Multiple sequence alignment - TraesCS3B01G015600

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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 TraesCS3B01G015600 chr3B 100.000 2955 0 0 1 2955 6405019 6407973 0.000000e+00 5457.0
1 TraesCS3B01G015600 chr3B 94.939 1956 60 12 353 2300 6336275 6338199 0.000000e+00 3027.0
2 TraesCS3B01G015600 chr3B 98.469 653 10 0 2303 2955 6412246 6412898 0.000000e+00 1151.0
3 TraesCS3B01G015600 chr3B 86.047 602 69 10 1703 2300 6533859 6534449 1.490000e-177 632.0
4 TraesCS3B01G015600 chr3B 84.431 668 51 24 335 978 6467853 6468491 2.520000e-170 608.0
5 TraesCS3B01G015600 chr3B 84.550 589 66 15 1535 2114 6469700 6470272 7.150000e-156 560.0
6 TraesCS3B01G015600 chr3B 96.167 287 11 0 47 333 173322538 173322824 1.240000e-128 470.0
7 TraesCS3B01G015600 chr3B 92.759 290 17 4 47 333 225170945 225171233 1.640000e-112 416.0
8 TraesCS3B01G015600 chr3B 87.366 372 33 9 335 695 6532288 6532656 5.890000e-112 414.0
9 TraesCS3B01G015600 chr3B 89.965 289 27 1 47 333 423798102 423798390 3.600000e-99 372.0
10 TraesCS3B01G015600 chr3B 89.583 288 25 2 47 333 370147923 370148206 7.790000e-96 361.0
11 TraesCS3B01G015600 chr3B 90.000 230 23 0 974 1203 6532984 6533213 6.190000e-77 298.0
12 TraesCS3B01G015600 chr3B 91.975 162 9 3 1260 1420 6468972 6469130 1.070000e-54 224.0
13 TraesCS3B01G015600 chr3B 87.363 182 19 4 1456 1635 6533668 6533847 3.860000e-49 206.0
14 TraesCS3B01G015600 chr3B 93.000 100 7 0 1288 1387 6533298 6533397 2.370000e-31 147.0
15 TraesCS3B01G015600 chr3B 93.750 48 3 0 2118 2165 6470346 6470393 4.090000e-09 73.1
16 TraesCS3B01G015600 chr3D 92.074 1779 95 11 335 2081 4111199 4112963 0.000000e+00 2462.0
17 TraesCS3B01G015600 chr3D 88.577 499 49 5 1623 2115 4134996 4135492 1.520000e-167 599.0
18 TraesCS3B01G015600 chr3D 87.989 358 32 9 1622 1972 4139545 4139898 2.120000e-111 412.0
19 TraesCS3B01G015600 chr3D 92.334 287 18 3 47 331 153504623 153504907 3.550000e-109 405.0
20 TraesCS3B01G015600 chr3D 81.390 446 39 21 542 972 4133868 4134284 1.020000e-84 324.0
21 TraesCS3B01G015600 chr3D 91.743 218 18 0 986 1203 4134328 4134545 1.330000e-78 303.0
22 TraesCS3B01G015600 chr3D 89.565 230 24 0 974 1203 4138738 4138967 2.880000e-75 292.0
23 TraesCS3B01G015600 chr3D 86.782 174 13 6 1260 1423 4139172 4139345 5.030000e-43 185.0
24 TraesCS3B01G015600 chr3D 84.000 200 18 10 1439 1633 4134851 4135041 2.340000e-41 180.0
25 TraesCS3B01G015600 chr3D 86.301 146 10 5 1288 1423 4134647 4134792 1.830000e-32 150.0
26 TraesCS3B01G015600 chr3D 91.429 105 8 1 340 443 4138142 4138246 3.070000e-30 143.0
27 TraesCS3B01G015600 chr3D 80.769 156 24 4 351 500 355752105 355751950 1.860000e-22 117.0
28 TraesCS3B01G015600 chr3D 91.139 79 7 0 1455 1533 4139423 4139501 1.120000e-19 108.0
29 TraesCS3B01G015600 chr3D 92.105 76 4 2 2129 2204 4153386 4153459 4.030000e-19 106.0
30 TraesCS3B01G015600 chr3A 93.032 1105 61 7 335 1424 9627266 9628369 0.000000e+00 1600.0
31 TraesCS3B01G015600 chr3A 89.588 874 72 11 1437 2300 9630889 9631753 0.000000e+00 1092.0
32 TraesCS3B01G015600 chr3A 91.349 289 21 3 47 333 176156243 176155957 2.760000e-105 392.0
33 TraesCS3B01G015600 chr3A 81.429 140 21 3 351 485 329495928 329495789 3.110000e-20 110.0
34 TraesCS3B01G015600 chr4A 98.165 654 11 1 2303 2955 740983026 740982373 0.000000e+00 1140.0
35 TraesCS3B01G015600 chr4A 98.009 653 13 0 2303 2955 733517981 733517329 0.000000e+00 1134.0
36 TraesCS3B01G015600 chr4A 97.121 660 18 1 2297 2955 733522912 733522253 0.000000e+00 1112.0
37 TraesCS3B01G015600 chr2B 97.859 654 11 3 2303 2955 793822248 793821597 0.000000e+00 1127.0
38 TraesCS3B01G015600 chr2B 97.401 654 15 2 2303 2955 793817325 793816673 0.000000e+00 1112.0
39 TraesCS3B01G015600 chr2B 82.086 374 52 13 1009 1372 707377353 707377721 3.700000e-79 305.0
40 TraesCS3B01G015600 chr5B 97.409 656 14 2 2303 2955 517706535 517705880 0.000000e+00 1114.0
41 TraesCS3B01G015600 chr5B 97.099 655 13 3 2303 2955 517701607 517700957 0.000000e+00 1099.0
42 TraesCS3B01G015600 chr5B 92.833 293 14 5 47 333 590276109 590276400 4.560000e-113 418.0
43 TraesCS3B01G015600 chr1D 96.799 656 21 0 2300 2955 439348822 439349477 0.000000e+00 1096.0
44 TraesCS3B01G015600 chrUn 84.431 668 51 24 335 978 35827064 35827702 2.520000e-170 608.0
45 TraesCS3B01G015600 chrUn 84.550 589 66 15 1535 2114 35828911 35829483 7.150000e-156 560.0
46 TraesCS3B01G015600 chrUn 91.975 162 9 3 1260 1420 35828183 35828341 1.070000e-54 224.0
47 TraesCS3B01G015600 chrUn 93.750 48 3 0 2118 2165 35829557 35829604 4.090000e-09 73.1
48 TraesCS3B01G015600 chr4D 93.080 289 19 1 47 335 23479845 23479558 3.520000e-114 422.0
49 TraesCS3B01G015600 chr7D 89.153 295 27 2 47 336 385033451 385033157 2.160000e-96 363.0
50 TraesCS3B01G015600 chr2A 89.558 249 20 3 1717 1965 719994275 719994517 7.950000e-81 311.0
51 TraesCS3B01G015600 chr2A 89.231 195 21 0 1009 1203 719993378 719993572 8.180000e-61 244.0
52 TraesCS3B01G015600 chr2D 81.402 371 54 13 1010 1372 585860394 585860757 3.730000e-74 289.0
53 TraesCS3B01G015600 chr5A 88.393 112 13 0 1431 1542 699318673 699318784 5.140000e-28 135.0
54 TraesCS3B01G015600 chr5A 78.333 240 25 12 552 780 699313878 699314101 2.390000e-26 130.0


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 TraesCS3B01G015600 chr3B 6405019 6407973 2954 False 5457.000 5457 100.0000 1 2955 1 chr3B.!!$F2 2954
