Multiple sequence alignment - TraesCS3D01G365400

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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 TraesCS3D01G365400 chr3D 100.000 3242 0 0 1 3242 479631173 479627932 0.000000e+00 5987.0
1 TraesCS3D01G365400 chr3B 96.591 3021 75 14 236 3242 640076473 640073467 0.000000e+00 4983.0
2 TraesCS3D01G365400 chr3B 91.579 95 8 0 1 95 446135679 446135773 7.300000e-27 132.0
3 TraesCS3D01G365400 chr3A 94.915 3048 107 17 232 3242 623062766 623059730 0.000000e+00 4726.0
4 TraesCS3D01G365400 chr2D 95.833 96 4 0 1 96 26366171 26366076 4.330000e-34 156.0
5 TraesCS3D01G365400 chr2D 95.745 94 4 0 1 94 26380015 26380108 5.600000e-33 152.0
6 TraesCS3D01G365400 chr7A 93.684 95 6 0 1 95 531101707 531101801 3.370000e-30 143.0
7 TraesCS3D01G365400 chr2B 92.708 96 7 0 1 96 250912666 250912571 4.360000e-29 139.0
8 TraesCS3D01G365400 chr1B 92.632 95 7 0 1 95 557412914 557412820 1.570000e-28 137.0
9 TraesCS3D01G365400 chr7B 90.526 95 9 0 1 95 422902764 422902858 3.400000e-25 126.0
10 TraesCS3D01G365400 chr7B 90.526 95 9 0 1 95 696630717 696630811 3.400000e-25 126.0
11 TraesCS3D01G365400 chr7B 89.474 95 10 0 1 95 641027954 641028048 1.580000e-23 121.0
12 TraesCS3D01G365400 chr1A 85.185 81 10 2 655 734 585988138 585988059 7.450000e-12 82.4


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 TraesCS3D01G365400 chr3D 479627932 479631173 3241 True 5987 5987 100.000 1 3242 1 chr3D.!!$R1 3241
1 TraesCS3D01G365400 chr3B 640073467 640076473 3006 True 4983 4983 96.591 236 3242 1 chr3B.!!$R1 3006
2 TraesCS3D01G365400 chr3A 623059730 623062766 3036 True 4726 4726 94.915 232 3242 1 chr3A.!!$R1 3010

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
125 126 0.038343 ACATTGCCGACAAACATGCC 60.038 50.0 0.00 0.00 39.77 4.40 F
222 223 0.039035 GGGCATAGGTGTTGTTGGGA 59.961 55.0 0.00 0.00 0.00 4.37 F
227 228 0.250553 TAGGTGTTGTTGGGAAGCGG 60.251 55.0 0.00 0.00 0.00 5.52 F
230 231 0.310854 GTGTTGTTGGGAAGCGGAAG 59.689 55.0 0.00 0.00 0.00 3.46 F
253 254 0.383860 GCCCGTTTTCGAAACGAGTG 60.384 55.0 24.48 16.58 45.64 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1867 1883 0.250166 ACACCCCAGAAACGTAGCAC 60.250 55.000 0.00 0.0 0.0 4.40 R
2067 2083 5.620738 TTTCAATCATTCCAAACACCCAA 57.379 34.783 0.00 0.0 0.0 4.12 R
2091 2107 6.547141 TGACAAGTTTCTTGAGATTTGGACAT 59.453 34.615 15.04 0.0 0.0 3.06 R
2178 2194 8.146053 TCCTCATGAGACAAACTATAAAGGAA 57.854 34.615 24.62 0.0 0.0 3.36 R
2263 2279 5.739959 TGAACGGAACAAGGATGATGAATA 58.260 37.500 0.00 0.0 0.0 1.75 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
24 25 7.583860 GAGACAAGTTGTAGGACTGTATTTC 57.416 40.000 8.88 0.00 0.00 2.17
25 26 6.157211 AGACAAGTTGTAGGACTGTATTTCG 58.843 40.000 8.88 0.00 0.00 3.46
26 27 5.235516 ACAAGTTGTAGGACTGTATTTCGG 58.764 41.667 6.75 0.00 0.00 4.30
27 28 4.467198 AGTTGTAGGACTGTATTTCGGG 57.533 45.455 0.00 0.00 0.00 5.14
28 29 3.836562 AGTTGTAGGACTGTATTTCGGGT 59.163 43.478 0.00 0.00 0.00 5.28
29 30 5.018809 AGTTGTAGGACTGTATTTCGGGTA 58.981 41.667 0.00 0.00 0.00 3.69
30 31 5.659971 AGTTGTAGGACTGTATTTCGGGTAT 59.340 40.000 0.00 0.00 0.00 2.73
31 32 6.155737 AGTTGTAGGACTGTATTTCGGGTATT 59.844 38.462 0.00 0.00 0.00 1.89
32 33 6.549433 TGTAGGACTGTATTTCGGGTATTT 57.451 37.500 0.00 0.00 0.00 1.40
33 34 6.342906 TGTAGGACTGTATTTCGGGTATTTG 58.657 40.000 0.00 0.00 0.00 2.32
34 35 4.196971 AGGACTGTATTTCGGGTATTTGC 58.803 43.478 0.00 0.00 0.00 3.68
35 36 3.942748 GGACTGTATTTCGGGTATTTGCA 59.057 43.478 0.00 0.00 0.00 4.08
36 37 4.396790 GGACTGTATTTCGGGTATTTGCAA 59.603 41.667 0.00 0.00 0.00 4.08
37 38 5.448632 GGACTGTATTTCGGGTATTTGCAAG 60.449 44.000 0.00 0.00 0.00 4.01
38 39 5.007682 ACTGTATTTCGGGTATTTGCAAGT 58.992 37.500 0.00 0.00 0.00 3.16
39 40 6.174760 ACTGTATTTCGGGTATTTGCAAGTA 58.825 36.000 0.00 0.00 0.00 2.24
40 41 6.093082 ACTGTATTTCGGGTATTTGCAAGTAC 59.907 38.462 20.53 20.53 0.00 2.73
41 42 4.609691 ATTTCGGGTATTTGCAAGTACG 57.390 40.909 21.48 13.73 0.00 3.67
42 43 2.012937 TCGGGTATTTGCAAGTACGG 57.987 50.000 21.48 16.76 0.00 4.02
43 44 1.011333 CGGGTATTTGCAAGTACGGG 58.989 55.000 21.48 13.82 0.00 5.28
44 45 1.405797 CGGGTATTTGCAAGTACGGGA 60.406 52.381 21.48 0.00 0.00 5.14
45 46 2.713877 GGGTATTTGCAAGTACGGGAA 58.286 47.619 21.48 0.00 0.00 3.97
46 47 2.681344 GGGTATTTGCAAGTACGGGAAG 59.319 50.000 21.48 0.00 0.00 3.46
47 48 3.602483 GGTATTTGCAAGTACGGGAAGA 58.398 45.455 21.48 0.00 0.00 2.87
48 49 4.004982 GGTATTTGCAAGTACGGGAAGAA 58.995 43.478 21.48 0.00 0.00 2.52
49 50 4.456566 GGTATTTGCAAGTACGGGAAGAAA 59.543 41.667 21.48 0.00 0.00 2.52
50 51 5.124936 GGTATTTGCAAGTACGGGAAGAAAT 59.875 40.000 21.48 1.99 0.00 2.17
51 52 4.497473 TTTGCAAGTACGGGAAGAAATG 57.503 40.909 0.00 0.00 0.00 2.32
