Multiple sequence alignment - TraesCS2D01G128800

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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 TraesCS2D01G128800 chr2D 100.000 4206 0 0 1 4206 74978623 74982828 0.000000e+00 7768.0
1 TraesCS2D01G128800 chr2D 85.932 263 34 1 3650 3912 79383975 79384234 1.150000e-70 278.0
2 TraesCS2D01G128800 chr2D 78.125 448 72 13 463 894 119824595 119824158 1.160000e-65 261.0
3 TraesCS2D01G128800 chr2D 90.741 54 3 2 45 97 469261287 469261235 2.100000e-08 71.3
4 TraesCS2D01G128800 chr2B 88.153 3140 267 59 89 3183 114373518 114376597 0.000000e+00 3640.0
5 TraesCS2D01G128800 chr2B 86.833 281 33 2 3650 3929 128374220 128374497 1.140000e-80 311.0
6 TraesCS2D01G128800 chr2B 96.721 183 6 0 3742 3924 114407660 114407842 5.280000e-79 305.0
7 TraesCS2D01G128800 chr2B 85.520 221 17 8 3532 3746 114395821 114396032 2.550000e-52 217.0
8 TraesCS2D01G128800 chr2B 96.330 109 2 2 3181 3289 114395556 114395662 1.200000e-40 178.0
9 TraesCS2D01G128800 chr2A 90.302 1887 109 27 1548 3399 74162973 74164820 0.000000e+00 2403.0
10 TraesCS2D01G128800 chr2A 93.772 578 24 5 949 1515 74162402 74162978 0.000000e+00 857.0
11 TraesCS2D01G128800 chr2A 90.476 420 32 7 3523 3935 74164930 74165348 7.950000e-152 547.0
12 TraesCS2D01G128800 chr2A 95.567 203 9 0 4004 4206 74165576 74165778 4.060000e-85 326.0
13 TraesCS2D01G128800 chr2A 80.769 442 56 15 326 764 74161848 74162263 6.790000e-83 318.0
14 TraesCS2D01G128800 chr2A 81.579 342 49 6 576 904 692242080 692242420 1.930000e-68 270.0
15 TraesCS2D01G128800 chr2A 87.850 107 10 3 2213 2318 676365562 676365666 5.710000e-24 122.0
16 TraesCS2D01G128800 chr7D 80.038 531 83 11 388 904 133886973 133887494 5.140000e-99 372.0
17 TraesCS2D01G128800 chr7D 78.993 576 91 14 351 912 632121427 632120868 2.390000e-97 366.0
18 TraesCS2D01G128800 chr7D 77.289 546 94 20 383 910 563708981 563708448 1.140000e-75 294.0
19 TraesCS2D01G128800 chr7D 77.045 379 76 8 387 763 162766218 162765849 1.530000e-49 207.0
20 TraesCS2D01G128800 chr4D 77.759 580 91 16 340 904 46026797 46027353 5.250000e-84 322.0
21 TraesCS2D01G128800 chr4D 89.928 139 11 3 768 904 496870167 496870030 4.320000e-40 176.0
22 TraesCS2D01G128800 chr4D 100.000 29 0 0 69 97 340081936 340081908 2.000000e-03 54.7
23 TraesCS2D01G128800 chr3D 78.108 539 94 11 387 912 29810793 29810266 1.890000e-83 320.0
24 TraesCS2D01G128800 chr3D 80.228 263 46 3 635 891 389257042 389257304 4.290000e-45 193.0
25 TraesCS2D01G128800 chr3D 100.000 29 0 0 69 97 252841300 252841272 2.000000e-03 54.7
26 TraesCS2D01G128800 chr3B 78.352 522 81 19 400 904 16101915 16102421 4.080000e-80 309.0
27 TraesCS2D01G128800 chr3B 88.350 103 9 3 2208 2309 229298781 229298681 2.050000e-23 121.0
28 TraesCS2D01G128800 chr1A 77.567 526 92 14 392 904 296915402 296915914 1.140000e-75 294.0
29 TraesCS2D01G128800 chr7A 77.509 538 87 21 386 904 576193398 576192876 4.110000e-75 292.0
30 TraesCS2D01G128800 chr7A 88.571 105 9 3 2219 2321 110813987 110814090 1.590000e-24 124.0
31 TraesCS2D01G128800 chr7A 94.737 38 2 0 63 100 643428893 643428930 4.540000e-05 60.2
32 TraesCS2D01G128800 chr7B 77.230 527 90 20 393 901 137516103 137516617 8.900000e-72 281.0
33 TraesCS2D01G128800 chr1D 76.952 538 84 23 386 904 468560926 468560410 1.930000e-68 270.0
34 TraesCS2D01G128800 chr1D 76.947 321 48 13 443 763 307665391 307665685 4.350000e-35 159.0
35 TraesCS2D01G128800 chr1D 82.143 84 8 7 52 129 495123845 495123763 9.760000e-07 65.8
36 TraesCS2D01G128800 chr5D 78.076 447 72 15 472 904 555200650 555200216 4.170000e-65 259.0
37 TraesCS2D01G128800 chr5B 74.775 555 106 20 370 904 455498854 455498314 7.080000e-53 219.0
38 TraesCS2D01G128800 chr6B 75.000 372 73 15 386 749 127106057 127106416 2.030000e-33 154.0
39 TraesCS2D01G128800 chr6B 91.071 56 4 1 42 97 182142444 182142390 1.620000e-09 75.0
40 TraesCS2D01G128800 chr6B 91.489 47 3 1 52 97 664896111 664896065 3.510000e-06 63.9
41 TraesCS2D01G128800 chr6D 71.887 530 124 20 386 904 468104358 468103843 3.410000e-26 130.0
42 TraesCS2D01G128800 chr6D 88.776 98 9 2 2213 2309 455888092 455888188 7.390000e-23 119.0
43 TraesCS2D01G128800 chr6D 93.478 46 1 2 55 99 354064396 354064352 2.710000e-07 67.6
44 TraesCS2D01G128800 chr3A 91.209 91 7 1 2218 2307 466063512 466063602 5.710000e-24 122.0
45 TraesCS2D01G128800 chr3A 100.000 33 0 0 54 86 53546200 53546168 1.260000e-05 62.1
46 TraesCS2D01G128800 chr1B 92.045 88 6 1 2220 2306 4594856 4594769 5.710000e-24 122.0
47 TraesCS2D01G128800 chr4A 90.323 93 7 2 2220 2310 547660665 547660757 2.050000e-23 121.0
48 TraesCS2D01G128800 chr5A 87.692 65 4 3 33 96 391993215 391993276 5.830000e-09 73.1
49 TraesCS2D01G128800 chr5A 94.737 38 2 0 60 97 537951756 537951719 4.540000e-05 60.2


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 TraesCS2D01G128800 chr2D 74978623 74982828 4205 False 7768.0 7768 100.0000 1 4206 1 chr2D.!!$F1 4205