1 TraesCS3B01G015600 chr3B 6336275 6338199 1924 False 3027.000 3027 94.9390 353 2300 1 chr3B.!!$F1 1947
2 TraesCS3B01G015600 chr3B 6412246 6412898 652 False 1151.000 1151 98.4690 2303 2955 1 chr3B.!!$F3 652
3 TraesCS3B01G015600 chr3B 6467853 6470393 2540 False 366.275 608 88.6765 335 2165 4 chr3B.!!$F8 1830
4 TraesCS3B01G015600 chr3B 6532288 6534449 2161 False 339.400 632 88.7552 335 2300 5 chr3B.!!$F9 1965
5 TraesCS3B01G015600 chr3D 4111199 4112963 1764 False 2462.000 2462 92.0740 335 2081 1 chr3D.!!$F1 1746
6 TraesCS3B01G015600 chr3D 4133868 4139898 6030 False 269.600 599 87.8915 340 2115 10 chr3D.!!$F4 1775
7 TraesCS3B01G015600 chr3A 9627266 9631753 4487 False 1346.000 1600 91.3100 335 2300 2 chr3A.!!$F1 1965
8 TraesCS3B01G015600 chr4A 740982373 740983026 653 True 1140.000 1140 98.1650 2303 2955 1 chr4A.!!$R3 652
9 TraesCS3B01G015600 chr4A 733517329 733517981 652 True 1134.000 1134 98.0090 2303 2955 1 chr4A.!!$R1 652
10 TraesCS3B01G015600 chr4A 733522253 733522912 659 True 1112.000 1112 97.1210 2297 2955 1 chr4A.!!$R2 658
11 TraesCS3B01G015600 chr2B 793821597 793822248 651 True 1127.000 1127 97.8590 2303 2955 1 chr2B.!!$R2 652
12 TraesCS3B01G015600 chr2B 793816673 793817325 652 True 1112.000 1112 97.4010 2303 2955 1 chr2B.!!$R1 652
13 TraesCS3B01G015600 chr5B 517705880 517706535 655 True 1114.000 1114 97.4090 2303 2955 1 chr5B.!!$R2 652
14 TraesCS3B01G015600 chr5B 517700957 517701607 650 True 1099.000 1099 97.0990 2303 2955 1 chr5B.!!$R1 652
15 TraesCS3B01G015600 chr1D 439348822 439349477 655 False 1096.000 1096 96.7990 2300 2955 1 chr1D.!!$F1 655
16 TraesCS3B01G015600 chrUn 35827064 35829604 2540 False 366.275 608 88.6765 335 2165 4 chrUn.!!$F1 1830
17 TraesCS3B01G015600 chr2A 719993378 719994517 1139 False 277.500 311 89.3945 1009 1965 2 chr2A.!!$F1 956

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
215 216 0.035739 TCCGTGGCTGTTCCTTTACC 59.964 55.0 0.00 0.0 35.26 2.85 F
216 217 0.036306 CCGTGGCTGTTCCTTTACCT 59.964 55.0 0.00 0.0 35.26 3.08 F
253 254 0.170116 GTGTGTTGTGTGGTGGTGTG 59.830 55.0 0.00 0.0 0.00 3.82 F
269 270 0.383590 TGTGGTGTGGCGTTGAATTG 59.616 50.0 0.00 0.0 0.00 2.32 F
270 271 0.383949 GTGGTGTGGCGTTGAATTGT 59.616 50.0 0.00 0.0 0.00 2.71 F
1041 1186 0.459899 TGATCGTCGGGAGGATTGTG 59.540 55.0 5.46 0.0 36.22 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1041 1186 1.086634 AGTAGTAGACGACGTCGCCC 61.087 60.000 35.92 26.82 44.43 6.13 R
1232 1629 1.202245 TGCAACTCGTTGGTTGAAAGC 60.202 47.619 17.49 7.08 46.55 3.51 R
1237 1634 2.548057 ACTATGTGCAACTCGTTGGTTG 59.452 45.455 11.35 11.88 46.41 3.77 R
1331 1767 2.809601 CGTTCGGAAGGGTCGCTG 60.810 66.667 2.57 0.00 0.00 5.18 R
1635 4878 4.976116 AGACAGTTTTGTATTTTTGCGAGC 59.024 37.500 0.00 0.00 37.76 5.03 R
2406 6388 3.030291 TGTGCAAAGTCCAAAATGACCT 58.970 40.909 0.00 0.00 35.83 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 9.719355 AAAAGTTTACATAAATGAATTGGGGTC 57.281 29.630 0.00 0.00 0.00 4.46
48 49 7.418337 AGTTTACATAAATGAATTGGGGTCC 57.582 36.000 0.00 0.00 0.00 4.46
49 50 7.189087 AGTTTACATAAATGAATTGGGGTCCT 58.811 34.615 0.00 0.00 0.00 3.85
50 51 7.678171 AGTTTACATAAATGAATTGGGGTCCTT 59.322 33.333 0.00 0.00 0.00 3.36
51 52 7.654022 TTACATAAATGAATTGGGGTCCTTC 57.346 36.000 0.00 0.00 0.00 3.46
52 53 5.842339 ACATAAATGAATTGGGGTCCTTCT 58.158 37.500 0.00 0.00 0.00 2.85
53 54 6.263754 ACATAAATGAATTGGGGTCCTTCTT 58.736 36.000 0.00 0.00 0.00 2.52
54 55 6.155049 ACATAAATGAATTGGGGTCCTTCTTG 59.845 38.462 0.00 0.00 0.00 3.02
55 56 4.402616 AATGAATTGGGGTCCTTCTTGA 57.597 40.909 0.00 0.00 0.00 3.02
56 57 3.893753 TGAATTGGGGTCCTTCTTGAA 57.106 42.857 0.00 0.00 0.00 2.69
57 58 3.766545 TGAATTGGGGTCCTTCTTGAAG 58.233 45.455 3.55 3.55 0.00 3.02
58 59 2.907458 ATTGGGGTCCTTCTTGAAGG 57.093 50.000 20.21 20.21 41.35 3.46
59 60 0.112412 TTGGGGTCCTTCTTGAAGGC 59.888 55.000 21.16 16.24 39.80 4.35
60 61 1.377333 GGGGTCCTTCTTGAAGGCG 60.377 63.158 21.16 3.04 39.80 5.52
61 62 1.375326 GGGTCCTTCTTGAAGGCGT 59.625 57.895 21.16 0.00 39.80 5.68
62 63 0.673956 GGGTCCTTCTTGAAGGCGTC 60.674 60.000 21.16 14.26 39.80 5.19
63 64 1.014564 GGTCCTTCTTGAAGGCGTCG 61.015 60.000 21.16 1.77 39.80 5.12
64 65 0.319641 GTCCTTCTTGAAGGCGTCGT 60.320 55.000 21.16 0.00 39.80 4.34
65 66 0.038526 TCCTTCTTGAAGGCGTCGTC 60.039 55.000 21.16 0.00 39.80 4.20
66 67 1.344942 CCTTCTTGAAGGCGTCGTCG 61.345 60.000 15.43 0.00 40.37 5.12
67 68 0.663568 CTTCTTGAAGGCGTCGTCGT 60.664 55.000 3.66 0.00 39.49 4.34
68 69 0.937699 TTCTTGAAGGCGTCGTCGTG 60.938 55.000 3.66 0.00 39.49 4.35
69 70 2.355363 TTGAAGGCGTCGTCGTGG 60.355 61.111 3.66 0.00 39.49 4.94
71 72 4.719369 GAAGGCGTCGTCGTGGCT 62.719 66.667 3.66 9.73 43.62 4.75
72 73 3.332493 GAAGGCGTCGTCGTGGCTA 62.332 63.158 14.42 0.00 40.50 3.93
73 74 3.621892 AAGGCGTCGTCGTGGCTAC 62.622 63.158 14.42 0.00 40.50 3.58
74 75 4.112341 GGCGTCGTCGTGGCTACT 62.112 66.667 3.66 0.00 39.49 2.57
75 76 2.576317 GCGTCGTCGTGGCTACTC 60.576 66.667 3.66 0.00 39.49 2.59
76 77 3.036783 GCGTCGTCGTGGCTACTCT 62.037 63.158 3.66 0.00 39.49 3.24
77 78 1.060622 CGTCGTCGTGGCTACTCTC 59.939 63.158 0.00 0.00 0.00 3.20
78 79 1.428620 GTCGTCGTGGCTACTCTCC 59.571 63.158 0.00 0.00 0.00 3.71
79 80 1.025647 GTCGTCGTGGCTACTCTCCT 61.026 60.000 0.00 0.00 0.00 3.69
80 81 0.743701 TCGTCGTGGCTACTCTCCTC 60.744 60.000 0.00 0.00 0.00 3.71
81 82 1.716826 CGTCGTGGCTACTCTCCTCC 61.717 65.000 0.00 0.00 0.00 4.30
