Multiple sequence alignment - TraesCS7D01G199200

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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 TraesCS7D01G199200 chr7D 100.000 7199 0 0 1 7199 156226218 156219020 0.000000e+00 13295.0
1 TraesCS7D01G199200 chr7D 91.477 528 26 8 930 1447 124164077 124164595 0.000000e+00 708.0
2 TraesCS7D01G199200 chr7D 92.857 266 18 1 6519 6784 351294515 351294251 1.130000e-102 385.0
3 TraesCS7D01G199200 chr7D 88.166 169 9 8 7032 7199 351293737 351293579 2.650000e-44 191.0
4 TraesCS7D01G199200 chr7D 89.032 155 9 3 2173 2327 156223893 156223747 1.230000e-42 185.0
5 TraesCS7D01G199200 chr7D 89.032 155 9 3 2326 2472 156224046 156223892 1.230000e-42 185.0
6 TraesCS7D01G199200 chr7D 88.991 109 8 2 6919 7027 351293914 351293810 1.630000e-26 132.0
7 TraesCS7D01G199200 chr7B 97.753 6187 107 14 621 6784 118653084 118646907 0.000000e+00 10626.0
8 TraesCS7D01G199200 chr7B 89.677 155 8 3 2326 2472 118651513 118651359 2.650000e-44 191.0
9 TraesCS7D01G199200 chr7B 87.742 155 11 2 2173 2327 118651360 118651214 2.670000e-39 174.0
10 TraesCS7D01G199200 chr7B 94.792 96 2 2 7105 7199 118646495 118646402 5.820000e-31 147.0
11 TraesCS7D01G199200 chr7B 88.073 109 9 2 6919 7027 118646695 118646591 7.580000e-25 126.0
12 TraesCS7D01G199200 chr7A 97.650 3575 79 3 3216 6787 210859295 210855723 0.000000e+00 6131.0
13 TraesCS7D01G199200 chr7A 94.825 2628 96 21 563 3173 210861898 210859294 0.000000e+00 4063.0
14 TraesCS7D01G199200 chr7A 82.740 365 50 6 220 572 210862462 210862099 5.420000e-81 313.0
15 TraesCS7D01G199200 chr7A 90.058 171 6 5 7032 7199 210855136 210854974 2.030000e-50 211.0
16 TraesCS7D01G199200 chr7A 89.103 156 8 3 2326 2472 210860293 210860138 1.230000e-42 185.0
17 TraesCS7D01G199200 chr7A 86.452 155 13 3 2173 2327 210860139 210859993 5.780000e-36 163.0
18 TraesCS7D01G199200 chr5D 92.857 266 18 1 6519 6784 438349433 438349697 1.130000e-102 385.0
19 TraesCS7D01G199200 chr1D 92.857 266 18 1 6519 6784 12786275 12786011 1.130000e-102 385.0
20 TraesCS7D01G199200 chr1D 91.124 169 5 7 7032 7199 12785498 12785339 3.380000e-53 220.0
21 TraesCS7D01G199200 chr1D 88.571 105 8 2 6919 7023 12785675 12785575 2.730000e-24 124.0
22 TraesCS7D01G199200 chr2A 92.395 263 19 1 6519 6781 274083547 274083808 2.450000e-99 374.0
23 TraesCS7D01G199200 chr2D 87.218 266 18 6 6519 6784 29241885 29241636 9.140000e-74 289.0
24 TraesCS7D01G199200 chr1B 93.023 43 2 1 370 411 502950953 502950995 2.170000e-05 62.1


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 TraesCS7D01G199200 chr7D 156219020 156226218 7198 True 4555.000000 13295 92.688000 1 7199 3 chr7D.!!$R1 7198
1 TraesCS7D01G199200 chr7D 124164077 124164595 518 False 708.000000 708 91.477000 930 1447 1 chr7D.!!$F1 517
2 TraesCS7D01G199200 chr7D 351293579 351294515 936 True 236.000000 385 90.004667 6519 7199 3 chr7D.!!$R2 680
3 TraesCS7D01G199200 chr7B 118646402 118653084 6682 True 2252.800000 10626 91.607400 621 7199 5 chr7B.!!$R1 6578
4 TraesCS7D01G199200 chr7A 210854974 210862462 7488 True 1844.333333 6131 90.138000 220 7199 6 chr7A.!!$R1 6979
5 TraesCS7D01G199200 chr1D 12785339 12786275 936 True 243.000000 385 90.850667 6519 7199 3 chr1D.!!$R1 680

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
166 167 0.030101 CCGTTCGCCAAACATGTTGT 59.970 50.000 12.82 0.0 37.77 3.32 F
179 180 0.179056 ATGTTGTAATCGGGAGGCCG 60.179 55.000 0.00 0.0 0.00 6.13 F
218 219 0.603707 ACCAACCAGCTCATCGTGTG 60.604 55.000 0.00 0.0 0.00 3.82 F
611 835 0.811616 GCGATTGATTGGACGGCTCT 60.812 55.000 0.00 0.0 0.00 4.09 F
754 987 1.001974 TCCACTCCACGATTCCTTGTG 59.998 52.381 0.00 0.0 36.64 3.33 F
755 988 1.001974 CCACTCCACGATTCCTTGTGA 59.998 52.381 0.00 0.0 38.85 3.58 F
797 1030 1.077357 ACCAAACACCGAGCCAACA 60.077 52.632 0.00 0.0 0.00 3.33 F
1680 1936 1.504900 GGCGAATTTTGTCCCGTCC 59.495 57.895 0.00 0.0 0.00 4.79 F
3621 3881 1.528129 AAAAGGAGCTTGCGAGGAAG 58.472 50.000 2.37 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 2014 0.250901 TTGGCAAACTCCTCCTGCTC 60.251 55.000 0.00 0.0 36.32 4.26 R
1840 2096 3.837213 AACCACGAGAATTTGCTCATG 57.163 42.857 0.00 0.0 34.56 3.07 R
2420 2677 3.118629 ACTGACTGACACAAAAGAGCTCA 60.119 43.478 17.77 0.0 0.00 4.26 R
2610 2867 5.445964 CCCAATAAGTAACAGGCCTACAAT 58.554 41.667 3.98 0.0 0.00 2.71 R
2866 3123 4.377022 GGTCATAACACGGCATATTTAGCG 60.377 45.833 0.00 0.0 0.00 4.26 R
3043 3302 5.472215 GCATGAGCAGAAACAGCATGGTT 62.472 47.826 0.00 0.0 46.30 3.67 R
3621 3881 6.501781 CCTCCACAAATATTCAAGATTCTGC 58.498 40.000 0.00 0.0 0.00 4.26 R
3831 4091 4.835678 TCATTGCTCTCTCTTGCACATTA 58.164 39.130 0.00 0.0 39.05 1.90 R
6364 6624 0.108233 CTCAGGCTGCTCAGAGGAAC 60.108 60.000 10.34 0.0 0.00 3.62 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
