Multiple sequence alignment - TraesCS3D01G125800

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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 TraesCS3D01G125800 chr3D 100.000 3632 0 0 1 3632 84113456 84109825 0.000000e+00 6708.0
1 TraesCS3D01G125800 chr3D 93.343 2809 109 17 860 3632 84121336 84118570 0.000000e+00 4080.0
2 TraesCS3D01G125800 chr3D 85.686 1020 146 0 1614 2633 84500391 84499372 0.000000e+00 1075.0
3 TraesCS3D01G125800 chr3D 86.717 527 59 11 1006 1525 84498179 84497657 3.150000e-160 575.0
4 TraesCS3D01G125800 chr3D 84.795 513 69 8 1006 1513 84501163 84500655 1.160000e-139 507.0
5 TraesCS3D01G125800 chr3D 84.600 513 69 8 1006 1513 84505654 84505147 5.410000e-138 501.0
6 TraesCS3D01G125800 chr3D 82.000 200 30 5 443 638 562530984 562530787 8.070000e-37 165.0
7 TraesCS3D01G125800 chr3D 97.778 45 1 0 1 45 268070173 268070129 1.080000e-10 78.7
8 TraesCS3D01G125800 chr3A 94.158 3235 108 19 443 3632 100420627 100417429 0.000000e+00 4852.0
9 TraesCS3D01G125800 chr3A 92.657 2996 155 20 671 3632 100435257 100432293 0.000000e+00 4253.0
10 TraesCS3D01G125800 chr3A 84.600 1026 157 1 1609 2633 100882050 100881025 0.000000e+00 1018.0
11 TraesCS3D01G125800 chr3A 85.115 524 70 8 1007 1526 100879804 100879285 2.480000e-146 529.0
12 TraesCS3D01G125800 chr3A 85.156 512 69 6 1006 1513 100844709 100844201 5.380000e-143 518.0
13 TraesCS3D01G125800 chr3A 93.458 107 3 4 28 131 170384393 170384498 4.860000e-34 156.0
14 TraesCS3D01G125800 chr3A 80.402 199 33 5 443 638 697637106 697636911 2.920000e-31 147.0
15 TraesCS3D01G125800 chr3A 97.778 45 1 0 1 45 439296640 439296596 1.080000e-10 78.7
16 TraesCS3D01G125800 chr3B 93.361 2922 117 16 770 3632 132518354 132521257 0.000000e+00 4250.0
17 TraesCS3D01G125800 chr3B 85.867 1026 144 1 1609 2633 133201040 133202065 0.000000e+00 1090.0
18 TraesCS3D01G125800 chr3B 85.131 1029 149 2 1609 2633 132006349 132007377 0.000000e+00 1050.0
19 TraesCS3D01G125800 chr3B 84.990 1026 153 1 1609 2633 132905433 132904408 0.000000e+00 1040.0
20 TraesCS3D01G125800 chr3B 85.441 522 68 8 1009 1526 133203613 133204130 1.480000e-148 536.0
21 TraesCS3D01G125800 chr3B 85.972 499 66 4 1006 1502 133200267 133200763 6.910000e-147 531.0
22 TraesCS3D01G125800 chr3B 83.499 503 72 9 1006 1502 132906218 132905721 3.300000e-125 459.0
23 TraesCS3D01G125800 chr3B 82.353 187 23 8 457 638 42167954 42167773 1.750000e-33 154.0
24 TraesCS3D01G125800 chr7D 74.332 561 86 33 127 638 104087998 104088549 6.190000e-43 185.0
25 TraesCS3D01G125800 chr7D 82.000 200 28 7 443 638 138505376 138505571 2.900000e-36 163.0
26 TraesCS3D01G125800 chr7D 96.842 95 3 0 42 136 519264632 519264538 3.750000e-35 159.0
27 TraesCS3D01G125800 chr7D 95.745 47 2 0 1 47 1043716 1043762 3.890000e-10 76.8
28 TraesCS3D01G125800 chr4A 97.872 94 2 0 41 134 556768042 556767949 2.900000e-36 163.0
29 TraesCS3D01G125800 chr4A 95.050 101 4 1 28 128 556767940 556768039 1.350000e-34 158.0
30 TraesCS3D01G125800 chr4A 92.391 92 7 0 3191 3282 697388889 697388798 8.180000e-27 132.0
31 TraesCS3D01G125800 chr5D 96.875 96 3 0 42 137 267846683 267846588 1.040000e-35 161.0
32 TraesCS3D01G125800 chr2B 82.051 195 29 6 441 632 667127461 667127270 1.040000e-35 161.0
33 TraesCS3D01G125800 chr2B 91.954 87 6 1 3188 3273 175632200 175632114 1.770000e-23 121.0
34 TraesCS3D01G125800 chr2B 97.778 45 1 0 1 45 440366920 440366964 1.080000e-10 78.7
35 TraesCS3D01G125800 chr5A 96.842 95 3 0 41 135 13410014 13409920 3.750000e-35 159.0
36 TraesCS3D01G125800 chr5A 88.430 121 12 2 21 140 178391601 178391482 1.050000e-30 145.0
37 TraesCS3D01G125800 chr2D 96.842 95 2 1 40 133 15682896 15682990 1.350000e-34 158.0
38 TraesCS3D01G125800 chr6A 73.693 574 78 41 127 638 526838120 526837558 4.860000e-34 156.0
39 TraesCS3D01G125800 chr6A 79.058 191 31 5 444 632 100428929 100429112 4.920000e-24 122.0
40 TraesCS3D01G125800 chrUn 92.523 107 4 4 28 131 397152074 397151969 2.260000e-32 150.0
41 TraesCS3D01G125800 chr7A 81.006 179 29 5 463 638 164821155 164821331 1.760000e-28 137.0
42 TraesCS3D01G125800 chr7A 97.674 43 1 0 3 45 164820701 164820743 1.400000e-09 75.0
43 TraesCS3D01G125800 chr1B 78.392 199 38 4 443 638 686790609 686790413 1.370000e-24 124.0
44 TraesCS3D01G125800 chr1B 88.636 88 10 0 3188 3275 392830059 392829972 1.380000e-19 108.0
