Multiple sequence alignment - TraesCS3D01G335800

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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 TraesCS3D01G335800 chr3D 100.000 3280 0 0 1 3280 447610475 447607196 0.000000e+00 6058
1 TraesCS3D01G335800 chr3D 92.883 1939 82 32 1374 3280 155676558 155678472 0.000000e+00 2765
2 TraesCS3D01G335800 chr3D 92.883 1939 82 32 1374 3280 374010167 374008253 0.000000e+00 2765
3 TraesCS3D01G335800 chr3D 92.519 1925 81 30 1401 3280 580651490 580649584 0.000000e+00 2699
4 TraesCS3D01G335800 chr3D 92.408 1541 68 23 1374 2885 609770575 609769055 0.000000e+00 2152
5 TraesCS3D01G335800 chr3D 90.710 183 5 7 2477 2657 580650446 580650274 1.970000e-57 233
6 TraesCS3D01G335800 chr3D 88.344 163 7 7 2474 2634 155677622 155677774 5.590000e-43 185
7 TraesCS3D01G335800 chrUn 94.901 2628 90 8 653 3280 112556593 112554010 0.000000e+00 4071
8 TraesCS3D01G335800 chr2A 91.875 2646 140 29 653 3280 751417376 751414788 0.000000e+00 3626
9 TraesCS3D01G335800 chr2A 93.340 1877 85 9 653 2529 54414730 54416566 0.000000e+00 2737
10 TraesCS3D01G335800 chr2A 93.798 1838 82 10 650 2487 202211687 202213492 0.000000e+00 2734
11 TraesCS3D01G335800 chr2A 94.168 1766 80 3 653 2418 184517048 184515306 0.000000e+00 2669
12 TraesCS3D01G335800 chr2A 94.688 979 50 2 653 1631 54411403 54412379 0.000000e+00 1519
13 TraesCS3D01G335800 chr2A 92.453 742 56 0 2538 3279 184515142 184514401 0.000000e+00 1061
14 TraesCS3D01G335800 chr1D 93.034 1938 84 26 1374 3280 422850084 422848167 0.000000e+00 2784
15 TraesCS3D01G335800 chr1D 88.679 159 9 8 2477 2634 422849016 422848866 5.590000e-43 185
16 TraesCS3D01G335800 chr2D 92.728 1939 86 31 1374 3280 535663028 535664943 0.000000e+00 2748
17 TraesCS3D01G335800 chr2D 92.087 1921 101 23 1374 3280 633747786 633749669 0.000000e+00 2658
18 TraesCS3D01G335800 chr6A 93.552 1861 73 16 652 2512 454845796 454843983 0.000000e+00 2728
19 TraesCS3D01G335800 chr6A 93.969 1144 42 11 1374 2504 532335626 532334497 0.000000e+00 1705
20 TraesCS3D01G335800 chr6D 92.002 1938 81 31 1374 3280 387623987 387622093 0.000000e+00 2652
21 TraesCS3D01G335800 chr6D 88.050 159 9 6 2477 2634 387622940 387622791 2.600000e-41 180
22 TraesCS3D01G335800 chr6D 88.125 160 7 9 2477 2634 445208227 445208078 2.600000e-41 180
23 TraesCS3D01G335800 chr4A 91.257 1853 127 14 653 2504 37984867 37983049 0.000000e+00 2492
24 TraesCS3D01G335800 chr5B 89.880 1996 114 44 653 2624 547624682 547622751 0.000000e+00 2486
25 TraesCS3D01G335800 chr5B 92.693 739 44 4 2546 3276 547622771 547622035 0.000000e+00 1057
26 TraesCS3D01G335800 chr7B 91.950 1764 78 27 1175 2894 66321419 66323162 0.000000e+00 2412
27 TraesCS3D01G335800 chr7B 92.469 810 55 1 2477 3280 11699750 11698941 0.000000e+00 1153
28 TraesCS3D01G335800 chr5A 93.111 871 47 7 653 1521 395004059 395004918 0.000000e+00 1264
29 TraesCS3D01G335800 chr1B 87.793 811 76 13 653 1447 176803728 176802925 0.000000e+00 928
30 TraesCS3D01G335800 chr3A 86.321 424 41 11 3 419 589314118 589313705 2.320000e-121 446
31 TraesCS3D01G335800 chr3A 91.089 202 18 0 419 620 589313539 589313338 1.160000e-69 274
32 TraesCS3D01G335800 chr3B 91.026 234 14 6 184 416 586854839 586854612 3.180000e-80 309


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 TraesCS3D01G335800 chr3D 447607196 447610475 3279 True 6058.0 6058 100.0000 1 3280 1 chr3D.!!$R2 3279
1 TraesCS3D01G335800 chr3D 374008253 374010167 1914 True 2765.0 2765 92.8830 1374 3280 1 chr3D.!!$R1 1906
2 TraesCS3D01G335800 chr3D 609769055 609770575 1520 True 2152.0 2152 92.4080 1374 2885 1 chr3D.!!$R3 1511
3 TraesCS3D01G335800 chr3D 155676558 155678472 1914 False 1475.0 2765 90.6135 1374 3280 2 chr3D.!!$F1 1906
4 TraesCS3D01G335800 chr3D 580649584 580651490 1906 True 1466.0 2699 91.6145 1401 3280 2 chr3D.!!$R4 1879
5 TraesCS3D01G335800 chrUn 112554010 112556593 2583 True 4071.0 4071 94.9010 653 3280 1 chrUn.!!$R1 2627
6 TraesCS3D01G335800 chr2A 751414788 751417376 2588 True 3626.0 3626 91.8750 653 3280 1 chr2A.!!$R1 2627
7 TraesCS3D01G335800 chr2A 202211687 202213492 1805 False 2734.0 2734 93.7980 650 2487 1 chr2A.!!$F1 1837
8 TraesCS3D01G335800 chr2A 54411403 54416566 5163 False 2128.0 2737 94.0140 653 2529 2 chr2A.!!$F2 1876
9 TraesCS3D01G335800 chr2A 184514401 184517048 2647 True 1865.0 2669 93.3105 653 3279 2 chr2A.!!$R2 2626
10 TraesCS3D01G335800 chr1D 422848167 422850084 1917 True 1484.5 2784 90.8565 1374 3280 2 chr1D.!!$R1 1906
11 TraesCS3D01G335800 chr2D 535663028 535664943 1915 False 2748.0 2748 92.7280 1374 3280 1 chr2D.!!$F1 1906
12 TraesCS3D01G335800 chr2D 633747786 633749669 1883 False 2658.0 2658 92.0870 1374 3280 1 chr2D.!!$F2 1906
13 TraesCS3D01G335800 chr6A 454843983 454845796 1813 True 2728.0 2728 93.5520 652 2512 1 chr6A.!!$R1 1860
14 TraesCS3D01G335800 chr6A 532334497 532335626 1129 True 1705.0 1705 93.9690 1374 2504 1 chr6A.!!$R2 1130
15 TraesCS3D01G335800 chr6D 387622093 387623987 1894 True 1416.0 2652 90.0260 1374 3280 2 chr6D.!!$R2 1906
