Multiple sequence alignment - TraesCS5D01G278000

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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 TraesCS5D01G278000 chr5D 100.000 2770 0 0 1 2770 379964258 379967027 0.000000e+00 5116.0
1 TraesCS5D01G278000 chr5A 90.510 2139 136 21 647 2764 480406156 480408248 0.000000e+00 2763.0
2 TraesCS5D01G278000 chr5A 93.500 200 12 1 1190 1388 139484863 139484664 2.090000e-76 296.0
3 TraesCS5D01G278000 chr5B 90.557 1525 86 18 291 1782 455760074 455761573 0.000000e+00 1965.0
4 TraesCS5D01G278000 chr5B 90.118 678 51 8 2097 2765 455764307 455764977 0.000000e+00 867.0
5 TraesCS5D01G278000 chr5B 92.050 239 17 2 1869 2106 455761950 455762187 4.420000e-88 335.0
6 TraesCS5D01G278000 chr7A 96.970 198 6 0 1313 1510 238537681 238537484 1.590000e-87 333.0
7 TraesCS5D01G278000 chr7A 93.500 200 12 1 1190 1388 238537879 238537680 2.090000e-76 296.0
8 TraesCS5D01G278000 chr2A 96.465 198 7 0 1313 1510 662939772 662939575 7.400000e-86 327.0
9 TraesCS5D01G278000 chr2A 93.103 203 13 1 1187 1388 668074063 668074265 2.090000e-76 296.0
10 TraesCS5D01G278000 chr6B 95.960 198 8 0 1313 1510 21194530 21194727 3.440000e-84 322.0
11 TraesCS5D01G278000 chr6B 92.611 203 14 1 1187 1388 21194329 21194531 9.700000e-75 291.0
12 TraesCS5D01G278000 chr6A 95.960 198 8 0 1313 1510 393233091 393233288 3.440000e-84 322.0
13 TraesCS5D01G278000 chr6A 93.103 203 13 1 1187 1388 393232890 393233092 2.090000e-76 296.0
14 TraesCS5D01G278000 chr4A 95.960 198 8 0 1313 1510 95156115 95156312 3.440000e-84 322.0
15 TraesCS5D01G278000 chr3B 95.960 198 8 0 1313 1510 1269812 1269615 3.440000e-84 322.0
16 TraesCS5D01G278000 chr3B 93.500 200 12 1 1190 1388 1270303 1270104 2.090000e-76 296.0
17 TraesCS5D01G278000 chr3A 95.960 198 8 0 1313 1510 363952202 363952399 3.440000e-84 322.0
18 TraesCS5D01G278000 chr4B 92.611 203 14 1 1187 1388 429597608 429597810 9.700000e-75 291.0
19 TraesCS5D01G278000 chr4B 94.545 55 3 0 233 287 622433519 622433465 4.920000e-13 86.1
20 TraesCS5D01G278000 chrUn 94.737 57 3 0 233 289 127027055 127026999 3.800000e-14 89.8
21 TraesCS5D01G278000 chrUn 94.545 55 3 0 233 287 338511689 338511743 4.920000e-13 86.1
22 TraesCS5D01G278000 chrUn 94.545 55 3 0 233 287 363201661 363201715 4.920000e-13 86.1
23 TraesCS5D01G278000 chrUn 94.545 55 3 0 233 287 453468264 453468210 4.920000e-13 86.1
24 TraesCS5D01G278000 chr2D 94.737 57 1 2 234 289 29833275 29833220 1.370000e-13 87.9
25 TraesCS5D01G278000 chr1B 92.453 53 3 1 233 285 394409222 394409273 1.060000e-09 75.0
26 TraesCS5D01G278000 chr6D 90.909 55 4 1 232 286 16572941 16572994 3.830000e-09 73.1
27 TraesCS5D01G278000 chr6D 90.909 55 3 2 233 286 452727382 452727435 3.830000e-09 73.1


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 TraesCS5D01G278000 chr5D 379964258 379967027 2769 False 5116.000000 5116 100.000000 1 2770 1 chr5D.!!$F1 2769
1 TraesCS5D01G278000 chr5A 480406156 480408248 2092 False 2763.000000 2763 90.510000 647 2764 1 chr5A.!!$F1 2117
2 TraesCS5D01G278000 chr5B 455760074 455764977 4903 False 1055.666667 1965 90.908333 291 2765 3 chr5B.!!$F1 2474
3 TraesCS5D01G278000 chr3B 1269615 1270303 688 True 309.000000 322 94.730000 1190 1510 2 chr3B.!!$R1 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
190 191 0.032130 GCACTTGGTGTCGACTGAGA 59.968 55.0 17.92 0.00 35.75 3.27 F
274 275 0.110678 CCCAGCCTCTGCATCATCAT 59.889 55.0 0.00 0.00 41.13 2.45 F
469 471 0.168128 GTTTTGTCCATTCTCGCGGG 59.832 55.0 6.13 1.01 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1114 1132 0.174617 CTCTTCTCTTCCCCTGCGAC 59.825 60.0 0.00 0.0 0.0 5.19 R
1676 2075 0.875059 GAGCTTAACCTTTGCACGCT 59.125 50.0 0.00 0.0 0.0 5.07 R
2446 5289 0.104855 GCCAGCTGATCGTCCATACA 59.895 55.0 17.39 0.0 0.0 2.29 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
28 29 4.828072 GGGAGTACCTTTCTCAGTTGAT 57.172 45.455 0.00 0.00 35.85 2.57
29 30 5.167303 GGGAGTACCTTTCTCAGTTGATT 57.833 43.478 0.00 0.00 35.85 2.57
30 31 5.561679 GGGAGTACCTTTCTCAGTTGATTT 58.438 41.667 0.00 0.00 35.85 2.17
31 32 5.644206 GGGAGTACCTTTCTCAGTTGATTTC 59.356 44.000 0.00 0.00 35.85 2.17
32 33 6.231211 GGAGTACCTTTCTCAGTTGATTTCA 58.769 40.000 0.00 0.00 34.04 2.69
33 34 6.147985 GGAGTACCTTTCTCAGTTGATTTCAC 59.852 42.308 0.00 0.00 34.04 3.18
34 35 5.696724 AGTACCTTTCTCAGTTGATTTCACG 59.303 40.000 0.00 0.00 0.00 4.35
35 36 4.703897 ACCTTTCTCAGTTGATTTCACGA 58.296 39.130 0.00 0.00 0.00 4.35
36 37 5.308825 ACCTTTCTCAGTTGATTTCACGAT 58.691 37.500 0.00 0.00 0.00 3.73
37 38 5.765182 ACCTTTCTCAGTTGATTTCACGATT 59.235 36.000 0.00 0.00 0.00 3.34
38 39 6.934645 ACCTTTCTCAGTTGATTTCACGATTA 59.065 34.615 0.00 0.00 0.00 1.75
39 40 7.607991 ACCTTTCTCAGTTGATTTCACGATTAT 59.392 33.333 0.00 0.00 0.00 1.28
40 41 7.907045 CCTTTCTCAGTTGATTTCACGATTATG 59.093 37.037 0.00 0.00 0.00 1.90
41 42 7.905604 TTCTCAGTTGATTTCACGATTATGT 57.094 32.000 0.00 0.00 0.00 2.29
42 43 7.294676 TCTCAGTTGATTTCACGATTATGTG 57.705 36.000 0.00 0.00 41.28 3.21
