Multiple sequence alignment - TraesCS3B01G444100

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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 TraesCS3B01G444100 chr3B 100.000 2633 0 0 1 2633 684269894 684267262 0.000000e+00 4863.0
1 TraesCS3B01G444100 chr3B 89.099 899 70 18 815 1694 684413414 684412525 0.000000e+00 1092.0
2 TraesCS3B01G444100 chr3B 87.201 961 94 12 954 1902 684411673 684410730 0.000000e+00 1066.0
3 TraesCS3B01G444100 chr3B 93.386 635 30 7 911 1533 684328290 684327656 0.000000e+00 929.0
4 TraesCS3B01G444100 chr3B 82.491 811 97 25 957 1750 684296921 684296139 0.000000e+00 669.0
5 TraesCS3B01G444100 chr3B 81.874 811 106 21 954 1756 684321175 684320398 0.000000e+00 645.0
6 TraesCS3B01G444100 chr3B 87.500 400 36 10 2245 2633 684614290 684613894 1.440000e-122 449.0
7 TraesCS3B01G444100 chr3B 97.006 167 5 0 1897 2063 684392271 684392105 5.550000e-72 281.0
8 TraesCS3B01G444100 chr3B 88.177 203 21 3 2432 2633 684251054 684250854 3.390000e-59 239.0
9 TraesCS3B01G444100 chr3B 81.570 293 43 9 1045 1332 684460243 684459957 5.670000e-57 231.0
10 TraesCS3B01G444100 chr3B 83.708 178 11 9 1524 1694 684322246 684322080 4.540000e-33 152.0
11 TraesCS3B01G444100 chr3B 96.875 64 2 0 2531 2594 684390002 684389939 9.970000e-20 108.0
12 TraesCS3B01G444100 chr3B 97.500 40 1 0 911 950 684462377 684462338 4.700000e-08 69.4
13 TraesCS3B01G444100 chr3A 88.569 1251 104 21 479 1701 655081426 655080187 0.000000e+00 1482.0
14 TraesCS3B01G444100 chr3A 86.702 752 83 8 954 1704 655079452 655078717 0.000000e+00 819.0
15 TraesCS3B01G444100 chr3A 91.409 582 18 8 2083 2633 654785060 654784480 0.000000e+00 769.0
16 TraesCS3B01G444100 chr3A 78.947 399 51 20 2238 2633 654570154 654569786 9.420000e-60 241.0
17 TraesCS3B01G444100 chr3D 87.822 1010 72 28 776 1750 519714256 519713263 0.000000e+00 1136.0
18 TraesCS3B01G444100 chr3D 97.222 396 11 0 2238 2633 519684938 519684543 0.000000e+00 671.0
19 TraesCS3B01G444100 chr3D 84.731 668 99 2 954 1621 519710315 519709651 0.000000e+00 665.0
20 TraesCS3B01G444100 chr3D 84.465 663 84 8 1045 1701 519876705 519876056 1.030000e-178 636.0
21 TraesCS3B01G444100 chr3D 87.847 288 23 3 510 787 519714755 519714470 7.030000e-86 327.0
22 TraesCS3B01G444100 chr3D 92.025 163 11 2 2066 2228 519685137 519684977 7.330000e-56 228.0
23 TraesCS3B01G444100 chr3D 89.623 106 7 3 2293 2396 519878382 519878279 5.910000e-27 132.0
24 TraesCS3B01G444100 chr3D 96.774 31 1 0 1716 1746 519876019 519875989 5.000000e-03 52.8
25 TraesCS3B01G444100 chr4D 86.154 130 18 0 365 494 212141449 212141320 9.830000e-30 141.0
26 TraesCS3B01G444100 chr4D 85.714 126 17 1 364 489 212141768 212141644 5.910000e-27 132.0
27 TraesCS3B01G444100 chr4B 83.471 121 18 2 364 484 121834977 121834859 7.700000e-21 111.0
28 TraesCS3B01G444100 chr2D 86.275 102 14 0 364 465 113334268 113334167 7.700000e-21 111.0
29 TraesCS3B01G444100 chr2D 80.469 128 23 2 364 490 113334591 113334465 2.160000e-16 97.1
30 TraesCS3B01G444100 chr2D 81.356 118 21 1 365 482 113346608 113346492 7.760000e-16 95.3
31 TraesCS3B01G444100 chr2A 80.342 117 23 0 366 482 713261621 713261737 3.610000e-14 89.8
32 TraesCS3B01G444100 chr1B 82.178 101 18 0 365 465 602878316 602878216 1.300000e-13 87.9
33 TraesCS3B01G444100 chr6B 85.075 67 10 0 370 436 509351670 509351604 4.700000e-08 69.4


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 TraesCS3B01G444100 chr3B 684267262 684269894 2632 True 4863.000000 4863 100.000000 1 2633 1 chr3B.!!$R2 2632
1 TraesCS3B01G444100 chr3B 684410730 684413414 2684 True 1079.000000 1092 88.150000 815 1902 2 chr3B.!!$R8 1087
2 TraesCS3B01G444100 chr3B 684327656 684328290 634 True 929.000000 929 93.386000 911 1533 1 chr3B.!!$R4 622
3 TraesCS3B01G444100 chr3B 684296139 684296921 782 True 669.000000 669 82.491000 957 1750 1 chr3B.!!$R3 793
4 TraesCS3B01G444100 chr3B 684320398 684322246 1848 True 398.500000 645 82.791000 954 1756 2 chr3B.!!$R6 802
5 TraesCS3B01G444100 chr3A 655078717 655081426 2709 True 1150.500000 1482 87.635500 479 1704 2 chr3A.!!$R3 1225
6 TraesCS3B01G444100 chr3A 654784480 654785060 580 True 769.000000 769 91.409000 2083 2633 1 chr3A.!!$R2 550
7 TraesCS3B01G444100 chr3D 519709651 519714755 5104 True 709.333333 1136 86.800000 510 1750 3 chr3D.!!$R2 1240
8 TraesCS3B01G444100 chr3D 519684543 519685137 594 True 449.500000 671 94.623500 2066 2633 2 chr3D.!!$R1 567
9 TraesCS3B01G444100 chr3D 519875989 519878382 2393 True 273.600000 636 90.287333 1045 2396 3 chr3D.!!$R3 1351

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
475 476 0.035317 ACACTGACCGCACATGATGT 59.965 50.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2056 7161 0.034186 CCTGGCATGGAACCTAAGCA 60.034 55.0 0.0 0.0 0.0 3.91 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
286 287 7.781324 AAAATGGAAGATGGTCTGTTGTATT 57.219 32.000 0.00 0.00 0.00 1.89
288 289 6.764308 ATGGAAGATGGTCTGTTGTATTTG 57.236 37.500 0.00 0.00 0.00 2.32
