Multiple sequence alignment - TraesCS5A01G269900

Loading Multiple Alignment...

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 TraesCS5A01G269900 chr5A 100.000 2582 0 0 1 2582 480405629 480408210 0.000000e+00 4769
1 TraesCS5A01G269900 chr5A 84.127 378 52 8 132 505 480406133 480405760 2.440000e-95 359
2 TraesCS5A01G269900 chr5A 93.467 199 12 1 1054 1251 139484863 139484665 6.990000e-76 294
3 TraesCS5A01G269900 chr5A 90.206 194 18 1 311 504 25078090 25077898 4.270000e-63 252
4 TraesCS5A01G269900 chr5A 79.464 336 49 10 104 437 667093531 667093848 1.200000e-53 220
5 TraesCS5A01G269900 chr5D 90.719 2101 128 21 528 2582 379964904 379966983 0.000000e+00 2737
6 TraesCS5A01G269900 chr5B 90.676 1169 46 14 528 1645 455760417 455761573 0.000000e+00 1496
7 TraesCS5A01G269900 chr5B 91.097 629 49 2 1961 2582 455764310 455764938 0.000000e+00 845
8 TraesCS5A01G269900 chr5B 93.333 225 13 2 1731 1954 455761950 455762173 5.330000e-87 331
9 TraesCS5A01G269900 chr5B 85.437 103 10 5 1632 1734 455761597 455761694 4.550000e-18 102
10 TraesCS5A01G269900 chr7B 89.724 399 34 7 108 504 169378525 169378132 1.070000e-138 503
11 TraesCS5A01G269900 chr7B 82.878 403 62 6 104 504 169378103 169378500 3.160000e-94 355
12 TraesCS5A01G269900 chr3B 89.673 397 36 5 104 500 665885014 665884623 3.840000e-138 501
13 TraesCS5A01G269900 chr3B 84.826 402 46 9 104 504 23164106 23163719 8.660000e-105 390
14 TraesCS5A01G269900 chr3B 97.980 198 4 0 1177 1374 1269812 1269615 6.840000e-91 344
15 TraesCS5A01G269900 chr3B 93.467 199 12 1 1054 1251 1270303 1270105 6.990000e-76 294
16 TraesCS5A01G269900 chr3B 80.833 360 57 12 97 452 23163684 23164035 3.270000e-69 272
17 TraesCS5A01G269900 chr2D 89.526 401 33 5 104 504 10734177 10734568 1.380000e-137 499
18 TraesCS5A01G269900 chr2D 80.941 404 62 13 104 504 10734597 10734206 3.230000e-79 305
19 TraesCS5A01G269900 chr1D 88.693 398 42 2 104 501 455154668 455155062 1.390000e-132 483
20 TraesCS5A01G269900 chr2A 98.485 198 3 0 1177 1374 662939772 662939575 1.470000e-92 350
21 TraesCS5A01G269900 chr2A 93.069 202 13 1 1051 1251 668074063 668074264 6.990000e-76 294
22 TraesCS5A01G269900 chr7A 97.980 198 4 0 1177 1374 238537681 238537484 6.840000e-91 344
23 TraesCS5A01G269900 chr7A 93.467 199 12 1 1054 1251 238537879 238537681 6.990000e-76 294
24 TraesCS5A01G269900 chr6B 97.980 198 4 0 1177 1374 21194530 21194727 6.840000e-91 344
25 TraesCS5A01G269900 chr6B 84.270 356 33 9 150 501 691792127 691792463 2.480000e-85 326
26 TraesCS5A01G269900 chr6B 92.574 202 14 1 1051 1251 21194329 21194530 3.250000e-74 289
27 TraesCS5A01G269900 chr6A 97.980 198 4 0 1177 1374 393233091 393233288 6.840000e-91 344
28 TraesCS5A01G269900 chr6A 93.069 202 13 1 1051 1251 393232890 393233091 6.990000e-76 294
29 TraesCS5A01G269900 chr4A 97.980 198 4 0 1177 1374 95156115 95156312 6.840000e-91 344
30 TraesCS5A01G269900 chr3A 97.980 198 4 0 1177 1374 363952202 363952399 6.840000e-91 344
31 TraesCS5A01G269900 chr4B 92.574 202 14 1 1051 1251 429597608 429597809 3.250000e-74 289


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 TraesCS5A01G269900 chr5A 480405629 480408210 2581 False 4769.0 4769 100.00000 1 2582 1 chr5A.!!$F1 2581
1 TraesCS5A01G269900 chr5D 379964904 379966983 2079 False 2737.0 2737 90.71900 528 2582 1 chr5D.!!$F1 2054
2 TraesCS5A01G269900 chr5B 455760417 455764938 4521 False 693.5 1496 90.13575 528 2582 4 chr5B.!!$F1 2054
3 TraesCS5A01G269900 chr3B 1269615 1270303 688 True 319.0 344 95.72350 1054 1374 2 chr3B.!!$R3 320

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
51 52 0.035725 AACTAAACTAGCGCCCCACC 60.036 55.0 2.29 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 4846 1.159285 TGCACTTTGAGATGGCGAAG 58.841 50.0 0.0 0.0 35.75 3.79 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 6.782298 CATACATGCATCTGTTAAGAGAGG 57.218 41.667 9.73 9.73 35.37 3.69
35 36 3.604582 GCATCTGTTAAGAGAGGCAACT 58.395 45.455 28.08 0.24 46.62 3.16
36 37 4.759782 GCATCTGTTAAGAGAGGCAACTA 58.240 43.478 28.08 0.00 46.62 2.24
37 38 5.178797 GCATCTGTTAAGAGAGGCAACTAA 58.821 41.667 28.08 0.00 46.62 2.24
38 39 5.643777 GCATCTGTTAAGAGAGGCAACTAAA 59.356 40.000 28.08 0.00 46.62 1.85
39 40 6.402658 GCATCTGTTAAGAGAGGCAACTAAAC 60.403 42.308 28.08 2.22 46.62 2.01
40 41 6.876257 CATCTGTTAAGAGAGGCAACTAAACT 59.124 38.462 8.44 0.00 40.35 2.66
41 42 8.035394 CATCTGTTAAGAGAGGCAACTAAACTA 58.965 37.037 8.44 0.00 40.35 2.24
42 43 8.254508 ATCTGTTAAGAGAGGCAACTAAACTAG 58.745 37.037 8.44 0.00 40.35 2.57
47 48 2.095750 GGCAACTAAACTAGCGCCC 58.904 57.895 2.29 0.00 40.15 6.13
48 49 1.374343 GGCAACTAAACTAGCGCCCC 61.374 60.000 2.29 0.00 40.15 5.80
49 50 0.675522 GCAACTAAACTAGCGCCCCA 60.676 55.000 2.29 0.00 0.00 4.96
50 51 1.084289 CAACTAAACTAGCGCCCCAC 58.916 55.000 2.29 0.00 0.00 4.61
51 52 0.035725 AACTAAACTAGCGCCCCACC 60.036 55.000 2.29 0.00 0.00 4.61
52 53 0.908180 ACTAAACTAGCGCCCCACCT 60.908 55.000 2.29 0.00 0.00 4.00
53 54 0.462047 CTAAACTAGCGCCCCACCTG 60.462 60.000 2.29 0.00 0.00 4.00
54 55 0.905809 TAAACTAGCGCCCCACCTGA 60.906 55.000 2.29 0.00 0.00 3.86
55 56 2.465055 AAACTAGCGCCCCACCTGAC 62.465 60.000 2.29 0.00 0.00 3.51
56 57 4.162690 CTAGCGCCCCACCTGACC 62.163 72.222 2.29 0.00 0.00 4.02
60 61 3.782443 CGCCCCACCTGACCCTAC 61.782 72.222 0.00 0.00 0.00 3.18
61 62 3.782443 GCCCCACCTGACCCTACG 61.782 72.222 0.00 0.00 0.00 3.51
