Multiple sequence alignment - TraesCS3D01G271100
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 | TraesCS3D01G271100 | chr3D | 100.000 | 5828 | 0 | 0 | 716 | 6543 | 376157356 | 376163183 | 0.000000e+00 | 10763.0 |
1 | TraesCS3D01G271100 | chr3D | 100.000 | 499 | 0 | 0 | 1 | 499 | 376156641 | 376157139 | 0.000000e+00 | 922.0 |
2 | TraesCS3D01G271100 | chr3D | 93.750 | 48 | 1 | 2 | 1660 | 1707 | 376158271 | 376158316 | 3.270000e-08 | 71.3 |
3 | TraesCS3D01G271100 | chr3D | 93.750 | 48 | 1 | 2 | 1631 | 1676 | 376158300 | 376158347 | 3.270000e-08 | 71.3 |
4 | TraesCS3D01G271100 | chr3B | 93.156 | 2776 | 116 | 35 | 2799 | 5528 | 490592291 | 490595038 | 0.000000e+00 | 4006.0 |
5 | TraesCS3D01G271100 | chr3B | 94.181 | 1117 | 35 | 7 | 1660 | 2760 | 490591188 | 490592290 | 0.000000e+00 | 1676.0 |
6 | TraesCS3D01G271100 | chr3B | 93.621 | 1019 | 26 | 6 | 5558 | 6543 | 490595220 | 490596232 | 0.000000e+00 | 1485.0 |
7 | TraesCS3D01G271100 | chr3B | 96.324 | 789 | 22 | 5 | 895 | 1676 | 490590446 | 490591234 | 0.000000e+00 | 1290.0 |
8 | TraesCS3D01G271100 | chr3B | 89.047 | 493 | 30 | 10 | 15 | 487 | 490589410 | 490589898 | 2.030000e-164 | 590.0 |
9 | TraesCS3D01G271100 | chr3B | 86.628 | 172 | 23 | 0 | 725 | 896 | 490590055 | 490590226 | 2.410000e-44 | 191.0 |
10 | TraesCS3D01G271100 | chr3B | 100.000 | 39 | 0 | 0 | 4448 | 4486 | 490593908 | 490593946 | 9.100000e-09 | 73.1 |
11 | TraesCS3D01G271100 | chr3A | 94.197 | 2068 | 75 | 14 | 1660 | 3711 | 500969888 | 500971926 | 0.000000e+00 | 3112.0 |
12 | TraesCS3D01G271100 | chr3A | 94.330 | 970 | 35 | 7 | 716 | 1676 | 500968976 | 500969934 | 0.000000e+00 | 1469.0 |
13 | TraesCS3D01G271100 | chr3A | 88.638 | 1153 | 68 | 33 | 4413 | 5531 | 500972639 | 500973762 | 0.000000e+00 | 1345.0 |
14 | TraesCS3D01G271100 | chr3A | 96.193 | 788 | 17 | 8 | 3739 | 4516 | 500971923 | 500972707 | 0.000000e+00 | 1277.0 |
15 | TraesCS3D01G271100 | chr3A | 89.628 | 1022 | 33 | 21 | 5558 | 6543 | 500973939 | 500974923 | 0.000000e+00 | 1232.0 |
16 | TraesCS3D01G271100 | chr3A | 84.407 | 295 | 43 | 3 | 66 | 359 | 730111280 | 730110988 | 2.990000e-73 | 287.0 |
17 | TraesCS3D01G271100 | chr3A | 84.828 | 290 | 35 | 7 | 211 | 492 | 500968542 | 500968830 | 3.860000e-72 | 283.0 |
18 | TraesCS3D01G271100 | chr3A | 87.692 | 195 | 9 | 2 | 2448 | 2630 | 503526127 | 503526318 | 5.140000e-51 | 213.0 |
19 | TraesCS3D01G271100 | chr3A | 97.436 | 39 | 1 | 0 | 4448 | 4486 | 500972604 | 500972642 | 4.230000e-07 | 67.6 |
20 | TraesCS3D01G271100 | chr5D | 93.322 | 569 | 10 | 9 | 3969 | 4516 | 22743866 | 22744427 | 0.000000e+00 | 815.0 |
21 | TraesCS3D01G271100 | chr5D | 82.335 | 334 | 48 | 6 | 33 | 358 | 548924691 | 548925021 | 5.000000e-71 | 279.0 |
22 | TraesCS3D01G271100 | chr5D | 97.436 | 39 | 1 | 0 | 4448 | 4486 | 22744321 | 22744359 | 4.230000e-07 | 67.6 |
23 | TraesCS3D01G271100 | chr5B | 89.845 | 453 | 28 | 4 | 2227 | 2666 | 528735284 | 528735731 | 3.420000e-157 | 566.0 |
24 | TraesCS3D01G271100 | chr2B | 89.183 | 453 | 30 | 5 | 2227 | 2666 | 132611328 | 132611774 | 1.240000e-151 | 547.0 |
25 | TraesCS3D01G271100 | chr4B | 88.962 | 453 | 32 | 4 | 2227 | 2666 | 112879306 | 112879753 | 1.600000e-150 | 544.0 |
26 | TraesCS3D01G271100 | chr4B | 84.393 | 346 | 45 | 8 | 19 | 361 | 140580555 | 140580216 | 1.360000e-86 | 331.0 |
27 | TraesCS3D01G271100 | chr7B | 88.433 | 268 | 15 | 5 | 2412 | 2666 | 708149797 | 708150061 | 6.370000e-80 | 309.0 |
28 | TraesCS3D01G271100 | chr2A | 88.312 | 231 | 12 | 2 | 2412 | 2630 | 27204687 | 27204460 | 5.030000e-66 | 263.0 |
29 | TraesCS3D01G271100 | chr1A | 88.312 | 231 | 12 | 2 | 2412 | 2630 | 45538186 | 45538413 | 5.030000e-66 | 263.0 |
30 | TraesCS3D01G271100 | chr7A | 85.903 | 227 | 30 | 2 | 135 | 360 | 686455607 | 686455382 | 2.360000e-59 | 241.0 |
31 | TraesCS3D01G271100 | chr5A | 86.147 | 231 | 17 | 2 | 2412 | 2630 | 546047839 | 546047612 | 1.100000e-57 | 235.0 |
32 | TraesCS3D01G271100 | chr7D | 79.545 | 352 | 43 | 20 | 14 | 361 | 8006813 | 8007139 | 2.370000e-54 | 224.0 |
33 | TraesCS3D01G271100 | chr4A | 78.378 | 333 | 47 | 16 | 33 | 361 | 732374489 | 732374800 | 6.700000e-45 | 193.0 |
34 | TraesCS3D01G271100 | chr6B | 93.548 | 62 | 4 | 0 | 300 | 361 | 222694940 | 222695001 | 6.990000e-15 | 93.5 |
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 | TraesCS3D01G271100 | chr3D | 376156641 | 376163183 | 6542 | False | 5842.500000 | 10763 | 100.000000 | 1 | 6543 | 2 | chr3D.!!$F1 | 6542 |
