Multiple sequence alignment - TraesCS2A01G323000

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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 TraesCS2A01G323000 chr2A 100.000 3571 0 0 1 3571 552841023 552837453 0.000000e+00 6595.0
1 TraesCS2A01G323000 chr2A 84.763 991 113 24 1000 1959 553280005 553279022 0.000000e+00 959.0
2 TraesCS2A01G323000 chr2A 90.000 190 18 1 2387 2576 553278680 553278492 9.900000e-61 244.0
3 TraesCS2A01G323000 chr2B 93.912 2316 89 24 409 2684 513252165 513254468 0.000000e+00 3448.0
4 TraesCS2A01G323000 chr2B 85.685 992 108 20 998 1959 512909351 512910338 0.000000e+00 1014.0
5 TraesCS2A01G323000 chr2B 83.529 510 56 18 2893 3385 513255051 513255549 5.440000e-123 451.0
6 TraesCS2A01G323000 chr2B 89.623 212 21 1 2365 2576 512910637 512910847 5.880000e-68 268.0
7 TraesCS2A01G323000 chr2B 90.323 155 11 2 244 394 513250202 513250356 2.170000e-47 200.0
8 TraesCS2A01G323000 chr2B 83.636 165 11 10 3409 3571 513255544 513255694 1.340000e-29 141.0
9 TraesCS2A01G323000 chr2D 91.453 2492 135 32 423 2893 434137932 434140366 0.000000e+00 3350.0
10 TraesCS2A01G323000 chr2D 85.020 988 114 20 1000 1959 433863295 433864276 0.000000e+00 974.0
11 TraesCS2A01G323000 chr2D 88.022 551 51 4 436 982 434080514 434081053 3.890000e-179 638.0
12 TraesCS2A01G323000 chr2D 83.857 700 71 22 2893 3571 434331641 434332319 2.340000e-176 628.0
13 TraesCS2A01G323000 chr2D 90.610 213 19 1 2365 2577 433864576 433864787 7.550000e-72 281.0
14 TraesCS2A01G323000 chr2D 97.744 133 2 1 977 1109 434135400 434135531 9.970000e-56 228.0
15 TraesCS2A01G323000 chr4D 88.889 243 24 3 1 242 431555517 431555277 2.700000e-76 296.0
16 TraesCS2A01G323000 chr7D 88.525 244 22 5 1 242 112330680 112330441 1.250000e-74 291.0
17 TraesCS2A01G323000 chr7D 88.186 237 26 2 1 236 115441660 115441425 7.550000e-72 281.0
18 TraesCS2A01G323000 chr7D 85.484 248 30 6 1 245 458522936 458523180 1.650000e-63 254.0
19 TraesCS2A01G323000 chr7D 84.000 75 10 2 365 438 555566117 555566044 1.780000e-08 71.3
20 TraesCS2A01G323000 chr5B 87.654 243 25 5 2 242 687765949 687766188 9.760000e-71 278.0
21 TraesCS2A01G323000 chr3B 86.939 245 29 3 1 243 388052871 388053114 4.540000e-69 272.0
22 TraesCS2A01G323000 chr3B 86.831 243 30 2 1 242 829336678 829336437 1.630000e-68 270.0
23 TraesCS2A01G323000 chr1D 86.275 255 29 6 1 252 110981210 110981461 4.540000e-69 272.0
24 TraesCS2A01G323000 chr7A 86.885 244 26 6 1 242 129611043 129610804 5.880000e-68 268.0
25 TraesCS2A01G323000 chr5A 97.143 35 1 0 412 446 398194060 398194026 3.850000e-05 60.2
26 TraesCS2A01G323000 chr4A 100.000 29 0 0 412 440 42263551 42263523 2.000000e-03 54.7


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 TraesCS2A01G323000 chr2A 552837453 552841023 3570 True 6595.0 6595 100.0000 1 3571 1 chr2A.!!$R1 3570
1 TraesCS2A01G323000 chr2A 553278492 553280005 1513 True 601.5 959 87.3815 1000 2576 2 chr2A.!!$R2 1576
2 TraesCS2A01G323000 chr2B 513250202 513255694 5492 False 1060.0 3448 87.8500 244 3571 4 chr2B.!!$F2 3327
3 TraesCS2A01G323000 chr2B 512909351 512910847 1496 False 641.0 1014 87.6540 998 2576 2 chr2B.!!$F1 1578
4 TraesCS2A01G323000 chr2D 434135400 434140366 4966 False 1789.0 3350 94.5985 423 2893 2 chr2D.!!$F4 2470
5 TraesCS2A01G323000 chr2D 434080514 434081053 539 False 638.0 638 88.0220 436 982 1 chr2D.!!$F1 546
6 TraesCS2A01G323000 chr2D 434331641 434332319 678 False 628.0 628 83.8570 2893 3571 1 chr2D.!!$F2 678
7 TraesCS2A01G323000 chr2D 433863295 433864787 1492 False 627.5 974 87.8150 1000 2577 2 chr2D.!!$F3 1577

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
989 3113 0.035317 AAGAGGATCGTGCAGTGCAA 59.965 50.0 21.67 5.49 41.47 4.08 F
1014 3138 0.443869 GATCAATGACGTTGTGCGCT 59.556 50.0 9.73 0.00 46.11 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2294 4500 0.167470 CAACTTGGCATGCGTCAGAG 59.833 55.0 12.44 7.18 0.0 3.35 R
2873 5099 0.250467 GAGCCCATCCACACGCATAT 60.250 55.0 0.00 0.00 0.0 1.78 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
36 37 1.006571 CGTAGTTGTGCCAGGACGT 60.007 57.895 0.00 0.00 0.00 4.34
37 38 1.282248 CGTAGTTGTGCCAGGACGTG 61.282 60.000 0.00 0.00 0.00 4.49
38 39 0.249741 GTAGTTGTGCCAGGACGTGT 60.250 55.000 0.00 0.00 0.00 4.49
39 40 0.249699 TAGTTGTGCCAGGACGTGTG 60.250 55.000 0.00 0.00 0.00 3.82
40 41 2.203139 TTGTGCCAGGACGTGTGG 60.203 61.111 8.89 8.89 38.21 4.17
