Multiple sequence alignment - TraesCS5B01G289700

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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 TraesCS5B01G289700 chr5B 100.000 6051 0 0 1 6051 475584922 475590972 0.000000e+00 11175.0
1 TraesCS5B01G289700 chr5B 79.654 1617 259 45 3453 5054 474577426 474578987 0.000000e+00 1099.0
2 TraesCS5B01G289700 chr5B 79.414 1637 264 39 3448 5053 474610742 474612336 0.000000e+00 1088.0
3 TraesCS5B01G289700 chr5D 98.241 5344 62 16 223 5540 395254159 395259496 0.000000e+00 9319.0
4 TraesCS5B01G289700 chr5D 92.213 244 15 3 12 254 276475370 276475610 5.810000e-90 342.0
5 TraesCS5B01G289700 chr5D 95.946 74 3 0 5582 5655 395259628 395259701 2.960000e-23 121.0
6 TraesCS5B01G289700 chr5D 100.000 29 0 0 5542 5570 395259486 395259514 3.000000e-03 54.7
7 TraesCS5B01G289700 chr5A 79.852 1618 265 36 3453 5053 501405637 501407210 0.000000e+00 1125.0
8 TraesCS5B01G289700 chr5A 79.779 1627 264 42 3453 5054 500631306 500632892 0.000000e+00 1122.0
9 TraesCS5B01G289700 chrUn 91.067 403 27 9 5655 6051 240149640 240149241 2.480000e-148 536.0
10 TraesCS5B01G289700 chrUn 91.067 403 27 9 5655 6051 263945005 263945404 2.480000e-148 536.0
11 TraesCS5B01G289700 chr1D 89.356 404 33 10 5655 6051 356942264 356941864 3.260000e-137 499.0
12 TraesCS5B01G289700 chr3D 89.109 404 32 12 5656 6051 61218233 61218632 5.450000e-135 492.0
13 TraesCS5B01G289700 chr3D 85.446 213 26 5 53 263 199250034 199249825 3.670000e-52 217.0
14 TraesCS5B01G289700 chr6B 88.614 404 34 12 5654 6051 297295572 297295969 1.180000e-131 481.0
15 TraesCS5B01G289700 chr6B 88.366 404 35 12 5654 6051 297291850 297292247 5.490000e-130 475.0
16 TraesCS5B01G289700 chr6B 97.297 37 1 0 3698 3734 218218598 218218634 5.060000e-06 63.9
17 TraesCS5B01G289700 chr4D 88.778 401 34 11 5658 6051 20431105 20430709 1.180000e-131 481.0
18 TraesCS5B01G289700 chr4A 88.337 403 37 10 5656 6051 656925055 656924656 5.490000e-130 475.0
19 TraesCS5B01G289700 chr4A 87.500 240 26 4 12 250 684267820 684268056 2.150000e-69 274.0
20 TraesCS5B01G289700 chr3A 87.711 415 41 10 5643 6050 365946111 365945700 5.490000e-130 475.0
21 TraesCS5B01G289700 chr3A 87.437 199 23 2 53 250 434067403 434067206 1.700000e-55 228.0
22 TraesCS5B01G289700 chr2D 92.339 248 15 3 12 258 640823333 640823577 3.470000e-92 350.0
23 TraesCS5B01G289700 chr2D 95.745 47 2 0 5503 5549 9925851 9925897 6.500000e-10 76.8
24 TraesCS5B01G289700 chr7B 86.321 212 24 5 53 260 538871867 538872077 6.100000e-55 226.0
25 TraesCS5B01G289700 chr7B 85.648 216 27 4 52 266 648387700 648387488 2.190000e-54 224.0
26 TraesCS5B01G289700 chr1A 86.124 209 25 4 53 258 416544804 416545011 7.890000e-54 222.0
27 TraesCS5B01G289700 chr7A 85.507 207 28 2 53 258 439343335 439343130 1.320000e-51 215.0
28 TraesCS5B01G289700 chr3B 92.647 68 5 0 5503 5570 823396002 823395935 1.390000e-16 99.0
29 TraesCS5B01G289700 chr3B 95.745 47 2 0 5503 5549 60743539 60743493 6.500000e-10 76.8


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 TraesCS5B01G289700 chr5B 475584922 475590972 6050 False 11175.0 11175 100.000000 1 6051 1 chr5B.!!$F3 6050
1 TraesCS5B01G289700 chr5B 474577426 474578987 1561 False 1099.0 1099 79.654000 3453 5054 1 chr5B.!!$F1 1601
2 TraesCS5B01G289700 chr5B 474610742 474612336 1594 False 1088.0 1088 79.414000 3448 5053 1 chr5B.!!$F2 1605
3 TraesCS5B01G289700 chr5D 395254159 395259701 5542 False 3164.9 9319 98.062333 223 5655 3 chr5D.!!$F2 5432
4 TraesCS5B01G289700 chr5A 501405637 501407210 1573 False 1125.0 1125 79.852000 3453 5053 1 chr5A.!!$F2 1600
5 TraesCS5B01G289700 chr5A 500631306 500632892 1586 False 1122.0 1122 79.779000 3453 5054 1 chr5A.!!$F1 1601
6 TraesCS5B01G289700 chr6B 297291850 297295969 4119 False 478.0 481 88.490000 5654 6051 2 chr6B.!!$F2 397

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
32 33 0.117340 AAGAGGGGGATAGATCGGGG 59.883 60.000 0.00 0.00 0.00 5.73 F
67 68 0.179018 AAAGTTTCTCGCCTGGCTGT 60.179 50.000 17.92 0.00 0.00 4.40 F
69 70 0.886490 AGTTTCTCGCCTGGCTGTTG 60.886 55.000 17.92 0.47 0.00 3.33 F
83 84 0.946221 CTGTTGTGCCCTCTGTCGAC 60.946 60.000 9.11 9.11 0.00 4.20 F
154 155 1.358152 AAAGGACCTCGGATGAACCA 58.642 50.000 0.00 0.00 38.90 3.67 F
155 156 1.584724 AAGGACCTCGGATGAACCAT 58.415 50.000 0.00 0.00 38.90 3.55 F
156 157 1.584724 AGGACCTCGGATGAACCATT 58.415 50.000 0.00 0.00 38.90 3.16 F
376 377 1.752498 TCCACGCCGCTCTAAAATCTA 59.248 47.619 0.00 0.00 0.00 1.98 F
1364 1368 2.621070 TGTTTCACCCTTCTAGCCTCT 58.379 47.619 0.00 0.00 0.00 3.69 F
