Multiple sequence alignment - TraesCS3D01G500300

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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 TraesCS3D01G500300 chr3D 100.000 2447 0 0 1 2447 589606927 589609373 0.000000e+00 4519.0
1 TraesCS3D01G500300 chr3D 90.314 795 52 8 696 1490 589579858 589580627 0.000000e+00 1018.0
2 TraesCS3D01G500300 chr3D 88.752 649 54 9 636 1283 589582589 589583219 0.000000e+00 776.0
3 TraesCS3D01G500300 chr3D 76.410 390 77 11 1064 1438 589417678 589417289 1.920000e-46 196.0
4 TraesCS3D01G500300 chr3D 98.958 96 1 0 2352 2447 602681335 602681430 3.230000e-39 172.0
5 TraesCS3D01G500300 chr3A 92.216 1002 51 7 497 1490 719482622 719483604 0.000000e+00 1393.0
6 TraesCS3D01G500300 chr3A 91.824 795 48 5 696 1490 719386827 719387604 0.000000e+00 1092.0
7 TraesCS3D01G500300 chr3A 89.165 683 52 20 1684 2351 719559360 719560035 0.000000e+00 832.0
8 TraesCS3D01G500300 chr3A 90.909 517 29 10 1174 1684 719555480 719555984 0.000000e+00 678.0
9 TraesCS3D01G500300 chr3A 87.892 446 52 2 984 1429 719461571 719462014 7.750000e-145 523.0
10 TraesCS3D01G500300 chr3A 95.437 263 12 0 240 502 719481587 719481849 1.050000e-113 420.0
11 TraesCS3D01G500300 chr3A 85.888 411 31 7 497 896 719534723 719535117 1.750000e-111 412.0
12 TraesCS3D01G500300 chr3A 91.038 212 18 1 962 1173 719535138 719535348 3.980000e-73 285.0
13 TraesCS3D01G500300 chr3B 82.762 905 78 35 696 1584 788106704 788107546 0.000000e+00 736.0
14 TraesCS3D01G500300 chr3B 87.294 669 46 21 497 1161 788138326 788138959 0.000000e+00 728.0
15 TraesCS3D01G500300 chr3B 88.946 389 24 8 1174 1559 788153555 788153927 1.710000e-126 462.0
16 TraesCS3D01G500300 chr3B 93.772 289 18 0 214 502 788136779 788137067 3.740000e-118 435.0
17 TraesCS3D01G500300 chr1D 89.640 222 16 4 1 217 275150329 275150548 2.400000e-70 276.0
18 TraesCS3D01G500300 chr1D 97.980 99 2 0 2349 2447 472325326 472325424 3.230000e-39 172.0
19 TraesCS3D01G500300 chr1D 97.030 101 1 2 2347 2447 468269457 468269555 4.180000e-38 169.0
20 TraesCS3D01G500300 chr4D 87.324 213 27 0 214 426 380442003 380441791 6.760000e-61 244.0
21 TraesCS3D01G500300 chr4D 97.030 101 3 0 2347 2447 125086778 125086878 1.160000e-38 171.0
22 TraesCS3D01G500300 chr4D 87.619 105 7 2 113 216 110140479 110140380 1.540000e-22 117.0
23 TraesCS3D01G500300 chr2D 85.581 215 26 4 3 215 505750242 505750453 1.140000e-53 220.0
24 TraesCS3D01G500300 chr2B 78.788 297 37 18 1685 1966 215591081 215591366 2.500000e-40 176.0
25 TraesCS3D01G500300 chr6D 98.969 97 1 0 2351 2447 432975089 432975185 8.990000e-40 174.0
26 TraesCS3D01G500300 chr7D 97.059 102 3 0 2346 2447 86602744 86602845 3.230000e-39 172.0
27 TraesCS3D01G500300 chr7A 98.958 96 1 0 2352 2447 44664562 44664657 3.230000e-39 172.0
28 TraesCS3D01G500300 chr7A 87.736 106 6 3 114 218 430327693 430327594 1.540000e-22 117.0
29 TraesCS3D01G500300 chrUn 97.980 99 1 1 2350 2447 97824226 97824128 1.160000e-38 171.0
30 TraesCS3D01G500300 chr5D 96.154 104 3 1 2344 2447 370321486 370321588 4.180000e-38 169.0
31 TraesCS3D01G500300 chr1A 87.736 106 6 3 113 216 12256241 12256141 1.540000e-22 117.0
32 TraesCS3D01G500300 chr5B 93.220 59 3 1 160 218 197825317 197825374 4.340000e-13 86.1
33 TraesCS3D01G500300 chr6B 83.951 81 11 2 137 217 696497230 696497308 2.610000e-10 76.8


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 TraesCS3D01G500300 chr3D 589606927 589609373 2446 False 4519.0 4519 100.0000 1 2447 1 chr3D.!!$F1 2446
1 TraesCS3D01G500300 chr3D 589579858 589583219 3361 False 897.0 1018 89.5330 636 1490 2 chr3D.!!$F3 854
2 TraesCS3D01G500300 chr3A 719386827 719387604 777 False 1092.0 1092 91.8240 696 1490 1 chr3A.!!$F1 794
3 TraesCS3D01G500300 chr3A 719481587 719483604 2017 False 906.5 1393 93.8265 240 1490 2 chr3A.!!$F3 1250
4 TraesCS3D01G500300 chr3A 719555480 719560035 4555 False 755.0 832 90.0370 1174 2351 2 chr3A.!!$F5 1177
5 TraesCS3D01G500300 chr3A 719534723 719535348 625 False 348.5 412 88.4630 497 1173 2 chr3A.!!$F4 676
6 TraesCS3D01G500300 chr3B 788106704 788107546 842 False 736.0 736 82.7620 696 1584 1 chr3B.!!$F1 888
7 TraesCS3D01G500300 chr3B 788136779 788138959 2180 False 581.5 728 90.5330 214 1161 2 chr3B.!!$F3 947

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
58 59 0.030101 GCGCAAAGTGCCTACAAACA 59.97 50.0 0.3 0.0 41.12 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 8562 1.971695 GGCCCTGAAAGTCAACGGG 60.972 63.158 0.0 0.0 37.97 5.28 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
19 20 3.630204 GCCATCCGTAGCGACATG 58.370 61.111 0.00 0.00 0.00 3.21
20 21 1.956170 GCCATCCGTAGCGACATGG 60.956 63.158 10.76 10.76 38.92 3.66
21 22 1.739667 CCATCCGTAGCGACATGGA 59.260 57.895 9.83 3.63 38.50 3.41
22 23 0.597637 CCATCCGTAGCGACATGGAC 60.598 60.000 9.83 0.00 38.50 4.02
23 24 0.385751 CATCCGTAGCGACATGGACT 59.614 55.000 0.00 0.00 36.42 3.85
24 25 0.385751 ATCCGTAGCGACATGGACTG 59.614 55.000 0.00 0.00 36.42 3.51
25 26 1.878522 CCGTAGCGACATGGACTGC 60.879 63.158 0.00 0.00 0.00 4.40
26 27 1.139734 CGTAGCGACATGGACTGCT 59.860 57.895 0.00 3.05 41.32 4.24
27 28 1.142185 CGTAGCGACATGGACTGCTG 61.142 60.000 11.85 0.00 38.33 4.41
28 29 0.807667 GTAGCGACATGGACTGCTGG 60.808 60.000 11.85 0.00 38.33 4.85
29 30 0.970427 TAGCGACATGGACTGCTGGA 60.970 55.000 11.85 0.00 38.33 3.86
