Multiple sequence alignment - TraesCS3A01G120800

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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 TraesCS3A01G120800 chr3A 100.000 2593 0 0 1 2593 95015173 95017765 0.000000e+00 4789.0
1 TraesCS3A01G120800 chr3D 88.507 1105 64 23 737 1813 80941364 80942433 0.000000e+00 1279.0
2 TraesCS3A01G120800 chr3D 95.138 617 26 3 1816 2431 127297741 127298354 0.000000e+00 970.0
3 TraesCS3A01G120800 chr3D 94.839 620 29 2 1813 2431 14531969 14532586 0.000000e+00 965.0
4 TraesCS3A01G120800 chr3D 88.816 608 54 8 150 752 80940752 80941350 0.000000e+00 734.0
5 TraesCS3A01G120800 chr3D 85.806 155 11 6 2431 2581 80942452 80942599 1.240000e-33 154.0
6 TraesCS3A01G120800 chr3D 88.732 71 7 1 17 86 80923435 80923505 4.600000e-13 86.1
7 TraesCS3A01G120800 chr3B 89.317 908 61 20 766 1663 126569644 126570525 0.000000e+00 1107.0
8 TraesCS3A01G120800 chr3B 90.870 471 41 1 307 775 126569150 126569620 4.710000e-177 630.0
9 TraesCS3A01G120800 chr3B 94.690 113 5 1 1703 1814 126570529 126570641 9.540000e-40 174.0
10 TraesCS3A01G120800 chr1A 96.607 619 19 2 1815 2431 548941083 548940465 0.000000e+00 1026.0
11 TraesCS3A01G120800 chr7A 96.434 617 20 2 1817 2431 27948976 27948360 0.000000e+00 1016.0
12 TraesCS3A01G120800 chr7A 95.652 621 26 1 1812 2431 527992943 527993563 0.000000e+00 996.0
13 TraesCS3A01G120800 chr7A 95.659 622 24 3 1811 2431 735502541 735503160 0.000000e+00 996.0
14 TraesCS3A01G120800 chr7A 95.087 631 28 3 1802 2431 729272387 729271759 0.000000e+00 990.0
15 TraesCS3A01G120800 chr7A 88.290 538 46 5 1090 1627 239860361 239859841 1.690000e-176 628.0
16 TraesCS3A01G120800 chr7A 94.643 224 12 0 861 1084 239869193 239868970 5.310000e-92 348.0
17 TraesCS3A01G120800 chr7D 92.683 615 43 2 1818 2431 519238085 519238698 0.000000e+00 885.0
18 TraesCS3A01G120800 chr2B 91.946 596 46 2 1818 2413 784700630 784701223 0.000000e+00 833.0


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 TraesCS3A01G120800 chr3A 95015173 95017765 2592 False 4789.000000 4789 100.000000 1 2593 1 chr3A.!!$F1 2592
1 TraesCS3A01G120800 chr3D 127297741 127298354 613 False 970.000000 970 95.138000 1816 2431 1 chr3D.!!$F3 615
2 TraesCS3A01G120800 chr3D 14531969 14532586 617 False 965.000000 965 94.839000 1813 2431 1 chr3D.!!$F1 618
3 TraesCS3A01G120800 chr3D 80940752 80942599 1847 False 722.333333 1279 87.709667 150 2581 3 chr3D.!!$F4 2431
4 TraesCS3A01G120800 chr3B 126569150 126570641 1491 False 637.000000 1107 91.625667 307 1814 3 chr3B.!!$F1 1507
5 TraesCS3A01G120800 chr1A 548940465 548941083 618 True 1026.000000 1026 96.607000 1815 2431 1 chr1A.!!$R1 616
6 TraesCS3A01G120800 chr7A 27948360 27948976 616 True 1016.000000 1016 96.434000 1817 2431 1 chr7A.!!$R1 614
7 TraesCS3A01G120800 chr7A 527992943 527993563 620 False 996.000000 996 95.652000 1812 2431 1 chr7A.!!$F1 619
8 TraesCS3A01G120800 chr7A 735502541 735503160 619 False 996.000000 996 95.659000 1811 2431 1 chr7A.!!$F2 620
9 TraesCS3A01G120800 chr7A 729271759 729272387 628 True 990.000000 990 95.087000 1802 2431 1 chr7A.!!$R4 629
10 TraesCS3A01G120800 chr7A 239859841 239860361 520 True 628.000000 628 88.290000 1090 1627 1 chr7A.!!$R2 537
11 TraesCS3A01G120800 chr7D 519238085 519238698 613 False 885.000000 885 92.683000 1818 2431 1 chr7D.!!$F1 613
12 TraesCS3A01G120800 chr2B 784700630 784701223 593 False 833.000000 833 91.946000 1818 2413 1 chr2B.!!$F1 595

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
21 22 0.035176 GCATGCTCCCCTCTCATCTC 59.965 60.0 11.37 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 1802 0.100861 TCGCACTACACACACGAACA 59.899 50.0 0.0 0.0 0.0 3.18 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
17 18 4.078167 ATGCATGCTCCCCTCTCA 57.922 55.556 20.33 0.00 0.00 3.27
18 19 2.553207 ATGCATGCTCCCCTCTCAT 58.447 52.632 20.33 0.00 0.00 2.90
19 20 0.400975 ATGCATGCTCCCCTCTCATC 59.599 55.000 20.33 0.00 0.00 2.92
20 21 0.693430 TGCATGCTCCCCTCTCATCT 60.693 55.000 20.33 0.00 0.00 2.90
21 22 0.035176 GCATGCTCCCCTCTCATCTC 59.965 60.000 11.37 0.00 0.00 2.75
22 23 1.719529 CATGCTCCCCTCTCATCTCT 58.280 55.000 0.00 0.00 0.00 3.10
23 24 1.619827 CATGCTCCCCTCTCATCTCTC 59.380 57.143 0.00 0.00 0.00 3.20
24 25 0.932955 TGCTCCCCTCTCATCTCTCT 59.067 55.000 0.00 0.00 0.00 3.10
25 26 1.290431 TGCTCCCCTCTCATCTCTCTT 59.710 52.381 0.00 0.00 0.00 2.85
26 27 2.292785 TGCTCCCCTCTCATCTCTCTTT 60.293 50.000 0.00 0.00 0.00 2.52