62 63 2.284405 CCCCACCTGACCCTACGT 60.284 66.667 0.00 0.00 0.00 3.57
63 64 2.656069 CCCCACCTGACCCTACGTG 61.656 68.421 0.00 0.00 0.00 4.49
64 65 2.264794 CCACCTGACCCTACGTGC 59.735 66.667 0.00 0.00 0.00 5.34
65 66 2.579657 CCACCTGACCCTACGTGCA 61.580 63.158 0.00 0.00 0.00 4.57
66 67 1.596934 CACCTGACCCTACGTGCAT 59.403 57.895 0.00 0.00 0.00 3.96
67 68 0.740868 CACCTGACCCTACGTGCATG 60.741 60.000 3.82 3.82 0.00 4.06
68 69 0.902984 ACCTGACCCTACGTGCATGA 60.903 55.000 14.17 0.00 0.00 3.07
69 70 0.179100 CCTGACCCTACGTGCATGAG 60.179 60.000 14.17 5.70 0.00 2.90
70 71 0.179100 CTGACCCTACGTGCATGAGG 60.179 60.000 14.17 14.20 0.00 3.86
71 72 0.613572 TGACCCTACGTGCATGAGGA 60.614 55.000 14.17 0.00 31.45 3.71
72 73 0.535335 GACCCTACGTGCATGAGGAA 59.465 55.000 14.17 0.00 31.45 3.36
73 74 0.537188 ACCCTACGTGCATGAGGAAG 59.463 55.000 14.17 6.12 31.45 3.46
74 75 0.537188 CCCTACGTGCATGAGGAAGT 59.463 55.000 14.17 0.00 31.45 3.01
75 76 1.066143 CCCTACGTGCATGAGGAAGTT 60.066 52.381 14.17 0.00 31.45 2.66
76 77 2.167693 CCCTACGTGCATGAGGAAGTTA 59.832 50.000 14.17 0.00 31.45 2.24
77 78 3.369052 CCCTACGTGCATGAGGAAGTTAA 60.369 47.826 14.17 0.00 31.45 2.01
78 79 4.442706 CCTACGTGCATGAGGAAGTTAAT 58.557 43.478 14.17 0.00 31.45 1.40
79 80 4.876107 CCTACGTGCATGAGGAAGTTAATT 59.124 41.667 14.17 0.00 31.45 1.40
80 81 6.046593 CCTACGTGCATGAGGAAGTTAATTA 58.953 40.000 14.17 0.00 31.45 1.40
81 82 6.201044 CCTACGTGCATGAGGAAGTTAATTAG 59.799 42.308 14.17 0.00 31.45 1.73
82 83 4.332819 ACGTGCATGAGGAAGTTAATTAGC 59.667 41.667 14.17 0.00 0.00 3.09
83 84 4.260784 CGTGCATGAGGAAGTTAATTAGCC 60.261 45.833 0.00 0.00 0.00 3.93
84 85 4.884164 GTGCATGAGGAAGTTAATTAGCCT 59.116 41.667 0.00 0.00 0.00 4.58
85 86 5.358160 GTGCATGAGGAAGTTAATTAGCCTT 59.642 40.000 0.00 0.00 0.00 4.35
86 87 5.590259 TGCATGAGGAAGTTAATTAGCCTTC 59.410 40.000 14.23 14.23 35.06 3.46
87 88 5.277538 GCATGAGGAAGTTAATTAGCCTTCG 60.278 44.000 15.32 7.25 36.34 3.79
88 89 4.766375 TGAGGAAGTTAATTAGCCTTCGG 58.234 43.478 15.32 0.00 36.34 4.30
89 90 4.468510 TGAGGAAGTTAATTAGCCTTCGGA 59.531 41.667 15.32 5.01 36.34 4.55
90 91 5.046159 TGAGGAAGTTAATTAGCCTTCGGAA 60.046 40.000 15.32 0.00 36.34 4.30
91 92 5.183969 AGGAAGTTAATTAGCCTTCGGAAC 58.816 41.667 15.32 6.77 36.34 3.62
105 106 3.221834 GGAACGTCGTGATCGAGAG 57.778 57.895 0.00 0.00 46.96 3.20
106 107 0.248134 GGAACGTCGTGATCGAGAGG 60.248 60.000 0.00 7.95 46.96 3.69
107 108 0.725686 GAACGTCGTGATCGAGAGGA 59.274 55.000 14.21 0.00 46.96 3.71
108 109 1.331138 GAACGTCGTGATCGAGAGGAT 59.669 52.381 14.21 5.11 46.96 3.24
109 110 2.235845 ACGTCGTGATCGAGAGGATA 57.764 50.000 14.21 0.00 46.96 2.59
110 111 2.768698 ACGTCGTGATCGAGAGGATAT 58.231 47.619 14.21 0.00 46.96 1.63
111 112 2.737783 ACGTCGTGATCGAGAGGATATC 59.262 50.000 14.21 0.00 46.96 1.63
112 113 2.737252 CGTCGTGATCGAGAGGATATCA 59.263 50.000 4.83 0.00 46.96 2.15
113 114 3.423776 CGTCGTGATCGAGAGGATATCAC 60.424 52.174 4.83 0.00 46.96 3.06
114 115 3.498777 GTCGTGATCGAGAGGATATCACA 59.501 47.826 12.17 0.00 46.34 3.58
115 116 4.155099 GTCGTGATCGAGAGGATATCACAT 59.845 45.833 12.17 0.00 46.34 3.21
116 117 4.154918 TCGTGATCGAGAGGATATCACATG 59.845 45.833 12.17 0.00 46.34 3.21
117 118 4.154918 CGTGATCGAGAGGATATCACATGA 59.845 45.833 12.17 1.37 46.34 3.07
118 119 5.163673 CGTGATCGAGAGGATATCACATGAT 60.164 44.000 12.17 0.00 46.34 2.45
119 120 6.037610 CGTGATCGAGAGGATATCACATGATA 59.962 42.308 12.17 4.11 46.34 2.15
120 121 7.192913 GTGATCGAGAGGATATCACATGATAC 58.807 42.308 4.83 0.00 45.66 2.24
121 122 6.319911 TGATCGAGAGGATATCACATGATACC 59.680 42.308 4.83 7.74 39.57 2.73
122 123 5.570320 TCGAGAGGATATCACATGATACCA 58.430 41.667 4.83 0.00 39.57 3.25
123 124 6.190587 TCGAGAGGATATCACATGATACCAT 58.809 40.000 4.83 2.68 39.57 3.55
124 125 6.319911 TCGAGAGGATATCACATGATACCATC 59.680 42.308 4.83 10.10 39.57 3.51
125 126 6.096001 CGAGAGGATATCACATGATACCATCA 59.904 42.308 9.89 0.00 44.55 3.07
148 149 8.560355 TCATTTAAATGATACCATGATACCCG 57.440 34.615 23.86 0.00 40.32 5.28
149 150 8.160765 TCATTTAAATGATACCATGATACCCGT 58.839 33.333 23.86 0.00 40.32 5.28
150 151 8.792633 CATTTAAATGATACCATGATACCCGTT 58.207 33.333 21.35 0.00 38.70 4.44
151 152 8.754991 TTTAAATGATACCATGATACCCGTTT 57.245 30.769 0.00 0.00 32.36 3.60
152 153 6.877611 AAATGATACCATGATACCCGTTTC 57.122 37.500 0.00 0.00 32.36 2.78
153 154 5.560722 ATGATACCATGATACCCGTTTCA 57.439 39.130 0.00 0.00 0.00 2.69
154 155 5.360649 TGATACCATGATACCCGTTTCAA 57.639 39.130 0.00 0.00 0.00 2.69
155 156 5.746284 TGATACCATGATACCCGTTTCAAA 58.254 37.500 0.00 0.00 0.00 2.69
156 157 6.181190 TGATACCATGATACCCGTTTCAAAA 58.819 36.000 0.00 0.00 0.00 2.44
157 158 6.659668 TGATACCATGATACCCGTTTCAAAAA 59.340 34.615 0.00 0.00 0.00 1.94
158 159 5.993748 ACCATGATACCCGTTTCAAAAAT 57.006 34.783 0.00 0.00 0.00 1.82
159 160 5.961272 ACCATGATACCCGTTTCAAAAATC 58.039 37.500 0.00 0.00 0.00 2.17
160 161 5.105513 ACCATGATACCCGTTTCAAAAATCC 60.106 40.000 0.00 0.00 0.00 3.01
161 162 5.105554 CCATGATACCCGTTTCAAAAATCCA 60.106 40.000 0.00 0.00 0.00 3.41
162 163 6.393990 CATGATACCCGTTTCAAAAATCCAA 58.606 36.000 0.00 0.00 0.00 3.53
163 164 6.597832 TGATACCCGTTTCAAAAATCCAAT 57.402 33.333 0.00 0.00 0.00 3.16
164 165 6.998802 TGATACCCGTTTCAAAAATCCAATT 58.001 32.000 0.00 0.00 0.00 2.32
165 166 7.445945 TGATACCCGTTTCAAAAATCCAATTT 58.554 30.769 0.00 0.00 0.00 1.82
166 167 7.934120 TGATACCCGTTTCAAAAATCCAATTTT 59.066 29.630 0.00 0.00 43.83 1.82
