Multiple sequence alignment - TraesCS3D01G289100

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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 TraesCS3D01G289100 chr3D 100.000 6118 0 0 1 6118 398407792 398401675 0.000000e+00 11298
1 TraesCS3D01G289100 chr3B 96.549 5883 149 26 246 6084 524454746 524448874 0.000000e+00 9690
2 TraesCS3D01G289100 chr3A 95.454 5587 184 29 278 5826 517667204 517661650 0.000000e+00 8846
3 TraesCS3D01G289100 chr3A 87.640 267 15 11 5830 6084 517661485 517661225 1.670000e-75 294
4 TraesCS3D01G289100 chr1B 81.304 2102 355 25 994 3091 581200599 581202666 0.000000e+00 1670
5 TraesCS3D01G289100 chr1A 81.377 1482 270 6 1613 3091 527951285 527952763 0.000000e+00 1203
6 TraesCS3D01G289100 chr1D 81.309 1482 271 6 1613 3091 430411219 430412697 0.000000e+00 1197
7 TraesCS3D01G289100 chr1D 84.919 557 76 5 994 1549 430410630 430411179 1.930000e-154 556
8 TraesCS3D01G289100 chr2D 97.561 246 6 0 1 246 395152516 395152761 7.330000e-114 422
9 TraesCS3D01G289100 chr6A 94.715 246 13 0 1 246 168010076 168010321 3.460000e-102 383
10 TraesCS3D01G289100 chr5A 89.388 245 24 2 1 244 471698487 471698730 2.140000e-79 307


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 TraesCS3D01G289100 chr3D 398401675 398407792 6117 True 11298.0 11298 100.000 1 6118 1 chr3D.!!$R1 6117
1 TraesCS3D01G289100 chr3B 524448874 524454746 5872 True 9690.0 9690 96.549 246 6084 1 chr3B.!!$R1 5838
2 TraesCS3D01G289100 chr3A 517661225 517667204 5979 True 4570.0 8846 91.547 278 6084 2 chr3A.!!$R1 5806
3 TraesCS3D01G289100 chr1B 581200599 581202666 2067 False 1670.0 1670 81.304 994 3091 1 chr1B.!!$F1 2097
4 TraesCS3D01G289100 chr1A 527951285 527952763 1478 False 1203.0 1203 81.377 1613 3091 1 chr1A.!!$F1 1478
5 TraesCS3D01G289100 chr1D 430410630 430412697 2067 False 876.5 1197 83.114 994 3091 2 chr1D.!!$F1 2097

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
180 181 0.032952 GACACCAGCGTGGACACTAA 59.967 55.000 10.46 0.00 44.86 2.24 F
181 182 0.033504 ACACCAGCGTGGACACTAAG 59.966 55.000 10.46 0.00 44.86 2.18 F
217 218 0.035439 TTCCTTTCCTAAGCGCCTGG 60.035 55.000 2.29 3.84 0.00 4.45 F
223 224 0.107848 TCCTAAGCGCCTGGTTAAGC 60.108 55.000 2.29 0.00 37.59 3.09 F
623 635 0.331616 AGCGCAAACCTTATCCCCTT 59.668 50.000 11.47 0.00 0.00 3.95 F
1923 1940 0.384669 GGCATTTCCTCTCATGCTGC 59.615 55.000 4.26 0.00 44.50 5.25 F
3268 3285 2.665165 TCATGGCTTGTTCTTGGTGTT 58.335 42.857 0.00 0.00 0.00 3.32 F
4440 4471 1.408422 GCTGCTTTGCCGTAGTTTTG 58.592 50.000 0.00 0.00 0.00 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 1526 1.220477 GTGGAAGAGAGGCCAGAGC 59.780 63.158 5.01 0.0 34.22 4.09 R
1923 1940 1.688735 TCGATTCCCAGCATCCTACTG 59.311 52.381 0.00 0.0 34.82 2.74 R
2274 2291 1.473258 AGCTCTCACGAATCTCAGCT 58.527 50.000 0.00 0.0 32.28 4.24 R
2889 2906 3.953612 GAGGCACCAATGTTCCATCATAA 59.046 43.478 0.00 0.0 29.00 1.90 R
3291 3308 6.106003 ACATTCCAGTTTCAGAAACCAAAAC 58.894 36.000 20.47 0.0 42.34 2.43 R
3673 3691 1.200948 GCCAAGCAAAGTTAGCAGAGG 59.799 52.381 0.00 0.0 0.00 3.69 R
4649 4681 1.250840 ACGCAATTTTGAGAGGGGGC 61.251 55.000 0.93 0.0 0.00 5.80 R
6090 6312 0.039764 TCCACTCCGACCATCAGACT 59.960 55.000 0.00 0.0 0.00 3.24 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
19 20 2.388310 GGCGCTAGGATCTAATTCCC 57.612 55.000 7.64 0.00 36.35 3.97
20 21 1.404315 GGCGCTAGGATCTAATTCCCG 60.404 57.143 7.64 0.00 36.35 5.14
21 22 1.404315 GCGCTAGGATCTAATTCCCGG 60.404 57.143 0.00 0.00 36.35 5.73
22 23 1.893801 CGCTAGGATCTAATTCCCGGT 59.106 52.381 0.00 0.00 36.35 5.28
23 24 3.087031 CGCTAGGATCTAATTCCCGGTA 58.913 50.000 0.00 0.00 36.35 4.02
24 25 3.128938 CGCTAGGATCTAATTCCCGGTAG 59.871 52.174 0.00 0.00 36.35 3.18
25 26 4.087907 GCTAGGATCTAATTCCCGGTAGT 58.912 47.826 0.00 0.00 36.35 2.73
26 27 4.527427 GCTAGGATCTAATTCCCGGTAGTT 59.473 45.833 0.00 0.00 36.35 2.24
27 28 5.011840 GCTAGGATCTAATTCCCGGTAGTTT 59.988 44.000 0.00 0.00 36.35 2.66
28 29 5.548181 AGGATCTAATTCCCGGTAGTTTC 57.452 43.478 0.00 0.00 36.35 2.78
29 30 4.966805 AGGATCTAATTCCCGGTAGTTTCA 59.033 41.667 0.00 0.00 36.35 2.69
30 31 5.427481 AGGATCTAATTCCCGGTAGTTTCAA 59.573 40.000 0.00 0.00 36.35 2.69
31 32 5.526479 GGATCTAATTCCCGGTAGTTTCAAC 59.474 44.000 0.00 0.00 0.00 3.18
32 33 5.486735 TCTAATTCCCGGTAGTTTCAACA 57.513 39.130 0.00 0.00 0.00 3.33
33 34 5.484715 TCTAATTCCCGGTAGTTTCAACAG 58.515 41.667 0.00 0.00 0.00 3.16
34 35 4.360951 AATTCCCGGTAGTTTCAACAGA 57.639 40.909 0.00 0.00 0.00 3.41
35 36 3.842007 TTCCCGGTAGTTTCAACAGAA 57.158 42.857 0.00 0.00 0.00 3.02
36 37 4.360951 TTCCCGGTAGTTTCAACAGAAT 57.639 40.909 0.00 0.00 0.00 2.40
37 38 3.934068 TCCCGGTAGTTTCAACAGAATC 58.066 45.455 0.00 0.00 0.00 2.52
38 39 3.007635 CCCGGTAGTTTCAACAGAATCC 58.992 50.000 0.00 0.00 0.00 3.01
39 40 3.007635 CCGGTAGTTTCAACAGAATCCC 58.992 50.000 0.00 0.00 0.00 3.85
40 41 3.558321 CCGGTAGTTTCAACAGAATCCCA 60.558 47.826 0.00 0.00 0.00 4.37
41 42 4.261801 CGGTAGTTTCAACAGAATCCCAT 58.738 43.478 0.00 0.00 0.00 4.00
42 43 4.700213 CGGTAGTTTCAACAGAATCCCATT 59.300 41.667 0.00 0.00 0.00 3.16
43 44 5.163754 CGGTAGTTTCAACAGAATCCCATTC 60.164 44.000 0.00 0.00 39.56 2.67
44 45 5.710099 GGTAGTTTCAACAGAATCCCATTCA 59.290 40.000 0.00 0.00 41.71 2.57
45 46 6.208599 GGTAGTTTCAACAGAATCCCATTCAA 59.791 38.462 0.00 0.00 41.71 2.69