16 TraesCS3D01G335800 chr4A 37983049 37984867 1818 True 2492.0 2492 91.2570 653 2504 1 chr4A.!!$R1 1851
17 TraesCS3D01G335800 chr5B 547622035 547624682 2647 True 1771.5 2486 91.2865 653 3276 2 chr5B.!!$R1 2623
18 TraesCS3D01G335800 chr7B 66321419 66323162 1743 False 2412.0 2412 91.9500 1175 2894 1 chr7B.!!$F1 1719
19 TraesCS3D01G335800 chr7B 11698941 11699750 809 True 1153.0 1153 92.4690 2477 3280 1 chr7B.!!$R1 803
20 TraesCS3D01G335800 chr5A 395004059 395004918 859 False 1264.0 1264 93.1110 653 1521 1 chr5A.!!$F1 868
21 TraesCS3D01G335800 chr1B 176802925 176803728 803 True 928.0 928 87.7930 653 1447 1 chr1B.!!$R1 794
22 TraesCS3D01G335800 chr3A 589313338 589314118 780 True 360.0 446 88.7050 3 620 2 chr3A.!!$R1 617

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
598 771 0.031857 TTGCAAGATGCCCAACAACG 59.968 50.0 0.00 0.0 44.23 4.10 F
1017 1265 0.107017 CCATGGTTTCCTGGAGCGAT 60.107 55.0 2.57 0.0 34.24 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 5303 1.746171 GCATTCTGCAGATGCTCTGGA 60.746 52.381 28.74 11.95 44.43 3.86 R
2767 6585 0.679321 GCCAAGAAGAAGAGGGCAGG 60.679 60.000 0.00 0.00 44.01 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
28 29 5.045872 AGGAACGCAAATACGGAATAGTAC 58.954 41.667 0.00 0.00 37.37 2.73
35 37 6.517714 CGCAAATACGGAATAGTACTACTACG 59.482 42.308 14.19 14.19 32.84 3.51
36 38 7.355778 GCAAATACGGAATAGTACTACTACGT 58.644 38.462 23.57 23.57 35.83 3.57
51 53 2.481919 CGTACTACGTGGCTCGCA 59.518 61.111 9.11 0.00 44.19 5.10
55 57 1.131126 GTACTACGTGGCTCGCACTAA 59.869 52.381 9.11 0.00 44.19 2.24
56 58 0.599558 ACTACGTGGCTCGCACTAAA 59.400 50.000 9.11 0.00 44.19 1.85
57 59 1.000060 ACTACGTGGCTCGCACTAAAA 60.000 47.619 9.11 0.00 44.19 1.52
58 60 1.654105 CTACGTGGCTCGCACTAAAAG 59.346 52.381 9.11 0.00 44.19 2.27
59 61 0.249741 ACGTGGCTCGCACTAAAAGT 60.250 50.000 9.11 0.00 44.19 2.66
60 62 1.000060 ACGTGGCTCGCACTAAAAGTA 60.000 47.619 9.11 0.00 44.19 2.24
61 63 2.063266 CGTGGCTCGCACTAAAAGTAA 58.937 47.619 0.00 0.00 0.00 2.24
62 64 2.671396 CGTGGCTCGCACTAAAAGTAAT 59.329 45.455 0.00 0.00 0.00 1.89
63 65 3.483574 CGTGGCTCGCACTAAAAGTAATG 60.484 47.826 0.00 0.00 0.00 1.90
64 66 3.006940 TGGCTCGCACTAAAAGTAATGG 58.993 45.455 0.00 0.00 0.00 3.16
65 67 2.354821 GGCTCGCACTAAAAGTAATGGG 59.645 50.000 0.00 0.00 0.00 4.00
93 95 5.235186 GTCATTATCTTGGACTGATCAACGG 59.765 44.000 0.00 0.00 0.00 4.44
135 137 1.301401 ACATGTCGACGGTGTTGGG 60.301 57.895 17.55 1.88 0.00 4.12
187 189 3.484229 GCACTCGACTTATGCACATTGTC 60.484 47.826 0.00 0.00 39.23 3.18
201 203 2.802816 ACATTGTCTCGCTGACTTTGTC 59.197 45.455 9.20 0.00 45.54 3.18
248 254 2.117423 CCAAACCCCTCCGGCTTT 59.883 61.111 0.00 0.00 33.26 3.51
250 256 0.251430 CCAAACCCCTCCGGCTTTAA 60.251 55.000 0.00 0.00 33.26 1.52
251 257 0.885879 CAAACCCCTCCGGCTTTAAC 59.114 55.000 0.00 0.00 33.26 2.01
252 258 0.775542 AAACCCCTCCGGCTTTAACT 59.224 50.000 0.00 0.00 33.26 2.24
253 259 1.660242 AACCCCTCCGGCTTTAACTA 58.340 50.000 0.00 0.00 33.26 2.24
254 260 1.660242 ACCCCTCCGGCTTTAACTAA 58.340 50.000 0.00 0.00 33.26 2.24
255 261 1.280133 ACCCCTCCGGCTTTAACTAAC 59.720 52.381 0.00 0.00 33.26 2.34
256 262 1.407851 CCCCTCCGGCTTTAACTAACC 60.408 57.143 0.00 0.00 0.00 2.85
257 263 1.407851 CCCTCCGGCTTTAACTAACCC 60.408 57.143 0.00 0.00 0.00 4.11
264 270 3.770046 GGCTTTAACTAACCCCCTTTGA 58.230 45.455 0.00 0.00 0.00 2.69
266 272 3.762288 GCTTTAACTAACCCCCTTTGAGG 59.238 47.826 0.00 0.00 34.30 3.86
267 273 4.751964 GCTTTAACTAACCCCCTTTGAGGT 60.752 45.833 0.00 0.00 38.27 3.85
272 278 3.780850 ACTAACCCCCTTTGAGGTATGAG 59.219 47.826 0.00 0.00 34.45 2.90
317 324 2.867472 CGACCCACGGCACATTTC 59.133 61.111 0.00 0.00 38.46 2.17
355 362 0.611714 GGGCCGGTTCTAGTTCAAGA 59.388 55.000 1.90 0.00 0.00 3.02
357 364 2.355818 GGGCCGGTTCTAGTTCAAGAAT 60.356 50.000 1.90 0.00 37.78 2.40
362 369 6.403309 GGCCGGTTCTAGTTCAAGAATTAAAG 60.403 42.308 1.90 0.00 37.78 1.85
380 387 3.078560 CCTAAAACCGCGACGCTC 58.921 61.111 19.02 0.00 0.00 5.03
382 389 1.411493 CCTAAAACCGCGACGCTCTC 61.411 60.000 19.02 0.00 0.00 3.20
383 390 0.456312 CTAAAACCGCGACGCTCTCT 60.456 55.000 19.02 1.00 0.00 3.10
385 392 2.143594 AAAACCGCGACGCTCTCTCT 62.144 55.000 19.02 0.00 0.00 3.10
386 393 2.804368 AAACCGCGACGCTCTCTCTG 62.804 60.000 19.02 0.00 0.00 3.35
429 602 4.673761 GCGTACGTATTCGAATCTTGATGA 59.326 41.667 15.25 0.00 40.62 2.92
437 610 7.148738 CGTATTCGAATCTTGATGAACCCTATG 60.149 40.741 15.25 0.00 39.71 2.23
442 615 5.715439 ATCTTGATGAACCCTATGTGGAA 57.285 39.130 0.00 0.00 38.35 3.53
460 633 2.480802 GGAAGCGTCCTTCTTCAACTTC 59.519 50.000 11.87 0.00 45.44 3.01
461 634 2.910688 AGCGTCCTTCTTCAACTTCA 57.089 45.000 0.00 0.00 0.00 3.02
462 635 3.194005 AGCGTCCTTCTTCAACTTCAA 57.806 42.857 0.00 0.00 0.00 2.69
463 636 3.744660 AGCGTCCTTCTTCAACTTCAAT 58.255 40.909 0.00 0.00 0.00 2.57
464 637 4.137543 AGCGTCCTTCTTCAACTTCAATT 58.862 39.130 0.00 0.00 0.00 2.32
465 638 4.214332 AGCGTCCTTCTTCAACTTCAATTC 59.786 41.667 0.00 0.00 0.00 2.17
466 639 4.024048 GCGTCCTTCTTCAACTTCAATTCA 60.024 41.667 0.00 0.00 0.00 2.57
467 640 5.444122 CGTCCTTCTTCAACTTCAATTCAC 58.556 41.667 0.00 0.00 0.00 3.18
