Multiple sequence alignment - TraesCS6B01G084800

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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 TraesCS6B01G084800 chr6B 100.000 2220 0 0 1 2220 61794663 61796882 0.000000e+00 4100
1 TraesCS6B01G084800 chr6B 94.215 968 47 7 436 1397 58778773 58777809 0.000000e+00 1469
2 TraesCS6B01G084800 chr6B 84.303 1134 123 36 553 1664 58310837 58309737 0.000000e+00 1057
3 TraesCS6B01G084800 chr6B 94.759 477 23 2 920 1396 59026857 59026383 0.000000e+00 741
4 TraesCS6B01G084800 chr6B 100.000 225 0 0 2398 2622 61797060 61797284 1.450000e-112 416
5 TraesCS6B01G084800 chr6B 89.286 112 12 0 749 860 59026970 59026859 9.780000e-30 141
6 TraesCS6B01G084800 chr6D 86.771 703 61 21 968 1664 29391511 29392187 0.000000e+00 754
7 TraesCS6B01G084800 chr6D 96.767 433 14 0 970 1402 28688497 28688065 0.000000e+00 723
8 TraesCS6B01G084800 chr6D 92.830 265 18 1 146 410 28690209 28689946 1.470000e-102 383
9 TraesCS6B01G084800 chr6D 87.296 307 32 3 533 834 28688873 28688569 6.950000e-91 344
10 TraesCS6B01G084800 chr6D 80.082 487 75 17 1735 2213 28687614 28687142 2.500000e-90 342
11 TraesCS6B01G084800 chr6D 91.371 197 16 1 2426 2622 28686277 28686082 4.300000e-68 268
12 TraesCS6B01G084800 chr6D 78.917 351 52 13 571 904 29391146 29391491 4.390000e-53 219
13 TraesCS6B01G084800 chr6A 85.933 718 53 25 971 1664 33001973 33001280 0.000000e+00 723
14 TraesCS6B01G084800 chr6A 92.105 266 19 2 146 410 33961554 33961818 8.860000e-100 374
15 TraesCS6B01G084800 chr6A 86.337 344 34 6 436 768 33962697 33963038 1.920000e-96 363
16 TraesCS6B01G084800 chr6A 91.765 85 7 0 759 843 33002138 33002054 4.580000e-23 119
17 TraesCS6B01G084800 chr4D 86.898 664 42 23 770 1420 444177896 444177265 0.000000e+00 702
18 TraesCS6B01G084800 chr4A 95.161 434 20 1 983 1416 23610808 23611240 0.000000e+00 684
19 TraesCS6B01G084800 chr1D 91.616 489 31 9 908 1396 321704474 321704952 0.000000e+00 667
20 TraesCS6B01G084800 chr2B 76.218 349 55 19 503 829 2243607 2243949 2.700000e-35 159
21 TraesCS6B01G084800 chr3D 75.701 321 50 17 522 820 19666995 19667309 4.550000e-28 135
22 TraesCS6B01G084800 chr3B 74.780 341 60 16 510 829 800628621 800628956 2.120000e-26 130


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 TraesCS6B01G084800 chr6B 61794663 61797284 2621 False 2258.0 4100 100.0000 1 2622 2 chr6B.!!$F1 2621
1 TraesCS6B01G084800 chr6B 58777809 58778773 964 True 1469.0 1469 94.2150 436 1397 1 chr6B.!!$R2 961
2 TraesCS6B01G084800 chr6B 58309737 58310837 1100 True 1057.0 1057 84.3030 553 1664 1 chr6B.!!$R1 1111
3 TraesCS6B01G084800 chr6B 59026383 59026970 587 True 441.0 741 92.0225 749 1396 2 chr6B.!!$R3 647
4 TraesCS6B01G084800 chr6D 29391146 29392187 1041 False 486.5 754 82.8440 571 1664 2 chr6D.!!$F1 1093
5 TraesCS6B01G084800 chr6D 28686082 28690209 4127 True 412.0 723 89.6692 146 2622 5 chr6D.!!$R1 2476
6 TraesCS6B01G084800 chr6A 33001280 33002138 858 True 421.0 723 88.8490 759 1664 2 chr6A.!!$R1 905
7 TraesCS6B01G084800 chr6A 33961554 33963038 1484 False 368.5 374 89.2210 146 768 2 chr6A.!!$F1 622
8 TraesCS6B01G084800 chr4D 444177265 444177896 631 True 702.0 702 86.8980 770 1420 1 chr4D.!!$R1 650

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
72 73 0.45541 TATGCGGCATTTGCACCTTC 59.545 50.0 21.99 0.0 46.57 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 3144 0.0297 CGTGGACGCCGACATACATA 59.97 55.0 0.0 0.0 0.0 2.29 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
30 31 9.322776 CACTTGCATATTTCTCTAATAAATCGC 57.677 33.333 0.00 0.00 32.63 4.58
31 32 8.223769 ACTTGCATATTTCTCTAATAAATCGCG 58.776 33.333 0.00 0.00 32.63 5.87
32 33 7.652300 TGCATATTTCTCTAATAAATCGCGT 57.348 32.000 5.77 0.00 32.63 6.01
33 34 7.729836 TGCATATTTCTCTAATAAATCGCGTC 58.270 34.615 5.77 0.00 32.63 5.19
34 35 6.889833 GCATATTTCTCTAATAAATCGCGTCG 59.110 38.462 5.77 0.00 32.63 5.12
35 36 7.410513 GCATATTTCTCTAATAAATCGCGTCGT 60.411 37.037 5.77 0.00 32.63 4.34
36 37 5.615495 TTTCTCTAATAAATCGCGTCGTG 57.385 39.130 5.77 0.00 0.00 4.35
37 38 4.282950 TCTCTAATAAATCGCGTCGTGT 57.717 40.909 5.77 0.00 0.00 4.49
38 39 4.033019 TCTCTAATAAATCGCGTCGTGTG 58.967 43.478 5.77 0.00 0.00 3.82
39 40 4.018649 TCTAATAAATCGCGTCGTGTGA 57.981 40.909 5.77 0.00 42.30 3.58
41 42 5.750650 TCTAATAAATCGCGTCGTGTGATA 58.249 37.500 5.77 0.00 46.95 2.15
42 43 6.200808 TCTAATAAATCGCGTCGTGTGATAA 58.799 36.000 5.77 1.03 46.95 1.75
43 44 5.900339 AATAAATCGCGTCGTGTGATAAT 57.100 34.783 5.77 2.88 46.95 1.28
44 45 6.996562 AATAAATCGCGTCGTGTGATAATA 57.003 33.333 5.77 5.06 46.95 0.98
45 46 7.576750 AATAAATCGCGTCGTGTGATAATAT 57.423 32.000 5.77 6.63 46.95 1.28
46 47 5.900339 AAATCGCGTCGTGTGATAATATT 57.100 34.783 5.77 0.00 46.95 1.28
47 48 5.900339 AATCGCGTCGTGTGATAATATTT 57.100 34.783 5.77 0.00 46.95 1.40
48 49 4.685824 TCGCGTCGTGTGATAATATTTG 57.314 40.909 5.77 0.00 30.48 2.32
49 50 4.106909 TCGCGTCGTGTGATAATATTTGT 58.893 39.130 5.77 0.00 30.48 2.83
50 51 4.563580 TCGCGTCGTGTGATAATATTTGTT 59.436 37.500 5.77 0.00 30.48 2.83
51 52 5.062433 TCGCGTCGTGTGATAATATTTGTTT 59.938 36.000 5.77 0.00 30.48 2.83