27 28 2.365293 GCTCCCCTCTCATCTCTCTTTC 59.635 54.545 0.00 0.00 0.00 2.62
28 29 2.965147 CTCCCCTCTCATCTCTCTTTCC 59.035 54.545 0.00 0.00 0.00 3.13
29 30 2.589664 TCCCCTCTCATCTCTCTTTCCT 59.410 50.000 0.00 0.00 0.00 3.36
30 31 2.965147 CCCCTCTCATCTCTCTTTCCTC 59.035 54.545 0.00 0.00 0.00 3.71
31 32 3.374098 CCCCTCTCATCTCTCTTTCCTCT 60.374 52.174 0.00 0.00 0.00 3.69
32 33 3.891366 CCCTCTCATCTCTCTTTCCTCTC 59.109 52.174 0.00 0.00 0.00 3.20
33 34 4.535781 CCTCTCATCTCTCTTTCCTCTCA 58.464 47.826 0.00 0.00 0.00 3.27
34 35 5.142639 CCTCTCATCTCTCTTTCCTCTCAT 58.857 45.833 0.00 0.00 0.00 2.90
35 36 5.242393 CCTCTCATCTCTCTTTCCTCTCATC 59.758 48.000 0.00 0.00 0.00 2.92
36 37 6.017211 TCTCATCTCTCTTTCCTCTCATCT 57.983 41.667 0.00 0.00 0.00 2.90
37 38 5.829391 TCTCATCTCTCTTTCCTCTCATCTG 59.171 44.000 0.00 0.00 0.00 2.90
38 39 4.894705 TCATCTCTCTTTCCTCTCATCTGG 59.105 45.833 0.00 0.00 0.00 3.86
39 40 4.599720 TCTCTCTTTCCTCTCATCTGGA 57.400 45.455 0.00 0.00 0.00 3.86
40 41 4.277476 TCTCTCTTTCCTCTCATCTGGAC 58.723 47.826 0.00 0.00 31.24 4.02
41 42 4.022603 CTCTCTTTCCTCTCATCTGGACA 58.977 47.826 0.00 0.00 31.24 4.02
42 43 3.766591 TCTCTTTCCTCTCATCTGGACAC 59.233 47.826 0.00 0.00 31.24 3.67
43 44 2.834549 TCTTTCCTCTCATCTGGACACC 59.165 50.000 0.00 0.00 31.24 4.16
44 45 2.325661 TTCCTCTCATCTGGACACCA 57.674 50.000 0.00 0.00 31.24 4.17
45 46 1.561643 TCCTCTCATCTGGACACCAC 58.438 55.000 0.00 0.00 0.00 4.16
46 47 1.203174 TCCTCTCATCTGGACACCACA 60.203 52.381 0.00 0.00 0.00 4.17
47 48 1.066573 CCTCTCATCTGGACACCACAC 60.067 57.143 0.00 0.00 0.00 3.82
48 49 0.976641 TCTCATCTGGACACCACACC 59.023 55.000 0.00 0.00 0.00 4.16
49 50 0.686789 CTCATCTGGACACCACACCA 59.313 55.000 0.00 0.00 34.81 4.17
50 51 1.280133 CTCATCTGGACACCACACCAT 59.720 52.381 0.00 0.00 35.54 3.55
51 52 2.501316 CTCATCTGGACACCACACCATA 59.499 50.000 0.00 0.00 35.54 2.74
52 53 2.909662 TCATCTGGACACCACACCATAA 59.090 45.455 0.00 0.00 35.54 1.90
53 54 3.523157 TCATCTGGACACCACACCATAAT 59.477 43.478 0.00 0.00 35.54 1.28
54 55 4.719273 TCATCTGGACACCACACCATAATA 59.281 41.667 0.00 0.00 35.54 0.98
55 56 5.369404 TCATCTGGACACCACACCATAATAT 59.631 40.000 0.00 0.00 35.54 1.28
56 57 5.290493 TCTGGACACCACACCATAATATC 57.710 43.478 0.00 0.00 35.54 1.63
57 58 4.968719 TCTGGACACCACACCATAATATCT 59.031 41.667 0.00 0.00 35.54 1.98
58 59 5.070446 TCTGGACACCACACCATAATATCTC 59.930 44.000 0.00 0.00 35.54 2.75
59 60 4.719273 TGGACACCACACCATAATATCTCA 59.281 41.667 0.00 0.00 0.00 3.27
60 61 5.057149 GGACACCACACCATAATATCTCAC 58.943 45.833 0.00 0.00 0.00 3.51
61 62 5.163301 GGACACCACACCATAATATCTCACT 60.163 44.000 0.00 0.00 0.00 3.41
62 63 6.041637 GGACACCACACCATAATATCTCACTA 59.958 42.308 0.00 0.00 0.00 2.74
63 64 6.817184 ACACCACACCATAATATCTCACTAC 58.183 40.000 0.00 0.00 0.00 2.73
64 65 6.382859 ACACCACACCATAATATCTCACTACA 59.617 38.462 0.00 0.00 0.00 2.74
65 66 7.071196 ACACCACACCATAATATCTCACTACAT 59.929 37.037 0.00 0.00 0.00 2.29
66 67 7.600375 CACCACACCATAATATCTCACTACATC 59.400 40.741 0.00 0.00 0.00 3.06
67 68 7.099764 CCACACCATAATATCTCACTACATCC 58.900 42.308 0.00 0.00 0.00 3.51
68 69 7.256296 CCACACCATAATATCTCACTACATCCA 60.256 40.741 0.00 0.00 0.00 3.41
69 70 8.316946 CACACCATAATATCTCACTACATCCAT 58.683 37.037 0.00 0.00 0.00 3.41
70 71 8.316946 ACACCATAATATCTCACTACATCCATG 58.683 37.037 0.00 0.00 0.00 3.66
71 72 7.767659 CACCATAATATCTCACTACATCCATGG 59.232 40.741 4.97 4.97 35.32 3.66
72 73 6.765036 CCATAATATCTCACTACATCCATGGC 59.235 42.308 6.96 0.00 0.00 4.40
73 74 4.833478 ATATCTCACTACATCCATGGCC 57.167 45.455 6.96 0.00 0.00 5.36
74 75 1.131638 TCTCACTACATCCATGGCCC 58.868 55.000 6.96 0.00 0.00 5.80
75 76 0.109342 CTCACTACATCCATGGCCCC 59.891 60.000 6.96 0.00 0.00 5.80
76 77 0.327480 TCACTACATCCATGGCCCCT 60.327 55.000 6.96 0.00 0.00 4.79
77 78 1.061735 TCACTACATCCATGGCCCCTA 60.062 52.381 6.96 0.00 0.00 3.53
78 79 1.988107 CACTACATCCATGGCCCCTAT 59.012 52.381 6.96 0.00 0.00 2.57
79 80 2.026822 CACTACATCCATGGCCCCTATC 60.027 54.545 6.96 0.00 0.00 2.08
80 81 2.157942 ACTACATCCATGGCCCCTATCT 60.158 50.000 6.96 0.00 0.00 1.98
81 82 2.741159 ACATCCATGGCCCCTATCTA 57.259 50.000 6.96 0.00 0.00 1.98
82 83 2.269940 ACATCCATGGCCCCTATCTAC 58.730 52.381 6.96 0.00 0.00 2.59
83 84 2.157942 ACATCCATGGCCCCTATCTACT 60.158 50.000 6.96 0.00 0.00 2.57
84 85 2.327325 TCCATGGCCCCTATCTACTC 57.673 55.000 6.96 0.00 0.00 2.59
85 86 1.795786 TCCATGGCCCCTATCTACTCT 59.204 52.381 6.96 0.00 0.00 3.24
