Multiple sequence alignment - TraesCS1B01G209200

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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 TraesCS1B01G209200 chr1B 100.000 2813 0 0 1 2813 378946045 378943233 0.000000e+00 5195.0
1 TraesCS1B01G209200 chr1B 94.821 560 28 1 1 559 665854854 665855413 0.000000e+00 872.0
2 TraesCS1B01G209200 chr1B 93.929 280 17 0 2504 2783 643404178 643403899 9.320000e-115 424.0
3 TraesCS1B01G209200 chr1A 92.804 1473 67 21 710 2170 351476362 351474917 0.000000e+00 2097.0
4 TraesCS1B01G209200 chr1A 92.949 312 17 1 2183 2494 351474863 351474557 1.540000e-122 449.0
5 TraesCS1B01G209200 chr1A 92.308 65 5 0 561 625 351476455 351476391 2.980000e-15 93.5
6 TraesCS1B01G209200 chr1D 92.120 1396 53 17 1059 2428 279235082 279233718 0.000000e+00 1916.0
7 TraesCS1B01G209200 chr1D 90.244 369 12 3 639 1003 279235826 279235478 7.100000e-126 460.0
8 TraesCS1B01G209200 chr1D 100.000 30 0 0 2426 2455 279232104 279232075 3.910000e-04 56.5
9 TraesCS1B01G209200 chr3B 96.250 560 20 1 1 559 559890149 559890708 0.000000e+00 917.0
10 TraesCS1B01G209200 chr3B 93.950 281 15 2 2505 2784 823673572 823673851 9.320000e-115 424.0
11 TraesCS1B01G209200 chr3B 93.594 281 18 0 2503 2783 122720460 122720740 1.200000e-113 420.0
12 TraesCS1B01G209200 chr3B 100.000 34 0 0 2780 2813 433534808 433534775 2.340000e-06 63.9
13 TraesCS1B01G209200 chr6B 95.365 561 24 2 1 559 106516433 106515873 0.000000e+00 891.0
14 TraesCS1B01G209200 chr5B 95.365 561 25 1 1 560 416324642 416324082 0.000000e+00 891.0
15 TraesCS1B01G209200 chr5B 95.000 560 26 2 1 559 401406490 401407048 0.000000e+00 878.0
16 TraesCS1B01G209200 chr5B 94.286 280 16 0 2505 2784 440289072 440289351 2.000000e-116 429.0
17 TraesCS1B01G209200 chr5B 95.939 197 8 0 1308 1504 390549366 390549170 1.260000e-83 320.0
18 TraesCS1B01G209200 chr5B 95.041 121 5 1 1500 1620 390543854 390543735 3.700000e-44 189.0
19 TraesCS1B01G209200 chr5B 77.143 245 42 13 2515 2752 446884876 446884639 2.270000e-26 130.0
20 TraesCS1B01G209200 chr2B 95.179 560 26 1 1 559 704424247 704423688 0.000000e+00 883.0
21 TraesCS1B01G209200 chr2B 94.831 561 28 1 1 560 195533587 195534147 0.000000e+00 874.0
22 TraesCS1B01G209200 chr2B 93.993 283 17 0 2503 2785 177180596 177180878 2.000000e-116 429.0
23 TraesCS1B01G209200 chr2B 93.929 280 17 0 2504 2783 565883625 565883904 9.320000e-115 424.0
24 TraesCS1B01G209200 chr2B 96.512 86 2 1 1474 1559 90442542 90442626 1.050000e-29 141.0
25 TraesCS1B01G209200 chr4B 95.000 560 27 1 1 559 611400128 611399569 0.000000e+00 878.0
26 TraesCS1B01G209200 chr4B 94.286 560 31 1 1 559 576470620 576470061 0.000000e+00 856.0
27 TraesCS1B01G209200 chr4B 93.950 281 17 0 2507 2787 670246924 670246644 2.590000e-115 425.0
28 TraesCS1B01G209200 chr4B 93.617 282 18 0 2503 2784 90460789 90460508 3.350000e-114 422.0
29 TraesCS1B01G209200 chr7B 94.265 279 16 0 2503 2781 196656784 196657062 7.200000e-116 427.0
30 TraesCS1B01G209200 chr7B 100.000 34 0 0 2780 2813 241112813 241112780 2.340000e-06 63.9
31 TraesCS1B01G209200 chr5D 100.000 35 0 0 2779 2813 104119038 104119004 6.500000e-07 65.8
32 TraesCS1B01G209200 chrUn 100.000 34 0 0 2780 2813 8618974 8618941 2.340000e-06 63.9
33 TraesCS1B01G209200 chrUn 100.000 34 0 0 2780 2813 13888297 13888330 2.340000e-06 63.9
34 TraesCS1B01G209200 chrUn 100.000 34 0 0 2780 2813 267218675 267218642 2.340000e-06 63.9


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 TraesCS1B01G209200 chr1B 378943233 378946045 2812 True 5195.000000 5195 100.000000 1 2813 1 chr1B.!!$R1 2812
1 TraesCS1B01G209200 chr1B 665854854 665855413 559 False 872.000000 872 94.821000 1 559 1 chr1B.!!$F1 558
2 TraesCS1B01G209200 chr1A 351474557 351476455 1898 True 879.833333 2097 92.687000 561 2494 3 chr1A.!!$R1 1933
3 TraesCS1B01G209200 chr1D 279232075 279235826 3751 True 810.833333 1916 94.121333 639 2455 3 chr1D.!!$R1 1816
4 TraesCS1B01G209200 chr3B 559890149 559890708 559 False 917.000000 917 96.250000 1 559 1 chr3B.!!$F2 558
5 TraesCS1B01G209200 chr6B 106515873 106516433 560 True 891.000000 891 95.365000 1 559 1 chr6B.!!$R1 558
6 TraesCS1B01G209200 chr5B 416324082 416324642 560 True 891.000000 891 95.365000 1 560 1 chr5B.!!$R3 559
7 TraesCS1B01G209200 chr5B 401406490 401407048 558 False 878.000000 878 95.000000 1 559 1 chr5B.!!$F1 558
8 TraesCS1B01G209200 chr2B 704423688 704424247 559 True 883.000000 883 95.179000 1 559 1 chr2B.!!$R1 558
9 TraesCS1B01G209200 chr2B 195533587 195534147 560 False 874.000000 874 94.831000 1 560 1 chr2B.!!$F3 559
10 TraesCS1B01G209200 chr4B 611399569 611400128 559 True 878.000000 878 95.000000 1 559 1 chr4B.!!$R3 558
11 TraesCS1B01G209200 chr4B 576470061 576470620 559 True 856.000000 856 94.286000 1 559 1 chr4B.!!$R2 558

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
617 620 0.030235 GTGGCTGTGAAACCGAAACC 59.97 55.0 0.0 0.0 34.36 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2488 4534 0.175989 CTAAGTTCCTCCGACCAGCC 59.824 60.0 0.0 0.0 0.0 4.85 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
268 269 3.556423 GCTTCCCACTTAAAGAAGGACGA 60.556 47.826 0.00 0.00 37.95 4.20
403 404 2.031919 TTTGCTGTCCGCCACGAT 59.968 55.556 0.00 0.00 38.05 3.73