289 290 5.875224 TGGAAGATGGTCTGTTGTATTTGA 58.125 37.500 0.00 0.00 0.00 2.69
290 291 6.484288 TGGAAGATGGTCTGTTGTATTTGAT 58.516 36.000 0.00 0.00 0.00 2.57
291 292 6.947733 TGGAAGATGGTCTGTTGTATTTGATT 59.052 34.615 0.00 0.00 0.00 2.57
292 293 8.106462 TGGAAGATGGTCTGTTGTATTTGATTA 58.894 33.333 0.00 0.00 0.00 1.75
294 295 9.774742 GAAGATGGTCTGTTGTATTTGATTAAC 57.225 33.333 0.00 0.00 0.00 2.01
296 297 9.520515 AGATGGTCTGTTGTATTTGATTAACTT 57.479 29.630 0.00 0.00 0.00 2.66
297 298 9.774742 GATGGTCTGTTGTATTTGATTAACTTC 57.225 33.333 0.00 0.00 0.00 3.01
298 299 8.918202 TGGTCTGTTGTATTTGATTAACTTCT 57.082 30.769 0.00 0.00 0.00 2.85
384 385 4.023137 GGTGACCATGGCAAGCAT 57.977 55.556 13.04 0.00 0.00 3.79
399 400 1.372582 AGCATGCATGACAAGTACCG 58.627 50.000 30.64 0.00 0.00 4.02
402 403 2.728846 GCATGCATGACAAGTACCGTTG 60.729 50.000 30.64 0.00 0.00 4.10
404 405 3.052455 TGCATGACAAGTACCGTTGAT 57.948 42.857 0.00 0.00 0.00 2.57
405 406 2.741517 TGCATGACAAGTACCGTTGATG 59.258 45.455 0.00 2.90 0.00 3.07
407 408 3.181520 GCATGACAAGTACCGTTGATGTC 60.182 47.826 0.00 0.00 40.53 3.06
409 410 5.407502 CATGACAAGTACCGTTGATGTCTA 58.592 41.667 2.13 0.00 40.70 2.59
410 411 5.456548 TGACAAGTACCGTTGATGTCTAA 57.543 39.130 2.13 0.00 40.70 2.10
411 412 5.224888 TGACAAGTACCGTTGATGTCTAAC 58.775 41.667 2.13 0.00 40.70 2.34
412 413 5.204409 ACAAGTACCGTTGATGTCTAACA 57.796 39.130 2.13 0.00 0.00 2.41
413 414 5.603596 ACAAGTACCGTTGATGTCTAACAA 58.396 37.500 2.13 0.00 0.00 2.83
415 416 6.367969 ACAAGTACCGTTGATGTCTAACAATC 59.632 38.462 2.13 0.00 0.00 2.67
417 418 4.280436 ACCGTTGATGTCTAACAATCCA 57.720 40.909 0.00 0.00 0.00 3.41
418 419 4.843728 ACCGTTGATGTCTAACAATCCAT 58.156 39.130 0.00 0.00 0.00 3.41
419 420 4.635765 ACCGTTGATGTCTAACAATCCATG 59.364 41.667 0.00 0.00 0.00 3.66
422 423 5.220912 CGTTGATGTCTAACAATCCATGCAT 60.221 40.000 0.00 0.00 0.00 3.96
424 425 6.778834 TGATGTCTAACAATCCATGCATTT 57.221 33.333 0.00 0.00 0.00 2.32
426 427 7.259882 TGATGTCTAACAATCCATGCATTTTC 58.740 34.615 0.00 0.00 0.00 2.29
427 428 6.839124 TGTCTAACAATCCATGCATTTTCT 57.161 33.333 0.00 0.00 0.00 2.52
429 430 7.988737 TGTCTAACAATCCATGCATTTTCTAG 58.011 34.615 0.00 0.00 0.00 2.43
430 431 7.067372 TGTCTAACAATCCATGCATTTTCTAGG 59.933 37.037 0.00 0.00 0.00 3.02
433 434 4.646492 ACAATCCATGCATTTTCTAGGGTC 59.354 41.667 0.00 0.00 0.00 4.46
435 436 4.591321 TCCATGCATTTTCTAGGGTCTT 57.409 40.909 0.00 0.00 0.00 3.01
436 437 4.272489 TCCATGCATTTTCTAGGGTCTTG 58.728 43.478 0.00 0.00 0.00 3.02
437 438 3.181483 CCATGCATTTTCTAGGGTCTTGC 60.181 47.826 0.00 0.00 0.00 4.01
438 439 2.446435 TGCATTTTCTAGGGTCTTGCC 58.554 47.619 0.00 0.00 0.00 4.52
439 440 1.401905 GCATTTTCTAGGGTCTTGCCG 59.598 52.381 0.00 0.00 38.44 5.69
441 442 3.545703 CATTTTCTAGGGTCTTGCCGAT 58.454 45.455 0.00 0.00 38.44 4.18
444 445 1.860641 TCTAGGGTCTTGCCGATGAA 58.139 50.000 0.00 0.00 38.44 2.57
445 446 2.184533 TCTAGGGTCTTGCCGATGAAA 58.815 47.619 0.00 0.00 38.44 2.69
464 465 3.513680 AAAAACCGGAAAACACTGACC 57.486 42.857 9.46 0.00 0.00 4.02
466 467 1.441732 AACCGGAAAACACTGACCGC 61.442 55.000 9.46 0.00 43.37 5.68
468 469 1.278637 CGGAAAACACTGACCGCAC 59.721 57.895 0.00 0.00 38.98 5.34
470 471 0.951558 GGAAAACACTGACCGCACAT 59.048 50.000 0.00 0.00 0.00 3.21
471 472 1.334960 GGAAAACACTGACCGCACATG 60.335 52.381 0.00 0.00 0.00 3.21
475 476 0.035317 ACACTGACCGCACATGATGT 59.965 50.000 0.00 0.00 0.00 3.06
477 478 2.289382 ACACTGACCGCACATGATGTAA 60.289 45.455 0.00 0.00 0.00 2.41
514 515 9.405587 GTTTTCGGTGATTTCAATGAGATTTTA 57.594 29.630 0.00 0.00 0.00 1.52
537 538 2.630158 TGGAAACAAAAACCGACGAGA 58.370 42.857 0.00 0.00 37.44 4.04
549 550 7.951530 AAAACCGACGAGATAACTTTAAAGA 57.048 32.000 21.92 0.30 0.00 2.52
553 554 5.393896 CCGACGAGATAACTTTAAAGACCCT 60.394 44.000 21.92 11.87 0.00 4.34
596 597 3.181434 TGTTTGGCAATACTCCACTCCTT 60.181 43.478 0.00 0.00 32.45 3.36
679 690 1.385528 TCAGCGGAGTTACATAGCGA 58.614 50.000 0.00 0.00 0.00 4.93
706 717 1.006832 CCGAACGGCCTCTAAATGTG 58.993 55.000 0.00 0.00 0.00 3.21
750 761 2.352388 TGTAAAAGGTCGCCTATGTGC 58.648 47.619 0.00 0.00 31.13 4.57
761 772 2.797156 CGCCTATGTGCATGTTACTCTC 59.203 50.000 0.00 0.00 0.00 3.20
766 777 1.337728 TGTGCATGTTACTCTCCACCG 60.338 52.381 0.00 0.00 0.00 4.94
791 1026 1.599419 GGTAACAAAACAGCCTGTGCG 60.599 52.381 0.00 0.00 44.33 5.34
841 1076 1.993956 ATGCTGCCGGCCATATTAAA 58.006 45.000 26.77 0.19 40.92 1.52
903 1145 3.400255 ACCGCTTGGTTAGTTTTCTCTC 58.600 45.455 0.00 0.00 46.51 3.20
905 1147 4.065789 CCGCTTGGTTAGTTTTCTCTCTT 58.934 43.478 0.00 0.00 0.00 2.85
909 1151 6.346999 CGCTTGGTTAGTTTTCTCTCTTTCTC 60.347 42.308 0.00 0.00 0.00 2.87
959 1216 1.367659 GAACTCTTGCAGCTAGCTGG 58.632 55.000 38.52 26.23 45.94 4.85
960 1217 0.676151 AACTCTTGCAGCTAGCTGGC 60.676 55.000 38.52 30.57 45.94 4.85
961 1218 2.125391 TCTTGCAGCTAGCTGGCG 60.125 61.111 38.52 19.80 45.94 5.69
1239 1880 4.765970 TGCCTGGCCTCCATCCCT 62.766 66.667 17.53 0.00 30.82 4.20
1248 1889 2.204291 TCCATCCCTGGGGCAGTT 60.204 61.111 14.00 0.00 43.34 3.16
