Multiple sequence alignment - TraesCS1D01G019300

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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 TraesCS1D01G019300 chr1D 100.000 3447 0 0 1 3447 8319806 8323252 0.000000e+00 6366
1 TraesCS1D01G019300 chr1D 100.000 416 0 0 3819 4234 8323624 8324039 0.000000e+00 769
2 TraesCS1D01G019300 chr1A 95.038 1713 51 5 1746 3438 9939765 9941463 0.000000e+00 2662
3 TraesCS1D01G019300 chr1A 90.154 1554 108 24 188 1719 9938241 9939771 0.000000e+00 1980
4 TraesCS1D01G019300 chr1A 86.516 1854 179 35 1638 3445 9856788 9858616 0.000000e+00 1973
5 TraesCS1D01G019300 chr1A 95.455 396 18 0 3839 4234 9941933 9942328 2.150000e-177 632
6 TraesCS1D01G019300 chr1A 94.842 349 16 2 944 1292 9855866 9856212 1.040000e-150 544
7 TraesCS1D01G019300 chr1A 78.285 898 131 34 2308 3188 10005927 10005077 1.740000e-143 520
8 TraesCS1D01G019300 chr1A 87.500 144 13 3 809 950 9855333 9855473 1.220000e-35 161
9 TraesCS1D01G019300 chr1B 89.101 1101 85 12 1772 2868 11217572 11218641 0.000000e+00 1336
10 TraesCS1D01G019300 chr1B 92.950 539 33 2 744 1281 11216705 11217239 0.000000e+00 780
11 TraesCS1D01G019300 chr1B 83.610 543 62 17 188 722 11216187 11216710 6.360000e-133 484
12 TraesCS1D01G019300 chr1B 82.536 418 47 15 2933 3326 11218674 11219089 1.130000e-90 344
13 TraesCS1D01G019300 chr1B 84.273 337 45 5 1000 1332 29263193 29263525 5.280000e-84 322
14 TraesCS1D01G019300 chr1B 81.940 299 45 7 3831 4123 11219790 11220085 1.180000e-60 244
15 TraesCS1D01G019300 chr3B 81.274 1052 122 42 1821 2835 4518795 4519808 0.000000e+00 782
16 TraesCS1D01G019300 chr3B 89.510 286 26 3 995 1276 4513259 4513544 4.030000e-95 359


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 TraesCS1D01G019300 chr1D 8319806 8324039 4233 False 3567.500000 6366 100.000000 1 4234 2 chr1D.!!$F1 4233
1 TraesCS1D01G019300 chr1A 9938241 9942328 4087 False 1758.000000 2662 93.549000 188 4234 3 chr1A.!!$F2 4046
2 TraesCS1D01G019300 chr1A 9855333 9858616 3283 False 892.666667 1973 89.619333 809 3445 3 chr1A.!!$F1 2636
3 TraesCS1D01G019300 chr1A 10005077 10005927 850 True 520.000000 520 78.285000 2308 3188 1 chr1A.!!$R1 880
4 TraesCS1D01G019300 chr1B 11216187 11220085 3898 False 637.600000 1336 86.027400 188 4123 5 chr1B.!!$F2 3935
5 TraesCS1D01G019300 chr3B 4518795 4519808 1013 False 782.000000 782 81.274000 1821 2835 1 chr3B.!!$F2 1014

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
161 162 0.190069 GGGGGAAAGGGGTTTGTCTT 59.810 55.0 0.0 0.0 0.00 3.01 F
563 579 0.322456 TGAAGATTTGGCCGGTGAGG 60.322 55.0 1.9 0.0 44.97 3.86 F
954 1374 0.461339 AAGTCACACACACACCGACC 60.461 55.0 0.0 0.0 0.00 4.79 F
1590 2270 1.262417 TGGACGATTGTGGTAGCAGA 58.738 50.0 0.0 0.0 0.00 4.26 F
2673 3413 1.323271 GGTGTGCCGAGATGAGAGGA 61.323 60.0 0.0 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1009 1429 1.215647 CGTACGGCTTCTTGCTCCT 59.784 57.895 7.57 0.00 42.39 3.69 R
1893 2592 2.036256 GGCATGGAGTTGGTGGCT 59.964 61.111 0.00 0.00 35.74 4.75 R
2673 3413 0.033504 ACATCGCGACAAAGACAGGT 59.966 50.000 12.93 0.00 0.00 4.00 R
2679 3419 0.716108 GACTCCACATCGCGACAAAG 59.284 55.000 12.93 7.63 0.00 2.77 R
3835 4609 3.070015 GCATGGGAGGATAATTTGGTTGG 59.930 47.826 0.00 0.00 0.00 3.77 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
29 30 2.202824 GCGCGCAGGGTACATGTA 60.203 61.111 29.10 0.08 44.71 2.29
30 31 1.594293 GCGCGCAGGGTACATGTAT 60.594 57.895 29.10 0.00 44.71 2.29
31 32 1.157870 GCGCGCAGGGTACATGTATT 61.158 55.000 29.10 0.00 44.71 1.89
32 33 1.295792 CGCGCAGGGTACATGTATTT 58.704 50.000 9.18 0.00 34.98 1.40
33 34 1.003972 CGCGCAGGGTACATGTATTTG 60.004 52.381 9.18 8.98 34.98 2.32
34 35 1.268539 GCGCAGGGTACATGTATTTGC 60.269 52.381 20.40 20.40 0.00 3.68
35 36 2.013400 CGCAGGGTACATGTATTTGCA 58.987 47.619 25.44 0.86 0.00 4.08
36 37 2.421775 CGCAGGGTACATGTATTTGCAA 59.578 45.455 25.44 0.00 0.00 4.08
37 38 3.066621 CGCAGGGTACATGTATTTGCAAT 59.933 43.478 25.44 0.00 0.00 3.56
38 39 4.610945 GCAGGGTACATGTATTTGCAATC 58.389 43.478 23.18 6.01 0.00 2.67
39 40 4.097741 GCAGGGTACATGTATTTGCAATCA 59.902 41.667 23.18 0.68 0.00 2.57
40 41 5.581605 CAGGGTACATGTATTTGCAATCAC 58.418 41.667 9.18 1.65 0.00 3.06
41 42 4.644685 AGGGTACATGTATTTGCAATCACC 59.355 41.667 9.18 3.69 0.00 4.02
42 43 4.644685 GGGTACATGTATTTGCAATCACCT 59.355 41.667 9.18 0.00 0.00 4.00
43 44 5.450412 GGGTACATGTATTTGCAATCACCTG 60.450 44.000 9.18 7.26 0.00 4.00
44 45 4.724074 ACATGTATTTGCAATCACCTGG 57.276 40.909 0.00 0.00 0.00 4.45
45 46 3.119029 ACATGTATTTGCAATCACCTGGC 60.119 43.478 0.00 0.00 0.00 4.85
46 47 2.806434 TGTATTTGCAATCACCTGGCT 58.194 42.857 0.00 0.00 0.00 4.75