30 31 1.375908 GCGACATGGACTGCTGGAA 60.376 57.895 0.00 0.00 0.00 3.53
31 32 1.364626 GCGACATGGACTGCTGGAAG 61.365 60.000 0.00 0.00 0.00 3.46
57 58 2.796227 GCGCAAAGTGCCTACAAAC 58.204 52.632 0.30 0.00 41.12 2.93
58 59 0.030101 GCGCAAAGTGCCTACAAACA 59.970 50.000 0.30 0.00 41.12 2.83
59 60 1.753956 CGCAAAGTGCCTACAAACAC 58.246 50.000 0.00 0.00 41.12 3.32
60 61 1.599419 CGCAAAGTGCCTACAAACACC 60.599 52.381 0.00 0.00 41.12 4.16
61 62 1.407258 GCAAAGTGCCTACAAACACCA 59.593 47.619 0.00 0.00 37.42 4.17
62 63 2.798145 GCAAAGTGCCTACAAACACCAC 60.798 50.000 0.00 0.00 37.42 4.16
63 64 2.687935 CAAAGTGCCTACAAACACCACT 59.312 45.455 0.00 0.00 38.30 4.00
64 65 2.256117 AGTGCCTACAAACACCACTC 57.744 50.000 0.00 0.00 37.51 3.51
65 66 0.865769 GTGCCTACAAACACCACTCG 59.134 55.000 0.00 0.00 0.00 4.18
66 67 0.250124 TGCCTACAAACACCACTCGG 60.250 55.000 0.00 0.00 38.77 4.63
75 76 2.923035 ACCACTCGGTGACCCAGG 60.923 66.667 0.39 0.00 46.79 4.45
76 77 4.394712 CCACTCGGTGACCCAGGC 62.395 72.222 0.39 0.00 35.23 4.85
77 78 3.314331 CACTCGGTGACCCAGGCT 61.314 66.667 0.39 0.00 35.23 4.58
78 79 3.314331 ACTCGGTGACCCAGGCTG 61.314 66.667 7.75 7.75 0.00 4.85
79 80 2.997315 CTCGGTGACCCAGGCTGA 60.997 66.667 17.94 0.00 0.00 4.26
80 81 2.997315 TCGGTGACCCAGGCTGAG 60.997 66.667 17.94 4.90 0.00 3.35
81 82 2.997315 CGGTGACCCAGGCTGAGA 60.997 66.667 17.94 0.00 0.00 3.27
82 83 2.362369 CGGTGACCCAGGCTGAGAT 61.362 63.158 17.94 0.00 0.00 2.75
83 84 1.222936 GGTGACCCAGGCTGAGATG 59.777 63.158 17.94 3.91 0.00 2.90
84 85 1.451028 GTGACCCAGGCTGAGATGC 60.451 63.158 17.94 1.00 0.00 3.91
95 96 2.720915 GCTGAGATGCCTTCTTTTCCT 58.279 47.619 0.00 0.00 33.74 3.36
96 97 3.087781 GCTGAGATGCCTTCTTTTCCTT 58.912 45.455 0.00 0.00 33.74 3.36
97 98 3.509184 GCTGAGATGCCTTCTTTTCCTTT 59.491 43.478 0.00 0.00 33.74 3.11
98 99 4.021632 GCTGAGATGCCTTCTTTTCCTTTT 60.022 41.667 0.00 0.00 33.74 2.27
99 100 5.707931 CTGAGATGCCTTCTTTTCCTTTTC 58.292 41.667 0.00 0.00 33.74 2.29
100 101 5.139727 TGAGATGCCTTCTTTTCCTTTTCA 58.860 37.500 0.00 0.00 33.74 2.69
101 102 5.242393 TGAGATGCCTTCTTTTCCTTTTCAG 59.758 40.000 0.00 0.00 33.74 3.02
102 103 5.143369 AGATGCCTTCTTTTCCTTTTCAGT 58.857 37.500 0.00 0.00 0.00 3.41
103 104 4.918810 TGCCTTCTTTTCCTTTTCAGTC 57.081 40.909 0.00 0.00 0.00 3.51
104 105 3.315191 TGCCTTCTTTTCCTTTTCAGTCG 59.685 43.478 0.00 0.00 0.00 4.18
105 106 3.564225 GCCTTCTTTTCCTTTTCAGTCGA 59.436 43.478 0.00 0.00 0.00 4.20
106 107 4.036380 GCCTTCTTTTCCTTTTCAGTCGAA 59.964 41.667 0.00 0.00 0.00 3.71
107 108 5.449999 GCCTTCTTTTCCTTTTCAGTCGAAA 60.450 40.000 0.00 0.00 39.38 3.46
108 109 5.971792 CCTTCTTTTCCTTTTCAGTCGAAAC 59.028 40.000 0.00 0.00 40.84 2.78
109 110 5.494632 TCTTTTCCTTTTCAGTCGAAACC 57.505 39.130 0.00 0.00 40.84 3.27
110 111 3.955771 TTTCCTTTTCAGTCGAAACCG 57.044 42.857 0.00 0.00 40.84 4.44
111 112 1.873698 TCCTTTTCAGTCGAAACCGG 58.126 50.000 0.00 0.00 40.84 5.28
112 113 1.139455 TCCTTTTCAGTCGAAACCGGT 59.861 47.619 0.00 0.00 40.84 5.28
113 114 1.944709 CCTTTTCAGTCGAAACCGGTT 59.055 47.619 15.86 15.86 40.84 4.44
114 115 2.286772 CCTTTTCAGTCGAAACCGGTTG 60.287 50.000 23.08 9.73 40.84 3.77
115 116 2.027003 TTTCAGTCGAAACCGGTTGT 57.973 45.000 23.08 11.24 36.19 3.32
116 117 2.886862 TTCAGTCGAAACCGGTTGTA 57.113 45.000 23.08 6.50 0.00 2.41
117 118 2.886862 TCAGTCGAAACCGGTTGTAA 57.113 45.000 23.08 6.12 0.00 2.41
118 119 2.472816 TCAGTCGAAACCGGTTGTAAC 58.527 47.619 23.08 18.08 0.00 2.50
119 120 1.528161 CAGTCGAAACCGGTTGTAACC 59.472 52.381 23.08 8.33 45.76 2.85
134 135 6.515272 GTTGTAACCACCATGATCAATCTT 57.485 37.500 0.00 0.00 0.00 2.40
135 136 6.924111 GTTGTAACCACCATGATCAATCTTT 58.076 36.000 0.00 0.00 0.00 2.52
136 137 7.378181 GTTGTAACCACCATGATCAATCTTTT 58.622 34.615 0.00 0.00 0.00 2.27
137 138 7.537596 TGTAACCACCATGATCAATCTTTTT 57.462 32.000 0.00 0.00 0.00 1.94
138 139 7.377398 TGTAACCACCATGATCAATCTTTTTG 58.623 34.615 0.00 0.00 0.00 2.44
139 140 6.669125 AACCACCATGATCAATCTTTTTGA 57.331 33.333 0.00 0.00 0.00 2.69
140 141 6.862469 ACCACCATGATCAATCTTTTTGAT 57.138 33.333 0.00 0.66 41.43 2.57
148 149 6.765424 GATCAATCTTTTTGATCGTGAACG 57.235 37.500 11.34 0.00 43.40 3.95
149 150 4.463209 TCAATCTTTTTGATCGTGAACGC 58.537 39.130 0.00 0.00 39.60 4.84
150 151 4.024472 TCAATCTTTTTGATCGTGAACGCA 60.024 37.500 0.00 0.00 39.60 5.24
151 152 4.685169 ATCTTTTTGATCGTGAACGCAT 57.315 36.364 0.00 0.00 39.60 4.73
152 153 4.481930 TCTTTTTGATCGTGAACGCATT 57.518 36.364 0.00 0.00 39.60 3.56
153 154 4.854399 TCTTTTTGATCGTGAACGCATTT 58.146 34.783 0.00 0.00 39.60 2.32
154 155 4.674662 TCTTTTTGATCGTGAACGCATTTG 59.325 37.500 0.00 0.00 39.60 2.32
155 156 1.962412 TTGATCGTGAACGCATTTGC 58.038 45.000 0.00 0.00 39.60 3.68
156 157 0.167908 TGATCGTGAACGCATTTGCC 59.832 50.000 0.00 0.00 39.60 4.52
157 158 0.167908 GATCGTGAACGCATTTGCCA 59.832 50.000 0.00 0.00 39.60 4.92
158 159 0.810648 ATCGTGAACGCATTTGCCAT 59.189 45.000 0.00 0.00 39.60 4.40
159 160 0.167908 TCGTGAACGCATTTGCCATC 59.832 50.000 0.00 0.00 39.60 3.51
160 161 0.168788 CGTGAACGCATTTGCCATCT 59.831 50.000 0.00 0.00 37.91 2.90
161 162 1.401409 CGTGAACGCATTTGCCATCTT 60.401 47.619 0.00 0.00 37.91 2.40
162 163 2.253603 GTGAACGCATTTGCCATCTTC 58.746 47.619 0.00 0.00 37.91 2.87
163 164 2.095059 GTGAACGCATTTGCCATCTTCT 60.095 45.455 0.00 0.00 37.91 2.85