46 47 6.923199 AGTTTCAACAGAATCCCATTCAAT 57.077 33.333 0.00 0.00 41.71 2.57
47 48 6.928520 AGTTTCAACAGAATCCCATTCAATC 58.071 36.000 0.00 0.00 41.71 2.67
48 49 5.920193 TTCAACAGAATCCCATTCAATCC 57.080 39.130 0.00 0.00 41.71 3.01
49 50 4.280819 TCAACAGAATCCCATTCAATCCC 58.719 43.478 0.00 0.00 41.71 3.85
50 51 4.025360 CAACAGAATCCCATTCAATCCCA 58.975 43.478 0.00 0.00 41.71 4.37
51 52 3.907221 ACAGAATCCCATTCAATCCCAG 58.093 45.455 0.00 0.00 41.71 4.45
52 53 3.270433 ACAGAATCCCATTCAATCCCAGT 59.730 43.478 0.00 0.00 41.71 4.00
53 54 4.478317 ACAGAATCCCATTCAATCCCAGTA 59.522 41.667 0.00 0.00 41.71 2.74
54 55 5.044179 ACAGAATCCCATTCAATCCCAGTAA 60.044 40.000 0.00 0.00 41.71 2.24
55 56 5.893255 CAGAATCCCATTCAATCCCAGTAAA 59.107 40.000 0.00 0.00 41.71 2.01
56 57 6.552350 CAGAATCCCATTCAATCCCAGTAAAT 59.448 38.462 0.00 0.00 41.71 1.40
57 58 6.779539 AGAATCCCATTCAATCCCAGTAAATC 59.220 38.462 0.00 0.00 41.71 2.17
58 59 5.464588 TCCCATTCAATCCCAGTAAATCA 57.535 39.130 0.00 0.00 0.00 2.57
59 60 5.448654 TCCCATTCAATCCCAGTAAATCAG 58.551 41.667 0.00 0.00 0.00 2.90
60 61 4.038402 CCCATTCAATCCCAGTAAATCAGC 59.962 45.833 0.00 0.00 0.00 4.26
61 62 4.891756 CCATTCAATCCCAGTAAATCAGCT 59.108 41.667 0.00 0.00 0.00 4.24
62 63 6.064060 CCATTCAATCCCAGTAAATCAGCTA 58.936 40.000 0.00 0.00 0.00 3.32
63 64 6.206243 CCATTCAATCCCAGTAAATCAGCTAG 59.794 42.308 0.00 0.00 0.00 3.42
64 65 4.708177 TCAATCCCAGTAAATCAGCTAGC 58.292 43.478 6.62 6.62 0.00 3.42
65 66 2.890808 TCCCAGTAAATCAGCTAGCG 57.109 50.000 9.55 4.60 0.00 4.26
66 67 2.108168 TCCCAGTAAATCAGCTAGCGT 58.892 47.619 9.55 0.00 0.00 5.07
67 68 2.100916 TCCCAGTAAATCAGCTAGCGTC 59.899 50.000 9.55 0.00 0.00 5.19
68 69 2.120232 CCAGTAAATCAGCTAGCGTCG 58.880 52.381 9.55 2.06 0.00 5.12
69 70 2.120232 CAGTAAATCAGCTAGCGTCGG 58.880 52.381 9.55 0.59 0.00 4.79
70 71 0.853419 GTAAATCAGCTAGCGTCGGC 59.147 55.000 9.55 0.00 40.37 5.54
71 72 0.594028 TAAATCAGCTAGCGTCGGCG 60.594 55.000 4.29 4.29 46.35 6.46
81 82 2.860293 CGTCGGCGCAAAAGATGT 59.140 55.556 10.83 0.00 0.00 3.06
82 83 1.225745 CGTCGGCGCAAAAGATGTC 60.226 57.895 10.83 0.00 0.00 3.06
83 84 1.866237 GTCGGCGCAAAAGATGTCA 59.134 52.632 10.83 0.00 0.00 3.58
84 85 0.452784 GTCGGCGCAAAAGATGTCAC 60.453 55.000 10.83 0.00 0.00 3.67
85 86 0.602638 TCGGCGCAAAAGATGTCACT 60.603 50.000 10.83 0.00 0.00 3.41
86 87 0.453282 CGGCGCAAAAGATGTCACTG 60.453 55.000 10.83 0.00 0.00 3.66
87 88 0.109597 GGCGCAAAAGATGTCACTGG 60.110 55.000 10.83 0.00 0.00 4.00
88 89 0.109597 GCGCAAAAGATGTCACTGGG 60.110 55.000 0.30 0.00 0.00 4.45
89 90 1.238439 CGCAAAAGATGTCACTGGGT 58.762 50.000 0.00 0.00 0.00 4.51
90 91 1.069022 CGCAAAAGATGTCACTGGGTG 60.069 52.381 0.00 0.00 34.45 4.61
91 92 1.336240 GCAAAAGATGTCACTGGGTGC 60.336 52.381 0.00 0.00 32.98 5.01
92 93 2.233271 CAAAAGATGTCACTGGGTGCT 58.767 47.619 0.00 0.00 32.98 4.40
93 94 3.411446 CAAAAGATGTCACTGGGTGCTA 58.589 45.455 0.00 0.00 32.98 3.49
94 95 3.340814 AAAGATGTCACTGGGTGCTAG 57.659 47.619 0.00 0.00 32.98 3.42
95 96 1.198713 AGATGTCACTGGGTGCTAGG 58.801 55.000 0.00 0.00 32.98 3.02
96 97 0.179000 GATGTCACTGGGTGCTAGGG 59.821 60.000 0.00 0.00 32.98 3.53
97 98 1.274703 ATGTCACTGGGTGCTAGGGG 61.275 60.000 0.00 0.00 32.98 4.79
98 99 1.918800 GTCACTGGGTGCTAGGGGT 60.919 63.158 0.00 0.00 32.98 4.95
99 100 1.918293 TCACTGGGTGCTAGGGGTG 60.918 63.158 0.00 0.00 32.98 4.61
100 101 2.207189 ACTGGGTGCTAGGGGTGT 59.793 61.111 0.00 0.00 0.00 4.16
101 102 1.463410 ACTGGGTGCTAGGGGTGTT 60.463 57.895 0.00 0.00 0.00 3.32
102 103 1.065997 ACTGGGTGCTAGGGGTGTTT 61.066 55.000 0.00 0.00 0.00 2.83
103 104 0.322546 CTGGGTGCTAGGGGTGTTTC 60.323 60.000 0.00 0.00 0.00 2.78
104 105 0.770557 TGGGTGCTAGGGGTGTTTCT 60.771 55.000 0.00 0.00 0.00 2.52
105 106 0.404426 GGGTGCTAGGGGTGTTTCTT 59.596 55.000 0.00 0.00 0.00 2.52
106 107 1.534729 GGTGCTAGGGGTGTTTCTTG 58.465 55.000 0.00 0.00 0.00 3.02
107 108 1.202891 GGTGCTAGGGGTGTTTCTTGT 60.203 52.381 0.00 0.00 0.00 3.16
108 109 2.583143 GTGCTAGGGGTGTTTCTTGTT 58.417 47.619 0.00 0.00 0.00 2.83
109 110 2.552743 GTGCTAGGGGTGTTTCTTGTTC 59.447 50.000 0.00 0.00 0.00 3.18
110 111 2.441750 TGCTAGGGGTGTTTCTTGTTCT 59.558 45.455 0.00 0.00 0.00 3.01
111 112 3.117663 TGCTAGGGGTGTTTCTTGTTCTT 60.118 43.478 0.00 0.00 0.00 2.52
112 113 3.889538 GCTAGGGGTGTTTCTTGTTCTTT 59.110 43.478 0.00 0.00 0.00 2.52
113 114 4.341235 GCTAGGGGTGTTTCTTGTTCTTTT 59.659 41.667 0.00 0.00 0.00 2.27
114 115 5.163447 GCTAGGGGTGTTTCTTGTTCTTTTT 60.163 40.000 0.00 0.00 0.00 1.94
115 116 5.339008 AGGGGTGTTTCTTGTTCTTTTTC 57.661 39.130 0.00 0.00 0.00 2.29
116 117 5.023452 AGGGGTGTTTCTTGTTCTTTTTCT 58.977 37.500 0.00 0.00 0.00 2.52
117 118 6.192044 AGGGGTGTTTCTTGTTCTTTTTCTA 58.808 36.000 0.00 0.00 0.00 2.10
118 119 6.096423 AGGGGTGTTTCTTGTTCTTTTTCTAC 59.904 38.462 0.00 0.00 0.00 2.59
119 120 6.096423 GGGGTGTTTCTTGTTCTTTTTCTACT 59.904 38.462 0.00 0.00 0.00 2.57
120 121 7.363530 GGGGTGTTTCTTGTTCTTTTTCTACTT 60.364 37.037 0.00 0.00 0.00 2.24
121 122 8.033038 GGGTGTTTCTTGTTCTTTTTCTACTTT 58.967 33.333 0.00 0.00 0.00 2.66
122 123 8.860128 GGTGTTTCTTGTTCTTTTTCTACTTTG 58.140 33.333 0.00 0.00 0.00 2.77
123 124 9.406828 GTGTTTCTTGTTCTTTTTCTACTTTGT 57.593 29.630 0.00 0.00 0.00 2.83
124 125 9.405587 TGTTTCTTGTTCTTTTTCTACTTTGTG 57.594 29.630 0.00 0.00 0.00 3.33
125 126 9.406828 GTTTCTTGTTCTTTTTCTACTTTGTGT 57.593 29.630 0.00 0.00 0.00 3.72
