Multiple sequence alignment - TraesCS7D01G411400

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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 TraesCS7D01G411400 chr7D 100.000 4031 0 0 1 4031 530119870 530123900 0.000000e+00 7444
1 TraesCS7D01G411400 chr7D 97.115 624 17 1 299 921 75345068 75345691 0.000000e+00 1051
2 TraesCS7D01G411400 chr7D 94.646 635 30 4 299 931 72163454 72164086 0.000000e+00 981
3 TraesCS7D01G411400 chr7D 98.485 66 1 0 3966 4031 494749952 494749887 2.550000e-22 117
4 TraesCS7D01G411400 chr7A 96.683 3105 95 3 928 4031 610443989 610447086 0.000000e+00 5156
5 TraesCS7D01G411400 chr7A 96.923 65 2 0 3966 4030 560306161 560306097 4.260000e-20 110
6 TraesCS7D01G411400 chr7B 95.900 3122 95 8 923 4031 568673413 568676514 0.000000e+00 5025
7 TraesCS7D01G411400 chr7B 98.485 66 1 0 3966 4031 522721481 522721416 2.550000e-22 117
8 TraesCS7D01G411400 chr7B 98.387 62 1 0 3970 4031 373075412 373075473 4.260000e-20 110
9 TraesCS7D01G411400 chr3A 94.961 635 30 2 299 931 8121661 8121027 0.000000e+00 994
10 TraesCS7D01G411400 chr3A 96.875 64 2 0 3968 4031 34532615 34532552 1.530000e-19 108
11 TraesCS7D01G411400 chr3A 92.958 71 4 1 3961 4031 547478206 547478275 7.130000e-18 102
12 TraesCS7D01G411400 chr6A 94.688 640 29 3 297 931 7972921 7972282 0.000000e+00 989
13 TraesCS7D01G411400 chr2B 94.937 632 30 2 299 929 95851828 95851198 0.000000e+00 989
14 TraesCS7D01G411400 chr2B 93.405 652 36 5 297 941 394099381 394100032 0.000000e+00 959
15 TraesCS7D01G411400 chr4B 94.210 639 33 3 297 931 450859232 450859870 0.000000e+00 972
16 TraesCS7D01G411400 chr4B 93.405 652 38 3 297 943 105357557 105356906 0.000000e+00 961
17 TraesCS7D01G411400 chr5B 94.192 637 32 4 299 931 163100287 163099652 0.000000e+00 966
18 TraesCS7D01G411400 chr2D 99.342 304 1 1 2 305 626754126 626753824 2.120000e-152 549
19 TraesCS7D01G411400 chrUn 99.013 304 2 1 2 305 89855708 89855406 9.850000e-151 544
20 TraesCS7D01G411400 chr5D 99.013 304 2 1 2 305 482685126 482684824 9.850000e-151 544
21 TraesCS7D01G411400 chr3D 99.013 304 2 1 2 305 525925423 525925121 9.850000e-151 544
22 TraesCS7D01G411400 chr3D 99.013 304 2 1 2 305 604641623 604641925 9.850000e-151 544
23 TraesCS7D01G411400 chr6D 98.684 304 3 1 2 305 205815738 205816040 4.580000e-149 538
24 TraesCS7D01G411400 chr1D 98.684 304 3 1 2 305 71706781 71707083 4.580000e-149 538
25 TraesCS7D01G411400 chr1D 98.684 304 3 1 2 305 73140600 73140298 4.580000e-149 538
26 TraesCS7D01G411400 chr1D 98.684 304 3 1 2 305 236086878 236086576 4.580000e-149 538
27 TraesCS7D01G411400 chr1D 96.875 64 2 0 3968 4031 60407174 60407237 1.530000e-19 108


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 TraesCS7D01G411400 chr7D 530119870 530123900 4030 False 7444 7444 100.000 1 4031 1 chr7D.!!$F3 4030
1 TraesCS7D01G411400 chr7D 75345068 75345691 623 False 1051 1051 97.115 299 921 1 chr7D.!!$F2 622
2 TraesCS7D01G411400 chr7D 72163454 72164086 632 False 981 981 94.646 299 931 1 chr7D.!!$F1 632
3 TraesCS7D01G411400 chr7A 610443989 610447086 3097 False 5156 5156 96.683 928 4031 1 chr7A.!!$F1 3103
4 TraesCS7D01G411400 chr7B 568673413 568676514 3101 False 5025 5025 95.900 923 4031 1 chr7B.!!$F2 3108
5 TraesCS7D01G411400 chr3A 8121027 8121661 634 True 994 994 94.961 299 931 1 chr3A.!!$R1 632
6 TraesCS7D01G411400 chr6A 7972282 7972921 639 True 989 989 94.688 297 931 1 chr6A.!!$R1 634
7 TraesCS7D01G411400 chr2B 95851198 95851828 630 True 989 989 94.937 299 929 1 chr2B.!!$R1 630
8 TraesCS7D01G411400 chr2B 394099381 394100032 651 False 959 959 93.405 297 941 1 chr2B.!!$F1 644
9 TraesCS7D01G411400 chr4B 450859232 450859870 638 False 972 972 94.210 297 931 1 chr4B.!!$F1 634
10 TraesCS7D01G411400 chr4B 105356906 105357557 651 True 961 961 93.405 297 943 1 chr4B.!!$R1 646
11 TraesCS7D01G411400 chr5B 163099652 163100287 635 True 966 966 94.192 299 931 1 chr5B.!!$R1 632

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
73 74 0.035152 TGGCGTCCTAGTCCGAACTA 60.035 55.0 2.77 0.00 36.92 2.24 F
91 92 0.035247 TACCGCGGCAAAAACCCTAT 60.035 50.0 28.58 2.85 0.00 2.57 F
290 291 0.035152 CATACTCAGGTGCCTGGCAA 60.035 55.0 25.23 6.80 41.47 4.52 F
1006 1018 0.038166 TTCCTGTCAAGACATGCCCC 59.962 55.0 3.01 0.00 41.01 5.80 F
1660 1672 0.247736 GTCTCCGACTGAGGCAACAT 59.752 55.0 0.00 0.00 45.44 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1313 1325 0.387202 CGCCATCTCTCGGAAGACAT 59.613 55.000 0.0 0.0 35.39 3.06 R
