Multiple sequence alignment - TraesCS6B01G276900

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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 TraesCS6B01G276900 chr6B 100.000 2624 0 0 1 2624 501103374 501105997 0.000000e+00 4846.0
1 TraesCS6B01G276900 chr6B 76.000 375 68 15 418 775 515158390 515158021 9.650000e-40 174.0
2 TraesCS6B01G276900 chr6A 90.021 2385 137 38 307 2624 459850340 459847990 0.000000e+00 2992.0
3 TraesCS6B01G276900 chr6A 86.022 93 8 2 148 236 459850430 459850339 7.730000e-16 95.3
4 TraesCS6B01G276900 chr6D 91.332 1892 84 23 791 2624 322461325 322459456 0.000000e+00 2512.0
5 TraesCS6B01G276900 chr6D 92.012 651 45 5 148 792 322462136 322461487 0.000000e+00 907.0
6 TraesCS6B01G276900 chr6D 94.643 168 7 2 1 167 120520056 120520222 2.590000e-65 259.0
7 TraesCS6B01G276900 chr6D 92.857 56 4 0 1094 1149 339002698 339002643 6.020000e-12 82.4
8 TraesCS6B01G276900 chr7B 96.835 158 4 1 1 157 395784663 395784506 2.000000e-66 263.0
9 TraesCS6B01G276900 chr5B 96.250 160 6 0 1 160 434867246 434867087 2.000000e-66 263.0
10 TraesCS6B01G276900 chr1D 96.835 158 4 1 1 157 369940942 369940785 2.000000e-66 263.0
11 TraesCS6B01G276900 chr1D 75.899 278 51 8 546 808 11743517 11743241 7.620000e-26 128.0
12 TraesCS6B01G276900 chr3D 95.732 164 4 3 1 162 387650080 387649918 7.200000e-66 261.0
13 TraesCS6B01G276900 chr3D 72.754 334 72 10 446 763 107655245 107654915 7.730000e-16 95.3
14 TraesCS6B01G276900 chr3D 79.208 101 19 2 649 748 482611510 482611411 4.690000e-08 69.4
15 TraesCS6B01G276900 chr2B 96.250 160 5 1 1 159 578909843 578910002 7.200000e-66 261.0
16 TraesCS6B01G276900 chr5D 95.679 162 6 1 1 161 289586151 289585990 2.590000e-65 259.0
17 TraesCS6B01G276900 chr2D 93.064 173 10 2 1 171 205756794 205756622 4.340000e-63 252.0
18 TraesCS6B01G276900 chr4D 89.796 196 11 7 1 193 391912640 391912451 2.610000e-60 243.0
19 TraesCS6B01G276900 chr3A 80.000 210 41 1 416 624 724831247 724831456 1.260000e-33 154.0
20 TraesCS6B01G276900 chr4B 77.005 187 35 5 634 820 41746822 41746644 1.660000e-17 100.0


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 TraesCS6B01G276900 chr6B 501103374 501105997 2623 False 4846.00 4846 100.0000 1 2624 1 chr6B.!!$F1 2623
1 TraesCS6B01G276900 chr6A 459847990 459850430 2440 True 1543.65 2992 88.0215 148 2624 2 chr6A.!!$R1 2476
2 TraesCS6B01G276900 chr6D 322459456 322462136 2680 True 1709.50 2512 91.6720 148 2624 2 chr6D.!!$R2 2476

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
617 625 0.03601 CGACTTCAGGGCATTGGTCT 60.036 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2407 2628 0.248866 AAAGGTCTTGCGGCAAAACG 60.249 50.0 17.13 5.5 0.0 3.6 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
23 24 6.187125 CACACATTTTTAGGGTCATCTCTG 57.813 41.667 0.00 0.00 0.00 3.35
24 25 4.702131 ACACATTTTTAGGGTCATCTCTGC 59.298 41.667 0.00 0.00 0.00 4.26
25 26 4.946157 CACATTTTTAGGGTCATCTCTGCT 59.054 41.667 0.00 0.00 0.00 4.24
26 27 6.115446 CACATTTTTAGGGTCATCTCTGCTA 58.885 40.000 0.00 0.00 0.00 3.49
27 28 6.259608 CACATTTTTAGGGTCATCTCTGCTAG 59.740 42.308 0.00 0.00 0.00 3.42
28 29 5.359194 TTTTTAGGGTCATCTCTGCTAGG 57.641 43.478 0.00 0.00 0.00 3.02
29 30 3.689872 TTAGGGTCATCTCTGCTAGGT 57.310 47.619 0.00 0.00 0.00 3.08
30 31 4.808767 TTAGGGTCATCTCTGCTAGGTA 57.191 45.455 0.00 0.00 0.00 3.08
31 32 3.689872 AGGGTCATCTCTGCTAGGTAA 57.310 47.619 0.00 0.00 0.00 2.85
32 33 3.995636 AGGGTCATCTCTGCTAGGTAAA 58.004 45.455 0.00 0.00 0.00 2.01
33 34 3.707102 AGGGTCATCTCTGCTAGGTAAAC 59.293 47.826 0.00 0.00 0.00 2.01
34 35 3.181464 GGGTCATCTCTGCTAGGTAAACC 60.181 52.174 0.00 0.00 0.00 3.27
35 36 3.491104 GGTCATCTCTGCTAGGTAAACCG 60.491 52.174 0.00 0.00 42.08 4.44
36 37 3.380637 GTCATCTCTGCTAGGTAAACCGA 59.619 47.826 0.00 0.00 42.08 4.69
37 38 4.021229 TCATCTCTGCTAGGTAAACCGAA 58.979 43.478 0.00 0.00 42.08 4.30
38 39 4.649674 TCATCTCTGCTAGGTAAACCGAAT 59.350 41.667 0.00 0.00 42.08 3.34
39 40 4.650754 TCTCTGCTAGGTAAACCGAATC 57.349 45.455 0.00 0.00 42.08 2.52
40 41 4.021229 TCTCTGCTAGGTAAACCGAATCA 58.979 43.478 0.00 0.00 42.08 2.57
41 42 4.464951 TCTCTGCTAGGTAAACCGAATCAA 59.535 41.667 0.00 0.00 42.08 2.57
42 43 5.128827 TCTCTGCTAGGTAAACCGAATCAAT 59.871 40.000 0.00 0.00 42.08 2.57
43 44 6.322969 TCTCTGCTAGGTAAACCGAATCAATA 59.677 38.462 0.00 0.00 42.08 1.90
44 45 7.015292 TCTCTGCTAGGTAAACCGAATCAATAT 59.985 37.037 0.00 0.00 42.08 1.28
45 46 6.929049 TCTGCTAGGTAAACCGAATCAATATG 59.071 38.462 0.00 0.00 42.08 1.78