43 44 5.868257 TCAGTTGATTTCACGATTATGTGC 58.132 37.500 0.00 0.00 39.73 4.57
44 45 5.411053 TCAGTTGATTTCACGATTATGTGCA 59.589 36.000 0.00 0.00 39.73 4.57
45 46 6.093909 TCAGTTGATTTCACGATTATGTGCAT 59.906 34.615 0.00 0.00 39.73 3.96
46 47 7.279758 TCAGTTGATTTCACGATTATGTGCATA 59.720 33.333 0.00 0.00 39.73 3.14
47 48 7.374228 CAGTTGATTTCACGATTATGTGCATAC 59.626 37.037 0.00 0.00 39.73 2.39
48 49 6.917217 TGATTTCACGATTATGTGCATACA 57.083 33.333 0.00 0.00 41.89 2.29
77 78 2.702592 AAAAGGTCACCGTGTTCTGA 57.297 45.000 0.00 0.00 0.00 3.27
78 79 2.702592 AAAGGTCACCGTGTTCTGAA 57.297 45.000 0.00 0.00 0.00 3.02
79 80 2.702592 AAGGTCACCGTGTTCTGAAA 57.297 45.000 0.00 0.00 0.00 2.69
80 81 1.949465 AGGTCACCGTGTTCTGAAAC 58.051 50.000 0.00 0.00 35.85 2.78
81 82 0.580104 GGTCACCGTGTTCTGAAACG 59.420 55.000 14.08 14.08 38.28 3.60
82 83 1.283736 GTCACCGTGTTCTGAAACGT 58.716 50.000 17.35 0.00 38.28 3.99
83 84 1.005347 GTCACCGTGTTCTGAAACGTG 60.005 52.381 17.35 15.43 38.28 4.49
84 85 1.003851 CACCGTGTTCTGAAACGTGT 58.996 50.000 17.35 13.61 38.28 4.49
85 86 1.395608 CACCGTGTTCTGAAACGTGTT 59.604 47.619 17.35 0.00 38.28 3.32
86 87 2.604011 CACCGTGTTCTGAAACGTGTTA 59.396 45.455 17.35 0.00 38.28 2.41
87 88 3.062369 CACCGTGTTCTGAAACGTGTTAA 59.938 43.478 17.35 0.00 38.28 2.01
88 89 3.872771 ACCGTGTTCTGAAACGTGTTAAT 59.127 39.130 17.35 0.00 38.28 1.40
89 90 4.025480 ACCGTGTTCTGAAACGTGTTAATC 60.025 41.667 17.35 0.00 38.28 1.75
90 91 4.210537 CCGTGTTCTGAAACGTGTTAATCT 59.789 41.667 17.35 0.00 38.28 2.40
91 92 5.403166 CCGTGTTCTGAAACGTGTTAATCTA 59.597 40.000 17.35 0.00 38.28 1.98
92 93 6.399669 CCGTGTTCTGAAACGTGTTAATCTAG 60.400 42.308 17.35 0.00 38.28 2.43
93 94 6.143438 CGTGTTCTGAAACGTGTTAATCTAGT 59.857 38.462 13.30 0.00 38.28 2.57
94 95 7.281484 GTGTTCTGAAACGTGTTAATCTAGTG 58.719 38.462 0.00 0.00 38.28 2.74
95 96 6.073980 TGTTCTGAAACGTGTTAATCTAGTGC 60.074 38.462 0.00 0.00 38.28 4.40
96 97 5.534407 TCTGAAACGTGTTAATCTAGTGCA 58.466 37.500 0.00 0.00 0.00 4.57
97 98 5.986741 TCTGAAACGTGTTAATCTAGTGCAA 59.013 36.000 0.00 0.00 0.00 4.08
98 99 6.480651 TCTGAAACGTGTTAATCTAGTGCAAA 59.519 34.615 0.00 0.00 0.00 3.68
99 100 7.011576 TCTGAAACGTGTTAATCTAGTGCAAAA 59.988 33.333 0.00 0.00 0.00 2.44
100 101 7.129622 TGAAACGTGTTAATCTAGTGCAAAAG 58.870 34.615 0.00 0.00 0.00 2.27
101 102 5.030874 ACGTGTTAATCTAGTGCAAAAGC 57.969 39.130 0.00 0.00 0.00 3.51
102 103 4.513692 ACGTGTTAATCTAGTGCAAAAGCA 59.486 37.500 0.00 0.00 0.00 3.91
103 104 5.082059 CGTGTTAATCTAGTGCAAAAGCAG 58.918 41.667 0.00 0.00 0.00 4.24
104 105 5.107104 CGTGTTAATCTAGTGCAAAAGCAGA 60.107 40.000 0.00 0.00 0.00 4.26
105 106 6.565811 CGTGTTAATCTAGTGCAAAAGCAGAA 60.566 38.462 0.00 0.00 0.00 3.02
106 107 7.308435 GTGTTAATCTAGTGCAAAAGCAGAAT 58.692 34.615 0.00 0.00 0.00 2.40
107 108 7.272084 GTGTTAATCTAGTGCAAAAGCAGAATG 59.728 37.037 0.00 0.00 40.87 2.67
108 109 5.972107 AATCTAGTGCAAAAGCAGAATGT 57.028 34.783 0.00 0.00 39.31 2.71
109 110 8.450964 GTTAATCTAGTGCAAAAGCAGAATGTA 58.549 33.333 0.00 0.00 39.31 2.29
110 111 6.674694 ATCTAGTGCAAAAGCAGAATGTAG 57.325 37.500 0.00 0.00 39.31 2.74
111 112 5.551233 TCTAGTGCAAAAGCAGAATGTAGT 58.449 37.500 0.00 0.00 39.31 2.73
112 113 4.494350 AGTGCAAAAGCAGAATGTAGTG 57.506 40.909 0.00 0.00 39.31 2.74
113 114 3.885297 AGTGCAAAAGCAGAATGTAGTGT 59.115 39.130 0.00 0.00 39.31 3.55
114 115 4.339247 AGTGCAAAAGCAGAATGTAGTGTT 59.661 37.500 0.00 0.00 39.31 3.32
115 116 5.043248 GTGCAAAAGCAGAATGTAGTGTTT 58.957 37.500 0.00 0.00 39.31 2.83
116 117 5.042593 TGCAAAAGCAGAATGTAGTGTTTG 58.957 37.500 0.00 0.00 39.31 2.93
117 118 4.084900 GCAAAAGCAGAATGTAGTGTTTGC 60.085 41.667 0.00 0.00 41.71 3.68
118 119 5.284079 CAAAAGCAGAATGTAGTGTTTGCT 58.716 37.500 0.00 0.00 43.13 3.91
120 121 5.520376 AAGCAGAATGTAGTGTTTGCTTT 57.480 34.783 3.89 0.00 46.31 3.51
121 122 5.520376 AGCAGAATGTAGTGTTTGCTTTT 57.480 34.783 0.00 0.00 38.64 2.27
122 123 6.633500 AGCAGAATGTAGTGTTTGCTTTTA 57.367 33.333 0.00 0.00 38.64 1.52
123 124 7.038154 AGCAGAATGTAGTGTTTGCTTTTAA 57.962 32.000 0.00 0.00 38.64 1.52
124 125 7.488322 AGCAGAATGTAGTGTTTGCTTTTAAA 58.512 30.769 0.00 0.00 38.64 1.52
125 126 7.978975 AGCAGAATGTAGTGTTTGCTTTTAAAA 59.021 29.630 0.00 0.00 38.64 1.52
126 127 8.764287 GCAGAATGTAGTGTTTGCTTTTAAAAT 58.236 29.630 0.09 0.00 39.31 1.82
131 132 8.988064 TGTAGTGTTTGCTTTTAAAATTCACA 57.012 26.923 0.09 0.42 0.00 3.58
132 133 9.081997 TGTAGTGTTTGCTTTTAAAATTCACAG 57.918 29.630 0.09 0.00 0.00 3.66
133 134 9.083080 GTAGTGTTTGCTTTTAAAATTCACAGT 57.917 29.630 0.09 7.83 0.00 3.55
135 136 9.646427 AGTGTTTGCTTTTAAAATTCACAGTAA 57.354 25.926 0.09 0.00 0.00 2.24
170 171 8.352137 ACATGGATCTCAACATCAAATTAACA 57.648 30.769 0.00 0.00 0.00 2.41
171 172 8.464404 ACATGGATCTCAACATCAAATTAACAG 58.536 33.333 0.00 0.00 0.00 3.16
172 173 6.855836 TGGATCTCAACATCAAATTAACAGC 58.144 36.000 0.00 0.00 0.00 4.40
173 174 6.433716 TGGATCTCAACATCAAATTAACAGCA 59.566 34.615 0.00 0.00 0.00 4.41
174 175 6.749118 GGATCTCAACATCAAATTAACAGCAC 59.251 38.462 0.00 0.00 0.00 4.40
