Multiple sequence alignment - TraesCS3D01G325200

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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 TraesCS3D01G325200 chr3D 100.000 3350 0 0 1 3350 438046038 438049387 0.000000e+00 6187.0
1 TraesCS3D01G325200 chr3D 85.640 1539 192 12 1125 2638 431628048 431629582 0.000000e+00 1591.0
2 TraesCS3D01G325200 chr3D 85.390 1540 194 14 1125 2638 431448401 431449935 0.000000e+00 1568.0
3 TraesCS3D01G325200 chr3D 83.831 1540 201 21 1125 2637 431832147 431833665 0.000000e+00 1421.0
4 TraesCS3D01G325200 chr3D 98.350 303 5 0 1 303 438031227 438031529 1.770000e-147 532.0
5 TraesCS3D01G325200 chr3A 92.769 2337 117 17 864 3177 576270156 576267849 0.000000e+00 3332.0
6 TraesCS3D01G325200 chr3A 92.498 1333 97 2 1194 2524 576273684 576275015 0.000000e+00 1905.0
7 TraesCS3D01G325200 chr3A 82.507 1835 248 39 864 2637 569229980 569231802 0.000000e+00 1543.0
8 TraesCS3D01G325200 chr3A 85.127 1533 193 15 1125 2634 569167755 569169275 0.000000e+00 1535.0
9 TraesCS3D01G325200 chr3A 85.440 1408 174 14 1128 2509 568972125 568973527 0.000000e+00 1435.0
10 TraesCS3D01G325200 chr3A 94.097 847 39 6 2508 3350 576275198 576276037 0.000000e+00 1277.0
11 TraesCS3D01G325200 chr3A 97.143 35 0 1 835 868 576270210 576270176 1.300000e-04 58.4
12 TraesCS3D01G325200 chr3B 92.044 1986 128 14 1184 3161 573467918 573469881 0.000000e+00 2765.0
13 TraesCS3D01G325200 chr3B 92.932 1344 90 3 1194 2534 573487526 573488867 0.000000e+00 1951.0
14 TraesCS3D01G325200 chr3B 83.075 1808 253 32 864 2638 564023138 564024925 0.000000e+00 1594.0
15 TraesCS3D01G325200 chr3B 84.550 1534 204 15 1125 2635 564038332 564039855 0.000000e+00 1489.0
16 TraesCS3D01G325200 chr3B 94.689 772 30 4 2582 3350 573488871 573489634 0.000000e+00 1188.0
17 TraesCS3D01G325200 chr3B 90.689 537 31 11 303 837 573463964 573464483 0.000000e+00 697.0
18 TraesCS3D01G325200 chr3B 95.286 297 13 1 832 1127 573467610 573467906 1.410000e-128 470.0
19 TraesCS3D01G325200 chr7D 98.350 303 5 0 1 303 215002464 215002766 1.770000e-147 532.0
20 TraesCS3D01G325200 chr7D 98.350 303 5 0 1 303 519662200 519662502 1.770000e-147 532.0
21 TraesCS3D01G325200 chr6D 98.350 303 5 0 1 303 408862737 408862435 1.770000e-147 532.0
22 TraesCS3D01G325200 chr6D 82.520 246 18 9 393 634 472745085 472745309 3.410000e-45 193.0
23 TraesCS3D01G325200 chr5D 98.350 303 5 0 1 303 25013237 25012935 1.770000e-147 532.0
24 TraesCS3D01G325200 chr2D 98.350 303 5 0 1 303 473973513 473973815 1.770000e-147 532.0
25 TraesCS3D01G325200 chr1D 98.350 303 5 0 1 303 278666115 278665813 1.770000e-147 532.0
26 TraesCS3D01G325200 chr1D 97.419 310 8 0 1 310 159065528 159065837 2.290000e-146 529.0
27 TraesCS3D01G325200 chr4D 97.727 308 7 0 1 308 156216002 156216309 6.360000e-147 531.0
28 TraesCS3D01G325200 chr5B 93.793 290 17 1 476 765 546802265 546801977 5.130000e-118 435.0
29 TraesCS3D01G325200 chr5B 94.323 229 13 0 476 704 546803123 546802895 5.320000e-93 351.0
30 TraesCS3D01G325200 chr5B 93.886 229 14 0 476 704 546803982 546803754 2.470000e-91 346.0
31 TraesCS3D01G325200 chr5B 93.878 196 12 0 509 704 546804808 546804613 2.530000e-76 296.0
32 TraesCS3D01G325200 chr6B 94.681 94 4 1 331 423 717895811 717895904 9.690000e-31 145.0
33 TraesCS3D01G325200 chr6B 89.815 108 8 2 529 634 717896882 717896988 5.830000e-28 135.0


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 TraesCS3D01G325200 chr3D 438046038 438049387 3349 False 6187.000000 6187 100.0000 1 3350 1 chr3D.!!$F5 3349
1 TraesCS3D01G325200 chr3D 431628048 431629582 1534 False 1591.000000 1591 85.6400 1125 2638 1 chr3D.!!$F2 1513
2 TraesCS3D01G325200 chr3D 431448401 431449935 1534 False 1568.000000 1568 85.3900 1125 2638 1 chr3D.!!$F1 1513
3 TraesCS3D01G325200 chr3D 431832147 431833665 1518 False 1421.000000 1421 83.8310 1125 2637 1 chr3D.!!$F3 1512
4 TraesCS3D01G325200 chr3A 576267849 576270210 2361 True 1695.200000 3332 94.9560 835 3177 2 chr3A.!!$R1 2342
5 TraesCS3D01G325200 chr3A 576273684 576276037 2353 False 1591.000000 1905 93.2975 1194 3350 2 chr3A.!!$F4 2156
