Multiple sequence alignment - TraesCS5A01G203400

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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 TraesCS5A01G203400 chr5A 100.000 3732 0 0 402 4133 412912840 412916571 0.000000e+00 6892.0
1 TraesCS5A01G203400 chr5A 100.000 75 0 0 1 75 412912439 412912513 5.570000e-29 139.0
2 TraesCS5A01G203400 chr5D 93.247 1851 82 20 2131 3956 318061034 318062866 0.000000e+00 2686.0
3 TraesCS5A01G203400 chr5D 93.143 1575 85 14 544 2106 318059386 318060949 0.000000e+00 2289.0
4 TraesCS5A01G203400 chr5D 93.789 161 10 0 3973 4133 318063043 318063203 4.130000e-60 243.0
5 TraesCS5A01G203400 chr5D 82.667 75 12 1 1 75 228255000 228255073 9.590000e-07 65.8
6 TraesCS5A01G203400 chr5B 92.223 1813 97 21 2261 4060 367910510 367912291 0.000000e+00 2527.0
7 TraesCS5A01G203400 chr5B 91.364 1598 78 17 531 2103 367908626 367910188 0.000000e+00 2132.0
8 TraesCS5A01G203400 chr2D 87.113 194 24 1 1048 1240 419783595 419783402 6.960000e-53 219.0
9 TraesCS5A01G203400 chr2A 86.802 197 25 1 1045 1240 570192959 570193155 6.960000e-53 219.0
10 TraesCS5A01G203400 chr2B 86.598 194 25 1 1048 1240 492148249 492148056 3.240000e-51 213.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G203400 chr5A 412912439 412916571 4132 False 3515.500000 6892 100.0000 1 4133 2 chr5A.!!$F1 4132
1 TraesCS5A01G203400 chr5D 318059386 318063203 3817 False 1739.333333 2686 93.3930 544 4133 3 chr5D.!!$F2 3589
2 TraesCS5A01G203400 chr5B 367908626 367912291 3665 False 2329.500000 2527 91.7935 531 4060 2 chr5B.!!$F1 3529

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
22 23 0.098200 TACGGTTCTGATGTCGAGCG 59.902 55.0 0.00 0.00 38.77 5.03 F
461 462 0.179134 CCTAGTGACGGCGAGAAAGG 60.179 60.0 16.62 9.74 0.00 3.11 F
484 485 0.323629 AAGACGGTGTGTATGGTGGG 59.676 55.0 0.00 0.00 0.00 4.61 F
518 519 0.971386 GGGGGTAGTCGTTTGTCTCA 59.029 55.0 0.00 0.00 0.00 3.27 F
1933 1955 0.988832 AACCCATCACGGTACCATGT 59.011 50.0 13.54 0.00 33.98 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1010 1012 0.247736 GTTCTCCTCGTCCTGCACAT 59.752 55.000 0.00 0.0 0.00 3.21 R
1980 2002 0.584785 CGATTCGCAGACGCACAATG 60.585 55.000 0.00 0.0 39.84 2.82 R
1981 2003 1.014044 ACGATTCGCAGACGCACAAT 61.014 50.000 5.86 0.0 39.84 2.71 R
1999 2025 1.923204 TGCACACGACAAAATTTGCAC 59.077 42.857 5.52 0.0 35.13 4.57 R
3687 3910 0.106519 ACAGAGTTGTTGGCTGCCTT 60.107 50.000 21.03 0.0 32.28 4.35 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
20 21 3.972950 AGATACGGTTCTGATGTCGAG 57.027 47.619 0.00 0.00 0.00 4.04
21 22 2.033550 AGATACGGTTCTGATGTCGAGC 59.966 50.000 0.00 0.00 0.00 5.03
22 23 0.098200 TACGGTTCTGATGTCGAGCG 59.902 55.000 0.00 0.00 38.77 5.03
23 24 2.508891 CGGTTCTGATGTCGAGCGC 61.509 63.158 0.00 0.00 0.00 5.92
24 25 1.446099 GGTTCTGATGTCGAGCGCA 60.446 57.895 11.47 0.00 0.00 6.09
25 26 1.687494 GGTTCTGATGTCGAGCGCAC 61.687 60.000 11.47 0.96 0.00 5.34
26 27 1.446099 TTCTGATGTCGAGCGCACC 60.446 57.895 11.47 0.00 0.00 5.01
27 28 1.877576 TTCTGATGTCGAGCGCACCT 61.878 55.000 11.47 0.00 0.00 4.00
28 29 1.875813 CTGATGTCGAGCGCACCTC 60.876 63.158 11.47 2.15 37.22 3.85
29 30 2.276863 CTGATGTCGAGCGCACCTCT 62.277 60.000 11.47 0.00 38.49 3.69
30 31 1.875813 GATGTCGAGCGCACCTCTG 60.876 63.158 11.47 0.00 38.49 3.35
31 32 3.997064 ATGTCGAGCGCACCTCTGC 62.997 63.158 11.47 0.00 38.49 4.26
35 36 4.704833 GAGCGCACCTCTGCCCAA 62.705 66.667 11.47 0.00 40.73 4.12
36 37 4.711949 AGCGCACCTCTGCCCAAG 62.712 66.667 11.47 0.00 40.73 3.61
37 38 4.704833 GCGCACCTCTGCCCAAGA 62.705 66.667 0.30 0.00 40.73 3.02
38 39 2.743928 CGCACCTCTGCCCAAGAC 60.744 66.667 0.00 0.00 40.73 3.01
39 40 2.360475 GCACCTCTGCCCAAGACC 60.360 66.667 0.00 0.00 37.45 3.85
40 41 3.160585 CACCTCTGCCCAAGACCA 58.839 61.111 0.00 0.00 0.00 4.02
41 42 1.687612 CACCTCTGCCCAAGACCAT 59.312 57.895 0.00 0.00 0.00 3.55
42 43 0.679002 CACCTCTGCCCAAGACCATG 60.679 60.000 0.00 0.00 0.00 3.66
43 44 1.751927 CCTCTGCCCAAGACCATGC 60.752 63.158 0.00 0.00 0.00 4.06
44 45 1.001764 CTCTGCCCAAGACCATGCA 60.002 57.895 0.00 0.00 0.00 3.96
45 46 1.303561 TCTGCCCAAGACCATGCAC 60.304 57.895 0.00 0.00 0.00 4.57
