Multiple sequence alignment - TraesCS3B01G239400

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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 TraesCS3B01G239400 chr3B 100.000 3593 0 0 1 3593 377709607 377713199 0.000000e+00 6636
1 TraesCS3B01G239400 chr3B 78.017 232 49 2 1661 1891 650071776 650072006 1.040000e-30 145
2 TraesCS3B01G239400 chr3D 95.492 3372 71 20 258 3593 283675093 283678419 0.000000e+00 5310
3 TraesCS3B01G239400 chr3A 94.450 2883 70 29 262 3097 371321223 371324062 0.000000e+00 4355
4 TraesCS3B01G239400 chr3A 87.451 255 31 1 3 256 165328374 165328628 3.510000e-75 292
5 TraesCS3B01G239400 chr3A 87.160 257 28 4 3 256 89665200 89664946 1.630000e-73 287
6 TraesCS3B01G239400 chr3A 87.109 256 29 4 3 256 715173420 715173673 1.630000e-73 287
7 TraesCS3B01G239400 chr3A 75.562 356 77 7 1541 1891 630807070 630807420 2.220000e-37 167
8 TraesCS3B01G239400 chr1A 81.373 1063 180 14 1530 2580 589791469 589792525 0.000000e+00 850
9 TraesCS3B01G239400 chr1D 81.144 1066 177 20 1530 2580 491794953 491796009 0.000000e+00 833
10 TraesCS3B01G239400 chr1B 80.316 1077 194 15 1530 2594 684098148 684097078 0.000000e+00 798
11 TraesCS3B01G239400 chr4A 90.196 255 24 1 3 256 96479428 96479174 7.440000e-87 331
12 TraesCS3B01G239400 chr4A 87.059 255 32 1 3 256 216015571 216015317 1.630000e-73 287
13 TraesCS3B01G239400 chr4B 88.627 255 26 3 1 254 658028132 658027880 1.250000e-79 307
14 TraesCS3B01G239400 chr5B 89.362 235 25 0 1 235 496148400 496148166 2.710000e-76 296
15 TraesCS3B01G239400 chr2A 87.302 252 26 6 3 251 473605480 473605728 2.110000e-72 283
16 TraesCS3B01G239400 chr5D 86.275 255 33 2 3 255 227451003 227451257 3.530000e-70 276


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 TraesCS3B01G239400 chr3B 377709607 377713199 3592 False 6636 6636 100.000 1 3593 1 chr3B.!!$F1 3592
1 TraesCS3B01G239400 chr3D 283675093 283678419 3326 False 5310 5310 95.492 258 3593 1 chr3D.!!$F1 3335
2 TraesCS3B01G239400 chr3A 371321223 371324062 2839 False 4355 4355 94.450 262 3097 1 chr3A.!!$F2 2835
3 TraesCS3B01G239400 chr1A 589791469 589792525 1056 False 850 850 81.373 1530 2580 1 chr1A.!!$F1 1050
4 TraesCS3B01G239400 chr1D 491794953 491796009 1056 False 833 833 81.144 1530 2580 1 chr1D.!!$F1 1050
5 TraesCS3B01G239400 chr1B 684097078 684098148 1070 True 798 798 80.316 1530 2594 1 chr1B.!!$R1 1064

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
388 389 0.176680 CAATCTCACCGCTGTAGGCT 59.823 55.000 0.00 0.0 39.13 4.58 F
1494 1532 1.070957 GGAGGCCGCCACTAATACC 59.929 63.158 22.24 0.0 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2349 2393 2.437359 GTGCGCTTCTGGAGGCAT 60.437 61.111 9.73 0.0 35.17 4.40 R
3113 3193 0.233590 TCGATTTTGTTGACGCCACG 59.766 50.000 0.00 0.0 0.00 4.94 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
20 21 3.990959 GGAGGGATTAGCTATGGGAAG 57.009 52.381 0.00 0.00 0.00 3.46
21 22 3.252351 GGAGGGATTAGCTATGGGAAGT 58.748 50.000 0.00 0.00 0.00 3.01
22 23 3.653352 GGAGGGATTAGCTATGGGAAGTT 59.347 47.826 0.00 0.00 0.00 2.66
23 24 4.505742 GGAGGGATTAGCTATGGGAAGTTG 60.506 50.000 0.00 0.00 0.00 3.16
24 25 4.307259 AGGGATTAGCTATGGGAAGTTGA 58.693 43.478 0.00 0.00 0.00 3.18
25 26 4.916424 AGGGATTAGCTATGGGAAGTTGAT 59.084 41.667 0.00 0.00 0.00 2.57
26 27 5.373854 AGGGATTAGCTATGGGAAGTTGATT 59.626 40.000 0.00 0.00 0.00 2.57
27 28 6.071320 GGGATTAGCTATGGGAAGTTGATTT 58.929 40.000 0.00 0.00 0.00 2.17
28 29 6.551227 GGGATTAGCTATGGGAAGTTGATTTT 59.449 38.462 0.00 0.00 0.00 1.82
29 30 7.069950 GGGATTAGCTATGGGAAGTTGATTTTT 59.930 37.037 0.00 0.00 0.00 1.94
30 31 9.131791 GGATTAGCTATGGGAAGTTGATTTTTA 57.868 33.333 0.00 0.00 0.00 1.52
31 32 9.952188 GATTAGCTATGGGAAGTTGATTTTTAC 57.048 33.333 0.00 0.00 0.00 2.01
32 33 9.700831 ATTAGCTATGGGAAGTTGATTTTTACT 57.299 29.630 0.00 0.00 0.00 2.24
33 34 7.631717 AGCTATGGGAAGTTGATTTTTACTC 57.368 36.000 0.00 0.00 0.00 2.59
34 35 6.603599 AGCTATGGGAAGTTGATTTTTACTCC 59.396 38.462 0.00 0.00 0.00 3.85
35 36 6.183360 GCTATGGGAAGTTGATTTTTACTCCC 60.183 42.308 0.00 0.00 34.76 4.30
36 37 5.068215 TGGGAAGTTGATTTTTACTCCCA 57.932 39.130 2.77 2.77 38.38 4.37
37 38 5.650283 TGGGAAGTTGATTTTTACTCCCAT 58.350 37.500 2.77 0.00 37.09 4.00
38 39 6.081356 TGGGAAGTTGATTTTTACTCCCATT 58.919 36.000 2.77 0.00 37.09 3.16
39 40 6.556874 TGGGAAGTTGATTTTTACTCCCATTT 59.443 34.615 2.77 0.00 37.09 2.32
40 41 7.097192 GGGAAGTTGATTTTTACTCCCATTTC 58.903 38.462 0.00 0.00 34.54 2.17
41 42 7.097192 GGAAGTTGATTTTTACTCCCATTTCC 58.903 38.462 0.00 0.00 0.00 3.13
42 43 7.039011 GGAAGTTGATTTTTACTCCCATTTCCT 60.039 37.037 0.00 0.00 0.00 3.36
43 44 7.855784 AGTTGATTTTTACTCCCATTTCCTT 57.144 32.000 0.00 0.00 0.00 3.36
44 45 7.670364 AGTTGATTTTTACTCCCATTTCCTTG 58.330 34.615 0.00 0.00 0.00 3.61
45 46 7.290014 AGTTGATTTTTACTCCCATTTCCTTGT 59.710 33.333 0.00 0.00 0.00 3.16