47 48 2.492881 TGTATTTGCAATCACCTGGCTG 59.507 45.455 0.00 0.00 0.00 4.85
48 49 1.927487 ATTTGCAATCACCTGGCTGA 58.073 45.000 0.00 0.00 0.00 4.26
49 50 1.702182 TTTGCAATCACCTGGCTGAA 58.298 45.000 0.00 0.00 0.00 3.02
50 51 1.702182 TTGCAATCACCTGGCTGAAA 58.298 45.000 0.00 0.00 0.00 2.69
51 52 1.702182 TGCAATCACCTGGCTGAAAA 58.298 45.000 0.00 0.00 0.00 2.29
52 53 1.614903 TGCAATCACCTGGCTGAAAAG 59.385 47.619 0.00 0.00 0.00 2.27
53 54 1.615392 GCAATCACCTGGCTGAAAAGT 59.385 47.619 0.00 0.00 0.00 2.66
54 55 2.608752 GCAATCACCTGGCTGAAAAGTG 60.609 50.000 0.00 0.00 0.00 3.16
55 56 2.886523 CAATCACCTGGCTGAAAAGTGA 59.113 45.455 0.00 4.29 41.35 3.41
56 57 2.727123 TCACCTGGCTGAAAAGTGAA 57.273 45.000 0.00 0.00 34.68 3.18
57 58 2.575532 TCACCTGGCTGAAAAGTGAAG 58.424 47.619 0.00 0.00 34.68 3.02
58 59 1.000938 CACCTGGCTGAAAAGTGAAGC 60.001 52.381 0.00 0.00 36.17 3.86
59 60 1.133668 ACCTGGCTGAAAAGTGAAGCT 60.134 47.619 0.00 0.00 37.12 3.74
60 61 1.959282 CCTGGCTGAAAAGTGAAGCTT 59.041 47.619 0.00 0.00 39.52 3.74
61 62 2.288030 CCTGGCTGAAAAGTGAAGCTTG 60.288 50.000 2.10 0.00 37.52 4.01
62 63 2.360165 CTGGCTGAAAAGTGAAGCTTGT 59.640 45.455 2.10 0.00 37.52 3.16
63 64 2.358898 TGGCTGAAAAGTGAAGCTTGTC 59.641 45.455 2.10 0.00 40.94 3.18
64 65 2.620585 GGCTGAAAAGTGAAGCTTGTCT 59.379 45.455 2.10 0.00 41.10 3.41
65 66 3.304324 GGCTGAAAAGTGAAGCTTGTCTC 60.304 47.826 2.10 0.00 41.10 3.36
66 67 3.563390 GCTGAAAAGTGAAGCTTGTCTCT 59.437 43.478 2.10 0.00 41.10 3.10
67 68 4.752101 GCTGAAAAGTGAAGCTTGTCTCTA 59.248 41.667 2.10 0.00 41.10 2.43
68 69 5.237344 GCTGAAAAGTGAAGCTTGTCTCTAA 59.763 40.000 2.10 0.00 41.10 2.10
69 70 6.565623 GCTGAAAAGTGAAGCTTGTCTCTAAG 60.566 42.308 2.10 0.00 41.10 2.18
70 71 5.760253 TGAAAAGTGAAGCTTGTCTCTAAGG 59.240 40.000 2.10 0.00 41.10 2.69
71 72 5.552870 AAAGTGAAGCTTGTCTCTAAGGA 57.447 39.130 2.10 0.00 37.52 3.36
72 73 4.529109 AGTGAAGCTTGTCTCTAAGGAC 57.471 45.455 2.10 0.00 36.81 3.85
73 74 3.898123 AGTGAAGCTTGTCTCTAAGGACA 59.102 43.478 2.10 0.00 43.41 4.02
74 75 4.530161 AGTGAAGCTTGTCTCTAAGGACAT 59.470 41.667 2.10 0.00 44.30 3.06
75 76 4.629200 GTGAAGCTTGTCTCTAAGGACATG 59.371 45.833 2.10 0.00 44.30 3.21
76 77 4.284490 TGAAGCTTGTCTCTAAGGACATGT 59.716 41.667 2.10 0.00 44.30 3.21
77 78 5.480422 TGAAGCTTGTCTCTAAGGACATGTA 59.520 40.000 2.10 0.00 44.30 2.29
78 79 6.155221 TGAAGCTTGTCTCTAAGGACATGTAT 59.845 38.462 2.10 0.00 44.30 2.29
79 80 7.342026 TGAAGCTTGTCTCTAAGGACATGTATA 59.658 37.037 2.10 0.00 44.30 1.47
80 81 7.283625 AGCTTGTCTCTAAGGACATGTATAG 57.716 40.000 0.00 2.38 44.30 1.31
81 82 6.836527 AGCTTGTCTCTAAGGACATGTATAGT 59.163 38.462 0.00 0.00 44.30 2.12
82 83 6.920758 GCTTGTCTCTAAGGACATGTATAGTG 59.079 42.308 0.00 3.72 44.30 2.74
83 84 7.201830 GCTTGTCTCTAAGGACATGTATAGTGA 60.202 40.741 0.00 5.98 44.30 3.41
84 85 8.768501 TTGTCTCTAAGGACATGTATAGTGAT 57.231 34.615 0.00 0.00 44.30 3.06
85 86 8.171164 TGTCTCTAAGGACATGTATAGTGATG 57.829 38.462 0.00 0.00 40.72 3.07
86 87 7.998964 TGTCTCTAAGGACATGTATAGTGATGA 59.001 37.037 0.00 0.00 40.72 2.92
87 88 9.019656 GTCTCTAAGGACATGTATAGTGATGAT 57.980 37.037 0.00 0.00 36.35 2.45
101 102 9.994432 GTATAGTGATGATATTTTAGCAATGCC 57.006 33.333 0.00 0.00 0.00 4.40
102 103 6.964807 AGTGATGATATTTTAGCAATGCCA 57.035 33.333 0.00 0.00 0.00 4.92
103 104 7.534723 AGTGATGATATTTTAGCAATGCCAT 57.465 32.000 0.00 0.00 0.00 4.40
104 105 7.375834 AGTGATGATATTTTAGCAATGCCATG 58.624 34.615 0.00 0.00 0.00 3.66
105 106 7.014905 AGTGATGATATTTTAGCAATGCCATGT 59.985 33.333 0.00 0.00 0.00 3.21
106 107 8.298854 GTGATGATATTTTAGCAATGCCATGTA 58.701 33.333 0.00 0.00 0.00 2.29
107 108 8.517056 TGATGATATTTTAGCAATGCCATGTAG 58.483 33.333 0.00 0.00 0.00 2.74
108 109 7.218228 TGATATTTTAGCAATGCCATGTAGG 57.782 36.000 0.00 0.00 41.84 3.18
109 110 7.003482 TGATATTTTAGCAATGCCATGTAGGA 58.997 34.615 0.00 0.00 41.22 2.94
110 111 7.670979 TGATATTTTAGCAATGCCATGTAGGAT 59.329 33.333 0.00 0.00 41.22 3.24
111 112 9.177608 GATATTTTAGCAATGCCATGTAGGATA 57.822 33.333 0.00 0.00 41.22 2.59
112 113 7.838079 ATTTTAGCAATGCCATGTAGGATAA 57.162 32.000 0.00 0.00 41.22 1.75
113 114 6.633500 TTTAGCAATGCCATGTAGGATAAC 57.367 37.500 0.00 0.00 41.22 1.89
114 115 4.443978 AGCAATGCCATGTAGGATAACT 57.556 40.909 0.00 0.00 41.22 2.24
115 116 4.139786 AGCAATGCCATGTAGGATAACTG 58.860 43.478 0.00 0.00 41.22 3.16
116 117 3.304928 GCAATGCCATGTAGGATAACTGC 60.305 47.826 0.00 0.00 41.22 4.40
117 118 4.139786 CAATGCCATGTAGGATAACTGCT 58.860 43.478 0.00 0.00 41.22 4.24
118 119 3.198409 TGCCATGTAGGATAACTGCTG 57.802 47.619 0.00 0.00 41.22 4.41
119 120 2.771372 TGCCATGTAGGATAACTGCTGA 59.229 45.455 0.00 0.00 41.22 4.26