46 47 2.283101 TGCCCAAGACCATGCACC 60.283 61.111 0.00 0.00 0.00 5.01
47 48 2.283101 GCCCAAGACCATGCACCA 60.283 61.111 0.00 0.00 0.00 4.17
48 49 1.907807 GCCCAAGACCATGCACCAA 60.908 57.895 0.00 0.00 0.00 3.67
49 50 1.966762 CCCAAGACCATGCACCAAC 59.033 57.895 0.00 0.00 0.00 3.77
50 51 0.827089 CCCAAGACCATGCACCAACA 60.827 55.000 0.00 0.00 0.00 3.33
51 52 0.314935 CCAAGACCATGCACCAACAC 59.685 55.000 0.00 0.00 0.00 3.32
52 53 0.314935 CAAGACCATGCACCAACACC 59.685 55.000 0.00 0.00 0.00 4.16
53 54 0.827507 AAGACCATGCACCAACACCC 60.828 55.000 0.00 0.00 0.00 4.61
54 55 1.228552 GACCATGCACCAACACCCT 60.229 57.895 0.00 0.00 0.00 4.34
55 56 1.228552 ACCATGCACCAACACCCTC 60.229 57.895 0.00 0.00 0.00 4.30
56 57 1.075482 CCATGCACCAACACCCTCT 59.925 57.895 0.00 0.00 0.00 3.69
57 58 0.540365 CCATGCACCAACACCCTCTT 60.540 55.000 0.00 0.00 0.00 2.85
58 59 0.883833 CATGCACCAACACCCTCTTC 59.116 55.000 0.00 0.00 0.00 2.87
59 60 0.773644 ATGCACCAACACCCTCTTCT 59.226 50.000 0.00 0.00 0.00 2.85
60 61 0.550914 TGCACCAACACCCTCTTCTT 59.449 50.000 0.00 0.00 0.00 2.52
61 62 1.239347 GCACCAACACCCTCTTCTTC 58.761 55.000 0.00 0.00 0.00 2.87
62 63 1.512926 CACCAACACCCTCTTCTTCG 58.487 55.000 0.00 0.00 0.00 3.79
63 64 1.070134 CACCAACACCCTCTTCTTCGA 59.930 52.381 0.00 0.00 0.00 3.71
64 65 1.978580 ACCAACACCCTCTTCTTCGAT 59.021 47.619 0.00 0.00 0.00 3.59
65 66 2.289694 ACCAACACCCTCTTCTTCGATG 60.290 50.000 0.00 0.00 0.00 3.84
66 67 2.028112 CCAACACCCTCTTCTTCGATGA 60.028 50.000 0.00 0.00 0.00 2.92
67 68 2.996621 CAACACCCTCTTCTTCGATGAC 59.003 50.000 0.00 0.00 0.00 3.06
68 69 2.530701 ACACCCTCTTCTTCGATGACT 58.469 47.619 0.00 0.00 0.00 3.41
69 70 2.232452 ACACCCTCTTCTTCGATGACTG 59.768 50.000 0.00 0.00 0.00 3.51
70 71 2.493675 CACCCTCTTCTTCGATGACTGA 59.506 50.000 0.00 2.37 0.00 3.41
71 72 2.757868 ACCCTCTTCTTCGATGACTGAG 59.242 50.000 16.82 16.82 0.00 3.35
72 73 2.481104 CCCTCTTCTTCGATGACTGAGC 60.481 54.545 17.70 0.00 0.00 4.26
73 74 2.481104 CCTCTTCTTCGATGACTGAGCC 60.481 54.545 17.70 0.00 0.00 4.70
74 75 2.165234 CTCTTCTTCGATGACTGAGCCA 59.835 50.000 13.68 0.00 0.00 4.75
418 419 4.609995 ATTAGCAACACCCCGTCG 57.390 55.556 0.00 0.00 0.00 5.12
419 420 1.976898 ATTAGCAACACCCCGTCGA 59.023 52.632 0.00 0.00 0.00 4.20
420 421 0.390735 ATTAGCAACACCCCGTCGAC 60.391 55.000 5.18 5.18 0.00 4.20
421 422 2.752322 TTAGCAACACCCCGTCGACG 62.752 60.000 30.33 30.33 39.44 5.12
429 430 4.675029 CCCGTCGACGCCAACCTT 62.675 66.667 31.73 0.00 38.18 3.50
430 431 3.411351 CCGTCGACGCCAACCTTG 61.411 66.667 31.73 12.14 38.18 3.61
431 432 4.072088 CGTCGACGCCAACCTTGC 62.072 66.667 26.59 0.00 0.00 4.01
432 433 2.970324 GTCGACGCCAACCTTGCA 60.970 61.111 0.00 0.00 0.00 4.08
433 434 2.970324 TCGACGCCAACCTTGCAC 60.970 61.111 0.00 0.00 0.00 4.57
434 435 4.368808 CGACGCCAACCTTGCACG 62.369 66.667 0.00 0.00 34.00 5.34
435 436 4.025401 GACGCCAACCTTGCACGG 62.025 66.667 7.87 7.87 32.69 4.94
439 440 2.912025 CCAACCTTGCACGGGCTT 60.912 61.111 12.74 0.00 41.91 4.35
440 441 2.498056 CCAACCTTGCACGGGCTTT 61.498 57.895 12.74 0.00 41.91 3.51
441 442 1.300080 CAACCTTGCACGGGCTTTG 60.300 57.895 12.74 5.31 41.91 2.77
442 443 3.150647 AACCTTGCACGGGCTTTGC 62.151 57.895 12.74 0.00 41.91 3.68
452 453 3.890674 GGCTTTGCCTAGTGACGG 58.109 61.111 0.73 0.00 46.69 4.79
453 454 2.399356 GGCTTTGCCTAGTGACGGC 61.399 63.158 0.73 0.00 46.69 5.68
458 459 2.882876 GCCTAGTGACGGCGAGAA 59.117 61.111 16.62 0.00 37.87 2.87
459 460 1.214589 GCCTAGTGACGGCGAGAAA 59.785 57.895 16.62 0.00 37.87 2.52
460 461 0.802607 GCCTAGTGACGGCGAGAAAG 60.803 60.000 16.62 3.92 37.87 2.62
461 462 0.179134 CCTAGTGACGGCGAGAAAGG 60.179 60.000 16.62 9.74 0.00 3.11
462 463 0.179134 CTAGTGACGGCGAGAAAGGG 60.179 60.000 16.62 0.00 0.00 3.95
463 464 0.609957 TAGTGACGGCGAGAAAGGGA 60.610 55.000 16.62 0.00 0.00 4.20
464 465 1.446272 GTGACGGCGAGAAAGGGAG 60.446 63.158 16.62 0.00 0.00 4.30
465 466 1.605451 TGACGGCGAGAAAGGGAGA 60.605 57.895 16.62 0.00 0.00 3.71
466 467 1.183030 TGACGGCGAGAAAGGGAGAA 61.183 55.000 16.62 0.00 0.00 2.87
467 468 0.458716 GACGGCGAGAAAGGGAGAAG 60.459 60.000 16.62 0.00 0.00 2.85
468 469 0.898789 ACGGCGAGAAAGGGAGAAGA 60.899 55.000 16.62 0.00 0.00 2.87