1437 1449 0.396811 CCAGGAGGTCGGTTGAAAGT 59.603 55.000 0.0 0.0 0.00 2.66 R
1869 1881 0.693622 TCCGAACAAGCCCACCAATA 59.306 50.000 0.0 0.0 0.00 1.90 R
2505 2517 1.452651 AGCATGTCCATTCCAGGCG 60.453 57.895 0.0 0.0 43.85 5.52 R
3638 3658 1.224592 CGACCAATCCCCCTCTTGG 59.775 63.158 0.0 0.0 46.03 3.61 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
33 34 4.891727 GGCCGTCCGCATCGTCAT 62.892 66.667 0.00 0.00 40.31 3.06
34 35 3.330853 GCCGTCCGCATCGTCATC 61.331 66.667 0.00 0.00 37.47 2.92
35 36 2.413351 CCGTCCGCATCGTCATCT 59.587 61.111 0.00 0.00 0.00 2.90
36 37 1.946156 CCGTCCGCATCGTCATCTG 60.946 63.158 0.00 0.00 0.00 2.90
37 38 1.226688 CGTCCGCATCGTCATCTGT 60.227 57.895 0.00 0.00 0.00 3.41
38 39 0.802222 CGTCCGCATCGTCATCTGTT 60.802 55.000 0.00 0.00 0.00 3.16
39 40 0.647410 GTCCGCATCGTCATCTGTTG 59.353 55.000 0.00 0.00 0.00 3.33
40 41 0.530288 TCCGCATCGTCATCTGTTGA 59.470 50.000 0.00 0.00 0.00 3.18
41 42 1.067213 TCCGCATCGTCATCTGTTGAA 60.067 47.619 0.00 0.00 35.70 2.69
42 43 1.061131 CCGCATCGTCATCTGTTGAAC 59.939 52.381 0.00 0.00 35.70 3.18
43 44 1.061131 CGCATCGTCATCTGTTGAACC 59.939 52.381 0.00 0.00 35.70 3.62
44 45 1.061131 GCATCGTCATCTGTTGAACCG 59.939 52.381 0.00 0.00 35.70 4.44
45 46 1.061131 CATCGTCATCTGTTGAACCGC 59.939 52.381 0.00 0.00 35.70 5.68
46 47 0.669318 TCGTCATCTGTTGAACCGCC 60.669 55.000 0.00 0.00 35.70 6.13
47 48 1.635663 CGTCATCTGTTGAACCGCCC 61.636 60.000 0.00 0.00 35.70 6.13
48 49 1.002624 TCATCTGTTGAACCGCCCC 60.003 57.895 0.00 0.00 0.00 5.80
49 50 2.046285 CATCTGTTGAACCGCCCCC 61.046 63.158 0.00 0.00 0.00 5.40
50 51 2.534396 ATCTGTTGAACCGCCCCCA 61.534 57.895 0.00 0.00 0.00 4.96
51 52 2.484287 ATCTGTTGAACCGCCCCCAG 62.484 60.000 0.00 0.00 0.00 4.45
52 53 4.278513 TGTTGAACCGCCCCCAGG 62.279 66.667 0.00 0.00 0.00 4.45
64 65 3.854669 CCCAGGCTGGCGTCCTAG 61.855 72.222 28.51 8.71 35.79 3.02
65 66 3.077556 CCAGGCTGGCGTCCTAGT 61.078 66.667 22.68 0.00 31.52 2.57
66 67 2.496817 CAGGCTGGCGTCCTAGTC 59.503 66.667 6.61 0.00 31.52 2.59
67 68 2.760385 AGGCTGGCGTCCTAGTCC 60.760 66.667 0.00 0.00 30.79 3.85
68 69 4.208686 GGCTGGCGTCCTAGTCCG 62.209 72.222 0.00 0.00 0.00 4.79
69 70 3.138798 GCTGGCGTCCTAGTCCGA 61.139 66.667 2.77 0.00 0.00 4.55
70 71 2.707849 GCTGGCGTCCTAGTCCGAA 61.708 63.158 2.77 0.00 0.00 4.30
71 72 1.139095 CTGGCGTCCTAGTCCGAAC 59.861 63.158 2.77 0.00 0.00 3.95
72 73 1.303888 TGGCGTCCTAGTCCGAACT 60.304 57.895 2.77 0.00 39.66 3.01
73 74 0.035152 TGGCGTCCTAGTCCGAACTA 60.035 55.000 2.77 0.00 36.92 2.24
74 75 0.380024 GGCGTCCTAGTCCGAACTAC 59.620 60.000 2.77 0.00 36.92 2.73
75 76 0.380024 GCGTCCTAGTCCGAACTACC 59.620 60.000 2.77 0.00 36.92 3.18
76 77 0.654683 CGTCCTAGTCCGAACTACCG 59.345 60.000 0.00 0.00 36.92 4.02
77 78 0.380024 GTCCTAGTCCGAACTACCGC 59.620 60.000 0.00 0.00 36.92 5.68
78 79 1.091771 TCCTAGTCCGAACTACCGCG 61.092 60.000 0.00 0.00 36.92 6.46
80 81 2.659017 CTAGTCCGAACTACCGCGGC 62.659 65.000 28.58 7.46 46.79 6.53
81 82 4.424566 GTCCGAACTACCGCGGCA 62.425 66.667 28.58 12.87 46.79 5.69
82 83 3.682885 TCCGAACTACCGCGGCAA 61.683 61.111 28.58 13.53 46.79 4.52
83 84 2.739287 CCGAACTACCGCGGCAAA 60.739 61.111 28.58 10.51 41.17 3.68
84 85 2.319096 CCGAACTACCGCGGCAAAA 61.319 57.895 28.58 7.56 41.17 2.44
85 86 1.570475 CGAACTACCGCGGCAAAAA 59.430 52.632 28.58 4.67 0.00 1.94
86 87 0.723459 CGAACTACCGCGGCAAAAAC 60.723 55.000 28.58 11.81 0.00 2.43
87 88 0.386352 GAACTACCGCGGCAAAAACC 60.386 55.000 28.58 4.82 0.00 3.27
88 89 1.798234 AACTACCGCGGCAAAAACCC 61.798 55.000 28.58 0.00 0.00 4.11
89 90 1.969589 CTACCGCGGCAAAAACCCT 60.970 57.895 28.58 4.37 0.00 4.34
90 91 0.674269 CTACCGCGGCAAAAACCCTA 60.674 55.000 28.58 5.51 0.00 3.53
91 92 0.035247 TACCGCGGCAAAAACCCTAT 60.035 50.000 28.58 2.85 0.00 2.57
92 93 1.310216 ACCGCGGCAAAAACCCTATC 61.310 55.000 28.58 0.00 0.00 2.08
93 94 1.029947 CCGCGGCAAAAACCCTATCT 61.030 55.000 14.67 0.00 0.00 1.98
94 95 1.658994 CGCGGCAAAAACCCTATCTA 58.341 50.000 0.00 0.00 0.00 1.98
95 96 1.329599 CGCGGCAAAAACCCTATCTAC 59.670 52.381 0.00 0.00 0.00 2.59
96 97 2.361789 GCGGCAAAAACCCTATCTACA 58.638 47.619 0.00 0.00 0.00 2.74
97 98 2.354821 GCGGCAAAAACCCTATCTACAG 59.645 50.000 0.00 0.00 0.00 2.74
98 99 2.943033 CGGCAAAAACCCTATCTACAGG 59.057 50.000 0.00 0.00 35.26 4.00
99 100 2.688446 GGCAAAAACCCTATCTACAGGC 59.312 50.000 0.00 0.00 34.02 4.85
