Multiple sequence alignment - TraesCS2D01G489300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


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 TraesCS2D01G489300 chr2D 100.000 3364 0 0 1 3364 588434927 588438290 0.000000e+00 6213.0
1 TraesCS2D01G489300 chr2D 82.476 1769 222 59 471 2201 588248461 588250179 0.000000e+00 1469.0
2 TraesCS2D01G489300 chr2D 96.837 664 12 7 2707 3364 588444662 588445322 0.000000e+00 1101.0
3 TraesCS2D01G489300 chr2D 77.034 1389 262 44 472 1814 635205735 635207112 0.000000e+00 745.0
4 TraesCS2D01G489300 chr2D 79.601 853 141 24 471 1306 588175583 588174747 6.260000e-162 580.0
5 TraesCS2D01G489300 chr2D 77.936 911 152 34 467 1346 588453153 588454045 1.070000e-144 523.0
6 TraesCS2D01G489300 chr2D 79.503 161 18 13 91 239 588235957 588236114 2.140000e-17 100.0
7 TraesCS2D01G489300 chr2D 75.269 186 32 9 61 239 588245669 588245847 3.600000e-10 76.8
8 TraesCS2D01G489300 chr2B 95.518 1852 61 8 437 2266 711867306 711869157 0.000000e+00 2940.0
9 TraesCS2D01G489300 chr2B 82.453 1761 237 47 471 2201 711726119 711727837 0.000000e+00 1474.0
10 TraesCS2D01G489300 chr2B 79.530 894 144 30 470 1346 711321093 711320222 4.800000e-168 601.0
11 TraesCS2D01G489300 chr2B 92.199 423 20 5 1 416 711866783 711867199 1.340000e-163 586.0
12 TraesCS2D01G489300 chr2B 89.450 218 16 3 2492 2708 711979308 711979519 5.530000e-68 268.0
13 TraesCS2D01G489300 chr2B 84.483 174 25 2 2321 2494 695838299 695838128 1.600000e-38 171.0
14 TraesCS2D01G489300 chr2B 77.564 156 21 7 91 239 711718048 711718196 7.740000e-12 82.4
15 TraesCS2D01G489300 chr2B 90.000 60 6 0 180 239 711723912 711723971 1.000000e-10 78.7
16 TraesCS2D01G489300 chr2A 94.470 1501 72 5 437 1927 723061423 723062922 0.000000e+00 2302.0
17 TraesCS2D01G489300 chr2A 81.700 1765 240 58 471 2201 722839861 722841576 0.000000e+00 1393.0
18 TraesCS2D01G489300 chr2A 76.691 1390 266 45 472 1814 777614756 777613378 0.000000e+00 719.0
19 TraesCS2D01G489300 chr2A 76.225 1388 272 40 472 1814 777809590 777808216 0.000000e+00 682.0
20 TraesCS2D01G489300 chr2A 75.540 1390 283 40 472 1814 777836909 777835530 6.130000e-177 630.0
21 TraesCS2D01G489300 chr2A 79.507 893 144 28 471 1346 722756484 722755614 1.730000e-167 599.0
22 TraesCS2D01G489300 chr2A 78.438 909 158 25 472 1347 778799516 778800419 2.930000e-155 558.0
23 TraesCS2D01G489300 chr2A 77.620 916 156 31 462 1346 723066375 723067272 8.330000e-141 510.0
24 TraesCS2D01G489300 chr2A 86.047 430 22 15 1 424 723060944 723061341 8.630000e-116 427.0
25 TraesCS2D01G489300 chr2A 95.181 249 11 1 2015 2263 723062986 723063233 3.150000e-105 392.0
26 TraesCS2D01G489300 chr2A 80.720 389 70 4 1438 1822 722755596 722755209 7.060000e-77 298.0
27 TraesCS2D01G489300 chr2A 79.950 404 72 3 1417 1814 778803079 778803479 4.250000e-74 289.0
28 TraesCS2D01G489300 chr2A 78.646 192 20 14 60 239 722830986 722831168 1.280000e-19 108.0
29 TraesCS2D01G489300 chr2A 75.676 185 31 11 62 239 722837590 722837767 2.780000e-11 80.5
30 TraesCS2D01G489300 chr2A 90.741 54 5 0 186 239 778798143 778798196 4.660000e-09 73.1
31 TraesCS2D01G489300 chr4D 96.692 665 9 7 2707 3364 272237057 272237715 0.000000e+00 1094.0
32 TraesCS2D01G489300 chr4D 96.536 664 15 6 2707 3364 27126703 27126042 0.000000e+00 1092.0
33 TraesCS2D01G489300 chr4D 95.958 668 16 7 2706 3364 27133728 27133063 0.000000e+00 1074.0
34 TraesCS2D01G489300 chr4D 84.146 164 22 4 2307 2468 34712167 34712006 4.490000e-34 156.0
35 TraesCS2D01G489300 chr4D 81.053 190 32 4 2311 2498 182068511 182068698 7.520000e-32 148.0
36 TraesCS2D01G489300 chr6D 96.541 665 12 7 2708 3364 306167713 306168374 0.000000e+00 1090.0
37 TraesCS2D01G489300 chr3D 96.536 664 14 6 2707 3364 586402720 586403380 0.000000e+00 1090.0
38 TraesCS2D01G489300 chr3D 82.540 189 28 5 2311 2496 54675337 54675151 9.660000e-36 161.0
39 TraesCS2D01G489300 chr3D 82.022 178 31 1 2321 2498 25341024 25340848 2.090000e-32 150.0
40 TraesCS2D01G489300 chr7D 96.526 662 15 4 2707 3364 5537475 5536818 0.000000e+00 1088.0
41 TraesCS2D01G489300 chr7D 96.526 662 14 6 2707 3364 567248525 567249181 0.000000e+00 1086.0
42 TraesCS2D01G489300 chr1D 96.531 663 13 6 2707 3364 382385813 382386470 0.000000e+00 1088.0
43 TraesCS2D01G489300 chr4A 86.286 175 22 2 2330 2503 561113660 561113833 4.430000e-44 189.0
44 TraesCS2D01G489300 chr3A 81.771 192 32 3 2310 2499 544423511 544423701 1.250000e-34 158.0
45 TraesCS2D01G489300 chrUn 81.383 188 32 3 2321 2506 199304443 199304629 2.090000e-32 150.0
