Multiple sequence alignment - TraesCS2D01G358900

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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 TraesCS2D01G358900 chr2D 100.000 2707 0 0 883 3589 460779149 460776443 0.000000e+00 5000
1 TraesCS2D01G358900 chr2D 100.000 586 0 0 1 586 460780031 460779446 0.000000e+00 1083
2 TraesCS2D01G358900 chr2B 95.357 2649 93 14 893 3525 542356382 542353748 0.000000e+00 4183
3 TraesCS2D01G358900 chr2B 89.646 367 20 9 226 582 542357051 542356693 5.460000e-123 451
4 TraesCS2D01G358900 chr2B 96.970 66 2 0 3524 3589 542353688 542353623 1.050000e-20 111
5 TraesCS2D01G358900 chr2A 94.723 2653 97 18 893 3525 603688572 603685943 0.000000e+00 4084
6 TraesCS2D01G358900 chr2A 86.648 352 16 8 237 565 603689250 603688907 9.470000e-96 361
7 TraesCS2D01G358900 chrUn 98.614 433 3 2 2147 2579 476327128 476327557 0.000000e+00 763
8 TraesCS2D01G358900 chrUn 100.000 62 0 0 2147 2208 305036885 305036824 8.140000e-22 115


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 TraesCS2D01G358900 chr2D 460776443 460780031 3588 True 3041.500000 5000 100.0000 1 3589 2 chr2D.!!$R1 3588
1 TraesCS2D01G358900 chr2B 542353623 542357051 3428 True 1581.666667 4183 93.9910 226 3589 3 chr2B.!!$R1 3363
2 TraesCS2D01G358900 chr2A 603685943 603689250 3307 True 2222.500000 4084 90.6855 237 3525 2 chr2A.!!$R1 3288

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
59 60 0.108329 GCGAGGGACTTTCGATTGGA 60.108 55.000 0.0 0.0 41.55 3.53 F
352 353 0.178995 TGACCATGAAGCACCTGCAA 60.179 50.000 0.0 0.0 45.16 4.08 F
1506 1545 1.063942 TCGGTCTGCCTCAAGGATCTA 60.064 52.381 0.0 0.0 37.39 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1594 1633 1.661341 GCAATGACCTCTAGTGGCAG 58.339 55.000 10.82 1.66 0.00 4.85 R
1713 1752 1.699634 TCAGGGGTCTTGACAAGGAAG 59.300 52.381 15.13 0.98 0.00 3.46 R
2972 3017 1.341080 CAGGAAATGGCACCTGGTTT 58.659 50.000 13.41 0.00 46.76 3.27 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
18 19 4.776322 TGGCTCACGGCAATCGGG 62.776 66.667 0.00 0.00 43.40 5.14
21 22 2.892425 CTCACGGCAATCGGGCTC 60.892 66.667 0.00 0.00 43.08 4.70
22 23 4.812476 TCACGGCAATCGGGCTCG 62.812 66.667 0.00 0.00 43.08 5.03
31 32 3.209812 TCGGGCTCGATCGGTCAG 61.210 66.667 16.41 6.61 40.88 3.51
32 33 3.518998 CGGGCTCGATCGGTCAGT 61.519 66.667 16.41 0.00 39.00 3.41
33 34 2.413765 GGGCTCGATCGGTCAGTC 59.586 66.667 16.41 6.82 0.00 3.51
34 35 2.024871 GGCTCGATCGGTCAGTCG 59.975 66.667 16.41 0.00 39.11 4.18
35 36 2.024871 GCTCGATCGGTCAGTCGG 59.975 66.667 16.41 0.00 38.34 4.79
36 37 2.762234 GCTCGATCGGTCAGTCGGT 61.762 63.158 16.41 0.00 38.34 4.69
37 38 1.434622 GCTCGATCGGTCAGTCGGTA 61.435 60.000 16.41 0.00 38.34 4.02
38 39 1.227639 CTCGATCGGTCAGTCGGTAT 58.772 55.000 16.41 0.00 38.34 2.73
39 40 1.194997 CTCGATCGGTCAGTCGGTATC 59.805 57.143 16.41 0.00 38.34 2.24
40 41 0.110778 CGATCGGTCAGTCGGTATCG 60.111 60.000 7.38 0.00 34.39 2.92
41 42 0.385723 GATCGGTCAGTCGGTATCGC 60.386 60.000 0.00 0.00 36.13 4.58
42 43 2.114331 ATCGGTCAGTCGGTATCGCG 62.114 60.000 0.00 0.00 36.13 5.87
43 44 2.816360 CGGTCAGTCGGTATCGCGA 61.816 63.158 13.09 13.09 36.13 5.87
44 45 1.009900 GGTCAGTCGGTATCGCGAG 60.010 63.158 16.66 0.00 36.13 5.03
45 46 1.009900 GTCAGTCGGTATCGCGAGG 60.010 63.158 16.66 3.80 36.13 4.63
46 47 2.184830 TCAGTCGGTATCGCGAGGG 61.185 63.158 16.66 3.41 36.13 4.30
47 48 2.184830 CAGTCGGTATCGCGAGGGA 61.185 63.158 16.66 6.01 36.13 4.20
48 49 2.185494 AGTCGGTATCGCGAGGGAC 61.185 63.158 16.66 17.64 36.13 4.46
49 50 2.185494 GTCGGTATCGCGAGGGACT 61.185 63.158 16.66 0.00 37.69 3.85
50 51 1.452651 TCGGTATCGCGAGGGACTT 60.453 57.895 16.66 0.00 35.55 3.01
51 52 1.033746 TCGGTATCGCGAGGGACTTT 61.034 55.000 16.66 0.00 35.55 2.66
52 53 0.594284 CGGTATCGCGAGGGACTTTC 60.594 60.000 16.66 0.00 41.55 2.62
53 54 0.594284 GGTATCGCGAGGGACTTTCG 60.594 60.000 16.66 0.00 41.55 3.46
54 55 0.379669 GTATCGCGAGGGACTTTCGA 59.620 55.000 16.66 0.00 41.55 3.71
55 56 2.116383 ATCGCGAGGGACTTTCGAT 58.884 52.632 16.66 0.00 43.66 3.59
56 57 0.460311 ATCGCGAGGGACTTTCGATT 59.540 50.000 16.66 0.00 45.53 3.34
57 58 0.457853 TCGCGAGGGACTTTCGATTG 60.458 55.000 3.71 0.00 41.55 2.67
