Multiple sequence alignment - TraesCS2D01G019400
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 | TraesCS2D01G019400 | chr2D | 100.000 | 3633 | 0 | 0 | 1 | 3633 | 9370494 | 9374126 | 0.000000e+00 | 6709.0 |
1 | TraesCS2D01G019400 | chr2D | 88.493 | 1738 | 175 | 13 | 883 | 2600 | 9277335 | 9279067 | 0.000000e+00 | 2078.0 |
2 | TraesCS2D01G019400 | chr2D | 88.789 | 1552 | 162 | 6 | 1006 | 2546 | 9502204 | 9503754 | 0.000000e+00 | 1892.0 |
3 | TraesCS2D01G019400 | chr2D | 83.237 | 1551 | 234 | 17 | 1006 | 2544 | 8686455 | 8687991 | 0.000000e+00 | 1400.0 |
4 | TraesCS2D01G019400 | chr2D | 84.392 | 756 | 109 | 9 | 2881 | 3633 | 29066265 | 29065516 | 0.000000e+00 | 734.0 |
5 | TraesCS2D01G019400 | chr2D | 85.033 | 608 | 84 | 6 | 3028 | 3633 | 318432768 | 318432166 | 2.400000e-171 | 612.0 |
6 | TraesCS2D01G019400 | chr2D | 85.507 | 552 | 48 | 13 | 371 | 915 | 9501137 | 9501663 | 6.860000e-152 | 547.0 |
7 | TraesCS2D01G019400 | chr2D | 93.704 | 270 | 10 | 3 | 2597 | 2863 | 9280133 | 9280398 | 7.310000e-107 | 398.0 |
8 | TraesCS2D01G019400 | chr2D | 84.437 | 302 | 34 | 12 | 568 | 864 | 9276992 | 9277285 | 5.940000e-73 | 285.0 |
9 | TraesCS2D01G019400 | chr2D | 78.409 | 176 | 28 | 10 | 2863 | 3034 | 318437155 | 318436986 | 4.960000e-19 | 106.0 |
10 | TraesCS2D01G019400 | chr2D | 80.460 | 87 | 13 | 3 | 481 | 563 | 9501695 | 9501781 | 3.030000e-06 | 63.9 |
11 | TraesCS2D01G019400 | chr2B | 91.803 | 2147 | 135 | 15 | 491 | 2600 | 11560116 | 11557974 | 0.000000e+00 | 2952.0 |
12 | TraesCS2D01G019400 | chr2B | 92.607 | 1772 | 97 | 9 | 861 | 2600 | 12914383 | 12916152 | 0.000000e+00 | 2516.0 |
13 | TraesCS2D01G019400 | chr2B | 93.291 | 1565 | 96 | 4 | 1013 | 2568 | 11573680 | 11572116 | 0.000000e+00 | 2300.0 |
14 | TraesCS2D01G019400 | chr2B | 91.987 | 312 | 21 | 4 | 684 | 993 | 11574041 | 11573732 | 5.570000e-118 | 435.0 |
15 | TraesCS2D01G019400 | chr2B | 90.335 | 269 | 19 | 5 | 2597 | 2863 | 12929093 | 12929356 | 2.690000e-91 | 346.0 |
16 | TraesCS2D01G019400 | chr2B | 87.200 | 250 | 26 | 5 | 582 | 827 | 12914136 | 12914383 | 2.760000e-71 | 279.0 |
17 | TraesCS2D01G019400 | chr2B | 80.537 | 149 | 18 | 9 | 548 | 692 | 11174712 | 11174571 | 1.780000e-18 | 104.0 |
18 | TraesCS2D01G019400 | chr2B | 96.875 | 32 | 1 | 0 | 524 | 555 | 11912746 | 11912715 | 2.000000e-03 | 54.7 |
19 | TraesCS2D01G019400 | chr2A | 94.819 | 1602 | 75 | 5 | 1006 | 2600 | 8627409 | 8629009 | 0.000000e+00 | 2492.0 |
20 | TraesCS2D01G019400 | chr2A | 79.612 | 1496 | 276 | 18 | 1019 | 2508 | 9111119 | 9109647 | 0.000000e+00 | 1046.0 |
21 | TraesCS2D01G019400 | chr2A | 81.176 | 765 | 69 | 36 | 266 | 1002 | 8626648 | 8627365 | 2.470000e-151 | 545.0 |
22 | TraesCS2D01G019400 | chr2A | 95.522 | 268 | 7 | 2 | 2597 | 2863 | 8630631 | 8630894 | 1.210000e-114 | 424.0 |
23 | TraesCS2D01G019400 | chr2A | 85.209 | 311 | 38 | 4 | 998 | 1303 | 8682702 | 8683009 | 2.720000e-81 | 313.0 |
24 | TraesCS2D01G019400 | chr2A | 83.165 | 297 | 40 | 6 | 1012 | 1303 | 8152317 | 8152608 | 2.780000e-66 | 263.0 |
25 | TraesCS2D01G019400 | chr2A | 84.689 | 209 | 31 | 1 | 2 | 210 | 8626419 | 8626626 | 1.320000e-49 | 207.0 |
26 | TraesCS2D01G019400 | chr2A | 100.000 | 28 | 0 | 0 | 524 | 551 | 8412913 | 8412940 | 7.000000e-03 | 52.8 |
27 | TraesCS2D01G019400 | chrUn | 84.910 | 1385 | 199 | 9 | 1166 | 2544 | 273231379 | 273229999 | 0.000000e+00 | 1391.0 |
28 | TraesCS2D01G019400 | chrUn | 84.870 | 1388 | 200 | 9 | 1163 | 2544 | 292878470 | 292879853 | 0.000000e+00 | 1391.0 |
29 | TraesCS2D01G019400 | chr6A | 84.974 | 772 | 113 | 3 | 2862 | 3633 | 73792031 | 73791263 | 0.000000e+00 | 780.0 |
30 | TraesCS2D01G019400 | chr3D | 82.990 | 776 | 123 | 9 | 2862 | 3633 | 580986100 | 580986870 | 0.000000e+00 | 693.0 |
31 | TraesCS2D01G019400 | chr3D | 84.211 | 114 | 18 | 0 | 2862 | 2975 | 152686820 | 152686707 | 1.070000e-20 | 111.0 |
32 | TraesCS2D01G019400 | chr7D | 81.912 | 774 | 125 | 12 | 2862 | 3630 | 80059167 | 80059930 | 1.100000e-179 | 640.0 |
33 | TraesCS2D01G019400 | chr4D | 80.824 | 777 | 128 | 14 | 2861 | 3633 | 57684871 | 57685630 | 1.120000e-164 | 590.0 |
