Multiple sequence alignment - TraesCS7B01G443100

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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 TraesCS7B01G443100 chr7B 100.000 2634 0 0 1 2634 707947658 707945025 0.000000e+00 4865.0
1 TraesCS7B01G443100 chr7B 89.516 620 60 5 2018 2634 720297944 720298561 0.000000e+00 780.0
2 TraesCS7B01G443100 chr7B 94.681 282 8 2 389 670 679698166 679697892 5.210000e-117 431.0
3 TraesCS7B01G443100 chr7B 92.881 295 13 5 378 672 214927924 214928210 3.130000e-114 422.0
4 TraesCS7B01G443100 chr7B 93.706 286 11 3 387 672 505255222 505255500 3.130000e-114 422.0
5 TraesCS7B01G443100 chr3B 86.224 1234 82 41 670 1868 50942796 50943976 0.000000e+00 1256.0
6 TraesCS7B01G443100 chr3B 85.576 929 78 29 673 1556 50959693 50958776 0.000000e+00 922.0
7 TraesCS7B01G443100 chr3B 90.098 717 46 10 670 1381 50654760 50654064 0.000000e+00 907.0
8 TraesCS7B01G443100 chr3B 83.593 707 65 28 700 1368 421532413 421531720 1.340000e-172 616.0
9 TraesCS7B01G443100 chr3B 93.728 287 11 2 387 673 565362714 565362993 8.720000e-115 424.0
10 TraesCS7B01G443100 chr3B 93.403 288 11 5 387 674 710386120 710386399 1.130000e-113 420.0
11 TraesCS7B01G443100 chr3B 84.275 407 32 13 1 390 50942408 50942799 4.140000e-98 368.0
12 TraesCS7B01G443100 chr3B 91.791 268 11 2 1607 1874 50653536 50653280 1.930000e-96 363.0
13 TraesCS7B01G443100 chr3B 78.671 286 32 16 78 357 421532737 421532475 2.100000e-36 163.0
14 TraesCS7B01G443100 chr3B 76.159 302 40 25 1589 1874 421531289 421531004 2.130000e-26 130.0
15 TraesCS7B01G443100 chr3A 90.748 735 46 12 670 1398 40390400 40389682 0.000000e+00 961.0
16 TraesCS7B01G443100 chr3A 89.444 720 48 14 670 1382 40556519 40555821 0.000000e+00 883.0
17 TraesCS7B01G443100 chr3A 90.023 441 25 10 1447 1874 40555668 40555234 1.070000e-153 553.0
18 TraesCS7B01G443100 chr3A 93.462 260 12 5 1873 2128 589365968 589366226 5.320000e-102 381.0
19 TraesCS7B01G443100 chr3A 84.770 348 24 13 50 390 40390722 40390397 3.270000e-84 322.0
20 TraesCS7B01G443100 chr3A 81.233 373 30 19 30 390 40556860 40556516 5.590000e-67 265.0
21 TraesCS7B01G443100 chr3A 83.108 296 26 14 1398 1689 436273556 436273281 5.630000e-62 248.0
22 TraesCS7B01G443100 chr3A 88.670 203 9 4 1685 1874 40389358 40389157 4.380000e-58 235.0
23 TraesCS7B01G443100 chr3A 79.233 313 23 14 1398 1704 40389646 40389370 2.080000e-41 180.0
24 TraesCS7B01G443100 chr3A 78.788 297 34 16 78 368 436274724 436274451 3.490000e-39 172.0
25 TraesCS7B01G443100 chr3A 76.159 302 40 25 1589 1874 436273287 436273002 2.130000e-26 130.0
26 TraesCS7B01G443100 chr3A 96.429 56 2 0 1 56 40390977 40390922 2.790000e-15 93.5
27 TraesCS7B01G443100 chr3D 89.762 713 53 9 670 1381 29801283 29800590 0.000000e+00 894.0
28 TraesCS7B01G443100 chr3D 89.286 728 50 20 670 1382 29812803 29812089 0.000000e+00 887.0
29 TraesCS7B01G443100 chr3D 89.700 699 58 10 670 1364 29790109 29789421 0.000000e+00 880.0
30 TraesCS7B01G443100 chr3D 89.514 658 44 10 670 1322 29861852 29861215 0.000000e+00 809.0
31 TraesCS7B01G443100 chr3D 91.837 490 22 9 1398 1874 29812033 29811549 0.000000e+00 667.0
32 TraesCS7B01G443100 chr3D 83.926 703 68 24 697 1368 299744815 299745503 4.780000e-177 630.0
33 TraesCS7B01G443100 chr3D 83.911 404 25 18 1 390 29813177 29812800 1.500000e-92 350.0
34 TraesCS7B01G443100 chr3D 88.014 292 17 6 2 292 29790434 29790160 1.950000e-86 329.0
35 TraesCS7B01G443100 chr3D 83.390 295 27 14 1398 1689 299745665 299745940 1.210000e-63 254.0
36 TraesCS7B01G443100 chr3D 86.740 181 14 7 210 390 29801450 29801280 2.680000e-45 193.0
37 TraesCS7B01G443100 chr3D 78.671 286 34 15 78 357 299744494 299744758 5.830000e-37 165.0
38 TraesCS7B01G443100 chr3D 90.385 104 4 2 1453 1556 29861106 29861009 5.920000e-27 132.0
39 TraesCS7B01G443100 chr3D 85.496 131 8 5 1398 1523 29800530 29800406 2.750000e-25 126.0
40 TraesCS7B01G443100 chr3D 75.748 301 41 25 1589 1874 299745934 299746217 3.560000e-24 122.0
41 TraesCS7B01G443100 chr3D 94.643 56 3 0 1 56 29803539 29803484 1.300000e-13 87.9
42 TraesCS7B01G443100 chr3D 94.545 55 3 0 1 55 29796792 29796738 4.670000e-13 86.1
43 TraesCS7B01G443100 chr3D 97.561 41 1 0 1516 1556 29800248 29800208 1.310000e-08 71.3
44 TraesCS7B01G443100 chr6D 91.131 654 53 5 1985 2634 442485735 442486387 0.000000e+00 881.0
45 TraesCS7B01G443100 chr1A 89.069 677 61 12 1966 2634 428187923 428187252 0.000000e+00 828.0
46 TraesCS7B01G443100 chr7D 86.695 699 77 11 1942 2631 312553357 312554048 0.000000e+00 761.0
47 TraesCS7B01G443100 chr7D 84.551 712 83 19 1942 2634 583964326 583963623 0.000000e+00 680.0
48 TraesCS7B01G443100 chr2B 85.633 703 78 17 1942 2631 668015837 668016529 0.000000e+00 717.0
49 TraesCS7B01G443100 chr2B 94.755 286 10 1 389 674 17029125 17028845 8.650000e-120 440.0
50 TraesCS7B01G443100 chr2B 93.772 289 10 3 387 675 679893712 679893992 6.740000e-116 427.0
51 TraesCS7B01G443100 chr2B 93.403 288 12 3 387 674 615402042 615402322 1.130000e-113 420.0
52 TraesCS7B01G443100 chr5D 85.411 706 79 18 1942 2634 298998727 298999421 0.000000e+00 712.0
53 TraesCS7B01G443100 chr1B 86.336 666 73 11 1982 2634 37761297 37760637 0.000000e+00 710.0
