Multiple sequence alignment - TraesCS2B01G424600

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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 TraesCS2B01G424600 chr2B 100.000 4227 0 0 1 4227 610696204 610691978 0.000000e+00 7806.0
1 TraesCS2B01G424600 chr2B 100.000 596 0 0 4482 5077 610691723 610691128 0.000000e+00 1101.0
2 TraesCS2B01G424600 chr2A 95.422 3517 120 13 739 4227 662747874 662744371 0.000000e+00 5565.0
3 TraesCS2B01G424600 chr2A 91.820 599 45 2 4482 5077 662744358 662743761 0.000000e+00 832.0
4 TraesCS2B01G424600 chr2A 91.398 93 7 1 650 742 662748008 662747917 5.340000e-25 126.0
5 TraesCS2B01G424600 chr2D 95.539 2197 71 6 739 2929 518601743 518599568 0.000000e+00 3489.0
6 TraesCS2B01G424600 chr2D 95.529 917 35 1 3302 4212 518599096 518598180 0.000000e+00 1461.0
7 TraesCS2B01G424600 chr2D 93.667 600 33 3 4482 5077 518598140 518597542 0.000000e+00 893.0
8 TraesCS2B01G424600 chr2D 97.923 337 6 1 2977 3313 518599495 518599160 2.630000e-162 582.0
9 TraesCS2B01G424600 chr2D 87.151 358 42 2 1 355 641575066 641574710 2.200000e-108 403.0
10 TraesCS2B01G424600 chr2D 90.980 255 10 2 500 742 518602035 518601782 1.050000e-86 331.0
11 TraesCS2B01G424600 chr2D 94.737 76 4 0 360 435 518602112 518602037 8.930000e-23 119.0
12 TraesCS2B01G424600 chr2D 100.000 30 0 0 4198 4227 518598182 518598153 7.100000e-04 56.5
13 TraesCS2B01G424600 chr5D 81.818 847 126 21 1538 2367 369725213 369726048 0.000000e+00 686.0
14 TraesCS2B01G424600 chr5D 80.606 330 61 3 27 355 245000730 245000403 8.440000e-63 252.0
15 TraesCS2B01G424600 chr5D 85.774 239 28 2 2480 2712 369726254 369726492 1.090000e-61 248.0
16 TraesCS2B01G424600 chr5A 81.680 857 123 25 1531 2367 472284059 472284901 0.000000e+00 682.0
17 TraesCS2B01G424600 chr5A 86.192 239 27 2 2480 2712 472285113 472285351 2.350000e-63 254.0
18 TraesCS2B01G424600 chr5A 82.301 226 40 0 129 354 603786801 603787026 4.010000e-46 196.0
19 TraesCS2B01G424600 chr5B 81.582 847 128 22 1538 2367 439067172 439068007 0.000000e+00 675.0
20 TraesCS2B01G424600 chr5B 86.364 352 46 1 1 352 28683826 28683477 2.870000e-102 383.0
21 TraesCS2B01G424600 chr5B 80.303 462 54 21 2480 2908 439068216 439068673 1.060000e-81 315.0
22 TraesCS2B01G424600 chr1B 87.701 374 32 3 1 360 599249405 599249032 1.690000e-114 424.0
23 TraesCS2B01G424600 chr1B 83.944 355 53 2 1 352 439428148 439428501 2.260000e-88 337.0
24 TraesCS2B01G424600 chr4D 79.362 596 102 16 1775 2367 494513387 494512810 2.850000e-107 399.0
25 TraesCS2B01G424600 chr6A 78.471 641 114 16 1733 2367 467043963 467044585 1.020000e-106 398.0
26 TraesCS2B01G424600 chr7B 86.723 354 47 0 1 354 134014609 134014962 1.320000e-105 394.0
27 TraesCS2B01G424600 chr7B 86.264 364 37 2 1 351 112336960 112337323 2.870000e-102 383.0
28 TraesCS2B01G424600 chr7B 87.209 344 35 8 1 341 158394721 158395058 2.870000e-102 383.0
29 TraesCS2B01G424600 chr1D 86.413 368 35 5 1 355 493225076 493224711 6.160000e-104 388.0
30 TraesCS2B01G424600 chr1D 83.180 327 53 1 9 333 478402563 478402237 1.070000e-76 298.0
31 TraesCS2B01G424600 chr6D 78.037 642 115 18 1733 2367 328330076 328330698 1.030000e-101 381.0
32 TraesCS2B01G424600 chr6B 78.072 643 113 19 1733 2367 492190531 492191153 1.030000e-101 381.0
33 TraesCS2B01G424600 chr6B 80.000 305 49 6 41 334 320728859 320729162 1.110000e-51 215.0


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 TraesCS2B01G424600 chr2B 610691128 610696204 5076 True 4453.500000 7806 100.000000 1 5077 2 chr2B.!!$R1 5076
1 TraesCS2B01G424600 chr2A 662743761 662748008 4247 True 2174.333333 5565 92.880000 650 5077 3 chr2A.!!$R1 4427
2 TraesCS2B01G424600 chr2D 518597542 518602112 4570 True 990.214286 3489 95.482143 360 5077 7 chr2D.!!$R2 4717
3 TraesCS2B01G424600 chr5D 369725213 369726492 1279 False 467.000000 686 83.796000 1538 2712 2 chr5D.!!$F1 1174
4 TraesCS2B01G424600 chr5A 472284059 472285351 1292 False 468.000000 682 83.936000 1531 2712 2 chr5A.!!$F2 1181
5 TraesCS2B01G424600 chr5B 439067172 439068673 1501 False 495.000000 675 80.942500 1538 2908 2 chr5B.!!$F1 1370
6 TraesCS2B01G424600 chr4D 494512810 494513387 577 True 399.000000 399 79.362000 1775 2367 1 chr4D.!!$R1 592
7 TraesCS2B01G424600 chr6A 467043963 467044585 622 False 398.000000 398 78.471000 1733 2367 1 chr6A.!!$F1 634
8 TraesCS2B01G424600 chr6D 328330076 328330698 622 False 381.000000 381 78.037000 1733 2367 1 chr6D.!!$F1 634
9 TraesCS2B01G424600 chr6B 492190531 492191153 622 False 381.000000 381 78.072000 1733 2367 1 chr6B.!!$F2 634

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
300 301 0.026285 CTTCACTTTTATCCGCGCCG 59.974 55.0 0.00 0.0 0.00 6.46 F
347 348 0.036483 GGGTCGCCCCGTTAAAGTTA 60.036 55.0 3.73 0.0 42.41 2.24 F
1438 1506 0.099968 CCGCGTCTCGTTCCAAGATA 59.900 55.0 4.92 0.0 36.19 1.98 F
1905 1979 0.100325 CGCTGGTGTGCAGTTTCAAA 59.900 50.0 0.00 0.0 0.00 2.69 F
3294 3544 0.530744 GTCAAAAATTCTCCCCGCCC 59.469 55.0 0.00 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 1839 0.388520 TCGTCGTCCTCGTCGTCTAA 60.389 55.0 7.05 0.0 45.27 2.10 R
1905 1979 0.618458 TCCCTTGCAGGCTTCGTATT 59.382 50.0 0.00 0.0 32.73 1.89 R
