Multiple sequence alignment - TraesCS4D01G266700

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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 TraesCS4D01G266700 chr4D 100.000 5969 0 0 1 5969 437520023 437514055 0.000000e+00 11023.0
1 TraesCS4D01G266700 chr4D 92.000 600 29 9 5385 5969 451680228 451680823 0.000000e+00 824.0
2 TraesCS4D01G266700 chr4D 97.297 37 1 0 5350 5386 437514722 437514686 4.990000e-06 63.9
3 TraesCS4D01G266700 chr4B 94.771 2639 105 14 2596 5233 539968263 539965657 0.000000e+00 4078.0
4 TraesCS4D01G266700 chr4B 91.566 2158 108 39 412 2507 539970482 539968337 0.000000e+00 2909.0
5 TraesCS4D01G266700 chr4B 94.221 398 17 3 1 398 539970932 539970541 2.380000e-168 603.0
6 TraesCS4D01G266700 chr4B 97.778 45 1 0 5231 5275 110230683 110230727 1.780000e-10 78.7
7 TraesCS4D01G266700 chr4A 88.919 2599 147 78 1 2507 30561602 30559053 0.000000e+00 3073.0
8 TraesCS4D01G266700 chr4A 93.289 1356 72 9 3896 5233 30557669 30556315 0.000000e+00 1982.0
9 TraesCS4D01G266700 chr4A 92.552 1383 51 16 2532 3893 30559057 30557706 0.000000e+00 1936.0
10 TraesCS4D01G266700 chr4A 97.826 46 0 1 5231 5275 18055288 18055243 1.780000e-10 78.7
11 TraesCS4D01G266700 chr7D 90.436 711 43 11 5275 5969 599719446 599718745 0.000000e+00 913.0
12 TraesCS4D01G266700 chr7D 80.296 203 27 8 5273 5467 17343652 17343455 2.240000e-29 141.0
13 TraesCS4D01G266700 chr7D 94.366 71 4 0 5273 5343 552304733 552304663 6.320000e-20 110.0
14 TraesCS4D01G266700 chr5D 89.790 715 55 5 5269 5969 424819121 424819831 0.000000e+00 900.0
15 TraesCS4D01G266700 chr5D 91.528 602 38 7 5377 5969 122627817 122627220 0.000000e+00 817.0
16 TraesCS4D01G266700 chr5D 79.808 208 23 12 5271 5467 63104658 63104857 3.750000e-27 134.0
17 TraesCS4D01G266700 chr5D 90.123 81 6 1 5273 5353 549550813 549550735 2.940000e-18 104.0
18 TraesCS4D01G266700 chr5D 97.778 45 1 0 5231 5275 27486821 27486865 1.780000e-10 78.7
19 TraesCS4D01G266700 chr6D 89.916 714 49 11 5273 5969 86639343 86638636 0.000000e+00 898.0
20 TraesCS4D01G266700 chr6D 81.856 722 92 28 5259 5969 87369580 87370273 6.710000e-159 571.0
21 TraesCS4D01G266700 chr6D 81.463 205 22 11 5273 5467 47079757 47079559 2.880000e-33 154.0
22 TraesCS4D01G266700 chr1D 89.718 710 47 12 5271 5965 236091274 236090576 0.000000e+00 883.0
23 TraesCS4D01G266700 chr1D 81.875 160 26 3 3977 4135 155340309 155340466 1.350000e-26 132.0
24 TraesCS4D01G266700 chr7A 88.592 710 58 11 5275 5969 65032528 65033229 0.000000e+00 841.0
25 TraesCS4D01G266700 chr7A 73.269 520 99 32 5271 5774 26979960 26979465 2.880000e-33 154.0
26 TraesCS4D01G266700 chr3D 92.894 577 27 2 5407 5969 358570154 358569578 0.000000e+00 826.0
27 TraesCS4D01G266700 chr3A 91.327 588 34 6 5396 5969 717900063 717900647 0.000000e+00 787.0
28 TraesCS4D01G266700 chrUn 76.395 466 85 19 3953 4406 6051303 6051755 1.670000e-55 228.0
29 TraesCS4D01G266700 chr2D 82.000 200 23 7 5271 5462 539154914 539155108 2.230000e-34 158.0
30 TraesCS4D01G266700 chr6A 73.524 525 88 39 5271 5774 593937873 593937379 1.040000e-32 152.0
31 TraesCS4D01G266700 chr5A 73.435 527 87 43 5271 5774 40057673 40058169 1.340000e-31 148.0
32 TraesCS4D01G266700 chr1B 95.918 49 2 0 5227 5275 449745360 449745408 4.960000e-11 80.5
33 TraesCS4D01G266700 chr1B 97.778 45 1 0 5231 5275 158157845 158157801 1.780000e-10 78.7
34 TraesCS4D01G266700 chr7B 97.778 45 1 0 5231 5275 504832546 504832502 1.780000e-10 78.7
35 TraesCS4D01G266700 chr7B 95.833 48 1 1 5229 5275 477972519 477972566 6.410000e-10 76.8
36 TraesCS4D01G266700 chr7B 94.000 50 2 1 5226 5274 194560827 194560876 2.310000e-09 75.0
37 TraesCS4D01G266700 chr2B 97.826 46 0 1 5231 5275 381299787 381299832 1.780000e-10 78.7


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 TraesCS4D01G266700 chr4D 437514055 437520023 5968 True 11023.000000 11023 100.000000 1 5969 1 chr4D.!!$R1 5968
1 TraesCS4D01G266700 chr4D 451680228 451680823 595 False 824.000000 824 92.000000 5385 5969 1 chr4D.!!$F1 584
2 TraesCS4D01G266700 chr4B 539965657 539970932 5275 True 2530.000000 4078 93.519333 1 5233 3 chr4B.!!$R1 5232
3 TraesCS4D01G266700 chr4A 30556315 30561602 5287 True 2330.333333 3073 91.586667 1 5233 3 chr4A.!!$R2 5232
4 TraesCS4D01G266700 chr7D 599718745 599719446 701 True 913.000000 913 90.436000 5275 5969 1 chr7D.!!$R3 694
