Multiple sequence alignment - TraesCS4D01G139600

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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 TraesCS4D01G139600 chr4D 100.000 2712 0 0 1 2712 123553392 123550681 0.000000e+00 5009.0
1 TraesCS4D01G139600 chr4D 98.065 310 6 0 1 310 135040380 135040071 8.540000e-150 540.0
2 TraesCS4D01G139600 chr7B 98.428 2417 29 2 301 2712 716875614 716878026 0.000000e+00 4244.0
3 TraesCS4D01G139600 chr7B 98.262 2417 37 1 301 2712 716835399 716837815 0.000000e+00 4226.0
4 TraesCS4D01G139600 chr7B 98.262 2417 34 2 301 2712 742992613 742990200 0.000000e+00 4224.0
5 TraesCS4D01G139600 chr1A 98.345 2417 31 2 301 2712 498688060 498690472 0.000000e+00 4233.0
6 TraesCS4D01G139600 chrUn 98.344 2415 31 2 301 2710 186205254 186207664 0.000000e+00 4229.0
7 TraesCS4D01G139600 chrUn 98.710 310 4 0 1 310 296252897 296253206 3.950000e-153 551.0
8 TraesCS4D01G139600 chrUn 98.065 310 6 0 1 310 246706119 246706428 8.540000e-150 540.0
9 TraesCS4D01G139600 chr7A 98.262 2417 33 2 301 2712 60282480 60280068 0.000000e+00 4222.0
10 TraesCS4D01G139600 chr4B 97.395 2418 52 3 301 2712 209302831 209300419 0.000000e+00 4106.0
11 TraesCS4D01G139600 chr3B 97.188 2418 56 6 301 2712 797589770 797592181 0.000000e+00 4078.0
12 TraesCS4D01G139600 chr3B 96.226 53 2 0 2542 2594 397341007 397341059 1.340000e-13 87.9
13 TraesCS4D01G139600 chr2B 97.679 2068 39 2 301 2363 391164176 391162113 0.000000e+00 3544.0
14 TraesCS4D01G139600 chr3D 98.387 310 5 0 1 310 202633337 202633646 1.840000e-151 545.0
15 TraesCS4D01G139600 chr1D 98.387 310 5 0 1 310 141349298 141348989 1.840000e-151 545.0
16 TraesCS4D01G139600 chr1D 98.065 310 6 0 1 310 350969819 350969510 8.540000e-150 540.0
17 TraesCS4D01G139600 chr6D 98.065 310 6 0 1 310 430477326 430477635 8.540000e-150 540.0
18 TraesCS4D01G139600 chr2D 98.065 310 6 0 1 310 634990744 634991053 8.540000e-150 540.0
19 TraesCS4D01G139600 chr3A 97.490 239 5 1 2421 2659 171786136 171785899 9.040000e-110 407.0
20 TraesCS4D01G139600 chr4A 97.835 231 5 0 2482 2712 302545604 302545374 1.510000e-107 399.0
21 TraesCS4D01G139600 chr4A 96.296 135 3 2 2314 2447 388429437 388429304 1.260000e-53 220.0


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 TraesCS4D01G139600 chr4D 123550681 123553392 2711 True 5009 5009 100.000 1 2712 1 chr4D.!!$R1 2711
1 TraesCS4D01G139600 chr7B 716875614 716878026 2412 False 4244 4244 98.428 301 2712 1 chr7B.!!$F2 2411
2 TraesCS4D01G139600 chr7B 716835399 716837815 2416 False 4226 4226 98.262 301 2712 1 chr7B.!!$F1 2411
3 TraesCS4D01G139600 chr7B 742990200 742992613 2413 True 4224 4224 98.262 301 2712 1 chr7B.!!$R1 2411
4 TraesCS4D01G139600 chr1A 498688060 498690472 2412 False 4233 4233 98.345 301 2712 1 chr1A.!!$F1 2411
5 TraesCS4D01G139600 chrUn 186205254 186207664 2410 False 4229 4229 98.344 301 2710 1 chrUn.!!$F1 2409
6 TraesCS4D01G139600 chr7A 60280068 60282480 2412 True 4222 4222 98.262 301 2712 1 chr7A.!!$R1 2411
7 TraesCS4D01G139600 chr4B 209300419 209302831 2412 True 4106 4106 97.395 301 2712 1 chr4B.!!$R1 2411
8 TraesCS4D01G139600 chr3B 797589770 797592181 2411 False 4078 4078 97.188 301 2712 1 chr3B.!!$F2 2411
9 TraesCS4D01G139600 chr2B 391162113 391164176 2063 True 3544 3544 97.679 301 2363 1 chr2B.!!$R1 2062

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
279 280 0.031857 TTGAAGGCCACACGCAATTG 59.968 50.0 5.01 0.0 40.31 2.32 F
286 287 0.238289 CCACACGCAATTGACTCACC 59.762 55.0 10.34 0.0 0.00 4.02 F
1572 1583 0.530288 CGTTTTCCGCCCCAAATGAT 59.470 50.0 0.00 0.0 0.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 1685 1.143373 CCAGTTACTGCGCGCGATAA 61.143 55.000 37.18 23.95 0.0 1.75 R
1675 1686 1.587876 CCAGTTACTGCGCGCGATA 60.588 57.895 37.18 20.67 0.0 2.92 R
2667 2678 2.350772 GCCGTCTGATGGAAAACAACTG 60.351 50.000 19.98 0.00 0.0 3.16 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
22 23 5.221891 CATTGTCGTCCATAGTTTCCTTG 57.778 43.478 0.00 0.00 0.00 3.61
23 24 4.345859 TTGTCGTCCATAGTTTCCTTGT 57.654 40.909 0.00 0.00 0.00 3.16
24 25 3.921677 TGTCGTCCATAGTTTCCTTGTC 58.078 45.455 0.00 0.00 0.00 3.18
25 26 2.921754 GTCGTCCATAGTTTCCTTGTCG 59.078 50.000 0.00 0.00 0.00 4.35
26 27 2.821378 TCGTCCATAGTTTCCTTGTCGA 59.179 45.455 0.00 0.00 0.00 4.20
27 28 2.921754 CGTCCATAGTTTCCTTGTCGAC 59.078 50.000 9.11 9.11 0.00 4.20
28 29 2.921754 GTCCATAGTTTCCTTGTCGACG 59.078 50.000 11.62 0.00 0.00 5.12
29 30 1.659098 CCATAGTTTCCTTGTCGACGC 59.341 52.381 11.62 0.00 0.00 5.19
30 31 1.320555 CATAGTTTCCTTGTCGACGCG 59.679 52.381 11.62 3.53 0.00 6.01
31 32 0.592637 TAGTTTCCTTGTCGACGCGA 59.407 50.000 15.93 2.92 0.00 5.87
32 33 0.249155 AGTTTCCTTGTCGACGCGAA 60.249 50.000 15.93 9.19 37.72 4.70