6 TraesCS3D01G325200 chr3A 569229980 569231802 1822 False 1543.000000 1543 82.5070 864 2637 1 chr3A.!!$F3 1773
7 TraesCS3D01G325200 chr3A 569167755 569169275 1520 False 1535.000000 1535 85.1270 1125 2634 1 chr3A.!!$F2 1509
8 TraesCS3D01G325200 chr3A 568972125 568973527 1402 False 1435.000000 1435 85.4400 1128 2509 1 chr3A.!!$F1 1381
9 TraesCS3D01G325200 chr3B 564023138 564024925 1787 False 1594.000000 1594 83.0750 864 2638 1 chr3B.!!$F1 1774
10 TraesCS3D01G325200 chr3B 573487526 573489634 2108 False 1569.500000 1951 93.8105 1194 3350 2 chr3B.!!$F4 2156
11 TraesCS3D01G325200 chr3B 564038332 564039855 1523 False 1489.000000 1489 84.5500 1125 2635 1 chr3B.!!$F2 1510
12 TraesCS3D01G325200 chr3B 573463964 573469881 5917 False 1310.666667 2765 92.6730 303 3161 3 chr3B.!!$F3 2858
13 TraesCS3D01G325200 chr5B 546801977 546804808 2831 True 357.000000 435 93.9700 476 765 4 chr5B.!!$R1 289

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
49 50 0.317938 GCGCCTCGTTCGATCTGTAT 60.318 55.0 0.00 0.00 0.0 2.29 F
133 134 0.382515 GCTTCCGCTGACTCGTCTAT 59.617 55.0 0.00 0.00 0.0 1.98 F
424 426 0.396417 GAGGCCCTAGACTGCAGAGA 60.396 60.0 23.35 3.63 0.0 3.10 F
2133 7418 0.399454 AGCTGGATTGTGCACTGAGT 59.601 50.0 19.41 0.74 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 7206 1.345741 CTCCAACCTCTCAAGCACAGA 59.654 52.381 0.00 0.0 0.00 3.41 R
2084 7369 0.249868 CAGAAGGTGTGGCACGAGAA 60.250 55.000 13.77 0.0 34.83 2.87 R
2298 7586 1.208052 TCATCAGTTCCAGCACTAGGC 59.792 52.381 0.00 0.0 45.30 3.93 R
3194 8713 0.325296 AAGGGAGGAGGATGCGTGTA 60.325 55.000 0.00 0.0 0.00 2.90 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
25 26 3.560989 GAGGATCCCAGGCAGGAG 58.439 66.667 8.55 0.00 39.95 3.69
26 27 2.040043 AGGATCCCAGGCAGGAGG 60.040 66.667 8.55 0.00 39.95 4.30
27 28 3.883549 GGATCCCAGGCAGGAGGC 61.884 72.222 0.00 0.00 39.95 4.70
44 45 2.956964 CCTGCGCCTCGTTCGATC 60.957 66.667 4.18 0.00 0.00 3.69
45 46 2.103143 CTGCGCCTCGTTCGATCT 59.897 61.111 4.18 0.00 0.00 2.75
46 47 2.202610 TGCGCCTCGTTCGATCTG 60.203 61.111 4.18 0.00 0.00 2.90
48 49 1.063649 GCGCCTCGTTCGATCTGTA 59.936 57.895 0.00 0.00 0.00 2.74
49 50 0.317938 GCGCCTCGTTCGATCTGTAT 60.318 55.000 0.00 0.00 0.00 2.29
50 51 1.676057 CGCCTCGTTCGATCTGTATC 58.324 55.000 0.00 0.00 0.00 2.24
51 52 1.663445 CGCCTCGTTCGATCTGTATCC 60.663 57.143 0.00 0.00 0.00 2.59
52 53 1.336056 GCCTCGTTCGATCTGTATCCC 60.336 57.143 0.00 0.00 0.00 3.85
53 54 1.954382 CCTCGTTCGATCTGTATCCCA 59.046 52.381 0.00 0.00 0.00 4.37
54 55 2.030717 CCTCGTTCGATCTGTATCCCAG 60.031 54.545 0.00 0.00 42.97 4.45
55 56 2.619177 CTCGTTCGATCTGTATCCCAGT 59.381 50.000 0.00 0.00 42.19 4.00
57 58 3.446161 TCGTTCGATCTGTATCCCAGTTT 59.554 43.478 0.00 0.00 42.19 2.66
58 59 3.551890 CGTTCGATCTGTATCCCAGTTTG 59.448 47.826 0.00 0.00 42.19 2.93
59 60 4.504858 GTTCGATCTGTATCCCAGTTTGT 58.495 43.478 0.00 0.00 42.19 2.83
60 61 4.123497 TCGATCTGTATCCCAGTTTGTG 57.877 45.455 0.00 0.00 42.19 3.33
61 62 2.609459 CGATCTGTATCCCAGTTTGTGC 59.391 50.000 0.00 0.00 42.19 4.57
63 64 4.441495 CGATCTGTATCCCAGTTTGTGCTA 60.441 45.833 0.00 0.00 42.19 3.49
64 65 4.471904 TCTGTATCCCAGTTTGTGCTAG 57.528 45.455 0.00 0.00 42.19 3.42
66 67 2.289565 GTATCCCAGTTTGTGCTAGCC 58.710 52.381 13.29 4.15 0.00 3.93
67 68 0.995024 ATCCCAGTTTGTGCTAGCCT 59.005 50.000 13.29 0.00 0.00 4.58
68 69 0.771127 TCCCAGTTTGTGCTAGCCTT 59.229 50.000 13.29 0.00 0.00 4.35
69 70 1.168714 CCCAGTTTGTGCTAGCCTTC 58.831 55.000 13.29 3.48 0.00 3.46
70 71 1.271597 CCCAGTTTGTGCTAGCCTTCT 60.272 52.381 13.29 0.83 0.00 2.85
72 73 3.559171 CCCAGTTTGTGCTAGCCTTCTTA 60.559 47.826 13.29 0.00 0.00 2.10
73 74 4.072131 CCAGTTTGTGCTAGCCTTCTTAA 58.928 43.478 13.29 0.00 0.00 1.85
74 75 4.154918 CCAGTTTGTGCTAGCCTTCTTAAG 59.845 45.833 13.29 0.00 0.00 1.85
90 91 7.489160 CCTTCTTAAGGCAAACTTGTTTAACT 58.511 34.615 1.85 0.00 42.78 2.24
94 95 9.959749 TCTTAAGGCAAACTTGTTTAACTTATG 57.040 29.630 15.68 16.48 40.37 1.90
95 96 9.744468 CTTAAGGCAAACTTGTTTAACTTATGT 57.256 29.630 15.68 0.00 40.37 2.29
96 97 9.738832 TTAAGGCAAACTTGTTTAACTTATGTC 57.261 29.630 15.68 1.30 40.37 3.06
