Multiple sequence alignment - TraesCS4D01G197900

Loading Multiple Alignment...

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 TraesCS4D01G197900 chr4D 100.000 5278 0 0 1 5278 343419426 343414149 0.000000e+00 9747.0
1 TraesCS4D01G197900 chr4D 90.244 123 10 1 4447 4567 484009352 484009474 5.470000e-35 159.0
2 TraesCS4D01G197900 chr4D 90.385 52 4 1 2060 2110 329317916 329317967 3.410000e-07 67.6
3 TraesCS4D01G197900 chr4B 94.738 3573 120 30 899 4441 425199559 425196025 0.000000e+00 5494.0
4 TraesCS4D01G197900 chr4B 94.253 261 13 2 646 906 425199850 425199592 1.070000e-106 398.0
5 TraesCS4D01G197900 chr4B 90.370 135 11 2 1 134 425199975 425199842 5.430000e-40 176.0
6 TraesCS4D01G197900 chr4B 89.922 129 11 2 4454 4580 606822143 606822015 1.180000e-36 165.0
7 TraesCS4D01G197900 chr4A 97.190 2242 55 7 2182 4421 122251369 122253604 0.000000e+00 3784.0
8 TraesCS4D01G197900 chr4A 91.676 853 42 13 899 1726 122249285 122250133 0.000000e+00 1155.0
9 TraesCS4D01G197900 chr4A 85.520 808 75 18 104 906 122248484 122249254 0.000000e+00 806.0
10 TraesCS4D01G197900 chr4A 73.477 558 116 29 1461 1999 474930967 474930423 1.170000e-41 182.0
11 TraesCS4D01G197900 chr4A 86.957 138 14 4 4447 4580 568196372 568196235 9.150000e-33 152.0
12 TraesCS4D01G197900 chr4A 93.590 78 5 0 1778 1855 122250132 122250209 3.340000e-22 117.0
13 TraesCS4D01G197900 chr7D 88.904 730 64 10 4565 5278 66976841 66976113 0.000000e+00 883.0
14 TraesCS4D01G197900 chr7D 84.753 728 82 19 4566 5278 171317587 171318300 0.000000e+00 702.0
15 TraesCS4D01G197900 chr7D 90.909 55 4 1 2057 2110 243007506 243007560 7.330000e-09 73.1
16 TraesCS4D01G197900 chr7D 87.273 55 4 2 2054 2107 78119596 78119648 5.710000e-05 60.2
17 TraesCS4D01G197900 chr3D 88.493 730 67 11 4564 5278 474539058 474538331 0.000000e+00 867.0
18 TraesCS4D01G197900 chr3D 86.357 733 74 16 4560 5278 586434117 586433397 0.000000e+00 776.0
19 TraesCS4D01G197900 chr3D 86.809 561 53 9 4563 5108 475893420 475892866 1.630000e-169 606.0
20 TraesCS4D01G197900 chr3D 74.187 492 111 12 1467 1952 9629741 9630222 1.940000e-44 191.0
21 TraesCS4D01G197900 chr3D 88.550 131 12 3 4447 4574 452368722 452368852 7.080000e-34 156.0
22 TraesCS4D01G197900 chr5D 88.340 729 65 13 4566 5278 532338544 532337820 0.000000e+00 857.0
23 TraesCS4D01G197900 chr5D 85.690 587 63 13 4599 5178 57581339 57581911 2.720000e-167 599.0
24 TraesCS4D01G197900 chr5D 90.244 123 10 2 4447 4567 377147857 377147979 5.470000e-35 159.0
25 TraesCS4D01G197900 chr5D 86.429 140 14 5 4447 4582 481980989 481981127 1.180000e-31 148.0
26 TraesCS4D01G197900 chr2B 87.222 720 82 10 4563 5278 496538047 496537334 0.000000e+00 811.0
27 TraesCS4D01G197900 chr2B 79.524 210 36 5 1450 1658 58315605 58315808 5.510000e-30 143.0
28 TraesCS4D01G197900 chr2D 87.787 696 77 6 4590 5278 159342700 159342006 0.000000e+00 808.0
29 TraesCS4D01G197900 chr2D 81.203 665 93 24 4563 5210 120547983 120548632 1.700000e-139 507.0
30 TraesCS4D01G197900 chr7A 85.948 733 75 21 4566 5278 105475172 105475896 0.000000e+00 758.0
31 TraesCS4D01G197900 chr7A 80.000 320 52 11 1398 1706 82932055 82932373 5.320000e-55 226.0
32 TraesCS4D01G197900 chr7A 95.455 44 2 0 57 100 646678522 646678479 2.640000e-08 71.3
33 TraesCS4D01G197900 chr7B 80.939 703 92 26 4599 5278 635907022 635906339 7.840000e-143 518.0
34 TraesCS4D01G197900 chr7B 91.489 47 3 1 57 102 700548553 700548507 4.410000e-06 63.9
35 TraesCS4D01G197900 chr1D 79.931 578 89 11 1398 1950 460879595 460879020 2.960000e-107 399.0
36 TraesCS4D01G197900 chr1D 90.323 124 7 5 4447 4567 8930475 8930354 1.970000e-34 158.0
37 TraesCS4D01G197900 chr1D 77.698 278 46 13 1661 1925 273920527 273920801 7.080000e-34 156.0
38 TraesCS4D01G197900 chr1D 91.489 47 3 1 2065 2110 256235846 256235800 4.410000e-06 63.9
39 TraesCS4D01G197900 chr1D 94.286 35 2 0 1589 1623 384127738 384127772 3.000000e-03 54.7
40 TraesCS4D01G197900 chr6D 75.125 599 97 25 1398 1954 138387336 138386748 3.180000e-57 233.0
41 TraesCS4D01G197900 chr1B 81.648 267 40 6 1661 1918 373318289 373318555 4.140000e-51 213.0
42 TraesCS4D01G197900 chr5A 90.909 121 9 2 4447 4565 539086292 539086412 1.520000e-35 161.0
43 TraesCS4D01G197900 chr5A 100.000 28 0 0 1596 1623 520466259 520466232 1.000000e-02 52.8
