Multiple sequence alignment - TraesCS3D01G336700

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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 TraesCS3D01G336700 chr3D 100.000 3935 0 0 1 3935 448426918 448430852 0.000000e+00 7267
1 TraesCS3D01G336700 chr3D 97.196 107 3 0 3829 3935 326723698 326723592 8.690000e-42 182
2 TraesCS3D01G336700 chr3D 97.170 106 3 0 3830 3935 551006379 551006274 3.120000e-41 180
3 TraesCS3D01G336700 chr3B 96.204 2608 92 2 853 3454 588470808 588473414 0.000000e+00 4261
4 TraesCS3D01G336700 chr3B 90.584 1816 131 15 1541 3334 588420649 588422446 0.000000e+00 2370
5 TraesCS3D01G336700 chr3B 95.109 552 26 1 981 1532 588420122 588420672 0.000000e+00 869
6 TraesCS3D01G336700 chr3B 96.328 463 15 1 338 800 588413671 588414131 0.000000e+00 760
7 TraesCS3D01G336700 chr3B 93.473 383 22 3 3452 3833 588473539 588473919 2.050000e-157 566
8 TraesCS3D01G336700 chr3B 98.266 173 2 1 165 336 588412296 588412468 6.390000e-78 302
9 TraesCS3D01G336700 chr3B 96.552 145 5 0 165 309 588470174 588470318 1.410000e-59 241
10 TraesCS3D01G336700 chr3B 93.464 153 10 0 3330 3482 588439671 588439823 1.100000e-55 228
11 TraesCS3D01G336700 chr3A 96.011 2281 82 2 853 3124 589792263 589794543 0.000000e+00 3699
12 TraesCS3D01G336700 chr3A 90.833 840 77 0 869 1708 589606161 589607000 0.000000e+00 1125
13 TraesCS3D01G336700 chr3A 91.956 634 50 1 1703 2336 589613372 589614004 0.000000e+00 887
14 TraesCS3D01G336700 chr3A 90.433 669 31 11 3169 3833 589794552 589795191 0.000000e+00 850
15 TraesCS3D01G336700 chr3A 98.769 325 4 0 336 660 589601650 589601974 2.640000e-161 579
16 TraesCS3D01G336700 chr3A 97.688 173 2 2 165 336 589791036 589791207 2.970000e-76 296
17 TraesCS3D01G336700 chr3A 96.599 147 4 1 165 311 589601424 589601569 3.930000e-60 243
18 TraesCS3D01G336700 chr3A 88.000 175 19 1 1 175 715797468 715797296 5.150000e-49 206
19 TraesCS3D01G336700 chr2B 81.450 1876 319 13 1075 2941 695889208 695891063 0.000000e+00 1509
20 TraesCS3D01G336700 chr2A 80.889 1889 323 23 1069 2941 716499572 716501438 0.000000e+00 1454
21 TraesCS3D01G336700 chr2A 97.196 107 3 0 3829 3935 57865498 57865392 8.690000e-42 182
22 TraesCS3D01G336700 chr2D 80.170 1881 338 23 1069 2941 578963134 578964987 0.000000e+00 1375
23 TraesCS3D01G336700 chr2D 98.113 106 2 0 3830 3935 45680998 45681103 6.710000e-43 185
24 TraesCS3D01G336700 chr2D 95.536 112 5 0 3824 3935 627971625 627971514 3.120000e-41 180
25 TraesCS3D01G336700 chr5D 91.975 162 12 1 1 162 436796635 436796475 3.960000e-55 226
26 TraesCS3D01G336700 chr6D 98.131 107 2 0 3829 3935 289718982 289718876 1.870000e-43 187
27 TraesCS3D01G336700 chr5B 96.396 111 4 0 3825 3935 441671896 441672006 2.420000e-42 183
28 TraesCS3D01G336700 chr5B 94.783 115 6 0 3821 3935 697184926 697185040 3.120000e-41 180
29 TraesCS3D01G336700 chr7D 95.495 111 5 0 3825 3935 227507232 227507122 1.120000e-40 178


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 TraesCS3D01G336700 chr3D 448426918 448430852 3934 False 7267.000000 7267 100.000000 1 3935 1 chr3D.!!$F1 3934
1 TraesCS3D01G336700 chr3B 588470174 588473919 3745 False 1689.333333 4261 95.409667 165 3833 3 chr3B.!!$F4 3668
2 TraesCS3D01G336700 chr3B 588420122 588422446 2324 False 1619.500000 2370 92.846500 981 3334 2 chr3B.!!$F3 2353
3 TraesCS3D01G336700 chr3B 588412296 588414131 1835 False 531.000000 760 97.297000 165 800 2 chr3B.!!$F2 635
4 TraesCS3D01G336700 chr3A 589791036 589795191 4155 False 1615.000000 3699 94.710667 165 3833 3 chr3A.!!$F4 3668
5 TraesCS3D01G336700 chr3A 589606161 589607000 839 False 1125.000000 1125 90.833000 869 1708 1 chr3A.!!$F1 839
6 TraesCS3D01G336700 chr3A 589613372 589614004 632 False 887.000000 887 91.956000 1703 2336 1 chr3A.!!$F2 633
7 TraesCS3D01G336700 chr3A 589601424 589601974 550 False 411.000000 579 97.684000 165 660 2 chr3A.!!$F3 495
8 TraesCS3D01G336700 chr2B 695889208 695891063 1855 False 1509.000000 1509 81.450000 1075 2941 1 chr2B.!!$F1 1866
9 TraesCS3D01G336700 chr2A 716499572 716501438 1866 False 1454.000000 1454 80.889000 1069 2941 1 chr2A.!!$F1 1872
10 TraesCS3D01G336700 chr2D 578963134 578964987 1853 False 1375.000000 1375 80.170000 1069 2941 1 chr2D.!!$F2 1872

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
135 136 0.032952 AGGTGCGCTCTAAACAACGA 59.967 50.0 9.73 0.0 0.0 3.85 F
1252 2970 0.103208 CCAGATACAGGCACTCGGTC 59.897 60.0 0.00 0.0 34.6 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 3467 1.153349 GAGATCAAGGGCGTCCACC 60.153 63.158 9.71 0.0 34.83 4.61 R
2988 4737 0.107456 CCTGTTCCAGTGCAGTGAGT 59.893 55.000 23.34 0.0 0.00 3.41 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