99 100 7.068226 AGGCAAACTTGTTTAACTTATGTCTGT 59.932 33.333 0.00 0.00 0.00 3.41
100 101 8.347035 GGCAAACTTGTTTAACTTATGTCTGTA 58.653 33.333 0.00 0.00 0.00 2.74
101 102 9.382244 GCAAACTTGTTTAACTTATGTCTGTAG 57.618 33.333 0.00 0.00 0.00 2.74
104 105 9.826574 AACTTGTTTAACTTATGTCTGTAGTCA 57.173 29.630 0.00 0.00 0.00 3.41
105 106 9.477484 ACTTGTTTAACTTATGTCTGTAGTCAG 57.523 33.333 0.00 0.00 42.54 3.51
106 107 9.692749 CTTGTTTAACTTATGTCTGTAGTCAGA 57.307 33.333 0.00 0.00 46.85 3.27
119 120 6.341316 TCTGTAGTCAGATATTGTTGCTTCC 58.659 40.000 0.00 0.00 44.58 3.46
121 122 2.939103 AGTCAGATATTGTTGCTTCCGC 59.061 45.455 0.00 0.00 0.00 5.54
122 123 2.939103 GTCAGATATTGTTGCTTCCGCT 59.061 45.455 0.00 0.00 36.97 5.52
123 124 2.938451 TCAGATATTGTTGCTTCCGCTG 59.062 45.455 0.00 0.00 36.97 5.18
125 126 2.939103 AGATATTGTTGCTTCCGCTGAC 59.061 45.455 0.00 0.00 36.97 3.51
126 127 2.472695 TATTGTTGCTTCCGCTGACT 57.527 45.000 0.00 0.00 36.97 3.41
127 128 1.160137 ATTGTTGCTTCCGCTGACTC 58.840 50.000 0.00 0.00 36.97 3.36
129 130 1.664965 GTTGCTTCCGCTGACTCGT 60.665 57.895 0.00 0.00 36.97 4.18
130 131 1.372997 TTGCTTCCGCTGACTCGTC 60.373 57.895 0.00 0.00 36.97 4.20
131 132 1.806461 TTGCTTCCGCTGACTCGTCT 61.806 55.000 0.00 0.00 36.97 4.18
132 133 0.958876 TGCTTCCGCTGACTCGTCTA 60.959 55.000 0.00 0.00 36.97 2.59
133 134 0.382515 GCTTCCGCTGACTCGTCTAT 59.617 55.000 0.00 0.00 0.00 1.98
134 135 1.862008 GCTTCCGCTGACTCGTCTATG 60.862 57.143 0.00 0.00 0.00 2.23
135 136 1.671328 CTTCCGCTGACTCGTCTATGA 59.329 52.381 0.00 0.00 0.00 2.15
136 137 1.968704 TCCGCTGACTCGTCTATGAT 58.031 50.000 0.00 0.00 0.00 2.45
137 138 1.874231 TCCGCTGACTCGTCTATGATC 59.126 52.381 0.00 0.00 0.00 2.92
138 139 1.399087 CCGCTGACTCGTCTATGATCG 60.399 57.143 0.00 0.00 0.00 3.69
139 140 1.527311 CGCTGACTCGTCTATGATCGA 59.473 52.381 0.00 0.00 34.88 3.59
145 146 3.617540 CTCGTCTATGATCGAGCACTT 57.382 47.619 5.03 0.00 44.82 3.16
146 147 3.295785 CTCGTCTATGATCGAGCACTTG 58.704 50.000 5.03 0.00 44.82 3.16
147 148 2.683362 TCGTCTATGATCGAGCACTTGT 59.317 45.455 5.03 0.00 0.00 3.16
148 149 3.875134 TCGTCTATGATCGAGCACTTGTA 59.125 43.478 5.03 0.00 0.00 2.41
149 150 4.515567 TCGTCTATGATCGAGCACTTGTAT 59.484 41.667 5.03 0.00 0.00 2.29
150 151 5.008712 TCGTCTATGATCGAGCACTTGTATT 59.991 40.000 5.03 0.00 0.00 1.89
151 152 5.340932 CGTCTATGATCGAGCACTTGTATTC 59.659 44.000 5.03 0.00 0.00 1.75
152 153 5.340932 GTCTATGATCGAGCACTTGTATTCG 59.659 44.000 5.03 0.00 34.56 3.34
154 155 3.695816 TGATCGAGCACTTGTATTCGAG 58.304 45.455 0.00 0.00 44.14 4.04
155 156 1.909376 TCGAGCACTTGTATTCGAGC 58.091 50.000 5.19 0.00 37.18 5.03
157 158 1.291132 GAGCACTTGTATTCGAGCCC 58.709 55.000 0.00 0.00 0.00 5.19
158 159 0.905357 AGCACTTGTATTCGAGCCCT 59.095 50.000 0.00 0.00 0.00 5.19
159 160 1.134670 AGCACTTGTATTCGAGCCCTC 60.135 52.381 0.00 0.00 0.00 4.30
182 183 2.656947 GCCCCTGGCTTGTATTATGA 57.343 50.000 0.00 0.00 46.69 2.15
185 186 2.821969 CCCCTGGCTTGTATTATGATGC 59.178 50.000 0.00 0.00 0.00 3.91
186 187 3.499202 CCCCTGGCTTGTATTATGATGCT 60.499 47.826 0.00 0.00 0.00 3.79
189 190 4.581824 CCTGGCTTGTATTATGATGCTTGT 59.418 41.667 0.00 0.00 0.00 3.16
190 191 5.764686 CCTGGCTTGTATTATGATGCTTGTA 59.235 40.000 0.00 0.00 0.00 2.41
191 192 6.432162 CCTGGCTTGTATTATGATGCTTGTAT 59.568 38.462 0.00 0.00 0.00 2.29
192 193 7.205737 TGGCTTGTATTATGATGCTTGTATG 57.794 36.000 0.00 0.00 0.00 2.39
194 195 7.041167 TGGCTTGTATTATGATGCTTGTATGAC 60.041 37.037 0.00 0.00 0.00 3.06
196 197 8.562892 GCTTGTATTATGATGCTTGTATGACTT 58.437 33.333 0.00 0.00 0.00 3.01
217 218 9.772973 TGACTTATTTATGTTGTAGAGTTGTGT 57.227 29.630 0.00 0.00 0.00 3.72
222 223 7.851387 TTTATGTTGTAGAGTTGTGTTGTGA 57.149 32.000 0.00 0.00 0.00 3.58
223 224 8.445275 TTTATGTTGTAGAGTTGTGTTGTGAT 57.555 30.769 0.00 0.00 0.00 3.06
224 225 9.549078 TTTATGTTGTAGAGTTGTGTTGTGATA 57.451 29.630 0.00 0.00 0.00 2.15
226 227 7.652300 TGTTGTAGAGTTGTGTTGTGATATC 57.348 36.000 0.00 0.00 0.00 1.63
227 228 7.441836 TGTTGTAGAGTTGTGTTGTGATATCT 58.558 34.615 3.98 0.00 0.00 1.98
229 230 9.419297 GTTGTAGAGTTGTGTTGTGATATCTTA 57.581 33.333 3.98 0.00 0.00 2.10
