Multiple sequence alignment - TraesCS3D01G226400

Loading Multiple Alignment...

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 TraesCS3D01G226400 chr3D 100.000 2249 0 0 1 2249 308263258 308265506 0.000000e+00 4154.0
1 TraesCS3D01G226400 chr3D 78.323 489 48 30 286 726 19332832 19332354 1.710000e-66 263.0
2 TraesCS3D01G226400 chr3D 82.468 154 14 5 1216 1365 16425344 16425200 3.030000e-24 122.0
3 TraesCS3D01G226400 chr3A 93.647 1401 44 15 862 2249 427759280 427760648 0.000000e+00 2052.0
4 TraesCS3D01G226400 chr3A 88.591 596 47 14 265 856 427758663 427759241 0.000000e+00 704.0
5 TraesCS3D01G226400 chr3B 95.560 901 22 6 862 1751 413042938 413042045 0.000000e+00 1426.0
6 TraesCS3D01G226400 chr3B 91.726 423 24 4 1829 2247 413041811 413041396 5.390000e-161 577.0
7 TraesCS3D01G226400 chr3B 83.524 613 55 27 265 856 413043564 413042977 4.250000e-147 531.0
8 TraesCS3D01G226400 chr3B 92.800 125 2 4 1681 1798 413042041 413041917 8.260000e-40 174.0
9 TraesCS3D01G226400 chr3B 82.707 133 19 4 275 405 62014441 62014571 5.080000e-22 115.0
10 TraesCS3D01G226400 chr6D 95.565 248 9 1 2 249 306677814 306678059 1.620000e-106 396.0
11 TraesCS3D01G226400 chr6D 95.565 248 9 1 1 248 361331025 361331270 1.620000e-106 396.0
12 TraesCS3D01G226400 chr2B 95.565 248 9 1 2 249 246580994 246581239 1.620000e-106 396.0
13 TraesCS3D01G226400 chr2B 84.962 133 17 3 275 405 351832047 351831916 5.040000e-27 132.0
14 TraesCS3D01G226400 chr2B 83.333 150 16 6 1216 1365 551273284 551273144 1.810000e-26 130.0
15 TraesCS3D01G226400 chr2B 77.612 134 19 10 364 491 670943096 670943224 1.110000e-08 71.3
16 TraesCS3D01G226400 chr1D 95.565 248 9 1 1 248 303376217 303376462 1.620000e-106 396.0
17 TraesCS3D01G226400 chr1D 88.742 151 8 4 2090 2238 471605935 471606078 2.300000e-40 176.0
18 TraesCS3D01G226400 chr7D 95.528 246 9 1 3 248 263485548 263485305 2.090000e-105 392.0
19 TraesCS3D01G226400 chr5D 95.181 249 10 1 1 249 107158353 107158599 2.090000e-105 392.0
20 TraesCS3D01G226400 chr5D 95.161 248 10 1 2 249 113259208 113258963 7.530000e-105 390.0
21 TraesCS3D01G226400 chr5D 77.512 418 49 24 275 652 560184619 560184207 2.260000e-50 209.0
22 TraesCS3D01G226400 chr5D 80.795 151 19 5 1216 1365 117738149 117738290 2.360000e-20 110.0
23 TraesCS3D01G226400 chr2D 95.181 249 10 2 1 249 317501738 317501984 2.090000e-105 392.0
24 TraesCS3D01G226400 chr2D 73.593 231 47 13 268 491 561900800 561901023 2.400000e-10 76.8
25 TraesCS3D01G226400 chr1B 95.547 247 8 2 1 247 171329044 171329287 2.090000e-105 392.0
26 TraesCS3D01G226400 chr1B 88.312 154 13 5 2090 2238 655778267 655778420 1.770000e-41 180.0
27 TraesCS3D01G226400 chr4B 78.116 361 38 25 275 600 103325866 103326220 8.200000e-45 191.0
28 TraesCS3D01G226400 chr4B 85.075 134 16 4 274 405 591488260 591488391 1.400000e-27 134.0
29 TraesCS3D01G226400 chr4A 77.839 361 35 29 278 600 675523665 675523312 4.930000e-42 182.0
30 TraesCS3D01G226400 chr4A 88.889 117 10 3 291 405 705228735 705228620 8.370000e-30 141.0
31 TraesCS3D01G226400 chr4A 82.667 150 17 2 1216 1365 697959557 697959417 8.430000e-25 124.0
32 TraesCS3D01G226400 chr1A 88.312 154 13 3 2090 2238 566006761 566006914 1.770000e-41 180.0
33 TraesCS3D01G226400 chr7A 84.000 150 14 5 1216 1365 343178961 343179100 3.900000e-28 135.0
34 TraesCS3D01G226400 chr5B 84.783 138 17 4 271 405 644472395 644472259 3.900000e-28 135.0
35 TraesCS3D01G226400 chr6B 83.444 151 14 5 1216 1365 10523181 10523041 1.810000e-26 130.0
36 TraesCS3D01G226400 chr6B 82.781 151 15 5 1216 1365 10457739 10457599 8.430000e-25 124.0
37 TraesCS3D01G226400 chr6B 82.119 151 16 5 1216 1365 10587411 10587271 3.920000e-23 119.0
38 TraesCS3D01G226400 chr6B 81.333 150 19 3 1216 1365 10394388 10394248 1.830000e-21 113.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G226400 chr3D 308263258 308265506 2248 False 4154 4154 100.0000 1 2249 1 chr3D.!!$F1 2248
1 TraesCS3D01G226400 chr3A 427758663 427760648 1985 False 1378 2052 91.1190 265 2249 2 chr3A.!!$F1 1984
2 TraesCS3D01G226400 chr3B 413041396 413043564 2168 True 677 1426 90.9025 265 2247 4 chr3B.!!$R1 1982

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
149 150 0.032912 TGGACCCGATGCACTAGGTA 60.033 55.0 3.48 0.0 31.1 3.08 F
247 248 0.177836 CACACACATAGATCCCGCCA 59.822 55.0 0.00 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1167 1252 0.521735 CGACGATGATGAGCGGGATA 59.478 55.0 0.0 0.0 34.48 2.59 R
2153 2403 0.320374 TCACCTCCGTTGATGTGGTC 59.680 55.0 0.0 0.0 37.62 4.02 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
22 23 4.954875 CTTCTATGTCTCCATCCTTGACC 58.045 47.826 0.00 0.00 32.29 4.02
23 24 4.271807 TCTATGTCTCCATCCTTGACCT 57.728 45.455 0.00 0.00 32.29 3.85
24 25 4.624913 TCTATGTCTCCATCCTTGACCTT 58.375 43.478 0.00 0.00 32.29 3.50
25 26 5.032846 TCTATGTCTCCATCCTTGACCTTT 58.967 41.667 0.00 0.00 32.29 3.11
26 27 4.664688 ATGTCTCCATCCTTGACCTTTT 57.335 40.909 0.00 0.00 0.00 2.27
27 28 4.021102 TGTCTCCATCCTTGACCTTTTC 57.979 45.455 0.00 0.00 0.00 2.29
28 29 3.394274 TGTCTCCATCCTTGACCTTTTCA 59.606 43.478 0.00 0.00 0.00 2.69