26 27 9.467796 TCTTCCTTTTCTCTTTTTCTTCTTCTT 57.532 29.630 0.00 0.00 0.00 2.52
27 28 9.729023 CTTCCTTTTCTCTTTTTCTTCTTCTTC 57.271 33.333 0.00 0.00 0.00 2.87
28 29 8.226819 TCCTTTTCTCTTTTTCTTCTTCTTCC 57.773 34.615 0.00 0.00 0.00 3.46
29 30 8.055790 TCCTTTTCTCTTTTTCTTCTTCTTCCT 58.944 33.333 0.00 0.00 0.00 3.36
30 31 8.690884 CCTTTTCTCTTTTTCTTCTTCTTCCTT 58.309 33.333 0.00 0.00 0.00 3.36
31 32 9.729023 CTTTTCTCTTTTTCTTCTTCTTCCTTC 57.271 33.333 0.00 0.00 0.00 3.46
32 33 8.807948 TTTCTCTTTTTCTTCTTCTTCCTTCA 57.192 30.769 0.00 0.00 0.00 3.02
33 34 7.793927 TCTCTTTTTCTTCTTCTTCCTTCAC 57.206 36.000 0.00 0.00 0.00 3.18
34 35 7.338710 TCTCTTTTTCTTCTTCTTCCTTCACA 58.661 34.615 0.00 0.00 0.00 3.58
35 36 7.281100 TCTCTTTTTCTTCTTCTTCCTTCACAC 59.719 37.037 0.00 0.00 0.00 3.82
36 37 7.112779 TCTTTTTCTTCTTCTTCCTTCACACT 58.887 34.615 0.00 0.00 0.00 3.55
37 38 6.683974 TTTTCTTCTTCTTCCTTCACACTG 57.316 37.500 0.00 0.00 0.00 3.66
38 39 3.733337 TCTTCTTCTTCCTTCACACTGC 58.267 45.455 0.00 0.00 0.00 4.40
39 40 3.134623 TCTTCTTCTTCCTTCACACTGCA 59.865 43.478 0.00 0.00 0.00 4.41
40 41 2.838736 TCTTCTTCCTTCACACTGCAC 58.161 47.619 0.00 0.00 0.00 4.57
41 42 1.876156 CTTCTTCCTTCACACTGCACC 59.124 52.381 0.00 0.00 0.00 5.01
42 43 0.836606 TCTTCCTTCACACTGCACCA 59.163 50.000 0.00 0.00 0.00 4.17
43 44 0.947244 CTTCCTTCACACTGCACCAC 59.053 55.000 0.00 0.00 0.00 4.16
44 45 0.254462 TTCCTTCACACTGCACCACA 59.746 50.000 0.00 0.00 0.00 4.17
45 46 0.463654 TCCTTCACACTGCACCACAC 60.464 55.000 0.00 0.00 0.00 3.82
46 47 0.747644 CCTTCACACTGCACCACACA 60.748 55.000 0.00 0.00 0.00 3.72
47 48 0.378257 CTTCACACTGCACCACACAC 59.622 55.000 0.00 0.00 0.00 3.82
48 49 1.029408 TTCACACTGCACCACACACC 61.029 55.000 0.00 0.00 0.00 4.16
49 50 1.748500 CACACTGCACCACACACCA 60.749 57.895 0.00 0.00 0.00 4.17
50 51 1.451927 ACACTGCACCACACACCAG 60.452 57.895 0.00 0.00 0.00 4.00
51 52 2.516930 ACTGCACCACACACCAGC 60.517 61.111 0.00 0.00 0.00 4.85
52 53 2.203252 CTGCACCACACACCAGCT 60.203 61.111 0.00 0.00 0.00 4.24
53 54 2.203195 TGCACCACACACCAGCTC 60.203 61.111 0.00 0.00 0.00 4.09
54 55 2.111878 GCACCACACACCAGCTCT 59.888 61.111 0.00 0.00 0.00 4.09
55 56 1.371183 GCACCACACACCAGCTCTA 59.629 57.895 0.00 0.00 0.00 2.43
56 57 0.036010 GCACCACACACCAGCTCTAT 60.036 55.000 0.00 0.00 0.00 1.98
57 58 2.009042 GCACCACACACCAGCTCTATC 61.009 57.143 0.00 0.00 0.00 2.08
58 59 0.532573 ACCACACACCAGCTCTATCG 59.467 55.000 0.00 0.00 0.00 2.92
59 60 0.807667 CCACACACCAGCTCTATCGC 60.808 60.000 0.00 0.00 0.00 4.58
60 61 0.174389 CACACACCAGCTCTATCGCT 59.826 55.000 0.00 0.00 41.90 4.93
61 62 0.457851 ACACACCAGCTCTATCGCTC 59.542 55.000 0.00 0.00 38.41 5.03
62 63 0.457443 CACACCAGCTCTATCGCTCA 59.543 55.000 0.00 0.00 38.41 4.26
63 64 0.457851 ACACCAGCTCTATCGCTCAC 59.542 55.000 0.00 0.00 38.41 3.51
64 65 0.249238 CACCAGCTCTATCGCTCACC 60.249 60.000 0.00 0.00 38.41 4.02
65 66 1.007964 CCAGCTCTATCGCTCACCG 60.008 63.158 0.00 0.00 38.41 4.94
66 67 1.659954 CAGCTCTATCGCTCACCGC 60.660 63.158 0.00 0.00 38.41 5.68
67 68 2.355244 GCTCTATCGCTCACCGCC 60.355 66.667 0.00 0.00 36.73 6.13
68 69 3.120105 CTCTATCGCTCACCGCCA 58.880 61.111 0.00 0.00 36.73 5.69
69 70 1.662608 CTCTATCGCTCACCGCCAT 59.337 57.895 0.00 0.00 36.73 4.40
70 71 0.387878 CTCTATCGCTCACCGCCATC 60.388 60.000 0.00 0.00 36.73 3.51
71 72 1.730902 CTATCGCTCACCGCCATCG 60.731 63.158 0.00 0.00 36.73 3.84
91 92 3.979497 GGTGGGGAGGGGGTGTTG 61.979 72.222 0.00 0.00 0.00 3.33
92 93 4.678743 GTGGGGAGGGGGTGTTGC 62.679 72.222 0.00 0.00 0.00 4.17
95 96 3.728373 GGGAGGGGGTGTTGCGAT 61.728 66.667 0.00 0.00 0.00 4.58
96 97 2.438434 GGAGGGGGTGTTGCGATG 60.438 66.667 0.00 0.00 0.00 3.84
97 98 2.351276 GAGGGGGTGTTGCGATGT 59.649 61.111 0.00 0.00 0.00 3.06
98 99 1.600107 GAGGGGGTGTTGCGATGTA 59.400 57.895 0.00 0.00 0.00 2.29
99 100 0.462047 GAGGGGGTGTTGCGATGTAG 60.462 60.000 0.00 0.00 0.00 2.74
100 101 1.451387 GGGGGTGTTGCGATGTAGG 60.451 63.158 0.00 0.00 0.00 3.18
101 102 1.600107 GGGGTGTTGCGATGTAGGA 59.400 57.895 0.00 0.00 0.00 2.94
102 103 0.462047 GGGGTGTTGCGATGTAGGAG 60.462 60.000 0.00 0.00 0.00 3.69
103 104 0.462047 GGGTGTTGCGATGTAGGAGG 60.462 60.000 0.00 0.00 0.00 4.30
104 105 1.090052 GGTGTTGCGATGTAGGAGGC 61.090 60.000 0.00 0.00 0.00 4.70
105 106 1.090052 GTGTTGCGATGTAGGAGGCC 61.090 60.000 0.00 0.00 0.00 5.19
106 107 1.523938 GTTGCGATGTAGGAGGCCC 60.524 63.158 0.00 0.00 0.00 5.80
107 108 2.742116 TTGCGATGTAGGAGGCCCC 61.742 63.158 0.00 0.00 0.00 5.80
108 109 4.301027 GCGATGTAGGAGGCCCCG 62.301 72.222 0.00 0.00 40.87 5.73
109 110 4.301027 CGATGTAGGAGGCCCCGC 62.301 72.222 0.00 0.05 40.87 6.13
110 111 4.301027 GATGTAGGAGGCCCCGCG 62.301 72.222 0.00 0.00 40.87 6.46
125 126 4.183686 GCGCGATGCTGCAACCAT 62.184 61.111 12.10 0.00 41.73 3.55
126 127 2.023741 CGCGATGCTGCAACCATC 59.976 61.111 6.36 14.11 36.58 3.51