52 53 5.730802 CGCGTCGTGTGATAATATTTGTTTT 59.269 36.000 0.00 0.00 0.00 2.43
53 54 6.247582 CGCGTCGTGTGATAATATTTGTTTTT 59.752 34.615 0.00 0.00 0.00 1.94
54 55 7.423030 CGCGTCGTGTGATAATATTTGTTTTTA 59.577 33.333 0.00 0.00 0.00 1.52
55 56 9.217223 GCGTCGTGTGATAATATTTGTTTTTAT 57.783 29.630 0.00 0.00 0.00 1.40
58 59 9.216087 TCGTGTGATAATATTTGTTTTTATGCG 57.784 29.630 0.00 0.00 0.00 4.73
59 60 8.468349 CGTGTGATAATATTTGTTTTTATGCGG 58.532 33.333 0.00 0.00 0.00 5.69
60 61 8.265998 GTGTGATAATATTTGTTTTTATGCGGC 58.734 33.333 0.00 0.00 0.00 6.53
61 62 7.976175 TGTGATAATATTTGTTTTTATGCGGCA 59.024 29.630 4.58 4.58 0.00 5.69
62 63 8.977505 GTGATAATATTTGTTTTTATGCGGCAT 58.022 29.630 20.57 20.57 0.00 4.40
63 64 9.539825 TGATAATATTTGTTTTTATGCGGCATT 57.460 25.926 21.99 5.49 0.00 3.56
66 67 3.802722 TTGTTTTTATGCGGCATTTGC 57.197 38.095 21.99 8.05 41.14 3.68
68 69 2.478134 TGTTTTTATGCGGCATTTGCAC 59.522 40.909 21.99 13.26 46.57 4.57
69 70 1.719600 TTTTATGCGGCATTTGCACC 58.280 45.000 21.99 0.00 46.57 5.01
70 71 0.894141 TTTATGCGGCATTTGCACCT 59.106 45.000 21.99 0.00 46.57 4.00
71 72 0.894141 TTATGCGGCATTTGCACCTT 59.106 45.000 21.99 0.00 46.57 3.50
72 73 0.455410 TATGCGGCATTTGCACCTTC 59.545 50.000 21.99 0.00 46.57 3.46
73 74 2.125952 GCGGCATTTGCACCTTCC 60.126 61.111 4.74 0.00 44.36 3.46
74 75 2.929903 GCGGCATTTGCACCTTCCA 61.930 57.895 4.74 0.00 44.36 3.53
75 76 1.080569 CGGCATTTGCACCTTCCAC 60.081 57.895 4.74 0.00 44.36 4.02
76 77 1.804396 CGGCATTTGCACCTTCCACA 61.804 55.000 4.74 0.00 44.36 4.17
77 78 0.609662 GGCATTTGCACCTTCCACAT 59.390 50.000 4.74 0.00 44.36 3.21
78 79 1.002315 GGCATTTGCACCTTCCACATT 59.998 47.619 4.74 0.00 44.36 2.71
79 80 2.070783 GCATTTGCACCTTCCACATTG 58.929 47.619 0.00 0.00 41.59 2.82
80 81 2.070783 CATTTGCACCTTCCACATTGC 58.929 47.619 0.00 0.00 35.45 3.56
81 82 1.117994 TTTGCACCTTCCACATTGCA 58.882 45.000 0.00 0.00 43.11 4.08
82 83 0.675083 TTGCACCTTCCACATTGCAG 59.325 50.000 0.00 0.00 45.29 4.41
83 84 0.467844 TGCACCTTCCACATTGCAGT 60.468 50.000 0.00 0.00 40.01 4.40
84 85 0.675633 GCACCTTCCACATTGCAGTT 59.324 50.000 0.00 0.00 34.97 3.16
85 86 1.885887 GCACCTTCCACATTGCAGTTA 59.114 47.619 0.00 0.00 34.97 2.24
86 87 2.295909 GCACCTTCCACATTGCAGTTAA 59.704 45.455 0.00 0.00 34.97 2.01
87 88 3.243704 GCACCTTCCACATTGCAGTTAAA 60.244 43.478 0.00 0.00 34.97 1.52
88 89 4.298332 CACCTTCCACATTGCAGTTAAAC 58.702 43.478 0.00 0.00 0.00 2.01
89 90 4.037923 CACCTTCCACATTGCAGTTAAACT 59.962 41.667 0.00 0.00 0.00 2.66
127 128 9.651913 AGTTCTAAGAAGCATTTTGTTGAAAAA 57.348 25.926 0.00 0.00 34.72 1.94
174 175 8.877864 TGGTACAAGATAATTCAACCTCAAAT 57.122 30.769 0.00 0.00 31.92 2.32
187 188 8.463930 TTCAACCTCAAATTTCAGATGTAGTT 57.536 30.769 0.00 0.00 0.00 2.24
193 194 7.230849 TCAAATTTCAGATGTAGTTTGGCAT 57.769 32.000 7.31 0.00 0.00 4.40
225 226 1.889262 GCCAATACGGTTTCACCCCTT 60.889 52.381 0.00 0.00 33.75 3.95
244 245 6.440328 ACCCCTTCATATTTTGCTTGTGTATT 59.560 34.615 0.00 0.00 0.00 1.89
422 436 2.047655 TAGCGTGCCCTGTTTCCG 60.048 61.111 0.00 0.00 0.00 4.30
451 1433 3.545703 GAGGGATAATGAACACTGGTGG 58.454 50.000 5.70 0.00 34.19 4.61
546 1557 3.103447 TCAGAGACTTCAGTTGCAGTG 57.897 47.619 0.00 0.00 0.00 3.66
611 1629 6.042638 ACTAATTGTGACAGTAGCATGACT 57.957 37.500 0.00 0.00 0.00 3.41
622 1640 0.689055 AGCATGACTGAGGAGCAACA 59.311 50.000 0.00 0.00 0.00 3.33
630 1649 2.008329 CTGAGGAGCAACAGAAGCATC 58.992 52.381 0.00 0.00 36.38 3.91
719 1747 2.480555 GCCGTGGATGAAGCAACG 59.519 61.111 0.00 0.00 35.85 4.10
725 1753 1.134694 GGATGAAGCAACGGTTCGC 59.865 57.895 7.05 7.05 42.15 4.70
734 1762 1.334599 GCAACGGTTCGCTGATTTTCA 60.335 47.619 7.68 0.00 0.00 2.69
740 1769 3.308530 GGTTCGCTGATTTTCAAGGTTG 58.691 45.455 0.00 0.00 0.00 3.77
850 1910 5.880332 ACACTACAACATAACATTAGCTGGG 59.120 40.000 0.00 0.00 0.00 4.45
860 1920 2.158900 ACATTAGCTGGGACGAGGAATG 60.159 50.000 0.00 0.00 0.00 2.67
1437 2497 0.320683 GGGTTTGCTTGGTGGATTGC 60.321 55.000 0.00 0.00 0.00 3.56
1438 2498 0.667184 GGTTTGCTTGGTGGATTGCG 60.667 55.000 0.00 0.00 0.00 4.85
1440 2500 0.313672 TTTGCTTGGTGGATTGCGTC 59.686 50.000 0.00 0.00 0.00 5.19
1450 2533 1.153249 GATTGCGTCGGGGATTGGA 60.153 57.895 0.00 0.00 0.00 3.53
1472 2555 1.381867 TTGGAGTGGATGGGGAATGT 58.618 50.000 0.00 0.00 0.00 2.71
1473 2556 0.625316 TGGAGTGGATGGGGAATGTG 59.375 55.000 0.00 0.00 0.00 3.21
1475 2558 0.918983 GAGTGGATGGGGAATGTGGA 59.081 55.000 0.00 0.00 0.00 4.02
1476 2559 1.284785 GAGTGGATGGGGAATGTGGAA 59.715 52.381 0.00 0.00 0.00 3.53
1477 2560 1.005924 AGTGGATGGGGAATGTGGAAC 59.994 52.381 0.00 0.00 37.35 3.62
1478 2561 0.334676 TGGATGGGGAATGTGGAACC 59.665 55.000 0.00 0.00 34.36 3.62
1480 2563 0.751643 GATGGGGAATGTGGAACCGG 60.752 60.000 0.00 0.00 34.36 5.28
1506 2589 2.234168 GGAGCGTTTTAAGGAGAGGAGT 59.766 50.000 0.00 0.00 0.00 3.85
1531 2625 3.028366 GAGCGAGCCTGGCGTTTTC 62.028 63.158 13.96 4.19 35.00 2.29
1542 2655 3.023591 GCGTTTTCGGCTTCGGGAG 62.024 63.158 0.00 0.00 44.29 4.30
1546 2659 4.707768 TTCGGCTTCGGGAGGGGA 62.708 66.667 0.00 0.00 34.13 4.81
1550 2663 3.787001 GCTTCGGGAGGGGAGGTG 61.787 72.222 0.00 0.00 0.00 4.00