510 511 2.095919 CGCCTTCTTTGTCCCTTTTACG 60.096 50.000 0.00 0.00 0.00 3.18
512 513 2.882137 CCTTCTTTGTCCCTTTTACGCA 59.118 45.455 0.00 0.00 0.00 5.24
515 516 5.508994 CCTTCTTTGTCCCTTTTACGCAAAT 60.509 40.000 0.00 0.00 0.00 2.32
525 528 0.402504 TTACGCAAATGGACTGGGGT 59.597 50.000 0.00 0.00 0.00 4.95
603 606 2.588877 GTGTGTGCGAGTGTGGCT 60.589 61.111 0.00 0.00 0.00 4.75
612 615 1.831389 CGAGTGTGGCTGTGAAACCG 61.831 60.000 0.00 0.00 34.36 4.44
613 616 0.531974 GAGTGTGGCTGTGAAACCGA 60.532 55.000 0.00 0.00 34.36 4.69
614 617 0.107410 AGTGTGGCTGTGAAACCGAA 60.107 50.000 0.00 0.00 34.36 4.30
615 618 0.736053 GTGTGGCTGTGAAACCGAAA 59.264 50.000 0.00 0.00 34.36 3.46
616 619 0.736053 TGTGGCTGTGAAACCGAAAC 59.264 50.000 0.00 0.00 34.36 2.78
617 620 0.030235 GTGGCTGTGAAACCGAAACC 59.970 55.000 0.00 0.00 34.36 3.27
618 621 0.394488 TGGCTGTGAAACCGAAACCA 60.394 50.000 0.00 0.00 34.36 3.67
619 622 0.310854 GGCTGTGAAACCGAAACCAG 59.689 55.000 0.00 0.00 34.36 4.00
620 623 0.317854 GCTGTGAAACCGAAACCAGC 60.318 55.000 0.00 0.00 38.58 4.85
621 624 1.021202 CTGTGAAACCGAAACCAGCA 58.979 50.000 0.00 0.00 34.36 4.41
622 625 1.002468 CTGTGAAACCGAAACCAGCAG 60.002 52.381 0.00 0.00 34.36 4.24
623 626 0.317854 GTGAAACCGAAACCAGCAGC 60.318 55.000 0.00 0.00 0.00 5.25
624 627 1.285950 GAAACCGAAACCAGCAGCC 59.714 57.895 0.00 0.00 0.00 4.85
625 628 1.452145 GAAACCGAAACCAGCAGCCA 61.452 55.000 0.00 0.00 0.00 4.75
626 629 0.827507 AAACCGAAACCAGCAGCCAT 60.828 50.000 0.00 0.00 0.00 4.40
627 630 1.244019 AACCGAAACCAGCAGCCATC 61.244 55.000 0.00 0.00 0.00 3.51
628 631 2.409870 CCGAAACCAGCAGCCATCC 61.410 63.158 0.00 0.00 0.00 3.51
629 632 1.377725 CGAAACCAGCAGCCATCCT 60.378 57.895 0.00 0.00 0.00 3.24
630 633 1.372087 CGAAACCAGCAGCCATCCTC 61.372 60.000 0.00 0.00 0.00 3.71
631 634 0.322816 GAAACCAGCAGCCATCCTCA 60.323 55.000 0.00 0.00 0.00 3.86
632 635 0.112995 AAACCAGCAGCCATCCTCAA 59.887 50.000 0.00 0.00 0.00 3.02
633 636 0.112995 AACCAGCAGCCATCCTCAAA 59.887 50.000 0.00 0.00 0.00 2.69
634 637 0.112995 ACCAGCAGCCATCCTCAAAA 59.887 50.000 0.00 0.00 0.00 2.44
635 638 1.259609 CCAGCAGCCATCCTCAAAAA 58.740 50.000 0.00 0.00 0.00 1.94
700 713 3.803082 GCACACGCATGCACCGAT 61.803 61.111 19.57 0.00 45.39 4.18
701 714 2.400798 CACACGCATGCACCGATC 59.599 61.111 19.57 0.00 0.00 3.69
702 715 3.188100 ACACGCATGCACCGATCG 61.188 61.111 19.57 8.51 0.00 3.69
703 716 2.885164 CACGCATGCACCGATCGA 60.885 61.111 18.66 0.00 0.00 3.59
704 717 2.885644 ACGCATGCACCGATCGAC 60.886 61.111 18.66 6.23 0.00 4.20
705 718 3.630148 CGCATGCACCGATCGACC 61.630 66.667 18.66 4.66 0.00 4.79
706 719 3.272334 GCATGCACCGATCGACCC 61.272 66.667 18.66 4.28 0.00 4.46
707 720 2.588877 CATGCACCGATCGACCCC 60.589 66.667 18.66 2.37 0.00 4.95
708 721 3.861797 ATGCACCGATCGACCCCC 61.862 66.667 18.66 0.50 0.00 5.40
829 842 2.651361 CTCCGACCTTCACGTGCT 59.349 61.111 11.67 0.00 0.00 4.40
1554 1917 4.404691 GCCAACCAGGACAAGGAG 57.595 61.111 0.00 0.00 41.22 3.69
1645 2008 4.551056 TCGTTCGCGACTATTTTGTTAC 57.449 40.909 9.15 0.00 45.62 2.50
1646 2009 4.229096 TCGTTCGCGACTATTTTGTTACT 58.771 39.130 9.15 0.00 45.62 2.24
1648 2011 4.552992 GTTCGCGACTATTTTGTTACTCG 58.447 43.478 9.15 0.00 0.00 4.18
1649 2012 3.825308 TCGCGACTATTTTGTTACTCGT 58.175 40.909 3.71 0.00 0.00 4.18
1650 2013 4.968626 TCGCGACTATTTTGTTACTCGTA 58.031 39.130 3.71 0.00 0.00 3.43
1662 2044 6.375945 TTGTTACTCGTACTTGACTGTGTA 57.624 37.500 0.00 0.00 0.00 2.90
1838 2223 1.215382 CGTTGATCTGGAGTGGCGA 59.785 57.895 0.00 0.00 0.00 5.54
1936 2321 0.744414 CATCCTCGGCCGTGTGAATT 60.744 55.000 27.15 5.60 0.00 2.17
1937 2322 0.462047 ATCCTCGGCCGTGTGAATTC 60.462 55.000 27.15 0.00 0.00 2.17
1938 2323 1.079127 CCTCGGCCGTGTGAATTCT 60.079 57.895 27.15 0.00 0.00 2.40
1939 2324 1.361668 CCTCGGCCGTGTGAATTCTG 61.362 60.000 27.15 3.09 0.00 3.02
1940 2325 0.389817 CTCGGCCGTGTGAATTCTGA 60.390 55.000 27.15 0.00 0.00 3.27
1941 2326 0.034198 TCGGCCGTGTGAATTCTGAA 59.966 50.000 27.15 0.00 0.00 3.02
1942 2327 1.086696 CGGCCGTGTGAATTCTGAAT 58.913 50.000 19.50 0.00 0.00 2.57
1972 2357 4.224594 GCTGATCAATCCAGGGATAGATCA 59.775 45.833 0.32 7.82 39.42 2.92
1983 2368 2.487934 GGATAGATCAACGCTGCATGT 58.512 47.619 0.00 0.00 0.00 3.21
1991 2376 2.103538 CGCTGCATGTCATTGCCC 59.896 61.111 0.00 0.00 42.06 5.36
1994 2379 3.420214 CTGCATGTCATTGCCCGCC 62.420 63.158 0.00 0.00 42.06 6.13
2013 2398 2.290577 GCCACAAGTTGAGGAAGGAGAT 60.291 50.000 21.95 0.00 28.90 2.75
2065 2450 5.050091 CACCTGAGGCGTCAATCAATAATAC 60.050 44.000 10.76 0.00 30.14 1.89
2067 2452 5.406780 CCTGAGGCGTCAATCAATAATACTC 59.593 44.000 10.76 0.00 30.14 2.59
2068 2453 5.297547 TGAGGCGTCAATCAATAATACTCC 58.702 41.667 6.64 0.00 0.00 3.85
2069 2454 5.070446 TGAGGCGTCAATCAATAATACTCCT 59.930 40.000 6.64 0.00 0.00 3.69
2070 2455 6.266786 TGAGGCGTCAATCAATAATACTCCTA 59.733 38.462 6.64 0.00 0.00 2.94
2071 2456 6.456501 AGGCGTCAATCAATAATACTCCTAC 58.543 40.000 0.00 0.00 0.00 3.18
2075 2460 7.541437 GCGTCAATCAATAATACTCCTACCTAC 59.459 40.741 0.00 0.00 0.00 3.18
2076 2461 8.794553 CGTCAATCAATAATACTCCTACCTACT 58.205 37.037 0.00 0.00 0.00 2.57
2081 2466 8.632906 TCAATAATACTCCTACCTACTACTGC 57.367 38.462 0.00 0.00 0.00 4.40
2082 2467 8.446394 TCAATAATACTCCTACCTACTACTGCT 58.554 37.037 0.00 0.00 0.00 4.24
2125 2510 4.095932 TGTTGCTACTCTATCGACAATCGT 59.904 41.667 0.00 0.00 41.35 3.73
