Multiple sequence alignment - TraesCS1D01G359700

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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 TraesCS1D01G359700 chr1D 100.000 2303 0 0 1 2303 443107825 443110127 0.000000e+00 4253
1 TraesCS1D01G359700 chr3D 93.763 1956 102 8 351 2303 55541117 55543055 0.000000e+00 2918
2 TraesCS1D01G359700 chr3D 94.365 1810 86 8 503 2303 2390486 2392288 0.000000e+00 2763
3 TraesCS1D01G359700 chr3D 95.460 1718 74 3 588 2303 571522087 571520372 0.000000e+00 2737
4 TraesCS1D01G359700 chr5D 97.909 1626 32 1 680 2303 371076650 371075025 0.000000e+00 2813
5 TraesCS1D01G359700 chr5D 97.093 1617 44 2 689 2303 193611367 193609752 0.000000e+00 2723
6 TraesCS1D01G359700 chr5D 94.504 1692 83 5 615 2303 417810466 417812150 0.000000e+00 2601
7 TraesCS1D01G359700 chr5D 97.486 358 9 0 2 359 552400754 552400397 1.510000e-171 612
8 TraesCS1D01G359700 chr2B 91.441 1916 125 21 257 2140 25567971 25569879 0.000000e+00 2593
9 TraesCS1D01G359700 chr7D 94.128 1703 96 3 603 2303 501413764 501412064 0.000000e+00 2588
10 TraesCS1D01G359700 chr7D 97.493 359 9 0 1 359 102558292 102558650 4.210000e-172 614
11 TraesCS1D01G359700 chr7D 97.214 359 10 0 1 359 397981352 397980994 1.960000e-170 608
12 TraesCS1D01G359700 chr7D 97.214 359 10 0 1 359 613117852 613117494 1.960000e-170 608
13 TraesCS1D01G359700 chr7D 96.936 359 11 0 1 359 230438115 230438473 9.100000e-169 603
14 TraesCS1D01G359700 chr7A 90.413 1961 146 27 351 2303 548053932 548055858 0.000000e+00 2542
15 TraesCS1D01G359700 chr7A 91.279 1525 77 23 351 1867 105259016 105260492 0.000000e+00 2028
16 TraesCS1D01G359700 chr4D 93.697 1666 97 6 640 2303 98461706 98460047 0.000000e+00 2488
17 TraesCS1D01G359700 chr4D 97.303 482 10 2 351 829 11926559 11927040 0.000000e+00 815
18 TraesCS1D01G359700 chr4D 96.936 359 11 0 1 359 85738946 85739304 9.100000e-169 603
19 TraesCS1D01G359700 chr3B 92.796 1527 85 18 351 1870 532656799 532658307 0.000000e+00 2187
20 TraesCS1D01G359700 chr3B 88.336 1689 119 33 351 2020 149237855 149239484 0.000000e+00 1956
21 TraesCS1D01G359700 chr2A 89.061 1682 114 26 351 2020 145432535 145434158 0.000000e+00 2023
22 TraesCS1D01G359700 chr2D 97.207 358 10 0 2 359 516816902 516817259 7.040000e-170 606
23 TraesCS1D01G359700 chr2D 96.936 359 11 0 1 359 2883954 2883596 9.100000e-169 603
24 TraesCS1D01G359700 chr2D 96.936 359 11 0 1 359 166115137 166115495 9.100000e-169 603


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 TraesCS1D01G359700 chr1D 443107825 443110127 2302 False 4253 4253 100.000 1 2303 1 chr1D.!!$F1 2302
1 TraesCS1D01G359700 chr3D 55541117 55543055 1938 False 2918 2918 93.763 351 2303 1 chr3D.!!$F2 1952
2 TraesCS1D01G359700 chr3D 2390486 2392288 1802 False 2763 2763 94.365 503 2303 1 chr3D.!!$F1 1800
3 TraesCS1D01G359700 chr3D 571520372 571522087 1715 True 2737 2737 95.460 588 2303 1 chr3D.!!$R1 1715
4 TraesCS1D01G359700 chr5D 371075025 371076650 1625 True 2813 2813 97.909 680 2303 1 chr5D.!!$R2 1623
5 TraesCS1D01G359700 chr5D 193609752 193611367 1615 True 2723 2723 97.093 689 2303 1 chr5D.!!$R1 1614
6 TraesCS1D01G359700 chr5D 417810466 417812150 1684 False 2601 2601 94.504 615 2303 1 chr5D.!!$F1 1688
7 TraesCS1D01G359700 chr2B 25567971 25569879 1908 False 2593 2593 91.441 257 2140 1 chr2B.!!$F1 1883
8 TraesCS1D01G359700 chr7D 501412064 501413764 1700 True 2588 2588 94.128 603 2303 1 chr7D.!!$R2 1700
9 TraesCS1D01G359700 chr7A 548053932 548055858 1926 False 2542 2542 90.413 351 2303 1 chr7A.!!$F2 1952
10 TraesCS1D01G359700 chr7A 105259016 105260492 1476 False 2028 2028 91.279 351 1867 1 chr7A.!!$F1 1516
11 TraesCS1D01G359700 chr4D 98460047 98461706 1659 True 2488 2488 93.697 640 2303 1 chr4D.!!$R1 1663
12 TraesCS1D01G359700 chr3B 532656799 532658307 1508 False 2187 2187 92.796 351 1870 1 chr3B.!!$F2 1519
13 TraesCS1D01G359700 chr3B 149237855 149239484 1629 False 1956 1956 88.336 351 2020 1 chr3B.!!$F1 1669
14 TraesCS1D01G359700 chr2A 145432535 145434158 1623 False 2023 2023 89.061 351 2020 1 chr2A.!!$F1 1669

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
246 247 0.107459 GTGCAGGGCCTCTTCCTTAG 60.107 60.0 0.95 0.0 31.06 2.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2114 2161 0.038618 TGCACAGTACAGTGTAGCGG 60.039 55.0 18.32 2.78 41.52 5.52 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 9.281075 CAATGTTTGTGTATGACTATGTGATTG 57.719 33.333 0.00 0.00 0.00 2.67
27 28 7.376435 TGTTTGTGTATGACTATGTGATTGG 57.624 36.000 0.00 0.00 0.00 3.16
28 29 7.164803 TGTTTGTGTATGACTATGTGATTGGA 58.835 34.615 0.00 0.00 0.00 3.53