58 59 1.421410 CGCGAGGGACTTTCGATTGG 61.421 60.000 0.00 0.00 41.55 3.16
59 60 0.108329 GCGAGGGACTTTCGATTGGA 60.108 55.000 0.00 0.00 41.55 3.53
60 61 1.641577 CGAGGGACTTTCGATTGGAC 58.358 55.000 0.00 0.00 41.55 4.02
61 62 1.641577 GAGGGACTTTCGATTGGACG 58.358 55.000 0.00 0.00 41.55 4.79
62 63 0.249398 AGGGACTTTCGATTGGACGG 59.751 55.000 0.00 0.00 27.25 4.79
63 64 1.366854 GGGACTTTCGATTGGACGGC 61.367 60.000 0.00 0.00 0.00 5.68
64 65 1.366854 GGACTTTCGATTGGACGGCC 61.367 60.000 0.00 0.00 0.00 6.13
65 66 0.672401 GACTTTCGATTGGACGGCCA 60.672 55.000 5.41 5.41 44.17 5.36
73 74 3.124686 TGGACGGCCAAAAGTTGC 58.875 55.556 8.12 0.00 42.49 4.17
74 75 1.454847 TGGACGGCCAAAAGTTGCT 60.455 52.632 8.12 0.00 42.49 3.91
75 76 0.179015 TGGACGGCCAAAAGTTGCTA 60.179 50.000 8.12 0.00 42.49 3.49
76 77 0.955905 GGACGGCCAAAAGTTGCTAA 59.044 50.000 0.00 0.00 0.00 3.09
77 78 1.544246 GGACGGCCAAAAGTTGCTAAT 59.456 47.619 0.00 0.00 0.00 1.73
78 79 2.415491 GGACGGCCAAAAGTTGCTAATC 60.415 50.000 0.00 0.00 0.00 1.75
79 80 2.488153 GACGGCCAAAAGTTGCTAATCT 59.512 45.455 2.24 0.00 0.00 2.40
80 81 2.488153 ACGGCCAAAAGTTGCTAATCTC 59.512 45.455 2.24 0.00 0.00 2.75
81 82 2.749621 CGGCCAAAAGTTGCTAATCTCT 59.250 45.455 2.24 0.00 0.00 3.10
82 83 3.426695 CGGCCAAAAGTTGCTAATCTCTG 60.427 47.826 2.24 0.00 0.00 3.35
83 84 3.507622 GGCCAAAAGTTGCTAATCTCTGT 59.492 43.478 0.00 0.00 0.00 3.41
84 85 4.479619 GCCAAAAGTTGCTAATCTCTGTG 58.520 43.478 0.00 0.00 0.00 3.66
85 86 4.216257 GCCAAAAGTTGCTAATCTCTGTGA 59.784 41.667 0.00 0.00 0.00 3.58
86 87 5.618640 GCCAAAAGTTGCTAATCTCTGTGAG 60.619 44.000 0.00 0.00 0.00 3.51
87 88 5.388944 CAAAAGTTGCTAATCTCTGTGAGC 58.611 41.667 0.00 0.00 35.43 4.26
88 89 2.886081 AGTTGCTAATCTCTGTGAGCG 58.114 47.619 0.00 0.00 37.77 5.03
89 90 2.232452 AGTTGCTAATCTCTGTGAGCGT 59.768 45.455 0.00 0.00 37.77 5.07
90 91 2.568696 TGCTAATCTCTGTGAGCGTC 57.431 50.000 0.00 0.00 37.77 5.19
91 92 1.135139 TGCTAATCTCTGTGAGCGTCC 59.865 52.381 0.00 0.00 37.77 4.79
92 93 1.862008 GCTAATCTCTGTGAGCGTCCG 60.862 57.143 0.00 0.00 0.00 4.79
93 94 0.738975 TAATCTCTGTGAGCGTCCGG 59.261 55.000 0.00 0.00 0.00 5.14
94 95 1.251527 AATCTCTGTGAGCGTCCGGT 61.252 55.000 0.00 0.00 0.00 5.28
95 96 1.938657 ATCTCTGTGAGCGTCCGGTG 61.939 60.000 0.00 0.00 0.00 4.94
96 97 4.357947 TCTGTGAGCGTCCGGTGC 62.358 66.667 12.59 12.59 0.00 5.01
104 105 4.796231 CGTCCGGTGCTCCCTTCG 62.796 72.222 0.00 0.00 0.00 3.79
105 106 3.692406 GTCCGGTGCTCCCTTCGT 61.692 66.667 0.00 0.00 0.00 3.85
106 107 2.920912 TCCGGTGCTCCCTTCGTT 60.921 61.111 0.00 0.00 0.00 3.85
107 108 2.032071 CCGGTGCTCCCTTCGTTT 59.968 61.111 0.00 0.00 0.00 3.60
108 109 2.325082 CCGGTGCTCCCTTCGTTTG 61.325 63.158 0.00 0.00 0.00 2.93
109 110 1.597027 CGGTGCTCCCTTCGTTTGT 60.597 57.895 0.00 0.00 0.00 2.83
110 111 1.164041 CGGTGCTCCCTTCGTTTGTT 61.164 55.000 0.00 0.00 0.00 2.83
111 112 0.591659 GGTGCTCCCTTCGTTTGTTC 59.408 55.000 0.00 0.00 0.00 3.18
112 113 1.594331 GTGCTCCCTTCGTTTGTTCT 58.406 50.000 0.00 0.00 0.00 3.01
113 114 1.531578 GTGCTCCCTTCGTTTGTTCTC 59.468 52.381 0.00 0.00 0.00 2.87
114 115 1.416401 TGCTCCCTTCGTTTGTTCTCT 59.584 47.619 0.00 0.00 0.00 3.10
115 116 2.158813 TGCTCCCTTCGTTTGTTCTCTT 60.159 45.455 0.00 0.00 0.00 2.85
116 117 2.879026 GCTCCCTTCGTTTGTTCTCTTT 59.121 45.455 0.00 0.00 0.00 2.52
117 118 3.315470 GCTCCCTTCGTTTGTTCTCTTTT 59.685 43.478 0.00 0.00 0.00 2.27
118 119 4.789802 GCTCCCTTCGTTTGTTCTCTTTTG 60.790 45.833 0.00 0.00 0.00 2.44
119 120 4.519213 TCCCTTCGTTTGTTCTCTTTTGA 58.481 39.130 0.00 0.00 0.00 2.69
120 121 5.130350 TCCCTTCGTTTGTTCTCTTTTGAT 58.870 37.500 0.00 0.00 0.00 2.57
121 122 6.292923 TCCCTTCGTTTGTTCTCTTTTGATA 58.707 36.000 0.00 0.00 0.00 2.15
122 123 6.940298 TCCCTTCGTTTGTTCTCTTTTGATAT 59.060 34.615 0.00 0.00 0.00 1.63
123 124 7.023575 CCCTTCGTTTGTTCTCTTTTGATATG 58.976 38.462 0.00 0.00 0.00 1.78
124 125 7.308589 CCCTTCGTTTGTTCTCTTTTGATATGT 60.309 37.037 0.00 0.00 0.00 2.29
125 126 7.535258 CCTTCGTTTGTTCTCTTTTGATATGTG 59.465 37.037 0.00 0.00 0.00 3.21
126 127 7.490962 TCGTTTGTTCTCTTTTGATATGTGT 57.509 32.000 0.00 0.00 0.00 3.72
127 128 8.596271 TCGTTTGTTCTCTTTTGATATGTGTA 57.404 30.769 0.00 0.00 0.00 2.90