1550 3811 2.267006 CCAGCAGTGCATCGACCT 59.733 61.111 19.20 0.00 0.00 3.85
1600 3861 1.971167 TGCCGGTGCAACATCTTCC 60.971 57.895 0.98 0.00 46.66 3.46
1637 3898 4.351192 GAAATGCAAATGGTATGACCGTC 58.649 43.478 0.00 0.00 42.58 4.79
1666 3929 2.877168 GGGTGATGCTTGTGATGAGATC 59.123 50.000 0.00 0.00 0.00 2.75
1675 3939 3.257469 TGTGATGAGATCAAGTGAGCC 57.743 47.619 0.00 0.00 41.69 4.70
1696 3960 4.381718 GCCCAGAGAACTAAAGACGTGTAT 60.382 45.833 0.00 0.00 0.00 2.29
1766 4062 3.627577 GCATGTTACGGACCTGAATTGAT 59.372 43.478 0.00 0.00 0.00 2.57
1772 4068 3.750371 ACGGACCTGAATTGATGAACAA 58.250 40.909 0.00 0.00 42.95 2.83
1808 4104 7.121315 TCTCTCACGAAATCAAGTCTCTGATTA 59.879 37.037 9.33 0.00 43.65 1.75
1899 7004 5.001874 CAGTAAGGAACCCTTGGAAGTTAC 58.998 45.833 8.41 0.00 44.44 2.50
1902 7007 3.323775 AGGAACCCTTGGAAGTTACAGA 58.676 45.455 0.00 0.00 0.00 3.41
1903 7008 3.720002 AGGAACCCTTGGAAGTTACAGAA 59.280 43.478 0.00 0.00 0.00 3.02
1904 7009 3.819337 GGAACCCTTGGAAGTTACAGAAC 59.181 47.826 0.00 0.00 35.64 3.01
1906 7011 4.513406 ACCCTTGGAAGTTACAGAACAA 57.487 40.909 0.00 0.00 38.10 2.83
1908 7013 4.887655 ACCCTTGGAAGTTACAGAACAAAG 59.112 41.667 0.00 0.00 38.10 2.77
1909 7014 4.261614 CCCTTGGAAGTTACAGAACAAAGC 60.262 45.833 0.00 0.00 38.10 3.51
1911 7016 3.892284 TGGAAGTTACAGAACAAAGCCA 58.108 40.909 0.00 0.00 38.10 4.75
1912 7017 4.469657 TGGAAGTTACAGAACAAAGCCAT 58.530 39.130 0.00 0.00 38.10 4.40
1914 7019 4.321230 GGAAGTTACAGAACAAAGCCATGG 60.321 45.833 7.63 7.63 38.10 3.66
1915 7020 3.832527 AGTTACAGAACAAAGCCATGGT 58.167 40.909 14.67 0.00 38.10 3.55
1916 7021 4.980573 AGTTACAGAACAAAGCCATGGTA 58.019 39.130 14.67 0.00 38.10 3.25
1917 7022 5.003804 AGTTACAGAACAAAGCCATGGTAG 58.996 41.667 14.67 3.50 38.10 3.18
1918 7023 2.795329 ACAGAACAAAGCCATGGTAGG 58.205 47.619 14.67 3.46 0.00 3.18
1919 7024 2.094675 CAGAACAAAGCCATGGTAGGG 58.905 52.381 14.67 3.85 0.00 3.53
1920 7025 1.992557 AGAACAAAGCCATGGTAGGGA 59.007 47.619 14.67 0.00 0.00 4.20
1921 7026 2.378547 AGAACAAAGCCATGGTAGGGAA 59.621 45.455 14.67 0.00 0.00 3.97
1924 7029 0.394352 AAAGCCATGGTAGGGAAGCG 60.394 55.000 14.67 0.00 0.00 4.68
1926 7031 1.227674 GCCATGGTAGGGAAGCGAG 60.228 63.158 14.67 0.00 0.00 5.03
1927 7032 1.972660 GCCATGGTAGGGAAGCGAGT 61.973 60.000 14.67 0.00 0.00 4.18
1928 7033 0.541863 CCATGGTAGGGAAGCGAGTT 59.458 55.000 2.57 0.00 0.00 3.01
1929 7034 1.656652 CATGGTAGGGAAGCGAGTTG 58.343 55.000 0.00 0.00 0.00 3.16
1930 7035 0.107654 ATGGTAGGGAAGCGAGTTGC 60.108 55.000 0.00 0.00 46.98 4.17
1934 7039 3.423154 GGGAAGCGAGTTGCCACG 61.423 66.667 0.00 0.00 46.01 4.94
1940 7045 4.308458 CGAGTTGCCACGGGTCCA 62.308 66.667 0.00 0.00 0.00 4.02
1942 7047 2.034066 AGTTGCCACGGGTCCATG 59.966 61.111 0.00 0.00 0.00 3.66
1943 7048 3.747976 GTTGCCACGGGTCCATGC 61.748 66.667 0.00 0.00 0.00 4.06
1944 7049 3.965258 TTGCCACGGGTCCATGCT 61.965 61.111 0.00 0.00 0.00 3.79
1945 7050 2.597818 TTGCCACGGGTCCATGCTA 61.598 57.895 0.00 0.00 0.00 3.49
1946 7051 2.130821 TTGCCACGGGTCCATGCTAA 62.131 55.000 0.00 0.00 0.00 3.09
1947 7052 1.377987 GCCACGGGTCCATGCTAAA 60.378 57.895 0.00 0.00 0.00 1.85
1948 7053 0.963355 GCCACGGGTCCATGCTAAAA 60.963 55.000 0.00 0.00 0.00 1.52
1949 7054 1.540267 CCACGGGTCCATGCTAAAAA 58.460 50.000 0.00 0.00 0.00 1.94
1951 7056 2.159382 CACGGGTCCATGCTAAAAAGT 58.841 47.619 0.00 0.00 0.00 2.66
1952 7057 2.095263 CACGGGTCCATGCTAAAAAGTG 60.095 50.000 0.00 0.00 0.00 3.16
1953 7058 1.135402 CGGGTCCATGCTAAAAAGTGC 60.135 52.381 0.00 0.00 0.00 4.40
1954 7059 2.171003 GGGTCCATGCTAAAAAGTGCT 58.829 47.619 0.00 0.00 0.00 4.40
1955 7060 3.352648 GGGTCCATGCTAAAAAGTGCTA 58.647 45.455 0.00 0.00 0.00 3.49
1956 7061 3.128764 GGGTCCATGCTAAAAAGTGCTAC 59.871 47.826 0.00 0.00 0.00 3.58
1957 7062 3.756434 GGTCCATGCTAAAAAGTGCTACA 59.244 43.478 0.00 0.00 0.00 2.74
1958 7063 4.379499 GGTCCATGCTAAAAAGTGCTACAC 60.379 45.833 0.00 0.00 34.10 2.90
1959 7064 3.756434 TCCATGCTAAAAAGTGCTACACC 59.244 43.478 0.00 0.00 34.49 4.16
1960 7065 3.758554 CCATGCTAAAAAGTGCTACACCT 59.241 43.478 0.00 0.00 34.49 4.00
1961 7066 4.941263 CCATGCTAAAAAGTGCTACACCTA 59.059 41.667 0.00 0.00 34.49 3.08
1962 7067 5.163754 CCATGCTAAAAAGTGCTACACCTAC 60.164 44.000 0.00 0.00 34.49 3.18
1963 7068 5.223449 TGCTAAAAAGTGCTACACCTACT 57.777 39.130 0.00 0.00 34.49 2.57
1964 7069 5.617252 TGCTAAAAAGTGCTACACCTACTT 58.383 37.500 0.00 0.00 36.29 2.24
1965 7070 6.761312 TGCTAAAAAGTGCTACACCTACTTA 58.239 36.000 0.00 0.00 33.82 2.24
1966 7071 6.647895 TGCTAAAAAGTGCTACACCTACTTAC 59.352 38.462 0.00 0.00 33.82 2.34
1967 7072 6.872547 GCTAAAAAGTGCTACACCTACTTACT 59.127 38.462 0.00 0.00 33.82 2.24
1968 7073 7.148623 GCTAAAAAGTGCTACACCTACTTACTG 60.149 40.741 0.00 0.00 33.82 2.74
1969 7074 6.415206 AAAAGTGCTACACCTACTTACTGA 57.585 37.500 0.00 0.00 33.82 3.41
1970 7075 6.415206 AAAGTGCTACACCTACTTACTGAA 57.585 37.500 0.00 0.00 33.82 3.02
1971 7076 6.607004 AAGTGCTACACCTACTTACTGAAT 57.393 37.500 0.00 0.00 34.49 2.57
1972 7077 6.607004 AGTGCTACACCTACTTACTGAATT 57.393 37.500 0.00 0.00 34.49 2.17