29 30 7.119116 TGTTTGTGTATGACTATGTGATTGGAC 59.881 37.037 0.00 0.00 0.00 4.02
30 31 6.544928 TGTGTATGACTATGTGATTGGACT 57.455 37.500 0.00 0.00 0.00 3.85
31 32 7.654022 TGTGTATGACTATGTGATTGGACTA 57.346 36.000 0.00 0.00 0.00 2.59
32 33 7.489160 TGTGTATGACTATGTGATTGGACTAC 58.511 38.462 0.00 0.00 0.00 2.73
33 34 7.342026 TGTGTATGACTATGTGATTGGACTACT 59.658 37.037 0.00 0.00 0.00 2.57
34 35 7.863375 GTGTATGACTATGTGATTGGACTACTC 59.137 40.741 0.00 0.00 0.00 2.59
35 36 7.780271 TGTATGACTATGTGATTGGACTACTCT 59.220 37.037 0.00 0.00 0.00 3.24
36 37 9.286170 GTATGACTATGTGATTGGACTACTCTA 57.714 37.037 0.00 0.00 0.00 2.43
37 38 8.948401 ATGACTATGTGATTGGACTACTCTAT 57.052 34.615 0.00 0.00 0.00 1.98
38 39 8.768501 TGACTATGTGATTGGACTACTCTATT 57.231 34.615 0.00 0.00 0.00 1.73
39 40 8.633561 TGACTATGTGATTGGACTACTCTATTG 58.366 37.037 0.00 0.00 0.00 1.90
40 41 7.437748 ACTATGTGATTGGACTACTCTATTGC 58.562 38.462 0.00 0.00 0.00 3.56
41 42 5.939764 TGTGATTGGACTACTCTATTGCT 57.060 39.130 0.00 0.00 0.00 3.91
42 43 7.603180 ATGTGATTGGACTACTCTATTGCTA 57.397 36.000 0.00 0.00 0.00 3.49
43 44 7.603180 TGTGATTGGACTACTCTATTGCTAT 57.397 36.000 0.00 0.00 0.00 2.97
44 45 7.436933 TGTGATTGGACTACTCTATTGCTATG 58.563 38.462 0.00 0.00 0.00 2.23
45 46 7.069950 TGTGATTGGACTACTCTATTGCTATGT 59.930 37.037 0.00 0.00 0.00 2.29
46 47 7.383572 GTGATTGGACTACTCTATTGCTATGTG 59.616 40.741 0.00 0.00 0.00 3.21
47 48 6.791867 TTGGACTACTCTATTGCTATGTGT 57.208 37.500 0.00 0.00 0.00 3.72
48 49 6.149129 TGGACTACTCTATTGCTATGTGTG 57.851 41.667 0.00 0.00 0.00 3.82
49 50 5.656859 TGGACTACTCTATTGCTATGTGTGT 59.343 40.000 0.00 0.00 0.00 3.72
50 51 6.831868 TGGACTACTCTATTGCTATGTGTGTA 59.168 38.462 0.00 0.00 0.00 2.90
51 52 7.505923 TGGACTACTCTATTGCTATGTGTGTAT 59.494 37.037 0.00 0.00 0.00 2.29
52 53 7.810282 GGACTACTCTATTGCTATGTGTGTATG 59.190 40.741 0.00 0.00 0.00 2.39
53 54 8.465273 ACTACTCTATTGCTATGTGTGTATGA 57.535 34.615 0.00 0.00 0.00 2.15
54 55 8.572185 ACTACTCTATTGCTATGTGTGTATGAG 58.428 37.037 0.00 0.00 0.00 2.90
55 56 7.353414 ACTCTATTGCTATGTGTGTATGAGT 57.647 36.000 0.00 0.00 0.00 3.41
56 57 8.465273 ACTCTATTGCTATGTGTGTATGAGTA 57.535 34.615 0.00 0.00 0.00 2.59
57 58 9.083422 ACTCTATTGCTATGTGTGTATGAGTAT 57.917 33.333 0.00 0.00 0.00 2.12
58 59 9.351570 CTCTATTGCTATGTGTGTATGAGTATG 57.648 37.037 0.00 0.00 0.00 2.39
59 60 8.860088 TCTATTGCTATGTGTGTATGAGTATGT 58.140 33.333 0.00 0.00 0.00 2.29
60 61 7.719778 ATTGCTATGTGTGTATGAGTATGTG 57.280 36.000 0.00 0.00 0.00 3.21
61 62 6.463995 TGCTATGTGTGTATGAGTATGTGA 57.536 37.500 0.00 0.00 0.00 3.58
62 63 7.054491 TGCTATGTGTGTATGAGTATGTGAT 57.946 36.000 0.00 0.00 0.00 3.06
63 64 7.500141 TGCTATGTGTGTATGAGTATGTGATT 58.500 34.615 0.00 0.00 0.00 2.57
64 65 7.986889 TGCTATGTGTGTATGAGTATGTGATTT 59.013 33.333 0.00 0.00 0.00 2.17
65 66 8.278408 GCTATGTGTGTATGAGTATGTGATTTG 58.722 37.037 0.00 0.00 0.00 2.32
66 67 6.983474 TGTGTGTATGAGTATGTGATTTGG 57.017 37.500 0.00 0.00 0.00 3.28
67 68 6.706295 TGTGTGTATGAGTATGTGATTTGGA 58.294 36.000 0.00 0.00 0.00 3.53
68 69 6.593770 TGTGTGTATGAGTATGTGATTTGGAC 59.406 38.462 0.00 0.00 0.00 4.02
69 70 6.818644 GTGTGTATGAGTATGTGATTTGGACT 59.181 38.462 0.00 0.00 0.00 3.85
70 71 7.979537 GTGTGTATGAGTATGTGATTTGGACTA 59.020 37.037 0.00 0.00 0.00 2.59
71 72 7.979537 TGTGTATGAGTATGTGATTTGGACTAC 59.020 37.037 0.00 0.00 0.00 2.73
72 73 8.198109 GTGTATGAGTATGTGATTTGGACTACT 58.802 37.037 0.00 0.00 0.00 2.57
73 74 9.416284 TGTATGAGTATGTGATTTGGACTACTA 57.584 33.333 0.00 0.00 0.00 1.82
80 81 7.969536 ATGTGATTTGGACTACTATATGTGC 57.030 36.000 0.00 0.00 0.00 4.57
81 82 7.124573 TGTGATTTGGACTACTATATGTGCT 57.875 36.000 0.00 0.00 0.00 4.40
82 83 8.245195 TGTGATTTGGACTACTATATGTGCTA 57.755 34.615 0.00 0.00 0.00 3.49
83 84 8.870116 TGTGATTTGGACTACTATATGTGCTAT 58.130 33.333 0.00 0.00 0.00 2.97
84 85 9.144747 GTGATTTGGACTACTATATGTGCTATG 57.855 37.037 0.00 0.00 0.00 2.23
85 86 8.870116 TGATTTGGACTACTATATGTGCTATGT 58.130 33.333 0.00 0.00 0.00 2.29
86 87 9.360093 GATTTGGACTACTATATGTGCTATGTC 57.640 37.037 0.00 0.00 0.00 3.06
87 88 8.478775 TTTGGACTACTATATGTGCTATGTCT 57.521 34.615 0.00 0.00 0.00 3.41
88 89 8.478775 TTGGACTACTATATGTGCTATGTCTT 57.521 34.615 0.00 0.00 0.00 3.01
89 90 8.112016 TGGACTACTATATGTGCTATGTCTTC 57.888 38.462 0.00 0.00 0.00 2.87
90 91 7.945109 TGGACTACTATATGTGCTATGTCTTCT 59.055 37.037 0.00 0.00 0.00 2.85
91 92 8.798402 GGACTACTATATGTGCTATGTCTTCTT 58.202 37.037 0.00 0.00 0.00 2.52
96 97 8.700051 ACTATATGTGCTATGTCTTCTTTCTGT 58.300 33.333 0.00 0.00 0.00 3.41
97 98 7.783090 ATATGTGCTATGTCTTCTTTCTGTG 57.217 36.000 0.00 0.00 0.00 3.66
