Multiple sequence alignment - TraesCS6A01G196600

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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 TraesCS6A01G196600 chr6A 100.000 6222 0 0 1 6222 289030967 289024746 0.000000e+00 11490.0
1 TraesCS6A01G196600 chr6A 88.293 709 75 7 1695 2398 250721508 250722213 0.000000e+00 843.0
2 TraesCS6A01G196600 chr6A 88.943 615 58 7 2474 3080 289028570 289029182 0.000000e+00 750.0
3 TraesCS6A01G196600 chr6A 89.062 64 3 2 5278 5341 59809632 59809691 6.690000e-10 76.8
4 TraesCS6A01G196600 chr6A 92.453 53 3 1 5311 5362 604890708 604890760 2.410000e-09 75.0
5 TraesCS6A01G196600 chr6A 100.000 28 0 0 1665 1692 98083573 98083546 1.100000e-02 52.8
6 TraesCS6A01G196600 chr6A 100.000 28 0 0 1697 1724 590211932 590211905 1.100000e-02 52.8
7 TraesCS6A01G196600 chr6D 96.955 2890 59 10 3150 6025 203749424 203746550 0.000000e+00 4822.0
8 TraesCS6A01G196600 chr6D 93.833 1135 59 4 1106 2238 203751860 203750735 0.000000e+00 1698.0
9 TraesCS6A01G196600 chr6D 90.705 979 85 6 115 1090 199247241 199248216 0.000000e+00 1299.0
10 TraesCS6A01G196600 chr6D 92.137 585 45 1 2443 3026 203753891 203754475 0.000000e+00 824.0
11 TraesCS6A01G196600 chr6D 86.779 711 80 11 1695 2398 60123019 60123722 0.000000e+00 780.0
12 TraesCS6A01G196600 chr6D 87.234 658 68 13 2437 3080 200489225 200489880 0.000000e+00 736.0
13 TraesCS6A01G196600 chr6D 98.507 335 5 0 5888 6222 203746626 203746292 5.370000e-165 592.0
14 TraesCS6A01G196600 chr6D 89.062 64 3 2 5278 5341 45479503 45479562 6.690000e-10 76.8
15 TraesCS6A01G196600 chr6D 91.837 49 2 2 5306 5353 104767464 104767511 4.030000e-07 67.6
16 TraesCS6A01G196600 chr6D 85.507 69 5 2 5273 5341 447883207 447883270 4.030000e-07 67.6
17 TraesCS6A01G196600 chr6D 95.238 42 1 1 5312 5352 294085211 294085170 1.450000e-06 65.8
18 TraesCS6A01G196600 chr6B 97.878 2121 30 4 3169 5286 316460825 316458717 0.000000e+00 3653.0
19 TraesCS6A01G196600 chr6B 95.996 899 29 4 5326 6222 316458717 316457824 0.000000e+00 1454.0
20 TraesCS6A01G196600 chr6B 93.686 586 35 2 1106 1691 480661892 480662475 0.000000e+00 876.0
21 TraesCS6A01G196600 chr6B 93.209 589 39 1 1106 1693 95584719 95585307 0.000000e+00 865.0
22 TraesCS6A01G196600 chr6B 88.872 656 66 7 1745 2398 316461082 316461732 0.000000e+00 800.0
23 TraesCS6A01G196600 chr6B 91.171 589 46 6 2440 3026 316461766 316461182 0.000000e+00 795.0
24 TraesCS6A01G196600 chr6B 90.179 112 11 0 1 112 159102005 159102116 5.030000e-31 147.0
25 TraesCS6A01G196600 chr7D 90.534 993 90 4 115 1105 177150972 177149982 0.000000e+00 1310.0
26 TraesCS6A01G196600 chr7D 90.030 993 95 4 115 1105 195830293 195829303 0.000000e+00 1282.0
27 TraesCS6A01G196600 chr7D 90.179 112 11 0 1 112 267869307 267869418 5.030000e-31 147.0
28 TraesCS6A01G196600 chr7D 93.421 76 4 1 5278 5352 545221964 545222039 1.830000e-20 111.0
29 TraesCS6A01G196600 chrUn 89.819 992 98 3 115 1105 311216660 311217649 0.000000e+00 1269.0
30 TraesCS6A01G196600 chr3A 89.759 996 95 5 115 1105 409579735 409578742 0.000000e+00 1267.0
31 TraesCS6A01G196600 chr3A 89.041 657 65 5 1745 2398 747601385 747602037 0.000000e+00 808.0
32 TraesCS6A01G196600 chr3A 89.286 112 12 0 1 112 500999406 500999295 2.340000e-29 141.0
33 TraesCS6A01G196600 chr3D 89.738 994 97 5 115 1105 31636052 31635061 0.000000e+00 1266.0
34 TraesCS6A01G196600 chr3D 89.759 996 91 8 115 1105 267428357 267427368 0.000000e+00 1264.0
35 TraesCS6A01G196600 chr3D 89.725 691 65 6 1712 2398 159768513 159769201 0.000000e+00 878.0
36 TraesCS6A01G196600 chr3D 87.671 657 69 9 2440 3086 159769235 159768581 0.000000e+00 754.0
37 TraesCS6A01G196600 chr3D 83.516 91 5 2 5273 5353 133538649 133538559 6.690000e-10 76.8
38 TraesCS6A01G196600 chr3D 97.674 43 0 1 5312 5353 598887882 598887924 8.650000e-09 73.1
39 TraesCS6A01G196600 chr3D 95.556 45 1 1 5311 5354 567408760 567408804 3.110000e-08 71.3
40 TraesCS6A01G196600 chr3D 100.000 29 0 0 5289 5317 606357856 606357828 3.000000e-03 54.7
41 TraesCS6A01G196600 chr3D 100.000 28 0 0 1665 1692 19016279 19016252 1.100000e-02 52.8
42 TraesCS6A01G196600 chr3D 91.892 37 3 0 1656 1692 389113525 389113561 1.100000e-02 52.8
43 TraesCS6A01G196600 chr2A 89.728 993 99 3 115 1105 395697183 395698174 0.000000e+00 1266.0
44 TraesCS6A01G196600 chr2A 89.752 644 59 5 1733 2375 122003305 122003942 0.000000e+00 817.0
45 TraesCS6A01G196600 chr2A 91.071 112 10 0 1 112 468258203 468258092 1.080000e-32 152.0
46 TraesCS6A01G196600 chr2A 89.381 113 10 2 1 112 241956714 241956603 2.340000e-29 141.0
47 TraesCS6A01G196600 chr5D 89.728 993 97 5 115 1105 190261181 190260192 0.000000e+00 1264.0
48 TraesCS6A01G196600 chr5D 86.402 706 81 9 1697 2398 470548721 470549415 0.000000e+00 758.0
49 TraesCS6A01G196600 chr5D 80.075 798 158 1 3902 4699 218260976 218260180 5.370000e-165 592.0
50 TraesCS6A01G196600 chr5D 90.501 379 27 6 5850 6222 173753523 173753148 5.600000e-135 492.0
51 TraesCS6A01G196600 chr5D 87.209 172 12 4 5156 5321 173756413 173756246 2.960000e-43 187.0
52 TraesCS6A01G196600 chr5D 90.141 142 6 7 5699 5838 173753622 173753487 1.780000e-40 178.0
