Multiple sequence alignment - TraesCS1A01G439900

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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 TraesCS1A01G439900 chr1A 100.000 3501 0 0 1 3501 589108732 589112232 0.000000e+00 6466.0
1 TraesCS1A01G439900 chr3A 98.266 3230 43 4 272 3501 711390349 711387133 0.000000e+00 5642.0
2 TraesCS1A01G439900 chr2B 98.164 1198 21 1 2304 3501 52656150 52657346 0.000000e+00 2089.0
3 TraesCS1A01G439900 chr6B 85.102 1470 178 18 2001 3468 33252193 33253623 0.000000e+00 1463.0
4 TraesCS1A01G439900 chr1B 84.095 1006 149 9 831 1833 7849007 7848010 0.000000e+00 961.0
5 TraesCS1A01G439900 chr1B 83.515 1007 153 11 831 1833 7746677 7745680 0.000000e+00 928.0
6 TraesCS1A01G439900 chr1B 83.416 1007 154 11 831 1833 7797832 7796835 0.000000e+00 922.0
7 TraesCS1A01G439900 chr1B 83.317 1007 154 12 831 1833 7835289 7834293 0.000000e+00 917.0
8 TraesCS1A01G439900 chr1B 82.920 1007 159 11 831 1833 7771743 7770746 0.000000e+00 894.0
9 TraesCS1A01G439900 chr1B 84.110 730 106 8 1107 1833 7824055 7823333 0.000000e+00 697.0
10 TraesCS1A01G439900 chr5A 84.864 403 26 10 268 659 478887660 478887282 1.190000e-99 374.0
11 TraesCS1A01G439900 chr1D 97.826 92 1 1 1 92 468129304 468129394 1.300000e-34 158.0
12 TraesCS1A01G439900 chr1D 86.400 125 13 3 3248 3372 255779491 255779371 2.190000e-27 134.0
13 TraesCS1A01G439900 chr4A 85.256 156 15 2 3346 3501 608980189 608980336 1.680000e-33 154.0
14 TraesCS1A01G439900 chr4A 79.433 141 25 4 3350 3488 659118170 659118308 2.880000e-16 97.1
15 TraesCS1A01G439900 chr3D 84.615 104 13 3 269 369 24896057 24896160 2.220000e-17 100.0
16 TraesCS1A01G439900 chr2D 83.000 100 14 3 274 370 120100669 120100570 1.730000e-13 87.9
17 TraesCS1A01G439900 chr7A 87.013 77 9 1 570 645 3844460 3844384 6.230000e-13 86.1
18 TraesCS1A01G439900 chr2A 84.091 88 13 1 272 358 28666833 28666746 2.240000e-12 84.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G439900 chr1A 589108732 589112232 3500 False 6466 6466 100.000 1 3501 1 chr1A.!!$F1 3500
1 TraesCS1A01G439900 chr3A 711387133 711390349 3216 True 5642 5642 98.266 272 3501 1 chr3A.!!$R1 3229
2 TraesCS1A01G439900 chr2B 52656150 52657346 1196 False 2089 2089 98.164 2304 3501 1 chr2B.!!$F1 1197
3 TraesCS1A01G439900 chr6B 33252193 33253623 1430 False 1463 1463 85.102 2001 3468 1 chr6B.!!$F1 1467
4 TraesCS1A01G439900 chr1B 7848010 7849007 997 True 961 961 84.095 831 1833 1 chr1B.!!$R6 1002
5 TraesCS1A01G439900 chr1B 7745680 7746677 997 True 928 928 83.515 831 1833 1 chr1B.!!$R1 1002
6 TraesCS1A01G439900 chr1B 7796835 7797832 997 True 922 922 83.416 831 1833 1 chr1B.!!$R3 1002
7 TraesCS1A01G439900 chr1B 7834293 7835289 996 True 917 917 83.317 831 1833 1 chr1B.!!$R5 1002
8 TraesCS1A01G439900 chr1B 7770746 7771743 997 True 894 894 82.920 831 1833 1 chr1B.!!$R2 1002
9 TraesCS1A01G439900 chr1B 7823333 7824055 722 True 697 697 84.110 1107 1833 1 chr1B.!!$R4 726

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
37 38 0.035056 GGTGGTCAAGGTGGATCCAG 60.035 60.0 16.81 3.10 39.02 3.86 F
62 63 0.035739 ACTTCCCCAACGCGTACAAT 59.964 50.0 14.46 0.00 0.00 2.71 F
419 420 0.100682 GAGCGCTACCTGAACGATCA 59.899 55.0 11.50 0.00 41.52 2.92 F
2197 2200 0.250945 TTTGCGTGGCCAAGGATACA 60.251 50.0 20.72 6.71 41.41 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1256 1259 0.596083 TTGCCAAATTTGTGGTCGCG 60.596 50.000 16.73 0.0 41.12 5.87 R
1439 1442 0.734889 ACAATAAGCACGATGGCTGC 59.265 50.000 0.00 0.0 45.07 5.25 R
2302 2305 1.442567 CTGCAGCAACAAGGGCAAA 59.557 52.632 0.00 0.0 35.59 3.68 R
3227 3234 5.010922 AGGCATCTACAAAGTGCAATCAAAA 59.989 36.000 0.00 0.0 40.53 2.44 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 3.971032 AGAAAAAGAAGAGCAACGGTG 57.029 42.857 0.00 0.00 0.00 4.94