1 | TraesCS3D01G271100 | chr3B | 490589410 | 490596232 | 6822 | False | 1330.157143 | 4006 | 93.279571 | 15 | 6543 | 7 | chr3B.!!$F1 | 6528 |
2 | TraesCS3D01G271100 | chr3A | 500968542 | 500974923 | 6381 | False | 1255.085714 | 3112 | 92.178571 | 211 | 6543 | 7 | chr3A.!!$F2 | 6332 |
3 | TraesCS3D01G271100 | chr5D | 22743866 | 22744427 | 561 | False | 441.300000 | 815 | 95.379000 | 3969 | 4516 | 2 | chr5D.!!$F2 | 547 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
430 | 461 | 0.537143 | AATGAAGGTGAGGTGCGCAA | 60.537 | 50.000 | 14.00 | 0.0 | 0.00 | 4.85 | F |
1264 | 1525 | 0.237235 | TTTCCAGATTGTTCGTGCGC | 59.763 | 50.000 | 0.00 | 0.0 | 0.00 | 6.09 | F |
1535 | 1798 | 0.250727 | AGGTGGTGGATTTGGTGTCG | 60.251 | 55.000 | 0.00 | 0.0 | 0.00 | 4.35 | F |
2586 | 2865 | 0.468648 | GCCGGAAACCATAGCTACCT | 59.531 | 55.000 | 5.05 | 0.0 | 0.00 | 3.08 | F |
3101 | 3383 | 0.459489 | GTGGTTGCCAAGAAACAGCA | 59.541 | 50.000 | 0.00 | 0.0 | 34.18 | 4.41 | F |
4722 | 5075 | 1.075374 | TCATCTGTGGGGTTTGGAAGG | 59.925 | 52.381 | 0.00 | 0.0 | 0.00 | 3.46 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
2245 | 2508 | 0.238553 | GAAGCCAAGAAACGACTGGC | 59.761 | 55.000 | 4.11 | 4.11 | 45.30 | 4.85 | R |
3035 | 3317 | 0.911769 | TCACTAGGTGGCCATGAAGG | 59.088 | 55.000 | 9.72 | 1.05 | 33.87 | 3.46 | R |
3101 | 3383 | 1.203441 | TGTTGCTCTGATCCTGGGCT | 61.203 | 55.000 | 8.77 | 0.00 | 30.04 | 5.19 | R |
4582 | 4934 | 3.621268 | GGTTGTTGTCATCAAGCGCTATA | 59.379 | 43.478 | 12.05 | 1.09 | 34.51 | 1.31 | R |
4775 | 5128 | 1.134580 | CATATAGGGCAGGGCTCATCG | 60.135 | 57.143 | 0.00 | 0.00 | 0.00 | 3.84 | R |
5579 | 6110 | 0.107214 | CACCTCCATTGCCGTATGGT | 60.107 | 55.000 | 2.17 | 0.00 | 44.48 | 3.55 | 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 |
---|---|---|---|---|---|---|---|---|---|
27 | 28 | 7.912383 | ACAAGATCTTTTTGTTGCAATGAAAG | 58.088 | 30.769 | 18.43 | 18.43 | 35.32 | 2.62 |
29 | 30 | 5.993441 | AGATCTTTTTGTTGCAATGAAAGGG | 59.007 | 36.000 | 21.55 | 13.89 | 0.00 | 3.95 |
35 | 36 | 1.412343 | GTTGCAATGAAAGGGGTGTGT | 59.588 | 47.619 | 0.59 | 0.00 | 0.00 | 3.72 |
36 | 37 | 1.039068 | TGCAATGAAAGGGGTGTGTG | 58.961 | 50.000 | 0.00 | 0.00 | 0.00 | 3.82 |
37 | 38 | 1.039856 | GCAATGAAAGGGGTGTGTGT | 58.960 | 50.000 | 0.00 | 0.00 | 0.00 | 3.72 |
38 | 39 | 1.269726 | GCAATGAAAGGGGTGTGTGTG | 60.270 | 52.381 | 0.00 | 0.00 | 0.00 | 3.82 |
39 | 40 | 2.031120 | CAATGAAAGGGGTGTGTGTGT | 58.969 | 47.619 | 0.00 | 0.00 | 0.00 | 3.72 |
44 | 45 | 2.341846 | AAGGGGTGTGTGTGTGTTAG | 57.658 | 50.000 | 0.00 | 0.00 | 0.00 | 2.34 |
93 | 94 | 1.621814 | TGTTTAGGTTGCTACTCGCCT | 59.378 | 47.619 | 0.00 | 0.00 | 38.05 | 5.52 |
156 | 160 | 7.141758 | AGTTGCAGAATTCAAGGGATAGATA | 57.858 | 36.000 | 8.44 | 0.00 | 0.00 | 1.98 |
168 | 172 | 8.473358 | TCAAGGGATAGATAATGTCGTTTCTA | 57.527 | 34.615 | 0.00 | 0.00 | 0.00 | 2.10 |
189 | 193 | 8.658499 | TTCTATCATGAGATTGACATGTTGAG | 57.342 | 34.615 | 0.00 | 0.00 | 43.56 | 3.02 |
191 | 195 | 3.943381 | TCATGAGATTGACATGTTGAGCC | 59.057 | 43.478 | 0.00 | 0.00 | 43.56 | 4.70 |
329 | 333 | 4.161189 | TGCAAAGTTGAATGGACCTTTGAA | 59.839 | 37.500 | 13.46 | 1.91 | 34.79 | 2.69 |
330 | 334 | 5.163322 | TGCAAAGTTGAATGGACCTTTGAAT | 60.163 | 36.000 | 13.46 | 0.00 | 34.79 | 2.57 |
411 | 442 | 5.888691 | AAATGTCCATGTTATAACGCACA | 57.111 | 34.783 | 10.92 | 10.22 | 0.00 | 4.57 |
412 | 443 | 5.888691 | AATGTCCATGTTATAACGCACAA | 57.111 | 34.783 | 10.92 | 0.00 | 0.00 | 3.33 |
429 | 460 | 1.073025 | AATGAAGGTGAGGTGCGCA | 59.927 | 52.632 | 5.66 | 5.66 | 0.00 | 6.09 |
430 | 461 | 0.537143 | AATGAAGGTGAGGTGCGCAA | 60.537 | 50.000 | 14.00 | 0.00 | 0.00 | 4.85 |
448 | 479 | 4.619336 | GCGCAACATCCGATTTTAAAGAAA | 59.381 | 37.500 | 0.30 | 0.00 | 0.00 | 2.52 |
738 | 769 | 2.233431 | CCGAGGCAATTGAATTTTGGGA | 59.767 | 45.455 | 10.34 | 0.00 | 0.00 | 4.37 |
742 | 773 | 3.652387 | AGGCAATTGAATTTTGGGAAGGT | 59.348 | 39.130 | 10.34 | 0.00 | 0.00 | 3.50 |
754 | 785 | 2.669240 | GAAGGTTACTGGGCGCCT | 59.331 | 61.111 | 28.56 | 9.55 | 0.00 | 5.52 |
777 | 808 | 5.701855 | TGTTTGATGTACGAACGTATGAGA | 58.298 | 37.500 | 10.14 | 0.00 | 43.67 | 3.27 |
885 | 916 | 5.620417 | GCAGCGTTCTACTAGTAATCTTACG | 59.380 | 44.000 | 3.76 | 9.90 | 38.65 | 3.18 |
941 | 1193 | 1.006086 | CGCACGCAGTATTTCCATGA | 58.994 | 50.000 | 0.00 | 0.00 | 41.61 | 3.07 |
948 | 1200 | 2.615912 | GCAGTATTTCCATGAGGACAGC | 59.384 | 50.000 | 0.00 | 0.00 | 45.73 | 4.40 |
1231 | 1492 | 5.825593 | AATTTTTCCTCCCTTCCCTTTTC | 57.174 | 39.130 | 0.00 | 0.00 | 0.00 | 2.29 |
1234 | 1495 | 0.849540 | TCCTCCCTTCCCTTTTCCCC | 60.850 | 60.000 | 0.00 | 0.00 | 0.00 | 4.81 |