2630 2634 2.682856 TCAGTTCTCCACACAACTTTGC 59.317 45.455 0.00 0.00 30.06 3.68 F
4510 4557 1.153958 CGCTTTTGCTTGCTAGGCC 60.154 57.895 0.00 0.00 44.80 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1558 1.619654 CACCAACCTTCAAGCCATCA 58.380 50.000 0.00 0.00 0.00 3.07 R
1599 1603 6.018832 GGTGCAGTTAACTTACGTAAACAAGA 60.019 38.462 5.07 0.00 0.00 3.02 R
1976 1980 8.525316 AGTGAAATGTCATTTTTATGCATCAGA 58.475 29.630 12.04 0.00 35.80 3.27 R
2101 2105 4.351874 AAGATGTTCTTTCCTCAACCGA 57.648 40.909 0.00 0.00 31.57 4.69 R
2436 2440 7.443302 AGAATCAAGTTGATATCAAGGGAGA 57.557 36.000 18.47 13.66 35.76 3.71 R
2589 2593 5.012148 ACTGAGCAAATACTACACAACCTCT 59.988 40.000 0.00 0.00 0.00 3.69 R
2630 2634 2.112426 ATCCTGGGATGATCCGAAGGG 61.112 57.143 23.85 12.15 39.95 3.95 R
2842 2857 0.250467 TGGCTGAAGGCTGTGTCTTC 60.250 55.000 5.41 5.11 43.66 2.87 R
3043 3058 0.685097 TAGCAGCAGGGTTTTCTCGT 59.315 50.000 0.00 0.00 0.00 4.18 R
4539 4586 0.826062 CATGCCAACAAATCTCCCCC 59.174 55.000 0.00 0.00 0.00 5.40 R
5697 5891 0.099791 AACTGCAACGACGGTTTTGG 59.900 50.000 0.00 0.00 35.60 3.28 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 4.963878 ATGTTGCCGCCTAAGAGG 57.036 55.556 0.00 0.00 38.80 3.69
19 20 0.468226 TATGTTGCCGCCTAAGAGGG 59.532 55.000 0.00 0.00 35.37 4.30
20 21 2.124695 GTTGCCGCCTAAGAGGGG 60.125 66.667 2.65 2.65 46.85 4.79
26 27 3.768008 CGCCTAAGAGGGGGATAGA 57.232 57.895 1.69 0.00 43.90 1.98
27 28 2.239681 CGCCTAAGAGGGGGATAGAT 57.760 55.000 1.69 0.00 43.90 1.98
28 29 2.104170 CGCCTAAGAGGGGGATAGATC 58.896 57.143 1.69 0.00 43.90 2.75
29 30 2.104170 GCCTAAGAGGGGGATAGATCG 58.896 57.143 0.00 0.00 35.37 3.69
30 31 2.741145 CCTAAGAGGGGGATAGATCGG 58.259 57.143 0.00 0.00 0.00 4.18
31 32 2.624557 CCTAAGAGGGGGATAGATCGGG 60.625 59.091 0.00 0.00 0.00 5.14
32 33 0.117340 AAGAGGGGGATAGATCGGGG 59.883 60.000 0.00 0.00 0.00 5.73
33 34 0.780494 AGAGGGGGATAGATCGGGGA 60.780 60.000 0.00 0.00 0.00 4.81
34 35 0.324830 GAGGGGGATAGATCGGGGAG 60.325 65.000 0.00 0.00 0.00 4.30
35 36 1.306226 GGGGGATAGATCGGGGAGG 60.306 68.421 0.00 0.00 0.00 4.30
36 37 1.306226 GGGGATAGATCGGGGAGGG 60.306 68.421 0.00 0.00 0.00 4.30
37 38 1.306226 GGGATAGATCGGGGAGGGG 60.306 68.421 0.00 0.00 0.00 4.79
38 39 1.306226 GGATAGATCGGGGAGGGGG 60.306 68.421 0.00 0.00 0.00 5.40
39 40 1.990614 GATAGATCGGGGAGGGGGC 60.991 68.421 0.00 0.00 0.00 5.80
40 41 3.564347 ATAGATCGGGGAGGGGGCC 62.564 68.421 0.00 0.00 0.00 5.80
43 44 3.864983 GATCGGGGAGGGGGCCATA 62.865 68.421 4.39 0.00 0.00 2.74
44 45 3.208342 ATCGGGGAGGGGGCCATAT 62.208 63.158 4.39 0.00 0.00 1.78
45 46 2.730196 ATCGGGGAGGGGGCCATATT 62.730 60.000 4.39 0.00 0.00 1.28
46 47 2.854076 GGGGAGGGGGCCATATTG 59.146 66.667 4.39 0.00 0.00 1.90
47 48 2.118294 GGGAGGGGGCCATATTGC 59.882 66.667 4.39 0.00 0.00 3.56
48 49 2.777960 GGGAGGGGGCCATATTGCA 61.778 63.158 4.39 0.00 0.00 4.08
49 50 1.232792 GGAGGGGGCCATATTGCAA 59.767 57.895 4.39 0.00 0.00 4.08
50 51 0.398381 GGAGGGGGCCATATTGCAAA 60.398 55.000 4.39 0.00 0.00 3.68
51 52 1.043022 GAGGGGGCCATATTGCAAAG 58.957 55.000 4.39 0.00 0.00 2.77
52 53 0.339510 AGGGGGCCATATTGCAAAGT 59.660 50.000 4.39 0.00 0.00 2.66
53 54 1.203237 GGGGGCCATATTGCAAAGTT 58.797 50.000 4.39 0.00 0.00 2.66
54 55 1.559219 GGGGGCCATATTGCAAAGTTT 59.441 47.619 4.39 0.00 0.00 2.66
55 56 2.419990 GGGGGCCATATTGCAAAGTTTC 60.420 50.000 4.39 0.00 0.00 2.78
56 57 2.501316 GGGGCCATATTGCAAAGTTTCT 59.499 45.455 4.39 0.00 0.00 2.52
57 58 3.430790 GGGGCCATATTGCAAAGTTTCTC 60.431 47.826 4.39 0.00 0.00 2.87
58 59 3.438360 GGCCATATTGCAAAGTTTCTCG 58.562 45.455 1.71 0.00 0.00 4.04
59 60 2.854185 GCCATATTGCAAAGTTTCTCGC 59.146 45.455 1.71 0.00 0.00 5.03
60 61 3.438360 CCATATTGCAAAGTTTCTCGCC 58.562 45.455 1.71 0.00 0.00 5.54
61 62 3.129287 CCATATTGCAAAGTTTCTCGCCT 59.871 43.478 1.71 0.00 0.00 5.52
62 63 2.712057 ATTGCAAAGTTTCTCGCCTG 57.288 45.000 1.71 0.00 0.00 4.85
63 64 0.667993 TTGCAAAGTTTCTCGCCTGG 59.332 50.000 0.00 0.00 0.00 4.45
64 65 1.081175 GCAAAGTTTCTCGCCTGGC 60.081 57.895 9.11 9.11 0.00 4.85
65 66 1.518903 GCAAAGTTTCTCGCCTGGCT 61.519 55.000 17.92 0.00 0.00 4.75
66 67 0.239347 CAAAGTTTCTCGCCTGGCTG 59.761 55.000 17.92 10.52 0.00 4.85
67 68 0.179018 AAAGTTTCTCGCCTGGCTGT 60.179 50.000 17.92 0.00 0.00 4.40
68 69 0.179018 AAGTTTCTCGCCTGGCTGTT 60.179 50.000 17.92 0.00 0.00 3.16
69 70 0.886490 AGTTTCTCGCCTGGCTGTTG 60.886 55.000 17.92 0.47 0.00 3.33
70 71 1.148273 TTTCTCGCCTGGCTGTTGT 59.852 52.632 17.92 0.00 0.00 3.32
71 72 1.165907 TTTCTCGCCTGGCTGTTGTG 61.166 55.000 17.92 0.00 0.00 3.33
72 73 3.730761 CTCGCCTGGCTGTTGTGC 61.731 66.667 17.92 0.00 0.00 4.57