167 168 9.425577 GATACCCGTTTCAAAAATCCAATTTTA 57.574 29.630 0.00 0.00 41.30 1.52
168 169 7.722795 ACCCGTTTCAAAAATCCAATTTTAG 57.277 32.000 0.00 0.00 41.30 1.85
169 170 7.501844 ACCCGTTTCAAAAATCCAATTTTAGA 58.498 30.769 0.00 0.00 41.30 2.10
170 171 8.154203 ACCCGTTTCAAAAATCCAATTTTAGAT 58.846 29.630 0.00 0.00 41.30 1.98
171 172 8.442384 CCCGTTTCAAAAATCCAATTTTAGATG 58.558 33.333 0.00 0.00 41.30 2.90
172 173 8.987890 CCGTTTCAAAAATCCAATTTTAGATGT 58.012 29.630 0.00 0.00 41.30 3.06
173 174 9.796062 CGTTTCAAAAATCCAATTTTAGATGTG 57.204 29.630 0.00 0.00 41.30 3.21
223 224 9.710900 TGAATGTTCATCACATATATGTCTACC 57.289 33.333 15.60 3.20 46.23 3.18
224 225 9.935241 GAATGTTCATCACATATATGTCTACCT 57.065 33.333 15.60 1.15 46.23 3.08
225 226 9.935241 AATGTTCATCACATATATGTCTACCTC 57.065 33.333 15.60 6.53 46.23 3.85
226 227 7.896811 TGTTCATCACATATATGTCTACCTCC 58.103 38.462 15.60 2.81 39.39 4.30
227 228 7.039011 TGTTCATCACATATATGTCTACCTCCC 60.039 40.741 15.60 1.60 39.39 4.30
228 229 5.958380 TCATCACATATATGTCTACCTCCCC 59.042 44.000 15.60 0.00 39.39 4.81
229 230 5.616975 TCACATATATGTCTACCTCCCCT 57.383 43.478 15.60 0.00 39.39 4.79
230 231 6.730001 TCACATATATGTCTACCTCCCCTA 57.270 41.667 15.60 0.00 39.39 3.53
231 232 7.111136 TCACATATATGTCTACCTCCCCTAA 57.889 40.000 15.60 0.00 39.39 2.69
232 233 7.541074 TCACATATATGTCTACCTCCCCTAAA 58.459 38.462 15.60 0.00 39.39 1.85
233 234 8.014263 TCACATATATGTCTACCTCCCCTAAAA 58.986 37.037 15.60 0.00 39.39 1.52
234 235 8.656806 CACATATATGTCTACCTCCCCTAAAAA 58.343 37.037 15.60 0.00 39.39 1.94
299 300 9.950680 AAAAGACAAATGTAGTTGTGAATAGTG 57.049 29.630 2.15 0.00 41.78 2.74
300 301 8.677148 AAGACAAATGTAGTTGTGAATAGTGT 57.323 30.769 2.15 0.00 41.78 3.55
301 302 8.677148 AGACAAATGTAGTTGTGAATAGTGTT 57.323 30.769 2.15 0.00 41.78 3.32
302 303 8.559536 AGACAAATGTAGTTGTGAATAGTGTTG 58.440 33.333 2.15 0.00 41.78 3.33
303 304 8.220755 ACAAATGTAGTTGTGAATAGTGTTGT 57.779 30.769 0.00 0.00 40.22 3.32
304 305 8.682710 ACAAATGTAGTTGTGAATAGTGTTGTT 58.317 29.630 0.00 0.00 40.22 2.83
305 306 9.515020 CAAATGTAGTTGTGAATAGTGTTGTTT 57.485 29.630 0.00 0.00 0.00 2.83
308 309 8.903570 TGTAGTTGTGAATAGTGTTGTTTTTG 57.096 30.769 0.00 0.00 0.00 2.44
309 310 7.971168 TGTAGTTGTGAATAGTGTTGTTTTTGG 59.029 33.333 0.00 0.00 0.00 3.28
310 311 5.810074 AGTTGTGAATAGTGTTGTTTTTGGC 59.190 36.000 0.00 0.00 0.00 4.52
311 312 5.330455 TGTGAATAGTGTTGTTTTTGGCA 57.670 34.783 0.00 0.00 0.00 4.92
312 313 5.105752 TGTGAATAGTGTTGTTTTTGGCAC 58.894 37.500 0.00 0.00 0.00 5.01
313 314 5.105554 TGTGAATAGTGTTGTTTTTGGCACT 60.106 36.000 0.00 0.00 43.55 4.40
314 315 6.095580 TGTGAATAGTGTTGTTTTTGGCACTA 59.904 34.615 5.85 5.85 44.96 2.74
318 319 5.590530 AGTGTTGTTTTTGGCACTATTCA 57.409 34.783 0.00 0.00 40.00 2.57
319 320 6.160576 AGTGTTGTTTTTGGCACTATTCAT 57.839 33.333 0.00 0.00 40.00 2.57
320 321 6.215845 AGTGTTGTTTTTGGCACTATTCATC 58.784 36.000 0.00 0.00 40.00 2.92
321 322 5.405269 GTGTTGTTTTTGGCACTATTCATCC 59.595 40.000 0.00 0.00 0.00 3.51
322 323 5.304101 TGTTGTTTTTGGCACTATTCATCCT 59.696 36.000 0.00 0.00 0.00 3.24
323 324 6.183360 TGTTGTTTTTGGCACTATTCATCCTT 60.183 34.615 0.00 0.00 0.00 3.36
324 325 6.418057 TGTTTTTGGCACTATTCATCCTTT 57.582 33.333 0.00 0.00 0.00 3.11
325 326 6.825610 TGTTTTTGGCACTATTCATCCTTTT 58.174 32.000 0.00 0.00 0.00 2.27
326 327 6.705381 TGTTTTTGGCACTATTCATCCTTTTG 59.295 34.615 0.00 0.00 0.00 2.44
327 328 6.418057 TTTTGGCACTATTCATCCTTTTGT 57.582 33.333 0.00 0.00 0.00 2.83
328 329 5.643379 TTGGCACTATTCATCCTTTTGTC 57.357 39.130 0.00 0.00 0.00 3.18
329 330 4.922206 TGGCACTATTCATCCTTTTGTCT 58.078 39.130 0.00 0.00 0.00 3.41
330 331 5.324409 TGGCACTATTCATCCTTTTGTCTT 58.676 37.500 0.00 0.00 0.00 3.01
331 332 5.774690 TGGCACTATTCATCCTTTTGTCTTT 59.225 36.000 0.00 0.00 0.00 2.52
332 333 6.945435 TGGCACTATTCATCCTTTTGTCTTTA 59.055 34.615 0.00 0.00 0.00 1.85
333 334 7.615365 TGGCACTATTCATCCTTTTGTCTTTAT 59.385 33.333 0.00 0.00 0.00 1.40
334 335 8.470002 GGCACTATTCATCCTTTTGTCTTTATT 58.530 33.333 0.00 0.00 0.00 1.40
335 336 9.294030 GCACTATTCATCCTTTTGTCTTTATTG 57.706 33.333 0.00 0.00 0.00 1.90
340 341 8.463930 TTCATCCTTTTGTCTTTATTGACACT 57.536 30.769 0.00 0.00 45.32 3.55
341 342 7.874940 TCATCCTTTTGTCTTTATTGACACTG 58.125 34.615 0.00 0.00 45.32 3.66
342 343 7.502226 TCATCCTTTTGTCTTTATTGACACTGT 59.498 33.333 0.00 0.00 45.32 3.55
343 344 7.639113 TCCTTTTGTCTTTATTGACACTGTT 57.361 32.000 0.00 0.00 45.32 3.16
344 345 7.703328 TCCTTTTGTCTTTATTGACACTGTTC 58.297 34.615 0.00 0.00 45.32 3.18
345 346 7.338196 TCCTTTTGTCTTTATTGACACTGTTCA 59.662 33.333 0.00 0.00 45.32 3.18
346 347 8.137437 CCTTTTGTCTTTATTGACACTGTTCAT 58.863 33.333 0.00 0.00 45.32 2.57
347 348 8.854979 TTTTGTCTTTATTGACACTGTTCATG 57.145 30.769 0.00 0.00 45.32 3.07
348 349 7.566760 TTGTCTTTATTGACACTGTTCATGT 57.433 32.000 0.00 0.00 45.32 3.21
349 350 7.566760 TGTCTTTATTGACACTGTTCATGTT 57.433 32.000 0.00 0.00 41.43 2.71
350 351 7.416817 TGTCTTTATTGACACTGTTCATGTTG 58.583 34.615 0.00 0.00 41.43 3.33
351 352 6.857964 GTCTTTATTGACACTGTTCATGTTGG 59.142 38.462 0.00 0.00 36.97 3.77
352 353 6.770303 TCTTTATTGACACTGTTCATGTTGGA 59.230 34.615 0.00 0.00 0.00 3.53
353 354 7.448161 TCTTTATTGACACTGTTCATGTTGGAT 59.552 33.333 0.00 0.00 0.00 3.41
354 355 7.523293 TTATTGACACTGTTCATGTTGGATT 57.477 32.000 0.00 0.00 0.00 3.01
355 356 5.850557 TTGACACTGTTCATGTTGGATTT 57.149 34.783 0.00 0.00 0.00 2.17
356 357 5.437289 TGACACTGTTCATGTTGGATTTC 57.563 39.130 0.00 0.00 0.00 2.17