53 TraesCS6A01G196600 chr5D 97.674 43 0 1 5312 5353 177683459 177683501 8.650000e-09 73.1
54 TraesCS6A01G196600 chr5D 97.619 42 0 1 5312 5352 482103317 482103358 3.110000e-08 71.3
55 TraesCS6A01G196600 chr1D 96.246 586 22 0 1106 1691 453228837 453228252 0.000000e+00 961.0
56 TraesCS6A01G196600 chr1D 88.136 708 74 10 1695 2397 296280751 296280049 0.000000e+00 833.0
57 TraesCS6A01G196600 chr1D 87.003 654 72 10 2437 3080 296280011 296280661 0.000000e+00 725.0
58 TraesCS6A01G196600 chr1D 97.727 44 0 1 5312 5354 253525987 253525944 2.410000e-09 75.0
59 TraesCS6A01G196600 chr1D 93.478 46 2 1 5311 5355 59951889 59951844 4.030000e-07 67.6
60 TraesCS6A01G196600 chr1D 95.349 43 1 1 5311 5352 326159392 326159434 4.030000e-07 67.6
61 TraesCS6A01G196600 chr1D 100.000 30 0 0 5312 5341 426584192 426584163 8.710000e-04 56.5
62 TraesCS6A01G196600 chr1D 90.476 42 2 2 5314 5354 416295912 416295952 3.000000e-03 54.7
63 TraesCS6A01G196600 chr5A 94.881 586 30 0 1106 1691 622825008 622824423 0.000000e+00 917.0
64 TraesCS6A01G196600 chr5A 79.975 799 157 3 3902 4699 291271966 291271170 2.500000e-163 586.0
65 TraesCS6A01G196600 chr5A 90.157 447 31 11 5699 6141 195632100 195631663 2.520000e-158 569.0
66 TraesCS6A01G196600 chr5A 92.405 158 12 0 5459 5616 195632473 195632316 6.280000e-55 226.0
67 TraesCS6A01G196600 chr4D 94.027 586 33 1 1106 1691 48511510 48510927 0.000000e+00 887.0
68 TraesCS6A01G196600 chr4D 96.875 32 1 0 1661 1692 134631888 134631919 3.000000e-03 54.7
69 TraesCS6A01G196600 chr4B 93.345 586 39 0 1106 1691 349113537 349112952 0.000000e+00 867.0
70 TraesCS6A01G196600 chr4B 90.179 112 11 0 1 112 591295035 591294924 5.030000e-31 147.0
71 TraesCS6A01G196600 chr2B 92.893 591 40 2 1106 1696 651320226 651319638 0.000000e+00 857.0
72 TraesCS6A01G196600 chr2B 93.003 586 40 1 1106 1691 480014423 480015007 0.000000e+00 854.0
73 TraesCS6A01G196600 chr1A 87.423 652 69 8 2440 3080 218210598 218209949 0.000000e+00 737.0
74 TraesCS6A01G196600 chr1A 91.071 112 10 0 1 112 287274218 287274107 1.080000e-32 152.0
75 TraesCS6A01G196600 chr1A 95.652 46 0 2 5312 5355 7183402 7183447 8.650000e-09 73.1
76 TraesCS6A01G196600 chr7B 87.176 655 72 7 2437 3079 126171812 126172466 0.000000e+00 734.0
77 TraesCS6A01G196600 chr7B 87.191 648 74 5 2440 3079 240940646 240940000 0.000000e+00 728.0
78 TraesCS6A01G196600 chr7A 87.925 588 64 7 1106 1691 49484025 49484607 0.000000e+00 686.0
79 TraesCS6A01G196600 chr7A 85.000 80 6 4 5278 5351 474730880 474730801 6.690000e-10 76.8
80 TraesCS6A01G196600 chr7A 92.683 41 3 0 2398 2438 736112973 736113013 6.740000e-05 60.2
81 TraesCS6A01G196600 chr5B 89.225 529 44 10 5699 6221 184769877 184770398 0.000000e+00 649.0
82 TraesCS6A01G196600 chr5B 79.289 816 164 5 3902 4715 234903947 234903135 3.260000e-157 566.0
83 TraesCS6A01G196600 chr5B 88.095 210 16 4 5451 5651 184769499 184769708 2.240000e-59 241.0
84 TraesCS6A01G196600 chr5B 78.912 294 26 14 5217 5497 184767098 184767368 3.860000e-37 167.0
85 TraesCS6A01G196600 chr5B 89.091 110 12 0 1 110 306456280 306456171 3.020000e-28 137.0
86 TraesCS6A01G196600 chr5B 93.333 45 2 1 5156 5200 184766101 184766144 1.450000e-06 65.8
87 TraesCS6A01G196600 chr5B 95.000 40 1 1 5278 5316 706353403 706353442 1.870000e-05 62.1
88 TraesCS6A01G196600 chr3B 90.179 112 11 0 1 112 530991834 530991723 5.030000e-31 147.0
89 TraesCS6A01G196600 chr2D 95.918 49 0 2 5308 5354 220977119 220977071 1.860000e-10 78.7
90 TraesCS6A01G196600 chr2D 97.561 41 1 0 2398 2438 384745512 384745552 3.110000e-08 71.3
91 TraesCS6A01G196600 chr2D 95.122 41 2 0 2398 2438 141471279 141471319 1.450000e-06 65.8
92 TraesCS6A01G196600 chr1B 88.235 68 5 1 5274 5341 9079219 9079283 1.860000e-10 78.7
93 TraesCS6A01G196600 chr1B 97.778 45 0 1 5311 5354 532174358 532174402 6.690000e-10 76.8
94 TraesCS6A01G196600 chr1B 93.750 48 1 2 5278 5324 620494909 620494955 3.110000e-08 71.3


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 TraesCS6A01G196600 chr6A 289024746 289030967 6221 True 11490.000000 11490 100.000000 1 6222 1 chr6A.!!$R2 6221
1 TraesCS6A01G196600 chr6A 250721508 250722213 705 False 843.000000 843 88.293000 1695 2398 1 chr6A.!!$F2 703
2 TraesCS6A01G196600 chr6A 289028570 289029182 612 False 750.000000 750 88.943000 2474 3080 1 chr6A.!!$F3 606
3 TraesCS6A01G196600 chr6D 203746292 203751860 5568 True 2370.666667 4822 96.431667 1106 6222 3 chr6D.!!$R2 5116
4 TraesCS6A01G196600 chr6D 199247241 199248216 975 False 1299.000000 1299 90.705000 115 1090 1 chr6D.!!$F4 975
5 TraesCS6A01G196600 chr6D 203753891 203754475 584 False 824.000000 824 92.137000 2443 3026 1 chr6D.!!$F6 583
6 TraesCS6A01G196600 chr6D 60123019 60123722 703 False 780.000000 780 86.779000 1695 2398 1 chr6D.!!$F2 703
7 TraesCS6A01G196600 chr6D 200489225 200489880 655 False 736.000000 736 87.234000 2437 3080 1 chr6D.!!$F5 643
8 TraesCS6A01G196600 chr6B 316457824 316461766 3942 True 1967.333333 3653 95.015000 2440 6222 3 chr6B.!!$R1 3782
9 TraesCS6A01G196600 chr6B 480661892 480662475 583 False 876.000000 876 93.686000 1106 1691 1 chr6B.!!$F4 585