468 641 5.007626 CGTCCTTCTTCAACTTCAATTCACA 59.992 40.000 0.00 0.00 0.00 3.58
469 642 6.202226 GTCCTTCTTCAACTTCAATTCACAC 58.798 40.000 0.00 0.00 0.00 3.82
470 643 5.885352 TCCTTCTTCAACTTCAATTCACACA 59.115 36.000 0.00 0.00 0.00 3.72
471 644 6.376864 TCCTTCTTCAACTTCAATTCACACAA 59.623 34.615 0.00 0.00 0.00 3.33
472 645 6.473455 CCTTCTTCAACTTCAATTCACACAAC 59.527 38.462 0.00 0.00 0.00 3.32
473 646 5.568482 TCTTCAACTTCAATTCACACAACG 58.432 37.500 0.00 0.00 0.00 4.10
474 647 4.285807 TCAACTTCAATTCACACAACGG 57.714 40.909 0.00 0.00 0.00 4.44
475 648 2.774439 ACTTCAATTCACACAACGGC 57.226 45.000 0.00 0.00 0.00 5.68
476 649 2.020720 ACTTCAATTCACACAACGGCA 58.979 42.857 0.00 0.00 0.00 5.69
477 650 2.223479 ACTTCAATTCACACAACGGCAC 60.223 45.455 0.00 0.00 0.00 5.01
478 651 1.674359 TCAATTCACACAACGGCACT 58.326 45.000 0.00 0.00 0.00 4.40
479 652 1.601903 TCAATTCACACAACGGCACTC 59.398 47.619 0.00 0.00 0.00 3.51
480 653 1.333308 CAATTCACACAACGGCACTCA 59.667 47.619 0.00 0.00 0.00 3.41
481 654 1.229428 ATTCACACAACGGCACTCAG 58.771 50.000 0.00 0.00 0.00 3.35
482 655 0.813610 TTCACACAACGGCACTCAGG 60.814 55.000 0.00 0.00 0.00 3.86
483 656 1.523711 CACACAACGGCACTCAGGT 60.524 57.895 0.00 0.00 0.00 4.00
484 657 1.523711 ACACAACGGCACTCAGGTG 60.524 57.895 0.00 0.00 45.53 4.00
485 658 1.227527 CACAACGGCACTCAGGTGA 60.228 57.895 0.00 0.00 45.61 4.02
486 659 0.813610 CACAACGGCACTCAGGTGAA 60.814 55.000 0.00 0.00 45.61 3.18
487 660 0.532862 ACAACGGCACTCAGGTGAAG 60.533 55.000 0.00 0.00 45.61 3.02
488 661 1.071471 AACGGCACTCAGGTGAAGG 59.929 57.895 0.00 0.00 45.61 3.46
489 662 1.696097 AACGGCACTCAGGTGAAGGT 61.696 55.000 0.00 0.00 45.61 3.50
490 663 1.374758 CGGCACTCAGGTGAAGGTC 60.375 63.158 0.00 0.00 45.61 3.85
491 664 1.754745 GGCACTCAGGTGAAGGTCA 59.245 57.895 0.00 0.00 45.61 4.02
492 665 0.108585 GGCACTCAGGTGAAGGTCAA 59.891 55.000 0.00 0.00 45.61 3.18
493 666 1.476833 GGCACTCAGGTGAAGGTCAAA 60.477 52.381 0.00 0.00 45.61 2.69
494 667 1.604278 GCACTCAGGTGAAGGTCAAAC 59.396 52.381 0.00 0.00 45.61 2.93
495 668 2.222027 CACTCAGGTGAAGGTCAAACC 58.778 52.381 0.00 0.00 45.61 3.27
496 669 1.143073 ACTCAGGTGAAGGTCAAACCC 59.857 52.381 0.00 0.00 39.75 4.11
497 670 1.421646 CTCAGGTGAAGGTCAAACCCT 59.578 52.381 0.00 0.00 39.75 4.34
499 672 2.243736 TCAGGTGAAGGTCAAACCCTTT 59.756 45.455 0.00 0.00 44.91 3.11
500 673 3.031013 CAGGTGAAGGTCAAACCCTTTT 58.969 45.455 0.00 0.00 44.91 2.27
501 674 3.450817 CAGGTGAAGGTCAAACCCTTTTT 59.549 43.478 0.00 0.00 44.91 1.94
520 693 3.825908 TTTTCCCTCTTTACATGGCCT 57.174 42.857 3.32 0.00 0.00 5.19
521 694 3.825908 TTTCCCTCTTTACATGGCCTT 57.174 42.857 3.32 0.00 0.00 4.35
522 695 3.825908 TTCCCTCTTTACATGGCCTTT 57.174 42.857 3.32 0.00 0.00 3.11
523 696 3.825908 TCCCTCTTTACATGGCCTTTT 57.174 42.857 3.32 0.00 0.00 2.27
524 697 3.430453 TCCCTCTTTACATGGCCTTTTG 58.570 45.455 3.32 1.36 0.00 2.44
525 698 3.165071 CCCTCTTTACATGGCCTTTTGT 58.835 45.455 3.32 8.06 0.00 2.83
526 699 4.043561 TCCCTCTTTACATGGCCTTTTGTA 59.956 41.667 3.32 6.99 0.00 2.41
527 700 4.157840 CCCTCTTTACATGGCCTTTTGTAC 59.842 45.833 3.32 0.00 0.00 2.90
528 701 4.142687 CCTCTTTACATGGCCTTTTGTACG 60.143 45.833 3.32 4.19 0.00 3.67
529 702 4.391155 TCTTTACATGGCCTTTTGTACGT 58.609 39.130 3.32 0.00 0.00 3.57
530 703 4.822896 TCTTTACATGGCCTTTTGTACGTT 59.177 37.500 3.32 0.00 0.00 3.99
531 704 4.752661 TTACATGGCCTTTTGTACGTTC 57.247 40.909 3.32 0.00 0.00 3.95
532 705 2.858745 ACATGGCCTTTTGTACGTTCT 58.141 42.857 3.32 0.00 0.00 3.01
533 706 2.812011 ACATGGCCTTTTGTACGTTCTC 59.188 45.455 3.32 0.00 0.00 2.87
534 707 2.922740 TGGCCTTTTGTACGTTCTCT 57.077 45.000 3.32 0.00 0.00 3.10
535 708 2.762745 TGGCCTTTTGTACGTTCTCTC 58.237 47.619 3.32 0.00 0.00 3.20
536 709 2.367567 TGGCCTTTTGTACGTTCTCTCT 59.632 45.455 3.32 0.00 0.00 3.10
537 710 2.737252 GGCCTTTTGTACGTTCTCTCTG 59.263 50.000 0.00 0.00 0.00 3.35
538 711 3.391049 GCCTTTTGTACGTTCTCTCTGT 58.609 45.455 0.00 0.00 0.00 3.41
539 712 3.808174 GCCTTTTGTACGTTCTCTCTGTT 59.192 43.478 0.00 0.00 0.00 3.16
540 713 4.986659 GCCTTTTGTACGTTCTCTCTGTTA 59.013 41.667 0.00 0.00 0.00 2.41
541 714 5.638234 GCCTTTTGTACGTTCTCTCTGTTAT 59.362 40.000 0.00 0.00 0.00 1.89
542 715 6.810182 GCCTTTTGTACGTTCTCTCTGTTATA 59.190 38.462 0.00 0.00 0.00 0.98
543 716 7.491696 GCCTTTTGTACGTTCTCTCTGTTATAT 59.508 37.037 0.00 0.00 0.00 0.86
544 717 8.808529 CCTTTTGTACGTTCTCTCTGTTATATG 58.191 37.037 0.00 0.00 0.00 1.78
545 718 9.355215 CTTTTGTACGTTCTCTCTGTTATATGT 57.645 33.333 0.00 0.00 0.00 2.29
546 719 8.683550 TTTGTACGTTCTCTCTGTTATATGTG 57.316 34.615 0.00 0.00 0.00 3.21
547 720 7.387119 TGTACGTTCTCTCTGTTATATGTGT 57.613 36.000 0.00 0.00 0.00 3.72
548 721 7.248437 TGTACGTTCTCTCTGTTATATGTGTG 58.752 38.462 0.00 0.00 0.00 3.82
549 722 6.510879 ACGTTCTCTCTGTTATATGTGTGA 57.489 37.500 0.00 0.00 0.00 3.58
550 723 6.920817 ACGTTCTCTCTGTTATATGTGTGAA 58.079 36.000 0.00 0.00 0.00 3.18
551 724 7.548097 ACGTTCTCTCTGTTATATGTGTGAAT 58.452 34.615 0.00 0.00 0.00 2.57
552 725 7.489435 ACGTTCTCTCTGTTATATGTGTGAATG 59.511 37.037 0.00 0.00 0.00 2.67