1598 2711 4.489771 GGCGGTGGGGATCTGGTG 62.490 72.222 0.00 0.00 0.00 4.17
1619 2732 4.143333 CGCGGATCGTGGGGAAGT 62.143 66.667 0.00 0.00 33.47 3.01
1632 2745 2.100631 GGAAGTGATCCGTGGCGTG 61.101 63.158 0.00 0.00 38.79 5.34
1633 2746 1.080093 GAAGTGATCCGTGGCGTGA 60.080 57.895 0.00 0.00 0.00 4.35
1639 2752 0.953960 GATCCGTGGCGTGAAGGTTT 60.954 55.000 0.00 0.00 0.00 3.27
1659 2772 2.261361 GCGTTCCCATTGGTTGGC 59.739 61.111 1.20 0.00 44.97 4.52
1664 2777 1.186917 TTCCCATTGGTTGGCTGCTG 61.187 55.000 1.20 0.00 44.97 4.41
1666 2779 2.280552 CCATTGGTTGGCTGCTGCT 61.281 57.895 15.64 0.00 39.09 4.24
1698 2811 4.408821 GTGGCCGTGGCATCCAGA 62.409 66.667 13.76 0.00 44.11 3.86
1699 2812 4.408821 TGGCCGTGGCATCCAGAC 62.409 66.667 13.76 0.00 44.11 3.51
1701 2814 2.512515 GCCGTGGCATCCAGACTC 60.513 66.667 5.89 0.00 41.49 3.36
1702 2815 3.023949 GCCGTGGCATCCAGACTCT 62.024 63.158 5.89 0.00 41.49 3.24
1705 2922 0.102120 CGTGGCATCCAGACTCTCTC 59.898 60.000 0.00 0.00 32.34 3.20
1706 2923 0.463620 GTGGCATCCAGACTCTCTCC 59.536 60.000 0.00 0.00 32.34 3.71
1708 2925 1.739049 GCATCCAGACTCTCTCCGG 59.261 63.158 0.00 0.00 0.00 5.14
1717 2934 0.540830 ACTCTCTCCGGTGCAACTCT 60.541 55.000 0.00 0.00 36.74 3.24
1721 2938 1.001406 CTCTCCGGTGCAACTCTCTTT 59.999 52.381 0.00 0.00 36.74 2.52
1722 2939 1.416401 TCTCCGGTGCAACTCTCTTTT 59.584 47.619 0.00 0.00 36.74 2.27
1725 2942 1.676006 CCGGTGCAACTCTCTTTTTGT 59.324 47.619 0.00 0.00 36.74 2.83
1727 2944 3.428862 CCGGTGCAACTCTCTTTTTGTTT 60.429 43.478 0.00 0.00 36.74 2.83
1730 2947 4.327087 GGTGCAACTCTCTTTTTGTTTGTG 59.673 41.667 0.00 0.00 36.74 3.33
1731 2948 4.923281 GTGCAACTCTCTTTTTGTTTGTGT 59.077 37.500 0.00 0.00 0.00 3.72
1732 2949 5.060940 GTGCAACTCTCTTTTTGTTTGTGTC 59.939 40.000 0.00 0.00 0.00 3.67
1733 2950 5.048083 TGCAACTCTCTTTTTGTTTGTGTCT 60.048 36.000 0.00 0.00 0.00 3.41
1739 2988 8.306761 ACTCTCTTTTTGTTTGTGTCTGAATTT 58.693 29.630 0.00 0.00 0.00 1.82
1743 2992 8.087750 TCTTTTTGTTTGTGTCTGAATTTGAGT 58.912 29.630 0.00 0.00 0.00 3.41
1761 3010 1.701847 AGTTGGCTCATGTCCTCTTGT 59.298 47.619 7.95 0.00 0.00 3.16
1764 3013 2.820178 TGGCTCATGTCCTCTTGTAGA 58.180 47.619 7.95 0.00 0.00 2.59
1765 3014 3.378512 TGGCTCATGTCCTCTTGTAGAT 58.621 45.455 7.95 0.00 0.00 1.98
1766 3015 3.776969 TGGCTCATGTCCTCTTGTAGATT 59.223 43.478 7.95 0.00 0.00 2.40
1767 3016 4.962362 TGGCTCATGTCCTCTTGTAGATTA 59.038 41.667 7.95 0.00 0.00 1.75
1768 3017 5.604231 TGGCTCATGTCCTCTTGTAGATTAT 59.396 40.000 7.95 0.00 0.00 1.28
1769 3018 5.931146 GGCTCATGTCCTCTTGTAGATTATG 59.069 44.000 0.00 0.00 0.00 1.90
1770 3019 6.463614 GGCTCATGTCCTCTTGTAGATTATGT 60.464 42.308 0.00 0.00 0.00 2.29
1771 3020 6.644592 GCTCATGTCCTCTTGTAGATTATGTC 59.355 42.308 0.00 0.00 0.00 3.06
1779 3029 7.342026 TCCTCTTGTAGATTATGTCTGTGCTTA 59.658 37.037 0.00 0.00 37.83 3.09
1785 3035 9.317936 TGTAGATTATGTCTGTGCTTAAATCTG 57.682 33.333 0.00 0.00 37.83 2.90
1788 3038 9.453572 AGATTATGTCTGTGCTTAAATCTGAAA 57.546 29.630 0.00 0.00 35.31 2.69
1791 3041 9.677567 TTATGTCTGTGCTTAAATCTGAAAAAC 57.322 29.630 0.00 0.00 0.00 2.43
1793 3043 7.542890 TGTCTGTGCTTAAATCTGAAAAACAA 58.457 30.769 0.00 0.00 0.00 2.83
1794 3044 8.031864 TGTCTGTGCTTAAATCTGAAAAACAAA 58.968 29.630 0.00 0.00 0.00 2.83
1796 3046 9.086336 TCTGTGCTTAAATCTGAAAAACAAAAG 57.914 29.630 0.00 0.00 0.00 2.27
1797 3047 8.770438 TGTGCTTAAATCTGAAAAACAAAAGT 57.230 26.923 0.00 0.00 0.00 2.66
1830 3080 1.383456 TTTTGCCACGCACTGCTCTT 61.383 50.000 0.00 0.00 38.71 2.85
1853 3103 2.665649 TTGTACACTAGCATCACCCG 57.334 50.000 0.00 0.00 0.00 5.28
1862 3112 2.117156 GCATCACCCGAGCAATGCT 61.117 57.895 7.79 7.79 43.88 3.79
1871 3121 1.006391 CCGAGCAATGCTACGTTTACG 60.006 52.381 8.12 5.43 39.88 3.18
1874 3124 3.000078 CGAGCAATGCTACGTTTACGAAT 60.000 43.478 8.12 0.00 39.88 3.34
1875 3125 4.258935 AGCAATGCTACGTTTACGAATG 57.741 40.909 5.69 0.15 43.39 2.67
1876 3126 3.063452 AGCAATGCTACGTTTACGAATGG 59.937 43.478 5.69 0.00 43.39 3.16
1879 3129 5.729454 GCAATGCTACGTTTACGAATGGAAT 60.729 40.000 9.53 0.00 43.02 3.01
1880 3130 6.255215 CAATGCTACGTTTACGAATGGAATT 58.745 36.000 9.53 0.00 43.02 2.17
1881 3131 5.866335 TGCTACGTTTACGAATGGAATTT 57.134 34.783 9.53 0.00 43.02 1.82
1883 3133 6.764094 TGCTACGTTTACGAATGGAATTTAC 58.236 36.000 9.53 0.00 43.02 2.01
1884 3134 6.368243 TGCTACGTTTACGAATGGAATTTACA 59.632 34.615 9.53 0.00 43.02 2.41
1885 3135 6.898189 GCTACGTTTACGAATGGAATTTACAG 59.102 38.462 9.53 0.00 43.02 2.74
1886 3136 6.173191 ACGTTTACGAATGGAATTTACAGG 57.827 37.500 9.53 0.00 43.02 4.00
1887 3137 5.122711 ACGTTTACGAATGGAATTTACAGGG 59.877 40.000 9.53 0.00 43.02 4.45
1888 3138 5.122711 CGTTTACGAATGGAATTTACAGGGT 59.877 40.000 0.00 0.00 43.02 4.34
1889 3139 6.348704 CGTTTACGAATGGAATTTACAGGGTT 60.349 38.462 0.00 0.00 43.02 4.11
1891 3141 8.680001 GTTTACGAATGGAATTTACAGGGTTAT 58.320 33.333 0.00 0.00 36.07 1.89
1892 3142 6.937436 ACGAATGGAATTTACAGGGTTATC 57.063 37.500 0.00 0.00 36.07 1.75
1893 3143 6.659824 ACGAATGGAATTTACAGGGTTATCT 58.340 36.000 0.00 0.00 36.07 1.98
1894 3144 7.116736 ACGAATGGAATTTACAGGGTTATCTT 58.883 34.615 0.00 0.00 36.07 2.40
1895 3145 8.269317 ACGAATGGAATTTACAGGGTTATCTTA 58.731 33.333 0.00 0.00 36.07 2.10