10 TraesCS6A01G196600 chr6B 95584719 95585307 588 False 865.000000 865 93.209000 1106 1693 1 chr6B.!!$F1 587
11 TraesCS6A01G196600 chr6B 316461082 316461732 650 False 800.000000 800 88.872000 1745 2398 1 chr6B.!!$F3 653
12 TraesCS6A01G196600 chr7D 177149982 177150972 990 True 1310.000000 1310 90.534000 115 1105 1 chr7D.!!$R1 990
13 TraesCS6A01G196600 chr7D 195829303 195830293 990 True 1282.000000 1282 90.030000 115 1105 1 chr7D.!!$R2 990
14 TraesCS6A01G196600 chrUn 311216660 311217649 989 False 1269.000000 1269 89.819000 115 1105 1 chrUn.!!$F1 990
15 TraesCS6A01G196600 chr3A 409578742 409579735 993 True 1267.000000 1267 89.759000 115 1105 1 chr3A.!!$R1 990
16 TraesCS6A01G196600 chr3A 747601385 747602037 652 False 808.000000 808 89.041000 1745 2398 1 chr3A.!!$F1 653
17 TraesCS6A01G196600 chr3D 31635061 31636052 991 True 1266.000000 1266 89.738000 115 1105 1 chr3D.!!$R2 990
18 TraesCS6A01G196600 chr3D 267427368 267428357 989 True 1264.000000 1264 89.759000 115 1105 1 chr3D.!!$R5 990
19 TraesCS6A01G196600 chr3D 159768513 159769201 688 False 878.000000 878 89.725000 1712 2398 1 chr3D.!!$F1 686
20 TraesCS6A01G196600 chr3D 159768581 159769235 654 True 754.000000 754 87.671000 2440 3086 1 chr3D.!!$R4 646
21 TraesCS6A01G196600 chr2A 395697183 395698174 991 False 1266.000000 1266 89.728000 115 1105 1 chr2A.!!$F2 990
22 TraesCS6A01G196600 chr2A 122003305 122003942 637 False 817.000000 817 89.752000 1733 2375 1 chr2A.!!$F1 642
23 TraesCS6A01G196600 chr5D 190260192 190261181 989 True 1264.000000 1264 89.728000 115 1105 1 chr5D.!!$R1 990
24 TraesCS6A01G196600 chr5D 470548721 470549415 694 False 758.000000 758 86.402000 1697 2398 1 chr5D.!!$F2 701
25 TraesCS6A01G196600 chr5D 218260180 218260976 796 True 592.000000 592 80.075000 3902 4699 1 chr5D.!!$R2 797
26 TraesCS6A01G196600 chr5D 173753148 173756413 3265 True 285.666667 492 89.283667 5156 6222 3 chr5D.!!$R3 1066
27 TraesCS6A01G196600 chr1D 453228252 453228837 585 True 961.000000 961 96.246000 1106 1691 1 chr1D.!!$R5 585
28 TraesCS6A01G196600 chr1D 296280049 296280751 702 True 833.000000 833 88.136000 1695 2397 1 chr1D.!!$R3 702
29 TraesCS6A01G196600 chr1D 296280011 296280661 650 False 725.000000 725 87.003000 2437 3080 1 chr1D.!!$F1 643
30 TraesCS6A01G196600 chr5A 622824423 622825008 585 True 917.000000 917 94.881000 1106 1691 1 chr5A.!!$R2 585
31 TraesCS6A01G196600 chr5A 291271170 291271966 796 True 586.000000 586 79.975000 3902 4699 1 chr5A.!!$R1 797
32 TraesCS6A01G196600 chr5A 195631663 195632473 810 True 397.500000 569 91.281000 5459 6141 2 chr5A.!!$R3 682
33 TraesCS6A01G196600 chr4D 48510927 48511510 583 True 887.000000 887 94.027000 1106 1691 1 chr4D.!!$R1 585
34 TraesCS6A01G196600 chr4B 349112952 349113537 585 True 867.000000 867 93.345000 1106 1691 1 chr4B.!!$R1 585
35 TraesCS6A01G196600 chr2B 651319638 651320226 588 True 857.000000 857 92.893000 1106 1696 1 chr2B.!!$R1 590
36 TraesCS6A01G196600 chr2B 480014423 480015007 584 False 854.000000 854 93.003000 1106 1691 1 chr2B.!!$F1 585
37 TraesCS6A01G196600 chr1A 218209949 218210598 649 True 737.000000 737 87.423000 2440 3080 1 chr1A.!!$R1 640
38 TraesCS6A01G196600 chr7B 126171812 126172466 654 False 734.000000 734 87.176000 2437 3079 1 chr7B.!!$F1 642
39 TraesCS6A01G196600 chr7B 240940000 240940646 646 True 728.000000 728 87.191000 2440 3079 1 chr7B.!!$R1 639
40 TraesCS6A01G196600 chr7A 49484025 49484607 582 False 686.000000 686 87.925000 1106 1691 1 chr7A.!!$F1 585
41 TraesCS6A01G196600 chr5B 234903135 234903947 812 True 566.000000 566 79.289000 3902 4715 1 chr5B.!!$R1 813
42 TraesCS6A01G196600 chr5B 184766101 184770398 4297 False 280.700000 649 87.391250 5156 6221 4 chr5B.!!$F2 1065

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
41 42 0.036306 ACGGGGTCACAAGCTTAAGG 59.964 55.0 0.00 0.00 0.00 2.69 F
42 43 0.036306 CGGGGTCACAAGCTTAAGGT 59.964 55.0 0.00 0.12 0.00 3.50 F
1438 1445 0.475906 AGATGGTAGGATGCCTTGGC 59.524 55.0 4.43 4.43 43.60 4.52 F
1841 1852 0.678366 AACCATATTTGCCGGCGTGA 60.678 50.0 23.90 10.59 0.00 4.35 F
2415 2596 0.034089 CTGAGGACAATCCCCAACCC 60.034 60.0 0.00 0.00 37.19 4.11 F
3757 4844 0.035056 CCTCCAGCGTCCTTTCCAAT 60.035 55.0 0.00 0.00 0.00 3.16 F
4087 5174 0.618458 CTGGTTACTGGGCCAAGCTA 59.382 55.0 7.20 0.00 33.93 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 1785 0.320374 ATCTCAAACAGGGCGAACGA 59.680 50.000 0.00 0.0 0.00 3.85 R
1778 1789 1.533625 CCAAATCTCAAACAGGGCGA 58.466 50.000 0.00 0.0 0.00 5.54 R
2398 2579 0.034089 CAGGGTTGGGGATTGTCCTC 60.034 60.000 0.00 0.0 37.60 3.71 R
3020 3883 0.041312 CATATTTACCGCGTGGCTGC 60.041 55.000 16.69 0.0 39.70 5.25 R
4033 5120 1.431440 GTGCGCAAGGTTGTGAACA 59.569 52.632 14.00 0.0 44.73 3.18 R
4790 5877 1.815003 CTTGGCCTTCACATCAAGGTC 59.185 52.381 3.32 0.0 46.89 3.85 R
6038 10644 0.106918 AACCAAGTCCGCAACCAAGA 60.107 50.000 0.00 0.0 0.00 3.02 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
24 25 6.548441 TGTCTTTGATTTACCAAACCTACG 57.452 37.500 0.00 0.00 33.07 3.51
25 26 5.470777 TGTCTTTGATTTACCAAACCTACGG 59.529 40.000 0.00 0.00 33.07 4.02
26 27 5.005094 TCTTTGATTTACCAAACCTACGGG 58.995 41.667 0.00 0.00 33.07 5.28
