Multiple sequence alignment - TraesCS3B01G375600

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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 TraesCS3B01G375600 chr3B 100.000 3949 0 0 1 3949 590502183 590498235 0.000000e+00 7293
1 TraesCS3B01G375600 chr3D 92.524 3371 155 53 625 3949 449344804 449341485 0.000000e+00 4739
2 TraesCS3B01G375600 chr3A 93.439 1570 69 13 409 1968 592492474 592490929 0.000000e+00 2298
3 TraesCS3B01G375600 chr3A 93.352 722 35 9 2372 3081 592490279 592489559 0.000000e+00 1055
4 TraesCS3B01G375600 chr3A 89.516 868 34 15 3092 3949 592489574 592488754 0.000000e+00 1046
5 TraesCS3B01G375600 chr3A 88.172 279 31 1 146 424 592492768 592492492 8.180000e-87 331
6 TraesCS3B01G375600 chr3A 80.696 316 19 11 2070 2375 592490828 592490545 1.440000e-49 207
7 TraesCS3B01G375600 chr3A 90.291 103 6 3 1996 2095 592490934 592490833 8.900000e-27 132
8 TraesCS3B01G375600 chr7A 89.333 150 13 2 2 151 252261535 252261681 6.740000e-43 185
9 TraesCS3B01G375600 chr7A 88.356 146 17 0 1 146 478879615 478879760 4.060000e-40 176
10 TraesCS3B01G375600 chr4D 89.583 144 12 2 8 151 226517263 226517403 3.140000e-41 180
11 TraesCS3B01G375600 chr4D 88.079 151 15 1 1 151 352983388 352983535 4.060000e-40 176
12 TraesCS3B01G375600 chr4D 88.889 144 13 2 8 151 31920046 31919906 1.460000e-39 174
13 TraesCS3B01G375600 chr4D 88.889 144 13 2 8 151 226434652 226434792 1.460000e-39 174
14 TraesCS3B01G375600 chr4D 87.417 151 16 3 1 151 386102207 386102060 1.890000e-38 171
15 TraesCS3B01G375600 chr2A 88.435 147 17 0 1 147 313957225 313957371 1.130000e-40 178
16 TraesCS3B01G375600 chr1B 87.333 150 16 2 2 151 405318394 405318540 6.790000e-38 169


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 TraesCS3B01G375600 chr3B 590498235 590502183 3948 True 7293.000000 7293 100.000000 1 3949 1 chr3B.!!$R1 3948
1 TraesCS3B01G375600 chr3D 449341485 449344804 3319 True 4739.000000 4739 92.524000 625 3949 1 chr3D.!!$R1 3324
2 TraesCS3B01G375600 chr3A 592488754 592492768 4014 True 844.833333 2298 89.244333 146 3949 6 chr3A.!!$R1 3803

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
242 243 0.174162 GTGGGATGCAATGCAGAACC 59.826 55.0 14.98 15.38 43.65 3.62 F
1972 2078 0.036732 AAGCATCGGCAAAGTGGAGA 59.963 50.0 0.00 0.00 44.61 3.71 F
1974 2080 0.391661 GCATCGGCAAAGTGGAGAGA 60.392 55.0 0.00 0.00 40.72 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 2290 0.033781 TAACGACCCAACCCTGTTCG 59.966 55.000 0.00 0.0 34.11 3.95 R
2825 3243 1.063764 GACGTATCGAGCGAAAGACCT 59.936 52.381 17.16 0.0 0.00 3.85 R