45 TraesCS3D01G125800 chr2A 91.011 89 7 1 3188 3275 127200389 127200301 6.370000e-23 119.0
46 TraesCS3D01G125800 chr7B 100.000 45 0 0 1 45 524226909 524226865 2.320000e-12 84.2
47 TraesCS3D01G125800 chr7B 100.000 42 0 0 1 42 649406906 649406865 1.080000e-10 78.7
48 TraesCS3D01G125800 chr5B 97.778 45 1 0 1 45 710729400 710729444 1.080000e-10 78.7
49 TraesCS3D01G125800 chr1A 82.955 88 13 2 3191 3276 372553206 372553119 1.080000e-10 78.7


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 TraesCS3D01G125800 chr3D 84109825 84113456 3631 True 6708.0 6708 100.0000 1 3632 1 chr3D.!!$R1 3631
1 TraesCS3D01G125800 chr3D 84118570 84121336 2766 True 4080.0 4080 93.3430 860 3632 1 chr3D.!!$R2 2772
2 TraesCS3D01G125800 chr3D 84497657 84505654 7997 True 664.5 1075 85.4495 1006 2633 4 chr3D.!!$R5 1627
3 TraesCS3D01G125800 chr3A 100417429 100420627 3198 True 4852.0 4852 94.1580 443 3632 1 chr3A.!!$R1 3189
4 TraesCS3D01G125800 chr3A 100432293 100435257 2964 True 4253.0 4253 92.6570 671 3632 1 chr3A.!!$R2 2961
5 TraesCS3D01G125800 chr3A 100879285 100882050 2765 True 773.5 1018 84.8575 1007 2633 2 chr3A.!!$R6 1626
6 TraesCS3D01G125800 chr3A 100844201 100844709 508 True 518.0 518 85.1560 1006 1513 1 chr3A.!!$R3 507
7 TraesCS3D01G125800 chr3B 132518354 132521257 2903 False 4250.0 4250 93.3610 770 3632 1 chr3B.!!$F2 2862
8 TraesCS3D01G125800 chr3B 132006349 132007377 1028 False 1050.0 1050 85.1310 1609 2633 1 chr3B.!!$F1 1024
9 TraesCS3D01G125800 chr3B 132904408 132906218 1810 True 749.5 1040 84.2445 1006 2633 2 chr3B.!!$R2 1627
10 TraesCS3D01G125800 chr3B 133200267 133204130 3863 False 719.0 1090 85.7600 1006 2633 3 chr3B.!!$F3 1627

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
58 59 0.115745 AAACTACTCCCTCCGTCCCA 59.884 55.0 0.00 0.0 0.00 4.37 F
468 469 0.320247 CAGGAGCGCTGTGTCTTCTT 60.320 55.0 18.48 0.0 0.00 2.52 F
469 470 0.320247 AGGAGCGCTGTGTCTTCTTG 60.320 55.0 18.48 0.0 0.00 3.02 F
1282 1304 0.504384 CGTCGACATGATCCAATCGC 59.496 55.0 17.16 0.0 34.59 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1262 1284 1.131771 CGATTGGATCATGTCGACGG 58.868 55.000 11.62 5.86 36.25 4.79 R
2177 6878 1.205655 TCATGCCTCTCTCTTTGACGG 59.794 52.381 0.00 0.00 0.00 4.79 R
2427 7128 8.325787 TCATTTCTTGTAACCATAGCCTCTTTA 58.674 33.333 0.00 0.00 0.00 1.85 R
2667 7411 1.909302 ACCAGTGACCCTGATACAAGG 59.091 52.381 0.00 0.00 44.49 3.61 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
52 53 9.847224 TTTATGAATGAATAAACTACTCCCTCC 57.153 33.333 0.00 0.00 29.18 4.30
53 54 5.914033 TGAATGAATAAACTACTCCCTCCG 58.086 41.667 0.00 0.00 0.00 4.63
54 55 5.424252 TGAATGAATAAACTACTCCCTCCGT 59.576 40.000 0.00 0.00 0.00 4.69
55 56 4.996788 TGAATAAACTACTCCCTCCGTC 57.003 45.455 0.00 0.00 0.00 4.79
56 57 3.703052 TGAATAAACTACTCCCTCCGTCC 59.297 47.826 0.00 0.00 0.00 4.79
57 58 2.149973 TAAACTACTCCCTCCGTCCC 57.850 55.000 0.00 0.00 0.00 4.46
58 59 0.115745 AAACTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
59 60 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
60 61 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
61 62 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
62 63 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
63 64 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
64 65 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
65 66 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
66 67 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
67 68 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
68 69 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
69 70 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
70 71 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
71 72 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
72 73 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
73 74 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
74 75 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
75 76 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
76 77 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
77 78 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
78 79 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
79 80 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
80 81 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