27 28 3.353370 TGATTTACCAAACCTACGGGG 57.647 47.619 0.00 0.00 41.89 5.73
36 37 3.388841 CCTACGGGGTCACAAGCT 58.611 61.111 0.00 0.00 0.00 3.74
37 38 1.677552 CCTACGGGGTCACAAGCTT 59.322 57.895 0.00 0.00 0.00 3.74
38 39 0.899720 CCTACGGGGTCACAAGCTTA 59.100 55.000 0.00 0.00 0.00 3.09
39 40 1.276989 CCTACGGGGTCACAAGCTTAA 59.723 52.381 0.00 0.00 0.00 1.85
40 41 2.618053 CTACGGGGTCACAAGCTTAAG 58.382 52.381 0.00 0.00 0.00 1.85
41 42 0.036306 ACGGGGTCACAAGCTTAAGG 59.964 55.000 0.00 0.00 0.00 2.69
42 43 0.036306 CGGGGTCACAAGCTTAAGGT 59.964 55.000 0.00 0.12 0.00 3.50
43 44 1.276989 CGGGGTCACAAGCTTAAGGTA 59.723 52.381 7.76 0.00 0.00 3.08
44 45 2.289819 CGGGGTCACAAGCTTAAGGTAA 60.290 50.000 7.76 0.00 0.00 2.85
45 46 3.621461 CGGGGTCACAAGCTTAAGGTAAT 60.621 47.826 7.76 0.00 0.00 1.89
46 47 3.945921 GGGGTCACAAGCTTAAGGTAATC 59.054 47.826 7.76 0.00 0.00 1.75
47 48 4.566907 GGGGTCACAAGCTTAAGGTAATCA 60.567 45.833 7.76 0.00 0.00 2.57
48 49 5.193679 GGGTCACAAGCTTAAGGTAATCAT 58.806 41.667 7.76 0.00 0.00 2.45
49 50 5.066505 GGGTCACAAGCTTAAGGTAATCATG 59.933 44.000 7.76 4.73 0.00 3.07
50 51 5.880332 GGTCACAAGCTTAAGGTAATCATGA 59.120 40.000 7.76 0.00 0.00 3.07
51 52 6.543831 GGTCACAAGCTTAAGGTAATCATGAT 59.456 38.462 7.76 1.18 0.00 2.45
52 53 7.254932 GGTCACAAGCTTAAGGTAATCATGATC 60.255 40.741 9.06 4.67 0.00 2.92
53 54 7.497249 GTCACAAGCTTAAGGTAATCATGATCT 59.503 37.037 9.06 0.00 0.00 2.75
54 55 7.496920 TCACAAGCTTAAGGTAATCATGATCTG 59.503 37.037 9.06 1.08 0.00 2.90
55 56 7.496920 CACAAGCTTAAGGTAATCATGATCTGA 59.503 37.037 9.06 0.00 38.53 3.27
56 57 8.216423 ACAAGCTTAAGGTAATCATGATCTGAT 58.784 33.333 9.06 0.00 46.87 2.90
57 58 8.504815 CAAGCTTAAGGTAATCATGATCTGATG 58.495 37.037 9.06 0.00 44.03 3.07
58 59 7.971201 AGCTTAAGGTAATCATGATCTGATGA 58.029 34.615 9.06 3.83 44.03 2.92
59 60 8.095792 AGCTTAAGGTAATCATGATCTGATGAG 58.904 37.037 9.06 3.94 44.03 2.90
60 61 7.877097 GCTTAAGGTAATCATGATCTGATGAGT 59.123 37.037 9.06 5.20 44.03 3.41
61 62 9.205719 CTTAAGGTAATCATGATCTGATGAGTG 57.794 37.037 9.06 0.00 44.03 3.51
62 63 6.744175 AGGTAATCATGATCTGATGAGTGT 57.256 37.500 9.06 0.00 44.03 3.55
63 64 7.134362 AGGTAATCATGATCTGATGAGTGTT 57.866 36.000 9.06 0.00 44.03 3.32
64 65 8.255111 AGGTAATCATGATCTGATGAGTGTTA 57.745 34.615 9.06 0.00 44.03 2.41
65 66 8.708378 AGGTAATCATGATCTGATGAGTGTTAA 58.292 33.333 9.06 0.00 44.03 2.01
66 67 9.499479 GGTAATCATGATCTGATGAGTGTTAAT 57.501 33.333 9.06 0.00 44.03 1.40
69 70 9.722184 AATCATGATCTGATGAGTGTTAATAGG 57.278 33.333 9.06 0.00 44.03 2.57
70 71 8.482852 TCATGATCTGATGAGTGTTAATAGGA 57.517 34.615 0.00 0.00 0.00 2.94
71 72 9.097946 TCATGATCTGATGAGTGTTAATAGGAT 57.902 33.333 0.00 0.00 0.00 3.24
77 78 9.593565 TCTGATGAGTGTTAATAGGATATGAGT 57.406 33.333 0.00 0.00 0.00 3.41
97 98 6.919721 TGAGTATCAAGGTTTTATTTGTGGC 58.080 36.000 0.00 0.00 45.97 5.01
98 99 6.491745 TGAGTATCAAGGTTTTATTTGTGGCA 59.508 34.615 0.00 0.00 45.97 4.92
99 100 7.178274 TGAGTATCAAGGTTTTATTTGTGGCAT 59.822 33.333 0.00 0.00 45.97 4.40
100 101 7.906327 AGTATCAAGGTTTTATTTGTGGCATT 58.094 30.769 0.00 0.00 0.00 3.56
101 102 8.374743 AGTATCAAGGTTTTATTTGTGGCATTT 58.625 29.630 0.00 0.00 0.00 2.32
102 103 8.998377 GTATCAAGGTTTTATTTGTGGCATTTT 58.002 29.630 0.00 0.00 0.00 1.82
103 104 7.872113 TCAAGGTTTTATTTGTGGCATTTTT 57.128 28.000 0.00 0.00 0.00 1.94
150 151 3.058085 TGCTAACGTGACACTACGATCAA 60.058 43.478 3.68 0.00 46.46 2.57
242 244 4.320935 GGTGCAAAACATTTACGATGGAGT 60.321 41.667 0.00 0.00 0.00 3.85
347 350 2.978010 AACAGAAACGGGCAGCCG 60.978 61.111 5.00 3.34 39.31 5.52
353 356 1.429148 GAAACGGGCAGCCGTATCAG 61.429 60.000 5.00 0.00 46.11 2.90
364 367 1.070821 CCGTATCAGTGTGTGTGCAG 58.929 55.000 0.00 0.00 0.00 4.41
367 370 2.661675 CGTATCAGTGTGTGTGCAGTAC 59.338 50.000 0.00 0.00 0.00 2.73
390 393 5.705441 ACACAACATACAATTCACTCCGATT 59.295 36.000 0.00 0.00 0.00 3.34
407 410 7.491372 CACTCCGATTAACTGTTTGCTATTAGA 59.509 37.037 0.00 0.00 0.00 2.10
538 541 7.564793 ACTTAATAAGAGGTGTGTGATATGCA 58.435 34.615 7.06 0.00 0.00 3.96
586 589 2.927553 GCGATGAGCCAAAAGAACAT 57.072 45.000 0.00 0.00 40.81 2.71
694 697 6.914757 ACAGACGGTTACTATAGTTAATTCGC 59.085 38.462 11.40 5.72 0.00 4.70
740 745 9.869757 AAAACTATGAAAAGTGCAAACTAGTTT 57.130 25.926 15.22 15.22 38.89 2.66
750 755 2.289547 GCAAACTAGTTTCTTGCGGTGA 59.710 45.455 18.00 0.00 36.44 4.02
908 913 1.500396 CACTTAGTTTTCCCGCGCC 59.500 57.895 0.00 0.00 0.00 6.53
967 972 0.698818 AAATCCACGCCTCTTCCCTT 59.301 50.000 0.00 0.00 0.00 3.95
977 982 2.170817 GCCTCTTCCCTTATCGGTTTCT 59.829 50.000 0.00 0.00 0.00 2.52
1039 1044 3.551796 GCATCATCGCGACACTCTA 57.448 52.632 12.93 0.00 0.00 2.43
1090 1095 3.091633 AGTTATTCCAAGCATGCCAGT 57.908 42.857 15.66 0.00 0.00 4.00
1097 1102 0.806868 CAAGCATGCCAGTCAACGAT 59.193 50.000 15.66 0.00 0.00 3.73
1099 1104 1.086067 AGCATGCCAGTCAACGATCG 61.086 55.000 15.66 14.88 0.00 3.69
1116 1121 5.168569 ACGATCGAAGCTAAAAACATGAGA 58.831 37.500 24.34 0.00 0.00 3.27
1438 1445 0.475906 AGATGGTAGGATGCCTTGGC 59.524 55.000 4.43 4.43 43.60 4.52
1709 1719 6.534634 ACTAGTGTTTAAGAGCAACTCCAAT 58.465 36.000 0.00 0.00 0.00 3.16
1710 1720 7.676947 ACTAGTGTTTAAGAGCAACTCCAATA 58.323 34.615 0.00 0.00 0.00 1.90
