Multiple sequence alignment - TraesCS6B01G302500

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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 TraesCS6B01G302500 chr6B 100.000 4525 0 0 1 4525 542229436 542224912 0.000000e+00 8357
1 TraesCS6B01G302500 chr6B 92.163 319 18 1 1 312 703666614 703666296 1.160000e-120 444
2 TraesCS6B01G302500 chr6A 95.084 3763 126 32 802 4525 501796861 501793119 0.000000e+00 5869
3 TraesCS6B01G302500 chr6A 84.615 442 32 18 324 748 501800285 501799863 1.520000e-109 407
4 TraesCS6B01G302500 chr6D 92.791 2899 131 28 1657 4525 360685021 360682171 0.000000e+00 4124
5 TraesCS6B01G302500 chr6D 87.809 1337 76 38 323 1608 360686471 360685171 0.000000e+00 1485
6 TraesCS6B01G302500 chr6D 93.103 290 20 0 1 290 455633547 455633258 4.180000e-115 425
7 TraesCS6B01G302500 chr5B 92.790 319 16 1 1 312 56690736 56690418 5.340000e-124 455
8 TraesCS6B01G302500 chr5B 93.793 290 17 1 1 290 96905469 96905181 6.950000e-118 435
9 TraesCS6B01G302500 chr5B 89.437 142 14 1 4384 4525 562454687 562454547 1.290000e-40 178
10 TraesCS6B01G302500 chr5B 79.916 239 28 12 4064 4298 562456474 562456252 1.690000e-34 158
11 TraesCS6B01G302500 chr2D 93.793 290 18 0 1 290 77182791 77182502 1.930000e-118 436
12 TraesCS6B01G302500 chr2D 93.793 290 17 1 1 290 590029021 590029309 6.950000e-118 435
13 TraesCS6B01G302500 chr2A 93.448 290 19 0 1 290 44180081 44180370 8.990000e-117 431
14 TraesCS6B01G302500 chr2A 93.448 290 19 0 1 290 765216096 765216385 8.990000e-117 431
15 TraesCS6B01G302500 chr2A 93.448 290 19 0 1 290 765241506 765241795 8.990000e-117 431
16 TraesCS6B01G302500 chr5D 80.982 489 47 25 4064 4525 458778518 458778049 3.350000e-91 346


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 TraesCS6B01G302500 chr6B 542224912 542229436 4524 True 8357.0 8357 100.0000 1 4525 1 chr6B.!!$R1 4524
1 TraesCS6B01G302500 chr6A 501793119 501800285 7166 True 3138.0 5869 89.8495 324 4525 2 chr6A.!!$R1 4201
2 TraesCS6B01G302500 chr6D 360682171 360686471 4300 True 2804.5 4124 90.3000 323 4525 2 chr6D.!!$R2 4202

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
57 58 0.030501 ATCCCCAACCATAGGACCGA 60.031 55.0 0.00 0.00 30.97 4.69 F
59 60 0.108585 CCCCAACCATAGGACCGATG 59.891 60.0 7.58 7.58 0.00 3.84 F
312 313 0.177373 GGAGAGGAAAACGCCCGTAT 59.823 55.0 0.00 0.00 0.00 3.06 F
809 910 0.179001 CGACAAAGGAACCAACCCCT 60.179 55.0 0.00 0.00 0.00 4.79 F
1276 4278 0.447011 CGTCCGACGCTTAGACTCTT 59.553 55.0 8.21 0.00 33.65 2.85 F
2792 5916 0.394899 ATGCAGGTTTAGCTGGGCTC 60.395 55.0 10.60 0.00 40.44 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1379 4381 0.307760 CGCCACAGAAGCTCGTTTTT 59.692 50.000 0.00 0.0 0.00 1.94 R
1466 4468 5.183140 GCACCTAGCAAGAGTTCCAATTTTA 59.817 40.000 0.00 0.0 44.79 1.52 R
1577 4579 5.552178 ACTCCGAATATGGGAATTAGAAGC 58.448 41.667 0.00 0.0 32.02 3.86 R
2792 5916 0.107214 ATGCTCCATAACCCACACGG 60.107 55.000 0.00 0.0 37.81 4.94 R
3255 6380 2.519377 TAACCCATATCGCAGTTCCG 57.481 50.000 0.00 0.0 0.00 4.30 R
4124 7267 0.618107 TTGCAATGGCCATCACCCAT 60.618 50.000 21.08 0.0 44.75 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.985877 CACGCCATCCTTGCTTGA 58.014 55.556 0.00 0.00 30.19 3.02
18 19 2.256391 CACGCCATCCTTGCTTGAA 58.744 52.632 0.00 0.00 30.19 2.69
19 20 0.109597 CACGCCATCCTTGCTTGAAC 60.110 55.000 0.00 0.00 30.19 3.18
20 21 0.537143 ACGCCATCCTTGCTTGAACA 60.537 50.000 0.00 0.00 0.00 3.18
21 22 0.169672 CGCCATCCTTGCTTGAACAG 59.830 55.000 0.00 0.00 0.00 3.16
22 23 1.538047 GCCATCCTTGCTTGAACAGA 58.462 50.000 0.00 0.00 0.00 3.41
23 24 1.200948 GCCATCCTTGCTTGAACAGAC 59.799 52.381 0.00 0.00 0.00 3.51
24 25 2.787994 CCATCCTTGCTTGAACAGACT 58.212 47.619 0.00 0.00 0.00 3.24
25 26 2.486982 CCATCCTTGCTTGAACAGACTG 59.513 50.000 0.00 0.00 0.00 3.51
26 27 2.260844 TCCTTGCTTGAACAGACTGG 57.739 50.000 7.51 0.00 0.00 4.00
27 28 1.490490 TCCTTGCTTGAACAGACTGGT 59.510 47.619 7.51 0.00 0.00 4.00
28 29 2.092429 TCCTTGCTTGAACAGACTGGTT 60.092 45.455 7.51 0.00 0.00 3.67
29 30 2.689983 CCTTGCTTGAACAGACTGGTTT 59.310 45.455 7.51 0.00 0.00 3.27
30 31 3.131046 CCTTGCTTGAACAGACTGGTTTT 59.869 43.478 7.51 0.00 0.00 2.43
31 32 4.354587 CTTGCTTGAACAGACTGGTTTTC 58.645 43.478 7.51 2.51 0.00 2.29
32 33 3.351740 TGCTTGAACAGACTGGTTTTCA 58.648 40.909 7.51 5.21 0.00 2.69
33 34 3.761218 TGCTTGAACAGACTGGTTTTCAA 59.239 39.130 15.19 15.19 36.70 2.69
34 35 4.219507 TGCTTGAACAGACTGGTTTTCAAA 59.780 37.500 16.21 4.97 37.48 2.69
35 36 5.105392 TGCTTGAACAGACTGGTTTTCAAAT 60.105 36.000 16.21 0.00 37.48 2.32