44 TraesCS4D01G197900 chr5B 89.516 124 11 2 4446 4567 347932724 347932601 7.080000e-34 156.0
45 TraesCS4D01G197900 chr5B 100.000 28 0 0 56 83 493475695 493475668 1.000000e-02 52.8
46 TraesCS4D01G197900 chr6B 86.957 46 6 0 56 101 588899584 588899539 1.000000e-02 52.8


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 TraesCS4D01G197900 chr4D 343414149 343419426 5277 True 9747.000000 9747 100.000000 1 5278 1 chr4D.!!$R1 5277
1 TraesCS4D01G197900 chr4B 425196025 425199975 3950 True 2022.666667 5494 93.120333 1 4441 3 chr4B.!!$R2 4440
2 TraesCS4D01G197900 chr4A 122248484 122253604 5120 False 1465.500000 3784 91.994000 104 4421 4 chr4A.!!$F1 4317
3 TraesCS4D01G197900 chr7D 66976113 66976841 728 True 883.000000 883 88.904000 4565 5278 1 chr7D.!!$R1 713
4 TraesCS4D01G197900 chr7D 171317587 171318300 713 False 702.000000 702 84.753000 4566 5278 1 chr7D.!!$F2 712
5 TraesCS4D01G197900 chr3D 474538331 474539058 727 True 867.000000 867 88.493000 4564 5278 1 chr3D.!!$R1 714
6 TraesCS4D01G197900 chr3D 586433397 586434117 720 True 776.000000 776 86.357000 4560 5278 1 chr3D.!!$R3 718
7 TraesCS4D01G197900 chr3D 475892866 475893420 554 True 606.000000 606 86.809000 4563 5108 1 chr3D.!!$R2 545
8 TraesCS4D01G197900 chr5D 532337820 532338544 724 True 857.000000 857 88.340000 4566 5278 1 chr5D.!!$R1 712
9 TraesCS4D01G197900 chr5D 57581339 57581911 572 False 599.000000 599 85.690000 4599 5178 1 chr5D.!!$F1 579
10 TraesCS4D01G197900 chr2B 496537334 496538047 713 True 811.000000 811 87.222000 4563 5278 1 chr2B.!!$R1 715
11 TraesCS4D01G197900 chr2D 159342006 159342700 694 True 808.000000 808 87.787000 4590 5278 1 chr2D.!!$R1 688
12 TraesCS4D01G197900 chr2D 120547983 120548632 649 False 507.000000 507 81.203000 4563 5210 1 chr2D.!!$F1 647
13 TraesCS4D01G197900 chr7A 105475172 105475896 724 False 758.000000 758 85.948000 4566 5278 1 chr7A.!!$F2 712
14 TraesCS4D01G197900 chr7B 635906339 635907022 683 True 518.000000 518 80.939000 4599 5278 1 chr7B.!!$R1 679
15 TraesCS4D01G197900 chr1D 460879020 460879595 575 True 399.000000 399 79.931000 1398 1950 1 chr1D.!!$R3 552
16 TraesCS4D01G197900 chr6D 138386748 138387336 588 True 233.000000 233 75.125000 1398 1954 1 chr6D.!!$R1 556

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
381 386 0.179054 GGGCTTTCATCCGTCCCTAC 60.179 60.000 0.00 0.0 34.19 3.18 F
1424 1511 0.532573 TCCATCAGCGAGTTGGAGAC 59.467 55.000 7.62 0.0 40.39 3.36 F
1999 2142 1.015085 CACGAACCGTAAATCCGCCA 61.015 55.000 0.00 0.0 38.32 5.69 F
3048 4189 1.151450 AACTGAAGCAGGGTGGTGG 59.849 57.895 0.00 0.0 35.51 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 2216 0.249155 TTATAAAGTCGGGCCTCGCG 60.249 55.0 0.84 0.00 41.10 5.87 R
3073 4214 2.153366 TATGCGCACGATCATGATGT 57.847 45.0 14.90 8.83 0.00 3.06 R
3482 4623 0.391661 CAGTGATGTGGACCTTCCCG 60.392 60.0 0.00 0.00 35.03 5.14 R
4981 6192 0.254747 ACGGGGACAGAGAGAGAGAG 59.745 60.0 0.00 0.00 0.00 3.20 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 5.389859 TTTATTCCAGCACATGAAACCTG 57.610 39.130 0.00 0.00 0.00 4.00
30 31 3.828451 AGCACATGAAACCTGTTATGCTT 59.172 39.130 0.00 0.00 0.00 3.91
44 45 2.820037 GCTTGCGGCAGACCCTAC 60.820 66.667 1.67 0.00 41.35 3.18
45 46 2.982130 CTTGCGGCAGACCCTACT 59.018 61.111 1.67 0.00 0.00 2.57
48 49 1.610554 TTGCGGCAGACCCTACTACC 61.611 60.000 1.67 0.00 0.00 3.18
50 51 1.328430 GCGGCAGACCCTACTACCTT 61.328 60.000 0.00 0.00 0.00 3.50
114 115 4.708601 CTGCCACGTACTTTTGTCAATAC 58.291 43.478 0.00 0.00 0.00 1.89
148 149 3.308866 GGTCCTTTCGGTCATTATGTTCG 59.691 47.826 0.00 0.00 0.00 3.95
155 156 2.490991 GGTCATTATGTTCGGGTAGGC 58.509 52.381 0.00 0.00 0.00 3.93
157 158 1.069513 TCATTATGTTCGGGTAGGCGG 59.930 52.381 0.00 0.00 0.00 6.13
166 167 0.179119 CGGGTAGGCGGTCTAAAGTG 60.179 60.000 0.00 0.00 0.00 3.16
168 169 1.134877 GGGTAGGCGGTCTAAAGTGAC 60.135 57.143 0.00 0.00 36.31 3.67
180 181 5.625311 GGTCTAAAGTGACAAAAATTCTGCG 59.375 40.000 0.00 0.00 38.61 5.18
206 207 3.303725 CGATGGCTCAAAACGTCTTCAAA 60.304 43.478 0.00 0.00 0.00 2.69
212 213 1.407258 CAAAACGTCTTCAAAGGGCCA 59.593 47.619 6.18 0.00 0.00 5.36
239 240 6.582295 CGCCGAATTTATTTTTCATATCCCAG 59.418 38.462 0.00 0.00 0.00 4.45
240 241 7.521423 CGCCGAATTTATTTTTCATATCCCAGA 60.521 37.037 0.00 0.00 0.00 3.86
250 251 7.792374 TTTTCATATCCCAGAGAAAAGATCG 57.208 36.000 0.00 0.00 35.68 3.69