79 80 2.113986 GGCTGTTGTGCCCTCTGT 59.886 61.111 0.00 0.00 46.82 3.41
80 81 1.968540 GGCTGTTGTGCCCTCTGTC 60.969 63.158 0.00 0.00 46.82 3.51
81 82 2.320587 GCTGTTGTGCCCTCTGTCG 61.321 63.158 0.00 0.00 0.00 4.35
82 83 1.367471 CTGTTGTGCCCTCTGTCGA 59.633 57.895 0.00 0.00 0.00 4.20
83 84 0.946221 CTGTTGTGCCCTCTGTCGAC 60.946 60.000 9.11 9.11 0.00 4.20
84 85 2.022129 GTTGTGCCCTCTGTCGACG 61.022 63.158 11.62 6.07 0.00 5.12
85 86 2.495409 TTGTGCCCTCTGTCGACGT 61.495 57.895 11.62 0.00 0.00 4.34
86 87 2.430921 GTGCCCTCTGTCGACGTG 60.431 66.667 11.62 6.55 0.00 4.49
87 88 3.680786 TGCCCTCTGTCGACGTGG 61.681 66.667 11.62 14.65 0.00 4.94
89 90 3.680786 CCCTCTGTCGACGTGGCA 61.681 66.667 11.62 0.00 0.00 4.92
90 91 2.573869 CCTCTGTCGACGTGGCAT 59.426 61.111 11.62 0.00 0.00 4.40
91 92 1.807165 CCTCTGTCGACGTGGCATG 60.807 63.158 11.62 4.87 0.00 4.06
92 93 1.807165 CTCTGTCGACGTGGCATGG 60.807 63.158 11.62 0.00 0.00 3.66
93 94 2.815211 CTGTCGACGTGGCATGGG 60.815 66.667 11.62 2.64 0.00 4.00
94 95 3.589654 CTGTCGACGTGGCATGGGT 62.590 63.158 11.62 0.00 0.00 4.51
95 96 2.813908 GTCGACGTGGCATGGGTC 60.814 66.667 12.05 8.72 0.00 4.46
96 97 3.307108 TCGACGTGGCATGGGTCA 61.307 61.111 12.05 0.00 0.00 4.02
97 98 2.358125 CGACGTGGCATGGGTCAA 60.358 61.111 12.05 0.00 0.00 3.18
98 99 2.677003 CGACGTGGCATGGGTCAAC 61.677 63.158 12.05 0.00 0.00 3.18
99 100 2.668212 ACGTGGCATGGGTCAACG 60.668 61.111 12.05 0.00 32.20 4.10
100 101 4.101790 CGTGGCATGGGTCAACGC 62.102 66.667 0.00 0.00 0.00 4.84
101 102 2.983030 GTGGCATGGGTCAACGCA 60.983 61.111 2.17 2.17 43.04 5.24
102 103 2.983030 TGGCATGGGTCAACGCAC 60.983 61.111 1.67 0.00 41.67 5.34
103 104 3.747976 GGCATGGGTCAACGCACC 61.748 66.667 1.67 0.00 41.67 5.01
104 105 2.983030 GCATGGGTCAACGCACCA 60.983 61.111 1.67 0.00 41.67 4.17
105 106 2.953821 CATGGGTCAACGCACCAC 59.046 61.111 1.67 0.00 41.67 4.16
135 136 5.963176 GGTCAACGACCCCTAATTAAAAA 57.037 39.130 1.47 0.00 46.19 1.94
153 154 2.491675 AAAAGGACCTCGGATGAACC 57.508 50.000 0.00 0.00 0.00 3.62
154 155 1.358152 AAAGGACCTCGGATGAACCA 58.642 50.000 0.00 0.00 38.90 3.67
155 156 1.584724 AAGGACCTCGGATGAACCAT 58.415 50.000 0.00 0.00 38.90 3.55
156 157 1.584724 AGGACCTCGGATGAACCATT 58.415 50.000 0.00 0.00 38.90 3.16
157 158 1.916181 AGGACCTCGGATGAACCATTT 59.084 47.619 0.00 0.00 38.90 2.32
158 159 3.112263 AGGACCTCGGATGAACCATTTA 58.888 45.455 0.00 0.00 38.90 1.40
159 160 3.118371 AGGACCTCGGATGAACCATTTAC 60.118 47.826 0.00 0.00 38.90 2.01
160 161 3.118371 GGACCTCGGATGAACCATTTACT 60.118 47.826 0.00 0.00 38.90 2.24
161 162 4.100498 GGACCTCGGATGAACCATTTACTA 59.900 45.833 0.00 0.00 38.90 1.82
162 163 5.395990 GGACCTCGGATGAACCATTTACTAA 60.396 44.000 0.00 0.00 38.90 2.24
163 164 6.057321 ACCTCGGATGAACCATTTACTAAA 57.943 37.500 0.00 0.00 38.90 1.85
164 165 6.113411 ACCTCGGATGAACCATTTACTAAAG 58.887 40.000 0.00 0.00 38.90 1.85
165 166 6.070424 ACCTCGGATGAACCATTTACTAAAGA 60.070 38.462 0.00 0.00 38.90 2.52
166 167 6.821665 CCTCGGATGAACCATTTACTAAAGAA 59.178 38.462 0.00 0.00 38.90 2.52
167 168 7.499232 CCTCGGATGAACCATTTACTAAAGAAT 59.501 37.037 0.00 0.00 38.90 2.40
168 169 8.801882 TCGGATGAACCATTTACTAAAGAATT 57.198 30.769 0.00 0.00 38.90 2.17
169 170 9.893634 TCGGATGAACCATTTACTAAAGAATTA 57.106 29.630 0.00 0.00 38.90 1.40
174 175 9.457436 TGAACCATTTACTAAAGAATTAGGACC 57.543 33.333 1.17 0.00 42.39 4.46
175 176 9.682465 GAACCATTTACTAAAGAATTAGGACCT 57.318 33.333 0.00 0.00 42.39 3.85
202 203 9.489084 AAAGGTGCATTTTTAAAGAAATAGGAC 57.511 29.630 0.00 0.00 0.00 3.85
203 204 8.422577 AGGTGCATTTTTAAAGAAATAGGACT 57.577 30.769 0.00 0.00 0.00 3.85
204 205 9.528489 AGGTGCATTTTTAAAGAAATAGGACTA 57.472 29.630 0.00 0.00 0.00 2.59
215 216 8.608844 AAAGAAATAGGACTAAAGTGACACAG 57.391 34.615 8.59 0.00 0.00 3.66
216 217 6.166982 AGAAATAGGACTAAAGTGACACAGC 58.833 40.000 8.59 0.00 0.00 4.40
217 218 2.440539 AGGACTAAAGTGACACAGCG 57.559 50.000 8.59 0.00 0.00 5.18
218 219 1.961394 AGGACTAAAGTGACACAGCGA 59.039 47.619 8.59 0.00 0.00 4.93
219 220 2.059541 GGACTAAAGTGACACAGCGAC 58.940 52.381 8.59 0.00 0.00 5.19
220 221 2.545113 GGACTAAAGTGACACAGCGACA 60.545 50.000 8.59 0.00 0.00 4.35
221 222 3.120792 GACTAAAGTGACACAGCGACAA 58.879 45.455 8.59 0.00 0.00 3.18
351 352 3.053619 ACCTACCCAAGTTCCAATCCATC 60.054 47.826 0.00 0.00 0.00 3.51
376 377 1.752498 TCCACGCCGCTCTAAAATCTA 59.248 47.619 0.00 0.00 0.00 1.98
395 396 3.699538 TCTATCGTGTAGCATCAGGTGTT 59.300 43.478 0.00 0.00 0.00 3.32
688 689 4.099824 GGTTGCGTTCTTTCTTTTTCGAA 58.900 39.130 0.00 0.00 0.00 3.71
1038 1042 3.162666 GGGTACCGATGATGGTCTCATA 58.837 50.000 5.65 0.00 41.79 2.15