36 37 5.460091 GCTTGAACAGACTGGTTTTCAAATC 59.540 40.000 16.21 10.07 37.48 2.17
37 38 5.514274 TGAACAGACTGGTTTTCAAATCC 57.486 39.130 7.51 0.00 0.00 3.01
38 39 4.952957 TGAACAGACTGGTTTTCAAATCCA 59.047 37.500 7.51 0.00 0.00 3.41
39 40 5.598005 TGAACAGACTGGTTTTCAAATCCAT 59.402 36.000 7.51 0.00 0.00 3.41
40 41 5.712152 ACAGACTGGTTTTCAAATCCATC 57.288 39.130 7.51 2.10 0.00 3.51
41 42 4.524328 ACAGACTGGTTTTCAAATCCATCC 59.476 41.667 7.51 0.00 0.00 3.51
42 43 4.082026 CAGACTGGTTTTCAAATCCATCCC 60.082 45.833 0.16 0.00 0.00 3.85
43 44 3.173151 ACTGGTTTTCAAATCCATCCCC 58.827 45.455 0.16 0.00 0.00 4.81
44 45 3.172339 CTGGTTTTCAAATCCATCCCCA 58.828 45.455 0.16 0.00 0.00 4.96
45 46 3.582208 CTGGTTTTCAAATCCATCCCCAA 59.418 43.478 0.16 0.00 0.00 4.12
46 47 3.326297 TGGTTTTCAAATCCATCCCCAAC 59.674 43.478 0.00 0.00 0.00 3.77
47 48 3.307410 GGTTTTCAAATCCATCCCCAACC 60.307 47.826 0.00 0.00 0.00 3.77
48 49 3.266477 TTTCAAATCCATCCCCAACCA 57.734 42.857 0.00 0.00 0.00 3.67
49 50 3.488355 TTCAAATCCATCCCCAACCAT 57.512 42.857 0.00 0.00 0.00 3.55
50 51 4.616671 TTCAAATCCATCCCCAACCATA 57.383 40.909 0.00 0.00 0.00 2.74
51 52 4.183223 TCAAATCCATCCCCAACCATAG 57.817 45.455 0.00 0.00 0.00 2.23
52 53 3.117169 TCAAATCCATCCCCAACCATAGG 60.117 47.826 0.00 0.00 0.00 2.57
53 54 2.531177 ATCCATCCCCAACCATAGGA 57.469 50.000 0.00 0.00 0.00 2.94
54 55 1.518367 TCCATCCCCAACCATAGGAC 58.482 55.000 0.00 0.00 30.97 3.85
55 56 0.478507 CCATCCCCAACCATAGGACC 59.521 60.000 0.00 0.00 30.97 4.46
56 57 0.108585 CATCCCCAACCATAGGACCG 59.891 60.000 0.00 0.00 30.97 4.79
57 58 0.030501 ATCCCCAACCATAGGACCGA 60.031 55.000 0.00 0.00 30.97 4.69
58 59 0.030501 TCCCCAACCATAGGACCGAT 60.031 55.000 0.00 0.00 0.00 4.18
59 60 0.108585 CCCCAACCATAGGACCGATG 59.891 60.000 7.58 7.58 0.00 3.84
61 62 0.535102 CCAACCATAGGACCGATGGC 60.535 60.000 28.23 0.00 46.76 4.40
62 63 0.535102 CAACCATAGGACCGATGGCC 60.535 60.000 28.23 0.00 46.76 5.36
63 64 0.694444 AACCATAGGACCGATGGCCT 60.694 55.000 28.23 16.00 46.76 5.19
64 65 1.122019 ACCATAGGACCGATGGCCTC 61.122 60.000 28.23 0.00 46.76 4.70
66 67 1.152525 ATAGGACCGATGGCCTCGT 60.153 57.895 18.94 6.61 46.18 4.18
67 68 1.179814 ATAGGACCGATGGCCTCGTC 61.180 60.000 18.94 15.85 46.18 4.20
68 69 2.561467 TAGGACCGATGGCCTCGTCA 62.561 60.000 18.94 0.00 46.18 4.35
69 70 2.105128 GACCGATGGCCTCGTCAG 59.895 66.667 18.94 9.61 46.18 3.51
70 71 2.362503 ACCGATGGCCTCGTCAGA 60.363 61.111 18.94 0.00 46.18 3.27
71 72 1.945354 GACCGATGGCCTCGTCAGAA 61.945 60.000 18.94 0.00 46.18 3.02
72 73 1.218047 CCGATGGCCTCGTCAGAAA 59.782 57.895 18.94 0.00 46.18 2.52
73 74 0.391130 CCGATGGCCTCGTCAGAAAA 60.391 55.000 18.94 0.00 46.18 2.29
74 75 1.438651 CGATGGCCTCGTCAGAAAAA 58.561 50.000 3.32 0.00 42.56 1.94
75 76 1.394917 CGATGGCCTCGTCAGAAAAAG 59.605 52.381 3.32 0.00 42.56 2.27
76 77 2.699954 GATGGCCTCGTCAGAAAAAGA 58.300 47.619 3.32 0.00 0.00 2.52
77 78 2.859165 TGGCCTCGTCAGAAAAAGAT 57.141 45.000 3.32 0.00 0.00 2.40
78 79 2.699954 TGGCCTCGTCAGAAAAAGATC 58.300 47.619 3.32 0.00 0.00 2.75
79 80 2.303022 TGGCCTCGTCAGAAAAAGATCT 59.697 45.455 3.32 0.00 0.00 2.75
80 81 3.513912 TGGCCTCGTCAGAAAAAGATCTA 59.486 43.478 3.32 0.00 0.00 1.98
81 82 4.020573 TGGCCTCGTCAGAAAAAGATCTAA 60.021 41.667 3.32 0.00 0.00 2.10
82 83 4.935808 GGCCTCGTCAGAAAAAGATCTAAA 59.064 41.667 0.00 0.00 0.00 1.85
83 84 5.064071 GGCCTCGTCAGAAAAAGATCTAAAG 59.936 44.000 0.00 0.00 0.00 1.85
84 85 5.869888 GCCTCGTCAGAAAAAGATCTAAAGA 59.130 40.000 0.00 0.00 0.00 2.52
85 86 6.369065 GCCTCGTCAGAAAAAGATCTAAAGAA 59.631 38.462 0.00 0.00 0.00 2.52
86 87 7.065204 GCCTCGTCAGAAAAAGATCTAAAGAAT 59.935 37.037 0.00 0.00 0.00 2.40
87 88 8.599774 CCTCGTCAGAAAAAGATCTAAAGAATC 58.400 37.037 0.00 0.00 0.00 2.52
88 89 9.364989 CTCGTCAGAAAAAGATCTAAAGAATCT 57.635 33.333 0.00 0.00 0.00 2.40
89 90 9.712305 TCGTCAGAAAAAGATCTAAAGAATCTT 57.288 29.630 0.00 0.00 36.32 2.40
107 108 8.085720 AGAATCTTTATTCAGCATTCTCATCG 57.914 34.615 1.35 0.00 43.44 3.84
108 109 7.714377 AGAATCTTTATTCAGCATTCTCATCGT 59.286 33.333 1.35 0.00 43.44 3.73
109 110 6.834959 TCTTTATTCAGCATTCTCATCGTC 57.165 37.500 0.00 0.00 0.00 4.20
110 111 5.460091 TCTTTATTCAGCATTCTCATCGTCG 59.540 40.000 0.00 0.00 0.00 5.12
111 112 1.280982 TTCAGCATTCTCATCGTCGC 58.719 50.000 0.00 0.00 0.00 5.19
112 113 0.528466 TCAGCATTCTCATCGTCGCC 60.528 55.000 0.00 0.00 0.00 5.54
113 114 1.589993 AGCATTCTCATCGTCGCCG 60.590 57.895 0.00 0.00 0.00 6.46
114 115 2.923854 CATTCTCATCGTCGCCGC 59.076 61.111 0.00 0.00 0.00 6.53
115 116 2.279517 ATTCTCATCGTCGCCGCC 60.280 61.111 0.00 0.00 0.00 6.13
116 117 4.847516 TTCTCATCGTCGCCGCCG 62.848 66.667 0.00 0.00 0.00 6.46