253 254 5.835819 TCATATCCCAGAGAAAAGATCGTCT 59.164 40.000 0.00 0.00 0.00 4.18
288 289 3.988819 TCTTGGCTTTAATGCAACCAAC 58.011 40.909 14.56 0.00 35.53 3.77
296 297 1.881591 AATGCAACCAACAACATGGC 58.118 45.000 0.00 0.00 44.75 4.40
297 298 0.319727 ATGCAACCAACAACATGGCG 60.320 50.000 0.00 0.00 44.75 5.69
298 299 1.664333 GCAACCAACAACATGGCGG 60.664 57.895 0.00 0.00 44.75 6.13
299 300 2.037053 CAACCAACAACATGGCGGA 58.963 52.632 0.00 0.00 44.75 5.54
300 301 0.602562 CAACCAACAACATGGCGGAT 59.397 50.000 0.00 0.00 44.75 4.18
301 302 1.815613 CAACCAACAACATGGCGGATA 59.184 47.619 0.00 0.00 44.75 2.59
302 303 2.426738 CAACCAACAACATGGCGGATAT 59.573 45.455 0.00 0.00 44.75 1.63
303 304 2.023673 ACCAACAACATGGCGGATATG 58.976 47.619 0.00 0.00 44.75 1.78
304 305 1.269206 CCAACAACATGGCGGATATGC 60.269 52.381 0.00 0.00 32.78 3.14
305 306 1.677576 CAACAACATGGCGGATATGCT 59.322 47.619 0.00 0.00 34.52 3.79
307 308 2.378038 ACAACATGGCGGATATGCTTT 58.622 42.857 0.00 0.00 34.52 3.51
308 309 2.358898 ACAACATGGCGGATATGCTTTC 59.641 45.455 0.00 0.00 34.52 2.62
319 324 3.491267 GGATATGCTTTCCTCGAACTTCG 59.509 47.826 4.72 4.72 42.10 3.79
329 334 0.601558 TCGAACTTCGTCCCTCCAAG 59.398 55.000 10.88 0.00 41.35 3.61
339 344 0.613260 TCCCTCCAAGTCAATGGTCG 59.387 55.000 0.00 0.00 41.46 4.79
346 351 2.349438 CCAAGTCAATGGTCGTTTGTCG 60.349 50.000 0.00 0.00 41.41 4.35
360 365 1.039068 TTGTCGTCTCCACGGGTAAA 58.961 50.000 0.00 0.00 46.70 2.01
368 373 1.076014 CCACGGGTAAAGGGGCTTT 59.924 57.895 0.00 0.00 37.46 3.51
381 386 0.179054 GGGCTTTCATCCGTCCCTAC 60.179 60.000 0.00 0.00 34.19 3.18
401 406 3.275143 ACAAGTCAATGGTCGTTTGTCA 58.725 40.909 0.00 0.00 0.00 3.58
405 410 4.389374 AGTCAATGGTCGTTTGTCATCTT 58.611 39.130 0.00 0.00 0.00 2.40
409 414 3.186702 TGGTCGTTTGTCATCTTCACA 57.813 42.857 0.00 0.00 0.00 3.58
411 416 2.480419 GGTCGTTTGTCATCTTCACAGG 59.520 50.000 0.00 0.00 0.00 4.00
414 419 4.386049 GTCGTTTGTCATCTTCACAGGTAG 59.614 45.833 0.00 0.00 0.00 3.18
415 420 3.679980 CGTTTGTCATCTTCACAGGTAGG 59.320 47.826 0.00 0.00 0.00 3.18
416 421 3.981071 TTGTCATCTTCACAGGTAGGG 57.019 47.619 0.00 0.00 0.00 3.53
434 439 2.477104 GGGGGTTTTCATCCATCCAT 57.523 50.000 0.00 0.00 0.00 3.41
435 440 3.611025 GGGGGTTTTCATCCATCCATA 57.389 47.619 0.00 0.00 0.00 2.74
449 454 4.227073 TCCATCCATACAAGTCAATGGTCA 59.773 41.667 1.56 0.00 42.77 4.02
452 457 6.097270 CCATCCATACAAGTCAATGGTCATTT 59.903 38.462 1.56 0.00 42.77 2.32
453 458 6.513806 TCCATACAAGTCAATGGTCATTTG 57.486 37.500 1.56 0.00 42.77 2.32
454 459 6.009589 TCCATACAAGTCAATGGTCATTTGT 58.990 36.000 1.56 0.00 42.77 2.83
455 460 6.150976 TCCATACAAGTCAATGGTCATTTGTC 59.849 38.462 1.56 0.00 42.77 3.18
456 461 4.488126 ACAAGTCAATGGTCATTTGTCG 57.512 40.909 0.00 0.00 0.00 4.35
457 462 3.882888 ACAAGTCAATGGTCATTTGTCGT 59.117 39.130 0.00 0.00 0.00 4.34
458 463 4.221342 CAAGTCAATGGTCATTTGTCGTG 58.779 43.478 0.00 0.00 0.00 4.35
459 464 3.476552 AGTCAATGGTCATTTGTCGTGT 58.523 40.909 0.00 0.00 0.00 4.49
460 465 4.637276 AGTCAATGGTCATTTGTCGTGTA 58.363 39.130 0.00 0.00 0.00 2.90
461 466 4.451096 AGTCAATGGTCATTTGTCGTGTAC 59.549 41.667 0.00 0.00 0.00 2.90
462 467 4.451096 GTCAATGGTCATTTGTCGTGTACT 59.549 41.667 0.00 0.00 0.00 2.73
470 475 4.992319 TCATTTGTCGTGTACTTGGGTAAG 59.008 41.667 0.00 0.00 39.86 2.34
472 477 2.318908 TGTCGTGTACTTGGGTAAGGT 58.681 47.619 0.00 0.00 38.26 3.50
474 479 1.619827 TCGTGTACTTGGGTAAGGTGG 59.380 52.381 0.00 0.00 38.26 4.61
477 482 2.059490 TGTACTTGGGTAAGGTGGCTT 58.941 47.619 0.00 0.00 38.26 4.35
551 556 3.372025 GGTAGAGGAGTACCCGGTAGAAA 60.372 52.174 0.00 0.00 40.87 2.52
587 592 8.066612 ACAGTATTAACCAATTTCAGGAATGG 57.933 34.615 1.12 1.12 0.00 3.16
635 640 7.469537 TCTTAAAAAGGAAAATTATGGGCGA 57.530 32.000 0.00 0.00 0.00 5.54
646 655 2.696989 TATGGGCGAGGATGCATATG 57.303 50.000 0.00 0.00 36.28 1.78
968 1024 4.292178 CCTCCCATCTCTCGCGCC 62.292 72.222 0.00 0.00 0.00 6.53
1283 1370 6.822442 TGGAATAGGATAAGCATGTTCGTAA 58.178 36.000 0.00 0.00 30.39 3.18
1304 1391 2.684843 CGGCAGCTTGGTCTTGCTC 61.685 63.158 0.00 0.00 37.44 4.26
1309 1396 0.892814 AGCTTGGTCTTGCTCTTGGC 60.893 55.000 0.00 0.00 42.22 4.52
1325 1412 7.116075 TGCTCTTGGCTTATTGAGGTTATTTA 58.884 34.615 0.00 0.00 42.39 1.40
1331 1418 6.661377 TGGCTTATTGAGGTTATTTAGTTGCA 59.339 34.615 0.00 0.00 0.00 4.08