81 82 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
82 83 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
85 86 8.997621 AATATAAGAGCGTTTTTGACACTAGA 57.002 30.769 0.00 0.00 0.00 2.43
86 87 6.707599 ATAAGAGCGTTTTTGACACTAGAC 57.292 37.500 0.00 0.00 0.00 2.59
87 88 4.323553 AGAGCGTTTTTGACACTAGACT 57.676 40.909 0.00 0.00 0.00 3.24
88 89 5.449107 AGAGCGTTTTTGACACTAGACTA 57.551 39.130 0.00 0.00 0.00 2.59
89 90 5.462405 AGAGCGTTTTTGACACTAGACTAG 58.538 41.667 8.00 8.00 0.00 2.57
90 91 5.009811 AGAGCGTTTTTGACACTAGACTAGT 59.990 40.000 9.45 9.45 40.28 2.57
103 104 5.117287 CACTAGACTAGTGTCAAAAACGCTC 59.883 44.000 27.70 0.00 45.69 5.03
104 105 4.323553 AGACTAGTGTCAAAAACGCTCT 57.676 40.909 0.00 0.00 45.69 4.09
105 106 4.694339 AGACTAGTGTCAAAAACGCTCTT 58.306 39.130 0.00 0.00 45.69 2.85
106 107 5.839621 AGACTAGTGTCAAAAACGCTCTTA 58.160 37.500 0.00 0.00 45.69 2.10
107 108 6.456501 AGACTAGTGTCAAAAACGCTCTTAT 58.543 36.000 0.00 0.00 45.69 1.73
108 109 7.600065 AGACTAGTGTCAAAAACGCTCTTATA 58.400 34.615 0.00 0.00 45.69 0.98
109 110 8.251721 AGACTAGTGTCAAAAACGCTCTTATAT 58.748 33.333 0.00 0.00 45.69 0.86
110 111 8.773404 ACTAGTGTCAAAAACGCTCTTATATT 57.227 30.769 0.00 0.00 45.69 1.28
111 112 9.865321 ACTAGTGTCAAAAACGCTCTTATATTA 57.135 29.630 0.00 0.00 45.69 0.98
114 115 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
115 116 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
116 117 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
117 118 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
118 119 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
119 120 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
120 121 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
121 122 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
122 123 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
123 124 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
124 125 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
125 126 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
126 127 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
127 128 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
128 129 3.562108 ATTATGGGACGGAGGGAGTAT 57.438 47.619 0.00 0.00 0.00 2.12
129 130 3.339713 TTATGGGACGGAGGGAGTATT 57.660 47.619 0.00 0.00 0.00 1.89
130 131 2.191981 ATGGGACGGAGGGAGTATTT 57.808 50.000 0.00 0.00 0.00 1.40
131 132 1.961133 TGGGACGGAGGGAGTATTTT 58.039 50.000 0.00 0.00 0.00 1.82
132 133 1.557832 TGGGACGGAGGGAGTATTTTG 59.442 52.381 0.00 0.00 0.00 2.44
133 134 1.558294 GGGACGGAGGGAGTATTTTGT 59.442 52.381 0.00 0.00 0.00 2.83
134 135 2.767960 GGGACGGAGGGAGTATTTTGTA 59.232 50.000 0.00 0.00 0.00 2.41
135 136 3.198417 GGGACGGAGGGAGTATTTTGTAA 59.802 47.826 0.00 0.00 0.00 2.41
136 137 4.439968 GGACGGAGGGAGTATTTTGTAAG 58.560 47.826 0.00 0.00 0.00 2.34
137 138 4.081254 GGACGGAGGGAGTATTTTGTAAGT 60.081 45.833 0.00 0.00 0.00 2.24
138 139 5.082251 ACGGAGGGAGTATTTTGTAAGTC 57.918 43.478 0.00 0.00 0.00 3.01
139 140 4.529377 ACGGAGGGAGTATTTTGTAAGTCA 59.471 41.667 0.00 0.00 0.00 3.41
140 141 4.868734 CGGAGGGAGTATTTTGTAAGTCAC 59.131 45.833 0.00 0.00 0.00 3.67
141 142 4.868734 GGAGGGAGTATTTTGTAAGTCACG 59.131 45.833 0.00 0.00 0.00 4.35
142 143 4.251268 AGGGAGTATTTTGTAAGTCACGC 58.749 43.478 0.00 0.00 0.00 5.34
143 144 3.373130 GGGAGTATTTTGTAAGTCACGCC 59.627 47.826 0.00 0.00 0.00 5.68
144 145 3.998341 GGAGTATTTTGTAAGTCACGCCA 59.002 43.478 0.00 0.00 0.00 5.69
145 146 4.092968 GGAGTATTTTGTAAGTCACGCCAG 59.907 45.833 0.00 0.00 0.00 4.85
146 147 4.638304 AGTATTTTGTAAGTCACGCCAGT 58.362 39.130 0.00 0.00 0.00 4.00
147 148 5.061179 AGTATTTTGTAAGTCACGCCAGTT 58.939 37.500 0.00 0.00 0.00 3.16
148 149 4.911514 ATTTTGTAAGTCACGCCAGTTT 57.088 36.364 0.00 0.00 0.00 2.66
149 150 4.705337 TTTTGTAAGTCACGCCAGTTTT 57.295 36.364 0.00 0.00 0.00 2.43
150 151 4.705337 TTTGTAAGTCACGCCAGTTTTT 57.295 36.364 0.00 0.00 0.00 1.94
151 152 3.684103 TGTAAGTCACGCCAGTTTTTG 57.316 42.857 0.00 0.00 0.00 2.44
152 153 3.271729 TGTAAGTCACGCCAGTTTTTGA 58.728 40.909 0.00 0.00 0.00 2.69
153 154 3.690139 TGTAAGTCACGCCAGTTTTTGAA 59.310 39.130 0.00 0.00 0.00 2.69
154 155 4.336993 TGTAAGTCACGCCAGTTTTTGAAT 59.663 37.500 0.00 0.00 0.00 2.57
155 156 4.385358 AAGTCACGCCAGTTTTTGAATT 57.615 36.364 0.00 0.00 0.00 2.17