18 19 1.749033 GGGGACAAGATCTAGGCCG 59.251 63.158 0.00 0.00 0.00 6.13
19 20 0.759436 GGGGACAAGATCTAGGCCGA 60.759 60.000 0.00 0.00 0.00 5.54
20 21 1.343069 GGGACAAGATCTAGGCCGAT 58.657 55.000 0.00 0.00 0.00 4.18
21 22 1.694696 GGGACAAGATCTAGGCCGATT 59.305 52.381 0.00 0.00 0.00 3.34
22 23 2.289133 GGGACAAGATCTAGGCCGATTC 60.289 54.545 0.00 0.00 0.00 2.52
23 24 2.630580 GGACAAGATCTAGGCCGATTCT 59.369 50.000 0.00 0.00 0.00 2.40
24 25 3.827302 GGACAAGATCTAGGCCGATTCTA 59.173 47.826 0.00 0.00 0.00 2.10
25 26 4.082463 GGACAAGATCTAGGCCGATTCTAG 60.082 50.000 0.00 0.00 36.46 2.43
26 27 3.257127 ACAAGATCTAGGCCGATTCTAGC 59.743 47.826 0.00 0.00 35.43 3.42
27 28 3.162147 AGATCTAGGCCGATTCTAGCA 57.838 47.619 0.00 0.00 35.43 3.49
28 29 3.088532 AGATCTAGGCCGATTCTAGCAG 58.911 50.000 0.00 0.00 35.43 4.24
29 30 2.366640 TCTAGGCCGATTCTAGCAGT 57.633 50.000 0.00 0.00 35.43 4.40
30 31 3.503800 TCTAGGCCGATTCTAGCAGTA 57.496 47.619 0.00 0.00 35.43 2.74
31 32 4.035612 TCTAGGCCGATTCTAGCAGTAT 57.964 45.455 0.00 0.00 35.43 2.12
32 33 4.011023 TCTAGGCCGATTCTAGCAGTATC 58.989 47.826 0.00 0.00 35.43 2.24
33 34 1.896465 AGGCCGATTCTAGCAGTATCC 59.104 52.381 0.00 0.00 0.00 2.59
34 35 1.618837 GGCCGATTCTAGCAGTATCCA 59.381 52.381 0.00 0.00 0.00 3.41
35 36 2.234908 GGCCGATTCTAGCAGTATCCAT 59.765 50.000 0.00 0.00 0.00 3.41
36 37 3.257393 GCCGATTCTAGCAGTATCCATG 58.743 50.000 0.00 0.00 0.00 3.66
37 38 3.306364 GCCGATTCTAGCAGTATCCATGT 60.306 47.826 0.00 0.00 0.00 3.21
38 39 4.240888 CCGATTCTAGCAGTATCCATGTG 58.759 47.826 0.00 0.00 0.00 3.21
39 40 3.677121 CGATTCTAGCAGTATCCATGTGC 59.323 47.826 0.00 0.00 37.48 4.57
40 41 2.800881 TCTAGCAGTATCCATGTGCG 57.199 50.000 0.15 0.00 42.26 5.34
41 42 1.143305 CTAGCAGTATCCATGTGCGC 58.857 55.000 0.00 0.00 42.26 6.09
42 43 0.249868 TAGCAGTATCCATGTGCGCC 60.250 55.000 4.18 0.00 42.26 6.53
43 44 1.819208 GCAGTATCCATGTGCGCCA 60.819 57.895 4.18 2.31 0.00 5.69
44 45 2.016961 CAGTATCCATGTGCGCCAC 58.983 57.895 4.18 3.72 34.56 5.01
45 46 1.521457 AGTATCCATGTGCGCCACG 60.521 57.895 4.18 0.00 37.14 4.94
46 47 2.203001 TATCCATGTGCGCCACGG 60.203 61.111 4.18 4.59 37.14 4.94
47 48 3.748660 TATCCATGTGCGCCACGGG 62.749 63.158 4.18 9.26 37.14 5.28
50 51 3.879682 CATGTGCGCCACGGGATG 61.880 66.667 4.18 0.02 37.14 3.51
51 52 4.408821 ATGTGCGCCACGGGATGT 62.409 61.111 4.18 0.00 37.14 3.06
59 60 3.813596 CACGGGATGTGGCTAAGC 58.186 61.111 0.00 0.00 45.21 3.09
60 61 1.078497 CACGGGATGTGGCTAAGCA 60.078 57.895 0.00 0.00 45.21 3.91
61 62 0.676466 CACGGGATGTGGCTAAGCAA 60.676 55.000 0.00 0.00 45.21 3.91
62 63 0.255890 ACGGGATGTGGCTAAGCAAT 59.744 50.000 0.00 0.00 0.00 3.56
63 64 1.340991 ACGGGATGTGGCTAAGCAATT 60.341 47.619 0.00 0.00 0.00 2.32
64 65 1.750778 CGGGATGTGGCTAAGCAATTT 59.249 47.619 0.00 0.00 0.00 1.82
65 66 2.223572 CGGGATGTGGCTAAGCAATTTC 60.224 50.000 0.00 0.00 0.00 2.17
66 67 2.101415 GGGATGTGGCTAAGCAATTTCC 59.899 50.000 0.00 0.00 0.00 3.13
67 68 3.026694 GGATGTGGCTAAGCAATTTCCT 58.973 45.455 0.00 0.00 0.00 3.36
68 69 3.448660 GGATGTGGCTAAGCAATTTCCTT 59.551 43.478 0.00 0.00 0.00 3.36
69 70 4.081476 GGATGTGGCTAAGCAATTTCCTTT 60.081 41.667 0.00 0.00 0.00 3.11
70 71 4.953940 TGTGGCTAAGCAATTTCCTTTT 57.046 36.364 0.00 0.00 0.00 2.27
71 72 6.350949 GGATGTGGCTAAGCAATTTCCTTTTA 60.351 38.462 0.00 0.00 0.00 1.52
72 73 6.603940 TGTGGCTAAGCAATTTCCTTTTAT 57.396 33.333 0.00 0.00 0.00 1.40
73 74 7.710676 TGTGGCTAAGCAATTTCCTTTTATA 57.289 32.000 0.00 0.00 0.00 0.98
74 75 7.771183 TGTGGCTAAGCAATTTCCTTTTATAG 58.229 34.615 0.00 0.00 0.00 1.31
75 76 7.396055 TGTGGCTAAGCAATTTCCTTTTATAGT 59.604 33.333 0.00 0.00 0.00 2.12
76 77 7.915923 GTGGCTAAGCAATTTCCTTTTATAGTC 59.084 37.037 0.00 0.00 0.00 2.59
77 78 7.834181 TGGCTAAGCAATTTCCTTTTATAGTCT 59.166 33.333 0.00 0.00 0.00 3.24
78 79 9.338622 GGCTAAGCAATTTCCTTTTATAGTCTA 57.661 33.333 0.00 0.00 0.00 2.59
81 82 8.807948 AAGCAATTTCCTTTTATAGTCTAGCA 57.192 30.769 0.00 0.00 0.00 3.49
82 83 8.443953 AGCAATTTCCTTTTATAGTCTAGCAG 57.556 34.615 0.00 0.00 0.00 4.24
83 84 7.012799 AGCAATTTCCTTTTATAGTCTAGCAGC 59.987 37.037 0.00 0.00 0.00 5.25
84 85 7.012799 GCAATTTCCTTTTATAGTCTAGCAGCT 59.987 37.037 0.00 0.00 0.00 4.24
85 86 8.341173 CAATTTCCTTTTATAGTCTAGCAGCTG 58.659 37.037 10.11 10.11 0.00 4.24
86 87 5.537300 TCCTTTTATAGTCTAGCAGCTGG 57.463 43.478 17.12 1.04 0.00 4.85
87 88 5.208890 TCCTTTTATAGTCTAGCAGCTGGA 58.791 41.667 17.12 3.93 0.00 3.86
88 89 5.069251 TCCTTTTATAGTCTAGCAGCTGGAC 59.931 44.000 27.23 27.23 41.33 4.02
89 90 5.163405 CCTTTTATAGTCTAGCAGCTGGACA 60.163 44.000 33.32 22.07 43.03 4.02
90 91 4.920640 TTATAGTCTAGCAGCTGGACAC 57.079 45.455 33.32 14.35 43.03 3.67
91 92 2.215942 TAGTCTAGCAGCTGGACACA 57.784 50.000 33.32 21.15 43.03 3.72