33 34 0.161024 GTTTCCTTGTCGACGCGAAG 59.839 55.000 15.93 9.00 37.72 3.79
34 35 0.942410 TTTCCTTGTCGACGCGAAGG 60.942 55.000 21.47 21.47 37.72 3.46
42 43 3.766691 GACGCGAAGGGGCCAGTA 61.767 66.667 15.93 0.00 45.79 2.74
43 44 3.718210 GACGCGAAGGGGCCAGTAG 62.718 68.421 15.93 0.00 45.79 2.57
53 54 2.362503 GCCAGTAGCCCCCAAACC 60.363 66.667 0.00 0.00 34.35 3.27
54 55 3.176297 CCAGTAGCCCCCAAACCA 58.824 61.111 0.00 0.00 0.00 3.67
55 56 1.462928 CCAGTAGCCCCCAAACCAA 59.537 57.895 0.00 0.00 0.00 3.67
56 57 0.178947 CCAGTAGCCCCCAAACCAAA 60.179 55.000 0.00 0.00 0.00 3.28
57 58 1.256812 CAGTAGCCCCCAAACCAAAG 58.743 55.000 0.00 0.00 0.00 2.77
58 59 0.857675 AGTAGCCCCCAAACCAAAGT 59.142 50.000 0.00 0.00 0.00 2.66
59 60 1.203013 AGTAGCCCCCAAACCAAAGTC 60.203 52.381 0.00 0.00 0.00 3.01
60 61 1.154430 TAGCCCCCAAACCAAAGTCT 58.846 50.000 0.00 0.00 0.00 3.24
61 62 0.469892 AGCCCCCAAACCAAAGTCTG 60.470 55.000 0.00 0.00 0.00 3.51
62 63 0.469144 GCCCCCAAACCAAAGTCTGA 60.469 55.000 0.00 0.00 0.00 3.27
63 64 1.620822 CCCCCAAACCAAAGTCTGAG 58.379 55.000 0.00 0.00 0.00 3.35
64 65 1.144913 CCCCCAAACCAAAGTCTGAGA 59.855 52.381 0.00 0.00 0.00 3.27
65 66 2.225117 CCCCCAAACCAAAGTCTGAGAT 60.225 50.000 0.00 0.00 0.00 2.75
66 67 3.084786 CCCCAAACCAAAGTCTGAGATC 58.915 50.000 0.00 0.00 0.00 2.75
67 68 3.498481 CCCCAAACCAAAGTCTGAGATCA 60.498 47.826 0.00 0.00 0.00 2.92
68 69 3.755378 CCCAAACCAAAGTCTGAGATCAG 59.245 47.826 3.33 3.33 45.08 2.90
80 81 3.637432 CTGAGATCAGAACTCATACCGC 58.363 50.000 10.63 0.00 46.59 5.68
81 82 2.033424 TGAGATCAGAACTCATACCGCG 59.967 50.000 6.29 0.00 39.10 6.46
82 83 1.338337 AGATCAGAACTCATACCGCGG 59.662 52.381 26.86 26.86 0.00 6.46
83 84 1.067212 GATCAGAACTCATACCGCGGT 59.933 52.381 36.01 36.01 0.00 5.68
84 85 0.892755 TCAGAACTCATACCGCGGTT 59.107 50.000 38.94 21.29 0.00 4.44
85 86 0.999406 CAGAACTCATACCGCGGTTG 59.001 55.000 38.94 30.41 0.00 3.77
86 87 0.606604 AGAACTCATACCGCGGTTGT 59.393 50.000 38.94 25.32 0.00 3.32
87 88 0.719465 GAACTCATACCGCGGTTGTG 59.281 55.000 38.94 32.12 0.00 3.33
94 95 3.283684 CCGCGGTTGTGGCTTGAA 61.284 61.111 19.50 0.00 39.30 2.69
95 96 2.252260 CGCGGTTGTGGCTTGAAG 59.748 61.111 0.00 0.00 0.00 3.02
96 97 2.644992 GCGGTTGTGGCTTGAAGG 59.355 61.111 0.00 0.00 0.00 3.46
97 98 2.644992 CGGTTGTGGCTTGAAGGC 59.355 61.111 12.27 12.27 41.77 4.35
104 105 4.503314 GGCTTGAAGGCCGCATGC 62.503 66.667 22.66 22.66 42.82 4.06
105 106 3.751246 GCTTGAAGGCCGCATGCA 61.751 61.111 24.52 7.94 43.89 3.96
106 107 2.964174 CTTGAAGGCCGCATGCAA 59.036 55.556 19.57 0.00 43.89 4.08
107 108 1.153901 CTTGAAGGCCGCATGCAAG 60.154 57.895 19.57 11.25 43.89 4.01
108 109 1.870055 CTTGAAGGCCGCATGCAAGT 61.870 55.000 19.57 0.00 43.89 3.16
109 110 1.462731 TTGAAGGCCGCATGCAAGTT 61.463 50.000 19.57 4.85 43.89 2.66
110 111 1.153958 GAAGGCCGCATGCAAGTTC 60.154 57.895 19.57 10.54 43.89 3.01
111 112 1.589716 GAAGGCCGCATGCAAGTTCT 61.590 55.000 19.57 7.56 43.89 3.01
112 113 1.181098 AAGGCCGCATGCAAGTTCTT 61.181 50.000 19.57 12.61 43.89 2.52
113 114 1.153958 GGCCGCATGCAAGTTCTTC 60.154 57.895 19.57 0.00 43.89 2.87
114 115 1.580942 GCCGCATGCAAGTTCTTCA 59.419 52.632 19.57 0.00 40.77 3.02
115 116 0.039256 GCCGCATGCAAGTTCTTCAA 60.039 50.000 19.57 0.00 40.77 2.69
116 117 1.403249 GCCGCATGCAAGTTCTTCAAT 60.403 47.619 19.57 0.00 40.77 2.57
117 118 2.159393 GCCGCATGCAAGTTCTTCAATA 60.159 45.455 19.57 0.00 40.77 1.90
118 119 3.489738 GCCGCATGCAAGTTCTTCAATAT 60.490 43.478 19.57 0.00 40.77 1.28
119 120 4.675510 CCGCATGCAAGTTCTTCAATATT 58.324 39.130 19.57 0.00 0.00 1.28
120 121 5.104374 CCGCATGCAAGTTCTTCAATATTT 58.896 37.500 19.57 0.00 0.00 1.40
121 122 6.264832 CCGCATGCAAGTTCTTCAATATTTA 58.735 36.000 19.57 0.00 0.00 1.40
122 123 6.415867 CCGCATGCAAGTTCTTCAATATTTAG 59.584 38.462 19.57 0.00 0.00 1.85
123 124 7.188834 CGCATGCAAGTTCTTCAATATTTAGA 58.811 34.615 19.57 0.00 0.00 2.10
124 125 7.375280 CGCATGCAAGTTCTTCAATATTTAGAG 59.625 37.037 19.57 0.00 0.00 2.43
125 126 8.400947 GCATGCAAGTTCTTCAATATTTAGAGA 58.599 33.333 14.21 0.00 0.00 3.10
126 127 9.932699 CATGCAAGTTCTTCAATATTTAGAGAG 57.067 33.333 0.00 0.00 0.00 3.20
127 128 9.678260 ATGCAAGTTCTTCAATATTTAGAGAGT 57.322 29.630 0.00 0.00 0.00 3.24
143 144 9.610705 ATTTAGAGAGTATGTGTTAGTACGAGA 57.389 33.333 0.00 0.00 0.00 4.04
144 145 9.610705 TTTAGAGAGTATGTGTTAGTACGAGAT 57.389 33.333 0.00 0.00 0.00 2.75
145 146 7.718272 AGAGAGTATGTGTTAGTACGAGATC 57.282 40.000 0.00 0.00 0.00 2.75
146 147 6.421501 AGAGAGTATGTGTTAGTACGAGATCG 59.578 42.308 0.00 0.00 46.33 3.69
147 148 5.050227 AGAGTATGTGTTAGTACGAGATCGC 60.050 44.000 1.39 0.00 44.43 4.58
148 149 2.447089 TGTGTTAGTACGAGATCGCG 57.553 50.000 17.67 17.67 44.43 5.87
149 150 1.110876 GTGTTAGTACGAGATCGCGC 58.889 55.000 19.16 0.00 44.43 6.86