128 129 9.214957 TCGTTTGTTCTCTTTTGATATGTGTAT 57.785 29.630 0.00 0.00 0.00 2.29
157 158 9.736023 ATGTATGTATGTATGTATGTATGAGCG 57.264 33.333 0.00 0.00 0.00 5.03
158 159 8.736244 TGTATGTATGTATGTATGTATGAGCGT 58.264 33.333 0.00 0.00 0.00 5.07
159 160 9.569167 GTATGTATGTATGTATGTATGAGCGTT 57.431 33.333 0.00 0.00 0.00 4.84
161 162 8.293114 TGTATGTATGTATGTATGAGCGTTTG 57.707 34.615 0.00 0.00 0.00 2.93
162 163 7.923878 TGTATGTATGTATGTATGAGCGTTTGT 59.076 33.333 0.00 0.00 0.00 2.83
163 164 9.401873 GTATGTATGTATGTATGAGCGTTTGTA 57.598 33.333 0.00 0.00 0.00 2.41
165 166 8.880878 TGTATGTATGTATGAGCGTTTGTATT 57.119 30.769 0.00 0.00 0.00 1.89
166 167 9.320352 TGTATGTATGTATGAGCGTTTGTATTT 57.680 29.630 0.00 0.00 0.00 1.40
167 168 9.580916 GTATGTATGTATGAGCGTTTGTATTTG 57.419 33.333 0.00 0.00 0.00 2.32
168 169 7.603963 TGTATGTATGAGCGTTTGTATTTGT 57.396 32.000 0.00 0.00 0.00 2.83
169 170 8.705048 TGTATGTATGAGCGTTTGTATTTGTA 57.295 30.769 0.00 0.00 0.00 2.41
170 171 8.597227 TGTATGTATGAGCGTTTGTATTTGTAC 58.403 33.333 0.00 0.00 0.00 2.90
171 172 7.603963 ATGTATGAGCGTTTGTATTTGTACA 57.396 32.000 0.00 0.00 0.00 2.90
172 173 7.056002 TGTATGAGCGTTTGTATTTGTACAG 57.944 36.000 0.00 0.00 0.00 2.74
173 174 6.647481 TGTATGAGCGTTTGTATTTGTACAGT 59.353 34.615 0.00 0.00 0.00 3.55
174 175 5.337219 TGAGCGTTTGTATTTGTACAGTG 57.663 39.130 0.00 0.00 0.00 3.66
175 176 4.812091 TGAGCGTTTGTATTTGTACAGTGT 59.188 37.500 0.00 0.00 0.00 3.55
176 177 5.050634 TGAGCGTTTGTATTTGTACAGTGTC 60.051 40.000 0.00 0.00 0.00 3.67
177 178 4.084745 AGCGTTTGTATTTGTACAGTGTCG 60.085 41.667 0.00 0.00 0.00 4.35
178 179 4.084952 GCGTTTGTATTTGTACAGTGTCGA 60.085 41.667 0.00 0.00 0.00 4.20
179 180 5.595993 CGTTTGTATTTGTACAGTGTCGAG 58.404 41.667 0.00 0.00 0.00 4.04
180 181 5.400188 CGTTTGTATTTGTACAGTGTCGAGA 59.600 40.000 0.00 0.00 0.00 4.04
181 182 6.074729 CGTTTGTATTTGTACAGTGTCGAGAA 60.075 38.462 0.00 0.00 0.00 2.87
182 183 7.515528 CGTTTGTATTTGTACAGTGTCGAGAAA 60.516 37.037 0.00 0.00 0.00 2.52
183 184 7.956420 TTGTATTTGTACAGTGTCGAGAAAT 57.044 32.000 0.00 2.70 0.00 2.17
184 185 9.478768 TTTGTATTTGTACAGTGTCGAGAAATA 57.521 29.630 0.00 1.68 0.00 1.40
185 186 8.456904 TGTATTTGTACAGTGTCGAGAAATAC 57.543 34.615 21.10 21.10 36.22 1.89
186 187 6.627690 ATTTGTACAGTGTCGAGAAATACG 57.372 37.500 0.00 0.00 0.00 3.06
187 188 4.087510 TGTACAGTGTCGAGAAATACGG 57.912 45.455 0.00 0.00 0.00 4.02
188 189 3.503363 TGTACAGTGTCGAGAAATACGGT 59.497 43.478 0.00 0.00 0.00 4.83
189 190 3.655276 ACAGTGTCGAGAAATACGGTT 57.345 42.857 0.00 0.00 0.00 4.44
190 191 3.314553 ACAGTGTCGAGAAATACGGTTG 58.685 45.455 0.00 0.00 0.00 3.77
191 192 2.666508 CAGTGTCGAGAAATACGGTTGG 59.333 50.000 0.00 0.00 0.00 3.77
192 193 1.392510 GTGTCGAGAAATACGGTTGGC 59.607 52.381 0.00 0.00 0.00 4.52
193 194 1.001068 TGTCGAGAAATACGGTTGGCA 59.999 47.619 0.00 0.00 0.00 4.92
194 195 2.277084 GTCGAGAAATACGGTTGGCAT 58.723 47.619 0.00 0.00 0.00 4.40
195 196 2.030457 GTCGAGAAATACGGTTGGCATG 59.970 50.000 0.00 0.00 0.00 4.06
196 197 2.093921 TCGAGAAATACGGTTGGCATGA 60.094 45.455 0.00 0.00 0.00 3.07
197 198 2.030457 CGAGAAATACGGTTGGCATGAC 59.970 50.000 0.00 0.00 0.00 3.06
198 199 2.354821 GAGAAATACGGTTGGCATGACC 59.645 50.000 0.00 0.00 39.84 4.02
203 204 3.263941 GGTTGGCATGACCGTGAC 58.736 61.111 0.00 0.00 43.94 3.67
204 205 2.677003 GGTTGGCATGACCGTGACG 61.677 63.158 0.00 0.00 43.94 4.35
205 206 3.047280 TTGGCATGACCGTGACGC 61.047 61.111 0.00 0.00 43.94 5.19
206 207 3.816367 TTGGCATGACCGTGACGCA 62.816 57.895 0.00 0.00 43.94 5.24
207 208 3.490759 GGCATGACCGTGACGCAG 61.491 66.667 0.00 0.00 0.00 5.18
223 224 2.579207 GCAGTATAAGCGTGACTCCA 57.421 50.000 0.00 0.00 0.00 3.86
224 225 3.099267 GCAGTATAAGCGTGACTCCAT 57.901 47.619 0.00 0.00 0.00 3.41
245 246 7.235079 TCCATAGAAATACCTGGAACACAAAA 58.765 34.615 0.00 0.00 34.91 2.44
254 255 6.232581 ACCTGGAACACAAAATGAAATTCA 57.767 33.333 0.00 0.00 33.67 2.57
333 334 3.126879 CGCGGCACCACATGACAT 61.127 61.111 0.00 0.00 35.12 3.06
334 335 2.486504 GCGGCACCACATGACATG 59.513 61.111 14.02 14.02 35.12 3.21
335 336 2.039974 GCGGCACCACATGACATGA 61.040 57.895 22.19 0.00 35.12 3.07
352 353 0.178995 TGACCATGAAGCACCTGCAA 60.179 50.000 0.00 0.00 45.16 4.08