230 231 8.981724 TGTAGAGTTGTGTTGTGATATCTTAC 57.018 34.615 3.98 0.00 0.00 2.34
232 233 6.100004 AGAGTTGTGTTGTGATATCTTACCG 58.900 40.000 3.98 0.00 0.00 4.02
233 234 5.790593 AGTTGTGTTGTGATATCTTACCGT 58.209 37.500 3.98 0.00 0.00 4.83
234 235 5.637810 AGTTGTGTTGTGATATCTTACCGTG 59.362 40.000 3.98 0.00 0.00 4.94
235 236 5.394224 TGTGTTGTGATATCTTACCGTGA 57.606 39.130 3.98 0.00 0.00 4.35
237 238 5.047590 TGTGTTGTGATATCTTACCGTGAGT 60.048 40.000 3.98 0.00 0.00 3.41
238 239 5.515626 GTGTTGTGATATCTTACCGTGAGTC 59.484 44.000 3.98 0.00 0.00 3.36
239 240 5.417894 TGTTGTGATATCTTACCGTGAGTCT 59.582 40.000 3.98 0.00 0.00 3.24
240 241 6.600427 TGTTGTGATATCTTACCGTGAGTCTA 59.400 38.462 3.98 0.00 0.00 2.59
241 242 7.284716 TGTTGTGATATCTTACCGTGAGTCTAT 59.715 37.037 3.98 0.00 0.00 1.98
243 244 6.996282 TGTGATATCTTACCGTGAGTCTATGA 59.004 38.462 3.98 0.00 0.00 2.15
244 245 7.665974 TGTGATATCTTACCGTGAGTCTATGAT 59.334 37.037 3.98 0.00 0.00 2.45
247 248 8.871629 ATATCTTACCGTGAGTCTATGATCTT 57.128 34.615 0.00 0.00 0.00 2.40
250 251 6.773200 TCTTACCGTGAGTCTATGATCTTGAT 59.227 38.462 0.00 0.00 0.00 2.57
251 252 5.446143 ACCGTGAGTCTATGATCTTGATC 57.554 43.478 3.82 3.82 0.00 2.92
252 253 4.023622 ACCGTGAGTCTATGATCTTGATCG 60.024 45.833 6.19 0.00 0.00 3.69
253 254 4.023622 CCGTGAGTCTATGATCTTGATCGT 60.024 45.833 9.84 9.84 0.00 3.73
254 255 5.179555 CCGTGAGTCTATGATCTTGATCGTA 59.820 44.000 10.88 10.88 0.00 3.43
255 256 6.074642 CGTGAGTCTATGATCTTGATCGTAC 58.925 44.000 8.09 3.87 0.00 3.67
259 260 7.229506 TGAGTCTATGATCTTGATCGTACACAT 59.770 37.037 15.49 0.00 0.00 3.21
260 261 7.946207 AGTCTATGATCTTGATCGTACACATT 58.054 34.615 15.49 0.59 0.00 2.71
261 262 8.417106 AGTCTATGATCTTGATCGTACACATTT 58.583 33.333 15.49 0.09 0.00 2.32
264 265 3.989705 TCTTGATCGTACACATTTGCG 57.010 42.857 0.00 0.00 0.00 4.85
265 266 3.322369 TCTTGATCGTACACATTTGCGT 58.678 40.909 0.00 0.00 0.00 5.24
266 267 3.122780 TCTTGATCGTACACATTTGCGTG 59.877 43.478 0.00 0.00 42.81 5.34
267 268 1.127766 TGATCGTACACATTTGCGTGC 59.872 47.619 0.00 0.00 40.73 5.34
268 269 1.127766 GATCGTACACATTTGCGTGCA 59.872 47.619 0.00 0.00 40.73 4.57
269 270 1.152510 TCGTACACATTTGCGTGCAT 58.847 45.000 0.00 0.00 40.73 3.96
270 271 1.136113 TCGTACACATTTGCGTGCATG 60.136 47.619 0.09 0.09 40.73 4.06
271 272 1.136113 CGTACACATTTGCGTGCATGA 60.136 47.619 10.93 0.00 40.73 3.07
272 273 2.476018 CGTACACATTTGCGTGCATGAT 60.476 45.455 10.93 0.00 40.73 2.45
274 275 3.846423 ACACATTTGCGTGCATGATTA 57.154 38.095 10.93 0.00 40.73 1.75
276 277 3.191162 ACACATTTGCGTGCATGATTAGT 59.809 39.130 10.93 0.00 40.73 2.24
277 278 3.544682 CACATTTGCGTGCATGATTAGTG 59.455 43.478 10.93 7.27 0.00 2.74
278 279 3.191162 ACATTTGCGTGCATGATTAGTGT 59.809 39.130 10.93 4.47 0.00 3.55
280 281 4.335082 TTTGCGTGCATGATTAGTGTAC 57.665 40.909 10.93 0.00 0.00 2.90
283 284 2.536365 CGTGCATGATTAGTGTACGGT 58.464 47.619 0.00 0.00 46.91 4.83
284 285 2.534349 CGTGCATGATTAGTGTACGGTC 59.466 50.000 0.00 0.00 46.91 4.79
285 286 2.534349 GTGCATGATTAGTGTACGGTCG 59.466 50.000 0.00 0.00 0.00 4.79
286 287 2.424246 TGCATGATTAGTGTACGGTCGA 59.576 45.455 0.00 0.00 0.00 4.20
287 288 3.119424 TGCATGATTAGTGTACGGTCGAA 60.119 43.478 0.00 0.00 0.00 3.71
288 289 4.049186 GCATGATTAGTGTACGGTCGAAT 58.951 43.478 0.00 0.00 0.00 3.34
289 290 4.148348 GCATGATTAGTGTACGGTCGAATC 59.852 45.833 0.00 9.54 0.00 2.52
291 292 2.830772 TTAGTGTACGGTCGAATCGG 57.169 50.000 1.76 0.00 0.00 4.18
292 293 1.016627 TAGTGTACGGTCGAATCGGG 58.983 55.000 1.76 0.00 0.00 5.14
293 294 1.226773 GTGTACGGTCGAATCGGGG 60.227 63.158 1.76 0.00 0.00 5.73
294 295 2.414594 GTACGGTCGAATCGGGGG 59.585 66.667 1.76 0.00 0.00 5.40
295 296 3.530260 TACGGTCGAATCGGGGGC 61.530 66.667 1.76 0.00 0.00 5.80
299 300 4.137872 GTCGAATCGGGGGCGTCA 62.138 66.667 1.76 0.00 0.00 4.35
300 301 4.137872 TCGAATCGGGGGCGTCAC 62.138 66.667 1.76 0.00 0.00 3.67
306 307 2.521958 ATCGGGGGCGTCACAAAGAG 62.522 60.000 0.00 0.00 0.00 2.85
343 344 4.456280 ACTGTATCGCTTCAAGATCACA 57.544 40.909 0.00 0.00 0.00 3.58
357 358 7.537596 TCAAGATCACATGGGTAATTTTGTT 57.462 32.000 0.00 0.00 0.00 2.83
415 417 1.964223 GTTCATCATCGAGGCCCTAGA 59.036 52.381 0.00 0.00 0.00 2.43
