Multiple sequence alignment - TraesCS5B01G520600

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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 TraesCS5B01G520600 chr5B 100.000 4143 0 0 453 4595 682817256 682821398 0.000000e+00 7651.0
1 TraesCS5B01G520600 chr5B 88.906 1271 136 4 1029 2298 682696407 682697673 0.000000e+00 1561.0
2 TraesCS5B01G520600 chr5B 93.900 836 44 7 3765 4594 689081116 689081950 0.000000e+00 1254.0
3 TraesCS5B01G520600 chr5B 100.000 152 0 0 1 152 682816804 682816955 9.730000e-72 281.0
4 TraesCS5B01G520600 chr5D 96.587 2901 75 6 717 3602 540339884 540342775 0.000000e+00 4787.0
5 TraesCS5B01G520600 chr5D 88.969 1251 119 13 1018 2266 540284947 540286180 0.000000e+00 1528.0
6 TraesCS5B01G520600 chr5D 94.451 829 38 7 3771 4594 232838417 232839242 0.000000e+00 1269.0
7 TraesCS5B01G520600 chr5D 94.111 832 39 8 3769 4594 335881590 335882417 0.000000e+00 1256.0
8 TraesCS5B01G520600 chr5D 89.333 150 14 1 551 698 540339649 540339798 2.180000e-43 187.0
9 TraesCS5B01G520600 chr5D 84.848 99 13 2 453 550 301108719 301108622 1.050000e-16 99.0
10 TraesCS5B01G520600 chr4A 96.307 2843 78 8 758 3593 628483611 628486433 0.000000e+00 4643.0
11 TraesCS5B01G520600 chr4A 87.127 1375 136 28 892 2243 628327326 628328682 0.000000e+00 1520.0
12 TraesCS5B01G520600 chr4A 74.214 318 51 24 2824 3133 567480176 567479882 2.260000e-18 104.0
13 TraesCS5B01G520600 chr4A 92.647 68 3 1 3660 3727 628486926 628486991 3.780000e-16 97.1
14 TraesCS5B01G520600 chr3B 94.231 832 39 7 3769 4594 829486967 829486139 0.000000e+00 1262.0
15 TraesCS5B01G520600 chr3B 72.694 553 118 28 2549 3092 673170768 673170240 2.210000e-33 154.0
16 TraesCS5B01G520600 chr3D 93.983 831 44 6 3768 4594 565791845 565792673 0.000000e+00 1253.0
17 TraesCS5B01G520600 chr3D 93.863 831 41 8 3770 4594 380491666 380490840 0.000000e+00 1243.0
18 TraesCS5B01G520600 chr3D 85.714 217 23 5 1017 1233 31112650 31112858 5.980000e-54 222.0
19 TraesCS5B01G520600 chr6B 94.254 818 43 4 3781 4594 620711906 620712723 0.000000e+00 1247.0
20 TraesCS5B01G520600 chr6B 93.750 832 44 6 3769 4594 657170273 657171102 0.000000e+00 1242.0
21 TraesCS5B01G520600 chr1D 93.630 832 47 6 3768 4594 107214862 107214032 0.000000e+00 1238.0
22 TraesCS5B01G520600 chr1D 83.333 774 98 9 1114 1879 75788809 75789559 0.000000e+00 686.0
23 TraesCS5B01G520600 chr1D 85.000 80 11 1 1260 1339 206494100 206494178 3.810000e-11 80.5
24 TraesCS5B01G520600 chr3A 82.776 778 103 9 1114 1883 11586032 11586786 0.000000e+00 665.0
25 TraesCS5B01G520600 chr2D 82.620 374 45 6 1267 1640 535646781 535647134 3.450000e-81 313.0
26 TraesCS5B01G520600 chr2D 75.290 259 51 11 2839 3092 598732959 598733209 1.350000e-20 111.0
27 TraesCS5B01G520600 chr2D 91.111 45 3 1 464 507 312448723 312448767 4.960000e-05 60.2
28 TraesCS5B01G520600 chr2D 92.683 41 3 0 464 504 606731321 606731281 4.960000e-05 60.2
29 TraesCS5B01G520600 chr4B 72.852 582 126 27 2501 3075 500869312 500868756 2.200000e-38 171.0
30 TraesCS5B01G520600 chr4B 74.847 326 61 18 2817 3133 50836465 50836152 1.340000e-25 128.0
31 TraesCS5B01G520600 chr2B 72.421 504 104 25 2599 3092 727241138 727241616 1.340000e-25 128.0
32 TraesCS5B01G520600 chr4D 74.613 323 61 17 2817 3130 35165672 35165982 6.240000e-24 122.0
33 TraesCS5B01G520600 chr1B 86.250 80 10 1 1260 1339 302205215 302205293 8.190000e-13 86.1
34 TraesCS5B01G520600 chr7B 96.970 33 1 0 470 502 440706483 440706451 6.420000e-04 56.5
35 TraesCS5B01G520600 chr2A 100.000 29 0 0 485 513 763449018 763449046 2.000000e-03 54.7


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 TraesCS5B01G520600 chr5B 682816804 682821398 4594 False 3966.00 7651 100.000 1 4595 2 chr5B.!!$F3 4594
1 TraesCS5B01G520600 chr5B 682696407 682697673 1266 False 1561.00 1561 88.906 1029 2298 1 chr5B.!!$F1 1269
2 TraesCS5B01G520600 chr5B 689081116 689081950 834 False 1254.00 1254 93.900 3765 4594 1 chr5B.!!$F2 829
3 TraesCS5B01G520600 chr5D 540339649 540342775 3126 False 2487.00 4787 92.960 551 3602 2 chr5D.!!$F4 3051
4 TraesCS5B01G520600 chr5D 540284947 540286180 1233 False 1528.00 1528 88.969 1018 2266 1 chr5D.!!$F3 1248
5 TraesCS5B01G520600 chr5D 232838417 232839242 825 False 1269.00 1269 94.451 3771 4594 1 chr5D.!!$F1 823
6 TraesCS5B01G520600 chr5D 335881590 335882417 827 False 1256.00 1256 94.111 3769 4594 1 chr5D.!!$F2 825
7 TraesCS5B01G520600 chr4A 628483611 628486991 3380 False 2370.05 4643 94.477 758 3727 2 chr4A.!!$F2 2969
8 TraesCS5B01G520600 chr4A 628327326 628328682 1356 False 1520.00 1520 87.127 892 2243 1 chr4A.!!$F1 1351
9 TraesCS5B01G520600 chr3B 829486139 829486967 828 True 1262.00 1262 94.231 3769 4594 1 chr3B.!!$R2 825
10 TraesCS5B01G520600 chr3D 565791845 565792673 828 False 1253.00 1253 93.983 3768 4594 1 chr3D.!!$F2 826
11 TraesCS5B01G520600 chr3D 380490840 380491666 826 True 1243.00 1243 93.863 3770 4594 1 chr3D.!!$R1 824
12 TraesCS5B01G520600 chr6B 620711906 620712723 817 False 1247.00 1247 94.254 3781 4594 1 chr6B.!!$F1 813
13 TraesCS5B01G520600 chr6B 657170273 657171102 829 False 1242.00 1242 93.750 3769 4594 1 chr6B.!!$F2 825
14 TraesCS5B01G520600 chr1D 107214032 107214862 830 True 1238.00 1238 93.630 3768 4594 1 chr1D.!!$R1 826
15 TraesCS5B01G520600 chr1D 75788809 75789559 750 False 686.00 686 83.333 1114 1879 1 chr1D.!!$F1 765