1896 3146 9.284968 CGAATGGAATTTACAGGGTTATCTTAT 57.715 33.333 0.00 0.00 36.07 1.73
1898 3148 9.936329 AATGGAATTTACAGGGTTATCTTATGT 57.064 29.630 0.00 0.00 26.74 2.29
1907 3157 3.924686 GGGTTATCTTATGTATGTCGGCG 59.075 47.826 0.00 0.00 0.00 6.46
1912 3162 2.124903 CTTATGTATGTCGGCGTCCAC 58.875 52.381 6.85 2.88 0.00 4.02
1915 3165 3.063704 TATGTCGGCGTCCACGGT 61.064 61.111 6.85 0.00 40.23 4.83
1926 3176 1.666054 GTCCACGGTTTAACCACACA 58.334 50.000 14.97 0.00 38.47 3.72
1927 3177 2.015587 GTCCACGGTTTAACCACACAA 58.984 47.619 14.97 0.00 38.47 3.33
1929 3179 1.268133 CCACGGTTTAACCACACAACG 60.268 52.381 14.97 0.72 38.47 4.10
1939 3189 6.627395 TTAACCACACAACGAGATGAAAAT 57.373 33.333 0.00 0.00 0.00 1.82
1942 3192 3.670055 CCACACAACGAGATGAAAATTGC 59.330 43.478 0.00 0.00 0.00 3.56
1943 3193 3.670055 CACACAACGAGATGAAAATTGCC 59.330 43.478 0.00 0.00 0.00 4.52
1948 3198 1.593070 CGAGATGAAAATTGCCGAGCG 60.593 52.381 0.00 0.00 0.00 5.03
1959 3209 3.470567 CCGAGCGCAGTCACGAAC 61.471 66.667 11.47 0.00 34.06 3.95
1961 3211 3.470567 GAGCGCAGTCACGAACGG 61.471 66.667 11.47 0.00 34.06 4.44
1976 3226 1.234615 AACGGAGAAACCATGGCACG 61.235 55.000 13.04 10.00 38.90 5.34
1977 3227 1.375396 CGGAGAAACCATGGCACGA 60.375 57.895 13.04 0.00 38.90 4.35
1982 3232 2.614057 GAGAAACCATGGCACGAATAGG 59.386 50.000 13.04 0.00 0.00 2.57
1983 3233 1.676006 GAAACCATGGCACGAATAGGG 59.324 52.381 13.04 0.00 0.00 3.53
2004 3255 0.673437 AACAATGCCCACACGAAAGG 59.327 50.000 0.00 0.00 0.00 3.11
2005 3256 0.467290 ACAATGCCCACACGAAAGGT 60.467 50.000 0.00 0.00 0.00 3.50
2008 3259 0.606401 ATGCCCACACGAAAGGTCAG 60.606 55.000 0.00 0.00 0.00 3.51
2021 3272 2.435059 GTCAGGACTGGCCGAAGC 60.435 66.667 0.00 0.00 43.43 3.86
2022 3273 2.922503 TCAGGACTGGCCGAAGCA 60.923 61.111 0.00 0.00 43.43 3.91
2055 3306 0.034863 ACCACCGACACACCAAAGTT 60.035 50.000 0.00 0.00 0.00 2.66
2056 3307 0.380378 CCACCGACACACCAAAGTTG 59.620 55.000 0.00 0.00 0.00 3.16
2062 3313 1.067060 GACACACCAAAGTTGCTTCCC 59.933 52.381 0.00 0.00 0.00 3.97
2080 3331 2.665000 CTCTCGCCCAGGCTCAAA 59.335 61.111 7.17 0.00 39.32 2.69
2083 3334 4.722700 TCGCCCAGGCTCAAAGGC 62.723 66.667 7.17 4.67 42.18 4.35
2093 3344 0.955428 GCTCAAAGGCCACATGTCGA 60.955 55.000 5.01 0.00 0.00 4.20
2096 3347 2.325082 AAAGGCCACATGTCGACGC 61.325 57.895 11.62 7.46 0.00 5.19
2097 3348 3.529341 AAGGCCACATGTCGACGCA 62.529 57.895 11.62 0.00 0.00 5.24
2098 3349 3.047280 GGCCACATGTCGACGCAA 61.047 61.111 11.62 0.00 0.00 4.85
2099 3350 2.612567 GGCCACATGTCGACGCAAA 61.613 57.895 11.62 0.00 0.00 3.68
2101 3352 1.497278 CCACATGTCGACGCAAAGG 59.503 57.895 11.62 5.31 0.00 3.11
2107 3362 4.697756 TCGACGCAAAGGGGCCAG 62.698 66.667 4.39 0.00 0.00 4.85
2121 3376 2.284921 CCAGGGTGGAGAGGAGCA 60.285 66.667 0.00 0.00 40.96 4.26
2124 3379 2.607750 GGGTGGAGAGGAGCACCA 60.608 66.667 2.07 0.00 39.35 4.17
2135 3390 3.330701 AGAGGAGCACCAATAACAAAGGA 59.669 43.478 2.07 0.00 38.94 3.36
2139 3394 4.072131 GAGCACCAATAACAAAGGACTCA 58.928 43.478 0.00 0.00 32.90 3.41
2140 3395 4.666512 AGCACCAATAACAAAGGACTCAT 58.333 39.130 0.00 0.00 0.00 2.90
2160 3415 1.134159 TCCGGACTAGCTAGTGGAGAC 60.134 57.143 30.70 15.28 36.50 3.36
2163 3418 2.356382 CGGACTAGCTAGTGGAGACAAG 59.644 54.545 30.70 9.84 46.06 3.16
2164 3419 3.622630 GGACTAGCTAGTGGAGACAAGA 58.377 50.000 30.70 0.00 46.06 3.02
2167 3422 3.764972 ACTAGCTAGTGGAGACAAGAACC 59.235 47.826 25.52 0.00 46.06 3.62
2177 3432 1.282930 GACAAGAACCTCGGTCACGC 61.283 60.000 0.00 0.00 40.69 5.34
2193 3448 2.345991 GCCGCAACTCACCCACTA 59.654 61.111 0.00 0.00 0.00 2.74
2194 3449 1.078426 GCCGCAACTCACCCACTAT 60.078 57.895 0.00 0.00 0.00 2.12
2196 3451 0.744414 CCGCAACTCACCCACTATGG 60.744 60.000 0.00 0.00 37.25 2.74
2213 3468 2.432456 GCGACAGTCATCGGCACA 60.432 61.111 0.41 0.00 42.49 4.57
2214 3469 2.027073 GCGACAGTCATCGGCACAA 61.027 57.895 0.41 0.00 42.49 3.33
2215 3470 1.959899 GCGACAGTCATCGGCACAAG 61.960 60.000 0.41 0.00 42.49 3.16
2216 3471 1.790387 GACAGTCATCGGCACAAGC 59.210 57.895 0.00 0.00 41.10 4.01
2217 3472 0.950555 GACAGTCATCGGCACAAGCA 60.951 55.000 0.00 0.00 44.61 3.91
2219 3474 0.167470 CAGTCATCGGCACAAGCAAG 59.833 55.000 0.00 0.00 44.61 4.01
2414 3669 4.887957 AACATGGACGAGAGGGGA 57.112 55.556 0.00 0.00 0.00 4.81
2417 3672 1.075970 CATGGACGAGAGGGGAGGA 60.076 63.158 0.00 0.00 0.00 3.71
2418 3673 0.687757 CATGGACGAGAGGGGAGGAA 60.688 60.000 0.00 0.00 0.00 3.36
2419 3674 0.688087 ATGGACGAGAGGGGAGGAAC 60.688 60.000 0.00 0.00 0.00 3.62
2421 3676 0.258194 GGACGAGAGGGGAGGAACTA 59.742 60.000 0.00 0.00 41.55 2.24
2422 3677 1.682740 GACGAGAGGGGAGGAACTAG 58.317 60.000 0.00 0.00 41.55 2.57
2423 3678 0.259356 ACGAGAGGGGAGGAACTAGG 59.741 60.000 0.00 0.00 41.55 3.02
2454 4361 1.586564 GAGTCGCCGAATGAGGACG 60.587 63.158 0.00 0.00 34.68 4.79
2455 4362 3.255379 GTCGCCGAATGAGGACGC 61.255 66.667 0.00 0.00 33.22 5.19
2459 4366 2.885644 CCGAATGAGGACGCCACG 60.886 66.667 0.00 0.00 0.00 4.94
2483 4390 3.316868 GGTCGGTTTCTCATTTCCAACAA 59.683 43.478 0.00 0.00 0.00 2.83
2520 4427 7.633193 ATTATTCCTAGACTCTACATAGGCG 57.367 40.000 0.00 0.00 36.75 5.52