3393 3718 0.248134 GTCGGAGGAAGATCGTCGTG 60.248 60.0 8.60 0.0 32.46 4.35 R
3792 4121 0.605319 GAAGTTGATGGTGTGGCGGA 60.605 55.0 0.00 0.0 0.00 5.54 R
4717 5064 0.321671 CATACAGGTAGGGATGCGGG 59.678 60.0 0.00 0.0 0.00 6.13 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
17 18 3.164269 AGCGTGGCCTAGATGGGG 61.164 66.667 3.32 0.00 36.00 4.96
18 19 3.161450 GCGTGGCCTAGATGGGGA 61.161 66.667 3.32 0.00 36.00 4.81
19 20 2.520536 GCGTGGCCTAGATGGGGAT 61.521 63.158 3.32 0.00 36.00 3.85
20 21 1.372683 CGTGGCCTAGATGGGGATG 59.627 63.158 3.32 0.00 36.00 3.51
21 22 1.763770 GTGGCCTAGATGGGGATGG 59.236 63.158 3.32 0.00 36.00 3.51
22 23 1.464001 TGGCCTAGATGGGGATGGG 60.464 63.158 3.32 0.00 36.00 4.00
23 24 1.151810 GGCCTAGATGGGGATGGGA 60.152 63.158 0.00 0.00 36.00 4.37
24 25 0.772124 GGCCTAGATGGGGATGGGAA 60.772 60.000 0.00 0.00 36.00 3.97
25 26 0.402121 GCCTAGATGGGGATGGGAAC 59.598 60.000 0.00 0.00 36.00 3.62
26 27 2.047742 GCCTAGATGGGGATGGGAACT 61.048 57.143 0.00 0.00 36.00 3.01
27 28 1.701847 CCTAGATGGGGATGGGAACTG 59.298 57.143 0.00 0.00 0.00 3.16
28 29 1.701847 CTAGATGGGGATGGGAACTGG 59.298 57.143 0.00 0.00 0.00 4.00
29 30 0.046242 AGATGGGGATGGGAACTGGA 59.954 55.000 0.00 0.00 0.00 3.86
30 31 1.152649 GATGGGGATGGGAACTGGAT 58.847 55.000 0.00 0.00 0.00 3.41
31 32 0.855598 ATGGGGATGGGAACTGGATG 59.144 55.000 0.00 0.00 0.00 3.51
32 33 0.253583 TGGGGATGGGAACTGGATGA 60.254 55.000 0.00 0.00 0.00 2.92
33 34 0.475906 GGGGATGGGAACTGGATGAG 59.524 60.000 0.00 0.00 0.00 2.90
34 35 0.475906 GGGATGGGAACTGGATGAGG 59.524 60.000 0.00 0.00 0.00 3.86
35 36 1.511613 GGATGGGAACTGGATGAGGA 58.488 55.000 0.00 0.00 0.00 3.71
36 37 1.141858 GGATGGGAACTGGATGAGGAC 59.858 57.143 0.00 0.00 0.00 3.85
37 38 0.833287 ATGGGAACTGGATGAGGACG 59.167 55.000 0.00 0.00 0.00 4.79
38 39 1.264749 TGGGAACTGGATGAGGACGG 61.265 60.000 0.00 0.00 0.00 4.79
39 40 1.153349 GGAACTGGATGAGGACGGC 60.153 63.158 0.00 0.00 0.00 5.68
40 41 1.153349 GAACTGGATGAGGACGGCC 60.153 63.158 0.00 0.00 0.00 6.13
41 42 2.595009 GAACTGGATGAGGACGGCCC 62.595 65.000 1.76 0.00 33.31 5.80
42 43 3.866582 CTGGATGAGGACGGCCCC 61.867 72.222 1.76 0.00 34.66 5.80
59 60 2.256158 CGCCACACGGTCGACTTA 59.744 61.111 16.46 0.00 38.44 2.24
60 61 1.372004 CGCCACACGGTCGACTTAA 60.372 57.895 16.46 0.00 38.44 1.85
61 62 0.940519 CGCCACACGGTCGACTTAAA 60.941 55.000 16.46 0.00 38.44 1.52
62 63 1.219646 GCCACACGGTCGACTTAAAA 58.780 50.000 16.46 0.00 33.28 1.52
63 64 1.598601 GCCACACGGTCGACTTAAAAA 59.401 47.619 16.46 0.00 33.28 1.94
102 103 4.388499 GCGTGTGTCCGGGGTCAT 62.388 66.667 0.00 0.00 0.00 3.06
103 104 3.009192 GCGTGTGTCCGGGGTCATA 62.009 63.158 0.00 0.00 0.00 2.15
104 105 1.592743 CGTGTGTCCGGGGTCATAA 59.407 57.895 0.00 0.00 0.00 1.90
105 106 0.037139 CGTGTGTCCGGGGTCATAAA 60.037 55.000 0.00 0.00 0.00 1.40
106 107 1.406341 CGTGTGTCCGGGGTCATAAAT 60.406 52.381 0.00 0.00 0.00 1.40
107 108 2.718563 GTGTGTCCGGGGTCATAAATT 58.281 47.619 0.00 0.00 0.00 1.82
108 109 3.679361 CGTGTGTCCGGGGTCATAAATTA 60.679 47.826 0.00 0.00 0.00 1.40
109 110 4.263435 GTGTGTCCGGGGTCATAAATTAA 58.737 43.478 0.00 0.00 0.00 1.40
110 111 4.334481 GTGTGTCCGGGGTCATAAATTAAG 59.666 45.833 0.00 0.00 0.00 1.85
111 112 3.314357 GTGTCCGGGGTCATAAATTAAGC 59.686 47.826 0.00 0.00 0.00 3.09
112 113 3.201266 TGTCCGGGGTCATAAATTAAGCT 59.799 43.478 0.00 0.00 0.00 3.74
113 114 3.564225 GTCCGGGGTCATAAATTAAGCTG 59.436 47.826 0.00 0.00 0.00 4.24
114 115 3.456644 TCCGGGGTCATAAATTAAGCTGA 59.543 43.478 0.00 0.00 0.00 4.26
115 116 3.564225 CCGGGGTCATAAATTAAGCTGAC 59.436 47.826 0.00 0.00 37.79 3.51
118 119 4.813296 GGTCATAAATTAAGCTGACCGG 57.187 45.455 0.00 0.00 45.79 5.28
119 120 3.003378 GGTCATAAATTAAGCTGACCGGC 59.997 47.826 0.00 0.00 45.79 6.13
120 121 3.625764 GTCATAAATTAAGCTGACCGGCA 59.374 43.478 0.00 0.00 33.51 5.69
121 122 4.095782 GTCATAAATTAAGCTGACCGGCAA 59.904 41.667 0.00 0.00 33.51 4.52
122 123 4.335315 TCATAAATTAAGCTGACCGGCAAG 59.665 41.667 0.00 0.00 34.17 4.01
124 125 0.394352 ATTAAGCTGACCGGCAAGGG 60.394 55.000 0.00 0.00 46.96 3.95
125 126 2.478335 TTAAGCTGACCGGCAAGGGG 62.478 60.000 0.00 0.00 46.96 4.79
135 136 4.043100 GCAAGGGGGCGGGTAGTT 62.043 66.667 0.00 0.00 0.00 2.24
136 137 2.045340 CAAGGGGGCGGGTAGTTG 60.045 66.667 0.00 0.00 0.00 3.16
137 138 3.335729 AAGGGGGCGGGTAGTTGG 61.336 66.667 0.00 0.00 0.00 3.77
138 139 4.669773 AGGGGGCGGGTAGTTGGT 62.670 66.667 0.00 0.00 0.00 3.67
139 140 4.105553 GGGGGCGGGTAGTTGGTC 62.106 72.222 0.00 0.00 0.00 4.02
140 141 4.462280 GGGGCGGGTAGTTGGTCG 62.462 72.222 0.00 0.00 0.00 4.79
141 142 3.384532 GGGCGGGTAGTTGGTCGA 61.385 66.667 0.00 0.00 0.00 4.20
142 143 2.125793 GGCGGGTAGTTGGTCGAC 60.126 66.667 7.13 7.13 0.00 4.20
143 144 2.125793 GCGGGTAGTTGGTCGACC 60.126 66.667 28.17 28.17 40.39 4.79
144 145 2.180017 CGGGTAGTTGGTCGACCG 59.820 66.667 28.70 11.24 41.72 4.79
145 146 2.629656 CGGGTAGTTGGTCGACCGT 61.630 63.158 28.70 18.19 41.72 4.83
146 147 1.213799 GGGTAGTTGGTCGACCGTC 59.786 63.158 28.70 22.50 41.72 4.79
147 148 1.526575 GGGTAGTTGGTCGACCGTCA 61.527 60.000 28.70 13.24 41.72 4.35
148 149 0.109412 GGTAGTTGGTCGACCGTCAG 60.109 60.000 28.70 0.00 39.43 3.51