82 83 0.394625 GTCGTGGCTACTCTCCTCCT 60.395 60.000 0.00 0.00 0.00 3.69
83 84 0.331954 TCGTGGCTACTCTCCTCCTT 59.668 55.000 0.00 0.00 0.00 3.36
84 85 0.741915 CGTGGCTACTCTCCTCCTTC 59.258 60.000 0.00 0.00 0.00 3.46
85 86 0.741915 GTGGCTACTCTCCTCCTTCG 59.258 60.000 0.00 0.00 0.00 3.79
86 87 0.395862 TGGCTACTCTCCTCCTTCGG 60.396 60.000 0.00 0.00 0.00 4.30
87 88 0.106619 GGCTACTCTCCTCCTTCGGA 60.107 60.000 0.00 0.00 0.00 4.55
88 89 1.479757 GGCTACTCTCCTCCTTCGGAT 60.480 57.143 0.00 0.00 31.43 4.18
89 90 1.611491 GCTACTCTCCTCCTTCGGATG 59.389 57.143 0.00 0.00 31.43 3.51
90 91 2.235016 CTACTCTCCTCCTTCGGATGG 58.765 57.143 3.59 3.59 31.43 3.51
91 92 0.336737 ACTCTCCTCCTTCGGATGGT 59.663 55.000 9.49 0.00 31.43 3.55
92 93 1.036707 CTCTCCTCCTTCGGATGGTC 58.963 60.000 9.49 0.00 31.43 4.02
93 94 0.397254 TCTCCTCCTTCGGATGGTCC 60.397 60.000 9.49 0.00 31.43 4.46
94 95 0.687757 CTCCTCCTTCGGATGGTCCA 60.688 60.000 9.49 0.00 35.91 4.02
95 96 0.687757 TCCTCCTTCGGATGGTCCAG 60.688 60.000 9.49 0.95 35.91 3.86
96 97 1.690219 CCTCCTTCGGATGGTCCAGG 61.690 65.000 9.49 5.93 35.91 4.45
97 98 0.978146 CTCCTTCGGATGGTCCAGGT 60.978 60.000 9.49 0.00 35.91 4.00
98 99 1.221840 CCTTCGGATGGTCCAGGTG 59.778 63.158 0.00 0.00 35.91 4.00
99 100 1.264749 CCTTCGGATGGTCCAGGTGA 61.265 60.000 0.00 0.00 35.91 4.02
100 101 0.613260 CTTCGGATGGTCCAGGTGAA 59.387 55.000 0.00 0.18 35.91 3.18
101 102 1.003118 CTTCGGATGGTCCAGGTGAAA 59.997 52.381 0.00 0.00 35.91 2.69
102 103 1.060729 TCGGATGGTCCAGGTGAAAA 58.939 50.000 0.00 0.00 35.91 2.29
103 104 1.165270 CGGATGGTCCAGGTGAAAAC 58.835 55.000 0.00 0.00 35.91 2.43
104 105 1.545841 GGATGGTCCAGGTGAAAACC 58.454 55.000 0.00 0.00 36.28 3.27
105 106 1.203001 GGATGGTCCAGGTGAAAACCA 60.203 52.381 0.00 0.00 45.32 3.67
106 107 2.999185 ATGGTCCAGGTGAAAACCAT 57.001 45.000 4.21 4.21 45.08 3.55
107 108 1.993956 TGGTCCAGGTGAAAACCATG 58.006 50.000 0.00 0.00 36.88 3.66
108 109 1.496857 TGGTCCAGGTGAAAACCATGA 59.503 47.619 0.00 0.00 36.88 3.07
109 110 2.109834 TGGTCCAGGTGAAAACCATGAT 59.890 45.455 0.00 0.00 36.88 2.45
110 111 2.755103 GGTCCAGGTGAAAACCATGATC 59.245 50.000 0.00 0.00 0.00 2.92
111 112 2.755103 GTCCAGGTGAAAACCATGATCC 59.245 50.000 0.00 0.00 0.00 3.36
112 113 2.649312 TCCAGGTGAAAACCATGATCCT 59.351 45.455 0.00 0.00 0.00 3.24
113 114 3.075882 TCCAGGTGAAAACCATGATCCTT 59.924 43.478 0.00 0.00 0.00 3.36
114 115 3.834231 CCAGGTGAAAACCATGATCCTTT 59.166 43.478 0.00 0.00 0.00 3.11
115 116 4.322198 CCAGGTGAAAACCATGATCCTTTG 60.322 45.833 0.00 0.00 0.00 2.77
116 117 3.834231 AGGTGAAAACCATGATCCTTTGG 59.166 43.478 0.00 5.20 39.02 3.28
117 118 3.831911 GGTGAAAACCATGATCCTTTGGA 59.168 43.478 12.06 0.00 36.79 3.53
118 119 4.467438 GGTGAAAACCATGATCCTTTGGAT 59.533 41.667 12.06 0.00 46.28 3.41
125 126 2.510906 ATCCTTTGGATCGGGCGG 59.489 61.111 0.00 0.00 38.09 6.13
126 127 3.774599 ATCCTTTGGATCGGGCGGC 62.775 63.158 0.00 0.00 38.09 6.53
128 129 4.830765 CTTTGGATCGGGCGGCGA 62.831 66.667 12.98 4.27 0.00 5.54
147 148 3.723348 GGCGCTCCGGTGTTGTTC 61.723 66.667 7.64 0.00 0.00 3.18
148 149 2.665185 GCGCTCCGGTGTTGTTCT 60.665 61.111 0.00 0.00 0.00 3.01
149 150 2.668280 GCGCTCCGGTGTTGTTCTC 61.668 63.158 0.00 0.00 0.00 2.87
150 151 2.027625 CGCTCCGGTGTTGTTCTCC 61.028 63.158 0.00 0.00 0.00 3.71
151 152 1.371558 GCTCCGGTGTTGTTCTCCT 59.628 57.895 0.00 0.00 0.00 3.69
152 153 0.250338 GCTCCGGTGTTGTTCTCCTT 60.250 55.000 0.00 0.00 0.00 3.36
153 154 1.797025 CTCCGGTGTTGTTCTCCTTC 58.203 55.000 0.00 0.00 0.00 3.46
154 155 1.344763 CTCCGGTGTTGTTCTCCTTCT 59.655 52.381 0.00 0.00 0.00 2.85
155 156 1.766496 TCCGGTGTTGTTCTCCTTCTT 59.234 47.619 0.00 0.00 0.00 2.52
156 157 1.873591 CCGGTGTTGTTCTCCTTCTTG 59.126 52.381 0.00 0.00 0.00 3.02
157 158 2.484770 CCGGTGTTGTTCTCCTTCTTGA 60.485 50.000 0.00 0.00 0.00 3.02
158 159 3.202906 CGGTGTTGTTCTCCTTCTTGAA 58.797 45.455 0.00 0.00 0.00 2.69
159 160 3.625764 CGGTGTTGTTCTCCTTCTTGAAA 59.374 43.478 0.00 0.00 0.00 2.69
160 161 4.260784 CGGTGTTGTTCTCCTTCTTGAAAG 60.261 45.833 0.00 0.00 0.00 2.62
161 162 4.498177 GGTGTTGTTCTCCTTCTTGAAAGC 60.498 45.833 0.00 0.00 0.00 3.51
162 163 3.312421 TGTTGTTCTCCTTCTTGAAAGCG 59.688 43.478 0.00 0.00 0.00 4.68
163 164 1.873591 TGTTCTCCTTCTTGAAAGCGC 59.126 47.619 0.00 0.00 0.00 5.92
164 165 1.197949 GTTCTCCTTCTTGAAAGCGCC 59.802 52.381 2.29 0.00 0.00 6.53
165 166 0.670546 TCTCCTTCTTGAAAGCGCCG 60.671 55.000 2.29 0.00 0.00 6.46
166 167 0.951040 CTCCTTCTTGAAAGCGCCGT 60.951 55.000 2.29 0.00 0.00 5.68
167 168 0.949105 TCCTTCTTGAAAGCGCCGTC 60.949 55.000 2.29 1.53 0.00 4.79
168 169 0.951040 CCTTCTTGAAAGCGCCGTCT 60.951 55.000 2.29 0.00 0.00 4.18
169 170 0.868406 CTTCTTGAAAGCGCCGTCTT 59.132 50.000 2.29 0.00 0.00 3.01
170 171 0.586319 TTCTTGAAAGCGCCGTCTTG 59.414 50.000 2.29 0.00 0.00 3.02
171 172 0.249699 TCTTGAAAGCGCCGTCTTGA 60.250 50.000 2.29 1.74 0.00 3.02
172 173 0.586319 CTTGAAAGCGCCGTCTTGAA 59.414 50.000 2.29 0.00 0.00 2.69
173 174 0.586319 TTGAAAGCGCCGTCTTGAAG 59.414 50.000 2.29 0.00 0.00 3.02
174 175 1.227999 TGAAAGCGCCGTCTTGAAGG 61.228 55.000 2.29 0.00 0.00 3.46
180 181 3.393360 CCGTCTTGAAGGCCTCCT 58.607 61.111 5.23 0.00 33.87 3.69
181 182 1.219393 CCGTCTTGAAGGCCTCCTC 59.781 63.158 5.23 0.21 30.89 3.71
182 183 1.261238 CCGTCTTGAAGGCCTCCTCT 61.261 60.000 5.23 0.00 30.89 3.69
183 184 0.174617 CGTCTTGAAGGCCTCCTCTC 59.825 60.000 5.23 0.00 30.89 3.20
184 185 0.174617 GTCTTGAAGGCCTCCTCTCG 59.825 60.000 5.23 0.00 30.89 4.04