46 47 5.995282 TGCTAGGTAAACCGAATCAATATGG 59.005 40.000 0.00 0.00 42.08 2.74
47 48 5.411669 GCTAGGTAAACCGAATCAATATGGG 59.588 44.000 0.00 0.00 42.08 4.00
48 49 5.640158 AGGTAAACCGAATCAATATGGGA 57.360 39.130 0.00 0.00 42.08 4.37
49 50 5.374071 AGGTAAACCGAATCAATATGGGAC 58.626 41.667 0.00 0.00 42.08 4.46
50 51 5.132144 AGGTAAACCGAATCAATATGGGACT 59.868 40.000 0.00 0.00 42.08 3.85
51 52 6.328148 AGGTAAACCGAATCAATATGGGACTA 59.672 38.462 0.00 0.00 42.08 2.59
52 53 6.426025 GGTAAACCGAATCAATATGGGACTAC 59.574 42.308 0.00 0.00 0.00 2.73
53 54 5.888982 AACCGAATCAATATGGGACTACT 57.111 39.130 0.00 0.00 0.00 2.57
54 55 6.989155 AACCGAATCAATATGGGACTACTA 57.011 37.500 0.00 0.00 0.00 1.82
55 56 6.342338 ACCGAATCAATATGGGACTACTAC 57.658 41.667 0.00 0.00 0.00 2.73
56 57 5.245526 ACCGAATCAATATGGGACTACTACC 59.754 44.000 0.00 0.00 0.00 3.18
57 58 5.480772 CCGAATCAATATGGGACTACTACCT 59.519 44.000 0.00 0.00 0.00 3.08
58 59 6.390721 CGAATCAATATGGGACTACTACCTG 58.609 44.000 0.00 0.00 0.00 4.00
59 60 6.015350 CGAATCAATATGGGACTACTACCTGT 60.015 42.308 0.00 0.00 0.00 4.00
60 61 6.672266 ATCAATATGGGACTACTACCTGTG 57.328 41.667 0.00 0.00 0.00 3.66
61 62 5.525484 TCAATATGGGACTACTACCTGTGT 58.475 41.667 0.00 0.00 0.00 3.72
62 63 5.962031 TCAATATGGGACTACTACCTGTGTT 59.038 40.000 0.00 0.00 0.00 3.32
63 64 7.127405 TCAATATGGGACTACTACCTGTGTTA 58.873 38.462 0.00 0.00 0.00 2.41
64 65 7.787904 TCAATATGGGACTACTACCTGTGTTAT 59.212 37.037 0.00 0.00 0.00 1.89
65 66 7.778185 ATATGGGACTACTACCTGTGTTATC 57.222 40.000 0.00 0.00 0.00 1.75
66 67 4.284178 TGGGACTACTACCTGTGTTATCC 58.716 47.826 0.00 0.00 0.00 2.59
67 68 4.016851 TGGGACTACTACCTGTGTTATCCT 60.017 45.833 0.00 0.00 0.00 3.24
68 69 4.341520 GGGACTACTACCTGTGTTATCCTG 59.658 50.000 0.00 0.00 0.00 3.86
69 70 4.202131 GGACTACTACCTGTGTTATCCTGC 60.202 50.000 0.00 0.00 0.00 4.85
70 71 4.350245 ACTACTACCTGTGTTATCCTGCA 58.650 43.478 0.00 0.00 0.00 4.41
71 72 4.775780 ACTACTACCTGTGTTATCCTGCAA 59.224 41.667 0.00 0.00 0.00 4.08
72 73 4.844349 ACTACCTGTGTTATCCTGCAAT 57.156 40.909 0.00 0.00 0.00 3.56
73 74 5.179452 ACTACCTGTGTTATCCTGCAATT 57.821 39.130 0.00 0.00 0.00 2.32
74 75 5.570320 ACTACCTGTGTTATCCTGCAATTT 58.430 37.500 0.00 0.00 0.00 1.82
75 76 6.010219 ACTACCTGTGTTATCCTGCAATTTT 58.990 36.000 0.00 0.00 0.00 1.82
76 77 5.391312 ACCTGTGTTATCCTGCAATTTTC 57.609 39.130 0.00 0.00 0.00 2.29
77 78 4.832266 ACCTGTGTTATCCTGCAATTTTCA 59.168 37.500 0.00 0.00 0.00 2.69
78 79 5.163513 CCTGTGTTATCCTGCAATTTTCAC 58.836 41.667 0.00 0.00 0.00 3.18
79 80 5.278907 CCTGTGTTATCCTGCAATTTTCACA 60.279 40.000 8.96 8.96 33.38 3.58
80 81 6.154203 TGTGTTATCCTGCAATTTTCACAA 57.846 33.333 7.48 0.00 31.85 3.33
81 82 6.577103 TGTGTTATCCTGCAATTTTCACAAA 58.423 32.000 7.48 0.00 31.85 2.83
82 83 6.478344 TGTGTTATCCTGCAATTTTCACAAAC 59.522 34.615 7.48 0.00 31.85 2.93
83 84 6.478344 GTGTTATCCTGCAATTTTCACAAACA 59.522 34.615 0.00 0.00 0.00 2.83
84 85 6.478344 TGTTATCCTGCAATTTTCACAAACAC 59.522 34.615 0.00 0.00 0.00 3.32
85 86 4.462508 TCCTGCAATTTTCACAAACACA 57.537 36.364 0.00 0.00 0.00 3.72
86 87 5.021033 TCCTGCAATTTTCACAAACACAT 57.979 34.783 0.00 0.00 0.00 3.21
87 88 5.426504 TCCTGCAATTTTCACAAACACATT 58.573 33.333 0.00 0.00 0.00 2.71
88 89 6.577103 TCCTGCAATTTTCACAAACACATTA 58.423 32.000 0.00 0.00 0.00 1.90
89 90 6.700960 TCCTGCAATTTTCACAAACACATTAG 59.299 34.615 0.00 0.00 0.00 1.73
90 91 6.479660 CCTGCAATTTTCACAAACACATTAGT 59.520 34.615 0.00 0.00 0.00 2.24
91 92 7.306749 CCTGCAATTTTCACAAACACATTAGTC 60.307 37.037 0.00 0.00 0.00 2.59
92 93 6.478344 TGCAATTTTCACAAACACATTAGTCC 59.522 34.615 0.00 0.00 0.00 3.85
93 94 6.701400 GCAATTTTCACAAACACATTAGTCCT 59.299 34.615 0.00 0.00 0.00 3.85
94 95 7.224557 GCAATTTTCACAAACACATTAGTCCTT 59.775 33.333 0.00 0.00 0.00 3.36
95 96 8.755018 CAATTTTCACAAACACATTAGTCCTTC 58.245 33.333 0.00 0.00 0.00 3.46
96 97 7.397892 TTTTCACAAACACATTAGTCCTTCA 57.602 32.000 0.00 0.00 0.00 3.02
97 98 7.397892 TTTCACAAACACATTAGTCCTTCAA 57.602 32.000 0.00 0.00 0.00 2.69
98 99 6.371809 TCACAAACACATTAGTCCTTCAAC 57.628 37.500 0.00 0.00 0.00 3.18
99 100 5.298276 TCACAAACACATTAGTCCTTCAACC 59.702 40.000 0.00 0.00 0.00 3.77
100 101 5.067153 CACAAACACATTAGTCCTTCAACCA 59.933 40.000 0.00 0.00 0.00 3.67
101 102 5.654650 ACAAACACATTAGTCCTTCAACCAA 59.345 36.000 0.00 0.00 0.00 3.67
102 103 6.183360 ACAAACACATTAGTCCTTCAACCAAG 60.183 38.462 0.00 0.00 0.00 3.61
103 104 5.048846 ACACATTAGTCCTTCAACCAAGT 57.951 39.130 0.00 0.00 0.00 3.16