130 131 1.349627 GATGCTGCAACCATCGACG 59.650 57.895 6.36 0.00 30.88 5.12
131 132 1.079197 ATGCTGCAACCATCGACGA 60.079 52.632 6.36 0.00 0.00 4.20
132 133 1.361668 ATGCTGCAACCATCGACGAC 61.362 55.000 6.36 0.00 0.00 4.34
133 134 3.071459 GCTGCAACCATCGACGACG 62.071 63.158 0.00 0.00 41.26 5.12
134 135 1.733041 CTGCAACCATCGACGACGT 60.733 57.895 0.00 0.00 40.69 4.34
135 136 1.282248 CTGCAACCATCGACGACGTT 61.282 55.000 0.13 2.76 40.69 3.99
136 137 1.129809 GCAACCATCGACGACGTTG 59.870 57.895 24.80 24.80 40.69 4.10
137 138 1.129809 CAACCATCGACGACGTTGC 59.870 57.895 20.39 0.00 40.69 4.17
138 139 1.300311 AACCATCGACGACGTTGCA 60.300 52.632 10.52 0.44 40.69 4.08
139 140 0.876777 AACCATCGACGACGTTGCAA 60.877 50.000 10.52 0.00 40.69 4.08
140 141 1.282248 ACCATCGACGACGTTGCAAG 61.282 55.000 10.52 3.84 40.69 4.01
141 142 1.416049 CATCGACGACGTTGCAAGG 59.584 57.895 17.21 17.21 40.69 3.61
142 143 2.380410 ATCGACGACGTTGCAAGGC 61.380 57.895 18.61 10.58 40.69 4.35
143 144 4.409588 CGACGACGTTGCAAGGCG 62.410 66.667 24.06 24.06 34.56 5.52
144 145 4.072088 GACGACGTTGCAAGGCGG 62.072 66.667 26.93 18.79 0.00 6.13
162 163 2.501650 CGCCGTTCGCCAAACATG 60.502 61.111 0.00 0.00 37.77 3.21
163 164 2.642700 GCCGTTCGCCAAACATGT 59.357 55.556 0.00 0.00 37.77 3.21
164 165 1.007849 GCCGTTCGCCAAACATGTT 60.008 52.632 4.92 4.92 37.77 2.71
165 166 1.274798 GCCGTTCGCCAAACATGTTG 61.275 55.000 12.82 6.46 37.77 3.33
166 167 0.030101 CCGTTCGCCAAACATGTTGT 59.970 50.000 12.82 0.00 37.77 3.32
167 168 1.264557 CCGTTCGCCAAACATGTTGTA 59.735 47.619 12.82 0.00 37.77 2.41
168 169 2.287069 CCGTTCGCCAAACATGTTGTAA 60.287 45.455 12.82 0.00 37.77 2.41
169 170 3.560503 CGTTCGCCAAACATGTTGTAAT 58.439 40.909 12.82 0.00 37.77 1.89
170 171 3.602062 CGTTCGCCAAACATGTTGTAATC 59.398 43.478 12.82 0.00 37.77 1.75
171 172 3.463533 TCGCCAAACATGTTGTAATCG 57.536 42.857 12.82 11.42 0.00 3.34
172 173 2.160615 TCGCCAAACATGTTGTAATCGG 59.839 45.455 12.82 7.35 0.00 4.18
173 174 2.730715 CGCCAAACATGTTGTAATCGGG 60.731 50.000 12.82 6.66 0.00 5.14
174 175 2.490115 GCCAAACATGTTGTAATCGGGA 59.510 45.455 12.82 0.00 0.00 5.14
175 176 3.427503 GCCAAACATGTTGTAATCGGGAG 60.428 47.826 12.82 0.00 0.00 4.30
176 177 3.128589 CCAAACATGTTGTAATCGGGAGG 59.871 47.826 12.82 0.00 0.00 4.30
177 178 2.038387 ACATGTTGTAATCGGGAGGC 57.962 50.000 0.00 0.00 0.00 4.70
178 179 1.308998 CATGTTGTAATCGGGAGGCC 58.691 55.000 0.00 0.00 0.00 5.19
179 180 0.179056 ATGTTGTAATCGGGAGGCCG 60.179 55.000 0.00 0.00 0.00 6.13
180 181 1.259142 TGTTGTAATCGGGAGGCCGA 61.259 55.000 0.00 0.00 46.30 5.54
186 187 2.519541 TCGGGAGGCCGATGAGAG 60.520 66.667 0.00 0.00 37.29 3.20
187 188 3.610669 CGGGAGGCCGATGAGAGG 61.611 72.222 0.00 0.00 34.88 3.69
188 189 2.123251 GGGAGGCCGATGAGAGGA 60.123 66.667 0.00 0.00 0.00 3.71
189 190 2.206536 GGGAGGCCGATGAGAGGAG 61.207 68.421 0.00 0.00 0.00 3.69
190 191 2.206536 GGAGGCCGATGAGAGGAGG 61.207 68.421 0.00 0.00 0.00 4.30
191 192 1.456705 GAGGCCGATGAGAGGAGGT 60.457 63.158 0.00 0.00 0.00 3.85
192 193 1.743321 GAGGCCGATGAGAGGAGGTG 61.743 65.000 0.00 0.00 0.00 4.00
193 194 2.060980 GGCCGATGAGAGGAGGTGT 61.061 63.158 0.00 0.00 0.00 4.16
194 195 1.142748 GCCGATGAGAGGAGGTGTG 59.857 63.158 0.00 0.00 0.00 3.82
195 196 1.323271 GCCGATGAGAGGAGGTGTGA 61.323 60.000 0.00 0.00 0.00 3.58
196 197 1.186200 CCGATGAGAGGAGGTGTGAA 58.814 55.000 0.00 0.00 0.00 3.18
197 198 1.550524 CCGATGAGAGGAGGTGTGAAA 59.449 52.381 0.00 0.00 0.00 2.69
198 199 2.169352 CCGATGAGAGGAGGTGTGAAAT 59.831 50.000 0.00 0.00 0.00 2.17
199 200 3.384789 CCGATGAGAGGAGGTGTGAAATA 59.615 47.826 0.00 0.00 0.00 1.40
200 201 4.363999 CGATGAGAGGAGGTGTGAAATAC 58.636 47.826 0.00 0.00 0.00 1.89
210 211 3.831715 GTGTGAAATACCAACCAGCTC 57.168 47.619 0.00 0.00 0.00 4.09
211 212 3.146066 GTGTGAAATACCAACCAGCTCA 58.854 45.455 0.00 0.00 0.00 4.26
212 213 3.758554 GTGTGAAATACCAACCAGCTCAT 59.241 43.478 0.00 0.00 0.00 2.90
213 214 4.009675 TGTGAAATACCAACCAGCTCATC 58.990 43.478 0.00 0.00 0.00 2.92
214 215 3.063997 GTGAAATACCAACCAGCTCATCG 59.936 47.826 0.00 0.00 0.00 3.84
215 216 3.270877 GAAATACCAACCAGCTCATCGT 58.729 45.455 0.00 0.00 0.00 3.73
216 217 2.315925 ATACCAACCAGCTCATCGTG 57.684 50.000 0.00 0.00 0.00 4.35
217 218 0.973632 TACCAACCAGCTCATCGTGT 59.026 50.000 0.00 0.00 0.00 4.49
218 219 0.603707 ACCAACCAGCTCATCGTGTG 60.604 55.000 0.00 0.00 0.00 3.82
227 228 3.478394 CATCGTGTGACGGTGCGG 61.478 66.667 0.00 0.00 46.21 5.69
332 333 2.670934 AAGCTGCAGGGAAGCGTG 60.671 61.111 17.12 0.00 45.59 5.34
356 357 4.659874 CCGACGTTGCGGTGTTGC 62.660 66.667 7.49 0.00 46.07 4.17
367 368 1.671054 GGTGTTGCAAGCTAGCCGA 60.671 57.895 12.13 0.00 0.00 5.54
392 393 2.979676 CAGCAGCCGGTGAAGCAA 60.980 61.111 1.90 0.00 43.56 3.91
401 402 1.244019 CGGTGAAGCAAAGGGGGAAG 61.244 60.000 0.00 0.00 0.00 3.46
