Multiple sequence alignment - TraesCS7A01G251200

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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 TraesCS7A01G251200 chr7A 100.000 4329 0 0 1 4329 234523418 234527746 0.000000e+00 7995.0
1 TraesCS7A01G251200 chr7A 83.491 527 45 17 3838 4329 148175262 148175781 1.840000e-123 453.0
2 TraesCS7A01G251200 chr7A 80.050 401 56 15 1 391 42841967 42841581 4.260000e-70 276.0
3 TraesCS7A01G251200 chr7A 79.167 96 10 6 3828 3923 706847840 706847755 1.680000e-04 58.4
4 TraesCS7A01G251200 chr7D 95.618 3355 97 14 236 3553 223836074 223839415 0.000000e+00 5336.0
5 TraesCS7A01G251200 chr7D 93.289 298 19 1 3537 3833 223839369 223839666 5.140000e-119 438.0
6 TraesCS7A01G251200 chr7B 95.537 3137 92 20 448 3553 176244067 176240948 0.000000e+00 4974.0
7 TraesCS7A01G251200 chr7B 91.304 161 12 2 3608 3767 176240940 176240781 7.290000e-53 219.0
8 TraesCS7A01G251200 chr7B 80.460 174 26 1 3836 4001 717896042 717895869 4.540000e-25 126.0
9 TraesCS7A01G251200 chr7B 95.833 72 3 0 3762 3833 176240604 176240533 2.740000e-22 117.0
10 TraesCS7A01G251200 chrUn 86.233 523 41 14 3838 4329 928692 928170 4.930000e-149 538.0
11 TraesCS7A01G251200 chrUn 86.122 526 42 14 3835 4329 951012 951537 4.930000e-149 538.0
12 TraesCS7A01G251200 chr1A 86.233 523 41 14 3838 4329 514591912 514591390 4.930000e-149 538.0
13 TraesCS7A01G251200 chr1A 84.866 522 44 13 3837 4327 9964972 9965489 1.080000e-135 494.0
14 TraesCS7A01G251200 chr5B 81.096 529 62 15 3837 4329 474051605 474051079 5.250000e-104 388.0
15 TraesCS7A01G251200 chr4B 84.031 382 44 8 19 392 14138767 14138395 6.890000e-93 351.0
16 TraesCS7A01G251200 chr4B 85.305 279 39 2 4005 4283 596781256 596781532 1.970000e-73 287.0
17 TraesCS7A01G251200 chr3A 81.034 464 49 13 3837 4270 680761203 680761657 2.490000e-87 333.0
18 TraesCS7A01G251200 chr3A 80.051 396 49 10 6 391 414811120 414810745 2.570000e-67 267.0
19 TraesCS7A01G251200 chr2B 81.888 392 55 8 1 385 775137024 775137406 2.510000e-82 316.0
20 TraesCS7A01G251200 chr1B 81.047 401 58 10 1 393 32397560 32397170 1.960000e-78 303.0
21 TraesCS7A01G251200 chr5D 79.302 401 45 20 1 389 545258134 545258508 3.340000e-61 246.0
22 TraesCS7A01G251200 chr6D 78.292 281 54 6 2693 2968 115314860 115314582 1.600000e-39 174.0
23 TraesCS7A01G251200 chr6D 73.903 433 79 15 3837 4257 445401546 445401956 4.510000e-30 143.0
24 TraesCS7A01G251200 chr3D 80.976 205 32 6 1 202 583915032 583915232 5.800000e-34 156.0
25 TraesCS7A01G251200 chr2D 89.286 56 6 0 34 89 592641306 592641251 2.160000e-08 71.3


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 TraesCS7A01G251200 chr7A 234523418 234527746 4328 False 7995 7995 100.000000 1 4329 1 chr7A.!!$F2 4328
1 TraesCS7A01G251200 chr7A 148175262 148175781 519 False 453 453 83.491000 3838 4329 1 chr7A.!!$F1 491
2 TraesCS7A01G251200 chr7D 223836074 223839666 3592 False 2887 5336 94.453500 236 3833 2 chr7D.!!$F1 3597
3 TraesCS7A01G251200 chr7B 176240533 176244067 3534 True 1770 4974 94.224667 448 3833 3 chr7B.!!$R2 3385
4 TraesCS7A01G251200 chrUn 928170 928692 522 True 538 538 86.233000 3838 4329 1 chrUn.!!$R1 491
5 TraesCS7A01G251200 chrUn 951012 951537 525 False 538 538 86.122000 3835 4329 1 chrUn.!!$F1 494
6 TraesCS7A01G251200 chr1A 514591390 514591912 522 True 538 538 86.233000 3838 4329 1 chr1A.!!$R1 491
7 TraesCS7A01G251200 chr1A 9964972 9965489 517 False 494 494 84.866000 3837 4327 1 chr1A.!!$F1 490
8 TraesCS7A01G251200 chr5B 474051079 474051605 526 True 388 388 81.096000 3837 4329 1 chr5B.!!$R1 492

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
746 784 0.108615 ACACGCTCCCGAATTCTCTG 60.109 55.000 3.52 0.0 38.29 3.35 F
1239 1290 0.748005 GCGTCATATGCCACAAGGGT 60.748 55.000 0.00 0.0 39.65 4.34 F
2155 2207 1.201899 CGAGAGTACGACACCGAGAAC 60.202 57.143 0.00 0.0 39.50 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2345 2397 0.749649 AGGTCCTGCAGCTCGAATAG 59.250 55.0 8.66 0.0 0.0 1.73 R
2491 2543 0.973496 GCTCCTCGAACTCCTCCCTT 60.973 60.0 0.00 0.0 0.0 3.95 R
