Multiple sequence alignment - TraesCS1B01G019900

Loading Multiple Alignment...

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 TraesCS1B01G019900 chr1B 100.000 2981 0 0 1 2981 9280244 9283224 0.000000e+00 5505.0
1 TraesCS1B01G019900 chr1B 91.409 1001 59 14 1994 2981 652476231 652477217 0.000000e+00 1347.0
2 TraesCS1B01G019900 chr1B 91.284 872 62 5 918 1778 548200003 548199135 0.000000e+00 1177.0
3 TraesCS1B01G019900 chr1B 90.564 869 69 7 918 1778 9175264 9176127 0.000000e+00 1138.0
4 TraesCS1B01G019900 chr1B 82.799 686 83 20 1041 1722 8855868 8855214 5.540000e-162 580.0
5 TraesCS1B01G019900 chr1B 83.256 215 30 3 501 714 8867674 8867465 3.030000e-45 193.0
6 TraesCS1B01G019900 chr1B 86.184 152 12 1 714 856 548200323 548200172 3.980000e-34 156.0
7 TraesCS1B01G019900 chr6B 93.517 1018 36 8 1994 2981 402214572 402213555 0.000000e+00 1487.0
8 TraesCS1B01G019900 chr3B 93.526 1004 46 8 1994 2979 46046703 46045701 0.000000e+00 1476.0
9 TraesCS1B01G019900 chr3B 92.412 1028 37 16 1994 2981 481312996 481311970 0.000000e+00 1428.0
10 TraesCS1B01G019900 chr3B 89.133 819 73 10 1994 2803 680932127 680932938 0.000000e+00 1005.0
11 TraesCS1B01G019900 chr3B 82.903 1006 141 19 1994 2981 130133894 130132902 0.000000e+00 876.0
12 TraesCS1B01G019900 chr3B 95.556 270 12 0 3 272 259231223 259230954 1.640000e-117 433.0
13 TraesCS1B01G019900 chr1A 95.052 869 33 4 918 1778 8327030 8327896 0.000000e+00 1358.0
14 TraesCS1B01G019900 chr1A 85.928 803 81 18 940 1721 8144593 8143802 0.000000e+00 828.0
15 TraesCS1B01G019900 chr1A 92.885 506 28 4 414 918 8326441 8326939 0.000000e+00 728.0
16 TraesCS1B01G019900 chr1A 92.308 221 13 4 1778 1994 8398049 8398269 8.020000e-81 311.0
17 TraesCS1B01G019900 chr1A 91.705 217 17 1 1779 1994 8547200 8547416 1.740000e-77 300.0
18 TraesCS1B01G019900 chr1A 91.364 220 15 2 1779 1994 8457202 8457421 6.250000e-77 298.0
19 TraesCS1B01G019900 chr1A 91.244 217 13 5 1780 1992 8382765 8382979 1.050000e-74 291.0
20 TraesCS1B01G019900 chr1A 90.000 220 18 2 1779 1994 8532124 8532343 6.290000e-72 281.0
21 TraesCS1B01G019900 chr1A 90.045 221 15 6 1779 1994 8472249 8472467 2.260000e-71 279.0
22 TraesCS1B01G019900 chr1A 77.778 432 65 20 501 918 8160294 8159880 1.380000e-58 237.0
23 TraesCS1B01G019900 chr1A 76.127 377 39 19 579 918 8089152 8088790 1.850000e-32 150.0
24 TraesCS1B01G019900 chr1A 86.667 105 8 3 299 402 8326303 8326402 8.730000e-21 111.0
25 TraesCS1B01G019900 chr2B 89.086 1017 80 15 1994 2981 571728 572742 0.000000e+00 1234.0
26 TraesCS1B01G019900 chr2B 86.587 999 120 9 1994 2979 691465833 691464836 0.000000e+00 1090.0
27 TraesCS1B01G019900 chr2B 89.756 859 70 12 1989 2837 668428352 668429202 0.000000e+00 1083.0
28 TraesCS1B01G019900 chr2B 95.638 298 12 1 3 299 21948017 21947720 7.480000e-131 477.0
29 TraesCS1B01G019900 chr2B 77.140 853 129 32 953 1778 729766526 729767339 4.560000e-118 435.0
30 TraesCS1B01G019900 chr1D 91.904 877 54 11 918 1778 6898342 6899217 0.000000e+00 1210.0
31 TraesCS1B01G019900 chr1D 86.691 819 83 16 918 1721 6714717 6713910 0.000000e+00 885.0
32 TraesCS1B01G019900 chr1D 90.802 511 36 6 414 918 6897742 6898247 0.000000e+00 673.0
33 TraesCS1B01G019900 chr1D 91.403 221 14 2 1779 1994 6968774 6968994 6.250000e-77 298.0
34 TraesCS1B01G019900 chr1D 91.244 217 16 3 1781 1995 6921649 6921864 2.910000e-75 292.0
35 TraesCS1B01G019900 chr1D 80.749 187 29 7 127 308 486680722 486680538 4.010000e-29 139.0
36 TraesCS1B01G019900 chr1D 88.073 109 8 1 294 402 6897594 6897697 1.120000e-24 124.0
37 TraesCS1B01G019900 chr1D 95.455 44 2 0 256 299 381106711 381106668 1.480000e-08 71.3
38 TraesCS1B01G019900 chr5B 90.708 861 67 8 919 1778 549547888 549548736 0.000000e+00 1134.0
39 TraesCS1B01G019900 chr5B 80.791 708 109 21 1028 1725 13776132 13775442 2.030000e-146 529.0
40 TraesCS1B01G019900 chr5B 94.539 293 16 0 3 295 595318562 595318270 1.260000e-123 453.0
41 TraesCS1B01G019900 chr5B 94.218 294 17 0 3 296 657400466 657400173 1.630000e-122 449.0
42 TraesCS1B01G019900 chr5B 94.175 206 12 0 713 918 549547587 549547792 6.200000e-82 315.0
43 TraesCS1B01G019900 chr4B 90.865 821 62 9 1994 2803 258857699 258858517 0.000000e+00 1088.0
44 TraesCS1B01G019900 chr4B 93.220 295 16 3 3 295 414267231 414267523 5.900000e-117 431.0
45 TraesCS1B01G019900 chr4B 79.775 445 50 16 501 918 36636304 36635873 1.350000e-73 287.0
46 TraesCS1B01G019900 chr4B 89.313 131 12 2 170 299 623073217 623073346 2.380000e-36 163.0
47 TraesCS1B01G019900 chr7A 86.037 1017 110 19 1994 2981 46959698 46960711 0.000000e+00 1062.0
48 TraesCS1B01G019900 chr6D 84.930 1002 123 18 1991 2981 98088486 98089470 0.000000e+00 989.0
49 TraesCS1B01G019900 chr6D 94.059 303 13 3 3 301 202472150 202472451 3.500000e-124 455.0
50 TraesCS1B01G019900 chr6D 87.937 315 19 2 3 299 406227677 406227364 1.310000e-93 353.0
51 TraesCS1B01G019900 chr6D 80.571 175 30 4 127 299 255007431 255007259 6.700000e-27 132.0
52 TraesCS1B01G019900 chr6D 97.059 34 1 0 262 295 406229682 406229715 1.150000e-04 58.4
53 TraesCS1B01G019900 chr2A 77.960 853 126 27 952 1778 733628833 733629649 7.480000e-131 477.0
54 TraesCS1B01G019900 chr2A 77.081 829 121 34 982 1778 611296112 611296903 5.950000e-112 414.0