149 150 0.109412 GTAGTTGGTCGACCGTCAGG 60.109 60.000 28.70 0.00 45.13 3.86
159 160 4.521075 CCGTCAGGTGGTGCTATG 57.479 61.111 0.00 0.00 0.00 2.23
160 161 1.153369 CCGTCAGGTGGTGCTATGG 60.153 63.158 0.00 0.00 0.00 2.74
161 162 1.815421 CGTCAGGTGGTGCTATGGC 60.815 63.158 0.00 0.00 39.26 4.40
162 163 1.815421 GTCAGGTGGTGCTATGGCG 60.815 63.158 0.00 0.00 42.25 5.69
163 164 2.514592 CAGGTGGTGCTATGGCGG 60.515 66.667 0.00 0.00 42.25 6.13
164 165 2.687200 AGGTGGTGCTATGGCGGA 60.687 61.111 0.00 0.00 42.25 5.54
165 166 2.513897 GGTGGTGCTATGGCGGAC 60.514 66.667 0.00 0.00 42.25 4.79
166 167 2.890474 GTGGTGCTATGGCGGACG 60.890 66.667 0.00 0.00 42.25 4.79
167 168 3.387091 TGGTGCTATGGCGGACGT 61.387 61.111 0.00 0.00 42.25 4.34
168 169 2.585247 GGTGCTATGGCGGACGTC 60.585 66.667 7.13 7.13 42.25 4.34
169 170 2.954868 GTGCTATGGCGGACGTCG 60.955 66.667 9.92 6.26 42.25 5.12
170 171 3.135457 TGCTATGGCGGACGTCGA 61.135 61.111 9.92 0.00 42.43 4.20
171 172 2.353607 GCTATGGCGGACGTCGAG 60.354 66.667 9.92 7.39 42.43 4.04
172 173 2.831366 GCTATGGCGGACGTCGAGA 61.831 63.158 9.92 0.00 42.43 4.04
173 174 1.725665 CTATGGCGGACGTCGAGAA 59.274 57.895 9.92 0.00 42.43 2.87
174 175 0.317103 CTATGGCGGACGTCGAGAAG 60.317 60.000 9.92 0.00 42.43 2.85
175 176 1.721664 TATGGCGGACGTCGAGAAGG 61.722 60.000 9.92 0.00 42.43 3.46
183 184 3.470567 GTCGAGAAGGCGCGTGTG 61.471 66.667 8.43 0.00 38.51 3.82
184 185 4.717629 TCGAGAAGGCGCGTGTGG 62.718 66.667 8.43 0.00 38.51 4.17
220 221 2.911198 CGCTAACGCATTTGGAACG 58.089 52.632 0.00 0.00 35.30 3.95
221 222 1.125847 CGCTAACGCATTTGGAACGC 61.126 55.000 0.00 0.00 35.30 4.84
222 223 0.109964 GCTAACGCATTTGGAACGCA 60.110 50.000 0.00 0.00 35.78 5.24
223 224 1.664588 GCTAACGCATTTGGAACGCAA 60.665 47.619 0.00 0.00 35.78 4.85
224 225 2.656085 CTAACGCATTTGGAACGCAAA 58.344 42.857 0.00 0.00 0.00 3.68
225 226 2.147436 AACGCATTTGGAACGCAAAT 57.853 40.000 0.00 0.00 33.03 2.32
226 227 1.417372 ACGCATTTGGAACGCAAATG 58.583 45.000 17.52 17.52 46.82 2.32
262 263 3.956317 GCGGACGCGTTTTGGGTT 61.956 61.111 15.53 0.00 44.90 4.11
263 264 2.716864 CGGACGCGTTTTGGGTTT 59.283 55.556 15.53 0.00 44.90 3.27
264 265 1.655959 CGGACGCGTTTTGGGTTTG 60.656 57.895 15.53 0.00 44.90 2.93
265 266 1.299544 GGACGCGTTTTGGGTTTGG 60.300 57.895 15.53 0.00 44.90 3.28
266 267 1.299544 GACGCGTTTTGGGTTTGGG 60.300 57.895 15.53 0.00 44.90 4.12
267 268 2.007113 GACGCGTTTTGGGTTTGGGT 62.007 55.000 15.53 0.00 44.90 4.51
268 269 1.299544 CGCGTTTTGGGTTTGGGTC 60.300 57.895 0.00 0.00 0.00 4.46
269 270 1.299544 GCGTTTTGGGTTTGGGTCG 60.300 57.895 0.00 0.00 0.00 4.79
270 271 1.360911 CGTTTTGGGTTTGGGTCGG 59.639 57.895 0.00 0.00 0.00 4.79
271 272 1.068417 GTTTTGGGTTTGGGTCGGC 59.932 57.895 0.00 0.00 0.00 5.54
272 273 2.134933 TTTTGGGTTTGGGTCGGCC 61.135 57.895 0.00 0.00 0.00 6.13
288 289 2.115266 CCCGTTGGGCCTTCACTT 59.885 61.111 4.53 0.00 35.35 3.16
289 290 1.530655 CCCGTTGGGCCTTCACTTT 60.531 57.895 4.53 0.00 35.35 2.66
290 291 1.112916 CCCGTTGGGCCTTCACTTTT 61.113 55.000 4.53 0.00 35.35 2.27
291 292 1.611519 CCGTTGGGCCTTCACTTTTA 58.388 50.000 4.53 0.00 0.00 1.52
292 293 2.167662 CCGTTGGGCCTTCACTTTTAT 58.832 47.619 4.53 0.00 0.00 1.40
293 294 2.163613 CCGTTGGGCCTTCACTTTTATC 59.836 50.000 4.53 0.00 0.00 1.75
294 295 2.163613 CGTTGGGCCTTCACTTTTATCC 59.836 50.000 4.53 0.00 0.00 2.59
295 296 2.122783 TGGGCCTTCACTTTTATCCG 57.877 50.000 4.53 0.00 0.00 4.18
296 297 0.738975 GGGCCTTCACTTTTATCCGC 59.261 55.000 0.84 0.00 0.00 5.54
297 298 0.377203 GGCCTTCACTTTTATCCGCG 59.623 55.000 0.00 0.00 0.00 6.46
298 299 0.248094 GCCTTCACTTTTATCCGCGC 60.248 55.000 0.00 0.00 0.00 6.86
299 300 0.377203 CCTTCACTTTTATCCGCGCC 59.623 55.000 0.00 0.00 0.00 6.53
300 301 0.026285 CTTCACTTTTATCCGCGCCG 59.974 55.000 0.00 0.00 0.00 6.46
301 302 0.390078 TTCACTTTTATCCGCGCCGA 60.390 50.000 0.00 0.00 0.00 5.54
302 303 1.079875 TCACTTTTATCCGCGCCGAC 61.080 55.000 0.00 0.00 0.00 4.79
303 304 1.812507 ACTTTTATCCGCGCCGACC 60.813 57.895 0.00 0.00 0.00 4.79
304 305 2.512057 TTTTATCCGCGCCGACCC 60.512 61.111 0.00 0.00 0.00 4.46
305 306 3.312285 TTTTATCCGCGCCGACCCA 62.312 57.895 0.00 0.00 0.00 4.51
306 307 2.799814 TTTTATCCGCGCCGACCCAA 62.800 55.000 0.00 0.00 0.00 4.12
307 308 2.799814 TTTATCCGCGCCGACCCAAA 62.800 55.000 0.00 0.00 0.00 3.28
333 334 3.486263 GGCAGACGAAATGGGTCG 58.514 61.111 0.00 0.00 46.54 4.79
334 335 2.750888 GGCAGACGAAATGGGTCGC 61.751 63.158 0.00 0.00 45.00 5.19
335 336 2.750888 GCAGACGAAATGGGTCGCC 61.751 63.158 0.00 0.00 45.00 5.54
336 337 2.106683 CAGACGAAATGGGTCGCCC 61.107 63.158 7.87 7.87 45.00 6.13
345 346 2.348620 GGGTCGCCCCGTTAAAGT 59.651 61.111 3.73 0.00 42.41 2.66
346 347 1.302752 GGGTCGCCCCGTTAAAGTT 60.303 57.895 3.73 0.00 42.41 2.66
347 348 0.036483 GGGTCGCCCCGTTAAAGTTA 60.036 55.000 3.73 0.00 42.41 2.24
348 349 1.078709 GGTCGCCCCGTTAAAGTTAC 58.921 55.000 0.00 0.00 0.00 2.50
349 350 1.338105 GGTCGCCCCGTTAAAGTTACT 60.338 52.381 0.00 0.00 0.00 2.24
350 351 1.995484 GTCGCCCCGTTAAAGTTACTC 59.005 52.381 0.00 0.00 0.00 2.59
351 352 1.895131 TCGCCCCGTTAAAGTTACTCT 59.105 47.619 0.00 0.00 0.00 3.24
352 353 3.088532 TCGCCCCGTTAAAGTTACTCTA 58.911 45.455 0.00 0.00 0.00 2.43