150 151 1.012086 TGTTAGTACGAGATCGCGCT 58.988 50.000 19.16 11.11 44.43 5.92
151 152 2.033407 GTGTTAGTACGAGATCGCGCTA 60.033 50.000 19.16 10.11 44.43 4.26
152 153 2.804527 TGTTAGTACGAGATCGCGCTAT 59.195 45.455 19.16 0.00 44.43 2.97
153 154 3.120752 TGTTAGTACGAGATCGCGCTATC 60.121 47.826 19.16 13.69 44.43 2.08
154 155 1.509703 AGTACGAGATCGCGCTATCA 58.490 50.000 22.25 0.33 44.43 2.15
155 156 1.871676 AGTACGAGATCGCGCTATCAA 59.128 47.619 22.25 3.86 44.43 2.57
156 157 1.970608 GTACGAGATCGCGCTATCAAC 59.029 52.381 22.25 14.59 44.43 3.18
157 158 0.663688 ACGAGATCGCGCTATCAACT 59.336 50.000 22.25 3.39 44.43 3.16
158 159 1.065701 ACGAGATCGCGCTATCAACTT 59.934 47.619 22.25 8.14 44.43 2.66
159 160 2.289820 ACGAGATCGCGCTATCAACTTA 59.710 45.455 22.25 0.00 44.43 2.24
160 161 3.058155 ACGAGATCGCGCTATCAACTTAT 60.058 43.478 22.25 1.94 44.43 1.73
161 162 3.299281 CGAGATCGCGCTATCAACTTATG 59.701 47.826 22.25 2.13 0.00 1.90
162 163 4.230657 GAGATCGCGCTATCAACTTATGT 58.769 43.478 22.25 0.51 0.00 2.29
163 164 4.230657 AGATCGCGCTATCAACTTATGTC 58.769 43.478 22.25 0.00 0.00 3.06
164 165 3.430333 TCGCGCTATCAACTTATGTCA 57.570 42.857 5.56 0.00 0.00 3.58
165 166 3.977427 TCGCGCTATCAACTTATGTCAT 58.023 40.909 5.56 0.00 0.00 3.06
166 167 3.981416 TCGCGCTATCAACTTATGTCATC 59.019 43.478 5.56 0.00 0.00 2.92
167 168 3.983988 CGCGCTATCAACTTATGTCATCT 59.016 43.478 5.56 0.00 0.00 2.90
168 169 4.445718 CGCGCTATCAACTTATGTCATCTT 59.554 41.667 5.56 0.00 0.00 2.40
169 170 5.050769 CGCGCTATCAACTTATGTCATCTTT 60.051 40.000 5.56 0.00 0.00 2.52
170 171 6.358762 GCGCTATCAACTTATGTCATCTTTC 58.641 40.000 0.00 0.00 0.00 2.62
171 172 6.201806 GCGCTATCAACTTATGTCATCTTTCT 59.798 38.462 0.00 0.00 0.00 2.52
172 173 7.568497 GCGCTATCAACTTATGTCATCTTTCTC 60.568 40.741 0.00 0.00 0.00 2.87
173 174 7.357941 CGCTATCAACTTATGTCATCTTTCTCG 60.358 40.741 0.00 0.00 0.00 4.04
174 175 7.649705 GCTATCAACTTATGTCATCTTTCTCGA 59.350 37.037 0.00 0.00 0.00 4.04
175 176 9.689976 CTATCAACTTATGTCATCTTTCTCGAT 57.310 33.333 0.00 0.00 0.00 3.59
176 177 7.761651 TCAACTTATGTCATCTTTCTCGATG 57.238 36.000 0.00 0.00 41.64 3.84
177 178 7.547227 TCAACTTATGTCATCTTTCTCGATGA 58.453 34.615 0.00 0.00 45.46 2.92
185 186 6.715347 TCATCTTTCTCGATGATTAGGACA 57.285 37.500 0.00 0.00 43.47 4.02
186 187 7.112452 TCATCTTTCTCGATGATTAGGACAA 57.888 36.000 0.00 0.00 43.47 3.18
187 188 7.555965 TCATCTTTCTCGATGATTAGGACAAA 58.444 34.615 0.00 0.00 43.47 2.83
188 189 8.040727 TCATCTTTCTCGATGATTAGGACAAAA 58.959 33.333 0.00 0.00 43.47 2.44
189 190 8.834465 CATCTTTCTCGATGATTAGGACAAAAT 58.166 33.333 0.00 0.00 42.63 1.82
190 191 8.792830 TCTTTCTCGATGATTAGGACAAAATT 57.207 30.769 0.00 0.00 0.00 1.82
191 192 8.668353 TCTTTCTCGATGATTAGGACAAAATTG 58.332 33.333 0.00 0.00 0.00 2.32
192 193 7.921786 TTCTCGATGATTAGGACAAAATTGT 57.078 32.000 0.00 0.00 45.65 2.71
193 194 9.443323 TTTCTCGATGATTAGGACAAAATTGTA 57.557 29.630 0.00 0.00 42.43 2.41
194 195 9.613428 TTCTCGATGATTAGGACAAAATTGTAT 57.387 29.630 0.00 0.00 42.43 2.29
195 196 9.261180 TCTCGATGATTAGGACAAAATTGTATC 57.739 33.333 0.00 0.00 42.43 2.24
196 197 8.378172 TCGATGATTAGGACAAAATTGTATCC 57.622 34.615 0.00 0.00 42.43 2.59
197 198 7.444183 TCGATGATTAGGACAAAATTGTATCCC 59.556 37.037 0.00 0.00 42.43 3.85
198 199 7.445402 CGATGATTAGGACAAAATTGTATCCCT 59.555 37.037 9.24 9.24 42.43 4.20
199 200 9.136323 GATGATTAGGACAAAATTGTATCCCTT 57.864 33.333 9.48 0.00 42.43 3.95
201 202 9.627123 TGATTAGGACAAAATTGTATCCCTTAG 57.373 33.333 9.48 0.00 42.43 2.18
202 203 8.996651 ATTAGGACAAAATTGTATCCCTTAGG 57.003 34.615 9.48 0.00 42.43 2.69
203 204 6.652205 AGGACAAAATTGTATCCCTTAGGA 57.348 37.500 0.00 0.00 44.15 2.94
204 205 7.039722 AGGACAAAATTGTATCCCTTAGGAA 57.960 36.000 0.00 0.00 43.57 3.36
205 206 6.890268 AGGACAAAATTGTATCCCTTAGGAAC 59.110 38.462 0.00 0.00 43.57 3.62
206 207 6.096423 GGACAAAATTGTATCCCTTAGGAACC 59.904 42.308 0.00 0.00 43.57 3.62
207 208 5.650703 ACAAAATTGTATCCCTTAGGAACCG 59.349 40.000 0.00 0.00 38.89 4.44
208 209 6.748908 ACAAAATTGTATCCCTTAGGAACCGT 60.749 38.462 0.00 0.00 38.89 4.83
209 210 7.529220 ACAAAATTGTATCCCTTAGGAACCGTA 60.529 37.037 0.00 0.00 38.89 4.02
214 215 1.483415 TCCCTTAGGAACCGTACATGC 59.517 52.381 0.00 0.00 40.08 4.06
215 216 1.208535 CCCTTAGGAACCGTACATGCA 59.791 52.381 0.00 0.00 33.47 3.96
216 217 2.277084 CCTTAGGAACCGTACATGCAC 58.723 52.381 0.00 0.00 0.00 4.57
217 218 2.277084 CTTAGGAACCGTACATGCACC 58.723 52.381 0.00 0.00 0.00 5.01
218 219 1.563924 TAGGAACCGTACATGCACCT 58.436 50.000 0.00 0.00 0.00 4.00
219 220 0.690762 AGGAACCGTACATGCACCTT 59.309 50.000 0.00 0.00 0.00 3.50
220 221 1.073284 AGGAACCGTACATGCACCTTT 59.927 47.619 0.00 0.00 0.00 3.11
221 222 1.199097 GGAACCGTACATGCACCTTTG 59.801 52.381 0.00 0.00 0.00 2.77