118 119 4.847516 CTCATCGTCGCCGCCGAA 62.848 66.667 0.00 0.00 46.34 4.30
119 120 4.847516 TCATCGTCGCCGCCGAAG 62.848 66.667 0.00 0.00 46.34 3.79
124 125 4.445545 GTCGCCGCCGAAGCAAAG 62.446 66.667 0.00 0.00 46.34 2.77
125 126 4.673298 TCGCCGCCGAAGCAAAGA 62.673 61.111 0.00 0.00 41.17 2.52
126 127 4.445545 CGCCGCCGAAGCAAAGAC 62.446 66.667 0.00 0.00 39.83 3.01
127 128 3.353836 GCCGCCGAAGCAAAGACA 61.354 61.111 0.00 0.00 39.83 3.41
128 129 2.903547 GCCGCCGAAGCAAAGACAA 61.904 57.895 0.00 0.00 39.83 3.18
129 130 1.875963 CCGCCGAAGCAAAGACAAT 59.124 52.632 0.00 0.00 39.83 2.71
130 131 0.454957 CCGCCGAAGCAAAGACAATG 60.455 55.000 0.00 0.00 39.83 2.82
131 132 0.516877 CGCCGAAGCAAAGACAATGA 59.483 50.000 0.00 0.00 39.83 2.57
132 133 1.069296 CGCCGAAGCAAAGACAATGAA 60.069 47.619 0.00 0.00 39.83 2.57
133 134 2.319472 GCCGAAGCAAAGACAATGAAC 58.681 47.619 0.00 0.00 39.53 3.18
134 135 2.287547 GCCGAAGCAAAGACAATGAACA 60.288 45.455 0.00 0.00 39.53 3.18
135 136 3.795150 GCCGAAGCAAAGACAATGAACAA 60.795 43.478 0.00 0.00 39.53 2.83
136 137 3.730715 CCGAAGCAAAGACAATGAACAAC 59.269 43.478 0.00 0.00 0.00 3.32
137 138 3.730715 CGAAGCAAAGACAATGAACAACC 59.269 43.478 0.00 0.00 0.00 3.77
138 139 4.498009 CGAAGCAAAGACAATGAACAACCT 60.498 41.667 0.00 0.00 0.00 3.50
139 140 5.277779 CGAAGCAAAGACAATGAACAACCTA 60.278 40.000 0.00 0.00 0.00 3.08
140 141 6.463995 AAGCAAAGACAATGAACAACCTAA 57.536 33.333 0.00 0.00 0.00 2.69
141 142 6.463995 AGCAAAGACAATGAACAACCTAAA 57.536 33.333 0.00 0.00 0.00 1.85
142 143 6.872920 AGCAAAGACAATGAACAACCTAAAA 58.127 32.000 0.00 0.00 0.00 1.52
143 144 7.327214 AGCAAAGACAATGAACAACCTAAAAA 58.673 30.769 0.00 0.00 0.00 1.94
144 145 7.277760 AGCAAAGACAATGAACAACCTAAAAAC 59.722 33.333 0.00 0.00 0.00 2.43
145 146 7.465379 GCAAAGACAATGAACAACCTAAAAACC 60.465 37.037 0.00 0.00 0.00 3.27
146 147 7.418337 AAGACAATGAACAACCTAAAAACCT 57.582 32.000 0.00 0.00 0.00 3.50
147 148 8.528044 AAGACAATGAACAACCTAAAAACCTA 57.472 30.769 0.00 0.00 0.00 3.08
148 149 8.166422 AGACAATGAACAACCTAAAAACCTAG 57.834 34.615 0.00 0.00 0.00 3.02
149 150 7.996644 AGACAATGAACAACCTAAAAACCTAGA 59.003 33.333 0.00 0.00 0.00 2.43
150 151 7.937649 ACAATGAACAACCTAAAAACCTAGAC 58.062 34.615 0.00 0.00 0.00 2.59
151 152 7.778382 ACAATGAACAACCTAAAAACCTAGACT 59.222 33.333 0.00 0.00 0.00 3.24
152 153 9.280174 CAATGAACAACCTAAAAACCTAGACTA 57.720 33.333 0.00 0.00 0.00 2.59
161 162 9.994017 ACCTAAAAACCTAGACTATAAGAGAGT 57.006 33.333 0.00 0.00 0.00 3.24
168 169 8.156994 ACCTAGACTATAAGAGAGTAAAAGCG 57.843 38.462 0.00 0.00 0.00 4.68
169 170 7.992033 ACCTAGACTATAAGAGAGTAAAAGCGA 59.008 37.037 0.00 0.00 0.00 4.93
170 171 9.005777 CCTAGACTATAAGAGAGTAAAAGCGAT 57.994 37.037 0.00 0.00 0.00 4.58
172 173 7.878036 AGACTATAAGAGAGTAAAAGCGATCC 58.122 38.462 0.00 0.00 0.00 3.36
173 174 7.502895 AGACTATAAGAGAGTAAAAGCGATCCA 59.497 37.037 0.00 0.00 0.00 3.41
174 175 7.427214 ACTATAAGAGAGTAAAAGCGATCCAC 58.573 38.462 0.00 0.00 0.00 4.02
175 176 4.537135 AAGAGAGTAAAAGCGATCCACA 57.463 40.909 0.00 0.00 0.00 4.17
176 177 3.851098 AGAGAGTAAAAGCGATCCACAC 58.149 45.455 0.00 0.00 0.00 3.82
177 178 2.599082 GAGAGTAAAAGCGATCCACACG 59.401 50.000 0.00 0.00 0.00 4.49
214 215 2.872557 GTCACCACCGACGATCGA 59.127 61.111 24.34 0.00 43.74 3.59
215 216 1.226323 GTCACCACCGACGATCGAG 60.226 63.158 24.34 14.83 43.74 4.04
216 217 2.102357 CACCACCGACGATCGAGG 59.898 66.667 24.34 24.65 43.74 4.63
217 218 2.360852 ACCACCGACGATCGAGGT 60.361 61.111 25.90 25.90 43.74 3.85
218 219 2.404995 ACCACCGACGATCGAGGTC 61.405 63.158 27.73 13.90 41.70 3.85
223 224 4.609247 GACGATCGAGGTCGCCGG 62.609 72.222 24.34 0.00 45.12 6.13
226 227 4.933064 GATCGAGGTCGCCGGCAG 62.933 72.222 28.98 19.33 39.60 4.85
253 254 4.821589 GCCGGAGAGCGTCCTTGG 62.822 72.222 5.05 2.91 44.35 3.61
254 255 3.068691 CCGGAGAGCGTCCTTGGA 61.069 66.667 0.00 0.00 44.35 3.53
255 256 2.646175 CCGGAGAGCGTCCTTGGAA 61.646 63.158 0.00 0.00 44.35 3.53
256 257 1.153745 CGGAGAGCGTCCTTGGAAG 60.154 63.158 6.59 0.00 44.35 3.46
257 258 1.595993 CGGAGAGCGTCCTTGGAAGA 61.596 60.000 6.78 0.00 44.35 2.87
258 259 0.827368 GGAGAGCGTCCTTGGAAGAT 59.173 55.000 6.78 0.00 42.99 2.40
259 260 1.202475 GGAGAGCGTCCTTGGAAGATC 60.202 57.143 11.77 11.77 42.99 2.75
260 261 0.457851 AGAGCGTCCTTGGAAGATCG 59.542 55.000 13.34 4.54 0.00 3.69
261 262 0.528684 GAGCGTCCTTGGAAGATCGG 60.529 60.000 6.78 0.00 0.00 4.18
262 263 2.174319 GCGTCCTTGGAAGATCGGC 61.174 63.158 6.78 0.00 0.00 5.54
263 264 1.521681 CGTCCTTGGAAGATCGGCC 60.522 63.158 0.00 0.00 0.00 6.13
264 265 1.908483 GTCCTTGGAAGATCGGCCT 59.092 57.895 0.00 0.00 0.00 5.19