1264 | 1525 | 0.237235 | TTTCCAGATTGTTCGTGCGC | 59.763 | 50.000 | 0.00 | 0.00 | 0.00 | 6.09 |
1314 | 1575 | 2.940994 | TTCTTCCCGGTCATTCAACA | 57.059 | 45.000 | 0.00 | 0.00 | 0.00 | 3.33 |
1535 | 1798 | 0.250727 | AGGTGGTGGATTTGGTGTCG | 60.251 | 55.000 | 0.00 | 0.00 | 0.00 | 4.35 |
1586 | 1849 | 2.107141 | CCTGATCGGAAGCGTCCC | 59.893 | 66.667 | 13.43 | 0.00 | 41.44 | 4.46 |
1656 | 1919 | 1.941999 | GACAAGCAGAATGGCCTGGC | 61.942 | 60.000 | 11.05 | 11.05 | 35.86 | 4.85 |
1677 | 1940 | 3.359523 | CGCAGCAGCCAAGCAGAA | 61.360 | 61.111 | 0.00 | 0.00 | 37.52 | 3.02 |
1678 | 1941 | 2.697761 | CGCAGCAGCCAAGCAGAAT | 61.698 | 57.895 | 0.00 | 0.00 | 37.52 | 2.40 |
1679 | 1942 | 1.153823 | GCAGCAGCCAAGCAGAATG | 60.154 | 57.895 | 0.00 | 0.00 | 36.85 | 2.67 |
1680 | 1943 | 1.511305 | CAGCAGCCAAGCAGAATGG | 59.489 | 57.895 | 0.00 | 0.00 | 41.08 | 3.16 |
1685 | 1948 | 3.612251 | CCAAGCAGAATGGCCTGG | 58.388 | 61.111 | 3.32 | 0.00 | 38.90 | 4.45 |
1802 | 2065 | 0.864455 | GATCGCATGCTTCTAGTGCC | 59.136 | 55.000 | 17.13 | 0.00 | 35.51 | 5.01 |
1884 | 2147 | 4.999751 | AGAGATGAAAGAAGTGAAACGC | 57.000 | 40.909 | 0.00 | 0.00 | 45.86 | 4.84 |
1975 | 2238 | 1.521010 | CGATGCCTGGACAGAGCTG | 60.521 | 63.158 | 0.00 | 0.00 | 0.00 | 4.24 |
1997 | 2260 | 0.543277 | TGGCCATTCCTGAGCTACTG | 59.457 | 55.000 | 0.00 | 0.00 | 35.26 | 2.74 |
2176 | 2439 | 2.497107 | CAGCAGGTTGTTTCTGTTGG | 57.503 | 50.000 | 0.00 | 0.00 | 38.98 | 3.77 |
2197 | 2460 | 6.109156 | TGGTTACTTCTCAATCTTGCTGTA | 57.891 | 37.500 | 0.00 | 0.00 | 0.00 | 2.74 |
2241 | 2504 | 7.595604 | TCCGTTTCTTAGTTGTTGTTTTCTTT | 58.404 | 30.769 | 0.00 | 0.00 | 0.00 | 2.52 |
2242 | 2505 | 7.751793 | TCCGTTTCTTAGTTGTTGTTTTCTTTC | 59.248 | 33.333 | 0.00 | 0.00 | 0.00 | 2.62 |
2245 | 2508 | 8.860128 | GTTTCTTAGTTGTTGTTTTCTTTCCTG | 58.140 | 33.333 | 0.00 | 0.00 | 0.00 | 3.86 |
2282 | 2549 | 4.813697 | GGCTTCTTCTGATGATTCACTACC | 59.186 | 45.833 | 0.00 | 0.00 | 0.00 | 3.18 |
2384 | 2651 | 4.527157 | GCTGCGCGTGCCAGAATC | 62.527 | 66.667 | 19.87 | 0.24 | 41.78 | 2.52 |
2422 | 2689 | 5.245531 | CCAATCTAGTTCTGTAAGTTGCCA | 58.754 | 41.667 | 0.00 | 0.00 | 33.76 | 4.92 |
2425 | 2692 | 5.546621 | TCTAGTTCTGTAAGTTGCCACTT | 57.453 | 39.130 | 8.41 | 8.41 | 45.73 | 3.16 |
2470 | 2737 | 5.125578 | GGGGATTCGCTTACTGAAAAATCTT | 59.874 | 40.000 | 0.40 | 0.00 | 0.00 | 2.40 |
2471 | 2738 | 6.030228 | GGGATTCGCTTACTGAAAAATCTTG | 58.970 | 40.000 | 0.00 | 0.00 | 0.00 | 3.02 |
2472 | 2739 | 5.513141 | GGATTCGCTTACTGAAAAATCTTGC | 59.487 | 40.000 | 0.00 | 0.00 | 0.00 | 4.01 |
2496 | 2763 | 6.680625 | GCTGCAAGAATCATGTGATCATCTTT | 60.681 | 38.462 | 0.00 | 0.00 | 32.32 | 2.52 |
2533 | 2800 | 6.821665 | GGCATGGTTTCAGTTAGTTATGAGTA | 59.178 | 38.462 | 0.00 | 0.00 | 0.00 | 2.59 |
2586 | 2865 | 0.468648 | GCCGGAAACCATAGCTACCT | 59.531 | 55.000 | 5.05 | 0.00 | 0.00 | 3.08 |
2640 | 2919 | 3.244875 | TGCAAATCAGGTAGCTGAAAGGA | 60.245 | 43.478 | 27.06 | 17.61 | 36.88 | 3.36 |
2827 | 3109 | 4.816385 | TGCTCTTACTCTTGAGTTTTGTGG | 59.184 | 41.667 | 8.66 | 0.00 | 33.22 | 4.17 |
2907 | 3189 | 4.790937 | TGGCTATGGCATTCTGTTGATTA | 58.209 | 39.130 | 4.78 | 0.00 | 40.87 | 1.75 |
2971 | 3253 | 3.393089 | ACTGTACTTTGTGCTCAGAGG | 57.607 | 47.619 | 10.63 | 0.00 | 31.18 | 3.69 |
3033 | 3315 | 1.144969 | CGCTCGCAAGTTCAAGGTTA | 58.855 | 50.000 | 0.00 | 0.00 | 39.48 | 2.85 |
3035 | 3317 | 2.222819 | CGCTCGCAAGTTCAAGGTTATC | 60.223 | 50.000 | 0.00 | 0.00 | 39.48 | 1.75 |
3053 | 3335 | 0.911769 | TCCTTCATGGCCACCTAGTG | 59.088 | 55.000 | 8.16 | 1.02 | 35.26 | 2.74 |
3101 | 3383 | 0.459489 | GTGGTTGCCAAGAAACAGCA | 59.541 | 50.000 | 0.00 | 0.00 | 34.18 | 4.41 |
3187 | 3473 | 3.498774 | ACTGAGGACTGACATTTGCTT | 57.501 | 42.857 | 0.00 | 0.00 | 0.00 | 3.91 |
3317 | 3603 | 2.696775 | TGGAATATCGAGGGGCCTTTA | 58.303 | 47.619 | 0.84 | 0.00 | 0.00 | 1.85 |
3321 | 3607 | 5.491078 | TGGAATATCGAGGGGCCTTTATATT | 59.509 | 40.000 | 13.54 | 13.54 | 31.91 | 1.28 |
3335 | 3621 | 7.122204 | GGGCCTTTATATTGTTGACTACTTGTT | 59.878 | 37.037 | 0.84 | 0.00 | 0.00 | 2.83 |
4008 | 4299 | 5.201713 | TGTGCCTCTATTACTGTCTATGC | 57.798 | 43.478 | 0.00 | 0.00 | 0.00 | 3.14 |
4250 | 4559 | 5.292101 | GTCATAGTTGCATACTTGTCCTGAC | 59.708 | 44.000 | 6.82 | 8.55 | 38.33 | 3.51 |
4290 | 4600 | 4.259930 | GCATGTGTTGTTTGTTTCTGCTTC | 60.260 | 41.667 | 0.00 | 0.00 | 0.00 | 3.86 |
4524 | 4873 | 9.801873 | ACTTGTTGGTTCATGCATATTTATTAC | 57.198 | 29.630 | 0.00 | 0.00 | 0.00 | 1.89 |
4559 | 4911 | 7.688372 | ACTAATATTTTCTCGTTGCTCACATG | 58.312 | 34.615 | 0.00 | 0.00 | 0.00 | 3.21 |