54 TraesCS7B01G443100 chr5A 85.258 658 68 21 1986 2634 603560093 603559456 0.000000e+00 651.0
55 TraesCS7B01G443100 chr5A 94.056 286 10 2 387 672 388137437 388137715 6.740000e-116 427.0
56 TraesCS7B01G443100 chr7A 82.988 676 94 16 1964 2631 94288752 94288090 2.260000e-165 592.0
57 TraesCS7B01G443100 chr4A 95.703 256 9 2 1874 2128 614982742 614982488 6.790000e-111 411.0
58 TraesCS7B01G443100 chr2A 92.996 257 11 5 1874 2128 571427595 571427344 4.140000e-98 368.0


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 TraesCS7B01G443100 chr7B 707945025 707947658 2633 True 4865.000000 4865 100.000000 1 2634 1 chr7B.!!$R2 2633
1 TraesCS7B01G443100 chr7B 720297944 720298561 617 False 780.000000 780 89.516000 2018 2634 1 chr7B.!!$F3 616
2 TraesCS7B01G443100 chr3B 50958776 50959693 917 True 922.000000 922 85.576000 673 1556 1 chr3B.!!$R1 883
3 TraesCS7B01G443100 chr3B 50942408 50943976 1568 False 812.000000 1256 85.249500 1 1868 2 chr3B.!!$F3 1867
4 TraesCS7B01G443100 chr3B 50653280 50654760 1480 True 635.000000 907 90.944500 670 1874 2 chr3B.!!$R2 1204
5 TraesCS7B01G443100 chr3B 421531004 421532737 1733 True 303.000000 616 79.474333 78 1874 3 chr3B.!!$R3 1796
6 TraesCS7B01G443100 chr3A 40555234 40556860 1626 True 567.000000 883 86.900000 30 1874 3 chr3A.!!$R2 1844
7 TraesCS7B01G443100 chr3A 40389157 40390977 1820 True 358.300000 961 87.970000 1 1874 5 chr3A.!!$R1 1873
8 TraesCS7B01G443100 chr3D 29811549 29813177 1628 True 634.666667 887 88.344667 1 1874 3 chr3D.!!$R3 1873
9 TraesCS7B01G443100 chr3D 29789421 29790434 1013 True 604.500000 880 88.857000 2 1364 2 chr3D.!!$R1 1362
10 TraesCS7B01G443100 chr3D 29861009 29861852 843 True 470.500000 809 89.949500 670 1556 2 chr3D.!!$R4 886
11 TraesCS7B01G443100 chr3D 299744494 299746217 1723 False 292.750000 630 80.433750 78 1874 4 chr3D.!!$F1 1796
12 TraesCS7B01G443100 chr3D 29796738 29803539 6801 True 243.050000 894 91.457833 1 1556 6 chr3D.!!$R2 1555
13 TraesCS7B01G443100 chr6D 442485735 442486387 652 False 881.000000 881 91.131000 1985 2634 1 chr6D.!!$F1 649
14 TraesCS7B01G443100 chr1A 428187252 428187923 671 True 828.000000 828 89.069000 1966 2634 1 chr1A.!!$R1 668
15 TraesCS7B01G443100 chr7D 312553357 312554048 691 False 761.000000 761 86.695000 1942 2631 1 chr7D.!!$F1 689
16 TraesCS7B01G443100 chr7D 583963623 583964326 703 True 680.000000 680 84.551000 1942 2634 1 chr7D.!!$R1 692
17 TraesCS7B01G443100 chr2B 668015837 668016529 692 False 717.000000 717 85.633000 1942 2631 1 chr2B.!!$F2 689
18 TraesCS7B01G443100 chr5D 298998727 298999421 694 False 712.000000 712 85.411000 1942 2634 1 chr5D.!!$F1 692
19 TraesCS7B01G443100 chr1B 37760637 37761297 660 True 710.000000 710 86.336000 1982 2634 1 chr1B.!!$R1 652
20 TraesCS7B01G443100 chr5A 603559456 603560093 637 True 651.000000 651 85.258000 1986 2634 1 chr5A.!!$R1 648
21 TraesCS7B01G443100 chr7A 94288090 94288752 662 True 592.000000 592 82.988000 1964 2631 1 chr7A.!!$R1 667

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
396 2378 0.105039 CATCTCCCGTTAGGCTGGTC 59.895 60.0 0.0 0.0 35.76 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 6257 0.100861 GGAAGCGTTCCTACTCTCCG 59.899 60.0 8.87 0.0 46.57 4.63 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
47 48 2.115291 GGGCAATCTTCCGGCACTC 61.115 63.158 0.00 0.00 0.00 3.51
70 2007 1.135527 CAACATTGCCGATTCCAGCAT 59.864 47.619 0.00 0.00 39.11 3.79
71 2008 1.477553 ACATTGCCGATTCCAGCATT 58.522 45.000 0.00 0.00 39.11 3.56
72 2009 2.653726 ACATTGCCGATTCCAGCATTA 58.346 42.857 0.00 0.00 39.11 1.90
73 2010 3.023119 ACATTGCCGATTCCAGCATTAA 58.977 40.909 0.00 0.00 39.11 1.40
74 2011 3.638160 ACATTGCCGATTCCAGCATTAAT 59.362 39.130 0.00 0.00 39.11 1.40
75 2012 4.826733 ACATTGCCGATTCCAGCATTAATA 59.173 37.500 0.00 0.00 39.11 0.98
76 2013 5.477984 ACATTGCCGATTCCAGCATTAATAT 59.522 36.000 0.00 0.00 39.11 1.28
172 2121 7.381678 CCTAATCGCCTTTGTTCATACTAGTAC 59.618 40.741 4.31 0.00 0.00 2.73
178 2127 6.268566 CCTTTGTTCATACTAGTACGTACCC 58.731 44.000 21.80 0.00 0.00 3.69
223 2179 1.958205 GATCGCCGGATGAAGCAGG 60.958 63.158 5.05 0.00 31.51 4.85
271 2231 5.651530 ACAGAATATATATCCGCACCGAAG 58.348 41.667 0.00 0.00 0.00 3.79
346 2322 3.744846 GCAGGACCTCGAGTCTACTGATA 60.745 52.174 19.32 0.00 45.54 2.15
386 2368 2.681097 GCTAGCTTTTTCCATCTCCCGT 60.681 50.000 7.70 0.00 0.00 5.28
387 2369 2.586648 AGCTTTTTCCATCTCCCGTT 57.413 45.000 0.00 0.00 0.00 4.44
388 2370 3.713826 AGCTTTTTCCATCTCCCGTTA 57.286 42.857 0.00 0.00 0.00 3.18
389 2371 3.610911 AGCTTTTTCCATCTCCCGTTAG 58.389 45.455 0.00 0.00 0.00 2.34
390 2372 2.683362 GCTTTTTCCATCTCCCGTTAGG 59.317 50.000 0.00 0.00 37.24 2.69
391 2373 2.413310 TTTTCCATCTCCCGTTAGGC 57.587 50.000 0.00 0.00 35.76 3.93
392 2374 1.580059 TTTCCATCTCCCGTTAGGCT 58.420 50.000 0.00 0.00 35.76 4.58
393 2375 0.830648 TTCCATCTCCCGTTAGGCTG 59.169 55.000 0.00 0.00 35.76 4.85
394 2376 1.048724 TCCATCTCCCGTTAGGCTGG 61.049 60.000 0.00 0.00 35.76 4.85
395 2377 1.338136 CCATCTCCCGTTAGGCTGGT 61.338 60.000 0.00 0.00 35.76 4.00
396 2378 0.105039 CATCTCCCGTTAGGCTGGTC 59.895 60.000 0.00 0.00 35.76 4.02