265 266 0.179070 GTCCTTGGAAGATCGGCCTC 60.179 60.000 0.00 0.00 0.00 4.70
266 267 1.147153 CCTTGGAAGATCGGCCTCC 59.853 63.158 0.00 0.00 0.00 4.30
267 268 1.147153 CTTGGAAGATCGGCCTCCC 59.853 63.158 0.00 0.00 0.00 4.30
268 269 2.330924 CTTGGAAGATCGGCCTCCCC 62.331 65.000 0.00 0.00 0.00 4.81
269 270 2.446802 GGAAGATCGGCCTCCCCT 60.447 66.667 0.00 0.00 0.00 4.79
270 271 2.812619 GGAAGATCGGCCTCCCCTG 61.813 68.421 0.00 0.00 0.00 4.45
271 272 2.770048 AAGATCGGCCTCCCCTGG 60.770 66.667 0.00 0.00 0.00 4.45
289 290 4.530857 CGGCGGCTAGGGTTCCAG 62.531 72.222 7.61 0.00 0.00 3.86
290 291 4.176752 GGCGGCTAGGGTTCCAGG 62.177 72.222 0.00 0.00 0.00 4.45
291 292 4.176752 GCGGCTAGGGTTCCAGGG 62.177 72.222 0.00 0.00 0.00 4.45
292 293 2.365105 CGGCTAGGGTTCCAGGGA 60.365 66.667 0.00 0.00 0.00 4.20
293 294 2.435693 CGGCTAGGGTTCCAGGGAG 61.436 68.421 0.00 0.00 0.00 4.30
294 295 2.073101 GGCTAGGGTTCCAGGGAGG 61.073 68.421 0.00 0.00 39.47 4.30
304 305 1.657804 TCCAGGGAGGAGAGGAAAAC 58.342 55.000 0.00 0.00 43.07 2.43
305 306 0.250513 CCAGGGAGGAGAGGAAAACG 59.749 60.000 0.00 0.00 41.22 3.60
306 307 0.391793 CAGGGAGGAGAGGAAAACGC 60.392 60.000 0.00 0.00 0.00 4.84
307 308 1.078356 GGGAGGAGAGGAAAACGCC 60.078 63.158 0.00 0.00 0.00 5.68
308 309 1.078356 GGAGGAGAGGAAAACGCCC 60.078 63.158 0.00 0.00 0.00 6.13
309 310 1.448013 GAGGAGAGGAAAACGCCCG 60.448 63.158 0.00 0.00 0.00 6.13
310 311 2.168666 GAGGAGAGGAAAACGCCCGT 62.169 60.000 0.00 0.00 0.00 5.28
311 312 0.901580 AGGAGAGGAAAACGCCCGTA 60.902 55.000 0.00 0.00 0.00 4.02
312 313 0.177373 GGAGAGGAAAACGCCCGTAT 59.823 55.000 0.00 0.00 0.00 3.06
313 314 1.410153 GGAGAGGAAAACGCCCGTATA 59.590 52.381 0.00 0.00 0.00 1.47
314 315 2.159057 GGAGAGGAAAACGCCCGTATAA 60.159 50.000 0.00 0.00 0.00 0.98
315 316 3.121544 GAGAGGAAAACGCCCGTATAAG 58.878 50.000 0.00 0.00 0.00 1.73
316 317 2.159000 AGAGGAAAACGCCCGTATAAGG 60.159 50.000 0.00 0.00 0.00 2.69
337 338 1.806623 GCTAACCATCCCGTAGCTGTG 60.807 57.143 0.00 0.00 0.00 3.66
351 352 2.752144 GCTGTGTAGCTGATGATTGC 57.248 50.000 0.00 0.00 46.57 3.56
393 408 4.828296 GGGCCGAGACGAGGGGTA 62.828 72.222 0.00 0.00 0.00 3.69
394 409 3.525545 GGCCGAGACGAGGGGTAC 61.526 72.222 0.00 0.00 0.00 3.34
434 449 1.369209 CAAAACTGACACGCCTGCG 60.369 57.895 10.40 10.40 46.03 5.18
802 903 0.322546 ATCAGGCCGACAAAGGAACC 60.323 55.000 0.00 0.00 0.00 3.62
809 910 0.179001 CGACAAAGGAACCAACCCCT 60.179 55.000 0.00 0.00 0.00 4.79
874 3864 1.070821 CACGAATCTCAAAGCGCAGA 58.929 50.000 11.47 3.34 0.00 4.26
879 3869 3.364366 CGAATCTCAAAGCGCAGAAAAGT 60.364 43.478 11.47 0.00 0.00 2.66
939 3929 2.358737 CGCCGCCTGTCCTTTTCT 60.359 61.111 0.00 0.00 0.00 2.52
942 3932 1.856265 GCCGCCTGTCCTTTTCTGTG 61.856 60.000 0.00 0.00 0.00 3.66
944 3934 0.886490 CGCCTGTCCTTTTCTGTGCT 60.886 55.000 0.00 0.00 0.00 4.40
951 3941 0.886490 CCTTTTCTGTGCTGCTCGGT 60.886 55.000 10.04 0.00 0.00 4.69
1014 4013 1.009078 CGTCGATGGACTGTACCGTA 58.991 55.000 6.29 0.00 41.16 4.02
1252 4254 0.760945 CCTGCCCTTCGAGGTATCCT 60.761 60.000 0.00 0.00 36.03 3.24
1276 4278 0.447011 CGTCCGACGCTTAGACTCTT 59.553 55.000 8.21 0.00 33.65 2.85
1363 4365 2.255252 GCGGCGTGATTGTGCTTT 59.745 55.556 9.37 0.00 0.00 3.51
1379 4381 6.166984 TGTGCTTTGGGAATGAAATGTTTA 57.833 33.333 0.00 0.00 0.00 2.01
1411 4413 1.079819 GTGGCGTCTCAGCTTGCTA 60.080 57.895 0.00 0.00 37.29 3.49
1462 4464 5.667539 TTCCTTGATGTTGTTTGACCAAA 57.332 34.783 0.00 0.00 0.00 3.28
1466 4468 5.816777 CCTTGATGTTGTTTGACCAAATTGT 59.183 36.000 0.00 0.00 32.36 2.71
1590 4592 1.448985 GTGCGTGCTTCTAATTCCCA 58.551 50.000 0.00 0.00 0.00 4.37
1785 4900 7.994425 TTTGAGCCTGTAACAGAAAATATCA 57.006 32.000 0.00 0.00 32.44 2.15
1822 4939 5.857268 AGCAACAAAAGCACCAAGATAATT 58.143 33.333 0.00 0.00 0.00 1.40
1840 4958 8.814448 AGATAATTCATACCTCCCCTTTTCTA 57.186 34.615 0.00 0.00 0.00 2.10
1846 4964 7.798710 TCATACCTCCCCTTTTCTATATCTG 57.201 40.000 0.00 0.00 0.00 2.90
2431 5550 0.540365 AACAACCCAGATGGCAGGTG 60.540 55.000 0.00 0.00 37.83 4.00
2712 5836 8.821147 TTGTGTTCTATCGTTTTAGTGTGTAT 57.179 30.769 0.00 0.00 0.00 2.29
2792 5916 0.394899 ATGCAGGTTTAGCTGGGCTC 60.395 55.000 10.60 0.00 40.44 4.70
2934 6058 7.493971 CAGTCTATTTGGAGGTACATCTTTCAG 59.506 40.741 7.56 0.00 0.00 3.02
2990 6115 5.789710 TTAAACTTGGCTAATACGTCTGC 57.210 39.130 0.00 0.00 0.00 4.26
3190 6315 1.024271 GCACTGTCCAAGTTTCTGCA 58.976 50.000 0.00 0.00 36.83 4.41
3255 6380 5.163457 TGAGGTGACAAAATTTTGAGAACCC 60.163 40.000 32.20 24.44 40.55 4.11
3342 6468 7.119553 GTGCAATTTATGTCCCATTGAACAATT 59.880 33.333 0.00 0.00 36.71 2.32