5 TraesCS4D01G266700 chr5D 424819121 424819831 710 False 900.000000 900 89.790000 5269 5969 1 chr5D.!!$F3 700
6 TraesCS4D01G266700 chr5D 122627220 122627817 597 True 817.000000 817 91.528000 5377 5969 1 chr5D.!!$R1 592
7 TraesCS4D01G266700 chr6D 86638636 86639343 707 True 898.000000 898 89.916000 5273 5969 1 chr6D.!!$R2 696
8 TraesCS4D01G266700 chr6D 87369580 87370273 693 False 571.000000 571 81.856000 5259 5969 1 chr6D.!!$F1 710
9 TraesCS4D01G266700 chr1D 236090576 236091274 698 True 883.000000 883 89.718000 5271 5965 1 chr1D.!!$R1 694
10 TraesCS4D01G266700 chr7A 65032528 65033229 701 False 841.000000 841 88.592000 5275 5969 1 chr7A.!!$F1 694
11 TraesCS4D01G266700 chr3D 358569578 358570154 576 True 826.000000 826 92.894000 5407 5969 1 chr3D.!!$R1 562
12 TraesCS4D01G266700 chr3A 717900063 717900647 584 False 787.000000 787 91.327000 5396 5969 1 chr3A.!!$F1 573

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
693 777 0.606401 ACACGATCTTTGTGGGCAGG 60.606 55.0 4.56 0.00 41.64 4.85 F
1337 1464 0.026415 TCCTCTCCTCCCCTCCCTAT 60.026 60.0 0.00 0.00 0.00 2.57 F
2120 2286 0.038618 TGGCTACGTGCAGTGTAGTG 60.039 55.0 21.09 4.97 45.15 2.74 F
2504 2679 0.106015 GCCTCCTGCCCATGGTAAAT 60.106 55.0 11.73 0.00 0.00 1.40 F
3796 3995 0.185901 ACAACTGCCTGATTGGTGGT 59.814 50.0 0.00 0.00 38.35 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 2286 0.032130 TCTGTCGACAAGTGGCTCAC 59.968 55.0 20.49 0.0 34.10 3.51 R
2564 2739 0.750850 TTGCTACGGGGATAGTGCTC 59.249 55.0 0.00 0.0 0.00 4.26 R
3738 3937 0.746063 CAGCCCTGCACACAAGAAAA 59.254 50.0 0.00 0.0 0.00 2.29 R
4402 4648 0.106419 CTCTTACCTCTCCCTCGGCT 60.106 60.0 0.00 0.0 0.00 5.52 R
5361 5613 0.663269 GCGCGCTAAAAGCCAAGTTT 60.663 50.0 26.67 0.0 38.18 2.66 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
286 288 1.109920 ATGGACCGCGTCTATGCTCT 61.110 55.000 4.92 0.00 32.68 4.09
287 289 1.299468 GGACCGCGTCTATGCTCTG 60.299 63.158 4.92 0.00 32.47 3.35
407 452 2.747855 CGCCACTTGGGAAGGAGC 60.748 66.667 0.00 0.00 40.01 4.70
542 609 4.181578 TCCTCGGAATTTCAGAATCGTTC 58.818 43.478 0.98 0.00 0.00 3.95
548 615 5.502606 GGAATTTCAGAATCGTTCGGAATC 58.497 41.667 11.60 8.63 42.05 2.52
549 616 5.294552 GGAATTTCAGAATCGTTCGGAATCT 59.705 40.000 11.60 0.00 42.05 2.40
550 617 6.479001 GGAATTTCAGAATCGTTCGGAATCTA 59.521 38.462 11.60 2.23 42.05 1.98
554 621 6.301687 TCAGAATCGTTCGGAATCTACTAG 57.698 41.667 0.00 0.00 33.07 2.57
693 777 0.606401 ACACGATCTTTGTGGGCAGG 60.606 55.000 4.56 0.00 41.64 4.85
709 793 1.394572 GCAGGGCATTTTTGCGATTTC 59.605 47.619 0.00 0.00 35.24 2.17
711 795 3.328505 CAGGGCATTTTTGCGATTTCTT 58.671 40.909 0.00 0.00 35.24 2.52
717 801 4.664891 GCATTTTTGCGATTTCTTGAGTGC 60.665 41.667 0.00 0.00 0.00 4.40
1026 1147 0.038744 CACAATTCACTCCAGCCCCT 59.961 55.000 0.00 0.00 0.00 4.79
1062 1184 2.246091 AACCTCTCTCTTCCTCCCTG 57.754 55.000 0.00 0.00 0.00 4.45
1069 1191 1.203237 TCTCTTCCTCCCTGCAAGAGT 60.203 52.381 11.41 0.00 42.57 3.24
1108 1230 1.335506 GGGAGAGATCGATCTTGCGTC 60.336 57.143 27.90 20.10 37.25 5.19
1154 1276 2.599281 TGGAGAGCCCGAACGTGA 60.599 61.111 0.00 0.00 37.93 4.35
1180 1302 3.607661 GCGGGGGAGATCGAGTCC 61.608 72.222 7.90 7.90 0.00 3.85
1287 1409 2.291282 ACCACTTCAAGACCAACACCAA 60.291 45.455 0.00 0.00 0.00 3.67
1336 1463 0.703056 CTCCTCTCCTCCCCTCCCTA 60.703 65.000 0.00 0.00 0.00 3.53
1337 1464 0.026415 TCCTCTCCTCCCCTCCCTAT 60.026 60.000 0.00 0.00 0.00 2.57
1362 1489 2.473378 CGCGCAGTGCTTCTCTTG 59.527 61.111 14.33 0.00 43.27 3.02
1373 1500 5.348179 CAGTGCTTCTCTTGTCTTCTGTATG 59.652 44.000 0.00 0.00 0.00 2.39
1374 1501 5.011533 AGTGCTTCTCTTGTCTTCTGTATGT 59.988 40.000 0.00 0.00 0.00 2.29
1378 1505 7.600375 TGCTTCTCTTGTCTTCTGTATGTAAAG 59.400 37.037 0.00 0.00 0.00 1.85
1430 1557 0.814457 AGATCAGTCACTCAGTCGCC 59.186 55.000 0.00 0.00 0.00 5.54
1472 1599 6.090628 GCGCTTCTCTTAATTATCTCCTGATG 59.909 42.308 0.00 0.00 34.32 3.07
1561 1695 2.970324 TCGTTGACGCTTGTGGGC 60.970 61.111 0.00 0.00 39.60 5.36
1630 1764 4.826569 TTCGTTTTCGTTTCTTTTTGGC 57.173 36.364 0.00 0.00 44.46 4.52
1634 1768 5.004916 TCGTTTTCGTTTCTTTTTGGCATTC 59.995 36.000 0.00 0.00 44.46 2.67
1704 1838 6.562640 CGAACGGTCTCATTTTCGACTTTTTA 60.563 38.462 0.00 0.00 42.72 1.52
1722 1856 2.309528 TAGGAGAATGCGATGCGTTT 57.690 45.000 0.00 0.00 37.94 3.60
