Multiple sequence alignment - TraesCS2A01G311600

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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 TraesCS2A01G311600 chr2A 100.000 2988 0 0 1 2988 535412063 535415050 0.000000e+00 5518.0
1 TraesCS2A01G311600 chr2A 79.683 315 55 6 2631 2940 1607017 1606707 5.010000e-53 219.0
2 TraesCS2A01G311600 chr2A 79.878 164 28 4 714 873 22589755 22589593 6.770000e-22 115.0
3 TraesCS2A01G311600 chr2D 93.203 1942 98 14 1064 2988 398310474 398312398 0.000000e+00 2824.0
4 TraesCS2A01G311600 chr2D 95.305 213 8 2 1 211 423864339 423864127 1.330000e-88 337.0
5 TraesCS2A01G311600 chr2D 74.966 743 151 23 1066 1784 650685488 650686219 2.890000e-80 309.0
6 TraesCS2A01G311600 chr2D 91.549 142 9 2 897 1036 575827253 575827113 3.040000e-45 193.0
7 TraesCS2A01G311600 chr2B 90.620 1983 102 18 1064 2988 470911678 470913634 0.000000e+00 2555.0
8 TraesCS2A01G311600 chr2B 89.011 728 40 7 197 892 744455274 744454555 0.000000e+00 865.0
9 TraesCS2A01G311600 chr2B 88.563 682 45 3 222 873 519156944 519157622 0.000000e+00 797.0
10 TraesCS2A01G311600 chr2B 77.463 741 91 43 1633 2337 470904374 470903674 1.010000e-99 374.0
11 TraesCS2A01G311600 chr2B 79.393 461 79 13 1326 1776 5731161 5731615 8.040000e-81 311.0
12 TraesCS2A01G311600 chr2B 78.882 322 56 8 2627 2940 357151422 357151105 1.090000e-49 207.0
13 TraesCS2A01G311600 chr2B 95.968 124 5 0 897 1020 401145850 401145973 5.050000e-48 202.0
14 TraesCS2A01G311600 chr2B 92.199 141 8 2 897 1035 787077622 787077483 2.350000e-46 196.0
15 TraesCS2A01G311600 chr2B 91.367 139 12 0 897 1035 72674097 72673959 1.090000e-44 191.0
16 TraesCS2A01G311600 chr2B 97.368 38 1 0 1034 1071 470911625 470911662 6.910000e-07 65.8
17 TraesCS2A01G311600 chr6A 92.666 709 20 11 197 873 577858716 577859424 0.000000e+00 992.0
18 TraesCS2A01G311600 chr6A 78.919 370 69 8 1329 1695 50408559 50408196 2.980000e-60 243.0
19 TraesCS2A01G311600 chr6A 78.610 374 66 11 1329 1698 50865145 50864782 4.980000e-58 235.0
20 TraesCS2A01G311600 chr7B 92.199 705 20 10 197 869 611980677 611981378 0.000000e+00 965.0
21 TraesCS2A01G311600 chr7B 88.856 682 43 3 222 873 659892282 659891604 0.000000e+00 808.0
22 TraesCS2A01G311600 chr7B 78.882 322 56 9 2627 2940 122422997 122423314 1.090000e-49 207.0
23 TraesCS2A01G311600 chr7B 92.086 139 11 0 897 1035 619359384 619359246 2.350000e-46 196.0
24 TraesCS2A01G311600 chr7B 78.947 171 30 6 705 873 197699661 197699495 8.760000e-21 111.0
25 TraesCS2A01G311600 chr5B 88.494 704 46 5 222 893 558265609 558264909 0.000000e+00 819.0
26 TraesCS2A01G311600 chr5B 95.122 123 6 0 898 1020 680837476 680837354 8.450000e-46 195.0
27 TraesCS2A01G311600 chr5B 79.412 170 30 5 705 873 705527637 705527472 6.770000e-22 115.0
28 TraesCS2A01G311600 chr5B 79.167 168 26 9 736 898 455492831 455492668 1.130000e-19 108.0
29 TraesCS2A01G311600 chr3B 82.700 711 53 24 197 870 562754242 562754919 4.320000e-158 568.0
30 TraesCS2A01G311600 chr3B 78.931 318 55 8 2631 2940 809071405 809071718 3.900000e-49 206.0
31 TraesCS2A01G311600 chr3B 79.532 171 30 4 706 873 555555136 555555304 1.880000e-22 117.0
32 TraesCS2A01G311600 chr6B 81.278 673 58 27 197 834 105362167 105362806 1.610000e-132 483.0
33 TraesCS2A01G311600 chr6B 95.161 124 6 0 897 1020 3671031 3670908 2.350000e-46 196.0
34 TraesCS2A01G311600 chr4D 98.485 198 3 0 1 198 32130046 32130243 1.700000e-92 350.0
35 TraesCS2A01G311600 chr4D 97.980 198 4 0 1 198 111718015 111718212 7.930000e-91 344.0
36 TraesCS2A01G311600 chr4D 97.980 198 4 0 1 198 291190713 291190910 7.930000e-91 344.0
37 TraesCS2A01G311600 chr4D 86.174 311 31 5 293 598 346199836 346199533 2.870000e-85 326.0
38 TraesCS2A01G311600 chr4D 86.458 96 11 2 197 290 346200013 346199918 1.470000e-18 104.0
39 TraesCS2A01G311600 chr4B 97.990 199 4 0 1 199 262671386 262671584 2.200000e-91 346.0
40 TraesCS2A01G311600 chr4B 77.202 193 30 12 705 892 462773241 462773424 1.900000e-17 100.0
41 TraesCS2A01G311600 chr3D 97.980 198 4 0 1 198 207713714 207713517 7.930000e-91 344.0
42 TraesCS2A01G311600 chr3D 97.980 198 4 0 1 198 337501235 337501038 7.930000e-91 344.0
43 TraesCS2A01G311600 chr1A 97.980 198 4 0 1 198 364223455 364223652 7.930000e-91 344.0
44 TraesCS2A01G311600 chr5D 97.059 204 4 2 1 204 360782510 360782309 2.850000e-90 342.0
45 TraesCS2A01G311600 chr5D 80.781 333 53 5 2631 2952 466561462 466561794 1.780000e-62 250.0
46 TraesCS2A01G311600 chr5D 92.029 138 11 0 897 1034 481520473 481520610 8.450000e-46 195.0
47 TraesCS2A01G311600 chr5D 80.162 247 38 8 2696 2936 54814939 54815180 1.100000e-39 174.0
48 TraesCS2A01G311600 chr5D 82.323 198 26 4 2764 2952 2276682 2276485 2.380000e-36 163.0
49 TraesCS2A01G311600 chr4A 73.522 744 176 16 1064 1796 687706959 687706226 2.280000e-66 263.0
50 TraesCS2A01G311600 chr4A 73.351 743 177 14 1065 1796 687627420 687626688 3.820000e-64 255.0