16 TraesCS5B01G520600 chr3A 11586032 11586786 754 False 665.00 665 82.776 1114 1883 1 chr3A.!!$F1 769

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
543 544 0.105658 ACTCGCCAGCCCCTAAGATA 60.106 55.000 0.00 0.0 0.00 1.98 F
545 546 0.187606 TCGCCAGCCCCTAAGATAGA 59.812 55.000 0.00 0.0 0.00 1.98 F
1050 1158 0.321387 TCTGCTGCTTCTTGCTCCTG 60.321 55.000 0.00 0.0 43.37 3.86 F
1233 1344 3.622514 GGCATCTCCGTCTGGTCT 58.377 61.111 0.00 0.0 36.30 3.85 F
3075 3193 1.138247 GGACGTGTACAGCTACGGG 59.862 63.158 11.18 0.0 44.07 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1473 1584 1.745489 GGTGAGGTTCATGCCGGAC 60.745 63.158 5.05 0.0 0.00 4.79 R
1524 1635 3.291101 GAGCGTGAGGTTGCCGGTA 62.291 63.158 1.90 0.0 45.11 4.02 R
2859 2977 2.680913 GCAGTGCACGATGGTGTCC 61.681 63.158 11.09 0.7 46.13 4.02 R
3134 3252 1.014564 CACCGAGAACTTCTTCCGGC 61.015 60.000 15.53 0.0 40.85 6.13 R
3980 4526 0.320421 ACCAGTTTGGATGACGGTCG 60.320 55.000 3.34 0.0 40.96 4.79 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
20 21 2.654802 ACCGTCTACAGGTCAGGTG 58.345 57.895 0.00 0.00 37.44 4.00
21 22 1.215647 CCGTCTACAGGTCAGGTGC 59.784 63.158 0.00 0.00 0.00 5.01
22 23 1.154016 CGTCTACAGGTCAGGTGCG 60.154 63.158 0.00 0.00 0.00 5.34
23 24 1.863662 CGTCTACAGGTCAGGTGCGT 61.864 60.000 0.00 0.00 0.00 5.24
24 25 0.388649 GTCTACAGGTCAGGTGCGTG 60.389 60.000 0.00 0.00 0.00 5.34
25 26 1.079819 CTACAGGTCAGGTGCGTGG 60.080 63.158 0.00 0.00 0.00 4.94
26 27 1.532078 TACAGGTCAGGTGCGTGGA 60.532 57.895 0.00 0.00 0.00 4.02
27 28 1.116536 TACAGGTCAGGTGCGTGGAA 61.117 55.000 0.00 0.00 0.00 3.53
28 29 1.227823 CAGGTCAGGTGCGTGGAAA 60.228 57.895 0.00 0.00 0.00 3.13
29 30 0.817634 CAGGTCAGGTGCGTGGAAAA 60.818 55.000 0.00 0.00 0.00 2.29
30 31 0.106918 AGGTCAGGTGCGTGGAAAAA 60.107 50.000 0.00 0.00 0.00 1.94
51 52 4.519540 AAAAATCAGCGTTAGCCACATT 57.480 36.364 0.00 0.00 46.67 2.71
52 53 3.764885 AAATCAGCGTTAGCCACATTC 57.235 42.857 0.00 0.00 46.67 2.67
53 54 2.698855 ATCAGCGTTAGCCACATTCT 57.301 45.000 0.00 0.00 46.67 2.40
54 55 2.472695 TCAGCGTTAGCCACATTCTT 57.527 45.000 0.00 0.00 46.67 2.52
55 56 2.778299 TCAGCGTTAGCCACATTCTTT 58.222 42.857 0.00 0.00 46.67 2.52
56 57 2.742053 TCAGCGTTAGCCACATTCTTTC 59.258 45.455 0.00 0.00 46.67 2.62
57 58 2.744202 CAGCGTTAGCCACATTCTTTCT 59.256 45.455 0.00 0.00 46.67 2.52
58 59 3.932710 CAGCGTTAGCCACATTCTTTCTA 59.067 43.478 0.00 0.00 46.67 2.10
59 60 3.933332 AGCGTTAGCCACATTCTTTCTAC 59.067 43.478 0.00 0.00 46.67 2.59
60 61 3.682858 GCGTTAGCCACATTCTTTCTACA 59.317 43.478 0.00 0.00 37.42 2.74
61 62 4.435651 GCGTTAGCCACATTCTTTCTACAC 60.436 45.833 0.00 0.00 37.42 2.90
62 63 4.092968 CGTTAGCCACATTCTTTCTACACC 59.907 45.833 0.00 0.00 0.00 4.16
63 64 3.788227 AGCCACATTCTTTCTACACCA 57.212 42.857 0.00 0.00 0.00 4.17
64 65 4.307032 AGCCACATTCTTTCTACACCAT 57.693 40.909 0.00 0.00 0.00 3.55
65 66 4.265073 AGCCACATTCTTTCTACACCATC 58.735 43.478 0.00 0.00 0.00 3.51
66 67 3.378427 GCCACATTCTTTCTACACCATCC 59.622 47.826 0.00 0.00 0.00 3.51
67 68 3.623060 CCACATTCTTTCTACACCATCCG 59.377 47.826 0.00 0.00 0.00 4.18
68 69 4.503910 CACATTCTTTCTACACCATCCGA 58.496 43.478 0.00 0.00 0.00 4.55
69 70 5.118990 CACATTCTTTCTACACCATCCGAT 58.881 41.667 0.00 0.00 0.00 4.18
70 71 5.586243 CACATTCTTTCTACACCATCCGATT 59.414 40.000 0.00 0.00 0.00 3.34
71 72 6.094048 CACATTCTTTCTACACCATCCGATTT 59.906 38.462 0.00 0.00 0.00 2.17
72 73 6.094048 ACATTCTTTCTACACCATCCGATTTG 59.906 38.462 0.00 0.00 0.00 2.32
73 74 3.938963 TCTTTCTACACCATCCGATTTGC 59.061 43.478 0.00 0.00 0.00 3.68
74 75 3.342377 TTCTACACCATCCGATTTGCA 57.658 42.857 0.00 0.00 0.00 4.08
75 76 3.558931 TCTACACCATCCGATTTGCAT 57.441 42.857 0.00 0.00 0.00 3.96
76 77 3.466836 TCTACACCATCCGATTTGCATC 58.533 45.455 0.00 0.00 0.00 3.91
77 78 1.392589 ACACCATCCGATTTGCATCC 58.607 50.000 0.00 0.00 0.00 3.51
78 79 1.340893 ACACCATCCGATTTGCATCCA 60.341 47.619 0.00 0.00 0.00 3.41
79 80 1.335810 CACCATCCGATTTGCATCCAG 59.664 52.381 0.00 0.00 0.00 3.86
80 81 0.313043 CCATCCGATTTGCATCCAGC 59.687 55.000 0.00 0.00 45.96 4.85
91 92 2.584492 GCATCCAGCGGCTAAAAATT 57.416 45.000 0.26 0.00 0.00 1.82
92 93 2.195922 GCATCCAGCGGCTAAAAATTG 58.804 47.619 0.26 0.00 0.00 2.32
93 94 2.159254 GCATCCAGCGGCTAAAAATTGA 60.159 45.455 0.26 0.00 0.00 2.57
94 95 3.491447 GCATCCAGCGGCTAAAAATTGAT 60.491 43.478 0.26 0.00 0.00 2.57
95 96 4.293415 CATCCAGCGGCTAAAAATTGATC 58.707 43.478 0.26 0.00 0.00 2.92
96 97 3.351740 TCCAGCGGCTAAAAATTGATCA 58.648 40.909 0.26 0.00 0.00 2.92
97 98 3.761218 TCCAGCGGCTAAAAATTGATCAA 59.239 39.130 11.26 11.26 0.00 2.57
98 99 4.219507 TCCAGCGGCTAAAAATTGATCAAA 59.780 37.500 13.09 0.00 0.00 2.69
99 100 4.327087 CCAGCGGCTAAAAATTGATCAAAC 59.673 41.667 13.09 0.00 0.00 2.93
100 101 4.030529 CAGCGGCTAAAAATTGATCAAACG 59.969 41.667 13.09 8.17 0.00 3.60
101 102 3.241646 GCGGCTAAAAATTGATCAAACGC 60.242 43.478 13.09 13.49 35.32 4.84
102 103 3.303229 CGGCTAAAAATTGATCAAACGCC 59.697 43.478 13.09 15.28 0.00 5.68
103 104 3.616821 GGCTAAAAATTGATCAAACGCCC 59.383 43.478 13.09 3.49 0.00 6.13
104 105 4.494484 GCTAAAAATTGATCAAACGCCCT 58.506 39.130 13.09 0.00 0.00 5.19
105 106 4.929211 GCTAAAAATTGATCAAACGCCCTT 59.071 37.500 13.09 0.00 0.00 3.95
106 107 5.408299 GCTAAAAATTGATCAAACGCCCTTT 59.592 36.000 13.09 4.47 0.00 3.11
107 108 5.922739 AAAAATTGATCAAACGCCCTTTC 57.077 34.783 13.09 0.00 0.00 2.62
108 109 4.871933 AAATTGATCAAACGCCCTTTCT 57.128 36.364 13.09 0.00 0.00 2.52
