Multiple sequence alignment - TraesCS3D01G014300

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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 TraesCS3D01G014300 chr3D 100.000 3610 0 0 1 3610 4994667 4998276 0.000000e+00 6667.0
1 TraesCS3D01G014300 chr3D 86.317 1469 155 21 551 2016 9679525 9678100 0.000000e+00 1557.0
2 TraesCS3D01G014300 chr3D 94.872 39 1 1 81 119 449302320 449302283 3.890000e-05 60.2
3 TraesCS3D01G014300 chr3B 92.511 1322 59 17 2308 3610 13820294 13818994 0.000000e+00 1857.0
4 TraesCS3D01G014300 chr3B 83.392 1987 191 92 281 2232 13822176 13820294 0.000000e+00 1712.0
5 TraesCS3D01G014300 chrUn 94.899 1039 52 1 1235 2273 257141385 257140348 0.000000e+00 1624.0
6 TraesCS3D01G014300 chrUn 94.184 1066 61 1 1208 2273 279872587 279873651 0.000000e+00 1624.0
7 TraesCS3D01G014300 chrUn 82.897 1795 243 41 307 2075 299357971 299359727 0.000000e+00 1555.0
8 TraesCS3D01G014300 chrUn 81.609 1827 276 37 281 2077 309801057 309802853 0.000000e+00 1458.0
9 TraesCS3D01G014300 chrUn 81.609 1827 276 37 281 2077 315209804 315211600 0.000000e+00 1458.0
10 TraesCS3D01G014300 chrUn 81.643 1716 252 38 397 2075 208776568 208774879 0.000000e+00 1365.0
11 TraesCS3D01G014300 chrUn 95.093 856 39 3 2273 3128 208774566 208773714 0.000000e+00 1345.0
12 TraesCS3D01G014300 chrUn 81.238 1519 246 26 580 2077 225561804 225560304 0.000000e+00 1190.0
13 TraesCS3D01G014300 chrUn 81.209 1522 247 26 577 2077 237462563 237464066 0.000000e+00 1190.0
14 TraesCS3D01G014300 chrUn 81.209 1522 247 26 577 2077 257674279 257675782 0.000000e+00 1190.0
15 TraesCS3D01G014300 chrUn 81.209 1522 247 26 577 2077 279684420 279685923 0.000000e+00 1190.0
16 TraesCS3D01G014300 chrUn 81.238 1519 246 26 580 2077 294339444 294337944 0.000000e+00 1190.0
17 TraesCS3D01G014300 chrUn 79.740 1614 260 41 486 2077 32290604 32289036 0.000000e+00 1107.0
18 TraesCS3D01G014300 chrUn 82.502 1263 195 20 774 2022 306116650 306115400 0.000000e+00 1085.0
19 TraesCS3D01G014300 chrUn 81.325 921 131 30 2547 3455 285726568 285725677 0.000000e+00 710.0
20 TraesCS3D01G014300 chrUn 91.886 493 38 2 3120 3610 208768544 208768052 0.000000e+00 688.0
21 TraesCS3D01G014300 chrUn 74.825 1426 300 40 666 2075 34704161 34705543 1.120000e-164 590.0
22 TraesCS3D01G014300 chrUn 84.631 488 50 18 2650 3129 265025232 265024762 2.540000e-126 462.0
23 TraesCS3D01G014300 chrUn 84.631 488 50 18 2650 3129 287939827 287940297 2.540000e-126 462.0
24 TraesCS3D01G014300 chrUn 79.200 750 84 52 2429 3129 260319278 260320004 4.250000e-124 455.0
25 TraesCS3D01G014300 chrUn 76.383 741 125 33 2393 3115 314990638 314989930 1.590000e-93 353.0
26 TraesCS3D01G014300 chrUn 97.436 195 4 1 2273 2466 257140143 257139949 7.470000e-87 331.0
27 TraesCS3D01G014300 chrUn 97.436 195 4 1 2273 2466 279873856 279874050 7.470000e-87 331.0
28 TraesCS3D01G014300 chrUn 76.355 609 108 26 2525 3115 225560098 225559508 9.800000e-76 294.0
29 TraesCS3D01G014300 chrUn 76.355 609 108 26 2525 3115 237464272 237464862 9.800000e-76 294.0
30 TraesCS3D01G014300 chrUn 76.355 609 108 26 2525 3115 257675988 257676578 9.800000e-76 294.0
31 TraesCS3D01G014300 chrUn 76.355 609 108 26 2525 3115 279686129 279686719 9.800000e-76 294.0
32 TraesCS3D01G014300 chrUn 75.493 608 105 29 2525 3115 32288830 32288250 1.290000e-64 257.0
33 TraesCS3D01G014300 chr3A 82.897 1795 243 41 307 2075 11126338 11128094 0.000000e+00 1555.0
34 TraesCS3D01G014300 chr3A 82.897 1795 243 42 307 2075 11134989 11136745 0.000000e+00 1555.0
35 TraesCS3D01G014300 chr3A 82.897 1795 243 42 307 2075 11141861 11143617 0.000000e+00 1555.0
36 TraesCS3D01G014300 chr3A 93.855 716 34 7 2611 3322 10879081 10879790 0.000000e+00 1070.0
37 TraesCS3D01G014300 chr3A 93.868 636 35 2 1638 2273 10877938 10878569 0.000000e+00 955.0
38 TraesCS3D01G014300 chr3A 79.598 1343 224 34 748 2075 10940553 10941860 0.000000e+00 917.0
39 TraesCS3D01G014300 chr3A 96.215 317 12 0 2273 2589 10878774 10879090 1.490000e-143 520.0
40 TraesCS3D01G014300 chr3A 89.370 254 24 3 3355 3605 10879793 10880046 2.090000e-82 316.0
41 TraesCS3D01G014300 chr3A 90.710 183 7 5 369 542 10940359 10940540 6.030000e-58 235.0
42 TraesCS3D01G014300 chr3A 90.909 88 7 1 2071 2157 507291577 507291490 2.280000e-22 117.0
43 TraesCS3D01G014300 chr3A 86.139 101 12 2 2063 2161 167915669 167915569 1.370000e-19 108.0
44 TraesCS3D01G014300 chr3A 94.286 35 0 2 83 115 615161025 615160991 7.000000e-03 52.8
45 TraesCS3D01G014300 chr4B 92.045 88 7 0 2073 2160 22844122 22844035 1.360000e-24 124.0
46 TraesCS3D01G014300 chr7B 92.941 85 5 1 2074 2157 428965929 428965845 4.890000e-24 122.0
47 TraesCS3D01G014300 chr5D 92.045 88 6 1 2072 2158 188826533 188826620 4.890000e-24 122.0
48 TraesCS3D01G014300 chr6A 100.000 30 0 0 81 110 460016008 460016037 5.040000e-04 56.5


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 TraesCS3D01G014300 chr3D 4994667 4998276 3609 False 6667.00 6667 100.0000 1 3610 1 chr3D.!!$F1 3609
1 TraesCS3D01G014300 chr3D 9678100 9679525 1425 True 1557.00 1557 86.3170 551 2016 1 chr3D.!!$R1 1465
2 TraesCS3D01G014300 chr3B 13818994 13822176 3182 True 1784.50 1857 87.9515 281 3610 2 chr3B.!!$R1 3329