353 354 3.509575 TCGCCCCGTTAAAGTTACTCTAA 59.490 43.478 0.00 0.00 0.00 2.10
354 355 3.861689 CGCCCCGTTAAAGTTACTCTAAG 59.138 47.826 0.00 0.00 0.00 2.18
355 356 4.619160 CGCCCCGTTAAAGTTACTCTAAGT 60.619 45.833 0.00 0.00 0.00 2.24
356 357 4.628766 GCCCCGTTAAAGTTACTCTAAGTG 59.371 45.833 0.00 0.00 0.00 3.16
357 358 5.787380 CCCCGTTAAAGTTACTCTAAGTGT 58.213 41.667 0.00 0.00 0.00 3.55
358 359 5.636543 CCCCGTTAAAGTTACTCTAAGTGTG 59.363 44.000 0.00 0.00 0.00 3.82
371 372 2.279582 AAGTGTGCGTATTCGAGAGG 57.720 50.000 0.00 0.00 39.71 3.69
435 436 0.734942 CAAATGCAAGCAAGGAGGCG 60.735 55.000 0.00 0.00 39.27 5.52
436 437 1.181098 AAATGCAAGCAAGGAGGCGT 61.181 50.000 0.00 0.00 39.27 5.68
437 438 1.589716 AATGCAAGCAAGGAGGCGTC 61.590 55.000 0.00 0.00 39.27 5.19
438 439 2.359230 GCAAGCAAGGAGGCGTCT 60.359 61.111 6.34 0.00 39.27 4.18
439 440 2.684843 GCAAGCAAGGAGGCGTCTG 61.685 63.158 0.00 0.00 39.27 3.51
440 441 2.359230 AAGCAAGGAGGCGTCTGC 60.359 61.111 0.00 0.00 39.27 4.26
441 442 4.749310 AGCAAGGAGGCGTCTGCG 62.749 66.667 1.86 0.00 44.10 5.18
458 459 4.436998 GCCGTGTCTCCGTCCCAG 62.437 72.222 0.00 0.00 0.00 4.45
459 460 2.989824 CCGTGTCTCCGTCCCAGT 60.990 66.667 0.00 0.00 0.00 4.00
460 461 2.258591 CGTGTCTCCGTCCCAGTG 59.741 66.667 0.00 0.00 0.00 3.66
461 462 2.561956 CGTGTCTCCGTCCCAGTGT 61.562 63.158 0.00 0.00 0.00 3.55
462 463 1.006102 GTGTCTCCGTCCCAGTGTG 60.006 63.158 0.00 0.00 0.00 3.82
463 464 2.207229 TGTCTCCGTCCCAGTGTGG 61.207 63.158 0.00 0.00 37.25 4.17
464 465 3.311110 TCTCCGTCCCAGTGTGGC 61.311 66.667 0.00 0.00 35.79 5.01
465 466 4.394712 CTCCGTCCCAGTGTGGCC 62.395 72.222 0.00 0.00 35.79 5.36
469 470 4.265056 GTCCCAGTGTGGCCGGTT 62.265 66.667 1.90 0.00 35.79 4.44
470 471 2.527123 TCCCAGTGTGGCCGGTTA 60.527 61.111 1.90 0.00 35.79 2.85
471 472 1.921346 TCCCAGTGTGGCCGGTTAT 60.921 57.895 1.90 0.00 35.79 1.89
472 473 1.451387 CCCAGTGTGGCCGGTTATC 60.451 63.158 1.90 0.00 35.79 1.75
473 474 1.451387 CCAGTGTGGCCGGTTATCC 60.451 63.158 1.90 0.00 0.00 2.59
474 475 1.451387 CAGTGTGGCCGGTTATCCC 60.451 63.158 1.90 0.00 0.00 3.85
485 486 1.718280 GGTTATCCCGGTCATCCTCT 58.282 55.000 0.00 0.00 0.00 3.69
486 487 1.619332 GGTTATCCCGGTCATCCTCTC 59.381 57.143 0.00 0.00 0.00 3.20
487 488 2.317040 GTTATCCCGGTCATCCTCTCA 58.683 52.381 0.00 0.00 0.00 3.27
488 489 2.294449 TATCCCGGTCATCCTCTCAG 57.706 55.000 0.00 0.00 0.00 3.35
489 490 0.558220 ATCCCGGTCATCCTCTCAGA 59.442 55.000 0.00 0.00 0.00 3.27
490 491 0.395862 TCCCGGTCATCCTCTCAGAC 60.396 60.000 0.00 0.00 0.00 3.51
491 492 1.395826 CCCGGTCATCCTCTCAGACC 61.396 65.000 0.00 0.00 46.48 3.85
495 496 1.484038 GTCATCCTCTCAGACCAGCT 58.516 55.000 0.00 0.00 0.00 4.24
496 497 2.660572 GTCATCCTCTCAGACCAGCTA 58.339 52.381 0.00 0.00 0.00 3.32
497 498 2.360801 GTCATCCTCTCAGACCAGCTAC 59.639 54.545 0.00 0.00 0.00 3.58
498 499 2.243478 TCATCCTCTCAGACCAGCTACT 59.757 50.000 0.00 0.00 0.00 2.57
555 556 1.348036 GCTCCTAGTCCACCACACTTT 59.652 52.381 0.00 0.00 0.00 2.66
570 583 1.376812 CTTTACCGACCACTGGCCC 60.377 63.158 0.00 0.00 0.00 5.80
574 587 2.444004 TACCGACCACTGGCCCACTA 62.444 60.000 0.00 0.00 0.00 2.74
628 641 0.535102 CTTCCCTTCAGCAACCACGT 60.535 55.000 0.00 0.00 0.00 4.49
629 642 0.106918 TTCCCTTCAGCAACCACGTT 60.107 50.000 0.00 0.00 0.00 3.99
635 648 2.184167 CAGCAACCACGTTTCCGGT 61.184 57.895 0.00 0.00 38.78 5.28
695 708 3.418675 CGTAGCCACACGTTCAGAT 57.581 52.632 0.00 0.00 37.16 2.90
985 1044 3.691342 CGCCGGGTGGTTCTCTCA 61.691 66.667 2.18 0.00 37.67 3.27
987 1046 1.072505 GCCGGGTGGTTCTCTCAAA 59.927 57.895 2.18 0.00 37.67 2.69
1011 1070 2.024117 CCGCGCAATGGATCATCAA 58.976 52.632 8.75 0.00 0.00 2.57
1438 1506 0.099968 CCGCGTCTCGTTCCAAGATA 59.900 55.000 4.92 0.00 36.19 1.98
1509 1577 1.366111 CCGCCGACCACAATCGAAAT 61.366 55.000 0.00 0.00 45.13 2.17
1518 1586 2.684374 CCACAATCGAAATCAGGATGCA 59.316 45.455 0.00 0.00 34.76 3.96
1617 1685 3.550431 CGGTCCCGGCTGATGGAT 61.550 66.667 0.00 0.00 35.56 3.41
1728 1802 0.909623 ATTTCCGGTCGGGTCTCATT 59.090 50.000 9.68 0.00 37.00 2.57
1767 1841 4.367023 AAGTCAGGCGGCGCGTTA 62.367 61.111 25.68 15.01 0.00 3.18
1905 1979 0.100325 CGCTGGTGTGCAGTTTCAAA 59.900 50.000 0.00 0.00 0.00 2.69
2158 2232 0.596600 GCTCTTCGACAACGGTGACA 60.597 55.000 7.88 0.00 40.21 3.58
2412 2549 3.474570 GCCATGCCGAGGGAGTCT 61.475 66.667 0.00 0.00 0.00 3.24
2419 2556 4.200283 CGAGGGAGTCTGCCGCTC 62.200 72.222 12.17 4.37 39.37 5.03
2475 2639 1.135257 CAGAAGCAGAAGTCGGACGAT 60.135 52.381 1.89 0.00 0.00 3.73
2696 2881 0.950836 CACAATGTCGCCAAACCTGA 59.049 50.000 0.00 0.00 0.00 3.86
2706 2891 2.420022 CGCCAAACCTGAATCCAAGTAG 59.580 50.000 0.00 0.00 0.00 2.57
2885 3097 1.490490 AGAACAACAGGGTGAGCAAGA 59.510 47.619 0.00 0.00 0.00 3.02
2971 3217 3.547746 TGTGGTGTGGGTTCTAAACTTC 58.452 45.455 0.00 0.00 0.00 3.01
3265 3511 2.352915 GATCGCTGCGAGGTCGAG 60.353 66.667 29.23 0.00 39.91 4.04
3281 3531 1.243342 CGAGGGCATGCAGGTCAAAA 61.243 55.000 21.36 0.00 0.00 2.44
3294 3544 0.530744 GTCAAAAATTCTCCCCGCCC 59.469 55.000 0.00 0.00 0.00 6.13
3483 3808 3.553096 CCATCATGAACTACTACCGGAGC 60.553 52.174 9.46 0.00 0.00 4.70
3646 3975 8.339714 TGGCTAATTACGTCACTTATATTTTGC 58.660 33.333 0.00 0.00 0.00 3.68