156 157 4.385358 AGTCACGCCAGTTTTTGAATTT 57.615 36.364 0.00 0.00 0.00 1.82
157 158 4.754322 AGTCACGCCAGTTTTTGAATTTT 58.246 34.783 0.00 0.00 0.00 1.82
158 159 5.175127 AGTCACGCCAGTTTTTGAATTTTT 58.825 33.333 0.00 0.00 0.00 1.94
159 160 6.334202 AGTCACGCCAGTTTTTGAATTTTTA 58.666 32.000 0.00 0.00 0.00 1.52
160 161 6.475402 AGTCACGCCAGTTTTTGAATTTTTAG 59.525 34.615 0.00 0.00 0.00 1.85
161 162 5.751028 TCACGCCAGTTTTTGAATTTTTAGG 59.249 36.000 0.00 0.00 0.00 2.69
162 163 5.751028 CACGCCAGTTTTTGAATTTTTAGGA 59.249 36.000 0.00 0.00 0.00 2.94
163 164 6.256757 CACGCCAGTTTTTGAATTTTTAGGAA 59.743 34.615 0.00 0.00 0.00 3.36
164 165 6.819146 ACGCCAGTTTTTGAATTTTTAGGAAA 59.181 30.769 0.00 0.00 0.00 3.13
165 166 7.497579 ACGCCAGTTTTTGAATTTTTAGGAAAT 59.502 29.630 0.00 0.00 0.00 2.17
166 167 8.341903 CGCCAGTTTTTGAATTTTTAGGAAATT 58.658 29.630 0.00 0.00 32.98 1.82
196 197 8.772705 TCATTCATAAACACTTTTTGAATTGGC 58.227 29.630 9.39 0.00 34.14 4.52
197 198 6.761731 TCATAAACACTTTTTGAATTGGCG 57.238 33.333 0.00 0.00 0.00 5.69
198 199 6.507900 TCATAAACACTTTTTGAATTGGCGA 58.492 32.000 0.00 0.00 0.00 5.54
199 200 7.151308 TCATAAACACTTTTTGAATTGGCGAT 58.849 30.769 0.00 0.00 0.00 4.58
200 201 7.655328 TCATAAACACTTTTTGAATTGGCGATT 59.345 29.630 0.00 0.00 0.00 3.34
201 202 6.676237 AAACACTTTTTGAATTGGCGATTT 57.324 29.167 0.58 0.00 0.00 2.17
202 203 6.676237 AACACTTTTTGAATTGGCGATTTT 57.324 29.167 0.58 0.00 0.00 1.82
203 204 6.676237 ACACTTTTTGAATTGGCGATTTTT 57.324 29.167 0.58 0.00 0.00 1.94
255 256 8.635877 ACACGAACTTTTAAAAATAATGCACA 57.364 26.923 1.66 0.00 0.00 4.57
256 257 9.255304 ACACGAACTTTTAAAAATAATGCACAT 57.745 25.926 1.66 0.00 0.00 3.21
285 286 7.903995 TGATTTCCCAAACAATTGAATAAGC 57.096 32.000 13.59 0.34 38.94 3.09
286 287 7.448420 TGATTTCCCAAACAATTGAATAAGCA 58.552 30.769 13.59 2.81 38.94 3.91
287 288 7.935755 TGATTTCCCAAACAATTGAATAAGCAA 59.064 29.630 13.59 0.00 38.94 3.91
288 289 8.688747 ATTTCCCAAACAATTGAATAAGCAAA 57.311 26.923 13.59 3.41 38.94 3.68
289 290 8.688747 TTTCCCAAACAATTGAATAAGCAAAT 57.311 26.923 13.59 0.00 38.94 2.32
290 291 9.784531 TTTCCCAAACAATTGAATAAGCAAATA 57.215 25.926 13.59 0.00 38.94 1.40
291 292 9.784531 TTCCCAAACAATTGAATAAGCAAATAA 57.215 25.926 13.59 0.00 38.94 1.40
292 293 9.784531 TCCCAAACAATTGAATAAGCAAATAAA 57.215 25.926 13.59 0.00 38.94 1.40
325 326 6.857777 AAATTGCGAACATTTTTGAATCCA 57.142 29.167 0.00 0.00 0.00 3.41
326 327 5.844301 ATTGCGAACATTTTTGAATCCAC 57.156 34.783 0.00 0.00 0.00 4.02
327 328 4.313277 TGCGAACATTTTTGAATCCACA 57.687 36.364 0.00 0.00 0.00 4.17
328 329 4.686972 TGCGAACATTTTTGAATCCACAA 58.313 34.783 0.00 0.00 0.00 3.33
329 330 5.111989 TGCGAACATTTTTGAATCCACAAA 58.888 33.333 0.00 0.00 37.87 2.83
330 331 5.582269 TGCGAACATTTTTGAATCCACAAAA 59.418 32.000 0.00 0.00 44.42 2.44
440 441 6.684609 ATAAACGAAATTCGAAAAACAGGC 57.315 33.333 22.92 0.00 43.74 4.85
441 442 3.701532 ACGAAATTCGAAAAACAGGCA 57.298 38.095 22.92 0.00 43.74 4.75
450 451 1.344114 GAAAAACAGGCAGCCCAATCA 59.656 47.619 8.22 0.00 0.00 2.57
453 454 1.792757 AACAGGCAGCCCAATCAGGA 61.793 55.000 8.22 0.00 41.22 3.86
468 469 0.320247 CAGGAGCGCTGTGTCTTCTT 60.320 55.000 18.48 0.00 0.00 2.52
469 470 0.320247 AGGAGCGCTGTGTCTTCTTG 60.320 55.000 18.48 0.00 0.00 3.02
520 521 4.292145 TGCATGGGCCGGTCCAAA 62.292 61.111 35.35 18.61 40.62 3.28
614 615 1.135888 GGGTAATTTTCGTGACGCACC 60.136 52.381 0.00 0.37 0.00 5.01
624 625 2.357034 GACGCACCGGAAGAAGCA 60.357 61.111 9.46 0.00 0.00 3.91
633 634 1.303309 CGGAAGAAGCAATAGCCCTG 58.697 55.000 0.00 0.00 43.56 4.45
642 643 2.040412 AGCAATAGCCCTGTTATAGCCC 59.960 50.000 0.00 0.00 43.56 5.19
1074 1096 1.146041 GATGGCGCAGGGTCACATA 59.854 57.895 10.83 0.00 29.38 2.29
1281 1303 1.131771 CCGTCGACATGATCCAATCG 58.868 55.000 17.16 0.00 35.91 3.34
1282 1304 0.504384 CGTCGACATGATCCAATCGC 59.496 55.000 17.16 0.00 34.59 4.58
1383 1405 1.525535 GCCTCCGAGCTGCATCATT 60.526 57.895 1.02 0.00 0.00 2.57
1445 1467 0.830648 CTTGGTATCCCGAGGCTCAA 59.169 55.000 15.95 0.00 38.46 3.02
1810 2030 1.565067 TCAAGAGGAGCTGAGATGCA 58.435 50.000 0.00 0.00 34.99 3.96
2177 6878 1.446272 CAGACGGCTTCGAGGAACC 60.446 63.158 0.00 0.00 37.63 3.62
2427 7128 0.322456 CACGGTGGGGACATGAACAT 60.322 55.000 0.00 0.00 46.14 2.71
2489 7190 0.105709 TACGCCCTGATGGATGAGGA 60.106 55.000 0.00 0.00 32.39 3.71