29 30 3.753797 GTCTCCATCCTTGACCTTTTCAC 59.246 47.826 0.00 0.00 32.26 3.18
30 31 2.744202 CTCCATCCTTGACCTTTTCACG 59.256 50.000 0.00 0.00 32.26 4.35
31 32 2.370519 TCCATCCTTGACCTTTTCACGA 59.629 45.455 0.00 0.00 32.26 4.35
32 33 3.146066 CCATCCTTGACCTTTTCACGAA 58.854 45.455 0.00 0.00 32.26 3.85
33 34 3.758554 CCATCCTTGACCTTTTCACGAAT 59.241 43.478 0.00 0.00 32.26 3.34
34 35 4.379813 CCATCCTTGACCTTTTCACGAATG 60.380 45.833 0.00 0.00 32.26 2.67
35 36 3.146066 TCCTTGACCTTTTCACGAATGG 58.854 45.455 0.00 0.00 38.27 3.16
36 37 3.146066 CCTTGACCTTTTCACGAATGGA 58.854 45.455 0.00 0.00 36.36 3.41
37 38 3.189287 CCTTGACCTTTTCACGAATGGAG 59.811 47.826 0.00 0.00 36.36 3.86
38 39 3.485463 TGACCTTTTCACGAATGGAGT 57.515 42.857 0.00 0.00 36.36 3.85
39 40 3.815809 TGACCTTTTCACGAATGGAGTT 58.184 40.909 0.00 0.00 36.36 3.01
40 41 3.563808 TGACCTTTTCACGAATGGAGTTG 59.436 43.478 0.00 0.00 36.36 3.16
41 42 3.813166 GACCTTTTCACGAATGGAGTTGA 59.187 43.478 0.00 0.00 36.36 3.18
42 43 4.204012 ACCTTTTCACGAATGGAGTTGAA 58.796 39.130 0.00 0.00 36.36 2.69
43 44 4.275936 ACCTTTTCACGAATGGAGTTGAAG 59.724 41.667 0.00 0.00 36.36 3.02
44 45 3.896648 TTTCACGAATGGAGTTGAAGC 57.103 42.857 0.00 0.00 0.00 3.86
45 46 1.428448 TCACGAATGGAGTTGAAGCG 58.572 50.000 0.00 0.00 0.00 4.68
46 47 1.148310 CACGAATGGAGTTGAAGCGT 58.852 50.000 0.00 0.00 0.00 5.07
47 48 1.126846 CACGAATGGAGTTGAAGCGTC 59.873 52.381 0.00 0.00 0.00 5.19
48 49 1.000955 ACGAATGGAGTTGAAGCGTCT 59.999 47.619 0.31 0.00 0.00 4.18
49 50 1.656095 CGAATGGAGTTGAAGCGTCTC 59.344 52.381 0.31 0.00 0.00 3.36
50 51 2.672478 CGAATGGAGTTGAAGCGTCTCT 60.672 50.000 0.31 0.00 0.00 3.10
51 52 3.330267 GAATGGAGTTGAAGCGTCTCTT 58.670 45.455 0.31 0.00 37.83 2.85
52 53 2.154854 TGGAGTTGAAGCGTCTCTTG 57.845 50.000 0.31 0.00 34.56 3.02
53 54 1.686587 TGGAGTTGAAGCGTCTCTTGA 59.313 47.619 0.31 0.00 34.56 3.02
54 55 2.300152 TGGAGTTGAAGCGTCTCTTGAT 59.700 45.455 0.31 0.00 34.56 2.57
55 56 2.670414 GGAGTTGAAGCGTCTCTTGATG 59.330 50.000 0.31 0.00 34.56 3.07
56 57 3.321497 GAGTTGAAGCGTCTCTTGATGT 58.679 45.455 0.31 0.00 34.56 3.06
57 58 3.062763 AGTTGAAGCGTCTCTTGATGTG 58.937 45.455 0.31 0.00 34.56 3.21
58 59 2.802816 GTTGAAGCGTCTCTTGATGTGT 59.197 45.455 0.31 0.00 34.56 3.72
59 60 3.111853 TGAAGCGTCTCTTGATGTGTT 57.888 42.857 0.31 0.00 34.56 3.32
60 61 3.466836 TGAAGCGTCTCTTGATGTGTTT 58.533 40.909 0.31 0.00 34.56 2.83
61 62 3.248363 TGAAGCGTCTCTTGATGTGTTTG 59.752 43.478 0.31 0.00 34.56 2.93
62 63 2.146342 AGCGTCTCTTGATGTGTTTGG 58.854 47.619 0.00 0.00 0.00 3.28
63 64 1.873591 GCGTCTCTTGATGTGTTTGGT 59.126 47.619 0.00 0.00 0.00 3.67
64 65 2.290641 GCGTCTCTTGATGTGTTTGGTT 59.709 45.455 0.00 0.00 0.00 3.67
65 66 3.607078 GCGTCTCTTGATGTGTTTGGTTC 60.607 47.826 0.00 0.00 0.00 3.62
66 67 3.809832 CGTCTCTTGATGTGTTTGGTTCT 59.190 43.478 0.00 0.00 0.00 3.01
67 68 4.084328 CGTCTCTTGATGTGTTTGGTTCTC 60.084 45.833 0.00 0.00 0.00 2.87
68 69 5.059833 GTCTCTTGATGTGTTTGGTTCTCT 58.940 41.667 0.00 0.00 0.00 3.10
69 70 5.529060 GTCTCTTGATGTGTTTGGTTCTCTT 59.471 40.000 0.00 0.00 0.00 2.85
70 71 5.528690 TCTCTTGATGTGTTTGGTTCTCTTG 59.471 40.000 0.00 0.00 0.00 3.02
71 72 5.192927 TCTTGATGTGTTTGGTTCTCTTGT 58.807 37.500 0.00 0.00 0.00 3.16
72 73 4.898829 TGATGTGTTTGGTTCTCTTGTG 57.101 40.909 0.00 0.00 0.00 3.33
73 74 4.522114 TGATGTGTTTGGTTCTCTTGTGA 58.478 39.130 0.00 0.00 0.00 3.58
74 75 4.946772 TGATGTGTTTGGTTCTCTTGTGAA 59.053 37.500 0.00 0.00 0.00 3.18
75 76 5.417266 TGATGTGTTTGGTTCTCTTGTGAAA 59.583 36.000 0.00 0.00 0.00 2.69
76 77 5.054390 TGTGTTTGGTTCTCTTGTGAAAC 57.946 39.130 0.00 0.00 34.47 2.78
77 78 4.082463 TGTGTTTGGTTCTCTTGTGAAACC 60.082 41.667 0.00 0.00 33.02 3.27
78 79 4.157840 GTGTTTGGTTCTCTTGTGAAACCT 59.842 41.667 5.23 0.00 33.02 3.50
79 80 4.157656 TGTTTGGTTCTCTTGTGAAACCTG 59.842 41.667 5.23 0.00 33.02 4.00
80 81 2.930950 TGGTTCTCTTGTGAAACCTGG 58.069 47.619 5.23 0.00 33.02 4.45
81 82 2.507886 TGGTTCTCTTGTGAAACCTGGA 59.492 45.455 0.00 0.00 33.02 3.86
82 83 3.138283 TGGTTCTCTTGTGAAACCTGGAT 59.862 43.478 0.00 0.00 33.02 3.41
83 84 4.145052 GGTTCTCTTGTGAAACCTGGATT 58.855 43.478 0.00 0.00 34.36 3.01
84 85 4.216472 GGTTCTCTTGTGAAACCTGGATTC 59.784 45.833 9.55 9.55 34.36 2.52
85 86 4.021102 TCTCTTGTGAAACCTGGATTCC 57.979 45.455 13.36 6.31 34.36 3.01
86 87 3.652869 TCTCTTGTGAAACCTGGATTCCT 59.347 43.478 13.36 0.00 34.36 3.36
87 88 4.104738 TCTCTTGTGAAACCTGGATTCCTT 59.895 41.667 13.36 0.00 34.36 3.36
88 89 4.398319 TCTTGTGAAACCTGGATTCCTTC 58.602 43.478 13.36 0.07 34.36 3.46
89 90 2.778299 TGTGAAACCTGGATTCCTTCG 58.222 47.619 13.36 0.00 34.36 3.79
90 91 1.468914 GTGAAACCTGGATTCCTTCGC 59.531 52.381 13.36 2.55 0.00 4.70
91 92 1.095600 GAAACCTGGATTCCTTCGCC 58.904 55.000 0.00 0.00 0.00 5.54
92 93 0.404040 AAACCTGGATTCCTTCGCCA 59.596 50.000 0.00 0.00 0.00 5.69
93 94 0.404040 AACCTGGATTCCTTCGCCAA 59.596 50.000 0.00 0.00 0.00 4.52
94 95 0.035056 ACCTGGATTCCTTCGCCAAG 60.035 55.000 0.00 0.00 0.00 3.61
101 102 4.895854 CCTTCGCCAAGGCAATTG 57.104 55.556 12.19 0.00 43.14 2.32
102 103 1.446618 CCTTCGCCAAGGCAATTGC 60.447 57.895 22.47 22.47 43.14 3.56
103 104 1.588082 CTTCGCCAAGGCAATTGCT 59.412 52.632 28.42 12.86 42.06 3.91
