Multiple sequence alignment - TraesCS1D01G054600

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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 TraesCS1D01G054600 chr1D 100.000 2753 0 0 1 2753 35928164 35925412 0.000000e+00 5084.0
1 TraesCS1D01G054600 chr1D 90.380 1289 93 16 597 1866 35789193 35787917 0.000000e+00 1664.0
2 TraesCS1D01G054600 chr1D 90.854 984 77 5 597 1571 35900920 35899941 0.000000e+00 1306.0
3 TraesCS1D01G054600 chr1D 95.951 247 9 1 6 251 22188948 22188702 1.540000e-107 399.0
4 TraesCS1D01G054600 chr1D 95.122 246 10 2 1 244 198902510 198902755 1.200000e-103 387.0
5 TraesCS1D01G054600 chr1D 93.651 252 14 2 1 250 88381976 88381725 2.590000e-100 375.0
6 TraesCS1D01G054600 chr1D 86.879 282 31 5 1905 2182 35886175 35885896 7.400000e-81 311.0
7 TraesCS1D01G054600 chr1A 90.553 2530 116 45 251 2753 34886833 34884400 0.000000e+00 3234.0
8 TraesCS1D01G054600 chr1A 87.539 1605 141 25 603 2182 34860976 34859406 0.000000e+00 1801.0
9 TraesCS1D01G054600 chr1A 87.360 1606 143 34 603 2182 34708474 34706903 0.000000e+00 1786.0
10 TraesCS1D01G054600 chr1B 92.027 1317 85 8 568 1866 54974258 54972944 0.000000e+00 1832.0
11 TraesCS1D01G054600 chr1B 92.706 1275 74 8 568 1826 55012787 55011516 0.000000e+00 1821.0
12 TraesCS1D01G054600 chr1B 83.969 786 114 7 975 1753 55206208 55205428 0.000000e+00 743.0
13 TraesCS1D01G054600 chr1B 92.123 292 11 3 251 538 54974535 54974252 4.270000e-108 401.0
14 TraesCS1D01G054600 chr1B 92.123 292 11 3 251 538 55013064 55012781 4.270000e-108 401.0
15 TraesCS1D01G054600 chr1B 93.281 253 14 3 1 250 642653334 642653082 1.200000e-98 370.0
16 TraesCS1D01G054600 chr2B 82.347 963 137 23 816 1752 550396961 550397916 0.000000e+00 806.0
17 TraesCS1D01G054600 chr2B 74.667 600 117 21 2181 2753 495965488 495966079 1.650000e-57 233.0
18 TraesCS1D01G054600 chr2B 72.461 581 128 24 2178 2751 663789639 663790194 1.020000e-34 158.0
19 TraesCS1D01G054600 chr6D 94.841 252 11 2 1 250 288592711 288592460 2.570000e-105 392.0
20 TraesCS1D01G054600 chr6D 75.169 592 103 32 2178 2753 386085515 386084952 3.540000e-59 239.0
21 TraesCS1D01G054600 chr3A 94.048 252 13 2 1 250 46873902 46874153 5.560000e-102 381.0
22 TraesCS1D01G054600 chr2D 94.048 252 13 2 1 250 218352281 218352030 5.560000e-102 381.0
23 TraesCS1D01G054600 chr2D 82.836 134 11 8 2179 2305 423863136 423863264 2.900000e-20 110.0
24 TraesCS1D01G054600 chr2A 94.048 252 13 2 1 250 760478215 760477964 5.560000e-102 381.0
25 TraesCS1D01G054600 chr4D 93.254 252 15 2 1 250 425281135 425281386 1.200000e-98 370.0
26 TraesCS1D01G054600 chrUn 78.070 456 69 16 2185 2622 41898678 41899120 2.720000e-65 259.0
27 TraesCS1D01G054600 chr6A 75.563 577 99 29 2179 2735 530609242 530608688 2.120000e-61 246.0
28 TraesCS1D01G054600 chr7B 81.148 122 17 4 2179 2299 724977484 724977600 2.920000e-15 93.5
29 TraesCS1D01G054600 chr3B 80.328 122 16 8 2181 2299 345009034 345009150 4.880000e-13 86.1
30 TraesCS1D01G054600 chr7A 94.286 35 2 0 2452 2486 25105799 25105833 1.000000e-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 TraesCS1D01G054600 chr1D 35925412 35928164 2752 True 5084.0 5084 100.0000 1 2753 1 chr1D.!!$R5 2752
1 TraesCS1D01G054600 chr1D 35787917 35789193 1276 True 1664.0 1664 90.3800 597 1866 1 chr1D.!!$R2 1269
2 TraesCS1D01G054600 chr1D 35899941 35900920 979 True 1306.0 1306 90.8540 597 1571 1 chr1D.!!$R4 974
3 TraesCS1D01G054600 chr1A 34884400 34886833 2433 True 3234.0 3234 90.5530 251 2753 1 chr1A.!!$R3 2502
4 TraesCS1D01G054600 chr1A 34859406 34860976 1570 True 1801.0 1801 87.5390 603 2182 1 chr1A.!!$R2 1579
5 TraesCS1D01G054600 chr1A 34706903 34708474 1571 True 1786.0 1786 87.3600 603 2182 1 chr1A.!!$R1 1579
6 TraesCS1D01G054600 chr1B 54972944 54974535 1591 True 1116.5 1832 92.0750 251 1866 2 chr1B.!!$R3 1615
7 TraesCS1D01G054600 chr1B 55011516 55013064 1548 True 1111.0 1821 92.4145 251 1826 2 chr1B.!!$R4 1575
8 TraesCS1D01G054600 chr1B 55205428 55206208 780 True 743.0 743 83.9690 975 1753 1 chr1B.!!$R1 778
9 TraesCS1D01G054600 chr2B 550396961 550397916 955 False 806.0 806 82.3470 816 1752 1 chr2B.!!$F2 936
10 TraesCS1D01G054600 chr2B 495965488 495966079 591 False 233.0 233 74.6670 2181 2753 1 chr2B.!!$F1 572
11 TraesCS1D01G054600 chr6D 386084952 386085515 563 True 239.0 239 75.1690 2178 2753 1 chr6D.!!$R2 575
12 TraesCS1D01G054600 chr6A 530608688 530609242 554 True 246.0 246 75.5630 2179 2735 1 chr6A.!!$R1 556

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
19 20 0.037232 GTAAGCTGAAGCCACCGTCT 60.037 55.0 0.0 0.0 43.38 4.18 F
109 110 0.037326 CCTCGCAGTCAAGCCTAACA 60.037 55.0 0.0 0.0 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 1717 1.533625 TGGTTTGCTTGGATCCGAAG 58.466 50.000 7.39 12.59 0.0 3.79 R
2017 2093 4.016113 AGTGACTTGAACAAAAGCGAAC 57.984 40.909 0.00 0.00 0.0 3.95 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