86 87 2.182312 TCCATGGCCCCTATCTACTCTT 59.818 50.000 6.96 0.00 0.00 2.85
87 88 2.982488 CCATGGCCCCTATCTACTCTTT 59.018 50.000 0.00 0.00 0.00 2.52
88 89 4.140543 TCCATGGCCCCTATCTACTCTTTA 60.141 45.833 6.96 0.00 0.00 1.85
89 90 4.785376 CCATGGCCCCTATCTACTCTTTAT 59.215 45.833 0.00 0.00 0.00 1.40
90 91 5.104735 CCATGGCCCCTATCTACTCTTTATC 60.105 48.000 0.00 0.00 0.00 1.75
91 92 4.426704 TGGCCCCTATCTACTCTTTATCC 58.573 47.826 0.00 0.00 0.00 2.59
92 93 3.775866 GGCCCCTATCTACTCTTTATCCC 59.224 52.174 0.00 0.00 0.00 3.85
93 94 3.775866 GCCCCTATCTACTCTTTATCCCC 59.224 52.174 0.00 0.00 0.00 4.81
94 95 4.363573 CCCCTATCTACTCTTTATCCCCC 58.636 52.174 0.00 0.00 0.00 5.40
95 96 4.202901 CCCCTATCTACTCTTTATCCCCCA 60.203 50.000 0.00 0.00 0.00 4.96
96 97 5.412384 CCCTATCTACTCTTTATCCCCCAA 58.588 45.833 0.00 0.00 0.00 4.12
97 98 5.248705 CCCTATCTACTCTTTATCCCCCAAC 59.751 48.000 0.00 0.00 0.00 3.77
98 99 5.248705 CCTATCTACTCTTTATCCCCCAACC 59.751 48.000 0.00 0.00 0.00 3.77
99 100 3.036091 TCTACTCTTTATCCCCCAACCG 58.964 50.000 0.00 0.00 0.00 4.44
100 101 0.916809 ACTCTTTATCCCCCAACCGG 59.083 55.000 0.00 0.00 0.00 5.28
101 102 1.209621 CTCTTTATCCCCCAACCGGA 58.790 55.000 9.46 0.00 0.00 5.14
102 103 0.913924 TCTTTATCCCCCAACCGGAC 59.086 55.000 9.46 0.00 30.39 4.79
103 104 0.916809 CTTTATCCCCCAACCGGACT 59.083 55.000 9.46 0.00 30.39 3.85
104 105 2.121129 CTTTATCCCCCAACCGGACTA 58.879 52.381 9.46 0.00 30.39 2.59
105 106 2.500269 TTATCCCCCAACCGGACTAT 57.500 50.000 9.46 0.00 30.39 2.12
106 107 2.500269 TATCCCCCAACCGGACTATT 57.500 50.000 9.46 0.00 30.39 1.73
107 108 1.603634 ATCCCCCAACCGGACTATTT 58.396 50.000 9.46 0.00 30.39 1.40
108 109 0.913924 TCCCCCAACCGGACTATTTC 59.086 55.000 9.46 0.00 0.00 2.17
109 110 0.621609 CCCCCAACCGGACTATTTCA 59.378 55.000 9.46 0.00 0.00 2.69
110 111 1.214424 CCCCCAACCGGACTATTTCAT 59.786 52.381 9.46 0.00 0.00 2.57
111 112 2.297701 CCCCAACCGGACTATTTCATG 58.702 52.381 9.46 0.00 0.00 3.07
112 113 2.092646 CCCCAACCGGACTATTTCATGA 60.093 50.000 9.46 0.00 0.00 3.07
113 114 3.616219 CCCAACCGGACTATTTCATGAA 58.384 45.455 9.46 3.38 0.00 2.57
114 115 4.207165 CCCAACCGGACTATTTCATGAAT 58.793 43.478 9.46 2.50 0.00 2.57
115 116 5.373222 CCCAACCGGACTATTTCATGAATA 58.627 41.667 9.46 0.91 0.00 1.75
133 134 3.105659 GCCTTCAATGGCGCTCTC 58.894 61.111 7.64 0.00 43.74 3.20
134 135 2.476320 GCCTTCAATGGCGCTCTCC 61.476 63.158 7.64 0.00 43.74 3.71
135 136 1.821332 CCTTCAATGGCGCTCTCCC 60.821 63.158 7.64 0.00 0.00 4.30
136 137 2.125147 TTCAATGGCGCTCTCCCG 60.125 61.111 7.64 0.00 0.00 5.14
137 138 2.859273 CTTCAATGGCGCTCTCCCGT 62.859 60.000 7.64 0.00 0.00 5.28
138 139 1.609635 TTCAATGGCGCTCTCCCGTA 61.610 55.000 7.64 0.00 0.00 4.02
139 140 1.069765 CAATGGCGCTCTCCCGTAT 59.930 57.895 7.64 0.00 0.00 3.06
140 141 0.946221 CAATGGCGCTCTCCCGTATC 60.946 60.000 7.64 0.00 0.00 2.24
141 142 1.399744 AATGGCGCTCTCCCGTATCA 61.400 55.000 7.64 0.00 0.00 2.15
142 143 1.188219 ATGGCGCTCTCCCGTATCAT 61.188 55.000 7.64 0.00 0.00 2.45
143 144 1.373497 GGCGCTCTCCCGTATCATG 60.373 63.158 7.64 0.00 0.00 3.07
144 145 1.364171 GCGCTCTCCCGTATCATGT 59.636 57.895 0.00 0.00 0.00 3.21
145 146 0.596577 GCGCTCTCCCGTATCATGTA 59.403 55.000 0.00 0.00 0.00 2.29
146 147 1.202582 GCGCTCTCCCGTATCATGTAT 59.797 52.381 0.00 0.00 0.00 2.29
147 148 2.868662 CGCTCTCCCGTATCATGTATG 58.131 52.381 0.00 0.00 0.00 2.39
148 149 2.229062 CGCTCTCCCGTATCATGTATGT 59.771 50.000 0.00 0.00 0.00 2.29
156 157 3.049912 CGTATCATGTATGTGGACCACG 58.950 50.000 19.67 4.44 37.14 4.94
167 168 3.340727 GGACCACGTCCGAACATAG 57.659 57.895 0.00 0.00 43.14 2.23
178 179 4.625742 CGTCCGAACATAGAAACAGACATT 59.374 41.667 0.00 0.00 0.00 2.71
182 183 5.088739 CGAACATAGAAACAGACATTTGCC 58.911 41.667 0.00 0.00 0.00 4.52
186 187 3.308438 AGAAACAGACATTTGCCATGC 57.692 42.857 0.00 0.00 0.00 4.06
187 188 2.895404 AGAAACAGACATTTGCCATGCT 59.105 40.909 0.00 0.00 0.00 3.79
202 203 1.660560 ATGCTCATTTGCGGGTCAGC 61.661 55.000 0.00 0.00 35.36 4.26
203 204 2.334946 GCTCATTTGCGGGTCAGCA 61.335 57.895 0.00 0.00 46.54 4.41
211 212 1.832883 TGCGGGTCAGCAATGTAAAT 58.167 45.000 0.00 0.00 45.06 1.40
223 224 6.777091 TCAGCAATGTAAATGCCCTTATATGT 59.223 34.615 0.00 0.00 44.91 2.29
249 250 0.321564 TCACATCTCGGCCAGTTTGG 60.322 55.000 2.24 0.00 41.55 3.28
254 255 1.533625 TCTCGGCCAGTTTGGATTTG 58.466 50.000 2.24 0.00 40.96 2.32
264 265 4.503643 CCAGTTTGGATTTGAAGCCATTGT 60.504 41.667 1.04 0.00 45.07 2.71
272 273 4.597404 TTTGAAGCCATTGTGCATAACA 57.403 36.364 0.00 0.00 36.85 2.41