1 TraesCS2D01G128800 chr2B 114373518 114376597 3079 False 3640.0 3640 88.1530 89 3183 1 chr2B.!!$F1 3094
2 TraesCS2D01G128800 chr2A 74161848 74165778 3930 False 890.2 2403 90.1772 326 4206 5 chr2A.!!$F3 3880
3 TraesCS2D01G128800 chr7D 133886973 133887494 521 False 372.0 372 80.0380 388 904 1 chr7D.!!$F1 516
4 TraesCS2D01G128800 chr7D 632120868 632121427 559 True 366.0 366 78.9930 351 912 1 chr7D.!!$R3 561
5 TraesCS2D01G128800 chr7D 563708448 563708981 533 True 294.0 294 77.2890 383 910 1 chr7D.!!$R2 527
6 TraesCS2D01G128800 chr4D 46026797 46027353 556 False 322.0 322 77.7590 340 904 1 chr4D.!!$F1 564
7 TraesCS2D01G128800 chr3D 29810266 29810793 527 True 320.0 320 78.1080 387 912 1 chr3D.!!$R1 525
8 TraesCS2D01G128800 chr3B 16101915 16102421 506 False 309.0 309 78.3520 400 904 1 chr3B.!!$F1 504
9 TraesCS2D01G128800 chr1A 296915402 296915914 512 False 294.0 294 77.5670 392 904 1 chr1A.!!$F1 512
10 TraesCS2D01G128800 chr7A 576192876 576193398 522 True 292.0 292 77.5090 386 904 1 chr7A.!!$R1 518
11 TraesCS2D01G128800 chr7B 137516103 137516617 514 False 281.0 281 77.2300 393 901 1 chr7B.!!$F1 508
12 TraesCS2D01G128800 chr1D 468560410 468560926 516 True 270.0 270 76.9520 386 904 1 chr1D.!!$R1 518
13 TraesCS2D01G128800 chr5B 455498314 455498854 540 True 219.0 219 74.7750 370 904 1 chr5B.!!$R1 534

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
436 444 1.227973 GGAGGCGTGATGGATTCCC 60.228 63.158 0.0 0.0 0.00 3.97 F
1655 1699 0.102120 TGCTTTGTGCTTTCCAACCG 59.898 50.000 0.0 0.0 43.37 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1743 0.179045 GCCAGTGGCGGACAATAGAT 60.179 55.0 20.55 0.0 39.62 1.98 R
3520 3615 0.386478 GAGCGTACCGTGTTTCGACT 60.386 55.0 0.00 0.0 42.86 4.18 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
22 23 3.769300 AGGCCACAACCTCATTTAATTCC 59.231 43.478 5.01 0.00 33.62 3.01
23 24 3.769300 GGCCACAACCTCATTTAATTCCT 59.231 43.478 0.00 0.00 0.00 3.36
24 25 4.222810 GGCCACAACCTCATTTAATTCCTT 59.777 41.667 0.00 0.00 0.00 3.36
25 26 5.279960 GGCCACAACCTCATTTAATTCCTTT 60.280 40.000 0.00 0.00 0.00 3.11
26 27 6.230472 GCCACAACCTCATTTAATTCCTTTT 58.770 36.000 0.00 0.00 0.00 2.27
27 28 6.368791 GCCACAACCTCATTTAATTCCTTTTC 59.631 38.462 0.00 0.00 0.00 2.29
28 29 7.670364 CCACAACCTCATTTAATTCCTTTTCT 58.330 34.615 0.00 0.00 0.00 2.52
29 30 8.150296 CCACAACCTCATTTAATTCCTTTTCTT 58.850 33.333 0.00 0.00 0.00 2.52
30 31 9.196552 CACAACCTCATTTAATTCCTTTTCTTC 57.803 33.333 0.00 0.00 0.00 2.87
31 32 9.147732 ACAACCTCATTTAATTCCTTTTCTTCT 57.852 29.630 0.00 0.00 0.00 2.85
194 199 9.769093 ATAAGAAAGTTGAACATAAACGCATAC 57.231 29.630 0.00 0.00 32.65 2.39
200 205 8.226543 AGTTGAACATAAACGCATACATTTTG 57.773 30.769 0.00 0.00 32.65 2.44
201 206 8.079203 AGTTGAACATAAACGCATACATTTTGA 58.921 29.630 0.00 0.00 32.65 2.69
218 223 8.970691 ACATTTTGAATAGTGATGTTTACTGC 57.029 30.769 0.00 0.00 0.00 4.40
220 225 9.282247 CATTTTGAATAGTGATGTTTACTGCTC 57.718 33.333 0.00 0.00 0.00 4.26
226 231 2.090658 GTGATGTTTACTGCTCGACACG 59.909 50.000 0.00 0.00 0.00 4.49
235 240 2.262211 CTGCTCGACACGATTCAATGA 58.738 47.619 0.00 0.00 34.61 2.57
278 283 3.691575 TCATAAATTCGGCAAGGTTGGA 58.308 40.909 0.00 0.00 0.00 3.53
366 371 1.342574 GCTCAGGGTTCCTCTACCTCT 60.343 57.143 0.00 0.00 38.30 3.69
413 420 1.757118 CTCATCTCCGGTGGCTTTAGA 59.243 52.381 0.00 0.00 0.00 2.10
433 441 1.528824 CCAGGAGGCGTGATGGATT 59.471 57.895 1.09 0.00 34.60 3.01
436 444 1.227973 GGAGGCGTGATGGATTCCC 60.228 63.158 0.00 0.00 0.00 3.97
492 501 5.232202 GCTGTTTCTTTGAGTTTTGTTAGGC 59.768 40.000 0.00 0.00 0.00 3.93
496 505 8.524487 TGTTTCTTTGAGTTTTGTTAGGCTTTA 58.476 29.630 0.00 0.00 0.00 1.85
562 574 7.995488 AGATCAAATAACATTCTTCCCACCTAG 59.005 37.037 0.00 0.00 0.00 3.02
571 583 2.243994 TCTTCCCACCTAGCTAGTAGCA 59.756 50.000 23.77 9.17 45.56 3.49
579 591 2.022195 CTAGCTAGTAGCACCCGTTCA 58.978 52.381 23.77 0.00 45.56 3.18
607 619 2.276201 CGTTTAGCATCATCGGTGGAA 58.724 47.619 0.00 0.00 0.00 3.53
624 636 1.338200 GGAAGCGTGGAGATGTGTCTT 60.338 52.381 0.00 0.00 33.97 3.01
653 665 4.437682 TCTGTCTTTGGTGGATCTGTTT 57.562 40.909 0.00 0.00 0.00 2.83
654 666 4.389374 TCTGTCTTTGGTGGATCTGTTTC 58.611 43.478 0.00 0.00 0.00 2.78
690 702 7.488150 GTCATTCGTCTACATTCATGTGTCTTA 59.512 37.037 2.50 0.00 41.89 2.10
701 713 7.667219 ACATTCATGTGTCTTAAAGTTGGATCT 59.333 33.333 0.00 0.00 40.03 2.75
1035 1067 1.344191 GCCTCTTCCCATCCAGCTCT 61.344 60.000 0.00 0.00 0.00 4.09
1266 1299 7.744087 TTGTTCATGGATTATCGAATTAGGG 57.256 36.000 0.00 0.00 0.00 3.53
1278 1311 1.873591 GAATTAGGGCATAGCGGTGTG 59.126 52.381 7.02 7.02 0.00 3.82
1355 1395 2.680841 CAGCAGCTTCTAGACGACTACT 59.319 50.000 0.00 0.00 0.00 2.57
1438 1482 5.416952 AGAACTTCAGTTATGCAATTCCCAG 59.583 40.000 0.00 0.00 38.56 4.45
1459 1503 3.199508 AGACAGATGTTCCAGAATCCAGG 59.800 47.826 0.00 0.00 0.00 4.45
1477 1521 1.683385 AGGCCTTGTCACTTTTGCTTC 59.317 47.619 0.00 0.00 0.00 3.86
