Multiple sequence alignment - TraesCS5B01G560700

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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 TraesCS5B01G560700 chr5B 100.000 4916 0 0 1 4916 707189867 707194782 0.000000e+00 9079.0
1 TraesCS5B01G560700 chr5B 82.848 3195 469 54 971 4122 707420160 707423318 0.000000e+00 2791.0
2 TraesCS5B01G560700 chr5B 83.566 2221 335 21 941 3155 707407858 707410054 0.000000e+00 2052.0
3 TraesCS5B01G560700 chr5B 82.694 1878 287 28 2256 4117 707415555 707417410 0.000000e+00 1633.0
4 TraesCS5B01G560700 chr5B 89.709 894 83 5 3226 4112 707410164 707411055 0.000000e+00 1133.0
5 TraesCS5B01G560700 chr5B 80.799 1276 235 9 972 2245 707414221 707415488 0.000000e+00 990.0
6 TraesCS5B01G560700 chr5B 96.084 332 13 0 2841 3172 707387297 707387628 4.330000e-150 542.0
7 TraesCS5B01G560700 chr5B 87.968 374 21 7 3908 4258 707387623 707387995 2.120000e-113 420.0
8 TraesCS5B01G560700 chr5D 94.871 2203 100 7 660 2856 565832222 565830027 0.000000e+00 3430.0
9 TraesCS5B01G560700 chr5D 82.905 3188 484 46 972 4122 565713986 565710823 0.000000e+00 2811.0
10 TraesCS5B01G560700 chr5D 82.430 2675 402 43 1491 4136 565736020 565733385 0.000000e+00 2274.0
11 TraesCS5B01G560700 chr5D 82.949 2340 363 26 1793 4117 565719869 565717551 0.000000e+00 2078.0
12 TraesCS5B01G560700 chr5D 92.051 1497 79 15 2844 4320 565824732 565823256 0.000000e+00 2069.0
13 TraesCS5B01G560700 chr5D 82.373 2326 365 30 1820 4131 565729348 565727054 0.000000e+00 1982.0
14 TraesCS5B01G560700 chr5D 80.796 854 138 18 977 1818 565732053 565731214 0.000000e+00 645.0
15 TraesCS5B01G560700 chr5D 86.667 555 44 15 264 798 565895899 565895355 5.480000e-164 588.0
16 TraesCS5B01G560700 chr5D 91.176 170 13 2 792 960 565885436 565885268 3.830000e-56 230.0
17 TraesCS5B01G560700 chr5D 92.308 156 12 0 949 1104 565841274 565841119 6.400000e-54 222.0
18 TraesCS5B01G560700 chr5D 89.262 149 15 1 61 208 421651316 421651464 8.400000e-43 185.0
19 TraesCS5B01G560700 chr4A 82.449 3168 508 37 972 4117 607279990 607276849 0.000000e+00 2726.0
20 TraesCS5B01G560700 chr4A 82.196 3196 496 52 972 4122 607274151 607270984 0.000000e+00 2682.0
21 TraesCS5B01G560700 chr4A 88.235 340 22 12 271 599 607357341 607357009 1.660000e-104 390.0
22 TraesCS5B01G560700 chr4A 81.481 297 31 12 3843 4136 607283745 607283470 6.400000e-54 222.0
23 TraesCS5B01G560700 chr6D 75.924 2380 511 52 1558 3905 24335147 24332798 0.000000e+00 1164.0
24 TraesCS5B01G560700 chr4D 82.293 593 85 15 4314 4891 468306680 468306093 3.420000e-136 496.0
25 TraesCS5B01G560700 chr4D 88.571 280 26 5 4314 4589 422507824 422508101 7.880000e-88 335.0
26 TraesCS5B01G560700 chr4D 87.446 231 23 5 4314 4540 396423790 396424018 1.360000e-65 261.0
27 TraesCS5B01G560700 chr1B 86.667 270 31 4 4314 4580 660884527 660884794 1.340000e-75 294.0
28 TraesCS5B01G560700 chr1B 81.250 288 31 10 1 267 629720358 629720073 1.390000e-50 211.0
29 TraesCS5B01G560700 chr7B 85.766 274 26 4 5 266 425362621 425362893 1.350000e-70 278.0
30 TraesCS5B01G560700 chr7B 85.782 211 29 1 1 210 675050427 675050637 6.400000e-54 222.0
31 TraesCS5B01G560700 chr3B 88.085 235 21 6 4314 4543 760166094 760166326 6.270000e-69 272.0
32 TraesCS5B01G560700 chr3B 87.448 239 25 4 4314 4548 760287340 760287577 2.260000e-68 270.0
33 TraesCS5B01G560700 chr3B 87.826 230 24 3 4313 4539 104645059 104644831 2.920000e-67 267.0
34 TraesCS5B01G560700 chr3B 82.443 262 33 4 1 250 379359803 379360063 2.980000e-52 217.0
35 TraesCS5B01G560700 chr7D 84.532 278 32 3 1 267 197295698 197295975 1.050000e-66 265.0
36 TraesCS5B01G560700 chr7D 84.375 288 24 8 1 267 43372765 43373052 3.770000e-66 263.0
37 TraesCS5B01G560700 chr7D 82.517 286 29 6 1 265 69078100 69078385 1.060000e-56 231.0
38 TraesCS5B01G560700 chr1D 87.500 232 23 5 4314 4542 198883812 198884040 3.770000e-66 263.0
39 TraesCS5B01G560700 chr1D 85.167 209 28 3 1 208 252483278 252483072 1.390000e-50 211.0
40 TraesCS5B01G560700 chr1D 94.828 58 3 0 210 267 418764136 418764079 1.880000e-14 91.6
41 TraesCS5B01G560700 chr1D 93.103 58 4 0 210 267 16341153 16341096 8.770000e-13 86.1
42 TraesCS5B01G560700 chr2D 83.793 290 24 6 1 267 19606827 19606538 2.270000e-63 254.0
43 TraesCS5B01G560700 chr2D 83.681 288 26 5 1 267 2335883 2336170 8.170000e-63 252.0
44 TraesCS5B01G560700 chr6B 85.246 244 30 5 4314 4554 711490402 711490162 3.800000e-61 246.0
45 TraesCS5B01G560700 chr3A 82.986 288 28 9 1 267 585565957 585566244 1.770000e-59 241.0
46 TraesCS5B01G560700 chr5A 85.567 194 27 1 1 193 568880564 568880371 8.340000e-48 202.0
47 TraesCS5B01G560700 chr5A 82.990 194 32 1 1 193 568757957 568757764 1.820000e-39 174.0
48 TraesCS5B01G560700 chr5A 80.822 219 31 3 1 208 121116647 121116429 1.420000e-35 161.0
49 TraesCS5B01G560700 chr3D 82.524 206 34 2 6 210 527231131 527231335 3.910000e-41 180.0
50 TraesCS5B01G560700 chr2A 79.167 288 38 11 1 267 779431581 779431295 3.910000e-41 180.0


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 TraesCS5B01G560700 chr5B 707189867 707194782 4915 False 9079.000000 9079 100.000000 1 4916 1 chr5B.!!$F1 4915