175 176 6.882610 TCTCAACATCAAATTAACAGCACT 57.117 33.333 0.00 0.00 0.00 4.40
176 177 7.275888 TCTCAACATCAAATTAACAGCACTT 57.724 32.000 0.00 0.00 0.00 3.16
177 178 7.140705 TCTCAACATCAAATTAACAGCACTTG 58.859 34.615 0.00 0.00 0.00 3.16
178 179 6.215121 TCAACATCAAATTAACAGCACTTGG 58.785 36.000 0.00 0.00 0.00 3.61
179 180 5.789643 ACATCAAATTAACAGCACTTGGT 57.210 34.783 0.00 0.00 0.00 3.67
186 187 4.758692 CAGCACTTGGTGTCGACT 57.241 55.556 17.92 0.00 38.61 4.18
187 188 2.229039 CAGCACTTGGTGTCGACTG 58.771 57.895 17.92 6.49 38.61 3.51
188 189 0.249447 CAGCACTTGGTGTCGACTGA 60.249 55.000 17.92 0.00 38.61 3.41
189 190 0.032678 AGCACTTGGTGTCGACTGAG 59.967 55.000 17.92 11.11 35.75 3.35
190 191 0.032130 GCACTTGGTGTCGACTGAGA 59.968 55.000 17.92 0.00 35.75 3.27
191 192 1.932604 GCACTTGGTGTCGACTGAGAG 60.933 57.143 17.92 11.79 35.75 3.20
192 193 1.338337 CACTTGGTGTCGACTGAGAGT 59.662 52.381 17.92 12.40 0.00 3.24
193 194 2.032620 ACTTGGTGTCGACTGAGAGTT 58.967 47.619 17.92 0.00 0.00 3.01
194 195 3.004419 CACTTGGTGTCGACTGAGAGTTA 59.996 47.826 17.92 0.00 0.00 2.24
195 196 3.635373 ACTTGGTGTCGACTGAGAGTTAA 59.365 43.478 17.92 0.57 0.00 2.01
196 197 3.637998 TGGTGTCGACTGAGAGTTAAC 57.362 47.619 17.92 0.00 0.00 2.01
197 198 3.220110 TGGTGTCGACTGAGAGTTAACT 58.780 45.455 17.92 8.13 0.00 2.24
198 199 4.392047 TGGTGTCGACTGAGAGTTAACTA 58.608 43.478 17.92 0.00 0.00 2.24
199 200 4.823442 TGGTGTCGACTGAGAGTTAACTAA 59.177 41.667 17.92 0.00 0.00 2.24
200 201 5.475909 TGGTGTCGACTGAGAGTTAACTAAT 59.524 40.000 17.92 0.00 0.00 1.73
201 202 6.015688 TGGTGTCGACTGAGAGTTAACTAATT 60.016 38.462 17.92 0.00 0.00 1.40
202 203 6.527372 GGTGTCGACTGAGAGTTAACTAATTC 59.473 42.308 17.92 7.60 0.00 2.17
203 204 7.306953 GTGTCGACTGAGAGTTAACTAATTCT 58.693 38.462 17.92 1.04 35.35 2.40
204 205 7.482428 GTGTCGACTGAGAGTTAACTAATTCTC 59.518 40.741 17.92 11.38 44.50 2.87
256 257 5.509716 TTTTTCGAAAAGGAGAAAGACCC 57.490 39.130 21.53 0.00 37.61 4.46
257 258 2.853235 TCGAAAAGGAGAAAGACCCC 57.147 50.000 0.00 0.00 0.00 4.95
258 259 2.051692 TCGAAAAGGAGAAAGACCCCA 58.948 47.619 0.00 0.00 0.00 4.96
259 260 2.038557 TCGAAAAGGAGAAAGACCCCAG 59.961 50.000 0.00 0.00 0.00 4.45
260 261 2.163509 GAAAAGGAGAAAGACCCCAGC 58.836 52.381 0.00 0.00 0.00 4.85
261 262 0.405973 AAAGGAGAAAGACCCCAGCC 59.594 55.000 0.00 0.00 0.00 4.85
262 263 0.476611 AAGGAGAAAGACCCCAGCCT 60.477 55.000 0.00 0.00 0.00 4.58
263 264 0.912006 AGGAGAAAGACCCCAGCCTC 60.912 60.000 0.00 0.00 0.00 4.70
264 265 0.912006 GGAGAAAGACCCCAGCCTCT 60.912 60.000 0.00 0.00 0.00 3.69
265 266 0.251634 GAGAAAGACCCCAGCCTCTG 59.748 60.000 0.00 0.00 0.00 3.35
266 267 1.377856 GAAAGACCCCAGCCTCTGC 60.378 63.158 0.00 0.00 37.95 4.26
267 268 2.129555 GAAAGACCCCAGCCTCTGCA 62.130 60.000 0.00 0.00 41.13 4.41
268 269 1.504275 AAAGACCCCAGCCTCTGCAT 61.504 55.000 0.00 0.00 41.13 3.96
269 270 1.919600 AAGACCCCAGCCTCTGCATC 61.920 60.000 0.00 0.00 41.13 3.91
270 271 2.611800 ACCCCAGCCTCTGCATCA 60.612 61.111 0.00 0.00 41.13 3.07
271 272 1.992519 GACCCCAGCCTCTGCATCAT 61.993 60.000 0.00 0.00 41.13 2.45
272 273 1.228184 CCCCAGCCTCTGCATCATC 60.228 63.158 0.00 0.00 41.13 2.92
273 274 1.530283 CCCAGCCTCTGCATCATCA 59.470 57.895 0.00 0.00 41.13 3.07
274 275 0.110678 CCCAGCCTCTGCATCATCAT 59.889 55.000 0.00 0.00 41.13 2.45
275 276 1.239347 CCAGCCTCTGCATCATCATG 58.761 55.000 0.00 0.00 41.13 3.07
276 277 1.202770 CCAGCCTCTGCATCATCATGA 60.203 52.381 0.00 0.00 41.13 3.07
277 278 2.553247 CCAGCCTCTGCATCATCATGAT 60.553 50.000 1.18 1.18 41.13 2.45
288 289 5.181690 CATCATCATGATGCACACAATCA 57.818 39.130 27.68 10.17 46.37 2.57
289 290 4.625972 TCATCATGATGCACACAATCAC 57.374 40.909 27.68 0.00 38.65 3.06
290 291 4.011023 TCATCATGATGCACACAATCACA 58.989 39.130 27.68 6.07 38.65 3.58
291 292 4.095782 TCATCATGATGCACACAATCACAG 59.904 41.667 27.68 2.50 38.65 3.66
292 293 2.162809 TCATGATGCACACAATCACAGC 59.837 45.455 0.00 0.00 0.00 4.40
293 294 1.606903 TGATGCACACAATCACAGCA 58.393 45.000 0.00 0.00 39.79 4.41
294 295 1.955080 TGATGCACACAATCACAGCAA 59.045 42.857 0.00 0.00 38.85 3.91
295 296 2.361438 TGATGCACACAATCACAGCAAA 59.639 40.909 0.00 0.00 38.85 3.68
296 297 2.206815 TGCACACAATCACAGCAAAC 57.793 45.000 0.00 0.00 31.42 2.93
297 298 1.122849 GCACACAATCACAGCAAACG 58.877 50.000 0.00 0.00 0.00 3.60
298 299 1.533756 GCACACAATCACAGCAAACGT 60.534 47.619 0.00 0.00 0.00 3.99
299 300 2.286713 GCACACAATCACAGCAAACGTA 60.287 45.455 0.00 0.00 0.00 3.57
300 301 3.790456 GCACACAATCACAGCAAACGTAA 60.790 43.478 0.00 0.00 0.00 3.18
301 302 3.723764 CACACAATCACAGCAAACGTAAC 59.276 43.478 0.00 0.00 0.00 2.50
322 323 3.255725 CTTTGCATGGTTACATTGGCAG 58.744 45.455 0.00 0.00 37.33 4.85
345 346 3.065019 ACAAAAATATGCGCACGATCC 57.935 42.857 14.90 0.00 0.00 3.36
381 382 9.773328 GCATCGCAAGCTTGATTAATTATATAA 57.227 29.630 30.39 0.00 37.18 0.98
468 470 0.871722 TGTTTTGTCCATTCTCGCGG 59.128 50.000 6.13 0.00 0.00 6.46
469 471 0.168128 GTTTTGTCCATTCTCGCGGG 59.832 55.000 6.13 1.01 0.00 6.13
528 530 4.453819 AGAAAGAAGGAAAGATGCTCGTTG 59.546 41.667 0.00 0.00 0.00 4.10