402 403 1.536073 GGTGAAGCAAAGGGGGAAGC 61.536 60.000 0.00 0.00 0.00 3.86
404 405 2.283173 AAGCAAAGGGGGAAGCCG 60.283 61.111 0.00 0.00 0.00 5.52
415 417 3.793144 GAAGCCGGAGTTGCAGCG 61.793 66.667 5.05 0.00 0.00 5.18
421 423 2.558313 GGAGTTGCAGCGAAGTGC 59.442 61.111 0.00 0.00 44.27 4.40
459 461 3.342627 CGCCGGAACTGCAACGAA 61.343 61.111 5.05 0.00 38.93 3.85
460 462 2.887889 CGCCGGAACTGCAACGAAA 61.888 57.895 5.05 0.00 38.93 3.46
463 465 1.721133 CGGAACTGCAACGAAACGC 60.721 57.895 0.00 0.00 0.00 4.84
464 466 1.370051 GGAACTGCAACGAAACGCC 60.370 57.895 0.00 0.00 0.00 5.68
473 475 1.522130 ACGAAACGCCGTTGGAGTT 60.522 52.632 1.95 0.00 46.99 3.01
474 476 1.083015 CGAAACGCCGTTGGAGTTG 60.083 57.895 1.95 0.00 44.43 3.16
475 477 1.370051 GAAACGCCGTTGGAGTTGC 60.370 57.895 1.95 0.05 44.43 4.17
476 478 2.054140 GAAACGCCGTTGGAGTTGCA 62.054 55.000 1.95 0.00 44.43 4.08
548 561 3.443045 GGGTGCTGCCATGGAACG 61.443 66.667 18.40 3.22 39.65 3.95
557 570 1.450312 CCATGGAACGGCTCCTGTC 60.450 63.158 5.56 0.00 45.64 3.51
568 581 4.314440 TCCTGTCGGTGCTGCCAC 62.314 66.667 0.00 0.00 41.32 5.01
611 835 0.811616 GCGATTGATTGGACGGCTCT 60.812 55.000 0.00 0.00 0.00 4.09
631 855 3.106827 CTGGGGGCAATTTATTTCTGGT 58.893 45.455 0.00 0.00 0.00 4.00
675 907 5.181690 TCGCCCATATAATTTGCTTGTTC 57.818 39.130 0.00 0.00 0.00 3.18
700 932 9.869757 TCAATGAAGTCAATAAAGATAGAACGA 57.130 29.630 0.00 0.00 0.00 3.85
720 953 1.608590 ACTCCGCAACACATTTCCTTG 59.391 47.619 0.00 0.00 0.00 3.61
730 963 1.009078 CATTTCCTTGCATCGCTCGA 58.991 50.000 0.00 0.00 0.00 4.04
744 977 1.062685 CTCGACGATCCACTCCACG 59.937 63.158 0.00 0.00 0.00 4.94
745 978 1.366854 CTCGACGATCCACTCCACGA 61.367 60.000 0.00 0.00 0.00 4.35
752 985 2.555199 GATCCACTCCACGATTCCTTG 58.445 52.381 0.00 0.00 0.00 3.61
753 986 1.348064 TCCACTCCACGATTCCTTGT 58.652 50.000 0.00 0.00 0.00 3.16
754 987 1.001974 TCCACTCCACGATTCCTTGTG 59.998 52.381 0.00 0.00 36.64 3.33
755 988 1.001974 CCACTCCACGATTCCTTGTGA 59.998 52.381 0.00 0.00 38.85 3.58
756 989 2.341257 CACTCCACGATTCCTTGTGAG 58.659 52.381 0.00 0.00 38.85 3.51
797 1030 1.077357 ACCAAACACCGAGCCAACA 60.077 52.632 0.00 0.00 0.00 3.33
800 1033 1.555477 CAAACACCGAGCCAACAAAC 58.445 50.000 0.00 0.00 0.00 2.93
1665 1921 2.556287 GCCTGTTTTCTGACGGCG 59.444 61.111 4.80 4.80 32.58 6.46
1680 1936 1.504900 GGCGAATTTTGTCCCGTCC 59.495 57.895 0.00 0.00 0.00 4.79
1840 2096 2.271800 GGTCATGAACGATGAGGTGAC 58.728 52.381 0.00 0.00 42.00 3.67
1911 2167 6.803154 AGCATAGTTTCTGTTTCCTTGTAC 57.197 37.500 0.00 0.00 0.00 2.90
2420 2677 4.697352 CCTGCAATAGTTTAGTTCTGCTGT 59.303 41.667 0.00 0.00 0.00 4.40
2508 2765 5.048846 ACTATGTCTGTTTGTTGTCCCTT 57.951 39.130 0.00 0.00 0.00 3.95
2866 3123 6.036470 GCATTATGTTTCAGTTTTCCCTAGC 58.964 40.000 0.00 0.00 0.00 3.42
3042 3301 8.876275 ATTGAATGCGTTTTCATGCTATTTAT 57.124 26.923 0.00 0.00 35.64 1.40
3043 3302 9.964303 ATTGAATGCGTTTTCATGCTATTTATA 57.036 25.926 0.00 0.00 35.64 0.98
3056 3315 8.352201 TCATGCTATTTATAACCATGCTGTTTC 58.648 33.333 8.58 0.00 34.72 2.78
3368 3628 2.036089 AGACTAAATAGCTAGTGCCGGC 59.964 50.000 22.73 22.73 40.80 6.13
3621 3881 1.528129 AAAAGGAGCTTGCGAGGAAG 58.472 50.000 2.37 0.00 0.00 3.46
3851 4111 6.376299 TCAAATAATGTGCAAGAGAGAGCAAT 59.624 34.615 0.00 0.00 43.20 3.56
4779 5039 3.096852 TGAGAAGATTTCTACTGGCCGA 58.903 45.455 0.00 0.00 40.87 5.54
5238 5498 1.857217 CTCTCACATAGCACACGCATC 59.143 52.381 0.00 0.00 42.27 3.91
5480 5740 3.350219 TGCCTTCTTACAGGATTCACC 57.650 47.619 0.00 0.00 35.71 4.02
5709 5969 5.181009 TCAATTACTCTTCAGCCATCACTG 58.819 41.667 0.00 0.00 39.12 3.66
6003 6263 2.743183 CGGGGAAGAGGCTGTAAATCTG 60.743 54.545 0.00 0.00 0.00 2.90
6066 6326 4.024472 GCAACTTCTCTGAACCTCTTGAAC 60.024 45.833 0.00 0.00 0.00 3.18
6162 6422 5.248020 ACCAATGGAAATTCAGGCATACAAA 59.752 36.000 6.16 0.00 0.00 2.83
6304 6564 0.671781 CTGGAACACCTGCTCTTCCG 60.672 60.000 0.00 0.00 36.94 4.30
6349 6609 5.698741 TGACATACAGTGAGGGATTGAAT 57.301 39.130 0.00 0.00 0.00 2.57
6350 6610 5.430886 TGACATACAGTGAGGGATTGAATG 58.569 41.667 0.00 0.00 0.00 2.67
6363 6623 4.273480 GGGATTGAATGTGATCGTCGAAAT 59.727 41.667 0.00 0.00 0.00 2.17
6364 6624 5.200454 GGATTGAATGTGATCGTCGAAATG 58.800 41.667 0.00 0.00 0.00 2.32
6389 6649 0.733729 CTGAGCAGCCTGAGAATTGC 59.266 55.000 0.00 0.00 36.83 3.56
6406 6666 3.907894 TTGCGGTTCAGTTATTTGACC 57.092 42.857 0.00 0.00 0.00 4.02
6419 6681 5.011635 AGTTATTTGACCGGCCTTTCATTTT 59.988 36.000 0.00 0.00 0.00 1.82
6490 6752 3.062042 GCAAATTGGAAGTTTGAGGCAG 58.938 45.455 3.03 0.00 38.51 4.85
6550 6812 2.673368 GCTGTCACCTCCACTTTTATCG 59.327 50.000 0.00 0.00 0.00 2.92
6688 6950 3.576078 TCACAGAACCTTGTGGACAAT 57.424 42.857 6.33 0.00 46.55 2.71
6705 6967 7.178451 TGTGGACAATATCTGAGACAGTTTAGA 59.822 37.037 0.00 0.00 32.61 2.10
6769 7031 8.579850 AATTCTGCCTGTATACATTTTCTGAA 57.420 30.769 5.91 10.88 0.00 3.02
