Multiple sequence alignment - TraesCS5B01G096100
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 | TraesCS5B01G096100 | chr5B | 100.000 | 4783 | 0 | 0 | 984 | 5766 | 127203262 | 127198480 | 0.000000e+00 | 8833.0 |
1 | TraesCS5B01G096100 | chr5B | 100.000 | 529 | 0 | 0 | 1 | 529 | 127204245 | 127203717 | 0.000000e+00 | 977.0 |
2 | TraesCS5B01G096100 | chr5B | 95.789 | 95 | 4 | 0 | 3100 | 3194 | 311070915 | 311070821 | 2.780000e-33 | 154.0 |
3 | TraesCS5B01G096100 | chr5D | 98.121 | 2608 | 18 | 8 | 3184 | 5766 | 115642826 | 115640225 | 0.000000e+00 | 4516.0 |
4 | TraesCS5B01G096100 | chr5D | 96.350 | 2137 | 30 | 13 | 984 | 3101 | 115644932 | 115642825 | 0.000000e+00 | 3470.0 |
5 | TraesCS5B01G096100 | chr5D | 96.954 | 197 | 6 | 0 | 333 | 529 | 115645313 | 115645117 | 1.200000e-86 | 331.0 |
6 | TraesCS5B01G096100 | chr5D | 90.667 | 150 | 9 | 3 | 169 | 316 | 115645446 | 115645300 | 1.640000e-45 | 195.0 |
7 | TraesCS5B01G096100 | chr5A | 94.559 | 2610 | 70 | 15 | 3184 | 5756 | 122330463 | 122327889 | 0.000000e+00 | 3967.0 |
8 | TraesCS5B01G096100 | chr5A | 95.372 | 2139 | 70 | 9 | 986 | 3101 | 122332594 | 122330462 | 0.000000e+00 | 3374.0 |
9 | TraesCS5B01G096100 | chr5A | 95.425 | 153 | 6 | 1 | 326 | 478 | 122338214 | 122338063 | 5.770000e-60 | 243.0 |
10 | TraesCS5B01G096100 | chr5A | 92.029 | 138 | 7 | 3 | 169 | 305 | 122338500 | 122338366 | 2.120000e-44 | 191.0 |
11 | TraesCS5B01G096100 | chr5A | 96.296 | 54 | 0 | 1 | 478 | 529 | 122332836 | 122332783 | 2.860000e-13 | 87.9 |
12 | TraesCS5B01G096100 | chr4B | 98.889 | 90 | 1 | 0 | 3097 | 3186 | 23323106 | 23323017 | 1.660000e-35 | 161.0 |
13 | TraesCS5B01G096100 | chr3B | 95.960 | 99 | 4 | 0 | 3100 | 3198 | 827868170 | 827868268 | 1.660000e-35 | 161.0 |
14 | TraesCS5B01G096100 | chr2B | 96.875 | 96 | 2 | 1 | 3091 | 3185 | 364949134 | 364949039 | 5.980000e-35 | 159.0 |
15 | TraesCS5B01G096100 | chr7A | 98.864 | 88 | 1 | 0 | 3098 | 3185 | 272502756 | 272502843 | 2.150000e-34 | 158.0 |
16 | TraesCS5B01G096100 | chr1B | 93.519 | 108 | 4 | 3 | 3084 | 3191 | 149606470 | 149606574 | 2.150000e-34 | 158.0 |
17 | TraesCS5B01G096100 | chr2D | 95.000 | 100 | 3 | 2 | 3095 | 3192 | 174430739 | 174430838 | 7.740000e-34 | 156.0 |
18 | TraesCS5B01G096100 | chr4A | 94.118 | 102 | 4 | 2 | 3100 | 3199 | 728648093 | 728647992 | 2.780000e-33 | 154.0 |
19 | TraesCS5B01G096100 | chr3D | 94.949 | 99 | 4 | 1 | 3087 | 3185 | 322709867 | 322709964 | 2.780000e-33 | 154.0 |
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 | TraesCS5B01G096100 | chr5B | 127198480 | 127204245 | 5765 | True | 4905.0 | 8833 | 100.000 | 1 | 5766 | 2 | chr5B.!!$R2 | 5765 |
1 | TraesCS5B01G096100 | chr5D | 115640225 | 115645446 | 5221 | True | 2128.0 | 4516 | 95.523 | 169 | 5766 | 4 | chr5D.!!$R1 | 5597 |
2 | TraesCS5B01G096100 | chr5A | 122327889 | 122332836 | 4947 | True | 2476.3 | 3967 | 95.409 | 478 | 5756 | 3 | chr5A.!!$R1 | 5278 |
AutoCloner calculated primer pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
308 | 310 | 0.313672 | TTGCCATTTTCTCACGTGCC | 59.686 | 50.000 | 11.67 | 0.00 | 0.00 | 5.01 | F |
321 | 323 | 0.323087 | ACGTGCCATTAGGTTTCCCC | 60.323 | 55.000 | 0.00 | 0.00 | 37.19 | 4.81 | F |
322 | 324 | 1.035385 | CGTGCCATTAGGTTTCCCCC | 61.035 | 60.000 | 0.00 | 0.00 | 37.19 | 5.40 | F |
423 | 425 | 1.136329 | ATCCACACTGGGCTTGAGGT | 61.136 | 55.000 | 0.00 | 0.00 | 38.32 | 3.85 | F |
463 | 465 | 1.202842 | CCCCGTAATTCCCACCATACC | 60.203 | 57.143 | 0.00 | 0.00 | 0.00 | 2.73 | F |
1741 | 1749 | 1.401409 | GCGCATGTTTGAGCTGCTTTA | 60.401 | 47.619 | 2.53 | 0.00 | 44.30 | 1.85 | F |
1772 | 1780 | 2.143122 | CTCAAGGTTCGCTTGCAAGTA | 58.857 | 47.619 | 26.55 | 13.33 | 0.00 | 2.24 | F |
3121 | 3161 | 3.178865 | ACTCCCTCCGTTCCAAAATAGA | 58.821 | 45.455 | 0.00 | 0.00 | 0.00 | 1.98 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1501 | 1509 | 1.604147 | CGGCCCAAATTCCCACCTTC | 61.604 | 60.000 | 0.00 | 0.0 | 0.00 | 3.46 | R |
1822 | 1830 | 1.911057 | AGTAAGCCAAGCCTTCAACC | 58.089 | 50.000 | 0.00 | 0.0 | 0.00 | 3.77 | R |
2993 | 3033 | 2.549064 | AAGAAAAATTGGCAGCCACC | 57.451 | 45.000 | 15.89 | 0.0 | 30.78 | 4.61 | R |
3033 | 3073 | 2.884894 | ACAACTACTATAGCGGCACC | 57.115 | 50.000 | 1.45 | 0.0 | 0.00 | 5.01 | R |
3102 | 3142 | 3.778075 | TCATCTATTTTGGAACGGAGGGA | 59.222 | 43.478 | 0.00 | 0.0 | 0.00 | 4.20 | R |
3169 | 3209 | 0.113776 | ACACTACTCCCTCCGTTCCA | 59.886 | 55.000 | 0.00 | 0.0 | 0.00 | 3.53 | R |