164 165 2.162208 TGAACGCATTTGCCATCTTCTC 59.838 45.455 0.00 0.00 37.91 2.87
165 166 1.098050 ACGCATTTGCCATCTTCTCC 58.902 50.000 0.00 0.00 37.91 3.71
166 167 0.383231 CGCATTTGCCATCTTCTCCC 59.617 55.000 0.00 0.00 37.91 4.30
167 168 1.772836 GCATTTGCCATCTTCTCCCT 58.227 50.000 0.00 0.00 34.31 4.20
168 169 1.407979 GCATTTGCCATCTTCTCCCTG 59.592 52.381 0.00 0.00 34.31 4.45
169 170 1.407979 CATTTGCCATCTTCTCCCTGC 59.592 52.381 0.00 0.00 0.00 4.85
170 171 0.700564 TTTGCCATCTTCTCCCTGCT 59.299 50.000 0.00 0.00 0.00 4.24
171 172 0.700564 TTGCCATCTTCTCCCTGCTT 59.299 50.000 0.00 0.00 0.00 3.91
172 173 1.583556 TGCCATCTTCTCCCTGCTTA 58.416 50.000 0.00 0.00 0.00 3.09
173 174 1.915489 TGCCATCTTCTCCCTGCTTAA 59.085 47.619 0.00 0.00 0.00 1.85
174 175 2.511218 TGCCATCTTCTCCCTGCTTAAT 59.489 45.455 0.00 0.00 0.00 1.40
175 176 3.716353 TGCCATCTTCTCCCTGCTTAATA 59.284 43.478 0.00 0.00 0.00 0.98
176 177 4.352001 TGCCATCTTCTCCCTGCTTAATAT 59.648 41.667 0.00 0.00 0.00 1.28
177 178 5.547666 TGCCATCTTCTCCCTGCTTAATATA 59.452 40.000 0.00 0.00 0.00 0.86
178 179 6.216251 TGCCATCTTCTCCCTGCTTAATATAT 59.784 38.462 0.00 0.00 0.00 0.86
179 180 6.541641 GCCATCTTCTCCCTGCTTAATATATG 59.458 42.308 0.00 0.00 0.00 1.78
180 181 7.582242 GCCATCTTCTCCCTGCTTAATATATGA 60.582 40.741 0.00 0.00 0.00 2.15
181 182 8.324306 CCATCTTCTCCCTGCTTAATATATGAA 58.676 37.037 0.00 0.00 0.00 2.57
182 183 9.902684 CATCTTCTCCCTGCTTAATATATGAAT 57.097 33.333 0.00 0.00 0.00 2.57
183 184 9.902684 ATCTTCTCCCTGCTTAATATATGAATG 57.097 33.333 0.00 0.00 0.00 2.67
184 185 7.826252 TCTTCTCCCTGCTTAATATATGAATGC 59.174 37.037 0.00 0.00 0.00 3.56
185 186 6.418101 TCTCCCTGCTTAATATATGAATGCC 58.582 40.000 0.00 0.00 0.00 4.40
186 187 6.012596 TCTCCCTGCTTAATATATGAATGCCA 60.013 38.462 0.00 0.00 0.00 4.92
187 188 6.182627 TCCCTGCTTAATATATGAATGCCAG 58.817 40.000 0.00 0.00 0.00 4.85
188 189 5.948162 CCCTGCTTAATATATGAATGCCAGT 59.052 40.000 0.00 0.00 0.00 4.00
189 190 6.127814 CCCTGCTTAATATATGAATGCCAGTG 60.128 42.308 0.00 0.00 0.00 3.66
190 191 6.656270 CCTGCTTAATATATGAATGCCAGTGA 59.344 38.462 0.00 0.00 0.00 3.41
191 192 7.338703 CCTGCTTAATATATGAATGCCAGTGAT 59.661 37.037 0.00 0.00 0.00 3.06
192 193 9.387257 CTGCTTAATATATGAATGCCAGTGATA 57.613 33.333 0.00 0.00 0.00 2.15
193 194 9.166173 TGCTTAATATATGAATGCCAGTGATAC 57.834 33.333 0.00 0.00 0.00 2.24
194 195 9.166173 GCTTAATATATGAATGCCAGTGATACA 57.834 33.333 0.00 0.00 0.00 2.29
208 209 5.808366 AGTGATACACTGGTTCTTTCAGA 57.192 39.130 3.54 0.00 43.63 3.27
209 210 6.174720 AGTGATACACTGGTTCTTTCAGAA 57.825 37.500 3.54 0.00 43.63 3.02
210 211 6.591935 AGTGATACACTGGTTCTTTCAGAAA 58.408 36.000 3.54 0.00 43.63 2.52
211 212 7.054124 AGTGATACACTGGTTCTTTCAGAAAA 58.946 34.615 3.54 0.00 43.63 2.29
212 213 7.556275 AGTGATACACTGGTTCTTTCAGAAAAA 59.444 33.333 3.54 0.00 43.63 1.94
238 239 4.965814 TGATGCACTCTATTCATCCTTCC 58.034 43.478 0.00 0.00 36.64 3.46
318 319 3.546815 CCACTATTGCTAAGTTCATGCGC 60.547 47.826 0.00 0.00 0.00 6.09
490 491 1.298859 GGCCAAAGACGTGCTACTGG 61.299 60.000 0.00 2.52 34.38 4.00
500 1765 1.202533 CGTGCTACTGGGATTAGGTGG 60.203 57.143 0.00 0.00 0.00 4.61
548 1813 8.574737 GGAGTAGACACCGAATAACATATTAGT 58.425 37.037 0.00 0.00 0.00 2.24
602 1868 2.905075 TGCCTGGAATATTCTGTCACG 58.095 47.619 14.95 1.21 0.00 4.35
644 1911 4.568359 GCATTATATACTCCCGATGTGCTG 59.432 45.833 0.00 0.00 0.00 4.41
675 1949 8.807667 ACTTTCAGCTTTCACAAAATATTCTG 57.192 30.769 0.00 0.00 0.00 3.02
705 1979 3.257561 ATGCATGCTCGACGACGC 61.258 61.111 20.33 10.97 39.58 5.19
896 2192 0.321671 ACCAGAAGCAAAGCTAGCGA 59.678 50.000 9.55 0.00 38.25 4.93
897 2193 1.005340 CCAGAAGCAAAGCTAGCGAG 58.995 55.000 9.55 4.37 38.25 5.03
898 2194 1.404717 CCAGAAGCAAAGCTAGCGAGA 60.405 52.381 9.55 0.00 38.25 4.04
931 2227 0.392998 AGGCTCCCAGCACATTAACG 60.393 55.000 0.00 0.00 44.75 3.18
935 2231 0.250510 TCCCAGCACATTAACGCACA 60.251 50.000 0.00 0.00 0.00 4.57
974 2270 1.556911 AGCCACGAATCTCAGGTGATT 59.443 47.619 0.00 0.00 39.14 2.57
992 2292 0.601576 TTACCGAAGCAAGCAAGCGA 60.602 50.000 0.00 0.00 40.15 4.93
993 2293 0.601576 TACCGAAGCAAGCAAGCGAA 60.602 50.000 0.00 0.00 40.15 4.70
994 2294 1.154338 CCGAAGCAAGCAAGCGAAG 60.154 57.895 0.00 0.00 40.15 3.79
1032 2332 3.612371 GACGACCGAGCGCTTCAGT 62.612 63.158 13.26 9.79 33.86 3.41
1350 2659 3.325753 AGGCTGGGGTCAGAGCAC 61.326 66.667 1.20 0.00 43.49 4.40
1490 2799 6.238897 CCAGTCTACTGAATACTGATCCTGAC 60.239 46.154 11.69 0.00 46.59 3.51
1492 2801 7.068103 CAGTCTACTGAATACTGATCCTGACTT 59.932 40.741 3.99 0.00 46.59 3.01
1493 2802 7.284489 AGTCTACTGAATACTGATCCTGACTTC 59.716 40.741 0.00 0.00 0.00 3.01
1494 2803 5.606348 ACTGAATACTGATCCTGACTTCC 57.394 43.478 0.00 0.00 0.00 3.46
1544 3124 7.655732 ACAAGATTAATTTAGTTTTGGGTGCAC 59.344 33.333 8.80 8.80 0.00 4.57
1671 5045 0.178879 AGGCATCTCCAGGGATAGGG 60.179 60.000 0.00 0.00 37.29 3.53
1674 5048 1.762827 GCATCTCCAGGGATAGGGACA 60.763 57.143 0.00 0.00 0.00 4.02
1873 8628 9.350951 AGTGTGTATAGTGACTTGTATATAGCA 57.649 33.333 0.00 0.00 0.00 3.49
1874 8629 9.961265 GTGTGTATAGTGACTTGTATATAGCAA 57.039 33.333 0.00 0.00 0.00 3.91
1897 8654 8.835439 GCAATAAATTTTGTCTTTTTCCCAGAA 58.165 29.630 0.00 0.00 0.00 3.02
1904 8661 3.625764 TGTCTTTTTCCCAGAAGTCAACG 59.374 43.478 0.00 0.00 0.00 4.10
1905 8662 3.626217 GTCTTTTTCCCAGAAGTCAACGT 59.374 43.478 0.00 0.00 0.00 3.99