4582 | 4934 | 7.482169 | TGTTAGTGATGACTATGAGAACCTT | 57.518 | 36.000 | 0.00 | 0.00 | 34.53 | 3.50 |
4606 | 4958 | 1.925946 | GCGCTTGATGACAACAACCAC | 60.926 | 52.381 | 0.00 | 0.00 | 32.27 | 4.16 |
4645 | 4997 | 1.267806 | AGTGAAATTGACAGCTTGCCG | 59.732 | 47.619 | 0.00 | 0.00 | 0.00 | 5.69 |
4703 | 5056 | 2.634815 | AGACAGGATGGATGTGCATC | 57.365 | 50.000 | 6.01 | 6.01 | 43.62 | 3.91 |
4720 | 5073 | 2.806434 | CATCATCTGTGGGGTTTGGAA | 58.194 | 47.619 | 0.00 | 0.00 | 0.00 | 3.53 |
4722 | 5075 | 1.075374 | TCATCTGTGGGGTTTGGAAGG | 59.925 | 52.381 | 0.00 | 0.00 | 0.00 | 3.46 |
4755 | 5108 | 2.919602 | TGCCTCTCCCCTCTTTACATTT | 59.080 | 45.455 | 0.00 | 0.00 | 0.00 | 2.32 |
4936 | 5290 | 3.311486 | AACATATTTTTGTGGGTGCGG | 57.689 | 42.857 | 0.00 | 0.00 | 0.00 | 5.69 |
5051 | 5405 | 0.963962 | CTGCAGCACCTGTTGGAATT | 59.036 | 50.000 | 0.00 | 0.00 | 37.04 | 2.17 |
5096 | 5451 | 1.066430 | GCCATTTCGACACTCCTGGTA | 60.066 | 52.381 | 0.00 | 0.00 | 0.00 | 3.25 |
5101 | 5456 | 2.577593 | GACACTCCTGGTACCGCC | 59.422 | 66.667 | 7.57 | 0.00 | 37.90 | 6.13 |
5146 | 5502 | 0.958382 | GTTACACAATGCTGGCCGGA | 60.958 | 55.000 | 18.31 | 2.96 | 0.00 | 5.14 |
5155 | 5511 | 2.420890 | CTGGCCGGATCTCTCTGC | 59.579 | 66.667 | 5.28 | 0.00 | 0.00 | 4.26 |
5156 | 5512 | 3.496875 | CTGGCCGGATCTCTCTGCG | 62.497 | 68.421 | 5.28 | 0.00 | 0.00 | 5.18 |
5157 | 5513 | 4.959596 | GGCCGGATCTCTCTGCGC | 62.960 | 72.222 | 5.05 | 0.00 | 0.00 | 6.09 |
5159 | 5515 | 4.637489 | CCGGATCTCTCTGCGCGG | 62.637 | 72.222 | 10.86 | 10.86 | 0.00 | 6.46 |
5160 | 5516 | 3.893763 | CGGATCTCTCTGCGCGGT | 61.894 | 66.667 | 17.37 | 0.00 | 0.00 | 5.68 |
5161 | 5517 | 2.279120 | GGATCTCTCTGCGCGGTG | 60.279 | 66.667 | 17.37 | 14.57 | 0.00 | 4.94 |
5185 | 5541 | 3.461061 | CAGTGAGCAGAGAGTGTTTGAA | 58.539 | 45.455 | 0.00 | 0.00 | 0.00 | 2.69 |
5238 | 5598 | 3.257933 | CTGCGAGAAACAGGGCAC | 58.742 | 61.111 | 0.00 | 0.00 | 0.00 | 5.01 |
5289 | 5650 | 3.517296 | TTTTTGTGCAGGGGAGATGTA | 57.483 | 42.857 | 0.00 | 0.00 | 0.00 | 2.29 |
5300 | 5661 | 4.346418 | CAGGGGAGATGTATGATATAGCCC | 59.654 | 50.000 | 0.00 | 0.00 | 0.00 | 5.19 |
5340 | 5701 | 2.766828 | GCCCTGTCCTGTAGTAGTGAAT | 59.233 | 50.000 | 0.00 | 0.00 | 0.00 | 2.57 |
5381 | 5742 | 3.007290 | TGCTGCAGACTTGTAGTTCATCT | 59.993 | 43.478 | 20.43 | 0.00 | 39.03 | 2.90 |
5383 | 5744 | 4.564041 | CTGCAGACTTGTAGTTCATCTGT | 58.436 | 43.478 | 8.42 | 0.00 | 36.26 | 3.41 |
5385 | 5746 | 6.096673 | TGCAGACTTGTAGTTCATCTGTTA | 57.903 | 37.500 | 0.00 | 0.00 | 36.26 | 2.41 |
5394 | 5755 | 5.958380 | TGTAGTTCATCTGTTACTGGGATCT | 59.042 | 40.000 | 0.00 | 0.00 | 0.00 | 2.75 |
5395 | 5756 | 5.606348 | AGTTCATCTGTTACTGGGATCTC | 57.394 | 43.478 | 0.00 | 0.00 | 0.00 | 2.75 |
5399 | 5760 | 4.895889 | TCATCTGTTACTGGGATCTCGAAT | 59.104 | 41.667 | 0.00 | 0.00 | 0.00 | 3.34 |
5402 | 5763 | 6.978674 | TCTGTTACTGGGATCTCGAATTAT | 57.021 | 37.500 | 0.00 | 0.00 | 0.00 | 1.28 |
5403 | 5764 | 7.361457 | TCTGTTACTGGGATCTCGAATTATT | 57.639 | 36.000 | 0.00 | 0.00 | 0.00 | 1.40 |
5406 | 5767 | 8.473358 | TGTTACTGGGATCTCGAATTATTAGA | 57.527 | 34.615 | 0.00 | 0.00 | 0.00 | 2.10 |
5408 | 5769 | 9.930693 | GTTACTGGGATCTCGAATTATTAGAAT | 57.069 | 33.333 | 0.00 | 0.00 | 0.00 | 2.40 |
5456 | 5830 | 3.055094 | TCCAGCCTGGTTCTTCAGTAATC | 60.055 | 47.826 | 11.27 | 0.00 | 39.03 | 1.75 |
5486 | 5865 | 1.303888 | CTGTCATGCCTGGCAACCT | 60.304 | 57.895 | 27.24 | 6.43 | 43.62 | 3.50 |
5487 | 5866 | 0.896940 | CTGTCATGCCTGGCAACCTT | 60.897 | 55.000 | 27.24 | 5.99 | 43.62 | 3.50 |
5492 | 5871 | 1.895131 | CATGCCTGGCAACCTTTAAGT | 59.105 | 47.619 | 27.24 | 2.08 | 43.62 | 2.24 |
5517 | 5896 | 6.898041 | TCGAACCAGTAAATTGTTCAGAATG | 58.102 | 36.000 | 6.46 | 0.00 | 38.59 | 2.67 |
5520 | 5899 | 7.519809 | CGAACCAGTAAATTGTTCAGAATGTCA | 60.520 | 37.037 | 6.46 | 0.00 | 38.59 | 3.58 |
5522 | 5901 | 8.862325 | ACCAGTAAATTGTTCAGAATGTCATA | 57.138 | 30.769 | 0.00 | 0.00 | 37.40 | 2.15 |
5533 | 5912 | 9.500785 | TGTTCAGAATGTCATATTACTTTGTGA | 57.499 | 29.630 | 9.91 | 9.91 | 36.01 | 3.58 |
5536 | 5915 | 9.889128 | TCAGAATGTCATATTACTTTGTGATCA | 57.111 | 29.630 | 9.91 | 0.00 | 34.19 | 2.92 |
5539 | 5918 | 9.888878 | GAATGTCATATTACTTTGTGATCATGG | 57.111 | 33.333 | 0.00 | 0.00 | 0.00 | 3.66 |
5540 | 5919 | 8.985315 | ATGTCATATTACTTTGTGATCATGGT | 57.015 | 30.769 | 0.00 | 0.00 | 0.00 | 3.55 |
5543 | 5922 | 4.989279 | ATTACTTTGTGATCATGGTGGC | 57.011 | 40.909 | 0.00 | 0.00 | 0.00 | 5.01 |
5544 | 5923 | 2.291209 | ACTTTGTGATCATGGTGGCA | 57.709 | 45.000 | 0.00 | 0.00 | 0.00 | 4.92 |