1094 1098 5.690464 ACTTGCATTGGTAGAGAAGAGAT 57.310 39.130 0.00 0.00 0.00 2.75
1095 1099 6.059787 ACTTGCATTGGTAGAGAAGAGATT 57.940 37.500 0.00 0.00 0.00 2.40
1144 1148 6.968904 GCCAACACTTCATTATTCTACACATG 59.031 38.462 0.00 0.00 0.00 3.21
1364 1368 2.621070 TGTTTCACCCTTCTAGCCTCT 58.379 47.619 0.00 0.00 0.00 3.69
1500 1504 3.807553 CCAGGTTCATTTTGCAAGGTTT 58.192 40.909 0.00 0.00 0.00 3.27
1554 1558 7.121382 TCAATGATCTTAAAAGAGAAGGCCAT 58.879 34.615 5.01 0.00 38.66 4.40
1599 1603 9.525409 GCTGCTAATCATCATTCACTTAATTTT 57.475 29.630 0.00 0.00 0.00 1.82
1775 1779 4.125703 GTGAAACTCTATCATCAGCTGGG 58.874 47.826 15.13 6.93 0.00 4.45
1976 1980 9.938280 TGTAACTATATGCACTGAAAAGTAACT 57.062 29.630 0.00 0.00 0.00 2.24
2101 2105 4.162131 ACTTTGTTGGCATGAACCTTTCTT 59.838 37.500 0.00 0.00 0.00 2.52
2589 2593 5.187186 GGTTTGTGATAGTCTCCTGAACCTA 59.813 44.000 0.00 0.00 33.14 3.08
2630 2634 2.682856 TCAGTTCTCCACACAACTTTGC 59.317 45.455 0.00 0.00 30.06 3.68
2657 2672 4.090090 CGGATCATCCCAGGATAACTAGT 58.910 47.826 0.00 0.00 31.13 2.57
2666 2681 4.525100 CCCAGGATAACTAGTCTTAGAGGC 59.475 50.000 0.00 0.00 0.00 4.70
2826 2841 3.007940 TCTTCATGTCAACCGAATCTGGT 59.992 43.478 0.00 0.00 46.67 4.00
2842 2857 4.394712 GTGCCACCTCCACCTCCG 62.395 72.222 0.00 0.00 0.00 4.63
2880 2895 4.081087 AGCCAACATCGATACAGTAAACCT 60.081 41.667 0.00 0.00 0.00 3.50
3014 3029 3.623060 CACTAATAACTGCCAATCTGCGT 59.377 43.478 0.00 0.00 0.00 5.24
3034 3049 6.513180 TGCGTTTAATCTCCCTGTCTAATAG 58.487 40.000 0.00 0.00 0.00 1.73
3043 3058 1.473257 CCTGTCTAATAGCAGCGCCAA 60.473 52.381 2.29 0.00 0.00 4.52
3201 3216 9.733556 ATAAGTACAATTACATGTCCACTTTCA 57.266 29.630 0.00 0.00 35.11 2.69
3330 3345 3.163594 GCTGCGTATGTGTGATGTTTTC 58.836 45.455 0.00 0.00 0.00 2.29
4127 4160 4.599047 ATTCCAAACGAAGGATGCAAAA 57.401 36.364 0.00 0.00 34.56 2.44
4210 4243 5.073311 TCCGTCCTCTTTGTTCATCTAAG 57.927 43.478 0.00 0.00 0.00 2.18
4386 4419 9.871238 CAGTTGTACAATCACTAAGGTTAGTAT 57.129 33.333 12.26 0.00 41.82 2.12
4510 4557 1.153958 CGCTTTTGCTTGCTAGGCC 60.154 57.895 0.00 0.00 44.80 5.19
4539 4586 1.075536 AGGGCCCCTGTTTGACTTTAG 59.924 52.381 21.43 0.00 29.57 1.85
4809 4884 1.603802 CGTTGATGAAGTTGGCAGTGT 59.396 47.619 0.00 0.00 0.00 3.55
4890 4973 4.956085 ACTGCCGATAACATTACTATGCA 58.044 39.130 0.00 0.00 35.03 3.96
5160 5243 3.181445 TGAACCTGTTGGCTGTCTTGTAT 60.181 43.478 0.00 0.00 36.63 2.29
5161 5244 3.508845 ACCTGTTGGCTGTCTTGTATT 57.491 42.857 0.00 0.00 36.63 1.89
5178 5270 9.394477 GTCTTGTATTCTAATGTTTGAACCAAC 57.606 33.333 0.00 0.00 0.00 3.77
5435 5527 3.308904 GCCCCTTCTACCTTGTAACCAAT 60.309 47.826 0.00 0.00 0.00 3.16
5530 5622 5.450171 ACATATAAACGCTGCTAGAGTACG 58.550 41.667 0.00 0.00 0.00 3.67
5531 5623 2.184385 TAAACGCTGCTAGAGTACGC 57.816 50.000 0.00 0.00 0.00 4.42
5533 5625 3.019545 CGCTGCTAGAGTACGCGC 61.020 66.667 5.73 0.00 37.29 6.86
5534 5626 2.655685 GCTGCTAGAGTACGCGCC 60.656 66.667 5.73 0.00 0.00 6.53
5535 5627 2.798689 CTGCTAGAGTACGCGCCA 59.201 61.111 5.73 0.00 0.00 5.69
5536 5628 1.360551 CTGCTAGAGTACGCGCCAT 59.639 57.895 5.73 0.00 0.00 4.40
5537 5629 0.249073 CTGCTAGAGTACGCGCCATT 60.249 55.000 5.73 0.00 0.00 3.16
5538 5630 0.248907 TGCTAGAGTACGCGCCATTC 60.249 55.000 5.73 0.02 0.00 2.67
5539 5631 0.940047 GCTAGAGTACGCGCCATTCC 60.940 60.000 5.73 0.00 0.00 3.01
5540 5632 0.384309 CTAGAGTACGCGCCATTCCA 59.616 55.000 5.73 0.00 0.00 3.53
5570 5662 2.621055 TCCGTTTCAAATTCACCCTGTG 59.379 45.455 0.00 0.00 34.45 3.66
5572 5664 2.754472 GTTTCAAATTCACCCTGTGCC 58.246 47.619 0.00 0.00 32.98 5.01
5573 5665 2.365293 GTTTCAAATTCACCCTGTGCCT 59.635 45.455 0.00 0.00 32.98 4.75
5575 5667 1.962807 TCAAATTCACCCTGTGCCTTG 59.037 47.619 0.00 0.00 32.98 3.61
5576 5668 0.681175 AAATTCACCCTGTGCCTTGC 59.319 50.000 0.00 0.00 32.98 4.01
5577 5669 1.526575 AATTCACCCTGTGCCTTGCG 61.527 55.000 0.00 0.00 32.98 4.85
5662 5856 1.611491 CGTGGGTTGGCAGTGTTAAAT 59.389 47.619 0.00 0.00 0.00 1.40
5663 5857 2.814919 CGTGGGTTGGCAGTGTTAAATA 59.185 45.455 0.00 0.00 0.00 1.40
5698 5892 4.686695 GGAAATCTCCCCTTGCCC 57.313 61.111 0.00 0.00 35.42 5.36
5699 5893 1.697297 GGAAATCTCCCCTTGCCCA 59.303 57.895 0.00 0.00 35.42 5.36
5713 5907 3.111939 CCCAAAACCGTCGTTGCA 58.888 55.556 0.00 0.00 30.72 4.08
5750 5944 1.455959 GCCTCCCTTCGCTCTCCTA 60.456 63.158 0.00 0.00 0.00 2.94
5758 5952 1.950909 CTTCGCTCTCCTAGAACCGAT 59.049 52.381 0.00 0.00 31.34 4.18
5760 5954 0.318275 CGCTCTCCTAGAACCGATGC 60.318 60.000 0.00 0.00 0.00 3.91
5763 5957 1.107538 TCTCCTAGAACCGATGCCCG 61.108 60.000 0.00 0.00 38.18 6.13