6776 7038 6.016777 CCTGTATACATTTTCTGAAGATGGCC 60.017 42.308 20.76 0.00 0.00 5.36
6781 7043 4.463891 ACATTTTCTGAAGATGGCCGAAAT 59.536 37.500 20.76 0.30 0.00 2.17
6784 7046 0.028505 CTGAAGATGGCCGAAATGCG 59.971 55.000 0.00 0.00 40.47 4.73
6799 7135 1.989706 ATGCGGGTTGTGTTTTAGGT 58.010 45.000 0.00 0.00 0.00 3.08
6814 7150 9.616156 TGTGTTTTAGGTTTTGTAGATCTGTTA 57.384 29.630 5.18 0.00 0.00 2.41
6822 7158 6.371825 GGTTTTGTAGATCTGTTACTTCCCTG 59.628 42.308 5.18 0.00 0.00 4.45
6828 7164 1.418637 TCTGTTACTTCCCTGGCGTTT 59.581 47.619 0.00 0.00 0.00 3.60
6884 7220 0.525761 TTTTATTGCCGAGCAGTGCC 59.474 50.000 12.58 2.23 40.61 5.01
6900 7243 0.948678 TGCCGTTGGTCAGCTTTTAC 59.051 50.000 0.00 0.00 0.00 2.01
6901 7244 0.948678 GCCGTTGGTCAGCTTTTACA 59.051 50.000 0.00 0.00 0.00 2.41
6910 7253 7.434013 CGTTGGTCAGCTTTTACAAGTTTTATT 59.566 33.333 0.00 0.00 31.86 1.40
6981 7524 5.534278 TGCATCCAAAATTACAAGTGAGTGA 59.466 36.000 0.00 0.00 0.00 3.41
6983 7526 5.689383 TCCAAAATTACAAGTGAGTGAGC 57.311 39.130 0.00 0.00 0.00 4.26
6984 7527 4.213270 TCCAAAATTACAAGTGAGTGAGCG 59.787 41.667 0.00 0.00 0.00 5.03
6985 7528 3.813529 AAATTACAAGTGAGTGAGCGC 57.186 42.857 0.00 0.00 0.00 5.92
6986 7529 2.455674 ATTACAAGTGAGTGAGCGCA 57.544 45.000 11.47 0.00 0.00 6.09
7003 7546 1.648504 GCAATGCAAAATGGAGGCTC 58.351 50.000 5.78 5.78 0.00 4.70
7004 7547 1.206371 GCAATGCAAAATGGAGGCTCT 59.794 47.619 15.23 0.00 0.00 4.09
7027 7592 0.804544 CGTCCGGCAACACGATGTAT 60.805 55.000 7.60 0.00 38.16 2.29
7028 7593 0.650512 GTCCGGCAACACGATGTATG 59.349 55.000 0.00 0.00 35.47 2.39
7030 7595 1.012343 CGGCAACACGATGTATGCG 60.012 57.895 0.00 0.00 36.20 4.73
7065 7699 2.815647 GCCACTCACGCAGTAGCC 60.816 66.667 0.00 0.00 41.61 3.93
7066 7700 2.656646 CCACTCACGCAGTAGCCA 59.343 61.111 0.00 0.00 41.61 4.75
7100 7737 0.871057 GAACCAAGAGACAGCAGCAC 59.129 55.000 0.00 0.00 0.00 4.40
7102 7739 0.399454 ACCAAGAGACAGCAGCACAT 59.601 50.000 0.00 0.00 0.00 3.21
7104 7741 2.238144 ACCAAGAGACAGCAGCACATAT 59.762 45.455 0.00 0.00 0.00 1.78
7105 7742 3.452264 ACCAAGAGACAGCAGCACATATA 59.548 43.478 0.00 0.00 0.00 0.86
7109 7746 4.691175 AGAGACAGCAGCACATATAACAG 58.309 43.478 0.00 0.00 0.00 3.16
7111 7748 5.070180 AGAGACAGCAGCACATATAACAGAT 59.930 40.000 0.00 0.00 0.00 2.90
7113 7750 5.027293 ACAGCAGCACATATAACAGATGA 57.973 39.130 0.00 0.00 0.00 2.92
7114 7751 5.430886 ACAGCAGCACATATAACAGATGAA 58.569 37.500 0.00 0.00 0.00 2.57
7115 7752 5.526479 ACAGCAGCACATATAACAGATGAAG 59.474 40.000 0.00 0.00 0.00 3.02
7116 7753 5.049612 CAGCAGCACATATAACAGATGAAGG 60.050 44.000 0.00 0.00 0.00 3.46
7117 7754 5.059161 GCAGCACATATAACAGATGAAGGA 58.941 41.667 0.00 0.00 0.00 3.36
7118 7755 5.528690 GCAGCACATATAACAGATGAAGGAA 59.471 40.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.467796 AAGAAGAAGAAAAAGAGAAAAGGAAGA 57.532 29.630 0.00 0.00 0.00 2.87
1 2 9.729023 GAAGAAGAAGAAAAAGAGAAAAGGAAG 57.271 33.333 0.00 0.00 0.00 3.46
2 3 8.687242 GGAAGAAGAAGAAAAAGAGAAAAGGAA 58.313 33.333 0.00 0.00 0.00 3.36
3 4 8.055790 AGGAAGAAGAAGAAAAAGAGAAAAGGA 58.944 33.333 0.00 0.00 0.00 3.36
4 5 8.231692 AGGAAGAAGAAGAAAAAGAGAAAAGG 57.768 34.615 0.00 0.00 0.00 3.11
5 6 9.729023 GAAGGAAGAAGAAGAAAAAGAGAAAAG 57.271 33.333 0.00 0.00 0.00 2.27
6 7 9.243105 TGAAGGAAGAAGAAGAAAAAGAGAAAA 57.757 29.630 0.00 0.00 0.00 2.29
7 8 8.678199 GTGAAGGAAGAAGAAGAAAAAGAGAAA 58.322 33.333 0.00 0.00 0.00 2.52
8 9 7.829211 TGTGAAGGAAGAAGAAGAAAAAGAGAA 59.171 33.333 0.00 0.00 0.00 2.87
9 10 7.281100 GTGTGAAGGAAGAAGAAGAAAAAGAGA 59.719 37.037 0.00 0.00 0.00 3.10
10 11 7.281999 AGTGTGAAGGAAGAAGAAGAAAAAGAG 59.718 37.037 0.00 0.00 0.00 2.85
11 12 7.066284 CAGTGTGAAGGAAGAAGAAGAAAAAGA 59.934 37.037 0.00 0.00 0.00 2.52
12 13 7.192232 CAGTGTGAAGGAAGAAGAAGAAAAAG 58.808 38.462 0.00 0.00 0.00 2.27
13 14 6.404734 GCAGTGTGAAGGAAGAAGAAGAAAAA 60.405 38.462 0.00 0.00 0.00 1.94
14 15 5.066505 GCAGTGTGAAGGAAGAAGAAGAAAA 59.933 40.000 0.00 0.00 0.00 2.29
15 16 4.576463 GCAGTGTGAAGGAAGAAGAAGAAA 59.424 41.667 0.00 0.00 0.00 2.52
16 17 4.130118 GCAGTGTGAAGGAAGAAGAAGAA 58.870 43.478 0.00 0.00 0.00 2.52
17 18 3.134623 TGCAGTGTGAAGGAAGAAGAAGA 59.865 43.478 0.00 0.00 0.00 2.87
18 19 3.249559 GTGCAGTGTGAAGGAAGAAGAAG 59.750 47.826 0.00 0.00 0.00 2.85
19 20 3.206150 GTGCAGTGTGAAGGAAGAAGAA 58.794 45.455 0.00 0.00 0.00 2.52
20 21 2.485479 GGTGCAGTGTGAAGGAAGAAGA 60.485 50.000 0.00 0.00 0.00 2.87
21 22 1.876156 GGTGCAGTGTGAAGGAAGAAG 59.124 52.381 0.00 0.00 0.00 2.85
22 23 1.211703 TGGTGCAGTGTGAAGGAAGAA 59.788 47.619 0.00 0.00 0.00 2.52
23 24 0.836606 TGGTGCAGTGTGAAGGAAGA 59.163 50.000 0.00 0.00 0.00 2.87
24 25 0.947244 GTGGTGCAGTGTGAAGGAAG 59.053 55.000 0.00 0.00 0.00 3.46
25 26 0.254462 TGTGGTGCAGTGTGAAGGAA 59.746 50.000 0.00 0.00 0.00 3.36
26 27 0.463654 GTGTGGTGCAGTGTGAAGGA 60.464 55.000 0.00 0.00 0.00 3.36