47 48 1.750193 CCAGGACGTGTGGCATATTT 58.250 50.000 0.00 0.00 0.00 1.40
48 49 1.401552 CCAGGACGTGTGGCATATTTG 59.598 52.381 0.00 0.00 0.00 2.32
59 60 1.548986 GCATATTTGCTTCGTGCCAC 58.451 50.000 0.35 0.00 45.77 5.01
60 61 1.135431 GCATATTTGCTTCGTGCCACA 60.135 47.619 0.35 0.00 45.77 4.17
61 62 2.518949 CATATTTGCTTCGTGCCACAC 58.481 47.619 0.00 0.00 42.00 3.82
76 77 4.715523 CACGTGCGGGGTGGGAAT 62.716 66.667 0.82 0.00 0.00 3.01
77 78 4.715523 ACGTGCGGGGTGGGAATG 62.716 66.667 0.00 0.00 0.00 2.67
78 79 4.402528 CGTGCGGGGTGGGAATGA 62.403 66.667 0.00 0.00 0.00 2.57
79 80 2.438434 GTGCGGGGTGGGAATGAG 60.438 66.667 0.00 0.00 0.00 2.90
80 81 2.933287 TGCGGGGTGGGAATGAGT 60.933 61.111 0.00 0.00 0.00 3.41
81 82 1.613928 TGCGGGGTGGGAATGAGTA 60.614 57.895 0.00 0.00 0.00 2.59
82 83 1.146263 GCGGGGTGGGAATGAGTAG 59.854 63.158 0.00 0.00 0.00 2.57
83 84 1.623542 GCGGGGTGGGAATGAGTAGT 61.624 60.000 0.00 0.00 0.00 2.73
84 85 1.784358 CGGGGTGGGAATGAGTAGTA 58.216 55.000 0.00 0.00 0.00 1.82
85 86 1.411612 CGGGGTGGGAATGAGTAGTAC 59.588 57.143 0.00 0.00 0.00 2.73
87 88 3.113043 GGGGTGGGAATGAGTAGTACTT 58.887 50.000 0.00 0.00 0.00 2.24
89 90 3.518303 GGGTGGGAATGAGTAGTACTTGT 59.482 47.826 0.00 0.00 0.00 3.16
90 91 4.019591 GGGTGGGAATGAGTAGTACTTGTT 60.020 45.833 0.00 2.72 0.00 2.83
91 92 4.935808 GGTGGGAATGAGTAGTACTTGTTG 59.064 45.833 0.00 0.00 0.00 3.33
94 95 5.176592 GGGAATGAGTAGTACTTGTTGGAC 58.823 45.833 0.00 0.00 0.00 4.02
95 96 4.863131 GGAATGAGTAGTACTTGTTGGACG 59.137 45.833 0.00 0.00 0.00 4.79
96 97 5.464030 AATGAGTAGTACTTGTTGGACGT 57.536 39.130 0.00 0.00 0.00 4.34
98 99 3.633525 TGAGTAGTACTTGTTGGACGTGT 59.366 43.478 0.00 0.00 0.00 4.49
100 101 3.633525 AGTAGTACTTGTTGGACGTGTGA 59.366 43.478 0.00 0.00 0.00 3.58
101 102 2.817901 AGTACTTGTTGGACGTGTGAC 58.182 47.619 0.00 0.00 0.00 3.67
102 103 2.166870 AGTACTTGTTGGACGTGTGACA 59.833 45.455 0.00 0.00 0.00 3.58
115 116 0.387565 TGTGACACGAAGTAGCTGCA 59.612 50.000 4.12 0.00 41.61 4.41
117 118 1.656095 GTGACACGAAGTAGCTGCATC 59.344 52.381 4.12 0.00 41.61 3.91
119 120 0.608130 ACACGAAGTAGCTGCATCCA 59.392 50.000 4.12 0.00 41.61 3.41
120 121 1.002366 CACGAAGTAGCTGCATCCAC 58.998 55.000 4.12 0.00 41.61 4.02
121 122 0.608130 ACGAAGTAGCTGCATCCACA 59.392 50.000 4.12 0.00 41.94 4.17
123 124 1.672737 CGAAGTAGCTGCATCCACACA 60.673 52.381 4.12 0.00 0.00 3.72
127 128 1.399440 GTAGCTGCATCCACACATGTG 59.601 52.381 24.25 24.25 45.23 3.21
141 142 5.904941 CACACATGTGGGCAATTATAATGT 58.095 37.500 28.64 0.31 42.10 2.71
143 144 6.817641 CACACATGTGGGCAATTATAATGTTT 59.182 34.615 28.64 0.00 42.10 2.83
144 145 7.010367 CACACATGTGGGCAATTATAATGTTTC 59.990 37.037 28.64 0.00 42.10 2.78
146 147 4.677584 TGTGGGCAATTATAATGTTTCGC 58.322 39.130 0.00 0.00 0.00 4.70
147 148 4.048504 GTGGGCAATTATAATGTTTCGCC 58.951 43.478 0.00 6.64 37.57 5.54
149 150 4.314740 GGCAATTATAATGTTTCGCCCA 57.685 40.909 0.00 0.00 32.01 5.36
150 151 4.048504 GGCAATTATAATGTTTCGCCCAC 58.951 43.478 0.00 0.00 32.01 4.61
151 152 4.440802 GGCAATTATAATGTTTCGCCCACA 60.441 41.667 0.00 0.00 32.01 4.17
154 155 4.688511 TTATAATGTTTCGCCCACACAC 57.311 40.909 0.00 0.00 0.00 3.82
155 156 0.869068 TAATGTTTCGCCCACACACG 59.131 50.000 0.00 0.00 0.00 4.49
156 157 1.791103 AATGTTTCGCCCACACACGG 61.791 55.000 0.00 0.00 0.00 4.94
157 158 2.898343 GTTTCGCCCACACACGGT 60.898 61.111 0.00 0.00 0.00 4.83
158 159 2.589442 TTTCGCCCACACACGGTC 60.589 61.111 0.00 0.00 0.00 4.79
159 160 3.387225 TTTCGCCCACACACGGTCA 62.387 57.895 0.00 0.00 0.00 4.02
160 161 3.800685 TTCGCCCACACACGGTCAG 62.801 63.158 0.00 0.00 0.00 3.51
161 162 4.602259 CGCCCACACACGGTCAGT 62.602 66.667 0.00 0.00 0.00 3.41
169 170 3.731136 CACGGTCAGTGTGGGTTG 58.269 61.111 0.00 0.00 45.51 3.77
171 172 1.145377 ACGGTCAGTGTGGGTTGTC 59.855 57.895 0.00 0.00 0.00 3.18
172 173 1.335132 ACGGTCAGTGTGGGTTGTCT 61.335 55.000 0.00 0.00 0.00 3.41
174 175 1.594331 GGTCAGTGTGGGTTGTCTTC 58.406 55.000 0.00 0.00 0.00 2.87
175 176 1.141053 GGTCAGTGTGGGTTGTCTTCT 59.859 52.381 0.00 0.00 0.00 2.85
176 177 2.213499 GTCAGTGTGGGTTGTCTTCTG 58.787 52.381 0.00 0.00 0.00 3.02
177 178 0.947244 CAGTGTGGGTTGTCTTCTGC 59.053 55.000 0.00 0.00 0.00 4.26
179 180 1.202698 AGTGTGGGTTGTCTTCTGCTC 60.203 52.381 0.00 0.00 0.00 4.26
180 181 0.836606 TGTGGGTTGTCTTCTGCTCA 59.163 50.000 0.00 0.00 0.00 4.26
181 182 1.230324 GTGGGTTGTCTTCTGCTCAC 58.770 55.000 0.00 0.00 0.00 3.51
182 183 0.249868 TGGGTTGTCTTCTGCTCACG 60.250 55.000 0.00 0.00 0.00 4.35