5546 | 5925 | 3.167485 | ACTTTGTGATCATGGTGGCAAT | 58.833 | 40.909 | 0.00 | 0.00 | 0.00 | 3.56 |
5547 | 5926 | 3.056393 | ACTTTGTGATCATGGTGGCAATG | 60.056 | 43.478 | 0.00 | 2.55 | 0.00 | 2.82 |
5548 | 5927 | 1.476477 | TGTGATCATGGTGGCAATGG | 58.524 | 50.000 | 0.00 | 0.00 | 0.00 | 3.16 |
5549 | 5928 | 1.005687 | TGTGATCATGGTGGCAATGGA | 59.994 | 47.619 | 0.00 | 0.00 | 0.00 | 3.41 |
5551 | 5930 | 1.325355 | GATCATGGTGGCAATGGAGG | 58.675 | 55.000 | 0.00 | 0.00 | 0.00 | 4.30 |
5552 | 5931 | 0.632835 | ATCATGGTGGCAATGGAGGT | 59.367 | 50.000 | 0.00 | 0.00 | 0.00 | 3.85 |
5553 | 5932 | 0.323633 | TCATGGTGGCAATGGAGGTG | 60.324 | 55.000 | 0.00 | 0.00 | 0.00 | 4.00 |
5579 | 6110 | 8.978874 | AAAATCAGCTGTATGTAATCATGGTA | 57.021 | 30.769 | 14.67 | 0.00 | 35.70 | 3.25 |
5581 | 6112 | 5.853936 | TCAGCTGTATGTAATCATGGTACC | 58.146 | 41.667 | 14.67 | 4.43 | 35.70 | 3.34 |
5585 | 6116 | 7.331934 | CAGCTGTATGTAATCATGGTACCATAC | 59.668 | 40.741 | 26.91 | 20.63 | 34.91 | 2.39 |
5604 | 6135 | 1.818674 | ACGGCAATGGAGGTGAAAATC | 59.181 | 47.619 | 0.00 | 0.00 | 0.00 | 2.17 |
5608 | 6139 | 3.259123 | GGCAATGGAGGTGAAAATCACTT | 59.741 | 43.478 | 10.06 | 2.69 | 46.19 | 3.16 |
5712 | 6245 | 1.600485 | TCGATACGCTGATAACTCGCA | 59.400 | 47.619 | 0.00 | 0.00 | 0.00 | 5.10 |
5714 | 6247 | 2.320367 | GATACGCTGATAACTCGCAGG | 58.680 | 52.381 | 0.00 | 0.00 | 32.83 | 4.85 |
6248 | 6794 | 4.838486 | GCGTCTCAGTCCCGCTCG | 62.838 | 72.222 | 0.00 | 0.00 | 43.81 | 5.03 |
6296 | 6842 | 1.187567 | AAATGTTCTGCAGTGGGGGC | 61.188 | 55.000 | 14.67 | 0.00 | 0.00 | 5.80 |
6306 | 6852 | 1.755179 | CAGTGGGGGCTGTTATTCTG | 58.245 | 55.000 | 0.00 | 0.00 | 0.00 | 3.02 |
6339 | 6885 | 1.896220 | AGCAATTCGTTTGAGCAGGA | 58.104 | 45.000 | 5.27 | 0.00 | 37.53 | 3.86 |
6414 | 6965 | 2.455557 | ACTCTCACCTCACCTCATCTG | 58.544 | 52.381 | 0.00 | 0.00 | 0.00 | 2.90 |
6415 | 6966 | 1.136695 | CTCTCACCTCACCTCATCTGC | 59.863 | 57.143 | 0.00 | 0.00 | 0.00 | 4.26 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
0 | 1 | 9.545105 | TTTCATTGCAACAAAAAGATCTTGTAT | 57.455 | 25.926 | 9.17 | 0.00 | 35.98 | 2.29 |
1 | 2 | 8.939201 | TTTCATTGCAACAAAAAGATCTTGTA | 57.061 | 26.923 | 9.17 | 0.00 | 35.98 | 2.41 |
2 | 3 | 7.011669 | CCTTTCATTGCAACAAAAAGATCTTGT | 59.988 | 33.333 | 22.22 | 0.00 | 38.65 | 3.16 |
3 | 4 | 7.349711 | CCTTTCATTGCAACAAAAAGATCTTG | 58.650 | 34.615 | 22.22 | 0.00 | 0.00 | 3.02 |
4 | 5 | 6.484308 | CCCTTTCATTGCAACAAAAAGATCTT | 59.516 | 34.615 | 22.22 | 0.88 | 0.00 | 2.40 |
5 | 6 | 5.993441 | CCCTTTCATTGCAACAAAAAGATCT | 59.007 | 36.000 | 22.22 | 0.00 | 0.00 | 2.75 |
6 | 7 | 5.179929 | CCCCTTTCATTGCAACAAAAAGATC | 59.820 | 40.000 | 22.22 | 0.00 | 0.00 | 2.75 |
7 | 8 | 5.065235 | CCCCTTTCATTGCAACAAAAAGAT | 58.935 | 37.500 | 22.22 | 0.00 | 0.00 | 2.40 |
8 | 9 | 4.080638 | ACCCCTTTCATTGCAACAAAAAGA | 60.081 | 37.500 | 22.22 | 5.80 | 0.00 | 2.52 |
9 | 10 | 4.035441 | CACCCCTTTCATTGCAACAAAAAG | 59.965 | 41.667 | 17.10 | 17.10 | 0.00 | 2.27 |
10 | 11 | 3.944015 | CACCCCTTTCATTGCAACAAAAA | 59.056 | 39.130 | 0.00 | 1.86 | 0.00 | 1.94 |
11 | 12 | 3.054802 | ACACCCCTTTCATTGCAACAAAA | 60.055 | 39.130 | 0.00 | 4.55 | 0.00 | 2.44 |
12 | 13 | 2.503356 | ACACCCCTTTCATTGCAACAAA | 59.497 | 40.909 | 0.00 | 3.09 | 0.00 | 2.83 |
13 | 14 | 2.114616 | ACACCCCTTTCATTGCAACAA | 58.885 | 42.857 | 0.00 | 0.00 | 0.00 | 2.83 |
27 | 28 | 1.542547 | CCTCTAACACACACACACCCC | 60.543 | 57.143 | 0.00 | 0.00 | 0.00 | 4.95 |
29 | 30 | 2.159014 | TCACCTCTAACACACACACACC | 60.159 | 50.000 | 0.00 | 0.00 | 0.00 | 4.16 |
35 | 36 | 3.838244 | AAGCTTCACCTCTAACACACA | 57.162 | 42.857 | 0.00 | 0.00 | 0.00 | 3.72 |
36 | 37 | 5.122396 | CCAATAAGCTTCACCTCTAACACAC | 59.878 | 44.000 | 0.00 | 0.00 | 0.00 | 3.82 |
37 | 38 | 5.221843 | ACCAATAAGCTTCACCTCTAACACA | 60.222 | 40.000 | 0.00 | 0.00 | 0.00 | 3.72 |
38 | 39 | 5.122396 | CACCAATAAGCTTCACCTCTAACAC | 59.878 | 44.000 | 0.00 | 0.00 | 0.00 | 3.32 |
39 | 40 | 5.012664 | TCACCAATAAGCTTCACCTCTAACA | 59.987 | 40.000 | 0.00 | 0.00 | 0.00 | 2.41 |
44 | 45 | 5.529060 | CCTATTCACCAATAAGCTTCACCTC | 59.471 | 44.000 | 0.00 | 0.00 | 0.00 | 3.85 |
93 | 94 | 1.002544 | TGCATACACATTGACGTGGGA | 59.997 | 47.619 | 0.00 | 0.00 | 41.38 | 4.37 |
139 | 143 | 8.608844 | AACGACATTATCTATCCCTTGAATTC | 57.391 | 34.615 | 0.00 | 0.00 | 0.00 | 2.17 |
156 | 160 | 7.765819 | TGTCAATCTCATGATAGAAACGACATT | 59.234 | 33.333 | 0.00 | 0.00 | 32.02 | 2.71 |
168 | 172 | 4.579340 | GGCTCAACATGTCAATCTCATGAT | 59.421 | 41.667 | 0.00 | 0.00 | 43.47 | 2.45 |
189 | 193 | 3.595108 | GAGTTTGCACGCCTTCGGC | 62.595 | 63.158 | 0.00 | 0.00 | 46.75 | 5.54 |