46 47 7.610580 TGATTTTTACTCCCATTTCCTTGTT 57.389 32.000 0.00 0.00 0.00 2.83
47 48 8.028652 TGATTTTTACTCCCATTTCCTTGTTT 57.971 30.769 0.00 0.00 0.00 2.83
48 49 7.930865 TGATTTTTACTCCCATTTCCTTGTTTG 59.069 33.333 0.00 0.00 0.00 2.93
49 50 5.799827 TTTACTCCCATTTCCTTGTTTGG 57.200 39.130 0.00 0.00 0.00 3.28
50 51 1.970640 ACTCCCATTTCCTTGTTTGGC 59.029 47.619 0.00 0.00 0.00 4.52
51 52 1.969923 CTCCCATTTCCTTGTTTGGCA 59.030 47.619 0.00 0.00 0.00 4.92
52 53 2.568509 CTCCCATTTCCTTGTTTGGCAT 59.431 45.455 0.00 0.00 0.00 4.40
53 54 3.768757 CTCCCATTTCCTTGTTTGGCATA 59.231 43.478 0.00 0.00 0.00 3.14
54 55 4.360889 TCCCATTTCCTTGTTTGGCATAT 58.639 39.130 0.00 0.00 0.00 1.78
55 56 4.161942 TCCCATTTCCTTGTTTGGCATATG 59.838 41.667 0.00 0.00 0.00 1.78
56 57 4.444536 CCATTTCCTTGTTTGGCATATGG 58.555 43.478 4.56 0.00 0.00 2.74
57 58 4.080975 CCATTTCCTTGTTTGGCATATGGT 60.081 41.667 4.56 0.00 31.01 3.55
58 59 4.533919 TTTCCTTGTTTGGCATATGGTG 57.466 40.909 4.56 0.00 0.00 4.17
59 60 2.455557 TCCTTGTTTGGCATATGGTGG 58.544 47.619 4.56 0.00 0.00 4.61
60 61 1.481772 CCTTGTTTGGCATATGGTGGG 59.518 52.381 4.56 0.00 0.00 4.61
61 62 2.455557 CTTGTTTGGCATATGGTGGGA 58.544 47.619 4.56 0.00 0.00 4.37
62 63 2.612285 TGTTTGGCATATGGTGGGAA 57.388 45.000 4.56 0.00 0.00 3.97
63 64 3.113191 TGTTTGGCATATGGTGGGAAT 57.887 42.857 4.56 0.00 0.00 3.01
64 65 3.448934 TGTTTGGCATATGGTGGGAATT 58.551 40.909 4.56 0.00 0.00 2.17
65 66 4.614475 TGTTTGGCATATGGTGGGAATTA 58.386 39.130 4.56 0.00 0.00 1.40
66 67 4.648762 TGTTTGGCATATGGTGGGAATTAG 59.351 41.667 4.56 0.00 0.00 1.73
67 68 4.534647 TTGGCATATGGTGGGAATTAGT 57.465 40.909 4.56 0.00 0.00 2.24
68 69 5.654901 TTGGCATATGGTGGGAATTAGTA 57.345 39.130 4.56 0.00 0.00 1.82
69 70 4.980573 TGGCATATGGTGGGAATTAGTAC 58.019 43.478 4.56 0.00 0.00 2.73
70 71 4.000988 GGCATATGGTGGGAATTAGTACG 58.999 47.826 4.56 0.00 0.00 3.67
71 72 4.000988 GCATATGGTGGGAATTAGTACGG 58.999 47.826 4.56 0.00 0.00 4.02
72 73 4.575885 CATATGGTGGGAATTAGTACGGG 58.424 47.826 0.00 0.00 0.00 5.28
73 74 2.250921 TGGTGGGAATTAGTACGGGA 57.749 50.000 0.00 0.00 0.00 5.14
74 75 2.766736 TGGTGGGAATTAGTACGGGAT 58.233 47.619 0.00 0.00 0.00 3.85
75 76 3.926198 TGGTGGGAATTAGTACGGGATA 58.074 45.455 0.00 0.00 0.00 2.59
76 77 4.296912 TGGTGGGAATTAGTACGGGATAA 58.703 43.478 0.00 0.00 0.00 1.75
77 78 4.720773 TGGTGGGAATTAGTACGGGATAAA 59.279 41.667 0.00 0.00 0.00 1.40
78 79 5.191323 TGGTGGGAATTAGTACGGGATAAAA 59.809 40.000 0.00 0.00 0.00 1.52
79 80 5.528690 GGTGGGAATTAGTACGGGATAAAAC 59.471 44.000 0.00 0.00 0.00 2.43
80 81 6.351711 GTGGGAATTAGTACGGGATAAAACT 58.648 40.000 0.00 0.00 0.00 2.66
81 82 6.481313 GTGGGAATTAGTACGGGATAAAACTC 59.519 42.308 0.00 0.00 0.00 3.01
82 83 6.384886 TGGGAATTAGTACGGGATAAAACTCT 59.615 38.462 0.00 0.00 0.00 3.24
83 84 6.704937 GGGAATTAGTACGGGATAAAACTCTG 59.295 42.308 0.00 0.00 0.00 3.35
84 85 6.202379 GGAATTAGTACGGGATAAAACTCTGC 59.798 42.308 0.00 0.00 0.00 4.26
85 86 5.927281 TTAGTACGGGATAAAACTCTGCT 57.073 39.130 0.00 0.00 0.00 4.24
86 87 4.388378 AGTACGGGATAAAACTCTGCTC 57.612 45.455 0.00 0.00 0.00 4.26
87 88 3.767673 AGTACGGGATAAAACTCTGCTCA 59.232 43.478 0.00 0.00 0.00 4.26
88 89 3.914426 ACGGGATAAAACTCTGCTCAT 57.086 42.857 0.00 0.00 0.00 2.90
89 90 3.798202 ACGGGATAAAACTCTGCTCATC 58.202 45.455 0.00 0.00 0.00 2.92
90 91 3.197766 ACGGGATAAAACTCTGCTCATCA 59.802 43.478 0.00 0.00 0.00 3.07
91 92 4.191544 CGGGATAAAACTCTGCTCATCAA 58.808 43.478 0.00 0.00 0.00 2.57
92 93 4.818546 CGGGATAAAACTCTGCTCATCAAT 59.181 41.667 0.00 0.00 0.00 2.57
93 94 5.297776 CGGGATAAAACTCTGCTCATCAATT 59.702 40.000 0.00 0.00 0.00 2.32
94 95 6.483307 CGGGATAAAACTCTGCTCATCAATTA 59.517 38.462 0.00 0.00 0.00 1.40
95 96 7.012327 CGGGATAAAACTCTGCTCATCAATTAA 59.988 37.037 0.00 0.00 0.00 1.40
96 97 8.131731 GGGATAAAACTCTGCTCATCAATTAAC 58.868 37.037 0.00 0.00 0.00 2.01
97 98 8.677300 GGATAAAACTCTGCTCATCAATTAACA 58.323 33.333 0.00 0.00 0.00 2.41
100 101 6.506500 AACTCTGCTCATCAATTAACAAGG 57.493 37.500 0.00 0.00 0.00 3.61
101 102 5.564550 ACTCTGCTCATCAATTAACAAGGT 58.435 37.500 0.00 0.00 0.00 3.50
102 103 6.711277 ACTCTGCTCATCAATTAACAAGGTA 58.289 36.000 0.00 0.00 0.00 3.08
103 104 6.595716 ACTCTGCTCATCAATTAACAAGGTAC 59.404 38.462 0.00 0.00 0.00 3.34
104 105 5.580691 TCTGCTCATCAATTAACAAGGTACG 59.419 40.000 0.00 0.00 0.00 3.67
105 106 4.094294 TGCTCATCAATTAACAAGGTACGC 59.906 41.667 0.00 0.00 0.00 4.42
106 107 4.495844 GCTCATCAATTAACAAGGTACGCC 60.496 45.833 0.00 0.00 0.00 5.68
107 108 4.580868 TCATCAATTAACAAGGTACGCCA 58.419 39.130 0.00 0.00 37.19 5.69
108 109 5.189928 TCATCAATTAACAAGGTACGCCAT 58.810 37.500 0.00 0.00 37.19 4.40
109 110 4.955925 TCAATTAACAAGGTACGCCATG 57.044 40.909 0.00 0.00 39.24 3.66
110 111 3.692101 TCAATTAACAAGGTACGCCATGG 59.308 43.478 7.63 7.63 37.76 3.66
111 112 3.637911 ATTAACAAGGTACGCCATGGA 57.362 42.857 18.40 0.00 37.76 3.41
112 113 3.420300 TTAACAAGGTACGCCATGGAA 57.580 42.857 18.40 0.00 37.76 3.53