418 420 1.271934 CATCATCGAGGCCCTAGACTG 59.728 57.143 0.00 0.00 0.00 3.51
424 426 0.396417 GAGGCCCTAGACTGCAGAGA 60.396 60.000 23.35 3.63 0.00 3.10
458 460 1.765314 GCTATGGAGAGTGGGTCACAT 59.235 52.381 0.78 0.00 36.74 3.21
464 466 4.588899 TGGAGAGTGGGTCACATAAAATG 58.411 43.478 0.78 0.00 36.74 2.32
539 1751 1.802960 CGATTGGGTGCAGCTCATATC 59.197 52.381 16.65 14.29 0.00 1.63
547 1759 2.799412 GTGCAGCTCATATCTTTCGAGG 59.201 50.000 0.00 0.00 0.00 4.63
578 1790 8.474710 AATCATATCTCTCAAATTTTCAGGGG 57.525 34.615 0.00 0.00 0.00 4.79
597 1809 5.525745 CAGGGGTTTTCGCTTGTTTTTATTT 59.474 36.000 0.00 0.00 36.43 1.40
618 1830 5.431420 TTCTAGAAGTGCGAATTTTGCAA 57.569 34.783 12.86 0.00 45.23 4.08
648 1860 1.032014 TGCAAAGGAAGCACTGAACC 58.968 50.000 0.00 0.00 37.02 3.62
695 2766 4.112634 TGTAATCCCTGCTTTCTTGGTT 57.887 40.909 0.00 0.00 0.00 3.67
746 2817 6.561902 CGCCGAATGTTTAATAAAATGCCATG 60.562 38.462 0.00 0.00 0.00 3.66
757 2828 4.931661 AAAATGCCATGATGGTGATCTC 57.068 40.909 13.84 0.00 40.46 2.75
793 2864 1.301401 TATCGCAGTATTGGGCCGC 60.301 57.895 0.00 0.00 37.19 6.53
809 2880 0.744414 CCGCTCCACCCACACTAATG 60.744 60.000 0.00 0.00 0.00 1.90
822 2893 3.019564 ACACTAATGGATTGAGCAAGGC 58.980 45.455 0.00 0.00 0.00 4.35
887 6117 1.128809 TGGGCTGGGAGACGGTTAAA 61.129 55.000 0.00 0.00 0.00 1.52
891 6121 0.981943 CTGGGAGACGGTTAAAGGGT 59.018 55.000 0.00 0.00 0.00 4.34
927 6157 5.604565 GGCCTAATTAAGAAGCATTGCATT 58.395 37.500 11.91 5.31 0.00 3.56
1078 6318 2.031768 GCCTCTCCCGCATCATCC 59.968 66.667 0.00 0.00 0.00 3.51
1126 6411 1.074775 AAGCGCAATCCCAAGACCA 59.925 52.632 11.47 0.00 0.00 4.02
1129 6414 1.303236 CGCAATCCCAAGACCACCA 60.303 57.895 0.00 0.00 0.00 4.17
1147 6432 2.281345 CCGATGCTGGCTCCATCC 60.281 66.667 10.77 0.00 36.58 3.51
1514 6799 2.044946 GGCCGCAACCTTCCATCT 60.045 61.111 0.00 0.00 0.00 2.90
1589 6874 2.892425 CGAGGCCGGAGATGTTGC 60.892 66.667 5.05 0.00 0.00 4.17
1782 7067 0.976641 TCAACTCGCTCTTGGATGGT 59.023 50.000 0.00 0.00 0.00 3.55
1817 7102 2.821546 CCGTAATGATGAAGCCGAGAA 58.178 47.619 0.00 0.00 0.00 2.87
1921 7206 2.584236 GGAGGATTGATGATGCAGCTT 58.416 47.619 2.53 0.00 0.00 3.74
2133 7418 0.399454 AGCTGGATTGTGCACTGAGT 59.601 50.000 19.41 0.74 0.00 3.41
2145 7430 5.793817 TGTGCACTGAGTTACTGTTATGAT 58.206 37.500 19.41 0.00 0.00 2.45
2298 7586 1.032114 GGAAGGGTTTGAGGATGCCG 61.032 60.000 0.00 0.00 0.00 5.69
2435 7748 4.015872 TCACCATGACCTGTTTTACTCC 57.984 45.455 0.00 0.00 0.00 3.85
2645 8159 4.631377 TCCTCGTTGCATCAAACTAGATTG 59.369 41.667 6.40 6.40 0.00 2.67
2758 8274 2.025155 AGTCGTCGATAATGAGTGCCT 58.975 47.619 0.00 0.00 0.00 4.75
2773 8289 4.471025 TGAGTGCCTCAATAGATGGAGAAA 59.529 41.667 2.78 0.00 37.57 2.52
2840 8356 4.340617 TGGACAATAAGGTGGTGAATTCC 58.659 43.478 2.27 0.00 0.00 3.01
2861 8377 3.294493 GCCCCGAGCAAGCACAAA 61.294 61.111 0.00 0.00 42.97 2.83
2937 8454 0.804989 GAAATTCTCGGCCACCACTG 59.195 55.000 2.24 0.00 0.00 3.66
3185 8704 4.440387 GGTCAACCGAGAGAGTATCCTTTC 60.440 50.000 0.00 0.00 33.66 2.62
3194 8713 6.350612 CGAGAGAGTATCCTTTCCTTGTTCTT 60.351 42.308 0.00 0.00 33.66 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.578703 TGCCTGGGATCCTCCTAACTA 59.421 52.381 12.58 0.00 36.57 2.24
2 3 0.343372 TGCCTGGGATCCTCCTAACT 59.657 55.000 12.58 0.00 36.57 2.24
4 5 0.400525 CCTGCCTGGGATCCTCCTAA 60.401 60.000 12.58 0.00 36.57 2.69
5 6 1.237163 CCTGCCTGGGATCCTCCTA 59.763 63.158 12.58 0.00 36.57 2.94
7 8 2.040464 TCCTGCCTGGGATCCTCC 60.040 66.667 12.58 0.00 36.20 4.30
10 11 3.883549 GCCTCCTGCCTGGGATCC 61.884 72.222 1.92 1.92 34.56 3.36
27 28 2.956964 GATCGAACGAGGCGCAGG 60.957 66.667 10.83 0.00 0.00 4.85
28 29 2.103143 AGATCGAACGAGGCGCAG 59.897 61.111 10.83 1.82 0.00 5.18
29 30 1.650314 TACAGATCGAACGAGGCGCA 61.650 55.000 10.83 0.00 0.00 6.09
30 31 0.317938 ATACAGATCGAACGAGGCGC 60.318 55.000 0.00 0.00 0.00 6.53
31 32 1.663445 GGATACAGATCGAACGAGGCG 60.663 57.143 2.94 0.00 32.28 5.52
32 33 1.336056 GGGATACAGATCGAACGAGGC 60.336 57.143 2.94 0.00 39.74 4.70
33 34 1.954382 TGGGATACAGATCGAACGAGG 59.046 52.381 2.94 0.00 39.74 4.63