52 53 1.810151 TGCAAGTACGGGAAGAAATGC 59.190 47.619 0.00 0.00 0.00 3.56
53 54 1.202031 GCAAGTACGGGAAGAAATGCG 60.202 52.381 0.00 0.00 0.00 4.73
54 55 1.396996 CAAGTACGGGAAGAAATGCGG 59.603 52.381 0.00 0.00 0.00 5.69
55 56 0.743345 AGTACGGGAAGAAATGCGGC 60.743 55.000 0.00 0.00 0.00 6.53
56 57 1.450669 TACGGGAAGAAATGCGGCC 60.451 57.895 0.00 0.00 0.00 6.13
57 58 2.186602 TACGGGAAGAAATGCGGCCA 62.187 55.000 2.24 0.00 0.00 5.36
58 59 2.339556 CGGGAAGAAATGCGGCCAA 61.340 57.895 2.24 0.00 0.00 4.52
59 60 1.215382 GGGAAGAAATGCGGCCAAC 59.785 57.895 2.24 0.00 0.00 3.77
60 61 1.531739 GGGAAGAAATGCGGCCAACA 61.532 55.000 2.24 0.00 0.00 3.33
61 62 0.388520 GGAAGAAATGCGGCCAACAC 60.389 55.000 2.24 0.00 0.00 3.32
62 63 0.729140 GAAGAAATGCGGCCAACACG 60.729 55.000 2.24 0.00 0.00 4.49
63 64 1.169661 AAGAAATGCGGCCAACACGA 61.170 50.000 2.24 0.00 0.00 4.35
64 65 1.442017 GAAATGCGGCCAACACGAC 60.442 57.895 2.24 0.00 0.00 4.34
65 66 3.248630 AAATGCGGCCAACACGACG 62.249 57.895 2.24 0.00 0.00 5.12
66 67 4.673298 ATGCGGCCAACACGACGA 62.673 61.111 2.24 0.00 0.00 4.20
69 70 2.256158 CGGCCAACACGACGAGTA 59.744 61.111 2.24 0.00 0.00 2.59
70 71 1.153901 CGGCCAACACGACGAGTAT 60.154 57.895 2.24 0.00 0.00 2.12
71 72 1.410737 CGGCCAACACGACGAGTATG 61.411 60.000 2.24 1.50 0.00 2.39
72 73 0.108992 GGCCAACACGACGAGTATGA 60.109 55.000 0.00 0.00 0.00 2.15
73 74 1.670674 GGCCAACACGACGAGTATGAA 60.671 52.381 0.00 0.00 0.00 2.57
74 75 1.654105 GCCAACACGACGAGTATGAAG 59.346 52.381 0.00 0.00 0.00 3.02
75 76 2.670229 GCCAACACGACGAGTATGAAGA 60.670 50.000 0.00 0.00 0.00 2.87
76 77 2.915463 CCAACACGACGAGTATGAAGAC 59.085 50.000 0.00 0.00 0.00 3.01
77 78 2.915463 CAACACGACGAGTATGAAGACC 59.085 50.000 0.00 0.00 0.00 3.85
78 79 2.434428 ACACGACGAGTATGAAGACCT 58.566 47.619 0.00 0.00 0.00 3.85
79 80 2.161808 ACACGACGAGTATGAAGACCTG 59.838 50.000 0.00 0.00 0.00 4.00
80 81 2.161808 CACGACGAGTATGAAGACCTGT 59.838 50.000 0.00 0.00 0.00 4.00
81 82 2.161808 ACGACGAGTATGAAGACCTGTG 59.838 50.000 0.00 0.00 0.00 3.66
82 83 2.478031 CGACGAGTATGAAGACCTGTGG 60.478 54.545 0.00 0.00 0.00 4.17
83 84 2.492484 GACGAGTATGAAGACCTGTGGT 59.508 50.000 0.00 0.00 39.44 4.16
84 85 2.231478 ACGAGTATGAAGACCTGTGGTG 59.769 50.000 0.00 0.00 35.25 4.17
85 86 2.492088 CGAGTATGAAGACCTGTGGTGA 59.508 50.000 0.00 0.00 35.25 4.02
86 87 3.056821 CGAGTATGAAGACCTGTGGTGAA 60.057 47.826 0.00 0.00 35.25 3.18
87 88 4.382040 CGAGTATGAAGACCTGTGGTGAAT 60.382 45.833 0.00 0.00 35.25 2.57
88 89 5.491982 GAGTATGAAGACCTGTGGTGAATT 58.508 41.667 0.00 0.00 35.25 2.17
89 90 5.880901 AGTATGAAGACCTGTGGTGAATTT 58.119 37.500 0.00 0.00 35.25 1.82
90 91 6.306987 AGTATGAAGACCTGTGGTGAATTTT 58.693 36.000 0.00 0.00 35.25 1.82
91 92 6.777580 AGTATGAAGACCTGTGGTGAATTTTT 59.222 34.615 0.00 0.00 35.25 1.94
92 93 5.514274 TGAAGACCTGTGGTGAATTTTTC 57.486 39.130 0.00 0.00 35.25 2.29
93 94 5.200483 TGAAGACCTGTGGTGAATTTTTCT 58.800 37.500 0.00 0.00 35.25 2.52
94 95 5.299279 TGAAGACCTGTGGTGAATTTTTCTC 59.701 40.000 0.00 0.00 35.25 2.87
95 96 3.815401 AGACCTGTGGTGAATTTTTCTCG 59.185 43.478 0.00 0.00 35.25 4.04
96 97 2.293399 ACCTGTGGTGAATTTTTCTCGC 59.707 45.455 0.00 0.00 32.98 5.03
97 98 2.351738 CCTGTGGTGAATTTTTCTCGCC 60.352 50.000 0.00 0.00 42.73 5.54
100 101 2.582052 TGGTGAATTTTTCTCGCCACT 58.418 42.857 1.04 0.00 46.14 4.00
101 102 3.745799 TGGTGAATTTTTCTCGCCACTA 58.254 40.909 1.04 0.00 46.14 2.74
102 103 4.138290 TGGTGAATTTTTCTCGCCACTAA 58.862 39.130 1.04 0.00 46.14 2.24
103 104 4.580995 TGGTGAATTTTTCTCGCCACTAAA 59.419 37.500 1.04 0.00 46.14 1.85
104 105 5.242838 TGGTGAATTTTTCTCGCCACTAAAT 59.757 36.000 1.04 0.00 46.14 1.40
105 106 6.156519 GGTGAATTTTTCTCGCCACTAAATT 58.843 36.000 0.00 0.00 42.11 1.82
106 107 7.040340 TGGTGAATTTTTCTCGCCACTAAATTA 60.040 33.333 1.04 0.00 46.14 1.40
107 108 7.272731 GGTGAATTTTTCTCGCCACTAAATTAC 59.727 37.037 0.00 0.00 42.11 1.89
108 109 7.806014 GTGAATTTTTCTCGCCACTAAATTACA 59.194 33.333 0.00 0.00 30.85 2.41
109 110 8.519526 TGAATTTTTCTCGCCACTAAATTACAT 58.480 29.630 0.00 0.00 30.85 2.29
110 111 9.353999 GAATTTTTCTCGCCACTAAATTACATT 57.646 29.630 0.00 0.00 30.85 2.71
111 112 8.687824 ATTTTTCTCGCCACTAAATTACATTG 57.312 30.769 0.00 0.00 0.00 2.82
112 113 4.875544 TCTCGCCACTAAATTACATTGC 57.124 40.909 0.00 0.00 0.00 3.56
113 114 3.625764 TCTCGCCACTAAATTACATTGCC 59.374 43.478 0.00 0.00 0.00 4.52
114 115 2.353269 TCGCCACTAAATTACATTGCCG 59.647 45.455 0.00 0.00 0.00 5.69
115 116 2.353269 CGCCACTAAATTACATTGCCGA 59.647 45.455 0.00 0.00 0.00 5.54
116 117 3.691498 GCCACTAAATTACATTGCCGAC 58.309 45.455 0.00 0.00 0.00 4.79
117 118 3.127895 GCCACTAAATTACATTGCCGACA 59.872 43.478 0.00 0.00 0.00 4.35
118 119 4.380023 GCCACTAAATTACATTGCCGACAA 60.380 41.667 0.00 0.00 40.87 3.18
