Multiple sequence alignment - TraesCS4D01G115000

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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 TraesCS4D01G115000 chr4D 100.000 2987 0 0 1 2987 95875583 95878569 0.000000e+00 5517.0
1 TraesCS4D01G115000 chr4A 92.967 2787 106 41 223 2986 483384262 483381543 0.000000e+00 3978.0
2 TraesCS4D01G115000 chr4A 89.831 177 18 0 1273 1449 455302761 455302937 8.330000e-56 228.0
3 TraesCS4D01G115000 chr4B 95.479 1703 60 7 522 2215 135811733 135813427 0.000000e+00 2702.0
4 TraesCS4D01G115000 chr4B 94.890 724 21 5 2272 2987 135814310 135815025 0.000000e+00 1118.0
5 TraesCS4D01G115000 chr4B 86.747 415 34 9 113 520 135803113 135803513 2.730000e-120 442.0
6 TraesCS4D01G115000 chr4B 89.831 177 18 0 1273 1449 142710325 142710149 8.330000e-56 228.0
7 TraesCS4D01G115000 chr5A 76.996 952 174 30 1045 1987 280238944 280238029 1.240000e-138 503.0
8 TraesCS4D01G115000 chr5A 92.241 116 9 0 1 116 501412813 501412698 6.620000e-37 165.0
9 TraesCS4D01G115000 chr5D 76.576 952 178 30 1045 1987 214360920 214360005 5.790000e-132 481.0
10 TraesCS4D01G115000 chr1A 90.547 201 18 1 1487 1686 323262164 323262364 6.350000e-67 265.0
11 TraesCS4D01G115000 chr1A 88.950 181 20 0 1273 1453 323261982 323262162 1.080000e-54 224.0
12 TraesCS4D01G115000 chr1B 93.491 169 10 1 1521 1688 613022925 613022757 1.780000e-62 250.0
13 TraesCS4D01G115000 chr1B 91.160 181 16 0 1273 1453 613023126 613022946 2.300000e-61 246.0
14 TraesCS4D01G115000 chr6A 94.074 135 7 1 1554 1687 591103881 591103747 1.400000e-48 204.0
15 TraesCS4D01G115000 chr6A 94.074 135 7 1 1554 1687 591127615 591127481 1.400000e-48 204.0
16 TraesCS4D01G115000 chr6A 94.074 135 7 1 1554 1687 591128942 591128808 1.400000e-48 204.0
17 TraesCS4D01G115000 chr7B 94.783 115 6 0 1 115 217425778 217425664 2.370000e-41 180.0
18 TraesCS4D01G115000 chr2A 92.982 114 8 0 1 114 8156262 8156149 1.840000e-37 167.0
19 TraesCS4D01G115000 chr6D 86.047 86 10 2 31 115 44418933 44419017 1.140000e-14 91.6


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 TraesCS4D01G115000 chr4D 95875583 95878569 2986 False 5517 5517 100.0000 1 2987 1 chr4D.!!$F1 2986
1 TraesCS4D01G115000 chr4A 483381543 483384262 2719 True 3978 3978 92.9670 223 2986 1 chr4A.!!$R1 2763
2 TraesCS4D01G115000 chr4B 135811733 135815025 3292 False 1910 2702 95.1845 522 2987 2 chr4B.!!$F2 2465
3 TraesCS4D01G115000 chr5A 280238029 280238944 915 True 503 503 76.9960 1045 1987 1 chr5A.!!$R1 942
4 TraesCS4D01G115000 chr5D 214360005 214360920 915 True 481 481 76.5760 1045 1987 1 chr5D.!!$R1 942
5 TraesCS4D01G115000 chr6A 591127481 591128942 1461 True 204 204 94.0740 1554 1687 2 chr6A.!!$R2 133

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
68 69 0.036483 ATGTGGACAGTGCGCATGTA 60.036 50.0 19.32 4.59 37.53 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2047 1.202382 ACCTTTACTAGTCGATGCGCC 60.202 52.381 4.18 0.0 0.0 6.53 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
18 19 3.933879 TGACGTGGAGATTGCATGT 57.066 47.368 0.00 0.00 40.72 3.21
19 20 2.183478 TGACGTGGAGATTGCATGTT 57.817 45.000 0.00 0.00 38.07 2.71
20 21 1.805943 TGACGTGGAGATTGCATGTTG 59.194 47.619 0.00 0.00 38.07 3.33
21 22 2.076100 GACGTGGAGATTGCATGTTGA 58.924 47.619 0.00 0.00 38.07 3.18
22 23 2.079158 ACGTGGAGATTGCATGTTGAG 58.921 47.619 0.00 0.00 34.12 3.02
23 24 2.289631 ACGTGGAGATTGCATGTTGAGA 60.290 45.455 0.00 0.00 34.12 3.27
24 25 2.350804 CGTGGAGATTGCATGTTGAGAG 59.649 50.000 0.00 0.00 0.00 3.20
25 26 3.603532 GTGGAGATTGCATGTTGAGAGA 58.396 45.455 0.00 0.00 0.00 3.10
26 27 3.622163 GTGGAGATTGCATGTTGAGAGAG 59.378 47.826 0.00 0.00 0.00 3.20
27 28 2.613133 GGAGATTGCATGTTGAGAGAGC 59.387 50.000 0.00 0.00 0.00 4.09
28 29 3.268330 GAGATTGCATGTTGAGAGAGCA 58.732 45.455 0.00 0.00 0.00 4.26
29 30 3.878103 GAGATTGCATGTTGAGAGAGCAT 59.122 43.478 0.00 0.00 34.87 3.79
30 31 4.270834 AGATTGCATGTTGAGAGAGCATT 58.729 39.130 0.00 0.00 34.87 3.56
31 32 3.842732 TTGCATGTTGAGAGAGCATTG 57.157 42.857 0.00 0.00 34.87 2.82
32 33 3.062122 TGCATGTTGAGAGAGCATTGA 57.938 42.857 0.00 0.00 0.00 2.57
33 34 3.617284 TGCATGTTGAGAGAGCATTGAT 58.383 40.909 0.00 0.00 0.00 2.57
34 35 3.377172 TGCATGTTGAGAGAGCATTGATG 59.623 43.478 0.00 0.00 0.00 3.07
35 36 3.377485 GCATGTTGAGAGAGCATTGATGT 59.623 43.478 0.00 0.00 0.00 3.06
36 37 4.730903 GCATGTTGAGAGAGCATTGATGTG 60.731 45.833 0.00 0.00 0.00 3.21
37 38 3.340928 TGTTGAGAGAGCATTGATGTGG 58.659 45.455 0.00 0.00 0.00 4.17
38 39 2.034104 TGAGAGAGCATTGATGTGGC 57.966 50.000 0.00 0.00 0.00 5.01
39 40 1.279846 TGAGAGAGCATTGATGTGGCA 59.720 47.619 0.00 0.00 0.00 4.92
40 41 2.092592 TGAGAGAGCATTGATGTGGCAT 60.093 45.455 0.00 0.00 0.00 4.40
41 42 2.548904 GAGAGAGCATTGATGTGGCATC 59.451 50.000 0.00 2.44 0.00 3.91
42 43 1.607628 GAGAGCATTGATGTGGCATCC 59.392 52.381 6.65 0.00 0.00 3.51