45 46 2.355716 GGCTAGCACAAACTGGGATACA 60.356 50.000 18.24 0.00 39.74 2.29
46 47 2.092914 AGGCTAGCACAAACTGGGATAC 60.093 50.000 18.24 0.00 0.00 2.24
48 49 0.995024 AGGCTAGCACAAACTGGGAT 59.005 50.000 18.24 0.00 0.00 3.85
49 50 0.771127 AAGGCTAGCACAAACTGGGA 59.229 50.000 18.24 0.00 0.00 4.37
50 51 1.168714 GAAGGCTAGCACAAACTGGG 58.831 55.000 18.24 0.00 0.00 4.45
51 52 2.191128 AGAAGGCTAGCACAAACTGG 57.809 50.000 18.24 0.00 0.00 4.00
52 53 4.154918 CCTTAAGAAGGCTAGCACAAACTG 59.845 45.833 18.24 0.00 42.78 3.16
53 54 4.327680 CCTTAAGAAGGCTAGCACAAACT 58.672 43.478 18.24 0.14 42.78 2.66
54 55 4.686839 CCTTAAGAAGGCTAGCACAAAC 57.313 45.455 18.24 0.00 42.78 2.93
66 67 8.926715 AAGTTAAACAAGTTTGCCTTAAGAAG 57.073 30.769 3.36 0.00 34.23 2.85
68 69 9.959749 CATAAGTTAAACAAGTTTGCCTTAAGA 57.040 29.630 3.36 4.25 33.73 2.10
69 70 9.744468 ACATAAGTTAAACAAGTTTGCCTTAAG 57.256 29.630 16.01 14.75 33.73 1.85
70 71 9.738832 GACATAAGTTAAACAAGTTTGCCTTAA 57.261 29.630 16.01 2.70 33.73 1.85
72 73 7.920682 CAGACATAAGTTAAACAAGTTTGCCTT 59.079 33.333 8.37 11.11 34.23 4.35
73 74 7.068226 ACAGACATAAGTTAAACAAGTTTGCCT 59.932 33.333 8.37 1.61 34.23 4.75
74 75 7.200455 ACAGACATAAGTTAAACAAGTTTGCC 58.800 34.615 8.37 0.00 34.23 4.52
75 76 9.382244 CTACAGACATAAGTTAAACAAGTTTGC 57.618 33.333 8.37 2.03 34.23 3.68
78 79 9.826574 TGACTACAGACATAAGTTAAACAAGTT 57.173 29.630 0.00 0.00 0.00 2.66
79 80 9.477484 CTGACTACAGACATAAGTTAAACAAGT 57.523 33.333 0.00 0.00 46.03 3.16
80 81 9.692749 TCTGACTACAGACATAAGTTAAACAAG 57.307 33.333 0.00 0.00 46.55 3.16
96 97 5.233050 CGGAAGCAACAATATCTGACTACAG 59.767 44.000 0.00 0.00 44.66 2.74
115 116 1.671328 TCATAGACGAGTCAGCGGAAG 59.329 52.381 5.99 0.00 35.12 3.46
116 117 1.746470 TCATAGACGAGTCAGCGGAA 58.254 50.000 5.99 0.00 35.12 4.30
118 119 1.399087 CGATCATAGACGAGTCAGCGG 60.399 57.143 5.99 0.00 35.12 5.52
119 120 1.527311 TCGATCATAGACGAGTCAGCG 59.473 52.381 5.99 0.00 34.49 5.18
126 127 2.683362 ACAAGTGCTCGATCATAGACGA 59.317 45.455 0.00 0.00 37.03 4.20
127 128 3.071786 ACAAGTGCTCGATCATAGACG 57.928 47.619 0.00 0.00 0.00 4.18
129 130 5.238650 TCGAATACAAGTGCTCGATCATAGA 59.761 40.000 0.00 0.00 35.52 1.98
130 131 5.452777 TCGAATACAAGTGCTCGATCATAG 58.547 41.667 0.00 0.00 35.52 2.23
131 132 5.432885 TCGAATACAAGTGCTCGATCATA 57.567 39.130 0.00 0.00 35.52 2.15
132 133 4.294232 CTCGAATACAAGTGCTCGATCAT 58.706 43.478 8.31 0.00 39.39 2.45
133 134 3.695816 CTCGAATACAAGTGCTCGATCA 58.304 45.455 8.31 0.00 39.39 2.92
134 135 2.469516 GCTCGAATACAAGTGCTCGATC 59.530 50.000 8.31 2.80 39.39 3.69
135 136 2.464865 GCTCGAATACAAGTGCTCGAT 58.535 47.619 8.31 0.00 39.39 3.59
136 137 1.469251 GGCTCGAATACAAGTGCTCGA 60.469 52.381 7.80 7.80 37.95 4.04
137 138 0.924090 GGCTCGAATACAAGTGCTCG 59.076 55.000 0.00 0.00 0.00 5.03
138 139 1.134670 AGGGCTCGAATACAAGTGCTC 60.135 52.381 0.00 0.00 0.00 4.26
139 140 0.905357 AGGGCTCGAATACAAGTGCT 59.095 50.000 0.00 0.00 0.00 4.40
140 141 1.291132 GAGGGCTCGAATACAAGTGC 58.709 55.000 0.00 0.00 0.00 4.40
164 165 2.821969 GCATCATAATACAAGCCAGGGG 59.178 50.000 0.00 0.00 0.00 4.79
165 166 3.759581 AGCATCATAATACAAGCCAGGG 58.240 45.455 0.00 0.00 0.00 4.45
166 167 4.581824 ACAAGCATCATAATACAAGCCAGG 59.418 41.667 0.00 0.00 0.00 4.45
167 168 5.762825 ACAAGCATCATAATACAAGCCAG 57.237 39.130 0.00 0.00 0.00 4.85
169 170 7.173907 AGTCATACAAGCATCATAATACAAGCC 59.826 37.037 0.00 0.00 0.00 4.35
170 171 8.092521 AGTCATACAAGCATCATAATACAAGC 57.907 34.615 0.00 0.00 0.00 4.01
191 192 9.772973 ACACAACTCTACAACATAAATAAGTCA 57.227 29.630 0.00 0.00 0.00 3.41
196 197 9.549078 TCACAACACAACTCTACAACATAAATA 57.451 29.630 0.00 0.00 0.00 1.40
198 199 7.851387 TCACAACACAACTCTACAACATAAA 57.149 32.000 0.00 0.00 0.00 1.40
199 200 9.719355 ATATCACAACACAACTCTACAACATAA 57.281 29.630 0.00 0.00 0.00 1.90
200 201 9.366216 GATATCACAACACAACTCTACAACATA 57.634 33.333 0.00 0.00 0.00 2.29
201 202 8.097038 AGATATCACAACACAACTCTACAACAT 58.903 33.333 5.32 0.00 0.00 2.71
202 203 7.441836 AGATATCACAACACAACTCTACAACA 58.558 34.615 5.32 0.00 0.00 3.33
203 204 7.891183 AGATATCACAACACAACTCTACAAC 57.109 36.000 5.32 0.00 0.00 3.32
204 205 9.419297 GTAAGATATCACAACACAACTCTACAA 57.581 33.333 5.32 0.00 0.00 2.41