3528 3983 1.808945 CTCCATTGTGTGCTTGGTCTC 59.191 52.381 0.00 0.0 0.00 3.36 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
24 25 6.927294 TCTGAAGTTCTCTTTTTCCTTGTC 57.073 37.500 4.17 0.00 33.64 3.18
25 26 5.823045 TCTGAAGTTCTCTTTTTCCTTGTCC 59.177 40.000 4.17 0.00 33.64 4.02
26 27 5.755849 TGAAGTTCTCTTTTTCCTTGTCCT 58.244 37.500 4.17 0.00 33.64 3.85
27 28 5.590259 TGAAGTTCTCTTTTTCCTTGTCCTG 59.410 40.000 4.17 0.00 33.64 3.86
28 29 4.464947 AGTTCTCTTTTTCCTTGTCCTGG 58.535 43.478 0.00 0.00 0.00 4.45
29 30 4.079730 AGTTCTCTTTTTCCTTGTCCTGGT 60.080 41.667 0.00 0.00 0.00 4.00
30 31 4.519906 TCTCTTTTTCCTTGTCCTGGTT 57.480 40.909 0.00 0.00 0.00 3.67
31 32 4.207165 TCTCTTTTTCCTTGTCCTGGTTG 58.793 43.478 0.00 0.00 0.00 3.77
32 33 2.693074 TCTTTTTCCTTGTCCTGGTTGC 59.307 45.455 0.00 0.00 0.00 4.17
33 34 2.452600 TTTTCCTTGTCCTGGTTGCT 57.547 45.000 0.00 0.00 0.00 3.91
34 35 3.586470 TTTTCCTTGTCCTGGTTGCTA 57.414 42.857 0.00 0.00 0.00 3.49
35 36 2.561478 TTCCTTGTCCTGGTTGCTAC 57.439 50.000 0.00 0.00 0.00 3.58
36 37 1.729586 TCCTTGTCCTGGTTGCTACT 58.270 50.000 0.00 0.00 0.00 2.57
37 38 2.054799 TCCTTGTCCTGGTTGCTACTT 58.945 47.619 0.00 0.00 0.00 2.24
38 39 2.441750 TCCTTGTCCTGGTTGCTACTTT 59.558 45.455 0.00 0.00 0.00 2.66
39 40 2.554032 CCTTGTCCTGGTTGCTACTTTG 59.446 50.000 0.00 0.00 0.00 2.77
40 41 2.270352 TGTCCTGGTTGCTACTTTGG 57.730 50.000 0.00 0.00 0.00 3.28
41 42 1.202879 TGTCCTGGTTGCTACTTTGGG 60.203 52.381 0.00 0.00 0.00 4.12
42 43 0.251165 TCCTGGTTGCTACTTTGGGC 60.251 55.000 0.00 0.00 0.00 5.36
43 44 0.539438 CCTGGTTGCTACTTTGGGCA 60.539 55.000 0.00 0.00 36.62 5.36
44 45 1.327303 CTGGTTGCTACTTTGGGCAA 58.673 50.000 0.00 0.00 44.64 4.52
45 46 1.270550 CTGGTTGCTACTTTGGGCAAG 59.729 52.381 0.48 0.00 46.87 4.01
46 47 1.328279 GGTTGCTACTTTGGGCAAGT 58.672 50.000 0.48 0.00 46.87 3.16
47 48 1.686587 GGTTGCTACTTTGGGCAAGTT 59.313 47.619 0.48 0.00 43.89 2.66
48 49 2.545742 GGTTGCTACTTTGGGCAAGTTG 60.546 50.000 0.00 0.00 43.89 3.16
51 52 2.712057 CTACTTTGGGCAAGTTGCTG 57.288 50.000 26.16 13.81 43.89 4.41
52 53 1.270550 CTACTTTGGGCAAGTTGCTGG 59.729 52.381 26.16 14.06 43.89 4.85
53 54 1.368579 CTTTGGGCAAGTTGCTGGG 59.631 57.895 26.16 9.52 44.28 4.45
54 55 1.075674 TTTGGGCAAGTTGCTGGGA 60.076 52.632 26.16 8.82 44.28 4.37
55 56 1.114722 TTTGGGCAAGTTGCTGGGAG 61.115 55.000 26.16 0.00 44.28 4.30
56 57 2.116125 GGGCAAGTTGCTGGGAGT 59.884 61.111 26.16 0.00 44.28 3.85
57 58 2.270986 GGGCAAGTTGCTGGGAGTG 61.271 63.158 26.16 0.00 44.28 3.51
58 59 2.647297 GCAAGTTGCTGGGAGTGC 59.353 61.111 20.71 0.00 40.96 4.40
59 60 1.900498 GCAAGTTGCTGGGAGTGCT 60.900 57.895 20.71 0.00 40.96 4.40
60 61 1.458639 GCAAGTTGCTGGGAGTGCTT 61.459 55.000 20.71 0.00 40.96 3.91