3 TraesCS3D01G014300 chrUn 299357971 299359727 1756 False 1555.00 1555 82.8970 307 2075 1 chrUn.!!$F4 1768
4 TraesCS3D01G014300 chrUn 309801057 309802853 1796 False 1458.00 1458 81.6090 281 2077 1 chrUn.!!$F5 1796
5 TraesCS3D01G014300 chrUn 315209804 315211600 1796 False 1458.00 1458 81.6090 281 2077 1 chrUn.!!$F6 1796
6 TraesCS3D01G014300 chrUn 208773714 208776568 2854 True 1355.00 1365 88.3680 397 3128 2 chrUn.!!$R8 2731
7 TraesCS3D01G014300 chrUn 294337944 294339444 1500 True 1190.00 1190 81.2380 580 2077 1 chrUn.!!$R4 1497
8 TraesCS3D01G014300 chrUn 306115400 306116650 1250 True 1085.00 1085 82.5020 774 2022 1 chrUn.!!$R5 1248
9 TraesCS3D01G014300 chrUn 257139949 257141385 1436 True 977.50 1624 96.1675 1235 2466 2 chrUn.!!$R10 1231
10 TraesCS3D01G014300 chrUn 279872587 279874050 1463 False 977.50 1624 95.8100 1208 2466 2 chrUn.!!$F10 1258
11 TraesCS3D01G014300 chrUn 225559508 225561804 2296 True 742.00 1190 78.7965 580 3115 2 chrUn.!!$R9 2535
12 TraesCS3D01G014300 chrUn 237462563 237464862 2299 False 742.00 1190 78.7820 577 3115 2 chrUn.!!$F7 2538
13 TraesCS3D01G014300 chrUn 257674279 257676578 2299 False 742.00 1190 78.7820 577 3115 2 chrUn.!!$F8 2538
14 TraesCS3D01G014300 chrUn 279684420 279686719 2299 False 742.00 1190 78.7820 577 3115 2 chrUn.!!$F9 2538
15 TraesCS3D01G014300 chrUn 285725677 285726568 891 True 710.00 710 81.3250 2547 3455 1 chrUn.!!$R3 908
16 TraesCS3D01G014300 chrUn 32288250 32290604 2354 True 682.00 1107 77.6165 486 3115 2 chrUn.!!$R7 2629
17 TraesCS3D01G014300 chrUn 34704161 34705543 1382 False 590.00 590 74.8250 666 2075 1 chrUn.!!$F1 1409
18 TraesCS3D01G014300 chrUn 260319278 260320004 726 False 455.00 455 79.2000 2429 3129 1 chrUn.!!$F2 700
19 TraesCS3D01G014300 chrUn 314989930 314990638 708 True 353.00 353 76.3830 2393 3115 1 chrUn.!!$R6 722
20 TraesCS3D01G014300 chr3A 11126338 11128094 1756 False 1555.00 1555 82.8970 307 2075 1 chr3A.!!$F1 1768
21 TraesCS3D01G014300 chr3A 11134989 11136745 1756 False 1555.00 1555 82.8970 307 2075 1 chr3A.!!$F2 1768
22 TraesCS3D01G014300 chr3A 11141861 11143617 1756 False 1555.00 1555 82.8970 307 2075 1 chr3A.!!$F3 1768
23 TraesCS3D01G014300 chr3A 10877938 10880046 2108 False 715.25 1070 93.3270 1638 3605 4 chr3A.!!$F4 1967
24 TraesCS3D01G014300 chr3A 10940359 10941860 1501 False 576.00 917 85.1540 369 2075 2 chr3A.!!$F5 1706

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
155 156 0.037590 TGAGGTCCGTTTTGGGGATG 59.962 55.0 0.00 0.0 38.76 3.51 F
167 168 0.184933 TGGGGATGCCCTAATTTCGG 59.815 55.0 24.41 0.0 44.66 4.30 F
168 169 0.185175 GGGGATGCCCTAATTTCGGT 59.815 55.0 16.52 0.0 44.66 4.69 F
1747 1896 0.034670 ACCTGCTCAGATTGAAGGGC 60.035 55.0 0.00 0.0 30.46 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1033 1131 2.185608 GAAGCGCTGAGGAGGGAC 59.814 66.667 12.58 0.0 33.95 4.46 R
1630 1778 2.431782 GCCACATTTGAATGGTATGGCT 59.568 45.455 20.73 0.0 45.39 4.75 R
1852 2001 5.289595 GGGCTTTTCACAAAGTTTTCTAGG 58.710 41.667 0.00 0.0 41.51 3.02 R
3457 3933 1.080501 TCAAGAGAAGCGCGACCAG 60.081 57.895 12.10 0.0 0.00 4.00 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
30 31 8.604640 TGCTCATTGAATTTAAATTTTGCTCA 57.395 26.923 14.45 5.29 0.00 4.26
31 32 9.221933 TGCTCATTGAATTTAAATTTTGCTCAT 57.778 25.926 14.45 0.00 0.00 2.90
32 33 9.698617 GCTCATTGAATTTAAATTTTGCTCATC 57.301 29.630 14.45 0.68 0.00 2.92
67 68 8.961294 AAATGTTCATTGAAATTCAAAGTGGA 57.039 26.923 12.75 0.00 40.12 4.02
68 69 9.563748 AAATGTTCATTGAAATTCAAAGTGGAT 57.436 25.926 12.75 0.56 40.12 3.41
87 88 9.712305 AAGTGGATATATAGAATTTCTCGTTGG 57.288 33.333 1.27 0.00 0.00 3.77
88 89 9.090103 AGTGGATATATAGAATTTCTCGTTGGA 57.910 33.333 1.27 0.00 0.00 3.53
89 90 9.877178 GTGGATATATAGAATTTCTCGTTGGAT 57.123 33.333 1.27 0.00 0.00 3.41
90 91 9.875691 TGGATATATAGAATTTCTCGTTGGATG 57.124 33.333 1.27 0.00 0.00 3.51
91 92 9.319143 GGATATATAGAATTTCTCGTTGGATGG 57.681 37.037 1.27 0.00 0.00 3.51
92 93 8.723942 ATATATAGAATTTCTCGTTGGATGGC 57.276 34.615 1.27 0.00 0.00 4.40
93 94 3.071874 AGAATTTCTCGTTGGATGGCA 57.928 42.857 0.00 0.00 0.00 4.92
94 95 3.420893 AGAATTTCTCGTTGGATGGCAA 58.579 40.909 0.00 0.00 0.00 4.52
95 96 3.826157 AGAATTTCTCGTTGGATGGCAAA 59.174 39.130 0.00 0.00 0.00 3.68
96 97 4.280677 AGAATTTCTCGTTGGATGGCAAAA 59.719 37.500 0.00 0.00 0.00 2.44
97 98 3.641437 TTTCTCGTTGGATGGCAAAAG 57.359 42.857 0.00 0.00 0.00 2.27
98 99 2.270352 TCTCGTTGGATGGCAAAAGT 57.730 45.000 0.00 0.00 0.00 2.66
99 100 1.879380 TCTCGTTGGATGGCAAAAGTG 59.121 47.619 0.00 0.00 0.00 3.16
100 101 0.958091 TCGTTGGATGGCAAAAGTGG 59.042 50.000 0.00 0.00 0.00 4.00
101 102 0.673437 CGTTGGATGGCAAAAGTGGT 59.327 50.000 0.00 0.00 0.00 4.16
102 103 1.335872 CGTTGGATGGCAAAAGTGGTC 60.336 52.381 0.00 0.00 0.00 4.02
103 104 1.000843 GTTGGATGGCAAAAGTGGTCC 59.999 52.381 0.00 0.00 0.00 4.46
104 105 0.893270 TGGATGGCAAAAGTGGTCCG 60.893 55.000 0.00 0.00 0.00 4.79
105 106 1.595093 GGATGGCAAAAGTGGTCCGG 61.595 60.000 0.00 0.00 0.00 5.14
106 107 0.608035 GATGGCAAAAGTGGTCCGGA 60.608 55.000 0.00 0.00 0.00 5.14
107 108 0.893727 ATGGCAAAAGTGGTCCGGAC 60.894 55.000 27.04 27.04 0.00 4.79
108 109 1.527380 GGCAAAAGTGGTCCGGACA 60.527 57.895 34.40 18.59 0.00 4.02