55 TraesCS1B01G019900 chr7D 95.254 295 11 2 3 295 133201069 133201362 5.820000e-127 464.0
56 TraesCS1B01G019900 chr4D 93.919 296 15 2 3 295 477027301 477027596 7.580000e-121 444.0
57 TraesCS1B01G019900 chr4D 95.185 270 12 1 3 272 335175202 335174934 2.750000e-115 425.0
58 TraesCS1B01G019900 chr4D 80.814 172 29 4 126 295 322668176 322668345 6.700000e-27 132.0
59 TraesCS1B01G019900 chr4D 80.405 148 25 4 127 272 60874405 60874260 3.140000e-20 110.0
60 TraesCS1B01G019900 chr3D 95.926 270 9 1 5 272 531361822 531362091 1.270000e-118 436.0
61 TraesCS1B01G019900 chr2D 77.049 854 130 31 952 1778 599926355 599927169 5.900000e-117 431.0
62 TraesCS1B01G019900 chr5D 92.642 299 16 5 3 299 496562067 496561773 2.750000e-115 425.0
63 TraesCS1B01G019900 chrUn 81.143 175 29 4 127 299 471104395 471104567 1.440000e-28 137.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G019900 chr1B 9280244 9283224 2980 False 5505.000000 5505 100.000000 1 2981 1 chr1B.!!$F2 2980
1 TraesCS1B01G019900 chr1B 652476231 652477217 986 False 1347.000000 1347 91.409000 1994 2981 1 chr1B.!!$F3 987
2 TraesCS1B01G019900 chr1B 9175264 9176127 863 False 1138.000000 1138 90.564000 918 1778 1 chr1B.!!$F1 860
3 TraesCS1B01G019900 chr1B 548199135 548200323 1188 True 666.500000 1177 88.734000 714 1778 2 chr1B.!!$R3 1064
4 TraesCS1B01G019900 chr1B 8855214 8855868 654 True 580.000000 580 82.799000 1041 1722 1 chr1B.!!$R1 681
5 TraesCS1B01G019900 chr6B 402213555 402214572 1017 True 1487.000000 1487 93.517000 1994 2981 1 chr6B.!!$R1 987
6 TraesCS1B01G019900 chr3B 46045701 46046703 1002 True 1476.000000 1476 93.526000 1994 2979 1 chr3B.!!$R1 985
7 TraesCS1B01G019900 chr3B 481311970 481312996 1026 True 1428.000000 1428 92.412000 1994 2981 1 chr3B.!!$R4 987
8 TraesCS1B01G019900 chr3B 680932127 680932938 811 False 1005.000000 1005 89.133000 1994 2803 1 chr3B.!!$F1 809
9 TraesCS1B01G019900 chr3B 130132902 130133894 992 True 876.000000 876 82.903000 1994 2981 1 chr3B.!!$R2 987
10 TraesCS1B01G019900 chr1A 8143802 8144593 791 True 828.000000 828 85.928000 940 1721 1 chr1A.!!$R2 781
11 TraesCS1B01G019900 chr1A 8326303 8327896 1593 False 732.333333 1358 91.534667 299 1778 3 chr1A.!!$F7 1479
12 TraesCS1B01G019900 chr2B 571728 572742 1014 False 1234.000000 1234 89.086000 1994 2981 1 chr2B.!!$F1 987
13 TraesCS1B01G019900 chr2B 691464836 691465833 997 True 1090.000000 1090 86.587000 1994 2979 1 chr2B.!!$R2 985
14 TraesCS1B01G019900 chr2B 668428352 668429202 850 False 1083.000000 1083 89.756000 1989 2837 1 chr2B.!!$F2 848
15 TraesCS1B01G019900 chr2B 729766526 729767339 813 False 435.000000 435 77.140000 953 1778 1 chr2B.!!$F3 825
16 TraesCS1B01G019900 chr1D 6713910 6714717 807 True 885.000000 885 86.691000 918 1721 1 chr1D.!!$R1 803
17 TraesCS1B01G019900 chr1D 6897594 6899217 1623 False 669.000000 1210 90.259667 294 1778 3 chr1D.!!$F3 1484
18 TraesCS1B01G019900 chr5B 549547587 549548736 1149 False 724.500000 1134 92.441500 713 1778 2 chr5B.!!$F1 1065
19 TraesCS1B01G019900 chr5B 13775442 13776132 690 True 529.000000 529 80.791000 1028 1725 1 chr5B.!!$R1 697
20 TraesCS1B01G019900 chr4B 258857699 258858517 818 False 1088.000000 1088 90.865000 1994 2803 1 chr4B.!!$F1 809
21 TraesCS1B01G019900 chr7A 46959698 46960711 1013 False 1062.000000 1062 86.037000 1994 2981 1 chr7A.!!$F1 987
22 TraesCS1B01G019900 chr6D 98088486 98089470 984 False 989.000000 989 84.930000 1991 2981 1 chr6D.!!$F1 990
23 TraesCS1B01G019900 chr2A 733628833 733629649 816 False 477.000000 477 77.960000 952 1778 1 chr2A.!!$F2 826
24 TraesCS1B01G019900 chr2A 611296112 611296903 791 False 414.000000 414 77.081000 982 1778 1 chr2A.!!$F1 796
25 TraesCS1B01G019900 chr2D 599926355 599927169 814 False 431.000000 431 77.049000 952 1778 1 chr2D.!!$F1 826

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
129 130 0.105913 GGGTTGTTTCCCCACTCCAA 60.106 55.0 0.0 0.0 42.15 3.53 F
132 133 0.105913 TTGTTTCCCCACTCCAACCC 60.106 55.0 0.0 0.0 0.00 4.11 F
279 280 0.187606 GGGTTTGAGGGTTTGAGGGT 59.812 55.0 0.0 0.0 0.00 4.34 F
732 773 0.464036 CCCTGCCGACTAGCACATAA 59.536 55.0 0.0 0.0 38.00 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1600 1870 0.464036 TGCGACTGAAACCAGTGACT 59.536 50.000 2.5 0.0 44.34 3.41 R
1955 2225 1.425066 TCTGGCTGTGGAAAGATTGGT 59.575 47.619 0.0 0.0 0.00 3.67 R
1956 2226 2.205022 TCTGGCTGTGGAAAGATTGG 57.795 50.000 0.0 0.0 0.00 3.16 R
2443 2715 2.288213 CGCACTCTTTGAGTCCTGTACA 60.288 50.000 0.0 0.0 41.37 2.90 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
73 74 4.296265 GGGCGACGAACCTGATTT 57.704 55.556 0.00 0.00 0.00 2.17
74 75 2.551644 GGGCGACGAACCTGATTTT 58.448 52.632 0.00 0.00 0.00 1.82
75 76 0.879090 GGGCGACGAACCTGATTTTT 59.121 50.000 0.00 0.00 0.00 1.94
76 77 1.135774 GGGCGACGAACCTGATTTTTC 60.136 52.381 0.00 0.00 0.00 2.29
77 78 1.135774 GGCGACGAACCTGATTTTTCC 60.136 52.381 0.00 0.00 0.00 3.13
78 79 1.135774 GCGACGAACCTGATTTTTCCC 60.136 52.381 0.00 0.00 0.00 3.97
79 80 2.423577 CGACGAACCTGATTTTTCCCT 58.576 47.619 0.00 0.00 0.00 4.20
80 81 2.415512 CGACGAACCTGATTTTTCCCTC 59.584 50.000 0.00 0.00 0.00 4.30