553 726 7.489435 CGTTCTCTCTGTTATATGTGTGAATGT 59.511 37.037 0.00 0.00 0.00 2.71
554 727 8.812329 GTTCTCTCTGTTATATGTGTGAATGTC 58.188 37.037 0.00 0.00 0.00 3.06
555 728 7.196331 TCTCTCTGTTATATGTGTGAATGTCG 58.804 38.462 0.00 0.00 0.00 4.35
556 729 7.067008 TCTCTCTGTTATATGTGTGAATGTCGA 59.933 37.037 0.00 0.00 0.00 4.20
557 730 7.716612 TCTCTGTTATATGTGTGAATGTCGAT 58.283 34.615 0.00 0.00 0.00 3.59
558 731 8.197439 TCTCTGTTATATGTGTGAATGTCGATT 58.803 33.333 0.00 0.00 0.00 3.34
559 732 8.130307 TCTGTTATATGTGTGAATGTCGATTG 57.870 34.615 0.00 0.00 0.00 2.67
560 733 6.714492 TGTTATATGTGTGAATGTCGATTGC 58.286 36.000 0.00 0.00 0.00 3.56
561 734 6.314896 TGTTATATGTGTGAATGTCGATTGCA 59.685 34.615 0.00 0.00 0.00 4.08
562 735 5.816449 ATATGTGTGAATGTCGATTGCAA 57.184 34.783 0.00 0.00 0.00 4.08
563 736 3.978718 TGTGTGAATGTCGATTGCAAA 57.021 38.095 1.71 0.00 0.00 3.68
564 737 4.502171 TGTGTGAATGTCGATTGCAAAT 57.498 36.364 1.71 0.00 0.00 2.32
565 738 4.869215 TGTGTGAATGTCGATTGCAAATT 58.131 34.783 1.71 0.00 0.00 1.82
566 739 5.288015 TGTGTGAATGTCGATTGCAAATTT 58.712 33.333 1.71 0.00 0.00 1.82
567 740 5.175308 TGTGTGAATGTCGATTGCAAATTTG 59.825 36.000 14.03 14.03 0.00 2.32
568 741 5.401972 GTGTGAATGTCGATTGCAAATTTGA 59.598 36.000 22.31 1.94 0.00 2.69
569 742 5.981915 TGTGAATGTCGATTGCAAATTTGAA 59.018 32.000 22.31 8.84 0.00 2.69
570 743 6.645827 TGTGAATGTCGATTGCAAATTTGAAT 59.354 30.769 22.31 16.55 0.00 2.57
571 744 6.951530 GTGAATGTCGATTGCAAATTTGAATG 59.048 34.615 22.31 4.93 0.00 2.67
572 745 6.867293 TGAATGTCGATTGCAAATTTGAATGA 59.133 30.769 22.31 7.21 0.00 2.57
573 746 7.384387 TGAATGTCGATTGCAAATTTGAATGAA 59.616 29.630 22.31 8.33 0.00 2.57
574 747 7.655236 ATGTCGATTGCAAATTTGAATGAAA 57.345 28.000 22.31 5.73 0.00 2.69
575 748 7.655236 TGTCGATTGCAAATTTGAATGAAAT 57.345 28.000 22.31 11.57 35.65 2.17
576 749 8.754230 TGTCGATTGCAAATTTGAATGAAATA 57.246 26.923 22.31 0.00 32.76 1.40
577 750 9.201127 TGTCGATTGCAAATTTGAATGAAATAA 57.799 25.926 22.31 0.00 32.76 1.40
583 756 9.961265 TTGCAAATTTGAATGAAATAAATTGCA 57.039 22.222 22.31 10.23 45.22 4.08
584 757 9.961265 TGCAAATTTGAATGAAATAAATTGCAA 57.039 22.222 22.31 0.00 44.60 4.08
589 762 9.997482 ATTTGAATGAAATAAATTGCAAGATGC 57.003 25.926 4.94 0.00 36.84 3.91
590 763 7.542534 TGAATGAAATAAATTGCAAGATGCC 57.457 32.000 4.94 0.00 44.23 4.40
591 764 6.539464 TGAATGAAATAAATTGCAAGATGCCC 59.461 34.615 4.94 0.00 44.23 5.36
592 765 5.417754 TGAAATAAATTGCAAGATGCCCA 57.582 34.783 4.94 0.00 44.23 5.36
593 766 5.802465 TGAAATAAATTGCAAGATGCCCAA 58.198 33.333 4.94 0.00 44.23 4.12
594 767 5.642919 TGAAATAAATTGCAAGATGCCCAAC 59.357 36.000 4.94 0.00 44.23 3.77
595 768 4.822685 ATAAATTGCAAGATGCCCAACA 57.177 36.364 4.94 0.00 44.23 3.33
596 769 3.488778 AAATTGCAAGATGCCCAACAA 57.511 38.095 4.94 0.00 44.23 2.83
597 770 2.460757 ATTGCAAGATGCCCAACAAC 57.539 45.000 4.94 0.00 44.23 3.32
598 771 0.031857 TTGCAAGATGCCCAACAACG 59.968 50.000 0.00 0.00 44.23 4.10
599 772 1.734117 GCAAGATGCCCAACAACGC 60.734 57.895 0.00 0.00 37.42 4.84
600 773 1.659233 CAAGATGCCCAACAACGCA 59.341 52.632 0.00 0.00 39.79 5.24
602 775 1.472082 CAAGATGCCCAACAACGCATA 59.528 47.619 0.00 0.00 45.52 3.14
603 776 1.094785 AGATGCCCAACAACGCATAC 58.905 50.000 0.00 0.00 45.52 2.39
604 777 0.808125 GATGCCCAACAACGCATACA 59.192 50.000 0.00 0.00 45.52 2.29
605 778 1.405105 GATGCCCAACAACGCATACAT 59.595 47.619 0.00 0.00 45.52 2.29
606 779 1.252175 TGCCCAACAACGCATACATT 58.748 45.000 0.00 0.00 0.00 2.71
607 780 2.437413 TGCCCAACAACGCATACATTA 58.563 42.857 0.00 0.00 0.00 1.90
608 781 2.820197 TGCCCAACAACGCATACATTAA 59.180 40.909 0.00 0.00 0.00 1.40
609 782 3.255888 TGCCCAACAACGCATACATTAAA 59.744 39.130 0.00 0.00 0.00 1.52
610 783 3.857093 GCCCAACAACGCATACATTAAAG 59.143 43.478 0.00 0.00 0.00 1.85
611 784 3.857093 CCCAACAACGCATACATTAAAGC 59.143 43.478 0.00 0.00 0.00 3.51
612 785 4.380444 CCCAACAACGCATACATTAAAGCT 60.380 41.667 0.00 0.00 0.00 3.74
613 786 5.163703 CCCAACAACGCATACATTAAAGCTA 60.164 40.000 0.00 0.00 0.00 3.32
614 787 6.459573 CCCAACAACGCATACATTAAAGCTAT 60.460 38.462 0.00 0.00 0.00 2.97
615 788 6.972328 CCAACAACGCATACATTAAAGCTATT 59.028 34.615 0.00 0.00 0.00 1.73
616 789 8.126074 CCAACAACGCATACATTAAAGCTATTA 58.874 33.333 0.00 0.00 0.00 0.98
617 790 9.663904 CAACAACGCATACATTAAAGCTATTAT 57.336 29.630 0.00 0.00 0.00 1.28
632 805 7.863901 AAGCTATTATTAGATGGAGGTGAGT 57.136 36.000 0.00 0.00 0.00 3.41
633 806 7.863901 AGCTATTATTAGATGGAGGTGAGTT 57.136 36.000 0.00 0.00 0.00 3.01
634 807 8.268878 AGCTATTATTAGATGGAGGTGAGTTT 57.731 34.615 0.00 0.00 0.00 2.66
635 808 8.718656 AGCTATTATTAGATGGAGGTGAGTTTT 58.281 33.333 0.00 0.00 0.00 2.43
636 809 9.343539 GCTATTATTAGATGGAGGTGAGTTTTT 57.656 33.333 0.00 0.00 0.00 1.94
639 812 9.981460 ATTATTAGATGGAGGTGAGTTTTTCTT 57.019 29.630 0.00 0.00 0.00 2.52
640 813 9.807921 TTATTAGATGGAGGTGAGTTTTTCTTT 57.192 29.630 0.00 0.00 0.00 2.52
642 815 8.617290 TTAGATGGAGGTGAGTTTTTCTTTAC 57.383 34.615 0.00 0.00 0.00 2.01
643 816 6.601332 AGATGGAGGTGAGTTTTTCTTTACA 58.399 36.000 0.00 0.00 0.00 2.41