22 23 2.618709 AGAAAAAGAAGAGCAACGGTGG 59.381 45.455 0.90 0.00 0.00 4.61
23 24 2.052782 AAAAGAAGAGCAACGGTGGT 57.947 45.000 3.99 3.99 38.47 4.16
29 30 2.915869 AGCAACGGTGGTCAAGGT 59.084 55.556 0.00 0.00 0.00 3.50
30 31 1.525995 AGCAACGGTGGTCAAGGTG 60.526 57.895 0.00 0.00 0.00 4.00
31 32 2.551912 GCAACGGTGGTCAAGGTGG 61.552 63.158 0.90 0.00 0.00 4.61
32 33 1.147376 CAACGGTGGTCAAGGTGGA 59.853 57.895 0.00 0.00 0.00 4.02
33 34 0.250727 CAACGGTGGTCAAGGTGGAT 60.251 55.000 0.00 0.00 0.00 3.41
34 35 0.036306 AACGGTGGTCAAGGTGGATC 59.964 55.000 0.00 0.00 0.00 3.36
35 36 1.078426 CGGTGGTCAAGGTGGATCC 60.078 63.158 4.20 4.20 0.00 3.36
36 37 1.836999 CGGTGGTCAAGGTGGATCCA 61.837 60.000 11.44 11.44 39.02 3.41
37 38 0.035056 GGTGGTCAAGGTGGATCCAG 60.035 60.000 16.81 3.10 39.02 3.86
38 39 0.678048 GTGGTCAAGGTGGATCCAGC 60.678 60.000 32.30 32.30 43.95 4.85
45 46 3.232279 GGTGGATCCAGCTCCTACT 57.768 57.895 32.11 0.00 40.83 2.57
46 47 1.501582 GGTGGATCCAGCTCCTACTT 58.498 55.000 32.11 0.00 40.83 2.24
47 48 1.414550 GGTGGATCCAGCTCCTACTTC 59.585 57.143 32.11 9.65 40.83 3.01
48 49 1.414550 GTGGATCCAGCTCCTACTTCC 59.585 57.143 16.81 0.00 36.20 3.46
49 50 1.052617 GGATCCAGCTCCTACTTCCC 58.947 60.000 6.95 0.00 32.18 3.97
50 51 1.052617 GATCCAGCTCCTACTTCCCC 58.947 60.000 0.00 0.00 0.00 4.81
51 52 0.343372 ATCCAGCTCCTACTTCCCCA 59.657 55.000 0.00 0.00 0.00 4.96
52 53 0.118346 TCCAGCTCCTACTTCCCCAA 59.882 55.000 0.00 0.00 0.00 4.12
53 54 0.253327 CCAGCTCCTACTTCCCCAAC 59.747 60.000 0.00 0.00 0.00 3.77
54 55 0.108138 CAGCTCCTACTTCCCCAACG 60.108 60.000 0.00 0.00 0.00 4.10
55 56 1.449778 GCTCCTACTTCCCCAACGC 60.450 63.158 0.00 0.00 0.00 4.84
56 57 1.153628 CTCCTACTTCCCCAACGCG 60.154 63.158 3.53 3.53 0.00 6.01
57 58 1.885163 CTCCTACTTCCCCAACGCGT 61.885 60.000 5.58 5.58 0.00 6.01
58 59 0.611618 TCCTACTTCCCCAACGCGTA 60.612 55.000 14.46 0.00 0.00 4.42
59 60 0.459063 CCTACTTCCCCAACGCGTAC 60.459 60.000 14.46 0.00 0.00 3.67
60 61 0.244450 CTACTTCCCCAACGCGTACA 59.756 55.000 14.46 0.00 0.00 2.90
61 62 0.678395 TACTTCCCCAACGCGTACAA 59.322 50.000 14.46 0.00 0.00 2.41
62 63 0.035739 ACTTCCCCAACGCGTACAAT 59.964 50.000 14.46 0.00 0.00 2.71
63 64 0.725117 CTTCCCCAACGCGTACAATC 59.275 55.000 14.46 0.00 0.00 2.67
64 65 0.674269 TTCCCCAACGCGTACAATCC 60.674 55.000 14.46 0.00 0.00 3.01
65 66 2.457778 CCCCAACGCGTACAATCCG 61.458 63.158 14.46 0.00 0.00 4.18
66 67 1.738830 CCCAACGCGTACAATCCGT 60.739 57.895 14.46 0.00 36.68 4.69
67 68 1.418367 CCAACGCGTACAATCCGTG 59.582 57.895 14.46 3.87 41.34 4.94
68 69 1.418367 CAACGCGTACAATCCGTGG 59.582 57.895 14.46 0.00 39.97 4.94
69 70 1.009903 CAACGCGTACAATCCGTGGA 61.010 55.000 14.46 0.00 39.97 4.02
70 71 1.010419 AACGCGTACAATCCGTGGAC 61.010 55.000 14.46 0.00 39.97 4.02
71 72 1.153901 CGCGTACAATCCGTGGACT 60.154 57.895 0.00 0.00 39.18 3.85
72 73 1.410737 CGCGTACAATCCGTGGACTG 61.411 60.000 0.00 0.00 39.18 3.51
73 74 1.082117 GCGTACAATCCGTGGACTGG 61.082 60.000 2.10 0.00 39.18 4.00
74 75 0.245539 CGTACAATCCGTGGACTGGT 59.754 55.000 2.10 0.00 39.18 4.00
75 76 1.734707 CGTACAATCCGTGGACTGGTC 60.735 57.143 2.10 0.00 39.18 4.02
76 77 1.274167 GTACAATCCGTGGACTGGTCA 59.726 52.381 2.10 0.00 38.17 4.02
77 78 0.321671 ACAATCCGTGGACTGGTCAG 59.678 55.000 2.10 0.00 0.00 3.51
78 79 0.608130 CAATCCGTGGACTGGTCAGA 59.392 55.000 4.84 0.00 0.00 3.27
79 80 1.208052 CAATCCGTGGACTGGTCAGAT 59.792 52.381 4.84 0.00 0.00 2.90
80 81 1.115467 ATCCGTGGACTGGTCAGATC 58.885 55.000 4.84 0.00 0.00 2.75
81 82 0.970937 TCCGTGGACTGGTCAGATCC 60.971 60.000 4.84 8.40 32.71 3.36
82 83 1.257750 CCGTGGACTGGTCAGATCCA 61.258 60.000 14.04 14.04 36.77 3.41
83 84 0.826715 CGTGGACTGGTCAGATCCAT 59.173 55.000 18.19 0.00 39.23 3.41
84 85 2.031870 CGTGGACTGGTCAGATCCATA 58.968 52.381 18.19 2.60 39.23 2.74
85 86 2.630098 CGTGGACTGGTCAGATCCATAT 59.370 50.000 18.19 0.00 39.23 1.78
