 GCCTACATATGGACTTCCTGCATT 60.748 45.833 7.80 0.00 36.82 3.56
116 117 3.244700 GCCTACATATGGACTTCCTGCAT 60.245 47.826 7.80 0.00 36.82 3.96
117 118 2.104792 GCCTACATATGGACTTCCTGCA 59.895 50.000 7.80 0.00 36.82 4.41
118 119 2.104792 TGCCTACATATGGACTTCCTGC 59.895 50.000 7.80 0.00 36.82 4.85
119 120 4.130118 GTTGCCTACATATGGACTTCCTG 58.870 47.826 7.80 0.00 36.82 3.86
120 121 3.136626 GGTTGCCTACATATGGACTTCCT 59.863 47.826 7.80 0.00 36.82 3.36
121 122 3.118038 TGGTTGCCTACATATGGACTTCC 60.118 47.826 7.80 1.81 0.00 3.46
122 123 4.150897 TGGTTGCCTACATATGGACTTC 57.849 45.455 7.80 0.00 0.00 3.01
123 124 4.584638 TTGGTTGCCTACATATGGACTT 57.415 40.909 7.80 0.00 0.00 3.01
124 125 4.263727 TGTTTGGTTGCCTACATATGGACT 60.264 41.667 7.80 0.00 0.00 3.85
125 126 4.013728 TGTTTGGTTGCCTACATATGGAC 58.986 43.478 7.80 0.00 0.00 4.02
126 127 4.308526 TGTTTGGTTGCCTACATATGGA 57.691 40.909 7.80 0.00 0.00 3.41
127 128 4.462483 AGTTGTTTGGTTGCCTACATATGG 59.538 41.667 7.80 0.00 0.00 2.74
128 129 5.643379 AGTTGTTTGGTTGCCTACATATG 57.357 39.130 0.00 0.00 0.00 1.78
129 130 5.772672 TCAAGTTGTTTGGTTGCCTACATAT 59.227 36.000 2.11 0.00 37.39 1.78
130 131 5.133941 TCAAGTTGTTTGGTTGCCTACATA 58.866 37.500 2.11 0.00 37.39 2.29
131 132 3.957497 TCAAGTTGTTTGGTTGCCTACAT 59.043 39.130 2.11 0.00 37.39 2.29
132 133 3.357203 TCAAGTTGTTTGGTTGCCTACA 58.643 40.909 2.11 0.00 37.39 2.74
133 134 3.630312 TCTCAAGTTGTTTGGTTGCCTAC 59.370 43.478 2.11 0.00 37.39 3.18
134 135 3.892284 TCTCAAGTTGTTTGGTTGCCTA 58.108 40.909 2.11 0.00 37.39 3.93
135 136 2.733956 TCTCAAGTTGTTTGGTTGCCT 58.266 42.857 2.11 0.00 37.39 4.75
136 137 3.181476 ACATCTCAAGTTGTTTGGTTGCC 60.181 43.478 2.11 0.00 37.39 4.52
137 138 4.044426 GACATCTCAAGTTGTTTGGTTGC 58.956 43.478 2.11 0.00 37.39 4.17
138 139 4.282068 CGACATCTCAAGTTGTTTGGTTG 58.718 43.478 2.11 0.00 37.39 3.77
139 140 3.243068 GCGACATCTCAAGTTGTTTGGTT 60.243 43.478 2.11 0.00 37.39 3.67
140 141 2.290641 GCGACATCTCAAGTTGTTTGGT 59.709 45.455 2.11 0.00 37.39 3.67
141 142 2.290367 TGCGACATCTCAAGTTGTTTGG 59.710 45.455 2.11 0.00 37.39 3.28
142 143 3.607422 TGCGACATCTCAAGTTGTTTG 57.393 42.857 2.11 2.28 38.17 2.93
143 144 5.163723 CCATATGCGACATCTCAAGTTGTTT 60.164 40.000 2.11 0.00 0.00 2.83
144 145 4.333649 CCATATGCGACATCTCAAGTTGTT 59.666 41.667 2.11 0.00 0.00 2.83
145 146 3.873361 CCATATGCGACATCTCAAGTTGT 59.127 43.478 2.11 0.00 0.00 3.32
146 147 3.249320 CCCATATGCGACATCTCAAGTTG 59.751 47.826 0.00 0.00 0.00 3.16
147 148 3.470709 CCCATATGCGACATCTCAAGTT 58.529 45.455 0.00 0.00 0.00 2.66
148 149 2.224378 CCCCATATGCGACATCTCAAGT 60.224 50.000 0.00 0.00 0.00 3.16