43 44 1.064240 AGAGCATTGATGTGGCATCCA 60.064 47.619 6.65 0.00 0.00 3.41
44 45 1.961394 GAGCATTGATGTGGCATCCAT 59.039 47.619 6.65 0.00 35.28 3.41
45 46 1.686587 AGCATTGATGTGGCATCCATG 59.313 47.619 14.86 14.86 35.28 3.66
57 58 2.047002 CATCCATGCTGATGTGGACA 57.953 50.000 4.32 0.00 46.55 4.02
58 59 1.947456 CATCCATGCTGATGTGGACAG 59.053 52.381 4.32 0.00 46.55 3.51
59 60 0.986527 TCCATGCTGATGTGGACAGT 59.013 50.000 0.00 0.00 39.51 3.55
60 61 1.092348 CCATGCTGATGTGGACAGTG 58.908 55.000 0.00 0.00 37.72 3.66
61 62 0.450583 CATGCTGATGTGGACAGTGC 59.549 55.000 0.00 0.00 37.64 4.40
62 63 1.022982 ATGCTGATGTGGACAGTGCG 61.023 55.000 0.00 0.00 37.64 5.34
63 64 3.031964 GCTGATGTGGACAGTGCGC 62.032 63.158 0.00 0.00 37.64 6.09
64 65 1.668793 CTGATGTGGACAGTGCGCA 60.669 57.895 5.66 5.66 31.54 6.09
65 66 1.003476 TGATGTGGACAGTGCGCAT 60.003 52.632 20.00 20.00 41.62 4.73
66 67 1.300266 TGATGTGGACAGTGCGCATG 61.300 55.000 24.23 15.54 39.03 4.06
67 68 1.300971 GATGTGGACAGTGCGCATGT 61.301 55.000 24.23 18.85 39.03 3.21
68 69 0.036483 ATGTGGACAGTGCGCATGTA 60.036 50.000 19.32 4.59 37.53 2.29
69 70 0.250081 TGTGGACAGTGCGCATGTAA 60.250 50.000 15.91 8.34 0.00 2.41
70 71 0.871722 GTGGACAGTGCGCATGTAAA 59.128 50.000 15.91 8.00 0.00 2.01
71 72 1.135972 GTGGACAGTGCGCATGTAAAG 60.136 52.381 15.91 2.60 0.00 1.85
72 73 1.270571 TGGACAGTGCGCATGTAAAGA 60.271 47.619 15.91 1.63 0.00 2.52
73 74 2.009774 GGACAGTGCGCATGTAAAGAT 58.990 47.619 15.91 0.00 0.00 2.40
74 75 3.194861 GGACAGTGCGCATGTAAAGATA 58.805 45.455 15.91 0.00 0.00 1.98
75 76 3.621268 GGACAGTGCGCATGTAAAGATAA 59.379 43.478 15.91 0.00 0.00 1.75
76 77 4.273480 GGACAGTGCGCATGTAAAGATAAT 59.727 41.667 15.91 0.00 0.00 1.28
77 78 5.220854 GGACAGTGCGCATGTAAAGATAATT 60.221 40.000 15.91 0.00 0.00 1.40
78 79 5.572211 ACAGTGCGCATGTAAAGATAATTG 58.428 37.500 15.91 0.00 0.00 2.32
79 80 4.438797 CAGTGCGCATGTAAAGATAATTGC 59.561 41.667 15.91 0.00 0.00 3.56
80 81 4.336433 AGTGCGCATGTAAAGATAATTGCT 59.664 37.500 15.91 0.00 0.00 3.91
81 82 5.527214 AGTGCGCATGTAAAGATAATTGCTA 59.473 36.000 15.91 0.00 0.00 3.49
82 83 6.205464 AGTGCGCATGTAAAGATAATTGCTAT 59.795 34.615 15.91 0.00 0.00 2.97
83 84 7.387673 AGTGCGCATGTAAAGATAATTGCTATA 59.612 33.333 15.91 0.00 0.00 1.31
84 85 7.689812 GTGCGCATGTAAAGATAATTGCTATAG 59.310 37.037 15.91 0.00 0.00 1.31
85 86 7.387673 TGCGCATGTAAAGATAATTGCTATAGT 59.612 33.333 5.66 0.00 0.00 2.12
86 87 7.689812 GCGCATGTAAAGATAATTGCTATAGTG 59.310 37.037 0.30 0.00 0.00 2.74
87 88 8.171196 CGCATGTAAAGATAATTGCTATAGTGG 58.829 37.037 0.84 0.00 0.00 4.00
88 89 8.454106 GCATGTAAAGATAATTGCTATAGTGGG 58.546 37.037 0.84 0.00 0.00 4.61
89 90 8.950210 CATGTAAAGATAATTGCTATAGTGGGG 58.050 37.037 0.84 0.00 0.00 4.96
90 91 8.270137 TGTAAAGATAATTGCTATAGTGGGGA 57.730 34.615 0.84 0.00 0.00 4.81
91 92 8.375506 TGTAAAGATAATTGCTATAGTGGGGAG 58.624 37.037 0.84 0.00 0.00 4.30
92 93 7.394144 AAAGATAATTGCTATAGTGGGGAGT 57.606 36.000 0.84 0.00 0.00 3.85
93 94 8.506196 AAAGATAATTGCTATAGTGGGGAGTA 57.494 34.615 0.84 0.00 0.00 2.59
94 95 8.506196 AAGATAATTGCTATAGTGGGGAGTAA 57.494 34.615 0.84 0.00 0.00 2.24
95 96 7.908453 AGATAATTGCTATAGTGGGGAGTAAC 58.092 38.462 0.84 0.00 0.00 2.50
96 97 7.735321 AGATAATTGCTATAGTGGGGAGTAACT 59.265 37.037 0.84 0.00 0.00 2.24
97 98 6.576778 AATTGCTATAGTGGGGAGTAACTT 57.423 37.500 0.84 0.00 0.00 2.66
98 99 5.609533 TTGCTATAGTGGGGAGTAACTTC 57.390 43.478 0.84 0.00 0.00 3.01
99 100 4.880164 TGCTATAGTGGGGAGTAACTTCT 58.120 43.478 0.84 0.00 0.00 2.85
100 101 5.278061 TGCTATAGTGGGGAGTAACTTCTT 58.722 41.667 0.84 0.00 0.00 2.52
101 102 6.437755 TGCTATAGTGGGGAGTAACTTCTTA 58.562 40.000 0.84 0.00 0.00 2.10
102 103 6.899075 TGCTATAGTGGGGAGTAACTTCTTAA 59.101 38.462 0.84 0.00 0.00 1.85
103 104 7.400915 TGCTATAGTGGGGAGTAACTTCTTAAA 59.599 37.037 0.84 0.00 0.00 1.52
104 105 8.262933 GCTATAGTGGGGAGTAACTTCTTAAAA 58.737 37.037 0.84 0.00 0.00 1.52
107 108 7.761038 AGTGGGGAGTAACTTCTTAAAAATG 57.239 36.000 0.00 0.00 0.00 2.32
108 109 7.523415 AGTGGGGAGTAACTTCTTAAAAATGA 58.477 34.615 0.00 0.00 0.00 2.57
109 110 8.170730 AGTGGGGAGTAACTTCTTAAAAATGAT 58.829 33.333 0.00 0.00 0.00 2.45
110 111 9.457436 GTGGGGAGTAACTTCTTAAAAATGATA 57.543 33.333 0.00 0.00 0.00 2.15
111 112 9.681062 TGGGGAGTAACTTCTTAAAAATGATAG 57.319 33.333 0.00 0.00 0.00 2.08
112 113 9.901172 GGGGAGTAACTTCTTAAAAATGATAGA 57.099 33.333 0.00 0.00 0.00 1.98
133 134 9.844257 GATAGATTTAAGATTGGGATATGGAGG 57.156 37.037 0.00 0.00 0.00 4.30
134 135 7.037342 AGATTTAAGATTGGGATATGGAGGG 57.963 40.000 0.00 0.00 0.00 4.30
135 136 6.799582 AGATTTAAGATTGGGATATGGAGGGA 59.200 38.462 0.00 0.00 0.00 4.20
136 137 7.466866 AGATTTAAGATTGGGATATGGAGGGAT 59.533 37.037 0.00 0.00 0.00 3.85
137 138 4.942363 AAGATTGGGATATGGAGGGATG 57.058 45.455 0.00 0.00 0.00 3.51
138 139 3.196300 AGATTGGGATATGGAGGGATGG 58.804 50.000 0.00 0.00 0.00 3.51
139 140 2.531177 TTGGGATATGGAGGGATGGT 57.469 50.000 0.00 0.00 0.00 3.55