119 120 5.704888 CCACTAAATTACATTGCCGACAAA 58.295 37.500 0.00 0.00 39.77 2.83
120 121 5.571357 CCACTAAATTACATTGCCGACAAAC 59.429 40.000 0.00 0.00 39.77 2.93
121 122 6.146216 CACTAAATTACATTGCCGACAAACA 58.854 36.000 0.00 0.00 39.77 2.83
122 123 6.806249 CACTAAATTACATTGCCGACAAACAT 59.194 34.615 0.00 0.00 39.77 2.71
123 124 6.806249 ACTAAATTACATTGCCGACAAACATG 59.194 34.615 0.00 0.00 39.77 3.21
124 125 2.627863 TACATTGCCGACAAACATGC 57.372 45.000 0.00 0.00 39.77 4.06
125 126 0.038343 ACATTGCCGACAAACATGCC 60.038 50.000 0.00 0.00 39.77 4.40
126 127 0.244450 CATTGCCGACAAACATGCCT 59.756 50.000 0.00 0.00 39.77 4.75
127 128 0.244450 ATTGCCGACAAACATGCCTG 59.756 50.000 0.00 0.00 39.77 4.85
128 129 0.821301 TTGCCGACAAACATGCCTGA 60.821 50.000 0.00 0.00 31.21 3.86
129 130 0.821301 TGCCGACAAACATGCCTGAA 60.821 50.000 0.00 0.00 0.00 3.02
130 131 0.527565 GCCGACAAACATGCCTGAAT 59.472 50.000 0.00 0.00 0.00 2.57
131 132 1.733389 GCCGACAAACATGCCTGAATG 60.733 52.381 0.00 0.00 0.00 2.67
132 133 1.541147 CCGACAAACATGCCTGAATGT 59.459 47.619 0.00 0.19 42.62 2.71
133 134 2.414559 CCGACAAACATGCCTGAATGTC 60.415 50.000 15.98 15.98 39.89 3.06
134 135 2.725759 CGACAAACATGCCTGAATGTCG 60.726 50.000 25.52 25.52 46.84 4.35
135 136 2.483877 GACAAACATGCCTGAATGTCGA 59.516 45.455 12.87 0.00 39.89 4.20
136 137 2.884012 ACAAACATGCCTGAATGTCGAA 59.116 40.909 0.00 0.00 39.89 3.71
137 138 3.058016 ACAAACATGCCTGAATGTCGAAG 60.058 43.478 0.00 0.00 39.89 3.79
138 139 2.768253 ACATGCCTGAATGTCGAAGA 57.232 45.000 0.00 0.00 35.92 2.87
139 140 3.272574 ACATGCCTGAATGTCGAAGAT 57.727 42.857 0.00 0.00 40.67 2.40
140 141 2.941064 ACATGCCTGAATGTCGAAGATG 59.059 45.455 0.00 0.00 40.67 2.90
141 142 2.768253 TGCCTGAATGTCGAAGATGT 57.232 45.000 0.00 0.00 40.67 3.06
142 143 2.349590 TGCCTGAATGTCGAAGATGTG 58.650 47.619 0.00 0.00 40.67 3.21
143 144 2.028203 TGCCTGAATGTCGAAGATGTGA 60.028 45.455 0.00 0.00 40.67 3.58
144 145 3.002791 GCCTGAATGTCGAAGATGTGAA 58.997 45.455 0.00 0.00 40.67 3.18
145 146 3.436704 GCCTGAATGTCGAAGATGTGAAA 59.563 43.478 0.00 0.00 40.67 2.69
146 147 4.083324 GCCTGAATGTCGAAGATGTGAAAA 60.083 41.667 0.00 0.00 40.67 2.29
147 148 5.385617 CCTGAATGTCGAAGATGTGAAAAC 58.614 41.667 0.00 0.00 40.67 2.43
148 149 5.180117 CCTGAATGTCGAAGATGTGAAAACT 59.820 40.000 0.00 0.00 40.67 2.66
149 150 6.368791 CCTGAATGTCGAAGATGTGAAAACTA 59.631 38.462 0.00 0.00 40.67 2.24
150 151 7.351414 TGAATGTCGAAGATGTGAAAACTAG 57.649 36.000 0.00 0.00 40.67 2.57
151 152 6.368791 TGAATGTCGAAGATGTGAAAACTAGG 59.631 38.462 0.00 0.00 40.67 3.02
152 153 4.566004 TGTCGAAGATGTGAAAACTAGGG 58.434 43.478 0.00 0.00 40.67 3.53
153 154 3.371285 GTCGAAGATGTGAAAACTAGGGC 59.629 47.826 0.00 0.00 40.67 5.19
154 155 2.678336 CGAAGATGTGAAAACTAGGGCC 59.322 50.000 0.00 0.00 0.00 5.80
155 156 2.403252 AGATGTGAAAACTAGGGCCG 57.597 50.000 0.00 0.00 0.00 6.13
156 157 0.733150 GATGTGAAAACTAGGGCCGC 59.267 55.000 0.00 0.00 0.00 6.53
157 158 0.328258 ATGTGAAAACTAGGGCCGCT 59.672 50.000 0.00 0.00 0.00 5.52
158 159 0.109723 TGTGAAAACTAGGGCCGCTT 59.890 50.000 0.00 0.00 0.00 4.68
159 160 0.521735 GTGAAAACTAGGGCCGCTTG 59.478 55.000 0.00 0.00 0.00 4.01
160 161 0.109723 TGAAAACTAGGGCCGCTTGT 59.890 50.000 0.00 0.00 0.00 3.16
161 162 1.244816 GAAAACTAGGGCCGCTTGTT 58.755 50.000 12.74 12.74 0.00 2.83
162 163 1.611977 GAAAACTAGGGCCGCTTGTTT 59.388 47.619 19.95 19.95 32.85 2.83
163 164 0.958822 AAACTAGGGCCGCTTGTTTG 59.041 50.000 22.78 2.57 31.00 2.93
164 165 0.109723 AACTAGGGCCGCTTGTTTGA 59.890 50.000 12.74 0.00 0.00 2.69
165 166 0.328258 ACTAGGGCCGCTTGTTTGAT 59.672 50.000 0.00 0.00 0.00 2.57
166 167 1.557832 ACTAGGGCCGCTTGTTTGATA 59.442 47.619 0.00 0.00 0.00 2.15
167 168 2.172717 ACTAGGGCCGCTTGTTTGATAT 59.827 45.455 0.00 0.00 0.00 1.63
168 169 2.143876 AGGGCCGCTTGTTTGATATT 57.856 45.000 0.00 0.00 0.00 1.28
169 170 2.024414 AGGGCCGCTTGTTTGATATTC 58.976 47.619 0.00 0.00 0.00 1.75
170 171 1.748493 GGGCCGCTTGTTTGATATTCA 59.252 47.619 0.00 0.00 0.00 2.57
171 172 2.479560 GGGCCGCTTGTTTGATATTCAC 60.480 50.000 0.00 0.00 0.00 3.18
172 173 2.440501 GCCGCTTGTTTGATATTCACG 58.559 47.619 0.00 0.00 0.00 4.35
173 174 2.159572 GCCGCTTGTTTGATATTCACGT 60.160 45.455 0.00 0.00 0.00 4.49
174 175 3.670203 CCGCTTGTTTGATATTCACGTC 58.330 45.455 0.00 0.00 0.00 4.34
175 176 3.370978 CCGCTTGTTTGATATTCACGTCT 59.629 43.478 0.00 0.00 0.00 4.18
176 177 4.142902 CCGCTTGTTTGATATTCACGTCTT 60.143 41.667 0.00 0.00 0.00 3.01
177 178 5.062934 CCGCTTGTTTGATATTCACGTCTTA 59.937 40.000 0.00 0.00 0.00 2.10
178 179 6.401688 CCGCTTGTTTGATATTCACGTCTTAA 60.402 38.462 0.00 0.00 0.00 1.85
179 180 6.678663 CGCTTGTTTGATATTCACGTCTTAAG 59.321 38.462 0.00 0.00 0.00 1.85
180 181 7.411480 CGCTTGTTTGATATTCACGTCTTAAGA 60.411 37.037 0.00 0.00 0.00 2.10