357 358 5.132502 TGACACTGTTCATGTTGGATTTCT 58.867 37.500 0.00 0.00 0.00 2.52
358 359 5.239306 TGACACTGTTCATGTTGGATTTCTC 59.761 40.000 0.00 0.00 0.00 2.87
359 360 5.380043 ACACTGTTCATGTTGGATTTCTCT 58.620 37.500 0.00 0.00 0.00 3.10
360 361 5.829924 ACACTGTTCATGTTGGATTTCTCTT 59.170 36.000 0.00 0.00 0.00 2.85
361 362 6.322201 ACACTGTTCATGTTGGATTTCTCTTT 59.678 34.615 0.00 0.00 0.00 2.52
362 363 7.147846 ACACTGTTCATGTTGGATTTCTCTTTT 60.148 33.333 0.00 0.00 0.00 2.27
363 364 7.707893 CACTGTTCATGTTGGATTTCTCTTTTT 59.292 33.333 0.00 0.00 0.00 1.94
426 427 8.808240 TTTTTAGGGGAGGTAGACATATATGT 57.192 34.615 18.31 18.31 45.16 2.29
427 428 7.792364 TTTAGGGGAGGTAGACATATATGTG 57.208 40.000 22.93 0.00 41.95 3.21
428 429 5.616975 AGGGGAGGTAGACATATATGTGA 57.383 43.478 22.93 7.93 41.95 3.58
429 430 6.172350 AGGGGAGGTAGACATATATGTGAT 57.828 41.667 22.93 13.19 41.95 3.06
430 431 5.960811 AGGGGAGGTAGACATATATGTGATG 59.039 44.000 22.93 0.00 41.95 3.07
431 432 5.958380 GGGGAGGTAGACATATATGTGATGA 59.042 44.000 22.93 2.65 41.95 2.92
432 433 6.440647 GGGGAGGTAGACATATATGTGATGAA 59.559 42.308 22.93 1.16 41.95 2.57
433 434 7.324178 GGGAGGTAGACATATATGTGATGAAC 58.676 42.308 22.93 12.08 41.95 3.18
434 435 7.039011 GGGAGGTAGACATATATGTGATGAACA 60.039 40.741 22.93 0.00 41.95 3.18
449 450 8.489990 TGTGATGAACATTCACAATTGTTTTT 57.510 26.923 8.77 0.00 40.81 1.94
450 451 8.388853 TGTGATGAACATTCACAATTGTTTTTG 58.611 29.630 8.77 8.89 40.81 2.44
451 452 8.602328 GTGATGAACATTCACAATTGTTTTTGA 58.398 29.630 8.77 0.00 40.49 2.69
452 453 9.159364 TGATGAACATTCACAATTGTTTTTGAA 57.841 25.926 8.77 9.87 40.49 2.69
453 454 9.640974 GATGAACATTCACAATTGTTTTTGAAG 57.359 29.630 8.77 6.43 40.49 3.02
454 455 8.545229 TGAACATTCACAATTGTTTTTGAAGT 57.455 26.923 8.77 6.98 35.58 3.01
455 456 8.997323 TGAACATTCACAATTGTTTTTGAAGTT 58.003 25.926 8.77 13.66 35.58 2.66
456 457 9.824534 GAACATTCACAATTGTTTTTGAAGTTT 57.175 25.926 8.77 6.71 35.58 2.66
497 498 9.643693 AATTAGCTTTTTGAAACTGGTATCATG 57.356 29.630 0.00 0.00 0.00 3.07
498 499 6.029346 AGCTTTTTGAAACTGGTATCATGG 57.971 37.500 0.00 0.00 0.00 3.66
499 500 5.539955 AGCTTTTTGAAACTGGTATCATGGT 59.460 36.000 0.00 0.00 0.00 3.55
500 501 6.719370 AGCTTTTTGAAACTGGTATCATGGTA 59.281 34.615 0.00 0.00 0.00 3.25
501 502 7.397192 AGCTTTTTGAAACTGGTATCATGGTAT 59.603 33.333 0.00 0.00 0.00 2.73
502 503 7.702348 GCTTTTTGAAACTGGTATCATGGTATC 59.298 37.037 0.00 0.00 0.00 2.24
503 504 8.642935 TTTTTGAAACTGGTATCATGGTATCA 57.357 30.769 0.00 0.00 0.00 2.15
504 505 8.821686 TTTTGAAACTGGTATCATGGTATCAT 57.178 30.769 0.00 0.00 0.00 2.45
518 519 5.762179 TGGTATCATGTGATATTCTCCCC 57.238 43.478 6.04 2.96 39.03 4.81
519 520 4.222810 TGGTATCATGTGATATTCTCCCCG 59.777 45.833 6.04 0.00 39.03 5.73
520 521 4.223032 GGTATCATGTGATATTCTCCCCGT 59.777 45.833 6.04 0.00 39.03 5.28
521 522 4.543590 ATCATGTGATATTCTCCCCGTC 57.456 45.455 0.00 0.00 32.01 4.79
522 523 2.632996 TCATGTGATATTCTCCCCGTCC 59.367 50.000 0.00 0.00 0.00 4.79
523 524 1.420430 TGTGATATTCTCCCCGTCCC 58.580 55.000 0.00 0.00 0.00 4.46
524 525 0.317479 GTGATATTCTCCCCGTCCCG 59.683 60.000 0.00 0.00 0.00 5.14
625 647 0.465287 CATGGCCCCAAAATAGTGCC 59.535 55.000 0.00 0.00 42.49 5.01
641 663 2.269241 CCCCCTCGAGCTCCAAAC 59.731 66.667 6.99 0.00 0.00 2.93
650 672 1.756430 GAGCTCCAAACCCCAAGATC 58.244 55.000 0.87 0.00 0.00 2.75
755 783 1.887242 TTGACACTGACAGCACGGC 60.887 57.895 1.25 0.00 0.00 5.68
847 876 4.514577 AGCTCCATCGTTCCGCCG 62.515 66.667 0.00 0.00 0.00 6.46
862 898 1.464376 CGCCGGTATCCAGAGTCCAT 61.464 60.000 1.90 0.00 0.00 3.41
871 907 1.686325 CCAGAGTCCATACCACCGGG 61.686 65.000 6.32 0.00 41.29 5.73
932 976 2.740981 AGACTAGGTAACACGTCGACAG 59.259 50.000 17.16 9.92 41.27 3.51
934 978 1.808945 CTAGGTAACACGTCGACAGGT 59.191 52.381 17.16 9.85 41.41 4.00
935 979 0.313043 AGGTAACACGTCGACAGGTG 59.687 55.000 17.16 17.89 42.97 4.00
936 980 0.311790 GGTAACACGTCGACAGGTGA 59.688 55.000 24.50 9.57 40.28 4.02
938 982 2.049228 GTAACACGTCGACAGGTGAAG 58.951 52.381 24.50 6.69 40.28 3.02
941 985 3.470567 CGTCGACAGGTGAAGCGC 61.471 66.667 17.16 0.00 0.00 5.92
952 996 0.937699 GTGAAGCGCACACGTAGACA 60.938 55.000 18.59 0.03 46.91 3.41
983 1027 3.393970 CAGCCTCGCAGGGGAAGA 61.394 66.667 0.00 0.00 35.37 2.87
984 1028 3.394836 AGCCTCGCAGGGGAAGAC 61.395 66.667 0.00 0.00 35.37 3.01
985 1029 4.475135 GCCTCGCAGGGGAAGACC 62.475 72.222 0.00 0.00 35.37 3.85
986 1030 4.148825 CCTCGCAGGGGAAGACCG 62.149 72.222 0.00 0.00 41.60 4.79
987 1031 4.148825 CTCGCAGGGGAAGACCGG 62.149 72.222 0.00 0.00 41.60 5.28
988 1032 4.689549 TCGCAGGGGAAGACCGGA 62.690 66.667 9.46 0.00 41.60 5.14
989 1033 3.702048 CGCAGGGGAAGACCGGAA 61.702 66.667 9.46 0.00 41.60 4.30
1251 1665 2.711922 CGGGTGGCTCTACTTCGCT 61.712 63.158 0.00 0.00 0.00 4.93
1389 1803 4.838486 CCGCTCGTCCTCGCTGAC 62.838 72.222 0.00 0.00 36.96 3.51
1499 1916 2.979649 GGTGGGGAAGACGAGGAC 59.020 66.667 0.00 0.00 0.00 3.85
1586 2009 1.305297 AGGCCGATGACTGAGTCCA 60.305 57.895 10.52 0.00 0.00 4.02
1660 2129 6.208994 AGTCTAGTTACTTGATTCAGTCGGTT 59.791 38.462 0.00 0.00 0.00 4.44
1696 2165 3.492309 GCTGAGGTGGAGATCAGTGTATG 60.492 52.174 0.00 0.00 43.94 2.39
1697 2166 3.033909 TGAGGTGGAGATCAGTGTATGG 58.966 50.000 0.00 0.00 0.00 2.74
1698 2167 1.765314 AGGTGGAGATCAGTGTATGGC 59.235 52.381 0.00 0.00 0.00 4.40
1699 2168 1.486310 GGTGGAGATCAGTGTATGGCA 59.514 52.381 0.00 0.00 0.00 4.92