5788 5982 0.248134 GGGATCGTCGTGTCTCTTCG 60.248 60.000 0.00 0.00 0.00 3.79
5817 6012 0.034477 AAAGGGGCCTGTAACCATCG 60.034 55.000 0.84 0.00 0.00 3.84
5822 6017 1.134220 GGGCCTGTAACCATCGATCAA 60.134 52.381 0.84 0.00 0.00 2.57
5823 6018 2.213499 GGCCTGTAACCATCGATCAAG 58.787 52.381 0.00 0.00 0.00 3.02
5824 6019 2.158957 GGCCTGTAACCATCGATCAAGA 60.159 50.000 0.00 0.00 0.00 3.02
5825 6020 3.126831 GCCTGTAACCATCGATCAAGAG 58.873 50.000 0.00 0.00 0.00 2.85
5826 6021 3.181475 GCCTGTAACCATCGATCAAGAGA 60.181 47.826 0.00 0.00 0.00 3.10
5827 6022 4.502259 GCCTGTAACCATCGATCAAGAGAT 60.502 45.833 0.00 0.00 37.13 2.75
5829 6024 6.738731 GCCTGTAACCATCGATCAAGAGATAA 60.739 42.308 0.00 0.00 33.72 1.75
5830 6025 7.210174 CCTGTAACCATCGATCAAGAGATAAA 58.790 38.462 0.00 0.00 33.72 1.40
5831 6026 7.875041 CCTGTAACCATCGATCAAGAGATAAAT 59.125 37.037 0.00 0.00 33.72 1.40
5832 6027 8.818141 TGTAACCATCGATCAAGAGATAAATC 57.182 34.615 0.00 0.00 33.72 2.17
5833 6028 8.421002 TGTAACCATCGATCAAGAGATAAATCA 58.579 33.333 0.00 0.00 33.72 2.57
5836 6031 7.504403 ACCATCGATCAAGAGATAAATCACTT 58.496 34.615 0.00 0.00 38.06 3.16
5837 6032 7.989741 ACCATCGATCAAGAGATAAATCACTTT 59.010 33.333 0.00 0.00 35.92 2.66
5838 6033 8.494347 CCATCGATCAAGAGATAAATCACTTTC 58.506 37.037 0.00 0.00 35.92 2.62
5839 6034 9.038803 CATCGATCAAGAGATAAATCACTTTCA 57.961 33.333 0.00 0.00 35.92 2.69
5859 6054 8.981647 ACTTTCAATTCAAAACATGTTATGAGC 58.018 29.630 12.39 0.00 0.00 4.26
5860 6055 8.883954 TTTCAATTCAAAACATGTTATGAGCA 57.116 26.923 12.39 0.00 0.00 4.26
5861 6056 7.872163 TCAATTCAAAACATGTTATGAGCAC 57.128 32.000 12.39 0.00 0.00 4.40
5862 6057 6.581919 TCAATTCAAAACATGTTATGAGCACG 59.418 34.615 12.39 0.00 0.00 5.34
5863 6058 5.431420 TTCAAAACATGTTATGAGCACGT 57.569 34.783 12.39 0.00 0.00 4.49
5864 6059 6.546972 TTCAAAACATGTTATGAGCACGTA 57.453 33.333 12.39 0.00 0.00 3.57
5865 6060 6.164408 TCAAAACATGTTATGAGCACGTAG 57.836 37.500 12.39 0.00 0.00 3.51
5866 6061 5.929415 TCAAAACATGTTATGAGCACGTAGA 59.071 36.000 12.39 0.00 0.00 2.59
5878 6073 1.493772 CACGTAGAACAACCAGCGAA 58.506 50.000 0.00 0.00 0.00 4.70
5941 6140 3.734776 CGTTTTCTACGGGGACAATTC 57.265 47.619 0.00 0.00 46.42 2.17
5974 6173 2.198827 TTATGCCTTGTGGACAGTGG 57.801 50.000 0.00 0.00 34.57 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.468226 CCCTCTTAGGCGGCAACATA 59.532 55.000 13.08 0.00 32.73 2.29
1 2 1.224592 CCCTCTTAGGCGGCAACAT 59.775 57.895 13.08 0.00 32.73 2.71
2 3 2.668632 CCCTCTTAGGCGGCAACA 59.331 61.111 13.08 0.00 32.73 3.33
3 4 2.124695 CCCCTCTTAGGCGGCAAC 60.125 66.667 13.08 0.00 32.73 4.17
4 5 3.407967 CCCCCTCTTAGGCGGCAA 61.408 66.667 13.08 2.54 32.73 4.52
5 6 2.320830 TATCCCCCTCTTAGGCGGCA 62.321 60.000 13.08 0.00 33.22 5.69
6 7 1.535687 TATCCCCCTCTTAGGCGGC 60.536 63.158 0.00 0.00 33.22 6.53
7 8 0.114560 TCTATCCCCCTCTTAGGCGG 59.885 60.000 0.00 0.00 34.53 6.13
8 9 2.104170 GATCTATCCCCCTCTTAGGCG 58.896 57.143 0.00 0.00 32.73 5.52
9 10 2.104170 CGATCTATCCCCCTCTTAGGC 58.896 57.143 0.00 0.00 32.73 3.93
10 11 2.624557 CCCGATCTATCCCCCTCTTAGG 60.625 59.091 0.00 0.00 34.30 2.69
11 12 2.624557 CCCCGATCTATCCCCCTCTTAG 60.625 59.091 0.00 0.00 0.00 2.18
12 13 1.361543 CCCCGATCTATCCCCCTCTTA 59.638 57.143 0.00 0.00 0.00 2.10
13 14 0.117340 CCCCGATCTATCCCCCTCTT 59.883 60.000 0.00 0.00 0.00 2.85
14 15 0.780494 TCCCCGATCTATCCCCCTCT 60.780 60.000 0.00 0.00 0.00 3.69
15 16 0.324830 CTCCCCGATCTATCCCCCTC 60.325 65.000 0.00 0.00 0.00 4.30
16 17 1.784387 CTCCCCGATCTATCCCCCT 59.216 63.158 0.00 0.00 0.00 4.79
17 18 1.306226 CCTCCCCGATCTATCCCCC 60.306 68.421 0.00 0.00 0.00 5.40
18 19 1.306226 CCCTCCCCGATCTATCCCC 60.306 68.421 0.00 0.00 0.00 4.81
19 20 1.306226 CCCCTCCCCGATCTATCCC 60.306 68.421 0.00 0.00 0.00 3.85
20 21 1.306226 CCCCCTCCCCGATCTATCC 60.306 68.421 0.00 0.00 0.00 2.59
21 22 1.990614 GCCCCCTCCCCGATCTATC 60.991 68.421 0.00 0.00 0.00 2.08
22 23 2.122954 GCCCCCTCCCCGATCTAT 59.877 66.667 0.00 0.00 0.00 1.98
23 24 4.250170 GGCCCCCTCCCCGATCTA 62.250 72.222 0.00 0.00 0.00 1.98
25 26 3.864983 TATGGCCCCCTCCCCGATC 62.865 68.421 0.00 0.00 0.00 3.69
26 27 2.730196 AATATGGCCCCCTCCCCGAT 62.730 60.000 0.00 0.00 0.00 4.18
27 28 3.436056 AATATGGCCCCCTCCCCGA 62.436 63.158 0.00 0.00 0.00 5.14
28 29 2.858974 AATATGGCCCCCTCCCCG 60.859 66.667 0.00 0.00 0.00 5.73
29 30 2.854076 CAATATGGCCCCCTCCCC 59.146 66.667 0.00 0.00 0.00 4.81
30 31 2.118294 GCAATATGGCCCCCTCCC 59.882 66.667 0.00 0.00 0.00 4.30
31 32 0.398381 TTTGCAATATGGCCCCCTCC 60.398 55.000 0.00 0.00 0.00 4.30
32 33 1.043022 CTTTGCAATATGGCCCCCTC 58.957 55.000 0.00 0.00 0.00 4.30