104 105 5.063880 ACACATTAGTCCTTCAACCAAGTC 58.936 41.667 0.00 0.00 0.00 3.01
105 106 5.163195 ACACATTAGTCCTTCAACCAAGTCT 60.163 40.000 0.00 0.00 0.00 3.24
106 107 5.180117 CACATTAGTCCTTCAACCAAGTCTG 59.820 44.000 0.00 0.00 0.00 3.51
107 108 5.163195 ACATTAGTCCTTCAACCAAGTCTGT 60.163 40.000 0.00 0.00 0.00 3.41
108 109 3.477210 AGTCCTTCAACCAAGTCTGTC 57.523 47.619 0.00 0.00 0.00 3.51
109 110 2.135933 GTCCTTCAACCAAGTCTGTCG 58.864 52.381 0.00 0.00 0.00 4.35
110 111 1.760613 TCCTTCAACCAAGTCTGTCGT 59.239 47.619 0.00 0.00 0.00 4.34
111 112 2.135933 CCTTCAACCAAGTCTGTCGTC 58.864 52.381 0.00 0.00 0.00 4.20
112 113 2.483013 CCTTCAACCAAGTCTGTCGTCA 60.483 50.000 0.00 0.00 0.00 4.35
113 114 2.971660 TCAACCAAGTCTGTCGTCAA 57.028 45.000 0.00 0.00 0.00 3.18
114 115 3.469008 TCAACCAAGTCTGTCGTCAAT 57.531 42.857 0.00 0.00 0.00 2.57
115 116 4.594123 TCAACCAAGTCTGTCGTCAATA 57.406 40.909 0.00 0.00 0.00 1.90
116 117 4.304110 TCAACCAAGTCTGTCGTCAATAC 58.696 43.478 0.00 0.00 0.00 1.89
117 118 4.038763 TCAACCAAGTCTGTCGTCAATACT 59.961 41.667 0.00 0.00 0.00 2.12
118 119 4.175787 ACCAAGTCTGTCGTCAATACTC 57.824 45.455 0.00 0.00 0.00 2.59
119 120 3.056749 ACCAAGTCTGTCGTCAATACTCC 60.057 47.826 0.00 0.00 0.00 3.85
120 121 3.056821 CCAAGTCTGTCGTCAATACTCCA 60.057 47.826 0.00 0.00 0.00 3.86
121 122 4.556233 CAAGTCTGTCGTCAATACTCCAA 58.444 43.478 0.00 0.00 0.00 3.53
122 123 4.866508 AGTCTGTCGTCAATACTCCAAA 57.133 40.909 0.00 0.00 0.00 3.28
123 124 5.209818 AGTCTGTCGTCAATACTCCAAAA 57.790 39.130 0.00 0.00 0.00 2.44
124 125 4.989168 AGTCTGTCGTCAATACTCCAAAAC 59.011 41.667 0.00 0.00 0.00 2.43
125 126 4.151867 GTCTGTCGTCAATACTCCAAAACC 59.848 45.833 0.00 0.00 0.00 3.27
126 127 4.062293 CTGTCGTCAATACTCCAAAACCA 58.938 43.478 0.00 0.00 0.00 3.67
127 128 4.452825 TGTCGTCAATACTCCAAAACCAA 58.547 39.130 0.00 0.00 0.00 3.67
128 129 4.273969 TGTCGTCAATACTCCAAAACCAAC 59.726 41.667 0.00 0.00 0.00 3.77
129 130 4.514066 GTCGTCAATACTCCAAAACCAACT 59.486 41.667 0.00 0.00 0.00 3.16
130 131 5.697633 GTCGTCAATACTCCAAAACCAACTA 59.302 40.000 0.00 0.00 0.00 2.24
131 132 5.929992 TCGTCAATACTCCAAAACCAACTAG 59.070 40.000 0.00 0.00 0.00 2.57
132 133 5.121768 CGTCAATACTCCAAAACCAACTAGG 59.878 44.000 0.00 0.00 45.67 3.02
133 134 5.414765 GTCAATACTCCAAAACCAACTAGGG 59.585 44.000 0.00 0.00 43.89 3.53
134 135 2.971901 ACTCCAAAACCAACTAGGGG 57.028 50.000 0.00 0.00 43.89 4.79
135 136 2.141067 ACTCCAAAACCAACTAGGGGT 58.859 47.619 2.70 2.70 43.89 4.95
136 137 2.158519 ACTCCAAAACCAACTAGGGGTG 60.159 50.000 8.90 0.00 43.89 4.61
137 138 1.146152 TCCAAAACCAACTAGGGGTGG 59.854 52.381 8.90 8.22 43.89 4.61
138 139 0.966179 CAAAACCAACTAGGGGTGGC 59.034 55.000 8.90 0.00 43.89 5.01
139 140 0.558712 AAAACCAACTAGGGGTGGCA 59.441 50.000 8.90 0.00 43.89 4.92
140 141 0.178973 AAACCAACTAGGGGTGGCAC 60.179 55.000 9.70 9.70 43.89 5.01
141 142 1.065997 AACCAACTAGGGGTGGCACT 61.066 55.000 18.45 0.00 43.89 4.40
142 143 0.178885 ACCAACTAGGGGTGGCACTA 60.179 55.000 18.45 0.98 43.89 2.74
143 144 0.541863 CCAACTAGGGGTGGCACTAG 59.458 60.000 18.45 13.59 41.83 2.57
144 145 1.568504 CAACTAGGGGTGGCACTAGA 58.431 55.000 18.45 0.00 39.16 2.43
145 146 2.119495 CAACTAGGGGTGGCACTAGAT 58.881 52.381 18.45 3.55 39.16 1.98
146 147 1.794714 ACTAGGGGTGGCACTAGATG 58.205 55.000 18.45 8.10 39.16 2.90
161 162 6.208988 CACTAGATGCACTTACACTAAGGA 57.791 41.667 0.00 0.00 40.08 3.36
162 163 6.037098 CACTAGATGCACTTACACTAAGGAC 58.963 44.000 0.00 0.00 40.08 3.85
163 164 5.952947 ACTAGATGCACTTACACTAAGGACT 59.047 40.000 0.00 0.00 40.08 3.85
164 165 5.746990 AGATGCACTTACACTAAGGACTT 57.253 39.130 0.00 0.00 40.08 3.01
165 166 5.725362 AGATGCACTTACACTAAGGACTTC 58.275 41.667 0.00 0.00 40.08 3.01
204 205 5.205517 TGGTTGGGTTTCTATGGAATCAT 57.794 39.130 0.00 0.00 37.40 2.45
211 216 7.741785 TGGGTTTCTATGGAATCATACGTAAT 58.258 34.615 0.00 0.00 34.96 1.89
224 229 5.657474 TCATACGTAATGTTTCCTCCTGTC 58.343 41.667 0.00 0.00 36.89 3.51
225 230 3.329929 ACGTAATGTTTCCTCCTGTCC 57.670 47.619 0.00 0.00 0.00 4.02
249 255 5.330233 CCCTAGGTGGTTAGGACAATTTTT 58.670 41.667 8.29 0.00 42.39 1.94
254 260 4.591498 GGTGGTTAGGACAATTTTTCCCTT 59.409 41.667 0.00 0.00 33.01 3.95
268 274 7.855784 ATTTTTCCCTTTAGAATTCACTGGT 57.144 32.000 8.44 0.00 0.00 4.00
275 281 1.067295 AGAATTCACTGGTGAGCCCA 58.933 50.000 8.44 0.00 41.13 5.36
290 296 0.756815 GCCCATGGATTTGTCTCCCC 60.757 60.000 15.22 0.00 34.12 4.81
394 401 2.994995 TCCTCGCCGGTGTGATGT 60.995 61.111 18.30 0.00 0.00 3.06