100 101 2.688446 GCAAAAACCCTATCTACAGGCC 59.312 50.000 0.00 0.00 34.02 5.19
101 102 2.943033 CAAAAACCCTATCTACAGGCCG 59.057 50.000 0.00 0.00 34.02 6.13
102 103 0.468648 AAACCCTATCTACAGGCCGC 59.531 55.000 0.00 0.00 34.02 6.53
103 104 1.408453 AACCCTATCTACAGGCCGCC 61.408 60.000 0.00 0.00 34.02 6.13
104 105 2.651361 CCTATCTACAGGCCGCCG 59.349 66.667 3.05 1.53 0.00 6.46
105 106 2.201022 CCTATCTACAGGCCGCCGT 61.201 63.158 3.05 7.90 0.00 5.68
106 107 1.286260 CTATCTACAGGCCGCCGTC 59.714 63.158 3.05 0.00 0.00 4.79
107 108 2.459421 CTATCTACAGGCCGCCGTCG 62.459 65.000 3.05 1.94 0.00 5.12
108 109 2.946172 TATCTACAGGCCGCCGTCGA 62.946 60.000 3.05 7.34 38.10 4.20
109 110 4.849329 CTACAGGCCGCCGTCGAC 62.849 72.222 5.18 5.18 38.10 4.20
123 124 3.170585 CGACTCGTTCGGTTCCGC 61.171 66.667 6.35 0.00 44.60 5.54
124 125 2.808321 GACTCGTTCGGTTCCGCC 60.808 66.667 6.35 0.00 0.00 6.13
125 126 3.278592 GACTCGTTCGGTTCCGCCT 62.279 63.158 6.35 0.00 34.25 5.52
126 127 1.926511 GACTCGTTCGGTTCCGCCTA 61.927 60.000 6.35 0.00 34.25 3.93
127 128 1.318158 ACTCGTTCGGTTCCGCCTAT 61.318 55.000 6.35 0.00 34.25 2.57
128 129 0.870307 CTCGTTCGGTTCCGCCTATG 60.870 60.000 6.35 0.98 34.25 2.23
129 130 1.140161 CGTTCGGTTCCGCCTATGA 59.860 57.895 6.35 0.00 34.25 2.15
130 131 1.143969 CGTTCGGTTCCGCCTATGAC 61.144 60.000 6.35 0.00 34.25 3.06
131 132 0.108520 GTTCGGTTCCGCCTATGACA 60.109 55.000 6.35 0.00 34.25 3.58
132 133 0.828022 TTCGGTTCCGCCTATGACAT 59.172 50.000 6.35 0.00 34.25 3.06
133 134 0.387929 TCGGTTCCGCCTATGACATC 59.612 55.000 6.35 0.00 34.25 3.06
134 135 0.104120 CGGTTCCGCCTATGACATCA 59.896 55.000 0.00 0.00 34.25 3.07
135 136 1.583054 GGTTCCGCCTATGACATCAC 58.417 55.000 0.00 0.00 0.00 3.06
136 137 1.583054 GTTCCGCCTATGACATCACC 58.417 55.000 0.00 0.00 0.00 4.02
137 138 1.134521 GTTCCGCCTATGACATCACCA 60.135 52.381 0.00 0.00 0.00 4.17
138 139 0.752658 TCCGCCTATGACATCACCAG 59.247 55.000 0.00 0.00 0.00 4.00
139 140 0.882042 CCGCCTATGACATCACCAGC 60.882 60.000 0.00 0.00 0.00 4.85
140 141 0.179076 CGCCTATGACATCACCAGCA 60.179 55.000 0.00 0.00 0.00 4.41
141 142 1.303309 GCCTATGACATCACCAGCAC 58.697 55.000 0.00 0.00 0.00 4.40
142 143 1.959042 CCTATGACATCACCAGCACC 58.041 55.000 0.00 0.00 0.00 5.01
143 144 1.575244 CTATGACATCACCAGCACCG 58.425 55.000 0.00 0.00 0.00 4.94
144 145 1.136891 CTATGACATCACCAGCACCGA 59.863 52.381 0.00 0.00 0.00 4.69
145 146 0.107993 ATGACATCACCAGCACCGAG 60.108 55.000 0.00 0.00 0.00 4.63
146 147 1.293498 GACATCACCAGCACCGAGT 59.707 57.895 0.00 0.00 0.00 4.18
147 148 0.737715 GACATCACCAGCACCGAGTC 60.738 60.000 0.00 0.00 0.00 3.36
148 149 1.448540 CATCACCAGCACCGAGTCC 60.449 63.158 0.00 0.00 0.00 3.85
149 150 1.610673 ATCACCAGCACCGAGTCCT 60.611 57.895 0.00 0.00 0.00 3.85
150 151 1.892819 ATCACCAGCACCGAGTCCTG 61.893 60.000 0.00 0.00 0.00 3.86
151 152 4.008933 ACCAGCACCGAGTCCTGC 62.009 66.667 0.00 0.00 0.00 4.85
152 153 4.007644 CCAGCACCGAGTCCTGCA 62.008 66.667 9.53 0.00 35.73 4.41
153 154 2.740055 CAGCACCGAGTCCTGCAC 60.740 66.667 9.53 0.00 35.73 4.57
154 155 4.008933 AGCACCGAGTCCTGCACC 62.009 66.667 9.53 0.00 35.73 5.01
155 156 4.314440 GCACCGAGTCCTGCACCA 62.314 66.667 3.11 0.00 33.31 4.17
156 157 2.357517 CACCGAGTCCTGCACCAC 60.358 66.667 0.00 0.00 0.00 4.16
157 158 3.626924 ACCGAGTCCTGCACCACC 61.627 66.667 0.00 0.00 0.00 4.61
158 159 4.394712 CCGAGTCCTGCACCACCC 62.395 72.222 0.00 0.00 0.00 4.61
159 160 3.625897 CGAGTCCTGCACCACCCA 61.626 66.667 0.00 0.00 0.00 4.51
160 161 2.032681 GAGTCCTGCACCACCCAC 59.967 66.667 0.00 0.00 0.00 4.61
161 162 3.553095 GAGTCCTGCACCACCCACC 62.553 68.421 0.00 0.00 0.00 4.61
162 163 3.884774 GTCCTGCACCACCCACCA 61.885 66.667 0.00 0.00 0.00 4.17
163 164 3.569210 TCCTGCACCACCCACCAG 61.569 66.667 0.00 0.00 0.00 4.00
164 165 3.889692 CCTGCACCACCCACCAGT 61.890 66.667 0.00 0.00 0.00 4.00
165 166 2.595463 CTGCACCACCCACCAGTG 60.595 66.667 0.00 0.00 37.51 3.66
168 169 2.281761 CACCACCCACCAGTGCTC 60.282 66.667 0.00 0.00 36.38 4.26
169 170 3.570212 ACCACCCACCAGTGCTCC 61.570 66.667 0.00 0.00 36.38 4.70
170 171 3.569210 CCACCCACCAGTGCTCCA 61.569 66.667 0.00 0.00 36.38 3.86
171 172 2.759114 CACCCACCAGTGCTCCAT 59.241 61.111 0.00 0.00 0.00 3.41
172 173 1.377725 CACCCACCAGTGCTCCATC 60.378 63.158 0.00 0.00 0.00 3.51
173 174 1.539869 ACCCACCAGTGCTCCATCT 60.540 57.895 0.00 0.00 0.00 2.90
174 175 1.077930 CCCACCAGTGCTCCATCTG 60.078 63.158 0.00 0.00 0.00 2.90