81 82 2.747989 GACGAACCTGATTTTTCCCTCC 59.252 50.000 0.00 0.00 0.00 4.30
82 83 2.092323 CGAACCTGATTTTTCCCTCCC 58.908 52.381 0.00 0.00 0.00 4.30
83 84 2.092323 GAACCTGATTTTTCCCTCCCG 58.908 52.381 0.00 0.00 0.00 5.14
84 85 0.323451 ACCTGATTTTTCCCTCCCGC 60.323 55.000 0.00 0.00 0.00 6.13
85 86 1.376609 CCTGATTTTTCCCTCCCGCG 61.377 60.000 0.00 0.00 0.00 6.46
86 87 1.993369 CTGATTTTTCCCTCCCGCGC 61.993 60.000 0.00 0.00 0.00 6.86
87 88 3.108357 GATTTTTCCCTCCCGCGCG 62.108 63.158 25.67 25.67 0.00 6.86
100 101 4.508326 GCGCGCGCAACGGATAAA 62.508 61.111 46.11 0.00 43.93 1.40
101 102 2.323105 CGCGCGCAACGGATAAAT 59.677 55.556 32.61 0.00 43.93 1.40
102 103 1.560770 CGCGCGCAACGGATAAATA 59.439 52.632 32.61 0.00 43.93 1.40
103 104 0.448861 CGCGCGCAACGGATAAATAG 60.449 55.000 32.61 5.56 43.93 1.73
104 105 0.856641 GCGCGCAACGGATAAATAGA 59.143 50.000 29.10 0.00 43.93 1.98
105 106 1.136611 GCGCGCAACGGATAAATAGAG 60.137 52.381 29.10 0.00 43.93 2.43
106 107 1.455786 CGCGCAACGGATAAATAGAGG 59.544 52.381 8.75 0.00 38.44 3.69
107 108 2.480845 GCGCAACGGATAAATAGAGGT 58.519 47.619 0.30 0.00 0.00 3.85
108 109 2.870411 GCGCAACGGATAAATAGAGGTT 59.130 45.455 0.30 0.00 0.00 3.50
109 110 3.303132 GCGCAACGGATAAATAGAGGTTG 60.303 47.826 0.30 0.00 38.16 3.77
110 111 3.247648 CGCAACGGATAAATAGAGGTTGG 59.752 47.826 4.19 0.00 36.26 3.77
111 112 3.564225 GCAACGGATAAATAGAGGTTGGG 59.436 47.826 4.19 0.00 36.26 4.12
112 113 4.134563 CAACGGATAAATAGAGGTTGGGG 58.865 47.826 0.00 0.00 33.12 4.96
113 114 3.390819 ACGGATAAATAGAGGTTGGGGT 58.609 45.455 0.00 0.00 0.00 4.95
114 115 3.784202 ACGGATAAATAGAGGTTGGGGTT 59.216 43.478 0.00 0.00 0.00 4.11
115 116 4.134563 CGGATAAATAGAGGTTGGGGTTG 58.865 47.826 0.00 0.00 0.00 3.77
116 117 4.384868 CGGATAAATAGAGGTTGGGGTTGT 60.385 45.833 0.00 0.00 0.00 3.32
117 118 5.516044 GGATAAATAGAGGTTGGGGTTGTT 58.484 41.667 0.00 0.00 0.00 2.83
118 119 5.955959 GGATAAATAGAGGTTGGGGTTGTTT 59.044 40.000 0.00 0.00 0.00 2.83
119 120 6.096423 GGATAAATAGAGGTTGGGGTTGTTTC 59.904 42.308 0.00 0.00 0.00 2.78
120 121 2.963599 TAGAGGTTGGGGTTGTTTCC 57.036 50.000 0.00 0.00 0.00 3.13
121 122 0.187606 AGAGGTTGGGGTTGTTTCCC 59.812 55.000 0.00 0.00 46.31 3.97
127 128 4.513777 GGGTTGTTTCCCCACTCC 57.486 61.111 0.00 0.00 42.15 3.85
128 129 1.539665 GGGTTGTTTCCCCACTCCA 59.460 57.895 0.00 0.00 42.15 3.86
129 130 0.105913 GGGTTGTTTCCCCACTCCAA 60.106 55.000 0.00 0.00 42.15 3.53
130 131 1.037493 GGTTGTTTCCCCACTCCAAC 58.963 55.000 0.00 0.00 35.75 3.77
131 132 1.037493 GTTGTTTCCCCACTCCAACC 58.963 55.000 0.00 0.00 31.50 3.77
132 133 0.105913 TTGTTTCCCCACTCCAACCC 60.106 55.000 0.00 0.00 0.00 4.11
133 134 0.996762 TGTTTCCCCACTCCAACCCT 60.997 55.000 0.00 0.00 0.00 4.34
134 135 0.251209 GTTTCCCCACTCCAACCCTC 60.251 60.000 0.00 0.00 0.00 4.30
135 136 0.699577 TTTCCCCACTCCAACCCTCA 60.700 55.000 0.00 0.00 0.00 3.86
136 137 1.133809 TTCCCCACTCCAACCCTCAG 61.134 60.000 0.00 0.00 0.00 3.35
137 138 1.847968 CCCCACTCCAACCCTCAGT 60.848 63.158 0.00 0.00 0.00 3.41
138 139 1.427072 CCCCACTCCAACCCTCAGTT 61.427 60.000 0.00 0.00 40.16 3.16
139 140 0.478507 CCCACTCCAACCCTCAGTTT 59.521 55.000 0.00 0.00 36.18 2.66
140 141 1.133482 CCCACTCCAACCCTCAGTTTT 60.133 52.381 0.00 0.00 36.18 2.43
141 142 2.107552 CCCACTCCAACCCTCAGTTTTA 59.892 50.000 0.00 0.00 36.18 1.52
142 143 3.412386 CCACTCCAACCCTCAGTTTTAG 58.588 50.000 0.00 0.00 36.18 1.85
143 144 3.072476 CCACTCCAACCCTCAGTTTTAGA 59.928 47.826 0.00 0.00 36.18 2.10
144 145 4.319177 CACTCCAACCCTCAGTTTTAGAG 58.681 47.826 0.00 0.00 36.18 2.43
150 151 2.409948 CCTCAGTTTTAGAGGCTGGG 57.590 55.000 0.00 0.00 45.51 4.45
151 152 1.909302 CCTCAGTTTTAGAGGCTGGGA 59.091 52.381 0.00 0.00 45.51 4.37
152 153 2.093235 CCTCAGTTTTAGAGGCTGGGAG 60.093 54.545 0.00 0.00 45.51 4.30
153 154 2.834549 CTCAGTTTTAGAGGCTGGGAGA 59.165 50.000 0.00 0.00 32.77 3.71
154 155 2.834549 TCAGTTTTAGAGGCTGGGAGAG 59.165 50.000 0.00 0.00 0.00 3.20
170 171 3.459063 AGCGACCCGGGCTCTAAC 61.459 66.667 24.08 4.17 35.37 2.34
171 172 4.525949 GCGACCCGGGCTCTAACC 62.526 72.222 24.08 0.00 0.00 2.85
205 206 8.425237 TTTTTACAGGTTTAGGGATTAAAGGG 57.575 34.615 0.00 0.00 32.07 3.95
206 207 6.723471 TTACAGGTTTAGGGATTAAAGGGT 57.277 37.500 0.00 0.00 32.07 4.34
207 208 5.610429 ACAGGTTTAGGGATTAAAGGGTT 57.390 39.130 0.00 0.00 32.07 4.11
208 209 5.577100 ACAGGTTTAGGGATTAAAGGGTTC 58.423 41.667 0.00 0.00 32.07 3.62
209 210 5.315109 ACAGGTTTAGGGATTAAAGGGTTCT 59.685 40.000 0.00 0.00 32.07 3.01
210 211 6.506413 ACAGGTTTAGGGATTAAAGGGTTCTA 59.494 38.462 0.00 0.00 32.07 2.10
211 212 7.054751 CAGGTTTAGGGATTAAAGGGTTCTAG 58.945 42.308 0.00 0.00 32.07 2.43
212 213 6.739042 AGGTTTAGGGATTAAAGGGTTCTAGT 59.261 38.462 0.00 0.00 32.07 2.57
213 214 7.052873 GGTTTAGGGATTAAAGGGTTCTAGTC 58.947 42.308 0.00 0.00 32.07 2.59
214 215 7.092533 GGTTTAGGGATTAAAGGGTTCTAGTCT 60.093 40.741 0.00 0.00 32.07 3.24
215 216 8.327271 GTTTAGGGATTAAAGGGTTCTAGTCTT 58.673 37.037 0.00 0.00 32.07 3.01
216 217 6.971932 AGGGATTAAAGGGTTCTAGTCTTT 57.028 37.500 0.00 0.00 35.29 2.52
217 218 6.722328 AGGGATTAAAGGGTTCTAGTCTTTG 58.278 40.000 0.00 0.00 33.44 2.77
218 219 5.357314 GGGATTAAAGGGTTCTAGTCTTTGC 59.643 44.000 0.00 0.00 33.44 3.68