17 18 4.695560 GTAAGCTGAAGCCACCGT 57.304 55.556 0.00 0.00 43.38 4.83
18 19 2.457080 GTAAGCTGAAGCCACCGTC 58.543 57.895 0.00 0.00 43.38 4.79
19 20 0.037232 GTAAGCTGAAGCCACCGTCT 60.037 55.000 0.00 0.00 43.38 4.18
20 21 1.203994 GTAAGCTGAAGCCACCGTCTA 59.796 52.381 0.00 0.00 43.38 2.59
21 22 0.247736 AAGCTGAAGCCACCGTCTAG 59.752 55.000 0.00 0.00 43.38 2.43
22 23 1.153549 GCTGAAGCCACCGTCTAGG 60.154 63.158 0.00 0.00 39.83 3.02
29 30 3.065575 CCACCGTCTAGGCAACATC 57.934 57.895 0.00 0.00 46.52 3.06
30 31 0.537188 CCACCGTCTAGGCAACATCT 59.463 55.000 0.00 0.00 46.52 2.90
31 32 1.645034 CACCGTCTAGGCAACATCTG 58.355 55.000 0.00 0.00 46.52 2.90
32 33 1.066858 CACCGTCTAGGCAACATCTGT 60.067 52.381 0.00 0.00 46.52 3.41
33 34 1.204941 ACCGTCTAGGCAACATCTGTC 59.795 52.381 0.00 0.00 46.52 3.51
34 35 1.550065 CGTCTAGGCAACATCTGTCG 58.450 55.000 0.00 0.00 41.41 4.35
35 36 1.281899 GTCTAGGCAACATCTGTCGC 58.718 55.000 0.00 0.00 41.41 5.19
36 37 1.134965 GTCTAGGCAACATCTGTCGCT 60.135 52.381 0.00 0.00 41.41 4.93
37 38 2.099263 GTCTAGGCAACATCTGTCGCTA 59.901 50.000 0.00 0.00 41.41 4.26
38 39 2.099263 TCTAGGCAACATCTGTCGCTAC 59.901 50.000 0.00 0.00 41.41 3.58
39 40 0.898320 AGGCAACATCTGTCGCTACT 59.102 50.000 0.00 0.00 41.41 2.57
40 41 1.134965 AGGCAACATCTGTCGCTACTC 60.135 52.381 0.00 0.00 41.41 2.59
41 42 1.404181 GGCAACATCTGTCGCTACTCA 60.404 52.381 0.00 0.00 0.00 3.41
42 43 2.544685 GCAACATCTGTCGCTACTCAT 58.455 47.619 0.00 0.00 0.00 2.90
43 44 3.490933 GGCAACATCTGTCGCTACTCATA 60.491 47.826 0.00 0.00 0.00 2.15
44 45 4.302455 GCAACATCTGTCGCTACTCATAT 58.698 43.478 0.00 0.00 0.00 1.78
45 46 4.384247 GCAACATCTGTCGCTACTCATATC 59.616 45.833 0.00 0.00 0.00 1.63
46 47 4.775058 ACATCTGTCGCTACTCATATCC 57.225 45.455 0.00 0.00 0.00 2.59
47 48 4.145052 ACATCTGTCGCTACTCATATCCA 58.855 43.478 0.00 0.00 0.00 3.41
48 49 4.217334 ACATCTGTCGCTACTCATATCCAG 59.783 45.833 0.00 0.00 0.00 3.86
49 50 3.821748 TCTGTCGCTACTCATATCCAGT 58.178 45.455 0.00 0.00 0.00 4.00
50 51 4.207955 TCTGTCGCTACTCATATCCAGTT 58.792 43.478 0.00 0.00 0.00 3.16
51 52 4.036852 TCTGTCGCTACTCATATCCAGTTG 59.963 45.833 0.00 0.00 0.00 3.16
52 53 3.951680 TGTCGCTACTCATATCCAGTTGA 59.048 43.478 0.00 0.00 0.00 3.18
53 54 4.584743 TGTCGCTACTCATATCCAGTTGAT 59.415 41.667 0.00 0.00 37.49 2.57
54 55 4.920340 GTCGCTACTCATATCCAGTTGATG 59.080 45.833 0.00 0.00 34.76 3.07
55 56 4.827284 TCGCTACTCATATCCAGTTGATGA 59.173 41.667 0.00 0.00 34.76 2.92
56 57 5.301805 TCGCTACTCATATCCAGTTGATGAA 59.698 40.000 0.00 0.00 34.76 2.57
57 58 5.632764 CGCTACTCATATCCAGTTGATGAAG 59.367 44.000 0.00 0.00 34.76 3.02
58 59 6.515696 CGCTACTCATATCCAGTTGATGAAGA 60.516 42.308 0.00 0.00 34.76 2.87
59 60 6.867816 GCTACTCATATCCAGTTGATGAAGAG 59.132 42.308 0.00 0.00 35.15 2.85
60 61 7.255766 GCTACTCATATCCAGTTGATGAAGAGA 60.256 40.741 0.00 0.00 34.12 3.10
61 62 7.615039 ACTCATATCCAGTTGATGAAGAGAT 57.385 36.000 0.00 0.00 34.12 2.75
62 63 7.443477 ACTCATATCCAGTTGATGAAGAGATG 58.557 38.462 0.00 0.00 34.12 2.90
63 64 6.228995 TCATATCCAGTTGATGAAGAGATGC 58.771 40.000 0.00 0.00 34.76 3.91
64 65 4.774660 ATCCAGTTGATGAAGAGATGCT 57.225 40.909 0.00 0.00 30.54 3.79
65 66 3.870274 TCCAGTTGATGAAGAGATGCTG 58.130 45.455 0.00 0.00 0.00 4.41
66 67 3.516700 TCCAGTTGATGAAGAGATGCTGA 59.483 43.478 0.00 0.00 0.00 4.26
67 68 4.163649 TCCAGTTGATGAAGAGATGCTGAT 59.836 41.667 0.00 0.00 0.00 2.90
68 69 5.364735 TCCAGTTGATGAAGAGATGCTGATA 59.635 40.000 0.00 0.00 0.00 2.15
69 70 5.697178 CCAGTTGATGAAGAGATGCTGATAG 59.303 44.000 0.00 0.00 0.00 2.08
70 71 6.282167 CAGTTGATGAAGAGATGCTGATAGT 58.718 40.000 0.00 0.00 0.00 2.12
71 72 6.421501 CAGTTGATGAAGAGATGCTGATAGTC 59.578 42.308 0.00 0.00 0.00 2.59
72 73 5.465532 TGATGAAGAGATGCTGATAGTCC 57.534 43.478 0.00 0.00 0.00 3.85
73 74 3.998099 TGAAGAGATGCTGATAGTCCG 57.002 47.619 0.00 0.00 0.00 4.79
74 75 2.625314 TGAAGAGATGCTGATAGTCCGG 59.375 50.000 0.00 0.00 0.00 5.14
75 76 1.626686 AGAGATGCTGATAGTCCGGG 58.373 55.000 0.00 0.00 0.00 5.73
76 77 0.037790 GAGATGCTGATAGTCCGGGC 60.038 60.000 0.00 0.00 0.00 6.13
77 78 1.004440 GATGCTGATAGTCCGGGCC 60.004 63.158 0.08 0.00 0.00 5.80
78 79 1.460305 ATGCTGATAGTCCGGGCCT 60.460 57.895 0.08 0.16 0.00 5.19
79 80 0.178932 ATGCTGATAGTCCGGGCCTA 60.179 55.000 0.08 2.94 0.00 3.93
80 81 0.397957 TGCTGATAGTCCGGGCCTAA 60.398 55.000 0.08 0.00 0.00 2.69
81 82 0.977395 GCTGATAGTCCGGGCCTAAT 59.023 55.000 0.08 0.00 0.00 1.73
82 83 2.176889 GCTGATAGTCCGGGCCTAATA 58.823 52.381 0.08 0.00 0.00 0.98
83 84 2.094130 GCTGATAGTCCGGGCCTAATAC 60.094 54.545 0.08 0.00 0.00 1.89
84 85 2.496470 CTGATAGTCCGGGCCTAATACC 59.504 54.545 0.08 0.00 0.00 2.73
85 86 2.158279 TGATAGTCCGGGCCTAATACCA 60.158 50.000 0.08 0.00 0.00 3.25
86 87 2.708037 TAGTCCGGGCCTAATACCAT 57.292 50.000 0.08 0.00 0.00 3.55
87 88 2.708037 AGTCCGGGCCTAATACCATA 57.292 50.000 0.08 0.00 0.00 2.74
