Multiple sequence alignment - TraesCS3D01G449700

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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 TraesCS3D01G449700 chr3D 100.000 3449 0 0 1 3449 557878046 557881494 0.000000e+00 6370.0
1 TraesCS3D01G449700 chr3D 84.848 2079 224 48 1006 3026 557914241 557916286 0.000000e+00 2010.0
2 TraesCS3D01G449700 chr3D 83.107 2066 224 59 1011 3010 557794909 557796915 0.000000e+00 1766.0
3 TraesCS3D01G449700 chr3D 80.173 1155 168 43 1206 2322 557764771 557763640 0.000000e+00 808.0
4 TraesCS3D01G449700 chr3D 87.805 328 36 4 1025 1350 557721142 557721467 6.980000e-102 381.0
5 TraesCS3D01G449700 chr3D 79.601 451 64 16 2388 2828 557922305 557922737 7.240000e-77 298.0
6 TraesCS3D01G449700 chr3D 85.549 173 22 2 2901 3072 557723013 557723183 9.840000e-41 178.0
7 TraesCS3D01G449700 chr3B 92.054 2517 149 24 964 3449 740502992 740505488 0.000000e+00 3493.0
8 TraesCS3D01G449700 chr3B 82.872 1337 168 34 1006 2307 740051427 740052737 0.000000e+00 1144.0
9 TraesCS3D01G449700 chr3B 83.025 1243 151 35 1003 2212 740514537 740515752 0.000000e+00 1072.0
10 TraesCS3D01G449700 chr3B 87.794 893 95 8 1620 2502 740101327 740102215 0.000000e+00 1033.0
11 TraesCS3D01G449700 chr3B 83.257 872 119 11 1620 2469 740040261 740041127 0.000000e+00 776.0
12 TraesCS3D01G449700 chr3B 84.334 766 61 22 2306 3026 740052861 740053612 0.000000e+00 695.0
13 TraesCS3D01G449700 chr3B 85.271 516 61 6 2502 3010 740494910 740495417 5.100000e-143 518.0
14 TraesCS3D01G449700 chr3B 86.935 398 41 9 1006 1393 708796719 708797115 1.470000e-118 436.0
15 TraesCS3D01G449700 chr3B 81.113 593 68 18 266 853 740501811 740502364 5.290000e-118 435.0
16 TraesCS3D01G449700 chr3B 83.540 322 40 7 2513 2828 740542147 740542461 4.360000e-74 289.0
17 TraesCS3D01G449700 chr3B 95.614 114 3 2 846 957 740502840 740502953 7.600000e-42 182.0
18 TraesCS3D01G449700 chr3B 85.816 141 11 2 2947 3086 740542509 740542641 1.290000e-29 141.0
19 TraesCS3D01G449700 chr3A 83.827 1756 191 43 1006 2705 693647044 693648762 0.000000e+00 1583.0
20 TraesCS3D01G449700 chr3A 85.105 1336 128 25 1625 2932 693581546 693582838 0.000000e+00 1299.0
21 TraesCS3D01G449700 chr3A 89.612 799 63 10 2652 3449 693614804 693615583 0.000000e+00 998.0
22 TraesCS3D01G449700 chr3A 82.420 876 124 16 1620 2469 693484698 693485569 0.000000e+00 737.0
23 TraesCS3D01G449700 chr3A 84.495 574 67 16 233 800 693614230 693614787 6.510000e-152 547.0
24 TraesCS3D01G449700 chr3A 79.073 626 82 25 1001 1600 693571885 693572487 5.400000e-103 385.0
25 TraesCS3D01G449700 chrUn 78.821 458 63 19 2388 2828 295852300 295852740 9.430000e-71 278.0
26 TraesCS3D01G449700 chrUn 83.099 142 15 2 2947 3087 295852788 295852921 1.680000e-23 121.0
27 TraesCS3D01G449700 chr5D 82.759 87 10 5 487 572 449944490 449944408 4.770000e-09 73.1
28 TraesCS3D01G449700 chr6B 91.667 48 4 0 508 555 504286286 504286239 2.220000e-07 67.6


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 TraesCS3D01G449700 chr3D 557878046 557881494 3448 False 6370.0 6370 100.000000 1 3449 1 chr3D.!!$F2 3448
1 TraesCS3D01G449700 chr3D 557914241 557916286 2045 False 2010.0 2010 84.848000 1006 3026 1 chr3D.!!$F3 2020
2 TraesCS3D01G449700 chr3D 557794909 557796915 2006 False 1766.0 1766 83.107000 1011 3010 1 chr3D.!!$F1 1999
3 TraesCS3D01G449700 chr3D 557763640 557764771 1131 True 808.0 808 80.173000 1206 2322 1 chr3D.!!$R1 1116
4 TraesCS3D01G449700 chr3D 557721142 557723183 2041 False 279.5 381 86.677000 1025 3072 2 chr3D.!!$F5 2047
5 TraesCS3D01G449700 chr3B 740501811 740505488 3677 False 1370.0 3493 89.593667 266 3449 3 chr3B.!!$F7 3183
6 TraesCS3D01G449700 chr3B 740514537 740515752 1215 False 1072.0 1072 83.025000 1003 2212 1 chr3B.!!$F5 1209
7 TraesCS3D01G449700 chr3B 740101327 740102215 888 False 1033.0 1033 87.794000 1620 2502 1 chr3B.!!$F3 882
8 TraesCS3D01G449700 chr3B 740051427 740053612 2185 False 919.5 1144 83.603000 1006 3026 2 chr3B.!!$F6 2020
9 TraesCS3D01G449700 chr3B 740040261 740041127 866 False 776.0 776 83.257000 1620 2469 1 chr3B.!!$F2 849
10 TraesCS3D01G449700 chr3B 740494910 740495417 507 False 518.0 518 85.271000 2502 3010 1 chr3B.!!$F4 508
11 TraesCS3D01G449700 chr3A 693647044 693648762 1718 False 1583.0 1583 83.827000 1006 2705 1 chr3A.!!$F4 1699
12 TraesCS3D01G449700 chr3A 693581546 693582838 1292 False 1299.0 1299 85.105000 1625 2932 1 chr3A.!!$F3 1307
13 TraesCS3D01G449700 chr3A 693614230 693615583 1353 False 772.5 998 87.053500 233 3449 2 chr3A.!!$F5 3216
14 TraesCS3D01G449700 chr3A 693484698 693485569 871 False 737.0 737 82.420000 1620 2469 1 chr3A.!!$F1 849
15 TraesCS3D01G449700 chr3A 693571885 693572487 602 False 385.0 385 79.073000 1001 1600 1 chr3A.!!$F2 599

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
130 131 0.181824 TACCCTAGCCCCGATTTTGC 59.818 55.0 0.00 0.0 0.00 3.68 F