400 407 2.112815 GCCGGTGTGATGTTAGGGC 61.113 63.158 1.90 0.00 0.00 5.19
442 449 2.218603 GAGTTTGTCTTTCGGGCTTCA 58.781 47.619 0.00 0.00 0.00 3.02
462 470 0.471211 ACCCTCCTCAAGTTCGTCCA 60.471 55.000 0.00 0.00 0.00 4.02
544 552 1.202639 ACAGTTTCTCGTCATGTGGCA 60.203 47.619 0.00 0.00 0.00 4.92
551 559 2.560981 TCTCGTCATGTGGCAAGAGTTA 59.439 45.455 0.00 0.00 0.00 2.24
556 564 3.815401 GTCATGTGGCAAGAGTTAGTGTT 59.185 43.478 0.00 0.00 0.00 3.32
617 625 0.036010 CGACTTCAGGGCATTGGTCT 60.036 55.000 0.00 0.00 0.00 3.85
661 669 1.006102 ACAAGGTCAAGTCGGCTCG 60.006 57.895 0.00 0.00 0.00 5.03
667 675 3.691342 CAAGTCGGCTCGGGTGGA 61.691 66.667 0.00 0.00 0.00 4.02
675 683 3.059982 CTCGGGTGGAGAGCAACA 58.940 61.111 0.00 0.00 46.23 3.33
679 687 0.817634 CGGGTGGAGAGCAACAACAA 60.818 55.000 0.00 0.00 0.00 2.83
682 690 1.748493 GGTGGAGAGCAACAACAACAA 59.252 47.619 0.00 0.00 0.00 2.83
689 697 1.468340 GCAACAACAACAACGCGTCC 61.468 55.000 14.44 0.00 0.00 4.79
781 789 6.600882 TTGAGATACTTTTTACTCCCGACT 57.399 37.500 0.00 0.00 0.00 4.18
863 1035 8.726068 TCTTCTTTGAAAACGATACATTGCATA 58.274 29.630 0.00 0.00 0.00 3.14
901 1073 8.909423 AATATTCAGATAAACCCCTTTCCAAA 57.091 30.769 0.00 0.00 0.00 3.28
902 1074 9.506042 AATATTCAGATAAACCCCTTTCCAAAT 57.494 29.630 0.00 0.00 0.00 2.32
903 1075 7.813087 ATTCAGATAAACCCCTTTCCAAATT 57.187 32.000 0.00 0.00 0.00 1.82
904 1076 6.850752 TCAGATAAACCCCTTTCCAAATTC 57.149 37.500 0.00 0.00 0.00 2.17
905 1077 5.719563 TCAGATAAACCCCTTTCCAAATTCC 59.280 40.000 0.00 0.00 0.00 3.01
906 1078 5.483583 CAGATAAACCCCTTTCCAAATTCCA 59.516 40.000 0.00 0.00 0.00 3.53
907 1079 6.013812 CAGATAAACCCCTTTCCAAATTCCAA 60.014 38.462 0.00 0.00 0.00 3.53
1074 1250 1.557269 CCAAGTCCACTCTCCTGGGG 61.557 65.000 0.00 0.00 31.41 4.96
1360 1536 2.488355 CGGACATGTACGTCGCCT 59.512 61.111 22.63 0.00 36.73 5.52
1500 1676 1.588082 GACTTCGGCGTCAAGGGTA 59.412 57.895 6.85 0.00 34.11 3.69
1649 1840 4.134379 TGCATGTTTTTGGTCACACAAT 57.866 36.364 0.00 0.00 0.00 2.71
1659 1850 5.731599 TTGGTCACACAATTGCATTTTTC 57.268 34.783 5.05 0.00 0.00 2.29
1695 1886 0.028902 GTTTGTGAGCACCCGTGTTC 59.971 55.000 4.88 4.88 40.58 3.18
1699 1890 0.814010 GTGAGCACCCGTGTTCTTGT 60.814 55.000 12.11 0.00 40.76 3.16
1734 1938 4.648651 TGATGAGTATGCCATGAAGGATG 58.351 43.478 0.00 0.00 41.22 3.51
1785 1996 4.393062 CACCCTGCACTTTTATGAGTACAG 59.607 45.833 0.00 0.00 39.63 2.74
1789 2000 5.356882 TGCACTTTTATGAGTACAGTTGC 57.643 39.130 0.00 0.00 0.00 4.17
1794 2005 6.649141 CACTTTTATGAGTACAGTTGCTGGTA 59.351 38.462 0.00 0.00 35.51 3.25
1800 2011 2.093447 AGTACAGTTGCTGGTAGATGGC 60.093 50.000 0.00 0.00 35.51 4.40
1811 2022 2.238646 TGGTAGATGGCGGTTTCTTCAT 59.761 45.455 0.00 0.00 0.00 2.57
1816 2027 4.082125 AGATGGCGGTTTCTTCATCTTTT 58.918 39.130 0.00 0.00 42.30 2.27
1888 2102 5.993055 TGATTACTCTTCCTTCATCATGCA 58.007 37.500 0.00 0.00 0.00 3.96
1921 2135 3.939066 AGATTTACGTTGCTTAGGCTGT 58.061 40.909 0.00 0.00 39.59 4.40
1969 2183 0.037734 CCAGGTGTTCTTACCCCCAC 59.962 60.000 0.00 0.00 41.83 4.61
1971 2185 2.471462 GGTGTTCTTACCCCCACCT 58.529 57.895 0.00 0.00 43.21 4.00
1990 2204 0.615331 TTGGGTAGGCAGCTCTTCTG 59.385 55.000 0.00 0.00 45.62 3.02
2020 2234 4.661993 TTTCACAGCGTAGTTGCTTATG 57.338 40.909 0.00 0.00 44.46 1.90
2022 2236 2.002586 CACAGCGTAGTTGCTTATGCT 58.997 47.619 1.96 4.90 44.46 3.79
2023 2237 3.119280 TCACAGCGTAGTTGCTTATGCTA 60.119 43.478 8.98 0.00 44.46 3.49
2024 2238 3.000322 CACAGCGTAGTTGCTTATGCTAC 60.000 47.826 7.02 7.02 44.46 3.58
2026 2240 3.000322 CAGCGTAGTTGCTTATGCTACAC 60.000 47.826 15.43 10.82 44.46 2.90
2027 2241 2.927477 GCGTAGTTGCTTATGCTACACA 59.073 45.455 15.43 2.72 45.02 3.72
2029 2243 4.034048 GCGTAGTTGCTTATGCTACACAAT 59.966 41.667 15.43 0.45 45.02 2.71
2031 2245 6.637365 CGTAGTTGCTTATGCTACACAATAC 58.363 40.000 15.43 9.05 45.02 1.89
2032 2246 6.475727 CGTAGTTGCTTATGCTACACAATACT 59.524 38.462 15.43 0.00 45.02 2.12
2033 2247 7.010183 CGTAGTTGCTTATGCTACACAATACTT 59.990 37.037 15.43 0.00 45.02 2.24
2091 2310 9.013229 TGCTACATATTCCATACCAATTTGATC 57.987 33.333 0.00 0.00 0.00 2.92
2110 2329 4.462834 TGATCTGTCAGGTTACATTCGAGT 59.537 41.667 0.00 0.00 0.00 4.18
2113 2332 2.631062 TGTCAGGTTACATTCGAGTGGT 59.369 45.455 12.90 2.06 0.00 4.16
2144 2363 1.407989 GCTATCAGCTGCAGGAGGTTT 60.408 52.381 17.12 0.00 38.45 3.27
2357 2578 0.173481 GTCTGCATCACTGGCGAGTA 59.827 55.000 0.00 0.00 0.00 2.59
2407 2628 1.822581 GATCGCGGCATTTTTGTACC 58.177 50.000 6.13 0.00 0.00 3.34