2132 2517 2.943033 TCTATCGACAATCGTCTGCTGA 59.057 45.455 0.00 0.00 41.35 4.26
2137 2522 3.128764 TCGACAATCGTCTGCTGATACTT 59.871 43.478 0.00 0.00 41.35 2.24
2138 2523 4.334481 TCGACAATCGTCTGCTGATACTTA 59.666 41.667 0.00 0.00 41.35 2.24
2139 2524 4.438145 CGACAATCGTCTGCTGATACTTAC 59.562 45.833 0.00 0.00 40.23 2.34
2214 2640 2.293677 GAGCTTGCTATCCGCTGTACTA 59.706 50.000 0.00 0.00 40.11 1.82
2268 2697 7.701539 TTTCCTTGATGTGTAATTACATGCT 57.298 32.000 20.72 9.03 41.15 3.79
2369 2799 9.715121 AATCTGTGCAATATCTTCAAACAAAAT 57.285 25.926 0.00 0.00 0.00 1.82
2371 2801 9.844790 TCTGTGCAATATCTTCAAACAAAATAG 57.155 29.630 0.00 0.00 0.00 1.73
2372 2802 9.844790 CTGTGCAATATCTTCAAACAAAATAGA 57.155 29.630 0.00 0.00 0.00 1.98
2373 2803 9.844790 TGTGCAATATCTTCAAACAAAATAGAG 57.155 29.630 0.00 0.00 0.00 2.43
2408 2838 2.277591 TGGAGCCATTTGCACAGCC 61.278 57.895 0.00 0.00 44.83 4.85
2489 4535 3.416119 CTGTCAAGCATGCATGTTAGG 57.584 47.619 26.79 16.76 0.00 2.69
2494 4540 0.033796 AGCATGCATGTTAGGCTGGT 60.034 50.000 26.79 3.43 33.43 4.00
2495 4541 0.383231 GCATGCATGTTAGGCTGGTC 59.617 55.000 26.79 3.32 0.00 4.02
2496 4542 0.659427 CATGCATGTTAGGCTGGTCG 59.341 55.000 18.91 0.00 0.00 4.79
2497 4543 0.464373 ATGCATGTTAGGCTGGTCGG 60.464 55.000 0.00 0.00 0.00 4.79
2498 4544 1.220749 GCATGTTAGGCTGGTCGGA 59.779 57.895 0.00 0.00 0.00 4.55
2499 4545 0.811616 GCATGTTAGGCTGGTCGGAG 60.812 60.000 0.00 0.00 0.00 4.63
2500 4546 0.179073 CATGTTAGGCTGGTCGGAGG 60.179 60.000 0.00 0.00 0.00 4.30
2501 4547 0.325296 ATGTTAGGCTGGTCGGAGGA 60.325 55.000 0.00 0.00 0.00 3.71
2502 4548 0.543410 TGTTAGGCTGGTCGGAGGAA 60.543 55.000 0.00 0.00 0.00 3.36
2503 4549 0.108281 GTTAGGCTGGTCGGAGGAAC 60.108 60.000 0.00 0.00 0.00 3.62
2505 4551 0.252103 TAGGCTGGTCGGAGGAACTT 60.252 55.000 0.00 0.00 41.55 2.66
2506 4552 0.252103 AGGCTGGTCGGAGGAACTTA 60.252 55.000 0.00 0.00 41.55 2.24
2507 4553 0.175989 GGCTGGTCGGAGGAACTTAG 59.824 60.000 0.00 0.00 41.55 2.18
2508 4554 1.183549 GCTGGTCGGAGGAACTTAGA 58.816 55.000 0.00 0.00 41.55 2.10
2509 4555 1.135053 GCTGGTCGGAGGAACTTAGAC 60.135 57.143 0.00 0.00 41.55 2.59
2510 4556 2.448453 CTGGTCGGAGGAACTTAGACT 58.552 52.381 0.00 0.00 41.55 3.24
2511 4557 3.618351 CTGGTCGGAGGAACTTAGACTA 58.382 50.000 0.00 0.00 41.55 2.59
2512 4558 3.618351 TGGTCGGAGGAACTTAGACTAG 58.382 50.000 0.00 0.00 41.55 2.57
2513 4559 2.358582 GGTCGGAGGAACTTAGACTAGC 59.641 54.545 0.00 0.00 41.55 3.42
2514 4560 2.358582 GTCGGAGGAACTTAGACTAGCC 59.641 54.545 0.00 0.00 41.55 3.93
2515 4561 2.025605 TCGGAGGAACTTAGACTAGCCA 60.026 50.000 0.00 0.00 41.55 4.75
2516 4562 2.099427 CGGAGGAACTTAGACTAGCCAC 59.901 54.545 0.00 0.00 41.55 5.01
2517 4563 3.097614 GGAGGAACTTAGACTAGCCACA 58.902 50.000 0.00 0.00 41.55 4.17
2518 4564 3.514309 GGAGGAACTTAGACTAGCCACAA 59.486 47.826 0.00 0.00 41.55 3.33
2519 4565 4.162509 GGAGGAACTTAGACTAGCCACAAT 59.837 45.833 0.00 0.00 41.55 2.71
2520 4566 5.091261 AGGAACTTAGACTAGCCACAATG 57.909 43.478 0.00 0.00 27.25 2.82
2521 4567 4.080863 AGGAACTTAGACTAGCCACAATGG 60.081 45.833 0.00 0.00 35.99 3.16
2522 4568 4.081087 GGAACTTAGACTAGCCACAATGGA 60.081 45.833 0.00 0.00 40.96 3.41
2523 4569 5.488341 GAACTTAGACTAGCCACAATGGAA 58.512 41.667 0.00 0.00 40.96 3.53
2524 4570 5.091261 ACTTAGACTAGCCACAATGGAAG 57.909 43.478 0.00 0.00 40.96 3.46
2525 4571 4.532521 ACTTAGACTAGCCACAATGGAAGT 59.467 41.667 0.00 1.09 40.96 3.01
2526 4572 5.720041 ACTTAGACTAGCCACAATGGAAGTA 59.280 40.000 0.00 0.00 40.96 2.24
2527 4573 6.212791 ACTTAGACTAGCCACAATGGAAGTAA 59.787 38.462 0.00 0.00 40.96 2.24
2528 4574 4.833390 AGACTAGCCACAATGGAAGTAAC 58.167 43.478 0.00 0.00 40.96 2.50
2529 4575 4.532521 AGACTAGCCACAATGGAAGTAACT 59.467 41.667 0.00 0.00 40.96 2.24
2530 4576 5.013183 AGACTAGCCACAATGGAAGTAACTT 59.987 40.000 0.00 0.00 40.96 2.66
2531 4577 5.246307 ACTAGCCACAATGGAAGTAACTTC 58.754 41.667 0.00 0.00 40.96 3.01
2532 4578 3.074412 AGCCACAATGGAAGTAACTTCG 58.926 45.455 0.00 0.00 40.96 3.79
2533 4579 2.161609 GCCACAATGGAAGTAACTTCGG 59.838 50.000 0.00 0.00 40.96 4.30
2534 4580 3.408634 CCACAATGGAAGTAACTTCGGT 58.591 45.455 0.00 0.00 40.96 4.69
2535 4581 4.571919 CCACAATGGAAGTAACTTCGGTA 58.428 43.478 0.00 0.00 40.96 4.02
2536 4582 4.630069 CCACAATGGAAGTAACTTCGGTAG 59.370 45.833 0.00 0.00 40.96 3.18
2537 4583 5.235516 CACAATGGAAGTAACTTCGGTAGT 58.764 41.667 0.00 0.00 40.99 2.73
2538 4584 6.392354 CACAATGGAAGTAACTTCGGTAGTA 58.608 40.000 0.00 0.00 40.99 1.82
2539 4585 6.869913 CACAATGGAAGTAACTTCGGTAGTAA 59.130 38.462 0.00 0.00 40.99 2.24
2540 4586 6.870439 ACAATGGAAGTAACTTCGGTAGTAAC 59.130 38.462 0.00 0.00 40.99 2.50
2541 4587 6.594788 ATGGAAGTAACTTCGGTAGTAACA 57.405 37.500 0.00 0.00 40.99 2.41
2542 4588 6.594788 TGGAAGTAACTTCGGTAGTAACAT 57.405 37.500 0.00 0.00 40.99 2.71
2543 4589 6.624423 TGGAAGTAACTTCGGTAGTAACATC 58.376 40.000 0.00 0.00 40.99 3.06
2544 4590 5.741040 GGAAGTAACTTCGGTAGTAACATCG 59.259 44.000 0.00 0.00 40.99 3.84
2545 4591 6.403636 GGAAGTAACTTCGGTAGTAACATCGA 60.404 42.308 0.00 0.00 40.99 3.59
2546 4592 6.116680 AGTAACTTCGGTAGTAACATCGAG 57.883 41.667 0.00 0.00 35.54 4.04
2547 4593 5.645497 AGTAACTTCGGTAGTAACATCGAGT 59.355 40.000 0.00 0.00 35.54 4.18
2548 4594 4.612932 ACTTCGGTAGTAACATCGAGTC 57.387 45.455 0.00 0.00 34.56 3.36
