Multiple sequence alignment - TraesCS5D01G195400
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 | TraesCS5D01G195400 | chr5D | 100.000 | 4111 | 0 | 0 | 948 | 5058 | 298939600 | 298943710 | 0.000000e+00 | 7592.0 |
1 | TraesCS5D01G195400 | chr5D | 100.000 | 643 | 0 | 0 | 1 | 643 | 298938653 | 298939295 | 0.000000e+00 | 1188.0 |
2 | TraesCS5D01G195400 | chr5A | 93.012 | 4164 | 174 | 57 | 948 | 5058 | 398887550 | 398883451 | 0.000000e+00 | 5969.0 |
3 | TraesCS5D01G195400 | chr5A | 92.291 | 454 | 19 | 8 | 202 | 643 | 398888053 | 398887604 | 9.240000e-177 | 630.0 |
4 | TraesCS5D01G195400 | chr5B | 93.080 | 2312 | 100 | 24 | 2794 | 5058 | 339905691 | 339907989 | 0.000000e+00 | 3328.0 |
5 | TraesCS5D01G195400 | chr5B | 89.363 | 1335 | 97 | 22 | 948 | 2255 | 339903782 | 339905098 | 0.000000e+00 | 1637.0 |
6 | TraesCS5D01G195400 | chr5B | 92.500 | 520 | 30 | 4 | 2254 | 2764 | 339905179 | 339905698 | 0.000000e+00 | 736.0 |
7 | TraesCS5D01G195400 | chr5B | 93.154 | 409 | 20 | 4 | 229 | 636 | 339903308 | 339903709 | 1.210000e-165 | 593.0 |
8 | TraesCS5D01G195400 | chr4D | 74.754 | 610 | 87 | 43 | 4442 | 5004 | 220344370 | 220343781 | 1.430000e-50 | 211.0 |
9 | TraesCS5D01G195400 | chr3B | 79.649 | 285 | 35 | 18 | 4551 | 4820 | 479293763 | 479293487 | 3.110000e-42 | 183.0 |
10 | TraesCS5D01G195400 | chr4B | 81.159 | 207 | 27 | 6 | 4546 | 4745 | 20229052 | 20229253 | 6.780000e-34 | 156.0 |
11 | TraesCS5D01G195400 | chr1D | 91.111 | 45 | 3 | 1 | 4696 | 4740 | 484320128 | 484320171 | 5.470000e-05 | 60.2 |
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 | TraesCS5D01G195400 | chr5D | 298938653 | 298943710 | 5057 | False | 4390.0 | 7592 | 100.00000 | 1 | 5058 | 2 | chr5D.!!$F1 | 5057 |
1 | TraesCS5D01G195400 | chr5A | 398883451 | 398888053 | 4602 | True | 3299.5 | 5969 | 92.65150 | 202 | 5058 | 2 | chr5A.!!$R1 | 4856 |
2 | TraesCS5D01G195400 | chr5B | 339903308 | 339907989 | 4681 | False | 1573.5 | 3328 | 92.02425 | 229 | 5058 | 4 | chr5B.!!$F1 | 4829 |
3 | TraesCS5D01G195400 | chr4D | 220343781 | 220344370 | 589 | True | 211.0 | 211 | 74.75400 | 4442 | 5004 | 1 | chr4D.!!$R1 | 562 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
297 | 298 | 0.173708 | ACGAAAGCTCCGAGCCTTAG | 59.826 | 55.0 | 16.99 | 12.82 | 43.77 | 2.18 | F |
628 | 650 | 0.983378 | CCCTCCCGACCTTCATCCTT | 60.983 | 60.0 | 0.00 | 0.00 | 0.00 | 3.36 | F |
2041 | 2091 | 0.035317 | AATGGCACGCAGAGAAGTCA | 59.965 | 50.0 | 0.00 | 0.00 | 0.00 | 3.41 | F |
2163 | 2216 | 0.188342 | AAGCCTGGATGTGGTTTGGT | 59.812 | 50.0 | 0.00 | 0.00 | 0.00 | 3.67 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1277 | 1317 | 0.036306 | AAATCCGGTCTCCCACACAC | 59.964 | 55.0 | 0.00 | 0.0 | 0.00 | 3.82 | R |
2147 | 2200 | 0.318120 | GCAACCAAACCACATCCAGG | 59.682 | 55.0 | 0.00 | 0.0 | 0.00 | 4.45 | R |
3134 | 3318 | 1.114119 | TTGCTGGCAGGTGCAATTCA | 61.114 | 50.0 | 17.64 | 0.0 | 43.17 | 2.57 | R |
4157 | 4362 | 0.036952 | CGGTGACAACAGGCATCTCT | 60.037 | 55.0 | 0.00 | 0.0 | 0.00 | 3.10 | 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 |
---|---|---|---|---|---|---|---|---|---|
20 | 21 | 3.034721 | ACAACTAAAGTCGCCATTCGA | 57.965 | 42.857 | 0.00 | 0.00 | 46.29 | 3.71 |
58 | 59 | 6.908870 | AAGAAAAACTGAAACTTGCAATCC | 57.091 | 33.333 | 0.00 | 0.00 | 0.00 | 3.01 |
59 | 60 | 5.043248 | AGAAAAACTGAAACTTGCAATCCG | 58.957 | 37.500 | 0.00 | 0.00 | 0.00 | 4.18 |
60 | 61 | 4.647424 | AAAACTGAAACTTGCAATCCGA | 57.353 | 36.364 | 0.00 | 0.00 | 0.00 | 4.55 |
61 | 62 | 4.647424 | AAACTGAAACTTGCAATCCGAA | 57.353 | 36.364 | 0.00 | 0.00 | 0.00 | 4.30 |
62 | 63 | 4.647424 | AACTGAAACTTGCAATCCGAAA | 57.353 | 36.364 | 0.00 | 0.00 | 0.00 | 3.46 |
63 | 64 | 4.647424 | ACTGAAACTTGCAATCCGAAAA | 57.353 | 36.364 | 0.00 | 0.00 | 0.00 | 2.29 |
64 | 65 | 4.610945 | ACTGAAACTTGCAATCCGAAAAG | 58.389 | 39.130 | 0.00 | 0.00 | 0.00 | 2.27 |
65 | 66 | 4.338118 | ACTGAAACTTGCAATCCGAAAAGA | 59.662 | 37.500 | 0.00 | 0.00 | 0.00 | 2.52 |
66 | 67 | 5.163561 | ACTGAAACTTGCAATCCGAAAAGAA | 60.164 | 36.000 | 0.00 | 0.00 | 0.00 | 2.52 |
67 | 68 | 5.280945 | TGAAACTTGCAATCCGAAAAGAAG | 58.719 | 37.500 | 0.00 | 0.00 | 0.00 | 2.85 |
68 | 69 | 4.918810 | AACTTGCAATCCGAAAAGAAGT | 57.081 | 36.364 | 0.00 | 0.00 | 0.00 | 3.01 |
69 | 70 | 4.918810 | ACTTGCAATCCGAAAAGAAGTT | 57.081 | 36.364 | 0.00 | 0.00 | 0.00 | 2.66 |
70 | 71 | 4.610945 | ACTTGCAATCCGAAAAGAAGTTG | 58.389 | 39.130 | 0.00 | 0.00 | 0.00 | 3.16 |
71 | 72 | 4.097892 | ACTTGCAATCCGAAAAGAAGTTGT | 59.902 | 37.500 | 0.00 | 0.00 | 0.00 | 3.32 |
72 | 73 | 4.223320 | TGCAATCCGAAAAGAAGTTGTC | 57.777 | 40.909 | 0.00 | 0.00 | 0.00 | 3.18 |
73 | 74 | 3.226347 | GCAATCCGAAAAGAAGTTGTCG | 58.774 | 45.455 | 0.00 | 0.00 | 0.00 | 4.35 |
74 | 75 | 3.303791 | GCAATCCGAAAAGAAGTTGTCGT | 60.304 | 43.478 | 0.00 | 0.00 | 0.00 | 4.34 |