183 184 1.569479 GGGTTGTCTTCTGCTCACGC 61.569 60.000 0.00 0.00 0.00 5.34
184 185 1.569479 GGTTGTCTTCTGCTCACGCC 61.569 60.000 0.00 0.00 34.43 5.68
185 186 0.880278 GTTGTCTTCTGCTCACGCCA 60.880 55.000 0.00 0.00 34.43 5.69
186 187 0.880278 TTGTCTTCTGCTCACGCCAC 60.880 55.000 0.00 0.00 34.43 5.01
188 189 1.300931 TCTTCTGCTCACGCCACAC 60.301 57.895 0.00 0.00 34.43 3.82
189 190 1.595109 CTTCTGCTCACGCCACACA 60.595 57.895 0.00 0.00 34.43 3.72
190 191 1.835483 CTTCTGCTCACGCCACACAC 61.835 60.000 0.00 0.00 34.43 3.82
191 192 3.705638 CTGCTCACGCCACACACG 61.706 66.667 0.00 0.00 34.43 4.49
208 209 2.094659 CGGTGTGTGAGCGGATGTC 61.095 63.158 0.00 0.00 42.02 3.06
209 210 1.293498 GGTGTGTGAGCGGATGTCT 59.707 57.895 0.00 0.00 0.00 3.41
210 211 0.530744 GGTGTGTGAGCGGATGTCTA 59.469 55.000 0.00 0.00 0.00 2.59
213 214 3.181479 GGTGTGTGAGCGGATGTCTAATA 60.181 47.826 0.00 0.00 0.00 0.98
214 215 4.501571 GGTGTGTGAGCGGATGTCTAATAT 60.502 45.833 0.00 0.00 0.00 1.28
215 216 4.445718 GTGTGTGAGCGGATGTCTAATATG 59.554 45.833 0.00 0.00 0.00 1.78
217 218 2.996621 GTGAGCGGATGTCTAATATGCC 59.003 50.000 0.00 0.00 0.00 4.40
218 219 2.632512 TGAGCGGATGTCTAATATGCCA 59.367 45.455 0.00 0.00 0.00 4.92
219 220 2.996621 GAGCGGATGTCTAATATGCCAC 59.003 50.000 0.00 0.00 0.00 5.01
220 221 2.368548 AGCGGATGTCTAATATGCCACA 59.631 45.455 0.00 0.00 0.00 4.17
222 223 3.125829 GCGGATGTCTAATATGCCACATG 59.874 47.826 0.00 0.00 29.43 3.21
223 224 4.318332 CGGATGTCTAATATGCCACATGT 58.682 43.478 0.00 0.00 29.43 3.21
225 226 5.065914 GGATGTCTAATATGCCACATGTGT 58.934 41.667 23.79 8.80 29.43 3.72
226 227 5.049198 GGATGTCTAATATGCCACATGTGTG 60.049 44.000 23.79 15.96 45.23 3.82
237 238 1.398041 CACATGTGTGGGCGTTATCAG 59.602 52.381 18.03 0.00 42.10 2.90
238 239 1.016627 CATGTGTGGGCGTTATCAGG 58.983 55.000 0.00 0.00 0.00 3.86
239 240 0.908910 ATGTGTGGGCGTTATCAGGA 59.091 50.000 0.00 0.00 0.00 3.86
240 241 0.036765 TGTGTGGGCGTTATCAGGAC 60.037 55.000 0.00 0.00 0.00 3.85
250 251 5.362263 GGCGTTATCAGGACCATTTACTTA 58.638 41.667 0.00 0.00 0.00 2.24
293 294 9.842775 AGCTGATGAATAGATTGAAAGTTATCA 57.157 29.630 0.00 0.00 0.00 2.15
345 350 8.337739 AGTACCAACTAGAAGAGAGGAATCTTA 58.662 37.037 0.00 0.00 35.35 2.10
369 374 1.134098 TCCCTCCTTCGATCCATTTGC 60.134 52.381 0.00 0.00 0.00 3.68
377 382 5.485353 TCCTTCGATCCATTTGCCTAGATAT 59.515 40.000 0.00 0.00 0.00 1.63
379 384 6.358974 TTCGATCCATTTGCCTAGATATGA 57.641 37.500 0.00 0.00 0.00 2.15
382 387 8.078060 TCGATCCATTTGCCTAGATATGAATA 57.922 34.615 0.00 0.00 0.00 1.75
438 2549 8.949421 ACAAGTAATATGGATCAAAGGGAGTAT 58.051 33.333 0.00 0.00 0.00 2.12
518 2632 1.593209 GGCTCAAACGTGTGTCCGA 60.593 57.895 5.45 0.00 0.00 4.55
559 2673 3.859411 AAGCAACAAAAGAACGGAACA 57.141 38.095 0.00 0.00 0.00 3.18
732 2846 1.480137 CTTCTCTTCCAGCCGTCTCAT 59.520 52.381 0.00 0.00 0.00 2.90
911 3034 3.512329 TCCACATCGCTTTGGTCTAGTTA 59.488 43.478 0.00 0.00 34.19 2.24
929 3052 5.259832 AGTTACCTTCGTCTATTGGCTAC 57.740 43.478 0.00 0.00 0.00 3.58
989 3113 0.035317 AAGAGGATCGTGCAGTGCAA 59.965 50.000 21.67 5.49 41.47 4.08
1014 3138 0.443869 GATCAATGACGTTGTGCGCT 59.556 50.000 9.73 0.00 46.11 5.92
1122 3246 2.593468 TAAGCCAGCCTGCCGATCAC 62.593 60.000 0.00 0.00 0.00 3.06
1161 3290 2.086869 TCTTCTTGCCTTGTGCTATGC 58.913 47.619 0.00 0.00 42.00 3.14
1724 3864 3.797353 GCCATGGCCTCCCTCGAA 61.797 66.667 27.24 0.00 34.56 3.71
2018 4173 2.051256 CGTCCCGTCCGATCGATG 60.051 66.667 18.66 8.15 0.00 3.84
2104 4279 1.129437 GTGCAGTCTGCCGAGATTTTC 59.871 52.381 21.99 0.00 44.23 2.29
2143 4320 2.278206 CATCGACCGACCTCTGCG 60.278 66.667 0.00 0.00 0.00 5.18
2233 4429 2.643933 ACGGACGTAGCTTTCTTACC 57.356 50.000 0.00 0.00 0.00 2.85
2258 4454 6.573664 TTTCATGAAAATGACTTGGACGAT 57.426 33.333 18.45 0.00 0.00 3.73
2263 4459 2.622064 AATGACTTGGACGATAGGGC 57.378 50.000 0.00 0.00 43.77 5.19
2294 4500 4.040339 ACCAAAAATCTCCACCCAAATGAC 59.960 41.667 0.00 0.00 0.00 3.06
2306 4512 1.202110 CCAAATGACTCTGACGCATGC 60.202 52.381 7.91 7.91 0.00 4.06
2307 4513 1.089920 AAATGACTCTGACGCATGCC 58.910 50.000 13.15 0.00 0.00 4.40
2308 4514 0.036105 AATGACTCTGACGCATGCCA 60.036 50.000 13.15 4.10 0.00 4.92
2309 4515 0.036105 ATGACTCTGACGCATGCCAA 60.036 50.000 13.15 0.00 0.00 4.52
2310 4516 0.671472 TGACTCTGACGCATGCCAAG 60.671 55.000 13.15 7.35 0.00 3.61
2311 4517 0.671781 GACTCTGACGCATGCCAAGT 60.672 55.000 13.15 3.94 0.00 3.16
2312 4518 0.250467 ACTCTGACGCATGCCAAGTT 60.250 50.000 13.15 0.00 0.00 2.66