1332 1419 7.341769 TGGCTTATTGAGGTTATTTAGTTGCAT 59.658 33.333 0.00 0.00 0.00 3.96
1370 1457 0.546122 ATAGCAGATCCCGCAAACCA 59.454 50.000 7.42 0.00 0.00 3.67
1392 1479 3.504520 ACGGTCCTGCAAATTTCGTTTAT 59.495 39.130 0.00 0.00 0.00 1.40
1424 1511 0.532573 TCCATCAGCGAGTTGGAGAC 59.467 55.000 7.62 0.00 40.39 3.36
1509 1602 4.838152 GCCGCCTCCTTCGCATCA 62.838 66.667 0.00 0.00 0.00 3.07
1690 1790 2.261361 CACCTCGTCGTCATGGCA 59.739 61.111 0.00 0.00 0.00 4.92
1822 1942 2.158755 GGGATTTGTCACCGGAGATGAT 60.159 50.000 9.46 0.97 0.00 2.45
1844 1986 4.954118 TGCGGCGGAGGGGGATAT 62.954 66.667 9.78 0.00 0.00 1.63
1899 2042 2.755650 CTCCGGTATATGTGCAGGAAC 58.244 52.381 0.00 0.00 34.32 3.62
1963 2106 2.941064 GGCCGTTTTTACAGGATCTACC 59.059 50.000 0.00 0.00 39.35 3.18
1971 2114 2.122813 AGGATCTACCCGGGCCTG 60.123 66.667 24.08 11.37 40.05 4.85
1973 2116 1.152398 GGATCTACCCGGGCCTGTA 60.152 63.158 24.08 4.00 0.00 2.74
1999 2142 1.015085 CACGAACCGTAAATCCGCCA 61.015 55.000 0.00 0.00 38.32 5.69
2028 2171 6.241645 GGTGAGCTTTTAAGGGATATGCTAT 58.758 40.000 0.00 0.00 0.00 2.97
2030 2173 7.550906 GGTGAGCTTTTAAGGGATATGCTATAG 59.449 40.741 0.00 0.00 0.00 1.31
2050 2193 7.255801 GCTATAGATGCTCTTAGTCCTGTCTTT 60.256 40.741 3.21 0.00 0.00 2.52
2058 2201 6.204882 GCTCTTAGTCCTGTCTTTGCTTTTTA 59.795 38.462 0.00 0.00 0.00 1.52
2080 2223 3.531262 TTTTTAGAGAAAACGCGAGGC 57.469 42.857 15.93 0.00 34.24 4.70
2085 2229 3.785499 GAAAACGCGAGGCCCGAC 61.785 66.667 15.93 7.63 41.76 4.79
2384 3525 5.916318 TGTTCTGCAATTGTGGAATTCTTT 58.084 33.333 7.40 0.00 28.65 2.52
2712 3853 3.135994 TCTACCCACGCTTGAGTTTTTC 58.864 45.455 0.00 0.00 0.00 2.29
3048 4189 1.151450 AACTGAAGCAGGGTGGTGG 59.849 57.895 0.00 0.00 35.51 4.61
3465 4606 2.636830 CAGTTGATACCTTCTGCCCTG 58.363 52.381 0.00 0.00 0.00 4.45
3482 4623 1.673168 CTGAGCACCTTCTTATGGGC 58.327 55.000 0.00 0.00 0.00 5.36
3738 4879 2.045926 GGTCAGACTGCGGGCATT 60.046 61.111 0.00 0.00 0.00 3.56
3758 4899 6.207221 GGCATTTGTTCATTTGGAGGAAAAAT 59.793 34.615 0.00 0.00 0.00 1.82
3819 4960 2.980568 TCGTTAATTGCATCGAACCCT 58.019 42.857 0.00 0.00 0.00 4.34
3859 5000 5.013287 TCCTAGCTACTAGTGGGATAGACAG 59.987 48.000 18.24 2.79 32.62 3.51
4067 5208 3.134127 GCGCGGGAGAGGCAATTT 61.134 61.111 8.83 0.00 0.00 1.82
4132 5273 7.082700 TGATGCGTATCTTAAGATTGCAAAA 57.917 32.000 31.66 24.17 43.16 2.44
4263 5404 1.134670 CGAACTCTGATCCCAGGGAAC 60.135 57.143 13.94 11.18 43.69 3.62
4416 5559 8.683550 TGTTAGTATGTTCAAATCTGTACTCG 57.316 34.615 0.00 0.00 0.00 4.18
4422 5565 6.525578 TGTTCAAATCTGTACTCGGTCTAT 57.474 37.500 0.00 0.00 0.00 1.98
4441 5584 7.517893 CGGTCTATTAAAATAAAGGCGTTCCTC 60.518 40.741 0.00 0.00 43.40 3.71
4442 5585 7.342942 GTCTATTAAAATAAAGGCGTTCCTCG 58.657 38.462 0.00 0.00 43.40 4.63
4470 5613 5.715434 TTTTTAAAAGAAGGATGACCCCG 57.285 39.130 0.14 0.00 36.73 5.73
4471 5614 3.359695 TTAAAAGAAGGATGACCCCGG 57.640 47.619 0.00 0.00 36.73 5.73
4472 5615 0.323451 AAAAGAAGGATGACCCCGGC 60.323 55.000 0.00 0.00 36.73 6.13
4473 5616 2.211468 AAAGAAGGATGACCCCGGCC 62.211 60.000 0.00 0.00 36.73 6.13
4474 5617 3.090532 GAAGGATGACCCCGGCCT 61.091 66.667 0.00 0.00 36.73 5.19
4475 5618 3.090532 AAGGATGACCCCGGCCTC 61.091 66.667 0.00 0.00 36.73 4.70
4476 5619 3.642741 AAGGATGACCCCGGCCTCT 62.643 63.158 0.00 0.00 36.73 3.69
4477 5620 3.090532 GGATGACCCCGGCCTCTT 61.091 66.667 0.00 0.00 0.00 2.85
4478 5621 2.506472 GATGACCCCGGCCTCTTC 59.494 66.667 0.00 0.00 0.00 2.87
4479 5622 2.285368 ATGACCCCGGCCTCTTCA 60.285 61.111 0.00 0.00 0.00 3.02
4480 5623 1.694169 ATGACCCCGGCCTCTTCAT 60.694 57.895 0.00 0.37 0.00 2.57
4481 5624 1.700042 ATGACCCCGGCCTCTTCATC 61.700 60.000 0.00 0.00 0.00 2.92
4482 5625 2.041265 ACCCCGGCCTCTTCATCT 59.959 61.111 0.00 0.00 0.00 2.90
4483 5626 2.317149 GACCCCGGCCTCTTCATCTG 62.317 65.000 0.00 0.00 0.00 2.90
4484 5627 2.507944 CCCGGCCTCTTCATCTGG 59.492 66.667 0.00 0.00 0.00 3.86
4485 5628 2.066393 CCCGGCCTCTTCATCTGGA 61.066 63.158 0.00 0.00 0.00 3.86
4486 5629 1.626356 CCCGGCCTCTTCATCTGGAA 61.626 60.000 0.00 0.00 0.00 3.53
4499 5642 2.034104 TCTGGAAGATGCATGCAGTC 57.966 50.000 26.69 20.83 38.67 3.51
4500 5643 1.279846 TCTGGAAGATGCATGCAGTCA 59.720 47.619 26.69 16.52 38.67 3.41
4501 5644 1.400846 CTGGAAGATGCATGCAGTCAC 59.599 52.381 26.69 16.23 34.07 3.67
4502 5645 1.003928 TGGAAGATGCATGCAGTCACT 59.996 47.619 26.69 17.98 0.00 3.41