1973 7078 6.631962 AGTGCTACACCTACTTACTGAATTC 58.368 40.000 0.00 0.00 34.49 2.17
1974 7079 6.437793 AGTGCTACACCTACTTACTGAATTCT 59.562 38.462 7.05 0.00 34.49 2.40
1975 7080 7.038941 AGTGCTACACCTACTTACTGAATTCTT 60.039 37.037 7.05 0.00 34.49 2.52
1976 7081 8.248945 GTGCTACACCTACTTACTGAATTCTTA 58.751 37.037 7.05 0.00 0.00 2.10
1977 7082 8.248945 TGCTACACCTACTTACTGAATTCTTAC 58.751 37.037 7.05 0.00 0.00 2.34
1978 7083 7.431668 GCTACACCTACTTACTGAATTCTTACG 59.568 40.741 7.05 0.00 0.00 3.18
1979 7084 7.224522 ACACCTACTTACTGAATTCTTACGT 57.775 36.000 7.05 0.00 0.00 3.57
1980 7085 8.340618 ACACCTACTTACTGAATTCTTACGTA 57.659 34.615 7.05 0.00 0.00 3.57
1981 7086 8.796475 ACACCTACTTACTGAATTCTTACGTAA 58.204 33.333 7.94 7.94 0.00 3.18
1982 7087 9.070149 CACCTACTTACTGAATTCTTACGTAAC 57.930 37.037 3.29 0.00 0.00 2.50
1983 7088 8.796475 ACCTACTTACTGAATTCTTACGTAACA 58.204 33.333 3.29 0.00 0.00 2.41
1984 7089 9.798994 CCTACTTACTGAATTCTTACGTAACAT 57.201 33.333 3.29 0.00 0.00 2.71
1987 7092 9.148104 ACTTACTGAATTCTTACGTAACATTCC 57.852 33.333 21.86 11.67 0.00 3.01
1988 7093 9.367444 CTTACTGAATTCTTACGTAACATTCCT 57.633 33.333 21.86 14.40 0.00 3.36
1991 7096 9.530633 ACTGAATTCTTACGTAACATTCCTATC 57.469 33.333 21.86 7.94 0.00 2.08
1992 7097 9.751542 CTGAATTCTTACGTAACATTCCTATCT 57.248 33.333 21.86 0.00 0.00 1.98
1993 7098 9.745880 TGAATTCTTACGTAACATTCCTATCTC 57.254 33.333 21.86 6.98 0.00 2.75
1994 7099 9.745880 GAATTCTTACGTAACATTCCTATCTCA 57.254 33.333 17.51 0.00 0.00 3.27
1995 7100 9.530633 AATTCTTACGTAACATTCCTATCTCAC 57.469 33.333 3.29 0.00 0.00 3.51
1996 7101 7.035840 TCTTACGTAACATTCCTATCTCACC 57.964 40.000 3.29 0.00 0.00 4.02
1997 7102 6.604396 TCTTACGTAACATTCCTATCTCACCA 59.396 38.462 3.29 0.00 0.00 4.17
1998 7103 5.670792 ACGTAACATTCCTATCTCACCAA 57.329 39.130 0.00 0.00 0.00 3.67
1999 7104 6.235231 ACGTAACATTCCTATCTCACCAAT 57.765 37.500 0.00 0.00 0.00 3.16
2000 7105 6.650120 ACGTAACATTCCTATCTCACCAATT 58.350 36.000 0.00 0.00 0.00 2.32
2001 7106 6.538742 ACGTAACATTCCTATCTCACCAATTG 59.461 38.462 0.00 0.00 0.00 2.32
2002 7107 6.761242 CGTAACATTCCTATCTCACCAATTGA 59.239 38.462 7.12 0.00 0.00 2.57
2003 7108 7.279981 CGTAACATTCCTATCTCACCAATTGAA 59.720 37.037 7.12 0.00 32.21 2.69
2004 7109 7.396540 AACATTCCTATCTCACCAATTGAAC 57.603 36.000 7.12 0.00 32.21 3.18
2005 7110 6.725364 ACATTCCTATCTCACCAATTGAACT 58.275 36.000 7.12 0.00 32.21 3.01
2006 7111 6.600822 ACATTCCTATCTCACCAATTGAACTG 59.399 38.462 7.12 0.00 32.21 3.16
2007 7112 5.102953 TCCTATCTCACCAATTGAACTGG 57.897 43.478 7.12 0.00 40.05 4.00
2008 7113 4.080356 TCCTATCTCACCAATTGAACTGGG 60.080 45.833 7.12 0.00 38.36 4.45
2009 7114 3.814504 ATCTCACCAATTGAACTGGGT 57.185 42.857 7.12 0.00 38.36 4.51
2012 7117 0.968405 CACCAATTGAACTGGGTGGG 59.032 55.000 7.12 0.00 45.48 4.61
2013 7118 0.831711 ACCAATTGAACTGGGTGGGC 60.832 55.000 7.12 0.00 38.36 5.36
2014 7119 1.543944 CCAATTGAACTGGGTGGGCC 61.544 60.000 7.12 0.00 0.00 5.80
2027 7132 4.523282 GGGCCCCCTCCTCCTGAT 62.523 72.222 12.23 0.00 0.00 2.90
2028 7133 2.368878 GGCCCCCTCCTCCTGATT 60.369 66.667 0.00 0.00 0.00 2.57
2029 7134 2.009302 GGCCCCCTCCTCCTGATTT 61.009 63.158 0.00 0.00 0.00 2.17
2030 7135 0.697854 GGCCCCCTCCTCCTGATTTA 60.698 60.000 0.00 0.00 0.00 1.40
2031 7136 1.222567 GCCCCCTCCTCCTGATTTAA 58.777 55.000 0.00 0.00 0.00 1.52
2032 7137 1.783365 GCCCCCTCCTCCTGATTTAAT 59.217 52.381 0.00 0.00 0.00 1.40
2033 7138 2.224892 GCCCCCTCCTCCTGATTTAATC 60.225 54.545 0.00 0.00 0.00 1.75
2034 7139 2.376855 CCCCCTCCTCCTGATTTAATCC 59.623 54.545 2.22 0.00 0.00 3.01
2035 7140 3.056080 CCCCTCCTCCTGATTTAATCCA 58.944 50.000 2.22 0.00 0.00 3.41
2036 7141 3.463329 CCCCTCCTCCTGATTTAATCCAA 59.537 47.826 2.22 0.00 0.00 3.53
2037 7142 4.464947 CCCTCCTCCTGATTTAATCCAAC 58.535 47.826 2.22 0.00 0.00 3.77
2038 7143 4.464947 CCTCCTCCTGATTTAATCCAACC 58.535 47.826 2.22 0.00 0.00 3.77
2039 7144 4.079787 CCTCCTCCTGATTTAATCCAACCA 60.080 45.833 2.22 0.00 0.00 3.67
2040 7145 5.509498 CTCCTCCTGATTTAATCCAACCAA 58.491 41.667 2.22 0.00 0.00 3.67
2041 7146 5.898120 TCCTCCTGATTTAATCCAACCAAA 58.102 37.500 2.22 0.00 0.00 3.28
2042 7147 6.318913 TCCTCCTGATTTAATCCAACCAAAA 58.681 36.000 2.22 0.00 0.00 2.44
2043 7148 6.210584 TCCTCCTGATTTAATCCAACCAAAAC 59.789 38.462 2.22 0.00 0.00 2.43
2044 7149 6.014669 CCTCCTGATTTAATCCAACCAAAACA 60.015 38.462 2.22 0.00 0.00 2.83
2045 7150 6.991938 TCCTGATTTAATCCAACCAAAACAG 58.008 36.000 2.22 0.00 33.99 3.16
2046 7151 5.639082 CCTGATTTAATCCAACCAAAACAGC 59.361 40.000 2.22 0.00 33.30 4.40
2047 7152 5.546526 TGATTTAATCCAACCAAAACAGCC 58.453 37.500 2.22 0.00 0.00 4.85
2048 7153 4.344359 TTTAATCCAACCAAAACAGCCC 57.656 40.909 0.00 0.00 0.00 5.19
2049 7154 1.799933 AATCCAACCAAAACAGCCCA 58.200 45.000 0.00 0.00 0.00 5.36
2050 7155 1.047801 ATCCAACCAAAACAGCCCAC 58.952 50.000 0.00 0.00 0.00 4.61
2051 7156 1.045911 TCCAACCAAAACAGCCCACC 61.046 55.000 0.00 0.00 0.00 4.61
2052 7157 1.048160 CCAACCAAAACAGCCCACCT 61.048 55.000 0.00 0.00 0.00 4.00
2053 7158 1.698506 CAACCAAAACAGCCCACCTA 58.301 50.000 0.00 0.00 0.00 3.08