1481 1525 3.067320 GCCTTGTCACTTTTGCTTCTCTT 59.933 43.478 0.00 0.00 0.00 2.85
1506 1550 3.957535 GGCGCCGGCTCATCAATG 61.958 66.667 26.68 7.15 39.81 2.82
1509 1553 2.549198 CGCCGGCTCATCAATGCAT 61.549 57.895 26.68 0.00 0.00 3.96
1518 1562 4.261322 GGCTCATCAATGCATTTGTCGTAT 60.261 41.667 9.83 0.00 36.65 3.06
1526 1570 9.616634 ATCAATGCATTTGTCGTATTGATTATC 57.383 29.630 9.83 0.00 42.59 1.75
1527 1571 8.619546 TCAATGCATTTGTCGTATTGATTATCA 58.380 29.630 9.83 0.00 34.04 2.15
1538 1582 5.877012 CGTATTGATTATCAGGGAAGGGATG 59.123 44.000 0.00 0.00 0.00 3.51
1545 1589 7.688534 TGATTATCAGGGAAGGGATGGTATAAT 59.311 37.037 0.00 0.00 0.00 1.28
1652 1696 2.098614 TCACTGCTTTGTGCTTTCCAA 58.901 42.857 0.00 0.00 43.37 3.53
1654 1698 1.136891 ACTGCTTTGTGCTTTCCAACC 59.863 47.619 0.00 0.00 43.37 3.77
1655 1699 0.102120 TGCTTTGTGCTTTCCAACCG 59.898 50.000 0.00 0.00 43.37 4.44
1656 1700 0.383949 GCTTTGTGCTTTCCAACCGA 59.616 50.000 0.00 0.00 38.95 4.69
1657 1701 1.864029 GCTTTGTGCTTTCCAACCGAC 60.864 52.381 0.00 0.00 38.95 4.79
1658 1702 1.403679 CTTTGTGCTTTCCAACCGACA 59.596 47.619 0.00 0.00 0.00 4.35
1659 1703 0.736053 TTGTGCTTTCCAACCGACAC 59.264 50.000 0.00 0.00 0.00 3.67
1708 1753 5.121811 ACTTGTCATGCTGATCTATTGTCC 58.878 41.667 0.00 0.00 0.00 4.02
1789 1834 6.035542 CCTGTTATGTTTGTTTTGTTGACACC 59.964 38.462 0.00 0.00 0.00 4.16
1850 1895 1.798813 CTTACTGGAGTCGGTTTGTGC 59.201 52.381 0.00 0.00 33.86 4.57
1851 1896 0.753867 TACTGGAGTCGGTTTGTGCA 59.246 50.000 0.00 0.00 33.86 4.57
1891 1936 6.023357 TGATTTGGAGCAAATTGAAATCGA 57.977 33.333 0.00 0.00 43.05 3.59
1916 1961 1.146041 TCAGCGAGCAACCAACTGT 59.854 52.632 0.00 0.00 0.00 3.55
1917 1962 0.880278 TCAGCGAGCAACCAACTGTC 60.880 55.000 0.00 0.00 0.00 3.51
1919 1964 2.244651 GCGAGCAACCAACTGTCGT 61.245 57.895 0.00 0.00 33.19 4.34
1956 2001 4.136796 TGCATATTATCTGTTGCCTGTCC 58.863 43.478 0.00 0.00 34.20 4.02
1959 2004 5.371526 CATATTATCTGTTGCCTGTCCAGT 58.628 41.667 0.00 0.00 0.00 4.00
1965 2010 1.529010 TTGCCTGTCCAGTTGCCTG 60.529 57.895 0.00 0.00 38.50 4.85
2136 2196 3.902881 TTTGGCAGTTCCACACATTTT 57.097 38.095 0.00 0.00 46.55 1.82
2145 2205 6.042143 CAGTTCCACACATTTTAAAAGCTGT 58.958 36.000 6.79 7.05 0.00 4.40
2146 2206 6.534793 CAGTTCCACACATTTTAAAAGCTGTT 59.465 34.615 6.79 0.00 0.00 3.16
2158 2218 7.945033 TTTAAAAGCTGTTCTTGCCTAATTG 57.055 32.000 0.00 0.00 34.67 2.32
2172 2232 5.200483 TGCCTAATTGAACTAATCTTGGGG 58.800 41.667 0.00 0.00 0.00 4.96
2186 2246 3.450904 TCTTGGGGTGTTGCTCTACTAT 58.549 45.455 0.00 0.00 0.00 2.12
2189 2249 2.766263 TGGGGTGTTGCTCTACTATCTG 59.234 50.000 0.00 0.00 0.00 2.90
2249 2315 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
2269 2336 8.238631 AGAACGTTTTTCAAACTGTTTTAGCTA 58.761 29.630 0.46 0.00 0.00 3.32
2270 2337 8.745464 AACGTTTTTCAAACTGTTTTAGCTAA 57.255 26.923 0.86 0.86 0.00 3.09
2332 2399 2.104267 CAATCCTGCAGCGATGCTT 58.896 52.632 27.55 9.80 36.40 3.91
2427 2494 4.332543 CGAAGGCACACTTATCATGCTTAA 59.667 41.667 0.00 0.00 40.21 1.85
2432 2499 8.292444 AGGCACACTTATCATGCTTAATTAAA 57.708 30.769 0.00 0.00 39.38 1.52
2516 2586 6.183361 TGTGTCCCCTAAATGTTTTCTGTCTA 60.183 38.462 0.00 0.00 0.00 2.59
2558 2628 2.123988 TTTTGCAGGCACGGTTAGCG 62.124 55.000 1.14 1.14 0.00 4.26
2583 2653 2.670934 AAGCCCTGCTGCTGAACG 60.671 61.111 8.20 0.00 41.80 3.95
2600 2670 8.780846 TGCTGAACGAAGGTAATCTTAAATAA 57.219 30.769 0.00 0.00 35.50 1.40
2603 2673 9.379791 CTGAACGAAGGTAATCTTAAATAAGGT 57.620 33.333 0.00 0.00 35.50 3.50
2617 2687 8.108364 TCTTAAATAAGGTTTTGGGTATTCCGA 58.892 33.333 0.62 0.00 34.53 4.55
2744 2814 0.804989 CGGCCACCAAAGAATGTCTC 59.195 55.000 2.24 0.00 0.00 3.36
2765 2835 2.482142 CGCTGAGAAGGAACAGGTATCC 60.482 54.545 0.00 0.00 37.22 2.59
2796 2866 2.178912 AACTAACCGTCACCACCATG 57.821 50.000 0.00 0.00 0.00 3.66
2798 2868 0.036388 CTAACCGTCACCACCATGCT 60.036 55.000 0.00 0.00 0.00 3.79
2799 2869 0.321210 TAACCGTCACCACCATGCTG 60.321 55.000 0.00 0.00 0.00 4.41
2804 2874 1.302752 TCACCACCATGCTGCTGTC 60.303 57.895 0.00 0.00 0.00 3.51
2805 2875 1.303074 CACCACCATGCTGCTGTCT 60.303 57.895 0.00 0.00 0.00 3.41
2806 2876 1.303074 ACCACCATGCTGCTGTCTG 60.303 57.895 0.00 0.00 0.00 3.51
2824 2894 2.688446 TCTGCTGATCCTAGTGTAACCG 59.312 50.000 0.00 0.00 37.80 4.44
2826 2896 1.136305 GCTGATCCTAGTGTAACCGCA 59.864 52.381 0.00 0.00 37.80 5.69
2837 2907 2.673368 GTGTAACCGCATTCTCCTCTTG 59.327 50.000 0.00 0.00 0.00 3.02
2843 2913 3.134458 CCGCATTCTCCTCTTGATTACC 58.866 50.000 0.00 0.00 0.00 2.85
2963 3033 4.692228 GAGAAGCCTCTGATAAGTTGGAG 58.308 47.826 0.00 0.00 36.50 3.86
2972 3042 5.408356 TCTGATAAGTTGGAGCTCGTAAAC 58.592 41.667 7.83 11.94 0.00 2.01
3030 3100 1.740025 GCAAACCTGTCTATGTGCTCC 59.260 52.381 0.00 0.00 0.00 4.70
3033 3103 0.818296 ACCTGTCTATGTGCTCCGTC 59.182 55.000 0.00 0.00 0.00 4.79
3040 3110 1.132453 CTATGTGCTCCGTCTTGACGA 59.868 52.381 22.54 9.28 34.64 4.20
3099 3179 3.127589 TGAAATGTGTCTGGTACGTGTG 58.872 45.455 0.00 0.00 0.00 3.82