2313 4519 0.167470 CTCTGACGCATGCCAAGTTG 59.833 55.000 13.15 0.00 0.00 3.16
2355 4573 9.857656 ATTTACTTGTGATGGTGATATCAGATT 57.142 29.630 5.42 0.00 37.72 2.40
2363 4581 4.377021 TGGTGATATCAGATTACCGCAAC 58.623 43.478 5.42 0.00 34.16 4.17
2458 4676 2.110967 CATGGCGGCTTCTGGTGAG 61.111 63.158 11.43 0.00 0.00 3.51
2497 4715 0.678048 GTGATGTCCTCCTTGGCCAC 60.678 60.000 3.88 0.00 35.26 5.01
2588 4806 5.307204 AGATGAGAAGATAATCAAGCCTGC 58.693 41.667 0.00 0.00 0.00 4.85
2589 4807 4.767578 TGAGAAGATAATCAAGCCTGCT 57.232 40.909 0.00 0.00 0.00 4.24
2600 4818 4.074526 GCCTGCTCGTCTCCAGCA 62.075 66.667 0.00 0.00 44.80 4.41
2647 4866 3.127548 GTGTAATCGTCAAGACCCGAGTA 59.872 47.826 0.00 0.00 36.41 2.59
2674 4893 1.048601 ACATCAGGTCACGGTCTTGT 58.951 50.000 0.00 0.00 0.00 3.16
2675 4894 1.270305 ACATCAGGTCACGGTCTTGTG 60.270 52.381 0.00 0.00 41.28 3.33
2676 4895 0.321671 ATCAGGTCACGGTCTTGTGG 59.678 55.000 0.00 0.00 40.31 4.17
2677 4896 1.301716 CAGGTCACGGTCTTGTGGG 60.302 63.158 0.00 0.00 40.31 4.61
2678 4897 1.764854 AGGTCACGGTCTTGTGGGT 60.765 57.895 0.00 0.00 40.31 4.51
2679 4898 1.301479 GGTCACGGTCTTGTGGGTC 60.301 63.158 0.00 0.00 40.31 4.46
2680 4899 1.746517 GTCACGGTCTTGTGGGTCT 59.253 57.895 0.00 0.00 40.31 3.85
2681 4900 0.963962 GTCACGGTCTTGTGGGTCTA 59.036 55.000 0.00 0.00 40.31 2.59
2682 4901 1.342174 GTCACGGTCTTGTGGGTCTAA 59.658 52.381 0.00 0.00 40.31 2.10
2683 4902 2.040939 TCACGGTCTTGTGGGTCTAAA 58.959 47.619 0.00 0.00 40.31 1.85
2684 4903 2.036733 TCACGGTCTTGTGGGTCTAAAG 59.963 50.000 0.00 0.00 40.31 1.85
2685 4904 2.044758 ACGGTCTTGTGGGTCTAAAGT 58.955 47.619 0.00 0.00 0.00 2.66
2686 4905 2.436911 ACGGTCTTGTGGGTCTAAAGTT 59.563 45.455 0.00 0.00 0.00 2.66
2687 4906 3.118149 ACGGTCTTGTGGGTCTAAAGTTT 60.118 43.478 0.00 0.00 0.00 2.66
2688 4907 3.881089 CGGTCTTGTGGGTCTAAAGTTTT 59.119 43.478 0.00 0.00 0.00 2.43
2689 4908 4.337274 CGGTCTTGTGGGTCTAAAGTTTTT 59.663 41.667 0.00 0.00 0.00 1.94
2755 4977 6.836527 AGCTGTATATTATAGGGTCAGGCTAG 59.163 42.308 0.00 0.00 0.00 3.42
2761 4984 3.529216 ATAGGGTCAGGCTAGAGGTAC 57.471 52.381 0.00 0.00 0.00 3.34
2773 4996 0.548031 AGAGGTACGTCCGGGTGATA 59.452 55.000 11.83 0.00 41.99 2.15
2781 5004 5.183904 GGTACGTCCGGGTGATATTTATACT 59.816 44.000 0.00 0.00 0.00 2.12
2782 5005 5.130292 ACGTCCGGGTGATATTTATACTG 57.870 43.478 0.00 0.00 0.00 2.74
2785 5011 5.105473 CGTCCGGGTGATATTTATACTGGAT 60.105 44.000 0.00 0.00 0.00 3.41
2812 5038 9.607988 TTTTCGATAATTATCCACAGTACATGT 57.392 29.630 17.83 2.69 45.43 3.21
2815 5041 9.855021 TCGATAATTATCCACAGTACATGTATG 57.145 33.333 17.83 10.61 41.41 2.39
2816 5042 9.855021 CGATAATTATCCACAGTACATGTATGA 57.145 33.333 17.83 2.14 41.41 2.15
2846 5072 7.970061 TGCAATCAAAGCTAGATTAACAACATC 59.030 33.333 12.43 0.00 34.14 3.06
2883 5109 2.214387 TGAGAGCTGATATGCGTGTG 57.786 50.000 0.00 0.00 38.13 3.82
2893 5119 1.337384 TATGCGTGTGGATGGGCTCT 61.337 55.000 0.00 0.00 0.00 4.09
2894 5120 1.337384 ATGCGTGTGGATGGGCTCTA 61.337 55.000 0.00 0.00 0.00 2.43
2895 5121 1.337384 TGCGTGTGGATGGGCTCTAT 61.337 55.000 0.00 0.00 0.00 1.98
2896 5122 0.179045 GCGTGTGGATGGGCTCTATT 60.179 55.000 0.00 0.00 0.00 1.73
2903 5538 2.972713 TGGATGGGCTCTATTAGGTGTC 59.027 50.000 0.00 0.00 0.00 3.67
2916 5551 8.314143 TCTATTAGGTGTCGGTAAAACTTTTG 57.686 34.615 0.00 0.00 0.00 2.44
2917 5552 5.754543 TTAGGTGTCGGTAAAACTTTTGG 57.245 39.130 0.00 0.00 0.00 3.28
2929 5564 6.890268 GGTAAAACTTTTGGGTGATAGAGGAT 59.110 38.462 0.00 0.00 0.00 3.24
2942 5577 4.767409 TGATAGAGGATCCTTGACGGTATG 59.233 45.833 17.42 0.00 33.66 2.39
2946 5582 2.040178 GGATCCTTGACGGTATGAGGT 58.960 52.381 3.84 0.00 0.00 3.85
2961 5597 0.307760 GAGGTCCAGTGTGCAAAACG 59.692 55.000 0.00 0.00 0.00 3.60
2964 5600 1.336755 GGTCCAGTGTGCAAAACGATT 59.663 47.619 0.00 0.00 0.00 3.34
2966 5602 1.336440 TCCAGTGTGCAAAACGATTGG 59.664 47.619 0.00 0.00 0.00 3.16
2967 5603 1.336440 CCAGTGTGCAAAACGATTGGA 59.664 47.619 0.00 0.00 0.00 3.53
2998 5636 9.396022 TCATAACCTCTTGATTTTCATACCTTC 57.604 33.333 0.00 0.00 0.00 3.46
3092 5730 2.225467 TCGAAACCATGCATGTGTTCA 58.775 42.857 26.56 16.86 0.00 3.18
3117 5756 2.947652 CCTTGACCACCTGATATTGCAG 59.052 50.000 0.00 0.00 35.66 4.41
3142 5793 5.045012 ACATATCATGACTCCACATGCTT 57.955 39.130 0.00 0.00 44.79 3.91
3149 5800 4.128925 TGACTCCACATGCTTATCTGTC 57.871 45.455 0.00 0.00 0.00 3.51
3150 5801 3.515104 TGACTCCACATGCTTATCTGTCA 59.485 43.478 0.00 0.00 0.00 3.58