109 110 4.871933 AATTGATCAAACGCCCTTTCTT 57.128 36.364 13.09 0.00 0.00 2.52
110 111 3.915437 TTGATCAAACGCCCTTTCTTC 57.085 42.857 5.45 0.00 0.00 2.87
111 112 3.140325 TGATCAAACGCCCTTTCTTCT 57.860 42.857 0.00 0.00 0.00 2.85
112 113 3.486383 TGATCAAACGCCCTTTCTTCTT 58.514 40.909 0.00 0.00 0.00 2.52
113 114 3.502211 TGATCAAACGCCCTTTCTTCTTC 59.498 43.478 0.00 0.00 0.00 2.87
114 115 2.227194 TCAAACGCCCTTTCTTCTTCC 58.773 47.619 0.00 0.00 0.00 3.46
115 116 2.158667 TCAAACGCCCTTTCTTCTTCCT 60.159 45.455 0.00 0.00 0.00 3.36
116 117 2.623416 CAAACGCCCTTTCTTCTTCCTT 59.377 45.455 0.00 0.00 0.00 3.36
117 118 2.186532 ACGCCCTTTCTTCTTCCTTC 57.813 50.000 0.00 0.00 0.00 3.46
118 119 1.700186 ACGCCCTTTCTTCTTCCTTCT 59.300 47.619 0.00 0.00 0.00 2.85
119 120 2.289756 ACGCCCTTTCTTCTTCCTTCTC 60.290 50.000 0.00 0.00 0.00 2.87
120 121 2.289694 CGCCCTTTCTTCTTCCTTCTCA 60.290 50.000 0.00 0.00 0.00 3.27
121 122 3.078097 GCCCTTTCTTCTTCCTTCTCAC 58.922 50.000 0.00 0.00 0.00 3.51
122 123 3.244735 GCCCTTTCTTCTTCCTTCTCACT 60.245 47.826 0.00 0.00 0.00 3.41
123 124 4.020128 GCCCTTTCTTCTTCCTTCTCACTA 60.020 45.833 0.00 0.00 0.00 2.74
124 125 5.338789 GCCCTTTCTTCTTCCTTCTCACTAT 60.339 44.000 0.00 0.00 0.00 2.12
125 126 6.345298 CCCTTTCTTCTTCCTTCTCACTATC 58.655 44.000 0.00 0.00 0.00 2.08
126 127 6.156083 CCCTTTCTTCTTCCTTCTCACTATCT 59.844 42.308 0.00 0.00 0.00 1.98
127 128 7.041107 CCTTTCTTCTTCCTTCTCACTATCTG 58.959 42.308 0.00 0.00 0.00 2.90
128 129 5.590530 TCTTCTTCCTTCTCACTATCTGC 57.409 43.478 0.00 0.00 0.00 4.26
129 130 4.404073 TCTTCTTCCTTCTCACTATCTGCC 59.596 45.833 0.00 0.00 0.00 4.85
130 131 3.713003 TCTTCCTTCTCACTATCTGCCA 58.287 45.455 0.00 0.00 0.00 4.92
131 132 3.703556 TCTTCCTTCTCACTATCTGCCAG 59.296 47.826 0.00 0.00 0.00 4.85
132 133 1.759445 TCCTTCTCACTATCTGCCAGC 59.241 52.381 0.00 0.00 0.00 4.85
133 134 1.202627 CCTTCTCACTATCTGCCAGCC 60.203 57.143 0.00 0.00 0.00 4.85
134 135 1.483827 CTTCTCACTATCTGCCAGCCA 59.516 52.381 0.00 0.00 0.00 4.75
135 136 1.571955 TCTCACTATCTGCCAGCCAA 58.428 50.000 0.00 0.00 0.00 4.52
136 137 1.208052 TCTCACTATCTGCCAGCCAAC 59.792 52.381 0.00 0.00 0.00 3.77
137 138 0.253044 TCACTATCTGCCAGCCAACC 59.747 55.000 0.00 0.00 0.00 3.77
138 139 0.749454 CACTATCTGCCAGCCAACCC 60.749 60.000 0.00 0.00 0.00 4.11
139 140 1.207488 ACTATCTGCCAGCCAACCCA 61.207 55.000 0.00 0.00 0.00 4.51
140 141 0.465097 CTATCTGCCAGCCAACCCAG 60.465 60.000 0.00 0.00 0.00 4.45
141 142 1.925285 TATCTGCCAGCCAACCCAGG 61.925 60.000 0.00 0.00 0.00 4.45
149 150 4.109675 CCAACCCAGGCCTACCCG 62.110 72.222 3.98 0.00 39.21 5.28
150 151 4.796495 CAACCCAGGCCTACCCGC 62.796 72.222 3.98 0.00 39.21 6.13
491 492 2.448542 GCCCCAGCCATCCCTCTA 60.449 66.667 0.00 0.00 0.00 2.43
492 493 2.078665 GCCCCAGCCATCCCTCTAA 61.079 63.158 0.00 0.00 0.00 2.10
493 494 2.061790 GCCCCAGCCATCCCTCTAAG 62.062 65.000 0.00 0.00 0.00 2.18
494 495 1.453669 CCCAGCCATCCCTCTAAGC 59.546 63.158 0.00 0.00 0.00 3.09
495 496 1.453669 CCAGCCATCCCTCTAAGCC 59.546 63.158 0.00 0.00 0.00 4.35
496 497 1.453669 CAGCCATCCCTCTAAGCCC 59.546 63.158 0.00 0.00 0.00 5.19
497 498 1.772156 AGCCATCCCTCTAAGCCCC 60.772 63.158 0.00 0.00 0.00 5.80
498 499 3.151906 CCATCCCTCTAAGCCCCG 58.848 66.667 0.00 0.00 0.00 5.73
499 500 2.427753 CATCCCTCTAAGCCCCGC 59.572 66.667 0.00 0.00 0.00 6.13
500 501 2.849646 ATCCCTCTAAGCCCCGCC 60.850 66.667 0.00 0.00 0.00 6.13
515 516 4.980805 GCCGCACAACTCCGGTGA 62.981 66.667 11.17 0.00 45.98 4.02
516 517 2.047274 CCGCACAACTCCGGTGAT 60.047 61.111 11.17 0.00 39.67 3.06
517 518 2.390599 CCGCACAACTCCGGTGATG 61.391 63.158 11.17 11.49 39.67 3.07
518 519 2.870372 GCACAACTCCGGTGATGC 59.130 61.111 11.17 12.59 38.54 3.91
519 520 2.690778 GCACAACTCCGGTGATGCC 61.691 63.158 11.17 0.10 38.54 4.40
520 521 2.040544 CACAACTCCGGTGATGCCC 61.041 63.158 11.17 0.00 38.54 5.36
521 522 2.224159 ACAACTCCGGTGATGCCCT 61.224 57.895 11.17 0.00 0.00 5.19
522 523 1.450312 CAACTCCGGTGATGCCCTC 60.450 63.158 11.17 0.00 0.00 4.30
523 524 3.019003 AACTCCGGTGATGCCCTCG 62.019 63.158 11.17 0.00 0.00 4.63
524 525 3.147595 CTCCGGTGATGCCCTCGA 61.148 66.667 0.00 0.00 0.00 4.04
525 526 3.432051 CTCCGGTGATGCCCTCGAC 62.432 68.421 0.00 0.00 0.00 4.20
526 527 3.461773 CCGGTGATGCCCTCGACT 61.462 66.667 0.00 0.00 0.00 4.18
527 528 2.105128 CGGTGATGCCCTCGACTC 59.895 66.667 0.00 0.00 0.00 3.36
528 529 2.105128 GGTGATGCCCTCGACTCG 59.895 66.667 0.00 0.00 0.00 4.18
529 530 2.583593 GTGATGCCCTCGACTCGC 60.584 66.667 0.00 0.00 0.00 5.03
530 531 3.838271 TGATGCCCTCGACTCGCC 61.838 66.667 0.00 0.00 0.00 5.54
531 532 3.838271 GATGCCCTCGACTCGCCA 61.838 66.667 0.00 0.00 0.00 5.69
532 533 3.781770 GATGCCCTCGACTCGCCAG 62.782 68.421 0.00 0.00 0.00 4.85
538 539 4.435970 TCGACTCGCCAGCCCCTA 62.436 66.667 0.00 0.00 0.00 3.53
539 540 3.458163 CGACTCGCCAGCCCCTAA 61.458 66.667 0.00 0.00 0.00 2.69
540 541 2.501610 GACTCGCCAGCCCCTAAG 59.498 66.667 0.00 0.00 0.00 2.18
541 542 2.038975 ACTCGCCAGCCCCTAAGA 59.961 61.111 0.00 0.00 0.00 2.10
542 543 1.383248 ACTCGCCAGCCCCTAAGAT 60.383 57.895 0.00 0.00 0.00 2.40
543 544 0.105658 ACTCGCCAGCCCCTAAGATA 60.106 55.000 0.00 0.00 0.00 1.98
544 545 0.605589 CTCGCCAGCCCCTAAGATAG 59.394 60.000 0.00 0.00 0.00 2.08
545 546 0.187606 TCGCCAGCCCCTAAGATAGA 59.812 55.000 0.00 0.00 0.00 1.98
546 547 1.203187 TCGCCAGCCCCTAAGATAGAT 60.203 52.381 0.00 0.00 0.00 1.98