546 548 6.535274 TCGTTGGCTTAAACTAGAAAGTTC 57.465 37.500 0.00 0.00 45.37 3.01
547 549 5.467735 TCGTTGGCTTAAACTAGAAAGTTCC 59.532 40.000 0.00 0.00 45.37 3.62
552 554 6.882678 TGGCTTAAACTAGAAAGTTCCCATAC 59.117 38.462 0.00 0.00 45.37 2.39
590 592 2.897436 GGCAACTAAACTAGTACCCCG 58.103 52.381 0.00 0.00 38.26 5.73
595 597 2.291800 ACTAAACTAGTACCCCGCCTGA 60.292 50.000 0.00 0.00 37.23 3.86
596 598 1.192428 AAACTAGTACCCCGCCTGAG 58.808 55.000 0.00 0.00 0.00 3.35
623 625 2.093306 CACCTACGTGCATGAGGAAA 57.907 50.000 23.20 1.89 34.24 3.13
627 629 4.816385 CACCTACGTGCATGAGGAAATTAT 59.184 41.667 23.20 4.94 34.24 1.28
634 636 5.532557 GTGCATGAGGAAATTATTTAGCCC 58.467 41.667 0.00 0.00 0.00 5.19
797 799 2.880890 CCAAAGCCCAATATTCCTCTCG 59.119 50.000 0.00 0.00 0.00 4.04
849 851 1.785041 GAAGCGGACAAAGTGCAGCA 61.785 55.000 0.00 0.00 0.00 4.41
850 852 1.789078 AAGCGGACAAAGTGCAGCAG 61.789 55.000 0.00 0.00 0.00 4.24
851 853 2.253452 CGGACAAAGTGCAGCAGC 59.747 61.111 0.00 0.00 42.57 5.25
877 879 1.309688 GCTCTCCCTCTCCCTGTCT 59.690 63.158 0.00 0.00 0.00 3.41
886 888 1.213013 CTCCCTGTCTCCGTTGACG 59.787 63.158 0.00 0.00 39.64 4.35
898 900 1.949133 GTTGACGCTGACAGCACGA 60.949 57.895 26.32 16.03 42.58 4.35
954 957 1.889105 ACCAACGTGCACTCTGCTG 60.889 57.895 16.19 0.89 45.31 4.41
991 994 3.077556 AGCTCCATCGTTCCGCCT 61.078 61.111 0.00 0.00 0.00 5.52
1035 1045 4.676459 CGGATAGATCATCAATCCAGTCCG 60.676 50.000 13.54 0.00 42.04 4.79
1037 1047 1.071385 AGATCATCAATCCAGTCCGCC 59.929 52.381 0.00 0.00 34.67 6.13
1053 1071 0.600557 CGCCTTCTCAGACAGACAGT 59.399 55.000 0.00 0.00 0.00 3.55
1065 1083 4.950434 GACAGACAGTCAGACTAGGTAC 57.050 50.000 1.67 0.00 46.77 3.34
1141 1167 2.628290 GGGGAAGAGAAGAGAGATGGGT 60.628 54.545 0.00 0.00 0.00 4.51
1393 1786 2.492090 CTCTACTTCGCGCTGCCT 59.508 61.111 5.56 0.00 0.00 4.75
1529 1925 2.047560 TCGTCGTCGCTGAGGAGA 60.048 61.111 0.00 1.10 36.96 3.71
1560 1956 0.970937 GAGGACGGTGGATGGAGTCA 60.971 60.000 0.00 0.00 35.49 3.41
1577 1973 1.127951 GTCACCACGCGTATGGAAAAG 59.872 52.381 21.34 8.77 43.02 2.27
1639 2035 1.517475 GAAGACGAGGAAGCGAGCC 60.517 63.158 0.00 0.00 34.83 4.70
1648 2047 4.699522 AAGCGAGCCGGTGGTTCC 62.700 66.667 1.90 0.00 37.73 3.62
1719 2118 2.107953 GGAGGCCGATGACTGAGC 59.892 66.667 0.00 0.00 0.00 4.26
1722 2121 4.554036 GGCCGATGACTGAGCCCC 62.554 72.222 0.00 0.00 39.60 5.80
1837 2282 9.639563 CTGAGGTGGAGATCAGTGTATATATAT 57.360 37.037 0.00 0.00 38.49 0.86
1951 2656 1.952367 GCCCCTTCACTTCCATGTCAG 60.952 57.143 0.00 0.00 0.00 3.51
2031 2736 4.597004 ACATGGACCTCTTCTACGAGTTA 58.403 43.478 0.00 0.00 0.00 2.24
2056 2761 1.134098 CCATAGCTCCGGACAATGGTT 60.134 52.381 20.02 4.88 33.81 3.67
2057 2762 1.942657 CATAGCTCCGGACAATGGTTG 59.057 52.381 0.00 0.00 0.00 3.77
2063 2768 3.000727 CTCCGGACAATGGTTGAACTAC 58.999 50.000 0.00 0.00 0.00 2.73
2096 2801 2.681421 GCCTTGGCTTGGGGGAAG 60.681 66.667 4.11 0.00 34.41 3.46
2098 2803 1.464722 CCTTGGCTTGGGGGAAGAA 59.535 57.895 0.00 0.00 32.82 2.52
2106 2811 0.251165 TTGGGGGAAGAAAGCCGAAG 60.251 55.000 0.00 0.00 0.00 3.79
2180 5016 5.221925 TGCTCTTTCTACTGGAAAATGGACT 60.222 40.000 0.00 0.00 42.52 3.85
2181 5017 6.013725 TGCTCTTTCTACTGGAAAATGGACTA 60.014 38.462 0.00 0.00 42.52 2.59
2182 5018 6.536941 GCTCTTTCTACTGGAAAATGGACTAG 59.463 42.308 0.00 0.00 42.52 2.57
2183 5019 6.947464 TCTTTCTACTGGAAAATGGACTAGG 58.053 40.000 0.00 0.00 42.52 3.02
2184 5020 6.729100 TCTTTCTACTGGAAAATGGACTAGGA 59.271 38.462 0.00 0.00 42.52 2.94
2185 5021 6.945636 TTCTACTGGAAAATGGACTAGGAA 57.054 37.500 0.00 0.00 0.00 3.36
2186 5022 6.295719 TCTACTGGAAAATGGACTAGGAAC 57.704 41.667 0.00 0.00 0.00 3.62
2206 5042 4.965119 ACATCAATTTAAGTTCGGGCTC 57.035 40.909 0.00 0.00 0.00 4.70
2225 5067 4.624364 TGGTCCACCACGCTGCTG 62.624 66.667 0.00 0.00 42.01 4.41
2241 5084 6.412943 CACGCTGCTGATTTATACAATCTTTG 59.587 38.462 0.00 0.00 0.00 2.77
2243 5086 6.458751 CGCTGCTGATTTATACAATCTTTGGT 60.459 38.462 0.00 0.00 34.12 3.67
2261 5104 7.732025 TCTTTGGTTGAGTCTACAAGATGTTA 58.268 34.615 7.04 0.00 0.00 2.41
2264 5107 7.905604 TGGTTGAGTCTACAAGATGTTAATG 57.094 36.000 7.04 0.00 0.00 1.90
2266 5109 7.936847 TGGTTGAGTCTACAAGATGTTAATGTT 59.063 33.333 7.04 0.00 0.00 2.71
2344 5187 1.070134 ACGAAGTCAGCTTACTTGGCA 59.930 47.619 17.81 0.00 39.78 4.92
2345 5188 2.289694 ACGAAGTCAGCTTACTTGGCAT 60.290 45.455 17.81 0.00 39.78 4.40
2361 5204 1.303309 GCATAGCTGGACACCATGAC 58.697 55.000 0.00 0.00 30.82 3.06
2392 5235 8.983724 TCAATTTTAAATCCGATTGTTTGGAAC 58.016 29.630 9.18 0.00 38.97 3.62
2437 5280 6.874288 AGATTCTTTGCCTAGCATATTCAC 57.126 37.500 0.00 0.00 38.76 3.18
2454 5297 5.599999 ATTCACTAGGACTGTGTATGGAC 57.400 43.478 0.00 0.00 36.83 4.02
2457 5300 3.632604 CACTAGGACTGTGTATGGACGAT 59.367 47.826 0.00 0.00 0.00 3.73
2459 5302 2.735151 AGGACTGTGTATGGACGATCA 58.265 47.619 0.00 0.00 0.00 2.92
2524 5367 0.606673 AAAAGGGAGCAAGAGTCCGC 60.607 55.000 0.00 0.00 34.56 5.54
2598 5441 0.468226 AGCTTGGTTTGTCCTCGTCA 59.532 50.000 0.00 0.00 37.07 4.35