3689 4018 5.898174 AGTTTCCCTTTTACTTTGTTTCGG 58.102 37.500 0.00 0.00 0.00 4.30
3791 4120 4.040461 ACCGACTCAAGATAACCATATGGG 59.960 45.833 25.55 8.07 44.81 4.00
3904 4233 3.565063 TCGACATCGAATACCGGATGTTA 59.435 43.478 9.46 0.00 46.30 2.41
4109 4438 1.387084 GATCGACAACTTGCTGACGAC 59.613 52.381 0.91 0.00 43.99 4.34
4147 4482 5.179452 ACAGCACATGAGGTAGGTTTTAT 57.821 39.130 0.00 0.00 0.00 1.40
4175 4510 0.039618 TTTGAGTGATGGGGGAAGGC 59.960 55.000 0.00 0.00 0.00 4.35
4176 4511 1.139498 TTGAGTGATGGGGGAAGGCA 61.139 55.000 0.00 0.00 0.00 4.75
4179 4514 0.846427 AGTGATGGGGGAAGGCAAGA 60.846 55.000 0.00 0.00 0.00 3.02
4194 4529 2.652590 GCAAGAGGAAGGCAAGATGAT 58.347 47.619 0.00 0.00 0.00 2.45
4526 4873 2.047154 AGGGGATTTAAAATGGGGGCTT 59.953 45.455 0.00 0.00 0.00 4.35
4580 4927 7.123830 CCGCGGATAATTACTTCTTAGTTTTG 58.876 38.462 24.07 0.00 35.78 2.44
4618 4965 0.661483 GAAAAGCACACTGCCTTCGC 60.661 55.000 0.00 0.00 46.52 4.70
4627 4974 4.373116 TGCCTTCGCTCCGTCCAC 62.373 66.667 0.00 0.00 35.36 4.02
4631 4978 1.153823 CTTCGCTCCGTCCACGAAT 60.154 57.895 0.00 0.00 43.98 3.34
4659 5006 2.750807 GCCACCATGACCTAATCTGCAT 60.751 50.000 0.00 0.00 0.00 3.96
4696 5043 0.393077 GCCGCACCCACTATCTACAT 59.607 55.000 0.00 0.00 0.00 2.29
4717 5064 9.906660 CTACATCCTCTTTCTCTATGTATGTTC 57.093 37.037 0.00 0.00 33.77 3.18
4719 5066 6.732896 TCCTCTTTCTCTATGTATGTTCCC 57.267 41.667 0.00 0.00 0.00 3.97
4731 5078 0.694444 ATGTTCCCGCATCCCTACCT 60.694 55.000 0.00 0.00 0.00 3.08
4735 5082 0.190069 TCCCGCATCCCTACCTGTAT 59.810 55.000 0.00 0.00 0.00 2.29
4826 5173 0.953471 GGCCACTCGCACATAACACA 60.953 55.000 0.00 0.00 40.31 3.72
4858 5205 4.354893 AAAGCAATTTCATGAAGGCCAA 57.645 36.364 19.11 2.83 0.00 4.52
4912 5261 9.712305 TTTTTCTTCAAAAAGGAATGTGTTGTA 57.288 25.926 0.00 0.00 36.70 2.41
4926 5275 6.707440 ATGTGTTGTATTTGACTTCACCAA 57.293 33.333 0.00 0.00 34.11 3.67
4955 5304 5.180271 TCCCACGGAAATATACAGAAACAC 58.820 41.667 0.00 0.00 0.00 3.32
5026 5376 6.147864 TGCATGATTTGTTAATTAGGGAGC 57.852 37.500 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.972589 ATCCCCATCTAGGCCACGCT 62.973 60.000 5.01 0.00 35.39 5.07
1 2 2.520536 ATCCCCATCTAGGCCACGC 61.521 63.158 5.01 0.00 35.39 5.34
3 4 1.763770 CCATCCCCATCTAGGCCAC 59.236 63.158 5.01 0.00 35.39 5.01
5 6 0.772124 TTCCCATCCCCATCTAGGCC 60.772 60.000 0.00 0.00 35.39 5.19
6 7 0.402121 GTTCCCATCCCCATCTAGGC 59.598 60.000 0.00 0.00 35.39 3.93
7 8 1.701847 CAGTTCCCATCCCCATCTAGG 59.298 57.143 0.00 0.00 37.03 3.02
8 9 1.701847 CCAGTTCCCATCCCCATCTAG 59.298 57.143 0.00 0.00 0.00 2.43
9 10 1.296832 TCCAGTTCCCATCCCCATCTA 59.703 52.381 0.00 0.00 0.00 1.98
10 11 0.046242 TCCAGTTCCCATCCCCATCT 59.954 55.000 0.00 0.00 0.00 2.90
11 12 1.152649 ATCCAGTTCCCATCCCCATC 58.847 55.000 0.00 0.00 0.00 3.51
12 13 0.855598 CATCCAGTTCCCATCCCCAT 59.144 55.000 0.00 0.00 0.00 4.00
13 14 0.253583 TCATCCAGTTCCCATCCCCA 60.254 55.000 0.00 0.00 0.00 4.96
14 15 0.475906 CTCATCCAGTTCCCATCCCC 59.524 60.000 0.00 0.00 0.00 4.81
15 16 0.475906 CCTCATCCAGTTCCCATCCC 59.524 60.000 0.00 0.00 0.00 3.85
16 17 1.141858 GTCCTCATCCAGTTCCCATCC 59.858 57.143 0.00 0.00 0.00 3.51
17 18 1.202580 CGTCCTCATCCAGTTCCCATC 60.203 57.143 0.00 0.00 0.00 3.51
18 19 0.833287 CGTCCTCATCCAGTTCCCAT 59.167 55.000 0.00 0.00 0.00 4.00
19 20 1.264749 CCGTCCTCATCCAGTTCCCA 61.265 60.000 0.00 0.00 0.00 4.37
20 21 1.522569 CCGTCCTCATCCAGTTCCC 59.477 63.158 0.00 0.00 0.00 3.97
21 22 1.153349 GCCGTCCTCATCCAGTTCC 60.153 63.158 0.00 0.00 0.00 3.62
22 23 1.153349 GGCCGTCCTCATCCAGTTC 60.153 63.158 0.00 0.00 0.00 3.01
23 24 2.670148 GGGCCGTCCTCATCCAGTT 61.670 63.158 0.00 0.00 0.00 3.16
24 25 3.083997 GGGCCGTCCTCATCCAGT 61.084 66.667 0.00 0.00 0.00 4.00
25 26 3.866582 GGGGCCGTCCTCATCCAG 61.867 72.222 0.00 0.00 35.33 3.86
42 43 0.940519 TTTAAGTCGACCGTGTGGCG 60.941 55.000 13.01 0.00 39.70 5.69
43 44 1.219646 TTTTAAGTCGACCGTGTGGC 58.780 50.000 13.01 0.00 39.70 5.01
85 86 2.510064 TTATGACCCCGGACACACGC 62.510 60.000 0.73 0.00 0.00 5.34
86 87 0.037139 TTTATGACCCCGGACACACG 60.037 55.000 0.73 0.00 0.00 4.49
87 88 2.413310 ATTTATGACCCCGGACACAC 57.587 50.000 0.73 0.00 0.00 3.82
88 89 4.519213 CTTAATTTATGACCCCGGACACA 58.481 43.478 0.73 0.00 0.00 3.72
89 90 3.314357 GCTTAATTTATGACCCCGGACAC 59.686 47.826 0.73 0.00 0.00 3.67
90 91 3.201266 AGCTTAATTTATGACCCCGGACA 59.799 43.478 0.73 0.00 0.00 4.02
91 92 3.564225 CAGCTTAATTTATGACCCCGGAC 59.436 47.826 0.73 0.00 0.00 4.79
92 93 3.456644 TCAGCTTAATTTATGACCCCGGA 59.543 43.478 0.73 0.00 0.00 5.14
93 94 3.564225 GTCAGCTTAATTTATGACCCCGG 59.436 47.826 0.00 0.00 36.83 5.73
94 95 4.813296 GTCAGCTTAATTTATGACCCCG 57.187 45.455 0.00 0.00 36.83 5.73
98 99 3.625764 TGCCGGTCAGCTTAATTTATGAC 59.374 43.478 1.90 0.00 41.03 3.06
99 100 3.879998 TGCCGGTCAGCTTAATTTATGA 58.120 40.909 1.90 0.00 0.00 2.15
100 101 4.498009 CCTTGCCGGTCAGCTTAATTTATG 60.498 45.833 1.90 0.00 0.00 1.90
101 102 3.632145 CCTTGCCGGTCAGCTTAATTTAT 59.368 43.478 1.90 0.00 0.00 1.40
102 103 3.013921 CCTTGCCGGTCAGCTTAATTTA 58.986 45.455 1.90 0.00 0.00 1.40
103 104 1.818674 CCTTGCCGGTCAGCTTAATTT 59.181 47.619 1.90 0.00 0.00 1.82