3174 | 3214 | 1.136500 | GCCTAAACACTACTCCCTCCG | 59.864 | 57.143 | 0.00 | 0.0 | 0.00 | 4.63 | R |
5550 | 5605 | 0.392595 | GGAAGGATGTGACGTTCCCC | 60.393 | 60.000 | 0.00 | 0.0 | 44.20 | 4.81 | R |
All possible primersListed 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. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
46 | 47 | 3.337398 | CGAGAGCCAACTGAGCTAC | 57.663 | 57.895 | 0.00 | 0.00 | 41.75 | 3.58 |
47 | 48 | 0.528017 | CGAGAGCCAACTGAGCTACA | 59.472 | 55.000 | 0.00 | 0.00 | 41.75 | 2.74 |
48 | 49 | 1.067565 | CGAGAGCCAACTGAGCTACAA | 60.068 | 52.381 | 0.00 | 0.00 | 41.75 | 2.41 |
49 | 50 | 2.615869 | GAGAGCCAACTGAGCTACAAG | 58.384 | 52.381 | 0.00 | 0.00 | 41.75 | 3.16 |
50 | 51 | 2.232452 | GAGAGCCAACTGAGCTACAAGA | 59.768 | 50.000 | 0.00 | 0.00 | 41.75 | 3.02 |
51 | 52 | 2.233431 | AGAGCCAACTGAGCTACAAGAG | 59.767 | 50.000 | 0.00 | 0.00 | 41.75 | 2.85 |
76 | 77 | 8.626093 | GCATTTTGCAAAATTTTAAAGTTCCA | 57.374 | 26.923 | 30.13 | 3.89 | 44.26 | 3.53 |
77 | 78 | 9.247126 | GCATTTTGCAAAATTTTAAAGTTCCAT | 57.753 | 25.926 | 30.13 | 6.85 | 44.26 | 3.41 |
113 | 114 | 8.833231 | ATTCCTTTATGGTCATAATACAGACG | 57.167 | 34.615 | 4.49 | 0.00 | 35.63 | 4.18 |
114 | 115 | 6.755206 | TCCTTTATGGTCATAATACAGACGG | 58.245 | 40.000 | 4.49 | 0.00 | 35.63 | 4.79 |
115 | 116 | 6.551975 | TCCTTTATGGTCATAATACAGACGGA | 59.448 | 38.462 | 4.49 | 0.00 | 35.63 | 4.69 |
116 | 117 | 7.070198 | TCCTTTATGGTCATAATACAGACGGAA | 59.930 | 37.037 | 4.49 | 0.00 | 35.63 | 4.30 |
117 | 118 | 7.878127 | CCTTTATGGTCATAATACAGACGGAAT | 59.122 | 37.037 | 4.49 | 0.00 | 35.63 | 3.01 |
118 | 119 | 9.923143 | CTTTATGGTCATAATACAGACGGAATA | 57.077 | 33.333 | 4.49 | 0.00 | 35.63 | 1.75 |
120 | 121 | 9.923143 | TTATGGTCATAATACAGACGGAATAAG | 57.077 | 33.333 | 0.00 | 0.00 | 35.63 | 1.73 |
121 | 122 | 6.755206 | TGGTCATAATACAGACGGAATAAGG | 58.245 | 40.000 | 0.00 | 0.00 | 35.63 | 2.69 |
122 | 123 | 5.638234 | GGTCATAATACAGACGGAATAAGGC | 59.362 | 44.000 | 0.00 | 0.00 | 35.63 | 4.35 |
123 | 124 | 5.638234 | GTCATAATACAGACGGAATAAGGCC | 59.362 | 44.000 | 0.00 | 0.00 | 0.00 | 5.19 |
124 | 125 | 5.542635 | TCATAATACAGACGGAATAAGGCCT | 59.457 | 40.000 | 0.00 | 0.00 | 0.00 | 5.19 |
125 | 126 | 4.772886 | AATACAGACGGAATAAGGCCTT | 57.227 | 40.909 | 24.18 | 24.18 | 0.00 | 4.35 |
126 | 127 | 5.881923 | AATACAGACGGAATAAGGCCTTA | 57.118 | 39.130 | 27.11 | 27.11 | 0.00 | 2.69 |
127 | 128 | 3.538634 | ACAGACGGAATAAGGCCTTAC | 57.461 | 47.619 | 27.46 | 15.38 | 0.00 | 2.34 |
128 | 129 | 3.105283 | ACAGACGGAATAAGGCCTTACT | 58.895 | 45.455 | 27.46 | 17.81 | 0.00 | 2.24 |
129 | 130 | 4.284178 | ACAGACGGAATAAGGCCTTACTA | 58.716 | 43.478 | 27.46 | 8.29 | 0.00 | 1.82 |
130 | 131 | 4.900054 | ACAGACGGAATAAGGCCTTACTAT | 59.100 | 41.667 | 27.46 | 16.26 | 0.00 | 2.12 |
131 | 132 | 5.010820 | ACAGACGGAATAAGGCCTTACTATC | 59.989 | 44.000 | 27.46 | 22.63 | 0.00 | 2.08 |
132 | 133 | 5.244178 | CAGACGGAATAAGGCCTTACTATCT | 59.756 | 44.000 | 27.46 | 20.29 | 0.00 | 1.98 |
133 | 134 | 5.244178 | AGACGGAATAAGGCCTTACTATCTG | 59.756 | 44.000 | 27.46 | 27.08 | 0.00 | 2.90 |
134 | 135 | 5.145564 | ACGGAATAAGGCCTTACTATCTGA | 58.854 | 41.667 | 31.28 | 14.32 | 0.00 | 3.27 |
135 | 136 | 5.244178 | ACGGAATAAGGCCTTACTATCTGAG | 59.756 | 44.000 | 31.28 | 22.86 | 0.00 | 3.35 |
136 | 137 | 5.336849 | CGGAATAAGGCCTTACTATCTGAGG | 60.337 | 48.000 | 27.46 | 12.11 | 0.00 | 3.86 |
137 | 138 | 5.780793 | GGAATAAGGCCTTACTATCTGAGGA | 59.219 | 44.000 | 27.46 | 2.70 | 32.11 | 3.71 |
138 | 139 | 6.270231 | GGAATAAGGCCTTACTATCTGAGGAA | 59.730 | 42.308 | 27.46 | 2.47 | 32.11 | 3.36 |
139 | 140 | 7.037945 | GGAATAAGGCCTTACTATCTGAGGAAT | 60.038 | 40.741 | 27.46 | 5.01 | 32.11 | 3.01 |
140 | 141 | 8.974292 | AATAAGGCCTTACTATCTGAGGAATA | 57.026 | 34.615 | 27.46 | 1.25 | 32.11 | 1.75 |
141 | 142 | 9.567702 | AATAAGGCCTTACTATCTGAGGAATAT | 57.432 | 33.333 | 27.46 | 3.85 | 32.11 | 1.28 |
202 | 203 | 0.951558 | GCTTCCGTTTTTCAGAGCCA | 59.048 | 50.000 | 0.00 | 0.00 | 0.00 | 4.75 |
238 | 240 | 7.859325 | AAGTTTGGTATACGTGCATTATTCT | 57.141 | 32.000 | 0.00 | 0.00 | 0.00 | 2.40 |
250 | 252 | 3.202906 | GCATTATTCTTGGACCTACGCA | 58.797 | 45.455 | 0.00 | 0.00 | 0.00 | 5.24 |
299 | 301 | 1.469767 | GGATGCCGAGTTGCCATTTTC | 60.470 | 52.381 | 0.00 | 0.00 | 0.00 | 2.29 |
300 | 302 | 1.474077 | GATGCCGAGTTGCCATTTTCT | 59.526 | 47.619 | 0.00 | 0.00 | 0.00 | 2.52 |
301 | 303 | 0.881118 | TGCCGAGTTGCCATTTTCTC | 59.119 | 50.000 | 0.00 | 0.00 | 0.00 | 2.87 |
302 | 304 | 0.881118 | GCCGAGTTGCCATTTTCTCA | 59.119 | 50.000 | 0.00 | 0.00 | 0.00 | 3.27 |