61 62 0.595095 CAAGTTGCTGGGAGTGCTTC 59.405 55.000 0.00 0.00 0.00 3.86
62 63 0.475906 AAGTTGCTGGGAGTGCTTCT 59.524 50.000 0.00 0.00 0.00 2.85
63 64 0.250640 AGTTGCTGGGAGTGCTTCTG 60.251 55.000 0.00 0.00 0.00 3.02
64 65 1.601759 TTGCTGGGAGTGCTTCTGC 60.602 57.895 0.00 0.00 40.20 4.26
65 66 2.060567 TTGCTGGGAGTGCTTCTGCT 62.061 55.000 0.00 0.00 40.48 4.24
66 67 1.744741 GCTGGGAGTGCTTCTGCTC 60.745 63.158 0.00 0.00 40.48 4.26
69 70 2.270527 GGAGTGCTTCTGCTCCCC 59.729 66.667 0.00 0.00 44.06 4.81
70 71 2.297129 GGAGTGCTTCTGCTCCCCT 61.297 63.158 0.00 0.00 44.06 4.79
71 72 1.220477 GAGTGCTTCTGCTCCCCTC 59.780 63.158 0.00 0.00 40.48 4.30
72 73 1.537397 AGTGCTTCTGCTCCCCTCA 60.537 57.895 0.00 0.00 40.48 3.86
73 74 0.913451 AGTGCTTCTGCTCCCCTCAT 60.913 55.000 0.00 0.00 40.48 2.90
74 75 0.463474 GTGCTTCTGCTCCCCTCATC 60.463 60.000 0.00 0.00 40.48 2.92
75 76 0.911045 TGCTTCTGCTCCCCTCATCA 60.911 55.000 0.00 0.00 40.48 3.07
76 77 0.463474 GCTTCTGCTCCCCTCATCAC 60.463 60.000 0.00 0.00 36.03 3.06
77 78 0.907486 CTTCTGCTCCCCTCATCACA 59.093 55.000 0.00 0.00 0.00 3.58
78 79 1.280133 CTTCTGCTCCCCTCATCACAA 59.720 52.381 0.00 0.00 0.00 3.33
79 80 0.615331 TCTGCTCCCCTCATCACAAC 59.385 55.000 0.00 0.00 0.00 3.32
80 81 0.617413 CTGCTCCCCTCATCACAACT 59.383 55.000 0.00 0.00 0.00 3.16
81 82 0.325933 TGCTCCCCTCATCACAACTG 59.674 55.000 0.00 0.00 0.00 3.16
82 83 1.028868 GCTCCCCTCATCACAACTGC 61.029 60.000 0.00 0.00 0.00 4.40
83 84 0.617413 CTCCCCTCATCACAACTGCT 59.383 55.000 0.00 0.00 0.00 4.24
84 85 1.833630 CTCCCCTCATCACAACTGCTA 59.166 52.381 0.00 0.00 0.00 3.49
85 86 2.437281 CTCCCCTCATCACAACTGCTAT 59.563 50.000 0.00 0.00 0.00 2.97
86 87 2.846206 TCCCCTCATCACAACTGCTATT 59.154 45.455 0.00 0.00 0.00 1.73
87 88 3.118261 TCCCCTCATCACAACTGCTATTC 60.118 47.826 0.00 0.00 0.00 1.75
88 89 2.868583 CCCTCATCACAACTGCTATTCG 59.131 50.000 0.00 0.00 0.00 3.34
89 90 3.430790 CCCTCATCACAACTGCTATTCGA 60.431 47.826 0.00 0.00 0.00 3.71
90 91 3.801050 CCTCATCACAACTGCTATTCGAG 59.199 47.826 0.00 0.00 0.00 4.04
91 92 3.785486 TCATCACAACTGCTATTCGAGG 58.215 45.455 0.00 0.00 0.00 4.63
92 93 2.672961 TCACAACTGCTATTCGAGGG 57.327 50.000 0.00 0.00 0.00 4.30
93 94 2.176045 TCACAACTGCTATTCGAGGGA 58.824 47.619 0.00 0.00 0.00 4.20
94 95 2.094182 TCACAACTGCTATTCGAGGGAC 60.094 50.000 0.00 0.00 0.00 4.46
96 97 3.130516 CACAACTGCTATTCGAGGGACTA 59.869 47.826 0.00 0.00 41.55 2.59
97 98 3.381908 ACAACTGCTATTCGAGGGACTAG 59.618 47.826 0.00 0.00 41.55 2.57
98 99 3.300239 ACTGCTATTCGAGGGACTAGT 57.700 47.619 0.00 0.00 41.55 2.57
99 100 2.952978 ACTGCTATTCGAGGGACTAGTG 59.047 50.000 0.00 0.00 41.55 2.74