222 223 1.877443 GAACCGTACATGCACCTTTGT 59.123 47.619 0.00 0.00 0.00 2.83
223 224 1.975660 ACCGTACATGCACCTTTGTT 58.024 45.000 0.00 0.00 0.00 2.83
224 225 2.303175 ACCGTACATGCACCTTTGTTT 58.697 42.857 0.00 0.00 0.00 2.83
225 226 2.034053 ACCGTACATGCACCTTTGTTTG 59.966 45.455 0.00 0.00 0.00 2.93
226 227 2.606795 CCGTACATGCACCTTTGTTTGG 60.607 50.000 0.00 0.00 0.00 3.28
227 228 2.292016 CGTACATGCACCTTTGTTTGGA 59.708 45.455 0.00 0.00 0.00 3.53
228 229 3.057596 CGTACATGCACCTTTGTTTGGAT 60.058 43.478 0.00 0.00 0.00 3.41
229 230 3.389925 ACATGCACCTTTGTTTGGATG 57.610 42.857 0.00 1.99 44.63 3.51
230 231 2.070783 CATGCACCTTTGTTTGGATGC 58.929 47.619 0.00 0.00 35.19 3.91
231 232 0.392336 TGCACCTTTGTTTGGATGCC 59.608 50.000 0.00 0.00 33.70 4.40
232 233 0.667184 GCACCTTTGTTTGGATGCCG 60.667 55.000 0.00 0.00 0.00 5.69
233 234 0.958091 CACCTTTGTTTGGATGCCGA 59.042 50.000 0.00 0.00 0.00 5.54
234 235 1.545582 CACCTTTGTTTGGATGCCGAT 59.454 47.619 0.00 0.00 0.00 4.18
235 236 1.818674 ACCTTTGTTTGGATGCCGATC 59.181 47.619 0.00 0.00 0.00 3.69
236 237 2.094675 CCTTTGTTTGGATGCCGATCT 58.905 47.619 0.00 0.00 0.00 2.75
237 238 3.278574 CCTTTGTTTGGATGCCGATCTA 58.721 45.455 0.00 0.00 0.00 1.98
238 239 3.694072 CCTTTGTTTGGATGCCGATCTAA 59.306 43.478 0.00 0.00 0.00 2.10
239 240 4.339247 CCTTTGTTTGGATGCCGATCTAAT 59.661 41.667 0.00 0.00 29.90 1.73
240 241 5.530915 CCTTTGTTTGGATGCCGATCTAATA 59.469 40.000 0.00 0.00 29.90 0.98
241 242 6.207417 CCTTTGTTTGGATGCCGATCTAATAT 59.793 38.462 0.00 0.00 29.90 1.28
242 243 7.255590 CCTTTGTTTGGATGCCGATCTAATATT 60.256 37.037 0.00 0.00 29.90 1.28
243 244 6.558771 TGTTTGGATGCCGATCTAATATTG 57.441 37.500 0.00 0.00 29.90 1.90
244 245 6.061441 TGTTTGGATGCCGATCTAATATTGT 58.939 36.000 0.00 0.00 29.90 2.71
245 246 6.545666 TGTTTGGATGCCGATCTAATATTGTT 59.454 34.615 0.00 0.00 29.90 2.83
246 247 7.717436 TGTTTGGATGCCGATCTAATATTGTTA 59.283 33.333 0.00 0.00 29.90 2.41
247 248 7.667043 TTGGATGCCGATCTAATATTGTTAC 57.333 36.000 0.00 0.00 0.00 2.50
248 249 6.764379 TGGATGCCGATCTAATATTGTTACA 58.236 36.000 0.00 0.00 0.00 2.41
249 250 7.220740 TGGATGCCGATCTAATATTGTTACAA 58.779 34.615 0.00 0.00 0.00 2.41
250 251 7.882791 TGGATGCCGATCTAATATTGTTACAAT 59.117 33.333 15.22 15.22 0.00 2.71
251 252 9.378551 GGATGCCGATCTAATATTGTTACAATA 57.621 33.333 18.47 18.47 0.00 1.90
254 255 9.936759 TGCCGATCTAATATTGTTACAATATGA 57.063 29.630 25.45 20.13 0.00 2.15
268 269 8.682710 TGTTACAATATGAAATACTTGAAGGCC 58.317 33.333 0.00 0.00 0.00 5.19
269 270 8.682710 GTTACAATATGAAATACTTGAAGGCCA 58.317 33.333 5.01 0.00 0.00 5.36
270 271 7.100458 ACAATATGAAATACTTGAAGGCCAC 57.900 36.000 5.01 0.00 0.00 5.01
271 272 6.663093 ACAATATGAAATACTTGAAGGCCACA 59.337 34.615 5.01 1.11 0.00 4.17
272 273 6.699575 ATATGAAATACTTGAAGGCCACAC 57.300 37.500 5.01 0.00 0.00 3.82
273 274 2.811431 TGAAATACTTGAAGGCCACACG 59.189 45.455 5.01 5.15 0.00 4.49
274 275 1.165270 AATACTTGAAGGCCACACGC 58.835 50.000 5.01 0.00 0.00 5.34
275 276 0.036164 ATACTTGAAGGCCACACGCA 59.964 50.000 5.01 0.00 40.31 5.24
276 277 0.179043 TACTTGAAGGCCACACGCAA 60.179 50.000 5.01 0.31 40.31 4.85
277 278 0.823356 ACTTGAAGGCCACACGCAAT 60.823 50.000 5.01 0.00 40.31 3.56
278 279 0.314935 CTTGAAGGCCACACGCAATT 59.685 50.000 5.01 0.00 40.31 2.32
279 280 0.031857 TTGAAGGCCACACGCAATTG 59.968 50.000 5.01 0.00 40.31 2.32
280 281 0.821301 TGAAGGCCACACGCAATTGA 60.821 50.000 10.34 0.00 40.31 2.57
281 282 0.387239 GAAGGCCACACGCAATTGAC 60.387 55.000 10.34 0.00 40.31 3.18
282 283 0.823356 AAGGCCACACGCAATTGACT 60.823 50.000 10.34 0.00 40.31 3.41
283 284 1.210155 GGCCACACGCAATTGACTC 59.790 57.895 10.34 0.00 40.31 3.36
284 285 1.514678 GGCCACACGCAATTGACTCA 61.515 55.000 10.34 0.00 40.31 3.41
285 286 0.385974 GCCACACGCAATTGACTCAC 60.386 55.000 10.34 0.00 37.47 3.51
286 287 0.238289 CCACACGCAATTGACTCACC 59.762 55.000 10.34 0.00 0.00 4.02
287 288 1.229428 CACACGCAATTGACTCACCT 58.771 50.000 10.34 0.00 0.00 4.00
288 289 2.412870 CACACGCAATTGACTCACCTA 58.587 47.619 10.34 0.00 0.00 3.08
289 290 2.157668 CACACGCAATTGACTCACCTAC 59.842 50.000 10.34 0.00 0.00 3.18
290 291 2.224185 ACACGCAATTGACTCACCTACA 60.224 45.455 10.34 0.00 0.00 2.74
291 292 3.002791 CACGCAATTGACTCACCTACAT 58.997 45.455 10.34 0.00 0.00 2.29
292 293 3.436704 CACGCAATTGACTCACCTACATT 59.563 43.478 10.34 0.00 0.00 2.71
293 294 4.072131 ACGCAATTGACTCACCTACATTT 58.928 39.130 10.34 0.00 0.00 2.32
294 295 4.518970 ACGCAATTGACTCACCTACATTTT 59.481 37.500 10.34 0.00 0.00 1.82
295 296 5.703592 ACGCAATTGACTCACCTACATTTTA 59.296 36.000 10.34 0.00 0.00 1.52
296 297 6.374333 ACGCAATTGACTCACCTACATTTTAT 59.626 34.615 10.34 0.00 0.00 1.40
297 298 6.688385 CGCAATTGACTCACCTACATTTTATG 59.312 38.462 10.34 0.00 0.00 1.90