191 | 195 | 1.144969 | TTAGAGTTTGCACGCCTTCG | 58.855 | 50.000 | 0.00 | 0.00 | 42.43 | 3.79 |
411 | 442 | 0.537143 | TTGCGCACCTCACCTTCATT | 60.537 | 50.000 | 11.12 | 0.00 | 0.00 | 2.57 |
412 | 443 | 1.073025 | TTGCGCACCTCACCTTCAT | 59.927 | 52.632 | 11.12 | 0.00 | 0.00 | 2.57 |
429 | 460 | 6.014584 | AGCCCTTTTCTTTAAAATCGGATGTT | 60.015 | 34.615 | 0.00 | 0.00 | 34.18 | 2.71 |
430 | 461 | 5.480422 | AGCCCTTTTCTTTAAAATCGGATGT | 59.520 | 36.000 | 0.00 | 0.00 | 34.18 | 3.06 |
448 | 479 | 0.393537 | CATTTCTCGCTGGAGCCCTT | 60.394 | 55.000 | 0.00 | 0.00 | 40.26 | 3.95 |
722 | 753 | 6.147656 | CAGTAACCTTCCCAAAATTCAATTGC | 59.852 | 38.462 | 0.00 | 0.00 | 0.00 | 3.56 |
738 | 769 | 2.064242 | AACAGGCGCCCAGTAACCTT | 62.064 | 55.000 | 26.15 | 3.69 | 0.00 | 3.50 |
742 | 773 | 0.037590 | ATCAAACAGGCGCCCAGTAA | 59.962 | 50.000 | 26.15 | 11.79 | 0.00 | 2.24 |
754 | 785 | 5.701855 | TCTCATACGTTCGTACATCAAACA | 58.298 | 37.500 | 7.21 | 0.00 | 0.00 | 2.83 |
840 | 871 | 3.933332 | GCGTTTCTATGGCCTATATGACC | 59.067 | 47.826 | 3.32 | 0.00 | 0.00 | 4.02 |
885 | 916 | 1.486726 | CTACCTCCTCCATCCCACAAC | 59.513 | 57.143 | 0.00 | 0.00 | 0.00 | 3.32 |
948 | 1200 | 1.530013 | CTTTGCCCCCTGCTTGTGAG | 61.530 | 60.000 | 0.00 | 0.00 | 42.00 | 3.51 |
1231 | 1492 | 6.665248 | ACAATCTGGAAAGAAAAATAGAGGGG | 59.335 | 38.462 | 0.00 | 0.00 | 0.00 | 4.79 |
1234 | 1495 | 8.507249 | ACGAACAATCTGGAAAGAAAAATAGAG | 58.493 | 33.333 | 0.00 | 0.00 | 0.00 | 2.43 |
1288 | 1549 | 2.489938 | TGACCGGGAAGAAAGATTGG | 57.510 | 50.000 | 6.32 | 0.00 | 0.00 | 3.16 |
1314 | 1575 | 4.247267 | TCGTGGTTCTCACTAAATCGTT | 57.753 | 40.909 | 0.00 | 0.00 | 43.94 | 3.85 |
1535 | 1798 | 2.435586 | TCGTCCTCGGAGTCGGAC | 60.436 | 66.667 | 15.80 | 10.98 | 42.47 | 4.79 |
1660 | 1923 | 2.697761 | ATTCTGCTTGGCTGCTGCG | 61.698 | 57.895 | 9.65 | 0.00 | 40.82 | 5.18 |
1661 | 1924 | 1.153823 | CATTCTGCTTGGCTGCTGC | 60.154 | 57.895 | 7.10 | 7.10 | 38.76 | 5.25 |
1662 | 1925 | 1.511305 | CCATTCTGCTTGGCTGCTG | 59.489 | 57.895 | 0.00 | 4.56 | 0.00 | 4.41 |
1663 | 1926 | 4.013702 | CCATTCTGCTTGGCTGCT | 57.986 | 55.556 | 0.00 | 0.00 | 0.00 | 4.24 |
1669 | 1932 | 2.890371 | GCCAGGCCATTCTGCTTG | 59.110 | 61.111 | 5.01 | 0.00 | 38.01 | 4.01 |
1792 | 2055 | 2.224066 | CCCAAGATACCGGCACTAGAAG | 60.224 | 54.545 | 0.00 | 0.00 | 0.00 | 2.85 |
1802 | 2065 | 0.318762 | GCCTAGCTCCCAAGATACCG | 59.681 | 60.000 | 0.00 | 0.00 | 0.00 | 4.02 |
1884 | 2147 | 1.599797 | GTCCCCAACAACACTCGGG | 60.600 | 63.158 | 0.00 | 0.00 | 38.52 | 5.14 |
1933 | 2196 | 0.251341 | ACCATCTTCCTTGGGCACAC | 60.251 | 55.000 | 0.00 | 0.00 | 38.64 | 3.82 |
1975 | 2238 | 2.370189 | AGTAGCTCAGGAATGGCCATAC | 59.630 | 50.000 | 21.15 | 15.45 | 40.02 | 2.39 |
1997 | 2260 | 1.863454 | CATGCGCTACTGTCTTCCATC | 59.137 | 52.381 | 9.73 | 0.00 | 0.00 | 3.51 |
2176 | 2439 | 6.166982 | AGGTACAGCAAGATTGAGAAGTAAC | 58.833 | 40.000 | 0.00 | 0.00 | 0.00 | 2.50 |
2241 | 2504 | 0.250295 | CCAAGAAACGACTGGCAGGA | 60.250 | 55.000 | 20.34 | 0.00 | 0.00 | 3.86 |
2242 | 2505 | 1.856265 | GCCAAGAAACGACTGGCAGG | 61.856 | 60.000 | 20.34 | 4.16 | 44.42 | 4.85 |
2245 | 2508 | 0.238553 | GAAGCCAAGAAACGACTGGC | 59.761 | 55.000 | 4.11 | 4.11 | 45.30 | 4.85 |
2282 | 2549 | 3.413558 | GCCGTTTAGTAAACTTGCATCG | 58.586 | 45.455 | 20.60 | 8.04 | 39.23 | 3.84 |
2309 | 2576 | 2.089980 | ACCTGCAAGATGTCAGCAATC | 58.910 | 47.619 | 0.00 | 0.00 | 37.89 | 2.67 |
2422 | 2689 | 6.384224 | CACAACATATGCATCAAGACAAAGT | 58.616 | 36.000 | 0.19 | 0.00 | 0.00 | 2.66 |
2425 | 2692 | 4.158209 | CCCACAACATATGCATCAAGACAA | 59.842 | 41.667 | 0.19 | 0.00 | 0.00 | 3.18 |
2470 | 2737 | 3.349022 | TGATCACATGATTCTTGCAGCA | 58.651 | 40.909 | 0.00 | 0.00 | 34.37 | 4.41 |
2471 | 2738 | 4.276183 | AGATGATCACATGATTCTTGCAGC | 59.724 | 41.667 | 0.00 | 0.00 | 36.82 | 5.25 |
2472 | 2739 | 6.378710 | AAGATGATCACATGATTCTTGCAG | 57.621 | 37.500 | 0.00 | 0.00 | 33.03 | 4.41 |
2496 | 2763 | 5.076182 | TGAAACCATGCCACTTCTCATAAA | 58.924 | 37.500 | 0.00 | 0.00 | 0.00 | 1.40 |
2503 | 2770 | 3.821033 | ACTAACTGAAACCATGCCACTTC | 59.179 | 43.478 | 0.00 | 0.00 | 0.00 | 3.01 |
2533 | 2800 | 6.039047 | GGCATCAACATATCAGTTCAGTCATT | 59.961 | 38.462 | 0.00 | 0.00 | 0.00 | 2.57 |
2586 | 2865 | 9.748708 | CAAAGGTTTCATCAATAAAACAGAGAA | 57.251 | 29.630 | 0.00 | 0.00 | 37.16 | 2.87 |
2640 | 2919 | 4.870123 | TTAGTTGGTGCAATGCAATTCT | 57.130 | 36.364 | 10.44 | 8.90 | 41.47 | 2.40 |
2907 | 3189 | 4.651045 | GGGGTGCAGATAAATGAGGAAAAT | 59.349 | 41.667 | 0.00 | 0.00 | 0.00 | 1.82 |