2054 7159 2.035632 CAACCAAAACAGCCCACCTAA 58.964 47.619 0.00 0.00 0.00 2.69
2055 7160 2.632512 CAACCAAAACAGCCCACCTAAT 59.367 45.455 0.00 0.00 0.00 1.73
2056 7161 2.970987 ACCAAAACAGCCCACCTAATT 58.029 42.857 0.00 0.00 0.00 1.40
2057 7162 2.632512 ACCAAAACAGCCCACCTAATTG 59.367 45.455 0.00 0.00 0.00 2.32
2058 7163 2.612721 CCAAAACAGCCCACCTAATTGC 60.613 50.000 0.00 0.00 0.00 3.56
2059 7164 2.299867 CAAAACAGCCCACCTAATTGCT 59.700 45.455 0.00 0.00 33.52 3.91
2060 7165 2.309136 AACAGCCCACCTAATTGCTT 57.691 45.000 0.00 0.00 30.08 3.91
2061 7166 3.449746 AACAGCCCACCTAATTGCTTA 57.550 42.857 0.00 0.00 30.08 3.09
2062 7167 3.004752 ACAGCCCACCTAATTGCTTAG 57.995 47.619 0.00 0.00 35.15 2.18
2092 7197 0.622665 AGGGCAATCAGAACTGGGAG 59.377 55.000 1.93 0.00 0.00 4.30
2097 7202 1.558756 CAATCAGAACTGGGAGGCTCT 59.441 52.381 15.23 0.00 0.00 4.09
2109 7214 4.893601 GGCTCTAACCTCCGGCGC 62.894 72.222 0.00 0.00 0.00 6.53
2124 7229 3.800863 CGCCAAGAGCTGCAGCAG 61.801 66.667 38.24 23.95 45.16 4.24
2126 7231 1.970114 GCCAAGAGCTGCAGCAGAA 60.970 57.895 38.24 0.00 45.16 3.02
2166 7271 3.963428 AAATCGCCTGACAGAGTTACT 57.037 42.857 3.32 0.00 0.00 2.24
2187 7292 2.558313 GTCCTGAAGCTGCAACGC 59.442 61.111 1.02 0.00 0.00 4.84
2209 7541 1.375853 GCGGTATGCATCACAGGCAA 61.376 55.000 0.19 0.00 45.60 4.52
2214 7546 1.940883 ATGCATCACAGGCAAAGGCG 61.941 55.000 0.00 0.00 45.60 5.52
2228 7565 1.299541 AAGGCGCCGATCAAACATAG 58.700 50.000 23.20 0.00 0.00 2.23
2229 7566 0.532862 AGGCGCCGATCAAACATAGG 60.533 55.000 23.20 0.00 0.00 2.57
2233 7570 0.663153 GCCGATCAAACATAGGCACC 59.337 55.000 0.00 0.00 46.48 5.01
2234 7571 0.937304 CCGATCAAACATAGGCACCG 59.063 55.000 0.00 0.00 0.00 4.94
2235 7572 1.472552 CCGATCAAACATAGGCACCGA 60.473 52.381 0.00 0.00 0.00 4.69
2236 7573 2.276201 CGATCAAACATAGGCACCGAA 58.724 47.619 0.00 0.00 0.00 4.30
2273 7639 2.544267 ACAGCGACTTCAACTAAACTGC 59.456 45.455 0.00 0.00 0.00 4.40
2283 7649 7.832769 ACTTCAACTAAACTGCAAAGGTAAAA 58.167 30.769 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 264 7.451255 TCAAATACAACAGACCATCTTCCATTT 59.549 33.333 0.00 0.00 0.00 2.32
264 265 6.947733 TCAAATACAACAGACCATCTTCCATT 59.052 34.615 0.00 0.00 0.00 3.16
268 269 9.774742 GTTAATCAAATACAACAGACCATCTTC 57.225 33.333 0.00 0.00 0.00 2.87
269 270 9.520515 AGTTAATCAAATACAACAGACCATCTT 57.479 29.630 0.00 0.00 0.00 2.40
271 272 9.774742 GAAGTTAATCAAATACAACAGACCATC 57.225 33.333 0.00 0.00 0.00 3.51
273 274 8.918202 AGAAGTTAATCAAATACAACAGACCA 57.082 30.769 0.00 0.00 0.00 4.02
346 347 9.682465 GTCACCCTAGAAAATAGGTAAGATTTT 57.318 33.333 0.00 0.00 38.81 1.82
347 348 8.272889 GGTCACCCTAGAAAATAGGTAAGATTT 58.727 37.037 0.00 0.00 32.88 2.17
349 350 6.906901 TGGTCACCCTAGAAAATAGGTAAGAT 59.093 38.462 0.00 0.00 32.88 2.40
350 351 6.266080 TGGTCACCCTAGAAAATAGGTAAGA 58.734 40.000 0.00 0.00 32.88 2.10
351 352 6.555463 TGGTCACCCTAGAAAATAGGTAAG 57.445 41.667 0.00 0.00 32.88 2.34
352 353 6.126594 CCATGGTCACCCTAGAAAATAGGTAA 60.127 42.308 2.57 0.00 32.88 2.85
354 355 4.166144 CCATGGTCACCCTAGAAAATAGGT 59.834 45.833 2.57 0.00 32.88 3.08
356 357 4.137543 GCCATGGTCACCCTAGAAAATAG 58.862 47.826 14.67 0.00 0.00 1.73
357 358 3.525609 TGCCATGGTCACCCTAGAAAATA 59.474 43.478 14.67 0.00 0.00 1.40
359 360 1.707989 TGCCATGGTCACCCTAGAAAA 59.292 47.619 14.67 0.00 0.00 2.29
360 361 1.367346 TGCCATGGTCACCCTAGAAA 58.633 50.000 14.67 0.00 0.00 2.52
363 364 0.749454 GCTTGCCATGGTCACCCTAG 60.749 60.000 14.67 7.31 0.00 3.02
364 365 1.302949 GCTTGCCATGGTCACCCTA 59.697 57.895 14.67 0.00 0.00 3.53
366 367 1.683365 ATGCTTGCCATGGTCACCC 60.683 57.895 14.67 6.05 31.48 4.61
378 379 2.476686 CGGTACTTGTCATGCATGCTTG 60.477 50.000 23.82 23.82 0.00 4.01
380 381 1.339055 ACGGTACTTGTCATGCATGCT 60.339 47.619 22.25 1.07 0.00 3.79
381 382 1.086696 ACGGTACTTGTCATGCATGC 58.913 50.000 22.25 11.82 0.00 4.06
382 383 2.741517 TCAACGGTACTTGTCATGCATG 59.258 45.455 21.07 21.07 0.00 4.06
384 385 2.535012 TCAACGGTACTTGTCATGCA 57.465 45.000 0.00 0.00 0.00 3.96
386 387 4.245660 AGACATCAACGGTACTTGTCATG 58.754 43.478 15.26 0.00 39.27 3.07
388 389 5.221283 TGTTAGACATCAACGGTACTTGTCA 60.221 40.000 15.26 4.09 39.27 3.58
389 390 5.224888 TGTTAGACATCAACGGTACTTGTC 58.775 41.667 8.41 8.41 37.54 3.18
392 393 5.873164 GGATTGTTAGACATCAACGGTACTT 59.127 40.000 0.00 0.00 0.00 2.24
394 395 5.172934 TGGATTGTTAGACATCAACGGTAC 58.827 41.667 0.00 0.00 0.00 3.34
395 396 5.408880 TGGATTGTTAGACATCAACGGTA 57.591 39.130 0.00 0.00 0.00 4.02
396 397 4.280436 TGGATTGTTAGACATCAACGGT 57.720 40.909 0.00 0.00 0.00 4.83
399 400 5.565592 TGCATGGATTGTTAGACATCAAC 57.434 39.130 0.00 0.00 0.00 3.18
402 403 7.486647 AGAAAATGCATGGATTGTTAGACATC 58.513 34.615 13.66 3.02 0.00 3.06
404 405 6.839124 AGAAAATGCATGGATTGTTAGACA 57.161 33.333 13.66 0.00 0.00 3.41
405 406 7.420800 CCTAGAAAATGCATGGATTGTTAGAC 58.579 38.462 13.66 0.00 0.00 2.59
407 408 6.322201 ACCCTAGAAAATGCATGGATTGTTAG 59.678 38.462 13.66 13.77 0.00 2.34
409 410 5.025453 ACCCTAGAAAATGCATGGATTGTT 58.975 37.500 13.66 9.63 0.00 2.83