175 176 1.748122 CCACCAGTGCTCCATCTGC 60.748 63.158 0.00 0.00 0.00 4.26
176 177 2.104859 CACCAGTGCTCCATCTGCG 61.105 63.158 0.00 0.00 0.00 5.18
177 178 2.513204 CCAGTGCTCCATCTGCGG 60.513 66.667 0.00 0.00 0.00 5.69
178 179 2.267006 CAGTGCTCCATCTGCGGT 59.733 61.111 0.00 0.00 0.00 5.68
179 180 1.376424 CAGTGCTCCATCTGCGGTT 60.376 57.895 0.00 0.00 0.00 4.44
180 181 1.376424 AGTGCTCCATCTGCGGTTG 60.376 57.895 0.00 0.00 0.00 3.77
181 182 2.747460 TGCTCCATCTGCGGTTGC 60.747 61.111 0.00 0.00 43.20 4.17
195 196 4.802051 TTGCATGGCGGCCTCCTC 62.802 66.667 21.46 7.33 0.00 3.71
197 198 4.575973 GCATGGCGGCCTCCTCAT 62.576 66.667 21.46 1.21 0.00 2.90
198 199 2.593725 CATGGCGGCCTCCTCATG 60.594 66.667 21.46 11.12 31.03 3.07
199 200 2.769621 ATGGCGGCCTCCTCATGA 60.770 61.111 21.46 0.00 0.00 3.07
200 201 2.152058 ATGGCGGCCTCCTCATGAT 61.152 57.895 21.46 0.00 0.00 2.45
201 202 2.031768 GGCGGCCTCCTCATGATC 59.968 66.667 12.87 0.00 0.00 2.92
202 203 2.031768 GCGGCCTCCTCATGATCC 59.968 66.667 0.00 0.00 0.00 3.36
203 204 2.515071 GCGGCCTCCTCATGATCCT 61.515 63.158 0.00 0.00 0.00 3.24
204 205 2.049627 GCGGCCTCCTCATGATCCTT 62.050 60.000 0.00 0.00 0.00 3.36
205 206 0.250209 CGGCCTCCTCATGATCCTTG 60.250 60.000 0.00 0.00 0.00 3.61
206 207 0.110104 GGCCTCCTCATGATCCTTGG 59.890 60.000 0.00 0.00 0.00 3.61
207 208 1.135094 GCCTCCTCATGATCCTTGGA 58.865 55.000 0.00 0.00 0.00 3.53
208 209 1.202746 GCCTCCTCATGATCCTTGGAC 60.203 57.143 0.00 0.00 0.00 4.02
209 210 1.069823 CCTCCTCATGATCCTTGGACG 59.930 57.143 0.00 0.00 0.00 4.79
210 211 1.069823 CTCCTCATGATCCTTGGACGG 59.930 57.143 0.00 0.00 0.00 4.79
211 212 0.107456 CCTCATGATCCTTGGACGGG 59.893 60.000 0.00 0.00 0.00 5.28
212 213 0.107456 CTCATGATCCTTGGACGGGG 59.893 60.000 0.00 0.00 0.00 5.73
213 214 1.526917 CATGATCCTTGGACGGGGC 60.527 63.158 0.00 0.00 0.00 5.80
214 215 1.694169 ATGATCCTTGGACGGGGCT 60.694 57.895 0.00 0.00 0.00 5.19
215 216 1.281925 ATGATCCTTGGACGGGGCTT 61.282 55.000 0.00 0.00 0.00 4.35
216 217 1.452108 GATCCTTGGACGGGGCTTG 60.452 63.158 0.00 0.00 0.00 4.01
217 218 2.198304 GATCCTTGGACGGGGCTTGT 62.198 60.000 0.00 0.00 0.00 3.16
218 219 1.789576 ATCCTTGGACGGGGCTTGTT 61.790 55.000 0.00 0.00 0.00 2.83
219 220 1.971695 CCTTGGACGGGGCTTGTTC 60.972 63.158 0.00 0.00 0.00 3.18
220 221 1.228124 CTTGGACGGGGCTTGTTCA 60.228 57.895 0.00 0.00 0.00 3.18
221 222 0.821711 CTTGGACGGGGCTTGTTCAA 60.822 55.000 3.89 3.89 33.84 2.69
222 223 0.821711 TTGGACGGGGCTTGTTCAAG 60.822 55.000 8.04 8.04 29.95 3.02
223 224 2.626780 GGACGGGGCTTGTTCAAGC 61.627 63.158 23.97 23.97 44.76 4.01
229 230 4.584688 GCTTGTTCAAGCATGGCC 57.415 55.556 26.10 0.00 44.85 5.36
230 231 1.079612 GCTTGTTCAAGCATGGCCC 60.080 57.895 26.10 1.57 44.85 5.80
231 232 1.818959 GCTTGTTCAAGCATGGCCCA 61.819 55.000 26.10 0.00 44.85 5.36
232 233 0.899720 CTTGTTCAAGCATGGCCCAT 59.100 50.000 0.00 0.00 0.00 4.00
233 234 0.609151 TTGTTCAAGCATGGCCCATG 59.391 50.000 19.72 19.72 43.91 3.66
246 247 4.864334 CCATGCCCTGGTCCGCTC 62.864 72.222 0.00 0.00 40.49 5.03
247 248 4.864334 CATGCCCTGGTCCGCTCC 62.864 72.222 0.00 0.00 0.00 4.70
253 254 4.436998 CTGGTCCGCTCCGTCCAC 62.437 72.222 0.00 0.00 0.00 4.02
276 277 4.530857 GTGCTCCGCCGGCATACT 62.531 66.667 28.98 0.00 41.86 2.12
277 278 4.221422 TGCTCCGCCGGCATACTC 62.221 66.667 28.98 11.42 34.56 2.59
278 279 4.221422 GCTCCGCCGGCATACTCA 62.221 66.667 28.98 1.22 0.00 3.41
279 280 2.028190 CTCCGCCGGCATACTCAG 59.972 66.667 28.98 7.87 0.00 3.35
280 281 3.506059 CTCCGCCGGCATACTCAGG 62.506 68.421 28.98 17.71 0.00 3.86
281 282 3.849951 CCGCCGGCATACTCAGGT 61.850 66.667 28.98 0.00 0.00 4.00
282 283 2.586079 CGCCGGCATACTCAGGTG 60.586 66.667 28.98 0.98 0.00 4.00
283 284 2.897350 GCCGGCATACTCAGGTGC 60.897 66.667 24.80 0.00 40.55 5.01
287 288 4.547859 GCATACTCAGGTGCCTGG 57.452 61.111 17.23 10.81 43.75 4.45
288 289 1.821332 GCATACTCAGGTGCCTGGC 60.821 63.158 12.87 12.87 43.75 4.85
289 290 1.603842 CATACTCAGGTGCCTGGCA 59.396 57.895 19.30 19.30 43.75 4.92
290 291 0.035152 CATACTCAGGTGCCTGGCAA 60.035 55.000 25.23 6.80 41.47 4.52
339 340 4.642429 ACAGTCGCTTCCTGACTTTAAAT 58.358 39.130 0.00 0.00 44.00 1.40
361 362 3.243839 TGAAAAGGAAAAGTGATGCCAGC 60.244 43.478 0.00 0.00 0.00 4.85
436 437 2.435372 AACTCAGGTTGGCTCAAACA 57.565 45.000 5.87 0.00 32.84 2.83
637 638 2.835764 ACCGGCCAGTAGTTATTGAGAA 59.164 45.455 0.00 0.00 0.00 2.87