181 182 7.688578 GCTTGTTTGATATTCACGTCTTAAGAC 59.311 37.037 23.25 23.25 41.47 3.01
182 183 8.827177 TTGTTTGATATTCACGTCTTAAGACT 57.173 30.769 28.30 14.93 42.66 3.24
183 184 8.827177 TGTTTGATATTCACGTCTTAAGACTT 57.173 30.769 28.30 19.49 42.66 3.01
184 185 9.268268 TGTTTGATATTCACGTCTTAAGACTTT 57.732 29.630 28.30 15.44 42.66 2.66
185 186 9.530129 GTTTGATATTCACGTCTTAAGACTTTG 57.470 33.333 28.30 23.98 42.66 2.77
186 187 8.827177 TTGATATTCACGTCTTAAGACTTTGT 57.173 30.769 28.30 18.33 42.66 2.83
187 188 8.827177 TGATATTCACGTCTTAAGACTTTGTT 57.173 30.769 28.30 18.78 42.66 2.83
188 189 8.708742 TGATATTCACGTCTTAAGACTTTGTTG 58.291 33.333 28.30 16.51 42.66 3.33
189 190 6.920569 ATTCACGTCTTAAGACTTTGTTGT 57.079 33.333 28.30 17.08 42.66 3.32
190 191 6.730960 TTCACGTCTTAAGACTTTGTTGTT 57.269 33.333 28.30 4.59 42.66 2.83
191 192 6.102006 TCACGTCTTAAGACTTTGTTGTTG 57.898 37.500 28.30 14.66 42.66 3.33
192 193 4.728608 CACGTCTTAAGACTTTGTTGTTGC 59.271 41.667 28.30 3.12 42.66 4.17
193 194 4.634443 ACGTCTTAAGACTTTGTTGTTGCT 59.366 37.500 28.30 3.41 42.66 3.91
194 195 4.963953 CGTCTTAAGACTTTGTTGTTGCTG 59.036 41.667 28.30 8.56 42.66 4.41
195 196 5.447279 CGTCTTAAGACTTTGTTGTTGCTGT 60.447 40.000 28.30 0.00 42.66 4.40
196 197 6.322491 GTCTTAAGACTTTGTTGTTGCTGTT 58.678 36.000 25.30 0.00 41.65 3.16
197 198 6.251376 GTCTTAAGACTTTGTTGTTGCTGTTG 59.749 38.462 25.30 0.00 41.65 3.33
198 199 4.519540 AAGACTTTGTTGTTGCTGTTGT 57.480 36.364 0.00 0.00 0.00 3.32
199 200 4.519540 AGACTTTGTTGTTGCTGTTGTT 57.480 36.364 0.00 0.00 0.00 2.83
200 201 4.236935 AGACTTTGTTGTTGCTGTTGTTG 58.763 39.130 0.00 0.00 0.00 3.33
201 202 3.987220 GACTTTGTTGTTGCTGTTGTTGT 59.013 39.130 0.00 0.00 0.00 3.32
202 203 4.376146 ACTTTGTTGTTGCTGTTGTTGTT 58.624 34.783 0.00 0.00 0.00 2.83
203 204 4.210955 ACTTTGTTGTTGCTGTTGTTGTTG 59.789 37.500 0.00 0.00 0.00 3.33
204 205 2.681706 TGTTGTTGCTGTTGTTGTTGG 58.318 42.857 0.00 0.00 0.00 3.77
205 206 1.999024 GTTGTTGCTGTTGTTGTTGGG 59.001 47.619 0.00 0.00 0.00 4.12
206 207 0.108424 TGTTGCTGTTGTTGTTGGGC 60.108 50.000 0.00 0.00 0.00 5.36
207 208 0.108424 GTTGCTGTTGTTGTTGGGCA 60.108 50.000 0.00 0.00 0.00 5.36
208 209 0.829333 TTGCTGTTGTTGTTGGGCAT 59.171 45.000 0.00 0.00 0.00 4.40
209 210 1.697284 TGCTGTTGTTGTTGGGCATA 58.303 45.000 0.00 0.00 0.00 3.14
210 211 1.612950 TGCTGTTGTTGTTGGGCATAG 59.387 47.619 0.00 0.00 0.00 2.23
211 212 1.067635 GCTGTTGTTGTTGGGCATAGG 60.068 52.381 0.00 0.00 0.00 2.57
212 213 2.238521 CTGTTGTTGTTGGGCATAGGT 58.761 47.619 0.00 0.00 0.00 3.08
213 214 1.959985 TGTTGTTGTTGGGCATAGGTG 59.040 47.619 0.00 0.00 0.00 4.00
214 215 1.960689 GTTGTTGTTGGGCATAGGTGT 59.039 47.619 0.00 0.00 0.00 4.16
215 216 2.364002 GTTGTTGTTGGGCATAGGTGTT 59.636 45.455 0.00 0.00 0.00 3.32
216 217 1.959985 TGTTGTTGGGCATAGGTGTTG 59.040 47.619 0.00 0.00 0.00 3.33
217 218 1.960689 GTTGTTGGGCATAGGTGTTGT 59.039 47.619 0.00 0.00 0.00 3.32
218 219 2.364002 GTTGTTGGGCATAGGTGTTGTT 59.636 45.455 0.00 0.00 0.00 2.83
219 220 1.959985 TGTTGGGCATAGGTGTTGTTG 59.040 47.619 0.00 0.00 0.00 3.33
220 221 1.272212 GTTGGGCATAGGTGTTGTTGG 59.728 52.381 0.00 0.00 0.00 3.77
221 222 0.251564 TGGGCATAGGTGTTGTTGGG 60.252 55.000 0.00 0.00 0.00 4.12
222 223 0.039035 GGGCATAGGTGTTGTTGGGA 59.961 55.000 0.00 0.00 0.00 4.37
223 224 1.549037 GGGCATAGGTGTTGTTGGGAA 60.549 52.381 0.00 0.00 0.00 3.97
224 225 1.818674 GGCATAGGTGTTGTTGGGAAG 59.181 52.381 0.00 0.00 0.00 3.46
225 226 1.202348 GCATAGGTGTTGTTGGGAAGC 59.798 52.381 0.00 0.00 0.00 3.86
226 227 1.468520 CATAGGTGTTGTTGGGAAGCG 59.531 52.381 0.00 0.00 0.00 4.68
227 228 0.250553 TAGGTGTTGTTGGGAAGCGG 60.251 55.000 0.00 0.00 0.00 5.52
228 229 1.527380 GGTGTTGTTGGGAAGCGGA 60.527 57.895 0.00 0.00 0.00 5.54
229 230 1.104577 GGTGTTGTTGGGAAGCGGAA 61.105 55.000 0.00 0.00 0.00 4.30
230 231 0.310854 GTGTTGTTGGGAAGCGGAAG 59.689 55.000 0.00 0.00 0.00 3.46
234 235 1.377333 GTTGGGAAGCGGAAGGGAG 60.377 63.158 0.00 0.00 0.00 4.30
252 253 0.531311 AGCCCGTTTTCGAAACGAGT 60.531 50.000 24.48 11.96 45.64 4.18
253 254 0.383860 GCCCGTTTTCGAAACGAGTG 60.384 55.000 24.48 16.58 45.64 3.51
269 270 3.507233 ACGAGTGAACGTAATACCTTGGA 59.493 43.478 0.00 0.00 44.72 3.53
270 271 4.022068 ACGAGTGAACGTAATACCTTGGAA 60.022 41.667 0.00 0.00 44.72 3.53
287 288 4.746535 TGGAATACGCTTCCATCAACTA 57.253 40.909 14.32 0.00 43.17 2.24
398 403 4.143333 CAACGAGATCCCGGCGGT 62.143 66.667 26.32 7.05 0.00 5.68
1528 1544 0.911769 TTGCCCCAAGATCGAGTCAT 59.088 50.000 0.00 0.00 0.00 3.06
1542 1558 2.485426 CGAGTCATTGGCACTTGATGTT 59.515 45.455 2.94 0.00 0.00 2.71
1838 1854 3.409026 AGTCTGGCCAAAGTTCTACAG 57.591 47.619 7.01 0.00 0.00 2.74
2090 2106 5.620738 TGGGTGTTTGGAATGATTGAAAA 57.379 34.783 0.00 0.00 0.00 2.29