2526 7227 0.762418 TCCGGGTGAGAGCAAAAGAA 59.238 50.000 0.00 0.00 0.00 2.52
2615 7316 7.234166 ACTGATTCAAGAAATGGGAAACAAGAT 59.766 33.333 0.00 0.00 0.00 2.40
2644 7345 1.068333 GTGGTTGATGCACATGGTGTC 60.068 52.381 0.00 0.00 35.75 3.67
2646 7347 1.068333 GGTTGATGCACATGGTGTCAC 60.068 52.381 0.00 0.00 35.75 3.67
2647 7348 1.881973 GTTGATGCACATGGTGTCACT 59.118 47.619 2.35 0.00 35.75 3.41
2649 7350 3.415457 TGATGCACATGGTGTCACTTA 57.585 42.857 2.35 0.00 35.75 2.24
2667 7411 9.005777 TGTCACTTAATTCCAAATAACCAGTAC 57.994 33.333 0.00 0.00 0.00 2.73
2709 7453 5.007682 GTGGTGGCCTAATTGTTTAGAGAA 58.992 41.667 3.32 0.00 37.59 2.87
2749 7493 8.613060 ATGAGTTGACAGCAATATCGATTATT 57.387 30.769 1.71 0.00 36.22 1.40
2802 7552 6.989759 TCAACATAATGTTACACACAGTCTGT 59.010 34.615 0.00 0.00 41.15 3.41
2928 7694 4.736793 CACACAAATCAAAACTGAGACTGC 59.263 41.667 0.00 0.00 0.00 4.40
3017 7789 8.734386 AGAAATTAGAAGCTTATGTTTGACTGG 58.266 33.333 3.25 0.00 0.00 4.00
3057 7829 7.749377 TTAAGTTTCAAGGATCTCTCCCATA 57.251 36.000 0.00 0.00 43.21 2.74
3088 7860 0.539669 AAAAGGTTTGAGGAGGGCCG 60.540 55.000 0.00 0.00 39.96 6.13
3128 7900 1.839424 AGCAATTACTTCAGGTGCCC 58.161 50.000 0.00 0.00 35.80 5.36
3130 7902 1.094785 CAATTACTTCAGGTGCCCCG 58.905 55.000 0.00 0.00 35.12 5.73
3135 7907 3.172106 TTCAGGTGCCCCGTTCCA 61.172 61.111 0.00 0.00 35.12 3.53
3247 8020 5.291614 GCACTTCAATTTGAACTGCAGAAAA 59.708 36.000 25.81 17.20 42.12 2.29
3273 8834 9.364653 AGTCTTATATTTTGATACGGAGGTAGT 57.635 33.333 0.00 0.00 30.81 2.73
3297 8858 0.823460 AACAACAGTGGGCACAAAGG 59.177 50.000 0.00 0.00 0.00 3.11
3322 8883 7.201696 GGTGTGTGAATAACTTATACCATGGTG 60.202 40.741 28.17 13.05 0.00 4.17
3355 8916 7.341445 TGTGTTTTAAATAGAGTGGCTGTTT 57.659 32.000 0.00 0.00 40.47 2.83
3358 8919 8.082242 GTGTTTTAAATAGAGTGGCTGTTTCAT 58.918 33.333 0.00 0.00 38.62 2.57
3415 8976 7.325660 ACTATGAACAAGCATGGTGAAATAG 57.674 36.000 0.00 5.20 38.36 1.73
3429 9610 8.950210 CATGGTGAAATAGTCTACAATCAAAGT 58.050 33.333 0.00 0.00 0.00 2.66
3452 9633 7.651808 AGTAGGTCAATGTTTTGAGTTCATTG 58.348 34.615 9.81 9.81 42.41 2.82
3462 9643 8.211116 TGTTTTGAGTTCATTGCAAATTCAAT 57.789 26.923 1.71 0.00 33.92 2.57
3617 9805 2.164827 GCTGTTGCACCATGATCATCAA 59.835 45.455 4.86 4.33 39.41 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.847224 GGAGGGAGTAGTTTATTCATTCATAAA 57.153 33.333 0.00 0.00 0.00 1.40
27 28 8.148351 CGGAGGGAGTAGTTTATTCATTCATAA 58.852 37.037 0.00 0.00 0.00 1.90
28 29 7.289317 ACGGAGGGAGTAGTTTATTCATTCATA 59.711 37.037 0.00 0.00 0.00 2.15
29 30 6.099845 ACGGAGGGAGTAGTTTATTCATTCAT 59.900 38.462 0.00 0.00 0.00 2.57
30 31 5.424252 ACGGAGGGAGTAGTTTATTCATTCA 59.576 40.000 0.00 0.00 0.00 2.57
31 32 5.915175 ACGGAGGGAGTAGTTTATTCATTC 58.085 41.667 0.00 0.00 0.00 2.67
32 33 5.163332 GGACGGAGGGAGTAGTTTATTCATT 60.163 44.000 0.00 0.00 0.00 2.57
33 34 4.344390 GGACGGAGGGAGTAGTTTATTCAT 59.656 45.833 0.00 0.00 0.00 2.57
34 35 3.703052 GGACGGAGGGAGTAGTTTATTCA 59.297 47.826 0.00 0.00 0.00 2.57
35 36 3.069300 GGGACGGAGGGAGTAGTTTATTC 59.931 52.174 0.00 0.00 0.00 1.75
36 37 3.036819 GGGACGGAGGGAGTAGTTTATT 58.963 50.000 0.00 0.00 0.00 1.40
37 38 2.023695 TGGGACGGAGGGAGTAGTTTAT 60.024 50.000 0.00 0.00 0.00 1.40
38 39 1.358787 TGGGACGGAGGGAGTAGTTTA 59.641 52.381 0.00 0.00 0.00 2.01
39 40 0.115745 TGGGACGGAGGGAGTAGTTT 59.884 55.000 0.00 0.00 0.00 2.66
40 41 0.338814 ATGGGACGGAGGGAGTAGTT 59.661 55.000 0.00 0.00 0.00 2.24
41 42 1.229131 TATGGGACGGAGGGAGTAGT 58.771 55.000 0.00 0.00 0.00 2.73
42 43 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
43 44 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
44 45 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
45 46 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
46 47 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
47 48 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
48 49 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
49 50 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
50 51 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
51 52 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
52 53 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
53 54 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
54 55 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