75 | 76 | 4.455124 | CAATCCGAAAAGAAGTTGTCGTC | 58.545 | 43.478 | 0.00 | 0.00 | 0.00 | 4.20 |
76 | 77 | 3.447918 | TCCGAAAAGAAGTTGTCGTCT | 57.552 | 42.857 | 0.00 | 0.00 | 34.13 | 4.18 |
77 | 78 | 3.788937 | TCCGAAAAGAAGTTGTCGTCTT | 58.211 | 40.909 | 0.00 | 0.00 | 42.36 | 3.01 |
79 | 80 | 4.269363 | TCCGAAAAGAAGTTGTCGTCTTTC | 59.731 | 41.667 | 8.87 | 0.00 | 46.03 | 2.62 |
80 | 81 | 4.033587 | CCGAAAAGAAGTTGTCGTCTTTCA | 59.966 | 41.667 | 8.87 | 0.00 | 46.03 | 2.69 |
81 | 82 | 5.446741 | CCGAAAAGAAGTTGTCGTCTTTCAA | 60.447 | 40.000 | 8.87 | 0.00 | 46.03 | 2.69 |
82 | 83 | 5.448162 | CGAAAAGAAGTTGTCGTCTTTCAAC | 59.552 | 40.000 | 8.87 | 0.00 | 46.03 | 3.18 |
103 | 104 | 5.786401 | ACTAAAGTTGTCATCATCGCTTC | 57.214 | 39.130 | 0.00 | 0.00 | 0.00 | 3.86 |
104 | 105 | 5.237815 | ACTAAAGTTGTCATCATCGCTTCA | 58.762 | 37.500 | 0.00 | 0.00 | 0.00 | 3.02 |
105 | 106 | 4.410492 | AAAGTTGTCATCATCGCTTCAC | 57.590 | 40.909 | 0.00 | 0.00 | 0.00 | 3.18 |
106 | 107 | 3.325293 | AGTTGTCATCATCGCTTCACT | 57.675 | 42.857 | 0.00 | 0.00 | 0.00 | 3.41 |
107 | 108 | 4.456280 | AGTTGTCATCATCGCTTCACTA | 57.544 | 40.909 | 0.00 | 0.00 | 0.00 | 2.74 |
108 | 109 | 4.820897 | AGTTGTCATCATCGCTTCACTAA | 58.179 | 39.130 | 0.00 | 0.00 | 0.00 | 2.24 |
109 | 110 | 5.237815 | AGTTGTCATCATCGCTTCACTAAA | 58.762 | 37.500 | 0.00 | 0.00 | 0.00 | 1.85 |
110 | 111 | 5.877012 | AGTTGTCATCATCGCTTCACTAAAT | 59.123 | 36.000 | 0.00 | 0.00 | 0.00 | 1.40 |
111 | 112 | 5.973651 | TGTCATCATCGCTTCACTAAATC | 57.026 | 39.130 | 0.00 | 0.00 | 0.00 | 2.17 |
112 | 113 | 5.664457 | TGTCATCATCGCTTCACTAAATCT | 58.336 | 37.500 | 0.00 | 0.00 | 0.00 | 2.40 |
113 | 114 | 5.521372 | TGTCATCATCGCTTCACTAAATCTG | 59.479 | 40.000 | 0.00 | 0.00 | 0.00 | 2.90 |
114 | 115 | 4.509230 | TCATCATCGCTTCACTAAATCTGC | 59.491 | 41.667 | 0.00 | 0.00 | 0.00 | 4.26 |
115 | 116 | 3.198068 | TCATCGCTTCACTAAATCTGCC | 58.802 | 45.455 | 0.00 | 0.00 | 0.00 | 4.85 |
116 | 117 | 2.760634 | TCGCTTCACTAAATCTGCCA | 57.239 | 45.000 | 0.00 | 0.00 | 0.00 | 4.92 |
117 | 118 | 3.266510 | TCGCTTCACTAAATCTGCCAT | 57.733 | 42.857 | 0.00 | 0.00 | 0.00 | 4.40 |
118 | 119 | 4.400529 | TCGCTTCACTAAATCTGCCATA | 57.599 | 40.909 | 0.00 | 0.00 | 0.00 | 2.74 |
119 | 120 | 4.765273 | TCGCTTCACTAAATCTGCCATAA | 58.235 | 39.130 | 0.00 | 0.00 | 0.00 | 1.90 |
120 | 121 | 5.182487 | TCGCTTCACTAAATCTGCCATAAA | 58.818 | 37.500 | 0.00 | 0.00 | 0.00 | 1.40 |
121 | 122 | 5.645929 | TCGCTTCACTAAATCTGCCATAAAA | 59.354 | 36.000 | 0.00 | 0.00 | 0.00 | 1.52 |
122 | 123 | 6.150307 | TCGCTTCACTAAATCTGCCATAAAAA | 59.850 | 34.615 | 0.00 | 0.00 | 0.00 | 1.94 |
123 | 124 | 6.974622 | CGCTTCACTAAATCTGCCATAAAAAT | 59.025 | 34.615 | 0.00 | 0.00 | 0.00 | 1.82 |
124 | 125 | 7.043854 | CGCTTCACTAAATCTGCCATAAAAATG | 60.044 | 37.037 | 0.00 | 0.00 | 0.00 | 2.32 |
125 | 126 | 7.761249 | GCTTCACTAAATCTGCCATAAAAATGT | 59.239 | 33.333 | 0.00 | 0.00 | 0.00 | 2.71 |
126 | 127 | 9.643693 | CTTCACTAAATCTGCCATAAAAATGTT | 57.356 | 29.630 | 0.00 | 0.00 | 0.00 | 2.71 |
127 | 128 | 9.995003 | TTCACTAAATCTGCCATAAAAATGTTT | 57.005 | 25.926 | 0.00 | 0.00 | 0.00 | 2.83 |
128 | 129 | 9.995003 | TCACTAAATCTGCCATAAAAATGTTTT | 57.005 | 25.926 | 0.00 | 0.00 | 0.00 | 2.43 |
130 | 131 | 9.995003 | ACTAAATCTGCCATAAAAATGTTTTGA | 57.005 | 25.926 | 0.00 | 0.00 | 0.00 | 2.69 |
135 | 136 | 7.583230 | TCTGCCATAAAAATGTTTTGAATTGC | 58.417 | 30.769 | 0.00 | 0.00 | 0.00 | 3.56 |
136 | 137 | 6.675987 | TGCCATAAAAATGTTTTGAATTGCC | 58.324 | 32.000 | 0.00 | 0.00 | 0.00 | 4.52 |
137 | 138 | 6.263842 | TGCCATAAAAATGTTTTGAATTGCCA | 59.736 | 30.769 | 0.00 | 0.00 | 0.00 | 4.92 |
138 | 139 | 7.039923 | TGCCATAAAAATGTTTTGAATTGCCAT | 60.040 | 29.630 | 0.00 | 0.00 | 0.00 | 4.40 |
139 | 140 | 7.273815 | GCCATAAAAATGTTTTGAATTGCCATG | 59.726 | 33.333 | 0.00 | 0.00 | 0.00 | 3.66 |
140 | 141 | 8.298140 | CCATAAAAATGTTTTGAATTGCCATGT | 58.702 | 29.630 | 0.00 | 0.00 | 0.00 | 3.21 |
141 | 142 | 9.119329 | CATAAAAATGTTTTGAATTGCCATGTG | 57.881 | 29.630 | 0.00 | 0.00 | 0.00 | 3.21 |
142 | 143 | 6.696441 | AAAATGTTTTGAATTGCCATGTGT | 57.304 | 29.167 | 0.00 | 0.00 | 0.00 | 3.72 |
143 | 144 | 6.696441 | AAATGTTTTGAATTGCCATGTGTT | 57.304 | 29.167 | 0.00 | 0.00 | 0.00 | 3.32 |
144 | 145 | 6.696441 | AATGTTTTGAATTGCCATGTGTTT | 57.304 | 29.167 | 0.00 | 0.00 | 0.00 | 2.83 |
145 | 146 | 7.798596 | AATGTTTTGAATTGCCATGTGTTTA | 57.201 | 28.000 | 0.00 | 0.00 | 0.00 | 2.01 |
146 | 147 | 7.982761 | ATGTTTTGAATTGCCATGTGTTTAT | 57.017 | 28.000 | 0.00 | 0.00 | 0.00 | 1.40 |
147 | 148 | 7.187244 | TGTTTTGAATTGCCATGTGTTTATG | 57.813 | 32.000 | 0.00 | 0.00 | 0.00 | 1.90 |
148 | 149 | 5.859521 | TTTGAATTGCCATGTGTTTATGC | 57.140 | 34.783 | 0.00 | 0.00 | 0.00 | 3.14 |
149 | 150 | 3.859443 | TGAATTGCCATGTGTTTATGCC | 58.141 | 40.909 | 0.00 | 0.00 | 0.00 | 4.40 |