51 TraesCS2A01G311600 chr4A 76.383 470 108 1 1327 1796 687660977 687660511 1.780000e-62 250.0
52 TraesCS2A01G311600 chr4A 79.688 320 54 8 2627 2940 374637117 374636803 1.390000e-53 220.0
53 TraesCS2A01G311600 chr4A 77.950 322 59 9 2627 2940 646533492 646533175 1.090000e-44 191.0
54 TraesCS2A01G311600 chr5A 79.062 320 56 8 2627 2940 648954087 648953773 3.020000e-50 209.0
55 TraesCS2A01G311600 chr3A 78.882 322 56 8 2627 2940 688456833 688456516 1.090000e-49 207.0
56 TraesCS2A01G311600 chr3A 92.806 139 7 2 897 1033 571916257 571916394 6.530000e-47 198.0
57 TraesCS2A01G311600 chr7A 78.571 322 60 6 2624 2940 299498689 299499006 1.400000e-48 204.0
58 TraesCS2A01G311600 chr1D 79.121 273 38 17 369 637 204022659 204022916 1.420000e-38 171.0
59 TraesCS2A01G311600 chr1D 83.333 180 23 4 2764 2940 468404241 468404066 3.080000e-35 159.0
60 TraesCS2A01G311600 chr7D 80.444 225 33 3 361 582 11127182 11127398 8.570000e-36 161.0


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 TraesCS2A01G311600 chr2A 535412063 535415050 2987 False 5518.0 5518 100.000 1 2988 1 chr2A.!!$F1 2987
1 TraesCS2A01G311600 chr2D 398310474 398312398 1924 False 2824.0 2824 93.203 1064 2988 1 chr2D.!!$F1 1924
2 TraesCS2A01G311600 chr2D 650685488 650686219 731 False 309.0 309 74.966 1066 1784 1 chr2D.!!$F2 718
3 TraesCS2A01G311600 chr2B 470911625 470913634 2009 False 1310.4 2555 93.994 1034 2988 2 chr2B.!!$F4 1954
4 TraesCS2A01G311600 chr2B 744454555 744455274 719 True 865.0 865 89.011 197 892 1 chr2B.!!$R4 695
5 TraesCS2A01G311600 chr2B 519156944 519157622 678 False 797.0 797 88.563 222 873 1 chr2B.!!$F3 651
6 TraesCS2A01G311600 chr2B 470903674 470904374 700 True 374.0 374 77.463 1633 2337 1 chr2B.!!$R3 704
7 TraesCS2A01G311600 chr6A 577858716 577859424 708 False 992.0 992 92.666 197 873 1 chr6A.!!$F1 676
8 TraesCS2A01G311600 chr7B 611980677 611981378 701 False 965.0 965 92.199 197 869 1 chr7B.!!$F2 672
9 TraesCS2A01G311600 chr7B 659891604 659892282 678 True 808.0 808 88.856 222 873 1 chr7B.!!$R3 651
10 TraesCS2A01G311600 chr5B 558264909 558265609 700 True 819.0 819 88.494 222 893 1 chr5B.!!$R2 671
11 TraesCS2A01G311600 chr3B 562754242 562754919 677 False 568.0 568 82.700 197 870 1 chr3B.!!$F2 673
12 TraesCS2A01G311600 chr6B 105362167 105362806 639 False 483.0 483 81.278 197 834 1 chr6B.!!$F1 637
13 TraesCS2A01G311600 chr4A 687706226 687706959 733 True 263.0 263 73.522 1064 1796 1 chr4A.!!$R5 732
14 TraesCS2A01G311600 chr4A 687626688 687627420 732 True 255.0 255 73.351 1065 1796 1 chr4A.!!$R3 731

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
984 1021 0.179078 TCGGTTTGTACGTGGCTTGT 60.179 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2660 2847 0.323302 TCGTCTGCCCTGCACAAATA 59.677 50.0 0.0 0.0 33.79 1.4 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
25 26 7.418408 GGCTAACTTTGACCAAATATTAGAGC 58.582 38.462 19.82 13.12 34.31 4.09
26 27 7.283354 GGCTAACTTTGACCAAATATTAGAGCT 59.717 37.037 19.82 0.00 34.31 4.09
27 28 9.326413 GCTAACTTTGACCAAATATTAGAGCTA 57.674 33.333 19.82 0.00 34.31 3.32
57 58 5.956068 TGACATGCAACTTACATAAAGCA 57.044 34.783 0.00 0.00 38.93 3.91
58 59 5.698832 TGACATGCAACTTACATAAAGCAC 58.301 37.500 0.00 0.00 38.93 4.40
59 60 5.240403 TGACATGCAACTTACATAAAGCACA 59.760 36.000 0.00 0.00 38.93 4.57
60 61 5.460646 ACATGCAACTTACATAAAGCACAC 58.539 37.500 0.00 0.00 38.93 3.82
61 62 4.497473 TGCAACTTACATAAAGCACACC 57.503 40.909 0.00 0.00 38.93 4.16
62 63 3.058570 TGCAACTTACATAAAGCACACCG 60.059 43.478 0.00 0.00 38.93 4.94
63 64 3.058501 GCAACTTACATAAAGCACACCGT 60.059 43.478 0.00 0.00 38.93 4.83
64 65 4.555906 GCAACTTACATAAAGCACACCGTT 60.556 41.667 0.00 0.00 38.93 4.44
65 66 5.334260 GCAACTTACATAAAGCACACCGTTA 60.334 40.000 0.00 0.00 38.93 3.18
66 67 6.660722 CAACTTACATAAAGCACACCGTTAA 58.339 36.000 0.00 0.00 38.93 2.01
67 68 6.864360 ACTTACATAAAGCACACCGTTAAA 57.136 33.333 0.00 0.00 38.93 1.52
68 69 7.443259 ACTTACATAAAGCACACCGTTAAAT 57.557 32.000 0.00 0.00 38.93 1.40
69 70 7.878036 ACTTACATAAAGCACACCGTTAAATT 58.122 30.769 0.00 0.00 38.93 1.82
70 71 8.019094 ACTTACATAAAGCACACCGTTAAATTC 58.981 33.333 0.00 0.00 38.93 2.17
71 72 5.387279 ACATAAAGCACACCGTTAAATTCG 58.613 37.500 0.00 0.00 0.00 3.34
72 73 3.974871 AAAGCACACCGTTAAATTCGT 57.025 38.095 0.00 0.00 0.00 3.85
73 74 2.961522 AGCACACCGTTAAATTCGTG 57.038 45.000 0.00 0.00 0.00 4.35
74 75 2.215196 AGCACACCGTTAAATTCGTGT 58.785 42.857 0.00 0.00 0.00 4.49
75 76 2.032377 AGCACACCGTTAAATTCGTGTG 60.032 45.455 13.39 13.39 40.02 3.82
76 77 2.286536 GCACACCGTTAAATTCGTGTGT 60.287 45.455 17.54 12.66 40.37 3.72
77 78 3.284914 CACACCGTTAAATTCGTGTGTG 58.715 45.455 17.05 17.05 44.50 3.82
78 79 3.196463 ACACCGTTAAATTCGTGTGTGA 58.804 40.909 9.71 0.00 39.31 3.58
79 80 3.622163 ACACCGTTAAATTCGTGTGTGAA 59.378 39.130 9.71 0.00 39.31 3.18
80 81 4.094590 ACACCGTTAAATTCGTGTGTGAAA 59.905 37.500 9.71 0.00 39.31 2.69