120 121 3.181462 TGCCATGTAGGATAACTGCTGAG 60.181 47.826 0.00 0.00 41.22 3.35
121 122 3.181461 GCCATGTAGGATAACTGCTGAGT 60.181 47.826 0.00 0.00 41.22 3.41
122 123 4.684485 GCCATGTAGGATAACTGCTGAGTT 60.684 45.833 0.00 0.00 42.19 3.01
123 124 4.813161 CCATGTAGGATAACTGCTGAGTTG 59.187 45.833 0.00 0.00 40.56 3.16
124 125 4.471904 TGTAGGATAACTGCTGAGTTGG 57.528 45.455 0.00 0.00 42.66 3.77
125 126 3.197766 TGTAGGATAACTGCTGAGTTGGG 59.802 47.826 0.00 0.00 42.66 4.12
126 127 2.551270 AGGATAACTGCTGAGTTGGGA 58.449 47.619 0.00 0.00 42.66 4.37
127 128 2.912956 AGGATAACTGCTGAGTTGGGAA 59.087 45.455 0.00 0.00 42.66 3.97
128 129 3.330701 AGGATAACTGCTGAGTTGGGAAA 59.669 43.478 0.00 0.00 42.66 3.13
129 130 4.018050 AGGATAACTGCTGAGTTGGGAAAT 60.018 41.667 0.00 0.00 42.66 2.17
130 131 4.096984 GGATAACTGCTGAGTTGGGAAATG 59.903 45.833 0.00 0.00 42.66 2.32
131 132 2.957402 ACTGCTGAGTTGGGAAATGA 57.043 45.000 0.00 0.00 0.00 2.57
132 133 3.446442 ACTGCTGAGTTGGGAAATGAT 57.554 42.857 0.00 0.00 0.00 2.45
133 134 4.574674 ACTGCTGAGTTGGGAAATGATA 57.425 40.909 0.00 0.00 0.00 2.15
134 135 4.922206 ACTGCTGAGTTGGGAAATGATAA 58.078 39.130 0.00 0.00 0.00 1.75
135 136 5.324409 ACTGCTGAGTTGGGAAATGATAAA 58.676 37.500 0.00 0.00 0.00 1.40
136 137 5.183904 ACTGCTGAGTTGGGAAATGATAAAC 59.816 40.000 0.00 0.00 0.00 2.01
137 138 5.076182 TGCTGAGTTGGGAAATGATAAACA 58.924 37.500 0.00 0.00 0.00 2.83
138 139 5.538053 TGCTGAGTTGGGAAATGATAAACAA 59.462 36.000 0.00 0.00 0.00 2.83
139 140 6.095377 GCTGAGTTGGGAAATGATAAACAAG 58.905 40.000 0.00 0.00 0.00 3.16
140 141 6.294731 GCTGAGTTGGGAAATGATAAACAAGT 60.295 38.462 0.00 0.00 0.00 3.16
141 142 6.980593 TGAGTTGGGAAATGATAAACAAGTG 58.019 36.000 0.00 0.00 0.00 3.16
142 143 6.015519 TGAGTTGGGAAATGATAAACAAGTGG 60.016 38.462 0.00 0.00 0.00 4.00
143 144 5.245977 AGTTGGGAAATGATAAACAAGTGGG 59.754 40.000 0.00 0.00 0.00 4.61
144 145 4.093011 TGGGAAATGATAAACAAGTGGGG 58.907 43.478 0.00 0.00 0.00 4.96
145 146 3.450817 GGGAAATGATAAACAAGTGGGGG 59.549 47.826 0.00 0.00 0.00 5.40
159 160 4.533318 GGGGGAAAGGGGTTTGTC 57.467 61.111 0.00 0.00 0.00 3.18
160 161 1.858505 GGGGGAAAGGGGTTTGTCT 59.141 57.895 0.00 0.00 0.00 3.41
161 162 0.190069 GGGGGAAAGGGGTTTGTCTT 59.810 55.000 0.00 0.00 0.00 3.01
162 163 1.413953 GGGGGAAAGGGGTTTGTCTTT 60.414 52.381 0.00 0.00 36.09 2.52
163 164 1.691976 GGGGAAAGGGGTTTGTCTTTG 59.308 52.381 0.00 0.00 33.85 2.77
164 165 2.673258 GGGAAAGGGGTTTGTCTTTGA 58.327 47.619 0.00 0.00 33.85 2.69
165 166 3.239449 GGGAAAGGGGTTTGTCTTTGAT 58.761 45.455 0.00 0.00 33.85 2.57
166 167 4.412843 GGGAAAGGGGTTTGTCTTTGATA 58.587 43.478 0.00 0.00 33.85 2.15
167 168 4.462834 GGGAAAGGGGTTTGTCTTTGATAG 59.537 45.833 0.00 0.00 33.85 2.08
168 169 5.321927 GGAAAGGGGTTTGTCTTTGATAGA 58.678 41.667 0.00 0.00 33.85 1.98
169 170 5.952347 GGAAAGGGGTTTGTCTTTGATAGAT 59.048 40.000 0.00 0.00 34.79 1.98
170 171 6.127619 GGAAAGGGGTTTGTCTTTGATAGATG 60.128 42.308 0.00 0.00 34.79 2.90
171 172 5.779241 AGGGGTTTGTCTTTGATAGATGA 57.221 39.130 0.00 0.00 34.79 2.92
172 173 6.332976 AGGGGTTTGTCTTTGATAGATGAT 57.667 37.500 0.00 0.00 34.79 2.45
173 174 7.451731 AGGGGTTTGTCTTTGATAGATGATA 57.548 36.000 0.00 0.00 34.79 2.15
174 175 8.050316 AGGGGTTTGTCTTTGATAGATGATAT 57.950 34.615 0.00 0.00 34.79 1.63
175 176 8.506083 AGGGGTTTGTCTTTGATAGATGATATT 58.494 33.333 0.00 0.00 34.79 1.28
176 177 9.136323 GGGGTTTGTCTTTGATAGATGATATTT 57.864 33.333 0.00 0.00 34.79 1.40
206 207 7.992754 AGGAATATTGAATTCATACTCCAGC 57.007 36.000 20.08 5.05 0.00 4.85
215 216 3.777106 TCATACTCCAGCCAATCCATC 57.223 47.619 0.00 0.00 0.00 3.51
228 229 4.692155 GCCAATCCATCCAAAAGTTTGAAG 59.308 41.667 5.34 0.00 40.55 3.02
230 231 6.518200 GCCAATCCATCCAAAAGTTTGAAGTA 60.518 38.462 5.34 0.00 40.55 2.24
264 265 7.781056 AGACGGGCAATATATTTCAACATTTT 58.219 30.769 0.00 0.00 0.00 1.82
277 278 7.504924 TTTCAACATTTTTCCTCACGTCTAT 57.495 32.000 0.00 0.00 0.00 1.98
279 280 4.946784 ACATTTTTCCTCACGTCTATGC 57.053 40.909 0.00 0.00 0.00 3.14
280 281 4.323417 ACATTTTTCCTCACGTCTATGCA 58.677 39.130 0.00 0.00 0.00 3.96
284 286 5.957842 TTTTCCTCACGTCTATGCATTTT 57.042 34.783 3.54 0.00 0.00 1.82
286 288 7.624360 TTTTCCTCACGTCTATGCATTTTAT 57.376 32.000 3.54 0.00 0.00 1.40
288 290 8.725405 TTTCCTCACGTCTATGCATTTTATTA 57.275 30.769 3.54 0.00 0.00 0.98
308 310 5.607939 TTACATAGATGTGGGATTGACGT 57.392 39.130 5.39 0.00 41.89 4.34
309 311 3.797039 ACATAGATGTGGGATTGACGTG 58.203 45.455 0.00 0.00 40.03 4.49
313 315 2.033448 GTGGGATTGACGTGGGCA 59.967 61.111 0.00 0.00 0.00 5.36
314 316 2.040544 GTGGGATTGACGTGGGCAG 61.041 63.158 0.00 0.00 0.00 4.85
315 317 2.351276 GGGATTGACGTGGGCAGT 59.649 61.111 0.00 0.00 0.00 4.40