3168 5820 4.948847 TGTCACAGTAGCATATCATGACC 58.051 43.478 0.00 0.00 35.26 4.02
3241 5893 7.887996 TCATCAAAACATGCTAAAACATTCC 57.112 32.000 0.00 0.00 0.00 3.01
3243 5895 4.683781 TCAAAACATGCTAAAACATTCCGC 59.316 37.500 0.00 0.00 0.00 5.54
3255 5907 1.153168 ATTCCGCCTCACAATCGGG 60.153 57.895 0.00 0.00 43.10 5.14
3267 5919 1.956477 ACAATCGGGCAAGCCATTATC 59.044 47.619 13.87 0.00 37.98 1.75
3268 5920 1.270550 CAATCGGGCAAGCCATTATCC 59.729 52.381 13.87 0.00 37.98 2.59
3273 5925 2.670939 GGGCAAGCCATTATCCTCTTT 58.329 47.619 13.87 0.00 37.98 2.52
3274 5926 3.747388 CGGGCAAGCCATTATCCTCTTTA 60.747 47.826 13.87 0.00 37.98 1.85
3275 5927 4.215109 GGGCAAGCCATTATCCTCTTTAA 58.785 43.478 13.87 0.00 37.98 1.52
3278 5930 6.151817 GGGCAAGCCATTATCCTCTTTAATAG 59.848 42.308 13.87 0.00 37.98 1.73
3309 5961 9.936759 TGATTTCCAATATTTAGTTTTGTTCCC 57.063 29.630 0.00 0.00 0.00 3.97
3311 5963 9.942850 ATTTCCAATATTTAGTTTTGTTCCCTG 57.057 29.630 0.00 0.00 0.00 4.45
3318 5970 7.786178 ATTTAGTTTTGTTCCCTGAAAAAGC 57.214 32.000 0.00 0.00 0.00 3.51
3321 5973 3.535280 TTTGTTCCCTGAAAAAGCACC 57.465 42.857 0.00 0.00 0.00 5.01
3334 5986 7.201785 CCTGAAAAAGCACCTAGTTTTGTTCTA 60.202 37.037 0.00 0.00 30.55 2.10
3339 5991 4.038883 AGCACCTAGTTTTGTTCTAGACGT 59.961 41.667 0.00 0.00 37.62 4.34
3347 5999 6.916440 AGTTTTGTTCTAGACGTTTTGGTTT 58.084 32.000 0.00 0.00 0.00 3.27
3404 6056 5.529430 TGAATGTATACCACAATTTAGCCCG 59.471 40.000 0.00 0.00 41.55 6.13
3407 6059 4.877251 TGTATACCACAATTTAGCCCGTTC 59.123 41.667 0.00 0.00 32.95 3.95
3424 6076 4.864247 CCCGTTCATGAATTTCAAATGGAC 59.136 41.667 12.12 10.83 29.05 4.02
3426 6078 6.127758 CCCGTTCATGAATTTCAAATGGACTA 60.128 38.462 12.12 0.00 29.05 2.59
3428 6080 8.620416 CCGTTCATGAATTTCAAATGGACTATA 58.380 33.333 12.12 0.00 29.05 1.31
3517 6169 6.419980 TGTTTGCTAATTATTTGCCAATGC 57.580 33.333 8.69 0.00 38.26 3.56
3518 6170 6.171921 TGTTTGCTAATTATTTGCCAATGCT 58.828 32.000 8.69 0.00 38.71 3.79
3521 6173 8.490355 GTTTGCTAATTATTTGCCAATGCTATC 58.510 33.333 8.69 0.00 38.71 2.08
3539 6191 1.933021 TCGCTTGTTCCTCCCTCTTA 58.067 50.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.063541 CTACGTTAGGTACCCGCGGG 62.064 65.000 42.17 42.17 42.03 6.13
4 5 1.356624 CTACGTTAGGTACCCGCGG 59.643 63.158 21.04 21.04 0.00 6.46
5 6 0.451783 AACTACGTTAGGTACCCGCG 59.548 55.000 8.74 13.16 0.00 6.46
6 7 1.202348 ACAACTACGTTAGGTACCCGC 59.798 52.381 8.74 0.00 0.00 6.13
7 8 2.867429 CACAACTACGTTAGGTACCCG 58.133 52.381 8.74 7.96 0.00 5.28
9 10 2.029110 TGGCACAACTACGTTAGGTACC 60.029 50.000 2.73 2.73 31.92 3.34
11 12 2.231964 CCTGGCACAACTACGTTAGGTA 59.768 50.000 0.00 0.00 38.70 3.08
13 14 1.274167 TCCTGGCACAACTACGTTAGG 59.726 52.381 0.00 0.00 38.70 2.69
15 16 1.336148 CGTCCTGGCACAACTACGTTA 60.336 52.381 0.00 0.00 38.70 3.18
17 18 1.006571 CGTCCTGGCACAACTACGT 60.007 57.895 0.00 0.00 38.70 3.57
18 19 1.006571 ACGTCCTGGCACAACTACG 60.007 57.895 0.93 0.93 41.43 3.51
20 21 0.249699 CACACGTCCTGGCACAACTA 60.250 55.000 0.00 0.00 38.70 2.24
21 22 1.523711 CACACGTCCTGGCACAACT 60.524 57.895 0.00 0.00 38.70 3.16
22 23 2.542907 CCACACGTCCTGGCACAAC 61.543 63.158 0.00 0.00 38.70 3.32
23 24 2.203139 CCACACGTCCTGGCACAA 60.203 61.111 0.00 0.00 38.70 3.33
29 30 2.830772 CAAATATGCCACACGTCCTG 57.169 50.000 0.00 0.00 0.00 3.86
59 60 4.715523 ATTCCCACCCCGCACGTG 62.716 66.667 12.28 12.28 0.00 4.49
60 61 4.715523 CATTCCCACCCCGCACGT 62.716 66.667 0.00 0.00 0.00 4.49
61 62 4.402528 TCATTCCCACCCCGCACG 62.403 66.667 0.00 0.00 0.00 5.34
63 64 1.613928 TACTCATTCCCACCCCGCA 60.614 57.895 0.00 0.00 0.00 5.69
65 66 1.411612 GTACTACTCATTCCCACCCCG 59.588 57.143 0.00 0.00 0.00 5.73
66 67 2.760581 AGTACTACTCATTCCCACCCC 58.239 52.381 0.00 0.00 0.00 4.95
69 70 4.935808 CCAACAAGTACTACTCATTCCCAC 59.064 45.833 0.00 0.00 0.00 4.61
70 71 4.841813 TCCAACAAGTACTACTCATTCCCA 59.158 41.667 0.00 0.00 0.00 4.37
72 73 4.863131 CGTCCAACAAGTACTACTCATTCC 59.137 45.833 0.00 0.00 0.00 3.01
74 75 5.221382 ACACGTCCAACAAGTACTACTCATT 60.221 40.000 0.00 0.00 0.00 2.57
75 76 4.280174 ACACGTCCAACAAGTACTACTCAT 59.720 41.667 0.00 0.00 0.00 2.90
76 77 3.633525 ACACGTCCAACAAGTACTACTCA 59.366 43.478 0.00 0.00 0.00 3.41
77 78 3.979495 CACACGTCCAACAAGTACTACTC 59.021 47.826 0.00 0.00 0.00 2.59
78 79 3.633525 TCACACGTCCAACAAGTACTACT 59.366 43.478 0.00 0.00 0.00 2.57
79 80 3.732721 GTCACACGTCCAACAAGTACTAC 59.267 47.826 0.00 0.00 0.00 2.73