1823 2554 0.482446 TCCATGTCAAGTGGGCCTTT 59.518 50.000 4.53 0.00 37.34 3.11
1829 2560 3.838565 TGTCAAGTGGGCCTTTTTATGA 58.161 40.909 4.53 0.00 0.00 2.15
1840 2571 2.023673 CTTTTTATGAGCCGGCATGGA 58.976 47.619 31.54 9.40 42.00 3.41
1909 2640 1.409427 AGTTGACTACCATAGCTCCGC 59.591 52.381 0.00 0.00 0.00 5.54
1954 2685 0.827507 GCTTTCACCTTGGCTTGGGA 60.828 55.000 1.86 0.00 0.00 4.37
1955 2686 1.703411 CTTTCACCTTGGCTTGGGAA 58.297 50.000 1.86 0.00 0.00 3.97
1958 2689 2.166907 TCACCTTGGCTTGGGAAAAA 57.833 45.000 1.86 0.00 0.00 1.94
1985 4846 5.277828 GCGGAAGGATATGGTGTTGTTTATC 60.278 44.000 0.00 0.00 0.00 1.75
1997 4858 4.391830 GTGTTGTTTATCTTCGCCATCTCA 59.608 41.667 0.00 0.00 0.00 3.27
2014 4877 4.156455 TCTCAAAGTGCAAGAAGAACCT 57.844 40.909 0.00 0.00 0.00 3.50
2015 4878 4.130118 TCTCAAAGTGCAAGAAGAACCTC 58.870 43.478 0.00 0.00 0.00 3.85
2021 4884 3.643792 AGTGCAAGAAGAACCTCTAGTGT 59.356 43.478 0.00 0.00 0.00 3.55
2066 4942 8.006298 ACATCAATTTAAATTCGGGCTATTGA 57.994 30.769 10.53 4.28 35.68 2.57
2100 4977 9.023967 CACTGCTAATTTATACAATCTTTTGCC 57.976 33.333 0.00 0.00 36.22 4.52
2211 5088 0.036164 TACTTGGCGCAACTGGACAT 59.964 50.000 10.83 0.00 0.00 3.06
2214 5091 1.514678 TTGGCGCAACTGGACATCAC 61.515 55.000 10.83 0.00 0.00 3.06
2292 5169 7.336427 GCATAGATTCTTTGCCTAGCATATTCT 59.664 37.037 15.72 0.00 38.76 2.40
2310 5187 5.552870 ATTCTTTAGGACTGCGTATGGAT 57.447 39.130 0.00 0.00 0.00 3.41
2378 5255 1.143684 TGCAAAAGGGAGCAAGAGTCT 59.856 47.619 0.00 0.00 37.90 3.24
2399 5276 6.040166 AGTCTGTTGCACATCTTCTTTTCAAT 59.960 34.615 0.00 0.00 0.00 2.57
2450 5327 4.793201 AGACTAAAGCTTGGTTTGTCCTT 58.207 39.130 0.00 0.00 37.07 3.36
2516 5393 1.197721 GAGTGGCGGAGTTTTGTGATG 59.802 52.381 0.00 0.00 0.00 3.07
2525 5402 5.762045 CGGAGTTTTGTGATGAAAGTCATT 58.238 37.500 6.72 0.00 37.20 2.57
2572 5449 8.623903 TGAATCCTTTGTGATGCTTGTATATTC 58.376 33.333 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.178996 GCCTCTCTTAACAGATGCATGTATG 59.821 44.000 2.46 2.43 34.95 2.39
8 9 5.163269 TGCCTCTCTTAACAGATGCATGTAT 60.163 40.000 2.46 0.00 38.63 2.29
9 10 4.162131 TGCCTCTCTTAACAGATGCATGTA 59.838 41.667 2.46 0.00 38.63 2.29
10 11 3.054875 TGCCTCTCTTAACAGATGCATGT 60.055 43.478 2.46 0.00 38.63 3.21
11 12 3.538591 TGCCTCTCTTAACAGATGCATG 58.461 45.455 2.46 0.00 38.63 4.06
12 13 3.920231 TGCCTCTCTTAACAGATGCAT 57.080 42.857 0.00 0.00 38.63 3.96
13 14 3.008375 AGTTGCCTCTCTTAACAGATGCA 59.992 43.478 6.60 6.60 40.88 3.96
14 15 3.604582 AGTTGCCTCTCTTAACAGATGC 58.395 45.455 1.87 1.87 35.29 3.91
15 16 6.876257 AGTTTAGTTGCCTCTCTTAACAGATG 59.124 38.462 0.00 0.00 0.00 2.90
16 17 7.010339 AGTTTAGTTGCCTCTCTTAACAGAT 57.990 36.000 0.00 0.00 0.00 2.90
17 18 6.420913 AGTTTAGTTGCCTCTCTTAACAGA 57.579 37.500 0.00 0.00 0.00 3.41
18 19 6.311690 GCTAGTTTAGTTGCCTCTCTTAACAG 59.688 42.308 0.00 0.00 0.00 3.16
19 20 6.164176 GCTAGTTTAGTTGCCTCTCTTAACA 58.836 40.000 0.00 0.00 0.00 2.41
20 21 5.288952 CGCTAGTTTAGTTGCCTCTCTTAAC 59.711 44.000 0.00 0.00 0.00 2.01
21 22 5.408356 CGCTAGTTTAGTTGCCTCTCTTAA 58.592 41.667 0.00 0.00 0.00 1.85
22 23 4.677250 GCGCTAGTTTAGTTGCCTCTCTTA 60.677 45.833 0.00 0.00 0.00 2.10
23 24 3.851098 CGCTAGTTTAGTTGCCTCTCTT 58.149 45.455 0.00 0.00 0.00 2.85
24 25 2.417515 GCGCTAGTTTAGTTGCCTCTCT 60.418 50.000 0.00 0.00 0.00 3.10
25 26 1.927838 GCGCTAGTTTAGTTGCCTCTC 59.072 52.381 0.00 0.00 0.00 3.20
26 27 1.405661 GGCGCTAGTTTAGTTGCCTCT 60.406 52.381 7.64 0.00 42.43 3.69
27 28 1.007580 GGCGCTAGTTTAGTTGCCTC 58.992 55.000 7.64 0.00 42.43 4.70
28 29 0.392595 GGGCGCTAGTTTAGTTGCCT 60.393 55.000 7.64 0.00 44.00 4.75
29 30 1.374343 GGGGCGCTAGTTTAGTTGCC 61.374 60.000 7.64 10.91 43.89 4.52
30 31 0.675522 TGGGGCGCTAGTTTAGTTGC 60.676 55.000 7.64 0.00 0.00 4.17
31 32 1.084289 GTGGGGCGCTAGTTTAGTTG 58.916 55.000 7.64 0.00 0.00 3.16
32 33 0.035725 GGTGGGGCGCTAGTTTAGTT 60.036 55.000 7.64 0.00 0.00 2.24
33 34 0.908180 AGGTGGGGCGCTAGTTTAGT 60.908 55.000 7.64 0.00 0.00 2.24
34 35 0.462047 CAGGTGGGGCGCTAGTTTAG 60.462 60.000 7.64 0.00 0.00 1.85
35 36 0.905809 TCAGGTGGGGCGCTAGTTTA 60.906 55.000 7.64 0.00 0.00 2.01
36 37 2.221299 TCAGGTGGGGCGCTAGTTT 61.221 57.895 7.64 0.00 0.00 2.66
37 38 2.606519 TCAGGTGGGGCGCTAGTT 60.607 61.111 7.64 0.00 0.00 2.24
38 39 3.391382 GTCAGGTGGGGCGCTAGT 61.391 66.667 7.64 0.00 0.00 2.57
39 40 4.162690 GGTCAGGTGGGGCGCTAG 62.163 72.222 7.64 0.00 0.00 3.42
43 44 3.782443 GTAGGGTCAGGTGGGGCG 61.782 72.222 0.00 0.00 0.00 6.13
44 45 3.782443 CGTAGGGTCAGGTGGGGC 61.782 72.222 0.00 0.00 0.00 5.80
45 46 2.284405 ACGTAGGGTCAGGTGGGG 60.284 66.667 0.00 0.00 0.00 4.96
46 47 2.978824 CACGTAGGGTCAGGTGGG 59.021 66.667 0.00 0.00 32.09 4.61
47 48 1.899437 ATGCACGTAGGGTCAGGTGG 61.899 60.000 0.00 0.00 35.39 4.61
48 49 0.740868 CATGCACGTAGGGTCAGGTG 60.741 60.000 0.00 0.00 37.36 4.00
49 50 0.902984 TCATGCACGTAGGGTCAGGT 60.903 55.000 0.00 0.00 0.00 4.00
50 51 0.179100 CTCATGCACGTAGGGTCAGG 60.179 60.000 0.00 0.00 0.00 3.86
51 52 0.179100 CCTCATGCACGTAGGGTCAG 60.179 60.000 0.00 0.00 0.00 3.51
52 53 0.613572 TCCTCATGCACGTAGGGTCA 60.614 55.000 10.15 0.00 0.00 4.02
53 54 0.535335 TTCCTCATGCACGTAGGGTC 59.465 55.000 10.15 0.00 0.00 4.46
54 55 0.537188 CTTCCTCATGCACGTAGGGT 59.463 55.000 10.15 0.00 0.00 4.34
55 56 0.537188 ACTTCCTCATGCACGTAGGG 59.463 55.000 10.15 0.00 0.00 3.53
56 57 2.386661 AACTTCCTCATGCACGTAGG 57.613 50.000 4.74 4.74 0.00 3.18
57 58 6.292381 GCTAATTAACTTCCTCATGCACGTAG 60.292 42.308 0.00 0.00 0.00 3.51