113 114 2.279935 AACAAGGTACGCCATGGAAA 57.720 45.000 18.40 0.00 37.76 3.13
114 115 2.279935 ACAAGGTACGCCATGGAAAA 57.720 45.000 18.40 0.00 37.76 2.29
115 116 2.588620 ACAAGGTACGCCATGGAAAAA 58.411 42.857 18.40 0.00 37.76 1.94
135 136 5.420725 AAAAATAGGTGGGAATTGGCTTC 57.579 39.130 0.00 0.00 0.00 3.86
145 146 3.857549 GAATTGGCTTCCTCAACTTCC 57.142 47.619 0.00 0.00 0.00 3.46
146 147 2.978156 ATTGGCTTCCTCAACTTCCA 57.022 45.000 0.00 0.00 0.00 3.53
147 148 2.978156 TTGGCTTCCTCAACTTCCAT 57.022 45.000 0.00 0.00 0.00 3.41
148 149 2.978156 TGGCTTCCTCAACTTCCATT 57.022 45.000 0.00 0.00 0.00 3.16
149 150 2.795329 TGGCTTCCTCAACTTCCATTC 58.205 47.619 0.00 0.00 0.00 2.67
150 151 2.095461 GGCTTCCTCAACTTCCATTCC 58.905 52.381 0.00 0.00 0.00 3.01
151 152 2.095461 GCTTCCTCAACTTCCATTCCC 58.905 52.381 0.00 0.00 0.00 3.97
152 153 2.728007 CTTCCTCAACTTCCATTCCCC 58.272 52.381 0.00 0.00 0.00 4.81
153 154 2.059756 TCCTCAACTTCCATTCCCCT 57.940 50.000 0.00 0.00 0.00 4.79
154 155 2.358258 TCCTCAACTTCCATTCCCCTT 58.642 47.619 0.00 0.00 0.00 3.95
155 156 2.308866 TCCTCAACTTCCATTCCCCTTC 59.691 50.000 0.00 0.00 0.00 3.46
156 157 2.621668 CCTCAACTTCCATTCCCCTTCC 60.622 54.545 0.00 0.00 0.00 3.46
157 158 1.004277 TCAACTTCCATTCCCCTTCCG 59.996 52.381 0.00 0.00 0.00 4.30
158 159 1.004277 CAACTTCCATTCCCCTTCCGA 59.996 52.381 0.00 0.00 0.00 4.55
159 160 0.618981 ACTTCCATTCCCCTTCCGAC 59.381 55.000 0.00 0.00 0.00 4.79
160 161 0.912486 CTTCCATTCCCCTTCCGACT 59.088 55.000 0.00 0.00 0.00 4.18
161 162 1.282157 CTTCCATTCCCCTTCCGACTT 59.718 52.381 0.00 0.00 0.00 3.01
162 163 2.257391 TCCATTCCCCTTCCGACTTA 57.743 50.000 0.00 0.00 0.00 2.24
163 164 2.553464 TCCATTCCCCTTCCGACTTAA 58.447 47.619 0.00 0.00 0.00 1.85
164 165 2.914278 TCCATTCCCCTTCCGACTTAAA 59.086 45.455 0.00 0.00 0.00 1.52
165 166 3.014623 CCATTCCCCTTCCGACTTAAAC 58.985 50.000 0.00 0.00 0.00 2.01
166 167 3.308188 CCATTCCCCTTCCGACTTAAACT 60.308 47.826 0.00 0.00 0.00 2.66
167 168 4.332828 CATTCCCCTTCCGACTTAAACTT 58.667 43.478 0.00 0.00 0.00 2.66
168 169 3.690475 TCCCCTTCCGACTTAAACTTC 57.310 47.619 0.00 0.00 0.00 3.01
169 170 2.303890 TCCCCTTCCGACTTAAACTTCC 59.696 50.000 0.00 0.00 0.00 3.46
170 171 2.039348 CCCCTTCCGACTTAAACTTCCA 59.961 50.000 0.00 0.00 0.00 3.53
171 172 3.308188 CCCCTTCCGACTTAAACTTCCAT 60.308 47.826 0.00 0.00 0.00 3.41
172 173 4.332828 CCCTTCCGACTTAAACTTCCATT 58.667 43.478 0.00 0.00 0.00 3.16
173 174 4.395231 CCCTTCCGACTTAAACTTCCATTC 59.605 45.833 0.00 0.00 0.00 2.67
174 175 4.395231 CCTTCCGACTTAAACTTCCATTCC 59.605 45.833 0.00 0.00 0.00 3.01
175 176 3.946606 TCCGACTTAAACTTCCATTCCC 58.053 45.455 0.00 0.00 0.00 3.97
176 177 3.585732 TCCGACTTAAACTTCCATTCCCT 59.414 43.478 0.00 0.00 0.00 4.20
177 178 3.939592 CCGACTTAAACTTCCATTCCCTC 59.060 47.826 0.00 0.00 0.00 4.30
178 179 4.323562 CCGACTTAAACTTCCATTCCCTCT 60.324 45.833 0.00 0.00 0.00 3.69
179 180 5.105064 CCGACTTAAACTTCCATTCCCTCTA 60.105 44.000 0.00 0.00 0.00 2.43
180 181 6.403878 CGACTTAAACTTCCATTCCCTCTAA 58.596 40.000 0.00 0.00 0.00 2.10
181 182 7.048512 CGACTTAAACTTCCATTCCCTCTAAT 58.951 38.462 0.00 0.00 0.00 1.73
182 183 7.553044 CGACTTAAACTTCCATTCCCTCTAATT 59.447 37.037 0.00 0.00 0.00 1.40
183 184 9.901172 GACTTAAACTTCCATTCCCTCTAATTA 57.099 33.333 0.00 0.00 0.00 1.40
187 188 8.950007 AAACTTCCATTCCCTCTAATTAAACA 57.050 30.769 0.00 0.00 0.00 2.83
188 189 8.581253 AACTTCCATTCCCTCTAATTAAACAG 57.419 34.615 0.00 0.00 0.00 3.16
189 190 7.699878 ACTTCCATTCCCTCTAATTAAACAGT 58.300 34.615 0.00 0.00 0.00 3.55
190 191 7.611855 ACTTCCATTCCCTCTAATTAAACAGTG 59.388 37.037 0.00 0.00 0.00 3.66
191 192 7.265599 TCCATTCCCTCTAATTAAACAGTGA 57.734 36.000 0.00 0.00 0.00 3.41
192 193 7.695055 TCCATTCCCTCTAATTAAACAGTGAA 58.305 34.615 0.00 0.00 0.00 3.18
193 194 7.610305 TCCATTCCCTCTAATTAAACAGTGAAC 59.390 37.037 0.00 0.00 0.00 3.18
194 195 7.611855 CCATTCCCTCTAATTAAACAGTGAACT 59.388 37.037 0.00 0.00 0.00 3.01
195 196 9.014297 CATTCCCTCTAATTAAACAGTGAACTT 57.986 33.333 0.00 0.00 0.00 2.66
196 197 8.990163 TTCCCTCTAATTAAACAGTGAACTTT 57.010 30.769 0.00 0.00 0.00 2.66
197 198 8.990163 TCCCTCTAATTAAACAGTGAACTTTT 57.010 30.769 0.00 0.00 0.00 2.27
207 208 9.621629 TTAAACAGTGAACTTTTAATCTCCTCA 57.378 29.630 0.00 0.00 0.00 3.86
208 209 7.497925 AACAGTGAACTTTTAATCTCCTCAC 57.502 36.000 0.00 0.00 33.51 3.51
209 210 5.998363 ACAGTGAACTTTTAATCTCCTCACC 59.002 40.000 0.00 0.00 33.75 4.02
210 211 5.412904 CAGTGAACTTTTAATCTCCTCACCC 59.587 44.000 0.00 0.00 33.75 4.61
211 212 4.700692 GTGAACTTTTAATCTCCTCACCCC 59.299 45.833 0.00 0.00 0.00 4.95
212 213 4.352595 TGAACTTTTAATCTCCTCACCCCA 59.647 41.667 0.00 0.00 0.00 4.96
213 214 5.015178 TGAACTTTTAATCTCCTCACCCCAT 59.985 40.000 0.00 0.00 0.00 4.00
214 215 6.216662 TGAACTTTTAATCTCCTCACCCCATA 59.783 38.462 0.00 0.00 0.00 2.74
215 216 6.652205 ACTTTTAATCTCCTCACCCCATAA 57.348 37.500 0.00 0.00 0.00 1.90