2091 2107 5.994250 TGGGTGTTTGGAATGATTGAAAAA 58.006 33.333 0.00 0.00 0.00 1.94
2178 2194 3.503748 GCAAGATGTTAGCAACCTTCACT 59.496 43.478 0.00 0.00 0.00 3.41
2181 2197 4.327680 AGATGTTAGCAACCTTCACTTCC 58.672 43.478 0.00 0.00 0.00 3.46
2298 2314 2.270352 TCCGTTCAACTCTTGCCATT 57.730 45.000 0.00 0.00 0.00 3.16
2319 2335 6.351796 CCATTAGGTAATCTTTTGGGGGTTTG 60.352 42.308 0.00 0.00 0.00 2.93
2528 2544 2.771943 TGTGAAGTCTTGGTTCCTCACT 59.228 45.455 0.00 0.00 0.00 3.41
2698 2716 5.109210 TGTTGTTATGGAACTCTGCTATCG 58.891 41.667 0.00 0.00 36.45 2.92
2736 2754 7.873719 TGGTTACTTGAACACCCATATAATG 57.126 36.000 0.00 0.00 40.09 1.90
2783 2801 0.181114 TCCTTGCGCATATCTGCCTT 59.819 50.000 12.75 0.00 46.07 4.35
2908 2933 7.751348 CAGAGAATAGACGATTCCCTTATAACG 59.249 40.741 4.83 0.00 44.54 3.18
3097 3142 8.871686 TGTAATTACATGCTGATACAGTAGTG 57.128 34.615 14.35 0.00 33.43 2.74
3132 3177 1.725641 TGAAGTTCAGTAGGCATGCG 58.274 50.000 12.44 0.00 0.00 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.308282 CGAAATACAGTCCTACAACTTGTCTC 59.692 42.308 0.00 0.00 0.00 3.36
1 2 6.157211 CGAAATACAGTCCTACAACTTGTCT 58.843 40.000 0.00 0.00 0.00 3.41
2 3 5.347907 CCGAAATACAGTCCTACAACTTGTC 59.652 44.000 0.00 0.00 0.00 3.18
3 4 5.235516 CCGAAATACAGTCCTACAACTTGT 58.764 41.667 0.00 0.00 0.00 3.16
4 5 4.630069 CCCGAAATACAGTCCTACAACTTG 59.370 45.833 0.00 0.00 0.00 3.16
5 6 4.285260 ACCCGAAATACAGTCCTACAACTT 59.715 41.667 0.00 0.00 0.00 2.66
6 7 3.836562 ACCCGAAATACAGTCCTACAACT 59.163 43.478 0.00 0.00 0.00 3.16
7 8 4.198028 ACCCGAAATACAGTCCTACAAC 57.802 45.455 0.00 0.00 0.00 3.32
8 9 6.549433 AATACCCGAAATACAGTCCTACAA 57.451 37.500 0.00 0.00 0.00 2.41
9 10 6.342906 CAAATACCCGAAATACAGTCCTACA 58.657 40.000 0.00 0.00 0.00 2.74
10 11 5.235831 GCAAATACCCGAAATACAGTCCTAC 59.764 44.000 0.00 0.00 0.00 3.18
11 12 5.104859 TGCAAATACCCGAAATACAGTCCTA 60.105 40.000 0.00 0.00 0.00 2.94
12 13 4.196971 GCAAATACCCGAAATACAGTCCT 58.803 43.478 0.00 0.00 0.00 3.85
13 14 3.942748 TGCAAATACCCGAAATACAGTCC 59.057 43.478 0.00 0.00 0.00 3.85
14 15 5.123344 ACTTGCAAATACCCGAAATACAGTC 59.877 40.000 0.00 0.00 0.00 3.51
15 16 5.007682 ACTTGCAAATACCCGAAATACAGT 58.992 37.500 0.00 0.00 0.00 3.55
16 17 5.560966 ACTTGCAAATACCCGAAATACAG 57.439 39.130 0.00 0.00 0.00 2.74
17 18 5.063691 CGTACTTGCAAATACCCGAAATACA 59.936 40.000 12.13 0.00 0.00 2.29
18 19 5.495502 CGTACTTGCAAATACCCGAAATAC 58.504 41.667 12.13 0.00 0.00 1.89
19 20 4.571580 CCGTACTTGCAAATACCCGAAATA 59.428 41.667 12.13 0.00 0.00 1.40
20 21 3.375922 CCGTACTTGCAAATACCCGAAAT 59.624 43.478 12.13 0.00 0.00 2.17
21 22 2.743126 CCGTACTTGCAAATACCCGAAA 59.257 45.455 12.13 0.00 0.00 3.46
22 23 2.348660 CCGTACTTGCAAATACCCGAA 58.651 47.619 12.13 0.00 0.00 4.30
23 24 1.405797 CCCGTACTTGCAAATACCCGA 60.406 52.381 12.13 0.00 0.00 5.14
24 25 1.011333 CCCGTACTTGCAAATACCCG 58.989 55.000 12.13 2.03 0.00 5.28
25 26 2.406596 TCCCGTACTTGCAAATACCC 57.593 50.000 12.13 0.00 0.00 3.69
26 27 3.602483 TCTTCCCGTACTTGCAAATACC 58.398 45.455 12.13 0.00 0.00 2.73
27 28 5.616488 TTTCTTCCCGTACTTGCAAATAC 57.384 39.130 7.99 7.99 0.00 1.89
28 29 5.392595 GCATTTCTTCCCGTACTTGCAAATA 60.393 40.000 0.00 0.00 0.00 1.40
29 30 4.618227 GCATTTCTTCCCGTACTTGCAAAT 60.618 41.667 0.00 0.00 0.00 2.32
30 31 3.305064 GCATTTCTTCCCGTACTTGCAAA 60.305 43.478 0.00 0.00 0.00 3.68
31 32 2.227865 GCATTTCTTCCCGTACTTGCAA 59.772 45.455 0.00 0.00 0.00 4.08
32 33 1.810151 GCATTTCTTCCCGTACTTGCA 59.190 47.619 0.00 0.00 0.00 4.08
33 34 1.202031 CGCATTTCTTCCCGTACTTGC 60.202 52.381 0.00 0.00 0.00 4.01
34 35 1.396996 CCGCATTTCTTCCCGTACTTG 59.603 52.381 0.00 0.00 0.00 3.16
35 36 1.734163 CCGCATTTCTTCCCGTACTT 58.266 50.000 0.00 0.00 0.00 2.24
36 37 0.743345 GCCGCATTTCTTCCCGTACT 60.743 55.000 0.00 0.00 0.00 2.73
37 38 1.712018 GGCCGCATTTCTTCCCGTAC 61.712 60.000 0.00 0.00 0.00 3.67
38 39 1.450669 GGCCGCATTTCTTCCCGTA 60.451 57.895 0.00 0.00 0.00 4.02
39 40 2.750237 GGCCGCATTTCTTCCCGT 60.750 61.111 0.00 0.00 0.00 5.28
40 41 2.339556 TTGGCCGCATTTCTTCCCG 61.340 57.895 0.00 0.00 0.00 5.14
41 42 1.215382 GTTGGCCGCATTTCTTCCC 59.785 57.895 0.00 0.00 0.00 3.97
42 43 0.388520 GTGTTGGCCGCATTTCTTCC 60.389 55.000 0.00 0.00 0.00 3.46
43 44 0.729140 CGTGTTGGCCGCATTTCTTC 60.729 55.000 0.00 0.00 0.00 2.87
44 45 1.169661 TCGTGTTGGCCGCATTTCTT 61.170 50.000 0.00 0.00 0.00 2.52
45 46 1.599518 TCGTGTTGGCCGCATTTCT 60.600 52.632 0.00 0.00 0.00 2.52
46 47 1.442017 GTCGTGTTGGCCGCATTTC 60.442 57.895 0.00 0.00 0.00 2.17
47 48 2.642700 GTCGTGTTGGCCGCATTT 59.357 55.556 0.00 0.00 0.00 2.32
48 49 3.722295 CGTCGTGTTGGCCGCATT 61.722 61.111 0.00 0.00 0.00 3.56
49 50 4.673298 TCGTCGTGTTGGCCGCAT 62.673 61.111 0.00 0.00 0.00 4.73
51 52 3.902162 TACTCGTCGTGTTGGCCGC 62.902 63.158 5.14 0.00 0.00 6.53