2443 2664 5.183904 AGACCTTTGATATTTCAGCAACACC 59.816 40.000 0.00 0.00 30.73 4.16
2444 2665 4.082787 ACCTTTGATATTTCAGCAACACCG 60.083 41.667 0.00 0.00 30.73 4.94
2573 2813 0.107897 TGACCTAACGCCGCATCATT 60.108 50.000 0.00 0.00 0.00 2.57
2574 2814 1.014352 GACCTAACGCCGCATCATTT 58.986 50.000 0.00 0.00 0.00 2.32
2575 2815 0.732571 ACCTAACGCCGCATCATTTG 59.267 50.000 0.00 0.00 0.00 2.32
2576 2816 0.732571 CCTAACGCCGCATCATTTGT 59.267 50.000 0.00 0.00 0.00 2.83
2577 2817 1.937223 CCTAACGCCGCATCATTTGTA 59.063 47.619 0.00 0.00 0.00 2.41
2578 2818 2.286184 CCTAACGCCGCATCATTTGTAC 60.286 50.000 0.00 0.00 0.00 2.90
2579 2819 0.450184 AACGCCGCATCATTTGTACC 59.550 50.000 0.00 0.00 0.00 3.34
2580 2820 0.675208 ACGCCGCATCATTTGTACCA 60.675 50.000 0.00 0.00 0.00 3.25
2608 2848 2.684374 TGATTGTTCCGATGATGCTTGG 59.316 45.455 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.184892 AGCAGAGATGACCCTAAAAATGT 57.815 39.130 0.00 0.00 0.00 2.71
4 5 5.762218 CCTAGCAGAGATGACCCTAAAAATG 59.238 44.000 0.00 0.00 0.00 2.32
5 6 5.430089 ACCTAGCAGAGATGACCCTAAAAAT 59.570 40.000 0.00 0.00 0.00 1.82
7 8 4.362677 ACCTAGCAGAGATGACCCTAAAA 58.637 43.478 0.00 0.00 0.00 1.52
9 10 3.689872 ACCTAGCAGAGATGACCCTAA 57.310 47.619 0.00 0.00 0.00 2.69
10 11 4.808767 TTACCTAGCAGAGATGACCCTA 57.191 45.455 0.00 0.00 0.00 3.53
11 12 3.689872 TTACCTAGCAGAGATGACCCT 57.310 47.619 0.00 0.00 0.00 4.34
13 14 3.491104 CGGTTTACCTAGCAGAGATGACC 60.491 52.174 0.00 0.00 0.00 4.02
14 15 3.380637 TCGGTTTACCTAGCAGAGATGAC 59.619 47.826 0.00 0.00 0.00 3.06
15 16 3.628008 TCGGTTTACCTAGCAGAGATGA 58.372 45.455 0.00 0.00 0.00 2.92
16 17 4.386867 TTCGGTTTACCTAGCAGAGATG 57.613 45.455 0.00 0.00 0.00 2.90
17 18 4.649674 TGATTCGGTTTACCTAGCAGAGAT 59.350 41.667 0.00 0.00 0.00 2.75
18 19 4.021229 TGATTCGGTTTACCTAGCAGAGA 58.979 43.478 0.00 0.00 0.00 3.10
19 20 4.386867 TGATTCGGTTTACCTAGCAGAG 57.613 45.455 0.00 0.00 0.00 3.35
20 21 4.811969 TTGATTCGGTTTACCTAGCAGA 57.188 40.909 0.00 0.00 0.00 4.26
21 22 6.147821 CCATATTGATTCGGTTTACCTAGCAG 59.852 42.308 0.00 0.00 0.00 4.24
22 23 5.995282 CCATATTGATTCGGTTTACCTAGCA 59.005 40.000 0.00 0.00 0.00 3.49
23 24 5.411669 CCCATATTGATTCGGTTTACCTAGC 59.588 44.000 0.00 0.00 0.00 3.42
24 25 6.649557 GTCCCATATTGATTCGGTTTACCTAG 59.350 42.308 0.00 0.00 0.00 3.02
25 26 6.328148 AGTCCCATATTGATTCGGTTTACCTA 59.672 38.462 0.00 0.00 0.00 3.08
26 27 5.132144 AGTCCCATATTGATTCGGTTTACCT 59.868 40.000 0.00 0.00 0.00 3.08
27 28 5.374071 AGTCCCATATTGATTCGGTTTACC 58.626 41.667 0.00 0.00 0.00 2.85
28 29 7.215085 AGTAGTCCCATATTGATTCGGTTTAC 58.785 38.462 0.00 0.00 0.00 2.01
29 30 7.369551 AGTAGTCCCATATTGATTCGGTTTA 57.630 36.000 0.00 0.00 0.00 2.01
30 31 6.248569 AGTAGTCCCATATTGATTCGGTTT 57.751 37.500 0.00 0.00 0.00 3.27
31 32 5.888982 AGTAGTCCCATATTGATTCGGTT 57.111 39.130 0.00 0.00 0.00 4.44
32 33 5.245526 GGTAGTAGTCCCATATTGATTCGGT 59.754 44.000 0.00 0.00 0.00 4.69
33 34 5.480772 AGGTAGTAGTCCCATATTGATTCGG 59.519 44.000 0.00 0.00 0.00 4.30
34 35 6.015350 ACAGGTAGTAGTCCCATATTGATTCG 60.015 42.308 0.00 0.00 0.00 3.34
35 36 7.155328 CACAGGTAGTAGTCCCATATTGATTC 58.845 42.308 0.00 0.00 0.00 2.52
36 37 6.615726 ACACAGGTAGTAGTCCCATATTGATT 59.384 38.462 0.00 0.00 0.00 2.57
37 38 6.143915 ACACAGGTAGTAGTCCCATATTGAT 58.856 40.000 0.00 0.00 0.00 2.57
38 39 5.525484 ACACAGGTAGTAGTCCCATATTGA 58.475 41.667 0.00 0.00 0.00 2.57
39 40 5.871396 ACACAGGTAGTAGTCCCATATTG 57.129 43.478 0.00 0.00 0.00 1.90
40 41 7.234988 GGATAACACAGGTAGTAGTCCCATATT 59.765 40.741 0.00 0.00 0.00 1.28
41 42 6.724905 GGATAACACAGGTAGTAGTCCCATAT 59.275 42.308 0.00 0.00 0.00 1.78
42 43 6.073314 GGATAACACAGGTAGTAGTCCCATA 58.927 44.000 0.00 0.00 0.00 2.74
43 44 4.900054 GGATAACACAGGTAGTAGTCCCAT 59.100 45.833 0.00 0.00 0.00 4.00
44 45 4.016851 AGGATAACACAGGTAGTAGTCCCA 60.017 45.833 0.00 0.00 0.00 4.37
45 46 4.341520 CAGGATAACACAGGTAGTAGTCCC 59.658 50.000 0.00 0.00 0.00 4.46
46 47 4.202131 GCAGGATAACACAGGTAGTAGTCC 60.202 50.000 0.00 0.00 0.00 3.85
47 48 4.401519 TGCAGGATAACACAGGTAGTAGTC 59.598 45.833 0.00 0.00 0.00 2.59
48 49 4.350245 TGCAGGATAACACAGGTAGTAGT 58.650 43.478 0.00 0.00 0.00 2.73
49 50 5.339008 TTGCAGGATAACACAGGTAGTAG 57.661 43.478 0.00 0.00 0.00 2.57
50 51 5.950544 ATTGCAGGATAACACAGGTAGTA 57.049 39.130 0.00 0.00 0.00 1.82
51 52 4.844349 ATTGCAGGATAACACAGGTAGT 57.156 40.909 0.00 0.00 0.00 2.73
52 53 6.150976 TGAAAATTGCAGGATAACACAGGTAG 59.849 38.462 0.00 0.00 0.00 3.18
53 54 6.007076 TGAAAATTGCAGGATAACACAGGTA 58.993 36.000 0.00 0.00 0.00 3.08