92 93 1.342074 AGTCTAGCAGCTGGACACAA 58.658 50.000 33.32 0.82 43.03 3.33
93 94 1.274728 AGTCTAGCAGCTGGACACAAG 59.725 52.381 33.32 10.37 43.03 3.16
94 95 0.610174 TCTAGCAGCTGGACACAAGG 59.390 55.000 17.12 0.00 0.00 3.61
95 96 0.610174 CTAGCAGCTGGACACAAGGA 59.390 55.000 17.12 0.00 0.00 3.36
96 97 0.321671 TAGCAGCTGGACACAAGGAC 59.678 55.000 17.12 0.00 0.00 3.85
97 98 1.227943 GCAGCTGGACACAAGGACA 60.228 57.895 17.12 0.00 0.00 4.02
98 99 1.510480 GCAGCTGGACACAAGGACAC 61.510 60.000 17.12 0.00 0.00 3.67
99 100 0.179048 CAGCTGGACACAAGGACACA 60.179 55.000 5.57 0.00 0.00 3.72
100 101 0.767375 AGCTGGACACAAGGACACAT 59.233 50.000 0.00 0.00 0.00 3.21
101 102 1.977854 AGCTGGACACAAGGACACATA 59.022 47.619 0.00 0.00 0.00 2.29
102 103 2.076863 GCTGGACACAAGGACACATAC 58.923 52.381 0.00 0.00 0.00 2.39
103 104 2.699954 CTGGACACAAGGACACATACC 58.300 52.381 0.00 0.00 0.00 2.73
104 105 2.303022 CTGGACACAAGGACACATACCT 59.697 50.000 0.00 0.00 39.69 3.08
105 106 3.512496 TGGACACAAGGACACATACCTA 58.488 45.455 0.00 0.00 36.67 3.08
106 107 3.259876 TGGACACAAGGACACATACCTAC 59.740 47.826 0.00 0.00 36.67 3.18
107 108 3.514309 GGACACAAGGACACATACCTACT 59.486 47.826 0.00 0.00 36.67 2.57
108 109 4.708421 GGACACAAGGACACATACCTACTA 59.292 45.833 0.00 0.00 36.67 1.82
109 110 5.363005 GGACACAAGGACACATACCTACTAT 59.637 44.000 0.00 0.00 36.67 2.12
110 111 6.548622 GGACACAAGGACACATACCTACTATA 59.451 42.308 0.00 0.00 36.67 1.31
111 112 7.232941 GGACACAAGGACACATACCTACTATAT 59.767 40.741 0.00 0.00 36.67 0.86
112 113 9.293404 GACACAAGGACACATACCTACTATATA 57.707 37.037 0.00 0.00 36.67 0.86
113 114 9.824216 ACACAAGGACACATACCTACTATATAT 57.176 33.333 0.00 0.00 36.67 0.86
118 119 9.702253 AGGACACATACCTACTATATATGAAGG 57.298 37.037 0.00 2.26 35.84 3.46
119 120 9.476928 GGACACATACCTACTATATATGAAGGT 57.523 37.037 15.64 15.64 43.00 3.50
121 122 8.750298 ACACATACCTACTATATATGAAGGTGC 58.250 37.037 18.63 0.00 40.71 5.01
122 123 7.915923 CACATACCTACTATATATGAAGGTGCG 59.084 40.741 18.63 13.73 40.71 5.34
123 124 5.326200 ACCTACTATATATGAAGGTGCGC 57.674 43.478 0.00 0.00 39.10 6.09
124 125 5.017490 ACCTACTATATATGAAGGTGCGCT 58.983 41.667 9.73 0.00 39.10 5.92
125 126 5.125739 ACCTACTATATATGAAGGTGCGCTC 59.874 44.000 9.73 4.47 39.10 5.03
126 127 5.358442 CCTACTATATATGAAGGTGCGCTCT 59.642 44.000 9.73 3.07 0.00 4.09
127 128 6.542735 CCTACTATATATGAAGGTGCGCTCTA 59.457 42.308 9.73 0.00 0.00 2.43
128 129 6.835819 ACTATATATGAAGGTGCGCTCTAA 57.164 37.500 9.73 0.00 0.00 2.10
129 130 7.228314 ACTATATATGAAGGTGCGCTCTAAA 57.772 36.000 9.73 0.00 0.00 1.85
130 131 7.091443 ACTATATATGAAGGTGCGCTCTAAAC 58.909 38.462 9.73 0.00 0.00 2.01
131 132 2.472695 ATGAAGGTGCGCTCTAAACA 57.527 45.000 9.73 8.28 0.00 2.83
132 133 2.248280 TGAAGGTGCGCTCTAAACAA 57.752 45.000 9.73 0.00 0.00 2.83
133 134 1.871039 TGAAGGTGCGCTCTAAACAAC 59.129 47.619 9.73 0.00 0.00 3.32
134 135 0.865769 AAGGTGCGCTCTAAACAACG 59.134 50.000 9.73 0.00 0.00 4.10
135 136 0.032952 AGGTGCGCTCTAAACAACGA 59.967 50.000 9.73 0.00 0.00 3.85
136 137 0.863144 GGTGCGCTCTAAACAACGAA 59.137 50.000 9.73 0.00 0.00 3.85
137 138 1.398071 GGTGCGCTCTAAACAACGAAC 60.398 52.381 9.73 0.00 33.20 3.95
138 139 0.505231 TGCGCTCTAAACAACGAACG 59.495 50.000 9.73 0.00 0.00 3.95
139 140 0.780002 GCGCTCTAAACAACGAACGA 59.220 50.000 0.00 0.00 0.00 3.85
140 141 1.201672 GCGCTCTAAACAACGAACGAG 60.202 52.381 0.00 0.00 0.00 4.18
141 142 1.201672 CGCTCTAAACAACGAACGAGC 60.202 52.381 0.14 0.00 40.19 5.03
142 143 1.201672 GCTCTAAACAACGAACGAGCG 60.202 52.381 0.14 0.00 35.21 5.03
144 145 3.228749 CTCTAAACAACGAACGAGCGTA 58.771 45.455 7.64 0.00 44.86 4.42
145 146 3.228749 TCTAAACAACGAACGAGCGTAG 58.771 45.455 7.64 0.00 44.86 3.51
158 159 4.310672 CGTAGCTGCGCTTCCTAG 57.689 61.111 12.24 0.00 40.44 3.02
159 160 1.946650 CGTAGCTGCGCTTCCTAGC 60.947 63.158 12.24 9.03 44.21 3.42
160 161 1.592939 GTAGCTGCGCTTCCTAGCC 60.593 63.158 9.73 0.00 44.86 3.93
161 162 2.058001 TAGCTGCGCTTCCTAGCCA 61.058 57.895 9.73 0.00 44.86 4.75
162 163 1.402896 TAGCTGCGCTTCCTAGCCAT 61.403 55.000 9.73 0.00 44.86 4.40
163 164 2.541120 GCTGCGCTTCCTAGCCATG 61.541 63.158 9.73 0.00 44.86 3.66
164 165 1.153289 CTGCGCTTCCTAGCCATGT 60.153 57.895 9.73 0.00 44.86 3.21
165 166 1.153369 TGCGCTTCCTAGCCATGTC 60.153 57.895 9.73 0.00 44.86 3.06
166 167 1.889573 GCGCTTCCTAGCCATGTCC 60.890 63.158 0.00 0.00 44.86 4.02
354 1558 1.079543 ACGAGCAGCTTTGCGATCT 60.080 52.632 8.86 0.00 40.27 2.75
447 1651 3.196469 CACCAGTGAGCTTCCTTATCTCA 59.804 47.826 0.00 0.00 34.78 3.27
462 1795 0.107993 TCTCATCTTGGAGCTTGGCG 60.108 55.000 0.00 0.00 34.84 5.69
762 2154 7.259290 TGATCTGAAACCAGAAACAAAGTAC 57.741 36.000 0.00 0.00 43.22 2.73
843 2510 2.203070 GAACCGCTCGGATGCCAT 60.203 61.111 15.95 0.00 38.96 4.40
