Multiple sequence alignment - TraesCS1A01G275700

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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 TraesCS1A01G275700 chr1A 100.000 2405 0 0 1 2405 470299495 470301899 0.000000e+00 4442.0
1 TraesCS1A01G275700 chr1D 96.480 2074 37 12 350 2405 371185701 371187756 0.000000e+00 3393.0
2 TraesCS1A01G275700 chr1B 94.676 2085 47 23 350 2405 495094257 495096306 0.000000e+00 3177.0
3 TraesCS1A01G275700 chr6D 85.039 381 28 10 1 353 69790791 69791170 6.320000e-96 361.0
4 TraesCS1A01G275700 chr6D 84.777 381 29 10 1 353 69752404 69752783 2.940000e-94 355.0
5 TraesCS1A01G275700 chr6D 84.777 381 29 10 1 353 69827231 69827610 2.940000e-94 355.0
6 TraesCS1A01G275700 chr5A 85.039 381 27 14 1 353 639190697 639190319 6.320000e-96 361.0
7 TraesCS1A01G275700 chr6B 91.770 243 19 1 1 242 144756198 144756440 1.070000e-88 337.0
8 TraesCS1A01G275700 chr3D 91.880 234 15 3 1 234 405557215 405557444 8.290000e-85 324.0
9 TraesCS1A01G275700 chr3D 77.285 361 54 19 997 1340 481711078 481711427 1.140000e-43 187.0
10 TraesCS1A01G275700 chr5D 90.871 241 21 1 1 241 377301338 377301577 2.980000e-84 322.0
11 TraesCS1A01G275700 chr5B 90.833 240 18 3 1 240 523447579 523447344 3.860000e-83 318.0
12 TraesCS1A01G275700 chr3A 89.712 243 20 4 1 242 654196471 654196709 3.000000e-79 305.0
13 TraesCS1A01G275700 chr3A 76.243 362 59 18 997 1340 624858891 624859243 1.480000e-37 167.0
14 TraesCS1A01G275700 chr3B 76.986 365 54 20 997 1340 643266203 643266558 5.280000e-42 182.0
15 TraesCS1A01G275700 chr2B 88.000 50 6 0 239 288 691811886 691811837 2.580000e-05 60.2


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 TraesCS1A01G275700 chr1A 470299495 470301899 2404 False 4442 4442 100.000 1 2405 1 chr1A.!!$F1 2404
1 TraesCS1A01G275700 chr1D 371185701 371187756 2055 False 3393 3393 96.480 350 2405 1 chr1D.!!$F1 2055
2 TraesCS1A01G275700 chr1B 495094257 495096306 2049 False 3177 3177 94.676 350 2405 1 chr1B.!!$F1 2055

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
257 258 0.040425 CGCCATATTTTACAGCGGCC 60.04 55.0 0.00 0.00 42.93 6.13 F
258 259 0.040425 GCCATATTTTACAGCGGCCG 60.04 55.0 24.05 24.05 33.31 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1317 1332 0.039074 CGTTGAAGTCGAGGAGCACT 60.039 55.0 0.0 0.0 0.0 4.40 R
1661 1700 0.387112 CCCGTACTACAAACGCACGA 60.387 55.0 0.0 0.0 39.0 4.35 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 5.927954 GATTGTTGATGTGCCATTTGTTT 57.072 34.783 0.00 0.00 0.00 2.83
23 24 5.676532 ATTGTTGATGTGCCATTTGTTTG 57.323 34.783 0.00 0.00 0.00 2.93
24 25 4.134379 TGTTGATGTGCCATTTGTTTGT 57.866 36.364 0.00 0.00 0.00 2.83
25 26 3.869832 TGTTGATGTGCCATTTGTTTGTG 59.130 39.130 0.00 0.00 0.00 3.33
26 27 3.815856 TGATGTGCCATTTGTTTGTGT 57.184 38.095 0.00 0.00 0.00 3.72
27 28 3.455327 TGATGTGCCATTTGTTTGTGTG 58.545 40.909 0.00 0.00 0.00 3.82
28 29 3.131755 TGATGTGCCATTTGTTTGTGTGA 59.868 39.130 0.00 0.00 0.00 3.58
29 30 3.599730 TGTGCCATTTGTTTGTGTGAA 57.400 38.095 0.00 0.00 0.00 3.18
30 31 3.257393 TGTGCCATTTGTTTGTGTGAAC 58.743 40.909 0.00 0.00 0.00 3.18
31 32 3.056250 TGTGCCATTTGTTTGTGTGAACT 60.056 39.130 0.00 0.00 0.00 3.01
32 33 3.932089 GTGCCATTTGTTTGTGTGAACTT 59.068 39.130 0.00 0.00 0.00 2.66
33 34 4.391523 GTGCCATTTGTTTGTGTGAACTTT 59.608 37.500 0.00 0.00 0.00 2.66
34 35 4.999950 TGCCATTTGTTTGTGTGAACTTTT 59.000 33.333 0.00 0.00 0.00 2.27
35 36 6.091441 GTGCCATTTGTTTGTGTGAACTTTTA 59.909 34.615 0.00 0.00 0.00 1.52
36 37 6.820656 TGCCATTTGTTTGTGTGAACTTTTAT 59.179 30.769 0.00 0.00 0.00 1.40
37 38 7.125113 GCCATTTGTTTGTGTGAACTTTTATG 58.875 34.615 0.00 0.00 0.00 1.90
38 39 7.201600 GCCATTTGTTTGTGTGAACTTTTATGT 60.202 33.333 0.00 0.00 0.00 2.29
39 40 8.115520 CCATTTGTTTGTGTGAACTTTTATGTG 58.884 33.333 0.00 0.00 0.00 3.21
40 41 8.655092 CATTTGTTTGTGTGAACTTTTATGTGT 58.345 29.630 0.00 0.00 0.00 3.72
41 42 7.804614 TTGTTTGTGTGAACTTTTATGTGTC 57.195 32.000 0.00 0.00 0.00 3.67
42 43 6.914259 TGTTTGTGTGAACTTTTATGTGTCA 58.086 32.000 0.00 0.00 0.00 3.58
43 44 7.542890 TGTTTGTGTGAACTTTTATGTGTCAT 58.457 30.769 0.00 0.00 0.00 3.06
44 45 7.487509 TGTTTGTGTGAACTTTTATGTGTCATG 59.512 33.333 0.00 0.00 0.00 3.07
45 46 6.934048 TGTGTGAACTTTTATGTGTCATGA 57.066 33.333 0.00 0.00 0.00 3.07
46 47 7.326968 TGTGTGAACTTTTATGTGTCATGAA 57.673 32.000 0.00 0.00 0.00 2.57
47 48 7.192913 TGTGTGAACTTTTATGTGTCATGAAC 58.807 34.615 0.00 0.00 0.00 3.18
48 49 7.066887 TGTGTGAACTTTTATGTGTCATGAACT 59.933 33.333 0.00 0.00 0.00 3.01
49 50 7.915397 GTGTGAACTTTTATGTGTCATGAACTT 59.085 33.333 0.00 0.00 0.00 2.66
50 51 7.914871 TGTGAACTTTTATGTGTCATGAACTTG 59.085 33.333 0.00 0.00 0.00 3.16
51 52 7.379529 GTGAACTTTTATGTGTCATGAACTTGG 59.620 37.037 0.00 0.00 0.00 3.61
52 53 6.959639 ACTTTTATGTGTCATGAACTTGGT 57.040 33.333 0.00 0.00 0.00 3.67
53 54 7.346751 ACTTTTATGTGTCATGAACTTGGTT 57.653 32.000 0.00 0.00 0.00 3.67