150 | 151 | 3.260128 | TGAATTGCCATGTGTTTATGCCA | 59.740 | 39.130 | 0.00 | 0.00 | 0.00 | 4.92 |
151 | 152 | 4.081031 | TGAATTGCCATGTGTTTATGCCAT | 60.081 | 37.500 | 0.00 | 0.00 | 0.00 | 4.40 |
152 | 153 | 3.523606 | TTGCCATGTGTTTATGCCATC | 57.476 | 42.857 | 0.00 | 0.00 | 0.00 | 3.51 |
153 | 154 | 1.755959 | TGCCATGTGTTTATGCCATCC | 59.244 | 47.619 | 0.00 | 0.00 | 0.00 | 3.51 |
154 | 155 | 1.755959 | GCCATGTGTTTATGCCATCCA | 59.244 | 47.619 | 0.00 | 0.00 | 0.00 | 3.41 |
155 | 156 | 2.366266 | GCCATGTGTTTATGCCATCCAT | 59.634 | 45.455 | 0.00 | 0.00 | 37.97 | 3.41 |
156 | 157 | 3.800949 | GCCATGTGTTTATGCCATCCATG | 60.801 | 47.826 | 0.00 | 0.00 | 35.34 | 3.66 |
157 | 158 | 3.385433 | CCATGTGTTTATGCCATCCATGT | 59.615 | 43.478 | 0.00 | 0.00 | 35.34 | 3.21 |
158 | 159 | 4.364860 | CATGTGTTTATGCCATCCATGTG | 58.635 | 43.478 | 0.00 | 0.00 | 35.34 | 3.21 |
159 | 160 | 3.694926 | TGTGTTTATGCCATCCATGTGA | 58.305 | 40.909 | 0.00 | 0.00 | 35.34 | 3.58 |
160 | 161 | 4.279982 | TGTGTTTATGCCATCCATGTGAT | 58.720 | 39.130 | 0.00 | 0.00 | 35.34 | 3.06 |
161 | 162 | 5.444176 | TGTGTTTATGCCATCCATGTGATA | 58.556 | 37.500 | 0.00 | 0.00 | 35.34 | 2.15 |
162 | 163 | 6.069994 | TGTGTTTATGCCATCCATGTGATAT | 58.930 | 36.000 | 0.00 | 0.00 | 35.34 | 1.63 |
163 | 164 | 6.550481 | TGTGTTTATGCCATCCATGTGATATT | 59.450 | 34.615 | 0.00 | 0.00 | 35.34 | 1.28 |
164 | 165 | 7.069702 | TGTGTTTATGCCATCCATGTGATATTT | 59.930 | 33.333 | 0.00 | 0.00 | 35.34 | 1.40 |
165 | 166 | 8.575589 | GTGTTTATGCCATCCATGTGATATTTA | 58.424 | 33.333 | 0.00 | 0.00 | 35.34 | 1.40 |
166 | 167 | 9.311676 | TGTTTATGCCATCCATGTGATATTTAT | 57.688 | 29.630 | 0.00 | 0.00 | 35.34 | 1.40 |
167 | 168 | 9.793252 | GTTTATGCCATCCATGTGATATTTATC | 57.207 | 33.333 | 0.00 | 0.00 | 35.34 | 1.75 |
168 | 169 | 9.531158 | TTTATGCCATCCATGTGATATTTATCA | 57.469 | 29.630 | 0.00 | 0.00 | 36.60 | 2.15 |
169 | 170 | 7.640597 | ATGCCATCCATGTGATATTTATCAG | 57.359 | 36.000 | 0.52 | 0.00 | 42.84 | 2.90 |
170 | 171 | 5.947566 | TGCCATCCATGTGATATTTATCAGG | 59.052 | 40.000 | 0.52 | 0.33 | 42.84 | 3.86 |
171 | 172 | 5.359009 | GCCATCCATGTGATATTTATCAGGG | 59.641 | 44.000 | 0.52 | 4.16 | 42.84 | 4.45 |
172 | 173 | 6.487828 | CCATCCATGTGATATTTATCAGGGT | 58.512 | 40.000 | 0.52 | 0.00 | 42.84 | 4.34 |
173 | 174 | 6.600822 | CCATCCATGTGATATTTATCAGGGTC | 59.399 | 42.308 | 0.52 | 0.00 | 42.84 | 4.46 |
174 | 175 | 7.400439 | CATCCATGTGATATTTATCAGGGTCT | 58.600 | 38.462 | 0.52 | 0.00 | 42.84 | 3.85 |
175 | 176 | 8.542926 | CATCCATGTGATATTTATCAGGGTCTA | 58.457 | 37.037 | 0.52 | 0.00 | 42.84 | 2.59 |
176 | 177 | 8.504811 | TCCATGTGATATTTATCAGGGTCTAA | 57.495 | 34.615 | 0.52 | 0.00 | 42.84 | 2.10 |
177 | 178 | 8.944138 | TCCATGTGATATTTATCAGGGTCTAAA | 58.056 | 33.333 | 0.52 | 0.00 | 42.84 | 1.85 |
178 | 179 | 9.573166 | CCATGTGATATTTATCAGGGTCTAAAA | 57.427 | 33.333 | 0.52 | 0.00 | 42.84 | 1.52 |
246 | 247 | 6.409704 | ACCAATCCAATGGATATCGATGTAG | 58.590 | 40.000 | 16.10 | 1.03 | 42.27 | 2.74 |
247 | 248 | 6.013379 | ACCAATCCAATGGATATCGATGTAGT | 60.013 | 38.462 | 16.10 | 1.62 | 42.27 | 2.73 |
248 | 249 | 7.180229 | ACCAATCCAATGGATATCGATGTAGTA | 59.820 | 37.037 | 16.10 | 0.00 | 42.27 | 1.82 |
262 | 263 | 8.858003 | ATCGATGTAGTATAAACAACTGACAG | 57.142 | 34.615 | 0.00 | 0.00 | 0.00 | 3.51 |
297 | 298 | 0.173708 | ACGAAAGCTCCGAGCCTTAG | 59.826 | 55.000 | 16.99 | 12.82 | 43.77 | 2.18 |
375 | 377 | 1.051556 | GTCAGTCCCCTCTCCCATCC | 61.052 | 65.000 | 0.00 | 0.00 | 0.00 | 3.51 |
378 | 381 | 2.964039 | TCCCCTCTCCCATCCCCA | 60.964 | 66.667 | 0.00 | 0.00 | 0.00 | 4.96 |
628 | 650 | 0.983378 | CCCTCCCGACCTTCATCCTT | 60.983 | 60.000 | 0.00 | 0.00 | 0.00 | 3.36 |
631 | 653 | 1.834263 | CTCCCGACCTTCATCCTTCTT | 59.166 | 52.381 | 0.00 | 0.00 | 0.00 | 2.52 |
636 | 658 | 2.545731 | GACCTTCATCCTTCTTCTCGC | 58.454 | 52.381 | 0.00 | 0.00 | 0.00 | 5.03 |
638 | 660 | 1.474143 | CCTTCATCCTTCTTCTCGCCC | 60.474 | 57.143 | 0.00 | 0.00 | 0.00 | 6.13 |
1193 | 1226 | 1.431036 | GCTCCTTCTTTCATGGCGC | 59.569 | 57.895 | 0.00 | 0.00 | 0.00 | 6.53 |
1209 | 1242 | 1.333115 | GCGCGGTTGTTGATTAAACC | 58.667 | 50.000 | 8.83 | 0.00 | 42.07 | 3.27 |
1277 | 1317 | 2.355197 | TGACTTGTGTTGTGTCAGTGG | 58.645 | 47.619 | 0.00 | 0.00 | 36.03 | 4.00 |
1278 | 1318 | 2.290008 | TGACTTGTGTTGTGTCAGTGGT | 60.290 | 45.455 | 0.00 | 0.00 | 36.03 | 4.16 |
1393 | 1433 | 4.837972 | AGGAATTTGAGTGCTAGAACCTC | 58.162 | 43.478 | 0.00 | 0.00 | 0.00 | 3.85 |
1394 | 1434 | 4.534103 | AGGAATTTGAGTGCTAGAACCTCT | 59.466 | 41.667 | 0.00 | 0.00 | 0.00 | 3.69 |
1396 | 1436 | 5.123027 | GGAATTTGAGTGCTAGAACCTCTTG | 59.877 | 44.000 | 0.00 | 0.00 | 0.00 | 3.02 |
1397 | 1437 | 4.689612 | TTTGAGTGCTAGAACCTCTTGT | 57.310 | 40.909 | 0.00 | 0.00 | 0.00 | 3.16 |
1398 | 1438 | 3.667497 | TGAGTGCTAGAACCTCTTGTG | 57.333 | 47.619 | 0.00 | 0.00 | 0.00 | 3.33 |