34 | TraesCS2D01G019400 | chr1B | 80.282 | 781 | 134 | 19 | 2862 | 3633 | 684906905 | 684906136 | 4.070000e-159 | 571.0 |
35 | TraesCS2D01G019400 | chr4B | 79.589 | 779 | 142 | 17 | 2862 | 3633 | 34804247 | 34803479 | 3.190000e-150 | 542.0 |
36 | TraesCS2D01G019400 | chr4B | 78.333 | 180 | 31 | 8 | 2862 | 3039 | 648562451 | 648562624 | 3.840000e-20 | 110.0 |
37 | TraesCS2D01G019400 | chr5B | 79.204 | 779 | 143 | 18 | 2862 | 3633 | 401081749 | 401080983 | 1.160000e-144 | 523.0 |
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 | TraesCS2D01G019400 | chr2D | 9370494 | 9374126 | 3632 | False | 6709.000000 | 6709 | 100.000000 | 1 | 3633 | 1 | chr2D.!!$F2 | 3632 |
1 | TraesCS2D01G019400 | chr2D | 8686455 | 8687991 | 1536 | False | 1400.000000 | 1400 | 83.237000 | 1006 | 2544 | 1 | chr2D.!!$F1 | 1538 |
2 | TraesCS2D01G019400 | chr2D | 9276992 | 9280398 | 3406 | False | 920.333333 | 2078 | 88.878000 | 568 | 2863 | 3 | chr2D.!!$F3 | 2295 |
3 | TraesCS2D01G019400 | chr2D | 9501137 | 9503754 | 2617 | False | 834.300000 | 1892 | 84.918667 | 371 | 2546 | 3 | chr2D.!!$F4 | 2175 |
4 | TraesCS2D01G019400 | chr2D | 29065516 | 29066265 | 749 | True | 734.000000 | 734 | 84.392000 | 2881 | 3633 | 1 | chr2D.!!$R1 | 752 |
5 | TraesCS2D01G019400 | chr2D | 318432166 | 318432768 | 602 | True | 612.000000 | 612 | 85.033000 | 3028 | 3633 | 1 | chr2D.!!$R2 | 605 |
6 | TraesCS2D01G019400 | chr2B | 11557974 | 11560116 | 2142 | True | 2952.000000 | 2952 | 91.803000 | 491 | 2600 | 1 | chr2B.!!$R2 | 2109 |
7 | TraesCS2D01G019400 | chr2B | 12914136 | 12916152 | 2016 | False | 1397.500000 | 2516 | 89.903500 | 582 | 2600 | 2 | chr2B.!!$F2 | 2018 |
8 | TraesCS2D01G019400 | chr2B | 11572116 | 11574041 | 1925 | True | 1367.500000 | 2300 | 92.639000 | 684 | 2568 | 2 | chr2B.!!$R4 | 1884 |
9 | TraesCS2D01G019400 | chr2A | 9109647 | 9111119 | 1472 | True | 1046.000000 | 1046 | 79.612000 | 1019 | 2508 | 1 | chr2A.!!$R1 | 1489 |
10 | TraesCS2D01G019400 | chr2A | 8626419 | 8630894 | 4475 | False | 917.000000 | 2492 | 89.051500 | 2 | 2863 | 4 | chr2A.!!$F4 | 2861 |
11 | TraesCS2D01G019400 | chrUn | 273229999 | 273231379 | 1380 | True | 1391.000000 | 1391 | 84.910000 | 1166 | 2544 | 1 | chrUn.!!$R1 | 1378 |
12 | TraesCS2D01G019400 | chrUn | 292878470 | 292879853 | 1383 | False | 1391.000000 | 1391 | 84.870000 | 1163 | 2544 | 1 | chrUn.!!$F1 | 1381 |
13 | TraesCS2D01G019400 | chr6A | 73791263 | 73792031 | 768 | True | 780.000000 | 780 | 84.974000 | 2862 | 3633 | 1 | chr6A.!!$R1 | 771 |
14 | TraesCS2D01G019400 | chr3D | 580986100 | 580986870 | 770 | False | 693.000000 | 693 | 82.990000 | 2862 | 3633 | 1 | chr3D.!!$F1 | 771 |
15 | TraesCS2D01G019400 | chr7D | 80059167 | 80059930 | 763 | False | 640.000000 | 640 | 81.912000 | 2862 | 3630 | 1 | chr7D.!!$F1 | 768 |
16 | TraesCS2D01G019400 | chr4D | 57684871 | 57685630 | 759 | False | 590.000000 | 590 | 80.824000 | 2861 | 3633 | 1 | chr4D.!!$F1 | 772 |
17 | TraesCS2D01G019400 | chr1B | 684906136 | 684906905 | 769 | True | 571.000000 | 571 | 80.282000 | 2862 | 3633 | 1 | chr1B.!!$R1 | 771 |
18 | TraesCS2D01G019400 | chr4B | 34803479 | 34804247 | 768 | True | 542.000000 | 542 | 79.589000 | 2862 | 3633 | 1 | chr4B.!!$R1 | 771 |
19 | TraesCS2D01G019400 | chr5B | 401080983 | 401081749 | 766 | True | 523.000000 | 523 | 79.204000 | 2862 | 3633 | 1 | chr5B.!!$R1 | 771 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
601 | 637 | 0.035630 | GCATGGAGCTGTGGTTCTCT | 60.036 | 55.0 | 0.0 | 0.0 | 41.15 | 3.10 | F |
1692 | 2238 | 0.723414 | CTCATGTGTGTGGCGATGAC | 59.277 | 55.0 | 0.0 | 0.0 | 0.00 | 3.06 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1698 | 2244 | 0.809385 | TAGAGGAGAAGCGTGAACGG | 59.191 | 55.0 | 4.84 | 0.0 | 40.23 | 4.44 | R |
2915 | 5156 | 0.240945 | CCGACATTGTGCCTGTTTCC | 59.759 | 55.0 | 0.00 | 0.0 | 0.00 | 3.13 | 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 |
---|---|---|---|---|---|---|---|---|---|
91 | 92 | 6.210796 | CAATGACTTTGAATTGCTTCTGTGA | 58.789 | 36.000 | 0.00 | 0.00 | 37.53 | 3.58 |
94 | 95 | 7.509141 | TGACTTTGAATTGCTTCTGTGATTA | 57.491 | 32.000 | 0.00 | 0.00 | 32.29 | 1.75 |
98 | 99 | 8.579006 | ACTTTGAATTGCTTCTGTGATTATTCA | 58.421 | 29.630 | 0.00 | 0.00 | 32.29 | 2.57 |