55 56 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
56 57 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
60 61 8.870879 GTCTAGTGTCAAAAACGCTCTTATATT 58.129 33.333 0.00 0.00 45.69 1.28
61 62 8.251721 AGTCTAGTGTCAAAAACGCTCTTATAT 58.748 33.333 0.00 0.00 45.69 0.86
62 63 7.600065 AGTCTAGTGTCAAAAACGCTCTTATA 58.400 34.615 0.00 0.00 45.69 0.98
63 64 6.456501 AGTCTAGTGTCAAAAACGCTCTTAT 58.543 36.000 0.00 0.00 45.69 1.73
64 65 5.839621 AGTCTAGTGTCAAAAACGCTCTTA 58.160 37.500 0.00 0.00 45.69 2.10
65 66 4.694339 AGTCTAGTGTCAAAAACGCTCTT 58.306 39.130 0.00 0.00 45.69 2.85
66 67 4.323553 AGTCTAGTGTCAAAAACGCTCT 57.676 40.909 0.00 0.00 45.69 4.09
67 68 5.117287 CACTAGTCTAGTGTCAAAAACGCTC 59.883 44.000 25.89 0.00 45.69 5.03
80 81 5.009811 AGAGCGTTTTTGACACTAGTCTAGT 59.990 40.000 6.71 6.71 45.20 2.57
81 82 5.462405 AGAGCGTTTTTGACACTAGTCTAG 58.538 41.667 5.27 5.27 45.20 2.43
82 83 5.449107 AGAGCGTTTTTGACACTAGTCTA 57.551 39.130 0.00 0.00 45.20 2.59
83 84 4.323553 AGAGCGTTTTTGACACTAGTCT 57.676 40.909 0.00 0.00 45.20 3.24
84 85 6.707599 ATAAGAGCGTTTTTGACACTAGTC 57.292 37.500 0.00 0.00 45.19 2.59
85 86 8.773404 AATATAAGAGCGTTTTTGACACTAGT 57.227 30.769 0.00 0.00 0.00 2.57
88 89 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
89 90 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
90 91 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
91 92 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
92 93 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
93 94 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
94 95 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
95 96 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
96 97 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
97 98 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
98 99 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
99 100 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
100 101 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
101 102 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
102 103 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
103 104 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
104 105 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
105 106 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
106 107 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
107 108 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
108 109 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
109 110 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
110 111 3.339713 AAATACTCCCTCCGTCCCATA 57.660 47.619 0.00 0.00 0.00 2.74
111 112 2.172717 CAAAATACTCCCTCCGTCCCAT 59.827 50.000 0.00 0.00 0.00 4.00
112 113 1.557832 CAAAATACTCCCTCCGTCCCA 59.442 52.381 0.00 0.00 0.00 4.37
113 114 1.558294 ACAAAATACTCCCTCCGTCCC 59.442 52.381 0.00 0.00 0.00 4.46
114 115 4.081254 ACTTACAAAATACTCCCTCCGTCC 60.081 45.833 0.00 0.00 0.00 4.79
115 116 5.082251 ACTTACAAAATACTCCCTCCGTC 57.918 43.478 0.00 0.00 0.00 4.79
116 117 4.529377 TGACTTACAAAATACTCCCTCCGT 59.471 41.667 0.00 0.00 0.00 4.69
117 118 4.868734 GTGACTTACAAAATACTCCCTCCG 59.131 45.833 0.00 0.00 0.00 4.63
118 119 4.868734 CGTGACTTACAAAATACTCCCTCC 59.131 45.833 0.00 0.00 0.00 4.30
119 120 4.329256 GCGTGACTTACAAAATACTCCCTC 59.671 45.833 0.00 0.00 0.00 4.30
120 121 4.251268 GCGTGACTTACAAAATACTCCCT 58.749 43.478 0.00 0.00 0.00 4.20
121 122 3.373130 GGCGTGACTTACAAAATACTCCC 59.627 47.826 0.00 0.00 0.00 4.30
122 123 3.998341 TGGCGTGACTTACAAAATACTCC 59.002 43.478 0.00 0.00 0.00 3.85
123 124 4.689345 ACTGGCGTGACTTACAAAATACTC 59.311 41.667 0.00 0.00 0.00 2.59
124 125 4.638304 ACTGGCGTGACTTACAAAATACT 58.362 39.130 0.00 0.00 0.00 2.12
125 126 5.352643 AACTGGCGTGACTTACAAAATAC 57.647 39.130 0.00 0.00 0.00 1.89
126 127 6.380095 AAAACTGGCGTGACTTACAAAATA 57.620 33.333 0.00 0.00 0.00 1.40
127 128 4.911514 AAACTGGCGTGACTTACAAAAT 57.088 36.364 0.00 0.00 0.00 1.82
128 129 4.705337 AAAACTGGCGTGACTTACAAAA 57.295 36.364 0.00 0.00 0.00 2.44
129 130 4.156190 TCAAAAACTGGCGTGACTTACAAA 59.844 37.500 0.00 0.00 0.00 2.83
130 131 3.690139 TCAAAAACTGGCGTGACTTACAA 59.310 39.130 0.00 0.00 0.00 2.41
131 132 3.271729 TCAAAAACTGGCGTGACTTACA 58.728 40.909 0.00 0.00 0.00 2.41
132 133 3.955771 TCAAAAACTGGCGTGACTTAC 57.044 42.857 0.00 0.00 0.00 2.34