128 129 8.395633 TCTTGTTCTTTTTCTACTTTGTGTAGC 58.604 33.333 0.00 0.00 46.15 3.58
129 130 6.711579 TGTTCTTTTTCTACTTTGTGTAGCG 58.288 36.000 0.00 0.00 46.15 4.26
130 131 5.338614 TCTTTTTCTACTTTGTGTAGCGC 57.661 39.130 0.00 0.00 46.15 5.92
131 132 4.212636 TCTTTTTCTACTTTGTGTAGCGCC 59.787 41.667 2.29 0.00 46.15 6.53
132 133 2.088950 TTCTACTTTGTGTAGCGCCC 57.911 50.000 2.29 0.00 46.15 6.13
133 134 0.108992 TCTACTTTGTGTAGCGCCCG 60.109 55.000 2.29 0.00 46.15 6.13
134 135 0.389426 CTACTTTGTGTAGCGCCCGT 60.389 55.000 2.29 0.00 41.68 5.28
135 136 0.887247 TACTTTGTGTAGCGCCCGTA 59.113 50.000 2.29 0.00 0.00 4.02
136 137 0.668401 ACTTTGTGTAGCGCCCGTAC 60.668 55.000 2.29 0.06 0.00 3.67
137 138 0.668096 CTTTGTGTAGCGCCCGTACA 60.668 55.000 2.29 3.38 0.00 2.90
138 139 0.037139 TTTGTGTAGCGCCCGTACAT 60.037 50.000 2.29 0.00 33.08 2.29
139 140 0.037139 TTGTGTAGCGCCCGTACATT 60.037 50.000 2.29 0.00 33.08 2.71
140 141 0.816373 TGTGTAGCGCCCGTACATTA 59.184 50.000 2.29 0.00 33.08 1.90
141 142 1.204231 TGTGTAGCGCCCGTACATTAA 59.796 47.619 2.29 0.00 33.08 1.40
142 143 2.159071 TGTGTAGCGCCCGTACATTAAT 60.159 45.455 2.29 0.00 33.08 1.40
143 144 2.867975 GTGTAGCGCCCGTACATTAATT 59.132 45.455 2.29 0.00 33.08 1.40
144 145 3.060070 GTGTAGCGCCCGTACATTAATTC 60.060 47.826 2.29 0.00 33.08 2.17
145 146 1.589803 AGCGCCCGTACATTAATTCC 58.410 50.000 2.29 0.00 0.00 3.01
146 147 1.134340 AGCGCCCGTACATTAATTCCA 60.134 47.619 2.29 0.00 0.00 3.53
147 148 1.263217 GCGCCCGTACATTAATTCCAG 59.737 52.381 0.00 0.00 0.00 3.86
148 149 1.263217 CGCCCGTACATTAATTCCAGC 59.737 52.381 0.00 0.00 0.00 4.85
149 150 1.263217 GCCCGTACATTAATTCCAGCG 59.737 52.381 0.00 0.00 0.00 5.18
150 151 2.557317 CCCGTACATTAATTCCAGCGT 58.443 47.619 0.00 0.00 0.00 5.07
151 152 2.940410 CCCGTACATTAATTCCAGCGTT 59.060 45.455 0.00 0.00 0.00 4.84
152 153 3.242608 CCCGTACATTAATTCCAGCGTTG 60.243 47.826 0.00 0.00 0.00 4.10
153 154 3.242608 CCGTACATTAATTCCAGCGTTGG 60.243 47.826 12.81 12.81 46.49 3.77
162 163 2.048222 CAGCGTTGGAAGCTCGGA 60.048 61.111 0.00 0.00 44.06 4.55
163 164 2.048127 AGCGTTGGAAGCTCGGAC 60.048 61.111 0.00 0.00 41.83 4.79
164 165 2.357034 GCGTTGGAAGCTCGGACA 60.357 61.111 0.00 0.00 0.00 4.02
165 166 2.668280 GCGTTGGAAGCTCGGACAC 61.668 63.158 0.00 0.00 0.00 3.67
166 167 2.027625 CGTTGGAAGCTCGGACACC 61.028 63.158 0.00 0.00 0.00 4.16
167 168 1.070786 GTTGGAAGCTCGGACACCA 59.929 57.895 0.00 0.00 0.00 4.17
168 169 0.951040 GTTGGAAGCTCGGACACCAG 60.951 60.000 0.00 0.00 32.16 4.00
169 170 2.435059 GGAAGCTCGGACACCAGC 60.435 66.667 0.00 0.00 35.73 4.85
170 171 2.811317 GAAGCTCGGACACCAGCG 60.811 66.667 0.00 0.00 40.84 5.18
171 172 3.575351 GAAGCTCGGACACCAGCGT 62.575 63.158 0.00 0.00 40.84 5.07
172 173 3.865929 AAGCTCGGACACCAGCGTG 62.866 63.158 0.00 0.00 46.11 5.34
174 175 3.680786 CTCGGACACCAGCGTGGA 61.681 66.667 10.46 0.00 44.86 4.02
175 176 3.916392 CTCGGACACCAGCGTGGAC 62.916 68.421 10.46 2.89 44.86 4.02
176 177 4.293648 CGGACACCAGCGTGGACA 62.294 66.667 10.46 0.00 44.86 4.02
177 178 2.665185 GGACACCAGCGTGGACAC 60.665 66.667 10.46 0.00 44.86 3.67
178 179 2.421739 GACACCAGCGTGGACACT 59.578 61.111 10.46 0.00 44.86 3.55
179 180 1.663739 GACACCAGCGTGGACACTA 59.336 57.895 10.46 0.00 44.86 2.74
180 181 0.032952 GACACCAGCGTGGACACTAA 59.967 55.000 10.46 0.00 44.86 2.24
181 182 0.033504 ACACCAGCGTGGACACTAAG 59.966 55.000 10.46 0.00 44.86 2.18
182 183 1.004918 ACCAGCGTGGACACTAAGC 60.005 57.895 10.46 0.00 40.96 3.09
183 184 1.741770 CCAGCGTGGACACTAAGCC 60.742 63.158 0.56 0.00 40.96 4.35
184 185 1.005037 CAGCGTGGACACTAAGCCA 60.005 57.895 0.56 0.00 0.00 4.75
185 186 0.602638 CAGCGTGGACACTAAGCCAA 60.603 55.000 0.56 0.00 35.63 4.52
186 187 0.107831 AGCGTGGACACTAAGCCAAA 59.892 50.000 0.56 0.00 35.63 3.28
187 188 0.948678 GCGTGGACACTAAGCCAAAA 59.051 50.000 0.56 0.00 35.63 2.44
188 189 1.335496 GCGTGGACACTAAGCCAAAAA 59.665 47.619 0.56 0.00 35.63 1.94
213 214 9.529325 AAATATTTATTTTCCTTTCCTAAGCGC 57.471 29.630 0.00 0.00 32.28 5.92
214 215 4.976224 TTATTTTCCTTTCCTAAGCGCC 57.024 40.909 2.29 0.00 0.00 6.53
215 216 2.579410 TTTTCCTTTCCTAAGCGCCT 57.421 45.000 2.29 0.00 0.00 5.52
216 217 1.821216 TTTCCTTTCCTAAGCGCCTG 58.179 50.000 2.29 0.00 0.00 4.85
217 218 0.035439 TTCCTTTCCTAAGCGCCTGG 60.035 55.000 2.29 3.84 0.00 4.45
218 219 1.198759 TCCTTTCCTAAGCGCCTGGT 61.199 55.000 2.29 0.00 0.00 4.00
219 220 0.322546 CCTTTCCTAAGCGCCTGGTT 60.323 55.000 2.29 0.00 39.56 3.67
220 221 1.065709 CCTTTCCTAAGCGCCTGGTTA 60.066 52.381 2.29 0.00 37.03 2.85
221 222 2.617021 CCTTTCCTAAGCGCCTGGTTAA 60.617 50.000 2.29 2.90 37.59 2.01
222 223 2.396590 TTCCTAAGCGCCTGGTTAAG 57.603 50.000 2.29 0.00 37.59 1.85
223 224 0.107848 TCCTAAGCGCCTGGTTAAGC 60.108 55.000 2.29 0.00 37.59 3.09
228 229 2.480555 CGCCTGGTTAAGCGCTTG 59.519 61.111 32.23 15.40 46.50 4.01
229 230 2.325082 CGCCTGGTTAAGCGCTTGT 61.325 57.895 32.23 10.24 46.50 3.16
230 231 1.210155 GCCTGGTTAAGCGCTTGTG 59.790 57.895 32.23 15.91 0.00 3.33
231 232 1.210155 CCTGGTTAAGCGCTTGTGC 59.790 57.895 32.23 20.03 0.00 4.57
276 277 7.575720 GCAGCAGAAGGAACAAAACAATACTAT 60.576 37.037 0.00 0.00 0.00 2.12
399 400 1.598685 GTTTTTCTCGCCCACCGGA 60.599 57.895 9.46 0.00 37.59 5.14
428 429 1.079127 ACGAAATGAGCCACCGGAG 60.079 57.895 9.46 0.00 0.00 4.63
444 446 1.133025 CGGAGCAGTTAAAATGGCCAG 59.867 52.381 13.05 0.00 0.00 4.85