3624 6750 4.767578 ACACTGGATGCAGTCTATCAAT 57.232 40.909 17.98 0.00 32.26 2.57
3759 6885 6.324819 CAACCATTTAGCCATAAACTCTGTG 58.675 40.000 0.00 0.00 33.78 3.66
3868 7007 3.304911 TGGTTGTTCATGGGAAAGTCA 57.695 42.857 0.00 0.00 34.13 3.41
3875 7014 6.968263 TGTTCATGGGAAAGTCAAATGTTA 57.032 33.333 0.00 0.00 34.13 2.41
3914 7053 6.922540 AGGCCATTACCATAATCTTACCTTT 58.077 36.000 5.01 0.00 0.00 3.11
3927 7066 5.148651 TCTTACCTTTCTTCTACCAGTGC 57.851 43.478 0.00 0.00 0.00 4.40
3941 7080 3.616219 ACCAGTGCTTTTGTCAGTACAA 58.384 40.909 0.00 0.00 43.85 2.41
3942 7081 4.207165 ACCAGTGCTTTTGTCAGTACAAT 58.793 39.130 0.00 0.00 44.85 2.71
3969 7108 3.558931 TGAGGAACTGCACTCTTCAAA 57.441 42.857 3.98 0.00 41.55 2.69
4039 7178 2.345641 CGAAATACAGCGAAGGACAGTG 59.654 50.000 0.00 0.00 0.00 3.66
4159 7302 0.319813 GCAACGGCCAAGCATCTTTT 60.320 50.000 2.24 0.00 0.00 2.27
4173 7316 8.306761 CCAAGCATCTTTTATTTAGTTTCTGGT 58.693 33.333 0.00 0.00 0.00 4.00
4177 7320 9.569167 GCATCTTTTATTTAGTTTCTGGTAACC 57.431 33.333 0.00 0.00 0.00 2.85
4182 7325 3.706600 TTAGTTTCTGGTAACCGGCAT 57.293 42.857 0.00 0.00 0.00 4.40
4184 7327 0.170339 GTTTCTGGTAACCGGCATGC 59.830 55.000 9.90 9.90 0.00 4.06
4187 7343 1.078497 CTGGTAACCGGCATGCTGA 60.078 57.895 28.32 5.05 0.00 4.26
4286 7442 3.003763 GGCTCCGGGAAGTCCTGT 61.004 66.667 0.00 0.00 40.86 4.00
4459 7616 1.224592 GGAGATGTGCGGGGTCATT 59.775 57.895 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.109597 GTTCAAGCAAGGATGGCGTG 60.110 55.000 0.00 0.00 46.47 5.34
1 2 0.537143 TGTTCAAGCAAGGATGGCGT 60.537 50.000 0.00 0.00 42.81 5.68
2 3 0.169672 CTGTTCAAGCAAGGATGGCG 59.830 55.000 0.00 0.00 42.81 5.69
3 4 1.200948 GTCTGTTCAAGCAAGGATGGC 59.799 52.381 0.00 0.00 32.57 4.40
4 5 2.486982 CAGTCTGTTCAAGCAAGGATGG 59.513 50.000 0.00 0.00 0.00 3.51
5 6 2.486982 CCAGTCTGTTCAAGCAAGGATG 59.513 50.000 0.00 0.00 0.00 3.51
6 7 2.107204 ACCAGTCTGTTCAAGCAAGGAT 59.893 45.455 0.00 0.00 0.00 3.24
7 8 1.490490 ACCAGTCTGTTCAAGCAAGGA 59.510 47.619 0.00 0.00 0.00 3.36
8 9 1.972872 ACCAGTCTGTTCAAGCAAGG 58.027 50.000 0.00 0.00 0.00 3.61
9 10 4.142403 TGAAAACCAGTCTGTTCAAGCAAG 60.142 41.667 0.00 0.00 0.00 4.01
10 11 3.761218 TGAAAACCAGTCTGTTCAAGCAA 59.239 39.130 0.00 0.00 0.00 3.91
11 12 3.351740 TGAAAACCAGTCTGTTCAAGCA 58.648 40.909 0.00 0.00 0.00 3.91
12 13 4.370364 TTGAAAACCAGTCTGTTCAAGC 57.630 40.909 11.23 0.00 35.60 4.01
13 14 5.979517 GGATTTGAAAACCAGTCTGTTCAAG 59.020 40.000 13.67 0.00 40.14 3.02
14 15 5.420421 TGGATTTGAAAACCAGTCTGTTCAA 59.580 36.000 2.51 11.23 38.01 2.69
15 16 4.952957 TGGATTTGAAAACCAGTCTGTTCA 59.047 37.500 2.51 0.00 0.00 3.18
16 17 5.514274 TGGATTTGAAAACCAGTCTGTTC 57.486 39.130 2.51 0.00 0.00 3.18
17 18 5.011023 GGATGGATTTGAAAACCAGTCTGTT 59.989 40.000 12.47 0.00 37.12 3.16
18 19 4.524328 GGATGGATTTGAAAACCAGTCTGT 59.476 41.667 12.47 0.00 37.12 3.41
19 20 4.082026 GGGATGGATTTGAAAACCAGTCTG 60.082 45.833 12.47 0.00 37.12 3.51
20 21 4.089361 GGGATGGATTTGAAAACCAGTCT 58.911 43.478 12.47 0.00 37.12 3.24
21 22 3.195610 GGGGATGGATTTGAAAACCAGTC 59.804 47.826 12.47 9.60 37.12 3.51
22 23 3.173151 GGGGATGGATTTGAAAACCAGT 58.827 45.455 12.47 1.76 37.12 4.00
23 24 3.172339 TGGGGATGGATTTGAAAACCAG 58.828 45.455 12.47 0.00 37.12 4.00
24 25 3.266477 TGGGGATGGATTTGAAAACCA 57.734 42.857 9.40 9.40 38.09 3.67
25 26 3.307410 GGTTGGGGATGGATTTGAAAACC 60.307 47.826 0.00 0.00 0.00 3.27
26 27 3.326297 TGGTTGGGGATGGATTTGAAAAC 59.674 43.478 0.00 0.00 0.00 2.43
27 28 3.591789 TGGTTGGGGATGGATTTGAAAA 58.408 40.909 0.00 0.00 0.00 2.29
28 29 3.266477 TGGTTGGGGATGGATTTGAAA 57.734 42.857 0.00 0.00 0.00 2.69
29 30 3.488355 ATGGTTGGGGATGGATTTGAA 57.512 42.857 0.00 0.00 0.00 2.69
30 31 3.117169 CCTATGGTTGGGGATGGATTTGA 60.117 47.826 0.00 0.00 0.00 2.69
31 32 3.117169 TCCTATGGTTGGGGATGGATTTG 60.117 47.826 0.00 0.00 0.00 2.32
32 33 3.117131 GTCCTATGGTTGGGGATGGATTT 60.117 47.826 0.00 0.00 0.00 2.17
33 34 2.447047 GTCCTATGGTTGGGGATGGATT 59.553 50.000 0.00 0.00 0.00 3.01
34 35 2.065799 GTCCTATGGTTGGGGATGGAT 58.934 52.381 0.00 0.00 0.00 3.41
35 36 1.518367 GTCCTATGGTTGGGGATGGA 58.482 55.000 0.00 0.00 0.00 3.41
36 37 0.478507 GGTCCTATGGTTGGGGATGG 59.521 60.000 0.00 0.00 0.00 3.51
37 38 0.108585 CGGTCCTATGGTTGGGGATG 59.891 60.000 0.00 0.00 0.00 3.51
38 39 0.030501 TCGGTCCTATGGTTGGGGAT 60.031 55.000 0.00 0.00 0.00 3.85
39 40 0.030501 ATCGGTCCTATGGTTGGGGA 60.031 55.000 0.00 0.00 0.00 4.81
40 41 0.108585 CATCGGTCCTATGGTTGGGG 59.891 60.000 0.00 0.00 0.00 4.96
41 42 0.108585 CCATCGGTCCTATGGTTGGG 59.891 60.000 13.32 0.00 39.30 4.12
42 43 0.535102 GCCATCGGTCCTATGGTTGG 60.535 60.000 20.67 5.91 44.87 3.77