88 89 2.537143 AGTCCGGGCCTAATACCATAG 58.463 52.381 0.08 0.00 0.00 2.23
89 90 2.111255 AGTCCGGGCCTAATACCATAGA 59.889 50.000 0.08 0.00 0.00 1.98
90 91 2.233186 GTCCGGGCCTAATACCATAGAC 59.767 54.545 0.84 0.00 0.00 2.59
91 92 1.553704 CCGGGCCTAATACCATAGACC 59.446 57.143 0.84 0.00 0.00 3.85
92 93 2.537143 CGGGCCTAATACCATAGACCT 58.463 52.381 0.84 0.00 0.00 3.85
93 94 2.496470 CGGGCCTAATACCATAGACCTC 59.504 54.545 0.84 0.00 0.00 3.85
94 95 2.496470 GGGCCTAATACCATAGACCTCG 59.504 54.545 0.84 0.00 0.00 4.63
95 96 2.094130 GGCCTAATACCATAGACCTCGC 60.094 54.545 0.00 0.00 0.00 5.03
96 97 2.561419 GCCTAATACCATAGACCTCGCA 59.439 50.000 0.00 0.00 0.00 5.10
97 98 3.367498 GCCTAATACCATAGACCTCGCAG 60.367 52.174 0.00 0.00 0.00 5.18
98 99 3.827302 CCTAATACCATAGACCTCGCAGT 59.173 47.826 0.00 0.00 0.00 4.40
99 100 4.082679 CCTAATACCATAGACCTCGCAGTC 60.083 50.000 0.00 0.00 37.01 3.51
100 101 2.430248 TACCATAGACCTCGCAGTCA 57.570 50.000 7.30 0.00 39.34 3.41
101 102 1.557099 ACCATAGACCTCGCAGTCAA 58.443 50.000 7.30 0.00 39.34 3.18
102 103 1.478510 ACCATAGACCTCGCAGTCAAG 59.521 52.381 7.30 0.00 39.34 3.02
103 104 1.565305 CATAGACCTCGCAGTCAAGC 58.435 55.000 7.30 0.00 39.34 4.01
104 105 0.461961 ATAGACCTCGCAGTCAAGCC 59.538 55.000 7.30 0.00 39.34 4.35
105 106 0.612174 TAGACCTCGCAGTCAAGCCT 60.612 55.000 7.30 0.00 39.34 4.58
106 107 0.612174 AGACCTCGCAGTCAAGCCTA 60.612 55.000 7.30 0.00 39.34 3.93
107 108 0.246635 GACCTCGCAGTCAAGCCTAA 59.753 55.000 0.36 0.00 36.73 2.69
108 109 0.037232 ACCTCGCAGTCAAGCCTAAC 60.037 55.000 0.00 0.00 0.00 2.34
109 110 0.037326 CCTCGCAGTCAAGCCTAACA 60.037 55.000 0.00 0.00 0.00 2.41
110 111 1.406069 CCTCGCAGTCAAGCCTAACAT 60.406 52.381 0.00 0.00 0.00 2.71
111 112 1.929836 CTCGCAGTCAAGCCTAACATC 59.070 52.381 0.00 0.00 0.00 3.06
112 113 1.550524 TCGCAGTCAAGCCTAACATCT 59.449 47.619 0.00 0.00 0.00 2.90
113 114 2.758423 TCGCAGTCAAGCCTAACATCTA 59.242 45.455 0.00 0.00 0.00 1.98
114 115 3.194755 TCGCAGTCAAGCCTAACATCTAA 59.805 43.478 0.00 0.00 0.00 2.10
115 116 3.553511 CGCAGTCAAGCCTAACATCTAAG 59.446 47.826 0.00 0.00 0.00 2.18
116 117 4.678044 CGCAGTCAAGCCTAACATCTAAGA 60.678 45.833 0.00 0.00 0.00 2.10
117 118 4.568760 GCAGTCAAGCCTAACATCTAAGAC 59.431 45.833 0.00 0.00 0.00 3.01
118 119 5.112686 CAGTCAAGCCTAACATCTAAGACC 58.887 45.833 0.00 0.00 0.00 3.85
119 120 5.026790 AGTCAAGCCTAACATCTAAGACCT 58.973 41.667 0.00 0.00 0.00 3.85
120 121 5.105146 AGTCAAGCCTAACATCTAAGACCTG 60.105 44.000 0.00 0.00 0.00 4.00
121 122 5.023452 TCAAGCCTAACATCTAAGACCTGA 58.977 41.667 0.00 0.00 0.00 3.86
122 123 5.127845 TCAAGCCTAACATCTAAGACCTGAG 59.872 44.000 0.00 0.00 0.00 3.35
123 124 4.873010 AGCCTAACATCTAAGACCTGAGA 58.127 43.478 0.00 0.00 0.00 3.27
124 125 4.647399 AGCCTAACATCTAAGACCTGAGAC 59.353 45.833 0.00 0.00 0.00 3.36
125 126 4.202172 GCCTAACATCTAAGACCTGAGACC 60.202 50.000 0.00 0.00 0.00 3.85
126 127 4.342665 CCTAACATCTAAGACCTGAGACCC 59.657 50.000 0.00 0.00 0.00 4.46
127 128 2.753247 ACATCTAAGACCTGAGACCCC 58.247 52.381 0.00 0.00 0.00 4.95
128 129 2.044492 ACATCTAAGACCTGAGACCCCA 59.956 50.000 0.00 0.00 0.00 4.96
129 130 3.107601 CATCTAAGACCTGAGACCCCAA 58.892 50.000 0.00 0.00 0.00 4.12
130 131 2.537143 TCTAAGACCTGAGACCCCAAC 58.463 52.381 0.00 0.00 0.00 3.77
131 132 2.158219 TCTAAGACCTGAGACCCCAACA 60.158 50.000 0.00 0.00 0.00 3.33
132 133 1.518367 AAGACCTGAGACCCCAACAA 58.482 50.000 0.00 0.00 0.00 2.83
133 134 1.059913 AGACCTGAGACCCCAACAAG 58.940 55.000 0.00 0.00 0.00 3.16
134 135 0.606673 GACCTGAGACCCCAACAAGC 60.607 60.000 0.00 0.00 0.00 4.01
135 136 1.303643 CCTGAGACCCCAACAAGCC 60.304 63.158 0.00 0.00 0.00 4.35
136 137 1.455849 CTGAGACCCCAACAAGCCA 59.544 57.895 0.00 0.00 0.00 4.75
137 138 0.890996 CTGAGACCCCAACAAGCCAC 60.891 60.000 0.00 0.00 0.00 5.01
138 139 1.352622 TGAGACCCCAACAAGCCACT 61.353 55.000 0.00 0.00 0.00 4.00
139 140 0.178990 GAGACCCCAACAAGCCACTT 60.179 55.000 0.00 0.00 0.00 3.16
140 141 0.468029 AGACCCCAACAAGCCACTTG 60.468 55.000 5.80 5.80 45.85 3.16
141 142 2.087462 GACCCCAACAAGCCACTTGC 62.087 60.000 7.23 0.00 44.43 4.01
142 143 2.736531 CCCAACAAGCCACTTGCC 59.263 61.111 7.23 0.00 44.43 4.52
143 144 2.336088 CCAACAAGCCACTTGCCG 59.664 61.111 7.23 0.00 44.43 5.69
144 145 2.336088 CAACAAGCCACTTGCCGG 59.664 61.111 7.23 0.00 44.43 6.13
145 146 2.912025 AACAAGCCACTTGCCGGG 60.912 61.111 2.18 0.00 44.43 5.73
146 147 3.731766 AACAAGCCACTTGCCGGGT 62.732 57.895 2.18 0.00 44.43 5.28
147 148 2.033448 CAAGCCACTTGCCGGGTA 59.967 61.111 2.18 0.00 42.71 3.69
148 149 1.378514 CAAGCCACTTGCCGGGTAT 60.379 57.895 2.18 0.00 42.71 2.73
149 150 1.378514 AAGCCACTTGCCGGGTATG 60.379 57.895 2.18 0.00 42.71 2.39
150 151 1.847798 AAGCCACTTGCCGGGTATGA 61.848 55.000 2.18 0.00 42.71 2.15
151 152 1.819632 GCCACTTGCCGGGTATGAG 60.820 63.158 2.18 0.00 0.00 2.90
152 153 1.153168 CCACTTGCCGGGTATGAGG 60.153 63.158 2.18 2.84 0.00 3.86
158 159 2.986290 CCGGGTATGAGGCACACA 59.014 61.111 0.00 0.00 0.00 3.72