394 398 4.965283 ATACTTTCCCCATTTTCCTCCA 57.035 40.909 0.00 0.00 0.00 3.86
485 518 4.119363 GGCAGGCAGGCAGATCCA 62.119 66.667 0.00 0.00 43.51 3.41
1335 1374 3.512516 GCATCCTGCACCTTCGGC 61.513 66.667 0.00 0.00 44.26 5.54
1506 1545 1.063942 TCGGTCTGCCTCAAGGATCTA 60.064 52.381 0.00 0.00 37.39 1.98
1679 1718 2.258591 CGGTGACCGTGGTCTGAG 59.741 66.667 17.28 7.11 44.80 3.35
1713 1752 1.086634 GTGCGAATCTGGAGGTGCTC 61.087 60.000 0.00 0.00 0.00 4.26
2001 2040 0.394192 CCGAGATTATCTGCCTGGCA 59.606 55.000 21.96 21.96 36.92 4.92
2121 2160 0.884704 TGAAGTTGAAGAGGTGCCGC 60.885 55.000 0.00 0.00 0.00 6.53
2139 2178 1.649171 CGCGGAGTATCGTATGAATGC 59.351 52.381 0.00 0.00 34.37 3.56
2410 2449 2.347114 CACCAGCGTGATGTGGGA 59.653 61.111 0.00 0.00 43.14 4.37
2411 2450 1.078214 CACCAGCGTGATGTGGGAT 60.078 57.895 0.00 0.00 43.14 3.85
2567 2610 1.346068 GCATCATCAGTAGTCTCCCCC 59.654 57.143 0.00 0.00 0.00 5.40
2591 2634 7.253422 CCTTGTTCTGATTTTACCTTGCTATG 58.747 38.462 0.00 0.00 0.00 2.23
2592 2635 6.757897 TGTTCTGATTTTACCTTGCTATGG 57.242 37.500 0.00 0.00 0.00 2.74
2593 2636 6.245408 TGTTCTGATTTTACCTTGCTATGGT 58.755 36.000 0.00 0.00 41.28 3.55
2594 2637 7.398829 TGTTCTGATTTTACCTTGCTATGGTA 58.601 34.615 0.00 0.00 38.88 3.25
2636 2681 1.048601 GCTTCCATCCGTATCCAGGA 58.951 55.000 0.00 0.00 42.69 3.86
2640 2685 4.718961 CTTCCATCCGTATCCAGGAAAAT 58.281 43.478 0.00 0.00 41.69 1.82
2642 2687 3.973973 TCCATCCGTATCCAGGAAAATCT 59.026 43.478 0.00 0.00 41.69 2.40
2733 2778 4.690748 CCTTCACTGTCGAACACATACATT 59.309 41.667 0.00 0.00 33.23 2.71
2802 2847 2.016318 TGGCACATGCTATGCAACTAC 58.984 47.619 8.81 0.00 45.27 2.73
2823 2868 5.840940 ACGCACAATAGTTTGAGTTAGTC 57.159 39.130 0.00 0.00 36.64 2.59
2830 2875 8.926710 CACAATAGTTTGAGTTAGTCTTGTAGG 58.073 37.037 0.00 0.00 36.64 3.18
2831 2876 7.603024 ACAATAGTTTGAGTTAGTCTTGTAGGC 59.397 37.037 0.00 0.00 36.64 3.93
2832 2877 5.810080 AGTTTGAGTTAGTCTTGTAGGCT 57.190 39.130 0.00 0.00 33.01 4.58
2833 2878 6.176014 AGTTTGAGTTAGTCTTGTAGGCTT 57.824 37.500 0.00 0.00 29.80 4.35
2834 2879 5.992217 AGTTTGAGTTAGTCTTGTAGGCTTG 59.008 40.000 0.00 0.00 29.80 4.01
2835 2880 5.546621 TTGAGTTAGTCTTGTAGGCTTGT 57.453 39.130 0.00 0.00 29.80 3.16
2836 2881 6.659745 TTGAGTTAGTCTTGTAGGCTTGTA 57.340 37.500 0.00 0.00 29.80 2.41
2837 2882 6.268825 TGAGTTAGTCTTGTAGGCTTGTAG 57.731 41.667 0.00 0.00 29.80 2.74
2838 2883 5.074584 AGTTAGTCTTGTAGGCTTGTAGC 57.925 43.478 0.00 0.00 41.46 3.58
2839 2884 4.527038 AGTTAGTCTTGTAGGCTTGTAGCA 59.473 41.667 0.00 0.00 44.75 3.49
2840 2885 5.011738 AGTTAGTCTTGTAGGCTTGTAGCAA 59.988 40.000 0.00 0.00 44.75 3.91
2841 2886 3.931578 AGTCTTGTAGGCTTGTAGCAAG 58.068 45.455 0.00 4.65 44.75 4.01
2842 2887 3.578716 AGTCTTGTAGGCTTGTAGCAAGA 59.421 43.478 12.45 3.35 44.75 3.02
2843 2888 4.040461 AGTCTTGTAGGCTTGTAGCAAGAA 59.960 41.667 12.45 0.00 44.75 2.52
2844 2889 4.152580 GTCTTGTAGGCTTGTAGCAAGAAC 59.847 45.833 12.45 7.50 44.75 3.01
2880 2925 8.963725 TGAGATTTGATATCTTTCTTTGTGCAT 58.036 29.630 3.98 0.00 0.00 3.96
3169 3214 7.442364 CGTCATCTTAACCAATCCATGATAACT 59.558 37.037 0.00 0.00 0.00 2.24
3170 3215 8.778358 GTCATCTTAACCAATCCATGATAACTC 58.222 37.037 0.00 0.00 0.00 3.01
3194 3239 7.306213 TCACATCTAGAAACAGAGTAAAGTCG 58.694 38.462 0.00 0.00 0.00 4.18
3310 3361 8.099364 AGACTTTGGTTAGTTGTTGTCATATG 57.901 34.615 0.00 0.00 0.00 1.78
3314 3365 7.433708 TTGGTTAGTTGTTGTCATATGACTG 57.566 36.000 30.67 0.00 44.99 3.51
3315 3366 5.937540 TGGTTAGTTGTTGTCATATGACTGG 59.062 40.000 30.67 0.00 44.99 4.00
3390 3446 3.236816 CATTTGAAAGTGCGCTTGTAGG 58.763 45.455 14.36 0.00 34.71 3.18
3409 3465 4.976224 AGGTTTGTTGTGTTTGGAGTAC 57.024 40.909 0.00 0.00 0.00 2.73
3424 3480 9.073475 TGTTTGGAGTACAAGTTAAGCAAATAT 57.927 29.630 0.00 0.00 40.82 1.28
3483 3544 6.424812 CACAAAGACATCATAGTCAGTTGTCA 59.575 38.462 11.01 0.00 42.28 3.58
3506 3571 1.072266 AATGCCTTGTCACTGGGGTA 58.928 50.000 0.00 0.00 0.00 3.69
3516 3581 3.967326 TGTCACTGGGGTATATCTTCCTG 59.033 47.826 0.00 0.00 0.00 3.86
3530 3656 9.628500 GTATATCTTCCTGGGTGAATAAAAGTT 57.372 33.333 0.00 0.00 0.00 2.66
3576 3702 9.722184 GTCTGGTCCTTAAGAAAAACTATTAGT 57.278 33.333 3.36 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.514592 CCGATTGCCGTGAGCCAT 60.515 61.111 0.00 0.00 42.71 4.40