100 101 1.681793 TGCTATTCGAGGGACTAGTGC 59.318 52.381 5.70 5.70 41.55 4.40
101 102 1.000052 GCTATTCGAGGGACTAGTGCC 60.000 57.143 24.99 24.99 41.55 5.01
102 103 1.614413 CTATTCGAGGGACTAGTGCCC 59.386 57.143 28.08 22.37 41.55 5.36
119 120 5.803020 GTGCCCTCACTAAGATTTACTTG 57.197 43.478 0.00 0.00 40.03 3.16
120 121 4.095036 GTGCCCTCACTAAGATTTACTTGC 59.905 45.833 0.00 0.00 40.03 4.01
121 122 4.019321 TGCCCTCACTAAGATTTACTTGCT 60.019 41.667 0.00 0.00 39.38 3.91
122 123 4.572795 GCCCTCACTAAGATTTACTTGCTC 59.427 45.833 0.00 0.00 39.38 4.26
123 124 5.627968 GCCCTCACTAAGATTTACTTGCTCT 60.628 44.000 0.00 0.00 39.38 4.09
124 125 6.410540 CCCTCACTAAGATTTACTTGCTCTT 58.589 40.000 0.00 0.00 39.38 2.85
125 126 6.536941 CCCTCACTAAGATTTACTTGCTCTTC 59.463 42.308 0.00 0.00 39.38 2.87
126 127 7.099764 CCTCACTAAGATTTACTTGCTCTTCA 58.900 38.462 0.00 0.00 39.38 3.02
127 128 7.277539 CCTCACTAAGATTTACTTGCTCTTCAG 59.722 40.741 0.00 0.00 39.38 3.02
128 129 7.896811 TCACTAAGATTTACTTGCTCTTCAGA 58.103 34.615 0.00 0.00 39.38 3.27
129 130 7.815068 TCACTAAGATTTACTTGCTCTTCAGAC 59.185 37.037 0.00 0.00 39.38 3.51
130 131 7.064016 CACTAAGATTTACTTGCTCTTCAGACC 59.936 40.741 0.00 0.00 39.38 3.85
131 132 5.753721 AGATTTACTTGCTCTTCAGACCT 57.246 39.130 0.00 0.00 0.00 3.85
132 133 5.486526 AGATTTACTTGCTCTTCAGACCTG 58.513 41.667 0.00 0.00 0.00 4.00
133 134 4.689612 TTTACTTGCTCTTCAGACCTGT 57.310 40.909 0.00 0.00 0.00 4.00
134 135 4.689612 TTACTTGCTCTTCAGACCTGTT 57.310 40.909 0.00 0.00 0.00 3.16
135 136 3.118905 ACTTGCTCTTCAGACCTGTTC 57.881 47.619 0.00 0.00 0.00 3.18
136 137 2.703007 ACTTGCTCTTCAGACCTGTTCT 59.297 45.455 0.00 0.00 33.33 3.01
161 162 2.893215 TCACTTCCCCGTCTTCTCTA 57.107 50.000 0.00 0.00 0.00 2.43
162 163 3.383698 TCACTTCCCCGTCTTCTCTAT 57.616 47.619 0.00 0.00 0.00 1.98
165 166 4.079901 TCACTTCCCCGTCTTCTCTATAGT 60.080 45.833 0.00 0.00 0.00 2.12
167 168 4.645588 ACTTCCCCGTCTTCTCTATAGTTG 59.354 45.833 0.00 0.00 0.00 3.16
172 173 4.496010 CCCGTCTTCTCTATAGTTGTGTCG 60.496 50.000 0.00 0.82 0.00 4.35
183 184 1.918293 TTGTGTCGGGGCATCTCCT 60.918 57.895 0.00 0.00 34.39 3.69
208 209 2.210102 ACTACCCCCTGCCCACTT 59.790 61.111 0.00 0.00 0.00 3.16
219 220 1.973812 GCCCACTTGTCTTCCCTGC 60.974 63.158 0.00 0.00 0.00 4.85
222 223 1.239968 CCACTTGTCTTCCCTGCAGC 61.240 60.000 8.66 0.00 0.00 5.25
238 239 2.103538 GCGTGGGATGCAATGCAG 59.896 61.111 14.98 0.00 43.65 4.41
242 243 0.174162 GTGGGATGCAATGCAGAACC 59.826 55.000 14.98 15.38 43.65 3.62
274 275 2.173669 CGCCACATGGGTTAGCTCG 61.174 63.158 0.00 0.00 39.65 5.03
275 276 1.078426 GCCACATGGGTTAGCTCGT 60.078 57.895 0.00 0.00 39.65 4.18