46 TraesCS2D01G489300 chr5B 81.383 188 32 3 2321 2506 102433730 102433544 2.090000e-32 150.0


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 TraesCS2D01G489300 chr2D 588434927 588438290 3363 False 6213.00 6213 100.0000 1 3364 1 chr2D.!!$F2 3363
1 TraesCS2D01G489300 chr2D 588444662 588445322 660 False 1101.00 1101 96.8370 2707 3364 1 chr2D.!!$F3 657
2 TraesCS2D01G489300 chr2D 588245669 588250179 4510 False 772.90 1469 78.8725 61 2201 2 chr2D.!!$F6 2140
3 TraesCS2D01G489300 chr2D 635205735 635207112 1377 False 745.00 745 77.0340 472 1814 1 chr2D.!!$F5 1342
4 TraesCS2D01G489300 chr2D 588174747 588175583 836 True 580.00 580 79.6010 471 1306 1 chr2D.!!$R1 835
5 TraesCS2D01G489300 chr2D 588453153 588454045 892 False 523.00 523 77.9360 467 1346 1 chr2D.!!$F4 879
6 TraesCS2D01G489300 chr2B 711866783 711869157 2374 False 1763.00 2940 93.8585 1 2266 2 chr2B.!!$F4 2265
7 TraesCS2D01G489300 chr2B 711723912 711727837 3925 False 776.35 1474 86.2265 180 2201 2 chr2B.!!$F3 2021
8 TraesCS2D01G489300 chr2B 711320222 711321093 871 True 601.00 601 79.5300 470 1346 1 chr2B.!!$R2 876
9 TraesCS2D01G489300 chr2A 723060944 723067272 6328 False 907.75 2302 88.3295 1 2263 4 chr2A.!!$F3 2262
10 TraesCS2D01G489300 chr2A 722837590 722841576 3986 False 736.75 1393 78.6880 62 2201 2 chr2A.!!$F2 2139
11 TraesCS2D01G489300 chr2A 777613378 777614756 1378 True 719.00 719 76.6910 472 1814 1 chr2A.!!$R1 1342
12 TraesCS2D01G489300 chr2A 777808216 777809590 1374 True 682.00 682 76.2250 472 1814 1 chr2A.!!$R2 1342
13 TraesCS2D01G489300 chr2A 777835530 777836909 1379 True 630.00 630 75.5400 472 1814 1 chr2A.!!$R3 1342
14 TraesCS2D01G489300 chr2A 722755209 722756484 1275 True 448.50 599 80.1135 471 1822 2 chr2A.!!$R4 1351
15 TraesCS2D01G489300 chr2A 778798143 778803479 5336 False 306.70 558 83.0430 186 1814 3 chr2A.!!$F4 1628
16 TraesCS2D01G489300 chr4D 272237057 272237715 658 False 1094.00 1094 96.6920 2707 3364 1 chr4D.!!$F2 657
17 TraesCS2D01G489300 chr4D 27126042 27126703 661 True 1092.00 1092 96.5360 2707 3364 1 chr4D.!!$R1 657
18 TraesCS2D01G489300 chr4D 27133063 27133728 665 True 1074.00 1074 95.9580 2706 3364 1 chr4D.!!$R2 658
19 TraesCS2D01G489300 chr6D 306167713 306168374 661 False 1090.00 1090 96.5410 2708 3364 1 chr6D.!!$F1 656
20 TraesCS2D01G489300 chr3D 586402720 586403380 660 False 1090.00 1090 96.5360 2707 3364 1 chr3D.!!$F1 657
21 TraesCS2D01G489300 chr7D 5536818 5537475 657 True 1088.00 1088 96.5260 2707 3364 1 chr7D.!!$R1 657
22 TraesCS2D01G489300 chr7D 567248525 567249181 656 False 1086.00 1086 96.5260 2707 3364 1 chr7D.!!$F1 657
23 TraesCS2D01G489300 chr1D 382385813 382386470 657 False 1088.00 1088 96.5310 2707 3364 1 chr1D.!!$F1 657

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
389 417 0.249489 ATCCGAATGGTACGCTCTGC 60.249 55.0 0.00 0.0 36.30 4.26 F
757 4199 0.749454 CCTTCCCCAAGAATGCCTCG 60.749 60.0 0.00 0.0 32.82 4.63 F
2141 8296 0.108041 ACGTGTTCAACAACGGGACT 60.108 50.0 14.31 0.0 34.95 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 8165 0.031585 TGGTCAACCTGTTCGTCGAG 59.968 55.000 0.1 0.0 36.82 4.04 R
2252 8407 0.106217 AAACCAGTCCCCACACCTTG 60.106 55.000 0.0 0.0 0.00 3.61 R
3091 9294 1.076777 AGGGCAGCAACACAACAGT 60.077 52.632 0.0 0.0 0.00 3.55 R

All possible primers

Listed 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.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
151 152 2.365105 CTCTCCGGTTAGCCCCCA 60.365 66.667 0.00 0.00 0.00 4.96
198 205 2.034532 CATGGCAGTGGCAGGACA 59.965 61.111 25.35 0.10 42.32 4.02
245 252 2.009774 CTGGCAGAACGGTAGGAATTG 58.990 52.381 9.42 0.00 0.00 2.32
321 328 3.865446 TGGCTAATCTGATCACTGTGTG 58.135 45.455 7.79 0.00 34.45 3.82
389 417 0.249489 ATCCGAATGGTACGCTCTGC 60.249 55.000 0.00 0.00 36.30 4.26
390 418 1.141881 CCGAATGGTACGCTCTGCT 59.858 57.895 0.00 0.00 0.00 4.24
392 420 0.924090 CGAATGGTACGCTCTGCTTC 59.076 55.000 0.00 0.00 0.00 3.86
424 463 4.706962 TCTGCATTCTGCTGAGTTACTAGA 59.293 41.667 0.00 0.00 44.54 2.43
426 465 4.706962 TGCATTCTGCTGAGTTACTAGAGA 59.293 41.667 0.00 0.00 45.31 3.10
432 471 5.820423 TCTGCTGAGTTACTAGAGATCAGAC 59.180 44.000 17.23 11.44 39.80 3.51
434 473 4.553938 GCTGAGTTACTAGAGATCAGACGC 60.554 50.000 17.23 5.27 39.80 5.19
435 474 3.878103 TGAGTTACTAGAGATCAGACGCC 59.122 47.826 0.00 0.00 0.00 5.68
487 3920 4.684623 GCAGGGCCAATGTACCAT 57.315 55.556 6.18 0.00 0.00 3.55
596 4029 1.371558 GACCTCGTGAACTGGGCTT 59.628 57.895 0.00 0.00 0.00 4.35