54 55 7.202526 ACTTTTATGTGTCATGAACTTGGTTG 58.797 34.615 0.00 0.00 0.00 3.77
55 56 5.703978 TTATGTGTCATGAACTTGGTTGG 57.296 39.130 0.00 0.00 0.00 3.77
56 57 2.305928 TGTGTCATGAACTTGGTTGGG 58.694 47.619 0.00 0.00 0.00 4.12
57 58 2.306847 GTGTCATGAACTTGGTTGGGT 58.693 47.619 0.00 0.00 0.00 4.51
58 59 2.034558 GTGTCATGAACTTGGTTGGGTG 59.965 50.000 0.00 0.00 0.00 4.61
59 60 2.092158 TGTCATGAACTTGGTTGGGTGA 60.092 45.455 0.00 0.00 0.00 4.02
60 61 3.157087 GTCATGAACTTGGTTGGGTGAT 58.843 45.455 0.00 0.00 0.00 3.06
61 62 3.573967 GTCATGAACTTGGTTGGGTGATT 59.426 43.478 0.00 0.00 0.00 2.57
62 63 4.039124 GTCATGAACTTGGTTGGGTGATTT 59.961 41.667 0.00 0.00 0.00 2.17
63 64 4.653341 TCATGAACTTGGTTGGGTGATTTT 59.347 37.500 0.00 0.00 0.00 1.82
64 65 4.399004 TGAACTTGGTTGGGTGATTTTG 57.601 40.909 0.00 0.00 0.00 2.44
65 66 4.026744 TGAACTTGGTTGGGTGATTTTGA 58.973 39.130 0.00 0.00 0.00 2.69
66 67 4.467795 TGAACTTGGTTGGGTGATTTTGAA 59.532 37.500 0.00 0.00 0.00 2.69
67 68 4.400529 ACTTGGTTGGGTGATTTTGAAC 57.599 40.909 0.00 0.00 0.00 3.18
68 69 4.030216 ACTTGGTTGGGTGATTTTGAACT 58.970 39.130 0.00 0.00 0.00 3.01
69 70 4.469586 ACTTGGTTGGGTGATTTTGAACTT 59.530 37.500 0.00 0.00 0.00 2.66
70 71 4.399004 TGGTTGGGTGATTTTGAACTTG 57.601 40.909 0.00 0.00 0.00 3.16
71 72 3.133721 TGGTTGGGTGATTTTGAACTTGG 59.866 43.478 0.00 0.00 0.00 3.61
72 73 3.133901 GGTTGGGTGATTTTGAACTTGGT 59.866 43.478 0.00 0.00 0.00 3.67
73 74 4.383661 GGTTGGGTGATTTTGAACTTGGTT 60.384 41.667 0.00 0.00 0.00 3.67
74 75 4.399004 TGGGTGATTTTGAACTTGGTTG 57.601 40.909 0.00 0.00 0.00 3.77
75 76 3.133721 TGGGTGATTTTGAACTTGGTTGG 59.866 43.478 0.00 0.00 0.00 3.77
76 77 3.386402 GGGTGATTTTGAACTTGGTTGGA 59.614 43.478 0.00 0.00 0.00 3.53
77 78 4.040339 GGGTGATTTTGAACTTGGTTGGAT 59.960 41.667 0.00 0.00 0.00 3.41
78 79 4.990426 GGTGATTTTGAACTTGGTTGGATG 59.010 41.667 0.00 0.00 0.00 3.51
79 80 5.221422 GGTGATTTTGAACTTGGTTGGATGA 60.221 40.000 0.00 0.00 0.00 2.92
80 81 6.458210 GTGATTTTGAACTTGGTTGGATGAT 58.542 36.000 0.00 0.00 0.00 2.45
81 82 6.366877 GTGATTTTGAACTTGGTTGGATGATG 59.633 38.462 0.00 0.00 0.00 3.07
82 83 6.267242 TGATTTTGAACTTGGTTGGATGATGA 59.733 34.615 0.00 0.00 0.00 2.92
83 84 6.669125 TTTTGAACTTGGTTGGATGATGAT 57.331 33.333 0.00 0.00 0.00 2.45
84 85 5.648178 TTGAACTTGGTTGGATGATGATG 57.352 39.130 0.00 0.00 0.00 3.07
85 86 4.665451 TGAACTTGGTTGGATGATGATGT 58.335 39.130 0.00 0.00 0.00 3.06
86 87 4.460034 TGAACTTGGTTGGATGATGATGTG 59.540 41.667 0.00 0.00 0.00 3.21
87 88 3.359033 ACTTGGTTGGATGATGATGTGG 58.641 45.455 0.00 0.00 0.00 4.17
88 89 1.766494 TGGTTGGATGATGATGTGGC 58.234 50.000 0.00 0.00 0.00 5.01
89 90 1.005687 TGGTTGGATGATGATGTGGCA 59.994 47.619 0.00 0.00 0.00 4.92
90 91 2.313317 GGTTGGATGATGATGTGGCAT 58.687 47.619 0.00 0.00 0.00 4.40
91 92 2.035449 GGTTGGATGATGATGTGGCATG 59.965 50.000 0.00 0.00 0.00 4.06
92 93 2.953648 GTTGGATGATGATGTGGCATGA 59.046 45.455 0.00 0.00 0.00 3.07
93 94 3.518992 TGGATGATGATGTGGCATGAT 57.481 42.857 0.00 0.00 0.00 2.45
94 95 3.839778 TGGATGATGATGTGGCATGATT 58.160 40.909 0.00 0.00 0.00 2.57
95 96 3.572255 TGGATGATGATGTGGCATGATTG 59.428 43.478 0.00 0.00 0.00 2.67
96 97 3.572682 GGATGATGATGTGGCATGATTGT 59.427 43.478 0.00 0.00 0.00 2.71
97 98 4.038763 GGATGATGATGTGGCATGATTGTT 59.961 41.667 0.00 0.00 0.00 2.83
98 99 4.379339 TGATGATGTGGCATGATTGTTG 57.621 40.909 0.00 0.00 0.00 3.33
99 100 4.017808 TGATGATGTGGCATGATTGTTGA 58.982 39.130 0.00 0.00 0.00 3.18
100 101 4.647399 TGATGATGTGGCATGATTGTTGAT 59.353 37.500 0.00 0.00 0.00 2.57
101 102 5.128008 TGATGATGTGGCATGATTGTTGATT 59.872 36.000 0.00 0.00 0.00 2.57
102 103 5.408880 TGATGTGGCATGATTGTTGATTT 57.591 34.783 0.00 0.00 0.00 2.17
103 104 5.172205 TGATGTGGCATGATTGTTGATTTG 58.828 37.500 0.00 0.00 0.00 2.32
104 105 3.327626 TGTGGCATGATTGTTGATTTGC 58.672 40.909 0.00 0.00 0.00 3.68
105 106 3.007074 TGTGGCATGATTGTTGATTTGCT 59.993 39.130 0.00 0.00 31.50 3.91
106 107 3.369756 GTGGCATGATTGTTGATTTGCTG 59.630 43.478 0.00 0.00 31.50 4.41
107 108 3.007074 TGGCATGATTGTTGATTTGCTGT 59.993 39.130 0.00 0.00 31.50 4.40
108 109 3.369756 GGCATGATTGTTGATTTGCTGTG 59.630 43.478 0.00 0.00 31.50 3.66
109 110 3.181524 GCATGATTGTTGATTTGCTGTGC 60.182 43.478 0.00 0.00 0.00 4.57
110 111 3.729862 TGATTGTTGATTTGCTGTGCA 57.270 38.095 0.00 0.00 36.47 4.57
122 123 4.852134 TTGCTGTGCAATTGAACTATGT 57.148 36.364 17.58 0.00 43.99 2.29
123 124 4.852134 TGCTGTGCAATTGAACTATGTT 57.148 36.364 17.58 0.00 34.76 2.71
124 125 5.956068 TGCTGTGCAATTGAACTATGTTA 57.044 34.783 17.58 0.00 34.76 2.41
125 126 6.513806 TGCTGTGCAATTGAACTATGTTAT 57.486 33.333 17.58 0.00 34.76 1.89
126 127 6.324042 TGCTGTGCAATTGAACTATGTTATG 58.676 36.000 17.58 0.07 34.76 1.90
127 128 5.230726 GCTGTGCAATTGAACTATGTTATGC 59.769 40.000 17.58 5.64 0.00 3.14
128 129 5.649557 TGTGCAATTGAACTATGTTATGCC 58.350 37.500 17.58 0.00 0.00 4.40