445 447 1.134995 GGAGCAGTTAAAATGGCCAGC 60.135 52.381 13.05 6.38 0.00 4.85
483 485 2.125269 CCACGACCGGTTGGATCC 60.125 66.667 25.74 4.20 39.21 3.36
515 517 4.393155 CCAGCCGCACCTGTAGCA 62.393 66.667 0.00 0.00 0.00 3.49
623 635 0.331616 AGCGCAAACCTTATCCCCTT 59.668 50.000 11.47 0.00 0.00 3.95
756 768 3.015145 GCCTCAGCCTAACCCCCA 61.015 66.667 0.00 0.00 0.00 4.96
918 932 3.885976 TCGGATAAGATCAGAGAGGGT 57.114 47.619 0.00 0.00 0.00 4.34
919 933 3.491342 TCGGATAAGATCAGAGAGGGTG 58.509 50.000 0.00 0.00 0.00 4.61
967 981 2.507547 CCGTTCCGCGAATCCGAA 60.508 61.111 8.23 0.00 44.77 4.30
984 998 2.330924 GAAGGGGCCAGATTCTCCGG 62.331 65.000 4.39 0.00 0.00 5.14
1264 1278 0.394899 CTCCAACCAGCTCCCAATCC 60.395 60.000 0.00 0.00 0.00 3.01
1587 1604 1.292941 CCTCCTCCTCCTCCTCCTCA 61.293 65.000 0.00 0.00 0.00 3.86
1590 1607 0.539438 CCTCCTCCTCCTCCTCATCG 60.539 65.000 0.00 0.00 0.00 3.84
1881 1898 3.129813 TGCTCAATTGTGATCTCATTGGC 59.870 43.478 11.59 15.16 31.85 4.52
1923 1940 0.384669 GGCATTTCCTCTCATGCTGC 59.615 55.000 4.26 0.00 44.50 5.25
2271 2288 3.137360 AGGGTAAAGATCTGGAAGCCATC 59.863 47.826 17.77 0.00 30.82 3.51
2274 2291 3.634397 AAAGATCTGGAAGCCATCGAA 57.366 42.857 0.00 0.00 30.82 3.71
2889 2906 7.233144 TCAGAGAGCAGAGCTATATTTCTTGAT 59.767 37.037 0.00 0.00 39.88 2.57
2979 2996 4.033009 TCAATACCCTCTGCTCAGATGAA 58.967 43.478 0.00 0.00 36.76 2.57
3268 3285 2.665165 TCATGGCTTGTTCTTGGTGTT 58.335 42.857 0.00 0.00 0.00 3.32
3291 3308 9.639601 TGTTACCTGCTATAATTATCAGAATCG 57.360 33.333 13.26 2.78 0.00 3.34
3403 3421 4.559153 GTGATGGTTCCTTTCATGTTTGG 58.441 43.478 0.00 0.00 0.00 3.28
3602 3620 7.372260 AGTCACCTGAAGAGCTCATATAAAT 57.628 36.000 17.77 0.00 32.14 1.40
4188 4208 5.160607 TCAGTCGTTTCCATATTTGTCCT 57.839 39.130 0.00 0.00 0.00 3.85
4232 4252 6.143919 GCTTTTGTTTTGCCACAGTAGATAAC 59.856 38.462 0.00 0.00 0.00 1.89
4258 4278 7.326789 CCTGTTTGTTTTGTAATCTGTATGCAG 59.673 37.037 4.14 4.14 43.87 4.41
4324 4350 6.200854 GCATTTGCTAGTTGTGTTTAGCTTTT 59.799 34.615 0.00 0.00 42.13 2.27
4440 4471 1.408422 GCTGCTTTGCCGTAGTTTTG 58.592 50.000 0.00 0.00 0.00 2.44
4517 4548 3.088532 CACATTGCAGGGCCTTAACTAA 58.911 45.455 1.32 0.00 0.00 2.24
4550 4581 5.817816 CCCACCTACTATCAACATTGTTCTC 59.182 44.000 0.00 0.00 0.00 2.87
4573 4604 5.023533 TCTTCTGCAAGTGTGTTAGTTCT 57.976 39.130 0.00 0.00 33.76 3.01
4649 4681 4.974368 TCTGGTTTAGTTTGTTGGTGTG 57.026 40.909 0.00 0.00 0.00 3.82
4667 4699 1.250154 TGCCCCCTCTCAAAATTGCG 61.250 55.000 0.00 0.00 0.00 4.85
4688 4720 4.084589 GCGTCGCATGTTTGATATGTGATA 60.085 41.667 13.44 0.00 44.14 2.15
4707 4739 8.072238 TGTGATATATGCTCAACGTTAACATC 57.928 34.615 0.00 0.00 0.00 3.06
4832 4864 8.579850 ACTTTGTATTGTGTATTGGTGATGAT 57.420 30.769 0.00 0.00 0.00 2.45
4883 4915 1.067060 GCGGACATAATCAAAAGGGGC 59.933 52.381 0.00 0.00 0.00 5.80
5015 5047 0.179089 CGGAGGCAACAGATCCTGAG 60.179 60.000 0.45 0.00 41.41 3.35
5190 5222 5.864474 GCTTCTACACATATATTCTGACGGG 59.136 44.000 0.00 0.00 0.00 5.28
5307 5339 4.075963 ACCATCTTTTGCTGCAAAATGT 57.924 36.364 33.05 24.73 41.53 2.71
5341 5373 1.394618 ATAGCTGACTCGTCACCTCC 58.605 55.000 0.00 0.00 35.46 4.30
5385 5417 9.470399 AAACCTTTTTCCTTCTCTAGTAAAACA 57.530 29.630 0.00 0.00 0.00 2.83
5700 5746 8.486210 ACAGCATATAGGATTCTAAACTTGACA 58.514 33.333 0.00 0.00 0.00 3.58
5703 5749 8.983724 GCATATAGGATTCTAAACTTGACAGTC 58.016 37.037 0.00 0.00 30.45 3.51
5828 6036 4.023536 GCGAATTTGTTCCTTCAGTACCAA 60.024 41.667 0.00 0.00 0.00 3.67
5857 6065 1.195448 GCTTCATCAGTTCGTGGTGTG 59.805 52.381 0.00 0.00 38.57 3.82
5901 6109 6.786967 ACGGATAGGTACAAAGTATGAACT 57.213 37.500 0.00 0.00 37.65 3.01
5910 6118 5.652744 ACAAAGTATGAACTGACAACGTC 57.347 39.130 0.00 0.00 35.62 4.34
5929 6137 3.368843 CGTCAGACAGATGATGTTTCCCT 60.369 47.826 0.41 0.00 44.17 4.20
5959 6167 3.680620 ATCGTGGTCATGGGGCACG 62.681 63.158 0.00 0.00 40.17 5.34
5960 6168 4.697756 CGTGGTCATGGGGCACGT 62.698 66.667 0.00 0.00 34.96 4.49
5979 6187 3.132646 ACGTTGTTGTGTGGGTAGAACTA 59.867 43.478 0.00 0.00 0.00 2.24
6020 6239 1.386533 TCCGTCTATCAGGAACGGAC 58.613 55.000 11.48 1.14 46.31 4.79
6021 6240 1.064906 TCCGTCTATCAGGAACGGACT 60.065 52.381 11.48 0.00 46.31 3.85
6022 6241 1.065701 CCGTCTATCAGGAACGGACTG 59.934 57.143 7.35 0.00 45.77 3.51
6023 6242 1.743958 CGTCTATCAGGAACGGACTGT 59.256 52.381 3.73 0.00 33.98 3.55
6024 6243 2.163815 CGTCTATCAGGAACGGACTGTT 59.836 50.000 0.00 0.00 45.61 3.16
6037 6259 0.521735 GACTGTTTTTGGCGGCTAGG 59.478 55.000 11.43 0.00 0.00 3.02
6045 6267 1.271840 TTGGCGGCTAGGATTGGACT 61.272 55.000 11.43 0.00 0.00 3.85
6048 6270 1.826024 CGGCTAGGATTGGACTGCT 59.174 57.895 0.00 0.00 0.00 4.24
6078 6300 3.425404 CGTTGGACTAATGGCATTTTCG 58.575 45.455 19.21 9.82 0.00 3.46
6084 6306 4.156008 GGACTAATGGCATTTTCGTGAAGT 59.844 41.667 19.21 13.26 0.00 3.01
6085 6307 5.353123 GGACTAATGGCATTTTCGTGAAGTA 59.647 40.000 19.21 0.00 0.00 2.24
6086 6308 6.422776 ACTAATGGCATTTTCGTGAAGTAG 57.577 37.500 19.21 7.82 0.00 2.57
6087 6309 6.170506 ACTAATGGCATTTTCGTGAAGTAGA 58.829 36.000 19.21 0.00 0.00 2.59
6088 6310 6.823689 ACTAATGGCATTTTCGTGAAGTAGAT 59.176 34.615 19.21 0.00 0.00 1.98
6089 6311 4.944962 TGGCATTTTCGTGAAGTAGATG 57.055 40.909 0.00 0.00 0.00 2.90
6090 6312 4.574892 TGGCATTTTCGTGAAGTAGATGA 58.425 39.130 0.00 0.00 0.00 2.92