216 217 6.424032 ACTTTTAATCTCCTCACCCCATAAC 58.576 40.000 0.00 0.00 0.00 1.89
217 218 6.217693 ACTTTTAATCTCCTCACCCCATAACT 59.782 38.462 0.00 0.00 0.00 2.24
218 219 5.888982 TTAATCTCCTCACCCCATAACTC 57.111 43.478 0.00 0.00 0.00 3.01
219 220 2.176247 TCTCCTCACCCCATAACTCC 57.824 55.000 0.00 0.00 0.00 3.85
220 221 1.132500 CTCCTCACCCCATAACTCCC 58.868 60.000 0.00 0.00 0.00 4.30
221 222 0.419865 TCCTCACCCCATAACTCCCA 59.580 55.000 0.00 0.00 0.00 4.37
222 223 1.010793 TCCTCACCCCATAACTCCCAT 59.989 52.381 0.00 0.00 0.00 4.00
223 224 1.852965 CCTCACCCCATAACTCCCATT 59.147 52.381 0.00 0.00 0.00 3.16
224 225 2.158608 CCTCACCCCATAACTCCCATTC 60.159 54.545 0.00 0.00 0.00 2.67
225 226 1.850345 TCACCCCATAACTCCCATTCC 59.150 52.381 0.00 0.00 0.00 3.01
226 227 1.133482 CACCCCATAACTCCCATTCCC 60.133 57.143 0.00 0.00 0.00 3.97
227 228 0.482887 CCCCATAACTCCCATTCCCC 59.517 60.000 0.00 0.00 0.00 4.81
228 229 1.231018 CCCATAACTCCCATTCCCCA 58.769 55.000 0.00 0.00 0.00 4.96
229 230 1.788915 CCCATAACTCCCATTCCCCAT 59.211 52.381 0.00 0.00 0.00 4.00
230 231 2.225117 CCCATAACTCCCATTCCCCATC 60.225 54.545 0.00 0.00 0.00 3.51
231 232 2.718609 CCATAACTCCCATTCCCCATCT 59.281 50.000 0.00 0.00 0.00 2.90
232 233 3.140895 CCATAACTCCCATTCCCCATCTT 59.859 47.826 0.00 0.00 0.00 2.40
233 234 4.387891 CCATAACTCCCATTCCCCATCTTT 60.388 45.833 0.00 0.00 0.00 2.52
234 235 5.162991 CCATAACTCCCATTCCCCATCTTTA 60.163 44.000 0.00 0.00 0.00 1.85
235 236 4.965283 AACTCCCATTCCCCATCTTTAA 57.035 40.909 0.00 0.00 0.00 1.52
236 237 5.487861 AACTCCCATTCCCCATCTTTAAT 57.512 39.130 0.00 0.00 0.00 1.40
237 238 5.487861 ACTCCCATTCCCCATCTTTAATT 57.512 39.130 0.00 0.00 0.00 1.40
238 239 5.458595 ACTCCCATTCCCCATCTTTAATTC 58.541 41.667 0.00 0.00 0.00 2.17
239 240 4.814967 TCCCATTCCCCATCTTTAATTCC 58.185 43.478 0.00 0.00 0.00 3.01
240 241 3.903714 CCCATTCCCCATCTTTAATTCCC 59.096 47.826 0.00 0.00 0.00 3.97
241 242 3.903714 CCATTCCCCATCTTTAATTCCCC 59.096 47.826 0.00 0.00 0.00 4.81
242 243 4.389034 CCATTCCCCATCTTTAATTCCCCT 60.389 45.833 0.00 0.00 0.00 4.79
243 244 5.162881 CCATTCCCCATCTTTAATTCCCCTA 60.163 44.000 0.00 0.00 0.00 3.53
244 245 6.381250 CATTCCCCATCTTTAATTCCCCTAA 58.619 40.000 0.00 0.00 0.00 2.69
245 246 5.397553 TCCCCATCTTTAATTCCCCTAAC 57.602 43.478 0.00 0.00 0.00 2.34
246 247 4.169264 TCCCCATCTTTAATTCCCCTAACC 59.831 45.833 0.00 0.00 0.00 2.85
247 248 4.078863 CCCCATCTTTAATTCCCCTAACCA 60.079 45.833 0.00 0.00 0.00 3.67
248 249 5.524535 CCCATCTTTAATTCCCCTAACCAA 58.475 41.667 0.00 0.00 0.00 3.67
249 250 5.961421 CCCATCTTTAATTCCCCTAACCAAA 59.039 40.000 0.00 0.00 0.00 3.28
250 251 6.127168 CCCATCTTTAATTCCCCTAACCAAAC 60.127 42.308 0.00 0.00 0.00 2.93
251 252 6.405397 CCATCTTTAATTCCCCTAACCAAACG 60.405 42.308 0.00 0.00 0.00 3.60
252 253 4.460034 TCTTTAATTCCCCTAACCAAACGC 59.540 41.667 0.00 0.00 0.00 4.84
253 254 1.170442 AATTCCCCTAACCAAACGCG 58.830 50.000 3.53 3.53 0.00 6.01
254 255 1.310216 ATTCCCCTAACCAAACGCGC 61.310 55.000 5.73 0.00 0.00 6.86
255 256 2.359478 CCCCTAACCAAACGCGCT 60.359 61.111 5.73 0.00 0.00 5.92
256 257 1.078988 CCCCTAACCAAACGCGCTA 60.079 57.895 5.73 0.00 0.00 4.26
272 273 1.635817 GCTATGGGTCCCTTGAGGCA 61.636 60.000 10.00 0.00 34.51 4.75
388 389 0.176680 CAATCTCACCGCTGTAGGCT 59.823 55.000 0.00 0.00 39.13 4.58
411 412 6.315144 GCTTACCACCAAATTTTGACAGTTTT 59.685 34.615 10.72 0.00 0.00 2.43
530 537 3.136123 TTCGTCCGCTAGTCCCCG 61.136 66.667 0.00 0.00 0.00 5.73
648 658 3.616721 ACCCGTTCGCTGTCAGCT 61.617 61.111 22.13 0.00 39.60 4.24
858 869 1.073763 TCCCCATTTCACACCAGTCTG 59.926 52.381 0.00 0.00 0.00 3.51
1422 1454 3.760035 GACTCCGAGGCCGCTGAA 61.760 66.667 4.53 0.00 0.00 3.02
1423 1455 3.708220 GACTCCGAGGCCGCTGAAG 62.708 68.421 4.53 1.49 0.00 3.02
1494 1532 1.070957 GGAGGCCGCCACTAATACC 59.929 63.158 22.24 0.00 0.00 2.73
2349 2393 4.680237 CTCAAGACGCGGTGGGCA 62.680 66.667 12.47 0.00 43.84 5.36
2836 2890 4.202010 TGTGAAGAGCAAAGCTGGTTTAAC 60.202 41.667 4.32 0.84 39.88 2.01
2839 2893 2.294512 AGAGCAAAGCTGGTTTAACTGC 59.705 45.455 4.32 5.27 39.88 4.40
2884 2938 4.537135 TCTGTACGCCATTCTCTCTTTT 57.463 40.909 0.00 0.00 0.00 2.27
3023 3093 0.458669 GACAATCTAAGGGACGCGGA 59.541 55.000 12.47 0.00 0.00 5.54
3113 3193 9.941664 CATTATCAGATGACATTAGTGGAAAAC 57.058 33.333 0.00 0.00 0.00 2.43
3120 3200 1.533731 CATTAGTGGAAAACGTGGCGT 59.466 47.619 0.00 0.00 43.97 5.68
3121 3201 1.219646 TTAGTGGAAAACGTGGCGTC 58.780 50.000 0.00 0.00 39.99 5.19
3138 3218 2.774007 CGTCAACAAAATCGATGCTCC 58.226 47.619 0.00 0.00 0.00 4.70
3145 3225 5.138125 ACAAAATCGATGCTCCAAAATGT 57.862 34.783 0.00 0.00 0.00 2.71
3237 3318 6.371809 AAACAACACTTTCGCAATCTAAGA 57.628 33.333 0.00 0.00 0.00 2.10
3273 3354 0.029300 CCTCAAATTGCCCGCATACG 59.971 55.000 0.00 0.00 39.67 3.06
3288 3369 3.243336 GCATACGATCCGGACATACTTC 58.757 50.000 6.12 0.00 0.00 3.01
3294 3375 3.566523 GATCCGGACATACTTCGTCATC 58.433 50.000 6.12 0.00 34.97 2.92