1399 | 1439 | 2.289072 | TGAGTGCTAGAACCTCTTGTGC | 60.289 | 50.000 | 0.00 | 0.00 | 0.00 | 4.57 |
1405 | 1449 | 4.202315 | TGCTAGAACCTCTTGTGCTTTGTA | 60.202 | 41.667 | 0.00 | 0.00 | 33.62 | 2.41 |
1412 | 1456 | 3.743396 | CCTCTTGTGCTTTGTAGTGAGTC | 59.257 | 47.826 | 0.00 | 0.00 | 0.00 | 3.36 |
1471 | 1515 | 1.152881 | ATGGCCCTTTCGCTGGATC | 60.153 | 57.895 | 0.00 | 0.00 | 0.00 | 3.36 |
1472 | 1516 | 1.925285 | ATGGCCCTTTCGCTGGATCA | 61.925 | 55.000 | 0.00 | 0.00 | 0.00 | 2.92 |
1473 | 1517 | 1.152881 | GGCCCTTTCGCTGGATCAT | 60.153 | 57.895 | 0.00 | 0.00 | 0.00 | 2.45 |
1507 | 1551 | 5.324409 | TGTTTCAGTTCTGGGCATATTTCT | 58.676 | 37.500 | 0.00 | 0.00 | 0.00 | 2.52 |
1510 | 1554 | 5.441718 | TCAGTTCTGGGCATATTTCTTCT | 57.558 | 39.130 | 0.00 | 0.00 | 0.00 | 2.85 |
1515 | 1559 | 5.902613 | TCTGGGCATATTTCTTCTGTTTG | 57.097 | 39.130 | 0.00 | 0.00 | 0.00 | 2.93 |
1554 | 1599 | 1.503818 | CTTTGCGGTTACGTGTGGCT | 61.504 | 55.000 | 0.00 | 0.00 | 43.45 | 4.75 |
1555 | 1600 | 1.500512 | TTTGCGGTTACGTGTGGCTC | 61.501 | 55.000 | 0.00 | 0.00 | 43.45 | 4.70 |
1556 | 1601 | 2.356553 | GCGGTTACGTGTGGCTCA | 60.357 | 61.111 | 0.00 | 0.00 | 43.45 | 4.26 |
1557 | 1602 | 2.664436 | GCGGTTACGTGTGGCTCAC | 61.664 | 63.158 | 9.57 | 9.57 | 43.45 | 3.51 |
1568 | 1613 | 2.880890 | GTGTGGCTCACAATTCTGAGTT | 59.119 | 45.455 | 14.37 | 0.00 | 46.28 | 3.01 |
1570 | 1615 | 3.565482 | TGTGGCTCACAATTCTGAGTTTC | 59.435 | 43.478 | 11.72 | 4.04 | 41.69 | 2.78 |
1574 | 1619 | 5.360714 | TGGCTCACAATTCTGAGTTTCTTTT | 59.639 | 36.000 | 11.72 | 0.00 | 40.03 | 2.27 |
1581 | 1626 | 3.963476 | TCTGAGTTTCTTTTTGGGGGA | 57.037 | 42.857 | 0.00 | 0.00 | 0.00 | 4.81 |
1587 | 1637 | 4.411013 | AGTTTCTTTTTGGGGGAGATGAG | 58.589 | 43.478 | 0.00 | 0.00 | 0.00 | 2.90 |
1595 | 1645 | 2.358258 | TGGGGGAGATGAGGACTTTTT | 58.642 | 47.619 | 0.00 | 0.00 | 0.00 | 1.94 |
1628 | 1678 | 2.609825 | CACACTGTGTGCTCTGACC | 58.390 | 57.895 | 26.02 | 0.00 | 41.89 | 4.02 |
1639 | 1689 | 3.771479 | TGTGCTCTGACCTCACTGAATAT | 59.229 | 43.478 | 0.00 | 0.00 | 0.00 | 1.28 |
1642 | 1692 | 6.070824 | TGTGCTCTGACCTCACTGAATATTAA | 60.071 | 38.462 | 0.00 | 0.00 | 0.00 | 1.40 |
1644 | 1694 | 7.497249 | GTGCTCTGACCTCACTGAATATTAAAT | 59.503 | 37.037 | 0.00 | 0.00 | 0.00 | 1.40 |
1666 | 1716 | 7.775397 | AATTTGATGTGCAATAGCCAATAAC | 57.225 | 32.000 | 0.00 | 0.00 | 41.13 | 1.89 |
1691 | 1741 | 1.274728 | AGAGCACTCTTGTACTGCTGG | 59.725 | 52.381 | 10.93 | 0.00 | 36.31 | 4.85 |
1731 | 1781 | 4.613437 | AGAATTGGCCATCTTTGTATGGT | 58.387 | 39.130 | 6.09 | 0.00 | 46.93 | 3.55 |
1739 | 1789 | 5.376625 | GCCATCTTTGTATGGTTATGGAGA | 58.623 | 41.667 | 0.00 | 0.00 | 46.93 | 3.71 |
1752 | 1802 | 2.988010 | ATGGAGAGTATGCAAAGCGA | 57.012 | 45.000 | 0.00 | 0.00 | 30.55 | 4.93 |
1798 | 1848 | 0.326264 | AGGTTGCTTCTGGGCTAGTG | 59.674 | 55.000 | 0.00 | 0.00 | 0.00 | 2.74 |
1806 | 1856 | 1.486211 | TCTGGGCTAGTGCTAAGGAC | 58.514 | 55.000 | 0.00 | 0.00 | 39.59 | 3.85 |
1925 | 1975 | 6.942532 | TGGCATTGGAATTCAGTATCTTAC | 57.057 | 37.500 | 7.93 | 0.00 | 0.00 | 2.34 |
1926 | 1976 | 6.422333 | TGGCATTGGAATTCAGTATCTTACA | 58.578 | 36.000 | 7.93 | 0.00 | 0.00 | 2.41 |
1928 | 1978 | 7.013559 | TGGCATTGGAATTCAGTATCTTACATG | 59.986 | 37.037 | 7.93 | 0.00 | 0.00 | 3.21 |
1929 | 1979 | 7.013655 | GGCATTGGAATTCAGTATCTTACATGT | 59.986 | 37.037 | 7.93 | 2.69 | 0.00 | 3.21 |
2012 | 2062 | 4.942483 | GCCTCTTCCTAGTTTTAGTTTCCC | 59.058 | 45.833 | 0.00 | 0.00 | 0.00 | 3.97 |
2034 | 2084 | 1.548719 | AGTACTACAATGGCACGCAGA | 59.451 | 47.619 | 0.00 | 0.00 | 0.00 | 4.26 |
2036 | 2086 | 0.608130 | ACTACAATGGCACGCAGAGA | 59.392 | 50.000 | 0.00 | 0.00 | 0.00 | 3.10 |
2038 | 2088 | 1.662629 | CTACAATGGCACGCAGAGAAG | 59.337 | 52.381 | 0.00 | 0.00 | 0.00 | 2.85 |
2040 | 2090 | 0.445436 | CAATGGCACGCAGAGAAGTC | 59.555 | 55.000 | 0.00 | 0.00 | 0.00 | 3.01 |
2041 | 2091 | 0.035317 | AATGGCACGCAGAGAAGTCA | 59.965 | 50.000 | 0.00 | 0.00 | 0.00 | 3.41 |
2042 | 2092 | 0.390866 | ATGGCACGCAGAGAAGTCAG | 60.391 | 55.000 | 0.00 | 0.00 | 0.00 | 3.51 |
2062 | 2113 | 9.435688 | AAGTCAGTTGCATTAAAATATTTTCCC | 57.564 | 29.630 | 16.56 | 5.21 | 0.00 | 3.97 |
2113 | 2164 | 5.106555 | CGAAACACTAGAAGATGCACCAATT | 60.107 | 40.000 | 0.00 | 0.00 | 0.00 | 2.32 |
2147 | 2200 | 3.436700 | ACAAACTGGCAAGTGTAAAGC | 57.563 | 42.857 | 0.00 | 0.00 | 36.51 | 3.51 |
2163 | 2216 | 0.188342 | AAGCCTGGATGTGGTTTGGT | 59.812 | 50.000 | 0.00 | 0.00 | 0.00 | 3.67 |
2165 | 2218 | 0.318120 | GCCTGGATGTGGTTTGGTTG | 59.682 | 55.000 | 0.00 | 0.00 | 0.00 | 3.77 |
2166 | 2219 | 0.318120 | CCTGGATGTGGTTTGGTTGC | 59.682 | 55.000 | 0.00 | 0.00 | 0.00 | 4.17 |
2167 | 2220 | 1.331214 | CTGGATGTGGTTTGGTTGCT | 58.669 | 50.000 | 0.00 | 0.00 | 0.00 | 3.91 |
2212 | 2270 | 6.619446 | GCACTCACTTGTGTTCATATGACTTC | 60.619 | 42.308 | 4.48 | 0.07 | 39.89 | 3.01 |