298 299 6.473455 GCAATTGACTCACCTACATTTTATGC 59.527 38.462 10.34 0.00 0.00 3.14
299 300 7.629222 GCAATTGACTCACCTACATTTTATGCT 60.629 37.037 10.34 0.00 0.00 3.79
739 740 6.459066 AGATGATTCTTTCTTTGTCGAGACA 58.541 36.000 1.24 1.24 39.98 3.41
765 767 2.755103 AGGAACCCATCTTTTCGATTGC 59.245 45.455 0.00 0.00 0.00 3.56
1125 1132 2.365105 CCCCTTCCCGGCTACTGA 60.365 66.667 0.00 0.00 0.00 3.41
1489 1500 3.780804 TTTCTTCATTGGAGGGTTCGA 57.219 42.857 0.00 0.00 0.00 3.71
1572 1583 0.530288 CGTTTTCCGCCCCAAATGAT 59.470 50.000 0.00 0.00 0.00 2.45
1674 1685 1.133136 ACGGGGAGCACCTCAGTATAT 60.133 52.381 0.00 0.00 40.03 0.86
1675 1686 1.971357 CGGGGAGCACCTCAGTATATT 59.029 52.381 0.00 0.00 40.03 1.28
1730 1741 0.609131 AGGCCAACTTCCATTCACCG 60.609 55.000 5.01 0.00 0.00 4.94
1783 1794 4.341520 GGACTCGTACAAGGATATGGAGTT 59.658 45.833 0.00 0.00 0.00 3.01
1953 1964 4.749099 ACGACCTATAACGCTAGTCACTAG 59.251 45.833 7.56 7.56 37.16 2.57
2429 2440 6.258727 ACGTGACATATTTGCAGAAATAGAGG 59.741 38.462 0.00 0.00 37.44 3.69
2667 2678 1.687628 CTCTCTGAACCGAACGTGAC 58.312 55.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.695455 ACAAGGAAACTATGGACGACAATG 59.305 41.667 0.00 0.00 42.68 2.82
1 2 4.906618 ACAAGGAAACTATGGACGACAAT 58.093 39.130 0.00 0.00 42.68 2.71
2 3 4.312443 GACAAGGAAACTATGGACGACAA 58.688 43.478 0.00 0.00 42.68 3.18
3 4 3.613193 CGACAAGGAAACTATGGACGACA 60.613 47.826 0.00 0.00 42.68 4.35
4 5 2.921754 CGACAAGGAAACTATGGACGAC 59.078 50.000 0.00 0.00 42.68 4.34
5 6 2.821378 TCGACAAGGAAACTATGGACGA 59.179 45.455 0.00 0.00 42.68 4.20
6 7 2.921754 GTCGACAAGGAAACTATGGACG 59.078 50.000 11.55 0.00 42.68 4.79
7 8 2.921754 CGTCGACAAGGAAACTATGGAC 59.078 50.000 17.16 0.00 42.68 4.02
8 9 2.673043 GCGTCGACAAGGAAACTATGGA 60.673 50.000 17.16 0.00 42.68 3.41
9 10 1.659098 GCGTCGACAAGGAAACTATGG 59.341 52.381 17.16 0.00 42.68 2.74
10 11 1.320555 CGCGTCGACAAGGAAACTATG 59.679 52.381 17.16 0.00 42.68 2.23
11 12 1.200716 TCGCGTCGACAAGGAAACTAT 59.799 47.619 17.16 0.00 42.68 2.12
12 13 0.592637 TCGCGTCGACAAGGAAACTA 59.407 50.000 17.16 0.00 42.68 2.24
13 14 0.249155 TTCGCGTCGACAAGGAAACT 60.249 50.000 17.16 0.00 37.87 2.66
14 15 0.161024 CTTCGCGTCGACAAGGAAAC 59.839 55.000 17.16 0.00 34.89 2.78
15 16 0.942410 CCTTCGCGTCGACAAGGAAA 60.942 55.000 22.52 6.52 36.36 3.13
16 17 1.372499 CCTTCGCGTCGACAAGGAA 60.372 57.895 22.52 16.63 36.36 3.36
17 18 2.257371 CCTTCGCGTCGACAAGGA 59.743 61.111 22.52 10.90 36.36 3.36
18 19 2.809601 CCCTTCGCGTCGACAAGG 60.810 66.667 20.84 20.84 34.89 3.61
19 20 2.809601 CCCCTTCGCGTCGACAAG 60.810 66.667 17.16 11.45 34.89 3.16
25 26 3.718210 CTACTGGCCCCTTCGCGTC 62.718 68.421 5.77 0.00 0.00 5.19
26 27 3.771160 CTACTGGCCCCTTCGCGT 61.771 66.667 5.77 0.00 0.00 6.01
36 37 2.362503 GGTTTGGGGGCTACTGGC 60.363 66.667 0.00 0.00 40.90 4.85
37 38 0.178947 TTTGGTTTGGGGGCTACTGG 60.179 55.000 0.00 0.00 0.00 4.00
38 39 1.256812 CTTTGGTTTGGGGGCTACTG 58.743 55.000 0.00 0.00 0.00 2.74
39 40 0.857675 ACTTTGGTTTGGGGGCTACT 59.142 50.000 0.00 0.00 0.00 2.57
40 41 1.203013 AGACTTTGGTTTGGGGGCTAC 60.203 52.381 0.00 0.00 0.00 3.58
41 42 1.154430 AGACTTTGGTTTGGGGGCTA 58.846 50.000 0.00 0.00 0.00 3.93
42 43 0.469892 CAGACTTTGGTTTGGGGGCT 60.470 55.000 0.00 0.00 0.00 5.19
43 44 0.469144 TCAGACTTTGGTTTGGGGGC 60.469 55.000 0.00 0.00 0.00 5.80
44 45 1.144913 TCTCAGACTTTGGTTTGGGGG 59.855 52.381 0.00 0.00 30.06 5.40
45 46 2.656947 TCTCAGACTTTGGTTTGGGG 57.343 50.000 0.00 0.00 30.06 4.96
46 47 3.754965 TGATCTCAGACTTTGGTTTGGG 58.245 45.455 0.00 0.00 30.26 4.12
59 60 3.637432 GCGGTATGAGTTCTGATCTCAG 58.363 50.000 19.74 10.11 43.66 3.35
60 61 2.033424 CGCGGTATGAGTTCTGATCTCA 59.967 50.000 17.97 17.97 44.37 3.27
61 62 2.605823 CCGCGGTATGAGTTCTGATCTC 60.606 54.545 19.50 8.48 0.00 2.75
62 63 1.338337 CCGCGGTATGAGTTCTGATCT 59.662 52.381 19.50 0.00 0.00 2.75
63 64 1.067212 ACCGCGGTATGAGTTCTGATC 59.933 52.381 33.34 0.00 0.00 2.92
64 65 1.112113 ACCGCGGTATGAGTTCTGAT 58.888 50.000 33.34 0.00 0.00 2.90
65 66 0.892755 AACCGCGGTATGAGTTCTGA 59.107 50.000 34.44 0.00 0.00 3.27
66 67 0.999406 CAACCGCGGTATGAGTTCTG 59.001 55.000 34.44 19.80 0.00 3.02
67 68 0.606604 ACAACCGCGGTATGAGTTCT 59.393 50.000 34.44 10.71 0.00 3.01
68 69 0.719465 CACAACCGCGGTATGAGTTC 59.281 55.000 34.44 0.00 0.00 3.01
69 70 0.672401 CCACAACCGCGGTATGAGTT 60.672 55.000 33.08 16.88 0.00 3.01
70 71 1.079405 CCACAACCGCGGTATGAGT 60.079 57.895 33.08 25.18 0.00 3.41
71 72 2.461110 GCCACAACCGCGGTATGAG 61.461 63.158 33.08 26.95 0.00 2.90
72 73 2.435234 GCCACAACCGCGGTATGA 60.435 61.111 33.08 0.00 0.00 2.15
73 74 2.038269 AAGCCACAACCGCGGTATG 61.038 57.895 34.44 30.22 0.00 2.39
74 75 2.038269 CAAGCCACAACCGCGGTAT 61.038 57.895 34.44 20.88 0.00 2.73