469 470 0.458716 CGGCGAGAAAGGGAGAAGAC 60.459 60.000 0.00 0.00 0.00 3.01
470 471 0.458716 GGCGAGAAAGGGAGAAGACG 60.459 60.000 0.00 0.00 0.00 4.18
471 472 0.458716 GCGAGAAAGGGAGAAGACGG 60.459 60.000 0.00 0.00 0.00 4.79
472 473 0.889306 CGAGAAAGGGAGAAGACGGT 59.111 55.000 0.00 0.00 0.00 4.83
473 474 1.402984 CGAGAAAGGGAGAAGACGGTG 60.403 57.143 0.00 0.00 0.00 4.94
474 475 1.619332 GAGAAAGGGAGAAGACGGTGT 59.381 52.381 0.00 0.00 0.00 4.16
475 476 1.344763 AGAAAGGGAGAAGACGGTGTG 59.655 52.381 0.00 0.00 0.00 3.82
476 477 1.070289 GAAAGGGAGAAGACGGTGTGT 59.930 52.381 0.00 0.00 0.00 3.72
477 478 2.005370 AAGGGAGAAGACGGTGTGTA 57.995 50.000 0.00 0.00 0.00 2.90
478 479 2.233305 AGGGAGAAGACGGTGTGTAT 57.767 50.000 0.00 0.00 0.00 2.29
479 480 1.825474 AGGGAGAAGACGGTGTGTATG 59.175 52.381 0.00 0.00 0.00 2.39
480 481 1.134788 GGGAGAAGACGGTGTGTATGG 60.135 57.143 0.00 0.00 0.00 2.74
481 482 1.549170 GGAGAAGACGGTGTGTATGGT 59.451 52.381 0.00 0.00 0.00 3.55
482 483 2.607187 GAGAAGACGGTGTGTATGGTG 58.393 52.381 0.00 0.00 0.00 4.17
483 484 1.275291 AGAAGACGGTGTGTATGGTGG 59.725 52.381 0.00 0.00 0.00 4.61
484 485 0.323629 AAGACGGTGTGTATGGTGGG 59.676 55.000 0.00 0.00 0.00 4.61
485 486 1.078708 GACGGTGTGTATGGTGGGG 60.079 63.158 0.00 0.00 0.00 4.96
486 487 2.270850 CGGTGTGTATGGTGGGGG 59.729 66.667 0.00 0.00 0.00 5.40
487 488 2.598787 CGGTGTGTATGGTGGGGGT 61.599 63.158 0.00 0.00 0.00 4.95
488 489 1.001393 GGTGTGTATGGTGGGGGTG 60.001 63.158 0.00 0.00 0.00 4.61
489 490 1.001393 GTGTGTATGGTGGGGGTGG 60.001 63.158 0.00 0.00 0.00 4.61
490 491 2.235028 TGTGTATGGTGGGGGTGGG 61.235 63.158 0.00 0.00 0.00 4.61
491 492 2.615608 TGTATGGTGGGGGTGGGG 60.616 66.667 0.00 0.00 0.00 4.96
492 493 3.425925 GTATGGTGGGGGTGGGGG 61.426 72.222 0.00 0.00 0.00 5.40
493 494 3.975145 TATGGTGGGGGTGGGGGT 61.975 66.667 0.00 0.00 0.00 4.95
517 518 3.828657 GGGGGTAGTCGTTTGTCTC 57.171 57.895 0.00 0.00 0.00 3.36
518 519 0.971386 GGGGGTAGTCGTTTGTCTCA 59.029 55.000 0.00 0.00 0.00 3.27
519 520 1.345415 GGGGGTAGTCGTTTGTCTCAA 59.655 52.381 0.00 0.00 0.00 3.02
520 521 2.410939 GGGGTAGTCGTTTGTCTCAAC 58.589 52.381 0.00 0.00 0.00 3.18
521 522 2.410939 GGGTAGTCGTTTGTCTCAACC 58.589 52.381 0.00 0.00 0.00 3.77
522 523 2.410939 GGTAGTCGTTTGTCTCAACCC 58.589 52.381 0.00 0.00 0.00 4.11
523 524 2.036862 GGTAGTCGTTTGTCTCAACCCT 59.963 50.000 0.00 0.00 0.00 4.34
524 525 2.528041 AGTCGTTTGTCTCAACCCTC 57.472 50.000 0.00 0.00 0.00 4.30
525 526 2.040178 AGTCGTTTGTCTCAACCCTCT 58.960 47.619 0.00 0.00 0.00 3.69
526 527 2.036089 AGTCGTTTGTCTCAACCCTCTC 59.964 50.000 0.00 0.00 0.00 3.20
527 528 2.036387 TCGTTTGTCTCAACCCTCTCA 58.964 47.619 0.00 0.00 0.00 3.27
528 529 2.135933 CGTTTGTCTCAACCCTCTCAC 58.864 52.381 0.00 0.00 0.00 3.51
529 530 2.483013 CGTTTGTCTCAACCCTCTCACA 60.483 50.000 0.00 0.00 0.00 3.58
547 548 1.147376 ACAAGGCGTTGTGGCACTA 59.853 52.632 23.02 8.69 45.58 2.74
636 637 3.000322 GTGCAATAACGATCGTTCTCTGG 60.000 47.826 34.78 21.14 39.31 3.86
657 658 3.243535 GGTCCCTTTGAGTTTCTGCAAAG 60.244 47.826 0.00 0.00 46.46 2.77
698 699 1.210967 GGATCCGTGGTTCCATGGTAA 59.789 52.381 24.13 10.90 42.20 2.85
775 777 4.937620 ACATACTCACCACACATTCACATC 59.062 41.667 0.00 0.00 0.00 3.06
777 779 1.733912 CTCACCACACATTCACATCGG 59.266 52.381 0.00 0.00 0.00 4.18
798 800 3.976701 CTCGCGTGCCCAAATCCCT 62.977 63.158 5.77 0.00 0.00 4.20
845 847 2.754254 GGACATTTCACCCGGCCC 60.754 66.667 0.00 0.00 0.00 5.80
912 914 1.273324 ACCAAAACCCACCCTTGTCAA 60.273 47.619 0.00 0.00 0.00 3.18
913 915 1.412343 CCAAAACCCACCCTTGTCAAG 59.588 52.381 5.53 5.53 0.00 3.02
936 938 3.490078 GCAGATCACGAGCTAGCTAACTT 60.490 47.826 19.38 1.49 0.00 2.66
937 939 4.041049 CAGATCACGAGCTAGCTAACTTG 58.959 47.826 19.38 10.30 0.00 3.16
1010 1012 1.675310 CCGGCAAGATGGTGAAGCA 60.675 57.895 0.00 0.00 0.00 3.91
1286 1288 3.297134 TTCTGGGCATATGTTTCCTCC 57.703 47.619 4.29 0.00 0.00 4.30
1420 1422 9.723601 ATGCAAAGGCTTAATTATTTCTGAAAA 57.276 25.926 6.95 0.00 41.91 2.29
1605 1609 5.010012 CCTTCCTGCATTGTTCACTAAGTTT 59.990 40.000 0.00 0.00 0.00 2.66
1788 1802 1.934589 CCCGATCTTTGCACGACATA 58.065 50.000 0.00 0.00 0.00 2.29