185 186 1.153469 CTTGAAGGCCTCCTCTCGC 60.153 63.158 5.23 0.00 30.89 5.03
186 187 2.585791 CTTGAAGGCCTCCTCTCGCC 62.586 65.000 5.23 0.00 46.09 5.54
192 193 3.591835 CCTCCTCTCGCCGAGCTC 61.592 72.222 9.77 2.73 38.49 4.09
193 194 2.826287 CTCCTCTCGCCGAGCTCA 60.826 66.667 15.40 0.00 38.49 4.26
194 195 2.826287 TCCTCTCGCCGAGCTCAG 60.826 66.667 15.40 2.93 38.49 3.35
195 196 4.567385 CCTCTCGCCGAGCTCAGC 62.567 72.222 15.40 13.71 38.49 4.26
196 197 3.517140 CTCTCGCCGAGCTCAGCT 61.517 66.667 19.34 0.00 43.88 4.24
210 211 2.925170 AGCTCCGTGGCTGTTCCT 60.925 61.111 0.00 0.00 41.43 3.36
211 212 2.032681 GCTCCGTGGCTGTTCCTT 59.967 61.111 0.00 0.00 35.26 3.36
212 213 1.600916 GCTCCGTGGCTGTTCCTTT 60.601 57.895 0.00 0.00 35.26 3.11
213 214 0.321298 GCTCCGTGGCTGTTCCTTTA 60.321 55.000 0.00 0.00 35.26 1.85
214 215 1.439679 CTCCGTGGCTGTTCCTTTAC 58.560 55.000 0.00 0.00 35.26 2.01
215 216 0.035739 TCCGTGGCTGTTCCTTTACC 59.964 55.000 0.00 0.00 35.26 2.85
216 217 0.036306 CCGTGGCTGTTCCTTTACCT 59.964 55.000 0.00 0.00 35.26 3.08
217 218 1.156736 CGTGGCTGTTCCTTTACCTG 58.843 55.000 0.00 0.00 35.26 4.00
218 219 1.542547 CGTGGCTGTTCCTTTACCTGT 60.543 52.381 0.00 0.00 35.26 4.00
219 220 2.583143 GTGGCTGTTCCTTTACCTGTT 58.417 47.619 0.00 0.00 35.26 3.16
220 221 2.293399 GTGGCTGTTCCTTTACCTGTTG 59.707 50.000 0.00 0.00 35.26 3.33
221 222 2.092103 TGGCTGTTCCTTTACCTGTTGT 60.092 45.455 0.00 0.00 35.26 3.32
222 223 3.136809 TGGCTGTTCCTTTACCTGTTGTA 59.863 43.478 0.00 0.00 35.26 2.41
223 224 4.202524 TGGCTGTTCCTTTACCTGTTGTAT 60.203 41.667 0.00 0.00 35.26 2.29
224 225 4.395231 GGCTGTTCCTTTACCTGTTGTATC 59.605 45.833 0.00 0.00 0.00 2.24
225 226 4.395231 GCTGTTCCTTTACCTGTTGTATCC 59.605 45.833 0.00 0.00 0.00 2.59
226 227 4.571919 TGTTCCTTTACCTGTTGTATCCG 58.428 43.478 0.00 0.00 0.00 4.18
227 228 4.040706 TGTTCCTTTACCTGTTGTATCCGT 59.959 41.667 0.00 0.00 0.00 4.69
228 229 4.460948 TCCTTTACCTGTTGTATCCGTC 57.539 45.455 0.00 0.00 0.00 4.79
229 230 3.196254 TCCTTTACCTGTTGTATCCGTCC 59.804 47.826 0.00 0.00 0.00 4.79
230 231 3.197116 CCTTTACCTGTTGTATCCGTCCT 59.803 47.826 0.00 0.00 0.00 3.85
231 232 4.323257 CCTTTACCTGTTGTATCCGTCCTT 60.323 45.833 0.00 0.00 0.00 3.36
232 233 2.762535 ACCTGTTGTATCCGTCCTTG 57.237 50.000 0.00 0.00 0.00 3.61
233 234 1.278127 ACCTGTTGTATCCGTCCTTGG 59.722 52.381 0.00 0.00 0.00 3.61
234 235 1.406887 CCTGTTGTATCCGTCCTTGGG 60.407 57.143 0.00 0.00 0.00 4.12
235 236 1.278127 CTGTTGTATCCGTCCTTGGGT 59.722 52.381 0.00 0.00 0.00 4.51
236 237 1.002659 TGTTGTATCCGTCCTTGGGTG 59.997 52.381 0.00 0.00 0.00 4.61
237 238 1.002773 GTTGTATCCGTCCTTGGGTGT 59.997 52.381 0.00 0.00 0.00 4.16
238 239 0.611200 TGTATCCGTCCTTGGGTGTG 59.389 55.000 0.00 0.00 0.00 3.82
239 240 0.611714 GTATCCGTCCTTGGGTGTGT 59.388 55.000 0.00 0.00 0.00 3.72
240 241 1.002773 GTATCCGTCCTTGGGTGTGTT 59.997 52.381 0.00 0.00 0.00 3.32
241 242 0.250727 ATCCGTCCTTGGGTGTGTTG 60.251 55.000 0.00 0.00 0.00 3.33
242 243 1.153046 CCGTCCTTGGGTGTGTTGT 60.153 57.895 0.00 0.00 0.00 3.32
243 244 1.444119 CCGTCCTTGGGTGTGTTGTG 61.444 60.000 0.00 0.00 0.00 3.33
244 245 0.746563 CGTCCTTGGGTGTGTTGTGT 60.747 55.000 0.00 0.00 0.00 3.72
245 246 0.738389 GTCCTTGGGTGTGTTGTGTG 59.262 55.000 0.00 0.00 0.00 3.82
246 247 0.395036 TCCTTGGGTGTGTTGTGTGG 60.395 55.000 0.00 0.00 0.00 4.17
247 248 0.682855 CCTTGGGTGTGTTGTGTGGT 60.683 55.000 0.00 0.00 0.00 4.16
248 249 0.455410 CTTGGGTGTGTTGTGTGGTG 59.545 55.000 0.00 0.00 0.00 4.17
249 250 0.967887 TTGGGTGTGTTGTGTGGTGG 60.968 55.000 0.00 0.00 0.00 4.61
250 251 1.379309 GGGTGTGTTGTGTGGTGGT 60.379 57.895 0.00 0.00 0.00 4.16
251 252 1.662438 GGGTGTGTTGTGTGGTGGTG 61.662 60.000 0.00 0.00 0.00 4.17
252 253 0.963355 GGTGTGTTGTGTGGTGGTGT 60.963 55.000 0.00 0.00 0.00 4.16
253 254 0.170116 GTGTGTTGTGTGGTGGTGTG 59.830 55.000 0.00 0.00 0.00 3.82
254 255 0.962855 TGTGTTGTGTGGTGGTGTGG 60.963 55.000 0.00 0.00 0.00 4.17
255 256 0.963355 GTGTTGTGTGGTGGTGTGGT 60.963 55.000 0.00 0.00 0.00 4.16
256 257 0.962855 TGTTGTGTGGTGGTGTGGTG 60.963 55.000 0.00 0.00 0.00 4.17
257 258 0.963355 GTTGTGTGGTGGTGTGGTGT 60.963 55.000 0.00 0.00 0.00 4.16
258 259 0.962855 TTGTGTGGTGGTGTGGTGTG 60.963 55.000 0.00 0.00 0.00 3.82
259 260 2.118404 GTGTGGTGGTGTGGTGTGG 61.118 63.158 0.00 0.00 0.00 4.17
260 261 3.216292 GTGGTGGTGTGGTGTGGC 61.216 66.667 0.00 0.00 0.00 5.01
261 262 4.866224 TGGTGGTGTGGTGTGGCG 62.866 66.667 0.00 0.00 0.00 5.69
262 263 4.868116 GGTGGTGTGGTGTGGCGT 62.868 66.667 0.00 0.00 0.00 5.68
263 264 2.826738 GTGGTGTGGTGTGGCGTT 60.827 61.111 0.00 0.00 0.00 4.84
264 265 2.826287 TGGTGTGGTGTGGCGTTG 60.826 61.111 0.00 0.00 0.00 4.10
265 266 2.515057 GGTGTGGTGTGGCGTTGA 60.515 61.111 0.00 0.00 0.00 3.18
266 267 2.115911 GGTGTGGTGTGGCGTTGAA 61.116 57.895 0.00 0.00 0.00 2.69
267 268 1.452145 GGTGTGGTGTGGCGTTGAAT 61.452 55.000 0.00 0.00 0.00 2.57
268 269 0.383949 GTGTGGTGTGGCGTTGAATT 59.616 50.000 0.00 0.00 0.00 2.17
269 270 0.383590 TGTGGTGTGGCGTTGAATTG 59.616 50.000 0.00 0.00 0.00 2.32
270 271 0.383949 GTGGTGTGGCGTTGAATTGT 59.616 50.000 0.00 0.00 0.00 2.71
271 272 1.107114 TGGTGTGGCGTTGAATTGTT 58.893 45.000 0.00 0.00 0.00 2.83
272 273 1.478510 TGGTGTGGCGTTGAATTGTTT 59.521 42.857 0.00 0.00 0.00 2.83
273 274 1.857837 GGTGTGGCGTTGAATTGTTTG 59.142 47.619 0.00 0.00 0.00 2.93
274 275 1.257675 GTGTGGCGTTGAATTGTTTGC 59.742 47.619 0.00 0.00 0.00 3.68
275 276 0.858583 GTGGCGTTGAATTGTTTGCC 59.141 50.000 0.00 0.00 42.76 4.52