4503 5646 2.089980 GGAAGATGCATGCAGTCACTT 58.910 47.619 26.69 24.15 0.00 3.16
4504 5647 2.490903 GGAAGATGCATGCAGTCACTTT 59.509 45.455 26.69 12.73 0.00 2.66
4505 5648 3.691118 GGAAGATGCATGCAGTCACTTTA 59.309 43.478 26.69 0.00 0.00 1.85
4506 5649 4.337555 GGAAGATGCATGCAGTCACTTTAT 59.662 41.667 26.69 5.33 0.00 1.40
4507 5650 5.163581 GGAAGATGCATGCAGTCACTTTATT 60.164 40.000 26.69 10.60 0.00 1.40
4508 5651 6.038603 GGAAGATGCATGCAGTCACTTTATTA 59.961 38.462 26.69 0.00 0.00 0.98
4509 5652 7.395190 AAGATGCATGCAGTCACTTTATTAA 57.605 32.000 26.69 0.00 0.00 1.40
4510 5653 7.578310 AGATGCATGCAGTCACTTTATTAAT 57.422 32.000 26.69 3.17 0.00 1.40
4511 5654 8.004087 AGATGCATGCAGTCACTTTATTAATT 57.996 30.769 26.69 2.43 0.00 1.40
4512 5655 9.123902 AGATGCATGCAGTCACTTTATTAATTA 57.876 29.630 26.69 0.00 0.00 1.40
4513 5656 9.903682 GATGCATGCAGTCACTTTATTAATTAT 57.096 29.630 26.69 1.61 0.00 1.28
4515 5658 9.734620 TGCATGCAGTCACTTTATTAATTATTC 57.265 29.630 18.46 0.00 0.00 1.75
4516 5659 9.734620 GCATGCAGTCACTTTATTAATTATTCA 57.265 29.630 14.21 0.00 0.00 2.57
4534 5677 9.715121 AATTATTCACAAAGACCTTACGAAGTA 57.285 29.630 0.00 0.00 45.11 2.24
4535 5678 8.752766 TTATTCACAAAGACCTTACGAAGTAG 57.247 34.615 0.00 0.00 46.93 2.57
4536 5679 5.779529 TCACAAAGACCTTACGAAGTAGT 57.220 39.130 0.00 0.00 46.93 2.73
4537 5680 6.882610 TCACAAAGACCTTACGAAGTAGTA 57.117 37.500 0.00 0.00 46.93 1.82
4538 5681 6.672147 TCACAAAGACCTTACGAAGTAGTAC 58.328 40.000 0.00 0.00 46.93 2.73
4539 5682 6.262944 TCACAAAGACCTTACGAAGTAGTACA 59.737 38.462 2.52 0.00 46.93 2.90
4540 5683 7.040201 TCACAAAGACCTTACGAAGTAGTACAT 60.040 37.037 2.52 0.00 46.93 2.29
4541 5684 7.272948 CACAAAGACCTTACGAAGTAGTACATC 59.727 40.741 2.52 0.00 46.93 3.06
4542 5685 7.040201 ACAAAGACCTTACGAAGTAGTACATCA 60.040 37.037 2.52 0.00 46.93 3.07
4543 5686 6.680874 AGACCTTACGAAGTAGTACATCAG 57.319 41.667 2.52 0.16 46.93 2.90
4544 5687 5.589452 AGACCTTACGAAGTAGTACATCAGG 59.411 44.000 2.52 6.03 46.93 3.86
4545 5688 5.259632 ACCTTACGAAGTAGTACATCAGGT 58.740 41.667 9.20 9.20 46.93 4.00
4546 5689 6.418101 ACCTTACGAAGTAGTACATCAGGTA 58.582 40.000 12.08 2.94 46.93 3.08
4547 5690 6.541641 ACCTTACGAAGTAGTACATCAGGTAG 59.458 42.308 12.08 2.34 46.93 3.18
4548 5691 6.541641 CCTTACGAAGTAGTACATCAGGTAGT 59.458 42.308 2.52 0.00 46.93 2.73
4549 5692 7.254727 CCTTACGAAGTAGTACATCAGGTAGTC 60.255 44.444 2.52 0.00 46.93 2.59
4550 5693 5.743117 ACGAAGTAGTACATCAGGTAGTCT 58.257 41.667 2.52 0.00 41.94 3.24
4551 5694 5.585445 ACGAAGTAGTACATCAGGTAGTCTG 59.415 44.000 2.52 0.00 41.94 3.51
4561 5704 3.834489 CAGGTAGTCTGAAGCCATCAT 57.166 47.619 0.00 0.00 46.18 2.45
4635 5792 2.264480 GCCCAAAAATCGGCCCAC 59.736 61.111 0.00 0.00 39.39 4.61
4638 5795 0.611896 CCCAAAAATCGGCCCACTCT 60.612 55.000 0.00 0.00 0.00 3.24
4863 6046 4.643784 GTCAGCCTTTCATTGATTCCTCAT 59.356 41.667 0.00 0.00 0.00 2.90
4940 6150 1.276622 CCCCCGGCTGCTATATAAGT 58.723 55.000 0.00 0.00 0.00 2.24
4985 6196 4.154347 CCCGCCCACAGCTCTCTC 62.154 72.222 0.00 0.00 40.39 3.20
4986 6197 3.073735 CCGCCCACAGCTCTCTCT 61.074 66.667 0.00 0.00 40.39 3.10
4989 6200 1.815866 GCCCACAGCTCTCTCTCTC 59.184 63.158 0.00 0.00 38.99 3.20
4993 6212 2.019249 CCACAGCTCTCTCTCTCTCTG 58.981 57.143 0.00 0.00 0.00 3.35
5226 6465 3.801997 CTCATTCCCCCGCTGCCT 61.802 66.667 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.880443 ACAGGTTTCATGTGCTGGAAT 58.120 42.857 0.00 0.00 0.00 3.01
11 12 3.366273 CGCAAGCATAACAGGTTTCATGT 60.366 43.478 0.00 0.00 0.00 3.21
30 31 2.056223 GGTAGTAGGGTCTGCCGCA 61.056 63.158 0.00 0.00 34.97 5.69
48 49 2.260869 CCTGCCACCACAACCGAAG 61.261 63.158 0.00 0.00 0.00 3.79
50 51 3.484806 ACCTGCCACCACAACCGA 61.485 61.111 0.00 0.00 0.00 4.69
134 135 2.750948 CCTACCCGAACATAATGACCG 58.249 52.381 0.00 0.00 0.00 4.79
136 137 2.132762 CGCCTACCCGAACATAATGAC 58.867 52.381 0.00 0.00 0.00 3.06
148 149 1.134877 GTCACTTTAGACCGCCTACCC 60.135 57.143 0.00 0.00 32.36 3.69
155 156 5.625311 GCAGAATTTTTGTCACTTTAGACCG 59.375 40.000 0.00 0.00 37.73 4.79
157 158 5.115622 GCGCAGAATTTTTGTCACTTTAGAC 59.884 40.000 0.30 0.00 38.99 2.59
166 167 1.196808 TCGAGGCGCAGAATTTTTGTC 59.803 47.619 10.83 0.00 0.00 3.18
168 169 2.179589 CATCGAGGCGCAGAATTTTTG 58.820 47.619 10.83 0.00 0.00 2.44
198 199 1.285950 GCGTTGGCCCTTTGAAGAC 59.714 57.895 0.00 0.00 0.00 3.01