1 2 4.776322 CCCGATTGCCGTGAGCCA 62.776 66.667 0.00 0.00 42.71 4.75
4 5 2.892425 GAGCCCGATTGCCGTGAG 60.892 66.667 0.00 0.00 36.31 3.51
5 6 4.812476 CGAGCCCGATTGCCGTGA 62.812 66.667 0.00 0.00 38.22 4.35
6 7 4.812476 TCGAGCCCGATTGCCGTG 62.812 66.667 0.00 0.00 40.30 4.94
15 16 3.471244 GACTGACCGATCGAGCCCG 62.471 68.421 18.66 1.10 37.07 6.13
16 17 2.413765 GACTGACCGATCGAGCCC 59.586 66.667 18.66 2.92 0.00 5.19
17 18 2.024871 CGACTGACCGATCGAGCC 59.975 66.667 18.66 5.55 40.86 4.70
18 19 1.434622 TACCGACTGACCGATCGAGC 61.435 60.000 18.66 8.49 40.86 5.03
19 20 1.194997 GATACCGACTGACCGATCGAG 59.805 57.143 18.66 8.84 40.86 4.04
20 21 1.224075 GATACCGACTGACCGATCGA 58.776 55.000 18.66 0.00 40.86 3.59
21 22 0.110778 CGATACCGACTGACCGATCG 60.111 60.000 8.51 8.51 38.22 3.69
22 23 0.385723 GCGATACCGACTGACCGATC 60.386 60.000 0.00 0.00 38.22 3.69
23 24 1.653115 GCGATACCGACTGACCGAT 59.347 57.895 0.00 0.00 38.22 4.18
24 25 2.816360 CGCGATACCGACTGACCGA 61.816 63.158 0.00 0.00 38.22 4.69
25 26 2.352001 CGCGATACCGACTGACCG 60.352 66.667 0.00 0.00 38.22 4.79
26 27 1.009900 CTCGCGATACCGACTGACC 60.010 63.158 10.36 0.00 38.22 4.02
27 28 1.009900 CCTCGCGATACCGACTGAC 60.010 63.158 10.36 0.00 38.22 3.51
28 29 2.184830 CCCTCGCGATACCGACTGA 61.185 63.158 10.36 0.00 38.22 3.41
29 30 2.184830 TCCCTCGCGATACCGACTG 61.185 63.158 10.36 0.00 38.22 3.51
30 31 2.185494 GTCCCTCGCGATACCGACT 61.185 63.158 10.36 0.00 38.22 4.18
31 32 1.722636 AAGTCCCTCGCGATACCGAC 61.723 60.000 10.36 12.68 38.22 4.79
32 33 1.033746 AAAGTCCCTCGCGATACCGA 61.034 55.000 10.36 0.00 38.22 4.69
33 34 0.594284 GAAAGTCCCTCGCGATACCG 60.594 60.000 10.36 0.00 39.16 4.02
34 35 0.594284 CGAAAGTCCCTCGCGATACC 60.594 60.000 10.36 0.00 0.00 2.73
35 36 0.379669 TCGAAAGTCCCTCGCGATAC 59.620 55.000 10.36 8.85 36.25 2.24
36 37 1.315690 ATCGAAAGTCCCTCGCGATA 58.684 50.000 10.36 0.00 39.60 2.92
37 38 0.460311 AATCGAAAGTCCCTCGCGAT 59.540 50.000 10.36 0.00 42.74 4.58
38 39 0.457853 CAATCGAAAGTCCCTCGCGA 60.458 55.000 9.26 9.26 36.25 5.87
39 40 1.421410 CCAATCGAAAGTCCCTCGCG 61.421 60.000 0.00 0.00 36.25 5.87
40 41 0.108329 TCCAATCGAAAGTCCCTCGC 60.108 55.000 0.00 0.00 36.25 5.03
41 42 1.641577 GTCCAATCGAAAGTCCCTCG 58.358 55.000 0.00 0.00 37.66 4.63
42 43 1.641577 CGTCCAATCGAAAGTCCCTC 58.358 55.000 0.00 0.00 0.00 4.30
43 44 0.249398 CCGTCCAATCGAAAGTCCCT 59.751 55.000 0.00 0.00 0.00 4.20
44 45 1.366854 GCCGTCCAATCGAAAGTCCC 61.367 60.000 0.00 0.00 0.00 4.46
45 46 1.366854 GGCCGTCCAATCGAAAGTCC 61.367 60.000 0.00 0.00 0.00 3.85
46 47 0.672401 TGGCCGTCCAATCGAAAGTC 60.672 55.000 0.00 0.00 39.99 3.01
47 48 0.250553 TTGGCCGTCCAATCGAAAGT 60.251 50.000 0.00 0.00 46.89 2.66
48 49 2.550487 TTGGCCGTCCAATCGAAAG 58.450 52.632 0.00 0.00 46.89 2.62
49 50 4.802678 TTGGCCGTCCAATCGAAA 57.197 50.000 0.00 0.00 46.89 3.46
56 57 0.179015 TAGCAACTTTTGGCCGTCCA 60.179 50.000 0.00 0.00 41.55 4.02
57 58 0.955905 TTAGCAACTTTTGGCCGTCC 59.044 50.000 0.00 0.00 0.00 4.79
58 59 2.488153 AGATTAGCAACTTTTGGCCGTC 59.512 45.455 0.00 0.00 0.00 4.79
59 60 2.488153 GAGATTAGCAACTTTTGGCCGT 59.512 45.455 0.00 0.00 0.00 5.68
60 61 2.749621 AGAGATTAGCAACTTTTGGCCG 59.250 45.455 0.00 0.00 0.00 6.13
61 62 3.507622 ACAGAGATTAGCAACTTTTGGCC 59.492 43.478 0.00 0.00 0.00 5.36
62 63 4.216257 TCACAGAGATTAGCAACTTTTGGC 59.784 41.667 0.00 0.00 0.00 4.52
63 64 5.618640 GCTCACAGAGATTAGCAACTTTTGG 60.619 44.000 0.00 0.00 35.05 3.28
64 65 5.388944 GCTCACAGAGATTAGCAACTTTTG 58.611 41.667 0.00 0.00 35.05 2.44
65 66 4.153117 CGCTCACAGAGATTAGCAACTTTT 59.847 41.667 0.00 0.00 34.60 2.27
66 67 3.681897 CGCTCACAGAGATTAGCAACTTT 59.318 43.478 0.00 0.00 34.60 2.66
67 68 3.257393 CGCTCACAGAGATTAGCAACTT 58.743 45.455 0.00 0.00 34.60 2.66
68 69 2.232452 ACGCTCACAGAGATTAGCAACT 59.768 45.455 0.00 0.00 34.60 3.16
69 70 2.600867 GACGCTCACAGAGATTAGCAAC 59.399 50.000 0.00 0.00 34.60 4.17
70 71 2.417379 GGACGCTCACAGAGATTAGCAA 60.417 50.000 0.00 0.00 34.60 3.91
71 72 1.135139 GGACGCTCACAGAGATTAGCA 59.865 52.381 0.00 0.00 34.60 3.49
72 73 1.846541 GGACGCTCACAGAGATTAGC 58.153 55.000 0.00 0.00 0.00 3.09
73 74 1.268794 CCGGACGCTCACAGAGATTAG 60.269 57.143 0.00 0.00 0.00 1.73