109 110 0.893727 GGCAAAAGTGGTCCGGACAT 60.894 55.000 34.40 17.85 0.00 3.06
110 111 0.958822 GCAAAAGTGGTCCGGACATT 59.041 50.000 34.40 22.37 0.00 2.71
111 112 1.335872 GCAAAAGTGGTCCGGACATTG 60.336 52.381 34.40 26.73 0.00 2.82
112 113 1.953686 CAAAAGTGGTCCGGACATTGT 59.046 47.619 34.40 18.35 0.00 2.71
113 114 1.604604 AAAGTGGTCCGGACATTGTG 58.395 50.000 34.40 0.00 0.00 3.33
114 115 0.250727 AAGTGGTCCGGACATTGTGG 60.251 55.000 34.40 0.00 0.00 4.17
115 116 1.072505 GTGGTCCGGACATTGTGGT 59.927 57.895 34.40 0.00 0.00 4.16
116 117 0.953960 GTGGTCCGGACATTGTGGTC 60.954 60.000 34.40 15.78 37.06 4.02
123 124 2.908817 GACATTGTGGTCCGAACGT 58.091 52.632 0.00 0.00 0.00 3.99
124 125 2.068837 GACATTGTGGTCCGAACGTA 57.931 50.000 0.00 0.00 0.00 3.57
125 126 2.613691 GACATTGTGGTCCGAACGTAT 58.386 47.619 0.00 0.00 0.00 3.06
126 127 3.772932 GACATTGTGGTCCGAACGTATA 58.227 45.455 0.00 0.00 0.00 1.47
127 128 3.777478 ACATTGTGGTCCGAACGTATAG 58.223 45.455 0.00 0.00 0.00 1.31
128 129 3.194116 ACATTGTGGTCCGAACGTATAGT 59.806 43.478 0.00 0.00 0.00 2.12
129 130 2.925578 TGTGGTCCGAACGTATAGTG 57.074 50.000 0.00 0.00 0.00 2.74
130 131 1.473677 TGTGGTCCGAACGTATAGTGG 59.526 52.381 0.00 0.00 0.00 4.00
131 132 1.745087 GTGGTCCGAACGTATAGTGGA 59.255 52.381 0.00 0.00 0.00 4.02
132 133 2.019249 TGGTCCGAACGTATAGTGGAG 58.981 52.381 0.00 0.00 0.00 3.86
133 134 1.336125 GGTCCGAACGTATAGTGGAGG 59.664 57.143 0.00 0.00 0.00 4.30
134 135 2.019984 GTCCGAACGTATAGTGGAGGT 58.980 52.381 0.00 0.00 0.00 3.85
135 136 2.424956 GTCCGAACGTATAGTGGAGGTT 59.575 50.000 0.00 0.00 0.00 3.50
136 137 3.091545 TCCGAACGTATAGTGGAGGTTT 58.908 45.455 0.00 0.00 0.00 3.27
137 138 3.119388 TCCGAACGTATAGTGGAGGTTTG 60.119 47.826 0.00 0.00 0.00 2.93
138 139 3.119388 CCGAACGTATAGTGGAGGTTTGA 60.119 47.826 0.00 0.00 30.80 2.69
139 140 4.103357 CGAACGTATAGTGGAGGTTTGAG 58.897 47.826 0.00 0.00 30.80 3.02
140 141 4.430908 GAACGTATAGTGGAGGTTTGAGG 58.569 47.826 0.00 0.00 0.00 3.86
141 142 3.438183 ACGTATAGTGGAGGTTTGAGGT 58.562 45.455 0.00 0.00 0.00 3.85
142 143 3.446516 ACGTATAGTGGAGGTTTGAGGTC 59.553 47.826 0.00 0.00 0.00 3.85
143 144 3.181478 CGTATAGTGGAGGTTTGAGGTCC 60.181 52.174 0.00 0.00 0.00 4.46
144 145 1.263356 TAGTGGAGGTTTGAGGTCCG 58.737 55.000 0.00 0.00 32.51 4.79
145 146 0.763223 AGTGGAGGTTTGAGGTCCGT 60.763 55.000 0.00 0.00 32.51 4.69
146 147 0.108019 GTGGAGGTTTGAGGTCCGTT 59.892 55.000 0.00 0.00 32.51 4.44
147 148 0.841289 TGGAGGTTTGAGGTCCGTTT 59.159 50.000 0.00 0.00 32.51 3.60
148 149 1.213430 TGGAGGTTTGAGGTCCGTTTT 59.787 47.619 0.00 0.00 32.51 2.43
149 150 1.607148 GGAGGTTTGAGGTCCGTTTTG 59.393 52.381 0.00 0.00 0.00 2.44
150 151 1.607148 GAGGTTTGAGGTCCGTTTTGG 59.393 52.381 0.00 0.00 40.09 3.28
151 152 0.671796 GGTTTGAGGTCCGTTTTGGG 59.328 55.000 0.00 0.00 38.76 4.12
152 153 0.671796 GTTTGAGGTCCGTTTTGGGG 59.328 55.000 0.00 0.00 38.76 4.96
153 154 0.551879 TTTGAGGTCCGTTTTGGGGA 59.448 50.000 0.00 0.00 38.76 4.81
154 155 0.774908 TTGAGGTCCGTTTTGGGGAT 59.225 50.000 0.00 0.00 38.76 3.85
155 156 0.037590 TGAGGTCCGTTTTGGGGATG 59.962 55.000 0.00 0.00 38.76 3.51
156 157 1.304134 AGGTCCGTTTTGGGGATGC 60.304 57.895 0.00 0.00 38.76 3.91
157 158 2.348104 GGTCCGTTTTGGGGATGCC 61.348 63.158 0.00 0.00 38.76 4.40
158 159 2.036572 TCCGTTTTGGGGATGCCC 59.963 61.111 16.99 16.99 44.51 5.36
159 160 2.037208 CCGTTTTGGGGATGCCCT 59.963 61.111 24.41 0.00 44.66 5.19
160 161 1.208844 TCCGTTTTGGGGATGCCCTA 61.209 55.000 24.41 13.87 44.66 3.53
161 162 0.323908 CCGTTTTGGGGATGCCCTAA 60.324 55.000 24.41 19.59 44.66 2.69
162 163 1.687996 CCGTTTTGGGGATGCCCTAAT 60.688 52.381 24.41 0.00 43.59 1.73
163 164 2.107366 CGTTTTGGGGATGCCCTAATT 58.893 47.619 24.41 0.00 43.59 1.40
164 165 2.499693 CGTTTTGGGGATGCCCTAATTT 59.500 45.455 24.41 0.00 43.59 1.82
165 166 3.430236 CGTTTTGGGGATGCCCTAATTTC 60.430 47.826 24.41 13.58 43.59 2.17
166 167 2.065899 TTGGGGATGCCCTAATTTCG 57.934 50.000 24.41 0.00 44.66 3.46
167 168 0.184933 TGGGGATGCCCTAATTTCGG 59.815 55.000 24.41 0.00 44.66 4.30
168 169 0.185175 GGGGATGCCCTAATTTCGGT 59.815 55.000 16.52 0.00 44.66 4.69
169 170 1.411074 GGGGATGCCCTAATTTCGGTT 60.411 52.381 16.52 0.00 44.66 4.44
170 171 1.954382 GGGATGCCCTAATTTCGGTTC 59.046 52.381 0.00 0.00 41.34 3.62
171 172 1.954382 GGATGCCCTAATTTCGGTTCC 59.046 52.381 0.00 0.00 0.00 3.62
172 173 2.422945 GGATGCCCTAATTTCGGTTCCT 60.423 50.000 0.00 0.00 0.00 3.36
173 174 2.891191 TGCCCTAATTTCGGTTCCTT 57.109 45.000 0.00 0.00 0.00 3.36
174 175 3.163616 TGCCCTAATTTCGGTTCCTTT 57.836 42.857 0.00 0.00 0.00 3.11
175 176 2.823154 TGCCCTAATTTCGGTTCCTTTG 59.177 45.455 0.00 0.00 0.00 2.77
176 177 2.165641 GCCCTAATTTCGGTTCCTTTGG 59.834 50.000 0.00 0.00 0.00 3.28
177 178 2.165641 CCCTAATTTCGGTTCCTTTGGC 59.834 50.000 0.00 0.00 0.00 4.52
178 179 2.823154 CCTAATTTCGGTTCCTTTGGCA 59.177 45.455 0.00 0.00 0.00 4.92
179 180 3.119495 CCTAATTTCGGTTCCTTTGGCAG 60.119 47.826 0.00 0.00 0.00 4.85
180 181 0.603065 ATTTCGGTTCCTTTGGCAGC 59.397 50.000 0.00 0.00 0.00 5.25
181 182 0.467290 TTTCGGTTCCTTTGGCAGCT 60.467 50.000 0.00 0.00 0.00 4.24
182 183 1.172180 TTCGGTTCCTTTGGCAGCTG 61.172 55.000 10.11 10.11 0.00 4.24
183 184 2.653115 GGTTCCTTTGGCAGCTGC 59.347 61.111 30.88 30.88 41.14 5.25