81 82 4.668837 CACCGTTAAATTCGTGTGTGAAAG 59.331 41.667 0.00 0.00 0.00 2.62
82 83 4.215965 CCGTTAAATTCGTGTGTGAAAGG 58.784 43.478 0.00 0.00 0.00 3.11
83 84 4.024725 CCGTTAAATTCGTGTGTGAAAGGA 60.025 41.667 0.00 0.00 0.00 3.36
84 85 5.137403 CGTTAAATTCGTGTGTGAAAGGAG 58.863 41.667 0.00 0.00 0.00 3.69
85 86 3.626028 AAATTCGTGTGTGAAAGGAGC 57.374 42.857 0.00 0.00 0.00 4.70
86 87 2.550830 ATTCGTGTGTGAAAGGAGCT 57.449 45.000 0.00 0.00 0.00 4.09
87 88 2.325583 TTCGTGTGTGAAAGGAGCTT 57.674 45.000 0.00 0.00 0.00 3.74
88 89 2.325583 TCGTGTGTGAAAGGAGCTTT 57.674 45.000 0.00 0.00 36.29 3.51
89 90 2.210116 TCGTGTGTGAAAGGAGCTTTC 58.790 47.619 0.00 0.00 46.88 2.62
118 119 9.518906 TGATATAATTTTCACATTGTGCATGTC 57.481 29.630 12.04 6.55 43.17 3.06
119 120 9.518906 GATATAATTTTCACATTGTGCATGTCA 57.481 29.630 12.04 0.00 43.17 3.58
121 122 6.474819 AATTTTCACATTGTGCATGTCATG 57.525 33.333 12.04 8.56 43.17 3.07
122 123 4.587584 TTTCACATTGTGCATGTCATGT 57.412 36.364 14.26 0.00 43.17 3.21
123 124 5.702349 TTTCACATTGTGCATGTCATGTA 57.298 34.783 14.26 7.11 43.17 2.29
124 125 4.683501 TCACATTGTGCATGTCATGTAC 57.316 40.909 22.84 22.84 43.17 2.90
125 126 4.325972 TCACATTGTGCATGTCATGTACT 58.674 39.130 27.47 11.55 43.17 2.73
126 127 5.486526 TCACATTGTGCATGTCATGTACTA 58.513 37.500 27.47 22.59 43.17 1.82
127 128 6.114767 TCACATTGTGCATGTCATGTACTAT 58.885 36.000 27.47 23.55 43.17 2.12
128 129 6.598850 TCACATTGTGCATGTCATGTACTATT 59.401 34.615 27.47 16.17 43.17 1.73
129 130 7.768120 TCACATTGTGCATGTCATGTACTATTA 59.232 33.333 27.47 14.37 43.17 0.98
130 131 8.397148 CACATTGTGCATGTCATGTACTATTAA 58.603 33.333 27.47 17.22 43.17 1.40
131 132 9.123902 ACATTGTGCATGTCATGTACTATTAAT 57.876 29.630 27.47 18.36 43.17 1.40
132 133 9.603298 CATTGTGCATGTCATGTACTATTAATC 57.397 33.333 27.47 6.34 44.74 1.75
133 134 8.962884 TTGTGCATGTCATGTACTATTAATCT 57.037 30.769 27.47 0.00 44.74 2.40
134 135 8.962884 TGTGCATGTCATGTACTATTAATCTT 57.037 30.769 27.47 0.00 44.74 2.40
135 136 8.829612 TGTGCATGTCATGTACTATTAATCTTG 58.170 33.333 27.47 0.00 44.74 3.02
136 137 8.830580 GTGCATGTCATGTACTATTAATCTTGT 58.169 33.333 22.47 0.00 41.79 3.16
137 138 9.045223 TGCATGTCATGTACTATTAATCTTGTC 57.955 33.333 14.26 0.00 0.00 3.18
138 139 9.045223 GCATGTCATGTACTATTAATCTTGTCA 57.955 33.333 14.26 0.00 0.00 3.58
151 152 5.551760 AATCTTGTCAATAGTCAAAGGCG 57.448 39.130 0.00 0.00 0.00 5.52
152 153 3.334691 TCTTGTCAATAGTCAAAGGCGG 58.665 45.455 0.00 0.00 0.00 6.13
153 154 2.851263 TGTCAATAGTCAAAGGCGGT 57.149 45.000 0.00 0.00 0.00 5.68
154 155 2.695359 TGTCAATAGTCAAAGGCGGTC 58.305 47.619 0.00 0.00 0.00 4.79
155 156 2.301870 TGTCAATAGTCAAAGGCGGTCT 59.698 45.455 0.00 0.00 0.00 3.85
156 157 3.244422 TGTCAATAGTCAAAGGCGGTCTT 60.244 43.478 0.00 0.00 37.28 3.01
157 158 4.020928 TGTCAATAGTCAAAGGCGGTCTTA 60.021 41.667 0.00 0.00 34.78 2.10
158 159 4.933400 GTCAATAGTCAAAGGCGGTCTTAA 59.067 41.667 0.00 0.00 34.78 1.85
159 160 5.410439 GTCAATAGTCAAAGGCGGTCTTAAA 59.590 40.000 0.00 0.00 34.78 1.52
160 161 5.998981 TCAATAGTCAAAGGCGGTCTTAAAA 59.001 36.000 0.00 0.00 34.78 1.52
161 162 6.487331 TCAATAGTCAAAGGCGGTCTTAAAAA 59.513 34.615 0.00 0.00 34.78 1.94
184 185 8.757982 AAAATGCATTAGGCCCTATATAGATG 57.242 34.615 13.39 6.87 43.89 2.90
185 186 5.894298 TGCATTAGGCCCTATATAGATGG 57.106 43.478 11.53 6.04 43.89 3.51
186 187 5.537914 TGCATTAGGCCCTATATAGATGGA 58.462 41.667 11.53 4.41 43.89 3.41
187 188 5.970021 TGCATTAGGCCCTATATAGATGGAA 59.030 40.000 11.53 0.00 43.89 3.53
188 189 6.100279 TGCATTAGGCCCTATATAGATGGAAG 59.900 42.308 11.53 0.00 43.89 3.46
189 190 6.327626 GCATTAGGCCCTATATAGATGGAAGA 59.672 42.308 11.53 0.00 36.11 2.87
190 191 7.147479 GCATTAGGCCCTATATAGATGGAAGAA 60.147 40.741 11.53 1.20 36.11 2.52
191 192 7.979786 TTAGGCCCTATATAGATGGAAGAAG 57.020 40.000 11.53 0.00 0.00 2.85
192 193 5.284582 AGGCCCTATATAGATGGAAGAAGG 58.715 45.833 11.53 1.87 0.00 3.46
193 194 4.410555 GGCCCTATATAGATGGAAGAAGGG 59.589 50.000 11.53 3.52 44.43 3.95
194 195 5.281314 GCCCTATATAGATGGAAGAAGGGA 58.719 45.833 11.53 0.00 44.39 4.20
195 196 5.365314 GCCCTATATAGATGGAAGAAGGGAG 59.635 48.000 11.53 0.00 44.39 4.30
208 209 6.836527 TGGAAGAAGGGAGTAAATCAAAACAA 59.163 34.615 0.00 0.00 0.00 2.83
220 221 3.320610 TCAAAACAATGGAAGGTCCCA 57.679 42.857 0.00 0.00 41.05 4.37
291 294 1.525077 TTGGCGACGGAGCAAAACT 60.525 52.632 6.70 0.00 39.27 2.66
454 457 1.749634 GCAAGCTCCTACCTAAGTCGA 59.250 52.381 0.00 0.00 0.00 4.20
712 745 4.578928 CCGTCCCGATTTAAAAAGGATCAT 59.421 41.667 12.32 0.00 0.00 2.45
734 767 5.570205 TGGGTTGAATACTCTAAACCACA 57.430 39.130 5.84 0.00 43.20 4.17
832 867 5.010012 CAGAGGGTCTTTTATGCAAAACAGT 59.990 40.000 0.00 0.00 30.52 3.55
876 911 7.665080 GCAATCGCTGGTTTATTAGTAAAAG 57.335 36.000 0.00 0.00 31.46 2.27
877 912 7.248437 GCAATCGCTGGTTTATTAGTAAAAGT 58.752 34.615 0.00 0.00 31.46 2.66
878 913 8.392612 GCAATCGCTGGTTTATTAGTAAAAGTA 58.607 33.333 0.00 0.00 31.46 2.24