104 105 0.457337 CTTCGCCAAGGCAATTGCTC 60.457 55.000 28.42 18.62 42.06 4.26
105 106 1.876497 TTCGCCAAGGCAATTGCTCC 61.876 55.000 28.42 14.00 42.06 4.70
106 107 2.638354 CGCCAAGGCAATTGCTCCA 61.638 57.895 28.42 0.00 42.06 3.86
107 108 1.217244 GCCAAGGCAATTGCTCCAG 59.783 57.895 28.42 16.45 41.70 3.86
108 109 1.538687 GCCAAGGCAATTGCTCCAGT 61.539 55.000 28.42 8.03 41.70 4.00
109 110 0.245539 CCAAGGCAATTGCTCCAGTG 59.754 55.000 28.42 17.90 41.70 3.66
110 111 0.963962 CAAGGCAATTGCTCCAGTGT 59.036 50.000 28.42 5.01 41.70 3.55
111 112 1.342174 CAAGGCAATTGCTCCAGTGTT 59.658 47.619 28.42 9.14 41.70 3.32
112 113 0.963962 AGGCAATTGCTCCAGTGTTG 59.036 50.000 28.42 0.00 41.70 3.33
113 114 0.675633 GGCAATTGCTCCAGTGTTGT 59.324 50.000 28.42 0.00 41.70 3.32
114 115 1.336240 GGCAATTGCTCCAGTGTTGTC 60.336 52.381 28.42 4.84 41.70 3.18
115 116 1.337703 GCAATTGCTCCAGTGTTGTCA 59.662 47.619 23.21 0.00 38.21 3.58
116 117 2.859806 GCAATTGCTCCAGTGTTGTCAC 60.860 50.000 23.21 0.00 40.24 3.67
117 118 2.346766 ATTGCTCCAGTGTTGTCACA 57.653 45.000 1.36 0.00 46.01 3.58
118 119 2.121291 TTGCTCCAGTGTTGTCACAA 57.879 45.000 0.00 0.00 46.01 3.33
119 120 2.121291 TGCTCCAGTGTTGTCACAAA 57.879 45.000 0.00 0.00 46.01 2.83
120 121 2.441410 TGCTCCAGTGTTGTCACAAAA 58.559 42.857 0.00 0.00 46.01 2.44
121 122 2.423185 TGCTCCAGTGTTGTCACAAAAG 59.577 45.455 0.00 0.00 46.01 2.27
122 123 2.682856 GCTCCAGTGTTGTCACAAAAGA 59.317 45.455 0.00 0.00 46.01 2.52
123 124 3.316308 GCTCCAGTGTTGTCACAAAAGAT 59.684 43.478 0.00 0.00 46.01 2.40
124 125 4.202050 GCTCCAGTGTTGTCACAAAAGATT 60.202 41.667 0.00 0.00 46.01 2.40
125 126 5.679638 GCTCCAGTGTTGTCACAAAAGATTT 60.680 40.000 0.00 0.00 46.01 2.17
126 127 6.279513 TCCAGTGTTGTCACAAAAGATTTT 57.720 33.333 0.00 0.00 46.01 1.82
127 128 6.329496 TCCAGTGTTGTCACAAAAGATTTTC 58.671 36.000 0.00 0.00 46.01 2.29
128 129 6.071672 TCCAGTGTTGTCACAAAAGATTTTCA 60.072 34.615 0.00 0.00 46.01 2.69
129 130 6.757947 CCAGTGTTGTCACAAAAGATTTTCAT 59.242 34.615 0.00 0.00 46.01 2.57
130 131 7.278424 CCAGTGTTGTCACAAAAGATTTTCATT 59.722 33.333 0.00 0.00 46.01 2.57
131 132 8.111836 CAGTGTTGTCACAAAAGATTTTCATTG 58.888 33.333 0.00 0.00 46.01 2.82
132 133 7.278424 AGTGTTGTCACAAAAGATTTTCATTGG 59.722 33.333 0.00 0.00 46.01 3.16
133 134 7.277539 GTGTTGTCACAAAAGATTTTCATTGGA 59.722 33.333 0.00 0.00 43.37 3.53
134 135 7.277539 TGTTGTCACAAAAGATTTTCATTGGAC 59.722 33.333 0.00 0.00 0.00 4.02
135 136 6.279882 TGTCACAAAAGATTTTCATTGGACC 58.720 36.000 0.00 0.00 0.00 4.46
136 137 5.696270 GTCACAAAAGATTTTCATTGGACCC 59.304 40.000 0.00 0.00 0.00 4.46
137 138 4.685628 CACAAAAGATTTTCATTGGACCCG 59.314 41.667 0.00 0.00 0.00 5.28
138 139 4.586841 ACAAAAGATTTTCATTGGACCCGA 59.413 37.500 0.00 0.00 0.00 5.14
139 140 5.245977 ACAAAAGATTTTCATTGGACCCGAT 59.754 36.000 0.00 0.00 0.00 4.18
140 141 4.989279 AAGATTTTCATTGGACCCGATG 57.011 40.909 9.53 9.53 38.77 3.84
141 142 2.689983 AGATTTTCATTGGACCCGATGC 59.310 45.455 10.74 0.00 37.65 3.91
142 143 1.916506 TTTTCATTGGACCCGATGCA 58.083 45.000 10.74 0.00 37.65 3.96
143 144 1.173043 TTTCATTGGACCCGATGCAC 58.827 50.000 10.74 0.00 37.65 4.57
144 145 0.327924 TTCATTGGACCCGATGCACT 59.672 50.000 10.74 0.00 37.65 4.40
145 146 1.199615 TCATTGGACCCGATGCACTA 58.800 50.000 10.74 0.00 37.65 2.74
146 147 1.138859 TCATTGGACCCGATGCACTAG 59.861 52.381 10.74 0.00 37.65 2.57
147 148 0.469917 ATTGGACCCGATGCACTAGG 59.530 55.000 0.00 0.00 0.00 3.02
148 149 0.907704 TTGGACCCGATGCACTAGGT 60.908 55.000 3.13 3.13 34.57 3.08
149 150 0.032912 TGGACCCGATGCACTAGGTA 60.033 55.000 3.48 0.00 31.10 3.08
150 151 1.339097 GGACCCGATGCACTAGGTAT 58.661 55.000 3.48 0.00 31.10 2.73
151 152 1.692519 GGACCCGATGCACTAGGTATT 59.307 52.381 3.48 0.00 31.10 1.89
152 153 2.895404 GGACCCGATGCACTAGGTATTA 59.105 50.000 3.48 0.00 31.10 0.98
153 154 3.305881 GGACCCGATGCACTAGGTATTAC 60.306 52.174 3.48 0.00 31.10 1.89
154 155 3.302161 ACCCGATGCACTAGGTATTACA 58.698 45.455 1.62 0.00 0.00 2.41
155 156 3.069158 ACCCGATGCACTAGGTATTACAC 59.931 47.826 1.62 0.00 0.00 2.90
170 171 7.876936 GGTATTACACCTAGATCGGATATGA 57.123 40.000 0.00 0.00 44.79 2.15
171 172 8.289939 GGTATTACACCTAGATCGGATATGAA 57.710 38.462 0.00 0.00 44.79 2.57
172 173 8.189460 GGTATTACACCTAGATCGGATATGAAC 58.811 40.741 0.00 0.00 44.79 3.18
173 174 8.958506 GTATTACACCTAGATCGGATATGAACT 58.041 37.037 0.00 0.00 0.00 3.01
174 175 5.968528 ACACCTAGATCGGATATGAACTC 57.031 43.478 0.00 0.00 0.00 3.01
175 176 4.767928 ACACCTAGATCGGATATGAACTCC 59.232 45.833 0.00 0.00 0.00 3.85
176 177 5.013547 CACCTAGATCGGATATGAACTCCT 58.986 45.833 0.00 0.00 0.00 3.69
177 178 5.478679 CACCTAGATCGGATATGAACTCCTT 59.521 44.000 0.00 0.00 0.00 3.36
178 179 5.712917 ACCTAGATCGGATATGAACTCCTTC 59.287 44.000 0.00 0.00 0.00 3.46
179 180 5.712446 CCTAGATCGGATATGAACTCCTTCA 59.288 44.000 0.00 0.00 40.77 3.02
180 181 6.379703 CCTAGATCGGATATGAACTCCTTCAT 59.620 42.308 0.00 1.78 46.84 2.57
181 182 6.279513 AGATCGGATATGAACTCCTTCATC 57.720 41.667 0.00 0.00 42.54 2.92
182 183 4.873746 TCGGATATGAACTCCTTCATCC 57.126 45.455 0.00 0.00 42.54 3.51
183 184 4.223144 TCGGATATGAACTCCTTCATCCA 58.777 43.478 0.00 0.00 42.54 3.41