757 4199 0.749454 CCTTCCCCAAGAATGCCTCG 60.749 60.000 0.00 0.00 32.82 4.63
942 4394 1.076332 ACGCTCATTACCGAAGCAAC 58.924 50.000 0.00 0.00 0.00 4.17
1176 4655 1.226030 CGACGGACACCTTTGAACCC 61.226 60.000 0.00 0.00 0.00 4.11
1371 4864 4.579384 CACCGCCACCACCCAACT 62.579 66.667 0.00 0.00 0.00 3.16
1732 7875 3.838271 GCTCGTCATGGCCTCCGA 61.838 66.667 3.32 5.37 0.00 4.55
1970 8118 6.475504 TGAATCTTTTGCTCTGGTTCAGATA 58.524 36.000 0.00 0.00 39.92 1.98
1971 8119 6.372659 TGAATCTTTTGCTCTGGTTCAGATAC 59.627 38.462 0.00 0.00 39.92 2.24
2010 8165 8.906636 TCGAGTACTTATTACAACTTGTGATC 57.093 34.615 4.57 0.00 32.41 2.92
2141 8296 0.108041 ACGTGTTCAACAACGGGACT 60.108 50.000 14.31 0.00 34.95 3.85
2252 8407 3.768632 CGCAGAGGTGAAGCGTAC 58.231 61.111 0.00 0.00 45.82 3.67
2266 8421 2.055299 CGTACAAGGTGTGGGGACT 58.945 57.895 0.00 0.00 0.00 3.85
2267 8422 0.320421 CGTACAAGGTGTGGGGACTG 60.320 60.000 0.00 0.00 0.00 3.51
2268 8423 0.036306 GTACAAGGTGTGGGGACTGG 59.964 60.000 0.00 0.00 0.00 4.00
2269 8424 0.400815 TACAAGGTGTGGGGACTGGT 60.401 55.000 0.00 0.00 0.00 4.00
2270 8425 1.286305 ACAAGGTGTGGGGACTGGTT 61.286 55.000 0.00 0.00 0.00 3.67
2271 8426 0.106217 CAAGGTGTGGGGACTGGTTT 60.106 55.000 0.00 0.00 0.00 3.27
2273 8428 0.106217 AGGTGTGGGGACTGGTTTTG 60.106 55.000 0.00 0.00 0.00 2.44
2274 8429 0.396556 GGTGTGGGGACTGGTTTTGT 60.397 55.000 0.00 0.00 0.00 2.83
2275 8430 1.480789 GTGTGGGGACTGGTTTTGTT 58.519 50.000 0.00 0.00 0.00 2.83
2276 8431 1.407618 GTGTGGGGACTGGTTTTGTTC 59.592 52.381 0.00 0.00 0.00 3.18
2277 8432 0.666374 GTGGGGACTGGTTTTGTTCG 59.334 55.000 0.00 0.00 0.00 3.95
2278 8433 0.256464 TGGGGACTGGTTTTGTTCGT 59.744 50.000 0.00 0.00 0.00 3.85
2279 8434 0.666374 GGGGACTGGTTTTGTTCGTG 59.334 55.000 0.00 0.00 0.00 4.35
2281 8436 0.030235 GGACTGGTTTTGTTCGTGCC 59.970 55.000 0.00 0.00 0.00 5.01
2282 8437 0.736053 GACTGGTTTTGTTCGTGCCA 59.264 50.000 0.00 0.00 0.00 4.92
2283 8438 1.336755 GACTGGTTTTGTTCGTGCCAT 59.663 47.619 0.00 0.00 0.00 4.40
2284 8439 1.066908 ACTGGTTTTGTTCGTGCCATG 59.933 47.619 0.00 0.00 0.00 3.66
2285 8440 0.387202 TGGTTTTGTTCGTGCCATGG 59.613 50.000 7.63 7.63 0.00 3.66
2286 8441 0.943835 GGTTTTGTTCGTGCCATGGC 60.944 55.000 30.54 30.54 42.35 4.40
2287 8442 0.943835 GTTTTGTTCGTGCCATGGCC 60.944 55.000 33.44 22.58 41.09 5.36
2306 8490 2.094675 CCCTCATGTCAAATTTCGGCT 58.905 47.619 0.00 0.00 0.00 5.52
2314 8498 2.091541 TCAAATTTCGGCTGGCTTAGG 58.908 47.619 0.00 0.00 0.00 2.69
2315 8499 1.818674 CAAATTTCGGCTGGCTTAGGT 59.181 47.619 0.00 0.00 0.00 3.08
2317 8501 0.107165 ATTTCGGCTGGCTTAGGTCC 60.107 55.000 0.00 0.00 0.00 4.46
2318 8502 2.193087 TTTCGGCTGGCTTAGGTCCC 62.193 60.000 0.00 0.00 0.00 4.46
2319 8503 3.083997 CGGCTGGCTTAGGTCCCT 61.084 66.667 0.00 0.00 0.00 4.20
2323 8507 0.909623 GCTGGCTTAGGTCCCTTACA 59.090 55.000 0.00 0.00 0.00 2.41
2324 8508 1.280998 GCTGGCTTAGGTCCCTTACAA 59.719 52.381 0.00 0.00 0.00 2.41
2325 8509 2.092375 GCTGGCTTAGGTCCCTTACAAT 60.092 50.000 0.00 0.00 0.00 2.71
2326 8510 3.545703 CTGGCTTAGGTCCCTTACAATG 58.454 50.000 0.00 0.00 0.00 2.82
2327 8511 2.298610 GGCTTAGGTCCCTTACAATGC 58.701 52.381 0.00 0.00 0.00 3.56
2328 8512 2.356741 GGCTTAGGTCCCTTACAATGCA 60.357 50.000 0.00 0.00 0.00 3.96
2329 8513 3.352648 GCTTAGGTCCCTTACAATGCAA 58.647 45.455 0.00 0.00 0.00 4.08
2330 8514 3.378427 GCTTAGGTCCCTTACAATGCAAG 59.622 47.826 0.00 0.00 0.00 4.01
2331 8515 2.514458 AGGTCCCTTACAATGCAAGG 57.486 50.000 5.26 5.26 41.97 3.61
2332 8516 1.710809 AGGTCCCTTACAATGCAAGGT 59.289 47.619 11.05 0.00 40.92 3.50
2333 8517 1.818674 GGTCCCTTACAATGCAAGGTG 59.181 52.381 11.05 3.51 40.92 4.00
2334 8518 1.202348 GTCCCTTACAATGCAAGGTGC 59.798 52.381 11.05 0.43 45.29 5.01
2335 8519 1.075374 TCCCTTACAATGCAAGGTGCT 59.925 47.619 11.05 0.00 45.31 4.40
2336 8520 1.895131 CCCTTACAATGCAAGGTGCTT 59.105 47.619 11.05 0.00 45.31 3.91
2337 8521 3.088532 CCCTTACAATGCAAGGTGCTTA 58.911 45.455 11.05 0.00 45.31 3.09
2338 8522 3.129287 CCCTTACAATGCAAGGTGCTTAG 59.871 47.826 11.05 0.00 45.31 2.18
2339 8523 4.009675 CCTTACAATGCAAGGTGCTTAGA 58.990 43.478 4.08 0.00 45.31 2.10
2340 8524 4.095483 CCTTACAATGCAAGGTGCTTAGAG 59.905 45.833 4.08 0.00 45.31 2.43
2341 8525 3.423539 ACAATGCAAGGTGCTTAGAGA 57.576 42.857 0.00 0.00 45.31 3.10
2342 8526 3.754965 ACAATGCAAGGTGCTTAGAGAA 58.245 40.909 0.00 0.00 45.31 2.87
2343 8527 4.144297 ACAATGCAAGGTGCTTAGAGAAA 58.856 39.130 0.00 0.00 45.31 2.52
2344 8528 4.768968 ACAATGCAAGGTGCTTAGAGAAAT 59.231 37.500 0.00 0.00 45.31 2.17
2345 8529 5.945784 ACAATGCAAGGTGCTTAGAGAAATA 59.054 36.000 0.00 0.00 45.31 1.40