129 130 5.418524 TGTGCAATTGAACTATGTTATGCCT 59.581 36.000 17.58 0.00 0.00 4.75
130 131 6.071447 TGTGCAATTGAACTATGTTATGCCTT 60.071 34.615 17.58 0.00 0.00 4.35
131 132 6.813152 GTGCAATTGAACTATGTTATGCCTTT 59.187 34.615 10.34 0.00 0.00 3.11
132 133 7.331687 GTGCAATTGAACTATGTTATGCCTTTT 59.668 33.333 10.34 0.00 0.00 2.27
133 134 8.526978 TGCAATTGAACTATGTTATGCCTTTTA 58.473 29.630 10.34 0.00 0.00 1.52
134 135 9.533253 GCAATTGAACTATGTTATGCCTTTTAT 57.467 29.630 10.34 0.00 0.00 1.40
139 140 9.364989 TGAACTATGTTATGCCTTTTATTTTGC 57.635 29.630 0.00 0.00 0.00 3.68
140 141 9.364989 GAACTATGTTATGCCTTTTATTTTGCA 57.635 29.630 0.00 0.00 38.23 4.08
141 142 9.889128 AACTATGTTATGCCTTTTATTTTGCAT 57.111 25.926 0.00 0.00 45.67 3.96
176 177 6.803642 TGTTTGAAACATCATCACATTGTCA 58.196 32.000 6.66 0.00 36.25 3.58
177 178 7.263496 TGTTTGAAACATCATCACATTGTCAA 58.737 30.769 6.66 0.00 36.25 3.18
178 179 7.763071 TGTTTGAAACATCATCACATTGTCAAA 59.237 29.630 6.66 0.00 36.25 2.69
179 180 8.602328 GTTTGAAACATCATCACATTGTCAAAA 58.398 29.630 2.68 0.00 0.00 2.44
180 181 8.890124 TTGAAACATCATCACATTGTCAAAAT 57.110 26.923 0.00 0.00 0.00 1.82
181 182 8.300495 TGAAACATCATCACATTGTCAAAATG 57.700 30.769 0.00 0.00 0.00 2.32
182 183 7.385478 TGAAACATCATCACATTGTCAAAATGG 59.615 33.333 0.00 0.00 32.14 3.16
183 184 6.593268 ACATCATCACATTGTCAAAATGGA 57.407 33.333 0.00 0.00 32.14 3.41
184 185 6.392354 ACATCATCACATTGTCAAAATGGAC 58.608 36.000 0.00 0.00 38.29 4.02
185 186 5.045668 TCATCACATTGTCAAAATGGACG 57.954 39.130 0.00 0.00 40.72 4.79
186 187 4.518590 TCATCACATTGTCAAAATGGACGT 59.481 37.500 0.00 0.00 40.72 4.34
187 188 4.221926 TCACATTGTCAAAATGGACGTG 57.778 40.909 0.00 0.00 40.72 4.49
188 189 3.629855 TCACATTGTCAAAATGGACGTGT 59.370 39.130 0.00 0.00 40.72 4.49
189 190 4.816925 TCACATTGTCAAAATGGACGTGTA 59.183 37.500 0.00 0.00 40.72 2.90
190 191 5.297029 TCACATTGTCAAAATGGACGTGTAA 59.703 36.000 0.00 0.00 40.72 2.41
191 192 5.974158 CACATTGTCAAAATGGACGTGTAAA 59.026 36.000 0.00 0.00 40.72 2.01
192 193 6.473778 CACATTGTCAAAATGGACGTGTAAAA 59.526 34.615 0.00 0.00 40.72 1.52
193 194 7.168972 CACATTGTCAAAATGGACGTGTAAAAT 59.831 33.333 0.00 0.00 40.72 1.82
194 195 7.381139 ACATTGTCAAAATGGACGTGTAAAATC 59.619 33.333 0.00 0.00 40.72 2.17
195 196 6.627395 TGTCAAAATGGACGTGTAAAATCT 57.373 33.333 0.00 0.00 40.72 2.40
196 197 7.033530 TGTCAAAATGGACGTGTAAAATCTT 57.966 32.000 0.00 0.00 40.72 2.40
197 198 8.155821 TGTCAAAATGGACGTGTAAAATCTTA 57.844 30.769 0.00 0.00 40.72 2.10
198 199 8.788806 TGTCAAAATGGACGTGTAAAATCTTAT 58.211 29.630 0.00 0.00 40.72 1.73
199 200 9.620660 GTCAAAATGGACGTGTAAAATCTTATT 57.379 29.630 0.00 0.00 0.00 1.40
202 203 8.460831 AAATGGACGTGTAAAATCTTATTTGC 57.539 30.769 0.00 0.00 0.00 3.68
203 204 6.561737 TGGACGTGTAAAATCTTATTTGCA 57.438 33.333 0.00 0.00 33.39 4.08
204 205 6.971602 TGGACGTGTAAAATCTTATTTGCAA 58.028 32.000 0.00 0.00 36.80 4.08
205 206 7.081349 TGGACGTGTAAAATCTTATTTGCAAG 58.919 34.615 0.00 0.00 39.14 4.01
206 207 6.033513 GGACGTGTAAAATCTTATTTGCAAGC 59.966 38.462 0.00 0.00 37.69 4.01
207 208 5.567534 ACGTGTAAAATCTTATTTGCAAGCG 59.432 36.000 0.00 2.90 37.69 4.68
208 209 5.496969 CGTGTAAAATCTTATTTGCAAGCGC 60.497 40.000 0.00 0.00 36.80 5.92
209 210 4.862018 TGTAAAATCTTATTTGCAAGCGCC 59.138 37.500 2.29 0.00 37.32 6.53
210 211 2.193306 AATCTTATTTGCAAGCGCCG 57.807 45.000 2.29 0.00 37.32 6.46
211 212 0.381801 ATCTTATTTGCAAGCGCCGG 59.618 50.000 2.29 0.00 37.32 6.13
212 213 1.873572 CTTATTTGCAAGCGCCGGC 60.874 57.895 19.07 19.07 37.32 6.13
231 232 4.196826 GCTCGCGCACGCTGTAAG 62.197 66.667 13.70 6.38 39.84 2.34
232 233 2.805353 CTCGCGCACGCTGTAAGT 60.805 61.111 13.70 0.00 39.84 2.24
233 234 2.355363 TCGCGCACGCTGTAAGTT 60.355 55.556 13.70 0.00 39.84 2.66
234 235 1.068832 CTCGCGCACGCTGTAAGTTA 61.069 55.000 13.70 0.00 39.84 2.24
235 236 1.068832 TCGCGCACGCTGTAAGTTAG 61.069 55.000 13.70 0.00 39.84 2.34
236 237 1.058903 GCGCACGCTGTAAGTTAGC 59.941 57.895 7.96 0.00 38.26 3.09
237 238 1.623081 GCGCACGCTGTAAGTTAGCA 61.623 55.000 7.96 0.00 41.18 3.49
238 239 0.093026 CGCACGCTGTAAGTTAGCAC 59.907 55.000 0.00 0.00 41.18 4.40
239 240 0.093026 GCACGCTGTAAGTTAGCACG 59.907 55.000 0.00 0.00 41.18 5.34
240 241 0.093026 CACGCTGTAAGTTAGCACGC 59.907 55.000 0.00 0.00 41.18 5.34
241 242 1.012486 ACGCTGTAAGTTAGCACGCC 61.012 55.000 0.00 0.00 41.18 5.68
242 243 1.011968 CGCTGTAAGTTAGCACGCCA 61.012 55.000 0.00 0.00 41.18 5.69
243 244 1.369625 GCTGTAAGTTAGCACGCCAT 58.630 50.000 0.00 0.00 40.81 4.40
244 245 2.546778 GCTGTAAGTTAGCACGCCATA 58.453 47.619 0.00 0.00 40.81 2.74
245 246 3.131396 GCTGTAAGTTAGCACGCCATAT 58.869 45.455 0.00 0.00 40.81 1.78
246 247 3.560068 GCTGTAAGTTAGCACGCCATATT 59.440 43.478 0.00 0.00 40.81 1.28
247 248 4.035208 GCTGTAAGTTAGCACGCCATATTT 59.965 41.667 0.00 0.00 40.81 1.40
248 249 5.448632 GCTGTAAGTTAGCACGCCATATTTT 60.449 40.000 0.00 0.00 40.81 1.82