2578 | 2725 | 4.576879 | ACTCTATGACTATGCATGCCATG | 58.423 | 43.478 | 16.68 | 0.00 | 35.34 | 3.66 |
2582 | 2729 | 7.124750 | ACTCTATGACTATGCATGCCATGTATA | 59.875 | 37.037 | 16.68 | 13.74 | 36.90 | 1.47 |
2787 | 2938 | 8.927411 | AGTACTAAAGTTTGTAGGAGTTGGTAA | 58.073 | 33.333 | 0.00 | 0.00 | 0.00 | 2.85 |
3049 | 3200 | 1.274167 | CGGGTGCCGGCTATATTAAGA | 59.726 | 52.381 | 29.70 | 0.00 | 44.15 | 2.10 |
3076 | 3260 | 5.917447 | CCACATGACATAGTGATTCTAGACG | 59.083 | 44.000 | 15.37 | 0.00 | 37.97 | 4.18 |
3098 | 3282 | 3.781079 | CGGTATACGTCCCAAGTGTTA | 57.219 | 47.619 | 0.00 | 0.00 | 37.93 | 2.41 |
3119 | 3303 | 6.042093 | TGTTAAACCATTTAATCCTGCCAACA | 59.958 | 34.615 | 0.00 | 0.00 | 37.44 | 3.33 |
3141 | 3325 | 3.067180 | ACGTGGAATCCATCATGAATTGC | 59.933 | 43.478 | 4.81 | 1.06 | 35.28 | 3.56 |
3148 | 3332 | 1.202486 | CCATCATGAATTGCACCTGCC | 60.202 | 52.381 | 0.00 | 0.00 | 41.18 | 4.85 |
3518 | 3715 | 5.947228 | TGCCATCTTGTTTCTTAGTGAAG | 57.053 | 39.130 | 0.00 | 0.00 | 35.89 | 3.02 |
3544 | 3741 | 8.459911 | AATGATGCATAATGAACAAGATGAGA | 57.540 | 30.769 | 0.00 | 0.00 | 0.00 | 3.27 |
3558 | 3755 | 6.516718 | ACAAGATGAGATTACCATCCTTACG | 58.483 | 40.000 | 0.00 | 0.00 | 40.85 | 3.18 |
3563 | 3760 | 4.051922 | GAGATTACCATCCTTACGCACAG | 58.948 | 47.826 | 0.00 | 0.00 | 0.00 | 3.66 |
3786 | 3983 | 0.389426 | GCAAGCCAAAGCACTCATGG | 60.389 | 55.000 | 0.00 | 0.00 | 43.56 | 3.66 |
3790 | 3987 | 0.811281 | GCCAAAGCACTCATGGTACC | 59.189 | 55.000 | 4.43 | 4.43 | 39.53 | 3.34 |
3979 | 4176 | 0.602905 | ACTTTGCGAACGGCTTAGCT | 60.603 | 50.000 | 3.59 | 0.00 | 44.05 | 3.32 |
4157 | 4362 | 0.951558 | GAAAGAAGAAACCGGCTGCA | 59.048 | 50.000 | 0.00 | 0.00 | 0.00 | 4.41 |
4178 | 4383 | 1.965930 | GATGCCTGTTGTCACCGCA | 60.966 | 57.895 | 0.00 | 0.00 | 0.00 | 5.69 |
4211 | 4416 | 1.473550 | TCAATTTAACCCCCACCCCT | 58.526 | 50.000 | 0.00 | 0.00 | 0.00 | 4.79 |
4390 | 4596 | 2.752354 | CTGTTGTCAAGTGTTTGGTGGA | 59.248 | 45.455 | 0.00 | 0.00 | 34.97 | 4.02 |
4468 | 4674 | 1.614996 | TACAGTGCACCAACCCAATG | 58.385 | 50.000 | 14.63 | 4.99 | 33.66 | 2.82 |
4661 | 4887 | 7.125507 | ACAAAGATGGCCATATATTTTGAACCA | 59.874 | 33.333 | 30.86 | 2.01 | 0.00 | 3.67 |
4830 | 5068 | 1.541672 | GGAGAGGGAGAGGGAGAGG | 59.458 | 68.421 | 0.00 | 0.00 | 0.00 | 3.69 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
32 | 33 | 9.045223 | GGATTGCAAGTTTCAGTTTTTCTTATT | 57.955 | 29.630 | 4.94 | 0.00 | 0.00 | 1.40 |
33 | 34 | 7.382218 | CGGATTGCAAGTTTCAGTTTTTCTTAT | 59.618 | 33.333 | 4.94 | 0.00 | 0.00 | 1.73 |
34 | 35 | 6.695278 | CGGATTGCAAGTTTCAGTTTTTCTTA | 59.305 | 34.615 | 4.94 | 0.00 | 0.00 | 2.10 |
35 | 36 | 5.519927 | CGGATTGCAAGTTTCAGTTTTTCTT | 59.480 | 36.000 | 4.94 | 0.00 | 0.00 | 2.52 |
36 | 37 | 5.043248 | CGGATTGCAAGTTTCAGTTTTTCT | 58.957 | 37.500 | 4.94 | 0.00 | 0.00 | 2.52 |
37 | 38 | 5.040635 | TCGGATTGCAAGTTTCAGTTTTTC | 58.959 | 37.500 | 4.94 | 0.00 | 0.00 | 2.29 |
38 | 39 | 5.004922 | TCGGATTGCAAGTTTCAGTTTTT | 57.995 | 34.783 | 4.94 | 0.00 | 0.00 | 1.94 |
39 | 40 | 4.647424 | TCGGATTGCAAGTTTCAGTTTT | 57.353 | 36.364 | 4.94 | 0.00 | 0.00 | 2.43 |
40 | 41 | 4.647424 | TTCGGATTGCAAGTTTCAGTTT | 57.353 | 36.364 | 4.94 | 0.00 | 0.00 | 2.66 |
41 | 42 | 4.647424 | TTTCGGATTGCAAGTTTCAGTT | 57.353 | 36.364 | 4.94 | 0.00 | 0.00 | 3.16 |
42 | 43 | 4.338118 | TCTTTTCGGATTGCAAGTTTCAGT | 59.662 | 37.500 | 4.94 | 0.00 | 0.00 | 3.41 |
43 | 44 | 4.858935 | TCTTTTCGGATTGCAAGTTTCAG | 58.141 | 39.130 | 4.94 | 0.00 | 0.00 | 3.02 |
44 | 45 | 4.909696 | TCTTTTCGGATTGCAAGTTTCA | 57.090 | 36.364 | 4.94 | 0.00 | 0.00 | 2.69 |
45 | 46 | 5.281727 | ACTTCTTTTCGGATTGCAAGTTTC | 58.718 | 37.500 | 4.94 | 0.00 | 0.00 | 2.78 |
46 | 47 | 5.262588 | ACTTCTTTTCGGATTGCAAGTTT | 57.737 | 34.783 | 4.94 | 0.00 | 0.00 | 2.66 |
47 | 48 | 4.918810 | ACTTCTTTTCGGATTGCAAGTT | 57.081 | 36.364 | 4.94 | 0.00 | 0.00 | 2.66 |
48 | 49 | 4.097892 | ACAACTTCTTTTCGGATTGCAAGT | 59.902 | 37.500 | 4.94 | 0.00 | 0.00 | 3.16 |
49 | 50 | 4.610945 | ACAACTTCTTTTCGGATTGCAAG | 58.389 | 39.130 | 4.94 | 0.00 | 0.00 | 4.01 |
50 | 51 | 4.606961 | GACAACTTCTTTTCGGATTGCAA | 58.393 | 39.130 | 0.00 | 0.00 | 0.00 | 4.08 |
51 | 52 | 3.303725 | CGACAACTTCTTTTCGGATTGCA | 60.304 | 43.478 | 0.00 | 0.00 | 0.00 | 4.08 |
52 | 53 | 3.226347 | CGACAACTTCTTTTCGGATTGC | 58.774 | 45.455 | 0.00 | 0.00 | 0.00 | 3.56 |
53 | 54 | 4.211374 | AGACGACAACTTCTTTTCGGATTG | 59.789 | 41.667 | 0.00 | 0.00 | 35.77 | 2.67 |
54 | 55 | 4.377897 | AGACGACAACTTCTTTTCGGATT | 58.622 | 39.130 | 0.00 | 0.00 | 35.77 | 3.01 |
55 | 56 | 3.991367 | AGACGACAACTTCTTTTCGGAT | 58.009 | 40.909 | 0.00 | 0.00 | 35.77 | 4.18 |
56 | 57 | 3.447918 | AGACGACAACTTCTTTTCGGA | 57.552 | 42.857 | 0.00 | 0.00 | 35.77 | 4.55 |
57 | 58 | 4.033587 | TGAAAGACGACAACTTCTTTTCGG | 59.966 | 41.667 | 0.00 | 0.00 | 42.07 | 4.30 |