27 28 0.747644 TGTGTGGTGCAGTGTGAAGG 60.748 55.000 0.00 0.00 0.00 3.46
28 29 0.378257 GTGTGTGGTGCAGTGTGAAG 59.622 55.000 0.00 0.00 0.00 3.02
29 30 1.029408 GGTGTGTGGTGCAGTGTGAA 61.029 55.000 0.00 0.00 0.00 3.18
30 31 1.451207 GGTGTGTGGTGCAGTGTGA 60.451 57.895 0.00 0.00 0.00 3.58
31 32 1.717791 CTGGTGTGTGGTGCAGTGTG 61.718 60.000 0.00 0.00 0.00 3.82
32 33 1.451927 CTGGTGTGTGGTGCAGTGT 60.452 57.895 0.00 0.00 0.00 3.55
33 34 2.837883 GCTGGTGTGTGGTGCAGTG 61.838 63.158 0.00 0.00 0.00 3.66
34 35 2.516930 GCTGGTGTGTGGTGCAGT 60.517 61.111 0.00 0.00 0.00 4.40
35 36 2.203252 AGCTGGTGTGTGGTGCAG 60.203 61.111 0.00 0.00 0.00 4.41
36 37 1.406860 TAGAGCTGGTGTGTGGTGCA 61.407 55.000 0.00 0.00 0.00 4.57
37 38 0.036010 ATAGAGCTGGTGTGTGGTGC 60.036 55.000 0.00 0.00 0.00 5.01
38 39 1.737029 CGATAGAGCTGGTGTGTGGTG 60.737 57.143 0.00 0.00 39.76 4.17
39 40 0.532573 CGATAGAGCTGGTGTGTGGT 59.467 55.000 0.00 0.00 39.76 4.16
40 41 0.807667 GCGATAGAGCTGGTGTGTGG 60.808 60.000 0.00 0.00 39.76 4.17
41 42 2.670635 GCGATAGAGCTGGTGTGTG 58.329 57.895 0.00 0.00 39.76 3.82
74 75 3.979497 CAACACCCCCTCCCCACC 61.979 72.222 0.00 0.00 0.00 4.61
75 76 4.678743 GCAACACCCCCTCCCCAC 62.679 72.222 0.00 0.00 0.00 4.61
78 79 3.728373 ATCGCAACACCCCCTCCC 61.728 66.667 0.00 0.00 0.00 4.30
79 80 1.906105 TACATCGCAACACCCCCTCC 61.906 60.000 0.00 0.00 0.00 4.30
80 81 0.462047 CTACATCGCAACACCCCCTC 60.462 60.000 0.00 0.00 0.00 4.30
81 82 1.602237 CTACATCGCAACACCCCCT 59.398 57.895 0.00 0.00 0.00 4.79
82 83 1.451387 CCTACATCGCAACACCCCC 60.451 63.158 0.00 0.00 0.00 5.40
83 84 0.462047 CTCCTACATCGCAACACCCC 60.462 60.000 0.00 0.00 0.00 4.95
84 85 0.462047 CCTCCTACATCGCAACACCC 60.462 60.000 0.00 0.00 0.00 4.61
85 86 1.090052 GCCTCCTACATCGCAACACC 61.090 60.000 0.00 0.00 0.00 4.16
86 87 1.090052 GGCCTCCTACATCGCAACAC 61.090 60.000 0.00 0.00 0.00 3.32
87 88 1.220749 GGCCTCCTACATCGCAACA 59.779 57.895 0.00 0.00 0.00 3.33
88 89 1.523938 GGGCCTCCTACATCGCAAC 60.524 63.158 0.84 0.00 0.00 4.17
89 90 2.742116 GGGGCCTCCTACATCGCAA 61.742 63.158 0.84 0.00 0.00 4.85
90 91 3.161450 GGGGCCTCCTACATCGCA 61.161 66.667 0.84 0.00 0.00 5.10
91 92 4.301027 CGGGGCCTCCTACATCGC 62.301 72.222 0.84 0.00 0.00 4.58
92 93 4.301027 GCGGGGCCTCCTACATCG 62.301 72.222 0.84 0.00 0.00 3.84
93 94 4.301027 CGCGGGGCCTCCTACATC 62.301 72.222 0.84 0.00 0.00 3.06
108 109 4.183686 ATGGTTGCAGCATCGCGC 62.184 61.111 0.00 0.00 42.91 6.86
109 110 2.023741 GATGGTTGCAGCATCGCG 59.976 61.111 0.00 0.00 42.29 5.87
112 113 1.083806 TCGTCGATGGTTGCAGCATC 61.084 55.000 4.48 14.47 46.48 3.91
113 114 1.079197 TCGTCGATGGTTGCAGCAT 60.079 52.632 4.48 1.61 39.30 3.79
114 115 2.027073 GTCGTCGATGGTTGCAGCA 61.027 57.895 4.48 0.00 0.00 4.41
115 116 2.778679 GTCGTCGATGGTTGCAGC 59.221 61.111 4.48 0.00 0.00 5.25
116 117 1.282248 AACGTCGTCGATGGTTGCAG 61.282 55.000 18.28 0.00 40.62 4.41
117 118 1.300311 AACGTCGTCGATGGTTGCA 60.300 52.632 18.28 0.00 40.62 4.08
118 119 1.129809 CAACGTCGTCGATGGTTGC 59.870 57.895 21.37 0.00 40.62 4.17
119 120 1.129809 GCAACGTCGTCGATGGTTG 59.870 57.895 25.51 25.51 39.59 3.77
120 121 0.876777 TTGCAACGTCGTCGATGGTT 60.877 50.000 18.28 12.94 39.59 3.67
121 122 1.282248 CTTGCAACGTCGTCGATGGT 61.282 55.000 18.28 9.45 39.59 3.55
122 123 1.416049 CTTGCAACGTCGTCGATGG 59.584 57.895 18.28 7.02 39.59 3.51
123 124 1.416049 CCTTGCAACGTCGTCGATG 59.584 57.895 12.90 12.90 41.56 3.84
124 125 2.380410 GCCTTGCAACGTCGTCGAT 61.380 57.895 9.47 0.00 40.62 3.59
125 126 3.033764 GCCTTGCAACGTCGTCGA 61.034 61.111 9.47 0.00 40.62 4.20
126 127 4.409588 CGCCTTGCAACGTCGTCG 62.410 66.667 0.00 0.00 43.34 5.12
127 128 4.072088 CCGCCTTGCAACGTCGTC 62.072 66.667 0.00 0.00 0.00 4.20
145 146 2.501650 CATGTTTGGCGAACGGCG 60.502 61.111 12.77 4.80 44.92 6.46
146 147 1.007849 AACATGTTTGGCGAACGGC 60.008 52.632 4.92 13.50 41.29 5.68
147 148 0.030101 ACAACATGTTTGGCGAACGG 59.970 50.000 8.77 9.83 41.29 4.44
148 149 2.672188 TACAACATGTTTGGCGAACG 57.328 45.000 8.77 2.34 41.29 3.95
149 150 3.602062 CGATTACAACATGTTTGGCGAAC 59.398 43.478 8.77 10.79 38.78 3.95
150 151 3.365465 CCGATTACAACATGTTTGGCGAA 60.365 43.478 8.77 0.00 0.00 4.70
151 152 2.160615 CCGATTACAACATGTTTGGCGA 59.839 45.455 8.77 0.00 0.00 5.54
152 153 2.514902 CCGATTACAACATGTTTGGCG 58.485 47.619 8.77 8.48 0.00 5.69
153 154 2.490115 TCCCGATTACAACATGTTTGGC 59.510 45.455 8.77 0.00 0.00 4.52
154 155 3.128589 CCTCCCGATTACAACATGTTTGG 59.871 47.826 8.77 0.88 0.00 3.28
155 156 3.427503 GCCTCCCGATTACAACATGTTTG 60.428 47.826 8.77 7.37 0.00 2.93
156 157 2.752903 GCCTCCCGATTACAACATGTTT 59.247 45.455 8.77 3.54 0.00 2.83
157 158 2.365582 GCCTCCCGATTACAACATGTT 58.634 47.619 4.92 4.92 0.00 2.71
158 159 1.408266 GGCCTCCCGATTACAACATGT 60.408 52.381 0.00 0.00 0.00 3.21
159 160 1.308998 GGCCTCCCGATTACAACATG 58.691 55.000 0.00 0.00 0.00 3.21