3106 3191 1.811359 GTCTGGTACGTGTGAGCTAGT 59.189 52.381 0.00 0.00 0.00 2.57
3110 3195 2.745821 TGGTACGTGTGAGCTAGTAGTG 59.254 50.000 0.00 0.00 0.00 2.74
3119 3204 5.980116 GTGTGAGCTAGTAGTGATGTATTGG 59.020 44.000 0.00 0.00 0.00 3.16
3185 3274 5.475273 CTATCGCAGCAAAAGATGAAGAA 57.525 39.130 0.00 0.00 0.00 2.52
3270 3359 2.358195 GGTGGAATGCTAGTTGGGGATT 60.358 50.000 0.00 0.00 0.00 3.01
3278 3367 4.272489 TGCTAGTTGGGGATTGATTTGAG 58.728 43.478 0.00 0.00 0.00 3.02
3279 3368 4.018506 TGCTAGTTGGGGATTGATTTGAGA 60.019 41.667 0.00 0.00 0.00 3.27
3291 3380 7.557719 GGGATTGATTTGAGAATTCAGGAGTTA 59.442 37.037 8.44 0.00 34.15 2.24
3292 3381 8.619546 GGATTGATTTGAGAATTCAGGAGTTAG 58.380 37.037 8.44 0.00 34.15 2.34
3296 3385 7.772292 TGATTTGAGAATTCAGGAGTTAGGATG 59.228 37.037 8.44 0.00 34.15 3.51
3297 3386 6.627087 TTGAGAATTCAGGAGTTAGGATGT 57.373 37.500 8.44 0.00 34.15 3.06
3300 3389 6.385176 TGAGAATTCAGGAGTTAGGATGTGAT 59.615 38.462 8.44 0.00 0.00 3.06
3301 3390 7.092712 TGAGAATTCAGGAGTTAGGATGTGATT 60.093 37.037 8.44 0.00 0.00 2.57
3302 3391 7.278875 AGAATTCAGGAGTTAGGATGTGATTC 58.721 38.462 8.44 0.00 0.00 2.52
3303 3392 4.655762 TCAGGAGTTAGGATGTGATTCG 57.344 45.455 0.00 0.00 0.00 3.34
3304 3393 4.278310 TCAGGAGTTAGGATGTGATTCGA 58.722 43.478 0.00 0.00 0.00 3.71
3305 3394 4.098044 TCAGGAGTTAGGATGTGATTCGAC 59.902 45.833 0.00 0.00 0.00 4.20
3306 3395 4.098654 CAGGAGTTAGGATGTGATTCGACT 59.901 45.833 0.00 0.00 0.00 4.18
3307 3396 4.098654 AGGAGTTAGGATGTGATTCGACTG 59.901 45.833 0.00 0.00 0.00 3.51
3315 3410 3.090210 TGTGATTCGACTGTAGGGGTA 57.910 47.619 0.00 0.00 0.00 3.69
3332 3427 2.037144 GGTATTCTCTCCCGGTTAGCA 58.963 52.381 0.00 0.00 0.00 3.49
3335 3430 4.282703 GGTATTCTCTCCCGGTTAGCATAA 59.717 45.833 0.00 0.00 0.00 1.90
3348 3443 1.456287 GCATAAGGCAGGGGGTAGG 59.544 63.158 0.00 0.00 43.97 3.18
3349 3444 2.069165 GCATAAGGCAGGGGGTAGGG 62.069 65.000 0.00 0.00 43.97 3.53
3350 3445 0.697854 CATAAGGCAGGGGGTAGGGT 60.698 60.000 0.00 0.00 0.00 4.34
3351 3446 0.954203 ATAAGGCAGGGGGTAGGGTA 59.046 55.000 0.00 0.00 0.00 3.69
3352 3447 0.030807 TAAGGCAGGGGGTAGGGTAC 60.031 60.000 0.00 0.00 0.00 3.34
3372 3467 1.410882 CCTTCTCATCCCTTCCGAGTC 59.589 57.143 0.00 0.00 0.00 3.36
3373 3468 1.410882 CTTCTCATCCCTTCCGAGTCC 59.589 57.143 0.00 0.00 0.00 3.85
3380 3475 1.040339 CCCTTCCGAGTCCCTCTCAG 61.040 65.000 0.00 0.00 42.88 3.35
3395 3490 0.108615 CTCAGAATCGGAACCAGCGT 60.109 55.000 0.00 0.00 0.00 5.07
3396 3491 0.389817 TCAGAATCGGAACCAGCGTG 60.390 55.000 0.00 0.00 0.00 5.34
3397 3492 1.741770 AGAATCGGAACCAGCGTGC 60.742 57.895 0.00 0.00 0.00 5.34
3398 3493 2.031919 AATCGGAACCAGCGTGCA 59.968 55.556 0.00 0.00 0.00 4.57
3400 3495 1.169661 AATCGGAACCAGCGTGCAAA 61.170 50.000 0.00 0.00 0.00 3.68
3402 3497 1.370414 CGGAACCAGCGTGCAAAAG 60.370 57.895 0.00 0.00 0.00 2.27
3403 3498 1.661509 GGAACCAGCGTGCAAAAGC 60.662 57.895 0.00 0.00 0.00 3.51
3404 3499 1.661509 GAACCAGCGTGCAAAAGCC 60.662 57.895 6.47 0.00 0.00 4.35
3405 3500 2.075426 GAACCAGCGTGCAAAAGCCT 62.075 55.000 6.47 0.00 0.00 4.58
3406 3501 2.075426 AACCAGCGTGCAAAAGCCTC 62.075 55.000 6.47 0.00 0.00 4.70
3407 3502 2.127118 CAGCGTGCAAAAGCCTCG 60.127 61.111 6.47 0.00 0.00 4.63
3408 3503 2.591715 AGCGTGCAAAAGCCTCGT 60.592 55.556 6.47 0.00 0.00 4.18
3409 3504 2.427410 GCGTGCAAAAGCCTCGTG 60.427 61.111 0.00 0.00 0.00 4.35
3410 3505 2.252260 CGTGCAAAAGCCTCGTGG 59.748 61.111 0.00 0.00 0.00 4.94
3420 3515 3.309582 CCTCGTGGCTGGTGGTAT 58.690 61.111 0.00 0.00 0.00 2.73
3421 3516 2.511818 CCTCGTGGCTGGTGGTATA 58.488 57.895 0.00 0.00 0.00 1.47
3422 3517 1.048601 CCTCGTGGCTGGTGGTATAT 58.951 55.000 0.00 0.00 0.00 0.86
3423 3518 2.244695 CCTCGTGGCTGGTGGTATATA 58.755 52.381 0.00 0.00 0.00 0.86
3424 3519 2.832129 CCTCGTGGCTGGTGGTATATAT 59.168 50.000 0.00 0.00 0.00 0.86
3425 3520 3.368427 CCTCGTGGCTGGTGGTATATATG 60.368 52.174 0.00 0.00 0.00 1.78
3426 3521 3.236047 TCGTGGCTGGTGGTATATATGT 58.764 45.455 0.00 0.00 0.00 2.29
3427 3522 4.409187 TCGTGGCTGGTGGTATATATGTA 58.591 43.478 0.00 0.00 0.00 2.29
3428 3523 4.461431 TCGTGGCTGGTGGTATATATGTAG 59.539 45.833 0.00 0.00 0.00 2.74
3429 3524 4.381612 CGTGGCTGGTGGTATATATGTAGG 60.382 50.000 0.00 0.00 0.00 3.18
3430 3525 4.775780 GTGGCTGGTGGTATATATGTAGGA 59.224 45.833 0.00 0.00 0.00 2.94
3431 3526 4.775780 TGGCTGGTGGTATATATGTAGGAC 59.224 45.833 0.00 0.00 0.00 3.85
3432 3527 4.142227 GGCTGGTGGTATATATGTAGGACG 60.142 50.000 0.00 0.00 0.00 4.79
3433 3528 4.677250 GCTGGTGGTATATATGTAGGACGC 60.677 50.000 0.00 0.00 0.00 5.19
3438 3533 4.021916 GGTATATATGTAGGACGCACCCT 58.978 47.826 0.00 0.00 40.05 4.34
3449 3544 4.101448 GCACCCTGGCCATCGAGT 62.101 66.667 5.51 0.00 0.00 4.18
3451 3546 3.461773 ACCCTGGCCATCGAGTCG 61.462 66.667 5.51 6.09 0.00 4.18
3452 3547 3.147595 CCCTGGCCATCGAGTCGA 61.148 66.667 19.06 19.06 41.13 4.20
3453 3548 2.415010 CCTGGCCATCGAGTCGAG 59.585 66.667 21.36 9.36 39.91 4.04