212 213 6.921307 GGGATATGAAAAATAAATTCGGCGTT 59.079 34.615 6.85 0.00 0.00 4.84
250 251 6.159988 AGCCAAGATATGCTTCGTATTAGAC 58.840 40.000 0.00 0.00 32.94 2.59
253 254 8.896320 TTAAAGCCAAGATATGCTTCGTATTA 57.104 30.769 0.00 0.00 46.58 0.98
288 289 2.287788 GGAAAGCATATCCGCCATGTTG 60.288 50.000 0.00 0.00 0.00 3.33
296 297 3.099267 AGTTCGAGGAAAGCATATCCG 57.901 47.619 0.00 0.00 42.03 4.18
297 298 3.491267 CGAAGTTCGAGGAAAGCATATCC 59.509 47.826 20.58 0.00 43.74 2.59
298 299 4.113354 ACGAAGTTCGAGGAAAGCATATC 58.887 43.478 30.77 0.00 43.74 1.63
299 300 4.124851 ACGAAGTTCGAGGAAAGCATAT 57.875 40.909 30.77 1.42 43.74 1.78
300 301 3.587797 ACGAAGTTCGAGGAAAGCATA 57.412 42.857 30.77 0.00 43.74 3.14
301 302 2.457366 ACGAAGTTCGAGGAAAGCAT 57.543 45.000 30.77 2.75 43.74 3.79
302 303 3.980583 ACGAAGTTCGAGGAAAGCA 57.019 47.368 30.77 0.00 43.74 3.91
319 324 1.676014 CGACCATTGACTTGGAGGGAC 60.676 57.143 0.00 0.00 39.25 4.46
329 334 2.132762 AGACGACAAACGACCATTGAC 58.867 47.619 0.00 0.00 45.77 3.18
346 351 1.600638 CCCCTTTACCCGTGGAGAC 59.399 63.158 0.00 0.00 0.00 3.36
360 365 2.680370 GGGACGGATGAAAGCCCCT 61.680 63.158 0.00 0.00 41.45 4.79
368 373 2.225382 TGACTTGTAGGGACGGATGA 57.775 50.000 0.00 0.00 0.00 2.92
381 386 3.961477 TGACAAACGACCATTGACTTG 57.039 42.857 0.00 0.00 0.00 3.16
415 420 2.477104 ATGGATGGATGAAAACCCCC 57.523 50.000 0.00 0.00 0.00 5.40
416 421 3.909732 TGTATGGATGGATGAAAACCCC 58.090 45.455 0.00 0.00 0.00 4.95
420 425 7.147863 CCATTGACTTGTATGGATGGATGAAAA 60.148 37.037 0.00 0.00 43.25 2.29
423 428 5.103982 ACCATTGACTTGTATGGATGGATGA 60.104 40.000 8.03 0.00 43.25 2.92
433 438 5.705441 ACGACAAATGACCATTGACTTGTAT 59.295 36.000 0.00 0.00 0.00 2.29
434 439 5.049749 CACGACAAATGACCATTGACTTGTA 60.050 40.000 0.00 0.00 0.00 2.41
435 440 3.882888 ACGACAAATGACCATTGACTTGT 59.117 39.130 0.00 0.00 0.00 3.16
449 454 4.202388 ACCTTACCCAAGTACACGACAAAT 60.202 41.667 0.00 0.00 0.00 2.32
452 457 2.036217 CACCTTACCCAAGTACACGACA 59.964 50.000 0.00 0.00 0.00 4.35
453 458 2.611224 CCACCTTACCCAAGTACACGAC 60.611 54.545 0.00 0.00 0.00 4.34
454 459 1.619827 CCACCTTACCCAAGTACACGA 59.380 52.381 0.00 0.00 0.00 4.35
455 460 1.942586 GCCACCTTACCCAAGTACACG 60.943 57.143 0.00 0.00 0.00 4.49
456 461 1.350019 AGCCACCTTACCCAAGTACAC 59.650 52.381 0.00 0.00 0.00 2.90
457 462 1.737199 AGCCACCTTACCCAAGTACA 58.263 50.000 0.00 0.00 0.00 2.90
458 463 2.617276 GGAAGCCACCTTACCCAAGTAC 60.617 54.545 0.00 0.00 0.00 2.73
459 464 1.631898 GGAAGCCACCTTACCCAAGTA 59.368 52.381 0.00 0.00 0.00 2.24
460 465 0.404426 GGAAGCCACCTTACCCAAGT 59.596 55.000 0.00 0.00 0.00 3.16
461 466 0.404040 TGGAAGCCACCTTACCCAAG 59.596 55.000 0.00 0.00 30.32 3.61
462 467 0.854218 TTGGAAGCCACCTTACCCAA 59.146 50.000 0.00 0.00 34.40 4.12
470 475 2.161609 CGATTTACAGTTGGAAGCCACC 59.838 50.000 0.00 0.00 30.78 4.61
472 477 3.071479 GTCGATTTACAGTTGGAAGCCA 58.929 45.455 0.00 0.00 0.00 4.75
474 479 3.071479 TGGTCGATTTACAGTTGGAAGC 58.929 45.455 0.00 0.00 0.00 3.86
477 482 4.069304 CCTTTGGTCGATTTACAGTTGGA 58.931 43.478 0.00 0.00 0.00 3.53
483 488 4.627284 TTCTCCCTTTGGTCGATTTACA 57.373 40.909 0.00 0.00 0.00 2.41
564 569 6.667414 TGCCATTCCTGAAATTGGTTAATACT 59.333 34.615 2.45 0.00 0.00 2.12
565 570 6.756542 GTGCCATTCCTGAAATTGGTTAATAC 59.243 38.462 2.45 0.00 0.00 1.89
579 584 3.057596 ACGTGTAAAATGTGCCATTCCTG 60.058 43.478 0.00 0.00 0.00 3.86
587 592 9.716507 AGATTCAATAATACGTGTAAAATGTGC 57.283 29.630 0.00 0.00 0.00 4.57
608 613 8.817100 CGCCCATAATTTTCCTTTTTAAGATTC 58.183 33.333 0.00 0.00 0.00 2.52
626 631 2.356022 CCATATGCATCCTCGCCCATAA 60.356 50.000 0.19 0.00 0.00 1.90
635 640 1.423584 TCACGGACCATATGCATCCT 58.576 50.000 17.57 6.55 0.00 3.24
674 683 3.968265 AGTGTTAATGGACAGGGGAATG 58.032 45.455 0.00 0.00 0.00 2.67
925 981 2.853159 CCGGGGTTTTAACGGGTAC 58.147 57.895 0.00 0.00 43.69 3.34
968 1024 1.548269 GGATGGGAGAATAGAGAGGCG 59.452 57.143 0.00 0.00 0.00 5.52
1283 1370 3.958860 AAGACCAAGCTGCCGCCT 61.959 61.111 0.00 0.00 36.60 5.52
1304 1391 7.702348 GCAACTAAATAACCTCAATAAGCCAAG 59.298 37.037 0.00 0.00 0.00 3.61
1351 1438 0.546122 TGGTTTGCGGGATCTGCTAT 59.454 50.000 10.94 0.00 0.00 2.97
1370 1457 1.314730 AACGAAATTTGCAGGACCGT 58.685 45.000 0.00 0.00 0.00 4.83
1506 1599 2.325082 GGAGCGCGTGTGGTTTGAT 61.325 57.895 8.43 0.00 0.00 2.57