2549 4595 3.376546 ACTTCGGTAGTAACATCGAGTCC 59.623 47.826 0.00 0.00 34.56 3.85
2550 4596 2.989909 TCGGTAGTAACATCGAGTCCA 58.010 47.619 0.00 0.00 0.00 4.02
2551 4597 3.346315 TCGGTAGTAACATCGAGTCCAA 58.654 45.455 0.00 0.00 0.00 3.53
2552 4598 3.127548 TCGGTAGTAACATCGAGTCCAAC 59.872 47.826 0.00 0.00 0.00 3.77
2553 4599 3.128242 CGGTAGTAACATCGAGTCCAACT 59.872 47.826 0.00 0.00 0.00 3.16
2554 4600 4.670347 GGTAGTAACATCGAGTCCAACTC 58.330 47.826 0.00 0.00 41.71 3.01
2555 4601 4.157289 GGTAGTAACATCGAGTCCAACTCA 59.843 45.833 7.78 0.00 45.30 3.41
2556 4602 4.442375 AGTAACATCGAGTCCAACTCAG 57.558 45.455 7.78 1.37 45.30 3.35
2557 4603 2.086054 AACATCGAGTCCAACTCAGC 57.914 50.000 7.78 0.00 45.30 4.26
2558 4604 0.969149 ACATCGAGTCCAACTCAGCA 59.031 50.000 7.78 0.00 45.30 4.41
2559 4605 1.344438 ACATCGAGTCCAACTCAGCAA 59.656 47.619 7.78 0.00 45.30 3.91
2560 4606 2.224281 ACATCGAGTCCAACTCAGCAAA 60.224 45.455 7.78 0.00 45.30 3.68
2561 4607 2.839486 TCGAGTCCAACTCAGCAAAT 57.161 45.000 7.78 0.00 45.30 2.32
2562 4608 3.126001 TCGAGTCCAACTCAGCAAATT 57.874 42.857 7.78 0.00 45.30 1.82
2563 4609 3.476552 TCGAGTCCAACTCAGCAAATTT 58.523 40.909 7.78 0.00 45.30 1.82
2564 4610 3.250762 TCGAGTCCAACTCAGCAAATTTG 59.749 43.478 14.03 14.03 45.30 2.32
2565 4611 3.311966 GAGTCCAACTCAGCAAATTTGC 58.688 45.455 31.36 31.36 44.45 3.68
2580 4626 6.102006 CAAATTTGCTTATGTGGCAATGAG 57.898 37.500 5.01 0.00 46.81 2.90
2581 4627 5.410355 AATTTGCTTATGTGGCAATGAGT 57.590 34.783 2.01 0.00 46.81 3.41
2582 4628 4.870123 TTTGCTTATGTGGCAATGAGTT 57.130 36.364 2.01 0.00 46.81 3.01
2583 4629 5.973899 TTTGCTTATGTGGCAATGAGTTA 57.026 34.783 2.01 0.00 46.81 2.24
2584 4630 5.973899 TTGCTTATGTGGCAATGAGTTAA 57.026 34.783 0.00 0.00 43.50 2.01
2585 4631 6.528537 TTGCTTATGTGGCAATGAGTTAAT 57.471 33.333 0.00 0.00 43.50 1.40
2586 4632 5.893687 TGCTTATGTGGCAATGAGTTAATG 58.106 37.500 0.00 0.00 36.71 1.90
2587 4633 5.651576 TGCTTATGTGGCAATGAGTTAATGA 59.348 36.000 0.00 0.00 36.71 2.57
2588 4634 6.152492 TGCTTATGTGGCAATGAGTTAATGAA 59.848 34.615 0.00 0.00 36.71 2.57
2589 4635 6.694411 GCTTATGTGGCAATGAGTTAATGAAG 59.306 38.462 0.00 0.00 0.00 3.02
2590 4636 7.415541 GCTTATGTGGCAATGAGTTAATGAAGA 60.416 37.037 0.00 0.00 0.00 2.87
2591 4637 5.885230 TGTGGCAATGAGTTAATGAAGAG 57.115 39.130 0.00 0.00 0.00 2.85
2592 4638 5.559770 TGTGGCAATGAGTTAATGAAGAGA 58.440 37.500 0.00 0.00 0.00 3.10
2593 4639 5.645067 TGTGGCAATGAGTTAATGAAGAGAG 59.355 40.000 0.00 0.00 0.00 3.20
2594 4640 5.877012 GTGGCAATGAGTTAATGAAGAGAGA 59.123 40.000 0.00 0.00 0.00 3.10
2595 4641 6.541641 GTGGCAATGAGTTAATGAAGAGAGAT 59.458 38.462 0.00 0.00 0.00 2.75
2596 4642 6.541278 TGGCAATGAGTTAATGAAGAGAGATG 59.459 38.462 0.00 0.00 0.00 2.90
2597 4643 6.541641 GGCAATGAGTTAATGAAGAGAGATGT 59.458 38.462 0.00 0.00 0.00 3.06
2598 4644 7.712639 GGCAATGAGTTAATGAAGAGAGATGTA 59.287 37.037 0.00 0.00 0.00 2.29
2599 4645 8.763356 GCAATGAGTTAATGAAGAGAGATGTAG 58.237 37.037 0.00 0.00 0.00 2.74
2600 4646 9.814899 CAATGAGTTAATGAAGAGAGATGTAGT 57.185 33.333 0.00 0.00 0.00 2.73
2603 4649 9.688091 TGAGTTAATGAAGAGAGATGTAGTACT 57.312 33.333 0.00 0.00 0.00 2.73
2614 4660 9.768662 AGAGAGATGTAGTACTAGTAACTTAGC 57.231 37.037 3.61 0.00 0.00 3.09
2615 4661 9.768662 GAGAGATGTAGTACTAGTAACTTAGCT 57.231 37.037 3.61 0.33 0.00 3.32
2633 4679 9.938280 AACTTAGCTAGTTAATGTAACATCACA 57.062 29.630 0.00 0.00 45.22 3.58
2637 4683 8.425577 AGCTAGTTAATGTAACATCACATGTC 57.574 34.615 0.00 0.00 44.07 3.06
2638 4684 7.495934 AGCTAGTTAATGTAACATCACATGTCC 59.504 37.037 0.00 0.00 44.07 4.02
2639 4685 7.254795 GCTAGTTAATGTAACATCACATGTCCC 60.255 40.741 0.00 0.00 44.07 4.46
2640 4686 6.480763 AGTTAATGTAACATCACATGTCCCA 58.519 36.000 0.00 0.00 44.07 4.37
2641 4687 6.945435 AGTTAATGTAACATCACATGTCCCAA 59.055 34.615 0.00 0.00 44.07 4.12
2642 4688 7.615365 AGTTAATGTAACATCACATGTCCCAAT 59.385 33.333 0.00 0.00 44.07 3.16
2643 4689 5.840243 ATGTAACATCACATGTCCCAATG 57.160 39.130 0.00 0.45 44.07 2.82
2644 4690 3.443329 TGTAACATCACATGTCCCAATGC 59.557 43.478 0.00 0.00 44.07 3.56
2645 4691 2.219080 ACATCACATGTCCCAATGCA 57.781 45.000 0.00 0.00 39.92 3.96
2646 4692 2.527497 ACATCACATGTCCCAATGCAA 58.473 42.857 0.00 0.00 39.92 4.08
2647 4693 3.101437 ACATCACATGTCCCAATGCAAT 58.899 40.909 0.00 0.00 39.92 3.56
2648 4694 4.279982 ACATCACATGTCCCAATGCAATA 58.720 39.130 0.00 0.00 39.92 1.90
2649 4695 4.897076 ACATCACATGTCCCAATGCAATAT 59.103 37.500 0.00 0.00 39.92 1.28
2650 4696 4.922471 TCACATGTCCCAATGCAATATG 57.078 40.909 0.00 0.00 0.00 1.78
2651 4697 4.534797 TCACATGTCCCAATGCAATATGA 58.465 39.130 0.00 0.00 0.00 2.15
2652 4698 4.581409 TCACATGTCCCAATGCAATATGAG 59.419 41.667 0.00 0.00 0.00 2.90
2653 4699 4.340097 CACATGTCCCAATGCAATATGAGT 59.660 41.667 0.00 0.00 0.00 3.41
2654 4700 4.581824 ACATGTCCCAATGCAATATGAGTC 59.418 41.667 0.00 0.00 0.00 3.36
2655 4701 4.508551 TGTCCCAATGCAATATGAGTCT 57.491 40.909 0.00 0.00 0.00 3.24
2656 4702 5.628797 TGTCCCAATGCAATATGAGTCTA 57.371 39.130 0.00 0.00 0.00 2.59
2657 4703 6.191657 TGTCCCAATGCAATATGAGTCTAT 57.808 37.500 0.00 0.00 0.00 1.98
2658 4704 7.315066 TGTCCCAATGCAATATGAGTCTATA 57.685 36.000 0.00 0.00 0.00 1.31
2659 4705 7.744733 TGTCCCAATGCAATATGAGTCTATAA 58.255 34.615 0.00 0.00 0.00 0.98
2660 4706 8.385491 TGTCCCAATGCAATATGAGTCTATAAT 58.615 33.333 0.00 0.00 0.00 1.28