184 185 4.840680 TCGGATATGAACTCCTTCATCCAT 59.159 41.667 0.00 0.00 42.54 3.41
185 186 6.016555 TCGGATATGAACTCCTTCATCCATA 58.983 40.000 0.00 0.00 42.54 2.74
186 187 6.071334 TCGGATATGAACTCCTTCATCCATAC 60.071 42.308 0.00 0.00 42.54 2.39
187 188 6.071108 CGGATATGAACTCCTTCATCCATACT 60.071 42.308 0.00 0.00 42.54 2.12
188 189 7.327214 GGATATGAACTCCTTCATCCATACTC 58.673 42.308 0.00 0.00 42.54 2.59
189 190 5.559148 ATGAACTCCTTCATCCATACTCC 57.441 43.478 0.00 0.00 42.54 3.85
190 191 4.624913 TGAACTCCTTCATCCATACTCCT 58.375 43.478 0.00 0.00 31.00 3.69
191 192 5.032846 TGAACTCCTTCATCCATACTCCTT 58.967 41.667 0.00 0.00 31.00 3.36
192 193 5.129485 TGAACTCCTTCATCCATACTCCTTC 59.871 44.000 0.00 0.00 31.00 3.46
193 194 4.624913 ACTCCTTCATCCATACTCCTTCA 58.375 43.478 0.00 0.00 0.00 3.02
194 195 4.653341 ACTCCTTCATCCATACTCCTTCAG 59.347 45.833 0.00 0.00 0.00 3.02
195 196 3.969976 TCCTTCATCCATACTCCTTCAGG 59.030 47.826 0.00 0.00 0.00 3.86
196 197 3.713764 CCTTCATCCATACTCCTTCAGGT 59.286 47.826 0.00 0.00 36.34 4.00
197 198 4.444022 CCTTCATCCATACTCCTTCAGGTG 60.444 50.000 0.00 0.00 36.34 4.00
198 199 3.724478 TCATCCATACTCCTTCAGGTGT 58.276 45.455 5.88 5.88 43.53 4.16
199 200 4.104086 TCATCCATACTCCTTCAGGTGTT 58.896 43.478 5.90 0.00 41.60 3.32
200 201 3.981071 TCCATACTCCTTCAGGTGTTG 57.019 47.619 5.90 5.06 41.60 3.33
201 202 2.027192 TCCATACTCCTTCAGGTGTTGC 60.027 50.000 5.90 0.00 41.60 4.17
202 203 2.026822 CCATACTCCTTCAGGTGTTGCT 60.027 50.000 5.90 0.00 41.60 3.91
203 204 3.560025 CCATACTCCTTCAGGTGTTGCTT 60.560 47.826 5.90 0.00 41.60 3.91
204 205 2.736670 ACTCCTTCAGGTGTTGCTTT 57.263 45.000 0.00 0.00 38.65 3.51
205 206 2.576615 ACTCCTTCAGGTGTTGCTTTC 58.423 47.619 0.00 0.00 38.65 2.62
206 207 1.532868 CTCCTTCAGGTGTTGCTTTCG 59.467 52.381 0.00 0.00 36.34 3.46
207 208 1.140052 TCCTTCAGGTGTTGCTTTCGA 59.860 47.619 0.00 0.00 36.34 3.71
208 209 1.946768 CCTTCAGGTGTTGCTTTCGAA 59.053 47.619 0.00 0.00 0.00 3.71
209 210 2.031682 CCTTCAGGTGTTGCTTTCGAAG 60.032 50.000 0.00 0.00 0.00 3.79
223 224 4.677584 CTTTCGAAGCAGCTATGTACTCT 58.322 43.478 0.00 0.00 0.00 3.24
224 225 3.699779 TCGAAGCAGCTATGTACTCTG 57.300 47.619 0.00 0.00 0.00 3.35
229 230 3.170791 GCAGCTATGTACTCTGCTTCA 57.829 47.619 16.79 0.00 46.93 3.02
230 231 2.863137 GCAGCTATGTACTCTGCTTCAC 59.137 50.000 16.79 4.23 46.93 3.18
231 232 3.677148 GCAGCTATGTACTCTGCTTCACA 60.677 47.826 16.79 0.00 46.93 3.58
232 233 3.862267 CAGCTATGTACTCTGCTTCACAC 59.138 47.826 0.00 0.00 33.03 3.82
233 234 3.511540 AGCTATGTACTCTGCTTCACACA 59.488 43.478 0.00 0.00 30.96 3.72
234 235 3.614616 GCTATGTACTCTGCTTCACACAC 59.385 47.826 0.00 0.00 0.00 3.82
235 236 3.751479 ATGTACTCTGCTTCACACACA 57.249 42.857 0.00 0.00 0.00 3.72
236 237 3.751479 TGTACTCTGCTTCACACACAT 57.249 42.857 0.00 0.00 0.00 3.21
237 238 4.864704 TGTACTCTGCTTCACACACATA 57.135 40.909 0.00 0.00 0.00 2.29
238 239 4.809673 TGTACTCTGCTTCACACACATAG 58.190 43.478 0.00 0.00 0.00 2.23
239 240 4.522789 TGTACTCTGCTTCACACACATAGA 59.477 41.667 0.00 0.00 0.00 1.98
240 241 4.815533 ACTCTGCTTCACACACATAGAT 57.184 40.909 0.00 0.00 0.00 1.98
241 242 4.753233 ACTCTGCTTCACACACATAGATC 58.247 43.478 0.00 0.00 0.00 2.75
242 243 4.118410 CTCTGCTTCACACACATAGATCC 58.882 47.826 0.00 0.00 0.00 3.36
243 244 3.118629 TCTGCTTCACACACATAGATCCC 60.119 47.826 0.00 0.00 0.00 3.85
244 245 2.205074 GCTTCACACACATAGATCCCG 58.795 52.381 0.00 0.00 0.00 5.14
245 246 2.205074 CTTCACACACATAGATCCCGC 58.795 52.381 0.00 0.00 0.00 6.13
246 247 0.464036 TCACACACATAGATCCCGCC 59.536 55.000 0.00 0.00 0.00 6.13
247 248 0.177836 CACACACATAGATCCCGCCA 59.822 55.000 0.00 0.00 0.00 5.69
248 249 0.178068 ACACACATAGATCCCGCCAC 59.822 55.000 0.00 0.00 0.00 5.01
249 250 0.465705 CACACATAGATCCCGCCACT 59.534 55.000 0.00 0.00 0.00 4.00
250 251 1.134401 CACACATAGATCCCGCCACTT 60.134 52.381 0.00 0.00 0.00 3.16
251 252 1.139058 ACACATAGATCCCGCCACTTC 59.861 52.381 0.00 0.00 0.00 3.01
252 253 1.414181 CACATAGATCCCGCCACTTCT 59.586 52.381 0.00 0.00 0.00 2.85
253 254 1.689273 ACATAGATCCCGCCACTTCTC 59.311 52.381 0.00 0.00 0.00 2.87
254 255 1.688735 CATAGATCCCGCCACTTCTCA 59.311 52.381 0.00 0.00 0.00 3.27
255 256 1.860641 TAGATCCCGCCACTTCTCAA 58.139 50.000 0.00 0.00 0.00 3.02
256 257 0.539051 AGATCCCGCCACTTCTCAAG 59.461 55.000 0.00 0.00 0.00 3.02
257 258 0.462759 GATCCCGCCACTTCTCAAGG 60.463 60.000 0.00 0.00 0.00 3.61
258 259 0.909610 ATCCCGCCACTTCTCAAGGA 60.910 55.000 0.00 0.00 0.00 3.36
259 260 1.125093 TCCCGCCACTTCTCAAGGAA 61.125 55.000 0.00 0.00 0.00 3.36
260 261 0.955919 CCCGCCACTTCTCAAGGAAC 60.956 60.000 0.00 0.00 0.00 3.62
262 263 1.151668 CGCCACTTCTCAAGGAACTG 58.848 55.000 0.00 0.00 40.86 3.16
263 264 0.877743 GCCACTTCTCAAGGAACTGC 59.122 55.000 0.00 0.00 40.86 4.40
264 265 1.544314 GCCACTTCTCAAGGAACTGCT 60.544 52.381 0.00 0.00 40.86 4.24
265 266 2.856222 CCACTTCTCAAGGAACTGCTT 58.144 47.619 0.00 0.00 40.86 3.91
266 267 2.810852 CCACTTCTCAAGGAACTGCTTC 59.189 50.000 0.00 0.00 40.86 3.86
267 268 3.495806 CCACTTCTCAAGGAACTGCTTCT 60.496 47.826 0.00 0.00 40.86 2.85
268 269 4.262635 CCACTTCTCAAGGAACTGCTTCTA 60.263 45.833 0.00 0.00 40.86 2.10