86 87 3.553715 CGTGGACTGGTCAGATCCATATG 60.554 52.174 18.19 0.00 39.23 1.78
87 88 3.389329 GTGGACTGGTCAGATCCATATGT 59.611 47.826 18.19 0.00 39.23 2.29
88 89 4.588951 GTGGACTGGTCAGATCCATATGTA 59.411 45.833 18.19 0.00 39.23 2.29
89 90 5.247110 GTGGACTGGTCAGATCCATATGTAT 59.753 44.000 18.19 0.00 39.23 2.29
90 91 5.481824 TGGACTGGTCAGATCCATATGTATC 59.518 44.000 14.04 0.63 35.34 2.24
91 92 5.105146 GGACTGGTCAGATCCATATGTATCC 60.105 48.000 4.76 0.00 36.84 2.59
92 93 4.780021 ACTGGTCAGATCCATATGTATCCC 59.220 45.833 4.76 0.86 36.84 3.85
93 94 4.762220 TGGTCAGATCCATATGTATCCCA 58.238 43.478 4.76 3.26 31.96 4.37
94 95 5.353125 TGGTCAGATCCATATGTATCCCAT 58.647 41.667 4.76 0.00 33.46 4.00
95 96 5.190330 TGGTCAGATCCATATGTATCCCATG 59.810 44.000 4.76 0.00 32.08 3.66
96 97 5.397221 GGTCAGATCCATATGTATCCCATGG 60.397 48.000 4.14 4.14 40.55 3.66
97 98 5.190528 GTCAGATCCATATGTATCCCATGGT 59.809 44.000 11.73 0.00 40.18 3.55
98 99 5.792188 TCAGATCCATATGTATCCCATGGTT 59.208 40.000 11.73 0.00 40.18 3.67
99 100 5.884232 CAGATCCATATGTATCCCATGGTTG 59.116 44.000 11.73 0.00 40.18 3.77
100 101 4.656100 TCCATATGTATCCCATGGTTGG 57.344 45.455 11.73 4.70 40.18 3.77
101 102 3.091545 CCATATGTATCCCATGGTTGGC 58.908 50.000 11.73 0.00 42.15 4.52
102 103 3.500108 CCATATGTATCCCATGGTTGGCA 60.500 47.826 11.73 4.91 42.15 4.92
103 104 2.844654 ATGTATCCCATGGTTGGCAA 57.155 45.000 11.73 0.00 42.15 4.52
104 105 2.844654 TGTATCCCATGGTTGGCAAT 57.155 45.000 11.73 0.00 42.15 3.56
105 106 2.386779 TGTATCCCATGGTTGGCAATG 58.613 47.619 11.73 0.00 42.15 2.82
106 107 1.688197 GTATCCCATGGTTGGCAATGG 59.312 52.381 11.73 10.72 44.24 3.16
107 108 1.339644 ATCCCATGGTTGGCAATGGC 61.340 55.000 11.73 0.00 43.46 4.40
108 109 2.291801 CCCATGGTTGGCAATGGCA 61.292 57.895 11.73 5.05 43.46 4.92
109 110 1.078988 CCATGGTTGGCAATGGCAC 60.079 57.895 9.62 4.93 39.20 5.01
110 111 1.446445 CATGGTTGGCAATGGCACG 60.446 57.895 9.62 0.00 43.71 5.34
111 112 3.299524 ATGGTTGGCAATGGCACGC 62.300 57.895 9.62 5.48 43.71 5.34
130 131 3.917760 CGCAGGGATCCTCGGTCC 61.918 72.222 12.58 0.00 34.92 4.46
131 132 2.764128 GCAGGGATCCTCGGTCCA 60.764 66.667 12.58 0.00 37.49 4.02
132 133 3.095347 GCAGGGATCCTCGGTCCAC 62.095 68.421 12.58 0.00 37.49 4.02
133 134 2.442272 AGGGATCCTCGGTCCACG 60.442 66.667 12.58 0.00 46.11 4.94
134 135 2.758737 GGGATCCTCGGTCCACGT 60.759 66.667 12.58 0.00 44.69 4.49
135 136 2.783288 GGGATCCTCGGTCCACGTC 61.783 68.421 12.58 0.00 44.69 4.34
136 137 2.783288 GGATCCTCGGTCCACGTCC 61.783 68.421 3.84 0.00 44.69 4.79
137 138 1.753463 GATCCTCGGTCCACGTCCT 60.753 63.158 0.00 0.00 44.69 3.85
138 139 0.465097 GATCCTCGGTCCACGTCCTA 60.465 60.000 0.00 0.00 44.69 2.94
139 140 0.750911 ATCCTCGGTCCACGTCCTAC 60.751 60.000 0.00 0.00 44.69 3.18
150 151 2.401967 CGTCCTACGGTCCTAGTGG 58.598 63.158 0.00 0.00 38.08 4.00
151 152 1.722636 CGTCCTACGGTCCTAGTGGC 61.723 65.000 0.00 0.00 38.08 5.01
152 153 0.395448 GTCCTACGGTCCTAGTGGCT 60.395 60.000 0.00 0.00 0.00 4.75
153 154 1.133976 GTCCTACGGTCCTAGTGGCTA 60.134 57.143 0.00 0.00 0.00 3.93
154 155 1.133976 TCCTACGGTCCTAGTGGCTAC 60.134 57.143 0.00 0.00 0.00 3.58
155 156 0.942962 CTACGGTCCTAGTGGCTACG 59.057 60.000 0.00 0.00 0.00 3.51
156 157 0.464373 TACGGTCCTAGTGGCTACGG 60.464 60.000 0.00 0.00 0.00 4.02
157 158 2.813200 GGTCCTAGTGGCTACGGC 59.187 66.667 0.00 0.00 37.82 5.68
158 159 1.757340 GGTCCTAGTGGCTACGGCT 60.757 63.158 0.00 0.00 38.73 5.52
159 160 1.734748 GTCCTAGTGGCTACGGCTC 59.265 63.158 0.00 0.00 38.73 4.70
160 161 1.035932 GTCCTAGTGGCTACGGCTCA 61.036 60.000 0.00 0.00 38.73 4.26
161 162 1.035932 TCCTAGTGGCTACGGCTCAC 61.036 60.000 0.00 0.00 38.77 3.51
162 163 1.437986 CTAGTGGCTACGGCTCACC 59.562 63.158 0.00 0.00 39.06 4.02
163 164 1.000019 TAGTGGCTACGGCTCACCT 60.000 57.895 0.00 0.00 39.06 4.00