159 160 1.449601 CCGGGTATGAGGCACACAC 60.450 63.158 0.00 0.00 0.00 3.82
160 161 1.449601 CGGGTATGAGGCACACACC 60.450 63.158 3.56 3.56 44.59 4.16
161 162 1.449601 GGGTATGAGGCACACACCG 60.450 63.158 6.29 0.00 46.11 4.94
162 163 1.449601 GGTATGAGGCACACACCGG 60.450 63.158 0.00 0.00 36.30 5.28
163 164 1.295423 GTATGAGGCACACACCGGT 59.705 57.895 0.00 0.00 33.69 5.28
164 165 0.739813 GTATGAGGCACACACCGGTC 60.740 60.000 2.59 0.00 33.69 4.79
165 166 1.895020 TATGAGGCACACACCGGTCC 61.895 60.000 2.59 1.58 33.69 4.46
208 209 4.641645 CCAACTGCCGCCACTCCA 62.642 66.667 0.00 0.00 0.00 3.86
209 210 2.360350 CAACTGCCGCCACTCCAT 60.360 61.111 0.00 0.00 0.00 3.41
210 211 2.045926 AACTGCCGCCACTCCATC 60.046 61.111 0.00 0.00 0.00 3.51
211 212 2.596851 AACTGCCGCCACTCCATCT 61.597 57.895 0.00 0.00 0.00 2.90
212 213 2.129555 AACTGCCGCCACTCCATCTT 62.130 55.000 0.00 0.00 0.00 2.40
213 214 1.817099 CTGCCGCCACTCCATCTTC 60.817 63.158 0.00 0.00 0.00 2.87
214 215 2.268920 GCCGCCACTCCATCTTCA 59.731 61.111 0.00 0.00 0.00 3.02
215 216 1.817099 GCCGCCACTCCATCTTCAG 60.817 63.158 0.00 0.00 0.00 3.02
216 217 1.900351 CCGCCACTCCATCTTCAGA 59.100 57.895 0.00 0.00 0.00 3.27
217 218 0.179089 CCGCCACTCCATCTTCAGAG 60.179 60.000 0.00 0.00 36.16 3.35
218 219 0.179089 CGCCACTCCATCTTCAGAGG 60.179 60.000 0.00 0.00 34.27 3.69
219 220 0.908198 GCCACTCCATCTTCAGAGGT 59.092 55.000 0.00 0.00 34.27 3.85
220 221 1.406614 GCCACTCCATCTTCAGAGGTG 60.407 57.143 0.00 0.00 34.27 4.00
221 222 1.905215 CCACTCCATCTTCAGAGGTGT 59.095 52.381 0.00 0.00 31.77 4.16
222 223 3.099905 CCACTCCATCTTCAGAGGTGTA 58.900 50.000 0.00 0.00 31.77 2.90
223 224 3.118956 CCACTCCATCTTCAGAGGTGTAC 60.119 52.174 0.00 0.00 31.77 2.90
224 225 3.766591 CACTCCATCTTCAGAGGTGTACT 59.233 47.826 0.00 0.00 31.77 2.73
225 226 3.766591 ACTCCATCTTCAGAGGTGTACTG 59.233 47.826 0.00 0.00 31.77 2.74
226 227 4.019858 CTCCATCTTCAGAGGTGTACTGA 58.980 47.826 0.00 0.00 41.70 3.41
227 228 3.764434 TCCATCTTCAGAGGTGTACTGAC 59.236 47.826 0.00 0.00 42.84 3.51
228 229 3.428180 CCATCTTCAGAGGTGTACTGACG 60.428 52.174 0.00 0.00 42.84 4.35
229 230 1.540267 TCTTCAGAGGTGTACTGACGC 59.460 52.381 0.00 0.00 42.84 5.19
230 231 1.269723 CTTCAGAGGTGTACTGACGCA 59.730 52.381 0.00 0.00 42.84 5.24
231 232 1.545841 TCAGAGGTGTACTGACGCAT 58.454 50.000 0.00 0.00 39.10 4.73
232 233 1.472878 TCAGAGGTGTACTGACGCATC 59.527 52.381 0.00 0.00 45.10 3.91
233 234 1.202348 CAGAGGTGTACTGACGCATCA 59.798 52.381 6.14 0.00 46.72 3.07
234 235 2.103373 AGAGGTGTACTGACGCATCAT 58.897 47.619 6.14 0.00 46.72 2.45
235 236 2.099921 AGAGGTGTACTGACGCATCATC 59.900 50.000 6.14 0.00 46.72 2.92
236 237 1.137086 AGGTGTACTGACGCATCATCC 59.863 52.381 0.00 0.00 37.85 3.51
237 238 1.137086 GGTGTACTGACGCATCATCCT 59.863 52.381 0.00 0.00 37.85 3.24
238 239 2.418746 GGTGTACTGACGCATCATCCTT 60.419 50.000 0.00 0.00 37.85 3.36
239 240 2.604914 GTGTACTGACGCATCATCCTTG 59.395 50.000 0.00 0.00 36.03 3.61
240 241 1.594862 GTACTGACGCATCATCCTTGC 59.405 52.381 0.00 0.00 33.22 4.01
241 242 0.745845 ACTGACGCATCATCCTTGCC 60.746 55.000 0.00 0.00 36.75 4.52
242 243 1.442526 CTGACGCATCATCCTTGCCC 61.443 60.000 0.00 0.00 36.75 5.36
243 244 2.514592 ACGCATCATCCTTGCCCG 60.515 61.111 0.00 0.00 36.75 6.13
244 245 3.282157 CGCATCATCCTTGCCCGG 61.282 66.667 0.00 0.00 36.75 5.73
245 246 2.124151 GCATCATCCTTGCCCGGT 60.124 61.111 0.00 0.00 33.95 5.28
246 247 2.189499 GCATCATCCTTGCCCGGTC 61.189 63.158 0.00 0.00 33.95 4.79
247 248 1.528824 CATCATCCTTGCCCGGTCT 59.471 57.895 0.00 0.00 0.00 3.85
248 249 0.758734 CATCATCCTTGCCCGGTCTA 59.241 55.000 0.00 0.00 0.00 2.59
249 250 1.051812 ATCATCCTTGCCCGGTCTAG 58.948 55.000 0.00 0.00 0.00 2.43
275 276 6.524101 AACGCATTCCATAACAAGGTAATT 57.476 33.333 0.00 0.00 0.00 1.40
293 294 8.396272 AGGTAATTATTTGGTCACTCATATGC 57.604 34.615 0.00 0.00 0.00 3.14
325 326 0.320697 ACGACACTTAAGGTCAGCCC 59.679 55.000 18.33 0.00 34.97 5.19
391 392 8.136800 GGCTTTCTAGGTATCTTTCTAGTGTAC 58.863 40.741 0.00 0.00 35.65 2.90
392 393 8.684520 GCTTTCTAGGTATCTTTCTAGTGTACA 58.315 37.037 0.00 0.00 35.65 2.90
438 439 8.971073 TGAAGAAAGAAAGAAAGAAGTTTGGAT 58.029 29.630 0.00 0.00 0.00 3.41
466 467 2.362736 CAGCAGAGTGGTGCATACAAT 58.637 47.619 6.80 0.80 46.60 2.71
467 468 3.534554 CAGCAGAGTGGTGCATACAATA 58.465 45.455 6.80 0.00 46.60 1.90
468 469 3.310774 CAGCAGAGTGGTGCATACAATAC 59.689 47.826 6.80 0.00 46.60 1.89
469 470 3.055167 AGCAGAGTGGTGCATACAATACA 60.055 43.478 6.80 0.00 46.60 2.29
470 471 3.689161 GCAGAGTGGTGCATACAATACAA 59.311 43.478 6.80 0.00 43.41 2.41
523 528 4.704833 GCCTGCTCCTGCACGGAA 62.705 66.667 6.39 0.00 45.31 4.30
674 679 0.532862 AAGTGTGGAGCCAAGACACG 60.533 55.000 0.00 0.00 43.88 4.49
698 704 5.020132 AGACAAGAGAGCCAGTACAAGTAT 58.980 41.667 0.00 0.00 0.00 2.12
848 858 4.272489 CATTTCCTTCTTATCCACAGGCA 58.728 43.478 0.00 0.00 0.00 4.75