2612 5455 2.131972 CTCGTCAATGTTCACACCGAA 58.868 47.619 0.00 0.00 0.00 4.30
2765 5608 6.183359 CGAGAGTCTTTAAAAGCACTTCTACG 60.183 42.308 0.00 0.00 0.00 3.51
2766 5609 6.514063 AGAGTCTTTAAAAGCACTTCTACGT 58.486 36.000 0.00 0.00 0.00 3.57
2767 5610 6.985059 AGAGTCTTTAAAAGCACTTCTACGTT 59.015 34.615 0.00 0.00 0.00 3.99
2768 5611 6.945072 AGTCTTTAAAAGCACTTCTACGTTG 58.055 36.000 0.00 0.00 0.00 4.10
2769 5612 6.537660 AGTCTTTAAAAGCACTTCTACGTTGT 59.462 34.615 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.006896 TGAGAAAGGTACTCCCTCTGTAA 57.993 43.478 0.00 0.00 45.47 2.41
1 2 4.044317 ACTGAGAAAGGTACTCCCTCTGTA 59.956 45.833 12.12 0.00 45.47 2.74
2 3 3.181416 ACTGAGAAAGGTACTCCCTCTGT 60.181 47.826 0.00 0.00 45.47 3.41
3 4 3.436243 ACTGAGAAAGGTACTCCCTCTG 58.564 50.000 0.00 0.00 45.47 3.35
7 8 4.828072 ATCAACTGAGAAAGGTACTCCC 57.172 45.455 0.00 0.00 38.49 4.30
8 9 6.147985 GTGAAATCAACTGAGAAAGGTACTCC 59.852 42.308 0.00 0.00 38.49 3.85
9 10 6.128795 CGTGAAATCAACTGAGAAAGGTACTC 60.129 42.308 0.00 0.00 38.49 2.59
12 13 5.849510 TCGTGAAATCAACTGAGAAAGGTA 58.150 37.500 0.00 0.00 0.00 3.08
13 14 4.703897 TCGTGAAATCAACTGAGAAAGGT 58.296 39.130 0.00 0.00 0.00 3.50
14 15 5.869753 ATCGTGAAATCAACTGAGAAAGG 57.130 39.130 0.00 0.00 0.00 3.11
15 16 8.446273 ACATAATCGTGAAATCAACTGAGAAAG 58.554 33.333 0.00 0.00 0.00 2.62
16 17 8.229811 CACATAATCGTGAAATCAACTGAGAAA 58.770 33.333 0.00 0.00 39.34 2.52
17 18 7.624134 GCACATAATCGTGAAATCAACTGAGAA 60.624 37.037 0.00 0.00 39.34 2.87
18 19 6.183360 GCACATAATCGTGAAATCAACTGAGA 60.183 38.462 0.00 0.00 39.34 3.27
19 20 5.961843 GCACATAATCGTGAAATCAACTGAG 59.038 40.000 0.00 0.00 39.34 3.35
20 21 5.411053 TGCACATAATCGTGAAATCAACTGA 59.589 36.000 0.00 0.00 39.34 3.41
21 22 5.630061 TGCACATAATCGTGAAATCAACTG 58.370 37.500 0.00 0.00 39.34 3.16
22 23 5.878332 TGCACATAATCGTGAAATCAACT 57.122 34.783 0.00 0.00 39.34 3.16
23 24 7.164171 GTGTATGCACATAATCGTGAAATCAAC 59.836 37.037 9.26 0.00 44.64 3.18
24 25 7.186128 GTGTATGCACATAATCGTGAAATCAA 58.814 34.615 9.26 0.00 44.64 2.57
25 26 6.714492 GTGTATGCACATAATCGTGAAATCA 58.286 36.000 9.26 0.00 44.64 2.57
57 58 2.993937 TCAGAACACGGTGACCTTTTT 58.006 42.857 16.29 0.00 0.00 1.94
58 59 2.702592 TCAGAACACGGTGACCTTTT 57.297 45.000 16.29 0.00 0.00 2.27
59 60 2.681344 GTTTCAGAACACGGTGACCTTT 59.319 45.455 16.29 0.00 35.79 3.11
60 61 2.285977 GTTTCAGAACACGGTGACCTT 58.714 47.619 16.29 0.00 35.79 3.50
61 62 1.805120 CGTTTCAGAACACGGTGACCT 60.805 52.381 16.29 8.09 35.44 3.85
62 63 0.580104 CGTTTCAGAACACGGTGACC 59.420 55.000 16.29 5.81 35.44 4.02
63 64 1.005347 CACGTTTCAGAACACGGTGAC 60.005 52.381 16.29 8.42 40.84 3.67
64 65 1.282817 CACGTTTCAGAACACGGTGA 58.717 50.000 16.29 0.00 40.84 4.02
65 66 1.003851 ACACGTTTCAGAACACGGTG 58.996 50.000 6.58 6.58 40.84 4.94
66 67 1.729284 AACACGTTTCAGAACACGGT 58.271 45.000 16.89 11.34 40.84 4.83
67 68 3.929417 TTAACACGTTTCAGAACACGG 57.071 42.857 16.89 10.92 40.84 4.94
68 69 5.324739 AGATTAACACGTTTCAGAACACG 57.675 39.130 13.16 13.16 42.29 4.49
69 70 7.281484 CACTAGATTAACACGTTTCAGAACAC 58.719 38.462 0.00 0.00 35.44 3.32
70 71 6.073980 GCACTAGATTAACACGTTTCAGAACA 60.074 38.462 0.00 0.00 35.44 3.18
71 72 6.073980 TGCACTAGATTAACACGTTTCAGAAC 60.074 38.462 0.00 0.00 0.00 3.01
72 73 5.986741 TGCACTAGATTAACACGTTTCAGAA 59.013 36.000 0.00 0.00 0.00 3.02
73 74 5.534407 TGCACTAGATTAACACGTTTCAGA 58.466 37.500 0.00 0.00 0.00 3.27
74 75 5.839262 TGCACTAGATTAACACGTTTCAG 57.161 39.130 0.00 0.00 0.00 3.02
75 76 6.606234 TTTGCACTAGATTAACACGTTTCA 57.394 33.333 0.00 0.00 0.00 2.69
76 77 6.086371 GCTTTTGCACTAGATTAACACGTTTC 59.914 38.462 0.00 0.00 46.58 2.78
77 78 5.912955 GCTTTTGCACTAGATTAACACGTTT 59.087 36.000 0.00 0.00 46.58 3.60
78 79 5.449304 GCTTTTGCACTAGATTAACACGTT 58.551 37.500 0.00 0.00 46.58 3.99
79 80 5.030874 GCTTTTGCACTAGATTAACACGT 57.969 39.130 0.00 0.00 46.58 4.49
94 95 6.244900 AGCAAACACTACATTCTGCTTTTGC 61.245 40.000 7.46 7.46 45.01 3.68
95 96 5.284079 AGCAAACACTACATTCTGCTTTTG 58.716 37.500 0.00 0.00 36.79 2.44
96 97 5.520376 AGCAAACACTACATTCTGCTTTT 57.480 34.783 0.00 0.00 36.79 2.27
97 98 5.520376 AAGCAAACACTACATTCTGCTTT 57.480 34.783 1.43 0.00 45.28 3.51
99 100 5.520376 AAAAGCAAACACTACATTCTGCT 57.480 34.783 0.00 0.00 41.72 4.24
100 101 7.692908 TTTAAAAGCAAACACTACATTCTGC 57.307 32.000 0.00 0.00 0.00 4.26
105 106 9.593134 TGTGAATTTTAAAAGCAAACACTACAT 57.407 25.926 6.79 0.00 0.00 2.29
106 107 8.988064 TGTGAATTTTAAAAGCAAACACTACA 57.012 26.923 6.79 0.00 0.00 2.74
107 108 9.083080 ACTGTGAATTTTAAAAGCAAACACTAC 57.917 29.630 6.79 0.00 0.00 2.73
109 110 9.646427 TTACTGTGAATTTTAAAAGCAAACACT 57.354 25.926 6.79 1.61 0.00 3.55
144 145 9.460019 TGTTAATTTGATGTTGAGATCCATGTA 57.540 29.630 0.00 0.00 0.00 2.29
145 146 8.352137 TGTTAATTTGATGTTGAGATCCATGT 57.648 30.769 0.00 0.00 0.00 3.21
146 147 7.434307 GCTGTTAATTTGATGTTGAGATCCATG 59.566 37.037 0.00 0.00 0.00 3.66
147 148 7.123098 TGCTGTTAATTTGATGTTGAGATCCAT 59.877 33.333 0.00 0.00 0.00 3.41
148 149 6.433716 TGCTGTTAATTTGATGTTGAGATCCA 59.566 34.615 0.00 0.00 0.00 3.41