104 105 1.463674 CCTTGCCGGTCAGCTTAATT 58.536 50.000 1.90 0.00 0.00 1.40
105 106 0.394352 CCCTTGCCGGTCAGCTTAAT 60.394 55.000 1.90 0.00 0.00 1.40
106 107 1.002624 CCCTTGCCGGTCAGCTTAA 60.003 57.895 1.90 0.00 0.00 1.85
107 108 2.668632 CCCTTGCCGGTCAGCTTA 59.331 61.111 1.90 0.00 0.00 3.09
108 109 4.351054 CCCCTTGCCGGTCAGCTT 62.351 66.667 1.90 0.00 0.00 3.74
118 119 4.043100 AACTACCCGCCCCCTTGC 62.043 66.667 0.00 0.00 0.00 4.01
119 120 2.045340 CAACTACCCGCCCCCTTG 60.045 66.667 0.00 0.00 0.00 3.61
120 121 3.335729 CCAACTACCCGCCCCCTT 61.336 66.667 0.00 0.00 0.00 3.95
121 122 4.669773 ACCAACTACCCGCCCCCT 62.670 66.667 0.00 0.00 0.00 4.79
122 123 4.105553 GACCAACTACCCGCCCCC 62.106 72.222 0.00 0.00 0.00 5.40
123 124 4.462280 CGACCAACTACCCGCCCC 62.462 72.222 0.00 0.00 0.00 5.80
124 125 3.384532 TCGACCAACTACCCGCCC 61.385 66.667 0.00 0.00 0.00 6.13
125 126 2.125793 GTCGACCAACTACCCGCC 60.126 66.667 3.51 0.00 0.00 6.13
126 127 2.125793 GGTCGACCAACTACCCGC 60.126 66.667 29.75 0.00 35.64 6.13
127 128 2.180017 CGGTCGACCAACTACCCG 59.820 66.667 32.80 13.73 35.14 5.28
128 129 1.213799 GACGGTCGACCAACTACCC 59.786 63.158 32.80 10.19 35.14 3.69
129 130 0.109412 CTGACGGTCGACCAACTACC 60.109 60.000 32.80 14.95 35.14 3.18
130 131 0.109412 CCTGACGGTCGACCAACTAC 60.109 60.000 32.80 18.23 35.14 2.73
131 132 0.538057 ACCTGACGGTCGACCAACTA 60.538 55.000 32.80 15.28 40.27 2.24
132 133 1.831286 ACCTGACGGTCGACCAACT 60.831 57.895 32.80 15.38 40.27 3.16
133 134 1.663702 CACCTGACGGTCGACCAAC 60.664 63.158 32.80 24.48 43.24 3.77
134 135 2.732016 CACCTGACGGTCGACCAA 59.268 61.111 32.80 17.21 43.24 3.67
135 136 3.299977 CCACCTGACGGTCGACCA 61.300 66.667 32.80 14.01 43.24 4.02
136 137 3.300765 ACCACCTGACGGTCGACC 61.301 66.667 25.28 25.28 43.24 4.79
137 138 2.049433 CACCACCTGACGGTCGAC 60.049 66.667 7.13 7.13 43.24 4.20
138 139 3.986006 GCACCACCTGACGGTCGA 61.986 66.667 3.34 0.00 43.24 4.20
139 140 1.945354 ATAGCACCACCTGACGGTCG 61.945 60.000 3.34 0.00 43.24 4.79
140 141 0.460284 CATAGCACCACCTGACGGTC 60.460 60.000 0.00 0.00 43.24 4.79
142 143 1.153369 CCATAGCACCACCTGACGG 60.153 63.158 0.00 0.00 0.00 4.79
143 144 1.815421 GCCATAGCACCACCTGACG 60.815 63.158 0.00 0.00 39.53 4.35
144 145 1.815421 CGCCATAGCACCACCTGAC 60.815 63.158 0.00 0.00 39.83 3.51
145 146 2.584064 CGCCATAGCACCACCTGA 59.416 61.111 0.00 0.00 39.83 3.86
146 147 2.514592 CCGCCATAGCACCACCTG 60.515 66.667 0.00 0.00 39.83 4.00
147 148 2.687200 TCCGCCATAGCACCACCT 60.687 61.111 0.00 0.00 39.83 4.00
148 149 2.513897 GTCCGCCATAGCACCACC 60.514 66.667 0.00 0.00 39.83 4.61
149 150 2.890474 CGTCCGCCATAGCACCAC 60.890 66.667 0.00 0.00 39.83 4.16
150 151 3.365291 GACGTCCGCCATAGCACCA 62.365 63.158 3.51 0.00 39.83 4.17
151 152 2.585247 GACGTCCGCCATAGCACC 60.585 66.667 3.51 0.00 39.83 5.01
152 153 2.954868 CGACGTCCGCCATAGCAC 60.955 66.667 10.58 0.00 39.83 4.40
153 154 3.120979 CTCGACGTCCGCCATAGCA 62.121 63.158 10.58 0.00 39.83 3.49
154 155 2.332362 TTCTCGACGTCCGCCATAGC 62.332 60.000 10.58 0.00 38.37 2.97
155 156 0.317103 CTTCTCGACGTCCGCCATAG 60.317 60.000 10.58 0.00 38.37 2.23
156 157 1.721664 CCTTCTCGACGTCCGCCATA 61.722 60.000 10.58 0.00 38.37 2.74
157 158 2.490217 CTTCTCGACGTCCGCCAT 59.510 61.111 10.58 0.00 38.37 4.40
158 159 3.744719 CCTTCTCGACGTCCGCCA 61.745 66.667 10.58 0.00 38.37 5.69
163 164 4.755614 ACGCGCCTTCTCGACGTC 62.756 66.667 5.73 5.18 37.54 4.34
166 167 3.470567 CACACGCGCCTTCTCGAC 61.471 66.667 5.73 0.00 0.00 4.20
167 168 4.717629 CCACACGCGCCTTCTCGA 62.718 66.667 5.73 0.00 0.00 4.04
203 204 0.109964 TGCGTTCCAAATGCGTTAGC 60.110 50.000 0.00 0.00 46.36 3.09
204 205 2.323939 TTGCGTTCCAAATGCGTTAG 57.676 45.000 0.00 0.00 46.36 2.34
205 206 2.776312 TTTGCGTTCCAAATGCGTTA 57.224 40.000 0.00 0.00 46.36 3.18
206 207 3.650409 TTTGCGTTCCAAATGCGTT 57.350 42.105 0.00 0.00 46.36 4.84
241 242 2.496794 CAAAACGCGTCCGCTTCG 60.497 61.111 14.44 0.00 39.32 3.79
242 243 2.127383 CCAAAACGCGTCCGCTTC 60.127 61.111 14.44 0.00 39.32 3.86
243 244 3.656045 CCCAAAACGCGTCCGCTT 61.656 61.111 14.44 0.00 39.32 4.68
244 245 4.922026 ACCCAAAACGCGTCCGCT 62.922 61.111 14.44 0.00 39.32 5.52
245 246 3.472736 AAACCCAAAACGCGTCCGC 62.473 57.895 14.44 0.68 38.22 5.54
246 247 1.655959 CAAACCCAAAACGCGTCCG 60.656 57.895 14.44 3.52 41.14 4.79
247 248 1.299544 CCAAACCCAAAACGCGTCC 60.300 57.895 14.44 0.00 0.00 4.79
248 249 1.299544 CCCAAACCCAAAACGCGTC 60.300 57.895 14.44 0.00 0.00 5.19
249 250 2.007113 GACCCAAACCCAAAACGCGT 62.007 55.000 5.58 5.58 0.00 6.01
250 251 1.299544 GACCCAAACCCAAAACGCG 60.300 57.895 3.53 3.53 0.00 6.01
251 252 1.299544 CGACCCAAACCCAAAACGC 60.300 57.895 0.00 0.00 0.00 4.84
252 253 1.360911 CCGACCCAAACCCAAAACG 59.639 57.895 0.00 0.00 0.00 3.60
253 254 1.068417 GCCGACCCAAACCCAAAAC 59.932 57.895 0.00 0.00 0.00 2.43
254 255 2.134933 GGCCGACCCAAACCCAAAA 61.135 57.895 0.00 0.00 0.00 2.44
255 256 2.522193 GGCCGACCCAAACCCAAA 60.522 61.111 0.00 0.00 0.00 3.28
272 273 1.611519 TAAAAGTGAAGGCCCAACGG 58.388 50.000 0.00 0.00 0.00 4.44
273 274 2.163613 GGATAAAAGTGAAGGCCCAACG 59.836 50.000 0.00 0.00 0.00 4.10
274 275 2.163613 CGGATAAAAGTGAAGGCCCAAC 59.836 50.000 0.00 0.00 0.00 3.77