592 600 0.258774 AGTGGGTTGTTTCCAGCACT 59.741 50.0 0.00 0.0 34.56 4.40 F
1004 1528 0.825840 CCCTTTCTTCCCAAACCGCA 60.826 55.0 0.00 0.0 0.00 5.69 F
1822 2451 0.812412 ACACGGGGTGAGTTTTGACG 60.812 55.0 2.29 0.0 36.96 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 2274 1.001764 CCAAGGTGAGATGCAGGCA 60.002 57.895 0.00 0.0 0.00 4.75 R
1696 2322 1.007387 GCACGCCTTTGGGACTTTG 60.007 57.895 0.00 0.0 33.58 2.77 R
1839 2468 1.146930 ATCATCAGCCCGCGACAAT 59.853 52.632 8.23 0.0 0.00 2.71 R
2719 3629 3.010584 GGGATCCACCATGGTAGCATATT 59.989 47.826 19.28 0.0 39.03 1.28 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
37 38 8.562052 AGATTTAGTAAACCAAGTAAAACACCG 58.438 33.333 0.00 0.00 30.24 4.94
38 39 6.616774 TTAGTAAACCAAGTAAAACACCGG 57.383 37.500 0.00 0.00 0.00 5.28
39 40 4.779696 AGTAAACCAAGTAAAACACCGGA 58.220 39.130 9.46 0.00 0.00 5.14
40 41 5.379187 AGTAAACCAAGTAAAACACCGGAT 58.621 37.500 9.46 0.00 0.00 4.18
41 42 4.841443 AAACCAAGTAAAACACCGGATC 57.159 40.909 9.46 0.00 0.00 3.36
42 43 3.495434 ACCAAGTAAAACACCGGATCA 57.505 42.857 9.46 0.00 0.00 2.92
43 44 3.408634 ACCAAGTAAAACACCGGATCAG 58.591 45.455 9.46 0.00 0.00 2.90
44 45 2.747446 CCAAGTAAAACACCGGATCAGG 59.253 50.000 9.46 10.69 37.30 3.86
45 46 2.747446 CAAGTAAAACACCGGATCAGGG 59.253 50.000 16.73 8.62 35.02 4.45
46 47 1.092348 GTAAAACACCGGATCAGGGC 58.908 55.000 16.73 0.00 35.02 5.19
47 48 0.988832 TAAAACACCGGATCAGGGCT 59.011 50.000 16.73 0.00 35.02 5.19
48 49 0.988832 AAAACACCGGATCAGGGCTA 59.011 50.000 16.73 0.00 35.02 3.93
49 50 1.213296 AAACACCGGATCAGGGCTAT 58.787 50.000 16.73 0.00 35.02 2.97
50 51 0.469917 AACACCGGATCAGGGCTATG 59.530 55.000 16.73 7.67 35.02 2.23
51 52 0.691078 ACACCGGATCAGGGCTATGT 60.691 55.000 16.73 8.31 35.02 2.29
52 53 0.250038 CACCGGATCAGGGCTATGTG 60.250 60.000 16.73 0.26 35.02 3.21
53 54 0.691078 ACCGGATCAGGGCTATGTGT 60.691 55.000 16.73 0.00 35.02 3.72
54 55 0.469917 CCGGATCAGGGCTATGTGTT 59.530 55.000 3.59 0.00 0.00 3.32
55 56 1.691976 CCGGATCAGGGCTATGTGTTA 59.308 52.381 3.59 0.00 0.00 2.41
56 57 2.548067 CCGGATCAGGGCTATGTGTTAC 60.548 54.545 3.59 0.00 0.00 2.50
57 58 2.102420 CGGATCAGGGCTATGTGTTACA 59.898 50.000 0.00 0.00 0.00 2.41
58 59 3.467803 GGATCAGGGCTATGTGTTACAC 58.532 50.000 8.76 8.76 34.56 2.90
72 73 4.638304 GTGTTACACACCTGACCTAATGT 58.362 43.478 10.96 0.00 43.05 2.71
73 74 5.786311 GTGTTACACACCTGACCTAATGTA 58.214 41.667 10.96 0.00 43.05 2.29
74 75 6.403878 GTGTTACACACCTGACCTAATGTAT 58.596 40.000 10.96 0.00 43.05 2.29
75 76 6.877322 GTGTTACACACCTGACCTAATGTATT 59.123 38.462 10.96 0.00 43.05 1.89
76 77 7.064253 GTGTTACACACCTGACCTAATGTATTC 59.936 40.741 10.96 0.00 43.05 1.75
77 78 7.038587 TGTTACACACCTGACCTAATGTATTCT 60.039 37.037 0.00 0.00 0.00 2.40
78 79 6.374417 ACACACCTGACCTAATGTATTCTT 57.626 37.500 0.00 0.00 0.00 2.52
79 80 6.779860 ACACACCTGACCTAATGTATTCTTT 58.220 36.000 0.00 0.00 0.00 2.52
80 81 7.231467 ACACACCTGACCTAATGTATTCTTTT 58.769 34.615 0.00 0.00 0.00 2.27
81 82 7.174946 ACACACCTGACCTAATGTATTCTTTTG 59.825 37.037 0.00 0.00 0.00 2.44
82 83 6.151144 ACACCTGACCTAATGTATTCTTTTGC 59.849 38.462 0.00 0.00 0.00 3.68
83 84 5.354234 ACCTGACCTAATGTATTCTTTTGCG 59.646 40.000 0.00 0.00 0.00 4.85
84 85 5.584649 CCTGACCTAATGTATTCTTTTGCGA 59.415 40.000 0.00 0.00 0.00 5.10
85 86 6.260936 CCTGACCTAATGTATTCTTTTGCGAT 59.739 38.462 0.00 0.00 0.00 4.58
86 87 7.201732 CCTGACCTAATGTATTCTTTTGCGATT 60.202 37.037 0.00 0.00 0.00 3.34
87 88 8.050778 TGACCTAATGTATTCTTTTGCGATTT 57.949 30.769 0.00 0.00 0.00 2.17
88 89 8.519526 TGACCTAATGTATTCTTTTGCGATTTT 58.480 29.630 0.00 0.00 0.00 1.82
89 90 8.911247 ACCTAATGTATTCTTTTGCGATTTTC 57.089 30.769 0.00 0.00 0.00 2.29
90 91 8.519526 ACCTAATGTATTCTTTTGCGATTTTCA 58.480 29.630 0.00 0.00 0.00 2.69
91 92 9.520204 CCTAATGTATTCTTTTGCGATTTTCAT 57.480 29.630 0.00 0.00 0.00 2.57
93 94 8.984891 AATGTATTCTTTTGCGATTTTCATCA 57.015 26.923 0.00 0.00 0.00 3.07
94 95 8.984891 ATGTATTCTTTTGCGATTTTCATCAA 57.015 26.923 0.00 0.00 0.00 2.57
95 96 8.451687 TGTATTCTTTTGCGATTTTCATCAAG 57.548 30.769 0.00 0.00 0.00 3.02
96 97 6.956299 ATTCTTTTGCGATTTTCATCAAGG 57.044 33.333 0.00 0.00 0.00 3.61
97 98 5.703978 TCTTTTGCGATTTTCATCAAGGA 57.296 34.783 0.00 0.00 0.00 3.36
98 99 6.271488 TCTTTTGCGATTTTCATCAAGGAT 57.729 33.333 0.00 0.00 0.00 3.24
99 100 6.690530 TCTTTTGCGATTTTCATCAAGGATT 58.309 32.000 0.00 0.00 0.00 3.01
100 101 7.153985 TCTTTTGCGATTTTCATCAAGGATTT 58.846 30.769 0.00 0.00 0.00 2.17
101 102 6.709145 TTTGCGATTTTCATCAAGGATTTG 57.291 33.333 0.00 0.00 35.57 2.32
102 103 4.746729 TGCGATTTTCATCAAGGATTTGG 58.253 39.130 0.00 0.00 34.97 3.28
103 104 4.220382 TGCGATTTTCATCAAGGATTTGGT 59.780 37.500 0.00 0.00 34.97 3.67
104 105 5.170748 GCGATTTTCATCAAGGATTTGGTT 58.829 37.500 0.00 0.00 34.97 3.67
105 106 5.289434 GCGATTTTCATCAAGGATTTGGTTC 59.711 40.000 0.00 0.00 34.97 3.62
106 107 5.807011 CGATTTTCATCAAGGATTTGGTTCC 59.193 40.000 0.00 0.00 34.97 3.62