54 55 4.832266 TGAAAATTGCAGGATAACACAGGT 59.168 37.500 0.00 0.00 0.00 4.00
55 56 5.163513 GTGAAAATTGCAGGATAACACAGG 58.836 41.667 0.00 0.00 0.00 4.00
56 57 5.771469 TGTGAAAATTGCAGGATAACACAG 58.229 37.500 0.00 0.00 33.10 3.66
57 58 5.781210 TGTGAAAATTGCAGGATAACACA 57.219 34.783 0.00 0.00 34.24 3.72
58 59 6.478344 TGTTTGTGAAAATTGCAGGATAACAC 59.522 34.615 0.00 0.00 0.00 3.32
59 60 6.478344 GTGTTTGTGAAAATTGCAGGATAACA 59.522 34.615 0.00 0.00 0.00 2.41
60 61 6.478344 TGTGTTTGTGAAAATTGCAGGATAAC 59.522 34.615 0.00 0.00 0.00 1.89
61 62 6.577103 TGTGTTTGTGAAAATTGCAGGATAA 58.423 32.000 0.00 0.00 0.00 1.75
62 63 6.154203 TGTGTTTGTGAAAATTGCAGGATA 57.846 33.333 0.00 0.00 0.00 2.59
63 64 5.021033 TGTGTTTGTGAAAATTGCAGGAT 57.979 34.783 0.00 0.00 0.00 3.24
64 65 4.462508 TGTGTTTGTGAAAATTGCAGGA 57.537 36.364 0.00 0.00 0.00 3.86
65 66 5.738118 AATGTGTTTGTGAAAATTGCAGG 57.262 34.783 0.00 0.00 0.00 4.85
66 67 7.306749 GGACTAATGTGTTTGTGAAAATTGCAG 60.307 37.037 0.00 0.00 0.00 4.41
67 68 6.478344 GGACTAATGTGTTTGTGAAAATTGCA 59.522 34.615 0.00 0.00 0.00 4.08
68 69 6.701400 AGGACTAATGTGTTTGTGAAAATTGC 59.299 34.615 0.00 0.00 0.00 3.56
69 70 8.647143 AAGGACTAATGTGTTTGTGAAAATTG 57.353 30.769 0.00 0.00 0.00 2.32
70 71 8.474025 TGAAGGACTAATGTGTTTGTGAAAATT 58.526 29.630 0.00 0.00 0.00 1.82
71 72 8.006298 TGAAGGACTAATGTGTTTGTGAAAAT 57.994 30.769 0.00 0.00 0.00 1.82
72 73 7.397892 TGAAGGACTAATGTGTTTGTGAAAA 57.602 32.000 0.00 0.00 0.00 2.29
73 74 7.254852 GTTGAAGGACTAATGTGTTTGTGAAA 58.745 34.615 0.00 0.00 0.00 2.69
74 75 6.183360 GGTTGAAGGACTAATGTGTTTGTGAA 60.183 38.462 0.00 0.00 0.00 3.18
75 76 5.298276 GGTTGAAGGACTAATGTGTTTGTGA 59.702 40.000 0.00 0.00 0.00 3.58
76 77 5.067153 TGGTTGAAGGACTAATGTGTTTGTG 59.933 40.000 0.00 0.00 0.00 3.33
77 78 5.197451 TGGTTGAAGGACTAATGTGTTTGT 58.803 37.500 0.00 0.00 0.00 2.83
78 79 5.766150 TGGTTGAAGGACTAATGTGTTTG 57.234 39.130 0.00 0.00 0.00 2.93
79 80 5.891551 ACTTGGTTGAAGGACTAATGTGTTT 59.108 36.000 0.00 0.00 35.78 2.83
80 81 5.445964 ACTTGGTTGAAGGACTAATGTGTT 58.554 37.500 0.00 0.00 35.78 3.32
81 82 5.048846 ACTTGGTTGAAGGACTAATGTGT 57.951 39.130 0.00 0.00 35.78 3.72
82 83 5.180117 CAGACTTGGTTGAAGGACTAATGTG 59.820 44.000 0.00 0.00 35.78 3.21
83 84 5.163195 ACAGACTTGGTTGAAGGACTAATGT 60.163 40.000 0.00 0.00 35.78 2.71
84 85 5.308825 ACAGACTTGGTTGAAGGACTAATG 58.691 41.667 0.00 0.00 35.78 1.90
85 86 5.552178 GACAGACTTGGTTGAAGGACTAAT 58.448 41.667 0.00 0.00 35.78 1.73
86 87 4.500887 CGACAGACTTGGTTGAAGGACTAA 60.501 45.833 0.00 0.00 35.78 2.24
87 88 3.005472 CGACAGACTTGGTTGAAGGACTA 59.995 47.826 0.00 0.00 35.78 2.59
88 89 2.224066 CGACAGACTTGGTTGAAGGACT 60.224 50.000 0.00 0.00 35.78 3.85
89 90 2.135933 CGACAGACTTGGTTGAAGGAC 58.864 52.381 0.00 0.00 35.78 3.85
90 91 1.760613 ACGACAGACTTGGTTGAAGGA 59.239 47.619 0.00 0.00 35.78 3.36
91 92 2.135933 GACGACAGACTTGGTTGAAGG 58.864 52.381 0.00 0.00 35.78 3.46
92 93 2.821546 TGACGACAGACTTGGTTGAAG 58.178 47.619 0.00 0.00 37.73 3.02
93 94 2.971660 TGACGACAGACTTGGTTGAA 57.028 45.000 0.00 0.00 0.00 2.69
94 95 2.971660 TTGACGACAGACTTGGTTGA 57.028 45.000 0.00 0.00 0.00 3.18
95 96 4.307432 AGTATTGACGACAGACTTGGTTG 58.693 43.478 0.00 0.00 0.00 3.77
96 97 4.557205 GAGTATTGACGACAGACTTGGTT 58.443 43.478 6.11 0.00 0.00 3.67
97 98 3.056749 GGAGTATTGACGACAGACTTGGT 60.057 47.826 6.11 0.00 0.00 3.67
98 99 3.056821 TGGAGTATTGACGACAGACTTGG 60.057 47.826 6.11 0.00 0.00 3.61
99 100 4.174411 TGGAGTATTGACGACAGACTTG 57.826 45.455 6.11 0.00 0.00 3.16
100 101 4.866508 TTGGAGTATTGACGACAGACTT 57.133 40.909 6.11 0.00 0.00 3.01
101 102 4.866508 TTTGGAGTATTGACGACAGACT 57.133 40.909 4.65 4.65 0.00 3.24
102 103 4.151867 GGTTTTGGAGTATTGACGACAGAC 59.848 45.833 0.00 0.00 0.00 3.51
103 104 4.202274 TGGTTTTGGAGTATTGACGACAGA 60.202 41.667 0.00 0.00 0.00 3.41
104 105 4.062293 TGGTTTTGGAGTATTGACGACAG 58.938 43.478 0.00 0.00 0.00 3.51
105 106 4.074627 TGGTTTTGGAGTATTGACGACA 57.925 40.909 0.00 0.00 0.00 4.35
106 107 4.514066 AGTTGGTTTTGGAGTATTGACGAC 59.486 41.667 0.00 0.00 0.00 4.34
107 108 4.710324 AGTTGGTTTTGGAGTATTGACGA 58.290 39.130 0.00 0.00 0.00 4.20
108 109 5.121768 CCTAGTTGGTTTTGGAGTATTGACG 59.878 44.000 0.00 0.00 0.00 4.35
109 110 5.414765 CCCTAGTTGGTTTTGGAGTATTGAC 59.585 44.000 0.00 0.00 0.00 3.18
110 111 5.515886 CCCCTAGTTGGTTTTGGAGTATTGA 60.516 44.000 0.00 0.00 0.00 2.57
111 112 4.705023 CCCCTAGTTGGTTTTGGAGTATTG 59.295 45.833 0.00 0.00 0.00 1.90