164 165 1.320344 TAGTGGCTACGGCTCACCTG 61.320 60.000 0.00 0.00 39.06 4.00
165 166 4.082523 TGGCTACGGCTCACCTGC 62.083 66.667 0.00 0.00 38.73 4.85
166 167 3.775654 GGCTACGGCTCACCTGCT 61.776 66.667 0.00 0.00 38.73 4.24
167 168 2.510238 GCTACGGCTCACCTGCTG 60.510 66.667 0.00 0.00 44.34 4.41
168 169 2.510238 CTACGGCTCACCTGCTGC 60.510 66.667 0.00 0.00 42.69 5.25
169 170 2.997315 TACGGCTCACCTGCTGCT 60.997 61.111 0.00 0.00 42.69 4.24
170 171 2.897641 CTACGGCTCACCTGCTGCTC 62.898 65.000 0.00 0.00 42.69 4.26
171 172 4.383861 CGGCTCACCTGCTGCTCA 62.384 66.667 0.00 0.00 32.21 4.26
172 173 2.033141 GGCTCACCTGCTGCTCAA 59.967 61.111 0.00 0.00 0.00 3.02
173 174 2.039405 GGCTCACCTGCTGCTCAAG 61.039 63.158 0.00 0.00 0.00 3.02
174 175 2.039405 GCTCACCTGCTGCTCAAGG 61.039 63.158 0.00 1.66 0.00 3.61
175 176 2.033141 TCACCTGCTGCTCAAGGC 59.967 61.111 0.00 0.00 42.22 4.35
176 177 2.033757 CACCTGCTGCTCAAGGCT 59.966 61.111 0.00 0.00 42.39 4.58
177 178 1.602888 CACCTGCTGCTCAAGGCTT 60.603 57.895 0.00 0.00 42.39 4.35
178 179 1.303155 ACCTGCTGCTCAAGGCTTC 60.303 57.895 0.00 0.00 42.39 3.86
179 180 2.396955 CCTGCTGCTCAAGGCTTCG 61.397 63.158 0.00 0.00 42.39 3.79
180 181 1.670406 CTGCTGCTCAAGGCTTCGT 60.670 57.895 0.00 0.00 42.39 3.85
181 182 1.633852 CTGCTGCTCAAGGCTTCGTC 61.634 60.000 0.00 0.00 42.39 4.20
182 183 2.734673 GCTGCTCAAGGCTTCGTCG 61.735 63.158 0.00 0.00 42.39 5.12
183 184 2.734673 CTGCTCAAGGCTTCGTCGC 61.735 63.158 0.00 0.00 42.39 5.19
184 185 3.843240 GCTCAAGGCTTCGTCGCG 61.843 66.667 0.00 0.00 38.06 5.87
185 186 3.181967 CTCAAGGCTTCGTCGCGG 61.182 66.667 6.13 0.00 0.00 6.46
212 213 3.746889 CGCACCCGTACCCGTACA 61.747 66.667 5.88 0.00 35.87 2.90
213 214 2.125952 GCACCCGTACCCGTACAC 60.126 66.667 5.88 0.00 35.87 2.90
214 215 2.573340 CACCCGTACCCGTACACC 59.427 66.667 5.88 0.00 35.87 4.16
215 216 3.061848 ACCCGTACCCGTACACCG 61.062 66.667 5.88 0.00 35.87 4.94
216 217 3.061848 CCCGTACCCGTACACCGT 61.062 66.667 5.88 0.00 35.87 4.83
217 218 2.485122 CCGTACCCGTACACCGTC 59.515 66.667 5.88 0.00 35.87 4.79
218 219 2.098298 CGTACCCGTACACCGTCG 59.902 66.667 5.88 0.00 35.87 5.12
219 220 2.202479 GTACCCGTACACCGTCGC 60.202 66.667 0.06 0.00 36.15 5.19
220 221 3.798650 TACCCGTACACCGTCGCG 61.799 66.667 0.00 0.00 33.66 5.87
238 239 4.426313 CCCGGCTTCTTCCCACCC 62.426 72.222 0.00 0.00 0.00 4.61
239 240 4.778143 CCGGCTTCTTCCCACCCG 62.778 72.222 0.00 0.00 38.71 5.28
251 252 4.673298 CACCCGCCGCACAGTACA 62.673 66.667 0.00 0.00 0.00 2.90
252 253 3.931247 ACCCGCCGCACAGTACAA 61.931 61.111 0.00 0.00 0.00 2.41
253 254 3.419759 CCCGCCGCACAGTACAAC 61.420 66.667 0.00 0.00 0.00 3.32
254 255 2.357034 CCGCCGCACAGTACAACT 60.357 61.111 0.00 0.00 0.00 3.16
255 256 1.080366 CCGCCGCACAGTACAACTA 60.080 57.895 0.00 0.00 0.00 2.24
256 257 1.349259 CCGCCGCACAGTACAACTAC 61.349 60.000 0.00 0.00 0.00 2.73
257 258 1.670971 CGCCGCACAGTACAACTACG 61.671 60.000 0.00 0.00 0.00 3.51
258 259 1.952266 GCCGCACAGTACAACTACGC 61.952 60.000 0.00 0.00 0.00 4.42
259 260 1.349259 CCGCACAGTACAACTACGCC 61.349 60.000 0.00 0.00 0.00 5.68
260 261 0.665068 CGCACAGTACAACTACGCCA 60.665 55.000 0.00 0.00 0.00 5.69
261 262 1.504359 GCACAGTACAACTACGCCAA 58.496 50.000 0.00 0.00 0.00 4.52
262 263 2.073816 GCACAGTACAACTACGCCAAT 58.926 47.619 0.00 0.00 0.00 3.16
263 264 2.159707 GCACAGTACAACTACGCCAATG 60.160 50.000 0.00 0.00 0.00 2.82
264 265 2.073816 ACAGTACAACTACGCCAATGC 58.926 47.619 0.00 0.00 0.00 3.56
265 266 1.396996 CAGTACAACTACGCCAATGCC 59.603 52.381 0.00 0.00 0.00 4.40
266 267 0.730840 GTACAACTACGCCAATGCCC 59.269 55.000 0.00 0.00 0.00 5.36
267 268 0.393267 TACAACTACGCCAATGCCCC 60.393 55.000 0.00 0.00 0.00 5.80
268 269 1.378514 CAACTACGCCAATGCCCCT 60.379 57.895 0.00 0.00 0.00 4.79
269 270 0.107410 CAACTACGCCAATGCCCCTA 60.107 55.000 0.00 0.00 0.00 3.53
270 271 0.107361 AACTACGCCAATGCCCCTAC 60.107 55.000 0.00 0.00 0.00 3.18