1794 1808 6.073369 CCGATCTTTGCACGACATATAAATG 58.927 40.000 0.00 0.00 39.17 2.32
1823 1837 1.075374 AGTGCCCTTTTCAGCCATACA 59.925 47.619 0.00 0.00 0.00 2.29
1848 1862 2.930950 TCCGGCTGGATTTAATCTTGG 58.069 47.619 11.27 1.10 40.17 3.61
1859 1873 8.642935 TGGATTTAATCTTGGTGTGTGAATTA 57.357 30.769 4.87 0.00 0.00 1.40
1867 1881 6.757237 TCTTGGTGTGTGAATTATGCATTTT 58.243 32.000 3.54 0.00 0.00 1.82
1908 1927 6.552350 GTGAGACCCCTACAATATAGTTGGTA 59.448 42.308 0.00 0.00 33.34 3.25
1920 1939 9.930158 ACAATATAGTTGGTATAACAAACCCAT 57.070 29.630 4.38 0.00 36.06 4.00
1923 1942 7.875327 ATAGTTGGTATAACAAACCCATCAC 57.125 36.000 4.38 0.00 36.06 3.06
1933 1955 0.988832 AACCCATCACGGTACCATGT 59.011 50.000 13.54 0.00 33.98 3.21
1943 1965 4.707934 TCACGGTACCATGTCTTGAATCTA 59.292 41.667 13.54 0.00 0.00 1.98
1980 2002 1.905637 CAACCCCTTTCCACCACTAC 58.094 55.000 0.00 0.00 0.00 2.73
1981 2003 1.144093 CAACCCCTTTCCACCACTACA 59.856 52.381 0.00 0.00 0.00 2.74
2106 2132 0.036164 TTCACCCACACTAAGCGCAT 59.964 50.000 11.47 0.00 0.00 4.73
2110 2201 1.229428 CCCACACTAAGCGCATATGG 58.771 55.000 11.47 7.00 0.00 2.74
2237 2328 7.069455 ACAGAGTTTATAGTTTTGCCCTGTTTT 59.931 33.333 0.00 0.00 0.00 2.43
2256 2452 5.976534 TGTTTTGCAATTACAAGCACTACTG 59.023 36.000 11.27 0.00 41.05 2.74
2259 2455 5.356882 TGCAATTACAAGCACTACTGTTC 57.643 39.130 0.00 0.00 35.51 3.18
2270 2466 8.345565 ACAAGCACTACTGTTCTTTAGAAAATG 58.654 33.333 0.00 0.00 35.58 2.32
2282 2478 6.677913 TCTTTAGAAAATGGCAAGCACTAAC 58.322 36.000 0.00 0.00 0.00 2.34
2283 2479 6.490040 TCTTTAGAAAATGGCAAGCACTAACT 59.510 34.615 0.00 0.00 0.00 2.24
2284 2480 7.663905 TCTTTAGAAAATGGCAAGCACTAACTA 59.336 33.333 0.00 0.00 0.00 2.24
2285 2481 5.629079 AGAAAATGGCAAGCACTAACTAC 57.371 39.130 0.00 0.00 0.00 2.73
2286 2482 5.316987 AGAAAATGGCAAGCACTAACTACT 58.683 37.500 0.00 0.00 0.00 2.57
2330 2526 1.232621 ACTAAAACGGGCCGAAGTGC 61.233 55.000 35.78 0.00 0.00 4.40
2343 2539 4.686554 GGCCGAAGTGCTGTCTATATTTAG 59.313 45.833 0.00 0.00 0.00 1.85
2547 2743 4.699735 GTCACTCTCTCACATTCTCTCTCA 59.300 45.833 0.00 0.00 0.00 3.27
2548 2744 4.699735 TCACTCTCTCACATTCTCTCTCAC 59.300 45.833 0.00 0.00 0.00 3.51
2549 2745 4.701651 CACTCTCTCACATTCTCTCTCACT 59.298 45.833 0.00 0.00 0.00 3.41
2551 2747 5.183713 ACTCTCTCACATTCTCTCTCACTTG 59.816 44.000 0.00 0.00 0.00 3.16
2552 2748 5.320277 TCTCTCACATTCTCTCTCACTTGA 58.680 41.667 0.00 0.00 0.00 3.02
2553 2749 5.182950 TCTCTCACATTCTCTCTCACTTGAC 59.817 44.000 0.00 0.00 0.00 3.18
2556 2766 4.586421 TCACATTCTCTCTCACTTGACACT 59.414 41.667 0.00 0.00 0.00 3.55
2816 3028 2.508439 TGATCGCGGCGGAACTTC 60.508 61.111 23.46 11.93 0.00 3.01
2838 3050 3.334751 CACGCACGCAGGTTCGAA 61.335 61.111 0.00 0.00 36.29 3.71
3178 3390 3.866539 CGGGGGACGGCTAAGTAT 58.133 61.111 0.00 0.00 39.42 2.12
3207 3419 6.743575 AAAATAAGTACAGCAAGCTACCTG 57.256 37.500 10.95 10.95 35.26 4.00
3224 3436 4.077300 ACCTGCCTGTGTATGTATGATG 57.923 45.455 0.00 0.00 0.00 3.07
3230 3442 4.024556 GCCTGTGTATGTATGATGAAGTGC 60.025 45.833 0.00 0.00 0.00 4.40
3367 3579 2.474410 AGCCCAAAGTGTACTACAGC 57.526 50.000 0.00 0.00 0.00 4.40
3427 3643 1.852895 CATCTGTCGCGTTAGGTAAGC 59.147 52.381 5.77 0.00 0.00 3.09
3471 3690 3.303526 GCGTTATTTAGGCGGTGGTAATG 60.304 47.826 0.00 0.00 0.00 1.90
3489 3708 5.069516 GGTAATGTGATGGGCTTTGAATCAT 59.930 40.000 0.00 0.00 33.19 2.45
3613 3835 7.891561 ACCATATCTGTGAAGTAAGAGATAGC 58.108 38.462 0.00 0.00 32.35 2.97
3636 3859 5.559417 GCGACGTCCTCTCACAAAATAAAAA 60.559 40.000 10.58 0.00 0.00 1.94
3681 3904 6.606796 TGACATACCACATTATCTTGGCAATT 59.393 34.615 0.00 0.00 36.20 2.32
3682 3905 6.808829 ACATACCACATTATCTTGGCAATTG 58.191 36.000 0.00 0.00 36.20 2.32
3687 3910 3.443329 ACATTATCTTGGCAATTGCGACA 59.557 39.130 23.48 14.25 43.26 4.35
3697 3920 1.462731 AATTGCGACAAGGCAGCCAA 61.463 50.000 15.80 0.00 44.94 4.52
3711 3934 1.670811 CAGCCAACAACTCTGTTTCGT 59.329 47.619 0.00 0.00 43.45 3.85
3751 3974 1.214367 TCGCACTCTCGAAAACAACC 58.786 50.000 0.00 0.00 35.31 3.77
3799 4022 6.533367 GGTAGTTCTTCTCAAGTCAATAGCAG 59.467 42.308 0.00 0.00 0.00 4.24
3810 4033 7.656412 TCAAGTCAATAGCAGCATAAAAACAA 58.344 30.769 0.00 0.00 0.00 2.83