74 75 0.738975 CCGGACGCTCACAGAGATTA 59.261 55.000 0.00 0.00 0.00 1.75
75 76 1.251527 ACCGGACGCTCACAGAGATT 61.252 55.000 9.46 0.00 0.00 2.40
76 77 1.679305 ACCGGACGCTCACAGAGAT 60.679 57.895 9.46 0.00 0.00 2.75
77 78 2.282251 ACCGGACGCTCACAGAGA 60.282 61.111 9.46 0.00 0.00 3.10
78 79 2.126307 CACCGGACGCTCACAGAG 60.126 66.667 9.46 0.00 0.00 3.35
79 80 4.357947 GCACCGGACGCTCACAGA 62.358 66.667 9.46 0.00 0.00 3.41
80 81 4.363990 AGCACCGGACGCTCACAG 62.364 66.667 9.46 0.00 33.35 3.66
87 88 4.796231 CGAAGGGAGCACCGGACG 62.796 72.222 9.46 0.00 46.96 4.79
88 89 2.726822 AAACGAAGGGAGCACCGGAC 62.727 60.000 9.46 0.00 46.96 4.79
89 90 2.513259 AAACGAAGGGAGCACCGGA 61.513 57.895 9.46 0.00 46.96 5.14
90 91 2.032071 AAACGAAGGGAGCACCGG 59.968 61.111 0.00 0.00 46.96 5.28
91 92 1.164041 AACAAACGAAGGGAGCACCG 61.164 55.000 0.00 0.00 46.96 4.94
92 93 0.591659 GAACAAACGAAGGGAGCACC 59.408 55.000 0.00 0.00 40.67 5.01
93 94 1.531578 GAGAACAAACGAAGGGAGCAC 59.468 52.381 0.00 0.00 0.00 4.40
94 95 1.416401 AGAGAACAAACGAAGGGAGCA 59.584 47.619 0.00 0.00 0.00 4.26
95 96 2.171341 AGAGAACAAACGAAGGGAGC 57.829 50.000 0.00 0.00 0.00 4.70
96 97 4.574828 TCAAAAGAGAACAAACGAAGGGAG 59.425 41.667 0.00 0.00 0.00 4.30
97 98 4.519213 TCAAAAGAGAACAAACGAAGGGA 58.481 39.130 0.00 0.00 0.00 4.20
98 99 4.893424 TCAAAAGAGAACAAACGAAGGG 57.107 40.909 0.00 0.00 0.00 3.95
99 100 7.535258 CACATATCAAAAGAGAACAAACGAAGG 59.465 37.037 0.00 0.00 0.00 3.46
100 101 8.070171 ACACATATCAAAAGAGAACAAACGAAG 58.930 33.333 0.00 0.00 0.00 3.79
101 102 7.925993 ACACATATCAAAAGAGAACAAACGAA 58.074 30.769 0.00 0.00 0.00 3.85
102 103 7.490962 ACACATATCAAAAGAGAACAAACGA 57.509 32.000 0.00 0.00 0.00 3.85
131 132 9.736023 CGCTCATACATACATACATACATACAT 57.264 33.333 0.00 0.00 0.00 2.29
132 133 8.736244 ACGCTCATACATACATACATACATACA 58.264 33.333 0.00 0.00 0.00 2.29
133 134 9.569167 AACGCTCATACATACATACATACATAC 57.431 33.333 0.00 0.00 0.00 2.39
135 136 8.925700 CAAACGCTCATACATACATACATACAT 58.074 33.333 0.00 0.00 0.00 2.29
136 137 7.923878 ACAAACGCTCATACATACATACATACA 59.076 33.333 0.00 0.00 0.00 2.29
137 138 8.294341 ACAAACGCTCATACATACATACATAC 57.706 34.615 0.00 0.00 0.00 2.39
139 140 9.489084 AATACAAACGCTCATACATACATACAT 57.511 29.630 0.00 0.00 0.00 2.29
140 141 8.880878 AATACAAACGCTCATACATACATACA 57.119 30.769 0.00 0.00 0.00 2.29
141 142 9.580916 CAAATACAAACGCTCATACATACATAC 57.419 33.333 0.00 0.00 0.00 2.39
142 143 9.320352 ACAAATACAAACGCTCATACATACATA 57.680 29.630 0.00 0.00 0.00 2.29
143 144 8.208718 ACAAATACAAACGCTCATACATACAT 57.791 30.769 0.00 0.00 0.00 2.29
144 145 7.603963 ACAAATACAAACGCTCATACATACA 57.396 32.000 0.00 0.00 0.00 2.29
145 146 8.597227 TGTACAAATACAAACGCTCATACATAC 58.403 33.333 0.00 0.00 38.40 2.39
146 147 8.705048 TGTACAAATACAAACGCTCATACATA 57.295 30.769 0.00 0.00 38.40 2.29
147 148 7.333423 ACTGTACAAATACAAACGCTCATACAT 59.667 33.333 0.00 0.00 40.84 2.29
148 149 6.647481 ACTGTACAAATACAAACGCTCATACA 59.353 34.615 0.00 0.00 40.84 2.29
149 150 6.953743 CACTGTACAAATACAAACGCTCATAC 59.046 38.462 0.00 0.00 40.84 2.39
150 151 6.647481 ACACTGTACAAATACAAACGCTCATA 59.353 34.615 0.00 0.00 40.84 2.15
151 152 5.468746 ACACTGTACAAATACAAACGCTCAT 59.531 36.000 0.00 0.00 40.84 2.90
152 153 4.812091 ACACTGTACAAATACAAACGCTCA 59.188 37.500 0.00 0.00 40.84 4.26
153 154 5.338614 ACACTGTACAAATACAAACGCTC 57.661 39.130 0.00 0.00 40.84 5.03
154 155 4.084745 CGACACTGTACAAATACAAACGCT 60.085 41.667 0.00 0.00 40.84 5.07
155 156 4.084952 TCGACACTGTACAAATACAAACGC 60.085 41.667 0.00 0.00 40.84 4.84
156 157 5.400188 TCTCGACACTGTACAAATACAAACG 59.600 40.000 0.00 0.00 40.84 3.60
157 158 6.758593 TCTCGACACTGTACAAATACAAAC 57.241 37.500 0.00 0.00 40.84 2.93
158 159 7.773864 TTTCTCGACACTGTACAAATACAAA 57.226 32.000 0.00 0.00 40.84 2.83
159 160 7.956420 ATTTCTCGACACTGTACAAATACAA 57.044 32.000 0.00 0.00 40.84 2.41
160 161 7.271868 CGTATTTCTCGACACTGTACAAATACA 59.728 37.037 15.94 0.00 39.06 2.29
161 162 7.253552 CCGTATTTCTCGACACTGTACAAATAC 60.254 40.741 0.00 4.39 34.24 1.89
162 163 6.748658 CCGTATTTCTCGACACTGTACAAATA 59.251 38.462 0.00 0.00 0.00 1.40
163 164 5.575606 CCGTATTTCTCGACACTGTACAAAT 59.424 40.000 0.00 0.00 0.00 2.32