644 817 7.060421 AGATGGAGGTGAGTTTTTCTTTACAA 58.940 34.615 0.00 0.00 0.00 2.41
645 818 7.559897 AGATGGAGGTGAGTTTTTCTTTACAAA 59.440 33.333 0.00 0.00 0.00 2.83
646 819 7.469537 TGGAGGTGAGTTTTTCTTTACAAAA 57.530 32.000 0.00 0.00 0.00 2.44
647 820 7.543756 TGGAGGTGAGTTTTTCTTTACAAAAG 58.456 34.615 0.00 0.00 0.00 2.27
648 821 7.177744 TGGAGGTGAGTTTTTCTTTACAAAAGT 59.822 33.333 0.00 0.00 30.86 2.66
649 822 8.033038 GGAGGTGAGTTTTTCTTTACAAAAGTT 58.967 33.333 0.00 0.00 28.79 2.66
650 823 9.419297 GAGGTGAGTTTTTCTTTACAAAAGTTT 57.581 29.630 0.00 0.00 28.79 2.66
748 921 1.129811 CCACCGCGGATTCAGTAAAAC 59.870 52.381 35.90 0.00 36.56 2.43
898 1073 4.838486 GCGAGAGACAGACCGCCG 62.838 72.222 0.00 0.00 41.59 6.46
920 1095 2.105128 CCGACCACATCTCGCTCC 59.895 66.667 0.00 0.00 0.00 4.70
921 1096 2.105128 CGACCACATCTCGCTCCC 59.895 66.667 0.00 0.00 0.00 4.30
925 1124 2.801631 CCACATCTCGCTCCCCTCC 61.802 68.421 0.00 0.00 0.00 4.30
942 1162 2.051518 CCCTCTGCTCTCACGCTCT 61.052 63.158 0.00 0.00 0.00 4.09
965 1185 2.364317 TCCCCTCCCTCTTGCTCG 60.364 66.667 0.00 0.00 0.00 5.03
971 1191 0.682855 CTCCCTCTTGCTCGTCTCCT 60.683 60.000 0.00 0.00 0.00 3.69
972 1192 0.681564 TCCCTCTTGCTCGTCTCCTC 60.682 60.000 0.00 0.00 0.00 3.71
973 1193 0.682855 CCCTCTTGCTCGTCTCCTCT 60.683 60.000 0.00 0.00 0.00 3.69
974 1194 0.738389 CCTCTTGCTCGTCTCCTCTC 59.262 60.000 0.00 0.00 0.00 3.20
975 1195 0.738389 CTCTTGCTCGTCTCCTCTCC 59.262 60.000 0.00 0.00 0.00 3.71
976 1196 1.027255 TCTTGCTCGTCTCCTCTCCG 61.027 60.000 0.00 0.00 0.00 4.63
977 1197 1.999071 CTTGCTCGTCTCCTCTCCGG 61.999 65.000 0.00 0.00 0.00 5.14
978 1198 2.438795 GCTCGTCTCCTCTCCGGT 60.439 66.667 0.00 0.00 0.00 5.28
979 1199 2.474612 GCTCGTCTCCTCTCCGGTC 61.475 68.421 0.00 0.00 0.00 4.79
980 1200 2.125229 TCGTCTCCTCTCCGGTCG 60.125 66.667 0.00 0.00 0.00 4.79
983 1203 2.125229 TCTCCTCTCCGGTCGTCG 60.125 66.667 0.00 0.00 38.88 5.12
1017 1265 0.107017 CCATGGTTTCCTGGAGCGAT 60.107 55.000 2.57 0.00 34.24 4.58
1080 1328 0.763223 ACGACTCCCCTGTCAAGGTT 60.763 55.000 0.00 0.00 42.74 3.50
1201 1451 1.102978 TGATGAGCCGTCATTCGAGA 58.897 50.000 0.00 0.00 43.92 4.04
1317 1567 1.270839 GCCTGTGCCACTGAAGTAAGA 60.271 52.381 2.97 0.00 0.00 2.10
1337 1587 5.581126 AGATTCAAGTTGTGTCTTTGCAA 57.419 34.783 2.11 0.00 0.00 4.08
1343 1593 4.989279 AGTTGTGTCTTTGCAACATTCT 57.011 36.364 0.00 0.00 45.16 2.40
1670 5303 2.681976 GCAGTGGGTAGATGAGCATTGT 60.682 50.000 0.00 0.00 0.00 2.71
1983 5617 7.946207 TGTTGACCAGTTAAAGCAAATTCATA 58.054 30.769 0.00 0.00 0.00 2.15
2148 5803 2.230508 CTGGATTGTTGCATTGCTGAGT 59.769 45.455 10.49 0.00 0.00 3.41
2183 5838 3.848975 AGGAGAAGTTGACCATGGAGAAT 59.151 43.478 21.47 0.00 0.00 2.40
2312 5967 2.095567 GTCTGACCATGTGTGTCAATGC 60.096 50.000 5.05 0.00 41.85 3.56
2401 6056 7.759489 TTATTTCTGTAGCAATGAACCTTGT 57.241 32.000 0.00 0.00 0.00 3.16
2426 6081 9.204570 GTATTGTATGTTGTTTGTGAGAGTACT 57.795 33.333 0.00 0.00 0.00 2.73
2427 6082 7.709269 TTGTATGTTGTTTGTGAGAGTACTC 57.291 36.000 15.41 15.41 42.88 2.59
2428 6083 7.050970 TGTATGTTGTTTGTGAGAGTACTCT 57.949 36.000 25.44 25.44 42.99 3.24
2429 6084 6.923508 TGTATGTTGTTTGTGAGAGTACTCTG 59.076 38.462 29.84 0.00 42.99 3.35
2430 6085 5.339008 TGTTGTTTGTGAGAGTACTCTGT 57.661 39.130 29.84 7.29 42.99 3.41
2431 6086 5.730550 TGTTGTTTGTGAGAGTACTCTGTT 58.269 37.500 29.84 6.46 42.99 3.16
2432 6087 6.170506 TGTTGTTTGTGAGAGTACTCTGTTT 58.829 36.000 29.84 6.05 42.99 2.83
2433 6088 6.092122 TGTTGTTTGTGAGAGTACTCTGTTTG 59.908 38.462 29.84 0.00 42.99 2.93
2434 6089 5.730550 TGTTTGTGAGAGTACTCTGTTTGT 58.269 37.500 29.84 4.81 42.99 2.83
2435 6090 5.580691 TGTTTGTGAGAGTACTCTGTTTGTG 59.419 40.000 29.84 0.00 42.99 3.33
2436 6091 5.592104 TTGTGAGAGTACTCTGTTTGTGA 57.408 39.130 29.84 6.46 42.99 3.58
2520 6175 6.573664 TGGATTAAGTTCAGTTTGTGATGG 57.426 37.500 0.00 0.00 34.17 3.51
2529 6184 7.397221 AGTTCAGTTTGTGATGGATTATCAGA 58.603 34.615 0.00 0.00 46.09 3.27
2767 6585 1.599419 GCACGTCATTGTTGTTCACCC 60.599 52.381 0.00 0.00 0.00 4.61
2769 6587 1.133915 ACGTCATTGTTGTTCACCCCT 60.134 47.619 0.00 0.00 0.00 4.79
2852 6682 1.504647 TTCACGACGACGAGCTCTGT 61.505 55.000 15.32 11.43 42.66 3.41
2916 6746 1.987855 CTTCTACCCCTCCACGGCA 60.988 63.158 0.00 0.00 0.00 5.69
2987 6817 1.678425 GGAGGAGAGTACGACGACCTT 60.678 57.143 0.00 0.00 0.00 3.50
3072 6908 0.673956 CGTCAGAGTCCTCGTCTGGA 60.674 60.000 0.47 0.00 41.62 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.801771 TCCGTATTTGCGTTCCTTGTG 59.198 47.619 0.00 0.00 0.00 3.33
35 37 4.068302 GTGCGAGCCACGTAGTAC 57.932 61.111 0.00 0.00 41.61 2.73
42 44 3.181510 CCATTACTTTTAGTGCGAGCCAC 60.182 47.826 0.00 0.00 45.01 5.01
47 49 4.250464 CACTCCCATTACTTTTAGTGCGA 58.750 43.478 0.00 0.00 0.00 5.10
51 53 9.614792 GATAATGACACTCCCATTACTTTTAGT 57.385 33.333 0.00 0.00 38.74 2.24
55 57 7.557719 CCAAGATAATGACACTCCCATTACTTT 59.442 37.037 0.00 0.00 38.74 2.66
56 58 7.056635 CCAAGATAATGACACTCCCATTACTT 58.943 38.462 0.00 0.00 38.74 2.24
57 59 6.386927 TCCAAGATAATGACACTCCCATTACT 59.613 38.462 0.00 0.00 38.74 2.24
58 60 6.483640 GTCCAAGATAATGACACTCCCATTAC 59.516 42.308 0.00 0.00 38.74 1.89