397 2379 1.392710 ATCTCCCGTTAGGCTGGTCG 61.393 60.000 0.00 0.00 35.76 4.79
398 2380 2.283388 TCCCGTTAGGCTGGTCGT 60.283 61.111 0.00 0.00 35.76 4.34
399 2381 1.001020 TCCCGTTAGGCTGGTCGTA 60.001 57.895 0.00 0.00 35.76 3.43
400 2382 0.611618 TCCCGTTAGGCTGGTCGTAA 60.612 55.000 0.00 0.00 35.76 3.18
401 2383 0.462789 CCCGTTAGGCTGGTCGTAAT 59.537 55.000 0.00 0.00 35.76 1.89
402 2384 1.567504 CCGTTAGGCTGGTCGTAATG 58.432 55.000 0.00 0.00 33.85 1.90
403 2385 1.567504 CGTTAGGCTGGTCGTAATGG 58.432 55.000 0.00 0.00 31.67 3.16
404 2386 1.134907 CGTTAGGCTGGTCGTAATGGT 60.135 52.381 0.00 0.00 31.67 3.55
405 2387 2.099592 CGTTAGGCTGGTCGTAATGGTA 59.900 50.000 0.00 0.00 31.67 3.25
406 2388 3.714391 GTTAGGCTGGTCGTAATGGTAG 58.286 50.000 0.00 0.00 0.00 3.18
407 2389 1.861982 AGGCTGGTCGTAATGGTAGT 58.138 50.000 0.00 0.00 0.00 2.73
408 2390 3.022557 AGGCTGGTCGTAATGGTAGTA 57.977 47.619 0.00 0.00 0.00 1.82
409 2391 3.573695 AGGCTGGTCGTAATGGTAGTAT 58.426 45.455 0.00 0.00 0.00 2.12
410 2392 3.573110 AGGCTGGTCGTAATGGTAGTATC 59.427 47.826 0.00 0.00 0.00 2.24
411 2393 3.319972 GGCTGGTCGTAATGGTAGTATCA 59.680 47.826 0.00 0.00 0.00 2.15
412 2394 4.021368 GGCTGGTCGTAATGGTAGTATCAT 60.021 45.833 0.00 0.00 0.00 2.45
413 2395 5.184479 GGCTGGTCGTAATGGTAGTATCATA 59.816 44.000 0.00 0.00 0.00 2.15
414 2396 6.323266 GCTGGTCGTAATGGTAGTATCATAG 58.677 44.000 0.00 0.00 0.00 2.23
415 2397 6.263516 TGGTCGTAATGGTAGTATCATAGC 57.736 41.667 0.00 0.00 0.00 2.97
416 2398 6.008331 TGGTCGTAATGGTAGTATCATAGCT 58.992 40.000 0.00 0.00 0.00 3.32
417 2399 7.170277 TGGTCGTAATGGTAGTATCATAGCTA 58.830 38.462 0.00 0.00 0.00 3.32
418 2400 7.666804 TGGTCGTAATGGTAGTATCATAGCTAA 59.333 37.037 0.00 0.00 0.00 3.09
419 2401 8.684520 GGTCGTAATGGTAGTATCATAGCTAAT 58.315 37.037 0.00 0.00 0.00 1.73
427 2409 9.200817 TGGTAGTATCATAGCTAATATCATGCA 57.799 33.333 0.00 0.00 0.00 3.96
430 2412 8.604640 AGTATCATAGCTAATATCATGCATGC 57.395 34.615 22.25 11.82 0.00 4.06
431 2413 6.879276 ATCATAGCTAATATCATGCATGCC 57.121 37.500 22.25 3.99 0.00 4.40
432 2414 5.747342 TCATAGCTAATATCATGCATGCCA 58.253 37.500 22.25 11.89 0.00 4.92
433 2415 6.181908 TCATAGCTAATATCATGCATGCCAA 58.818 36.000 22.25 9.67 0.00 4.52
434 2416 6.831868 TCATAGCTAATATCATGCATGCCAAT 59.168 34.615 22.25 12.74 0.00 3.16
435 2417 5.995565 AGCTAATATCATGCATGCCAATT 57.004 34.783 22.25 19.98 0.00 2.32
436 2418 8.626526 CATAGCTAATATCATGCATGCCAATTA 58.373 33.333 22.25 20.02 0.00 1.40
437 2419 7.096884 AGCTAATATCATGCATGCCAATTAG 57.903 36.000 28.77 28.77 32.63 1.73
438 2420 6.096423 AGCTAATATCATGCATGCCAATTAGG 59.904 38.462 30.86 22.00 41.84 2.69
453 2435 5.981174 CCAATTAGGCAATTTTGATGAGGT 58.019 37.500 0.00 0.00 31.82 3.85
454 2436 5.813672 CCAATTAGGCAATTTTGATGAGGTG 59.186 40.000 0.00 0.00 31.82 4.00
455 2437 5.603170 ATTAGGCAATTTTGATGAGGTGG 57.397 39.130 0.00 0.00 0.00 4.61
456 2438 1.551883 AGGCAATTTTGATGAGGTGGC 59.448 47.619 0.00 0.00 0.00 5.01
457 2439 1.275856 GGCAATTTTGATGAGGTGGCA 59.724 47.619 0.00 0.00 0.00 4.92
458 2440 2.093341 GGCAATTTTGATGAGGTGGCAT 60.093 45.455 0.00 0.00 0.00 4.40
459 2441 3.132646 GGCAATTTTGATGAGGTGGCATA 59.867 43.478 0.00 0.00 0.00 3.14
460 2442 4.365723 GCAATTTTGATGAGGTGGCATAG 58.634 43.478 0.00 0.00 0.00 2.23
461 2443 4.365723 CAATTTTGATGAGGTGGCATAGC 58.634 43.478 0.00 0.00 0.00 2.97
462 2444 2.804986 TTTGATGAGGTGGCATAGCA 57.195 45.000 0.00 0.00 0.00 3.49
463 2445 3.301794 TTTGATGAGGTGGCATAGCAT 57.698 42.857 0.00 0.00 0.00 3.79
464 2446 3.301794 TTGATGAGGTGGCATAGCATT 57.698 42.857 0.00 0.00 0.00 3.56
465 2447 4.436113 TTGATGAGGTGGCATAGCATTA 57.564 40.909 0.00 0.00 0.00 1.90
466 2448 4.436113 TGATGAGGTGGCATAGCATTAA 57.564 40.909 0.00 0.00 0.00 1.40
467 2449 4.790937 TGATGAGGTGGCATAGCATTAAA 58.209 39.130 0.00 0.00 0.00 1.52
468 2450 5.387788 TGATGAGGTGGCATAGCATTAAAT 58.612 37.500 0.00 0.00 0.00 1.40
469 2451 5.242171 TGATGAGGTGGCATAGCATTAAATG 59.758 40.000 0.00 0.00 0.00 2.32
470 2452 4.790937 TGAGGTGGCATAGCATTAAATGA 58.209 39.130 0.00 0.00 0.00 2.57
471 2453 5.199723 TGAGGTGGCATAGCATTAAATGAA 58.800 37.500 0.00 0.00 0.00 2.57
472 2454 5.300034 TGAGGTGGCATAGCATTAAATGAAG 59.700 40.000 0.00 0.00 0.00 3.02
473 2455 5.448654 AGGTGGCATAGCATTAAATGAAGA 58.551 37.500 0.00 0.00 0.00 2.87
474 2456 5.893255 AGGTGGCATAGCATTAAATGAAGAA 59.107 36.000 0.00 0.00 0.00 2.52
475 2457 6.380846 AGGTGGCATAGCATTAAATGAAGAAA 59.619 34.615 0.00 0.00 0.00 2.52
476 2458 6.698766 GGTGGCATAGCATTAAATGAAGAAAG 59.301 38.462 0.00 0.00 0.00 2.62
477 2459 7.416664 GGTGGCATAGCATTAAATGAAGAAAGA 60.417 37.037 0.00 0.00 0.00 2.52
478 2460 7.646922 GTGGCATAGCATTAAATGAAGAAAGAG 59.353 37.037 0.00 0.00 0.00 2.85
479 2461 7.557358 TGGCATAGCATTAAATGAAGAAAGAGA 59.443 33.333 0.00 0.00 0.00 3.10
480 2462 8.574737 GGCATAGCATTAAATGAAGAAAGAGAT 58.425 33.333 0.00 0.00 0.00 2.75
481 2463 9.395707 GCATAGCATTAAATGAAGAAAGAGATG 57.604 33.333 0.00 0.00 0.00 2.90
482 2464 9.894783 CATAGCATTAAATGAAGAAAGAGATGG 57.105 33.333 0.00 0.00 0.00 3.51
483 2465 7.951347 AGCATTAAATGAAGAAAGAGATGGT 57.049 32.000 0.00 0.00 0.00 3.55
484 2466 7.769220 AGCATTAAATGAAGAAAGAGATGGTG 58.231 34.615 0.00 0.00 0.00 4.17
485 2467 7.395489 AGCATTAAATGAAGAAAGAGATGGTGT 59.605 33.333 0.00 0.00 0.00 4.16