376 377 4.082523 TCGTGGCCCAGTAGCAGC 62.083 66.667 0.00 0.00 0.00 5.25
397 398 3.259633 AAACTGAGAGGCCCAGGCG 62.260 63.158 11.60 0.00 43.06 5.52
416 417 2.483745 CGAGCGCTACCTGAACGA 59.516 61.111 11.50 0.00 0.00 3.85
419 420 0.100682 GAGCGCTACCTGAACGATCA 59.899 55.000 11.50 0.00 41.52 2.92
474 475 2.890766 TTCTGTTCGCCTGTCCCCC 61.891 63.158 0.00 0.00 0.00 5.40
495 496 2.345244 CGCACTCCACTGCTCCTT 59.655 61.111 0.00 0.00 34.77 3.36
497 498 1.673665 GCACTCCACTGCTCCTTGG 60.674 63.158 0.00 0.00 34.06 3.61
522 523 3.695606 GCACTGCTCCTCCGGTCA 61.696 66.667 0.00 0.00 0.00 4.02
634 635 1.291335 CCACTAGTCCCCTACTTCCCT 59.709 57.143 0.00 0.00 39.80 4.20
641 642 1.003573 CCCTACTTCCCTGGCTCCT 59.996 63.158 0.00 0.00 0.00 3.69
760 761 0.803117 CAGTGCAAGTGGATCTGCAG 59.197 55.000 7.63 7.63 38.00 4.41
808 809 2.539302 CCAAATTTGTGGGGGATCTGT 58.461 47.619 16.73 0.00 34.77 3.41
876 877 8.831550 GTTCTATCTTGCTAAGTTAATTGGAGG 58.168 37.037 0.00 0.00 0.00 4.30
1569 1572 5.362430 AGTTAAAAATGGAGAAAGGTGTGCA 59.638 36.000 0.00 0.00 0.00 4.57
1576 1579 2.887152 GGAGAAAGGTGTGCATTCTTGT 59.113 45.455 1.26 0.00 33.73 3.16
1671 1674 5.644636 ACCAACCCACATAGTAAACGTTATG 59.355 40.000 0.00 4.05 34.28 1.90
1834 1837 8.180267 ACTTCATTGAATTGATAAAGCTTCTCG 58.820 33.333 0.00 0.00 0.00 4.04
1848 1851 2.941720 GCTTCTCGCAGAATTCAATCCT 59.058 45.455 8.44 0.00 38.92 3.24
1952 1955 3.712016 TTATGCACTGAAGGTTAGGCA 57.288 42.857 0.00 0.00 35.54 4.75
2197 2200 0.250945 TTTGCGTGGCCAAGGATACA 60.251 50.000 20.72 6.71 41.41 2.29
2386 2389 8.492673 TCTCTACATCATAAACATTGTTGACC 57.507 34.615 2.13 0.00 0.00 4.02
2572 2575 4.036262 GCCTTATGGATATGTTCAACGCAA 59.964 41.667 0.00 0.00 34.57 4.85
2807 2810 4.936685 AGGCCCTTCTAGAAAAACTGAT 57.063 40.909 6.63 0.00 0.00 2.90
3227 3234 7.951347 ATGAAGATCTAAAGAAGCCAACAAT 57.049 32.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.066760 CCACCGTTGCTCTTCTTTTTCTT 59.933 43.478 0.00 0.00 0.00 2.52
1 2 2.618709 CCACCGTTGCTCTTCTTTTTCT 59.381 45.455 0.00 0.00 0.00 2.52
2 3 2.357952 ACCACCGTTGCTCTTCTTTTTC 59.642 45.455 0.00 0.00 0.00 2.29
3 4 2.357952 GACCACCGTTGCTCTTCTTTTT 59.642 45.455 0.00 0.00 0.00 1.94
4 5 1.947456 GACCACCGTTGCTCTTCTTTT 59.053 47.619 0.00 0.00 0.00 2.27
6 7 0.468226 TGACCACCGTTGCTCTTCTT 59.532 50.000 0.00 0.00 0.00 2.52
7 8 0.468226 TTGACCACCGTTGCTCTTCT 59.532 50.000 0.00 0.00 0.00 2.85
8 9 0.868406 CTTGACCACCGTTGCTCTTC 59.132 55.000 0.00 0.00 0.00 2.87
9 10 0.535102 CCTTGACCACCGTTGCTCTT 60.535 55.000 0.00 0.00 0.00 2.85
10 11 1.071471 CCTTGACCACCGTTGCTCT 59.929 57.895 0.00 0.00 0.00 4.09
11 12 1.227853 ACCTTGACCACCGTTGCTC 60.228 57.895 0.00 0.00 0.00 4.26
12 13 1.525995 CACCTTGACCACCGTTGCT 60.526 57.895 0.00 0.00 0.00 3.91
13 14 2.551912 CCACCTTGACCACCGTTGC 61.552 63.158 0.00 0.00 0.00 4.17
14 15 0.250727 ATCCACCTTGACCACCGTTG 60.251 55.000 0.00 0.00 0.00 4.10
15 16 0.036306 GATCCACCTTGACCACCGTT 59.964 55.000 0.00 0.00 0.00 4.44
16 17 1.677552 GATCCACCTTGACCACCGT 59.322 57.895 0.00 0.00 0.00 4.83
17 18 1.078426 GGATCCACCTTGACCACCG 60.078 63.158 6.95 0.00 35.41 4.94
18 19 0.035056 CTGGATCCACCTTGACCACC 60.035 60.000 11.44 0.00 39.86 4.61
19 20 0.678048 GCTGGATCCACCTTGACCAC 60.678 60.000 11.44 0.00 39.86 4.16
20 21 0.842030 AGCTGGATCCACCTTGACCA 60.842 55.000 11.44 0.00 39.86 4.02
21 22 0.107459 GAGCTGGATCCACCTTGACC 60.107 60.000 11.44 0.00 39.86 4.02
22 23 0.107459 GGAGCTGGATCCACCTTGAC 60.107 60.000 11.44 1.13 39.34 3.18
23 24 0.252881 AGGAGCTGGATCCACCTTGA 60.253 55.000 11.44 0.00 42.26 3.02
24 25 1.139853 GTAGGAGCTGGATCCACCTTG 59.860 57.143 23.55 10.57 42.26 3.61
25 26 1.008938 AGTAGGAGCTGGATCCACCTT 59.991 52.381 23.55 7.77 42.26 3.50
26 27 0.639392 AGTAGGAGCTGGATCCACCT 59.361 55.000 22.37 22.37 42.26 4.00