317 319 0.462047 GGGATTGACGTGGGCAGTAG 60.462 60.000 0.00 0.00 0.00 2.57
326 328 4.202121 TGACGTGGGCAGTAGAATATCTTC 60.202 45.833 0.00 0.00 0.00 2.87
358 361 3.788227 TGTTGGCAGGTCTTGAACTAT 57.212 42.857 0.00 0.00 0.00 2.12
373 376 7.224949 GTCTTGAACTATTGTACTCCTAATGGC 59.775 40.741 0.00 0.00 0.00 4.40
380 383 9.026121 ACTATTGTACTCCTAATGGCACTATAG 57.974 37.037 0.00 0.00 34.91 1.31
381 384 5.723672 TGTACTCCTAATGGCACTATAGC 57.276 43.478 0.00 0.00 0.00 2.97
382 385 5.144832 TGTACTCCTAATGGCACTATAGCA 58.855 41.667 0.00 0.00 35.83 3.49
402 406 8.915871 ATAGCATTTTGTATAGTGCAAAACAG 57.084 30.769 7.85 5.90 44.99 3.16
405 409 8.023128 AGCATTTTGTATAGTGCAAAACAGTAG 58.977 33.333 7.85 0.22 44.99 2.57
406 410 7.201350 GCATTTTGTATAGTGCAAAACAGTAGC 60.201 37.037 7.85 5.09 44.99 3.58
407 411 5.524511 TTGTATAGTGCAAAACAGTAGCG 57.475 39.130 0.00 0.00 37.60 4.26
408 412 3.369756 TGTATAGTGCAAAACAGTAGCGC 59.630 43.478 0.00 0.00 37.60 5.92
409 413 3.006672 AGTGCAAAACAGTAGCGCT 57.993 47.368 17.26 17.26 43.59 5.92
410 414 2.163818 AGTGCAAAACAGTAGCGCTA 57.836 45.000 14.45 14.45 46.20 4.26
411 415 2.699954 AGTGCAAAACAGTAGCGCTAT 58.300 42.857 21.96 6.98 46.20 2.97
412 416 3.857052 AGTGCAAAACAGTAGCGCTATA 58.143 40.909 21.96 0.00 46.20 1.31
413 417 4.442706 AGTGCAAAACAGTAGCGCTATAT 58.557 39.130 21.96 9.94 46.20 0.86
414 418 5.597806 AGTGCAAAACAGTAGCGCTATATA 58.402 37.500 21.96 0.00 46.20 0.86
415 419 6.223852 AGTGCAAAACAGTAGCGCTATATAT 58.776 36.000 21.96 5.17 46.20 0.86
416 420 7.375834 AGTGCAAAACAGTAGCGCTATATATA 58.624 34.615 21.96 0.00 46.20 0.86
439 443 8.706492 ATAGCACATGTTCAATATGTTTTTGG 57.294 30.769 0.00 0.00 36.67 3.28
440 444 6.523840 AGCACATGTTCAATATGTTTTTGGT 58.476 32.000 0.00 0.00 36.67 3.67
441 445 7.665690 AGCACATGTTCAATATGTTTTTGGTA 58.334 30.769 0.00 0.00 36.67 3.25
443 447 7.411804 GCACATGTTCAATATGTTTTTGGTAGC 60.412 37.037 0.00 0.00 36.67 3.58
444 448 7.598118 CACATGTTCAATATGTTTTTGGTAGCA 59.402 33.333 0.00 0.00 36.67 3.49
446 450 9.153721 CATGTTCAATATGTTTTTGGTAGCAAT 57.846 29.630 8.40 0.00 0.00 3.56
448 452 7.117523 TGTTCAATATGTTTTTGGTAGCAATGC 59.882 33.333 8.40 0.00 0.00 3.56
451 455 1.000283 TGTTTTTGGTAGCAATGCCCG 60.000 47.619 8.40 0.00 0.00 6.13
454 458 1.745232 TTTGGTAGCAATGCCCGTAG 58.255 50.000 8.40 0.00 0.00 3.51
476 480 3.924073 GTGTTTCCATTTTGGTTATCCGC 59.076 43.478 0.00 0.00 39.03 5.54
479 483 5.124776 TGTTTCCATTTTGGTTATCCGCTAG 59.875 40.000 0.00 0.00 39.03 3.42
481 485 5.105567 TCCATTTTGGTTATCCGCTAGAA 57.894 39.130 0.00 0.00 39.03 2.10
485 489 6.039270 CCATTTTGGTTATCCGCTAGAAATCA 59.961 38.462 0.00 0.00 36.30 2.57
488 492 4.693283 TGGTTATCCGCTAGAAATCAGTG 58.307 43.478 0.00 0.00 36.30 3.66
490 494 4.745620 GGTTATCCGCTAGAAATCAGTGAC 59.254 45.833 0.00 0.00 0.00 3.67
495 501 3.487574 CCGCTAGAAATCAGTGACGATTC 59.512 47.826 0.00 0.92 34.49 2.52
505 511 7.645058 AATCAGTGACGATTCCCAATAATTT 57.355 32.000 0.00 0.00 29.42 1.82
510 526 6.546034 AGTGACGATTCCCAATAATTTTAGGG 59.454 38.462 0.00 0.00 42.86 3.53
533 549 9.768215 AGGGAGGAGATATTTAATGTTCAAAAA 57.232 29.630 0.00 0.00 0.00 1.94
563 579 0.322456 TGAAGATTTGGCCGGTGAGG 60.322 55.000 1.90 0.00 44.97 3.86
572 588 2.700773 GCCGGTGAGGAATTGGCAC 61.701 63.158 1.90 0.00 45.06 5.01
632 648 4.135153 CTGGTCAGTCCCTCCGCG 62.135 72.222 0.00 0.00 34.77 6.46
634 650 4.436998 GGTCAGTCCCTCCGCGTG 62.437 72.222 4.92 0.00 0.00 5.34
708 724 3.118038 AGAAGGGTGTGAAACTTGTGCTA 60.118 43.478 0.00 0.00 38.04 3.49
711 727 2.293399 GGGTGTGAAACTTGTGCTAAGG 59.707 50.000 6.31 0.00 38.04 2.69
720 736 5.656213 AACTTGTGCTAAGGTATAGACGT 57.344 39.130 0.00 0.00 0.00 4.34
721 737 5.656213 ACTTGTGCTAAGGTATAGACGTT 57.344 39.130 0.70 0.70 37.44 3.99
722 738 6.764308 ACTTGTGCTAAGGTATAGACGTTA 57.236 37.500 2.96 2.96 35.38 3.18
742 758 5.910723 CGTTATGTAAACCACAAAAGTCACC 59.089 40.000 0.00 0.00 41.55 4.02
876 893 5.905913 ACCTTCTAGCTCCATACAAATAGGT 59.094 40.000 0.00 0.00 0.00 3.08
878 895 5.707242 TCTAGCTCCATACAAATAGGTCG 57.293 43.478 0.00 0.00 0.00 4.79
918 935 0.856641 CACACCAGAACCAACGTACG 59.143 55.000 15.01 15.01 0.00 3.67
939 958 4.144555 CGATCTTCACTTTTTCGCAAGTC 58.855 43.478 0.00 0.00 34.60 3.01
950 969 1.087202 TCGCAAGTCACACACACACC 61.087 55.000 0.00 0.00 39.48 4.16
951 970 1.351707 GCAAGTCACACACACACCG 59.648 57.895 0.00 0.00 0.00 4.94
954 1374 0.461339 AAGTCACACACACACCGACC 60.461 55.000 0.00 0.00 0.00 4.79
1359 2026 6.767902 AGAAATACAACTGAGCTCAAACTCAA 59.232 34.615 18.85 2.38 45.72 3.02
1478 2147 8.718734 ACTTCCACATTAAGTTTAGACGATTTC 58.281 33.333 0.00 0.00 33.39 2.17
1521 2194 8.624367 TTGAATCTAGTCCCAAATTTTTACGA 57.376 30.769 0.00 0.00 0.00 3.43