854 865 0.331278 CTTATCCACAGGCACCCCAA 59.669 55.000 0.00 0.00 0.00 4.12
900 923 5.434044 TCCTCCATGTCCCTATATATACCGA 59.566 44.000 0.00 0.00 0.00 4.69
902 925 6.209589 CCTCCATGTCCCTATATATACCGATG 59.790 46.154 0.00 0.00 0.00 3.84
905 928 6.294010 CCATGTCCCTATATATACCGATGTCG 60.294 46.154 0.00 0.00 39.44 4.35
914 938 1.936436 TACCGATGTCGTCCAACCCG 61.936 60.000 1.44 0.00 37.74 5.28
969 1011 6.719829 TCTTCTCTACCTGATCAAACACACTA 59.280 38.462 0.00 0.00 0.00 2.74
970 1012 6.268825 TCTCTACCTGATCAAACACACTAC 57.731 41.667 0.00 0.00 0.00 2.73
1121 1164 8.633561 TGACAAGACATCTCAAGGTATGTATAG 58.366 37.037 0.00 0.00 36.48 1.31
1206 1264 9.549509 TGTTAACTGTTCGAAATTTGTATATGC 57.450 29.630 7.22 0.00 0.00 3.14
1398 1456 3.932710 TCTCATTGGCTCGTGTTGATTAC 59.067 43.478 0.00 0.00 0.00 1.89
1422 1480 1.076350 CCCTATGGTCAAAACCCACCA 59.924 52.381 0.00 0.00 46.84 4.17
1659 1717 0.463654 TCACCATAGCCAATGCGGTC 60.464 55.000 0.00 0.00 44.33 4.79
2017 2093 1.399215 GGCATTACGGTTGTGTGTTCG 60.399 52.381 0.00 0.00 0.00 3.95
2075 2151 0.892755 AAGTGCCCATGTGCTCAATG 59.107 50.000 0.86 0.00 0.00 2.82
2266 2349 2.038329 CACCTAGTCGGTCCCCCA 59.962 66.667 0.00 0.00 44.93 4.96
2345 2429 1.490693 AAATATCCTCACTGCGCGCG 61.491 55.000 28.44 28.44 0.00 6.86
2385 2469 2.586792 CTTCTCTCCCGCCCTTGG 59.413 66.667 0.00 0.00 0.00 3.61
2407 2491 4.329545 GCTCCACTCCCGCCACAA 62.330 66.667 0.00 0.00 0.00 3.33
2421 2505 0.321210 CCACAACCACTATCACGCCA 60.321 55.000 0.00 0.00 0.00 5.69
2516 2615 1.894756 CCGCCGAAAACAACCCTCA 60.895 57.895 0.00 0.00 0.00 3.86
2522 2621 2.125202 GAAAACAACCCTCACGCCGG 62.125 60.000 0.00 0.00 0.00 6.13
2523 2622 2.897172 AAAACAACCCTCACGCCGGT 62.897 55.000 1.90 0.00 0.00 5.28
2566 2666 5.333566 TGGGGATAAGAAAAAGTCCACTT 57.666 39.130 0.00 0.00 35.17 3.16
2674 2786 4.517453 CCAAACAGGATAGAAAACCAACGA 59.483 41.667 0.00 0.00 41.22 3.85
2740 2852 2.961559 AAAGGCCACAATGGTGCCCA 62.962 55.000 5.01 0.00 44.87 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.037232 AGACGGTGGCTTCAGCTTAC 60.037 55.000 0.00 0.00 41.70 2.34
1 2 1.476891 CTAGACGGTGGCTTCAGCTTA 59.523 52.381 0.00 0.00 41.70 3.09
2 3 0.247736 CTAGACGGTGGCTTCAGCTT 59.752 55.000 0.00 0.00 41.70 3.74
3 4 1.608717 CCTAGACGGTGGCTTCAGCT 61.609 60.000 0.00 0.00 41.70 4.24
4 5 1.153549 CCTAGACGGTGGCTTCAGC 60.154 63.158 0.00 0.00 41.14 4.26
5 6 1.153549 GCCTAGACGGTGGCTTCAG 60.154 63.158 1.01 0.00 45.26 3.02
6 7 2.978824 GCCTAGACGGTGGCTTCA 59.021 61.111 1.01 0.00 45.26 3.02
11 12 0.537188 AGATGTTGCCTAGACGGTGG 59.463 55.000 0.00 0.00 34.25 4.61
12 13 1.066858 ACAGATGTTGCCTAGACGGTG 60.067 52.381 0.00 0.00 34.25 4.94
13 14 1.204941 GACAGATGTTGCCTAGACGGT 59.795 52.381 0.00 0.00 34.25 4.83
14 15 1.799181 CGACAGATGTTGCCTAGACGG 60.799 57.143 0.00 0.00 0.00 4.79
15 16 1.550065 CGACAGATGTTGCCTAGACG 58.450 55.000 0.00 0.00 0.00 4.18
23 24 4.920340 GGATATGAGTAGCGACAGATGTTG 59.080 45.833 0.00 0.00 0.00 3.33
24 25 4.584743 TGGATATGAGTAGCGACAGATGTT 59.415 41.667 0.00 0.00 0.00 2.71
25 26 4.145052 TGGATATGAGTAGCGACAGATGT 58.855 43.478 0.00 0.00 0.00 3.06
26 27 4.217334 ACTGGATATGAGTAGCGACAGATG 59.783 45.833 0.00 0.00 0.00 2.90
27 28 4.402829 ACTGGATATGAGTAGCGACAGAT 58.597 43.478 0.00 0.00 0.00 2.90
28 29 3.821748 ACTGGATATGAGTAGCGACAGA 58.178 45.455 0.00 0.00 0.00 3.41
29 30 4.036852 TCAACTGGATATGAGTAGCGACAG 59.963 45.833 0.00 0.00 0.00 3.51
30 31 3.951680 TCAACTGGATATGAGTAGCGACA 59.048 43.478 0.00 0.00 0.00 4.35
31 32 4.569761 TCAACTGGATATGAGTAGCGAC 57.430 45.455 0.00 0.00 0.00 5.19
32 33 4.827284 TCATCAACTGGATATGAGTAGCGA 59.173 41.667 0.00 0.00 33.95 4.93
33 34 5.126396 TCATCAACTGGATATGAGTAGCG 57.874 43.478 0.00 0.00 33.95 4.26
34 35 6.753180 TCTTCATCAACTGGATATGAGTAGC 58.247 40.000 0.00 0.00 33.95 3.58
35 36 8.175925 TCTCTTCATCAACTGGATATGAGTAG 57.824 38.462 0.00 0.00 33.95 2.57
36 37 8.583296 CATCTCTTCATCAACTGGATATGAGTA 58.417 37.037 0.00 0.00 33.95 2.59
37 38 7.443477 CATCTCTTCATCAACTGGATATGAGT 58.557 38.462 0.00 0.00 33.95 3.41
38 39 6.369340 GCATCTCTTCATCAACTGGATATGAG 59.631 42.308 0.00 0.00 33.95 2.90
39 40 6.042897 AGCATCTCTTCATCAACTGGATATGA 59.957 38.462 0.00 0.00 33.95 2.15
40 41 6.147985 CAGCATCTCTTCATCAACTGGATATG 59.852 42.308 0.00 0.00 33.95 1.78
41 42 6.042897 TCAGCATCTCTTCATCAACTGGATAT 59.957 38.462 0.00 0.00 33.95 1.63
42 43 5.364735 TCAGCATCTCTTCATCAACTGGATA 59.635 40.000 0.00 0.00 33.95 2.59
43 44 4.163649 TCAGCATCTCTTCATCAACTGGAT 59.836 41.667 0.00 0.00 36.39 3.41
44 45 3.516700 TCAGCATCTCTTCATCAACTGGA 59.483 43.478 0.00 0.00 0.00 3.86
45 46 3.870274 TCAGCATCTCTTCATCAACTGG 58.130 45.455 0.00 0.00 0.00 4.00
46 47 6.282167 ACTATCAGCATCTCTTCATCAACTG 58.718 40.000 0.00 0.00 0.00 3.16
47 48 6.462768 GGACTATCAGCATCTCTTCATCAACT 60.463 42.308 0.00 0.00 0.00 3.16
48 49 5.695816 GGACTATCAGCATCTCTTCATCAAC 59.304 44.000 0.00 0.00 0.00 3.18
49 50 5.508657 CGGACTATCAGCATCTCTTCATCAA 60.509 44.000 0.00 0.00 0.00 2.57