80 81 3.380954 TGTCACACGTCCAACAAGTACTA 59.619 43.478 0.00 0.00 0.00 1.82
81 82 2.166870 TGTCACACGTCCAACAAGTACT 59.833 45.455 0.00 0.00 0.00 2.73
82 83 2.283351 GTGTCACACGTCCAACAAGTAC 59.717 50.000 0.00 0.00 0.00 2.73
83 84 2.542597 GTGTCACACGTCCAACAAGTA 58.457 47.619 0.00 0.00 0.00 2.24
84 85 1.365699 GTGTCACACGTCCAACAAGT 58.634 50.000 0.00 0.00 0.00 3.16
95 96 0.784778 GCAGCTACTTCGTGTCACAC 59.215 55.000 0.00 0.00 0.00 3.82
96 97 0.387565 TGCAGCTACTTCGTGTCACA 59.612 50.000 3.42 0.00 0.00 3.58
98 99 1.404181 GGATGCAGCTACTTCGTGTCA 60.404 52.381 0.22 0.00 0.00 3.58
100 101 0.608130 TGGATGCAGCTACTTCGTGT 59.392 50.000 0.22 0.00 0.00 4.49
101 102 1.002366 GTGGATGCAGCTACTTCGTG 58.998 55.000 11.58 0.00 0.00 4.35
102 103 0.608130 TGTGGATGCAGCTACTTCGT 59.392 50.000 19.47 0.00 0.00 3.85
105 106 2.290514 ACATGTGTGGATGCAGCTACTT 60.291 45.455 19.47 1.90 0.00 2.24
106 107 1.280133 ACATGTGTGGATGCAGCTACT 59.720 47.619 19.47 0.00 0.00 2.57
108 109 1.741528 CACATGTGTGGATGCAGCTA 58.258 50.000 18.03 0.00 42.10 3.32
109 110 2.563297 CACATGTGTGGATGCAGCT 58.437 52.632 18.03 0.00 42.10 4.24
119 120 6.543430 AACATTATAATTGCCCACATGTGT 57.457 33.333 23.79 7.33 0.00 3.72
120 121 6.198778 CGAAACATTATAATTGCCCACATGTG 59.801 38.462 19.31 19.31 0.00 3.21
121 122 6.272318 CGAAACATTATAATTGCCCACATGT 58.728 36.000 0.00 0.00 0.00 3.21
123 124 5.288804 GCGAAACATTATAATTGCCCACAT 58.711 37.500 0.00 0.00 0.00 3.21
128 129 4.048504 GTGGGCGAAACATTATAATTGCC 58.951 43.478 6.53 6.53 40.48 4.52
131 132 5.646606 GTGTGTGGGCGAAACATTATAATT 58.353 37.500 0.00 0.00 0.00 1.40
132 133 4.201871 CGTGTGTGGGCGAAACATTATAAT 60.202 41.667 0.00 0.00 0.00 1.28
133 134 3.125487 CGTGTGTGGGCGAAACATTATAA 59.875 43.478 0.00 0.00 0.00 0.98
134 135 2.673862 CGTGTGTGGGCGAAACATTATA 59.326 45.455 0.00 0.00 0.00 0.98
135 136 1.466950 CGTGTGTGGGCGAAACATTAT 59.533 47.619 0.00 0.00 0.00 1.28
136 137 0.869068 CGTGTGTGGGCGAAACATTA 59.131 50.000 0.00 0.00 0.00 1.90
137 138 1.652012 CGTGTGTGGGCGAAACATT 59.348 52.632 0.00 0.00 0.00 2.71
138 139 2.258013 CCGTGTGTGGGCGAAACAT 61.258 57.895 0.00 0.00 0.00 2.71
139 140 2.897846 CCGTGTGTGGGCGAAACA 60.898 61.111 0.00 0.00 0.00 2.83
140 141 2.888998 GACCGTGTGTGGGCGAAAC 61.889 63.158 0.00 0.00 0.00 2.78
141 142 2.589442 GACCGTGTGTGGGCGAAA 60.589 61.111 0.00 0.00 0.00 3.46
143 144 4.293648 CTGACCGTGTGTGGGCGA 62.294 66.667 0.00 0.00 41.34 5.54
144 145 4.602259 ACTGACCGTGTGTGGGCG 62.602 66.667 0.00 0.00 41.34 6.13
154 155 0.179056 AAGACAACCCACACTGACCG 60.179 55.000 0.00 0.00 0.00 4.79
155 156 1.141053 AGAAGACAACCCACACTGACC 59.859 52.381 0.00 0.00 0.00 4.02
156 157 2.213499 CAGAAGACAACCCACACTGAC 58.787 52.381 0.00 0.00 0.00 3.51
157 158 1.475034 GCAGAAGACAACCCACACTGA 60.475 52.381 0.00 0.00 0.00 3.41
158 159 0.947244 GCAGAAGACAACCCACACTG 59.053 55.000 0.00 0.00 0.00 3.66
159 160 0.839946 AGCAGAAGACAACCCACACT 59.160 50.000 0.00 0.00 0.00 3.55
160 161 1.230324 GAGCAGAAGACAACCCACAC 58.770 55.000 0.00 0.00 0.00 3.82
161 162 0.836606 TGAGCAGAAGACAACCCACA 59.163 50.000 0.00 0.00 0.00 4.17
162 163 1.230324 GTGAGCAGAAGACAACCCAC 58.770 55.000 0.00 0.00 0.00 4.61
163 164 0.249868 CGTGAGCAGAAGACAACCCA 60.250 55.000 0.00 0.00 0.00 4.51
164 165 2.533318 CGTGAGCAGAAGACAACCC 58.467 57.895 0.00 0.00 0.00 4.11
177 178 3.337889 CACCGTGTGTGGCGTGAG 61.338 66.667 0.00 0.00 41.52 3.51
189 190 2.048222 CATCCGCTCACACACCGT 60.048 61.111 0.00 0.00 0.00 4.83
190 191 2.048222 ACATCCGCTCACACACCG 60.048 61.111 0.00 0.00 0.00 4.94
191 192 0.530744 TAGACATCCGCTCACACACC 59.469 55.000 0.00 0.00 0.00 4.16
193 194 4.620982 CATATTAGACATCCGCTCACACA 58.379 43.478 0.00 0.00 0.00 3.72
194 195 3.430218 GCATATTAGACATCCGCTCACAC 59.570 47.826 0.00 0.00 0.00 3.82
195 196 3.554960 GGCATATTAGACATCCGCTCACA 60.555 47.826 0.00 0.00 0.00 3.58
196 197 2.996621 GGCATATTAGACATCCGCTCAC 59.003 50.000 0.00 0.00 0.00 3.51
197 198 2.632512 TGGCATATTAGACATCCGCTCA 59.367 45.455 0.00 0.00 0.00 4.26
198 199 2.996621 GTGGCATATTAGACATCCGCTC 59.003 50.000 0.00 0.00 0.00 5.03
200 201 2.766313 TGTGGCATATTAGACATCCGC 58.234 47.619 0.00 0.00 0.00 5.54
201 202 4.152938 CACATGTGGCATATTAGACATCCG 59.847 45.833 18.51 0.00 0.00 4.18
202 203 5.049198 CACACATGTGGCATATTAGACATCC 60.049 44.000 28.64 0.00 42.10 3.51
217 218 1.398041 CTGATAACGCCCACACATGTG 59.602 52.381 24.25 24.25 45.23 3.21
218 219 1.678728 CCTGATAACGCCCACACATGT 60.679 52.381 0.00 0.00 0.00 3.21
219 220 1.016627 CCTGATAACGCCCACACATG 58.983 55.000 0.00 0.00 0.00 3.21