3454 3549 2.418910 CCTGGCCATCGAGTCGAGT 61.419 63.158 21.36 6.52 39.91 4.18
3455 3550 1.064946 CTGGCCATCGAGTCGAGTC 59.935 63.158 21.36 10.37 39.91 3.36
3456 3551 1.657751 CTGGCCATCGAGTCGAGTCA 61.658 60.000 21.36 14.43 39.91 3.41
3457 3552 1.064946 GGCCATCGAGTCGAGTCAG 59.935 63.158 21.36 12.33 39.91 3.51
3458 3553 1.658686 GGCCATCGAGTCGAGTCAGT 61.659 60.000 21.36 0.00 39.91 3.41
3459 3554 0.248296 GCCATCGAGTCGAGTCAGTC 60.248 60.000 21.36 3.18 39.91 3.51
3483 3578 3.706698 TCTCAAAATCCACGATCGCTAG 58.293 45.455 16.60 5.38 0.00 3.42
3489 3584 2.543802 CCACGATCGCTAGCTCGGA 61.544 63.158 24.75 11.51 39.98 4.55
3490 3585 1.082431 CACGATCGCTAGCTCGGAG 60.082 63.158 24.75 15.55 39.98 4.63
3500 3595 2.425668 GCTAGCTCGGAGTTCTCTTCTT 59.574 50.000 7.70 0.00 0.00 2.52
3501 3596 3.119280 GCTAGCTCGGAGTTCTCTTCTTT 60.119 47.826 7.70 0.00 0.00 2.52
3502 3597 4.619628 GCTAGCTCGGAGTTCTCTTCTTTT 60.620 45.833 7.70 0.00 0.00 2.27
3503 3598 4.344359 AGCTCGGAGTTCTCTTCTTTTT 57.656 40.909 6.90 0.00 0.00 1.94
3518 3613 4.271964 TTTTTGAACACGACGCGC 57.728 50.000 5.73 0.00 0.00 6.86
3519 3614 1.716760 TTTTTGAACACGACGCGCT 59.283 47.368 5.73 0.00 0.00 5.92
3520 3615 0.928922 TTTTTGAACACGACGCGCTA 59.071 45.000 5.73 0.00 0.00 4.26
3522 3617 0.595567 TTTGAACACGACGCGCTAGT 60.596 50.000 5.73 0.00 0.00 2.57
3523 3618 1.000233 TTGAACACGACGCGCTAGTC 61.000 55.000 5.73 5.50 37.76 2.59
3593 3706 1.897137 TGCACGACGGAGACAGAGT 60.897 57.895 0.00 0.00 0.00 3.24
3594 3707 1.154188 GCACGACGGAGACAGAGTC 60.154 63.158 0.00 0.00 0.00 3.36
3595 3708 1.579084 GCACGACGGAGACAGAGTCT 61.579 60.000 0.00 0.00 46.42 3.24
3635 3748 1.081376 GACACTGACACGACGGAGG 60.081 63.158 0.00 0.00 0.00 4.30
3884 4015 1.210478 TCTCCAGCTTCAACATAGCCC 59.790 52.381 0.00 0.00 39.47 5.19
3908 4039 0.109689 CGACCTCGACCAAGAGTGTC 60.110 60.000 0.00 5.91 43.02 3.67
3920 4051 3.428999 CCAAGAGTGTCAGTATACCACCG 60.429 52.174 0.00 0.00 0.00 4.94
3929 4060 2.997986 CAGTATACCACCGTTCACAACC 59.002 50.000 0.00 0.00 0.00 3.77
3935 4066 1.270839 CCACCGTTCACAACCATCTCT 60.271 52.381 0.00 0.00 0.00 3.10
3936 4067 2.069273 CACCGTTCACAACCATCTCTC 58.931 52.381 0.00 0.00 0.00 3.20
3937 4068 1.002087 ACCGTTCACAACCATCTCTCC 59.998 52.381 0.00 0.00 0.00 3.71
3938 4069 1.276421 CCGTTCACAACCATCTCTCCT 59.724 52.381 0.00 0.00 0.00 3.69
3939 4070 2.496070 CCGTTCACAACCATCTCTCCTA 59.504 50.000 0.00 0.00 0.00 2.94
3941 4072 3.193691 CGTTCACAACCATCTCTCCTACT 59.806 47.826 0.00 0.00 0.00 2.57
3942 4073 4.398358 CGTTCACAACCATCTCTCCTACTA 59.602 45.833 0.00 0.00 0.00 1.82
3943 4074 5.105877 CGTTCACAACCATCTCTCCTACTAA 60.106 44.000 0.00 0.00 0.00 2.24
3946 4077 6.728411 TCACAACCATCTCTCCTACTAACTA 58.272 40.000 0.00 0.00 0.00 2.24
3949 4080 8.478877 CACAACCATCTCTCCTACTAACTAATT 58.521 37.037 0.00 0.00 0.00 1.40
3950 4081 9.710818 ACAACCATCTCTCCTACTAACTAATTA 57.289 33.333 0.00 0.00 0.00 1.40
3976 4178 5.931441 ATCTCGTTTAATAGCTGATTGGC 57.069 39.130 0.00 0.00 0.00 4.52
3977 4179 5.023533 TCTCGTTTAATAGCTGATTGGCT 57.976 39.130 0.00 0.00 45.29 4.75
3978 4180 4.811024 TCTCGTTTAATAGCTGATTGGCTG 59.189 41.667 0.00 0.00 43.01 4.85
3980 4182 4.570772 TCGTTTAATAGCTGATTGGCTGAC 59.429 41.667 0.00 0.00 43.01 3.51
3981 4183 4.332543 CGTTTAATAGCTGATTGGCTGACA 59.667 41.667 0.00 0.00 43.01 3.58
3982 4184 5.008019 CGTTTAATAGCTGATTGGCTGACAT 59.992 40.000 0.00 0.00 43.01 3.06
3993 4266 5.655090 TGATTGGCTGACATGAATGAATTCT 59.345 36.000 7.05 0.00 37.67 2.40
4002 4275 7.884257 TGACATGAATGAATTCTTTTACAGCA 58.116 30.769 7.05 1.49 37.67 4.41
4006 4296 3.201726 TGAATTCTTTTACAGCAGCGC 57.798 42.857 7.05 0.00 0.00 5.92
4039 4329 0.461135 CCTCTTCTCAGCAGAGCTCC 59.539 60.000 10.93 0.00 41.81 4.70
4042 4332 2.904470 CTTCTCAGCAGAGCTCCGCC 62.904 65.000 18.31 3.05 41.81 6.13
4080 4370 1.177401 GTCATTTCCCTCAAGGTGGC 58.823 55.000 0.00 0.00 36.75 5.01
4114 4404 1.641577 GCTACCCGATCAGTGTGTTC 58.358 55.000 0.00 0.00 0.00 3.18
4153 4443 1.939785 CGACGCCGACTACAGATGC 60.940 63.158 0.00 0.00 38.22 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.769300 AGGAATTAAATGAGGTTGTGGCC 59.231 43.478 0.00 0.00 0.00 5.36
3 4 7.670364 AGAAAAGGAATTAAATGAGGTTGTGG 58.330 34.615 0.00 0.00 0.00 4.17
4 5 9.196552 GAAGAAAAGGAATTAAATGAGGTTGTG 57.803 33.333 0.00 0.00 0.00 3.33
5 6 9.147732 AGAAGAAAAGGAATTAAATGAGGTTGT 57.852 29.630 0.00 0.00 0.00 3.32
65 66 9.558396 TTTTCCAAATGCTTGATTAACATTCTT 57.442 25.926 0.00 0.00 33.01 2.52
66 67 9.558396 TTTTTCCAAATGCTTGATTAACATTCT 57.442 25.926 0.00 0.00 33.01 2.40
168 173 9.769093 GTATGCGTTTATGTTCAACTTTCTTAT 57.231 29.630 0.00 0.00 0.00 1.73
172 177 8.447787 AATGTATGCGTTTATGTTCAACTTTC 57.552 30.769 0.00 0.00 0.00 2.62
194 199 9.282247 GAGCAGTAAACATCACTATTCAAAATG 57.718 33.333 0.00 0.00 0.00 2.32
200 205 5.805486 TGTCGAGCAGTAAACATCACTATTC 59.195 40.000 0.00 0.00 0.00 1.75
201 206 5.577164 GTGTCGAGCAGTAAACATCACTATT 59.423 40.000 0.00 0.00 0.00 1.73