277 278 0.744414 CCACATGGGTTAGCTCGTGG 60.744 60.000 3.52 0.00 36.43 4.94
278 279 0.249120 CACATGGGTTAGCTCGTGGA 59.751 55.000 3.52 0.00 36.43 4.02
289 290 4.686695 TCGTGGAGAGAGGGATGG 57.313 61.111 0.00 0.00 0.00 3.51
295 296 0.825840 GGAGAGAGGGATGGAGGTCG 60.826 65.000 0.00 0.00 0.00 4.79
306 307 3.771160 GAGGTCGCCCATGGTCGT 61.771 66.667 15.77 0.00 0.00 4.34
310 311 3.144871 TCGCCCATGGTCGTCGAT 61.145 61.111 15.77 0.00 0.00 3.59
315 316 0.459899 CCCATGGTCGTCGATGAAGA 59.540 55.000 9.35 0.00 32.72 2.87
324 325 6.160684 TGGTCGTCGATGAAGAAAAGAATAA 58.839 36.000 9.35 0.00 0.00 1.40
362 363 4.081972 TGAAGAGGATATAGAATGAGCGGC 60.082 45.833 0.00 0.00 0.00 6.53
369 370 2.572095 TAGAATGAGCGGCGTGTGGG 62.572 60.000 9.37 0.00 0.00 4.61
385 386 1.611977 GTGGGTCCTACCAAAACTTGC 59.388 52.381 0.00 0.00 43.34 4.01
389 390 2.303175 GTCCTACCAAAACTTGCCACA 58.697 47.619 0.00 0.00 0.00 4.17
392 393 2.627699 CCTACCAAAACTTGCCACATGT 59.372 45.455 0.00 0.00 0.00 3.21
393 394 2.600470 ACCAAAACTTGCCACATGTG 57.400 45.000 19.31 19.31 0.00 3.21
404 405 2.467962 CACATGTGGAGCTCAGCTG 58.532 57.895 18.51 7.63 39.88 4.24
435 469 2.014335 TGTCACTTGATCTGATGGCG 57.986 50.000 0.00 0.00 0.00 5.69
554 591 8.790718 TGTGTATAATCTTACGGAGGAGTTATC 58.209 37.037 0.00 0.00 0.00 1.75
581 618 4.336433 TGACCAAAAGCTCTCTTTGTTGAG 59.664 41.667 8.22 0.00 41.40 3.02
1335 1379 4.908877 GCGCGCCGTCCTAGAGAC 62.909 72.222 23.24 0.00 42.54 3.36
1391 1438 6.304624 TGCTAGTACTACTACATACCTGCAT 58.695 40.000 0.00 0.00 30.32 3.96
1412 1466 9.322773 CTGCATTAGAGTAGAAGAAAATGATCA 57.677 33.333 0.00 0.00 0.00 2.92
1485 1539 7.681939 TTGTTTCTTCAACAGAGTAACAGTT 57.318 32.000 0.00 0.00 46.37 3.16
1497 1551 2.233186 AGTAACAGTTACTTCCTCGCCC 59.767 50.000 18.79 0.00 43.70 6.13
1515 1569 1.099879 CCTACTCGGACGGGTACCAG 61.100 65.000 15.35 13.03 43.08 4.00
1576 1630 4.401925 CTTCCCAAGGTCAGTTCATTTCT 58.598 43.478 0.00 0.00 0.00 2.52
1577 1631 5.560724 CTTCCCAAGGTCAGTTCATTTCTA 58.439 41.667 0.00 0.00 0.00 2.10
1578 1632 4.906618 TCCCAAGGTCAGTTCATTTCTAC 58.093 43.478 0.00 0.00 0.00 2.59
1579 1633 3.684788 CCCAAGGTCAGTTCATTTCTACG 59.315 47.826 0.00 0.00 0.00 3.51
1618 1672 5.918608 TCCTGTTGCTTATCTTATCCAGAC 58.081 41.667 0.00 0.00 32.83 3.51
1649 1703 3.084070 TCGACGGATGATGAGTGATTG 57.916 47.619 0.00 0.00 0.00 2.67
1677 1733 4.142600 GCCATGTCGCTCTAACAAGAAAAT 60.143 41.667 0.00 0.00 0.00 1.82
1722 1778 2.279582 AGGTTTAGATCGTGACGCTG 57.720 50.000 0.00 0.00 0.00 5.18
1749 1805 0.457337 GCGCGTACGGGATAATAGGG 60.457 60.000 33.24 4.03 40.57 3.53
1752 1808 2.030007 CGCGTACGGGATAATAGGGAAA 60.030 50.000 26.40 0.00 34.97 3.13