219 220 5.064834 GGATTAAAGGGTTCTAGTCTTTGCG 59.935 44.000 0.00 0.00 33.44 4.85
220 221 3.487120 AAAGGGTTCTAGTCTTTGCGT 57.513 42.857 0.00 0.00 30.56 5.24
221 222 3.487120 AAGGGTTCTAGTCTTTGCGTT 57.513 42.857 0.00 0.00 0.00 4.84
222 223 3.487120 AGGGTTCTAGTCTTTGCGTTT 57.513 42.857 0.00 0.00 0.00 3.60
223 224 3.816994 AGGGTTCTAGTCTTTGCGTTTT 58.183 40.909 0.00 0.00 0.00 2.43
224 225 4.204799 AGGGTTCTAGTCTTTGCGTTTTT 58.795 39.130 0.00 0.00 0.00 1.94
263 264 4.948341 AAAAGCGGTTATTTTTGAGGGT 57.052 36.364 0.00 0.00 0.00 4.34
264 265 4.948341 AAAGCGGTTATTTTTGAGGGTT 57.052 36.364 0.00 0.00 0.00 4.11
265 266 4.948341 AAGCGGTTATTTTTGAGGGTTT 57.052 36.364 0.00 0.00 0.00 3.27
266 267 4.251543 AGCGGTTATTTTTGAGGGTTTG 57.748 40.909 0.00 0.00 0.00 2.93
267 268 3.892588 AGCGGTTATTTTTGAGGGTTTGA 59.107 39.130 0.00 0.00 0.00 2.69
268 269 4.022329 AGCGGTTATTTTTGAGGGTTTGAG 60.022 41.667 0.00 0.00 0.00 3.02
269 270 4.805219 CGGTTATTTTTGAGGGTTTGAGG 58.195 43.478 0.00 0.00 0.00 3.86
270 271 4.321675 CGGTTATTTTTGAGGGTTTGAGGG 60.322 45.833 0.00 0.00 0.00 4.30
271 272 4.591498 GGTTATTTTTGAGGGTTTGAGGGT 59.409 41.667 0.00 0.00 0.00 4.34
272 273 5.071250 GGTTATTTTTGAGGGTTTGAGGGTT 59.929 40.000 0.00 0.00 0.00 4.11
273 274 6.408776 GGTTATTTTTGAGGGTTTGAGGGTTT 60.409 38.462 0.00 0.00 0.00 3.27
274 275 4.479786 TTTTTGAGGGTTTGAGGGTTTG 57.520 40.909 0.00 0.00 0.00 2.93
275 276 3.390175 TTTGAGGGTTTGAGGGTTTGA 57.610 42.857 0.00 0.00 0.00 2.69
276 277 2.656947 TGAGGGTTTGAGGGTTTGAG 57.343 50.000 0.00 0.00 0.00 3.02
277 278 1.144913 TGAGGGTTTGAGGGTTTGAGG 59.855 52.381 0.00 0.00 0.00 3.86
278 279 0.482887 AGGGTTTGAGGGTTTGAGGG 59.517 55.000 0.00 0.00 0.00 4.30
279 280 0.187606 GGGTTTGAGGGTTTGAGGGT 59.812 55.000 0.00 0.00 0.00 4.34
280 281 1.426215 GGGTTTGAGGGTTTGAGGGTA 59.574 52.381 0.00 0.00 0.00 3.69
281 282 2.511659 GGTTTGAGGGTTTGAGGGTAC 58.488 52.381 0.00 0.00 0.00 3.34
282 283 2.107726 GGTTTGAGGGTTTGAGGGTACT 59.892 50.000 0.00 0.00 0.00 2.73
283 284 3.328637 GGTTTGAGGGTTTGAGGGTACTA 59.671 47.826 0.00 0.00 0.00 1.82
284 285 4.321718 GTTTGAGGGTTTGAGGGTACTAC 58.678 47.826 0.00 0.00 0.00 2.73
285 286 3.555117 TGAGGGTTTGAGGGTACTACT 57.445 47.619 0.00 0.00 0.00 2.57
286 287 4.680278 TGAGGGTTTGAGGGTACTACTA 57.320 45.455 0.00 0.00 0.00 1.82
287 288 4.607239 TGAGGGTTTGAGGGTACTACTAG 58.393 47.826 0.00 0.00 0.00 2.57
288 289 4.045079 TGAGGGTTTGAGGGTACTACTAGT 59.955 45.833 0.00 0.00 0.00 2.57
289 290 5.253798 TGAGGGTTTGAGGGTACTACTAGTA 59.746 44.000 1.89 1.89 0.00 1.82
290 291 6.157862 AGGGTTTGAGGGTACTACTAGTAA 57.842 41.667 3.76 0.00 31.62 2.24
291 292 6.750009 AGGGTTTGAGGGTACTACTAGTAAT 58.250 40.000 3.76 0.00 31.62 1.89
292 293 6.610425 AGGGTTTGAGGGTACTACTAGTAATG 59.390 42.308 3.76 0.00 31.62 1.90
296 297 7.729124 TTGAGGGTACTACTAGTAATGCTTT 57.271 36.000 3.76 0.00 31.62 3.51
313 314 9.207042 GTAATGCTTTTAACATCTTAGTTACGC 57.793 33.333 0.00 0.00 33.96 4.42
353 354 6.152154 AGCAAATATTGTGGGTTGGTTAGTAC 59.848 38.462 0.00 0.00 0.00 2.73
354 355 6.152154 GCAAATATTGTGGGTTGGTTAGTACT 59.848 38.462 0.00 0.00 0.00 2.73
355 356 7.535139 CAAATATTGTGGGTTGGTTAGTACTG 58.465 38.462 5.39 0.00 0.00 2.74
397 398 5.152623 TGTATCAGAAGACAACCCTTGAG 57.847 43.478 0.00 0.00 0.00 3.02
402 403 4.020218 TCAGAAGACAACCCTTGAGTATGG 60.020 45.833 0.00 0.00 0.00 2.74
403 404 3.910627 AGAAGACAACCCTTGAGTATGGT 59.089 43.478 0.00 0.00 0.00 3.55
404 405 3.703001 AGACAACCCTTGAGTATGGTG 57.297 47.619 0.00 0.00 31.32 4.17
405 406 2.305927 AGACAACCCTTGAGTATGGTGG 59.694 50.000 0.00 0.00 31.32 4.61
406 407 1.354368 ACAACCCTTGAGTATGGTGGG 59.646 52.381 0.00 0.00 43.26 4.61
407 408 3.513453 ACCCTTGAGTATGGTGGGT 57.487 52.632 0.00 0.00 45.47 4.51
411 445 1.354368 CCTTGAGTATGGTGGGTTGGT 59.646 52.381 0.00 0.00 0.00 3.67
412 446 2.618045 CCTTGAGTATGGTGGGTTGGTC 60.618 54.545 0.00 0.00 0.00 4.02
434 468 4.693566 TCGACCCTTTTTACAGTTAGCATG 59.306 41.667 0.00 0.00 0.00 4.06
436 470 5.390567 CGACCCTTTTTACAGTTAGCATGTC 60.391 44.000 0.00 0.00 32.02 3.06
438 472 6.775708 ACCCTTTTTACAGTTAGCATGTCTA 58.224 36.000 0.00 0.00 32.02 2.59
560 601 2.859165 TCCTGTTAAGCTTGGTGGAG 57.141 50.000 9.86 0.00 0.00 3.86
592 633 1.379916 CTTGACCATGGCCCACAGA 59.620 57.895 13.04 0.00 0.00 3.41
641 682 1.203162 TGACCAAATTCCATGGCCACT 60.203 47.619 8.16 0.00 41.89 4.00
665 706 1.277273 TGGAAGCCTCATGACTGACTG 59.723 52.381 0.00 0.00 0.00 3.51
666 707 1.552337 GGAAGCCTCATGACTGACTGA 59.448 52.381 0.00 0.00 0.00 3.41
667 708 2.615869 GAAGCCTCATGACTGACTGAC 58.384 52.381 0.00 0.00 0.00 3.51
668 709 1.935799 AGCCTCATGACTGACTGACT 58.064 50.000 0.00 0.00 0.00 3.41
677 718 2.362397 TGACTGACTGACTTGGACACTC 59.638 50.000 0.00 0.00 0.00 3.51
682 723 0.946221 CTGACTTGGACACTCGGTGC 60.946 60.000 4.23 0.00 36.98 5.01
732 773 0.464036 CCCTGCCGACTAGCACATAA 59.536 55.000 0.00 0.00 38.00 1.90
826 876 4.400251 TGTCCTGATCTGAATTTGATTGGC 59.600 41.667 0.38 0.00 0.00 4.52
840 890 1.402107 ATTGGCCCCAAATGGATCGC 61.402 55.000 0.00 0.00 39.55 4.58
846 896 1.683943 CCCAAATGGATCGCAGTGAT 58.316 50.000 0.00 0.00 41.06 3.06
905 982 9.303116 TCTACATATACATCCTCTTCTTCCTTC 57.697 37.037 0.00 0.00 0.00 3.46
1019 1219 2.357075 CAGAGCAGAGCACATTCACAT 58.643 47.619 0.00 0.00 0.00 3.21