845 2512 0.320771 GAACCGCTCGGATGCCATAT 60.321 55.000 15.95 0.00 38.96 1.78
847 2514 1.742880 CCGCTCGGATGCCATATGG 60.743 63.158 18.07 18.07 37.50 2.74
848 2515 1.004560 CGCTCGGATGCCATATGGT 60.005 57.895 22.79 3.89 37.57 3.55
850 2517 0.674895 GCTCGGATGCCATATGGTCC 60.675 60.000 22.79 20.01 37.57 4.46
875 2585 2.349755 GCGACCTGGGCCTTGTTA 59.650 61.111 4.53 0.00 0.00 2.41
937 2647 1.226030 GCACCGTTTCGCAACTAGGT 61.226 55.000 0.00 0.00 29.24 3.08
968 2678 5.237236 TCTCGTCCCCTCAAAATTTACTT 57.763 39.130 0.00 0.00 0.00 2.24
1008 2726 1.340017 TGCTGGCTAAAGATGACCACC 60.340 52.381 0.00 0.00 0.00 4.61
1020 2738 2.526873 ACCACCGAGCCTTCCACT 60.527 61.111 0.00 0.00 0.00 4.00
1027 2745 3.296709 GAGCCTTCCACTTCCGCGA 62.297 63.158 8.23 0.00 0.00 5.87
1036 2754 4.831307 CTTCCGCGACGACCTCCG 62.831 72.222 8.23 0.00 45.44 4.63
1145 2863 4.286320 CCTAGCCCTGCTACGCGG 62.286 72.222 12.47 0.00 40.44 6.46
1252 2970 0.103208 CCAGATACAGGCACTCGGTC 59.897 60.000 0.00 0.00 34.60 4.79
1253 2971 0.817654 CAGATACAGGCACTCGGTCA 59.182 55.000 0.00 0.00 34.60 4.02
1536 3266 3.160047 CTCCCTGCCGCTCCTCAT 61.160 66.667 0.00 0.00 0.00 2.90
1540 3270 2.030262 CTGCCGCTCCTCATAGCC 59.970 66.667 0.00 0.00 39.43 3.93
2457 4187 2.534349 GGCGAACATATACACAGACACG 59.466 50.000 0.00 0.00 0.00 4.49
2852 4600 0.250901 AAGGCGGTCTCTGCAATTGT 60.251 50.000 7.40 0.00 0.00 2.71
2988 4737 4.956700 AGATTTCACTCCGGATCTTCAGTA 59.043 41.667 3.57 0.00 0.00 2.74
3294 5064 0.527113 TGGAAATGCAATGCTCCACG 59.473 50.000 10.18 0.00 35.01 4.94
3314 5084 0.108138 CACGCCCTTGGACCTTCTAG 60.108 60.000 0.00 0.00 0.00 2.43
3322 5092 2.552093 TGGACCTTCTAGGGAGGAAG 57.448 55.000 16.90 1.62 40.58 3.46
3397 5167 1.070134 GTGGTTCAGAGTACACCAGCA 59.930 52.381 2.38 0.00 41.37 4.41
3415 5185 1.814394 GCAATGGTCAGCATGTTCTGA 59.186 47.619 0.00 0.00 40.50 3.27
3429 5199 0.810648 TTCTGAATCGTTGGCATGGC 59.189 50.000 13.29 13.29 0.00 4.40
3507 5405 0.323725 GCTGATGGAAGGGCAAAGGA 60.324 55.000 0.00 0.00 0.00 3.36
3539 5437 1.857217 CGTGATGCTGAGCTGTATGTC 59.143 52.381 5.83 0.00 0.00 3.06
3544 5442 0.942962 GCTGAGCTGTATGTCCATGC 59.057 55.000 0.00 0.00 0.00 4.06
3545 5443 1.744798 GCTGAGCTGTATGTCCATGCA 60.745 52.381 0.00 0.00 32.58 3.96
3707 5605 3.713248 AGGATATCAAGATCAGGCACACA 59.287 43.478 4.83 0.00 0.00 3.72
3718 5616 0.178981 AGGCACACAAGGAATGCAGT 60.179 50.000 0.00 0.00 41.27 4.40
3729 5627 1.639298 GAATGCAGTGGCGTCAGGTC 61.639 60.000 0.00 0.00 45.35 3.85
3833 5732 1.135373 TGCGCTTACTGACAGCTACTC 60.135 52.381 9.73 0.00 34.88 2.59
3834 5733 1.799548 GCGCTTACTGACAGCTACTCC 60.800 57.143 0.00 0.00 34.88 3.85
3835 5734 1.202313 CGCTTACTGACAGCTACTCCC 60.202 57.143 1.25 0.00 34.88 4.30
3836 5735 2.104170 GCTTACTGACAGCTACTCCCT 58.896 52.381 1.25 0.00 34.15 4.20
3837 5736 2.100087 GCTTACTGACAGCTACTCCCTC 59.900 54.545 1.25 0.00 34.15 4.30
3838 5737 2.438800 TACTGACAGCTACTCCCTCC 57.561 55.000 1.25 0.00 0.00 4.30
3839 5738 0.681564 ACTGACAGCTACTCCCTCCG 60.682 60.000 1.25 0.00 0.00 4.63
3840 5739 0.681564 CTGACAGCTACTCCCTCCGT 60.682 60.000 0.00 0.00 0.00 4.69
3841 5740 0.251653 TGACAGCTACTCCCTCCGTT 60.252 55.000 0.00 0.00 0.00 4.44
3842 5741 0.456628 GACAGCTACTCCCTCCGTTC 59.543 60.000 0.00 0.00 0.00 3.95
3843 5742 1.313812 ACAGCTACTCCCTCCGTTCG 61.314 60.000 0.00 0.00 0.00 3.95
3844 5743 1.753463 AGCTACTCCCTCCGTTCGG 60.753 63.158 4.74 4.74 0.00 4.30
3845 5744 1.751927 GCTACTCCCTCCGTTCGGA 60.752 63.158 13.34 13.34 0.00 4.55
3846 5745 1.318158 GCTACTCCCTCCGTTCGGAA 61.318 60.000 14.79 0.04 33.41 4.30
3847 5746 1.400737 CTACTCCCTCCGTTCGGAAT 58.599 55.000 14.79 2.09 33.41 3.01
3848 5747 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
3849 5748 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3850 5749 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3851 5750 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3852 5751 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3853 5752 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3854 5753 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3855 5754 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3856 5755 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
3857 5756 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
3858 5757 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
3859 5758 2.222508 CGTTCGGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
3860 5759 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
3861 5760 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
3862 5761 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
3863 5762 4.250464 TCGGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