3299 3380 2.858344 GGACATACTTCGTCATCCAACG 59.142 50.000 0.00 0.00 43.92 4.10
3374 3457 1.149627 CACCCAAAACCACTCCCGA 59.850 57.895 0.00 0.00 0.00 5.14
3388 3471 1.205655 CTCCCGAAGCTCACATCTCAA 59.794 52.381 0.00 0.00 0.00 3.02
3390 3473 2.237143 TCCCGAAGCTCACATCTCAATT 59.763 45.455 0.00 0.00 0.00 2.32
3405 3488 3.142028 TCTCAATTCCTTCCCCCTTGTTT 59.858 43.478 0.00 0.00 0.00 2.83
3508 3591 3.063743 GCCATGCCGGTTTGCCTAC 62.064 63.158 1.90 0.00 36.97 3.18
3539 3622 4.193334 CTCTCGTCCATCCGCGCA 62.193 66.667 8.75 0.00 0.00 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.252351 ACTTCCCATAGCTAATCCCTCC 58.748 50.000 0.00 0.00 0.00 4.30
1 2 4.348168 TCAACTTCCCATAGCTAATCCCTC 59.652 45.833 0.00 0.00 0.00 4.30
2 3 4.307259 TCAACTTCCCATAGCTAATCCCT 58.693 43.478 0.00 0.00 0.00 4.20
3 4 4.706842 TCAACTTCCCATAGCTAATCCC 57.293 45.455 0.00 0.00 0.00 3.85
4 5 7.588497 AAAATCAACTTCCCATAGCTAATCC 57.412 36.000 0.00 0.00 0.00 3.01
5 6 9.952188 GTAAAAATCAACTTCCCATAGCTAATC 57.048 33.333 0.00 0.00 0.00 1.75
6 7 9.700831 AGTAAAAATCAACTTCCCATAGCTAAT 57.299 29.630 0.00 0.00 0.00 1.73
7 8 9.174166 GAGTAAAAATCAACTTCCCATAGCTAA 57.826 33.333 0.00 0.00 0.00 3.09
8 9 7.773690 GGAGTAAAAATCAACTTCCCATAGCTA 59.226 37.037 0.00 0.00 0.00 3.32
9 10 6.603599 GGAGTAAAAATCAACTTCCCATAGCT 59.396 38.462 0.00 0.00 0.00 3.32
10 11 6.183360 GGGAGTAAAAATCAACTTCCCATAGC 60.183 42.308 1.89 0.00 35.59 2.97
11 12 6.889722 TGGGAGTAAAAATCAACTTCCCATAG 59.110 38.462 5.28 0.00 40.25 2.23
12 13 6.795590 TGGGAGTAAAAATCAACTTCCCATA 58.204 36.000 5.28 0.00 40.25 2.74
13 14 5.650283 TGGGAGTAAAAATCAACTTCCCAT 58.350 37.500 5.28 0.00 40.25 4.00
14 15 5.068215 TGGGAGTAAAAATCAACTTCCCA 57.932 39.130 5.28 5.28 40.25 4.37
15 16 6.605471 AATGGGAGTAAAAATCAACTTCCC 57.395 37.500 0.00 0.00 40.25 3.97
16 17 7.039011 AGGAAATGGGAGTAAAAATCAACTTCC 60.039 37.037 0.00 0.00 41.22 3.46
17 18 7.896811 AGGAAATGGGAGTAAAAATCAACTTC 58.103 34.615 0.00 0.00 0.00 3.01
18 19 7.855784 AGGAAATGGGAGTAAAAATCAACTT 57.144 32.000 0.00 0.00 0.00 2.66
19 20 7.290014 ACAAGGAAATGGGAGTAAAAATCAACT 59.710 33.333 0.00 0.00 0.00 3.16
20 21 7.441836 ACAAGGAAATGGGAGTAAAAATCAAC 58.558 34.615 0.00 0.00 0.00 3.18
21 22 7.610580 ACAAGGAAATGGGAGTAAAAATCAA 57.389 32.000 0.00 0.00 0.00 2.57
22 23 7.610580 AACAAGGAAATGGGAGTAAAAATCA 57.389 32.000 0.00 0.00 0.00 2.57
23 24 7.387673 CCAAACAAGGAAATGGGAGTAAAAATC 59.612 37.037 0.00 0.00 0.00 2.17
24 25 7.223584 CCAAACAAGGAAATGGGAGTAAAAAT 58.776 34.615 0.00 0.00 0.00 1.82
25 26 6.587273 CCAAACAAGGAAATGGGAGTAAAAA 58.413 36.000 0.00 0.00 0.00 1.94
26 27 5.454045 GCCAAACAAGGAAATGGGAGTAAAA 60.454 40.000 0.00 0.00 33.45 1.52
27 28 4.039852 GCCAAACAAGGAAATGGGAGTAAA 59.960 41.667 0.00 0.00 33.45 2.01
28 29 3.576550 GCCAAACAAGGAAATGGGAGTAA 59.423 43.478 0.00 0.00 33.45 2.24
29 30 3.161866 GCCAAACAAGGAAATGGGAGTA 58.838 45.455 0.00 0.00 33.45 2.59
30 31 1.970640 GCCAAACAAGGAAATGGGAGT 59.029 47.619 0.00 0.00 33.45 3.85
31 32 1.969923 TGCCAAACAAGGAAATGGGAG 59.030 47.619 0.00 0.00 33.45 4.30
32 33 2.094100 TGCCAAACAAGGAAATGGGA 57.906 45.000 0.00 0.00 33.45 4.37
33 34 4.444536 CATATGCCAAACAAGGAAATGGG 58.555 43.478 0.00 0.00 33.45 4.00
34 35 4.080975 ACCATATGCCAAACAAGGAAATGG 60.081 41.667 0.00 0.00 38.58 3.16
35 36 4.871557 CACCATATGCCAAACAAGGAAATG 59.128 41.667 0.00 0.00 0.00 2.32
36 37 4.080975 CCACCATATGCCAAACAAGGAAAT 60.081 41.667 0.00 0.00 0.00 2.17
37 38 3.260380 CCACCATATGCCAAACAAGGAAA 59.740 43.478 0.00 0.00 0.00 3.13
38 39 2.830923 CCACCATATGCCAAACAAGGAA 59.169 45.455 0.00 0.00 0.00 3.36
39 40 2.455557 CCACCATATGCCAAACAAGGA 58.544 47.619 0.00 0.00 0.00 3.36
40 41 1.481772 CCCACCATATGCCAAACAAGG 59.518 52.381 0.00 0.00 0.00 3.61
41 42 2.455557 TCCCACCATATGCCAAACAAG 58.544 47.619 0.00 0.00 0.00 3.16
42 43 2.612285 TCCCACCATATGCCAAACAA 57.388 45.000 0.00 0.00 0.00 2.83
43 44 2.612285 TTCCCACCATATGCCAAACA 57.388 45.000 0.00 0.00 0.00 2.83
44 45 4.649218 ACTAATTCCCACCATATGCCAAAC 59.351 41.667 0.00 0.00 0.00 2.93
45 46 4.877773 ACTAATTCCCACCATATGCCAAA 58.122 39.130 0.00 0.00 0.00 3.28
46 47 4.534647 ACTAATTCCCACCATATGCCAA 57.465 40.909 0.00 0.00 0.00 4.52
47 48 4.504165 CGTACTAATTCCCACCATATGCCA 60.504 45.833 0.00 0.00 0.00 4.92
48 49 4.000988 CGTACTAATTCCCACCATATGCC 58.999 47.826 0.00 0.00 0.00 4.40
49 50 4.000988 CCGTACTAATTCCCACCATATGC 58.999 47.826 0.00 0.00 0.00 3.14
50 51 4.285003 TCCCGTACTAATTCCCACCATATG 59.715 45.833 0.00 0.00 0.00 1.78
51 52 4.495565 TCCCGTACTAATTCCCACCATAT 58.504 43.478 0.00 0.00 0.00 1.78
52 53 3.926198 TCCCGTACTAATTCCCACCATA 58.074 45.455 0.00 0.00 0.00 2.74
53 54 2.766736 TCCCGTACTAATTCCCACCAT 58.233 47.619 0.00 0.00 0.00 3.55
54 55 2.250921 TCCCGTACTAATTCCCACCA 57.749 50.000 0.00 0.00 0.00 4.17
55 56 4.961438 TTATCCCGTACTAATTCCCACC 57.039 45.455 0.00 0.00 0.00 4.61
56 57 6.351711 AGTTTTATCCCGTACTAATTCCCAC 58.648 40.000 0.00 0.00 0.00 4.61