303 | 305 | 1.401539 | GCCGAGTTGCCATTTTCTCAC | 60.402 | 52.381 | 0.00 | 0.00 | 0.00 | 3.51 |
304 | 306 | 1.135972 | CCGAGTTGCCATTTTCTCACG | 60.136 | 52.381 | 0.00 | 0.00 | 0.00 | 4.35 |
305 | 307 | 1.531149 | CGAGTTGCCATTTTCTCACGT | 59.469 | 47.619 | 0.00 | 0.00 | 0.00 | 4.49 |
306 | 308 | 2.662791 | CGAGTTGCCATTTTCTCACGTG | 60.663 | 50.000 | 9.94 | 9.94 | 0.00 | 4.49 |
307 | 309 | 1.001378 | AGTTGCCATTTTCTCACGTGC | 60.001 | 47.619 | 11.67 | 0.00 | 0.00 | 5.34 |
308 | 310 | 0.313672 | TTGCCATTTTCTCACGTGCC | 59.686 | 50.000 | 11.67 | 0.00 | 0.00 | 5.01 |
309 | 311 | 0.821301 | TGCCATTTTCTCACGTGCCA | 60.821 | 50.000 | 11.67 | 0.00 | 0.00 | 4.92 |
310 | 312 | 0.527565 | GCCATTTTCTCACGTGCCAT | 59.472 | 50.000 | 11.67 | 0.00 | 0.00 | 4.40 |
311 | 313 | 1.067635 | GCCATTTTCTCACGTGCCATT | 60.068 | 47.619 | 11.67 | 0.00 | 0.00 | 3.16 |
312 | 314 | 2.163412 | GCCATTTTCTCACGTGCCATTA | 59.837 | 45.455 | 11.67 | 0.00 | 0.00 | 1.90 |
313 | 315 | 3.731867 | GCCATTTTCTCACGTGCCATTAG | 60.732 | 47.826 | 11.67 | 2.36 | 0.00 | 1.73 |
314 | 316 | 3.181497 | CCATTTTCTCACGTGCCATTAGG | 60.181 | 47.826 | 11.67 | 3.52 | 38.23 | 2.69 |
315 | 317 | 2.851263 | TTTCTCACGTGCCATTAGGT | 57.149 | 45.000 | 11.67 | 0.00 | 37.19 | 3.08 |
316 | 318 | 2.851263 | TTCTCACGTGCCATTAGGTT | 57.149 | 45.000 | 11.67 | 0.00 | 37.19 | 3.50 |
317 | 319 | 2.851263 | TCTCACGTGCCATTAGGTTT | 57.149 | 45.000 | 11.67 | 0.00 | 37.19 | 3.27 |
318 | 320 | 2.695359 | TCTCACGTGCCATTAGGTTTC | 58.305 | 47.619 | 11.67 | 0.00 | 37.19 | 2.78 |
319 | 321 | 1.737793 | CTCACGTGCCATTAGGTTTCC | 59.262 | 52.381 | 11.67 | 0.00 | 37.19 | 3.13 |
320 | 322 | 0.808755 | CACGTGCCATTAGGTTTCCC | 59.191 | 55.000 | 0.82 | 0.00 | 37.19 | 3.97 |
321 | 323 | 0.323087 | ACGTGCCATTAGGTTTCCCC | 60.323 | 55.000 | 0.00 | 0.00 | 37.19 | 4.81 |
322 | 324 | 1.035385 | CGTGCCATTAGGTTTCCCCC | 61.035 | 60.000 | 0.00 | 0.00 | 37.19 | 5.40 |
341 | 343 | 2.069273 | CCCTCAGTGAAACGTGTCATC | 58.931 | 52.381 | 12.49 | 5.98 | 45.86 | 2.92 |
423 | 425 | 1.136329 | ATCCACACTGGGCTTGAGGT | 61.136 | 55.000 | 0.00 | 0.00 | 38.32 | 3.85 |
424 | 426 | 1.302832 | CCACACTGGGCTTGAGGTC | 60.303 | 63.158 | 0.00 | 0.00 | 32.67 | 3.85 |
463 | 465 | 1.202842 | CCCCGTAATTCCCACCATACC | 60.203 | 57.143 | 0.00 | 0.00 | 0.00 | 2.73 |
1195 | 1199 | 2.671177 | GGAGACCGACGACGACGAA | 61.671 | 63.158 | 20.63 | 0.00 | 42.66 | 3.85 |
1391 | 1395 | 7.201696 | CGCATCTAGCTCAAAAATTAGGGTTTA | 60.202 | 37.037 | 0.00 | 0.00 | 42.61 | 2.01 |
1486 | 1494 | 7.490725 | TGTGTGGTGATTTTACTTGTCATTTTG | 59.509 | 33.333 | 0.00 | 0.00 | 0.00 | 2.44 |
1565 | 1573 | 5.244785 | ACTATGCATGTTTGAGATGCTTG | 57.755 | 39.130 | 10.16 | 4.55 | 45.45 | 4.01 |
1637 | 1645 | 3.135348 | TGCATAGGGTTCTTCTCCTCATG | 59.865 | 47.826 | 0.00 | 0.00 | 34.75 | 3.07 |
1680 | 1688 | 8.286191 | AGAAATGTGCTTAATCTTCCTTTAGG | 57.714 | 34.615 | 0.00 | 0.00 | 0.00 | 2.69 |
1741 | 1749 | 1.401409 | GCGCATGTTTGAGCTGCTTTA | 60.401 | 47.619 | 2.53 | 0.00 | 44.30 | 1.85 |
1761 | 1769 | 8.730680 | TGCTTTAATTTATCACTCTCAAGGTTC | 58.269 | 33.333 | 0.00 | 0.00 | 0.00 | 3.62 |
1772 | 1780 | 2.143122 | CTCAAGGTTCGCTTGCAAGTA | 58.857 | 47.619 | 26.55 | 13.33 | 0.00 | 2.24 |
1822 | 1830 | 5.022021 | GCTTGCGTGTTAAGTTATAAGCTG | 58.978 | 41.667 | 0.00 | 3.11 | 37.06 | 4.24 |
2121 | 2130 | 4.696899 | TCACGTGTGAAGATTAGATCGT | 57.303 | 40.909 | 16.51 | 0.00 | 36.53 | 3.73 |
2124 | 2133 | 5.096169 | CACGTGTGAAGATTAGATCGTTCT | 58.904 | 41.667 | 7.58 | 0.97 | 35.90 | 3.01 |
2764 | 2803 | 5.636903 | AATGGCAGTGGTGAGTATAAGAT | 57.363 | 39.130 | 0.00 | 0.00 | 0.00 | 2.40 |
2765 | 2804 | 5.636903 | ATGGCAGTGGTGAGTATAAGATT | 57.363 | 39.130 | 0.00 | 0.00 | 0.00 | 2.40 |
3101 | 3141 | 5.233988 | TGTGCATGTGGCCTTTTAAAATAC | 58.766 | 37.500 | 3.32 | 0.00 | 43.89 | 1.89 |
3102 | 3142 | 5.011533 | TGTGCATGTGGCCTTTTAAAATACT | 59.988 | 36.000 | 3.32 | 0.00 | 43.89 | 2.12 |
3103 | 3143 | 5.576774 | GTGCATGTGGCCTTTTAAAATACTC | 59.423 | 40.000 | 3.32 | 0.00 | 43.89 | 2.59 |
3104 | 3144 | 5.109210 | GCATGTGGCCTTTTAAAATACTCC | 58.891 | 41.667 | 3.32 | 1.75 | 36.11 | 3.85 |
3105 | 3145 | 5.660460 | CATGTGGCCTTTTAAAATACTCCC | 58.340 | 41.667 | 3.32 | 0.00 | 0.00 | 4.30 |
3106 | 3146 | 5.005628 | TGTGGCCTTTTAAAATACTCCCT | 57.994 | 39.130 | 3.32 | 0.00 | 0.00 | 4.20 |
3107 | 3147 | 5.014202 | TGTGGCCTTTTAAAATACTCCCTC | 58.986 | 41.667 | 3.32 | 0.79 | 0.00 | 4.30 |
3108 | 3148 | 4.401519 | GTGGCCTTTTAAAATACTCCCTCC | 59.598 | 45.833 | 3.32 | 0.00 | 0.00 | 4.30 |