50 51 4.022503 CGGACTATCAGCATCTCTTCATCA 60.023 45.833 0.00 0.00 0.00 3.07
51 52 4.484236 CGGACTATCAGCATCTCTTCATC 58.516 47.826 0.00 0.00 0.00 2.92
52 53 3.257873 CCGGACTATCAGCATCTCTTCAT 59.742 47.826 0.00 0.00 0.00 2.57
53 54 2.625314 CCGGACTATCAGCATCTCTTCA 59.375 50.000 0.00 0.00 0.00 3.02
54 55 2.029470 CCCGGACTATCAGCATCTCTTC 60.029 54.545 0.73 0.00 0.00 2.87
55 56 1.967066 CCCGGACTATCAGCATCTCTT 59.033 52.381 0.73 0.00 0.00 2.85
56 57 1.626686 CCCGGACTATCAGCATCTCT 58.373 55.000 0.73 0.00 0.00 3.10
57 58 0.037790 GCCCGGACTATCAGCATCTC 60.038 60.000 0.73 0.00 0.00 2.75
58 59 1.476007 GGCCCGGACTATCAGCATCT 61.476 60.000 0.73 0.00 0.00 2.90
59 60 1.004440 GGCCCGGACTATCAGCATC 60.004 63.158 0.73 0.00 0.00 3.91
60 61 0.178932 TAGGCCCGGACTATCAGCAT 60.179 55.000 0.73 0.00 0.00 3.79
61 62 0.397957 TTAGGCCCGGACTATCAGCA 60.398 55.000 0.73 0.00 0.00 4.41
62 63 0.977395 ATTAGGCCCGGACTATCAGC 59.023 55.000 0.73 0.00 0.00 4.26
63 64 2.496470 GGTATTAGGCCCGGACTATCAG 59.504 54.545 0.73 0.00 0.00 2.90
64 65 2.158279 TGGTATTAGGCCCGGACTATCA 60.158 50.000 0.73 0.00 0.00 2.15
65 66 2.532843 TGGTATTAGGCCCGGACTATC 58.467 52.381 0.73 0.00 0.00 2.08
66 67 2.708037 TGGTATTAGGCCCGGACTAT 57.292 50.000 0.73 0.00 0.00 2.12
67 68 2.708037 ATGGTATTAGGCCCGGACTA 57.292 50.000 0.73 0.00 0.00 2.59
68 69 2.111255 TCTATGGTATTAGGCCCGGACT 59.889 50.000 0.73 0.00 0.00 3.85
69 70 2.233186 GTCTATGGTATTAGGCCCGGAC 59.767 54.545 0.73 0.00 0.00 4.79
70 71 2.532843 GTCTATGGTATTAGGCCCGGA 58.467 52.381 0.73 0.00 0.00 5.14
71 72 1.553704 GGTCTATGGTATTAGGCCCGG 59.446 57.143 0.00 0.00 37.90 5.73
72 73 2.496470 GAGGTCTATGGTATTAGGCCCG 59.504 54.545 0.00 0.00 43.72 6.13
73 74 2.496470 CGAGGTCTATGGTATTAGGCCC 59.504 54.545 0.00 0.00 43.72 5.80
74 75 2.094130 GCGAGGTCTATGGTATTAGGCC 60.094 54.545 0.00 0.00 43.12 5.19
75 76 2.561419 TGCGAGGTCTATGGTATTAGGC 59.439 50.000 0.00 0.00 0.00 3.93
76 77 3.827302 ACTGCGAGGTCTATGGTATTAGG 59.173 47.826 0.00 0.00 0.00 2.69
77 78 4.519350 TGACTGCGAGGTCTATGGTATTAG 59.481 45.833 9.06 0.00 37.16 1.73
78 79 4.466827 TGACTGCGAGGTCTATGGTATTA 58.533 43.478 9.06 0.00 37.16 0.98
79 80 3.296854 TGACTGCGAGGTCTATGGTATT 58.703 45.455 9.06 0.00 37.16 1.89
80 81 2.945456 TGACTGCGAGGTCTATGGTAT 58.055 47.619 9.06 0.00 37.16 2.73
81 82 2.430248 TGACTGCGAGGTCTATGGTA 57.570 50.000 9.06 0.00 37.16 3.25
82 83 1.478510 CTTGACTGCGAGGTCTATGGT 59.521 52.381 9.06 0.00 37.16 3.55
83 84 1.804372 GCTTGACTGCGAGGTCTATGG 60.804 57.143 9.06 0.00 37.16 2.74
84 85 1.565305 GCTTGACTGCGAGGTCTATG 58.435 55.000 9.06 2.35 37.16 2.23
85 86 0.461961 GGCTTGACTGCGAGGTCTAT 59.538 55.000 9.06 0.00 37.16 1.98
86 87 0.612174 AGGCTTGACTGCGAGGTCTA 60.612 55.000 9.06 2.15 37.16 2.59
87 88 0.612174 TAGGCTTGACTGCGAGGTCT 60.612 55.000 0.00 0.00 37.16 3.85
88 89 0.246635 TTAGGCTTGACTGCGAGGTC 59.753 55.000 0.00 0.00 36.81 3.85
89 90 0.037232 GTTAGGCTTGACTGCGAGGT 60.037 55.000 0.00 0.00 0.00 3.85
90 91 0.037326 TGTTAGGCTTGACTGCGAGG 60.037 55.000 0.00 0.00 0.00 4.63
91 92 1.929836 GATGTTAGGCTTGACTGCGAG 59.070 52.381 0.00 0.00 0.00 5.03
92 93 1.550524 AGATGTTAGGCTTGACTGCGA 59.449 47.619 0.00 0.00 0.00 5.10
93 94 2.015736 AGATGTTAGGCTTGACTGCG 57.984 50.000 0.00 0.00 0.00 5.18
94 95 4.568760 GTCTTAGATGTTAGGCTTGACTGC 59.431 45.833 0.00 0.00 0.00 4.40
95 96 5.105146 AGGTCTTAGATGTTAGGCTTGACTG 60.105 44.000 0.00 0.00 0.00 3.51
96 97 5.026790 AGGTCTTAGATGTTAGGCTTGACT 58.973 41.667 0.00 0.00 0.00 3.41
97 98 5.105310 TCAGGTCTTAGATGTTAGGCTTGAC 60.105 44.000 0.00 0.00 28.69 3.18
98 99 5.023452 TCAGGTCTTAGATGTTAGGCTTGA 58.977 41.667 0.00 0.00 30.84 3.02
99 100 5.127845 TCTCAGGTCTTAGATGTTAGGCTTG 59.872 44.000 0.00 0.00 0.00 4.01
100 101 5.128008 GTCTCAGGTCTTAGATGTTAGGCTT 59.872 44.000 0.00 0.00 0.00 4.35
101 102 4.647399 GTCTCAGGTCTTAGATGTTAGGCT 59.353 45.833 0.00 0.00 0.00 4.58
102 103 4.202172 GGTCTCAGGTCTTAGATGTTAGGC 60.202 50.000 0.00 0.00 0.00 3.93
103 104 4.342665 GGGTCTCAGGTCTTAGATGTTAGG 59.657 50.000 0.00 0.00 0.00 2.69
104 105 4.342665 GGGGTCTCAGGTCTTAGATGTTAG 59.657 50.000 0.00 0.00 0.00 2.34
105 106 4.264668 TGGGGTCTCAGGTCTTAGATGTTA 60.265 45.833 0.00 0.00 0.00 2.41
106 107 3.108376 GGGGTCTCAGGTCTTAGATGTT 58.892 50.000 0.00 0.00 0.00 2.71
107 108 2.044492 TGGGGTCTCAGGTCTTAGATGT 59.956 50.000 0.00 0.00 0.00 3.06
108 109 2.752030 TGGGGTCTCAGGTCTTAGATG 58.248 52.381 0.00 0.00 0.00 2.90
109 110 3.108376 GTTGGGGTCTCAGGTCTTAGAT 58.892 50.000 0.00 0.00 0.00 1.98
110 111 2.158219 TGTTGGGGTCTCAGGTCTTAGA 60.158 50.000 0.00 0.00 0.00 2.10
111 112 2.257207 TGTTGGGGTCTCAGGTCTTAG 58.743 52.381 0.00 0.00 0.00 2.18
112 113 2.409064 TGTTGGGGTCTCAGGTCTTA 57.591 50.000 0.00 0.00 0.00 2.10
113 114 1.421646 CTTGTTGGGGTCTCAGGTCTT 59.578 52.381 0.00 0.00 0.00 3.01
114 115 1.059913 CTTGTTGGGGTCTCAGGTCT 58.940 55.000 0.00 0.00 0.00 3.85
115 116 0.606673 GCTTGTTGGGGTCTCAGGTC 60.607 60.000 0.00 0.00 0.00 3.85