57 58 6.384886 AGAGTTTTATCCCGTACTAATTCCCA 59.615 38.462 0.00 0.00 0.00 4.37
58 59 6.704937 CAGAGTTTTATCCCGTACTAATTCCC 59.295 42.308 0.00 0.00 0.00 3.97
59 60 6.202379 GCAGAGTTTTATCCCGTACTAATTCC 59.798 42.308 0.00 0.00 0.00 3.01
60 61 6.985059 AGCAGAGTTTTATCCCGTACTAATTC 59.015 38.462 0.00 0.00 0.00 2.17
61 62 6.885922 AGCAGAGTTTTATCCCGTACTAATT 58.114 36.000 0.00 0.00 0.00 1.40
62 63 6.097839 TGAGCAGAGTTTTATCCCGTACTAAT 59.902 38.462 0.00 0.00 0.00 1.73
63 64 5.419788 TGAGCAGAGTTTTATCCCGTACTAA 59.580 40.000 0.00 0.00 0.00 2.24
64 65 4.951715 TGAGCAGAGTTTTATCCCGTACTA 59.048 41.667 0.00 0.00 0.00 1.82
65 66 3.767673 TGAGCAGAGTTTTATCCCGTACT 59.232 43.478 0.00 0.00 0.00 2.73
66 67 4.119442 TGAGCAGAGTTTTATCCCGTAC 57.881 45.455 0.00 0.00 0.00 3.67
67 68 4.404394 TGATGAGCAGAGTTTTATCCCGTA 59.596 41.667 0.00 0.00 0.00 4.02
68 69 3.197766 TGATGAGCAGAGTTTTATCCCGT 59.802 43.478 0.00 0.00 0.00 5.28
69 70 3.797039 TGATGAGCAGAGTTTTATCCCG 58.203 45.455 0.00 0.00 0.00 5.14
70 71 6.705863 AATTGATGAGCAGAGTTTTATCCC 57.294 37.500 0.00 0.00 0.00 3.85
71 72 8.677300 TGTTAATTGATGAGCAGAGTTTTATCC 58.323 33.333 0.00 0.00 0.00 2.59
74 75 8.514594 CCTTGTTAATTGATGAGCAGAGTTTTA 58.485 33.333 0.00 0.00 0.00 1.52
75 76 7.014615 ACCTTGTTAATTGATGAGCAGAGTTTT 59.985 33.333 0.00 0.00 0.00 2.43
76 77 6.491403 ACCTTGTTAATTGATGAGCAGAGTTT 59.509 34.615 0.00 0.00 0.00 2.66
77 78 6.006449 ACCTTGTTAATTGATGAGCAGAGTT 58.994 36.000 0.00 0.00 0.00 3.01
78 79 5.564550 ACCTTGTTAATTGATGAGCAGAGT 58.435 37.500 0.00 0.00 0.00 3.24
79 80 6.237942 CGTACCTTGTTAATTGATGAGCAGAG 60.238 42.308 0.00 0.00 0.00 3.35
80 81 5.580691 CGTACCTTGTTAATTGATGAGCAGA 59.419 40.000 0.00 0.00 0.00 4.26
81 82 5.727791 GCGTACCTTGTTAATTGATGAGCAG 60.728 44.000 0.00 0.00 0.00 4.24
82 83 4.094294 GCGTACCTTGTTAATTGATGAGCA 59.906 41.667 0.00 0.00 0.00 4.26
83 84 4.495844 GGCGTACCTTGTTAATTGATGAGC 60.496 45.833 0.00 0.00 0.00 4.26
84 85 4.634004 TGGCGTACCTTGTTAATTGATGAG 59.366 41.667 0.00 0.00 36.63 2.90
85 86 4.580868 TGGCGTACCTTGTTAATTGATGA 58.419 39.130 0.00 0.00 36.63 2.92
86 87 4.955925 TGGCGTACCTTGTTAATTGATG 57.044 40.909 0.00 0.00 36.63 3.07
87 88 4.338118 CCATGGCGTACCTTGTTAATTGAT 59.662 41.667 0.00 0.00 39.04 2.57
88 89 3.692101 CCATGGCGTACCTTGTTAATTGA 59.308 43.478 0.00 0.00 39.04 2.57
89 90 3.692101 TCCATGGCGTACCTTGTTAATTG 59.308 43.478 6.96 0.00 39.04 2.32
90 91 3.958018 TCCATGGCGTACCTTGTTAATT 58.042 40.909 6.96 0.00 39.04 1.40
91 92 3.637911 TCCATGGCGTACCTTGTTAAT 57.362 42.857 6.96 0.00 39.04 1.40
92 93 3.420300 TTCCATGGCGTACCTTGTTAA 57.580 42.857 6.96 0.00 39.04 2.01
93 94 3.420300 TTTCCATGGCGTACCTTGTTA 57.580 42.857 6.96 0.00 39.04 2.41
94 95 2.279935 TTTCCATGGCGTACCTTGTT 57.720 45.000 6.96 0.00 39.04 2.83
95 96 2.279935 TTTTCCATGGCGTACCTTGT 57.720 45.000 6.96 0.00 39.04 3.16
113 114 5.420725 GAAGCCAATTCCCACCTATTTTT 57.579 39.130 0.00 0.00 31.14 1.94
125 126 3.157087 TGGAAGTTGAGGAAGCCAATTC 58.843 45.455 0.00 0.00 37.17 2.17
126 127 3.243359 TGGAAGTTGAGGAAGCCAATT 57.757 42.857 0.00 0.00 0.00 2.32
127 128 2.978156 TGGAAGTTGAGGAAGCCAAT 57.022 45.000 0.00 0.00 0.00 3.16
128 129 2.978156 ATGGAAGTTGAGGAAGCCAA 57.022 45.000 0.00 0.00 0.00 4.52
129 130 2.555227 GGAATGGAAGTTGAGGAAGCCA 60.555 50.000 0.00 0.00 0.00 4.75
130 131 2.095461 GGAATGGAAGTTGAGGAAGCC 58.905 52.381 0.00 0.00 0.00 4.35
131 132 2.095461 GGGAATGGAAGTTGAGGAAGC 58.905 52.381 0.00 0.00 0.00 3.86
132 133 2.310052 AGGGGAATGGAAGTTGAGGAAG 59.690 50.000 0.00 0.00 0.00 3.46
133 134 2.358258 AGGGGAATGGAAGTTGAGGAA 58.642 47.619 0.00 0.00 0.00 3.36
134 135 2.059756 AGGGGAATGGAAGTTGAGGA 57.940 50.000 0.00 0.00 0.00 3.71
135 136 2.621668 GGAAGGGGAATGGAAGTTGAGG 60.622 54.545 0.00 0.00 0.00 3.86
136 137 2.728007 GGAAGGGGAATGGAAGTTGAG 58.272 52.381 0.00 0.00 0.00 3.02
137 138 1.004277 CGGAAGGGGAATGGAAGTTGA 59.996 52.381 0.00 0.00 0.00 3.18
138 139 1.004277 TCGGAAGGGGAATGGAAGTTG 59.996 52.381 0.00 0.00 0.00 3.16
139 140 1.004394 GTCGGAAGGGGAATGGAAGTT 59.996 52.381 0.00 0.00 0.00 2.66
140 141 0.618981 GTCGGAAGGGGAATGGAAGT 59.381 55.000 0.00 0.00 0.00 3.01
141 142 0.912486 AGTCGGAAGGGGAATGGAAG 59.088 55.000 0.00 0.00 0.00 3.46
142 143 1.368374 AAGTCGGAAGGGGAATGGAA 58.632 50.000 0.00 0.00 0.00 3.53
143 144 2.257391 TAAGTCGGAAGGGGAATGGA 57.743 50.000 0.00 0.00 0.00 3.41
144 145 3.014623 GTTTAAGTCGGAAGGGGAATGG 58.985 50.000 0.00 0.00 0.00 3.16
145 146 3.951663 AGTTTAAGTCGGAAGGGGAATG 58.048 45.455 0.00 0.00 0.00 2.67
146 147 4.567116 GGAAGTTTAAGTCGGAAGGGGAAT 60.567 45.833 0.00 0.00 0.00 3.01
147 148 3.244665 GGAAGTTTAAGTCGGAAGGGGAA 60.245 47.826 0.00 0.00 0.00 3.97
148 149 2.303890 GGAAGTTTAAGTCGGAAGGGGA 59.696 50.000 0.00 0.00 0.00 4.81
149 150 2.039348 TGGAAGTTTAAGTCGGAAGGGG 59.961 50.000 0.00 0.00 0.00 4.79
150 151 3.412237 TGGAAGTTTAAGTCGGAAGGG 57.588 47.619 0.00 0.00 0.00 3.95