2589 4496 3.250280 GCTATTGTGGCATCTCACATCAG 59.750 47.826 0.00 0.00 45.63 2.90
2593 4500 4.492494 TGTGGCATCTCACATCAGTTAT 57.508 40.909 0.00 0.00 42.05 1.89
2602 4509 7.013083 GCATCTCACATCAGTTATGAATCCTTT 59.987 37.037 0.00 0.00 39.39 3.11
2619 4526 5.964958 TCCTTTATTTTCAAGTGCAGAGG 57.035 39.130 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.322776 GCGATTTATTAGAGAAATATGCAAGTG 57.677 33.333 0.00 0.00 32.28 3.16
5 6 8.223769 CGCGATTTATTAGAGAAATATGCAAGT 58.776 33.333 0.00 0.00 31.84 3.16
6 7 8.223769 ACGCGATTTATTAGAGAAATATGCAAG 58.776 33.333 15.93 0.00 31.84 4.01
7 8 8.083462 ACGCGATTTATTAGAGAAATATGCAA 57.917 30.769 15.93 0.00 31.84 4.08
8 9 7.410407 CGACGCGATTTATTAGAGAAATATGCA 60.410 37.037 15.93 0.00 31.84 3.96
9 10 6.889833 CGACGCGATTTATTAGAGAAATATGC 59.110 38.462 15.93 0.00 30.11 3.14
10 11 7.888209 CACGACGCGATTTATTAGAGAAATATG 59.112 37.037 15.93 0.00 30.11 1.78
11 12 7.594015 ACACGACGCGATTTATTAGAGAAATAT 59.406 33.333 15.93 0.00 30.11 1.28
12 13 6.914215 ACACGACGCGATTTATTAGAGAAATA 59.086 34.615 15.93 0.00 0.00 1.40
13 14 5.747197 ACACGACGCGATTTATTAGAGAAAT 59.253 36.000 15.93 0.00 0.00 2.17
14 15 5.004061 CACACGACGCGATTTATTAGAGAAA 59.996 40.000 15.93 0.00 0.00 2.52
15 16 4.497966 CACACGACGCGATTTATTAGAGAA 59.502 41.667 15.93 0.00 0.00 2.87
16 17 4.033019 CACACGACGCGATTTATTAGAGA 58.967 43.478 15.93 0.00 0.00 3.10
17 18 4.033019 TCACACGACGCGATTTATTAGAG 58.967 43.478 15.93 0.00 0.00 2.43
18 19 4.018649 TCACACGACGCGATTTATTAGA 57.981 40.909 15.93 0.00 0.00 2.10
19 20 4.948864 ATCACACGACGCGATTTATTAG 57.051 40.909 15.93 0.00 0.00 1.73
20 21 6.996562 ATTATCACACGACGCGATTTATTA 57.003 33.333 15.93 0.00 0.00 0.98
21 22 5.900339 ATTATCACACGACGCGATTTATT 57.100 34.783 15.93 0.00 0.00 1.40
22 23 7.576750 AATATTATCACACGACGCGATTTAT 57.423 32.000 15.93 0.00 0.00 1.40
23 24 6.996562 AATATTATCACACGACGCGATTTA 57.003 33.333 15.93 0.00 0.00 1.40
24 25 5.900339 AATATTATCACACGACGCGATTT 57.100 34.783 15.93 0.00 0.00 2.17
25 26 5.233476 ACAAATATTATCACACGACGCGATT 59.767 36.000 15.93 0.00 0.00 3.34
26 27 4.743151 ACAAATATTATCACACGACGCGAT 59.257 37.500 15.93 0.00 0.00 4.58
27 28 4.106909 ACAAATATTATCACACGACGCGA 58.893 39.130 15.93 0.00 0.00 5.87
28 29 4.431894 ACAAATATTATCACACGACGCG 57.568 40.909 3.53 3.53 0.00 6.01
29 30 7.487180 AAAAACAAATATTATCACACGACGC 57.513 32.000 0.00 0.00 0.00 5.19
32 33 9.216087 CGCATAAAAACAAATATTATCACACGA 57.784 29.630 0.00 0.00 0.00 4.35
33 34 8.468349 CCGCATAAAAACAAATATTATCACACG 58.532 33.333 0.00 0.00 0.00 4.49
34 35 8.265998 GCCGCATAAAAACAAATATTATCACAC 58.734 33.333 0.00 0.00 0.00 3.82
35 36 7.976175 TGCCGCATAAAAACAAATATTATCACA 59.024 29.630 0.00 0.00 0.00 3.58
36 37 8.346476 TGCCGCATAAAAACAAATATTATCAC 57.654 30.769 0.00 0.00 0.00 3.06
37 38 9.539825 AATGCCGCATAAAAACAAATATTATCA 57.460 25.926 6.22 0.00 0.00 2.15
40 41 8.119226 GCAAATGCCGCATAAAAACAAATATTA 58.881 29.630 6.22 0.00 34.31 0.98
41 42 6.966066 GCAAATGCCGCATAAAAACAAATATT 59.034 30.769 6.22 0.00 34.31 1.28
42 43 6.093219 TGCAAATGCCGCATAAAAACAAATAT 59.907 30.769 6.22 0.00 41.18 1.28
43 44 5.409520 TGCAAATGCCGCATAAAAACAAATA 59.590 32.000 6.22 0.00 41.18 1.40
44 45 4.214971 TGCAAATGCCGCATAAAAACAAAT 59.785 33.333 6.22 0.00 41.18 2.32
45 46 3.561310 TGCAAATGCCGCATAAAAACAAA 59.439 34.783 6.22 0.00 41.18 2.83
46 47 3.059325 GTGCAAATGCCGCATAAAAACAA 60.059 39.130 6.22 0.00 42.32 2.83
47 48 2.478134 GTGCAAATGCCGCATAAAAACA 59.522 40.909 6.22 0.00 42.32 2.83
48 49 2.159720 GGTGCAAATGCCGCATAAAAAC 60.160 45.455 6.22 3.72 42.32 2.43
49 50 2.072298 GGTGCAAATGCCGCATAAAAA 58.928 42.857 6.22 0.00 42.32 1.94
50 51 1.274728 AGGTGCAAATGCCGCATAAAA 59.725 42.857 6.22 0.00 42.32 1.52
51 52 0.894141 AGGTGCAAATGCCGCATAAA 59.106 45.000 6.22 0.00 42.32 1.40
52 53 0.894141 AAGGTGCAAATGCCGCATAA 59.106 45.000 6.22 0.00 42.32 1.90
53 54 0.455410 GAAGGTGCAAATGCCGCATA 59.545 50.000 6.22 0.00 42.32 3.14
54 55 1.216178 GAAGGTGCAAATGCCGCAT 59.784 52.632 0.00 0.00 42.32 4.73
55 56 2.650196 GAAGGTGCAAATGCCGCA 59.350 55.556 2.46 0.00 41.18 5.69
56 57 2.125952 GGAAGGTGCAAATGCCGC 60.126 61.111 2.46 0.00 41.18 6.53
57 58 1.080569 GTGGAAGGTGCAAATGCCG 60.081 57.895 2.46 0.00 41.18 5.69
58 59 0.609662 ATGTGGAAGGTGCAAATGCC 59.390 50.000 2.46 0.00 41.18 4.40
59 60 2.070783 CAATGTGGAAGGTGCAAATGC 58.929 47.619 0.00 0.00 42.50 3.56
60 61 2.070783 GCAATGTGGAAGGTGCAAATG 58.929 47.619 0.00 0.00 36.97 2.32
61 62 1.693062 TGCAATGTGGAAGGTGCAAAT 59.307 42.857 0.00 0.00 43.65 2.32
62 63 1.068895 CTGCAATGTGGAAGGTGCAAA 59.931 47.619 0.00 0.00 45.71 3.68
63 64 0.675083 CTGCAATGTGGAAGGTGCAA 59.325 50.000 0.00 0.00 45.71 4.08
64 65 0.467844 ACTGCAATGTGGAAGGTGCA 60.468 50.000 0.00 0.00 44.36 4.57
65 66 0.675633 AACTGCAATGTGGAAGGTGC 59.324 50.000 0.00 0.00 37.51 5.01
66 67 4.037923 AGTTTAACTGCAATGTGGAAGGTG 59.962 41.667 0.00 0.00 0.00 4.00
67 68 4.037923 CAGTTTAACTGCAATGTGGAAGGT 59.962 41.667 12.37 0.00 39.62 3.50
68 69 4.278170 TCAGTTTAACTGCAATGTGGAAGG 59.722 41.667 19.24 0.00 45.54 3.46
69 70 5.437289 TCAGTTTAACTGCAATGTGGAAG 57.563 39.130 19.24 0.00 45.54 3.46
70 71 5.843673 TTCAGTTTAACTGCAATGTGGAA 57.156 34.783 19.24 4.15 45.54 3.53