149 150 2.420642 CCCCATATGCGACATCTCAAG 58.579 52.381 0.00 0.00 0.00 3.02
150 151 1.543208 GCCCCATATGCGACATCTCAA 60.543 52.381 0.00 0.00 0.00 3.02
151 152 0.035317 GCCCCATATGCGACATCTCA 59.965 55.000 0.00 0.00 0.00 3.27
152 153 0.322975 AGCCCCATATGCGACATCTC 59.677 55.000 0.00 0.00 0.00 2.75
153 154 0.035881 CAGCCCCATATGCGACATCT 59.964 55.000 0.00 0.00 0.00 2.90
154 155 0.250467 ACAGCCCCATATGCGACATC 60.250 55.000 0.00 0.00 0.00 3.06
155 156 0.183492 AACAGCCCCATATGCGACAT 59.817 50.000 0.00 0.00 0.00 3.06
156 157 0.034574 AAACAGCCCCATATGCGACA 60.035 50.000 0.00 0.00 0.00 4.35
157 158 1.102978 AAAACAGCCCCATATGCGAC 58.897 50.000 0.00 0.00 0.00 5.19
158 159 1.748493 GAAAAACAGCCCCATATGCGA 59.252 47.619 0.00 0.00 0.00 5.10
159 160 1.202405 GGAAAAACAGCCCCATATGCG 60.202 52.381 0.00 0.00 0.00 4.73
160 161 1.830477 TGGAAAAACAGCCCCATATGC 59.170 47.619 0.00 0.00 0.00 3.14
161 162 3.364549 TCTGGAAAAACAGCCCCATATG 58.635 45.455 0.00 0.00 38.36 1.78
162 163 3.635591 CTCTGGAAAAACAGCCCCATAT 58.364 45.455 0.00 0.00 38.36 1.78
163 164 2.883888 GCTCTGGAAAAACAGCCCCATA 60.884 50.000 0.00 0.00 38.36 2.74
164 165 1.928868 CTCTGGAAAAACAGCCCCAT 58.071 50.000 0.00 0.00 38.36 4.00
165 166 0.827507 GCTCTGGAAAAACAGCCCCA 60.828 55.000 0.00 0.00 38.36 4.96
166 167 1.536073 GGCTCTGGAAAAACAGCCCC 61.536 60.000 0.00 0.00 45.04 5.80
167 168 1.967535 GGCTCTGGAAAAACAGCCC 59.032 57.895 0.00 0.00 45.04 5.19
169 170 0.600057 CCTGGCTCTGGAAAAACAGC 59.400 55.000 0.00 0.00 38.36 4.40
170 171 0.600057 GCCTGGCTCTGGAAAAACAG 59.400 55.000 12.43 0.00 39.84 3.16
171 172 0.185901 AGCCTGGCTCTGGAAAAACA 59.814 50.000 17.22 0.00 30.62 2.83
172 173 2.200373 TAGCCTGGCTCTGGAAAAAC 57.800 50.000 27.16 0.00 40.44 2.43
173 174 2.108250 ACTTAGCCTGGCTCTGGAAAAA 59.892 45.455 27.16 11.08 40.44 1.94
174 175 1.705186 ACTTAGCCTGGCTCTGGAAAA 59.295 47.619 27.16 11.85 40.44 2.29
175 176 1.003580 CACTTAGCCTGGCTCTGGAAA 59.996 52.381 27.16 12.63 40.44 3.13
176 177 0.615331 CACTTAGCCTGGCTCTGGAA 59.385 55.000 27.16 13.04 40.44 3.53
177 178 1.267574 CCACTTAGCCTGGCTCTGGA 61.268 60.000 27.16 4.24 40.44 3.86
178 179 1.222936 CCACTTAGCCTGGCTCTGG 59.777 63.158 27.16 22.60 40.44 3.86
179 180 0.177604 CTCCACTTAGCCTGGCTCTG 59.822 60.000 27.16 20.51 40.44 3.35
180 181 0.041833 TCTCCACTTAGCCTGGCTCT 59.958 55.000 27.16 4.80 40.44 4.09
181 182 0.905357 TTCTCCACTTAGCCTGGCTC 59.095 55.000 27.16 0.00 40.44 4.70
182 183 1.280421 CTTTCTCCACTTAGCCTGGCT 59.720 52.381 26.52 26.52 43.41 4.75
183 184 1.680249 CCTTTCTCCACTTAGCCTGGC 60.680 57.143 11.65 11.65 0.00 4.85