1578 2258 5.966742 TCGAATTCTAGATCATGGACGAT 57.033 39.130 3.52 0.00 0.00 3.73
1590 2270 1.262417 TGGACGATTGTGGTAGCAGA 58.738 50.000 0.00 0.00 0.00 4.26
1599 2279 4.640771 TTGTGGTAGCAGAAGGAAGAAT 57.359 40.909 0.00 0.00 0.00 2.40
1853 2552 2.404215 CTTCACCCTGAACGTGTACAG 58.596 52.381 0.00 9.65 32.21 2.74
1923 2622 4.344865 ATGCCCGTCGCCACCTTT 62.345 61.111 0.00 0.00 36.24 3.11
1927 2626 2.657237 CCGTCGCCACCTTTCTCT 59.343 61.111 0.00 0.00 0.00 3.10
2265 2966 9.232473 TGCATGTGTATGTTAATTAGGTTTACA 57.768 29.630 0.00 0.00 36.65 2.41
2266 2967 9.498307 GCATGTGTATGTTAATTAGGTTTACAC 57.502 33.333 15.75 15.75 38.77 2.90
2568 3304 7.807977 AATTGAAGTGTACAAAGTGATGAGT 57.192 32.000 0.00 0.00 0.00 3.41
2673 3413 1.323271 GGTGTGCCGAGATGAGAGGA 61.323 60.000 0.00 0.00 0.00 3.71
2679 3419 1.028905 CCGAGATGAGAGGACCTGTC 58.971 60.000 11.76 11.76 0.00 3.51
2790 3530 7.176690 AGGTAATCCTTTGAAACACACCATAAG 59.823 37.037 0.00 0.00 42.12 1.73
2883 3623 6.624297 TGAGAGGAGGGATGACTATTCATTA 58.376 40.000 0.00 0.00 42.95 1.90
2934 3674 1.381327 TTTTTGGGGGAACGTGCCA 60.381 52.632 16.38 0.00 0.00 4.92
2948 3688 1.044611 GTGCCAAAACCCCTAAAGCA 58.955 50.000 0.00 0.00 0.00 3.91
3010 3750 8.796475 ACAAGATAGAAGCTCAAGCATTTTAAA 58.204 29.630 4.59 0.00 45.16 1.52
3230 4001 4.960938 ACATCACAAGTGTAAAGCTCAGA 58.039 39.130 0.00 0.00 0.00 3.27
3259 4030 7.066887 ACACATGTTAAATTGACAAGACACTCA 59.933 33.333 0.00 0.00 0.00 3.41
3380 4154 4.097892 GTGTCCCATGTTGATTTGGATACC 59.902 45.833 0.00 0.00 34.81 2.73
3857 4893 3.070015 CCAACCAAATTATCCTCCCATGC 59.930 47.826 0.00 0.00 0.00 4.06
4039 5081 8.465273 AACCTTCTCTTAGTTAACAAAGCATT 57.535 30.769 8.61 0.00 0.00 3.56
4110 5152 6.317088 CAATCCATAAATCATACGCATCACC 58.683 40.000 0.00 0.00 0.00 4.02
4187 5229 8.470805 ACATACTAGATCATTTATCCGATGGAC 58.529 37.037 0.00 0.00 34.90 4.02
4223 5265 7.779798 ACAACTGCCATTACATGAAATATACCT 59.220 33.333 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.654412 CTGCGCGCCCCTAGCTAG 62.654 72.222 30.77 14.20 40.39 3.42
11 12 2.989055 ATACATGTACCCTGCGCGCC 62.989 60.000 30.77 12.65 0.00 6.53
12 13 1.157870 AATACATGTACCCTGCGCGC 61.158 55.000 27.26 27.26 0.00 6.86
13 14 1.003972 CAAATACATGTACCCTGCGCG 60.004 52.381 7.96 0.00 0.00 6.86
14 15 1.268539 GCAAATACATGTACCCTGCGC 60.269 52.381 7.96 0.00 0.00 6.09
15 16 2.013400 TGCAAATACATGTACCCTGCG 58.987 47.619 21.49 6.66 0.00 5.18
16 17 4.097741 TGATTGCAAATACATGTACCCTGC 59.902 41.667 20.75 20.75 0.00 4.85
17 18 5.450412 GGTGATTGCAAATACATGTACCCTG 60.450 44.000 7.96 6.98 0.00 4.45
18 19 4.644685 GGTGATTGCAAATACATGTACCCT 59.355 41.667 7.96 0.00 0.00 4.34
19 20 4.644685 AGGTGATTGCAAATACATGTACCC 59.355 41.667 7.96 2.20 0.00 3.69
20 21 5.450412 CCAGGTGATTGCAAATACATGTACC 60.450 44.000 21.54 3.25 0.00 3.34
21 22 5.581605 CCAGGTGATTGCAAATACATGTAC 58.418 41.667 21.54 0.00 0.00 2.90
22 23 4.097741 GCCAGGTGATTGCAAATACATGTA 59.902 41.667 21.54 8.27 0.00 2.29
23 24 3.119029 GCCAGGTGATTGCAAATACATGT 60.119 43.478 21.54 2.69 0.00 3.21
24 25 3.131577 AGCCAGGTGATTGCAAATACATG 59.868 43.478 18.44 18.44 0.00 3.21
25 26 3.131577 CAGCCAGGTGATTGCAAATACAT 59.868 43.478 1.71 0.00 0.00 2.29
26 27 2.492881 CAGCCAGGTGATTGCAAATACA 59.507 45.455 1.71 1.43 0.00 2.29
27 28 2.754552 TCAGCCAGGTGATTGCAAATAC 59.245 45.455 1.71 5.51 0.00 1.89
28 29 3.084536 TCAGCCAGGTGATTGCAAATA 57.915 42.857 1.71 0.00 0.00 1.40
29 30 1.927487 TCAGCCAGGTGATTGCAAAT 58.073 45.000 1.71 0.00 0.00 2.32
30 31 1.702182 TTCAGCCAGGTGATTGCAAA 58.298 45.000 1.71 0.00 0.00 3.68
31 32 1.702182 TTTCAGCCAGGTGATTGCAA 58.298 45.000 0.00 0.00 0.00 4.08
32 33 1.614903 CTTTTCAGCCAGGTGATTGCA 59.385 47.619 0.00 0.00 0.00 4.08
33 34 1.615392 ACTTTTCAGCCAGGTGATTGC 59.385 47.619 0.00 0.00 0.00 3.56
34 35 2.886523 TCACTTTTCAGCCAGGTGATTG 59.113 45.455 0.00 0.00 32.91 2.67
35 36 3.228188 TCACTTTTCAGCCAGGTGATT 57.772 42.857 0.00 0.00 32.91 2.57
36 37 2.957402 TCACTTTTCAGCCAGGTGAT 57.043 45.000 0.00 0.00 32.91 3.06
37 38 2.575532 CTTCACTTTTCAGCCAGGTGA 58.424 47.619 0.00 0.00 35.51 4.02
38 39 1.000938 GCTTCACTTTTCAGCCAGGTG 60.001 52.381 0.00 0.00 0.00 4.00
39 40 1.133668 AGCTTCACTTTTCAGCCAGGT 60.134 47.619 0.00 0.00 33.73 4.00
40 41 1.613836 AGCTTCACTTTTCAGCCAGG 58.386 50.000 0.00 0.00 33.73 4.45
41 42 2.360165 ACAAGCTTCACTTTTCAGCCAG 59.640 45.455 0.00 0.00 36.04 4.85
42 43 2.358898 GACAAGCTTCACTTTTCAGCCA 59.641 45.455 0.00 0.00 36.04 4.75
43 44 2.620585 AGACAAGCTTCACTTTTCAGCC 59.379 45.455 0.00 0.00 37.51 4.85
44 45 3.563390 AGAGACAAGCTTCACTTTTCAGC 59.437 43.478 0.00 0.00 37.51 4.26
45 46 6.073331 CCTTAGAGACAAGCTTCACTTTTCAG 60.073 42.308 0.00 0.00 37.51 3.02