1087 1293 0.881796 TACACACTCCTCACTGCTCG 59.118 55.000 0.00 0.00 0.00 5.03
1359 1595 5.163713 ACTCAACAAAGCTCAAGTTCTCAAC 60.164 40.000 0.00 0.00 0.00 3.18
1441 1693 4.707934 TGGTCCACTCGTATTGTGAATAGA 59.292 41.667 0.00 0.00 37.60 1.98
1476 1728 3.523564 AGCATAAACACCACCACCTCTAT 59.476 43.478 0.00 0.00 0.00 1.98
1542 1812 1.696063 AGCAAAGTGATGTTGTGGCT 58.304 45.000 0.00 0.00 0.00 4.75
1551 1821 0.957395 ATGTTGTGGCTGAGCTTCGG 60.957 55.000 3.72 0.00 0.00 4.30
1584 1854 4.389576 CGCGCTTTCTGGTGCCAC 62.390 66.667 5.56 0.00 39.27 5.01
1600 1870 2.192861 CACGCTTGGCTGGGACAAA 61.193 57.895 2.72 0.00 38.70 2.83
1778 2048 8.985315 AACATCATCAATGAGTGTTATACCAT 57.015 30.769 13.98 0.00 40.64 3.55
1779 2049 8.387190 ACATCATCAATGAGTGTTATACCATG 57.613 34.615 0.00 0.00 40.64 3.66
1780 2050 8.212995 ACATCATCAATGAGTGTTATACCATGA 58.787 33.333 0.00 0.00 40.64 3.07
1781 2051 9.227777 CATCATCAATGAGTGTTATACCATGAT 57.772 33.333 0.00 0.00 40.64 2.45
1782 2052 9.803507 ATCATCAATGAGTGTTATACCATGATT 57.196 29.630 0.00 0.00 40.64 2.57
1783 2053 9.631257 TCATCAATGAGTGTTATACCATGATTT 57.369 29.630 0.00 0.00 32.11 2.17
1877 2147 9.341899 CAATGTTACCACTTTTAGAAATGTAGC 57.658 33.333 0.00 0.00 0.00 3.58
1878 2148 8.630054 ATGTTACCACTTTTAGAAATGTAGCA 57.370 30.769 0.00 0.00 0.00 3.49
1879 2149 8.453238 TGTTACCACTTTTAGAAATGTAGCAA 57.547 30.769 0.00 0.00 0.00 3.91
1880 2150 8.904834 TGTTACCACTTTTAGAAATGTAGCAAA 58.095 29.630 0.00 0.00 0.00 3.68
1881 2151 9.738832 GTTACCACTTTTAGAAATGTAGCAAAA 57.261 29.630 0.00 0.00 0.00 2.44
1883 2153 8.642908 ACCACTTTTAGAAATGTAGCAAAAAC 57.357 30.769 0.00 0.00 0.00 2.43
1884 2154 8.254508 ACCACTTTTAGAAATGTAGCAAAAACA 58.745 29.630 0.00 0.00 0.00 2.83
1885 2155 9.092876 CCACTTTTAGAAATGTAGCAAAAACAA 57.907 29.630 0.00 0.00 0.00 2.83
1948 2218 8.224389 AGCATTACTATACATTTGTTCATGCA 57.776 30.769 0.00 0.00 34.43 3.96
1949 2219 8.131100 AGCATTACTATACATTTGTTCATGCAC 58.869 33.333 0.00 0.00 34.43 4.57
1950 2220 8.131100 GCATTACTATACATTTGTTCATGCACT 58.869 33.333 0.00 0.00 33.30 4.40
1957 2227 6.843069 ACATTTGTTCATGCACTTTAAACC 57.157 33.333 0.00 0.00 0.00 3.27
1958 2228 6.344500 ACATTTGTTCATGCACTTTAAACCA 58.656 32.000 0.00 0.00 0.00 3.67
1959 2229 6.820656 ACATTTGTTCATGCACTTTAAACCAA 59.179 30.769 0.00 0.00 0.00 3.67
1960 2230 7.498570 ACATTTGTTCATGCACTTTAAACCAAT 59.501 29.630 0.00 0.00 0.00 3.16
1961 2231 7.475771 TTTGTTCATGCACTTTAAACCAATC 57.524 32.000 0.00 0.00 0.00 2.67
1962 2232 6.403866 TGTTCATGCACTTTAAACCAATCT 57.596 33.333 0.00 0.00 0.00 2.40
1963 2233 6.815089 TGTTCATGCACTTTAAACCAATCTT 58.185 32.000 0.00 0.00 0.00 2.40
1964 2234 7.271511 TGTTCATGCACTTTAAACCAATCTTT 58.728 30.769 0.00 0.00 0.00 2.52
1965 2235 7.437862 TGTTCATGCACTTTAAACCAATCTTTC 59.562 33.333 0.00 0.00 0.00 2.62
1966 2236 6.454795 TCATGCACTTTAAACCAATCTTTCC 58.545 36.000 0.00 0.00 0.00 3.13
1967 2237 5.860941 TGCACTTTAAACCAATCTTTCCA 57.139 34.783 0.00 0.00 0.00 3.53
1968 2238 5.596845 TGCACTTTAAACCAATCTTTCCAC 58.403 37.500 0.00 0.00 0.00 4.02
1969 2239 5.127845 TGCACTTTAAACCAATCTTTCCACA 59.872 36.000 0.00 0.00 0.00 4.17
1970 2240 5.691754 GCACTTTAAACCAATCTTTCCACAG 59.308 40.000 0.00 0.00 0.00 3.66
1971 2241 5.691754 CACTTTAAACCAATCTTTCCACAGC 59.308 40.000 0.00 0.00 0.00 4.40
1972 2242 4.864704 TTAAACCAATCTTTCCACAGCC 57.135 40.909 0.00 0.00 0.00 4.85
1973 2243 2.380064 AACCAATCTTTCCACAGCCA 57.620 45.000 0.00 0.00 0.00 4.75
1974 2244 1.915141 ACCAATCTTTCCACAGCCAG 58.085 50.000 0.00 0.00 0.00 4.85
1975 2245 1.425066 ACCAATCTTTCCACAGCCAGA 59.575 47.619 0.00 0.00 0.00 3.86
1976 2246 2.158475 ACCAATCTTTCCACAGCCAGAA 60.158 45.455 0.00 0.00 0.00 3.02
1977 2247 2.892852 CCAATCTTTCCACAGCCAGAAA 59.107 45.455 0.00 0.00 0.00 2.52
1978 2248 3.321682 CCAATCTTTCCACAGCCAGAAAA 59.678 43.478 0.00 0.00 31.91 2.29
1979 2249 4.202243 CCAATCTTTCCACAGCCAGAAAAA 60.202 41.667 0.00 0.00 31.91 1.94
2133 2403 4.558697 CGTCCGCATATATGAACTTGAGGA 60.559 45.833 17.10 3.60 35.99 3.71
2157 2427 7.656137 GGAAAACACATCTAGAACAGTCACTAA 59.344 37.037 0.00 0.00 0.00 2.24
2215 2485 4.321750 CGTAGGACAGAAACTAGAGCCAAA 60.322 45.833 0.00 0.00 0.00 3.28
2262 2532 1.337821 GAGAAGAACACGTACGGCAG 58.662 55.000 21.06 11.42 0.00 4.85
2324 2596 2.105128 CCATGTCGTCGAGGAGGC 59.895 66.667 8.30 0.00 0.00 4.70
2351 2623 2.506438 CGGGGAAGAAGTCGTCGC 60.506 66.667 3.27 3.27 36.78 5.19
2443 2715 5.325239 CAAAAACCTTATCACCCTTCTCCT 58.675 41.667 0.00 0.00 0.00 3.69
2551 2825 2.789917 GCGCAGTGCTCAGGAATG 59.210 61.111 14.33 0.00 41.73 2.67
2557 2831 1.064906 CAGTGCTCAGGAATGGATGGT 60.065 52.381 0.00 0.00 0.00 3.55
2971 3299 2.203480 ACAAATGGGCTGCGTGGT 60.203 55.556 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 4.814294 ATCAGGTTCGTCGCCCGC 62.814 66.667 0.00 0.00 36.19 6.13
55 56 1.296056 AAAATCAGGTTCGTCGCCCG 61.296 55.000 0.00 0.00 38.13 6.13
56 57 0.879090 AAAAATCAGGTTCGTCGCCC 59.121 50.000 0.00 0.00 0.00 6.13
57 58 1.135774 GGAAAAATCAGGTTCGTCGCC 60.136 52.381 0.00 0.00 0.00 5.54
58 59 1.135774 GGGAAAAATCAGGTTCGTCGC 60.136 52.381 0.00 0.00 0.00 5.19
59 60 2.415512 GAGGGAAAAATCAGGTTCGTCG 59.584 50.000 0.00 0.00 0.00 5.12
60 61 2.747989 GGAGGGAAAAATCAGGTTCGTC 59.252 50.000 0.00 0.00 0.00 4.20
61 62 2.554564 GGGAGGGAAAAATCAGGTTCGT 60.555 50.000 0.00 0.00 0.00 3.85