164 165 4.919168 CCGTATTTCTCGACACTGTACAAA 59.081 41.667 0.00 0.00 0.00 2.83
165 166 4.022935 ACCGTATTTCTCGACACTGTACAA 60.023 41.667 0.00 0.00 0.00 2.41
166 167 3.503363 ACCGTATTTCTCGACACTGTACA 59.497 43.478 0.00 0.00 0.00 2.90
167 168 4.088823 ACCGTATTTCTCGACACTGTAC 57.911 45.455 0.00 0.00 0.00 2.90
168 169 4.478699 CAACCGTATTTCTCGACACTGTA 58.521 43.478 0.00 0.00 0.00 2.74
169 170 3.314553 CAACCGTATTTCTCGACACTGT 58.685 45.455 0.00 0.00 0.00 3.55
170 171 2.666508 CCAACCGTATTTCTCGACACTG 59.333 50.000 0.00 0.00 0.00 3.66
171 172 2.929592 GCCAACCGTATTTCTCGACACT 60.930 50.000 0.00 0.00 0.00 3.55
172 173 1.392510 GCCAACCGTATTTCTCGACAC 59.607 52.381 0.00 0.00 0.00 3.67
173 174 1.001068 TGCCAACCGTATTTCTCGACA 59.999 47.619 0.00 0.00 0.00 4.35
174 175 1.717194 TGCCAACCGTATTTCTCGAC 58.283 50.000 0.00 0.00 0.00 4.20
175 176 2.093921 TCATGCCAACCGTATTTCTCGA 60.094 45.455 0.00 0.00 0.00 4.04
176 177 2.030457 GTCATGCCAACCGTATTTCTCG 59.970 50.000 0.00 0.00 0.00 4.04
177 178 2.354821 GGTCATGCCAACCGTATTTCTC 59.645 50.000 1.78 0.00 37.17 2.87
178 179 2.365582 GGTCATGCCAACCGTATTTCT 58.634 47.619 1.78 0.00 37.17 2.52
179 180 2.844122 GGTCATGCCAACCGTATTTC 57.156 50.000 1.78 0.00 37.17 2.17
186 187 2.677003 CGTCACGGTCATGCCAACC 61.677 63.158 6.92 0.04 36.97 3.77
187 188 2.860293 CGTCACGGTCATGCCAAC 59.140 61.111 6.92 1.78 36.97 3.77
188 189 3.047280 GCGTCACGGTCATGCCAA 61.047 61.111 0.00 0.00 36.97 4.52
189 190 4.306967 TGCGTCACGGTCATGCCA 62.307 61.111 0.00 0.00 36.97 4.92
190 191 2.829043 TACTGCGTCACGGTCATGCC 62.829 60.000 0.00 0.00 39.22 4.40
191 192 0.806102 ATACTGCGTCACGGTCATGC 60.806 55.000 0.00 0.00 39.22 4.06
192 193 2.485266 TATACTGCGTCACGGTCATG 57.515 50.000 0.00 0.00 39.22 3.07
193 194 2.798499 GCTTATACTGCGTCACGGTCAT 60.798 50.000 0.00 0.00 39.22 3.06
194 195 1.468565 GCTTATACTGCGTCACGGTCA 60.469 52.381 0.00 0.00 39.22 4.02
195 196 1.197910 GCTTATACTGCGTCACGGTC 58.802 55.000 0.00 0.00 39.22 4.79
196 197 3.340727 GCTTATACTGCGTCACGGT 57.659 52.632 0.00 0.00 42.04 4.83
204 205 2.579207 TGGAGTCACGCTTATACTGC 57.421 50.000 0.00 0.00 32.76 4.40
205 206 5.690997 TCTATGGAGTCACGCTTATACTG 57.309 43.478 0.00 0.00 0.00 2.74
206 207 6.710597 TTTCTATGGAGTCACGCTTATACT 57.289 37.500 0.00 0.00 0.00 2.12
207 208 7.541437 GGTATTTCTATGGAGTCACGCTTATAC 59.459 40.741 0.00 0.00 0.00 1.47
208 209 7.450634 AGGTATTTCTATGGAGTCACGCTTATA 59.549 37.037 0.00 0.00 0.00 0.98
209 210 6.267928 AGGTATTTCTATGGAGTCACGCTTAT 59.732 38.462 0.00 0.00 0.00 1.73
210 211 5.597182 AGGTATTTCTATGGAGTCACGCTTA 59.403 40.000 0.00 0.00 0.00 3.09
211 212 4.406003 AGGTATTTCTATGGAGTCACGCTT 59.594 41.667 0.00 0.00 0.00 4.68
212 213 3.961408 AGGTATTTCTATGGAGTCACGCT 59.039 43.478 0.00 0.00 0.00 5.07
213 214 4.051922 CAGGTATTTCTATGGAGTCACGC 58.948 47.826 0.00 0.00 0.00 5.34
214 215 4.341235 TCCAGGTATTTCTATGGAGTCACG 59.659 45.833 0.00 0.00 36.92 4.35
215 216 5.871396 TCCAGGTATTTCTATGGAGTCAC 57.129 43.478 0.00 0.00 36.92 3.67
216 217 5.724370 TGTTCCAGGTATTTCTATGGAGTCA 59.276 40.000 0.00 0.00 42.54 3.41
217 218 6.049790 GTGTTCCAGGTATTTCTATGGAGTC 58.950 44.000 0.00 0.00 42.54 3.36
218 219 5.487488 TGTGTTCCAGGTATTTCTATGGAGT 59.513 40.000 0.00 0.00 42.54 3.85
219 220 5.989477 TGTGTTCCAGGTATTTCTATGGAG 58.011 41.667 0.00 0.00 42.54 3.86
220 221 6.381498 TTGTGTTCCAGGTATTTCTATGGA 57.619 37.500 0.00 0.00 40.04 3.41
221 222 7.461182 TTTTGTGTTCCAGGTATTTCTATGG 57.539 36.000 0.00 0.00 0.00 2.74
222 223 8.739039 TCATTTTGTGTTCCAGGTATTTCTATG 58.261 33.333 0.00 0.00 0.00 2.23
223 224 8.877864 TCATTTTGTGTTCCAGGTATTTCTAT 57.122 30.769 0.00 0.00 0.00 1.98
224 225 8.698973 TTCATTTTGTGTTCCAGGTATTTCTA 57.301 30.769 0.00 0.00 0.00 2.10
245 246 5.049060 TCGGTCGTTTGTTGATGAATTTCAT 60.049 36.000 11.64 11.64 40.34 2.57
254 255 2.140717 GGAACTCGGTCGTTTGTTGAT 58.859 47.619 0.00 0.00 0.00 2.57
329 330 1.741706 CAGGTGCTTCATGGTCATGTC 59.258 52.381 10.32 0.00 39.72 3.06
330 331 1.830279 CAGGTGCTTCATGGTCATGT 58.170 50.000 10.32 0.00 39.72 3.21
331 332 0.454600 GCAGGTGCTTCATGGTCATG 59.545 55.000 4.67 4.67 37.86 3.07
332 333 0.038599 TGCAGGTGCTTCATGGTCAT 59.961 50.000 3.18 0.00 42.66 3.06