3884 4109 7.080353 TGACATTTCTGAACAAGCATATCAG 57.920 36.000 0.00 0.00 41.49 2.90
3896 4121 7.864108 ACAAGCATATCAGCATAAACTTGTA 57.136 32.000 0.00 0.00 40.02 2.41
3985 4370 7.751768 AACAAGATCCCTCTGAAAGTAAAAG 57.248 36.000 0.00 0.00 33.76 2.27
4046 4431 5.753438 GCACATCATTCTCATTGCAAATGAT 59.247 36.000 14.88 14.88 46.06 2.45
4060 4445 9.158233 CATTGCAAATGATAGAAAGTTTCCAAT 57.842 29.630 12.05 6.40 0.00 3.16
4097 4482 5.979993 GGCTACTAGGCTAGAACTTTCTTT 58.020 41.667 27.59 4.72 38.70 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.033550 GCTCGACATCAGAACCGTATCT 59.966 50.000 0.00 0.00 0.00 1.98
1 2 2.386249 GCTCGACATCAGAACCGTATC 58.614 52.381 0.00 0.00 0.00 2.24
2 3 1.268589 CGCTCGACATCAGAACCGTAT 60.269 52.381 0.00 0.00 0.00 3.06
3 4 0.098200 CGCTCGACATCAGAACCGTA 59.902 55.000 0.00 0.00 0.00 4.02
4 5 1.154016 CGCTCGACATCAGAACCGT 60.154 57.895 0.00 0.00 0.00 4.83
5 6 2.508891 GCGCTCGACATCAGAACCG 61.509 63.158 0.00 0.00 0.00 4.44
6 7 1.446099 TGCGCTCGACATCAGAACC 60.446 57.895 9.73 0.00 0.00 3.62
7 8 1.687494 GGTGCGCTCGACATCAGAAC 61.687 60.000 9.73 0.00 0.00 3.01
8 9 1.446099 GGTGCGCTCGACATCAGAA 60.446 57.895 9.73 0.00 0.00 3.02
9 10 2.181777 GGTGCGCTCGACATCAGA 59.818 61.111 9.73 0.00 0.00 3.27
10 11 1.875813 GAGGTGCGCTCGACATCAG 60.876 63.158 9.73 0.00 0.00 2.90
11 12 2.181777 GAGGTGCGCTCGACATCA 59.818 61.111 9.73 0.00 0.00 3.07
12 13 1.875813 CAGAGGTGCGCTCGACATC 60.876 63.158 9.73 5.86 0.00 3.06
13 14 2.182791 CAGAGGTGCGCTCGACAT 59.817 61.111 9.73 0.00 0.00 3.06
14 15 4.724602 GCAGAGGTGCGCTCGACA 62.725 66.667 9.73 0.00 40.71 4.35
23 24 0.679002 CATGGTCTTGGGCAGAGGTG 60.679 60.000 0.00 0.00 29.34 4.00
24 25 1.687612 CATGGTCTTGGGCAGAGGT 59.312 57.895 0.00 0.00 29.34 3.85
25 26 1.751927 GCATGGTCTTGGGCAGAGG 60.752 63.158 0.00 0.00 29.34 3.69
26 27 1.001764 TGCATGGTCTTGGGCAGAG 60.002 57.895 0.00 0.00 29.34 3.35
27 28 1.303561 GTGCATGGTCTTGGGCAGA 60.304 57.895 0.00 0.00 36.86 4.26
28 29 2.345760 GGTGCATGGTCTTGGGCAG 61.346 63.158 0.00 0.00 36.86 4.85
29 30 2.283101 GGTGCATGGTCTTGGGCA 60.283 61.111 0.00 0.00 0.00 5.36
30 31 1.907807 TTGGTGCATGGTCTTGGGC 60.908 57.895 0.00 0.00 0.00 5.36
31 32 0.827089 TGTTGGTGCATGGTCTTGGG 60.827 55.000 0.00 0.00 0.00 4.12
32 33 0.314935 GTGTTGGTGCATGGTCTTGG 59.685 55.000 0.00 0.00 0.00 3.61
33 34 0.314935 GGTGTTGGTGCATGGTCTTG 59.685 55.000 0.00 0.00 0.00 3.02
34 35 0.827507 GGGTGTTGGTGCATGGTCTT 60.828 55.000 0.00 0.00 0.00 3.01
35 36 1.228552 GGGTGTTGGTGCATGGTCT 60.229 57.895 0.00 0.00 0.00 3.85
36 37 1.228552 AGGGTGTTGGTGCATGGTC 60.229 57.895 0.00 0.00 0.00 4.02
37 38 1.228552 GAGGGTGTTGGTGCATGGT 60.229 57.895 0.00 0.00 0.00 3.55
38 39 0.540365 AAGAGGGTGTTGGTGCATGG 60.540 55.000 0.00 0.00 0.00 3.66
39 40 0.883833 GAAGAGGGTGTTGGTGCATG 59.116 55.000 0.00 0.00 0.00 4.06
40 41 0.773644 AGAAGAGGGTGTTGGTGCAT 59.226 50.000 0.00 0.00 0.00 3.96
41 42 0.550914 AAGAAGAGGGTGTTGGTGCA 59.449 50.000 0.00 0.00 0.00 4.57
42 43 1.239347 GAAGAAGAGGGTGTTGGTGC 58.761 55.000 0.00 0.00 0.00 5.01
43 44 1.070134 TCGAAGAAGAGGGTGTTGGTG 59.930 52.381 0.00 0.00 0.00 4.17
44 45 1.420430 TCGAAGAAGAGGGTGTTGGT 58.580 50.000 0.00 0.00 0.00 3.67
45 46 2.028112 TCATCGAAGAAGAGGGTGTTGG 60.028 50.000 0.00 0.00 43.58 3.77
46 47 2.996621 GTCATCGAAGAAGAGGGTGTTG 59.003 50.000 0.00 0.00 43.58 3.33
47 48 2.900546 AGTCATCGAAGAAGAGGGTGTT 59.099 45.455 0.00 0.00 43.58 3.32
48 49 2.232452 CAGTCATCGAAGAAGAGGGTGT 59.768 50.000 0.00 0.00 43.58 4.16
49 50 2.493675 TCAGTCATCGAAGAAGAGGGTG 59.506 50.000 0.00 0.00 43.58 4.61
50 51 2.757868 CTCAGTCATCGAAGAAGAGGGT 59.242 50.000 11.47 0.00 43.58 4.34
51 52 2.481104 GCTCAGTCATCGAAGAAGAGGG 60.481 54.545 17.65 3.15 43.58 4.30
52 53 2.481104 GGCTCAGTCATCGAAGAAGAGG 60.481 54.545 17.65 5.55 43.58 3.69
53 54 2.165234 TGGCTCAGTCATCGAAGAAGAG 59.835 50.000 13.85 13.85 43.58 2.85
54 55 2.171003 TGGCTCAGTCATCGAAGAAGA 58.829 47.619 0.00 0.00 43.58 2.87
55 56 2.662006 TGGCTCAGTCATCGAAGAAG 57.338 50.000 0.00 0.00 43.58 2.85
401 402 0.390735 GTCGACGGGGTGTTGCTAAT 60.391 55.000 0.00 0.00 31.43 1.73
402 403 1.005867 GTCGACGGGGTGTTGCTAA 60.006 57.895 0.00 0.00 31.43 3.09