276 277 3.280920 GGCGTTGAATTGTTTGCCA 57.719 47.368 4.06 0.00 42.03 4.92
277 278 1.069823 TGGCGTTGAATTGTTTGCCAT 59.930 42.857 6.90 0.00 46.74 4.40
278 279 1.460359 GGCGTTGAATTGTTTGCCATG 59.540 47.619 4.06 0.00 42.03 3.66
279 280 2.402305 GCGTTGAATTGTTTGCCATGA 58.598 42.857 0.00 0.00 0.00 3.07
280 281 2.995258 GCGTTGAATTGTTTGCCATGAT 59.005 40.909 0.00 0.00 0.00 2.45
281 282 3.432933 GCGTTGAATTGTTTGCCATGATT 59.567 39.130 0.00 0.00 0.00 2.57
282 283 4.667161 GCGTTGAATTGTTTGCCATGATTG 60.667 41.667 0.00 0.00 0.00 2.67
283 284 4.448395 CGTTGAATTGTTTGCCATGATTGT 59.552 37.500 0.00 0.00 0.00 2.71
284 285 5.632764 CGTTGAATTGTTTGCCATGATTGTA 59.367 36.000 0.00 0.00 0.00 2.41
285 286 6.145209 CGTTGAATTGTTTGCCATGATTGTAA 59.855 34.615 0.00 0.00 0.00 2.41
286 287 7.148606 CGTTGAATTGTTTGCCATGATTGTAAT 60.149 33.333 0.00 0.00 0.00 1.89
287 288 7.830940 TGAATTGTTTGCCATGATTGTAATC 57.169 32.000 0.00 0.00 35.97 1.75
288 289 6.530887 TGAATTGTTTGCCATGATTGTAATCG 59.469 34.615 0.00 0.00 38.26 3.34
289 290 4.368874 TGTTTGCCATGATTGTAATCGG 57.631 40.909 0.00 0.00 38.26 4.18
290 291 3.761218 TGTTTGCCATGATTGTAATCGGT 59.239 39.130 0.00 0.00 38.26 4.69
291 292 4.104776 GTTTGCCATGATTGTAATCGGTG 58.895 43.478 0.00 2.56 38.26 4.94
292 293 3.274095 TGCCATGATTGTAATCGGTGA 57.726 42.857 0.00 0.00 38.26 4.02
293 294 3.819368 TGCCATGATTGTAATCGGTGAT 58.181 40.909 0.00 0.00 38.26 3.06
294 295 3.565063 TGCCATGATTGTAATCGGTGATG 59.435 43.478 0.00 4.47 38.26 3.07
295 296 3.058016 GCCATGATTGTAATCGGTGATGG 60.058 47.826 13.35 13.35 37.86 3.51
296 297 4.136796 CCATGATTGTAATCGGTGATGGT 58.863 43.478 10.98 0.00 38.26 3.55
297 298 4.023792 CCATGATTGTAATCGGTGATGGTG 60.024 45.833 10.98 0.00 38.26 4.17
298 299 2.942376 TGATTGTAATCGGTGATGGTGC 59.058 45.455 0.65 0.00 38.26 5.01
299 300 2.779755 TTGTAATCGGTGATGGTGCT 57.220 45.000 0.00 0.00 0.00 4.40
300 301 2.779755 TGTAATCGGTGATGGTGCTT 57.220 45.000 0.00 0.00 0.00 3.91
301 302 3.066291 TGTAATCGGTGATGGTGCTTT 57.934 42.857 0.00 0.00 0.00 3.51
302 303 4.209307 TGTAATCGGTGATGGTGCTTTA 57.791 40.909 0.00 0.00 0.00 1.85
303 304 4.776349 TGTAATCGGTGATGGTGCTTTAT 58.224 39.130 0.00 0.00 0.00 1.40
304 305 5.919755 TGTAATCGGTGATGGTGCTTTATA 58.080 37.500 0.00 0.00 0.00 0.98
305 306 6.530120 TGTAATCGGTGATGGTGCTTTATAT 58.470 36.000 0.00 0.00 0.00 0.86
306 307 7.672240 TGTAATCGGTGATGGTGCTTTATATA 58.328 34.615 0.00 0.00 0.00 0.86
307 308 8.318412 TGTAATCGGTGATGGTGCTTTATATAT 58.682 33.333 0.00 0.00 0.00 0.86
308 309 9.811995 GTAATCGGTGATGGTGCTTTATATATA 57.188 33.333 0.00 0.00 0.00 0.86
310 311 9.733556 AATCGGTGATGGTGCTTTATATATAAA 57.266 29.630 15.47 15.47 0.00 1.40
312 313 8.372459 TCGGTGATGGTGCTTTATATATAAAGT 58.628 33.333 31.63 19.57 46.78 2.66
313 314 8.443160 CGGTGATGGTGCTTTATATATAAAGTG 58.557 37.037 31.63 18.06 46.78 3.16
314 315 8.730680 GGTGATGGTGCTTTATATATAAAGTGG 58.269 37.037 31.63 17.53 46.78 4.00
315 316 8.730680 GTGATGGTGCTTTATATATAAAGTGGG 58.269 37.037 31.63 17.26 46.78 4.61
316 317 7.888021 TGATGGTGCTTTATATATAAAGTGGGG 59.112 37.037 31.63 16.99 46.78 4.96
317 318 6.548321 TGGTGCTTTATATATAAAGTGGGGG 58.452 40.000 31.63 16.46 46.78 5.40
344 345 4.071423 CCCTTTTTCGGCAAATTGGAAAT 58.929 39.130 0.00 0.00 30.55 2.17
345 346 4.154015 CCCTTTTTCGGCAAATTGGAAATC 59.846 41.667 0.00 0.00 30.55 2.17
447 448 2.494073 GGAAGTCTCGAGACCAGACAAT 59.506 50.000 35.83 17.29 45.85 2.71
553 562 5.098663 GGGGGTATACATGGAGAGGAAATA 58.901 45.833 5.01 0.00 0.00 1.40
596 605 0.681243 GGGTTCAGATTCTGCCCACC 60.681 60.000 19.20 17.45 35.02 4.61
613 622 4.853007 CCCACCACTACTACTAGTGTACT 58.147 47.826 5.39 0.00 46.07 2.73
818 877 3.849911 CCATCACATGTTAGTGTCGTCT 58.150 45.455 0.00 0.00 40.37 4.18
893 960 5.164233 CGTAGTCACACTCAAGATGATTGT 58.836 41.667 0.00 0.00 40.28 2.71
1041 1186 0.459899 TGATCGTCGGGAGGATTGTG 59.540 55.000 5.46 0.00 36.22 3.33
1054 1199 2.814183 GATTGTGGGCGACGTCGTCT 62.814 60.000 37.51 21.04 44.45 4.18
1175 1320 2.045926 GCGCATCACAGGAAGGGT 60.046 61.111 0.30 0.00 0.00 4.34
1232 1629 2.028763 CCACGTTTCGGTCATATCGTTG 59.971 50.000 0.00 0.00 0.00 4.10
1237 1634 4.331962 GTTTCGGTCATATCGTTGCTTTC 58.668 43.478 0.00 0.00 0.00 2.62
1270 1705 6.855836 AGTTGCACATAGTTATTTGTCCATG 58.144 36.000 0.00 0.00 0.00 3.66
1331 1767 0.620700 ACCCTGATGTACCTGGACCC 60.621 60.000 0.00 0.00 0.00 4.46
1566 4802 6.129352 CGATCGAATACTACATGTGTCATGTG 60.129 42.308 20.90 14.41 33.76 3.21
1637 4880 6.685527 AAGAAAAGTCTTCTTTCTTTCGCT 57.314 33.333 6.48 0.00 40.18 4.93
2275 6257 5.041191 TCTATTTCTTCAGAATCCTGGCC 57.959 43.478 0.00 0.00 40.76 5.36
2465 6616 0.621571 TTACCCTCCATCCAGCAGCT 60.622 55.000 0.00 0.00 0.00 4.24
2799 8394 1.001393 GGATTTGGGTGGCTTCGGA 60.001 57.895 0.00 0.00 0.00 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.719355 GACCCCAATTCATTTATGTAAACTTTT 57.281 29.630 0.00 0.00 0.00 2.27
22 23 8.318412 GGACCCCAATTCATTTATGTAAACTTT 58.682 33.333 0.00 0.00 0.00 2.66
23 24 7.678171 AGGACCCCAATTCATTTATGTAAACTT 59.322 33.333 0.00 0.00 0.00 2.66
24 25 7.189087 AGGACCCCAATTCATTTATGTAAACT 58.811 34.615 0.00 0.00 0.00 2.66
25 26 7.418337 AGGACCCCAATTCATTTATGTAAAC 57.582 36.000 0.00 0.00 0.00 2.01
26 27 7.898636 AGAAGGACCCCAATTCATTTATGTAAA 59.101 33.333 0.00 0.00 0.00 2.01
27 28 7.418378 AGAAGGACCCCAATTCATTTATGTAA 58.582 34.615 0.00 0.00 0.00 2.41
28 29 6.980577 AGAAGGACCCCAATTCATTTATGTA 58.019 36.000 0.00 0.00 0.00 2.29