486 2468 8.677300 GCATTAAATGAAGAAAGAGATGGTGTA 58.323 33.333 0.00 0.00 0.00 2.90
488 2470 9.965902 ATTAAATGAAGAAAGAGATGGTGTAGT 57.034 29.630 0.00 0.00 0.00 2.73
491 2473 9.606631 AAATGAAGAAAGAGATGGTGTAGTATC 57.393 33.333 0.00 0.00 0.00 2.24
492 2474 7.718334 TGAAGAAAGAGATGGTGTAGTATCA 57.282 36.000 0.00 0.00 0.00 2.15
493 2475 8.311395 TGAAGAAAGAGATGGTGTAGTATCAT 57.689 34.615 0.00 0.00 31.12 2.45
494 2476 9.421399 TGAAGAAAGAGATGGTGTAGTATCATA 57.579 33.333 0.00 0.00 27.68 2.15
497 2479 9.593565 AGAAAGAGATGGTGTAGTATCATATCA 57.406 33.333 0.00 0.00 39.95 2.15
500 2482 9.539194 AAGAGATGGTGTAGTATCATATCATGA 57.461 33.333 0.00 0.00 39.95 3.07
537 2519 7.680442 TTAAATGCTATGCTACTTTGTGTCA 57.320 32.000 0.00 0.00 0.00 3.58
538 2520 6.764308 AAATGCTATGCTACTTTGTGTCAT 57.236 33.333 0.00 0.00 0.00 3.06
539 2521 5.746307 ATGCTATGCTACTTTGTGTCATG 57.254 39.130 0.00 0.00 0.00 3.07
540 2522 3.374988 TGCTATGCTACTTTGTGTCATGC 59.625 43.478 0.00 0.00 0.00 4.06
541 2523 3.374988 GCTATGCTACTTTGTGTCATGCA 59.625 43.478 0.00 0.00 35.34 3.96
542 2524 4.036027 GCTATGCTACTTTGTGTCATGCAT 59.964 41.667 0.00 0.00 40.50 3.96
543 2525 3.835378 TGCTACTTTGTGTCATGCATG 57.165 42.857 21.07 21.07 0.00 4.06
544 2526 3.410508 TGCTACTTTGTGTCATGCATGA 58.589 40.909 25.42 25.42 0.00 3.07
561 2543 9.612066 TCATGCATGACAATAAATAGAGTACAA 57.388 29.630 25.42 0.00 0.00 2.41
562 2544 9.655769 CATGCATGACAATAAATAGAGTACAAC 57.344 33.333 22.59 0.00 0.00 3.32
563 2545 8.785329 TGCATGACAATAAATAGAGTACAACA 57.215 30.769 0.00 0.00 0.00 3.33
564 2546 9.394767 TGCATGACAATAAATAGAGTACAACAT 57.605 29.630 0.00 0.00 0.00 2.71
565 2547 9.655769 GCATGACAATAAATAGAGTACAACATG 57.344 33.333 0.00 0.00 34.20 3.21
598 2580 9.904732 ATATATGATACTATGCATTAGGGAGGT 57.095 33.333 3.54 0.00 31.68 3.85
600 2582 7.667575 ATGATACTATGCATTAGGGAGGTAG 57.332 40.000 3.54 0.00 31.68 3.18
601 2583 6.562228 TGATACTATGCATTAGGGAGGTAGT 58.438 40.000 3.54 0.88 31.68 2.73
602 2584 7.705700 TGATACTATGCATTAGGGAGGTAGTA 58.294 38.462 3.54 3.44 31.68 1.82
603 2585 8.344546 TGATACTATGCATTAGGGAGGTAGTAT 58.655 37.037 3.54 8.56 36.89 2.12
604 2586 8.770010 ATACTATGCATTAGGGAGGTAGTATC 57.230 38.462 3.54 0.00 31.70 2.24
605 2587 6.562228 ACTATGCATTAGGGAGGTAGTATCA 58.438 40.000 3.54 0.00 31.68 2.15
606 2588 7.192628 ACTATGCATTAGGGAGGTAGTATCAT 58.807 38.462 3.54 0.00 31.68 2.45
607 2589 8.344546 ACTATGCATTAGGGAGGTAGTATCATA 58.655 37.037 3.54 0.00 31.68 2.15
608 2590 6.852420 TGCATTAGGGAGGTAGTATCATAC 57.148 41.667 0.00 0.00 0.00 2.39
609 2591 6.319715 TGCATTAGGGAGGTAGTATCATACA 58.680 40.000 0.00 0.00 0.00 2.29
610 2592 6.210784 TGCATTAGGGAGGTAGTATCATACAC 59.789 42.308 0.00 0.00 0.00 2.90
611 2593 6.437793 GCATTAGGGAGGTAGTATCATACACT 59.562 42.308 0.00 0.00 0.00 3.55
612 2594 7.614583 GCATTAGGGAGGTAGTATCATACACTA 59.385 40.741 0.00 0.00 0.00 2.74
613 2595 9.179909 CATTAGGGAGGTAGTATCATACACTAG 57.820 40.741 0.00 0.00 0.00 2.57
614 2596 6.783517 AGGGAGGTAGTATCATACACTAGT 57.216 41.667 0.00 0.00 0.00 2.57
615 2597 7.885209 AGGGAGGTAGTATCATACACTAGTA 57.115 40.000 0.00 0.00 34.10 1.82
616 2598 8.465798 AGGGAGGTAGTATCATACACTAGTAT 57.534 38.462 0.00 0.00 41.57 2.12
617 2599 8.550585 AGGGAGGTAGTATCATACACTAGTATC 58.449 40.741 0.00 0.00 38.88 2.24
618 2600 8.327271 GGGAGGTAGTATCATACACTAGTATCA 58.673 40.741 0.00 0.00 38.88 2.15
619 2601 9.908747 GGAGGTAGTATCATACACTAGTATCAT 57.091 37.037 0.00 0.00 38.88 2.45
652 2634 9.908747 ATGATACTAGTGTATGATACTACCTCC 57.091 37.037 5.39 0.00 39.29 4.30
653 2635 8.327271 TGATACTAGTGTATGATACTACCTCCC 58.673 40.741 5.39 0.00 39.29 4.30
654 2636 5.890049 ACTAGTGTATGATACTACCTCCCC 58.110 45.833 4.03 0.00 0.00 4.81
655 2637 4.129317 AGTGTATGATACTACCTCCCCC 57.871 50.000 4.03 0.00 0.00 5.40
656 2638 3.469771 AGTGTATGATACTACCTCCCCCA 59.530 47.826 4.03 0.00 0.00 4.96
657 2639 4.109765 AGTGTATGATACTACCTCCCCCAT 59.890 45.833 4.03 0.00 0.00 4.00
658 2640 4.844655 GTGTATGATACTACCTCCCCCATT 59.155 45.833 4.03 0.00 0.00 3.16
659 2641 6.021030 GTGTATGATACTACCTCCCCCATTA 58.979 44.000 4.03 0.00 0.00 1.90
660 2642 6.021030 TGTATGATACTACCTCCCCCATTAC 58.979 44.000 4.03 0.00 0.00 1.89
661 2643 4.562934 TGATACTACCTCCCCCATTACA 57.437 45.455 0.00 0.00 0.00 2.41
662 2644 4.898268 TGATACTACCTCCCCCATTACAA 58.102 43.478 0.00 0.00 0.00 2.41
663 2645 4.657039 TGATACTACCTCCCCCATTACAAC 59.343 45.833 0.00 0.00 0.00 3.32
664 2646 2.202707 ACTACCTCCCCCATTACAACC 58.797 52.381 0.00 0.00 0.00 3.77
665 2647 2.201830 CTACCTCCCCCATTACAACCA 58.798 52.381 0.00 0.00 0.00 3.67
666 2648 0.999712 ACCTCCCCCATTACAACCAG 59.000 55.000 0.00 0.00 0.00 4.00
667 2649 0.395724 CCTCCCCCATTACAACCAGC 60.396 60.000 0.00 0.00 0.00 4.85
668 2650 0.395724 CTCCCCCATTACAACCAGCC 60.396 60.000 0.00 0.00 0.00 4.85
845 2849 2.363795 CTCCCCGGCTGGTGACTA 60.364 66.667 11.58 0.00 0.00 2.59
853 2857 2.184322 CTGGTGACTATGCGGCGT 59.816 61.111 9.37 0.00 0.00 5.68
942 2947 4.459331 CGTGCCGCCACATTTCCG 62.459 66.667 0.00 0.00 42.17 4.30
1042 3083 2.923035 CCCCACCAACACCACTGA 59.077 61.111 0.00 0.00 0.00 3.41
1124 3188 2.651701 CCGCATACGTACTCAAGCTAG 58.348 52.381 0.00 0.00 37.70 3.42
1125 3189 2.044860 CGCATACGTACTCAAGCTAGC 58.955 52.381 6.62 6.62 33.53 3.42