98 99 4.960938 TGTGCTATGTCTTCTTTCTGTGT 58.039 39.130 0.00 0.00 0.00 3.72
99 100 5.368145 TGTGCTATGTCTTCTTTCTGTGTT 58.632 37.500 0.00 0.00 0.00 3.32
100 101 5.822519 TGTGCTATGTCTTCTTTCTGTGTTT 59.177 36.000 0.00 0.00 0.00 2.83
101 102 6.318648 TGTGCTATGTCTTCTTTCTGTGTTTT 59.681 34.615 0.00 0.00 0.00 2.43
102 103 6.634436 GTGCTATGTCTTCTTTCTGTGTTTTG 59.366 38.462 0.00 0.00 0.00 2.44
103 104 6.145535 GCTATGTCTTCTTTCTGTGTTTTGG 58.854 40.000 0.00 0.00 0.00 3.28
104 105 6.017109 GCTATGTCTTCTTTCTGTGTTTTGGA 60.017 38.462 0.00 0.00 0.00 3.53
105 106 5.560966 TGTCTTCTTTCTGTGTTTTGGAC 57.439 39.130 0.00 0.00 0.00 4.02
106 107 5.253330 TGTCTTCTTTCTGTGTTTTGGACT 58.747 37.500 0.00 0.00 0.00 3.85
107 108 6.411376 TGTCTTCTTTCTGTGTTTTGGACTA 58.589 36.000 0.00 0.00 0.00 2.59
108 109 6.315393 TGTCTTCTTTCTGTGTTTTGGACTAC 59.685 38.462 0.00 0.00 0.00 2.73
109 110 6.539103 GTCTTCTTTCTGTGTTTTGGACTACT 59.461 38.462 0.00 0.00 0.00 2.57
110 111 7.709613 GTCTTCTTTCTGTGTTTTGGACTACTA 59.290 37.037 0.00 0.00 0.00 1.82
111 112 7.709613 TCTTCTTTCTGTGTTTTGGACTACTAC 59.290 37.037 0.00 0.00 0.00 2.73
112 113 6.880484 TCTTTCTGTGTTTTGGACTACTACA 58.120 36.000 0.00 0.00 0.00 2.74
113 114 7.506114 TCTTTCTGTGTTTTGGACTACTACAT 58.494 34.615 0.00 0.00 0.00 2.29
114 115 7.441157 TCTTTCTGTGTTTTGGACTACTACATG 59.559 37.037 0.00 0.00 0.00 3.21
115 116 6.169557 TCTGTGTTTTGGACTACTACATGT 57.830 37.500 2.69 2.69 0.00 3.21
116 117 5.989168 TCTGTGTTTTGGACTACTACATGTG 59.011 40.000 9.11 0.93 0.00 3.21
117 118 5.919755 TGTGTTTTGGACTACTACATGTGA 58.080 37.500 9.11 0.00 0.00 3.58
118 119 6.530120 TGTGTTTTGGACTACTACATGTGAT 58.470 36.000 9.11 0.00 0.00 3.06
119 120 6.995686 TGTGTTTTGGACTACTACATGTGATT 59.004 34.615 9.11 0.00 0.00 2.57
120 121 7.500892 TGTGTTTTGGACTACTACATGTGATTT 59.499 33.333 9.11 0.00 0.00 2.17
121 122 7.803189 GTGTTTTGGACTACTACATGTGATTTG 59.197 37.037 9.11 0.00 0.00 2.32
122 123 7.040755 TGTTTTGGACTACTACATGTGATTTGG 60.041 37.037 9.11 0.00 0.00 3.28
123 124 6.367374 TTGGACTACTACATGTGATTTGGA 57.633 37.500 9.11 0.00 0.00 3.53
124 125 6.560003 TGGACTACTACATGTGATTTGGAT 57.440 37.500 9.11 0.00 0.00 3.41
125 126 7.669089 TGGACTACTACATGTGATTTGGATA 57.331 36.000 9.11 0.00 0.00 2.59
126 127 8.262601 TGGACTACTACATGTGATTTGGATAT 57.737 34.615 9.11 0.00 0.00 1.63
127 128 8.150296 TGGACTACTACATGTGATTTGGATATG 58.850 37.037 9.11 0.00 0.00 1.78
128 129 8.367911 GGACTACTACATGTGATTTGGATATGA 58.632 37.037 9.11 0.00 0.00 2.15
129 130 9.935241 GACTACTACATGTGATTTGGATATGAT 57.065 33.333 9.11 0.00 0.00 2.45
136 137 8.301720 ACATGTGATTTGGATATGATTATGTGC 58.698 33.333 0.00 0.00 0.00 4.57
137 138 7.218228 TGTGATTTGGATATGATTATGTGCC 57.782 36.000 0.00 0.00 0.00 5.01
138 139 6.776603 TGTGATTTGGATATGATTATGTGCCA 59.223 34.615 0.00 0.00 0.00 4.92
139 140 7.452189 TGTGATTTGGATATGATTATGTGCCAT 59.548 33.333 0.00 0.00 0.00 4.40
140 141 7.972277 GTGATTTGGATATGATTATGTGCCATC 59.028 37.037 0.00 0.00 0.00 3.51
141 142 7.891712 TGATTTGGATATGATTATGTGCCATCT 59.108 33.333 0.00 0.00 0.00 2.90
142 143 9.399797 GATTTGGATATGATTATGTGCCATCTA 57.600 33.333 0.00 0.00 0.00 1.98
143 144 9.931698 ATTTGGATATGATTATGTGCCATCTAT 57.068 29.630 0.00 0.00 0.00 1.98
144 145 8.741603 TTGGATATGATTATGTGCCATCTATG 57.258 34.615 0.00 0.00 0.00 2.23
145 146 7.864770 TGGATATGATTATGTGCCATCTATGT 58.135 34.615 0.00 0.00 0.00 2.29
146 147 7.771826 TGGATATGATTATGTGCCATCTATGTG 59.228 37.037 0.00 0.00 0.00 3.21
147 148 7.989170 GGATATGATTATGTGCCATCTATGTGA 59.011 37.037 0.00 0.00 0.00 3.58
148 149 9.387257 GATATGATTATGTGCCATCTATGTGAA 57.613 33.333 0.00 0.00 0.00 3.18
149 150 9.916360 ATATGATTATGTGCCATCTATGTGAAT 57.084 29.630 0.00 0.00 0.00 2.57
150 151 7.677454 TGATTATGTGCCATCTATGTGAATC 57.323 36.000 0.00 0.00 0.00 2.52
151 152 7.225725 TGATTATGTGCCATCTATGTGAATCA 58.774 34.615 0.00 0.00 0.00 2.57
152 153 6.866010 TTATGTGCCATCTATGTGAATCAC 57.134 37.500 6.41 6.41 34.56 3.06
168 169 7.904094 TGTGAATCACAAAACATAAAAAGCAC 58.096 30.769 14.37 0.00 41.69 4.40
169 170 7.763528 TGTGAATCACAAAACATAAAAAGCACT 59.236 29.630 14.37 0.00 41.69 4.40
170 171 8.603181 GTGAATCACAAAACATAAAAAGCACTT 58.397 29.630 8.74 0.00 34.08 3.16
171 172 9.160496 TGAATCACAAAACATAAAAAGCACTTT 57.840 25.926 0.00 0.00 0.00 2.66
172 173 9.424659 GAATCACAAAACATAAAAAGCACTTTG 57.575 29.630 0.00 0.00 32.36 2.77
173 174 7.897575 TCACAAAACATAAAAAGCACTTTGT 57.102 28.000 0.00 0.00 36.29 2.83
174 175 8.988064 TCACAAAACATAAAAAGCACTTTGTA 57.012 26.923 0.00 0.00 34.65 2.41
175 176 9.593134 TCACAAAACATAAAAAGCACTTTGTAT 57.407 25.926 0.76 0.76 34.26 2.29
186 187 6.588348 AAGCACTTTGTATTTGAAAACAGC 57.412 33.333 0.00 0.00 0.00 4.40