43 44 0.535102 GGCCATCGGTCCTATGGTTG 60.535 60.000 20.67 0.07 44.87 3.77
44 45 0.694444 AGGCCATCGGTCCTATGGTT 60.694 55.000 20.67 9.30 44.87 3.67
45 46 1.074471 AGGCCATCGGTCCTATGGT 60.074 57.895 20.67 2.52 44.87 3.55
46 47 1.674057 GAGGCCATCGGTCCTATGG 59.326 63.158 16.59 16.59 45.68 2.74
56 57 2.699954 TCTTTTTCTGACGAGGCCATC 58.300 47.619 5.01 0.00 0.00 3.51
57 58 2.859165 TCTTTTTCTGACGAGGCCAT 57.141 45.000 5.01 0.00 0.00 4.40
58 59 2.303022 AGATCTTTTTCTGACGAGGCCA 59.697 45.455 5.01 0.00 0.00 5.36
59 60 2.979240 AGATCTTTTTCTGACGAGGCC 58.021 47.619 0.00 0.00 0.00 5.19
60 61 5.869888 TCTTTAGATCTTTTTCTGACGAGGC 59.130 40.000 0.00 0.00 0.00 4.70
61 62 7.891183 TTCTTTAGATCTTTTTCTGACGAGG 57.109 36.000 0.00 0.00 0.00 4.63
62 63 9.364989 AGATTCTTTAGATCTTTTTCTGACGAG 57.635 33.333 0.00 0.00 0.00 4.18
63 64 9.712305 AAGATTCTTTAGATCTTTTTCTGACGA 57.288 29.630 0.00 0.00 31.21 4.20
81 82 8.557864 CGATGAGAATGCTGAATAAAGATTCTT 58.442 33.333 0.00 0.00 41.87 2.52
82 83 7.714377 ACGATGAGAATGCTGAATAAAGATTCT 59.286 33.333 0.00 0.00 41.87 2.40
83 84 7.859598 ACGATGAGAATGCTGAATAAAGATTC 58.140 34.615 0.00 0.00 41.72 2.52
84 85 7.307042 CGACGATGAGAATGCTGAATAAAGATT 60.307 37.037 0.00 0.00 0.00 2.40
85 86 6.145209 CGACGATGAGAATGCTGAATAAAGAT 59.855 38.462 0.00 0.00 0.00 2.40
86 87 5.460091 CGACGATGAGAATGCTGAATAAAGA 59.540 40.000 0.00 0.00 0.00 2.52
87 88 5.664262 CGACGATGAGAATGCTGAATAAAG 58.336 41.667 0.00 0.00 0.00 1.85
88 89 4.025730 GCGACGATGAGAATGCTGAATAAA 60.026 41.667 0.00 0.00 0.00 1.40
89 90 3.490896 GCGACGATGAGAATGCTGAATAA 59.509 43.478 0.00 0.00 0.00 1.40
90 91 3.052745 GCGACGATGAGAATGCTGAATA 58.947 45.455 0.00 0.00 0.00 1.75
91 92 1.863454 GCGACGATGAGAATGCTGAAT 59.137 47.619 0.00 0.00 0.00 2.57
92 93 1.280982 GCGACGATGAGAATGCTGAA 58.719 50.000 0.00 0.00 0.00 3.02
93 94 0.528466 GGCGACGATGAGAATGCTGA 60.528 55.000 0.00 0.00 0.00 4.26
94 95 1.930100 GGCGACGATGAGAATGCTG 59.070 57.895 0.00 0.00 0.00 4.41
95 96 4.427394 GGCGACGATGAGAATGCT 57.573 55.556 0.00 0.00 0.00 3.79
107 108 4.445545 CTTTGCTTCGGCGGCGAC 62.446 66.667 34.85 23.49 45.37 5.19
108 109 4.673298 TCTTTGCTTCGGCGGCGA 62.673 61.111 31.46 31.46 45.37 5.54
109 110 4.445545 GTCTTTGCTTCGGCGGCG 62.446 66.667 27.15 27.15 45.37 6.46
110 111 2.200170 ATTGTCTTTGCTTCGGCGGC 62.200 55.000 7.21 3.69 45.37 6.53
111 112 0.454957 CATTGTCTTTGCTTCGGCGG 60.455 55.000 7.21 0.00 45.37 6.13
112 113 0.516877 TCATTGTCTTTGCTTCGGCG 59.483 50.000 0.00 0.00 45.37 6.46
113 114 2.287547 TGTTCATTGTCTTTGCTTCGGC 60.288 45.455 0.00 0.00 42.19 5.54
114 115 3.624326 TGTTCATTGTCTTTGCTTCGG 57.376 42.857 0.00 0.00 0.00 4.30
115 116 3.730715 GGTTGTTCATTGTCTTTGCTTCG 59.269 43.478 0.00 0.00 0.00 3.79
116 117 4.936891 AGGTTGTTCATTGTCTTTGCTTC 58.063 39.130 0.00 0.00 0.00 3.86
117 118 6.463995 TTAGGTTGTTCATTGTCTTTGCTT 57.536 33.333 0.00 0.00 0.00 3.91
118 119 6.463995 TTTAGGTTGTTCATTGTCTTTGCT 57.536 33.333 0.00 0.00 0.00 3.91
119 120 7.398746 GTTTTTAGGTTGTTCATTGTCTTTGC 58.601 34.615 0.00 0.00 0.00 3.68
120 121 7.763985 AGGTTTTTAGGTTGTTCATTGTCTTTG 59.236 33.333 0.00 0.00 0.00 2.77
121 122 7.847096 AGGTTTTTAGGTTGTTCATTGTCTTT 58.153 30.769 0.00 0.00 0.00 2.52
122 123 7.418337 AGGTTTTTAGGTTGTTCATTGTCTT 57.582 32.000 0.00 0.00 0.00 3.01
123 124 7.996644 TCTAGGTTTTTAGGTTGTTCATTGTCT 59.003 33.333 0.00 0.00 0.00 3.41
124 125 8.074370 GTCTAGGTTTTTAGGTTGTTCATTGTC 58.926 37.037 0.00 0.00 0.00 3.18
125 126 7.778382 AGTCTAGGTTTTTAGGTTGTTCATTGT 59.222 33.333 0.00 0.00 0.00 2.71
126 127 8.166422 AGTCTAGGTTTTTAGGTTGTTCATTG 57.834 34.615 0.00 0.00 0.00 2.82
135 136 9.994017 ACTCTCTTATAGTCTAGGTTTTTAGGT 57.006 33.333 0.00 0.00 0.00 3.08
142 143 8.623030 CGCTTTTACTCTCTTATAGTCTAGGTT 58.377 37.037 0.00 0.00 0.00 3.50
143 144 7.992033 TCGCTTTTACTCTCTTATAGTCTAGGT 59.008 37.037 0.00 0.00 0.00 3.08
144 145 8.380743 TCGCTTTTACTCTCTTATAGTCTAGG 57.619 38.462 0.00 0.00 0.00 3.02
146 147 9.001542 GGATCGCTTTTACTCTCTTATAGTCTA 57.998 37.037 0.00 0.00 0.00 2.59
147 148 7.502895 TGGATCGCTTTTACTCTCTTATAGTCT 59.497 37.037 0.00 0.00 0.00 3.24
148 149 7.592164 GTGGATCGCTTTTACTCTCTTATAGTC 59.408 40.741 0.00 0.00 0.00 2.59
149 150 7.068348 TGTGGATCGCTTTTACTCTCTTATAGT 59.932 37.037 0.00 0.00 0.00 2.12
150 151 7.380065 GTGTGGATCGCTTTTACTCTCTTATAG 59.620 40.741 0.00 0.00 0.00 1.31
151 152 7.201145 GTGTGGATCGCTTTTACTCTCTTATA 58.799 38.462 0.00 0.00 0.00 0.98
152 153 6.043411 GTGTGGATCGCTTTTACTCTCTTAT 58.957 40.000 0.00 0.00 0.00 1.73
153 154 5.408356 GTGTGGATCGCTTTTACTCTCTTA 58.592 41.667 0.00 0.00 0.00 2.10