1 TraesCS5B01G560700 chr5B 707407858 707423318 15460 False 1719.800000 2791 83.923200 941 4122 5 chr5B.!!$F3 3181
2 TraesCS5B01G560700 chr5B 707387297 707387995 698 False 481.000000 542 92.026000 2841 4258 2 chr5B.!!$F2 1417
3 TraesCS5B01G560700 chr5D 565830027 565832222 2195 True 3430.000000 3430 94.871000 660 2856 1 chr5D.!!$R2 2196
4 TraesCS5B01G560700 chr5D 565710823 565719869 9046 True 2444.500000 2811 82.927000 972 4122 2 chr5D.!!$R6 3150
5 TraesCS5B01G560700 chr5D 565823256 565824732 1476 True 2069.000000 2069 92.051000 2844 4320 1 chr5D.!!$R1 1476
6 TraesCS5B01G560700 chr5D 565727054 565736020 8966 True 1633.666667 2274 81.866333 977 4136 3 chr5D.!!$R7 3159
7 TraesCS5B01G560700 chr5D 565895355 565895899 544 True 588.000000 588 86.667000 264 798 1 chr5D.!!$R5 534
8 TraesCS5B01G560700 chr4A 607270984 607283745 12761 True 1876.666667 2726 82.042000 972 4136 3 chr4A.!!$R2 3164
9 TraesCS5B01G560700 chr6D 24332798 24335147 2349 True 1164.000000 1164 75.924000 1558 3905 1 chr6D.!!$R1 2347
10 TraesCS5B01G560700 chr4D 468306093 468306680 587 True 496.000000 496 82.293000 4314 4891 1 chr4D.!!$R1 577

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
110 111 0.028110 GCCATCGGCTCGATTTTCAC 59.972 55.0 7.27 0.0 44.59 3.18 F
129 130 0.251916 CCGGCAACTATGTCTTCCCA 59.748 55.0 0.00 0.0 0.00 4.37 F
875 895 0.320421 CCGTGAACATGGACCGAACT 60.320 55.0 7.21 0.0 39.90 3.01 F
2137 4934 0.605319 CTTAAGCAACCTGACCGGCA 60.605 55.0 0.00 0.0 35.61 5.69 F
3488 28701 0.874390 CACAATGAGTTGTCCGGTGG 59.126 55.0 0.00 0.0 45.14 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1206 3991 0.694771 AGCAGTCATCAGCCTTCCAA 59.305 50.000 0.0 0.0 0.00 3.53 R
1401 4186 2.107950 TTTGCACCCCATAGAACTCG 57.892 50.000 0.0 0.0 0.00 4.18 R
2215 5012 3.420893 CCTCCAGGTTATTGTTGCTCAA 58.579 45.455 0.0 0.0 40.53 3.02 R
3636 28851 0.250513 ATTCCTGCGACAAGGGAGAC 59.749 55.000 0.0 0.0 37.96 3.36 R
4781 30067 0.033405 AGGATCGACGGGAAGGAAGA 60.033 55.000 0.0 0.0 0.00 2.87 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
20 21 3.786213 ACCAGATCCTAGAGTTTCCCT 57.214 47.619 0.00 0.00 0.00 4.20
22 23 2.625790 CCAGATCCTAGAGTTTCCCTCG 59.374 54.545 0.00 0.00 45.44 4.63
23 24 2.625790 CAGATCCTAGAGTTTCCCTCGG 59.374 54.545 0.00 0.00 45.44 4.63
24 25 2.514582 AGATCCTAGAGTTTCCCTCGGA 59.485 50.000 0.00 0.00 45.44 4.55
26 27 0.747852 CCTAGAGTTTCCCTCGGAGC 59.252 60.000 0.00 0.00 45.44 4.70
27 28 1.475403 CTAGAGTTTCCCTCGGAGCA 58.525 55.000 0.00 0.00 45.44 4.26
28 29 1.407258 CTAGAGTTTCCCTCGGAGCAG 59.593 57.143 0.00 0.00 45.44 4.24
29 30 1.448717 GAGTTTCCCTCGGAGCAGC 60.449 63.158 0.00 0.00 31.21 5.25
30 31 2.172483 GAGTTTCCCTCGGAGCAGCA 62.172 60.000 0.00 0.00 31.21 4.41
32 33 2.515979 TTTCCCTCGGAGCAGCACA 61.516 57.895 0.00 0.00 31.21 4.57
33 34 2.050836 TTTCCCTCGGAGCAGCACAA 62.051 55.000 0.00 0.00 31.21 3.33
35 36 2.345244 CCTCGGAGCAGCACAAGT 59.655 61.111 0.00 0.00 0.00 3.16
36 37 2.031516 CCTCGGAGCAGCACAAGTG 61.032 63.158 0.00 0.00 0.00 3.16
37 38 2.031012 TCGGAGCAGCACAAGTGG 59.969 61.111 2.00 0.00 0.00 4.00
38 39 3.052082 CGGAGCAGCACAAGTGGG 61.052 66.667 2.00 0.00 0.00 4.61
39 40 2.113986 GGAGCAGCACAAGTGGGT 59.886 61.111 2.00 0.00 0.00 4.51
40 41 1.529244 GGAGCAGCACAAGTGGGTT 60.529 57.895 2.00 0.00 0.00 4.11
41 42 1.656441 GAGCAGCACAAGTGGGTTG 59.344 57.895 2.00 0.00 42.48 3.77
42 43 1.799258 GAGCAGCACAAGTGGGTTGG 61.799 60.000 2.00 0.00 40.90 3.77
43 44 2.730094 CAGCACAAGTGGGTTGGC 59.270 61.111 2.00 0.00 40.90 4.52
45 46 1.829533 AGCACAAGTGGGTTGGCAG 60.830 57.895 2.00 0.00 40.90 4.85
46 47 2.127232 GCACAAGTGGGTTGGCAGT 61.127 57.895 2.00 0.00 40.90 4.40
48 49 1.238439 CACAAGTGGGTTGGCAGTAG 58.762 55.000 0.00 0.00 40.90 2.57
49 50 0.843984 ACAAGTGGGTTGGCAGTAGT 59.156 50.000 0.00 0.00 40.90 2.73
50 51 1.214424 ACAAGTGGGTTGGCAGTAGTT 59.786 47.619 0.00 0.00 40.90 2.24
51 52 2.440253 ACAAGTGGGTTGGCAGTAGTTA 59.560 45.455 0.00 0.00 40.90 2.24
54 55 2.642807 AGTGGGTTGGCAGTAGTTACAT 59.357 45.455 0.00 0.00 0.00 2.29
55 56 2.747446 GTGGGTTGGCAGTAGTTACATG 59.253 50.000 0.00 0.00 0.00 3.21
56 57 2.290641 TGGGTTGGCAGTAGTTACATGG 60.291 50.000 0.00 0.00 0.00 3.66
57 58 1.743394 GGTTGGCAGTAGTTACATGGC 59.257 52.381 0.00 2.76 39.75 4.40
58 59 1.396996 GTTGGCAGTAGTTACATGGCG 59.603 52.381 0.00 0.00 42.03 5.69
60 61 1.002659 TGGCAGTAGTTACATGGCGTT 59.997 47.619 0.00 0.00 42.03 4.84
61 62 1.396996 GGCAGTAGTTACATGGCGTTG 59.603 52.381 0.00 0.00 0.00 4.10
62 63 1.202031 GCAGTAGTTACATGGCGTTGC 60.202 52.381 0.00 0.00 0.00 4.17
83 84 4.114058 CCTTCATTAAGGTAACGACGGA 57.886 45.455 0.00 0.00 46.34 4.69
85 86 4.142315 CCTTCATTAAGGTAACGACGGAGA 60.142 45.833 0.00 0.00 46.34 3.71
86 87 5.389859 TTCATTAAGGTAACGACGGAGAA 57.610 39.130 0.00 0.00 46.39 2.87
109 110 2.393557 GCCATCGGCTCGATTTTCA 58.606 52.632 7.27 0.00 44.59 2.69
110 111 0.028110 GCCATCGGCTCGATTTTCAC 59.972 55.000 7.27 0.00 44.59 3.18
111 112 0.657840 CCATCGGCTCGATTTTCACC 59.342 55.000 7.27 0.00 44.59 4.02
114 115 2.791927 GGCTCGATTTTCACCGGC 59.208 61.111 0.00 0.00 0.00 6.13
115 116 2.038269 GGCTCGATTTTCACCGGCA 61.038 57.895 0.00 0.00 0.00 5.69
117 118 0.454452 GCTCGATTTTCACCGGCAAC 60.454 55.000 0.00 0.00 0.00 4.17