249 250 6.238266 GCTGTAAGTTAGCACGCCATATTTTA 60.238 38.462 0.00 0.00 40.81 1.52
250 251 7.007313 TGTAAGTTAGCACGCCATATTTTAC 57.993 36.000 0.00 0.00 0.00 2.01
251 252 6.594547 TGTAAGTTAGCACGCCATATTTTACA 59.405 34.615 0.00 0.00 0.00 2.41
252 253 5.734855 AGTTAGCACGCCATATTTTACAG 57.265 39.130 0.00 0.00 0.00 2.74
253 254 4.035208 AGTTAGCACGCCATATTTTACAGC 59.965 41.667 0.00 0.00 0.00 4.40
256 257 3.454941 CGCCATATTTTACAGCGGC 57.545 52.632 0.00 0.00 42.93 6.53
257 258 0.040425 CGCCATATTTTACAGCGGCC 60.040 55.000 0.00 0.00 42.93 6.13
258 259 0.040425 GCCATATTTTACAGCGGCCG 60.040 55.000 24.05 24.05 33.31 6.13
259 260 0.040425 CCATATTTTACAGCGGCCGC 60.040 55.000 42.34 42.34 42.33 6.53
276 277 2.125753 CTGGAGTCAGCGTCCTGC 60.126 66.667 0.00 0.00 46.98 4.85
287 288 3.416382 GTCCTGCCGCGCGTAAAA 61.416 61.111 29.95 9.90 0.00 1.52
288 289 2.665520 TCCTGCCGCGCGTAAAAA 60.666 55.556 29.95 8.26 0.00 1.94
289 290 2.501008 CCTGCCGCGCGTAAAAAC 60.501 61.111 29.95 10.88 0.00 2.43
290 291 2.554272 CTGCCGCGCGTAAAAACT 59.446 55.556 29.95 0.00 0.00 2.66
291 292 1.792057 CTGCCGCGCGTAAAAACTG 60.792 57.895 29.95 11.72 0.00 3.16
292 293 3.163358 GCCGCGCGTAAAAACTGC 61.163 61.111 29.95 18.18 0.00 4.40
293 294 2.554272 CCGCGCGTAAAAACTGCT 59.446 55.556 29.95 0.00 0.00 4.24
294 295 1.782807 CCGCGCGTAAAAACTGCTA 59.217 52.632 29.95 0.00 0.00 3.49
295 296 0.372334 CCGCGCGTAAAAACTGCTAT 59.628 50.000 29.95 0.00 0.00 2.97
296 297 1.201987 CCGCGCGTAAAAACTGCTATT 60.202 47.619 29.95 0.00 0.00 1.73
297 298 2.501881 CGCGCGTAAAAACTGCTATTT 58.498 42.857 24.19 0.00 0.00 1.40
298 299 2.520754 CGCGCGTAAAAACTGCTATTTC 59.479 45.455 24.19 0.00 0.00 2.17
299 300 2.844223 GCGCGTAAAAACTGCTATTTCC 59.156 45.455 8.43 0.00 0.00 3.13
300 301 3.668491 GCGCGTAAAAACTGCTATTTCCA 60.668 43.478 8.43 0.00 0.00 3.53
301 302 4.658071 CGCGTAAAAACTGCTATTTCCAT 58.342 39.130 0.00 0.00 0.00 3.41
302 303 4.495472 CGCGTAAAAACTGCTATTTCCATG 59.505 41.667 0.00 0.00 0.00 3.66
303 304 4.265320 GCGTAAAAACTGCTATTTCCATGC 59.735 41.667 0.00 0.00 0.00 4.06
304 305 5.640732 CGTAAAAACTGCTATTTCCATGCT 58.359 37.500 0.00 0.00 0.00 3.79
305 306 5.512788 CGTAAAAACTGCTATTTCCATGCTG 59.487 40.000 0.00 0.00 0.00 4.41
306 307 5.473066 AAAAACTGCTATTTCCATGCTGT 57.527 34.783 0.00 0.00 39.81 4.40
307 308 6.588719 AAAAACTGCTATTTCCATGCTGTA 57.411 33.333 0.00 0.00 37.78 2.74
308 309 6.588719 AAAACTGCTATTTCCATGCTGTAA 57.411 33.333 0.00 0.00 37.78 2.41
309 310 6.588719 AAACTGCTATTTCCATGCTGTAAA 57.411 33.333 0.00 0.00 37.78 2.01
310 311 6.588719 AACTGCTATTTCCATGCTGTAAAA 57.411 33.333 0.00 0.00 37.78 1.52
311 312 6.588719 ACTGCTATTTCCATGCTGTAAAAA 57.411 33.333 0.00 0.00 37.17 1.94
312 313 6.624423 ACTGCTATTTCCATGCTGTAAAAAG 58.376 36.000 0.00 0.00 37.17 2.27
313 314 5.964758 TGCTATTTCCATGCTGTAAAAAGG 58.035 37.500 0.00 0.00 0.00 3.11
314 315 5.480073 TGCTATTTCCATGCTGTAAAAAGGT 59.520 36.000 0.00 0.00 0.00 3.50
315 316 6.014669 TGCTATTTCCATGCTGTAAAAAGGTT 60.015 34.615 0.00 0.00 0.00 3.50
316 317 6.873605 GCTATTTCCATGCTGTAAAAAGGTTT 59.126 34.615 0.00 0.00 0.00 3.27
317 318 7.387673 GCTATTTCCATGCTGTAAAAAGGTTTT 59.612 33.333 0.00 0.00 0.00 2.43
318 319 9.921637 CTATTTCCATGCTGTAAAAAGGTTTTA 57.078 29.630 0.00 0.00 0.00 1.52
319 320 8.831715 ATTTCCATGCTGTAAAAAGGTTTTAG 57.168 30.769 0.00 0.00 0.00 1.85
320 321 6.969993 TCCATGCTGTAAAAAGGTTTTAGT 57.030 33.333 0.00 0.00 0.00 2.24
321 322 6.744112 TCCATGCTGTAAAAAGGTTTTAGTG 58.256 36.000 0.00 0.00 0.00 2.74
322 323 5.405269 CCATGCTGTAAAAAGGTTTTAGTGC 59.595 40.000 0.00 9.10 0.00 4.40
323 324 4.602995 TGCTGTAAAAAGGTTTTAGTGCG 58.397 39.130 10.39 0.00 0.00 5.34
324 325 3.424198 GCTGTAAAAAGGTTTTAGTGCGC 59.576 43.478 0.00 0.00 0.00 6.09
325 326 3.619729 TGTAAAAAGGTTTTAGTGCGCG 58.380 40.909 0.00 0.00 0.00 6.86
326 327 2.855660 AAAAAGGTTTTAGTGCGCGT 57.144 40.000 8.43 0.00 0.00 6.01
327 328 2.113910 AAAAGGTTTTAGTGCGCGTG 57.886 45.000 8.43 0.00 0.00 5.34
328 329 0.309612 AAAGGTTTTAGTGCGCGTGG 59.690 50.000 8.43 0.00 0.00 4.94
329 330 0.816421 AAGGTTTTAGTGCGCGTGGT 60.816 50.000 8.43 0.00 0.00 4.16
330 331 0.816421 AGGTTTTAGTGCGCGTGGTT 60.816 50.000 8.43 0.00 0.00 3.67
331 332 0.659123 GGTTTTAGTGCGCGTGGTTG 60.659 55.000 8.43 0.00 0.00 3.77
332 333 1.009449 TTTTAGTGCGCGTGGTTGC 60.009 52.632 8.43 0.00 0.00 4.17
345 346 3.558411 GTTGCGCGCCTGCTAGAG 61.558 66.667 30.77 0.00 39.65 2.43
346 347 3.758931 TTGCGCGCCTGCTAGAGA 61.759 61.111 30.77 2.53 39.65 3.10
347 348 3.081311 TTGCGCGCCTGCTAGAGAT 62.081 57.895 30.77 0.00 39.65 2.75
348 349 3.034923 GCGCGCCTGCTAGAGATG 61.035 66.667 23.24 0.00 39.65 2.90
359 360 3.153130 TGCTAGAGATGCTCTTAGCGAT 58.847 45.455 1.88 0.00 46.26 4.58
649 658 2.266055 GGCTCTCACTTGGTCCGG 59.734 66.667 0.00 0.00 0.00 5.14
760 772 1.351017 CACCTCCACACCCACATTAGT 59.649 52.381 0.00 0.00 0.00 2.24