107 108 6.572119 CGATTTTCATCAAGGATTTGGTTCCA 60.572 38.462 0.00 0.00 38.32 3.53
108 109 6.684897 TTTTCATCAAGGATTTGGTTCCAT 57.315 33.333 0.00 0.00 38.32 3.41
109 110 5.664294 TTCATCAAGGATTTGGTTCCATG 57.336 39.130 0.00 0.00 38.32 3.66
110 111 4.933134 TCATCAAGGATTTGGTTCCATGA 58.067 39.130 0.00 1.39 44.88 3.07
112 113 6.671605 TCATCAAGGATTTGGTTCCATGATA 58.328 36.000 10.00 0.00 46.96 2.15
113 114 6.547141 TCATCAAGGATTTGGTTCCATGATAC 59.453 38.462 10.00 0.00 46.96 2.24
114 115 5.200483 TCAAGGATTTGGTTCCATGATACC 58.800 41.667 8.73 8.73 38.29 2.73
115 116 4.184649 AGGATTTGGTTCCATGATACCC 57.815 45.455 12.05 0.01 38.32 3.69
116 117 3.793827 AGGATTTGGTTCCATGATACCCT 59.206 43.478 12.05 0.00 38.32 4.34
117 118 4.981647 AGGATTTGGTTCCATGATACCCTA 59.018 41.667 12.05 3.02 38.32 3.53
118 119 5.073691 AGGATTTGGTTCCATGATACCCTAG 59.926 44.000 12.05 0.00 38.32 3.02
119 120 3.857157 TTGGTTCCATGATACCCTAGC 57.143 47.619 12.05 0.00 33.34 3.42
120 121 2.054799 TGGTTCCATGATACCCTAGCC 58.945 52.381 12.05 0.00 33.34 3.93
121 122 1.351350 GGTTCCATGATACCCTAGCCC 59.649 57.143 0.00 0.00 0.00 5.19
122 123 1.351350 GTTCCATGATACCCTAGCCCC 59.649 57.143 0.00 0.00 0.00 5.80
123 124 0.544357 TCCATGATACCCTAGCCCCG 60.544 60.000 0.00 0.00 0.00 5.73
124 125 0.544357 CCATGATACCCTAGCCCCGA 60.544 60.000 0.00 0.00 0.00 5.14
125 126 1.573108 CATGATACCCTAGCCCCGAT 58.427 55.000 0.00 0.00 0.00 4.18
126 127 1.909302 CATGATACCCTAGCCCCGATT 59.091 52.381 0.00 0.00 0.00 3.34
127 128 2.112279 TGATACCCTAGCCCCGATTT 57.888 50.000 0.00 0.00 0.00 2.17
128 129 2.414612 TGATACCCTAGCCCCGATTTT 58.585 47.619 0.00 0.00 0.00 1.82
129 130 2.105821 TGATACCCTAGCCCCGATTTTG 59.894 50.000 0.00 0.00 0.00 2.44
130 131 0.181824 TACCCTAGCCCCGATTTTGC 59.818 55.000 0.00 0.00 0.00 3.68
131 132 1.077068 CCCTAGCCCCGATTTTGCA 60.077 57.895 0.00 0.00 0.00 4.08
132 133 0.468029 CCCTAGCCCCGATTTTGCAT 60.468 55.000 0.00 0.00 0.00 3.96
133 134 1.402787 CCTAGCCCCGATTTTGCATT 58.597 50.000 0.00 0.00 0.00 3.56
134 135 1.756538 CCTAGCCCCGATTTTGCATTT 59.243 47.619 0.00 0.00 0.00 2.32
135 136 2.168313 CCTAGCCCCGATTTTGCATTTT 59.832 45.455 0.00 0.00 0.00 1.82
136 137 2.857186 AGCCCCGATTTTGCATTTTT 57.143 40.000 0.00 0.00 0.00 1.94
179 180 8.538409 AAACAATTGCAAGATGAATAAGTTCC 57.462 30.769 18.76 0.00 33.26 3.62
180 181 7.230849 ACAATTGCAAGATGAATAAGTTCCA 57.769 32.000 18.76 0.00 33.26 3.53
181 182 7.669427 ACAATTGCAAGATGAATAAGTTCCAA 58.331 30.769 18.76 0.00 33.26 3.53
182 183 7.816031 ACAATTGCAAGATGAATAAGTTCCAAG 59.184 33.333 18.76 0.00 33.26 3.61
183 184 6.899393 TTGCAAGATGAATAAGTTCCAAGT 57.101 33.333 0.00 0.00 33.26 3.16
184 185 6.899393 TGCAAGATGAATAAGTTCCAAGTT 57.101 33.333 0.00 0.00 33.26 2.66
185 186 6.680810 TGCAAGATGAATAAGTTCCAAGTTG 58.319 36.000 0.00 0.00 33.26 3.16
186 187 6.265196 TGCAAGATGAATAAGTTCCAAGTTGT 59.735 34.615 1.45 0.00 33.26 3.32
187 188 7.446931 TGCAAGATGAATAAGTTCCAAGTTGTA 59.553 33.333 1.45 0.00 33.26 2.41
188 189 7.965107 GCAAGATGAATAAGTTCCAAGTTGTAG 59.035 37.037 1.45 0.00 33.26 2.74
189 190 9.003658 CAAGATGAATAAGTTCCAAGTTGTAGT 57.996 33.333 1.45 0.00 33.26 2.73
195 196 8.959705 AATAAGTTCCAAGTTGTAGTATAGGC 57.040 34.615 1.45 0.00 0.00 3.93
196 197 6.368779 AAGTTCCAAGTTGTAGTATAGGCA 57.631 37.500 1.45 0.00 0.00 4.75
197 198 5.731591 AGTTCCAAGTTGTAGTATAGGCAC 58.268 41.667 1.45 0.00 0.00 5.01
198 199 4.380841 TCCAAGTTGTAGTATAGGCACG 57.619 45.455 1.45 0.00 0.00 5.34
199 200 2.864343 CCAAGTTGTAGTATAGGCACGC 59.136 50.000 1.45 0.00 0.00 5.34
200 201 2.864343 CAAGTTGTAGTATAGGCACGCC 59.136 50.000 0.00 0.00 0.00 5.68
209 210 4.025858 AGGCACGCCTGCTCACAT 62.026 61.111 10.47 0.00 46.22 3.21
210 211 2.125147 GGCACGCCTGCTCACATA 60.125 61.111 7.62 0.00 43.66 2.29
211 212 2.464459 GGCACGCCTGCTCACATAC 61.464 63.158 7.62 0.00 43.66 2.39
212 213 1.741401 GCACGCCTGCTCACATACA 60.741 57.895 0.00 0.00 40.63 2.29
213 214 1.298157 GCACGCCTGCTCACATACAA 61.298 55.000 0.00 0.00 40.63 2.41
214 215 1.155889 CACGCCTGCTCACATACAAA 58.844 50.000 0.00 0.00 0.00 2.83
215 216 1.535028 CACGCCTGCTCACATACAAAA 59.465 47.619 0.00 0.00 0.00 2.44
216 217 1.535462 ACGCCTGCTCACATACAAAAC 59.465 47.619 0.00 0.00 0.00 2.43
217 218 1.535028 CGCCTGCTCACATACAAAACA 59.465 47.619 0.00 0.00 0.00 2.83
218 219 2.665519 CGCCTGCTCACATACAAAACAC 60.666 50.000 0.00 0.00 0.00 3.32
219 220 2.293122 GCCTGCTCACATACAAAACACA 59.707 45.455 0.00 0.00 0.00 3.72
220 221 3.057315 GCCTGCTCACATACAAAACACAT 60.057 43.478 0.00 0.00 0.00 3.21
221 222 4.155826 GCCTGCTCACATACAAAACACATA 59.844 41.667 0.00 0.00 0.00 2.29
222 223 5.163622 GCCTGCTCACATACAAAACACATAT 60.164 40.000 0.00 0.00 0.00 1.78
223 224 6.260377 CCTGCTCACATACAAAACACATATG 58.740 40.000 0.00 0.00 33.38 1.78
224 225 6.127925 CCTGCTCACATACAAAACACATATGT 60.128 38.462 1.41 1.41 42.46 2.29
225 226 7.065683 CCTGCTCACATACAAAACACATATGTA 59.934 37.037 8.32 0.00 38.45 2.29