112 113 4.355889 ACCCCTAGTTGGTTTTGGAGTATT 59.644 41.667 0.00 0.00 29.75 1.89
113 114 3.920841 ACCCCTAGTTGGTTTTGGAGTAT 59.079 43.478 0.00 0.00 29.75 2.12
114 115 3.073356 CACCCCTAGTTGGTTTTGGAGTA 59.927 47.826 0.00 0.00 32.46 2.59
115 116 2.141067 ACCCCTAGTTGGTTTTGGAGT 58.859 47.619 0.00 0.00 29.75 3.85
116 117 2.514803 CACCCCTAGTTGGTTTTGGAG 58.485 52.381 0.00 0.00 32.46 3.86
117 118 1.146152 CCACCCCTAGTTGGTTTTGGA 59.854 52.381 0.00 0.00 32.46 3.53
118 119 1.627864 CCACCCCTAGTTGGTTTTGG 58.372 55.000 0.00 0.00 32.46 3.28
119 120 0.966179 GCCACCCCTAGTTGGTTTTG 59.034 55.000 0.00 0.00 32.46 2.44
120 121 0.558712 TGCCACCCCTAGTTGGTTTT 59.441 50.000 0.00 0.00 32.46 2.43
121 122 0.178973 GTGCCACCCCTAGTTGGTTT 60.179 55.000 0.00 0.00 32.46 3.27
122 123 1.065997 AGTGCCACCCCTAGTTGGTT 61.066 55.000 0.00 0.00 32.46 3.67
123 124 0.178885 TAGTGCCACCCCTAGTTGGT 60.179 55.000 0.00 0.53 36.21 3.67
124 125 0.541863 CTAGTGCCACCCCTAGTTGG 59.458 60.000 0.00 0.00 0.00 3.77
125 126 1.568504 TCTAGTGCCACCCCTAGTTG 58.431 55.000 0.00 0.00 33.81 3.16
126 127 2.119495 CATCTAGTGCCACCCCTAGTT 58.881 52.381 0.00 0.00 33.81 2.24
127 128 1.794714 CATCTAGTGCCACCCCTAGT 58.205 55.000 0.00 0.00 33.81 2.57
135 136 8.520199 CCTTAGTGTAAGTGCATCTAGTGCCA 62.520 46.154 12.71 3.24 41.73 4.92
136 137 6.193519 CCTTAGTGTAAGTGCATCTAGTGCC 61.194 48.000 12.71 6.37 41.73 5.01
137 138 4.806247 CCTTAGTGTAAGTGCATCTAGTGC 59.194 45.833 9.52 9.52 42.24 4.40
138 139 6.037098 GTCCTTAGTGTAAGTGCATCTAGTG 58.963 44.000 0.00 0.00 33.96 2.74
139 140 5.952947 AGTCCTTAGTGTAAGTGCATCTAGT 59.047 40.000 0.00 0.00 33.96 2.57
140 141 6.458232 AGTCCTTAGTGTAAGTGCATCTAG 57.542 41.667 0.00 0.00 33.96 2.43
141 142 6.663953 AGAAGTCCTTAGTGTAAGTGCATCTA 59.336 38.462 0.00 0.00 33.96 1.98
142 143 5.482175 AGAAGTCCTTAGTGTAAGTGCATCT 59.518 40.000 0.00 0.00 33.96 2.90
143 144 5.725362 AGAAGTCCTTAGTGTAAGTGCATC 58.275 41.667 0.00 0.00 33.96 3.91
144 145 5.746990 AGAAGTCCTTAGTGTAAGTGCAT 57.253 39.130 0.00 0.00 33.96 3.96
145 146 5.546621 AAGAAGTCCTTAGTGTAAGTGCA 57.453 39.130 0.00 0.00 33.96 4.57
146 147 5.989777 TCAAAGAAGTCCTTAGTGTAAGTGC 59.010 40.000 0.00 0.00 34.00 4.40
147 148 7.171678 CCTTCAAAGAAGTCCTTAGTGTAAGTG 59.828 40.741 6.08 0.00 34.00 3.16
148 149 7.217906 CCTTCAAAGAAGTCCTTAGTGTAAGT 58.782 38.462 6.08 0.00 34.00 2.24
149 150 6.147985 GCCTTCAAAGAAGTCCTTAGTGTAAG 59.852 42.308 6.08 0.00 34.00 2.34
150 151 5.995897 GCCTTCAAAGAAGTCCTTAGTGTAA 59.004 40.000 6.08 0.00 34.00 2.41
151 152 5.307196 AGCCTTCAAAGAAGTCCTTAGTGTA 59.693 40.000 6.08 0.00 34.00 2.90
152 153 4.103311 AGCCTTCAAAGAAGTCCTTAGTGT 59.897 41.667 6.08 0.00 34.00 3.55
153 154 4.646572 AGCCTTCAAAGAAGTCCTTAGTG 58.353 43.478 6.08 0.00 34.00 2.74
154 155 4.984146 AGCCTTCAAAGAAGTCCTTAGT 57.016 40.909 6.08 0.00 34.00 2.24
155 156 5.049129 CACAAGCCTTCAAAGAAGTCCTTAG 60.049 44.000 6.08 6.00 34.00 2.18
156 157 4.821805 CACAAGCCTTCAAAGAAGTCCTTA 59.178 41.667 6.08 0.00 34.00 2.69
157 158 3.633986 CACAAGCCTTCAAAGAAGTCCTT 59.366 43.478 6.08 5.41 36.47 3.36
158 159 3.217626 CACAAGCCTTCAAAGAAGTCCT 58.782 45.455 6.08 0.02 0.00 3.85
159 160 2.294512 CCACAAGCCTTCAAAGAAGTCC 59.705 50.000 6.08 0.00 0.00 3.85
160 161 2.952310 ACCACAAGCCTTCAAAGAAGTC 59.048 45.455 6.08 0.00 0.00 3.01
161 162 3.018423 ACCACAAGCCTTCAAAGAAGT 57.982 42.857 6.08 0.00 0.00 3.01
162 163 3.491447 CCAACCACAAGCCTTCAAAGAAG 60.491 47.826 0.00 0.00 0.00 2.85
163 164 2.430332 CCAACCACAAGCCTTCAAAGAA 59.570 45.455 0.00 0.00 0.00 2.52
164 165 2.031120 CCAACCACAAGCCTTCAAAGA 58.969 47.619 0.00 0.00 0.00 2.52
165 166 1.756538 ACCAACCACAAGCCTTCAAAG 59.243 47.619 0.00 0.00 0.00 2.77
204 205 3.196254 GGGACAGGAGGAAACATTACGTA 59.804 47.826 0.00 0.00 0.00 3.57
211 216 0.494551 TAGGGGGACAGGAGGAAACA 59.505 55.000 0.00 0.00 0.00 2.83
224 229 0.043637 TGTCCTAACCACCTAGGGGG 59.956 60.000 29.78 29.78 43.89 5.40
225 230 1.961133 TTGTCCTAACCACCTAGGGG 58.039 55.000 14.81 9.46 43.89 4.79
249 255 4.565652 GCTCACCAGTGAATTCTAAAGGGA 60.566 45.833 7.05 0.00 39.39 4.20
254 260 2.642311 TGGGCTCACCAGTGAATTCTAA 59.358 45.455 7.05 0.00 46.80 2.10
268 274 1.064463 GGAGACAAATCCATGGGCTCA 60.064 52.381 13.02 0.00 39.34 4.26
275 281 1.213926 GCAGAGGGGAGACAAATCCAT 59.786 52.381 0.00 0.00 41.52 3.41
384 391 0.249120 TCTGCCCTAACATCACACCG 59.751 55.000 0.00 0.00 0.00 4.94
394 401 1.141019 GCGTCATCGTCTGCCCTAA 59.859 57.895 0.00 0.00 39.49 2.69
400 407 2.270275 AGAAGAAGCGTCATCGTCTG 57.730 50.000 1.61 0.00 34.91 3.51