1906 8663 4.812626 GTCTTTTTCCCAGAAGTCAACGTA 59.187 41.667 0.00 0.00 0.00 3.57
1911 8668 7.804843 TTTTCCCAGAAGTCAACGTATTTTA 57.195 32.000 0.00 0.00 0.00 1.52
1916 8673 9.321562 TCCCAGAAGTCAACGTATTTTATATTC 57.678 33.333 0.00 0.00 0.00 1.75
2074 8835 0.470080 CCGGATCTCTAGCCCCTTCA 60.470 60.000 0.00 0.00 0.00 3.02
2111 8873 9.458374 TTTTTCGTTTAAAAGCTAATTCCTCAG 57.542 29.630 0.00 0.00 38.29 3.35
2119 8881 1.475930 GCTAATTCCTCAGAGCACCCC 60.476 57.143 0.00 0.00 34.96 4.95
2137 8899 3.647590 ACCCCCAAAACTTAACTACTCGA 59.352 43.478 0.00 0.00 0.00 4.04
2191 8953 5.106876 ACCCCTAAAACGTACATAGCATT 57.893 39.130 0.00 0.00 0.00 3.56
2203 8965 4.282950 ACATAGCATTCGTCTGCAAATG 57.717 40.909 13.02 15.48 44.77 2.32
2208 8970 2.318578 CATTCGTCTGCAAATGCGTTT 58.681 42.857 0.00 0.00 45.83 3.60
2209 8971 1.752753 TTCGTCTGCAAATGCGTTTG 58.247 45.000 24.17 24.17 45.92 2.93
2258 9020 3.421567 GGCCATCTAACCATGGACC 57.578 57.895 21.47 2.56 45.48 4.46
2261 9023 1.490490 GCCATCTAACCATGGACCTCA 59.510 52.381 21.47 0.00 45.79 3.86
2301 9063 5.527951 TCGAATGGAATTTGAACAAACCAG 58.472 37.500 12.63 3.62 43.55 4.00
2304 9066 5.867903 ATGGAATTTGAACAAACCAGACA 57.132 34.783 12.63 5.61 32.33 3.41
2353 9115 9.801873 ATTTATTTAAATCGGACCACATTCTTG 57.198 29.630 3.39 0.00 30.50 3.02
2354 9116 4.695217 TTAAATCGGACCACATTCTTGC 57.305 40.909 0.00 0.00 0.00 4.01
2355 9117 2.198827 AATCGGACCACATTCTTGCA 57.801 45.000 0.00 0.00 0.00 4.08
2356 9118 1.453155 ATCGGACCACATTCTTGCAC 58.547 50.000 0.00 0.00 0.00 4.57
2357 9119 0.396435 TCGGACCACATTCTTGCACT 59.604 50.000 0.00 0.00 0.00 4.40
2358 9120 1.621317 TCGGACCACATTCTTGCACTA 59.379 47.619 0.00 0.00 0.00 2.74
2359 9121 2.002586 CGGACCACATTCTTGCACTAG 58.997 52.381 0.00 0.00 0.00 2.57
2360 9122 2.612972 CGGACCACATTCTTGCACTAGT 60.613 50.000 0.00 0.00 0.00 2.57
2361 9123 3.368013 CGGACCACATTCTTGCACTAGTA 60.368 47.826 0.00 0.00 0.00 1.82
2362 9124 4.184629 GGACCACATTCTTGCACTAGTAG 58.815 47.826 0.00 0.00 0.00 2.57
2363 9125 4.081642 GGACCACATTCTTGCACTAGTAGA 60.082 45.833 3.59 0.00 0.00 2.59
2364 9126 5.479306 GACCACATTCTTGCACTAGTAGAA 58.521 41.667 3.59 8.63 32.91 2.10
2365 9127 5.865085 ACCACATTCTTGCACTAGTAGAAA 58.135 37.500 9.97 0.00 32.20 2.52
2366 9128 6.296026 ACCACATTCTTGCACTAGTAGAAAA 58.704 36.000 9.97 0.00 32.20 2.29
2367 9129 6.770785 ACCACATTCTTGCACTAGTAGAAAAA 59.229 34.615 9.97 0.00 32.20 1.94
2368 9130 7.041098 ACCACATTCTTGCACTAGTAGAAAAAG 60.041 37.037 9.97 4.45 32.20 2.27
2369 9131 7.301054 CACATTCTTGCACTAGTAGAAAAAGG 58.699 38.462 9.97 4.53 32.20 3.11
2370 9132 6.431234 ACATTCTTGCACTAGTAGAAAAAGGG 59.569 38.462 9.97 2.67 32.20 3.95
2371 9133 5.562298 TCTTGCACTAGTAGAAAAAGGGT 57.438 39.130 3.59 0.00 0.00 4.34
2372 9134 5.548406 TCTTGCACTAGTAGAAAAAGGGTC 58.452 41.667 3.59 0.00 0.00 4.46
2373 9135 4.967084 TGCACTAGTAGAAAAAGGGTCA 57.033 40.909 3.59 0.00 0.00 4.02
2374 9136 5.499004 TGCACTAGTAGAAAAAGGGTCAT 57.501 39.130 3.59 0.00 0.00 3.06
2375 9137 5.488341 TGCACTAGTAGAAAAAGGGTCATC 58.512 41.667 3.59 0.00 0.00 2.92
2376 9138 5.248477 TGCACTAGTAGAAAAAGGGTCATCT 59.752 40.000 3.59 0.00 0.00 2.90
2377 9139 5.582665 GCACTAGTAGAAAAAGGGTCATCTG 59.417 44.000 3.59 0.00 0.00 2.90
2378 9140 6.702329 CACTAGTAGAAAAAGGGTCATCTGT 58.298 40.000 3.59 0.00 0.00 3.41
2379 9141 6.814146 CACTAGTAGAAAAAGGGTCATCTGTC 59.186 42.308 3.59 0.00 0.00 3.51
2380 9142 5.167303 AGTAGAAAAAGGGTCATCTGTCC 57.833 43.478 0.00 0.00 0.00 4.02
2381 9143 3.441500 AGAAAAAGGGTCATCTGTCCC 57.558 47.619 4.52 4.52 42.66 4.46
2382 9144 2.084546 GAAAAAGGGTCATCTGTCCCG 58.915 52.381 6.82 0.00 46.13 5.14
2383 9145 0.328258 AAAAGGGTCATCTGTCCCGG 59.672 55.000 6.82 0.00 46.13 5.73
2384 9146 0.840722 AAAGGGTCATCTGTCCCGGT 60.841 55.000 0.00 0.00 46.13 5.28
2385 9147 0.840722 AAGGGTCATCTGTCCCGGTT 60.841 55.000 0.00 0.00 46.13 4.44
2386 9148 1.078426 GGGTCATCTGTCCCGGTTG 60.078 63.158 0.00 0.00 33.91 3.77
2387 9149 1.078426 GGTCATCTGTCCCGGTTGG 60.078 63.158 0.00 0.00 0.00 3.77
2388 9150 1.677552 GTCATCTGTCCCGGTTGGT 59.322 57.895 0.00 0.00 34.77 3.67
2389 9151 0.899720 GTCATCTGTCCCGGTTGGTA 59.100 55.000 0.00 0.00 34.77 3.25
2390 9152 1.276989 GTCATCTGTCCCGGTTGGTAA 59.723 52.381 0.00 0.00 34.77 2.85
2391 9153 1.553248 TCATCTGTCCCGGTTGGTAAG 59.447 52.381 0.00 0.00 34.77 2.34
2392 9154 0.909623 ATCTGTCCCGGTTGGTAAGG 59.090 55.000 0.00 0.00 34.77 2.69
2393 9155 1.196104 TCTGTCCCGGTTGGTAAGGG 61.196 60.000 0.00 0.00 46.40 3.95
2394 9156 2.045634 GTCCCGGTTGGTAAGGGC 60.046 66.667 0.00 0.00 44.70 5.19
2395 9157 3.332385 TCCCGGTTGGTAAGGGCC 61.332 66.667 0.00 0.00 44.70 5.80
2396 9158 3.335729 CCCGGTTGGTAAGGGCCT 61.336 66.667 0.00 0.00 38.51 5.19
2397 9159 2.761160 CCGGTTGGTAAGGGCCTT 59.239 61.111 24.44 24.44 0.00 4.35
2398 9160 1.076014 CCGGTTGGTAAGGGCCTTT 59.924 57.895 26.29 5.08 0.00 3.11
2399 9161 0.541063 CCGGTTGGTAAGGGCCTTTT 60.541 55.000 26.29 2.86 0.00 2.27
2400 9162 0.601057 CGGTTGGTAAGGGCCTTTTG 59.399 55.000 26.29 3.03 0.00 2.44
2401 9163 1.712056 GGTTGGTAAGGGCCTTTTGT 58.288 50.000 26.29 1.50 0.00 2.83
2402 9164 1.616865 GGTTGGTAAGGGCCTTTTGTC 59.383 52.381 26.29 12.32 0.00 3.18
2403 9165 1.616865 GTTGGTAAGGGCCTTTTGTCC 59.383 52.381 26.29 20.31 0.00 4.02
2404 9166 0.113580 TGGTAAGGGCCTTTTGTCCC 59.886 55.000 26.29 16.23 42.94 4.46
2408 9170 2.203582 GGGCCTTTTGTCCCGGTT 60.204 61.111 0.84 0.00 32.00 4.44