160 161 3.800826 GGCCTCCCGATTACAACAT 57.199 52.632 0.00 0.00 0.00 2.71
171 172 2.123251 TCCTCTCATCGGCCTCCC 60.123 66.667 0.00 0.00 0.00 4.30
172 173 2.206536 CCTCCTCTCATCGGCCTCC 61.207 68.421 0.00 0.00 0.00 4.30
173 174 1.456705 ACCTCCTCTCATCGGCCTC 60.457 63.158 0.00 0.00 0.00 4.70
174 175 1.760086 CACCTCCTCTCATCGGCCT 60.760 63.158 0.00 0.00 0.00 5.19
175 176 2.060980 ACACCTCCTCTCATCGGCC 61.061 63.158 0.00 0.00 0.00 6.13
176 177 1.142748 CACACCTCCTCTCATCGGC 59.857 63.158 0.00 0.00 0.00 5.54
177 178 1.186200 TTCACACCTCCTCTCATCGG 58.814 55.000 0.00 0.00 0.00 4.18
178 179 3.533606 ATTTCACACCTCCTCTCATCG 57.466 47.619 0.00 0.00 0.00 3.84
179 180 4.162320 TGGTATTTCACACCTCCTCTCATC 59.838 45.833 0.00 0.00 36.96 2.92
180 181 4.104086 TGGTATTTCACACCTCCTCTCAT 58.896 43.478 0.00 0.00 36.96 2.90
181 182 3.516586 TGGTATTTCACACCTCCTCTCA 58.483 45.455 0.00 0.00 36.96 3.27
182 183 4.254492 GTTGGTATTTCACACCTCCTCTC 58.746 47.826 0.00 0.00 36.96 3.20
183 184 3.009143 GGTTGGTATTTCACACCTCCTCT 59.991 47.826 0.00 0.00 36.96 3.69
184 185 3.244770 TGGTTGGTATTTCACACCTCCTC 60.245 47.826 0.00 0.00 36.96 3.71
185 186 2.714250 TGGTTGGTATTTCACACCTCCT 59.286 45.455 0.00 0.00 36.96 3.69
186 187 3.081804 CTGGTTGGTATTTCACACCTCC 58.918 50.000 0.00 0.00 36.96 4.30
187 188 2.488153 GCTGGTTGGTATTTCACACCTC 59.512 50.000 0.00 0.00 36.96 3.85
188 189 2.108250 AGCTGGTTGGTATTTCACACCT 59.892 45.455 0.00 0.00 36.96 4.00
189 190 2.488153 GAGCTGGTTGGTATTTCACACC 59.512 50.000 0.00 0.00 36.54 4.16
190 191 3.146066 TGAGCTGGTTGGTATTTCACAC 58.854 45.455 0.00 0.00 0.00 3.82
191 192 3.500448 TGAGCTGGTTGGTATTTCACA 57.500 42.857 0.00 0.00 0.00 3.58
192 193 3.063997 CGATGAGCTGGTTGGTATTTCAC 59.936 47.826 0.00 0.00 0.00 3.18
193 194 3.270027 CGATGAGCTGGTTGGTATTTCA 58.730 45.455 0.00 0.00 0.00 2.69
194 195 3.063997 CACGATGAGCTGGTTGGTATTTC 59.936 47.826 0.00 0.00 0.00 2.17
195 196 3.009723 CACGATGAGCTGGTTGGTATTT 58.990 45.455 0.00 0.00 0.00 1.40
196 197 2.027192 ACACGATGAGCTGGTTGGTATT 60.027 45.455 0.00 0.00 0.00 1.89
197 198 1.555075 ACACGATGAGCTGGTTGGTAT 59.445 47.619 0.00 0.00 0.00 2.73
198 199 0.973632 ACACGATGAGCTGGTTGGTA 59.026 50.000 0.00 0.00 0.00 3.25
199 200 0.603707 CACACGATGAGCTGGTTGGT 60.604 55.000 0.00 0.00 0.00 3.67
200 201 0.320683 TCACACGATGAGCTGGTTGG 60.321 55.000 0.00 0.00 31.91 3.77
201 202 0.792640 GTCACACGATGAGCTGGTTG 59.207 55.000 0.00 0.00 38.28 3.77
202 203 0.667487 CGTCACACGATGAGCTGGTT 60.667 55.000 0.00 0.00 46.05 3.67
203 204 1.080501 CGTCACACGATGAGCTGGT 60.081 57.895 0.00 0.00 46.05 4.00
204 205 1.807165 CCGTCACACGATGAGCTGG 60.807 63.158 0.00 0.00 46.05 4.85
205 206 1.080501 ACCGTCACACGATGAGCTG 60.081 57.895 0.00 0.00 46.05 4.24
206 207 1.080501 CACCGTCACACGATGAGCT 60.081 57.895 0.00 0.00 46.05 4.09
207 208 2.730672 GCACCGTCACACGATGAGC 61.731 63.158 0.00 0.00 46.05 4.26
208 209 2.436539 CGCACCGTCACACGATGAG 61.437 63.158 0.00 0.00 46.05 2.90
209 210 2.430075 CGCACCGTCACACGATGA 60.430 61.111 0.00 0.00 46.05 2.92
210 211 3.478394 CCGCACCGTCACACGATG 61.478 66.667 0.00 0.00 46.05 3.84
244 245 1.450312 ACAGACTATTGCAGCCCGC 60.450 57.895 0.00 0.00 42.89 6.13
254 255 3.917300 CCCCCTCTACTTCACAGACTAT 58.083 50.000 0.00 0.00 0.00 2.12
286 287 1.368345 CCCATGATGCTTCGTCGCAA 61.368 55.000 0.00 0.00 44.06 4.85
311 312 3.130160 CTTCCCTGCAGCTTCGGC 61.130 66.667 8.66 0.00 42.17 5.54
353 354 2.434185 CCGTCGGCTAGCTTGCAA 60.434 61.111 21.53 6.43 34.04 4.08
380 381 3.373565 CCCCTTTGCTTCACCGGC 61.374 66.667 0.00 0.00 0.00 6.13
390 391 2.044946 CTCCGGCTTCCCCCTTTG 60.045 66.667 0.00 0.00 0.00 2.77
392 393 2.531942 AACTCCGGCTTCCCCCTT 60.532 61.111 0.00 0.00 0.00 3.95
401 402 3.793144 CTTCGCTGCAACTCCGGC 61.793 66.667 0.00 0.00 0.00 6.13
402 403 2.357517 ACTTCGCTGCAACTCCGG 60.358 61.111 0.00 0.00 0.00 5.14
404 405 2.558313 GCACTTCGCTGCAACTCC 59.442 61.111 0.00 0.00 37.11 3.85
449 451 2.893404 ACGGCGTTTCGTTGCAGT 60.893 55.556 6.77 0.00 40.85 4.40
457 459 1.370051 GCAACTCCAACGGCGTTTC 60.370 57.895 24.49 2.71 27.10 2.78
458 460 1.452145 ATGCAACTCCAACGGCGTTT 61.452 50.000 24.49 5.57 27.10 3.60
459 461 1.452145 AATGCAACTCCAACGGCGTT 61.452 50.000 21.19 21.19 30.03 4.84
460 462 1.896660 AATGCAACTCCAACGGCGT 60.897 52.632 6.77 6.77 0.00 5.68
463 465 1.666888 GCTTCAATGCAACTCCAACGG 60.667 52.381 0.00 0.00 0.00 4.44
464 466 1.267806 AGCTTCAATGCAACTCCAACG 59.732 47.619 0.00 0.00 34.99 4.10
595 819 0.107017 CCCAGAGCCGTCCAATCAAT 60.107 55.000 0.00 0.00 0.00 2.57
611 835 3.197927 ACCAGAAATAAATTGCCCCCA 57.802 42.857 0.00 0.00 0.00 4.96
631 855 6.183360 GCGATGTTACCAGTGGATGATTTTAA 60.183 38.462 18.40 0.00 0.00 1.52
645 869 5.048364 GCAAATTATATGGGCGATGTTACCA 60.048 40.000 0.00 0.00 38.88 3.25
675 907 9.907576 GTCGTTCTATCTTTATTGACTTCATTG 57.092 33.333 0.00 0.00 0.00 2.82