1753 1809 3.552684 CGCGTACGGGATAATAGGGAAAA 60.553 47.826 26.40 0.00 34.97 2.29
1754 1810 3.742882 GCGTACGGGATAATAGGGAAAAC 59.257 47.826 18.39 0.00 0.00 2.43
1776 1832 4.154195 ACACGTGCAAGATTAGGTTCATTC 59.846 41.667 17.22 0.00 0.00 2.67
1777 1833 4.154015 CACGTGCAAGATTAGGTTCATTCA 59.846 41.667 6.65 0.00 0.00 2.57
1778 1834 4.393062 ACGTGCAAGATTAGGTTCATTCAG 59.607 41.667 6.65 0.00 0.00 3.02
1779 1835 4.631377 CGTGCAAGATTAGGTTCATTCAGA 59.369 41.667 0.00 0.00 0.00 3.27
1780 1836 5.295292 CGTGCAAGATTAGGTTCATTCAGAT 59.705 40.000 0.00 0.00 0.00 2.90
1781 1837 6.183360 CGTGCAAGATTAGGTTCATTCAGATT 60.183 38.462 0.00 0.00 0.00 2.40
1782 1838 7.542025 GTGCAAGATTAGGTTCATTCAGATTT 58.458 34.615 0.00 0.00 0.00 2.17
1783 1839 8.031277 GTGCAAGATTAGGTTCATTCAGATTTT 58.969 33.333 0.00 0.00 0.00 1.82
1784 1840 8.246180 TGCAAGATTAGGTTCATTCAGATTTTC 58.754 33.333 0.00 0.00 0.00 2.29
1785 1841 7.430502 GCAAGATTAGGTTCATTCAGATTTTCG 59.569 37.037 0.00 0.00 0.00 3.46
1786 1842 7.559590 AGATTAGGTTCATTCAGATTTTCGG 57.440 36.000 0.00 0.00 0.00 4.30
1787 1843 7.338710 AGATTAGGTTCATTCAGATTTTCGGA 58.661 34.615 0.00 0.00 0.00 4.55
1788 1844 7.995488 AGATTAGGTTCATTCAGATTTTCGGAT 59.005 33.333 0.00 0.00 0.00 4.18
1789 1845 5.824904 AGGTTCATTCAGATTTTCGGATG 57.175 39.130 0.00 0.00 0.00 3.51
1790 1846 4.641989 AGGTTCATTCAGATTTTCGGATGG 59.358 41.667 0.00 0.00 0.00 3.51
1924 1996 1.466851 ATGAGCAGCCGATCGGATCA 61.467 55.000 37.64 29.67 37.50 2.92
1965 2071 1.066303 ACGTTTGAAAGCATCGGCAAA 59.934 42.857 0.00 0.00 44.61 3.68
1966 2072 1.715519 CGTTTGAAAGCATCGGCAAAG 59.284 47.619 0.00 0.00 44.61 2.77
1967 2073 2.742774 GTTTGAAAGCATCGGCAAAGT 58.257 42.857 0.00 0.00 44.61 2.66
1968 2074 2.420628 TTGAAAGCATCGGCAAAGTG 57.579 45.000 0.00 0.00 44.61 3.16
1969 2075 0.597568 TGAAAGCATCGGCAAAGTGG 59.402 50.000 0.00 0.00 44.61 4.00
1970 2076 0.881118 GAAAGCATCGGCAAAGTGGA 59.119 50.000 0.00 0.00 44.61 4.02
1971 2077 0.883833 AAAGCATCGGCAAAGTGGAG 59.116 50.000 0.00 0.00 44.61 3.86
1972 2078 0.036732 AAGCATCGGCAAAGTGGAGA 59.963 50.000 0.00 0.00 44.61 3.71
1973 2079 0.392193 AGCATCGGCAAAGTGGAGAG 60.392 55.000 0.00 0.00 44.61 3.20
1974 2080 0.391661 GCATCGGCAAAGTGGAGAGA 60.392 55.000 0.00 0.00 40.72 3.10
1975 2081 1.745141 GCATCGGCAAAGTGGAGAGAT 60.745 52.381 0.00 0.00 40.72 2.75
1976 2082 1.938577 CATCGGCAAAGTGGAGAGATG 59.061 52.381 0.00 0.00 0.00 2.90
1977 2083 0.976641 TCGGCAAAGTGGAGAGATGT 59.023 50.000 0.00 0.00 0.00 3.06
1978 2084 1.081892 CGGCAAAGTGGAGAGATGTG 58.918 55.000 0.00 0.00 0.00 3.21
1979 2085 1.609061 CGGCAAAGTGGAGAGATGTGT 60.609 52.381 0.00 0.00 0.00 3.72