2661 4707 8.887717 GTCCCAATGCAATATGAGTCTATAATC 58.112 37.037 0.00 0.00 0.00 1.75
2662 4708 8.829746 TCCCAATGCAATATGAGTCTATAATCT 58.170 33.333 0.00 0.00 0.00 2.40
2690 4736 7.499321 AAATGAAGTTTCGTATGTTACCACA 57.501 32.000 0.00 0.00 37.31 4.17
2691 4737 5.910637 TGAAGTTTCGTATGTTACCACAC 57.089 39.130 0.00 0.00 35.03 3.82
2692 4738 5.603596 TGAAGTTTCGTATGTTACCACACT 58.396 37.500 0.00 0.00 35.03 3.55
2693 4739 6.050432 TGAAGTTTCGTATGTTACCACACTT 58.950 36.000 0.00 0.00 35.03 3.16
2694 4740 7.208777 TGAAGTTTCGTATGTTACCACACTTA 58.791 34.615 0.00 0.00 35.03 2.24
2695 4741 7.874016 TGAAGTTTCGTATGTTACCACACTTAT 59.126 33.333 0.00 0.00 35.03 1.73
2696 4742 7.591006 AGTTTCGTATGTTACCACACTTATG 57.409 36.000 0.00 0.00 35.03 1.90
2697 4743 7.156673 AGTTTCGTATGTTACCACACTTATGT 58.843 34.615 0.00 0.00 40.80 2.29
2698 4744 7.658575 AGTTTCGTATGTTACCACACTTATGTT 59.341 33.333 0.00 0.00 36.72 2.71
2699 4745 8.924691 GTTTCGTATGTTACCACACTTATGTTA 58.075 33.333 0.00 0.00 36.72 2.41
2700 4746 8.464770 TTCGTATGTTACCACACTTATGTTAC 57.535 34.615 0.00 0.00 36.72 2.50
2701 4747 7.829725 TCGTATGTTACCACACTTATGTTACT 58.170 34.615 0.00 0.00 36.72 2.24
2702 4748 8.955388 TCGTATGTTACCACACTTATGTTACTA 58.045 33.333 0.00 0.00 36.72 1.82
2703 4749 9.740239 CGTATGTTACCACACTTATGTTACTAT 57.260 33.333 0.00 0.00 36.72 2.12
2706 4752 8.136563 TGTTACCACACTTATGTTACTATCCA 57.863 34.615 0.00 0.00 36.72 3.41
2707 4753 8.036575 TGTTACCACACTTATGTTACTATCCAC 58.963 37.037 0.00 0.00 36.72 4.02
2708 4754 6.869206 ACCACACTTATGTTACTATCCACT 57.131 37.500 0.00 0.00 36.72 4.00
2709 4755 7.966339 ACCACACTTATGTTACTATCCACTA 57.034 36.000 0.00 0.00 36.72 2.74
2710 4756 8.548880 ACCACACTTATGTTACTATCCACTAT 57.451 34.615 0.00 0.00 36.72 2.12
2711 4757 8.421784 ACCACACTTATGTTACTATCCACTATG 58.578 37.037 0.00 0.00 36.72 2.23
2712 4758 8.638873 CCACACTTATGTTACTATCCACTATGA 58.361 37.037 0.00 0.00 36.72 2.15
2745 4791 8.958060 AACATAGTCTAGGGATATGTGTATGT 57.042 34.615 12.94 0.00 39.46 2.29
2746 4792 8.958060 ACATAGTCTAGGGATATGTGTATGTT 57.042 34.615 11.97 0.00 38.40 2.71
2751 4797 9.742144 AGTCTAGGGATATGTGTATGTTACTAG 57.258 37.037 0.00 0.00 0.00 2.57
2752 4798 9.517868 GTCTAGGGATATGTGTATGTTACTAGT 57.482 37.037 0.00 0.00 0.00 2.57
2753 4799 9.516546 TCTAGGGATATGTGTATGTTACTAGTG 57.483 37.037 5.39 0.00 0.00 2.74
2754 4800 9.298250 CTAGGGATATGTGTATGTTACTAGTGT 57.702 37.037 5.39 0.00 0.00 3.55
2756 4802 9.824216 AGGGATATGTGTATGTTACTAGTGTAT 57.176 33.333 5.39 0.00 0.00 2.29
2757 4803 9.856488 GGGATATGTGTATGTTACTAGTGTATG 57.144 37.037 5.39 0.00 0.00 2.39
2767 4813 8.827832 ATGTTACTAGTGTATGTTACTACCCA 57.172 34.615 5.39 0.00 0.00 4.51
2768 4814 8.827832 TGTTACTAGTGTATGTTACTACCCAT 57.172 34.615 5.39 0.00 0.00 4.00
2769 4815 9.258629 TGTTACTAGTGTATGTTACTACCCATT 57.741 33.333 5.39 0.00 0.00 3.16
2770 4816 9.741647 GTTACTAGTGTATGTTACTACCCATTC 57.258 37.037 5.39 0.00 0.00 2.67
2771 4817 9.705103 TTACTAGTGTATGTTACTACCCATTCT 57.295 33.333 5.39 0.00 0.00 2.40
2772 4818 8.008513 ACTAGTGTATGTTACTACCCATTCTG 57.991 38.462 0.00 0.00 0.00 3.02
2773 4819 6.235231 AGTGTATGTTACTACCCATTCTGG 57.765 41.667 0.00 0.00 37.25 3.86
2774 4820 5.724854 AGTGTATGTTACTACCCATTCTGGT 59.275 40.000 0.00 0.00 42.62 4.00
2775 4821 6.214819 AGTGTATGTTACTACCCATTCTGGTT 59.785 38.462 0.00 0.00 39.91 3.67
2776 4822 7.400915 AGTGTATGTTACTACCCATTCTGGTTA 59.599 37.037 0.00 0.00 39.91 2.85
2777 4823 7.709613 GTGTATGTTACTACCCATTCTGGTTAG 59.290 40.741 0.00 0.00 39.91 2.34
2778 4824 6.886178 ATGTTACTACCCATTCTGGTTAGT 57.114 37.500 8.24 8.24 39.91 2.24
2779 4825 6.290294 TGTTACTACCCATTCTGGTTAGTC 57.710 41.667 6.66 0.00 39.91 2.59
2780 4826 6.021030 TGTTACTACCCATTCTGGTTAGTCT 58.979 40.000 6.66 0.00 39.91 3.24
2781 4827 6.499350 TGTTACTACCCATTCTGGTTAGTCTT 59.501 38.462 6.66 0.00 39.91 3.01
2782 4828 7.675195 TGTTACTACCCATTCTGGTTAGTCTTA 59.325 37.037 6.66 0.00 39.91 2.10
2783 4829 6.793505 ACTACCCATTCTGGTTAGTCTTAG 57.206 41.667 0.00 0.00 39.91 2.18
2784 4830 5.661759 ACTACCCATTCTGGTTAGTCTTAGG 59.338 44.000 0.00 0.00 39.91 2.69
2785 4831 4.695606 ACCCATTCTGGTTAGTCTTAGGA 58.304 43.478 0.00 0.00 33.91 2.94
2786 4832 4.717280 ACCCATTCTGGTTAGTCTTAGGAG 59.283 45.833 0.00 0.00 33.91 3.69
2787 4833 4.717280 CCCATTCTGGTTAGTCTTAGGAGT 59.283 45.833 0.00 0.00 35.17 3.85
2788 4834 5.897824 CCCATTCTGGTTAGTCTTAGGAGTA 59.102 44.000 0.00 0.00 35.17 2.59
2789 4835 6.383147 CCCATTCTGGTTAGTCTTAGGAGTAA 59.617 42.308 0.00 0.00 35.17 2.24
2798 4844 7.770366 TTAGTCTTAGGAGTAACATCACACA 57.230 36.000 0.00 0.00 33.80 3.72
2799 4845 6.026947 AGTCTTAGGAGTAACATCACACAC 57.973 41.667 0.00 0.00 0.00 3.82
2800 4846 5.775701 AGTCTTAGGAGTAACATCACACACT 59.224 40.000 0.00 0.00 0.00 3.55
2801 4847 6.071840 AGTCTTAGGAGTAACATCACACACTC 60.072 42.308 0.00 0.00 37.32 3.51
2807 4853 6.648725 GAGTAACATCACACACTCCAATAC 57.351 41.667 0.00 0.00 32.93 1.89
2808 4854 6.109156 AGTAACATCACACACTCCAATACA 57.891 37.500 0.00 0.00 0.00 2.29
2809 4855 6.530120 AGTAACATCACACACTCCAATACAA 58.470 36.000 0.00 0.00 0.00 2.41
2810 4856 5.689383 AACATCACACACTCCAATACAAC 57.311 39.130 0.00 0.00 0.00 3.32
2811 4857 4.973168 ACATCACACACTCCAATACAACT 58.027 39.130 0.00 0.00 0.00 3.16
2812 4858 5.376625 ACATCACACACTCCAATACAACTT 58.623 37.500 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