3851 4099 0.387239 GCGCCAAGTTTAAGCACCAG 60.387 55.0 0.00 0.0 0.0 4.00 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
18 19 2.555123 CACATGGTCCCTTCGTTGG 58.445 57.895 0.00 0.00 0.00 3.77
19 20 1.303317 ACATGGTCCCTTCGTTGGC 60.303 57.895 0.00 0.00 0.00 4.52
20 21 1.002134 CATGGTCCCTTCGTTGGCT 60.002 57.895 0.00 0.00 0.00 4.75
21 22 1.026718 CATGGTCCCTTCGTTGGCTC 61.027 60.000 0.00 0.00 0.00 4.70
22 23 2.046217 GGTCCCTTCGTTGGCTCC 60.046 66.667 0.00 0.00 0.00 4.70
23 24 2.046217 GTCCCTTCGTTGGCTCCC 60.046 66.667 0.00 0.00 0.00 4.30
24 25 3.702048 TCCCTTCGTTGGCTCCCG 61.702 66.667 0.00 0.00 0.00 5.14
27 28 4.735132 CTTCGTTGGCTCCCGCGA 62.735 66.667 8.23 0.00 36.88 5.87
28 29 4.735132 TTCGTTGGCTCCCGCGAG 62.735 66.667 8.23 0.00 35.70 5.03
63 64 4.563337 GGGACCCGATTGCTTTTTATAC 57.437 45.455 0.00 0.00 0.00 1.47
64 65 4.204799 GGGACCCGATTGCTTTTTATACT 58.795 43.478 0.00 0.00 0.00 2.12
65 66 4.643334 GGGACCCGATTGCTTTTTATACTT 59.357 41.667 0.00 0.00 0.00 2.24
66 67 5.126545 GGGACCCGATTGCTTTTTATACTTT 59.873 40.000 0.00 0.00 0.00 2.66
67 68 6.350696 GGGACCCGATTGCTTTTTATACTTTT 60.351 38.462 0.00 0.00 0.00 2.27
68 69 7.094631 GGACCCGATTGCTTTTTATACTTTTT 58.905 34.615 0.00 0.00 0.00 1.94
69 70 7.274904 GGACCCGATTGCTTTTTATACTTTTTC 59.725 37.037 0.00 0.00 0.00 2.29
70 71 6.804783 ACCCGATTGCTTTTTATACTTTTTCG 59.195 34.615 0.00 0.00 0.00 3.46
71 72 6.237463 CCCGATTGCTTTTTATACTTTTTCGC 60.237 38.462 0.00 0.00 0.00 4.70
72 73 6.306837 CCGATTGCTTTTTATACTTTTTCGCA 59.693 34.615 0.00 0.00 0.00 5.10
73 74 7.157699 CGATTGCTTTTTATACTTTTTCGCAC 58.842 34.615 0.00 0.00 0.00 5.34
74 75 6.427300 TTGCTTTTTATACTTTTTCGCACG 57.573 33.333 0.00 0.00 0.00 5.34
75 76 4.912766 TGCTTTTTATACTTTTTCGCACGG 59.087 37.500 0.00 0.00 0.00 4.94
76 77 5.148568 GCTTTTTATACTTTTTCGCACGGA 58.851 37.500 0.00 0.00 0.00 4.69
77 78 5.058856 GCTTTTTATACTTTTTCGCACGGAC 59.941 40.000 0.00 0.00 0.00 4.79
78 79 4.666928 TTTATACTTTTTCGCACGGACC 57.333 40.909 0.00 0.00 0.00 4.46
79 80 1.445871 ATACTTTTTCGCACGGACCC 58.554 50.000 0.00 0.00 0.00 4.46
80 81 0.945265 TACTTTTTCGCACGGACCCG 60.945 55.000 6.94 6.94 46.03 5.28
81 82 1.957186 CTTTTTCGCACGGACCCGA 60.957 57.895 16.07 1.37 42.83 5.14
82 83 1.296056 CTTTTTCGCACGGACCCGAT 61.296 55.000 16.07 0.00 42.83 4.18
83 84 0.885596 TTTTTCGCACGGACCCGATT 60.886 50.000 16.07 0.00 42.83 3.34
84 85 1.570347 TTTTCGCACGGACCCGATTG 61.570 55.000 16.07 5.10 42.83 2.67
87 88 2.746277 GCACGGACCCGATTGCTT 60.746 61.111 16.07 0.00 42.83 3.91
88 89 2.332654 GCACGGACCCGATTGCTTT 61.333 57.895 16.07 0.00 42.83 3.51
89 90 1.022451 GCACGGACCCGATTGCTTTA 61.022 55.000 16.07 0.00 42.83 1.85
90 91 1.444836 CACGGACCCGATTGCTTTAA 58.555 50.000 16.07 0.00 42.83 1.52
91 92 1.807742 CACGGACCCGATTGCTTTAAA 59.192 47.619 16.07 0.00 42.83 1.52
92 93 2.226912 CACGGACCCGATTGCTTTAAAA 59.773 45.455 16.07 0.00 42.83 1.52
93 94 2.885894 ACGGACCCGATTGCTTTAAAAA 59.114 40.909 16.07 0.00 42.83 1.94
113 114 5.405935 AAAAATTACAGGGACCTGATTGC 57.594 39.130 24.31 0.00 46.30 3.56
114 115 2.736670 ATTACAGGGACCTGATTGCC 57.263 50.000 24.31 0.00 46.30 4.52
115 116 1.668826 TTACAGGGACCTGATTGCCT 58.331 50.000 24.31 3.88 46.30 4.75
116 117 1.668826 TACAGGGACCTGATTGCCTT 58.331 50.000 24.31 3.16 46.30 4.35
117 118 0.779997 ACAGGGACCTGATTGCCTTT 59.220 50.000 24.31 0.00 46.30 3.11
118 119 1.147817 ACAGGGACCTGATTGCCTTTT 59.852 47.619 24.31 0.00 46.30 2.27
119 120 2.250924 CAGGGACCTGATTGCCTTTTT 58.749 47.619 13.06 0.00 46.30 1.94
146 147 9.807921 TTTTCTTATTTCTAGGGACATGAAAGT 57.192 29.630 0.00 0.00 35.92 2.66
147 148 9.449719 TTTCTTATTTCTAGGGACATGAAAGTC 57.550 33.333 0.00 0.00 35.92 3.01
148 149 8.380742 TCTTATTTCTAGGGACATGAAAGTCT 57.619 34.615 0.00 0.00 38.57 3.24
149 150 8.826765 TCTTATTTCTAGGGACATGAAAGTCTT 58.173 33.333 0.00 0.00 38.57 3.01
150 151 9.454859 CTTATTTCTAGGGACATGAAAGTCTTT 57.545 33.333 0.00 0.00 38.57 2.52
151 152 7.929941 ATTTCTAGGGACATGAAAGTCTTTC 57.070 36.000 16.99 16.99 38.57 2.62
165 166 7.441017 TGAAAGTCTTTCAAAAATATGTGGGG 58.559 34.615 22.87 0.00 45.94 4.96