1764 1898 4.505808 TGTTCGGTTTTGGATTATCGCTA 58.494 39.130 0.00 0.00 0.00 4.26
1765 1899 4.569162 TGTTCGGTTTTGGATTATCGCTAG 59.431 41.667 0.00 0.00 0.00 3.42
1833 1967 6.363167 TTTCCCCGATCTACTAGTTTTTCA 57.637 37.500 0.00 0.00 0.00 2.69
1857 1991 2.949106 GCATGTGCACGTGAGCTT 59.051 55.556 37.09 6.06 41.59 3.74
1861 1995 1.733912 CATGTGCACGTGAGCTTGTAT 59.266 47.619 31.17 3.09 34.90 2.29
1877 2013 8.443160 TGAGCTTGTATTTTAAGATTCAGAACG 58.557 33.333 0.00 0.00 0.00 3.95
1882 2018 8.251750 TGTATTTTAAGATTCAGAACGGACTG 57.748 34.615 5.03 5.03 39.02 3.51
1916 2053 4.412796 TTAGATGAGATGCAGAACAGGG 57.587 45.455 0.00 0.00 0.00 4.45
1935 2072 2.041216 GGGTTTTGACTCCACCTGGTAT 59.959 50.000 0.00 0.00 36.34 2.73
1942 2081 8.621286 GTTTTGACTCCACCTGGTATAATAATG 58.379 37.037 0.00 0.00 36.34 1.90
1946 2085 7.015292 TGACTCCACCTGGTATAATAATGAGAC 59.985 40.741 0.00 0.00 36.34 3.36
1966 2105 4.028852 ACGTCAGCCTTTTTCTTTTGAC 57.971 40.909 0.00 0.00 33.44 3.18
1969 2108 4.500477 CGTCAGCCTTTTTCTTTTGACAAG 59.500 41.667 3.72 0.00 35.80 3.16
1974 2113 3.466836 CTTTTTCTTTTGACAAGGGCCC 58.533 45.455 16.46 16.46 0.00 5.80
1975 2114 2.166907 TTTCTTTTGACAAGGGCCCA 57.833 45.000 27.56 0.00 0.00 5.36
1977 2116 1.408969 TCTTTTGACAAGGGCCCAAC 58.591 50.000 27.56 12.48 0.00 3.77
1983 2122 1.427368 TGACAAGGGCCCAACTATGTT 59.573 47.619 27.56 4.03 0.00 2.71
1994 2133 3.308117 CCCAACTATGTTAGCCTGACCAA 60.308 47.826 0.00 0.00 0.00 3.67
1996 2135 4.565652 CCAACTATGTTAGCCTGACCAAGT 60.566 45.833 0.00 0.00 0.00 3.16
2042 2181 2.231215 TGCATTTGTTTGTTTCCCCG 57.769 45.000 0.00 0.00 0.00 5.73
2047 2186 1.112950 TTGTTTGTTTCCCCGGGTTC 58.887 50.000 21.85 7.12 0.00 3.62
2078 2217 7.687941 TTCCTCTTTGTTTTCATCTACATCC 57.312 36.000 0.00 0.00 0.00 3.51
2082 2221 7.824289 CCTCTTTGTTTTCATCTACATCCACTA 59.176 37.037 0.00 0.00 0.00 2.74
2084 2223 6.985188 TTGTTTTCATCTACATCCACTAGC 57.015 37.500 0.00 0.00 0.00 3.42
2120 2286 0.038618 TGGCTACGTGCAGTGTAGTG 60.039 55.000 21.09 4.97 45.15 2.74
2141 2307 1.344438 TGAGCCACTTGTCGACAGAAT 59.656 47.619 19.11 5.40 0.00 2.40
2164 2330 8.445275 AATACGCTGATTATTTGTGGTAATCA 57.555 30.769 7.95 7.95 42.92 2.57
2168 2334 7.701924 ACGCTGATTATTTGTGGTAATCATTTG 59.298 33.333 8.50 5.39 43.65 2.32
2169 2335 7.167968 CGCTGATTATTTGTGGTAATCATTTGG 59.832 37.037 8.50 0.82 43.65 3.28
2263 2429 0.535335 TCATCGCCAACAGGGAGTAC 59.465 55.000 0.00 0.00 41.35 2.73
2270 2436 1.069513 CCAACAGGGAGTACGTTGTCA 59.930 52.381 0.00 0.00 38.65 3.58
2292 2463 3.073503 ACCATCCACATCGATTCCATCAT 59.926 43.478 0.00 0.00 0.00 2.45
2295 2466 5.122869 CCATCCACATCGATTCCATCATTAC 59.877 44.000 0.00 0.00 0.00 1.89
2299 2470 6.772233 TCCACATCGATTCCATCATTACAATT 59.228 34.615 0.00 0.00 0.00 2.32
2303 2474 7.922278 ACATCGATTCCATCATTACAATTTTGG 59.078 33.333 0.00 0.00 0.00 3.28
2309 2480 9.657419 ATTCCATCATTACAATTTTGGTTCTTC 57.343 29.630 0.00 0.00 0.00 2.87
2312 2483 8.096414 CCATCATTACAATTTTGGTTCTTCCTT 58.904 33.333 0.00 0.00 37.07 3.36
2313 2484 8.928733 CATCATTACAATTTTGGTTCTTCCTTG 58.071 33.333 0.00 0.00 37.07 3.61
2316 2487 5.930837 ACAATTTTGGTTCTTCCTTGTCA 57.069 34.783 0.00 0.00 37.07 3.58
2329 2504 5.128827 TCTTCCTTGTCAACAGTAGTGTCTT 59.871 40.000 3.07 0.00 35.08 3.01
2381 2556 2.443394 GGGGATCTCATGGGCGACA 61.443 63.158 0.00 0.00 0.00 4.35
2399 2574 0.746063 CAAAGGACAAGGTGCAGCAA 59.254 50.000 19.63 0.00 0.00 3.91
2474 2649 2.625314 CAACGGAGAGGAGATCTATGCA 59.375 50.000 0.00 0.00 38.84 3.96
2503 2678 1.214305 AGCCTCCTGCCCATGGTAAA 61.214 55.000 11.73 0.00 42.71 2.01
2504 2679 0.106015 GCCTCCTGCCCATGGTAAAT 60.106 55.000 11.73 0.00 0.00 1.40
2505 2680 1.144913 GCCTCCTGCCCATGGTAAATA 59.855 52.381 11.73 0.00 0.00 1.40
2506 2681 2.863809 CCTCCTGCCCATGGTAAATAC 58.136 52.381 11.73 0.00 0.00 1.89
2507 2682 2.174639 CCTCCTGCCCATGGTAAATACA 59.825 50.000 11.73 0.00 0.00 2.29
2508 2683 3.480470 CTCCTGCCCATGGTAAATACAG 58.520 50.000 11.73 7.89 0.00 2.74
2509 2684 2.849943 TCCTGCCCATGGTAAATACAGT 59.150 45.455 11.73 0.00 0.00 3.55
2510 2685 3.268334 TCCTGCCCATGGTAAATACAGTT 59.732 43.478 11.73 0.00 0.00 3.16
2511 2686 4.023291 CCTGCCCATGGTAAATACAGTTT 58.977 43.478 11.73 0.00 0.00 2.66
2512 2687 4.466015 CCTGCCCATGGTAAATACAGTTTT 59.534 41.667 11.73 0.00 0.00 2.43
2513 2688 5.394115 CCTGCCCATGGTAAATACAGTTTTC 60.394 44.000 11.73 0.00 0.00 2.29
2514 2689 5.329399 TGCCCATGGTAAATACAGTTTTCT 58.671 37.500 11.73 0.00 0.00 2.52