547 548 2.042569 TCGCCAGCCCCTAAGATAGATA 59.957 50.000 0.00 0.00 0.00 1.98
548 549 2.832129 CGCCAGCCCCTAAGATAGATAA 59.168 50.000 0.00 0.00 0.00 1.75
549 550 3.452627 CGCCAGCCCCTAAGATAGATAAT 59.547 47.826 0.00 0.00 0.00 1.28
601 602 5.276348 GCAACTTTTGATTTTGAGTTCGTGG 60.276 40.000 0.00 0.00 30.41 4.94
606 607 6.928979 TTTGATTTTGAGTTCGTGGACTAA 57.071 33.333 0.00 0.00 0.00 2.24
609 610 7.504924 TGATTTTGAGTTCGTGGACTAAAAT 57.495 32.000 0.00 0.00 31.64 1.82
611 612 8.500773 TGATTTTGAGTTCGTGGACTAAAATAC 58.499 33.333 0.00 0.00 31.64 1.89
613 614 7.416154 TTTGAGTTCGTGGACTAAAATACAG 57.584 36.000 0.00 0.00 27.40 2.74
614 615 5.475719 TGAGTTCGTGGACTAAAATACAGG 58.524 41.667 0.00 0.00 0.00 4.00
615 616 4.828829 AGTTCGTGGACTAAAATACAGGG 58.171 43.478 0.00 0.00 0.00 4.45
639 642 5.347342 CCAAACAAGTGTGCATTTTACTCA 58.653 37.500 0.00 0.00 0.00 3.41
655 658 8.469200 CATTTTACTCAGCTAAAATTCCCATCA 58.531 33.333 2.78 0.00 35.16 3.07
671 674 3.474600 CCATCAGGAAGCATTGGTCTAG 58.525 50.000 0.00 0.00 36.89 2.43
673 676 4.202440 CCATCAGGAAGCATTGGTCTAGAT 60.202 45.833 0.00 0.00 36.89 1.98
676 679 4.039730 TCAGGAAGCATTGGTCTAGATAGC 59.960 45.833 0.00 0.00 0.00 2.97
682 685 6.678568 AGCATTGGTCTAGATAGCTGTTAT 57.321 37.500 0.00 0.00 0.00 1.89
699 702 8.723942 AGCTGTTATTTACTAGTCCATTTCTG 57.276 34.615 0.00 0.00 0.00 3.02
700 703 7.770897 AGCTGTTATTTACTAGTCCATTTCTGG 59.229 37.037 0.00 0.00 44.64 3.86
730 800 4.028993 AGTCCACAAACATACGGGAATT 57.971 40.909 0.00 0.00 0.00 2.17
753 823 2.232941 GACCGATCAACTACAAGGACCA 59.767 50.000 0.00 0.00 0.00 4.02
786 866 2.179517 CGTCACAGTCGCTCTCCC 59.820 66.667 0.00 0.00 0.00 4.30
787 867 2.574399 GTCACAGTCGCTCTCCCC 59.426 66.667 0.00 0.00 0.00 4.81
799 879 3.541713 CTCCCCTGCTCCGGCTAC 61.542 72.222 0.00 0.00 39.59 3.58
806 886 1.000486 TGCTCCGGCTACTTCCTCT 60.000 57.895 0.00 0.00 39.59 3.69
828 912 2.282958 TTCCTCCCTCGCTCACGT 60.283 61.111 0.00 0.00 41.18 4.49
853 937 3.093172 CTCCCCTCCCCTGCTTCC 61.093 72.222 0.00 0.00 0.00 3.46
906 990 1.987807 ATTCACGCCATGAGAGGGGG 61.988 60.000 0.00 0.00 45.21 5.40
961 1051 2.032681 AGCTCCCGGTGCAAGAAC 59.967 61.111 17.16 0.00 0.00 3.01
1005 1095 1.019278 TCCGTCCAAGAAAGATGCGC 61.019 55.000 0.00 0.00 0.00 6.09
1008 1098 1.745115 TCCAAGAAAGATGCGCCCG 60.745 57.895 4.18 0.00 0.00 6.13
1040 1148 4.749310 CGCCGTCCTCTGCTGCTT 62.749 66.667 0.00 0.00 0.00 3.91
1044 1152 1.018226 CCGTCCTCTGCTGCTTCTTG 61.018 60.000 0.00 0.00 0.00 3.02
1050 1158 0.321387 TCTGCTGCTTCTTGCTCCTG 60.321 55.000 0.00 0.00 43.37 3.86
1233 1344 3.622514 GGCATCTCCGTCTGGTCT 58.377 61.111 0.00 0.00 36.30 3.85
1506 1617 4.709604 ACCTCGGGCCCCTACGTT 62.710 66.667 18.66 0.00 0.00 3.99
3075 3193 1.138247 GGACGTGTACAGCTACGGG 59.862 63.158 11.18 0.00 44.07 5.28
3603 3721 5.726980 ACATGACAATGTAACATTGCCTT 57.273 34.783 0.38 0.00 45.41 4.35
3606 3724 5.781210 TGACAATGTAACATTGCCTTTGA 57.219 34.783 0.38 0.00 32.55 2.69
3607 3725 5.771469 TGACAATGTAACATTGCCTTTGAG 58.229 37.500 0.38 0.00 32.55 3.02
3609 3727 4.588528 ACAATGTAACATTGCCTTTGAGGT 59.411 37.500 0.38 0.00 37.80 3.85
3610 3728 5.163513 CAATGTAACATTGCCTTTGAGGTC 58.836 41.667 0.00 0.00 37.80 3.85
3616 3915 4.751431 GCCTTTGAGGTCTGGCAT 57.249 55.556 0.00 0.00 44.34 4.40
3618 3917 1.673168 GCCTTTGAGGTCTGGCATAG 58.327 55.000 0.00 0.00 44.34 2.23
3621 3920 3.012518 CCTTTGAGGTCTGGCATAGTTG 58.987 50.000 0.00 0.00 0.00 3.16
3629 3928 3.539604 GTCTGGCATAGTTGAGAAGCAT 58.460 45.455 0.00 0.00 0.00 3.79
3631 3930 2.019249 TGGCATAGTTGAGAAGCATGC 58.981 47.619 10.51 10.51 40.96 4.06
3641 3940 2.356695 TGAGAAGCATGCATGTATGTGC 59.643 45.455 26.79 13.90 45.25 4.57
3643 3942 0.382873 AAGCATGCATGTATGTGCCG 59.617 50.000 26.79 0.00 44.43 5.69
3644 3943 1.008194 GCATGCATGTATGTGCCGG 60.008 57.895 26.79 0.00 44.43 6.13
3649 3948 1.308047 GCATGTATGTGCCGGATGAA 58.692 50.000 5.05 0.00 39.18 2.57
3653 3952 1.014352 GTATGTGCCGGATGAACCAC 58.986 55.000 5.05 2.56 38.90 4.16
3655 3954 0.251121 ATGTGCCGGATGAACCACAA 60.251 50.000 5.05 0.00 41.02 3.33
3657 3956 0.887933 GTGCCGGATGAACCACAATT 59.112 50.000 5.05 0.00 38.90 2.32
3659 3958 1.271934 TGCCGGATGAACCACAATTTG 59.728 47.619 5.05 0.00 38.90 2.32
3660 3959 1.272212 GCCGGATGAACCACAATTTGT 59.728 47.619 5.05 0.00 38.90 2.83
3663 3962 4.732784 CCGGATGAACCACAATTTGTAAG 58.267 43.478 0.00 0.00 38.90 2.34
3664 3963 4.217550 CCGGATGAACCACAATTTGTAAGT 59.782 41.667 0.00 0.30 38.90 2.24
3665 3964 5.413213 CCGGATGAACCACAATTTGTAAGTA 59.587 40.000 0.00 0.00 38.90 2.24
3666 3965 6.072397 CCGGATGAACCACAATTTGTAAGTAA 60.072 38.462 0.00 0.00 38.90 2.24
3727 4269 9.202273 TGTACAAATAATTCAAATTTGAGGCAC 57.798 29.630 19.64 9.93 43.79 5.01
3728 4270 9.202273 GTACAAATAATTCAAATTTGAGGCACA 57.798 29.630 19.64 6.48 43.79 4.57
3729 4271 8.674263 ACAAATAATTCAAATTTGAGGCACAA 57.326 26.923 19.64 5.77 43.79 3.33
3730 4272 8.776470 ACAAATAATTCAAATTTGAGGCACAAG 58.224 29.630 19.64 12.12 43.79 3.16
3731 4273 8.991026 CAAATAATTCAAATTTGAGGCACAAGA 58.009 29.630 19.64 4.36 43.79 3.02
3732 4274 8.538409 AATAATTCAAATTTGAGGCACAAGAC 57.462 30.769 19.64 0.00 39.77 3.01
3733 4275 4.998671 TTCAAATTTGAGGCACAAGACA 57.001 36.364 19.64 0.00 39.77 3.41
3734 4276 4.998671 TCAAATTTGAGGCACAAGACAA 57.001 36.364 16.91 0.00 39.77 3.18
3735 4277 5.336150 TCAAATTTGAGGCACAAGACAAA 57.664 34.783 16.91 0.00 39.77 2.83
3736 4278 5.728471 TCAAATTTGAGGCACAAGACAAAA 58.272 33.333 16.91 0.00 39.77 2.44