403 404 2.652530 GTCGACGGGGTGTTGCTA 59.347 61.111 0.00 0.00 31.43 3.49
404 405 4.657824 CGTCGACGGGGTGTTGCT 62.658 66.667 29.70 0.00 35.37 3.91
412 413 4.675029 AAGGTTGGCGTCGACGGG 62.675 66.667 36.13 13.02 40.23 5.28
413 414 3.411351 CAAGGTTGGCGTCGACGG 61.411 66.667 36.13 19.71 40.23 4.79
414 415 4.072088 GCAAGGTTGGCGTCGACG 62.072 66.667 32.57 32.57 43.27 5.12
415 416 2.970324 TGCAAGGTTGGCGTCGAC 60.970 61.111 5.18 5.18 0.00 4.20
416 417 2.970324 GTGCAAGGTTGGCGTCGA 60.970 61.111 0.00 0.00 0.00 4.20
417 418 4.368808 CGTGCAAGGTTGGCGTCG 62.369 66.667 0.00 0.00 0.00 5.12
418 419 4.025401 CCGTGCAAGGTTGGCGTC 62.025 66.667 10.93 0.00 0.00 5.19
422 423 2.498056 AAAGCCCGTGCAAGGTTGG 61.498 57.895 17.81 3.51 41.13 3.77
423 424 1.300080 CAAAGCCCGTGCAAGGTTG 60.300 57.895 17.81 11.47 41.13 3.77
424 425 3.128375 CAAAGCCCGTGCAAGGTT 58.872 55.556 17.81 3.26 41.13 3.50
425 426 3.605664 GCAAAGCCCGTGCAAGGT 61.606 61.111 17.81 0.00 41.80 3.50
426 427 4.362476 GGCAAAGCCCGTGCAAGG 62.362 66.667 12.27 12.27 44.06 3.61
442 443 0.179134 CCTTTCTCGCCGTCACTAGG 60.179 60.000 0.00 0.00 0.00 3.02
443 444 0.179134 CCCTTTCTCGCCGTCACTAG 60.179 60.000 0.00 0.00 0.00 2.57
444 445 0.609957 TCCCTTTCTCGCCGTCACTA 60.610 55.000 0.00 0.00 0.00 2.74
445 446 1.878656 CTCCCTTTCTCGCCGTCACT 61.879 60.000 0.00 0.00 0.00 3.41
446 447 1.446272 CTCCCTTTCTCGCCGTCAC 60.446 63.158 0.00 0.00 0.00 3.67
447 448 1.183030 TTCTCCCTTTCTCGCCGTCA 61.183 55.000 0.00 0.00 0.00 4.35
448 449 0.458716 CTTCTCCCTTTCTCGCCGTC 60.459 60.000 0.00 0.00 0.00 4.79
449 450 0.898789 TCTTCTCCCTTTCTCGCCGT 60.899 55.000 0.00 0.00 0.00 5.68
450 451 0.458716 GTCTTCTCCCTTTCTCGCCG 60.459 60.000 0.00 0.00 0.00 6.46
451 452 0.458716 CGTCTTCTCCCTTTCTCGCC 60.459 60.000 0.00 0.00 0.00 5.54
452 453 0.458716 CCGTCTTCTCCCTTTCTCGC 60.459 60.000 0.00 0.00 0.00 5.03
453 454 0.889306 ACCGTCTTCTCCCTTTCTCG 59.111 55.000 0.00 0.00 0.00 4.04
454 455 1.619332 ACACCGTCTTCTCCCTTTCTC 59.381 52.381 0.00 0.00 0.00 2.87
455 456 1.344763 CACACCGTCTTCTCCCTTTCT 59.655 52.381 0.00 0.00 0.00 2.52
456 457 1.070289 ACACACCGTCTTCTCCCTTTC 59.930 52.381 0.00 0.00 0.00 2.62
457 458 1.129058 ACACACCGTCTTCTCCCTTT 58.871 50.000 0.00 0.00 0.00 3.11
458 459 2.005370 TACACACCGTCTTCTCCCTT 57.995 50.000 0.00 0.00 0.00 3.95
459 460 1.825474 CATACACACCGTCTTCTCCCT 59.175 52.381 0.00 0.00 0.00 4.20
460 461 1.134788 CCATACACACCGTCTTCTCCC 60.135 57.143 0.00 0.00 0.00 4.30
461 462 1.549170 ACCATACACACCGTCTTCTCC 59.451 52.381 0.00 0.00 0.00 3.71
462 463 2.607187 CACCATACACACCGTCTTCTC 58.393 52.381 0.00 0.00 0.00 2.87
463 464 1.275291 CCACCATACACACCGTCTTCT 59.725 52.381 0.00 0.00 0.00 2.85
464 465 1.674817 CCCACCATACACACCGTCTTC 60.675 57.143 0.00 0.00 0.00 2.87
465 466 0.323629 CCCACCATACACACCGTCTT 59.676 55.000 0.00 0.00 0.00 3.01
466 467 1.550130 CCCCACCATACACACCGTCT 61.550 60.000 0.00 0.00 0.00 4.18
467 468 1.078708 CCCCACCATACACACCGTC 60.079 63.158 0.00 0.00 0.00 4.79
468 469 2.598787 CCCCCACCATACACACCGT 61.599 63.158 0.00 0.00 0.00 4.83
469 470 2.270850 CCCCCACCATACACACCG 59.729 66.667 0.00 0.00 0.00 4.94
470 471 1.001393 CACCCCCACCATACACACC 60.001 63.158 0.00 0.00 0.00 4.16
471 472 1.001393 CCACCCCCACCATACACAC 60.001 63.158 0.00 0.00 0.00 3.82
472 473 2.235028 CCCACCCCCACCATACACA 61.235 63.158 0.00 0.00 0.00 3.72
473 474 2.680965 CCCACCCCCACCATACAC 59.319 66.667 0.00 0.00 0.00 2.90
474 475 2.615608 CCCCACCCCCACCATACA 60.616 66.667 0.00 0.00 0.00 2.29
475 476 3.425925 CCCCCACCCCCACCATAC 61.426 72.222 0.00 0.00 0.00 2.39
476 477 3.975145 ACCCCCACCCCCACCATA 61.975 66.667 0.00 0.00 0.00 2.74
499 500 0.971386 TGAGACAAACGACTACCCCC 59.029 55.000 0.00 0.00 0.00 5.40
500 501 2.410939 GTTGAGACAAACGACTACCCC 58.589 52.381 0.00 0.00 0.00 4.95
501 502 2.410939 GGTTGAGACAAACGACTACCC 58.589 52.381 0.00 0.00 0.00 3.69
502 503 2.036862 AGGGTTGAGACAAACGACTACC 59.963 50.000 0.00 0.00 0.00 3.18
503 504 3.005578 AGAGGGTTGAGACAAACGACTAC 59.994 47.826 0.00 0.00 0.00 2.73
504 505 3.228453 AGAGGGTTGAGACAAACGACTA 58.772 45.455 0.00 0.00 0.00 2.59
505 506 2.036089 GAGAGGGTTGAGACAAACGACT 59.964 50.000 0.00 0.00 0.00 4.18