1980 2086 2.079925 GGCAAAGTGGAGAGATGTGTC 58.920 52.381 0.00 0.00 0.00 3.67
1981 2087 2.079925 GCAAAGTGGAGAGATGTGTCC 58.920 52.381 0.00 0.00 36.61 4.02
1982 2088 2.550855 GCAAAGTGGAGAGATGTGTCCA 60.551 50.000 4.38 4.38 43.86 4.02
1986 2092 1.177401 TGGAGAGATGTGTCCACTCG 58.823 55.000 4.38 0.00 41.22 4.18
1987 2093 1.271926 TGGAGAGATGTGTCCACTCGA 60.272 52.381 4.38 0.00 41.22 4.04
1988 2094 1.819288 GGAGAGATGTGTCCACTCGAA 59.181 52.381 0.46 0.00 36.08 3.71
1989 2095 2.428890 GGAGAGATGTGTCCACTCGAAT 59.571 50.000 0.46 0.00 36.08 3.34
1990 2096 3.443037 GAGAGATGTGTCCACTCGAATG 58.557 50.000 0.00 0.00 36.03 2.67
1991 2097 2.167281 AGAGATGTGTCCACTCGAATGG 59.833 50.000 6.56 6.56 41.57 3.16
1992 2098 2.166459 GAGATGTGTCCACTCGAATGGA 59.834 50.000 12.44 12.44 46.92 3.41
2044 2151 7.291566 TGACCCATGTTCTCTTTTAGGTAAAA 58.708 34.615 0.00 0.00 34.35 1.52
2063 2170 5.845391 AAAAGGAATGTTTTCTCGACCAA 57.155 34.783 0.00 0.00 32.16 3.67
2077 2215 4.215399 TCTCGACCAACCACAATTTTCATC 59.785 41.667 0.00 0.00 0.00 2.92
2101 2239 2.676839 TGAAAGTTACGTTTTGTGGCGA 59.323 40.909 0.00 0.00 0.00 5.54
2132 2271 1.993370 GATCCTCGTGTGTGTTACTGC 59.007 52.381 0.00 0.00 0.00 4.40
2135 2274 1.205657 CTCGTGTGTGTTACTGCGTT 58.794 50.000 0.00 0.00 32.90 4.84
2137 2276 0.924777 CGTGTGTGTTACTGCGTTCA 59.075 50.000 0.00 0.00 0.00 3.18
2138 2277 1.331680 CGTGTGTGTTACTGCGTTCAC 60.332 52.381 0.00 0.00 0.00 3.18
2139 2278 1.004292 GTGTGTGTTACTGCGTTCACC 60.004 52.381 0.00 0.00 0.00 4.02
2140 2279 1.292061 GTGTGTTACTGCGTTCACCA 58.708 50.000 0.00 0.00 0.00 4.17
2142 2281 2.096417 GTGTGTTACTGCGTTCACCATC 60.096 50.000 0.00 0.00 0.00 3.51
2143 2282 2.139917 GTGTTACTGCGTTCACCATCA 58.860 47.619 0.00 0.00 0.00 3.07
2144 2283 2.742053 GTGTTACTGCGTTCACCATCAT 59.258 45.455 0.00 0.00 0.00 2.45
2146 2285 4.032900 GTGTTACTGCGTTCACCATCATAG 59.967 45.833 0.00 0.00 0.00 2.23
2147 2286 4.181578 GTTACTGCGTTCACCATCATAGT 58.818 43.478 0.00 0.00 0.00 2.12
2149 2288 2.233676 ACTGCGTTCACCATCATAGTGA 59.766 45.455 0.00 0.00 42.36 3.41
2156 2295 4.529109 TCACCATCATAGTGAACGAACA 57.471 40.909 0.00 0.00 41.17 3.18
2157 2296 4.494484 TCACCATCATAGTGAACGAACAG 58.506 43.478 0.00 0.00 41.17 3.16
2158 2297 3.618594 CACCATCATAGTGAACGAACAGG 59.381 47.826 0.00 0.00 37.42 4.00
2159 2298 3.198068 CCATCATAGTGAACGAACAGGG 58.802 50.000 0.00 0.00 0.00 4.45
2171 2310 1.540797 CGAACAGGGTTGGGTCGTTAA 60.541 52.381 0.00 0.00 33.70 2.01
2172 2311 1.875514 GAACAGGGTTGGGTCGTTAAC 59.124 52.381 0.00 0.00 0.00 2.01
2188 2327 5.927030 TCGTTAACGATTTGACGTAGTAGT 58.073 37.500 26.00 0.00 42.93 2.73
2189 2328 7.056002 TCGTTAACGATTTGACGTAGTAGTA 57.944 36.000 26.00 0.00 42.93 1.82