2409 9171 2.273179 GGGCCTTTTGTCCCGGTTC 61.273 63.158 0.84 0.00 32.00 3.62
2410 9172 1.228459 GGCCTTTTGTCCCGGTTCT 60.228 57.895 0.00 0.00 0.00 3.01
2411 9173 0.826256 GGCCTTTTGTCCCGGTTCTT 60.826 55.000 0.00 0.00 0.00 2.52
2412 9174 0.313987 GCCTTTTGTCCCGGTTCTTG 59.686 55.000 0.00 0.00 0.00 3.02
2413 9175 1.975660 CCTTTTGTCCCGGTTCTTGA 58.024 50.000 0.00 0.00 0.00 3.02
2414 9176 2.303175 CCTTTTGTCCCGGTTCTTGAA 58.697 47.619 0.00 0.00 0.00 2.69
2415 9177 2.034179 CCTTTTGTCCCGGTTCTTGAAC 59.966 50.000 0.00 5.03 0.00 3.18
2416 9178 1.682740 TTTGTCCCGGTTCTTGAACC 58.317 50.000 19.50 19.50 39.44 3.62
2424 9186 2.845363 GGTTCTTGAACCGGGACTAA 57.155 50.000 15.61 0.00 32.47 2.24
2425 9187 3.130280 GGTTCTTGAACCGGGACTAAA 57.870 47.619 15.61 0.00 32.47 1.85
2426 9188 3.072211 GGTTCTTGAACCGGGACTAAAG 58.928 50.000 15.61 2.23 32.47 1.85
2427 9189 3.072211 GTTCTTGAACCGGGACTAAAGG 58.928 50.000 6.32 0.00 0.00 3.11
2428 9190 1.626825 TCTTGAACCGGGACTAAAGGG 59.373 52.381 6.32 0.00 0.00 3.95
2429 9191 1.350019 CTTGAACCGGGACTAAAGGGT 59.650 52.381 6.32 0.00 0.00 4.34
2430 9192 0.978907 TGAACCGGGACTAAAGGGTC 59.021 55.000 6.32 0.00 41.92 4.46
2431 9193 0.108472 GAACCGGGACTAAAGGGTCG 60.108 60.000 6.32 0.00 37.12 4.79
2432 9194 0.833409 AACCGGGACTAAAGGGTCGT 60.833 55.000 6.32 0.00 37.12 4.34
2433 9195 0.833409 ACCGGGACTAAAGGGTCGTT 60.833 55.000 6.32 0.00 37.12 3.85
2434 9196 1.185315 CCGGGACTAAAGGGTCGTTA 58.815 55.000 0.00 0.00 37.12 3.18
2435 9197 1.134995 CCGGGACTAAAGGGTCGTTAC 60.135 57.143 0.00 0.00 37.12 2.50
2436 9198 1.821136 CGGGACTAAAGGGTCGTTACT 59.179 52.381 0.00 0.00 37.12 2.24
2437 9199 3.016736 CGGGACTAAAGGGTCGTTACTA 58.983 50.000 0.00 0.00 37.12 1.82
2438 9200 3.443681 CGGGACTAAAGGGTCGTTACTAA 59.556 47.826 0.00 0.00 37.12 2.24
2439 9201 4.098501 CGGGACTAAAGGGTCGTTACTAAT 59.901 45.833 0.00 0.00 37.12 1.73
2440 9202 5.354767 GGGACTAAAGGGTCGTTACTAATG 58.645 45.833 0.00 0.00 37.12 1.90
2441 9203 4.807834 GGACTAAAGGGTCGTTACTAATGC 59.192 45.833 0.00 0.00 37.12 3.56
2442 9204 4.763073 ACTAAAGGGTCGTTACTAATGCC 58.237 43.478 0.00 0.00 0.00 4.40
2443 9205 2.704464 AAGGGTCGTTACTAATGCCC 57.296 50.000 10.40 10.40 35.35 5.36
2444 9206 1.875488 AGGGTCGTTACTAATGCCCT 58.125 50.000 13.37 13.37 38.46 5.19
2445 9207 3.036452 AGGGTCGTTACTAATGCCCTA 57.964 47.619 15.90 0.00 40.21 3.53
2446 9208 2.963782 AGGGTCGTTACTAATGCCCTAG 59.036 50.000 15.90 0.00 40.21 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.597637 GTCCATGTCGCTACGGATGG 60.598 60.000 10.78 10.78 38.06 3.51
4 5 0.385751 AGTCCATGTCGCTACGGATG 59.614 55.000 0.00 0.00 0.00 3.51
5 6 0.385751 CAGTCCATGTCGCTACGGAT 59.614 55.000 0.00 0.00 0.00 4.18
6 7 1.807226 CAGTCCATGTCGCTACGGA 59.193 57.895 0.00 0.00 0.00 4.69
7 8 1.878522 GCAGTCCATGTCGCTACGG 60.879 63.158 0.00 0.00 0.00 4.02
8 9 1.139734 AGCAGTCCATGTCGCTACG 59.860 57.895 0.00 0.00 31.60 3.51
9 10 0.807667 CCAGCAGTCCATGTCGCTAC 60.808 60.000 0.00 0.00 32.29 3.58
10 11 0.970427 TCCAGCAGTCCATGTCGCTA 60.970 55.000 0.00 0.00 32.29 4.26
11 12 1.830587 TTCCAGCAGTCCATGTCGCT 61.831 55.000 0.00 0.00 34.29 4.93
12 13 1.364626 CTTCCAGCAGTCCATGTCGC 61.365 60.000 0.00 0.00 0.00 5.19
13 14 1.364626 GCTTCCAGCAGTCCATGTCG 61.365 60.000 0.00 0.00 41.89 4.35
14 15 0.035630 AGCTTCCAGCAGTCCATGTC 60.036 55.000 0.00 0.00 45.56 3.06
15 16 0.403271 AAGCTTCCAGCAGTCCATGT 59.597 50.000 0.00 0.00 45.56 3.21
16 17 0.809385 CAAGCTTCCAGCAGTCCATG 59.191 55.000 0.00 0.00 45.56 3.66
17 18 0.964358 GCAAGCTTCCAGCAGTCCAT 60.964 55.000 0.00 0.00 45.56 3.41
18 19 1.601759 GCAAGCTTCCAGCAGTCCA 60.602 57.895 0.00 0.00 45.56 4.02
19 20 2.338785 GGCAAGCTTCCAGCAGTCC 61.339 63.158 9.23 0.00 45.56 3.85
20 21 2.684843 CGGCAAGCTTCCAGCAGTC 61.685 63.158 9.23 0.00 45.56 3.51
21 22 2.670934 CGGCAAGCTTCCAGCAGT 60.671 61.111 9.23 0.00 45.56 4.40
22 23 3.437795 CCGGCAAGCTTCCAGCAG 61.438 66.667 9.23 5.21 45.56 4.24
39 40 0.030101 TGTTTGTAGGCACTTTGCGC 59.970 50.000 0.00 0.00 46.21 6.09
40 41 1.599419 GGTGTTTGTAGGCACTTTGCG 60.599 52.381 0.00 0.00 46.21 4.85
41 42 1.407258 TGGTGTTTGTAGGCACTTTGC 59.593 47.619 0.00 0.00 44.08 3.68
42 43 2.687935 AGTGGTGTTTGTAGGCACTTTG 59.312 45.455 0.00 0.00 41.75 2.77
43 44 2.949644 GAGTGGTGTTTGTAGGCACTTT 59.050 45.455 0.00 0.00 41.75 2.66
44 45 2.572290 GAGTGGTGTTTGTAGGCACTT 58.428 47.619 0.00 0.00 41.75 3.16
45 46 1.540363 CGAGTGGTGTTTGTAGGCACT 60.540 52.381 0.00 0.00 46.37 4.40
46 47 0.865769 CGAGTGGTGTTTGTAGGCAC 59.134 55.000 0.00 0.00 35.07 5.01
47 48 0.250124 CCGAGTGGTGTTTGTAGGCA 60.250 55.000 0.00 0.00 0.00 4.75
48 49 2.540145 CCGAGTGGTGTTTGTAGGC 58.460 57.895 0.00 0.00 0.00 3.93
59 60 4.394712 GCCTGGGTCACCGAGTGG 62.395 72.222 4.97 0.00 40.75 4.00
60 61 3.314331 AGCCTGGGTCACCGAGTG 61.314 66.667 4.97 0.00 40.75 3.51
61 62 3.314331 CAGCCTGGGTCACCGAGT 61.314 66.667 4.97 0.00 40.75 4.18
62 63 2.997315 TCAGCCTGGGTCACCGAG 60.997 66.667 0.00 0.00 40.75 4.63
63 64 2.805313 ATCTCAGCCTGGGTCACCGA 62.805 60.000 0.00 0.00 40.75 4.69
64 65 2.362369 ATCTCAGCCTGGGTCACCG 61.362 63.158 0.00 0.00 40.75 4.94
65 66 1.222936 CATCTCAGCCTGGGTCACC 59.777 63.158 0.00 0.00 37.24 4.02
66 67 1.451028 GCATCTCAGCCTGGGTCAC 60.451 63.158 0.00 0.00 0.00 3.67
67 68 2.993008 GCATCTCAGCCTGGGTCA 59.007 61.111 0.00 0.00 0.00 4.02
75 76 2.720915 AGGAAAAGAAGGCATCTCAGC 58.279 47.619 0.00 0.00 37.42 4.26
