Multiple sequence alignment - TraesCS2D01G569700
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 | TraesCS2D01G569700 | chr2D | 100.000 | 2963 | 0 | 0 | 1 | 2963 | 637423912 | 637420950 | 0.000000e+00 | 5472 |
1 | TraesCS2D01G569700 | chr2D | 81.738 | 564 | 56 | 30 | 201 | 758 | 577522453 | 577522975 | 7.590000e-116 | 427 |
2 | TraesCS2D01G569700 | chr2D | 79.004 | 462 | 53 | 27 | 201 | 657 | 131967173 | 131966751 | 2.910000e-70 | 276 |
3 | TraesCS2D01G569700 | chr2D | 96.364 | 165 | 4 | 1 | 2489 | 2653 | 637391019 | 637390857 | 1.350000e-68 | 270 |
4 | TraesCS2D01G569700 | chr2A | 85.691 | 1838 | 121 | 61 | 609 | 2362 | 762644951 | 762646730 | 0.000000e+00 | 1807 |
5 | TraesCS2D01G569700 | chr2A | 89.453 | 256 | 24 | 2 | 1 | 253 | 762644443 | 762644698 | 1.330000e-83 | 320 |
6 | TraesCS2D01G569700 | chr2A | 80.769 | 312 | 55 | 3 | 2656 | 2963 | 353482673 | 353482983 | 3.820000e-59 | 239 |
7 | TraesCS2D01G569700 | chr2A | 79.412 | 238 | 35 | 8 | 1853 | 2087 | 762722230 | 762722456 | 3.950000e-34 | 156 |
8 | TraesCS2D01G569700 | chrUn | 84.165 | 1863 | 125 | 72 | 588 | 2354 | 234386359 | 234388147 | 0.000000e+00 | 1650 |
9 | TraesCS2D01G569700 | chrUn | 85.091 | 550 | 45 | 15 | 4 | 547 | 234385506 | 234386024 | 7.270000e-146 | 527 |
10 | TraesCS2D01G569700 | chrUn | 85.371 | 499 | 47 | 8 | 2489 | 2963 | 39590420 | 39590916 | 7.380000e-136 | 494 |
11 | TraesCS2D01G569700 | chrUn | 93.220 | 177 | 11 | 1 | 2489 | 2665 | 39595704 | 39595879 | 2.930000e-65 | 259 |
12 | TraesCS2D01G569700 | chrUn | 93.617 | 94 | 3 | 2 | 2376 | 2469 | 234388222 | 234388312 | 1.430000e-28 | 137 |
13 | TraesCS2D01G569700 | chr5D | 89.648 | 483 | 42 | 2 | 2489 | 2963 | 204284086 | 204284568 | 2.530000e-170 | 608 |
14 | TraesCS2D01G569700 | chr5D | 79.654 | 462 | 50 | 28 | 201 | 657 | 444011028 | 444010606 | 2.890000e-75 | 292 |
15 | TraesCS2D01G569700 | chr5D | 83.168 | 303 | 24 | 16 | 359 | 657 | 507902487 | 507902208 | 4.900000e-63 | 252 |
16 | TraesCS2D01G569700 | chr4D | 86.785 | 507 | 34 | 22 | 2489 | 2963 | 478098822 | 478099327 | 4.350000e-148 | 534 |
17 | TraesCS2D01G569700 | chr4D | 88.889 | 261 | 23 | 5 | 2489 | 2745 | 47982461 | 47982719 | 1.710000e-82 | 316 |
18 | TraesCS2D01G569700 | chr4D | 86.555 | 119 | 6 | 6 | 548 | 657 | 373890991 | 373891108 | 4.010000e-24 | 122 |
19 | TraesCS2D01G569700 | chr1D | 83.202 | 506 | 46 | 21 | 2489 | 2963 | 33961610 | 33962107 | 7.590000e-116 | 427 |
20 | TraesCS2D01G569700 | chr1D | 79.221 | 462 | 52 | 28 | 201 | 657 | 120851759 | 120851337 | 6.250000e-72 | 281 |
21 | TraesCS2D01G569700 | chr1D | 83.775 | 302 | 25 | 13 | 359 | 657 | 5743837 | 5743557 | 6.300000e-67 | 265 |
22 | TraesCS2D01G569700 | chr7D | 80.492 | 569 | 55 | 32 | 201 | 758 | 620009756 | 620010279 | 4.630000e-103 | 385 |
23 | TraesCS2D01G569700 | chr6D | 86.817 | 311 | 38 | 1 | 2656 | 2963 | 395366984 | 395367294 | 7.860000e-91 | 344 |
24 | TraesCS2D01G569700 | chr3A | 79.002 | 481 | 83 | 15 | 2489 | 2961 | 534336559 | 534337029 | 2.220000e-81 | 313 |
25 | TraesCS2D01G569700 | chr3A | 85.374 | 294 | 40 | 1 | 2656 | 2946 | 358289670 | 358289377 | 4.800000e-78 | 302 |
26 | TraesCS2D01G569700 | chr3A | 91.489 | 188 | 11 | 4 | 359 | 543 | 731329662 | 731329477 | 1.360000e-63 | 254 |
27 | TraesCS2D01G569700 | chr7A | 84.731 | 334 | 19 | 20 | 2489 | 2790 | 192882937 | 192883270 | 3.710000e-79 | 305 |
28 | TraesCS2D01G569700 | chr7A | 83.775 | 302 | 23 | 15 | 359 | 657 | 178997028 | 178996750 | 2.260000e-66 | 263 |
29 | TraesCS2D01G569700 | chr1A | 85.417 | 288 | 38 | 4 | 2504 | 2787 | 123052922 | 123052635 | 2.230000e-76 | 296 |
30 | TraesCS2D01G569700 | chr5B | 83.175 | 315 | 47 | 6 | 2653 | 2963 | 146262690 | 146262378 | 1.740000e-72 | 283 |
31 | TraesCS2D01G569700 | chr4A | 78.747 | 447 | 47 | 31 | 218 | 657 | 201030599 | 201030194 | 3.790000e-64 | 255 |
32 | TraesCS2D01G569700 | chr7B | 86.441 | 118 | 7 | 6 | 548 | 657 | 248170619 | 248170735 | 1.440000e-23 | 121 |
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 | TraesCS2D01G569700 | chr2D | 637420950 | 637423912 | 2962 | True | 5472.000000 | 5472 | 100.000000 | 1 | 2963 | 1 | chr2D.!!$R3 | 2962 |
1 | TraesCS2D01G569700 | chr2D | 577522453 | 577522975 | 522 | False | 427.000000 | 427 | 81.738000 | 201 | 758 | 1 | chr2D.!!$F1 | 557 |
2 | TraesCS2D01G569700 | chr2A | 762644443 | 762646730 | 2287 | False | 1063.500000 | 1807 | 87.572000 | 1 | 2362 | 2 | chr2A.!!$F3 | 2361 |
3 | TraesCS2D01G569700 | chrUn | 234385506 | 234388312 | 2806 | False | 771.333333 | 1650 | 87.624333 | 4 | 2469 | 3 | chrUn.!!$F3 | 2465 |
4 | TraesCS2D01G569700 | chr4D | 478098822 | 478099327 | 505 | False | 534.000000 | 534 | 86.785000 | 2489 | 2963 | 1 | chr4D.!!$F3 | 474 |
5 | TraesCS2D01G569700 | chr7D | 620009756 | 620010279 | 523 | False | 385.000000 | 385 | 80.492000 | 201 | 758 | 1 | chr7D.!!$F1 | 557 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