6091 6313 4.631377 TGGCATTTTCGTGAAGTAGATGAG 59.369 41.667 0.00 0.00 0.00 2.90
6092 6314 4.631813 GGCATTTTCGTGAAGTAGATGAGT 59.368 41.667 0.00 0.00 0.00 3.41
6093 6315 5.220491 GGCATTTTCGTGAAGTAGATGAGTC 60.220 44.000 0.00 0.00 0.00 3.36
6094 6316 5.578727 GCATTTTCGTGAAGTAGATGAGTCT 59.421 40.000 0.00 0.00 38.52 3.24
6095 6317 6.454848 GCATTTTCGTGAAGTAGATGAGTCTG 60.455 42.308 0.00 0.00 35.87 3.51
6096 6318 5.959618 TTTCGTGAAGTAGATGAGTCTGA 57.040 39.130 0.00 0.00 35.87 3.27
6097 6319 6.516739 TTTCGTGAAGTAGATGAGTCTGAT 57.483 37.500 0.00 0.00 35.87 2.90
6098 6320 5.491635 TCGTGAAGTAGATGAGTCTGATG 57.508 43.478 0.00 0.00 35.87 3.07
6099 6321 4.336713 TCGTGAAGTAGATGAGTCTGATGG 59.663 45.833 0.00 0.00 35.87 3.51
6100 6322 4.097135 CGTGAAGTAGATGAGTCTGATGGT 59.903 45.833 0.00 0.00 35.87 3.55
6101 6323 5.587289 GTGAAGTAGATGAGTCTGATGGTC 58.413 45.833 0.00 0.00 35.87 4.02
6102 6324 4.336713 TGAAGTAGATGAGTCTGATGGTCG 59.663 45.833 0.00 0.00 35.87 4.79
6103 6325 3.218453 AGTAGATGAGTCTGATGGTCGG 58.782 50.000 0.00 0.00 35.87 4.79
6104 6326 2.443958 AGATGAGTCTGATGGTCGGA 57.556 50.000 0.00 0.00 32.13 4.55
6105 6327 2.305928 AGATGAGTCTGATGGTCGGAG 58.694 52.381 0.00 0.00 31.37 4.63
6106 6328 2.028130 GATGAGTCTGATGGTCGGAGT 58.972 52.381 0.00 0.00 38.10 3.85
6107 6329 1.177401 TGAGTCTGATGGTCGGAGTG 58.823 55.000 1.03 0.00 35.66 3.51
6108 6330 0.457851 GAGTCTGATGGTCGGAGTGG 59.542 60.000 1.03 0.00 35.66 4.00
6109 6331 0.039764 AGTCTGATGGTCGGAGTGGA 59.960 55.000 0.00 0.00 34.30 4.02
6110 6332 0.457851 GTCTGATGGTCGGAGTGGAG 59.542 60.000 0.00 0.00 31.37 3.86
6111 6333 0.331616 TCTGATGGTCGGAGTGGAGA 59.668 55.000 0.00 0.00 0.00 3.71
6112 6334 1.186200 CTGATGGTCGGAGTGGAGAA 58.814 55.000 0.00 0.00 0.00 2.87
6113 6335 0.895530 TGATGGTCGGAGTGGAGAAC 59.104 55.000 0.00 0.00 0.00 3.01
6114 6336 1.187087 GATGGTCGGAGTGGAGAACT 58.813 55.000 0.00 0.00 43.85 3.01
6115 6337 0.898320 ATGGTCGGAGTGGAGAACTG 59.102 55.000 0.00 0.00 40.07 3.16
6116 6338 0.469331 TGGTCGGAGTGGAGAACTGT 60.469 55.000 0.00 0.00 40.07 3.55
6117 6339 0.680061 GGTCGGAGTGGAGAACTGTT 59.320 55.000 0.00 0.00 40.07 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.404315 CGGGAATTAGATCCTAGCGCC 60.404 57.143 2.29 0.00 39.57 6.53
1 2 1.404315 CCGGGAATTAGATCCTAGCGC 60.404 57.143 0.00 0.00 39.57 5.92
2 3 1.893801 ACCGGGAATTAGATCCTAGCG 59.106 52.381 6.32 0.00 39.57 4.26
3 4 4.087907 ACTACCGGGAATTAGATCCTAGC 58.912 47.826 6.32 0.00 39.57 3.42
4 5 6.267014 TGAAACTACCGGGAATTAGATCCTAG 59.733 42.308 6.32 0.00 39.57 3.02
5 6 6.138263 TGAAACTACCGGGAATTAGATCCTA 58.862 40.000 6.32 0.00 39.57 2.94
6 7 4.966805 TGAAACTACCGGGAATTAGATCCT 59.033 41.667 6.32 0.00 39.57 3.24
7 8 5.286267 TGAAACTACCGGGAATTAGATCC 57.714 43.478 6.32 0.00 38.86 3.36
8 9 6.110707 TGTTGAAACTACCGGGAATTAGATC 58.889 40.000 6.32 3.78 0.00 2.75
9 10 6.057321 TGTTGAAACTACCGGGAATTAGAT 57.943 37.500 6.32 0.00 0.00 1.98
10 11 5.246656 TCTGTTGAAACTACCGGGAATTAGA 59.753 40.000 6.32 0.00 0.00 2.10
11 12 5.484715 TCTGTTGAAACTACCGGGAATTAG 58.515 41.667 6.32 0.00 0.00 1.73
12 13 5.486735 TCTGTTGAAACTACCGGGAATTA 57.513 39.130 6.32 0.00 0.00 1.40
13 14 4.360951 TCTGTTGAAACTACCGGGAATT 57.639 40.909 6.32 0.00 0.00 2.17
14 15 4.360951 TTCTGTTGAAACTACCGGGAAT 57.639 40.909 6.32 0.00 0.00 3.01
15 16 3.842007 TTCTGTTGAAACTACCGGGAA 57.158 42.857 6.32 0.00 0.00 3.97
16 17 3.307199 GGATTCTGTTGAAACTACCGGGA 60.307 47.826 6.32 0.00 35.63 5.14
17 18 3.007635 GGATTCTGTTGAAACTACCGGG 58.992 50.000 6.32 0.00 35.63 5.73
18 19 3.007635 GGGATTCTGTTGAAACTACCGG 58.992 50.000 0.00 0.00 35.63 5.28
19 20 3.670625 TGGGATTCTGTTGAAACTACCG 58.329 45.455 0.00 0.00 35.63 4.02
20 21 5.710099 TGAATGGGATTCTGTTGAAACTACC 59.290 40.000 0.00 0.00 39.96 3.18
21 22 6.817765 TGAATGGGATTCTGTTGAAACTAC 57.182 37.500 0.00 0.00 39.96 2.73
22 23 7.122650 GGATTGAATGGGATTCTGTTGAAACTA 59.877 37.037 0.00 0.00 39.96 2.24
23 24 6.071165 GGATTGAATGGGATTCTGTTGAAACT 60.071 38.462 0.00 0.00 39.96 2.66
24 25 6.101997 GGATTGAATGGGATTCTGTTGAAAC 58.898 40.000 0.00 0.00 39.96 2.78
25 26 5.187576 GGGATTGAATGGGATTCTGTTGAAA 59.812 40.000 0.00 0.00 39.96 2.69
26 27 4.711355 GGGATTGAATGGGATTCTGTTGAA 59.289 41.667 0.00 0.00 39.96 2.69
27 28 4.264307 TGGGATTGAATGGGATTCTGTTGA 60.264 41.667 0.00 0.00 39.96 3.18
28 29 4.025360 TGGGATTGAATGGGATTCTGTTG 58.975 43.478 0.00 0.00 39.96 3.33
29 30 4.264532 ACTGGGATTGAATGGGATTCTGTT 60.265 41.667 0.00 0.00 39.96 3.16
30 31 3.270433 ACTGGGATTGAATGGGATTCTGT 59.730 43.478 0.00 0.00 39.96 3.41
31 32 3.907221 ACTGGGATTGAATGGGATTCTG 58.093 45.455 0.00 0.00 39.96 3.02
32 33 5.732331 TTACTGGGATTGAATGGGATTCT 57.268 39.130 0.00 0.00 39.96 2.40
33 34 6.550854 TGATTTACTGGGATTGAATGGGATTC 59.449 38.462 0.00 0.00 39.70 2.52
34 35 6.442961 TGATTTACTGGGATTGAATGGGATT 58.557 36.000 0.00 0.00 0.00 3.01
35 36 6.029492 TGATTTACTGGGATTGAATGGGAT 57.971 37.500 0.00 0.00 0.00 3.85
36 37 5.448654 CTGATTTACTGGGATTGAATGGGA 58.551 41.667 0.00 0.00 0.00 4.37
37 38 4.038402 GCTGATTTACTGGGATTGAATGGG 59.962 45.833 0.00 0.00 0.00 4.00
38 39 4.891756 AGCTGATTTACTGGGATTGAATGG 59.108 41.667 0.00 0.00 0.00 3.16
39 40 6.293845 GCTAGCTGATTTACTGGGATTGAATG 60.294 42.308 7.70 0.00 0.00 2.67
40 41 5.767168 GCTAGCTGATTTACTGGGATTGAAT 59.233 40.000 7.70 0.00 0.00 2.57
41 42 5.126067 GCTAGCTGATTTACTGGGATTGAA 58.874 41.667 7.70 0.00 0.00 2.69