918 955 9.788960 AAAGATTTTACTTCTTGACTGTTGTTC 57.211 29.630 0.00 0.00 33.79 3.18
919 956 7.931275 AGATTTTACTTCTTGACTGTTGTTCC 58.069 34.615 0.00 0.00 0.00 3.62
920 957 7.775561 AGATTTTACTTCTTGACTGTTGTTCCT 59.224 33.333 0.00 0.00 0.00 3.36
921 958 7.696992 TTTTACTTCTTGACTGTTGTTCCTT 57.303 32.000 0.00 0.00 0.00 3.36
922 959 7.696992 TTTACTTCTTGACTGTTGTTCCTTT 57.303 32.000 0.00 0.00 0.00 3.11
923 960 5.567138 ACTTCTTGACTGTTGTTCCTTTG 57.433 39.130 0.00 0.00 0.00 2.77
924 961 5.010282 ACTTCTTGACTGTTGTTCCTTTGT 58.990 37.500 0.00 0.00 0.00 2.83
925 962 4.963276 TCTTGACTGTTGTTCCTTTGTG 57.037 40.909 0.00 0.00 0.00 3.33
926 963 3.128589 TCTTGACTGTTGTTCCTTTGTGC 59.871 43.478 0.00 0.00 0.00 4.57
927 964 2.441410 TGACTGTTGTTCCTTTGTGCA 58.559 42.857 0.00 0.00 0.00 4.57
928 965 2.822561 TGACTGTTGTTCCTTTGTGCAA 59.177 40.909 0.00 0.00 0.00 4.08
929 966 3.256879 TGACTGTTGTTCCTTTGTGCAAA 59.743 39.130 0.00 0.00 0.00 3.68
930 967 3.848726 ACTGTTGTTCCTTTGTGCAAAG 58.151 40.909 15.53 15.53 45.47 2.77
937 974 3.389741 CTTTGTGCAAAGGCTAGCG 57.610 52.632 9.00 0.00 42.96 4.26
938 975 0.593128 CTTTGTGCAAAGGCTAGCGT 59.407 50.000 9.00 6.32 42.96 5.07
939 976 1.001378 CTTTGTGCAAAGGCTAGCGTT 60.001 47.619 16.67 16.67 42.96 4.84
940 977 1.028905 TTGTGCAAAGGCTAGCGTTT 58.971 45.000 25.57 25.57 41.91 3.60
941 978 1.028905 TGTGCAAAGGCTAGCGTTTT 58.971 45.000 27.94 18.53 41.91 2.43
942 979 1.268999 TGTGCAAAGGCTAGCGTTTTG 60.269 47.619 27.94 27.12 41.91 2.44
943 980 0.318614 TGCAAAGGCTAGCGTTTTGC 60.319 50.000 36.42 36.42 42.46 3.68
963 1000 3.009301 CTGTCTTTTCAGCTTTGCCAG 57.991 47.619 0.00 0.00 0.00 4.85
964 1001 1.682854 TGTCTTTTCAGCTTTGCCAGG 59.317 47.619 0.00 0.00 0.00 4.45
965 1002 1.683385 GTCTTTTCAGCTTTGCCAGGT 59.317 47.619 0.00 0.00 0.00 4.00
966 1003 1.956477 TCTTTTCAGCTTTGCCAGGTC 59.044 47.619 0.00 0.00 0.00 3.85
967 1004 0.667993 TTTTCAGCTTTGCCAGGTCG 59.332 50.000 0.00 0.00 0.00 4.79
968 1005 1.172180 TTTCAGCTTTGCCAGGTCGG 61.172 55.000 0.00 0.00 38.11 4.79
969 1006 2.281761 CAGCTTTGCCAGGTCGGT 60.282 61.111 0.00 0.00 36.97 4.69
970 1007 1.898574 CAGCTTTGCCAGGTCGGTT 60.899 57.895 0.00 0.00 36.97 4.44
971 1008 1.152756 AGCTTTGCCAGGTCGGTTT 60.153 52.632 0.00 0.00 36.97 3.27
972 1009 1.007387 GCTTTGCCAGGTCGGTTTG 60.007 57.895 0.00 0.00 36.97 2.93
973 1010 1.734388 GCTTTGCCAGGTCGGTTTGT 61.734 55.000 0.00 0.00 36.97 2.83
974 1011 1.600023 CTTTGCCAGGTCGGTTTGTA 58.400 50.000 0.00 0.00 36.97 2.41
975 1012 1.265905 CTTTGCCAGGTCGGTTTGTAC 59.734 52.381 0.00 0.00 36.97 2.90
976 1013 0.881159 TTGCCAGGTCGGTTTGTACG 60.881 55.000 0.00 0.00 36.97 3.67
977 1014 1.301165 GCCAGGTCGGTTTGTACGT 60.301 57.895 0.00 0.00 36.97 3.57
978 1015 1.562575 GCCAGGTCGGTTTGTACGTG 61.563 60.000 0.00 0.00 36.97 4.49
979 1016 0.947180 CCAGGTCGGTTTGTACGTGG 60.947 60.000 0.00 0.00 43.04 4.94
980 1017 1.301165 AGGTCGGTTTGTACGTGGC 60.301 57.895 0.00 0.00 0.00 5.01
981 1018 1.301165 GGTCGGTTTGTACGTGGCT 60.301 57.895 0.00 0.00 0.00 4.75
982 1019 0.881600 GGTCGGTTTGTACGTGGCTT 60.882 55.000 0.00 0.00 0.00 4.35
983 1020 0.233848 GTCGGTTTGTACGTGGCTTG 59.766 55.000 0.00 0.00 0.00 4.01
984 1021 0.179078 TCGGTTTGTACGTGGCTTGT 60.179 50.000 0.00 0.00 0.00 3.16
985 1022 1.068281 TCGGTTTGTACGTGGCTTGTA 59.932 47.619 0.00 0.00 0.00 2.41
986 1023 1.192980 CGGTTTGTACGTGGCTTGTAC 59.807 52.381 0.00 11.33 41.97 2.90
987 1024 2.486918 GGTTTGTACGTGGCTTGTACT 58.513 47.619 16.75 0.00 42.09 2.73
988 1025 3.652274 GGTTTGTACGTGGCTTGTACTA 58.348 45.455 16.75 9.53 42.09 1.82
989 1026 4.248058 GGTTTGTACGTGGCTTGTACTAT 58.752 43.478 16.75 0.00 42.09 2.12
990 1027 4.092383 GGTTTGTACGTGGCTTGTACTATG 59.908 45.833 16.75 0.00 42.09 2.23
991 1028 4.787260 TTGTACGTGGCTTGTACTATGA 57.213 40.909 16.75 0.00 42.09 2.15
992 1029 4.994907 TGTACGTGGCTTGTACTATGAT 57.005 40.909 16.75 0.00 42.09 2.45
993 1030 4.928601 TGTACGTGGCTTGTACTATGATC 58.071 43.478 16.75 0.00 42.09 2.92
994 1031 3.454371 ACGTGGCTTGTACTATGATCC 57.546 47.619 0.00 0.00 0.00 3.36
995 1032 3.031736 ACGTGGCTTGTACTATGATCCT 58.968 45.455 0.00 0.00 0.00 3.24
996 1033 3.451178 ACGTGGCTTGTACTATGATCCTT 59.549 43.478 0.00 0.00 0.00 3.36
997 1034 4.647853 ACGTGGCTTGTACTATGATCCTTA 59.352 41.667 0.00 0.00 0.00 2.69
998 1035 5.304614 ACGTGGCTTGTACTATGATCCTTAT 59.695 40.000 0.00 0.00 0.00 1.73
999 1036 5.635280 CGTGGCTTGTACTATGATCCTTATG 59.365 44.000 0.00 0.00 0.00 1.90
1000 1037 6.516693 CGTGGCTTGTACTATGATCCTTATGA 60.517 42.308 0.00 0.00 0.00 2.15
1001 1038 7.390027 GTGGCTTGTACTATGATCCTTATGAT 58.610 38.462 0.00 0.00 36.01 2.45
1002 1039 8.531982 GTGGCTTGTACTATGATCCTTATGATA 58.468 37.037 0.00 0.00 32.41 2.15
1003 1040 9.271921 TGGCTTGTACTATGATCCTTATGATAT 57.728 33.333 0.00 0.00 32.41 1.63
1025 1062 9.533983 GATATAAATGAGACATGTATTGTTGCG 57.466 33.333 0.00 0.00 39.18 4.85
1026 1063 5.878332 AAATGAGACATGTATTGTTGCGA 57.122 34.783 0.00 0.00 39.18 5.10