3864 5763 4.092821 TCGGAATTACTTGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
3865 5764 4.662145 GGAATTACTTGTCGCAGAAATGG 58.338 43.478 0.00 0.00 39.69 3.16
3866 5765 4.394920 GGAATTACTTGTCGCAGAAATGGA 59.605 41.667 0.00 0.00 39.69 3.41
3867 5766 5.066505 GGAATTACTTGTCGCAGAAATGGAT 59.933 40.000 0.00 0.00 39.69 3.41
3868 5767 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
3869 5768 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
3870 5769 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
3871 5770 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
3872 5771 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
3873 5772 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
3874 5773 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
3875 5774 5.289595 TGTCGCAGAAATGGATGTATCTAC 58.710 41.667 0.00 0.00 39.69 2.59
3876 5775 5.163457 TGTCGCAGAAATGGATGTATCTACA 60.163 40.000 0.00 0.00 39.69 2.74
3877 5776 5.175856 GTCGCAGAAATGGATGTATCTACAC 59.824 44.000 0.00 0.00 39.69 2.90
3878 5777 4.148871 CGCAGAAATGGATGTATCTACACG 59.851 45.833 0.00 0.00 39.30 4.49
3879 5778 5.050490 GCAGAAATGGATGTATCTACACGT 58.950 41.667 0.00 0.00 39.30 4.49
3880 5779 6.213677 GCAGAAATGGATGTATCTACACGTA 58.786 40.000 0.00 0.00 39.30 3.57
3881 5780 6.868864 GCAGAAATGGATGTATCTACACGTAT 59.131 38.462 0.00 0.00 39.30 3.06
3882 5781 7.385205 GCAGAAATGGATGTATCTACACGTATT 59.615 37.037 0.00 0.00 39.30 1.89
3883 5782 9.261180 CAGAAATGGATGTATCTACACGTATTT 57.739 33.333 0.00 1.02 39.30 1.40
3884 5783 9.832445 AGAAATGGATGTATCTACACGTATTTT 57.168 29.630 0.00 0.00 39.30 1.82
3889 5788 9.740239 TGGATGTATCTACACGTATTTTAGTTC 57.260 33.333 0.00 0.00 39.30 3.01
3890 5789 9.962783 GGATGTATCTACACGTATTTTAGTTCT 57.037 33.333 0.00 0.00 39.30 3.01
3922 5821 6.494893 TCATTTCCAAGACAAGTAATTCCG 57.505 37.500 0.00 0.00 0.00 4.30
3923 5822 6.234920 TCATTTCCAAGACAAGTAATTCCGA 58.765 36.000 0.00 0.00 0.00 4.55
3924 5823 6.712998 TCATTTCCAAGACAAGTAATTCCGAA 59.287 34.615 0.00 0.00 0.00 4.30
3925 5824 5.934935 TTCCAAGACAAGTAATTCCGAAC 57.065 39.130 0.00 0.00 0.00 3.95
3926 5825 3.991773 TCCAAGACAAGTAATTCCGAACG 59.008 43.478 0.00 0.00 0.00 3.95
3927 5826 3.124636 CCAAGACAAGTAATTCCGAACGG 59.875 47.826 6.94 6.94 0.00 4.44
3928 5827 3.947910 AGACAAGTAATTCCGAACGGA 57.052 42.857 12.04 12.04 43.52 4.69
3929 5828 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
3930 5829 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3931 5830 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3932 5831 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3933 5832 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
3934 5833 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.759436 TCGGCCTAGATCTTGTCCCC 60.759 60.000 0.00 0.00 0.00 4.81
1 2 1.343069 ATCGGCCTAGATCTTGTCCC 58.657 55.000 0.00 0.78 0.00 4.46
2 3 2.630580 AGAATCGGCCTAGATCTTGTCC 59.369 50.000 0.00 0.00 0.00 4.02
3 4 4.617298 GCTAGAATCGGCCTAGATCTTGTC 60.617 50.000 0.00 0.00 36.58 3.18
4 5 3.257127 GCTAGAATCGGCCTAGATCTTGT 59.743 47.826 0.00 0.00 36.58 3.16
6 7 3.501349 TGCTAGAATCGGCCTAGATCTT 58.499 45.455 0.00 0.00 36.58 2.40
7 8 3.088532 CTGCTAGAATCGGCCTAGATCT 58.911 50.000 0.00 0.00 36.58 2.75
8 9 2.823154 ACTGCTAGAATCGGCCTAGATC 59.177 50.000 0.00 0.00 36.58 2.75
9 10 2.883026 ACTGCTAGAATCGGCCTAGAT 58.117 47.619 0.00 0.00 36.58 1.98
10 11 2.366640 ACTGCTAGAATCGGCCTAGA 57.633 50.000 0.00 0.00 36.58 2.43
11 12 3.129638 GGATACTGCTAGAATCGGCCTAG 59.870 52.174 0.00 0.00 37.31 3.02
12 13 3.090037 GGATACTGCTAGAATCGGCCTA 58.910 50.000 0.00 0.00 0.00 3.93
13 14 1.896465 GGATACTGCTAGAATCGGCCT 59.104 52.381 0.00 0.00 0.00 5.19
14 15 1.618837 TGGATACTGCTAGAATCGGCC 59.381 52.381 0.00 0.00 37.61 6.13
15 16 3.257393 CATGGATACTGCTAGAATCGGC 58.743 50.000 0.00 0.00 37.61 5.54
16 17 4.240888 CACATGGATACTGCTAGAATCGG 58.759 47.826 0.00 0.00 37.61 4.18
17 18 3.677121 GCACATGGATACTGCTAGAATCG 59.323 47.826 0.00 0.00 37.61 3.34
18 19 3.677121 CGCACATGGATACTGCTAGAATC 59.323 47.826 0.00 0.00 37.61 2.52
19 20 3.657634 CGCACATGGATACTGCTAGAAT 58.342 45.455 0.00 0.00 37.61 2.40
20 21 2.803133 GCGCACATGGATACTGCTAGAA 60.803 50.000 0.30 0.00 37.61 2.10
21 22 1.269778 GCGCACATGGATACTGCTAGA 60.270 52.381 0.30 0.00 37.61 2.43
22 23 1.143305 GCGCACATGGATACTGCTAG 58.857 55.000 0.30 0.00 37.61 3.42
23 24 0.249868 GGCGCACATGGATACTGCTA 60.250 55.000 10.83 0.00 37.61 3.49
24 25 1.524621 GGCGCACATGGATACTGCT 60.525 57.895 10.83 0.00 37.61 4.24
25 26 1.819208 TGGCGCACATGGATACTGC 60.819 57.895 10.83 0.00 37.61 4.40
26 27 1.765161 CGTGGCGCACATGGATACTG 61.765 60.000 10.83 0.00 33.40 2.74
27 28 1.521457 CGTGGCGCACATGGATACT 60.521 57.895 10.83 0.00 33.40 2.12