174 | 175 | 6.672147 | AGCAATGACTCTGAATTGTTTGTAC | 58.328 | 36.000 | 3.34 | 0.00 | 36.39 | 2.90 |
185 | 186 | 7.931407 | TCTGAATTGTTTGTACATATATCCGCT | 59.069 | 33.333 | 0.00 | 0.00 | 33.44 | 5.52 |
196 | 197 | 2.638480 | ATATCCGCTAAGCAAAGGCA | 57.362 | 45.000 | 0.00 | 0.00 | 44.61 | 4.75 |
199 | 200 | 1.094785 | TCCGCTAAGCAAAGGCAATC | 58.905 | 50.000 | 0.00 | 0.00 | 44.61 | 2.67 |
205 | 206 | 4.176271 | GCTAAGCAAAGGCAATCGAAAAT | 58.824 | 39.130 | 0.00 | 0.00 | 44.61 | 1.82 |
210 | 211 | 5.240121 | AGCAAAGGCAATCGAAAATTCAAT | 58.760 | 33.333 | 0.00 | 0.00 | 44.61 | 2.57 |
211 | 212 | 5.121142 | AGCAAAGGCAATCGAAAATTCAATG | 59.879 | 36.000 | 0.00 | 0.00 | 44.61 | 2.82 |
212 | 213 | 5.318349 | CAAAGGCAATCGAAAATTCAATGC | 58.682 | 37.500 | 0.00 | 6.36 | 0.00 | 3.56 |
213 | 214 | 4.191033 | AGGCAATCGAAAATTCAATGCA | 57.809 | 36.364 | 13.34 | 0.00 | 33.80 | 3.96 |
214 | 215 | 4.761975 | AGGCAATCGAAAATTCAATGCAT | 58.238 | 34.783 | 0.00 | 0.00 | 33.80 | 3.96 |
215 | 216 | 4.569162 | AGGCAATCGAAAATTCAATGCATG | 59.431 | 37.500 | 0.00 | 0.00 | 33.80 | 4.06 |
216 | 217 | 4.268522 | GCAATCGAAAATTCAATGCATGC | 58.731 | 39.130 | 11.82 | 11.82 | 32.96 | 4.06 |
217 | 218 | 4.201734 | GCAATCGAAAATTCAATGCATGCA | 60.202 | 37.500 | 25.04 | 25.04 | 32.96 | 3.96 |
218 | 219 | 5.252583 | CAATCGAAAATTCAATGCATGCAC | 58.747 | 37.500 | 25.37 | 5.76 | 0.00 | 4.57 |
219 | 220 | 3.252400 | TCGAAAATTCAATGCATGCACC | 58.748 | 40.909 | 25.37 | 2.99 | 0.00 | 5.01 |
220 | 221 | 3.056678 | TCGAAAATTCAATGCATGCACCT | 60.057 | 39.130 | 25.37 | 10.76 | 0.00 | 4.00 |
221 | 222 | 4.157472 | TCGAAAATTCAATGCATGCACCTA | 59.843 | 37.500 | 25.37 | 8.16 | 0.00 | 3.08 |
222 | 223 | 5.045215 | CGAAAATTCAATGCATGCACCTAT | 58.955 | 37.500 | 25.37 | 11.35 | 0.00 | 2.57 |
223 | 224 | 6.039159 | TCGAAAATTCAATGCATGCACCTATA | 59.961 | 34.615 | 25.37 | 8.18 | 0.00 | 1.31 |
239 | 240 | 7.053498 | TGCACCTATAATAGATGCAGACAAAA | 58.947 | 34.615 | 2.57 | 0.00 | 41.18 | 2.44 |
240 | 241 | 7.720957 | TGCACCTATAATAGATGCAGACAAAAT | 59.279 | 33.333 | 2.57 | 0.00 | 41.18 | 1.82 |
241 | 242 | 8.019669 | GCACCTATAATAGATGCAGACAAAATG | 58.980 | 37.037 | 0.00 | 0.00 | 36.30 | 2.32 |
243 | 244 | 9.851686 | ACCTATAATAGATGCAGACAAAATGAA | 57.148 | 29.630 | 0.00 | 0.00 | 0.00 | 2.57 |
247 | 248 | 4.627611 | AGATGCAGACAAAATGAATCGG | 57.372 | 40.909 | 0.00 | 0.00 | 37.72 | 4.18 |
248 | 249 | 4.012374 | AGATGCAGACAAAATGAATCGGT | 58.988 | 39.130 | 0.00 | 0.00 | 37.72 | 4.69 |
249 | 250 | 5.185454 | AGATGCAGACAAAATGAATCGGTA | 58.815 | 37.500 | 0.00 | 0.00 | 37.72 | 4.02 |
250 | 251 | 5.647658 | AGATGCAGACAAAATGAATCGGTAA | 59.352 | 36.000 | 0.00 | 0.00 | 37.72 | 2.85 |
251 | 252 | 5.697473 | TGCAGACAAAATGAATCGGTAAA | 57.303 | 34.783 | 0.00 | 0.00 | 0.00 | 2.01 |
252 | 253 | 6.266168 | TGCAGACAAAATGAATCGGTAAAT | 57.734 | 33.333 | 0.00 | 0.00 | 0.00 | 1.40 |
253 | 254 | 7.384439 | TGCAGACAAAATGAATCGGTAAATA | 57.616 | 32.000 | 0.00 | 0.00 | 0.00 | 1.40 |
254 | 255 | 7.821652 | TGCAGACAAAATGAATCGGTAAATAA | 58.178 | 30.769 | 0.00 | 0.00 | 0.00 | 1.40 |
255 | 256 | 8.465999 | TGCAGACAAAATGAATCGGTAAATAAT | 58.534 | 29.630 | 0.00 | 0.00 | 0.00 | 1.28 |
256 | 257 | 8.958043 | GCAGACAAAATGAATCGGTAAATAATC | 58.042 | 33.333 | 0.00 | 0.00 | 0.00 | 1.75 |
268 | 269 | 7.359262 | TCGGTAAATAATCAATAAGATGGCG | 57.641 | 36.000 | 0.00 | 0.00 | 36.96 | 5.69 |
286 | 287 | 2.607180 | GGCGCAACAAACTGTTCAAAAT | 59.393 | 40.909 | 10.83 | 0.00 | 38.77 | 1.82 |
287 | 288 | 3.799420 | GGCGCAACAAACTGTTCAAAATA | 59.201 | 39.130 | 10.83 | 0.00 | 38.77 | 1.40 |
288 | 289 | 4.085107 | GGCGCAACAAACTGTTCAAAATAG | 60.085 | 41.667 | 10.83 | 0.00 | 38.77 | 1.73 |
289 | 290 | 4.737765 | GCGCAACAAACTGTTCAAAATAGA | 59.262 | 37.500 | 0.30 | 0.00 | 38.77 | 1.98 |
290 | 291 | 5.402270 | GCGCAACAAACTGTTCAAAATAGAT | 59.598 | 36.000 | 0.30 | 0.00 | 38.77 | 1.98 |
309 | 310 | 8.804912 | AATAGATGATGAGATTCATAAAGGCC | 57.195 | 34.615 | 0.00 | 0.00 | 37.20 | 5.19 |
310 | 311 | 6.196918 | AGATGATGAGATTCATAAAGGCCA | 57.803 | 37.500 | 5.01 | 0.00 | 37.20 | 5.36 |
343 | 344 | 2.104963 | ACCTCACCTCTCTGTTTGTTCC | 59.895 | 50.000 | 0.00 | 0.00 | 0.00 | 3.62 |