326 | 336 | 0.610232 | GAGCTGGCCACCAACATCTT | 60.610 | 55.0 | 0.0 | 0.0 | 30.8 | 2.40 | F |
908 | 1283 | 0.634465 | GGAGGAGGAGGAGAAGGAGT | 59.366 | 60.0 | 0.0 | 0.0 | 0.0 | 3.85 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1195 | 1576 | 0.036952 | CCGATTGTCAGGTGTGAGCT | 60.037 | 55.0 | 0.0 | 0.0 | 31.53 | 4.09 | R |
2684 | 3259 | 0.115745 | TGTAGGGAAACGAGGGAGGT | 59.884 | 55.0 | 0.0 | 0.0 | 0.00 | 3.85 | 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 |
---|---|---|---|---|---|---|---|---|---|
47 | 48 | 3.492337 | ACTTCAGAGAGACCGTCTTCTT | 58.508 | 45.455 | 1.71 | 0.00 | 34.71 | 2.52 |
51 | 52 | 0.806241 | GAGAGACCGTCTTCTTCGCT | 59.194 | 55.000 | 1.71 | 0.00 | 34.71 | 4.93 |
89 | 90 | 1.614317 | CCAGCAAAACTTCCGAGGGAT | 60.614 | 52.381 | 0.00 | 0.00 | 0.00 | 3.85 |
97 | 98 | 1.103803 | CTTCCGAGGGATCGTCTTCA | 58.896 | 55.000 | 0.00 | 0.00 | 0.00 | 3.02 |
124 | 125 | 1.065418 | CCCCAAGCGAGGTTAAGTGAT | 60.065 | 52.381 | 0.00 | 0.00 | 0.00 | 3.06 |
127 | 128 | 2.932614 | CCAAGCGAGGTTAAGTGATCTG | 59.067 | 50.000 | 0.00 | 0.00 | 0.00 | 2.90 |
130 | 131 | 1.207329 | GCGAGGTTAAGTGATCTGGGT | 59.793 | 52.381 | 0.00 | 0.00 | 0.00 | 4.51 |
262 | 272 | 2.320781 | CCACTAGTGCACCCTATAGCT | 58.679 | 52.381 | 17.86 | 0.00 | 0.00 | 3.32 |
287 | 297 | 1.209990 | AGCTCTTGATTGAGGCTGAGG | 59.790 | 52.381 | 0.00 | 0.00 | 34.82 | 3.86 |
293 | 303 | 2.923121 | TGATTGAGGCTGAGGTTATGC | 58.077 | 47.619 | 0.00 | 0.00 | 0.00 | 3.14 |
304 | 314 | 5.227238 | CTGAGGTTATGCAGCAAGTAAAG | 57.773 | 43.478 | 0.00 | 0.00 | 0.00 | 1.85 |
305 | 315 | 4.651778 | TGAGGTTATGCAGCAAGTAAAGT | 58.348 | 39.130 | 0.00 | 0.00 | 0.00 | 2.66 |
306 | 316 | 5.070001 | TGAGGTTATGCAGCAAGTAAAGTT | 58.930 | 37.500 | 0.00 | 0.00 | 0.00 | 2.66 |
307 | 317 | 5.048782 | TGAGGTTATGCAGCAAGTAAAGTTG | 60.049 | 40.000 | 0.00 | 0.00 | 0.00 | 3.16 |
308 | 318 | 5.070001 | AGGTTATGCAGCAAGTAAAGTTGA | 58.930 | 37.500 | 0.00 | 0.00 | 0.00 | 3.18 |
309 | 319 | 5.182001 | AGGTTATGCAGCAAGTAAAGTTGAG | 59.818 | 40.000 | 0.00 | 0.00 | 0.00 | 3.02 |
310 | 320 | 3.565905 | ATGCAGCAAGTAAAGTTGAGC | 57.434 | 42.857 | 0.00 | 5.37 | 33.24 | 4.26 |
311 | 321 | 2.575532 | TGCAGCAAGTAAAGTTGAGCT | 58.424 | 42.857 | 0.00 | 0.00 | 33.58 | 4.09 |
326 | 336 | 0.610232 | GAGCTGGCCACCAACATCTT | 60.610 | 55.000 | 0.00 | 0.00 | 30.80 | 2.40 |
327 | 337 | 0.698238 | AGCTGGCCACCAACATCTTA | 59.302 | 50.000 | 0.00 | 0.00 | 30.80 | 2.10 |
328 | 338 | 0.811281 | GCTGGCCACCAACATCTTAC | 59.189 | 55.000 | 0.00 | 0.00 | 30.80 | 2.34 |
330 | 340 | 2.726821 | CTGGCCACCAACATCTTACAT | 58.273 | 47.619 | 0.00 | 0.00 | 30.80 | 2.29 |
331 | 341 | 2.684881 | CTGGCCACCAACATCTTACATC | 59.315 | 50.000 | 0.00 | 0.00 | 30.80 | 3.06 |
332 | 342 | 2.308570 | TGGCCACCAACATCTTACATCT | 59.691 | 45.455 | 0.00 | 0.00 | 0.00 | 2.90 |
333 | 343 | 2.684881 | GGCCACCAACATCTTACATCTG | 59.315 | 50.000 | 0.00 | 0.00 | 0.00 | 2.90 |
342 | 352 | 7.387948 | ACCAACATCTTACATCTGTGAAGTTAC | 59.612 | 37.037 | 0.00 | 0.00 | 0.00 | 2.50 |
355 | 365 | 4.439057 | GTGAAGTTACTCCACAGTTCACA | 58.561 | 43.478 | 12.80 | 0.00 | 46.26 | 3.58 |
380 | 401 | 5.832060 | TGGCCCATGAAAATGAAAATTTTGT | 59.168 | 32.000 | 8.47 | 0.00 | 34.24 | 2.83 |
389 | 410 | 9.985318 | TGAAAATGAAAATTTTGTTTGCTGTAG | 57.015 | 25.926 | 8.47 | 0.00 | 34.24 | 2.74 |
578 | 610 | 8.284945 | AGCAGCATTTTTAGATGATTGTTAGA | 57.715 | 30.769 | 0.00 | 0.00 | 0.00 | 2.10 |
579 | 611 | 8.910944 | AGCAGCATTTTTAGATGATTGTTAGAT | 58.089 | 29.630 | 0.00 | 0.00 | 0.00 | 1.98 |
581 | 613 | 8.965172 | CAGCATTTTTAGATGATTGTTAGATGC | 58.035 | 33.333 | 0.00 | 0.00 | 36.25 | 3.91 |
585 | 942 | 8.593945 | TTTTTAGATGATTGTTAGATGCCCTT | 57.406 | 30.769 | 0.00 | 0.00 | 0.00 | 3.95 |
586 | 943 | 9.693739 | TTTTTAGATGATTGTTAGATGCCCTTA | 57.306 | 29.630 | 0.00 | 0.00 | 0.00 | 2.69 |
598 | 955 | 3.203040 | AGATGCCCTTAATGTAGCTGGTT | 59.797 | 43.478 | 0.00 | 0.00 | 0.00 | 3.67 |
644 | 1004 | 2.452116 | CCTTGGTGTCAGTGAGGGA | 58.548 | 57.895 | 0.00 | 0.00 | 0.00 | 4.20 |
653 | 1013 | 1.073923 | GTCAGTGAGGGAATTGGGTGT | 59.926 | 52.381 | 0.00 | 0.00 | 0.00 | 4.16 |
843 | 1214 | 2.464459 | GCAGCAGCCACGTACATCC | 61.464 | 63.158 | 0.00 | 0.00 | 33.58 | 3.51 |
908 | 1283 | 0.634465 | GGAGGAGGAGGAGAAGGAGT | 59.366 | 60.000 | 0.00 | 0.00 | 0.00 | 3.85 |
911 | 1286 | 2.499693 | GAGGAGGAGGAGAAGGAGTTTG | 59.500 | 54.545 | 0.00 | 0.00 | 0.00 | 2.93 |
1160 | 1541 | 1.183549 | TCCTCCCTCGTAAGCTCAAC | 58.816 | 55.000 | 0.00 | 0.00 | 37.18 | 3.18 |
1163 | 1544 | 2.359531 | CCTCCCTCGTAAGCTCAACTAG | 59.640 | 54.545 | 0.00 | 0.00 | 37.18 | 2.57 |
1178 | 1559 | 4.319177 | TCAACTAGCTTGCTTCTTCTTCC | 58.681 | 43.478 | 0.00 | 0.00 | 0.00 | 3.46 |
1190 | 1571 | 5.994668 | TGCTTCTTCTTCCTTTCTTCTTCTC | 59.005 | 40.000 | 0.00 | 0.00 | 0.00 | 2.87 |
1191 | 1572 | 5.411361 | GCTTCTTCTTCCTTTCTTCTTCTCC | 59.589 | 44.000 | 0.00 | 0.00 | 0.00 | 3.71 |
1192 | 1573 | 5.491323 | TCTTCTTCCTTTCTTCTTCTCCC | 57.509 | 43.478 | 0.00 | 0.00 | 0.00 | 4.30 |