1027 1064 5.878332 AATGAGACATGTATTGTTGCGAA 57.122 34.783 0.00 0.00 39.18 4.70
1028 1065 5.878332 ATGAGACATGTATTGTTGCGAAA 57.122 34.783 0.00 0.00 39.18 3.46
1029 1066 5.681337 TGAGACATGTATTGTTGCGAAAA 57.319 34.783 0.00 0.00 39.18 2.29
1030 1067 6.066054 TGAGACATGTATTGTTGCGAAAAA 57.934 33.333 0.00 0.00 39.18 1.94
1193 1269 3.068691 TCAGAGTTCCTCGGCGGG 61.069 66.667 7.21 1.99 35.36 6.13
1229 1305 2.238353 GGCCATCATCGAATGGACG 58.762 57.895 18.43 0.00 44.78 4.79
1493 1584 1.395826 GGGACATCGGGAGAGACAGG 61.396 65.000 0.00 0.00 45.48 4.00
1523 1614 1.437986 GGATCCCGACGAGTTCCAG 59.562 63.158 0.00 0.00 0.00 3.86
1617 1708 4.418401 CGTTTGGTGCGGGGCATG 62.418 66.667 0.00 0.00 41.91 4.06
1732 1829 4.444838 CGGCGGGGTCGACATGAA 62.445 66.667 18.91 0.00 46.65 2.57
1784 1881 1.826487 GCCACTTTCCACCCGTGTT 60.826 57.895 0.00 0.00 0.00 3.32
1909 2026 1.470098 GATGTGCCAGTGTCATGTTCC 59.530 52.381 0.00 0.00 0.00 3.62
1943 2062 3.303990 GGCACGTGCAAAGATACCATATG 60.304 47.826 38.60 0.00 44.36 1.78
1944 2063 3.312421 GCACGTGCAAAGATACCATATGT 59.688 43.478 34.52 0.00 41.59 2.29
1949 2068 5.239306 CGTGCAAAGATACCATATGTCCAAT 59.761 40.000 1.24 0.00 0.00 3.16
1969 2089 1.709994 CCCCCAAGGCTCCACTATCC 61.710 65.000 0.00 0.00 0.00 2.59
1973 2093 1.766461 AAGGCTCCACTATCCCCCG 60.766 63.158 0.00 0.00 0.00 5.73
1994 2114 3.574614 GCACAGGCACACGAAATTAATT 58.425 40.909 0.00 0.00 40.72 1.40
1995 2115 4.670478 CGCACAGGCACACGAAATTAATTA 60.670 41.667 0.01 0.00 41.24 1.40
1996 2116 4.793216 GCACAGGCACACGAAATTAATTAG 59.207 41.667 0.01 1.82 40.72 1.73
1997 2117 5.619086 GCACAGGCACACGAAATTAATTAGT 60.619 40.000 0.01 2.45 40.72 2.24
1998 2118 6.402766 GCACAGGCACACGAAATTAATTAGTA 60.403 38.462 0.01 0.00 40.72 1.82
1999 2119 6.959311 CACAGGCACACGAAATTAATTAGTAC 59.041 38.462 0.01 0.00 0.00 2.73
2000 2120 6.877322 ACAGGCACACGAAATTAATTAGTACT 59.123 34.615 0.01 0.00 0.00 2.73
2001 2121 7.148474 ACAGGCACACGAAATTAATTAGTACTG 60.148 37.037 5.39 12.10 0.00 2.74
2284 2422 5.551760 AGAGCAATGTTTAATCGGAAGTG 57.448 39.130 0.00 0.00 0.00 3.16
2346 2511 4.081198 TGCCCACAAAATTATTCATCCCAC 60.081 41.667 0.00 0.00 0.00 4.61
2379 2564 2.616969 GCTCCAAACAAGAGCGTGA 58.383 52.632 0.00 0.00 46.58 4.35
2430 2615 0.252197 ATCGGACCAAGGTAAGCACC 59.748 55.000 0.00 0.00 46.19 5.01
2470 2655 8.222433 CGATATTGAAGAGAAGATGCATCTTTC 58.778 37.037 35.91 30.63 46.47 2.62
2476 2661 9.708092 TGAAGAGAAGATGCATCTTTCTATATG 57.292 33.333 35.91 0.00 46.47 1.78
2560 2747 2.279037 ATTGGGGGCCTTACGCGAAT 62.279 55.000 15.93 0.00 38.94 3.34
2660 2847 2.575532 CAACACCTCACAACCTGACAT 58.424 47.619 0.00 0.00 0.00 3.06
2675 2862 2.093890 TGACATATTTGTGCAGGGCAG 58.906 47.619 0.00 0.00 40.08 4.85
2701 2888 2.391616 TGCAGAGTTAGTGATGCCAG 57.608 50.000 0.00 0.00 37.89 4.85
2726 2913 8.448615 AGTCAGCGTTATTAATTGGTTTAGTTC 58.551 33.333 0.00 0.00 0.00 3.01
2812 2999 2.496899 TTCCAGAAGCCATCAAGTCC 57.503 50.000 0.00 0.00 0.00 3.85
2862 3049 4.201744 GCCATAACTTGCATTGTCATTTGC 60.202 41.667 0.00 2.16 39.33 3.68
2967 3157 5.455392 CATGTAACTGAACCAAAAGAGCTG 58.545 41.667 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.283354 AGCTCTAATATTTGGTCAAAGTTAGCC 59.717 37.037 17.32 13.39 35.14 3.93
1 2 8.214721 AGCTCTAATATTTGGTCAAAGTTAGC 57.785 34.615 17.32 13.21 35.14 3.09
31 32 9.336171 TGCTTTATGTAAGTTGCATGTCATATA 57.664 29.630 15.82 0.00 36.19 0.86
32 33 8.131100 GTGCTTTATGTAAGTTGCATGTCATAT 58.869 33.333 15.82 0.00 36.19 1.78
33 34 7.120432 TGTGCTTTATGTAAGTTGCATGTCATA 59.880 33.333 15.82 4.86 36.19 2.15
34 35 6.072008 TGTGCTTTATGTAAGTTGCATGTCAT 60.072 34.615 15.82 0.00 36.19 3.06
35 36 5.240403 TGTGCTTTATGTAAGTTGCATGTCA 59.760 36.000 15.82 6.08 36.19 3.58
36 37 5.569059 GTGTGCTTTATGTAAGTTGCATGTC 59.431 40.000 15.82 3.87 36.19 3.06
37 38 5.460646 GTGTGCTTTATGTAAGTTGCATGT 58.539 37.500 15.82 0.00 36.19 3.21
38 39 4.858692 GGTGTGCTTTATGTAAGTTGCATG 59.141 41.667 15.82 1.56 36.19 4.06
39 40 4.379394 CGGTGTGCTTTATGTAAGTTGCAT 60.379 41.667 11.37 11.37 36.19 3.96
40 41 3.058570 CGGTGTGCTTTATGTAAGTTGCA 60.059 43.478 0.00 0.00 36.19 4.08
41 42 3.058501 ACGGTGTGCTTTATGTAAGTTGC 60.059 43.478 0.00 0.00 36.19 4.17
42 43 4.742438 ACGGTGTGCTTTATGTAAGTTG 57.258 40.909 0.00 0.00 36.19 3.16
43 44 6.864360 TTAACGGTGTGCTTTATGTAAGTT 57.136 33.333 0.00 0.00 36.19 2.66
44 45 6.864360 TTTAACGGTGTGCTTTATGTAAGT 57.136 33.333 0.00 0.00 36.19 2.24
45 46 7.215568 CGAATTTAACGGTGTGCTTTATGTAAG 59.784 37.037 0.00 0.00 36.90 2.34
46 47 7.016466 CGAATTTAACGGTGTGCTTTATGTAA 58.984 34.615 0.00 0.00 0.00 2.41
47 48 6.147492 ACGAATTTAACGGTGTGCTTTATGTA 59.853 34.615 0.00 0.00 34.93 2.29
48 49 5.049267 ACGAATTTAACGGTGTGCTTTATGT 60.049 36.000 0.00 0.00 34.93 2.29
49 50 5.282778 CACGAATTTAACGGTGTGCTTTATG 59.717 40.000 0.00 0.00 34.93 1.90
50 51 5.049267 ACACGAATTTAACGGTGTGCTTTAT 60.049 36.000 0.00 0.00 34.93 1.40
51 52 4.272991 ACACGAATTTAACGGTGTGCTTTA 59.727 37.500 0.00 0.00 34.93 1.85