390 391 1.375396 TTTGGATCGTGGCGGACAG 60.375 57.895 0.00 0.00 0.00 3.51
403 404 4.572571 ACTTGCGCCGGGTTTGGA 62.573 61.111 4.18 0.00 0.00 3.53
445 446 2.360801 CCCATCCTGTTCGTTTTGTGTT 59.639 45.455 0.00 0.00 0.00 3.32
510 511 1.076549 TCCACCCCAGTCCATTTGC 59.923 57.895 0.00 0.00 0.00 3.68
512 513 0.405585 CTGTCCACCCCAGTCCATTT 59.594 55.000 0.00 0.00 0.00 2.32
515 516 0.475632 ATTCTGTCCACCCCAGTCCA 60.476 55.000 0.00 0.00 0.00 4.02
525 528 1.813859 CGCGACCCTATTCTGTCCA 59.186 57.895 0.00 0.00 0.00 4.02
591 594 1.153269 TTTCACAGCCACACTCGCA 60.153 52.632 0.00 0.00 0.00 5.10
593 596 1.831389 CGGTTTCACAGCCACACTCG 61.831 60.000 0.00 0.00 0.00 4.18
603 606 1.021202 CTGCTGGTTTCGGTTTCACA 58.979 50.000 0.00 0.00 0.00 3.58
612 615 0.322816 TGAGGATGGCTGCTGGTTTC 60.323 55.000 0.00 0.00 0.00 2.78
613 616 0.112995 TTGAGGATGGCTGCTGGTTT 59.887 50.000 0.00 0.00 0.00 3.27
614 617 0.112995 TTTGAGGATGGCTGCTGGTT 59.887 50.000 0.00 0.00 0.00 3.67
615 618 0.112995 TTTTGAGGATGGCTGCTGGT 59.887 50.000 0.00 0.00 0.00 4.00
616 619 1.259609 TTTTTGAGGATGGCTGCTGG 58.740 50.000 0.00 0.00 0.00 4.85
633 636 0.389025 CGGGCTGCTGGTTTCTTTTT 59.611 50.000 0.00 0.00 0.00 1.94
634 637 1.463553 CCGGGCTGCTGGTTTCTTTT 61.464 55.000 0.00 0.00 0.00 2.27
635 638 1.903404 CCGGGCTGCTGGTTTCTTT 60.903 57.895 0.00 0.00 0.00 2.52
636 639 2.282462 CCGGGCTGCTGGTTTCTT 60.282 61.111 0.00 0.00 0.00 2.52
685 698 3.188100 CGATCGGTGCATGCGTGT 61.188 61.111 14.09 0.00 0.00 4.49
686 699 2.885164 TCGATCGGTGCATGCGTG 60.885 61.111 16.41 0.09 0.00 5.34
687 700 2.885644 GTCGATCGGTGCATGCGT 60.886 61.111 16.41 0.00 0.00 5.24
688 701 3.630148 GGTCGATCGGTGCATGCG 61.630 66.667 16.41 0.00 0.00 4.73
689 702 3.272334 GGGTCGATCGGTGCATGC 61.272 66.667 16.41 11.82 0.00 4.06
690 703 2.588877 GGGGTCGATCGGTGCATG 60.589 66.667 16.41 0.00 0.00 4.06
691 704 3.861797 GGGGGTCGATCGGTGCAT 61.862 66.667 16.41 0.00 0.00 3.96
706 719 3.929334 TTTCCGGTGGCGAATGGGG 62.929 63.158 0.00 0.00 0.00 4.96
707 720 1.974343 TTTTCCGGTGGCGAATGGG 60.974 57.895 0.00 0.00 0.00 4.00
708 721 1.211709 GTTTTCCGGTGGCGAATGG 59.788 57.895 0.00 0.00 0.00 3.16
709 722 1.211709 GGTTTTCCGGTGGCGAATG 59.788 57.895 0.00 0.00 0.00 2.67
710 723 1.228306 TGGTTTTCCGGTGGCGAAT 60.228 52.632 0.00 0.00 44.36 3.34
711 724 1.894756 CTGGTTTTCCGGTGGCGAA 60.895 57.895 0.00 0.00 44.36 4.70
712 725 2.281208 CTGGTTTTCCGGTGGCGA 60.281 61.111 0.00 0.00 44.36 5.54
721 734 2.556287 CGGACGCTGCTGGTTTTC 59.444 61.111 0.00 0.00 0.00 2.29
722 735 3.660111 GCGGACGCTGCTGGTTTT 61.660 61.111 9.76 0.00 38.26 2.43
800 813 2.028484 TCGGAGGACACGTGTTGC 59.972 61.111 24.26 12.31 0.00 4.17
829 842 2.885861 GCGCGAAGGAAGAGAGGA 59.114 61.111 12.10 0.00 0.00 3.71
999 1022 1.299976 GGACGAGGTGGCTTCCATT 59.700 57.895 0.00 0.00 35.28 3.16
1071 1434 3.134127 GGCATGTGCGGGGACTTC 61.134 66.667 0.00 0.00 43.26 3.01
1216 1579 4.779733 TCTCTCCCCGAGGGTGCC 62.780 72.222 7.48 0.00 44.74 5.01
1251 1614 2.569134 GAGCCGTCGAAGCAGTCT 59.431 61.111 10.96 0.00 0.00 3.24
1283 1646 2.594592 GGCCGGAGCTGTTGTTGT 60.595 61.111 5.05 0.00 39.73 3.32
1561 1924 2.719979 GCGCTCGAAGTATCCGGA 59.280 61.111 6.61 6.61 0.00 5.14
1596 1959 4.456253 CGCGCGTACCAGTCGTCT 62.456 66.667 24.19 0.00 0.00 4.18
1635 1998 7.922278 ACACAGTCAAGTACGAGTAACAAAATA 59.078 33.333 0.00 0.00 0.00 1.40
1641 2004 5.995055 ACTACACAGTCAAGTACGAGTAAC 58.005 41.667 0.00 0.00 0.00 2.50
1662 2044 2.949451 AGCAAGTGATTCGATCGACT 57.051 45.000 19.26 13.34 0.00 4.18
1817 2202 1.450312 CCACTCCAGATCAACGGCC 60.450 63.158 0.00 0.00 0.00 6.13
1895 2280 3.790437 CGACCAGCTGCCATCCCT 61.790 66.667 8.66 0.00 0.00 4.20
1936 2321 1.282738 TGATCAGCCTGCCAATTCAGA 59.717 47.619 0.00 0.00 36.19 3.27
1937 2322 1.758936 TGATCAGCCTGCCAATTCAG 58.241 50.000 0.00 0.00 0.00 3.02
1938 2323 2.219080 TTGATCAGCCTGCCAATTCA 57.781 45.000 0.00 0.00 0.00 2.57
1939 2324 2.035576 GGATTGATCAGCCTGCCAATTC 59.964 50.000 11.56 7.54 30.29 2.17
1940 2325 2.037144 GGATTGATCAGCCTGCCAATT 58.963 47.619 11.56 0.23 30.29 2.32
1941 2326 1.063492 TGGATTGATCAGCCTGCCAAT 60.063 47.619 15.26 10.52 32.54 3.16
1942 2327 0.332293 TGGATTGATCAGCCTGCCAA 59.668 50.000 15.26 2.67 0.00 4.52
1972 2357 4.874534 GCAATGACATGCAGCGTT 57.125 50.000 0.00 0.00 45.70 4.84
1983 2368 1.530419 AACTTGTGGCGGGCAATGA 60.530 52.632 5.57 0.00 0.00 2.57
1991 2376 0.250295 TCCTTCCTCAACTTGTGGCG 60.250 55.000 5.16 0.17 31.43 5.69
1994 2379 3.999663 GTCATCTCCTTCCTCAACTTGTG 59.000 47.826 0.00 0.00 0.00 3.33
2013 2398 3.544684 CCGGATCCATTCAAATCTGTCA 58.455 45.455 13.41 0.00 0.00 3.58
2065 2450 2.882137 GCAGAGCAGTAGTAGGTAGGAG 59.118 54.545 0.00 0.00 0.00 3.69
2067 2452 2.882137 GAGCAGAGCAGTAGTAGGTAGG 59.118 54.545 0.00 0.00 0.00 3.18
2068 2453 3.815809 AGAGCAGAGCAGTAGTAGGTAG 58.184 50.000 0.00 0.00 0.00 3.18
2069 2454 3.935818 AGAGCAGAGCAGTAGTAGGTA 57.064 47.619 0.00 0.00 0.00 3.08
2070 2455 2.818751 AGAGCAGAGCAGTAGTAGGT 57.181 50.000 0.00 0.00 0.00 3.08
2071 2456 3.563808 CAGTAGAGCAGAGCAGTAGTAGG 59.436 52.174 0.00 0.00 0.00 3.18
2075 2460 3.694072 ACTTCAGTAGAGCAGAGCAGTAG 59.306 47.826 0.00 0.00 0.00 2.57
2076 2461 3.691575 ACTTCAGTAGAGCAGAGCAGTA 58.308 45.455 0.00 0.00 0.00 2.74
2077 2462 2.524306 ACTTCAGTAGAGCAGAGCAGT 58.476 47.619 0.00 0.00 0.00 4.40