300 301 6.419413 GTCATCTAGTCGGCATAAGAAGAAAG 59.581 42.308 0.00 0.00 0.00 2.62
341 342 1.078214 ACATCAGCGGTGGTCCATG 60.078 57.895 15.67 13.07 0.00 3.66
359 360 6.206498 GTCCATGAAGTTTTGGTTTGACTAC 58.794 40.000 0.00 0.00 34.48 2.73
378 379 1.132262 ACAACGACAAAGTGGCAACTG 59.868 47.619 0.00 0.00 36.51 3.16
392 393 0.961753 CAACTGCTTCCAACCTTCCC 59.038 55.000 0.00 0.00 0.00 3.97
450 451 1.000163 CACTGTCGAGTGCTAACTGGT 60.000 52.381 0.00 0.00 43.24 4.00
452 453 0.601558 TGTCGAGTGCTAACTGGTCC 59.398 55.000 0.00 0.00 36.52 4.46
455 456 1.218316 GAGTGCTAACTGGTCCCCG 59.782 63.158 0.00 0.00 36.52 5.73
464 470 1.558233 ACTGGTCCCCGTCTTAGAAG 58.442 55.000 0.00 0.00 0.00 2.85
466 472 2.176889 CTGGTCCCCGTCTTAGAAGAA 58.823 52.381 0.00 0.00 36.68 2.52
469 475 3.585732 TGGTCCCCGTCTTAGAAGAAAAT 59.414 43.478 0.00 0.00 36.68 1.82
470 476 4.042435 TGGTCCCCGTCTTAGAAGAAAATT 59.958 41.667 0.00 0.00 36.68 1.82
507 515 1.404315 GGTAGCTCAAACCAGTCTCCG 60.404 57.143 0.00 0.00 36.96 4.63
511 519 2.030562 CAAACCAGTCTCCGCCGT 59.969 61.111 0.00 0.00 0.00 5.68
515 523 4.477975 CCAGTCTCCGCCGTCGAC 62.478 72.222 5.18 5.18 38.10 4.20
525 533 2.308039 GCCGTCGACCACAGTGAAC 61.308 63.158 10.58 0.00 0.00 3.18
529 537 2.032071 CGACCACAGTGAACCCCC 59.968 66.667 0.62 0.00 0.00 5.40
535 543 3.047877 CAGTGAACCCCCGCGTTC 61.048 66.667 4.92 2.37 42.10 3.95
672 680 1.542915 CTGGTCACTTGGATGCTTTGG 59.457 52.381 0.00 0.00 0.00 3.28
760 800 1.089920 CGACTGGCTGGAATCTTTGG 58.910 55.000 0.00 0.00 0.00 3.28
854 933 2.879756 GCTCCTGGTCCATTGCTTAACA 60.880 50.000 0.00 0.00 0.00 2.41
858 937 2.884012 CTGGTCCATTGCTTAACACACA 59.116 45.455 0.00 0.00 0.00 3.72
859 938 2.884012 TGGTCCATTGCTTAACACACAG 59.116 45.455 0.00 0.00 0.00 3.66
860 939 2.884639 GGTCCATTGCTTAACACACAGT 59.115 45.455 0.00 0.00 0.00 3.55
872 951 2.587522 ACACACAGTACTCAGCTGAGA 58.412 47.619 42.76 26.27 44.74 3.27
907 987 3.381335 ACAATATGAGGGTACGGGTTCT 58.619 45.455 0.00 0.00 0.00 3.01
948 1028 4.545610 TCGAAATTTTGTGTGGATTCTGC 58.454 39.130 5.33 0.00 0.00 4.26
951 1031 5.117592 CGAAATTTTGTGTGGATTCTGCTTC 59.882 40.000 0.00 0.00 0.00 3.86
1146 1249 2.105006 ATTGCTCAATGCGTCTGAGT 57.895 45.000 15.14 0.00 46.63 3.41
1149 1252 1.001293 TGCTCAATGCGTCTGAGTTCT 59.999 47.619 15.14 0.00 46.63 3.01
1150 1253 1.392853 GCTCAATGCGTCTGAGTTCTG 59.607 52.381 15.14 0.00 42.01 3.02
1151 1254 2.928301 GCTCAATGCGTCTGAGTTCTGA 60.928 50.000 15.14 0.00 42.01 3.27
1152 1255 2.665537 CTCAATGCGTCTGAGTTCTGAC 59.334 50.000 8.58 8.58 40.18 3.51
1153 1256 2.035832 TCAATGCGTCTGAGTTCTGACA 59.964 45.455 16.15 2.19 42.61 3.58
1154 1257 2.998670 CAATGCGTCTGAGTTCTGACAT 59.001 45.455 16.15 4.04 42.61 3.06
1155 1258 4.082245 TCAATGCGTCTGAGTTCTGACATA 60.082 41.667 16.15 7.16 42.61 2.29
1160 1263 4.108336 CGTCTGAGTTCTGACATATGTGG 58.892 47.826 14.43 6.10 42.61 4.17
1163 1266 2.205074 GAGTTCTGACATATGTGGCGG 58.795 52.381 14.43 5.03 41.44 6.13
1170 1273 1.792949 GACATATGTGGCGGATTCGAC 59.207 52.381 14.43 0.00 46.45 4.20
1371 1474 2.359967 GGAGCCGGCTACCACTCTT 61.360 63.158 32.97 3.02 30.13 2.85
1450 1553 0.680921 TACACTACGGCCGGCTACTT 60.681 55.000 31.76 9.87 0.00 2.24
1560 1663 1.951510 GTCCACCACGAGTACACGA 59.048 57.895 19.65 0.00 37.03 4.35
1670 1777 8.286097 TGCGTTCATTTTTCTTTGTTTTTCTTT 58.714 25.926 0.00 0.00 0.00 2.52
1677 1784 9.689976 ATTTTTCTTTGTTTTTCTTTTGTTGGG 57.310 25.926 0.00 0.00 0.00 4.12
1679 1786 6.115448 TCTTTGTTTTTCTTTTGTTGGGGA 57.885 33.333 0.00 0.00 0.00 4.81
1692 1799 0.249120 TTGGGGAGTGCACTGTATCG 59.751 55.000 27.27 0.00 0.00 2.92
1693 1800 0.902984 TGGGGAGTGCACTGTATCGT 60.903 55.000 27.27 0.00 0.00 3.73
1694 1801 0.460284 GGGGAGTGCACTGTATCGTG 60.460 60.000 27.27 0.00 37.94 4.35
1695 1802 0.246635 GGGAGTGCACTGTATCGTGT 59.753 55.000 27.27 0.00 37.24 4.49
1696 1803 1.350193 GGAGTGCACTGTATCGTGTG 58.650 55.000 27.27 0.00 37.24 3.82
1697 1804 1.336887 GGAGTGCACTGTATCGTGTGT 60.337 52.381 27.27 0.00 37.24 3.72
1698 1805 2.404215 GAGTGCACTGTATCGTGTGTT 58.596 47.619 27.27 0.00 37.24 3.32
1699 1806 2.404215 AGTGCACTGTATCGTGTGTTC 58.596 47.619 20.97 0.00 37.24 3.18
1700 1807 1.124297 GTGCACTGTATCGTGTGTTCG 59.876 52.381 10.32 0.00 37.24 3.95
1701 1808 1.269361 TGCACTGTATCGTGTGTTCGT 60.269 47.619 0.00 0.00 37.24 3.85
1735 1843 0.744057 CCATCGGGGCCAATTTTTGC 60.744 55.000 4.39 0.00 0.00 3.68
1756 1864 0.539986 GGCCCTCGTTGGATCTGTAA 59.460 55.000 0.00 0.00 38.35 2.41