1194 | 1575 | 5.608860 | TCTTCTTCCTTTCTTCTTCTCCCTT | 59.391 | 40.000 | 0.00 | 0.00 | 0.00 | 3.95 |
1195 | 1576 | 6.787957 | TCTTCTTCCTTTCTTCTTCTCCCTTA | 59.212 | 38.462 | 0.00 | 0.00 | 0.00 | 2.69 |
1196 | 1577 | 6.613153 | TCTTCCTTTCTTCTTCTCCCTTAG | 57.387 | 41.667 | 0.00 | 0.00 | 0.00 | 2.18 |
1198 | 1579 | 4.430441 | TCCTTTCTTCTTCTCCCTTAGCT | 58.570 | 43.478 | 0.00 | 0.00 | 0.00 | 3.32 |
1199 | 1580 | 4.468153 | TCCTTTCTTCTTCTCCCTTAGCTC | 59.532 | 45.833 | 0.00 | 0.00 | 0.00 | 4.09 |
1200 | 1581 | 4.223923 | CCTTTCTTCTTCTCCCTTAGCTCA | 59.776 | 45.833 | 0.00 | 0.00 | 0.00 | 4.26 |
1201 | 1582 | 4.810191 | TTCTTCTTCTCCCTTAGCTCAC | 57.190 | 45.455 | 0.00 | 0.00 | 0.00 | 3.51 |
1203 | 1584 | 3.511934 | TCTTCTTCTCCCTTAGCTCACAC | 59.488 | 47.826 | 0.00 | 0.00 | 0.00 | 3.82 |
1206 | 1587 | 1.561643 | TCTCCCTTAGCTCACACCTG | 58.438 | 55.000 | 0.00 | 0.00 | 0.00 | 4.00 |
1209 | 1590 | 0.976641 | CCCTTAGCTCACACCTGACA | 59.023 | 55.000 | 0.00 | 0.00 | 0.00 | 3.58 |
1211 | 1596 | 2.026822 | CCCTTAGCTCACACCTGACAAT | 60.027 | 50.000 | 0.00 | 0.00 | 0.00 | 2.71 |
1213 | 1598 | 2.654749 | TAGCTCACACCTGACAATCG | 57.345 | 50.000 | 0.00 | 0.00 | 0.00 | 3.34 |
1217 | 1602 | 0.037326 | TCACACCTGACAATCGGAGC | 60.037 | 55.000 | 0.00 | 0.00 | 0.00 | 4.70 |
1222 | 1607 | 2.434185 | TGACAATCGGAGCGGCAC | 60.434 | 61.111 | 1.45 | 0.00 | 0.00 | 5.01 |
1226 | 1611 | 2.040544 | CAATCGGAGCGGCACCTTT | 61.041 | 57.895 | 14.50 | 5.43 | 0.00 | 3.11 |
1228 | 1613 | 0.893727 | AATCGGAGCGGCACCTTTTT | 60.894 | 50.000 | 14.50 | 2.75 | 0.00 | 1.94 |
1230 | 1615 | 1.966451 | CGGAGCGGCACCTTTTTCT | 60.966 | 57.895 | 14.50 | 0.00 | 0.00 | 2.52 |
1231 | 1616 | 1.581447 | GGAGCGGCACCTTTTTCTG | 59.419 | 57.895 | 9.34 | 0.00 | 0.00 | 3.02 |
1232 | 1617 | 1.081175 | GAGCGGCACCTTTTTCTGC | 60.081 | 57.895 | 1.45 | 0.00 | 0.00 | 4.26 |
1299 | 1686 | 2.356313 | CGAAGCTGACGGTGCAGT | 60.356 | 61.111 | 5.79 | 0.00 | 38.17 | 4.40 |
1358 | 1745 | 2.029844 | GAGCCACTGCGACTTCACC | 61.030 | 63.158 | 0.00 | 0.00 | 44.33 | 4.02 |
1514 | 1901 | 3.349006 | CACCTGCACTGCCACGTC | 61.349 | 66.667 | 0.00 | 0.00 | 0.00 | 4.34 |
1653 | 2040 | 4.147449 | CCGAGCTCATGGACGCCA | 62.147 | 66.667 | 15.40 | 1.01 | 38.19 | 5.69 |
1655 | 2042 | 2.202987 | GAGCTCATGGACGCCAGG | 60.203 | 66.667 | 9.40 | 4.47 | 36.75 | 4.45 |
1658 | 2045 | 2.124983 | CTCATGGACGCCAGGGTG | 60.125 | 66.667 | 9.95 | 0.00 | 36.75 | 4.61 |
1736 | 2123 | 4.077184 | CGCGAGGCCACCAAGGTA | 62.077 | 66.667 | 5.01 | 0.00 | 40.61 | 3.08 |
1737 | 2124 | 2.125106 | GCGAGGCCACCAAGGTAG | 60.125 | 66.667 | 5.01 | 0.00 | 40.61 | 3.18 |
1738 | 2125 | 2.955881 | GCGAGGCCACCAAGGTAGT | 61.956 | 63.158 | 5.01 | 0.00 | 40.61 | 2.73 |
1739 | 2126 | 1.079127 | CGAGGCCACCAAGGTAGTG | 60.079 | 63.158 | 5.01 | 0.00 | 40.61 | 2.74 |
1740 | 2127 | 1.377333 | GAGGCCACCAAGGTAGTGC | 60.377 | 63.158 | 5.01 | 0.00 | 40.61 | 4.40 |
1741 | 2128 | 1.842381 | GAGGCCACCAAGGTAGTGCT | 61.842 | 60.000 | 5.01 | 0.00 | 40.61 | 4.40 |
1742 | 2129 | 1.074951 | GGCCACCAAGGTAGTGCTT | 59.925 | 57.895 | 0.00 | 0.00 | 40.61 | 3.91 |
1743 | 2130 | 0.960861 | GGCCACCAAGGTAGTGCTTC | 60.961 | 60.000 | 0.00 | 0.00 | 40.61 | 3.86 |
1744 | 2131 | 0.036875 | GCCACCAAGGTAGTGCTTCT | 59.963 | 55.000 | 0.00 | 0.00 | 40.61 | 2.85 |
1745 | 2132 | 1.545651 | GCCACCAAGGTAGTGCTTCTT | 60.546 | 52.381 | 0.00 | 0.00 | 40.61 | 2.52 |
1746 | 2133 | 2.427506 | CCACCAAGGTAGTGCTTCTTC | 58.572 | 52.381 | 0.00 | 0.00 | 33.75 | 2.87 |
1747 | 2134 | 2.224523 | CCACCAAGGTAGTGCTTCTTCA | 60.225 | 50.000 | 0.00 | 0.00 | 33.75 | 3.02 |
1748 | 2135 | 3.560025 | CCACCAAGGTAGTGCTTCTTCAT | 60.560 | 47.826 | 0.00 | 0.00 | 33.75 | 2.57 |
1762 | 2149 | 4.162131 | GCTTCTTCATCTTCTTCCTCCTCT | 59.838 | 45.833 | 0.00 | 0.00 | 0.00 | 3.69 |
1772 | 2159 | 3.102972 | TCTTCCTCCTCTTCTGTCATGG | 58.897 | 50.000 | 0.00 | 0.00 | 0.00 | 3.66 |
1786 | 2204 | 6.048732 | TCTGTCATGGTTTGCATCTACTAA | 57.951 | 37.500 | 0.00 | 0.00 | 0.00 | 2.24 |
1788 | 2206 | 7.112122 | TCTGTCATGGTTTGCATCTACTAATT | 58.888 | 34.615 | 0.00 | 0.00 | 0.00 | 1.40 |
1791 | 2209 | 6.968904 | GTCATGGTTTGCATCTACTAATTGTG | 59.031 | 38.462 | 0.00 | 0.00 | 0.00 | 3.33 |
1792 | 2210 | 6.883756 | TCATGGTTTGCATCTACTAATTGTGA | 59.116 | 34.615 | 0.00 | 0.00 | 0.00 | 3.58 |
1793 | 2211 | 7.392953 | TCATGGTTTGCATCTACTAATTGTGAA | 59.607 | 33.333 | 0.00 | 0.00 | 0.00 | 3.18 |
1794 | 2212 | 7.701539 | TGGTTTGCATCTACTAATTGTGAAT | 57.298 | 32.000 | 0.00 | 0.00 | 0.00 | 2.57 |
1838 | 2256 | 1.084018 | ATTCTGATGTGGTTGGGGGT | 58.916 | 50.000 | 0.00 | 0.00 | 0.00 | 4.95 |
1839 | 2257 | 0.856982 | TTCTGATGTGGTTGGGGGTT | 59.143 | 50.000 | 0.00 | 0.00 | 0.00 | 4.11 |
1912 | 2330 | 1.098129 | CCAGAGCGAGATCACCGAGA | 61.098 | 60.000 | 11.02 | 0.00 | 0.00 | 4.04 |
1920 | 2338 | 1.332375 | GAGATCACCGAGAGACGAAGG | 59.668 | 57.143 | 0.00 | 0.00 | 45.77 | 3.46 |
1967 | 2385 | 2.034685 | TCTCGTTTCTGCTATGATCGGG | 59.965 | 50.000 | 0.00 | 0.00 | 0.00 | 5.14 |
2023 | 2459 | 5.923204 | TGAGAAAGATTTGAGAGATAGGGC | 58.077 | 41.667 | 0.00 | 0.00 | 0.00 | 5.19 |