1527 1620 2.659016 CTCAAGCGTCTCTGGGCA 59.341 61.111 0.00 0.00 0.00 5.36
1781 1899 1.679032 CCTTTCCTCCGGTAGCCTTTG 60.679 57.143 0.00 0.00 0.00 2.77
1822 1942 4.794648 CCCCTCCGCCGCAAATCA 62.795 66.667 0.00 0.00 0.00 2.57
1844 1986 2.828095 CGCATCCGGCATTTCCCA 60.828 61.111 0.00 0.00 45.17 4.37
1963 2106 0.808755 GTGTCAAAATACAGGCCCGG 59.191 55.000 0.00 0.00 0.00 5.73
1971 2114 6.017325 GGATTTACGGTTCGTGTCAAAATAC 58.983 40.000 3.03 0.00 41.39 1.89
1973 2116 4.377635 CGGATTTACGGTTCGTGTCAAAAT 60.378 41.667 3.03 1.55 41.39 1.82
1999 2142 0.322546 CCTTAAAAGCTCACCGGCCT 60.323 55.000 0.00 0.00 0.00 5.19
2006 2149 8.435931 TCTATAGCATATCCCTTAAAAGCTCA 57.564 34.615 0.00 0.00 32.49 4.26
2010 2153 9.323985 GAGCATCTATAGCATATCCCTTAAAAG 57.676 37.037 0.00 0.00 0.00 2.27
2030 2173 3.620821 GCAAAGACAGGACTAAGAGCATC 59.379 47.826 0.00 0.00 0.00 3.91
2073 2216 0.249155 TTATAAAGTCGGGCCTCGCG 60.249 55.000 0.84 0.00 41.10 5.87
2102 2246 4.348486 ACTAAGAACATCTCTCTGCCTCA 58.652 43.478 0.00 0.00 31.02 3.86
2113 2257 5.241662 AGCAAAGACAGGACTAAGAACATC 58.758 41.667 0.00 0.00 0.00 3.06
2384 3525 3.563808 AGCAAACAGTAAGCATGAAACGA 59.436 39.130 0.00 0.00 0.00 3.85
2905 4046 9.958180 TCATTCCATACATAACCAATATCGAAT 57.042 29.630 0.00 0.00 0.00 3.34
3073 4214 2.153366 TATGCGCACGATCATGATGT 57.847 45.000 14.90 8.83 0.00 3.06
3211 4352 9.775854 AACAAATATTCAATCCAAATGTGTGAA 57.224 25.926 0.00 0.00 33.08 3.18
3422 4563 6.115446 TGGTAGGTTCATATTGCTTGAAGAG 58.885 40.000 0.00 0.00 33.95 2.85
3465 4606 0.815615 CCGCCCATAAGAAGGTGCTC 60.816 60.000 0.00 0.00 32.04 4.26
3482 4623 0.391661 CAGTGATGTGGACCTTCCCG 60.392 60.000 0.00 0.00 35.03 5.14
3738 4879 6.464180 CCTCCATTTTTCCTCCAAATGAACAA 60.464 38.462 6.90 0.00 42.10 2.83
3758 4899 3.781965 TGATCCTCATCAATTCACCTCCA 59.218 43.478 0.00 0.00 35.99 3.86
3819 4960 3.496160 GCTAGGAAGGGAAAATGCGGATA 60.496 47.826 0.00 0.00 0.00 2.59
3859 5000 3.763897 AGGTGTCCAAATCTTAATGGTGC 59.236 43.478 0.00 0.00 37.94 5.01
4132 5273 4.816392 TGCGTACAGTTCAGATTGTGTAT 58.184 39.130 0.00 0.00 0.00 2.29
4263 5404 1.307355 TGGCCTCATGTCACAATGCG 61.307 55.000 3.32 0.00 0.00 4.73
4416 5559 7.563888 AGGAACGCCTTTATTTTAATAGACC 57.436 36.000 0.00 0.00 43.90 3.85
4448 5591 4.525100 CCGGGGTCATCCTTCTTTTAAAAA 59.475 41.667 1.66 0.00 35.33 1.94
4449 5592 4.083565 CCGGGGTCATCCTTCTTTTAAAA 58.916 43.478 0.00 0.00 35.33 1.52
4450 5593 3.692690 CCGGGGTCATCCTTCTTTTAAA 58.307 45.455 0.00 0.00 35.33 1.52
4451 5594 2.619590 GCCGGGGTCATCCTTCTTTTAA 60.620 50.000 2.18 0.00 35.33 1.52
4452 5595 1.064979 GCCGGGGTCATCCTTCTTTTA 60.065 52.381 2.18 0.00 35.33 1.52
4453 5596 0.323451 GCCGGGGTCATCCTTCTTTT 60.323 55.000 2.18 0.00 35.33 2.27
4454 5597 1.303282 GCCGGGGTCATCCTTCTTT 59.697 57.895 2.18 0.00 35.33 2.52
4455 5598 2.680370 GGCCGGGGTCATCCTTCTT 61.680 63.158 2.18 0.00 35.33 2.52
4456 5599 3.090532 GGCCGGGGTCATCCTTCT 61.091 66.667 2.18 0.00 35.33 2.85
4457 5600 3.090532 AGGCCGGGGTCATCCTTC 61.091 66.667 2.18 0.00 35.33 3.46
4458 5601 3.090532 GAGGCCGGGGTCATCCTT 61.091 66.667 2.18 0.00 35.33 3.36
4459 5602 3.642741 AAGAGGCCGGGGTCATCCT 62.643 63.158 2.18 0.00 35.33 3.24
4460 5603 3.090532 AAGAGGCCGGGGTCATCC 61.091 66.667 2.18 0.00 0.00 3.51
4461 5604 1.700042 ATGAAGAGGCCGGGGTCATC 61.700 60.000 2.18 0.00 0.00 2.92
4462 5605 1.694169 ATGAAGAGGCCGGGGTCAT 60.694 57.895 2.18 2.58 0.00 3.06
4463 5606 2.285368 ATGAAGAGGCCGGGGTCA 60.285 61.111 2.18 0.00 0.00 4.02
4464 5607 2.066999 AGATGAAGAGGCCGGGGTC 61.067 63.158 2.18 0.00 0.00 4.46
4465 5608 2.041265 AGATGAAGAGGCCGGGGT 59.959 61.111 2.18 0.00 0.00 4.95
4466 5609 2.507944 CAGATGAAGAGGCCGGGG 59.492 66.667 2.18 0.00 0.00 5.73
4467 5610 1.626356 TTCCAGATGAAGAGGCCGGG 61.626 60.000 2.18 0.00 0.00 5.73
4468 5611 1.907739 TTCCAGATGAAGAGGCCGG 59.092 57.895 0.00 0.00 0.00 6.13
4479 5622 2.092592 TGACTGCATGCATCTTCCAGAT 60.093 45.455 22.97 0.00 34.74 2.90
4480 5623 1.279846 TGACTGCATGCATCTTCCAGA 59.720 47.619 22.97 0.01 0.00 3.86
4481 5624 1.400846 GTGACTGCATGCATCTTCCAG 59.599 52.381 22.97 10.18 0.00 3.86
4482 5625 1.003928 AGTGACTGCATGCATCTTCCA 59.996 47.619 22.97 11.65 0.00 3.53
4483 5626 1.747709 AGTGACTGCATGCATCTTCC 58.252 50.000 22.97 8.53 0.00 3.46
4484 5627 3.844577 AAAGTGACTGCATGCATCTTC 57.155 42.857 22.97 17.65 0.00 2.87
4485 5628 5.909621 AATAAAGTGACTGCATGCATCTT 57.090 34.783 22.97 18.67 0.00 2.40