731 733 2.165998 GAATTCAGAGTTTGCTGGGCT 58.834 47.619 0.00 0.00 36.55 5.19
740 743 1.280998 GTTTGCTGGGCTAACTCCCTA 59.719 52.381 8.94 0.00 46.67 3.53
845 848 1.873591 GTGTGTTGATCGGCTCAGTTT 59.126 47.619 0.00 0.00 34.68 2.66
1006 1018 0.038166 TTCCTGTCAAGACATGCCCC 59.962 55.000 3.01 0.00 41.01 5.80
1208 1220 2.758770 TTCGACGCTGTTCCCCTTCG 62.759 60.000 0.00 0.00 0.00 3.79
1404 1416 1.289380 GTCGGAGTTTGAGCTCGGT 59.711 57.895 9.64 0.00 37.20 4.69
1437 1449 1.519246 CGAAGCATGCTCCAGAGGA 59.481 57.895 22.93 0.00 0.00 3.71
1443 1455 1.339438 GCATGCTCCAGAGGACTTTCA 60.339 52.381 11.37 0.00 0.00 2.69
1614 1626 2.367241 GGGAGAGGCTCTCAGGTTATTC 59.633 54.545 37.55 21.46 45.12 1.75
1660 1672 0.247736 GTCTCCGACTGAGGCAACAT 59.752 55.000 0.00 0.00 45.44 2.71
1719 1731 6.753913 TCTTGGAAGGTCTGCTATATGATT 57.246 37.500 0.00 0.00 0.00 2.57
1818 1830 0.957888 GCTGTTTGAGGGAGGCTGTC 60.958 60.000 0.00 0.00 0.00 3.51
1841 1853 2.104111 TGTTGTTTCGTCAGATGGAGGT 59.896 45.455 0.00 0.00 33.18 3.85
1899 1911 0.668096 TTGTTCGGAATGGACGACCG 60.668 55.000 0.00 0.00 46.71 4.79
2316 2328 9.179909 GAGATCCTACCTATGATTTCTTCGATA 57.820 37.037 0.00 0.00 0.00 2.92
2375 2387 6.426937 CAGATCGTTAAAAGAGGTTTCCAGAA 59.573 38.462 0.00 0.00 0.00 3.02
2403 2415 7.472334 AAGGACAATTGCTAATTCACTCATT 57.528 32.000 5.05 0.00 0.00 2.57
2505 2517 8.861086 TCTTGGACTTCTATGATTCAGGTATAC 58.139 37.037 0.00 0.00 0.00 1.47
2525 2537 0.682209 GCCTGGAATGGACATGCTGT 60.682 55.000 0.00 0.00 0.00 4.40
2536 2548 2.349817 GGACATGCTGTTGAAGTTGTCG 60.350 50.000 0.00 0.00 39.83 4.35
2741 2753 0.240145 CGTACTGGACGCTTGACTGA 59.760 55.000 0.00 0.00 46.27 3.41
2742 2754 1.135373 CGTACTGGACGCTTGACTGAT 60.135 52.381 0.00 0.00 46.27 2.90
2743 2755 2.263077 GTACTGGACGCTTGACTGATG 58.737 52.381 0.00 0.00 0.00 3.07
2744 2756 0.671781 ACTGGACGCTTGACTGATGC 60.672 55.000 0.00 0.00 0.00 3.91
2745 2757 0.671472 CTGGACGCTTGACTGATGCA 60.671 55.000 0.00 0.00 0.00 3.96
2746 2758 0.036105 TGGACGCTTGACTGATGCAT 60.036 50.000 0.00 0.00 0.00 3.96
3040 3052 3.005684 TGAAGGTGGCTAAATGTTGCAAG 59.994 43.478 0.00 0.00 0.00 4.01
3042 3054 2.297033 AGGTGGCTAAATGTTGCAAGTG 59.703 45.455 0.00 0.00 0.00 3.16
3247 3259 2.227388 CCAACTTACAGCTCTTTGCCTG 59.773 50.000 0.00 0.00 44.23 4.85
3301 3318 6.183360 CCGACCTTAAGCACAGTTATTTGTAG 60.183 42.308 0.00 0.00 0.00 2.74
3532 3549 5.966335 CAAAAGTCTTTTGCATTTTCTCGG 58.034 37.500 21.85 0.00 42.91 4.63
3547 3567 3.469899 TCTCGGAAAACATCAAATGCG 57.530 42.857 0.00 0.00 0.00 4.73
3673 3693 7.041098 GGATTGGTCGTAATGCTAAAATCTCAT 60.041 37.037 0.00 0.00 0.00 2.90
3741 3762 4.188247 TGAATCAAGTTAGACGACCCAG 57.812 45.455 0.00 0.00 0.00 4.45
3783 3804 1.604593 GGTGGCAAGCATGACCACT 60.605 57.895 24.47 0.00 45.34 4.00
3784 3805 1.582968 GTGGCAAGCATGACCACTG 59.417 57.895 20.82 0.00 43.97 3.66
3790 3811 1.802960 CAAGCATGACCACTGTCTCAC 59.197 52.381 0.00 0.00 42.28 3.51
3796 3817 1.202371 TGACCACTGTCTCACACGTTC 60.202 52.381 0.00 0.00 42.28 3.95
3854 3875 2.177044 GTGATTAACCGCCACCACC 58.823 57.895 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.891727 ATGACGATGCGGACGGCC 62.892 66.667 0.00 0.00 42.61 6.13
17 18 3.330853 GATGACGATGCGGACGGC 61.331 66.667 0.00 0.00 43.96 5.68
18 19 1.946156 CAGATGACGATGCGGACGG 60.946 63.158 0.00 0.00 34.93 4.79
19 20 0.802222 AACAGATGACGATGCGGACG 60.802 55.000 0.00 0.00 0.00 4.79
20 21 0.647410 CAACAGATGACGATGCGGAC 59.353 55.000 0.00 0.00 0.00 4.79
21 22 0.530288 TCAACAGATGACGATGCGGA 59.470 50.000 0.00 0.00 31.50 5.54
22 23 1.061131 GTTCAACAGATGACGATGCGG 59.939 52.381 0.00 0.00 37.92 5.69
23 24 1.061131 GGTTCAACAGATGACGATGCG 59.939 52.381 0.00 0.00 37.92 4.73
24 25 1.061131 CGGTTCAACAGATGACGATGC 59.939 52.381 0.00 0.00 37.92 3.91
25 26 1.061131 GCGGTTCAACAGATGACGATG 59.939 52.381 0.00 0.00 37.92 3.84
26 27 1.359848 GCGGTTCAACAGATGACGAT 58.640 50.000 0.00 0.00 37.92 3.73
27 28 0.669318 GGCGGTTCAACAGATGACGA 60.669 55.000 0.00 0.00 37.92 4.20
28 29 1.635663 GGGCGGTTCAACAGATGACG 61.636 60.000 0.00 0.00 37.92 4.35
29 30 1.305930 GGGGCGGTTCAACAGATGAC 61.306 60.000 0.00 0.00 37.92 3.06
30 31 1.002624 GGGGCGGTTCAACAGATGA 60.003 57.895 0.00 0.00 35.85 2.92
31 32 2.046285 GGGGGCGGTTCAACAGATG 61.046 63.158 0.00 0.00 0.00 2.90
32 33 2.355115 GGGGGCGGTTCAACAGAT 59.645 61.111 0.00 0.00 0.00 2.90
33 34 3.172106 TGGGGGCGGTTCAACAGA 61.172 61.111 0.00 0.00 0.00 3.41
34 35 2.672996 CTGGGGGCGGTTCAACAG 60.673 66.667 0.00 0.00 0.00 3.16