58 | 59 | 5.138800 | TGAAAGACGACAACTTCTTTTCG | 57.861 | 39.130 | 0.00 | 0.00 | 42.07 | 3.46 |
59 | 60 | 6.776271 | GTTGAAAGACGACAACTTCTTTTC | 57.224 | 37.500 | 0.00 | 0.00 | 42.07 | 2.29 |
80 | 81 | 5.700832 | TGAAGCGATGATGACAACTTTAGTT | 59.299 | 36.000 | 0.00 | 0.00 | 39.12 | 2.24 |
81 | 82 | 5.120830 | GTGAAGCGATGATGACAACTTTAGT | 59.879 | 40.000 | 0.00 | 0.00 | 0.00 | 2.24 |
82 | 83 | 5.349817 | AGTGAAGCGATGATGACAACTTTAG | 59.650 | 40.000 | 0.00 | 0.00 | 0.00 | 1.85 |
83 | 84 | 5.237815 | AGTGAAGCGATGATGACAACTTTA | 58.762 | 37.500 | 0.00 | 0.00 | 0.00 | 1.85 |
84 | 85 | 4.067896 | AGTGAAGCGATGATGACAACTTT | 58.932 | 39.130 | 0.00 | 0.00 | 0.00 | 2.66 |
85 | 86 | 3.668447 | AGTGAAGCGATGATGACAACTT | 58.332 | 40.909 | 0.00 | 0.00 | 0.00 | 2.66 |
86 | 87 | 3.325293 | AGTGAAGCGATGATGACAACT | 57.675 | 42.857 | 0.00 | 0.00 | 0.00 | 3.16 |
87 | 88 | 5.530519 | TTTAGTGAAGCGATGATGACAAC | 57.469 | 39.130 | 0.00 | 0.00 | 0.00 | 3.32 |
88 | 89 | 6.036408 | CAGATTTAGTGAAGCGATGATGACAA | 59.964 | 38.462 | 0.00 | 0.00 | 0.00 | 3.18 |
89 | 90 | 5.521372 | CAGATTTAGTGAAGCGATGATGACA | 59.479 | 40.000 | 0.00 | 0.00 | 0.00 | 3.58 |
90 | 91 | 5.557893 | GCAGATTTAGTGAAGCGATGATGAC | 60.558 | 44.000 | 0.00 | 0.00 | 0.00 | 3.06 |
91 | 92 | 4.509230 | GCAGATTTAGTGAAGCGATGATGA | 59.491 | 41.667 | 0.00 | 0.00 | 0.00 | 2.92 |
92 | 93 | 4.319333 | GGCAGATTTAGTGAAGCGATGATG | 60.319 | 45.833 | 0.00 | 0.00 | 0.00 | 3.07 |
93 | 94 | 3.812053 | GGCAGATTTAGTGAAGCGATGAT | 59.188 | 43.478 | 0.00 | 0.00 | 0.00 | 2.45 |
94 | 95 | 3.198068 | GGCAGATTTAGTGAAGCGATGA | 58.802 | 45.455 | 0.00 | 0.00 | 0.00 | 2.92 |
95 | 96 | 2.938451 | TGGCAGATTTAGTGAAGCGATG | 59.062 | 45.455 | 0.00 | 0.00 | 0.00 | 3.84 |
96 | 97 | 3.266510 | TGGCAGATTTAGTGAAGCGAT | 57.733 | 42.857 | 0.00 | 0.00 | 0.00 | 4.58 |
97 | 98 | 2.760634 | TGGCAGATTTAGTGAAGCGA | 57.239 | 45.000 | 0.00 | 0.00 | 0.00 | 4.93 |
98 | 99 | 5.484173 | TTTATGGCAGATTTAGTGAAGCG | 57.516 | 39.130 | 0.00 | 0.00 | 0.00 | 4.68 |
99 | 100 | 7.761249 | ACATTTTTATGGCAGATTTAGTGAAGC | 59.239 | 33.333 | 0.00 | 0.00 | 0.00 | 3.86 |
100 | 101 | 9.643693 | AACATTTTTATGGCAGATTTAGTGAAG | 57.356 | 29.630 | 0.00 | 0.00 | 0.00 | 3.02 |
101 | 102 | 9.995003 | AAACATTTTTATGGCAGATTTAGTGAA | 57.005 | 25.926 | 0.00 | 0.00 | 0.00 | 3.18 |
102 | 103 | 9.995003 | AAAACATTTTTATGGCAGATTTAGTGA | 57.005 | 25.926 | 0.00 | 0.00 | 0.00 | 3.41 |
104 | 105 | 9.995003 | TCAAAACATTTTTATGGCAGATTTAGT | 57.005 | 25.926 | 0.00 | 0.00 | 0.00 | 2.24 |
109 | 110 | 8.238631 | GCAATTCAAAACATTTTTATGGCAGAT | 58.761 | 29.630 | 0.00 | 0.00 | 0.00 | 2.90 |
110 | 111 | 7.308469 | GGCAATTCAAAACATTTTTATGGCAGA | 60.308 | 33.333 | 0.00 | 0.00 | 0.00 | 4.26 |
111 | 112 | 6.802834 | GGCAATTCAAAACATTTTTATGGCAG | 59.197 | 34.615 | 0.00 | 0.00 | 0.00 | 4.85 |
112 | 113 | 6.263842 | TGGCAATTCAAAACATTTTTATGGCA | 59.736 | 30.769 | 0.00 | 0.00 | 0.00 | 4.92 |
113 | 114 | 6.675987 | TGGCAATTCAAAACATTTTTATGGC | 58.324 | 32.000 | 0.00 | 0.00 | 0.00 | 4.40 |
114 | 115 | 8.298140 | ACATGGCAATTCAAAACATTTTTATGG | 58.702 | 29.630 | 0.00 | 0.00 | 0.00 | 2.74 |
115 | 116 | 9.119329 | CACATGGCAATTCAAAACATTTTTATG | 57.881 | 29.630 | 0.00 | 0.00 | 0.00 | 1.90 |
116 | 117 | 8.848182 | ACACATGGCAATTCAAAACATTTTTAT | 58.152 | 25.926 | 0.00 | 0.00 | 0.00 | 1.40 |
117 | 118 | 8.218338 | ACACATGGCAATTCAAAACATTTTTA | 57.782 | 26.923 | 0.00 | 0.00 | 0.00 | 1.52 |
118 | 119 | 7.098074 | ACACATGGCAATTCAAAACATTTTT | 57.902 | 28.000 | 0.00 | 0.00 | 0.00 | 1.94 |
119 | 120 | 6.696441 | ACACATGGCAATTCAAAACATTTT | 57.304 | 29.167 | 0.00 | 0.00 | 0.00 | 1.82 |
120 | 121 | 6.696441 | AACACATGGCAATTCAAAACATTT | 57.304 | 29.167 | 0.00 | 0.00 | 0.00 | 2.32 |
121 | 122 | 6.696441 | AAACACATGGCAATTCAAAACATT | 57.304 | 29.167 | 0.00 | 0.00 | 0.00 | 2.71 |
122 | 123 | 7.573469 | GCATAAACACATGGCAATTCAAAACAT | 60.573 | 33.333 | 0.00 | 0.00 | 0.00 | 2.71 |
123 | 124 | 6.293298 | GCATAAACACATGGCAATTCAAAACA | 60.293 | 34.615 | 0.00 | 0.00 | 0.00 | 2.83 |
124 | 125 | 6.079120 | GCATAAACACATGGCAATTCAAAAC | 58.921 | 36.000 | 0.00 | 0.00 | 0.00 | 2.43 |
125 | 126 | 6.238610 | GCATAAACACATGGCAATTCAAAA | 57.761 | 33.333 | 0.00 | 0.00 | 0.00 | 2.44 |
126 | 127 | 5.859521 | GCATAAACACATGGCAATTCAAA | 57.140 | 34.783 | 0.00 | 0.00 | 0.00 | 2.69 |
135 | 136 | 3.385433 | ACATGGATGGCATAAACACATGG | 59.615 | 43.478 | 21.57 | 11.26 | 38.72 | 3.66 |
136 | 137 | 4.098196 | TCACATGGATGGCATAAACACATG | 59.902 | 41.667 | 18.59 | 18.59 | 39.88 | 3.21 |
137 | 138 | 4.279982 | TCACATGGATGGCATAAACACAT | 58.720 | 39.130 | 0.00 | 0.00 | 0.00 | 3.21 |
138 | 139 | 3.694926 | TCACATGGATGGCATAAACACA | 58.305 | 40.909 | 0.00 | 0.00 | 0.00 | 3.72 |
139 | 140 | 4.924305 | ATCACATGGATGGCATAAACAC | 57.076 | 40.909 | 0.00 | 0.00 | 34.06 | 3.32 |
140 | 141 | 7.600231 | AAATATCACATGGATGGCATAAACA | 57.400 | 32.000 | 0.00 | 0.14 | 36.72 | 2.83 |