861 873 5.082059 GTCGGCTATTTAATTGCATCGATG 58.918 41.667 21.27 21.27 31.02 3.84
888 900 8.901472 ATCATTAGTATAGCTAGGTTGATGGA 57.099 34.615 0.00 0.00 30.94 3.41
932 944 6.073494 TGTTTTATGTTTGAGATCGAGCGAAA 60.073 34.615 0.00 0.00 0.00 3.46
1061 1073 2.876645 GAGCTTCTCGCGGTCACG 60.877 66.667 6.13 0.00 45.59 4.35
1311 1326 2.203538 AAGTGCCCCAAGTGCCAG 60.204 61.111 0.00 0.00 0.00 4.85
1341 1356 0.040692 TCCTCGACTTCAACGACGTG 60.041 55.000 0.00 0.00 35.88 4.49
1478 1510 1.112113 CCTAGCTGCCGTCCTCTTTA 58.888 55.000 0.00 0.00 0.00 1.85
1661 1700 2.165641 TCTGTTGTGTGAGTCGTGACTT 59.834 45.455 3.69 0.00 42.66 3.01
1738 1777 5.527582 AGGTTTTATAGAAGGCAGTAATGCG 59.472 40.000 9.33 0.00 35.24 4.73
1879 1918 1.959985 GCTCTGGCTAGCTATGTCAGA 59.040 52.381 15.72 19.60 42.91 3.27
1938 1977 1.721476 CTACGTACGCCGCATCGAG 60.721 63.158 16.72 0.00 41.42 4.04
1978 2017 1.807981 GTACGTACGCCTGCATGCA 60.808 57.895 21.29 21.29 0.00 3.96
1998 2037 9.918630 GCATGCATAATAACCTTTTCTGAATAT 57.081 29.630 14.21 0.00 0.00 1.28
2025 2064 7.408756 ACTGTATGTATGGTTTTTGCATGAT 57.591 32.000 0.00 0.00 0.00 2.45
2058 2098 8.093118 ACTACTAGTACTCCTACTCAGAACAT 57.907 38.462 0.00 0.00 34.79 2.71
2221 2265 2.158957 GGTTCAGACTTCAGACCACACA 60.159 50.000 0.00 0.00 0.00 3.72
2222 2266 2.866762 GTTCAGACTTCAGACCACACAC 59.133 50.000 0.00 0.00 0.00 3.82
2286 2330 1.559682 GGAAGATGCTGGGTGGTTAGA 59.440 52.381 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.520569 AGTTCACACAAACAAATGGCAC 58.479 40.909 0.00 0.00 0.00 5.01
11 12 3.883830 AGTTCACACAAACAAATGGCA 57.116 38.095 0.00 0.00 0.00 4.92
12 13 5.544136 AAAAGTTCACACAAACAAATGGC 57.456 34.783 0.00 0.00 0.00 4.40
13 14 8.115520 CACATAAAAGTTCACACAAACAAATGG 58.884 33.333 0.00 0.00 0.00 3.16
14 15 8.655092 ACACATAAAAGTTCACACAAACAAATG 58.345 29.630 0.00 0.00 0.00 2.32
15 16 8.770438 ACACATAAAAGTTCACACAAACAAAT 57.230 26.923 0.00 0.00 0.00 2.32
16 17 7.867909 TGACACATAAAAGTTCACACAAACAAA 59.132 29.630 0.00 0.00 0.00 2.83
17 18 7.371159 TGACACATAAAAGTTCACACAAACAA 58.629 30.769 0.00 0.00 0.00 2.83
18 19 6.914259 TGACACATAAAAGTTCACACAAACA 58.086 32.000 0.00 0.00 0.00 2.83
19 20 7.700234 TCATGACACATAAAAGTTCACACAAAC 59.300 33.333 0.00 0.00 0.00 2.93
20 21 7.766283 TCATGACACATAAAAGTTCACACAAA 58.234 30.769 0.00 0.00 0.00 2.83
21 22 7.326968 TCATGACACATAAAAGTTCACACAA 57.673 32.000 0.00 0.00 0.00 3.33
22 23 6.934048 TCATGACACATAAAAGTTCACACA 57.066 33.333 0.00 0.00 0.00 3.72
23 24 7.417612 AGTTCATGACACATAAAAGTTCACAC 58.582 34.615 0.00 0.00 0.00 3.82
24 25 7.566760 AGTTCATGACACATAAAAGTTCACA 57.433 32.000 0.00 0.00 0.00 3.58
25 26 7.379529 CCAAGTTCATGACACATAAAAGTTCAC 59.620 37.037 0.00 0.00 0.00 3.18
26 27 7.068103 ACCAAGTTCATGACACATAAAAGTTCA 59.932 33.333 0.00 0.00 0.00 3.18
27 28 7.425606 ACCAAGTTCATGACACATAAAAGTTC 58.574 34.615 0.00 0.00 0.00 3.01
28 29 7.346751 ACCAAGTTCATGACACATAAAAGTT 57.653 32.000 0.00 0.00 0.00 2.66
29 30 6.959639 ACCAAGTTCATGACACATAAAAGT 57.040 33.333 0.00 0.00 0.00 2.66
30 31 6.642131 CCAACCAAGTTCATGACACATAAAAG 59.358 38.462 0.00 0.00 0.00 2.27
31 32 6.462207 CCCAACCAAGTTCATGACACATAAAA 60.462 38.462 0.00 0.00 0.00 1.52
32 33 5.010516 CCCAACCAAGTTCATGACACATAAA 59.989 40.000 0.00 0.00 0.00 1.40
33 34 4.522405 CCCAACCAAGTTCATGACACATAA 59.478 41.667 0.00 0.00 0.00 1.90
34 35 4.078537 CCCAACCAAGTTCATGACACATA 58.921 43.478 0.00 0.00 0.00 2.29
35 36 2.892852 CCCAACCAAGTTCATGACACAT 59.107 45.455 0.00 0.00 0.00 3.21
36 37 2.305928 CCCAACCAAGTTCATGACACA 58.694 47.619 0.00 0.00 0.00 3.72
37 38 2.034558 CACCCAACCAAGTTCATGACAC 59.965 50.000 0.00 0.00 0.00 3.67
38 39 2.092158 TCACCCAACCAAGTTCATGACA 60.092 45.455 0.00 0.00 0.00 3.58
39 40 2.582052 TCACCCAACCAAGTTCATGAC 58.418 47.619 0.00 0.00 0.00 3.06
40 41 3.524095 ATCACCCAACCAAGTTCATGA 57.476 42.857 0.00 0.00 0.00 3.07
41 42 4.605640 AAATCACCCAACCAAGTTCATG 57.394 40.909 0.00 0.00 0.00 3.07
42 43 4.653341 TCAAAATCACCCAACCAAGTTCAT 59.347 37.500 0.00 0.00 0.00 2.57
43 44 4.026744 TCAAAATCACCCAACCAAGTTCA 58.973 39.130 0.00 0.00 0.00 3.18
44 45 4.664150 TCAAAATCACCCAACCAAGTTC 57.336 40.909 0.00 0.00 0.00 3.01
45 46 4.469586 AGTTCAAAATCACCCAACCAAGTT 59.530 37.500 0.00 0.00 0.00 2.66
46 47 4.030216 AGTTCAAAATCACCCAACCAAGT 58.970 39.130 0.00 0.00 0.00 3.16
47 48 4.670896 AGTTCAAAATCACCCAACCAAG 57.329 40.909 0.00 0.00 0.00 3.61
48 49 4.383552 CCAAGTTCAAAATCACCCAACCAA 60.384 41.667 0.00 0.00 0.00 3.67
49 50 3.133721 CCAAGTTCAAAATCACCCAACCA 59.866 43.478 0.00 0.00 0.00 3.67
50 51 3.133901 ACCAAGTTCAAAATCACCCAACC 59.866 43.478 0.00 0.00 0.00 3.77
51 52 4.400529 ACCAAGTTCAAAATCACCCAAC 57.599 40.909 0.00 0.00 0.00 3.77
52 53 4.383552 CCAACCAAGTTCAAAATCACCCAA 60.384 41.667 0.00 0.00 0.00 4.12
53 54 3.133721 CCAACCAAGTTCAAAATCACCCA 59.866 43.478 0.00 0.00 0.00 4.51
54 55 3.386402 TCCAACCAAGTTCAAAATCACCC 59.614 43.478 0.00 0.00 0.00 4.61