2515 2690 5.777732 TGCCCATGGTAAATACAGTTTTCTT 59.222 36.000 11.73 0.00 0.00 2.52
2516 2691 6.071616 TGCCCATGGTAAATACAGTTTTCTTC 60.072 38.462 11.73 0.00 0.00 2.87
2517 2692 6.551736 CCCATGGTAAATACAGTTTTCTTCG 58.448 40.000 11.73 0.00 0.00 3.79
2518 2693 6.373216 CCCATGGTAAATACAGTTTTCTTCGA 59.627 38.462 11.73 0.00 0.00 3.71
2519 2694 7.414098 CCCATGGTAAATACAGTTTTCTTCGAG 60.414 40.741 11.73 0.00 0.00 4.04
2520 2695 7.119262 CCATGGTAAATACAGTTTTCTTCGAGT 59.881 37.037 2.57 0.00 0.00 4.18
2521 2696 7.647907 TGGTAAATACAGTTTTCTTCGAGTC 57.352 36.000 0.00 0.00 0.00 3.36
2522 2697 7.211573 TGGTAAATACAGTTTTCTTCGAGTCA 58.788 34.615 0.00 0.00 0.00 3.41
2523 2698 7.170320 TGGTAAATACAGTTTTCTTCGAGTCAC 59.830 37.037 0.00 0.00 0.00 3.67
2524 2699 7.384387 GGTAAATACAGTTTTCTTCGAGTCACT 59.616 37.037 0.00 0.00 0.00 3.41
2525 2700 6.771188 AATACAGTTTTCTTCGAGTCACTG 57.229 37.500 9.48 9.48 38.09 3.66
2526 2701 2.866762 ACAGTTTTCTTCGAGTCACTGC 59.133 45.455 10.48 0.00 35.98 4.40
2527 2702 2.866156 CAGTTTTCTTCGAGTCACTGCA 59.134 45.455 0.00 0.00 0.00 4.41
2528 2703 3.309682 CAGTTTTCTTCGAGTCACTGCAA 59.690 43.478 0.00 0.00 0.00 4.08
2529 2704 4.024556 CAGTTTTCTTCGAGTCACTGCAAT 60.025 41.667 0.00 0.00 0.00 3.56
2530 2705 4.212214 AGTTTTCTTCGAGTCACTGCAATC 59.788 41.667 0.00 0.00 0.00 2.67
2531 2706 3.385193 TTCTTCGAGTCACTGCAATCA 57.615 42.857 0.00 0.00 0.00 2.57
2532 2707 3.385193 TCTTCGAGTCACTGCAATCAA 57.615 42.857 0.00 0.00 0.00 2.57
2536 2711 4.456280 TCGAGTCACTGCAATCAATACT 57.544 40.909 0.00 0.00 0.00 2.12
2542 2717 7.201556 CGAGTCACTGCAATCAATACTAACATT 60.202 37.037 0.00 0.00 0.00 2.71
2578 2753 0.824759 GTGAAGAGCACTATCCCCGT 59.175 55.000 0.00 0.00 44.27 5.28
2579 2754 2.029623 GTGAAGAGCACTATCCCCGTA 58.970 52.381 0.00 0.00 44.27 4.02
2580 2755 2.034812 GTGAAGAGCACTATCCCCGTAG 59.965 54.545 0.00 0.00 44.27 3.51
2609 2798 3.138884 TGCTGCATGTTAGTTGAAGGA 57.861 42.857 0.00 0.00 0.00 3.36
2629 2818 4.768968 AGGACAGCTAAGTCATGCAAAAAT 59.231 37.500 6.54 0.00 40.29 1.82
2630 2819 5.945784 AGGACAGCTAAGTCATGCAAAAATA 59.054 36.000 6.54 0.00 40.29 1.40
2631 2820 6.434028 AGGACAGCTAAGTCATGCAAAAATAA 59.566 34.615 6.54 0.00 40.29 1.40
2633 2822 7.598493 GGACAGCTAAGTCATGCAAAAATAAAA 59.402 33.333 6.54 0.00 40.29 1.52
2652 2841 3.441496 AAAAAGACAGTGCACCATGTG 57.559 42.857 15.71 9.19 36.51 3.21
2832 3021 2.029892 TTGTGTTTGGGGGCTGGGAT 62.030 55.000 0.00 0.00 0.00 3.85
3134 3329 4.464069 AGAGTACTCTGAGTTTGATGCC 57.536 45.455 24.62 0.00 38.75 4.40
3186 3382 3.118775 TCTGTAACCACTGCGAATATGCT 60.119 43.478 0.00 0.00 35.36 3.79
3267 3463 4.460382 AGTGGCTTTTGTATGATTGGACAG 59.540 41.667 0.00 0.00 0.00 3.51
3389 3588 3.875134 ACCAGTCCTTGTTAGTTTCAACG 59.125 43.478 0.00 0.00 0.00 4.10
3416 3615 5.632347 CCATGCTGAAAACTTCATCAACTTC 59.368 40.000 0.00 0.00 39.02 3.01
3601 3800 2.097304 CGAGGCAGAGATATCTCCATCG 59.903 54.545 25.88 23.92 43.88 3.84
3699 3898 1.277273 TGTGTAGCTTGCTCTGCTGAT 59.723 47.619 0.00 0.00 41.32 2.90
3713 3912 5.636965 GCTCTGCTGATTGTACCTGTATATG 59.363 44.000 0.00 0.00 0.00 1.78
3745 3944 8.519526 TGGTTACAGGCTTATGTTATTTTCTTG 58.480 33.333 0.00 0.00 34.56 3.02
3769 3968 0.883814 CAGGGCTGATCGATCTTGCC 60.884 60.000 34.30 34.30 42.21 4.52
3796 3995 0.185901 ACAACTGCCTGATTGGTGGT 59.814 50.000 0.00 0.00 38.35 4.16
3820 4019 2.373169 TGATTTCAAGAGTGGCCAGACT 59.627 45.455 5.11 5.59 0.00 3.24
3953 4197 5.376854 ACATATGTGGTTTCTGTTCTTGC 57.623 39.130 7.78 0.00 0.00 4.01
4156 4402 3.197983 TCTGTCGATCTGTCTCTCACCTA 59.802 47.826 0.00 0.00 0.00 3.08
4194 4440 3.594134 TGTTGGTGCAAAAACTTGGAAG 58.406 40.909 12.52 0.00 0.00 3.46
4354 4600 2.969238 CTCGCCGCACCCATCATC 60.969 66.667 0.00 0.00 0.00 2.92
4360 4606 1.097547 CCGCACCCATCATCCTTGAC 61.098 60.000 0.00 0.00 33.85 3.18
4402 4648 1.074405 AGCACCAGGATTCAGCTGAAA 59.926 47.619 31.55 16.04 37.61 2.69
4449 4695 6.017852 TGACGAGATATGTTGCTAGTCTACTG 60.018 42.308 0.00 0.00 37.56 2.74
4616 4862 6.810182 TCGACTGTTTGCTCTAAATAACCTAC 59.190 38.462 0.00 0.00 0.00 3.18
4655 4901 5.493133 TTAACTGACGTGCAACTGAATTT 57.507 34.783 0.00 0.00 31.75 1.82
4656 4902 3.338818 ACTGACGTGCAACTGAATTTG 57.661 42.857 0.00 0.00 31.75 2.32
4739 4985 0.548031 TGGAGAACATCATGAGGGCC 59.452 55.000 12.66 7.92 0.00 5.80
4831 5077 1.493950 CCGAGAGCGACCGTACGTAT 61.494 60.000 15.21 1.14 40.82 3.06