347 | 348 | 1.344763 | ACCTCTCTGTTTGTTCCGGAG | 59.655 | 52.381 | 3.34 | 0.00 | 36.79 | 4.63 |
361 | 362 | 2.276869 | CGGAGGATGAGGTGTGTCA | 58.723 | 57.895 | 0.00 | 0.00 | 0.00 | 3.58 |
362 | 363 | 0.826715 | CGGAGGATGAGGTGTGTCAT | 59.173 | 55.000 | 0.00 | 0.00 | 40.00 | 3.06 |
363 | 364 | 2.031870 | CGGAGGATGAGGTGTGTCATA | 58.968 | 52.381 | 0.00 | 0.00 | 37.29 | 2.15 |
365 | 366 | 3.553715 | CGGAGGATGAGGTGTGTCATATG | 60.554 | 52.174 | 0.00 | 0.00 | 37.29 | 1.78 |
367 | 368 | 4.588951 | GGAGGATGAGGTGTGTCATATGTA | 59.411 | 45.833 | 1.90 | 0.00 | 37.29 | 2.29 |
368 | 369 | 5.070446 | GGAGGATGAGGTGTGTCATATGTAA | 59.930 | 44.000 | 1.90 | 0.00 | 37.29 | 2.41 |
388 | 422 | 7.403312 | TGTAAAATATGGGAAATGAGGTGTG | 57.597 | 36.000 | 0.00 | 0.00 | 0.00 | 3.82 |
506 | 541 | 3.074412 | CGGTTAAAGACTGAACTGGCAT | 58.926 | 45.455 | 0.00 | 0.00 | 36.72 | 4.40 |
510 | 545 | 6.612306 | GGTTAAAGACTGAACTGGCATAAAG | 58.388 | 40.000 | 0.00 | 0.00 | 0.00 | 1.85 |
519 | 554 | 1.086696 | CTGGCATAAAGTGGACCACG | 58.913 | 55.000 | 18.93 | 5.56 | 39.64 | 4.94 |
521 | 556 | 1.654023 | GGCATAAAGTGGACCACGGC | 61.654 | 60.000 | 18.93 | 16.76 | 39.64 | 5.68 |
556 | 591 | 4.339530 | GGTTCTGAAGAAACCAAAAGAGCT | 59.660 | 41.667 | 0.00 | 0.00 | 35.78 | 4.09 |
558 | 593 | 6.431278 | GTTCTGAAGAAACCAAAAGAGCTAC | 58.569 | 40.000 | 0.00 | 0.00 | 35.58 | 3.58 |
562 | 597 | 6.588204 | TGAAGAAACCAAAAGAGCTACTGTA | 58.412 | 36.000 | 0.00 | 0.00 | 0.00 | 2.74 |
563 | 598 | 6.706270 | TGAAGAAACCAAAAGAGCTACTGTAG | 59.294 | 38.462 | 10.48 | 10.48 | 0.00 | 2.74 |
601 | 637 | 0.035630 | GCATGGAGCTGTGGTTCTCT | 60.036 | 55.000 | 0.00 | 0.00 | 41.15 | 3.10 |
661 | 698 | 5.350365 | TCATTTACTTACGATGACTTGTGCC | 59.650 | 40.000 | 0.00 | 0.00 | 0.00 | 5.01 |
719 | 759 | 3.153919 | AGCAAATTCCCACGTGTGTAAT | 58.846 | 40.909 | 15.65 | 8.01 | 0.00 | 1.89 |
727 | 767 | 8.514330 | AATTCCCACGTGTGTAATATGTAAAT | 57.486 | 30.769 | 15.65 | 0.00 | 0.00 | 1.40 |
779 | 826 | 9.429359 | GATGATTAGATATCATTTCTGAACGGT | 57.571 | 33.333 | 5.32 | 0.00 | 38.73 | 4.83 |
1027 | 1554 | 1.692395 | TCAATCCCGGCCATGGAGA | 60.692 | 57.895 | 18.40 | 6.28 | 34.80 | 3.71 |
1124 | 1654 | 1.202639 | TGCGCAGTCAGAGGAAAAGAA | 60.203 | 47.619 | 5.66 | 0.00 | 0.00 | 2.52 |
1337 | 1867 | 2.941064 | GCAGCAATGACTCATCTAGCAA | 59.059 | 45.455 | 11.44 | 0.00 | 0.00 | 3.91 |
1379 | 1918 | 2.476619 | CAGTCAAGCGTTCTCGAACAAT | 59.523 | 45.455 | 10.10 | 0.00 | 41.20 | 2.71 |
1380 | 1919 | 2.476619 | AGTCAAGCGTTCTCGAACAATG | 59.523 | 45.455 | 10.10 | 5.64 | 41.20 | 2.82 |
1500 | 2039 | 1.810853 | TGGATGTGAGCGCATGTCG | 60.811 | 57.895 | 11.47 | 5.35 | 42.12 | 4.35 |
1692 | 2238 | 0.723414 | CTCATGTGTGTGGCGATGAC | 59.277 | 55.000 | 0.00 | 0.00 | 0.00 | 3.06 |
1698 | 2244 | 1.741770 | GTGTGGCGATGACAGGGTC | 60.742 | 63.158 | 0.00 | 0.00 | 0.00 | 4.46 |
1778 | 2324 | 0.479815 | GATGGGAGGGCCATGATTGA | 59.520 | 55.000 | 6.18 | 0.00 | 35.15 | 2.57 |
1834 | 2380 | 5.089970 | TGTAGGTGATGATGACTGGAAAG | 57.910 | 43.478 | 0.00 | 0.00 | 0.00 | 2.62 |
1876 | 2422 | 0.324091 | AATGGGCAGAGGAAGCAAGG | 60.324 | 55.000 | 0.00 | 0.00 | 0.00 | 3.61 |
1965 | 2511 | 4.040217 | GGGCTATCTCATGATGAGTTGACT | 59.960 | 45.833 | 20.82 | 6.04 | 44.58 | 3.41 |
1996 | 2542 | 1.214589 | GCACTCGCCTTCGGAAGTA | 59.785 | 57.895 | 16.07 | 1.45 | 36.13 | 2.24 |
2055 | 2603 | 4.682320 | GCAGATGAATTTGCCATGGTGATT | 60.682 | 41.667 | 14.67 | 10.96 | 34.28 | 2.57 |
2058 | 2606 | 5.365605 | AGATGAATTTGCCATGGTGATTCAT | 59.634 | 36.000 | 30.80 | 30.80 | 45.22 | 2.57 |
2106 | 2655 | 7.301789 | CAACAAATATGTTCACGGATGTGTTA | 58.698 | 34.615 | 0.00 | 0.00 | 46.78 | 2.41 |
2121 | 2670 | 3.128349 | TGTGTTAAGAAGCAACCTCGAC | 58.872 | 45.455 | 0.00 | 0.00 | 0.00 | 4.20 |
2153 | 2702 | 3.275999 | GGCGTTGTATATTGGACAAGGT | 58.724 | 45.455 | 9.91 | 0.00 | 42.10 | 3.50 |
2680 | 4919 | 5.945144 | TCAATTTGGACCTACCTACCTAC | 57.055 | 43.478 | 0.00 | 0.00 | 39.86 | 3.18 |
2681 | 4920 | 4.718276 | TCAATTTGGACCTACCTACCTACC | 59.282 | 45.833 | 0.00 | 0.00 | 39.86 | 3.18 |
2682 | 4921 | 4.639019 | ATTTGGACCTACCTACCTACCT | 57.361 | 45.455 | 0.00 | 0.00 | 39.86 | 3.08 |
2683 | 4922 | 5.756314 | ATTTGGACCTACCTACCTACCTA | 57.244 | 43.478 | 0.00 | 0.00 | 39.86 | 3.08 |