52 53 1.153901 ATACTCGTCGTGTTGGCCG 60.154 57.895 5.14 0.00 0.00 6.13
53 54 0.108992 TCATACTCGTCGTGTTGGCC 60.109 55.000 5.14 0.00 0.00 5.36
54 55 1.654105 CTTCATACTCGTCGTGTTGGC 59.346 52.381 5.14 0.00 0.00 4.52
55 56 2.915463 GTCTTCATACTCGTCGTGTTGG 59.085 50.000 5.14 0.00 0.00 3.77
56 57 2.915463 GGTCTTCATACTCGTCGTGTTG 59.085 50.000 5.14 4.66 0.00 3.33
57 58 2.818432 AGGTCTTCATACTCGTCGTGTT 59.182 45.455 5.14 0.00 0.00 3.32
58 59 2.161808 CAGGTCTTCATACTCGTCGTGT 59.838 50.000 5.19 5.19 0.00 4.49
59 60 2.161808 ACAGGTCTTCATACTCGTCGTG 59.838 50.000 0.00 0.00 0.00 4.35
60 61 2.161808 CACAGGTCTTCATACTCGTCGT 59.838 50.000 0.00 0.00 0.00 4.34
61 62 2.478031 CCACAGGTCTTCATACTCGTCG 60.478 54.545 0.00 0.00 0.00 5.12
62 63 2.492484 ACCACAGGTCTTCATACTCGTC 59.508 50.000 0.00 0.00 0.00 4.20
63 64 2.231478 CACCACAGGTCTTCATACTCGT 59.769 50.000 0.00 0.00 31.02 4.18
64 65 2.492088 TCACCACAGGTCTTCATACTCG 59.508 50.000 0.00 0.00 31.02 4.18
65 66 4.537135 TTCACCACAGGTCTTCATACTC 57.463 45.455 0.00 0.00 31.02 2.59
66 67 5.505181 AATTCACCACAGGTCTTCATACT 57.495 39.130 0.00 0.00 31.02 2.12
67 68 6.575162 AAAATTCACCACAGGTCTTCATAC 57.425 37.500 0.00 0.00 31.02 2.39
68 69 7.004086 AGAAAAATTCACCACAGGTCTTCATA 58.996 34.615 0.00 0.00 31.02 2.15
69 70 5.835280 AGAAAAATTCACCACAGGTCTTCAT 59.165 36.000 0.00 0.00 31.02 2.57
70 71 5.200483 AGAAAAATTCACCACAGGTCTTCA 58.800 37.500 0.00 0.00 31.02 3.02
71 72 5.560953 CGAGAAAAATTCACCACAGGTCTTC 60.561 44.000 0.00 0.00 31.02 2.87
72 73 4.275936 CGAGAAAAATTCACCACAGGTCTT 59.724 41.667 0.00 0.00 31.02 3.01
73 74 3.815401 CGAGAAAAATTCACCACAGGTCT 59.185 43.478 0.00 0.00 31.02 3.85
74 75 3.609409 GCGAGAAAAATTCACCACAGGTC 60.609 47.826 0.00 0.00 31.02 3.85
75 76 2.293399 GCGAGAAAAATTCACCACAGGT 59.707 45.455 0.00 0.00 35.62 4.00
76 77 2.351738 GGCGAGAAAAATTCACCACAGG 60.352 50.000 0.00 0.00 0.00 4.00
77 78 2.293122 TGGCGAGAAAAATTCACCACAG 59.707 45.455 0.00 0.00 0.00 3.66
78 79 2.034053 GTGGCGAGAAAAATTCACCACA 59.966 45.455 17.66 1.94 43.77 4.17
79 80 2.293399 AGTGGCGAGAAAAATTCACCAC 59.707 45.455 16.03 16.03 44.22 4.16
80 81 2.582052 AGTGGCGAGAAAAATTCACCA 58.418 42.857 0.00 0.00 0.00 4.17
81 82 4.759516 TTAGTGGCGAGAAAAATTCACC 57.240 40.909 0.00 0.00 0.00 4.02
82 83 7.806014 TGTAATTTAGTGGCGAGAAAAATTCAC 59.194 33.333 0.00 0.00 33.24 3.18
83 84 7.877003 TGTAATTTAGTGGCGAGAAAAATTCA 58.123 30.769 0.00 0.00 33.24 2.57
84 85 8.911247 ATGTAATTTAGTGGCGAGAAAAATTC 57.089 30.769 0.00 0.00 33.24 2.17
85 86 9.139174 CAATGTAATTTAGTGGCGAGAAAAATT 57.861 29.630 0.00 0.00 31.22 1.82
86 87 7.275560 GCAATGTAATTTAGTGGCGAGAAAAAT 59.724 33.333 0.00 0.00 31.22 1.82
87 88 6.584563 GCAATGTAATTTAGTGGCGAGAAAAA 59.415 34.615 0.00 0.00 31.22 1.94
88 89 6.090129 GCAATGTAATTTAGTGGCGAGAAAA 58.910 36.000 0.00 0.00 31.22 2.29
89 90 5.392595 GGCAATGTAATTTAGTGGCGAGAAA 60.393 40.000 0.00 0.00 31.22 2.52
90 91 4.095782 GGCAATGTAATTTAGTGGCGAGAA 59.904 41.667 0.00 0.00 31.22 2.87
91 92 3.625764 GGCAATGTAATTTAGTGGCGAGA 59.374 43.478 0.00 0.00 31.22 4.04
92 93 3.952535 GGCAATGTAATTTAGTGGCGAG 58.047 45.455 0.00 0.00 31.22 5.03
95 96 3.127895 TGTCGGCAATGTAATTTAGTGGC 59.872 43.478 0.00 6.40 31.22 5.01
96 97 4.955925 TGTCGGCAATGTAATTTAGTGG 57.044 40.909 0.00 0.00 31.22 4.00
97 98 6.146216 TGTTTGTCGGCAATGTAATTTAGTG 58.854 36.000 1.89 0.00 31.22 2.74
98 99 6.320494 TGTTTGTCGGCAATGTAATTTAGT 57.680 33.333 1.89 0.00 31.22 2.24
99 100 6.237542 GCATGTTTGTCGGCAATGTAATTTAG 60.238 38.462 1.89 0.00 31.22 1.85
100 101 5.574830 GCATGTTTGTCGGCAATGTAATTTA 59.425 36.000 1.89 0.00 31.22 1.40
101 102 4.388469 GCATGTTTGTCGGCAATGTAATTT 59.612 37.500 1.89 0.00 31.22 1.82
102 103 3.925913 GCATGTTTGTCGGCAATGTAATT 59.074 39.130 1.89 0.00 36.63 1.40
103 104 3.510719 GCATGTTTGTCGGCAATGTAAT 58.489 40.909 1.89 0.00 34.18 1.89
104 105 2.352225 GGCATGTTTGTCGGCAATGTAA 60.352 45.455 1.89 0.00 34.18 2.41
105 106 1.201181 GGCATGTTTGTCGGCAATGTA 59.799 47.619 1.89 0.00 34.18 2.29
106 107 0.038343 GGCATGTTTGTCGGCAATGT 60.038 50.000 1.89 0.00 34.18 2.71
107 108 0.244450 AGGCATGTTTGTCGGCAATG 59.756 50.000 1.89 0.00 34.18 2.82
108 109 0.244450 CAGGCATGTTTGTCGGCAAT 59.756 50.000 1.89 0.00 34.18 3.56
109 110 0.821301 TCAGGCATGTTTGTCGGCAA 60.821 50.000 0.00 0.00 30.85 4.52
110 111 0.821301 TTCAGGCATGTTTGTCGGCA 60.821 50.000 0.00 0.00 30.85 5.69
111 112 0.527565 ATTCAGGCATGTTTGTCGGC 59.472 50.000 0.00 0.00 30.85 5.54
112 113 1.541147 ACATTCAGGCATGTTTGTCGG 59.459 47.619 0.00 0.00 33.29 4.79
113 114 2.725759 CGACATTCAGGCATGTTTGTCG 60.726 50.000 29.02 29.02 46.04 4.35
114 115 2.483877 TCGACATTCAGGCATGTTTGTC 59.516 45.455 19.33 19.33 37.52 3.18
115 116 2.503331 TCGACATTCAGGCATGTTTGT 58.497 42.857 8.29 8.29 37.52 2.83