119 120 2.343101 CTCGATTTTCACCGGCAACTA 58.657 47.619 0.00 0.00 0.00 2.24
120 121 2.936498 CTCGATTTTCACCGGCAACTAT 59.064 45.455 0.00 0.00 0.00 2.12
121 122 2.675844 TCGATTTTCACCGGCAACTATG 59.324 45.455 0.00 0.00 0.00 2.23
122 123 2.418628 CGATTTTCACCGGCAACTATGT 59.581 45.455 0.00 0.00 0.00 2.29
123 124 3.485216 CGATTTTCACCGGCAACTATGTC 60.485 47.826 0.00 0.00 0.00 3.06
125 126 2.851263 TTCACCGGCAACTATGTCTT 57.149 45.000 0.00 0.00 0.00 3.01
126 127 2.380084 TCACCGGCAACTATGTCTTC 57.620 50.000 0.00 0.00 0.00 2.87
127 128 1.066430 TCACCGGCAACTATGTCTTCC 60.066 52.381 0.00 0.00 0.00 3.46
128 129 0.252197 ACCGGCAACTATGTCTTCCC 59.748 55.000 0.00 0.00 0.00 3.97
129 130 0.251916 CCGGCAACTATGTCTTCCCA 59.748 55.000 0.00 0.00 0.00 4.37
133 134 3.010420 GGCAACTATGTCTTCCCAACTC 58.990 50.000 0.00 0.00 0.00 3.01
134 135 2.673368 GCAACTATGTCTTCCCAACTCG 59.327 50.000 0.00 0.00 0.00 4.18
135 136 2.673368 CAACTATGTCTTCCCAACTCGC 59.327 50.000 0.00 0.00 0.00 5.03
137 138 2.093973 ACTATGTCTTCCCAACTCGCAG 60.094 50.000 0.00 0.00 0.00 5.18
138 139 0.674895 ATGTCTTCCCAACTCGCAGC 60.675 55.000 0.00 0.00 0.00 5.25
139 140 2.035442 GTCTTCCCAACTCGCAGCC 61.035 63.158 0.00 0.00 0.00 4.85
140 141 3.121030 CTTCCCAACTCGCAGCCG 61.121 66.667 0.00 0.00 0.00 5.52
141 142 4.697756 TTCCCAACTCGCAGCCGG 62.698 66.667 0.00 0.00 34.56 6.13
145 146 2.357517 CAACTCGCAGCCGGAACT 60.358 61.111 5.05 0.00 34.56 3.01
146 147 1.080093 CAACTCGCAGCCGGAACTA 60.080 57.895 5.05 0.00 34.56 2.24
147 148 1.078759 CAACTCGCAGCCGGAACTAG 61.079 60.000 5.05 0.00 34.56 2.57
148 149 1.248785 AACTCGCAGCCGGAACTAGA 61.249 55.000 5.05 0.00 34.56 2.43
149 150 1.226717 CTCGCAGCCGGAACTAGAC 60.227 63.158 5.05 0.00 34.56 2.59
150 151 2.579787 CGCAGCCGGAACTAGACG 60.580 66.667 5.05 0.00 0.00 4.18
156 157 1.008767 CCGGAACTAGACGGCGATC 60.009 63.158 16.62 7.71 43.96 3.69
157 158 1.445716 CCGGAACTAGACGGCGATCT 61.446 60.000 16.62 15.26 43.96 2.75
158 159 0.381089 CGGAACTAGACGGCGATCTT 59.619 55.000 16.62 0.00 0.00 2.40
160 161 1.404391 GGAACTAGACGGCGATCTTGA 59.596 52.381 16.62 0.00 0.00 3.02
161 162 2.541999 GGAACTAGACGGCGATCTTGAG 60.542 54.545 16.62 10.34 0.00 3.02
162 163 2.039818 ACTAGACGGCGATCTTGAGA 57.960 50.000 16.62 0.00 0.00 3.27
164 165 2.550606 ACTAGACGGCGATCTTGAGATC 59.449 50.000 16.62 10.32 45.60 2.75
165 166 0.671251 AGACGGCGATCTTGAGATCC 59.329 55.000 16.62 7.78 46.16 3.36
167 168 1.101635 ACGGCGATCTTGAGATCCGA 61.102 55.000 21.12 0.00 46.16 4.55
169 170 0.671251 GGCGATCTTGAGATCCGACT 59.329 55.000 13.80 0.00 46.16 4.18
170 171 1.880675 GGCGATCTTGAGATCCGACTA 59.119 52.381 13.80 0.00 46.16 2.59
171 172 2.490115 GGCGATCTTGAGATCCGACTAT 59.510 50.000 13.80 0.00 46.16 2.12
172 173 3.057174 GGCGATCTTGAGATCCGACTATT 60.057 47.826 13.80 0.00 46.16 1.73
173 174 4.162812 GCGATCTTGAGATCCGACTATTC 58.837 47.826 13.80 0.00 46.16 1.75
175 176 5.389778 CGATCTTGAGATCCGACTATTCAG 58.610 45.833 13.80 0.00 46.16 3.02
176 177 4.576216 TCTTGAGATCCGACTATTCAGC 57.424 45.455 0.00 0.00 0.00 4.26
177 178 3.319405 TCTTGAGATCCGACTATTCAGCC 59.681 47.826 0.00 0.00 0.00 4.85
178 179 2.950781 TGAGATCCGACTATTCAGCCT 58.049 47.619 0.00 0.00 0.00 4.58
179 180 2.887783 TGAGATCCGACTATTCAGCCTC 59.112 50.000 0.00 0.00 0.00 4.70
181 182 2.890311 AGATCCGACTATTCAGCCTCAG 59.110 50.000 0.00 0.00 0.00 3.35
182 183 1.403814 TCCGACTATTCAGCCTCAGG 58.596 55.000 0.00 0.00 0.00 3.86
193 194 3.775654 CCTCAGGCCGACCACCTC 61.776 72.222 0.00 0.00 39.06 3.85
194 195 3.775654 CTCAGGCCGACCACCTCC 61.776 72.222 0.00 0.00 39.06 4.30
209 210 2.833582 TCCGACGGAGGAGATGGC 60.834 66.667 13.88 0.00 34.92 4.40
210 211 3.147595 CCGACGGAGGAGATGGCA 61.148 66.667 8.64 0.00 0.00 4.92
211 212 2.415010 CGACGGAGGAGATGGCAG 59.585 66.667 0.00 0.00 0.00 4.85
212 213 2.107953 GACGGAGGAGATGGCAGC 59.892 66.667 0.00 0.00 0.00 5.25
213 214 3.781770 GACGGAGGAGATGGCAGCG 62.782 68.421 0.00 0.00 0.00 5.18
216 217 4.166888 GAGGAGATGGCAGCGGCA 62.167 66.667 11.88 9.25 43.71 5.69
217 218 4.479993 AGGAGATGGCAGCGGCAC 62.480 66.667 11.88 0.45 41.84 5.01
231 232 2.507944 GCACCGGCCAGATCAGAT 59.492 61.111 0.00 0.00 0.00 2.90
232 233 1.596477 GCACCGGCCAGATCAGATC 60.596 63.158 0.00 1.64 0.00 2.75
233 234 2.037620 GCACCGGCCAGATCAGATCT 62.038 60.000 7.15 7.15 41.15 2.75
243 244 1.686052 AGATCAGATCTGACCGAAGGC 59.314 52.381 27.37 10.69 46.60 4.35
260 261 2.879462 CGCCGCCGACTAGTCAAC 60.879 66.667 22.37 12.20 36.29 3.18
262 263 2.967397 CCGCCGACTAGTCAACCA 59.033 61.111 22.37 0.00 0.00 3.67
263 264 1.515954 CCGCCGACTAGTCAACCAT 59.484 57.895 22.37 0.00 0.00 3.55
264 265 0.806102 CCGCCGACTAGTCAACCATG 60.806 60.000 22.37 5.06 0.00 3.66
266 267 1.090052 GCCGACTAGTCAACCATGGC 61.090 60.000 22.37 19.83 0.00 4.40
269 270 1.740380 CGACTAGTCAACCATGGCAGG 60.740 57.143 22.37 0.99 31.99 4.85
278 279 2.675423 CATGGCAGGTGCAGCTGT 60.675 61.111 37.97 21.91 44.36 4.40
323 324 3.489229 CGAATGCTGTCTTCCTCGTATCA 60.489 47.826 0.00 0.00 0.00 2.15
324 325 4.626042 GAATGCTGTCTTCCTCGTATCAT 58.374 43.478 0.00 0.00 0.00 2.45
325 326 5.562890 CGAATGCTGTCTTCCTCGTATCATA 60.563 44.000 0.00 0.00 0.00 2.15
329 330 6.216569 TGCTGTCTTCCTCGTATCATATTTC 58.783 40.000 0.00 0.00 0.00 2.17