2765 | 5006 | 5.598005 | TCCTTGTCACATCTTTGGACATTTT | 59.402 | 36.000 | 0.00 | 0.00 | 40.84 | 1.82 |
2836 | 5077 | 5.412594 | TCAAATCATCCCTTGAGACTTTTCG | 59.587 | 40.000 | 0.00 | 0.00 | 37.89 | 3.46 |
2850 | 5091 | 5.402398 | AGACTTTTCGATTTTGCCAATAGC | 58.598 | 37.500 | 0.00 | 0.00 | 44.14 | 2.97 |
2851 | 5092 | 5.183904 | AGACTTTTCGATTTTGCCAATAGCT | 59.816 | 36.000 | 0.00 | 0.00 | 44.23 | 3.32 |
2852 | 5093 | 5.783111 | ACTTTTCGATTTTGCCAATAGCTT | 58.217 | 33.333 | 0.00 | 0.00 | 44.23 | 3.74 |
2853 | 5094 | 6.223120 | ACTTTTCGATTTTGCCAATAGCTTT | 58.777 | 32.000 | 0.00 | 0.00 | 44.23 | 3.51 |
2854 | 5095 | 6.146021 | ACTTTTCGATTTTGCCAATAGCTTTG | 59.854 | 34.615 | 0.00 | 0.00 | 44.23 | 2.77 |
2855 | 5096 | 3.510719 | TCGATTTTGCCAATAGCTTTGC | 58.489 | 40.909 | 0.00 | 0.00 | 44.23 | 3.68 |
2856 | 5097 | 2.604462 | CGATTTTGCCAATAGCTTTGCC | 59.396 | 45.455 | 0.00 | 0.00 | 44.23 | 4.52 |
2857 | 5098 | 3.598299 | GATTTTGCCAATAGCTTTGCCA | 58.402 | 40.909 | 0.00 | 0.00 | 44.23 | 4.92 |
2858 | 5099 | 2.747396 | TTTGCCAATAGCTTTGCCAG | 57.253 | 45.000 | 0.00 | 0.00 | 44.23 | 4.85 |
2859 | 5100 | 1.921982 | TTGCCAATAGCTTTGCCAGA | 58.078 | 45.000 | 0.00 | 0.00 | 44.23 | 3.86 |
2926 | 5167 | 2.041153 | CCCACAAGGAAACAGGCAC | 58.959 | 57.895 | 0.00 | 0.00 | 38.24 | 5.01 |
2928 | 5169 | 1.110442 | CCACAAGGAAACAGGCACAA | 58.890 | 50.000 | 0.00 | 0.00 | 36.89 | 3.33 |
2934 | 5175 | 0.240945 | GGAAACAGGCACAATGTCGG | 59.759 | 55.000 | 0.00 | 0.00 | 0.00 | 4.79 |
2938 | 5179 | 3.281727 | AACAGGCACAATGTCGGATAT | 57.718 | 42.857 | 0.00 | 0.00 | 0.00 | 1.63 |
2951 | 5192 | 4.866921 | TGTCGGATATTCGGACATTACAG | 58.133 | 43.478 | 12.22 | 0.00 | 46.93 | 2.74 |
2959 | 5200 | 3.226346 | TCGGACATTACAGAACGAAGG | 57.774 | 47.619 | 0.00 | 0.00 | 0.00 | 3.46 |
2994 | 5240 | 6.267070 | GGCTACACACTAATACAGAAGTCTC | 58.733 | 44.000 | 0.00 | 0.00 | 0.00 | 3.36 |
3034 | 5281 | 2.534903 | GCGAGCGGAATACAAGGCC | 61.535 | 63.158 | 0.00 | 0.00 | 0.00 | 5.19 |
3196 | 5445 | 0.609151 | TTCGCCAACGGACTCCATTA | 59.391 | 50.000 | 0.00 | 0.00 | 40.63 | 1.90 |
3200 | 5449 | 1.338769 | GCCAACGGACTCCATTACTGT | 60.339 | 52.381 | 0.00 | 0.00 | 0.00 | 3.55 |
3220 | 5469 | 4.447054 | CTGTAAGAGGATAGAGCATTTGCG | 59.553 | 45.833 | 0.00 | 0.00 | 41.39 | 4.85 |
3265 | 5514 | 3.522553 | GGAACAGTCCTTCGATGGTAAG | 58.477 | 50.000 | 16.29 | 9.82 | 41.24 | 2.34 |
3274 | 5523 | 3.252215 | CCTTCGATGGTAAGTTTGTTGCA | 59.748 | 43.478 | 9.17 | 0.00 | 0.00 | 4.08 |
3276 | 5525 | 4.902443 | TCGATGGTAAGTTTGTTGCAAA | 57.098 | 36.364 | 0.00 | 0.00 | 0.00 | 3.68 |
3317 | 5566 | 3.162666 | CATCGCCCCTATACTAGTCCAA | 58.837 | 50.000 | 0.00 | 0.00 | 0.00 | 3.53 |
3346 | 5595 | 1.978455 | TTGTGCTGACCCTGAACCGT | 61.978 | 55.000 | 0.00 | 0.00 | 0.00 | 4.83 |
3475 | 5724 | 0.693622 | TGGTTTGCATTCTCGGGGTA | 59.306 | 50.000 | 0.00 | 0.00 | 0.00 | 3.69 |
3524 | 5773 | 4.121317 | CCGTACCATTCCGTTTAGCAATA | 58.879 | 43.478 | 0.00 | 0.00 | 0.00 | 1.90 |
3533 | 5782 | 8.356657 | CCATTCCGTTTAGCAATATTAATGGAA | 58.643 | 33.333 | 18.33 | 18.33 | 44.98 | 3.53 |
3556 | 5805 | 1.595357 | GAAGACGGTCCCGGAACAT | 59.405 | 57.895 | 0.73 | 0.00 | 44.69 | 2.71 |
3625 | 5874 | 4.340617 | AGACCTTTGACCTCTCTCTGTAG | 58.659 | 47.826 | 0.00 | 0.00 | 0.00 | 2.74 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
22 | 23 | 3.860930 | TTTCCCAAGTGGAGCCGCC | 62.861 | 63.158 | 0.00 | 0.00 | 46.24 | 6.13 |
24 | 25 | 2.727103 | TTTTTCCCAAGTGGAGCCG | 58.273 | 52.632 | 0.00 | 0.00 | 46.24 | 5.52 |
74 | 75 | 9.361315 | CATGAATAATCACAGAAGCAATTCAAA | 57.639 | 29.630 | 0.00 | 0.00 | 38.69 | 2.69 |
83 | 84 | 9.529325 | AAATCAATGCATGAATAATCACAGAAG | 57.471 | 29.630 | 0.00 | 0.00 | 42.54 | 2.85 |
129 | 130 | 4.321008 | GCTTATGATCCATGATGCCACAAG | 60.321 | 45.833 | 0.00 | 0.00 | 0.00 | 3.16 |
133 | 134 | 3.512219 | TGCTTATGATCCATGATGCCA | 57.488 | 42.857 | 0.00 | 0.00 | 0.00 | 4.92 |
134 | 135 | 4.461431 | TCATTGCTTATGATCCATGATGCC | 59.539 | 41.667 | 0.00 | 0.00 | 38.35 | 4.40 |
159 | 160 | 7.931407 | AGCGGATATATGTACAAACAATTCAGA | 59.069 | 33.333 | 0.00 | 0.00 | 39.58 | 3.27 |
160 | 161 | 8.087982 | AGCGGATATATGTACAAACAATTCAG | 57.912 | 34.615 | 0.00 | 0.00 | 39.58 | 3.02 |