166 167 5.405935 AGTCTTTCAAAAATATGTGGGGC 57.594 39.130 0.00 0.00 0.00 5.80
167 168 4.222810 AGTCTTTCAAAAATATGTGGGGCC 59.777 41.667 0.00 0.00 0.00 5.80
168 169 3.517500 TCTTTCAAAAATATGTGGGGCCC 59.482 43.478 18.17 18.17 0.00 5.80
169 170 2.630889 TCAAAAATATGTGGGGCCCA 57.369 45.000 24.76 24.76 0.00 5.36
170 171 3.127791 TCAAAAATATGTGGGGCCCAT 57.872 42.857 31.48 17.17 35.28 4.00
171 172 2.770802 TCAAAAATATGTGGGGCCCATG 59.229 45.455 31.48 20.18 35.28 3.66
172 173 2.504996 CAAAAATATGTGGGGCCCATGT 59.495 45.455 31.48 22.30 35.28 3.21
173 174 3.697190 AAAATATGTGGGGCCCATGTA 57.303 42.857 31.48 23.74 35.28 2.29
174 175 3.921287 AAATATGTGGGGCCCATGTAT 57.079 42.857 31.48 24.85 35.28 2.29
175 176 3.456380 AATATGTGGGGCCCATGTATC 57.544 47.619 31.48 16.36 35.28 2.24
176 177 1.826447 TATGTGGGGCCCATGTATCA 58.174 50.000 31.48 22.03 35.28 2.15
177 178 1.160702 ATGTGGGGCCCATGTATCAT 58.839 50.000 31.48 23.35 35.28 2.45
178 179 0.185658 TGTGGGGCCCATGTATCATG 59.814 55.000 31.48 3.11 35.28 3.07
179 180 0.540365 GTGGGGCCCATGTATCATGG 60.540 60.000 31.48 18.51 35.28 3.66
180 181 1.607467 GGGGCCCATGTATCATGGC 60.607 63.158 26.86 15.24 43.26 4.40
183 184 2.649831 GCCCATGTATCATGGCCTG 58.350 57.895 19.65 10.07 37.94 4.85
184 185 0.178981 GCCCATGTATCATGGCCTGT 60.179 55.000 19.65 0.00 37.94 4.00
185 186 1.755265 GCCCATGTATCATGGCCTGTT 60.755 52.381 19.65 0.00 37.94 3.16
186 187 2.488891 GCCCATGTATCATGGCCTGTTA 60.489 50.000 19.65 0.00 37.94 2.41
187 188 3.831323 CCCATGTATCATGGCCTGTTAA 58.169 45.455 19.65 0.00 37.85 2.01
188 189 3.569701 CCCATGTATCATGGCCTGTTAAC 59.430 47.826 19.65 0.00 37.85 2.01
189 190 3.250762 CCATGTATCATGGCCTGTTAACG 59.749 47.826 14.50 0.00 31.75 3.18
190 191 2.912771 TGTATCATGGCCTGTTAACGG 58.087 47.619 3.32 7.51 0.00 4.44
191 192 2.237643 TGTATCATGGCCTGTTAACGGT 59.762 45.455 13.35 0.00 0.00 4.83
192 193 2.038387 ATCATGGCCTGTTAACGGTC 57.962 50.000 13.35 12.78 0.00 4.79
193 194 0.687920 TCATGGCCTGTTAACGGTCA 59.312 50.000 20.58 20.58 40.98 4.02
194 195 1.072489 TCATGGCCTGTTAACGGTCAA 59.928 47.619 21.64 1.59 39.97 3.18
195 196 1.199097 CATGGCCTGTTAACGGTCAAC 59.801 52.381 21.64 7.58 39.97 3.18
196 197 0.535553 TGGCCTGTTAACGGTCAACC 60.536 55.000 17.50 11.78 32.23 3.77
197 198 0.250597 GGCCTGTTAACGGTCAACCT 60.251 55.000 13.35 0.00 0.00 3.50
198 199 1.002315 GGCCTGTTAACGGTCAACCTA 59.998 52.381 13.35 0.00 0.00 3.08
199 200 2.550639 GGCCTGTTAACGGTCAACCTAA 60.551 50.000 13.35 0.00 0.00 2.69
200 201 2.481568 GCCTGTTAACGGTCAACCTAAC 59.518 50.000 13.35 1.65 31.18 2.34
201 202 2.733026 CCTGTTAACGGTCAACCTAACG 59.267 50.000 13.35 0.00 32.42 3.18
202 203 2.733026 CTGTTAACGGTCAACCTAACGG 59.267 50.000 6.25 6.02 32.42 4.44
204 205 2.723124 TAACGGTCAACCTAACGGTC 57.277 50.000 0.00 0.00 44.73 4.79
205 206 0.752054 AACGGTCAACCTAACGGTCA 59.248 50.000 0.00 0.00 44.73 4.02
206 207 0.752054 ACGGTCAACCTAACGGTCAA 59.248 50.000 0.00 0.00 44.73 3.18
207 208 1.138661 ACGGTCAACCTAACGGTCAAA 59.861 47.619 0.00 0.00 44.73 2.69
208 209 1.796459 CGGTCAACCTAACGGTCAAAG 59.204 52.381 0.00 0.00 44.73 2.77
209 210 1.534163 GGTCAACCTAACGGTCAAAGC 59.466 52.381 0.00 0.00 44.73 3.51
210 211 2.490991 GTCAACCTAACGGTCAAAGCT 58.509 47.619 0.00 0.00 44.73 3.74
211 212 3.555586 GGTCAACCTAACGGTCAAAGCTA 60.556 47.826 0.00 0.00 44.73 3.32
212 213 4.251268 GTCAACCTAACGGTCAAAGCTAT 58.749 43.478 0.00 0.00 44.73 2.97
213 214 4.329256 GTCAACCTAACGGTCAAAGCTATC 59.671 45.833 0.00 0.00 44.73 2.08
214 215 4.020928 TCAACCTAACGGTCAAAGCTATCA 60.021 41.667 0.00 0.00 44.73 2.15
215 216 4.124851 ACCTAACGGTCAAAGCTATCAG 57.875 45.455 0.00 0.00 40.27 2.90
216 217 3.514309 ACCTAACGGTCAAAGCTATCAGT 59.486 43.478 0.00 0.00 40.27 3.41
217 218 4.113354 CCTAACGGTCAAAGCTATCAGTC 58.887 47.826 0.00 0.00 0.00 3.51
218 219 3.678056 AACGGTCAAAGCTATCAGTCA 57.322 42.857 0.00 0.00 0.00 3.41
219 220 3.678056 ACGGTCAAAGCTATCAGTCAA 57.322 42.857 0.00 0.00 0.00 3.18
220 221 4.207891 ACGGTCAAAGCTATCAGTCAAT 57.792 40.909 0.00 0.00 0.00 2.57