187 188 5.659463 AGCACTTTGTATTTGAAAACAGCA 58.341 33.333 0.00 0.00 0.00 4.41
188 189 5.750067 AGCACTTTGTATTTGAAAACAGCAG 59.250 36.000 0.00 0.00 0.00 4.24
189 190 5.748152 GCACTTTGTATTTGAAAACAGCAGA 59.252 36.000 0.00 0.00 0.00 4.26
190 191 6.255453 GCACTTTGTATTTGAAAACAGCAGAA 59.745 34.615 0.00 0.00 0.00 3.02
191 192 7.201513 GCACTTTGTATTTGAAAACAGCAGAAA 60.202 33.333 0.00 0.00 0.00 2.52
192 193 8.323140 CACTTTGTATTTGAAAACAGCAGAAAG 58.677 33.333 0.00 0.00 0.00 2.62
193 194 8.034804 ACTTTGTATTTGAAAACAGCAGAAAGT 58.965 29.630 0.00 0.00 0.00 2.66
194 195 7.754069 TTGTATTTGAAAACAGCAGAAAGTG 57.246 32.000 0.00 0.00 0.00 3.16
195 196 6.862209 TGTATTTGAAAACAGCAGAAAGTGT 58.138 32.000 0.00 0.00 0.00 3.55
196 197 7.990917 TGTATTTGAAAACAGCAGAAAGTGTA 58.009 30.769 0.00 0.00 0.00 2.90
197 198 8.128582 TGTATTTGAAAACAGCAGAAAGTGTAG 58.871 33.333 0.00 0.00 0.00 2.74
198 199 4.552166 TGAAAACAGCAGAAAGTGTAGC 57.448 40.909 0.00 0.00 0.00 3.58
199 200 3.002246 TGAAAACAGCAGAAAGTGTAGCG 59.998 43.478 0.00 0.00 0.00 4.26
200 201 0.868406 AACAGCAGAAAGTGTAGCGC 59.132 50.000 0.00 0.00 0.00 5.92
201 202 0.951040 ACAGCAGAAAGTGTAGCGCC 60.951 55.000 2.29 0.00 0.00 6.53
202 203 0.671781 CAGCAGAAAGTGTAGCGCCT 60.672 55.000 2.29 0.00 0.00 5.52
203 204 0.895530 AGCAGAAAGTGTAGCGCCTA 59.104 50.000 2.29 0.00 0.00 3.93
204 205 1.275291 AGCAGAAAGTGTAGCGCCTAA 59.725 47.619 2.29 0.00 0.00 2.69
205 206 1.661112 GCAGAAAGTGTAGCGCCTAAG 59.339 52.381 2.29 0.00 0.00 2.18
206 207 2.271800 CAGAAAGTGTAGCGCCTAAGG 58.728 52.381 2.29 0.00 0.00 2.69
207 208 1.207329 AGAAAGTGTAGCGCCTAAGGG 59.793 52.381 2.29 0.00 0.00 3.95
208 209 0.981943 AAAGTGTAGCGCCTAAGGGT 59.018 50.000 2.29 0.00 34.45 4.34
209 210 1.856629 AAGTGTAGCGCCTAAGGGTA 58.143 50.000 2.29 0.00 34.45 3.69
210 211 1.856629 AGTGTAGCGCCTAAGGGTAA 58.143 50.000 2.29 0.00 34.45 2.85
211 212 1.755380 AGTGTAGCGCCTAAGGGTAAG 59.245 52.381 2.29 0.00 34.45 2.34
212 213 1.117150 TGTAGCGCCTAAGGGTAAGG 58.883 55.000 2.29 0.00 37.17 2.69
217 218 3.316029 CCTAAGGGTAAGGCGCCA 58.684 61.111 31.54 5.56 0.00 5.69
218 219 1.153229 CCTAAGGGTAAGGCGCCAC 60.153 63.158 31.54 19.41 0.00 5.01
219 220 1.600107 CTAAGGGTAAGGCGCCACA 59.400 57.895 31.54 13.31 0.00 4.17
220 221 0.743345 CTAAGGGTAAGGCGCCACAC 60.743 60.000 31.54 24.47 0.00 3.82
221 222 1.196104 TAAGGGTAAGGCGCCACACT 61.196 55.000 31.54 23.08 0.00 3.55
222 223 1.196104 AAGGGTAAGGCGCCACACTA 61.196 55.000 31.54 11.39 0.00 2.74
223 224 1.449070 GGGTAAGGCGCCACACTAC 60.449 63.158 31.54 21.85 0.00 2.73
224 225 1.595357 GGTAAGGCGCCACACTACT 59.405 57.895 31.54 1.71 0.00 2.57
225 226 0.459759 GGTAAGGCGCCACACTACTC 60.460 60.000 31.54 13.25 0.00 2.59
226 227 0.245539 GTAAGGCGCCACACTACTCA 59.754 55.000 31.54 0.00 0.00 3.41
227 228 0.530744 TAAGGCGCCACACTACTCAG 59.469 55.000 31.54 0.00 0.00 3.35
228 229 1.472662 AAGGCGCCACACTACTCAGT 61.473 55.000 31.54 0.00 34.42 3.41
235 236 4.606071 CACTACTCAGTGCAGGGC 57.394 61.111 0.00 0.00 45.44 5.19
236 237 1.078848 CACTACTCAGTGCAGGGCC 60.079 63.158 0.00 0.00 45.44 5.80
237 238 1.229336 ACTACTCAGTGCAGGGCCT 60.229 57.895 0.00 0.00 32.25 5.19
238 239 1.261238 ACTACTCAGTGCAGGGCCTC 61.261 60.000 0.95 0.00 32.25 4.70
239 240 0.975040 CTACTCAGTGCAGGGCCTCT 60.975 60.000 0.95 0.00 0.00 3.69
240 241 0.545309 TACTCAGTGCAGGGCCTCTT 60.545 55.000 0.95 0.00 0.00 2.85
241 242 1.078567 CTCAGTGCAGGGCCTCTTC 60.079 63.158 0.95 0.00 0.00 2.87
242 243 2.045536 CAGTGCAGGGCCTCTTCC 60.046 66.667 0.95 0.00 0.00 3.46
243 244 2.204059 AGTGCAGGGCCTCTTCCT 60.204 61.111 0.95 0.00 34.39 3.36
244 245 1.849823 AGTGCAGGGCCTCTTCCTT 60.850 57.895 0.95 0.00 31.06 3.36
245 246 0.547712 AGTGCAGGGCCTCTTCCTTA 60.548 55.000 0.95 0.00 31.06 2.69
246 247 0.107459 GTGCAGGGCCTCTTCCTTAG 60.107 60.000 0.95 0.00 31.06 2.18
247 248 1.274703 TGCAGGGCCTCTTCCTTAGG 61.275 60.000 0.95 0.00 37.17 2.69
252 253 4.844420 CCTCTTCCTTAGGCGCTG 57.156 61.111 7.64 0.00 0.00 5.18
253 254 1.522580 CCTCTTCCTTAGGCGCTGC 60.523 63.158 7.64 0.00 0.00 5.25
254 255 1.219124 CTCTTCCTTAGGCGCTGCA 59.781 57.895 7.64 0.00 0.00 4.41
255 256 0.179062 CTCTTCCTTAGGCGCTGCAT 60.179 55.000 7.64 0.00 0.00 3.96
259 260 0.389391 TCCTTAGGCGCTGCATACTC 59.611 55.000 7.64 0.00 0.00 2.59
266 267 0.579156 GCGCTGCATACTCACTTAGC 59.421 55.000 0.00 0.00 0.00 3.09
269 270 2.672874 CGCTGCATACTCACTTAGCAAA 59.327 45.455 0.00 0.00 34.45 3.68
297 298 0.591170 TGCAAAAGCTACTGGAACGC 59.409 50.000 0.00 0.00 0.00 4.84
336 337 1.601759 GCATGTCCAGGTGTGCAGT 60.602 57.895 8.11 0.00 37.52 4.40
340 341 4.269523 TCCAGGTGTGCAGTGCCC 62.270 66.667 13.72 6.73 0.00 5.36