184 185 1.630878 ACCTTTCTCCACTTAGCCTGG 59.369 52.381 0.00 0.00 0.00 4.45
185 186 4.446371 CATACCTTTCTCCACTTAGCCTG 58.554 47.826 0.00 0.00 0.00 4.85
186 187 3.118223 GCATACCTTTCTCCACTTAGCCT 60.118 47.826 0.00 0.00 0.00 4.58
187 188 3.206964 GCATACCTTTCTCCACTTAGCC 58.793 50.000 0.00 0.00 0.00 3.93
188 189 3.873910 TGCATACCTTTCTCCACTTAGC 58.126 45.455 0.00 0.00 0.00 3.09
189 190 4.330074 CGTTGCATACCTTTCTCCACTTAG 59.670 45.833 0.00 0.00 0.00 2.18
190 191 4.250464 CGTTGCATACCTTTCTCCACTTA 58.750 43.478 0.00 0.00 0.00 2.24
191 192 3.074412 CGTTGCATACCTTTCTCCACTT 58.926 45.455 0.00 0.00 0.00 3.16
192 193 2.699954 CGTTGCATACCTTTCTCCACT 58.300 47.619 0.00 0.00 0.00 4.00
193 194 1.130561 GCGTTGCATACCTTTCTCCAC 59.869 52.381 0.00 0.00 0.00 4.02
194 195 1.271108 TGCGTTGCATACCTTTCTCCA 60.271 47.619 0.00 0.00 31.71 3.86
195 196 1.398390 CTGCGTTGCATACCTTTCTCC 59.602 52.381 0.00 0.00 38.13 3.71
196 197 1.398390 CCTGCGTTGCATACCTTTCTC 59.602 52.381 0.00 0.00 38.13 2.87
197 198 1.271379 ACCTGCGTTGCATACCTTTCT 60.271 47.619 0.00 0.00 38.13 2.52
198 199 1.165270 ACCTGCGTTGCATACCTTTC 58.835 50.000 0.00 0.00 38.13 2.62
199 200 2.081462 GTACCTGCGTTGCATACCTTT 58.919 47.619 0.00 0.00 38.13 3.11
200 201 1.734163 GTACCTGCGTTGCATACCTT 58.266 50.000 0.00 0.00 38.13 3.50
201 202 0.459585 CGTACCTGCGTTGCATACCT 60.460 55.000 0.00 0.00 38.13 3.08
202 203 1.426041 CCGTACCTGCGTTGCATACC 61.426 60.000 0.00 0.00 38.13 2.73
203 204 0.738412 ACCGTACCTGCGTTGCATAC 60.738 55.000 0.00 0.00 38.13 2.39
204 205 0.816373 TACCGTACCTGCGTTGCATA 59.184 50.000 0.00 0.00 38.13 3.14
205 206 0.459585 CTACCGTACCTGCGTTGCAT 60.460 55.000 0.00 0.00 38.13 3.96
206 207 1.080366 CTACCGTACCTGCGTTGCA 60.080 57.895 0.00 0.00 36.92 4.08
207 208 2.450345 GCTACCGTACCTGCGTTGC 61.450 63.158 0.00 0.00 0.00 4.17
208 209 1.808390 GGCTACCGTACCTGCGTTG 60.808 63.158 0.00 0.00 0.00 4.10
209 210 2.575461 GGCTACCGTACCTGCGTT 59.425 61.111 0.00 0.00 0.00 4.84
210 211 3.818787 CGGCTACCGTACCTGCGT 61.819 66.667 0.00 0.00 42.73 5.24
225 226 0.736325 CTAGGACTGTTTGCCGTCGG 60.736 60.000 6.99 6.99 0.00 4.79
226 227 0.242825 TCTAGGACTGTTTGCCGTCG 59.757 55.000 0.00 0.00 0.00 5.12
227 228 2.450609 TTCTAGGACTGTTTGCCGTC 57.549 50.000 0.00 0.00 0.00 4.79
228 229 2.354805 GGATTCTAGGACTGTTTGCCGT 60.355 50.000 0.00 0.00 0.00 5.68
229 230 2.280628 GGATTCTAGGACTGTTTGCCG 58.719 52.381 0.00 0.00 0.00 5.69
230 231 2.280628 CGGATTCTAGGACTGTTTGCC 58.719 52.381 0.00 0.00 0.00 4.52
231 232 1.666189 GCGGATTCTAGGACTGTTTGC 59.334 52.381 0.00 0.00 0.00 3.68
232 233 1.927174 CGCGGATTCTAGGACTGTTTG 59.073 52.381 0.00 0.00 0.00 2.93