2346 8530 6.434028 ACAATGCAAGGTGCTTAGAGAAATAA 59.566 34.615 0.00 0.00 45.31 1.40
2347 8531 7.039784 ACAATGCAAGGTGCTTAGAGAAATAAA 60.040 33.333 0.00 0.00 45.31 1.40
2348 8532 6.254281 TGCAAGGTGCTTAGAGAAATAAAC 57.746 37.500 1.43 0.00 45.31 2.01
2349 8533 5.183140 TGCAAGGTGCTTAGAGAAATAAACC 59.817 40.000 1.43 0.00 45.31 3.27
2350 8534 5.183140 GCAAGGTGCTTAGAGAAATAAACCA 59.817 40.000 0.00 0.00 40.96 3.67
2351 8535 6.294508 GCAAGGTGCTTAGAGAAATAAACCAA 60.295 38.462 0.00 0.00 40.96 3.67
2352 8536 7.308435 CAAGGTGCTTAGAGAAATAAACCAAG 58.692 38.462 0.00 0.00 0.00 3.61
2353 8537 6.543735 AGGTGCTTAGAGAAATAAACCAAGT 58.456 36.000 0.00 0.00 0.00 3.16
2354 8538 7.004691 AGGTGCTTAGAGAAATAAACCAAGTT 58.995 34.615 0.00 0.00 0.00 2.66
2355 8539 7.505923 AGGTGCTTAGAGAAATAAACCAAGTTT 59.494 33.333 0.00 0.00 39.24 2.66
2356 8540 8.141909 GGTGCTTAGAGAAATAAACCAAGTTTT 58.858 33.333 0.00 0.00 37.01 2.43
2357 8541 9.529325 GTGCTTAGAGAAATAAACCAAGTTTTT 57.471 29.630 0.00 0.00 37.01 1.94
2371 8555 9.830975 AAACCAAGTTTTTATTTAAGCATCAGT 57.169 25.926 0.00 0.00 31.10 3.41
2372 8556 8.816640 ACCAAGTTTTTATTTAAGCATCAGTG 57.183 30.769 0.00 0.00 0.00 3.66
2390 8574 8.994429 CATCAGTGCTTATTTATAGAGGGTAG 57.006 38.462 0.00 0.00 0.00 3.18
2391 8575 6.994221 TCAGTGCTTATTTATAGAGGGTAGC 58.006 40.000 0.00 0.00 0.00 3.58
2392 8576 6.014499 TCAGTGCTTATTTATAGAGGGTAGCC 60.014 42.308 1.60 1.60 0.00 3.93
2393 8577 5.047235 AGTGCTTATTTATAGAGGGTAGCCG 60.047 44.000 5.06 0.00 0.00 5.52
2394 8578 4.182339 GCTTATTTATAGAGGGTAGCCGC 58.818 47.826 6.59 6.59 0.00 6.53
2395 8579 4.081586 GCTTATTTATAGAGGGTAGCCGCT 60.082 45.833 21.21 21.21 36.41 5.52
2396 8580 5.569026 GCTTATTTATAGAGGGTAGCCGCTT 60.569 44.000 22.58 12.45 33.35 4.68
2397 8581 6.350780 GCTTATTTATAGAGGGTAGCCGCTTA 60.351 42.308 22.58 11.53 33.35 3.09
2398 8582 7.543359 TTATTTATAGAGGGTAGCCGCTTAA 57.457 36.000 22.58 16.07 33.35 1.85
2399 8583 5.464030 TTTATAGAGGGTAGCCGCTTAAG 57.536 43.478 22.58 0.00 33.35 1.85
2400 8584 2.449137 TAGAGGGTAGCCGCTTAAGT 57.551 50.000 22.58 0.38 33.35 2.24
2401 8585 2.449137 AGAGGGTAGCCGCTTAAGTA 57.551 50.000 11.83 0.00 33.35 2.24
2402 8586 2.743553 AGAGGGTAGCCGCTTAAGTAA 58.256 47.619 11.83 0.00 33.35 2.24
2403 8587 2.694109 AGAGGGTAGCCGCTTAAGTAAG 59.306 50.000 11.83 0.00 33.35 2.34
2415 8599 4.175787 CTTAAGTAAGCGTCTGTCCTGT 57.824 45.455 0.00 0.00 0.00 4.00
2416 8600 5.306532 CTTAAGTAAGCGTCTGTCCTGTA 57.693 43.478 0.00 0.00 0.00 2.74
2417 8601 3.851976 AAGTAAGCGTCTGTCCTGTAG 57.148 47.619 0.00 0.00 0.00 2.74
2418 8602 3.069079 AGTAAGCGTCTGTCCTGTAGA 57.931 47.619 0.00 0.00 0.00 2.59
2419 8603 3.418995 AGTAAGCGTCTGTCCTGTAGAA 58.581 45.455 0.00 0.00 0.00 2.10
2420 8604 3.825014 AGTAAGCGTCTGTCCTGTAGAAA 59.175 43.478 0.00 0.00 0.00 2.52
2421 8605 3.963428 AAGCGTCTGTCCTGTAGAAAT 57.037 42.857 0.00 0.00 0.00 2.17
2422 8606 5.651139 AGTAAGCGTCTGTCCTGTAGAAATA 59.349 40.000 0.00 0.00 0.00 1.40
2423 8607 5.401531 AAGCGTCTGTCCTGTAGAAATAA 57.598 39.130 0.00 0.00 0.00 1.40
2424 8608 5.000012 AGCGTCTGTCCTGTAGAAATAAG 58.000 43.478 0.00 0.00 0.00 1.73
2425 8609 4.463186 AGCGTCTGTCCTGTAGAAATAAGT 59.537 41.667 0.00 0.00 0.00 2.24
2426 8610 5.651139 AGCGTCTGTCCTGTAGAAATAAGTA 59.349 40.000 0.00 0.00 0.00 2.24
2427 8611 5.742926 GCGTCTGTCCTGTAGAAATAAGTAC 59.257 44.000 0.00 0.00 0.00 2.73
2428 8612 6.264088 CGTCTGTCCTGTAGAAATAAGTACC 58.736 44.000 0.00 0.00 0.00 3.34
2429 8613 6.264088 GTCTGTCCTGTAGAAATAAGTACCG 58.736 44.000 0.00 0.00 0.00 4.02
2430 8614 5.359009 TCTGTCCTGTAGAAATAAGTACCGG 59.641 44.000 0.00 0.00 0.00 5.28
2431 8615 5.018809 TGTCCTGTAGAAATAAGTACCGGT 58.981 41.667 13.98 13.98 0.00 5.28
2432 8616 5.105635 TGTCCTGTAGAAATAAGTACCGGTG 60.106 44.000 19.93 0.00 0.00 4.94
2433 8617 4.117685 CCTGTAGAAATAAGTACCGGTGC 58.882 47.826 19.93 17.74 0.00 5.01
2434 8618 4.142004 CCTGTAGAAATAAGTACCGGTGCT 60.142 45.833 20.57 20.57 0.00 4.40
2435 8619 5.410355 TGTAGAAATAAGTACCGGTGCTT 57.590 39.130 35.22 35.22 38.94 3.91
2436 8620 6.406177 CCTGTAGAAATAAGTACCGGTGCTTA 60.406 42.308 36.78 36.78 40.91 3.09
2437 8621 6.934056 TGTAGAAATAAGTACCGGTGCTTAA 58.066 36.000 37.77 23.91 40.26 1.85
2438 8622 7.037438 TGTAGAAATAAGTACCGGTGCTTAAG 58.963 38.462 37.77 0.00 40.26 1.85
2439 8623 6.290294 AGAAATAAGTACCGGTGCTTAAGA 57.710 37.500 37.77 24.45 40.26 2.10
2440 8624 6.704310 AGAAATAAGTACCGGTGCTTAAGAA 58.296 36.000 37.77 24.13 40.26 2.52
2441 8625 7.163441 AGAAATAAGTACCGGTGCTTAAGAAA 58.837 34.615 37.77 23.80 40.26 2.52