184 185 2.202395 GGTTCCTTTGGCAGCTGCA 61.202 57.895 37.63 22.06 44.36 4.41
185 186 1.538687 GGTTCCTTTGGCAGCTGCAT 61.539 55.000 37.63 0.00 44.36 3.96
186 187 0.319405 GTTCCTTTGGCAGCTGCATT 59.681 50.000 37.63 0.00 44.36 3.56
187 188 0.604578 TTCCTTTGGCAGCTGCATTC 59.395 50.000 37.63 22.24 44.36 2.67
188 189 0.540133 TCCTTTGGCAGCTGCATTCA 60.540 50.000 37.63 24.58 44.36 2.57
189 190 0.319083 CCTTTGGCAGCTGCATTCAA 59.681 50.000 37.63 28.42 44.36 2.69
190 191 1.066430 CCTTTGGCAGCTGCATTCAAT 60.066 47.619 37.63 0.00 44.36 2.57
191 192 2.268298 CTTTGGCAGCTGCATTCAATC 58.732 47.619 37.63 20.06 44.36 2.67
192 193 0.533491 TTGGCAGCTGCATTCAATCC 59.467 50.000 37.63 19.33 44.36 3.01
193 194 1.065273 GGCAGCTGCATTCAATCCG 59.935 57.895 37.63 0.00 44.36 4.18
194 195 1.378882 GGCAGCTGCATTCAATCCGA 61.379 55.000 37.63 0.00 44.36 4.55
195 196 0.666913 GCAGCTGCATTCAATCCGAT 59.333 50.000 33.36 0.00 41.59 4.18
196 197 1.875514 GCAGCTGCATTCAATCCGATA 59.124 47.619 33.36 0.00 41.59 2.92
197 198 2.486982 GCAGCTGCATTCAATCCGATAT 59.513 45.455 33.36 0.00 41.59 1.63
198 199 3.686241 GCAGCTGCATTCAATCCGATATA 59.314 43.478 33.36 0.00 41.59 0.86
199 200 4.201792 GCAGCTGCATTCAATCCGATATAG 60.202 45.833 33.36 0.00 41.59 1.31
200 201 4.934001 CAGCTGCATTCAATCCGATATAGT 59.066 41.667 0.00 0.00 0.00 2.12
201 202 6.101997 CAGCTGCATTCAATCCGATATAGTA 58.898 40.000 0.00 0.00 0.00 1.82
202 203 6.035435 CAGCTGCATTCAATCCGATATAGTAC 59.965 42.308 0.00 0.00 0.00 2.73
203 204 5.869344 GCTGCATTCAATCCGATATAGTACA 59.131 40.000 0.00 0.00 0.00 2.90
204 205 6.368791 GCTGCATTCAATCCGATATAGTACAA 59.631 38.462 0.00 0.00 0.00 2.41
205 206 7.622256 GCTGCATTCAATCCGATATAGTACAAC 60.622 40.741 0.00 0.00 0.00 3.32
206 207 7.441836 TGCATTCAATCCGATATAGTACAACT 58.558 34.615 0.00 0.00 0.00 3.16
207 208 8.581578 TGCATTCAATCCGATATAGTACAACTA 58.418 33.333 0.00 0.00 34.82 2.24
208 209 9.587772 GCATTCAATCCGATATAGTACAACTAT 57.412 33.333 5.04 5.04 43.36 2.12
223 224 8.478775 AGTACAACTATACATATTGCCTGAGA 57.521 34.615 0.00 0.00 0.00 3.27
224 225 8.924303 AGTACAACTATACATATTGCCTGAGAA 58.076 33.333 0.00 0.00 0.00 2.87
225 226 9.542462 GTACAACTATACATATTGCCTGAGAAA 57.458 33.333 0.00 0.00 0.00 2.52
227 228 9.060347 ACAACTATACATATTGCCTGAGAAATG 57.940 33.333 0.00 0.00 0.00 2.32
228 229 9.060347 CAACTATACATATTGCCTGAGAAATGT 57.940 33.333 0.00 0.00 0.00 2.71
229 230 9.632638 AACTATACATATTGCCTGAGAAATGTT 57.367 29.630 0.00 0.00 0.00 2.71
233 234 7.559590 ACATATTGCCTGAGAAATGTTAGTC 57.440 36.000 0.00 0.00 0.00 2.59
234 235 7.112122 ACATATTGCCTGAGAAATGTTAGTCA 58.888 34.615 0.00 0.00 0.00 3.41
235 236 7.611467 ACATATTGCCTGAGAAATGTTAGTCAA 59.389 33.333 0.00 0.00 0.00 3.18
236 237 5.947228 TTGCCTGAGAAATGTTAGTCAAG 57.053 39.130 0.00 0.00 0.00 3.02
237 238 4.326826 TGCCTGAGAAATGTTAGTCAAGG 58.673 43.478 0.00 0.00 0.00 3.61
238 239 4.041567 TGCCTGAGAAATGTTAGTCAAGGA 59.958 41.667 0.00 0.00 0.00 3.36
239 240 5.003804 GCCTGAGAAATGTTAGTCAAGGAA 58.996 41.667 0.00 0.00 0.00 3.36
240 241 5.473504 GCCTGAGAAATGTTAGTCAAGGAAA 59.526 40.000 0.00 0.00 0.00 3.13
241 242 6.568653 GCCTGAGAAATGTTAGTCAAGGAAAC 60.569 42.308 0.00 0.00 0.00 2.78
243 244 7.878127 CCTGAGAAATGTTAGTCAAGGAAACTA 59.122 37.037 0.00 0.00 42.68 2.24
244 245 8.833231 TGAGAAATGTTAGTCAAGGAAACTAG 57.167 34.615 0.00 0.00 42.68 2.57
245 246 8.647796 TGAGAAATGTTAGTCAAGGAAACTAGA 58.352 33.333 0.00 0.00 42.68 2.43
246 247 9.490379 GAGAAATGTTAGTCAAGGAAACTAGAA 57.510 33.333 0.00 0.00 42.68 2.10
247 248 9.847224 AGAAATGTTAGTCAAGGAAACTAGAAA 57.153 29.630 0.00 0.00 42.68 2.52
250 251 9.793259 AATGTTAGTCAAGGAAACTAGAAATCA 57.207 29.630 0.00 0.00 42.68 2.57
251 252 9.965902 ATGTTAGTCAAGGAAACTAGAAATCAT 57.034 29.630 0.00 0.00 42.68 2.45
252 253 9.436957 TGTTAGTCAAGGAAACTAGAAATCATC 57.563 33.333 0.00 0.00 42.68 2.92
253 254 9.436957 GTTAGTCAAGGAAACTAGAAATCATCA 57.563 33.333 0.00 0.00 42.68 3.07
255 256 8.729805 AGTCAAGGAAACTAGAAATCATCATC 57.270 34.615 0.00 0.00 42.68 2.92
256 257 8.324306 AGTCAAGGAAACTAGAAATCATCATCA 58.676 33.333 0.00 0.00 42.68 3.07
257 258 9.118300 GTCAAGGAAACTAGAAATCATCATCAT 57.882 33.333 0.00 0.00 42.68 2.45
258 259 9.334947 TCAAGGAAACTAGAAATCATCATCATC 57.665 33.333 0.00 0.00 42.68 2.92
259 260 9.117183 CAAGGAAACTAGAAATCATCATCATCA 57.883 33.333 0.00 0.00 42.68 3.07
260 261 9.863650 AAGGAAACTAGAAATCATCATCATCAT 57.136 29.630 0.00 0.00 42.68 2.45
261 262 9.504708 AGGAAACTAGAAATCATCATCATCATC 57.495 33.333 0.00 0.00 40.61 2.92
262 263 9.281371 GGAAACTAGAAATCATCATCATCATCA 57.719 33.333 0.00 0.00 0.00 3.07
264 265 9.848710 AAACTAGAAATCATCATCATCATCAGT 57.151 29.630 0.00 0.00 0.00 3.41
265 266 8.834749 ACTAGAAATCATCATCATCATCAGTG 57.165 34.615 0.00 0.00 0.00 3.66
266 267 7.878644 ACTAGAAATCATCATCATCATCAGTGG 59.121 37.037 0.00 0.00 0.00 4.00
267 268 6.004574 AGAAATCATCATCATCATCAGTGGG 58.995 40.000 0.00 0.00 0.00 4.61
268 269 3.136009 TCATCATCATCATCAGTGGGC 57.864 47.619 0.00 0.00 0.00 5.36
269 270 2.709397 TCATCATCATCATCAGTGGGCT 59.291 45.455 0.00 0.00 0.00 5.19
270 271 3.137728 TCATCATCATCATCAGTGGGCTT 59.862 43.478 0.00 0.00 0.00 4.35
271 272 3.657398 TCATCATCATCAGTGGGCTTT 57.343 42.857 0.00 0.00 0.00 3.51