46 47 5.760253 CCTTAGAGACAAGCTTCACTTTTCA 59.240 40.000 0.00 0.00 37.51 2.69
47 48 5.992217 TCCTTAGAGACAAGCTTCACTTTTC 59.008 40.000 0.00 0.00 36.04 2.29
48 49 5.760743 GTCCTTAGAGACAAGCTTCACTTTT 59.239 40.000 0.00 0.00 36.04 2.27
49 50 5.163301 TGTCCTTAGAGACAAGCTTCACTTT 60.163 40.000 0.00 0.00 43.65 2.66
50 51 4.345257 TGTCCTTAGAGACAAGCTTCACTT 59.655 41.667 0.00 0.00 43.65 3.16
51 52 3.898123 TGTCCTTAGAGACAAGCTTCACT 59.102 43.478 0.00 0.00 43.65 3.41
52 53 4.258702 TGTCCTTAGAGACAAGCTTCAC 57.741 45.455 0.00 0.00 43.65 3.18
61 62 8.397575 TCATCACTATACATGTCCTTAGAGAC 57.602 38.462 0.00 0.00 37.28 3.36
75 76 9.994432 GGCATTGCTAAAATATCATCACTATAC 57.006 33.333 8.82 0.00 0.00 1.47
76 77 9.737844 TGGCATTGCTAAAATATCATCACTATA 57.262 29.630 8.82 0.00 0.00 1.31
77 78 8.640063 TGGCATTGCTAAAATATCATCACTAT 57.360 30.769 8.82 0.00 0.00 2.12
78 79 8.517056 CATGGCATTGCTAAAATATCATCACTA 58.483 33.333 8.82 0.00 0.00 2.74
79 80 6.964807 TGGCATTGCTAAAATATCATCACT 57.035 33.333 8.82 0.00 0.00 3.41
80 81 7.149973 ACATGGCATTGCTAAAATATCATCAC 58.850 34.615 8.82 0.00 0.00 3.06
81 82 7.292713 ACATGGCATTGCTAAAATATCATCA 57.707 32.000 8.82 0.00 0.00 3.07
82 83 7.972277 CCTACATGGCATTGCTAAAATATCATC 59.028 37.037 8.82 0.00 0.00 2.92
83 84 7.670979 TCCTACATGGCATTGCTAAAATATCAT 59.329 33.333 8.82 0.00 35.26 2.45
84 85 7.003482 TCCTACATGGCATTGCTAAAATATCA 58.997 34.615 8.82 0.00 35.26 2.15
85 86 7.452880 TCCTACATGGCATTGCTAAAATATC 57.547 36.000 8.82 0.00 35.26 1.63
86 87 9.532494 TTATCCTACATGGCATTGCTAAAATAT 57.468 29.630 8.82 0.00 35.26 1.28
87 88 8.792633 GTTATCCTACATGGCATTGCTAAAATA 58.207 33.333 8.82 0.00 35.26 1.40
88 89 7.506938 AGTTATCCTACATGGCATTGCTAAAAT 59.493 33.333 8.82 0.00 35.26 1.82
89 90 6.833416 AGTTATCCTACATGGCATTGCTAAAA 59.167 34.615 8.82 0.00 35.26 1.52
90 91 6.262944 CAGTTATCCTACATGGCATTGCTAAA 59.737 38.462 8.82 0.00 35.26 1.85
91 92 5.764686 CAGTTATCCTACATGGCATTGCTAA 59.235 40.000 8.82 0.00 35.26 3.09
92 93 5.308014 CAGTTATCCTACATGGCATTGCTA 58.692 41.667 8.82 2.16 35.26 3.49
93 94 4.139786 CAGTTATCCTACATGGCATTGCT 58.860 43.478 8.82 0.00 35.26 3.91
94 95 3.304928 GCAGTTATCCTACATGGCATTGC 60.305 47.826 0.00 0.00 35.26 3.56
95 96 4.023450 CAGCAGTTATCCTACATGGCATTG 60.023 45.833 0.00 0.00 35.26 2.82
96 97 4.139786 CAGCAGTTATCCTACATGGCATT 58.860 43.478 0.00 0.00 35.26 3.56
97 98 3.392285 TCAGCAGTTATCCTACATGGCAT 59.608 43.478 0.00 0.00 35.26 4.40
98 99 2.771372 TCAGCAGTTATCCTACATGGCA 59.229 45.455 0.00 0.00 35.26 4.92
99 100 3.181461 ACTCAGCAGTTATCCTACATGGC 60.181 47.826 0.00 0.00 35.26 4.40
100 101 4.679373 ACTCAGCAGTTATCCTACATGG 57.321 45.455 0.00 0.00 37.10 3.66
101 102 4.813161 CCAACTCAGCAGTTATCCTACATG 59.187 45.833 0.00 0.00 41.24 3.21
102 103 4.141620 CCCAACTCAGCAGTTATCCTACAT 60.142 45.833 0.00 0.00 41.24 2.29
103 104 3.197766 CCCAACTCAGCAGTTATCCTACA 59.802 47.826 0.00 0.00 41.24 2.74
104 105 3.451178 TCCCAACTCAGCAGTTATCCTAC 59.549 47.826 0.00 0.00 41.24 3.18
105 106 3.719871 TCCCAACTCAGCAGTTATCCTA 58.280 45.455 0.00 0.00 41.24 2.94
106 107 2.551270 TCCCAACTCAGCAGTTATCCT 58.449 47.619 0.00 0.00 41.24 3.24
107 108 3.350219 TTCCCAACTCAGCAGTTATCC 57.650 47.619 0.00 0.00 41.24 2.59
108 109 4.943705 TCATTTCCCAACTCAGCAGTTATC 59.056 41.667 0.00 0.00 41.24 1.75
109 110 4.922206 TCATTTCCCAACTCAGCAGTTAT 58.078 39.130 0.00 0.00 41.24 1.89
110 111 4.365514 TCATTTCCCAACTCAGCAGTTA 57.634 40.909 0.00 0.00 41.24 2.24
111 112 3.228188 TCATTTCCCAACTCAGCAGTT 57.772 42.857 0.00 0.00 44.26 3.16
112 113 2.957402 TCATTTCCCAACTCAGCAGT 57.043 45.000 0.00 0.00 0.00 4.40
113 114 5.183713 TGTTTATCATTTCCCAACTCAGCAG 59.816 40.000 0.00 0.00 0.00 4.24
114 115 5.076182 TGTTTATCATTTCCCAACTCAGCA 58.924 37.500 0.00 0.00 0.00 4.41
115 116 5.643379 TGTTTATCATTTCCCAACTCAGC 57.357 39.130 0.00 0.00 0.00 4.26
116 117 7.086376 CACTTGTTTATCATTTCCCAACTCAG 58.914 38.462 0.00 0.00 0.00 3.35
117 118 6.015519 CCACTTGTTTATCATTTCCCAACTCA 60.016 38.462 0.00 0.00 0.00 3.41
118 119 6.389906 CCACTTGTTTATCATTTCCCAACTC 58.610 40.000 0.00 0.00 0.00 3.01
119 120 5.245977 CCCACTTGTTTATCATTTCCCAACT 59.754 40.000 0.00 0.00 0.00 3.16
120 121 5.478407 CCCACTTGTTTATCATTTCCCAAC 58.522 41.667 0.00 0.00 0.00 3.77
121 122 4.530161 CCCCACTTGTTTATCATTTCCCAA 59.470 41.667 0.00 0.00 0.00 4.12
122 123 4.093011 CCCCACTTGTTTATCATTTCCCA 58.907 43.478 0.00 0.00 0.00 4.37
123 124 3.450817 CCCCCACTTGTTTATCATTTCCC 59.549 47.826 0.00 0.00 0.00 3.97
124 125 4.736126 CCCCCACTTGTTTATCATTTCC 57.264 45.455 0.00 0.00 0.00 3.13
142 143 0.190069 AAGACAAACCCCTTTCCCCC 59.810 55.000 0.00 0.00 0.00 5.40
143 144 1.691976 CAAAGACAAACCCCTTTCCCC 59.308 52.381 0.00 0.00 30.89 4.81