506 507 2.223971 TGAGAGGGTTGAGACAAACGAC 60.224 50.000 0.00 0.00 0.00 4.34
507 508 2.036387 TGAGAGGGTTGAGACAAACGA 58.964 47.619 0.00 0.00 0.00 3.85
508 509 2.135933 GTGAGAGGGTTGAGACAAACG 58.864 52.381 0.00 0.00 0.00 3.60
509 510 2.872858 GTGTGAGAGGGTTGAGACAAAC 59.127 50.000 0.00 0.00 0.00 2.93
510 511 2.503765 TGTGTGAGAGGGTTGAGACAAA 59.496 45.455 0.00 0.00 0.00 2.83
511 512 2.115427 TGTGTGAGAGGGTTGAGACAA 58.885 47.619 0.00 0.00 0.00 3.18
512 513 1.788229 TGTGTGAGAGGGTTGAGACA 58.212 50.000 0.00 0.00 0.00 3.41
513 514 2.548920 CCTTGTGTGAGAGGGTTGAGAC 60.549 54.545 0.00 0.00 0.00 3.36
514 515 1.694150 CCTTGTGTGAGAGGGTTGAGA 59.306 52.381 0.00 0.00 0.00 3.27
515 516 1.879796 GCCTTGTGTGAGAGGGTTGAG 60.880 57.143 0.00 0.00 33.52 3.02
516 517 0.108585 GCCTTGTGTGAGAGGGTTGA 59.891 55.000 0.00 0.00 33.52 3.18
517 518 1.230635 CGCCTTGTGTGAGAGGGTTG 61.231 60.000 0.00 0.00 33.52 3.77
518 519 1.071471 CGCCTTGTGTGAGAGGGTT 59.929 57.895 0.00 0.00 33.52 4.11
519 520 1.696097 AACGCCTTGTGTGAGAGGGT 61.696 55.000 0.00 0.00 33.52 4.34
520 521 1.071471 AACGCCTTGTGTGAGAGGG 59.929 57.895 0.00 0.00 33.52 4.30
521 522 0.532862 ACAACGCCTTGTGTGAGAGG 60.533 55.000 0.00 0.00 39.28 3.69
522 523 2.992089 ACAACGCCTTGTGTGAGAG 58.008 52.632 0.00 0.00 39.28 3.20
529 530 0.884704 CTAGTGCCACAACGCCTTGT 60.885 55.000 0.00 0.00 41.61 3.16
547 548 3.511934 CAGGAGTAGGAACTAGCACAACT 59.488 47.826 0.00 0.00 44.14 3.16
564 565 9.657419 ATTTAAAGGATTTGTAAAATGCAGGAG 57.343 29.630 6.93 0.00 39.63 3.69
636 637 3.796844 GCTTTGCAGAAACTCAAAGGGAC 60.797 47.826 14.17 0.00 45.49 4.46
657 658 3.243301 CCATCTCATGCCAAGTTGTATGC 60.243 47.826 1.45 0.00 0.00 3.14
698 699 9.023962 TCACTTTATTATTTGCTGAGACCAATT 57.976 29.630 0.00 0.00 0.00 2.32
777 779 2.746277 ATTTGGGCACGCGAGGTC 60.746 61.111 15.93 5.72 0.00 3.85
798 800 0.619255 TGGGAAGTCGGGGCAATCTA 60.619 55.000 0.00 0.00 0.00 1.98
869 871 1.290324 GCGAAGTGGACAGAGCTGA 59.710 57.895 4.21 0.00 0.00 4.26
912 914 0.754957 AGCTAGCTCGTGATCTGCCT 60.755 55.000 12.68 0.00 0.00 4.75
913 915 0.955178 TAGCTAGCTCGTGATCTGCC 59.045 55.000 23.26 0.00 0.00 4.85
936 938 1.953559 CTTAGCTATTTCCTGCGCCA 58.046 50.000 4.18 0.00 0.00 5.69
937 939 0.588737 GCTTAGCTATTTCCTGCGCC 59.411 55.000 4.18 0.00 0.00 6.53
1010 1012 0.247736 GTTCTCCTCGTCCTGCACAT 59.752 55.000 0.00 0.00 0.00 3.21
1218 1220 3.089874 CCTCCGAGCCCCATGGAA 61.090 66.667 15.22 0.00 0.00 3.53
1273 1275 6.423905 ACGACATTAATCGGAGGAAACATATG 59.576 38.462 0.00 0.00 46.56 1.78
1350 1352 3.064987 GCATCCAGCAAGCCAGCAG 62.065 63.158 0.55 0.00 44.79 4.24
1381 1383 4.713321 AGCCTTTGCATACAAATCCAGATT 59.287 37.500 0.00 0.00 44.54 2.40
1382 1384 4.284178 AGCCTTTGCATACAAATCCAGAT 58.716 39.130 0.00 0.00 44.54 2.90
1420 1422 4.159244 AGCTACTCTCACTAATCTCCGT 57.841 45.455 0.00 0.00 0.00 4.69
1527 1529 4.391830 TGGTACTCATCAGAAAACATTCGC 59.608 41.667 0.00 0.00 0.00 4.70
1564 1567 5.479375 CAGGAAGGTACTAACACTGTAGGAA 59.521 44.000 0.00 0.00 38.49 3.36
1605 1609 6.471233 CAGACTCTGGACTATAAATGACCA 57.529 41.667 0.00 0.00 0.00 4.02
1744 1748 2.914059 AGTACTGTGCGTGGAACTTTT 58.086 42.857 0.00 0.00 31.75 2.27
1745 1749 2.612212 CAAGTACTGTGCGTGGAACTTT 59.388 45.455 0.00 0.00 31.75 2.66
1757 1771 1.267121 AGATCGGGCACAAGTACTGT 58.733 50.000 0.00 0.00 39.56 3.55
1759 1773 2.699954 CAAAGATCGGGCACAAGTACT 58.300 47.619 0.00 0.00 0.00 2.73
1788 1802 0.947244 GCACTAGCCGCTGCATTTAT 59.053 50.000 2.16 0.00 41.13 1.40
1823 1837 2.799126 TTAAATCCAGCCGGACATGT 57.201 45.000 5.05 0.00 46.79 3.21
1867 1881 6.769341 GGGGTCTCACTTACAGTCTTTTTAAA 59.231 38.462 0.00 0.00 0.00 1.52
1888 1907 8.802057 TGTTATACCAACTATATTGTAGGGGT 57.198 34.615 10.94 11.01 33.18 4.95
1894 1913 9.930158 ATGGGTTTGTTATACCAACTATATTGT 57.070 29.630 0.00 0.00 37.40 2.71
1897 1916 9.569122 GTGATGGGTTTGTTATACCAACTATAT 57.431 33.333 0.00 0.00 37.40 0.86
1898 1917 7.711772 CGTGATGGGTTTGTTATACCAACTATA 59.288 37.037 0.00 0.00 37.40 1.31
1899 1918 6.540914 CGTGATGGGTTTGTTATACCAACTAT 59.459 38.462 0.00 0.00 37.40 2.12
1908 1927 3.009253 TGGTACCGTGATGGGTTTGTTAT 59.991 43.478 7.57 0.00 44.64 1.89