116 117 3.189080 TCTTCGACATTCAGGCATGTTTG 59.811 43.478 0.00 0.00 37.52 2.93
117 118 3.411446 TCTTCGACATTCAGGCATGTTT 58.589 40.909 0.00 0.00 37.52 2.83
118 119 3.057969 TCTTCGACATTCAGGCATGTT 57.942 42.857 0.00 0.00 37.52 2.71
119 120 2.768253 TCTTCGACATTCAGGCATGT 57.232 45.000 0.00 0.00 40.25 3.21
120 121 2.941064 ACATCTTCGACATTCAGGCATG 59.059 45.455 0.00 0.00 0.00 4.06
121 122 2.941064 CACATCTTCGACATTCAGGCAT 59.059 45.455 0.00 0.00 0.00 4.40
122 123 2.028203 TCACATCTTCGACATTCAGGCA 60.028 45.455 0.00 0.00 0.00 4.75
123 124 2.621338 TCACATCTTCGACATTCAGGC 58.379 47.619 0.00 0.00 0.00 4.85
124 125 5.180117 AGTTTTCACATCTTCGACATTCAGG 59.820 40.000 0.00 0.00 0.00 3.86
125 126 6.233430 AGTTTTCACATCTTCGACATTCAG 57.767 37.500 0.00 0.00 0.00 3.02
126 127 6.368791 CCTAGTTTTCACATCTTCGACATTCA 59.631 38.462 0.00 0.00 0.00 2.57
127 128 6.183360 CCCTAGTTTTCACATCTTCGACATTC 60.183 42.308 0.00 0.00 0.00 2.67
128 129 5.643777 CCCTAGTTTTCACATCTTCGACATT 59.356 40.000 0.00 0.00 0.00 2.71
129 130 5.178797 CCCTAGTTTTCACATCTTCGACAT 58.821 41.667 0.00 0.00 0.00 3.06
130 131 4.566004 CCCTAGTTTTCACATCTTCGACA 58.434 43.478 0.00 0.00 0.00 4.35
131 132 3.371285 GCCCTAGTTTTCACATCTTCGAC 59.629 47.826 0.00 0.00 0.00 4.20
132 133 3.596214 GCCCTAGTTTTCACATCTTCGA 58.404 45.455 0.00 0.00 0.00 3.71
133 134 2.678336 GGCCCTAGTTTTCACATCTTCG 59.322 50.000 0.00 0.00 0.00 3.79
134 135 2.678336 CGGCCCTAGTTTTCACATCTTC 59.322 50.000 0.00 0.00 0.00 2.87
135 136 2.711542 CGGCCCTAGTTTTCACATCTT 58.288 47.619 0.00 0.00 0.00 2.40
136 137 1.679032 GCGGCCCTAGTTTTCACATCT 60.679 52.381 0.00 0.00 0.00 2.90
137 138 0.733150 GCGGCCCTAGTTTTCACATC 59.267 55.000 0.00 0.00 0.00 3.06
138 139 0.328258 AGCGGCCCTAGTTTTCACAT 59.672 50.000 0.00 0.00 0.00 3.21
139 140 0.109723 AAGCGGCCCTAGTTTTCACA 59.890 50.000 0.00 0.00 0.00 3.58
140 141 0.521735 CAAGCGGCCCTAGTTTTCAC 59.478 55.000 0.00 0.00 0.00 3.18
141 142 0.109723 ACAAGCGGCCCTAGTTTTCA 59.890 50.000 0.00 0.00 0.00 2.69
142 143 1.244816 AACAAGCGGCCCTAGTTTTC 58.755 50.000 0.00 0.00 0.00 2.29
143 144 1.339929 CAAACAAGCGGCCCTAGTTTT 59.660 47.619 0.00 0.00 30.68 2.43
144 145 0.958822 CAAACAAGCGGCCCTAGTTT 59.041 50.000 0.00 0.42 33.09 2.66
145 146 0.109723 TCAAACAAGCGGCCCTAGTT 59.890 50.000 0.00 0.00 0.00 2.24
146 147 0.328258 ATCAAACAAGCGGCCCTAGT 59.672 50.000 0.00 0.00 0.00 2.57
147 148 2.325583 TATCAAACAAGCGGCCCTAG 57.674 50.000 0.00 0.00 0.00 3.02
148 149 3.211045 GAATATCAAACAAGCGGCCCTA 58.789 45.455 0.00 0.00 0.00 3.53
149 150 2.024414 GAATATCAAACAAGCGGCCCT 58.976 47.619 0.00 0.00 0.00 5.19
150 151 1.748493 TGAATATCAAACAAGCGGCCC 59.252 47.619 0.00 0.00 0.00 5.80
151 152 2.791158 CGTGAATATCAAACAAGCGGCC 60.791 50.000 0.00 0.00 0.00 6.13
152 153 2.159572 ACGTGAATATCAAACAAGCGGC 60.160 45.455 0.00 0.00 0.00 6.53
153 154 3.370978 AGACGTGAATATCAAACAAGCGG 59.629 43.478 0.00 0.00 0.00 5.52
154 155 4.584029 AGACGTGAATATCAAACAAGCG 57.416 40.909 0.00 0.00 0.00 4.68
155 156 7.688578 GTCTTAAGACGTGAATATCAAACAAGC 59.311 37.037 19.39 0.00 35.12 4.01
172 173 5.880341 ACAGCAACAACAAAGTCTTAAGAC 58.120 37.500 25.24 25.24 45.08 3.01
173 174 6.072175 ACAACAGCAACAACAAAGTCTTAAGA 60.072 34.615 0.00 0.00 0.00 2.10
174 175 6.092748 ACAACAGCAACAACAAAGTCTTAAG 58.907 36.000 0.00 0.00 0.00 1.85
175 176 6.019779 ACAACAGCAACAACAAAGTCTTAA 57.980 33.333 0.00 0.00 0.00 1.85
176 177 5.637006 ACAACAGCAACAACAAAGTCTTA 57.363 34.783 0.00 0.00 0.00 2.10
177 178 4.519540 ACAACAGCAACAACAAAGTCTT 57.480 36.364 0.00 0.00 0.00 3.01
178 179 4.236935 CAACAACAGCAACAACAAAGTCT 58.763 39.130 0.00 0.00 0.00 3.24
179 180 3.987220 ACAACAACAGCAACAACAAAGTC 59.013 39.130 0.00 0.00 0.00 3.01
180 181 3.988819 ACAACAACAGCAACAACAAAGT 58.011 36.364 0.00 0.00 0.00 2.66
181 182 4.377226 CCAACAACAACAGCAACAACAAAG 60.377 41.667 0.00 0.00 0.00 2.77
182 183 3.496130 CCAACAACAACAGCAACAACAAA 59.504 39.130 0.00 0.00 0.00 2.83
183 184 3.062763 CCAACAACAACAGCAACAACAA 58.937 40.909 0.00 0.00 0.00 2.83
184 185 2.611473 CCCAACAACAACAGCAACAACA 60.611 45.455 0.00 0.00 0.00 3.33
185 186 1.999024 CCCAACAACAACAGCAACAAC 59.001 47.619 0.00 0.00 0.00 3.32
186 187 1.674221 GCCCAACAACAACAGCAACAA 60.674 47.619 0.00 0.00 0.00 2.83
187 188 0.108424 GCCCAACAACAACAGCAACA 60.108 50.000 0.00 0.00 0.00 3.33
188 189 0.108424 TGCCCAACAACAACAGCAAC 60.108 50.000 0.00 0.00 0.00 4.17
189 190 0.829333 ATGCCCAACAACAACAGCAA 59.171 45.000 0.00 0.00 33.35 3.91
190 191 1.612950 CTATGCCCAACAACAACAGCA 59.387 47.619 0.00 0.00 34.28 4.41
191 192 1.067635 CCTATGCCCAACAACAACAGC 60.068 52.381 0.00 0.00 0.00 4.40
192 193 2.030007 CACCTATGCCCAACAACAACAG 60.030 50.000 0.00 0.00 0.00 3.16
193 194 1.959985 CACCTATGCCCAACAACAACA 59.040 47.619 0.00 0.00 0.00 3.33