33 34 0.339510 ACTTTGCAATATGGCCCCCT 59.660 50.000 0.00 0.00 0.00 4.79
34 35 1.203237 AACTTTGCAATATGGCCCCC 58.797 50.000 0.00 0.00 0.00 5.40
35 36 2.501316 AGAAACTTTGCAATATGGCCCC 59.499 45.455 0.00 0.00 0.00 5.80
36 37 3.734902 CGAGAAACTTTGCAATATGGCCC 60.735 47.826 0.00 0.00 0.00 5.80
37 38 3.438360 CGAGAAACTTTGCAATATGGCC 58.562 45.455 0.00 0.00 0.00 5.36
38 39 2.854185 GCGAGAAACTTTGCAATATGGC 59.146 45.455 0.00 0.00 0.00 4.40
39 40 3.129287 AGGCGAGAAACTTTGCAATATGG 59.871 43.478 0.00 0.00 0.00 2.74
40 41 4.100529 CAGGCGAGAAACTTTGCAATATG 58.899 43.478 0.00 0.00 0.00 1.78
41 42 3.129287 CCAGGCGAGAAACTTTGCAATAT 59.871 43.478 0.00 0.00 0.00 1.28
42 43 2.487762 CCAGGCGAGAAACTTTGCAATA 59.512 45.455 0.00 0.00 0.00 1.90
43 44 1.270550 CCAGGCGAGAAACTTTGCAAT 59.729 47.619 0.00 0.00 0.00 3.56
44 45 0.667993 CCAGGCGAGAAACTTTGCAA 59.332 50.000 0.00 0.00 0.00 4.08
45 46 1.795170 GCCAGGCGAGAAACTTTGCA 61.795 55.000 0.00 0.00 0.00 4.08
46 47 1.081175 GCCAGGCGAGAAACTTTGC 60.081 57.895 0.00 0.00 0.00 3.68
47 48 0.239347 CAGCCAGGCGAGAAACTTTG 59.761 55.000 5.55 0.00 0.00 2.77
48 49 0.179018 ACAGCCAGGCGAGAAACTTT 60.179 50.000 5.55 0.00 0.00 2.66
49 50 0.179018 AACAGCCAGGCGAGAAACTT 60.179 50.000 5.55 0.00 0.00 2.66
50 51 0.886490 CAACAGCCAGGCGAGAAACT 60.886 55.000 5.55 0.00 0.00 2.66
51 52 1.166531 ACAACAGCCAGGCGAGAAAC 61.167 55.000 5.55 0.00 0.00 2.78
52 53 1.148273 ACAACAGCCAGGCGAGAAA 59.852 52.632 5.55 0.00 0.00 2.52
53 54 1.597854 CACAACAGCCAGGCGAGAA 60.598 57.895 5.55 0.00 0.00 2.87
54 55 2.031012 CACAACAGCCAGGCGAGA 59.969 61.111 5.55 0.00 0.00 4.04
55 56 3.730761 GCACAACAGCCAGGCGAG 61.731 66.667 5.55 5.50 0.00 5.03
63 64 2.320587 CGACAGAGGGCACAACAGC 61.321 63.158 0.00 0.00 0.00 4.40
64 65 0.946221 GTCGACAGAGGGCACAACAG 60.946 60.000 11.55 0.00 0.00 3.16
65 66 1.069090 GTCGACAGAGGGCACAACA 59.931 57.895 11.55 0.00 0.00 3.33
66 67 2.022129 CGTCGACAGAGGGCACAAC 61.022 63.158 17.16 0.00 0.00 3.32
67 68 2.338620 CGTCGACAGAGGGCACAA 59.661 61.111 17.16 0.00 0.00 3.33
68 69 2.910479 ACGTCGACAGAGGGCACA 60.910 61.111 17.16 0.00 36.64 4.57
69 70 2.430921 CACGTCGACAGAGGGCAC 60.431 66.667 17.16 0.00 36.64 5.01
70 71 3.680786 CCACGTCGACAGAGGGCA 61.681 66.667 17.16 0.00 36.64 5.36
72 73 3.006756 ATGCCACGTCGACAGAGGG 62.007 63.158 17.16 11.47 36.64 4.30
73 74 1.807165 CATGCCACGTCGACAGAGG 60.807 63.158 17.16 16.16 38.17 3.69
74 75 1.807165 CCATGCCACGTCGACAGAG 60.807 63.158 17.16 7.07 0.00 3.35
75 76 2.261361 CCATGCCACGTCGACAGA 59.739 61.111 17.16 0.00 0.00 3.41
76 77 2.815211 CCCATGCCACGTCGACAG 60.815 66.667 17.16 10.90 0.00 3.51
77 78 3.583276 GACCCATGCCACGTCGACA 62.583 63.158 17.16 0.00 0.00 4.35
78 79 2.813908 GACCCATGCCACGTCGAC 60.814 66.667 5.18 5.18 0.00 4.20
79 80 2.873525 TTGACCCATGCCACGTCGA 61.874 57.895 0.00 0.00 0.00 4.20
80 81 2.358125 TTGACCCATGCCACGTCG 60.358 61.111 0.00 0.00 0.00 5.12
81 82 2.677003 CGTTGACCCATGCCACGTC 61.677 63.158 0.00 0.00 0.00 4.34
82 83 2.668212 CGTTGACCCATGCCACGT 60.668 61.111 0.00 0.00 0.00 4.49
83 84 4.101790 GCGTTGACCCATGCCACG 62.102 66.667 0.00 0.00 0.00 4.94
84 85 2.983030 TGCGTTGACCCATGCCAC 60.983 61.111 0.00 0.00 0.00 5.01
85 86 2.983030 GTGCGTTGACCCATGCCA 60.983 61.111 0.00 0.00 0.00 4.92
86 87 3.747976 GGTGCGTTGACCCATGCC 61.748 66.667 0.00 0.00 0.00 4.40
87 88 2.983030 TGGTGCGTTGACCCATGC 60.983 61.111 0.00 0.00 34.79 4.06
88 89 2.953821 GTGGTGCGTTGACCCATG 59.046 61.111 0.00 0.00 34.79 3.66
89 90 2.668212 CGTGGTGCGTTGACCCAT 60.668 61.111 0.00 0.00 34.79 4.00
133 134 2.107552 TGGTTCATCCGAGGTCCTTTTT 59.892 45.455 0.00 0.00 39.52 1.94
134 135 1.702957 TGGTTCATCCGAGGTCCTTTT 59.297 47.619 0.00 0.00 39.52 2.27
135 136 1.358152 TGGTTCATCCGAGGTCCTTT 58.642 50.000 0.00 0.00 39.52 3.11
136 137 1.584724 ATGGTTCATCCGAGGTCCTT 58.415 50.000 0.00 0.00 39.52 3.36
137 138 1.584724 AATGGTTCATCCGAGGTCCT 58.415 50.000 0.00 0.00 39.52 3.85
138 139 2.420058 AAATGGTTCATCCGAGGTCC 57.580 50.000 0.00 0.00 39.52 4.46
139 140 4.138487 AGTAAATGGTTCATCCGAGGTC 57.862 45.455 0.00 0.00 39.52 3.85
140 141 5.687166 TTAGTAAATGGTTCATCCGAGGT 57.313 39.130 0.00 0.00 39.52 3.85
141 142 6.346096 TCTTTAGTAAATGGTTCATCCGAGG 58.654 40.000 0.00 0.00 39.52 4.63
142 143 7.843490 TTCTTTAGTAAATGGTTCATCCGAG 57.157 36.000 0.00 0.00 39.52 4.63
143 144 8.801882 AATTCTTTAGTAAATGGTTCATCCGA 57.198 30.769 0.00 0.00 39.52 4.55
148 149 9.457436 GGTCCTAATTCTTTAGTAAATGGTTCA 57.543 33.333 0.00 0.00 34.20 3.18
149 150 9.682465 AGGTCCTAATTCTTTAGTAAATGGTTC 57.318 33.333 0.00 0.00 34.20 3.62
176 177 9.489084 GTCCTATTTCTTTAAAAATGCACCTTT 57.511 29.630 0.00 0.00 31.50 3.11