221 222 4.184629 ACGGTCAAAGCTATCAGTCAATC 58.815 43.478 0.00 0.00 0.00 2.67
222 223 4.081420 ACGGTCAAAGCTATCAGTCAATCT 60.081 41.667 0.00 0.00 0.00 2.40
223 224 4.269603 CGGTCAAAGCTATCAGTCAATCTG 59.730 45.833 0.00 0.00 44.85 2.90
307 308 5.615289 TGGAACAACCAACCAAATTTATGG 58.385 37.500 12.78 12.78 46.75 2.74
375 376 8.705594 ACATACATAGCTTGTAATGAGGTAGTT 58.294 33.333 11.18 0.00 43.84 2.24
429 430 2.972505 GCACACCACACCACGAGG 60.973 66.667 0.00 0.00 42.21 4.63
456 482 2.156697 GCAGAGAAAAGAAGTCGACTGC 59.843 50.000 20.85 18.55 40.25 4.40
457 483 3.648009 CAGAGAAAAGAAGTCGACTGCT 58.352 45.455 21.04 21.04 31.69 4.24
490 517 4.430441 AGTCAGTCCCAATTTCTAGAGGT 58.570 43.478 0.00 0.00 0.00 3.85
502 529 2.536066 TCTAGAGGTACTGCTGCCAAA 58.464 47.619 0.00 0.00 41.55 3.28
509 536 2.288213 GGTACTGCTGCCAAAAAGGTTC 60.288 50.000 0.00 0.00 40.61 3.62
518 545 3.386402 TGCCAAAAAGGTTCCTCGAAAAT 59.614 39.130 0.00 0.00 40.61 1.82
746 784 0.108615 ACACGCTCCCGAATTCTCTG 60.109 55.000 3.52 0.00 38.29 3.35
1239 1290 0.748005 GCGTCATATGCCACAAGGGT 60.748 55.000 0.00 0.00 39.65 4.34
1332 1383 3.459063 GGCCTCCGCTCGGTTAGT 61.459 66.667 8.28 0.00 36.47 2.24
1807 1859 1.403323 GGTGCAGGCAATAAGAAGCTC 59.597 52.381 0.00 0.00 0.00 4.09
1864 1916 2.910479 ACGTCACTGACTCCGGCA 60.910 61.111 7.58 0.00 0.00 5.69
2155 2207 1.201899 CGAGAGTACGACACCGAGAAC 60.202 57.143 0.00 0.00 39.50 3.01
2167 2219 2.506438 GAGAACTTCGGCCCGTCG 60.506 66.667 1.63 0.00 0.00 5.12
2491 2543 2.577059 GAGATGAACCGCGTGGGA 59.423 61.111 21.14 2.72 40.75 4.37
3081 3133 2.435059 GGAGAAGTGGCTGCGGAC 60.435 66.667 0.00 0.00 0.00 4.79
3129 3181 4.821589 CGAGGCGGACAAGGAGGC 62.822 72.222 0.00 0.00 0.00 4.70
3313 3365 0.389948 GCGACGAGGACTTCACCAAT 60.390 55.000 0.00 0.00 0.00 3.16
3392 3444 2.424956 GTCCGTCTAACGACCCAACTAT 59.575 50.000 0.24 0.00 46.05 2.12
3519 3584 4.797800 TCTTCTCTCAGTTCACCATCTG 57.202 45.455 0.00 0.00 0.00 2.90
3526 3591 6.042093 TCTCTCAGTTCACCATCTGTAGTTTT 59.958 38.462 0.00 0.00 33.89 2.43
3527 3592 6.591935 TCTCAGTTCACCATCTGTAGTTTTT 58.408 36.000 0.00 0.00 33.89 1.94
3528 3593 6.706270 TCTCAGTTCACCATCTGTAGTTTTTC 59.294 38.462 0.00 0.00 33.89 2.29
3529 3594 6.591935 TCAGTTCACCATCTGTAGTTTTTCT 58.408 36.000 0.00 0.00 33.89 2.52
3530 3595 7.054124 TCAGTTCACCATCTGTAGTTTTTCTT 58.946 34.615 0.00 0.00 33.89 2.52
3531 3596 7.556275 TCAGTTCACCATCTGTAGTTTTTCTTT 59.444 33.333 0.00 0.00 33.89 2.52
3532 3597 8.836413 CAGTTCACCATCTGTAGTTTTTCTTTA 58.164 33.333 0.00 0.00 0.00 1.85
3533 3598 9.403583 AGTTCACCATCTGTAGTTTTTCTTTAA 57.596 29.630 0.00 0.00 0.00 1.52
3534 3599 9.447040 GTTCACCATCTGTAGTTTTTCTTTAAC 57.553 33.333 0.00 0.00 0.00 2.01
3535 3600 8.740123 TCACCATCTGTAGTTTTTCTTTAACA 57.260 30.769 0.00 0.00 0.00 2.41
3536 3601 8.617809 TCACCATCTGTAGTTTTTCTTTAACAC 58.382 33.333 0.00 0.00 0.00 3.32
3537 3602 8.402472 CACCATCTGTAGTTTTTCTTTAACACA 58.598 33.333 0.00 0.00 0.00 3.72
3538 3603 8.621286 ACCATCTGTAGTTTTTCTTTAACACAG 58.379 33.333 0.00 0.00 36.76 3.66
3539 3604 8.621286 CCATCTGTAGTTTTTCTTTAACACAGT 58.379 33.333 0.00 0.00 36.77 3.55
3542 3607 9.444600 TCTGTAGTTTTTCTTTAACACAGTTCT 57.555 29.630 0.00 0.00 36.77 3.01
3543 3608 9.704098 CTGTAGTTTTTCTTTAACACAGTTCTC 57.296 33.333 0.00 0.00 34.13 2.87
3544 3609 8.671028 TGTAGTTTTTCTTTAACACAGTTCTCC 58.329 33.333 0.00 0.00 0.00 3.71
3545 3610 6.782150 AGTTTTTCTTTAACACAGTTCTCCG 58.218 36.000 0.00 0.00 0.00 4.63
3546 3611 6.373495 AGTTTTTCTTTAACACAGTTCTCCGT 59.627 34.615 0.00 0.00 0.00 4.69
3547 3612 5.978934 TTTCTTTAACACAGTTCTCCGTC 57.021 39.130 0.00 0.00 0.00 4.79
3548 3613 4.931661 TCTTTAACACAGTTCTCCGTCT 57.068 40.909 0.00 0.00 0.00 4.18
3549 3614 5.272283 TCTTTAACACAGTTCTCCGTCTT 57.728 39.130 0.00 0.00 0.00 3.01
3550 3615 5.667466 TCTTTAACACAGTTCTCCGTCTTT 58.333 37.500 0.00 0.00 0.00 2.52
3551 3616 6.808829 TCTTTAACACAGTTCTCCGTCTTTA 58.191 36.000 0.00 0.00 0.00 1.85
3552 3617 6.921857 TCTTTAACACAGTTCTCCGTCTTTAG 59.078 38.462 0.00 0.00 0.00 1.85
3592 3657 9.118300 AGTTCTCCATCTTTAGCTAATTGATTG 57.882 33.333 7.08 10.03 0.00 2.67