1974 2087 1.531602 GGTGACCCAAAGGCTTGCT 60.532 57.895 0.00 0.00 36.11 3.91
1992 2105 1.948611 GCTTCGGCCACAATGGAGTTA 60.949 52.381 2.24 0.00 40.96 2.24
2003 2116 5.183713 CCACAATGGAGTTAAGCAGAATTGA 59.816 40.000 0.00 0.00 40.96 2.57
2170 2283 1.672356 AAGTGCCATGAGGTCGTGC 60.672 57.895 0.00 0.00 37.19 5.34
2171 2284 2.046892 GTGCCATGAGGTCGTGCT 60.047 61.111 0.00 0.00 37.19 4.40
2437 2551 2.636647 ACCAGGCCCAAAATGTTTTG 57.363 45.000 0.00 10.48 45.34 2.44
2469 2583 6.812656 TGCATTGGATTGTCATATTTTGTCAC 59.187 34.615 0.00 0.00 0.00 3.67
2471 2585 7.493320 GCATTGGATTGTCATATTTTGTCACAT 59.507 33.333 0.00 0.00 0.00 3.21
2474 2588 8.224389 TGGATTGTCATATTTTGTCACATAGG 57.776 34.615 0.00 0.00 0.00 2.57
2475 2589 8.052141 TGGATTGTCATATTTTGTCACATAGGA 58.948 33.333 0.00 0.00 0.00 2.94
2476 2590 8.562892 GGATTGTCATATTTTGTCACATAGGAG 58.437 37.037 0.00 0.00 0.00 3.69
2477 2591 9.113838 GATTGTCATATTTTGTCACATAGGAGT 57.886 33.333 0.00 0.00 0.00 3.85
2543 2661 7.187824 TCATAAGTTGACAAGCCTAAGAGAT 57.812 36.000 0.00 0.00 0.00 2.75
2551 2669 4.151883 ACAAGCCTAAGAGATTTTTGCCA 58.848 39.130 0.00 0.00 0.00 4.92
2581 2699 1.405821 TGTCCAAACGCCACGAATTTT 59.594 42.857 0.00 0.00 0.00 1.82
2582 2700 2.159226 TGTCCAAACGCCACGAATTTTT 60.159 40.909 0.00 0.00 0.00 1.94
2583 2701 2.217620 GTCCAAACGCCACGAATTTTTG 59.782 45.455 0.00 0.00 0.00 2.44
2584 2702 1.070909 CCAAACGCCACGAATTTTTGC 60.071 47.619 0.00 0.00 0.00 3.68
2585 2703 1.590238 CAAACGCCACGAATTTTTGCA 59.410 42.857 0.00 0.00 0.00 4.08
2586 2704 1.204792 AACGCCACGAATTTTTGCAC 58.795 45.000 0.00 0.00 0.00 4.57
2587 2705 0.932585 ACGCCACGAATTTTTGCACG 60.933 50.000 0.00 0.00 0.00 5.34
2588 2706 1.486801 GCCACGAATTTTTGCACGC 59.513 52.632 0.00 0.00 0.00 5.34
2589 2707 1.211818 GCCACGAATTTTTGCACGCA 61.212 50.000 0.00 0.00 0.00 5.24
2590 2708 0.502275 CCACGAATTTTTGCACGCAC 59.498 50.000 0.00 0.00 0.00 5.34
2591 2709 1.195347 CACGAATTTTTGCACGCACA 58.805 45.000 0.00 0.00 0.00 4.57
2592 2710 1.786004 CACGAATTTTTGCACGCACAT 59.214 42.857 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.400975 GATGAGAGGGGAGCATGCAT 59.599 55.000 21.98 4.75 0.00 3.96
2 3 0.035176 GAGATGAGAGGGGAGCATGC 59.965 60.000 10.51 10.51 0.00 4.06
3 4 1.619827 GAGAGATGAGAGGGGAGCATG 59.380 57.143 0.00 0.00 0.00 4.06
4 5 1.504660 AGAGAGATGAGAGGGGAGCAT 59.495 52.381 0.00 0.00 0.00 3.79
6 7 2.086610 AAGAGAGATGAGAGGGGAGC 57.913 55.000 0.00 0.00 0.00 4.70
7 8 2.965147 GGAAAGAGAGATGAGAGGGGAG 59.035 54.545 0.00 0.00 0.00 4.30
8 9 2.589664 AGGAAAGAGAGATGAGAGGGGA 59.410 50.000 0.00 0.00 0.00 4.81
9 10 2.965147 GAGGAAAGAGAGATGAGAGGGG 59.035 54.545 0.00 0.00 0.00 4.79
10 11 3.891366 GAGAGGAAAGAGAGATGAGAGGG 59.109 52.174 0.00 0.00 0.00 4.30
11 12 4.535781 TGAGAGGAAAGAGAGATGAGAGG 58.464 47.826 0.00 0.00 0.00 3.69
12 13 6.016527 CAGATGAGAGGAAAGAGAGATGAGAG 60.017 46.154 0.00 0.00 0.00 3.20
13 14 5.829391 CAGATGAGAGGAAAGAGAGATGAGA 59.171 44.000 0.00 0.00 0.00 3.27
14 15 5.010314 CCAGATGAGAGGAAAGAGAGATGAG 59.990 48.000 0.00 0.00 0.00 2.90
15 16 4.894705 CCAGATGAGAGGAAAGAGAGATGA 59.105 45.833 0.00 0.00 0.00 2.92
16 17 4.894705 TCCAGATGAGAGGAAAGAGAGATG 59.105 45.833 0.00 0.00 0.00 2.90
17 18 4.895297 GTCCAGATGAGAGGAAAGAGAGAT 59.105 45.833 0.00 0.00 35.29 2.75
18 19 4.264128 TGTCCAGATGAGAGGAAAGAGAGA 60.264 45.833 0.00 0.00 35.29 3.10
19 20 4.022603 TGTCCAGATGAGAGGAAAGAGAG 58.977 47.826 0.00 0.00 35.29 3.20
20 21 3.766591 GTGTCCAGATGAGAGGAAAGAGA 59.233 47.826 0.00 0.00 35.29 3.10
21 22 3.118811 GGTGTCCAGATGAGAGGAAAGAG 60.119 52.174 0.00 0.00 35.29 2.85
22 23 2.834549 GGTGTCCAGATGAGAGGAAAGA 59.165 50.000 0.00 0.00 35.29 2.52
23 24 2.568956 TGGTGTCCAGATGAGAGGAAAG 59.431 50.000 0.00 0.00 35.29 2.62
24 25 2.303022 GTGGTGTCCAGATGAGAGGAAA 59.697 50.000 0.00 0.00 35.29 3.13
25 26 1.902508 GTGGTGTCCAGATGAGAGGAA 59.097 52.381 0.00 0.00 35.29 3.36
26 27 1.203174 TGTGGTGTCCAGATGAGAGGA 60.203 52.381 0.00 0.00 32.34 3.71
27 28 1.066573 GTGTGGTGTCCAGATGAGAGG 60.067 57.143 0.00 0.00 32.34 3.69
28 29 1.066573 GGTGTGGTGTCCAGATGAGAG 60.067 57.143 0.00 0.00 32.34 3.20
29 30 0.976641 GGTGTGGTGTCCAGATGAGA 59.023 55.000 0.00 0.00 32.34 3.27
30 31 0.686789 TGGTGTGGTGTCCAGATGAG 59.313 55.000 0.00 0.00 32.34 2.90
31 32 1.361204 ATGGTGTGGTGTCCAGATGA 58.639 50.000 0.00 0.00 37.14 2.92
32 33 3.348647 TTATGGTGTGGTGTCCAGATG 57.651 47.619 0.00 0.00 37.14 2.90
33 34 5.608437 AGATATTATGGTGTGGTGTCCAGAT 59.392 40.000 0.00 0.00 37.14 2.90
34 35 4.968719 AGATATTATGGTGTGGTGTCCAGA 59.031 41.667 0.00 0.00 37.14 3.86