59 61 6.386927 AGTCCAAGATAATGACACTCCCATTA 59.613 38.462 0.00 0.00 39.79 1.90
60 62 5.192522 AGTCCAAGATAATGACACTCCCATT 59.807 40.000 0.00 0.00 37.86 3.16
61 63 4.723789 AGTCCAAGATAATGACACTCCCAT 59.276 41.667 0.00 0.00 0.00 4.00
62 64 4.080919 CAGTCCAAGATAATGACACTCCCA 60.081 45.833 0.00 0.00 0.00 4.37
63 65 4.162320 TCAGTCCAAGATAATGACACTCCC 59.838 45.833 0.00 0.00 0.00 4.30
64 66 5.344743 TCAGTCCAAGATAATGACACTCC 57.655 43.478 0.00 0.00 0.00 3.85
65 67 6.577103 TGATCAGTCCAAGATAATGACACTC 58.423 40.000 0.00 0.00 0.00 3.51
93 95 3.602924 TTTCATTTCGGTGCCGCGC 62.603 57.895 0.00 0.00 39.59 6.86
102 104 3.155998 GACATGTGCGACTTTCATTTCG 58.844 45.455 1.15 0.00 38.31 3.46
103 105 3.120683 TCGACATGTGCGACTTTCATTTC 60.121 43.478 1.15 0.00 32.09 2.17
106 108 2.078849 TCGACATGTGCGACTTTCAT 57.921 45.000 1.15 0.00 32.09 2.57
126 128 2.830827 TGGCAACACCCAACACCG 60.831 61.111 0.00 0.00 46.17 4.94
146 148 1.217882 CGACGAGCCAAGAAACAGTT 58.782 50.000 0.00 0.00 0.00 3.16
148 150 1.493311 GCGACGAGCCAAGAAACAG 59.507 57.895 0.00 0.00 40.81 3.16
187 189 3.159984 GCGGACAAAGTCAGCGAG 58.840 61.111 6.53 0.00 42.77 5.03
201 203 2.907917 TCCCAAAACAACCGGCGG 60.908 61.111 27.06 27.06 0.00 6.13
248 254 5.352264 TCATACCTCAAAGGGGGTTAGTTA 58.648 41.667 0.00 0.00 40.58 2.24
250 256 3.780850 CTCATACCTCAAAGGGGGTTAGT 59.219 47.826 0.00 0.00 40.58 2.24
251 257 4.037927 TCTCATACCTCAAAGGGGGTTAG 58.962 47.826 0.00 0.00 40.58 2.34
252 258 4.083080 TCTCATACCTCAAAGGGGGTTA 57.917 45.455 0.00 0.00 40.58 2.85
253 259 2.929301 TCTCATACCTCAAAGGGGGTT 58.071 47.619 0.00 0.00 40.58 4.11
254 260 2.576648 GTTCTCATACCTCAAAGGGGGT 59.423 50.000 0.00 0.00 40.58 4.95
255 261 2.846827 AGTTCTCATACCTCAAAGGGGG 59.153 50.000 0.00 0.00 40.58 5.40
256 262 3.370953 CCAGTTCTCATACCTCAAAGGGG 60.371 52.174 0.00 0.00 40.58 4.79
257 263 3.264450 ACCAGTTCTCATACCTCAAAGGG 59.736 47.826 0.00 0.00 40.58 3.95
264 270 3.791320 TCCTCAACCAGTTCTCATACCT 58.209 45.455 0.00 0.00 0.00 3.08
266 272 5.412904 CCTTTTCCTCAACCAGTTCTCATAC 59.587 44.000 0.00 0.00 0.00 2.39
267 273 5.073144 ACCTTTTCCTCAACCAGTTCTCATA 59.927 40.000 0.00 0.00 0.00 2.15
272 278 3.551846 TGACCTTTTCCTCAACCAGTTC 58.448 45.455 0.00 0.00 0.00 3.01
295 302 0.387929 ATGTGCCGTGGGTCGTATAG 59.612 55.000 0.00 0.00 37.94 1.31
297 304 0.035820 AAATGTGCCGTGGGTCGTAT 60.036 50.000 0.00 0.00 37.94 3.06
317 324 4.381292 GGCCCAGAAATCAATCAAGACTTG 60.381 45.833 9.03 9.03 0.00 3.16
355 362 3.425227 CGTCGCGGTTTTAGGCTTTAATT 60.425 43.478 6.13 0.00 0.00 1.40
357 364 1.460359 CGTCGCGGTTTTAGGCTTTAA 59.540 47.619 6.13 0.00 0.00 1.52
362 369 3.079941 GAGCGTCGCGGTTTTAGGC 62.080 63.158 12.30 3.44 37.83 3.93
380 387 1.954362 CTTGGTCTCCCGGCAGAGAG 61.954 65.000 10.35 4.98 43.47 3.20
382 389 2.581354 CTTGGTCTCCCGGCAGAG 59.419 66.667 0.00 0.00 35.04 3.35
383 390 3.706373 GCTTGGTCTCCCGGCAGA 61.706 66.667 0.00 0.00 33.83 4.26
385 392 3.551496 CTTGCTTGGTCTCCCGGCA 62.551 63.158 0.00 0.00 39.31 5.69
386 393 2.747855 CTTGCTTGGTCTCCCGGC 60.748 66.667 0.00 0.00 34.11 6.13
387 394 2.045926 CCTTGCTTGGTCTCCCGG 60.046 66.667 0.00 0.00 0.00 5.73
388 395 1.078848 CTCCTTGCTTGGTCTCCCG 60.079 63.158 0.00 0.00 0.00 5.14
389 396 1.377856 GCTCCTTGCTTGGTCTCCC 60.378 63.158 0.00 0.00 38.95 4.30
397 404 2.537401 GAATACGTACGCTCCTTGCTT 58.463 47.619 16.72 0.00 40.11 3.91
398 405 1.533338 CGAATACGTACGCTCCTTGCT 60.533 52.381 16.72 0.00 35.61 3.91
412 419 7.657761 ACATAGGGTTCATCAAGATTCGAATAC 59.342 37.037 11.38 2.73 0.00 1.89
416 423 5.359756 CACATAGGGTTCATCAAGATTCGA 58.640 41.667 0.00 0.00 0.00 3.71
429 602 0.252197 GGACGCTTCCACATAGGGTT 59.748 55.000 3.96 0.00 42.30 4.11
437 610 1.531578 GTTGAAGAAGGACGCTTCCAC 59.468 52.381 12.41 5.25 45.72 4.02
442 615 2.910688 TGAAGTTGAAGAAGGACGCT 57.089 45.000 0.00 0.00 0.00 5.07
460 633 1.333308 TGAGTGCCGTTGTGTGAATTG 59.667 47.619 0.00 0.00 0.00 2.32
461 634 1.603802 CTGAGTGCCGTTGTGTGAATT 59.396 47.619 0.00 0.00 0.00 2.17
462 635 1.229428 CTGAGTGCCGTTGTGTGAAT 58.771 50.000 0.00 0.00 0.00 2.57
463 636 0.813610 CCTGAGTGCCGTTGTGTGAA 60.814 55.000 0.00 0.00 0.00 3.18
464 637 1.227527 CCTGAGTGCCGTTGTGTGA 60.228 57.895 0.00 0.00 0.00 3.58
465 638 1.523711 ACCTGAGTGCCGTTGTGTG 60.524 57.895 0.00 0.00 0.00 3.82
466 639 1.523711 CACCTGAGTGCCGTTGTGT 60.524 57.895 0.00 0.00 37.14 3.72
467 640 0.813610 TTCACCTGAGTGCCGTTGTG 60.814 55.000 0.00 0.00 44.16 3.33
468 641 0.532862 CTTCACCTGAGTGCCGTTGT 60.533 55.000 0.00 0.00 44.16 3.32
469 642 1.230635 CCTTCACCTGAGTGCCGTTG 61.231 60.000 0.00 0.00 44.16 4.10
470 643 1.071471 CCTTCACCTGAGTGCCGTT 59.929 57.895 0.00 0.00 44.16 4.44
471 644 2.100879 GACCTTCACCTGAGTGCCGT 62.101 60.000 0.00 0.00 44.16 5.68
472 645 1.374758 GACCTTCACCTGAGTGCCG 60.375 63.158 0.00 0.00 44.16 5.69
473 646 0.108585 TTGACCTTCACCTGAGTGCC 59.891 55.000 0.00 0.00 44.16 5.01
474 647 1.604278 GTTTGACCTTCACCTGAGTGC 59.396 52.381 0.00 0.00 44.16 4.40
475 648 2.222027 GGTTTGACCTTCACCTGAGTG 58.778 52.381 0.00 0.00 39.30 3.51
476 649 1.143073 GGGTTTGACCTTCACCTGAGT 59.857 52.381 0.00 0.00 38.64 3.41