4956 5205 5.391577 TCCCTTGTTTAAGTTTACCCTGT 57.608 39.130 0.00 0.00 31.80 4.00
4957 5206 6.512514 TCCCTTGTTTAAGTTTACCCTGTA 57.487 37.500 0.00 0.00 31.80 2.74
5030 5281 2.739932 CGACTTGGTAGCTTCTCATGGG 60.740 54.545 0.00 0.00 0.00 4.00
5066 5317 0.621862 GATGTGGAGGGAGGAGGGTT 60.622 60.000 0.00 0.00 0.00 4.11
5151 5402 9.192642 TGTGTGCTACTAGTATATGGAACTTTA 57.807 33.333 2.33 0.00 0.00 1.85
5201 5452 3.620488 TGCTTTTATCATGTCACCTCCC 58.380 45.455 0.00 0.00 0.00 4.30
5230 5481 2.567049 GACGGCGAGCAGTACTGT 59.433 61.111 23.44 10.82 0.00 3.55
5233 5484 0.249741 ACGGCGAGCAGTACTGTTTT 60.250 50.000 23.44 10.19 0.00 2.43
5234 5485 0.865769 CGGCGAGCAGTACTGTTTTT 59.134 50.000 23.44 7.75 0.00 1.94
5257 5508 5.529014 TTTGAAACAAGCAAAAGACTTGC 57.471 34.783 3.52 1.19 46.81 4.01
5258 5509 3.520569 TGAAACAAGCAAAAGACTTGCC 58.479 40.909 5.87 0.00 46.81 4.52
5259 5510 3.056250 TGAAACAAGCAAAAGACTTGCCA 60.056 39.130 5.87 0.00 46.81 4.92
5260 5511 3.825143 AACAAGCAAAAGACTTGCCAT 57.175 38.095 5.87 0.00 46.81 4.40
5261 5512 3.825143 ACAAGCAAAAGACTTGCCATT 57.175 38.095 5.87 0.00 46.81 3.16
5262 5513 4.141233 ACAAGCAAAAGACTTGCCATTT 57.859 36.364 5.87 0.00 46.81 2.32
5263 5514 4.122046 ACAAGCAAAAGACTTGCCATTTC 58.878 39.130 5.87 0.00 46.81 2.17
5264 5515 4.121317 CAAGCAAAAGACTTGCCATTTCA 58.879 39.130 5.87 0.00 45.98 2.69
5265 5516 4.612264 AGCAAAAGACTTGCCATTTCAT 57.388 36.364 5.87 0.00 45.98 2.57
5266 5517 4.964593 AGCAAAAGACTTGCCATTTCATT 58.035 34.783 5.87 0.00 45.98 2.57
5267 5518 4.753107 AGCAAAAGACTTGCCATTTCATTG 59.247 37.500 5.87 0.00 45.98 2.82
5268 5519 4.751098 GCAAAAGACTTGCCATTTCATTGA 59.249 37.500 0.00 0.00 39.38 2.57
5269 5520 5.410439 GCAAAAGACTTGCCATTTCATTGAT 59.590 36.000 0.00 0.00 39.38 2.57
5300 5551 3.216292 AACAGCCGCGCCAAAAGT 61.216 55.556 0.00 0.00 0.00 2.66
5354 5606 4.104633 GACGTTCAGTCGCGCGTG 62.105 66.667 30.98 21.82 40.43 5.34
5365 5617 3.708734 GCGCGTGCGTGGTAAACT 61.709 61.111 16.27 0.00 42.09 2.66
5366 5618 2.932905 CGCGTGCGTGGTAAACTT 59.067 55.556 6.00 0.00 34.35 2.66
5367 5619 1.438059 CGCGTGCGTGGTAAACTTG 60.438 57.895 6.00 0.00 34.35 3.16
5368 5620 1.082366 GCGTGCGTGGTAAACTTGG 60.082 57.895 0.00 0.00 0.00 3.61
5369 5621 1.082366 CGTGCGTGGTAAACTTGGC 60.082 57.895 0.00 0.00 0.00 4.52
5370 5622 1.503818 CGTGCGTGGTAAACTTGGCT 61.504 55.000 0.00 0.00 0.00 4.75
5373 5625 1.751924 TGCGTGGTAAACTTGGCTTTT 59.248 42.857 0.00 0.00 0.00 2.27
5374 5626 2.950309 TGCGTGGTAAACTTGGCTTTTA 59.050 40.909 0.00 0.00 0.00 1.52
5404 5659 4.605967 AACAGTTTGCGCGCGTGG 62.606 61.111 32.35 15.97 0.00 4.94
5499 5761 3.181471 CCTATTCCACACGCATCTCTTCT 60.181 47.826 0.00 0.00 0.00 2.85
5695 5967 4.052229 CGGCACCTTCGAGACGGT 62.052 66.667 0.00 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 2.589159 GGGAATCTTCGGGCGCTC 60.589 66.667 7.64 0.06 0.00 5.03
252 254 2.895865 CATGGGCTCGCTGCAGAG 60.896 66.667 20.43 15.90 45.15 3.35
254 256 4.478371 TCCATGGGCTCGCTGCAG 62.478 66.667 13.02 10.11 45.15 4.41
286 288 2.067605 ACACACGTCCTTCCCCACA 61.068 57.895 0.00 0.00 0.00 4.17
287 289 1.597027 CACACACGTCCTTCCCCAC 60.597 63.158 0.00 0.00 0.00 4.61
542 609 6.074729 CGCGAGATAGATACTAGTAGATTCCG 60.075 46.154 0.00 7.04 0.00 4.30
548 615 4.033129 GGCACGCGAGATAGATACTAGTAG 59.967 50.000 15.93 0.00 0.00 2.57
549 616 3.931468 GGCACGCGAGATAGATACTAGTA 59.069 47.826 15.93 4.77 0.00 1.82
550 617 2.743126 GGCACGCGAGATAGATACTAGT 59.257 50.000 15.93 0.00 0.00 2.57
554 621 0.454620 CGGGCACGCGAGATAGATAC 60.455 60.000 15.93 0.00 0.00 2.24
641 724 1.082561 GCGTCACATGCACACAGTG 60.083 57.895 0.00 0.00 36.51 3.66
693 777 3.989817 ACTCAAGAAATCGCAAAAATGCC 59.010 39.130 0.00 0.00 0.00 4.40
709 793 4.905866 CACAGTTACGATTTTGCACTCAAG 59.094 41.667 0.00 0.00 33.12 3.02
711 795 3.874543 ACACAGTTACGATTTTGCACTCA 59.125 39.130 0.00 0.00 0.00 3.41
717 801 4.083484 GGGAGGAACACAGTTACGATTTTG 60.083 45.833 0.00 0.00 0.00 2.44
796 893 4.787735 TCGAAGAGGAGGAAGGGG 57.212 61.111 0.00 0.00 0.00 4.79
988 1109 0.036765 GTGTGATCTGCGGTGGGTAA 60.037 55.000 0.00 0.00 0.00 2.85
1062 1184 3.409026 TTCTTTCCTGGAGACTCTTGC 57.591 47.619 1.74 0.00 0.00 4.01
1069 1191 3.177228 CCCTCTCTTTCTTTCCTGGAGA 58.823 50.000 0.00 0.00 0.00 3.71
1108 1230 1.857217 CTCTCGATGAACATCTTGGCG 59.143 52.381 12.05 0.94 35.72 5.69
1180 1302 1.061570 GGTGTCGTAGCGGTACTCG 59.938 63.158 21.36 10.41 42.76 4.18