220 221 0.908910 TCCTGATAACGCCCACACAT 59.091 50.000 0.00 0.00 0.00 3.21
222 223 0.743345 GGTCCTGATAACGCCCACAC 60.743 60.000 0.00 0.00 0.00 3.82
223 224 1.195442 TGGTCCTGATAACGCCCACA 61.195 55.000 0.00 0.00 0.00 4.17
225 226 0.916086 AATGGTCCTGATAACGCCCA 59.084 50.000 0.00 0.00 0.00 5.36
226 227 2.052782 AAATGGTCCTGATAACGCCC 57.947 50.000 0.00 0.00 0.00 6.13
228 229 6.073222 CCATAAGTAAATGGTCCTGATAACGC 60.073 42.308 0.00 0.00 41.38 4.84
229 230 7.421530 CCATAAGTAAATGGTCCTGATAACG 57.578 40.000 0.00 0.00 41.38 3.18
250 251 5.483685 TCAGCTAGTACAAAGAACACCAT 57.516 39.130 0.00 0.00 0.00 3.55
257 258 9.755804 CAATCTATTCATCAGCTAGTACAAAGA 57.244 33.333 0.00 0.00 0.00 2.52
267 268 9.842775 TGATAACTTTCAATCTATTCATCAGCT 57.157 29.630 0.00 0.00 0.00 4.24
293 294 6.208599 TGGATGGAAGCTTTTTCTTTTACGAT 59.791 34.615 0.00 0.00 0.00 3.73
299 300 5.876651 ACTTGGATGGAAGCTTTTTCTTT 57.123 34.783 0.00 0.00 0.00 2.52
302 303 4.522789 TGGTACTTGGATGGAAGCTTTTTC 59.477 41.667 0.00 0.00 0.00 2.29
345 350 3.551635 ATGGATCGAAGGAGGGAGTAT 57.448 47.619 0.00 0.00 0.00 2.12
407 412 9.799106 CCCTTTGATCCATATTACTTGTCTTAT 57.201 33.333 0.00 0.00 0.00 1.73
518 2632 0.036732 TGGCCGAAGATTTGCTGACT 59.963 50.000 0.00 0.00 0.00 3.41
559 2673 4.229582 TGGGGTAGAGCAGGAAATATTTGT 59.770 41.667 5.17 0.00 0.00 2.83
911 3034 1.407979 CGGTAGCCAATAGACGAAGGT 59.592 52.381 0.00 0.00 0.00 3.50
929 3052 2.290641 CTGGTGAACTCTTTGGTTTCGG 59.709 50.000 0.00 0.00 0.00 4.30
989 3113 2.813754 CACAACGTCATTGATCCCTTGT 59.186 45.455 0.00 0.00 41.23 3.16
1014 3138 1.882625 CCGGAGCGCATCGAAATCA 60.883 57.895 20.92 0.00 0.00 2.57
1122 3246 5.698545 AGAAGATCCAGACAAAGAAGAAACG 59.301 40.000 0.00 0.00 0.00 3.60
1161 3290 1.237285 CCAGACCAAAAGGTCAGCGG 61.237 60.000 16.23 9.70 40.96 5.52
1177 3306 2.644992 GTTGCCGCCAAGTTCCAG 59.355 61.111 0.00 0.00 0.00 3.86
1260 3394 3.490759 GACGCGGATGGTGCAGTG 61.491 66.667 12.47 0.00 0.00 3.66
1724 3864 3.000819 TCGCCGGGGAAGATGTGT 61.001 61.111 20.34 0.00 0.00 3.72
1773 3928 3.368571 GCAAGTGCACCCTGCCTC 61.369 66.667 24.31 4.17 44.23 4.70
1831 3986 2.983592 CCGGCGCCACCTTTTTCT 60.984 61.111 28.98 0.00 35.61 2.52
2004 4159 2.335369 GTCCATCGATCGGACGGG 59.665 66.667 22.64 11.59 43.36 5.28
2090 4265 1.812571 GGCAAAGAAAATCTCGGCAGA 59.187 47.619 5.83 0.00 30.12 4.26
2094 4269 0.451783 CGGGGCAAAGAAAATCTCGG 59.548 55.000 0.00 0.00 0.00 4.63
2124 4301 1.517257 GCAGAGGTCGGTCGATGTG 60.517 63.158 0.00 0.00 0.00 3.21
2143 4320 2.887568 CCTGCTGCATCGACCGAC 60.888 66.667 1.31 0.00 0.00 4.79
2233 4429 6.437928 TCGTCCAAGTCATTTTCATGAAAAG 58.562 36.000 31.05 23.58 41.30 2.27
2258 4454 0.400975 TTTTGGTAGCGTTGGCCCTA 59.599 50.000 0.00 0.00 41.24 3.53
2263 4459 2.817258 TGGAGATTTTTGGTAGCGTTGG 59.183 45.455 0.00 0.00 0.00 3.77
2294 4500 0.167470 CAACTTGGCATGCGTCAGAG 59.833 55.000 12.44 7.18 0.00 3.35
2355 4573 2.522836 TGAAACGTTAGGTTGCGGTA 57.477 45.000 0.00 0.00 36.93 4.02
2363 4581 3.485216 GCCAATCACGATGAAACGTTAGG 60.485 47.826 0.00 0.00 44.76 2.69
2458 4676 2.837371 CTTCGCCCTCGTCACCTTCC 62.837 65.000 0.00 0.00 36.96 3.46
2497 4715 1.033574 CTCCGGCACTACCTTCCTAG 58.966 60.000 0.00 0.00 35.61 3.02
2588 4806 4.378978 GCAGTATACTATGCTGGAGACGAG 60.379 50.000 14.04 0.00 42.36 4.18
2589 4807 3.502595 GCAGTATACTATGCTGGAGACGA 59.497 47.826 14.04 0.00 42.36 4.20
2647 4866 2.878406 CCGTGACCTGATGTTTTGAAGT 59.122 45.455 0.00 0.00 0.00 3.01
2689 4908 9.211485 GCTAACTTTAGACCTATACACACAAAA 57.789 33.333 0.00 0.00 32.47 2.44
2690 4909 8.369424 TGCTAACTTTAGACCTATACACACAAA 58.631 33.333 0.00 0.00 32.47 2.83
2691 4910 7.898918 TGCTAACTTTAGACCTATACACACAA 58.101 34.615 0.00 0.00 32.47 3.33
2692 4911 7.470935 TGCTAACTTTAGACCTATACACACA 57.529 36.000 0.00 0.00 32.47 3.72
2693 4912 7.491696 CCTTGCTAACTTTAGACCTATACACAC 59.508 40.741 0.00 0.00 32.47 3.82
2694 4913 7.179694 ACCTTGCTAACTTTAGACCTATACACA 59.820 37.037 0.00 0.00 32.47 3.72
2695 4914 7.554211 ACCTTGCTAACTTTAGACCTATACAC 58.446 38.462 0.00 0.00 32.47 2.90
2696 4915 7.729124 ACCTTGCTAACTTTAGACCTATACA 57.271 36.000 0.00 0.00 32.47 2.29
2697 4916 8.911965 ACTACCTTGCTAACTTTAGACCTATAC 58.088 37.037 0.00 0.00 32.47 1.47
2698 4917 8.910944 CACTACCTTGCTAACTTTAGACCTATA 58.089 37.037 0.00 0.00 32.47 1.31
2699 4918 7.618512 TCACTACCTTGCTAACTTTAGACCTAT 59.381 37.037 0.00 0.00 32.47 2.57
2744 4966 0.395448 ACGTACCTCTAGCCTGACCC 60.395 60.000 0.00 0.00 0.00 4.46