140 141 2.531177 TGGGATATGGAGGGATGGTT 57.469 50.000 0.00 0.00 0.00 3.67
141 142 2.065007 TGGGATATGGAGGGATGGTTG 58.935 52.381 0.00 0.00 0.00 3.77
142 143 2.065799 GGGATATGGAGGGATGGTTGT 58.934 52.381 0.00 0.00 0.00 3.32
143 144 2.224867 GGGATATGGAGGGATGGTTGTG 60.225 54.545 0.00 0.00 0.00 3.33
144 145 2.224867 GGATATGGAGGGATGGTTGTGG 60.225 54.545 0.00 0.00 0.00 4.17
145 146 2.278657 TATGGAGGGATGGTTGTGGA 57.721 50.000 0.00 0.00 0.00 4.02
146 147 0.625849 ATGGAGGGATGGTTGTGGAC 59.374 55.000 0.00 0.00 0.00 4.02
147 148 0.770166 TGGAGGGATGGTTGTGGACA 60.770 55.000 0.00 0.00 0.00 4.02
148 149 0.625849 GGAGGGATGGTTGTGGACAT 59.374 55.000 0.00 0.00 0.00 3.06
149 150 1.683011 GGAGGGATGGTTGTGGACATG 60.683 57.143 0.00 0.00 0.00 3.21
150 151 0.332632 AGGGATGGTTGTGGACATGG 59.667 55.000 0.00 0.00 0.00 3.66
151 152 0.331278 GGGATGGTTGTGGACATGGA 59.669 55.000 0.00 0.00 0.00 3.41
152 153 1.463674 GGATGGTTGTGGACATGGAC 58.536 55.000 0.00 0.00 0.00 4.02
153 154 1.271871 GGATGGTTGTGGACATGGACA 60.272 52.381 0.00 0.00 0.00 4.02
154 155 2.513753 GATGGTTGTGGACATGGACAA 58.486 47.619 0.00 0.19 0.00 3.18
155 156 2.443958 TGGTTGTGGACATGGACAAA 57.556 45.000 8.32 0.00 33.96 2.83
156 157 2.956132 TGGTTGTGGACATGGACAAAT 58.044 42.857 8.32 0.00 33.96 2.32
157 158 2.627221 TGGTTGTGGACATGGACAAATG 59.373 45.455 8.32 0.00 33.96 2.32
158 159 2.890311 GGTTGTGGACATGGACAAATGA 59.110 45.455 8.32 0.00 33.96 2.57
159 160 3.511146 GGTTGTGGACATGGACAAATGAT 59.489 43.478 8.32 0.00 33.96 2.45
160 161 4.487948 GTTGTGGACATGGACAAATGATG 58.512 43.478 8.32 0.00 33.96 3.07
161 162 4.031636 TGTGGACATGGACAAATGATGA 57.968 40.909 0.00 0.00 0.00 2.92
162 163 4.011698 TGTGGACATGGACAAATGATGAG 58.988 43.478 0.00 0.00 0.00 2.90
163 164 4.012374 GTGGACATGGACAAATGATGAGT 58.988 43.478 0.00 0.00 0.00 3.41
164 165 4.011698 TGGACATGGACAAATGATGAGTG 58.988 43.478 0.00 0.00 0.00 3.51
165 166 4.263418 TGGACATGGACAAATGATGAGTGA 60.263 41.667 0.00 0.00 0.00 3.41
166 167 4.885907 GGACATGGACAAATGATGAGTGAT 59.114 41.667 0.00 0.00 0.00 3.06
167 168 5.008415 GGACATGGACAAATGATGAGTGATC 59.992 44.000 0.00 0.00 0.00 2.92
168 169 4.573607 ACATGGACAAATGATGAGTGATCG 59.426 41.667 0.00 0.00 33.17 3.69
169 170 3.534554 TGGACAAATGATGAGTGATCGG 58.465 45.455 0.00 0.00 33.17 4.18
170 171 3.197549 TGGACAAATGATGAGTGATCGGA 59.802 43.478 0.00 0.00 33.17 4.55
171 172 3.557595 GGACAAATGATGAGTGATCGGAC 59.442 47.826 0.00 0.00 33.17 4.79
172 173 3.190079 ACAAATGATGAGTGATCGGACG 58.810 45.455 0.00 0.00 33.17 4.79
173 174 3.190079 CAAATGATGAGTGATCGGACGT 58.810 45.455 0.00 0.00 33.17 4.34
174 175 3.526931 AATGATGAGTGATCGGACGTT 57.473 42.857 0.00 0.00 33.17 3.99
175 176 2.278026 TGATGAGTGATCGGACGTTG 57.722 50.000 0.00 0.00 33.17 4.10
176 177 1.544246 TGATGAGTGATCGGACGTTGT 59.456 47.619 0.00 0.00 33.17 3.32
177 178 2.029380 TGATGAGTGATCGGACGTTGTT 60.029 45.455 0.00 0.00 33.17 2.83
178 179 2.060326 TGAGTGATCGGACGTTGTTC 57.940 50.000 0.00 0.00 0.00 3.18
179 180 1.338655 TGAGTGATCGGACGTTGTTCA 59.661 47.619 0.00 0.00 0.00 3.18
180 181 1.719780 GAGTGATCGGACGTTGTTCAC 59.280 52.381 18.06 18.06 37.54 3.18
188 189 2.462468 CGTTGTTCACGTACGCGG 59.538 61.111 16.72 8.28 44.49 6.46
189 190 2.010286 CGTTGTTCACGTACGCGGA 61.010 57.895 16.72 10.81 44.49 5.54
190 191 1.484232 GTTGTTCACGTACGCGGAC 59.516 57.895 16.72 12.68 43.45 4.79
192 193 2.127270 GTTCACGTACGCGGACGA 60.127 61.111 46.78 26.08 45.82 4.20
193 194 2.127270 TTCACGTACGCGGACGAC 60.127 61.111 46.78 20.42 45.82 4.34
194 195 3.909421 TTCACGTACGCGGACGACG 62.909 63.158 46.78 34.81 45.82 5.12
205 206 2.364243 CGGACGACGCGGATATATAG 57.636 55.000 12.47 0.00 34.82 1.31
206 207 1.004185 CGGACGACGCGGATATATAGG 60.004 57.143 12.47 0.00 34.82 2.57
207 208 1.332997 GGACGACGCGGATATATAGGG 59.667 57.143 12.47 4.01 0.00 3.53
208 209 2.012673 GACGACGCGGATATATAGGGT 58.987 52.381 12.47 9.24 0.00 4.34
209 210 2.012673 ACGACGCGGATATATAGGGTC 58.987 52.381 12.47 19.36 42.16 4.46
210 211 2.011947 CGACGCGGATATATAGGGTCA 58.988 52.381 24.40 0.00 44.64 4.02
211 212 2.617308 CGACGCGGATATATAGGGTCAT 59.383 50.000 24.40 3.74 44.64 3.06
212 213 3.811497 CGACGCGGATATATAGGGTCATA 59.189 47.826 24.40 0.00 44.64 2.15
213 214 4.319333 CGACGCGGATATATAGGGTCATAC 60.319 50.000 24.40 9.54 44.64 2.39
214 215 4.789807 ACGCGGATATATAGGGTCATACT 58.210 43.478 12.47 0.00 0.00 2.12
215 216 4.579340 ACGCGGATATATAGGGTCATACTG 59.421 45.833 12.47 0.00 0.00 2.74
216 217 4.579340 CGCGGATATATAGGGTCATACTGT 59.421 45.833 0.00 0.00 0.00 3.55
217 218 5.761726 CGCGGATATATAGGGTCATACTGTA 59.238 44.000 0.00 0.00 0.00 2.74
218 219 6.430308 CGCGGATATATAGGGTCATACTGTAT 59.570 42.308 0.00 0.00 0.00 2.29
219 220 7.040617 CGCGGATATATAGGGTCATACTGTATT 60.041 40.741 0.00 0.00 0.00 1.89
220 221 9.293404 GCGGATATATAGGGTCATACTGTATTA 57.707 37.037 0.00 0.00 0.00 0.98
228 229 7.349412 AGGGTCATACTGTATTAGACAAGTC 57.651 40.000 15.81 0.00 37.70 3.01