141 | 142 | 9.793252 | GATAAATATCACATGGATGGCATAAAC | 57.207 | 33.333 | 0.00 | 0.00 | 36.72 | 2.01 |
142 | 143 | 9.531158 | TGATAAATATCACATGGATGGCATAAA | 57.469 | 29.630 | 0.00 | 0.00 | 37.76 | 1.40 |
143 | 144 | 9.181061 | CTGATAAATATCACATGGATGGCATAA | 57.819 | 33.333 | 0.00 | 0.00 | 37.76 | 1.90 |
144 | 145 | 7.776500 | CCTGATAAATATCACATGGATGGCATA | 59.224 | 37.037 | 0.00 | 0.00 | 37.76 | 3.14 |
145 | 146 | 6.605995 | CCTGATAAATATCACATGGATGGCAT | 59.394 | 38.462 | 0.00 | 0.00 | 37.76 | 4.40 |
146 | 147 | 5.947566 | CCTGATAAATATCACATGGATGGCA | 59.052 | 40.000 | 0.00 | 0.00 | 37.76 | 4.92 |
147 | 148 | 5.359009 | CCCTGATAAATATCACATGGATGGC | 59.641 | 44.000 | 0.00 | 0.00 | 37.76 | 4.40 |
148 | 149 | 6.487828 | ACCCTGATAAATATCACATGGATGG | 58.512 | 40.000 | 0.00 | 6.04 | 37.76 | 3.51 |
149 | 150 | 7.400439 | AGACCCTGATAAATATCACATGGATG | 58.600 | 38.462 | 0.00 | 0.00 | 37.76 | 3.51 |
150 | 151 | 7.579940 | AGACCCTGATAAATATCACATGGAT | 57.420 | 36.000 | 0.00 | 0.00 | 37.76 | 3.41 |
151 | 152 | 8.504811 | TTAGACCCTGATAAATATCACATGGA | 57.495 | 34.615 | 0.00 | 0.00 | 37.76 | 3.41 |
152 | 153 | 9.573166 | TTTTAGACCCTGATAAATATCACATGG | 57.427 | 33.333 | 0.00 | 3.93 | 37.76 | 3.66 |
208 | 209 | 8.859090 | CCATTGGATTGGTAAGCTAATCAATAA | 58.141 | 33.333 | 8.76 | 2.61 | 42.24 | 1.40 |
209 | 210 | 8.224025 | TCCATTGGATTGGTAAGCTAATCAATA | 58.776 | 33.333 | 0.00 | 0.00 | 42.24 | 1.90 |
219 | 220 | 6.881065 | ACATCGATATCCATTGGATTGGTAAG | 59.119 | 38.462 | 22.87 | 12.01 | 39.79 | 2.34 |
220 | 221 | 6.778821 | ACATCGATATCCATTGGATTGGTAA | 58.221 | 36.000 | 22.87 | 5.55 | 39.79 | 2.85 |
246 | 247 | 8.161699 | TCCTTTTTCCTGTCAGTTGTTTATAC | 57.838 | 34.615 | 0.00 | 0.00 | 0.00 | 1.47 |
247 | 248 | 7.996644 | ACTCCTTTTTCCTGTCAGTTGTTTATA | 59.003 | 33.333 | 0.00 | 0.00 | 0.00 | 0.98 |
248 | 249 | 6.833933 | ACTCCTTTTTCCTGTCAGTTGTTTAT | 59.166 | 34.615 | 0.00 | 0.00 | 0.00 | 1.40 |
262 | 263 | 0.601841 | TCGTGCCGACTCCTTTTTCC | 60.602 | 55.000 | 0.00 | 0.00 | 0.00 | 3.13 |
297 | 298 | 1.193874 | CTACTCGGCGGTGTGTTTTTC | 59.806 | 52.381 | 7.21 | 0.00 | 0.00 | 2.29 |
375 | 377 | 0.325933 | TGAGGCTGATGTGACTTGGG | 59.674 | 55.000 | 0.00 | 0.00 | 0.00 | 4.12 |
378 | 381 | 0.681733 | ACGTGAGGCTGATGTGACTT | 59.318 | 50.000 | 0.00 | 0.00 | 0.00 | 3.01 |
621 | 630 | 1.338136 | GGGGGCGAGAAGAAGGATGA | 61.338 | 60.000 | 0.00 | 0.00 | 0.00 | 2.92 |
985 | 1007 | 2.123077 | CATCTCTCCCCCGCTCCT | 60.123 | 66.667 | 0.00 | 0.00 | 0.00 | 3.69 |
988 | 1010 | 2.835431 | CGTCATCTCTCCCCCGCT | 60.835 | 66.667 | 0.00 | 0.00 | 0.00 | 5.52 |
1176 | 1207 | 1.709147 | CCGCGCCATGAAAGAAGGAG | 61.709 | 60.000 | 0.00 | 0.00 | 0.00 | 3.69 |
1179 | 1212 | 0.454957 | CAACCGCGCCATGAAAGAAG | 60.455 | 55.000 | 0.00 | 0.00 | 0.00 | 2.85 |
1209 | 1242 | 2.568696 | ATCAGTCCGTCAGTCAATCG | 57.431 | 50.000 | 0.00 | 0.00 | 0.00 | 3.34 |
1224 | 1260 | 2.031314 | AGCGCACGAATCAATCAATCAG | 59.969 | 45.455 | 11.47 | 0.00 | 0.00 | 2.90 |
1277 | 1317 | 0.036306 | AAATCCGGTCTCCCACACAC | 59.964 | 55.000 | 0.00 | 0.00 | 0.00 | 3.82 |
1278 | 1318 | 0.768622 | AAAATCCGGTCTCCCACACA | 59.231 | 50.000 | 0.00 | 0.00 | 0.00 | 3.72 |
1393 | 1433 | 5.773575 | TCTAGACTCACTACAAAGCACAAG | 58.226 | 41.667 | 0.00 | 0.00 | 0.00 | 3.16 |
1394 | 1434 | 5.784578 | TCTAGACTCACTACAAAGCACAA | 57.215 | 39.130 | 0.00 | 0.00 | 0.00 | 3.33 |
1396 | 1436 | 6.159988 | ACAATCTAGACTCACTACAAAGCAC | 58.840 | 40.000 | 0.00 | 0.00 | 0.00 | 4.40 |
1397 | 1437 | 6.346477 | ACAATCTAGACTCACTACAAAGCA | 57.654 | 37.500 | 0.00 | 0.00 | 0.00 | 3.91 |
1398 | 1438 | 7.093992 | AGAACAATCTAGACTCACTACAAAGC | 58.906 | 38.462 | 0.00 | 0.00 | 32.88 | 3.51 |
1399 | 1439 | 8.920665 | CAAGAACAATCTAGACTCACTACAAAG | 58.079 | 37.037 | 0.00 | 0.00 | 33.77 | 2.77 |
1435 | 1479 | 1.841302 | ATCTCGCTTGCCCCTGAACA | 61.841 | 55.000 | 0.00 | 0.00 | 0.00 | 3.18 |
1494 | 1538 | 4.427312 | GCAAACAGAAGAAATATGCCCAG | 58.573 | 43.478 | 0.00 | 0.00 | 0.00 | 4.45 |
1507 | 1551 | 3.719924 | CAGAATTTGCAGGCAAACAGAA | 58.280 | 40.909 | 20.45 | 0.00 | 46.80 | 3.02 |
1532 | 1576 | 1.064357 | CCACACGTAACCGCAAAGTTT | 59.936 | 47.619 | 0.00 | 0.00 | 37.70 | 2.66 |
1554 | 1599 | 6.406849 | CCCCAAAAAGAAACTCAGAATTGTGA | 60.407 | 38.462 | 5.05 | 5.05 | 0.00 | 3.58 |
1555 | 1600 | 5.754890 | CCCCAAAAAGAAACTCAGAATTGTG | 59.245 | 40.000 | 0.00 | 0.00 | 0.00 | 3.33 |
1556 | 1601 | 5.163311 | CCCCCAAAAAGAAACTCAGAATTGT | 60.163 | 40.000 | 0.00 | 0.00 | 0.00 | 2.71 |
1557 | 1602 | 5.070313 | TCCCCCAAAAAGAAACTCAGAATTG | 59.930 | 40.000 | 0.00 | 0.00 | 0.00 | 2.32 |
1568 | 1613 | 2.993146 | TCCTCATCTCCCCCAAAAAGAA | 59.007 | 45.455 | 0.00 | 0.00 | 0.00 | 2.52 |
1570 | 1615 | 2.310052 | AGTCCTCATCTCCCCCAAAAAG | 59.690 | 50.000 | 0.00 | 0.00 | 0.00 | 2.27 |