55 56 4.664150 TCCAACCAAGTTCAAAATCACC 57.336 40.909 0.00 0.00 0.00 4.02
56 57 5.841810 TCATCCAACCAAGTTCAAAATCAC 58.158 37.500 0.00 0.00 0.00 3.06
57 58 6.267242 TCATCATCCAACCAAGTTCAAAATCA 59.733 34.615 0.00 0.00 0.00 2.57
58 59 6.690530 TCATCATCCAACCAAGTTCAAAATC 58.309 36.000 0.00 0.00 0.00 2.17
59 60 6.669125 TCATCATCCAACCAAGTTCAAAAT 57.331 33.333 0.00 0.00 0.00 1.82
60 61 6.041865 ACATCATCATCCAACCAAGTTCAAAA 59.958 34.615 0.00 0.00 0.00 2.44
61 62 5.539574 ACATCATCATCCAACCAAGTTCAAA 59.460 36.000 0.00 0.00 0.00 2.69
62 63 5.047872 CACATCATCATCCAACCAAGTTCAA 60.048 40.000 0.00 0.00 0.00 2.69
63 64 4.460034 CACATCATCATCCAACCAAGTTCA 59.540 41.667 0.00 0.00 0.00 3.18
64 65 4.142315 CCACATCATCATCCAACCAAGTTC 60.142 45.833 0.00 0.00 0.00 3.01
65 66 3.765511 CCACATCATCATCCAACCAAGTT 59.234 43.478 0.00 0.00 0.00 2.66
66 67 3.359033 CCACATCATCATCCAACCAAGT 58.641 45.455 0.00 0.00 0.00 3.16
67 68 2.100252 GCCACATCATCATCCAACCAAG 59.900 50.000 0.00 0.00 0.00 3.61
68 69 2.101783 GCCACATCATCATCCAACCAA 58.898 47.619 0.00 0.00 0.00 3.67
69 70 1.005687 TGCCACATCATCATCCAACCA 59.994 47.619 0.00 0.00 0.00 3.67
70 71 1.766494 TGCCACATCATCATCCAACC 58.234 50.000 0.00 0.00 0.00 3.77
71 72 2.953648 TCATGCCACATCATCATCCAAC 59.046 45.455 0.00 0.00 0.00 3.77
72 73 3.300239 TCATGCCACATCATCATCCAA 57.700 42.857 0.00 0.00 0.00 3.53
73 74 3.518992 ATCATGCCACATCATCATCCA 57.481 42.857 0.00 0.00 0.00 3.41
74 75 3.572682 ACAATCATGCCACATCATCATCC 59.427 43.478 0.00 0.00 0.00 3.51
75 76 4.848562 ACAATCATGCCACATCATCATC 57.151 40.909 0.00 0.00 0.00 2.92
76 77 4.647399 TCAACAATCATGCCACATCATCAT 59.353 37.500 0.00 0.00 0.00 2.45
77 78 4.017808 TCAACAATCATGCCACATCATCA 58.982 39.130 0.00 0.00 0.00 3.07
78 79 4.642445 TCAACAATCATGCCACATCATC 57.358 40.909 0.00 0.00 0.00 2.92
79 80 5.607939 AATCAACAATCATGCCACATCAT 57.392 34.783 0.00 0.00 0.00 2.45
80 81 5.172205 CAAATCAACAATCATGCCACATCA 58.828 37.500 0.00 0.00 0.00 3.07
81 82 4.033587 GCAAATCAACAATCATGCCACATC 59.966 41.667 0.00 0.00 0.00 3.06
82 83 3.936453 GCAAATCAACAATCATGCCACAT 59.064 39.130 0.00 0.00 0.00 3.21
83 84 3.007074 AGCAAATCAACAATCATGCCACA 59.993 39.130 0.00 0.00 32.99 4.17
84 85 3.369756 CAGCAAATCAACAATCATGCCAC 59.630 43.478 0.00 0.00 32.99 5.01
85 86 3.007074 ACAGCAAATCAACAATCATGCCA 59.993 39.130 0.00 0.00 32.99 4.92
86 87 3.369756 CACAGCAAATCAACAATCATGCC 59.630 43.478 0.00 0.00 32.99 4.40
87 88 3.181524 GCACAGCAAATCAACAATCATGC 60.182 43.478 0.00 0.00 32.82 4.06
88 89 3.991121 TGCACAGCAAATCAACAATCATG 59.009 39.130 0.00 0.00 34.76 3.07
89 90 4.260139 TGCACAGCAAATCAACAATCAT 57.740 36.364 0.00 0.00 34.76 2.45
90 91 3.729862 TGCACAGCAAATCAACAATCA 57.270 38.095 0.00 0.00 34.76 2.57
102 103 4.852134 AACATAGTTCAATTGCACAGCA 57.148 36.364 10.86 0.00 36.47 4.41
103 104 5.230726 GCATAACATAGTTCAATTGCACAGC 59.769 40.000 10.86 0.00 0.00 4.40
104 105 5.745294 GGCATAACATAGTTCAATTGCACAG 59.255 40.000 10.86 2.93 0.00 3.66
105 106 5.418524 AGGCATAACATAGTTCAATTGCACA 59.581 36.000 10.86 0.00 0.00 4.57
106 107 5.894807 AGGCATAACATAGTTCAATTGCAC 58.105 37.500 0.00 0.00 0.00 4.57
107 108 6.528537 AAGGCATAACATAGTTCAATTGCA 57.471 33.333 0.00 0.00 0.00 4.08
108 109 7.832503 AAAAGGCATAACATAGTTCAATTGC 57.167 32.000 0.00 0.00 0.00 3.56
113 114 9.364989 GCAAAATAAAAGGCATAACATAGTTCA 57.635 29.630 0.00 0.00 0.00 3.18
114 115 9.364989 TGCAAAATAAAAGGCATAACATAGTTC 57.635 29.630 0.00 0.00 0.00 3.01
115 116 9.889128 ATGCAAAATAAAAGGCATAACATAGTT 57.111 25.926 0.00 0.00 44.52 2.24
152 153 6.803642 TGACAATGTGATGATGTTTCAAACA 58.196 32.000 5.18 5.18 46.94 2.83
153 154 7.697352 TTGACAATGTGATGATGTTTCAAAC 57.303 32.000 0.00 0.00 34.96 2.93
154 155 8.713737 TTTTGACAATGTGATGATGTTTCAAA 57.286 26.923 0.00 0.00 34.96 2.69
155 156 8.766151 CATTTTGACAATGTGATGATGTTTCAA 58.234 29.630 0.00 0.00 34.96 2.69
156 157 7.385478 CCATTTTGACAATGTGATGATGTTTCA 59.615 33.333 0.00 0.00 36.00 2.69
157 158 7.599621 TCCATTTTGACAATGTGATGATGTTTC 59.400 33.333 0.00 0.00 0.00 2.78
158 159 7.385752 GTCCATTTTGACAATGTGATGATGTTT 59.614 33.333 0.00 0.00 35.29 2.83
159 160 6.869913 GTCCATTTTGACAATGTGATGATGTT 59.130 34.615 0.00 0.00 35.29 2.71
160 161 6.392354 GTCCATTTTGACAATGTGATGATGT 58.608 36.000 0.00 0.00 35.29 3.06
161 162 5.513849 CGTCCATTTTGACAATGTGATGATG 59.486 40.000 0.00 0.00 34.88 3.07
162 163 5.183713 ACGTCCATTTTGACAATGTGATGAT 59.816 36.000 0.00 0.00 34.88 2.45
163 164 4.518590 ACGTCCATTTTGACAATGTGATGA 59.481 37.500 0.00 0.00 34.88 2.92
164 165 4.618067 CACGTCCATTTTGACAATGTGATG 59.382 41.667 0.00 0.00 34.88 3.07
165 166 4.278170 ACACGTCCATTTTGACAATGTGAT 59.722 37.500 0.00 0.00 34.61 3.06
166 167 3.629855 ACACGTCCATTTTGACAATGTGA 59.370 39.130 0.00 0.00 34.61 3.58
167 168 3.963665 ACACGTCCATTTTGACAATGTG 58.036 40.909 0.00 0.00 34.61 3.21
168 169 5.759506 TTACACGTCCATTTTGACAATGT 57.240 34.783 0.00 0.00 37.72 2.71