62 63 2.092323 GGGAGGGAAAAATCAGGTTCG 58.908 52.381 0.00 0.00 0.00 3.95
63 64 2.092323 CGGGAGGGAAAAATCAGGTTC 58.908 52.381 0.00 0.00 0.00 3.62
64 65 1.891011 GCGGGAGGGAAAAATCAGGTT 60.891 52.381 0.00 0.00 0.00 3.50
65 66 0.323451 GCGGGAGGGAAAAATCAGGT 60.323 55.000 0.00 0.00 0.00 4.00
66 67 2.493547 GCGGGAGGGAAAAATCAGG 58.506 57.895 0.00 0.00 0.00 3.86
83 84 2.419100 TATTTATCCGTTGCGCGCGC 62.419 55.000 45.02 45.02 39.71 6.86
84 85 0.448861 CTATTTATCCGTTGCGCGCG 60.449 55.000 28.44 28.44 39.71 6.86
85 86 0.856641 TCTATTTATCCGTTGCGCGC 59.143 50.000 27.26 27.26 39.71 6.86
86 87 1.455786 CCTCTATTTATCCGTTGCGCG 59.544 52.381 0.00 0.00 40.95 6.86
87 88 2.480845 ACCTCTATTTATCCGTTGCGC 58.519 47.619 0.00 0.00 0.00 6.09
88 89 3.247648 CCAACCTCTATTTATCCGTTGCG 59.752 47.826 0.00 0.00 31.45 4.85
89 90 3.564225 CCCAACCTCTATTTATCCGTTGC 59.436 47.826 0.00 0.00 31.45 4.17
90 91 4.134563 CCCCAACCTCTATTTATCCGTTG 58.865 47.826 0.00 0.00 0.00 4.10
91 92 3.784202 ACCCCAACCTCTATTTATCCGTT 59.216 43.478 0.00 0.00 0.00 4.44
92 93 3.390819 ACCCCAACCTCTATTTATCCGT 58.609 45.455 0.00 0.00 0.00 4.69
93 94 4.134563 CAACCCCAACCTCTATTTATCCG 58.865 47.826 0.00 0.00 0.00 4.18
94 95 5.125367 ACAACCCCAACCTCTATTTATCC 57.875 43.478 0.00 0.00 0.00 2.59
95 96 6.096423 GGAAACAACCCCAACCTCTATTTATC 59.904 42.308 0.00 0.00 0.00 1.75
96 97 5.955959 GGAAACAACCCCAACCTCTATTTAT 59.044 40.000 0.00 0.00 0.00 1.40
97 98 5.326900 GGAAACAACCCCAACCTCTATTTA 58.673 41.667 0.00 0.00 0.00 1.40
98 99 4.157246 GGAAACAACCCCAACCTCTATTT 58.843 43.478 0.00 0.00 0.00 1.40
99 100 3.501568 GGGAAACAACCCCAACCTCTATT 60.502 47.826 0.00 0.00 43.81 1.73
100 101 2.042569 GGGAAACAACCCCAACCTCTAT 59.957 50.000 0.00 0.00 43.81 1.98
101 102 1.426215 GGGAAACAACCCCAACCTCTA 59.574 52.381 0.00 0.00 43.81 2.43
102 103 0.187606 GGGAAACAACCCCAACCTCT 59.812 55.000 0.00 0.00 43.81 3.69
103 104 2.741433 GGGAAACAACCCCAACCTC 58.259 57.895 0.00 0.00 43.81 3.85
111 112 1.037493 GTTGGAGTGGGGAAACAACC 58.963 55.000 0.00 0.00 36.37 3.77
112 113 1.037493 GGTTGGAGTGGGGAAACAAC 58.963 55.000 0.00 0.00 40.35 3.32
113 114 0.105913 GGGTTGGAGTGGGGAAACAA 60.106 55.000 0.00 0.00 0.00 2.83
114 115 0.996762 AGGGTTGGAGTGGGGAAACA 60.997 55.000 0.00 0.00 0.00 2.83
115 116 0.251209 GAGGGTTGGAGTGGGGAAAC 60.251 60.000 0.00 0.00 0.00 2.78
116 117 0.699577 TGAGGGTTGGAGTGGGGAAA 60.700 55.000 0.00 0.00 0.00 3.13
117 118 1.073319 TGAGGGTTGGAGTGGGGAA 60.073 57.895 0.00 0.00 0.00 3.97
118 119 1.538876 CTGAGGGTTGGAGTGGGGA 60.539 63.158 0.00 0.00 0.00 4.81
119 120 1.427072 AACTGAGGGTTGGAGTGGGG 61.427 60.000 0.00 0.00 36.70 4.96
120 121 0.478507 AAACTGAGGGTTGGAGTGGG 59.521 55.000 0.00 0.00 38.29 4.61
121 122 2.364972 AAAACTGAGGGTTGGAGTGG 57.635 50.000 0.00 0.00 38.29 4.00
122 123 4.319177 CTCTAAAACTGAGGGTTGGAGTG 58.681 47.826 3.61 0.00 38.29 3.51
123 124 3.328050 CCTCTAAAACTGAGGGTTGGAGT 59.672 47.826 8.96 0.00 45.39 3.85
124 125 3.944087 CCTCTAAAACTGAGGGTTGGAG 58.056 50.000 2.09 4.49 45.39 3.86
132 133 2.834549 TCTCCCAGCCTCTAAAACTGAG 59.165 50.000 0.00 0.00 33.10 3.35
133 134 2.834549 CTCTCCCAGCCTCTAAAACTGA 59.165 50.000 0.00 0.00 33.10 3.41
134 135 2.679349 GCTCTCCCAGCCTCTAAAACTG 60.679 54.545 0.00 0.00 43.17 3.16
135 136 1.557371 GCTCTCCCAGCCTCTAAAACT 59.443 52.381 0.00 0.00 43.17 2.66
136 137 1.740718 CGCTCTCCCAGCCTCTAAAAC 60.741 57.143 0.00 0.00 46.74 2.43
137 138 0.537188 CGCTCTCCCAGCCTCTAAAA 59.463 55.000 0.00 0.00 46.74 1.52
138 139 0.324368 TCGCTCTCCCAGCCTCTAAA 60.324 55.000 0.00 0.00 46.74 1.85
139 140 1.038130 GTCGCTCTCCCAGCCTCTAA 61.038 60.000 0.00 0.00 46.74 2.10
140 141 1.454111 GTCGCTCTCCCAGCCTCTA 60.454 63.158 0.00 0.00 46.74 2.43
141 142 2.757917 GTCGCTCTCCCAGCCTCT 60.758 66.667 0.00 0.00 46.74 3.69
142 143 3.844090 GGTCGCTCTCCCAGCCTC 61.844 72.222 0.00 0.00 46.74 4.70
153 154 3.459063 GTTAGAGCCCGGGTCGCT 61.459 66.667 24.63 22.34 39.95 4.93
154 155 4.525949 GGTTAGAGCCCGGGTCGC 62.526 72.222 24.63 16.21 35.00 5.19
155 156 3.846430 GGGTTAGAGCCCGGGTCG 61.846 72.222 24.63 0.00 39.17 4.79
180 181 8.011883 ACCCTTTAATCCCTAAACCTGTAAAAA 58.988 33.333 0.00 0.00 0.00 1.94
181 182 7.537513 ACCCTTTAATCCCTAAACCTGTAAAA 58.462 34.615 0.00 0.00 0.00 1.52
182 183 7.106204 ACCCTTTAATCCCTAAACCTGTAAA 57.894 36.000 0.00 0.00 0.00 2.01
183 184 6.723471 ACCCTTTAATCCCTAAACCTGTAA 57.277 37.500 0.00 0.00 0.00 2.41
184 185 6.506413 AGAACCCTTTAATCCCTAAACCTGTA 59.494 38.462 0.00 0.00 0.00 2.74
185 186 5.315109 AGAACCCTTTAATCCCTAAACCTGT 59.685 40.000 0.00 0.00 0.00 4.00
186 187 5.827756 AGAACCCTTTAATCCCTAAACCTG 58.172 41.667 0.00 0.00 0.00 4.00
187 188 6.739042 ACTAGAACCCTTTAATCCCTAAACCT 59.261 38.462 0.00 0.00 0.00 3.50
188 189 6.966751 ACTAGAACCCTTTAATCCCTAAACC 58.033 40.000 0.00 0.00 0.00 3.27
189 190 7.859540 AGACTAGAACCCTTTAATCCCTAAAC 58.140 38.462 0.00 0.00 0.00 2.01
190 191 8.458951 AAGACTAGAACCCTTTAATCCCTAAA 57.541 34.615 0.00 0.00 0.00 1.85
191 192 8.326529 CAAAGACTAGAACCCTTTAATCCCTAA 58.673 37.037 0.00 0.00 0.00 2.69
192 193 7.582828 GCAAAGACTAGAACCCTTTAATCCCTA 60.583 40.741 0.00 0.00 0.00 3.53
193 194 6.722328 CAAAGACTAGAACCCTTTAATCCCT 58.278 40.000 0.00 0.00 0.00 4.20