2442 8626 7.662669 AGAAATAAGTACCGGTGCTTAAGAAAA 59.337 33.333 37.77 23.16 40.26 2.29
2443 8627 6.732531 ATAAGTACCGGTGCTTAAGAAAAC 57.267 37.500 37.77 17.27 40.26 2.43
2444 8628 4.347360 AGTACCGGTGCTTAAGAAAACT 57.653 40.909 20.57 6.43 0.00 2.66
2445 8629 4.313282 AGTACCGGTGCTTAAGAAAACTC 58.687 43.478 20.57 0.00 0.00 3.01
2446 8630 2.140717 ACCGGTGCTTAAGAAAACTCG 58.859 47.619 6.12 6.90 0.00 4.18
2447 8631 1.463444 CCGGTGCTTAAGAAAACTCGG 59.537 52.381 6.67 11.36 0.00 4.63
2448 8632 2.140717 CGGTGCTTAAGAAAACTCGGT 58.859 47.619 6.67 0.00 0.00 4.69
2449 8633 2.546789 CGGTGCTTAAGAAAACTCGGTT 59.453 45.455 6.67 0.00 0.00 4.44
2450 8634 3.002965 CGGTGCTTAAGAAAACTCGGTTT 59.997 43.478 6.67 0.00 37.34 3.27
2451 8635 4.211794 CGGTGCTTAAGAAAACTCGGTTTA 59.788 41.667 6.67 0.00 34.43 2.01
2452 8636 5.106830 CGGTGCTTAAGAAAACTCGGTTTAT 60.107 40.000 6.67 0.00 34.43 1.40
2453 8637 6.567132 CGGTGCTTAAGAAAACTCGGTTTATT 60.567 38.462 6.67 0.00 34.43 1.40
2454 8638 7.143340 GGTGCTTAAGAAAACTCGGTTTATTT 58.857 34.615 6.67 4.11 34.43 1.40
2455 8639 7.650504 GGTGCTTAAGAAAACTCGGTTTATTTT 59.349 33.333 6.67 0.00 34.43 1.82
2456 8640 9.667989 GTGCTTAAGAAAACTCGGTTTATTTTA 57.332 29.630 6.67 1.56 34.43 1.52
2457 8641 9.667989 TGCTTAAGAAAACTCGGTTTATTTTAC 57.332 29.630 6.67 0.00 34.43 2.01
2458 8642 9.888878 GCTTAAGAAAACTCGGTTTATTTTACT 57.111 29.630 6.67 0.00 34.43 2.24
2480 8664 7.354751 ACTAATCATCTCTCTAAACACCTCC 57.645 40.000 0.00 0.00 0.00 4.30
2481 8665 5.622346 AATCATCTCTCTAAACACCTCCC 57.378 43.478 0.00 0.00 0.00 4.30
2482 8666 4.061131 TCATCTCTCTAAACACCTCCCA 57.939 45.455 0.00 0.00 0.00 4.37
2483 8667 4.624913 TCATCTCTCTAAACACCTCCCAT 58.375 43.478 0.00 0.00 0.00 4.00
2484 8668 5.032846 TCATCTCTCTAAACACCTCCCATT 58.967 41.667 0.00 0.00 0.00 3.16
2485 8669 6.202331 TCATCTCTCTAAACACCTCCCATTA 58.798 40.000 0.00 0.00 0.00 1.90
2486 8670 6.846505 TCATCTCTCTAAACACCTCCCATTAT 59.153 38.462 0.00 0.00 0.00 1.28
2487 8671 8.010697 TCATCTCTCTAAACACCTCCCATTATA 58.989 37.037 0.00 0.00 0.00 0.98
2488 8672 7.598759 TCTCTCTAAACACCTCCCATTATAC 57.401 40.000 0.00 0.00 0.00 1.47
2489 8673 7.130099 TCTCTCTAAACACCTCCCATTATACA 58.870 38.462 0.00 0.00 0.00 2.29
2490 8674 7.622081 TCTCTCTAAACACCTCCCATTATACAA 59.378 37.037 0.00 0.00 0.00 2.41
2491 8675 7.792032 TCTCTAAACACCTCCCATTATACAAG 58.208 38.462 0.00 0.00 0.00 3.16
2492 8676 6.895782 TCTAAACACCTCCCATTATACAAGG 58.104 40.000 0.00 0.00 0.00 3.61
2493 8677 3.577805 ACACCTCCCATTATACAAGGC 57.422 47.619 0.00 0.00 0.00 4.35
2494 8678 3.123273 ACACCTCCCATTATACAAGGCT 58.877 45.455 0.00 0.00 0.00 4.58
2495 8679 3.527665 ACACCTCCCATTATACAAGGCTT 59.472 43.478 0.00 0.00 0.00 4.35
2496 8680 4.017499 ACACCTCCCATTATACAAGGCTTT 60.017 41.667 0.00 0.00 0.00 3.51
2497 8681 5.192923 ACACCTCCCATTATACAAGGCTTTA 59.807 40.000 0.00 0.00 0.00 1.85
2498 8682 5.765182 CACCTCCCATTATACAAGGCTTTAG 59.235 44.000 0.00 0.00 0.00 1.85
2499 8683 5.670361 ACCTCCCATTATACAAGGCTTTAGA 59.330 40.000 0.00 0.00 0.00 2.10
2500 8684 6.183361 ACCTCCCATTATACAAGGCTTTAGAG 60.183 42.308 0.00 0.00 0.00 2.43
2533 8717 2.483106 GCCTCAAACCGGTCTTAAACTC 59.517 50.000 8.04 0.00 0.00 3.01
2534 8718 3.072211 CCTCAAACCGGTCTTAAACTCC 58.928 50.000 8.04 0.00 0.00 3.85
2535 8719 3.495453 CCTCAAACCGGTCTTAAACTCCA 60.495 47.826 8.04 0.00 0.00 3.86
2536 8720 3.469739 TCAAACCGGTCTTAAACTCCAC 58.530 45.455 8.04 0.00 0.00 4.02
2537 8721 2.159327 AACCGGTCTTAAACTCCACG 57.841 50.000 8.04 0.00 0.00 4.94
2539 8723 1.688197 ACCGGTCTTAAACTCCACGAA 59.312 47.619 0.00 0.00 0.00 3.85
2543 8727 2.074576 GTCTTAAACTCCACGAAGGCC 58.925 52.381 0.00 0.00 37.29 5.19
2559 8743 2.046314 CCGCCCGGTCACTCAATT 60.046 61.111 0.00 0.00 0.00 2.32
2564 8748 2.156098 GCCCGGTCACTCAATTGTAAA 58.844 47.619 5.13 0.00 0.00 2.01
2607 8791 3.547746 ACGCCTCAAACCAGTCTTAAAA 58.452 40.909 0.00 0.00 0.00 1.52
2609 8793 3.609409 CGCCTCAAACCAGTCTTAAAAGC 60.609 47.826 0.00 0.00 0.00 3.51
2611 8795 3.255888 CCTCAAACCAGTCTTAAAAGCCC 59.744 47.826 0.00 0.00 0.00 5.19
2615 8799 0.037734 CCAGTCTTAAAAGCCCGGGT 59.962 55.000 24.63 5.98 0.00 5.28
2619 8803 1.958579 GTCTTAAAAGCCCGGGTTGTT 59.041 47.619 24.63 20.98 0.00 2.83
2621 8805 0.953003 TTAAAAGCCCGGGTTGTTCG 59.047 50.000 24.63 0.00 0.00 3.95
2630 8814 2.046217 GGTTGTTCGGAGCCCCTC 60.046 66.667 0.00 0.00 0.00 4.30
2636 8820 0.038159 GTTCGGAGCCCCTCATATCG 60.038 60.000 0.00 0.00 31.08 2.92
2639 8823 1.594310 GGAGCCCCTCATATCGAGC 59.406 63.158 0.00 0.00 40.78 5.03
2650 8834 4.248859 CTCATATCGAGCCCAAATGTAGG 58.751 47.826 0.00 0.00 34.18 3.18