332 333 7.115663 GCTGTCTTCCTCGTATCATATTTCTTC 59.884 40.741 0.00 0.00 0.00 2.87
334 335 8.696374 TGTCTTCCTCGTATCATATTTCTTCTT 58.304 33.333 0.00 0.00 0.00 2.52
339 340 9.534565 TCCTCGTATCATATTTCTTCTTGAAAG 57.465 33.333 0.00 0.00 46.39 2.62
352 353 9.942850 TTTCTTCTTGAAAGTTTTGGAATTCTT 57.057 25.926 5.23 0.00 39.50 2.52
353 354 9.942850 TTCTTCTTGAAAGTTTTGGAATTCTTT 57.057 25.926 5.23 0.00 33.64 2.52
427 428 7.049754 TGATGAGCTCATTCTGCATAACTAAA 58.950 34.615 29.26 0.00 36.57 1.85
444 445 5.763876 ACTAAAAGATTGGCTAGTGGAGT 57.236 39.130 0.00 0.00 0.00 3.85
445 446 6.869206 ACTAAAAGATTGGCTAGTGGAGTA 57.131 37.500 0.00 0.00 0.00 2.59
446 447 6.641474 ACTAAAAGATTGGCTAGTGGAGTAC 58.359 40.000 0.00 0.00 0.00 2.73
448 449 6.869206 AAAAGATTGGCTAGTGGAGTACTA 57.131 37.500 0.00 0.00 40.89 1.82
477 487 2.749280 TACTGGACATGCAGACACAG 57.251 50.000 7.46 9.01 0.00 3.66
478 488 0.761187 ACTGGACATGCAGACACAGT 59.239 50.000 7.46 10.09 34.63 3.55
493 503 2.747446 ACACAGTTTCTTTCTGCGTTGT 59.253 40.909 0.00 0.00 36.50 3.32
495 505 4.201783 ACACAGTTTCTTTCTGCGTTGTAC 60.202 41.667 0.00 0.00 36.50 2.90
496 506 3.311596 ACAGTTTCTTTCTGCGTTGTACC 59.688 43.478 0.00 0.00 36.50 3.34
502 512 4.553323 TCTTTCTGCGTTGTACCTACTTC 58.447 43.478 0.00 0.00 0.00 3.01
516 526 3.853784 ACCTACTTCTGGAGGTAGAGACT 59.146 47.826 17.59 0.00 44.51 3.24
519 529 4.120946 ACTTCTGGAGGTAGAGACTTGT 57.879 45.455 0.00 0.00 0.00 3.16
520 530 4.083565 ACTTCTGGAGGTAGAGACTTGTC 58.916 47.826 0.00 0.00 0.00 3.18
543 554 6.472486 GTCAATTGATGTCTCGATCGTTTAGA 59.528 38.462 15.94 7.99 0.00 2.10
571 582 3.368248 ACCCATTCATCAGGTCCAATTG 58.632 45.455 0.00 0.00 0.00 2.32
572 583 3.011595 ACCCATTCATCAGGTCCAATTGA 59.988 43.478 7.12 0.00 0.00 2.57
577 589 2.301583 TCATCAGGTCCAATTGACGTCA 59.698 45.455 15.76 15.76 45.46 4.35
697 717 4.405680 ACAGGGTCTTGGAAAAGGAAAAAG 59.594 41.667 0.00 0.00 0.00 2.27
718 738 3.395941 AGAAGAGGAAACTTGGTGGACAT 59.604 43.478 0.00 0.00 44.43 3.06
737 757 1.609208 TGGACAGAAGCAGGCTTTTC 58.391 50.000 8.09 5.51 36.26 2.29
740 760 1.195674 GACAGAAGCAGGCTTTTCGAC 59.804 52.381 8.09 0.00 36.26 4.20
759 779 4.717313 GGCCGCCGGTCTCCTTTT 62.717 66.667 4.45 0.00 0.00 2.27
761 781 2.813908 CCGCCGGTCTCCTTTTCG 60.814 66.667 1.90 0.00 0.00 3.46
770 790 2.415224 GGTCTCCTTTTCGTCGGTAGAC 60.415 54.545 0.00 0.00 43.72 2.59
790 810 5.885465 AGACATTTTCATTTCCTCTCCACT 58.115 37.500 0.00 0.00 0.00 4.00
809 829 6.237154 TCCACTTGTAATCACATCATGACAA 58.763 36.000 0.00 0.00 41.24 3.18
825 845 1.669115 CAAGCAGGTCAGTGTCCCG 60.669 63.158 2.50 0.00 0.00 5.14
833 853 0.741915 GTCAGTGTCCCGGAGATCTC 59.258 60.000 14.75 14.75 0.00 2.75
850 870 9.788960 CGGAGATCTCGTTCAATAATATATCAA 57.211 33.333 16.46 0.00 0.00 2.57
875 895 0.320421 CCGTGAACATGGACCGAACT 60.320 55.000 7.21 0.00 39.90 3.01
878 898 1.535462 GTGAACATGGACCGAACTTGG 59.465 52.381 0.00 0.00 0.00 3.61
923 943 8.297426 GGGAGAAAATAGAACACTTACTTTTGG 58.703 37.037 0.00 0.00 0.00 3.28
932 952 3.573967 ACACTTACTTTTGGATGGCTTGG 59.426 43.478 0.00 0.00 0.00 3.61
1029 3814 2.101582 GCGTCTACTCTCCAACATCCAT 59.898 50.000 0.00 0.00 0.00 3.41
1032 3817 4.568359 CGTCTACTCTCCAACATCCATTTG 59.432 45.833 0.00 0.00 0.00 2.32
1047 3832 7.059788 ACATCCATTTGGTAACTATATGTGCA 58.940 34.615 0.00 0.00 36.34 4.57
1099 3884 7.388224 GCTTTGTAGAGTCATCATCATCATCAT 59.612 37.037 0.00 0.00 0.00 2.45
1100 3885 8.828688 TTTGTAGAGTCATCATCATCATCATC 57.171 34.615 0.00 0.00 0.00 2.92
1117 3902 3.173151 TCATCCTCTAGCCACTCAAACA 58.827 45.455 0.00 0.00 0.00 2.83
1137 3922 7.919091 TCAAACAATACGGTCACTAGATGTATC 59.081 37.037 0.00 0.00 31.20 2.24
1206 3991 2.441001 CCCTGCAAACCTCCTATCATCT 59.559 50.000 0.00 0.00 0.00 2.90
1254 4039 1.362224 AGGGTGTCCATTGCAGTAGT 58.638 50.000 0.00 0.00 34.83 2.73
1401 4186 1.818642 ATCTCAACCTCAGCTGCAAC 58.181 50.000 9.47 0.00 0.00 4.17
1714 4508 3.257393 AGCGACTGCAATCTTAGAACTG 58.743 45.455 0.00 0.00 46.23 3.16
1721 4515 6.162777 ACTGCAATCTTAGAACTGACTCTTC 58.837 40.000 0.00 0.00 0.00 2.87
1727 4521 6.961360 TCTTAGAACTGACTCTTCTTCACA 57.039 37.500 0.00 0.00 0.00 3.58
1884 4678 2.135933 CAATTTCCGGACGAGATAGGC 58.864 52.381 1.83 0.00 0.00 3.93
2137 4934 0.605319 CTTAAGCAACCTGACCGGCA 60.605 55.000 0.00 0.00 35.61 5.69
2215 5012 2.037772 ACGAAGCTGACTGAATTGGACT 59.962 45.455 0.00 0.00 0.00 3.85
2698 11892 1.968493 ACTTTGGAGCACCGAGTCTAA 59.032 47.619 3.68 0.00 39.42 2.10
2847 17928 7.418337 TGCTATTACCTCTGAGACAAACATA 57.582 36.000 6.17 0.00 0.00 2.29
3119 18206 6.945636 TTCCTACAATAATATGACGGGGAT 57.054 37.500 0.00 0.00 0.00 3.85
3387 18493 5.926542 CAGTCTTGTCGAATTGAAGAACCTA 59.073 40.000 0.00 0.00 0.00 3.08
3483 28696 4.579869 ACCTATCACACAATGAGTTGTCC 58.420 43.478 0.00 0.00 45.14 4.02
3488 28701 0.874390 CACAATGAGTTGTCCGGTGG 59.126 55.000 0.00 0.00 45.14 4.61
3498 28711 3.407967 TCCGGTGGAATCCCTGCC 61.408 66.667 0.00 0.00 0.00 4.85
3652 28867 2.266055 GGTCTCCCTTGTCGCAGG 59.734 66.667 0.00 0.00 0.00 4.85
3719 28937 5.063204 TGAAGATTTGAACGATGTGGTCTT 58.937 37.500 0.00 0.00 0.00 3.01
3756 28974 4.311613 TGGGTTCTGGATATGTAATGGGA 58.688 43.478 0.00 0.00 0.00 4.37
3971 29193 5.200483 AGTGTGGGGATTTTACCATGTATG 58.800 41.667 0.00 0.00 39.30 2.39