226 227 8.504812 TGCTCACATACAAAACACATATGTAT 57.495 30.769 8.32 0.00 38.45 2.29
247 248 8.712285 TGTATGCAGTATTTCTTACCTTGTAC 57.288 34.615 0.00 0.00 0.00 2.90
248 249 8.537016 TGTATGCAGTATTTCTTACCTTGTACT 58.463 33.333 0.00 0.00 0.00 2.73
252 253 8.755028 TGCAGTATTTCTTACCTTGTACTATCA 58.245 33.333 0.00 0.00 0.00 2.15
346 349 8.845227 TGAAAAACACAGTACAATCACATATGT 58.155 29.630 1.41 1.41 0.00 2.29
405 409 1.196104 TACACACACCCTGCCCCTAC 61.196 60.000 0.00 0.00 0.00 3.18
408 412 2.203877 ACACCCTGCCCCTACGAA 60.204 61.111 0.00 0.00 0.00 3.85
415 419 1.874345 CTGCCCCTACGAACACGTCT 61.874 60.000 0.00 0.00 40.72 4.18
460 466 4.437682 TGAGATTGACAAAGTCCCACTT 57.562 40.909 0.00 0.00 40.80 3.16
461 467 4.389374 TGAGATTGACAAAGTCCCACTTC 58.611 43.478 0.00 0.00 37.47 3.01
467 473 1.489230 ACAAAGTCCCACTTCCGTCTT 59.511 47.619 0.00 0.00 37.47 3.01
471 477 1.893801 AGTCCCACTTCCGTCTTGTAG 59.106 52.381 0.00 0.00 0.00 2.74
485 491 3.432252 GTCTTGTAGTTGACGGGAACATG 59.568 47.826 0.00 0.00 0.00 3.21
488 494 2.631062 TGTAGTTGACGGGAACATGTCT 59.369 45.455 0.00 0.00 36.44 3.41
517 523 3.810941 TGAACGAACATAGCCGAAAAGTT 59.189 39.130 0.00 0.00 0.00 2.66
527 533 9.705290 AACATAGCCGAAAAGTTTGAAATAAAT 57.295 25.926 0.00 0.00 0.00 1.40
560 568 2.805295 CGAACACCAGTGCCAAGTCTTA 60.805 50.000 0.00 0.00 0.00 2.10
587 595 1.145571 AGCCTAGTGGGTTGTTTCCA 58.854 50.000 0.00 0.00 42.12 3.53
588 596 1.073923 AGCCTAGTGGGTTGTTTCCAG 59.926 52.381 0.00 0.00 42.12 3.86
589 597 1.534729 CCTAGTGGGTTGTTTCCAGC 58.465 55.000 0.00 0.00 34.56 4.85
590 598 1.202879 CCTAGTGGGTTGTTTCCAGCA 60.203 52.381 0.00 0.00 34.56 4.41
591 599 1.880027 CTAGTGGGTTGTTTCCAGCAC 59.120 52.381 0.00 0.00 34.56 4.40
592 600 0.258774 AGTGGGTTGTTTCCAGCACT 59.741 50.000 0.00 0.00 34.56 4.40
593 601 1.493022 AGTGGGTTGTTTCCAGCACTA 59.507 47.619 0.00 0.00 34.56 2.74
594 602 1.880027 GTGGGTTGTTTCCAGCACTAG 59.120 52.381 0.00 0.00 34.56 2.57
595 603 1.202879 TGGGTTGTTTCCAGCACTAGG 60.203 52.381 0.00 0.00 0.00 3.02
596 604 1.073284 GGGTTGTTTCCAGCACTAGGA 59.927 52.381 0.00 0.00 0.00 2.94
597 605 2.488347 GGGTTGTTTCCAGCACTAGGAA 60.488 50.000 0.00 0.00 43.13 3.36
602 610 2.743636 TTCCAGCACTAGGAAACTCG 57.256 50.000 0.00 0.00 41.94 4.18
603 611 1.919240 TCCAGCACTAGGAAACTCGA 58.081 50.000 0.00 0.00 43.67 4.04
604 612 1.544691 TCCAGCACTAGGAAACTCGAC 59.455 52.381 0.00 0.00 43.67 4.20
605 613 1.404315 CCAGCACTAGGAAACTCGACC 60.404 57.143 0.00 0.00 43.67 4.79
606 614 1.546476 CAGCACTAGGAAACTCGACCT 59.454 52.381 0.00 0.00 43.67 3.85
617 625 4.807304 GGAAACTCGACCTAAAATGCGATA 59.193 41.667 0.00 0.00 31.87 2.92
637 645 2.265589 TCAAGGACCCCGAAAAACTC 57.734 50.000 0.00 0.00 0.00 3.01
652 660 5.399604 AAAAACTCGAAAACACTCTACGG 57.600 39.130 0.00 0.00 0.00 4.02
667 675 4.223032 ACTCTACGGCCATATTTAGGATGG 59.777 45.833 2.24 0.00 45.79 3.51
668 676 4.164981 TCTACGGCCATATTTAGGATGGT 58.835 43.478 2.24 0.00 44.96 3.55
669 677 3.418684 ACGGCCATATTTAGGATGGTC 57.581 47.619 2.24 0.00 44.96 4.02
673 681 3.562176 GGCCATATTTAGGATGGTCAGGG 60.562 52.174 0.00 0.00 46.49 4.45
681 689 1.005924 AGGATGGTCAGGGCGATTTTT 59.994 47.619 0.00 0.00 0.00 1.94
696 704 3.629398 CGATTTTTAAGGCCATCTGAGCT 59.371 43.478 5.01 0.00 0.00 4.09
698 706 5.471456 CGATTTTTAAGGCCATCTGAGCTAT 59.529 40.000 5.01 0.00 0.00 2.97
757 765 7.183460 AGTAGTACCAGGTACAGAAGAAAGAT 58.817 38.462 28.36 8.90 41.03 2.40
758 766 6.532988 AGTACCAGGTACAGAAGAAAGATC 57.467 41.667 28.36 0.10 41.03 2.75
763 771 6.670027 ACCAGGTACAGAAGAAAGATCTACAT 59.330 38.462 0.00 0.00 33.77 2.29
766 774 8.908903 CAGGTACAGAAGAAAGATCTACATACT 58.091 37.037 0.00 0.00 33.77 2.12
767 775 8.908903 AGGTACAGAAGAAAGATCTACATACTG 58.091 37.037 0.00 6.63 33.77 2.74
774 782 4.576216 AAGATCTACATACTGAGCACCG 57.424 45.455 0.00 0.00 0.00 4.94
913 1405 3.181440 TGATACTTGGATGGGCCTTGATC 60.181 47.826 4.53 0.00 37.63 2.92
957 1449 2.751806 CCTTGATTTGCTCTTCACTCCC 59.248 50.000 0.00 0.00 0.00 4.30
958 1450 3.415212 CTTGATTTGCTCTTCACTCCCA 58.585 45.455 0.00 0.00 0.00 4.37
959 1451 3.507162 TGATTTGCTCTTCACTCCCAA 57.493 42.857 0.00 0.00 0.00 4.12
960 1452 3.831323 TGATTTGCTCTTCACTCCCAAA 58.169 40.909 0.00 0.00 0.00 3.28
974 1498 4.459337 CACTCCCAAACTGATCCCTAAAAC 59.541 45.833 0.00 0.00 0.00 2.43
1004 1528 0.825840 CCCTTTCTTCCCAAACCGCA 60.826 55.000 0.00 0.00 0.00 5.69
1090 1614 3.036783 GACGACGACGACCTCCTGG 62.037 68.421 15.32 0.00 42.66 4.45
1209 1733 2.509336 CGTTTCCGCGAGCTCCAT 60.509 61.111 8.23 0.00 0.00 3.41
1533 2132 1.006832 GCAGTATGTACAGTTGGGCG 58.993 55.000 0.33 0.00 39.31 6.13
1582 2184 3.449737 TGGGTGGTCCTACTTTTATCTCG 59.550 47.826 0.00 0.00 36.20 4.04
1657 2274 3.194116 GCAAAATGGTGATGATGTCTGGT 59.806 43.478 0.00 0.00 0.00 4.00
1696 2322 2.300437 GCCTCAGACCTGTATCCATACC 59.700 54.545 0.00 0.00 32.33 2.73
1717 2343 3.056328 GTCCCAAAGGCGTGCTCC 61.056 66.667 0.00 0.00 0.00 4.70
1756 2385 1.656263 GCGACCGACGATGCGATTA 60.656 57.895 0.00 0.00 45.77 1.75