35 36 4.278513 CCTGGGGGCGGTTCAACA 62.279 66.667 0.00 0.00 0.00 3.33
47 48 3.854669 CTAGGACGCCAGCCTGGG 61.855 72.222 13.78 5.25 38.19 4.45
48 49 3.077556 ACTAGGACGCCAGCCTGG 61.078 66.667 6.32 6.32 41.55 4.45
49 50 2.496817 GACTAGGACGCCAGCCTG 59.503 66.667 0.00 0.00 36.96 4.85
50 51 2.760385 GGACTAGGACGCCAGCCT 60.760 66.667 0.00 0.00 39.56 4.58
51 52 4.208686 CGGACTAGGACGCCAGCC 62.209 72.222 0.00 0.00 0.00 4.85
52 53 2.707849 TTCGGACTAGGACGCCAGC 61.708 63.158 0.00 0.00 0.00 4.85
53 54 1.139095 GTTCGGACTAGGACGCCAG 59.861 63.158 0.00 0.00 0.00 4.85
54 55 0.035152 TAGTTCGGACTAGGACGCCA 60.035 55.000 0.00 0.00 37.33 5.69
55 56 0.380024 GTAGTTCGGACTAGGACGCC 59.620 60.000 3.04 0.00 38.98 5.68
56 57 0.380024 GGTAGTTCGGACTAGGACGC 59.620 60.000 3.04 0.00 38.98 5.19
57 58 0.654683 CGGTAGTTCGGACTAGGACG 59.345 60.000 3.04 6.01 38.98 4.79
58 59 0.380024 GCGGTAGTTCGGACTAGGAC 59.620 60.000 3.04 0.00 38.98 3.85
59 60 1.091771 CGCGGTAGTTCGGACTAGGA 61.092 60.000 3.04 0.00 38.98 2.94
60 61 1.354506 CGCGGTAGTTCGGACTAGG 59.645 63.158 3.04 0.42 38.98 3.02
61 62 4.991760 CGCGGTAGTTCGGACTAG 57.008 61.111 3.04 0.00 38.98 2.57
67 68 0.723459 GTTTTTGCCGCGGTAGTTCG 60.723 55.000 28.70 0.00 0.00 3.95
68 69 0.386352 GGTTTTTGCCGCGGTAGTTC 60.386 55.000 28.70 10.19 0.00 3.01
69 70 1.655885 GGTTTTTGCCGCGGTAGTT 59.344 52.632 28.70 0.00 0.00 2.24
70 71 2.263021 GGGTTTTTGCCGCGGTAGT 61.263 57.895 28.70 0.00 0.00 2.73
71 72 0.674269 TAGGGTTTTTGCCGCGGTAG 60.674 55.000 28.70 0.72 0.00 3.18
72 73 0.035247 ATAGGGTTTTTGCCGCGGTA 60.035 50.000 28.70 21.83 0.00 4.02
73 74 1.303806 ATAGGGTTTTTGCCGCGGT 60.304 52.632 28.70 5.57 0.00 5.68
74 75 1.029947 AGATAGGGTTTTTGCCGCGG 61.030 55.000 24.05 24.05 0.00 6.46
75 76 1.329599 GTAGATAGGGTTTTTGCCGCG 59.670 52.381 0.00 0.00 0.00 6.46
76 77 2.354821 CTGTAGATAGGGTTTTTGCCGC 59.645 50.000 0.00 0.00 0.00 6.53
77 78 2.943033 CCTGTAGATAGGGTTTTTGCCG 59.057 50.000 0.00 0.00 34.06 5.69
78 79 2.688446 GCCTGTAGATAGGGTTTTTGCC 59.312 50.000 0.00 0.00 38.32 4.52
79 80 2.688446 GGCCTGTAGATAGGGTTTTTGC 59.312 50.000 0.00 0.00 38.32 3.68
80 81 2.943033 CGGCCTGTAGATAGGGTTTTTG 59.057 50.000 0.00 0.00 38.32 2.44
81 82 2.682858 GCGGCCTGTAGATAGGGTTTTT 60.683 50.000 0.00 0.00 38.32 1.94
82 83 1.134189 GCGGCCTGTAGATAGGGTTTT 60.134 52.381 0.00 0.00 38.32 2.43
83 84 0.468648 GCGGCCTGTAGATAGGGTTT 59.531 55.000 0.00 0.00 38.32 3.27
84 85 1.408453 GGCGGCCTGTAGATAGGGTT 61.408 60.000 12.87 0.00 38.32 4.11
85 86 1.837499 GGCGGCCTGTAGATAGGGT 60.837 63.158 12.87 0.00 38.32 4.34
86 87 2.932234 CGGCGGCCTGTAGATAGGG 61.932 68.421 18.34 0.00 38.32 3.53
87 88 2.143594 GACGGCGGCCTGTAGATAGG 62.144 65.000 18.34 0.00 40.95 2.57
88 89 1.286260 GACGGCGGCCTGTAGATAG 59.714 63.158 18.34 0.73 0.00 2.08
89 90 2.549198 CGACGGCGGCCTGTAGATA 61.549 63.158 18.34 0.00 0.00 1.98
90 91 3.900892 CGACGGCGGCCTGTAGAT 61.901 66.667 18.34 0.00 0.00 1.98
92 93 4.849329 GTCGACGGCGGCCTGTAG 62.849 72.222 12.58 15.91 35.76 2.74
107 108 1.926511 TAGGCGGAACCGAACGAGTC 61.927 60.000 17.63 0.00 46.52 3.36
108 109 1.318158 ATAGGCGGAACCGAACGAGT 61.318 55.000 17.63 0.00 46.52 4.18
109 110 0.870307 CATAGGCGGAACCGAACGAG 60.870 60.000 17.63 0.00 46.52 4.18
110 111 1.140161 CATAGGCGGAACCGAACGA 59.860 57.895 17.63 5.65 46.52 3.85
111 112 1.140161 TCATAGGCGGAACCGAACG 59.860 57.895 17.63 0.46 46.52 3.95
112 113 0.108520 TGTCATAGGCGGAACCGAAC 60.109 55.000 17.63 8.66 46.52 3.95
113 114 0.828022 ATGTCATAGGCGGAACCGAA 59.172 50.000 17.63 1.84 46.52 4.30
114 115 0.387929 GATGTCATAGGCGGAACCGA 59.612 55.000 17.63 0.00 46.52 4.69
115 116 0.104120 TGATGTCATAGGCGGAACCG 59.896 55.000 9.00 9.00 46.52 4.44
116 117 1.583054 GTGATGTCATAGGCGGAACC 58.417 55.000 0.00 0.00 39.61 3.62
117 118 1.134521 TGGTGATGTCATAGGCGGAAC 60.135 52.381 0.00 0.00 0.00 3.62
118 119 1.138859 CTGGTGATGTCATAGGCGGAA 59.861 52.381 0.00 0.00 0.00 4.30
119 120 0.752658 CTGGTGATGTCATAGGCGGA 59.247 55.000 0.00 0.00 0.00 5.54
120 121 0.882042 GCTGGTGATGTCATAGGCGG 60.882 60.000 0.00 0.00 0.00 6.13
121 122 0.179076 TGCTGGTGATGTCATAGGCG 60.179 55.000 0.00 0.00 0.00 5.52
122 123 1.303309 GTGCTGGTGATGTCATAGGC 58.697 55.000 0.00 0.00 0.00 3.93
123 124 1.807755 CGGTGCTGGTGATGTCATAGG 60.808 57.143 0.00 0.00 0.00 2.57
124 125 1.136891 TCGGTGCTGGTGATGTCATAG 59.863 52.381 0.00 0.00 0.00 2.23
125 126 1.136891 CTCGGTGCTGGTGATGTCATA 59.863 52.381 0.00 0.00 0.00 2.15