3109 | 3149 | 3.630769 | GGCCTTTTAAAATACTCCCTCCG | 59.369 | 47.826 | 0.09 | 0.00 | 0.00 | 4.63 |
3110 | 3150 | 4.267536 | GCCTTTTAAAATACTCCCTCCGT | 58.732 | 43.478 | 0.09 | 0.00 | 0.00 | 4.69 |
3111 | 3151 | 4.703575 | GCCTTTTAAAATACTCCCTCCGTT | 59.296 | 41.667 | 0.09 | 0.00 | 0.00 | 4.44 |
3112 | 3152 | 5.163683 | GCCTTTTAAAATACTCCCTCCGTTC | 60.164 | 44.000 | 0.09 | 0.00 | 0.00 | 3.95 |
3113 | 3153 | 5.356190 | CCTTTTAAAATACTCCCTCCGTTCC | 59.644 | 44.000 | 0.09 | 0.00 | 0.00 | 3.62 |
3114 | 3154 | 5.502089 | TTTAAAATACTCCCTCCGTTCCA | 57.498 | 39.130 | 0.00 | 0.00 | 0.00 | 3.53 |
3115 | 3155 | 5.502089 | TTAAAATACTCCCTCCGTTCCAA | 57.498 | 39.130 | 0.00 | 0.00 | 0.00 | 3.53 |
3116 | 3156 | 4.376225 | AAAATACTCCCTCCGTTCCAAA | 57.624 | 40.909 | 0.00 | 0.00 | 0.00 | 3.28 |
3117 | 3157 | 4.376225 | AAATACTCCCTCCGTTCCAAAA | 57.624 | 40.909 | 0.00 | 0.00 | 0.00 | 2.44 |
3118 | 3158 | 4.586306 | AATACTCCCTCCGTTCCAAAAT | 57.414 | 40.909 | 0.00 | 0.00 | 0.00 | 1.82 |
3119 | 3159 | 5.703730 | AATACTCCCTCCGTTCCAAAATA | 57.296 | 39.130 | 0.00 | 0.00 | 0.00 | 1.40 |
3120 | 3160 | 3.629142 | ACTCCCTCCGTTCCAAAATAG | 57.371 | 47.619 | 0.00 | 0.00 | 0.00 | 1.73 |
3121 | 3161 | 3.178865 | ACTCCCTCCGTTCCAAAATAGA | 58.821 | 45.455 | 0.00 | 0.00 | 0.00 | 1.98 |
3122 | 3162 | 3.780850 | ACTCCCTCCGTTCCAAAATAGAT | 59.219 | 43.478 | 0.00 | 0.00 | 0.00 | 1.98 |
3123 | 3163 | 4.130118 | CTCCCTCCGTTCCAAAATAGATG | 58.870 | 47.826 | 0.00 | 0.00 | 0.00 | 2.90 |
3124 | 3164 | 3.778075 | TCCCTCCGTTCCAAAATAGATGA | 59.222 | 43.478 | 0.00 | 0.00 | 0.00 | 2.92 |
3125 | 3165 | 3.877508 | CCCTCCGTTCCAAAATAGATGAC | 59.122 | 47.826 | 0.00 | 0.00 | 0.00 | 3.06 |
3126 | 3166 | 4.384208 | CCCTCCGTTCCAAAATAGATGACT | 60.384 | 45.833 | 0.00 | 0.00 | 0.00 | 3.41 |
3127 | 3167 | 4.811557 | CCTCCGTTCCAAAATAGATGACTC | 59.188 | 45.833 | 0.00 | 0.00 | 0.00 | 3.36 |
3128 | 3168 | 5.414789 | TCCGTTCCAAAATAGATGACTCA | 57.585 | 39.130 | 0.00 | 0.00 | 0.00 | 3.41 |
3129 | 3169 | 5.800296 | TCCGTTCCAAAATAGATGACTCAA | 58.200 | 37.500 | 0.00 | 0.00 | 0.00 | 3.02 |
3130 | 3170 | 5.642063 | TCCGTTCCAAAATAGATGACTCAAC | 59.358 | 40.000 | 0.00 | 0.00 | 0.00 | 3.18 |
3131 | 3171 | 5.643777 | CCGTTCCAAAATAGATGACTCAACT | 59.356 | 40.000 | 0.00 | 0.00 | 0.00 | 3.16 |
3132 | 3172 | 6.149474 | CCGTTCCAAAATAGATGACTCAACTT | 59.851 | 38.462 | 0.00 | 0.00 | 0.00 | 2.66 |
3133 | 3173 | 7.308589 | CCGTTCCAAAATAGATGACTCAACTTT | 60.309 | 37.037 | 0.00 | 0.00 | 0.00 | 2.66 |
3134 | 3174 | 7.535258 | CGTTCCAAAATAGATGACTCAACTTTG | 59.465 | 37.037 | 0.00 | 0.00 | 0.00 | 2.77 |
3135 | 3175 | 8.352942 | GTTCCAAAATAGATGACTCAACTTTGT | 58.647 | 33.333 | 0.00 | 0.00 | 0.00 | 2.83 |
3136 | 3176 | 9.567776 | TTCCAAAATAGATGACTCAACTTTGTA | 57.432 | 29.630 | 0.00 | 0.00 | 0.00 | 2.41 |
3137 | 3177 | 8.999431 | TCCAAAATAGATGACTCAACTTTGTAC | 58.001 | 33.333 | 0.00 | 0.00 | 0.00 | 2.90 |
3138 | 3178 | 9.003658 | CCAAAATAGATGACTCAACTTTGTACT | 57.996 | 33.333 | 0.00 | 0.00 | 0.00 | 2.73 |
3159 | 3199 | 9.850198 | TGTACTAACTTTAATACAAAGTTGGGT | 57.150 | 29.630 | 21.95 | 19.76 | 46.38 | 4.51 |
3161 | 3201 | 8.983702 | ACTAACTTTAATACAAAGTTGGGTCA | 57.016 | 30.769 | 21.95 | 6.46 | 46.38 | 4.02 |
3162 | 3202 | 9.582648 | ACTAACTTTAATACAAAGTTGGGTCAT | 57.417 | 29.630 | 21.95 | 6.17 | 46.38 | 3.06 |
3164 | 3204 | 8.706322 | AACTTTAATACAAAGTTGGGTCATCT | 57.294 | 30.769 | 12.88 | 0.00 | 45.58 | 2.90 |
3165 | 3205 | 9.802039 | AACTTTAATACAAAGTTGGGTCATCTA | 57.198 | 29.630 | 12.88 | 0.00 | 45.58 | 1.98 |
3166 | 3206 | 9.975218 | ACTTTAATACAAAGTTGGGTCATCTAT | 57.025 | 29.630 | 0.00 | 0.00 | 37.18 | 1.98 |
3171 | 3211 | 6.345096 | ACAAAGTTGGGTCATCTATTTTGG | 57.655 | 37.500 | 0.00 | 0.00 | 0.00 | 3.28 |
3172 | 3212 | 6.074648 | ACAAAGTTGGGTCATCTATTTTGGA | 58.925 | 36.000 | 0.00 | 0.00 | 0.00 | 3.53 |
3173 | 3213 | 6.553100 | ACAAAGTTGGGTCATCTATTTTGGAA | 59.447 | 34.615 | 0.00 | 0.00 | 0.00 | 3.53 |
3174 | 3214 | 6.590234 | AAGTTGGGTCATCTATTTTGGAAC | 57.410 | 37.500 | 0.00 | 0.00 | 0.00 | 3.62 |
3175 | 3215 | 4.700213 | AGTTGGGTCATCTATTTTGGAACG | 59.300 | 41.667 | 0.00 | 0.00 | 0.00 | 3.95 |
3176 | 3216 | 3.616219 | TGGGTCATCTATTTTGGAACGG | 58.384 | 45.455 | 0.00 | 0.00 | 0.00 | 4.44 |
3177 | 3217 | 3.264706 | TGGGTCATCTATTTTGGAACGGA | 59.735 | 43.478 | 0.00 | 0.00 | 0.00 | 4.69 |
3178 | 3218 | 3.877508 | GGGTCATCTATTTTGGAACGGAG | 59.122 | 47.826 | 0.00 | 0.00 | 0.00 | 4.63 |
3179 | 3219 | 3.877508 | GGTCATCTATTTTGGAACGGAGG | 59.122 | 47.826 | 0.00 | 0.00 | 0.00 | 4.30 |