71 72 5.769662 AGATTCAGTTTAACTGCAATGTGGA 59.230 36.000 19.24 0.00 45.54 4.02
72 73 6.017400 AGATTCAGTTTAACTGCAATGTGG 57.983 37.500 19.24 0.00 45.54 4.17
73 74 6.671190 TGAGATTCAGTTTAACTGCAATGTG 58.329 36.000 19.24 0.00 45.54 3.21
74 75 6.882610 TGAGATTCAGTTTAACTGCAATGT 57.117 33.333 19.24 16.38 45.54 2.71
77 78 9.890629 ACTATATGAGATTCAGTTTAACTGCAA 57.109 29.630 19.24 14.25 45.54 4.08
78 79 9.890629 AACTATATGAGATTCAGTTTAACTGCA 57.109 29.630 19.24 10.06 45.54 4.41
101 102 9.651913 TTTTTCAACAAAATGCTTCTTAGAACT 57.348 25.926 0.00 0.00 31.39 3.01
125 126 9.161629 CCAAAATCTGTTGAACTTTTACCTTTT 57.838 29.630 0.00 0.00 0.00 2.27
126 127 8.318412 ACCAAAATCTGTTGAACTTTTACCTTT 58.682 29.630 0.00 0.00 0.00 3.11
127 128 7.847096 ACCAAAATCTGTTGAACTTTTACCTT 58.153 30.769 0.00 0.00 0.00 3.50
128 129 7.418337 ACCAAAATCTGTTGAACTTTTACCT 57.582 32.000 0.00 0.00 0.00 3.08
129 130 8.192110 TGTACCAAAATCTGTTGAACTTTTACC 58.808 33.333 0.00 0.00 0.00 2.85
130 131 9.575783 TTGTACCAAAATCTGTTGAACTTTTAC 57.424 29.630 0.00 0.00 0.00 2.01
131 132 9.796120 CTTGTACCAAAATCTGTTGAACTTTTA 57.204 29.630 0.00 0.00 0.00 1.52
132 133 8.527810 TCTTGTACCAAAATCTGTTGAACTTTT 58.472 29.630 0.00 0.00 0.00 2.27
133 134 8.062065 TCTTGTACCAAAATCTGTTGAACTTT 57.938 30.769 0.00 0.00 0.00 2.66
134 135 7.639113 TCTTGTACCAAAATCTGTTGAACTT 57.361 32.000 0.00 0.00 0.00 2.66
135 136 7.823745 ATCTTGTACCAAAATCTGTTGAACT 57.176 32.000 0.00 0.00 0.00 3.01
142 143 9.573133 GGTTGAATTATCTTGTACCAAAATCTG 57.427 33.333 0.00 0.00 0.00 2.90
143 144 9.533831 AGGTTGAATTATCTTGTACCAAAATCT 57.466 29.630 0.00 0.00 0.00 2.40
144 145 9.788960 GAGGTTGAATTATCTTGTACCAAAATC 57.211 33.333 0.00 0.00 0.00 2.17
187 188 1.378882 GCGGATGCTTCAGATGCCAA 61.379 55.000 5.86 0.00 38.39 4.52
193 194 1.806247 CGTATTGGCGGATGCTTCAGA 60.806 52.381 3.92 0.00 42.25 3.27
195 196 2.689083 CGTATTGGCGGATGCTTCA 58.311 52.632 1.64 0.00 42.25 3.02
225 226 5.186603 TGGGCAATACACAAGCAAAATATGA 59.813 36.000 0.00 0.00 0.00 2.15
244 245 3.114606 TGATAGGAGTTCTTCATGGGCA 58.885 45.455 0.00 0.00 0.00 5.36
354 355 8.533657 TGCCTTTTGAAATGACATAATGAAGAT 58.466 29.630 0.00 0.00 0.00 2.40
355 356 7.894708 TGCCTTTTGAAATGACATAATGAAGA 58.105 30.769 0.00 0.00 0.00 2.87
408 422 3.423154 GAGCGGAAACAGGGCACG 61.423 66.667 0.00 0.00 0.00 5.34
422 436 3.117888 TGTTCATTATCCCTCCCTTGAGC 60.118 47.826 0.00 0.00 37.29 4.26
451 1433 4.931002 ACCATTGCATTTGCTGTATTTCAC 59.069 37.500 3.94 0.00 42.66 3.18
546 1557 5.408299 GGACTGATATTTTTGTTTGGCAACC 59.592 40.000 0.00 0.00 36.72 3.77
551 1562 9.191995 GTTTAGTGGACTGATATTTTTGTTTGG 57.808 33.333 0.00 0.00 0.00 3.28
611 1629 1.348696 TGATGCTTCTGTTGCTCCTCA 59.651 47.619 0.88 0.00 0.00 3.86
622 1640 7.692460 TTGTTTGATCTAATGTGATGCTTCT 57.308 32.000 0.88 0.00 0.00 2.85
719 1747 3.004315 TCAACCTTGAAAATCAGCGAACC 59.996 43.478 0.00 0.00 33.55 3.62
720 1748 3.975035 GTCAACCTTGAAAATCAGCGAAC 59.025 43.478 0.00 0.00 39.21 3.95
740 1769 6.091986 TCCATTTTCTGCTTTTGTTGTTTGTC 59.908 34.615 0.00 0.00 0.00 3.18
860 1920 2.825861 TCTGGTTTCGTGGTAGGAAC 57.174 50.000 0.00 0.00 0.00 3.62
1410 2470 2.282462 AAGCAAACCCCAGCCTCG 60.282 61.111 0.00 0.00 0.00 4.63
1411 2471 2.278330 CCAAGCAAACCCCAGCCTC 61.278 63.158 0.00 0.00 0.00 4.70
1412 2472 2.203684 CCAAGCAAACCCCAGCCT 60.204 61.111 0.00 0.00 0.00 4.58
1413 2473 2.524148 ACCAAGCAAACCCCAGCC 60.524 61.111 0.00 0.00 0.00 4.85
1414 2474 2.736531 CACCAAGCAAACCCCAGC 59.263 61.111 0.00 0.00 0.00 4.85
1415 2475 0.542702 ATCCACCAAGCAAACCCCAG 60.543 55.000 0.00 0.00 0.00 4.45
1416 2476 0.105246 AATCCACCAAGCAAACCCCA 60.105 50.000 0.00 0.00 0.00 4.96
1417 2477 0.321346 CAATCCACCAAGCAAACCCC 59.679 55.000 0.00 0.00 0.00 4.95
1418 2478 0.320683 GCAATCCACCAAGCAAACCC 60.321 55.000 0.00 0.00 0.00 4.11
1419 2479 0.667184 CGCAATCCACCAAGCAAACC 60.667 55.000 0.00 0.00 0.00 3.27
1420 2480 0.031994 ACGCAATCCACCAAGCAAAC 59.968 50.000 0.00 0.00 0.00 2.93
1437 2497 0.532862 CCAATCTCCAATCCCCGACG 60.533 60.000 0.00 0.00 0.00 5.12
1438 2498 0.837272 TCCAATCTCCAATCCCCGAC 59.163 55.000 0.00 0.00 0.00 4.79
1440 2500 0.839946 ACTCCAATCTCCAATCCCCG 59.160 55.000 0.00 0.00 0.00 5.73
1450 2533 1.985622 TTCCCCATCCACTCCAATCT 58.014 50.000 0.00 0.00 0.00 2.40
1477 2560 2.784889 TTAAAACGCTCCCCGACCGG 62.785 60.000 0.00 0.00 41.02 5.28
1478 2561 1.356527 CTTAAAACGCTCCCCGACCG 61.357 60.000 0.00 0.00 41.02 4.79
1480 2563 0.037046 TCCTTAAAACGCTCCCCGAC 60.037 55.000 0.00 0.00 41.02 4.79
1526 2620 2.038837 CCCTCCCGAAGCCGAAAAC 61.039 63.158 0.00 0.00 38.22 2.43
1527 2621 2.349755 CCCTCCCGAAGCCGAAAA 59.650 61.111 0.00 0.00 38.22 2.29
1528 2622 3.712907 CCCCTCCCGAAGCCGAAA 61.713 66.667 0.00 0.00 38.22 3.46
1529 2623 4.707768 TCCCCTCCCGAAGCCGAA 62.708 66.667 0.00 0.00 38.22 4.30
1534 2647 3.083997 CCACCTCCCCTCCCGAAG 61.084 72.222 0.00 0.00 0.00 3.79
1542 2655 3.327404 TCGAAAGCCCACCTCCCC 61.327 66.667 0.00 0.00 0.00 4.81
1546 2659 3.178540 AACGCTCGAAAGCCCACCT 62.179 57.895 0.00 0.00 46.34 4.00
1547 2660 2.668550 AACGCTCGAAAGCCCACC 60.669 61.111 0.00 0.00 46.34 4.61
1549 2662 2.463589 ATCCAACGCTCGAAAGCCCA 62.464 55.000 0.00 0.00 46.34 5.36