442 449 0.685660 GGACGAACTTGAGGAGGGTT 59.314 55.000 0.00 0.00 0.00 4.11
462 470 2.007049 GCTCGTCGACCACATCCAAAT 61.007 52.381 10.58 0.00 0.00 2.32
472 480 1.303799 TACACTGGAGCTCGTCGACC 61.304 60.000 10.58 0.00 0.00 4.79
544 552 9.810545 GATCTTAAGCATCTAACACTAACTCTT 57.189 33.333 0.00 0.00 0.00 2.85
551 559 7.730084 TGCATAGATCTTAAGCATCTAACACT 58.270 34.615 19.56 8.26 36.62 3.55
556 564 6.214208 ACCCATGCATAGATCTTAAGCATCTA 59.786 38.462 19.93 18.67 43.43 1.98
617 625 3.833650 TGATAGTTCCACGTGTCCCTAAA 59.166 43.478 15.65 1.93 0.00 1.85
661 669 0.668535 GTTGTTGTTGCTCTCCACCC 59.331 55.000 0.00 0.00 0.00 4.61
667 675 0.248054 CGCGTTGTTGTTGTTGCTCT 60.248 50.000 0.00 0.00 0.00 4.09
673 681 2.704616 CGGACGCGTTGTTGTTGT 59.295 55.556 15.53 0.00 0.00 3.32
689 697 2.277884 CCGCCAAAATAAGCCGCG 60.278 61.111 0.00 0.00 42.37 6.46
863 1035 4.532834 TCTGAATATTAAGGGCCGCTTTT 58.467 39.130 11.15 1.12 0.00 2.27
1074 1250 3.961414 TCCAGAACCCCAACGCCC 61.961 66.667 0.00 0.00 0.00 6.13
1360 1536 2.280524 CCAGTGGTCAACGGCGAA 60.281 61.111 16.62 0.00 0.00 4.70
1500 1676 2.606519 TAGTGCCGGCCCAGAAGT 60.607 61.111 26.77 10.40 0.00 3.01
1659 1850 4.050553 ACAAACGTGAATCAATTGCAAGG 58.949 39.130 4.94 0.00 0.00 3.61
1688 1879 2.869801 TCAAGCACTAACAAGAACACGG 59.130 45.455 0.00 0.00 0.00 4.94
1690 1881 5.064707 TCAGTTCAAGCACTAACAAGAACAC 59.935 40.000 0.00 0.00 38.18 3.32
1695 1886 5.468072 ACTCATCAGTTCAAGCACTAACAAG 59.532 40.000 0.00 0.00 0.00 3.16
1699 1890 5.582269 GCATACTCATCAGTTCAAGCACTAA 59.418 40.000 0.00 0.00 33.62 2.24
1768 1972 5.385617 CAGCAACTGTACTCATAAAAGTGC 58.614 41.667 0.00 0.00 33.06 4.40
1769 1973 5.470098 ACCAGCAACTGTACTCATAAAAGTG 59.530 40.000 0.00 0.00 0.00 3.16
1770 1974 5.621193 ACCAGCAACTGTACTCATAAAAGT 58.379 37.500 0.00 0.00 0.00 2.66
1771 1975 7.097192 TCTACCAGCAACTGTACTCATAAAAG 58.903 38.462 0.00 0.00 0.00 2.27
1774 1985 6.406961 CCATCTACCAGCAACTGTACTCATAA 60.407 42.308 0.00 0.00 0.00 1.90
1785 1996 0.676782 AACCGCCATCTACCAGCAAC 60.677 55.000 0.00 0.00 0.00 4.17
1789 2000 2.280628 GAAGAAACCGCCATCTACCAG 58.719 52.381 0.00 0.00 0.00 4.00
1794 2005 3.356529 AAGATGAAGAAACCGCCATCT 57.643 42.857 0.00 0.00 45.25 2.90
1800 2011 8.020819 TGCAATAACTAAAAGATGAAGAAACCG 58.979 33.333 0.00 0.00 0.00 4.44
1816 2027 9.190858 GTTGTCAATTGTCATTTGCAATAACTA 57.809 29.630 0.00 0.00 35.73 2.24
1888 2102 5.109903 CAACGTAAATCTAGCTAGCACCTT 58.890 41.667 18.83 8.43 0.00 3.50
1921 2135 3.834489 AACCAATGTTTCCAATGCACA 57.166 38.095 0.00 0.00 0.00 4.57
1971 2185 0.615331 CAGAAGAGCTGCCTACCCAA 59.385 55.000 0.00 0.00 37.90 4.12
1999 2213 3.120338 GCATAAGCAACTACGCTGTGAAA 60.120 43.478 0.00 0.00 42.89 2.69
2006 2220 2.927477 TGTGTAGCATAAGCAACTACGC 59.073 45.455 6.11 6.11 45.49 4.42
2020 2234 9.685828 TCCATTTTACAAAAAGTATTGTGTAGC 57.314 29.630 3.10 0.00 43.13 3.58
2029 2243 9.030452 ACCAGCATATCCATTTTACAAAAAGTA 57.970 29.630 0.00 0.00 0.00 2.24
2031 2245 9.520204 CTACCAGCATATCCATTTTACAAAAAG 57.480 33.333 0.00 0.00 0.00 2.27
2032 2246 7.978975 GCTACCAGCATATCCATTTTACAAAAA 59.021 33.333 0.00 0.00 41.89 1.94
2033 2247 7.488322 GCTACCAGCATATCCATTTTACAAAA 58.512 34.615 0.00 0.00 41.89 2.44
2070 2287 9.070179 TGACAGATCAAATTGGTATGGAATATG 57.930 33.333 5.82 0.00 0.00 1.78
2080 2299 5.630121 TGTAACCTGACAGATCAAATTGGT 58.370 37.500 3.32 0.00 32.44 3.67
2091 2310 3.254060 CCACTCGAATGTAACCTGACAG 58.746 50.000 0.00 0.00 31.51 3.51
2110 2329 5.412594 CAGCTGATAGCACTTCTTAAAACCA 59.587 40.000 8.42 0.00 45.56 3.67
2113 2332 5.003160 TGCAGCTGATAGCACTTCTTAAAA 58.997 37.500 20.43 0.00 45.56 1.52
2144 2363 1.349026 CAGGTGCCCTTTTCTGAGAGA 59.651 52.381 0.00 0.00 0.00 3.10
2168 2387 8.012957 AGAGTGAACAGACTAATATAACTGGG 57.987 38.462 0.00 0.00 35.08 4.45
2357 2578 1.043116 TCTCATCCGGGATTGTCGCT 61.043 55.000 6.84 0.00 0.00 4.93
2407 2628 0.248866 AAAGGTCTTGCGGCAAAACG 60.249 50.000 17.13 5.50 0.00 3.60
2443 2664 5.966636 TTGTTACTGTAGCTGATTATGCG 57.033 39.130 0.00 0.00 35.28 4.73
2444 2665 8.066595 CAGAATTGTTACTGTAGCTGATTATGC 58.933 37.037 0.00 0.00 0.00 3.14
2576 2816 5.408880 TCGGAACAATCAGTACAATGGTA 57.591 39.130 0.00 0.00 0.00 3.25
2577 2817 4.280436 TCGGAACAATCAGTACAATGGT 57.720 40.909 0.00 0.00 0.00 3.55
2578 2818 4.875536 TCATCGGAACAATCAGTACAATGG 59.124 41.667 0.00 0.00 0.00 3.16
2579 2819 6.424683 CATCATCGGAACAATCAGTACAATG 58.575 40.000 0.00 0.00 0.00 2.82
2580 2820 5.008019 GCATCATCGGAACAATCAGTACAAT 59.992 40.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.