75 76 2.661840 TTCAAGCCACAACCGCGGTA 62.662 55.000 34.44 9.82 0.00 4.02
76 77 4.555709 TCAAGCCACAACCGCGGT 62.556 61.111 28.70 28.70 0.00 5.68
77 78 3.254014 CTTCAAGCCACAACCGCGG 62.254 63.158 26.86 26.86 0.00 6.46
78 79 2.252260 CTTCAAGCCACAACCGCG 59.748 61.111 0.00 0.00 0.00 6.46
79 80 2.644992 CCTTCAAGCCACAACCGC 59.355 61.111 0.00 0.00 0.00 5.68
80 81 2.644992 GCCTTCAAGCCACAACCG 59.355 61.111 0.00 0.00 0.00 4.44
88 89 3.285523 TTGCATGCGGCCTTCAAGC 62.286 57.895 14.09 13.08 43.89 4.01
89 90 1.153901 CTTGCATGCGGCCTTCAAG 60.154 57.895 14.09 5.24 43.89 3.02
90 91 1.462731 AACTTGCATGCGGCCTTCAA 61.463 50.000 14.09 0.00 43.89 2.69
91 92 1.865788 GAACTTGCATGCGGCCTTCA 61.866 55.000 14.09 0.00 43.89 3.02
92 93 1.153958 GAACTTGCATGCGGCCTTC 60.154 57.895 14.09 7.27 43.89 3.46
93 94 1.181098 AAGAACTTGCATGCGGCCTT 61.181 50.000 14.09 11.78 43.89 4.35
94 95 1.589716 GAAGAACTTGCATGCGGCCT 61.590 55.000 14.09 6.67 43.89 5.19
95 96 1.153958 GAAGAACTTGCATGCGGCC 60.154 57.895 14.09 0.00 43.89 6.13
96 97 0.039256 TTGAAGAACTTGCATGCGGC 60.039 50.000 14.09 0.00 45.13 6.53
97 98 2.642139 ATTGAAGAACTTGCATGCGG 57.358 45.000 14.09 10.98 0.00 5.69
98 99 7.188834 TCTAAATATTGAAGAACTTGCATGCG 58.811 34.615 14.09 1.59 0.00 4.73
99 100 8.400947 TCTCTAAATATTGAAGAACTTGCATGC 58.599 33.333 11.82 11.82 0.00 4.06
100 101 9.932699 CTCTCTAAATATTGAAGAACTTGCATG 57.067 33.333 0.00 0.00 0.00 4.06
101 102 9.678260 ACTCTCTAAATATTGAAGAACTTGCAT 57.322 29.630 0.00 0.00 0.00 3.96
117 118 9.610705 TCTCGTACTAACACATACTCTCTAAAT 57.389 33.333 0.00 0.00 0.00 1.40
118 119 9.610705 ATCTCGTACTAACACATACTCTCTAAA 57.389 33.333 0.00 0.00 0.00 1.85
119 120 9.258826 GATCTCGTACTAACACATACTCTCTAA 57.741 37.037 0.00 0.00 0.00 2.10
120 121 7.594386 CGATCTCGTACTAACACATACTCTCTA 59.406 40.741 0.00 0.00 34.11 2.43
121 122 6.421501 CGATCTCGTACTAACACATACTCTCT 59.578 42.308 0.00 0.00 34.11 3.10
122 123 6.583160 CGATCTCGTACTAACACATACTCTC 58.417 44.000 0.00 0.00 34.11 3.20
123 124 5.050227 GCGATCTCGTACTAACACATACTCT 60.050 44.000 1.14 0.00 42.22 3.24
124 125 5.138788 GCGATCTCGTACTAACACATACTC 58.861 45.833 1.14 0.00 42.22 2.59
125 126 4.318618 CGCGATCTCGTACTAACACATACT 60.319 45.833 0.00 0.00 42.22 2.12
126 127 3.898946 CGCGATCTCGTACTAACACATAC 59.101 47.826 0.00 0.00 42.22 2.39
127 128 3.605461 GCGCGATCTCGTACTAACACATA 60.605 47.826 12.10 0.00 42.22 2.29
128 129 2.853662 GCGCGATCTCGTACTAACACAT 60.854 50.000 12.10 0.00 42.22 3.21
129 130 1.530441 GCGCGATCTCGTACTAACACA 60.530 52.381 12.10 0.00 42.22 3.72
130 131 1.110876 GCGCGATCTCGTACTAACAC 58.889 55.000 12.10 0.00 42.22 3.32
131 132 1.012086 AGCGCGATCTCGTACTAACA 58.988 50.000 12.10 0.00 42.22 2.41
132 133 2.937994 TAGCGCGATCTCGTACTAAC 57.062 50.000 12.10 0.00 42.22 2.34
133 134 3.062042 TGATAGCGCGATCTCGTACTAA 58.938 45.455 27.21 5.55 42.22 2.24
134 135 2.680577 TGATAGCGCGATCTCGTACTA 58.319 47.619 27.21 6.24 42.22 1.82
135 136 1.509703 TGATAGCGCGATCTCGTACT 58.490 50.000 27.21 0.00 42.22 2.73
136 137 1.970608 GTTGATAGCGCGATCTCGTAC 59.029 52.381 27.21 16.94 42.22 3.67
137 138 1.871676 AGTTGATAGCGCGATCTCGTA 59.128 47.619 27.21 7.97 42.22 3.43
138 139 0.663688 AGTTGATAGCGCGATCTCGT 59.336 50.000 27.21 11.53 42.22 4.18
139 140 1.759994 AAGTTGATAGCGCGATCTCG 58.240 50.000 27.21 0.00 43.27 4.04
140 141 4.230657 ACATAAGTTGATAGCGCGATCTC 58.769 43.478 27.21 20.13 0.00 2.75
141 142 4.230657 GACATAAGTTGATAGCGCGATCT 58.769 43.478 27.21 12.53 0.00 2.75
142 143 3.981416 TGACATAAGTTGATAGCGCGATC 59.019 43.478 21.90 21.90 0.00 3.69
143 144 3.977427 TGACATAAGTTGATAGCGCGAT 58.023 40.909 12.10 5.99 0.00 4.58
144 145 3.430333 TGACATAAGTTGATAGCGCGA 57.570 42.857 12.10 0.00 0.00 5.87
145 146 3.983988 AGATGACATAAGTTGATAGCGCG 59.016 43.478 0.00 0.00 0.00 6.86
146 147 5.914085 AAGATGACATAAGTTGATAGCGC 57.086 39.130 0.00 0.00 0.00 5.92
147 148 7.357941 CGAGAAAGATGACATAAGTTGATAGCG 60.358 40.741 0.00 0.00 0.00 4.26
148 149 7.649705 TCGAGAAAGATGACATAAGTTGATAGC 59.350 37.037 0.00 0.00 0.00 2.97
149 150 9.689976 ATCGAGAAAGATGACATAAGTTGATAG 57.310 33.333 0.00 0.00 0.00 2.08
163 164 7.776933 TTTGTCCTAATCATCGAGAAAGATG 57.223 36.000 0.00 0.89 46.90 2.90
164 165 8.970859 ATTTTGTCCTAATCATCGAGAAAGAT 57.029 30.769 0.00 0.00 0.00 2.40
165 166 8.668353 CAATTTTGTCCTAATCATCGAGAAAGA 58.332 33.333 0.00 0.00 0.00 2.52
166 167 8.454106 ACAATTTTGTCCTAATCATCGAGAAAG 58.546 33.333 0.00 0.00 36.50 2.62
167 168 8.335532 ACAATTTTGTCCTAATCATCGAGAAA 57.664 30.769 0.00 0.00 36.50 2.52
168 169 7.921786 ACAATTTTGTCCTAATCATCGAGAA 57.078 32.000 0.00 0.00 36.50 2.87
169 170 9.261180 GATACAATTTTGTCCTAATCATCGAGA 57.739 33.333 0.00 0.00 42.35 4.04
170 171 8.499162 GGATACAATTTTGTCCTAATCATCGAG 58.501 37.037 0.00 0.00 42.35 4.04