217 222 2.860136 TCATCATTGAATCGTGTCGAGC 59.140 45.455 0.00 0.00 39.91 5.03
260 265 4.939052 TTTTCCAACCTTGCCGAATTTA 57.061 36.364 0.00 0.00 0.00 1.40
300 305 7.222611 GCAAACTTCTGAATGAAACTAGCAAAA 59.777 33.333 0.00 0.00 33.79 2.44
311 316 3.305539 GGTGCATGCAAACTTCTGAATGA 60.306 43.478 24.58 0.00 34.63 2.57
315 320 1.881973 GAGGTGCATGCAAACTTCTGA 59.118 47.619 24.58 0.00 0.00 3.27
562 574 0.179108 CCTGAACGGGTGCTACTAGC 60.179 60.000 0.61 0.61 42.82 3.42
571 583 4.619227 CGCACCACCTGAACGGGT 62.619 66.667 0.00 0.00 40.73 5.28
607 619 0.109086 CGAAGACACATCTCCACGCT 60.109 55.000 0.00 0.00 32.34 5.07
624 636 1.001974 CACCAAAGACAGATCCACCGA 59.998 52.381 0.00 0.00 0.00 4.69
938 967 2.230660 GTTGCAAGCTTAGACCAACCT 58.769 47.619 0.00 0.00 31.96 3.50
943 972 2.997485 CAAGGTTGCAAGCTTAGACC 57.003 50.000 35.85 17.44 44.21 3.85
1035 1067 0.476771 GGGGAGTTGACAAGTGGGAA 59.523 55.000 0.00 0.00 0.00 3.97
1102 1134 1.661341 CTCGAAGGATTTCAGGGCTG 58.339 55.000 0.00 0.00 32.67 4.85
1266 1299 1.241315 ACAAACCCACACCGCTATGC 61.241 55.000 0.00 0.00 0.00 3.14
1278 1311 4.622456 CCACGCACGCACAAACCC 62.622 66.667 0.00 0.00 0.00 4.11
1384 1428 2.753043 GGGTGGTCTCGCGGACTA 60.753 66.667 21.54 15.78 43.97 2.59
1399 1443 3.551496 TTCTGTTCCAGCAGCCGGG 62.551 63.158 2.18 0.00 36.49 5.73
1438 1482 3.539604 CCTGGATTCTGGAACATCTGTC 58.460 50.000 0.00 0.00 38.20 3.51
1459 1503 2.620585 AGAGAAGCAAAAGTGACAAGGC 59.379 45.455 0.00 0.00 0.00 4.35
1477 1521 2.464459 CGGCGCCTTGGCTAAAGAG 61.464 63.158 26.68 0.00 42.02 2.85
1506 1550 6.204688 TCCCTGATAATCAATACGACAAATGC 59.795 38.462 0.00 0.00 0.00 3.56
1509 1553 6.765989 CCTTCCCTGATAATCAATACGACAAA 59.234 38.462 0.00 0.00 0.00 2.83
1518 1562 4.054369 ACCATCCCTTCCCTGATAATCAA 58.946 43.478 0.00 0.00 0.00 2.57
1526 1570 6.462909 GCAAAAATTATACCATCCCTTCCCTG 60.463 42.308 0.00 0.00 0.00 4.45
1527 1571 5.602561 GCAAAAATTATACCATCCCTTCCCT 59.397 40.000 0.00 0.00 0.00 4.20
1538 1582 7.334171 AGCTTCAAATGTGGCAAAAATTATACC 59.666 33.333 0.00 0.00 0.00 2.73
1545 1589 4.121317 CAGAGCTTCAAATGTGGCAAAAA 58.879 39.130 0.00 0.00 0.00 1.94
1652 1696 4.906618 AGTCATTTGGAAATAGTGTCGGT 58.093 39.130 0.00 0.00 0.00 4.69
1654 1698 6.183360 GGGTTAGTCATTTGGAAATAGTGTCG 60.183 42.308 0.00 0.00 0.00 4.35
1655 1699 6.657541 TGGGTTAGTCATTTGGAAATAGTGTC 59.342 38.462 0.00 0.00 0.00 3.67
1656 1700 6.548321 TGGGTTAGTCATTTGGAAATAGTGT 58.452 36.000 0.00 0.00 0.00 3.55
1657 1701 7.461182 TTGGGTTAGTCATTTGGAAATAGTG 57.539 36.000 0.00 0.00 0.00 2.74
1658 1702 6.152831 GCTTGGGTTAGTCATTTGGAAATAGT 59.847 38.462 0.00 0.00 0.00 2.12
1659 1703 6.152661 TGCTTGGGTTAGTCATTTGGAAATAG 59.847 38.462 0.00 0.00 0.00 1.73
1698 1743 0.179045 GCCAGTGGCGGACAATAGAT 60.179 55.000 20.55 0.00 39.62 1.98
1789 1834 3.189080 TGGCAGATCATTTTGAACGTCAG 59.811 43.478 0.00 0.00 0.00 3.51
1850 1895 6.128769 CCAAATCAAGCACAACATAACACATG 60.129 38.462 0.00 0.00 0.00 3.21
1851 1896 5.927689 CCAAATCAAGCACAACATAACACAT 59.072 36.000 0.00 0.00 0.00 3.21
1891 1936 1.738099 GTTGCTCGCTGACCGACAT 60.738 57.895 0.00 0.00 41.89 3.06
1916 1961 8.887036 AATATGCATCTAAACATCTGTTACGA 57.113 30.769 0.19 0.00 37.25 3.43
1927 1972 8.019669 CAGGCAACAGATAATATGCATCTAAAC 58.980 37.037 0.19 0.00 40.51 2.01
1930 1975 6.772605 ACAGGCAACAGATAATATGCATCTA 58.227 36.000 0.19 0.00 40.51 1.98
1944 1989 1.656441 GCAACTGGACAGGCAACAG 59.344 57.895 4.14 0.00 41.41 3.16
1959 2004 2.288666 GGATCGTATTTCTGCAGGCAA 58.711 47.619 15.13 7.82 0.00 4.52
1965 2010 4.335315 TGGTTTGATGGATCGTATTTCTGC 59.665 41.667 0.00 0.00 0.00 4.26
2136 2196 6.892658 TCAATTAGGCAAGAACAGCTTTTA 57.107 33.333 0.00 0.00 33.60 1.52
2145 2205 7.122650 CCCAAGATTAGTTCAATTAGGCAAGAA 59.877 37.037 0.00 0.00 0.00 2.52
2146 2206 6.603201 CCCAAGATTAGTTCAATTAGGCAAGA 59.397 38.462 0.00 0.00 0.00 3.02
2158 2218 3.421844 AGCAACACCCCAAGATTAGTTC 58.578 45.455 0.00 0.00 0.00 3.01
2172 2232 5.578005 TGGTACAGATAGTAGAGCAACAC 57.422 43.478 0.00 0.00 32.19 3.32
2186 2246 1.134818 CAGCATAGCCGTTGGTACAGA 60.135 52.381 0.00 0.00 42.39 3.41
2189 2249 2.589798 TACAGCATAGCCGTTGGTAC 57.410 50.000 0.00 0.00 0.00 3.34
2332 2399 6.041069 ACCATCAATAAAGAAACAAAACGGGA 59.959 34.615 0.00 0.00 0.00 5.14
2487 2557 6.432783 CAGAAAACATTTAGGGGACACATGTA 59.567 38.462 0.00 0.00 0.00 2.29
2600 2670 2.645797 TCCTTCGGAATACCCAAAACCT 59.354 45.455 0.00 0.00 34.14 3.50
2603 2673 2.040545 TGCTCCTTCGGAATACCCAAAA 59.959 45.455 0.00 0.00 34.14 2.44
2614 2684 1.522668 TCACAAACATGCTCCTTCGG 58.477 50.000 0.00 0.00 0.00 4.30
2615 2685 3.250762 TCTTTCACAAACATGCTCCTTCG 59.749 43.478 0.00 0.00 0.00 3.79
2617 2687 4.276926 GTCTCTTTCACAAACATGCTCCTT 59.723 41.667 0.00 0.00 0.00 3.36
2726 2796 0.804989 CGAGACATTCTTTGGTGGCC 59.195 55.000 0.00 0.00 0.00 5.36
2744 2814 2.482142 GGATACCTGTTCCTTCTCAGCG 60.482 54.545 0.00 0.00 0.00 5.18
2765 2835 4.925054 TGACGGTTAGTTTCAGGTAAATCG 59.075 41.667 0.00 0.00 0.00 3.34
2799 2869 1.480137 ACACTAGGATCAGCAGACAGC 59.520 52.381 0.00 0.00 46.19 4.40