169 170 7.594758 AGATTTTACACGTCCATTTTGACAATG 59.405 33.333 0.00 0.00 34.88 2.82
170 171 7.657336 AGATTTTACACGTCCATTTTGACAAT 58.343 30.769 0.00 0.00 34.88 2.71
171 172 7.033530 AGATTTTACACGTCCATTTTGACAA 57.966 32.000 0.00 0.00 34.88 3.18
172 173 6.627395 AGATTTTACACGTCCATTTTGACA 57.373 33.333 0.00 0.00 34.88 3.58
173 174 9.620660 AATAAGATTTTACACGTCCATTTTGAC 57.379 29.630 0.00 0.00 0.00 3.18
176 177 8.921670 GCAAATAAGATTTTACACGTCCATTTT 58.078 29.630 0.00 0.00 0.00 1.82
177 178 8.085296 TGCAAATAAGATTTTACACGTCCATTT 58.915 29.630 0.00 0.00 0.00 2.32
178 179 7.598278 TGCAAATAAGATTTTACACGTCCATT 58.402 30.769 0.00 0.00 0.00 3.16
179 180 7.151999 TGCAAATAAGATTTTACACGTCCAT 57.848 32.000 0.00 0.00 0.00 3.41
180 181 6.561737 TGCAAATAAGATTTTACACGTCCA 57.438 33.333 0.00 0.00 0.00 4.02
181 182 6.033513 GCTTGCAAATAAGATTTTACACGTCC 59.966 38.462 0.00 0.00 0.00 4.79
182 183 6.236941 CGCTTGCAAATAAGATTTTACACGTC 60.237 38.462 0.00 0.00 0.00 4.34
183 184 5.567534 CGCTTGCAAATAAGATTTTACACGT 59.432 36.000 0.00 0.00 0.00 4.49
184 185 5.496969 GCGCTTGCAAATAAGATTTTACACG 60.497 40.000 0.00 0.00 38.92 4.49
185 186 5.220209 GGCGCTTGCAAATAAGATTTTACAC 60.220 40.000 7.64 0.00 41.71 2.90
186 187 4.862018 GGCGCTTGCAAATAAGATTTTACA 59.138 37.500 7.64 0.00 41.71 2.41
187 188 4.027702 CGGCGCTTGCAAATAAGATTTTAC 60.028 41.667 7.64 0.00 41.71 2.01
188 189 4.101942 CGGCGCTTGCAAATAAGATTTTA 58.898 39.130 7.64 0.00 41.71 1.52
189 190 2.923020 CGGCGCTTGCAAATAAGATTTT 59.077 40.909 7.64 0.00 41.71 1.82
190 191 2.529151 CGGCGCTTGCAAATAAGATTT 58.471 42.857 7.64 0.00 41.71 2.17
191 192 1.202290 CCGGCGCTTGCAAATAAGATT 60.202 47.619 7.64 0.00 41.71 2.40
192 193 0.381801 CCGGCGCTTGCAAATAAGAT 59.618 50.000 7.64 0.00 41.71 2.40
193 194 1.800032 CCGGCGCTTGCAAATAAGA 59.200 52.632 7.64 0.00 41.71 2.10
194 195 1.873572 GCCGGCGCTTGCAAATAAG 60.874 57.895 12.58 0.00 41.71 1.73
195 196 2.180518 GCCGGCGCTTGCAAATAA 59.819 55.556 12.58 0.00 41.71 1.40
196 197 2.749839 AGCCGGCGCTTGCAAATA 60.750 55.556 23.20 0.00 45.55 1.40
197 198 4.424566 CAGCCGGCGCTTGCAAAT 62.425 61.111 23.20 0.00 45.55 2.32
218 219 1.058903 GCTAACTTACAGCGTGCGC 59.941 57.895 8.67 8.67 42.33 6.09
219 220 0.093026 GTGCTAACTTACAGCGTGCG 59.907 55.000 0.00 0.00 42.13 5.34
220 221 0.093026 CGTGCTAACTTACAGCGTGC 59.907 55.000 0.00 0.00 42.13 5.34
221 222 0.093026 GCGTGCTAACTTACAGCGTG 59.907 55.000 0.00 0.00 42.13 5.34
222 223 1.012486 GGCGTGCTAACTTACAGCGT 61.012 55.000 0.00 0.00 42.13 5.07
223 224 1.011968 TGGCGTGCTAACTTACAGCG 61.012 55.000 0.00 0.00 42.13 5.18
224 225 1.369625 ATGGCGTGCTAACTTACAGC 58.630 50.000 0.00 0.00 39.56 4.40
225 226 5.734855 AAATATGGCGTGCTAACTTACAG 57.265 39.130 0.00 0.00 0.00 2.74
226 227 6.594547 TGTAAAATATGGCGTGCTAACTTACA 59.405 34.615 0.00 0.00 0.00 2.41
227 228 7.007313 TGTAAAATATGGCGTGCTAACTTAC 57.993 36.000 0.00 0.00 0.00 2.34
228 229 6.238266 GCTGTAAAATATGGCGTGCTAACTTA 60.238 38.462 0.00 0.00 0.00 2.24
229 230 5.448632 GCTGTAAAATATGGCGTGCTAACTT 60.449 40.000 0.00 0.00 0.00 2.66
230 231 4.035208 GCTGTAAAATATGGCGTGCTAACT 59.965 41.667 0.00 0.00 0.00 2.24
231 232 4.279659 GCTGTAAAATATGGCGTGCTAAC 58.720 43.478 0.00 0.00 0.00 2.34
232 233 3.001838 CGCTGTAAAATATGGCGTGCTAA 59.998 43.478 0.00 0.00 40.78 3.09
233 234 2.542178 CGCTGTAAAATATGGCGTGCTA 59.458 45.455 0.00 0.00 40.78 3.49
234 235 1.330521 CGCTGTAAAATATGGCGTGCT 59.669 47.619 0.00 0.00 40.78 4.40
235 236 1.596954 CCGCTGTAAAATATGGCGTGC 60.597 52.381 0.00 0.00 43.57 5.34
236 237 1.596954 GCCGCTGTAAAATATGGCGTG 60.597 52.381 0.00 0.00 43.57 5.34
237 238 0.661020 GCCGCTGTAAAATATGGCGT 59.339 50.000 0.00 0.00 43.57 5.68
238 239 0.040425 GGCCGCTGTAAAATATGGCG 60.040 55.000 0.00 0.00 43.36 5.69
239 240 0.040425 CGGCCGCTGTAAAATATGGC 60.040 55.000 14.67 0.00 41.72 4.40
240 241 0.040425 GCGGCCGCTGTAAAATATGG 60.040 55.000 41.71 0.75 38.26 2.74
241 242 3.454941 GCGGCCGCTGTAAAATATG 57.545 52.632 41.71 1.28 38.26 1.78
259 260 2.125753 GCAGGACGCTGACTCCAG 60.126 66.667 0.00 0.00 43.22 3.86
260 261 3.695606 GGCAGGACGCTGACTCCA 61.696 66.667 0.00 0.00 41.91 3.86
270 271 2.957052 TTTTTACGCGCGGCAGGAC 61.957 57.895 35.22 0.00 0.00 3.85
271 272 2.665520 TTTTTACGCGCGGCAGGA 60.666 55.556 35.22 14.09 0.00 3.86
272 273 2.501008 GTTTTTACGCGCGGCAGG 60.501 61.111 35.22 6.16 0.00 4.85
273 274 1.792057 CAGTTTTTACGCGCGGCAG 60.792 57.895 35.22 6.61 0.00 4.85
274 275 2.249896 CAGTTTTTACGCGCGGCA 59.750 55.556 35.22 19.03 0.00 5.69
275 276 2.230484 TAGCAGTTTTTACGCGCGGC 62.230 55.000 35.22 23.85 0.00 6.53
276 277 0.372334 ATAGCAGTTTTTACGCGCGG 59.628 50.000 35.22 16.31 0.00 6.46
277 278 2.153680 AATAGCAGTTTTTACGCGCG 57.846 45.000 30.96 30.96 0.00 6.86
278 279 2.844223 GGAAATAGCAGTTTTTACGCGC 59.156 45.455 5.73 0.00 0.00 6.86
279 280 4.073169 TGGAAATAGCAGTTTTTACGCG 57.927 40.909 3.53 3.53 0.00 6.01
280 281 4.265320 GCATGGAAATAGCAGTTTTTACGC 59.735 41.667 0.00 0.00 0.00 4.42