58 59 5.522460 GCTAATTAACTTCCTCATGCACGTA 59.478 40.000 0.00 0.00 0.00 3.57
59 60 4.332819 GCTAATTAACTTCCTCATGCACGT 59.667 41.667 0.00 0.00 0.00 4.49
60 61 4.260784 GGCTAATTAACTTCCTCATGCACG 60.261 45.833 0.00 0.00 0.00 5.34
61 62 4.884164 AGGCTAATTAACTTCCTCATGCAC 59.116 41.667 0.00 0.00 0.00 4.57
62 63 5.116084 AGGCTAATTAACTTCCTCATGCA 57.884 39.130 0.00 0.00 0.00 3.96
63 64 5.277538 CGAAGGCTAATTAACTTCCTCATGC 60.278 44.000 17.39 2.14 37.84 4.06
64 65 5.237344 CCGAAGGCTAATTAACTTCCTCATG 59.763 44.000 17.39 0.00 46.14 3.07
65 66 5.368989 CCGAAGGCTAATTAACTTCCTCAT 58.631 41.667 17.39 0.00 46.14 2.90
66 67 4.766375 CCGAAGGCTAATTAACTTCCTCA 58.234 43.478 17.39 0.00 46.14 3.86
83 84 0.179207 TCGATCACGACGTTCCGAAG 60.179 55.000 11.93 0.00 43.81 3.79
84 85 0.179207 CTCGATCACGACGTTCCGAA 60.179 55.000 14.25 0.00 43.81 4.30
85 86 1.015607 TCTCGATCACGACGTTCCGA 61.016 55.000 0.00 6.85 43.81 4.55
86 87 0.586748 CTCTCGATCACGACGTTCCG 60.587 60.000 0.00 2.25 43.81 4.30
87 88 0.248134 CCTCTCGATCACGACGTTCC 60.248 60.000 0.00 0.00 43.81 3.62
88 89 0.725686 TCCTCTCGATCACGACGTTC 59.274 55.000 0.00 0.00 43.81 3.95
89 90 1.380524 ATCCTCTCGATCACGACGTT 58.619 50.000 0.00 0.00 43.81 3.99
90 91 2.235845 TATCCTCTCGATCACGACGT 57.764 50.000 0.00 0.00 43.81 4.34
91 92 2.737252 TGATATCCTCTCGATCACGACG 59.263 50.000 0.00 0.00 43.81 5.12
92 93 4.073169 GTGATATCCTCTCGATCACGAC 57.927 50.000 0.00 0.00 43.81 4.34
95 96 5.635417 TCATGTGATATCCTCTCGATCAC 57.365 43.478 6.20 6.20 46.34 3.06
96 97 6.319911 GGTATCATGTGATATCCTCTCGATCA 59.680 42.308 6.04 0.00 39.03 2.92
97 98 6.319911 TGGTATCATGTGATATCCTCTCGATC 59.680 42.308 10.03 0.00 37.34 3.69
98 99 6.190587 TGGTATCATGTGATATCCTCTCGAT 58.809 40.000 10.03 0.00 37.34 3.59
99 100 5.570320 TGGTATCATGTGATATCCTCTCGA 58.430 41.667 10.03 0.00 37.34 4.04
100 101 5.904362 TGGTATCATGTGATATCCTCTCG 57.096 43.478 10.03 0.00 37.34 4.04
101 102 7.415592 TGATGGTATCATGTGATATCCTCTC 57.584 40.000 15.12 13.22 37.34 3.20
124 125 8.335532 ACGGGTATCATGGTATCATTTAAATG 57.664 34.615 20.13 20.13 37.75 2.32
125 126 8.934023 AACGGGTATCATGGTATCATTTAAAT 57.066 30.769 0.00 0.00 0.00 1.40
126 127 8.754991 AAACGGGTATCATGGTATCATTTAAA 57.245 30.769 0.00 0.00 0.00 1.52
127 128 7.993758 TGAAACGGGTATCATGGTATCATTTAA 59.006 33.333 0.00 0.00 0.00 1.52
128 129 7.510407 TGAAACGGGTATCATGGTATCATTTA 58.490 34.615 0.00 0.00 0.00 1.40
129 130 6.361433 TGAAACGGGTATCATGGTATCATTT 58.639 36.000 0.00 0.00 0.00 2.32
130 131 5.935945 TGAAACGGGTATCATGGTATCATT 58.064 37.500 0.00 0.00 0.00 2.57
131 132 5.560722 TGAAACGGGTATCATGGTATCAT 57.439 39.130 0.00 0.00 0.00 2.45
132 133 5.360649 TTGAAACGGGTATCATGGTATCA 57.639 39.130 0.00 0.00 0.00 2.15
133 134 6.687081 TTTTGAAACGGGTATCATGGTATC 57.313 37.500 0.00 0.00 0.00 2.24
134 135 7.201875 GGATTTTTGAAACGGGTATCATGGTAT 60.202 37.037 0.00 0.00 0.00 2.73
135 136 6.095720 GGATTTTTGAAACGGGTATCATGGTA 59.904 38.462 0.00 0.00 0.00 3.25
136 137 5.105513 GGATTTTTGAAACGGGTATCATGGT 60.106 40.000 0.00 0.00 0.00 3.55
137 138 5.105554 TGGATTTTTGAAACGGGTATCATGG 60.106 40.000 0.00 0.00 0.00 3.66
138 139 5.960113 TGGATTTTTGAAACGGGTATCATG 58.040 37.500 0.00 0.00 0.00 3.07
139 140 6.597832 TTGGATTTTTGAAACGGGTATCAT 57.402 33.333 0.00 0.00 0.00 2.45
140 141 6.597832 ATTGGATTTTTGAAACGGGTATCA 57.402 33.333 0.00 0.00 0.00 2.15
141 142 7.899178 AAATTGGATTTTTGAAACGGGTATC 57.101 32.000 0.00 0.00 0.00 2.24
142 143 9.430623 CTAAAATTGGATTTTTGAAACGGGTAT 57.569 29.630 4.21 0.00 42.13 2.73
143 144 8.639761 TCTAAAATTGGATTTTTGAAACGGGTA 58.360 29.630 4.21 0.00 42.13 3.69
144 145 7.501844 TCTAAAATTGGATTTTTGAAACGGGT 58.498 30.769 4.21 0.00 42.13 5.28
145 146 7.954788 TCTAAAATTGGATTTTTGAAACGGG 57.045 32.000 4.21 0.00 42.13 5.28
146 147 8.987890 ACATCTAAAATTGGATTTTTGAAACGG 58.012 29.630 11.98 7.07 43.42 4.44
147 148 9.796062 CACATCTAAAATTGGATTTTTGAAACG 57.204 29.630 11.98 8.03 43.42 3.60
201 202 7.039011 GGGAGGTAGACATATATGTGATGAACA 60.039 40.741 22.93 0.00 41.95 3.18
202 203 7.324178 GGGAGGTAGACATATATGTGATGAAC 58.676 42.308 22.93 12.08 41.95 3.18
203 204 6.440647 GGGGAGGTAGACATATATGTGATGAA 59.559 42.308 22.93 1.16 41.95 2.57
204 205 5.958380 GGGGAGGTAGACATATATGTGATGA 59.042 44.000 22.93 2.65 41.95 2.92
205 206 5.960811 AGGGGAGGTAGACATATATGTGATG 59.039 44.000 22.93 0.00 41.95 3.07
206 207 6.172350 AGGGGAGGTAGACATATATGTGAT 57.828 41.667 22.93 13.19 41.95 3.06
207 208 5.616975 AGGGGAGGTAGACATATATGTGA 57.383 43.478 22.93 7.93 41.95 3.58
208 209 7.792364 TTTAGGGGAGGTAGACATATATGTG 57.208 40.000 22.93 0.00 41.95 3.21
209 210 8.808240 TTTTTAGGGGAGGTAGACATATATGT 57.192 34.615 18.31 18.31 45.16 2.29
273 274 9.950680 CACTATTCACAACTACATTTGTCTTTT 57.049 29.630 0.00 0.00 37.62 2.27
274 275 9.120538 ACACTATTCACAACTACATTTGTCTTT 57.879 29.630 0.00 0.00 37.62 2.52
275 276 8.677148 ACACTATTCACAACTACATTTGTCTT 57.323 30.769 0.00 0.00 37.62 3.01
276 277 8.559536 CAACACTATTCACAACTACATTTGTCT 58.440 33.333 0.00 0.00 37.62 3.41
277 278 8.342634 ACAACACTATTCACAACTACATTTGTC 58.657 33.333 0.00 0.00 37.62 3.18
278 279 8.220755 ACAACACTATTCACAACTACATTTGT 57.779 30.769 0.00 0.00 40.46 2.83
279 280 9.515020 AAACAACACTATTCACAACTACATTTG 57.485 29.630 0.00 0.00 0.00 2.32
282 283 9.515020 CAAAAACAACACTATTCACAACTACAT 57.485 29.630 0.00 0.00 0.00 2.29
283 284 7.971168 CCAAAAACAACACTATTCACAACTACA 59.029 33.333 0.00 0.00 0.00 2.74