3627 3693 6.660949 TCTCAGTGTTCATCTGATGTTCTCTA 59.339 38.462 16.66 0.00 40.46 2.43
3698 3764 3.845781 ACAGATCCTGTTCACAGTTGT 57.154 42.857 6.22 2.88 42.59 3.32
3717 3783 6.426633 CAGTTGTAAAATTTAGGGCCTTTTGG 59.573 38.462 13.45 0.00 44.18 3.28
3735 3801 9.435688 GCCTTTTGGTTCACATAATTCTAAAAT 57.564 29.630 0.00 0.00 42.99 1.82
3741 3807 7.148154 TGGTTCACATAATTCTAAAATCACGGG 60.148 37.037 0.00 0.00 0.00 5.28
3745 3811 5.885912 ACATAATTCTAAAATCACGGGCAGT 59.114 36.000 0.00 0.00 0.00 4.40
3748 3814 4.811969 TTCTAAAATCACGGGCAGTAGA 57.188 40.909 0.00 0.00 0.00 2.59
3779 4027 3.687572 AGATTGAAATGTCATGCTCGC 57.312 42.857 0.00 0.00 32.48 5.03
3872 4120 2.796227 GTGCTTAAACTTGGCGCAC 58.204 52.632 10.83 0.00 43.22 5.34
3924 4180 2.195567 GGTGCAGCAACTTGGCTCA 61.196 57.895 11.86 0.00 43.68 4.26
3933 4189 0.882042 AACTTGGCTCAGACGTGCAG 60.882 55.000 0.00 0.00 33.19 4.41
3937 4193 1.114627 TGGCTCAGACGTGCAGATAT 58.885 50.000 0.00 0.00 33.19 1.63
3981 4237 1.808411 AATCGATGTTGACTTGGCGT 58.192 45.000 0.00 0.00 0.00 5.68
4044 4327 3.301274 TGTGAAAACCCCCTCGAAAAAT 58.699 40.909 0.00 0.00 0.00 1.82
4081 4365 1.972872 CCCCTATCAACATGACAGCC 58.027 55.000 0.00 0.00 0.00 4.85
4082 4366 1.477558 CCCCTATCAACATGACAGCCC 60.478 57.143 0.00 0.00 0.00 5.19
4107 4391 7.069085 CCCCATTTCATTTTGACTCTATGACAT 59.931 37.037 0.00 0.00 0.00 3.06
4151 4437 6.961576 ACGTGAAAATAAAAACGGATCAGAA 58.038 32.000 0.00 0.00 40.25 3.02
4183 4469 2.807967 CTCGAACTCAAGACCAATTGCA 59.192 45.455 0.00 0.00 0.00 4.08
4203 4489 2.037772 CAGGATAGCTAGCCGTCCAAAT 59.962 50.000 28.14 12.44 36.72 2.32
4219 4507 4.157840 GTCCAAATAACTCCACCATTCACC 59.842 45.833 0.00 0.00 0.00 4.02
4241 4529 6.750501 CACCTTTGCAATGAGAATTACTGATG 59.249 38.462 13.58 0.00 0.00 3.07
4242 4530 6.127535 ACCTTTGCAATGAGAATTACTGATGG 60.128 38.462 13.58 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.586154 GCCAACGAAGGGACCATGTG 61.586 60.000 0.00 0.00 0.00 3.21
1 2 1.303317 GCCAACGAAGGGACCATGT 60.303 57.895 0.00 0.00 0.00 3.21
2 3 1.002134 AGCCAACGAAGGGACCATG 60.002 57.895 0.00 0.00 0.00 3.66
3 4 1.299976 GAGCCAACGAAGGGACCAT 59.700 57.895 0.00 0.00 0.00 3.55
4 5 2.747686 GAGCCAACGAAGGGACCA 59.252 61.111 0.00 0.00 0.00 4.02
5 6 2.046217 GGAGCCAACGAAGGGACC 60.046 66.667 0.00 0.00 0.00 4.46
6 7 2.046217 GGGAGCCAACGAAGGGAC 60.046 66.667 0.00 0.00 0.00 4.46
7 8 3.702048 CGGGAGCCAACGAAGGGA 61.702 66.667 0.00 0.00 0.00 4.20
41 42 1.842052 TAAAAAGCAATCGGGTCCCC 58.158 50.000 1.00 0.00 0.00 4.81
42 43 4.204799 AGTATAAAAAGCAATCGGGTCCC 58.795 43.478 0.00 0.00 0.00 4.46
43 44 5.830000 AAGTATAAAAAGCAATCGGGTCC 57.170 39.130 0.00 0.00 0.00 4.46
44 45 7.007995 CGAAAAAGTATAAAAAGCAATCGGGTC 59.992 37.037 0.00 0.00 0.00 4.46
45 46 6.804783 CGAAAAAGTATAAAAAGCAATCGGGT 59.195 34.615 0.00 0.00 0.00 5.28
46 47 6.237463 GCGAAAAAGTATAAAAAGCAATCGGG 60.237 38.462 0.00 0.00 0.00 5.14
47 48 6.306837 TGCGAAAAAGTATAAAAAGCAATCGG 59.693 34.615 0.00 0.00 0.00 4.18
48 49 7.157699 GTGCGAAAAAGTATAAAAAGCAATCG 58.842 34.615 0.00 0.00 33.75 3.34
49 50 7.157699 CGTGCGAAAAAGTATAAAAAGCAATC 58.842 34.615 0.00 0.00 33.75 2.67
50 51 6.088883 CCGTGCGAAAAAGTATAAAAAGCAAT 59.911 34.615 0.00 0.00 33.75 3.56
51 52 5.399892 CCGTGCGAAAAAGTATAAAAAGCAA 59.600 36.000 0.00 0.00 33.75 3.91
52 53 4.912766 CCGTGCGAAAAAGTATAAAAAGCA 59.087 37.500 0.00 0.00 0.00 3.91
53 54 5.058856 GTCCGTGCGAAAAAGTATAAAAAGC 59.941 40.000 0.00 0.00 0.00 3.51
54 55 5.566395 GGTCCGTGCGAAAAAGTATAAAAAG 59.434 40.000 0.00 0.00 0.00 2.27
55 56 5.451039 GGTCCGTGCGAAAAAGTATAAAAA 58.549 37.500 0.00 0.00 0.00 1.94
56 57 4.083377 GGGTCCGTGCGAAAAAGTATAAAA 60.083 41.667 0.00 0.00 0.00 1.52
57 58 3.436359 GGGTCCGTGCGAAAAAGTATAAA 59.564 43.478 0.00 0.00 0.00 1.40
58 59 3.002102 GGGTCCGTGCGAAAAAGTATAA 58.998 45.455 0.00 0.00 0.00 0.98
59 60 2.620242 GGGTCCGTGCGAAAAAGTATA 58.380 47.619 0.00 0.00 0.00 1.47
60 61 1.445871 GGGTCCGTGCGAAAAAGTAT 58.554 50.000 0.00 0.00 0.00 2.12
61 62 0.945265 CGGGTCCGTGCGAAAAAGTA 60.945 55.000 0.55 0.00 34.35 2.24