29 30 5.842339 AGAAGGACCCCAATTCATTTATGT 58.158 37.500 0.00 0.00 0.00 2.29
30 31 6.380846 TCAAGAAGGACCCCAATTCATTTATG 59.619 38.462 0.00 0.00 0.00 1.90
31 32 6.502138 TCAAGAAGGACCCCAATTCATTTAT 58.498 36.000 0.00 0.00 0.00 1.40
32 33 5.898120 TCAAGAAGGACCCCAATTCATTTA 58.102 37.500 0.00 0.00 0.00 1.40
33 34 4.750941 TCAAGAAGGACCCCAATTCATTT 58.249 39.130 0.00 0.00 0.00 2.32
34 35 4.402616 TCAAGAAGGACCCCAATTCATT 57.597 40.909 0.00 0.00 0.00 2.57
35 36 4.347607 CTTCAAGAAGGACCCCAATTCAT 58.652 43.478 1.86 0.00 34.87 2.57
36 37 3.766545 CTTCAAGAAGGACCCCAATTCA 58.233 45.455 1.86 0.00 34.87 2.57
48 49 0.663568 ACGACGACGCCTTCAAGAAG 60.664 55.000 7.30 2.83 43.96 2.85
49 50 0.937699 CACGACGACGCCTTCAAGAA 60.938 55.000 7.30 0.00 43.96 2.52
50 51 1.371267 CACGACGACGCCTTCAAGA 60.371 57.895 7.30 0.00 43.96 3.02
51 52 2.372690 CCACGACGACGCCTTCAAG 61.373 63.158 7.30 0.00 43.96 3.02
52 53 2.355363 CCACGACGACGCCTTCAA 60.355 61.111 7.30 0.00 43.96 2.69
54 55 3.332493 TAGCCACGACGACGCCTTC 62.332 63.158 7.30 0.00 43.96 3.46
55 56 3.367743 TAGCCACGACGACGCCTT 61.368 61.111 7.30 0.00 43.96 4.35
56 57 4.112341 GTAGCCACGACGACGCCT 62.112 66.667 7.30 4.21 43.96 5.52
57 58 4.112341 AGTAGCCACGACGACGCC 62.112 66.667 7.30 0.00 43.96 5.68
58 59 2.576317 GAGTAGCCACGACGACGC 60.576 66.667 7.30 1.89 43.96 5.19
59 60 1.060622 GAGAGTAGCCACGACGACG 59.939 63.158 5.58 5.58 45.75 5.12
60 61 1.025647 AGGAGAGTAGCCACGACGAC 61.026 60.000 0.00 0.00 0.00 4.34
61 62 0.743701 GAGGAGAGTAGCCACGACGA 60.744 60.000 0.00 0.00 0.00 4.20
62 63 1.716826 GGAGGAGAGTAGCCACGACG 61.717 65.000 0.00 0.00 0.00 5.12
63 64 0.394625 AGGAGGAGAGTAGCCACGAC 60.395 60.000 0.00 0.00 0.00 4.34
64 65 0.331954 AAGGAGGAGAGTAGCCACGA 59.668 55.000 0.00 0.00 0.00 4.35
65 66 0.741915 GAAGGAGGAGAGTAGCCACG 59.258 60.000 0.00 0.00 0.00 4.94
66 67 0.741915 CGAAGGAGGAGAGTAGCCAC 59.258 60.000 0.00 0.00 0.00 5.01
67 68 3.192799 CGAAGGAGGAGAGTAGCCA 57.807 57.895 0.00 0.00 0.00 4.75
81 82 0.613260 TTCACCTGGACCATCCGAAG 59.387 55.000 0.00 0.00 40.17 3.79
82 83 1.060729 TTTCACCTGGACCATCCGAA 58.939 50.000 0.00 0.00 40.17 4.30
83 84 1.060729 TTTTCACCTGGACCATCCGA 58.939 50.000 0.00 0.00 40.17 4.55
84 85 1.165270 GTTTTCACCTGGACCATCCG 58.835 55.000 0.00 0.00 40.17 4.18
85 86 1.203001 TGGTTTTCACCTGGACCATCC 60.203 52.381 0.00 0.00 44.61 3.51
86 87 2.286365 TGGTTTTCACCTGGACCATC 57.714 50.000 0.00 0.00 44.61 3.51
87 88 2.999185 ATGGTTTTCACCTGGACCAT 57.001 45.000 10.37 10.37 45.18 3.55
88 89 1.496857 TCATGGTTTTCACCTGGACCA 59.503 47.619 0.00 3.29 44.61 4.02
89 90 2.286365 TCATGGTTTTCACCTGGACC 57.714 50.000 0.00 0.00 44.61 4.46
90 91 2.755103 GGATCATGGTTTTCACCTGGAC 59.245 50.000 0.00 0.00 44.61 4.02
91 92 2.649312 AGGATCATGGTTTTCACCTGGA 59.351 45.455 0.00 0.00 44.61 3.86
92 93 3.091633 AGGATCATGGTTTTCACCTGG 57.908 47.619 0.00 0.00 44.61 4.45
93 94 4.322198 CCAAAGGATCATGGTTTTCACCTG 60.322 45.833 0.00 0.00 44.61 4.00
94 95 3.834231 CCAAAGGATCATGGTTTTCACCT 59.166 43.478 0.00 0.00 44.61 4.00
95 96 3.831911 TCCAAAGGATCATGGTTTTCACC 59.168 43.478 10.22 0.00 44.56 4.02
96 97 5.665916 ATCCAAAGGATCATGGTTTTCAC 57.334 39.130 10.22 0.00 38.09 3.18
108 109 2.510906 CCGCCCGATCCAAAGGAT 59.489 61.111 0.00 0.00 46.28 3.24
109 110 4.483243 GCCGCCCGATCCAAAGGA 62.483 66.667 0.00 0.00 35.55 3.36
111 112 4.830765 TCGCCGCCCGATCCAAAG 62.831 66.667 0.00 0.00 41.89 2.77
130 131 3.723348 GAACAACACCGGAGCGCC 61.723 66.667 9.46 0.00 0.00 6.53
131 132 2.665185 AGAACAACACCGGAGCGC 60.665 61.111 9.46 0.00 0.00 5.92
132 133 2.027625 GGAGAACAACACCGGAGCG 61.028 63.158 9.46 0.00 0.00 5.03
133 134 0.250338 AAGGAGAACAACACCGGAGC 60.250 55.000 9.46 0.00 34.46 4.70
134 135 1.344763 AGAAGGAGAACAACACCGGAG 59.655 52.381 9.46 1.26 34.46 4.63
135 136 1.420430 AGAAGGAGAACAACACCGGA 58.580 50.000 9.46 0.00 34.46 5.14
136 137 1.873591 CAAGAAGGAGAACAACACCGG 59.126 52.381 0.00 0.00 34.46 5.28
137 138 2.833794 TCAAGAAGGAGAACAACACCG 58.166 47.619 0.00 0.00 34.46 4.94
138 139 4.498177 GCTTTCAAGAAGGAGAACAACACC 60.498 45.833 0.00 0.00 0.00 4.16
139 140 4.602006 GCTTTCAAGAAGGAGAACAACAC 58.398 43.478 0.00 0.00 0.00 3.32
140 141 3.312421 CGCTTTCAAGAAGGAGAACAACA 59.688 43.478 0.00 0.00 0.00 3.33
141 142 3.850010 GCGCTTTCAAGAAGGAGAACAAC 60.850 47.826 0.00 0.00 0.00 3.32
142 143 2.290641 GCGCTTTCAAGAAGGAGAACAA 59.709 45.455 0.00 0.00 0.00 2.83
143 144 1.873591 GCGCTTTCAAGAAGGAGAACA 59.126 47.619 0.00 0.00 0.00 3.18
144 145 1.197949 GGCGCTTTCAAGAAGGAGAAC 59.802 52.381 7.64 0.00 0.00 3.01
145 146 1.523758 GGCGCTTTCAAGAAGGAGAA 58.476 50.000 7.64 0.00 0.00 2.87
146 147 0.670546 CGGCGCTTTCAAGAAGGAGA 60.671 55.000 7.64 0.00 0.00 3.71
147 148 0.951040 ACGGCGCTTTCAAGAAGGAG 60.951 55.000 6.90 0.00 0.00 3.69
148 149 0.949105 GACGGCGCTTTCAAGAAGGA 60.949 55.000 6.90 0.00 0.00 3.36
149 150 0.951040 AGACGGCGCTTTCAAGAAGG 60.951 55.000 6.90 0.00 0.00 3.46
150 151 0.868406 AAGACGGCGCTTTCAAGAAG 59.132 50.000 6.90 0.00 0.00 2.85
151 152 0.586319 CAAGACGGCGCTTTCAAGAA 59.414 50.000 6.90 0.00 0.00 2.52
152 153 0.249699 TCAAGACGGCGCTTTCAAGA 60.250 50.000 6.90 2.50 0.00 3.02
153 154 0.586319 TTCAAGACGGCGCTTTCAAG 59.414 50.000 6.90 0.04 0.00 3.02
154 155 0.586319 CTTCAAGACGGCGCTTTCAA 59.414 50.000 6.90 6.02 0.00 2.69
155 156 1.227999 CCTTCAAGACGGCGCTTTCA 61.228 55.000 6.90 0.00 0.00 2.69
156 157 1.497722 CCTTCAAGACGGCGCTTTC 59.502 57.895 6.90 3.72 0.00 2.62
157 158 2.617274 GCCTTCAAGACGGCGCTTT 61.617 57.895 6.90 0.00 36.45 3.51