1724 1734 0.956410 CCAATACGCCGACCCAAACA 60.956 55.000 0.00 0.00 0.00 2.83
1751 1762 5.391312 ACACTTTTGTCTGCTTTTTGTCT 57.609 34.783 0.00 0.00 0.00 3.41
1760 1771 3.513515 TCTGCTTTTTGTCTGTTTGGGTT 59.486 39.130 0.00 0.00 0.00 4.11
1761 1772 4.707448 TCTGCTTTTTGTCTGTTTGGGTTA 59.293 37.500 0.00 0.00 0.00 2.85
1841 1852 0.678366 AACCATATTTGCCGGCGTGA 60.678 50.000 23.90 10.59 0.00 4.35
2024 2043 8.567285 AATAGTCTAACATAGTTTTGCAAGCT 57.433 30.769 0.00 5.05 0.00 3.74
2346 2481 3.057315 CCTCATCGAGGTTGCAAAACATT 60.057 43.478 0.00 0.00 44.25 2.71
2382 2563 3.280295 CGTCCTTCCTAGCACTCTCTTA 58.720 50.000 0.00 0.00 0.00 2.10
2391 2572 2.896039 AGCACTCTCTTACTCTTGGGT 58.104 47.619 0.00 0.00 0.00 4.51
2398 2579 5.186797 ACTCTCTTACTCTTGGGTGAATCTG 59.813 44.000 0.00 0.00 0.00 2.90
2399 2580 5.333581 TCTCTTACTCTTGGGTGAATCTGA 58.666 41.667 0.00 0.00 0.00 3.27
2400 2581 5.420421 TCTCTTACTCTTGGGTGAATCTGAG 59.580 44.000 0.00 0.00 0.00 3.35
2401 2582 4.467795 TCTTACTCTTGGGTGAATCTGAGG 59.532 45.833 0.00 0.00 0.00 3.86
2402 2583 2.907892 ACTCTTGGGTGAATCTGAGGA 58.092 47.619 0.00 0.00 0.00 3.71
2405 2586 2.978978 TCTTGGGTGAATCTGAGGACAA 59.021 45.455 0.00 0.00 0.00 3.18
2406 2587 3.588842 TCTTGGGTGAATCTGAGGACAAT 59.411 43.478 0.00 0.00 0.00 2.71
2409 2590 2.422093 GGGTGAATCTGAGGACAATCCC 60.422 54.545 0.00 0.00 37.19 3.85
2410 2591 2.422093 GGTGAATCTGAGGACAATCCCC 60.422 54.545 0.00 0.00 37.19 4.81
2411 2592 2.239654 GTGAATCTGAGGACAATCCCCA 59.760 50.000 0.00 0.00 37.19 4.96
2413 2594 3.282885 GAATCTGAGGACAATCCCCAAC 58.717 50.000 0.00 0.00 37.19 3.77
2414 2595 0.991920 TCTGAGGACAATCCCCAACC 59.008 55.000 0.00 0.00 37.19 3.77
2415 2596 0.034089 CTGAGGACAATCCCCAACCC 60.034 60.000 0.00 0.00 37.19 4.11
2418 2599 0.776080 AGGACAATCCCCAACCCTGT 60.776 55.000 0.00 0.00 37.19 4.00
2425 2606 0.771127 TCCCCAACCCTGTTGAAGAG 59.229 55.000 8.47 0.00 0.00 2.85
2426 2607 0.771127 CCCCAACCCTGTTGAAGAGA 59.229 55.000 8.47 0.00 0.00 3.10
2427 2608 1.144913 CCCCAACCCTGTTGAAGAGAA 59.855 52.381 8.47 0.00 0.00 2.87
2429 2610 2.106511 CCCAACCCTGTTGAAGAGAAGA 59.893 50.000 8.47 0.00 0.00 2.87
2430 2611 3.406764 CCAACCCTGTTGAAGAGAAGAG 58.593 50.000 8.47 0.00 0.00 2.85
2431 2612 3.406764 CAACCCTGTTGAAGAGAAGAGG 58.593 50.000 0.70 0.00 36.37 3.69
2433 2614 3.318313 ACCCTGTTGAAGAGAAGAGGAA 58.682 45.455 0.00 0.00 38.42 3.36
2434 2615 3.716872 ACCCTGTTGAAGAGAAGAGGAAA 59.283 43.478 0.00 0.00 38.42 3.13
2435 2616 4.166144 ACCCTGTTGAAGAGAAGAGGAAAA 59.834 41.667 0.00 0.00 38.42 2.29
2437 2618 5.455326 CCCTGTTGAAGAGAAGAGGAAAAGA 60.455 44.000 0.00 0.00 38.42 2.52
2438 2619 5.700373 CCTGTTGAAGAGAAGAGGAAAAGAG 59.300 44.000 0.00 0.00 38.42 2.85
2546 2765 2.487762 GTGTTTTGCAATCTCGATGGGA 59.512 45.455 0.00 0.00 0.00 4.37
2564 2783 1.407979 GGACATCGTTCGGTATCCTGT 59.592 52.381 0.00 0.00 0.00 4.00
2619 2838 4.872124 GTGATGACTGCTTGTGTGATCATA 59.128 41.667 0.00 0.00 39.43 2.15
2685 2905 5.118729 TCAAGGGTTTCAGTTTCAAGGTA 57.881 39.130 0.00 0.00 0.00 3.08
2714 2934 1.077930 GCCTGAGCATGAAGGAGCA 60.078 57.895 12.35 0.00 39.53 4.26
2736 2956 5.562113 GCAGCAACGTTTAAATAGTTCACCT 60.562 40.000 0.00 4.58 0.00 4.00
2822 3047 2.291209 TGTGGGCTCATGTTGACAAT 57.709 45.000 0.00 0.00 0.00 2.71
2831 3056 6.712095 GGGCTCATGTTGACAATCAATAGATA 59.288 38.462 0.00 0.00 38.79 1.98
3020 3883 0.894835 ATTTGCTACAAAAGGGCGGG 59.105 50.000 0.00 0.00 0.00 6.13
3040 3908 1.577468 CAGCCACGCGGTAAATATGA 58.423 50.000 12.47 0.00 33.28 2.15
3062 3930 2.517598 GACGCATTCGACACACTGT 58.482 52.632 0.00 0.00 39.41 3.55
3063 3931 0.859232 GACGCATTCGACACACTGTT 59.141 50.000 0.00 0.00 39.41 3.16
3080 3948 5.531287 ACACTGTTGACCTAAATCTCAAACC 59.469 40.000 0.00 0.00 0.00 3.27
3082 3950 4.963373 TGTTGACCTAAATCTCAAACCGA 58.037 39.130 0.00 0.00 0.00 4.69
3086 3954 1.327764 CCTAAATCTCAAACCGAGCGC 59.672 52.381 0.00 0.00 41.98 5.92
3102 3984 2.677003 CGCGCGGACAAAACCAGAT 61.677 57.895 24.84 0.00 0.00 2.90
3110 3992 3.058501 CGGACAAAACCAGATAAAAGCGT 60.059 43.478 0.00 0.00 0.00 5.07
3111 3993 4.152759 CGGACAAAACCAGATAAAAGCGTA 59.847 41.667 0.00 0.00 0.00 4.42
3114 3996 6.293790 GGACAAAACCAGATAAAAGCGTAGTT 60.294 38.462 0.00 0.00 0.00 2.24
3128 4172 2.331194 CGTAGTTCGTTTTGGATCGGT 58.669 47.619 0.00 0.00 34.52 4.69
3131 4175 0.452122 GTTCGTTTTGGATCGGTGCG 60.452 55.000 0.00 0.00 0.00 5.34
3135 4179 0.589223 GTTTTGGATCGGTGCGTTGA 59.411 50.000 0.00 0.00 0.00 3.18
3145 4189 0.235926 GGTGCGTTGAAGTTGCTCTC 59.764 55.000 0.00 0.00 0.00 3.20
3147 4191 1.330521 GTGCGTTGAAGTTGCTCTCAA 59.669 47.619 0.00 0.00 0.00 3.02
3148 4192 2.031682 GTGCGTTGAAGTTGCTCTCAAT 60.032 45.455 0.00 0.00 34.29 2.57
3301 4388 4.467062 CGCTCTCGCTCACGCTCA 62.467 66.667 0.00 0.00 39.84 4.26
3303 4390 2.101965 CTCTCGCTCACGCTCAGG 59.898 66.667 0.00 0.00 39.84 3.86
3304 4391 4.121669 TCTCGCTCACGCTCAGGC 62.122 66.667 0.00 0.00 39.84 4.85
3305 4392 4.127040 CTCGCTCACGCTCAGGCT 62.127 66.667 0.00 0.00 39.84 4.58
3306 4393 4.426112 TCGCTCACGCTCAGGCTG 62.426 66.667 8.58 8.58 39.84 4.85
3307 4394 4.426112 CGCTCACGCTCAGGCTGA 62.426 66.667 17.68 17.68 36.09 4.26
3309 4396 2.505777 CTCACGCTCAGGCTGACG 60.506 66.667 26.50 26.50 36.09 4.35