35 36 5.163311 TGAGATATTATGGTGTGGTGTCCAG 60.163 44.000 0.00 0.00 37.14 3.86
36 37 4.719273 TGAGATATTATGGTGTGGTGTCCA 59.281 41.667 0.00 0.00 38.14 4.02
37 38 5.057149 GTGAGATATTATGGTGTGGTGTCC 58.943 45.833 0.00 0.00 0.00 4.02
38 39 5.918608 AGTGAGATATTATGGTGTGGTGTC 58.081 41.667 0.00 0.00 0.00 3.67
39 40 5.957771 AGTGAGATATTATGGTGTGGTGT 57.042 39.130 0.00 0.00 0.00 4.16
40 41 6.816136 TGTAGTGAGATATTATGGTGTGGTG 58.184 40.000 0.00 0.00 0.00 4.17
41 42 7.256332 GGATGTAGTGAGATATTATGGTGTGGT 60.256 40.741 0.00 0.00 0.00 4.16
42 43 7.099764 GGATGTAGTGAGATATTATGGTGTGG 58.900 42.308 0.00 0.00 0.00 4.17
43 44 7.670364 TGGATGTAGTGAGATATTATGGTGTG 58.330 38.462 0.00 0.00 0.00 3.82
44 45 7.855784 TGGATGTAGTGAGATATTATGGTGT 57.144 36.000 0.00 0.00 0.00 4.16
45 46 7.767659 CCATGGATGTAGTGAGATATTATGGTG 59.232 40.741 5.56 0.00 0.00 4.17
46 47 7.582242 GCCATGGATGTAGTGAGATATTATGGT 60.582 40.741 18.40 0.00 34.25 3.55
47 48 6.765036 GCCATGGATGTAGTGAGATATTATGG 59.235 42.308 18.40 0.00 34.73 2.74
48 49 6.765036 GGCCATGGATGTAGTGAGATATTATG 59.235 42.308 18.40 0.00 0.00 1.90
49 50 6.126652 GGGCCATGGATGTAGTGAGATATTAT 60.127 42.308 18.40 0.00 0.00 1.28
50 51 5.189736 GGGCCATGGATGTAGTGAGATATTA 59.810 44.000 18.40 0.00 0.00 0.98
51 52 4.018960 GGGCCATGGATGTAGTGAGATATT 60.019 45.833 18.40 0.00 0.00 1.28
52 53 3.521126 GGGCCATGGATGTAGTGAGATAT 59.479 47.826 18.40 0.00 0.00 1.63
53 54 2.906389 GGGCCATGGATGTAGTGAGATA 59.094 50.000 18.40 0.00 0.00 1.98
54 55 1.701847 GGGCCATGGATGTAGTGAGAT 59.298 52.381 18.40 0.00 0.00 2.75
55 56 1.131638 GGGCCATGGATGTAGTGAGA 58.868 55.000 18.40 0.00 0.00 3.27
56 57 0.109342 GGGGCCATGGATGTAGTGAG 59.891 60.000 18.40 0.00 0.00 3.51
57 58 0.327480 AGGGGCCATGGATGTAGTGA 60.327 55.000 18.40 0.00 0.00 3.41
58 59 1.434188 TAGGGGCCATGGATGTAGTG 58.566 55.000 18.40 0.00 0.00 2.74
59 60 2.157942 AGATAGGGGCCATGGATGTAGT 60.158 50.000 18.40 0.00 0.00 2.73
60 61 2.555664 AGATAGGGGCCATGGATGTAG 58.444 52.381 18.40 0.00 0.00 2.74
61 62 2.741159 AGATAGGGGCCATGGATGTA 57.259 50.000 18.40 0.58 0.00 2.29
62 63 2.157942 AGTAGATAGGGGCCATGGATGT 60.158 50.000 18.40 0.00 0.00 3.06
63 64 2.503356 GAGTAGATAGGGGCCATGGATG 59.497 54.545 18.40 0.00 0.00 3.51
64 65 2.388563 AGAGTAGATAGGGGCCATGGAT 59.611 50.000 18.40 0.00 0.00 3.41
65 66 1.795786 AGAGTAGATAGGGGCCATGGA 59.204 52.381 18.40 0.00 0.00 3.41
66 67 2.334006 AGAGTAGATAGGGGCCATGG 57.666 55.000 7.63 7.63 0.00 3.66
67 68 5.104735 GGATAAAGAGTAGATAGGGGCCATG 60.105 48.000 4.39 0.00 0.00 3.66
68 69 5.033522 GGATAAAGAGTAGATAGGGGCCAT 58.966 45.833 4.39 0.00 0.00 4.40
69 70 4.426704 GGATAAAGAGTAGATAGGGGCCA 58.573 47.826 4.39 0.00 0.00 5.36
70 71 3.775866 GGGATAAAGAGTAGATAGGGGCC 59.224 52.174 0.00 0.00 0.00 5.80
71 72 3.775866 GGGGATAAAGAGTAGATAGGGGC 59.224 52.174 0.00 0.00 0.00 5.80
72 73 4.202901 TGGGGGATAAAGAGTAGATAGGGG 60.203 50.000 0.00 0.00 0.00 4.79
73 74 5.024803 TGGGGGATAAAGAGTAGATAGGG 57.975 47.826 0.00 0.00 0.00 3.53
74 75 5.248705 GGTTGGGGGATAAAGAGTAGATAGG 59.751 48.000 0.00 0.00 0.00 2.57
75 76 5.047235 CGGTTGGGGGATAAAGAGTAGATAG 60.047 48.000 0.00 0.00 0.00 2.08
76 77 4.836736 CGGTTGGGGGATAAAGAGTAGATA 59.163 45.833 0.00 0.00 0.00 1.98
77 78 3.646637 CGGTTGGGGGATAAAGAGTAGAT 59.353 47.826 0.00 0.00 0.00 1.98
78 79 3.036091 CGGTTGGGGGATAAAGAGTAGA 58.964 50.000 0.00 0.00 0.00 2.59
79 80 2.104281 CCGGTTGGGGGATAAAGAGTAG 59.896 54.545 0.00 0.00 0.00 2.57
80 81 2.121129 CCGGTTGGGGGATAAAGAGTA 58.879 52.381 0.00 0.00 0.00 2.59
81 82 0.916809 CCGGTTGGGGGATAAAGAGT 59.083 55.000 0.00 0.00 0.00 3.24
82 83 1.134189 GTCCGGTTGGGGGATAAAGAG 60.134 57.143 0.00 0.00 35.67 2.85
83 84 0.913924 GTCCGGTTGGGGGATAAAGA 59.086 55.000 0.00 0.00 35.67 2.52
84 85 0.916809 AGTCCGGTTGGGGGATAAAG 59.083 55.000 0.00 0.00 35.67 1.85
85 86 2.267160 TAGTCCGGTTGGGGGATAAA 57.733 50.000 0.00 0.00 35.67 1.40
86 87 2.500269 ATAGTCCGGTTGGGGGATAA 57.500 50.000 0.00 0.00 35.67 1.75
87 88 2.500269 AATAGTCCGGTTGGGGGATA 57.500 50.000 0.00 0.00 35.67 2.59
88 89 1.493446 GAAATAGTCCGGTTGGGGGAT 59.507 52.381 0.00 0.00 35.67 3.85
89 90 0.913924 GAAATAGTCCGGTTGGGGGA 59.086 55.000 0.00 0.00 36.01 4.81
90 91 0.621609 TGAAATAGTCCGGTTGGGGG 59.378 55.000 0.00 0.00 36.01 5.40
91 92 2.092646 TCATGAAATAGTCCGGTTGGGG 60.093 50.000 0.00 0.00 36.01 4.96
92 93 3.275617 TCATGAAATAGTCCGGTTGGG 57.724 47.619 0.00 0.00 35.24 4.12
93 94 5.049405 GCTATTCATGAAATAGTCCGGTTGG 60.049 44.000 13.09 0.00 45.89 3.77