76 77 5.242393 TGAAAAGGAAAAGAAGGCATCTCAG 59.758 40.000 0.00 0.00 37.42 3.35
77 78 5.139727 TGAAAAGGAAAAGAAGGCATCTCA 58.860 37.500 0.00 0.00 37.42 3.27
78 79 5.242615 ACTGAAAAGGAAAAGAAGGCATCTC 59.757 40.000 0.00 0.00 37.42 2.75
79 80 5.143369 ACTGAAAAGGAAAAGAAGGCATCT 58.857 37.500 0.00 0.00 41.32 2.90
80 81 5.459536 ACTGAAAAGGAAAAGAAGGCATC 57.540 39.130 0.00 0.00 0.00 3.91
81 82 4.022849 CGACTGAAAAGGAAAAGAAGGCAT 60.023 41.667 0.00 0.00 0.00 4.40
82 83 3.315191 CGACTGAAAAGGAAAAGAAGGCA 59.685 43.478 0.00 0.00 0.00 4.75
83 84 3.564225 TCGACTGAAAAGGAAAAGAAGGC 59.436 43.478 0.00 0.00 0.00 4.35
84 85 5.751243 TTCGACTGAAAAGGAAAAGAAGG 57.249 39.130 0.00 0.00 0.00 3.46
85 86 5.971792 GGTTTCGACTGAAAAGGAAAAGAAG 59.028 40.000 0.00 0.00 45.22 2.85
86 87 5.448089 CGGTTTCGACTGAAAAGGAAAAGAA 60.448 40.000 0.00 0.00 45.22 2.52
87 88 4.034742 CGGTTTCGACTGAAAAGGAAAAGA 59.965 41.667 0.00 0.00 45.22 2.52
88 89 4.279659 CGGTTTCGACTGAAAAGGAAAAG 58.720 43.478 0.00 0.00 45.22 2.27
89 90 3.065648 CCGGTTTCGACTGAAAAGGAAAA 59.934 43.478 0.00 0.00 45.22 2.29
90 91 2.614983 CCGGTTTCGACTGAAAAGGAAA 59.385 45.455 0.00 0.00 45.22 3.13
91 92 2.215196 CCGGTTTCGACTGAAAAGGAA 58.785 47.619 0.00 0.00 45.22 3.36
92 93 1.139455 ACCGGTTTCGACTGAAAAGGA 59.861 47.619 0.00 0.00 45.22 3.36
93 94 1.589803 ACCGGTTTCGACTGAAAAGG 58.410 50.000 0.00 10.20 45.22 3.11
94 95 2.353579 ACAACCGGTTTCGACTGAAAAG 59.646 45.455 19.55 4.07 45.22 2.27
95 96 2.358015 ACAACCGGTTTCGACTGAAAA 58.642 42.857 19.55 0.00 45.22 2.29
96 97 2.027003 ACAACCGGTTTCGACTGAAA 57.973 45.000 19.55 0.00 41.69 2.69
97 98 2.865551 GTTACAACCGGTTTCGACTGAA 59.134 45.455 19.55 1.23 39.00 3.02
98 99 2.472816 GTTACAACCGGTTTCGACTGA 58.527 47.619 19.55 0.00 39.00 3.41
99 100 1.528161 GGTTACAACCGGTTTCGACTG 59.472 52.381 19.55 8.85 39.66 3.51
100 101 1.869774 GGTTACAACCGGTTTCGACT 58.130 50.000 19.55 0.13 39.66 4.18
111 112 6.515272 AAGATTGATCATGGTGGTTACAAC 57.485 37.500 0.00 0.00 33.91 3.32
112 113 7.537596 AAAAGATTGATCATGGTGGTTACAA 57.462 32.000 0.00 0.00 0.00 2.41
113 114 7.232330 TCAAAAAGATTGATCATGGTGGTTACA 59.768 33.333 0.00 0.00 0.00 2.41
114 115 7.601856 TCAAAAAGATTGATCATGGTGGTTAC 58.398 34.615 0.00 0.00 0.00 2.50
115 116 7.773489 TCAAAAAGATTGATCATGGTGGTTA 57.227 32.000 0.00 0.00 0.00 2.85
116 117 6.669125 TCAAAAAGATTGATCATGGTGGTT 57.331 33.333 0.00 0.00 0.00 3.67
117 118 6.862469 ATCAAAAAGATTGATCATGGTGGT 57.138 33.333 0.00 0.00 34.28 4.16
125 126 5.225949 GCGTTCACGATCAAAAAGATTGATC 59.774 40.000 17.18 17.18 46.85 2.92
126 127 5.088739 GCGTTCACGATCAAAAAGATTGAT 58.911 37.500 2.87 3.48 40.08 2.57
127 128 4.024472 TGCGTTCACGATCAAAAAGATTGA 60.024 37.500 2.87 0.00 40.08 2.57
128 129 4.218265 TGCGTTCACGATCAAAAAGATTG 58.782 39.130 2.87 0.00 42.84 2.67
129 130 4.481930 TGCGTTCACGATCAAAAAGATT 57.518 36.364 2.87 0.00 43.02 2.40
130 131 4.685169 ATGCGTTCACGATCAAAAAGAT 57.315 36.364 2.87 0.00 43.02 2.40
131 132 4.481930 AATGCGTTCACGATCAAAAAGA 57.518 36.364 2.87 0.00 43.02 2.52
132 133 4.661402 GCAAATGCGTTCACGATCAAAAAG 60.661 41.667 2.87 0.00 43.02 2.27
133 134 3.181377 GCAAATGCGTTCACGATCAAAAA 59.819 39.130 2.87 0.00 43.02 1.94
134 135 2.723658 GCAAATGCGTTCACGATCAAAA 59.276 40.909 2.87 0.00 43.02 2.44
135 136 2.315011 GCAAATGCGTTCACGATCAAA 58.685 42.857 2.87 0.00 43.02 2.69
136 137 1.400888 GGCAAATGCGTTCACGATCAA 60.401 47.619 2.87 0.00 43.26 2.57
137 138 0.167908 GGCAAATGCGTTCACGATCA 59.832 50.000 2.87 0.00 43.26 2.92
138 139 0.167908 TGGCAAATGCGTTCACGATC 59.832 50.000 2.87 0.00 43.26 3.69
139 140 0.810648 ATGGCAAATGCGTTCACGAT 59.189 45.000 2.87 0.00 43.26 3.73
140 141 0.167908 GATGGCAAATGCGTTCACGA 59.832 50.000 2.87 0.00 43.26 4.35
141 142 0.168788 AGATGGCAAATGCGTTCACG 59.831 50.000 0.00 0.00 43.26 4.35
142 143 2.095059 AGAAGATGGCAAATGCGTTCAC 60.095 45.455 0.00 0.00 43.26 3.18
143 144 2.161855 AGAAGATGGCAAATGCGTTCA 58.838 42.857 0.00 0.00 43.26 3.18
144 145 2.478539 GGAGAAGATGGCAAATGCGTTC 60.479 50.000 0.00 0.00 43.26 3.95
145 146 1.474077 GGAGAAGATGGCAAATGCGTT 59.526 47.619 0.00 0.00 43.26 4.84
146 147 1.098050 GGAGAAGATGGCAAATGCGT 58.902 50.000 0.00 0.00 43.26 5.24
147 148 0.383231 GGGAGAAGATGGCAAATGCG 59.617 55.000 0.00 0.00 43.26 4.73
148 149 1.407979 CAGGGAGAAGATGGCAAATGC 59.592 52.381 0.00 0.00 41.14 3.56
149 150 1.407979 GCAGGGAGAAGATGGCAAATG 59.592 52.381 0.00 0.00 0.00 2.32
150 151 1.287146 AGCAGGGAGAAGATGGCAAAT 59.713 47.619 0.00 0.00 0.00 2.32
151 152 0.700564 AGCAGGGAGAAGATGGCAAA 59.299 50.000 0.00 0.00 0.00 3.68
152 153 0.700564 AAGCAGGGAGAAGATGGCAA 59.299 50.000 0.00 0.00 0.00 4.52
153 154 1.583556 TAAGCAGGGAGAAGATGGCA 58.416 50.000 0.00 0.00 0.00 4.92
154 155 2.717639 TTAAGCAGGGAGAAGATGGC 57.282 50.000 0.00 0.00 0.00 4.40
155 156 7.855375 TCATATATTAAGCAGGGAGAAGATGG 58.145 38.462 0.00 0.00 0.00 3.51
156 157 9.902684 ATTCATATATTAAGCAGGGAGAAGATG 57.097 33.333 0.00 0.00 0.00 2.90
157 158 9.902684 CATTCATATATTAAGCAGGGAGAAGAT 57.097 33.333 0.00 0.00 0.00 2.40
158 159 7.826252 GCATTCATATATTAAGCAGGGAGAAGA 59.174 37.037 0.00 0.00 0.00 2.87
159 160 7.066766 GGCATTCATATATTAAGCAGGGAGAAG 59.933 40.741 0.00 0.00 0.00 2.85
160 161 6.886459 GGCATTCATATATTAAGCAGGGAGAA 59.114 38.462 0.00 0.00 0.00 2.87
161 162 6.012596 TGGCATTCATATATTAAGCAGGGAGA 60.013 38.462 0.00 0.00 0.00 3.71
162 163 6.182627 TGGCATTCATATATTAAGCAGGGAG 58.817 40.000 0.00 0.00 0.00 4.30