1920 1939 3.513912 AGATTCAAGACATGGTACCGTGA 59.486 43.478 35.58 16.06 36.80 4.35
1921 1940 3.861840 AGATTCAAGACATGGTACCGTG 58.138 45.455 29.02 29.02 38.78 4.94
1922 1941 5.187186 ACTTAGATTCAAGACATGGTACCGT 59.813 40.000 7.57 3.49 0.00 4.83
1923 1942 5.661458 ACTTAGATTCAAGACATGGTACCG 58.339 41.667 7.57 0.00 0.00 4.02
1933 1955 5.425539 CCTTCCCACCTACTTAGATTCAAGA 59.574 44.000 0.00 0.00 0.00 3.02
1943 1965 1.133809 TGCTGCCTTCCCACCTACTT 61.134 55.000 0.00 0.00 0.00 2.24
1980 2002 0.584785 CGATTCGCAGACGCACAATG 60.585 55.000 0.00 0.00 39.84 2.82
1981 2003 1.014044 ACGATTCGCAGACGCACAAT 61.014 50.000 5.86 0.00 39.84 2.71
1999 2025 1.923204 TGCACACGACAAAATTTGCAC 59.077 42.857 5.52 0.00 35.13 4.57
2125 2216 6.482973 ACATCAACGAAAAATTGGCAATTCTT 59.517 30.769 24.51 18.00 0.00 2.52
2126 2217 5.990996 ACATCAACGAAAAATTGGCAATTCT 59.009 32.000 24.51 15.25 0.00 2.40
2127 2218 6.226988 ACATCAACGAAAAATTGGCAATTC 57.773 33.333 24.51 13.15 0.00 2.17
2128 2219 7.903995 ATACATCAACGAAAAATTGGCAATT 57.096 28.000 19.39 19.39 0.00 2.32
2227 2318 3.726607 CTTGTAATTGCAAAACAGGGCA 58.273 40.909 15.51 4.27 38.46 5.36
2228 2319 2.480037 GCTTGTAATTGCAAAACAGGGC 59.520 45.455 21.23 20.09 0.00 5.19
2237 2328 5.063204 AGAACAGTAGTGCTTGTAATTGCA 58.937 37.500 0.00 0.00 36.79 4.08
2256 2452 5.532557 AGTGCTTGCCATTTTCTAAAGAAC 58.467 37.500 0.00 0.00 33.13 3.01
2259 2455 6.681777 AGTTAGTGCTTGCCATTTTCTAAAG 58.318 36.000 0.00 0.00 0.00 1.85
2330 2526 3.327757 TGGGCTGGGCTAAATATAGACAG 59.672 47.826 0.00 0.00 39.10 3.51
2580 2791 7.997773 ACATCTCAGCCGTTAGATACTTATA 57.002 36.000 0.00 0.00 31.25 0.98
2581 2792 6.902771 ACATCTCAGCCGTTAGATACTTAT 57.097 37.500 0.00 0.00 31.25 1.73
2635 2846 3.811083 CCCGTACTCAGAGAGTATGTCT 58.189 50.000 19.45 0.00 45.47 3.41
2895 3107 3.437795 CCGACGACGTAGGCCAGT 61.438 66.667 14.35 0.82 37.88 4.00
3178 3390 7.510549 AGCTTGCTGTACTTATTTTTCTTGA 57.489 32.000 0.00 0.00 0.00 3.02
3207 3419 4.024556 GCACTTCATCATACATACACAGGC 60.025 45.833 0.00 0.00 0.00 4.85
3224 3436 0.798771 CTCGACTACGGCAGCACTTC 60.799 60.000 0.00 0.00 40.21 3.01
3230 3442 0.377554 CTACCACTCGACTACGGCAG 59.622 60.000 0.00 0.00 40.21 4.85
3367 3579 5.245531 ACACCCAAATACACTACTGACATG 58.754 41.667 0.00 0.00 0.00 3.21
3372 3584 6.228258 ACAAGTACACCCAAATACACTACTG 58.772 40.000 0.00 0.00 0.00 2.74
3427 3643 5.965334 CGCAACTTGCCTTACAAATAGTATG 59.035 40.000 8.20 0.00 41.12 2.39
3471 3690 3.067742 CCAGATGATTCAAAGCCCATCAC 59.932 47.826 0.00 0.00 38.22 3.06
3489 3708 1.159285 CGCAAGACTCATTTGCCAGA 58.841 50.000 4.57 0.00 46.20 3.86
3589 3808 7.026562 CGCTATCTCTTACTTCACAGATATGG 58.973 42.308 0.00 0.00 29.49 2.74
3590 3809 7.748683 GTCGCTATCTCTTACTTCACAGATATG 59.251 40.741 0.00 0.00 29.49 1.78
3593 3812 5.277586 CGTCGCTATCTCTTACTTCACAGAT 60.278 44.000 0.00 0.00 0.00 2.90
3613 3835 5.585500 TTTTATTTTGTGAGAGGACGTCG 57.415 39.130 9.92 0.00 0.00 5.12
3649 3872 9.770097 CAAGATAATGTGGTATGTCACTATCTT 57.230 33.333 13.13 13.13 41.07 2.40
3681 3904 3.286751 GTTGGCTGCCTTGTCGCA 61.287 61.111 21.03 0.00 37.19 5.10
3682 3905 2.844451 TTGTTGGCTGCCTTGTCGC 61.844 57.895 21.03 4.25 0.00 5.19
3687 3910 0.106519 ACAGAGTTGTTGGCTGCCTT 60.107 50.000 21.03 0.00 32.28 4.35
3697 3920 3.006940 TGCTTTCACGAAACAGAGTTGT 58.993 40.909 0.00 0.00 39.87 3.32
3711 3934 5.698832 CGATATTTCTTGTGGTTGCTTTCA 58.301 37.500 0.00 0.00 0.00 2.69
3751 3974 4.628074 TCACTCTGGTCTTCCGTTTTTAG 58.372 43.478 0.00 0.00 36.30 1.85
3799 4022 3.622612 GGGGATGTGCATTGTTTTTATGC 59.377 43.478 0.00 0.00 46.63 3.14
3810 4033 2.360138 TTTTTGCGGGGATGTGCAT 58.640 47.368 0.00 0.00 41.42 3.96
3896 4121 8.767085 CAATTGTTTGCTGTGTCAGATATTTTT 58.233 29.630 0.00 0.00 32.44 1.94
3985 4370 1.270358 GGACGGTTATGATCTGAGGCC 60.270 57.143 0.00 0.00 0.00 5.19
4060 4445 6.062095 GCCTAGTAGCCTTTCCATTGAATAA 58.938 40.000 0.00 0.00 0.00 1.40
4065 4450 3.567478 AGCCTAGTAGCCTTTCCATTG 57.433 47.619 0.00 0.00 0.00 2.82
4071 4456 5.722441 AGAAAGTTCTAGCCTAGTAGCCTTT 59.278 40.000 0.00 3.66 35.34 3.11
4097 4482 4.141597 TGAAACCAAGTGTGATACCACTGA 60.142 41.667 0.00 0.00 44.74 3.41


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

AutoCloner maintained by Alex Coulton.