3987 29213 5.120674 CCATGTATGAATGTATAGCACCGTG 59.879 44.000 0.00 0.00 0.00 4.94
4087 29319 5.371176 TGTAATGAATAATGCCAGGGGTAGA 59.629 40.000 0.00 0.00 0.00 2.59
4091 29323 0.834612 TAATGCCAGGGGTAGAACCG 59.165 55.000 0.00 0.00 39.83 4.44
4125 29357 1.748493 GGGTGTGTGTGTCAATGTGTT 59.252 47.619 0.00 0.00 0.00 3.32
4126 29358 2.165437 GGGTGTGTGTGTCAATGTGTTT 59.835 45.455 0.00 0.00 0.00 2.83
4131 29377 6.183360 GGTGTGTGTGTCAATGTGTTTAGTTA 60.183 38.462 0.00 0.00 0.00 2.24
4132 29378 7.244898 GTGTGTGTGTCAATGTGTTTAGTTAA 58.755 34.615 0.00 0.00 0.00 2.01
4133 29379 7.217447 GTGTGTGTGTCAATGTGTTTAGTTAAC 59.783 37.037 0.00 0.00 37.26 2.01
4134 29380 7.119992 TGTGTGTGTCAATGTGTTTAGTTAACT 59.880 33.333 13.68 13.68 37.64 2.24
4135 29381 7.428183 GTGTGTGTCAATGTGTTTAGTTAACTG 59.572 37.037 18.56 0.00 37.64 3.16
4219 29474 0.733909 GAATTTGGTCTGCGCAAGGC 60.734 55.000 13.05 7.27 43.96 4.35
4253 29508 9.739276 TTTATTGTGTTGATTCTTACTCTGGAT 57.261 29.630 0.00 0.00 0.00 3.41
4270 29525 1.284982 GATGCAGTATACTGGGCGCG 61.285 60.000 29.45 0.00 43.94 6.86
4279 29534 4.201679 CTGGGCGCGGACGTGATA 62.202 66.667 8.83 0.00 42.83 2.15
4328 29584 6.979238 GGGTTCAGACTGTTAGATGTGTATAC 59.021 42.308 1.59 0.00 0.00 1.47
4331 29587 7.569639 TCAGACTGTTAGATGTGTATACTCC 57.430 40.000 4.17 0.00 0.00 3.85
4348 29604 3.937751 ACTCCCTTTTCGGTATATCCCT 58.062 45.455 0.00 0.00 0.00 4.20
4375 29631 6.544650 TGTATAAGGGGTTTTCTGCACTTTA 58.455 36.000 0.00 0.00 0.00 1.85
4415 29671 0.615827 GCCTTTGGCCCTCAGGAAAT 60.616 55.000 14.77 0.00 44.06 2.17
4416 29672 1.188863 CCTTTGGCCCTCAGGAAATG 58.811 55.000 0.00 0.00 33.47 2.32
4417 29673 0.533951 CTTTGGCCCTCAGGAAATGC 59.466 55.000 0.00 0.00 33.47 3.56
4463 29721 2.320781 TCATGTTAGGCTAGCCTCTCC 58.679 52.381 39.25 26.10 44.43 3.71
4464 29722 2.091055 TCATGTTAGGCTAGCCTCTCCT 60.091 50.000 39.25 21.73 44.43 3.69
4504 29762 1.533033 GCTCCCTCCTCCTAGCCTC 60.533 68.421 0.00 0.00 0.00 4.70
4510 29768 2.915137 CCTCCTAGCCTCCCTCGC 60.915 72.222 0.00 0.00 0.00 5.03
4536 29794 1.714794 CTGTTTCTGCTCGATTCCGT 58.285 50.000 0.00 0.00 37.05 4.69
4543 29801 3.833645 CTCGATTCCGTCCGCCCA 61.834 66.667 0.00 0.00 37.05 5.36
4554 29812 3.854669 CCGCCCAGGCTCGATTCT 61.855 66.667 7.17 0.00 39.32 2.40
4561 29819 3.577313 GGCTCGATTCTTGCCGGC 61.577 66.667 22.73 22.73 37.11 6.13
4564 29822 3.391665 CTCGATTCTTGCCGGCCCT 62.392 63.158 26.77 3.11 0.00 5.19
4622 29901 4.143333 CGTCCGGATCCGCCACTT 62.143 66.667 29.12 0.00 38.24 3.16
4625 29911 4.473520 CCGGATCCGCCACTTGCT 62.474 66.667 29.12 0.00 38.05 3.91
4636 29922 4.586235 ACTTGCTGCTGCCCCGTT 62.586 61.111 13.47 0.00 38.71 4.44
4637 29923 3.741476 CTTGCTGCTGCCCCGTTC 61.741 66.667 13.47 0.00 38.71 3.95
4644 29930 4.796231 CTGCCCCGTTCGACCTCG 62.796 72.222 0.00 0.00 41.45 4.63
4648 29934 4.493747 CCCGTTCGACCTCGGCTC 62.494 72.222 14.74 0.00 44.63 4.70
4649 29935 4.831307 CCGTTCGACCTCGGCTCG 62.831 72.222 9.35 0.00 40.28 5.03
4650 29936 4.831307 CGTTCGACCTCGGCTCGG 62.831 72.222 0.00 0.00 40.29 4.63
4691 29977 4.394712 CTTCCCCGGCTCAAGCGT 62.395 66.667 0.00 0.00 43.26 5.07
4700 29986 2.047465 CTCAAGCGTGCTCCTGCT 60.047 61.111 0.00 0.00 44.97 4.24
4703 29989 3.946201 AAGCGTGCTCCTGCTGGT 61.946 61.111 9.73 0.00 41.46 4.00
4716 30002 4.436998 CTGGTCTCGGGTGCGTCC 62.437 72.222 0.00 0.00 0.00 4.79
4730 30016 4.452733 GTCCCCTCTGCCCGTTCG 62.453 72.222 0.00 0.00 0.00 3.95
4793 30079 1.375326 GCCACTTCTTCCTTCCCGT 59.625 57.895 0.00 0.00 0.00 5.28
4796 30082 0.601558 CACTTCTTCCTTCCCGTCGA 59.398 55.000 0.00 0.00 0.00 4.20
4797 30083 1.204941 CACTTCTTCCTTCCCGTCGAT 59.795 52.381 0.00 0.00 0.00 3.59
4805 30091 0.108138 CTTCCCGTCGATCCTGCTTT 60.108 55.000 0.00 0.00 0.00 3.51
4808 30094 1.517832 CCGTCGATCCTGCTTTCCT 59.482 57.895 0.00 0.00 0.00 3.36
4810 30096 0.528684 CGTCGATCCTGCTTTCCTCC 60.529 60.000 0.00 0.00 0.00 4.30
4815 30101 2.883267 ATCCTGCTTTCCTCCGCTGC 62.883 60.000 0.00 0.00 0.00 5.25
4816 30102 2.046507 CTGCTTTCCTCCGCTGCT 60.047 61.111 0.00 0.00 0.00 4.24
4856 30142 4.116328 CCAAGTCGAGCGAGCGGA 62.116 66.667 0.00 0.00 0.00 5.54
4858 30144 3.362797 AAGTCGAGCGAGCGGACA 61.363 61.111 18.93 0.00 0.00 4.02
4910 30196 2.049063 GCGGGCGCTCGATCTATT 60.049 61.111 37.54 0.00 38.26 1.73
4911 30197 2.375766 GCGGGCGCTCGATCTATTG 61.376 63.158 37.54 0.89 38.26 1.90
4912 30198 1.285950 CGGGCGCTCGATCTATTGA 59.714 57.895 29.20 0.00 0.00 2.57
4913 30199 0.730834 CGGGCGCTCGATCTATTGAG 60.731 60.000 29.20 3.21 40.56 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.952116 CTCCGAGGGAAACTCTAGGAT 58.048 52.381 1.34 0.00 44.33 3.24
7 8 0.747852 GCTCCGAGGGAAACTCTAGG 59.252 60.000 0.00 0.00 44.33 3.02
9 10 1.475403 CTGCTCCGAGGGAAACTCTA 58.525 55.000 0.00 0.00 44.33 2.43
11 12 1.448717 GCTGCTCCGAGGGAAACTC 60.449 63.158 0.00 0.00 43.02 3.01
12 13 2.217038 TGCTGCTCCGAGGGAAACT 61.217 57.895 0.00 0.00 0.00 2.66
14 15 2.050836 TTGTGCTGCTCCGAGGGAAA 62.051 55.000 0.00 0.00 0.00 3.13
15 16 2.454832 CTTGTGCTGCTCCGAGGGAA 62.455 60.000 0.00 0.00 0.00 3.97
16 17 2.922503 TTGTGCTGCTCCGAGGGA 60.923 61.111 0.00 0.00 0.00 4.20
17 18 2.435586 CTTGTGCTGCTCCGAGGG 60.436 66.667 0.00 0.00 0.00 4.30
18 19 2.031516 CACTTGTGCTGCTCCGAGG 61.032 63.158 0.00 0.00 0.00 4.63