116 117 1.456287 GCTTGTTGGGGTCTCAGGT 59.544 57.895 0.00 0.00 0.00 4.00
117 118 1.303643 GGCTTGTTGGGGTCTCAGG 60.304 63.158 0.00 0.00 0.00 3.86
118 119 0.890996 GTGGCTTGTTGGGGTCTCAG 60.891 60.000 0.00 0.00 0.00 3.35
119 120 1.150536 GTGGCTTGTTGGGGTCTCA 59.849 57.895 0.00 0.00 0.00 3.27
120 121 0.178990 AAGTGGCTTGTTGGGGTCTC 60.179 55.000 0.00 0.00 0.00 3.36
121 122 0.468029 CAAGTGGCTTGTTGGGGTCT 60.468 55.000 1.06 0.00 36.79 3.85
122 123 2.041153 CAAGTGGCTTGTTGGGGTC 58.959 57.895 1.06 0.00 36.79 4.46
123 124 2.133641 GCAAGTGGCTTGTTGGGGT 61.134 57.895 10.10 0.00 42.77 4.95
124 125 2.736531 GCAAGTGGCTTGTTGGGG 59.263 61.111 10.10 0.00 42.77 4.96
125 126 2.736531 GGCAAGTGGCTTGTTGGG 59.263 61.111 10.10 0.00 42.77 4.12
126 127 2.336088 CGGCAAGTGGCTTGTTGG 59.664 61.111 10.10 0.00 42.77 3.77
127 128 2.336088 CCGGCAAGTGGCTTGTTG 59.664 61.111 10.10 3.88 42.77 3.33
128 129 2.346284 TACCCGGCAAGTGGCTTGTT 62.346 55.000 0.00 0.00 42.77 2.83
129 130 2.137177 ATACCCGGCAAGTGGCTTGT 62.137 55.000 0.00 2.84 42.77 3.16
130 131 1.378514 ATACCCGGCAAGTGGCTTG 60.379 57.895 0.00 4.65 43.57 4.01
131 132 1.378514 CATACCCGGCAAGTGGCTT 60.379 57.895 0.00 0.00 44.01 4.35
132 133 2.257409 CTCATACCCGGCAAGTGGCT 62.257 60.000 0.00 0.00 44.01 4.75
133 134 1.819632 CTCATACCCGGCAAGTGGC 60.820 63.158 0.00 0.00 43.74 5.01
134 135 1.153168 CCTCATACCCGGCAAGTGG 60.153 63.158 0.00 0.00 0.00 4.00
135 136 1.819632 GCCTCATACCCGGCAAGTG 60.820 63.158 0.00 0.00 45.59 3.16
136 137 2.590092 GCCTCATACCCGGCAAGT 59.410 61.111 0.00 0.00 45.59 3.16
140 141 2.513897 GTGTGCCTCATACCCGGC 60.514 66.667 0.00 0.00 46.46 6.13
141 142 1.449601 GTGTGTGCCTCATACCCGG 60.450 63.158 0.00 0.00 33.07 5.73
142 143 4.201951 GTGTGTGCCTCATACCCG 57.798 61.111 0.00 0.00 33.07 5.28
145 146 0.739813 GACCGGTGTGTGCCTCATAC 60.740 60.000 14.63 0.00 37.42 2.39
146 147 1.594833 GACCGGTGTGTGCCTCATA 59.405 57.895 14.63 0.00 0.00 2.15
147 148 2.347490 GACCGGTGTGTGCCTCAT 59.653 61.111 14.63 0.00 0.00 2.90
148 149 3.936203 GGACCGGTGTGTGCCTCA 61.936 66.667 14.63 0.00 0.00 3.86
191 192 3.925630 ATGGAGTGGCGGCAGTTGG 62.926 63.158 21.38 0.00 0.00 3.77
192 193 2.360350 ATGGAGTGGCGGCAGTTG 60.360 61.111 21.38 0.00 0.00 3.16
193 194 2.045926 GATGGAGTGGCGGCAGTT 60.046 61.111 21.38 8.30 0.00 3.16
194 195 2.527951 GAAGATGGAGTGGCGGCAGT 62.528 60.000 20.57 20.57 0.00 4.40
195 196 1.817099 GAAGATGGAGTGGCGGCAG 60.817 63.158 13.91 0.00 0.00 4.85
196 197 2.268920 GAAGATGGAGTGGCGGCA 59.731 61.111 7.97 7.97 0.00 5.69
197 198 1.817099 CTGAAGATGGAGTGGCGGC 60.817 63.158 0.00 0.00 0.00 6.53
198 199 0.179089 CTCTGAAGATGGAGTGGCGG 60.179 60.000 0.00 0.00 0.00 6.13
199 200 0.179089 CCTCTGAAGATGGAGTGGCG 60.179 60.000 0.00 0.00 0.00 5.69
200 201 0.908198 ACCTCTGAAGATGGAGTGGC 59.092 55.000 0.00 0.00 0.00 5.01
201 202 1.905215 ACACCTCTGAAGATGGAGTGG 59.095 52.381 0.00 0.00 0.00 4.00
202 203 3.766591 AGTACACCTCTGAAGATGGAGTG 59.233 47.826 0.00 0.00 0.00 3.51
203 204 3.766591 CAGTACACCTCTGAAGATGGAGT 59.233 47.826 0.00 0.00 35.20 3.85
204 205 4.019858 TCAGTACACCTCTGAAGATGGAG 58.980 47.826 0.00 0.00 38.71 3.86
205 206 3.764434 GTCAGTACACCTCTGAAGATGGA 59.236 47.826 0.00 0.00 42.42 3.41
206 207 3.428180 CGTCAGTACACCTCTGAAGATGG 60.428 52.174 0.00 0.00 42.42 3.51
207 208 3.763902 CGTCAGTACACCTCTGAAGATG 58.236 50.000 0.00 0.00 42.42 2.90
208 209 2.164624 GCGTCAGTACACCTCTGAAGAT 59.835 50.000 11.57 0.00 42.42 2.40
209 210 1.540267 GCGTCAGTACACCTCTGAAGA 59.460 52.381 11.57 0.00 42.42 2.87
210 211 1.269723 TGCGTCAGTACACCTCTGAAG 59.730 52.381 0.00 0.00 42.42 3.02
211 212 1.324383 TGCGTCAGTACACCTCTGAA 58.676 50.000 0.00 0.00 42.42 3.02
212 213 1.472878 GATGCGTCAGTACACCTCTGA 59.527 52.381 0.00 0.00 39.25 3.27
213 214 1.202348 TGATGCGTCAGTACACCTCTG 59.798 52.381 3.97 0.00 0.00 3.35
214 215 1.545841 TGATGCGTCAGTACACCTCT 58.454 50.000 3.97 0.00 0.00 3.69
215 216 2.464865 GATGATGCGTCAGTACACCTC 58.535 52.381 15.04 1.23 37.87 3.85
216 217 1.137086 GGATGATGCGTCAGTACACCT 59.863 52.381 15.04 0.00 37.87 4.00
217 218 1.137086 AGGATGATGCGTCAGTACACC 59.863 52.381 15.04 11.58 37.87 4.16
218 219 2.586258 AGGATGATGCGTCAGTACAC 57.414 50.000 15.04 2.77 37.87 2.90
219 220 2.892374 CAAGGATGATGCGTCAGTACA 58.108 47.619 15.04 0.00 37.87 2.90
220 221 1.594862 GCAAGGATGATGCGTCAGTAC 59.405 52.381 15.04 6.94 37.87 2.73
221 222 1.473257 GGCAAGGATGATGCGTCAGTA 60.473 52.381 15.04 0.00 44.75 2.74
222 223 0.745845 GGCAAGGATGATGCGTCAGT 60.746 55.000 15.04 2.78 44.75 3.41
223 224 1.442526 GGGCAAGGATGATGCGTCAG 61.443 60.000 15.04 1.18 44.75 3.51
224 225 1.451927 GGGCAAGGATGATGCGTCA 60.452 57.895 11.83 11.83 44.75 4.35
225 226 2.537560 CGGGCAAGGATGATGCGTC 61.538 63.158 0.00 0.00 44.75 5.19
226 227 2.514592 CGGGCAAGGATGATGCGT 60.515 61.111 0.00 0.00 44.75 5.24
227 228 3.282157 CCGGGCAAGGATGATGCG 61.282 66.667 0.00 0.00 44.75 4.73