28 29 3.014036 CGTGGCGCACATGGATAC 58.986 61.111 10.83 0.00 33.40 2.24
33 34 3.879682 CATCCCGTGGCGCACATG 61.880 66.667 10.83 10.40 33.40 3.21
34 35 4.408821 ACATCCCGTGGCGCACAT 62.409 61.111 10.83 0.00 33.40 3.21
42 43 0.676466 TTGCTTAGCCACATCCCGTG 60.676 55.000 0.29 0.00 45.92 4.94
43 44 0.255890 ATTGCTTAGCCACATCCCGT 59.744 50.000 0.29 0.00 0.00 5.28
44 45 1.392589 AATTGCTTAGCCACATCCCG 58.607 50.000 0.29 0.00 0.00 5.14
45 46 2.101415 GGAAATTGCTTAGCCACATCCC 59.899 50.000 0.29 0.00 0.00 3.85
46 47 3.026694 AGGAAATTGCTTAGCCACATCC 58.973 45.455 0.29 4.99 0.00 3.51
47 48 4.725790 AAGGAAATTGCTTAGCCACATC 57.274 40.909 0.29 0.00 0.00 3.06
48 49 5.488262 AAAAGGAAATTGCTTAGCCACAT 57.512 34.783 0.29 0.00 0.00 3.21
49 50 4.953940 AAAAGGAAATTGCTTAGCCACA 57.046 36.364 0.29 0.00 0.00 4.17
50 51 7.772166 ACTATAAAAGGAAATTGCTTAGCCAC 58.228 34.615 0.29 0.00 0.00 5.01
51 52 7.834181 AGACTATAAAAGGAAATTGCTTAGCCA 59.166 33.333 0.29 0.00 0.00 4.75
52 53 8.226819 AGACTATAAAAGGAAATTGCTTAGCC 57.773 34.615 0.29 0.00 0.00 3.93
55 56 9.899661 TGCTAGACTATAAAAGGAAATTGCTTA 57.100 29.630 0.00 0.00 0.00 3.09
56 57 8.807948 TGCTAGACTATAAAAGGAAATTGCTT 57.192 30.769 0.00 0.00 0.00 3.91
57 58 7.012799 GCTGCTAGACTATAAAAGGAAATTGCT 59.987 37.037 0.00 0.00 0.00 3.91
58 59 7.012799 AGCTGCTAGACTATAAAAGGAAATTGC 59.987 37.037 0.00 0.00 0.00 3.56
59 60 8.341173 CAGCTGCTAGACTATAAAAGGAAATTG 58.659 37.037 0.00 0.00 0.00 2.32
60 61 7.500559 CCAGCTGCTAGACTATAAAAGGAAATT 59.499 37.037 8.66 0.00 0.00 1.82
61 62 6.995091 CCAGCTGCTAGACTATAAAAGGAAAT 59.005 38.462 8.66 0.00 0.00 2.17
62 63 6.156256 TCCAGCTGCTAGACTATAAAAGGAAA 59.844 38.462 8.66 0.00 0.00 3.13
63 64 5.661312 TCCAGCTGCTAGACTATAAAAGGAA 59.339 40.000 8.66 0.00 0.00 3.36
64 65 5.069251 GTCCAGCTGCTAGACTATAAAAGGA 59.931 44.000 18.90 6.88 0.00 3.36
65 66 5.163405 TGTCCAGCTGCTAGACTATAAAAGG 60.163 44.000 24.63 8.53 0.00 3.11
66 67 5.751028 GTGTCCAGCTGCTAGACTATAAAAG 59.249 44.000 24.63 0.00 0.00 2.27
67 68 5.186992 TGTGTCCAGCTGCTAGACTATAAAA 59.813 40.000 24.63 4.94 0.00 1.52
68 69 4.709886 TGTGTCCAGCTGCTAGACTATAAA 59.290 41.667 24.63 5.60 0.00 1.40
69 70 4.278310 TGTGTCCAGCTGCTAGACTATAA 58.722 43.478 24.63 5.94 0.00 0.98
70 71 3.898482 TGTGTCCAGCTGCTAGACTATA 58.102 45.455 24.63 11.22 0.00 1.31
71 72 2.739943 TGTGTCCAGCTGCTAGACTAT 58.260 47.619 24.63 0.00 0.00 2.12
72 73 2.215942 TGTGTCCAGCTGCTAGACTA 57.784 50.000 24.63 13.61 0.00 2.59
73 74 1.274728 CTTGTGTCCAGCTGCTAGACT 59.725 52.381 24.63 0.00 0.00 3.24
74 75 1.674221 CCTTGTGTCCAGCTGCTAGAC 60.674 57.143 19.26 19.26 0.00 2.59
75 76 0.610174 CCTTGTGTCCAGCTGCTAGA 59.390 55.000 8.66 0.00 0.00 2.43
76 77 0.610174 TCCTTGTGTCCAGCTGCTAG 59.390 55.000 8.66 0.00 0.00 3.42
77 78 0.321671 GTCCTTGTGTCCAGCTGCTA 59.678 55.000 8.66 0.00 0.00 3.49
78 79 1.072159 GTCCTTGTGTCCAGCTGCT 59.928 57.895 8.66 0.00 0.00 4.24
79 80 1.227943 TGTCCTTGTGTCCAGCTGC 60.228 57.895 8.66 0.00 0.00 5.25
80 81 0.179048 TGTGTCCTTGTGTCCAGCTG 60.179 55.000 6.78 6.78 0.00 4.24
81 82 0.767375 ATGTGTCCTTGTGTCCAGCT 59.233 50.000 0.00 0.00 0.00 4.24
82 83 2.076863 GTATGTGTCCTTGTGTCCAGC 58.923 52.381 0.00 0.00 0.00 4.85
83 84 2.303022 AGGTATGTGTCCTTGTGTCCAG 59.697 50.000 0.00 0.00 30.18 3.86
84 85 2.334977 AGGTATGTGTCCTTGTGTCCA 58.665 47.619 0.00 0.00 30.18 4.02
85 86 3.514309 AGTAGGTATGTGTCCTTGTGTCC 59.486 47.826 0.00 0.00 36.60 4.02
86 87 4.803098 AGTAGGTATGTGTCCTTGTGTC 57.197 45.455 0.00 0.00 36.60 3.67
87 88 9.824216 ATATATAGTAGGTATGTGTCCTTGTGT 57.176 33.333 0.00 0.00 36.60 3.72
92 93 9.702253 CCTTCATATATAGTAGGTATGTGTCCT 57.298 37.037 0.00 0.00 38.91 3.85
93 94 9.476928 ACCTTCATATATAGTAGGTATGTGTCC 57.523 37.037 10.09 0.00 37.45 4.02
95 96 8.750298 GCACCTTCATATATAGTAGGTATGTGT 58.250 37.037 11.01 1.16 37.12 3.72
96 97 7.915923 CGCACCTTCATATATAGTAGGTATGTG 59.084 40.741 11.01 5.65 37.12 3.21
97 98 7.416438 GCGCACCTTCATATATAGTAGGTATGT 60.416 40.741 0.30 0.00 37.12 2.29
98 99 6.918569 GCGCACCTTCATATATAGTAGGTATG 59.081 42.308 0.30 8.69 37.12 2.39
99 100 6.834451 AGCGCACCTTCATATATAGTAGGTAT 59.166 38.462 11.47 0.29 37.12 2.73
100 101 6.185511 AGCGCACCTTCATATATAGTAGGTA 58.814 40.000 11.47 0.00 37.12 3.08
101 102 5.017490 AGCGCACCTTCATATATAGTAGGT 58.983 41.667 11.47 7.18 39.74 3.08
102 103 5.358442 AGAGCGCACCTTCATATATAGTAGG 59.642 44.000 11.47 6.19 0.00 3.18
103 104 6.443934 AGAGCGCACCTTCATATATAGTAG 57.556 41.667 11.47 0.00 0.00 2.57
104 105 7.933215 TTAGAGCGCACCTTCATATATAGTA 57.067 36.000 11.47 0.00 0.00 1.82
105 106 6.835819 TTAGAGCGCACCTTCATATATAGT 57.164 37.500 11.47 0.00 0.00 2.12
106 107 7.090808 TGTTTAGAGCGCACCTTCATATATAG 58.909 38.462 11.47 0.00 0.00 1.31