3737 4279 5.811613 TCAAATTTGAGGCACAAGACAAAAG 59.188 36.000 16.91 0.00 39.77 2.27
3738 4280 5.343307 AATTTGAGGCACAAGACAAAAGT 57.657 34.783 0.00 0.00 39.77 2.66
3739 4281 3.781079 TTGAGGCACAAGACAAAAGTG 57.219 42.857 0.00 0.00 34.20 3.16
3745 4287 2.878580 CACAAGACAAAAGTGCAAGCA 58.121 42.857 0.00 0.00 0.00 3.91
3746 4288 3.450578 CACAAGACAAAAGTGCAAGCAT 58.549 40.909 0.00 0.00 0.00 3.79
3747 4289 3.244345 CACAAGACAAAAGTGCAAGCATG 59.756 43.478 0.00 0.00 0.00 4.06
3748 4290 3.130869 ACAAGACAAAAGTGCAAGCATGA 59.869 39.130 0.00 0.00 0.00 3.07
3749 4291 3.637998 AGACAAAAGTGCAAGCATGAG 57.362 42.857 0.00 0.00 0.00 2.90
3750 4292 2.295349 AGACAAAAGTGCAAGCATGAGG 59.705 45.455 0.00 0.00 0.00 3.86
3751 4293 2.294233 GACAAAAGTGCAAGCATGAGGA 59.706 45.455 0.00 0.00 0.00 3.71
3752 4294 2.035066 ACAAAAGTGCAAGCATGAGGAC 59.965 45.455 0.00 0.00 0.00 3.85
3753 4295 1.985473 AAAGTGCAAGCATGAGGACA 58.015 45.000 0.00 0.00 0.00 4.02
3754 4296 1.531423 AAGTGCAAGCATGAGGACAG 58.469 50.000 0.00 0.00 0.00 3.51
3755 4297 0.689055 AGTGCAAGCATGAGGACAGA 59.311 50.000 0.00 0.00 0.00 3.41
3756 4298 1.281287 AGTGCAAGCATGAGGACAGAT 59.719 47.619 0.00 0.00 0.00 2.90
3757 4299 1.400846 GTGCAAGCATGAGGACAGATG 59.599 52.381 0.00 0.00 0.00 2.90
3758 4300 1.279846 TGCAAGCATGAGGACAGATGA 59.720 47.619 0.00 0.00 0.00 2.92
3759 4301 2.092592 TGCAAGCATGAGGACAGATGAT 60.093 45.455 0.00 0.00 0.00 2.45
3760 4302 2.290916 GCAAGCATGAGGACAGATGATG 59.709 50.000 0.00 0.00 0.00 3.07
3761 4303 2.879026 CAAGCATGAGGACAGATGATGG 59.121 50.000 0.00 0.00 0.00 3.51
3762 4304 2.405559 AGCATGAGGACAGATGATGGA 58.594 47.619 0.00 0.00 0.00 3.41
3763 4305 2.104451 AGCATGAGGACAGATGATGGAC 59.896 50.000 0.00 0.00 0.00 4.02
3767 4309 2.502947 TGAGGACAGATGATGGACAAGG 59.497 50.000 0.00 0.00 0.00 3.61
3938 4484 2.662596 CCAGAGCCACAACCGCTA 59.337 61.111 0.00 0.00 36.48 4.26
3986 4532 3.496130 CGTCTATCCTATTACACGACCGT 59.504 47.826 0.00 0.00 0.00 4.83
3996 4542 0.391597 ACACGACCGTCATCCAAACT 59.608 50.000 0.00 0.00 0.00 2.66
4045 4591 1.762957 CCACCGGACAGATCCAGTAAT 59.237 52.381 9.46 0.00 46.67 1.89
4090 4636 3.767673 GGAGTGAGTAAGGACCACATACA 59.232 47.826 0.00 0.00 32.33 2.29
4096 4642 5.719563 TGAGTAAGGACCACATACAGATCAA 59.280 40.000 0.00 0.00 0.00 2.57
4099 4645 3.096852 AGGACCACATACAGATCAACGA 58.903 45.455 0.00 0.00 0.00 3.85
4100 4646 3.706594 AGGACCACATACAGATCAACGAT 59.293 43.478 0.00 0.00 0.00 3.73
4107 4653 5.750547 CACATACAGATCAACGATGTAGCTT 59.249 40.000 0.00 0.00 33.24 3.74
4181 4727 4.039488 TCATTTCTGCAGTTCCAAATTGCT 59.961 37.500 14.67 0.00 43.65 3.91
4243 4789 4.712829 TGTATCGGACTCTATCCCAACAAA 59.287 41.667 0.00 0.00 46.04 2.83
4330 4876 0.863144 TACAAAACTCTCGCCAACGC 59.137 50.000 0.00 0.00 39.84 4.84
4537 5085 7.772166 TGACACTAGAGTTAATGACATCGATT 58.228 34.615 0.00 0.00 0.00 3.34
4594 5142 6.119536 AGTAAGTTTCCAACACAACTGATCA 58.880 36.000 0.00 0.00 33.38 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.533469 GCACCTGACCTGTAGACGGT 61.533 60.000 0.00 0.00 37.50 4.83
3 4 1.215647 GCACCTGACCTGTAGACGG 59.784 63.158 0.00 0.00 0.00 4.79
4 5 1.154016 CGCACCTGACCTGTAGACG 60.154 63.158 0.00 0.00 0.00 4.18
5 6 0.388649 CACGCACCTGACCTGTAGAC 60.389 60.000 0.00 0.00 0.00 2.59
7 8 1.079819 CCACGCACCTGACCTGTAG 60.080 63.158 0.00 0.00 0.00 2.74
9 10 1.978455 TTTCCACGCACCTGACCTGT 61.978 55.000 0.00 0.00 0.00 4.00
10 11 0.817634 TTTTCCACGCACCTGACCTG 60.818 55.000 0.00 0.00 0.00 4.00
11 12 0.106918 TTTTTCCACGCACCTGACCT 60.107 50.000 0.00 0.00 0.00 3.85
12 13 2.410466 TTTTTCCACGCACCTGACC 58.590 52.632 0.00 0.00 0.00 4.02
30 31 4.218417 AGAATGTGGCTAACGCTGATTTTT 59.782 37.500 0.00 0.00 36.09 1.94
31 32 3.758554 AGAATGTGGCTAACGCTGATTTT 59.241 39.130 0.00 0.00 36.09 1.82
32 33 3.347216 AGAATGTGGCTAACGCTGATTT 58.653 40.909 0.00 0.00 36.09 2.17
33 34 2.991250 AGAATGTGGCTAACGCTGATT 58.009 42.857 0.00 0.00 36.09 2.57
34 35 2.698855 AGAATGTGGCTAACGCTGAT 57.301 45.000 0.00 0.00 36.09 2.90
35 36 2.472695 AAGAATGTGGCTAACGCTGA 57.527 45.000 0.00 0.00 36.09 4.26
36 37 2.744202 AGAAAGAATGTGGCTAACGCTG 59.256 45.455 0.00 0.00 36.09 5.18
37 38 3.059352 AGAAAGAATGTGGCTAACGCT 57.941 42.857 0.00 0.00 36.09 5.07
38 39 3.682858 TGTAGAAAGAATGTGGCTAACGC 59.317 43.478 0.00 0.00 0.00 4.84
39 40 4.092968 GGTGTAGAAAGAATGTGGCTAACG 59.907 45.833 0.00 0.00 0.00 3.18
40 41 5.001232 TGGTGTAGAAAGAATGTGGCTAAC 58.999 41.667 0.00 0.00 0.00 2.34
41 42 5.235850 TGGTGTAGAAAGAATGTGGCTAA 57.764 39.130 0.00 0.00 0.00 3.09
42 43 4.901197 TGGTGTAGAAAGAATGTGGCTA 57.099 40.909 0.00 0.00 0.00 3.93
43 44 3.788227 TGGTGTAGAAAGAATGTGGCT 57.212 42.857 0.00 0.00 0.00 4.75
44 45 3.378427 GGATGGTGTAGAAAGAATGTGGC 59.622 47.826 0.00 0.00 0.00 5.01
45 46 3.623060 CGGATGGTGTAGAAAGAATGTGG 59.377 47.826 0.00 0.00 0.00 4.17
46 47 4.503910 TCGGATGGTGTAGAAAGAATGTG 58.496 43.478 0.00 0.00 0.00 3.21
47 48 4.819105 TCGGATGGTGTAGAAAGAATGT 57.181 40.909 0.00 0.00 0.00 2.71
48 49 6.489675 CAAATCGGATGGTGTAGAAAGAATG 58.510 40.000 0.00 0.00 0.00 2.67
49 50 5.066505 GCAAATCGGATGGTGTAGAAAGAAT 59.933 40.000 0.00 0.00 0.00 2.40
50 51 4.394920 GCAAATCGGATGGTGTAGAAAGAA 59.605 41.667 0.00 0.00 0.00 2.52
51 52 3.938963 GCAAATCGGATGGTGTAGAAAGA 59.061 43.478 0.00 0.00 0.00 2.52
52 53 3.689161 TGCAAATCGGATGGTGTAGAAAG 59.311 43.478 0.00 0.00 0.00 2.62
53 54 3.680490 TGCAAATCGGATGGTGTAGAAA 58.320 40.909 0.00 0.00 0.00 2.52