2024 | 2460 | 4.954875 | AGAAAGATTTGAGAGATAGGGCG | 58.045 | 43.478 | 0.00 | 0.00 | 0.00 | 6.13 |
2025 | 2461 | 2.829741 | AGATTTGAGAGATAGGGCGC | 57.170 | 50.000 | 0.00 | 0.00 | 0.00 | 6.53 |
2046 | 2505 | 5.546434 | CGCGAAAGAGAGAAAGAAAGAATC | 58.454 | 41.667 | 0.00 | 0.00 | 0.00 | 2.52 |
2133 | 2595 | 5.544176 | AGGAACTCTAGACACCATTCTTCAA | 59.456 | 40.000 | 0.00 | 0.00 | 0.00 | 2.69 |
2141 | 2603 | 6.814506 | AGACACCATTCTTCAATTCTTGAG | 57.185 | 37.500 | 0.00 | 0.00 | 41.38 | 3.02 |
2153 | 2621 | 9.383519 | TCTTCAATTCTTGAGATGTACATTACC | 57.616 | 33.333 | 10.30 | 3.22 | 41.38 | 2.85 |
2154 | 2622 | 9.166173 | CTTCAATTCTTGAGATGTACATTACCA | 57.834 | 33.333 | 10.30 | 5.81 | 41.38 | 3.25 |
2155 | 2623 | 9.513906 | TTCAATTCTTGAGATGTACATTACCAA | 57.486 | 29.630 | 10.30 | 12.64 | 41.38 | 3.67 |
2157 | 2625 | 7.865706 | ATTCTTGAGATGTACATTACCAACC | 57.134 | 36.000 | 10.30 | 0.00 | 0.00 | 3.77 |
2159 | 2627 | 6.774673 | TCTTGAGATGTACATTACCAACCAA | 58.225 | 36.000 | 10.30 | 6.17 | 0.00 | 3.67 |
2160 | 2628 | 7.227873 | TCTTGAGATGTACATTACCAACCAAA | 58.772 | 34.615 | 10.30 | 0.00 | 0.00 | 3.28 |
2161 | 2629 | 7.390440 | TCTTGAGATGTACATTACCAACCAAAG | 59.610 | 37.037 | 10.30 | 6.22 | 0.00 | 2.77 |
2162 | 2630 | 6.539173 | TGAGATGTACATTACCAACCAAAGT | 58.461 | 36.000 | 10.30 | 0.00 | 0.00 | 2.66 |
2202 | 2685 | 3.011708 | AGCATTTCACCCCCTGTTTATCT | 59.988 | 43.478 | 0.00 | 0.00 | 0.00 | 1.98 |
2207 | 2690 | 5.789574 | TTCACCCCCTGTTTATCTAATGT | 57.210 | 39.130 | 0.00 | 0.00 | 0.00 | 2.71 |
2209 | 2692 | 6.147437 | TCACCCCCTGTTTATCTAATGTTT | 57.853 | 37.500 | 0.00 | 0.00 | 0.00 | 2.83 |
2232 | 2715 | 8.487176 | GTTTACGACATTTGCTGATTTGATTTT | 58.513 | 29.630 | 0.00 | 0.00 | 0.00 | 1.82 |
2237 | 2720 | 8.862074 | CGACATTTGCTGATTTGATTTTGATTA | 58.138 | 29.630 | 0.00 | 0.00 | 0.00 | 1.75 |
2244 | 2727 | 9.932207 | TGCTGATTTGATTTTGATTATTGTTCT | 57.068 | 25.926 | 0.00 | 0.00 | 0.00 | 3.01 |
2256 | 2739 | 5.803461 | TGATTATTGTTCTTCAGTACCGTCG | 59.197 | 40.000 | 0.00 | 0.00 | 0.00 | 5.12 |
2268 | 2751 | 4.083643 | TCAGTACCGTCGTCTGTTTTCTAG | 60.084 | 45.833 | 8.42 | 0.00 | 0.00 | 2.43 |
2269 | 2752 | 3.817647 | AGTACCGTCGTCTGTTTTCTAGT | 59.182 | 43.478 | 0.00 | 0.00 | 0.00 | 2.57 |
2270 | 2753 | 4.997395 | AGTACCGTCGTCTGTTTTCTAGTA | 59.003 | 41.667 | 0.00 | 0.00 | 0.00 | 1.82 |
2272 | 2755 | 4.979388 | ACCGTCGTCTGTTTTCTAGTATC | 58.021 | 43.478 | 0.00 | 0.00 | 0.00 | 2.24 |
2275 | 2758 | 6.091437 | CCGTCGTCTGTTTTCTAGTATCTTT | 58.909 | 40.000 | 0.00 | 0.00 | 0.00 | 2.52 |
2276 | 2759 | 7.094634 | ACCGTCGTCTGTTTTCTAGTATCTTTA | 60.095 | 37.037 | 0.00 | 0.00 | 0.00 | 1.85 |
2278 | 2761 | 7.961827 | CGTCGTCTGTTTTCTAGTATCTTTACT | 59.038 | 37.037 | 0.00 | 0.00 | 41.57 | 2.24 |
2284 | 2776 | 9.360093 | CTGTTTTCTAGTATCTTTACTCACCAG | 57.640 | 37.037 | 0.00 | 0.00 | 39.42 | 4.00 |
2295 | 2787 | 0.533755 | ACTCACCAGTCTTGCTGCAC | 60.534 | 55.000 | 0.00 | 0.00 | 43.71 | 4.57 |
2316 | 2808 | 9.149225 | CTGCACATTTCTCAAGATATATACCTC | 57.851 | 37.037 | 0.00 | 0.00 | 0.00 | 3.85 |
2317 | 2809 | 8.097038 | TGCACATTTCTCAAGATATATACCTCC | 58.903 | 37.037 | 0.00 | 0.00 | 0.00 | 4.30 |
2318 | 2810 | 7.276658 | GCACATTTCTCAAGATATATACCTCCG | 59.723 | 40.741 | 0.00 | 0.00 | 0.00 | 4.63 |
2319 | 2811 | 8.523658 | CACATTTCTCAAGATATATACCTCCGA | 58.476 | 37.037 | 0.00 | 0.00 | 0.00 | 4.55 |
2320 | 2812 | 9.261035 | ACATTTCTCAAGATATATACCTCCGAT | 57.739 | 33.333 | 0.00 | 0.00 | 0.00 | 4.18 |
2328 | 2820 | 8.478066 | CAAGATATATACCTCCGATCCAATTGA | 58.522 | 37.037 | 7.12 | 0.00 | 0.00 | 2.57 |
2346 | 2838 | 6.094603 | CCAATTGAGTTTCAGGACTGGATAAG | 59.905 | 42.308 | 7.12 | 0.00 | 0.00 | 1.73 |
2354 | 2852 | 1.842562 | AGGACTGGATAAGCACAGCAT | 59.157 | 47.619 | 0.00 | 0.00 | 38.25 | 3.79 |
2355 | 2853 | 1.945394 | GGACTGGATAAGCACAGCATG | 59.055 | 52.381 | 0.00 | 0.00 | 46.00 | 4.06 |
2373 | 2908 | 6.286758 | CAGCATGTGTCTTAATCCTCTATGT | 58.713 | 40.000 | 0.00 | 0.00 | 0.00 | 2.29 |
2380 | 2915 | 9.197306 | TGTGTCTTAATCCTCTATGTTAAGCTA | 57.803 | 33.333 | 0.00 | 0.00 | 36.09 | 3.32 |
2381 | 2916 | 9.685828 | GTGTCTTAATCCTCTATGTTAAGCTAG | 57.314 | 37.037 | 0.00 | 0.00 | 36.09 | 3.42 |
2382 | 2917 | 8.361139 | TGTCTTAATCCTCTATGTTAAGCTAGC | 58.639 | 37.037 | 6.62 | 6.62 | 36.09 | 3.42 |
2383 | 2918 | 8.581578 | GTCTTAATCCTCTATGTTAAGCTAGCT | 58.418 | 37.037 | 12.68 | 12.68 | 36.09 | 3.32 |
2384 | 2919 | 8.580720 | TCTTAATCCTCTATGTTAAGCTAGCTG | 58.419 | 37.037 | 20.16 | 3.56 | 36.09 | 4.24 |
2385 | 2920 | 4.592485 | TCCTCTATGTTAAGCTAGCTGC | 57.408 | 45.455 | 20.16 | 12.31 | 43.29 | 5.25 |
2435 | 2978 | 2.276201 | GTTTCAAGGTTTGTTGGTGGC | 58.724 | 47.619 | 0.00 | 0.00 | 0.00 | 5.01 |
2450 | 2993 | 2.890311 | TGGTGGCAAATTTACAGTCAGG | 59.110 | 45.455 | 0.00 | 0.00 | 0.00 | 3.86 |
2469 | 3012 | 3.312421 | CAGGTTAGATTGTTGCGTATGGG | 59.688 | 47.826 | 0.00 | 0.00 | 0.00 | 4.00 |
2470 | 3013 | 2.032924 | GGTTAGATTGTTGCGTATGGGC | 59.967 | 50.000 | 0.00 | 0.00 | 0.00 | 5.36 |