477 650 1.421646 AGGGTTTGACCTTCACCTGAG 59.578 52.381 0.00 0.00 37.69 3.35
478 651 1.518367 AGGGTTTGACCTTCACCTGA 58.482 50.000 0.00 0.00 37.69 3.86
499 672 4.126520 AGGCCATGTAAAGAGGGAAAAA 57.873 40.909 5.01 0.00 0.00 1.94
500 673 3.825908 AGGCCATGTAAAGAGGGAAAA 57.174 42.857 5.01 0.00 0.00 2.29
501 674 3.825908 AAGGCCATGTAAAGAGGGAAA 57.174 42.857 5.01 0.00 0.00 3.13
502 675 3.825908 AAAGGCCATGTAAAGAGGGAA 57.174 42.857 5.01 0.00 0.00 3.97
503 676 3.181423 ACAAAAGGCCATGTAAAGAGGGA 60.181 43.478 5.01 0.00 0.00 4.20
504 677 3.165071 ACAAAAGGCCATGTAAAGAGGG 58.835 45.455 5.01 0.00 0.00 4.30
505 678 4.142687 CGTACAAAAGGCCATGTAAAGAGG 60.143 45.833 15.14 1.47 34.08 3.69
506 679 4.454504 ACGTACAAAAGGCCATGTAAAGAG 59.545 41.667 15.14 10.62 34.08 2.85
507 680 4.391155 ACGTACAAAAGGCCATGTAAAGA 58.609 39.130 15.14 0.00 34.08 2.52
508 681 4.759516 ACGTACAAAAGGCCATGTAAAG 57.240 40.909 15.14 14.21 34.08 1.85
509 682 4.822896 AGAACGTACAAAAGGCCATGTAAA 59.177 37.500 15.14 0.00 34.08 2.01
510 683 4.391155 AGAACGTACAAAAGGCCATGTAA 58.609 39.130 15.14 1.28 34.08 2.41
511 684 3.998341 GAGAACGTACAAAAGGCCATGTA 59.002 43.478 5.01 8.81 0.00 2.29
512 685 2.812011 GAGAACGTACAAAAGGCCATGT 59.188 45.455 5.01 9.93 0.00 3.21
513 686 3.074412 AGAGAACGTACAAAAGGCCATG 58.926 45.455 5.01 3.18 0.00 3.66
514 687 3.008049 AGAGAGAACGTACAAAAGGCCAT 59.992 43.478 5.01 0.00 0.00 4.40
515 688 2.367567 AGAGAGAACGTACAAAAGGCCA 59.632 45.455 5.01 0.00 0.00 5.36
516 689 2.737252 CAGAGAGAACGTACAAAAGGCC 59.263 50.000 0.00 0.00 0.00 5.19
517 690 3.391049 ACAGAGAGAACGTACAAAAGGC 58.609 45.455 0.00 0.00 0.00 4.35
518 691 8.808529 CATATAACAGAGAGAACGTACAAAAGG 58.191 37.037 0.00 0.00 0.00 3.11
519 692 9.355215 ACATATAACAGAGAGAACGTACAAAAG 57.645 33.333 0.00 0.00 0.00 2.27
520 693 9.135843 CACATATAACAGAGAGAACGTACAAAA 57.864 33.333 0.00 0.00 0.00 2.44
521 694 8.301720 ACACATATAACAGAGAGAACGTACAAA 58.698 33.333 0.00 0.00 0.00 2.83
522 695 7.753580 CACACATATAACAGAGAGAACGTACAA 59.246 37.037 0.00 0.00 0.00 2.41
523 696 7.120138 TCACACATATAACAGAGAGAACGTACA 59.880 37.037 0.00 0.00 0.00 2.90
524 697 7.470079 TCACACATATAACAGAGAGAACGTAC 58.530 38.462 0.00 0.00 0.00 3.67
525 698 7.619964 TCACACATATAACAGAGAGAACGTA 57.380 36.000 0.00 0.00 0.00 3.57
526 699 6.510879 TCACACATATAACAGAGAGAACGT 57.489 37.500 0.00 0.00 0.00 3.99
527 700 7.489435 ACATTCACACATATAACAGAGAGAACG 59.511 37.037 0.00 0.00 0.00 3.95
528 701 8.709386 ACATTCACACATATAACAGAGAGAAC 57.291 34.615 0.00 0.00 0.00 3.01
529 702 7.702348 CGACATTCACACATATAACAGAGAGAA 59.298 37.037 0.00 0.00 0.00 2.87
530 703 7.067008 TCGACATTCACACATATAACAGAGAGA 59.933 37.037 0.00 0.00 0.00 3.10
531 704 7.196331 TCGACATTCACACATATAACAGAGAG 58.804 38.462 0.00 0.00 0.00 3.20
532 705 7.095695 TCGACATTCACACATATAACAGAGA 57.904 36.000 0.00 0.00 0.00 3.10
533 706 7.936950 ATCGACATTCACACATATAACAGAG 57.063 36.000 0.00 0.00 0.00 3.35
534 707 7.254421 GCAATCGACATTCACACATATAACAGA 60.254 37.037 0.00 0.00 0.00 3.41
535 708 6.847792 GCAATCGACATTCACACATATAACAG 59.152 38.462 0.00 0.00 0.00 3.16
536 709 6.314896 TGCAATCGACATTCACACATATAACA 59.685 34.615 0.00 0.00 0.00 2.41
537 710 6.714492 TGCAATCGACATTCACACATATAAC 58.286 36.000 0.00 0.00 0.00 1.89
538 711 6.917217 TGCAATCGACATTCACACATATAA 57.083 33.333 0.00 0.00 0.00 0.98
539 712 6.917217 TTGCAATCGACATTCACACATATA 57.083 33.333 0.00 0.00 0.00 0.86
540 713 5.816449 TTGCAATCGACATTCACACATAT 57.184 34.783 0.00 0.00 0.00 1.78
541 714 5.619625 TTTGCAATCGACATTCACACATA 57.380 34.783 0.00 0.00 0.00 2.29
542 715 4.502171 TTTGCAATCGACATTCACACAT 57.498 36.364 0.00 0.00 0.00 3.21
543 716 3.978718 TTTGCAATCGACATTCACACA 57.021 38.095 0.00 0.00 0.00 3.72
544 717 5.401972 TCAAATTTGCAATCGACATTCACAC 59.598 36.000 13.54 0.00 0.00 3.82
545 718 5.527033 TCAAATTTGCAATCGACATTCACA 58.473 33.333 13.54 0.00 0.00 3.58
546 719 6.450845 TTCAAATTTGCAATCGACATTCAC 57.549 33.333 13.54 0.00 0.00 3.18
547 720 6.867293 TCATTCAAATTTGCAATCGACATTCA 59.133 30.769 13.54 0.00 0.00 2.57
548 721 7.280730 TCATTCAAATTTGCAATCGACATTC 57.719 32.000 13.54 0.00 0.00 2.67
549 722 7.655236 TTCATTCAAATTTGCAATCGACATT 57.345 28.000 13.54 0.00 0.00 2.71
550 723 7.655236 TTTCATTCAAATTTGCAATCGACAT 57.345 28.000 13.54 0.00 0.00 3.06
551 724 7.655236 ATTTCATTCAAATTTGCAATCGACA 57.345 28.000 13.54 8.01 29.60 4.35
557 730 9.961265 TGCAATTTATTTCATTCAAATTTGCAA 57.039 22.222 13.54 9.03 44.87 4.08
558 731 9.961265 TTGCAATTTATTTCATTCAAATTTGCA 57.039 22.222 13.54 2.71 45.50 4.08
563 736 9.997482 GCATCTTGCAATTTATTTCATTCAAAT 57.003 25.926 0.00 0.00 44.26 2.32
581 754 1.734117 GCGTTGTTGGGCATCTTGC 60.734 57.895 0.00 0.00 44.08 4.01
582 755 0.244450 ATGCGTTGTTGGGCATCTTG 59.756 50.000 0.00 0.00 46.31 3.02
583 756 1.472480 GTATGCGTTGTTGGGCATCTT 59.528 47.619 1.30 0.00 46.31 2.40
584 757 1.094785 GTATGCGTTGTTGGGCATCT 58.905 50.000 1.30 0.00 46.31 2.90
585 758 0.808125 TGTATGCGTTGTTGGGCATC 59.192 50.000 1.30 0.00 46.31 3.91
587 760 1.252175 AATGTATGCGTTGTTGGGCA 58.748 45.000 0.00 0.00 44.29 5.36
588 761 3.495670 TTAATGTATGCGTTGTTGGGC 57.504 42.857 0.00 0.00 0.00 5.36