174 | 175 | 4.002982 | TGCCTTTGCTTAGCGGATATATG | 58.997 | 43.478 | 0.00 | 0.00 | 38.71 | 1.78 |
182 | 183 | 0.726827 | TCGATTGCCTTTGCTTAGCG | 59.273 | 50.000 | 0.00 | 0.00 | 38.71 | 4.26 |
185 | 186 | 5.777802 | TGAATTTTCGATTGCCTTTGCTTA | 58.222 | 33.333 | 0.00 | 0.00 | 38.71 | 3.09 |
196 | 197 | 4.330620 | GGTGCATGCATTGAATTTTCGATT | 59.669 | 37.500 | 25.64 | 0.00 | 0.00 | 3.34 |
199 | 200 | 3.255725 | AGGTGCATGCATTGAATTTTCG | 58.744 | 40.909 | 25.64 | 0.00 | 0.00 | 3.46 |
205 | 206 | 8.047413 | CATCTATTATAGGTGCATGCATTGAA | 57.953 | 34.615 | 25.64 | 13.91 | 28.88 | 2.69 |
216 | 217 | 9.276590 | TCATTTTGTCTGCATCTATTATAGGTG | 57.723 | 33.333 | 8.07 | 8.07 | 39.92 | 4.00 |
217 | 218 | 9.851686 | TTCATTTTGTCTGCATCTATTATAGGT | 57.148 | 29.630 | 0.00 | 0.00 | 0.00 | 3.08 |
221 | 222 | 8.509690 | CCGATTCATTTTGTCTGCATCTATTAT | 58.490 | 33.333 | 0.00 | 0.00 | 0.00 | 1.28 |
222 | 223 | 7.498900 | ACCGATTCATTTTGTCTGCATCTATTA | 59.501 | 33.333 | 0.00 | 0.00 | 0.00 | 0.98 |
223 | 224 | 6.319658 | ACCGATTCATTTTGTCTGCATCTATT | 59.680 | 34.615 | 0.00 | 0.00 | 0.00 | 1.73 |
241 | 242 | 9.774742 | GCCATCTTATTGATTATTTACCGATTC | 57.225 | 33.333 | 0.00 | 0.00 | 32.05 | 2.52 |
243 | 244 | 7.414098 | GCGCCATCTTATTGATTATTTACCGAT | 60.414 | 37.037 | 0.00 | 0.00 | 32.05 | 4.18 |
244 | 245 | 6.128391 | GCGCCATCTTATTGATTATTTACCGA | 60.128 | 38.462 | 0.00 | 0.00 | 32.05 | 4.69 |
245 | 246 | 6.021596 | GCGCCATCTTATTGATTATTTACCG | 58.978 | 40.000 | 0.00 | 0.00 | 32.05 | 4.02 |
246 | 247 | 6.908825 | TGCGCCATCTTATTGATTATTTACC | 58.091 | 36.000 | 4.18 | 0.00 | 32.05 | 2.85 |
247 | 248 | 7.860373 | TGTTGCGCCATCTTATTGATTATTTAC | 59.140 | 33.333 | 4.18 | 0.00 | 32.05 | 2.01 |
248 | 249 | 7.935520 | TGTTGCGCCATCTTATTGATTATTTA | 58.064 | 30.769 | 4.18 | 0.00 | 32.05 | 1.40 |
249 | 250 | 6.804677 | TGTTGCGCCATCTTATTGATTATTT | 58.195 | 32.000 | 4.18 | 0.00 | 32.05 | 1.40 |
250 | 251 | 6.389830 | TGTTGCGCCATCTTATTGATTATT | 57.610 | 33.333 | 4.18 | 0.00 | 32.05 | 1.40 |
251 | 252 | 6.389830 | TTGTTGCGCCATCTTATTGATTAT | 57.610 | 33.333 | 4.18 | 0.00 | 32.05 | 1.28 |
252 | 253 | 5.826601 | TTGTTGCGCCATCTTATTGATTA | 57.173 | 34.783 | 4.18 | 0.00 | 32.05 | 1.75 |
253 | 254 | 4.717233 | TTGTTGCGCCATCTTATTGATT | 57.283 | 36.364 | 4.18 | 0.00 | 32.05 | 2.57 |
254 | 255 | 4.158394 | AGTTTGTTGCGCCATCTTATTGAT | 59.842 | 37.500 | 4.18 | 0.00 | 35.40 | 2.57 |
255 | 256 | 3.505680 | AGTTTGTTGCGCCATCTTATTGA | 59.494 | 39.130 | 4.18 | 0.00 | 0.00 | 2.57 |
256 | 257 | 3.609373 | CAGTTTGTTGCGCCATCTTATTG | 59.391 | 43.478 | 4.18 | 0.00 | 0.00 | 1.90 |
257 | 258 | 3.255642 | ACAGTTTGTTGCGCCATCTTATT | 59.744 | 39.130 | 4.18 | 0.00 | 0.00 | 1.40 |
258 | 259 | 2.819608 | ACAGTTTGTTGCGCCATCTTAT | 59.180 | 40.909 | 4.18 | 0.00 | 0.00 | 1.73 |
259 | 260 | 2.226330 | ACAGTTTGTTGCGCCATCTTA | 58.774 | 42.857 | 4.18 | 0.00 | 0.00 | 2.10 |
260 | 261 | 1.032014 | ACAGTTTGTTGCGCCATCTT | 58.968 | 45.000 | 4.18 | 0.00 | 0.00 | 2.40 |
261 | 262 | 1.001378 | GAACAGTTTGTTGCGCCATCT | 60.001 | 47.619 | 4.18 | 0.00 | 41.28 | 2.90 |
262 | 263 | 1.268999 | TGAACAGTTTGTTGCGCCATC | 60.269 | 47.619 | 4.18 | 0.00 | 41.28 | 3.51 |
263 | 264 | 0.743688 | TGAACAGTTTGTTGCGCCAT | 59.256 | 45.000 | 4.18 | 0.00 | 41.28 | 4.40 |
264 | 265 | 0.528017 | TTGAACAGTTTGTTGCGCCA | 59.472 | 45.000 | 4.18 | 0.00 | 41.28 | 5.69 |
268 | 269 | 7.928908 | TCATCTATTTTGAACAGTTTGTTGC | 57.071 | 32.000 | 0.00 | 0.00 | 41.28 | 4.17 |
286 | 287 | 7.320384 | TGGCCTTTATGAATCTCATCATCTA | 57.680 | 36.000 | 3.32 | 0.00 | 40.44 | 1.98 |
287 | 288 | 6.196918 | TGGCCTTTATGAATCTCATCATCT | 57.803 | 37.500 | 3.32 | 0.00 | 40.44 | 2.90 |
288 | 289 | 6.889301 | TTGGCCTTTATGAATCTCATCATC | 57.111 | 37.500 | 3.32 | 0.00 | 40.44 | 2.92 |
289 | 290 | 7.664552 | TTTTGGCCTTTATGAATCTCATCAT | 57.335 | 32.000 | 3.32 | 0.00 | 42.52 | 2.45 |
290 | 291 | 7.664552 | ATTTTGGCCTTTATGAATCTCATCA | 57.335 | 32.000 | 3.32 | 0.00 | 38.26 | 3.07 |
320 | 321 | 4.202326 | GGAACAAACAGAGAGGTGAGGTAA | 60.202 | 45.833 | 0.00 | 0.00 | 0.00 | 2.85 |
321 | 322 | 3.323979 | GGAACAAACAGAGAGGTGAGGTA | 59.676 | 47.826 | 0.00 | 0.00 | 0.00 | 3.08 |
323 | 324 | 2.772287 | GGAACAAACAGAGAGGTGAGG | 58.228 | 52.381 | 0.00 | 0.00 | 0.00 | 3.86 |