346 347 3.578286 TGTGCAGTGCCCATGGGA 61.578 61.111 36.00 16.78 37.50 4.37
391 422 2.097038 CAGTACAGTGCAGCGCCTC 61.097 63.158 2.29 0.00 0.00 4.70
431 462 4.631131 ACTGACTTAGCAAATTTTTGGGC 58.369 39.130 5.28 0.00 38.57 5.36
478 509 1.857965 CTCTCTGGACTGGGATGTCA 58.142 55.000 0.00 0.00 38.61 3.58
481 512 0.615331 TCTGGACTGGGATGTCAAGC 59.385 55.000 0.00 0.00 37.79 4.01
482 513 0.393537 CTGGACTGGGATGTCAAGCC 60.394 60.000 0.00 0.00 38.61 4.35
557 588 1.719709 CGCTGCACATCTGGACATG 59.280 57.895 0.00 0.00 0.00 3.21
663 699 2.404750 GCCCTCCTCTCTCCCCCTA 61.405 68.421 0.00 0.00 0.00 3.53
704 740 4.435425 CGGAGTATTTGACCGTGGATTTA 58.565 43.478 0.00 0.00 41.47 1.40
705 741 5.054477 CGGAGTATTTGACCGTGGATTTAT 58.946 41.667 0.00 0.00 41.47 1.40
872 912 7.095695 TCTTTGCTAATTTGGTATGGTTAGC 57.904 36.000 8.57 8.57 45.64 3.09
1031 1071 1.296715 GTTCCATGACGAGGCCACT 59.703 57.895 5.01 0.00 0.00 4.00
1273 1314 3.177487 CCGGTAAGCTCGAGAAGTAAAC 58.823 50.000 18.75 4.52 0.00 2.01
1505 1546 3.028130 GGAAGAAACGAGAGGAGGAGAT 58.972 50.000 0.00 0.00 0.00 2.75
1583 1624 2.581354 CGAGGCACAAGAGGAGGG 59.419 66.667 0.00 0.00 0.00 4.30
1713 1754 1.676746 GCATGTGAGATGCTGGTGAT 58.323 50.000 7.37 0.00 41.52 3.06
2164 2211 1.330234 TTGGGCGTCACACAGTACTA 58.670 50.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.281075 CAATCACATAGTCATACACAAACATTG 57.719 33.333 0.00 0.00 0.00 2.82
1 2 8.461222 CCAATCACATAGTCATACACAAACATT 58.539 33.333 0.00 0.00 0.00 2.71
2 3 7.828717 TCCAATCACATAGTCATACACAAACAT 59.171 33.333 0.00 0.00 0.00 2.71
3 4 7.119116 GTCCAATCACATAGTCATACACAAACA 59.881 37.037 0.00 0.00 0.00 2.83
4 5 7.334421 AGTCCAATCACATAGTCATACACAAAC 59.666 37.037 0.00 0.00 0.00 2.93
5 6 7.394016 AGTCCAATCACATAGTCATACACAAA 58.606 34.615 0.00 0.00 0.00 2.83
6 7 6.946340 AGTCCAATCACATAGTCATACACAA 58.054 36.000 0.00 0.00 0.00 3.33
7 8 6.544928 AGTCCAATCACATAGTCATACACA 57.455 37.500 0.00 0.00 0.00 3.72
8 9 7.717568 AGTAGTCCAATCACATAGTCATACAC 58.282 38.462 0.00 0.00 0.00 2.90
9 10 7.780271 AGAGTAGTCCAATCACATAGTCATACA 59.220 37.037 0.00 0.00 0.00 2.29
10 11 8.172352 AGAGTAGTCCAATCACATAGTCATAC 57.828 38.462 0.00 0.00 0.00 2.39
12 13 8.948401 ATAGAGTAGTCCAATCACATAGTCAT 57.052 34.615 0.00 0.00 0.00 3.06
13 14 8.633561 CAATAGAGTAGTCCAATCACATAGTCA 58.366 37.037 0.00 0.00 0.00 3.41
14 15 7.596995 GCAATAGAGTAGTCCAATCACATAGTC 59.403 40.741 0.00 0.00 0.00 2.59
15 16 7.288852 AGCAATAGAGTAGTCCAATCACATAGT 59.711 37.037 0.00 0.00 0.00 2.12
16 17 7.665690 AGCAATAGAGTAGTCCAATCACATAG 58.334 38.462 0.00 0.00 0.00 2.23
17 18 7.603180 AGCAATAGAGTAGTCCAATCACATA 57.397 36.000 0.00 0.00 0.00 2.29
18 19 6.491714 AGCAATAGAGTAGTCCAATCACAT 57.508 37.500 0.00 0.00 0.00 3.21
19 20 5.939764 AGCAATAGAGTAGTCCAATCACA 57.060 39.130 0.00 0.00 0.00 3.58
20 21 7.383572 CACATAGCAATAGAGTAGTCCAATCAC 59.616 40.741 0.00 0.00 0.00 3.06
21 22 7.069950 ACACATAGCAATAGAGTAGTCCAATCA 59.930 37.037 0.00 0.00 0.00 2.57
22 23 7.383572 CACACATAGCAATAGAGTAGTCCAATC 59.616 40.741 0.00 0.00 0.00 2.67
23 24 7.147655 ACACACATAGCAATAGAGTAGTCCAAT 60.148 37.037 0.00 0.00 0.00 3.16
24 25 6.154534 ACACACATAGCAATAGAGTAGTCCAA 59.845 38.462 0.00 0.00 0.00 3.53
25 26 5.656859 ACACACATAGCAATAGAGTAGTCCA 59.343 40.000 0.00 0.00 0.00 4.02
26 27 6.150396 ACACACATAGCAATAGAGTAGTCC 57.850 41.667 0.00 0.00 0.00 3.85
27 28 8.568794 TCATACACACATAGCAATAGAGTAGTC 58.431 37.037 0.00 0.00 0.00 2.59
28 29 8.465273 TCATACACACATAGCAATAGAGTAGT 57.535 34.615 0.00 0.00 0.00 2.73
29 30 8.572185 ACTCATACACACATAGCAATAGAGTAG 58.428 37.037 0.00 0.00 30.50 2.57
30 31 8.465273 ACTCATACACACATAGCAATAGAGTA 57.535 34.615 0.00 0.00 30.50 2.59
31 32 7.353414 ACTCATACACACATAGCAATAGAGT 57.647 36.000 0.00 0.00 0.00 3.24
32 33 9.351570 CATACTCATACACACATAGCAATAGAG 57.648 37.037 0.00 0.00 0.00 2.43
33 34 8.860088 ACATACTCATACACACATAGCAATAGA 58.140 33.333 0.00 0.00 0.00 1.98
34 35 8.919661 CACATACTCATACACACATAGCAATAG 58.080 37.037 0.00 0.00 0.00 1.73
35 36 8.637986 TCACATACTCATACACACATAGCAATA 58.362 33.333 0.00 0.00 0.00 1.90
36 37 7.500141 TCACATACTCATACACACATAGCAAT 58.500 34.615 0.00 0.00 0.00 3.56
37 38 6.872920 TCACATACTCATACACACATAGCAA 58.127 36.000 0.00 0.00 0.00 3.91
38 39 6.463995 TCACATACTCATACACACATAGCA 57.536 37.500 0.00 0.00 0.00 3.49
39 40 7.953158 AATCACATACTCATACACACATAGC 57.047 36.000 0.00 0.00 0.00 2.97
40 41 8.768019 CCAAATCACATACTCATACACACATAG 58.232 37.037 0.00 0.00 0.00 2.23
41 42 8.482128 TCCAAATCACATACTCATACACACATA 58.518 33.333 0.00 0.00 0.00 2.29
42 43 7.280876 GTCCAAATCACATACTCATACACACAT 59.719 37.037 0.00 0.00 0.00 3.21
43 44 6.593770 GTCCAAATCACATACTCATACACACA 59.406 38.462 0.00 0.00 0.00 3.72