2471 | 3014 | 2.680841 | GTTAGATTGTTGCGTATGGGCA | 59.319 | 45.455 | 0.00 | 0.00 | 42.12 | 5.36 |
2472 | 3015 | 2.057137 | AGATTGTTGCGTATGGGCAT | 57.943 | 45.000 | 0.00 | 0.00 | 43.52 | 4.40 |
2473 | 3016 | 1.677576 | AGATTGTTGCGTATGGGCATG | 59.322 | 47.619 | 0.00 | 0.00 | 43.52 | 4.06 |
2474 | 3017 | 0.746063 | ATTGTTGCGTATGGGCATGG | 59.254 | 50.000 | 0.00 | 0.00 | 43.52 | 3.66 |
2475 | 3018 | 1.943116 | TTGTTGCGTATGGGCATGGC | 61.943 | 55.000 | 11.56 | 11.56 | 43.52 | 4.40 |
2476 | 3019 | 2.120909 | GTTGCGTATGGGCATGGCT | 61.121 | 57.895 | 19.78 | 2.39 | 43.52 | 4.75 |
2477 | 3020 | 1.823470 | TTGCGTATGGGCATGGCTC | 60.823 | 57.895 | 19.78 | 9.85 | 43.52 | 4.70 |
2478 | 3021 | 2.203195 | GCGTATGGGCATGGCTCA | 60.203 | 61.111 | 19.78 | 15.27 | 45.75 | 4.26 |
2479 | 3022 | 2.256591 | GCGTATGGGCATGGCTCAG | 61.257 | 63.158 | 19.78 | 7.67 | 44.52 | 3.35 |
2480 | 3023 | 1.447217 | CGTATGGGCATGGCTCAGA | 59.553 | 57.895 | 19.78 | 9.87 | 44.52 | 3.27 |
2481 | 3024 | 0.882042 | CGTATGGGCATGGCTCAGAC | 60.882 | 60.000 | 19.78 | 19.22 | 44.52 | 3.51 |
2482 | 3025 | 0.471617 | GTATGGGCATGGCTCAGACT | 59.528 | 55.000 | 19.78 | 3.77 | 46.25 | 3.24 |
2483 | 3026 | 0.471191 | TATGGGCATGGCTCAGACTG | 59.529 | 55.000 | 19.78 | 0.00 | 44.52 | 3.51 |
2484 | 3027 | 1.569030 | ATGGGCATGGCTCAGACTGT | 61.569 | 55.000 | 19.78 | 0.00 | 44.52 | 3.55 |
2485 | 3028 | 1.001641 | GGGCATGGCTCAGACTGTT | 60.002 | 57.895 | 19.78 | 0.00 | 0.00 | 3.16 |
2486 | 3029 | 0.253044 | GGGCATGGCTCAGACTGTTA | 59.747 | 55.000 | 19.78 | 0.00 | 0.00 | 2.41 |
2487 | 3030 | 1.133976 | GGGCATGGCTCAGACTGTTAT | 60.134 | 52.381 | 19.78 | 0.00 | 0.00 | 1.89 |
2492 | 3035 | 0.464554 | GGCTCAGACTGTTATGCCCC | 60.465 | 60.000 | 15.39 | 0.96 | 34.81 | 5.80 |
2521 | 3064 | 3.951663 | AGTTTAGCCCGCAAGTTATCTT | 58.048 | 40.909 | 0.00 | 0.00 | 0.00 | 2.40 |
2642 | 3185 | 1.918467 | AACCCTAAACCCTAGCCGCC | 61.918 | 60.000 | 0.00 | 0.00 | 0.00 | 6.13 |
2647 | 3190 | 1.209747 | CTAAACCCTAGCCGCCTCTTT | 59.790 | 52.381 | 0.00 | 0.00 | 0.00 | 2.52 |
2648 | 3191 | 0.035343 | AAACCCTAGCCGCCTCTTTC | 60.035 | 55.000 | 0.00 | 0.00 | 0.00 | 2.62 |
2653 | 3196 | 0.537188 | CTAGCCGCCTCTTTCCTTCA | 59.463 | 55.000 | 0.00 | 0.00 | 0.00 | 3.02 |
2654 | 3197 | 0.537188 | TAGCCGCCTCTTTCCTTCAG | 59.463 | 55.000 | 0.00 | 0.00 | 0.00 | 3.02 |
2696 | 3271 | 4.016706 | CGCCCACCTCCCTCGTTT | 62.017 | 66.667 | 0.00 | 0.00 | 0.00 | 3.60 |
2704 | 3279 | 0.824759 | CCTCCCTCGTTTCCCTACAG | 59.175 | 60.000 | 0.00 | 0.00 | 0.00 | 2.74 |
2719 | 3294 | 0.251354 | TACAGCCTACGTCCGAGACT | 59.749 | 55.000 | 0.00 | 0.00 | 0.00 | 3.24 |
2770 | 3345 | 2.370281 | TCAGCTAGCTTGGTTTCGAG | 57.630 | 50.000 | 16.46 | 0.00 | 0.00 | 4.04 |
2793 | 3368 | 1.385347 | TCCTCACCACCACCAACCT | 60.385 | 57.895 | 0.00 | 0.00 | 0.00 | 3.50 |
2795 | 3370 | 1.301716 | CTCACCACCACCAACCTCG | 60.302 | 63.158 | 0.00 | 0.00 | 0.00 | 4.63 |
2838 | 3413 | 2.104132 | CCGTGACATCGCCGATCA | 59.896 | 61.111 | 0.00 | 0.00 | 0.00 | 2.92 |
2842 | 3417 | 0.530650 | GTGACATCGCCGATCACCAT | 60.531 | 55.000 | 9.19 | 0.00 | 37.39 | 3.55 |
2947 | 3522 | 2.272146 | GCCATCACCGTCCACCAT | 59.728 | 61.111 | 0.00 | 0.00 | 0.00 | 3.55 |
2951 | 3526 | 3.680620 | ATCACCGTCCACCATGCCG | 62.681 | 63.158 | 0.00 | 0.00 | 0.00 | 5.69 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
2 | 3 | 3.961414 | GGTGGCCGGAACTTGGGA | 61.961 | 66.667 | 5.05 | 0.00 | 0.00 | 4.37 |
9 | 10 | 1.529713 | GTTTTCCTGGTGGCCGGAA | 60.530 | 57.895 | 5.05 | 5.78 | 35.57 | 4.30 |
47 | 48 | 4.722700 | GGAAGCTTGGGGCAGCGA | 62.723 | 66.667 | 2.10 | 0.00 | 45.24 | 4.93 |
51 | 52 | 3.506743 | TGGTGGAAGCTTGGGGCA | 61.507 | 61.111 | 2.10 | 0.00 | 44.79 | 5.36 |
65 | 66 | 0.106918 | TCGGAAGTTTTGCTGGTGGT | 60.107 | 50.000 | 0.00 | 0.00 | 0.00 | 4.16 |
89 | 90 | 3.998672 | GGGCGGTGGTGAAGACGA | 61.999 | 66.667 | 0.00 | 0.00 | 0.00 | 4.20 |
124 | 125 | 0.251165 | GCAAAGGCTACCAACCCAGA | 60.251 | 55.000 | 0.00 | 0.00 | 36.96 | 3.86 |
130 | 131 | 9.802468 | AACATGAGTTCTAGCAAAGGCTACCAA | 62.802 | 40.741 | 0.00 | 0.00 | 46.65 | 3.67 |
148 | 149 | 0.998928 | TGCACCCCCATAACATGAGT | 59.001 | 50.000 | 0.00 | 0.00 | 0.00 | 3.41 |
156 | 157 | 3.752622 | TGCTCATGCACCCCCATA | 58.247 | 55.556 | 0.00 | 0.00 | 45.31 | 2.74 |
240 | 249 | 2.320781 | CTATAGGGTGCACTAGTGGCT | 58.679 | 52.381 | 23.95 | 4.00 | 0.00 | 4.75 |
262 | 272 | 2.238144 | AGCCTCAATCAAGAGCTGCTAA | 59.762 | 45.455 | 0.15 | 0.00 | 33.33 | 3.09 |
287 | 297 | 4.853743 | GCTCAACTTTACTTGCTGCATAAC | 59.146 | 41.667 | 1.84 | 0.00 | 0.00 | 1.89 |
293 | 303 | 2.351157 | GCCAGCTCAACTTTACTTGCTG | 60.351 | 50.000 | 0.00 | 0.00 | 44.97 | 4.41 |
300 | 310 | 0.476338 | TGGTGGCCAGCTCAACTTTA | 59.524 | 50.000 | 33.29 | 9.88 | 0.00 | 1.85 |
301 | 311 | 0.396974 | TTGGTGGCCAGCTCAACTTT | 60.397 | 50.000 | 33.29 | 0.00 | 33.81 | 2.66 |
302 | 312 | 1.109323 | GTTGGTGGCCAGCTCAACTT | 61.109 | 55.000 | 33.29 | 0.00 | 37.21 | 2.66 |
304 | 314 | 1.181098 | ATGTTGGTGGCCAGCTCAAC | 61.181 | 55.000 | 33.29 | 29.45 | 39.68 | 3.18 |