3180 | 3220 | 3.877508 | GTCATCTATTTTGGAACGGAGGG | 59.122 | 47.826 | 0.00 | 0.00 | 0.00 | 4.30 |
3181 | 3221 | 3.778075 | TCATCTATTTTGGAACGGAGGGA | 59.222 | 43.478 | 0.00 | 0.00 | 0.00 | 4.20 |
3182 | 3222 | 3.906720 | TCTATTTTGGAACGGAGGGAG | 57.093 | 47.619 | 0.00 | 0.00 | 0.00 | 4.30 |
3183 | 3223 | 3.178865 | TCTATTTTGGAACGGAGGGAGT | 58.821 | 45.455 | 0.00 | 0.00 | 0.00 | 3.85 |
3184 | 3224 | 4.355549 | TCTATTTTGGAACGGAGGGAGTA | 58.644 | 43.478 | 0.00 | 0.00 | 0.00 | 2.59 |
3269 | 3309 | 7.283127 | GTGGATTTCAGGATTGCTAAGATAACA | 59.717 | 37.037 | 0.00 | 0.00 | 0.00 | 2.41 |
5433 | 5488 | 4.988029 | AGACTCGTATAGTAATCCAGCCT | 58.012 | 43.478 | 0.00 | 0.00 | 39.07 | 4.58 |
5550 | 5605 | 2.621998 | TCCTAGGCCGTTCTAAAGATCG | 59.378 | 50.000 | 2.96 | 3.93 | 37.10 | 3.69 |
5591 | 5646 | 1.946768 | CTTCGCTTTGTGGTGAGGAAA | 59.053 | 47.619 | 0.00 | 0.00 | 0.00 | 3.13 |
5629 | 5684 | 8.571336 | CAATTGATTCAGAACCTAGTTGAAGTT | 58.429 | 33.333 | 0.00 | 0.00 | 34.64 | 2.66 |
5648 | 5703 | 5.485209 | AGTTCTACGAGGTCCTGAAAAAT | 57.515 | 39.130 | 0.00 | 0.00 | 0.00 | 1.82 |
5742 | 5821 | 6.017275 | CGACCTCCGTAATTCTATTCACTAGT | 60.017 | 42.308 | 0.00 | 0.00 | 0.00 | 2.57 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
13 | 14 | 0.454600 | TCTCGCACCCGCTTAGTAAG | 59.545 | 55.000 | 5.47 | 5.47 | 35.30 | 2.34 |
14 | 15 | 0.454600 | CTCTCGCACCCGCTTAGTAA | 59.545 | 55.000 | 0.00 | 0.00 | 35.30 | 2.24 |
15 | 16 | 2.001361 | GCTCTCGCACCCGCTTAGTA | 62.001 | 60.000 | 0.00 | 0.00 | 35.30 | 1.82 |
16 | 17 | 2.885861 | CTCTCGCACCCGCTTAGT | 59.114 | 61.111 | 0.00 | 0.00 | 35.30 | 2.24 |
17 | 18 | 2.583593 | GCTCTCGCACCCGCTTAG | 60.584 | 66.667 | 0.00 | 0.00 | 35.30 | 2.18 |
18 | 19 | 4.143333 | GGCTCTCGCACCCGCTTA | 62.143 | 66.667 | 0.00 | 0.00 | 38.10 | 3.09 |
22 | 23 | 4.379243 | AGTTGGCTCTCGCACCCG | 62.379 | 66.667 | 0.00 | 0.00 | 38.10 | 5.28 |
23 | 24 | 2.743928 | CAGTTGGCTCTCGCACCC | 60.744 | 66.667 | 0.00 | 0.00 | 38.10 | 4.61 |
24 | 25 | 1.739562 | CTCAGTTGGCTCTCGCACC | 60.740 | 63.158 | 0.00 | 0.00 | 38.10 | 5.01 |
25 | 26 | 2.386660 | GCTCAGTTGGCTCTCGCAC | 61.387 | 63.158 | 0.00 | 0.00 | 38.10 | 5.34 |
26 | 27 | 1.250840 | TAGCTCAGTTGGCTCTCGCA | 61.251 | 55.000 | 0.00 | 0.00 | 40.74 | 5.10 |
27 | 28 | 0.804156 | GTAGCTCAGTTGGCTCTCGC | 60.804 | 60.000 | 0.00 | 0.00 | 40.74 | 5.03 |
28 | 29 | 0.528017 | TGTAGCTCAGTTGGCTCTCG | 59.472 | 55.000 | 0.00 | 0.00 | 40.74 | 4.04 |
29 | 30 | 2.232452 | TCTTGTAGCTCAGTTGGCTCTC | 59.768 | 50.000 | 0.00 | 0.00 | 40.74 | 3.20 |
30 | 31 | 2.233431 | CTCTTGTAGCTCAGTTGGCTCT | 59.767 | 50.000 | 0.00 | 0.00 | 40.74 | 4.09 |
31 | 32 | 2.615869 | CTCTTGTAGCTCAGTTGGCTC | 58.384 | 52.381 | 0.00 | 0.00 | 40.74 | 4.70 |
32 | 33 | 2.758736 | CTCTTGTAGCTCAGTTGGCT | 57.241 | 50.000 | 0.00 | 0.00 | 43.02 | 4.75 |
45 | 46 | 9.505995 | CTTTAAAATTTTGCAAAATGCTCTTGT | 57.494 | 25.926 | 32.23 | 17.66 | 45.31 | 3.16 |
46 | 47 | 9.505995 | ACTTTAAAATTTTGCAAAATGCTCTTG | 57.494 | 25.926 | 32.23 | 23.03 | 45.31 | 3.02 |
48 | 49 | 9.720667 | GAACTTTAAAATTTTGCAAAATGCTCT | 57.279 | 25.926 | 32.23 | 17.47 | 45.31 | 4.09 |
49 | 50 | 8.957028 | GGAACTTTAAAATTTTGCAAAATGCTC | 58.043 | 29.630 | 32.23 | 19.99 | 45.31 | 4.26 |
50 | 51 | 8.465201 | TGGAACTTTAAAATTTTGCAAAATGCT | 58.535 | 25.926 | 32.23 | 24.36 | 45.31 | 3.79 |
51 | 52 | 8.626093 | TGGAACTTTAAAATTTTGCAAAATGC | 57.374 | 26.923 | 32.23 | 16.88 | 45.29 | 3.56 |
87 | 88 | 9.273016 | CGTCTGTATTATGACCATAAAGGAATT | 57.727 | 33.333 | 6.55 | 0.00 | 41.22 | 2.17 |
88 | 89 | 7.878127 | CCGTCTGTATTATGACCATAAAGGAAT | 59.122 | 37.037 | 6.55 | 0.00 | 41.22 | 3.01 |
89 | 90 | 7.070198 | TCCGTCTGTATTATGACCATAAAGGAA | 59.930 | 37.037 | 6.55 | 0.00 | 41.22 | 3.36 |
90 | 91 | 6.551975 | TCCGTCTGTATTATGACCATAAAGGA | 59.448 | 38.462 | 6.55 | 5.19 | 41.22 | 3.36 |
91 | 92 | 6.755206 | TCCGTCTGTATTATGACCATAAAGG | 58.245 | 40.000 | 6.55 | 0.00 | 45.67 | 3.11 |
92 | 93 | 8.833231 | ATTCCGTCTGTATTATGACCATAAAG | 57.167 | 34.615 | 6.55 | 1.32 | 36.90 | 1.85 |
94 | 95 | 9.923143 | CTTATTCCGTCTGTATTATGACCATAA | 57.077 | 33.333 | 5.08 | 5.08 | 37.64 | 1.90 |
95 | 96 | 8.528643 | CCTTATTCCGTCTGTATTATGACCATA | 58.471 | 37.037 | 0.00 | 0.00 | 0.00 | 2.74 |
96 | 97 | 7.386851 | CCTTATTCCGTCTGTATTATGACCAT | 58.613 | 38.462 | 0.00 | 0.00 | 0.00 | 3.55 |
97 | 98 | 6.740401 | GCCTTATTCCGTCTGTATTATGACCA | 60.740 | 42.308 | 0.00 | 0.00 | 0.00 | 4.02 |
98 | 99 | 5.638234 | GCCTTATTCCGTCTGTATTATGACC | 59.362 | 44.000 | 0.00 | 0.00 | 0.00 | 4.02 |