19 20 2.031516 CCACTTGTGCTGCTCCGAG 61.032 63.158 0.00 3.53 0.00 4.63
20 21 2.031012 CCACTTGTGCTGCTCCGA 59.969 61.111 0.00 0.00 0.00 4.55
22 23 1.529244 AACCCACTTGTGCTGCTCC 60.529 57.895 0.00 0.00 0.00 4.70
23 24 1.656441 CAACCCACTTGTGCTGCTC 59.344 57.895 0.00 0.00 0.00 4.26
24 25 1.829533 CCAACCCACTTGTGCTGCT 60.830 57.895 0.00 0.00 0.00 4.24
26 27 2.079020 CTGCCAACCCACTTGTGCTG 62.079 60.000 0.00 0.00 31.08 4.41
27 28 1.829533 CTGCCAACCCACTTGTGCT 60.830 57.895 0.00 0.00 31.08 4.40
28 29 0.821711 TACTGCCAACCCACTTGTGC 60.822 55.000 0.00 0.00 0.00 4.57
29 30 1.238439 CTACTGCCAACCCACTTGTG 58.762 55.000 0.00 0.00 0.00 3.33
30 31 0.843984 ACTACTGCCAACCCACTTGT 59.156 50.000 0.00 0.00 0.00 3.16
32 33 2.440253 TGTAACTACTGCCAACCCACTT 59.560 45.455 0.00 0.00 0.00 3.16
33 34 2.051692 TGTAACTACTGCCAACCCACT 58.948 47.619 0.00 0.00 0.00 4.00
35 36 2.290641 CCATGTAACTACTGCCAACCCA 60.291 50.000 0.00 0.00 0.00 4.51
36 37 2.365582 CCATGTAACTACTGCCAACCC 58.634 52.381 0.00 0.00 0.00 4.11
37 38 1.743394 GCCATGTAACTACTGCCAACC 59.257 52.381 0.00 0.00 0.00 3.77
38 39 1.396996 CGCCATGTAACTACTGCCAAC 59.603 52.381 0.00 0.00 0.00 3.77
39 40 1.002659 ACGCCATGTAACTACTGCCAA 59.997 47.619 0.00 0.00 0.00 4.52
40 41 0.611200 ACGCCATGTAACTACTGCCA 59.389 50.000 0.00 0.00 0.00 4.92
41 42 1.396996 CAACGCCATGTAACTACTGCC 59.603 52.381 0.00 0.00 0.00 4.85
42 43 1.202031 GCAACGCCATGTAACTACTGC 60.202 52.381 0.00 0.00 0.00 4.40
43 44 2.806288 GCAACGCCATGTAACTACTG 57.194 50.000 0.00 0.00 0.00 2.74
63 64 4.990257 TCTCCGTCGTTACCTTAATGAAG 58.010 43.478 0.00 0.00 35.63 3.02
64 65 5.163513 GTTCTCCGTCGTTACCTTAATGAA 58.836 41.667 0.00 0.00 35.63 2.57
65 66 4.672542 CGTTCTCCGTCGTTACCTTAATGA 60.673 45.833 0.00 0.00 0.00 2.57
66 67 3.545078 CGTTCTCCGTCGTTACCTTAATG 59.455 47.826 0.00 0.00 0.00 1.90
69 70 1.135689 GCGTTCTCCGTCGTTACCTTA 60.136 52.381 0.00 0.00 39.32 2.69
70 71 0.387750 GCGTTCTCCGTCGTTACCTT 60.388 55.000 0.00 0.00 39.32 3.50
71 72 1.211190 GCGTTCTCCGTCGTTACCT 59.789 57.895 0.00 0.00 39.32 3.08
72 73 1.803117 GGCGTTCTCCGTCGTTACC 60.803 63.158 0.00 0.00 39.32 2.85
73 74 3.759353 GGCGTTCTCCGTCGTTAC 58.241 61.111 0.00 0.00 39.32 2.50
91 92 0.028110 GTGAAAATCGAGCCGATGGC 59.972 55.000 10.25 0.00 46.30 4.40
92 93 0.657840 GGTGAAAATCGAGCCGATGG 59.342 55.000 10.25 0.00 46.30 3.51
93 94 0.301687 CGGTGAAAATCGAGCCGATG 59.698 55.000 10.25 0.00 46.30 3.84
97 98 1.582610 TTGCCGGTGAAAATCGAGCC 61.583 55.000 1.90 0.00 0.00 4.70
98 99 0.454452 GTTGCCGGTGAAAATCGAGC 60.454 55.000 1.90 0.00 0.00 5.03
100 101 2.459060 TAGTTGCCGGTGAAAATCGA 57.541 45.000 1.90 0.00 0.00 3.59
101 102 2.418628 ACATAGTTGCCGGTGAAAATCG 59.581 45.455 1.90 0.00 0.00 3.34
102 103 3.689649 AGACATAGTTGCCGGTGAAAATC 59.310 43.478 1.90 0.00 0.00 2.17
103 104 3.686016 AGACATAGTTGCCGGTGAAAAT 58.314 40.909 1.90 0.00 0.00 1.82
105 106 2.851263 AGACATAGTTGCCGGTGAAA 57.149 45.000 1.90 0.00 0.00 2.69
106 107 2.614481 GGAAGACATAGTTGCCGGTGAA 60.614 50.000 1.90 0.00 0.00 3.18
108 109 1.369625 GGAAGACATAGTTGCCGGTG 58.630 55.000 1.90 0.00 0.00 4.94
109 110 0.252197 GGGAAGACATAGTTGCCGGT 59.748 55.000 1.90 0.00 0.00 5.28
110 111 0.251916 TGGGAAGACATAGTTGCCGG 59.748 55.000 0.00 0.00 38.20 6.13
111 112 1.737793 GTTGGGAAGACATAGTTGCCG 59.262 52.381 0.00 0.00 38.20 5.69
114 115 2.673368 GCGAGTTGGGAAGACATAGTTG 59.327 50.000 0.00 0.00 0.00 3.16
115 116 2.301870 TGCGAGTTGGGAAGACATAGTT 59.698 45.455 0.00 0.00 0.00 2.24
117 118 2.544685 CTGCGAGTTGGGAAGACATAG 58.455 52.381 0.00 0.00 0.00 2.23
119 120 0.674895 GCTGCGAGTTGGGAAGACAT 60.675 55.000 0.00 0.00 0.00 3.06
120 121 1.301716 GCTGCGAGTTGGGAAGACA 60.302 57.895 0.00 0.00 0.00 3.41
121 122 2.035442 GGCTGCGAGTTGGGAAGAC 61.035 63.158 0.00 0.00 0.00 3.01
122 123 2.347490 GGCTGCGAGTTGGGAAGA 59.653 61.111 0.00 0.00 0.00 2.87
123 124 3.121030 CGGCTGCGAGTTGGGAAG 61.121 66.667 0.00 0.00 0.00 3.46
126 127 4.697756 TTCCGGCTGCGAGTTGGG 62.698 66.667 0.00 0.00 0.00 4.12
127 128 2.501223 TAGTTCCGGCTGCGAGTTGG 62.501 60.000 0.00 0.00 0.00 3.77
128 129 1.078759 CTAGTTCCGGCTGCGAGTTG 61.079 60.000 0.00 0.00 0.00 3.16
129 130 1.215647 CTAGTTCCGGCTGCGAGTT 59.784 57.895 0.00 0.00 0.00 3.01
133 134 2.579787 CGTCTAGTTCCGGCTGCG 60.580 66.667 0.00 0.00 0.00 5.18
134 135 2.202756 CCGTCTAGTTCCGGCTGC 60.203 66.667 0.00 0.00 37.43 5.25
138 139 1.008767 GATCGCCGTCTAGTTCCGG 60.009 63.158 12.01 12.01 46.90 5.14
139 140 0.381089 AAGATCGCCGTCTAGTTCCG 59.619 55.000 0.00 0.00 0.00 4.30
140 141 1.404391 TCAAGATCGCCGTCTAGTTCC 59.596 52.381 0.00 0.00 0.00 3.62
141 142 2.355132 TCTCAAGATCGCCGTCTAGTTC 59.645 50.000 0.00 0.00 0.00 3.01
142 143 2.366533 TCTCAAGATCGCCGTCTAGTT 58.633 47.619 0.00 0.00 0.00 2.24
154 155 4.021544 GGCTGAATAGTCGGATCTCAAGAT 60.022 45.833 2.51 0.00 37.51 2.40
156 157 3.320541 AGGCTGAATAGTCGGATCTCAAG 59.679 47.826 2.51 0.00 32.48 3.02
157 158 3.300388 AGGCTGAATAGTCGGATCTCAA 58.700 45.455 2.51 0.00 32.48 3.02
158 159 2.887783 GAGGCTGAATAGTCGGATCTCA 59.112 50.000 2.51 0.00 34.62 3.27
160 161 2.890311 CTGAGGCTGAATAGTCGGATCT 59.110 50.000 2.51 0.00 32.48 2.75
161 162 2.029470 CCTGAGGCTGAATAGTCGGATC 60.029 54.545 2.51 0.66 32.48 3.36