3311 4398 4.731612 CACGCTCAGGCTGACGCT 62.732 66.667 27.42 17.35 36.09 5.07
3312 4399 4.427661 ACGCTCAGGCTGACGCTC 62.428 66.667 27.42 12.78 36.09 5.03
3313 4400 4.127040 CGCTCAGGCTGACGCTCT 62.127 66.667 25.57 0.00 36.09 4.09
3314 4401 2.508887 GCTCAGGCTGACGCTCTG 60.509 66.667 23.09 11.77 36.43 3.35
3315 4402 2.508887 CTCAGGCTGACGCTCTGC 60.509 66.667 14.43 7.86 40.10 4.26
3316 4403 3.292500 CTCAGGCTGACGCTCTGCA 62.293 63.158 14.43 0.00 42.21 4.41
3317 4404 2.357881 CAGGCTGACGCTCTGCAA 60.358 61.111 9.42 0.00 42.21 4.08
3318 4405 2.358003 AGGCTGACGCTCTGCAAC 60.358 61.111 14.94 3.57 42.21 4.17
3319 4406 3.426568 GGCTGACGCTCTGCAACC 61.427 66.667 14.94 0.00 42.21 3.77
3320 4407 3.426568 GCTGACGCTCTGCAACCC 61.427 66.667 10.40 0.00 40.47 4.11
3321 4408 2.031012 CTGACGCTCTGCAACCCA 59.969 61.111 0.00 0.00 0.00 4.51
3327 4414 2.358737 CTCTGCAACCCACCGTCC 60.359 66.667 0.00 0.00 0.00 4.79
3757 4844 0.035056 CCTCCAGCGTCCTTTCCAAT 60.035 55.000 0.00 0.00 0.00 3.16
4033 5120 1.799181 CGCTTCCACGACATCGAGATT 60.799 52.381 8.54 0.00 43.02 2.40
4087 5174 0.618458 CTGGTTACTGGGCCAAGCTA 59.382 55.000 7.20 0.00 33.93 3.32
4790 5877 3.821421 AGCCTATTAACGACAAGGAGG 57.179 47.619 0.00 0.00 0.00 4.30
5082 6180 3.009805 GGACAAGTACCCCTAATGTGGTT 59.990 47.826 0.00 0.00 36.04 3.67
5116 6214 9.639601 CTTGTAGTGATTTGTGTTCTATGTAGA 57.360 33.333 0.00 0.00 0.00 2.59
5285 7328 3.502595 GCTCCAAACTTTGTTACTCCCTC 59.497 47.826 0.88 0.00 0.00 4.30
5286 7329 4.747009 GCTCCAAACTTTGTTACTCCCTCT 60.747 45.833 0.88 0.00 0.00 3.69
5287 7330 5.377478 CTCCAAACTTTGTTACTCCCTCTT 58.623 41.667 0.88 0.00 0.00 2.85
5288 7331 6.503560 TCCAAACTTTGTTACTCCCTCTTA 57.496 37.500 0.88 0.00 0.00 2.10
5289 7332 7.086685 TCCAAACTTTGTTACTCCCTCTTAT 57.913 36.000 0.88 0.00 0.00 1.73
5290 7333 7.166167 TCCAAACTTTGTTACTCCCTCTTATC 58.834 38.462 0.88 0.00 0.00 1.75
5291 7334 6.374613 CCAAACTTTGTTACTCCCTCTTATCC 59.625 42.308 0.88 0.00 0.00 2.59
5292 7335 6.697641 AACTTTGTTACTCCCTCTTATCCA 57.302 37.500 0.00 0.00 0.00 3.41
5293 7336 6.893020 ACTTTGTTACTCCCTCTTATCCAT 57.107 37.500 0.00 0.00 0.00 3.41
5294 7337 7.989947 ACTTTGTTACTCCCTCTTATCCATA 57.010 36.000 0.00 0.00 0.00 2.74
5295 7338 8.568617 ACTTTGTTACTCCCTCTTATCCATAT 57.431 34.615 0.00 0.00 0.00 1.78
5296 7339 9.004231 ACTTTGTTACTCCCTCTTATCCATATT 57.996 33.333 0.00 0.00 0.00 1.28
5304 7347 8.314751 ACTCCCTCTTATCCATATTAATTGTCG 58.685 37.037 0.00 0.00 0.00 4.35
5305 7348 8.202461 TCCCTCTTATCCATATTAATTGTCGT 57.798 34.615 0.00 0.00 0.00 4.34
5306 7349 8.656806 TCCCTCTTATCCATATTAATTGTCGTT 58.343 33.333 0.00 0.00 0.00 3.85
5307 7350 8.721478 CCCTCTTATCCATATTAATTGTCGTTG 58.279 37.037 0.00 0.00 0.00 4.10
5308 7351 9.489084 CCTCTTATCCATATTAATTGTCGTTGA 57.511 33.333 0.00 0.00 0.00 3.18
5545 9923 2.908688 AAACTTGGCATGGGTGTTTC 57.091 45.000 5.31 0.00 0.00 2.78
5798 10344 7.610305 ACAGAGGTGTTTCGTTAAATAATCCAT 59.390 33.333 0.00 0.00 30.30 3.41
6038 10644 8.510243 TCTAAACATCTTGCATTGTACATGAT 57.490 30.769 0.00 0.00 33.55 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.141100 CGTAGGTTTGGTAAATCAAAGACAT 57.859 36.000 0.00 0.00 37.31 3.06
1 2 6.548441 CGTAGGTTTGGTAAATCAAAGACA 57.452 37.500 0.00 0.00 37.31 3.41
20 21 2.618053 CTTAAGCTTGTGACCCCGTAG 58.382 52.381 9.86 0.00 0.00 3.51
21 22 1.276989 CCTTAAGCTTGTGACCCCGTA 59.723 52.381 9.86 0.00 0.00 4.02
22 23 0.036306 CCTTAAGCTTGTGACCCCGT 59.964 55.000 9.86 0.00 0.00 5.28
23 24 0.036306 ACCTTAAGCTTGTGACCCCG 59.964 55.000 9.86 0.00 0.00 5.73
24 25 3.428413 TTACCTTAAGCTTGTGACCCC 57.572 47.619 9.86 0.00 0.00 4.95
25 26 4.585879 TGATTACCTTAAGCTTGTGACCC 58.414 43.478 9.86 0.00 0.00 4.46
26 27 5.880332 TCATGATTACCTTAAGCTTGTGACC 59.120 40.000 9.86 0.00 32.92 4.02
27 28 6.985188 TCATGATTACCTTAAGCTTGTGAC 57.015 37.500 9.86 0.00 32.92 3.67
28 29 7.496920 CAGATCATGATTACCTTAAGCTTGTGA 59.503 37.037 10.14 0.00 32.92 3.58
29 30 7.496920 TCAGATCATGATTACCTTAAGCTTGTG 59.503 37.037 10.14 1.13 32.92 3.33
30 31 7.568349 TCAGATCATGATTACCTTAAGCTTGT 58.432 34.615 10.14 0.59 32.92 3.16
31 32 8.504815 CATCAGATCATGATTACCTTAAGCTTG 58.495 37.037 10.14 0.00 46.97 4.01
32 33 8.435187 TCATCAGATCATGATTACCTTAAGCTT 58.565 33.333 10.14 3.48 46.97 3.74
33 34 7.971201 TCATCAGATCATGATTACCTTAAGCT 58.029 34.615 10.14 0.00 46.97 3.74
34 35 7.877097 ACTCATCAGATCATGATTACCTTAAGC 59.123 37.037 10.14 0.00 46.97 3.09
35 36 9.205719 CACTCATCAGATCATGATTACCTTAAG 57.794 37.037 10.14 5.63 46.97 1.85
36 37 8.708378 ACACTCATCAGATCATGATTACCTTAA 58.292 33.333 10.14 0.00 46.97 1.85
37 38 8.255111 ACACTCATCAGATCATGATTACCTTA 57.745 34.615 10.14 0.00 46.97 2.69
38 39 7.134362 ACACTCATCAGATCATGATTACCTT 57.866 36.000 10.14 0.00 46.97 3.50
39 40 6.744175 ACACTCATCAGATCATGATTACCT 57.256 37.500 10.14 0.00 46.97 3.08
40 41 8.893219 TTAACACTCATCAGATCATGATTACC 57.107 34.615 10.14 0.00 46.97 2.85
43 44 9.722184 CCTATTAACACTCATCAGATCATGATT 57.278 33.333 10.14 0.00 46.97 2.57
45 46 8.482852 TCCTATTAACACTCATCAGATCATGA 57.517 34.615 0.00 0.00 43.70 3.07
51 52 9.593565 ACTCATATCCTATTAACACTCATCAGA 57.406 33.333 0.00 0.00 0.00 3.27
71 72 8.682710 GCCACAAATAAAACCTTGATACTCATA 58.317 33.333 0.00 0.00 0.00 2.15