281 282 5.512788 CAGCATGGAAATAGCAGTTTTTACG 59.487 40.000 0.00 0.00 0.00 3.18
282 283 6.389906 ACAGCATGGAAATAGCAGTTTTTAC 58.610 36.000 0.00 0.00 43.62 2.01
283 284 6.588719 ACAGCATGGAAATAGCAGTTTTTA 57.411 33.333 0.00 0.00 43.62 1.52
284 285 5.473066 ACAGCATGGAAATAGCAGTTTTT 57.527 34.783 0.00 0.00 43.62 1.94
285 286 6.588719 TTACAGCATGGAAATAGCAGTTTT 57.411 33.333 0.00 0.00 34.71 2.43
286 287 6.588719 TTTACAGCATGGAAATAGCAGTTT 57.411 33.333 0.00 0.00 45.75 2.66
296 297 7.206687 CACTAAAACCTTTTTACAGCATGGAA 58.793 34.615 0.00 0.00 43.62 3.53
297 298 6.737346 GCACTAAAACCTTTTTACAGCATGGA 60.737 38.462 0.00 0.00 43.62 3.41
298 299 5.405269 GCACTAAAACCTTTTTACAGCATGG 59.595 40.000 0.00 0.00 43.62 3.66
299 300 5.116983 CGCACTAAAACCTTTTTACAGCATG 59.883 40.000 0.00 0.00 46.00 4.06
300 301 5.219633 CGCACTAAAACCTTTTTACAGCAT 58.780 37.500 0.00 0.00 0.00 3.79
301 302 4.602995 CGCACTAAAACCTTTTTACAGCA 58.397 39.130 0.00 0.00 0.00 4.41
302 303 3.424198 GCGCACTAAAACCTTTTTACAGC 59.576 43.478 0.30 0.00 0.00 4.40
303 304 3.662186 CGCGCACTAAAACCTTTTTACAG 59.338 43.478 8.75 0.00 0.00 2.74
304 305 3.065095 ACGCGCACTAAAACCTTTTTACA 59.935 39.130 5.73 0.00 0.00 2.41
305 306 3.419596 CACGCGCACTAAAACCTTTTTAC 59.580 43.478 5.73 0.00 0.00 2.01
306 307 3.548415 CCACGCGCACTAAAACCTTTTTA 60.548 43.478 5.73 0.00 0.00 1.52
307 308 2.456010 CACGCGCACTAAAACCTTTTT 58.544 42.857 5.73 0.00 0.00 1.94
308 309 1.268845 CCACGCGCACTAAAACCTTTT 60.269 47.619 5.73 0.00 0.00 2.27
309 310 0.309612 CCACGCGCACTAAAACCTTT 59.690 50.000 5.73 0.00 0.00 3.11
310 311 0.816421 ACCACGCGCACTAAAACCTT 60.816 50.000 5.73 0.00 0.00 3.50
311 312 0.816421 AACCACGCGCACTAAAACCT 60.816 50.000 5.73 0.00 0.00 3.50
312 313 0.659123 CAACCACGCGCACTAAAACC 60.659 55.000 5.73 0.00 0.00 3.27
313 314 1.266124 GCAACCACGCGCACTAAAAC 61.266 55.000 5.73 0.00 0.00 2.43
314 315 1.009449 GCAACCACGCGCACTAAAA 60.009 52.632 5.73 0.00 0.00 1.52
315 316 2.634777 GCAACCACGCGCACTAAA 59.365 55.556 5.73 0.00 0.00 1.85
328 329 3.558411 CTCTAGCAGGCGCGCAAC 61.558 66.667 34.42 20.95 45.49 4.17
329 330 3.081311 ATCTCTAGCAGGCGCGCAA 62.081 57.895 34.42 11.19 45.49 4.85
330 331 3.531207 ATCTCTAGCAGGCGCGCA 61.531 61.111 34.42 11.15 45.49 6.09
331 332 3.034923 CATCTCTAGCAGGCGCGC 61.035 66.667 25.94 25.94 45.49 6.86
332 333 3.034923 GCATCTCTAGCAGGCGCG 61.035 66.667 0.00 0.00 45.49 6.86
333 334 1.664333 GAGCATCTCTAGCAGGCGC 60.664 63.158 0.00 0.00 38.99 6.53
334 335 4.651585 GAGCATCTCTAGCAGGCG 57.348 61.111 0.00 0.00 0.00 5.52
345 346 4.230314 TGTAGTCATCGCTAAGAGCATC 57.770 45.455 0.00 0.00 42.58 3.91
346 347 4.655762 TTGTAGTCATCGCTAAGAGCAT 57.344 40.909 0.00 0.00 42.58 3.79
347 348 4.655762 ATTGTAGTCATCGCTAAGAGCA 57.344 40.909 0.00 0.00 42.58 4.26
348 349 5.975410 AAATTGTAGTCATCGCTAAGAGC 57.025 39.130 0.00 0.00 38.02 4.09
359 360 8.911918 ATGTGTGTTAGGTTAAATTGTAGTCA 57.088 30.769 0.00 0.00 0.00 3.41
467 476 1.817099 CTGTCGCTTCCCTCCATGC 60.817 63.158 0.00 0.00 0.00 4.06
468 477 1.153289 CCTGTCGCTTCCCTCCATG 60.153 63.158 0.00 0.00 0.00 3.66
760 772 1.005137 GAACGTGTACGCGAAACCAAA 60.005 47.619 33.44 0.00 44.43 3.28
861 873 8.200792 CCATCAACCTAGCTATACTAATGATCC 58.799 40.741 0.00 0.00 31.41 3.36
888 900 7.823745 AAAACAACATCAACAGAATACTCCT 57.176 32.000 0.00 0.00 0.00 3.69
932 944 5.472478 CACCAAATATAGCTCATGTCATGCT 59.528 40.000 8.03 5.48 40.43 3.79
1317 1332 0.039074 CGTTGAAGTCGAGGAGCACT 60.039 55.000 0.00 0.00 0.00 4.40
1478 1510 2.413112 CGCACACGATTGATGAGAAACT 59.587 45.455 0.00 0.00 43.93 2.66
1661 1700 0.387112 CCCGTACTACAAACGCACGA 60.387 55.000 0.00 0.00 39.00 4.35
1879 1918 3.070734 ACGAGAATGAATGAGCTGCCTAT 59.929 43.478 0.00 0.00 0.00 2.57
1998 2037 9.620259 TCATGCAAAAACCATACATACAGTATA 57.380 29.630 0.00 0.00 41.47 1.47
1999 2038 8.518430 TCATGCAAAAACCATACATACAGTAT 57.482 30.769 0.00 0.00 44.20 2.12
2000 2039 7.929941 TCATGCAAAAACCATACATACAGTA 57.070 32.000 0.00 0.00 37.06 2.74
2001 2040 6.832520 TCATGCAAAAACCATACATACAGT 57.167 33.333 0.00 0.00 0.00 3.55
2002 2041 9.800433 TTTATCATGCAAAAACCATACATACAG 57.200 29.630 0.00 0.00 0.00 2.74
2006 2045 9.669887 ACAATTTATCATGCAAAAACCATACAT 57.330 25.926 0.00 0.00 0.00 2.29
2034 2073 7.041644 GCATGTTCTGAGTAGGAGTACTAGTAG 60.042 44.444 1.87 0.00 39.78 2.57
2040 2079 4.720649 TGCATGTTCTGAGTAGGAGTAC 57.279 45.455 0.00 0.00 0.00 2.73
2045 2084 5.181009 TGATCTTTGCATGTTCTGAGTAGG 58.819 41.667 0.00 0.00 0.00 3.18
2058 2098 7.868906 TGTTAATCTCATGATGATCTTTGCA 57.131 32.000 0.00 0.00 32.44 4.08
2221 2265 2.224402 GCTTCTTTCTCTCTGGTGTGGT 60.224 50.000 0.00 0.00 0.00 4.16
2222 2266 2.224378 TGCTTCTTTCTCTCTGGTGTGG 60.224 50.000 0.00 0.00 0.00 4.17
2286 2330 5.749462 CAATAGTCTCCCCTTTGAATGACT 58.251 41.667 0.00 0.00 38.21 3.41


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

AutoCloner maintained by Alex Coulton.