251 252 7.928307 TCTAGTTGTAGACACCGTTAATACT 57.072 36.000 0.00 0.00 29.69 2.12
252 253 7.978982 TCTAGTTGTAGACACCGTTAATACTC 58.021 38.462 0.00 0.00 29.69 2.59
253 254 5.958955 AGTTGTAGACACCGTTAATACTCC 58.041 41.667 0.00 0.00 0.00 3.85
254 255 5.477984 AGTTGTAGACACCGTTAATACTCCA 59.522 40.000 0.00 0.00 0.00 3.86
255 256 6.154021 AGTTGTAGACACCGTTAATACTCCAT 59.846 38.462 0.00 0.00 0.00 3.41
256 257 7.340232 AGTTGTAGACACCGTTAATACTCCATA 59.660 37.037 0.00 0.00 0.00 2.74
257 258 7.828508 TGTAGACACCGTTAATACTCCATAT 57.171 36.000 0.00 0.00 0.00 1.78
258 259 7.654568 TGTAGACACCGTTAATACTCCATATG 58.345 38.462 0.00 0.00 0.00 1.78
259 260 6.971726 AGACACCGTTAATACTCCATATGA 57.028 37.500 3.65 0.00 0.00 2.15
277 278 1.340600 TGACCCCGGCCAAGAAAATAG 60.341 52.381 2.24 0.00 0.00 1.73
278 279 0.702316 ACCCCGGCCAAGAAAATAGT 59.298 50.000 2.24 0.00 0.00 2.12
279 280 1.917568 ACCCCGGCCAAGAAAATAGTA 59.082 47.619 2.24 0.00 0.00 1.82
308 309 7.386299 CCTATCAGCTATCATGGTGTTAGTTTC 59.614 40.741 0.00 0.00 36.65 2.78
311 312 6.939730 TCAGCTATCATGGTGTTAGTTTCAAA 59.060 34.615 0.00 0.00 36.85 2.69
323 324 5.531659 TGTTAGTTTCAAATACCGCTTCCAA 59.468 36.000 0.00 0.00 0.00 3.53
339 340 0.830023 CCAAAGGCGGGGAAGGAAAA 60.830 55.000 0.00 0.00 0.00 2.29
346 347 2.353704 GGCGGGGAAGGAAAATTTTCTG 60.354 50.000 25.86 9.54 37.35 3.02
390 392 1.696644 CGAAACAGACAGCGCTACG 59.303 57.895 10.99 0.00 0.00 3.51
391 393 1.002250 CGAAACAGACAGCGCTACGT 61.002 55.000 10.99 4.34 0.00 3.57
446 448 2.182496 TCGCTCCGTACGATTTCCA 58.818 52.632 18.76 0.00 33.96 3.53
447 449 0.742505 TCGCTCCGTACGATTTCCAT 59.257 50.000 18.76 0.00 33.96 3.41
452 454 4.033129 CGCTCCGTACGATTTCCATTTTTA 59.967 41.667 18.76 0.00 0.00 1.52
453 455 5.277154 CGCTCCGTACGATTTCCATTTTTAT 60.277 40.000 18.76 0.00 0.00 1.40
454 456 6.074195 CGCTCCGTACGATTTCCATTTTTATA 60.074 38.462 18.76 0.00 0.00 0.98
455 457 7.067728 GCTCCGTACGATTTCCATTTTTATAC 58.932 38.462 18.76 0.00 0.00 1.47
477 479 1.241990 ACGAGCTACAGGTGCGAAGA 61.242 55.000 0.00 0.00 35.28 2.87
481 483 0.798771 GCTACAGGTGCGAAGACGAG 60.799 60.000 0.00 0.00 42.66 4.18
482 484 0.522180 CTACAGGTGCGAAGACGAGT 59.478 55.000 0.00 0.00 42.66 4.18
483 485 0.520404 TACAGGTGCGAAGACGAGTC 59.480 55.000 0.00 0.00 42.66 3.36
484 486 1.444553 CAGGTGCGAAGACGAGTCC 60.445 63.158 0.00 0.00 42.66 3.85
485 487 1.604023 AGGTGCGAAGACGAGTCCT 60.604 57.895 0.00 0.00 42.66 3.85
525 528 2.187946 CGCCATGTCTGTCTCCCC 59.812 66.667 0.00 0.00 0.00 4.81
554 557 1.202879 TGTGCCGGTTTGATTTCTCCT 60.203 47.619 1.90 0.00 0.00 3.69
564 568 6.528072 CGGTTTGATTTCTCCTTTTAAGATGC 59.472 38.462 0.00 0.00 0.00 3.91
592 596 1.153823 GTGTCGACTCCATCCCACG 60.154 63.158 17.92 0.00 0.00 4.94
616 620 3.380479 TCACCCACAAGACTAGAAACG 57.620 47.619 0.00 0.00 0.00 3.60
645 649 2.888834 TGAGCAACTTGGCCTTTTTC 57.111 45.000 3.32 0.00 0.00 2.29
658 662 4.140947 TGGCCTTTTTCTATATGGCAGGAT 60.141 41.667 3.32 0.00 44.85 3.24
720 724 1.153369 CGGCCCATTCGTCAGTGAT 60.153 57.895 0.00 0.00 0.00 3.06
722 726 1.472552 CGGCCCATTCGTCAGTGATTA 60.473 52.381 0.00 0.00 0.00 1.75
953 971 0.319211 TAACCAACTCACAGGTCGCG 60.319 55.000 0.00 0.00 37.07 5.87
1269 1293 2.359850 AATTCTTGCTGCCGCGGA 60.360 55.556 33.48 13.59 39.65 5.54
1548 1575 2.047465 CTCACGCTGAGCTGGCTT 60.047 61.111 1.78 0.00 37.72 4.35
1896 1951 2.358247 GCGCGGAAGGAGTGGAAA 60.358 61.111 8.83 0.00 0.00 3.13
2060 2190 1.415374 CGTGTTCGTCCAGTAGGTTG 58.585 55.000 0.00 0.00 35.89 3.77
2068 2198 1.002134 CCAGTAGGTTGCACAGGGG 60.002 63.158 0.00 0.00 0.00 4.79
2077 2207 3.009115 GCACAGGGGCAGAGGGTA 61.009 66.667 0.00 0.00 0.00 3.69
2092 2222 1.065418 AGGGTAGCTGCCACAATGTAC 60.065 52.381 23.21 2.18 0.00 2.90
2100 2230 4.081142 AGCTGCCACAATGTACATGTACTA 60.081 41.667 30.69 19.85 37.00 1.82
2105 2235 6.183360 TGCCACAATGTACATGTACTATAGCT 60.183 38.462 30.69 10.50 37.00 3.32
2108 2238 7.926018 CCACAATGTACATGTACTATAGCTCAA 59.074 37.037 30.69 12.33 37.00 3.02
2172 2302 6.371825 GGAAACTTGAGAAGATACCGTTGAAT 59.628 38.462 0.00 0.00 0.00 2.57
2177 2307 4.391830 TGAGAAGATACCGTTGAATGTTGC 59.608 41.667 0.00 0.00 0.00 4.17
2215 2346 3.698029 TTTGAAGCTCAGTTTCACTGC 57.302 42.857 2.97 0.00 45.54 4.40
2218 2349 2.158914 TGAAGCTCAGTTTCACTGCTGA 60.159 45.455 0.00 0.00 45.54 4.26
2219 2350 2.855209 AGCTCAGTTTCACTGCTGAT 57.145 45.000 0.00 0.00 45.54 2.90
2220 2351 3.969287 AGCTCAGTTTCACTGCTGATA 57.031 42.857 0.00 0.00 45.54 2.15
2221 2352 4.484537 AGCTCAGTTTCACTGCTGATAT 57.515 40.909 0.00 0.00 45.54 1.63
2222 2353 4.841422 AGCTCAGTTTCACTGCTGATATT 58.159 39.130 0.00 0.00 45.54 1.28
2223 2354 5.251764 AGCTCAGTTTCACTGCTGATATTT 58.748 37.500 0.00 0.00 45.54 1.40
2224 2355 5.353678 AGCTCAGTTTCACTGCTGATATTTC 59.646 40.000 0.00 0.00 45.54 2.17
2225 2356 5.448360 GCTCAGTTTCACTGCTGATATTTCC 60.448 44.000 0.00 0.00 45.54 3.13
2226 2357 5.559770 TCAGTTTCACTGCTGATATTTCCA 58.440 37.500 0.00 0.00 45.54 3.53