144 145 2.673258 TCAAAGACAAACCCCTTTCCC 58.327 47.619 0.00 0.00 30.89 3.97
145 146 5.321927 TCTATCAAAGACAAACCCCTTTCC 58.678 41.667 0.00 0.00 30.89 3.13
146 147 6.659242 TCATCTATCAAAGACAAACCCCTTTC 59.341 38.462 0.00 0.00 36.93 2.62
147 148 6.552008 TCATCTATCAAAGACAAACCCCTTT 58.448 36.000 0.00 0.00 36.93 3.11
148 149 6.139679 TCATCTATCAAAGACAAACCCCTT 57.860 37.500 0.00 0.00 36.93 3.95
149 150 5.779241 TCATCTATCAAAGACAAACCCCT 57.221 39.130 0.00 0.00 36.93 4.79
150 151 8.697507 AATATCATCTATCAAAGACAAACCCC 57.302 34.615 0.00 0.00 36.93 4.95
180 181 9.507329 GCTGGAGTATGAATTCAATATTCCTTA 57.493 33.333 23.75 13.65 0.00 2.69
181 182 7.449704 GGCTGGAGTATGAATTCAATATTCCTT 59.550 37.037 23.75 8.95 0.00 3.36
182 183 6.944862 GGCTGGAGTATGAATTCAATATTCCT 59.055 38.462 23.75 12.48 0.00 3.36
183 184 6.716628 TGGCTGGAGTATGAATTCAATATTCC 59.283 38.462 13.09 18.08 0.00 3.01
184 185 7.750229 TGGCTGGAGTATGAATTCAATATTC 57.250 36.000 13.09 10.88 0.00 1.75
185 186 8.716674 ATTGGCTGGAGTATGAATTCAATATT 57.283 30.769 13.09 0.00 0.00 1.28
186 187 7.395489 GGATTGGCTGGAGTATGAATTCAATAT 59.605 37.037 13.09 0.54 0.00 1.28
196 197 2.107031 TGGATGGATTGGCTGGAGTATG 59.893 50.000 0.00 0.00 0.00 2.39
202 203 2.181975 ACTTTTGGATGGATTGGCTGG 58.818 47.619 0.00 0.00 0.00 4.85
206 207 5.857268 ACTTCAAACTTTTGGATGGATTGG 58.143 37.500 1.94 0.00 38.66 3.16
215 216 9.231297 TCTATCTCCATTACTTCAAACTTTTGG 57.769 33.333 1.94 0.00 38.66 3.28
228 229 3.746045 TTGCCCGTCTATCTCCATTAC 57.254 47.619 0.00 0.00 0.00 1.89
230 231 6.814954 ATATATTGCCCGTCTATCTCCATT 57.185 37.500 0.00 0.00 0.00 3.16
264 265 7.766738 TGTAATAAAATGCATAGACGTGAGGAA 59.233 33.333 0.00 0.00 0.00 3.36
277 278 8.938801 ATCCCACATCTATGTAATAAAATGCA 57.061 30.769 0.00 0.00 39.39 3.96
284 286 7.151976 CACGTCAATCCCACATCTATGTAATA 58.848 38.462 0.00 0.00 39.39 0.98
286 288 5.356426 CACGTCAATCCCACATCTATGTAA 58.644 41.667 0.00 0.00 39.39 2.41
288 290 3.432186 CCACGTCAATCCCACATCTATGT 60.432 47.826 0.00 0.00 42.84 2.29
295 297 2.033448 GCCCACGTCAATCCCACA 59.967 61.111 0.00 0.00 0.00 4.17
306 308 4.592485 AGAAGATATTCTACTGCCCACG 57.408 45.455 0.00 0.00 0.00 4.94
326 328 7.865706 AGACCTGCCAACATAGTATTAAAAG 57.134 36.000 0.00 0.00 0.00 2.27
339 341 3.821033 ACAATAGTTCAAGACCTGCCAAC 59.179 43.478 0.00 0.00 0.00 3.77
358 361 5.600898 TGCTATAGTGCCATTAGGAGTACAA 59.399 40.000 0.84 0.00 36.89 2.41
380 383 7.201350 GCTACTGTTTTGCACTATACAAAATGC 60.201 37.037 5.11 0.00 45.70 3.56
381 384 7.007367 CGCTACTGTTTTGCACTATACAAAATG 59.993 37.037 5.11 4.78 45.70 2.32
382 385 7.021196 CGCTACTGTTTTGCACTATACAAAAT 58.979 34.615 5.11 0.00 45.70 1.82
413 417 9.800433 CCAAAAACATATTGAACATGTGCTATA 57.200 29.630 9.99 9.99 36.74 1.31
414 418 8.313292 ACCAAAAACATATTGAACATGTGCTAT 58.687 29.630 5.18 5.65 36.74 2.97
415 419 7.665690 ACCAAAAACATATTGAACATGTGCTA 58.334 30.769 5.18 0.00 36.74 3.49
416 420 6.523840 ACCAAAAACATATTGAACATGTGCT 58.476 32.000 5.18 0.00 36.74 4.40
436 440 0.616371 ACTACGGGCATTGCTACCAA 59.384 50.000 8.82 0.00 35.01 3.67
438 442 0.107848 ACACTACGGGCATTGCTACC 60.108 55.000 8.82 1.08 0.00 3.18
439 443 1.734163 AACACTACGGGCATTGCTAC 58.266 50.000 8.82 1.31 0.00 3.58
440 444 2.352388 GAAACACTACGGGCATTGCTA 58.648 47.619 8.82 0.00 0.00 3.49
441 445 1.165270 GAAACACTACGGGCATTGCT 58.835 50.000 8.82 0.00 0.00 3.91
443 447 1.529226 TGGAAACACTACGGGCATTG 58.471 50.000 0.00 0.00 33.40 2.82
448 452 9.439994 GGATAACCAAAATGGAAACACTACGGG 62.440 44.444 2.85 0.00 40.96 5.28
451 455 6.319399 CGGATAACCAAAATGGAAACACTAC 58.681 40.000 2.85 0.00 40.96 2.73
454 458 3.924073 GCGGATAACCAAAATGGAAACAC 59.076 43.478 2.85 0.00 40.96 3.32
476 480 5.011090 TGGGAATCGTCACTGATTTCTAG 57.989 43.478 2.10 0.00 38.65 2.43
479 483 6.677781 TTATTGGGAATCGTCACTGATTTC 57.322 37.500 0.00 0.00 38.65 2.17
481 485 7.645058 AAATTATTGGGAATCGTCACTGATT 57.355 32.000 0.00 0.00 41.16 2.57
485 489 6.546034 CCCTAAAATTATTGGGAATCGTCACT 59.454 38.462 4.13 0.00 42.11 3.41
488 492 6.206829 CCTCCCTAAAATTATTGGGAATCGTC 59.793 42.308 11.74 0.00 46.80 4.20
490 494 6.303839 TCCTCCCTAAAATTATTGGGAATCG 58.696 40.000 11.74 3.39 46.80 3.34
495 501 9.828691 AAATATCTCCTCCCTAAAATTATTGGG 57.171 33.333 3.85 3.85 40.95 4.12
527 543 9.748708 CAAATCTTCAAGTAGGACAATTTTTGA 57.251 29.630 0.00 0.00 0.00 2.69
533 549 4.706962 GGCCAAATCTTCAAGTAGGACAAT 59.293 41.667 0.00 0.00 0.00 2.71
539 555 2.420022 CACCGGCCAAATCTTCAAGTAG 59.580 50.000 0.00 0.00 0.00 2.57
540 556 2.039216 TCACCGGCCAAATCTTCAAGTA 59.961 45.455 0.00 0.00 0.00 2.24
541 557 1.202879 TCACCGGCCAAATCTTCAAGT 60.203 47.619 0.00 0.00 0.00 3.16
572 588 2.355756 CAGTGTGTTCACACTCCCAAAG 59.644 50.000 28.39 16.36 46.96 2.77