1550 2663 1.706287 GATCCAACGCTCGAAAGCCC 61.706 60.000 0.00 0.00 46.34 5.19
1553 2666 1.999051 CGGATCCAACGCTCGAAAG 59.001 57.895 13.41 0.00 0.00 2.62
1576 2689 4.176752 GATCCCCACCGCCCACTC 62.177 72.222 0.00 0.00 0.00 3.51
1582 2695 3.682292 GACACCAGATCCCCACCGC 62.682 68.421 0.00 0.00 0.00 5.68
1616 2729 0.670546 CTTCACGCCACGGATCACTT 60.671 55.000 0.00 0.00 0.00 3.16
1619 2732 2.107041 AACCTTCACGCCACGGATCA 62.107 55.000 0.00 0.00 0.00 2.92
1630 2743 0.591659 GGGAACGCAGAAACCTTCAC 59.408 55.000 0.00 0.00 0.00 3.18
1632 2745 1.534729 ATGGGAACGCAGAAACCTTC 58.465 50.000 0.00 0.00 0.00 3.46
1633 2746 1.613437 CAATGGGAACGCAGAAACCTT 59.387 47.619 0.00 0.00 0.00 3.50
1639 2752 0.893270 CCAACCAATGGGAACGCAGA 60.893 55.000 3.55 0.00 46.27 4.26
1681 2794 4.408821 TCTGGATGCCACGGCCAC 62.409 66.667 2.24 0.00 41.09 5.01
1685 2798 1.142748 GAGAGTCTGGATGCCACGG 59.857 63.158 0.00 0.00 0.00 4.94
1689 2802 1.739049 CGGAGAGAGTCTGGATGCC 59.261 63.158 0.00 0.00 0.00 4.40
1698 2811 0.540830 AGAGTTGCACCGGAGAGAGT 60.541 55.000 9.46 0.00 0.00 3.24
1699 2812 0.172352 GAGAGTTGCACCGGAGAGAG 59.828 60.000 9.46 0.00 0.00 3.20
1701 2814 0.605589 AAGAGAGTTGCACCGGAGAG 59.394 55.000 9.46 0.00 0.00 3.20
1702 2815 1.048601 AAAGAGAGTTGCACCGGAGA 58.951 50.000 9.46 0.00 0.00 3.71
1705 2922 1.676006 ACAAAAAGAGAGTTGCACCGG 59.324 47.619 0.00 0.00 0.00 5.28
1706 2923 3.420839 AACAAAAAGAGAGTTGCACCG 57.579 42.857 0.00 0.00 0.00 4.94
1708 2925 4.923281 ACACAAACAAAAAGAGAGTTGCAC 59.077 37.500 0.00 0.00 0.00 4.57
1717 2934 8.087750 ACTCAAATTCAGACACAAACAAAAAGA 58.912 29.630 0.00 0.00 0.00 2.52
1721 2938 6.589523 CCAACTCAAATTCAGACACAAACAAA 59.410 34.615 0.00 0.00 0.00 2.83
1722 2939 6.098679 CCAACTCAAATTCAGACACAAACAA 58.901 36.000 0.00 0.00 0.00 2.83
1725 2942 4.402155 AGCCAACTCAAATTCAGACACAAA 59.598 37.500 0.00 0.00 0.00 2.83
1727 2944 3.554934 AGCCAACTCAAATTCAGACACA 58.445 40.909 0.00 0.00 0.00 3.72
1743 2992 3.173151 TCTACAAGAGGACATGAGCCAA 58.827 45.455 0.00 0.00 0.00 4.52
1750 2999 7.495901 CACAGACATAATCTACAAGAGGACAT 58.504 38.462 0.00 0.00 35.15 3.06
1755 3004 8.932945 TTAAGCACAGACATAATCTACAAGAG 57.067 34.615 0.00 0.00 35.15 2.85
1765 3014 9.677567 GTTTTTCAGATTTAAGCACAGACATAA 57.322 29.630 0.00 0.00 0.00 1.90
1766 3015 8.845227 TGTTTTTCAGATTTAAGCACAGACATA 58.155 29.630 0.00 0.00 0.00 2.29
1767 3016 7.715657 TGTTTTTCAGATTTAAGCACAGACAT 58.284 30.769 0.00 0.00 0.00 3.06
1768 3017 7.094508 TGTTTTTCAGATTTAAGCACAGACA 57.905 32.000 0.00 0.00 0.00 3.41
1769 3018 7.985634 TTGTTTTTCAGATTTAAGCACAGAC 57.014 32.000 0.00 0.00 0.00 3.51
1770 3019 8.994429 TTTTGTTTTTCAGATTTAAGCACAGA 57.006 26.923 0.00 0.00 0.00 3.41
1771 3020 8.872845 ACTTTTGTTTTTCAGATTTAAGCACAG 58.127 29.630 0.00 0.00 0.00 3.66
1812 3062 1.823470 AAGAGCAGTGCGTGGCAAA 60.823 52.632 10.00 0.00 41.47 3.68
1816 3066 1.129251 CAATACAAGAGCAGTGCGTGG 59.871 52.381 10.00 1.06 0.00 4.94
1825 3075 6.019479 GTGATGCTAGTGTACAATACAAGAGC 60.019 42.308 7.83 7.83 43.57 4.09
1830 3080 4.440940 CGGGTGATGCTAGTGTACAATACA 60.441 45.833 0.00 2.69 36.08 2.29
1853 3103 3.984018 TTCGTAAACGTAGCATTGCTC 57.016 42.857 15.81 6.25 37.89 4.26
1862 3112 6.313411 CCCTGTAAATTCCATTCGTAAACGTA 59.687 38.462 2.02 0.00 40.80 3.57
1879 3129 8.145767 CCGACATACATAAGATAACCCTGTAAA 58.854 37.037 0.00 0.00 0.00 2.01
1880 3130 7.663827 CCGACATACATAAGATAACCCTGTAA 58.336 38.462 0.00 0.00 0.00 2.41
1881 3131 6.294899 GCCGACATACATAAGATAACCCTGTA 60.295 42.308 0.00 0.00 0.00 2.74
1883 3133 4.929808 GCCGACATACATAAGATAACCCTG 59.070 45.833 0.00 0.00 0.00 4.45
1884 3134 4.321750 CGCCGACATACATAAGATAACCCT 60.322 45.833 0.00 0.00 0.00 4.34
1885 3135 3.924686 CGCCGACATACATAAGATAACCC 59.075 47.826 0.00 0.00 0.00 4.11
1886 3136 4.553323 ACGCCGACATACATAAGATAACC 58.447 43.478 0.00 0.00 0.00 2.85
1887 3137 4.620184 GGACGCCGACATACATAAGATAAC 59.380 45.833 0.00 0.00 0.00 1.89
1888 3138 4.278919 TGGACGCCGACATACATAAGATAA 59.721 41.667 0.00 0.00 0.00 1.75
1889 3139 3.822167 TGGACGCCGACATACATAAGATA 59.178 43.478 0.00 0.00 0.00 1.98
1891 3141 2.025898 TGGACGCCGACATACATAAGA 58.974 47.619 0.00 0.00 0.00 2.10
1892 3142 2.124903 GTGGACGCCGACATACATAAG 58.875 52.381 0.00 0.00 0.00 1.73
1893 3143 1.534385 CGTGGACGCCGACATACATAA 60.534 52.381 0.00 0.00 0.00 1.90
1894 3144 0.029700 CGTGGACGCCGACATACATA 59.970 55.000 0.00 0.00 0.00 2.29
1895 3145 1.226859 CGTGGACGCCGACATACAT 60.227 57.895 0.00 0.00 0.00 2.29
1896 3146 2.179767 CGTGGACGCCGACATACA 59.820 61.111 0.00 0.00 0.00 2.29
1897 3147 2.581409 CCGTGGACGCCGACATAC 60.581 66.667 0.00 0.00 38.18 2.39
1898 3148 2.157305 AAACCGTGGACGCCGACATA 62.157 55.000 0.00 0.00 38.18 2.29
1899 3149 2.157305 TAAACCGTGGACGCCGACAT 62.157 55.000 0.00 0.00 38.18 3.06
1900 3150 2.360949 TTAAACCGTGGACGCCGACA 62.361 55.000 0.00 0.00 38.18 4.35
1907 3157 1.666054 TGTGTGGTTAAACCGTGGAC 58.334 50.000 0.00 0.00 42.58 4.02
1912 3162 2.203401 TCTCGTTGTGTGGTTAAACCG 58.797 47.619 0.00 0.00 42.58 4.44
1915 3165 6.438259 TTTTCATCTCGTTGTGTGGTTAAA 57.562 33.333 0.00 0.00 0.00 1.52
1926 3176 2.159517 GCTCGGCAATTTTCATCTCGTT 60.160 45.455 0.00 0.00 0.00 3.85
1927 3177 1.398390 GCTCGGCAATTTTCATCTCGT 59.602 47.619 0.00 0.00 0.00 4.18