2804 2874 2.799917 GCGGTTACACTAGGATCAGCAG 60.800 54.545 0.00 0.00 0.00 4.24
2805 2875 1.136305 GCGGTTACACTAGGATCAGCA 59.864 52.381 0.00 0.00 0.00 4.41
2806 2876 1.136305 TGCGGTTACACTAGGATCAGC 59.864 52.381 0.00 0.00 0.00 4.26
2824 2894 4.060038 TCGGTAATCAAGAGGAGAATGC 57.940 45.455 0.00 0.00 0.00 3.56
2826 2896 4.717280 AGGTTCGGTAATCAAGAGGAGAAT 59.283 41.667 0.00 0.00 0.00 2.40
2837 2907 2.418976 GGTTCTGCAAGGTTCGGTAATC 59.581 50.000 0.00 0.00 0.00 1.75
2843 2913 0.882927 TTCCGGTTCTGCAAGGTTCG 60.883 55.000 0.00 0.00 0.00 3.95
2958 3028 2.494870 GGACTAGGTTTACGAGCTCCAA 59.505 50.000 8.47 0.00 37.30 3.53
2963 3033 5.522824 CCAAAATAGGACTAGGTTTACGAGC 59.477 44.000 0.00 0.00 0.00 5.03
2972 3042 6.265649 TCTCTCGAATCCAAAATAGGACTAGG 59.734 42.308 0.00 0.00 41.30 3.02
3033 3103 1.867233 CCAACTCCAACAGTCGTCAAG 59.133 52.381 0.00 0.00 32.30 3.02
3040 3110 5.014202 ACAGTTTAAACCAACTCCAACAGT 58.986 37.500 14.72 0.00 34.60 3.55
3099 3179 6.263392 TCTGACCAATACATCACTACTAGCTC 59.737 42.308 0.00 0.00 0.00 4.09
3106 3191 6.901081 ATCGATCTGACCAATACATCACTA 57.099 37.500 0.00 0.00 0.00 2.74
3184 3273 6.183360 GCTTGCACACGTAGAATATCTTTCTT 60.183 38.462 0.00 0.00 0.00 2.52
3185 3274 5.292101 GCTTGCACACGTAGAATATCTTTCT 59.708 40.000 0.00 0.00 0.00 2.52
3270 3359 7.257790 TCCTAACTCCTGAATTCTCAAATCA 57.742 36.000 7.05 0.00 0.00 2.57
3278 3367 6.201806 CGAATCACATCCTAACTCCTGAATTC 59.798 42.308 0.00 0.00 0.00 2.17
3279 3368 6.051717 CGAATCACATCCTAACTCCTGAATT 58.948 40.000 0.00 0.00 0.00 2.17
3291 3380 2.695666 CCCTACAGTCGAATCACATCCT 59.304 50.000 0.00 0.00 0.00 3.24
3292 3381 2.224066 CCCCTACAGTCGAATCACATCC 60.224 54.545 0.00 0.00 0.00 3.51
3296 3385 4.341520 AGAATACCCCTACAGTCGAATCAC 59.658 45.833 0.00 0.00 0.00 3.06
3297 3386 4.543689 AGAATACCCCTACAGTCGAATCA 58.456 43.478 0.00 0.00 0.00 2.57
3300 3389 4.205587 GAGAGAATACCCCTACAGTCGAA 58.794 47.826 0.00 0.00 0.00 3.71
3301 3390 3.434739 GGAGAGAATACCCCTACAGTCGA 60.435 52.174 0.00 0.00 0.00 4.20
3302 3391 2.885894 GGAGAGAATACCCCTACAGTCG 59.114 54.545 0.00 0.00 0.00 4.18
3303 3392 3.232662 GGGAGAGAATACCCCTACAGTC 58.767 54.545 0.00 0.00 40.19 3.51
3304 3393 2.424523 CGGGAGAGAATACCCCTACAGT 60.425 54.545 0.00 0.00 42.86 3.55
3305 3394 2.240279 CGGGAGAGAATACCCCTACAG 58.760 57.143 0.00 0.00 42.86 2.74
3306 3395 1.133262 CCGGGAGAGAATACCCCTACA 60.133 57.143 0.00 0.00 42.86 2.74
3307 3396 1.133231 ACCGGGAGAGAATACCCCTAC 60.133 57.143 6.32 0.00 42.86 3.18
3315 3410 3.325135 CCTTATGCTAACCGGGAGAGAAT 59.675 47.826 6.32 2.00 0.00 2.40
3332 3427 0.954203 TACCCTACCCCCTGCCTTAT 59.046 55.000 0.00 0.00 0.00 1.73
3335 3430 2.371453 GTACCCTACCCCCTGCCT 59.629 66.667 0.00 0.00 0.00 4.75
3347 3442 1.769465 GGAAGGGATGAGAAGGTACCC 59.231 57.143 8.74 0.00 40.71 3.69
3348 3443 1.413077 CGGAAGGGATGAGAAGGTACC 59.587 57.143 2.73 2.73 0.00 3.34
3349 3444 2.362717 CTCGGAAGGGATGAGAAGGTAC 59.637 54.545 0.00 0.00 31.31 3.34
3350 3445 2.024273 ACTCGGAAGGGATGAGAAGGTA 60.024 50.000 0.00 0.00 33.93 3.08
3351 3446 1.273324 ACTCGGAAGGGATGAGAAGGT 60.273 52.381 0.00 0.00 33.93 3.50
3352 3447 1.410882 GACTCGGAAGGGATGAGAAGG 59.589 57.143 0.00 0.00 33.93 3.46
3353 3448 1.410882 GGACTCGGAAGGGATGAGAAG 59.589 57.143 0.00 0.00 33.93 2.85
3354 3449 1.486211 GGACTCGGAAGGGATGAGAA 58.514 55.000 0.00 0.00 33.93 2.87
3357 3452 1.704082 AGGGACTCGGAAGGGATGA 59.296 57.895 0.00 0.00 33.92 2.92
3372 3467 1.137872 CTGGTTCCGATTCTGAGAGGG 59.862 57.143 0.00 0.00 0.00 4.30
3373 3468 1.472376 GCTGGTTCCGATTCTGAGAGG 60.472 57.143 0.00 0.00 0.00 3.69
3380 3475 1.573829 TTGCACGCTGGTTCCGATTC 61.574 55.000 0.00 0.00 0.00 2.52
3403 3498 1.048601 ATATACCACCAGCCACGAGG 58.951 55.000 0.00 0.00 38.23 4.63
3404 3499 3.258372 ACATATATACCACCAGCCACGAG 59.742 47.826 0.00 0.00 0.00 4.18
3405 3500 3.236047 ACATATATACCACCAGCCACGA 58.764 45.455 0.00 0.00 0.00 4.35
3406 3501 3.678056 ACATATATACCACCAGCCACG 57.322 47.619 0.00 0.00 0.00 4.94
3407 3502 4.775780 TCCTACATATATACCACCAGCCAC 59.224 45.833 0.00 0.00 0.00 5.01
3408 3503 4.775780 GTCCTACATATATACCACCAGCCA 59.224 45.833 0.00 0.00 0.00 4.75
3409 3504 4.142227 CGTCCTACATATATACCACCAGCC 60.142 50.000 0.00 0.00 0.00 4.85
3410 3505 4.677250 GCGTCCTACATATATACCACCAGC 60.677 50.000 0.00 0.00 0.00 4.85
3411 3506 4.461431 TGCGTCCTACATATATACCACCAG 59.539 45.833 0.00 0.00 0.00 4.00
3412 3507 4.219070 GTGCGTCCTACATATATACCACCA 59.781 45.833 0.00 0.00 0.00 4.17
3413 3508 4.381292 GGTGCGTCCTACATATATACCACC 60.381 50.000 0.00 0.00 33.20 4.61
3414 3509 4.381292 GGGTGCGTCCTACATATATACCAC 60.381 50.000 0.00 0.00 36.25 4.16
3415 3510 3.765511 GGGTGCGTCCTACATATATACCA 59.234 47.826 0.00 0.00 36.25 3.25
3416 3511 4.021916 AGGGTGCGTCCTACATATATACC 58.978 47.826 0.00 0.00 34.92 2.73
3417 3512 4.142227 CCAGGGTGCGTCCTACATATATAC 60.142 50.000 0.00 0.00 34.92 1.47
3418 3513 4.021229 CCAGGGTGCGTCCTACATATATA 58.979 47.826 0.00 0.00 34.92 0.86