333 334 0.178995 TTGCAGGTGCTTCATGGTCA 60.179 50.000 3.18 0.00 42.66 4.02
334 335 0.961019 TTTGCAGGTGCTTCATGGTC 59.039 50.000 3.18 0.00 42.66 4.02
335 336 1.069049 GTTTTGCAGGTGCTTCATGGT 59.931 47.619 3.18 0.00 42.66 3.55
358 359 4.831710 GGAAAGTATACATACGGAGGAGGT 59.168 45.833 5.50 0.00 38.28 3.85
394 398 2.572290 CTCCTTTGGTTGTTCGGAGTT 58.428 47.619 0.00 0.00 37.17 3.01
422 435 4.825679 GGTGGGGAGGGGAGGGAG 62.826 77.778 0.00 0.00 0.00 4.30
485 518 0.104197 GGATGGGAGGGAGGAAGGAT 60.104 60.000 0.00 0.00 0.00 3.24
889 922 3.339093 GAAGGTGGAGGGGGTGGG 61.339 72.222 0.00 0.00 0.00 4.61
890 923 3.717294 CGAAGGTGGAGGGGGTGG 61.717 72.222 0.00 0.00 0.00 4.61
931 970 2.682494 GGGGAGGTCCTGCGTGTA 60.682 66.667 4.05 0.00 35.95 2.90
1357 1396 3.403558 GAGGGGGCAGGACTGGAC 61.404 72.222 1.01 0.00 0.00 4.02
1428 1467 4.424711 ATGGCGGTGGCGGTGATT 62.425 61.111 0.00 0.00 41.24 2.57
1586 1625 1.965754 CTCTAGTGGCAGGTCCCAGC 61.966 65.000 0.00 0.00 35.05 4.85
1594 1633 1.661341 GCAATGACCTCTAGTGGCAG 58.339 55.000 10.82 1.66 0.00 4.85
1602 1641 4.473520 CGGGCGGCAATGACCTCT 62.474 66.667 12.47 0.00 33.52 3.69
1679 1718 2.740055 CACAGGCCGAGACAGCAC 60.740 66.667 0.00 0.00 0.00 4.40
1713 1752 1.699634 TCAGGGGTCTTGACAAGGAAG 59.300 52.381 15.13 0.98 0.00 3.46
2121 2160 2.929960 ACGCATTCATACGATACTCCG 58.070 47.619 0.00 0.00 0.00 4.63
2567 2610 7.094205 ACCATAGCAAGGTAAAATCAGAACAAG 60.094 37.037 0.00 0.00 37.67 3.16
2733 2778 7.931407 AGTGTTTGGCATCGATATATTGACTAA 59.069 33.333 4.71 0.00 0.00 2.24
2773 2818 4.500205 GCATAGCATGTGCCAACATTGTAT 60.500 41.667 0.57 0.00 44.94 2.29
2802 2847 6.073765 ACAAGACTAACTCAAACTATTGTGCG 60.074 38.462 0.00 0.00 37.79 5.34
2823 2868 4.065088 TGTTCTTGCTACAAGCCTACAAG 58.935 43.478 2.41 0.00 41.51 3.16
2830 2875 1.466360 CCGCATGTTCTTGCTACAAGC 60.466 52.381 2.41 0.00 42.82 4.01
2831 2876 2.076100 TCCGCATGTTCTTGCTACAAG 58.924 47.619 0.81 0.81 40.54 3.16
2832 2877 2.177394 TCCGCATGTTCTTGCTACAA 57.823 45.000 8.57 0.00 40.54 2.41
2833 2878 2.177394 TTCCGCATGTTCTTGCTACA 57.823 45.000 8.57 0.00 40.54 2.74
2834 2879 3.126858 TCAATTCCGCATGTTCTTGCTAC 59.873 43.478 8.57 0.00 40.54 3.58
2835 2880 3.342719 TCAATTCCGCATGTTCTTGCTA 58.657 40.909 8.57 0.00 40.54 3.49
2836 2881 2.161855 TCAATTCCGCATGTTCTTGCT 58.838 42.857 8.57 0.00 40.54 3.91
2837 2882 2.162208 TCTCAATTCCGCATGTTCTTGC 59.838 45.455 0.00 1.40 39.29 4.01
2838 2883 4.627611 ATCTCAATTCCGCATGTTCTTG 57.372 40.909 0.00 0.00 0.00 3.02
2839 2884 5.183713 TCAAATCTCAATTCCGCATGTTCTT 59.816 36.000 0.00 0.00 0.00 2.52
2840 2885 4.701651 TCAAATCTCAATTCCGCATGTTCT 59.298 37.500 0.00 0.00 0.00 3.01
2841 2886 4.985413 TCAAATCTCAATTCCGCATGTTC 58.015 39.130 0.00 0.00 0.00 3.18
2842 2887 5.587388 ATCAAATCTCAATTCCGCATGTT 57.413 34.783 0.00 0.00 0.00 2.71
2843 2888 6.713903 AGATATCAAATCTCAATTCCGCATGT 59.286 34.615 5.32 0.00 0.00 3.21
2844 2889 7.142306 AGATATCAAATCTCAATTCCGCATG 57.858 36.000 5.32 0.00 0.00 4.06
2880 2925 7.608153 TGGACAAACTGAATAAGAATCGTCTA 58.392 34.615 0.00 0.00 32.16 2.59
2972 3017 1.341080 CAGGAAATGGCACCTGGTTT 58.659 50.000 13.41 0.00 46.76 3.27
3159 3204 8.200120 TCTGTTTCTAGATGTGAGTTATCATGG 58.800 37.037 0.00 0.00 37.87 3.66
3169 3214 7.306213 CGACTTTACTCTGTTTCTAGATGTGA 58.694 38.462 0.00 0.00 0.00 3.58
3170 3215 6.528423 CCGACTTTACTCTGTTTCTAGATGTG 59.472 42.308 0.00 0.00 0.00 3.21
3194 3239 8.999431 TGAAACACAAGAGAATAAGTAATCACC 58.001 33.333 0.00 0.00 0.00 4.02
3361 3417 1.978782 GCACTTTCAAATGTAGCGTGC 59.021 47.619 0.00 0.00 39.31 5.34
3390 3446 5.705902 ACTTGTACTCCAAACACAACAAAC 58.294 37.500 0.00 0.00 31.20 2.93
3424 3480 9.509956 GAGGAGAGCTACTCTTATATGAACTTA 57.490 37.037 2.41 0.00 41.35 2.24
3442 3499 2.550830 TGTGACAAAAGGAGGAGAGC 57.449 50.000 0.00 0.00 0.00 4.09
3443 3500 4.513318 GTCTTTGTGACAAAAGGAGGAGAG 59.487 45.833 12.26 0.00 44.73 3.20
3445 3502 4.820284 GTCTTTGTGACAAAAGGAGGAG 57.180 45.455 12.26 0.00 44.73 3.69
3483 3544 2.555227 CCCCAGTGACAAGGCATTTACT 60.555 50.000 0.00 0.00 0.00 2.24
3506 3571 9.853177 CTAACTTTTATTCACCCAGGAAGATAT 57.147 33.333 0.00 0.00 0.00 1.63
3530 3656 8.372459 ACCAGACACAAGTACAACAAATATCTA 58.628 33.333 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.