Multiple sequence alignment - TraesCS3A01G099500

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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 TraesCS3A01G099500 chr3A 100.000 2727 0 0 1 2727 64286519 64283793 0.000000e+00 5036.0
1 TraesCS3A01G099500 chr3B 89.541 2046 153 32 406 2423 82630641 82628629 0.000000e+00 2536.0
2 TraesCS3A01G099500 chr3B 91.606 274 10 3 2454 2727 82628497 82628237 1.540000e-97 366.0
3 TraesCS3A01G099500 chr3B 87.719 171 11 4 90 252 207672120 207672288 9.970000e-45 191.0
4 TraesCS3A01G099500 chr3B 87.647 170 12 6 90 252 21549597 21549430 3.580000e-44 189.0
5 TraesCS3A01G099500 chr3D 92.585 1497 89 9 941 2423 51687007 51685519 0.000000e+00 2130.0
6 TraesCS3A01G099500 chr3D 89.339 469 21 12 422 885 51687457 51687013 1.830000e-156 562.0
7 TraesCS3A01G099500 chr3D 90.291 309 14 7 2423 2727 51685440 51685144 9.160000e-105 390.0
8 TraesCS3A01G099500 chr3D 88.235 170 11 5 90 252 335816073 335816240 7.700000e-46 195.0
9 TraesCS3A01G099500 chr3D 90.741 54 3 1 324 375 51688044 51687991 1.350000e-08 71.3
10 TraesCS3A01G099500 chr5A 78.965 1526 215 51 957 2423 504955200 504956678 0.000000e+00 942.0
11 TraesCS3A01G099500 chr5B 80.165 1089 159 31 962 2007 479714983 479716057 0.000000e+00 761.0
12 TraesCS3A01G099500 chr5D 80.065 923 138 19 1155 2042 399327902 399328813 0.000000e+00 643.0
13 TraesCS3A01G099500 chr5D 85.407 418 49 8 520 926 12992841 12992425 9.030000e-115 424.0
14 TraesCS3A01G099500 chr5D 82.996 247 37 4 957 1201 399327656 399327899 4.570000e-53 219.0
15 TraesCS3A01G099500 chr6A 85.645 411 48 8 520 926 579956493 579956090 3.250000e-114 422.0
16 TraesCS3A01G099500 chr1D 85.343 423 40 13 520 924 452340801 452341219 4.200000e-113 418.0
17 TraesCS3A01G099500 chr1D 80.294 340 35 16 448 781 406559612 406559299 7.600000e-56 228.0
18 TraesCS3A01G099500 chr1A 85.266 414 51 8 520 924 547253678 547254090 4.200000e-113 418.0
19 TraesCS3A01G099500 chr1A 84.726 419 46 13 518 924 547241569 547241981 1.180000e-108 403.0
20 TraesCS3A01G099500 chr1A 84.010 419 50 12 518 924 547219678 547220091 1.180000e-103 387.0
21 TraesCS3A01G099500 chr1B 84.689 418 48 9 520 923 622188352 622187937 1.180000e-108 403.0
22 TraesCS3A01G099500 chr7D 77.263 453 55 22 480 926 591455702 591455292 3.530000e-54 222.0
23 TraesCS3A01G099500 chr2B 88.690 168 12 5 90 252 234706640 234706805 5.960000e-47 198.0
24 TraesCS3A01G099500 chr7B 88.344 163 17 2 93 254 8369195 8369356 7.700000e-46 195.0
25 TraesCS3A01G099500 chr7B 88.623 167 10 6 91 251 75156723 75156560 7.700000e-46 195.0
26 TraesCS3A01G099500 chr7B 87.791 172 10 7 92 255 490680522 490680690 9.970000e-45 191.0
27 TraesCS3A01G099500 chr7B 87.574 169 13 4 90 252 221044325 221044491 3.580000e-44 189.0
28 TraesCS3A01G099500 chr4B 87.647 170 12 6 90 252 229962920 229962753 3.580000e-44 189.0


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 TraesCS3A01G099500 chr3A 64283793 64286519 2726 True 5036.000 5036 100.0000 1 2727 1 chr3A.!!$R1 2726
1 TraesCS3A01G099500 chr3B 82628237 82630641 2404 True 1451.000 2536 90.5735 406 2727 2 chr3B.!!$R2 2321
2 TraesCS3A01G099500 chr3D 51685144 51688044 2900 True 788.325 2130 90.7390 324 2727 4 chr3D.!!$R1 2403
3 TraesCS3A01G099500 chr5A 504955200 504956678 1478 False 942.000 942 78.9650 957 2423 1 chr5A.!!$F1 1466
4 TraesCS3A01G099500 chr5B 479714983 479716057 1074 False 761.000 761 80.1650 962 2007 1 chr5B.!!$F1 1045
5 TraesCS3A01G099500 chr5D 399327656 399328813 1157 False 431.000 643 81.5305 957 2042 2 chr5D.!!$F1 1085

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
373 374 0.101399 CAGTCCGTCGATCCAAGAGG 59.899 60.0 0.0 0.0 0.0 3.69 F
938 1516 0.318441 GTAGCAGCCTATCCGCATCA 59.682 55.0 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1206 1838 0.037590 ATCCAAGCGCCACTACCAAA 59.962 50.0 2.29 0.0 0.0 3.28 R
2517 3370 0.823356 GCCAAGCCAGGAACAGAACA 60.823 55.0 0.00 0.0 0.0 3.18 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
19 20 2.563297 GGGAAACAACCCGGATCAC 58.437 57.895 0.73 0.00 40.49 3.06
20 21 0.963856 GGGAAACAACCCGGATCACC 60.964 60.000 0.73 0.00 40.49 4.02
30 31 4.857251 GGATCACCGGCGAAGATT 57.143 55.556 9.30 0.00 0.00 2.40
31 32 3.080647 GGATCACCGGCGAAGATTT 57.919 52.632 9.30 0.00 0.00 2.17
32 33 1.379527 GGATCACCGGCGAAGATTTT 58.620 50.000 9.30 0.00 0.00 1.82
33 34 1.743394 GGATCACCGGCGAAGATTTTT 59.257 47.619 9.30 0.00 0.00 1.94