151 152 4.395231 GGAATGGAAGTTTAAGTCGGAAGG 59.605 45.833 0.00 0.00 0.00 3.46
152 153 4.395231 GGGAATGGAAGTTTAAGTCGGAAG 59.605 45.833 0.00 0.00 0.00 3.46
153 154 4.042435 AGGGAATGGAAGTTTAAGTCGGAA 59.958 41.667 0.00 0.00 0.00 4.30
154 155 3.585732 AGGGAATGGAAGTTTAAGTCGGA 59.414 43.478 0.00 0.00 0.00 4.55
155 156 3.939592 GAGGGAATGGAAGTTTAAGTCGG 59.060 47.826 0.00 0.00 0.00 4.79
156 157 4.833390 AGAGGGAATGGAAGTTTAAGTCG 58.167 43.478 0.00 0.00 0.00 4.18
157 158 8.809468 AATTAGAGGGAATGGAAGTTTAAGTC 57.191 34.615 0.00 0.00 0.00 3.01
162 163 8.950007 TGTTTAATTAGAGGGAATGGAAGTTT 57.050 30.769 0.00 0.00 0.00 2.66
163 164 8.170730 ACTGTTTAATTAGAGGGAATGGAAGTT 58.829 33.333 0.00 0.00 0.00 2.66
164 165 7.611855 CACTGTTTAATTAGAGGGAATGGAAGT 59.388 37.037 0.00 0.00 0.00 3.01
165 166 7.829211 TCACTGTTTAATTAGAGGGAATGGAAG 59.171 37.037 0.00 0.00 0.00 3.46
166 167 7.695055 TCACTGTTTAATTAGAGGGAATGGAA 58.305 34.615 0.00 0.00 0.00 3.53
167 168 7.265599 TCACTGTTTAATTAGAGGGAATGGA 57.734 36.000 0.00 0.00 0.00 3.41
168 169 7.611855 AGTTCACTGTTTAATTAGAGGGAATGG 59.388 37.037 8.39 0.00 0.00 3.16
169 170 8.567285 AGTTCACTGTTTAATTAGAGGGAATG 57.433 34.615 8.39 0.00 0.00 2.67
170 171 9.588096 AAAGTTCACTGTTTAATTAGAGGGAAT 57.412 29.630 8.39 0.00 0.00 3.01
171 172 8.990163 AAAGTTCACTGTTTAATTAGAGGGAA 57.010 30.769 3.12 3.12 0.00 3.97
172 173 8.990163 AAAAGTTCACTGTTTAATTAGAGGGA 57.010 30.769 0.00 0.00 0.00 4.20
181 182 9.621629 TGAGGAGATTAAAAGTTCACTGTTTAA 57.378 29.630 0.00 0.19 32.79 1.52
182 183 9.052759 GTGAGGAGATTAAAAGTTCACTGTTTA 57.947 33.333 0.00 0.00 32.79 2.01
183 184 7.013369 GGTGAGGAGATTAAAAGTTCACTGTTT 59.987 37.037 0.00 0.00 35.16 2.83
184 185 6.486993 GGTGAGGAGATTAAAAGTTCACTGTT 59.513 38.462 0.00 0.00 35.16 3.16
185 186 5.998363 GGTGAGGAGATTAAAAGTTCACTGT 59.002 40.000 0.00 0.00 35.16 3.55
186 187 5.412904 GGGTGAGGAGATTAAAAGTTCACTG 59.587 44.000 0.00 0.00 35.16 3.66
187 188 5.515008 GGGGTGAGGAGATTAAAAGTTCACT 60.515 44.000 0.00 0.00 35.16 3.41
188 189 4.700692 GGGGTGAGGAGATTAAAAGTTCAC 59.299 45.833 0.00 0.00 34.30 3.18
189 190 4.352595 TGGGGTGAGGAGATTAAAAGTTCA 59.647 41.667 0.00 0.00 0.00 3.18
190 191 4.918588 TGGGGTGAGGAGATTAAAAGTTC 58.081 43.478 0.00 0.00 0.00 3.01
191 192 5.536497 ATGGGGTGAGGAGATTAAAAGTT 57.464 39.130 0.00 0.00 0.00 2.66
192 193 6.217693 AGTTATGGGGTGAGGAGATTAAAAGT 59.782 38.462 0.00 0.00 0.00 2.66
193 194 6.663734 AGTTATGGGGTGAGGAGATTAAAAG 58.336 40.000 0.00 0.00 0.00 2.27
194 195 6.353602 GGAGTTATGGGGTGAGGAGATTAAAA 60.354 42.308 0.00 0.00 0.00 1.52
195 196 5.132144 GGAGTTATGGGGTGAGGAGATTAAA 59.868 44.000 0.00 0.00 0.00 1.52
196 197 4.658901 GGAGTTATGGGGTGAGGAGATTAA 59.341 45.833 0.00 0.00 0.00 1.40
197 198 4.232091 GGAGTTATGGGGTGAGGAGATTA 58.768 47.826 0.00 0.00 0.00 1.75
198 199 3.049344 GGAGTTATGGGGTGAGGAGATT 58.951 50.000 0.00 0.00 0.00 2.40
199 200 2.695585 GGAGTTATGGGGTGAGGAGAT 58.304 52.381 0.00 0.00 0.00 2.75
200 201 1.344087 GGGAGTTATGGGGTGAGGAGA 60.344 57.143 0.00 0.00 0.00 3.71
201 202 1.132500 GGGAGTTATGGGGTGAGGAG 58.868 60.000 0.00 0.00 0.00 3.69
202 203 0.419865 TGGGAGTTATGGGGTGAGGA 59.580 55.000 0.00 0.00 0.00 3.71
203 204 1.522900 ATGGGAGTTATGGGGTGAGG 58.477 55.000 0.00 0.00 0.00 3.86
204 205 2.158608 GGAATGGGAGTTATGGGGTGAG 60.159 54.545 0.00 0.00 0.00 3.51
205 206 1.850345 GGAATGGGAGTTATGGGGTGA 59.150 52.381 0.00 0.00 0.00 4.02
206 207 1.133482 GGGAATGGGAGTTATGGGGTG 60.133 57.143 0.00 0.00 0.00 4.61
207 208 1.231963 GGGAATGGGAGTTATGGGGT 58.768 55.000 0.00 0.00 0.00 4.95
208 209 0.482887 GGGGAATGGGAGTTATGGGG 59.517 60.000 0.00 0.00 0.00 4.96
209 210 1.231018 TGGGGAATGGGAGTTATGGG 58.769 55.000 0.00 0.00 0.00 4.00
210 211 2.718609 AGATGGGGAATGGGAGTTATGG 59.281 50.000 0.00 0.00 0.00 2.74
211 212 4.459852 AAGATGGGGAATGGGAGTTATG 57.540 45.455 0.00 0.00 0.00 1.90
212 213 6.606241 TTAAAGATGGGGAATGGGAGTTAT 57.394 37.500 0.00 0.00 0.00 1.89
213 214 6.606241 ATTAAAGATGGGGAATGGGAGTTA 57.394 37.500 0.00 0.00 0.00 2.24
214 215 4.965283 TTAAAGATGGGGAATGGGAGTT 57.035 40.909 0.00 0.00 0.00 3.01
215 216 5.458595 GAATTAAAGATGGGGAATGGGAGT 58.541 41.667 0.00 0.00 0.00 3.85
216 217 4.835056 GGAATTAAAGATGGGGAATGGGAG 59.165 45.833 0.00 0.00 0.00 4.30
217 218 4.388575 GGGAATTAAAGATGGGGAATGGGA 60.389 45.833 0.00 0.00 0.00 4.37
218 219 3.903714 GGGAATTAAAGATGGGGAATGGG 59.096 47.826 0.00 0.00 0.00 4.00
219 220 3.903714 GGGGAATTAAAGATGGGGAATGG 59.096 47.826 0.00 0.00 0.00 3.16
220 221 4.819610 AGGGGAATTAAAGATGGGGAATG 58.180 43.478 0.00 0.00 0.00 2.67
221 222 6.382087 GTTAGGGGAATTAAAGATGGGGAAT 58.618 40.000 0.00 0.00 0.00 3.01
222 223 5.341369 GGTTAGGGGAATTAAAGATGGGGAA 60.341 44.000 0.00 0.00 0.00 3.97
223 224 4.169264 GGTTAGGGGAATTAAAGATGGGGA 59.831 45.833 0.00 0.00 0.00 4.81
224 225 4.078863 TGGTTAGGGGAATTAAAGATGGGG 60.079 45.833 0.00 0.00 0.00 4.96
225 226 5.137412 TGGTTAGGGGAATTAAAGATGGG 57.863 43.478 0.00 0.00 0.00 4.00