52 53 3.065648 ACACGAATTTAACGGTGTGCTTT 59.934 39.130 0.00 0.00 34.93 3.51
53 54 2.614983 ACACGAATTTAACGGTGTGCTT 59.385 40.909 0.00 0.00 34.93 3.91
54 55 2.032377 CACACGAATTTAACGGTGTGCT 60.032 45.455 9.81 0.00 36.70 4.40
55 56 2.286536 ACACACGAATTTAACGGTGTGC 60.287 45.455 19.53 0.00 41.40 4.57
56 57 3.284914 CACACACGAATTTAACGGTGTG 58.715 45.455 18.39 18.39 45.49 3.82
57 58 3.196463 TCACACACGAATTTAACGGTGT 58.804 40.909 0.00 0.00 41.61 4.16
58 59 3.863396 TCACACACGAATTTAACGGTG 57.137 42.857 0.00 0.00 37.66 4.94
59 60 4.260866 CCTTTCACACACGAATTTAACGGT 60.261 41.667 0.00 0.00 34.93 4.83
60 61 4.024725 TCCTTTCACACACGAATTTAACGG 60.025 41.667 0.00 0.00 34.93 4.44
61 62 5.085636 TCCTTTCACACACGAATTTAACG 57.914 39.130 0.00 0.00 0.00 3.18
62 63 4.909880 GCTCCTTTCACACACGAATTTAAC 59.090 41.667 0.00 0.00 0.00 2.01
63 64 4.819630 AGCTCCTTTCACACACGAATTTAA 59.180 37.500 0.00 0.00 0.00 1.52
64 65 4.385825 AGCTCCTTTCACACACGAATTTA 58.614 39.130 0.00 0.00 0.00 1.40
65 66 3.214328 AGCTCCTTTCACACACGAATTT 58.786 40.909 0.00 0.00 0.00 1.82
66 67 2.851195 AGCTCCTTTCACACACGAATT 58.149 42.857 0.00 0.00 0.00 2.17
67 68 2.550830 AGCTCCTTTCACACACGAAT 57.449 45.000 0.00 0.00 0.00 3.34
68 69 2.325583 AAGCTCCTTTCACACACGAA 57.674 45.000 0.00 0.00 0.00 3.85
69 70 2.210116 GAAAGCTCCTTTCACACACGA 58.790 47.619 11.65 0.00 46.23 4.35
70 71 2.670401 GAAAGCTCCTTTCACACACG 57.330 50.000 11.65 0.00 46.23 4.49
106 107 9.603298 GATTAATAGTACATGACATGCACAATG 57.397 33.333 18.79 0.00 42.48 2.82
107 108 9.565090 AGATTAATAGTACATGACATGCACAAT 57.435 29.630 18.79 10.52 0.00 2.71
108 109 8.962884 AGATTAATAGTACATGACATGCACAA 57.037 30.769 18.79 6.65 0.00 3.33
109 110 8.829612 CAAGATTAATAGTACATGACATGCACA 58.170 33.333 18.79 7.29 0.00 4.57
110 111 8.830580 ACAAGATTAATAGTACATGACATGCAC 58.169 33.333 15.49 12.79 0.00 4.57
111 112 8.962884 ACAAGATTAATAGTACATGACATGCA 57.037 30.769 15.49 0.00 0.00 3.96
112 113 9.045223 TGACAAGATTAATAGTACATGACATGC 57.955 33.333 15.49 0.11 0.00 4.06
125 126 8.826710 CGCCTTTGACTATTGACAAGATTAATA 58.173 33.333 0.00 0.00 0.00 0.98
126 127 7.201732 CCGCCTTTGACTATTGACAAGATTAAT 60.202 37.037 0.00 0.00 0.00 1.40
127 128 6.093495 CCGCCTTTGACTATTGACAAGATTAA 59.907 38.462 0.00 0.00 0.00 1.40
128 129 5.584649 CCGCCTTTGACTATTGACAAGATTA 59.415 40.000 0.00 0.00 0.00 1.75
129 130 4.396166 CCGCCTTTGACTATTGACAAGATT 59.604 41.667 0.00 0.00 0.00 2.40
130 131 3.941483 CCGCCTTTGACTATTGACAAGAT 59.059 43.478 0.00 0.00 0.00 2.40
131 132 3.244422 ACCGCCTTTGACTATTGACAAGA 60.244 43.478 0.00 0.00 0.00 3.02
132 133 3.074412 ACCGCCTTTGACTATTGACAAG 58.926 45.455 0.00 0.00 0.00 3.16
133 134 3.071479 GACCGCCTTTGACTATTGACAA 58.929 45.455 0.00 0.00 0.00 3.18
134 135 2.301870 AGACCGCCTTTGACTATTGACA 59.698 45.455 0.00 0.00 0.00 3.58
135 136 2.973945 AGACCGCCTTTGACTATTGAC 58.026 47.619 0.00 0.00 0.00 3.18
136 137 3.695830 AAGACCGCCTTTGACTATTGA 57.304 42.857 0.00 0.00 0.00 2.57
137 138 5.873179 TTTAAGACCGCCTTTGACTATTG 57.127 39.130 0.00 0.00 36.34 1.90
138 139 6.887626 TTTTTAAGACCGCCTTTGACTATT 57.112 33.333 0.00 0.00 36.34 1.73
158 159 9.193806 CATCTATATAGGGCCTAATGCATTTTT 57.806 33.333 18.91 0.00 43.89 1.94
159 160 7.781693 CCATCTATATAGGGCCTAATGCATTTT 59.218 37.037 18.91 0.30 43.89 1.82
160 161 7.129349 TCCATCTATATAGGGCCTAATGCATTT 59.871 37.037 18.91 1.12 43.89 2.32
161 162 6.621098 TCCATCTATATAGGGCCTAATGCATT 59.379 38.462 18.91 17.56 43.89 3.56
162 163 6.153204 TCCATCTATATAGGGCCTAATGCAT 58.847 40.000 18.91 10.87 43.89 3.96
163 164 5.537914 TCCATCTATATAGGGCCTAATGCA 58.462 41.667 18.91 0.00 43.89 3.96
164 165 6.327626 TCTTCCATCTATATAGGGCCTAATGC 59.672 42.308 18.91 0.00 40.16 3.56
165 166 7.921041 TCTTCCATCTATATAGGGCCTAATG 57.079 40.000 18.91 15.42 0.00 1.90
166 167 7.570607 CCTTCTTCCATCTATATAGGGCCTAAT 59.429 40.741 18.91 14.19 0.00 1.73
167 168 6.903534 CCTTCTTCCATCTATATAGGGCCTAA 59.096 42.308 18.91 7.61 0.00 2.69
168 169 6.444704 CCTTCTTCCATCTATATAGGGCCTA 58.555 44.000 17.16 17.16 0.00 3.93
169 170 5.284582 CCTTCTTCCATCTATATAGGGCCT 58.715 45.833 12.58 12.58 0.00 5.19
170 171 4.410555 CCCTTCTTCCATCTATATAGGGCC 59.589 50.000 9.89 0.00 35.11 5.80
171 172 5.281314 TCCCTTCTTCCATCTATATAGGGC 58.719 45.833 9.89 0.00 40.71 5.19
172 173 6.507568 ACTCCCTTCTTCCATCTATATAGGG 58.492 44.000 9.89 4.49 41.98 3.53
173 174 9.548631 TTTACTCCCTTCTTCCATCTATATAGG 57.451 37.037 9.89 0.00 0.00 2.57
176 177 9.621239 TGATTTACTCCCTTCTTCCATCTATAT 57.379 33.333 0.00 0.00 0.00 0.86
177 178 9.447279 TTGATTTACTCCCTTCTTCCATCTATA 57.553 33.333 0.00 0.00 0.00 1.31
178 179 7.937700 TGATTTACTCCCTTCTTCCATCTAT 57.062 36.000 0.00 0.00 0.00 1.98
179 180 7.749377 TTGATTTACTCCCTTCTTCCATCTA 57.251 36.000 0.00 0.00 0.00 1.98
180 181 6.642733 TTGATTTACTCCCTTCTTCCATCT 57.357 37.500 0.00 0.00 0.00 2.90
181 182 7.176690 TGTTTTGATTTACTCCCTTCTTCCATC 59.823 37.037 0.00 0.00 0.00 3.51