194 195 5.357314 GCAAAGACTAGAACCCTTTAATCCC 59.643 44.000 0.00 0.00 0.00 3.85
195 196 5.064834 CGCAAAGACTAGAACCCTTTAATCC 59.935 44.000 0.00 0.00 0.00 3.01
196 197 5.642491 ACGCAAAGACTAGAACCCTTTAATC 59.358 40.000 0.00 0.00 0.00 1.75
197 198 5.557866 ACGCAAAGACTAGAACCCTTTAAT 58.442 37.500 0.00 0.00 0.00 1.40
198 199 4.964593 ACGCAAAGACTAGAACCCTTTAA 58.035 39.130 0.00 0.00 0.00 1.52
199 200 4.612264 ACGCAAAGACTAGAACCCTTTA 57.388 40.909 0.00 0.00 0.00 1.85
200 201 3.487120 ACGCAAAGACTAGAACCCTTT 57.513 42.857 0.00 0.00 0.00 3.11
201 202 3.487120 AACGCAAAGACTAGAACCCTT 57.513 42.857 0.00 0.00 0.00 3.95
202 203 3.487120 AAACGCAAAGACTAGAACCCT 57.513 42.857 0.00 0.00 0.00 4.34
203 204 4.563337 AAAAACGCAAAGACTAGAACCC 57.437 40.909 0.00 0.00 0.00 4.11
241 242 5.284861 ACCCTCAAAAATAACCGCTTTTT 57.715 34.783 0.00 0.00 36.50 1.94
242 243 4.948341 ACCCTCAAAAATAACCGCTTTT 57.052 36.364 0.00 0.00 0.00 2.27
243 244 4.948341 AACCCTCAAAAATAACCGCTTT 57.052 36.364 0.00 0.00 0.00 3.51
244 245 4.342665 TCAAACCCTCAAAAATAACCGCTT 59.657 37.500 0.00 0.00 0.00 4.68
245 246 3.892588 TCAAACCCTCAAAAATAACCGCT 59.107 39.130 0.00 0.00 0.00 5.52
246 247 4.234574 CTCAAACCCTCAAAAATAACCGC 58.765 43.478 0.00 0.00 0.00 5.68
247 248 4.321675 CCCTCAAACCCTCAAAAATAACCG 60.322 45.833 0.00 0.00 0.00 4.44
248 249 4.591498 ACCCTCAAACCCTCAAAAATAACC 59.409 41.667 0.00 0.00 0.00 2.85
249 250 5.801531 ACCCTCAAACCCTCAAAAATAAC 57.198 39.130 0.00 0.00 0.00 1.89
250 251 6.384305 TCAAACCCTCAAACCCTCAAAAATAA 59.616 34.615 0.00 0.00 0.00 1.40
251 252 5.900123 TCAAACCCTCAAACCCTCAAAAATA 59.100 36.000 0.00 0.00 0.00 1.40
252 253 4.719273 TCAAACCCTCAAACCCTCAAAAAT 59.281 37.500 0.00 0.00 0.00 1.82
253 254 4.097418 TCAAACCCTCAAACCCTCAAAAA 58.903 39.130 0.00 0.00 0.00 1.94
254 255 3.704061 CTCAAACCCTCAAACCCTCAAAA 59.296 43.478 0.00 0.00 0.00 2.44
255 256 3.295973 CTCAAACCCTCAAACCCTCAAA 58.704 45.455 0.00 0.00 0.00 2.69
256 257 2.424234 CCTCAAACCCTCAAACCCTCAA 60.424 50.000 0.00 0.00 0.00 3.02
257 258 1.144913 CCTCAAACCCTCAAACCCTCA 59.855 52.381 0.00 0.00 0.00 3.86
258 259 1.547901 CCCTCAAACCCTCAAACCCTC 60.548 57.143 0.00 0.00 0.00 4.30
259 260 0.482887 CCCTCAAACCCTCAAACCCT 59.517 55.000 0.00 0.00 0.00 4.34
260 261 0.187606 ACCCTCAAACCCTCAAACCC 59.812 55.000 0.00 0.00 0.00 4.11
261 262 2.107726 AGTACCCTCAAACCCTCAAACC 59.892 50.000 0.00 0.00 0.00 3.27
262 263 3.503800 AGTACCCTCAAACCCTCAAAC 57.496 47.619 0.00 0.00 0.00 2.93
263 264 4.237018 AGTAGTACCCTCAAACCCTCAAA 58.763 43.478 0.00 0.00 0.00 2.69
264 265 3.865571 AGTAGTACCCTCAAACCCTCAA 58.134 45.455 0.00 0.00 0.00 3.02
265 266 3.555117 AGTAGTACCCTCAAACCCTCA 57.445 47.619 0.00 0.00 0.00 3.86
266 267 4.608269 ACTAGTAGTACCCTCAAACCCTC 58.392 47.826 0.00 0.00 0.00 4.30
267 268 4.689014 ACTAGTAGTACCCTCAAACCCT 57.311 45.455 0.00 0.00 0.00 4.34
268 269 6.684865 GCATTACTAGTAGTACCCTCAAACCC 60.685 46.154 9.62 0.00 28.93 4.11
269 270 6.097981 AGCATTACTAGTAGTACCCTCAAACC 59.902 42.308 9.62 0.00 28.93 3.27
270 271 7.110043 AGCATTACTAGTAGTACCCTCAAAC 57.890 40.000 9.62 0.00 28.93 2.93
271 272 7.729124 AAGCATTACTAGTAGTACCCTCAAA 57.271 36.000 9.62 0.00 28.93 2.69
272 273 7.729124 AAAGCATTACTAGTAGTACCCTCAA 57.271 36.000 9.62 0.00 28.93 3.02
273 274 7.729124 AAAAGCATTACTAGTAGTACCCTCA 57.271 36.000 9.62 0.00 28.93 3.86
274 275 9.526713 GTTAAAAGCATTACTAGTAGTACCCTC 57.473 37.037 9.62 0.72 28.93 4.30
275 276 9.039165 TGTTAAAAGCATTACTAGTAGTACCCT 57.961 33.333 9.62 4.06 28.93 4.34
276 277 9.828039 ATGTTAAAAGCATTACTAGTAGTACCC 57.172 33.333 9.62 1.92 28.93 3.69
287 288 9.207042 GCGTAACTAAGATGTTAAAAGCATTAC 57.793 33.333 0.00 0.00 34.67 1.89
288 289 9.158233 AGCGTAACTAAGATGTTAAAAGCATTA 57.842 29.630 0.00 0.00 34.67 1.90
289 290 8.040716 AGCGTAACTAAGATGTTAAAAGCATT 57.959 30.769 0.00 0.00 34.67 3.56
290 291 7.201617 GGAGCGTAACTAAGATGTTAAAAGCAT 60.202 37.037 0.00 0.00 34.67 3.79
291 292 6.091713 GGAGCGTAACTAAGATGTTAAAAGCA 59.908 38.462 0.00 0.00 34.67 3.91
292 293 6.313164 AGGAGCGTAACTAAGATGTTAAAAGC 59.687 38.462 0.00 0.00 34.67 3.51
296 297 7.201767 GGTCTAGGAGCGTAACTAAGATGTTAA 60.202 40.741 0.00 0.00 34.67 2.01
310 311 1.134670 GCTTCAATGGTCTAGGAGCGT 60.135 52.381 0.00 0.00 32.15 5.07
313 314 7.284034 ACAATATTTGCTTCAATGGTCTAGGAG 59.716 37.037 0.00 0.00 0.00 3.69
381 382 3.910627 ACCATACTCAAGGGTTGTCTTCT 59.089 43.478 0.00 0.00 0.00 2.85
397 398 0.392060 GGTCGACCAACCCACCATAC 60.392 60.000 29.75 0.00 35.64 2.39
405 406 2.551032 CTGTAAAAAGGGTCGACCAACC 59.449 50.000 34.40 18.34 43.89 3.77
406 407 3.208594 ACTGTAAAAAGGGTCGACCAAC 58.791 45.455 34.40 19.09 43.89 3.77
407 408 3.564053 ACTGTAAAAAGGGTCGACCAA 57.436 42.857 34.40 10.52 43.89 3.67
411 445 4.339872 TGCTAACTGTAAAAAGGGTCGA 57.660 40.909 0.00 0.00 0.00 4.20
412 446 4.454504 ACATGCTAACTGTAAAAAGGGTCG 59.545 41.667 0.00 0.00 0.00 4.79
560 601 5.163683 CCATGGTCAAGTCAATCATGAGTTC 60.164 44.000 2.57 0.00 45.36 3.01
641 682 3.055819 GTCAGTCATGAGGCTTCCACTAA 60.056 47.826 0.00 0.00 35.66 2.24
665 706 0.531974 TTGCACCGAGTGTCCAAGTC 60.532 55.000 6.02 0.00 35.75 3.01
666 707 0.107410 TTTGCACCGAGTGTCCAAGT 60.107 50.000 6.02 0.00 35.75 3.16
667 708 0.588252 CTTTGCACCGAGTGTCCAAG 59.412 55.000 6.02 3.16 35.75 3.61