2078 2463 3.193267 AGAACTTCAGTAGAGCAGAGCAG 59.807 47.826 0.00 0.00 0.00 4.24
2079 2464 3.161067 AGAACTTCAGTAGAGCAGAGCA 58.839 45.455 0.00 0.00 0.00 4.26
2080 2465 3.866883 AGAACTTCAGTAGAGCAGAGC 57.133 47.619 0.00 0.00 0.00 4.09
2081 2466 5.537188 ACAAAGAACTTCAGTAGAGCAGAG 58.463 41.667 0.00 0.00 0.00 3.35
2082 2467 5.537300 ACAAAGAACTTCAGTAGAGCAGA 57.463 39.130 0.00 0.00 0.00 4.26
2164 2549 9.941325 TCTATAGGTACTGTAACATCTAGTAGC 57.059 37.037 5.55 0.00 42.61 3.58
2214 2640 2.125229 CAGCAGCATCAGCCGAGT 60.125 61.111 0.00 0.00 43.56 4.18
2268 2697 0.988832 AGCAAAGGTTATCCCGACCA 59.011 50.000 0.00 0.00 39.71 4.02
2488 4534 0.175989 CTAAGTTCCTCCGACCAGCC 59.824 60.000 0.00 0.00 0.00 4.85
2489 4535 1.135053 GTCTAAGTTCCTCCGACCAGC 60.135 57.143 0.00 0.00 0.00 4.85
2494 4540 2.025605 TGGCTAGTCTAAGTTCCTCCGA 60.026 50.000 0.00 0.00 0.00 4.55
2495 4541 2.099427 GTGGCTAGTCTAAGTTCCTCCG 59.901 54.545 0.00 0.00 0.00 4.63
2496 4542 3.097614 TGTGGCTAGTCTAAGTTCCTCC 58.902 50.000 0.00 0.00 0.00 4.30
2497 4543 4.803098 TTGTGGCTAGTCTAAGTTCCTC 57.197 45.455 0.00 0.00 0.00 3.71
2498 4544 4.080863 CCATTGTGGCTAGTCTAAGTTCCT 60.081 45.833 0.00 0.00 0.00 3.36
2499 4545 4.081087 TCCATTGTGGCTAGTCTAAGTTCC 60.081 45.833 0.00 0.00 37.47 3.62
2500 4546 5.086104 TCCATTGTGGCTAGTCTAAGTTC 57.914 43.478 0.00 0.00 37.47 3.01
2501 4547 5.013183 ACTTCCATTGTGGCTAGTCTAAGTT 59.987 40.000 0.00 0.00 37.47 2.66
2502 4548 4.532521 ACTTCCATTGTGGCTAGTCTAAGT 59.467 41.667 0.00 0.00 37.47 2.24
2503 4549 5.091261 ACTTCCATTGTGGCTAGTCTAAG 57.909 43.478 0.00 0.00 37.47 2.18
2504 4550 6.212791 AGTTACTTCCATTGTGGCTAGTCTAA 59.787 38.462 0.00 0.00 37.47 2.10
2505 4551 5.720041 AGTTACTTCCATTGTGGCTAGTCTA 59.280 40.000 0.00 0.00 37.47 2.59
2506 4552 4.532521 AGTTACTTCCATTGTGGCTAGTCT 59.467 41.667 0.00 0.00 37.47 3.24
2507 4553 4.833390 AGTTACTTCCATTGTGGCTAGTC 58.167 43.478 6.80 0.00 37.47 2.59
2508 4554 4.910458 AGTTACTTCCATTGTGGCTAGT 57.090 40.909 8.11 8.11 37.47 2.57
2509 4555 4.330074 CGAAGTTACTTCCATTGTGGCTAG 59.670 45.833 18.11 0.00 37.20 3.42
2510 4556 4.250464 CGAAGTTACTTCCATTGTGGCTA 58.750 43.478 18.11 0.00 37.20 3.93
2511 4557 3.074412 CGAAGTTACTTCCATTGTGGCT 58.926 45.455 18.11 0.00 37.20 4.75
2512 4558 2.161609 CCGAAGTTACTTCCATTGTGGC 59.838 50.000 18.11 0.00 37.20 5.01
2513 4559 3.408634 ACCGAAGTTACTTCCATTGTGG 58.591 45.455 18.11 14.29 37.20 4.17
2514 4560 5.235516 ACTACCGAAGTTACTTCCATTGTG 58.764 41.667 18.11 4.32 37.20 3.33
2515 4561 5.479124 ACTACCGAAGTTACTTCCATTGT 57.521 39.130 18.11 12.59 37.20 2.71
2516 4562 6.869913 TGTTACTACCGAAGTTACTTCCATTG 59.130 38.462 18.11 10.31 39.80 2.82
2517 4563 6.996509 TGTTACTACCGAAGTTACTTCCATT 58.003 36.000 18.11 6.32 39.80 3.16
2518 4564 6.594788 TGTTACTACCGAAGTTACTTCCAT 57.405 37.500 18.11 9.69 39.80 3.41
2519 4565 6.594788 ATGTTACTACCGAAGTTACTTCCA 57.405 37.500 18.11 8.77 39.80 3.53
2520 4566 5.741040 CGATGTTACTACCGAAGTTACTTCC 59.259 44.000 18.11 3.62 39.80 3.46
2521 4567 6.546395 TCGATGTTACTACCGAAGTTACTTC 58.454 40.000 14.56 14.56 39.80 3.01
2522 4568 6.150140 ACTCGATGTTACTACCGAAGTTACTT 59.850 38.462 0.00 0.00 39.80 2.24
2523 4569 5.645497 ACTCGATGTTACTACCGAAGTTACT 59.355 40.000 8.00 0.00 39.80 2.24
2524 4570 5.873732 ACTCGATGTTACTACCGAAGTTAC 58.126 41.667 0.00 0.00 39.80 2.50
2525 4571 5.065218 GGACTCGATGTTACTACCGAAGTTA 59.935 44.000 0.00 0.00 39.80 2.24
2526 4572 4.142513 GGACTCGATGTTACTACCGAAGTT 60.143 45.833 0.00 0.00 39.80 2.66
2527 4573 3.376546 GGACTCGATGTTACTACCGAAGT 59.623 47.826 0.00 0.00 42.62 3.01
2528 4574 3.376234 TGGACTCGATGTTACTACCGAAG 59.624 47.826 0.00 0.00 0.00 3.79
2529 4575 3.346315 TGGACTCGATGTTACTACCGAA 58.654 45.455 0.00 0.00 0.00 4.30
2530 4576 2.989909 TGGACTCGATGTTACTACCGA 58.010 47.619 0.00 0.00 0.00 4.69
2531 4577 3.128242 AGTTGGACTCGATGTTACTACCG 59.872 47.826 0.00 0.00 0.00 4.02
2532 4578 4.670347 GAGTTGGACTCGATGTTACTACC 58.330 47.826 0.00 0.00 35.28 3.18
2563 4609 5.651576 TCATTAACTCATTGCCACATAAGCA 59.348 36.000 0.00 0.00 38.81 3.91
2564 4610 6.135290 TCATTAACTCATTGCCACATAAGC 57.865 37.500 0.00 0.00 0.00 3.09
2565 4611 7.988737 TCTTCATTAACTCATTGCCACATAAG 58.011 34.615 0.00 0.00 0.00 1.73
2566 4612 7.828717 TCTCTTCATTAACTCATTGCCACATAA 59.171 33.333 0.00 0.00 0.00 1.90
2567 4613 7.337938 TCTCTTCATTAACTCATTGCCACATA 58.662 34.615 0.00 0.00 0.00 2.29
2568 4614 6.182627 TCTCTTCATTAACTCATTGCCACAT 58.817 36.000 0.00 0.00 0.00 3.21
2569 4615 5.559770 TCTCTTCATTAACTCATTGCCACA 58.440 37.500 0.00 0.00 0.00 4.17
2570 4616 5.877012 TCTCTCTTCATTAACTCATTGCCAC 59.123 40.000 0.00 0.00 0.00 5.01
2571 4617 6.053632 TCTCTCTTCATTAACTCATTGCCA 57.946 37.500 0.00 0.00 0.00 4.92
2572 4618 6.541641 ACATCTCTCTTCATTAACTCATTGCC 59.458 38.462 0.00 0.00 0.00 4.52
2573 4619 7.551035 ACATCTCTCTTCATTAACTCATTGC 57.449 36.000 0.00 0.00 0.00 3.56
2574 4620 9.814899 ACTACATCTCTCTTCATTAACTCATTG 57.185 33.333 0.00 0.00 0.00 2.82
2577 4623 9.688091 AGTACTACATCTCTCTTCATTAACTCA 57.312 33.333 0.00 0.00 0.00 3.41
2588 4634 9.768662 GCTAAGTTACTAGTACTACATCTCTCT 57.231 37.037 0.91 0.00 0.00 3.10
2589 4635 9.768662 AGCTAAGTTACTAGTACTACATCTCTC 57.231 37.037 0.91 0.00 0.00 3.20
2610 4656 9.884636 ACATGTGATGTTACATTAACTAGCTAA 57.115 29.630 0.00 0.00 41.63 3.09
2611 4657 9.529325 GACATGTGATGTTACATTAACTAGCTA 57.471 33.333 1.15 0.00 45.03 3.32