62 63 2.248835 CGGGTCCGTGCGAAAAAGT 61.249 57.895 0.55 0.00 34.35 2.66
63 64 1.296056 ATCGGGTCCGTGCGAAAAAG 61.296 55.000 9.36 0.00 40.74 2.27
64 65 0.885596 AATCGGGTCCGTGCGAAAAA 60.886 50.000 9.36 0.00 40.74 1.94
65 66 1.301874 AATCGGGTCCGTGCGAAAA 60.302 52.632 9.36 0.00 40.74 2.29
66 67 2.030401 CAATCGGGTCCGTGCGAAA 61.030 57.895 9.36 0.00 40.74 3.46
67 68 2.433491 CAATCGGGTCCGTGCGAA 60.433 61.111 9.36 0.00 40.74 4.70
70 71 1.022451 TAAAGCAATCGGGTCCGTGC 61.022 55.000 14.54 14.54 40.27 5.34
71 72 1.444836 TTAAAGCAATCGGGTCCGTG 58.555 50.000 9.36 2.66 40.74 4.94
72 73 2.188062 TTTAAAGCAATCGGGTCCGT 57.812 45.000 9.36 0.00 40.74 4.69
73 74 3.562567 TTTTTAAAGCAATCGGGTCCG 57.437 42.857 2.52 2.52 41.35 4.79
91 92 4.222810 GGCAATCAGGTCCCTGTAATTTTT 59.777 41.667 12.88 0.00 43.96 1.94
92 93 3.769300 GGCAATCAGGTCCCTGTAATTTT 59.231 43.478 12.88 0.00 43.96 1.82
93 94 3.011708 AGGCAATCAGGTCCCTGTAATTT 59.988 43.478 12.88 1.54 43.96 1.82
94 95 2.582636 AGGCAATCAGGTCCCTGTAATT 59.417 45.455 12.88 4.14 43.96 1.40
95 96 2.208872 AGGCAATCAGGTCCCTGTAAT 58.791 47.619 12.88 0.00 43.96 1.89
96 97 1.668826 AGGCAATCAGGTCCCTGTAA 58.331 50.000 12.88 0.00 43.96 2.41
97 98 1.668826 AAGGCAATCAGGTCCCTGTA 58.331 50.000 12.88 1.17 43.96 2.74
98 99 0.779997 AAAGGCAATCAGGTCCCTGT 59.220 50.000 12.88 0.00 43.96 4.00
99 100 1.928868 AAAAGGCAATCAGGTCCCTG 58.071 50.000 7.02 7.02 44.86 4.45
100 101 2.702270 AAAAAGGCAATCAGGTCCCT 57.298 45.000 0.00 0.00 0.00 4.20
120 121 9.807921 ACTTTCATGTCCCTAGAAATAAGAAAA 57.192 29.630 0.00 0.00 31.58 2.29
121 122 9.449719 GACTTTCATGTCCCTAGAAATAAGAAA 57.550 33.333 0.00 0.00 31.58 2.52
122 123 8.826765 AGACTTTCATGTCCCTAGAAATAAGAA 58.173 33.333 0.00 0.00 37.66 2.52
123 124 8.380742 AGACTTTCATGTCCCTAGAAATAAGA 57.619 34.615 0.00 0.00 37.66 2.10
124 125 9.454859 AAAGACTTTCATGTCCCTAGAAATAAG 57.545 33.333 0.00 0.00 37.66 1.73
125 126 9.449719 GAAAGACTTTCATGTCCCTAGAAATAA 57.550 33.333 20.70 0.00 39.45 1.40
126 127 8.602424 TGAAAGACTTTCATGTCCCTAGAAATA 58.398 33.333 23.67 0.00 44.21 1.40
127 128 7.461749 TGAAAGACTTTCATGTCCCTAGAAAT 58.538 34.615 23.67 0.00 44.21 2.17
128 129 6.837312 TGAAAGACTTTCATGTCCCTAGAAA 58.163 36.000 23.67 0.00 44.21 2.52
129 130 6.433847 TGAAAGACTTTCATGTCCCTAGAA 57.566 37.500 23.67 0.00 44.21 2.10
141 142 6.368791 GCCCCACATATTTTTGAAAGACTTTC 59.631 38.462 19.17 19.17 40.08 2.62
142 143 6.230472 GCCCCACATATTTTTGAAAGACTTT 58.770 36.000 0.00 0.00 0.00 2.66
143 144 5.279960 GGCCCCACATATTTTTGAAAGACTT 60.280 40.000 0.00 0.00 0.00 3.01
144 145 4.222810 GGCCCCACATATTTTTGAAAGACT 59.777 41.667 0.00 0.00 0.00 3.24
145 146 4.503910 GGCCCCACATATTTTTGAAAGAC 58.496 43.478 0.00 0.00 0.00 3.01
146 147 3.517500 GGGCCCCACATATTTTTGAAAGA 59.482 43.478 12.23 0.00 0.00 2.52
147 148 3.262915 TGGGCCCCACATATTTTTGAAAG 59.737 43.478 22.27 0.00 0.00 2.62
148 149 3.251484 TGGGCCCCACATATTTTTGAAA 58.749 40.909 22.27 0.00 0.00 2.69
149 150 2.907892 TGGGCCCCACATATTTTTGAA 58.092 42.857 22.27 0.00 0.00 2.69
150 151 2.630889 TGGGCCCCACATATTTTTGA 57.369 45.000 22.27 0.00 0.00 2.69
151 152 2.504996 ACATGGGCCCCACATATTTTTG 59.495 45.455 22.27 0.00 35.80 2.44
152 153 2.844369 ACATGGGCCCCACATATTTTT 58.156 42.857 22.27 0.00 35.80 1.94
153 154 2.566708 ACATGGGCCCCACATATTTT 57.433 45.000 22.27 0.00 35.80 1.82
154 155 3.141838 TGATACATGGGCCCCACATATTT 59.858 43.478 22.27 0.41 35.80 1.40
155 156 2.721355 TGATACATGGGCCCCACATATT 59.279 45.455 22.27 0.00 35.80 1.28
156 157 2.357274 TGATACATGGGCCCCACATAT 58.643 47.619 22.27 11.98 35.80 1.78
157 158 1.826447 TGATACATGGGCCCCACATA 58.174 50.000 22.27 6.99 35.80 2.29
158 159 1.160702 ATGATACATGGGCCCCACAT 58.839 50.000 22.27 12.42 35.80 3.21
159 160 0.185658 CATGATACATGGGCCCCACA 59.814 55.000 22.27 10.57 35.80 4.17
160 161 0.540365 CCATGATACATGGGCCCCAC 60.540 60.000 22.27 4.66 35.80 4.61
161 162 1.852707 CCATGATACATGGGCCCCA 59.147 57.895 22.27 4.05 38.19 4.96
162 163 1.607467 GCCATGATACATGGGCCCC 60.607 63.158 22.27 2.17 40.55 5.80
163 164 4.102113 GCCATGATACATGGGCCC 57.898 61.111 25.48 17.59 40.55 5.80