177 178 8.870116 AGTCCTATTTCTTTAAAAATGCACCTT 58.130 29.630 0.00 0.00 31.50 3.50
178 179 8.422577 AGTCCTATTTCTTTAAAAATGCACCT 57.577 30.769 0.00 0.00 31.50 4.00
189 190 9.706691 CTGTGTCACTTTAGTCCTATTTCTTTA 57.293 33.333 4.27 0.00 0.00 1.85
190 191 7.173390 GCTGTGTCACTTTAGTCCTATTTCTTT 59.827 37.037 4.27 0.00 0.00 2.52
191 192 6.651225 GCTGTGTCACTTTAGTCCTATTTCTT 59.349 38.462 4.27 0.00 0.00 2.52
192 193 6.166982 GCTGTGTCACTTTAGTCCTATTTCT 58.833 40.000 4.27 0.00 0.00 2.52
193 194 5.062308 CGCTGTGTCACTTTAGTCCTATTTC 59.938 44.000 4.27 0.00 0.00 2.17
194 195 4.929808 CGCTGTGTCACTTTAGTCCTATTT 59.070 41.667 4.27 0.00 0.00 1.40
195 196 4.219944 TCGCTGTGTCACTTTAGTCCTATT 59.780 41.667 4.27 0.00 0.00 1.73
196 197 3.762288 TCGCTGTGTCACTTTAGTCCTAT 59.238 43.478 4.27 0.00 0.00 2.57
197 198 3.057736 GTCGCTGTGTCACTTTAGTCCTA 60.058 47.826 4.27 0.00 0.00 2.94
198 199 1.961394 TCGCTGTGTCACTTTAGTCCT 59.039 47.619 4.27 0.00 0.00 3.85
199 200 2.059541 GTCGCTGTGTCACTTTAGTCC 58.940 52.381 4.27 0.00 0.00 3.85
200 201 2.739292 TGTCGCTGTGTCACTTTAGTC 58.261 47.619 4.27 0.00 0.00 2.59
201 202 2.882927 TGTCGCTGTGTCACTTTAGT 57.117 45.000 4.27 0.00 0.00 2.24
202 203 3.555956 AGTTTGTCGCTGTGTCACTTTAG 59.444 43.478 4.27 0.00 0.00 1.85
203 204 3.527533 AGTTTGTCGCTGTGTCACTTTA 58.472 40.909 4.27 0.00 0.00 1.85
204 205 2.356135 AGTTTGTCGCTGTGTCACTTT 58.644 42.857 4.27 0.00 0.00 2.66
205 206 2.024176 AGTTTGTCGCTGTGTCACTT 57.976 45.000 4.27 0.00 0.00 3.16
206 207 2.024176 AAGTTTGTCGCTGTGTCACT 57.976 45.000 4.27 0.00 0.00 3.41
207 208 2.825086 AAAGTTTGTCGCTGTGTCAC 57.175 45.000 0.00 0.00 0.00 3.67
208 209 3.311322 CCTAAAAGTTTGTCGCTGTGTCA 59.689 43.478 0.00 0.00 0.00 3.58
209 210 3.558418 TCCTAAAAGTTTGTCGCTGTGTC 59.442 43.478 0.00 0.00 0.00 3.67
210 211 3.311596 GTCCTAAAAGTTTGTCGCTGTGT 59.688 43.478 0.00 0.00 0.00 3.72
211 212 3.303791 GGTCCTAAAAGTTTGTCGCTGTG 60.304 47.826 0.00 0.00 0.00 3.66
212 213 2.876550 GGTCCTAAAAGTTTGTCGCTGT 59.123 45.455 0.00 0.00 0.00 4.40
213 214 3.139077 AGGTCCTAAAAGTTTGTCGCTG 58.861 45.455 0.00 0.00 0.00 5.18
214 215 3.400255 GAGGTCCTAAAAGTTTGTCGCT 58.600 45.455 0.00 0.00 0.00 4.93
215 216 2.483106 GGAGGTCCTAAAAGTTTGTCGC 59.517 50.000 0.00 0.00 0.00 5.19
216 217 2.735134 CGGAGGTCCTAAAAGTTTGTCG 59.265 50.000 0.00 0.00 0.00 4.35
258 259 5.223225 GAGGAAAGGTATTTCTTCGCAAG 57.777 43.478 1.20 0.00 43.67 4.01
376 377 2.418746 GGAACACCTGATGCTACACGAT 60.419 50.000 0.00 0.00 0.00 3.73
395 396 2.583298 TAAGGCGGCAGCTCTAGGGA 62.583 60.000 13.08 0.00 44.37 4.20
587 588 1.537990 GGTGCGCATCCAAAACTTGTT 60.538 47.619 15.91 0.00 0.00 2.83
688 689 4.040445 ACGCACAAATTTTAACTGCTGT 57.960 36.364 0.00 0.00 0.00 4.40
804 807 6.327154 CAAAATTAACTTGGATAACCCCGAC 58.673 40.000 0.00 0.00 34.81 4.79
1023 1027 7.150640 TGAGATTTTCTATGAGACCATCATCG 58.849 38.462 0.00 0.00 46.01 3.84
1038 1042 7.814264 TTTTGAGCTTTCTCTGAGATTTTCT 57.186 32.000 8.42 3.87 40.03 2.52
1094 1098 5.997746 AGACCTGAAATCGACAAATCAAGAA 59.002 36.000 0.00 0.00 0.00 2.52
1095 1099 5.409520 CAGACCTGAAATCGACAAATCAAGA 59.590 40.000 0.00 0.00 0.00 3.02
1144 1148 5.649831 AGTGCTCCAATAGATCTGGAAAAAC 59.350 40.000 5.18 3.61 42.43 2.43
1500 1504 3.206150 GACCAAACTTGCTGAAGTCAGA 58.794 45.455 12.54 0.00 46.59 3.27
1554 1558 1.619654 CACCAACCTTCAAGCCATCA 58.380 50.000 0.00 0.00 0.00 3.07
1599 1603 6.018832 GGTGCAGTTAACTTACGTAAACAAGA 60.019 38.462 5.07 0.00 0.00 3.02
1976 1980 8.525316 AGTGAAATGTCATTTTTATGCATCAGA 58.475 29.630 12.04 0.00 35.80 3.27
2101 2105 4.351874 AAGATGTTCTTTCCTCAACCGA 57.648 40.909 0.00 0.00 31.57 4.69
2436 2440 7.443302 AGAATCAAGTTGATATCAAGGGAGA 57.557 36.000 18.47 13.66 35.76 3.71
2589 2593 5.012148 ACTGAGCAAATACTACACAACCTCT 59.988 40.000 0.00 0.00 0.00 3.69
2630 2634 2.112426 ATCCTGGGATGATCCGAAGGG 61.112 57.143 23.85 12.15 39.95 3.95
2657 2672 0.615331 CCACTGCAAGGCCTCTAAGA 59.385 55.000 5.23 0.00 39.30 2.10
2760 2775 4.679662 CGGTACAACCATACTACCTTCAG 58.320 47.826 0.00 0.00 38.47 3.02
2826 2841 4.631740 TCGGAGGTGGAGGTGGCA 62.632 66.667 0.00 0.00 0.00 4.92
2842 2857 0.250467 TGGCTGAAGGCTGTGTCTTC 60.250 55.000 5.41 5.11 43.66 2.87
2880 2895 1.290203 GCTACAGCGCATCTGCTTAA 58.710 50.000 11.47 0.00 44.46 1.85
2932 2947 2.980568 ACGAAGGTGACAAACTGACAA 58.019 42.857 0.00 0.00 0.00 3.18
3014 3029 6.525629 GCTGCTATTAGACAGGGAGATTAAA 58.474 40.000 13.45 0.00 34.38 1.52
3034 3049 1.725973 GTTTTCTCGTTGGCGCTGC 60.726 57.895 7.64 0.00 38.14 5.25
3043 3058 0.685097 TAGCAGCAGGGTTTTCTCGT 59.315 50.000 0.00 0.00 0.00 4.18
3201 3216 7.934120 GGAGATAAGTTATTTGTCTGCCTGTAT 59.066 37.037 0.00 0.00 38.74 2.29