54 55 3.342377 TGCAAATCGGATGGTGTAGAA 57.658 42.857 0.00 0.00 0.00 2.10
55 56 3.466836 GATGCAAATCGGATGGTGTAGA 58.533 45.455 0.00 0.00 0.00 2.59
56 57 2.549754 GGATGCAAATCGGATGGTGTAG 59.450 50.000 0.00 0.00 0.00 2.74
57 58 2.092699 TGGATGCAAATCGGATGGTGTA 60.093 45.455 0.00 0.00 0.00 2.90
58 59 1.340893 TGGATGCAAATCGGATGGTGT 60.341 47.619 0.00 0.00 0.00 4.16
59 60 1.335810 CTGGATGCAAATCGGATGGTG 59.664 52.381 0.00 0.00 0.00 4.17
60 61 1.683943 CTGGATGCAAATCGGATGGT 58.316 50.000 0.00 0.00 0.00 3.55
61 62 0.313043 GCTGGATGCAAATCGGATGG 59.687 55.000 0.00 0.00 42.31 3.51
62 63 0.040692 CGCTGGATGCAAATCGGATG 60.041 55.000 0.00 0.00 43.06 3.51
63 64 1.168407 CCGCTGGATGCAAATCGGAT 61.168 55.000 14.21 0.00 43.06 4.18
64 65 1.819208 CCGCTGGATGCAAATCGGA 60.819 57.895 14.21 0.00 43.06 4.55
65 66 2.717485 CCGCTGGATGCAAATCGG 59.283 61.111 7.58 7.58 43.06 4.18
66 67 1.159713 TAGCCGCTGGATGCAAATCG 61.160 55.000 2.16 0.00 43.06 3.34
67 68 1.024271 TTAGCCGCTGGATGCAAATC 58.976 50.000 2.16 0.00 43.06 2.17
68 69 1.473258 TTTAGCCGCTGGATGCAAAT 58.527 45.000 2.16 0.00 43.06 2.32
69 70 1.252175 TTTTAGCCGCTGGATGCAAA 58.748 45.000 2.16 0.00 43.06 3.68
70 71 1.252175 TTTTTAGCCGCTGGATGCAA 58.748 45.000 2.16 0.00 43.06 4.08
71 72 1.473258 ATTTTTAGCCGCTGGATGCA 58.527 45.000 2.16 0.00 43.06 3.96
72 73 2.159254 TCAATTTTTAGCCGCTGGATGC 60.159 45.455 2.16 0.00 38.57 3.91
73 74 3.781079 TCAATTTTTAGCCGCTGGATG 57.219 42.857 2.16 0.00 0.00 3.51
74 75 3.953612 TGATCAATTTTTAGCCGCTGGAT 59.046 39.130 2.16 0.00 0.00 3.41
75 76 3.351740 TGATCAATTTTTAGCCGCTGGA 58.648 40.909 2.16 0.00 0.00 3.86
76 77 3.781079 TGATCAATTTTTAGCCGCTGG 57.219 42.857 2.16 0.00 0.00 4.85
77 78 4.030529 CGTTTGATCAATTTTTAGCCGCTG 59.969 41.667 9.40 0.00 0.00 5.18
78 79 4.165779 CGTTTGATCAATTTTTAGCCGCT 58.834 39.130 9.40 0.00 0.00 5.52
79 80 3.241646 GCGTTTGATCAATTTTTAGCCGC 60.242 43.478 9.40 9.15 0.00 6.53
80 81 3.303229 GGCGTTTGATCAATTTTTAGCCG 59.697 43.478 9.40 3.52 0.00 5.52
81 82 3.616821 GGGCGTTTGATCAATTTTTAGCC 59.383 43.478 9.40 15.90 40.04 3.93
82 83 4.494484 AGGGCGTTTGATCAATTTTTAGC 58.506 39.130 9.40 8.52 0.00 3.09
83 84 6.868339 AGAAAGGGCGTTTGATCAATTTTTAG 59.132 34.615 9.40 0.00 0.00 1.85
84 85 6.754193 AGAAAGGGCGTTTGATCAATTTTTA 58.246 32.000 9.40 0.00 0.00 1.52
85 86 5.610398 AGAAAGGGCGTTTGATCAATTTTT 58.390 33.333 9.40 4.39 0.00 1.94
86 87 5.213891 AGAAAGGGCGTTTGATCAATTTT 57.786 34.783 9.40 4.06 0.00 1.82
87 88 4.871933 AGAAAGGGCGTTTGATCAATTT 57.128 36.364 9.40 5.58 0.00 1.82
88 89 4.524328 AGAAGAAAGGGCGTTTGATCAATT 59.476 37.500 9.40 0.00 0.00 2.32
89 90 4.082125 AGAAGAAAGGGCGTTTGATCAAT 58.918 39.130 9.40 0.00 0.00 2.57
90 91 3.486383 AGAAGAAAGGGCGTTTGATCAA 58.514 40.909 10.26 3.38 0.00 2.57
91 92 3.140325 AGAAGAAAGGGCGTTTGATCA 57.860 42.857 10.26 0.00 0.00 2.92
92 93 3.119814 GGAAGAAGAAAGGGCGTTTGATC 60.120 47.826 10.26 7.86 0.00 2.92
93 94 2.820197 GGAAGAAGAAAGGGCGTTTGAT 59.180 45.455 10.26 0.00 0.00 2.57
94 95 2.158667 AGGAAGAAGAAAGGGCGTTTGA 60.159 45.455 10.26 0.00 0.00 2.69
95 96 2.230660 AGGAAGAAGAAAGGGCGTTTG 58.769 47.619 10.26 0.00 0.00 2.93
96 97 2.658807 AGGAAGAAGAAAGGGCGTTT 57.341 45.000 4.63 4.63 0.00 3.60
97 98 2.106684 AGAAGGAAGAAGAAAGGGCGTT 59.893 45.455 0.00 0.00 0.00 4.84
98 99 1.700186 AGAAGGAAGAAGAAAGGGCGT 59.300 47.619 0.00 0.00 0.00 5.68
99 100 2.289694 TGAGAAGGAAGAAGAAAGGGCG 60.290 50.000 0.00 0.00 0.00 6.13
100 101 3.078097 GTGAGAAGGAAGAAGAAAGGGC 58.922 50.000 0.00 0.00 0.00 5.19
101 102 4.632327 AGTGAGAAGGAAGAAGAAAGGG 57.368 45.455 0.00 0.00 0.00 3.95
102 103 7.041107 CAGATAGTGAGAAGGAAGAAGAAAGG 58.959 42.308 0.00 0.00 0.00 3.11
103 104 6.534793 GCAGATAGTGAGAAGGAAGAAGAAAG 59.465 42.308 0.00 0.00 0.00 2.62
104 105 6.402222 GCAGATAGTGAGAAGGAAGAAGAAA 58.598 40.000 0.00 0.00 0.00 2.52
105 106 5.105146 GGCAGATAGTGAGAAGGAAGAAGAA 60.105 44.000 0.00 0.00 0.00 2.52
106 107 4.404073 GGCAGATAGTGAGAAGGAAGAAGA 59.596 45.833 0.00 0.00 0.00 2.87
107 108 4.161189 TGGCAGATAGTGAGAAGGAAGAAG 59.839 45.833 0.00 0.00 0.00 2.85
108 109 4.096681 TGGCAGATAGTGAGAAGGAAGAA 58.903 43.478 0.00 0.00 0.00 2.52
109 110 3.703556 CTGGCAGATAGTGAGAAGGAAGA 59.296 47.826 9.42 0.00 0.00 2.87
110 111 3.740764 GCTGGCAGATAGTGAGAAGGAAG 60.741 52.174 20.86 0.00 0.00 3.46
111 112 2.169352 GCTGGCAGATAGTGAGAAGGAA 59.831 50.000 20.86 0.00 0.00 3.36
112 113 1.759445 GCTGGCAGATAGTGAGAAGGA 59.241 52.381 20.86 0.00 0.00 3.36
113 114 1.202627 GGCTGGCAGATAGTGAGAAGG 60.203 57.143 20.86 0.00 0.00 3.46
114 115 1.483827 TGGCTGGCAGATAGTGAGAAG 59.516 52.381 20.86 0.00 0.00 2.85
115 116 1.571955 TGGCTGGCAGATAGTGAGAA 58.428 50.000 20.86 0.00 0.00 2.87
116 117 1.208052 GTTGGCTGGCAGATAGTGAGA 59.792 52.381 20.86 0.00 0.00 3.27
117 118 1.661341 GTTGGCTGGCAGATAGTGAG 58.339 55.000 20.86 0.00 0.00 3.51
118 119 0.253044 GGTTGGCTGGCAGATAGTGA 59.747 55.000 20.86 0.00 0.00 3.41
119 120 0.749454 GGGTTGGCTGGCAGATAGTG 60.749 60.000 20.86 0.00 0.00 2.74
120 121 1.207488 TGGGTTGGCTGGCAGATAGT 61.207 55.000 20.86 0.00 0.00 2.12
121 122 0.465097 CTGGGTTGGCTGGCAGATAG 60.465 60.000 20.86 0.92 0.00 2.08
122 123 1.609239 CTGGGTTGGCTGGCAGATA 59.391 57.895 20.86 2.37 0.00 1.98
123 124 2.357836 CTGGGTTGGCTGGCAGAT 59.642 61.111 20.86 0.00 0.00 2.90
124 125 3.970410 CCTGGGTTGGCTGGCAGA 61.970 66.667 20.86 0.00 0.00 4.26
132 133 4.109675 CGGGTAGGCCTGGGTTGG 62.110 72.222 17.99 0.00 37.50 3.77