226 227 6.405397 CGTTTGGTTAGGGGAATTAAAGATGG 60.405 42.308 0.00 0.00 0.00 3.51
227 228 6.560711 CGTTTGGTTAGGGGAATTAAAGATG 58.439 40.000 0.00 0.00 0.00 2.90
228 229 5.126545 GCGTTTGGTTAGGGGAATTAAAGAT 59.873 40.000 0.00 0.00 0.00 2.40
229 230 4.460034 GCGTTTGGTTAGGGGAATTAAAGA 59.540 41.667 0.00 0.00 0.00 2.52
230 231 4.673320 CGCGTTTGGTTAGGGGAATTAAAG 60.673 45.833 0.00 0.00 0.00 1.85
231 232 3.190953 CGCGTTTGGTTAGGGGAATTAAA 59.809 43.478 0.00 0.00 0.00 1.52
232 233 2.748532 CGCGTTTGGTTAGGGGAATTAA 59.251 45.455 0.00 0.00 0.00 1.40
233 234 2.358015 CGCGTTTGGTTAGGGGAATTA 58.642 47.619 0.00 0.00 0.00 1.40
234 235 1.170442 CGCGTTTGGTTAGGGGAATT 58.830 50.000 0.00 0.00 0.00 2.17
235 236 1.310216 GCGCGTTTGGTTAGGGGAAT 61.310 55.000 8.43 0.00 0.00 3.01
236 237 1.967494 GCGCGTTTGGTTAGGGGAA 60.967 57.895 8.43 0.00 0.00 3.97
237 238 1.543065 TAGCGCGTTTGGTTAGGGGA 61.543 55.000 8.43 0.00 0.00 4.81
238 239 0.463116 ATAGCGCGTTTGGTTAGGGG 60.463 55.000 8.43 0.00 0.00 4.79
239 240 0.655733 CATAGCGCGTTTGGTTAGGG 59.344 55.000 8.43 0.00 0.00 3.53
240 241 0.655733 CCATAGCGCGTTTGGTTAGG 59.344 55.000 8.43 0.00 0.00 2.69
241 242 0.655733 CCCATAGCGCGTTTGGTTAG 59.344 55.000 20.08 6.24 0.00 2.34
242 243 0.036199 ACCCATAGCGCGTTTGGTTA 60.036 50.000 20.08 0.00 0.00 2.85
243 244 1.302993 ACCCATAGCGCGTTTGGTT 60.303 52.632 20.08 7.79 0.00 3.67
244 245 1.743995 GACCCATAGCGCGTTTGGT 60.744 57.895 20.08 17.00 0.00 3.67
245 246 2.469516 GGACCCATAGCGCGTTTGG 61.470 63.158 8.43 16.42 0.00 3.28
246 247 2.469516 GGGACCCATAGCGCGTTTG 61.470 63.158 8.43 2.82 0.00 2.93
247 248 2.124860 GGGACCCATAGCGCGTTT 60.125 61.111 8.43 0.00 0.00 3.60
248 249 2.666098 AAGGGACCCATAGCGCGTT 61.666 57.895 14.60 3.54 0.00 4.84
249 250 3.081409 AAGGGACCCATAGCGCGT 61.081 61.111 14.60 0.00 0.00 6.01
250 251 2.588877 CAAGGGACCCATAGCGCG 60.589 66.667 14.60 0.00 0.00 6.86
251 252 1.227674 CTCAAGGGACCCATAGCGC 60.228 63.158 14.60 0.00 0.00 5.92
252 253 1.447643 CCTCAAGGGACCCATAGCG 59.552 63.158 14.60 0.00 37.23 4.26
253 254 1.149401 GCCTCAAGGGACCCATAGC 59.851 63.158 14.60 4.23 37.23 2.97
254 255 1.143813 ATGCCTCAAGGGACCCATAG 58.856 55.000 14.60 6.55 38.75 2.23
255 256 0.846015 CATGCCTCAAGGGACCCATA 59.154 55.000 14.60 0.00 38.75 2.74
256 257 1.616921 CATGCCTCAAGGGACCCAT 59.383 57.895 14.60 0.00 38.75 4.00
272 273 0.110823 GTCGCTGACGTTTTTCGCAT 60.111 50.000 0.00 0.00 44.19 4.73
367 368 1.202580 GCCTACAGCGGTGAGATTGAT 60.203 52.381 23.44 0.00 0.00 2.57
413 414 8.876275 ACGTACAAACTGTCAAAATTACTCTA 57.124 30.769 0.00 0.00 0.00 2.43
414 415 7.781548 ACGTACAAACTGTCAAAATTACTCT 57.218 32.000 0.00 0.00 0.00 3.24
420 421 8.715088 GGAGTAATACGTACAAACTGTCAAAAT 58.285 33.333 10.14 0.00 34.88 1.82
421 422 7.710044 TGGAGTAATACGTACAAACTGTCAAAA 59.290 33.333 10.14 0.00 34.88 2.44
422 423 7.208777 TGGAGTAATACGTACAAACTGTCAAA 58.791 34.615 10.14 0.00 34.88 2.69
423 424 6.747125 TGGAGTAATACGTACAAACTGTCAA 58.253 36.000 10.14 0.00 34.88 3.18
424 425 6.016024 ACTGGAGTAATACGTACAAACTGTCA 60.016 38.462 10.14 7.95 34.88 3.58
692 702 2.964310 GCAGGAGCAGCCAGGAAGA 61.964 63.158 0.00 0.00 41.58 2.87
858 869 2.017559 ATTCGTAGGTGGAGGCGAGC 62.018 60.000 0.00 0.00 34.78 5.03
1187 1219 1.972660 GCTACCGTCCTTGATGGGCT 61.973 60.000 7.24 0.00 42.60 5.19
2349 2393 2.437359 GTGCGCTTCTGGAGGCAT 60.437 61.111 9.73 0.00 35.17 4.40
2836 2890 3.332919 ACACACTAGAAATGCTCTGCAG 58.667 45.455 7.63 7.63 43.65 4.41
2839 2893 3.499537 TGCAACACACTAGAAATGCTCTG 59.500 43.478 0.00 0.00 35.41 3.35
2884 2938 9.764363 AGATGAATTTATAAGAGCATGTCGTTA 57.236 29.630 0.00 0.00 0.00 3.18
3092 3172 5.408299 CACGTTTTCCACTAATGTCATCTGA 59.592 40.000 0.00 0.00 0.00 3.27
3113 3193 0.233590 TCGATTTTGTTGACGCCACG 59.766 50.000 0.00 0.00 0.00 4.94
3120 3200 4.844998 TTTGGAGCATCGATTTTGTTGA 57.155 36.364 0.00 0.00 34.37 3.18
3121 3201 5.406175 ACATTTTGGAGCATCGATTTTGTTG 59.594 36.000 0.00 0.00 34.37 3.33
3178 3259 6.739112 TCATGTGAAGTCGGATGAATAGTAG 58.261 40.000 0.00 0.00 0.00 2.57
3190 3271 2.084610 TCCAAGCTCATGTGAAGTCG 57.915 50.000 0.00 0.00 0.00 4.18
3194 3275 5.068855 TGTTTTGATTCCAAGCTCATGTGAA 59.931 36.000 0.00 0.00 33.23 3.18
3195 3276 4.583907 TGTTTTGATTCCAAGCTCATGTGA 59.416 37.500 0.00 0.00 33.23 3.58
3237 3318 1.078143 GGCTCGGCTTTGGAGATGT 60.078 57.895 0.00 0.00 33.27 3.06
3294 3375 2.482721 GACAAATACCTGTCCACGTTGG 59.517 50.000 0.00 0.00 39.93 3.77
3374 3457 4.268359 GGAAGGAATTGAGATGTGAGCTT 58.732 43.478 0.00 0.00 0.00 3.74
3388 3471 2.454772 AGGAAAACAAGGGGGAAGGAAT 59.545 45.455 0.00 0.00 0.00 3.01
3390 3473 1.541275 AGGAAAACAAGGGGGAAGGA 58.459 50.000 0.00 0.00 0.00 3.36
3508 3591 3.966026 GAGAGGTGGAACGACGGCG 62.966 68.421 10.39 10.39 44.79 6.46
3539 3622 2.172717 GTGCTGGGTGAATGGTACCTAT 59.827 50.000 14.36 1.01 38.30 2.57


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

AutoCloner maintained by Alex Coulton.