149 150 6.749118 GTGCTGTTAATTTGATGTTGAGATCC 59.251 38.462 0.00 0.00 0.00 3.36
150 151 7.533426 AGTGCTGTTAATTTGATGTTGAGATC 58.467 34.615 0.00 0.00 0.00 2.75
151 152 7.458409 AGTGCTGTTAATTTGATGTTGAGAT 57.542 32.000 0.00 0.00 0.00 2.75
152 153 6.882610 AGTGCTGTTAATTTGATGTTGAGA 57.117 33.333 0.00 0.00 0.00 3.27
153 154 6.364165 CCAAGTGCTGTTAATTTGATGTTGAG 59.636 38.462 0.00 0.00 0.00 3.02
154 155 6.183360 ACCAAGTGCTGTTAATTTGATGTTGA 60.183 34.615 0.00 0.00 0.00 3.18
155 156 5.984926 ACCAAGTGCTGTTAATTTGATGTTG 59.015 36.000 0.00 0.00 0.00 3.33
156 157 5.984926 CACCAAGTGCTGTTAATTTGATGTT 59.015 36.000 0.00 0.00 0.00 2.71
157 158 5.068987 ACACCAAGTGCTGTTAATTTGATGT 59.931 36.000 0.00 0.00 36.98 3.06
158 159 5.531634 ACACCAAGTGCTGTTAATTTGATG 58.468 37.500 0.00 0.00 36.98 3.07
159 160 5.562696 CGACACCAAGTGCTGTTAATTTGAT 60.563 40.000 0.00 0.00 36.98 2.57
160 161 4.260990 CGACACCAAGTGCTGTTAATTTGA 60.261 41.667 0.00 0.00 36.98 2.69
161 162 3.974401 CGACACCAAGTGCTGTTAATTTG 59.026 43.478 0.00 0.00 36.98 2.32
162 163 3.880490 TCGACACCAAGTGCTGTTAATTT 59.120 39.130 0.00 0.00 36.98 1.82
163 164 3.250040 GTCGACACCAAGTGCTGTTAATT 59.750 43.478 11.55 0.00 36.98 1.40
164 165 2.806244 GTCGACACCAAGTGCTGTTAAT 59.194 45.455 11.55 0.00 36.98 1.40
165 166 2.159014 AGTCGACACCAAGTGCTGTTAA 60.159 45.455 19.50 0.00 36.98 2.01
166 167 1.411246 AGTCGACACCAAGTGCTGTTA 59.589 47.619 19.50 0.00 36.98 2.41
167 168 0.178068 AGTCGACACCAAGTGCTGTT 59.822 50.000 19.50 0.00 36.98 3.16
168 169 0.530650 CAGTCGACACCAAGTGCTGT 60.531 55.000 19.50 0.00 36.98 4.40
169 170 0.249447 TCAGTCGACACCAAGTGCTG 60.249 55.000 19.50 3.74 36.98 4.41
170 171 0.032678 CTCAGTCGACACCAAGTGCT 59.967 55.000 19.50 0.00 36.98 4.40
171 172 0.032130 TCTCAGTCGACACCAAGTGC 59.968 55.000 19.50 0.00 36.98 4.40
172 173 1.338337 ACTCTCAGTCGACACCAAGTG 59.662 52.381 19.50 6.09 39.75 3.16
173 174 1.693627 ACTCTCAGTCGACACCAAGT 58.306 50.000 19.50 12.50 0.00 3.16
174 175 2.802787 AACTCTCAGTCGACACCAAG 57.197 50.000 19.50 11.86 0.00 3.61
175 176 3.635373 AGTTAACTCTCAGTCGACACCAA 59.365 43.478 19.50 0.00 0.00 3.67
176 177 3.220110 AGTTAACTCTCAGTCGACACCA 58.780 45.455 19.50 0.00 0.00 4.17
177 178 3.919223 AGTTAACTCTCAGTCGACACC 57.081 47.619 19.50 0.00 0.00 4.16
178 179 7.306953 AGAATTAGTTAACTCTCAGTCGACAC 58.693 38.462 19.50 3.44 0.00 3.67
179 180 7.174426 TGAGAATTAGTTAACTCTCAGTCGACA 59.826 37.037 19.50 9.18 41.79 4.35
180 181 7.528307 TGAGAATTAGTTAACTCTCAGTCGAC 58.472 38.462 12.39 7.70 41.79 4.20
181 182 7.683437 TGAGAATTAGTTAACTCTCAGTCGA 57.317 36.000 12.39 0.00 41.79 4.20
182 183 8.918961 ATTGAGAATTAGTTAACTCTCAGTCG 57.081 34.615 12.39 0.00 45.55 4.18
201 202 8.730680 GGTTTGCTAATTCTTAGTCAATTGAGA 58.269 33.333 8.80 0.00 35.66 3.27
202 203 8.734386 AGGTTTGCTAATTCTTAGTCAATTGAG 58.266 33.333 8.80 0.00 35.66 3.02
203 204 8.635765 AGGTTTGCTAATTCTTAGTCAATTGA 57.364 30.769 3.38 3.38 35.66 2.57
206 207 9.740710 ACTTAGGTTTGCTAATTCTTAGTCAAT 57.259 29.630 0.00 0.00 35.66 2.57
207 208 9.569122 AACTTAGGTTTGCTAATTCTTAGTCAA 57.431 29.630 6.43 0.00 32.13 3.18
208 209 9.569122 AAACTTAGGTTTGCTAATTCTTAGTCA 57.431 29.630 1.63 0.00 43.16 3.41
234 235 4.340097 GGGGTCTTTCTCCTTTTCGAAAAA 59.660 41.667 22.67 9.49 32.92 1.94
235 236 3.887110 GGGGTCTTTCTCCTTTTCGAAAA 59.113 43.478 21.35 21.35 32.92 2.29
236 237 3.117813 TGGGGTCTTTCTCCTTTTCGAAA 60.118 43.478 6.47 6.47 37.63 3.46
237 238 2.440253 TGGGGTCTTTCTCCTTTTCGAA 59.560 45.455 0.00 0.00 37.63 3.71
238 239 2.038557 CTGGGGTCTTTCTCCTTTTCGA 59.961 50.000 0.00 0.00 37.63 3.71
239 240 2.427506 CTGGGGTCTTTCTCCTTTTCG 58.572 52.381 0.00 0.00 37.63 3.46
240 241 2.163509 GCTGGGGTCTTTCTCCTTTTC 58.836 52.381 0.00 0.00 37.63 2.29
241 242 1.203063 GGCTGGGGTCTTTCTCCTTTT 60.203 52.381 0.00 0.00 37.63 2.27
242 243 0.405973 GGCTGGGGTCTTTCTCCTTT 59.594 55.000 0.00 0.00 37.63 3.11
243 244 0.476611 AGGCTGGGGTCTTTCTCCTT 60.477 55.000 0.00 0.00 37.63 3.36
244 245 0.912006 GAGGCTGGGGTCTTTCTCCT 60.912 60.000 0.00 0.00 37.63 3.69
245 246 0.912006 AGAGGCTGGGGTCTTTCTCC 60.912 60.000 0.00 0.00 37.17 3.71
246 247 0.251634 CAGAGGCTGGGGTCTTTCTC 59.748 60.000 0.00 0.00 0.00 2.87
247 248 1.846712 GCAGAGGCTGGGGTCTTTCT 61.847 60.000 0.00 0.00 36.96 2.52
248 249 1.377856 GCAGAGGCTGGGGTCTTTC 60.378 63.158 0.00 0.00 36.96 2.62
249 250 1.504275 ATGCAGAGGCTGGGGTCTTT 61.504 55.000 0.00 0.00 41.91 2.52
250 251 1.919600 GATGCAGAGGCTGGGGTCTT 61.920 60.000 0.00 0.00 41.91 3.01
251 252 2.285969 ATGCAGAGGCTGGGGTCT 60.286 61.111 0.00 0.00 41.91 3.85
252 253 1.992519 ATGATGCAGAGGCTGGGGTC 61.993 60.000 0.00 0.00 41.91 4.46
253 254 1.992519 GATGATGCAGAGGCTGGGGT 61.993 60.000 0.00 0.00 41.91 4.95
254 255 1.228184 GATGATGCAGAGGCTGGGG 60.228 63.158 0.00 0.00 41.91 4.96
255 256 0.110678 ATGATGATGCAGAGGCTGGG 59.889 55.000 0.00 0.00 41.91 4.45
256 257 1.202770 TCATGATGATGCAGAGGCTGG 60.203 52.381 0.00 0.00 41.91 4.85
257 258 2.256117 TCATGATGATGCAGAGGCTG 57.744 50.000 0.00 0.00 41.91 4.85