269 270 4.928615 CACTTCTCAAGGAACTGCTTCTAG 59.071 45.833 0.00 0.00 40.86 2.43
270 271 4.835615 ACTTCTCAAGGAACTGCTTCTAGA 59.164 41.667 0.00 0.00 40.86 2.43
271 272 5.305644 ACTTCTCAAGGAACTGCTTCTAGAA 59.694 40.000 4.81 4.81 40.86 2.10
272 273 5.140747 TCTCAAGGAACTGCTTCTAGAAC 57.859 43.478 0.00 0.00 40.86 3.01
357 358 5.578727 TGAAACCACGAACATTTTTGGAAAG 59.421 36.000 0.00 0.00 33.02 2.62
361 362 3.735746 CACGAACATTTTTGGAAAGCTCC 59.264 43.478 0.00 0.00 42.81 4.70
405 406 9.358872 GTGAACAAATTTCAGAAAAAGAGAACT 57.641 29.630 0.00 0.00 0.00 3.01
406 407 9.927668 TGAACAAATTTCAGAAAAAGAGAACTT 57.072 25.926 0.00 0.00 38.05 2.66
671 695 0.552848 AAATCGGGATCCTGTGGCAT 59.447 50.000 20.32 3.53 0.00 4.40
728 772 1.071471 CTCGCACCTGTTCCCTGTT 59.929 57.895 0.00 0.00 0.00 3.16
737 781 2.032924 CCTGTTCCCTGTTCGTTTCAAC 59.967 50.000 0.00 0.00 0.00 3.18
775 819 8.697067 GCAGTTAGCGTAAAATAGAATATTCGA 58.303 33.333 9.78 5.24 0.00 3.71
856 900 2.941480 AGCCCAATAGCATTTGAGGAG 58.059 47.619 0.60 0.00 34.23 3.69
857 901 2.511218 AGCCCAATAGCATTTGAGGAGA 59.489 45.455 0.60 0.00 34.23 3.71
858 902 2.883386 GCCCAATAGCATTTGAGGAGAG 59.117 50.000 0.60 0.00 0.00 3.20
859 903 3.484407 CCCAATAGCATTTGAGGAGAGG 58.516 50.000 0.60 0.00 0.00 3.69
864 941 6.222389 CAATAGCATTTGAGGAGAGGTCTAG 58.778 44.000 0.00 0.00 0.00 2.43
1302 1387 8.707796 TCGATCCATCTCCTTTTAGTTACTAT 57.292 34.615 0.00 0.00 0.00 2.12
1303 1388 9.803507 TCGATCCATCTCCTTTTAGTTACTATA 57.196 33.333 0.00 0.00 0.00 1.31
1500 1585 7.730364 ACTATGTTGAACTTTCAGTGTTAGG 57.270 36.000 0.00 0.00 38.61 2.69
1506 1591 5.741011 TGAACTTTCAGTGTTAGGTGTCTT 58.259 37.500 0.00 0.00 32.50 3.01
1605 1690 3.192001 ACTGCTCATTATTGCTGTGTTGG 59.808 43.478 0.00 0.00 39.30 3.77
1612 1698 6.164876 TCATTATTGCTGTGTTGGGAATTTG 58.835 36.000 0.00 0.00 0.00 2.32
1617 1703 2.831526 GCTGTGTTGGGAATTTGGGTAT 59.168 45.455 0.00 0.00 0.00 2.73
1631 1717 1.707989 TGGGTATTCTTGGTGCCTGAA 59.292 47.619 0.00 0.00 0.00 3.02
1634 1720 2.689983 GGTATTCTTGGTGCCTGAATGG 59.310 50.000 14.98 0.00 39.35 3.16
1663 1749 3.808466 TCAGTCTACAATGCTAGCAGG 57.192 47.619 23.89 19.19 0.00 4.85
1744 1908 2.057137 TGAGGCCATGGCATTAGTTC 57.943 50.000 36.56 21.96 44.11 3.01
1860 2107 4.151689 GCACTTGCAAATAGTAAGACGTGA 59.848 41.667 11.05 0.00 41.88 4.35
1899 2146 5.917541 TGAAATTTTGTGACGAGGACTAC 57.082 39.130 0.00 0.00 0.00 2.73
1914 2161 6.072508 ACGAGGACTACATAGACAACGTTTTA 60.073 38.462 0.00 0.00 32.20 1.52
1915 2162 6.803320 CGAGGACTACATAGACAACGTTTTAA 59.197 38.462 0.00 0.00 0.00 1.52
1941 2188 7.820386 ACGTTGTATGGTGTCTAATTTCATACA 59.180 33.333 9.51 9.51 44.48 2.29
2077 2327 6.452242 TCTGTTTGTGTACATGTACTTCGAT 58.548 36.000 30.69 0.00 37.00 3.59
2153 2403 9.784531 ACAAATTACAGGTATCCATCTATTCTG 57.215 33.333 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.680812 TGAAAAGGTCAAGGATGGAGACATAGA 61.681 40.741 0.00 0.00 42.24 1.98
3 4 6.577039 TGAAAAGGTCAAGGATGGAGACATAG 60.577 42.308 0.00 0.00 42.24 2.23
4 5 5.250543 TGAAAAGGTCAAGGATGGAGACATA 59.749 40.000 0.00 0.00 42.24 2.29
5 6 4.043310 TGAAAAGGTCAAGGATGGAGACAT 59.957 41.667 0.00 0.00 44.03 3.06
6 7 3.394274 TGAAAAGGTCAAGGATGGAGACA 59.606 43.478 0.00 0.00 37.95 3.41
7 8 3.753797 GTGAAAAGGTCAAGGATGGAGAC 59.246 47.826 0.00 0.00 38.23 3.36
8 9 3.557054 CGTGAAAAGGTCAAGGATGGAGA 60.557 47.826 0.00 0.00 38.23 3.71
9 10 2.744202 CGTGAAAAGGTCAAGGATGGAG 59.256 50.000 0.00 0.00 38.23 3.86
10 11 2.370519 TCGTGAAAAGGTCAAGGATGGA 59.629 45.455 0.00 0.00 38.23 3.41
11 12 2.778299 TCGTGAAAAGGTCAAGGATGG 58.222 47.619 0.00 0.00 38.23 3.51
12 13 4.379813 CCATTCGTGAAAAGGTCAAGGATG 60.380 45.833 4.19 4.19 46.09 3.51
13 14 3.758554 CCATTCGTGAAAAGGTCAAGGAT 59.241 43.478 0.00 0.00 38.23 3.24
14 15 3.146066 CCATTCGTGAAAAGGTCAAGGA 58.854 45.455 0.00 0.00 38.23 3.36
15 16 3.146066 TCCATTCGTGAAAAGGTCAAGG 58.854 45.455 4.90 0.00 38.23 3.61
16 17 3.815401 ACTCCATTCGTGAAAAGGTCAAG 59.185 43.478 4.90 0.00 38.23 3.02
17 18 3.815809 ACTCCATTCGTGAAAAGGTCAA 58.184 40.909 4.90 0.00 38.23 3.18
18 19 3.485463 ACTCCATTCGTGAAAAGGTCA 57.515 42.857 4.90 0.00 0.00 4.02
19 20 3.813166 TCAACTCCATTCGTGAAAAGGTC 59.187 43.478 4.90 0.00 0.00 3.85
20 21 3.815809 TCAACTCCATTCGTGAAAAGGT 58.184 40.909 4.90 0.00 0.00 3.50
21 22 4.787598 CTTCAACTCCATTCGTGAAAAGG 58.212 43.478 0.00 0.00 0.00 3.11
22 23 4.222114 GCTTCAACTCCATTCGTGAAAAG 58.778 43.478 0.00 0.00 0.00 2.27
23 24 3.303725 CGCTTCAACTCCATTCGTGAAAA 60.304 43.478 0.00 0.00 0.00 2.29
24 25 2.223144 CGCTTCAACTCCATTCGTGAAA 59.777 45.455 0.00 0.00 0.00 2.69
25 26 1.798223 CGCTTCAACTCCATTCGTGAA 59.202 47.619 0.00 0.00 0.00 3.18
26 27 1.270094 ACGCTTCAACTCCATTCGTGA 60.270 47.619 0.00 0.00 0.00 4.35
27 28 1.126846 GACGCTTCAACTCCATTCGTG 59.873 52.381 0.00 0.00 0.00 4.35
28 29 1.000955 AGACGCTTCAACTCCATTCGT 59.999 47.619 0.00 0.00 0.00 3.85
29 30 1.656095 GAGACGCTTCAACTCCATTCG 59.344 52.381 0.00 0.00 0.00 3.34
30 31 2.966050 AGAGACGCTTCAACTCCATTC 58.034 47.619 0.00 0.00 0.00 2.67
31 32 3.070018 CAAGAGACGCTTCAACTCCATT 58.930 45.455 0.00 0.00 33.60 3.16
32 33 2.300152 TCAAGAGACGCTTCAACTCCAT 59.700 45.455 0.00 0.00 33.60 3.41