69 70 8.606040 AATTTTACATCATTTGTTGGAGTTGG 57.394 30.769 0.00 0.00 39.87 3.77
70 71 6.968263 TTTACATCATTTGTTGGAGTTGGA 57.032 33.333 0.00 0.00 39.87 3.53
71 72 6.573664 TTACATCATTTGTTGGAGTTGGAG 57.426 37.500 0.00 0.00 39.87 3.86
72 73 3.828451 ACATCATTTGTTGGAGTTGGAGG 59.172 43.478 0.00 0.00 33.74 4.30
73 74 3.593442 TCATTTGTTGGAGTTGGAGGT 57.407 42.857 0.00 0.00 0.00 3.85
74 75 3.909732 TCATTTGTTGGAGTTGGAGGTT 58.090 40.909 0.00 0.00 0.00 3.50
75 76 4.285863 TCATTTGTTGGAGTTGGAGGTTT 58.714 39.130 0.00 0.00 0.00 3.27
76 77 4.714308 TCATTTGTTGGAGTTGGAGGTTTT 59.286 37.500 0.00 0.00 0.00 2.43
77 78 5.188751 TCATTTGTTGGAGTTGGAGGTTTTT 59.811 36.000 0.00 0.00 0.00 1.94
78 79 4.464069 TTGTTGGAGTTGGAGGTTTTTG 57.536 40.909 0.00 0.00 0.00 2.44
79 80 2.763448 TGTTGGAGTTGGAGGTTTTTGG 59.237 45.455 0.00 0.00 0.00 3.28
80 81 2.764010 GTTGGAGTTGGAGGTTTTTGGT 59.236 45.455 0.00 0.00 0.00 3.67
81 82 3.955524 TGGAGTTGGAGGTTTTTGGTA 57.044 42.857 0.00 0.00 0.00 3.25
82 83 4.252570 TGGAGTTGGAGGTTTTTGGTAA 57.747 40.909 0.00 0.00 0.00 2.85
83 84 4.810345 TGGAGTTGGAGGTTTTTGGTAAT 58.190 39.130 0.00 0.00 0.00 1.89
84 85 4.586841 TGGAGTTGGAGGTTTTTGGTAATG 59.413 41.667 0.00 0.00 0.00 1.90
85 86 4.587262 GGAGTTGGAGGTTTTTGGTAATGT 59.413 41.667 0.00 0.00 0.00 2.71
86 87 5.771165 GGAGTTGGAGGTTTTTGGTAATGTA 59.229 40.000 0.00 0.00 0.00 2.29
87 88 6.265876 GGAGTTGGAGGTTTTTGGTAATGTAA 59.734 38.462 0.00 0.00 0.00 2.41
88 89 7.201929 GGAGTTGGAGGTTTTTGGTAATGTAAA 60.202 37.037 0.00 0.00 0.00 2.01
89 90 8.080363 AGTTGGAGGTTTTTGGTAATGTAAAA 57.920 30.769 0.00 0.00 0.00 1.52
90 91 8.710239 AGTTGGAGGTTTTTGGTAATGTAAAAT 58.290 29.630 0.00 0.00 0.00 1.82
91 92 8.984764 GTTGGAGGTTTTTGGTAATGTAAAATC 58.015 33.333 0.00 0.00 0.00 2.17
92 93 8.485578 TGGAGGTTTTTGGTAATGTAAAATCT 57.514 30.769 0.00 0.00 35.52 2.40
93 94 9.589461 TGGAGGTTTTTGGTAATGTAAAATCTA 57.411 29.630 0.00 0.00 33.60 1.98
94 95 9.850628 GGAGGTTTTTGGTAATGTAAAATCTAC 57.149 33.333 0.00 0.00 33.60 2.59
97 98 9.850628 GGTTTTTGGTAATGTAAAATCTACTCC 57.149 33.333 0.00 0.00 0.00 3.85
98 99 9.850628 GTTTTTGGTAATGTAAAATCTACTCCC 57.149 33.333 0.00 0.00 0.00 4.30
99 100 9.816787 TTTTTGGTAATGTAAAATCTACTCCCT 57.183 29.630 0.00 0.00 0.00 4.20
100 101 9.457436 TTTTGGTAATGTAAAATCTACTCCCTC 57.543 33.333 0.00 0.00 0.00 4.30
101 102 7.133133 TGGTAATGTAAAATCTACTCCCTCC 57.867 40.000 0.00 0.00 0.00 4.30
102 103 6.674861 TGGTAATGTAAAATCTACTCCCTCCA 59.325 38.462 0.00 0.00 0.00 3.86
103 104 7.349859 TGGTAATGTAAAATCTACTCCCTCCAT 59.650 37.037 0.00 0.00 0.00 3.41
104 105 8.218488 GGTAATGTAAAATCTACTCCCTCCATT 58.782 37.037 0.00 0.00 0.00 3.16
105 106 9.628500 GTAATGTAAAATCTACTCCCTCCATTT 57.372 33.333 0.00 0.00 0.00 2.32
150 151 8.873830 AGAGATTTCAACAAATGACTACATACG 58.126 33.333 0.00 0.00 37.92 3.06
151 152 7.974675 AGATTTCAACAAATGACTACATACGG 58.025 34.615 0.00 0.00 37.92 4.02
152 153 7.822334 AGATTTCAACAAATGACTACATACGGA 59.178 33.333 0.00 0.00 37.92 4.69
153 154 6.961359 TTCAACAAATGACTACATACGGAG 57.039 37.500 0.00 0.00 37.92 4.63
154 155 4.868171 TCAACAAATGACTACATACGGAGC 59.132 41.667 0.00 0.00 35.50 4.70
155 156 4.465632 ACAAATGACTACATACGGAGCA 57.534 40.909 0.00 0.00 35.50 4.26
156 157 4.827692 ACAAATGACTACATACGGAGCAA 58.172 39.130 0.00 0.00 35.50 3.91
157 158 5.242434 ACAAATGACTACATACGGAGCAAA 58.758 37.500 0.00 0.00 35.50 3.68
158 159 5.703592 ACAAATGACTACATACGGAGCAAAA 59.296 36.000 0.00 0.00 35.50 2.44
159 160 6.374333 ACAAATGACTACATACGGAGCAAAAT 59.626 34.615 0.00 0.00 35.50 1.82
160 161 5.991328 ATGACTACATACGGAGCAAAATG 57.009 39.130 0.00 0.00 34.71 2.32
161 162 5.079689 TGACTACATACGGAGCAAAATGA 57.920 39.130 0.00 0.00 0.00 2.57
162 163 5.109210 TGACTACATACGGAGCAAAATGAG 58.891 41.667 0.00 0.00 0.00 2.90
163 164 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
164 165 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
165 166 3.674997 ACATACGGAGCAAAATGAGTGT 58.325 40.909 0.00 0.00 0.00 3.55
166 167 4.072131 ACATACGGAGCAAAATGAGTGTT 58.928 39.130 0.00 0.00 0.00 3.32
167 168 4.154195 ACATACGGAGCAAAATGAGTGTTC 59.846 41.667 0.00 0.00 0.00 3.18
168 169 2.851195 ACGGAGCAAAATGAGTGTTCT 58.149 42.857 0.00 0.00 0.00 3.01
169 170 4.002906 ACGGAGCAAAATGAGTGTTCTA 57.997 40.909 0.00 0.00 0.00 2.10
170 171 4.385825 ACGGAGCAAAATGAGTGTTCTAA 58.614 39.130 0.00 0.00 0.00 2.10
171 172 4.819630 ACGGAGCAAAATGAGTGTTCTAAA 59.180 37.500 0.00 0.00 0.00 1.85
172 173 5.298276 ACGGAGCAAAATGAGTGTTCTAAAA 59.702 36.000 0.00 0.00 0.00 1.52