272 273 3.548770 TCATCATCATCAGTGGGCTTTC 58.451 45.455 0.00 0.00 0.00 2.62
273 274 3.201487 TCATCATCATCAGTGGGCTTTCT 59.799 43.478 0.00 0.00 0.00 2.52
274 275 3.726557 TCATCATCAGTGGGCTTTCTT 57.273 42.857 0.00 0.00 0.00 2.52
275 276 4.038271 TCATCATCAGTGGGCTTTCTTT 57.962 40.909 0.00 0.00 0.00 2.52
276 277 3.760151 TCATCATCAGTGGGCTTTCTTTG 59.240 43.478 0.00 0.00 0.00 2.77
277 278 2.517959 TCATCAGTGGGCTTTCTTTGG 58.482 47.619 0.00 0.00 0.00 3.28
278 279 1.067354 CATCAGTGGGCTTTCTTTGGC 60.067 52.381 0.00 0.00 0.00 4.52
279 280 1.172180 TCAGTGGGCTTTCTTTGGCG 61.172 55.000 0.00 0.00 0.00 5.69
308 309 4.504340 GCCCAACACCACTTTACTCTTCTA 60.504 45.833 0.00 0.00 0.00 2.10
348 365 1.343506 CAACGCCAACTAGGTACGAC 58.656 55.000 9.19 0.00 40.61 4.34
394 411 0.392193 GACCACTGCACTGCTGCTAT 60.392 55.000 7.76 0.00 44.57 2.97
542 582 4.473520 CGAGTGAGGCGGGCCAAT 62.474 66.667 12.97 0.00 38.92 3.16
822 920 2.471818 CTCGAAGACGACGATCTCCTA 58.528 52.381 0.00 0.00 43.81 2.94
868 966 1.344191 GCAGCCCTCCTCTCTTCCAT 61.344 60.000 0.00 0.00 0.00 3.41
873 971 1.519246 CTCCTCTCTTCCATGCGCA 59.481 57.895 14.96 14.96 0.00 6.09
899 997 3.869272 CTGCAAGCGGTGGCGATC 61.869 66.667 9.83 0.00 46.35 3.69
987 1085 1.808799 CTTCGAGCACAGCGCAGAT 60.809 57.895 11.47 0.00 46.13 2.90
1017 1115 2.178912 TCATGTTCAAACCCGTCCTC 57.821 50.000 0.00 0.00 0.00 3.71
1033 1131 2.675423 TCGACCCTCCCGACTGTG 60.675 66.667 0.00 0.00 0.00 3.66
1078 1176 2.095415 CGACTCCACGACATTGACAGTA 60.095 50.000 0.00 0.00 35.09 2.74
1088 1186 0.253044 ATTGACAGTAGCCGTGGCAT 59.747 50.000 14.29 0.90 44.88 4.40
1135 1233 1.826024 GGTCGCCTCCTCATCATGT 59.174 57.895 0.00 0.00 0.00 3.21
1142 1240 1.068281 CCTCCTCATCATGTCCTCACG 59.932 57.143 0.00 0.00 0.00 4.35
1630 1778 6.210584 TGGTCTCGCCATATTGTCTCATAATA 59.789 38.462 0.00 0.00 43.61 0.98
1746 1895 3.274288 GTTACCTGCTCAGATTGAAGGG 58.726 50.000 0.00 0.00 30.46 3.95
1747 1896 0.034670 ACCTGCTCAGATTGAAGGGC 60.035 55.000 0.00 0.00 30.46 5.19
1871 2020 6.692486 TGCAACCTAGAAAACTTTGTGAAAA 58.308 32.000 0.00 0.00 0.00 2.29
2133 2298 5.077424 GCTATGTTAGGTTGAAAAACGTCG 58.923 41.667 0.00 0.00 39.71 5.12
2147 2312 7.267128 TGAAAAACGTCGTATATTATGGGACT 58.733 34.615 0.00 0.00 0.00 3.85
2245 2411 9.829507 TCAAATGTCAAATGGTTAACTCATTTT 57.170 25.926 22.10 12.01 41.28 1.82
2265 2431 1.619654 CCATGTTTGGAACCTCAGCA 58.380 50.000 0.00 0.00 46.92 4.41
2589 3036 7.661437 ACTCACTGTTGTCTTTTCATGCTTATA 59.339 33.333 0.00 0.00 0.00 0.98
2609 3056 3.610040 ACTTCTACGCACATCCATTGA 57.390 42.857 0.00 0.00 0.00 2.57
2711 3160 3.782656 AACGGTTCACCAGGTAAGAAT 57.217 42.857 0.00 0.00 35.14 2.40
2980 3448 9.174166 GGCTTAGTTGTTCCAGAATCTAATAAA 57.826 33.333 0.00 0.00 0.00 1.40
3070 3538 4.815846 ACCCAACAAATTCATGTGAAAAGC 59.184 37.500 0.00 0.00 37.61 3.51
3205 3676 6.656270 TGAGCTGATCTTGAATTTGTACACAT 59.344 34.615 0.00 0.00 0.00 3.21
3206 3677 7.081526 AGCTGATCTTGAATTTGTACACATC 57.918 36.000 0.00 0.00 0.00 3.06
3220 3693 9.719355 ATTTGTACACATCTTGTTCATACACTA 57.281 29.630 0.00 0.00 39.91 2.74
3307 3780 9.481340 AAATTTATTTTCTCCAGCTGAAGAAAC 57.519 29.630 25.72 0.00 31.11 2.78
3308 3781 7.581213 TTTATTTTCTCCAGCTGAAGAAACA 57.419 32.000 25.72 17.26 31.11 2.83
3311 3784 4.955811 TTCTCCAGCTGAAGAAACAGTA 57.044 40.909 13.62 0.00 39.73 2.74
3322 3795 3.565905 AGAAACAGTAGCTGCAATTGC 57.434 42.857 23.69 23.69 42.50 3.56
3324 3797 3.571401 AGAAACAGTAGCTGCAATTGCTT 59.429 39.130 29.37 17.57 41.46 3.91
3378 3852 4.019231 TGTGGTGGTGGCAGTGTTATAATA 60.019 41.667 0.00 0.00 0.00 0.98
3457 3933 5.009110 GCTTTTGAATAGCTAATCCAGGGAC 59.991 44.000 6.35 0.00 35.74 4.46
3492 3969 1.352083 TGACCCAGGAGAGTTTCAGG 58.648 55.000 0.00 0.00 0.00 3.86
3547 4024 0.318762 ACGGTGAGAGTTTCTGAGCC 59.681 55.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.221933 TGAGCAAAATTTAAATTCAATGAGCAT 57.778 25.926 13.68 0.00 0.00 3.79
5 6 8.604640 TGAGCAAAATTTAAATTCAATGAGCA 57.395 26.923 13.68 11.08 0.00 4.26
6 7 9.698617 GATGAGCAAAATTTAAATTCAATGAGC 57.301 29.630 13.68 11.01 0.00 4.26
41 42 9.393512 TCCACTTTGAATTTCAATGAACATTTT 57.606 25.926 24.02 4.79 36.11 1.82
42 43 8.961294 TCCACTTTGAATTTCAATGAACATTT 57.039 26.923 24.02 5.34 36.11 2.32
61 62 9.712305 CCAACGAGAAATTCTATATATCCACTT 57.288 33.333 0.00 0.00 0.00 3.16
62 63 9.090103 TCCAACGAGAAATTCTATATATCCACT 57.910 33.333 0.00 0.00 0.00 4.00
63 64 9.877178 ATCCAACGAGAAATTCTATATATCCAC 57.123 33.333 0.00 0.00 0.00 4.02
64 65 9.875691 CATCCAACGAGAAATTCTATATATCCA 57.124 33.333 0.00 0.00 0.00 3.41
65 66 9.319143 CCATCCAACGAGAAATTCTATATATCC 57.681 37.037 0.00 0.00 0.00 2.59
66 67 8.821894 GCCATCCAACGAGAAATTCTATATATC 58.178 37.037 0.00 0.00 0.00 1.63
67 68 8.321353 TGCCATCCAACGAGAAATTCTATATAT 58.679 33.333 0.00 0.00 0.00 0.86
68 69 7.676004 TGCCATCCAACGAGAAATTCTATATA 58.324 34.615 0.00 0.00 0.00 0.86
69 70 6.533730 TGCCATCCAACGAGAAATTCTATAT 58.466 36.000 0.00 0.00 0.00 0.86
70 71 5.924356 TGCCATCCAACGAGAAATTCTATA 58.076 37.500 0.00 0.00 0.00 1.31
71 72 4.780815 TGCCATCCAACGAGAAATTCTAT 58.219 39.130 0.00 0.00 0.00 1.98
72 73 4.214986 TGCCATCCAACGAGAAATTCTA 57.785 40.909 0.00 0.00 0.00 2.10
73 74 3.071874 TGCCATCCAACGAGAAATTCT 57.928 42.857 0.00 0.00 0.00 2.40