107 108 6.988522 TGTTTAGAGCGCACCTTCATATATA 58.011 36.000 11.47 0.00 0.00 0.86
108 109 5.853936 TGTTTAGAGCGCACCTTCATATAT 58.146 37.500 11.47 0.00 0.00 0.86
109 110 5.270893 TGTTTAGAGCGCACCTTCATATA 57.729 39.130 11.47 0.00 0.00 0.86
110 111 4.137116 TGTTTAGAGCGCACCTTCATAT 57.863 40.909 11.47 0.00 0.00 1.78
111 112 3.603158 TGTTTAGAGCGCACCTTCATA 57.397 42.857 11.47 0.00 0.00 2.15
112 113 2.472695 TGTTTAGAGCGCACCTTCAT 57.527 45.000 11.47 0.00 0.00 2.57
113 114 1.871039 GTTGTTTAGAGCGCACCTTCA 59.129 47.619 11.47 4.34 0.00 3.02
114 115 1.136336 CGTTGTTTAGAGCGCACCTTC 60.136 52.381 11.47 0.00 0.00 3.46
115 116 0.865769 CGTTGTTTAGAGCGCACCTT 59.134 50.000 11.47 0.00 0.00 3.50
116 117 0.032952 TCGTTGTTTAGAGCGCACCT 59.967 50.000 11.47 9.06 0.00 4.00
117 118 0.863144 TTCGTTGTTTAGAGCGCACC 59.137 50.000 11.47 0.00 0.00 5.01
118 119 1.717429 CGTTCGTTGTTTAGAGCGCAC 60.717 52.381 11.47 2.25 34.69 5.34
119 120 0.505231 CGTTCGTTGTTTAGAGCGCA 59.495 50.000 11.47 0.00 34.69 6.09
120 121 0.780002 TCGTTCGTTGTTTAGAGCGC 59.220 50.000 0.00 0.00 40.13 5.92
121 122 1.201672 GCTCGTTCGTTGTTTAGAGCG 60.202 52.381 0.00 0.00 41.03 5.03
122 123 1.201672 CGCTCGTTCGTTGTTTAGAGC 60.202 52.381 5.30 5.30 45.21 4.09
123 124 2.049228 ACGCTCGTTCGTTGTTTAGAG 58.951 47.619 0.00 0.00 40.07 2.43
124 125 2.124011 ACGCTCGTTCGTTGTTTAGA 57.876 45.000 0.00 0.00 40.07 2.10
125 126 2.222223 GCTACGCTCGTTCGTTGTTTAG 60.222 50.000 9.59 3.23 43.15 1.85
126 127 1.715519 GCTACGCTCGTTCGTTGTTTA 59.284 47.619 9.59 0.00 43.15 2.01
127 128 0.505655 GCTACGCTCGTTCGTTGTTT 59.494 50.000 9.59 0.00 43.15 2.83
128 129 0.318445 AGCTACGCTCGTTCGTTGTT 60.318 50.000 9.59 4.18 43.15 2.83
129 130 1.002250 CAGCTACGCTCGTTCGTTGT 61.002 55.000 9.59 0.00 43.15 3.32
130 131 1.696644 CAGCTACGCTCGTTCGTTG 59.303 57.895 9.59 9.01 43.15 4.10
131 132 2.087009 GCAGCTACGCTCGTTCGTT 61.087 57.895 9.59 0.00 43.15 3.85
132 133 2.504244 GCAGCTACGCTCGTTCGT 60.504 61.111 0.00 9.31 45.49 3.85
133 134 3.598562 CGCAGCTACGCTCGTTCG 61.599 66.667 0.00 0.00 36.40 3.95
151 152 3.634397 TTGAAGGACATGGCTAGGAAG 57.366 47.619 0.00 0.00 0.00 3.46
152 153 4.380843 TTTTGAAGGACATGGCTAGGAA 57.619 40.909 0.00 0.00 0.00 3.36
153 154 4.380843 TTTTTGAAGGACATGGCTAGGA 57.619 40.909 0.00 0.00 0.00 2.94
354 1558 0.889186 GCGTCTTGAAGGCTTGGGAA 60.889 55.000 3.46 0.00 35.85 3.97
447 1651 1.448540 CGTCGCCAAGCTCCAAGAT 60.449 57.895 0.00 0.00 0.00 2.40
462 1795 4.274865 CAAAGAAAAGCAAGAGTGACGTC 58.725 43.478 9.11 9.11 0.00 4.34
762 2154 0.244994 CGATCCCCTTCCTCTATGCG 59.755 60.000 0.00 0.00 0.00 4.73
826 2493 0.320771 ATATGGCATCCGAGCGGTTC 60.321 55.000 1.65 0.00 36.47 3.62
827 2494 0.603707 CATATGGCATCCGAGCGGTT 60.604 55.000 1.65 0.00 36.47 4.44
828 2495 1.004560 CATATGGCATCCGAGCGGT 60.005 57.895 1.65 0.00 36.47 5.68
829 2496 1.742880 CCATATGGCATCCGAGCGG 60.743 63.158 9.29 1.74 34.64 5.52
830 2497 1.004560 ACCATATGGCATCCGAGCG 60.005 57.895 22.18 0.00 39.32 5.03
831 2498 0.674895 GGACCATATGGCATCCGAGC 60.675 60.000 22.18 1.39 39.32 5.03
832 2499 0.036010 GGGACCATATGGCATCCGAG 60.036 60.000 22.18 0.00 39.32 4.63
833 2500 1.826340 CGGGACCATATGGCATCCGA 61.826 60.000 30.98 0.00 43.25 4.55
834 2501 1.375908 CGGGACCATATGGCATCCG 60.376 63.158 25.98 25.98 39.32 4.18
837 2504 2.224769 CCTAAACGGGACCATATGGCAT 60.225 50.000 22.18 4.88 39.32 4.40
840 2507 1.876416 CGCCTAAACGGGACCATATGG 60.876 57.143 20.68 20.68 42.17 2.74
841 2508 1.069513 TCGCCTAAACGGGACCATATG 59.930 52.381 0.00 0.00 0.00 1.78
843 2510 0.461135 GTCGCCTAAACGGGACCATA 59.539 55.000 0.00 0.00 30.91 2.74
845 2512 2.658422 GTCGCCTAAACGGGACCA 59.342 61.111 0.00 0.00 30.91 4.02
847 2514 1.447314 CAGGTCGCCTAAACGGGAC 60.447 63.158 0.00 0.00 34.25 4.46
848 2515 2.652095 CCAGGTCGCCTAAACGGGA 61.652 63.158 0.00 0.00 29.64 5.14
850 2517 2.125269 CCCAGGTCGCCTAAACGG 60.125 66.667 0.00 0.00 29.64 4.44
917 2627 0.949105 CCTAGTTGCGAAACGGTGCT 60.949 55.000 0.00 0.00 0.00 4.40
937 2647 4.175988 GGGACGAGATGATCCCGA 57.824 61.111 2.67 0.00 45.26 5.14
1008 2726 2.815647 GCGGAAGTGGAAGGCTCG 60.816 66.667 0.00 0.00 0.00 5.03
1656 3386 2.096496 GGTCAATGGCATCTCGTCAAAG 59.904 50.000 0.00 0.00 28.89 2.77
1737 3467 1.153349 GAGATCAAGGGCGTCCACC 60.153 63.158 9.71 0.00 34.83 4.61
1783 3513 3.626924 GTCCGGCTCCACACCACT 61.627 66.667 0.00 0.00 0.00 4.00
1821 3551 1.557269 GGTGGGCACATGAGGAGAGT 61.557 60.000 0.00 0.00 0.00 3.24
2343 4073 7.512130 TCTCCACATTCTTATGTATCTTGCAT 58.488 34.615 0.00 0.00 43.07 3.96
2457 4187 0.107848 CTACACCATCCGGTTGTCCC 60.108 60.000 11.51 0.00 46.31 4.46
2988 4737 0.107456 CCTGTTCCAGTGCAGTGAGT 59.893 55.000 23.34 0.00 0.00 3.41
3188 4958 2.476619 CAGTTTGTTCTACTGGCTGTCG 59.523 50.000 0.00 0.00 39.42 4.35