2927 | 3209 | 4.278310 | ACGAAATTAAAGGAAGGATGGGG | 58.722 | 43.478 | 0.00 | 0.00 | 0.00 | 4.96 |
3033 | 3315 | 1.492176 | CACTAGGTGGCCATGAAGGAT | 59.508 | 52.381 | 9.72 | 0.00 | 41.22 | 3.24 |
3035 | 3317 | 0.911769 | TCACTAGGTGGCCATGAAGG | 59.088 | 55.000 | 9.72 | 1.05 | 33.87 | 3.46 |
3053 | 3335 | 4.437930 | GCTTGTTATTGGAGCTGATGTGTC | 60.438 | 45.833 | 0.00 | 0.00 | 33.72 | 3.67 |
3101 | 3383 | 1.203441 | TGTTGCTCTGATCCTGGGCT | 61.203 | 55.000 | 8.77 | 0.00 | 30.04 | 5.19 |
3155 | 3441 | 4.654262 | TCAGTCCTCAGTTAAGTGAAGGTT | 59.346 | 41.667 | 13.85 | 7.99 | 0.00 | 3.50 |
3166 | 3452 | 3.498774 | AGCAAATGTCAGTCCTCAGTT | 57.501 | 42.857 | 0.00 | 0.00 | 0.00 | 3.16 |
3317 | 3603 | 7.036220 | CGAGAGGAACAAGTAGTCAACAATAT | 58.964 | 38.462 | 0.00 | 0.00 | 0.00 | 1.28 |
3321 | 3607 | 3.635373 | ACGAGAGGAACAAGTAGTCAACA | 59.365 | 43.478 | 0.00 | 0.00 | 0.00 | 3.33 |
3335 | 3621 | 8.459911 | TCATACATGATAAGTAAACGAGAGGA | 57.540 | 34.615 | 0.00 | 0.00 | 0.00 | 3.71 |
3431 | 3717 | 6.796785 | ATTGTTGGGATAAAAGGAATGGAG | 57.203 | 37.500 | 0.00 | 0.00 | 0.00 | 3.86 |
3665 | 3954 | 4.017126 | CAATCCCCTTTTTCCTACCACTC | 58.983 | 47.826 | 0.00 | 0.00 | 0.00 | 3.51 |
3856 | 4147 | 7.093377 | TGCTTTCCAGATACAATTGGCTAATTT | 60.093 | 33.333 | 10.83 | 1.05 | 34.34 | 1.82 |
4250 | 4559 | 8.800972 | CAACACATGCAAATAAGTATAGCAAAG | 58.199 | 33.333 | 0.00 | 0.00 | 38.85 | 2.77 |
4290 | 4600 | 6.750501 | CAGCAATATGAAACAATCCAGAACAG | 59.249 | 38.462 | 0.00 | 0.00 | 0.00 | 3.16 |
4429 | 4739 | 6.786843 | ATTGGGAGTATGAGGATAACCATT | 57.213 | 37.500 | 0.00 | 0.00 | 38.94 | 3.16 |
4434 | 4744 | 8.877195 | GTTAACCTATTGGGAGTATGAGGATAA | 58.123 | 37.037 | 0.00 | 0.00 | 38.76 | 1.75 |
4524 | 4873 | 8.395940 | ACGAGAAAATATTAGTCAGAAACTCG | 57.604 | 34.615 | 0.00 | 0.00 | 44.62 | 4.18 |
4541 | 4893 | 4.814234 | ACTAACATGTGAGCAACGAGAAAA | 59.186 | 37.500 | 10.40 | 0.00 | 0.00 | 2.29 |
4582 | 4934 | 3.621268 | GGTTGTTGTCATCAAGCGCTATA | 59.379 | 43.478 | 12.05 | 1.09 | 34.51 | 1.31 |
4606 | 4958 | 1.153667 | GTCAGAAGCTCCTCTGCGG | 60.154 | 63.158 | 10.11 | 0.00 | 42.25 | 5.69 |
4645 | 4997 | 3.258971 | AGAACCTCAGCAACAGATAGC | 57.741 | 47.619 | 0.00 | 0.00 | 0.00 | 2.97 |
4703 | 5056 | 1.549203 | CCTTCCAAACCCCACAGATG | 58.451 | 55.000 | 0.00 | 0.00 | 0.00 | 2.90 |
4755 | 5108 | 2.347490 | GCGGCTTTCTCCCTGACA | 59.653 | 61.111 | 0.00 | 0.00 | 0.00 | 3.58 |
4775 | 5128 | 1.134580 | CATATAGGGCAGGGCTCATCG | 60.135 | 57.143 | 0.00 | 0.00 | 0.00 | 3.84 |
4778 | 5131 | 1.492133 | GGCATATAGGGCAGGGCTCA | 61.492 | 60.000 | 6.02 | 0.00 | 0.00 | 4.26 |
4955 | 5309 | 1.191489 | TCATCCGAAGCCACCTGTCA | 61.191 | 55.000 | 0.00 | 0.00 | 0.00 | 3.58 |
5101 | 5456 | 3.427528 | ACATTACAAGTTGTCTACGCACG | 59.572 | 43.478 | 12.82 | 0.00 | 0.00 | 5.34 |
5146 | 5502 | 2.804167 | CTCACCGCGCAGAGAGAT | 59.196 | 61.111 | 17.79 | 0.00 | 33.74 | 2.75 |
5156 | 5512 | 3.117171 | CTGCTCACTGCTCACCGC | 61.117 | 66.667 | 0.00 | 0.00 | 43.37 | 5.68 |
5157 | 5513 | 1.445754 | CTCTGCTCACTGCTCACCG | 60.446 | 63.158 | 0.00 | 0.00 | 43.37 | 4.94 |
5158 | 5514 | 0.108709 | CTCTCTGCTCACTGCTCACC | 60.109 | 60.000 | 0.00 | 0.00 | 43.37 | 4.02 |
5159 | 5515 | 0.602562 | ACTCTCTGCTCACTGCTCAC | 59.397 | 55.000 | 0.00 | 0.00 | 43.37 | 3.51 |
5160 | 5516 | 0.602060 | CACTCTCTGCTCACTGCTCA | 59.398 | 55.000 | 0.00 | 0.00 | 43.37 | 4.26 |
5161 | 5517 | 0.602562 | ACACTCTCTGCTCACTGCTC | 59.397 | 55.000 | 0.00 | 0.00 | 43.37 | 4.26 |
5176 | 5532 | 1.470098 | GCTCCGCATCATTCAAACACT | 59.530 | 47.619 | 0.00 | 0.00 | 0.00 | 3.55 |
5185 | 5541 | 2.447379 | AGAGGGGCTCCGCATCAT | 60.447 | 61.111 | 9.79 | 0.00 | 38.33 | 2.45 |
5198 | 5554 | 4.244862 | GCAACAGAAGAGAAAGAGAGAGG | 58.755 | 47.826 | 0.00 | 0.00 | 0.00 | 3.69 |
5203 | 5563 | 2.483491 | GCAGGCAACAGAAGAGAAAGAG | 59.517 | 50.000 | 0.00 | 0.00 | 41.41 | 2.85 |
5207 | 5567 | 0.392706 | TCGCAGGCAACAGAAGAGAA | 59.607 | 50.000 | 0.00 | 0.00 | 41.41 | 2.87 |
5240 | 5600 | 6.018016 | GCAGCAAAAAGGAACACAATATTTGT | 60.018 | 34.615 | 0.00 | 0.00 | 46.75 | 2.83 |
5273 | 5634 | 1.878211 | TCATACATCTCCCCTGCACA | 58.122 | 50.000 | 0.00 | 0.00 | 0.00 | 4.57 |
5289 | 5650 | 5.045651 | TGACATGGAAATCGGGCTATATCAT | 60.046 | 40.000 | 0.00 | 0.00 | 0.00 | 2.45 |
5300 | 5661 | 1.066002 | GCCCACATGACATGGAAATCG | 59.934 | 52.381 | 19.39 | 2.33 | 39.87 | 3.34 |
5340 | 5701 | 4.706476 | CAGCAGAATAAACCTTTCATCCCA | 59.294 | 41.667 | 0.00 | 0.00 | 0.00 | 4.37 |
5381 | 5742 | 8.473358 | TCTAATAATTCGAGATCCCAGTAACA | 57.527 | 34.615 | 0.00 | 0.00 | 0.00 | 2.41 |
5406 | 5767 | 8.246871 | GCTTTCAGCTAAAAAGACCAGATAATT | 58.753 | 33.333 | 19.71 | 0.00 | 38.45 | 1.40 |