158 159 3.050275 GCCTTCAAGACGGCGCTT 61.050 61.111 6.90 8.91 36.45 4.68
162 163 2.436824 GGAGGCCTTCAAGACGGC 60.437 66.667 6.77 8.92 45.55 5.68
163 164 1.219393 GAGGAGGCCTTCAAGACGG 59.781 63.158 15.31 0.00 31.76 4.79
164 165 0.174617 GAGAGGAGGCCTTCAAGACG 59.825 60.000 15.31 0.00 31.76 4.18
165 166 0.174617 CGAGAGGAGGCCTTCAAGAC 59.825 60.000 15.31 1.47 31.76 3.01
166 167 1.608717 GCGAGAGGAGGCCTTCAAGA 61.609 60.000 15.31 0.00 31.76 3.02
167 168 1.153469 GCGAGAGGAGGCCTTCAAG 60.153 63.158 15.31 4.40 31.76 3.02
168 169 2.660064 GGCGAGAGGAGGCCTTCAA 61.660 63.158 15.31 0.00 45.93 2.69
169 170 3.077556 GGCGAGAGGAGGCCTTCA 61.078 66.667 15.31 0.00 45.93 3.02
175 176 3.591835 GAGCTCGGCGAGAGGAGG 61.592 72.222 38.56 14.21 46.91 4.30
176 177 2.826287 TGAGCTCGGCGAGAGGAG 60.826 66.667 38.56 15.00 46.91 3.69
177 178 2.826287 CTGAGCTCGGCGAGAGGA 60.826 66.667 38.56 19.59 46.91 3.71
178 179 4.567385 GCTGAGCTCGGCGAGAGG 62.567 72.222 38.56 23.42 46.91 3.69
193 194 2.056906 AAAGGAACAGCCACGGAGCT 62.057 55.000 0.00 0.00 46.45 4.09
194 195 0.321298 TAAAGGAACAGCCACGGAGC 60.321 55.000 0.00 0.00 40.02 4.70
195 196 1.439679 GTAAAGGAACAGCCACGGAG 58.560 55.000 0.00 0.00 40.02 4.63
196 197 0.035739 GGTAAAGGAACAGCCACGGA 59.964 55.000 0.00 0.00 40.02 4.69
197 198 0.036306 AGGTAAAGGAACAGCCACGG 59.964 55.000 0.00 0.00 40.02 4.94
198 199 1.156736 CAGGTAAAGGAACAGCCACG 58.843 55.000 0.00 0.00 40.02 4.94
199 200 2.271944 ACAGGTAAAGGAACAGCCAC 57.728 50.000 0.00 0.00 40.02 5.01
200 201 2.092103 ACAACAGGTAAAGGAACAGCCA 60.092 45.455 0.00 0.00 40.02 4.75
201 202 2.583143 ACAACAGGTAAAGGAACAGCC 58.417 47.619 0.00 0.00 0.00 4.85
202 203 4.395231 GGATACAACAGGTAAAGGAACAGC 59.605 45.833 0.00 0.00 35.14 4.40
203 204 4.630069 CGGATACAACAGGTAAAGGAACAG 59.370 45.833 0.00 0.00 35.14 3.16
204 205 4.040706 ACGGATACAACAGGTAAAGGAACA 59.959 41.667 0.00 0.00 35.14 3.18
205 206 4.572909 ACGGATACAACAGGTAAAGGAAC 58.427 43.478 0.00 0.00 35.14 3.62
206 207 4.322953 GGACGGATACAACAGGTAAAGGAA 60.323 45.833 0.00 0.00 35.14 3.36
207 208 3.196254 GGACGGATACAACAGGTAAAGGA 59.804 47.826 0.00 0.00 35.14 3.36
208 209 3.197116 AGGACGGATACAACAGGTAAAGG 59.803 47.826 0.00 0.00 35.14 3.11
209 210 4.467198 AGGACGGATACAACAGGTAAAG 57.533 45.455 0.00 0.00 35.14 1.85
210 211 4.563993 CCAAGGACGGATACAACAGGTAAA 60.564 45.833 0.00 0.00 35.14 2.01
211 212 3.055675 CCAAGGACGGATACAACAGGTAA 60.056 47.826 0.00 0.00 35.14 2.85
212 213 2.498481 CCAAGGACGGATACAACAGGTA 59.502 50.000 0.00 0.00 36.16 3.08
213 214 1.278127 CCAAGGACGGATACAACAGGT 59.722 52.381 0.00 0.00 0.00 4.00
214 215 1.406887 CCCAAGGACGGATACAACAGG 60.407 57.143 0.00 0.00 0.00 4.00
215 216 1.278127 ACCCAAGGACGGATACAACAG 59.722 52.381 0.00 0.00 0.00 3.16
216 217 1.002659 CACCCAAGGACGGATACAACA 59.997 52.381 0.00 0.00 0.00 3.33
217 218 1.002773 ACACCCAAGGACGGATACAAC 59.997 52.381 0.00 0.00 0.00 3.32
218 219 1.002659 CACACCCAAGGACGGATACAA 59.997 52.381 0.00 0.00 0.00 2.41
219 220 0.611200 CACACCCAAGGACGGATACA 59.389 55.000 0.00 0.00 0.00 2.29
220 221 0.611714 ACACACCCAAGGACGGATAC 59.388 55.000 0.00 0.00 0.00 2.24
221 222 1.002659 CAACACACCCAAGGACGGATA 59.997 52.381 0.00 0.00 0.00 2.59
222 223 0.250727 CAACACACCCAAGGACGGAT 60.251 55.000 0.00 0.00 0.00 4.18
223 224 1.147376 CAACACACCCAAGGACGGA 59.853 57.895 0.00 0.00 0.00 4.69
224 225 1.153046 ACAACACACCCAAGGACGG 60.153 57.895 0.00 0.00 0.00 4.79
225 226 0.746563 ACACAACACACCCAAGGACG 60.747 55.000 0.00 0.00 0.00 4.79
226 227 0.738389 CACACAACACACCCAAGGAC 59.262 55.000 0.00 0.00 0.00 3.85
227 228 0.395036 CCACACAACACACCCAAGGA 60.395 55.000 0.00 0.00 0.00 3.36
228 229 0.682855 ACCACACAACACACCCAAGG 60.683 55.000 0.00 0.00 0.00 3.61
229 230 0.455410 CACCACACAACACACCCAAG 59.545 55.000 0.00 0.00 0.00 3.61
230 231 0.967887 CCACCACACAACACACCCAA 60.968 55.000 0.00 0.00 0.00 4.12
231 232 1.379176 CCACCACACAACACACCCA 60.379 57.895 0.00 0.00 0.00 4.51
232 233 1.379309 ACCACCACACAACACACCC 60.379 57.895 0.00 0.00 0.00 4.61
233 234 0.963355 ACACCACCACACAACACACC 60.963 55.000 0.00 0.00 0.00 4.16
234 235 0.170116 CACACCACCACACAACACAC 59.830 55.000 0.00 0.00 0.00 3.82
235 236 0.962855 CCACACCACCACACAACACA 60.963 55.000 0.00 0.00 0.00 3.72
236 237 0.963355 ACCACACCACCACACAACAC 60.963 55.000 0.00 0.00 0.00 3.32
237 238 0.962855 CACCACACCACCACACAACA 60.963 55.000 0.00 0.00 0.00 3.33
238 239 0.963355 ACACCACACCACCACACAAC 60.963 55.000 0.00 0.00 0.00 3.32
239 240 0.962855 CACACCACACCACCACACAA 60.963 55.000 0.00 0.00 0.00 3.33
240 241 1.377856 CACACCACACCACCACACA 60.378 57.895 0.00 0.00 0.00 3.72
241 242 2.118404 CCACACCACACCACCACAC 61.118 63.158 0.00 0.00 0.00 3.82
242 243 2.273776 CCACACCACACCACCACA 59.726 61.111 0.00 0.00 0.00 4.17
243 244 3.216292 GCCACACCACACCACCAC 61.216 66.667 0.00 0.00 0.00 4.16
244 245 4.866224 CGCCACACCACACCACCA 62.866 66.667 0.00 0.00 0.00 4.17
245 246 4.868116 ACGCCACACCACACCACC 62.868 66.667 0.00 0.00 0.00 4.61
246 247 2.826738 AACGCCACACCACACCAC 60.827 61.111 0.00 0.00 0.00 4.16
247 248 2.821679 TTCAACGCCACACCACACCA 62.822 55.000 0.00 0.00 0.00 4.17
248 249 1.452145 ATTCAACGCCACACCACACC 61.452 55.000 0.00 0.00 0.00 4.16
249 250 0.383949 AATTCAACGCCACACCACAC 59.616 50.000 0.00 0.00 0.00 3.82
250 251 0.383590 CAATTCAACGCCACACCACA 59.616 50.000 0.00 0.00 0.00 4.17
251 252 0.383949 ACAATTCAACGCCACACCAC 59.616 50.000 0.00 0.00 0.00 4.16