284 285 7.043656 GCCAAAAACAACACTATTCACAACTAC 60.044 37.037 0.00 0.00 0.00 2.73
285 286 6.975772 GCCAAAAACAACACTATTCACAACTA 59.024 34.615 0.00 0.00 0.00 2.24
286 287 5.810074 GCCAAAAACAACACTATTCACAACT 59.190 36.000 0.00 0.00 0.00 3.16
287 288 5.578727 TGCCAAAAACAACACTATTCACAAC 59.421 36.000 0.00 0.00 0.00 3.32
288 289 5.578727 GTGCCAAAAACAACACTATTCACAA 59.421 36.000 0.00 0.00 0.00 3.33
289 290 5.105554 AGTGCCAAAAACAACACTATTCACA 60.106 36.000 0.00 0.00 41.41 3.58
290 291 5.348164 AGTGCCAAAAACAACACTATTCAC 58.652 37.500 0.00 0.00 41.41 3.18
291 292 5.590530 AGTGCCAAAAACAACACTATTCA 57.409 34.783 0.00 0.00 41.41 2.57
295 296 6.701145 TGAATAGTGCCAAAAACAACACTA 57.299 33.333 4.38 4.38 46.42 2.74
296 297 5.590530 TGAATAGTGCCAAAAACAACACT 57.409 34.783 0.00 0.00 45.02 3.55
297 298 5.405269 GGATGAATAGTGCCAAAAACAACAC 59.595 40.000 0.00 0.00 0.00 3.32
298 299 5.304101 AGGATGAATAGTGCCAAAAACAACA 59.696 36.000 0.00 0.00 0.00 3.33
299 300 5.783111 AGGATGAATAGTGCCAAAAACAAC 58.217 37.500 0.00 0.00 0.00 3.32
300 301 6.418057 AAGGATGAATAGTGCCAAAAACAA 57.582 33.333 0.00 0.00 0.00 2.83
301 302 6.418057 AAAGGATGAATAGTGCCAAAAACA 57.582 33.333 0.00 0.00 0.00 2.83
302 303 6.705825 ACAAAAGGATGAATAGTGCCAAAAAC 59.294 34.615 0.00 0.00 0.00 2.43
303 304 6.825610 ACAAAAGGATGAATAGTGCCAAAAA 58.174 32.000 0.00 0.00 0.00 1.94
304 305 6.267471 AGACAAAAGGATGAATAGTGCCAAAA 59.733 34.615 0.00 0.00 0.00 2.44
305 306 5.774690 AGACAAAAGGATGAATAGTGCCAAA 59.225 36.000 0.00 0.00 0.00 3.28
306 307 5.324409 AGACAAAAGGATGAATAGTGCCAA 58.676 37.500 0.00 0.00 0.00 4.52
307 308 4.922206 AGACAAAAGGATGAATAGTGCCA 58.078 39.130 0.00 0.00 0.00 4.92
308 309 5.904362 AAGACAAAAGGATGAATAGTGCC 57.096 39.130 0.00 0.00 0.00 5.01
309 310 9.294030 CAATAAAGACAAAAGGATGAATAGTGC 57.706 33.333 0.00 0.00 0.00 4.40
325 326 7.416817 CAACATGAACAGTGTCAATAAAGACA 58.583 34.615 0.00 0.00 45.64 3.41
326 327 6.857964 CCAACATGAACAGTGTCAATAAAGAC 59.142 38.462 0.00 0.00 38.99 3.01
327 328 6.770303 TCCAACATGAACAGTGTCAATAAAGA 59.230 34.615 0.00 0.00 0.00 2.52
328 329 6.969366 TCCAACATGAACAGTGTCAATAAAG 58.031 36.000 0.00 0.00 0.00 1.85
329 330 6.951062 TCCAACATGAACAGTGTCAATAAA 57.049 33.333 0.00 0.00 0.00 1.40
330 331 7.523293 AATCCAACATGAACAGTGTCAATAA 57.477 32.000 0.00 0.00 0.00 1.40
331 332 7.448161 AGAAATCCAACATGAACAGTGTCAATA 59.552 33.333 0.00 0.00 0.00 1.90
332 333 6.266103 AGAAATCCAACATGAACAGTGTCAAT 59.734 34.615 0.00 0.00 0.00 2.57
333 334 5.593909 AGAAATCCAACATGAACAGTGTCAA 59.406 36.000 0.00 0.00 0.00 3.18
334 335 5.132502 AGAAATCCAACATGAACAGTGTCA 58.867 37.500 0.00 0.00 0.00 3.58
335 336 5.471456 AGAGAAATCCAACATGAACAGTGTC 59.529 40.000 0.00 0.00 0.00 3.67
336 337 5.380043 AGAGAAATCCAACATGAACAGTGT 58.620 37.500 0.00 0.00 0.00 3.55
337 338 5.954296 AGAGAAATCCAACATGAACAGTG 57.046 39.130 0.00 0.00 0.00 3.66
338 339 6.966534 AAAGAGAAATCCAACATGAACAGT 57.033 33.333 0.00 0.00 0.00 3.55
401 402 8.656806 CACATATATGTCTACCTCCCCTAAAAA 58.343 37.037 15.60 0.00 39.39 1.94
402 403 8.014263 TCACATATATGTCTACCTCCCCTAAAA 58.986 37.037 15.60 0.00 39.39 1.52
403 404 7.541074 TCACATATATGTCTACCTCCCCTAAA 58.459 38.462 15.60 0.00 39.39 1.85
404 405 7.111136 TCACATATATGTCTACCTCCCCTAA 57.889 40.000 15.60 0.00 39.39 2.69
405 406 6.730001 TCACATATATGTCTACCTCCCCTA 57.270 41.667 15.60 0.00 39.39 3.53
406 407 5.616975 TCACATATATGTCTACCTCCCCT 57.383 43.478 15.60 0.00 39.39 4.79
407 408 5.958380 TCATCACATATATGTCTACCTCCCC 59.042 44.000 15.60 0.00 39.39 4.81
408 409 7.039011 TGTTCATCACATATATGTCTACCTCCC 60.039 40.741 15.60 1.60 39.39 4.30
409 410 7.896811 TGTTCATCACATATATGTCTACCTCC 58.103 38.462 15.60 2.81 39.39 4.30
410 411 9.935241 AATGTTCATCACATATATGTCTACCTC 57.065 33.333 15.60 6.53 46.23 3.85
411 412 9.935241 GAATGTTCATCACATATATGTCTACCT 57.065 33.333 15.60 1.15 46.23 3.08
412 413 9.710900 TGAATGTTCATCACATATATGTCTACC 57.289 33.333 15.60 3.20 46.23 3.18
425 426 8.602328 TCAAAAACAATTGTGAATGTTCATCAC 58.398 29.630 12.82 0.00 45.82 3.06
426 427 8.713737 TCAAAAACAATTGTGAATGTTCATCA 57.286 26.923 12.82 0.00 38.75 3.07
427 428 9.640974 CTTCAAAAACAATTGTGAATGTTCATC 57.359 29.630 12.82 0.00 40.98 2.92
428 429 9.165035 ACTTCAAAAACAATTGTGAATGTTCAT 57.835 25.926 12.82 0.00 40.98 2.57
429 430 8.545229 ACTTCAAAAACAATTGTGAATGTTCA 57.455 26.923 12.82 0.00 40.98 3.18
430 431 9.824534 AAACTTCAAAAACAATTGTGAATGTTC 57.175 25.926 12.82 0.00 40.98 3.18
471 472 9.643693 CATGATACCAGTTTCAAAAAGCTAATT 57.356 29.630 0.00 0.00 0.00 1.40
472 473 8.253113 CCATGATACCAGTTTCAAAAAGCTAAT 58.747 33.333 0.00 0.00 0.00 1.73
473 474 7.232534 ACCATGATACCAGTTTCAAAAAGCTAA 59.767 33.333 0.00 0.00 0.00 3.09
474 475 6.719370 ACCATGATACCAGTTTCAAAAAGCTA 59.281 34.615 0.00 0.00 0.00 3.32
475 476 5.539955 ACCATGATACCAGTTTCAAAAAGCT 59.460 36.000 0.00 0.00 0.00 3.74
476 477 5.783111 ACCATGATACCAGTTTCAAAAAGC 58.217 37.500 0.00 0.00 0.00 3.51
477 478 8.739039 TGATACCATGATACCAGTTTCAAAAAG 58.261 33.333 0.00 0.00 0.00 2.27
478 479 8.642935 TGATACCATGATACCAGTTTCAAAAA 57.357 30.769 0.00 0.00 0.00 1.94
479 480 8.821686 ATGATACCATGATACCAGTTTCAAAA 57.178 30.769 0.00 0.00 0.00 2.44
495 496 5.104776 CGGGGAGAATATCACATGATACCAT 60.105 44.000 0.00 0.00 39.57 3.55
496 497 4.222810 CGGGGAGAATATCACATGATACCA 59.777 45.833 0.00 0.00 39.57 3.25
497 498 4.223032 ACGGGGAGAATATCACATGATACC 59.777 45.833 0.00 1.52 39.57 2.73
498 499 5.407407 ACGGGGAGAATATCACATGATAC 57.593 43.478 0.00 0.00 39.57 2.24