2660 8844 1.464608 CCAAATGTAGGCGGATATGCG 59.535 52.381 12.80 12.80 35.06 4.73
2972 9175 1.284841 CCAGCAAGGGGGAAGGAGAT 61.285 60.000 0.00 0.00 0.00 2.75
3016 9219 1.743995 GGCGTGGTGGTGGATGTAC 60.744 63.158 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.884514 GACCAAAAGCTGCTTCCTCC 59.115 55.000 16.28 1.05 0.00 4.30
100 101 3.891366 GAGAAGAGAAGGAGGAGATGGAG 59.109 52.174 0.00 0.00 0.00 3.86
151 152 4.803426 CGAGCTCTCCGCCGCTTT 62.803 66.667 12.85 0.00 40.39 3.51
183 190 4.648626 GCTGTCCTGCCACTGCCA 62.649 66.667 0.00 0.00 35.71 4.92
193 200 0.178903 TGGAAGTGGTAGGCTGTCCT 60.179 55.000 0.00 0.00 46.57 3.85
198 205 2.301738 GGGCTGGAAGTGGTAGGCT 61.302 63.158 0.00 0.00 37.20 4.58
245 252 2.055100 TGCGGCAAATTAAAAAGCGTC 58.945 42.857 0.00 0.00 0.00 5.19
290 297 5.771666 TGATCAGATTAGCCAAATCCATTCC 59.228 40.000 0.00 0.00 44.44 3.01
321 328 2.386661 ATTCCACCACGATCAGACAC 57.613 50.000 0.00 0.00 0.00 3.67
389 417 3.940221 CAGAATGCAGAGAAGGAAGGAAG 59.060 47.826 0.00 0.00 0.00 3.46
390 418 3.947868 CAGAATGCAGAGAAGGAAGGAA 58.052 45.455 0.00 0.00 0.00 3.36
424 463 1.556911 AGTTCCATTGGCGTCTGATCT 59.443 47.619 0.00 0.00 0.00 2.75
426 465 1.278985 TCAGTTCCATTGGCGTCTGAT 59.721 47.619 15.23 0.00 0.00 2.90
432 471 1.234615 AACCGTCAGTTCCATTGGCG 61.235 55.000 0.00 0.00 42.86 5.69
434 473 1.604604 ACAACCGTCAGTTCCATTGG 58.395 50.000 0.00 0.00 36.18 3.16
435 474 3.708563 AAACAACCGTCAGTTCCATTG 57.291 42.857 0.00 0.00 36.18 2.82
487 3920 2.843401 ACAAGTGGTACATGCCGTTA 57.157 45.000 0.00 0.00 44.52 3.18
596 4029 3.838271 GATGGCAGCGTCGAGGGA 61.838 66.667 7.31 0.00 0.00 4.20
610 4043 4.899239 GGCGAGGTGGGCTCGATG 62.899 72.222 0.00 0.00 46.06 3.84
942 4394 3.649277 CTCCCACAGCCGGAAGTCG 62.649 68.421 5.05 0.00 38.88 4.18
1362 4855 6.758254 AGTTGATCAAAAATTAGTTGGGTGG 58.242 36.000 10.35 0.00 0.00 4.61
1899 8044 0.315568 ACCAGTGTTCTGAGCGAGAC 59.684 55.000 0.00 0.00 43.76 3.36
1970 8118 1.891150 ACTCGATTTACAGTCGGTGGT 59.109 47.619 0.00 0.00 39.45 4.16
1971 8119 2.649331 ACTCGATTTACAGTCGGTGG 57.351 50.000 0.00 0.00 39.45 4.61
2010 8165 0.031585 TGGTCAACCTGTTCGTCGAG 59.968 55.000 0.10 0.00 36.82 4.04
2141 8296 4.947147 GCCACCTTCACCGCACCA 62.947 66.667 0.00 0.00 0.00 4.17
2252 8407 0.106217 AAACCAGTCCCCACACCTTG 60.106 55.000 0.00 0.00 0.00 3.61
2266 8421 0.387202 CCATGGCACGAACAAAACCA 59.613 50.000 0.00 0.00 34.28 3.67
2267 8422 0.943835 GCCATGGCACGAACAAAACC 60.944 55.000 32.08 0.00 41.49 3.27
2268 8423 0.943835 GGCCATGGCACGAACAAAAC 60.944 55.000 36.56 12.63 44.11 2.43
2269 8424 1.365633 GGCCATGGCACGAACAAAA 59.634 52.632 36.56 0.00 44.11 2.44
2270 8425 2.569354 GGGCCATGGCACGAACAAA 61.569 57.895 36.56 0.00 44.11 2.83
2271 8426 2.988684 GGGCCATGGCACGAACAA 60.989 61.111 36.56 0.00 44.11 2.83
2282 8437 2.428171 CGAAATTTGACATGAGGGCCAT 59.572 45.455 6.18 0.00 35.44 4.40
2283 8438 1.818060 CGAAATTTGACATGAGGGCCA 59.182 47.619 6.18 0.00 0.00 5.36
2284 8439 1.134946 CCGAAATTTGACATGAGGGCC 59.865 52.381 0.00 0.00 0.00 5.80
2285 8440 1.469767 GCCGAAATTTGACATGAGGGC 60.470 52.381 0.00 0.00 0.00 5.19
2286 8441 2.094675 AGCCGAAATTTGACATGAGGG 58.905 47.619 0.00 0.00 0.00 4.30
2287 8442 2.159338 CCAGCCGAAATTTGACATGAGG 60.159 50.000 0.00 0.00 0.00 3.86
2306 8490 2.356741 GCATTGTAAGGGACCTAAGCCA 60.357 50.000 0.00 0.00 0.00 4.75
2326 8510 5.183140 TGGTTTATTTCTCTAAGCACCTTGC 59.817 40.000 0.00 0.00 45.46 4.01
2327 8511 6.817765 TGGTTTATTTCTCTAAGCACCTTG 57.182 37.500 0.00 0.00 0.00 3.61
2328 8512 7.004691 ACTTGGTTTATTTCTCTAAGCACCTT 58.995 34.615 0.00 0.00 0.00 3.50
2329 8513 6.543735 ACTTGGTTTATTTCTCTAAGCACCT 58.456 36.000 0.00 0.00 0.00 4.00
2330 8514 6.819397 ACTTGGTTTATTTCTCTAAGCACC 57.181 37.500 0.00 0.00 0.00 5.01
2331 8515 9.529325 AAAAACTTGGTTTATTTCTCTAAGCAC 57.471 29.630 0.00 0.00 34.43 4.40
2345 8529 9.830975 ACTGATGCTTAAATAAAAACTTGGTTT 57.169 25.926 0.00 0.00 37.34 3.27
2346 8530 9.260002 CACTGATGCTTAAATAAAAACTTGGTT 57.740 29.630 0.00 0.00 0.00 3.67
2347 8531 8.816640 CACTGATGCTTAAATAAAAACTTGGT 57.183 30.769 0.00 0.00 0.00 3.67
2365 8549 7.547370 GCTACCCTCTATAAATAAGCACTGATG 59.453 40.741 0.00 0.00 0.00 3.07
2366 8550 7.310734 GGCTACCCTCTATAAATAAGCACTGAT 60.311 40.741 0.00 0.00 0.00 2.90
2367 8551 6.014499 GGCTACCCTCTATAAATAAGCACTGA 60.014 42.308 0.00 0.00 0.00 3.41
2368 8552 6.166982 GGCTACCCTCTATAAATAAGCACTG 58.833 44.000 0.00 0.00 0.00 3.66
2369 8553 5.047235 CGGCTACCCTCTATAAATAAGCACT 60.047 44.000 0.00 0.00 0.00 4.40
2370 8554 5.169295 CGGCTACCCTCTATAAATAAGCAC 58.831 45.833 0.00 0.00 0.00 4.40