163 164 6.138391 TGGCATTCATATATTAAGCAGGGA 57.862 37.500 0.00 0.00 0.00 4.20
164 165 5.948162 ACTGGCATTCATATATTAAGCAGGG 59.052 40.000 0.00 0.00 0.00 4.45
165 166 6.656270 TCACTGGCATTCATATATTAAGCAGG 59.344 38.462 0.00 0.00 0.00 4.85
166 167 7.677454 TCACTGGCATTCATATATTAAGCAG 57.323 36.000 0.00 0.00 0.00 4.24
167 168 9.166173 GTATCACTGGCATTCATATATTAAGCA 57.834 33.333 0.00 0.00 0.00 3.91
168 169 9.166173 TGTATCACTGGCATTCATATATTAAGC 57.834 33.333 0.00 0.00 0.00 3.09
186 187 5.808366 TCTGAAAGAACCAGTGTATCACT 57.192 39.130 0.00 0.00 43.00 3.41
211 212 7.893124 AGGATGAATAGAGTGCATCATTTTT 57.107 32.000 0.00 0.00 40.03 1.94
212 213 7.014038 GGAAGGATGAATAGAGTGCATCATTTT 59.986 37.037 0.00 0.00 41.38 1.82
419 420 3.699038 TGCCATTTGCAAGGTTATACCTC 59.301 43.478 0.00 0.00 46.04 3.85
490 491 2.093128 ACGTGTCATTCCCACCTAATCC 60.093 50.000 0.00 0.00 0.00 3.01
500 1765 2.411547 CGAAGCTTTGACGTGTCATTCC 60.412 50.000 8.08 0.00 39.64 3.01
548 1813 1.214589 GGACTTTCGTCGGCTGCTA 59.785 57.895 0.00 0.00 41.16 3.49
602 1868 1.827394 ATGCATGCATGGGCCTTTC 59.173 52.632 31.74 9.80 40.13 2.62
644 1911 4.370364 TGTGAAAGCTGAAAGTTGAACC 57.630 40.909 0.00 0.00 35.30 3.62
675 1949 1.131883 GCATGCATGGTCTTCTGTGAC 59.868 52.381 27.34 2.90 36.31 3.67
705 1979 2.289547 ACGGTGTCAATTCGTTTTCAGG 59.710 45.455 0.00 0.00 32.95 3.86
896 2192 0.466124 GCCTGGGATTACTCGCTTCT 59.534 55.000 0.00 0.00 35.45 2.85
897 2193 0.466124 AGCCTGGGATTACTCGCTTC 59.534 55.000 0.00 0.00 35.45 3.86
898 2194 0.466124 GAGCCTGGGATTACTCGCTT 59.534 55.000 0.00 0.00 35.45 4.68
935 2231 1.524621 GTGGCAGCAGTGTGTGACT 60.525 57.895 0.00 0.00 34.02 3.41
974 2270 0.601576 TTCGCTTGCTTGCTTCGGTA 60.602 50.000 0.00 0.00 0.00 4.02
992 2292 2.680913 GCGTGCACCATCTTCGCTT 61.681 57.895 12.15 0.00 42.88 4.68
993 2293 3.121030 GCGTGCACCATCTTCGCT 61.121 61.111 12.15 0.00 42.88 4.93
994 2294 4.166011 GGCGTGCACCATCTTCGC 62.166 66.667 12.15 9.28 44.95 4.70
995 2295 3.853330 CGGCGTGCACCATCTTCG 61.853 66.667 12.15 0.00 0.00 3.79
996 2296 4.166011 GCGGCGTGCACCATCTTC 62.166 66.667 12.15 0.00 45.45 2.87
1344 2653 2.755876 TCCTCGATGCCGTGCTCT 60.756 61.111 0.00 0.00 37.05 4.09
1490 2799 6.115446 TCTGGCATGTTAAATACTCAGGAAG 58.885 40.000 0.00 0.00 0.00 3.46
1492 2801 5.425217 TCTCTGGCATGTTAAATACTCAGGA 59.575 40.000 0.00 0.00 0.00 3.86
1493 2802 5.674525 TCTCTGGCATGTTAAATACTCAGG 58.325 41.667 0.00 0.00 0.00 3.86
1494 2803 7.119699 TGTTTCTCTGGCATGTTAAATACTCAG 59.880 37.037 0.00 0.00 0.00 3.35
1544 3124 7.780064 TGGTGAATATGTGAAATATGTTTGGG 58.220 34.615 0.00 0.00 0.00 4.12
1753 8503 9.836864 AAAGAAGGTCAAGCTTATTTCAAAAAT 57.163 25.926 0.00 0.00 0.00 1.82
1766 8516 7.823149 TTTACGAGTATAAAGAAGGTCAAGC 57.177 36.000 0.00 0.00 0.00 4.01
1810 8562 1.971695 GGCCCTGAAAGTCAACGGG 60.972 63.158 0.00 0.00 37.97 5.28
1834 8586 7.717875 TCACTATACACACTTTTTAGCCAAGTT 59.282 33.333 0.00 0.00 31.83 2.66
1836 8588 7.387948 AGTCACTATACACACTTTTTAGCCAAG 59.612 37.037 0.00 0.00 0.00 3.61
1837 8589 7.221450 AGTCACTATACACACTTTTTAGCCAA 58.779 34.615 0.00 0.00 0.00 4.52
1838 8590 6.765403 AGTCACTATACACACTTTTTAGCCA 58.235 36.000 0.00 0.00 0.00 4.75
1839 8591 7.172703 ACAAGTCACTATACACACTTTTTAGCC 59.827 37.037 0.00 0.00 0.00 3.93
1840 8592 8.084590 ACAAGTCACTATACACACTTTTTAGC 57.915 34.615 0.00 0.00 0.00 3.09
1871 8626 8.376889 TCTGGGAAAAAGACAAAATTTATTGC 57.623 30.769 0.00 0.00 33.52 3.56
1874 8629 9.764363 GACTTCTGGGAAAAAGACAAAATTTAT 57.236 29.630 0.00 0.00 0.00 1.40
1875 8630 8.754080 TGACTTCTGGGAAAAAGACAAAATTTA 58.246 29.630 0.00 0.00 0.00 1.40
1877 8632 7.181569 TGACTTCTGGGAAAAAGACAAAATT 57.818 32.000 0.00 0.00 0.00 1.82
1879 8634 6.394809 GTTGACTTCTGGGAAAAAGACAAAA 58.605 36.000 0.00 0.00 38.32 2.44
1883 8638 3.626217 ACGTTGACTTCTGGGAAAAAGAC 59.374 43.478 0.00 0.00 0.00 3.01
1884 8639 3.881220 ACGTTGACTTCTGGGAAAAAGA 58.119 40.909 0.00 0.00 0.00 2.52
1885 8640 5.941948 ATACGTTGACTTCTGGGAAAAAG 57.058 39.130 0.00 0.00 0.00 2.27
1890 8647 9.321562 GAATATAAAATACGTTGACTTCTGGGA 57.678 33.333 0.00 0.00 0.00 4.37
1893 8650 7.522884 CGCGAATATAAAATACGTTGACTTCTG 59.477 37.037 0.00 0.00 0.00 3.02
1897 8654 7.453980 TTCGCGAATATAAAATACGTTGACT 57.546 32.000 19.38 0.00 0.00 3.41
2058 8819 5.071115 ACTTGTATTGAAGGGGCTAGAGATC 59.929 44.000 0.00 0.00 0.00 2.75
2098 8860 1.488393 GGGTGCTCTGAGGAATTAGCT 59.512 52.381 6.83 0.00 35.95 3.32
2104 8866 1.065410 TTTGGGGGTGCTCTGAGGAA 61.065 55.000 6.83 0.00 0.00 3.36
2111 8873 2.594131 AGTTAAGTTTTGGGGGTGCTC 58.406 47.619 0.00 0.00 0.00 4.26
2119 8881 9.807386 CTTAAATGTCGAGTAGTTAAGTTTTGG 57.193 33.333 15.80 0.00 33.45 3.28
2137 8899 7.187824 TGAGATGCTCTAACTCCTTAAATGT 57.812 36.000 0.00 0.00 0.00 2.71
2166 8928 3.133542 GCTATGTACGTTTTAGGGGTCCT 59.866 47.826 0.00 0.00 37.71 3.85
2191 8953 0.040514 CCAAACGCATTTGCAGACGA 60.041 50.000 0.00 0.00 43.38 4.20
2203 8965 2.699212 GCGGACGTATCCAAACGC 59.301 61.111 0.00 0.00 46.67 4.84
2208 8970 2.122797 ATGTCCGCGGACGTATCCA 61.123 57.895 43.58 29.82 46.67 3.41
2223 8985 0.179045 GCCGCCTCTTGTATCCATGT 60.179 55.000 0.00 0.00 0.00 3.21
2258 9020 4.935205 TCGAAATGTGTAGGGATGTTTGAG 59.065 41.667 0.00 0.00 0.00 3.02
2261 9023 5.125417 CCATTCGAAATGTGTAGGGATGTTT 59.875 40.000 0.00 0.00 0.00 2.83
2301 9063 1.068055 CCTGCTTGCATGGAAGTTGTC 60.068 52.381 25.43 11.29 0.00 3.18