173 174 6.016276 ACGGAGCAAAATGAGTGTTCTAAAAT 60.016 34.615 0.00 0.00 0.00 1.82
174 175 7.174253 ACGGAGCAAAATGAGTGTTCTAAAATA 59.826 33.333 0.00 0.00 0.00 1.40
175 176 8.184192 CGGAGCAAAATGAGTGTTCTAAAATAT 58.816 33.333 0.00 0.00 0.00 1.28
176 177 9.294030 GGAGCAAAATGAGTGTTCTAAAATATG 57.706 33.333 0.00 0.00 0.00 1.78
177 178 9.846248 GAGCAAAATGAGTGTTCTAAAATATGT 57.154 29.630 0.00 0.00 0.00 2.29
178 179 9.846248 AGCAAAATGAGTGTTCTAAAATATGTC 57.154 29.630 0.00 0.00 0.00 3.06
179 180 9.846248 GCAAAATGAGTGTTCTAAAATATGTCT 57.154 29.630 0.00 0.00 0.00 3.41
199 200 8.651589 ATGTCTATATATACATCCGTATGGGG 57.348 38.462 7.71 0.00 38.79 4.96
200 201 7.589081 TGTCTATATATACATCCGTATGGGGT 58.411 38.462 0.00 2.88 38.79 4.95
201 202 8.726202 TGTCTATATATACATCCGTATGGGGTA 58.274 37.037 0.00 5.11 38.79 3.69
202 203 9.228949 GTCTATATATACATCCGTATGGGGTAG 57.771 40.741 0.00 0.00 38.79 3.18
203 204 8.952602 TCTATATATACATCCGTATGGGGTAGT 58.047 37.037 0.00 0.00 38.79 2.73
204 205 9.228949 CTATATATACATCCGTATGGGGTAGTC 57.771 40.741 0.00 0.00 38.79 2.59
205 206 1.713297 ACATCCGTATGGGGTAGTCC 58.287 55.000 0.00 0.00 37.43 3.85
206 207 1.062734 ACATCCGTATGGGGTAGTCCA 60.063 52.381 0.00 0.00 41.60 4.02
208 209 2.482414 TCCGTATGGGGTAGTCCATT 57.518 50.000 0.00 0.00 44.55 3.16
209 210 2.766736 TCCGTATGGGGTAGTCCATTT 58.233 47.619 0.00 0.00 44.55 2.32
210 211 2.436542 TCCGTATGGGGTAGTCCATTTG 59.563 50.000 0.00 0.00 44.55 2.32
211 212 2.436542 CCGTATGGGGTAGTCCATTTGA 59.563 50.000 1.49 0.00 44.55 2.69
212 213 3.118186 CCGTATGGGGTAGTCCATTTGAA 60.118 47.826 1.49 0.00 44.55 2.69
213 214 4.519213 CGTATGGGGTAGTCCATTTGAAA 58.481 43.478 1.49 0.00 44.55 2.69
214 215 5.130350 CGTATGGGGTAGTCCATTTGAAAT 58.870 41.667 1.49 0.00 44.55 2.17
215 216 6.292923 CGTATGGGGTAGTCCATTTGAAATA 58.707 40.000 1.49 0.00 44.55 1.40
216 217 6.940298 CGTATGGGGTAGTCCATTTGAAATAT 59.060 38.462 1.49 0.00 44.55 1.28
217 218 7.119262 CGTATGGGGTAGTCCATTTGAAATATC 59.881 40.741 1.49 0.00 44.55 1.63
218 219 6.590656 TGGGGTAGTCCATTTGAAATATCT 57.409 37.500 0.00 0.00 37.22 1.98
219 220 6.364701 TGGGGTAGTCCATTTGAAATATCTG 58.635 40.000 0.00 0.00 37.22 2.90
220 221 6.159575 TGGGGTAGTCCATTTGAAATATCTGA 59.840 38.462 0.00 0.00 37.22 3.27
221 222 7.060421 GGGGTAGTCCATTTGAAATATCTGAA 58.940 38.462 0.00 0.00 37.22 3.02
222 223 7.559897 GGGGTAGTCCATTTGAAATATCTGAAA 59.440 37.037 0.00 0.00 37.22 2.69
223 224 8.966868 GGGTAGTCCATTTGAAATATCTGAAAA 58.033 33.333 0.00 0.00 35.00 2.29
227 228 9.300681 AGTCCATTTGAAATATCTGAAAAGACA 57.699 29.630 0.00 0.00 0.00 3.41
228 229 9.912634 GTCCATTTGAAATATCTGAAAAGACAA 57.087 29.630 0.00 0.00 0.00 3.18
246 247 9.483916 AAAAGACAAATATTTTAAAACGGAGGG 57.516 29.630 1.97 0.00 27.44 4.30
247 248 8.411991 AAGACAAATATTTTAAAACGGAGGGA 57.588 30.769 1.97 0.00 0.00 4.20
248 249 8.051901 AGACAAATATTTTAAAACGGAGGGAG 57.948 34.615 1.97 0.00 0.00 4.30
249 250 7.668469 AGACAAATATTTTAAAACGGAGGGAGT 59.332 33.333 1.97 0.00 0.00 3.85
250 251 8.866970 ACAAATATTTTAAAACGGAGGGAGTA 57.133 30.769 1.97 0.00 0.00 2.59
251 252 9.470399 ACAAATATTTTAAAACGGAGGGAGTAT 57.530 29.630 1.97 0.00 0.00 2.12
325 326 8.746922 TTTTACATCATCTGTTGAATTTGCTC 57.253 30.769 0.00 0.00 39.39 4.26
326 327 7.692460 TTACATCATCTGTTGAATTTGCTCT 57.308 32.000 0.00 0.00 39.39 4.09
327 328 6.585695 ACATCATCTGTTGAATTTGCTCTT 57.414 33.333 0.00 0.00 38.03 2.85
328 329 7.692460 ACATCATCTGTTGAATTTGCTCTTA 57.308 32.000 0.00 0.00 38.03 2.10
329 330 7.759465 ACATCATCTGTTGAATTTGCTCTTAG 58.241 34.615 0.00 0.00 38.03 2.18
361 362 4.159135 CCCACTAAGTACATTACAGTCCGT 59.841 45.833 0.00 0.00 0.00 4.69
370 371 2.933495 TTACAGTCCGTCGATCCAAG 57.067 50.000 0.00 0.00 0.00 3.61
371 372 2.118313 TACAGTCCGTCGATCCAAGA 57.882 50.000 0.00 0.00 0.00 3.02
372 373 0.811915 ACAGTCCGTCGATCCAAGAG 59.188 55.000 0.00 0.00 0.00 2.85
373 374 0.101399 CAGTCCGTCGATCCAAGAGG 59.899 60.000 0.00 0.00 0.00 3.69
384 385 2.403252 TCCAAGAGGAGAAAATCGGC 57.597 50.000 0.00 0.00 39.61 5.54
385 386 1.909302 TCCAAGAGGAGAAAATCGGCT 59.091 47.619 0.00 0.00 39.61 5.52
386 387 2.093447 TCCAAGAGGAGAAAATCGGCTC 60.093 50.000 0.00 0.00 39.61 4.70
724 1275 5.268118 TGGATGAGTACTTGCTGTAGATG 57.732 43.478 0.00 0.00 0.00 2.90
784 1335 2.297033 AGTACTTGCTGCATGGTTTTGG 59.703 45.455 18.21 0.00 0.00 3.28
848 1426 8.121305 TGATAGGTGTTTTTGATAATGCTTGT 57.879 30.769 0.00 0.00 0.00 3.16
849 1427 9.237187 TGATAGGTGTTTTTGATAATGCTTGTA 57.763 29.630 0.00 0.00 0.00 2.41