74 75 3.848272 TTGCCATCCAACGAGAAATTC 57.152 42.857 0.00 0.00 0.00 2.17
75 76 4.039124 ACTTTTGCCATCCAACGAGAAATT 59.961 37.500 0.00 0.00 31.97 1.82
76 77 3.573967 ACTTTTGCCATCCAACGAGAAAT 59.426 39.130 0.00 0.00 31.97 2.17
77 78 2.955660 ACTTTTGCCATCCAACGAGAAA 59.044 40.909 0.00 0.00 31.97 2.52
78 79 2.293122 CACTTTTGCCATCCAACGAGAA 59.707 45.455 0.00 0.00 31.97 2.87
79 80 1.879380 CACTTTTGCCATCCAACGAGA 59.121 47.619 0.00 0.00 31.97 4.04
80 81 1.068333 CCACTTTTGCCATCCAACGAG 60.068 52.381 0.00 0.00 31.97 4.18
81 82 0.958091 CCACTTTTGCCATCCAACGA 59.042 50.000 0.00 0.00 31.97 3.85
82 83 0.673437 ACCACTTTTGCCATCCAACG 59.327 50.000 0.00 0.00 31.97 4.10
83 84 1.000843 GGACCACTTTTGCCATCCAAC 59.999 52.381 0.00 0.00 31.97 3.77
84 85 1.337118 GGACCACTTTTGCCATCCAA 58.663 50.000 0.00 0.00 0.00 3.53
85 86 0.893270 CGGACCACTTTTGCCATCCA 60.893 55.000 0.00 0.00 0.00 3.41
86 87 1.595093 CCGGACCACTTTTGCCATCC 61.595 60.000 0.00 0.00 0.00 3.51
87 88 0.608035 TCCGGACCACTTTTGCCATC 60.608 55.000 0.00 0.00 0.00 3.51
88 89 0.893727 GTCCGGACCACTTTTGCCAT 60.894 55.000 24.75 0.00 0.00 4.40
89 90 1.527380 GTCCGGACCACTTTTGCCA 60.527 57.895 24.75 0.00 0.00 4.92
90 91 0.893727 ATGTCCGGACCACTTTTGCC 60.894 55.000 31.19 3.08 0.00 4.52
91 92 0.958822 AATGTCCGGACCACTTTTGC 59.041 50.000 31.19 3.89 0.00 3.68
92 93 1.953686 ACAATGTCCGGACCACTTTTG 59.046 47.619 31.19 24.54 0.00 2.44
93 94 1.953686 CACAATGTCCGGACCACTTTT 59.046 47.619 31.19 13.92 0.00 2.27
94 95 1.604604 CACAATGTCCGGACCACTTT 58.395 50.000 31.19 16.31 0.00 2.66
95 96 0.250727 CCACAATGTCCGGACCACTT 60.251 55.000 31.19 18.59 0.00 3.16
96 97 1.374947 CCACAATGTCCGGACCACT 59.625 57.895 31.19 13.59 0.00 4.00
97 98 0.953960 GACCACAATGTCCGGACCAC 60.954 60.000 31.19 8.63 0.00 4.16
98 99 1.373435 GACCACAATGTCCGGACCA 59.627 57.895 31.19 19.32 0.00 4.02
99 100 1.376812 GGACCACAATGTCCGGACC 60.377 63.158 31.19 14.15 44.98 4.46
100 101 4.296265 GGACCACAATGTCCGGAC 57.704 61.111 28.17 28.17 44.98 4.79
105 106 2.068837 TACGTTCGGACCACAATGTC 57.931 50.000 0.00 0.00 34.42 3.06
106 107 2.754946 ATACGTTCGGACCACAATGT 57.245 45.000 0.00 0.00 0.00 2.71
107 108 3.550275 CACTATACGTTCGGACCACAATG 59.450 47.826 0.00 0.00 0.00 2.82
108 109 3.429822 CCACTATACGTTCGGACCACAAT 60.430 47.826 0.00 0.00 0.00 2.71
109 110 2.094597 CCACTATACGTTCGGACCACAA 60.095 50.000 0.00 0.00 0.00 3.33
110 111 1.473677 CCACTATACGTTCGGACCACA 59.526 52.381 0.00 0.00 0.00 4.17
111 112 1.745087 TCCACTATACGTTCGGACCAC 59.255 52.381 0.00 0.00 0.00 4.16
112 113 2.019249 CTCCACTATACGTTCGGACCA 58.981 52.381 0.00 0.00 0.00 4.02
113 114 1.336125 CCTCCACTATACGTTCGGACC 59.664 57.143 0.00 0.00 0.00 4.46
114 115 2.019984 ACCTCCACTATACGTTCGGAC 58.980 52.381 0.00 0.00 0.00 4.79
115 116 2.425143 ACCTCCACTATACGTTCGGA 57.575 50.000 0.00 0.00 0.00 4.55
116 117 3.119388 TCAAACCTCCACTATACGTTCGG 60.119 47.826 0.00 0.00 0.00 4.30
117 118 4.100707 TCAAACCTCCACTATACGTTCG 57.899 45.455 0.00 0.00 0.00 3.95
118 119 4.081807 ACCTCAAACCTCCACTATACGTTC 60.082 45.833 0.00 0.00 0.00 3.95
119 120 3.836562 ACCTCAAACCTCCACTATACGTT 59.163 43.478 0.00 0.00 0.00 3.99
120 121 3.438183 ACCTCAAACCTCCACTATACGT 58.562 45.455 0.00 0.00 0.00 3.57
121 122 3.181478 GGACCTCAAACCTCCACTATACG 60.181 52.174 0.00 0.00 0.00 3.06
122 123 3.181478 CGGACCTCAAACCTCCACTATAC 60.181 52.174 0.00 0.00 0.00 1.47
123 124 3.028850 CGGACCTCAAACCTCCACTATA 58.971 50.000 0.00 0.00 0.00 1.31
124 125 1.831736 CGGACCTCAAACCTCCACTAT 59.168 52.381 0.00 0.00 0.00 2.12
125 126 1.263356 CGGACCTCAAACCTCCACTA 58.737 55.000 0.00 0.00 0.00 2.74
126 127 0.763223 ACGGACCTCAAACCTCCACT 60.763 55.000 0.00 0.00 0.00 4.00
127 128 0.108019 AACGGACCTCAAACCTCCAC 59.892 55.000 0.00 0.00 0.00 4.02
128 129 0.841289 AAACGGACCTCAAACCTCCA 59.159 50.000 0.00 0.00 0.00 3.86
129 130 1.607148 CAAAACGGACCTCAAACCTCC 59.393 52.381 0.00 0.00 0.00 4.30
130 131 1.607148 CCAAAACGGACCTCAAACCTC 59.393 52.381 0.00 0.00 36.56 3.85
131 132 1.687563 CCAAAACGGACCTCAAACCT 58.312 50.000 0.00 0.00 36.56 3.50
132 133 0.671796 CCCAAAACGGACCTCAAACC 59.328 55.000 0.00 0.00 36.56 3.27
133 134 0.671796 CCCCAAAACGGACCTCAAAC 59.328 55.000 0.00 0.00 36.56 2.93
134 135 0.551879 TCCCCAAAACGGACCTCAAA 59.448 50.000 0.00 0.00 36.56 2.69
135 136 0.774908 ATCCCCAAAACGGACCTCAA 59.225 50.000 0.00 0.00 36.56 3.02
136 137 0.037590 CATCCCCAAAACGGACCTCA 59.962 55.000 0.00 0.00 36.56 3.86
137 138 1.313091 GCATCCCCAAAACGGACCTC 61.313 60.000 0.00 0.00 36.56 3.85
138 139 1.304134 GCATCCCCAAAACGGACCT 60.304 57.895 0.00 0.00 36.56 3.85
139 140 2.348104 GGCATCCCCAAAACGGACC 61.348 63.158 0.00 0.00 36.56 4.46
140 141 3.284336 GGCATCCCCAAAACGGAC 58.716 61.111 0.00 0.00 36.56 4.79
150 151 1.954382 GAACCGAAATTAGGGCATCCC 59.046 52.381 0.00 0.00 45.90 3.85
151 152 1.954382 GGAACCGAAATTAGGGCATCC 59.046 52.381 0.00 5.08 0.00 3.51
152 153 2.932261 AGGAACCGAAATTAGGGCATC 58.068 47.619 0.00 0.39 0.00 3.91
153 154 3.382083 AAGGAACCGAAATTAGGGCAT 57.618 42.857 0.00 0.00 0.00 4.40
154 155 2.823154 CAAAGGAACCGAAATTAGGGCA 59.177 45.455 0.00 0.00 0.00 5.36
155 156 2.165641 CCAAAGGAACCGAAATTAGGGC 59.834 50.000 0.00 0.00 0.00 5.19
156 157 2.165641 GCCAAAGGAACCGAAATTAGGG 59.834 50.000 0.00 0.00 0.00 3.53