44 45 6.818644 AGTCCAAATCACATACTCATACACAC 59.181 38.462 0.00 0.00 0.00 3.82
45 46 6.946340 AGTCCAAATCACATACTCATACACA 58.054 36.000 0.00 0.00 0.00 3.72
46 47 8.198109 AGTAGTCCAAATCACATACTCATACAC 58.802 37.037 0.00 0.00 0.00 2.90
47 48 8.306313 AGTAGTCCAAATCACATACTCATACA 57.694 34.615 0.00 0.00 0.00 2.29
54 55 8.926710 GCACATATAGTAGTCCAAATCACATAC 58.073 37.037 0.00 0.00 0.00 2.39
55 56 8.870116 AGCACATATAGTAGTCCAAATCACATA 58.130 33.333 0.00 0.00 0.00 2.29
56 57 7.739825 AGCACATATAGTAGTCCAAATCACAT 58.260 34.615 0.00 0.00 0.00 3.21
57 58 7.124573 AGCACATATAGTAGTCCAAATCACA 57.875 36.000 0.00 0.00 0.00 3.58
58 59 9.144747 CATAGCACATATAGTAGTCCAAATCAC 57.855 37.037 0.00 0.00 0.00 3.06
59 60 8.870116 ACATAGCACATATAGTAGTCCAAATCA 58.130 33.333 0.00 0.00 0.00 2.57
60 61 9.360093 GACATAGCACATATAGTAGTCCAAATC 57.640 37.037 0.00 0.00 0.00 2.17
61 62 9.094578 AGACATAGCACATATAGTAGTCCAAAT 57.905 33.333 0.00 0.00 0.00 2.32
62 63 8.478775 AGACATAGCACATATAGTAGTCCAAA 57.521 34.615 0.00 0.00 0.00 3.28
63 64 8.478775 AAGACATAGCACATATAGTAGTCCAA 57.521 34.615 0.00 0.00 0.00 3.53
64 65 7.945109 AGAAGACATAGCACATATAGTAGTCCA 59.055 37.037 0.00 0.00 0.00 4.02
65 66 8.343168 AGAAGACATAGCACATATAGTAGTCC 57.657 38.462 0.00 0.00 0.00 3.85
70 71 8.700051 ACAGAAAGAAGACATAGCACATATAGT 58.300 33.333 0.00 0.00 0.00 2.12
71 72 8.976471 CACAGAAAGAAGACATAGCACATATAG 58.024 37.037 0.00 0.00 0.00 1.31
72 73 8.478066 ACACAGAAAGAAGACATAGCACATATA 58.522 33.333 0.00 0.00 0.00 0.86
73 74 7.334090 ACACAGAAAGAAGACATAGCACATAT 58.666 34.615 0.00 0.00 0.00 1.78
74 75 6.701340 ACACAGAAAGAAGACATAGCACATA 58.299 36.000 0.00 0.00 0.00 2.29
75 76 5.555017 ACACAGAAAGAAGACATAGCACAT 58.445 37.500 0.00 0.00 0.00 3.21
76 77 4.960938 ACACAGAAAGAAGACATAGCACA 58.039 39.130 0.00 0.00 0.00 4.57
77 78 5.931441 AACACAGAAAGAAGACATAGCAC 57.069 39.130 0.00 0.00 0.00 4.40
78 79 6.238731 CCAAAACACAGAAAGAAGACATAGCA 60.239 38.462 0.00 0.00 0.00 3.49
79 80 6.017109 TCCAAAACACAGAAAGAAGACATAGC 60.017 38.462 0.00 0.00 0.00 2.97
80 81 7.227512 AGTCCAAAACACAGAAAGAAGACATAG 59.772 37.037 0.00 0.00 0.00 2.23
81 82 7.054124 AGTCCAAAACACAGAAAGAAGACATA 58.946 34.615 0.00 0.00 0.00 2.29
82 83 5.888161 AGTCCAAAACACAGAAAGAAGACAT 59.112 36.000 0.00 0.00 0.00 3.06
83 84 5.253330 AGTCCAAAACACAGAAAGAAGACA 58.747 37.500 0.00 0.00 0.00 3.41
84 85 5.819825 AGTCCAAAACACAGAAAGAAGAC 57.180 39.130 0.00 0.00 0.00 3.01
85 86 6.650120 AGTAGTCCAAAACACAGAAAGAAGA 58.350 36.000 0.00 0.00 0.00 2.87
86 87 6.927294 AGTAGTCCAAAACACAGAAAGAAG 57.073 37.500 0.00 0.00 0.00 2.85
87 88 7.332557 TGTAGTAGTCCAAAACACAGAAAGAA 58.667 34.615 0.00 0.00 0.00 2.52
88 89 6.880484 TGTAGTAGTCCAAAACACAGAAAGA 58.120 36.000 0.00 0.00 0.00 2.52
89 90 7.226720 ACATGTAGTAGTCCAAAACACAGAAAG 59.773 37.037 0.00 0.00 0.00 2.62
90 91 7.011950 CACATGTAGTAGTCCAAAACACAGAAA 59.988 37.037 0.00 0.00 0.00 2.52
91 92 6.481976 CACATGTAGTAGTCCAAAACACAGAA 59.518 38.462 0.00 0.00 0.00 3.02
92 93 5.989168 CACATGTAGTAGTCCAAAACACAGA 59.011 40.000 0.00 0.00 0.00 3.41
93 94 5.989168 TCACATGTAGTAGTCCAAAACACAG 59.011 40.000 0.00 0.00 0.00 3.66
94 95 5.919755 TCACATGTAGTAGTCCAAAACACA 58.080 37.500 0.00 0.00 0.00 3.72
95 96 7.435068 AATCACATGTAGTAGTCCAAAACAC 57.565 36.000 0.00 0.00 0.00 3.32
96 97 7.040755 CCAAATCACATGTAGTAGTCCAAAACA 60.041 37.037 0.00 0.00 0.00 2.83
97 98 7.174253 TCCAAATCACATGTAGTAGTCCAAAAC 59.826 37.037 0.00 0.00 0.00 2.43
98 99 7.227873 TCCAAATCACATGTAGTAGTCCAAAA 58.772 34.615 0.00 0.00 0.00 2.44
99 100 6.774673 TCCAAATCACATGTAGTAGTCCAAA 58.225 36.000 0.00 0.00 0.00 3.28
100 101 6.367374 TCCAAATCACATGTAGTAGTCCAA 57.633 37.500 0.00 0.00 0.00 3.53
101 102 6.560003 ATCCAAATCACATGTAGTAGTCCA 57.440 37.500 0.00 0.00 0.00 4.02
102 103 8.367911 TCATATCCAAATCACATGTAGTAGTCC 58.632 37.037 0.00 0.00 0.00 3.85
103 104 9.935241 ATCATATCCAAATCACATGTAGTAGTC 57.065 33.333 0.00 0.00 0.00 2.59
110 111 8.301720 GCACATAATCATATCCAAATCACATGT 58.698 33.333 0.00 0.00 0.00 3.21
111 112 7.758076 GGCACATAATCATATCCAAATCACATG 59.242 37.037 0.00 0.00 0.00 3.21
112 113 7.452189 TGGCACATAATCATATCCAAATCACAT 59.548 33.333 0.00 0.00 0.00 3.21
113 114 6.776603 TGGCACATAATCATATCCAAATCACA 59.223 34.615 0.00 0.00 0.00 3.58
114 115 7.218228 TGGCACATAATCATATCCAAATCAC 57.782 36.000 0.00 0.00 0.00 3.06
126 127 7.173735 GTGATTCACATAGATGGCACATAATCA 59.826 37.037 11.93 0.00 37.46 2.57
127 128 7.173735 TGTGATTCACATAGATGGCACATAATC 59.826 37.037 15.41 0.00 41.00 1.75
128 129 6.999871 TGTGATTCACATAGATGGCACATAAT 59.000 34.615 15.41 0.00 41.00 1.28
129 130 6.355747 TGTGATTCACATAGATGGCACATAA 58.644 36.000 15.41 0.00 41.00 1.90