154 155 4.246458 GTGTGGATCGCTTTTACTCTCTT 58.754 43.478 0.00 0.00 0.00 2.85
155 156 3.673594 CGTGTGGATCGCTTTTACTCTCT 60.674 47.826 0.00 0.00 0.00 3.10
156 157 2.599082 CGTGTGGATCGCTTTTACTCTC 59.401 50.000 0.00 0.00 0.00 3.20
157 158 2.607187 CGTGTGGATCGCTTTTACTCT 58.393 47.619 0.00 0.00 0.00 3.24
197 198 1.226323 CTCGATCGTCGGTGGTGAC 60.226 63.158 15.94 0.00 40.88 3.67
198 199 2.404186 CCTCGATCGTCGGTGGTGA 61.404 63.158 15.94 0.00 40.88 4.02
199 200 2.102357 CCTCGATCGTCGGTGGTG 59.898 66.667 15.94 0.00 40.88 4.17
200 201 2.360852 ACCTCGATCGTCGGTGGT 60.361 61.111 23.96 17.48 40.88 4.16
201 202 2.408022 GACCTCGATCGTCGGTGG 59.592 66.667 27.68 18.83 40.88 4.61
206 207 4.609247 CCGGCGACCTCGATCGTC 62.609 72.222 15.94 6.62 44.13 4.20
209 210 4.933064 CTGCCGGCGACCTCGATC 62.933 72.222 23.90 0.00 43.02 3.69
236 237 4.821589 CCAAGGACGCTCTCCGGC 62.822 72.222 0.00 0.00 45.10 6.13
237 238 2.564553 CTTCCAAGGACGCTCTCCGG 62.565 65.000 0.00 0.00 45.10 5.14
238 239 1.153745 CTTCCAAGGACGCTCTCCG 60.154 63.158 0.00 0.00 45.10 4.63
239 240 0.827368 ATCTTCCAAGGACGCTCTCC 59.173 55.000 0.00 0.00 39.81 3.71
240 241 1.535015 CGATCTTCCAAGGACGCTCTC 60.535 57.143 0.00 0.00 0.00 3.20
241 242 0.457851 CGATCTTCCAAGGACGCTCT 59.542 55.000 0.00 0.00 0.00 4.09
242 243 0.528684 CCGATCTTCCAAGGACGCTC 60.529 60.000 0.00 0.00 0.00 5.03
243 244 1.517832 CCGATCTTCCAAGGACGCT 59.482 57.895 0.00 0.00 0.00 5.07
244 245 2.174319 GCCGATCTTCCAAGGACGC 61.174 63.158 0.00 0.00 0.00 5.19
245 246 1.521681 GGCCGATCTTCCAAGGACG 60.522 63.158 0.00 0.00 0.00 4.79
246 247 0.179070 GAGGCCGATCTTCCAAGGAC 60.179 60.000 0.00 0.00 0.00 3.85
247 248 1.338136 GGAGGCCGATCTTCCAAGGA 61.338 60.000 0.00 0.00 0.00 3.36
248 249 1.147153 GGAGGCCGATCTTCCAAGG 59.853 63.158 0.00 0.00 0.00 3.61
249 250 1.147153 GGGAGGCCGATCTTCCAAG 59.853 63.158 9.99 0.00 32.55 3.61
250 251 2.375345 GGGGAGGCCGATCTTCCAA 61.375 63.158 9.99 0.00 33.99 3.53
251 252 2.768344 GGGGAGGCCGATCTTCCA 60.768 66.667 9.99 0.00 33.99 3.53
252 253 2.446802 AGGGGAGGCCGATCTTCC 60.447 66.667 0.00 0.00 0.00 3.46
253 254 2.812619 CCAGGGGAGGCCGATCTTC 61.813 68.421 0.00 0.00 0.00 2.87
254 255 2.770048 CCAGGGGAGGCCGATCTT 60.770 66.667 0.00 0.00 0.00 2.40
272 273 4.530857 CTGGAACCCTAGCCGCCG 62.531 72.222 0.00 0.00 0.00 6.46
273 274 4.176752 CCTGGAACCCTAGCCGCC 62.177 72.222 0.00 0.00 0.00 6.13
274 275 4.176752 CCCTGGAACCCTAGCCGC 62.177 72.222 0.00 0.00 0.00 6.53
275 276 2.365105 TCCCTGGAACCCTAGCCG 60.365 66.667 0.00 0.00 0.00 5.52
276 277 2.073101 CCTCCCTGGAACCCTAGCC 61.073 68.421 0.00 0.00 38.35 3.93
277 278 1.003051 TCCTCCCTGGAACCCTAGC 59.997 63.158 0.00 0.00 42.94 3.42
278 279 0.637195 TCTCCTCCCTGGAACCCTAG 59.363 60.000 0.00 0.00 45.63 3.02
279 280 0.637195 CTCTCCTCCCTGGAACCCTA 59.363 60.000 0.00 0.00 45.63 3.53
280 281 1.394151 CTCTCCTCCCTGGAACCCT 59.606 63.158 0.00 0.00 45.63 4.34
281 282 1.690985 CCTCTCCTCCCTGGAACCC 60.691 68.421 0.00 0.00 45.63 4.11
282 283 0.252742 TTCCTCTCCTCCCTGGAACC 60.253 60.000 0.00 0.00 45.63 3.62
283 284 1.657804 TTTCCTCTCCTCCCTGGAAC 58.342 55.000 0.00 0.00 45.63 3.62
284 285 1.985895 GTTTTCCTCTCCTCCCTGGAA 59.014 52.381 0.00 0.00 45.63 3.53
285 286 1.657804 GTTTTCCTCTCCTCCCTGGA 58.342 55.000 0.00 0.00 43.86 3.86
286 287 0.250513 CGTTTTCCTCTCCTCCCTGG 59.749 60.000 0.00 0.00 37.10 4.45
287 288 0.391793 GCGTTTTCCTCTCCTCCCTG 60.392 60.000 0.00 0.00 0.00 4.45
288 289 1.554583 GGCGTTTTCCTCTCCTCCCT 61.555 60.000 0.00 0.00 0.00 4.20
289 290 1.078356 GGCGTTTTCCTCTCCTCCC 60.078 63.158 0.00 0.00 0.00 4.30
290 291 1.078356 GGGCGTTTTCCTCTCCTCC 60.078 63.158 0.00 0.00 0.00 4.30
291 292 1.448013 CGGGCGTTTTCCTCTCCTC 60.448 63.158 0.00 0.00 0.00 3.71
292 293 0.901580 TACGGGCGTTTTCCTCTCCT 60.902 55.000 0.00 0.00 0.00 3.69
293 294 0.177373 ATACGGGCGTTTTCCTCTCC 59.823 55.000 0.00 0.00 0.00 3.71
294 295 2.877043 TATACGGGCGTTTTCCTCTC 57.123 50.000 0.00 0.00 0.00 3.20
295 296 2.159000 CCTTATACGGGCGTTTTCCTCT 60.159 50.000 0.00 0.00 0.00 3.69
296 297 2.207590 CCTTATACGGGCGTTTTCCTC 58.792 52.381 0.00 0.00 0.00 3.71
297 298 1.134310 CCCTTATACGGGCGTTTTCCT 60.134 52.381 0.49 0.00 37.41 3.36
298 299 1.302366 CCCTTATACGGGCGTTTTCC 58.698 55.000 0.49 0.00 37.41 3.13
307 308 3.329929 GGATGGTTAGCCCTTATACGG 57.670 52.381 0.00 0.00 0.00 4.02
316 317 0.249911 CAGCTACGGGATGGTTAGCC 60.250 60.000 0.00 0.00 34.56 3.93
317 318 0.464452 ACAGCTACGGGATGGTTAGC 59.536 55.000 0.00 0.00 35.35 3.09
318 319 1.480954 ACACAGCTACGGGATGGTTAG 59.519 52.381 0.00 0.00 35.35 2.34
319 320 1.563924 ACACAGCTACGGGATGGTTA 58.436 50.000 0.00 0.00 35.35 2.85