2745 4967 1.023502 GACGTACCTCTAGCCTGACC 58.976 60.000 0.00 0.00 0.00 4.02
2755 4977 1.613836 ATATCACCCGGACGTACCTC 58.386 55.000 0.73 0.00 36.31 3.85
2761 4984 4.219070 TCCAGTATAAATATCACCCGGACG 59.781 45.833 0.73 0.00 0.00 4.79
2781 5004 8.746052 ACTGTGGATAATTATCGAAAAATCCA 57.254 30.769 17.25 8.47 37.49 3.41
2798 5024 6.041979 TGCAGTATCATACATGTACTGTGGAT 59.958 38.462 21.11 14.94 40.46 3.41
2813 5039 9.565090 TTAATCTAGCTTTGATTGCAGTATCAT 57.435 29.630 18.85 0.00 34.67 2.45
2814 5040 8.830580 GTTAATCTAGCTTTGATTGCAGTATCA 58.169 33.333 18.85 0.00 35.90 2.15
2815 5041 8.830580 TGTTAATCTAGCTTTGATTGCAGTATC 58.169 33.333 18.85 0.00 35.90 2.24
2816 5042 8.737168 TGTTAATCTAGCTTTGATTGCAGTAT 57.263 30.769 18.85 0.95 35.90 2.12
2846 5072 7.126726 GCTCTCAAGCTACCAATATAACATG 57.873 40.000 0.00 0.00 45.55 3.21
2873 5099 0.250467 GAGCCCATCCACACGCATAT 60.250 55.000 0.00 0.00 0.00 1.78
2883 5109 2.028930 CGACACCTAATAGAGCCCATCC 60.029 54.545 0.00 0.00 0.00 3.51
2893 5119 6.430616 CCCAAAAGTTTTACCGACACCTAATA 59.569 38.462 0.00 0.00 0.00 0.98
2894 5120 5.242171 CCCAAAAGTTTTACCGACACCTAAT 59.758 40.000 0.00 0.00 0.00 1.73
2895 5121 4.579753 CCCAAAAGTTTTACCGACACCTAA 59.420 41.667 0.00 0.00 0.00 2.69
2896 5122 4.136051 CCCAAAAGTTTTACCGACACCTA 58.864 43.478 0.00 0.00 0.00 3.08
2903 5538 5.123344 CCTCTATCACCCAAAAGTTTTACCG 59.877 44.000 0.00 0.00 0.00 4.02
2916 5551 2.297597 CGTCAAGGATCCTCTATCACCC 59.702 54.545 16.52 0.00 36.20 4.61
2917 5552 2.297597 CCGTCAAGGATCCTCTATCACC 59.702 54.545 16.52 0.00 45.00 4.02
2929 5564 1.272816 TGGACCTCATACCGTCAAGGA 60.273 52.381 0.00 0.00 45.00 3.36
2942 5577 0.307760 CGTTTTGCACACTGGACCTC 59.692 55.000 0.00 0.00 0.00 3.85
2946 5582 1.336440 CCAATCGTTTTGCACACTGGA 59.664 47.619 0.00 0.00 0.00 3.86
2964 5600 9.927668 GAAAATCAAGAGGTTATGAAAAATCCA 57.072 29.630 0.00 0.00 0.00 3.41
3034 5672 6.922957 GTGTTTAGATTCAATTCTTGGTGCAA 59.077 34.615 0.00 0.00 0.00 4.08
3048 5686 7.164498 CGATACGAGTCTTCAGTGTTTAGATTC 59.836 40.741 0.00 0.00 0.00 2.52
3060 5698 4.421058 CATGGTTTCGATACGAGTCTTCA 58.579 43.478 0.00 0.00 37.14 3.02
3092 5730 4.848357 CAATATCAGGTGGTCAAGGAAGT 58.152 43.478 0.00 0.00 0.00 3.01
3117 5756 4.556104 GCATGTGGAGTCATGATATGTTGC 60.556 45.833 0.00 0.00 45.41 4.17
3142 5793 7.309438 GGTCATGATATGCTACTGTGACAGATA 60.309 40.741 20.97 6.88 36.97 1.98
3149 5800 4.341366 TGGGTCATGATATGCTACTGTG 57.659 45.455 0.00 0.00 0.00 3.66
3150 5801 4.655649 TCTTGGGTCATGATATGCTACTGT 59.344 41.667 0.00 0.00 0.00 3.55
3168 5820 1.100510 CATGTGTGGGAGCATCTTGG 58.899 55.000 0.00 0.00 33.73 3.61
3215 5867 8.938906 GGAATGTTTTAGCATGTTTTGATGAAT 58.061 29.630 0.00 0.00 0.00 2.57
3218 5870 6.670452 GCGGAATGTTTTAGCATGTTTTGATG 60.670 38.462 0.00 0.00 0.00 3.07
3226 5878 2.423185 TGAGGCGGAATGTTTTAGCATG 59.577 45.455 0.00 0.00 0.00 4.06
3232 5884 2.095263 CGATTGTGAGGCGGAATGTTTT 60.095 45.455 0.00 0.00 0.00 2.43
3243 5895 2.409870 GGCTTGCCCGATTGTGAGG 61.410 63.158 0.00 0.00 0.00 3.86
3255 5907 7.751768 ACTATTAAAGAGGATAATGGCTTGC 57.248 36.000 0.00 0.00 0.00 4.01
3294 5946 7.279981 GTGCTTTTTCAGGGAACAAAACTAAAT 59.720 33.333 0.00 0.00 0.00 1.40
3295 5947 6.592220 GTGCTTTTTCAGGGAACAAAACTAAA 59.408 34.615 0.00 0.00 0.00 1.85
3309 5961 6.564328 AGAACAAAACTAGGTGCTTTTTCAG 58.436 36.000 0.00 0.00 0.00 3.02
3310 5962 6.524101 AGAACAAAACTAGGTGCTTTTTCA 57.476 33.333 0.00 0.00 0.00 2.69
3311 5963 7.856398 GTCTAGAACAAAACTAGGTGCTTTTTC 59.144 37.037 0.00 0.00 38.19 2.29
3317 5969 4.304939 ACGTCTAGAACAAAACTAGGTGC 58.695 43.478 0.00 0.00 38.19 5.01
3318 5970 6.839820 AAACGTCTAGAACAAAACTAGGTG 57.160 37.500 0.00 0.00 38.19 4.00
3321 5973 7.242914 ACCAAAACGTCTAGAACAAAACTAG 57.757 36.000 0.00 0.00 38.76 2.57
3385 6037 4.877251 TGAACGGGCTAAATTGTGGTATAC 59.123 41.667 0.00 0.00 0.00 1.47
3393 6045 6.098679 TGAAATTCATGAACGGGCTAAATTG 58.901 36.000 11.07 0.00 0.00 2.32
3396 6048 5.713792 TTGAAATTCATGAACGGGCTAAA 57.286 34.783 11.07 0.00 0.00 1.85
3399 6051 4.497300 CATTTGAAATTCATGAACGGGCT 58.503 39.130 11.07 0.00 0.00 5.19
3495 6147 6.667007 AGCATTGGCAAATAATTAGCAAAC 57.333 33.333 3.01 0.00 44.61 2.93
3517 6169 2.035632 AGAGGGAGGAACAAGCGATAG 58.964 52.381 0.00 0.00 0.00 2.08
3518 6170 2.160721 AGAGGGAGGAACAAGCGATA 57.839 50.000 0.00 0.00 0.00 2.92
3521 6173 2.990066 ATAAGAGGGAGGAACAAGCG 57.010 50.000 0.00 0.00 0.00 4.68


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

AutoCloner maintained by Alex Coulton.