94 95 5.049405 GGCTATTCATGAAATAGTCCGGTTG 60.049 44.000 13.09 0.00 43.78 3.77
95 96 5.063880 GGCTATTCATGAAATAGTCCGGTT 58.936 41.667 13.09 0.00 43.78 4.44
96 97 4.642429 GGCTATTCATGAAATAGTCCGGT 58.358 43.478 13.09 0.00 43.78 5.28
101 102 8.174733 CCATTGAAGGCTATTCATGAAATAGT 57.825 34.615 13.09 0.00 45.89 2.12
117 118 1.821332 GGGAGAGCGCCATTGAAGG 60.821 63.158 2.29 0.00 0.00 3.46
118 119 2.176273 CGGGAGAGCGCCATTGAAG 61.176 63.158 2.29 0.00 0.00 3.02
119 120 1.609635 TACGGGAGAGCGCCATTGAA 61.610 55.000 2.29 0.00 0.00 2.69
120 121 1.399744 ATACGGGAGAGCGCCATTGA 61.400 55.000 2.29 0.00 0.00 2.57
121 122 0.946221 GATACGGGAGAGCGCCATTG 60.946 60.000 2.29 0.00 0.00 2.82
122 123 1.367840 GATACGGGAGAGCGCCATT 59.632 57.895 2.29 0.00 0.00 3.16
123 124 1.188219 ATGATACGGGAGAGCGCCAT 61.188 55.000 2.29 0.00 0.00 4.40
124 125 1.832608 ATGATACGGGAGAGCGCCA 60.833 57.895 2.29 0.00 0.00 5.69
125 126 1.373497 CATGATACGGGAGAGCGCC 60.373 63.158 2.29 0.00 0.00 6.53
126 127 0.596577 TACATGATACGGGAGAGCGC 59.403 55.000 0.00 0.00 0.00 5.92
127 128 2.229062 ACATACATGATACGGGAGAGCG 59.771 50.000 0.00 0.00 0.00 5.03
128 129 3.579709 CACATACATGATACGGGAGAGC 58.420 50.000 0.00 0.00 0.00 4.09
129 130 3.826729 TCCACATACATGATACGGGAGAG 59.173 47.826 0.00 0.00 0.00 3.20
130 131 3.572682 GTCCACATACATGATACGGGAGA 59.427 47.826 0.00 0.00 0.00 3.71
131 132 3.306088 GGTCCACATACATGATACGGGAG 60.306 52.174 0.00 0.00 0.00 4.30
132 133 2.631062 GGTCCACATACATGATACGGGA 59.369 50.000 0.00 0.00 0.00 5.14
133 134 2.367241 TGGTCCACATACATGATACGGG 59.633 50.000 0.00 0.00 0.00 5.28
134 135 3.390135 GTGGTCCACATACATGATACGG 58.610 50.000 17.59 0.00 34.08 4.02
135 136 3.049912 CGTGGTCCACATACATGATACG 58.950 50.000 21.91 0.00 33.40 3.06
136 137 4.049186 GACGTGGTCCACATACATGATAC 58.951 47.826 21.91 0.00 33.40 2.24
137 138 4.316205 GACGTGGTCCACATACATGATA 57.684 45.455 21.91 0.00 33.40 2.15
138 139 3.179443 GACGTGGTCCACATACATGAT 57.821 47.619 21.91 0.00 33.40 2.45
139 140 2.665649 GACGTGGTCCACATACATGA 57.334 50.000 21.91 0.00 33.40 3.07
156 157 6.307155 CAAATGTCTGTTTCTATGTTCGGAC 58.693 40.000 0.00 0.00 36.91 4.79
161 162 6.392354 CATGGCAAATGTCTGTTTCTATGTT 58.608 36.000 0.00 0.00 0.00 2.71
167 168 3.248266 GAGCATGGCAAATGTCTGTTTC 58.752 45.455 0.00 0.00 0.00 2.78
178 179 1.215912 CCGCAAATGAGCATGGCAA 59.784 52.632 0.00 0.00 0.00 4.52
182 183 0.099968 CTGACCCGCAAATGAGCATG 59.900 55.000 0.00 0.00 0.00 4.06
186 187 2.256391 TTGCTGACCCGCAAATGAG 58.744 52.632 0.00 0.00 46.00 2.90
187 188 4.490696 TTGCTGACCCGCAAATGA 57.509 50.000 0.00 0.00 46.00 2.57
202 203 7.171337 GGCAAACATATAAGGGCATTTACATTG 59.829 37.037 0.00 0.00 0.00 2.82
203 204 7.216494 GGCAAACATATAAGGGCATTTACATT 58.784 34.615 0.00 0.00 0.00 2.71
207 208 5.463154 AGGGCAAACATATAAGGGCATTTA 58.537 37.500 0.00 0.00 0.00 1.40
209 210 3.897505 GAGGGCAAACATATAAGGGCATT 59.102 43.478 0.00 0.00 0.00 3.56
211 212 2.243478 TGAGGGCAAACATATAAGGGCA 59.757 45.455 0.00 0.00 0.00 5.36
223 224 1.377202 GCCGAGATGTGAGGGCAAA 60.377 57.895 0.00 0.00 44.91 3.68
249 250 5.170021 TGTTATGCACAATGGCTTCAAATC 58.830 37.500 0.00 0.00 29.87 2.17
254 255 2.159198 CCCTGTTATGCACAATGGCTTC 60.159 50.000 0.00 0.00 33.87 3.86
264 265 3.068165 CGACTAGATGACCCTGTTATGCA 59.932 47.826 0.00 0.00 0.00 3.96
272 273 2.677542 TATGCCGACTAGATGACCCT 57.322 50.000 0.00 0.00 0.00 4.34
300 301 3.796844 GCTCCACAAGCCTTCAAAACTTC 60.797 47.826 0.00 0.00 45.92 3.01
329 330 0.958822 AAAACTTCATGGACCACCGC 59.041 50.000 0.00 0.00 39.42 5.68
341 342 5.735892 GTCGTTGTAGTCAAACCAAAACTTC 59.264 40.000 0.00 0.00 35.20 3.01
359 360 1.826327 CAGTTGCCACTTTGTCGTTG 58.174 50.000 0.00 0.00 0.00 4.10
378 379 1.971695 CCACGGGAAGGTTGGAAGC 60.972 63.158 0.00 0.00 0.00 3.86
392 393 5.457473 GTGACCAACTTAAACAAATTCCACG 59.543 40.000 0.00 0.00 0.00 4.94
450 451 8.694581 TTTTTAATTTTCTTCTAAGACGGGGA 57.305 30.769 0.00 0.00 34.13 4.81
478 486 1.798813 GTTTGAGCTACCGACCTGTTG 59.201 52.381 0.00 0.00 0.00 3.33
490 498 1.004440 GCGGAGACTGGTTTGAGCT 60.004 57.895 0.00 0.00 0.00 4.09
507 515 2.028484 TTCACTGTGGTCGACGGC 59.972 61.111 9.92 5.25 33.72 5.68
511 519 2.513259 GGGGGTTCACTGTGGTCGA 61.513 63.158 8.11 0.00 0.00 4.20
535 543 1.521423 GGCGATAAATCTCGGACGTTG 59.479 52.381 0.00 0.00 39.05 4.10
621 629 2.661709 CGTGGCGATTTGTATATTGCGG 60.662 50.000 0.00 0.00 36.04 5.69
672 680 2.973419 TTTTTACCGTGGATTCGTGC 57.027 45.000 0.00 0.00 0.00 5.34
780 859 3.119708 GCCTTATATATTGCAGCAGTGGC 60.120 47.826 0.00 0.00 41.61 5.01