233 234 1.822990 TCGCGGATTCTAGGACTGTTT 59.177 47.619 6.13 0.00 0.00 2.83
234 235 1.405821 CTCGCGGATTCTAGGACTGTT 59.594 52.381 6.13 0.00 0.00 3.16
235 236 1.025812 CTCGCGGATTCTAGGACTGT 58.974 55.000 6.13 0.00 0.00 3.55
236 237 1.309950 TCTCGCGGATTCTAGGACTG 58.690 55.000 6.13 0.00 0.00 3.51
237 238 2.156098 GATCTCGCGGATTCTAGGACT 58.844 52.381 6.13 0.00 34.33 3.85
238 239 1.200484 GGATCTCGCGGATTCTAGGAC 59.800 57.143 6.13 0.00 34.33 3.85
239 240 1.202891 TGGATCTCGCGGATTCTAGGA 60.203 52.381 6.13 0.00 34.33 2.94
240 241 1.248486 TGGATCTCGCGGATTCTAGG 58.752 55.000 6.13 0.00 34.33 3.02
241 242 2.477021 CGATGGATCTCGCGGATTCTAG 60.477 54.545 6.13 0.00 34.33 2.43
403 411 7.931578 ACCGATACAATGAAAGGTCAATTTA 57.068 32.000 0.00 0.00 37.30 1.40
406 414 7.931578 TTTACCGATACAATGAAAGGTCAAT 57.068 32.000 0.00 0.00 37.30 2.57
475 484 8.783093 TCACACTATTTTGATCGATTTTTGTCT 58.217 29.630 0.00 0.00 0.00 3.41
543 552 1.461091 AACCAGCGTCGACTTCAGGA 61.461 55.000 14.70 0.00 0.00 3.86
666 677 9.613428 TGATTTTTGGGTGTATATAGTCTCTTG 57.387 33.333 0.00 0.00 0.00 3.02
672 683 7.878495 TCCCTTGATTTTTGGGTGTATATAGT 58.122 34.615 0.00 0.00 41.58 2.12
789 803 5.222151 ACTCCCTCCGTCTCAAGATATGATA 60.222 44.000 0.00 0.00 37.44 2.15
793 1009 3.603965 ACTCCCTCCGTCTCAAGATAT 57.396 47.619 0.00 0.00 0.00 1.63
941 1274 1.303317 ATGCCGGTGGTTTGAGTCC 60.303 57.895 1.90 0.00 0.00 3.85
942 1275 0.605319 TGATGCCGGTGGTTTGAGTC 60.605 55.000 1.90 0.00 0.00 3.36
1176 1518 3.402681 TGGCCAGGGCTGTAGAGC 61.403 66.667 15.38 2.57 45.40 4.09
1481 1823 2.022918 AGCTGGATCTAGGGGTTGTAGT 60.023 50.000 8.31 0.00 0.00 2.73
1527 1869 1.460504 ACGACTAAGATCACCGAGCA 58.539 50.000 0.00 0.00 0.00 4.26
1548 1890 4.686972 TGATAACTAACTAGCAGCTGCAG 58.313 43.478 38.24 31.41 45.16 4.41
1581 1924 3.436496 GACACGACAGTACAATAGCTCC 58.564 50.000 0.00 0.00 0.00 4.70
1604 1947 0.586319 ACAGCAAATCCGACACAACG 59.414 50.000 0.00 0.00 0.00 4.10
1607 1950 1.960417 TGAACAGCAAATCCGACACA 58.040 45.000 0.00 0.00 0.00 3.72
1608 1951 3.559238 ATTGAACAGCAAATCCGACAC 57.441 42.857 0.00 0.00 40.48 3.67
1609 1952 4.759693 ACTAATTGAACAGCAAATCCGACA 59.240 37.500 0.00 0.00 40.48 4.35
1610 1953 5.296813 ACTAATTGAACAGCAAATCCGAC 57.703 39.130 0.00 0.00 40.48 4.79
1611 1954 6.170506 ACTACTAATTGAACAGCAAATCCGA 58.829 36.000 0.00 0.00 40.48 4.55
1612 1955 6.422776 ACTACTAATTGAACAGCAAATCCG 57.577 37.500 0.00 0.00 40.48 4.18
1613 1956 6.528072 GCAACTACTAATTGAACAGCAAATCC 59.472 38.462 0.00 0.00 40.48 3.01
1650 1993 2.868583 CCATGAAACATCTCTAGCCACG 59.131 50.000 0.00 0.00 0.00 4.94