1246 3319 1.223487 GGCGGGTGGCATAGAAAGA 59.777 57.895 0.00 0.00 46.16 2.52
1428 3778 1.193203 CCGTGCTCGCTAAATATGCTG 59.807 52.381 1.89 0.00 35.54 4.41
1431 3781 3.384668 GTGCTCGCTAAATATGCTGAGA 58.615 45.455 0.00 0.00 35.09 3.27
1432 3782 3.804325 GTGCTCGCTAAATATGCTGAGAA 59.196 43.478 0.00 0.00 35.09 2.87
1485 3867 3.549299 CTGAAAGTAGGCTTGTGCTTG 57.451 47.619 0.00 0.00 39.59 4.01
1486 3868 2.227388 CTGAAAGTAGGCTTGTGCTTGG 59.773 50.000 0.00 0.00 39.59 3.61
1487 3869 2.158682 TGAAAGTAGGCTTGTGCTTGGA 60.159 45.455 0.00 0.00 39.59 3.53
1488 3870 2.191128 AAGTAGGCTTGTGCTTGGAG 57.809 50.000 0.00 0.00 39.59 3.86
1561 4194 8.475639 AGTACATCACTACCTTACTGTTTATGG 58.524 37.037 0.00 0.00 34.98 2.74
1591 4233 0.804364 TGTTGCTGTGCCGATCATTC 59.196 50.000 0.00 0.00 0.00 2.67
1618 4426 9.212641 CATGCTCCTATATATATGTTGGCATAC 57.787 37.037 18.50 0.00 40.05 2.39
1668 4484 1.134699 TGCATCTGGGAAGAGTTAGCG 60.135 52.381 0.00 0.00 0.00 4.26
1728 4677 7.205297 TCTTGAAGCAGAATTCCTTTTTCTTG 58.795 34.615 0.65 0.00 31.11 3.02
1766 4753 8.088981 TCAGGCTACGATATATTCTTTCTTTCC 58.911 37.037 0.00 0.00 0.00 3.13
1918 5980 9.436957 TTGTAATCTCAACTGTTTATCTTCTCC 57.563 33.333 0.00 0.00 0.00 3.71
1919 5981 8.041323 TGTAATCTCAACTGTTTATCTTCTCCC 58.959 37.037 0.00 0.00 0.00 4.30
1920 5982 6.882768 ATCTCAACTGTTTATCTTCTCCCT 57.117 37.500 0.00 0.00 0.00 4.20
1921 5983 6.287589 TCTCAACTGTTTATCTTCTCCCTC 57.712 41.667 0.00 0.00 0.00 4.30
1923 5985 6.153680 TCTCAACTGTTTATCTTCTCCCTCTC 59.846 42.308 0.00 0.00 0.00 3.20
1924 5986 5.187967 TCAACTGTTTATCTTCTCCCTCTCC 59.812 44.000 0.00 0.00 0.00 3.71
1925 5987 4.034410 ACTGTTTATCTTCTCCCTCTCCC 58.966 47.826 0.00 0.00 0.00 4.30
1927 5989 3.032459 GTTTATCTTCTCCCTCTCCCGT 58.968 50.000 0.00 0.00 0.00 5.28
1928 5990 4.213513 GTTTATCTTCTCCCTCTCCCGTA 58.786 47.826 0.00 0.00 0.00 4.02
1929 5991 4.531357 TTATCTTCTCCCTCTCCCGTAA 57.469 45.455 0.00 0.00 0.00 3.18
1930 5992 2.140839 TCTTCTCCCTCTCCCGTAAC 57.859 55.000 0.00 0.00 0.00 2.50
1931 5993 1.356738 TCTTCTCCCTCTCCCGTAACA 59.643 52.381 0.00 0.00 0.00 2.41
1932 5994 2.176889 CTTCTCCCTCTCCCGTAACAA 58.823 52.381 0.00 0.00 0.00 2.83
1933 5995 1.553706 TCTCCCTCTCCCGTAACAAC 58.446 55.000 0.00 0.00 0.00 3.32
1934 5996 0.535797 CTCCCTCTCCCGTAACAACC 59.464 60.000 0.00 0.00 0.00 3.77
1935 5997 0.115745 TCCCTCTCCCGTAACAACCT 59.884 55.000 0.00 0.00 0.00 3.50
1936 5998 0.981943 CCCTCTCCCGTAACAACCTT 59.018 55.000 0.00 0.00 0.00 3.50
1937 5999 1.338769 CCCTCTCCCGTAACAACCTTG 60.339 57.143 0.00 0.00 0.00 3.61
1938 6000 1.338769 CCTCTCCCGTAACAACCTTGG 60.339 57.143 0.00 0.00 0.00 3.61
1939 6001 1.346722 CTCTCCCGTAACAACCTTGGT 59.653 52.381 0.00 0.00 0.00 3.67
1940 6002 1.345415 TCTCCCGTAACAACCTTGGTC 59.655 52.381 0.00 0.00 0.00 4.02
1949 6011 5.105877 CGTAACAACCTTGGTCTCTATCTCA 60.106 44.000 0.00 0.00 0.00 3.27
1950 6012 6.405953 CGTAACAACCTTGGTCTCTATCTCAT 60.406 42.308 0.00 0.00 0.00 2.90
1952 6014 5.738909 ACAACCTTGGTCTCTATCTCATTG 58.261 41.667 0.00 0.00 0.00 2.82
1956 6018 5.364157 ACCTTGGTCTCTATCTCATTGTACC 59.636 44.000 0.00 0.00 0.00 3.34
1957 6019 5.508153 CCTTGGTCTCTATCTCATTGTACCG 60.508 48.000 0.00 0.00 0.00 4.02
1960 6022 5.067413 TGGTCTCTATCTCATTGTACCGAAC 59.933 44.000 0.00 0.00 0.00 3.95
1962 6024 5.299782 GTCTCTATCTCATTGTACCGAACCT 59.700 44.000 0.00 0.00 0.00 3.50
1977 6136 2.128035 GAACCTGTATCCTTGCGATCG 58.872 52.381 11.69 11.69 31.92 3.69
2001 6163 2.666862 CCTTGTACGCCACGGCAA 60.667 61.111 9.11 1.20 42.06 4.52
2011 6218 2.348998 CACGGCAAGGGCTCTTCT 59.651 61.111 0.00 0.00 40.87 2.85
2036 6247 3.432252 CCTCGATCAATATAAACCCACGC 59.568 47.826 0.00 0.00 0.00 5.34
2038 6249 2.156891 CGATCAATATAAACCCACGCGG 59.843 50.000 12.47 0.00 37.81 6.46
2044 6255 1.614241 ATAAACCCACGCGGCTCTCT 61.614 55.000 12.47 0.00 33.26 3.10
2046 6257 2.502692 AAACCCACGCGGCTCTCTAC 62.503 60.000 12.47 0.00 33.26 2.59
2049 6260 3.506096 CACGCGGCTCTCTACGGA 61.506 66.667 12.47 0.00 0.00 4.69
2182 7780 0.680921 ACCAGAACCAATCGCCATGG 60.681 55.000 7.63 7.63 43.84 3.66
2197 7807 1.997874 ATGGCTTCCTCCTCGGCTT 60.998 57.895 0.00 0.00 0.00 4.35
2219 7829 0.323908 CTCTCCCTCAACCTCGGAGT 60.324 60.000 4.02 0.00 43.20 3.85
2378 7988 1.157870 ACGGACAAAACGACAGCCAG 61.158 55.000 0.00 0.00 34.93 4.85
2400 8010 2.742116 GCCGAACCCCCTCTATGCA 61.742 63.158 0.00 0.00 0.00 3.96
2468 8078 5.713792 TCTCTGTCAAAAGAGATTCTCGT 57.286 39.130 8.01 2.02 46.13 4.18
2478 8088 5.723672 AAGAGATTCTCGTCCAAGTTGTA 57.276 39.130 8.01 0.00 35.36 2.41
2601 8220 0.324738 AGAAGGGCTCCATGTCGAGA 60.325 55.000 3.41 0.00 30.97 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
187 2136 3.731216 CGATCAATGTTAATCGAGTCGCT 59.269 43.478 7.92 0.00 45.83 4.93
271 2231 5.463392 TGAGATATCTCGCACTTTATTGCAC 59.537 40.000 24.27 0.00 45.72 4.57
324 2298 0.736053 CAGTAGACTCGAGGTCCTGC 59.264 60.000 18.41 13.48 45.54 4.85
346 2322 0.029035 CTAGCTAACCGTCGACGCAT 59.971 55.000 31.73 23.07 38.18 4.73
371 2353 2.307686 AGCCTAACGGGAGATGGAAAAA 59.692 45.455 0.00 0.00 37.23 1.94
386 2368 3.368248 ACTACCATTACGACCAGCCTAA 58.632 45.455 0.00 0.00 0.00 2.69
387 2369 3.022557 ACTACCATTACGACCAGCCTA 57.977 47.619 0.00 0.00 0.00 3.93