3294 5064 2.180159 TAGAAGGTCCAAGGGCGTGC 62.180 60.000 0.00 0.00 0.00 5.34
3314 5084 3.477346 GGCCGGGTACTTCCTCCC 61.477 72.222 2.18 0.00 40.26 4.30
3322 5092 1.376812 CTCAAACAGGGCCGGGTAC 60.377 63.158 8.94 0.00 0.00 3.34
3397 5167 3.376234 CGATTCAGAACATGCTGACCATT 59.624 43.478 2.84 0.00 44.08 3.16
3415 5185 1.033746 CCTGAGCCATGCCAACGATT 61.034 55.000 0.00 0.00 0.00 3.34
3429 5199 3.380479 TGACTAAACAACCGACCTGAG 57.620 47.619 0.00 0.00 0.00 3.35
3544 5442 2.871080 CTGAAATTGGCGCGCGTG 60.871 61.111 32.35 16.86 0.00 5.34
3545 5443 3.027170 CTCTGAAATTGGCGCGCGT 62.027 57.895 32.35 10.40 0.00 6.01
3559 5457 7.065085 CACACCAGTGGAATCTAATAAACTCTG 59.935 40.741 18.40 0.00 42.13 3.35
3679 5577 4.722220 CCTGATCTTGATATCCTGGCAAA 58.278 43.478 0.00 0.00 0.00 3.68
3691 5589 1.699083 TCCTTGTGTGCCTGATCTTGA 59.301 47.619 0.00 0.00 0.00 3.02
3707 5605 0.957395 CTGACGCCACTGCATTCCTT 60.957 55.000 0.00 0.00 37.32 3.36
3729 5627 1.315497 CGACGGACAGTATTATCGCG 58.685 55.000 0.00 0.00 0.00 5.87
3833 5732 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3834 5733 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3835 5734 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
3836 5735 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
3837 5736 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
3838 5737 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
3839 5738 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
3840 5739 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
3841 5740 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
3842 5741 4.334443 CATTTCTGCGACAAGTAATTCCG 58.666 43.478 0.00 0.00 0.00 4.30
3843 5742 4.394920 TCCATTTCTGCGACAAGTAATTCC 59.605 41.667 0.00 0.00 0.00 3.01
3844 5743 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
3845 5744 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
3846 5745 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
3847 5746 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
3848 5747 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
3849 5748 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
3850 5749 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
3851 5750 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
3852 5751 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
3853 5752 5.175856 GTGTAGATACATCCATTTCTGCGAC 59.824 44.000 0.00 0.00 38.63 5.19
3854 5753 5.289595 GTGTAGATACATCCATTTCTGCGA 58.710 41.667 0.00 0.00 38.63 5.10
3855 5754 4.148871 CGTGTAGATACATCCATTTCTGCG 59.851 45.833 0.00 0.00 38.63 5.18
3856 5755 5.050490 ACGTGTAGATACATCCATTTCTGC 58.950 41.667 0.00 0.00 38.63 4.26
3857 5756 8.818141 AATACGTGTAGATACATCCATTTCTG 57.182 34.615 0.00 0.00 38.63 3.02
3858 5757 9.832445 AAAATACGTGTAGATACATCCATTTCT 57.168 29.630 0.00 0.00 38.63 2.52
3863 5762 9.740239 GAACTAAAATACGTGTAGATACATCCA 57.260 33.333 0.00 0.00 38.63 3.41
3864 5763 9.962783 AGAACTAAAATACGTGTAGATACATCC 57.037 33.333 0.00 0.00 38.63 3.51
3896 5795 8.673711 CGGAATTACTTGTCTTGGAAATGAATA 58.326 33.333 0.00 0.00 0.00 1.75
3897 5796 7.393234 TCGGAATTACTTGTCTTGGAAATGAAT 59.607 33.333 0.00 0.00 0.00 2.57
3898 5797 6.712998 TCGGAATTACTTGTCTTGGAAATGAA 59.287 34.615 0.00 0.00 0.00 2.57
3899 5798 6.234920 TCGGAATTACTTGTCTTGGAAATGA 58.765 36.000 0.00 0.00 0.00 2.57
3900 5799 6.494893 TCGGAATTACTTGTCTTGGAAATG 57.505 37.500 0.00 0.00 0.00 2.32
3901 5800 6.348213 CGTTCGGAATTACTTGTCTTGGAAAT 60.348 38.462 0.00 0.00 0.00 2.17
3902 5801 5.049954 CGTTCGGAATTACTTGTCTTGGAAA 60.050 40.000 0.00 0.00 0.00 3.13
3903 5802 4.449743 CGTTCGGAATTACTTGTCTTGGAA 59.550 41.667 0.00 0.00 0.00 3.53
3904 5803 3.991773 CGTTCGGAATTACTTGTCTTGGA 59.008 43.478 0.00 0.00 0.00 3.53
3905 5804 3.124636 CCGTTCGGAATTACTTGTCTTGG 59.875 47.826 5.19 0.00 0.00 3.61
3906 5805 3.991773 TCCGTTCGGAATTACTTGTCTTG 59.008 43.478 11.66 0.00 0.00 3.02
3907 5806 4.243270 CTCCGTTCGGAATTACTTGTCTT 58.757 43.478 14.79 0.00 33.41 3.01
3908 5807 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
3909 5808 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3910 5809 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3911 5810 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3912 5811 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3913 5812 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3914 5813 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3915 5814 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3916 5815 2.680066 ACTCCCTCCGTTCGGAATT 58.320 52.632 14.79 0.00 33.41 2.17
3917 5816 4.455366 ACTCCCTCCGTTCGGAAT 57.545 55.556 14.79 0.00 33.41 3.01


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

AutoCloner maintained by Alex Coulton.