2227 2358 6.182627 TCAGTTTCACTGCTGATATTTCCAT 58.817 36.000 0.00 0.00 45.54 3.41
2236 2367 8.768955 CACTGCTGATATTTCCATAACTCTTAC 58.231 37.037 0.00 0.00 0.00 2.34
2258 2389 3.636153 AAGGTATCTGGAGCAAGGTTC 57.364 47.619 0.00 0.00 0.00 3.62
2289 2420 6.418101 TGCCTCAAGCTTCAATAGAACTTAT 58.582 36.000 0.00 0.00 44.23 1.73
2290 2421 6.886459 TGCCTCAAGCTTCAATAGAACTTATT 59.114 34.615 0.00 0.00 44.23 1.40
2291 2422 7.148188 TGCCTCAAGCTTCAATAGAACTTATTG 60.148 37.037 0.00 1.44 44.23 1.90
2318 3817 4.479619 GCCACAGCTCAAATTGTAAAGAG 58.520 43.478 0.00 0.00 35.50 2.85
2320 3819 5.278463 GCCACAGCTCAAATTGTAAAGAGAA 60.278 40.000 0.00 0.00 35.50 2.87
2742 4252 3.118075 TCACTCTGTTGGGAAACATGACA 60.118 43.478 0.00 0.00 31.47 3.58
2744 4254 3.213506 CTCTGTTGGGAAACATGACACA 58.786 45.455 0.00 0.00 31.47 3.72
2860 4370 1.626321 TCCCGTGAAATAACAGAGCCA 59.374 47.619 0.00 0.00 0.00 4.75
2863 4373 3.270027 CCGTGAAATAACAGAGCCATCA 58.730 45.455 0.00 0.00 0.00 3.07
2896 4406 1.903877 CGAAGGATGGAGGTGGTGCT 61.904 60.000 0.00 0.00 0.00 4.40
2973 4483 8.484641 TGAGTAGATGATGAAGTTGAATGAAC 57.515 34.615 0.00 0.00 34.40 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.805943 CAACATGCAATCTCCACGTCA 59.194 47.619 0.00 0.00 0.00 4.35
1 2 2.076100 TCAACATGCAATCTCCACGTC 58.924 47.619 0.00 0.00 0.00 4.34
3 4 2.349590 TCTCAACATGCAATCTCCACG 58.650 47.619 0.00 0.00 0.00 4.94
6 7 2.613133 GCTCTCTCAACATGCAATCTCC 59.387 50.000 0.00 0.00 0.00 3.71
7 8 3.268330 TGCTCTCTCAACATGCAATCTC 58.732 45.455 0.00 0.00 0.00 2.75
8 9 3.345508 TGCTCTCTCAACATGCAATCT 57.654 42.857 0.00 0.00 0.00 2.40
9 10 4.095932 TCAATGCTCTCTCAACATGCAATC 59.904 41.667 0.00 0.00 37.20 2.67
10 11 4.014406 TCAATGCTCTCTCAACATGCAAT 58.986 39.130 0.00 0.00 37.20 3.56
11 12 3.414269 TCAATGCTCTCTCAACATGCAA 58.586 40.909 0.00 0.00 37.20 4.08
12 13 3.062122 TCAATGCTCTCTCAACATGCA 57.938 42.857 0.00 0.00 38.05 3.96
13 14 3.377485 ACATCAATGCTCTCTCAACATGC 59.623 43.478 0.00 0.00 0.00 4.06
14 15 4.201920 CCACATCAATGCTCTCTCAACATG 60.202 45.833 0.00 0.00 0.00 3.21
15 16 3.945921 CCACATCAATGCTCTCTCAACAT 59.054 43.478 0.00 0.00 0.00 2.71
16 17 3.340928 CCACATCAATGCTCTCTCAACA 58.659 45.455 0.00 0.00 0.00 3.33
17 18 2.097142 GCCACATCAATGCTCTCTCAAC 59.903 50.000 0.00 0.00 0.00 3.18
18 19 2.290450 TGCCACATCAATGCTCTCTCAA 60.290 45.455 0.00 0.00 0.00 3.02
19 20 1.279846 TGCCACATCAATGCTCTCTCA 59.720 47.619 0.00 0.00 0.00 3.27
20 21 2.034104 TGCCACATCAATGCTCTCTC 57.966 50.000 0.00 0.00 0.00 3.20
21 22 2.573369 GATGCCACATCAATGCTCTCT 58.427 47.619 2.74 0.00 0.00 3.10
22 23 1.607628 GGATGCCACATCAATGCTCTC 59.392 52.381 9.60 0.00 0.00 3.20
23 24 1.064240 TGGATGCCACATCAATGCTCT 60.064 47.619 9.60 0.00 0.00 4.09
24 25 1.395635 TGGATGCCACATCAATGCTC 58.604 50.000 9.60 0.00 0.00 4.26
25 26 1.686587 CATGGATGCCACATCAATGCT 59.313 47.619 11.07 0.00 35.80 3.79
26 27 2.148916 CATGGATGCCACATCAATGC 57.851 50.000 11.07 0.00 35.80 3.56
38 39 1.947456 CTGTCCACATCAGCATGGATG 59.053 52.381 9.61 9.61 46.55 3.51
39 40 1.562942 ACTGTCCACATCAGCATGGAT 59.437 47.619 0.00 0.00 46.55 3.41
40 41 0.986527 ACTGTCCACATCAGCATGGA 59.013 50.000 0.00 0.00 42.88 3.41
41 42 1.092348 CACTGTCCACATCAGCATGG 58.908 55.000 0.00 0.00 36.50 3.66
42 43 0.450583 GCACTGTCCACATCAGCATG 59.549 55.000 0.00 0.00 36.50 4.06
43 44 1.022982 CGCACTGTCCACATCAGCAT 61.023 55.000 0.00 0.00 36.50 3.79
44 45 1.668793 CGCACTGTCCACATCAGCA 60.669 57.895 0.00 0.00 36.50 4.41
45 46 3.031964 GCGCACTGTCCACATCAGC 62.032 63.158 0.30 0.00 36.50 4.26
46 47 1.022982 ATGCGCACTGTCCACATCAG 61.023 55.000 14.90 0.00 38.68 2.90
47 48 1.003476 ATGCGCACTGTCCACATCA 60.003 52.632 14.90 0.00 0.00 3.07
48 49 1.300971 ACATGCGCACTGTCCACATC 61.301 55.000 14.90 0.00 0.00 3.06
49 50 0.036483 TACATGCGCACTGTCCACAT 60.036 50.000 22.74 0.00 0.00 3.21
50 51 0.250081 TTACATGCGCACTGTCCACA 60.250 50.000 22.74 8.32 0.00 4.17
51 52 0.871722 TTTACATGCGCACTGTCCAC 59.128 50.000 22.74 0.00 0.00 4.02
52 53 1.155889 CTTTACATGCGCACTGTCCA 58.844 50.000 22.74 12.26 0.00 4.02
53 54 1.438651 TCTTTACATGCGCACTGTCC 58.561 50.000 22.74 0.00 0.00 4.02
54 55 4.857871 TTATCTTTACATGCGCACTGTC 57.142 40.909 22.74 0.00 0.00 3.51
55 56 5.572211 CAATTATCTTTACATGCGCACTGT 58.428 37.500 14.90 20.26 0.00 3.55
56 57 4.438797 GCAATTATCTTTACATGCGCACTG 59.561 41.667 14.90 15.19 0.00 3.66
57 58 4.336433 AGCAATTATCTTTACATGCGCACT 59.664 37.500 14.90 2.74 38.74 4.40
58 59 4.601019 AGCAATTATCTTTACATGCGCAC 58.399 39.130 14.90 0.00 38.74 5.34
59 60 4.898829 AGCAATTATCTTTACATGCGCA 57.101 36.364 14.96 14.96 38.74 6.09
60 61 7.689812 CACTATAGCAATTATCTTTACATGCGC 59.310 37.037 0.00 0.00 38.74 6.09
61 62 8.171196 CCACTATAGCAATTATCTTTACATGCG 58.829 37.037 0.00 0.00 38.74 4.73
62 63 8.454106 CCCACTATAGCAATTATCTTTACATGC 58.546 37.037 0.00 0.00 0.00 4.06
63 64 8.950210 CCCCACTATAGCAATTATCTTTACATG 58.050 37.037 0.00 0.00 0.00 3.21