335 | 336 | 1.003233 | ACCTCATCCTCCGGAACAAAC | 59.997 | 52.381 | 5.23 | 0.00 | 34.34 | 2.93 |
343 | 344 | 0.826715 | ATGACACACCTCATCCTCCG | 59.173 | 55.000 | 0.00 | 0.00 | 0.00 | 4.63 |
347 | 348 | 7.807977 | ATTTTACATATGACACACCTCATCC | 57.192 | 36.000 | 10.38 | 0.00 | 32.86 | 3.51 |
361 | 362 | 9.881773 | ACACCTCATTTCCCATATTTTACATAT | 57.118 | 29.630 | 0.00 | 0.00 | 0.00 | 1.78 |
362 | 363 | 9.130661 | CACACCTCATTTCCCATATTTTACATA | 57.869 | 33.333 | 0.00 | 0.00 | 0.00 | 2.29 |
363 | 364 | 7.619302 | ACACACCTCATTTCCCATATTTTACAT | 59.381 | 33.333 | 0.00 | 0.00 | 0.00 | 2.29 |
365 | 366 | 7.122055 | TGACACACCTCATTTCCCATATTTTAC | 59.878 | 37.037 | 0.00 | 0.00 | 0.00 | 2.01 |
367 | 368 | 6.015918 | TGACACACCTCATTTCCCATATTTT | 58.984 | 36.000 | 0.00 | 0.00 | 0.00 | 1.82 |
368 | 369 | 5.579047 | TGACACACCTCATTTCCCATATTT | 58.421 | 37.500 | 0.00 | 0.00 | 0.00 | 1.40 |
431 | 465 | 5.413213 | CGGTTGTTCCATGTGGTTCTTAATA | 59.587 | 40.000 | 0.00 | 0.00 | 36.34 | 0.98 |
506 | 541 | 1.180456 | TCTCGCCGTGGTCCACTTTA | 61.180 | 55.000 | 19.82 | 2.18 | 31.34 | 1.85 |
510 | 545 | 3.681835 | AGTCTCGCCGTGGTCCAC | 61.682 | 66.667 | 12.40 | 12.40 | 0.00 | 4.02 |
519 | 554 | 0.250513 | AGAACCCAATCAGTCTCGCC | 59.749 | 55.000 | 0.00 | 0.00 | 0.00 | 5.54 |
521 | 556 | 3.056536 | TCTTCAGAACCCAATCAGTCTCG | 60.057 | 47.826 | 0.00 | 0.00 | 0.00 | 4.04 |
556 | 591 | 7.939784 | TCAGTAATCTTTCAGAGCTACAGTA | 57.060 | 36.000 | 0.00 | 0.00 | 0.00 | 2.74 |
558 | 593 | 6.255453 | GCTTCAGTAATCTTTCAGAGCTACAG | 59.745 | 42.308 | 0.00 | 0.00 | 0.00 | 2.74 |
562 | 597 | 5.157940 | TGCTTCAGTAATCTTTCAGAGCT | 57.842 | 39.130 | 0.00 | 0.00 | 0.00 | 4.09 |
563 | 598 | 5.220815 | CCATGCTTCAGTAATCTTTCAGAGC | 60.221 | 44.000 | 0.00 | 0.00 | 0.00 | 4.09 |
627 | 663 | 7.598869 | TCATCGTAAGTAAATGATATGTGCCTC | 59.401 | 37.037 | 0.00 | 0.00 | 39.48 | 4.70 |
643 | 679 | 1.623811 | AGGGCACAAGTCATCGTAAGT | 59.376 | 47.619 | 0.00 | 0.00 | 39.48 | 2.24 |
661 | 698 | 2.421619 | GAACTTCAGTGGAGAAGCAGG | 58.578 | 52.381 | 5.11 | 0.00 | 46.97 | 4.85 |
719 | 759 | 7.721842 | TGTCTTTTGTTGGACTCCATTTACATA | 59.278 | 33.333 | 0.00 | 0.00 | 31.53 | 2.29 |
727 | 767 | 3.278574 | CACTGTCTTTTGTTGGACTCCA | 58.721 | 45.455 | 0.00 | 0.00 | 34.01 | 3.86 |
779 | 826 | 7.214460 | TGGTAGGTCCAAATCCATTATTGTA | 57.786 | 36.000 | 0.00 | 0.00 | 44.12 | 2.41 |
1027 | 1554 | 2.380941 | TGCAACTGCTGATATGGCAAT | 58.619 | 42.857 | 2.95 | 0.00 | 42.66 | 3.56 |
1124 | 1654 | 0.178953 | ATGCTGCAACCTTTCCACCT | 60.179 | 50.000 | 6.36 | 0.00 | 0.00 | 4.00 |
1161 | 1691 | 1.721664 | CCGCCTCCTCGACGATTGTA | 61.722 | 60.000 | 0.00 | 0.00 | 0.00 | 2.41 |
1164 | 1694 | 2.439701 | TCCGCCTCCTCGACGATT | 60.440 | 61.111 | 0.00 | 0.00 | 0.00 | 3.34 |
1299 | 1829 | 0.321298 | TGCTAACCTTGTCGAAGCCC | 60.321 | 55.000 | 0.86 | 0.00 | 32.14 | 5.19 |
1309 | 1839 | 3.423539 | TGAGTCATTGCTGCTAACCTT | 57.576 | 42.857 | 0.00 | 0.00 | 0.00 | 3.50 |
1337 | 1867 | 7.936847 | TGACTGGAATGACTAAATACAAACTGT | 59.063 | 33.333 | 0.00 | 0.00 | 0.00 | 3.55 |
1379 | 1918 | 1.321474 | CTTGTTGCCTTTCTCTGCCA | 58.679 | 50.000 | 0.00 | 0.00 | 0.00 | 4.92 |
1380 | 1919 | 0.600057 | CCTTGTTGCCTTTCTCTGCC | 59.400 | 55.000 | 0.00 | 0.00 | 0.00 | 4.85 |
1500 | 2039 | 5.178797 | AGATAAACATCATATGGCCTACGC | 58.821 | 41.667 | 3.32 | 0.00 | 33.60 | 4.42 |
1692 | 2238 | 2.027625 | GAAGCGTGAACGGACCCTG | 61.028 | 63.158 | 4.84 | 0.00 | 40.23 | 4.45 |
1698 | 2244 | 0.809385 | TAGAGGAGAAGCGTGAACGG | 59.191 | 55.000 | 4.84 | 0.00 | 40.23 | 4.44 |
1800 | 2346 | 6.358974 | TCATCACCTACATCAGAAGTGAAA | 57.641 | 37.500 | 0.00 | 0.00 | 40.56 | 2.69 |
1996 | 2542 | 1.069823 | CGGATGTTCTGCTGGCTCTAT | 59.930 | 52.381 | 0.00 | 0.00 | 0.00 | 1.98 |
2079 | 2628 | 3.840890 | TCCGTGAACATATTTGTTGCC | 57.159 | 42.857 | 6.25 | 0.00 | 46.01 | 4.52 |
2106 | 2655 | 1.202486 | TGAACGTCGAGGTTGCTTCTT | 60.202 | 47.619 | 26.63 | 1.97 | 0.00 | 2.52 |
2121 | 2670 | 1.493772 | TACAACGCCAGAACTGAACG | 58.506 | 50.000 | 3.19 | 9.04 | 36.49 | 3.95 |
2153 | 2702 | 5.606505 | GGTTTCTTTTAACCATTCTTGCCA | 58.393 | 37.500 | 0.00 | 0.00 | 45.59 | 4.92 |
2191 | 2744 | 2.208132 | ATACGCATGGTTGGGTTCAA | 57.792 | 45.000 | 0.91 | 0.00 | 45.88 | 2.69 |