305 | 315 | 0.895100 | GATGTTGGTGGCCAGCTCAA | 60.895 | 55.000 | 33.29 | 21.42 | 35.72 | 3.02 |
306 | 316 | 1.303561 | GATGTTGGTGGCCAGCTCA | 60.304 | 57.895 | 33.29 | 29.15 | 35.72 | 4.26 |
307 | 317 | 0.610232 | AAGATGTTGGTGGCCAGCTC | 60.610 | 55.000 | 33.29 | 25.15 | 35.72 | 4.09 |
308 | 318 | 0.698238 | TAAGATGTTGGTGGCCAGCT | 59.302 | 50.000 | 33.29 | 15.37 | 35.72 | 4.24 |
309 | 319 | 0.811281 | GTAAGATGTTGGTGGCCAGC | 59.189 | 55.000 | 28.15 | 28.15 | 33.81 | 4.85 |
310 | 320 | 2.198827 | TGTAAGATGTTGGTGGCCAG | 57.801 | 50.000 | 5.11 | 0.00 | 33.81 | 4.85 |
311 | 321 | 2.308570 | AGATGTAAGATGTTGGTGGCCA | 59.691 | 45.455 | 0.00 | 0.00 | 0.00 | 5.36 |
312 | 322 | 2.684881 | CAGATGTAAGATGTTGGTGGCC | 59.315 | 50.000 | 0.00 | 0.00 | 0.00 | 5.36 |
327 | 337 | 4.955811 | TGTGGAGTAACTTCACAGATGT | 57.044 | 40.909 | 5.02 | 0.00 | 44.11 | 3.06 |
332 | 342 | 4.081365 | TGTGAACTGTGGAGTAACTTCACA | 60.081 | 41.667 | 8.57 | 8.57 | 46.44 | 3.58 |
333 | 343 | 4.439057 | TGTGAACTGTGGAGTAACTTCAC | 58.561 | 43.478 | 0.00 | 0.00 | 40.21 | 3.18 |
342 | 352 | 0.962356 | GGGCCATGTGAACTGTGGAG | 60.962 | 60.000 | 4.39 | 0.00 | 34.94 | 3.86 |
355 | 365 | 6.494146 | ACAAAATTTTCATTTTCATGGGCCAT | 59.506 | 30.769 | 14.78 | 14.78 | 40.09 | 4.40 |
422 | 449 | 5.309806 | AGGAGTACAATGAGTTTACAGGGTT | 59.690 | 40.000 | 0.00 | 0.00 | 0.00 | 4.11 |
552 | 584 | 9.394767 | TCTAACAATCATCTAAAAATGCTGCTA | 57.605 | 29.630 | 0.00 | 0.00 | 0.00 | 3.49 |
553 | 585 | 8.284945 | TCTAACAATCATCTAAAAATGCTGCT | 57.715 | 30.769 | 0.00 | 0.00 | 0.00 | 4.24 |
554 | 586 | 8.965172 | CATCTAACAATCATCTAAAAATGCTGC | 58.035 | 33.333 | 0.00 | 0.00 | 0.00 | 5.25 |
555 | 587 | 8.965172 | GCATCTAACAATCATCTAAAAATGCTG | 58.035 | 33.333 | 0.00 | 0.00 | 33.62 | 4.41 |
556 | 588 | 8.139989 | GGCATCTAACAATCATCTAAAAATGCT | 58.860 | 33.333 | 0.00 | 0.00 | 35.97 | 3.79 |
557 | 589 | 7.383300 | GGGCATCTAACAATCATCTAAAAATGC | 59.617 | 37.037 | 0.00 | 0.00 | 35.17 | 3.56 |
558 | 590 | 8.636213 | AGGGCATCTAACAATCATCTAAAAATG | 58.364 | 33.333 | 0.00 | 0.00 | 0.00 | 2.32 |
559 | 591 | 8.773033 | AGGGCATCTAACAATCATCTAAAAAT | 57.227 | 30.769 | 0.00 | 0.00 | 0.00 | 1.82 |
560 | 592 | 8.593945 | AAGGGCATCTAACAATCATCTAAAAA | 57.406 | 30.769 | 0.00 | 0.00 | 0.00 | 1.94 |
561 | 593 | 9.693739 | TTAAGGGCATCTAACAATCATCTAAAA | 57.306 | 29.630 | 0.00 | 0.00 | 0.00 | 1.52 |
562 | 594 | 9.866655 | ATTAAGGGCATCTAACAATCATCTAAA | 57.133 | 29.630 | 0.00 | 0.00 | 0.00 | 1.85 |
563 | 595 | 9.288576 | CATTAAGGGCATCTAACAATCATCTAA | 57.711 | 33.333 | 0.00 | 0.00 | 0.00 | 2.10 |
576 | 608 | 2.780010 | ACCAGCTACATTAAGGGCATCT | 59.220 | 45.455 | 0.00 | 0.00 | 0.00 | 2.90 |
577 | 609 | 3.214696 | ACCAGCTACATTAAGGGCATC | 57.785 | 47.619 | 0.00 | 0.00 | 0.00 | 3.91 |
578 | 610 | 3.669939 | AACCAGCTACATTAAGGGCAT | 57.330 | 42.857 | 0.00 | 0.00 | 0.00 | 4.40 |
579 | 611 | 3.088532 | CAAACCAGCTACATTAAGGGCA | 58.911 | 45.455 | 0.00 | 0.00 | 0.00 | 5.36 |
581 | 613 | 4.843728 | TCTCAAACCAGCTACATTAAGGG | 58.156 | 43.478 | 0.00 | 0.00 | 0.00 | 3.95 |
585 | 942 | 6.206634 | CCAGTTTTCTCAAACCAGCTACATTA | 59.793 | 38.462 | 0.00 | 0.00 | 43.08 | 1.90 |
586 | 943 | 5.010012 | CCAGTTTTCTCAAACCAGCTACATT | 59.990 | 40.000 | 0.00 | 0.00 | 43.08 | 2.71 |
598 | 955 | 2.374184 | CACCACACCCAGTTTTCTCAA | 58.626 | 47.619 | 0.00 | 0.00 | 0.00 | 3.02 |
644 | 1004 | 2.520069 | TGGATAACGCAACACCCAATT | 58.480 | 42.857 | 0.00 | 0.00 | 0.00 | 2.32 |
653 | 1013 | 1.202279 | GCACATGCATGGATAACGCAA | 60.202 | 47.619 | 29.41 | 0.00 | 39.48 | 4.85 |
753 | 1113 | 2.685743 | TGCCGCTTGCCCCTAGTA | 60.686 | 61.111 | 0.00 | 0.00 | 40.16 | 1.82 |
1160 | 1541 | 5.244755 | AGAAAGGAAGAAGAAGCAAGCTAG | 58.755 | 41.667 | 0.00 | 0.00 | 0.00 | 3.42 |
1163 | 1544 | 4.518590 | AGAAGAAAGGAAGAAGAAGCAAGC | 59.481 | 41.667 | 0.00 | 0.00 | 0.00 | 4.01 |
1178 | 1559 | 5.175127 | GTGAGCTAAGGGAGAAGAAGAAAG | 58.825 | 45.833 | 0.00 | 0.00 | 0.00 | 2.62 |
1190 | 1571 | 0.976641 | TGTCAGGTGTGAGCTAAGGG | 59.023 | 55.000 | 0.00 | 0.00 | 31.53 | 3.95 |
1191 | 1572 | 2.839486 | TTGTCAGGTGTGAGCTAAGG | 57.161 | 50.000 | 0.00 | 0.00 | 31.53 | 2.69 |
1192 | 1573 | 2.926200 | CGATTGTCAGGTGTGAGCTAAG | 59.074 | 50.000 | 0.00 | 0.00 | 31.53 | 2.18 |
1194 | 1575 | 1.204704 | CCGATTGTCAGGTGTGAGCTA | 59.795 | 52.381 | 0.00 | 0.00 | 31.53 | 3.32 |
1195 | 1576 | 0.036952 | CCGATTGTCAGGTGTGAGCT | 60.037 | 55.000 | 0.00 | 0.00 | 31.53 | 4.09 |
1196 | 1577 | 0.037326 | TCCGATTGTCAGGTGTGAGC | 60.037 | 55.000 | 0.00 | 0.00 | 31.53 | 4.26 |
1198 | 1579 | 0.037326 | GCTCCGATTGTCAGGTGTGA | 60.037 | 55.000 | 0.00 | 0.00 | 0.00 | 3.58 |
1199 | 1580 | 1.354337 | CGCTCCGATTGTCAGGTGTG | 61.354 | 60.000 | 0.00 | 0.00 | 0.00 | 3.82 |
1200 | 1581 | 1.079819 | CGCTCCGATTGTCAGGTGT | 60.080 | 57.895 | 0.00 | 0.00 | 0.00 | 4.16 |
1201 | 1582 | 1.811266 | CCGCTCCGATTGTCAGGTG | 60.811 | 63.158 | 0.00 | 0.00 | 0.00 | 4.00 |
1203 | 1584 | 2.892425 | GCCGCTCCGATTGTCAGG | 60.892 | 66.667 | 0.00 | 0.00 | 0.00 | 3.86 |