2304 9066 1.822990 CATCCTGCTTGCATGGAAGTT 59.177 47.619 25.43 5.90 33.20 2.66
2351 9113 5.298989 TGACCCTTTTTCTACTAGTGCAA 57.701 39.130 5.39 0.00 0.00 4.08
2352 9114 4.967084 TGACCCTTTTTCTACTAGTGCA 57.033 40.909 5.39 0.00 0.00 4.57
2353 9115 5.582665 CAGATGACCCTTTTTCTACTAGTGC 59.417 44.000 5.39 0.00 0.00 4.40
2354 9116 6.702329 ACAGATGACCCTTTTTCTACTAGTG 58.298 40.000 5.39 0.00 0.00 2.74
2355 9117 6.070710 GGACAGATGACCCTTTTTCTACTAGT 60.071 42.308 0.00 0.00 0.00 2.57
2356 9118 6.342111 GGACAGATGACCCTTTTTCTACTAG 58.658 44.000 0.00 0.00 0.00 2.57
2357 9119 5.189145 GGGACAGATGACCCTTTTTCTACTA 59.811 44.000 12.40 0.00 44.84 1.82
2358 9120 4.019231 GGGACAGATGACCCTTTTTCTACT 60.019 45.833 12.40 0.00 44.84 2.57
2359 9121 4.262617 GGGACAGATGACCCTTTTTCTAC 58.737 47.826 12.40 0.00 44.84 2.59
2360 9122 3.055385 CGGGACAGATGACCCTTTTTCTA 60.055 47.826 16.56 0.00 45.84 2.10
2361 9123 2.290323 CGGGACAGATGACCCTTTTTCT 60.290 50.000 16.56 0.00 45.84 2.52
2362 9124 2.084546 CGGGACAGATGACCCTTTTTC 58.915 52.381 16.56 0.00 45.84 2.29
2363 9125 1.271926 CCGGGACAGATGACCCTTTTT 60.272 52.381 16.56 0.00 45.84 1.94
2364 9126 0.328258 CCGGGACAGATGACCCTTTT 59.672 55.000 16.56 0.00 45.84 2.27
2365 9127 0.840722 ACCGGGACAGATGACCCTTT 60.841 55.000 16.56 2.55 45.84 3.11
2366 9128 0.840722 AACCGGGACAGATGACCCTT 60.841 55.000 16.56 4.36 45.84 3.95
2367 9129 1.229529 AACCGGGACAGATGACCCT 60.230 57.895 16.56 0.00 45.84 4.34
2368 9130 1.078426 CAACCGGGACAGATGACCC 60.078 63.158 6.32 9.97 44.81 4.46
2369 9131 1.078426 CCAACCGGGACAGATGACC 60.078 63.158 6.32 0.00 40.01 4.02
2370 9132 0.899720 TACCAACCGGGACAGATGAC 59.100 55.000 6.32 0.00 41.15 3.06
2371 9133 1.553248 CTTACCAACCGGGACAGATGA 59.447 52.381 6.32 0.00 41.15 2.92
2372 9134 1.406887 CCTTACCAACCGGGACAGATG 60.407 57.143 6.32 0.00 41.15 2.90
2373 9135 0.909623 CCTTACCAACCGGGACAGAT 59.090 55.000 6.32 0.00 41.15 2.90
2374 9136 1.196104 CCCTTACCAACCGGGACAGA 61.196 60.000 6.32 0.00 40.55 3.41
2375 9137 1.298667 CCCTTACCAACCGGGACAG 59.701 63.158 6.32 0.00 40.55 3.51
2376 9138 2.897762 GCCCTTACCAACCGGGACA 61.898 63.158 6.32 0.00 40.55 4.02
2377 9139 2.045634 GCCCTTACCAACCGGGAC 60.046 66.667 6.32 0.00 40.55 4.46
2378 9140 3.332385 GGCCCTTACCAACCGGGA 61.332 66.667 6.32 0.00 40.55 5.14
2379 9141 2.435120 AAAGGCCCTTACCAACCGGG 62.435 60.000 6.32 0.00 44.81 5.73
2380 9142 0.541063 AAAAGGCCCTTACCAACCGG 60.541 55.000 0.00 0.00 38.77 5.28
2381 9143 0.601057 CAAAAGGCCCTTACCAACCG 59.399 55.000 0.00 0.00 0.00 4.44
2382 9144 1.616865 GACAAAAGGCCCTTACCAACC 59.383 52.381 0.00 0.00 0.00 3.77
2383 9145 1.616865 GGACAAAAGGCCCTTACCAAC 59.383 52.381 0.00 0.00 0.00 3.77
2384 9146 1.481615 GGGACAAAAGGCCCTTACCAA 60.482 52.381 0.00 0.00 41.31 3.67
2385 9147 0.113580 GGGACAAAAGGCCCTTACCA 59.886 55.000 0.00 0.00 41.31 3.25
2386 9148 0.963856 CGGGACAAAAGGCCCTTACC 60.964 60.000 4.64 0.00 42.40 2.85
2387 9149 0.963856 CCGGGACAAAAGGCCCTTAC 60.964 60.000 4.64 0.00 42.40 2.34
2388 9150 1.381076 CCGGGACAAAAGGCCCTTA 59.619 57.895 4.64 0.00 42.40 2.69
2389 9151 2.117423 CCGGGACAAAAGGCCCTT 59.883 61.111 4.64 0.00 42.40 3.95
2390 9152 2.708593 GAACCGGGACAAAAGGCCCT 62.709 60.000 6.32 0.00 42.40 5.19
2391 9153 2.203582 AACCGGGACAAAAGGCCC 60.204 61.111 6.32 0.00 41.11 5.80
2392 9154 0.826256 AAGAACCGGGACAAAAGGCC 60.826 55.000 6.32 0.00 0.00 5.19
2393 9155 0.313987 CAAGAACCGGGACAAAAGGC 59.686 55.000 6.32 0.00 0.00 4.35
2394 9156 1.975660 TCAAGAACCGGGACAAAAGG 58.024 50.000 6.32 0.00 0.00 3.11
2395 9157 3.349488 GTTCAAGAACCGGGACAAAAG 57.651 47.619 6.32 0.00 35.36 2.27
2406 9168 3.072211 CCTTTAGTCCCGGTTCAAGAAC 58.928 50.000 0.00 4.39 40.45 3.01
2407 9169 2.039348 CCCTTTAGTCCCGGTTCAAGAA 59.961 50.000 0.00 0.00 0.00 2.52
2408 9170 1.626825 CCCTTTAGTCCCGGTTCAAGA 59.373 52.381 0.00 0.00 0.00 3.02
2409 9171 1.350019 ACCCTTTAGTCCCGGTTCAAG 59.650 52.381 0.00 0.00 0.00 3.02
2410 9172 1.348696 GACCCTTTAGTCCCGGTTCAA 59.651 52.381 0.00 0.00 0.00 2.69
2411 9173 0.978907 GACCCTTTAGTCCCGGTTCA 59.021 55.000 0.00 0.00 0.00 3.18
2412 9174 0.108472 CGACCCTTTAGTCCCGGTTC 60.108 60.000 0.00 0.00 32.91 3.62
2413 9175 0.833409 ACGACCCTTTAGTCCCGGTT 60.833 55.000 0.00 0.00 32.91 4.44
2414 9176 0.833409 AACGACCCTTTAGTCCCGGT 60.833 55.000 0.00 0.00 32.91 5.28
2415 9177 1.134995 GTAACGACCCTTTAGTCCCGG 60.135 57.143 0.00 0.00 32.91 5.73
2416 9178 1.821136 AGTAACGACCCTTTAGTCCCG 59.179 52.381 0.00 0.00 32.91 5.14
2417 9179 5.354767 CATTAGTAACGACCCTTTAGTCCC 58.645 45.833 0.00 0.00 32.91 4.46
2418 9180 4.807834 GCATTAGTAACGACCCTTTAGTCC 59.192 45.833 0.00 0.00 32.91 3.85
2419 9181 4.807834 GGCATTAGTAACGACCCTTTAGTC 59.192 45.833 0.00 0.00 0.00 2.59
2420 9182 4.383444 GGGCATTAGTAACGACCCTTTAGT 60.383 45.833 8.75 0.00 34.34 2.24
2421 9183 4.124970 GGGCATTAGTAACGACCCTTTAG 58.875 47.826 8.75 0.00 34.34 1.85
2422 9184 3.776417 AGGGCATTAGTAACGACCCTTTA 59.224 43.478 11.72 0.00 45.55 1.85
2423 9185 2.574824 AGGGCATTAGTAACGACCCTTT 59.425 45.455 11.72 0.00 45.55 3.11
2424 9186 2.193993 AGGGCATTAGTAACGACCCTT 58.806 47.619 11.72 0.48 45.55 3.95
2425 9187 1.875488 AGGGCATTAGTAACGACCCT 58.125 50.000 11.72 11.72 42.97 4.34
2426 9188 3.382048 CTAGGGCATTAGTAACGACCC 57.618 52.381 0.00 3.07 37.63 4.46


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

AutoCloner maintained by Alex Coulton.