589 762 3.857093 GCTTTAATGTATGCGTTGTTGGG 59.143 43.478 0.00 0.00 0.00 4.12
590 763 4.732784 AGCTTTAATGTATGCGTTGTTGG 58.267 39.130 0.00 0.00 0.00 3.77
591 764 7.969387 AATAGCTTTAATGTATGCGTTGTTG 57.031 32.000 0.00 0.00 0.00 3.33
606 779 9.381038 ACTCACCTCCATCTAATAATAGCTTTA 57.619 33.333 0.00 0.00 0.00 1.85
607 780 8.268878 ACTCACCTCCATCTAATAATAGCTTT 57.731 34.615 0.00 0.00 0.00 3.51
608 781 7.863901 ACTCACCTCCATCTAATAATAGCTT 57.136 36.000 0.00 0.00 0.00 3.74
609 782 7.863901 AACTCACCTCCATCTAATAATAGCT 57.136 36.000 0.00 0.00 0.00 3.32
610 783 8.910351 AAAACTCACCTCCATCTAATAATAGC 57.090 34.615 0.00 0.00 0.00 2.97
613 786 9.981460 AAGAAAAACTCACCTCCATCTAATAAT 57.019 29.630 0.00 0.00 0.00 1.28
614 787 9.807921 AAAGAAAAACTCACCTCCATCTAATAA 57.192 29.630 0.00 0.00 0.00 1.40
616 789 9.232473 GTAAAGAAAAACTCACCTCCATCTAAT 57.768 33.333 0.00 0.00 0.00 1.73
617 790 8.215050 TGTAAAGAAAAACTCACCTCCATCTAA 58.785 33.333 0.00 0.00 0.00 2.10
618 791 7.741785 TGTAAAGAAAAACTCACCTCCATCTA 58.258 34.615 0.00 0.00 0.00 1.98
619 792 6.601332 TGTAAAGAAAAACTCACCTCCATCT 58.399 36.000 0.00 0.00 0.00 2.90
620 793 6.877611 TGTAAAGAAAAACTCACCTCCATC 57.122 37.500 0.00 0.00 0.00 3.51
621 794 7.654022 TTTGTAAAGAAAAACTCACCTCCAT 57.346 32.000 0.00 0.00 0.00 3.41
622 795 7.177744 ACTTTTGTAAAGAAAAACTCACCTCCA 59.822 33.333 6.20 0.00 0.00 3.86
623 796 7.544622 ACTTTTGTAAAGAAAAACTCACCTCC 58.455 34.615 6.20 0.00 0.00 4.30
624 797 8.981724 AACTTTTGTAAAGAAAAACTCACCTC 57.018 30.769 6.20 0.00 0.00 3.85
625 798 9.772973 AAAACTTTTGTAAAGAAAAACTCACCT 57.227 25.926 6.20 0.00 0.00 4.00
626 799 9.805966 CAAAACTTTTGTAAAGAAAAACTCACC 57.194 29.630 6.14 0.00 0.00 4.02
636 809 8.868916 GCAATTCACTCAAAACTTTTGTAAAGA 58.131 29.630 12.88 5.98 0.00 2.52
637 810 8.655092 TGCAATTCACTCAAAACTTTTGTAAAG 58.345 29.630 12.88 6.93 0.00 1.85
638 811 8.539770 TGCAATTCACTCAAAACTTTTGTAAA 57.460 26.923 12.88 5.44 0.00 2.01
639 812 8.539770 TTGCAATTCACTCAAAACTTTTGTAA 57.460 26.923 12.88 5.70 0.00 2.41
640 813 8.031864 TCTTGCAATTCACTCAAAACTTTTGTA 58.968 29.630 12.88 1.57 0.00 2.41
641 814 6.873076 TCTTGCAATTCACTCAAAACTTTTGT 59.127 30.769 12.88 0.00 0.00 2.83
642 815 7.293402 TCTTGCAATTCACTCAAAACTTTTG 57.707 32.000 0.00 7.80 0.00 2.44
643 816 7.903995 TTCTTGCAATTCACTCAAAACTTTT 57.096 28.000 0.00 0.00 0.00 2.27
644 817 7.148423 GGTTTCTTGCAATTCACTCAAAACTTT 60.148 33.333 0.00 0.00 0.00 2.66
645 818 6.313658 GGTTTCTTGCAATTCACTCAAAACTT 59.686 34.615 0.00 0.00 0.00 2.66
646 819 5.812127 GGTTTCTTGCAATTCACTCAAAACT 59.188 36.000 0.00 0.00 0.00 2.66
647 820 5.580297 TGGTTTCTTGCAATTCACTCAAAAC 59.420 36.000 0.00 1.75 0.00 2.43
648 821 5.580297 GTGGTTTCTTGCAATTCACTCAAAA 59.420 36.000 0.00 0.00 0.00 2.44
649 822 5.108517 GTGGTTTCTTGCAATTCACTCAAA 58.891 37.500 0.00 0.00 0.00 2.69
650 823 4.441356 GGTGGTTTCTTGCAATTCACTCAA 60.441 41.667 0.00 0.00 0.00 3.02
920 1095 2.422231 CGTGAGAGCAGAGGGAGGG 61.422 68.421 0.00 0.00 0.00 4.30
921 1096 3.074999 GCGTGAGAGCAGAGGGAGG 62.075 68.421 0.00 0.00 37.05 4.30
925 1124 1.031571 AGAGAGCGTGAGAGCAGAGG 61.032 60.000 0.00 0.00 40.15 3.69
942 1162 2.627476 AAGAGGGAGGGGAGCGAGA 61.627 63.158 0.00 0.00 0.00 4.04
965 1185 2.462782 CGACGACCGGAGAGGAGAC 61.463 68.421 9.46 0.00 45.00 3.36
1005 1253 0.465642 TCTCGCTATCGCTCCAGGAA 60.466 55.000 0.00 0.00 35.26 3.36
1017 1265 2.418910 GCCCTCAGTGCTCTCGCTA 61.419 63.158 0.00 0.00 36.97 4.26
1080 1328 7.665559 ACACAAATGAGCAATAAGAAGGTTCTA 59.334 33.333 0.00 0.00 36.28 2.10
1201 1451 1.040646 TTCAGGTCGTCAGCAAGACT 58.959 50.000 7.58 0.00 45.32 3.24
1216 1466 4.421058 CCATGCTCACAAATCACATTCAG 58.579 43.478 0.00 0.00 0.00 3.02
1317 1567 5.070770 TGTTGCAAAGACACAACTTGAAT 57.929 34.783 0.00 0.00 45.07 2.57
1337 1587 9.014297 CAAACCCTAGAACAAGAATTAGAATGT 57.986 33.333 0.00 0.00 0.00 2.71
1343 1593 7.981142 ACCTACAAACCCTAGAACAAGAATTA 58.019 34.615 0.00 0.00 0.00 1.40
1626 5259 5.531634 CACTAATCCACAATTTGCAACACT 58.468 37.500 0.00 0.00 0.00 3.55
1670 5303 1.746171 GCATTCTGCAGATGCTCTGGA 60.746 52.381 28.74 11.95 44.43 3.86
1983 5617 3.572632 AATGACAGTGGCATGAGCTAT 57.427 42.857 13.53 0.00 41.70 2.97
1991 5625 4.661222 TCAAATTCCTAATGACAGTGGCA 58.339 39.130 0.00 0.00 0.00 4.92
2148 5803 6.260936 GTCAACTTCTCCTTCACTTTCATCAA 59.739 38.462 0.00 0.00 0.00 2.57
2312 5967 6.096987 TCCTCCATAGCTACTACAAAAGACAG 59.903 42.308 0.00 0.00 0.00 3.51
2401 6056 9.419297 GAGTACTCTCACAAACAACATACAATA 57.581 33.333 15.91 0.00 40.18 1.90
2426 6081 9.065798 TGAAACTGATAATTCATCACAAACAGA 57.934 29.630 0.00 0.00 38.79 3.41
2427 6082 9.681692 TTGAAACTGATAATTCATCACAAACAG 57.318 29.630 0.00 0.00 38.79 3.16
2767 6585 0.679321 GCCAAGAAGAAGAGGGCAGG 60.679 60.000 0.00 0.00 44.01 4.85
2769 6587 1.380302 GGCCAAGAAGAAGAGGGCA 59.620 57.895 0.00 0.00 46.37 5.36
2987 6817 1.228033 TCTGACGACGAGGTGGACA 60.228 57.895 0.00 0.00 0.00 4.02
3072 6908 1.915228 CAATCCATGGGTCCTCGGT 59.085 57.895 13.02 0.00 0.00 4.69
3164 7000 3.770040 CATCCACCACGCCTCCGA 61.770 66.667 0.00 0.00 38.29 4.55
3168 7004 4.457496 CGCTCATCCACCACGCCT 62.457 66.667 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.