410 411 4.613437 ACCCTAGAAAATGCATGGATTGT 58.387 39.130 13.66 7.90 0.00 2.71
411 412 4.891756 AGACCCTAGAAAATGCATGGATTG 59.108 41.667 13.66 1.61 0.00 2.67
412 413 5.134725 AGACCCTAGAAAATGCATGGATT 57.865 39.130 6.63 6.63 0.00 3.01
413 414 4.803329 AGACCCTAGAAAATGCATGGAT 57.197 40.909 0.00 0.00 0.00 3.41
415 416 3.181483 GCAAGACCCTAGAAAATGCATGG 60.181 47.826 0.00 0.00 32.80 3.66
417 418 3.026694 GGCAAGACCCTAGAAAATGCAT 58.973 45.455 0.00 0.00 34.14 3.96
418 419 2.446435 GGCAAGACCCTAGAAAATGCA 58.554 47.619 0.00 0.00 34.14 3.96
419 420 1.401905 CGGCAAGACCCTAGAAAATGC 59.598 52.381 0.00 0.00 33.26 3.56
422 423 2.569853 TCATCGGCAAGACCCTAGAAAA 59.430 45.455 0.00 0.00 33.26 2.29
424 425 1.860641 TCATCGGCAAGACCCTAGAA 58.139 50.000 0.00 0.00 33.26 2.10
426 427 2.691409 TTTCATCGGCAAGACCCTAG 57.309 50.000 0.00 0.00 33.26 3.02
427 428 3.426787 TTTTTCATCGGCAAGACCCTA 57.573 42.857 0.00 0.00 33.26 3.53
444 445 2.159352 CGGTCAGTGTTTTCCGGTTTTT 60.159 45.455 0.00 0.00 39.41 1.94
445 446 1.402613 CGGTCAGTGTTTTCCGGTTTT 59.597 47.619 0.00 0.00 39.41 2.43
448 449 1.890510 GCGGTCAGTGTTTTCCGGT 60.891 57.895 0.00 0.00 42.71 5.28
449 450 1.890041 TGCGGTCAGTGTTTTCCGG 60.890 57.895 15.67 0.00 42.71 5.14
450 451 1.278637 GTGCGGTCAGTGTTTTCCG 59.721 57.895 11.88 11.88 44.86 4.30
452 453 1.601903 TCATGTGCGGTCAGTGTTTTC 59.398 47.619 0.00 0.00 0.00 2.29
454 455 1.536766 CATCATGTGCGGTCAGTGTTT 59.463 47.619 0.00 0.00 0.00 2.83
456 457 0.035317 ACATCATGTGCGGTCAGTGT 59.965 50.000 0.00 0.00 0.00 3.55
457 458 2.008752 TACATCATGTGCGGTCAGTG 57.991 50.000 0.00 0.00 0.00 3.66
458 459 2.346803 GTTACATCATGTGCGGTCAGT 58.653 47.619 0.00 0.00 0.00 3.41
459 460 1.324435 CGTTACATCATGTGCGGTCAG 59.676 52.381 0.00 0.00 0.00 3.51
462 463 1.075542 CACGTTACATCATGTGCGGT 58.924 50.000 17.15 3.33 35.51 5.68
463 464 0.247655 GCACGTTACATCATGTGCGG 60.248 55.000 17.15 9.62 46.84 5.69
464 465 3.203275 GCACGTTACATCATGTGCG 57.797 52.632 12.99 12.99 46.84 5.34
466 467 1.355005 TCCGCACGTTACATCATGTG 58.645 50.000 0.00 0.00 36.83 3.21
468 469 2.351418 ACAATCCGCACGTTACATCATG 59.649 45.455 0.00 0.00 0.00 3.07
470 471 2.087501 ACAATCCGCACGTTACATCA 57.912 45.000 0.00 0.00 0.00 3.07
471 472 3.465122 AAACAATCCGCACGTTACATC 57.535 42.857 0.00 0.00 0.00 3.06
475 476 1.194997 CCGAAAACAATCCGCACGTTA 59.805 47.619 0.00 0.00 0.00 3.18
477 478 1.161563 ACCGAAAACAATCCGCACGT 61.162 50.000 0.00 0.00 0.00 4.49
482 483 4.153958 TGAAATCACCGAAAACAATCCG 57.846 40.909 0.00 0.00 0.00 4.18
514 515 4.998672 TCTCGTCGGTTTTTGTTTCCATAT 59.001 37.500 0.00 0.00 0.00 1.78
523 524 8.277713 TCTTTAAAGTTATCTCGTCGGTTTTTG 58.722 33.333 14.74 0.00 0.00 2.44
549 550 6.704056 AGCCTTAATATACAGCATTAGGGT 57.296 37.500 5.48 0.00 37.40 4.34
596 597 3.249189 ACTCCGCTCCCTGGCAAA 61.249 61.111 0.00 0.00 0.00 3.68
623 634 0.454452 GGCGGAATTTTGACGAGCAC 60.454 55.000 0.00 0.00 0.00 4.40
624 635 1.873165 GGCGGAATTTTGACGAGCA 59.127 52.632 0.00 0.00 0.00 4.26
679 690 0.175989 GAGGCCGTTCGGAATCTCTT 59.824 55.000 15.69 0.00 0.00 2.85
706 717 0.729690 GAATGGCGCAGAGACCTTTC 59.270 55.000 10.83 0.75 34.25 2.62
750 761 3.254060 CTCAACGGTGGAGAGTAACATG 58.746 50.000 6.70 0.00 34.24 3.21
766 777 3.380320 ACAGGCTGTTTTGTTACCTCAAC 59.620 43.478 15.88 0.00 37.67 3.18
791 1026 4.095610 CGACCTTTTACATTTCGAATGGC 58.904 43.478 0.00 0.00 0.00 4.40
841 1076 9.817809 AGTACGATGAAATGTTGTGTAGATATT 57.182 29.630 0.00 0.00 0.00 1.28
959 1216 0.442699 GATTTGACCGTGGAACTCGC 59.557 55.000 0.00 0.00 44.50 5.03
960 1217 1.790755 TGATTTGACCGTGGAACTCG 58.209 50.000 0.00 0.00 45.50 4.18
961 1218 3.186613 GTCTTGATTTGACCGTGGAACTC 59.813 47.826 0.00 0.00 31.75 3.01
1032 1290 2.325082 GCAGACGGTGTTGGCGATT 61.325 57.895 0.00 0.00 0.00 3.34
1215 1850 4.021925 GAGGCCAGGCACCGACTT 62.022 66.667 15.19 0.00 0.00 3.01
1637 3898 2.352651 CACAAGCATCACCCATACGAAG 59.647 50.000 0.00 0.00 0.00 3.79
1666 3929 3.685139 TTAGTTCTCTGGGCTCACTTG 57.315 47.619 0.00 0.00 0.00 3.16
1675 3939 7.086230 ACTATACACGTCTTTAGTTCTCTGG 57.914 40.000 0.00 0.00 0.00 3.86
1714 4000 1.004440 GAAGCCTCACTCGCAGGTT 60.004 57.895 0.00 0.00 32.98 3.50
1750 4036 4.545208 TGTTCATCAATTCAGGTCCGTA 57.455 40.909 0.00 0.00 0.00 4.02
1766 4062 4.816385 GTGAGAGAAATCTGTGGTTGTTCA 59.184 41.667 0.00 0.00 0.00 3.18
1772 4068 4.336889 TTTCGTGAGAGAAATCTGTGGT 57.663 40.909 0.00 0.00 43.69 4.16
1808 4104 6.609212 TGTCTCTCAAGAACTCCTATGCTATT 59.391 38.462 0.00 0.00 31.93 1.73
1899 7004 2.094675 CCCTACCATGGCTTTGTTCTG 58.905 52.381 13.04 0.00 0.00 3.02
1902 7007 2.807676 CTTCCCTACCATGGCTTTGTT 58.192 47.619 13.04 0.00 0.00 2.83
1903 7008 1.616994 GCTTCCCTACCATGGCTTTGT 60.617 52.381 13.04 0.00 0.00 2.83
1904 7009 1.106285 GCTTCCCTACCATGGCTTTG 58.894 55.000 13.04 0.00 0.00 2.77
1906 7011 1.224592 CGCTTCCCTACCATGGCTT 59.775 57.895 13.04 0.00 0.00 4.35
1908 7013 1.227674 CTCGCTTCCCTACCATGGC 60.228 63.158 13.04 0.00 0.00 4.40
1909 7014 0.541863 AACTCGCTTCCCTACCATGG 59.458 55.000 11.19 11.19 0.00 3.66