866 1444 5.393962 GCTTGTAGGAGCAAATGTTTACAG 58.606 41.667 0.00 0.00 42.25 2.74
870 1448 7.144722 TGTAGGAGCAAATGTTTACAGATTG 57.855 36.000 6.76 6.76 32.84 2.67
908 1486 6.847956 TTTTCAGATGAGCAAATGTTTTGG 57.152 33.333 2.50 0.00 0.00 3.28
909 1487 5.534207 TTCAGATGAGCAAATGTTTTGGT 57.466 34.783 4.50 4.50 0.00 3.67
910 1488 5.534207 TCAGATGAGCAAATGTTTTGGTT 57.466 34.783 6.18 0.00 0.00 3.67
911 1489 5.916318 TCAGATGAGCAAATGTTTTGGTTT 58.084 33.333 6.18 0.00 0.00 3.27
912 1490 7.048629 TCAGATGAGCAAATGTTTTGGTTTA 57.951 32.000 6.18 0.80 0.00 2.01
913 1491 7.495901 TCAGATGAGCAAATGTTTTGGTTTAA 58.504 30.769 6.18 0.00 0.00 1.52
914 1492 7.984050 TCAGATGAGCAAATGTTTTGGTTTAAA 59.016 29.630 6.18 0.00 0.00 1.52
915 1493 8.063630 CAGATGAGCAAATGTTTTGGTTTAAAC 58.936 33.333 9.98 9.98 38.26 2.01
924 1502 6.222038 TGTTTTGGTTTAAACATGGTAGCA 57.778 33.333 19.57 0.00 41.65 3.49
925 1503 6.276847 TGTTTTGGTTTAAACATGGTAGCAG 58.723 36.000 19.57 0.00 41.65 4.24
926 1504 4.513198 TTGGTTTAAACATGGTAGCAGC 57.487 40.909 19.57 0.00 0.00 5.25
927 1505 2.823154 TGGTTTAAACATGGTAGCAGCC 59.177 45.455 19.57 0.00 0.00 4.85
928 1506 3.089284 GGTTTAAACATGGTAGCAGCCT 58.911 45.455 19.57 0.00 0.00 4.58
929 1507 4.263550 TGGTTTAAACATGGTAGCAGCCTA 60.264 41.667 19.57 0.00 0.00 3.93
930 1508 4.887655 GGTTTAAACATGGTAGCAGCCTAT 59.112 41.667 19.57 0.00 0.00 2.57
931 1509 5.008712 GGTTTAAACATGGTAGCAGCCTATC 59.991 44.000 19.57 0.00 0.00 2.08
932 1510 2.938956 AACATGGTAGCAGCCTATCC 57.061 50.000 0.00 0.00 0.00 2.59
933 1511 0.681733 ACATGGTAGCAGCCTATCCG 59.318 55.000 0.00 0.00 0.00 4.18
934 1512 0.671781 CATGGTAGCAGCCTATCCGC 60.672 60.000 0.00 0.00 0.00 5.54
935 1513 1.121407 ATGGTAGCAGCCTATCCGCA 61.121 55.000 0.00 0.00 0.00 5.69
936 1514 1.121407 TGGTAGCAGCCTATCCGCAT 61.121 55.000 0.00 0.00 0.00 4.73
937 1515 0.390472 GGTAGCAGCCTATCCGCATC 60.390 60.000 0.00 0.00 0.00 3.91
938 1516 0.318441 GTAGCAGCCTATCCGCATCA 59.682 55.000 0.00 0.00 0.00 3.07
939 1517 0.605083 TAGCAGCCTATCCGCATCAG 59.395 55.000 0.00 0.00 0.00 2.90
963 1541 6.936335 AGTGCATTTTAGGCTTTAATTTGCTT 59.064 30.769 0.00 0.00 0.00 3.91
1024 1606 7.937394 AGATGAAGCACATATTCAAGATCATCA 59.063 33.333 12.72 0.00 41.76 3.07
1085 1667 2.036387 TGAAACCTCGACAGTTCCTCA 58.964 47.619 0.00 0.00 0.00 3.86
1092 1674 3.566523 CTCGACAGTTCCTCACAGTTAC 58.433 50.000 0.00 0.00 0.00 2.50
1095 1677 3.391049 GACAGTTCCTCACAGTTACACC 58.609 50.000 0.00 0.00 0.00 4.16
1118 1700 0.798776 CTGGTGAGTGCCACGAATTC 59.201 55.000 0.00 0.00 46.62 2.17
1130 1713 3.558505 CCACGAATTCTTTCACTTGCTG 58.441 45.455 3.52 0.00 0.00 4.41
1206 1838 5.435686 TGTTGTTGTAGCTTCCCATCTAT 57.564 39.130 0.00 0.00 0.00 1.98
1251 1883 2.164827 CGGCCTTTTTATGGTTGGGTAC 59.835 50.000 0.00 0.00 0.00 3.34
1299 1931 5.955959 TCCTCAAGAAGCCATACTACTACAA 59.044 40.000 0.00 0.00 0.00 2.41
1335 1967 8.941995 ATGTAGTCCTAGTAGCATAATTCTCA 57.058 34.615 0.00 0.00 0.00 3.27
1336 1968 8.397575 TGTAGTCCTAGTAGCATAATTCTCAG 57.602 38.462 0.00 0.00 0.00 3.35
1560 2230 1.830477 TGGCTTTTCATAATGGCCACC 59.170 47.619 8.16 0.00 46.35 4.61
1582 2252 3.383185 CACAAAGAAAACCAAGCCACCTA 59.617 43.478 0.00 0.00 0.00 3.08
1588 2258 6.247229 AGAAAACCAAGCCACCTAATTTTT 57.753 33.333 0.00 0.00 0.00 1.94
1633 2303 2.577449 ACAGTTTTGCTTTGTTCCCG 57.423 45.000 0.00 0.00 0.00 5.14
1635 2305 2.159296 ACAGTTTTGCTTTGTTCCCGTC 60.159 45.455 0.00 0.00 0.00 4.79
1652 2322 5.250200 TCCCGTCTGTAATTATTTGTGCTT 58.750 37.500 0.00 0.00 0.00 3.91
1654 2324 5.331902 CCGTCTGTAATTATTTGTGCTTGG 58.668 41.667 0.00 0.00 0.00 3.61
1681 2351 5.035556 ACTATGCAGGATATTATGGAGGCT 58.964 41.667 0.00 0.00 0.00 4.58
1889 2567 0.036732 GAGGTGGATGGCTTGTCACA 59.963 55.000 0.00 0.00 32.29 3.58
1891 2569 0.598065 GGTGGATGGCTTGTCACAAC 59.402 55.000 0.00 0.00 32.29 3.32
1914 2593 6.533819 CACTACTTGTGTCCGAAAACATTA 57.466 37.500 0.00 0.00 41.53 1.90
1952 2639 5.533154 TGAATGGTTCGTTAACAAGTCCATT 59.467 36.000 22.48 22.48 43.75 3.16
1973 2661 3.272439 AGTGTTCATGACATGTTTGCG 57.728 42.857 14.98 0.00 41.10 4.85
2001 2690 3.220110 CCATCTGGATTTCATCACTGGG 58.780 50.000 0.00 0.00 37.39 4.45
2005 2694 3.843619 TCTGGATTTCATCACTGGGTGTA 59.156 43.478 0.00 0.00 34.79 2.90
2171 2874 1.466167 CCGTCTCATTGGCACTTTGAG 59.534 52.381 12.69 12.69 38.66 3.02
2248 2951 8.649841 CATTATTGCTCCATGTTTACAAAACAG 58.350 33.333 10.60 4.04 33.18 3.16
2286 3001 2.286418 GCAGTGAACCTGTTTCAACTCG 60.286 50.000 0.00 0.00 46.09 4.18