33 34 1.686587 TCAAGAGACGCTTCAACTCCA 59.313 47.619 0.00 0.00 33.60 3.86
34 35 2.440539 TCAAGAGACGCTTCAACTCC 57.559 50.000 0.00 0.00 33.60 3.85
35 36 3.122613 CACATCAAGAGACGCTTCAACTC 59.877 47.826 0.00 0.00 33.60 3.01
36 37 3.062763 CACATCAAGAGACGCTTCAACT 58.937 45.455 0.00 0.00 33.60 3.16
37 38 2.802816 ACACATCAAGAGACGCTTCAAC 59.197 45.455 0.00 0.00 33.60 3.18
38 39 3.111853 ACACATCAAGAGACGCTTCAA 57.888 42.857 0.00 0.00 33.60 2.69
39 40 2.820059 ACACATCAAGAGACGCTTCA 57.180 45.000 0.00 0.00 33.60 3.02
40 41 3.364366 CCAAACACATCAAGAGACGCTTC 60.364 47.826 0.00 0.00 33.60 3.86
41 42 2.549754 CCAAACACATCAAGAGACGCTT 59.450 45.455 0.00 0.00 37.29 4.68
42 43 2.146342 CCAAACACATCAAGAGACGCT 58.854 47.619 0.00 0.00 0.00 5.07
43 44 1.873591 ACCAAACACATCAAGAGACGC 59.126 47.619 0.00 0.00 0.00 5.19
44 45 3.809832 AGAACCAAACACATCAAGAGACG 59.190 43.478 0.00 0.00 0.00 4.18
45 46 5.059833 AGAGAACCAAACACATCAAGAGAC 58.940 41.667 0.00 0.00 0.00 3.36
46 47 5.296151 AGAGAACCAAACACATCAAGAGA 57.704 39.130 0.00 0.00 0.00 3.10
47 48 5.297776 ACAAGAGAACCAAACACATCAAGAG 59.702 40.000 0.00 0.00 0.00 2.85
48 49 5.066375 CACAAGAGAACCAAACACATCAAGA 59.934 40.000 0.00 0.00 0.00 3.02
49 50 5.066375 TCACAAGAGAACCAAACACATCAAG 59.934 40.000 0.00 0.00 0.00 3.02
50 51 4.946772 TCACAAGAGAACCAAACACATCAA 59.053 37.500 0.00 0.00 0.00 2.57
51 52 4.522114 TCACAAGAGAACCAAACACATCA 58.478 39.130 0.00 0.00 0.00 3.07
52 53 5.499139 TTCACAAGAGAACCAAACACATC 57.501 39.130 0.00 0.00 0.00 3.06
53 54 5.394115 GGTTTCACAAGAGAACCAAACACAT 60.394 40.000 0.00 0.00 0.00 3.21
54 55 4.082463 GGTTTCACAAGAGAACCAAACACA 60.082 41.667 0.00 0.00 0.00 3.72
55 56 4.157840 AGGTTTCACAAGAGAACCAAACAC 59.842 41.667 7.19 0.00 0.00 3.32
56 57 4.157656 CAGGTTTCACAAGAGAACCAAACA 59.842 41.667 7.19 0.00 0.00 2.83
57 58 4.440112 CCAGGTTTCACAAGAGAACCAAAC 60.440 45.833 7.19 0.00 0.00 2.93
58 59 3.699038 CCAGGTTTCACAAGAGAACCAAA 59.301 43.478 7.19 0.00 0.00 3.28
59 60 3.053991 TCCAGGTTTCACAAGAGAACCAA 60.054 43.478 7.19 0.00 0.00 3.67
60 61 2.507886 TCCAGGTTTCACAAGAGAACCA 59.492 45.455 7.19 0.00 0.00 3.67
61 62 3.208747 TCCAGGTTTCACAAGAGAACC 57.791 47.619 0.00 0.00 0.00 3.62
62 63 4.216472 GGAATCCAGGTTTCACAAGAGAAC 59.784 45.833 11.69 0.00 0.00 3.01
63 64 4.104738 AGGAATCCAGGTTTCACAAGAGAA 59.895 41.667 11.69 0.00 0.00 2.87
64 65 3.652869 AGGAATCCAGGTTTCACAAGAGA 59.347 43.478 11.69 0.00 0.00 3.10
65 66 4.026356 AGGAATCCAGGTTTCACAAGAG 57.974 45.455 11.69 0.00 0.00 2.85
66 67 4.398319 GAAGGAATCCAGGTTTCACAAGA 58.602 43.478 11.69 0.00 0.00 3.02
67 68 3.189287 CGAAGGAATCCAGGTTTCACAAG 59.811 47.826 11.69 0.00 0.00 3.16
68 69 3.146066 CGAAGGAATCCAGGTTTCACAA 58.854 45.455 11.69 0.00 0.00 3.33
69 70 2.778299 CGAAGGAATCCAGGTTTCACA 58.222 47.619 11.69 0.00 0.00 3.58
70 71 1.468914 GCGAAGGAATCCAGGTTTCAC 59.531 52.381 11.69 2.60 0.00 3.18
71 72 1.613255 GGCGAAGGAATCCAGGTTTCA 60.613 52.381 11.69 0.00 0.00 2.69
72 73 1.095600 GGCGAAGGAATCCAGGTTTC 58.904 55.000 0.61 1.89 0.00 2.78
73 74 0.404040 TGGCGAAGGAATCCAGGTTT 59.596 50.000 0.61 0.00 0.00 3.27
74 75 0.404040 TTGGCGAAGGAATCCAGGTT 59.596 50.000 0.61 0.00 0.00 3.50
75 76 0.035056 CTTGGCGAAGGAATCCAGGT 60.035 55.000 0.61 0.00 0.00 4.00
76 77 2.785868 CTTGGCGAAGGAATCCAGG 58.214 57.895 0.61 0.00 0.00 4.45
85 86 0.457337 GAGCAATTGCCTTGGCGAAG 60.457 55.000 26.45 0.74 43.38 3.79
86 87 1.586028 GAGCAATTGCCTTGGCGAA 59.414 52.632 26.45 2.70 43.38 4.70
87 88 2.342650 GGAGCAATTGCCTTGGCGA 61.343 57.895 26.45 3.80 43.38 5.54
88 89 2.182537 GGAGCAATTGCCTTGGCG 59.817 61.111 26.45 0.00 43.38 5.69
89 90 1.217244 CTGGAGCAATTGCCTTGGC 59.783 57.895 26.45 10.94 43.38 4.52
90 91 0.245539 CACTGGAGCAATTGCCTTGG 59.754 55.000 26.45 16.32 43.38 3.61
91 92 0.963962 ACACTGGAGCAATTGCCTTG 59.036 50.000 26.45 17.37 43.38 3.61
92 93 1.342174 CAACACTGGAGCAATTGCCTT 59.658 47.619 26.45 9.54 43.38 4.35
93 94 0.963962 CAACACTGGAGCAATTGCCT 59.036 50.000 26.45 13.95 43.38 4.75
94 95 0.675633 ACAACACTGGAGCAATTGCC 59.324 50.000 26.45 17.19 43.38 4.52
95 96 1.337703 TGACAACACTGGAGCAATTGC 59.662 47.619 23.05 23.05 42.49 3.56
96 97 2.358582 TGTGACAACACTGGAGCAATTG 59.641 45.455 0.00 0.00 46.07 2.32
97 98 2.653726 TGTGACAACACTGGAGCAATT 58.346 42.857 0.00 0.00 46.07 2.32
98 99 2.346766 TGTGACAACACTGGAGCAAT 57.653 45.000 0.00 0.00 46.07 3.56
99 100 2.121291 TTGTGACAACACTGGAGCAA 57.879 45.000 0.00 0.00 46.07 3.91
100 101 2.121291 TTTGTGACAACACTGGAGCA 57.879 45.000 0.00 0.00 46.07 4.26
101 102 2.682856 TCTTTTGTGACAACACTGGAGC 59.317 45.455 0.00 0.00 46.07 4.70
102 103 5.505173 AATCTTTTGTGACAACACTGGAG 57.495 39.130 0.00 0.00 46.07 3.86
103 104 5.913137 AAATCTTTTGTGACAACACTGGA 57.087 34.783 0.00 0.00 46.07 3.86
104 105 6.098679 TGAAAATCTTTTGTGACAACACTGG 58.901 36.000 0.00 0.00 46.07 4.00
105 106 7.760131 ATGAAAATCTTTTGTGACAACACTG 57.240 32.000 0.00 0.00 46.07 3.66
106 107 7.278424 CCAATGAAAATCTTTTGTGACAACACT 59.722 33.333 0.00 0.00 46.07 3.55
107 108 7.277539 TCCAATGAAAATCTTTTGTGACAACAC 59.722 33.333 0.00 0.00 46.09 3.32
108 109 7.277539 GTCCAATGAAAATCTTTTGTGACAACA 59.722 33.333 0.00 0.00 0.00 3.33