2612 4658 7.495934 GGACATGTGATGTTACATTAACTAGCT 59.504 37.037 1.15 0.00 45.03 3.32
2613 4659 7.254795 GGGACATGTGATGTTACATTAACTAGC 60.255 40.741 1.15 0.00 45.03 3.42
2614 4660 7.768582 TGGGACATGTGATGTTACATTAACTAG 59.231 37.037 1.15 0.00 45.03 2.57
2615 4661 7.625469 TGGGACATGTGATGTTACATTAACTA 58.375 34.615 1.15 0.00 45.03 2.24
2616 4662 6.480763 TGGGACATGTGATGTTACATTAACT 58.519 36.000 1.15 0.00 45.03 2.24
2617 4663 6.751514 TGGGACATGTGATGTTACATTAAC 57.248 37.500 1.15 2.44 45.03 2.01
2618 4664 7.630297 GCATTGGGACATGTGATGTTACATTAA 60.630 37.037 1.15 0.00 45.03 1.40
2619 4665 6.183360 GCATTGGGACATGTGATGTTACATTA 60.183 38.462 1.15 0.00 45.03 1.90
2620 4666 5.394443 GCATTGGGACATGTGATGTTACATT 60.394 40.000 1.15 0.00 45.03 2.71
2621 4667 4.098349 GCATTGGGACATGTGATGTTACAT 59.902 41.667 1.15 0.00 45.03 2.29
2622 4668 3.443329 GCATTGGGACATGTGATGTTACA 59.557 43.478 1.15 0.00 45.03 2.41
2623 4669 3.443329 TGCATTGGGACATGTGATGTTAC 59.557 43.478 1.15 0.00 45.03 2.50
2624 4670 3.694926 TGCATTGGGACATGTGATGTTA 58.305 40.909 1.15 0.00 45.03 2.41
2625 4671 2.527497 TGCATTGGGACATGTGATGTT 58.473 42.857 1.15 0.00 45.03 2.71
2627 4673 3.812156 ATTGCATTGGGACATGTGATG 57.188 42.857 1.15 3.48 39.30 3.07
2628 4674 5.141910 TCATATTGCATTGGGACATGTGAT 58.858 37.500 1.15 0.00 39.30 3.06
2629 4675 4.534797 TCATATTGCATTGGGACATGTGA 58.465 39.130 1.15 0.00 39.30 3.58
2630 4676 4.340097 ACTCATATTGCATTGGGACATGTG 59.660 41.667 1.15 0.00 39.30 3.21
2631 4677 4.539726 ACTCATATTGCATTGGGACATGT 58.460 39.130 0.00 0.00 39.30 3.21
2632 4678 4.825634 AGACTCATATTGCATTGGGACATG 59.174 41.667 0.00 0.00 39.30 3.21
2633 4679 5.057843 AGACTCATATTGCATTGGGACAT 57.942 39.130 0.00 0.00 39.30 3.06
2634 4680 4.508551 AGACTCATATTGCATTGGGACA 57.491 40.909 0.00 0.00 0.00 4.02
2635 4681 8.798859 ATTATAGACTCATATTGCATTGGGAC 57.201 34.615 0.00 0.00 0.00 4.46
2636 4682 8.829746 AGATTATAGACTCATATTGCATTGGGA 58.170 33.333 0.00 0.00 0.00 4.37
2682 4728 8.255905 AGTGGATAGTAACATAAGTGTGGTAAC 58.744 37.037 0.00 0.00 38.92 2.50
2683 4729 8.370266 AGTGGATAGTAACATAAGTGTGGTAA 57.630 34.615 0.00 0.00 38.92 2.85
2684 4730 7.966339 AGTGGATAGTAACATAAGTGTGGTA 57.034 36.000 0.00 0.00 38.92 3.25
2685 4731 6.869206 AGTGGATAGTAACATAAGTGTGGT 57.131 37.500 0.00 0.00 38.92 4.16
2686 4732 8.638873 TCATAGTGGATAGTAACATAAGTGTGG 58.361 37.037 0.00 0.00 38.92 4.17
2720 4766 8.958060 ACATACACATATCCCTAGACTATGTT 57.042 34.615 8.30 5.15 34.66 2.71
2721 4767 8.958060 AACATACACATATCCCTAGACTATGT 57.042 34.615 0.00 0.00 36.72 2.29
2725 4771 9.742144 CTAGTAACATACACATATCCCTAGACT 57.258 37.037 0.00 0.00 0.00 3.24
2726 4772 9.517868 ACTAGTAACATACACATATCCCTAGAC 57.482 37.037 0.00 0.00 0.00 2.59
2727 4773 9.516546 CACTAGTAACATACACATATCCCTAGA 57.483 37.037 0.00 0.00 0.00 2.43
2728 4774 9.298250 ACACTAGTAACATACACATATCCCTAG 57.702 37.037 0.00 0.00 0.00 3.02
2730 4776 9.824216 ATACACTAGTAACATACACATATCCCT 57.176 33.333 0.00 0.00 33.13 4.20
2731 4777 9.856488 CATACACTAGTAACATACACATATCCC 57.144 37.037 0.00 0.00 33.13 3.85
2741 4787 9.919416 TGGGTAGTAACATACACTAGTAACATA 57.081 33.333 0.00 0.00 33.13 2.29
2742 4788 8.827832 TGGGTAGTAACATACACTAGTAACAT 57.172 34.615 0.00 0.00 33.13 2.71
2743 4789 8.827832 ATGGGTAGTAACATACACTAGTAACA 57.172 34.615 0.00 0.00 33.13 2.41
2744 4790 9.741647 GAATGGGTAGTAACATACACTAGTAAC 57.258 37.037 0.00 0.00 33.13 2.50
2745 4791 9.705103 AGAATGGGTAGTAACATACACTAGTAA 57.295 33.333 0.00 0.00 33.13 2.24
2746 4792 9.128404 CAGAATGGGTAGTAACATACACTAGTA 57.872 37.037 0.00 0.00 30.00 1.82
2747 4793 8.008513 CAGAATGGGTAGTAACATACACTAGT 57.991 38.462 0.00 0.00 30.00 2.57
2766 4812 7.837863 TGTTACTCCTAAGACTAACCAGAATG 58.162 38.462 0.00 0.00 0.00 2.67
2767 4813 8.611051 ATGTTACTCCTAAGACTAACCAGAAT 57.389 34.615 0.00 0.00 0.00 2.40
2768 4814 7.672660 TGATGTTACTCCTAAGACTAACCAGAA 59.327 37.037 0.00 0.00 0.00 3.02
2769 4815 7.122353 GTGATGTTACTCCTAAGACTAACCAGA 59.878 40.741 0.00 0.00 0.00 3.86
2770 4816 7.093902 TGTGATGTTACTCCTAAGACTAACCAG 60.094 40.741 0.00 0.00 0.00 4.00
2771 4817 6.722590 TGTGATGTTACTCCTAAGACTAACCA 59.277 38.462 0.00 0.00 0.00 3.67
2772 4818 7.034397 GTGTGATGTTACTCCTAAGACTAACC 58.966 42.308 0.00 0.00 0.00 2.85
2773 4819 7.541437 GTGTGTGATGTTACTCCTAAGACTAAC 59.459 40.741 0.00 0.00 0.00 2.34
2774 4820 7.450634 AGTGTGTGATGTTACTCCTAAGACTAA 59.549 37.037 0.00 0.00 0.00 2.24
2775 4821 6.946583 AGTGTGTGATGTTACTCCTAAGACTA 59.053 38.462 0.00 0.00 0.00 2.59
2776 4822 5.775701 AGTGTGTGATGTTACTCCTAAGACT 59.224 40.000 0.00 0.00 0.00 3.24
2777 4823 6.026947 AGTGTGTGATGTTACTCCTAAGAC 57.973 41.667 0.00 0.00 0.00 3.01
2778 4824 6.268825 GAGTGTGTGATGTTACTCCTAAGA 57.731 41.667 0.00 0.00 34.84 2.10
2784 4830 6.163476 TGTATTGGAGTGTGTGATGTTACTC 58.837 40.000 0.00 0.00 38.98 2.59
2785 4831 6.109156 TGTATTGGAGTGTGTGATGTTACT 57.891 37.500 0.00 0.00 0.00 2.24
2786 4832 6.426937 AGTTGTATTGGAGTGTGTGATGTTAC 59.573 38.462 0.00 0.00 0.00 2.50
2787 4833 6.530120 AGTTGTATTGGAGTGTGTGATGTTA 58.470 36.000 0.00 0.00 0.00 2.41
2788 4834 5.376625 AGTTGTATTGGAGTGTGTGATGTT 58.623 37.500 0.00 0.00 0.00 2.71
2789 4835 4.973168 AGTTGTATTGGAGTGTGTGATGT 58.027 39.130 0.00 0.00 0.00 3.06
2790 4836 5.947228 AAGTTGTATTGGAGTGTGTGATG 57.053 39.130 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.