5408 | 5769 | 6.714810 | TGCTTTCAGCTAAAAAGACCAGATAA | 59.285 | 34.615 | 19.71 | 0.00 | 42.97 | 1.75 |
5412 | 5773 | 4.836125 | TGCTTTCAGCTAAAAAGACCAG | 57.164 | 40.909 | 19.71 | 0.18 | 42.97 | 4.00 |
5413 | 5774 | 4.218417 | GGATGCTTTCAGCTAAAAAGACCA | 59.782 | 41.667 | 19.71 | 11.81 | 42.97 | 4.02 |
5414 | 5775 | 4.218417 | TGGATGCTTTCAGCTAAAAAGACC | 59.782 | 41.667 | 19.71 | 17.63 | 42.97 | 3.85 |
5415 | 5776 | 5.376854 | TGGATGCTTTCAGCTAAAAAGAC | 57.623 | 39.130 | 19.71 | 13.08 | 42.97 | 3.01 |
5438 | 5812 | 3.944087 | ACAGATTACTGAAGAACCAGGC | 58.056 | 45.455 | 0.00 | 0.00 | 46.03 | 4.85 |
5486 | 5865 | 8.675504 | TGAACAATTTACTGGTTCGAACTTAAA | 58.324 | 29.630 | 26.32 | 23.38 | 42.86 | 1.52 |
5487 | 5866 | 8.211116 | TGAACAATTTACTGGTTCGAACTTAA | 57.789 | 30.769 | 26.32 | 17.61 | 42.86 | 1.85 |
5492 | 5871 | 6.928979 | TTCTGAACAATTTACTGGTTCGAA | 57.071 | 33.333 | 0.00 | 0.00 | 42.86 | 3.71 |
5517 | 5896 | 7.642669 | CCACCATGATCACAAAGTAATATGAC | 58.357 | 38.462 | 0.00 | 0.00 | 0.00 | 3.06 |
5520 | 5899 | 6.128486 | TGCCACCATGATCACAAAGTAATAT | 58.872 | 36.000 | 0.00 | 0.00 | 0.00 | 1.28 |
5522 | 5901 | 4.343231 | TGCCACCATGATCACAAAGTAAT | 58.657 | 39.130 | 0.00 | 0.00 | 0.00 | 1.89 |
5531 | 5910 | 1.410507 | CCTCCATTGCCACCATGATCA | 60.411 | 52.381 | 0.00 | 0.00 | 0.00 | 2.92 |
5532 | 5911 | 1.325355 | CCTCCATTGCCACCATGATC | 58.675 | 55.000 | 0.00 | 0.00 | 0.00 | 2.92 |
5533 | 5912 | 0.632835 | ACCTCCATTGCCACCATGAT | 59.367 | 50.000 | 0.00 | 0.00 | 0.00 | 2.45 |
5534 | 5913 | 0.323633 | CACCTCCATTGCCACCATGA | 60.324 | 55.000 | 0.00 | 0.00 | 0.00 | 3.07 |
5535 | 5914 | 0.323633 | TCACCTCCATTGCCACCATG | 60.324 | 55.000 | 0.00 | 0.00 | 0.00 | 3.66 |
5536 | 5915 | 0.409092 | TTCACCTCCATTGCCACCAT | 59.591 | 50.000 | 0.00 | 0.00 | 0.00 | 3.55 |
5537 | 5916 | 0.187117 | TTTCACCTCCATTGCCACCA | 59.813 | 50.000 | 0.00 | 0.00 | 0.00 | 4.17 |
5538 | 5917 | 1.337118 | TTTTCACCTCCATTGCCACC | 58.663 | 50.000 | 0.00 | 0.00 | 0.00 | 4.61 |
5539 | 5918 | 2.562298 | TGATTTTCACCTCCATTGCCAC | 59.438 | 45.455 | 0.00 | 0.00 | 0.00 | 5.01 |
5540 | 5919 | 2.827322 | CTGATTTTCACCTCCATTGCCA | 59.173 | 45.455 | 0.00 | 0.00 | 0.00 | 4.92 |
5543 | 5922 | 3.508793 | ACAGCTGATTTTCACCTCCATTG | 59.491 | 43.478 | 23.35 | 0.00 | 0.00 | 2.82 |
5544 | 5923 | 3.771216 | ACAGCTGATTTTCACCTCCATT | 58.229 | 40.909 | 23.35 | 0.00 | 0.00 | 3.16 |
5546 | 5925 | 2.957402 | ACAGCTGATTTTCACCTCCA | 57.043 | 45.000 | 23.35 | 0.00 | 0.00 | 3.86 |
5547 | 5926 | 4.265073 | ACATACAGCTGATTTTCACCTCC | 58.735 | 43.478 | 23.35 | 0.00 | 0.00 | 4.30 |
5548 | 5927 | 6.985188 | TTACATACAGCTGATTTTCACCTC | 57.015 | 37.500 | 23.35 | 0.00 | 0.00 | 3.85 |
5549 | 5928 | 7.112122 | TGATTACATACAGCTGATTTTCACCT | 58.888 | 34.615 | 23.35 | 0.00 | 0.00 | 4.00 |
5551 | 5930 | 7.859377 | CCATGATTACATACAGCTGATTTTCAC | 59.141 | 37.037 | 23.35 | 5.97 | 35.09 | 3.18 |
5552 | 5931 | 7.557358 | ACCATGATTACATACAGCTGATTTTCA | 59.443 | 33.333 | 23.35 | 13.24 | 35.09 | 2.69 |
5553 | 5932 | 7.934457 | ACCATGATTACATACAGCTGATTTTC | 58.066 | 34.615 | 23.35 | 8.08 | 35.09 | 2.29 |
5568 | 6099 | 3.997762 | TGCCGTATGGTACCATGATTAC | 58.002 | 45.455 | 33.41 | 22.91 | 37.82 | 1.89 |
5579 | 6110 | 0.107214 | CACCTCCATTGCCGTATGGT | 60.107 | 55.000 | 2.17 | 0.00 | 44.48 | 3.55 |
5581 | 6112 | 2.036958 | TTCACCTCCATTGCCGTATG | 57.963 | 50.000 | 0.00 | 0.00 | 0.00 | 2.39 |
5585 | 6116 | 1.818060 | TGATTTTCACCTCCATTGCCG | 59.182 | 47.619 | 0.00 | 0.00 | 0.00 | 5.69 |
5604 | 6135 | 2.166459 | TCCGAGTTGCATAGGAGAAGTG | 59.834 | 50.000 | 0.00 | 0.00 | 0.00 | 3.16 |
5608 | 6139 | 3.197766 | ACATTTCCGAGTTGCATAGGAGA | 59.802 | 43.478 | 0.00 | 0.00 | 33.89 | 3.71 |
5659 | 6192 | 5.923204 | ACTGCTGGAAAATATCTACTCCTG | 58.077 | 41.667 | 0.00 | 0.00 | 0.00 | 3.86 |
5661 | 6194 | 6.481644 | CAGAACTGCTGGAAAATATCTACTCC | 59.518 | 42.308 | 0.00 | 0.00 | 41.07 | 3.85 |
6180 | 6726 | 3.583086 | GAATGGGCTTACCGGCGC | 61.583 | 66.667 | 0.00 | 0.00 | 44.64 | 6.53 |
6237 | 6783 | 0.673644 | AAATTCACCGAGCGGGACTG | 60.674 | 55.000 | 14.07 | 2.83 | 39.97 | 3.51 |
6296 | 6842 | 5.734720 | TGGTTAGGAGCTTCAGAATAACAG | 58.265 | 41.667 | 0.00 | 0.00 | 0.00 | 3.16 |
6306 | 6852 | 3.181506 | CGAATTGCTTGGTTAGGAGCTTC | 60.182 | 47.826 | 0.00 | 0.00 | 39.60 | 3.86 |
6339 | 6885 | 0.178929 | AAACCCTGAGTCCTCGTCCT | 60.179 | 55.000 | 0.00 | 0.00 | 0.00 | 3.85 |
6414 | 6965 | 4.626628 | GCGAAACGATTGTCGAGC | 57.373 | 55.556 | 6.34 | 2.89 | 43.74 | 5.03 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.