157 158 2.823154 TGCCAAAGGAACCGAAATTAGG 59.177 45.455 0.00 0.00 0.00 2.69
158 159 3.673323 GCTGCCAAAGGAACCGAAATTAG 60.673 47.826 0.00 0.00 0.00 1.73
159 160 2.230266 GCTGCCAAAGGAACCGAAATTA 59.770 45.455 0.00 0.00 0.00 1.40
160 161 1.000843 GCTGCCAAAGGAACCGAAATT 59.999 47.619 0.00 0.00 0.00 1.82
161 162 0.603065 GCTGCCAAAGGAACCGAAAT 59.397 50.000 0.00 0.00 0.00 2.17
162 163 0.467290 AGCTGCCAAAGGAACCGAAA 60.467 50.000 0.00 0.00 0.00 3.46
163 164 1.150536 AGCTGCCAAAGGAACCGAA 59.849 52.632 0.00 0.00 0.00 4.30
164 165 1.600636 CAGCTGCCAAAGGAACCGA 60.601 57.895 0.00 0.00 0.00 4.69
165 166 2.956987 CAGCTGCCAAAGGAACCG 59.043 61.111 0.00 0.00 0.00 4.44
166 167 1.538687 ATGCAGCTGCCAAAGGAACC 61.539 55.000 34.64 4.94 41.18 3.62
167 168 0.319405 AATGCAGCTGCCAAAGGAAC 59.681 50.000 34.64 5.72 41.18 3.62
168 169 0.604578 GAATGCAGCTGCCAAAGGAA 59.395 50.000 34.64 15.72 41.18 3.36
169 170 0.540133 TGAATGCAGCTGCCAAAGGA 60.540 50.000 34.64 16.51 41.18 3.36
170 171 0.319083 TTGAATGCAGCTGCCAAAGG 59.681 50.000 34.64 0.00 41.18 3.11
171 172 2.268298 GATTGAATGCAGCTGCCAAAG 58.732 47.619 34.64 0.00 41.18 2.77
172 173 1.066716 GGATTGAATGCAGCTGCCAAA 60.067 47.619 34.64 22.46 41.18 3.28
173 174 0.533491 GGATTGAATGCAGCTGCCAA 59.467 50.000 34.64 29.04 41.18 4.52
174 175 1.659622 CGGATTGAATGCAGCTGCCA 61.660 55.000 34.64 22.81 41.18 4.92
175 176 1.065273 CGGATTGAATGCAGCTGCC 59.935 57.895 34.64 20.39 41.18 4.85
176 177 0.666913 ATCGGATTGAATGCAGCTGC 59.333 50.000 31.89 31.89 42.50 5.25
177 178 4.934001 ACTATATCGGATTGAATGCAGCTG 59.066 41.667 10.11 10.11 0.00 4.24
178 179 5.157940 ACTATATCGGATTGAATGCAGCT 57.842 39.130 0.00 0.00 0.00 4.24
179 180 5.869344 TGTACTATATCGGATTGAATGCAGC 59.131 40.000 0.00 0.00 0.00 5.25
180 181 7.600375 AGTTGTACTATATCGGATTGAATGCAG 59.400 37.037 0.00 0.00 0.00 4.41
181 182 7.441836 AGTTGTACTATATCGGATTGAATGCA 58.558 34.615 0.00 0.00 0.00 3.96
182 183 7.891183 AGTTGTACTATATCGGATTGAATGC 57.109 36.000 0.00 0.00 0.00 3.56
197 198 9.582648 TCTCAGGCAATATGTATAGTTGTACTA 57.417 33.333 0.00 0.00 34.82 1.82
198 199 8.478775 TCTCAGGCAATATGTATAGTTGTACT 57.521 34.615 0.00 0.00 0.00 2.73
199 200 9.542462 TTTCTCAGGCAATATGTATAGTTGTAC 57.458 33.333 0.00 0.00 0.00 2.90
201 202 9.060347 CATTTCTCAGGCAATATGTATAGTTGT 57.940 33.333 0.00 0.00 0.00 3.32
202 203 9.060347 ACATTTCTCAGGCAATATGTATAGTTG 57.940 33.333 0.00 0.00 0.00 3.16
203 204 9.632638 AACATTTCTCAGGCAATATGTATAGTT 57.367 29.630 0.00 0.00 0.00 2.24
207 208 9.277783 GACTAACATTTCTCAGGCAATATGTAT 57.722 33.333 0.00 0.00 0.00 2.29
208 209 8.264347 TGACTAACATTTCTCAGGCAATATGTA 58.736 33.333 0.00 0.00 0.00 2.29
209 210 7.112122 TGACTAACATTTCTCAGGCAATATGT 58.888 34.615 0.00 0.00 0.00 2.29
210 211 7.558161 TGACTAACATTTCTCAGGCAATATG 57.442 36.000 0.00 0.00 0.00 1.78
211 212 7.284034 CCTTGACTAACATTTCTCAGGCAATAT 59.716 37.037 0.00 0.00 35.55 1.28
212 213 6.599244 CCTTGACTAACATTTCTCAGGCAATA 59.401 38.462 0.00 0.00 35.55 1.90
213 214 5.416952 CCTTGACTAACATTTCTCAGGCAAT 59.583 40.000 0.00 0.00 35.55 3.56
214 215 4.761739 CCTTGACTAACATTTCTCAGGCAA 59.238 41.667 0.00 0.00 34.87 4.52
215 216 4.041567 TCCTTGACTAACATTTCTCAGGCA 59.958 41.667 0.00 0.00 0.00 4.75
216 217 4.579869 TCCTTGACTAACATTTCTCAGGC 58.420 43.478 0.00 0.00 0.00 4.85
217 218 6.712547 AGTTTCCTTGACTAACATTTCTCAGG 59.287 38.462 0.00 0.00 0.00 3.86
218 219 7.736447 AGTTTCCTTGACTAACATTTCTCAG 57.264 36.000 0.00 0.00 0.00 3.35
219 220 8.647796 TCTAGTTTCCTTGACTAACATTTCTCA 58.352 33.333 0.00 0.00 0.00 3.27
220 221 9.490379 TTCTAGTTTCCTTGACTAACATTTCTC 57.510 33.333 0.00 0.00 0.00 2.87
221 222 9.847224 TTTCTAGTTTCCTTGACTAACATTTCT 57.153 29.630 0.00 0.00 0.00 2.52
224 225 9.793259 TGATTTCTAGTTTCCTTGACTAACATT 57.207 29.630 0.00 0.00 0.00 2.71
225 226 9.965902 ATGATTTCTAGTTTCCTTGACTAACAT 57.034 29.630 0.00 0.00 0.00 2.71
226 227 9.436957 GATGATTTCTAGTTTCCTTGACTAACA 57.563 33.333 0.00 0.00 0.00 2.41
227 228 9.436957 TGATGATTTCTAGTTTCCTTGACTAAC 57.563 33.333 0.00 0.00 0.00 2.34
229 230 9.823647 GATGATGATTTCTAGTTTCCTTGACTA 57.176 33.333 0.00 0.00 0.00 2.59
230 231 8.324306 TGATGATGATTTCTAGTTTCCTTGACT 58.676 33.333 0.00 0.00 0.00 3.41
231 232 8.498054 TGATGATGATTTCTAGTTTCCTTGAC 57.502 34.615 0.00 0.00 0.00 3.18
232 233 9.334947 GATGATGATGATTTCTAGTTTCCTTGA 57.665 33.333 0.00 0.00 0.00 3.02
233 234 9.117183 TGATGATGATGATTTCTAGTTTCCTTG 57.883 33.333 0.00 0.00 0.00 3.61
234 235 9.863650 ATGATGATGATGATTTCTAGTTTCCTT 57.136 29.630 0.00 0.00 0.00 3.36
235 236 9.504708 GATGATGATGATGATTTCTAGTTTCCT 57.495 33.333 0.00 0.00 0.00 3.36
236 237 9.281371 TGATGATGATGATGATTTCTAGTTTCC 57.719 33.333 0.00 0.00 0.00 3.13
238 239 9.848710 ACTGATGATGATGATGATTTCTAGTTT 57.151 29.630 0.00 0.00 0.00 2.66
239 240 9.274206 CACTGATGATGATGATGATTTCTAGTT 57.726 33.333 0.00 0.00 0.00 2.24
240 241 7.878644 CCACTGATGATGATGATGATTTCTAGT 59.121 37.037 0.00 0.00 0.00 2.57
241 242 7.334671 CCCACTGATGATGATGATGATTTCTAG 59.665 40.741 0.00 0.00 0.00 2.43
242 243 7.166167 CCCACTGATGATGATGATGATTTCTA 58.834 38.462 0.00 0.00 0.00 2.10
243 244 6.004574 CCCACTGATGATGATGATGATTTCT 58.995 40.000 0.00 0.00 0.00 2.52
244 245 5.335740 GCCCACTGATGATGATGATGATTTC 60.336 44.000 0.00 0.00 0.00 2.17