3284 3299 8.540492 GCATCAGATGAATAGAATTGCAAAAAG 58.460 33.333 15.12 0.00 0.00 2.27
3330 3345 4.481930 TGCAACTCAAGTAAAATGGACG 57.518 40.909 0.00 0.00 0.00 4.79
4156 4189 6.389830 ACATCAACAAGAGCAACATTGTAA 57.610 33.333 0.00 0.00 38.66 2.41
4210 4243 4.218635 GGGTCCCACTTTTCTTCAAGAATC 59.781 45.833 1.78 0.00 33.67 2.52
4223 4256 4.175962 TCAAGAATTCTAGGGTCCCACTT 58.824 43.478 11.55 1.33 0.00 3.16
4386 4419 5.023533 ACTAAGAATATCGCCAAGAGCAA 57.976 39.130 0.00 0.00 44.04 3.91
4539 4586 0.826062 CATGCCAACAAATCTCCCCC 59.174 55.000 0.00 0.00 0.00 5.40
4890 4973 8.381636 TGTTTCCATCATTTGGTAATTTTCCAT 58.618 29.630 0.00 0.00 46.52 3.41
5178 5270 4.232221 GACAGCAGATGAACACCAAAATG 58.768 43.478 0.00 0.00 0.00 2.32
5354 5446 7.828712 TCACCCACCCTTTAAAATTTTATACG 58.171 34.615 11.33 3.71 0.00 3.06
5404 5496 2.172082 AGGTAGAAGGGGCGTAAAATCC 59.828 50.000 0.00 0.00 0.00 3.01
5435 5527 2.241176 ACACAAGAGGGAAAAGTGGACA 59.759 45.455 0.00 0.00 34.65 4.02
5532 5624 2.517875 AGATGGCGCTGGAATGGC 60.518 61.111 7.64 0.00 0.00 4.40
5533 5625 1.895707 GGAGATGGCGCTGGAATGG 60.896 63.158 7.64 0.00 0.00 3.16
5534 5626 2.249535 CGGAGATGGCGCTGGAATG 61.250 63.158 7.64 0.00 0.00 2.67
5535 5627 2.109799 CGGAGATGGCGCTGGAAT 59.890 61.111 7.64 0.00 0.00 3.01
5536 5628 2.463589 AAACGGAGATGGCGCTGGAA 62.464 55.000 7.64 0.00 0.00 3.53
5537 5629 2.852495 GAAACGGAGATGGCGCTGGA 62.852 60.000 7.64 0.00 0.00 3.86
5538 5630 2.436646 AAACGGAGATGGCGCTGG 60.437 61.111 7.64 0.00 0.00 4.85
5539 5631 1.298157 TTGAAACGGAGATGGCGCTG 61.298 55.000 7.64 0.00 0.00 5.18
5540 5632 0.605319 TTTGAAACGGAGATGGCGCT 60.605 50.000 7.64 0.00 0.00 5.92
5580 5672 4.845580 CACTGCTAGGCTGGCCCG 62.846 72.222 20.71 13.44 39.21 6.13
5596 5790 2.888051 CACGCACACACCGTGTCA 60.888 61.111 0.00 0.00 43.92 3.58
5614 5808 2.280524 CTTTCGCCCGGACACACA 60.281 61.111 0.73 0.00 0.00 3.72
5626 5820 2.170985 CGAACACCGCTGCTTTCG 59.829 61.111 0.00 3.36 35.36 3.46
5696 5890 1.008995 CTGCAACGACGGTTTTGGG 60.009 57.895 0.00 0.00 32.98 4.12
5697 5891 0.099791 AACTGCAACGACGGTTTTGG 59.900 50.000 0.00 0.00 35.60 3.28
5698 5892 1.581602 CAAACTGCAACGACGGTTTTG 59.418 47.619 0.00 0.00 44.75 2.44
5699 5893 1.200484 ACAAACTGCAACGACGGTTTT 59.800 42.857 0.00 0.00 44.75 2.43
5713 5907 1.890510 GTCGGTTGCGGGACAAACT 60.891 57.895 0.00 0.00 44.32 2.66
5743 5937 0.676736 GGGCATCGGTTCTAGGAGAG 59.323 60.000 0.00 0.00 0.00 3.20
5788 5982 2.177016 ACAGGCCCCTTTTATATGTCCC 59.823 50.000 0.00 0.00 0.00 4.46
5833 6028 8.981647 GCTCATAACATGTTTTGAATTGAAAGT 58.018 29.630 25.37 0.00 31.89 2.66
5836 6031 7.114670 CGTGCTCATAACATGTTTTGAATTGAA 59.885 33.333 25.37 11.54 31.89 2.69
5837 6032 6.581919 CGTGCTCATAACATGTTTTGAATTGA 59.418 34.615 25.37 14.50 31.89 2.57
5838 6033 6.363088 ACGTGCTCATAACATGTTTTGAATTG 59.637 34.615 25.37 17.68 33.51 2.32
5839 6034 6.446318 ACGTGCTCATAACATGTTTTGAATT 58.554 32.000 25.37 10.60 33.51 2.17
5850 6045 3.991773 GGTTGTTCTACGTGCTCATAACA 59.008 43.478 0.00 0.00 0.00 2.41
5856 6051 0.790814 GCTGGTTGTTCTACGTGCTC 59.209 55.000 0.00 0.00 0.00 4.26
5858 6053 0.942410 TCGCTGGTTGTTCTACGTGC 60.942 55.000 0.00 0.00 0.00 5.34
5859 6054 1.455786 CTTCGCTGGTTGTTCTACGTG 59.544 52.381 0.00 0.00 0.00 4.49
5860 6055 1.338973 TCTTCGCTGGTTGTTCTACGT 59.661 47.619 0.00 0.00 0.00 3.57
5861 6056 1.986378 CTCTTCGCTGGTTGTTCTACG 59.014 52.381 0.00 0.00 0.00 3.51
5862 6057 1.727335 GCTCTTCGCTGGTTGTTCTAC 59.273 52.381 0.00 0.00 35.14 2.59
5863 6058 1.668919 CGCTCTTCGCTGGTTGTTCTA 60.669 52.381 0.00 0.00 36.13 2.10
5864 6059 0.946221 CGCTCTTCGCTGGTTGTTCT 60.946 55.000 0.00 0.00 36.13 3.01
5865 6060 0.944311 TCGCTCTTCGCTGGTTGTTC 60.944 55.000 0.00 0.00 38.27 3.18
5866 6061 0.531974 TTCGCTCTTCGCTGGTTGTT 60.532 50.000 0.00 0.00 38.27 2.83
5896 6091 0.988063 GAGTGCTCTTTCCCTCCCTT 59.012 55.000 0.00 0.00 0.00 3.95
5899 6094 1.448717 GCGAGTGCTCTTTCCCTCC 60.449 63.158 0.00 0.00 38.39 4.30
5901 6096 2.665603 GGCGAGTGCTCTTTCCCT 59.334 61.111 0.00 0.00 42.25 4.20
5902 6097 2.815647 CGGCGAGTGCTCTTTCCC 60.816 66.667 0.00 0.00 42.25 3.97
5904 6099 3.491652 GGCGGCGAGTGCTCTTTC 61.492 66.667 12.98 0.00 42.25 2.62
5940 6139 3.648067 AGGCATAATTCCTCTTCCATCGA 59.352 43.478 0.00 0.00 0.00 3.59
5941 6140 4.013267 AGGCATAATTCCTCTTCCATCG 57.987 45.455 0.00 0.00 0.00 3.84
5974 6173 4.504858 CCTCAGTATGGAGTTTGTGGTAC 58.495 47.826 0.00 0.00 36.16 3.34
6011 6210 7.720957 TCTCCATTCATCTTTTTCAGAGTTTGA 59.279 33.333 0.00 0.00 33.87 2.69


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

AutoCloner maintained by Alex Coulton.