27 28 1.414550 GAAGTAGGAGCTGGATCCACC 59.585 57.143 11.44 11.30 42.26 4.61
28 29 1.414550 GGAAGTAGGAGCTGGATCCAC 59.585 57.143 11.44 8.29 42.26 4.02
29 30 1.692762 GGGAAGTAGGAGCTGGATCCA 60.693 57.143 15.27 15.27 42.26 3.41
30 31 1.052617 GGGAAGTAGGAGCTGGATCC 58.947 60.000 4.20 4.20 39.89 3.36
31 32 1.052617 GGGGAAGTAGGAGCTGGATC 58.947 60.000 0.00 0.00 0.00 3.36
32 33 0.343372 TGGGGAAGTAGGAGCTGGAT 59.657 55.000 0.00 0.00 0.00 3.41
33 34 0.118346 TTGGGGAAGTAGGAGCTGGA 59.882 55.000 0.00 0.00 0.00 3.86
34 35 0.253327 GTTGGGGAAGTAGGAGCTGG 59.747 60.000 0.00 0.00 0.00 4.85
35 36 0.108138 CGTTGGGGAAGTAGGAGCTG 60.108 60.000 0.00 0.00 0.00 4.24
36 37 1.900545 GCGTTGGGGAAGTAGGAGCT 61.901 60.000 0.00 0.00 0.00 4.09
37 38 1.449778 GCGTTGGGGAAGTAGGAGC 60.450 63.158 0.00 0.00 0.00 4.70
38 39 1.153628 CGCGTTGGGGAAGTAGGAG 60.154 63.158 0.00 0.00 0.00 3.69
39 40 0.611618 TACGCGTTGGGGAAGTAGGA 60.612 55.000 20.78 0.00 0.00 2.94
40 41 0.459063 GTACGCGTTGGGGAAGTAGG 60.459 60.000 20.78 0.00 0.00 3.18
41 42 0.244450 TGTACGCGTTGGGGAAGTAG 59.756 55.000 20.78 0.00 0.00 2.57
42 43 0.678395 TTGTACGCGTTGGGGAAGTA 59.322 50.000 20.78 0.00 0.00 2.24
43 44 0.035739 ATTGTACGCGTTGGGGAAGT 59.964 50.000 20.78 0.00 0.00 3.01
44 45 0.725117 GATTGTACGCGTTGGGGAAG 59.275 55.000 20.78 0.00 0.00 3.46
45 46 0.674269 GGATTGTACGCGTTGGGGAA 60.674 55.000 20.78 3.67 0.00 3.97
46 47 1.078988 GGATTGTACGCGTTGGGGA 60.079 57.895 20.78 0.00 0.00 4.81
47 48 2.457778 CGGATTGTACGCGTTGGGG 61.458 63.158 20.78 0.00 0.00 4.96
48 49 1.738830 ACGGATTGTACGCGTTGGG 60.739 57.895 20.78 2.68 34.00 4.12
49 50 1.418367 CACGGATTGTACGCGTTGG 59.582 57.895 20.78 1.51 34.00 3.77
50 51 1.009903 TCCACGGATTGTACGCGTTG 61.010 55.000 20.78 6.71 34.00 4.10
51 52 1.010419 GTCCACGGATTGTACGCGTT 61.010 55.000 20.78 0.00 34.00 4.84
52 53 1.444895 GTCCACGGATTGTACGCGT 60.445 57.895 19.17 19.17 34.00 6.01
53 54 1.153901 AGTCCACGGATTGTACGCG 60.154 57.895 3.53 3.53 34.00 6.01
54 55 1.082117 CCAGTCCACGGATTGTACGC 61.082 60.000 7.69 0.00 31.13 4.42
55 56 0.245539 ACCAGTCCACGGATTGTACG 59.754 55.000 7.69 0.00 31.13 3.67
56 57 1.274167 TGACCAGTCCACGGATTGTAC 59.726 52.381 7.69 2.61 31.13 2.90
57 58 1.548719 CTGACCAGTCCACGGATTGTA 59.451 52.381 7.69 0.00 31.13 2.41
58 59 0.321671 CTGACCAGTCCACGGATTGT 59.678 55.000 7.69 0.00 31.13 2.71
59 60 0.608130 TCTGACCAGTCCACGGATTG 59.392 55.000 1.71 1.71 0.00 2.67
60 61 1.482593 GATCTGACCAGTCCACGGATT 59.517 52.381 0.00 0.00 31.03 3.01
61 62 1.115467 GATCTGACCAGTCCACGGAT 58.885 55.000 0.00 0.00 33.15 4.18
62 63 0.970937 GGATCTGACCAGTCCACGGA 60.971 60.000 11.26 0.00 32.51 4.69
63 64 1.257750 TGGATCTGACCAGTCCACGG 61.258 60.000 13.51 0.00 35.34 4.94
64 65 0.826715 ATGGATCTGACCAGTCCACG 59.173 55.000 17.34 0.00 43.49 4.94
65 66 3.389329 ACATATGGATCTGACCAGTCCAC 59.611 47.826 17.34 2.05 43.49 4.02
66 67 3.657610 ACATATGGATCTGACCAGTCCA 58.342 45.455 17.32 17.32 43.49 4.02
67 68 5.105146 GGATACATATGGATCTGACCAGTCC 60.105 48.000 24.17 5.40 43.49 3.85
68 69 5.105146 GGGATACATATGGATCTGACCAGTC 60.105 48.000 24.17 7.72 40.51 3.51
69 70 4.780021 GGGATACATATGGATCTGACCAGT 59.220 45.833 24.17 0.00 40.51 4.00
70 71 4.779489 TGGGATACATATGGATCTGACCAG 59.221 45.833 24.17 0.00 40.51 4.00
71 72 4.762220 TGGGATACATATGGATCTGACCA 58.238 43.478 24.17 20.02 41.18 4.02
72 73 5.678583 CATGGGATACATATGGATCTGACC 58.321 45.833 24.17 17.99 37.84 4.02
92 93 1.446445 CGTGCCATTGCCAACCATG 60.446 57.895 0.00 0.00 36.33 3.66
93 94 2.972267 CGTGCCATTGCCAACCAT 59.028 55.556 0.00 0.00 36.33 3.55
94 95 3.988525 GCGTGCCATTGCCAACCA 61.989 61.111 0.00 0.00 36.33 3.67
112 113 3.917760 GACCGAGGATCCCTGCGG 61.918 72.222 27.33 27.33 44.11 5.69
113 114 3.917760 GGACCGAGGATCCCTGCG 61.918 72.222 8.55 10.17 31.76 5.18
114 115 2.764128 TGGACCGAGGATCCCTGC 60.764 66.667 8.55 0.00 35.12 4.85