42 43 4.708177 GCTAGCTGATTTACTGGGATTGA 58.292 43.478 7.70 0.00 0.00 2.57
43 44 3.496130 CGCTAGCTGATTTACTGGGATTG 59.504 47.826 13.93 0.00 0.00 2.67
44 45 3.134804 ACGCTAGCTGATTTACTGGGATT 59.865 43.478 13.93 0.00 0.00 3.01
45 46 2.700897 ACGCTAGCTGATTTACTGGGAT 59.299 45.455 13.93 0.00 0.00 3.85
46 47 2.100916 GACGCTAGCTGATTTACTGGGA 59.899 50.000 13.93 0.00 0.00 4.37
47 48 2.474816 GACGCTAGCTGATTTACTGGG 58.525 52.381 13.93 0.00 0.00 4.45
48 49 2.120232 CGACGCTAGCTGATTTACTGG 58.880 52.381 13.93 0.00 0.00 4.00
49 50 2.120232 CCGACGCTAGCTGATTTACTG 58.880 52.381 13.93 0.00 0.00 2.74
50 51 1.536284 GCCGACGCTAGCTGATTTACT 60.536 52.381 13.93 0.00 0.00 2.24
51 52 0.853419 GCCGACGCTAGCTGATTTAC 59.147 55.000 13.93 0.00 0.00 2.01
52 53 0.594028 CGCCGACGCTAGCTGATTTA 60.594 55.000 13.93 0.00 0.00 1.40
53 54 1.878522 CGCCGACGCTAGCTGATTT 60.879 57.895 13.93 0.00 0.00 2.17
54 55 2.278857 CGCCGACGCTAGCTGATT 60.279 61.111 13.93 0.00 0.00 2.57
64 65 1.225745 GACATCTTTTGCGCCGACG 60.226 57.895 4.18 0.00 44.07 5.12
65 66 0.452784 GTGACATCTTTTGCGCCGAC 60.453 55.000 4.18 0.00 0.00 4.79
66 67 0.602638 AGTGACATCTTTTGCGCCGA 60.603 50.000 4.18 0.00 0.00 5.54
67 68 0.453282 CAGTGACATCTTTTGCGCCG 60.453 55.000 4.18 0.00 0.00 6.46
68 69 0.109597 CCAGTGACATCTTTTGCGCC 60.110 55.000 4.18 0.00 0.00 6.53
69 70 0.109597 CCCAGTGACATCTTTTGCGC 60.110 55.000 0.00 0.00 0.00 6.09
70 71 1.069022 CACCCAGTGACATCTTTTGCG 60.069 52.381 0.00 0.00 35.23 4.85
71 72 1.336240 GCACCCAGTGACATCTTTTGC 60.336 52.381 0.00 0.00 35.23 3.68
72 73 2.233271 AGCACCCAGTGACATCTTTTG 58.767 47.619 0.00 0.00 35.23 2.44
73 74 2.664402 AGCACCCAGTGACATCTTTT 57.336 45.000 0.00 0.00 35.23 2.27
74 75 2.026822 CCTAGCACCCAGTGACATCTTT 60.027 50.000 0.00 0.00 35.23 2.52
75 76 1.556911 CCTAGCACCCAGTGACATCTT 59.443 52.381 0.00 0.00 35.23 2.40
76 77 1.198713 CCTAGCACCCAGTGACATCT 58.801 55.000 0.00 0.00 35.23 2.90
77 78 0.179000 CCCTAGCACCCAGTGACATC 59.821 60.000 0.00 0.00 35.23 3.06
78 79 1.274703 CCCCTAGCACCCAGTGACAT 61.275 60.000 0.00 0.00 35.23 3.06
79 80 1.918293 CCCCTAGCACCCAGTGACA 60.918 63.158 0.00 0.00 35.23 3.58
80 81 1.918800 ACCCCTAGCACCCAGTGAC 60.919 63.158 0.00 0.00 35.23 3.67
81 82 1.918293 CACCCCTAGCACCCAGTGA 60.918 63.158 0.00 0.00 35.23 3.41
82 83 1.779061 AACACCCCTAGCACCCAGTG 61.779 60.000 0.00 0.00 36.51 3.66
83 84 1.065997 AAACACCCCTAGCACCCAGT 61.066 55.000 0.00 0.00 0.00 4.00
84 85 0.322546 GAAACACCCCTAGCACCCAG 60.323 60.000 0.00 0.00 0.00 4.45
85 86 0.770557 AGAAACACCCCTAGCACCCA 60.771 55.000 0.00 0.00 0.00 4.51
86 87 0.404426 AAGAAACACCCCTAGCACCC 59.596 55.000 0.00 0.00 0.00 4.61
87 88 1.202891 ACAAGAAACACCCCTAGCACC 60.203 52.381 0.00 0.00 0.00 5.01
88 89 2.271944 ACAAGAAACACCCCTAGCAC 57.728 50.000 0.00 0.00 0.00 4.40
89 90 2.441750 AGAACAAGAAACACCCCTAGCA 59.558 45.455 0.00 0.00 0.00 3.49
90 91 3.141767 AGAACAAGAAACACCCCTAGC 57.858 47.619 0.00 0.00 0.00 3.42
91 92 6.321435 AGAAAAAGAACAAGAAACACCCCTAG 59.679 38.462 0.00 0.00 0.00 3.02
92 93 6.192044 AGAAAAAGAACAAGAAACACCCCTA 58.808 36.000 0.00 0.00 0.00 3.53
93 94 5.023452 AGAAAAAGAACAAGAAACACCCCT 58.977 37.500 0.00 0.00 0.00 4.79
94 95 5.339008 AGAAAAAGAACAAGAAACACCCC 57.661 39.130 0.00 0.00 0.00 4.95
95 96 7.096884 AGTAGAAAAAGAACAAGAAACACCC 57.903 36.000 0.00 0.00 0.00 4.61
96 97 8.860128 CAAAGTAGAAAAAGAACAAGAAACACC 58.140 33.333 0.00 0.00 0.00 4.16
97 98 9.406828 ACAAAGTAGAAAAAGAACAAGAAACAC 57.593 29.630 0.00 0.00 0.00 3.32
98 99 9.405587 CACAAAGTAGAAAAAGAACAAGAAACA 57.594 29.630 0.00 0.00 0.00 2.83
99 100 9.406828 ACACAAAGTAGAAAAAGAACAAGAAAC 57.593 29.630 0.00 0.00 0.00 2.78
116 117 0.887247 TACGGGCGCTACACAAAGTA 59.113 50.000 7.64 0.00 0.00 2.24
117 118 0.668401 GTACGGGCGCTACACAAAGT 60.668 55.000 7.64 0.00 0.00 2.66
118 119 0.668096 TGTACGGGCGCTACACAAAG 60.668 55.000 7.64 0.00 0.00 2.77
119 120 0.037139 ATGTACGGGCGCTACACAAA 60.037 50.000 7.64 0.00 0.00 2.83
120 121 0.037139 AATGTACGGGCGCTACACAA 60.037 50.000 7.64 0.00 0.00 3.33
121 122 0.816373 TAATGTACGGGCGCTACACA 59.184 50.000 7.64 7.25 0.00 3.72
122 123 1.925229 TTAATGTACGGGCGCTACAC 58.075 50.000 7.64 0.89 0.00 2.90
123 124 2.894763 ATTAATGTACGGGCGCTACA 57.105 45.000 7.64 9.09 0.00 2.74
124 125 2.477754 GGAATTAATGTACGGGCGCTAC 59.522 50.000 7.64 2.35 0.00 3.58
125 126 2.102757 TGGAATTAATGTACGGGCGCTA 59.897 45.455 7.64 0.00 0.00 4.26
126 127 1.134340 TGGAATTAATGTACGGGCGCT 60.134 47.619 7.64 0.00 0.00 5.92
127 128 1.263217 CTGGAATTAATGTACGGGCGC 59.737 52.381 0.00 0.00 0.00 6.53
128 129 1.263217 GCTGGAATTAATGTACGGGCG 59.737 52.381 0.00 0.00 0.00 6.13
129 130 1.263217 CGCTGGAATTAATGTACGGGC 59.737 52.381 0.00 0.00 0.00 6.13
130 131 2.557317 ACGCTGGAATTAATGTACGGG 58.443 47.619 0.00 0.00 0.00 5.28
131 132 3.242608 CCAACGCTGGAATTAATGTACGG 60.243 47.826 0.00 0.00 46.92 4.02
132 133 3.935450 CCAACGCTGGAATTAATGTACG 58.065 45.455 0.00 0.00 46.92 3.67
144 145 3.121030 CCGAGCTTCCAACGCTGG 61.121 66.667 0.00 0.00 45.08 4.85
145 146 2.048222 TCCGAGCTTCCAACGCTG 60.048 61.111 0.00 0.00 37.96 5.18
146 147 2.048127 GTCCGAGCTTCCAACGCT 60.048 61.111 0.00 0.00 41.15 5.07
147 148 2.357034 TGTCCGAGCTTCCAACGC 60.357 61.111 0.00 0.00 0.00 4.84
148 149 2.027625 GGTGTCCGAGCTTCCAACG 61.028 63.158 0.00 0.00 0.00 4.10
149 150 0.951040 CTGGTGTCCGAGCTTCCAAC 60.951 60.000 0.00 0.00 0.00 3.77