171 172 7.444183 GGGATACAATTTTGTCCTAATCATCGA 59.556 37.037 7.25 0.00 42.35 3.59
172 173 7.445402 AGGGATACAATTTTGTCCTAATCATCG 59.555 37.037 7.25 0.00 42.35 3.84
173 174 8.697507 AGGGATACAATTTTGTCCTAATCATC 57.302 34.615 7.25 0.00 42.35 2.92
175 176 9.627123 CTAAGGGATACAATTTTGTCCTAATCA 57.373 33.333 7.25 0.00 42.35 2.57
176 177 9.067986 CCTAAGGGATACAATTTTGTCCTAATC 57.932 37.037 7.25 0.00 37.42 1.75
177 178 8.787818 TCCTAAGGGATACAATTTTGTCCTAAT 58.212 33.333 7.25 0.00 38.43 1.73
178 179 8.165267 TCCTAAGGGATACAATTTTGTCCTAA 57.835 34.615 7.25 0.00 38.43 2.69
179 180 7.758820 TCCTAAGGGATACAATTTTGTCCTA 57.241 36.000 7.25 0.00 38.43 2.94
180 181 6.652205 TCCTAAGGGATACAATTTTGTCCT 57.348 37.500 7.25 0.00 38.43 3.85
181 182 6.096423 GGTTCCTAAGGGATACAATTTTGTCC 59.904 42.308 0.00 0.00 41.87 4.02
182 183 6.183360 CGGTTCCTAAGGGATACAATTTTGTC 60.183 42.308 0.00 0.00 41.87 3.18
183 184 5.650703 CGGTTCCTAAGGGATACAATTTTGT 59.349 40.000 1.08 1.08 41.87 2.83
184 185 5.650703 ACGGTTCCTAAGGGATACAATTTTG 59.349 40.000 0.00 0.00 41.87 2.44
185 186 5.823312 ACGGTTCCTAAGGGATACAATTTT 58.177 37.500 0.00 0.00 41.87 1.82
186 187 5.446260 ACGGTTCCTAAGGGATACAATTT 57.554 39.130 0.00 0.00 41.87 1.82
187 188 5.426185 TGTACGGTTCCTAAGGGATACAATT 59.574 40.000 0.00 0.00 41.87 2.32
188 189 4.964262 TGTACGGTTCCTAAGGGATACAAT 59.036 41.667 0.00 0.00 41.87 2.71
189 190 4.352009 TGTACGGTTCCTAAGGGATACAA 58.648 43.478 0.00 0.00 41.87 2.41
190 191 3.979911 TGTACGGTTCCTAAGGGATACA 58.020 45.455 0.00 0.00 41.87 2.29
191 192 4.798593 GCATGTACGGTTCCTAAGGGATAC 60.799 50.000 0.00 0.00 41.87 2.24
192 193 3.322828 GCATGTACGGTTCCTAAGGGATA 59.677 47.826 0.00 0.00 41.87 2.59
193 194 2.104281 GCATGTACGGTTCCTAAGGGAT 59.896 50.000 0.00 0.00 41.87 3.85
194 195 1.483415 GCATGTACGGTTCCTAAGGGA 59.517 52.381 0.00 0.00 40.36 4.20
195 196 1.208535 TGCATGTACGGTTCCTAAGGG 59.791 52.381 0.00 0.00 0.00 3.95
196 197 2.277084 GTGCATGTACGGTTCCTAAGG 58.723 52.381 0.00 0.00 0.00 2.69
197 198 2.093658 AGGTGCATGTACGGTTCCTAAG 60.094 50.000 7.89 0.00 0.00 2.18
198 199 1.903860 AGGTGCATGTACGGTTCCTAA 59.096 47.619 7.89 0.00 0.00 2.69
199 200 1.563924 AGGTGCATGTACGGTTCCTA 58.436 50.000 7.89 0.00 0.00 2.94
200 201 0.690762 AAGGTGCATGTACGGTTCCT 59.309 50.000 7.89 0.00 0.00 3.36
201 202 1.199097 CAAAGGTGCATGTACGGTTCC 59.801 52.381 7.89 0.00 0.00 3.62
202 203 1.877443 ACAAAGGTGCATGTACGGTTC 59.123 47.619 7.89 0.00 0.00 3.62
203 204 1.975660 ACAAAGGTGCATGTACGGTT 58.024 45.000 7.89 1.32 0.00 4.44
204 205 1.975660 AACAAAGGTGCATGTACGGT 58.024 45.000 7.89 1.11 0.00 4.83
205 206 2.606795 CCAAACAAAGGTGCATGTACGG 60.607 50.000 7.89 0.00 0.00 4.02
206 207 2.292016 TCCAAACAAAGGTGCATGTACG 59.708 45.455 7.89 0.00 0.00 3.67
207 208 4.236935 CATCCAAACAAAGGTGCATGTAC 58.763 43.478 5.22 5.22 0.00 2.90
208 209 3.305950 GCATCCAAACAAAGGTGCATGTA 60.306 43.478 0.00 0.00 35.03 2.29
209 210 2.548493 GCATCCAAACAAAGGTGCATGT 60.548 45.455 0.00 0.00 35.03 3.21
210 211 2.070783 GCATCCAAACAAAGGTGCATG 58.929 47.619 0.00 0.00 35.03 4.06
211 212 1.002315 GGCATCCAAACAAAGGTGCAT 59.998 47.619 0.00 0.00 35.94 3.96
212 213 0.392336 GGCATCCAAACAAAGGTGCA 59.608 50.000 0.00 0.00 35.94 4.57
213 214 0.667184 CGGCATCCAAACAAAGGTGC 60.667 55.000 0.00 0.00 34.54 5.01
214 215 0.958091 TCGGCATCCAAACAAAGGTG 59.042 50.000 0.00 0.00 0.00 4.00
215 216 1.818674 GATCGGCATCCAAACAAAGGT 59.181 47.619 0.00 0.00 0.00 3.50
216 217 2.094675 AGATCGGCATCCAAACAAAGG 58.905 47.619 0.00 0.00 0.00 3.11
217 218 4.963276 TTAGATCGGCATCCAAACAAAG 57.037 40.909 0.00 0.00 0.00 2.77
218 219 7.068103 ACAATATTAGATCGGCATCCAAACAAA 59.932 33.333 0.00 0.00 0.00 2.83
219 220 6.545666 ACAATATTAGATCGGCATCCAAACAA 59.454 34.615 0.00 0.00 0.00 2.83
220 221 6.061441 ACAATATTAGATCGGCATCCAAACA 58.939 36.000 0.00 0.00 0.00 2.83
221 222 6.560253 ACAATATTAGATCGGCATCCAAAC 57.440 37.500 0.00 0.00 0.00 2.93
222 223 7.717436 TGTAACAATATTAGATCGGCATCCAAA 59.283 33.333 0.00 0.00 0.00 3.28
223 224 7.220740 TGTAACAATATTAGATCGGCATCCAA 58.779 34.615 0.00 0.00 0.00 3.53
224 225 6.764379 TGTAACAATATTAGATCGGCATCCA 58.236 36.000 0.00 0.00 0.00 3.41
225 226 7.667043 TTGTAACAATATTAGATCGGCATCC 57.333 36.000 0.00 0.00 0.00 3.51
228 229 9.936759 TCATATTGTAACAATATTAGATCGGCA 57.063 29.630 0.00 0.00 0.00 5.69
242 243 8.682710 GGCCTTCAAGTATTTCATATTGTAACA 58.317 33.333 0.00 0.00 0.00 2.41
243 244 8.682710 TGGCCTTCAAGTATTTCATATTGTAAC 58.317 33.333 3.32 0.00 0.00 2.50
244 245 8.682710 GTGGCCTTCAAGTATTTCATATTGTAA 58.317 33.333 3.32 0.00 0.00 2.41
245 246 7.831690 TGTGGCCTTCAAGTATTTCATATTGTA 59.168 33.333 3.32 0.00 0.00 2.41
246 247 6.663093 TGTGGCCTTCAAGTATTTCATATTGT 59.337 34.615 3.32 0.00 0.00 2.71
247 248 6.974622 GTGTGGCCTTCAAGTATTTCATATTG 59.025 38.462 3.32 0.00 0.00 1.90