668 709 1.444119 GCTTTGCACCGAGTGTCCAA 61.444 55.000 6.02 1.08 35.75 3.53
677 718 0.592637 TTGAGTGATGCTTTGCACCG 59.407 50.000 0.00 0.00 43.04 4.94
682 723 3.190118 GGAGGACTTTGAGTGATGCTTTG 59.810 47.826 0.00 0.00 0.00 2.77
732 773 3.891366 GGCAGGCAGTATACCATGAAAAT 59.109 43.478 0.00 0.00 0.00 1.82
800 850 4.564782 TCAAATTCAGATCAGGACAGCT 57.435 40.909 0.00 0.00 0.00 4.24
809 859 3.033184 TGGGGCCAATCAAATTCAGATC 58.967 45.455 4.39 0.00 0.00 2.75
826 876 0.394216 TCACTGCGATCCATTTGGGG 60.394 55.000 0.00 0.00 37.22 4.96
840 890 6.558771 TTTGGATTATGCGGAATATCACTG 57.441 37.500 4.50 0.00 0.00 3.66
905 982 1.535636 CTCACGCGCTCTGCTATTCG 61.536 60.000 5.73 0.00 43.27 3.34
980 1167 5.255710 TCTGCTATTCGAAGAAGGAAGAG 57.744 43.478 3.35 0.00 45.90 2.85
1019 1219 0.850883 AGGGGAGGCATGGGAAAGAA 60.851 55.000 0.00 0.00 0.00 2.52
1209 1424 0.616891 GGTGGTGTTCCGGGACTTAT 59.383 55.000 15.59 0.00 36.30 1.73
1359 1595 2.485426 ACAATGACAAGATTGCCGTCAG 59.515 45.455 0.00 0.00 42.53 3.51
1441 1693 4.023193 GTGTTTATGCTACTGGCTTGTGTT 60.023 41.667 0.00 0.00 42.39 3.32
1476 1728 3.395210 TTCAAGAGAACAGCGGCAA 57.605 47.368 1.45 0.00 0.00 4.52
1551 1821 1.419374 CGCGATATCTGTTGGGTAGC 58.581 55.000 0.00 0.00 0.00 3.58
1584 1854 1.856265 GACTTTGTCCCAGCCAAGCG 61.856 60.000 0.00 0.00 0.00 4.68
1595 1865 3.001330 CGACTGAAACCAGTGACTTTGTC 59.999 47.826 2.50 0.00 44.34 3.18
1600 1870 0.464036 TGCGACTGAAACCAGTGACT 59.536 50.000 2.50 0.00 44.34 3.41
1855 2125 9.738832 TTTTGCTACATTTCTAAAAGTGGTAAC 57.261 29.630 0.00 0.00 27.09 2.50
1857 2127 9.738832 GTTTTTGCTACATTTCTAAAAGTGGTA 57.261 29.630 0.00 0.00 0.00 3.25
1858 2128 8.254508 TGTTTTTGCTACATTTCTAAAAGTGGT 58.745 29.630 0.00 0.00 0.00 4.16
1859 2129 8.641499 TGTTTTTGCTACATTTCTAAAAGTGG 57.359 30.769 0.00 0.00 0.00 4.00
1922 2192 9.336171 TGCATGAACAAATGTATAGTAATGCTA 57.664 29.630 0.00 0.00 36.86 3.49
1923 2193 8.131100 GTGCATGAACAAATGTATAGTAATGCT 58.869 33.333 0.00 0.00 36.86 3.79
1924 2194 8.131100 AGTGCATGAACAAATGTATAGTAATGC 58.869 33.333 6.60 0.00 36.65 3.56
1931 2201 9.632807 GGTTTAAAGTGCATGAACAAATGTATA 57.367 29.630 6.60 0.00 0.00 1.47
1932 2202 8.147058 TGGTTTAAAGTGCATGAACAAATGTAT 58.853 29.630 6.60 0.00 0.00 2.29
1933 2203 7.492524 TGGTTTAAAGTGCATGAACAAATGTA 58.507 30.769 6.60 0.00 0.00 2.29
1934 2204 6.344500 TGGTTTAAAGTGCATGAACAAATGT 58.656 32.000 6.60 0.00 0.00 2.71
1935 2205 6.841443 TGGTTTAAAGTGCATGAACAAATG 57.159 33.333 6.60 0.00 0.00 2.32
1936 2206 7.933033 AGATTGGTTTAAAGTGCATGAACAAAT 59.067 29.630 6.60 0.14 0.00 2.32
1937 2207 7.271511 AGATTGGTTTAAAGTGCATGAACAAA 58.728 30.769 6.60 0.00 0.00 2.83
1938 2208 6.815089 AGATTGGTTTAAAGTGCATGAACAA 58.185 32.000 6.60 0.00 0.00 2.83
1939 2209 6.403866 AGATTGGTTTAAAGTGCATGAACA 57.596 33.333 6.60 0.00 0.00 3.18
1940 2210 7.095649 GGAAAGATTGGTTTAAAGTGCATGAAC 60.096 37.037 0.00 0.00 0.00 3.18
1941 2211 6.928492 GGAAAGATTGGTTTAAAGTGCATGAA 59.072 34.615 0.00 0.00 0.00 2.57
1942 2212 6.041409 TGGAAAGATTGGTTTAAAGTGCATGA 59.959 34.615 0.00 0.00 0.00 3.07
1943 2213 6.146021 GTGGAAAGATTGGTTTAAAGTGCATG 59.854 38.462 0.00 0.00 0.00 4.06
1944 2214 6.183360 TGTGGAAAGATTGGTTTAAAGTGCAT 60.183 34.615 0.00 0.00 0.00 3.96
1945 2215 5.127845 TGTGGAAAGATTGGTTTAAAGTGCA 59.872 36.000 0.00 0.00 0.00 4.57
1946 2216 5.596845 TGTGGAAAGATTGGTTTAAAGTGC 58.403 37.500 0.00 0.00 0.00 4.40
1947 2217 5.691754 GCTGTGGAAAGATTGGTTTAAAGTG 59.308 40.000 0.00 0.00 0.00 3.16
1948 2218 5.221441 GGCTGTGGAAAGATTGGTTTAAAGT 60.221 40.000 0.00 0.00 0.00 2.66
1949 2219 5.221422 TGGCTGTGGAAAGATTGGTTTAAAG 60.221 40.000 0.00 0.00 0.00 1.85
1950 2220 4.651503 TGGCTGTGGAAAGATTGGTTTAAA 59.348 37.500 0.00 0.00 0.00 1.52
1951 2221 4.219115 TGGCTGTGGAAAGATTGGTTTAA 58.781 39.130 0.00 0.00 0.00 1.52
1952 2222 3.826157 CTGGCTGTGGAAAGATTGGTTTA 59.174 43.478 0.00 0.00 0.00 2.01
1953 2223 2.629617 CTGGCTGTGGAAAGATTGGTTT 59.370 45.455 0.00 0.00 0.00 3.27
1954 2224 2.158475 TCTGGCTGTGGAAAGATTGGTT 60.158 45.455 0.00 0.00 0.00 3.67
1955 2225 1.425066 TCTGGCTGTGGAAAGATTGGT 59.575 47.619 0.00 0.00 0.00 3.67
1956 2226 2.205022 TCTGGCTGTGGAAAGATTGG 57.795 50.000 0.00 0.00 0.00 3.16
1957 2227 4.589216 TTTTCTGGCTGTGGAAAGATTG 57.411 40.909 0.00 0.00 33.77 2.67
1983 2253 9.962809 TGCTCATATTTCCAACATATATCATGA 57.037 29.630 0.00 0.00 0.00 3.07
1991 2261 8.349245 CGGTAAATTGCTCATATTTCCAACATA 58.651 33.333 0.00 0.00 0.00 2.29
1992 2262 7.068103 TCGGTAAATTGCTCATATTTCCAACAT 59.932 33.333 0.00 0.00 0.00 2.71
2133 2403 8.958119 TTTAGTGACTGTTCTAGATGTGTTTT 57.042 30.769 0.00 0.00 0.00 2.43
2157 2427 6.558009 TCTACGTCGTATAAGCAACTTCATT 58.442 36.000 5.39 0.00 0.00 2.57
2215 2485 7.120923 TCTGTTAGAAGTCCTGTTACAGTTT 57.879 36.000 11.68 2.97 34.54 2.66
2262 2532 4.163319 GCGCTTCTGCTGCTGCTC 62.163 66.667 17.00 0.61 40.48 4.26
2351 2623 2.768492 CCGACGACTACTTCCCGGG 61.768 68.421 16.85 16.85 34.78 5.73
2443 2715 2.288213 CGCACTCTTTGAGTCCTGTACA 60.288 50.000 0.00 0.00 41.37 2.90
2551 2825 4.027437 ACTACTTCTTCCTCTCACCATCC 58.973 47.826 0.00 0.00 0.00 3.51
2557 2831 4.021016 GCAAGGAACTACTTCTTCCTCTCA 60.021 45.833 0.19 0.00 45.81 3.27


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

AutoCloner maintained by Alex Coulton.