854 933 3.119673 CGATTCTCAGCTGAGTACTGTGT 60.120 47.826 36.32 16.78 42.60 3.72
858 937 3.616219 ACTCGATTCTCAGCTGAGTACT 58.384 45.455 36.32 24.14 42.60 2.73
859 938 3.242936 GGACTCGATTCTCAGCTGAGTAC 60.243 52.174 36.32 26.69 39.83 2.73
860 939 2.946329 GGACTCGATTCTCAGCTGAGTA 59.054 50.000 36.32 30.06 39.83 2.59
872 951 0.742505 TATTGTCGCCGGACTCGATT 59.257 50.000 5.05 0.00 43.79 3.34
907 987 9.906660 AATTTCGAAAGATATTGCAAGTAAACA 57.093 25.926 16.80 0.00 39.71 2.83
948 1028 9.793252 AAATCGATCAAAAATAGACCAATGAAG 57.207 29.630 0.00 0.00 0.00 3.02
951 1031 9.229784 CAGAAATCGATCAAAAATAGACCAATG 57.770 33.333 0.00 0.00 0.00 2.82
1074 1172 1.202325 TGTATAGGTTGCTGCGTACCG 60.202 52.381 15.30 0.00 39.46 4.02
1083 1181 6.599638 AGAACAGAGGAATTTGTATAGGTTGC 59.400 38.462 0.00 0.00 0.00 4.17
1085 1183 8.383175 TCAAGAACAGAGGAATTTGTATAGGTT 58.617 33.333 0.00 0.00 0.00 3.50
1086 1184 7.824779 GTCAAGAACAGAGGAATTTGTATAGGT 59.175 37.037 0.00 0.00 0.00 3.08
1087 1185 7.010552 CGTCAAGAACAGAGGAATTTGTATAGG 59.989 40.741 0.00 0.00 0.00 2.57
1146 1249 3.466836 GAATCCGCCACATATGTCAGAA 58.533 45.455 5.07 0.00 0.00 3.02
1149 1252 1.410882 TCGAATCCGCCACATATGTCA 59.589 47.619 5.07 0.00 35.37 3.58
1150 1253 1.792949 GTCGAATCCGCCACATATGTC 59.207 52.381 5.07 0.00 35.37 3.06
1151 1254 1.540363 GGTCGAATCCGCCACATATGT 60.540 52.381 1.41 1.41 33.96 2.29
1152 1255 1.148310 GGTCGAATCCGCCACATATG 58.852 55.000 0.00 0.00 33.96 1.78
1153 1256 0.756294 TGGTCGAATCCGCCACATAT 59.244 50.000 0.00 0.00 37.17 1.78
1154 1257 0.104120 CTGGTCGAATCCGCCACATA 59.896 55.000 0.00 0.00 37.17 2.29
1155 1258 1.153369 CTGGTCGAATCCGCCACAT 60.153 57.895 0.00 0.00 37.17 3.21
1160 1263 1.519455 CACTCCTGGTCGAATCCGC 60.519 63.158 0.00 0.00 35.37 5.54
1163 1266 1.135333 GACTCCACTCCTGGTCGAATC 59.865 57.143 0.00 0.00 38.90 2.52
1170 1273 1.606601 TCACCGACTCCACTCCTGG 60.607 63.158 0.00 0.00 39.23 4.45
1232 1335 3.998672 TGGTTGGAGTCGACGCCC 61.999 66.667 31.74 24.98 34.71 6.13
1496 1599 2.789893 CGGGTAGTACTCGTACTCGTAC 59.210 54.545 14.61 11.46 44.58 3.67
1571 1674 1.890979 CATGATGGAGCAGCCGGTC 60.891 63.158 1.90 0.00 40.66 4.79
1670 1777 0.840617 TACAGTGCACTCCCCAACAA 59.159 50.000 18.64 0.00 0.00 2.83
1677 1784 1.336887 ACACACGATACAGTGCACTCC 60.337 52.381 18.64 5.71 45.45 3.85
1679 1786 2.404215 GAACACACGATACAGTGCACT 58.596 47.619 15.25 15.25 45.45 4.40
1692 1799 1.005347 GCACTACACACACGAACACAC 60.005 52.381 0.00 0.00 0.00 3.82
1693 1800 1.282817 GCACTACACACACGAACACA 58.717 50.000 0.00 0.00 0.00 3.72
1694 1801 0.228742 CGCACTACACACACGAACAC 59.771 55.000 0.00 0.00 0.00 3.32
1695 1802 0.100861 TCGCACTACACACACGAACA 59.899 50.000 0.00 0.00 0.00 3.18
1696 1803 1.385743 GATCGCACTACACACACGAAC 59.614 52.381 0.00 0.00 36.22 3.95
1697 1804 1.667756 GGATCGCACTACACACACGAA 60.668 52.381 0.00 0.00 36.22 3.85
1698 1805 0.109458 GGATCGCACTACACACACGA 60.109 55.000 0.00 0.00 37.15 4.35
1699 1806 0.388006 TGGATCGCACTACACACACG 60.388 55.000 0.00 0.00 0.00 4.49
1700 1807 1.927174 GATGGATCGCACTACACACAC 59.073 52.381 0.00 0.00 0.00 3.82
1701 1808 1.469079 CGATGGATCGCACTACACACA 60.469 52.381 0.00 0.00 43.84 3.72
1735 1843 3.470888 AGATCCAACGAGGGCCGG 61.471 66.667 0.00 0.00 43.93 6.13
1756 1864 4.463891 CAGGCACCCATTTGACTAAGAAAT 59.536 41.667 0.00 0.00 30.77 2.17
1974 2087 2.432444 CTTAACTCCATTGTGGCCGAA 58.568 47.619 0.00 0.00 37.47 4.30
1992 2105 2.652590 GCTCCTCCATCAATTCTGCTT 58.347 47.619 0.00 0.00 0.00 3.91
2003 2116 1.220206 CACAAGAGCGCTCCTCCAT 59.780 57.895 32.94 12.34 41.74 3.41
2170 2283 5.299531 AGAGATTTGGCATTGATGACATGAG 59.700 40.000 0.00 0.00 46.90 2.90
2171 2284 5.067283 CAGAGATTTGGCATTGATGACATGA 59.933 40.000 0.00 0.00 46.90 3.07
2437 2551 5.779529 ATGACAATCCAATGCATAGAACC 57.220 39.130 0.00 0.00 0.00 3.62
2522 2640 8.567948 CAAAAATCTCTTAGGCTTGTCAACTTA 58.432 33.333 0.00 0.00 0.00 2.24
2530 2648 4.022068 TGTGGCAAAAATCTCTTAGGCTTG 60.022 41.667 0.00 0.00 0.00 4.01
2532 2650 3.507622 GTGTGGCAAAAATCTCTTAGGCT 59.492 43.478 0.00 0.00 0.00 4.58
2533 2651 3.255642 TGTGTGGCAAAAATCTCTTAGGC 59.744 43.478 0.00 0.00 0.00 3.93
2535 2653 7.439056 ACAAAATGTGTGGCAAAAATCTCTTAG 59.561 33.333 0.00 0.00 39.72 2.18
2536 2654 7.271511 ACAAAATGTGTGGCAAAAATCTCTTA 58.728 30.769 0.00 0.00 39.72 2.10
2538 2656 5.673514 ACAAAATGTGTGGCAAAAATCTCT 58.326 33.333 0.00 0.00 39.72 3.10


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

AutoCloner maintained by Alex Coulton.