275 276 2.442413 CGGATAAAAGTGAAGGCCCAA 58.558 47.619 0.00 0.00 0.00 4.12
276 277 1.953311 GCGGATAAAAGTGAAGGCCCA 60.953 52.381 0.00 0.00 0.00 5.36
277 278 0.738975 GCGGATAAAAGTGAAGGCCC 59.261 55.000 0.00 0.00 0.00 5.80
278 279 0.377203 CGCGGATAAAAGTGAAGGCC 59.623 55.000 0.00 0.00 0.00 5.19
279 280 0.248094 GCGCGGATAAAAGTGAAGGC 60.248 55.000 8.83 0.00 0.00 4.35
280 281 0.377203 GGCGCGGATAAAAGTGAAGG 59.623 55.000 8.83 0.00 0.00 3.46
281 282 0.026285 CGGCGCGGATAAAAGTGAAG 59.974 55.000 9.72 0.00 0.00 3.02
282 283 0.390078 TCGGCGCGGATAAAAGTGAA 60.390 50.000 14.27 0.00 0.00 3.18
283 284 1.079875 GTCGGCGCGGATAAAAGTGA 61.080 55.000 21.12 0.00 0.00 3.41
284 285 1.347221 GTCGGCGCGGATAAAAGTG 59.653 57.895 21.12 0.00 0.00 3.16
285 286 1.812507 GGTCGGCGCGGATAAAAGT 60.813 57.895 21.12 0.00 0.00 2.66
286 287 2.531376 GGGTCGGCGCGGATAAAAG 61.531 63.158 21.12 0.00 0.00 2.27
287 288 2.512057 GGGTCGGCGCGGATAAAA 60.512 61.111 21.12 0.00 0.00 1.52
288 289 2.799814 TTTGGGTCGGCGCGGATAAA 62.800 55.000 21.12 17.74 0.00 1.40
289 290 3.312285 TTTGGGTCGGCGCGGATAA 62.312 57.895 21.12 13.29 0.00 1.75
290 291 3.772281 TTTGGGTCGGCGCGGATA 61.772 61.111 21.12 8.05 0.00 2.59
311 312 4.520846 CATTTCGTCTGCCGCCGC 62.521 66.667 0.00 0.00 36.19 6.53
312 313 3.864686 CCATTTCGTCTGCCGCCG 61.865 66.667 0.00 0.00 36.19 6.46
313 314 3.508840 CCCATTTCGTCTGCCGCC 61.509 66.667 0.00 0.00 36.19 6.13
314 315 2.746277 ACCCATTTCGTCTGCCGC 60.746 61.111 0.00 0.00 36.19 6.53
315 316 2.452813 CGACCCATTTCGTCTGCCG 61.453 63.158 0.00 0.00 34.16 5.69
316 317 2.750888 GCGACCCATTTCGTCTGCC 61.751 63.158 0.00 0.00 41.26 4.85
317 318 2.750888 GGCGACCCATTTCGTCTGC 61.751 63.158 0.00 0.00 40.53 4.26
318 319 3.486263 GGCGACCCATTTCGTCTG 58.514 61.111 0.00 0.00 40.53 3.51
330 331 1.995484 GAGTAACTTTAACGGGGCGAC 59.005 52.381 0.00 0.00 0.00 5.19
331 332 1.895131 AGAGTAACTTTAACGGGGCGA 59.105 47.619 0.00 0.00 0.00 5.54
332 333 2.375173 AGAGTAACTTTAACGGGGCG 57.625 50.000 0.00 0.00 0.00 6.13
333 334 4.628766 CACTTAGAGTAACTTTAACGGGGC 59.371 45.833 0.00 0.00 0.00 5.80
334 335 5.636543 CACACTTAGAGTAACTTTAACGGGG 59.363 44.000 0.00 0.00 0.00 5.73
335 336 5.119743 GCACACTTAGAGTAACTTTAACGGG 59.880 44.000 0.00 0.00 0.00 5.28
336 337 5.164119 CGCACACTTAGAGTAACTTTAACGG 60.164 44.000 0.00 0.00 0.00 4.44
337 338 5.400485 ACGCACACTTAGAGTAACTTTAACG 59.600 40.000 0.00 0.00 0.00 3.18
338 339 6.760161 ACGCACACTTAGAGTAACTTTAAC 57.240 37.500 0.00 0.00 0.00 2.01
339 340 9.132521 GAATACGCACACTTAGAGTAACTTTAA 57.867 33.333 0.00 0.00 0.00 1.52
340 341 7.482743 CGAATACGCACACTTAGAGTAACTTTA 59.517 37.037 0.00 0.00 0.00 1.85
341 342 6.307318 CGAATACGCACACTTAGAGTAACTTT 59.693 38.462 0.00 0.00 0.00 2.66
342 343 5.798934 CGAATACGCACACTTAGAGTAACTT 59.201 40.000 0.00 0.00 0.00 2.66
343 344 5.122869 TCGAATACGCACACTTAGAGTAACT 59.877 40.000 0.00 0.00 39.58 2.24
344 345 5.327091 TCGAATACGCACACTTAGAGTAAC 58.673 41.667 0.00 0.00 39.58 2.50
345 346 5.352293 TCTCGAATACGCACACTTAGAGTAA 59.648 40.000 0.00 0.00 39.58 2.24
346 347 4.872124 TCTCGAATACGCACACTTAGAGTA 59.128 41.667 0.00 0.00 39.58 2.59
347 348 3.688185 TCTCGAATACGCACACTTAGAGT 59.312 43.478 0.00 0.00 39.58 3.24
348 349 4.274421 TCTCGAATACGCACACTTAGAG 57.726 45.455 0.00 0.00 39.58 2.43
349 350 3.064958 CCTCTCGAATACGCACACTTAGA 59.935 47.826 0.00 0.00 39.58 2.10
350 351 3.064958 TCCTCTCGAATACGCACACTTAG 59.935 47.826 0.00 0.00 39.58 2.18
351 352 3.011818 TCCTCTCGAATACGCACACTTA 58.988 45.455 0.00 0.00 39.58 2.24
352 353 1.816835 TCCTCTCGAATACGCACACTT 59.183 47.619 0.00 0.00 39.58 3.16
353 354 1.460504 TCCTCTCGAATACGCACACT 58.539 50.000 0.00 0.00 39.58 3.55
354 355 2.273370 TTCCTCTCGAATACGCACAC 57.727 50.000 0.00 0.00 39.58 3.82
355 356 3.306917 TTTTCCTCTCGAATACGCACA 57.693 42.857 0.00 0.00 39.58 4.57
379 380 1.365368 CCGTTGCATGCCGTGTGATA 61.365 55.000 16.68 0.00 0.00 2.15
441 442 4.436998 CTGGGACGGAGACACGGC 62.437 72.222 0.00 0.00 42.35 5.68
442 443 2.989824 ACTGGGACGGAGACACGG 60.990 66.667 0.00 0.00 38.11 4.94
443 444 2.258591 CACTGGGACGGAGACACG 59.741 66.667 0.00 0.00 38.67 4.49
444 445 1.006102 CACACTGGGACGGAGACAC 60.006 63.158 0.00 0.00 38.67 3.67
445 446 2.207229 CCACACTGGGACGGAGACA 61.207 63.158 0.00 0.00 38.67 3.41
446 447 2.657237 CCACACTGGGACGGAGAC 59.343 66.667 0.00 0.00 38.67 3.36
447 448 3.311110 GCCACACTGGGACGGAGA 61.311 66.667 0.00 0.00 38.19 3.71
448 449 4.394712 GGCCACACTGGGACGGAG 62.395 72.222 0.00 0.00 38.19 4.63
456 457 1.451387 GGGATAACCGGCCACACTG 60.451 63.158 0.00 0.00 36.97 3.66
457 458 2.995547 GGGATAACCGGCCACACT 59.004 61.111 0.00 0.00 36.97 3.55
466 467 1.619332 GAGAGGATGACCGGGATAACC 59.381 57.143 6.32 2.36 41.83 2.85
467 468 2.297597 CTGAGAGGATGACCGGGATAAC 59.702 54.545 6.32 0.00 41.83 1.89
468 469 2.177016 TCTGAGAGGATGACCGGGATAA 59.823 50.000 6.32 0.00 41.83 1.75
469 470 1.780919 TCTGAGAGGATGACCGGGATA 59.219 52.381 6.32 0.00 41.83 2.59
470 471 0.558220 TCTGAGAGGATGACCGGGAT 59.442 55.000 6.32 0.00 41.83 3.85
471 472 0.395862 GTCTGAGAGGATGACCGGGA 60.396 60.000 6.32 0.00 41.83 5.14
472 473 1.395826 GGTCTGAGAGGATGACCGGG 61.396 65.000 6.32 0.00 40.44 5.73
473 474 2.119886 GGTCTGAGAGGATGACCGG 58.880 63.158 0.00 0.00 40.44 5.28