126 127 0.107993 CTCGGTGCTGGTGATGTCAT 60.108 55.000 0.00 0.00 0.00 3.06
127 128 1.293179 CTCGGTGCTGGTGATGTCA 59.707 57.895 0.00 0.00 0.00 3.58
128 129 0.737715 GACTCGGTGCTGGTGATGTC 60.738 60.000 0.00 0.00 0.00 3.06
129 130 1.293498 GACTCGGTGCTGGTGATGT 59.707 57.895 0.00 0.00 0.00 3.06
130 131 1.448540 GGACTCGGTGCTGGTGATG 60.449 63.158 0.00 0.00 0.00 3.07
131 132 1.610673 AGGACTCGGTGCTGGTGAT 60.611 57.895 0.00 0.00 31.84 3.06
132 133 2.203640 AGGACTCGGTGCTGGTGA 60.204 61.111 0.00 0.00 31.84 4.02
133 134 2.047844 CAGGACTCGGTGCTGGTG 60.048 66.667 14.73 0.00 45.87 4.17
137 138 4.008933 GGTGCAGGACTCGGTGCT 62.009 66.667 0.00 0.00 40.54 4.40
138 139 4.314440 TGGTGCAGGACTCGGTGC 62.314 66.667 0.00 0.00 40.29 5.01
139 140 2.357517 GTGGTGCAGGACTCGGTG 60.358 66.667 0.00 0.00 0.00 4.94
140 141 3.626924 GGTGGTGCAGGACTCGGT 61.627 66.667 0.00 0.00 0.00 4.69
141 142 4.394712 GGGTGGTGCAGGACTCGG 62.395 72.222 0.00 0.00 0.00 4.63
142 143 3.625897 TGGGTGGTGCAGGACTCG 61.626 66.667 0.00 0.00 0.00 4.18
143 144 2.032681 GTGGGTGGTGCAGGACTC 59.967 66.667 0.00 0.00 0.00 3.36
144 145 3.570212 GGTGGGTGGTGCAGGACT 61.570 66.667 0.00 0.00 0.00 3.85
145 146 3.850098 CTGGTGGGTGGTGCAGGAC 62.850 68.421 0.00 0.00 0.00 3.85
146 147 3.569210 CTGGTGGGTGGTGCAGGA 61.569 66.667 0.00 0.00 0.00 3.86
147 148 3.889692 ACTGGTGGGTGGTGCAGG 61.890 66.667 0.00 0.00 0.00 4.85
148 149 2.595463 CACTGGTGGGTGGTGCAG 60.595 66.667 0.00 0.00 33.95 4.41
151 152 2.281761 GAGCACTGGTGGGTGGTG 60.282 66.667 4.07 0.00 46.04 4.17
153 154 2.826777 GATGGAGCACTGGTGGGTGG 62.827 65.000 2.84 0.00 37.65 4.61
154 155 1.377725 GATGGAGCACTGGTGGGTG 60.378 63.158 2.84 0.00 39.91 4.61
155 156 1.539869 AGATGGAGCACTGGTGGGT 60.540 57.895 2.84 0.00 0.00 4.51
156 157 1.077930 CAGATGGAGCACTGGTGGG 60.078 63.158 2.84 0.00 0.00 4.61
157 158 1.748122 GCAGATGGAGCACTGGTGG 60.748 63.158 2.84 0.00 35.05 4.61
158 159 2.104859 CGCAGATGGAGCACTGGTG 61.105 63.158 0.00 0.00 35.05 4.17
159 160 2.267006 CGCAGATGGAGCACTGGT 59.733 61.111 0.00 0.00 35.05 4.00
160 161 2.513204 CCGCAGATGGAGCACTGG 60.513 66.667 0.00 0.00 35.05 4.00
161 162 1.376424 AACCGCAGATGGAGCACTG 60.376 57.895 0.00 0.00 37.22 3.66
162 163 1.376424 CAACCGCAGATGGAGCACT 60.376 57.895 0.00 0.00 0.00 4.40
163 164 3.044059 GCAACCGCAGATGGAGCAC 62.044 63.158 0.00 0.00 38.36 4.40
164 165 2.747460 GCAACCGCAGATGGAGCA 60.747 61.111 0.00 0.00 38.36 4.26
165 166 2.747460 TGCAACCGCAGATGGAGC 60.747 61.111 0.00 0.00 45.36 4.70
178 179 4.802051 GAGGAGGCCGCCATGCAA 62.802 66.667 28.68 0.00 0.00 4.08
180 181 4.575973 ATGAGGAGGCCGCCATGC 62.576 66.667 28.68 16.40 0.00 4.06
181 182 2.407440 ATCATGAGGAGGCCGCCATG 62.407 60.000 28.68 22.07 39.18 3.66
182 183 2.121992 GATCATGAGGAGGCCGCCAT 62.122 60.000 28.68 11.88 0.00 4.40
183 184 2.769621 ATCATGAGGAGGCCGCCA 60.770 61.111 28.68 8.35 0.00 5.69
184 185 2.031768 GATCATGAGGAGGCCGCC 59.968 66.667 19.43 19.43 0.00 6.13
185 186 2.031768 GGATCATGAGGAGGCCGC 59.968 66.667 0.09 0.00 0.00 6.53
186 187 0.250209 CAAGGATCATGAGGAGGCCG 60.250 60.000 0.09 0.00 0.00 6.13
187 188 0.110104 CCAAGGATCATGAGGAGGCC 59.890 60.000 0.09 0.00 0.00 5.19
188 189 1.135094 TCCAAGGATCATGAGGAGGC 58.865 55.000 0.09 0.00 0.00 4.70
189 190 1.069823 CGTCCAAGGATCATGAGGAGG 59.930 57.143 0.09 3.97 0.00 4.30
190 191 1.069823 CCGTCCAAGGATCATGAGGAG 59.930 57.143 0.09 0.00 0.00 3.69
191 192 1.123077 CCGTCCAAGGATCATGAGGA 58.877 55.000 0.09 0.00 0.00 3.71
192 193 0.107456 CCCGTCCAAGGATCATGAGG 59.893 60.000 0.09 0.00 0.00 3.86
193 194 0.107456 CCCCGTCCAAGGATCATGAG 59.893 60.000 0.09 0.00 0.00 2.90
194 195 1.983119 GCCCCGTCCAAGGATCATGA 61.983 60.000 0.00 0.00 0.00 3.07
195 196 1.526917 GCCCCGTCCAAGGATCATG 60.527 63.158 0.00 0.00 0.00 3.07
196 197 1.281925 AAGCCCCGTCCAAGGATCAT 61.282 55.000 0.00 0.00 0.00 2.45
197 198 1.923395 AAGCCCCGTCCAAGGATCA 60.923 57.895 0.00 0.00 0.00 2.92
198 199 1.452108 CAAGCCCCGTCCAAGGATC 60.452 63.158 0.00 0.00 0.00 3.36
199 200 1.789576 AACAAGCCCCGTCCAAGGAT 61.790 55.000 0.00 0.00 0.00 3.24
200 201 2.406002 GAACAAGCCCCGTCCAAGGA 62.406 60.000 0.00 0.00 0.00 3.36
201 202 1.971695 GAACAAGCCCCGTCCAAGG 60.972 63.158 0.00 0.00 0.00 3.61
202 203 0.821711 TTGAACAAGCCCCGTCCAAG 60.822 55.000 0.00 0.00 0.00 3.61
203 204 0.821711 CTTGAACAAGCCCCGTCCAA 60.822 55.000 1.60 0.00 0.00 3.53
204 205 1.228124 CTTGAACAAGCCCCGTCCA 60.228 57.895 1.60 0.00 0.00 4.02