72 73 7.178274 TGCCACAAATAAAACCTTGATACTCAT 59.822 33.333 0.00 0.00 0.00 2.90
73 74 6.491745 TGCCACAAATAAAACCTTGATACTCA 59.508 34.615 0.00 0.00 0.00 3.41
74 75 6.919721 TGCCACAAATAAAACCTTGATACTC 58.080 36.000 0.00 0.00 0.00 2.59
75 76 6.909550 TGCCACAAATAAAACCTTGATACT 57.090 33.333 0.00 0.00 0.00 2.12
76 77 8.546597 AAATGCCACAAATAAAACCTTGATAC 57.453 30.769 0.00 0.00 0.00 2.24
77 78 9.566432 AAAAATGCCACAAATAAAACCTTGATA 57.434 25.926 0.00 0.00 0.00 2.15
78 79 8.462589 AAAAATGCCACAAATAAAACCTTGAT 57.537 26.923 0.00 0.00 0.00 2.57
79 80 7.872113 AAAAATGCCACAAATAAAACCTTGA 57.128 28.000 0.00 0.00 0.00 3.02
100 101 7.094508 TCCTGCAATAGCGATTAATGAAAAA 57.905 32.000 0.00 0.00 46.23 1.94
101 102 6.691754 TCCTGCAATAGCGATTAATGAAAA 57.308 33.333 0.00 0.00 46.23 2.29
102 103 6.671190 CATCCTGCAATAGCGATTAATGAAA 58.329 36.000 0.00 0.00 46.23 2.69
103 104 5.335113 GCATCCTGCAATAGCGATTAATGAA 60.335 40.000 0.00 0.00 44.26 2.57
104 105 4.154737 GCATCCTGCAATAGCGATTAATGA 59.845 41.667 0.00 0.00 44.26 2.57
105 106 4.409570 GCATCCTGCAATAGCGATTAATG 58.590 43.478 0.00 0.00 44.26 1.90
106 107 4.691860 GCATCCTGCAATAGCGATTAAT 57.308 40.909 0.00 0.00 44.26 1.40
150 151 4.082245 CACACAGTTTTGTCAAAGGGTCTT 60.082 41.667 0.00 0.00 34.62 3.01
220 222 4.794169 ACTCCATCGTAAATGTTTTGCAC 58.206 39.130 0.00 0.00 0.00 4.57
233 235 4.495422 GTGTTTGATGTCTACTCCATCGT 58.505 43.478 0.00 0.00 41.28 3.73
242 244 4.594123 TCTGAACCGTGTTTGATGTCTA 57.406 40.909 0.00 0.00 0.00 2.59
347 350 3.649073 TGTACTGCACACACACTGATAC 58.351 45.455 0.00 0.00 30.04 2.24
364 367 5.636121 TCGGAGTGAATTGTATGTTGTGTAC 59.364 40.000 0.00 0.00 0.00 2.90
367 370 5.801350 ATCGGAGTGAATTGTATGTTGTG 57.199 39.130 0.00 0.00 0.00 3.33
378 381 5.003804 AGCAAACAGTTAATCGGAGTGAAT 58.996 37.500 0.00 0.00 0.00 2.57
382 385 7.553334 TCTAATAGCAAACAGTTAATCGGAGT 58.447 34.615 0.00 0.00 0.00 3.85
390 393 8.450964 GTTGCATTCTCTAATAGCAAACAGTTA 58.549 33.333 0.00 0.00 39.04 2.24
407 410 6.699575 AGTTAACTGTTTCTGTTGCATTCT 57.300 33.333 7.48 0.00 0.00 2.40
524 527 3.205338 TGTATGCTGCATATCACACACC 58.795 45.455 23.74 10.02 0.00 4.16
538 541 8.151141 CAGTTCATCTATGTGAATTGTATGCT 57.849 34.615 4.57 0.00 39.54 3.79
586 589 7.042590 ACACATCTTGTTTACACGAATCGTTTA 60.043 33.333 5.20 0.52 33.81 2.01
635 638 4.064388 TCATCGCAAACAGTTCATCTGAA 58.936 39.130 1.79 0.00 46.27 3.02
694 697 6.795114 AGTTTTTGTACAAATAGAATCGCACG 59.205 34.615 21.17 0.00 0.00 5.34
705 708 9.593134 TGCACTTTTCATAGTTTTTGTACAAAT 57.407 25.926 21.17 9.73 0.00 2.32
727 732 2.032924 ACCGCAAGAAACTAGTTTGCAC 59.967 45.455 25.17 11.11 45.58 4.57
740 745 2.502142 TACTCCTAGTCACCGCAAGA 57.498 50.000 0.00 0.00 43.02 3.02
750 755 2.034104 TCGTGTGCGATACTCCTAGT 57.966 50.000 0.00 0.00 42.81 2.57
945 950 2.509964 AGGGAAGAGGCGTGGATTTTAT 59.490 45.455 0.00 0.00 0.00 1.40
1039 1044 2.324541 GGGTGAGGACTAGATCTGCAT 58.675 52.381 5.18 0.00 0.00 3.96
1090 1095 5.407084 TCATGTTTTTAGCTTCGATCGTTGA 59.593 36.000 15.94 1.79 0.00 3.18
1097 1102 9.817809 AGTATTATCTCATGTTTTTAGCTTCGA 57.182 29.630 0.00 0.00 0.00 3.71
1179 1186 4.570930 AGGAAGCAACTAGAAAGTAGTGC 58.429 43.478 0.00 0.00 38.99 4.40
1438 1445 3.270027 TCAGGCATTACCGAATCAACAG 58.730 45.455 0.00 0.00 46.52 3.16
1505 1512 4.703645 ATACATCACCGACATCTATCCG 57.296 45.455 0.00 0.00 0.00 4.18
1611 1620 9.612066 ACTTTAAAGCTTGAATTTTCAATCCAA 57.388 25.926 15.24 0.00 45.26 3.53
1709 1719 1.005867 GTCTGTTTGGGTCGGCGTA 60.006 57.895 6.85 0.00 0.00 4.42
1710 1720 2.280592 GTCTGTTTGGGTCGGCGT 60.281 61.111 6.85 0.00 0.00 5.68
1774 1785 0.320374 ATCTCAAACAGGGCGAACGA 59.680 50.000 0.00 0.00 0.00 3.85
1778 1789 1.533625 CCAAATCTCAAACAGGGCGA 58.466 50.000 0.00 0.00 0.00 5.54
1950 1967 9.793252 ACTATGCTATTTATTTGCTTGAAACTG 57.207 29.630 0.00 0.00 0.00 3.16
2334 2469 3.603629 GCGTGCCTTTAATGTTTTGCAAC 60.604 43.478 0.00 0.00 0.00 4.17
2382 2563 2.569404 GTCCTCAGATTCACCCAAGAGT 59.431 50.000 0.00 0.00 0.00 3.24
2391 2572 2.561187 TGGGGATTGTCCTCAGATTCA 58.439 47.619 0.00 0.00 43.43 2.57
2398 2579 0.034089 CAGGGTTGGGGATTGTCCTC 60.034 60.000 0.00 0.00 37.60 3.71
2399 2580 0.776080 ACAGGGTTGGGGATTGTCCT 60.776 55.000 0.00 0.00 36.57 3.85
2400 2581 0.114364 AACAGGGTTGGGGATTGTCC 59.886 55.000 0.00 0.00 35.23 4.02
2401 2582 1.203001 TCAACAGGGTTGGGGATTGTC 60.203 52.381 9.03 0.00 0.00 3.18
2402 2583 0.856982 TCAACAGGGTTGGGGATTGT 59.143 50.000 9.03 0.00 0.00 2.71
2405 2586 1.355720 CTCTTCAACAGGGTTGGGGAT 59.644 52.381 9.03 0.00 0.00 3.85
2406 2587 0.771127 CTCTTCAACAGGGTTGGGGA 59.229 55.000 9.03 6.91 0.00 4.81
2409 2590 3.406764 CTCTTCTCTTCAACAGGGTTGG 58.593 50.000 9.03 0.00 0.00 3.77
2410 2591 3.071602 TCCTCTTCTCTTCAACAGGGTTG 59.928 47.826 2.77 2.77 0.00 3.77
2411 2592 3.318313 TCCTCTTCTCTTCAACAGGGTT 58.682 45.455 0.00 0.00 0.00 4.11
2413 2594 4.357918 TTTCCTCTTCTCTTCAACAGGG 57.642 45.455 0.00 0.00 0.00 4.45
2414 2595 5.615289 TCTTTTCCTCTTCTCTTCAACAGG 58.385 41.667 0.00 0.00 0.00 4.00
2415 2596 5.700373 CCTCTTTTCCTCTTCTCTTCAACAG 59.300 44.000 0.00 0.00 0.00 3.16
2418 2599 5.366768 TGTCCTCTTTTCCTCTTCTCTTCAA 59.633 40.000 0.00 0.00 0.00 2.69
2425 2606 4.265893 GGGATTGTCCTCTTTTCCTCTTC 58.734 47.826 0.00 0.00 36.57 2.87