166 167 2.369983 AACAGGCCATGATACATGGG 57.630 50.000 25.48 15.03 39.53 4.00
167 168 3.250762 CGTTAACAGGCCATGATACATGG 59.749 47.826 21.86 21.86 41.99 3.66
168 169 3.250762 CCGTTAACAGGCCATGATACATG 59.749 47.826 5.01 4.94 0.00 3.21
169 170 3.118038 ACCGTTAACAGGCCATGATACAT 60.118 43.478 5.01 0.00 0.00 2.29
170 171 2.237643 ACCGTTAACAGGCCATGATACA 59.762 45.455 5.01 0.00 0.00 2.29
171 172 2.870411 GACCGTTAACAGGCCATGATAC 59.130 50.000 5.01 0.00 0.00 2.24
172 173 2.502130 TGACCGTTAACAGGCCATGATA 59.498 45.455 5.01 0.00 0.00 2.15
173 174 1.280710 TGACCGTTAACAGGCCATGAT 59.719 47.619 5.01 0.00 0.00 2.45
174 175 0.687920 TGACCGTTAACAGGCCATGA 59.312 50.000 5.01 0.00 0.00 3.07
175 176 1.199097 GTTGACCGTTAACAGGCCATG 59.801 52.381 5.01 2.64 0.00 3.66
176 177 1.530323 GTTGACCGTTAACAGGCCAT 58.470 50.000 5.01 0.00 0.00 4.40
177 178 0.535553 GGTTGACCGTTAACAGGCCA 60.536 55.000 5.01 8.39 0.00 5.36
178 179 0.250597 AGGTTGACCGTTAACAGGCC 60.251 55.000 14.00 0.00 42.08 5.19
179 180 2.460757 TAGGTTGACCGTTAACAGGC 57.539 50.000 14.00 2.21 42.08 4.85
180 181 2.733026 CGTTAGGTTGACCGTTAACAGG 59.267 50.000 6.39 10.27 42.08 4.00
181 182 2.733026 CCGTTAGGTTGACCGTTAACAG 59.267 50.000 6.39 0.00 42.08 3.16
182 183 2.753296 CCGTTAGGTTGACCGTTAACA 58.247 47.619 6.39 0.00 42.08 2.41
195 196 4.113354 GACTGATAGCTTTGACCGTTAGG 58.887 47.826 0.00 0.00 45.13 2.69
196 197 4.744570 TGACTGATAGCTTTGACCGTTAG 58.255 43.478 0.00 0.00 0.00 2.34
197 198 4.794278 TGACTGATAGCTTTGACCGTTA 57.206 40.909 0.00 0.00 0.00 3.18
198 199 3.678056 TGACTGATAGCTTTGACCGTT 57.322 42.857 0.00 0.00 0.00 4.44
199 200 3.678056 TTGACTGATAGCTTTGACCGT 57.322 42.857 0.00 0.00 0.00 4.83
200 201 4.437239 AGATTGACTGATAGCTTTGACCG 58.563 43.478 0.00 0.00 0.00 4.79
216 217 2.054021 TGGGTCCACTTGTCAGATTGA 58.946 47.619 0.00 0.00 0.00 2.57
217 218 2.566833 TGGGTCCACTTGTCAGATTG 57.433 50.000 0.00 0.00 0.00 2.67
218 219 2.443255 ACTTGGGTCCACTTGTCAGATT 59.557 45.455 0.00 0.00 0.00 2.40
219 220 2.057922 ACTTGGGTCCACTTGTCAGAT 58.942 47.619 0.00 0.00 0.00 2.90
220 221 1.507140 ACTTGGGTCCACTTGTCAGA 58.493 50.000 0.00 0.00 0.00 3.27
221 222 1.949525 CAACTTGGGTCCACTTGTCAG 59.050 52.381 0.00 0.00 0.00 3.51
222 223 1.283613 ACAACTTGGGTCCACTTGTCA 59.716 47.619 6.47 0.00 0.00 3.58
223 224 1.947456 GACAACTTGGGTCCACTTGTC 59.053 52.381 17.22 17.22 37.03 3.18
224 225 1.283613 TGACAACTTGGGTCCACTTGT 59.716 47.619 10.43 10.43 34.36 3.16
225 226 2.051334 TGACAACTTGGGTCCACTTG 57.949 50.000 0.00 0.00 34.36 3.16
226 227 4.447138 TTATGACAACTTGGGTCCACTT 57.553 40.909 0.00 0.00 34.36 3.16
227 228 4.657814 ATTATGACAACTTGGGTCCACT 57.342 40.909 0.00 0.00 34.36 4.00
228 229 5.722021 AAATTATGACAACTTGGGTCCAC 57.278 39.130 0.00 0.00 34.36 4.02
229 230 5.510520 GCAAAATTATGACAACTTGGGTCCA 60.511 40.000 0.00 0.00 34.36 4.02
230 231 4.929211 GCAAAATTATGACAACTTGGGTCC 59.071 41.667 0.00 0.00 34.36 4.46
231 232 5.783111 AGCAAAATTATGACAACTTGGGTC 58.217 37.500 0.00 0.00 35.83 4.46
232 233 5.806654 AGCAAAATTATGACAACTTGGGT 57.193 34.783 0.00 0.00 0.00 4.51
233 234 8.600449 TTTAAGCAAAATTATGACAACTTGGG 57.400 30.769 0.00 0.00 0.00 4.12
234 235 9.862585 GTTTTAAGCAAAATTATGACAACTTGG 57.137 29.630 0.00 0.00 36.10 3.61
345 346 7.829211 ACCTCATTACAAGCTATGTATGTTTGT 59.171 33.333 8.82 0.00 43.84 2.83
346 347 8.213518 ACCTCATTACAAGCTATGTATGTTTG 57.786 34.615 8.82 2.23 43.84 2.93
347 348 9.547753 CTACCTCATTACAAGCTATGTATGTTT 57.452 33.333 8.82 0.00 43.84 2.83
348 349 8.705594 ACTACCTCATTACAAGCTATGTATGTT 58.294 33.333 8.82 0.00 43.84 2.71
349 350 8.251383 ACTACCTCATTACAAGCTATGTATGT 57.749 34.615 8.82 2.08 43.84 2.29
352 353 9.953565 AAAAACTACCTCATTACAAGCTATGTA 57.046 29.630 0.00 0.00 43.63 2.29
375 376 4.101898 TCGGGCTGGAGTATATAGCAAAAA 59.898 41.667 0.00 0.00 39.15 1.94
429 430 3.666374 CGACTTCTTTTCTCTGCATGCAC 60.666 47.826 18.46 0.75 0.00 4.57
438 439 3.185391 CCAAGCAGTCGACTTCTTTTCTC 59.815 47.826 24.96 4.23 27.07 2.87
490 517 1.960689 GGAACCTTTTTGGCAGCAGTA 59.039 47.619 0.00 0.00 40.22 2.74