388 2370 1.861982 ACTACCATTACGACCAGCCT 58.138 50.000 0.00 0.00 0.00 4.58
389 2371 3.319972 TGATACTACCATTACGACCAGCC 59.680 47.826 0.00 0.00 0.00 4.85
390 2372 4.579454 TGATACTACCATTACGACCAGC 57.421 45.455 0.00 0.00 0.00 4.85
391 2373 6.151312 AGCTATGATACTACCATTACGACCAG 59.849 42.308 0.00 0.00 0.00 4.00
392 2374 6.008331 AGCTATGATACTACCATTACGACCA 58.992 40.000 0.00 0.00 0.00 4.02
393 2375 6.512342 AGCTATGATACTACCATTACGACC 57.488 41.667 0.00 0.00 0.00 4.79
401 2383 9.200817 TGCATGATATTAGCTATGATACTACCA 57.799 33.333 0.00 0.00 0.00 3.25
404 2386 9.702494 GCATGCATGATATTAGCTATGATACTA 57.298 33.333 30.64 0.00 0.00 1.82
405 2387 7.660617 GGCATGCATGATATTAGCTATGATACT 59.339 37.037 30.64 0.00 0.00 2.12
406 2388 7.443272 TGGCATGCATGATATTAGCTATGATAC 59.557 37.037 30.64 5.71 0.00 2.24
407 2389 7.511268 TGGCATGCATGATATTAGCTATGATA 58.489 34.615 30.64 0.00 0.00 2.15
408 2390 6.362248 TGGCATGCATGATATTAGCTATGAT 58.638 36.000 30.64 0.00 0.00 2.45
409 2391 5.747342 TGGCATGCATGATATTAGCTATGA 58.253 37.500 30.64 0.00 0.00 2.15
410 2392 6.445357 TTGGCATGCATGATATTAGCTATG 57.555 37.500 30.64 0.23 0.00 2.23
411 2393 7.655521 AATTGGCATGCATGATATTAGCTAT 57.344 32.000 30.64 7.83 0.00 2.97
412 2394 7.283807 CCTAATTGGCATGCATGATATTAGCTA 59.716 37.037 30.64 7.90 30.83 3.32
413 2395 5.995565 AATTGGCATGCATGATATTAGCT 57.004 34.783 30.64 3.18 0.00 3.32
414 2396 6.270815 CCTAATTGGCATGCATGATATTAGC 58.729 40.000 30.64 12.56 30.83 3.09
430 2412 5.813672 CACCTCATCAAAATTGCCTAATTGG 59.186 40.000 0.00 0.00 36.65 3.16
431 2413 5.813672 CCACCTCATCAAAATTGCCTAATTG 59.186 40.000 0.00 0.00 36.65 2.32
432 2414 5.627503 GCCACCTCATCAAAATTGCCTAATT 60.628 40.000 0.00 0.00 38.11 1.40
433 2415 4.141869 GCCACCTCATCAAAATTGCCTAAT 60.142 41.667 0.00 0.00 0.00 1.73
434 2416 3.195396 GCCACCTCATCAAAATTGCCTAA 59.805 43.478 0.00 0.00 0.00 2.69
435 2417 2.760092 GCCACCTCATCAAAATTGCCTA 59.240 45.455 0.00 0.00 0.00 3.93
436 2418 1.551883 GCCACCTCATCAAAATTGCCT 59.448 47.619 0.00 0.00 0.00 4.75
437 2419 1.275856 TGCCACCTCATCAAAATTGCC 59.724 47.619 0.00 0.00 0.00 4.52
438 2420 2.747396 TGCCACCTCATCAAAATTGC 57.253 45.000 0.00 0.00 0.00 3.56
439 2421 4.142116 TGCTATGCCACCTCATCAAAATTG 60.142 41.667 0.00 0.00 0.00 2.32
440 2422 4.025360 TGCTATGCCACCTCATCAAAATT 58.975 39.130 0.00 0.00 0.00 1.82
441 2423 3.634504 TGCTATGCCACCTCATCAAAAT 58.365 40.909 0.00 0.00 0.00 1.82
442 2424 3.084536 TGCTATGCCACCTCATCAAAA 57.915 42.857 0.00 0.00 0.00 2.44
443 2425 2.804986 TGCTATGCCACCTCATCAAA 57.195 45.000 0.00 0.00 0.00 2.69
444 2426 3.301794 AATGCTATGCCACCTCATCAA 57.698 42.857 0.00 0.00 0.00 2.57
445 2427 4.436113 TTAATGCTATGCCACCTCATCA 57.564 40.909 0.00 0.00 0.00 3.07
446 2428 5.474532 TCATTTAATGCTATGCCACCTCATC 59.525 40.000 0.00 0.00 0.00 2.92
447 2429 5.387788 TCATTTAATGCTATGCCACCTCAT 58.612 37.500 0.00 0.00 0.00 2.90
448 2430 4.790937 TCATTTAATGCTATGCCACCTCA 58.209 39.130 0.00 0.00 0.00 3.86
449 2431 5.532406 TCTTCATTTAATGCTATGCCACCTC 59.468 40.000 0.00 0.00 0.00 3.85
450 2432 5.448654 TCTTCATTTAATGCTATGCCACCT 58.551 37.500 0.00 0.00 0.00 4.00
451 2433 5.772825 TCTTCATTTAATGCTATGCCACC 57.227 39.130 0.00 0.00 0.00 4.61
452 2434 7.483307 TCTTTCTTCATTTAATGCTATGCCAC 58.517 34.615 0.00 0.00 0.00 5.01
453 2435 7.557358 TCTCTTTCTTCATTTAATGCTATGCCA 59.443 33.333 0.00 0.00 0.00 4.92
454 2436 7.934457 TCTCTTTCTTCATTTAATGCTATGCC 58.066 34.615 0.00 0.00 0.00 4.40
455 2437 9.395707 CATCTCTTTCTTCATTTAATGCTATGC 57.604 33.333 0.00 0.00 0.00 3.14
456 2438 9.894783 CCATCTCTTTCTTCATTTAATGCTATG 57.105 33.333 0.00 0.00 0.00 2.23
457 2439 9.638176 ACCATCTCTTTCTTCATTTAATGCTAT 57.362 29.630 0.00 0.00 0.00 2.97
458 2440 8.896744 CACCATCTCTTTCTTCATTTAATGCTA 58.103 33.333 0.00 0.00 0.00 3.49
459 2441 7.395489 ACACCATCTCTTTCTTCATTTAATGCT 59.605 33.333 0.00 0.00 0.00 3.79
460 2442 7.542025 ACACCATCTCTTTCTTCATTTAATGC 58.458 34.615 0.00 0.00 0.00 3.56
462 2444 9.965902 ACTACACCATCTCTTTCTTCATTTAAT 57.034 29.630 0.00 0.00 0.00 1.40
465 2447 9.606631 GATACTACACCATCTCTTTCTTCATTT 57.393 33.333 0.00 0.00 0.00 2.32
466 2448 8.762645 TGATACTACACCATCTCTTTCTTCATT 58.237 33.333 0.00 0.00 0.00 2.57
467 2449 8.311395 TGATACTACACCATCTCTTTCTTCAT 57.689 34.615 0.00 0.00 0.00 2.57
468 2450 7.718334 TGATACTACACCATCTCTTTCTTCA 57.282 36.000 0.00 0.00 0.00 3.02
471 2453 9.593565 TGATATGATACTACACCATCTCTTTCT 57.406 33.333 0.00 0.00 0.00 2.52
474 2456 9.539194 TCATGATATGATACTACACCATCTCTT 57.461 33.333 0.00 0.00 33.59 2.85
511 2493 9.389755 TGACACAAAGTAGCATAGCATTTAATA 57.610 29.630 0.00 0.00 0.00 0.98
512 2494 8.279970 TGACACAAAGTAGCATAGCATTTAAT 57.720 30.769 0.00 0.00 0.00 1.40
513 2495 7.680442 TGACACAAAGTAGCATAGCATTTAA 57.320 32.000 0.00 0.00 0.00 1.52
514 2496 7.679400 GCATGACACAAAGTAGCATAGCATTTA 60.679 37.037 0.00 0.00 0.00 1.40
515 2497 6.558009 CATGACACAAAGTAGCATAGCATTT 58.442 36.000 0.00 0.00 0.00 2.32
516 2498 5.449588 GCATGACACAAAGTAGCATAGCATT 60.450 40.000 0.00 0.00 0.00 3.56
517 2499 4.036027 GCATGACACAAAGTAGCATAGCAT 59.964 41.667 0.00 0.00 0.00 3.79
518 2500 3.374988 GCATGACACAAAGTAGCATAGCA 59.625 43.478 0.00 0.00 0.00 3.49
519 2501 3.374988 TGCATGACACAAAGTAGCATAGC 59.625 43.478 0.00 0.00 30.65 2.97