252 253 1.107114 AACAATTCAACGCCACACCA 58.893 45.000 0.00 0.00 0.00 4.17
253 254 1.857837 CAAACAATTCAACGCCACACC 59.142 47.619 0.00 0.00 0.00 4.16
254 255 1.257675 GCAAACAATTCAACGCCACAC 59.742 47.619 0.00 0.00 0.00 3.82
255 256 1.565305 GCAAACAATTCAACGCCACA 58.435 45.000 0.00 0.00 0.00 4.17
256 257 0.858583 GGCAAACAATTCAACGCCAC 59.141 50.000 0.00 0.00 39.38 5.01
257 258 0.461548 TGGCAAACAATTCAACGCCA 59.538 45.000 0.00 0.00 46.80 5.69
258 259 1.460359 CATGGCAAACAATTCAACGCC 59.540 47.619 0.00 0.00 40.02 5.68
259 260 2.402305 TCATGGCAAACAATTCAACGC 58.598 42.857 0.00 0.00 0.00 4.84
260 261 4.448395 ACAATCATGGCAAACAATTCAACG 59.552 37.500 0.00 0.00 0.00 4.10
261 262 5.927954 ACAATCATGGCAAACAATTCAAC 57.072 34.783 0.00 0.00 0.00 3.18
262 263 7.063191 CGATTACAATCATGGCAAACAATTCAA 59.937 33.333 0.00 0.00 35.11 2.69
263 264 6.530887 CGATTACAATCATGGCAAACAATTCA 59.469 34.615 0.00 0.00 35.11 2.57
264 265 6.019640 CCGATTACAATCATGGCAAACAATTC 60.020 38.462 0.00 0.00 35.11 2.17
265 266 5.811613 CCGATTACAATCATGGCAAACAATT 59.188 36.000 0.00 0.00 35.11 2.32
266 267 5.105392 ACCGATTACAATCATGGCAAACAAT 60.105 36.000 0.00 0.00 35.11 2.71
267 268 4.219507 ACCGATTACAATCATGGCAAACAA 59.780 37.500 0.00 0.00 35.11 2.83
268 269 3.761218 ACCGATTACAATCATGGCAAACA 59.239 39.130 0.00 0.00 35.11 2.83
269 270 4.104776 CACCGATTACAATCATGGCAAAC 58.895 43.478 0.00 0.00 35.11 2.93
270 271 4.013050 TCACCGATTACAATCATGGCAAA 58.987 39.130 0.00 0.00 35.11 3.68
271 272 3.615155 TCACCGATTACAATCATGGCAA 58.385 40.909 0.00 0.00 35.11 4.52
272 273 3.274095 TCACCGATTACAATCATGGCA 57.726 42.857 0.00 0.00 35.11 4.92
273 274 3.058016 CCATCACCGATTACAATCATGGC 60.058 47.826 3.07 0.00 35.11 4.40
274 275 4.023792 CACCATCACCGATTACAATCATGG 60.024 45.833 13.51 13.51 35.11 3.66
275 276 4.555313 GCACCATCACCGATTACAATCATG 60.555 45.833 3.07 0.00 35.11 3.07
276 277 3.565482 GCACCATCACCGATTACAATCAT 59.435 43.478 3.07 0.00 35.11 2.45
277 278 2.942376 GCACCATCACCGATTACAATCA 59.058 45.455 3.07 0.00 35.11 2.57
278 279 3.206150 AGCACCATCACCGATTACAATC 58.794 45.455 0.00 0.00 0.00 2.67
279 280 3.281727 AGCACCATCACCGATTACAAT 57.718 42.857 0.00 0.00 0.00 2.71
280 281 2.779755 AGCACCATCACCGATTACAA 57.220 45.000 0.00 0.00 0.00 2.41
281 282 2.779755 AAGCACCATCACCGATTACA 57.220 45.000 0.00 0.00 0.00 2.41
282 283 8.718102 ATATATAAAGCACCATCACCGATTAC 57.282 34.615 0.00 0.00 0.00 1.89
284 285 9.733556 TTTATATATAAAGCACCATCACCGATT 57.266 29.630 12.90 0.00 0.00 3.34
285 286 9.383519 CTTTATATATAAAGCACCATCACCGAT 57.616 33.333 25.10 0.00 41.69 4.18
286 287 8.771920 CTTTATATATAAAGCACCATCACCGA 57.228 34.615 25.10 0.00 41.69 4.69
316 317 0.753867 TTGCCGAAAAAGGGTTTCCC 59.246 50.000 0.00 0.00 45.90 3.97
317 318 2.605837 TTTGCCGAAAAAGGGTTTCC 57.394 45.000 0.00 0.00 0.00 3.13
318 319 3.249799 CCAATTTGCCGAAAAAGGGTTTC 59.750 43.478 0.00 0.00 0.00 2.78
319 320 3.118223 TCCAATTTGCCGAAAAAGGGTTT 60.118 39.130 0.00 0.00 31.31 3.27
320 321 2.436173 TCCAATTTGCCGAAAAAGGGTT 59.564 40.909 0.00 0.00 31.31 4.11
321 322 2.043227 TCCAATTTGCCGAAAAAGGGT 58.957 42.857 0.00 0.00 31.31 4.34
322 323 2.829741 TCCAATTTGCCGAAAAAGGG 57.170 45.000 0.00 0.00 31.31 3.95
323 324 4.143137 CGATTTCCAATTTGCCGAAAAAGG 60.143 41.667 5.35 0.00 0.00 3.11
324 325 4.666402 GCGATTTCCAATTTGCCGAAAAAG 60.666 41.667 5.35 4.52 0.00 2.27
325 326 3.185391 GCGATTTCCAATTTGCCGAAAAA 59.815 39.130 5.35 0.00 0.00 1.94
326 327 2.734079 GCGATTTCCAATTTGCCGAAAA 59.266 40.909 5.35 0.00 0.00 2.29
327 328 2.333014 GCGATTTCCAATTTGCCGAAA 58.667 42.857 4.12 4.12 0.00 3.46
328 329 1.403514 GGCGATTTCCAATTTGCCGAA 60.404 47.619 0.00 0.00 32.14 4.30
329 330 0.172352 GGCGATTTCCAATTTGCCGA 59.828 50.000 0.00 0.00 32.14 5.54
330 331 0.108898 TGGCGATTTCCAATTTGCCG 60.109 50.000 7.61 0.00 45.34 5.69
331 332 1.204467 TCTGGCGATTTCCAATTTGCC 59.796 47.619 5.75 5.75 42.76 4.52
332 333 2.094545 AGTCTGGCGATTTCCAATTTGC 60.095 45.455 0.00 0.00 35.36 3.68
333 334 3.191162 TGAGTCTGGCGATTTCCAATTTG 59.809 43.478 0.00 0.00 35.36 2.32
344 345 0.179234 TTTGGTTGTGAGTCTGGCGA 59.821 50.000 0.00 0.00 0.00 5.54
345 346 0.307760 GTTTGGTTGTGAGTCTGGCG 59.692 55.000 0.00 0.00 0.00 5.69
493 498 2.167487 TCAGGCGTTGACAGCACATATA 59.833 45.455 0.00 0.00 36.08 0.86
553 562 0.806868 CGTGCTGGAGATTGCAACAT 59.193 50.000 0.00 0.00 41.10 2.71
613 622 7.400915 TCCCAATAAGTTCAGCCTAAAGTAGTA 59.599 37.037 0.00 0.00 0.00 1.82
737 780 2.149578 GATTTCTGATCGGATGGCCAG 58.850 52.381 13.05 0.00 0.00 4.85
850 909 2.616376 CGGTTCAAAAGATGGTGTGACA 59.384 45.455 0.00 0.00 0.00 3.58
1041 1186 1.086634 AGTAGTAGACGACGTCGCCC 61.087 60.000 35.92 26.82 44.43 6.13
1175 1320 1.666189 CGAGCGTGTAGAGTGATCTCA 59.334 52.381 0.00 0.00 42.66 3.27
1177 1322 1.398739 CACGAGCGTGTAGAGTGATCT 59.601 52.381 14.36 0.00 40.91 2.75
1232 1629 1.202245 TGCAACTCGTTGGTTGAAAGC 60.202 47.619 17.49 7.08 46.55 3.51
1237 1634 2.548057 ACTATGTGCAACTCGTTGGTTG 59.452 45.455 11.35 11.88 46.41 3.77
1331 1767 2.809601 CGTTCGGAAGGGTCGCTG 60.810 66.667 2.57 0.00 0.00 5.18
1566 4802 8.245195 AGAAAGTTGGAGAGGATATCTAGTTC 57.755 38.462 2.05 0.00 38.84 3.01
1635 4878 4.976116 AGACAGTTTTGTATTTTTGCGAGC 59.024 37.500 0.00 0.00 37.76 5.03
1637 4880 6.556212 TGAAGACAGTTTTGTATTTTTGCGA 58.444 32.000 0.00 0.00 38.76 5.10
2406 6388 3.030291 TGTGCAAAGTCCAAAATGACCT 58.970 40.909 0.00 0.00 35.83 3.85


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

AutoCloner maintained by Alex Coulton.