115 116 2.786495 CGTGGACCGAGGATCCCTG 61.786 68.421 8.55 0.21 39.56 4.45
116 117 2.442272 CGTGGACCGAGGATCCCT 60.442 66.667 8.55 0.00 39.56 4.20
117 118 2.758737 ACGTGGACCGAGGATCCC 60.759 66.667 8.55 0.00 40.70 3.85
118 119 2.783288 GGACGTGGACCGAGGATCC 61.783 68.421 2.48 2.48 40.70 3.36
119 120 0.465097 TAGGACGTGGACCGAGGATC 60.465 60.000 0.00 0.00 40.70 3.36
120 121 0.750911 GTAGGACGTGGACCGAGGAT 60.751 60.000 0.00 0.00 40.70 3.24
121 122 1.377725 GTAGGACGTGGACCGAGGA 60.378 63.158 0.00 0.00 40.70 3.71
122 123 2.758089 CGTAGGACGTGGACCGAGG 61.758 68.421 0.00 0.00 40.70 4.63
123 124 2.789917 CGTAGGACGTGGACCGAG 59.210 66.667 0.00 0.00 40.70 4.63
132 133 1.722636 GCCACTAGGACCGTAGGACG 61.723 65.000 0.00 0.00 46.68 4.79
133 134 0.395448 AGCCACTAGGACCGTAGGAC 60.395 60.000 0.00 0.00 46.68 3.85
134 135 1.133976 GTAGCCACTAGGACCGTAGGA 60.134 57.143 0.00 0.00 46.68 2.94
135 136 1.316651 GTAGCCACTAGGACCGTAGG 58.683 60.000 0.00 0.00 46.31 3.18
136 137 0.942962 CGTAGCCACTAGGACCGTAG 59.057 60.000 0.00 0.00 36.89 3.51
137 138 0.464373 CCGTAGCCACTAGGACCGTA 60.464 60.000 0.00 0.00 36.89 4.02
138 139 1.751927 CCGTAGCCACTAGGACCGT 60.752 63.158 0.00 0.00 36.89 4.83
139 140 3.117372 CCGTAGCCACTAGGACCG 58.883 66.667 0.00 0.00 36.89 4.79
140 141 1.736365 GAGCCGTAGCCACTAGGACC 61.736 65.000 0.00 0.00 41.25 4.46
141 142 1.035932 TGAGCCGTAGCCACTAGGAC 61.036 60.000 0.00 0.00 41.25 3.85
142 143 1.035932 GTGAGCCGTAGCCACTAGGA 61.036 60.000 0.00 0.00 41.25 2.94
143 144 1.437986 GTGAGCCGTAGCCACTAGG 59.562 63.158 0.00 0.00 41.25 3.02
144 145 1.038130 AGGTGAGCCGTAGCCACTAG 61.038 60.000 0.00 0.00 41.25 2.57
145 146 1.000019 AGGTGAGCCGTAGCCACTA 60.000 57.895 0.00 0.00 41.25 2.74
146 147 2.283966 AGGTGAGCCGTAGCCACT 60.284 61.111 0.00 0.00 41.25 4.00
147 148 2.125512 CAGGTGAGCCGTAGCCAC 60.126 66.667 0.00 0.00 41.25 5.01
148 149 4.082523 GCAGGTGAGCCGTAGCCA 62.083 66.667 0.00 0.00 41.25 4.75
149 150 3.775654 AGCAGGTGAGCCGTAGCC 61.776 66.667 0.00 0.00 41.25 3.93
150 151 2.510238 CAGCAGGTGAGCCGTAGC 60.510 66.667 0.00 0.00 40.50 3.58
151 152 2.510238 GCAGCAGGTGAGCCGTAG 60.510 66.667 3.02 0.00 40.50 3.51
152 153 2.997315 AGCAGCAGGTGAGCCGTA 60.997 61.111 3.02 0.00 40.50 4.02
153 154 4.385405 GAGCAGCAGGTGAGCCGT 62.385 66.667 3.02 0.00 40.50 5.68
154 155 3.889134 TTGAGCAGCAGGTGAGCCG 62.889 63.158 3.02 0.00 40.50 5.52
155 156 2.033141 TTGAGCAGCAGGTGAGCC 59.967 61.111 3.02 0.00 34.23 4.70
156 157 2.039405 CCTTGAGCAGCAGGTGAGC 61.039 63.158 3.02 0.00 0.00 4.26
157 158 2.039405 GCCTTGAGCAGCAGGTGAG 61.039 63.158 3.02 0.00 42.97 3.51
158 159 2.033141 GCCTTGAGCAGCAGGTGA 59.967 61.111 3.02 0.00 42.97 4.02
167 168 3.843240 CGCGACGAAGCCTTGAGC 61.843 66.667 0.00 0.00 44.25 4.26
168 169 3.181967 CCGCGACGAAGCCTTGAG 61.182 66.667 8.23 0.00 0.00 3.02
195 196 3.746889 TGTACGGGTACGGGTGCG 61.747 66.667 4.67 0.00 46.48 5.34
196 197 2.125952 GTGTACGGGTACGGGTGC 60.126 66.667 4.67 0.00 46.48 5.01
197 198 2.573340 GGTGTACGGGTACGGGTG 59.427 66.667 4.67 0.00 46.48 4.61
198 199 3.061848 CGGTGTACGGGTACGGGT 61.062 66.667 4.67 0.00 46.48 5.28
221 222 4.426313 GGGTGGGAAGAAGCCGGG 62.426 72.222 2.18 0.00 0.00 5.73
234 235 4.673298 TGTACTGTGCGGCGGGTG 62.673 66.667 9.78 0.00 0.00 4.61
235 236 3.931247 TTGTACTGTGCGGCGGGT 61.931 61.111 9.78 0.00 0.00 5.28
236 237 2.495366 TAGTTGTACTGTGCGGCGGG 62.495 60.000 9.78 0.00 0.00 6.13
237 238 1.080366 TAGTTGTACTGTGCGGCGG 60.080 57.895 9.78 0.00 0.00 6.13
238 239 1.670971 CGTAGTTGTACTGTGCGGCG 61.671 60.000 0.51 0.51 0.00 6.46
239 240 1.952266 GCGTAGTTGTACTGTGCGGC 61.952 60.000 0.00 0.00 0.00 6.53
240 241 1.349259 GGCGTAGTTGTACTGTGCGG 61.349 60.000 0.00 0.00 32.63 5.69
241 242 0.665068 TGGCGTAGTTGTACTGTGCG 60.665 55.000 0.00 0.00 32.63 5.34
242 243 1.504359 TTGGCGTAGTTGTACTGTGC 58.496 50.000 0.00 0.00 0.00 4.57