2371 8555 4.322499 GCGGCTACCCTCTATAAATAAGCA 60.322 45.833 0.00 0.00 0.00 3.91
2372 8556 4.081586 AGCGGCTACCCTCTATAAATAAGC 60.082 45.833 0.00 0.00 0.00 3.09
2373 8557 5.662674 AGCGGCTACCCTCTATAAATAAG 57.337 43.478 0.00 0.00 0.00 1.73
2374 8558 7.234166 ACTTAAGCGGCTACCCTCTATAAATAA 59.766 37.037 1.35 0.00 0.00 1.40
2375 8559 6.723052 ACTTAAGCGGCTACCCTCTATAAATA 59.277 38.462 1.35 0.00 0.00 1.40
2376 8560 5.543020 ACTTAAGCGGCTACCCTCTATAAAT 59.457 40.000 1.35 0.00 0.00 1.40
2377 8561 4.897670 ACTTAAGCGGCTACCCTCTATAAA 59.102 41.667 1.35 0.00 0.00 1.40
2378 8562 4.477249 ACTTAAGCGGCTACCCTCTATAA 58.523 43.478 1.35 0.00 0.00 0.98
2379 8563 4.109877 ACTTAAGCGGCTACCCTCTATA 57.890 45.455 1.35 0.00 0.00 1.31
2380 8564 2.960163 ACTTAAGCGGCTACCCTCTAT 58.040 47.619 1.35 0.00 0.00 1.98
2381 8565 2.449137 ACTTAAGCGGCTACCCTCTA 57.551 50.000 1.35 0.00 0.00 2.43
2382 8566 2.449137 TACTTAAGCGGCTACCCTCT 57.551 50.000 1.35 0.00 0.00 3.69
2383 8567 3.095102 CTTACTTAAGCGGCTACCCTC 57.905 52.381 1.35 0.00 0.00 4.30
2394 8578 4.175787 ACAGGACAGACGCTTACTTAAG 57.824 45.455 0.00 0.00 36.40 1.85
2395 8579 5.005740 TCTACAGGACAGACGCTTACTTAA 58.994 41.667 0.00 0.00 0.00 1.85
2396 8580 4.582869 TCTACAGGACAGACGCTTACTTA 58.417 43.478 0.00 0.00 0.00 2.24
2397 8581 3.418995 TCTACAGGACAGACGCTTACTT 58.581 45.455 0.00 0.00 0.00 2.24
2398 8582 3.069079 TCTACAGGACAGACGCTTACT 57.931 47.619 0.00 0.00 0.00 2.24
2399 8583 3.844577 TTCTACAGGACAGACGCTTAC 57.155 47.619 0.00 0.00 0.00 2.34
2400 8584 6.152323 ACTTATTTCTACAGGACAGACGCTTA 59.848 38.462 0.00 0.00 0.00 3.09
2401 8585 3.963428 ATTTCTACAGGACAGACGCTT 57.037 42.857 0.00 0.00 0.00 4.68
2402 8586 4.463186 ACTTATTTCTACAGGACAGACGCT 59.537 41.667 0.00 0.00 0.00 5.07
2403 8587 4.745649 ACTTATTTCTACAGGACAGACGC 58.254 43.478 0.00 0.00 0.00 5.19
2404 8588 6.264088 GGTACTTATTTCTACAGGACAGACG 58.736 44.000 0.00 0.00 0.00 4.18
2405 8589 6.264088 CGGTACTTATTTCTACAGGACAGAC 58.736 44.000 0.00 0.00 0.00 3.51
2406 8590 5.359009 CCGGTACTTATTTCTACAGGACAGA 59.641 44.000 0.00 0.00 31.78 3.41
2407 8591 5.126707 ACCGGTACTTATTTCTACAGGACAG 59.873 44.000 4.49 0.00 33.71 3.51
2408 8592 5.018809 ACCGGTACTTATTTCTACAGGACA 58.981 41.667 4.49 0.00 33.71 4.02
2409 8593 5.346522 CACCGGTACTTATTTCTACAGGAC 58.653 45.833 6.87 0.00 33.71 3.85
2410 8594 4.142093 GCACCGGTACTTATTTCTACAGGA 60.142 45.833 6.87 0.00 33.71 3.86
2411 8595 4.117685 GCACCGGTACTTATTTCTACAGG 58.882 47.826 6.87 0.00 35.14 4.00
2412 8596 5.007385 AGCACCGGTACTTATTTCTACAG 57.993 43.478 6.87 0.00 0.00 2.74
2413 8597 5.410355 AAGCACCGGTACTTATTTCTACA 57.590 39.130 18.76 0.00 0.00 2.74
2414 8598 7.260603 TCTTAAGCACCGGTACTTATTTCTAC 58.739 38.462 24.60 0.00 0.00 2.59
2415 8599 7.408756 TCTTAAGCACCGGTACTTATTTCTA 57.591 36.000 24.60 11.00 0.00 2.10
2416 8600 6.290294 TCTTAAGCACCGGTACTTATTTCT 57.710 37.500 24.60 4.04 0.00 2.52
2417 8601 6.973229 TTCTTAAGCACCGGTACTTATTTC 57.027 37.500 24.60 0.57 0.00 2.17
2418 8602 7.446319 AGTTTTCTTAAGCACCGGTACTTATTT 59.554 33.333 24.60 5.12 0.00 1.40
2419 8603 6.938596 AGTTTTCTTAAGCACCGGTACTTATT 59.061 34.615 24.60 5.48 0.00 1.40
2420 8604 6.470278 AGTTTTCTTAAGCACCGGTACTTAT 58.530 36.000 24.60 8.19 0.00 1.73
2421 8605 5.857268 AGTTTTCTTAAGCACCGGTACTTA 58.143 37.500 21.15 21.15 0.00 2.24
2422 8606 4.711399 AGTTTTCTTAAGCACCGGTACTT 58.289 39.130 23.25 23.25 0.00 2.24
2423 8607 4.313282 GAGTTTTCTTAAGCACCGGTACT 58.687 43.478 6.87 3.13 0.00 2.73
2424 8608 3.122445 CGAGTTTTCTTAAGCACCGGTAC 59.878 47.826 6.87 0.00 0.00 3.34
2425 8609 3.319755 CGAGTTTTCTTAAGCACCGGTA 58.680 45.455 6.87 0.00 0.00 4.02
2426 8610 2.140717 CGAGTTTTCTTAAGCACCGGT 58.859 47.619 0.00 0.00 0.00 5.28
2427 8611 1.463444 CCGAGTTTTCTTAAGCACCGG 59.537 52.381 0.00 0.00 31.19 5.28
2428 8612 2.140717 ACCGAGTTTTCTTAAGCACCG 58.859 47.619 0.00 1.59 0.00 4.94
2429 8613 4.563337 AAACCGAGTTTTCTTAAGCACC 57.437 40.909 0.00 0.00 31.10 5.01
2430 8614 8.570096 AAAATAAACCGAGTTTTCTTAAGCAC 57.430 30.769 7.22 0.00 37.01 4.40
2431 8615 9.667989 GTAAAATAAACCGAGTTTTCTTAAGCA 57.332 29.630 7.22 0.00 37.01 3.91
2432 8616 9.888878 AGTAAAATAAACCGAGTTTTCTTAAGC 57.111 29.630 7.22 0.00 37.01 3.09
2454 8638 8.915036 GGAGGTGTTTAGAGAGATGATTAGTAA 58.085 37.037 0.00 0.00 0.00 2.24
2455 8639 7.506261 GGGAGGTGTTTAGAGAGATGATTAGTA 59.494 40.741 0.00 0.00 0.00 1.82
2456 8640 6.325286 GGGAGGTGTTTAGAGAGATGATTAGT 59.675 42.308 0.00 0.00 0.00 2.24
2457 8641 6.325028 TGGGAGGTGTTTAGAGAGATGATTAG 59.675 42.308 0.00 0.00 0.00 1.73
2458 8642 6.202331 TGGGAGGTGTTTAGAGAGATGATTA 58.798 40.000 0.00 0.00 0.00 1.75