1362 1489 9.649167 TTAAACTAGGCTTTACATACAGAAGAC 57.351 33.333 0.00 0.00 0.00 3.01
1378 1505 8.966069 ACAGAATCTAAAGGATTAAACTAGGC 57.034 34.615 0.00 0.00 43.90 3.93
1446 1573 4.688413 CAGGAGATAATTAAGAGAAGCGCC 59.312 45.833 2.29 0.00 0.00 6.53
1472 1599 9.931210 CAGGACCGAATTAAATCAAGTAAATAC 57.069 33.333 0.00 0.00 0.00 1.89
1479 1609 6.371548 TCTTGACAGGACCGAATTAAATCAAG 59.628 38.462 0.00 0.00 41.08 3.02
1482 1612 6.538742 TGATCTTGACAGGACCGAATTAAATC 59.461 38.462 0.00 0.00 0.00 2.17
1561 1695 0.587285 CGATCCGAGAACGACCTAGG 59.413 60.000 7.41 7.41 42.66 3.02
1630 1764 3.442977 CCTCTCTTGGCAAGGAAAGAATG 59.557 47.826 25.92 11.81 32.23 2.67
1634 1768 2.304180 TCTCCTCTCTTGGCAAGGAAAG 59.696 50.000 25.92 18.90 38.69 2.62
1704 1838 0.729116 CAAACGCATCGCATTCTCCT 59.271 50.000 0.00 0.00 0.00 3.69
1722 1856 0.867746 GCATCTTGCAGACGACAACA 59.132 50.000 0.00 0.00 44.26 3.33
1786 1920 4.476862 CATGTCGTATTACGGAGATGGAG 58.523 47.826 15.69 0.00 42.81 3.86
1833 1967 3.043713 CGTGCACATGCGACAGGT 61.044 61.111 18.64 0.00 45.83 4.00
1857 1991 7.148474 GCAGTCCGTTCTGAATCTTAAAATACA 60.148 37.037 8.02 0.00 37.61 2.29
1861 1995 5.305585 AGCAGTCCGTTCTGAATCTTAAAA 58.694 37.500 8.02 0.00 37.61 1.52
1896 2032 3.378512 ACCCTGTTCTGCATCTCATCTA 58.621 45.455 0.00 0.00 0.00 1.98
1897 2033 2.194859 ACCCTGTTCTGCATCTCATCT 58.805 47.619 0.00 0.00 0.00 2.90
1898 2034 2.706339 ACCCTGTTCTGCATCTCATC 57.294 50.000 0.00 0.00 0.00 2.92
1899 2035 3.446442 AAACCCTGTTCTGCATCTCAT 57.554 42.857 0.00 0.00 0.00 2.90
1900 2036 2.886523 CAAAACCCTGTTCTGCATCTCA 59.113 45.455 0.00 0.00 0.00 3.27
1901 2037 3.057946 GTCAAAACCCTGTTCTGCATCTC 60.058 47.826 0.00 0.00 0.00 2.75
1902 2038 2.887152 GTCAAAACCCTGTTCTGCATCT 59.113 45.455 0.00 0.00 0.00 2.90
1903 2039 2.887152 AGTCAAAACCCTGTTCTGCATC 59.113 45.455 0.00 0.00 0.00 3.91
1906 2042 1.609072 GGAGTCAAAACCCTGTTCTGC 59.391 52.381 0.00 0.00 0.00 4.26
1916 2053 8.621286 CATTATTATACCAGGTGGAGTCAAAAC 58.379 37.037 0.76 0.00 38.94 2.43
1935 2072 7.103641 AGAAAAAGGCTGACGTCTCATTATTA 58.896 34.615 17.92 0.00 0.00 0.98
1942 2081 4.035208 TCAAAAGAAAAAGGCTGACGTCTC 59.965 41.667 17.92 8.42 0.00 3.36
1946 2085 4.027572 TGTCAAAAGAAAAAGGCTGACG 57.972 40.909 0.00 0.00 36.76 4.35
1966 2105 2.024414 GCTAACATAGTTGGGCCCTTG 58.976 52.381 25.70 14.68 0.00 3.61
1969 2108 0.551396 AGGCTAACATAGTTGGGCCC 59.449 55.000 17.59 17.59 37.62 5.80
1974 2113 4.579869 ACTTGGTCAGGCTAACATAGTTG 58.420 43.478 0.00 0.00 0.00 3.16
1975 2114 4.910458 ACTTGGTCAGGCTAACATAGTT 57.090 40.909 0.00 0.00 0.00 2.24
1977 2116 9.561069 AAATTATACTTGGTCAGGCTAACATAG 57.439 33.333 0.00 0.00 0.00 2.23
1983 2122 6.990349 GCAGTAAATTATACTTGGTCAGGCTA 59.010 38.462 0.00 0.00 0.00 3.93
1996 2135 9.154632 TGGGATTCAGAGTAGCAGTAAATTATA 57.845 33.333 0.00 0.00 0.00 0.98
2042 2181 4.657013 ACAAAGAGGAAATCAGAGAACCC 58.343 43.478 0.00 0.00 0.00 4.11
2047 2186 8.108551 AGATGAAAACAAAGAGGAAATCAGAG 57.891 34.615 0.00 0.00 0.00 3.35
2084 2223 1.352114 CCAACATGCAAAGCAATCCG 58.648 50.000 0.00 0.00 43.62 4.18
2092 2253 0.039617 GCACGTAGCCAACATGCAAA 60.040 50.000 3.26 0.00 36.30 3.68
2093 2254 1.169034 TGCACGTAGCCAACATGCAA 61.169 50.000 7.95 0.00 43.00 4.08
2120 2286 0.032130 TCTGTCGACAAGTGGCTCAC 59.968 55.000 20.49 0.00 34.10 3.51
2141 2307 8.445275 AATGATTACCACAAATAATCAGCGTA 57.555 30.769 11.76 0.00 46.77 4.42
2164 2330 4.030216 ACCACCAAAAACAGAGTCCAAAT 58.970 39.130 0.00 0.00 0.00 2.32
2168 2334 1.067060 GCACCACCAAAAACAGAGTCC 59.933 52.381 0.00 0.00 0.00 3.85
2169 2335 1.748493 TGCACCACCAAAAACAGAGTC 59.252 47.619 0.00 0.00 0.00 3.36
2270 2436 3.131709 GATGGAATCGATGTGGATGGT 57.868 47.619 0.00 0.00 31.13 3.55
2292 2463 7.411486 TGACAAGGAAGAACCAAAATTGTAA 57.589 32.000 0.00 0.00 42.04 2.41
2295 2466 6.105333 TGTTGACAAGGAAGAACCAAAATTG 58.895 36.000 0.00 0.00 42.04 2.32
2299 2470 4.340617 ACTGTTGACAAGGAAGAACCAAA 58.659 39.130 0.00 0.00 42.04 3.28
2303 2474 5.116882 ACACTACTGTTGACAAGGAAGAAC 58.883 41.667 0.00 0.00 0.00 3.01
2309 2480 7.441157 TCAAATAAGACACTACTGTTGACAAGG 59.559 37.037 0.00 0.00 0.00 3.61
2312 2483 7.652105 GTCTCAAATAAGACACTACTGTTGACA 59.348 37.037 0.00 0.00 44.20 3.58
2313 2484 7.868415 AGTCTCAAATAAGACACTACTGTTGAC 59.132 37.037 6.79 0.00 46.65 3.18
2316 2487 7.952671 TCAGTCTCAAATAAGACACTACTGTT 58.047 34.615 6.79 0.00 46.65 3.16