182 183 7.010160 TGTTTTGATTTACTCCCTTCTTCCAT 58.990 34.615 0.00 0.00 0.00 3.41
183 184 6.369629 TGTTTTGATTTACTCCCTTCTTCCA 58.630 36.000 0.00 0.00 0.00 3.53
184 185 6.894339 TGTTTTGATTTACTCCCTTCTTCC 57.106 37.500 0.00 0.00 0.00 3.46
185 186 7.814587 CCATTGTTTTGATTTACTCCCTTCTTC 59.185 37.037 0.00 0.00 0.00 2.87
186 187 7.508977 TCCATTGTTTTGATTTACTCCCTTCTT 59.491 33.333 0.00 0.00 0.00 2.52
187 188 7.010160 TCCATTGTTTTGATTTACTCCCTTCT 58.990 34.615 0.00 0.00 0.00 2.85
188 189 7.227049 TCCATTGTTTTGATTTACTCCCTTC 57.773 36.000 0.00 0.00 0.00 3.46
189 190 7.256296 CCTTCCATTGTTTTGATTTACTCCCTT 60.256 37.037 0.00 0.00 0.00 3.95
190 191 6.211384 CCTTCCATTGTTTTGATTTACTCCCT 59.789 38.462 0.00 0.00 0.00 4.20
191 192 6.014584 ACCTTCCATTGTTTTGATTTACTCCC 60.015 38.462 0.00 0.00 0.00 4.30
192 193 6.993079 ACCTTCCATTGTTTTGATTTACTCC 58.007 36.000 0.00 0.00 0.00 3.85
193 194 7.090808 GGACCTTCCATTGTTTTGATTTACTC 58.909 38.462 0.00 0.00 36.28 2.59
194 195 6.014584 GGGACCTTCCATTGTTTTGATTTACT 60.015 38.462 0.00 0.00 38.64 2.24
195 196 6.163476 GGGACCTTCCATTGTTTTGATTTAC 58.837 40.000 0.00 0.00 38.64 2.01
208 209 2.965147 CACTGTTTTTGGGACCTTCCAT 59.035 45.455 0.00 0.00 38.64 3.41
220 221 2.689983 CTCTTGCCACTCCACTGTTTTT 59.310 45.455 0.00 0.00 0.00 1.94
621 624 2.281070 GGCGGATCCATGCGATGT 60.281 61.111 13.41 0.00 44.78 3.06
712 745 5.514136 CCTGTGGTTTAGAGTATTCAACCCA 60.514 44.000 5.39 3.32 38.36 4.51
734 767 2.028930 TCGTTTTTGCACAAAACACCCT 60.029 40.909 24.05 0.00 39.70 4.34
821 856 1.574428 GTCGCCGACTGTTTTGCAT 59.426 52.632 10.56 0.00 0.00 3.96
832 867 3.740397 CTGGTGGTACGTCGCCGA 61.740 66.667 0.00 0.00 40.02 5.54
898 935 7.175990 ACAAAGGAACAACAGTCAAGAAGTAAA 59.824 33.333 0.00 0.00 0.00 2.01
899 936 6.657541 ACAAAGGAACAACAGTCAAGAAGTAA 59.342 34.615 0.00 0.00 0.00 2.24
900 937 6.093495 CACAAAGGAACAACAGTCAAGAAGTA 59.907 38.462 0.00 0.00 0.00 2.24
901 938 5.010282 ACAAAGGAACAACAGTCAAGAAGT 58.990 37.500 0.00 0.00 0.00 3.01
902 939 5.335127 CACAAAGGAACAACAGTCAAGAAG 58.665 41.667 0.00 0.00 0.00 2.85
903 940 4.380444 GCACAAAGGAACAACAGTCAAGAA 60.380 41.667 0.00 0.00 0.00 2.52
904 941 3.128589 GCACAAAGGAACAACAGTCAAGA 59.871 43.478 0.00 0.00 0.00 3.02
905 942 3.119531 TGCACAAAGGAACAACAGTCAAG 60.120 43.478 0.00 0.00 0.00 3.02
906 943 2.822561 TGCACAAAGGAACAACAGTCAA 59.177 40.909 0.00 0.00 0.00 3.18
907 944 2.441410 TGCACAAAGGAACAACAGTCA 58.559 42.857 0.00 0.00 0.00 3.41
908 945 3.502191 TTGCACAAAGGAACAACAGTC 57.498 42.857 0.00 0.00 0.00 3.51
909 946 3.848726 CTTTGCACAAAGGAACAACAGT 58.151 40.909 14.08 0.00 42.96 3.55
919 956 0.593128 ACGCTAGCCTTTGCACAAAG 59.407 50.000 14.79 14.79 45.47 2.77
920 957 1.028905 AACGCTAGCCTTTGCACAAA 58.971 45.000 9.66 0.00 41.13 2.83
921 958 1.028905 AAACGCTAGCCTTTGCACAA 58.971 45.000 9.66 0.00 41.13 3.33
922 959 1.028905 AAAACGCTAGCCTTTGCACA 58.971 45.000 9.66 0.00 41.13 4.57
923 960 1.408422 CAAAACGCTAGCCTTTGCAC 58.592 50.000 18.76 0.00 41.13 4.57
924 961 3.863681 CAAAACGCTAGCCTTTGCA 57.136 47.368 18.76 0.00 41.13 4.08
925 962 2.434688 GCAAAACGCTAGCCTTTGC 58.565 52.632 30.69 30.69 45.61 3.68
943 980 2.288030 CCTGGCAAAGCTGAAAAGACAG 60.288 50.000 0.00 0.00 40.43 3.51
944 981 1.682854 CCTGGCAAAGCTGAAAAGACA 59.317 47.619 0.00 0.00 0.00 3.41
945 982 1.683385 ACCTGGCAAAGCTGAAAAGAC 59.317 47.619 0.00 0.00 0.00 3.01
946 983 1.956477 GACCTGGCAAAGCTGAAAAGA 59.044 47.619 0.00 0.00 0.00 2.52
947 984 1.335324 CGACCTGGCAAAGCTGAAAAG 60.335 52.381 0.00 0.00 0.00 2.27
948 985 0.667993 CGACCTGGCAAAGCTGAAAA 59.332 50.000 0.00 0.00 0.00 2.29
949 986 1.172180 CCGACCTGGCAAAGCTGAAA 61.172 55.000 0.00 0.00 0.00 2.69
950 987 1.600636 CCGACCTGGCAAAGCTGAA 60.601 57.895 0.00 0.00 0.00 3.02
951 988 2.032528 CCGACCTGGCAAAGCTGA 59.967 61.111 0.00 0.00 0.00 4.26
952 989 1.455383 AAACCGACCTGGCAAAGCTG 61.455 55.000 0.00 0.00 43.94 4.24
953 990 1.152756 AAACCGACCTGGCAAAGCT 60.153 52.632 0.00 0.00 43.94 3.74
954 991 1.007387 CAAACCGACCTGGCAAAGC 60.007 57.895 0.00 0.00 43.94 3.51
955 992 1.265905 GTACAAACCGACCTGGCAAAG 59.734 52.381 0.00 0.00 43.94 2.77
956 993 1.310904 GTACAAACCGACCTGGCAAA 58.689 50.000 0.00 0.00 43.94 3.68
957 994 0.881159 CGTACAAACCGACCTGGCAA 60.881 55.000 0.00 0.00 43.94 4.52
958 995 1.301087 CGTACAAACCGACCTGGCA 60.301 57.895 0.00 0.00 43.94 4.92
959 996 1.301165 ACGTACAAACCGACCTGGC 60.301 57.895 0.00 0.00 43.94 4.85
960 997 0.947180 CCACGTACAAACCGACCTGG 60.947 60.000 0.00 0.00 46.41 4.45
961 998 1.562575 GCCACGTACAAACCGACCTG 61.563 60.000 0.00 0.00 0.00 4.00
962 999 1.301165 GCCACGTACAAACCGACCT 60.301 57.895 0.00 0.00 0.00 3.85
963 1000 0.881600 AAGCCACGTACAAACCGACC 60.882 55.000 0.00 0.00 0.00 4.79
964 1001 0.233848 CAAGCCACGTACAAACCGAC 59.766 55.000 0.00 0.00 0.00 4.79
965 1002 0.179078 ACAAGCCACGTACAAACCGA 60.179 50.000 0.00 0.00 0.00 4.69
966 1003 1.192980 GTACAAGCCACGTACAAACCG 59.807 52.381 0.00 0.00 39.24 4.44