1929 3179 1.857602 GCGCTCGGCAATTTTCATCTC 60.858 52.381 0.00 0.00 42.87 2.75
1942 3192 3.470567 GTTCGTGACTGCGCTCGG 61.471 66.667 9.73 1.02 0.00 4.63
1943 3193 3.816920 CGTTCGTGACTGCGCTCG 61.817 66.667 9.73 1.70 0.00 5.03
1948 3198 0.507358 GTTTCTCCGTTCGTGACTGC 59.493 55.000 0.00 0.00 0.00 4.40
1950 3200 0.748450 TGGTTTCTCCGTTCGTGACT 59.252 50.000 0.00 0.00 39.52 3.41
1959 3209 0.953471 TTCGTGCCATGGTTTCTCCG 60.953 55.000 14.67 7.01 39.52 4.63
1961 3211 2.614057 CCTATTCGTGCCATGGTTTCTC 59.386 50.000 14.67 0.00 0.00 2.87
1989 3239 0.606401 CTGACCTTTCGTGTGGGCAT 60.606 55.000 0.00 0.00 41.09 4.40
1999 3250 1.376037 CGGCCAGTCCTGACCTTTC 60.376 63.158 2.24 0.00 30.27 2.62
2004 3255 2.435059 GCTTCGGCCAGTCCTGAC 60.435 66.667 2.24 0.00 34.32 3.51
2005 3256 2.922503 TGCTTCGGCCAGTCCTGA 60.923 61.111 2.24 0.00 40.91 3.86
2021 3272 2.032071 GGTGGTGAGAACCCGGTG 59.968 66.667 0.00 0.00 0.00 4.94
2022 3273 2.446994 TGGTGGTGAGAACCCGGT 60.447 61.111 0.00 0.00 36.83 5.28
2056 3307 4.168291 CTGGGCGAGAGGGGAAGC 62.168 72.222 0.00 0.00 0.00 3.86
2078 3329 2.325082 GCGTCGACATGTGGCCTTT 61.325 57.895 17.16 0.00 0.00 3.11
2080 3331 3.529341 TTGCGTCGACATGTGGCCT 62.529 57.895 17.16 0.00 0.00 5.19
2083 3334 1.497278 CCTTTGCGTCGACATGTGG 59.503 57.895 17.16 0.87 0.00 4.17
2084 3335 1.497278 CCCTTTGCGTCGACATGTG 59.503 57.895 17.16 0.00 0.00 3.21
2085 3336 1.671054 CCCCTTTGCGTCGACATGT 60.671 57.895 17.16 0.00 0.00 3.21
2087 3338 2.746277 GCCCCTTTGCGTCGACAT 60.746 61.111 17.16 0.00 0.00 3.06
2090 3341 4.697756 CTGGCCCCTTTGCGTCGA 62.698 66.667 0.00 0.00 0.00 4.20
2096 3347 3.589542 TCCACCCTGGCCCCTTTG 61.590 66.667 0.00 0.00 37.47 2.77
2097 3348 3.268032 CTCCACCCTGGCCCCTTT 61.268 66.667 0.00 0.00 37.47 3.11
2098 3349 4.285790 TCTCCACCCTGGCCCCTT 62.286 66.667 0.00 0.00 37.47 3.95
2099 3350 4.748798 CTCTCCACCCTGGCCCCT 62.749 72.222 0.00 0.00 37.47 4.79
2101 3352 4.741239 TCCTCTCCACCCTGGCCC 62.741 72.222 0.00 0.00 37.47 5.80
2121 3376 4.261801 CGGATGAGTCCTTTGTTATTGGT 58.738 43.478 0.00 0.00 42.73 3.67
2124 3379 4.225267 AGTCCGGATGAGTCCTTTGTTATT 59.775 41.667 7.81 0.00 42.73 1.40
2135 3390 2.577700 CACTAGCTAGTCCGGATGAGT 58.422 52.381 23.68 2.14 33.46 3.41
2139 3394 1.775459 TCTCCACTAGCTAGTCCGGAT 59.225 52.381 25.47 3.79 33.46 4.18
2140 3395 1.134159 GTCTCCACTAGCTAGTCCGGA 60.134 57.143 23.68 24.06 33.46 5.14
2145 3400 3.764972 GGTTCTTGTCTCCACTAGCTAGT 59.235 47.826 20.95 20.95 36.90 2.57
2148 3403 2.829120 GAGGTTCTTGTCTCCACTAGCT 59.171 50.000 0.00 0.00 0.00 3.32
2160 3415 2.027625 GGCGTGACCGAGGTTCTTG 61.028 63.158 0.00 0.00 35.63 3.02
2177 3432 0.744414 CCATAGTGGGTGAGTTGCGG 60.744 60.000 0.00 0.00 32.67 5.69
2193 3448 2.202932 GCCGATGACTGTCGCCAT 60.203 61.111 2.98 0.00 40.17 4.40
2194 3449 3.690280 TGCCGATGACTGTCGCCA 61.690 61.111 2.98 0.00 40.17 5.69
2196 3451 1.959899 CTTGTGCCGATGACTGTCGC 61.960 60.000 2.98 0.98 40.17 5.19
2397 3652 0.978146 CCTCCCCTCTCGTCCATGTT 60.978 60.000 0.00 0.00 0.00 2.71
2398 3653 1.381872 CCTCCCCTCTCGTCCATGT 60.382 63.158 0.00 0.00 0.00 3.21
2399 3654 0.687757 TTCCTCCCCTCTCGTCCATG 60.688 60.000 0.00 0.00 0.00 3.66
2400 3655 0.688087 GTTCCTCCCCTCTCGTCCAT 60.688 60.000 0.00 0.00 0.00 3.41
2401 3656 1.305046 GTTCCTCCCCTCTCGTCCA 60.305 63.158 0.00 0.00 0.00 4.02
2402 3657 0.258194 TAGTTCCTCCCCTCTCGTCC 59.742 60.000 0.00 0.00 0.00 4.79
2404 3659 0.259356 CCTAGTTCCTCCCCTCTCGT 59.741 60.000 0.00 0.00 0.00 4.18
2405 3660 0.259356 ACCTAGTTCCTCCCCTCTCG 59.741 60.000 0.00 0.00 0.00 4.04
2406 3661 2.553911 AACCTAGTTCCTCCCCTCTC 57.446 55.000 0.00 0.00 0.00 3.20
2407 3662 3.886548 GCTAAACCTAGTTCCTCCCCTCT 60.887 52.174 0.00 0.00 0.00 3.69
2409 3664 2.046025 AGCTAAACCTAGTTCCTCCCCT 59.954 50.000 0.00 0.00 0.00 4.79
2411 3666 2.435069 GGAGCTAAACCTAGTTCCTCCC 59.565 54.545 7.56 0.00 46.77 4.30
2412 3667 3.823281 GGAGCTAAACCTAGTTCCTCC 57.177 52.381 7.56 0.00 46.77 4.30
2417 3672 3.108376 CTCAGGGGAGCTAAACCTAGTT 58.892 50.000 3.26 0.00 33.67 2.24
2418 3673 2.044630 ACTCAGGGGAGCTAAACCTAGT 59.955 50.000 3.26 5.50 45.42 2.57
2419 3674 2.696187 GACTCAGGGGAGCTAAACCTAG 59.304 54.545 3.26 5.01 45.42 3.02
2420 3675 2.748388 GACTCAGGGGAGCTAAACCTA 58.252 52.381 3.26 0.00 45.42 3.08
2421 3676 1.574263 GACTCAGGGGAGCTAAACCT 58.426 55.000 0.00 0.00 45.42 3.50
2422 3677 0.175989 CGACTCAGGGGAGCTAAACC 59.824 60.000 0.00 0.00 45.42 3.27
2423 3678 0.460459 GCGACTCAGGGGAGCTAAAC 60.460 60.000 0.00 0.00 45.42 2.01
2454 4361 4.324991 AGAAACCGACCCCGTGGC 62.325 66.667 0.00 0.00 33.59 5.01
2455 4362 2.047560 GAGAAACCGACCCCGTGG 60.048 66.667 0.00 0.00 37.80 4.94
2459 4366 1.271707 TGGAAATGAGAAACCGACCCC 60.272 52.381 0.00 0.00 0.00 4.95
2547 4454 2.233922 GCATCTATACCCGTGCCACTAT 59.766 50.000 0.00 0.00 0.00 2.12
2554 4461 4.245660 CCACAATAGCATCTATACCCGTG 58.754 47.826 0.00 0.00 0.00 4.94
2557 4464 4.286297 TGCCACAATAGCATCTATACCC 57.714 45.455 0.00 0.00 34.69 3.69
2589 4496 9.638239 TGCACTTGAAAATAAAGGATTCATAAC 57.362 29.630 0.00 0.00 33.45 1.89
2593 4500 7.309377 CCTCTGCACTTGAAAATAAAGGATTCA 60.309 37.037 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.