150 151 1.371183 CTGGTGTCCGAGCTTCCAA 59.629 57.895 0.00 0.00 0.00 3.53
151 152 3.059982 CTGGTGTCCGAGCTTCCA 58.940 61.111 0.00 0.00 0.00 3.53
152 153 2.435059 GCTGGTGTCCGAGCTTCC 60.435 66.667 0.00 0.00 32.12 3.46
153 154 2.811317 CGCTGGTGTCCGAGCTTC 60.811 66.667 0.00 0.00 32.70 3.86
154 155 3.616721 ACGCTGGTGTCCGAGCTT 61.617 61.111 0.00 0.00 32.70 3.74
155 156 4.363990 CACGCTGGTGTCCGAGCT 62.364 66.667 0.00 0.00 39.38 4.09
157 158 3.680786 TCCACGCTGGTGTCCGAG 61.681 66.667 4.33 0.00 42.80 4.63
158 159 3.986006 GTCCACGCTGGTGTCCGA 61.986 66.667 4.33 0.00 42.80 4.55
159 160 4.293648 TGTCCACGCTGGTGTCCG 62.294 66.667 4.33 0.00 42.80 4.79
160 161 1.812686 TAGTGTCCACGCTGGTGTCC 61.813 60.000 2.93 0.00 42.80 4.02
161 162 0.032952 TTAGTGTCCACGCTGGTGTC 59.967 55.000 2.93 0.00 42.80 3.67
162 163 0.033504 CTTAGTGTCCACGCTGGTGT 59.966 55.000 2.93 0.00 42.80 4.16
163 164 1.291877 GCTTAGTGTCCACGCTGGTG 61.292 60.000 2.93 0.00 43.99 4.17
164 165 1.004918 GCTTAGTGTCCACGCTGGT 60.005 57.895 2.93 0.00 39.03 4.00
165 166 1.741770 GGCTTAGTGTCCACGCTGG 60.742 63.158 2.93 0.00 39.43 4.85
166 167 0.602638 TTGGCTTAGTGTCCACGCTG 60.603 55.000 2.93 0.00 37.28 5.18
167 168 0.107831 TTTGGCTTAGTGTCCACGCT 59.892 50.000 0.00 0.00 40.27 5.07
168 169 0.948678 TTTTGGCTTAGTGTCCACGC 59.051 50.000 0.00 0.00 36.20 5.34
187 188 9.529325 GCGCTTAGGAAAGGAAAATAAATATTT 57.471 29.630 0.00 5.89 34.03 1.40
188 189 8.141909 GGCGCTTAGGAAAGGAAAATAAATATT 58.858 33.333 7.64 0.00 32.98 1.28
189 190 7.505923 AGGCGCTTAGGAAAGGAAAATAAATAT 59.494 33.333 7.64 0.00 32.98 1.28
190 191 6.831868 AGGCGCTTAGGAAAGGAAAATAAATA 59.168 34.615 7.64 0.00 32.98 1.40
191 192 5.656859 AGGCGCTTAGGAAAGGAAAATAAAT 59.343 36.000 7.64 0.00 32.98 1.40
192 193 5.014202 AGGCGCTTAGGAAAGGAAAATAAA 58.986 37.500 7.64 0.00 32.98 1.40
193 194 4.398044 CAGGCGCTTAGGAAAGGAAAATAA 59.602 41.667 7.64 0.00 32.98 1.40
194 195 3.945285 CAGGCGCTTAGGAAAGGAAAATA 59.055 43.478 7.64 0.00 32.98 1.40
195 196 2.755103 CAGGCGCTTAGGAAAGGAAAAT 59.245 45.455 7.64 0.00 32.98 1.82
196 197 2.159382 CAGGCGCTTAGGAAAGGAAAA 58.841 47.619 7.64 0.00 32.98 2.29
197 198 1.613255 CCAGGCGCTTAGGAAAGGAAA 60.613 52.381 7.64 0.00 32.98 3.13
198 199 0.035439 CCAGGCGCTTAGGAAAGGAA 60.035 55.000 7.64 0.00 32.98 3.36
199 200 1.198759 ACCAGGCGCTTAGGAAAGGA 61.199 55.000 17.74 0.00 32.98 3.36
200 201 0.322546 AACCAGGCGCTTAGGAAAGG 60.323 55.000 17.74 5.17 32.98 3.11
201 202 2.396590 TAACCAGGCGCTTAGGAAAG 57.603 50.000 17.74 0.00 35.68 2.62
202 203 2.706890 CTTAACCAGGCGCTTAGGAAA 58.293 47.619 17.74 11.05 0.00 3.13
203 204 1.677820 GCTTAACCAGGCGCTTAGGAA 60.678 52.381 17.74 4.41 0.00 3.36
204 205 0.107848 GCTTAACCAGGCGCTTAGGA 60.108 55.000 17.74 0.00 0.00 2.94
205 206 1.429148 CGCTTAACCAGGCGCTTAGG 61.429 60.000 7.64 9.68 44.64 2.69
206 207 2.006772 CGCTTAACCAGGCGCTTAG 58.993 57.895 7.64 0.00 44.64 2.18
207 208 4.195308 CGCTTAACCAGGCGCTTA 57.805 55.556 7.64 0.00 44.64 3.09
212 213 1.210155 CACAAGCGCTTAACCAGGC 59.790 57.895 24.55 0.00 0.00 4.85
213 214 1.210155 GCACAAGCGCTTAACCAGG 59.790 57.895 24.55 11.98 0.00 4.45
214 215 4.847255 GCACAAGCGCTTAACCAG 57.153 55.556 24.55 12.78 0.00 4.00
224 225 1.059942 GGCATTTACAACGCACAAGC 58.940 50.000 0.00 0.00 37.42 4.01
225 226 1.269448 AGGGCATTTACAACGCACAAG 59.731 47.619 0.00 0.00 0.00 3.16
226 227 1.323412 AGGGCATTTACAACGCACAA 58.677 45.000 0.00 0.00 0.00 3.33
227 228 2.186532 TAGGGCATTTACAACGCACA 57.813 45.000 0.00 0.00 0.00 4.57
228 229 3.562567 TTTAGGGCATTTACAACGCAC 57.437 42.857 0.00 0.00 0.00 5.34
229 230 3.674682 GCATTTAGGGCATTTACAACGCA 60.675 43.478 0.00 0.00 0.00 5.24
230 231 2.857748 GCATTTAGGGCATTTACAACGC 59.142 45.455 0.00 0.00 0.00 4.84
231 232 4.103365 TGCATTTAGGGCATTTACAACG 57.897 40.909 0.00 0.00 36.11 4.10
232 233 3.865164 GCTGCATTTAGGGCATTTACAAC 59.135 43.478 0.00 0.00 41.06 3.32
233 234 3.513119 TGCTGCATTTAGGGCATTTACAA 59.487 39.130 0.00 0.00 41.06 2.41
234 235 3.095332 TGCTGCATTTAGGGCATTTACA 58.905 40.909 0.00 0.00 41.06 2.41
235 236 3.381272 TCTGCTGCATTTAGGGCATTTAC 59.619 43.478 1.31 0.00 41.06 2.01
236 237 3.630168 TCTGCTGCATTTAGGGCATTTA 58.370 40.909 1.31 0.00 41.06 1.40
237 238 2.459644 TCTGCTGCATTTAGGGCATTT 58.540 42.857 1.31 0.00 41.06 2.32
238 239 2.148446 TCTGCTGCATTTAGGGCATT 57.852 45.000 1.31 0.00 41.06 3.56
239 240 2.029623 CTTCTGCTGCATTTAGGGCAT 58.970 47.619 1.31 0.00 41.06 4.40
240 241 1.466856 CTTCTGCTGCATTTAGGGCA 58.533 50.000 1.31 0.00 39.32 5.36
241 242 0.743097 CCTTCTGCTGCATTTAGGGC 59.257 55.000 1.31 0.00 0.00 5.19
242 243 2.424956 GTTCCTTCTGCTGCATTTAGGG 59.575 50.000 18.69 11.38 0.00 3.53
243 244 3.084039 TGTTCCTTCTGCTGCATTTAGG 58.916 45.455 1.31 10.37 0.00 2.69
244 245 4.771590 TTGTTCCTTCTGCTGCATTTAG 57.228 40.909 1.31 0.77 0.00 1.85
276 277 3.259064 GCTCCTGTATGCTCGTTTGTAA 58.741 45.455 0.00 0.00 0.00 2.41
399 400 3.753797 GGCTCATTTCGTCCTCTCTTTTT 59.246 43.478 0.00 0.00 0.00 1.94
428 429 2.453983 TTGCTGGCCATTTTAACTGC 57.546 45.000 5.51 3.69 0.00 4.40
444 446 2.805845 CCTGCTTGCTCACATAATTGC 58.194 47.619 0.00 0.00 0.00 3.56
445 447 2.480759 GGCCTGCTTGCTCACATAATTG 60.481 50.000 0.00 0.00 0.00 2.32
497 499 4.082523 GCTACAGGTGCGGCTGGA 62.083 66.667 0.00 0.00 0.00 3.86
506 508 3.391665 GATGCGGGCTGCTACAGGT 62.392 63.158 20.66 0.00 46.63 4.00