1206 | 1587 | 3.195698 | GGTGCCGCTCCGATTGTC | 61.196 | 66.667 | 0.00 | 0.00 | 0.00 | 3.18 |
1209 | 1590 | 0.893727 | AAAAAGGTGCCGCTCCGATT | 60.894 | 50.000 | 5.84 | 3.26 | 0.00 | 3.34 |
1211 | 1596 | 1.964373 | GAAAAAGGTGCCGCTCCGA | 60.964 | 57.895 | 5.84 | 0.00 | 0.00 | 4.55 |
1213 | 1598 | 1.581447 | CAGAAAAAGGTGCCGCTCC | 59.419 | 57.895 | 3.10 | 3.10 | 0.00 | 4.70 |
1217 | 1602 | 0.239347 | CAGAGCAGAAAAAGGTGCCG | 59.761 | 55.000 | 0.00 | 0.00 | 40.81 | 5.69 |
1222 | 1607 | 2.157738 | CCTGGACAGAGCAGAAAAAGG | 58.842 | 52.381 | 0.00 | 0.00 | 0.00 | 3.11 |
1226 | 1611 | 1.004560 | CGCCTGGACAGAGCAGAAA | 60.005 | 57.895 | 0.00 | 0.00 | 0.00 | 2.52 |
1228 | 1613 | 3.385384 | CCGCCTGGACAGAGCAGA | 61.385 | 66.667 | 0.00 | 0.00 | 37.49 | 4.26 |
1376 | 1763 | 1.153823 | CGTGATGGTCTCCGACACC | 60.154 | 63.158 | 0.00 | 0.00 | 33.68 | 4.16 |
1436 | 1823 | 1.153745 | CTCCTTCCACTCGGCGAAG | 60.154 | 63.158 | 12.13 | 4.63 | 36.13 | 3.79 |
1481 | 1868 | 2.685017 | TGCAGCGTCATCTCCCCT | 60.685 | 61.111 | 0.00 | 0.00 | 0.00 | 4.79 |
1547 | 1934 | 4.421365 | ACGTAGTAGCGGAACCCA | 57.579 | 55.556 | 0.00 | 0.00 | 41.94 | 4.51 |
1653 | 2040 | 2.515901 | GAAGTGCACCCACACCCT | 59.484 | 61.111 | 14.63 | 0.00 | 44.53 | 4.34 |
1655 | 2042 | 2.194597 | TGGAAGTGCACCCACACC | 59.805 | 61.111 | 14.63 | 10.46 | 44.53 | 4.16 |
1736 | 2123 | 4.323409 | GGAGGAAGAAGATGAAGAAGCACT | 60.323 | 45.833 | 0.00 | 0.00 | 0.00 | 4.40 |
1737 | 2124 | 3.938334 | GGAGGAAGAAGATGAAGAAGCAC | 59.062 | 47.826 | 0.00 | 0.00 | 0.00 | 4.40 |
1738 | 2125 | 3.843027 | AGGAGGAAGAAGATGAAGAAGCA | 59.157 | 43.478 | 0.00 | 0.00 | 0.00 | 3.91 |
1739 | 2126 | 4.162131 | AGAGGAGGAAGAAGATGAAGAAGC | 59.838 | 45.833 | 0.00 | 0.00 | 0.00 | 3.86 |
1740 | 2127 | 5.937975 | AGAGGAGGAAGAAGATGAAGAAG | 57.062 | 43.478 | 0.00 | 0.00 | 0.00 | 2.85 |
1741 | 2128 | 6.022315 | AGAAGAGGAGGAAGAAGATGAAGAA | 58.978 | 40.000 | 0.00 | 0.00 | 0.00 | 2.52 |
1742 | 2129 | 5.421693 | CAGAAGAGGAGGAAGAAGATGAAGA | 59.578 | 44.000 | 0.00 | 0.00 | 0.00 | 2.87 |
1743 | 2130 | 5.187576 | ACAGAAGAGGAGGAAGAAGATGAAG | 59.812 | 44.000 | 0.00 | 0.00 | 0.00 | 3.02 |
1744 | 2131 | 5.090139 | ACAGAAGAGGAGGAAGAAGATGAA | 58.910 | 41.667 | 0.00 | 0.00 | 0.00 | 2.57 |
1745 | 2132 | 4.682563 | ACAGAAGAGGAGGAAGAAGATGA | 58.317 | 43.478 | 0.00 | 0.00 | 0.00 | 2.92 |
1746 | 2133 | 4.465660 | TGACAGAAGAGGAGGAAGAAGATG | 59.534 | 45.833 | 0.00 | 0.00 | 0.00 | 2.90 |
1747 | 2134 | 4.682563 | TGACAGAAGAGGAGGAAGAAGAT | 58.317 | 43.478 | 0.00 | 0.00 | 0.00 | 2.40 |
1748 | 2135 | 4.119556 | TGACAGAAGAGGAGGAAGAAGA | 57.880 | 45.455 | 0.00 | 0.00 | 0.00 | 2.87 |
1762 | 2149 | 4.910195 | AGTAGATGCAAACCATGACAGAA | 58.090 | 39.130 | 0.00 | 0.00 | 33.29 | 3.02 |
1772 | 2159 | 9.410556 | ACAAATTCACAATTAGTAGATGCAAAC | 57.589 | 29.630 | 0.00 | 0.00 | 0.00 | 2.93 |
1838 | 2256 | 7.520798 | ACTCCTCTGCAATCCATTCATATAAA | 58.479 | 34.615 | 0.00 | 0.00 | 0.00 | 1.40 |
1839 | 2257 | 7.016957 | AGACTCCTCTGCAATCCATTCATATAA | 59.983 | 37.037 | 0.00 | 0.00 | 0.00 | 0.98 |
1912 | 2330 | 5.104941 | TGAATATGTTCCATGTCCTTCGTCT | 60.105 | 40.000 | 0.00 | 0.00 | 33.26 | 4.18 |
1920 | 2338 | 4.949856 | AGGGTGTTGAATATGTTCCATGTC | 59.050 | 41.667 | 0.00 | 0.00 | 33.26 | 3.06 |
1939 | 2357 | 1.179814 | AGCAGAAACGAGACGAGGGT | 61.180 | 55.000 | 0.00 | 0.00 | 0.00 | 4.34 |
1984 | 2407 | 1.078988 | TCAATGTTACCCGGACCGC | 60.079 | 57.895 | 8.86 | 0.00 | 0.00 | 5.68 |
2023 | 2459 | 4.974103 | TTCTTTCTTTCTCTCTTTCGCG | 57.026 | 40.909 | 0.00 | 0.00 | 0.00 | 5.87 |
2024 | 2460 | 6.473397 | TGATTCTTTCTTTCTCTCTTTCGC | 57.527 | 37.500 | 0.00 | 0.00 | 0.00 | 4.70 |
2025 | 2461 | 6.960431 | GCATGATTCTTTCTTTCTCTCTTTCG | 59.040 | 38.462 | 0.00 | 0.00 | 0.00 | 3.46 |
2046 | 2505 | 7.117812 | AGAGCAAAAGAATGAAATGAAAGCATG | 59.882 | 33.333 | 0.00 | 0.00 | 34.26 | 4.06 |
2133 | 2595 | 7.402054 | TGGTTGGTAATGTACATCTCAAGAAT | 58.598 | 34.615 | 9.23 | 0.00 | 0.00 | 2.40 |
2141 | 2603 | 6.569179 | ACACTTTGGTTGGTAATGTACATC | 57.431 | 37.500 | 9.23 | 0.00 | 0.00 | 3.06 |
2153 | 2621 | 4.186856 | AACAAGGTGAACACTTTGGTTG | 57.813 | 40.909 | 25.24 | 14.28 | 44.43 | 3.77 |
2154 | 2622 | 5.623596 | GCTTAACAAGGTGAACACTTTGGTT | 60.624 | 40.000 | 25.24 | 19.70 | 44.43 | 3.67 |
2187 | 2669 | 6.037830 | CGTAAACATTAGATAAACAGGGGGTG | 59.962 | 42.308 | 0.00 | 0.00 | 0.00 | 4.61 |
2207 | 2690 | 8.486383 | CAAAATCAAATCAGCAAATGTCGTAAA | 58.514 | 29.630 | 0.00 | 0.00 | 0.00 | 2.01 |
2209 | 2692 | 7.366513 | TCAAAATCAAATCAGCAAATGTCGTA | 58.633 | 30.769 | 0.00 | 0.00 | 0.00 | 3.43 |
2232 | 2715 | 5.803461 | CGACGGTACTGAAGAACAATAATCA | 59.197 | 40.000 | 9.17 | 0.00 | 0.00 | 2.57 |
2237 | 2720 | 3.255149 | AGACGACGGTACTGAAGAACAAT | 59.745 | 43.478 | 9.17 | 0.00 | 0.00 | 2.71 |
2238 | 2721 | 2.620115 | AGACGACGGTACTGAAGAACAA | 59.380 | 45.455 | 9.17 | 0.00 | 0.00 | 2.83 |
2240 | 2723 | 2.031333 | ACAGACGACGGTACTGAAGAAC | 60.031 | 50.000 | 19.81 | 2.72 | 35.85 | 3.01 |