205 206 8.033038 GGTAAGATATCACAACACAACTCTACA 58.967 37.037 5.32 0.00 0.00 2.74
207 208 7.094075 ACGGTAAGATATCACAACACAACTCTA 60.094 37.037 5.32 0.00 0.00 2.43
208 209 6.100004 CGGTAAGATATCACAACACAACTCT 58.900 40.000 5.32 0.00 0.00 3.24
212 213 5.785243 TCACGGTAAGATATCACAACACAA 58.215 37.500 5.32 0.00 0.00 3.33
213 214 5.047590 ACTCACGGTAAGATATCACAACACA 60.048 40.000 5.32 0.00 0.00 3.72
215 216 5.417894 AGACTCACGGTAAGATATCACAACA 59.582 40.000 5.32 0.00 0.00 3.33
216 217 5.892568 AGACTCACGGTAAGATATCACAAC 58.107 41.667 5.32 0.00 0.00 3.32
217 218 7.501225 TCATAGACTCACGGTAAGATATCACAA 59.499 37.037 5.32 0.00 0.00 3.33
218 219 6.996282 TCATAGACTCACGGTAAGATATCACA 59.004 38.462 5.32 0.00 0.00 3.58
219 220 7.436430 TCATAGACTCACGGTAAGATATCAC 57.564 40.000 5.32 0.00 0.00 3.06
221 222 8.500753 AGATCATAGACTCACGGTAAGATATC 57.499 38.462 0.00 0.00 0.00 1.63
222 223 8.735315 CAAGATCATAGACTCACGGTAAGATAT 58.265 37.037 0.00 0.00 0.00 1.63
223 224 7.937394 TCAAGATCATAGACTCACGGTAAGATA 59.063 37.037 0.00 0.00 0.00 1.98
224 225 6.773200 TCAAGATCATAGACTCACGGTAAGAT 59.227 38.462 0.00 0.00 0.00 2.40
226 227 6.378710 TCAAGATCATAGACTCACGGTAAG 57.621 41.667 0.00 0.00 0.00 2.34
227 228 6.293462 CGATCAAGATCATAGACTCACGGTAA 60.293 42.308 10.39 0.00 37.69 2.85
229 230 4.023622 CGATCAAGATCATAGACTCACGGT 60.024 45.833 10.39 0.00 37.69 4.83
230 231 4.023622 ACGATCAAGATCATAGACTCACGG 60.024 45.833 10.39 0.00 37.69 4.94
232 233 6.853872 GTGTACGATCAAGATCATAGACTCAC 59.146 42.308 10.39 1.17 37.69 3.51
233 234 6.542370 TGTGTACGATCAAGATCATAGACTCA 59.458 38.462 12.52 7.61 32.97 3.41
234 235 6.960468 TGTGTACGATCAAGATCATAGACTC 58.040 40.000 12.52 5.80 32.97 3.36
235 236 6.944234 TGTGTACGATCAAGATCATAGACT 57.056 37.500 12.52 0.00 32.97 3.24
237 238 7.169813 GCAAATGTGTACGATCAAGATCATAGA 59.830 37.037 10.39 0.00 37.69 1.98
238 239 7.286508 GCAAATGTGTACGATCAAGATCATAG 58.713 38.462 10.39 0.00 37.69 2.23
239 240 6.074356 CGCAAATGTGTACGATCAAGATCATA 60.074 38.462 10.39 0.00 37.69 2.15
240 241 5.277011 CGCAAATGTGTACGATCAAGATCAT 60.277 40.000 10.39 0.00 37.69 2.45
241 242 4.032786 CGCAAATGTGTACGATCAAGATCA 59.967 41.667 10.39 0.00 37.69 2.92
243 244 3.932710 ACGCAAATGTGTACGATCAAGAT 59.067 39.130 0.00 0.00 36.94 2.40
244 245 3.122780 CACGCAAATGTGTACGATCAAGA 59.877 43.478 0.00 0.00 36.94 3.02
247 248 1.127766 GCACGCAAATGTGTACGATCA 59.872 47.619 0.00 0.00 41.94 2.92
250 251 1.136113 CATGCACGCAAATGTGTACGA 60.136 47.619 0.00 0.00 41.94 3.43
251 252 1.136113 TCATGCACGCAAATGTGTACG 60.136 47.619 0.00 0.00 41.94 3.67
252 253 2.610219 TCATGCACGCAAATGTGTAC 57.390 45.000 0.00 0.00 41.94 2.90
253 254 3.846423 AATCATGCACGCAAATGTGTA 57.154 38.095 0.00 0.00 41.94 2.90
254 255 2.728690 AATCATGCACGCAAATGTGT 57.271 40.000 0.00 0.00 41.94 3.72
255 256 3.544682 CACTAATCATGCACGCAAATGTG 59.455 43.478 0.00 0.00 42.81 3.21
259 260 3.181525 CGTACACTAATCATGCACGCAAA 60.182 43.478 0.00 0.00 30.70 3.68
260 261 2.347150 CGTACACTAATCATGCACGCAA 59.653 45.455 0.00 0.00 30.70 4.85
261 262 1.923864 CGTACACTAATCATGCACGCA 59.076 47.619 0.00 0.00 30.70 5.24
264 265 2.534349 CGACCGTACACTAATCATGCAC 59.466 50.000 0.00 0.00 0.00 4.57
265 266 2.424246 TCGACCGTACACTAATCATGCA 59.576 45.455 0.00 0.00 0.00 3.96
266 267 3.074504 TCGACCGTACACTAATCATGC 57.925 47.619 0.00 0.00 0.00 4.06
267 268 4.378910 CGATTCGACCGTACACTAATCATG 59.621 45.833 0.00 0.00 0.00 3.07
268 269 4.534168 CGATTCGACCGTACACTAATCAT 58.466 43.478 0.00 0.00 0.00 2.45
269 270 3.242837 CCGATTCGACCGTACACTAATCA 60.243 47.826 7.83 0.00 0.00 2.57
270 271 3.294943 CCGATTCGACCGTACACTAATC 58.705 50.000 7.83 0.00 0.00 1.75
271 272 2.033801 CCCGATTCGACCGTACACTAAT 59.966 50.000 7.83 0.00 0.00 1.73
272 273 1.401552 CCCGATTCGACCGTACACTAA 59.598 52.381 7.83 0.00 0.00 2.24
274 275 1.660560 CCCCGATTCGACCGTACACT 61.661 60.000 7.83 0.00 0.00 3.55
276 277 2.417257 CCCCCGATTCGACCGTACA 61.417 63.158 7.83 0.00 0.00 2.90
277 278 2.414594 CCCCCGATTCGACCGTAC 59.585 66.667 7.83 0.00 0.00 3.67
278 279 3.530260 GCCCCCGATTCGACCGTA 61.530 66.667 7.83 0.00 0.00 4.02