109 110 7.254421 GGTCCAATGAAAATCTTTTGTGACAAC 60.254 37.037 0.00 0.00 0.00 3.32
110 111 6.760770 GGTCCAATGAAAATCTTTTGTGACAA 59.239 34.615 0.00 0.00 0.00 3.18
111 112 6.279882 GGTCCAATGAAAATCTTTTGTGACA 58.720 36.000 0.00 0.00 0.00 3.58
112 113 5.696270 GGGTCCAATGAAAATCTTTTGTGAC 59.304 40.000 0.00 0.00 0.00 3.67
113 114 5.508825 CGGGTCCAATGAAAATCTTTTGTGA 60.509 40.000 0.00 0.00 0.00 3.58
114 115 4.685628 CGGGTCCAATGAAAATCTTTTGTG 59.314 41.667 0.00 0.00 0.00 3.33
115 116 4.586841 TCGGGTCCAATGAAAATCTTTTGT 59.413 37.500 0.00 0.00 0.00 2.83
116 117 5.132897 TCGGGTCCAATGAAAATCTTTTG 57.867 39.130 0.00 0.00 0.00 2.44
117 118 5.723295 CATCGGGTCCAATGAAAATCTTTT 58.277 37.500 0.00 0.00 0.00 2.27
118 119 4.381932 GCATCGGGTCCAATGAAAATCTTT 60.382 41.667 7.49 0.00 0.00 2.52
119 120 3.131046 GCATCGGGTCCAATGAAAATCTT 59.869 43.478 7.49 0.00 0.00 2.40
120 121 2.689983 GCATCGGGTCCAATGAAAATCT 59.310 45.455 7.49 0.00 0.00 2.40
121 122 2.426738 TGCATCGGGTCCAATGAAAATC 59.573 45.455 7.49 0.00 0.00 2.17
122 123 2.166254 GTGCATCGGGTCCAATGAAAAT 59.834 45.455 7.49 0.00 0.00 1.82
123 124 1.543802 GTGCATCGGGTCCAATGAAAA 59.456 47.619 7.49 0.00 0.00 2.29
124 125 1.173043 GTGCATCGGGTCCAATGAAA 58.827 50.000 7.49 0.00 0.00 2.69
125 126 0.327924 AGTGCATCGGGTCCAATGAA 59.672 50.000 7.49 0.00 0.00 2.57
126 127 1.138859 CTAGTGCATCGGGTCCAATGA 59.861 52.381 7.49 0.00 0.00 2.57
127 128 1.586422 CTAGTGCATCGGGTCCAATG 58.414 55.000 0.00 0.00 0.00 2.82
128 129 0.469917 CCTAGTGCATCGGGTCCAAT 59.530 55.000 0.00 0.00 0.00 3.16
129 130 0.907704 ACCTAGTGCATCGGGTCCAA 60.908 55.000 0.00 0.00 0.00 3.53
130 131 0.032912 TACCTAGTGCATCGGGTCCA 60.033 55.000 10.03 0.00 33.74 4.02
131 132 1.339097 ATACCTAGTGCATCGGGTCC 58.661 55.000 10.03 0.00 33.74 4.46
132 133 3.319972 TGTAATACCTAGTGCATCGGGTC 59.680 47.826 10.03 0.00 33.74 4.46
133 134 3.069158 GTGTAATACCTAGTGCATCGGGT 59.931 47.826 11.18 11.18 36.02 5.28
134 135 3.554337 GGTGTAATACCTAGTGCATCGGG 60.554 52.174 0.00 0.00 46.51 5.14
135 136 3.650139 GGTGTAATACCTAGTGCATCGG 58.350 50.000 0.00 0.00 46.51 4.18
147 148 8.958506 AGTTCATATCCGATCTAGGTGTAATAC 58.041 37.037 0.00 0.00 0.00 1.89
148 149 9.175312 GAGTTCATATCCGATCTAGGTGTAATA 57.825 37.037 0.00 0.00 0.00 0.98
149 150 7.122948 GGAGTTCATATCCGATCTAGGTGTAAT 59.877 40.741 0.00 0.00 0.00 1.89
150 151 6.433404 GGAGTTCATATCCGATCTAGGTGTAA 59.567 42.308 0.00 0.00 0.00 2.41
151 152 5.944599 GGAGTTCATATCCGATCTAGGTGTA 59.055 44.000 0.00 0.00 0.00 2.90
152 153 4.767928 GGAGTTCATATCCGATCTAGGTGT 59.232 45.833 0.00 0.00 0.00 4.16
153 154 5.013547 AGGAGTTCATATCCGATCTAGGTG 58.986 45.833 0.00 0.00 42.02 4.00
154 155 5.263872 AGGAGTTCATATCCGATCTAGGT 57.736 43.478 0.00 0.00 42.02 3.08
155 156 5.712446 TGAAGGAGTTCATATCCGATCTAGG 59.288 44.000 0.00 0.00 42.02 3.02
156 157 6.825944 TGAAGGAGTTCATATCCGATCTAG 57.174 41.667 0.00 0.00 42.02 2.43
168 169 4.624913 AGGAGTATGGATGAAGGAGTTCA 58.375 43.478 0.00 0.00 46.81 3.18
169 170 5.129485 TGAAGGAGTATGGATGAAGGAGTTC 59.871 44.000 0.00 0.00 0.00 3.01
170 171 5.032846 TGAAGGAGTATGGATGAAGGAGTT 58.967 41.667 0.00 0.00 0.00 3.01
171 172 4.624913 TGAAGGAGTATGGATGAAGGAGT 58.375 43.478 0.00 0.00 0.00 3.85
172 173 4.040217 CCTGAAGGAGTATGGATGAAGGAG 59.960 50.000 0.00 0.00 37.39 3.69
173 174 3.969976 CCTGAAGGAGTATGGATGAAGGA 59.030 47.826 0.00 0.00 37.39 3.36
174 175 3.713764 ACCTGAAGGAGTATGGATGAAGG 59.286 47.826 2.62 0.00 38.94 3.46
175 176 4.163078 ACACCTGAAGGAGTATGGATGAAG 59.837 45.833 2.62 0.00 37.24 3.02
176 177 4.104086 ACACCTGAAGGAGTATGGATGAA 58.896 43.478 2.62 0.00 37.24 2.57
177 178 3.724478 ACACCTGAAGGAGTATGGATGA 58.276 45.455 2.62 0.00 37.24 2.92
178 179 4.194640 CAACACCTGAAGGAGTATGGATG 58.805 47.826 2.62 0.00 38.05 3.51
179 180 3.370953 GCAACACCTGAAGGAGTATGGAT 60.371 47.826 2.62 0.00 38.05 3.41
180 181 2.027192 GCAACACCTGAAGGAGTATGGA 60.027 50.000 2.62 0.00 38.05 3.41
181 182 2.026822 AGCAACACCTGAAGGAGTATGG 60.027 50.000 2.62 0.00 38.05 2.74
182 183 3.340814 AGCAACACCTGAAGGAGTATG 57.659 47.619 2.62 4.47 38.05 2.39
183 184 4.327680 GAAAGCAACACCTGAAGGAGTAT 58.672 43.478 2.62 0.00 38.05 2.12
184 185 3.740115 GAAAGCAACACCTGAAGGAGTA 58.260 45.455 2.62 0.00 38.05 2.59
185 186 2.576615 GAAAGCAACACCTGAAGGAGT 58.423 47.619 2.62 0.00 40.79 3.85
186 187 1.532868 CGAAAGCAACACCTGAAGGAG 59.467 52.381 2.62 0.00 38.94 3.69
187 188 1.140052 TCGAAAGCAACACCTGAAGGA 59.860 47.619 2.62 0.00 38.94 3.36
188 189 1.593196 TCGAAAGCAACACCTGAAGG 58.407 50.000 0.00 0.00 42.17 3.46
189 190 3.259207 CTTCGAAAGCAACACCTGAAG 57.741 47.619 0.00 0.00 0.00 3.02
201 202 4.502282 CAGAGTACATAGCTGCTTCGAAAG 59.498 45.833 7.79 0.00 0.00 2.62
202 203 4.424626 CAGAGTACATAGCTGCTTCGAAA 58.575 43.478 7.79 0.00 0.00 3.46
203 204 4.033990 CAGAGTACATAGCTGCTTCGAA 57.966 45.455 7.79 0.00 0.00 3.71
204 205 3.699779 CAGAGTACATAGCTGCTTCGA 57.300 47.619 7.79 0.00 0.00 3.71
210 211 3.862267 GTGTGAAGCAGAGTACATAGCTG 59.138 47.826 0.00 4.24 37.41 4.24
211 212 3.511540 TGTGTGAAGCAGAGTACATAGCT 59.488 43.478 0.00 0.00 39.37 3.32
212 213 3.614616 GTGTGTGAAGCAGAGTACATAGC 59.385 47.826 0.00 0.00 0.00 2.97