2329 2504 9.383519 GATTAAACTCACCATCAGTCTCAAATA 57.616 33.333 0.00 0.00 0.00 1.40
2381 2556 1.035139 CTTGCTGCACCTTGTCCTTT 58.965 50.000 0.00 0.00 0.00 3.11
2474 2649 1.846712 GCAGGAGGCTCTTGAAGGGT 61.847 60.000 28.47 0.00 40.25 4.34
2503 2678 4.686554 GCAGTGACTCGAAGAAAACTGTAT 59.313 41.667 0.00 0.00 40.87 2.29
2504 2679 4.049186 GCAGTGACTCGAAGAAAACTGTA 58.951 43.478 0.00 0.00 40.87 2.74
2505 2680 2.866762 GCAGTGACTCGAAGAAAACTGT 59.133 45.455 0.00 0.00 40.87 3.55
2506 2681 2.866156 TGCAGTGACTCGAAGAAAACTG 59.134 45.455 0.00 8.31 41.36 3.16
2507 2682 3.179443 TGCAGTGACTCGAAGAAAACT 57.821 42.857 0.00 0.00 34.09 2.66
2508 2683 3.944422 TTGCAGTGACTCGAAGAAAAC 57.056 42.857 0.00 0.00 34.09 2.43
2509 2684 4.126437 TGATTGCAGTGACTCGAAGAAAA 58.874 39.130 0.00 0.00 34.09 2.29
2510 2685 3.727726 TGATTGCAGTGACTCGAAGAAA 58.272 40.909 0.00 0.00 34.09 2.52
2511 2686 3.385193 TGATTGCAGTGACTCGAAGAA 57.615 42.857 0.00 0.00 34.09 2.52
2512 2687 3.385193 TTGATTGCAGTGACTCGAAGA 57.615 42.857 0.00 0.00 0.00 2.87
2513 2688 4.867047 AGTATTGATTGCAGTGACTCGAAG 59.133 41.667 0.00 0.00 0.00 3.79
2514 2689 4.820897 AGTATTGATTGCAGTGACTCGAA 58.179 39.130 0.00 0.00 0.00 3.71
2515 2690 4.456280 AGTATTGATTGCAGTGACTCGA 57.544 40.909 0.00 0.00 0.00 4.04
2516 2691 5.576774 TGTTAGTATTGATTGCAGTGACTCG 59.423 40.000 0.00 0.00 0.00 4.18
2517 2692 6.968131 TGTTAGTATTGATTGCAGTGACTC 57.032 37.500 0.00 0.00 0.00 3.36
2518 2693 7.928307 AATGTTAGTATTGATTGCAGTGACT 57.072 32.000 0.00 0.00 0.00 3.41
2542 2717 9.394767 TGCTCTTCACATAGCAATATCTTTTTA 57.605 29.630 0.00 0.00 45.36 1.52
2564 2739 0.750850 TTGCTACGGGGATAGTGCTC 59.249 55.000 0.00 0.00 0.00 4.26
2566 2741 2.256117 AATTGCTACGGGGATAGTGC 57.744 50.000 0.00 0.00 0.00 4.40
2571 2746 1.956477 GCATCAAATTGCTACGGGGAT 59.044 47.619 0.00 0.00 39.57 3.85
2572 2747 1.388547 GCATCAAATTGCTACGGGGA 58.611 50.000 0.00 0.00 39.57 4.81
2580 2755 4.178540 ACTAACATGCAGCATCAAATTGC 58.821 39.130 4.38 0.00 43.09 3.56
2600 2776 4.573900 CATGACTTAGCTGTCCTTCAACT 58.426 43.478 0.00 0.00 36.21 3.16
2609 2798 8.885494 TTTTTATTTTTGCATGACTTAGCTGT 57.115 26.923 0.00 0.00 0.00 4.40
2643 2832 4.695455 TCTTTACTAAAGAGCACATGGTGC 59.305 41.667 13.16 13.16 45.82 5.01
2762 2951 6.540438 TTCTAACACCGTCAGAATAGGATT 57.460 37.500 0.00 0.00 0.00 3.01
2832 3021 2.173356 AGCCAGGTTCATGCTGCTAATA 59.827 45.455 0.00 0.00 33.23 0.98
3114 3303 4.081972 TCAGGCATCAAACTCAGAGTACTC 60.082 45.833 15.41 15.41 0.00 2.59
3115 3304 3.834813 TCAGGCATCAAACTCAGAGTACT 59.165 43.478 2.64 0.00 0.00 2.73
3116 3305 4.180057 CTCAGGCATCAAACTCAGAGTAC 58.820 47.826 2.64 0.00 0.00 2.73
3117 3306 3.368843 GCTCAGGCATCAAACTCAGAGTA 60.369 47.826 2.64 0.00 38.54 2.59
3134 3329 4.692155 TCCATATTAATCATGCGTGCTCAG 59.308 41.667 0.00 0.00 0.00 3.35
3167 3363 4.616181 AAAGCATATTCGCAGTGGTTAC 57.384 40.909 0.00 0.00 33.67 2.50
3267 3463 2.371910 GCCGGTGGCTATAGAGAATC 57.628 55.000 1.90 0.00 46.69 2.52
3353 3552 4.652822 AGGACTGGTGGAGTAACATTTTC 58.347 43.478 0.00 0.00 33.83 2.29
3416 3615 3.612479 GCCATATGAGGGCGCAAATTTAG 60.612 47.826 10.83 0.00 42.39 1.85
3441 3640 6.240549 TCTCCTTGAACTCCCTATTTCATC 57.759 41.667 0.00 0.00 31.87 2.92
3699 3898 5.027460 ACCAGACACCATATACAGGTACAA 58.973 41.667 0.00 0.00 37.23 2.41
3713 3912 3.270877 CATAAGCCTGTAACCAGACACC 58.729 50.000 0.00 0.00 41.50 4.16
3738 3937 0.746063 CAGCCCTGCACACAAGAAAA 59.254 50.000 0.00 0.00 0.00 2.29
3745 3944 1.153289 ATCGATCAGCCCTGCACAC 60.153 57.895 0.00 0.00 0.00 3.82
3769 3968 5.047802 ACCAATCAGGCAGTTGTTCTTAATG 60.048 40.000 0.00 0.00 43.14 1.90
3796 3995 3.009363 TCTGGCCACTCTTGAAATCATCA 59.991 43.478 0.00 0.00 35.85 3.07
3820 4019 6.373005 TCCACCAAGACAGATTTCATCTTA 57.627 37.500 0.00 0.00 37.58 2.10
3915 4148 6.456449 CCACATATGTTTAGGCTTCGTAACAC 60.456 42.308 5.37 0.00 0.00 3.32
3953 4197 1.171308 CTGACAATTGAGGTGGGCTG 58.829 55.000 13.59 0.00 0.00 4.85
4156 4402 0.679505 ACAGTGCATGTGTCCGTAGT 59.320 50.000 0.00 0.00 41.91 2.73
4194 4440 6.040878 ACAACGGTGAAGCTTCAGTATATAC 58.959 40.000 29.13 15.05 37.98 1.47
4354 4600 1.002868 CAGGAGCACCAGGTCAAGG 60.003 63.158 2.07 0.00 43.97 3.61
4402 4648 0.106419 CTCTTACCTCTCCCTCGGCT 60.106 60.000 0.00 0.00 0.00 5.52
4449 4695 4.051922 CCCAAAGTATATCTCGACTGCAC 58.948 47.826 0.00 0.00 0.00 4.57
4655 4901 3.764237 GGAGGAACCTGTTAACAGACA 57.236 47.619 32.50 0.61 46.59 3.41