99 | 100 | 5.638234 | GGCCTTATTCCGTCTGTATTATGAC | 59.362 | 44.000 | 0.00 | 0.00 | 0.00 | 3.06 |
100 | 101 | 5.542635 | AGGCCTTATTCCGTCTGTATTATGA | 59.457 | 40.000 | 0.00 | 0.00 | 0.00 | 2.15 |
101 | 102 | 5.794894 | AGGCCTTATTCCGTCTGTATTATG | 58.205 | 41.667 | 0.00 | 0.00 | 0.00 | 1.90 |
102 | 103 | 6.435292 | AAGGCCTTATTCCGTCTGTATTAT | 57.565 | 37.500 | 18.87 | 0.00 | 0.00 | 1.28 |
103 | 104 | 5.881923 | AAGGCCTTATTCCGTCTGTATTA | 57.118 | 39.130 | 18.87 | 0.00 | 0.00 | 0.98 |
104 | 105 | 4.772886 | AAGGCCTTATTCCGTCTGTATT | 57.227 | 40.909 | 18.87 | 0.00 | 0.00 | 1.89 |
105 | 106 | 4.900054 | AGTAAGGCCTTATTCCGTCTGTAT | 59.100 | 41.667 | 27.60 | 0.00 | 0.00 | 2.29 |
106 | 107 | 4.284178 | AGTAAGGCCTTATTCCGTCTGTA | 58.716 | 43.478 | 27.60 | 0.00 | 0.00 | 2.74 |
107 | 108 | 3.105283 | AGTAAGGCCTTATTCCGTCTGT | 58.895 | 45.455 | 27.60 | 0.00 | 0.00 | 3.41 |
108 | 109 | 3.821421 | AGTAAGGCCTTATTCCGTCTG | 57.179 | 47.619 | 27.60 | 0.00 | 0.00 | 3.51 |
109 | 110 | 5.244178 | CAGATAGTAAGGCCTTATTCCGTCT | 59.756 | 44.000 | 27.60 | 21.38 | 0.00 | 4.18 |
110 | 111 | 5.243283 | TCAGATAGTAAGGCCTTATTCCGTC | 59.757 | 44.000 | 27.60 | 19.80 | 0.00 | 4.79 |
111 | 112 | 5.145564 | TCAGATAGTAAGGCCTTATTCCGT | 58.854 | 41.667 | 27.60 | 13.22 | 0.00 | 4.69 |
112 | 113 | 5.336849 | CCTCAGATAGTAAGGCCTTATTCCG | 60.337 | 48.000 | 27.60 | 16.37 | 0.00 | 4.30 |
113 | 114 | 5.780793 | TCCTCAGATAGTAAGGCCTTATTCC | 59.219 | 44.000 | 27.60 | 17.66 | 0.00 | 3.01 |
114 | 115 | 6.919775 | TCCTCAGATAGTAAGGCCTTATTC | 57.080 | 41.667 | 27.60 | 22.10 | 0.00 | 1.75 |
115 | 116 | 7.880265 | ATTCCTCAGATAGTAAGGCCTTATT | 57.120 | 36.000 | 27.60 | 24.90 | 0.00 | 1.40 |
160 | 161 | 9.938280 | AAGCTGTTACTCTTGTGTATAATAACA | 57.062 | 29.630 | 0.00 | 0.00 | 31.99 | 2.41 |
162 | 163 | 9.595823 | GGAAGCTGTTACTCTTGTGTATAATAA | 57.404 | 33.333 | 0.00 | 0.00 | 0.00 | 1.40 |
163 | 164 | 7.919091 | CGGAAGCTGTTACTCTTGTGTATAATA | 59.081 | 37.037 | 0.00 | 0.00 | 0.00 | 0.98 |
164 | 165 | 6.757010 | CGGAAGCTGTTACTCTTGTGTATAAT | 59.243 | 38.462 | 0.00 | 0.00 | 0.00 | 1.28 |
165 | 166 | 6.097356 | CGGAAGCTGTTACTCTTGTGTATAA | 58.903 | 40.000 | 0.00 | 0.00 | 0.00 | 0.98 |
166 | 167 | 5.184479 | ACGGAAGCTGTTACTCTTGTGTATA | 59.816 | 40.000 | 0.00 | 0.00 | 0.00 | 1.47 |
167 | 168 | 4.021368 | ACGGAAGCTGTTACTCTTGTGTAT | 60.021 | 41.667 | 0.00 | 0.00 | 0.00 | 2.29 |
168 | 169 | 3.319972 | ACGGAAGCTGTTACTCTTGTGTA | 59.680 | 43.478 | 0.00 | 0.00 | 0.00 | 2.90 |
169 | 170 | 2.102588 | ACGGAAGCTGTTACTCTTGTGT | 59.897 | 45.455 | 0.00 | 0.00 | 0.00 | 3.72 |
170 | 171 | 2.755650 | ACGGAAGCTGTTACTCTTGTG | 58.244 | 47.619 | 0.00 | 0.00 | 0.00 | 3.33 |
171 | 172 | 3.470645 | AACGGAAGCTGTTACTCTTGT | 57.529 | 42.857 | 0.00 | 0.00 | 30.44 | 3.16 |
172 | 173 | 4.813296 | AAAACGGAAGCTGTTACTCTTG | 57.187 | 40.909 | 0.00 | 0.00 | 32.14 | 3.02 |
173 | 174 | 4.879545 | TGAAAAACGGAAGCTGTTACTCTT | 59.120 | 37.500 | 0.00 | 0.00 | 32.14 | 2.85 |
174 | 175 | 4.448210 | TGAAAAACGGAAGCTGTTACTCT | 58.552 | 39.130 | 0.00 | 0.00 | 32.14 | 3.24 |
175 | 176 | 4.510340 | TCTGAAAAACGGAAGCTGTTACTC | 59.490 | 41.667 | 0.00 | 0.00 | 32.14 | 2.59 |
176 | 177 | 4.448210 | TCTGAAAAACGGAAGCTGTTACT | 58.552 | 39.130 | 0.00 | 0.00 | 32.14 | 2.24 |
202 | 203 | 9.498176 | ACGTATACCAAACTTTGTTTTAGAGAT | 57.502 | 29.630 | 0.00 | 0.00 | 0.00 | 2.75 |
219 | 220 | 5.756347 | GTCCAAGAATAATGCACGTATACCA | 59.244 | 40.000 | 0.00 | 0.00 | 0.00 | 3.25 |
257 | 259 | 3.670625 | TCACATGGCGTAGTAGCTTTTT | 58.329 | 40.909 | 0.00 | 0.00 | 37.29 | 1.94 |
260 | 262 | 1.137086 | CCTCACATGGCGTAGTAGCTT | 59.863 | 52.381 | 0.00 | 0.00 | 37.29 | 3.74 |
261 | 263 | 0.747255 | CCTCACATGGCGTAGTAGCT | 59.253 | 55.000 | 0.00 | 0.00 | 37.29 | 3.32 |
262 | 264 | 0.744874 | TCCTCACATGGCGTAGTAGC | 59.255 | 55.000 | 0.00 | 0.00 | 0.00 | 3.58 |
299 | 301 | 1.737793 | GGAAACCTAATGGCACGTGAG | 59.262 | 52.381 | 22.23 | 7.01 | 36.63 | 3.51 |
300 | 302 | 1.816074 | GGAAACCTAATGGCACGTGA | 58.184 | 50.000 | 22.23 | 0.00 | 36.63 | 4.35 |
319 | 321 | 0.602905 | GACACGTTTCACTGAGGGGG | 60.603 | 60.000 | 0.00 | 0.00 | 0.00 | 5.40 |
320 | 322 | 0.105964 | TGACACGTTTCACTGAGGGG | 59.894 | 55.000 | 0.00 | 0.00 | 0.00 | 4.79 |
321 | 323 | 2.069273 | GATGACACGTTTCACTGAGGG | 58.931 | 52.381 | 6.54 | 0.00 | 0.00 | 4.30 |
322 | 324 | 2.754472 | TGATGACACGTTTCACTGAGG | 58.246 | 47.619 | 6.54 | 0.00 | 0.00 | 3.86 |
323 | 325 | 3.742882 | ACATGATGACACGTTTCACTGAG | 59.257 | 43.478 | 6.54 | 0.92 | 0.00 | 3.35 |