700 932 1.608590 CAAGGAAATGTGTTGCGGAGT 59.391 47.619 0.00 0.00 0.00 3.85
730 963 0.460311 GGAATCGTGGAGTGGATCGT 59.540 55.000 0.00 0.00 0.00 3.73
744 977 0.036388 TCACGGCCTCACAAGGAATC 60.036 55.000 0.00 0.00 46.67 2.52
745 978 0.321653 GTCACGGCCTCACAAGGAAT 60.322 55.000 0.00 0.00 46.67 3.01
752 985 1.444119 TTTGCAAGTCACGGCCTCAC 61.444 55.000 0.00 0.00 0.00 3.51
753 986 0.749818 TTTTGCAAGTCACGGCCTCA 60.750 50.000 0.00 0.00 0.00 3.86
754 987 0.598065 ATTTTGCAAGTCACGGCCTC 59.402 50.000 0.00 0.00 0.00 4.70
755 988 0.598065 GATTTTGCAAGTCACGGCCT 59.402 50.000 0.00 0.00 0.00 5.19
756 989 0.388520 GGATTTTGCAAGTCACGGCC 60.389 55.000 13.72 0.00 0.00 6.13
1665 1921 1.200020 CTGCAGGACGGGACAAAATTC 59.800 52.381 5.57 0.00 0.00 2.17
1758 2014 0.250901 TTGGCAAACTCCTCCTGCTC 60.251 55.000 0.00 0.00 36.32 4.26
1840 2096 3.837213 AACCACGAGAATTTGCTCATG 57.163 42.857 0.00 0.00 34.56 3.07
2420 2677 3.118629 ACTGACTGACACAAAAGAGCTCA 60.119 43.478 17.77 0.00 0.00 4.26
2472 2729 5.764686 ACAGACATAGTTTTCACAATGCTCA 59.235 36.000 0.00 0.00 0.00 4.26
2607 2864 6.038271 CCAATAAGTAACAGGCCTACAATGTC 59.962 42.308 3.98 0.00 0.00 3.06
2610 2867 5.445964 CCCAATAAGTAACAGGCCTACAAT 58.554 41.667 3.98 0.00 0.00 2.71
2866 3123 4.377022 GGTCATAACACGGCATATTTAGCG 60.377 45.833 0.00 0.00 0.00 4.26
3042 3301 6.164984 GCATGAGCAGAAACAGCATGGTTA 62.165 45.833 0.00 0.00 44.36 2.85
3043 3302 5.472215 GCATGAGCAGAAACAGCATGGTT 62.472 47.826 0.00 0.00 46.30 3.67
3621 3881 6.501781 CCTCCACAAATATTCAAGATTCTGC 58.498 40.000 0.00 0.00 0.00 4.26
3831 4091 4.835678 TCATTGCTCTCTCTTGCACATTA 58.164 39.130 0.00 0.00 39.05 1.90
4779 5039 1.204941 GCTCTCCAATACAGACGGTGT 59.795 52.381 0.00 0.00 43.86 4.16
5238 5498 5.008331 TGTATAGAGTCCCCGCAACTATAG 58.992 45.833 0.00 0.00 30.23 1.31
5480 5740 1.265905 GTACTGAAAACCGGTTGCCAG 59.734 52.381 31.42 31.42 35.60 4.85
6003 6263 7.148407 ACCGATAGATCTTTGAACATGTCAAAC 60.148 37.037 15.17 9.11 44.85 2.93
6048 6308 4.280929 TCATCGTTCAAGAGGTTCAGAGAA 59.719 41.667 0.00 0.00 0.00 2.87
6066 6326 2.487934 CCTAGCATTTCAGGGTCATCG 58.512 52.381 0.00 0.00 0.00 3.84
6162 6422 3.384168 TGATGGTGGCTGTAGGTCTAAT 58.616 45.455 0.00 0.00 0.00 1.73
6304 6564 3.317149 ACCAGATGAACACATATGCATGC 59.683 43.478 11.82 11.82 35.39 4.06
6349 6609 3.056821 AGAGGAACATTTCGACGATCACA 60.057 43.478 0.00 0.00 0.00 3.58
6350 6610 3.304559 CAGAGGAACATTTCGACGATCAC 59.695 47.826 0.00 0.00 0.00 3.06
6363 6623 0.833409 TCAGGCTGCTCAGAGGAACA 60.833 55.000 10.34 0.00 0.00 3.18
6364 6624 0.108233 CTCAGGCTGCTCAGAGGAAC 60.108 60.000 10.34 0.00 0.00 3.62
6389 6649 1.129811 GCCGGTCAAATAACTGAACCG 59.870 52.381 1.90 5.31 38.56 4.44
6406 6666 1.543802 TGCAGGTAAAATGAAAGGCCG 59.456 47.619 0.00 0.00 0.00 6.13
6490 6752 2.280628 CTCCAATAACCTGCTCCGAAC 58.719 52.381 0.00 0.00 0.00 3.95
6550 6812 1.273455 CTGTGAGCGCAAAAAGCTGC 61.273 55.000 11.47 0.00 46.13 5.25
6649 6911 2.288579 TGATGTCGCTACAAAACTCGGT 60.289 45.455 0.00 0.00 39.58 4.69
6705 6967 8.097038 AGCGGTCATATAACAAGAATCATGTAT 58.903 33.333 0.00 0.00 0.00 2.29
6728 6990 5.615495 CAGAATTTGCATATGTGAAAGCG 57.385 39.130 4.29 0.00 0.00 4.68
6756 7018 4.780815 TCGGCCATCTTCAGAAAATGTAT 58.219 39.130 2.24 0.00 0.00 2.29
6757 7019 4.214986 TCGGCCATCTTCAGAAAATGTA 57.785 40.909 2.24 0.00 0.00 2.29
6776 7038 1.846541 AAAACACAACCCGCATTTCG 58.153 45.000 0.00 0.00 38.08 3.46
6781 7043 1.765230 AACCTAAAACACAACCCGCA 58.235 45.000 0.00 0.00 0.00 5.69
6784 7046 6.453926 TCTACAAAACCTAAAACACAACCC 57.546 37.500 0.00 0.00 0.00 4.11
6799 7135 6.472887 CCAGGGAAGTAACAGATCTACAAAA 58.527 40.000 0.00 0.00 0.00 2.44
6814 7150 1.053424 TACAGAAACGCCAGGGAAGT 58.947 50.000 0.00 0.00 0.00 3.01
6822 7158 1.448985 TTCCAGCATACAGAAACGCC 58.551 50.000 0.00 0.00 0.00 5.68
6828 7164 6.543465 CCTGATAATGTTTTCCAGCATACAGA 59.457 38.462 0.00 0.00 0.00 3.41
6884 7220 3.963383 ACTTGTAAAAGCTGACCAACG 57.037 42.857 0.00 0.00 0.00 4.10
6981 7524 0.108520 CCTCCATTTTGCATTGCGCT 60.109 50.000 9.73 0.00 43.06 5.92
6983 7526 0.108520 AGCCTCCATTTTGCATTGCG 60.109 50.000 3.84 0.00 0.00 4.85
6984 7527 1.206371 AGAGCCTCCATTTTGCATTGC 59.794 47.619 0.46 0.46 0.00 3.56
6985 7528 2.232941 ACAGAGCCTCCATTTTGCATTG 59.767 45.455 0.00 0.00 0.00 2.82
6986 7529 2.532843 ACAGAGCCTCCATTTTGCATT 58.467 42.857 0.00 0.00 0.00 3.56
6997 7540 2.182030 CCGGACGAACAGAGCCTC 59.818 66.667 0.00 0.00 0.00 4.70
7003 7546 2.935955 GTGTTGCCGGACGAACAG 59.064 61.111 5.05 0.00 32.81 3.16
7004 7547 2.702751 ATCGTGTTGCCGGACGAACA 62.703 55.000 18.48 13.76 46.83 3.18
7058 7692 2.031682 GCTTGTTTGAGTGTGGCTACTG 60.032 50.000 0.64 0.00 0.00 2.74
7065 7699 2.423185 TGGTTCTGCTTGTTTGAGTGTG 59.577 45.455 0.00 0.00 0.00 3.82
7066 7700 2.722094 TGGTTCTGCTTGTTTGAGTGT 58.278 42.857 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.