213 214 4.809673 TGTGTGTGAAGCAGAGTACATAG 58.190 43.478 0.00 0.00 0.00 2.23
214 215 4.864704 TGTGTGTGAAGCAGAGTACATA 57.135 40.909 0.00 0.00 0.00 2.29
215 216 3.751479 TGTGTGTGAAGCAGAGTACAT 57.249 42.857 0.00 0.00 0.00 2.29
216 217 3.751479 ATGTGTGTGAAGCAGAGTACA 57.249 42.857 0.00 0.00 0.00 2.90
217 218 5.060662 TCTATGTGTGTGAAGCAGAGTAC 57.939 43.478 0.00 0.00 0.00 2.73
218 219 5.163509 GGATCTATGTGTGTGAAGCAGAGTA 60.164 44.000 0.00 0.00 0.00 2.59
219 220 4.382470 GGATCTATGTGTGTGAAGCAGAGT 60.382 45.833 0.00 0.00 0.00 3.24
220 221 4.118410 GGATCTATGTGTGTGAAGCAGAG 58.882 47.826 0.00 0.00 0.00 3.35
221 222 3.118629 GGGATCTATGTGTGTGAAGCAGA 60.119 47.826 0.00 0.00 0.00 4.26
222 223 3.201290 GGGATCTATGTGTGTGAAGCAG 58.799 50.000 0.00 0.00 0.00 4.24
223 224 2.418609 CGGGATCTATGTGTGTGAAGCA 60.419 50.000 0.00 0.00 0.00 3.91
224 225 2.205074 CGGGATCTATGTGTGTGAAGC 58.795 52.381 0.00 0.00 0.00 3.86
225 226 2.205074 GCGGGATCTATGTGTGTGAAG 58.795 52.381 0.00 0.00 0.00 3.02
226 227 1.134521 GGCGGGATCTATGTGTGTGAA 60.135 52.381 0.00 0.00 0.00 3.18
227 228 0.464036 GGCGGGATCTATGTGTGTGA 59.536 55.000 0.00 0.00 0.00 3.58
228 229 0.177836 TGGCGGGATCTATGTGTGTG 59.822 55.000 0.00 0.00 0.00 3.82
229 230 0.178068 GTGGCGGGATCTATGTGTGT 59.822 55.000 0.00 0.00 0.00 3.72
230 231 0.465705 AGTGGCGGGATCTATGTGTG 59.534 55.000 0.00 0.00 0.00 3.82
231 232 1.139058 GAAGTGGCGGGATCTATGTGT 59.861 52.381 0.00 0.00 0.00 3.72
232 233 1.414181 AGAAGTGGCGGGATCTATGTG 59.586 52.381 0.00 0.00 0.00 3.21
233 234 1.689273 GAGAAGTGGCGGGATCTATGT 59.311 52.381 0.00 0.00 0.00 2.29
234 235 1.688735 TGAGAAGTGGCGGGATCTATG 59.311 52.381 0.00 0.00 0.00 2.23
235 236 2.088104 TGAGAAGTGGCGGGATCTAT 57.912 50.000 0.00 0.00 0.00 1.98
236 237 1.757118 CTTGAGAAGTGGCGGGATCTA 59.243 52.381 0.00 0.00 0.00 1.98
237 238 0.539051 CTTGAGAAGTGGCGGGATCT 59.461 55.000 0.00 0.00 0.00 2.75
238 239 0.462759 CCTTGAGAAGTGGCGGGATC 60.463 60.000 0.00 0.00 0.00 3.36
239 240 0.909610 TCCTTGAGAAGTGGCGGGAT 60.910 55.000 0.00 0.00 0.00 3.85
240 241 1.125093 TTCCTTGAGAAGTGGCGGGA 61.125 55.000 0.00 0.00 0.00 5.14
241 242 0.955919 GTTCCTTGAGAAGTGGCGGG 60.956 60.000 0.00 0.00 34.29 6.13
242 243 0.035458 AGTTCCTTGAGAAGTGGCGG 59.965 55.000 0.00 0.00 36.74 6.13
243 244 3.614399 AGTTCCTTGAGAAGTGGCG 57.386 52.632 0.00 0.00 36.74 5.69
247 248 4.835615 TCTAGAAGCAGTTCCTTGAGAAGT 59.164 41.667 0.00 0.00 38.77 3.01
248 249 5.398603 TCTAGAAGCAGTTCCTTGAGAAG 57.601 43.478 0.00 0.00 34.29 2.85
249 250 5.305644 AGTTCTAGAAGCAGTTCCTTGAGAA 59.694 40.000 5.12 0.00 32.48 2.87
250 251 4.835615 AGTTCTAGAAGCAGTTCCTTGAGA 59.164 41.667 5.12 0.00 32.48 3.27
251 252 5.146010 AGTTCTAGAAGCAGTTCCTTGAG 57.854 43.478 5.12 0.00 32.48 3.02
252 253 5.552870 AAGTTCTAGAAGCAGTTCCTTGA 57.447 39.130 5.12 0.00 32.48 3.02
253 254 6.625873 AAAAGTTCTAGAAGCAGTTCCTTG 57.374 37.500 5.12 0.00 32.48 3.61
330 331 5.932303 TCCAAAAATGTTCGTGGTTTCAAAA 59.068 32.000 0.00 0.00 32.68 2.44
357 358 8.309163 TCACAAATTCAAAATATGTTTGGAGC 57.691 30.769 9.18 0.00 32.23 4.70
604 628 5.826601 TTTTTGGCTTTTCACATTTTCCC 57.173 34.783 0.00 0.00 0.00 3.97
628 652 0.038618 CCCAAGGCGGTTTTTACTGC 60.039 55.000 0.52 0.52 41.06 4.40
655 679 2.745308 CCATGCCACAGGATCCCGA 61.745 63.158 8.55 0.00 0.00 5.14
737 781 2.560896 GCTAACTGCGACAAACTTTCG 58.439 47.619 0.00 0.00 39.56 3.46
775 819 2.048023 CGCTGGGCATTGTGGACAT 61.048 57.895 0.00 0.00 0.00 3.06
802 846 2.928801 ATTGGGCCAAACTTTCCAAC 57.071 45.000 24.97 0.00 41.38 3.77
856 900 1.544691 TCTCGTGTTTGGCTAGACCTC 59.455 52.381 0.00 0.00 40.22 3.85
857 901 1.629043 TCTCGTGTTTGGCTAGACCT 58.371 50.000 0.00 0.00 40.22 3.85
858 902 2.338500 CTTCTCGTGTTTGGCTAGACC 58.662 52.381 0.00 0.00 39.84 3.85
859 903 2.029290 TCCTTCTCGTGTTTGGCTAGAC 60.029 50.000 0.00 0.00 0.00 2.59
864 941 0.868406 CAGTCCTTCTCGTGTTTGGC 59.132 55.000 0.00 0.00 0.00 4.52
1167 1252 0.521735 CGACGATGATGAGCGGGATA 59.478 55.000 0.00 0.00 34.48 2.59
1500 1585 5.106908 GGCAGAGAAATACAACTCAAGACAC 60.107 44.000 0.00 0.00 35.83 3.67
1506 1591 4.890158 TCAGGCAGAGAAATACAACTCA 57.110 40.909 0.00 0.00 35.83 3.41
1605 1690 3.118775 GGCACCAAGAATACCCAAATTCC 60.119 47.826 0.00 0.00 36.68 3.01
1612 1698 2.507407 TTCAGGCACCAAGAATACCC 57.493 50.000 0.00 0.00 0.00 3.69
1617 1703 1.144708 TGACCATTCAGGCACCAAGAA 59.855 47.619 0.00 0.00 43.14 2.52
1631 1717 6.039047 GCATTGTAGACTGAATGAATGACCAT 59.961 38.462 11.39 0.00 32.24 3.55
1634 1720 6.674694 AGCATTGTAGACTGAATGAATGAC 57.325 37.500 11.39 0.00 32.24 3.06
1744 1908 3.615099 GTGTCCCAACAACACAACG 57.385 52.632 1.72 0.00 45.05 4.10
1860 2107 7.903995 AAATTTCAATGTGGCAATCGTTAAT 57.096 28.000 0.00 0.00 0.00 1.40
1877 2124 5.361427 TGTAGTCCTCGTCACAAAATTTCA 58.639 37.500 0.00 0.00 0.00 2.69
1914 2161 7.681939 ATGAAATTAGACACCATACAACGTT 57.318 32.000 0.00 0.00 0.00 3.99
1915 2162 7.820386 TGTATGAAATTAGACACCATACAACGT 59.180 33.333 0.00 0.00 43.49 3.99
2077 2327 9.037737 GTATATTCGACTTGTATAAGTTGGCAA 57.962 33.333 16.96 0.00 46.79 4.52
2153 2403 0.320374 TCACCTCCGTTGATGTGGTC 59.680 55.000 0.00 0.00 37.62 4.02


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

AutoCloner maintained by Alex Coulton.