582 598 2.802816 GTGACCAGATCAGTGTGTTCAC 59.197 50.000 0.00 0.00 44.15 3.18
708 724 7.839907 TGTGGTTTACATAACGTCTATACCTT 58.160 34.615 0.00 0.00 33.42 3.50
711 727 9.962759 CTTTTGTGGTTTACATAACGTCTATAC 57.037 33.333 0.00 0.00 39.48 1.47
720 736 7.041916 CGTAGGTGACTTTTGTGGTTTACATAA 60.042 37.037 0.00 0.00 43.67 1.90
721 737 6.424509 CGTAGGTGACTTTTGTGGTTTACATA 59.575 38.462 0.00 0.00 43.67 2.29
722 738 5.237779 CGTAGGTGACTTTTGTGGTTTACAT 59.762 40.000 0.00 0.00 43.67 2.29
856 873 4.022242 GCGACCTATTTGTATGGAGCTAGA 60.022 45.833 0.00 0.00 0.00 2.43
876 893 1.985662 ATTGGTACGGTCCTGGCGA 60.986 57.895 0.64 0.00 0.00 5.54
878 895 2.112815 GCATTGGTACGGTCCTGGC 61.113 63.158 0.00 0.00 0.00 4.85
918 935 4.906437 GTGACTTGCGAAAAAGTGAAGATC 59.094 41.667 3.66 0.00 40.48 2.75
939 958 2.590575 GGGGTCGGTGTGTGTGTG 60.591 66.667 0.00 0.00 0.00 3.82
951 970 4.767255 CTCTGCTGCGGTGGGGTC 62.767 72.222 8.55 0.00 0.00 4.46
954 1374 2.172483 AACTACTCTGCTGCGGTGGG 62.172 60.000 14.33 9.15 0.00 4.61
1009 1429 1.215647 CGTACGGCTTCTTGCTCCT 59.784 57.895 7.57 0.00 42.39 3.69
1031 1451 2.182842 GCCTGGATTGCTACTGCCG 61.183 63.158 0.00 0.00 38.71 5.69
1430 2099 3.245229 TGACTGATATTTTGGTGTGGGCT 60.245 43.478 0.00 0.00 0.00 5.19
1478 2147 7.542025 AGATTCAAACTAAATGCTTTAGCCAG 58.458 34.615 12.68 5.94 45.05 4.85
1552 2231 5.923114 CGTCCATGATCTAGAATTCGAACAT 59.077 40.000 0.00 0.51 0.00 2.71
1554 2233 5.520632 TCGTCCATGATCTAGAATTCGAAC 58.479 41.667 0.00 0.00 0.00 3.95
1557 2236 5.923114 ACAATCGTCCATGATCTAGAATTCG 59.077 40.000 0.00 0.00 0.00 3.34
1558 2237 6.146837 CCACAATCGTCCATGATCTAGAATTC 59.853 42.308 0.00 0.00 0.00 2.17
1578 2258 4.640771 ATTCTTCCTTCTGCTACCACAA 57.359 40.909 0.00 0.00 0.00 3.33
1599 2279 8.093927 CCAGCCCTTTTTCTTTTCACAATTATA 58.906 33.333 0.00 0.00 0.00 0.98
1740 2420 9.495754 GACTGCTGTAAAATTGAAATCATACTC 57.504 33.333 0.00 0.00 0.00 2.59
1744 2424 7.230849 TGGACTGCTGTAAAATTGAAATCAT 57.769 32.000 0.00 0.00 0.00 2.45
1747 2427 7.230849 TCATGGACTGCTGTAAAATTGAAAT 57.769 32.000 0.00 0.00 0.00 2.17
1751 2431 7.622672 GCAAAATCATGGACTGCTGTAAAATTG 60.623 37.037 0.00 0.00 0.00 2.32
1762 2442 4.368315 CATGGATGCAAAATCATGGACTG 58.632 43.478 11.58 0.00 34.89 3.51
1853 2552 2.047844 TCTGCTTCAGGCTCACGC 60.048 61.111 0.00 0.00 42.39 5.34
1893 2592 2.036256 GGCATGGAGTTGGTGGCT 59.964 61.111 0.00 0.00 35.74 4.75
1923 2622 3.684990 AGCAGCACCGCGAAGAGA 61.685 61.111 8.23 0.00 36.85 3.10
2069 2768 3.876589 TTGTGAGCGAAGACGGGGC 62.877 63.158 0.00 0.00 40.15 5.80
2568 3304 2.102925 TGAGTGAGTTGTGTGCATCAGA 59.897 45.455 0.00 0.00 0.00 3.27
2673 3413 0.033504 ACATCGCGACAAAGACAGGT 59.966 50.000 12.93 0.00 0.00 4.00
2679 3419 0.716108 GACTCCACATCGCGACAAAG 59.284 55.000 12.93 7.63 0.00 2.77
2790 3530 5.921004 TGTTGCCATTTCATAAAAGTTGC 57.079 34.783 0.00 0.00 0.00 4.17
2883 3623 8.145767 CCACTCCATGCACATATCATTTATTTT 58.854 33.333 0.00 0.00 0.00 1.82
2934 3674 8.491134 AGTATTTTCTTTTGCTTTAGGGGTTTT 58.509 29.630 0.00 0.00 0.00 2.43
2948 3688 6.779860 TGGTAGGAGAGCAGTATTTTCTTTT 58.220 36.000 0.00 0.00 0.00 2.27
3021 3761 7.750014 TCATAAACACAATCATTCACGACATTG 59.250 33.333 0.00 0.00 33.27 2.82
3230 4001 9.677567 GTGTCTTGTCAATTTAACATGTGTTAT 57.322 29.630 0.00 0.00 39.89 1.89
3380 4154 2.668250 TGAAGGTCGTGTCGTGTATTG 58.332 47.619 0.00 0.00 0.00 1.90
3824 4598 9.707957 AGGATAATTTGGTTGGTATGTTCATAA 57.292 29.630 0.00 0.00 0.00 1.90
3826 4600 7.287696 GGAGGATAATTTGGTTGGTATGTTCAT 59.712 37.037 0.00 0.00 0.00 2.57
3827 4601 6.605594 GGAGGATAATTTGGTTGGTATGTTCA 59.394 38.462 0.00 0.00 0.00 3.18
3828 4602 6.040504 GGGAGGATAATTTGGTTGGTATGTTC 59.959 42.308 0.00 0.00 0.00 3.18
3831 4605 5.454062 TGGGAGGATAATTTGGTTGGTATG 58.546 41.667 0.00 0.00 0.00 2.39
3833 4607 5.454062 CATGGGAGGATAATTTGGTTGGTA 58.546 41.667 0.00 0.00 0.00 3.25
3834 4608 4.289245 CATGGGAGGATAATTTGGTTGGT 58.711 43.478 0.00 0.00 0.00 3.67
3835 4609 3.070015 GCATGGGAGGATAATTTGGTTGG 59.930 47.826 0.00 0.00 0.00 3.77
3836 4610 3.705579 TGCATGGGAGGATAATTTGGTTG 59.294 43.478 0.00 0.00 0.00 3.77
3837 4611 3.962718 CTGCATGGGAGGATAATTTGGTT 59.037 43.478 0.00 0.00 0.00 3.67
3857 4893 6.754209 AGAATGAAGTCGTACAGCTAATTCTG 59.246 38.462 15.79 0.00 39.86 3.02
3971 5011 9.383519 AGATGCTTCTGATTTTACGAGATTTTA 57.616 29.630 0.48 0.00 0.00 1.52
4039 5081 5.242434 ACAAGTTACAATGATCTAACGGCA 58.758 37.500 0.00 0.00 0.00 5.69
4157 5199 8.056407 TCGGATAAATGATCTAGTATGTCTGG 57.944 38.462 0.00 0.00 34.66 3.86
4158 5200 9.513727 CATCGGATAAATGATCTAGTATGTCTG 57.486 37.037 0.00 0.00 34.66 3.51
4187 5229 6.215121 TGTAATGGCAGTTGTGATTTTTCAG 58.785 36.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.