248 249 6.183360 CGTGTGGCCTTCAAGTATTTCATATT 60.183 38.462 3.32 0.00 0.00 1.28
249 250 5.296780 CGTGTGGCCTTCAAGTATTTCATAT 59.703 40.000 3.32 0.00 0.00 1.78
250 251 4.634004 CGTGTGGCCTTCAAGTATTTCATA 59.366 41.667 3.32 0.00 0.00 2.15
251 252 3.440173 CGTGTGGCCTTCAAGTATTTCAT 59.560 43.478 3.32 0.00 0.00 2.57
252 253 2.811431 CGTGTGGCCTTCAAGTATTTCA 59.189 45.455 3.32 0.00 0.00 2.69
253 254 2.414161 GCGTGTGGCCTTCAAGTATTTC 60.414 50.000 3.32 0.00 34.80 2.17
254 255 1.539827 GCGTGTGGCCTTCAAGTATTT 59.460 47.619 3.32 0.00 34.80 1.40
255 256 1.165270 GCGTGTGGCCTTCAAGTATT 58.835 50.000 3.32 0.00 34.80 1.89
256 257 0.036164 TGCGTGTGGCCTTCAAGTAT 59.964 50.000 3.32 0.00 42.61 2.12
257 258 0.179043 TTGCGTGTGGCCTTCAAGTA 60.179 50.000 3.32 2.68 42.61 2.24
258 259 0.823356 ATTGCGTGTGGCCTTCAAGT 60.823 50.000 3.32 0.00 42.61 3.16
259 260 0.314935 AATTGCGTGTGGCCTTCAAG 59.685 50.000 3.32 7.18 42.61 3.02
260 261 0.031857 CAATTGCGTGTGGCCTTCAA 59.968 50.000 3.32 1.15 42.61 2.69
261 262 0.821301 TCAATTGCGTGTGGCCTTCA 60.821 50.000 3.32 0.00 42.61 3.02
262 263 0.387239 GTCAATTGCGTGTGGCCTTC 60.387 55.000 3.32 0.00 42.61 3.46
263 264 0.823356 AGTCAATTGCGTGTGGCCTT 60.823 50.000 3.32 0.00 42.61 4.35
264 265 1.228245 AGTCAATTGCGTGTGGCCT 60.228 52.632 3.32 0.00 42.61 5.19
265 266 1.210155 GAGTCAATTGCGTGTGGCC 59.790 57.895 0.00 0.00 42.61 5.36
266 267 0.385974 GTGAGTCAATTGCGTGTGGC 60.386 55.000 0.00 0.00 43.96 5.01
267 268 0.238289 GGTGAGTCAATTGCGTGTGG 59.762 55.000 0.00 0.00 0.00 4.17
268 269 1.229428 AGGTGAGTCAATTGCGTGTG 58.771 50.000 0.00 0.00 0.00 3.82
269 270 2.224185 TGTAGGTGAGTCAATTGCGTGT 60.224 45.455 0.00 0.00 0.00 4.49
270 271 2.412870 TGTAGGTGAGTCAATTGCGTG 58.587 47.619 0.00 0.00 0.00 5.34
271 272 2.831685 TGTAGGTGAGTCAATTGCGT 57.168 45.000 0.00 0.00 0.00 5.24
272 273 4.685169 AAATGTAGGTGAGTCAATTGCG 57.315 40.909 0.00 0.00 0.00 4.85
273 274 6.473455 GCATAAAATGTAGGTGAGTCAATTGC 59.527 38.462 0.00 0.00 0.00 3.56
274 275 7.765307 AGCATAAAATGTAGGTGAGTCAATTG 58.235 34.615 0.00 0.00 0.00 2.32
275 276 7.067494 GGAGCATAAAATGTAGGTGAGTCAATT 59.933 37.037 0.00 0.00 0.00 2.32
276 277 6.543831 GGAGCATAAAATGTAGGTGAGTCAAT 59.456 38.462 0.00 0.00 0.00 2.57
277 278 5.880332 GGAGCATAAAATGTAGGTGAGTCAA 59.120 40.000 0.00 0.00 0.00 3.18
278 279 5.428253 GGAGCATAAAATGTAGGTGAGTCA 58.572 41.667 0.00 0.00 0.00 3.41
279 280 4.816925 GGGAGCATAAAATGTAGGTGAGTC 59.183 45.833 0.00 0.00 0.00 3.36
280 281 4.227300 TGGGAGCATAAAATGTAGGTGAGT 59.773 41.667 0.00 0.00 0.00 3.41
281 282 4.576463 GTGGGAGCATAAAATGTAGGTGAG 59.424 45.833 0.00 0.00 0.00 3.51
282 283 4.523083 GTGGGAGCATAAAATGTAGGTGA 58.477 43.478 0.00 0.00 0.00 4.02
283 284 3.632145 GGTGGGAGCATAAAATGTAGGTG 59.368 47.826 0.00 0.00 0.00 4.00
284 285 3.372675 GGGTGGGAGCATAAAATGTAGGT 60.373 47.826 0.00 0.00 0.00 3.08
285 286 3.117512 AGGGTGGGAGCATAAAATGTAGG 60.118 47.826 0.00 0.00 0.00 3.18
286 287 4.170468 AGGGTGGGAGCATAAAATGTAG 57.830 45.455 0.00 0.00 0.00 2.74
287 288 4.601406 AAGGGTGGGAGCATAAAATGTA 57.399 40.909 0.00 0.00 0.00 2.29
288 289 3.473113 AAGGGTGGGAGCATAAAATGT 57.527 42.857 0.00 0.00 0.00 2.71
289 290 4.026052 AGAAAGGGTGGGAGCATAAAATG 58.974 43.478 0.00 0.00 0.00 2.32
290 291 4.337264 AGAAAGGGTGGGAGCATAAAAT 57.663 40.909 0.00 0.00 0.00 1.82
291 292 3.825908 AGAAAGGGTGGGAGCATAAAA 57.174 42.857 0.00 0.00 0.00 1.52
292 293 3.825908 AAGAAAGGGTGGGAGCATAAA 57.174 42.857 0.00 0.00 0.00 1.40
293 294 3.075283 TCAAAGAAAGGGTGGGAGCATAA 59.925 43.478 0.00 0.00 0.00 1.90
294 295 2.647299 TCAAAGAAAGGGTGGGAGCATA 59.353 45.455 0.00 0.00 0.00 3.14
295 296 1.428912 TCAAAGAAAGGGTGGGAGCAT 59.571 47.619 0.00 0.00 0.00 3.79
296 297 0.850100 TCAAAGAAAGGGTGGGAGCA 59.150 50.000 0.00 0.00 0.00 4.26
297 298 1.613925 GTTCAAAGAAAGGGTGGGAGC 59.386 52.381 0.00 0.00 0.00 4.70
298 299 2.158460 AGGTTCAAAGAAAGGGTGGGAG 60.158 50.000 0.00 0.00 0.00 4.30
299 300 1.856920 AGGTTCAAAGAAAGGGTGGGA 59.143 47.619 0.00 0.00 0.00 4.37
765 767 3.803778 GGGCAAAACAGACTCACATTTTG 59.196 43.478 4.36 4.36 42.36 2.44
1489 1500 1.804748 GAAAGAACGGCGAAGTCCATT 59.195 47.619 16.62 6.16 0.00 3.16
1572 1583 4.631234 ACAGAGGTGACTAATTCCCCATA 58.369 43.478 0.00 0.00 44.43 2.74
1640 1651 1.524165 CCCGTCGGTTGTTGGAACA 60.524 57.895 11.06 0.00 37.08 3.18
1674 1685 1.143373 CCAGTTACTGCGCGCGATAA 61.143 55.000 37.18 23.95 0.00 1.75
1675 1686 1.587876 CCAGTTACTGCGCGCGATA 60.588 57.895 37.18 20.67 0.00 2.92
1783 1794 3.181500 CGAGTCTGATACATCAACCGTCA 60.181 47.826 0.00 0.00 36.18 4.35
2429 2440 4.957759 TCCTTTCTATTGCGCCTAAAAC 57.042 40.909 4.18 0.00 0.00 2.43
2667 2678 2.350772 GCCGTCTGATGGAAAACAACTG 60.351 50.000 19.98 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.