515 517 1.947597 TAACGGTTACGATGCGGGCT 61.948 55.000 0.00 0.00 44.60 5.19
520 522 5.517770 ACTCACTTATTAACGGTTACGATGC 59.482 40.000 0.00 0.00 44.60 3.91
959 973 0.183731 AATCTGGCCCCTTCGGATTC 59.816 55.000 0.00 0.00 35.91 2.52
973 987 3.854669 AGGCGCCCGGAGAATCTG 61.855 66.667 26.15 0.00 42.57 2.90
1512 1526 1.220477 GTGGAAGAGAGGCCAGAGC 59.780 63.158 5.01 0.00 34.22 4.09
1881 1898 2.093783 GGCGTAATCGAAAGTGTGGAAG 59.906 50.000 0.00 0.00 39.71 3.46
1923 1940 1.688735 TCGATTCCCAGCATCCTACTG 59.311 52.381 0.00 0.00 34.82 2.74
2274 2291 1.473258 AGCTCTCACGAATCTCAGCT 58.527 50.000 0.00 0.00 32.28 4.24
2889 2906 3.953612 GAGGCACCAATGTTCCATCATAA 59.046 43.478 0.00 0.00 29.00 1.90
2979 2996 7.305474 CGCTGACAATAAAAACTATGTTCCTT 58.695 34.615 0.00 0.00 0.00 3.36
3291 3308 6.106003 ACATTCCAGTTTCAGAAACCAAAAC 58.894 36.000 20.47 0.00 42.34 2.43
3445 3463 7.040686 TGCTTGAACTGGTTTAAAGATAACTCC 60.041 37.037 11.43 0.00 0.00 3.85
3673 3691 1.200948 GCCAAGCAAAGTTAGCAGAGG 59.799 52.381 0.00 0.00 0.00 3.69
3738 3756 6.223852 CACCTACACATGTTTAGACAGAACT 58.776 40.000 18.59 0.00 39.58 3.01
4183 4203 6.350780 GCTACTGGCTAAAGTTAGTAAGGACA 60.351 42.308 0.32 0.00 38.06 4.02
4232 4252 7.144661 TGCATACAGATTACAAAACAAACAGG 58.855 34.615 0.00 0.00 0.00 4.00
4258 4278 4.324267 AGCAGAACCACACCTAACATAAC 58.676 43.478 0.00 0.00 0.00 1.89
4324 4350 2.418669 AGGTCTTTCCCAACCAAGAGA 58.581 47.619 0.00 0.00 38.06 3.10
4517 4548 3.051341 TGATAGTAGGTGGGGAGGTGAAT 60.051 47.826 0.00 0.00 0.00 2.57
4550 4581 5.053145 AGAACTAACACACTTGCAGAAGAG 58.947 41.667 0.00 0.00 32.98 2.85
4649 4681 1.250840 ACGCAATTTTGAGAGGGGGC 61.251 55.000 0.93 0.00 0.00 5.80
4667 4699 7.637519 GCATATATCACATATCAAACATGCGAC 59.362 37.037 0.00 0.00 0.00 5.19
4688 4720 6.701841 AGATTCGATGTTAACGTTGAGCATAT 59.298 34.615 11.99 8.32 0.00 1.78
4707 4739 9.994432 AATTAGCATAAAGAAACAAGAGATTCG 57.006 29.630 0.00 0.00 32.36 3.34
5029 5061 2.089980 ACGTAGCTAACTCATCGGTGT 58.910 47.619 0.00 0.00 0.00 4.16
5190 5222 7.867909 TCGTTCATTGAGTATCCATCTTCATAC 59.132 37.037 0.00 0.00 0.00 2.39
5341 5373 6.581171 AGGTTTAAGAGAAAGATGCAAAGG 57.419 37.500 0.00 0.00 0.00 3.11
5385 5417 2.519771 TGCCTTCCATGAAGCATCTT 57.480 45.000 0.00 0.00 38.24 2.40
5641 5675 3.895998 AGCATCAAAGGAGGGAGAAATC 58.104 45.455 0.00 0.00 0.00 2.17
5700 5746 1.285641 CAATTTTGCCCGTGCGACT 59.714 52.632 0.00 0.00 41.78 4.18
5783 5830 3.495100 CCAGTACTCCAAGCAAAGTGTCT 60.495 47.826 0.00 0.00 0.00 3.41
5828 6036 4.999950 ACGAACTGATGAAGCAAAGAGATT 59.000 37.500 0.00 0.00 0.00 2.40
5857 6065 3.974871 TGTTCAGCCGTTTTCTAAACC 57.025 42.857 0.00 0.00 0.00 3.27
5901 6109 3.005791 ACATCATCTGTCTGACGTTGTCA 59.994 43.478 2.98 0.00 40.76 3.58
5910 6118 6.314896 GTCTAAAGGGAAACATCATCTGTCTG 59.685 42.308 0.00 0.00 36.98 3.51
5912 6120 6.410540 AGTCTAAAGGGAAACATCATCTGTC 58.589 40.000 0.00 0.00 36.98 3.51
5926 6134 3.129988 ACCACGATTCGTAGTCTAAAGGG 59.870 47.826 11.99 8.02 38.32 3.95
5929 6137 5.337554 CATGACCACGATTCGTAGTCTAAA 58.662 41.667 28.82 15.68 45.51 1.85
5948 6156 1.152860 ACAACAACGTGCCCCATGA 60.153 52.632 0.00 0.00 0.00 3.07
5959 6167 4.024302 GCTTAGTTCTACCCACACAACAAC 60.024 45.833 0.00 0.00 0.00 3.32
5960 6168 4.131596 GCTTAGTTCTACCCACACAACAA 58.868 43.478 0.00 0.00 0.00 2.83
5979 6187 3.005155 ACGTGTAGTTTAAGACGAGGCTT 59.995 43.478 0.00 0.00 35.77 4.35
6019 6238 0.109723 TCCTAGCCGCCAAAAACAGT 59.890 50.000 0.00 0.00 0.00 3.55
6020 6239 1.463674 ATCCTAGCCGCCAAAAACAG 58.536 50.000 0.00 0.00 0.00 3.16
6021 6240 1.543802 CAATCCTAGCCGCCAAAAACA 59.456 47.619 0.00 0.00 0.00 2.83
6022 6241 1.135112 CCAATCCTAGCCGCCAAAAAC 60.135 52.381 0.00 0.00 0.00 2.43
6023 6242 1.181786 CCAATCCTAGCCGCCAAAAA 58.818 50.000 0.00 0.00 0.00 1.94
6024 6243 0.329931 TCCAATCCTAGCCGCCAAAA 59.670 50.000 0.00 0.00 0.00 2.44
6037 6259 3.869272 CGCCGCAGCAGTCCAATC 61.869 66.667 0.00 0.00 39.83 2.67
6066 6288 5.647658 TCATCTACTTCACGAAAATGCCATT 59.352 36.000 0.00 0.00 0.00 3.16
6074 6296 5.959618 TCAGACTCATCTACTTCACGAAA 57.040 39.130 0.00 0.00 32.25 3.46
6078 6300 5.587289 GACCATCAGACTCATCTACTTCAC 58.413 45.833 0.00 0.00 32.25 3.18
6084 6306 3.117851 ACTCCGACCATCAGACTCATCTA 60.118 47.826 0.00 0.00 32.25 1.98
6085 6307 2.305928 CTCCGACCATCAGACTCATCT 58.694 52.381 0.00 0.00 34.57 2.90
6086 6308 2.028130 ACTCCGACCATCAGACTCATC 58.972 52.381 0.00 0.00 0.00 2.92
6087 6309 1.753649 CACTCCGACCATCAGACTCAT 59.246 52.381 0.00 0.00 0.00 2.90
6088 6310 1.177401 CACTCCGACCATCAGACTCA 58.823 55.000 0.00 0.00 0.00 3.41
6089 6311 0.457851 CCACTCCGACCATCAGACTC 59.542 60.000 0.00 0.00 0.00 3.36
6090 6312 0.039764 TCCACTCCGACCATCAGACT 59.960 55.000 0.00 0.00 0.00 3.24
6091 6313 0.457851 CTCCACTCCGACCATCAGAC 59.542 60.000 0.00 0.00 0.00 3.51
6092 6314 0.331616 TCTCCACTCCGACCATCAGA 59.668 55.000 0.00 0.00 0.00 3.27
6093 6315 1.134965 GTTCTCCACTCCGACCATCAG 60.135 57.143 0.00 0.00 0.00 2.90
6094 6316 0.895530 GTTCTCCACTCCGACCATCA 59.104 55.000 0.00 0.00 0.00 3.07
6095 6317 1.134965 CAGTTCTCCACTCCGACCATC 60.135 57.143 0.00 0.00 30.92 3.51
6096 6318 0.898320 CAGTTCTCCACTCCGACCAT 59.102 55.000 0.00 0.00 30.92 3.55
6097 6319 0.469331 ACAGTTCTCCACTCCGACCA 60.469 55.000 0.00 0.00 30.92 4.02
6098 6320 0.680061 AACAGTTCTCCACTCCGACC 59.320 55.000 0.00 0.00 30.92 4.79


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

AutoCloner maintained by Alex Coulton.