2241 | 2724 | 2.224606 | ACAGACGACGGTACTGAAGAA | 58.775 | 47.619 | 19.81 | 0.00 | 35.85 | 2.52 |
2244 | 2727 | 3.067180 | AGAAAACAGACGACGGTACTGAA | 59.933 | 43.478 | 19.81 | 0.00 | 35.85 | 3.02 |
2245 | 2728 | 2.620115 | AGAAAACAGACGACGGTACTGA | 59.380 | 45.455 | 19.81 | 0.00 | 35.85 | 3.41 |
2246 | 2729 | 3.009301 | AGAAAACAGACGACGGTACTG | 57.991 | 47.619 | 14.15 | 14.15 | 37.62 | 2.74 |
2256 | 2739 | 9.356433 | GGTGAGTAAAGATACTAGAAAACAGAC | 57.644 | 37.037 | 0.00 | 0.00 | 42.47 | 3.51 |
2268 | 2751 | 5.725362 | AGCAAGACTGGTGAGTAAAGATAC | 58.275 | 41.667 | 0.00 | 0.00 | 30.16 | 2.24 |
2270 | 2753 | 4.899352 | AGCAAGACTGGTGAGTAAAGAT | 57.101 | 40.909 | 0.00 | 0.00 | 30.16 | 2.40 |
2284 | 2776 | 3.251729 | TCTTGAGAAATGTGCAGCAAGAC | 59.748 | 43.478 | 0.00 | 0.00 | 37.43 | 3.01 |
2295 | 2787 | 9.743057 | GATCGGAGGTATATATCTTGAGAAATG | 57.257 | 37.037 | 0.00 | 0.00 | 0.00 | 2.32 |
2316 | 2808 | 3.375299 | GTCCTGAAACTCAATTGGATCGG | 59.625 | 47.826 | 5.42 | 4.42 | 0.00 | 4.18 |
2317 | 2809 | 4.093998 | CAGTCCTGAAACTCAATTGGATCG | 59.906 | 45.833 | 5.42 | 0.00 | 0.00 | 3.69 |
2318 | 2810 | 4.397417 | CCAGTCCTGAAACTCAATTGGATC | 59.603 | 45.833 | 5.42 | 0.18 | 0.00 | 3.36 |
2319 | 2811 | 4.043310 | TCCAGTCCTGAAACTCAATTGGAT | 59.957 | 41.667 | 5.42 | 0.00 | 0.00 | 3.41 |
2320 | 2812 | 3.394274 | TCCAGTCCTGAAACTCAATTGGA | 59.606 | 43.478 | 5.42 | 0.00 | 0.00 | 3.53 |
2328 | 2820 | 3.327757 | TGTGCTTATCCAGTCCTGAAACT | 59.672 | 43.478 | 0.00 | 0.00 | 0.00 | 2.66 |
2354 | 2852 | 8.079211 | AGCTTAACATAGAGGATTAAGACACA | 57.921 | 34.615 | 7.07 | 0.00 | 37.89 | 3.72 |
2355 | 2853 | 9.685828 | CTAGCTTAACATAGAGGATTAAGACAC | 57.314 | 37.037 | 0.00 | 0.00 | 37.89 | 3.67 |
2356 | 2854 | 8.361139 | GCTAGCTTAACATAGAGGATTAAGACA | 58.639 | 37.037 | 7.70 | 0.00 | 37.89 | 3.41 |
2357 | 2855 | 8.581578 | AGCTAGCTTAACATAGAGGATTAAGAC | 58.418 | 37.037 | 12.68 | 0.29 | 37.89 | 3.01 |
2358 | 2856 | 8.580720 | CAGCTAGCTTAACATAGAGGATTAAGA | 58.419 | 37.037 | 16.46 | 0.00 | 37.89 | 2.10 |
2359 | 2857 | 7.330700 | GCAGCTAGCTTAACATAGAGGATTAAG | 59.669 | 40.741 | 16.46 | 0.00 | 41.15 | 1.85 |
2360 | 2858 | 7.155328 | GCAGCTAGCTTAACATAGAGGATTAA | 58.845 | 38.462 | 16.46 | 0.00 | 41.15 | 1.40 |
2362 | 2860 | 5.546526 | GCAGCTAGCTTAACATAGAGGATT | 58.453 | 41.667 | 16.46 | 0.00 | 41.15 | 3.01 |
2381 | 2916 | 2.738013 | AATCAAAGAAAGCCAGCAGC | 57.262 | 45.000 | 0.00 | 0.00 | 44.25 | 5.25 |
2382 | 2917 | 6.459298 | CCATACTAATCAAAGAAAGCCAGCAG | 60.459 | 42.308 | 0.00 | 0.00 | 0.00 | 4.24 |
2383 | 2918 | 5.357878 | CCATACTAATCAAAGAAAGCCAGCA | 59.642 | 40.000 | 0.00 | 0.00 | 0.00 | 4.41 |
2384 | 2919 | 5.590259 | TCCATACTAATCAAAGAAAGCCAGC | 59.410 | 40.000 | 0.00 | 0.00 | 0.00 | 4.85 |
2385 | 2920 | 6.599244 | TGTCCATACTAATCAAAGAAAGCCAG | 59.401 | 38.462 | 0.00 | 0.00 | 0.00 | 4.85 |
2386 | 2921 | 6.480763 | TGTCCATACTAATCAAAGAAAGCCA | 58.519 | 36.000 | 0.00 | 0.00 | 0.00 | 4.75 |
2387 | 2922 | 7.573968 | ATGTCCATACTAATCAAAGAAAGCC | 57.426 | 36.000 | 0.00 | 0.00 | 0.00 | 4.35 |
2416 | 2959 | 1.902508 | TGCCACCAACAAACCTTGAAA | 59.097 | 42.857 | 0.00 | 0.00 | 0.00 | 2.69 |
2435 | 2978 | 9.398170 | CAACAATCTAACCTGACTGTAAATTTG | 57.602 | 33.333 | 0.00 | 0.00 | 0.00 | 2.32 |
2450 | 2993 | 2.680841 | TGCCCATACGCAACAATCTAAC | 59.319 | 45.455 | 0.00 | 0.00 | 35.32 | 2.34 |
2469 | 3012 | 1.332997 | GCATAACAGTCTGAGCCATGC | 59.667 | 52.381 | 6.91 | 10.99 | 0.00 | 4.06 |
2470 | 3013 | 1.945394 | GGCATAACAGTCTGAGCCATG | 59.055 | 52.381 | 18.56 | 11.67 | 41.63 | 3.66 |
2471 | 3014 | 1.133976 | GGGCATAACAGTCTGAGCCAT | 60.134 | 52.381 | 22.21 | 4.44 | 43.72 | 4.40 |
2472 | 3015 | 0.253044 | GGGCATAACAGTCTGAGCCA | 59.747 | 55.000 | 22.21 | 2.67 | 43.72 | 4.75 |
2473 | 3016 | 0.464554 | GGGGCATAACAGTCTGAGCC | 60.465 | 60.000 | 6.91 | 13.21 | 41.29 | 4.70 |
2474 | 3017 | 0.464554 | GGGGGCATAACAGTCTGAGC | 60.465 | 60.000 | 6.91 | 4.96 | 0.00 | 4.26 |
2475 | 3018 | 3.788672 | GGGGGCATAACAGTCTGAG | 57.211 | 57.895 | 6.91 | 0.00 | 0.00 | 3.35 |
2502 | 3045 | 5.093849 | ACTAAGATAACTTGCGGGCTAAA | 57.906 | 39.130 | 0.00 | 0.00 | 37.53 | 1.85 |
2642 | 3185 | 2.103042 | CCGGCGCTGAAGGAAAGAG | 61.103 | 63.158 | 20.25 | 0.00 | 0.00 | 2.85 |
2684 | 3259 | 0.115745 | TGTAGGGAAACGAGGGAGGT | 59.884 | 55.000 | 0.00 | 0.00 | 0.00 | 3.85 |
2696 | 3271 | 1.452651 | CGGACGTAGGCTGTAGGGA | 60.453 | 63.158 | 0.00 | 0.00 | 0.00 | 4.20 |
2704 | 3279 | 2.772691 | CCCAGTCTCGGACGTAGGC | 61.773 | 68.421 | 0.00 | 0.00 | 37.67 | 3.93 |
2740 | 3315 | 2.472029 | AGCTAGCTGATACCAAGGTGT | 58.528 | 47.619 | 18.57 | 0.00 | 0.00 | 4.16 |
2770 | 3345 | 1.675641 | GGTGGTGGTGAGGACATGC | 60.676 | 63.158 | 0.00 | 0.00 | 0.00 | 4.06 |
2824 | 3399 | 0.530431 | CATGGTGATCGGCGATGTCA | 60.530 | 55.000 | 29.20 | 18.39 | 0.00 | 3.58 |
2826 | 3401 | 1.227645 | CCATGGTGATCGGCGATGT | 60.228 | 57.895 | 29.20 | 4.46 | 0.00 | 3.06 |
2929 | 3504 | 2.601702 | ATGGTGGACGGTGATGGCA | 61.602 | 57.895 | 0.00 | 0.00 | 0.00 | 4.92 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.