324 | 326 | 3.494251 | CACATGATGACACGTTTCACTGA | 59.506 | 43.478 | 6.54 | 0.00 | 0.00 | 3.41 |
325 | 327 | 3.802423 | CACATGATGACACGTTTCACTG | 58.198 | 45.455 | 6.54 | 7.72 | 0.00 | 3.66 |
326 | 328 | 2.224079 | GCACATGATGACACGTTTCACT | 59.776 | 45.455 | 6.54 | 0.00 | 0.00 | 3.41 |
327 | 329 | 2.032117 | TGCACATGATGACACGTTTCAC | 60.032 | 45.455 | 6.54 | 2.28 | 0.00 | 3.18 |
328 | 330 | 2.216898 | TGCACATGATGACACGTTTCA | 58.783 | 42.857 | 6.89 | 6.89 | 0.00 | 2.69 |
329 | 331 | 2.967459 | TGCACATGATGACACGTTTC | 57.033 | 45.000 | 0.00 | 0.00 | 0.00 | 2.78 |
330 | 332 | 2.553602 | ACATGCACATGATGACACGTTT | 59.446 | 40.909 | 17.19 | 0.00 | 41.20 | 3.60 |
331 | 333 | 2.095617 | CACATGCACATGATGACACGTT | 60.096 | 45.455 | 17.19 | 0.00 | 41.20 | 3.99 |
341 | 343 | 2.352030 | GGTTCTTGTCCACATGCACATG | 60.352 | 50.000 | 9.06 | 9.06 | 44.15 | 3.21 |
377 | 379 | 2.165030 | CTGCCCATTCTTGTCCACATTC | 59.835 | 50.000 | 0.00 | 0.00 | 0.00 | 2.67 |
389 | 391 | 1.530183 | GGATCCAGCCTGCCCATTC | 60.530 | 63.158 | 6.95 | 0.00 | 0.00 | 2.67 |
423 | 425 | 0.739462 | CGCTGTAAATGGGCTGACGA | 60.739 | 55.000 | 0.00 | 0.00 | 0.00 | 4.20 |
424 | 426 | 1.715585 | CGCTGTAAATGGGCTGACG | 59.284 | 57.895 | 0.00 | 0.00 | 0.00 | 4.35 |
1391 | 1395 | 7.724305 | ACGTGTTACACAAGAGATTAACAAT | 57.276 | 32.000 | 16.09 | 0.00 | 36.46 | 2.71 |
1413 | 1417 | 4.223320 | AGAAACAACAACAATGCCTACG | 57.777 | 40.909 | 0.00 | 0.00 | 0.00 | 3.51 |
1486 | 1494 | 6.801575 | TCCCACCTTCGCAATTAAAAATATC | 58.198 | 36.000 | 0.00 | 0.00 | 0.00 | 1.63 |
1501 | 1509 | 1.604147 | CGGCCCAAATTCCCACCTTC | 61.604 | 60.000 | 0.00 | 0.00 | 0.00 | 3.46 |
1565 | 1573 | 8.669243 | ACAGCAATATCTTAGCTCAAAAACTAC | 58.331 | 33.333 | 0.00 | 0.00 | 36.26 | 2.73 |
1637 | 1645 | 8.804743 | CACATTTCTACAAAATCAGATGCAATC | 58.195 | 33.333 | 0.00 | 0.00 | 46.04 | 2.67 |
1680 | 1688 | 6.402658 | GCACTCTAAATTCCTAGCTCAAACAC | 60.403 | 42.308 | 0.00 | 0.00 | 0.00 | 3.32 |
1741 | 1749 | 5.491982 | AGCGAACCTTGAGAGTGATAAATT | 58.508 | 37.500 | 0.00 | 0.00 | 0.00 | 1.82 |
1761 | 1769 | 7.850982 | CCAAAAATACTATACTACTTGCAAGCG | 59.149 | 37.037 | 26.27 | 18.98 | 0.00 | 4.68 |
1822 | 1830 | 1.911057 | AGTAAGCCAAGCCTTCAACC | 58.089 | 50.000 | 0.00 | 0.00 | 0.00 | 3.77 |
2993 | 3033 | 2.549064 | AAGAAAAATTGGCAGCCACC | 57.451 | 45.000 | 15.89 | 0.00 | 30.78 | 4.61 |
3033 | 3073 | 2.884894 | ACAACTACTATAGCGGCACC | 57.115 | 50.000 | 1.45 | 0.00 | 0.00 | 5.01 |
3101 | 3141 | 3.906720 | TCTATTTTGGAACGGAGGGAG | 57.093 | 47.619 | 0.00 | 0.00 | 0.00 | 4.30 |
3102 | 3142 | 3.778075 | TCATCTATTTTGGAACGGAGGGA | 59.222 | 43.478 | 0.00 | 0.00 | 0.00 | 4.20 |
3103 | 3143 | 3.877508 | GTCATCTATTTTGGAACGGAGGG | 59.122 | 47.826 | 0.00 | 0.00 | 0.00 | 4.30 |
3104 | 3144 | 4.770795 | AGTCATCTATTTTGGAACGGAGG | 58.229 | 43.478 | 0.00 | 0.00 | 0.00 | 4.30 |
3105 | 3145 | 5.419542 | TGAGTCATCTATTTTGGAACGGAG | 58.580 | 41.667 | 0.00 | 0.00 | 0.00 | 4.63 |
3106 | 3146 | 5.414789 | TGAGTCATCTATTTTGGAACGGA | 57.585 | 39.130 | 0.00 | 0.00 | 0.00 | 4.69 |
3107 | 3147 | 5.643777 | AGTTGAGTCATCTATTTTGGAACGG | 59.356 | 40.000 | 1.70 | 0.00 | 0.00 | 4.44 |
3108 | 3148 | 6.727824 | AGTTGAGTCATCTATTTTGGAACG | 57.272 | 37.500 | 1.70 | 0.00 | 0.00 | 3.95 |
3109 | 3149 | 8.352942 | ACAAAGTTGAGTCATCTATTTTGGAAC | 58.647 | 33.333 | 14.35 | 0.00 | 40.00 | 3.62 |
3110 | 3150 | 8.463930 | ACAAAGTTGAGTCATCTATTTTGGAA | 57.536 | 30.769 | 14.35 | 0.00 | 40.00 | 3.53 |
3111 | 3151 | 8.999431 | GTACAAAGTTGAGTCATCTATTTTGGA | 58.001 | 33.333 | 14.35 | 6.88 | 40.00 | 3.53 |
3112 | 3152 | 9.003658 | AGTACAAAGTTGAGTCATCTATTTTGG | 57.996 | 33.333 | 14.35 | 0.00 | 40.00 | 3.28 |
3133 | 3173 | 9.850198 | ACCCAACTTTGTATTAAAGTTAGTACA | 57.150 | 29.630 | 15.03 | 3.15 | 45.57 | 2.90 |
3136 | 3176 | 8.983702 | TGACCCAACTTTGTATTAAAGTTAGT | 57.016 | 30.769 | 15.03 | 14.80 | 45.57 | 2.24 |
3138 | 3178 | 9.802039 | AGATGACCCAACTTTGTATTAAAGTTA | 57.198 | 29.630 | 15.03 | 3.25 | 45.57 | 2.24 |
3140 | 3180 | 9.975218 | ATAGATGACCCAACTTTGTATTAAAGT | 57.025 | 29.630 | 0.00 | 0.00 | 41.82 | 2.66 |
3145 | 3185 | 8.531146 | CCAAAATAGATGACCCAACTTTGTATT | 58.469 | 33.333 | 0.00 | 0.00 | 0.00 | 1.89 |
3146 | 3186 | 7.893302 | TCCAAAATAGATGACCCAACTTTGTAT | 59.107 | 33.333 | 0.00 | 0.00 | 0.00 | 2.29 |
3147 | 3187 | 7.235079 | TCCAAAATAGATGACCCAACTTTGTA | 58.765 | 34.615 | 0.00 | 0.00 | 0.00 | 2.41 |
3148 | 3188 | 6.074648 | TCCAAAATAGATGACCCAACTTTGT | 58.925 | 36.000 | 0.00 | 0.00 | 0.00 | 2.83 |
3149 | 3189 | 6.588719 | TCCAAAATAGATGACCCAACTTTG | 57.411 | 37.500 | 0.00 | 0.00 | 0.00 | 2.77 |