3419 3514 2.832129 CCAGGGTGCGTCCTACATATAT 59.168 50.000 0.00 0.00 34.92 0.86
3420 3515 2.244695 CCAGGGTGCGTCCTACATATA 58.755 52.381 0.00 0.00 34.92 0.86
3421 3516 1.048601 CCAGGGTGCGTCCTACATAT 58.951 55.000 0.00 0.00 34.92 1.78
3422 3517 1.682451 GCCAGGGTGCGTCCTACATA 61.682 60.000 0.00 0.00 34.92 2.29
3423 3518 3.031417 GCCAGGGTGCGTCCTACAT 62.031 63.158 0.00 0.00 34.92 2.29
3424 3519 3.702048 GCCAGGGTGCGTCCTACA 61.702 66.667 0.00 0.00 34.92 2.74
3425 3520 4.468689 GGCCAGGGTGCGTCCTAC 62.469 72.222 0.00 0.00 34.92 3.18
3432 3527 4.101448 ACTCGATGGCCAGGGTGC 62.101 66.667 13.05 0.00 0.00 5.01
3433 3528 2.187946 GACTCGATGGCCAGGGTG 59.812 66.667 13.05 8.94 0.00 4.61
3438 3533 1.657751 CTGACTCGACTCGATGGCCA 61.658 60.000 8.56 8.56 34.61 5.36
3449 3544 2.287977 TTTGAGAGGGACTGACTCGA 57.712 50.000 0.00 0.00 41.55 4.04
3451 3546 3.261897 TGGATTTTGAGAGGGACTGACTC 59.738 47.826 0.00 0.00 41.55 3.36
3452 3547 3.008485 GTGGATTTTGAGAGGGACTGACT 59.992 47.826 0.00 0.00 41.55 3.41
3453 3548 3.339141 GTGGATTTTGAGAGGGACTGAC 58.661 50.000 0.00 0.00 41.55 3.51
3454 3549 2.028112 CGTGGATTTTGAGAGGGACTGA 60.028 50.000 0.00 0.00 41.55 3.41
3455 3550 2.028112 TCGTGGATTTTGAGAGGGACTG 60.028 50.000 0.00 0.00 41.55 3.51
3457 3552 2.762535 TCGTGGATTTTGAGAGGGAC 57.237 50.000 0.00 0.00 0.00 4.46
3458 3553 2.159099 CGATCGTGGATTTTGAGAGGGA 60.159 50.000 7.03 0.00 0.00 4.20
3459 3554 2.205074 CGATCGTGGATTTTGAGAGGG 58.795 52.381 7.03 0.00 0.00 4.30
3501 3596 0.928922 TAGCGCGTCGTGTTCAAAAA 59.071 45.000 8.43 0.00 0.00 1.94
3502 3597 0.505231 CTAGCGCGTCGTGTTCAAAA 59.495 50.000 8.43 0.00 0.00 2.44
3503 3598 0.595567 ACTAGCGCGTCGTGTTCAAA 60.596 50.000 8.43 0.00 0.00 2.69
3504 3599 1.000233 GACTAGCGCGTCGTGTTCAA 61.000 55.000 8.43 0.00 0.00 2.69
3512 3607 1.694962 GTGTTTCGACTAGCGCGTC 59.305 57.895 8.43 3.15 40.61 5.19
3513 3608 2.078914 CGTGTTTCGACTAGCGCGT 61.079 57.895 8.43 0.00 42.86 6.01
3516 3611 1.253999 GTACCGTGTTTCGACTAGCG 58.746 55.000 0.00 0.00 42.86 4.26
3518 3613 1.135859 AGCGTACCGTGTTTCGACTAG 60.136 52.381 0.00 0.00 42.86 2.57
3519 3614 0.874390 AGCGTACCGTGTTTCGACTA 59.126 50.000 0.00 0.00 42.86 2.59
3520 3615 0.386478 GAGCGTACCGTGTTTCGACT 60.386 55.000 0.00 0.00 42.86 4.18
3522 3617 1.081242 GGAGCGTACCGTGTTTCGA 60.081 57.895 0.00 0.00 42.86 3.71
3523 3618 1.069378 GAGGAGCGTACCGTGTTTCG 61.069 60.000 0.00 0.00 39.52 3.46
3524 3619 1.069378 CGAGGAGCGTACCGTGTTTC 61.069 60.000 0.00 0.00 34.64 2.78
3544 3657 1.078143 AGCCATCTCGCTTTCCCAC 60.078 57.895 0.00 0.00 34.73 4.61
3576 3689 1.154188 GACTCTGTCTCCGTCGTGC 60.154 63.158 0.00 0.00 0.00 5.34
3593 3706 3.062466 CTCCGTGTCCGCCAGAGA 61.062 66.667 0.00 0.00 0.00 3.10
3594 3707 4.135153 CCTCCGTGTCCGCCAGAG 62.135 72.222 0.00 0.00 0.00 3.35
3602 3715 4.773117 GTCCGTCGCCTCCGTGTC 62.773 72.222 0.00 0.00 35.54 3.67
3662 3793 4.899239 CGTCTCTGCCCCCGATGC 62.899 72.222 0.00 0.00 0.00 3.91
3669 3800 3.775654 CTGACCCCGTCTCTGCCC 61.776 72.222 0.00 0.00 33.15 5.36
3675 3806 2.114625 TCGTGTCTGACCCCGTCT 59.885 61.111 5.17 0.00 33.15 4.18
3681 3812 1.371389 GTGTCCGTCGTGTCTGACC 60.371 63.158 5.17 0.00 35.40 4.02
3827 3958 1.959226 CGTTGGACTTGGGGTCGTG 60.959 63.158 0.00 0.00 45.35 4.35
3908 4039 2.997986 GGTTGTGAACGGTGGTATACTG 59.002 50.000 2.25 0.00 41.64 2.74
3920 4051 4.810191 AGTAGGAGAGATGGTTGTGAAC 57.190 45.455 0.00 0.00 0.00 3.18
3950 4081 8.507249 GCCAATCAGCTATTAAACGAGATTATT 58.493 33.333 0.00 0.00 0.00 1.40
3959 4161 5.818136 TGTCAGCCAATCAGCTATTAAAC 57.182 39.130 0.00 0.00 42.61 2.01
3965 4167 3.632643 TTCATGTCAGCCAATCAGCTA 57.367 42.857 0.00 0.00 42.61 3.32
3966 4168 2.502142 TTCATGTCAGCCAATCAGCT 57.498 45.000 0.00 0.00 46.45 4.24
3967 4169 2.686405 TCATTCATGTCAGCCAATCAGC 59.314 45.455 0.00 0.00 0.00 4.26
3968 4170 4.976224 TTCATTCATGTCAGCCAATCAG 57.024 40.909 0.00 0.00 0.00 2.90
3973 4175 5.988310 AAAGAATTCATTCATGTCAGCCA 57.012 34.783 8.44 0.00 39.23 4.75
3974 4176 7.315142 TGTAAAAGAATTCATTCATGTCAGCC 58.685 34.615 8.44 0.00 39.23 4.85
3975 4177 7.008992 GCTGTAAAAGAATTCATTCATGTCAGC 59.991 37.037 8.44 12.99 39.23 4.26
3976 4178 8.024865 TGCTGTAAAAGAATTCATTCATGTCAG 58.975 33.333 8.44 8.08 39.23 3.51
3977 4179 7.884257 TGCTGTAAAAGAATTCATTCATGTCA 58.116 30.769 8.44 0.00 39.23 3.58
3978 4180 7.008992 GCTGCTGTAAAAGAATTCATTCATGTC 59.991 37.037 8.44 0.00 39.23 3.06
3980 4182 6.020916 CGCTGCTGTAAAAGAATTCATTCATG 60.021 38.462 8.44 0.00 39.23 3.07
3981 4183 6.032094 CGCTGCTGTAAAAGAATTCATTCAT 58.968 36.000 8.44 0.00 39.23 2.57
3982 4184 5.393124 CGCTGCTGTAAAAGAATTCATTCA 58.607 37.500 8.44 0.00 39.23 2.57
3993 4266 0.874390 CTGAAGGCGCTGCTGTAAAA 59.126 50.000 7.64 0.00 0.00 1.52
4006 4296 1.206849 GAAGAGGTGAGCTCCTGAAGG 59.793 57.143 12.15 0.00 38.02 3.46
4042 4332 0.247262 CGTTGACCGATGATTGCACG 60.247 55.000 0.00 0.00 39.56 5.34
4153 4443 2.442188 GCGGCGGAACAAGTAGACG 61.442 63.158 9.78 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.