245 246 4.523173 GCCCACTGATGATGATGATGATTT 59.477 41.667 0.00 0.00 0.00 2.17
246 247 4.079970 GCCCACTGATGATGATGATGATT 58.920 43.478 0.00 0.00 0.00 2.57
247 248 3.330998 AGCCCACTGATGATGATGATGAT 59.669 43.478 0.00 0.00 0.00 2.45
248 249 2.709397 AGCCCACTGATGATGATGATGA 59.291 45.455 0.00 0.00 0.00 2.92
249 250 3.141767 AGCCCACTGATGATGATGATG 57.858 47.619 0.00 0.00 0.00 3.07
250 251 3.878237 AAGCCCACTGATGATGATGAT 57.122 42.857 0.00 0.00 0.00 2.45
251 252 3.201487 AGAAAGCCCACTGATGATGATGA 59.799 43.478 0.00 0.00 0.00 2.92
252 253 3.552875 AGAAAGCCCACTGATGATGATG 58.447 45.455 0.00 0.00 0.00 3.07
253 254 3.947612 AGAAAGCCCACTGATGATGAT 57.052 42.857 0.00 0.00 0.00 2.45
254 255 3.726557 AAGAAAGCCCACTGATGATGA 57.273 42.857 0.00 0.00 0.00 2.92
255 256 3.119245 CCAAAGAAAGCCCACTGATGATG 60.119 47.826 0.00 0.00 0.00 3.07
256 257 3.094572 CCAAAGAAAGCCCACTGATGAT 58.905 45.455 0.00 0.00 0.00 2.45
257 258 2.517959 CCAAAGAAAGCCCACTGATGA 58.482 47.619 0.00 0.00 0.00 2.92
258 259 1.067354 GCCAAAGAAAGCCCACTGATG 60.067 52.381 0.00 0.00 0.00 3.07
259 260 1.260544 GCCAAAGAAAGCCCACTGAT 58.739 50.000 0.00 0.00 0.00 2.90
260 261 1.172180 CGCCAAAGAAAGCCCACTGA 61.172 55.000 0.00 0.00 0.00 3.41
261 262 1.286880 CGCCAAAGAAAGCCCACTG 59.713 57.895 0.00 0.00 0.00 3.66
262 263 1.152756 ACGCCAAAGAAAGCCCACT 60.153 52.632 0.00 0.00 0.00 4.00
263 264 1.007387 CACGCCAAAGAAAGCCCAC 60.007 57.895 0.00 0.00 0.00 4.61
264 265 2.199652 CCACGCCAAAGAAAGCCCA 61.200 57.895 0.00 0.00 0.00 5.36
265 266 2.650778 CCACGCCAAAGAAAGCCC 59.349 61.111 0.00 0.00 0.00 5.19
266 267 2.650778 CCCACGCCAAAGAAAGCC 59.349 61.111 0.00 0.00 0.00 4.35
267 268 2.650778 CCCCACGCCAAAGAAAGC 59.349 61.111 0.00 0.00 0.00 3.51
268 269 2.931068 GCCCCCACGCCAAAGAAAG 61.931 63.158 0.00 0.00 0.00 2.62
269 270 2.915137 GCCCCCACGCCAAAGAAA 60.915 61.111 0.00 0.00 0.00 2.52
348 365 1.065854 AGGATTTCTGGCTTCACTCCG 60.066 52.381 0.00 0.00 0.00 4.63
394 411 4.415332 GAAGACGCCGCGGAGTGA 62.415 66.667 39.23 0.00 43.07 3.41
710 808 4.436998 CCTCACTCGCGTGGACCC 62.437 72.222 13.32 0.00 41.53 4.46
861 959 2.896854 GCGGATGCGCATGGAAGA 60.897 61.111 30.76 0.00 34.62 2.87
906 1004 1.914764 GTGGAACCTGGGGTCGGTA 60.915 63.158 0.00 0.00 33.12 4.02
987 1085 4.331968 GTTTGAACATGATACCACCTCCA 58.668 43.478 0.00 0.00 0.00 3.86
988 1086 3.694566 GGTTTGAACATGATACCACCTCC 59.305 47.826 0.00 0.00 0.00 4.30
989 1087 3.694566 GGGTTTGAACATGATACCACCTC 59.305 47.826 0.00 0.00 0.00 3.85
990 1088 3.697166 GGGTTTGAACATGATACCACCT 58.303 45.455 0.00 0.00 0.00 4.00
991 1089 2.422127 CGGGTTTGAACATGATACCACC 59.578 50.000 0.00 0.00 0.00 4.61
992 1090 3.078837 ACGGGTTTGAACATGATACCAC 58.921 45.455 0.00 0.00 0.00 4.16
1017 1115 2.989824 ACACAGTCGGGAGGGTCG 60.990 66.667 0.00 0.00 0.00 4.79
1033 1131 2.185608 GAAGCGCTGAGGAGGGAC 59.814 66.667 12.58 0.00 33.95 4.46
1142 1240 2.614829 TACAATAAGCTCTTCCCGCC 57.385 50.000 0.00 0.00 0.00 6.13
1347 1472 2.926200 CTCTGAGGAGTAAACATGTGCG 59.074 50.000 0.00 0.00 35.03 5.34
1433 1567 5.415701 AGTGCATTACCAATAAGTGAACCAG 59.584 40.000 0.00 0.00 0.00 4.00
1630 1778 2.431782 GCCACATTTGAATGGTATGGCT 59.568 45.455 20.73 0.00 45.39 4.75
1746 1895 9.067986 AGTATAAATATTAACCTTGCCTTCTGC 57.932 33.333 0.00 0.00 41.77 4.26
1852 2001 5.289595 GGGCTTTTCACAAAGTTTTCTAGG 58.710 41.667 0.00 0.00 41.51 3.02
1871 2020 5.605540 ATGATAGTGATTATTTGGGGGCT 57.394 39.130 0.00 0.00 0.00 5.19
2133 2298 7.183460 ACTACTCCCTCAGTCCCATAATATAC 58.817 42.308 0.00 0.00 36.43 1.47
2218 2383 9.480053 AAATGAGTTAACCATTTGACATTTGAG 57.520 29.630 23.07 0.00 41.20 3.02
2245 2411 1.144708 TGCTGAGGTTCCAAACATGGA 59.855 47.619 0.00 0.00 35.93 3.41
2246 2412 1.619654 TGCTGAGGTTCCAAACATGG 58.380 50.000 0.00 0.00 0.00 3.66
2265 2431 8.244113 GCCAAAACTCATAAACACTTATAGCTT 58.756 33.333 0.00 0.00 0.00 3.74
2300 2674 4.883759 TCCCTCCTCATGTGAAGAAGATA 58.116 43.478 0.00 0.00 0.00 1.98
2589 3036 3.610040 TCAATGGATGTGCGTAGAAGT 57.390 42.857 0.00 0.00 0.00 3.01
2609 3056 2.236146 TCAGCTCCAACATAACCACGAT 59.764 45.455 0.00 0.00 0.00 3.73
2888 3353 8.463930 TCATTTATTGTTGAAAAGGAGTCACT 57.536 30.769 0.00 0.00 0.00 3.41
2982 3450 8.043710 AGCTGGGCTACTAATATATTGCTTTAG 58.956 37.037 8.28 0.00 36.99 1.85
2983 3451 7.918076 AGCTGGGCTACTAATATATTGCTTTA 58.082 34.615 8.28 0.00 36.99 1.85
3070 3538 6.155475 TGACAACAAAATAAACCCTTCAGG 57.845 37.500 0.00 0.00 43.78 3.86
3243 3716 8.740906 AGTAACCCGATACAGATGAATATACAG 58.259 37.037 0.00 0.00 0.00 2.74
3298 3771 5.152097 CAATTGCAGCTACTGTTTCTTCAG 58.848 41.667 0.00 0.00 40.80 3.02
3307 3780 2.984471 CAACAAGCAATTGCAGCTACTG 59.016 45.455 30.89 18.54 42.53 2.74
3308 3781 2.624838 ACAACAAGCAATTGCAGCTACT 59.375 40.909 30.89 7.52 42.53 2.57
3311 3784 1.409790 TGACAACAAGCAATTGCAGCT 59.590 42.857 30.89 13.05 45.97 4.24
3322 3795 2.675844 TGACAAACTCGGTGACAACAAG 59.324 45.455 0.00 0.00 0.00 3.16
3324 3797 2.004017 GTGACAAACTCGGTGACAACA 58.996 47.619 0.00 0.00 0.00 3.33
3457 3933 1.080501 TCAAGAGAAGCGCGACCAG 60.081 57.895 12.10 0.00 0.00 4.00
3492 3969 6.017109 CACCAAGTATATGTGATACTTTGGGC 60.017 42.308 19.09 0.00 41.40 5.36
3547 4024 8.208718 TCCTACAGAATCATTCATTTAAACCG 57.791 34.615 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.