130 131 5.927819 TGTGATTCACATAGATGGCACATA 58.072 37.500 15.41 0.00 41.00 2.29
131 132 4.784177 TGTGATTCACATAGATGGCACAT 58.216 39.130 15.41 0.00 41.00 3.21
132 133 4.219264 TGTGATTCACATAGATGGCACA 57.781 40.909 15.41 0.00 40.94 4.57
133 134 5.565592 TTTGTGATTCACATAGATGGCAC 57.434 39.130 19.63 0.00 44.16 5.01
134 135 5.476254 TGTTTTGTGATTCACATAGATGGCA 59.524 36.000 19.63 9.56 44.16 4.92
135 136 5.953183 TGTTTTGTGATTCACATAGATGGC 58.047 37.500 19.63 7.45 44.16 4.40
141 142 9.755804 TGCTTTTTATGTTTTGTGATTCACATA 57.244 25.926 19.63 12.60 44.16 2.29
142 143 8.550376 GTGCTTTTTATGTTTTGTGATTCACAT 58.450 29.630 19.63 7.60 44.16 3.21
143 144 7.763528 AGTGCTTTTTATGTTTTGTGATTCACA 59.236 29.630 15.41 15.41 43.02 3.58
144 145 8.130307 AGTGCTTTTTATGTTTTGTGATTCAC 57.870 30.769 9.93 9.93 34.56 3.18
145 146 8.715191 AAGTGCTTTTTATGTTTTGTGATTCA 57.285 26.923 0.00 0.00 0.00 2.57
146 147 9.424659 CAAAGTGCTTTTTATGTTTTGTGATTC 57.575 29.630 0.00 0.00 0.00 2.52
147 148 8.945057 ACAAAGTGCTTTTTATGTTTTGTGATT 58.055 25.926 0.00 0.00 36.33 2.57
148 149 8.491331 ACAAAGTGCTTTTTATGTTTTGTGAT 57.509 26.923 0.00 0.00 36.33 3.06
149 150 7.897575 ACAAAGTGCTTTTTATGTTTTGTGA 57.102 28.000 0.00 0.00 36.33 3.58
160 161 7.962373 GCTGTTTTCAAATACAAAGTGCTTTTT 59.038 29.630 0.00 0.00 0.00 1.94
161 162 7.118971 TGCTGTTTTCAAATACAAAGTGCTTTT 59.881 29.630 0.00 0.00 0.00 2.27
162 163 6.593382 TGCTGTTTTCAAATACAAAGTGCTTT 59.407 30.769 0.00 0.00 0.00 3.51
163 164 6.105333 TGCTGTTTTCAAATACAAAGTGCTT 58.895 32.000 0.00 0.00 0.00 3.91
164 165 5.659463 TGCTGTTTTCAAATACAAAGTGCT 58.341 33.333 0.00 0.00 0.00 4.40
165 166 5.748152 TCTGCTGTTTTCAAATACAAAGTGC 59.252 36.000 0.00 0.00 0.00 4.40
166 167 7.754069 TTCTGCTGTTTTCAAATACAAAGTG 57.246 32.000 0.00 0.00 0.00 3.16
167 168 8.034804 ACTTTCTGCTGTTTTCAAATACAAAGT 58.965 29.630 0.00 0.00 0.00 2.66
168 169 8.323140 CACTTTCTGCTGTTTTCAAATACAAAG 58.677 33.333 0.00 0.00 0.00 2.77
169 170 7.816995 ACACTTTCTGCTGTTTTCAAATACAAA 59.183 29.630 0.00 0.00 0.00 2.83
170 171 7.319646 ACACTTTCTGCTGTTTTCAAATACAA 58.680 30.769 0.00 0.00 0.00 2.41
171 172 6.862209 ACACTTTCTGCTGTTTTCAAATACA 58.138 32.000 0.00 0.00 0.00 2.29
172 173 7.113544 GCTACACTTTCTGCTGTTTTCAAATAC 59.886 37.037 0.00 0.00 0.00 1.89
173 174 7.138736 GCTACACTTTCTGCTGTTTTCAAATA 58.861 34.615 0.00 0.00 0.00 1.40
174 175 5.979517 GCTACACTTTCTGCTGTTTTCAAAT 59.020 36.000 0.00 0.00 0.00 2.32
175 176 5.339990 GCTACACTTTCTGCTGTTTTCAAA 58.660 37.500 0.00 0.00 0.00 2.69
176 177 4.495679 CGCTACACTTTCTGCTGTTTTCAA 60.496 41.667 0.00 0.00 0.00 2.69
177 178 3.002246 CGCTACACTTTCTGCTGTTTTCA 59.998 43.478 0.00 0.00 0.00 2.69
178 179 3.545633 CGCTACACTTTCTGCTGTTTTC 58.454 45.455 0.00 0.00 0.00 2.29
179 180 2.287009 GCGCTACACTTTCTGCTGTTTT 60.287 45.455 0.00 0.00 0.00 2.43
180 181 1.264288 GCGCTACACTTTCTGCTGTTT 59.736 47.619 0.00 0.00 0.00 2.83
181 182 0.868406 GCGCTACACTTTCTGCTGTT 59.132 50.000 0.00 0.00 0.00 3.16
182 183 0.951040 GGCGCTACACTTTCTGCTGT 60.951 55.000 7.64 0.00 0.00 4.40
183 184 0.671781 AGGCGCTACACTTTCTGCTG 60.672 55.000 7.64 0.00 0.00 4.41
184 185 0.895530 TAGGCGCTACACTTTCTGCT 59.104 50.000 7.64 0.00 0.00 4.24
185 186 1.661112 CTTAGGCGCTACACTTTCTGC 59.339 52.381 7.64 0.00 0.00 4.26
186 187 2.271800 CCTTAGGCGCTACACTTTCTG 58.728 52.381 7.64 0.00 0.00 3.02
187 188 1.207329 CCCTTAGGCGCTACACTTTCT 59.793 52.381 7.64 0.00 0.00 2.52
188 189 1.066358 ACCCTTAGGCGCTACACTTTC 60.066 52.381 7.64 0.00 36.11 2.62
189 190 0.981943 ACCCTTAGGCGCTACACTTT 59.018 50.000 7.64 0.00 36.11 2.66
190 191 1.856629 TACCCTTAGGCGCTACACTT 58.143 50.000 7.64 0.00 36.11 3.16
191 192 1.755380 CTTACCCTTAGGCGCTACACT 59.245 52.381 7.64 0.00 36.11 3.55
192 193 1.202498 CCTTACCCTTAGGCGCTACAC 60.202 57.143 7.64 0.00 36.11 2.90
193 194 1.117150 CCTTACCCTTAGGCGCTACA 58.883 55.000 7.64 0.00 36.11 2.74
194 195 3.982709 CCTTACCCTTAGGCGCTAC 57.017 57.895 7.64 0.00 36.11 3.58
200 201 1.153229 GTGGCGCCTTACCCTTAGG 60.153 63.158 29.70 0.00 40.04 2.69
201 202 0.743345 GTGTGGCGCCTTACCCTTAG 60.743 60.000 29.70 0.00 0.00 2.18
202 203 1.196104 AGTGTGGCGCCTTACCCTTA 61.196 55.000 29.70 0.07 0.00 2.69
203 204 1.196104 TAGTGTGGCGCCTTACCCTT 61.196 55.000 29.70 12.69 0.00 3.95
204 205 1.611261 TAGTGTGGCGCCTTACCCT 60.611 57.895 29.70 17.28 0.00 4.34
205 206 1.449070 GTAGTGTGGCGCCTTACCC 60.449 63.158 29.70 9.89 0.00 3.69
206 207 0.459759 GAGTAGTGTGGCGCCTTACC 60.460 60.000 29.70 13.27 0.00 2.85
207 208 0.245539 TGAGTAGTGTGGCGCCTTAC 59.754 55.000 29.70 24.73 0.00 2.34
208 209 0.530744 CTGAGTAGTGTGGCGCCTTA 59.469 55.000 29.70 13.97 0.00 2.69