1911 7016 0.107654 GCAACTCGCTTCCCTACCAT 60.108 55.000 0.00 0.00 37.77 3.55
1912 7017 1.295423 GCAACTCGCTTCCCTACCA 59.705 57.895 0.00 0.00 37.77 3.25
1914 7019 1.019805 GTGGCAACTCGCTTCCCTAC 61.020 60.000 0.00 0.00 41.91 3.18
1915 7020 1.295423 GTGGCAACTCGCTTCCCTA 59.705 57.895 0.00 0.00 41.91 3.53
1916 7021 2.032681 GTGGCAACTCGCTTCCCT 59.967 61.111 0.00 0.00 41.91 4.20
1924 7029 2.040544 CATGGACCCGTGGCAACTC 61.041 63.158 0.00 0.00 37.61 3.01
1926 7031 2.813226 TAGCATGGACCCGTGGCAAC 62.813 60.000 10.03 0.00 33.81 4.17
1927 7032 2.130821 TTAGCATGGACCCGTGGCAA 62.131 55.000 10.03 0.00 33.81 4.52
1928 7033 2.130821 TTTAGCATGGACCCGTGGCA 62.131 55.000 10.03 0.00 33.81 4.92
1929 7034 0.963355 TTTTAGCATGGACCCGTGGC 60.963 55.000 10.03 3.18 33.81 5.01
1930 7035 1.472480 CTTTTTAGCATGGACCCGTGG 59.528 52.381 10.03 0.00 33.81 4.94
1931 7036 2.095263 CACTTTTTAGCATGGACCCGTG 60.095 50.000 3.93 3.93 36.13 4.94
1932 7037 2.159382 CACTTTTTAGCATGGACCCGT 58.841 47.619 0.00 0.00 0.00 5.28
1934 7039 2.171003 AGCACTTTTTAGCATGGACCC 58.829 47.619 0.00 0.00 0.00 4.46
1935 7040 3.756434 TGTAGCACTTTTTAGCATGGACC 59.244 43.478 0.00 0.00 0.00 4.46
1936 7041 4.379499 GGTGTAGCACTTTTTAGCATGGAC 60.379 45.833 0.00 0.00 34.40 4.02
1937 7042 3.756434 GGTGTAGCACTTTTTAGCATGGA 59.244 43.478 0.00 0.00 34.40 3.41
1938 7043 3.758554 AGGTGTAGCACTTTTTAGCATGG 59.241 43.478 0.00 0.00 34.40 3.66
1940 7045 5.805728 AGTAGGTGTAGCACTTTTTAGCAT 58.194 37.500 0.00 0.00 34.40 3.79
1942 7047 6.872547 AGTAAGTAGGTGTAGCACTTTTTAGC 59.127 38.462 0.00 0.00 34.48 3.09
1943 7048 8.086522 TCAGTAAGTAGGTGTAGCACTTTTTAG 58.913 37.037 0.00 0.00 34.48 1.85
1944 7049 7.954835 TCAGTAAGTAGGTGTAGCACTTTTTA 58.045 34.615 0.00 0.00 34.48 1.52
1945 7050 6.823497 TCAGTAAGTAGGTGTAGCACTTTTT 58.177 36.000 0.00 0.00 34.48 1.94
1946 7051 6.415206 TCAGTAAGTAGGTGTAGCACTTTT 57.585 37.500 0.00 0.00 34.48 2.27
1947 7052 6.415206 TTCAGTAAGTAGGTGTAGCACTTT 57.585 37.500 0.00 0.00 34.48 2.66
1948 7053 6.607004 ATTCAGTAAGTAGGTGTAGCACTT 57.393 37.500 0.00 0.00 36.51 3.16
1949 7054 6.437793 AGAATTCAGTAAGTAGGTGTAGCACT 59.562 38.462 8.44 0.00 34.40 4.40
1951 7056 6.852420 AGAATTCAGTAAGTAGGTGTAGCA 57.148 37.500 8.44 0.00 0.00 3.49
1952 7057 7.431668 CGTAAGAATTCAGTAAGTAGGTGTAGC 59.568 40.741 8.44 0.00 43.02 3.58
1953 7058 8.457261 ACGTAAGAATTCAGTAAGTAGGTGTAG 58.543 37.037 8.44 0.00 43.62 2.74
1954 7059 8.340618 ACGTAAGAATTCAGTAAGTAGGTGTA 57.659 34.615 8.44 0.00 43.62 2.90
1955 7060 7.224522 ACGTAAGAATTCAGTAAGTAGGTGT 57.775 36.000 8.44 0.00 43.62 4.16
1956 7061 9.070149 GTTACGTAAGAATTCAGTAAGTAGGTG 57.930 37.037 8.60 0.00 43.62 4.00
1957 7062 8.796475 TGTTACGTAAGAATTCAGTAAGTAGGT 58.204 33.333 8.60 4.59 43.62 3.08
1958 7063 9.798994 ATGTTACGTAAGAATTCAGTAAGTAGG 57.201 33.333 8.60 0.00 43.62 3.18
1961 7066 9.148104 GGAATGTTACGTAAGAATTCAGTAAGT 57.852 33.333 28.05 9.95 43.62 2.24
1962 7067 9.367444 AGGAATGTTACGTAAGAATTCAGTAAG 57.633 33.333 28.05 4.62 43.62 2.34
1965 7070 9.530633 GATAGGAATGTTACGTAAGAATTCAGT 57.469 33.333 28.05 21.47 43.62 3.41
1966 7071 9.751542 AGATAGGAATGTTACGTAAGAATTCAG 57.248 33.333 28.05 0.00 43.62 3.02
1967 7072 9.745880 GAGATAGGAATGTTACGTAAGAATTCA 57.254 33.333 28.05 17.05 43.62 2.57
1968 7073 9.745880 TGAGATAGGAATGTTACGTAAGAATTC 57.254 33.333 23.40 23.40 43.62 2.17
1969 7074 9.530633 GTGAGATAGGAATGTTACGTAAGAATT 57.469 33.333 8.60 11.58 43.62 2.17
1970 7075 8.142551 GGTGAGATAGGAATGTTACGTAAGAAT 58.857 37.037 8.60 0.00 43.62 2.40
1971 7076 7.123098 TGGTGAGATAGGAATGTTACGTAAGAA 59.877 37.037 8.60 0.28 43.62 2.52
1972 7077 6.604396 TGGTGAGATAGGAATGTTACGTAAGA 59.396 38.462 8.60 8.12 43.62 2.10
1974 7079 6.778834 TGGTGAGATAGGAATGTTACGTAA 57.221 37.500 3.29 3.29 0.00 3.18
1975 7080 6.778834 TTGGTGAGATAGGAATGTTACGTA 57.221 37.500 0.00 0.00 0.00 3.57
1976 7081 5.670792 TTGGTGAGATAGGAATGTTACGT 57.329 39.130 0.00 0.00 0.00 3.57
1977 7082 6.761242 TCAATTGGTGAGATAGGAATGTTACG 59.239 38.462 5.42 0.00 0.00 3.18
1978 7083 8.398665 GTTCAATTGGTGAGATAGGAATGTTAC 58.601 37.037 5.42 0.00 37.61 2.50
1979 7084 8.328758 AGTTCAATTGGTGAGATAGGAATGTTA 58.671 33.333 5.42 0.00 37.61 2.41
1980 7085 7.121759 CAGTTCAATTGGTGAGATAGGAATGTT 59.878 37.037 5.42 0.00 37.61 2.71
1981 7086 6.600822 CAGTTCAATTGGTGAGATAGGAATGT 59.399 38.462 5.42 0.00 37.61 2.71
1982 7087 6.039047 CCAGTTCAATTGGTGAGATAGGAATG 59.961 42.308 5.42 0.00 37.61 2.67
1983 7088 6.125029 CCAGTTCAATTGGTGAGATAGGAAT 58.875 40.000 5.42 0.00 37.61 3.01
1984 7089 5.500234 CCAGTTCAATTGGTGAGATAGGAA 58.500 41.667 5.42 0.00 37.61 3.36
1985 7090 4.080356 CCCAGTTCAATTGGTGAGATAGGA 60.080 45.833 5.42 0.00 37.61 2.94
1986 7091 4.202441 CCCAGTTCAATTGGTGAGATAGG 58.798 47.826 5.42 0.00 37.61 2.57
1987 7092 4.848357 ACCCAGTTCAATTGGTGAGATAG 58.152 43.478 5.42 0.00 37.61 2.08
1988 7093 4.927267 ACCCAGTTCAATTGGTGAGATA 57.073 40.909 5.42 0.00 37.61 1.98
1989 7094 3.814504 ACCCAGTTCAATTGGTGAGAT 57.185 42.857 5.42 0.00 37.61 2.75
1993 7098 0.968405 CCCACCCAGTTCAATTGGTG 59.032 55.000 5.42 4.53 46.22 4.17