1776 2405 3.703001 ATTGTCCTGGATTTGACGTCT 57.297 42.857 17.92 0.00 34.18 4.18
1799 2428 5.991328 TCAATCTTATCGACAATTCAGCC 57.009 39.130 0.00 0.00 0.00 4.85
1822 2451 0.812412 ACACGGGGTGAGTTTTGACG 60.812 55.000 2.29 0.00 36.96 4.35
2238 2875 8.900781 GGTGATCTGTATAGTGTACTTGTAGAA 58.099 37.037 0.00 0.00 0.00 2.10
2305 3084 6.782988 AGTATAGCTATGGAGTGGTGTTACAT 59.217 38.462 16.77 0.00 0.00 2.29
2306 3085 7.948447 AGTATAGCTATGGAGTGGTGTTACATA 59.052 37.037 16.77 0.00 0.00 2.29
2364 3144 7.928706 GTCAAGCCACATATAGTATTCTTGTCT 59.071 37.037 0.00 0.00 34.45 3.41
2403 3183 9.793259 AAATCACTTCTGTATTGTTTCCTTAGA 57.207 29.630 0.00 0.00 0.00 2.10
2405 3185 7.732025 TCACTTCTGTATTGTTTCCTTAGACA 58.268 34.615 0.00 0.00 0.00 3.41
2428 3301 9.698617 GACATTTTTAACAATACTAGTAAGCGG 57.301 33.333 6.70 0.00 0.00 5.52
2541 3430 7.521529 AGATGATTTGAAATCACTTGTGTACG 58.478 34.615 21.54 0.00 0.00 3.67
2617 3516 3.135994 GTTGTCGGTGTGTAATGGTTCT 58.864 45.455 0.00 0.00 0.00 3.01
2620 3519 4.958509 TGTCGGTGTGTAATGGTTCTTTA 58.041 39.130 0.00 0.00 0.00 1.85
2624 3523 5.998981 TCGGTGTGTAATGGTTCTTTACAAT 59.001 36.000 7.60 0.00 40.26 2.71
2698 3608 7.971722 GCAGGTTTGTTTCTTAGTCACTAAAAA 59.028 33.333 0.00 0.65 0.00 1.94
2876 3805 3.627577 ACGGGCTCAATATTAGTTGCAAG 59.372 43.478 0.00 0.00 0.00 4.01
3019 3957 5.415701 GTCATGCTTCCTGAATTTGGTCTTA 59.584 40.000 0.00 0.00 0.00 2.10
3062 4000 4.035441 GCAATTTGTGGTTGTGCTCAAAAT 59.965 37.500 2.18 0.00 35.20 1.82
3077 4015 7.589587 TGTGCTCAAAATTTACTTGTTGTATCG 59.410 33.333 0.00 0.00 0.00 2.92
3111 4049 5.789643 ACTATGTGGTGCTGAAAATTGTT 57.210 34.783 0.00 0.00 0.00 2.83
3237 4178 8.540507 TCTTGTATAAGAGGATTAAGAGCTGT 57.459 34.615 0.00 0.00 37.99 4.40
3250 4191 1.339610 AGAGCTGTAAGATGCCTAGCG 59.660 52.381 0.00 0.00 39.27 4.26
3253 4194 1.594862 GCTGTAAGATGCCTAGCGTTG 59.405 52.381 0.00 0.00 34.07 4.10
3312 4253 4.518970 GCACAGAAATAGTCAGAAACCCAA 59.481 41.667 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.562052 CGGTGTTTTACTTGGTTTACTAAATCT 58.438 33.333 0.00 0.00 0.00 2.40
12 13 7.804600 CCGGTGTTTTACTTGGTTTACTAAATC 59.195 37.037 0.00 0.00 0.00 2.17
13 14 7.501892 TCCGGTGTTTTACTTGGTTTACTAAAT 59.498 33.333 0.00 0.00 0.00 1.40
14 15 6.825721 TCCGGTGTTTTACTTGGTTTACTAAA 59.174 34.615 0.00 0.00 0.00 1.85
15 16 6.352516 TCCGGTGTTTTACTTGGTTTACTAA 58.647 36.000 0.00 0.00 0.00 2.24
16 17 5.923204 TCCGGTGTTTTACTTGGTTTACTA 58.077 37.500 0.00 0.00 0.00 1.82
17 18 4.779696 TCCGGTGTTTTACTTGGTTTACT 58.220 39.130 0.00 0.00 0.00 2.24
18 19 5.239087 TGATCCGGTGTTTTACTTGGTTTAC 59.761 40.000 0.00 0.00 0.00 2.01
19 20 5.374921 TGATCCGGTGTTTTACTTGGTTTA 58.625 37.500 0.00 0.00 0.00 2.01
20 21 4.208746 TGATCCGGTGTTTTACTTGGTTT 58.791 39.130 0.00 0.00 0.00 3.27
21 22 3.818773 CTGATCCGGTGTTTTACTTGGTT 59.181 43.478 0.00 0.00 0.00 3.67
22 23 3.408634 CTGATCCGGTGTTTTACTTGGT 58.591 45.455 0.00 0.00 0.00 3.67
23 24 2.747446 CCTGATCCGGTGTTTTACTTGG 59.253 50.000 0.00 0.00 0.00 3.61
24 25 2.747446 CCCTGATCCGGTGTTTTACTTG 59.253 50.000 0.00 0.00 0.00 3.16
25 26 2.878526 GCCCTGATCCGGTGTTTTACTT 60.879 50.000 0.00 0.00 0.00 2.24
26 27 1.339727 GCCCTGATCCGGTGTTTTACT 60.340 52.381 0.00 0.00 0.00 2.24
27 28 1.092348 GCCCTGATCCGGTGTTTTAC 58.908 55.000 0.00 0.00 0.00 2.01
28 29 0.988832 AGCCCTGATCCGGTGTTTTA 59.011 50.000 0.00 0.00 0.00 1.52
29 30 0.988832 TAGCCCTGATCCGGTGTTTT 59.011 50.000 0.00 0.00 0.00 2.43
30 31 1.134098 CATAGCCCTGATCCGGTGTTT 60.134 52.381 0.00 0.00 0.00 2.83
31 32 0.469917 CATAGCCCTGATCCGGTGTT 59.530 55.000 0.00 0.00 0.00 3.32
32 33 0.691078 ACATAGCCCTGATCCGGTGT 60.691 55.000 0.00 0.00 0.00 4.16
33 34 0.250038 CACATAGCCCTGATCCGGTG 60.250 60.000 0.00 0.00 0.00 4.94
34 35 0.691078 ACACATAGCCCTGATCCGGT 60.691 55.000 0.00 0.00 0.00 5.28
35 36 0.469917 AACACATAGCCCTGATCCGG 59.530 55.000 0.00 0.00 0.00 5.14
36 37 2.102420 TGTAACACATAGCCCTGATCCG 59.898 50.000 0.00 0.00 0.00 4.18
37 38 3.118408 TGTGTAACACATAGCCCTGATCC 60.118 47.826 0.00 0.00 45.67 3.36
38 39 4.137116 TGTGTAACACATAGCCCTGATC 57.863 45.455 0.00 0.00 45.67 2.92
52 53 7.328737 AGAATACATTAGGTCAGGTGTGTAAC 58.671 38.462 0.00 0.00 37.35 2.50
53 54 7.490657 AGAATACATTAGGTCAGGTGTGTAA 57.509 36.000 0.00 0.00 0.00 2.41
54 55 7.490657 AAGAATACATTAGGTCAGGTGTGTA 57.509 36.000 0.00 0.00 0.00 2.90
55 56 6.374417 AAGAATACATTAGGTCAGGTGTGT 57.626 37.500 0.00 0.00 0.00 3.72
56 57 7.530010 CAAAAGAATACATTAGGTCAGGTGTG 58.470 38.462 0.00 0.00 0.00 3.82
57 58 6.151144 GCAAAAGAATACATTAGGTCAGGTGT 59.849 38.462 0.00 0.00 0.00 4.16
58 59 6.555315 GCAAAAGAATACATTAGGTCAGGTG 58.445 40.000 0.00 0.00 0.00 4.00
59 60 5.354234 CGCAAAAGAATACATTAGGTCAGGT 59.646 40.000 0.00 0.00 0.00 4.00
60 61 5.584649 TCGCAAAAGAATACATTAGGTCAGG 59.415 40.000 0.00 0.00 0.00 3.86
61 62 6.662414 TCGCAAAAGAATACATTAGGTCAG 57.338 37.500 0.00 0.00 0.00 3.51
62 63 7.624360 AATCGCAAAAGAATACATTAGGTCA 57.376 32.000 0.00 0.00 0.00 4.02