243 244 2.159707 GCATTGGCGTAGTTGTACTGTG 60.160 50.000 0.00 0.00 0.00 3.66
244 245 2.073816 GCATTGGCGTAGTTGTACTGT 58.926 47.619 0.00 0.00 0.00 3.55
245 246 1.396996 GGCATTGGCGTAGTTGTACTG 59.603 52.381 0.00 0.00 42.47 2.74
246 247 1.677820 GGGCATTGGCGTAGTTGTACT 60.678 52.381 3.93 0.00 42.47 2.73
247 248 0.730840 GGGCATTGGCGTAGTTGTAC 59.269 55.000 3.93 0.00 42.47 2.90
248 249 0.393267 GGGGCATTGGCGTAGTTGTA 60.393 55.000 3.93 0.00 42.47 2.41
249 250 1.677633 GGGGCATTGGCGTAGTTGT 60.678 57.895 3.93 0.00 42.47 3.32
250 251 0.107410 TAGGGGCATTGGCGTAGTTG 60.107 55.000 3.93 0.00 42.47 3.16
251 252 0.107361 GTAGGGGCATTGGCGTAGTT 60.107 55.000 3.93 0.00 42.47 2.24
252 253 1.525442 GTAGGGGCATTGGCGTAGT 59.475 57.895 3.93 0.00 42.47 2.73
253 254 1.227853 GGTAGGGGCATTGGCGTAG 60.228 63.158 3.93 0.00 42.47 3.51
254 255 1.996187 TGGTAGGGGCATTGGCGTA 60.996 57.895 3.93 0.00 42.47 4.42
255 256 3.334891 TGGTAGGGGCATTGGCGT 61.335 61.111 3.93 0.00 42.47 5.68
256 257 2.828549 GTGGTAGGGGCATTGGCG 60.829 66.667 3.93 0.00 42.47 5.69
257 258 1.754234 CAGTGGTAGGGGCATTGGC 60.754 63.158 0.70 0.70 40.13 4.52
258 259 1.076777 CCAGTGGTAGGGGCATTGG 60.077 63.158 0.00 0.00 0.00 3.16
259 260 1.754234 GCCAGTGGTAGGGGCATTG 60.754 63.158 11.74 0.00 46.92 2.82
260 261 2.683475 GCCAGTGGTAGGGGCATT 59.317 61.111 11.74 0.00 46.92 3.56
264 265 3.470888 CTCCGCCAGTGGTAGGGG 61.471 72.222 20.81 16.14 38.69 4.79
265 266 4.162690 GCTCCGCCAGTGGTAGGG 62.163 72.222 20.81 15.25 0.00 3.53
266 267 4.514577 CGCTCCGCCAGTGGTAGG 62.515 72.222 11.74 14.72 0.00 3.18
267 268 3.296709 AACGCTCCGCCAGTGGTAG 62.297 63.158 11.74 7.45 36.88 3.18
268 269 3.307906 AACGCTCCGCCAGTGGTA 61.308 61.111 11.74 0.00 36.88 3.25
269 270 4.988598 CAACGCTCCGCCAGTGGT 62.989 66.667 11.74 0.00 36.88 4.16
270 271 4.988598 ACAACGCTCCGCCAGTGG 62.989 66.667 4.20 4.20 36.88 4.00
376 377 0.035630 CCTGGGCCTCTCAGTTTCTG 60.036 60.000 4.53 0.00 0.00 3.02
397 398 2.886124 GTTCAGGTAGCGCTCGGC 60.886 66.667 16.34 5.46 44.05 5.54
403 404 2.389059 CTCATGATCGTTCAGGTAGCG 58.611 52.381 7.90 0.00 35.22 4.26
416 417 2.160853 CACGTGACGCGCTCATGAT 61.161 57.895 26.55 14.36 46.11 2.45
497 498 4.828925 GGAGCAGTGCGGAGGAGC 62.829 72.222 10.00 0.00 37.71 4.70
634 635 3.512329 TCACGTAGTTTATCAAGGAGCCA 59.488 43.478 0.00 0.00 41.61 4.75
641 642 4.091549 AGGGGACTCACGTAGTTTATCAA 58.908 43.478 0.00 0.00 41.61 2.57
760 761 3.248602 CCCACGAATTTGCTGCTATAGAC 59.751 47.826 3.21 0.00 0.00 2.59
770 771 1.374125 GCAACCCCCACGAATTTGC 60.374 57.895 0.00 0.00 36.14 3.68
958 959 7.783090 TTTGCAAACAAATTTTCATCAGCTA 57.217 28.000 8.05 0.00 40.84 3.32
1191 1193 2.032030 AGGCTCATTTGTTTGTCGTTCG 60.032 45.455 0.00 0.00 0.00 3.95
1256 1259 0.596083 TTGCCAAATTTGTGGTCGCG 60.596 50.000 16.73 0.00 41.12 5.87
1439 1442 0.734889 ACAATAAGCACGATGGCTGC 59.265 50.000 0.00 0.00 45.07 5.25
1569 1572 6.715280 ACTACATCCAACATGAGACAAGAAT 58.285 36.000 0.00 0.00 0.00 2.40
1671 1674 3.142174 CTCCTTGTTGTCTTGAACCTCC 58.858 50.000 0.00 0.00 0.00 4.30
1834 1837 4.040376 GCGATTTCAGGATTGAATTCTGC 58.960 43.478 8.63 0.00 42.60 4.26
1848 1851 5.234752 TCTAAAACTACAGCTGCGATTTCA 58.765 37.500 15.27 0.00 0.00 2.69
1952 1955 4.543590 CCAATCTCTTGGCGGATATACT 57.456 45.455 0.00 0.00 45.28 2.12
2092 2095 7.023575 GCTTTGGTGTTCTTTACATGTATCAG 58.976 38.462 6.36 6.34 39.39 2.90
2197 2200 2.381911 CTTCATGTTGCTAGCCCCATT 58.618 47.619 13.29 0.00 0.00 3.16
2302 2305 1.442567 CTGCAGCAACAAGGGCAAA 59.557 52.632 0.00 0.00 35.59 3.68
2485 2488 5.182487 TGGACGCTTTAATGCTTTGATCTA 58.818 37.500 11.16 0.00 0.00 1.98
2807 2810 9.659135 AAAAATCATCCCAACCATTATCTGATA 57.341 29.630 0.00 0.00 0.00 2.15
3227 3234 5.010922 AGGCATCTACAAAGTGCAATCAAAA 59.989 36.000 0.00 0.00 40.53 2.44
3344 3351 8.155510 TGATAATCTTCAAGCTAGAGAATGCAT 58.844 33.333 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.