2299 3014 8.612619 CCTGTTTCAACTCGTAATGCTATTATT 58.387 33.333 0.00 0.00 0.00 1.40
2332 3049 4.232221 GTTCAGTCACATGCCAATTTGAG 58.768 43.478 0.00 0.00 0.00 3.02
2337 3054 3.093814 TCACATGCCAATTTGAGAGCAT 58.906 40.909 5.97 5.97 46.50 3.79
2364 3081 0.826715 CCTGCTACCTTGAGCTAGCA 59.173 55.000 18.83 6.45 42.46 3.49
2516 3369 4.621068 TGCTTAAACATGTATGCTGCTC 57.379 40.909 0.00 0.00 0.00 4.26
2517 3370 4.264253 TGCTTAAACATGTATGCTGCTCT 58.736 39.130 0.00 0.00 0.00 4.09
2531 3384 0.250467 TGCTCTGTTCTGTTCCTGGC 60.250 55.000 0.00 0.00 0.00 4.85
2551 3404 3.627123 GGCTTGGCATGTCAAAAGTTTTT 59.373 39.130 14.69 0.00 0.00 1.94
2597 3451 4.570369 GTGTTGTTGAATTTTTGGGTCCTG 59.430 41.667 0.00 0.00 0.00 3.86
2647 3501 7.345914 AGGTTTACCTAATGCTAGTCATTCTCT 59.654 37.037 13.42 3.51 46.48 3.10
2648 3502 7.439655 GGTTTACCTAATGCTAGTCATTCTCTG 59.560 40.741 13.42 6.21 43.90 3.35
2649 3503 4.954875 ACCTAATGCTAGTCATTCTCTGC 58.045 43.478 13.42 0.00 43.90 4.26
2650 3504 4.406972 ACCTAATGCTAGTCATTCTCTGCA 59.593 41.667 13.42 0.00 43.90 4.41
2651 3505 5.104776 ACCTAATGCTAGTCATTCTCTGCAA 60.105 40.000 13.42 0.00 43.90 4.08
2652 3506 5.996513 CCTAATGCTAGTCATTCTCTGCAAT 59.003 40.000 13.42 0.00 43.90 3.56
2653 3507 6.485984 CCTAATGCTAGTCATTCTCTGCAATT 59.514 38.462 13.42 0.00 43.90 2.32
2654 3508 6.374565 AATGCTAGTCATTCTCTGCAATTC 57.625 37.500 6.58 0.00 41.34 2.17
2655 3509 5.095145 TGCTAGTCATTCTCTGCAATTCT 57.905 39.130 0.00 0.00 34.59 2.40
2656 3510 5.114780 TGCTAGTCATTCTCTGCAATTCTC 58.885 41.667 0.00 0.00 34.59 2.87
2657 3511 4.511082 GCTAGTCATTCTCTGCAATTCTCC 59.489 45.833 0.00 0.00 0.00 3.71
2718 3575 1.955778 TGCTGACATTTTGTGGACAGG 59.044 47.619 0.00 0.00 37.07 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.037734 GTGATCCGGGTTGTTTCCCT 59.962 55.000 0.00 0.00 44.95 4.20
1 2 0.963856 GGTGATCCGGGTTGTTTCCC 60.964 60.000 0.00 0.00 43.78 3.97
2 3 2.563297 GGTGATCCGGGTTGTTTCC 58.437 57.895 0.00 0.00 0.00 3.13
13 14 1.379527 AAAATCTTCGCCGGTGATCC 58.620 50.000 20.33 0.00 0.00 3.36
43 44 9.054922 CCAACTCCAACAAATGATGTAAAATTT 57.945 29.630 0.00 0.00 42.99 1.82
44 45 8.428063 TCCAACTCCAACAAATGATGTAAAATT 58.572 29.630 0.00 0.00 42.99 1.82
45 46 7.961351 TCCAACTCCAACAAATGATGTAAAAT 58.039 30.769 0.00 0.00 42.99 1.82
46 47 7.353414 TCCAACTCCAACAAATGATGTAAAA 57.647 32.000 0.00 0.00 42.99 1.52
47 48 6.015519 CCTCCAACTCCAACAAATGATGTAAA 60.016 38.462 0.00 0.00 42.99 2.01
48 49 5.476599 CCTCCAACTCCAACAAATGATGTAA 59.523 40.000 0.00 0.00 42.99 2.41
49 50 5.009631 CCTCCAACTCCAACAAATGATGTA 58.990 41.667 0.00 0.00 42.99 2.29
50 51 3.828451 CCTCCAACTCCAACAAATGATGT 59.172 43.478 0.00 0.00 46.82 3.06
51 52 3.828451 ACCTCCAACTCCAACAAATGATG 59.172 43.478 0.00 0.00 0.00 3.07
52 53 4.118168 ACCTCCAACTCCAACAAATGAT 57.882 40.909 0.00 0.00 0.00 2.45
53 54 3.593442 ACCTCCAACTCCAACAAATGA 57.407 42.857 0.00 0.00 0.00 2.57
54 55 4.670896 AAACCTCCAACTCCAACAAATG 57.329 40.909 0.00 0.00 0.00 2.32
55 56 5.427378 CAAAAACCTCCAACTCCAACAAAT 58.573 37.500 0.00 0.00 0.00 2.32
56 57 4.323104 CCAAAAACCTCCAACTCCAACAAA 60.323 41.667 0.00 0.00 0.00 2.83
57 58 3.196685 CCAAAAACCTCCAACTCCAACAA 59.803 43.478 0.00 0.00 0.00 2.83
58 59 2.763448 CCAAAAACCTCCAACTCCAACA 59.237 45.455 0.00 0.00 0.00 3.33
59 60 2.764010 ACCAAAAACCTCCAACTCCAAC 59.236 45.455 0.00 0.00 0.00 3.77
60 61 3.108847 ACCAAAAACCTCCAACTCCAA 57.891 42.857 0.00 0.00 0.00 3.53
61 62 2.838637 ACCAAAAACCTCCAACTCCA 57.161 45.000 0.00 0.00 0.00 3.86
62 63 4.587262 ACATTACCAAAAACCTCCAACTCC 59.413 41.667 0.00 0.00 0.00 3.85
63 64 5.784578 ACATTACCAAAAACCTCCAACTC 57.215 39.130 0.00 0.00 0.00 3.01
64 65 7.663043 TTTACATTACCAAAAACCTCCAACT 57.337 32.000 0.00 0.00 0.00 3.16
65 66 8.896320 ATTTTACATTACCAAAAACCTCCAAC 57.104 30.769 0.00 0.00 0.00 3.77
66 67 8.929487 AGATTTTACATTACCAAAAACCTCCAA 58.071 29.630 0.00 0.00 0.00 3.53
67 68 8.485578 AGATTTTACATTACCAAAAACCTCCA 57.514 30.769 0.00 0.00 0.00 3.86
68 69 9.850628 GTAGATTTTACATTACCAAAAACCTCC 57.149 33.333 0.00 0.00 0.00 4.30
71 72 9.850628 GGAGTAGATTTTACATTACCAAAAACC 57.149 33.333 0.00 0.00 0.00 3.27
72 73 9.850628 GGGAGTAGATTTTACATTACCAAAAAC 57.149 33.333 0.00 0.00 0.00 2.43
73 74 9.816787 AGGGAGTAGATTTTACATTACCAAAAA 57.183 29.630 0.00 0.00 0.00 1.94
74 75 9.457436 GAGGGAGTAGATTTTACATTACCAAAA 57.543 33.333 0.00 0.00 0.00 2.44
75 76 8.050930 GGAGGGAGTAGATTTTACATTACCAAA 58.949 37.037 0.00 0.00 0.00 3.28