63 64 8.911247 AAAATCGCAAAAGAATACATTAGGTC 57.089 30.769 0.00 0.00 0.00 3.85
64 65 8.519526 TGAAAATCGCAAAAGAATACATTAGGT 58.480 29.630 0.00 0.00 0.00 3.08
65 66 8.909708 TGAAAATCGCAAAAGAATACATTAGG 57.090 30.769 0.00 0.00 0.00 2.69
68 69 8.984891 TGATGAAAATCGCAAAAGAATACATT 57.015 26.923 0.00 0.00 0.00 2.71
69 70 8.984891 TTGATGAAAATCGCAAAAGAATACAT 57.015 26.923 0.00 0.00 0.00 2.29
70 71 7.541783 CCTTGATGAAAATCGCAAAAGAATACA 59.458 33.333 0.00 0.00 0.00 2.29
71 72 7.754924 TCCTTGATGAAAATCGCAAAAGAATAC 59.245 33.333 0.00 0.00 0.00 1.89
72 73 7.825681 TCCTTGATGAAAATCGCAAAAGAATA 58.174 30.769 0.00 0.00 0.00 1.75
73 74 6.690530 TCCTTGATGAAAATCGCAAAAGAAT 58.309 32.000 0.00 0.00 0.00 2.40
74 75 6.083098 TCCTTGATGAAAATCGCAAAAGAA 57.917 33.333 0.00 0.00 0.00 2.52
75 76 5.703978 TCCTTGATGAAAATCGCAAAAGA 57.296 34.783 0.00 0.00 0.00 2.52
76 77 6.956299 AATCCTTGATGAAAATCGCAAAAG 57.044 33.333 0.00 0.00 0.00 2.27
77 78 6.147492 CCAAATCCTTGATGAAAATCGCAAAA 59.853 34.615 0.00 0.00 34.14 2.44
78 79 5.638657 CCAAATCCTTGATGAAAATCGCAAA 59.361 36.000 0.00 0.00 34.14 3.68
79 80 5.170021 CCAAATCCTTGATGAAAATCGCAA 58.830 37.500 0.00 0.00 34.14 4.85
80 81 4.220382 ACCAAATCCTTGATGAAAATCGCA 59.780 37.500 0.00 0.00 34.14 5.10
81 82 4.747810 ACCAAATCCTTGATGAAAATCGC 58.252 39.130 0.00 0.00 34.14 4.58
82 83 5.807011 GGAACCAAATCCTTGATGAAAATCG 59.193 40.000 0.00 0.00 36.50 3.34
83 84 6.700352 TGGAACCAAATCCTTGATGAAAATC 58.300 36.000 0.00 0.00 40.35 2.17
84 85 6.684897 TGGAACCAAATCCTTGATGAAAAT 57.315 33.333 0.00 0.00 40.35 1.82
85 86 6.269538 TCATGGAACCAAATCCTTGATGAAAA 59.730 34.615 7.58 0.00 44.33 2.29
86 87 5.779260 TCATGGAACCAAATCCTTGATGAAA 59.221 36.000 7.58 0.00 44.33 2.69
87 88 5.331906 TCATGGAACCAAATCCTTGATGAA 58.668 37.500 7.58 0.00 44.33 2.57
88 89 4.933134 TCATGGAACCAAATCCTTGATGA 58.067 39.130 7.58 0.70 44.33 2.92
92 93 4.342092 GGGTATCATGGAACCAAATCCTTG 59.658 45.833 16.26 3.52 42.88 3.61
93 94 4.232820 AGGGTATCATGGAACCAAATCCTT 59.767 41.667 16.26 0.00 40.35 3.36
94 95 3.793827 AGGGTATCATGGAACCAAATCCT 59.206 43.478 16.26 4.31 40.35 3.24
95 96 4.184649 AGGGTATCATGGAACCAAATCC 57.815 45.455 16.26 0.00 37.51 3.01
96 97 4.762251 GCTAGGGTATCATGGAACCAAATC 59.238 45.833 16.26 2.76 37.51 2.17
97 98 4.447762 GGCTAGGGTATCATGGAACCAAAT 60.448 45.833 16.26 6.87 37.51 2.32
98 99 3.117663 GGCTAGGGTATCATGGAACCAAA 60.118 47.826 16.26 5.61 37.51 3.28
99 100 2.441750 GGCTAGGGTATCATGGAACCAA 59.558 50.000 16.26 5.89 37.51 3.67
100 101 2.054799 GGCTAGGGTATCATGGAACCA 58.945 52.381 16.26 0.00 37.51 3.67
101 102 1.351350 GGGCTAGGGTATCATGGAACC 59.649 57.143 8.44 8.44 34.85 3.62
102 103 1.351350 GGGGCTAGGGTATCATGGAAC 59.649 57.143 0.00 0.00 0.00 3.62
103 104 1.742308 GGGGCTAGGGTATCATGGAA 58.258 55.000 0.00 0.00 0.00 3.53
104 105 0.544357 CGGGGCTAGGGTATCATGGA 60.544 60.000 0.00 0.00 0.00 3.41
105 106 0.544357 TCGGGGCTAGGGTATCATGG 60.544 60.000 0.00 0.00 0.00 3.66
106 107 1.573108 ATCGGGGCTAGGGTATCATG 58.427 55.000 0.00 0.00 0.00 3.07
107 108 2.344093 AATCGGGGCTAGGGTATCAT 57.656 50.000 0.00 0.00 0.00 2.45
108 109 2.105821 CAAAATCGGGGCTAGGGTATCA 59.894 50.000 0.00 0.00 0.00 2.15
109 110 2.779506 CAAAATCGGGGCTAGGGTATC 58.220 52.381 0.00 0.00 0.00 2.24
110 111 1.202891 GCAAAATCGGGGCTAGGGTAT 60.203 52.381 0.00 0.00 0.00 2.73
111 112 0.181824 GCAAAATCGGGGCTAGGGTA 59.818 55.000 0.00 0.00 0.00 3.69
112 113 1.076995 GCAAAATCGGGGCTAGGGT 60.077 57.895 0.00 0.00 0.00 4.34
113 114 0.468029 ATGCAAAATCGGGGCTAGGG 60.468 55.000 0.00 0.00 0.00 3.53
114 115 1.402787 AATGCAAAATCGGGGCTAGG 58.597 50.000 0.00 0.00 0.00 3.02
115 116 3.525268 AAAATGCAAAATCGGGGCTAG 57.475 42.857 0.00 0.00 0.00 3.42
116 117 3.971245 AAAAATGCAAAATCGGGGCTA 57.029 38.095 0.00 0.00 0.00 3.93
117 118 2.857186 AAAAATGCAAAATCGGGGCT 57.143 40.000 0.00 0.00 0.00 5.19
153 154 9.638239 GGAACTTATTCATCTTGCAATTGTTTA 57.362 29.630 7.40 0.00 36.46 2.01
154 155 8.149647 TGGAACTTATTCATCTTGCAATTGTTT 58.850 29.630 7.40 0.00 36.46 2.83
155 156 7.669427 TGGAACTTATTCATCTTGCAATTGTT 58.331 30.769 7.40 0.00 36.46 2.83
156 157 7.230849 TGGAACTTATTCATCTTGCAATTGT 57.769 32.000 7.40 0.00 36.46 2.71
157 158 7.816031 ACTTGGAACTTATTCATCTTGCAATTG 59.184 33.333 0.00 0.00 36.46 2.32
158 159 7.899973 ACTTGGAACTTATTCATCTTGCAATT 58.100 30.769 0.00 0.00 36.46 2.32
159 160 7.472334 ACTTGGAACTTATTCATCTTGCAAT 57.528 32.000 0.00 0.00 36.46 3.56
160 161 6.899393 ACTTGGAACTTATTCATCTTGCAA 57.101 33.333 0.00 0.00 36.46 4.08
161 162 6.265196 ACAACTTGGAACTTATTCATCTTGCA 59.735 34.615 0.00 0.00 36.46 4.08
162 163 6.681777 ACAACTTGGAACTTATTCATCTTGC 58.318 36.000 0.00 0.00 36.46 4.01
163 164 9.003658 ACTACAACTTGGAACTTATTCATCTTG 57.996 33.333 0.00 0.00 36.46 3.02
169 170 9.043079 GCCTATACTACAACTTGGAACTTATTC 57.957 37.037 0.00 0.00 0.00 1.75
170 171 8.545472 TGCCTATACTACAACTTGGAACTTATT 58.455 33.333 0.00 0.00 0.00 1.40