2459 8643 5.032846 TGGGAGGTGTTTAGAGAGATGATT 58.967 41.667 0.00 0.00 0.00 2.57
2460 8644 4.624913 TGGGAGGTGTTTAGAGAGATGAT 58.375 43.478 0.00 0.00 0.00 2.45
2461 8645 4.061131 TGGGAGGTGTTTAGAGAGATGA 57.939 45.455 0.00 0.00 0.00 2.92
2462 8646 5.365021 AATGGGAGGTGTTTAGAGAGATG 57.635 43.478 0.00 0.00 0.00 2.90
2463 8647 7.789831 TGTATAATGGGAGGTGTTTAGAGAGAT 59.210 37.037 0.00 0.00 0.00 2.75
2464 8648 7.130099 TGTATAATGGGAGGTGTTTAGAGAGA 58.870 38.462 0.00 0.00 0.00 3.10
2465 8649 7.361457 TGTATAATGGGAGGTGTTTAGAGAG 57.639 40.000 0.00 0.00 0.00 3.20
2466 8650 7.147549 CCTTGTATAATGGGAGGTGTTTAGAGA 60.148 40.741 0.00 0.00 0.00 3.10
2467 8651 6.992715 CCTTGTATAATGGGAGGTGTTTAGAG 59.007 42.308 0.00 0.00 0.00 2.43
2468 8652 6.634039 GCCTTGTATAATGGGAGGTGTTTAGA 60.634 42.308 0.00 0.00 0.00 2.10
2469 8653 5.531287 GCCTTGTATAATGGGAGGTGTTTAG 59.469 44.000 0.00 0.00 0.00 1.85
2470 8654 5.192923 AGCCTTGTATAATGGGAGGTGTTTA 59.807 40.000 0.00 0.00 0.00 2.01
2471 8655 4.017499 AGCCTTGTATAATGGGAGGTGTTT 60.017 41.667 0.00 0.00 0.00 2.83
2472 8656 3.527665 AGCCTTGTATAATGGGAGGTGTT 59.472 43.478 0.00 0.00 0.00 3.32
2473 8657 3.123273 AGCCTTGTATAATGGGAGGTGT 58.877 45.455 0.00 0.00 0.00 4.16
2474 8658 3.864789 AGCCTTGTATAATGGGAGGTG 57.135 47.619 0.00 0.00 0.00 4.00
2475 8659 4.881157 AAAGCCTTGTATAATGGGAGGT 57.119 40.909 0.00 0.00 0.00 3.85
2476 8660 6.187727 TCTAAAGCCTTGTATAATGGGAGG 57.812 41.667 0.00 0.00 0.00 4.30
2477 8661 5.703130 GCTCTAAAGCCTTGTATAATGGGAG 59.297 44.000 0.00 0.00 43.10 4.30
2478 8662 5.621193 GCTCTAAAGCCTTGTATAATGGGA 58.379 41.667 0.00 0.00 43.10 4.37
2479 8663 5.948992 GCTCTAAAGCCTTGTATAATGGG 57.051 43.478 0.00 0.00 43.10 4.00
2493 8677 2.872858 GGCTCCGGTAAATGCTCTAAAG 59.127 50.000 0.00 0.00 0.00 1.85
2494 8678 2.504175 AGGCTCCGGTAAATGCTCTAAA 59.496 45.455 0.00 0.00 0.00 1.85
2495 8679 2.102588 GAGGCTCCGGTAAATGCTCTAA 59.897 50.000 2.15 0.00 0.00 2.10
2496 8680 1.687123 GAGGCTCCGGTAAATGCTCTA 59.313 52.381 2.15 0.00 0.00 2.43
2497 8681 0.466124 GAGGCTCCGGTAAATGCTCT 59.534 55.000 2.15 0.00 0.00 4.09
2498 8682 0.178068 TGAGGCTCCGGTAAATGCTC 59.822 55.000 12.86 0.00 0.00 4.26
2499 8683 0.618458 TTGAGGCTCCGGTAAATGCT 59.382 50.000 12.86 0.00 0.00 3.79
2500 8684 1.132453 GTTTGAGGCTCCGGTAAATGC 59.868 52.381 12.86 0.00 0.00 3.56
2501 8685 1.743394 GGTTTGAGGCTCCGGTAAATG 59.257 52.381 12.86 0.00 0.00 2.32
2502 8686 1.677820 CGGTTTGAGGCTCCGGTAAAT 60.678 52.381 12.86 0.00 40.49 1.40
2503 8687 0.320946 CGGTTTGAGGCTCCGGTAAA 60.321 55.000 12.86 2.70 40.49 2.01
2504 8688 1.294138 CGGTTTGAGGCTCCGGTAA 59.706 57.895 12.86 0.00 40.49 2.85
2505 8689 2.975536 CGGTTTGAGGCTCCGGTA 59.024 61.111 12.86 0.00 40.49 4.02
2508 8692 2.434359 GACCGGTTTGAGGCTCCG 60.434 66.667 9.42 8.81 43.30 4.63
2509 8693 0.611714 TAAGACCGGTTTGAGGCTCC 59.388 55.000 9.42 0.00 0.00 4.70
2510 8694 2.467566 TTAAGACCGGTTTGAGGCTC 57.532 50.000 9.42 7.79 0.00 4.70
2511 8695 2.105993 AGTTTAAGACCGGTTTGAGGCT 59.894 45.455 9.42 0.00 0.00 4.58
2543 8727 0.390603 TACAATTGAGTGACCGGGCG 60.391 55.000 13.59 0.00 0.00 6.13
2575 8759 1.264749 TTGAGGCGTACAGATGGGCT 61.265 55.000 0.00 0.00 39.50 5.19
2576 8760 0.392461 TTTGAGGCGTACAGATGGGC 60.392 55.000 0.00 0.00 0.00 5.36
2577 8761 1.369625 GTTTGAGGCGTACAGATGGG 58.630 55.000 0.00 0.00 0.00 4.00
2578 8762 1.338674 TGGTTTGAGGCGTACAGATGG 60.339 52.381 0.00 0.00 0.00 3.51
2582 8766 1.000955 AGACTGGTTTGAGGCGTACAG 59.999 52.381 0.00 0.00 0.00 2.74
2583 8767 1.045407 AGACTGGTTTGAGGCGTACA 58.955 50.000 0.00 0.00 0.00 2.90
2607 8791 4.016706 CTCCGAACAACCCGGGCT 62.017 66.667 24.08 4.98 46.47 5.19
2615 8799 1.416401 GATATGAGGGGCTCCGAACAA 59.584 52.381 0.00 0.00 38.33 2.83
2619 8803 0.609406 CTCGATATGAGGGGCTCCGA 60.609 60.000 0.00 0.00 41.29 4.55
2621 8805 1.594310 GCTCGATATGAGGGGCTCC 59.406 63.158 0.00 0.00 45.38 4.70
2623 8807 1.915769 GGGCTCGATATGAGGGGCT 60.916 63.158 0.00 0.00 45.38 5.19
2630 8814 2.744202 GCCTACATTTGGGCTCGATATG 59.256 50.000 0.00 0.00 44.48 1.78
2636 8820 0.179018 ATCCGCCTACATTTGGGCTC 60.179 55.000 4.61 0.00 45.57 4.70
2639 8823 1.812571 GCATATCCGCCTACATTTGGG 59.187 52.381 0.00 0.00 0.00 4.12
2679 8863 4.314440 TGGACCAGGCTGACGTGC 62.314 66.667 17.94 12.16 0.00 5.34
2704 8888 0.616395 TGCTACGATCCCCAACAGGA 60.616 55.000 0.00 0.00 41.18 3.86
2972 9175 1.407851 GCTGCTGGATCTCCATCAACA 60.408 52.381 0.00 0.00 46.46 3.33
3091 9294 1.076777 AGGGCAGCAACACAACAGT 60.077 52.632 0.00 0.00 0.00 3.55


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.