76 77 7.183112 TGGAGGGAGTAGATTTTACATTACCAA 59.817 37.037 0.00 0.00 0.00 3.67
77 78 6.674861 TGGAGGGAGTAGATTTTACATTACCA 59.325 38.462 0.00 0.00 0.00 3.25
78 79 7.133133 TGGAGGGAGTAGATTTTACATTACC 57.867 40.000 0.00 0.00 0.00 2.85
79 80 9.628500 AAATGGAGGGAGTAGATTTTACATTAC 57.372 33.333 0.00 0.00 0.00 1.89
124 125 8.873830 CGTATGTAGTCATTTGTTGAAATCTCT 58.126 33.333 0.00 0.00 35.70 3.10
125 126 8.116753 CCGTATGTAGTCATTTGTTGAAATCTC 58.883 37.037 0.00 0.00 35.70 2.75
126 127 7.822334 TCCGTATGTAGTCATTTGTTGAAATCT 59.178 33.333 0.00 0.00 35.70 2.40
127 128 7.970384 TCCGTATGTAGTCATTTGTTGAAATC 58.030 34.615 0.00 0.00 35.70 2.17
128 129 7.414098 GCTCCGTATGTAGTCATTTGTTGAAAT 60.414 37.037 0.00 0.00 35.70 2.17
129 130 6.128391 GCTCCGTATGTAGTCATTTGTTGAAA 60.128 38.462 0.00 0.00 35.70 2.69
130 131 5.350365 GCTCCGTATGTAGTCATTTGTTGAA 59.650 40.000 0.00 0.00 35.70 2.69
131 132 4.868171 GCTCCGTATGTAGTCATTTGTTGA 59.132 41.667 0.00 0.00 35.70 3.18
132 133 4.629634 TGCTCCGTATGTAGTCATTTGTTG 59.370 41.667 0.00 0.00 35.70 3.33
133 134 4.827692 TGCTCCGTATGTAGTCATTTGTT 58.172 39.130 0.00 0.00 35.70 2.83
134 135 4.465632 TGCTCCGTATGTAGTCATTTGT 57.534 40.909 0.00 0.00 35.70 2.83
135 136 5.794687 TTTGCTCCGTATGTAGTCATTTG 57.205 39.130 0.00 0.00 35.70 2.32
136 137 6.597672 TCATTTTGCTCCGTATGTAGTCATTT 59.402 34.615 0.00 0.00 35.70 2.32
137 138 6.112734 TCATTTTGCTCCGTATGTAGTCATT 58.887 36.000 0.00 0.00 35.70 2.57
138 139 5.670485 TCATTTTGCTCCGTATGTAGTCAT 58.330 37.500 0.00 0.00 38.00 3.06
139 140 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
140 141 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
141 142 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
142 143 4.870426 ACACTCATTTTGCTCCGTATGTAG 59.130 41.667 0.00 0.00 0.00 2.74
143 144 4.827692 ACACTCATTTTGCTCCGTATGTA 58.172 39.130 0.00 0.00 0.00 2.29
144 145 3.674997 ACACTCATTTTGCTCCGTATGT 58.325 40.909 0.00 0.00 0.00 2.29
145 146 4.393062 AGAACACTCATTTTGCTCCGTATG 59.607 41.667 0.00 0.00 0.00 2.39
146 147 4.579869 AGAACACTCATTTTGCTCCGTAT 58.420 39.130 0.00 0.00 0.00 3.06
147 148 4.002906 AGAACACTCATTTTGCTCCGTA 57.997 40.909 0.00 0.00 0.00 4.02
148 149 2.851195 AGAACACTCATTTTGCTCCGT 58.149 42.857 0.00 0.00 0.00 4.69
149 150 5.356882 TTTAGAACACTCATTTTGCTCCG 57.643 39.130 0.00 0.00 0.00 4.63
150 151 9.294030 CATATTTTAGAACACTCATTTTGCTCC 57.706 33.333 0.00 0.00 0.00 4.70
151 152 9.846248 ACATATTTTAGAACACTCATTTTGCTC 57.154 29.630 0.00 0.00 0.00 4.26
152 153 9.846248 GACATATTTTAGAACACTCATTTTGCT 57.154 29.630 0.00 0.00 0.00 3.91
153 154 9.846248 AGACATATTTTAGAACACTCATTTTGC 57.154 29.630 0.00 0.00 0.00 3.68
173 174 9.749340 CCCCATACGGATGTATATATAGACATA 57.251 37.037 20.17 7.81 39.28 2.29
174 175 8.232412 ACCCCATACGGATGTATATATAGACAT 58.768 37.037 20.23 20.23 39.28 3.06
175 176 7.589081 ACCCCATACGGATGTATATATAGACA 58.411 38.462 12.35 12.35 39.28 3.41
176 177 9.228949 CTACCCCATACGGATGTATATATAGAC 57.771 40.741 6.92 0.35 39.28 2.59
177 178 8.952602 ACTACCCCATACGGATGTATATATAGA 58.047 37.037 6.92 0.00 39.28 1.98
178 179 9.228949 GACTACCCCATACGGATGTATATATAG 57.771 40.741 6.92 2.53 39.28 1.31
179 180 8.166061 GGACTACCCCATACGGATGTATATATA 58.834 40.741 6.92 0.00 39.28 0.86
180 181 7.008941 GGACTACCCCATACGGATGTATATAT 58.991 42.308 6.92 0.00 39.28 0.86
181 182 6.068912 TGGACTACCCCATACGGATGTATATA 60.069 42.308 6.92 0.00 36.02 0.86
182 183 5.206587 GGACTACCCCATACGGATGTATAT 58.793 45.833 6.92 0.00 39.28 0.86
183 184 4.044444 TGGACTACCCCATACGGATGTATA 59.956 45.833 6.92 0.00 36.02 1.47
184 185 3.181415 TGGACTACCCCATACGGATGTAT 60.181 47.826 6.92 0.00 37.27 2.29
185 186 2.177451 TGGACTACCCCATACGGATGTA 59.823 50.000 6.92 0.00 34.81 2.29
186 187 1.062734 TGGACTACCCCATACGGATGT 60.063 52.381 6.92 0.00 34.81 3.06
187 188 1.712056 TGGACTACCCCATACGGATG 58.288 55.000 0.00 0.00 34.81 3.51
188 189 2.715763 ATGGACTACCCCATACGGAT 57.284 50.000 0.00 0.00 44.66 4.18
189 190 2.436542 CAAATGGACTACCCCATACGGA 59.563 50.000 0.00 0.00 45.69 4.69
190 191 2.436542 TCAAATGGACTACCCCATACGG 59.563 50.000 0.00 0.00 45.69 4.02
191 192 3.830744 TCAAATGGACTACCCCATACG 57.169 47.619 0.00 0.00 45.69 3.06
192 193 8.164070 AGATATTTCAAATGGACTACCCCATAC 58.836 37.037 0.00 0.00 45.69 2.39
193 194 8.163408 CAGATATTTCAAATGGACTACCCCATA 58.837 37.037 0.00 0.00 45.69 2.74
195 196 6.159575 TCAGATATTTCAAATGGACTACCCCA 59.840 38.462 0.00 0.00 41.05 4.96
196 197 6.601332 TCAGATATTTCAAATGGACTACCCC 58.399 40.000 0.00 0.00 34.81 4.95