1670 2013 2.126346 GCAGTTCATTGCACGGCC 60.126 61.111 0.49 0.00 43.53 6.13
1750 2095 0.893270 TCGGTGACCCAGCCAAATTG 60.893 55.000 0.00 0.00 0.00 2.32
1798 2147 3.100817 GTGCATGCACGTTGAATGATAC 58.899 45.455 33.20 7.70 37.19 2.24
1799 2148 3.403613 GTGCATGCACGTTGAATGATA 57.596 42.857 33.20 0.00 37.19 2.15
1800 2149 2.267188 GTGCATGCACGTTGAATGAT 57.733 45.000 33.20 0.00 37.19 2.45
1801 2150 3.771171 GTGCATGCACGTTGAATGA 57.229 47.368 33.20 0.00 37.19 2.57
1850 2201 1.826921 GAGGGCATCTGGGCATGTG 60.827 63.158 0.00 0.00 45.66 3.21
1851 2202 2.599597 GAGGGCATCTGGGCATGT 59.400 61.111 0.00 0.00 45.66 3.21
1852 2203 2.203451 GGAGGGCATCTGGGCATG 60.203 66.667 0.00 0.00 45.66 4.06
1853 2204 3.505773 GGGAGGGCATCTGGGCAT 61.506 66.667 0.00 0.00 45.66 4.40
1854 2205 4.765970 AGGGAGGGCATCTGGGCA 62.766 66.667 0.00 0.00 45.66 5.36
1855 2206 3.883549 GAGGGAGGGCATCTGGGC 61.884 72.222 0.00 0.00 42.44 5.36
1856 2207 2.040043 AGAGGGAGGGCATCTGGG 60.040 66.667 0.00 0.00 0.00 4.45
1857 2208 2.146061 GGAGAGGGAGGGCATCTGG 61.146 68.421 0.00 0.00 0.00 3.86
1860 2211 2.206536 CGAGGAGAGGGAGGGCATC 61.207 68.421 0.00 0.00 0.00 3.91
1908 2259 6.472686 TTTTACACCATTTTTGCTACCAGT 57.527 33.333 0.00 0.00 0.00 4.00
1909 2260 6.928492 ACATTTTACACCATTTTTGCTACCAG 59.072 34.615 0.00 0.00 0.00 4.00
2021 2373 8.184192 AGAAATTAATCATCGTTCCACATTGTC 58.816 33.333 0.00 0.00 0.00 3.18
2036 2440 4.081142 TCTCACTGCGGGAGAAATTAATCA 60.081 41.667 2.65 0.00 38.40 2.57
2050 2454 1.713597 TGTGCATAGTTCTCACTGCG 58.286 50.000 0.00 0.00 34.06 5.18
2055 2459 4.871933 TCTGTCTTGTGCATAGTTCTCA 57.128 40.909 0.00 0.00 0.00 3.27
2098 2694 5.630121 TGGGTTGAAGATGCTTTAGAAGAA 58.370 37.500 0.00 0.00 0.00 2.52
2119 2715 2.233676 GAGGCCAAATTTACCCAGTTGG 59.766 50.000 5.01 0.00 42.87 3.77
2154 2750 6.860023 GGCCTTCGAATCTTCAAATATTGATG 59.140 38.462 0.00 0.00 39.84 3.07
2191 2787 7.470147 GCAGTAGTACAATATGAGCTAGGAACA 60.470 40.741 2.52 0.00 0.00 3.18
2193 2789 6.549736 TGCAGTAGTACAATATGAGCTAGGAA 59.450 38.462 2.52 0.00 0.00 3.36
2278 2882 0.756294 TCCGGCAAGAGAGAACAACA 59.244 50.000 0.00 0.00 0.00 3.33
2281 2885 0.321671 CCTTCCGGCAAGAGAGAACA 59.678 55.000 13.28 0.00 33.29 3.18
2285 2889 0.898320 TCTTCCTTCCGGCAAGAGAG 59.102 55.000 13.28 10.55 33.29 3.20
2356 2962 3.309296 GTGGGATAAGGATGGAGACTGA 58.691 50.000 0.00 0.00 0.00 3.41
2362 2968 2.168458 TGTCGTGGGATAAGGATGGA 57.832 50.000 0.00 0.00 0.00 3.41
2465 3071 4.072088 GTACACGCGTGCACCTGC 62.072 66.667 37.35 18.74 42.50 4.85


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

AutoCloner maintained by Alex Coulton.