162 163 1.967066 CCTGAGGCTGAATAGTCGGAT 59.033 52.381 2.51 0.00 32.48 4.18
164 165 0.249657 GCCTGAGGCTGAATAGTCGG 60.250 60.000 17.96 0.00 46.69 4.79
165 166 3.280920 GCCTGAGGCTGAATAGTCG 57.719 57.895 17.96 0.00 46.69 4.18
176 177 3.775654 GAGGTGGTCGGCCTGAGG 61.776 72.222 7.97 0.00 36.29 3.86
177 178 3.775654 GGAGGTGGTCGGCCTGAG 61.776 72.222 7.97 0.00 36.29 3.35
184 185 3.812019 CTCCGTCGGAGGTGGTCG 61.812 72.222 30.23 6.72 45.43 4.79
192 193 2.833582 GCCATCTCCTCCGTCGGA 60.834 66.667 14.54 14.54 0.00 4.55
193 194 3.144120 CTGCCATCTCCTCCGTCGG 62.144 68.421 4.39 4.39 0.00 4.79
194 195 2.415010 CTGCCATCTCCTCCGTCG 59.585 66.667 0.00 0.00 0.00 5.12
195 196 2.107953 GCTGCCATCTCCTCCGTC 59.892 66.667 0.00 0.00 0.00 4.79
196 197 3.842923 CGCTGCCATCTCCTCCGT 61.843 66.667 0.00 0.00 0.00 4.69
197 198 4.598894 CCGCTGCCATCTCCTCCG 62.599 72.222 0.00 0.00 0.00 4.63
198 199 4.925861 GCCGCTGCCATCTCCTCC 62.926 72.222 0.00 0.00 0.00 4.30
199 200 4.166888 TGCCGCTGCCATCTCCTC 62.167 66.667 0.00 0.00 36.33 3.71
200 201 4.479993 GTGCCGCTGCCATCTCCT 62.480 66.667 0.00 0.00 36.33 3.69
216 217 4.716025 AGATCTGATCTGGCCGGT 57.284 55.556 18.93 0.00 38.44 5.28
225 226 0.387202 CGCCTTCGGTCAGATCTGAT 59.613 55.000 27.51 0.00 42.18 2.90
226 227 1.809869 CGCCTTCGGTCAGATCTGA 59.190 57.895 21.67 21.67 37.24 3.27
228 229 2.496817 GCGCCTTCGGTCAGATCT 59.503 61.111 0.00 0.00 35.95 2.75
229 230 2.586357 GGCGCCTTCGGTCAGATC 60.586 66.667 22.15 0.00 35.95 2.75
242 243 4.789075 TTGACTAGTCGGCGGCGC 62.789 66.667 28.25 26.17 0.00 6.53
243 244 2.879462 GTTGACTAGTCGGCGGCG 60.879 66.667 27.15 27.15 0.00 6.46
245 246 0.806102 CATGGTTGACTAGTCGGCGG 60.806 60.000 17.85 2.01 0.00 6.13
246 247 0.806102 CCATGGTTGACTAGTCGGCG 60.806 60.000 17.85 0.00 0.00 6.46
248 249 0.249120 TGCCATGGTTGACTAGTCGG 59.751 55.000 17.85 12.32 0.00 4.79
249 250 1.645034 CTGCCATGGTTGACTAGTCG 58.355 55.000 17.85 3.06 0.00 4.18
250 251 1.279271 ACCTGCCATGGTTGACTAGTC 59.721 52.381 16.32 16.32 36.89 2.59
251 252 1.003580 CACCTGCCATGGTTGACTAGT 59.996 52.381 14.67 0.00 38.45 2.57
252 253 1.742761 CACCTGCCATGGTTGACTAG 58.257 55.000 14.67 2.82 38.45 2.57
253 254 0.322456 GCACCTGCCATGGTTGACTA 60.322 55.000 14.67 0.00 38.45 2.59
254 255 1.604593 GCACCTGCCATGGTTGACT 60.605 57.895 14.67 0.00 38.45 3.41
255 256 1.870055 CTGCACCTGCCATGGTTGAC 61.870 60.000 14.67 0.00 38.45 3.18
260 261 2.825075 TACAGCTGCACCTGCCATGG 62.825 60.000 15.27 7.63 41.18 3.66
262 263 1.077930 CTACAGCTGCACCTGCCAT 60.078 57.895 15.27 0.00 41.18 4.40
263 264 2.348620 CTACAGCTGCACCTGCCA 59.651 61.111 15.27 0.00 41.18 4.92
264 265 2.037136 CACTACAGCTGCACCTGCC 61.037 63.158 15.27 0.00 41.18 4.85
266 267 1.296755 CTGCACTACAGCTGCACCTG 61.297 60.000 15.27 7.50 39.76 4.00
269 270 1.005340 GATCTGCACTACAGCTGCAC 58.995 55.000 15.27 0.00 46.76 4.57
295 296 2.499289 AGGAAGACAGCATTCGATCACT 59.501 45.455 0.00 0.00 0.00 3.41
353 354 1.680735 ACGATTGTGCAGAGCCAAAAA 59.319 42.857 0.00 0.00 0.00 1.94
361 362 2.029110 TCAGTGATCACGATTGTGCAGA 60.029 45.455 19.85 5.74 46.01 4.26
416 417 6.318648 CCACTAGCCAATCTTTTAGTTATGCA 59.681 38.462 0.00 0.00 0.00 3.96
427 428 8.728596 ATATTAGTACTCCACTAGCCAATCTT 57.271 34.615 0.00 0.00 40.83 2.40
448 449 8.870116 TGTCTGCATGTCCAGTATAGTTATATT 58.130 33.333 0.00 0.00 34.47 1.28
477 487 4.748600 AGTAGGTACAACGCAGAAAGAAAC 59.251 41.667 0.00 0.00 0.00 2.78
478 488 4.952460 AGTAGGTACAACGCAGAAAGAAA 58.048 39.130 0.00 0.00 0.00 2.52
493 503 5.038279 AGTCTCTACCTCCAGAAGTAGGTA 58.962 45.833 4.09 0.00 44.40 3.08
495 505 4.513406 AGTCTCTACCTCCAGAAGTAGG 57.487 50.000 4.09 0.00 37.22 3.18
496 506 5.258051 ACAAGTCTCTACCTCCAGAAGTAG 58.742 45.833 0.00 0.00 37.83 2.57
502 512 5.047021 TCAATTGACAAGTCTCTACCTCCAG 60.047 44.000 3.38 0.00 0.00 3.86
516 526 4.494484 ACGATCGAGACATCAATTGACAA 58.506 39.130 24.34 0.00 0.00 3.18
519 529 6.560711 TCTAAACGATCGAGACATCAATTGA 58.439 36.000 24.34 11.26 0.00 2.57
520 530 6.812481 TCTAAACGATCGAGACATCAATTG 57.188 37.500 24.34 0.00 0.00 2.32
543 554 4.026052 GACCTGATGAATGGGTTGGAATT 58.974 43.478 0.00 0.00 33.01 2.17
577 589 6.398234 ACTGACTAATAGCATGAAGACGAT 57.602 37.500 0.00 0.00 0.00 3.73
697 717 3.208747 TGTCCACCAAGTTTCCTCTTC 57.791 47.619 0.00 0.00 0.00 2.87
718 738 1.609208 GAAAAGCCTGCTTCTGTCCA 58.391 50.000 4.63 0.00 34.84 4.02
759 779 4.628333 GGAAATGAAAATGTCTACCGACGA 59.372 41.667 0.00 0.00 43.21 4.20
761 781 5.875359 AGAGGAAATGAAAATGTCTACCGAC 59.125 40.000 0.00 0.00 40.64 4.79
770 790 6.336842 ACAAGTGGAGAGGAAATGAAAATG 57.663 37.500 0.00 0.00 0.00 2.32
790 810 5.124297 CCTGCTTGTCATGATGTGATTACAA 59.876 40.000 0.00 0.00 40.84 2.41
809 829 3.314331 CCGGGACACTGACCTGCT 61.314 66.667 0.00 0.00 32.89 4.24
850 870 2.227194 GGTCCATGTTCACGGAGTTTT 58.773 47.619 0.00 0.00 41.61 2.43
857 877 1.194547 CAAGTTCGGTCCATGTTCACG 59.805 52.381 0.00 0.00 0.00 4.35
863 883 2.185004 AACTCCAAGTTCGGTCCATG 57.815 50.000 0.00 0.00 31.77 3.66
894 914 7.981102 AGTAAGTGTTCTATTTTCTCCCAAC 57.019 36.000 0.00 0.00 0.00 3.77
906 926 5.876357 AGCCATCCAAAAGTAAGTGTTCTA 58.124 37.500 0.00 0.00 0.00 2.10
923 943 6.259608 GCATGATATATGTAGTCCAAGCCATC 59.740 42.308 0.00 0.00 0.00 3.51
926 946 4.878397 GGCATGATATATGTAGTCCAAGCC 59.122 45.833 0.00 0.00 0.00 4.35