171 172 7.985752 GTGCCTATACTACAACTTGGAACTTAT 59.014 37.037 0.00 0.00 0.00 1.73
172 173 7.325694 GTGCCTATACTACAACTTGGAACTTA 58.674 38.462 0.00 0.00 0.00 2.24
173 174 6.171213 GTGCCTATACTACAACTTGGAACTT 58.829 40.000 0.00 0.00 0.00 2.66
174 175 5.623824 CGTGCCTATACTACAACTTGGAACT 60.624 44.000 0.00 0.00 0.00 3.01
175 176 4.565564 CGTGCCTATACTACAACTTGGAAC 59.434 45.833 0.00 0.00 0.00 3.62
176 177 4.751060 CGTGCCTATACTACAACTTGGAA 58.249 43.478 0.00 0.00 0.00 3.53
177 178 3.429822 GCGTGCCTATACTACAACTTGGA 60.430 47.826 0.00 0.00 0.00 3.53
178 179 2.864343 GCGTGCCTATACTACAACTTGG 59.136 50.000 0.00 0.00 0.00 3.61
179 180 2.864343 GGCGTGCCTATACTACAACTTG 59.136 50.000 2.98 0.00 0.00 3.16
180 181 2.764572 AGGCGTGCCTATACTACAACTT 59.235 45.455 12.68 0.00 46.14 2.66
181 182 2.100916 CAGGCGTGCCTATACTACAACT 59.899 50.000 14.07 0.00 46.28 3.16
182 183 2.470821 CAGGCGTGCCTATACTACAAC 58.529 52.381 14.07 0.00 46.28 3.32
183 184 1.202486 GCAGGCGTGCCTATACTACAA 60.202 52.381 20.50 0.00 46.28 2.41
184 185 0.387929 GCAGGCGTGCCTATACTACA 59.612 55.000 20.50 0.00 46.28 2.74
185 186 3.196613 GCAGGCGTGCCTATACTAC 57.803 57.895 20.50 0.00 46.28 2.73
195 196 1.155889 TTTGTATGTGAGCAGGCGTG 58.844 50.000 1.01 1.01 0.00 5.34
196 197 1.535462 GTTTTGTATGTGAGCAGGCGT 59.465 47.619 0.00 0.00 0.00 5.68
197 198 1.535028 TGTTTTGTATGTGAGCAGGCG 59.465 47.619 0.00 0.00 0.00 5.52
198 199 2.293122 TGTGTTTTGTATGTGAGCAGGC 59.707 45.455 0.00 0.00 0.00 4.85
199 200 4.771590 ATGTGTTTTGTATGTGAGCAGG 57.228 40.909 0.00 0.00 0.00 4.85
200 201 6.845302 ACATATGTGTTTTGTATGTGAGCAG 58.155 36.000 7.78 0.00 37.58 4.24
201 202 6.816134 ACATATGTGTTTTGTATGTGAGCA 57.184 33.333 7.78 0.00 37.58 4.26
202 203 8.772306 CATACATATGTGTTTTGTATGTGAGC 57.228 34.615 18.81 0.00 44.01 4.26
210 211 9.787532 GAAATACTGCATACATATGTGTTTTGT 57.212 29.630 18.81 13.10 39.77 2.83
215 216 9.273016 GGTAAGAAATACTGCATACATATGTGT 57.727 33.333 18.81 9.13 37.23 3.72
216 217 9.494271 AGGTAAGAAATACTGCATACATATGTG 57.506 33.333 18.81 3.75 34.23 3.21
221 222 9.326413 GTACAAGGTAAGAAATACTGCATACAT 57.674 33.333 0.00 0.00 34.74 2.29
222 223 8.537016 AGTACAAGGTAAGAAATACTGCATACA 58.463 33.333 0.00 0.00 34.74 2.29
223 224 8.943909 AGTACAAGGTAAGAAATACTGCATAC 57.056 34.615 0.00 0.00 34.74 2.39
225 226 9.765795 GATAGTACAAGGTAAGAAATACTGCAT 57.234 33.333 0.00 0.00 34.74 3.96
226 227 8.755028 TGATAGTACAAGGTAAGAAATACTGCA 58.245 33.333 0.00 0.00 34.74 4.41
227 228 9.032420 GTGATAGTACAAGGTAAGAAATACTGC 57.968 37.037 0.00 0.00 34.74 4.40
346 349 5.579119 GTGATTGTATGTCCGTGTATGTGAA 59.421 40.000 0.00 0.00 0.00 3.18
405 409 3.741805 TCAGTATCTCAGACGTGTTCG 57.258 47.619 0.00 0.00 43.34 3.95
408 412 2.161808 CGGTTCAGTATCTCAGACGTGT 59.838 50.000 0.00 0.00 0.00 4.49
415 419 1.621317 TGTTGCCGGTTCAGTATCTCA 59.379 47.619 1.90 0.00 0.00 3.27
467 473 2.631062 AGACATGTTCCCGTCAACTACA 59.369 45.455 0.00 0.00 34.48 2.74
471 477 1.804748 GGAAGACATGTTCCCGTCAAC 59.195 52.381 0.00 0.00 40.31 3.18
477 483 3.140325 TCAGTTGGAAGACATGTTCCC 57.860 47.619 12.99 9.08 44.93 3.97
485 491 4.143094 GCTATGTTCGTTCAGTTGGAAGAC 60.143 45.833 0.00 0.00 35.82 3.01
488 494 3.071479 GGCTATGTTCGTTCAGTTGGAA 58.929 45.455 0.00 0.00 0.00 3.53
527 533 4.513692 CACTGGTGTTCGTATTTTTCTGGA 59.486 41.667 0.00 0.00 0.00 3.86
538 545 0.814010 GACTTGGCACTGGTGTTCGT 60.814 55.000 2.64 0.00 0.00 3.85
560 568 3.222603 CAACCCACTAGGCTTCAAGTTT 58.777 45.455 0.00 0.00 40.58 2.66
584 592 1.544691 GTCGAGTTTCCTAGTGCTGGA 59.455 52.381 0.00 0.00 0.00 3.86
587 595 1.926108 AGGTCGAGTTTCCTAGTGCT 58.074 50.000 0.00 0.00 31.66 4.40
588 596 3.863142 TTAGGTCGAGTTTCCTAGTGC 57.137 47.619 0.39 0.00 37.57 4.40
589 597 5.063564 GCATTTTAGGTCGAGTTTCCTAGTG 59.936 44.000 0.39 3.37 37.57 2.74
590 598 5.176592 GCATTTTAGGTCGAGTTTCCTAGT 58.823 41.667 0.39 0.00 37.57 2.57
591 599 4.267928 CGCATTTTAGGTCGAGTTTCCTAG 59.732 45.833 0.39 0.00 37.57 3.02
592 600 4.082081 TCGCATTTTAGGTCGAGTTTCCTA 60.082 41.667 0.00 0.00 35.51 2.94
593 601 3.000727 CGCATTTTAGGTCGAGTTTCCT 58.999 45.455 0.00 0.00 37.80 3.36
594 602 2.997986 TCGCATTTTAGGTCGAGTTTCC 59.002 45.455 0.00 0.00 0.00 3.13
595 603 4.859629 ATCGCATTTTAGGTCGAGTTTC 57.140 40.909 0.00 0.00 34.30 2.78
596 604 6.046593 TGATATCGCATTTTAGGTCGAGTTT 58.953 36.000 0.00 0.00 34.30 2.66
597 605 5.597806 TGATATCGCATTTTAGGTCGAGTT 58.402 37.500 0.00 0.00 34.30 3.01
598 606 5.196341 TGATATCGCATTTTAGGTCGAGT 57.804 39.130 0.00 0.00 34.30 4.18
599 607 5.119279 CCTTGATATCGCATTTTAGGTCGAG 59.881 44.000 0.00 0.00 34.30 4.04
600 608 4.988540 CCTTGATATCGCATTTTAGGTCGA 59.011 41.667 0.00 0.00 35.34 4.20
601 609 4.988540 TCCTTGATATCGCATTTTAGGTCG 59.011 41.667 0.00 0.00 0.00 4.79
602 610 5.179555 GGTCCTTGATATCGCATTTTAGGTC 59.820 44.000 0.00 0.00 0.00 3.85
603 611 5.063880 GGTCCTTGATATCGCATTTTAGGT 58.936 41.667 0.00 0.00 0.00 3.08
604 612 4.455877 GGGTCCTTGATATCGCATTTTAGG 59.544 45.833 0.00 0.00 0.00 2.69