133 134 4.796495 GCGGGTAGGCCTGGGTTG 62.796 72.222 17.99 2.18 41.51 3.77
474 475 2.061790 CTTAGAGGGATGGCTGGGGC 62.062 65.000 0.00 0.00 37.82 5.80
475 476 2.061790 GCTTAGAGGGATGGCTGGGG 62.062 65.000 0.00 0.00 0.00 4.96
476 477 1.453669 GCTTAGAGGGATGGCTGGG 59.546 63.158 0.00 0.00 0.00 4.45
477 478 1.453669 GGCTTAGAGGGATGGCTGG 59.546 63.158 0.00 0.00 0.00 4.85
478 479 1.453669 GGGCTTAGAGGGATGGCTG 59.546 63.158 0.00 0.00 0.00 4.85
479 480 1.772156 GGGGCTTAGAGGGATGGCT 60.772 63.158 0.00 0.00 0.00 4.75
480 481 2.839836 GGGGCTTAGAGGGATGGC 59.160 66.667 0.00 0.00 0.00 4.40
481 482 3.151906 CGGGGCTTAGAGGGATGG 58.848 66.667 0.00 0.00 0.00 3.51
482 483 2.427753 GCGGGGCTTAGAGGGATG 59.572 66.667 0.00 0.00 0.00 3.51
483 484 2.849646 GGCGGGGCTTAGAGGGAT 60.850 66.667 0.00 0.00 0.00 3.85
500 501 3.027170 GCATCACCGGAGTTGTGCG 62.027 63.158 9.46 0.00 37.24 5.34
501 502 2.690778 GGCATCACCGGAGTTGTGC 61.691 63.158 9.46 12.90 34.54 4.57
502 503 2.040544 GGGCATCACCGGAGTTGTG 61.041 63.158 9.46 2.77 40.62 3.33
503 504 2.185310 GAGGGCATCACCGGAGTTGT 62.185 60.000 9.46 0.00 40.62 3.32
504 505 1.450312 GAGGGCATCACCGGAGTTG 60.450 63.158 9.46 7.09 40.62 3.16
505 506 2.990479 GAGGGCATCACCGGAGTT 59.010 61.111 9.46 0.00 40.62 3.01
506 507 3.461773 CGAGGGCATCACCGGAGT 61.462 66.667 9.46 0.00 40.62 3.85
507 508 3.147595 TCGAGGGCATCACCGGAG 61.148 66.667 9.46 0.00 40.62 4.63
508 509 3.458163 GTCGAGGGCATCACCGGA 61.458 66.667 9.46 0.00 40.62 5.14
509 510 3.432051 GAGTCGAGGGCATCACCGG 62.432 68.421 0.00 0.00 40.62 5.28
510 511 2.105128 GAGTCGAGGGCATCACCG 59.895 66.667 0.00 0.00 40.62 4.94
511 512 2.105128 CGAGTCGAGGGCATCACC 59.895 66.667 6.73 0.00 37.93 4.02
512 513 2.583593 GCGAGTCGAGGGCATCAC 60.584 66.667 18.61 0.00 0.00 3.06
513 514 3.838271 GGCGAGTCGAGGGCATCA 61.838 66.667 18.61 0.00 0.00 3.07
514 515 3.781770 CTGGCGAGTCGAGGGCATC 62.782 68.421 18.61 0.00 38.11 3.91
515 516 3.842923 CTGGCGAGTCGAGGGCAT 61.843 66.667 18.61 0.00 38.11 4.40
521 522 3.949885 TTAGGGGCTGGCGAGTCGA 62.950 63.158 18.61 0.00 0.00 4.20
522 523 3.432051 CTTAGGGGCTGGCGAGTCG 62.432 68.421 8.54 8.54 0.00 4.18
523 524 1.403687 ATCTTAGGGGCTGGCGAGTC 61.404 60.000 0.00 0.00 0.00 3.36
524 525 0.105658 TATCTTAGGGGCTGGCGAGT 60.106 55.000 0.00 0.00 0.00 4.18
525 526 0.605589 CTATCTTAGGGGCTGGCGAG 59.394 60.000 0.00 0.00 0.00 5.03
526 527 0.187606 TCTATCTTAGGGGCTGGCGA 59.812 55.000 0.00 0.00 0.00 5.54
527 528 1.270907 ATCTATCTTAGGGGCTGGCG 58.729 55.000 0.00 0.00 0.00 5.69
528 529 5.663556 ACTATTATCTATCTTAGGGGCTGGC 59.336 44.000 0.00 0.00 0.00 4.85
529 530 6.098982 CCACTATTATCTATCTTAGGGGCTGG 59.901 46.154 0.00 0.00 28.98 4.85
530 531 6.897966 TCCACTATTATCTATCTTAGGGGCTG 59.102 42.308 0.00 0.00 35.58 4.85
531 532 7.057732 TCCACTATTATCTATCTTAGGGGCT 57.942 40.000 0.00 0.00 35.58 5.19
532 533 7.565398 TGATCCACTATTATCTATCTTAGGGGC 59.435 40.741 0.00 0.00 35.58 5.80
533 534 8.919145 GTGATCCACTATTATCTATCTTAGGGG 58.081 40.741 0.00 0.00 36.71 4.79
534 535 9.707957 AGTGATCCACTATTATCTATCTTAGGG 57.292 37.037 0.00 0.00 43.46 3.53
594 595 3.373130 GCCCTGTATTTTAGTCCACGAAC 59.627 47.826 0.00 0.00 0.00 3.95
601 602 5.243060 ACTTGTTTGGCCCTGTATTTTAGTC 59.757 40.000 0.00 0.00 0.00 2.59
606 607 3.069443 CACACTTGTTTGGCCCTGTATTT 59.931 43.478 0.00 0.00 0.00 1.40
609 610 1.686355 CACACTTGTTTGGCCCTGTA 58.314 50.000 0.00 0.00 0.00 2.74
611 612 1.067916 GCACACTTGTTTGGCCCTG 59.932 57.895 0.00 0.00 0.00 4.45
613 614 0.106521 AATGCACACTTGTTTGGCCC 59.893 50.000 0.00 0.00 0.00 5.80
614 615 1.952193 AAATGCACACTTGTTTGGCC 58.048 45.000 0.00 0.00 0.00 5.36
615 616 4.119136 AGTAAAATGCACACTTGTTTGGC 58.881 39.130 0.00 0.00 0.00 4.52
655 658 4.040217 CAGCTATCTAGACCAATGCTTCCT 59.960 45.833 0.00 0.00 0.00 3.36
673 676 9.817809 CAGAAATGGACTAGTAAATAACAGCTA 57.182 33.333 0.00 0.00 0.00 3.32
676 679 9.667107 TTCCAGAAATGGACTAGTAAATAACAG 57.333 33.333 0.00 0.00 37.76 3.16
706 709 2.635915 TCCCGTATGTTTGTGGACTTCT 59.364 45.455 0.00 0.00 0.00 2.85
707 710 3.048337 TCCCGTATGTTTGTGGACTTC 57.952 47.619 0.00 0.00 0.00 3.01
708 711 3.495434 TTCCCGTATGTTTGTGGACTT 57.505 42.857 0.00 0.00 0.00 3.01
709 712 3.713826 ATTCCCGTATGTTTGTGGACT 57.286 42.857 0.00 0.00 0.00 3.85
710 713 4.216687 TCAAATTCCCGTATGTTTGTGGAC 59.783 41.667 0.00 0.00 34.20 4.02
711 714 4.216687 GTCAAATTCCCGTATGTTTGTGGA 59.783 41.667 0.00 0.00 34.20 4.02
712 715 4.481463 GTCAAATTCCCGTATGTTTGTGG 58.519 43.478 0.00 0.00 34.20 4.17
713 716 4.481463 GGTCAAATTCCCGTATGTTTGTG 58.519 43.478 0.00 0.00 34.20 3.33
730 800 3.306502 GGTCCTTGTAGTTGATCGGTCAA 60.307 47.826 7.11 7.11 41.89 3.18
738 808 2.805295 CGTGCTTGGTCCTTGTAGTTGA 60.805 50.000 0.00 0.00 0.00 3.18
786 866 2.022240 GAGGAAGTAGCCGGAGCAGG 62.022 65.000 5.05 0.00 43.56 4.85
787 867 1.040339 AGAGGAAGTAGCCGGAGCAG 61.040 60.000 5.05 0.00 43.56 4.24
799 879 1.208706 GGGAGGAAGGGAAGAGGAAG 58.791 60.000 0.00 0.00 0.00 3.46
806 886 1.686110 GAGCGAGGGAGGAAGGGAA 60.686 63.158 0.00 0.00 0.00 3.97
828 912 2.376842 GGGAGGGGAGGGGATGAA 59.623 66.667 0.00 0.00 0.00 2.57
961 1051 4.840005 GAGGAAGAAGGCCGCGGG 62.840 72.222 29.38 8.95 0.00 6.13
968 1058 4.162690 CGGGGGCGAGGAAGAAGG 62.163 72.222 0.00 0.00 0.00 3.46
1040 1148 1.992277 GGGAGGAGCAGGAGCAAGA 60.992 63.158 0.00 0.00 45.49 3.02
1044 1152 1.223211 GAAAGGGAGGAGCAGGAGC 59.777 63.158 0.00 0.00 42.56 4.70
1050 1158 1.604915 GGACAGGAAAGGGAGGAGC 59.395 63.158 0.00 0.00 0.00 4.70