205 206 3.668386 CTTGAACAAGCCCCGTCC 58.332 61.111 1.60 0.00 0.00 4.79
213 214 0.899720 ATGGGCCATGCTTGAACAAG 59.100 50.000 20.49 9.82 41.24 3.16
214 215 0.609151 CATGGGCCATGCTTGAACAA 59.391 50.000 31.96 0.00 35.02 2.83
215 216 2.278849 CATGGGCCATGCTTGAACA 58.721 52.632 31.96 0.00 35.02 3.18
230 231 4.864334 GGAGCGGACCAGGGCATG 62.864 72.222 0.00 0.00 0.00 4.06
236 237 4.436998 GTGGACGGAGCGGACCAG 62.437 72.222 0.00 0.00 37.84 4.00
262 263 2.028190 CTGAGTATGCCGGCGGAG 59.972 66.667 33.44 12.64 0.00 4.63
263 264 3.536917 CCTGAGTATGCCGGCGGA 61.537 66.667 33.44 15.74 0.00 5.54
264 265 3.849951 ACCTGAGTATGCCGGCGG 61.850 66.667 24.35 24.35 0.00 6.13
265 266 2.586079 CACCTGAGTATGCCGGCG 60.586 66.667 23.90 7.09 0.00 6.46
266 267 2.897350 GCACCTGAGTATGCCGGC 60.897 66.667 22.73 22.73 35.73 6.13
270 271 1.821332 GCCAGGCACCTGAGTATGC 60.821 63.158 18.44 8.55 46.30 3.14
271 272 0.035152 TTGCCAGGCACCTGAGTATG 60.035 55.000 15.89 1.99 46.30 2.39
272 273 0.035056 GTTGCCAGGCACCTGAGTAT 60.035 55.000 15.89 0.00 46.30 2.12
273 274 1.374947 GTTGCCAGGCACCTGAGTA 59.625 57.895 15.89 5.19 46.30 2.59
274 275 2.113986 GTTGCCAGGCACCTGAGT 59.886 61.111 15.89 0.00 46.30 3.41
275 276 2.674380 GGTTGCCAGGCACCTGAG 60.674 66.667 15.89 9.23 46.30 3.35
276 277 4.284550 GGGTTGCCAGGCACCTGA 62.285 66.667 24.22 6.26 46.30 3.86
297 298 2.589492 CCGCTCTAATCGCCGCAAG 61.589 63.158 0.00 0.00 0.00 4.01
339 340 3.243839 GCTGGCATCACTTTTCCTTTTCA 60.244 43.478 0.00 0.00 0.00 2.69
361 362 2.814805 AGTCTCATGGGGTGAAATGG 57.185 50.000 0.00 0.00 36.14 3.16
436 437 6.927416 TGAATAAAGCTTGCATCAACATTCT 58.073 32.000 0.00 0.00 0.00 2.40
495 496 0.916086 ACCGCCCCATTTGTATCTCA 59.084 50.000 0.00 0.00 0.00 3.27
637 638 1.350193 GATGACATTCGCACAGTCGT 58.650 50.000 0.00 0.00 35.09 4.34
845 848 4.600576 TCGCAACACGCAGGCTGA 62.601 61.111 20.86 0.00 42.60 4.26
1006 1018 0.806868 TGGTACTGGTAAGTCGCGAG 59.193 55.000 10.24 0.00 37.88 5.03
1313 1325 0.387202 CGCCATCTCTCGGAAGACAT 59.613 55.000 0.00 0.00 35.39 3.06
1425 1437 2.290577 GGTTGAAAGTCCTCTGGAGCAT 60.291 50.000 0.00 0.00 29.39 3.79
1437 1449 0.396811 CCAGGAGGTCGGTTGAAAGT 59.603 55.000 0.00 0.00 0.00 2.66
1545 1557 2.034066 AGGGCATTCCACACCACG 59.966 61.111 0.00 0.00 38.24 4.94
1614 1626 2.039418 TCCACCATCCTCATCCTTACG 58.961 52.381 0.00 0.00 0.00 3.18
1656 1668 2.365293 GGAAACCAAGCTCACCAATGTT 59.635 45.455 0.00 0.00 0.00 2.71
1660 1672 0.821711 CCGGAAACCAAGCTCACCAA 60.822 55.000 0.00 0.00 0.00 3.67
1719 1731 4.256110 CAGACCTAATCACAACAGCATGA 58.744 43.478 0.00 0.00 39.69 3.07
1818 1830 3.125829 CCTCCATCTGACGAAACAACATG 59.874 47.826 0.00 0.00 0.00 3.21
1869 1881 0.693622 TCCGAACAAGCCCACCAATA 59.306 50.000 0.00 0.00 0.00 1.90
1899 1911 6.207614 AGTGGAAAAGGTTAAGAGCAGAATTC 59.792 38.462 0.00 0.00 0.00 2.17
2316 2328 2.044793 TCCCCTTCTTCAGTGATGGT 57.955 50.000 6.21 0.00 31.60 3.55
2375 2387 7.177216 TGAGTGAATTAGCAATTGTCCTTTCAT 59.823 33.333 7.40 3.67 0.00 2.57
2421 2433 6.122277 GTCAAATGAATGTCTAAGATCCCCA 58.878 40.000 0.00 0.00 0.00 4.96
2505 2517 1.452651 AGCATGTCCATTCCAGGCG 60.453 57.895 0.00 0.00 43.85 5.52
2525 2537 4.908736 CTCAAAAAGCTCGACAACTTCAA 58.091 39.130 0.00 0.00 0.00 2.69
2743 2755 8.517878 ACTTTTTATCAGGTCATATGCATATGC 58.482 33.333 32.95 27.19 39.90 3.14
3040 3052 3.993081 GAGTCATACCATCTAGCATGCAC 59.007 47.826 21.98 4.28 0.00 4.57
3042 3054 4.263018 TGAGTCATACCATCTAGCATGC 57.737 45.455 10.51 10.51 0.00 4.06
3301 3318 6.034683 GTCACATCAGTAGTATTTTCCACGTC 59.965 42.308 0.00 0.00 0.00 4.34
3422 3439 9.856488 GTTCACAACTTATAGTTCTATCAGTGA 57.144 33.333 0.00 0.00 36.03 3.41
3532 3549 5.790495 GTCTAGTCACGCATTTGATGTTTTC 59.210 40.000 0.00 0.00 0.00 2.29
3547 3567 3.990469 CACTCAACACATGGTCTAGTCAC 59.010 47.826 0.00 0.00 0.00 3.67
3638 3658 1.224592 CGACCAATCCCCCTCTTGG 59.775 63.158 0.00 0.00 46.03 3.61
3741 3762 6.365050 CAAAGTTGGAATAAAAGCAACATGC 58.635 36.000 0.00 0.00 45.46 4.06
3783 3804 2.030628 TCTATTGCGAACGTGTGAGACA 60.031 45.455 0.00 0.00 0.00 3.41
3784 3805 2.592194 TCTATTGCGAACGTGTGAGAC 58.408 47.619 0.00 0.00 0.00 3.36
3790 3811 3.839954 GCCGTTAATCTATTGCGAACGTG 60.840 47.826 0.00 0.00 40.87 4.49
3796 3817 2.863740 TGTGAGCCGTTAATCTATTGCG 59.136 45.455 0.00 0.00 0.00 4.85
3854 3875 8.074370 TCATTACTCCTATAAAGACGTCAATCG 58.926 37.037 19.50 4.43 46.00 3.34


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

AutoCloner maintained by Alex Coulton.