4831 5077 4.028490 CCCCCGCCACTTGCTACA 62.028 66.667 0.00 0.00 38.05 2.74
4892 5138 3.508744 AGACAAGCCGCCAAATAATTG 57.491 42.857 0.00 0.00 36.25 2.32
4956 5205 2.899976 CAAGGACACACACACACACTA 58.100 47.619 0.00 0.00 0.00 2.74
4957 5206 1.737838 CAAGGACACACACACACACT 58.262 50.000 0.00 0.00 0.00 3.55
5066 5317 4.763793 AGTGGACTAACTTAGCTAACACGA 59.236 41.667 0.86 0.00 0.00 4.35
5233 5484 6.369799 GCAAGTCTTTTGCTTGTTTCAAAAA 58.630 32.000 4.73 0.00 43.65 1.94
5234 5485 5.106752 GGCAAGTCTTTTGCTTGTTTCAAAA 60.107 36.000 11.18 0.00 43.65 2.44
5235 5486 4.391523 GGCAAGTCTTTTGCTTGTTTCAAA 59.608 37.500 11.18 0.00 43.65 2.69
5236 5487 3.932089 GGCAAGTCTTTTGCTTGTTTCAA 59.068 39.130 11.18 0.00 43.65 2.69
5237 5488 3.056250 TGGCAAGTCTTTTGCTTGTTTCA 60.056 39.130 11.18 0.00 43.65 2.69
5238 5489 3.520569 TGGCAAGTCTTTTGCTTGTTTC 58.479 40.909 11.18 0.00 43.65 2.78
5239 5490 3.608316 TGGCAAGTCTTTTGCTTGTTT 57.392 38.095 11.18 0.00 43.65 2.83
5240 5491 3.825143 ATGGCAAGTCTTTTGCTTGTT 57.175 38.095 11.18 0.00 43.65 2.83
5241 5492 3.825143 AATGGCAAGTCTTTTGCTTGT 57.175 38.095 11.18 0.00 43.65 3.16
5242 5493 4.121317 TGAAATGGCAAGTCTTTTGCTTG 58.879 39.130 11.18 0.00 44.36 4.01
5243 5494 4.405116 TGAAATGGCAAGTCTTTTGCTT 57.595 36.364 11.18 0.00 44.36 3.91
5244 5495 4.612264 ATGAAATGGCAAGTCTTTTGCT 57.388 36.364 11.18 0.00 44.36 3.91
5245 5496 4.751098 TCAATGAAATGGCAAGTCTTTTGC 59.249 37.500 3.39 3.39 44.22 3.68
5246 5497 7.429636 AATCAATGAAATGGCAAGTCTTTTG 57.570 32.000 0.00 1.55 0.00 2.44
5247 5498 9.211485 CTTAATCAATGAAATGGCAAGTCTTTT 57.789 29.630 0.00 0.00 0.00 2.27
5248 5499 8.587608 TCTTAATCAATGAAATGGCAAGTCTTT 58.412 29.630 0.00 0.00 0.00 2.52
5249 5500 8.125978 TCTTAATCAATGAAATGGCAAGTCTT 57.874 30.769 0.00 0.00 0.00 3.01
5250 5501 7.630082 GCTCTTAATCAATGAAATGGCAAGTCT 60.630 37.037 0.00 0.00 0.00 3.24
5251 5502 6.474751 GCTCTTAATCAATGAAATGGCAAGTC 59.525 38.462 0.00 0.00 0.00 3.01
5252 5503 6.071221 TGCTCTTAATCAATGAAATGGCAAGT 60.071 34.615 0.00 0.00 0.00 3.16
5253 5504 6.334989 TGCTCTTAATCAATGAAATGGCAAG 58.665 36.000 0.00 0.00 0.00 4.01
5254 5505 6.283544 TGCTCTTAATCAATGAAATGGCAA 57.716 33.333 0.00 0.00 0.00 4.52
5255 5506 5.918426 TGCTCTTAATCAATGAAATGGCA 57.082 34.783 0.00 0.00 0.00 4.92
5256 5507 6.746120 AGATGCTCTTAATCAATGAAATGGC 58.254 36.000 0.00 0.00 0.00 4.40
5257 5508 7.013942 TGGAGATGCTCTTAATCAATGAAATGG 59.986 37.037 0.00 0.00 0.00 3.16
5258 5509 7.937649 TGGAGATGCTCTTAATCAATGAAATG 58.062 34.615 0.00 0.00 0.00 2.32
5259 5510 8.411683 GTTGGAGATGCTCTTAATCAATGAAAT 58.588 33.333 0.00 0.00 0.00 2.17
5260 5511 7.394077 TGTTGGAGATGCTCTTAATCAATGAAA 59.606 33.333 0.00 0.00 0.00 2.69
5261 5512 6.885918 TGTTGGAGATGCTCTTAATCAATGAA 59.114 34.615 0.00 0.00 0.00 2.57
5262 5513 6.417258 TGTTGGAGATGCTCTTAATCAATGA 58.583 36.000 0.00 0.00 0.00 2.57
5263 5514 6.688637 TGTTGGAGATGCTCTTAATCAATG 57.311 37.500 0.00 0.00 0.00 2.82
5264 5515 5.298777 GCTGTTGGAGATGCTCTTAATCAAT 59.701 40.000 0.00 0.00 0.00 2.57
5265 5516 4.637534 GCTGTTGGAGATGCTCTTAATCAA 59.362 41.667 0.00 0.00 0.00 2.57
5266 5517 4.194640 GCTGTTGGAGATGCTCTTAATCA 58.805 43.478 0.00 0.00 0.00 2.57
5267 5518 3.563390 GGCTGTTGGAGATGCTCTTAATC 59.437 47.826 0.00 0.00 0.00 1.75
5268 5519 3.549794 GGCTGTTGGAGATGCTCTTAAT 58.450 45.455 0.00 0.00 0.00 1.40
5269 5520 2.677902 CGGCTGTTGGAGATGCTCTTAA 60.678 50.000 0.00 0.00 0.00 1.85
5305 5556 1.448922 AAAGCCAAGTTTACCGCGCA 61.449 50.000 8.75 0.00 0.00 6.09
5352 5604 0.666374 AAGCCAAGTTTACCACGCAC 59.334 50.000 0.00 0.00 0.00 5.34
5354 5606 2.502213 AAAAGCCAAGTTTACCACGC 57.498 45.000 0.00 0.00 0.00 5.34
5355 5607 3.561503 GCTAAAAGCCAAGTTTACCACG 58.438 45.455 0.00 0.00 34.48 4.94
5361 5613 0.663269 GCGCGCTAAAAGCCAAGTTT 60.663 50.000 26.67 0.00 38.18 2.66
5362 5614 1.081442 GCGCGCTAAAAGCCAAGTT 60.081 52.632 26.67 0.00 38.18 2.66
5363 5615 2.561373 GCGCGCTAAAAGCCAAGT 59.439 55.556 26.67 0.00 38.18 3.16
5364 5616 2.574212 CGCGCGCTAAAAGCCAAG 60.574 61.111 30.48 5.07 38.18 3.61
5365 5617 4.752142 GCGCGCGCTAAAAGCCAA 62.752 61.111 44.38 0.00 38.18 4.52
5404 5659 2.034221 ACCTGCCGCCTTTTCCTC 59.966 61.111 0.00 0.00 0.00 3.71
5405 5660 2.034221 GACCTGCCGCCTTTTCCT 59.966 61.111 0.00 0.00 0.00 3.36
5491 5753 2.027745 TGGCAGCGAAAGAAGAAGAGAT 60.028 45.455 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.