1994 7099 0.831711 GCCCACCCAGTTCAATTGGT 60.832 55.000 5.42 0.00 33.73 3.67
1995 7100 1.543944 GGCCCACCCAGTTCAATTGG 61.544 60.000 5.42 0.00 35.41 3.16
1996 7101 1.974543 GGCCCACCCAGTTCAATTG 59.025 57.895 0.00 0.00 0.00 2.32
1997 7102 4.539235 GGCCCACCCAGTTCAATT 57.461 55.556 0.00 0.00 0.00 2.32
2010 7115 4.523282 ATCAGGAGGAGGGGGCCC 62.523 72.222 15.76 15.76 0.00 5.80
2011 7116 0.697854 TAAATCAGGAGGAGGGGGCC 60.698 60.000 0.00 0.00 0.00 5.80
2012 7117 1.222567 TTAAATCAGGAGGAGGGGGC 58.777 55.000 0.00 0.00 0.00 5.80
2013 7118 2.376855 GGATTAAATCAGGAGGAGGGGG 59.623 54.545 0.00 0.00 0.00 5.40
2014 7119 3.056080 TGGATTAAATCAGGAGGAGGGG 58.944 50.000 0.00 0.00 0.00 4.79
2015 7120 4.464947 GTTGGATTAAATCAGGAGGAGGG 58.535 47.826 0.00 0.00 0.00 4.30
2016 7121 4.079787 TGGTTGGATTAAATCAGGAGGAGG 60.080 45.833 0.00 0.00 0.00 4.30
2017 7122 5.116084 TGGTTGGATTAAATCAGGAGGAG 57.884 43.478 0.00 0.00 0.00 3.69
2018 7123 5.528600 TTGGTTGGATTAAATCAGGAGGA 57.471 39.130 0.00 0.00 0.00 3.71
2019 7124 6.014669 TGTTTTGGTTGGATTAAATCAGGAGG 60.015 38.462 0.00 0.00 0.00 4.30
2020 7125 6.991938 TGTTTTGGTTGGATTAAATCAGGAG 58.008 36.000 0.00 0.00 0.00 3.69
2021 7126 6.518200 GCTGTTTTGGTTGGATTAAATCAGGA 60.518 38.462 0.00 0.00 34.28 3.86
2022 7127 5.639082 GCTGTTTTGGTTGGATTAAATCAGG 59.361 40.000 0.00 0.00 34.28 3.86
2023 7128 5.639082 GGCTGTTTTGGTTGGATTAAATCAG 59.361 40.000 0.00 0.00 35.65 2.90
2024 7129 5.512232 GGGCTGTTTTGGTTGGATTAAATCA 60.512 40.000 0.00 0.00 0.00 2.57
2025 7130 4.935205 GGGCTGTTTTGGTTGGATTAAATC 59.065 41.667 0.00 0.00 0.00 2.17
2026 7131 4.349342 TGGGCTGTTTTGGTTGGATTAAAT 59.651 37.500 0.00 0.00 0.00 1.40
2027 7132 3.711704 TGGGCTGTTTTGGTTGGATTAAA 59.288 39.130 0.00 0.00 0.00 1.52
2028 7133 3.070302 GTGGGCTGTTTTGGTTGGATTAA 59.930 43.478 0.00 0.00 0.00 1.40
2029 7134 2.630580 GTGGGCTGTTTTGGTTGGATTA 59.369 45.455 0.00 0.00 0.00 1.75
2030 7135 1.416030 GTGGGCTGTTTTGGTTGGATT 59.584 47.619 0.00 0.00 0.00 3.01
2031 7136 1.047801 GTGGGCTGTTTTGGTTGGAT 58.952 50.000 0.00 0.00 0.00 3.41
2032 7137 1.045911 GGTGGGCTGTTTTGGTTGGA 61.046 55.000 0.00 0.00 0.00 3.53
2033 7138 1.048160 AGGTGGGCTGTTTTGGTTGG 61.048 55.000 0.00 0.00 0.00 3.77
2034 7139 1.698506 TAGGTGGGCTGTTTTGGTTG 58.301 50.000 0.00 0.00 0.00 3.77
2035 7140 2.463047 TTAGGTGGGCTGTTTTGGTT 57.537 45.000 0.00 0.00 0.00 3.67
2036 7141 2.632512 CAATTAGGTGGGCTGTTTTGGT 59.367 45.455 0.00 0.00 0.00 3.67
2037 7142 2.612721 GCAATTAGGTGGGCTGTTTTGG 60.613 50.000 0.00 0.00 0.00 3.28
2038 7143 2.299867 AGCAATTAGGTGGGCTGTTTTG 59.700 45.455 0.00 0.00 34.83 2.44
2039 7144 2.608623 AGCAATTAGGTGGGCTGTTTT 58.391 42.857 0.00 0.00 34.83 2.43
2040 7145 2.309136 AGCAATTAGGTGGGCTGTTT 57.691 45.000 0.00 0.00 34.83 2.83
2041 7146 2.309136 AAGCAATTAGGTGGGCTGTT 57.691 45.000 0.00 0.00 36.58 3.16
2042 7147 2.357154 CCTAAGCAATTAGGTGGGCTGT 60.357 50.000 5.98 0.00 39.33 4.40
2043 7148 2.301346 CCTAAGCAATTAGGTGGGCTG 58.699 52.381 5.98 0.00 39.33 4.85
2044 7149 2.736670 CCTAAGCAATTAGGTGGGCT 57.263 50.000 5.98 0.00 39.33 5.19
2051 7156 3.953612 TGGCATGGAACCTAAGCAATTAG 59.046 43.478 0.00 0.00 0.00 1.73
2052 7157 3.953612 CTGGCATGGAACCTAAGCAATTA 59.046 43.478 0.00 0.00 0.00 1.40
2053 7158 2.762327 CTGGCATGGAACCTAAGCAATT 59.238 45.455 0.00 0.00 0.00 2.32
2054 7159 2.381911 CTGGCATGGAACCTAAGCAAT 58.618 47.619 0.00 0.00 0.00 3.56
2055 7160 1.616725 CCTGGCATGGAACCTAAGCAA 60.617 52.381 0.00 0.00 0.00 3.91
2056 7161 0.034186 CCTGGCATGGAACCTAAGCA 60.034 55.000 0.00 0.00 0.00 3.91
2057 7162 0.753111 CCCTGGCATGGAACCTAAGC 60.753 60.000 2.14 0.00 0.00 3.09
2058 7163 0.753111 GCCCTGGCATGGAACCTAAG 60.753 60.000 13.44 0.00 41.49 2.18
2059 7164 1.306296 GCCCTGGCATGGAACCTAA 59.694 57.895 13.44 0.00 41.49 2.69
2060 7165 3.006677 GCCCTGGCATGGAACCTA 58.993 61.111 13.44 0.00 41.49 3.08
2109 7214 0.605860 ACTTCTGCTGCAGCTCTTGG 60.606 55.000 36.61 23.87 42.66 3.61
2124 7229 1.511305 TCATCGCTCCGGTGACTTC 59.489 57.895 7.92 0.00 42.26 3.01
2166 7271 0.250467 GTTGCAGCTTCAGGACCTCA 60.250 55.000 0.00 0.00 0.00 3.86
2187 7292 2.203001 TGTGATGCATACCGCCCG 60.203 61.111 0.00 0.00 41.33 6.13
2209 7541 1.299541 CTATGTTTGATCGGCGCCTT 58.700 50.000 26.68 12.25 0.00 4.35
2214 7546 0.663153 GGTGCCTATGTTTGATCGGC 59.337 55.000 0.00 0.00 41.06 5.54
2228 7565 2.526304 TATGCTCTGTATTCGGTGCC 57.474 50.000 3.20 0.00 38.29 5.01
2229 7566 4.511454 TGAAATATGCTCTGTATTCGGTGC 59.489 41.667 0.00 0.00 39.16 5.01
2232 7569 5.333645 GCTGTGAAATATGCTCTGTATTCGG 60.334 44.000 0.00 0.00 0.00 4.30
2233 7570 5.611197 CGCTGTGAAATATGCTCTGTATTCG 60.611 44.000 0.00 0.00 0.00 3.34
2234 7571 5.463392 TCGCTGTGAAATATGCTCTGTATTC 59.537 40.000 0.00 0.00 0.00 1.75
2235 7572 5.235186 GTCGCTGTGAAATATGCTCTGTATT 59.765 40.000 0.00 0.00 0.00 1.89
2236 7573 4.747108 GTCGCTGTGAAATATGCTCTGTAT 59.253 41.667 0.00 0.00 0.00 2.29
2273 7639 4.642885 TGTGTTGGGAGTCTTTTACCTTTG 59.357 41.667 0.00 0.00 0.00 2.77
2283 7649 1.140312 ATGTGGTGTGTTGGGAGTCT 58.860 50.000 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.