228 229 2.124151 ACCGGGCAAGGATGATGC 60.124 61.111 6.32 0.00 43.08 3.91
229 230 0.758734 TAGACCGGGCAAGGATGATG 59.241 55.000 11.69 0.00 34.73 3.07
230 231 1.051812 CTAGACCGGGCAAGGATGAT 58.948 55.000 11.69 0.00 34.73 2.45
231 232 0.325296 ACTAGACCGGGCAAGGATGA 60.325 55.000 11.69 0.00 34.73 2.92
232 233 1.410004 TACTAGACCGGGCAAGGATG 58.590 55.000 11.69 0.00 34.73 3.51
233 234 2.169978 GTTTACTAGACCGGGCAAGGAT 59.830 50.000 11.69 0.00 34.73 3.24
234 235 1.551883 GTTTACTAGACCGGGCAAGGA 59.448 52.381 11.69 0.00 34.73 3.36
235 236 1.738030 CGTTTACTAGACCGGGCAAGG 60.738 57.143 11.69 0.26 37.30 3.61
236 237 1.636988 CGTTTACTAGACCGGGCAAG 58.363 55.000 11.69 3.48 0.00 4.01
237 238 0.390209 GCGTTTACTAGACCGGGCAA 60.390 55.000 11.69 0.00 0.00 4.52
238 239 1.216178 GCGTTTACTAGACCGGGCA 59.784 57.895 11.69 0.00 0.00 5.36
239 240 0.179092 ATGCGTTTACTAGACCGGGC 60.179 55.000 6.32 0.52 0.00 6.13
240 241 2.199236 GAATGCGTTTACTAGACCGGG 58.801 52.381 6.32 0.00 0.00 5.73
241 242 2.199236 GGAATGCGTTTACTAGACCGG 58.801 52.381 0.00 0.00 0.00 5.28
242 243 2.883574 TGGAATGCGTTTACTAGACCG 58.116 47.619 0.00 0.00 0.00 4.79
243 244 5.813672 TGTTATGGAATGCGTTTACTAGACC 59.186 40.000 0.00 0.00 0.00 3.85
244 245 6.897259 TGTTATGGAATGCGTTTACTAGAC 57.103 37.500 0.00 0.00 0.00 2.59
245 246 6.537301 CCTTGTTATGGAATGCGTTTACTAGA 59.463 38.462 0.00 0.00 0.00 2.43
246 247 6.315393 ACCTTGTTATGGAATGCGTTTACTAG 59.685 38.462 0.00 0.00 0.00 2.57
247 248 6.174760 ACCTTGTTATGGAATGCGTTTACTA 58.825 36.000 0.00 0.00 0.00 1.82
248 249 5.007682 ACCTTGTTATGGAATGCGTTTACT 58.992 37.500 0.00 0.00 0.00 2.24
249 250 5.305139 ACCTTGTTATGGAATGCGTTTAC 57.695 39.130 0.00 0.00 0.00 2.01
275 276 3.138304 GCCGCATATGAGTGACCAAATA 58.862 45.455 6.97 0.00 0.00 1.40
325 326 0.744874 TCTCGCCTGGGACGATTAAG 59.255 55.000 0.00 0.00 39.12 1.85
391 392 3.601443 ACTAGCACTTGGAAGCTACTG 57.399 47.619 0.00 0.00 42.05 2.74
392 393 3.578716 TCAACTAGCACTTGGAAGCTACT 59.421 43.478 0.00 0.00 42.05 2.57
393 394 3.926616 TCAACTAGCACTTGGAAGCTAC 58.073 45.455 0.00 0.00 42.05 3.58
395 396 3.071602 TCTTCAACTAGCACTTGGAAGCT 59.928 43.478 0.00 0.00 44.55 3.74
438 439 0.689055 ACCACTCTGCTGCATCTTCA 59.311 50.000 1.31 0.00 0.00 3.02
466 467 6.013725 TCCAGTGGAAAGCTTTCTATCTTGTA 60.014 38.462 32.28 14.67 37.35 2.41
467 468 5.006386 CCAGTGGAAAGCTTTCTATCTTGT 58.994 41.667 32.28 12.16 37.35 3.16
468 469 5.248640 TCCAGTGGAAAGCTTTCTATCTTG 58.751 41.667 32.28 24.59 37.35 3.02
469 470 5.505181 TCCAGTGGAAAGCTTTCTATCTT 57.495 39.130 32.28 17.03 37.35 2.40
470 471 5.249420 GTTCCAGTGGAAAGCTTTCTATCT 58.751 41.667 32.28 23.47 43.86 1.98
551 556 9.874205 AGCTGTAATAGTAACAAAACGGTAATA 57.126 29.630 0.00 0.00 0.00 0.98
552 557 8.662141 CAGCTGTAATAGTAACAAAACGGTAAT 58.338 33.333 5.25 0.00 0.00 1.89
557 562 6.884187 ACACAGCTGTAATAGTAACAAAACG 58.116 36.000 21.20 3.49 0.00 3.60
569 574 6.072673 GGCTAACTTGTAAACACAGCTGTAAT 60.073 38.462 21.20 8.13 0.00 1.89
674 679 3.257127 ACTTGTACTGGCTCTCTTGTCTC 59.743 47.826 0.00 0.00 0.00 3.36
721 727 7.857734 TCCGTATTTTAATTTCTCTGCATGA 57.142 32.000 0.00 0.00 0.00 3.07
743 749 4.336280 GGCCAACTAATAGATCCCAATCC 58.664 47.826 0.00 0.00 31.78 3.01
848 858 3.771577 TTGTGTTTGTTTTGTTGGGGT 57.228 38.095 0.00 0.00 0.00 4.95
854 865 8.389779 AGGAAAATCTTTTGTGTTTGTTTTGT 57.610 26.923 0.00 0.00 0.00 2.83
900 923 0.107081 TTCAACGGGTTGGACGACAT 59.893 50.000 11.31 0.00 40.78 3.06
902 925 1.838568 GCTTCAACGGGTTGGACGAC 61.839 60.000 11.31 0.00 40.78 4.34
905 928 0.521735 GATGCTTCAACGGGTTGGAC 59.478 55.000 11.31 2.85 40.78 4.02
914 938 1.127582 GCTCGACAGTGATGCTTCAAC 59.872 52.381 3.51 0.00 32.48 3.18
969 1011 4.201589 CGAACGTTGATTCTCGCTAAATGT 60.202 41.667 5.00 0.00 0.00 2.71
970 1012 4.255999 CGAACGTTGATTCTCGCTAAATG 58.744 43.478 5.00 0.00 0.00 2.32
1206 1264 4.925054 CCATTGACAAAAACTGCAGGTATG 59.075 41.667 19.93 16.64 0.00 2.39
1659 1717 1.533625 TGGTTTGCTTGGATCCGAAG 58.466 50.000 7.39 12.59 0.00 3.79
1906 1972 8.686334 GGAAATAATATCCAGCACAAAAGAGAA 58.314 33.333 0.00 0.00 36.92 2.87
2017 2093 4.016113 AGTGACTTGAACAAAAGCGAAC 57.984 40.909 0.00 0.00 0.00 3.95
2075 2151 8.324567 GTGACTTGAATTCTCGATGAAGAATAC 58.675 37.037 7.05 0.79 43.53 1.89
2119 2199 3.566351 AGCTTTAACACTTGAGCCCTTT 58.434 40.909 0.00 0.00 35.79 3.11
2259 2340 3.244457 CCTCTATTCGGTTTATGGGGGAC 60.244 52.174 0.00 0.00 0.00 4.46
2345 2429 2.785258 CCGCTTTTACTCAGCCGC 59.215 61.111 0.00 0.00 33.29 6.53
2407 2491 2.125673 GCGTGGCGTGATAGTGGT 60.126 61.111 0.00 0.00 0.00 4.16
2421 2505 1.377594 TCATCAATGGCAGCAGCGT 60.378 52.632 0.00 0.00 43.41 5.07
2522 2621 1.120437 CTTTTCTTTGCCGCGAACAC 58.880 50.000 8.23 0.00 0.00 3.32
2523 2622 0.593773 GCTTTTCTTTGCCGCGAACA 60.594 50.000 8.23 1.70 0.00 3.18
2566 2666 1.423584 TGGAGACAGAGCTTGAACCA 58.576 50.000 0.00 0.00 35.01 3.67


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

AutoCloner maintained by Alex Coulton.