258 259 2.784347 CATCATGATGATGCAGAGGCT 58.216 47.619 28.37 0.00 46.37 4.58
267 268 4.642885 TGTGATTGTGTGCATCATGATGAT 59.357 37.500 34.65 19.82 41.20 2.45
268 269 4.011023 TGTGATTGTGTGCATCATGATGA 58.989 39.130 34.65 18.94 41.20 2.92
269 270 4.351192 CTGTGATTGTGTGCATCATGATG 58.649 43.478 28.04 28.04 41.60 3.07
270 271 3.181490 GCTGTGATTGTGTGCATCATGAT 60.181 43.478 1.18 1.18 0.00 2.45
271 272 2.162809 GCTGTGATTGTGTGCATCATGA 59.837 45.455 0.00 0.00 0.00 3.07
272 273 2.094957 TGCTGTGATTGTGTGCATCATG 60.095 45.455 0.00 0.00 0.00 3.07
273 274 2.164338 TGCTGTGATTGTGTGCATCAT 58.836 42.857 0.00 0.00 0.00 2.45
274 275 1.606903 TGCTGTGATTGTGTGCATCA 58.393 45.000 0.00 0.00 0.00 3.07
275 276 2.710220 TTGCTGTGATTGTGTGCATC 57.290 45.000 0.00 0.00 33.50 3.91
276 277 2.746269 GTTTGCTGTGATTGTGTGCAT 58.254 42.857 0.00 0.00 33.50 3.96
277 278 1.533547 CGTTTGCTGTGATTGTGTGCA 60.534 47.619 0.00 0.00 0.00 4.57
278 279 1.122849 CGTTTGCTGTGATTGTGTGC 58.877 50.000 0.00 0.00 0.00 4.57
279 280 2.473530 ACGTTTGCTGTGATTGTGTG 57.526 45.000 0.00 0.00 0.00 3.82
280 281 3.625764 AGTTACGTTTGCTGTGATTGTGT 59.374 39.130 0.00 0.00 0.00 3.72
281 282 4.209452 AGTTACGTTTGCTGTGATTGTG 57.791 40.909 0.00 0.00 0.00 3.33
282 283 4.893424 AAGTTACGTTTGCTGTGATTGT 57.107 36.364 0.00 0.00 0.00 2.71
283 284 5.544738 CAAAGTTACGTTTGCTGTGATTG 57.455 39.130 0.00 0.00 30.94 2.67
292 293 5.799542 GTAACCATGCAAAGTTACGTTTG 57.200 39.130 20.19 0.00 39.06 2.93
297 298 4.625311 GCCAATGTAACCATGCAAAGTTAC 59.375 41.667 24.73 24.73 45.51 2.50
298 299 4.281941 TGCCAATGTAACCATGCAAAGTTA 59.718 37.500 7.62 7.62 29.80 2.24
299 300 3.070734 TGCCAATGTAACCATGCAAAGTT 59.929 39.130 9.39 9.39 29.80 2.66
300 301 2.632028 TGCCAATGTAACCATGCAAAGT 59.368 40.909 0.00 0.00 29.80 2.66
301 302 3.255725 CTGCCAATGTAACCATGCAAAG 58.744 45.455 0.00 0.00 31.78 2.77
322 323 3.046285 TCGTGCGCATATTTTTGTAGC 57.954 42.857 15.91 0.00 0.00 3.58
352 353 2.042686 AATCAAGCTTGCGATGCCTA 57.957 45.000 21.99 1.87 0.00 3.93
381 382 1.349357 GCTCCTCAAAGGGACAAGAGT 59.651 52.381 0.00 0.00 35.59 3.24
393 395 0.689080 CTGCCCCTCTAGCTCCTCAA 60.689 60.000 0.00 0.00 0.00 3.02
468 470 2.246719 ATAAGCCAACGAGCATCTCC 57.753 50.000 0.00 0.00 34.23 3.71
469 471 4.090642 CGAATATAAGCCAACGAGCATCTC 59.909 45.833 0.00 0.00 34.23 2.75
501 503 5.411053 CGAGCATCTTTCCTTCTTTCTTTCT 59.589 40.000 0.00 0.00 0.00 2.52
502 504 5.180304 ACGAGCATCTTTCCTTCTTTCTTTC 59.820 40.000 0.00 0.00 0.00 2.62
503 505 5.066593 ACGAGCATCTTTCCTTCTTTCTTT 58.933 37.500 0.00 0.00 0.00 2.52
504 506 4.646572 ACGAGCATCTTTCCTTCTTTCTT 58.353 39.130 0.00 0.00 0.00 2.52
505 507 4.278975 ACGAGCATCTTTCCTTCTTTCT 57.721 40.909 0.00 0.00 0.00 2.52
506 508 4.378874 CCAACGAGCATCTTTCCTTCTTTC 60.379 45.833 0.00 0.00 0.00 2.62
507 509 3.503748 CCAACGAGCATCTTTCCTTCTTT 59.496 43.478 0.00 0.00 0.00 2.52
508 510 3.077359 CCAACGAGCATCTTTCCTTCTT 58.923 45.455 0.00 0.00 0.00 2.52
509 511 2.704572 CCAACGAGCATCTTTCCTTCT 58.295 47.619 0.00 0.00 0.00 2.85
510 512 1.131315 GCCAACGAGCATCTTTCCTTC 59.869 52.381 0.00 0.00 0.00 3.46
511 513 1.168714 GCCAACGAGCATCTTTCCTT 58.831 50.000 0.00 0.00 0.00 3.36
512 514 0.326264 AGCCAACGAGCATCTTTCCT 59.674 50.000 0.00 0.00 34.23 3.36
513 515 1.168714 AAGCCAACGAGCATCTTTCC 58.831 50.000 0.00 0.00 34.23 3.13
514 516 4.083271 AGTTTAAGCCAACGAGCATCTTTC 60.083 41.667 0.00 0.00 34.23 2.62
528 530 6.882678 TGTATGGGAACTTTCTAGTTTAAGCC 59.117 38.462 0.00 0.00 44.51 4.35
546 548 5.125356 TCTCTTAACACATGCATGTATGGG 58.875 41.667 30.92 22.74 39.39 4.00
547 549 5.237996 CCTCTCTTAACACATGCATGTATGG 59.762 44.000 30.92 21.07 39.39 2.74
552 554 3.011818 TGCCTCTCTTAACACATGCATG 58.988 45.455 25.09 25.09 0.00 4.06
595 597 2.989824 ACGTAGGTGCACGAGGCT 60.990 61.111 11.45 4.59 44.69 4.58
596 598 2.809601 CACGTAGGTGCACGAGGC 60.810 66.667 11.45 0.00 44.69 4.70
719 721 2.766875 TTAATGTGTGGCGACCGCGA 62.767 55.000 8.23 1.16 43.06 5.87
721 723 1.133869 GTTAATGTGTGGCGACCGC 59.866 57.895 5.75 5.75 41.06 5.68
722 724 1.009903 TCGTTAATGTGTGGCGACCG 61.010 55.000 0.00 0.00 0.00 4.79
723 725 0.441145 GTCGTTAATGTGTGGCGACC 59.559 55.000 0.00 0.00 43.94 4.79
787 789 1.215673 AGTGAGGAGGCGAGAGGAATA 59.784 52.381 0.00 0.00 0.00 1.75
797 799 1.078848 ACGCAATCAGTGAGGAGGC 60.079 57.895 0.00 0.00 0.00 4.70
853 855 1.220477 GGAGAGGGAGAGCACTTGC 59.780 63.158 0.00 0.00 42.49 4.01
854 856 0.617249 AGGGAGAGGGAGAGCACTTG 60.617 60.000 0.00 0.00 0.00 3.16
855 857 0.617249 CAGGGAGAGGGAGAGCACTT 60.617 60.000 0.00 0.00 0.00 3.16
856 858 1.001503 CAGGGAGAGGGAGAGCACT 59.998 63.158 0.00 0.00 0.00 4.40
857 859 1.305718 ACAGGGAGAGGGAGAGCAC 60.306 63.158 0.00 0.00 0.00 4.40
858 860 1.000993 GACAGGGAGAGGGAGAGCA 59.999 63.158 0.00 0.00 0.00 4.26
860 862 0.106217 GGAGACAGGGAGAGGGAGAG 60.106 65.000 0.00 0.00 0.00 3.20
861 863 1.927569 CGGAGACAGGGAGAGGGAGA 61.928 65.000 0.00 0.00 0.00 3.71
862 864 1.454847 CGGAGACAGGGAGAGGGAG 60.455 68.421 0.00 0.00 0.00 4.30
863 865 1.801302 AACGGAGACAGGGAGAGGGA 61.801 60.000 0.00 0.00 0.00 4.20