133 134 5.508200 AATTCAAAAACTGGCGTGACTTA 57.492 34.783 0.00 0.00 0.00 2.24
134 135 4.385358 AATTCAAAAACTGGCGTGACTT 57.615 36.364 0.00 0.00 0.00 3.01
135 136 4.385358 AAATTCAAAAACTGGCGTGACT 57.615 36.364 0.00 0.00 0.00 3.41
136 137 5.463499 AAAAATTCAAAAACTGGCGTGAC 57.537 34.783 0.00 0.00 0.00 3.67
137 138 5.751028 CCTAAAAATTCAAAAACTGGCGTGA 59.249 36.000 0.00 0.00 0.00 4.35
138 139 5.751028 TCCTAAAAATTCAAAAACTGGCGTG 59.249 36.000 0.00 0.00 0.00 5.34
139 140 5.908341 TCCTAAAAATTCAAAAACTGGCGT 58.092 33.333 0.00 0.00 0.00 5.68
140 141 6.836577 TTCCTAAAAATTCAAAAACTGGCG 57.163 33.333 0.00 0.00 0.00 5.69
170 171 8.772705 GCCAATTCAAAAAGTGTTTATGAATGA 58.227 29.630 0.00 0.00 36.15 2.57
171 172 7.741216 CGCCAATTCAAAAAGTGTTTATGAATG 59.259 33.333 0.00 0.00 36.15 2.67
172 173 7.655328 TCGCCAATTCAAAAAGTGTTTATGAAT 59.345 29.630 0.00 0.00 36.77 2.57
173 174 6.980978 TCGCCAATTCAAAAAGTGTTTATGAA 59.019 30.769 0.00 0.00 32.93 2.57
174 175 6.507900 TCGCCAATTCAAAAAGTGTTTATGA 58.492 32.000 0.00 0.00 0.00 2.15
175 176 6.761731 TCGCCAATTCAAAAAGTGTTTATG 57.238 33.333 0.00 0.00 0.00 1.90
176 177 7.961325 AATCGCCAATTCAAAAAGTGTTTAT 57.039 28.000 0.00 0.00 0.00 1.40
177 178 7.778470 AAATCGCCAATTCAAAAAGTGTTTA 57.222 28.000 0.00 0.00 0.00 2.01
178 179 6.676237 AAATCGCCAATTCAAAAAGTGTTT 57.324 29.167 0.00 0.00 0.00 2.83
179 180 6.676237 AAAATCGCCAATTCAAAAAGTGTT 57.324 29.167 0.00 0.00 0.00 3.32
180 181 6.676237 AAAAATCGCCAATTCAAAAAGTGT 57.324 29.167 0.00 0.00 0.00 3.55
229 230 9.731819 TGTGCATTATTTTTAAAAGTTCGTGTA 57.268 25.926 0.94 0.00 0.00 2.90
230 231 8.635877 TGTGCATTATTTTTAAAAGTTCGTGT 57.364 26.923 0.94 0.00 0.00 4.49
259 260 8.782144 GCTTATTCAATTGTTTGGGAAATCAAA 58.218 29.630 5.13 0.00 34.64 2.69
260 261 7.935755 TGCTTATTCAATTGTTTGGGAAATCAA 59.064 29.630 5.13 0.00 33.44 2.57
261 262 7.448420 TGCTTATTCAATTGTTTGGGAAATCA 58.552 30.769 5.13 0.00 33.44 2.57
262 263 7.903995 TGCTTATTCAATTGTTTGGGAAATC 57.096 32.000 5.13 0.00 33.44 2.17
263 264 8.688747 TTTGCTTATTCAATTGTTTGGGAAAT 57.311 26.923 5.13 0.00 33.44 2.17
264 265 8.688747 ATTTGCTTATTCAATTGTTTGGGAAA 57.311 26.923 5.13 7.58 33.44 3.13
265 266 9.784531 TTATTTGCTTATTCAATTGTTTGGGAA 57.215 25.926 5.13 0.00 33.44 3.97
266 267 9.784531 TTTATTTGCTTATTCAATTGTTTGGGA 57.215 25.926 5.13 0.00 33.44 4.37
299 300 8.997323 TGGATTCAAAAATGTTCGCAATTTTAT 58.003 25.926 3.87 0.00 37.92 1.40
300 301 8.279103 GTGGATTCAAAAATGTTCGCAATTTTA 58.721 29.630 3.87 0.00 37.92 1.52
301 302 7.131565 GTGGATTCAAAAATGTTCGCAATTTT 58.868 30.769 0.00 0.00 39.87 1.82
302 303 6.259608 TGTGGATTCAAAAATGTTCGCAATTT 59.740 30.769 0.00 0.00 32.06 1.82
303 304 5.757320 TGTGGATTCAAAAATGTTCGCAATT 59.243 32.000 0.00 0.00 0.00 2.32
304 305 5.295950 TGTGGATTCAAAAATGTTCGCAAT 58.704 33.333 0.00 0.00 0.00 3.56
305 306 4.686972 TGTGGATTCAAAAATGTTCGCAA 58.313 34.783 0.00 0.00 0.00 4.85
306 307 4.313277 TGTGGATTCAAAAATGTTCGCA 57.687 36.364 0.00 0.00 0.00 5.10
307 308 5.649602 TTTGTGGATTCAAAAATGTTCGC 57.350 34.783 0.00 0.00 34.90 4.70
414 415 8.856247 GCCTGTTTTTCGAATTTCGTTTATTAT 58.144 29.630 17.61 0.00 41.35 1.28
415 416 7.861372 TGCCTGTTTTTCGAATTTCGTTTATTA 59.139 29.630 17.61 0.00 41.35 0.98
416 417 6.697892 TGCCTGTTTTTCGAATTTCGTTTATT 59.302 30.769 17.61 0.00 41.35 1.40
417 418 6.210078 TGCCTGTTTTTCGAATTTCGTTTAT 58.790 32.000 17.61 0.00 41.35 1.40
418 419 5.579718 TGCCTGTTTTTCGAATTTCGTTTA 58.420 33.333 17.61 3.32 41.35 2.01
419 420 4.425520 TGCCTGTTTTTCGAATTTCGTTT 58.574 34.783 17.61 0.00 41.35 3.60
420 421 4.035278 TGCCTGTTTTTCGAATTTCGTT 57.965 36.364 17.61 0.00 41.35 3.85
421 422 3.628017 CTGCCTGTTTTTCGAATTTCGT 58.372 40.909 17.61 0.00 41.35 3.85
422 423 2.405025 GCTGCCTGTTTTTCGAATTTCG 59.595 45.455 12.54 12.54 42.10 3.46
423 424 2.731451 GGCTGCCTGTTTTTCGAATTTC 59.269 45.455 12.43 0.00 0.00 2.17
424 425 2.547855 GGGCTGCCTGTTTTTCGAATTT 60.548 45.455 19.68 0.00 0.00 1.82
425 426 1.000843 GGGCTGCCTGTTTTTCGAATT 59.999 47.619 19.68 0.00 0.00 2.17
426 427 0.603065 GGGCTGCCTGTTTTTCGAAT 59.397 50.000 19.68 0.00 0.00 3.34
427 428 0.753479 TGGGCTGCCTGTTTTTCGAA 60.753 50.000 19.68 0.00 0.00 3.71
428 429 0.753479 TTGGGCTGCCTGTTTTTCGA 60.753 50.000 19.68 0.00 0.00 3.71
429 430 0.318120 ATTGGGCTGCCTGTTTTTCG 59.682 50.000 19.68 0.00 0.00 3.46
430 431 1.344114 TGATTGGGCTGCCTGTTTTTC 59.656 47.619 19.68 7.94 0.00 2.29