499 500 4.466370 GGACGGGGAGAATATCACATGATA 59.534 45.833 0.00 4.11 40.85 2.15
500 501 3.261897 GGACGGGGAGAATATCACATGAT 59.738 47.826 0.00 0.00 38.51 2.45
501 502 2.632996 GGACGGGGAGAATATCACATGA 59.367 50.000 0.00 0.00 30.31 3.07
502 503 2.289694 GGGACGGGGAGAATATCACATG 60.290 54.545 0.00 0.00 30.31 3.21
503 504 1.978580 GGGACGGGGAGAATATCACAT 59.021 52.381 0.00 0.00 30.31 3.21
504 505 1.420430 GGGACGGGGAGAATATCACA 58.580 55.000 0.00 0.00 30.31 3.58
519 520 2.105128 CAGCTGATCGTCCGGGAC 59.895 66.667 17.38 17.38 0.00 4.46
520 521 3.838271 GCAGCTGATCGTCCGGGA 61.838 66.667 20.43 0.00 0.00 5.14
521 522 4.899239 GGCAGCTGATCGTCCGGG 62.899 72.222 20.43 0.00 0.00 5.73
525 526 4.854784 TCGCGGCAGCTGATCGTC 62.855 66.667 20.43 14.27 42.32 4.20
526 527 4.862092 CTCGCGGCAGCTGATCGT 62.862 66.667 20.43 0.00 42.32 3.73
625 647 2.269241 GGTTTGGAGCTCGAGGGG 59.731 66.667 15.58 0.00 0.00 4.79
641 663 0.267356 AGGAGAGAGGGATCTTGGGG 59.733 60.000 0.00 0.00 0.00 4.96
650 672 0.628522 TCAGTGAGGAGGAGAGAGGG 59.371 60.000 0.00 0.00 0.00 4.30
755 783 1.208259 TTCGTCATCGATCAATGCGG 58.792 50.000 0.00 0.00 45.65 5.69
799 828 4.577246 GGCCAGGAGTAGAGCGCG 62.577 72.222 0.00 0.00 0.00 6.86
802 831 2.923634 TACGGGGCCAGGAGTAGAGC 62.924 65.000 4.39 0.00 0.00 4.09
847 876 2.633481 GGTGGTATGGACTCTGGATACC 59.367 54.545 0.00 0.00 41.39 2.73
862 898 3.212377 GGTGATCTACCCGGTGGTA 57.788 57.895 0.00 0.00 45.45 3.25
871 907 5.041191 AGTGGATTGGATTGGTGATCTAC 57.959 43.478 0.00 0.00 35.02 2.59
879 915 4.397417 GTCTGAGAAAGTGGATTGGATTGG 59.603 45.833 0.00 0.00 0.00 3.16
887 923 4.021544 GTCTGTCTGTCTGAGAAAGTGGAT 60.022 45.833 0.00 0.00 37.33 3.41
932 976 1.372499 TCTACGTGTGCGCTTCACC 60.372 57.895 22.80 10.97 45.03 4.02
934 978 0.038618 ATGTCTACGTGTGCGCTTCA 60.039 50.000 9.73 5.24 42.83 3.02
935 979 0.640768 GATGTCTACGTGTGCGCTTC 59.359 55.000 9.73 2.14 42.83 3.86
936 980 1.071019 CGATGTCTACGTGTGCGCTT 61.071 55.000 9.73 0.00 42.83 4.68
938 982 2.987593 CGATGTCTACGTGTGCGC 59.012 61.111 0.00 0.00 42.83 6.09
941 985 1.872234 CGGGCGATGTCTACGTGTG 60.872 63.158 0.00 0.00 0.00 3.82
982 1026 2.360801 CCATCTCTCTTCTCTTCCGGTC 59.639 54.545 0.00 0.00 0.00 4.79
983 1027 2.383855 CCATCTCTCTTCTCTTCCGGT 58.616 52.381 0.00 0.00 0.00 5.28
984 1028 1.686052 CCCATCTCTCTTCTCTTCCGG 59.314 57.143 0.00 0.00 0.00 5.14
985 1029 1.068434 GCCCATCTCTCTTCTCTTCCG 59.932 57.143 0.00 0.00 0.00 4.30
986 1030 2.365293 GAGCCCATCTCTCTTCTCTTCC 59.635 54.545 0.00 0.00 38.78 3.46
987 1031 2.034558 CGAGCCCATCTCTCTTCTCTTC 59.965 54.545 0.00 0.00 39.70 2.87
988 1032 2.031120 CGAGCCCATCTCTCTTCTCTT 58.969 52.381 0.00 0.00 39.70 2.85
989 1033 1.064017 ACGAGCCCATCTCTCTTCTCT 60.064 52.381 0.00 0.00 39.70 3.10
1070 1117 3.834799 CGTCTAGGCCGACCACCC 61.835 72.222 0.00 0.00 39.06 4.61
1082 1129 4.143333 GCGCCAAGGAGCCGTCTA 62.143 66.667 3.21 0.00 34.89 2.59
1251 1665 1.225426 GAGCATGGACATGGGCAGA 59.775 57.895 13.63 0.00 39.16 4.26
1392 1809 3.649277 CTCTGTTCCGGTGCCCTCG 62.649 68.421 0.00 0.00 0.00 4.63
1499 1916 2.158959 CCGTAAGAACCAGCTCGCG 61.159 63.158 0.00 0.00 43.02 5.87
1586 2009 2.159114 ACCGTTTGCAAAAATCAGCAGT 60.159 40.909 14.67 0.00 42.39 4.40
1823 2554 1.608055 CATCCATGCCGGCTCATAAA 58.392 50.000 29.70 6.08 33.14 1.40
1829 2560 1.305213 AAAACCATCCATGCCGGCT 60.305 52.632 29.70 10.60 33.14 5.52
1864 2595 8.547481 TCATAGAAGAGGTCCATGTTAACATA 57.453 34.615 20.39 3.83 34.26 2.29
1887 2618 2.688446 CGGAGCTATGGTAGTCAACTCA 59.312 50.000 0.00 0.00 0.00 3.41
1958 2689 3.016736 CAACACCATATCCTTCCGCTTT 58.983 45.455 0.00 0.00 0.00 3.51
1963 4824 7.254795 CGAAGATAAACAACACCATATCCTTCC 60.255 40.741 0.00 0.00 0.00 3.46
1967 4828 5.277828 GGCGAAGATAAACAACACCATATCC 60.278 44.000 0.00 0.00 0.00 2.59
1968 4829 5.295787 TGGCGAAGATAAACAACACCATATC 59.704 40.000 0.00 0.00 0.00 1.63
1973 4834 3.689649 AGATGGCGAAGATAAACAACACC 59.310 43.478 0.00 0.00 0.00 4.16
1985 4846 1.159285 TGCACTTTGAGATGGCGAAG 58.841 50.000 0.00 0.00 35.75 3.79
1997 4858 5.059833 CACTAGAGGTTCTTCTTGCACTTT 58.940 41.667 0.00 0.00 0.00 2.66
2014 4877 4.955811 TTCCAGCAGAAAGAACACTAGA 57.044 40.909 0.00 0.00 0.00 2.43
2015 4878 6.376978 CATTTTCCAGCAGAAAGAACACTAG 58.623 40.000 2.68 0.00 45.11 2.57
2021 4884 4.214310 TGTCCATTTTCCAGCAGAAAGAA 58.786 39.130 2.68 0.00 45.11 2.52
2029 4892 7.903995 TTTAAATTGATGTCCATTTTCCAGC 57.096 32.000 0.00 0.00 32.51 4.85
2066 4942 6.658849 TGTATAAATTAGCAGTGTGGTGGAT 58.341 36.000 0.00 0.00 0.00 3.41
2097 4974 2.560981 TGAACATCTTGTAGACTCGGCA 59.439 45.455 0.00 0.00 0.00 5.69
2180 5057 1.967597 GCCAAGTAAGCCGACTTCGC 61.968 60.000 2.89 2.89 37.57 4.70
2203 5080 7.630242 AATTGAAATATTCGTGATGTCCAGT 57.370 32.000 0.00 0.00 0.00 4.00
2211 5088 8.237949 TCGGCTTTAAAATTGAAATATTCGTGA 58.762 29.630 0.00 0.00 0.00 4.35
2214 5091 9.833894 CAATCGGCTTTAAAATTGAAATATTCG 57.166 29.630 4.90 0.00 32.14 3.34
2292 5169 3.181469 GGTCATCCATACGCAGTCCTAAA 60.181 47.826 0.00 0.00 43.93 1.85
2310 5187 4.329545 GAACCAGCCAGCCGGTCA 62.330 66.667 1.90 0.00 33.17 4.02
2325 5202 0.321564 CGCCACCAATGTCTCTGGAA 60.322 55.000 0.00 0.00 37.40 3.53
2328 5205 0.957395 AAGCGCCACCAATGTCTCTG 60.957 55.000 2.29 0.00 0.00 3.35
2399 5276 1.974265 TGCGTCAAGAAAATCCACCA 58.026 45.000 0.00 0.00 0.00 4.17
2469 5346 4.686191 TCAAATTGAAATGGCACCAAGT 57.314 36.364 0.00 0.00 0.00 3.16
2548 5425 8.523915 TGAATATACAAGCATCACAAAGGATT 57.476 30.769 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.