197 198 8.519799 TTTCAGATATTTCAAATGGACTACCC 57.480 34.615 0.00 0.00 34.81 3.69
201 202 9.300681 TGTCTTTTCAGATATTTCAAATGGACT 57.699 29.630 0.00 0.00 0.00 3.85
202 203 9.912634 TTGTCTTTTCAGATATTTCAAATGGAC 57.087 29.630 0.00 0.00 0.00 4.02
220 221 9.483916 CCCTCCGTTTTAAAATATTTGTCTTTT 57.516 29.630 3.52 0.00 0.00 2.27
221 222 8.862085 TCCCTCCGTTTTAAAATATTTGTCTTT 58.138 29.630 3.52 0.00 0.00 2.52
222 223 8.411991 TCCCTCCGTTTTAAAATATTTGTCTT 57.588 30.769 3.52 0.00 0.00 3.01
223 224 7.668469 ACTCCCTCCGTTTTAAAATATTTGTCT 59.332 33.333 3.52 0.00 0.00 3.41
224 225 7.823665 ACTCCCTCCGTTTTAAAATATTTGTC 58.176 34.615 3.52 0.00 0.00 3.18
225 226 7.770366 ACTCCCTCCGTTTTAAAATATTTGT 57.230 32.000 3.52 0.00 0.00 2.83
299 300 9.362539 GAGCAAATTCAACAGATGATGTAAAAT 57.637 29.630 0.00 0.00 43.00 1.82
300 301 8.579006 AGAGCAAATTCAACAGATGATGTAAAA 58.421 29.630 0.00 0.00 43.00 1.52
301 302 8.114331 AGAGCAAATTCAACAGATGATGTAAA 57.886 30.769 0.00 0.00 43.00 2.01
302 303 7.692460 AGAGCAAATTCAACAGATGATGTAA 57.308 32.000 0.00 0.00 43.00 2.41
303 304 7.692460 AAGAGCAAATTCAACAGATGATGTA 57.308 32.000 0.00 0.00 43.00 2.29
304 305 6.585695 AAGAGCAAATTCAACAGATGATGT 57.414 33.333 0.00 0.00 46.97 3.06
305 306 6.691818 GCTAAGAGCAAATTCAACAGATGATG 59.308 38.462 0.00 0.00 41.89 3.07
306 307 6.793349 GCTAAGAGCAAATTCAACAGATGAT 58.207 36.000 0.00 0.00 41.89 2.45
307 308 6.187125 GCTAAGAGCAAATTCAACAGATGA 57.813 37.500 0.00 0.00 41.89 2.92
322 323 4.790765 AGTGGGAAAAATTGCTAAGAGC 57.209 40.909 0.00 0.00 42.82 4.09
323 324 7.454260 ACTTAGTGGGAAAAATTGCTAAGAG 57.546 36.000 13.79 0.00 38.24 2.85
324 325 7.940137 TGTACTTAGTGGGAAAAATTGCTAAGA 59.060 33.333 13.79 0.00 38.24 2.10
325 326 8.106247 TGTACTTAGTGGGAAAAATTGCTAAG 57.894 34.615 0.00 0.00 40.41 2.18
326 327 8.644374 ATGTACTTAGTGGGAAAAATTGCTAA 57.356 30.769 0.00 0.00 0.00 3.09
327 328 8.644374 AATGTACTTAGTGGGAAAAATTGCTA 57.356 30.769 0.00 0.00 0.00 3.49
328 329 7.539034 AATGTACTTAGTGGGAAAAATTGCT 57.461 32.000 0.00 0.00 0.00 3.91
329 330 8.301002 TGTAATGTACTTAGTGGGAAAAATTGC 58.699 33.333 0.00 0.00 0.00 3.56
361 362 3.181475 CCGATTTTCTCCTCTTGGATCGA 60.181 47.826 0.00 0.00 40.39 3.59
370 371 3.388272 GGGAGCCGATTTTCTCCTC 57.612 57.895 8.04 0.00 46.22 3.71
396 397 3.694566 GTCCTCACTCTTGGTGTGTTTTT 59.305 43.478 0.00 0.00 45.50 1.94
397 398 3.279434 GTCCTCACTCTTGGTGTGTTTT 58.721 45.455 0.00 0.00 45.50 2.43
398 399 2.741878 CGTCCTCACTCTTGGTGTGTTT 60.742 50.000 0.00 0.00 45.50 2.83
399 400 1.202533 CGTCCTCACTCTTGGTGTGTT 60.203 52.381 0.00 0.00 45.50 3.32
400 401 0.389391 CGTCCTCACTCTTGGTGTGT 59.611 55.000 0.00 0.00 45.50 3.72
401 402 0.389391 ACGTCCTCACTCTTGGTGTG 59.611 55.000 0.00 0.00 45.50 3.82
402 403 0.674534 GACGTCCTCACTCTTGGTGT 59.325 55.000 3.51 0.00 45.50 4.16
403 404 0.038159 GGACGTCCTCACTCTTGGTG 60.038 60.000 27.64 0.00 46.60 4.17
404 405 1.186267 GGGACGTCCTCACTCTTGGT 61.186 60.000 32.52 0.00 35.95 3.67
609 1154 0.544223 GGGAAGAAGGAGGAAGGAGC 59.456 60.000 0.00 0.00 0.00 4.70
750 1301 7.165485 TGCAGCAAGTACTCCTTAAGAAATAA 58.835 34.615 3.36 0.00 0.00 1.40
759 1310 1.352352 ACCATGCAGCAAGTACTCCTT 59.648 47.619 0.00 0.00 0.00 3.36
761 1312 1.826385 AACCATGCAGCAAGTACTCC 58.174 50.000 0.00 0.00 0.00 3.85
848 1426 8.100791 ACTACAATCTGTAAACATTTGCTCCTA 58.899 33.333 6.07 0.00 31.67 2.94
849 1427 6.942576 ACTACAATCTGTAAACATTTGCTCCT 59.057 34.615 6.07 0.00 31.67 3.69
886 1464 5.916318 ACCAAAACATTTGCTCATCTGAAA 58.084 33.333 0.00 0.00 0.00 2.69
888 1466 5.534207 AACCAAAACATTTGCTCATCTGA 57.466 34.783 0.00 0.00 0.00 3.27
889 1467 7.712264 TTAAACCAAAACATTTGCTCATCTG 57.288 32.000 0.00 0.00 0.00 2.90
890 1468 7.768120 TGTTTAAACCAAAACATTTGCTCATCT 59.232 29.630 15.59 0.00 42.78 2.90
891 1469 7.914465 TGTTTAAACCAAAACATTTGCTCATC 58.086 30.769 15.59 0.00 42.78 2.92
892 1470 7.856145 TGTTTAAACCAAAACATTTGCTCAT 57.144 28.000 15.59 0.00 42.78 2.90
902 1480 5.176774 GCTGCTACCATGTTTAAACCAAAAC 59.823 40.000 15.59 0.77 39.35 2.43
903 1481 5.293560 GCTGCTACCATGTTTAAACCAAAA 58.706 37.500 15.59 0.00 0.00 2.44
904 1482 4.262249 GGCTGCTACCATGTTTAAACCAAA 60.262 41.667 15.59 0.00 0.00 3.28
905 1483 3.257127 GGCTGCTACCATGTTTAAACCAA 59.743 43.478 15.59 0.00 0.00 3.67
906 1484 2.823154 GGCTGCTACCATGTTTAAACCA 59.177 45.455 15.59 4.61 0.00 3.67
907 1485 3.089284 AGGCTGCTACCATGTTTAAACC 58.911 45.455 15.59 0.00 0.00 3.27
908 1486 5.008712 GGATAGGCTGCTACCATGTTTAAAC 59.991 44.000 11.54 11.54 0.00 2.01