1473 1584 1.745489 GGTGAGGTTCATGCCGGAC 60.745 63.158 5.05 0.00 0.00 4.79
1524 1635 3.291101 GAGCGTGAGGTTGCCGGTA 62.291 63.158 1.90 0.00 45.11 4.02
2625 2743 2.743538 TGCGTGCTGCTGATGGTC 60.744 61.111 0.00 0.00 46.63 4.02
2755 2873 4.030452 GTCGCTGGTGTTGCTGCC 62.030 66.667 0.00 0.00 0.00 4.85
2859 2977 2.680913 GCAGTGCACGATGGTGTCC 61.681 63.158 11.09 0.70 46.13 4.02
3075 3193 1.142748 CGTCTCCAGCAGGACCATC 59.857 63.158 0.00 0.00 39.61 3.51
3104 3222 1.710339 GAGATGTCGAAGTTGCGGC 59.290 57.895 0.00 0.00 36.22 6.53
3134 3252 1.014564 CACCGAGAACTTCTTCCGGC 61.015 60.000 15.53 0.00 40.85 6.13
3300 3418 1.379044 CTGCACCACCTTCCCCATC 60.379 63.158 0.00 0.00 0.00 3.51
3306 3424 1.310933 CCAGCATCTGCACCACCTTC 61.311 60.000 4.79 0.00 45.16 3.46
3602 3720 3.582647 TCTCAACTATGCCAGACCTCAAA 59.417 43.478 0.00 0.00 0.00 2.69
3603 3721 3.173151 TCTCAACTATGCCAGACCTCAA 58.827 45.455 0.00 0.00 0.00 3.02
3606 3724 2.093235 GCTTCTCAACTATGCCAGACCT 60.093 50.000 0.00 0.00 0.00 3.85
3607 3725 2.284190 GCTTCTCAACTATGCCAGACC 58.716 52.381 0.00 0.00 0.00 3.85
3609 3727 3.538591 CATGCTTCTCAACTATGCCAGA 58.461 45.455 0.00 0.00 0.00 3.86
3610 3728 2.033049 GCATGCTTCTCAACTATGCCAG 59.967 50.000 11.37 0.00 38.48 4.85
3616 3915 5.295045 CACATACATGCATGCTTCTCAACTA 59.705 40.000 26.53 8.37 0.00 2.24
3618 3917 4.348656 CACATACATGCATGCTTCTCAAC 58.651 43.478 26.53 0.00 0.00 3.18
3621 3920 2.996155 GCACATACATGCATGCTTCTC 58.004 47.619 26.53 8.01 45.39 2.87
3631 3930 1.603802 GGTTCATCCGGCACATACATG 59.396 52.381 0.00 0.00 0.00 3.21
3641 3940 4.217550 ACTTACAAATTGTGGTTCATCCGG 59.782 41.667 9.15 0.00 39.52 5.14
3643 3942 9.705290 ATTTTACTTACAAATTGTGGTTCATCC 57.295 29.630 9.15 0.00 0.00 3.51
3659 3958 9.513727 CCTTCGGTCTAGTTCTATTTTACTTAC 57.486 37.037 0.00 0.00 0.00 2.34
3660 3959 8.193438 GCCTTCGGTCTAGTTCTATTTTACTTA 58.807 37.037 0.00 0.00 0.00 2.24
3663 3962 6.571605 AGCCTTCGGTCTAGTTCTATTTTAC 58.428 40.000 0.00 0.00 0.00 2.01
3664 3963 6.786967 AGCCTTCGGTCTAGTTCTATTTTA 57.213 37.500 0.00 0.00 0.00 1.52
3665 3964 5.678955 AGCCTTCGGTCTAGTTCTATTTT 57.321 39.130 0.00 0.00 0.00 1.82
3666 3965 5.892686 AGTAGCCTTCGGTCTAGTTCTATTT 59.107 40.000 0.00 0.00 0.00 1.40
3684 4226 6.897259 TTGTACAAATTACGATGAGTAGCC 57.103 37.500 5.64 0.00 36.56 3.93
3727 4269 3.708890 TCATGCTTGCACTTTTGTCTTG 58.291 40.909 0.00 0.00 0.00 3.02
3728 4270 3.243636 CCTCATGCTTGCACTTTTGTCTT 60.244 43.478 0.00 0.00 0.00 3.01
3729 4271 2.295349 CCTCATGCTTGCACTTTTGTCT 59.705 45.455 0.00 0.00 0.00 3.41
3730 4272 2.294233 TCCTCATGCTTGCACTTTTGTC 59.706 45.455 0.00 0.00 0.00 3.18
3731 4273 2.035066 GTCCTCATGCTTGCACTTTTGT 59.965 45.455 0.00 0.00 0.00 2.83
3732 4274 2.034939 TGTCCTCATGCTTGCACTTTTG 59.965 45.455 0.00 0.00 0.00 2.44
3733 4275 2.295349 CTGTCCTCATGCTTGCACTTTT 59.705 45.455 0.00 0.00 0.00 2.27
3734 4276 1.884579 CTGTCCTCATGCTTGCACTTT 59.115 47.619 0.00 0.00 0.00 2.66
3735 4277 1.072806 TCTGTCCTCATGCTTGCACTT 59.927 47.619 0.00 0.00 0.00 3.16
3736 4278 0.689055 TCTGTCCTCATGCTTGCACT 59.311 50.000 0.00 0.00 0.00 4.40
3737 4279 1.400846 CATCTGTCCTCATGCTTGCAC 59.599 52.381 0.00 0.00 0.00 4.57
3738 4280 1.279846 TCATCTGTCCTCATGCTTGCA 59.720 47.619 0.00 0.00 0.00 4.08
3739 4281 2.034104 TCATCTGTCCTCATGCTTGC 57.966 50.000 0.00 0.00 0.00 4.01
3740 4282 2.879026 CCATCATCTGTCCTCATGCTTG 59.121 50.000 0.00 0.00 0.00 4.01
3741 4283 2.775960 TCCATCATCTGTCCTCATGCTT 59.224 45.455 0.00 0.00 0.00 3.91
3742 4284 2.104451 GTCCATCATCTGTCCTCATGCT 59.896 50.000 0.00 0.00 0.00 3.79
3743 4285 2.158856 TGTCCATCATCTGTCCTCATGC 60.159 50.000 0.00 0.00 0.00 4.06
3744 4286 3.832615 TGTCCATCATCTGTCCTCATG 57.167 47.619 0.00 0.00 0.00 3.07
3745 4287 3.136077 CCTTGTCCATCATCTGTCCTCAT 59.864 47.826 0.00 0.00 0.00 2.90
3746 4288 2.502947 CCTTGTCCATCATCTGTCCTCA 59.497 50.000 0.00 0.00 0.00 3.86
3747 4289 2.503356 ACCTTGTCCATCATCTGTCCTC 59.497 50.000 0.00 0.00 0.00 3.71
3748 4290 2.555664 ACCTTGTCCATCATCTGTCCT 58.444 47.619 0.00 0.00 0.00 3.85
3749 4291 3.356529 AACCTTGTCCATCATCTGTCC 57.643 47.619 0.00 0.00 0.00 4.02
3750 4292 5.712152 AAAAACCTTGTCCATCATCTGTC 57.288 39.130 0.00 0.00 0.00 3.51
3900 4443 3.385577 GGCATTTTTGTCTTTGGCGTTA 58.614 40.909 0.00 0.00 0.00 3.18
3966 4512 4.707105 TGACGGTCGTGTAATAGGATAGA 58.293 43.478 0.00 0.00 0.00 1.98
3980 4526 0.320421 ACCAGTTTGGATGACGGTCG 60.320 55.000 3.34 0.00 40.96 4.79
3986 4532 6.122277 GGATATCTTCAACCAGTTTGGATGA 58.878 40.000 2.05 4.19 45.84 2.92
3996 4542 0.531974 GCGCGGGATATCTTCAACCA 60.532 55.000 8.83 0.00 0.00 3.67
4045 4591 3.249189 AGGCCAGGGAGCGTTTGA 61.249 61.111 5.01 0.00 0.00 2.69
4090 4636 4.471904 TTCCAAGCTACATCGTTGATCT 57.528 40.909 0.00 0.00 0.00 2.75
4096 4642 5.354234 CAGGTTTTATTCCAAGCTACATCGT 59.646 40.000 0.00 0.00 30.75 3.73
4099 4645 5.016173 TGCAGGTTTTATTCCAAGCTACAT 58.984 37.500 0.00 0.00 30.75 2.29
4100 4646 4.402829 TGCAGGTTTTATTCCAAGCTACA 58.597 39.130 0.00 0.00 30.75 2.74
4181 4727 4.465632 AGGAGTATGTGCGTTGTTATGA 57.534 40.909 0.00 0.00 0.00 2.15
4311 4857 0.863144 GCGTTGGCGAGAGTTTTGTA 59.137 50.000 0.00 0.00 41.33 2.41
4330 4876 0.514691 GCACCTCTTCTTTGAGTGCG 59.485 55.000 0.00 0.00 34.33 5.34
4492 5040 5.705441 TGTCATTCCTAGTTCCAAACATGTC 59.295 40.000 0.00 0.00 0.00 3.06
4537 5085 7.489113 GGAGAATTTACGGTTAAGTCGATGTAA 59.511 37.037 5.32 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.