3150 | 3190 | 6.294508 | CGTTCCAAAATAGATGACCCAACTTT | 60.295 | 38.462 | 0.00 | 0.00 | 0.00 | 2.66 |
3151 | 3191 | 5.183140 | CGTTCCAAAATAGATGACCCAACTT | 59.817 | 40.000 | 0.00 | 0.00 | 0.00 | 2.66 |
3152 | 3192 | 4.700213 | CGTTCCAAAATAGATGACCCAACT | 59.300 | 41.667 | 0.00 | 0.00 | 0.00 | 3.16 |
3153 | 3193 | 4.142469 | CCGTTCCAAAATAGATGACCCAAC | 60.142 | 45.833 | 0.00 | 0.00 | 0.00 | 3.77 |
3154 | 3194 | 4.013728 | CCGTTCCAAAATAGATGACCCAA | 58.986 | 43.478 | 0.00 | 0.00 | 0.00 | 4.12 |
3155 | 3195 | 3.264706 | TCCGTTCCAAAATAGATGACCCA | 59.735 | 43.478 | 0.00 | 0.00 | 0.00 | 4.51 |
3156 | 3196 | 3.877508 | CTCCGTTCCAAAATAGATGACCC | 59.122 | 47.826 | 0.00 | 0.00 | 0.00 | 4.46 |
3157 | 3197 | 3.877508 | CCTCCGTTCCAAAATAGATGACC | 59.122 | 47.826 | 0.00 | 0.00 | 0.00 | 4.02 |
3158 | 3198 | 3.877508 | CCCTCCGTTCCAAAATAGATGAC | 59.122 | 47.826 | 0.00 | 0.00 | 0.00 | 3.06 |
3159 | 3199 | 3.778075 | TCCCTCCGTTCCAAAATAGATGA | 59.222 | 43.478 | 0.00 | 0.00 | 0.00 | 2.92 |
3160 | 3200 | 4.130118 | CTCCCTCCGTTCCAAAATAGATG | 58.870 | 47.826 | 0.00 | 0.00 | 0.00 | 2.90 |
3161 | 3201 | 3.780850 | ACTCCCTCCGTTCCAAAATAGAT | 59.219 | 43.478 | 0.00 | 0.00 | 0.00 | 1.98 |
3162 | 3202 | 3.178865 | ACTCCCTCCGTTCCAAAATAGA | 58.821 | 45.455 | 0.00 | 0.00 | 0.00 | 1.98 |
3163 | 3203 | 3.629142 | ACTCCCTCCGTTCCAAAATAG | 57.371 | 47.619 | 0.00 | 0.00 | 0.00 | 1.73 |
3164 | 3204 | 4.081309 | CACTACTCCCTCCGTTCCAAAATA | 60.081 | 45.833 | 0.00 | 0.00 | 0.00 | 1.40 |
3165 | 3205 | 2.910977 | ACTACTCCCTCCGTTCCAAAAT | 59.089 | 45.455 | 0.00 | 0.00 | 0.00 | 1.82 |
3166 | 3206 | 2.038033 | CACTACTCCCTCCGTTCCAAAA | 59.962 | 50.000 | 0.00 | 0.00 | 0.00 | 2.44 |
3167 | 3207 | 1.621814 | CACTACTCCCTCCGTTCCAAA | 59.378 | 52.381 | 0.00 | 0.00 | 0.00 | 3.28 |
3168 | 3208 | 1.263356 | CACTACTCCCTCCGTTCCAA | 58.737 | 55.000 | 0.00 | 0.00 | 0.00 | 3.53 |
3169 | 3209 | 0.113776 | ACACTACTCCCTCCGTTCCA | 59.886 | 55.000 | 0.00 | 0.00 | 0.00 | 3.53 |
3170 | 3210 | 1.264295 | AACACTACTCCCTCCGTTCC | 58.736 | 55.000 | 0.00 | 0.00 | 0.00 | 3.62 |
3171 | 3211 | 3.119209 | CCTAAACACTACTCCCTCCGTTC | 60.119 | 52.174 | 0.00 | 0.00 | 0.00 | 3.95 |
3172 | 3212 | 2.830321 | CCTAAACACTACTCCCTCCGTT | 59.170 | 50.000 | 0.00 | 0.00 | 0.00 | 4.44 |
3173 | 3213 | 2.454538 | CCTAAACACTACTCCCTCCGT | 58.545 | 52.381 | 0.00 | 0.00 | 0.00 | 4.69 |
3174 | 3214 | 1.136500 | GCCTAAACACTACTCCCTCCG | 59.864 | 57.143 | 0.00 | 0.00 | 0.00 | 4.63 |
3175 | 3215 | 2.185387 | TGCCTAAACACTACTCCCTCC | 58.815 | 52.381 | 0.00 | 0.00 | 0.00 | 4.30 |
3176 | 3216 | 3.975168 | TTGCCTAAACACTACTCCCTC | 57.025 | 47.619 | 0.00 | 0.00 | 0.00 | 4.30 |
3177 | 3217 | 3.054361 | CCATTGCCTAAACACTACTCCCT | 60.054 | 47.826 | 0.00 | 0.00 | 0.00 | 4.20 |
3178 | 3218 | 3.054655 | TCCATTGCCTAAACACTACTCCC | 60.055 | 47.826 | 0.00 | 0.00 | 0.00 | 4.30 |
3179 | 3219 | 4.216411 | TCCATTGCCTAAACACTACTCC | 57.784 | 45.455 | 0.00 | 0.00 | 0.00 | 3.85 |
3180 | 3220 | 5.122396 | CAGTTCCATTGCCTAAACACTACTC | 59.878 | 44.000 | 0.00 | 0.00 | 0.00 | 2.59 |
3181 | 3221 | 5.003804 | CAGTTCCATTGCCTAAACACTACT | 58.996 | 41.667 | 0.00 | 0.00 | 0.00 | 2.57 |
3182 | 3222 | 4.379499 | GCAGTTCCATTGCCTAAACACTAC | 60.379 | 45.833 | 0.00 | 0.00 | 35.54 | 2.73 |
3183 | 3223 | 3.756434 | GCAGTTCCATTGCCTAAACACTA | 59.244 | 43.478 | 0.00 | 0.00 | 35.54 | 2.74 |
3184 | 3224 | 2.558359 | GCAGTTCCATTGCCTAAACACT | 59.442 | 45.455 | 0.00 | 0.00 | 35.54 | 3.55 |
3251 | 3291 | 7.765307 | ACACAAATGTTATCTTAGCAATCCTG | 58.235 | 34.615 | 0.00 | 0.00 | 34.46 | 3.86 |
5433 | 5488 | 1.585297 | GTTCGGAACACGGAAGGAAA | 58.415 | 50.000 | 15.70 | 0.00 | 44.45 | 3.13 |
5473 | 5528 | 9.531942 | CCACATACGTGTAACTAATAAACCATA | 57.468 | 33.333 | 0.00 | 0.00 | 41.93 | 2.74 |
5538 | 5593 | 3.185330 | GACGTTCCCCGATCTTTAGAAC | 58.815 | 50.000 | 0.00 | 0.00 | 40.70 | 3.01 |
5541 | 5596 | 2.094390 | TGTGACGTTCCCCGATCTTTAG | 60.094 | 50.000 | 0.00 | 0.00 | 40.70 | 1.85 |
5550 | 5605 | 0.392595 | GGAAGGATGTGACGTTCCCC | 60.393 | 60.000 | 0.00 | 0.00 | 44.20 | 4.81 |
5591 | 5646 | 6.108687 | TCTGAATCAATTGAGACGTAAGCAT | 58.891 | 36.000 | 14.54 | 0.00 | 45.62 | 3.79 |
5629 | 5684 | 6.605995 | TCTGATATTTTTCAGGACCTCGTAGA | 59.394 | 38.462 | 0.00 | 0.00 | 42.78 | 2.59 |
5648 | 5703 | 6.017109 | GGTTTGCAACTCTTGTTCTTCTGATA | 60.017 | 38.462 | 0.00 | 0.00 | 33.52 | 2.15 |
5717 | 5796 | 5.184340 | AGTGAATAGAATTACGGAGGTCG | 57.816 | 43.478 | 0.00 | 0.00 | 45.88 | 4.79 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.