64 65 8.890472 TCCCCACTATAGCAATTATCTTTACAT 58.110 33.333 0.00 0.00 0.00 2.29
65 66 8.270137 TCCCCACTATAGCAATTATCTTTACA 57.730 34.615 0.00 0.00 0.00 2.41
66 67 8.376270 ACTCCCCACTATAGCAATTATCTTTAC 58.624 37.037 0.00 0.00 0.00 2.01
67 68 8.506196 ACTCCCCACTATAGCAATTATCTTTA 57.494 34.615 0.00 0.00 0.00 1.85
68 69 7.394144 ACTCCCCACTATAGCAATTATCTTT 57.606 36.000 0.00 0.00 0.00 2.52
69 70 8.376270 GTTACTCCCCACTATAGCAATTATCTT 58.624 37.037 0.00 0.00 0.00 2.40
70 71 7.735321 AGTTACTCCCCACTATAGCAATTATCT 59.265 37.037 0.00 0.00 0.00 1.98
71 72 7.908453 AGTTACTCCCCACTATAGCAATTATC 58.092 38.462 0.00 0.00 0.00 1.75
72 73 7.873699 AGTTACTCCCCACTATAGCAATTAT 57.126 36.000 0.00 0.00 0.00 1.28
73 74 7.567622 AGAAGTTACTCCCCACTATAGCAATTA 59.432 37.037 0.00 0.00 0.00 1.40
74 75 6.387220 AGAAGTTACTCCCCACTATAGCAATT 59.613 38.462 0.00 0.00 0.00 2.32
75 76 5.905913 AGAAGTTACTCCCCACTATAGCAAT 59.094 40.000 0.00 0.00 0.00 3.56
76 77 5.278061 AGAAGTTACTCCCCACTATAGCAA 58.722 41.667 0.00 0.00 0.00 3.91
77 78 4.880164 AGAAGTTACTCCCCACTATAGCA 58.120 43.478 0.00 0.00 0.00 3.49
78 79 5.873146 AAGAAGTTACTCCCCACTATAGC 57.127 43.478 0.00 0.00 0.00 2.97
81 82 9.462606 CATTTTTAAGAAGTTACTCCCCACTAT 57.537 33.333 0.00 0.00 0.00 2.12
82 83 8.662255 TCATTTTTAAGAAGTTACTCCCCACTA 58.338 33.333 0.00 0.00 0.00 2.74
83 84 7.523415 TCATTTTTAAGAAGTTACTCCCCACT 58.477 34.615 0.00 0.00 0.00 4.00
84 85 7.754851 TCATTTTTAAGAAGTTACTCCCCAC 57.245 36.000 0.00 0.00 0.00 4.61
85 86 9.681062 CTATCATTTTTAAGAAGTTACTCCCCA 57.319 33.333 0.00 0.00 0.00 4.96
86 87 9.901172 TCTATCATTTTTAAGAAGTTACTCCCC 57.099 33.333 0.00 0.00 0.00 4.81
107 108 9.844257 CCTCCATATCCCAATCTTAAATCTATC 57.156 37.037 0.00 0.00 0.00 2.08
108 109 8.785859 CCCTCCATATCCCAATCTTAAATCTAT 58.214 37.037 0.00 0.00 0.00 1.98
109 110 7.967170 TCCCTCCATATCCCAATCTTAAATCTA 59.033 37.037 0.00 0.00 0.00 1.98
110 111 6.799582 TCCCTCCATATCCCAATCTTAAATCT 59.200 38.462 0.00 0.00 0.00 2.40
111 112 7.032598 TCCCTCCATATCCCAATCTTAAATC 57.967 40.000 0.00 0.00 0.00 2.17
112 113 7.416731 CATCCCTCCATATCCCAATCTTAAAT 58.583 38.462 0.00 0.00 0.00 1.40
113 114 6.240556 CCATCCCTCCATATCCCAATCTTAAA 60.241 42.308 0.00 0.00 0.00 1.52
114 115 5.253798 CCATCCCTCCATATCCCAATCTTAA 59.746 44.000 0.00 0.00 0.00 1.85
115 116 4.790246 CCATCCCTCCATATCCCAATCTTA 59.210 45.833 0.00 0.00 0.00 2.10
116 117 3.595138 CCATCCCTCCATATCCCAATCTT 59.405 47.826 0.00 0.00 0.00 2.40
117 118 3.196300 CCATCCCTCCATATCCCAATCT 58.804 50.000 0.00 0.00 0.00 2.40
118 119 2.922283 ACCATCCCTCCATATCCCAATC 59.078 50.000 0.00 0.00 0.00 2.67
119 120 3.023931 ACCATCCCTCCATATCCCAAT 57.976 47.619 0.00 0.00 0.00 3.16
120 121 2.446666 CAACCATCCCTCCATATCCCAA 59.553 50.000 0.00 0.00 0.00 4.12
121 122 2.065007 CAACCATCCCTCCATATCCCA 58.935 52.381 0.00 0.00 0.00 4.37
122 123 2.065799 ACAACCATCCCTCCATATCCC 58.934 52.381 0.00 0.00 0.00 3.85
123 124 2.224867 CCACAACCATCCCTCCATATCC 60.225 54.545 0.00 0.00 0.00 2.59
124 125 2.711009 TCCACAACCATCCCTCCATATC 59.289 50.000 0.00 0.00 0.00 1.63
125 126 2.443255 GTCCACAACCATCCCTCCATAT 59.557 50.000 0.00 0.00 0.00 1.78
126 127 1.843851 GTCCACAACCATCCCTCCATA 59.156 52.381 0.00 0.00 0.00 2.74
127 128 0.625849 GTCCACAACCATCCCTCCAT 59.374 55.000 0.00 0.00 0.00 3.41
128 129 0.770166 TGTCCACAACCATCCCTCCA 60.770 55.000 0.00 0.00 0.00 3.86
129 130 0.625849 ATGTCCACAACCATCCCTCC 59.374 55.000 0.00 0.00 0.00 4.30
130 131 1.683011 CCATGTCCACAACCATCCCTC 60.683 57.143 0.00 0.00 0.00 4.30
131 132 0.332632 CCATGTCCACAACCATCCCT 59.667 55.000 0.00 0.00 0.00 4.20
132 133 0.331278 TCCATGTCCACAACCATCCC 59.669 55.000 0.00 0.00 0.00 3.85
133 134 1.271871 TGTCCATGTCCACAACCATCC 60.272 52.381 0.00 0.00 0.00 3.51
134 135 2.198827 TGTCCATGTCCACAACCATC 57.801 50.000 0.00 0.00 0.00 3.51
135 136 2.673775 TTGTCCATGTCCACAACCAT 57.326 45.000 0.00 0.00 0.00 3.55
136 137 2.443958 TTTGTCCATGTCCACAACCA 57.556 45.000 2.47 0.00 32.19 3.67
137 138 2.890311 TCATTTGTCCATGTCCACAACC 59.110 45.455 2.47 0.00 32.19 3.77
138 139 4.218200 TCATCATTTGTCCATGTCCACAAC 59.782 41.667 2.47 0.00 32.19 3.32
139 140 4.405548 TCATCATTTGTCCATGTCCACAA 58.594 39.130 0.00 0.00 0.00 3.33
140 141 4.011698 CTCATCATTTGTCCATGTCCACA 58.988 43.478 0.00 0.00 0.00 4.17
141 142 4.012374 ACTCATCATTTGTCCATGTCCAC 58.988 43.478 0.00 0.00 0.00 4.02
142 143 4.011698 CACTCATCATTTGTCCATGTCCA 58.988 43.478 0.00 0.00 0.00 4.02
143 144 4.264253 TCACTCATCATTTGTCCATGTCC 58.736 43.478 0.00 0.00 0.00 4.02
144 145 5.277202 CGATCACTCATCATTTGTCCATGTC 60.277 44.000 0.00 0.00 0.00 3.06
145 146 4.573607 CGATCACTCATCATTTGTCCATGT 59.426 41.667 0.00 0.00 0.00 3.21
146 147 4.024302 CCGATCACTCATCATTTGTCCATG 60.024 45.833 0.00 0.00 0.00 3.66
147 148 4.132336 CCGATCACTCATCATTTGTCCAT 58.868 43.478 0.00 0.00 0.00 3.41
148 149 3.197549 TCCGATCACTCATCATTTGTCCA 59.802 43.478 0.00 0.00 0.00 4.02