932 952 5.998454 GCCATGGCATGATATATGTAGTC 57.002 43.478 32.08 0.00 41.49 2.59
1029 3814 9.461312 AAGAGAATTGCACATATAGTTACCAAA 57.539 29.630 0.00 0.00 0.00 3.28
1032 3817 8.438676 ACAAGAGAATTGCACATATAGTTACC 57.561 34.615 0.00 0.00 0.00 2.85
1047 3832 3.244770 TGGCTCGGGTAAACAAGAGAATT 60.245 43.478 7.85 0.00 32.84 2.17
1099 3884 4.381612 CGTATTGTTTGAGTGGCTAGAGGA 60.382 45.833 0.00 0.00 0.00 3.71
1100 3885 3.865745 CGTATTGTTTGAGTGGCTAGAGG 59.134 47.826 0.00 0.00 0.00 3.69
1117 3902 4.082895 GGCGATACATCTAGTGACCGTATT 60.083 45.833 0.00 0.00 29.50 1.89
1206 3991 0.694771 AGCAGTCATCAGCCTTCCAA 59.305 50.000 0.00 0.00 0.00 3.53
1254 4039 2.867287 TGACGACGTGGTTGTTTCTA 57.133 45.000 4.58 0.00 29.24 2.10
1401 4186 2.107950 TTTGCACCCCATAGAACTCG 57.892 50.000 0.00 0.00 0.00 4.18
1714 4508 7.664082 TTGAAATCTGATGTGAAGAAGAGTC 57.336 36.000 0.00 0.00 0.00 3.36
1884 4678 6.365970 AGCCTTACTATGGAGGTCATATTG 57.634 41.667 0.00 0.00 37.67 1.90
2137 4934 8.322091 AGTGAGCTTGTTACTACCAAGAATAAT 58.678 33.333 4.43 0.00 41.44 1.28
2215 5012 3.420893 CCTCCAGGTTATTGTTGCTCAA 58.579 45.455 0.00 0.00 40.53 3.02
2561 11755 3.825014 ACTGAGATCAATTGCAGTTGCTT 59.175 39.130 16.52 6.96 38.34 3.91
2698 11892 7.389053 GGAGTTGTCAAATAGAATCAGTCTTGT 59.611 37.037 0.00 0.00 37.84 3.16
2970 18057 3.099141 CCCTATCCATGTTGGCAAAGTT 58.901 45.455 0.00 0.00 37.47 2.66
3018 18105 5.617028 AAAACTTATTCGATCGTAGTCGC 57.383 39.130 15.94 0.00 41.22 5.19
3210 18312 4.780815 TCATGTCACCAGGACCAATAATC 58.219 43.478 0.00 0.00 46.38 1.75
3387 18493 5.183904 GCTGAAGGTGTTCCATGATAAGTTT 59.816 40.000 0.00 0.00 35.89 2.66
3425 28638 1.008538 GCCAAGGCGCCAATATTCG 60.009 57.895 31.54 7.89 0.00 3.34
3483 28696 2.124570 CTGGCAGGGATTCCACCG 60.125 66.667 6.61 0.00 35.10 4.94
3488 28701 1.070758 TCGATAAGCTGGCAGGGATTC 59.929 52.381 17.64 0.00 0.00 2.52
3498 28711 4.298744 TGATGTGAGAGTCGATAAGCTG 57.701 45.455 0.00 0.00 0.00 4.24
3636 28851 0.250513 ATTCCTGCGACAAGGGAGAC 59.749 55.000 0.00 0.00 37.96 3.36
3652 28867 0.521735 GGCTCGGGTTGTGAACATTC 59.478 55.000 0.00 0.00 0.00 2.67
3719 28937 1.529226 ACCCATCGCGATGAAAAACA 58.471 45.000 42.44 5.65 41.20 2.83
3756 28974 1.896465 GTGCAGAAGACTACCCAGAGT 59.104 52.381 0.00 0.00 0.00 3.24
4135 29381 4.335037 GGTTGGATTGAGAGCTTGAGAATC 59.665 45.833 0.00 0.00 0.00 2.52
4245 29500 2.968574 CCCAGTATACTGCATCCAGAGT 59.031 50.000 24.85 0.00 41.77 3.24
4253 29508 2.106131 CGCGCCCAGTATACTGCA 59.894 61.111 24.85 0.00 42.47 4.41
4279 29534 7.450014 CCCTGTACATGTCTATCTAGTGAAGAT 59.550 40.741 0.00 0.00 46.95 2.40
4328 29584 6.013639 ACAATAGGGATATACCGAAAAGGGAG 60.014 42.308 0.00 0.00 46.96 4.30
4348 29604 6.727394 AGTGCAGAAAACCCCTTATACAATA 58.273 36.000 0.00 0.00 0.00 1.90
4375 29631 6.364701 AGGCCATTACATATACATGTGTGTT 58.635 36.000 9.11 0.00 45.17 3.32
4415 29671 7.630458 CCATGTTGGATAATGAGCAACTAGCA 61.630 42.308 0.00 0.00 43.26 3.49
4416 29672 5.278169 CCATGTTGGATAATGAGCAACTAGC 60.278 44.000 0.00 0.00 40.96 3.42
4417 29673 5.824624 ACCATGTTGGATAATGAGCAACTAG 59.175 40.000 0.00 0.00 40.96 2.57
4518 29776 1.671850 GGACGGAATCGAGCAGAAACA 60.672 52.381 0.00 0.00 40.11 2.83
4543 29801 2.187946 CCGGCAAGAATCGAGCCT 59.812 61.111 14.94 0.00 46.14 4.58
4619 29898 4.586235 AACGGGGCAGCAGCAAGT 62.586 61.111 2.65 0.00 44.61 3.16
4640 29926 4.856607 GAACGAGCCGAGCCGAGG 62.857 72.222 11.42 0.00 0.00 4.63
4641 29927 4.856607 GGAACGAGCCGAGCCGAG 62.857 72.222 11.42 0.00 0.00 4.63
4681 29967 3.123620 CAGGAGCACGCTTGAGCC 61.124 66.667 0.00 0.00 37.91 4.70
4691 29977 3.385384 CCGAGACCAGCAGGAGCA 61.385 66.667 0.35 0.00 45.49 4.26
4694 29980 2.997315 CACCCGAGACCAGCAGGA 60.997 66.667 0.35 0.00 38.69 3.86
4695 29981 4.767255 GCACCCGAGACCAGCAGG 62.767 72.222 0.00 0.00 42.21 4.85
4724 30010 3.839432 GGAGGAGCTCCCGAACGG 61.839 72.222 29.54 6.25 44.36 4.44
4774 30060 1.374947 CGGGAAGGAAGAAGTGGCA 59.625 57.895 0.00 0.00 0.00 4.92
4778 30064 1.477295 GATCGACGGGAAGGAAGAAGT 59.523 52.381 0.00 0.00 0.00 3.01
4781 30067 0.033405 AGGATCGACGGGAAGGAAGA 60.033 55.000 0.00 0.00 0.00 2.87
4784 30070 2.423898 GCAGGATCGACGGGAAGGA 61.424 63.158 0.00 0.00 0.00 3.36
4785 30071 1.961180 AAGCAGGATCGACGGGAAGG 61.961 60.000 0.00 0.00 0.00 3.46
4793 30079 1.816537 CGGAGGAAAGCAGGATCGA 59.183 57.895 0.00 0.00 0.00 3.59
4796 30082 1.222936 CAGCGGAGGAAAGCAGGAT 59.777 57.895 0.00 0.00 35.48 3.24
4797 30083 2.665000 CAGCGGAGGAAAGCAGGA 59.335 61.111 0.00 0.00 35.48 3.86
4829 30115 1.004560 TCGACTTGGCAAGCAGAGG 60.005 57.895 26.45 11.45 0.00 3.69
4834 30120 2.734673 CTCGCTCGACTTGGCAAGC 61.735 63.158 26.45 17.49 0.00 4.01
4840 30126 2.874010 ATGTCCGCTCGCTCGACTTG 62.874 60.000 7.28 0.00 0.00 3.16
4841 30127 2.701780 ATGTCCGCTCGCTCGACTT 61.702 57.895 7.28 0.33 0.00 3.01
4893 30179 2.049063 AATAGATCGAGCGCCCGC 60.049 61.111 6.39 4.20 42.33 6.13
4894 30180 0.730834 CTCAATAGATCGAGCGCCCG 60.731 60.000 4.37 4.37 0.00 6.13
4895 30181 1.011451 GCTCAATAGATCGAGCGCCC 61.011 60.000 2.29 0.00 44.68 6.13
4896 30182 2.439964 GCTCAATAGATCGAGCGCC 58.560 57.895 2.29 0.00 44.68 6.53


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

AutoCloner maintained by Alex Coulton.