909 1487 5.130350 GGATAGGCTGCTACCATGTTTAAA 58.870 41.667 0.00 0.00 0.00 1.52
910 1488 4.714632 GGATAGGCTGCTACCATGTTTAA 58.285 43.478 0.00 0.00 0.00 1.52
911 1489 3.244078 CGGATAGGCTGCTACCATGTTTA 60.244 47.826 0.00 0.00 0.00 2.01
912 1490 2.485479 CGGATAGGCTGCTACCATGTTT 60.485 50.000 0.00 0.00 0.00 2.83
913 1491 1.070758 CGGATAGGCTGCTACCATGTT 59.929 52.381 0.00 0.00 0.00 2.71
914 1492 0.681733 CGGATAGGCTGCTACCATGT 59.318 55.000 0.00 0.00 0.00 3.21
915 1493 0.671781 GCGGATAGGCTGCTACCATG 60.672 60.000 0.00 0.00 45.70 3.66
916 1494 1.674057 GCGGATAGGCTGCTACCAT 59.326 57.895 0.00 0.00 45.70 3.55
917 1495 3.138625 GCGGATAGGCTGCTACCA 58.861 61.111 0.00 0.00 45.70 3.25
923 1501 1.226686 GCACTGATGCGGATAGGCTG 61.227 60.000 0.00 0.00 43.33 4.85
924 1502 1.070445 GCACTGATGCGGATAGGCT 59.930 57.895 0.00 0.00 43.33 4.58
925 1503 3.647824 GCACTGATGCGGATAGGC 58.352 61.111 0.00 0.00 43.33 3.93
934 1512 8.385111 CAAATTAAAGCCTAAAATGCACTGATG 58.615 33.333 0.00 0.00 0.00 3.07
935 1513 7.064966 GCAAATTAAAGCCTAAAATGCACTGAT 59.935 33.333 0.00 0.00 0.00 2.90
936 1514 6.368516 GCAAATTAAAGCCTAAAATGCACTGA 59.631 34.615 0.00 0.00 0.00 3.41
937 1515 6.369615 AGCAAATTAAAGCCTAAAATGCACTG 59.630 34.615 13.99 0.00 33.89 3.66
938 1516 6.466812 AGCAAATTAAAGCCTAAAATGCACT 58.533 32.000 13.99 0.00 33.89 4.40
939 1517 6.726258 AGCAAATTAAAGCCTAAAATGCAC 57.274 33.333 13.99 0.00 33.89 4.57
963 1541 4.187694 GTTTGTCTGCCATCAACCAAAAA 58.812 39.130 0.00 0.00 0.00 1.94
969 1547 0.593128 AGCGTTTGTCTGCCATCAAC 59.407 50.000 0.00 0.00 0.00 3.18
1055 1637 1.630244 CGAGGTTTCAAGGAGCGCAG 61.630 60.000 11.47 0.00 0.00 5.18
1112 1694 8.581263 CAATAAATCAGCAAGTGAAAGAATTCG 58.419 33.333 0.00 0.00 39.19 3.34
1113 1695 9.630098 TCAATAAATCAGCAAGTGAAAGAATTC 57.370 29.630 0.00 0.00 39.19 2.17
1118 1700 8.807667 AACTTCAATAAATCAGCAAGTGAAAG 57.192 30.769 0.00 0.00 39.19 2.62
1167 1750 4.737054 ACAACAAAAGTCACAAGCAAGAG 58.263 39.130 0.00 0.00 0.00 2.85
1168 1751 4.782019 ACAACAAAAGTCACAAGCAAGA 57.218 36.364 0.00 0.00 0.00 3.02
1169 1752 4.685628 ACAACAACAAAAGTCACAAGCAAG 59.314 37.500 0.00 0.00 0.00 4.01
1206 1838 0.037590 ATCCAAGCGCCACTACCAAA 59.962 50.000 2.29 0.00 0.00 3.28
1251 1883 0.322456 TGGGAAAGAACATCAGCCCG 60.322 55.000 0.00 0.00 38.42 6.13
1520 2190 5.707298 AGCCATACAATCATACACATAAGGC 59.293 40.000 0.00 0.00 36.22 4.35
1560 2230 2.168313 AGGTGGCTTGGTTTTCTTTGTG 59.832 45.455 0.00 0.00 0.00 3.33
1617 2287 2.159296 ACAGACGGGAACAAAGCAAAAC 60.159 45.455 0.00 0.00 0.00 2.43
1618 2288 2.096248 ACAGACGGGAACAAAGCAAAA 58.904 42.857 0.00 0.00 0.00 2.44
1633 2303 5.102313 GGCCAAGCACAAATAATTACAGAC 58.898 41.667 0.00 0.00 0.00 3.51
1635 2305 5.329035 AGGCCAAGCACAAATAATTACAG 57.671 39.130 5.01 0.00 0.00 2.74
1652 2322 5.130975 CCATAATATCCTGCATAGTAGGCCA 59.869 44.000 5.01 0.00 35.23 5.36
1654 2324 6.463614 CCTCCATAATATCCTGCATAGTAGGC 60.464 46.154 0.00 0.00 35.23 3.93
1681 2351 6.895204 CACCCCTTTTGGATAAGAATTCCTTA 59.105 38.462 0.65 1.19 44.07 2.69
1914 2593 6.655003 ACGAACCATTCATTAGTTGTTCTCAT 59.345 34.615 0.00 0.00 32.11 2.90
1952 2639 3.812609 ACGCAAACATGTCATGAACACTA 59.187 39.130 19.77 0.00 41.75 2.74
1973 2661 6.375455 AGTGATGAAATCCAGATGGTTACAAC 59.625 38.462 0.00 0.00 44.73 3.32
2001 2690 4.631377 TGCAGAGCACAAACTGATATACAC 59.369 41.667 0.00 0.00 36.38 2.90
2005 2694 3.947868 ACTGCAGAGCACAAACTGATAT 58.052 40.909 23.35 0.00 36.38 1.63
2171 2874 7.214467 TGTTAAATCATGAGGAGTTCAAACC 57.786 36.000 0.09 0.00 39.77 3.27
2248 2951 3.187227 CACTGCACAGTCCATTCTACAAC 59.813 47.826 0.00 0.00 40.20 3.32
2364 3081 2.930562 AAGTCCCTGCCGGAAGCT 60.931 61.111 5.05 0.00 44.47 3.74
2447 3290 6.710295 ACGGAACACATAACATATATGCACAT 59.290 34.615 12.79 0.99 0.00 3.21
2448 3291 6.052360 ACGGAACACATAACATATATGCACA 58.948 36.000 12.79 0.00 0.00 4.57
2462 3313 1.140252 GGCCAGGTATACGGAACACAT 59.860 52.381 0.00 0.00 0.00 3.21
2469 3320 1.450211 CCAAGGGCCAGGTATACGG 59.550 63.158 6.18 0.00 0.00 4.02
2516 3369 1.242076 CCAAGCCAGGAACAGAACAG 58.758 55.000 0.00 0.00 0.00 3.16
2517 3370 0.823356 GCCAAGCCAGGAACAGAACA 60.823 55.000 0.00 0.00 0.00 3.18
2531 3384 9.786105 ATTTTTAAAAACTTTTGACATGCCAAG 57.214 25.926 15.35 0.00 0.00 3.61
2564 3418 5.659440 AATTCAACAACACCACAAACTCT 57.341 34.783 0.00 0.00 0.00 3.24
2597 3451 1.009829 CTCACATAGAAGGCGCCAAC 58.990 55.000 31.54 21.55 0.00 3.77


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

AutoCloner maintained by Alex Coulton.