431 432 1.345415 CTGATTGGGCTGCCTGTTTTT 59.655 47.619 19.68 0.00 0.00 1.94
432 433 0.971386 CTGATTGGGCTGCCTGTTTT 59.029 50.000 19.68 0.00 0.00 2.43
433 434 0.901580 CCTGATTGGGCTGCCTGTTT 60.902 55.000 19.68 0.95 0.00 2.83
434 435 1.304713 CCTGATTGGGCTGCCTGTT 60.305 57.895 19.68 2.91 0.00 3.16
435 436 2.207501 CTCCTGATTGGGCTGCCTGT 62.208 60.000 19.68 4.61 36.20 4.00
436 437 1.453379 CTCCTGATTGGGCTGCCTG 60.453 63.158 19.68 2.42 36.20 4.85
437 438 3.004951 CTCCTGATTGGGCTGCCT 58.995 61.111 19.68 0.00 36.20 4.75
438 439 2.832201 GCTCCTGATTGGGCTGCC 60.832 66.667 11.05 11.05 36.20 4.85
439 440 3.207669 CGCTCCTGATTGGGCTGC 61.208 66.667 0.00 0.00 36.20 5.25
440 441 3.207669 GCGCTCCTGATTGGGCTG 61.208 66.667 0.00 0.00 38.77 4.85
441 442 3.406200 AGCGCTCCTGATTGGGCT 61.406 61.111 2.64 0.00 45.46 5.19
450 451 0.320247 CAAGAAGACACAGCGCTCCT 60.320 55.000 7.13 0.00 0.00 3.69
453 454 1.226686 CTGCAAGAAGACACAGCGCT 61.227 55.000 2.64 2.64 34.07 5.92
469 470 1.220529 TATTACGCTCTGCATGCTGC 58.779 50.000 20.33 18.20 45.29 5.25
502 503 4.738998 TTGGACCGGCCCATGCAG 62.739 66.667 11.52 0.00 40.13 4.41
525 526 2.820178 AGTTTCACATGGGGGAATTCC 58.180 47.619 16.74 16.74 0.00 3.01
551 552 5.279306 CCCGCTAATGCTACCTAAGTGATAA 60.279 44.000 0.00 0.00 36.97 1.75
552 553 4.219944 CCCGCTAATGCTACCTAAGTGATA 59.780 45.833 0.00 0.00 36.97 2.15
572 573 5.295540 CCCCAAAATTGCAAAATATTACCCG 59.704 40.000 1.71 0.00 0.00 5.28
614 615 1.303309 CAGGGCTATTGCTTCTTCCG 58.697 55.000 0.00 0.00 39.59 4.30
624 625 3.005529 AGGGGCTATAACAGGGCTATT 57.994 47.619 0.00 0.00 0.00 1.73
1262 1284 1.131771 CGATTGGATCATGTCGACGG 58.868 55.000 11.62 5.86 36.25 4.79
1282 1304 2.094286 AGAAGTTCGACAGCAGATCCTG 60.094 50.000 0.00 0.00 38.78 3.86
1383 1405 1.805943 CACCAATGCATCGTGTCAGAA 59.194 47.619 15.45 0.00 0.00 3.02
1445 1467 1.421646 AGCCACAGAAGCCACTAAAGT 59.578 47.619 0.00 0.00 0.00 2.66
1810 2030 1.821216 CTGTTAAGGACCACGCCATT 58.179 50.000 0.00 0.00 0.00 3.16
2177 6878 1.205655 TCATGCCTCTCTCTTTGACGG 59.794 52.381 0.00 0.00 0.00 4.79
2427 7128 8.325787 TCATTTCTTGTAACCATAGCCTCTTTA 58.674 33.333 0.00 0.00 0.00 1.85
2489 7190 2.777094 GGAACTGCTCTTGAGCTTTCT 58.223 47.619 21.17 5.68 35.49 2.52
2615 7316 2.658373 GCATCAACCACATGCATTCA 57.342 45.000 0.00 0.00 45.19 2.57
2644 7345 8.575649 AGGTACTGGTTATTTGGAATTAAGTG 57.424 34.615 0.00 0.00 37.18 3.16
2646 7347 9.020731 ACAAGGTACTGGTTATTTGGAATTAAG 57.979 33.333 0.00 0.00 41.93 1.85
2647 7348 8.943594 ACAAGGTACTGGTTATTTGGAATTAA 57.056 30.769 0.00 0.00 41.93 1.40
2649 7350 9.185680 GATACAAGGTACTGGTTATTTGGAATT 57.814 33.333 0.00 0.00 41.93 2.17
2667 7411 1.909302 ACCAGTGACCCTGATACAAGG 59.091 52.381 0.00 0.00 44.49 3.61
2709 7453 5.882557 GTCAACTCATTTGGACCATGTCTAT 59.117 40.000 0.00 0.00 35.69 1.98
2802 7552 6.552008 AGGGAGAACATAACATCTGGAAAAA 58.448 36.000 0.00 0.00 0.00 1.94
2913 7679 2.642427 TGCTTGCAGTCTCAGTTTTGA 58.358 42.857 0.00 0.00 0.00 2.69
2928 7694 5.235186 CGATTATTCACCTACCTCTTGCTTG 59.765 44.000 0.00 0.00 0.00 4.01
3017 7789 6.201425 TGAAACTTAATGTTCGTCACACTACC 59.799 38.462 0.00 0.00 38.61 3.18
3088 7860 7.383102 TGCTTTCCTCATTAATCTTGAGTTC 57.617 36.000 4.34 0.00 39.16 3.01
3128 7900 3.206150 AGTGCATATTTAGCTGGAACGG 58.794 45.455 0.00 0.00 38.10 4.44
3130 7902 6.972901 GGTTAAAGTGCATATTTAGCTGGAAC 59.027 38.462 15.67 9.08 0.00 3.62
3135 7907 9.681062 TTAGAAGGTTAAAGTGCATATTTAGCT 57.319 29.630 15.67 9.12 0.00 3.32
3172 7944 9.930693 GAGGGAGTAATACATACTTTTATCTGG 57.069 37.037 0.00 0.00 45.00 3.86
3247 8020 9.364653 ACTACCTCCGTATCAAAATATAAGACT 57.635 33.333 0.00 0.00 0.00 3.24
3272 8833 3.670625 TGTGCCCACTGTTGTTAGATAC 58.329 45.455 0.00 0.00 0.00 2.24
3273 8834 4.359434 TTGTGCCCACTGTTGTTAGATA 57.641 40.909 0.00 0.00 0.00 1.98
3274 8835 2.949177 TGTGCCCACTGTTGTTAGAT 57.051 45.000 0.00 0.00 0.00 1.98
3297 8858 7.335924 ACACCATGGTATAAGTTATTCACACAC 59.664 37.037 19.28 0.00 0.00 3.82
3333 8894 7.575414 TGAAACAGCCACTCTATTTAAAACA 57.425 32.000 0.00 0.00 0.00 2.83
3415 8976 7.907214 ACATTGACCTACTTTGATTGTAGAC 57.093 36.000 0.00 0.00 39.61 2.59
3452 9633 5.719173 TGCCTAGTTGGTAATTGAATTTGC 58.281 37.500 0.00 0.00 38.35 3.68
3462 9643 1.350071 TCCCGTTGCCTAGTTGGTAA 58.650 50.000 0.00 0.00 38.10 2.85


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

AutoCloner maintained by Alex Coulton.