4486 5629 7.578310 ATTAATAAAGTGACTGCATGCATCT 57.422 32.000 22.97 14.03 0.00 2.90
4487 5630 9.903682 ATAATTAATAAAGTGACTGCATGCATC 57.096 29.630 22.97 19.75 0.00 3.91
4489 5632 9.734620 GAATAATTAATAAAGTGACTGCATGCA 57.265 29.630 21.29 21.29 0.00 3.96
4490 5633 9.734620 TGAATAATTAATAAAGTGACTGCATGC 57.265 29.630 11.82 11.82 0.00 4.06
4507 5650 9.715121 ACTTCGTAAGGTCTTTGTGAATAATTA 57.285 29.630 0.00 0.00 38.47 1.40
4508 5651 8.617290 ACTTCGTAAGGTCTTTGTGAATAATT 57.383 30.769 0.00 0.00 38.47 1.40
4509 5652 9.367444 CTACTTCGTAAGGTCTTTGTGAATAAT 57.633 33.333 0.00 0.00 38.47 1.28
4510 5653 8.362639 ACTACTTCGTAAGGTCTTTGTGAATAA 58.637 33.333 0.00 0.00 38.47 1.40
4511 5654 7.889469 ACTACTTCGTAAGGTCTTTGTGAATA 58.111 34.615 0.00 0.00 38.47 1.75
4512 5655 6.756221 ACTACTTCGTAAGGTCTTTGTGAAT 58.244 36.000 0.00 0.00 38.47 2.57
4513 5656 6.152932 ACTACTTCGTAAGGTCTTTGTGAA 57.847 37.500 0.00 0.00 38.47 3.18
4514 5657 5.779529 ACTACTTCGTAAGGTCTTTGTGA 57.220 39.130 0.00 0.00 38.47 3.58
4515 5658 6.441274 TGTACTACTTCGTAAGGTCTTTGTG 58.559 40.000 0.00 0.00 38.47 3.33
4516 5659 6.639632 TGTACTACTTCGTAAGGTCTTTGT 57.360 37.500 0.00 0.00 38.47 2.83
4517 5660 7.310664 TGATGTACTACTTCGTAAGGTCTTTG 58.689 38.462 0.00 0.00 38.47 2.77
4518 5661 7.362747 CCTGATGTACTACTTCGTAAGGTCTTT 60.363 40.741 0.00 0.00 38.47 2.52
4519 5662 6.095160 CCTGATGTACTACTTCGTAAGGTCTT 59.905 42.308 0.00 0.00 38.47 3.01
4520 5663 5.589452 CCTGATGTACTACTTCGTAAGGTCT 59.411 44.000 0.00 0.00 38.47 3.85
4521 5664 5.356470 ACCTGATGTACTACTTCGTAAGGTC 59.644 44.000 0.00 0.00 27.26 3.85
4522 5665 5.259632 ACCTGATGTACTACTTCGTAAGGT 58.740 41.667 0.00 6.72 38.47 3.50
4523 5666 5.831702 ACCTGATGTACTACTTCGTAAGG 57.168 43.478 0.00 5.84 38.47 2.69
4524 5667 7.495279 AGACTACCTGATGTACTACTTCGTAAG 59.505 40.741 0.00 0.00 0.00 2.34
4525 5668 7.279536 CAGACTACCTGATGTACTACTTCGTAA 59.720 40.741 0.00 0.00 45.78 3.18
4526 5669 6.760298 CAGACTACCTGATGTACTACTTCGTA 59.240 42.308 0.00 0.00 45.78 3.43
4527 5670 5.585445 CAGACTACCTGATGTACTACTTCGT 59.415 44.000 0.00 0.00 45.78 3.85
4528 5671 5.816258 TCAGACTACCTGATGTACTACTTCG 59.184 44.000 0.00 0.00 46.38 3.79
4541 5684 3.387374 AGATGATGGCTTCAGACTACCTG 59.613 47.826 9.09 0.00 44.27 4.00
4542 5685 3.652055 AGATGATGGCTTCAGACTACCT 58.348 45.455 9.09 0.00 37.89 3.08
4543 5686 4.414337 AAGATGATGGCTTCAGACTACC 57.586 45.455 9.09 0.00 37.89 3.18
4544 5687 6.398234 TCTAAGATGATGGCTTCAGACTAC 57.602 41.667 9.09 0.00 37.89 2.73
4545 5688 5.010516 GCTCTAAGATGATGGCTTCAGACTA 59.989 44.000 9.09 0.02 37.89 2.59
4546 5689 4.202243 GCTCTAAGATGATGGCTTCAGACT 60.202 45.833 9.09 7.86 37.89 3.24
4547 5690 4.057432 GCTCTAAGATGATGGCTTCAGAC 58.943 47.826 9.09 5.89 37.89 3.51
4548 5691 3.708121 TGCTCTAAGATGATGGCTTCAGA 59.292 43.478 9.09 0.06 37.89 3.27
4549 5692 4.069300 TGCTCTAAGATGATGGCTTCAG 57.931 45.455 9.09 0.00 37.89 3.02
4550 5693 4.347292 AGATGCTCTAAGATGATGGCTTCA 59.653 41.667 5.47 5.47 39.12 3.02
4551 5694 4.897140 AGATGCTCTAAGATGATGGCTTC 58.103 43.478 0.00 0.00 0.00 3.86
4552 5695 4.978438 AGATGCTCTAAGATGATGGCTT 57.022 40.909 0.00 0.00 0.00 4.35
4553 5696 4.978438 AAGATGCTCTAAGATGATGGCT 57.022 40.909 0.00 0.00 0.00 4.75
4554 5697 5.122082 GCTAAAGATGCTCTAAGATGATGGC 59.878 44.000 0.00 0.00 0.00 4.40
4555 5698 6.369340 CAGCTAAAGATGCTCTAAGATGATGG 59.631 42.308 0.00 0.00 38.92 3.51
4556 5699 7.354025 CAGCTAAAGATGCTCTAAGATGATG 57.646 40.000 0.00 0.00 38.92 3.07
4619 5774 0.611896 AGAGTGGGCCGATTTTTGGG 60.612 55.000 0.00 0.00 0.00 4.12
4638 5795 3.714078 AATAGGCTCCTGGGGGCGA 62.714 63.158 15.17 10.34 0.00 5.54
4940 6150 4.075793 AGGCGAGGGGAGGTGCTA 62.076 66.667 0.00 0.00 0.00 3.49
4981 6192 0.254747 ACGGGGACAGAGAGAGAGAG 59.745 60.000 0.00 0.00 0.00 3.20
4984 6195 1.679305 GCACGGGGACAGAGAGAGA 60.679 63.158 0.00 0.00 0.00 3.10
4985 6196 2.888863 GCACGGGGACAGAGAGAG 59.111 66.667 0.00 0.00 0.00 3.20
4986 6197 3.062466 CGCACGGGGACAGAGAGA 61.062 66.667 0.00 0.00 0.00 3.10
5205 6444 2.285368 AGCGGGGGAATGAGGACA 60.285 61.111 0.00 0.00 0.00 4.02
5210 6449 4.113815 CAGGCAGCGGGGGAATGA 62.114 66.667 0.00 0.00 0.00 2.57
5243 6482 2.246841 TCGTCGGCGAAGTAGTTGA 58.753 52.632 21.47 4.31 44.92 3.18


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

AutoCloner maintained by Alex Coulton.