209 210 1.293498 CTGAGTAGTGTGGCGCCTT 59.707 57.895 29.70 13.03 0.00 4.35
210 211 1.908793 ACTGAGTAGTGTGGCGCCT 60.909 57.895 29.70 9.99 35.34 5.52
211 212 2.657237 ACTGAGTAGTGTGGCGCC 59.343 61.111 22.73 22.73 35.34 6.53
219 220 1.229336 AGGCCCTGCACTGAGTAGT 60.229 57.895 0.00 0.00 37.75 2.73
220 221 0.975040 AGAGGCCCTGCACTGAGTAG 60.975 60.000 0.00 0.00 0.00 2.57
221 222 0.545309 AAGAGGCCCTGCACTGAGTA 60.545 55.000 0.00 0.00 0.00 2.59
222 223 1.835927 GAAGAGGCCCTGCACTGAGT 61.836 60.000 0.00 0.00 0.00 3.41
223 224 1.078567 GAAGAGGCCCTGCACTGAG 60.079 63.158 0.00 0.00 0.00 3.35
224 225 2.596851 GGAAGAGGCCCTGCACTGA 61.597 63.158 0.00 0.00 0.00 3.41
225 226 2.045536 GGAAGAGGCCCTGCACTG 60.046 66.667 0.00 0.00 0.00 3.66
226 227 0.547712 TAAGGAAGAGGCCCTGCACT 60.548 55.000 0.00 0.00 33.55 4.40
227 228 0.107459 CTAAGGAAGAGGCCCTGCAC 60.107 60.000 0.00 0.00 33.55 4.57
228 229 1.274703 CCTAAGGAAGAGGCCCTGCA 61.275 60.000 0.00 0.00 33.55 4.41
229 230 1.529309 CCTAAGGAAGAGGCCCTGC 59.471 63.158 0.00 0.00 33.55 4.85
235 236 1.522580 GCAGCGCCTAAGGAAGAGG 60.523 63.158 2.29 0.00 37.12 3.69
236 237 0.179062 ATGCAGCGCCTAAGGAAGAG 60.179 55.000 2.29 0.00 0.00 2.85
237 238 1.119684 TATGCAGCGCCTAAGGAAGA 58.880 50.000 2.29 0.00 0.00 2.87
238 239 1.202580 AGTATGCAGCGCCTAAGGAAG 60.203 52.381 2.29 0.00 0.00 3.46
239 240 0.830648 AGTATGCAGCGCCTAAGGAA 59.169 50.000 2.29 0.00 0.00 3.36
240 241 0.389391 GAGTATGCAGCGCCTAAGGA 59.611 55.000 2.29 0.00 0.00 3.36
241 242 0.104855 TGAGTATGCAGCGCCTAAGG 59.895 55.000 2.29 0.00 0.00 2.69
242 243 1.202463 AGTGAGTATGCAGCGCCTAAG 60.202 52.381 2.29 0.00 0.00 2.18
243 244 0.824109 AGTGAGTATGCAGCGCCTAA 59.176 50.000 2.29 0.00 0.00 2.69
244 245 0.824109 AAGTGAGTATGCAGCGCCTA 59.176 50.000 2.29 0.00 0.00 3.93
245 246 0.824109 TAAGTGAGTATGCAGCGCCT 59.176 50.000 2.29 0.00 0.00 5.52
246 247 1.212616 CTAAGTGAGTATGCAGCGCC 58.787 55.000 2.29 0.00 0.00 6.53
247 248 0.579156 GCTAAGTGAGTATGCAGCGC 59.421 55.000 0.00 0.00 0.00 5.92
248 249 1.926561 TGCTAAGTGAGTATGCAGCG 58.073 50.000 0.00 0.00 0.00 5.18
249 250 4.889832 ATTTGCTAAGTGAGTATGCAGC 57.110 40.909 0.00 0.00 35.02 5.25
250 251 7.062605 CCAAAAATTTGCTAAGTGAGTATGCAG 59.937 37.037 0.00 0.00 36.86 4.41
251 252 6.867816 CCAAAAATTTGCTAAGTGAGTATGCA 59.132 34.615 0.00 0.00 36.86 3.96
252 253 6.311200 CCCAAAAATTTGCTAAGTGAGTATGC 59.689 38.462 0.29 0.00 36.86 3.14
253 254 7.329226 CACCCAAAAATTTGCTAAGTGAGTATG 59.671 37.037 0.29 0.00 36.86 2.39
254 255 7.378181 CACCCAAAAATTTGCTAAGTGAGTAT 58.622 34.615 0.29 0.00 36.86 2.12
255 256 6.737346 GCACCCAAAAATTTGCTAAGTGAGTA 60.737 38.462 14.91 0.00 36.86 2.59
259 260 4.125703 TGCACCCAAAAATTTGCTAAGTG 58.874 39.130 0.29 6.37 36.86 3.16
266 267 4.635833 AGCTTTTGCACCCAAAAATTTG 57.364 36.364 0.00 0.00 46.84 2.32
269 270 4.379652 CAGTAGCTTTTGCACCCAAAAAT 58.620 39.130 0.00 0.00 46.84 1.82
297 298 2.612471 CCAGTCCAGAGAGCAACAGAAG 60.612 54.545 0.00 0.00 0.00 2.85
330 331 2.753043 CTCCCATGGGCACTGCAC 60.753 66.667 27.41 0.00 34.68 4.57
340 341 3.473647 TGAGGCGCCTCTCCCATG 61.474 66.667 46.04 0.00 43.12 3.66
346 347 4.079850 CAGCAGTGAGGCGCCTCT 62.080 66.667 46.04 31.14 43.12 3.69
408 439 4.686091 GCCCAAAAATTTGCTAAGTCAGTC 59.314 41.667 0.29 0.00 36.86 3.51
431 462 0.794473 GCGTTCCAGTAGGTTTTCGG 59.206 55.000 0.00 0.00 35.89 4.30
613 646 1.414919 ACTGAGCTTCGGGTTTGTGTA 59.585 47.619 0.00 0.00 0.00 2.90
663 699 2.636893 CCGGATCTGAGGAGGATTTGAT 59.363 50.000 2.08 0.00 0.00 2.57
704 740 2.296943 TAAGGGAGGGGTTGGCTTAT 57.703 50.000 0.00 0.00 0.00 1.73
705 741 1.920351 CTTAAGGGAGGGGTTGGCTTA 59.080 52.381 0.00 0.00 0.00 3.09
872 912 6.295916 CCCTAACCCTAGCATACTATGAAAGG 60.296 46.154 0.00 5.44 34.98 3.11
1031 1071 3.552132 TGTCTTCTTGGTTAGCACACA 57.448 42.857 0.00 0.00 0.00 3.72
1273 1314 7.860613 TGTTGACACACATTTGATAGTAACAG 58.139 34.615 0.00 0.00 0.00 3.16
1572 1613 3.394836 GCCGAGCCCTCCTCTTGT 61.395 66.667 0.00 0.00 38.49 3.16
1583 1624 3.876589 TTCTTGTCACGGGCCGAGC 62.877 63.158 35.78 20.57 0.00 5.03
1713 1754 2.158900 GCAGCTTGCCCTAGAAGATACA 60.159 50.000 0.00 0.00 37.42 2.29
1790 1831 6.582636 TGCCGATGAGTTCATAACTTAAGAT 58.417 36.000 10.09 0.00 43.03 2.40
1963 2006 2.690881 ACGCCTATCCCTTGGGCA 60.691 61.111 0.00 0.00 45.50 5.36
2012 2055 0.321671 ACCAAGTCATAGTGCAGCGT 59.678 50.000 0.00 0.00 0.00 5.07
2105 2152 2.506438 GTGTAGCGGCCGTCTCAC 60.506 66.667 28.70 25.67 0.00 3.51
2114 2161 0.038618 TGCACAGTACAGTGTAGCGG 60.039 55.000 18.32 2.78 41.52 5.52
2164 2211 2.033141 AACAGACAGGCGCTGCAT 59.967 55.556 7.64 0.00 36.86 3.96


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

AutoCloner maintained by Alex Coulton.