502 529 4.142469 CGCCATTATTTTCGAGGAACCTTT 60.142 41.667 0.00 0.00 0.00 3.11
509 536 0.934496 TCGCGCCATTATTTTCGAGG 59.066 50.000 0.00 0.00 0.00 4.63
518 545 1.826054 CCCCCATTTCGCGCCATTA 60.826 57.895 0.00 0.00 0.00 1.90
638 672 2.311688 AATAGACCAAGGCCTCCGCG 62.312 60.000 5.23 0.00 35.02 6.46
639 673 0.533085 GAATAGACCAAGGCCTCCGC 60.533 60.000 5.23 0.00 0.00 5.54
640 674 1.123928 AGAATAGACCAAGGCCTCCG 58.876 55.000 5.23 0.49 0.00 4.63
641 675 2.422093 CCAAGAATAGACCAAGGCCTCC 60.422 54.545 5.23 0.00 0.00 4.30
645 679 1.340991 TGCCCAAGAATAGACCAAGGC 60.341 52.381 0.00 0.00 39.64 4.35
1032 1071 2.951745 CAGACGGCGATCGACAGC 60.952 66.667 23.01 12.02 42.43 4.40
1033 1072 2.951745 GCAGACGGCGATCGACAG 60.952 66.667 23.01 16.05 42.43 3.51
1136 1187 2.126071 CGTCGTCCTTGATGCCGT 60.126 61.111 0.00 0.00 0.00 5.68
1239 1290 3.535629 CTGCAGGCCCGTCACTTCA 62.536 63.158 5.57 0.00 0.00 3.02
1332 1383 3.501828 CGGTGAACTGATTGTCCATGAAA 59.498 43.478 0.00 0.00 0.00 2.69
1807 1859 1.338674 TGGTCAAGTAATCCACCGCAG 60.339 52.381 0.00 0.00 0.00 5.18
2155 2207 2.026301 GAGATCGACGGGCCGAAG 59.974 66.667 35.78 24.69 42.22 3.79
2167 2219 1.025812 TCGAGGGCTTCTTCGAGATC 58.974 55.000 0.00 0.00 0.00 2.75
2345 2397 0.749649 AGGTCCTGCAGCTCGAATAG 59.250 55.000 8.66 0.00 0.00 1.73
2491 2543 0.973496 GCTCCTCGAACTCCTCCCTT 60.973 60.000 0.00 0.00 0.00 3.95
3129 3181 1.699656 CTTGATCAGCTTCACCGCCG 61.700 60.000 0.00 0.00 0.00 6.46
3512 3577 8.514330 TGTGTTAAAGAAAAACTACAGATGGT 57.486 30.769 0.00 0.00 0.00 3.55
3519 3584 7.849515 CGGAGAACTGTGTTAAAGAAAAACTAC 59.150 37.037 0.00 0.00 0.00 2.73
3526 3591 5.272283 AGACGGAGAACTGTGTTAAAGAA 57.728 39.130 0.00 0.00 35.56 2.52
3527 3592 4.931661 AGACGGAGAACTGTGTTAAAGA 57.068 40.909 0.00 0.00 35.56 2.52
3528 3593 5.986004 AAAGACGGAGAACTGTGTTAAAG 57.014 39.130 0.00 0.00 37.80 1.85
3529 3594 6.576185 ACTAAAGACGGAGAACTGTGTTAAA 58.424 36.000 0.00 0.00 37.80 1.52
3530 3595 6.152932 ACTAAAGACGGAGAACTGTGTTAA 57.847 37.500 0.00 0.00 37.80 2.01
3531 3596 5.779529 ACTAAAGACGGAGAACTGTGTTA 57.220 39.130 0.00 0.00 37.80 2.41
3532 3597 4.667519 ACTAAAGACGGAGAACTGTGTT 57.332 40.909 0.00 0.00 39.94 3.32
3533 3598 4.667519 AACTAAAGACGGAGAACTGTGT 57.332 40.909 0.00 0.00 35.56 3.72
3534 3599 5.986004 AAAACTAAAGACGGAGAACTGTG 57.014 39.130 0.00 0.00 35.56 3.66
3627 3693 4.713792 ATTCTGAATCCCTAATCCGCTT 57.286 40.909 0.00 0.00 0.00 4.68
3698 3764 6.099845 TGTGAACCAAAAGGCCCTAAATTTTA 59.900 34.615 0.00 0.00 0.00 1.52
3717 3783 6.691388 GCCCGTGATTTTAGAATTATGTGAAC 59.309 38.462 0.00 0.00 0.00 3.18
3760 3826 3.409851 TGCGAGCATGACATTTCAATC 57.590 42.857 0.00 0.00 34.61 2.67
3833 4081 5.109210 CACCAGCGATGTAATTGACTCTTA 58.891 41.667 0.00 0.00 0.00 2.10
3851 4099 0.387239 GCGCCAAGTTTAAGCACCAG 60.387 55.000 0.00 0.00 0.00 4.00
3872 4120 3.713858 TCAAGCACCAAAGTGATTGTG 57.286 42.857 19.86 1.25 45.93 3.33
3924 4180 5.241728 TGATTAGCACTATATCTGCACGTCT 59.758 40.000 7.78 0.00 37.08 4.18
3959 4215 2.159430 CGCCAAGTCAACATCGATTTCA 59.841 45.455 0.00 0.00 0.00 2.69
4025 4308 6.673839 ATAAATTTTTCGAGGGGGTTTTCA 57.326 33.333 0.00 0.00 0.00 2.69
4038 4321 9.663904 GGGCTTTTTGTGAGAAATAAATTTTTC 57.336 29.630 0.00 0.00 36.13 2.29
4044 4327 7.453126 TGATAGGGGCTTTTTGTGAGAAATAAA 59.547 33.333 0.00 0.00 0.00 1.40
4081 4365 6.377996 TGTCATAGAGTCAAAATGAAATGGGG 59.622 38.462 4.88 0.00 31.77 4.96
4082 4366 7.395190 TGTCATAGAGTCAAAATGAAATGGG 57.605 36.000 4.88 0.00 31.77 4.00
4151 4437 2.010582 GAGTTCGAGATGCGGAGGCT 62.011 60.000 0.00 0.00 41.33 4.58
4183 4469 1.789523 TTTGGACGGCTAGCTATCCT 58.210 50.000 27.43 0.00 32.06 3.24
4203 4489 3.153919 GCAAAGGTGAATGGTGGAGTTA 58.846 45.455 0.00 0.00 0.00 2.24
4219 4507 5.747197 GCCATCAGTAATTCTCATTGCAAAG 59.253 40.000 1.71 0.00 0.00 2.77
4241 4529 6.403878 TCCTTGTAGTACATTAAAGACTGCC 58.596 40.000 3.28 0.00 0.00 4.85
4242 4530 6.535508 CCTCCTTGTAGTACATTAAAGACTGC 59.464 42.308 3.28 0.00 0.00 4.40
4248 4536 5.047164 TGCGTCCTCCTTGTAGTACATTAAA 60.047 40.000 3.28 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.