2342 | 2895 | 1.630878 | AGTCTCCTTTGGGCCTAACAG | 59.369 | 52.381 | 0.00 | 2.60 | 0.00 | 3.16 |
2352 | 2905 | 5.702670 | TGCAATTAGAGTGAAGTCTCCTTTG | 59.297 | 40.000 | 0.00 | 0.00 | 35.28 | 2.77 |
2562 | 3121 | 7.274468 | CACTGTATGTCACTTGAGATCTGTAAC | 59.726 | 40.741 | 0.00 | 0.00 | 30.22 | 2.50 |
2568 | 3127 | 6.393990 | AGTTCACTGTATGTCACTTGAGATC | 58.606 | 40.000 | 0.00 | 0.00 | 30.22 | 2.75 |
2653 | 4892 | 7.746703 | AGGTAGGTAGGTCCAAATTGATTATC | 58.253 | 38.462 | 0.00 | 0.00 | 39.02 | 1.75 |
2683 | 4922 | 9.860650 | TTGGCCAATATTTATAATACTCACAGT | 57.139 | 29.630 | 16.05 | 0.00 | 0.00 | 3.55 |
2765 | 5006 | 8.030692 | ACACACGCATACTTGTCTAGTTTAATA | 58.969 | 33.333 | 0.00 | 0.00 | 38.33 | 0.98 |
2850 | 5091 | 5.418310 | TCGTTCTAAAAAGTCTGGCAAAG | 57.582 | 39.130 | 0.00 | 0.00 | 0.00 | 2.77 |
2851 | 5092 | 5.587043 | TCTTCGTTCTAAAAAGTCTGGCAAA | 59.413 | 36.000 | 0.00 | 0.00 | 0.00 | 3.68 |
2852 | 5093 | 5.007332 | GTCTTCGTTCTAAAAAGTCTGGCAA | 59.993 | 40.000 | 0.00 | 0.00 | 0.00 | 4.52 |
2853 | 5094 | 4.510340 | GTCTTCGTTCTAAAAAGTCTGGCA | 59.490 | 41.667 | 0.00 | 0.00 | 0.00 | 4.92 |
2854 | 5095 | 4.376109 | CGTCTTCGTTCTAAAAAGTCTGGC | 60.376 | 45.833 | 0.00 | 0.00 | 0.00 | 4.85 |
2855 | 5096 | 4.376109 | GCGTCTTCGTTCTAAAAAGTCTGG | 60.376 | 45.833 | 0.00 | 0.00 | 39.49 | 3.86 |
2856 | 5097 | 4.444720 | AGCGTCTTCGTTCTAAAAAGTCTG | 59.555 | 41.667 | 0.00 | 0.00 | 39.49 | 3.51 |
2857 | 5098 | 4.618965 | AGCGTCTTCGTTCTAAAAAGTCT | 58.381 | 39.130 | 0.00 | 0.00 | 39.49 | 3.24 |
2858 | 5099 | 4.968660 | AGCGTCTTCGTTCTAAAAAGTC | 57.031 | 40.909 | 0.00 | 0.00 | 39.49 | 3.01 |
2859 | 5100 | 4.922103 | CCTAGCGTCTTCGTTCTAAAAAGT | 59.078 | 41.667 | 0.00 | 0.00 | 39.49 | 2.66 |
2915 | 5156 | 0.240945 | CCGACATTGTGCCTGTTTCC | 59.759 | 55.000 | 0.00 | 0.00 | 0.00 | 3.13 |
2926 | 5167 | 5.694458 | TGTAATGTCCGAATATCCGACATTG | 59.306 | 40.000 | 24.38 | 0.00 | 43.56 | 2.82 |
2928 | 5169 | 5.243060 | TCTGTAATGTCCGAATATCCGACAT | 59.757 | 40.000 | 8.03 | 8.03 | 38.01 | 3.06 |
2934 | 5175 | 6.144080 | CCTTCGTTCTGTAATGTCCGAATATC | 59.856 | 42.308 | 0.00 | 0.00 | 34.33 | 1.63 |
2938 | 5179 | 3.581755 | CCTTCGTTCTGTAATGTCCGAA | 58.418 | 45.455 | 0.00 | 0.00 | 33.79 | 4.30 |
2976 | 5222 | 6.350277 | CCCTTTCGAGACTTCTGTATTAGTGT | 60.350 | 42.308 | 0.00 | 0.00 | 0.00 | 3.55 |
2979 | 5225 | 6.210287 | ACCCTTTCGAGACTTCTGTATTAG | 57.790 | 41.667 | 0.00 | 0.00 | 0.00 | 1.73 |
2981 | 5227 | 5.011738 | TGAACCCTTTCGAGACTTCTGTATT | 59.988 | 40.000 | 0.00 | 0.00 | 34.04 | 1.89 |
2983 | 5229 | 3.893200 | TGAACCCTTTCGAGACTTCTGTA | 59.107 | 43.478 | 0.00 | 0.00 | 34.04 | 2.74 |
2994 | 5240 | 0.598065 | CCAGGCTTTGAACCCTTTCG | 59.402 | 55.000 | 0.00 | 0.00 | 34.04 | 3.46 |
3117 | 5366 | 1.696884 | TGTGCACCAGGTCTATGTGAA | 59.303 | 47.619 | 15.69 | 0.00 | 31.66 | 3.18 |
3118 | 5367 | 1.001974 | GTGTGCACCAGGTCTATGTGA | 59.998 | 52.381 | 15.69 | 0.00 | 31.66 | 3.58 |
3196 | 5445 | 5.363939 | GCAAATGCTCTATCCTCTTACAGT | 58.636 | 41.667 | 0.00 | 0.00 | 38.21 | 3.55 |
3200 | 5449 | 4.937201 | TCGCAAATGCTCTATCCTCTTA | 57.063 | 40.909 | 3.63 | 0.00 | 39.32 | 2.10 |
3220 | 5469 | 3.332034 | ACGCACCCGGCTAATATTATTC | 58.668 | 45.455 | 0.00 | 0.00 | 41.67 | 1.75 |
3241 | 5490 | 0.530744 | CATCGAAGGACTGTTCCCGA | 59.469 | 55.000 | 4.09 | 4.09 | 44.10 | 5.14 |
3249 | 5498 | 4.618920 | ACAAACTTACCATCGAAGGACT | 57.381 | 40.909 | 14.76 | 0.00 | 0.00 | 3.85 |
3274 | 5523 | 3.954258 | GCTATGGTCCTTGTGGCTTATTT | 59.046 | 43.478 | 0.00 | 0.00 | 0.00 | 1.40 |
3276 | 5525 | 2.509548 | TGCTATGGTCCTTGTGGCTTAT | 59.490 | 45.455 | 0.00 | 0.00 | 0.00 | 1.73 |
3346 | 5595 | 1.490490 | AGCTTGTGGAACTCCTTGACA | 59.510 | 47.619 | 0.00 | 0.00 | 38.04 | 3.58 |
3505 | 5754 | 8.788806 | CCATTAATATTGCTAAACGGAATGGTA | 58.211 | 33.333 | 10.65 | 0.00 | 37.22 | 3.25 |
3506 | 5755 | 7.504238 | TCCATTAATATTGCTAAACGGAATGGT | 59.496 | 33.333 | 15.48 | 0.00 | 40.95 | 3.55 |
3524 | 5773 | 5.163332 | GGACCGTCTTCCTACTTCCATTAAT | 60.163 | 44.000 | 0.00 | 0.00 | 32.24 | 1.40 |
3533 | 5782 | 1.379576 | CCGGGACCGTCTTCCTACT | 60.380 | 63.158 | 10.17 | 0.00 | 35.76 | 2.57 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.