967 1004 2.486918 AGTACAAGCCACGTACAAACC 58.513 47.619 9.73 0.00 41.40 3.27
968 1005 4.925054 TCATAGTACAAGCCACGTACAAAC 59.075 41.667 9.73 0.00 41.40 2.93
969 1006 5.136816 TCATAGTACAAGCCACGTACAAA 57.863 39.130 9.73 0.15 41.40 2.83
970 1007 4.787260 TCATAGTACAAGCCACGTACAA 57.213 40.909 9.73 0.00 41.40 2.41
971 1008 4.202080 GGATCATAGTACAAGCCACGTACA 60.202 45.833 9.73 0.00 41.40 2.90
972 1009 4.037684 AGGATCATAGTACAAGCCACGTAC 59.962 45.833 0.00 0.00 39.64 3.67
973 1010 4.212716 AGGATCATAGTACAAGCCACGTA 58.787 43.478 0.00 0.00 0.00 3.57
974 1011 3.031736 AGGATCATAGTACAAGCCACGT 58.968 45.455 0.00 0.00 0.00 4.49
975 1012 3.735237 AGGATCATAGTACAAGCCACG 57.265 47.619 0.00 0.00 0.00 4.94
976 1013 6.759272 TCATAAGGATCATAGTACAAGCCAC 58.241 40.000 0.00 0.00 0.00 5.01
977 1014 6.994421 TCATAAGGATCATAGTACAAGCCA 57.006 37.500 0.00 0.00 0.00 4.75
999 1036 9.533983 CGCAACAATACATGTCTCATTTATATC 57.466 33.333 0.00 0.00 42.99 1.63
1000 1037 9.271828 TCGCAACAATACATGTCTCATTTATAT 57.728 29.630 0.00 0.00 42.99 0.86
1001 1038 8.655651 TCGCAACAATACATGTCTCATTTATA 57.344 30.769 0.00 0.00 42.99 0.98
1002 1039 7.552458 TCGCAACAATACATGTCTCATTTAT 57.448 32.000 0.00 0.00 42.99 1.40
1003 1040 6.976636 TCGCAACAATACATGTCTCATTTA 57.023 33.333 0.00 0.00 42.99 1.40
1004 1041 5.878332 TCGCAACAATACATGTCTCATTT 57.122 34.783 0.00 0.00 42.99 2.32
1005 1042 5.878332 TTCGCAACAATACATGTCTCATT 57.122 34.783 0.00 0.00 42.99 2.57
1006 1043 5.878332 TTTCGCAACAATACATGTCTCAT 57.122 34.783 0.00 0.00 42.99 2.90
1007 1044 5.681337 TTTTCGCAACAATACATGTCTCA 57.319 34.783 0.00 0.00 42.99 3.27
1031 1068 2.713708 AGGGAGGAAGAGCTCAGTTTTT 59.286 45.455 17.77 0.00 0.00 1.94
1032 1069 2.304470 GAGGGAGGAAGAGCTCAGTTTT 59.696 50.000 17.77 0.20 0.00 2.43
1033 1070 1.905894 GAGGGAGGAAGAGCTCAGTTT 59.094 52.381 17.77 0.63 0.00 2.66
1034 1071 1.078656 AGAGGGAGGAAGAGCTCAGTT 59.921 52.381 17.77 1.49 0.00 3.16
1035 1072 0.709992 AGAGGGAGGAAGAGCTCAGT 59.290 55.000 17.77 2.52 0.00 3.41
1132 1195 4.216687 CGTCTCTAAGAGGATGTCCATACC 59.783 50.000 1.30 0.00 38.89 2.73
1134 1197 5.064558 GTCGTCTCTAAGAGGATGTCCATA 58.935 45.833 1.30 0.00 40.66 2.74
1193 1269 4.338539 ACGATCGTATCCGCGCCC 62.339 66.667 21.32 0.00 0.00 6.13
1229 1305 1.587613 GATGACGAGGTGAGCGAGC 60.588 63.158 0.00 0.00 0.00 5.03
1682 1773 4.373116 GGCGCCCACTCGAACTCA 62.373 66.667 18.11 0.00 0.00 3.41
1732 1829 1.142060 TGAAGAACACGTTGGGGTCAT 59.858 47.619 0.00 0.00 0.00 3.06
1738 1835 2.285083 TCACCTTGAAGAACACGTTGG 58.715 47.619 0.00 0.00 0.00 3.77
1784 1881 2.050168 GAACGGGTGCGTCGTGTA 60.050 61.111 0.00 0.00 40.96 2.90
1909 2026 0.867753 CACGTGCCGCTAGCTAGAAG 60.868 60.000 25.15 16.09 44.23 2.85
1943 2062 1.076705 GAGCCTTGGGGGATTGGAC 60.077 63.158 0.00 0.00 37.23 4.02
1944 2063 2.316586 GGAGCCTTGGGGGATTGGA 61.317 63.158 0.00 0.00 37.23 3.53
1949 2068 0.694444 GATAGTGGAGCCTTGGGGGA 60.694 60.000 0.00 0.00 37.23 4.81
1973 2093 2.697431 TTAATTTCGTGTGCCTGTGC 57.303 45.000 0.00 0.00 38.26 4.57
1994 2114 4.401519 GGCAGGAACACAGATACAGTACTA 59.598 45.833 0.00 0.00 0.00 1.82
1995 2115 3.195825 GGCAGGAACACAGATACAGTACT 59.804 47.826 0.00 0.00 0.00 2.73
1996 2116 3.195825 AGGCAGGAACACAGATACAGTAC 59.804 47.826 0.00 0.00 0.00 2.73
1997 2117 3.441101 AGGCAGGAACACAGATACAGTA 58.559 45.455 0.00 0.00 0.00 2.74
1998 2118 2.260822 AGGCAGGAACACAGATACAGT 58.739 47.619 0.00 0.00 0.00 3.55
1999 2119 3.265791 GAAGGCAGGAACACAGATACAG 58.734 50.000 0.00 0.00 0.00 2.74
2000 2120 2.353704 CGAAGGCAGGAACACAGATACA 60.354 50.000 0.00 0.00 0.00 2.29
2001 2121 2.271800 CGAAGGCAGGAACACAGATAC 58.728 52.381 0.00 0.00 0.00 2.24
2284 2422 6.407202 TGAGCTGGAAGAAAGATTTACTACC 58.593 40.000 0.00 0.00 34.07 3.18
2346 2511 1.081242 GAGCCACCACAAATGTGCG 60.081 57.895 8.03 4.57 44.34 5.34
2379 2564 5.339008 TTCAGGTATTCGAGTGTAGCATT 57.661 39.130 0.00 0.00 0.00 3.56
2454 2639 9.872721 TCATCATATAGAAAGATGCATCTTCTC 57.127 33.333 35.67 30.49 45.83 2.87
2474 2659 8.701908 AACTATATTTGCACCTTCATCATCAT 57.298 30.769 0.00 0.00 0.00 2.45
2475 2660 8.523915 AAACTATATTTGCACCTTCATCATCA 57.476 30.769 0.00 0.00 0.00 3.07
2476 2661 9.884465 GTAAACTATATTTGCACCTTCATCATC 57.116 33.333 0.00 0.00 0.00 2.92
2560 2747 1.008995 GCGCAAGAAAGCAAACCGA 60.009 52.632 0.30 0.00 43.02 4.69
2660 2847 0.323302 TCGTCTGCCCTGCACAAATA 59.677 50.000 0.00 0.00 33.79 1.40
2675 2862 4.493220 GCATCACTAACTCTGCAATTCGTC 60.493 45.833 0.00 0.00 34.77 4.20
2701 2888 7.424452 CGAACTAAACCAATTAATAACGCTGAC 59.576 37.037 0.00 0.00 0.00 3.51
2726 2913 9.712305 ATGGTTAAAATAATCCTATGTCTCTCG 57.288 33.333 0.00 0.00 0.00 4.04
2758 2945 8.739039 CCATCAAAGGTTAGTGAAACAATGATA 58.261 33.333 0.00 0.00 41.43 2.15
2812 2999 3.414272 GCCAACGGCTGCTATGAG 58.586 61.111 0.00 0.00 46.69 2.90
2862 3049 1.954528 CTGCTGTTGAAGGTGCTGG 59.045 57.895 0.00 0.00 0.00 4.85
2920 3107 6.072175 TGCACATTTGTCTGGTAAACTATTCC 60.072 38.462 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.