520 2502 5.295045 TCATGCATGACACAAAGTAGCATAG 59.705 40.000 25.42 0.00 39.67 2.23
521 2503 5.184711 TCATGCATGACACAAAGTAGCATA 58.815 37.500 25.42 0.00 39.67 3.14
522 2504 4.011698 TCATGCATGACACAAAGTAGCAT 58.988 39.130 25.42 0.00 41.24 3.79
523 2505 3.410508 TCATGCATGACACAAAGTAGCA 58.589 40.909 25.42 0.00 37.13 3.49
535 2517 9.612066 TTGTACTCTATTTATTGTCATGCATGA 57.388 29.630 25.42 25.42 0.00 3.07
536 2518 9.655769 GTTGTACTCTATTTATTGTCATGCATG 57.344 33.333 21.07 21.07 0.00 4.06
537 2519 9.394767 TGTTGTACTCTATTTATTGTCATGCAT 57.605 29.630 0.00 0.00 0.00 3.96
538 2520 8.785329 TGTTGTACTCTATTTATTGTCATGCA 57.215 30.769 0.00 0.00 0.00 3.96
539 2521 9.655769 CATGTTGTACTCTATTTATTGTCATGC 57.344 33.333 0.00 0.00 0.00 4.06
572 2554 9.904732 ACCTCCCTAATGCATAGTATCATATAT 57.095 33.333 0.00 0.00 0.00 0.86
574 2556 9.373450 CTACCTCCCTAATGCATAGTATCATAT 57.627 37.037 0.00 0.00 0.00 1.78
575 2557 8.344546 ACTACCTCCCTAATGCATAGTATCATA 58.655 37.037 0.00 0.00 0.00 2.15
576 2558 7.192628 ACTACCTCCCTAATGCATAGTATCAT 58.807 38.462 0.00 0.00 0.00 2.45
577 2559 6.562228 ACTACCTCCCTAATGCATAGTATCA 58.438 40.000 0.00 0.00 0.00 2.15
578 2560 8.770010 ATACTACCTCCCTAATGCATAGTATC 57.230 38.462 0.00 0.00 31.76 2.24
579 2561 8.344546 TGATACTACCTCCCTAATGCATAGTAT 58.655 37.037 11.08 11.08 37.18 2.12
580 2562 7.705700 TGATACTACCTCCCTAATGCATAGTA 58.294 38.462 0.00 0.81 0.00 1.82
581 2563 6.562228 TGATACTACCTCCCTAATGCATAGT 58.438 40.000 0.00 0.00 0.00 2.12
582 2564 7.667575 ATGATACTACCTCCCTAATGCATAG 57.332 40.000 0.00 0.00 0.00 2.23
583 2565 8.119891 TGTATGATACTACCTCCCTAATGCATA 58.880 37.037 0.00 0.00 0.00 3.14
584 2566 6.959954 TGTATGATACTACCTCCCTAATGCAT 59.040 38.462 4.03 0.00 0.00 3.96
585 2567 6.210784 GTGTATGATACTACCTCCCTAATGCA 59.789 42.308 4.03 0.00 0.00 3.96
586 2568 6.437793 AGTGTATGATACTACCTCCCTAATGC 59.562 42.308 4.03 0.00 0.00 3.56
587 2569 9.179909 CTAGTGTATGATACTACCTCCCTAATG 57.820 40.741 4.03 0.00 0.00 1.90
588 2570 8.902881 ACTAGTGTATGATACTACCTCCCTAAT 58.097 37.037 4.03 0.00 0.00 1.73
589 2571 8.285350 ACTAGTGTATGATACTACCTCCCTAA 57.715 38.462 4.03 0.00 0.00 2.69
590 2572 7.885209 ACTAGTGTATGATACTACCTCCCTA 57.115 40.000 4.03 0.00 0.00 3.53
591 2573 6.783517 ACTAGTGTATGATACTACCTCCCT 57.216 41.667 4.03 0.00 0.00 4.20
592 2574 8.327271 TGATACTAGTGTATGATACTACCTCCC 58.673 40.741 5.39 0.00 39.29 4.30
593 2575 9.908747 ATGATACTAGTGTATGATACTACCTCC 57.091 37.037 5.39 0.00 39.29 4.30
626 2608 9.908747 GGAGGTAGTATCATACACTAGTATCAT 57.091 37.037 0.00 0.00 38.88 2.45
627 2609 8.327271 GGGAGGTAGTATCATACACTAGTATCA 58.673 40.741 0.00 0.00 38.88 2.15
628 2610 7.774625 GGGGAGGTAGTATCATACACTAGTATC 59.225 44.444 0.00 0.00 38.88 2.24
629 2611 7.312439 GGGGGAGGTAGTATCATACACTAGTAT 60.312 44.444 0.00 0.00 41.57 2.12
630 2612 6.012157 GGGGGAGGTAGTATCATACACTAGTA 60.012 46.154 0.00 0.00 34.10 1.82
631 2613 5.222296 GGGGGAGGTAGTATCATACACTAGT 60.222 48.000 0.00 0.00 0.00 2.57
632 2614 5.222275 TGGGGGAGGTAGTATCATACACTAG 60.222 48.000 0.00 0.00 0.00 2.57
633 2615 4.671207 TGGGGGAGGTAGTATCATACACTA 59.329 45.833 0.00 0.00 0.00 2.74
634 2616 3.469771 TGGGGGAGGTAGTATCATACACT 59.530 47.826 0.00 0.00 0.00 3.55
635 2617 3.853207 TGGGGGAGGTAGTATCATACAC 58.147 50.000 0.00 0.00 0.00 2.90
636 2618 4.777877 ATGGGGGAGGTAGTATCATACA 57.222 45.455 0.00 0.00 0.00 2.29
637 2619 6.021030 TGTAATGGGGGAGGTAGTATCATAC 58.979 44.000 0.00 0.00 0.00 2.39
638 2620 6.235765 TGTAATGGGGGAGGTAGTATCATA 57.764 41.667 0.00 0.00 0.00 2.15
639 2621 5.101254 TGTAATGGGGGAGGTAGTATCAT 57.899 43.478 0.00 0.00 0.00 2.45
640 2622 4.562934 TGTAATGGGGGAGGTAGTATCA 57.437 45.455 0.00 0.00 0.00 2.15
641 2623 4.041321 GGTTGTAATGGGGGAGGTAGTATC 59.959 50.000 0.00 0.00 0.00 2.24
642 2624 3.978672 GGTTGTAATGGGGGAGGTAGTAT 59.021 47.826 0.00 0.00 0.00 2.12
643 2625 3.246424 TGGTTGTAATGGGGGAGGTAGTA 60.246 47.826 0.00 0.00 0.00 1.82
644 2626 2.202707 GGTTGTAATGGGGGAGGTAGT 58.797 52.381 0.00 0.00 0.00 2.73
645 2627 2.172717 CTGGTTGTAATGGGGGAGGTAG 59.827 54.545 0.00 0.00 0.00 3.18
646 2628 2.201830 CTGGTTGTAATGGGGGAGGTA 58.798 52.381 0.00 0.00 0.00 3.08
647 2629 0.999712 CTGGTTGTAATGGGGGAGGT 59.000 55.000 0.00 0.00 0.00 3.85
648 2630 0.395724 GCTGGTTGTAATGGGGGAGG 60.396 60.000 0.00 0.00 0.00 4.30
649 2631 0.395724 GGCTGGTTGTAATGGGGGAG 60.396 60.000 0.00 0.00 0.00 4.30
650 2632 0.849094 AGGCTGGTTGTAATGGGGGA 60.849 55.000 0.00 0.00 0.00 4.81
651 2633 0.041090 AAGGCTGGTTGTAATGGGGG 59.959 55.000 0.00 0.00 0.00 5.40
652 2634 2.654863 CTAAGGCTGGTTGTAATGGGG 58.345 52.381 0.00 0.00 0.00 4.96
653 2635 2.024414 GCTAAGGCTGGTTGTAATGGG 58.976 52.381 0.00 0.00 35.22 4.00
1124 3188 2.796651 CTGGCGCCATGAGAAAGC 59.203 61.111 32.87 0.00 0.00 3.51
1125 3189 2.796651 GCTGGCGCCATGAGAAAG 59.203 61.111 32.87 17.85 0.00 2.62
1257 3330 3.424859 TCATCGTCGTCGTCGCCA 61.425 61.111 7.01 0.00 38.33 5.69
1329 3406 0.466963 AGGTTCCAGGTTCGTTTCGT 59.533 50.000 0.00 0.00 0.00 3.85
1428 3778 4.249661 GGCAACTAGGCATAGCTATTCTC 58.750 47.826 2.64 0.00 43.51 2.87
1485 3867 3.512033 ACAAGCTAGTCGATGAACTCC 57.488 47.619 0.00 0.00 0.00 3.85
1486 3868 7.377397 CAGTATAACAAGCTAGTCGATGAACTC 59.623 40.741 0.00 0.00 0.00 3.01