194 195 1.960689 ACACCTATGCCCAACAACAAC 59.039 47.619 0.00 0.00 0.00 3.32
195 196 2.363680 CAACACCTATGCCCAACAACAA 59.636 45.455 0.00 0.00 0.00 2.83
196 197 1.959985 CAACACCTATGCCCAACAACA 59.040 47.619 0.00 0.00 0.00 3.33
197 198 1.960689 ACAACACCTATGCCCAACAAC 59.039 47.619 0.00 0.00 0.00 3.32
198 199 2.363680 CAACAACACCTATGCCCAACAA 59.636 45.455 0.00 0.00 0.00 2.83
199 200 1.959985 CAACAACACCTATGCCCAACA 59.040 47.619 0.00 0.00 0.00 3.33
200 201 1.272212 CCAACAACACCTATGCCCAAC 59.728 52.381 0.00 0.00 0.00 3.77
201 202 1.626686 CCAACAACACCTATGCCCAA 58.373 50.000 0.00 0.00 0.00 4.12
202 203 0.251564 CCCAACAACACCTATGCCCA 60.252 55.000 0.00 0.00 0.00 5.36
203 204 0.039035 TCCCAACAACACCTATGCCC 59.961 55.000 0.00 0.00 0.00 5.36
204 205 1.818674 CTTCCCAACAACACCTATGCC 59.181 52.381 0.00 0.00 0.00 4.40
205 206 1.202348 GCTTCCCAACAACACCTATGC 59.798 52.381 0.00 0.00 0.00 3.14
206 207 1.468520 CGCTTCCCAACAACACCTATG 59.531 52.381 0.00 0.00 0.00 2.23
207 208 1.613255 CCGCTTCCCAACAACACCTAT 60.613 52.381 0.00 0.00 0.00 2.57
208 209 0.250553 CCGCTTCCCAACAACACCTA 60.251 55.000 0.00 0.00 0.00 3.08
209 210 1.528309 CCGCTTCCCAACAACACCT 60.528 57.895 0.00 0.00 0.00 4.00
210 211 1.104577 TTCCGCTTCCCAACAACACC 61.105 55.000 0.00 0.00 0.00 4.16
211 212 0.310854 CTTCCGCTTCCCAACAACAC 59.689 55.000 0.00 0.00 0.00 3.32
212 213 0.821711 CCTTCCGCTTCCCAACAACA 60.822 55.000 0.00 0.00 0.00 3.33
213 214 1.524008 CCCTTCCGCTTCCCAACAAC 61.524 60.000 0.00 0.00 0.00 3.32
214 215 1.228429 CCCTTCCGCTTCCCAACAA 60.228 57.895 0.00 0.00 0.00 2.83
215 216 2.124507 CTCCCTTCCGCTTCCCAACA 62.125 60.000 0.00 0.00 0.00 3.33
216 217 1.377333 CTCCCTTCCGCTTCCCAAC 60.377 63.158 0.00 0.00 0.00 3.77
217 218 3.077907 CTCCCTTCCGCTTCCCAA 58.922 61.111 0.00 0.00 0.00 4.12
218 219 3.717294 GCTCCCTTCCGCTTCCCA 61.717 66.667 0.00 0.00 0.00 4.37
219 220 4.491409 GGCTCCCTTCCGCTTCCC 62.491 72.222 0.00 0.00 0.00 3.97
220 221 4.491409 GGGCTCCCTTCCGCTTCC 62.491 72.222 0.00 0.00 0.00 3.46
221 222 4.840005 CGGGCTCCCTTCCGCTTC 62.840 72.222 3.11 0.00 39.78 3.86
226 227 2.038837 CGAAAACGGGCTCCCTTCC 61.039 63.158 3.11 0.00 0.00 3.46
227 228 0.604511 TTCGAAAACGGGCTCCCTTC 60.605 55.000 0.00 0.00 0.00 3.46
228 229 0.179012 TTTCGAAAACGGGCTCCCTT 60.179 50.000 8.44 0.00 0.00 3.95
229 230 0.887836 GTTTCGAAAACGGGCTCCCT 60.888 55.000 13.10 0.00 0.00 4.20
230 231 1.577922 GTTTCGAAAACGGGCTCCC 59.422 57.895 13.10 0.00 0.00 4.30
234 235 4.812308 CTCGTTTCGAAAACGGGC 57.188 55.556 23.08 8.59 43.24 6.13
252 253 4.805192 GCGTATTCCAAGGTATTACGTTCA 59.195 41.667 0.00 0.00 32.79 3.18
253 254 5.045872 AGCGTATTCCAAGGTATTACGTTC 58.954 41.667 0.00 5.01 32.79 3.95
269 270 4.189231 GTGGTAGTTGATGGAAGCGTATT 58.811 43.478 0.00 0.00 0.00 1.89
270 271 3.196901 TGTGGTAGTTGATGGAAGCGTAT 59.803 43.478 0.00 0.00 0.00 3.06
816 827 1.814429 TCACCTTCCTTCCCTGTGAA 58.186 50.000 0.00 0.00 33.35 3.18
868 879 4.563061 TCAGGATGTGCGATCATCAATAG 58.437 43.478 17.44 7.74 44.00 1.73
961 977 8.899427 TTGATGTCCAATTTTATCAGCAAAAA 57.101 26.923 0.00 0.00 32.84 1.94
1528 1544 3.819368 TCTCAAGAACATCAAGTGCCAA 58.181 40.909 0.00 0.00 0.00 4.52
1542 1558 5.866092 CGAATCAGAAGTGACAATCTCAAGA 59.134 40.000 0.00 0.00 34.75 3.02
1838 1854 7.412781 GCAAGTTGCATGCTCTAGATATCATAC 60.413 40.741 22.90 0.00 44.26 2.39
1867 1883 0.250166 ACACCCCAGAAACGTAGCAC 60.250 55.000 0.00 0.00 0.00 4.40
2067 2083 5.620738 TTTCAATCATTCCAAACACCCAA 57.379 34.783 0.00 0.00 0.00 4.12
2090 2106 7.068593 TGACAAGTTTCTTGAGATTTGGACATT 59.931 33.333 15.04 0.00 0.00 2.71
2091 2107 6.547141 TGACAAGTTTCTTGAGATTTGGACAT 59.453 34.615 15.04 0.00 0.00 3.06
2178 2194 8.146053 TCCTCATGAGACAAACTATAAAGGAA 57.854 34.615 24.62 0.00 0.00 3.36
2263 2279 5.739959 TGAACGGAACAAGGATGATGAATA 58.260 37.500 0.00 0.00 0.00 1.75
2298 2314 4.357399 TCCAAACCCCCAAAAGATTACCTA 59.643 41.667 0.00 0.00 0.00 3.08
2319 2335 2.099756 GCTGGAATACATGCCAAAGTCC 59.900 50.000 0.00 0.00 32.95 3.85
2403 2419 4.830046 ACACGAAGATAGCCAGATATGAGT 59.170 41.667 0.00 0.00 0.00 3.41
2409 2425 8.958119 TTAATTTTACACGAAGATAGCCAGAT 57.042 30.769 0.00 0.00 0.00 2.90
2528 2544 2.504367 TCGACTCATGTGACTGACTCA 58.496 47.619 0.94 0.00 0.00 3.41
2639 2657 6.238897 GCTACAACTATATCACTCTCAGCAGT 60.239 42.308 0.00 0.00 0.00 4.40
2698 2716 8.391106 GTTCAAGTAACCATTGATGACTACATC 58.609 37.037 0.00 0.00 41.19 3.06
2736 2754 0.250901 TGTGAAAAGGCAGCCTCTCC 60.251 55.000 16.53 7.20 30.89 3.71
3081 3126 4.889995 TGCTAGTCACTACTGTATCAGCAT 59.110 41.667 0.00 0.00 36.36 3.79
3114 3159 0.375106 GCGCATGCCTACTGAACTTC 59.625 55.000 13.15 0.00 33.98 3.01
3132 3177 2.945668 ACCGAATGGAAAGAGCATAAGC 59.054 45.455 0.00 0.00 39.21 3.09


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

AutoCloner maintained by Alex Coulton.