1574 | 1619 | 2.059756 | AAAGTCCTCATCTCCCCCAA | 57.940 | 50.000 | 0.00 | 0.00 | 0.00 | 4.12 |
1595 | 1645 | 5.116180 | CACAGTGTGACAAGGAACTTAGAA | 58.884 | 41.667 | 18.83 | 0.00 | 41.06 | 2.10 |
1596 | 1646 | 4.161565 | ACACAGTGTGACAAGGAACTTAGA | 59.838 | 41.667 | 29.58 | 0.00 | 41.50 | 2.10 |
1598 | 1648 | 4.481368 | ACACAGTGTGACAAGGAACTTA | 57.519 | 40.909 | 29.58 | 0.00 | 41.50 | 2.24 |
1614 | 1664 | 0.678395 | AGTGAGGTCAGAGCACACAG | 59.322 | 55.000 | 25.81 | 0.00 | 35.08 | 3.66 |
1628 | 1678 | 9.791820 | TGCACATCAAATTTAATATTCAGTGAG | 57.208 | 29.630 | 0.00 | 0.00 | 0.00 | 3.51 |
1639 | 1689 | 9.881649 | TTATTGGCTATTGCACATCAAATTTAA | 57.118 | 25.926 | 0.66 | 0.00 | 41.91 | 1.52 |
1642 | 1692 | 7.558604 | AGTTATTGGCTATTGCACATCAAATT | 58.441 | 30.769 | 0.66 | 0.00 | 41.91 | 1.82 |
1644 | 1694 | 6.152492 | TGAGTTATTGGCTATTGCACATCAAA | 59.848 | 34.615 | 0.66 | 0.00 | 41.91 | 2.69 |
1691 | 1741 | 7.626452 | GCCAATTCTAATCAGAGTTGTTGTACC | 60.626 | 40.741 | 0.87 | 0.00 | 43.47 | 3.34 |
1731 | 1781 | 4.400529 | TCGCTTTGCATACTCTCCATAA | 57.599 | 40.909 | 0.00 | 0.00 | 0.00 | 1.90 |
1739 | 1789 | 2.359900 | CCCTCTTTCGCTTTGCATACT | 58.640 | 47.619 | 0.00 | 0.00 | 0.00 | 2.12 |
1752 | 1802 | 1.353091 | AAGCGAAGTCTCCCCTCTTT | 58.647 | 50.000 | 0.00 | 0.00 | 0.00 | 2.52 |
1806 | 1856 | 6.808008 | TGAAGTAAAGCTGAAAAGGATGAG | 57.192 | 37.500 | 0.00 | 0.00 | 0.00 | 2.90 |
1925 | 1975 | 6.739112 | TCTGACCAGAACGATAGATAACATG | 58.261 | 40.000 | 0.00 | 0.00 | 33.91 | 3.21 |
1926 | 1976 | 6.961360 | TCTGACCAGAACGATAGATAACAT | 57.039 | 37.500 | 0.00 | 0.00 | 33.91 | 2.71 |
2012 | 2062 | 3.116300 | CTGCGTGCCATTGTAGTACTAG | 58.884 | 50.000 | 1.87 | 0.00 | 0.00 | 2.57 |
2036 | 2086 | 9.435688 | GGGAAAATATTTTAATGCAACTGACTT | 57.564 | 29.630 | 13.34 | 0.00 | 0.00 | 3.01 |
2038 | 2088 | 7.757624 | TCGGGAAAATATTTTAATGCAACTGAC | 59.242 | 33.333 | 13.34 | 0.00 | 0.00 | 3.51 |
2040 | 2090 | 7.973388 | TCTCGGGAAAATATTTTAATGCAACTG | 59.027 | 33.333 | 13.34 | 4.36 | 0.00 | 3.16 |
2041 | 2091 | 8.062065 | TCTCGGGAAAATATTTTAATGCAACT | 57.938 | 30.769 | 13.34 | 0.00 | 0.00 | 3.16 |
2042 | 2092 | 8.696410 | TTCTCGGGAAAATATTTTAATGCAAC | 57.304 | 30.769 | 13.34 | 0.00 | 0.00 | 4.17 |
2062 | 2113 | 3.778618 | TGAGTTGAGCAGATGATTCTCG | 58.221 | 45.455 | 0.00 | 0.00 | 0.00 | 4.04 |
2113 | 2164 | 8.948631 | TTGCCAGTTTGTAAATAAATGTTTGA | 57.051 | 26.923 | 0.00 | 0.00 | 0.00 | 2.69 |
2147 | 2200 | 0.318120 | GCAACCAAACCACATCCAGG | 59.682 | 55.000 | 0.00 | 0.00 | 0.00 | 4.45 |
2149 | 2202 | 1.786937 | AAGCAACCAAACCACATCCA | 58.213 | 45.000 | 0.00 | 0.00 | 0.00 | 3.41 |
2176 | 2234 | 3.062763 | CAAGTGAGTGCTTCTACACCAG | 58.937 | 50.000 | 0.00 | 0.00 | 41.67 | 4.00 |
2212 | 2270 | 9.950680 | CTGCAATGTAAACCCACTATAAAATAG | 57.049 | 33.333 | 0.00 | 0.00 | 0.00 | 1.73 |
2553 | 2700 | 4.101430 | TGGCATGCATAGTCATAGAGTTGA | 59.899 | 41.667 | 21.36 | 0.00 | 0.00 | 3.18 |
2578 | 2725 | 8.375465 | GTGAAGTACCGTGTGTGTAAAATATAC | 58.625 | 37.037 | 0.00 | 0.00 | 0.00 | 1.47 |
2582 | 2729 | 5.117584 | TGTGAAGTACCGTGTGTGTAAAAT | 58.882 | 37.500 | 0.00 | 0.00 | 0.00 | 1.82 |
2666 | 2816 | 7.822658 | ACACGGCTGTTAATTACATACAAAAT | 58.177 | 30.769 | 0.00 | 0.00 | 35.85 | 1.82 |
2680 | 2830 | 0.398696 | ATGACCCAACACGGCTGTTA | 59.601 | 50.000 | 0.00 | 0.00 | 38.66 | 2.41 |
2812 | 2963 | 6.434302 | TCATGTGATGAATTAATCCCCTGTT | 58.566 | 36.000 | 0.00 | 0.00 | 36.11 | 3.16 |
2864 | 3015 | 9.147364 | CGTATCAGATTCGTATTTTGATTGTTG | 57.853 | 33.333 | 1.40 | 0.00 | 31.49 | 3.33 |
2967 | 3118 | 3.681594 | CGCCCAAGCAGTTAGGATAAGAA | 60.682 | 47.826 | 0.00 | 0.00 | 39.83 | 2.52 |
3049 | 3200 | 5.901413 | AGAATCACTATGTCATGTGGGAT | 57.099 | 39.130 | 12.51 | 7.30 | 35.15 | 3.85 |
3098 | 3282 | 4.560513 | CGTGTTGGCAGGATTAAATGGTTT | 60.561 | 41.667 | 0.00 | 0.00 | 32.67 | 3.27 |
3119 | 3303 | 3.067180 | GCAATTCATGATGGATTCCACGT | 59.933 | 43.478 | 7.76 | 1.05 | 35.80 | 4.49 |
3134 | 3318 | 1.114119 | TTGCTGGCAGGTGCAATTCA | 61.114 | 50.000 | 17.64 | 0.00 | 43.17 | 2.57 |
3518 | 3715 | 8.565416 | TCTCATCTTGTTCATTATGCATCATTC | 58.435 | 33.333 | 0.19 | 0.00 | 0.00 | 2.67 |
3544 | 3741 | 2.093181 | TGCTGTGCGTAAGGATGGTAAT | 60.093 | 45.455 | 0.00 | 0.00 | 42.42 | 1.89 |
3979 | 4176 | 4.508128 | GTGGGATTCGGCTCGCGA | 62.508 | 66.667 | 9.26 | 9.26 | 0.00 | 5.87 |
4157 | 4362 | 0.036952 | CGGTGACAACAGGCATCTCT | 60.037 | 55.000 | 0.00 | 0.00 | 0.00 | 3.10 |
4178 | 4383 | 7.832685 | GGGGTTAAATTGAATACTCCTACTTGT | 59.167 | 37.037 | 0.00 | 0.00 | 0.00 | 3.16 |
4359 | 4565 | 1.860950 | CTTGACAACAGACCGACAGTG | 59.139 | 52.381 | 0.00 | 0.00 | 0.00 | 3.66 |
4830 | 5068 | 6.403878 | TGTCTTATAAGTTCTGTAACCCTGC | 58.596 | 40.000 | 12.19 | 0.00 | 36.15 | 4.85 |
4913 | 5169 | 3.567585 | TGTTCGAAACAAGATCAATGCCA | 59.432 | 39.130 | 0.00 | 0.00 | 38.72 | 4.92 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.