2426 2607 3.010696 GGGGATTGTCCTCTTTTCCTCTT 59.989 47.826 0.00 0.00 33.02 2.85
2427 2608 2.578480 GGGGATTGTCCTCTTTTCCTCT 59.422 50.000 0.00 0.00 33.02 3.69
2429 2610 2.358258 TGGGGATTGTCCTCTTTTCCT 58.642 47.619 0.00 0.00 38.07 3.36
2430 2611 2.826128 GTTGGGGATTGTCCTCTTTTCC 59.174 50.000 0.00 0.00 38.07 3.13
2431 2612 2.826128 GGTTGGGGATTGTCCTCTTTTC 59.174 50.000 0.00 0.00 38.07 2.29
2433 2614 1.077169 GGGTTGGGGATTGTCCTCTTT 59.923 52.381 0.00 0.00 38.07 2.52
2434 2615 0.704664 GGGTTGGGGATTGTCCTCTT 59.295 55.000 0.00 0.00 38.07 2.85
2435 2616 0.178831 AGGGTTGGGGATTGTCCTCT 60.179 55.000 0.00 0.00 38.07 3.69
2437 2618 0.776080 ACAGGGTTGGGGATTGTCCT 60.776 55.000 0.00 0.00 36.57 3.85
2438 2619 0.323451 GACAGGGTTGGGGATTGTCC 60.323 60.000 0.00 0.00 33.74 4.02
2546 2765 3.067742 CCTAACAGGATACCGAACGATGT 59.932 47.826 0.00 0.00 37.67 3.06
2564 2783 4.307432 CTTCTTCGTGCTTCAAGTCCTAA 58.693 43.478 0.00 0.00 0.00 2.69
2574 2793 0.886490 CCCACAGCTTCTTCGTGCTT 60.886 55.000 0.00 0.00 37.44 3.91
2619 2838 7.064371 GCGCTCATCTTCTATGATCATATTGTT 59.936 37.037 15.71 2.63 0.00 2.83
2685 2905 1.985473 TGCTCAGGCACAACATTCTT 58.015 45.000 0.00 0.00 44.28 2.52
2714 2934 7.733402 TTAGGTGAACTATTTAAACGTTGCT 57.267 32.000 0.00 0.00 0.00 3.91
3020 3883 0.041312 CATATTTACCGCGTGGCTGC 60.041 55.000 16.69 0.00 39.70 5.25
3027 3890 1.707117 CGTCGACTCATATTTACCGCG 59.293 52.381 14.70 0.00 0.00 6.46
3086 3954 3.488489 CTTTTATCTGGTTTTGTCCGCG 58.512 45.455 0.00 0.00 0.00 6.46
3089 3971 4.499037 ACGCTTTTATCTGGTTTTGTCC 57.501 40.909 0.00 0.00 0.00 4.02
3092 3974 5.788531 CGAACTACGCTTTTATCTGGTTTTG 59.211 40.000 0.00 0.00 34.51 2.44
3093 3975 5.467735 ACGAACTACGCTTTTATCTGGTTTT 59.532 36.000 0.00 0.00 46.94 2.43
3094 3976 4.992951 ACGAACTACGCTTTTATCTGGTTT 59.007 37.500 0.00 0.00 46.94 3.27
3097 3979 5.526010 AAACGAACTACGCTTTTATCTGG 57.474 39.130 0.00 0.00 46.94 3.86
3099 3981 5.697633 TCCAAAACGAACTACGCTTTTATCT 59.302 36.000 0.00 0.00 46.94 1.98
3102 3984 5.388682 CGATCCAAAACGAACTACGCTTTTA 60.389 40.000 0.00 0.00 46.94 1.52
3110 3992 2.070783 GCACCGATCCAAAACGAACTA 58.929 47.619 0.00 0.00 0.00 2.24
3111 3993 0.872388 GCACCGATCCAAAACGAACT 59.128 50.000 0.00 0.00 0.00 3.01
3114 3996 0.881159 AACGCACCGATCCAAAACGA 60.881 50.000 0.00 0.00 0.00 3.85
3123 4167 0.884704 AGCAACTTCAACGCACCGAT 60.885 50.000 0.00 0.00 0.00 4.18
3124 4168 1.495584 GAGCAACTTCAACGCACCGA 61.496 55.000 0.00 0.00 0.00 4.69
3128 4172 1.662517 TTGAGAGCAACTTCAACGCA 58.337 45.000 0.00 0.00 0.00 5.24
3163 4250 1.469940 CGGACGGAGAAATGAGAGGTG 60.470 57.143 0.00 0.00 0.00 4.00
3171 4258 2.022934 GAGGTAGACGGACGGAGAAAT 58.977 52.381 0.00 0.00 0.00 2.17
3301 4388 2.358003 GTTGCAGAGCGTCAGCCT 60.358 61.111 0.00 0.00 46.67 4.58
3303 4390 3.426568 GGGTTGCAGAGCGTCAGC 61.427 66.667 0.00 0.00 45.58 4.26
3304 4391 2.031012 TGGGTTGCAGAGCGTCAG 59.969 61.111 0.00 0.00 0.00 3.51
3305 4392 2.280797 GTGGGTTGCAGAGCGTCA 60.281 61.111 0.00 0.00 0.00 4.35
3306 4393 3.050275 GGTGGGTTGCAGAGCGTC 61.050 66.667 0.00 0.00 0.00 5.19
3307 4394 4.988598 CGGTGGGTTGCAGAGCGT 62.989 66.667 0.00 0.00 0.00 5.07
3309 4396 3.050275 GACGGTGGGTTGCAGAGC 61.050 66.667 0.00 0.00 0.00 4.09
3311 4398 3.164977 TGGACGGTGGGTTGCAGA 61.165 61.111 0.00 0.00 0.00 4.26
3312 4399 2.978010 GTGGACGGTGGGTTGCAG 60.978 66.667 0.00 0.00 0.00 4.41
3313 4400 4.920112 CGTGGACGGTGGGTTGCA 62.920 66.667 0.00 0.00 35.37 4.08
3327 4414 2.972505 AGTTGGAACAGCCGCGTG 60.973 61.111 4.92 0.00 41.77 5.34
4033 5120 1.431440 GTGCGCAAGGTTGTGAACA 59.569 52.632 14.00 0.00 44.73 3.18
4096 5183 1.437986 GGAGAGCATAAGTCGGCGT 59.562 57.895 6.85 0.00 34.54 5.68
4790 5877 1.815003 CTTGGCCTTCACATCAAGGTC 59.185 52.381 3.32 0.00 46.89 3.85
5082 6180 8.458573 AACACAAATCACTACAAGATACCAAA 57.541 30.769 0.00 0.00 0.00 3.28
5116 6214 3.193267 TGCTTCAAAACTGCACTTCAACT 59.807 39.130 0.00 0.00 0.00 3.16
5307 7350 8.895932 AATTGTCGCTGATTTAGTACAAAATC 57.104 30.769 0.00 3.02 43.28 2.17
5314 7357 9.990360 TCCATATTAATTGTCGCTGATTTAGTA 57.010 29.630 0.00 0.00 0.00 1.82
5315 7358 8.774586 GTCCATATTAATTGTCGCTGATTTAGT 58.225 33.333 0.00 0.00 0.00 2.24
5316 7359 7.952101 CGTCCATATTAATTGTCGCTGATTTAG 59.048 37.037 0.00 0.00 0.00 1.85
5317 7360 7.095397 CCGTCCATATTAATTGTCGCTGATTTA 60.095 37.037 0.00 0.00 0.00 1.40
5318 7361 6.293407 CCGTCCATATTAATTGTCGCTGATTT 60.293 38.462 0.00 0.00 0.00 2.17
5319 7362 5.179368 CCGTCCATATTAATTGTCGCTGATT 59.821 40.000 0.00 0.00 0.00 2.57
5320 7363 4.690748 CCGTCCATATTAATTGTCGCTGAT 59.309 41.667 0.00 0.00 0.00 2.90
5321 7364 4.055360 CCGTCCATATTAATTGTCGCTGA 58.945 43.478 0.00 0.00 0.00 4.26
5322 7365 4.055360 TCCGTCCATATTAATTGTCGCTG 58.945 43.478 0.00 0.00 0.00 5.18
5323 7366 4.307432 CTCCGTCCATATTAATTGTCGCT 58.693 43.478 0.00 0.00 0.00 4.93
5324 7367 3.432252 CCTCCGTCCATATTAATTGTCGC 59.568 47.826 0.00 0.00 0.00 5.19
5735 10281 6.524101 TGTTGTAAATAAGGGCCATCTTTC 57.476 37.500 6.18 0.00 0.00 2.62
5913 10519 5.354842 ACCTTAGGCACCAGTACTTATTC 57.645 43.478 0.00 0.00 0.00 1.75
6038 10644 0.106918 AACCAAGTCCGCAACCAAGA 60.107 50.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.