864 866 1.305381 AACGGAGACAGGGAGAGGG 60.305 63.158 0.00 0.00 0.00 4.30
865 867 0.612174 TCAACGGAGACAGGGAGAGG 60.612 60.000 0.00 0.00 0.00 3.69
877 879 2.355837 GCTGTCAGCGTCAACGGA 60.356 61.111 9.53 0.00 40.23 4.69
898 900 0.249031 TCGTCATCGATCAATGCGCT 60.249 50.000 9.73 0.00 41.35 5.92
951 954 0.541863 ATATATACGGGGCCAGCAGC 59.458 55.000 4.39 0.00 42.60 5.25
954 957 1.760613 TGCTATATATACGGGGCCAGC 59.239 52.381 4.39 2.35 0.00 4.85
1035 1045 1.615883 TGACTGTCTGTCTGAGAAGGC 59.384 52.381 9.51 0.00 45.54 4.35
1053 1071 1.276138 TCGACGTGGTACCTAGTCTGA 59.724 52.381 26.27 22.59 0.00 3.27
1065 1083 1.545614 CGTTCACCTTGTCGACGTGG 61.546 60.000 20.54 20.54 0.00 4.94
1114 1132 0.174617 CTCTTCTCTTCCCCTGCGAC 59.825 60.000 0.00 0.00 0.00 5.19
1298 1324 2.812609 CTCGTCTGCGCTGCACAT 60.813 61.111 9.73 0.00 38.14 3.21
1475 1868 3.431725 CTTCCGCCCTTTGCCGTC 61.432 66.667 0.00 0.00 36.24 4.79
1525 1918 3.708220 CTCTGTTCCGGCGCTCTCC 62.708 68.421 7.64 0.00 0.00 3.71
1529 1925 4.070552 GTCCTCTGTTCCGGCGCT 62.071 66.667 7.64 0.00 0.00 5.92
1532 1928 3.692406 ACCGTCCTCTGTTCCGGC 61.692 66.667 0.00 0.00 44.14 6.13
1560 1956 1.303091 GCCTTTTCCATACGCGTGGT 61.303 55.000 24.59 7.70 40.27 4.16
1648 2047 2.579787 CTCGTGCCGCTTCCGTAG 60.580 66.667 0.00 0.00 0.00 3.51
1676 2075 0.875059 GAGCTTAACCTTTGCACGCT 59.125 50.000 0.00 0.00 0.00 5.07
1722 2121 1.856802 GTTTGCAAAAGTCAGCAGGG 58.143 50.000 14.67 0.00 42.39 4.45
1731 2138 9.240159 ACTTTACTAATTAACCGTTTGCAAAAG 57.760 29.630 14.67 15.98 0.00 2.27
1951 2656 1.455773 GCCCATAAGAAGGCCCACC 60.456 63.158 0.00 0.00 43.76 4.61
2031 2736 2.154567 TGTCCGGAGCTATGGTAGTT 57.845 50.000 3.06 0.00 0.00 2.24
2056 2761 5.350091 GCCAAAGCAAAACTTTTGTAGTTCA 59.650 36.000 14.36 0.00 46.73 3.18
2057 2762 5.220586 GGCCAAAGCAAAACTTTTGTAGTTC 60.221 40.000 14.36 0.00 46.73 3.01
2063 2768 3.181498 CCAAGGCCAAAGCAAAACTTTTG 60.181 43.478 5.01 9.54 46.73 2.44
2078 2783 4.315264 TTCCCCCAAGCCAAGGCC 62.315 66.667 7.62 0.00 43.17 5.19
2096 2801 2.822764 ACACGATATCCTTCGGCTTTC 58.177 47.619 0.00 0.00 43.33 2.62
2098 2803 2.093658 ACAACACGATATCCTTCGGCTT 60.094 45.455 0.00 0.00 43.33 4.35
2106 2811 5.679792 GGCGAAAATAAACAACACGATATCC 59.320 40.000 0.00 0.00 0.00 2.59
2107 2812 6.252281 TGGCGAAAATAAACAACACGATATC 58.748 36.000 0.00 0.00 0.00 1.63
2109 2814 5.608676 TGGCGAAAATAAACAACACGATA 57.391 34.783 0.00 0.00 0.00 2.92
2110 2815 4.491234 TGGCGAAAATAAACAACACGAT 57.509 36.364 0.00 0.00 0.00 3.73
2111 2816 3.965292 TGGCGAAAATAAACAACACGA 57.035 38.095 0.00 0.00 0.00 4.35
2112 2817 4.472286 AGATGGCGAAAATAAACAACACG 58.528 39.130 0.00 0.00 0.00 4.49
2180 5016 5.355910 GCCCGAACTTAAATTGATGTTCCTA 59.644 40.000 13.43 0.00 36.43 2.94
2181 5017 4.157840 GCCCGAACTTAAATTGATGTTCCT 59.842 41.667 13.43 0.00 36.43 3.36
2182 5018 4.157840 AGCCCGAACTTAAATTGATGTTCC 59.842 41.667 13.43 3.34 36.43 3.62
2183 5019 5.123979 AGAGCCCGAACTTAAATTGATGTTC 59.876 40.000 10.34 10.34 36.44 3.18
2184 5020 5.010282 AGAGCCCGAACTTAAATTGATGTT 58.990 37.500 0.00 0.00 0.00 2.71
2185 5021 4.589908 AGAGCCCGAACTTAAATTGATGT 58.410 39.130 0.00 0.00 0.00 3.06
2186 5022 5.335127 CAAGAGCCCGAACTTAAATTGATG 58.665 41.667 0.00 0.00 0.00 3.07
2197 5033 1.671379 GTGGACCAAGAGCCCGAAC 60.671 63.158 0.00 0.00 0.00 3.95
2219 5061 6.799512 ACCAAAGATTGTATAAATCAGCAGC 58.200 36.000 1.30 0.00 0.00 5.25
2241 5084 7.907214 ACATTAACATCTTGTAGACTCAACC 57.093 36.000 0.00 0.00 0.00 3.77
2261 5104 6.611381 CATCCAAAGTGTCGTCATTAACATT 58.389 36.000 0.00 0.00 0.00 2.71
2264 5107 4.403453 GCATCCAAAGTGTCGTCATTAAC 58.597 43.478 0.00 0.00 0.00 2.01
2266 5109 3.006940 GGCATCCAAAGTGTCGTCATTA 58.993 45.455 0.00 0.00 0.00 1.90
2311 5154 1.802960 GACTTCGTCGAGTAGTCACCA 59.197 52.381 18.06 0.00 43.90 4.17
2332 5175 1.839994 TCCAGCTATGCCAAGTAAGCT 59.160 47.619 0.00 0.00 45.94 3.74
2344 5187 5.130975 TGAAATAGTCATGGTGTCCAGCTAT 59.869 40.000 0.00 0.96 36.75 2.97
2345 5188 4.469586 TGAAATAGTCATGGTGTCCAGCTA 59.530 41.667 0.00 0.00 36.75 3.32
2377 5220 5.584253 TTCAAAAGTTCCAAACAATCGGA 57.416 34.783 0.00 0.00 0.00 4.55
2392 5235 1.069296 TGCTTCGACGGCATTCAAAAG 60.069 47.619 8.00 0.00 34.56 2.27
2437 5280 3.883489 TGATCGTCCATACACAGTCCTAG 59.117 47.826 0.00 0.00 0.00 3.02
2446 5289 0.104855 GCCAGCTGATCGTCCATACA 59.895 55.000 17.39 0.00 0.00 2.29
2454 5297 2.588314 GAGCCAGCCAGCTGATCG 60.588 66.667 21.01 5.66 45.15 3.69
2457 5300 3.767806 CTCGAGCCAGCCAGCTGA 61.768 66.667 21.01 0.00 45.15 4.26
2500 5343 2.560105 GACTCTTGCTCCCTTTTGCATT 59.440 45.455 0.00 0.00 39.07 3.56
2524 5367 3.003689 ACCGTTGAAAAGAAGATGTGCAG 59.996 43.478 0.00 0.00 0.00 4.41
2598 5441 1.608590 CCAAGCTTCGGTGTGAACATT 59.391 47.619 0.00 0.00 31.87 2.71
2612 5455 3.071312 TCAAATTGAAATGCCACCAAGCT 59.929 39.130 0.00 0.00 0.00 3.74
2621 5464 5.522460 CCACTCCATGATCAAATTGAAATGC 59.478 40.000 13.42 0.82 0.00 3.56
2733 5576 4.725169 GCTTTTAAAGACTCTCGCATTCCG 60.725 45.833 9.10 0.00 38.61 4.30


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

AutoCloner maintained by Alex Coulton.