149 150 3.557595 GTCCGATCACTCATCATTTGTCC 59.442 47.826 0.00 0.00 0.00 4.02
150 151 3.243877 CGTCCGATCACTCATCATTTGTC 59.756 47.826 0.00 0.00 0.00 3.18
151 152 3.190079 CGTCCGATCACTCATCATTTGT 58.810 45.455 0.00 0.00 0.00 2.83
152 153 3.190079 ACGTCCGATCACTCATCATTTG 58.810 45.455 0.00 0.00 0.00 2.32
153 154 3.526931 ACGTCCGATCACTCATCATTT 57.473 42.857 0.00 0.00 0.00 2.32
154 155 3.190079 CAACGTCCGATCACTCATCATT 58.810 45.455 0.00 0.00 0.00 2.57
155 156 2.166459 ACAACGTCCGATCACTCATCAT 59.834 45.455 0.00 0.00 0.00 2.45
156 157 1.544246 ACAACGTCCGATCACTCATCA 59.456 47.619 0.00 0.00 0.00 3.07
157 158 2.279582 ACAACGTCCGATCACTCATC 57.720 50.000 0.00 0.00 0.00 2.92
158 159 2.029380 TGAACAACGTCCGATCACTCAT 60.029 45.455 0.00 0.00 0.00 2.90
159 160 1.338655 TGAACAACGTCCGATCACTCA 59.661 47.619 0.00 0.00 0.00 3.41
160 161 1.719780 GTGAACAACGTCCGATCACTC 59.280 52.381 16.33 0.00 37.87 3.51
161 162 1.779569 GTGAACAACGTCCGATCACT 58.220 50.000 16.33 0.00 37.87 3.41
172 173 1.484232 GTCCGCGTACGTGAACAAC 59.516 57.895 29.24 16.73 37.70 3.32
173 174 2.010286 CGTCCGCGTACGTGAACAA 61.010 57.895 29.24 9.42 38.07 2.83
174 175 2.427245 CGTCCGCGTACGTGAACA 60.427 61.111 29.24 10.40 38.07 3.18
175 176 2.127270 TCGTCCGCGTACGTGAAC 60.127 61.111 29.24 19.43 43.31 3.18
176 177 2.127270 GTCGTCCGCGTACGTGAA 60.127 61.111 29.24 7.12 43.31 3.18
177 178 4.428922 CGTCGTCCGCGTACGTGA 62.429 66.667 29.24 16.96 43.31 4.35
186 187 1.004185 CCTATATATCCGCGTCGTCCG 60.004 57.143 4.92 0.00 40.40 4.79
187 188 1.332997 CCCTATATATCCGCGTCGTCC 59.667 57.143 4.92 0.00 0.00 4.79
188 189 2.012673 ACCCTATATATCCGCGTCGTC 58.987 52.381 4.92 0.00 0.00 4.20
189 190 2.012673 GACCCTATATATCCGCGTCGT 58.987 52.381 4.92 0.00 0.00 4.34
190 191 2.011947 TGACCCTATATATCCGCGTCG 58.988 52.381 4.92 0.00 0.00 5.12
191 192 4.820716 AGTATGACCCTATATATCCGCGTC 59.179 45.833 4.92 0.00 0.00 5.19
192 193 4.579340 CAGTATGACCCTATATATCCGCGT 59.421 45.833 4.92 0.00 39.69 6.01
193 194 4.579340 ACAGTATGACCCTATATATCCGCG 59.421 45.833 0.00 0.00 39.69 6.46
194 195 7.762588 ATACAGTATGACCCTATATATCCGC 57.237 40.000 0.00 0.00 39.69 5.54
202 203 9.080097 GACTTGTCTAATACAGTATGACCCTAT 57.920 37.037 8.05 0.00 39.69 2.57
203 204 8.280084 AGACTTGTCTAATACAGTATGACCCTA 58.720 37.037 0.89 0.00 39.69 3.53
204 205 7.126733 AGACTTGTCTAATACAGTATGACCCT 58.873 38.462 0.89 0.60 39.69 4.34
205 206 7.349412 AGACTTGTCTAATACAGTATGACCC 57.651 40.000 0.89 0.00 39.69 4.46
206 207 9.122779 ACTAGACTTGTCTAATACAGTATGACC 57.877 37.037 11.09 0.00 39.69 4.02
212 213 9.736414 TCTACAACTAGACTTGTCTAATACAGT 57.264 33.333 11.09 4.99 39.87 3.55
213 214 9.991388 GTCTACAACTAGACTTGTCTAATACAG 57.009 37.037 11.09 4.44 44.02 2.74
214 215 9.511272 TGTCTACAACTAGACTTGTCTAATACA 57.489 33.333 11.09 1.14 46.53 2.29
215 216 9.771915 GTGTCTACAACTAGACTTGTCTAATAC 57.228 37.037 11.09 1.32 46.53 1.89
216 217 8.954350 GGTGTCTACAACTAGACTTGTCTAATA 58.046 37.037 11.09 2.74 46.53 0.98
217 218 7.361885 CGGTGTCTACAACTAGACTTGTCTAAT 60.362 40.741 11.09 0.00 46.53 1.73
218 219 6.072838 CGGTGTCTACAACTAGACTTGTCTAA 60.073 42.308 11.09 0.00 46.53 2.10
219 220 5.410746 CGGTGTCTACAACTAGACTTGTCTA 59.589 44.000 9.75 9.75 46.53 2.59
220 221 4.215827 CGGTGTCTACAACTAGACTTGTCT 59.784 45.833 8.41 8.41 46.53 3.41
221 222 4.023365 ACGGTGTCTACAACTAGACTTGTC 60.023 45.833 0.00 0.00 46.53 3.18
222 223 3.887716 ACGGTGTCTACAACTAGACTTGT 59.112 43.478 0.00 0.00 46.53 3.16
223 224 4.500603 ACGGTGTCTACAACTAGACTTG 57.499 45.455 0.00 0.00 46.53 3.16
224 225 6.639632 TTAACGGTGTCTACAACTAGACTT 57.360 37.500 0.00 0.00 46.53 3.01
225 226 6.830873 ATTAACGGTGTCTACAACTAGACT 57.169 37.500 0.00 0.00 46.53 3.24
226 227 7.756558 AGTATTAACGGTGTCTACAACTAGAC 58.243 38.462 0.00 1.57 46.56 2.59
227 228 7.066284 GGAGTATTAACGGTGTCTACAACTAGA 59.934 40.741 0.00 0.00 0.00 2.43
228 229 7.148188 TGGAGTATTAACGGTGTCTACAACTAG 60.148 40.741 0.00 0.00 0.00 2.57
247 248 1.276622 GCCGGGGTCATATGGAGTAT 58.723 55.000 2.18 0.00 0.00 2.12
248 249 0.834687 GGCCGGGGTCATATGGAGTA 60.835 60.000 2.18 0.00 0.00 2.59
249 250 2.147387 GGCCGGGGTCATATGGAGT 61.147 63.158 2.18 0.00 0.00 3.85
250 251 1.705002 TTGGCCGGGGTCATATGGAG 61.705 60.000 2.18 0.00 0.00 3.86
251 252 1.694525 TTGGCCGGGGTCATATGGA 60.695 57.895 2.18 0.00 0.00 3.41
252 253 1.228245 CTTGGCCGGGGTCATATGG 60.228 63.158 2.18 0.00 0.00 2.74
253 254 0.182537 TTCTTGGCCGGGGTCATATG 59.817 55.000 2.18 0.00 0.00 1.78
254 255 0.923358 TTTCTTGGCCGGGGTCATAT 59.077 50.000 2.18 0.00 0.00 1.78
255 256 0.699399 TTTTCTTGGCCGGGGTCATA 59.301 50.000 2.18 0.00 0.00 2.15
256 257 0.041090 ATTTTCTTGGCCGGGGTCAT 59.959 50.000 2.18 0.00 0.00 3.06
257 258 0.699399 TATTTTCTTGGCCGGGGTCA 59.301 50.000 2.18 0.00 0.00 4.02
258 259 1.340697 ACTATTTTCTTGGCCGGGGTC 60.341 52.381 2.18 0.00 0.00 4.46
259 260 0.702316 ACTATTTTCTTGGCCGGGGT 59.298 50.000 2.18 0.00 0.00 4.95