320 321 1.480954 CTACACAGCTACGGGATGGTT 59.519 52.381 0.00 0.00 35.35 3.67
321 322 1.112113 CTACACAGCTACGGGATGGT 58.888 55.000 0.00 0.02 35.35 3.55
337 338 3.128242 ACAAGCAAGCAATCATCAGCTAC 59.872 43.478 0.00 0.00 40.90 3.58
392 407 4.201714 CGGAACTTGATCTGTACGTACGTA 60.202 45.833 23.60 23.60 0.00 3.57
393 408 3.425359 CGGAACTTGATCTGTACGTACGT 60.425 47.826 25.98 25.98 0.00 3.57
394 409 3.096461 CGGAACTTGATCTGTACGTACG 58.904 50.000 20.18 15.01 0.00 3.67
412 427 2.539338 GGCGTGTCAGTTTTGCGGA 61.539 57.895 0.00 0.00 0.00 5.54
413 428 2.051345 GGCGTGTCAGTTTTGCGG 60.051 61.111 0.00 0.00 0.00 5.69
434 449 3.712881 GAGCGCGGTGGTCACAAC 61.713 66.667 18.92 0.00 44.60 3.32
591 631 2.493030 GAGTACGGCAAGGCGCTA 59.507 61.111 16.18 5.25 41.91 4.26
607 647 1.600957 CGAGGCGACTTACTATTCGGA 59.399 52.381 0.00 0.00 44.43 4.55
809 910 1.629043 CCTCTTGCCCGCCTAGTATA 58.371 55.000 0.00 0.00 0.00 1.47
851 3841 0.095935 CGCTTTGAGATTCGTGCTGG 59.904 55.000 0.00 0.00 0.00 4.85
942 3932 3.782244 CGAGTGCAACCGAGCAGC 61.782 66.667 3.18 0.00 46.69 5.25
967 3957 4.612412 TTGGTGCCACGGACGGAC 62.612 66.667 0.00 0.00 0.00 4.79
968 3958 4.612412 GTTGGTGCCACGGACGGA 62.612 66.667 0.00 0.00 0.00 4.69
1049 4048 4.214327 CCTCTCCGGAGAAGCGGC 62.214 72.222 32.94 0.00 41.86 6.53
1252 4254 1.331756 GTCTAAGCGTCGGACGGATAA 59.668 52.381 29.30 0.00 42.82 1.75
1276 4278 4.927425 GCATCTTTCACTACACGGTAGAAA 59.073 41.667 15.28 7.68 0.00 2.52
1349 4351 0.313672 TTCCCAAAGCACAATCACGC 59.686 50.000 0.00 0.00 0.00 5.34
1354 4356 5.231702 ACATTTCATTCCCAAAGCACAAT 57.768 34.783 0.00 0.00 0.00 2.71
1363 4365 6.422400 GCTCGTTTTTAAACATTTCATTCCCA 59.578 34.615 6.21 0.00 38.81 4.37
1379 4381 0.307760 CGCCACAGAAGCTCGTTTTT 59.692 50.000 0.00 0.00 0.00 1.94
1411 4413 9.394477 GCAGATTACAACTTCGAAACTAAATTT 57.606 29.630 0.00 0.00 0.00 1.82
1462 4464 7.451566 ACCTAGCAAGAGTTCCAATTTTACAAT 59.548 33.333 0.00 0.00 0.00 2.71
1466 4468 5.183140 GCACCTAGCAAGAGTTCCAATTTTA 59.817 40.000 0.00 0.00 44.79 1.52
1577 4579 5.552178 ACTCCGAATATGGGAATTAGAAGC 58.448 41.667 0.00 0.00 32.02 3.86
1590 4592 8.675504 CGTATGGATTTAGACTACTCCGAATAT 58.324 37.037 6.02 0.00 0.00 1.28
1752 4867 8.268850 TCTGTTACAGGCTCAAAAAGATATTC 57.731 34.615 12.79 0.00 31.51 1.75
1822 4939 7.544650 TCAGATATAGAAAAGGGGAGGTATGA 58.455 38.462 0.00 0.00 0.00 2.15
1840 4958 9.415008 GTACAGATACAGGTATCCATCAGATAT 57.585 37.037 14.21 0.00 42.13 1.63
2278 5397 5.779529 ATGGCATATCAAATCAGGTTCAC 57.220 39.130 0.00 0.00 0.00 3.18
2431 5550 5.050490 ACGACTATTGAGTGGCAATGATAC 58.950 41.667 0.00 0.00 46.38 2.24
2511 5635 7.119699 TCCTCATCATTGATTACACTGACAAAC 59.880 37.037 0.00 0.00 38.23 2.93
2757 5881 2.352651 CTGCATCACCAGTAATTCGTGG 59.647 50.000 4.74 4.74 39.98 4.94
2792 5916 0.107214 ATGCTCCATAACCCACACGG 60.107 55.000 0.00 0.00 37.81 4.94
2970 6095 3.684788 CAGCAGACGTATTAGCCAAGTTT 59.315 43.478 0.00 0.00 0.00 2.66
2990 6115 4.155644 GCTCTTCAAGAATGAAAGGTCCAG 59.844 45.833 0.00 0.00 44.64 3.86
3255 6380 2.519377 TAACCCATATCGCAGTTCCG 57.481 50.000 0.00 0.00 0.00 4.30
3326 6452 2.562298 GCCTGAATTGTTCAATGGGACA 59.438 45.455 12.75 0.00 39.58 4.02
3342 6468 3.193267 GTGAATAAAGTTGCATGGCCTGA 59.807 43.478 3.32 0.00 0.00 3.86
3624 6750 2.024176 TGGAGGGAAGCAGTGTCTAA 57.976 50.000 0.00 0.00 0.00 2.10
3759 6885 2.872245 TCTGCACAGTAACTTTGCTGAC 59.128 45.455 13.26 6.12 42.54 3.51
3868 7007 8.860088 GGCCTCTTTATTCACCATATAACATTT 58.140 33.333 0.00 0.00 0.00 2.32
3875 7014 6.948309 GGTAATGGCCTCTTTATTCACCATAT 59.052 38.462 3.32 0.00 36.91 1.78
3891 7030 7.004691 AGAAAGGTAAGATTATGGTAATGGCC 58.995 38.462 0.00 0.00 0.00 5.36
3914 7053 4.141711 ACTGACAAAAGCACTGGTAGAAGA 60.142 41.667 0.00 0.00 0.00 2.87
3941 7080 6.931790 AGAGTGCAGTTCCTCATGATATAT 57.068 37.500 0.00 0.00 0.00 0.86
3942 7081 6.324770 TGAAGAGTGCAGTTCCTCATGATATA 59.675 38.462 0.00 0.00 0.00 0.86
3955 7094 3.281727 TGAACCTTTGAAGAGTGCAGT 57.718 42.857 0.00 0.00 0.00 4.40
4028 7167 2.983402 TTCTCGTACACTGTCCTTCG 57.017 50.000 0.00 0.00 0.00 3.79
4039 7178 6.476243 TCCTTTGCTGTATTTTTCTCGTAC 57.524 37.500 0.00 0.00 0.00 3.67
4124 7267 0.618107 TTGCAATGGCCATCACCCAT 60.618 50.000 21.08 0.00 44.75 4.00
4128 7271 1.153784 CCGTTGCAATGGCCATCAC 60.154 57.895 24.31 14.81 40.13 3.06
4159 7302 5.163281 TGCCGGTTACCAGAAACTAAATA 57.837 39.130 1.90 0.00 0.00 1.40
4286 7442 2.821437 CTGGAGAGGTACTTCAAGGGA 58.179 52.381 7.82 0.00 41.55 4.20
4459 7616 1.519751 GGTACATGCCCAACAACGCA 61.520 55.000 0.00 0.00 39.79 5.24


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

AutoCloner maintained by Alex Coulton.