1487 3869 7.197017 CAGTATAACAAGCTAGTCGATGAACT 58.803 38.462 0.00 0.00 0.00 3.01
1488 3870 6.074782 GCAGTATAACAAGCTAGTCGATGAAC 60.075 42.308 0.00 0.00 0.00 3.18
1561 4194 1.136252 CACAGCAACAGCACATACGTC 60.136 52.381 0.00 0.00 0.00 4.34
1591 4233 6.594744 TGCCAACATATATATAGGAGCATGG 58.405 40.000 11.22 12.74 0.00 3.66
1668 4484 0.467290 TGAAATTGGATAGCCGGCCC 60.467 55.000 26.15 18.69 36.79 5.80
1728 4677 2.349886 CGTAGCCTGAGAAGATTTGTGC 59.650 50.000 0.00 0.00 0.00 4.57
1893 5955 8.041323 GGGAGAAGATAAACAGTTGAGATTACA 58.959 37.037 0.00 0.00 0.00 2.41
1894 5956 8.261522 AGGGAGAAGATAAACAGTTGAGATTAC 58.738 37.037 0.00 0.00 0.00 1.89
1895 5957 8.380742 AGGGAGAAGATAAACAGTTGAGATTA 57.619 34.615 0.00 0.00 0.00 1.75
1897 5959 6.671779 AGAGGGAGAAGATAAACAGTTGAGAT 59.328 38.462 0.00 0.00 0.00 2.75
1898 5960 6.019748 AGAGGGAGAAGATAAACAGTTGAGA 58.980 40.000 0.00 0.00 0.00 3.27
1899 5961 6.293004 AGAGGGAGAAGATAAACAGTTGAG 57.707 41.667 0.00 0.00 0.00 3.02
1900 5962 5.187967 GGAGAGGGAGAAGATAAACAGTTGA 59.812 44.000 0.00 0.00 0.00 3.18
1901 5963 5.423886 GGAGAGGGAGAAGATAAACAGTTG 58.576 45.833 0.00 0.00 0.00 3.16
1903 5965 4.034410 GGGAGAGGGAGAAGATAAACAGT 58.966 47.826 0.00 0.00 0.00 3.55
1904 5966 3.068873 CGGGAGAGGGAGAAGATAAACAG 59.931 52.174 0.00 0.00 0.00 3.16
1905 5967 3.031736 CGGGAGAGGGAGAAGATAAACA 58.968 50.000 0.00 0.00 0.00 2.83
1906 5968 3.032459 ACGGGAGAGGGAGAAGATAAAC 58.968 50.000 0.00 0.00 0.00 2.01
1907 5969 3.399952 ACGGGAGAGGGAGAAGATAAA 57.600 47.619 0.00 0.00 0.00 1.40
1908 5970 4.213513 GTTACGGGAGAGGGAGAAGATAA 58.786 47.826 0.00 0.00 0.00 1.75
1910 5972 2.024273 TGTTACGGGAGAGGGAGAAGAT 60.024 50.000 0.00 0.00 0.00 2.40
1911 5973 1.356738 TGTTACGGGAGAGGGAGAAGA 59.643 52.381 0.00 0.00 0.00 2.87
1912 5974 1.848652 TGTTACGGGAGAGGGAGAAG 58.151 55.000 0.00 0.00 0.00 2.85
1915 5977 0.535797 GGTTGTTACGGGAGAGGGAG 59.464 60.000 0.00 0.00 0.00 4.30
1916 5978 0.115745 AGGTTGTTACGGGAGAGGGA 59.884 55.000 0.00 0.00 0.00 4.20
1917 5979 0.981943 AAGGTTGTTACGGGAGAGGG 59.018 55.000 0.00 0.00 0.00 4.30
1918 5980 1.338769 CCAAGGTTGTTACGGGAGAGG 60.339 57.143 0.00 0.00 0.00 3.69
1919 5981 1.346722 ACCAAGGTTGTTACGGGAGAG 59.653 52.381 0.00 0.00 0.00 3.20
1920 5982 1.345415 GACCAAGGTTGTTACGGGAGA 59.655 52.381 0.00 0.00 0.00 3.71
1921 5983 1.346722 AGACCAAGGTTGTTACGGGAG 59.653 52.381 0.00 0.00 0.00 4.30
1923 5985 1.346722 AGAGACCAAGGTTGTTACGGG 59.653 52.381 0.00 0.00 0.00 5.28
1924 5986 2.833631 AGAGACCAAGGTTGTTACGG 57.166 50.000 0.00 0.00 0.00 4.02
1925 5987 5.105877 TGAGATAGAGACCAAGGTTGTTACG 60.106 44.000 0.00 0.00 0.00 3.18
1927 5989 7.038302 ACAATGAGATAGAGACCAAGGTTGTTA 60.038 37.037 0.00 0.00 0.00 2.41
1928 5990 6.176183 CAATGAGATAGAGACCAAGGTTGTT 58.824 40.000 0.00 0.00 0.00 2.83
1929 5991 5.249393 ACAATGAGATAGAGACCAAGGTTGT 59.751 40.000 0.00 0.00 0.00 3.32
1930 5992 5.738909 ACAATGAGATAGAGACCAAGGTTG 58.261 41.667 0.00 0.00 0.00 3.77
1931 5993 6.127026 GGTACAATGAGATAGAGACCAAGGTT 60.127 42.308 0.00 0.00 0.00 3.50
1932 5994 5.364157 GGTACAATGAGATAGAGACCAAGGT 59.636 44.000 0.00 0.00 0.00 3.50
1933 5995 5.508153 CGGTACAATGAGATAGAGACCAAGG 60.508 48.000 0.00 0.00 0.00 3.61
1934 5996 5.299531 TCGGTACAATGAGATAGAGACCAAG 59.700 44.000 0.00 0.00 0.00 3.61
1935 5997 5.198207 TCGGTACAATGAGATAGAGACCAA 58.802 41.667 0.00 0.00 0.00 3.67
1936 5998 4.788679 TCGGTACAATGAGATAGAGACCA 58.211 43.478 0.00 0.00 0.00 4.02
1937 5999 5.507650 GGTTCGGTACAATGAGATAGAGACC 60.508 48.000 0.00 0.00 0.00 3.85
1938 6000 5.299782 AGGTTCGGTACAATGAGATAGAGAC 59.700 44.000 0.00 0.00 0.00 3.36
1939 6001 5.299531 CAGGTTCGGTACAATGAGATAGAGA 59.700 44.000 0.00 0.00 0.00 3.10
1940 6002 5.067936 ACAGGTTCGGTACAATGAGATAGAG 59.932 44.000 0.00 0.00 0.00 2.43
1949 6011 4.766375 CAAGGATACAGGTTCGGTACAAT 58.234 43.478 0.00 0.00 41.41 2.71
1950 6012 3.618019 GCAAGGATACAGGTTCGGTACAA 60.618 47.826 0.00 0.00 41.41 2.41
1952 6014 2.547826 GCAAGGATACAGGTTCGGTAC 58.452 52.381 0.00 0.00 41.41 3.34
1956 6018 2.128035 GATCGCAAGGATACAGGTTCG 58.872 52.381 0.00 0.00 34.82 3.95
1957 6019 2.128035 CGATCGCAAGGATACAGGTTC 58.872 52.381 0.26 0.00 34.82 3.62
1960 6022 0.319900 CCCGATCGCAAGGATACAGG 60.320 60.000 10.32 0.00 34.82 4.00
1962 6024 1.694844 TACCCGATCGCAAGGATACA 58.305 50.000 10.32 0.00 34.82 2.29
1977 6136 1.159285 GTGGCGTACAAGGTTTACCC 58.841 55.000 0.00 0.00 36.42 3.69
2011 6218 4.819630 GTGGGTTTATATTGATCGAGGCAA 59.180 41.667 6.03 6.03 0.00 4.52
2044 6255 2.012673 GAAGCGTTCCTACTCTCCGTA 58.987 52.381 0.00 0.00 0.00 4.02
2046 6257 0.100861 GGAAGCGTTCCTACTCTCCG 59.899 60.000 8.87 0.00 46.57 4.63
2182 7780 2.202810 CGAAGCCGAGGAGGAAGC 60.203 66.667 0.00 0.00 45.00 3.86
2197 7807 2.046864 CGAGGTTGAGGGAGAGCGA 61.047 63.158 0.00 0.00 0.00 4.93
2219 7829 4.388499 GCTTCTCGGCGGGTGGAA 62.388 66.667 6.68 6.05 0.00 3.53
2337 7947 1.302033 CTGCTGCTCCACCGTCTTT 60.302 57.895 0.00 0.00 0.00 2.52
2378 7988 1.049289 ATAGAGGGGGTTCGGCACTC 61.049 60.000 0.00 0.00 0.00 3.51
2468 8078 9.328845 ACGTATTTTCTTTACTTACAACTTGGA 57.671 29.630 0.00 0.00 0.00 3.53
2601 8220 1.496060 TCCAGGCGATGTATGAGGTT 58.504 50.000 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.