476 477 1.484038 AGCTGGTCTGAGAGGATGAC 58.516 55.000 0.00 0.00 0.00 3.06
477 478 2.243478 AGTAGCTGGTCTGAGAGGATGA 59.757 50.000 0.00 0.00 0.00 2.92
478 479 2.361757 CAGTAGCTGGTCTGAGAGGATG 59.638 54.545 0.00 0.00 34.02 3.51
479 480 2.665165 CAGTAGCTGGTCTGAGAGGAT 58.335 52.381 0.00 0.00 34.02 3.24
480 481 1.341482 CCAGTAGCTGGTCTGAGAGGA 60.341 57.143 14.13 0.00 45.82 3.71
481 482 1.110442 CCAGTAGCTGGTCTGAGAGG 58.890 60.000 14.13 0.00 45.82 3.69
491 492 0.175302 CTCTGCTGGACCAGTAGCTG 59.825 60.000 29.26 21.11 42.46 4.24
492 493 0.040351 TCTCTGCTGGACCAGTAGCT 59.960 55.000 29.26 0.00 42.46 3.32
493 494 0.459489 CTCTCTGCTGGACCAGTAGC 59.541 60.000 29.26 14.99 42.46 3.58
494 495 0.459489 GCTCTCTGCTGGACCAGTAG 59.541 60.000 28.46 28.46 43.73 2.57
495 496 0.972983 GGCTCTCTGCTGGACCAGTA 60.973 60.000 22.58 17.50 42.39 2.74
496 497 2.289532 GGCTCTCTGCTGGACCAGT 61.290 63.158 22.58 0.00 42.39 4.00
497 498 1.988956 AGGCTCTCTGCTGGACCAG 60.989 63.158 17.83 17.83 42.39 4.00
498 499 2.121385 AGGCTCTCTGCTGGACCA 59.879 61.111 0.00 0.00 42.39 4.02
555 556 2.444004 TAGTGGGCCAGTGGTCGGTA 62.444 60.000 24.22 0.00 0.00 4.02
570 583 0.297820 GACGGCGAGCGAATTTAGTG 59.702 55.000 16.62 0.00 0.00 2.74
574 587 3.186047 CGGACGGCGAGCGAATTT 61.186 61.111 16.62 0.00 0.00 1.82
603 616 1.613925 GTTGCTGAAGGGAAGGGAAAC 59.386 52.381 0.00 0.00 0.00 2.78
635 648 2.490718 GCAGTGGATATATTTGGGGGCA 60.491 50.000 0.00 0.00 0.00 5.36
695 708 3.646715 CCGGGGCAGGTGGAGAAA 61.647 66.667 0.00 0.00 0.00 2.52
1034 1093 1.364901 GACGACTTGTTGGACCCGA 59.635 57.895 0.00 0.00 0.00 5.14
1158 1226 2.365105 GATCCAGACCCCGACCCA 60.365 66.667 0.00 0.00 0.00 4.51
1395 1463 4.201951 CGGGAATTGGTGACGGAG 57.798 61.111 0.00 0.00 0.00 4.63
1438 1506 4.681978 GCCGAGACGCTTGTGGGT 62.682 66.667 0.00 0.00 42.25 4.51
1498 1566 4.359971 TTGCATCCTGATTTCGATTGTG 57.640 40.909 0.00 0.00 0.00 3.33
1518 1586 1.890510 GGTGTCGACCCTTGCGTTT 60.891 57.895 14.12 0.00 36.03 3.60
1728 1802 0.530744 CGATCAGACCCGACTTTCCA 59.469 55.000 0.00 0.00 0.00 3.53
1765 1839 0.388520 TCGTCGTCCTCGTCGTCTAA 60.389 55.000 7.05 0.00 45.27 2.10
1767 1841 2.048784 TCGTCGTCCTCGTCGTCT 60.049 61.111 7.05 0.00 45.27 4.18
1905 1979 0.618458 TCCCTTGCAGGCTTCGTATT 59.382 50.000 0.00 0.00 32.73 1.89
2158 2232 3.753434 CGTCTGCGTCTCCAGCCT 61.753 66.667 0.00 0.00 32.87 4.58
2395 2493 3.474570 AGACTCCCTCGGCATGGC 61.475 66.667 9.69 9.69 0.00 4.40
2475 2639 1.456196 GCTGGTCGATCGAGATCCCA 61.456 60.000 20.09 20.19 34.40 4.37
2696 2881 1.129058 CGGGGCTACCTACTTGGATT 58.871 55.000 0.00 0.00 39.71 3.01
2706 2891 0.958876 CACCAAAGTTCGGGGCTACC 60.959 60.000 0.00 0.00 0.00 3.18
2885 3097 2.348998 CCAGTTCTTGAGCGCCCT 59.651 61.111 2.29 0.00 0.00 5.19
2971 3217 1.133253 CGCGTTCACCTGCAATCAG 59.867 57.895 0.00 0.00 40.02 2.90
3265 3511 2.027837 AGAATTTTTGACCTGCATGCCC 60.028 45.455 16.68 2.33 0.00 5.36
3281 3531 4.129148 GCAGGGGCGGGGAGAATT 62.129 66.667 0.00 0.00 0.00 2.17
3294 3544 2.481952 GTCAACTCAGTAAAGCAGCAGG 59.518 50.000 0.00 0.00 0.00 4.85
3393 3718 0.248134 GTCGGAGGAAGATCGTCGTG 60.248 60.000 8.60 0.00 32.46 4.35
3646 3975 9.717892 GGAAACTCAACAAAGTTAAAGTAGAAG 57.282 33.333 0.00 0.00 38.52 2.85
3689 4018 7.582435 TCTTGTTGTCGAGATAACTGAAATC 57.418 36.000 12.61 0.00 34.16 2.17
3755 4084 5.637810 TCTTGAGTCGGTTTGTATCATCAAC 59.362 40.000 0.00 0.00 0.00 3.18
3791 4120 0.889186 AAGTTGATGGTGTGGCGGAC 60.889 55.000 0.00 0.00 0.00 4.79
3792 4121 0.605319 GAAGTTGATGGTGTGGCGGA 60.605 55.000 0.00 0.00 0.00 5.54
4083 4412 5.215160 GTCAGCAAGTTGTCGATCAAAATT 58.785 37.500 4.48 0.00 37.81 1.82
4109 4438 2.416202 TGCTGTTACTCGCATCATGTTG 59.584 45.455 0.00 0.00 0.00 3.33
4147 4482 3.084039 CCCATCACTCAAAAGCTAAGCA 58.916 45.455 0.00 0.00 0.00 3.91
4175 4510 3.882444 TGATCATCTTGCCTTCCTCTTG 58.118 45.455 0.00 0.00 0.00 3.02
4176 4511 4.792513 ATGATCATCTTGCCTTCCTCTT 57.207 40.909 1.18 0.00 0.00 2.85
4179 4514 4.246712 ACAATGATCATCTTGCCTTCCT 57.753 40.909 9.06 0.00 0.00 3.36
4194 4529 5.398603 AACTCCAACAACAACAACAATGA 57.601 34.783 0.00 0.00 0.00 2.57
4580 4927 6.255237 GCTTTTCATACGAACTAGAGGTTACC 59.745 42.308 0.00 0.00 38.41 2.85
4618 4965 2.456119 GCAGCATTCGTGGACGGAG 61.456 63.158 0.00 0.00 40.29 4.63
4696 5043 5.302059 CGGGAACATACATAGAGAAAGAGGA 59.698 44.000 0.00 0.00 0.00 3.71
4717 5064 0.321671 CATACAGGTAGGGATGCGGG 59.678 60.000 0.00 0.00 0.00 6.13
4719 5066 1.412710 ACACATACAGGTAGGGATGCG 59.587 52.381 0.00 0.00 0.00 4.73
4731 5078 5.300539 ACATAACAACAAGCCAACACATACA 59.699 36.000 0.00 0.00 0.00 2.29
4735 5082 3.445450 ACACATAACAACAAGCCAACACA 59.555 39.130 0.00 0.00 0.00 3.72
4771 5118 3.319031 AATTCATGGATCCAACCCTCC 57.681 47.619 20.67 0.00 0.00 4.30
4812 5159 5.120053 TGTGAAATACTGTGTTATGTGCGAG 59.880 40.000 0.00 0.00 0.00 5.03
4814 5161 5.276240 TGTGAAATACTGTGTTATGTGCG 57.724 39.130 0.00 0.00 0.00 5.34
4826 5173 9.545105 TTCATGAAATTGCTTTTGTGAAATACT 57.455 25.926 5.45 0.00 31.14 2.12
4912 5261 6.378280 GTGGGATAATCTTGGTGAAGTCAAAT 59.622 38.462 0.00 0.00 0.00 2.32
4926 5275 7.792364 TCTGTATATTTCCGTGGGATAATCT 57.208 36.000 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.