281 282 4.886121 GACGCCCCCGATTCGACC 62.886 72.222 7.83 0.00 38.29 4.79
282 283 4.137872 TGACGCCCCCGATTCGAC 62.138 66.667 7.83 0.00 38.29 4.20
283 284 4.137872 GTGACGCCCCCGATTCGA 62.138 66.667 7.83 0.00 38.29 3.71
284 285 3.943479 TTGTGACGCCCCCGATTCG 62.943 63.158 0.00 0.00 38.29 3.34
285 286 1.644786 CTTTGTGACGCCCCCGATTC 61.645 60.000 0.00 0.00 38.29 2.52
286 287 1.674322 CTTTGTGACGCCCCCGATT 60.674 57.895 0.00 0.00 38.29 3.34
287 288 2.046314 CTTTGTGACGCCCCCGAT 60.046 61.111 0.00 0.00 38.29 4.18
288 289 3.234630 CTCTTTGTGACGCCCCCGA 62.235 63.158 0.00 0.00 38.29 5.14
289 290 2.742372 CTCTTTGTGACGCCCCCG 60.742 66.667 0.00 0.00 41.14 5.73
291 292 2.359975 CCCTCTTTGTGACGCCCC 60.360 66.667 0.00 0.00 0.00 5.80
292 293 1.671379 GTCCCTCTTTGTGACGCCC 60.671 63.158 0.00 0.00 0.00 6.13
293 294 2.027625 CGTCCCTCTTTGTGACGCC 61.028 63.158 0.00 0.00 44.29 5.68
294 295 3.550656 CGTCCCTCTTTGTGACGC 58.449 61.111 0.00 0.00 44.29 5.19
296 297 1.784525 CTCACGTCCCTCTTTGTGAC 58.215 55.000 0.00 0.00 36.50 3.67
297 298 0.033504 GCTCACGTCCCTCTTTGTGA 59.966 55.000 0.00 0.00 38.91 3.58
299 300 1.006102 CGCTCACGTCCCTCTTTGT 60.006 57.895 0.00 0.00 33.53 2.83
300 301 0.734253 CTCGCTCACGTCCCTCTTTG 60.734 60.000 0.00 0.00 41.18 2.77
306 307 3.112709 GTTGCTCGCTCACGTCCC 61.113 66.667 0.00 0.00 41.18 4.46
343 344 2.036475 TGCGTGCAACAAAATTACCCAT 59.964 40.909 0.00 0.00 35.74 4.00
415 417 2.775890 CTTGAACACCATCTCTGCAGT 58.224 47.619 14.67 0.00 0.00 4.40
418 420 1.467734 CTGCTTGAACACCATCTCTGC 59.532 52.381 0.00 0.00 0.00 4.26
424 426 2.025981 TCCATAGCTGCTTGAACACCAT 60.026 45.455 7.79 0.00 0.00 3.55
458 460 5.586243 GCTATCAGTCTCAAGCACCATTTTA 59.414 40.000 0.00 0.00 35.05 1.52
464 466 1.208052 TGGCTATCAGTCTCAAGCACC 59.792 52.381 0.00 0.00 36.68 5.01
533 1745 7.066307 TGATTTCATCCCTCGAAAGATATGA 57.934 36.000 0.00 0.00 40.84 2.15
539 1751 7.385267 AGAGATATGATTTCATCCCTCGAAAG 58.615 38.462 0.00 0.00 38.65 2.62
597 1809 4.515191 AGTTGCAAAATTCGCACTTCTAGA 59.485 37.500 0.00 0.00 39.59 2.43
695 2766 1.250328 CTTCTGATTGCACTTGGGCA 58.750 50.000 0.00 0.00 43.19 5.36
773 2844 0.249699 CGGCCCAATACTGCGATACA 60.250 55.000 0.00 0.00 0.00 2.29
778 2849 3.272334 GAGCGGCCCAATACTGCG 61.272 66.667 0.00 0.00 44.36 5.18
779 2850 2.902343 GGAGCGGCCCAATACTGC 60.902 66.667 0.00 0.00 39.82 4.40
793 2864 3.054434 TCAATCCATTAGTGTGGGTGGAG 60.054 47.826 0.00 0.00 43.42 3.86
805 2876 3.370840 ACAGCCTTGCTCAATCCATTA 57.629 42.857 0.00 0.00 36.40 1.90
809 2880 1.009829 CGTACAGCCTTGCTCAATCC 58.990 55.000 0.00 0.00 36.40 3.01
822 2893 0.595053 CACCCAGCTATCGCGTACAG 60.595 60.000 5.77 2.81 42.32 2.74
887 6117 1.890489 GGCCGTCAAAATGTTAACCCT 59.110 47.619 2.48 0.00 0.00 4.34
891 6121 8.338072 TCTTAATTAGGCCGTCAAAATGTTAA 57.662 30.769 0.00 0.00 0.00 2.01
1129 6414 2.507944 GATGGAGCCAGCATCGGT 59.492 61.111 0.00 0.00 31.91 4.69
1782 7067 2.039818 TACGGCCACTGTTGTGAAAA 57.960 45.000 2.24 0.00 46.55 2.29
1817 7102 6.774656 CCTCTCCTTAATCATTTGCCATACTT 59.225 38.462 0.00 0.00 0.00 2.24
1825 7110 8.297470 TCCAAATTCCTCTCCTTAATCATTTG 57.703 34.615 0.00 0.00 32.52 2.32
1921 7206 1.345741 CTCCAACCTCTCAAGCACAGA 59.654 52.381 0.00 0.00 0.00 3.41
2084 7369 0.249868 CAGAAGGTGTGGCACGAGAA 60.250 55.000 13.77 0.00 34.83 2.87
2145 7430 7.094805 CCACAGCACTTTTTACTAGCAAAGATA 60.095 37.037 13.82 0.00 34.60 1.98
2298 7586 1.208052 TCATCAGTTCCAGCACTAGGC 59.792 52.381 0.00 0.00 45.30 3.93
2435 7748 6.688637 TCTATCATGCCAACAGAAGAAATG 57.311 37.500 0.00 0.00 0.00 2.32
2564 8078 1.556911 GGCTTCCTGTGGATCTCTTCA 59.443 52.381 0.00 0.00 0.00 3.02
2645 8159 5.465056 GCTCATGAACTTGATTAGCTAGGAC 59.535 44.000 0.00 0.00 0.00 3.85
2773 8289 7.231317 GGTGGAATGTATGAACAATGGATATGT 59.769 37.037 0.00 0.00 39.58 2.29
2937 8454 3.807538 CGATGCTGCCAGTGTGCC 61.808 66.667 0.00 0.00 0.00 5.01
3185 8704 2.673368 GAGGATGCGTGTAAGAACAAGG 59.327 50.000 0.00 0.00 37.36 3.61
3194 8713 0.325296 AAGGGAGGAGGATGCGTGTA 60.325 55.000 0.00 0.00 0.00 2.90
3250 8769 4.504916 CGGCGCCAGAGGAGACTG 62.505 72.222 28.98 0.98 44.43 3.51


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

AutoCloner maintained by Alex Coulton.