277 278 5.478679 ACACCATGATAGCTGATAGGAGTAC 59.521 44.000 0.00 0.00 0.00 2.73
278 279 5.645201 ACACCATGATAGCTGATAGGAGTA 58.355 41.667 0.00 0.00 0.00 2.59
279 280 4.487804 ACACCATGATAGCTGATAGGAGT 58.512 43.478 0.00 0.00 0.00 3.85
296 297 4.391155 AGCGGTATTTGAAACTAACACCA 58.609 39.130 0.00 0.00 0.00 4.17
308 309 2.278026 GCCTTTGGAAGCGGTATTTG 57.722 50.000 0.00 0.00 0.00 2.32
323 324 2.024176 AAATTTTCCTTCCCCGCCTT 57.976 45.000 0.00 0.00 0.00 4.35
339 340 2.365293 GTGTTCCAGGGTTGCAGAAAAT 59.635 45.455 0.00 0.00 0.00 1.82
346 347 2.268076 ATGCGTGTTCCAGGGTTGC 61.268 57.895 0.00 0.00 0.00 4.17
399 401 3.124921 GTGTCGGGATGGCAACGG 61.125 66.667 9.20 2.49 42.51 4.44
445 447 8.487970 CACCTGTAGCTCGTATGTATAAAAATG 58.512 37.037 0.00 0.00 0.00 2.32
446 448 7.170998 GCACCTGTAGCTCGTATGTATAAAAAT 59.829 37.037 0.00 0.00 0.00 1.82
447 449 6.477688 GCACCTGTAGCTCGTATGTATAAAAA 59.522 38.462 0.00 0.00 0.00 1.94
452 454 2.031069 CGCACCTGTAGCTCGTATGTAT 60.031 50.000 0.00 0.00 0.00 2.29
453 455 1.332686 CGCACCTGTAGCTCGTATGTA 59.667 52.381 0.00 0.00 0.00 2.29
454 456 0.100682 CGCACCTGTAGCTCGTATGT 59.899 55.000 0.00 0.00 0.00 2.29
455 457 0.380733 TCGCACCTGTAGCTCGTATG 59.619 55.000 0.00 0.00 0.00 2.39
477 479 1.335689 GCGTTACAGAACAGGACTCGT 60.336 52.381 0.00 0.00 35.06 4.18
481 483 0.782384 CGTGCGTTACAGAACAGGAC 59.218 55.000 0.00 0.00 35.06 3.85
482 484 0.319211 CCGTGCGTTACAGAACAGGA 60.319 55.000 0.00 0.00 35.06 3.86
483 485 1.897398 GCCGTGCGTTACAGAACAGG 61.897 60.000 0.00 0.00 35.06 4.00
484 486 1.218875 TGCCGTGCGTTACAGAACAG 61.219 55.000 0.00 0.00 35.06 3.16
485 487 0.810426 TTGCCGTGCGTTACAGAACA 60.810 50.000 0.00 0.00 35.06 3.18
517 519 0.191064 ACAAGAGGACTGGGGAGACA 59.809 55.000 0.00 0.00 0.00 3.41
525 528 0.535102 AAACCGGCACAAGAGGACTG 60.535 55.000 0.00 0.00 0.00 3.51
554 557 1.136474 CGTCACGCGTGCATCTTAAAA 60.136 47.619 33.63 11.01 35.54 1.52
578 582 2.978452 GATGCCGTGGGATGGAGTCG 62.978 65.000 0.00 0.00 0.00 4.18
592 596 1.555075 TCTAGTCTTGTGGGTGATGCC 59.445 52.381 0.00 0.00 0.00 4.40
645 649 5.191426 CAAGGGATTCATCCTGCCATATAG 58.809 45.833 5.80 0.00 46.35 1.31
658 662 0.321564 CGTGTCAGCCAAGGGATTCA 60.322 55.000 0.00 0.00 0.00 2.57
720 724 9.535878 GTGATGTTTCTGGGTTTGTTTTATTAA 57.464 29.630 0.00 0.00 0.00 1.40
722 726 6.699642 CGTGATGTTTCTGGGTTTGTTTTATT 59.300 34.615 0.00 0.00 0.00 1.40
906 924 8.122952 GCACCTGTGAATTGAGTATGTTTATAC 58.877 37.037 0.51 0.00 39.57 1.47
941 959 4.056125 TCCTGCGCGACCTGTGAG 62.056 66.667 12.10 0.00 0.00 3.51
953 971 0.881118 TGCAATTCCTTTCGTCCTGC 59.119 50.000 0.00 0.00 0.00 4.85
982 1000 1.000843 CATGGTGGACAGACACGAAGA 59.999 52.381 0.00 0.00 42.23 2.87
1485 1512 2.354401 CGAGAAGCCCTCCTGCAGA 61.354 63.158 17.39 0.00 38.71 4.26
1548 1575 3.429141 GACGTCGGGTCGAGCAGA 61.429 66.667 17.59 15.50 36.23 4.26
1845 1900 2.602568 AACTCCCCGTACTGCCGT 60.603 61.111 0.00 0.00 0.00 5.68
1992 2047 1.202382 ACCTTTACTAGTCGATGCGCC 60.202 52.381 4.18 0.00 0.00 6.53
2060 2190 3.009115 TACCCTCTGCCCCTGTGC 61.009 66.667 0.00 0.00 0.00 4.57
2077 2207 2.205022 ACATGTACATTGTGGCAGCT 57.795 45.000 5.37 0.00 0.00 4.24
2092 2222 4.607293 TGGCCTTGAGCTATAGTACATG 57.393 45.455 3.32 0.00 43.05 3.21
2100 2230 4.657969 AGATAACTCTTGGCCTTGAGCTAT 59.342 41.667 20.37 18.09 43.05 2.97
2191 2321 4.370364 GTGAAACTGAGCTTCAAAACCA 57.630 40.909 0.00 0.00 34.68 3.67
2221 2352 9.667107 CAGATACCTTTGTAAGAGTTATGGAAA 57.333 33.333 0.00 0.00 0.00 3.13
2222 2353 8.265055 CCAGATACCTTTGTAAGAGTTATGGAA 58.735 37.037 0.00 0.00 0.00 3.53
2223 2354 7.622081 TCCAGATACCTTTGTAAGAGTTATGGA 59.378 37.037 0.00 0.00 0.00 3.41
2224 2355 7.792032 TCCAGATACCTTTGTAAGAGTTATGG 58.208 38.462 0.00 0.00 0.00 2.74
2225 2356 7.439655 GCTCCAGATACCTTTGTAAGAGTTATG 59.560 40.741 0.00 0.00 0.00 1.90
2226 2357 7.125811 TGCTCCAGATACCTTTGTAAGAGTTAT 59.874 37.037 0.00 0.00 0.00 1.89
2227 2358 6.439375 TGCTCCAGATACCTTTGTAAGAGTTA 59.561 38.462 0.00 0.00 0.00 2.24
2236 2367 3.356529 ACCTTGCTCCAGATACCTTTG 57.643 47.619 0.00 0.00 0.00 2.77
2243 2374 0.034670 GGCAGAACCTTGCTCCAGAT 60.035 55.000 0.00 0.00 43.57 2.90
2258 2389 1.307097 GAAGCTTGAGGCATAGGCAG 58.693 55.000 2.10 0.00 44.79 4.85
2265 2396 4.292186 AGTTCTATTGAAGCTTGAGGCA 57.708 40.909 2.10 0.00 44.79 4.75
2290 2421 0.698238 ATTTGAGCTGTGGCCTACCA 59.302 50.000 3.32 0.00 46.51 3.25
2291 2422 1.474077 CAATTTGAGCTGTGGCCTACC 59.526 52.381 3.32 0.00 39.73 3.18
2371 3871 6.684613 GCATCAGGTCTTGGAATGCAAATATT 60.685 38.462 0.00 0.00 34.12 1.28
2570 4080 8.079211 TCTGGAACTTCTGTATAGCTTTGTAT 57.921 34.615 0.00 0.00 0.00 2.29
2824 4334 2.498885 ACGGGATAAAGTTAAGGACGCT 59.501 45.455 0.00 0.00 0.00 5.07
2860 4370 2.048023 CGCCCCTGCACACAATGAT 61.048 57.895 0.00 0.00 37.32 2.45
2863 4373 1.973281 CTTCGCCCCTGCACACAAT 60.973 57.895 0.00 0.00 37.32 2.71
2896 4406 0.631753 TCCAACCTTTTCCACCACCA 59.368 50.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.