605 613 4.455877 GGGGTCCTTGATATCGCATTTTAG 59.544 45.833 0.00 0.00 0.00 1.85
606 614 4.394729 GGGGTCCTTGATATCGCATTTTA 58.605 43.478 0.00 0.00 0.00 1.52
617 625 2.791655 GAGTTTTTCGGGGTCCTTGAT 58.208 47.619 0.00 0.00 0.00 2.57
637 645 1.722011 ATGGCCGTAGAGTGTTTTCG 58.278 50.000 0.00 0.00 0.00 3.46
647 655 4.020573 TGACCATCCTAAATATGGCCGTAG 60.021 45.833 11.11 0.00 46.63 3.51
648 656 3.904965 TGACCATCCTAAATATGGCCGTA 59.095 43.478 7.25 7.25 46.63 4.02
652 660 3.690460 CCCTGACCATCCTAAATATGGC 58.310 50.000 2.03 0.00 46.63 4.40
667 675 1.134367 GGCCTTAAAAATCGCCCTGAC 59.866 52.381 0.00 0.00 35.23 3.51
668 676 1.272203 TGGCCTTAAAAATCGCCCTGA 60.272 47.619 3.32 0.00 40.87 3.86
669 677 1.181786 TGGCCTTAAAAATCGCCCTG 58.818 50.000 3.32 0.00 40.87 4.45
673 681 3.793465 GCTCAGATGGCCTTAAAAATCGC 60.793 47.826 3.32 0.00 0.00 4.58
681 689 2.333069 AGCATAGCTCAGATGGCCTTA 58.667 47.619 3.32 0.00 30.62 2.69
737 745 7.179966 TGTAGATCTTTCTTCTGTACCTGGTA 58.820 38.462 0.00 1.49 33.17 3.25
738 746 6.017192 TGTAGATCTTTCTTCTGTACCTGGT 58.983 40.000 4.05 4.05 33.17 4.00
739 747 6.531503 TGTAGATCTTTCTTCTGTACCTGG 57.468 41.667 0.00 0.00 33.17 4.45
743 751 9.944663 CTCAGTATGTAGATCTTTCTTCTGTAC 57.055 37.037 0.00 0.00 37.40 2.90
748 756 6.699642 GGTGCTCAGTATGTAGATCTTTCTTC 59.300 42.308 0.00 0.00 37.40 2.87
757 765 1.470051 TGCGGTGCTCAGTATGTAGA 58.530 50.000 0.00 0.00 37.40 2.59
758 766 2.293677 TTGCGGTGCTCAGTATGTAG 57.706 50.000 0.00 0.00 37.40 2.74
844 852 9.077885 TCTCCAGTTCATTTTAGCACTAAAAAT 57.922 29.630 17.01 1.83 44.92 1.82
849 1340 6.595326 CACATCTCCAGTTCATTTTAGCACTA 59.405 38.462 0.00 0.00 0.00 2.74
854 1345 6.808008 ACACACATCTCCAGTTCATTTTAG 57.192 37.500 0.00 0.00 0.00 1.85
913 1405 3.133691 CCATCCAAGTCCATATGTGACG 58.866 50.000 14.70 5.85 37.80 4.35
957 1449 7.367285 TCGATTTTGTTTTAGGGATCAGTTTG 58.633 34.615 0.00 0.00 0.00 2.93
958 1450 7.519032 TCGATTTTGTTTTAGGGATCAGTTT 57.481 32.000 0.00 0.00 0.00 2.66
959 1451 7.148069 GGATCGATTTTGTTTTAGGGATCAGTT 60.148 37.037 0.00 0.00 32.70 3.16
960 1452 6.318900 GGATCGATTTTGTTTTAGGGATCAGT 59.681 38.462 0.00 0.00 32.70 3.41
974 1498 3.381590 GGGAAGAAAGGGGATCGATTTTG 59.618 47.826 0.00 0.00 0.00 2.44
1261 1786 1.741770 GCATCGGGAAGAAGCGTGT 60.742 57.895 0.00 0.00 33.70 4.49
1411 2002 1.680338 ACAAGCTTGAAGGTGTCCAC 58.320 50.000 32.50 0.00 0.00 4.02
1533 2132 4.900635 TTCTTGTTTGGAGAAGAGTTGC 57.099 40.909 0.00 0.00 36.63 4.17
1582 2184 1.813513 CCCATGATATCCTTCACGGC 58.186 55.000 0.00 0.00 27.53 5.68
1657 2274 1.001764 CCAAGGTGAGATGCAGGCA 60.002 57.895 0.00 0.00 0.00 4.75
1696 2322 1.007387 GCACGCCTTTGGGACTTTG 60.007 57.895 0.00 0.00 33.58 2.77
1717 2343 5.122239 TCGCCAGATAGATTTTGTTGTCAAG 59.878 40.000 0.00 0.00 34.88 3.02
1752 2381 5.817816 AGACGTCAAATCCAGGACAATAATC 59.182 40.000 19.50 0.00 33.66 1.75
1756 2385 3.703001 AGACGTCAAATCCAGGACAAT 57.297 42.857 19.50 0.00 33.66 2.71
1776 2405 5.296780 GGGCTGAATTGTCGATAAGATTGAA 59.703 40.000 0.02 0.00 0.00 2.69
1839 2468 1.146930 ATCATCAGCCCGCGACAAT 59.853 52.632 8.23 0.00 0.00 2.71
2403 3183 8.179615 GCCGCTTACTAGTATTGTTAAAAATGT 58.820 33.333 2.79 0.00 0.00 2.71
2405 3185 8.271312 TGCCGCTTACTAGTATTGTTAAAAAT 57.729 30.769 2.79 0.00 0.00 1.82
2510 3399 9.071276 ACAAGTGATTTCAAATCATCTTACACT 57.929 29.630 15.91 4.53 36.63 3.55
2511 3400 9.121517 CACAAGTGATTTCAAATCATCTTACAC 57.878 33.333 15.91 2.26 0.00 2.90
2541 3430 3.891049 AGACACCTTGCAATATTCCTCC 58.109 45.455 0.00 0.00 0.00 4.30
2620 3519 8.506437 CGCTTACATATCCATAACATCAATTGT 58.494 33.333 5.13 0.00 41.53 2.71
2624 3523 8.669946 TTTCGCTTACATATCCATAACATCAA 57.330 30.769 0.00 0.00 0.00 2.57
2705 3615 8.918202 TGGTAGCATATTTAAAGGGATACTTG 57.082 34.615 10.04 0.00 39.96 3.16
2710 3620 6.721208 CACCATGGTAGCATATTTAAAGGGAT 59.279 38.462 19.28 0.00 0.00 3.85
2719 3629 3.010584 GGGATCCACCATGGTAGCATATT 59.989 47.826 19.28 0.00 39.03 1.28
3062 4000 7.815549 TCAGTAATCTGCGATACAACAAGTAAA 59.184 33.333 0.00 0.00 41.10 2.01
3077 4015 4.034510 GCACCACATAGTTCAGTAATCTGC 59.965 45.833 0.00 0.00 41.10 4.26
3111 4049 4.690748 TCCATGCGAAAAACAACAAACAAA 59.309 33.333 0.00 0.00 0.00 2.83
3127 4065 3.109044 ACAGAATGAGAGATCCATGCG 57.891 47.619 0.00 0.00 39.69 4.73
3237 4178 5.753438 CAGATTAACAACGCTAGGCATCTTA 59.247 40.000 0.00 0.00 0.00 2.10
3250 4191 8.730680 AGGTCAACATGATAACAGATTAACAAC 58.269 33.333 0.00 0.00 0.00 3.32
3253 4194 8.723942 AGAGGTCAACATGATAACAGATTAAC 57.276 34.615 0.00 0.00 0.00 2.01
3312 4253 6.838401 AGAAATAGGAGATTCCAGGATTGT 57.162 37.500 0.00 0.00 39.61 2.71
3368 4309 7.150640 AGCTTGAGGTTCAAATTTGAGAAATC 58.849 34.615 19.64 16.00 35.73 2.17
3424 4365 5.738619 AAAAGAACATACCATTGGGGAAC 57.261 39.130 7.78 0.00 41.15 3.62
3425 4366 6.353404 GAAAAAGAACATACCATTGGGGAA 57.647 37.500 7.78 0.00 41.15 3.97


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

AutoCloner maintained by Alex Coulton.