2190 2329 7.173419 TCGTTAACGATTTGACGTAGTAGTAG 58.827 38.462 26.00 0.00 42.93 2.57
2246 2385 2.271800 GCATCTCCTTACGTCACCAAG 58.728 52.381 0.00 0.00 0.00 3.61
2251 2390 1.626654 CCTTACGTCACCAAGCGCTG 61.627 60.000 12.58 0.57 0.00 5.18
2327 2476 7.229707 GTGCTAAGATGAGACAGAATACTCCTA 59.770 40.741 0.00 0.00 32.84 2.94
2332 2481 8.041143 AGATGAGACAGAATACTCCTACTACT 57.959 38.462 0.00 0.00 32.84 2.57
2333 2482 9.161572 AGATGAGACAGAATACTCCTACTACTA 57.838 37.037 0.00 0.00 32.84 1.82
2334 2483 9.781633 GATGAGACAGAATACTCCTACTACTAA 57.218 37.037 0.00 0.00 32.84 2.24
2754 3172 2.592993 GGCCACCACCAGAGCTACA 61.593 63.158 0.00 0.00 0.00 2.74
3012 3444 2.176055 GAGAGTCGCGAACGCAGA 59.824 61.111 12.06 13.29 42.06 4.26
3321 3766 5.722290 TCCCCTTATTTTCCTCTTTGGTTT 58.278 37.500 0.00 0.00 37.07 3.27
3357 3802 5.716703 AGGTGTTCTCATTTTATCAAAGGGG 59.283 40.000 0.00 0.00 0.00 4.79
3362 3807 5.579047 TCTCATTTTATCAAAGGGGCTTCA 58.421 37.500 0.00 0.00 0.00 3.02
3426 3875 9.687210 TTTTTCATCTTCATCTTCAATCTGTTG 57.313 29.630 0.00 0.00 36.65 3.33
3428 3877 7.991084 TCATCTTCATCTTCAATCTGTTGTT 57.009 32.000 0.00 0.00 36.69 2.83
3466 3915 9.751542 TGATTTTCTCTCTCGGTATTTTCTATC 57.248 33.333 0.00 0.00 0.00 2.08
3467 3916 9.751542 GATTTTCTCTCTCGGTATTTTCTATCA 57.248 33.333 0.00 0.00 0.00 2.15
3624 4080 5.488341 AGCAACGAAAAGTGTAGTGGATAT 58.512 37.500 0.00 0.00 0.00 1.63
3625 4081 5.351465 AGCAACGAAAAGTGTAGTGGATATG 59.649 40.000 0.00 0.00 0.00 1.78
3862 4320 7.771361 TGAAACAAAGACAATAGTGAAGTGGTA 59.229 33.333 0.00 0.00 0.00 3.25
3873 4331 9.988815 CAATAGTGAAGTGGTATTAGAATAGCT 57.011 33.333 11.58 0.00 39.47 3.32
3886 4344 9.182933 GTATTAGAATAGCTCGTTTAGTCCAAG 57.817 37.037 0.00 0.00 0.00 3.61
3935 4393 5.008316 AGTCACATTTTCGGAAAGTTGGTAC 59.992 40.000 15.48 12.94 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.318900 GGACAAGGAAAAAGAGAACTTCAGAA 59.681 38.462 0.00 0.00 35.05 3.02
2 3 5.825151 AGGACAAGGAAAAAGAGAACTTCAG 59.175 40.000 0.00 0.00 35.05 3.02
3 4 5.590259 CAGGACAAGGAAAAAGAGAACTTCA 59.410 40.000 0.00 0.00 35.05 3.02
4 5 5.009110 CCAGGACAAGGAAAAAGAGAACTTC 59.991 44.000 0.00 0.00 35.05 3.01
5 6 4.889995 CCAGGACAAGGAAAAAGAGAACTT 59.110 41.667 0.00 0.00 38.05 2.66
6 7 4.079730 ACCAGGACAAGGAAAAAGAGAACT 60.080 41.667 0.00 0.00 0.00 3.01
7 8 4.207955 ACCAGGACAAGGAAAAAGAGAAC 58.792 43.478 0.00 0.00 0.00 3.01
8 9 4.519906 ACCAGGACAAGGAAAAAGAGAA 57.480 40.909 0.00 0.00 0.00 2.87
9 10 4.207165 CAACCAGGACAAGGAAAAAGAGA 58.793 43.478 0.00 0.00 0.00 3.10
10 11 3.243535 GCAACCAGGACAAGGAAAAAGAG 60.244 47.826 0.00 0.00 0.00 2.85
11 12 2.693074 GCAACCAGGACAAGGAAAAAGA 59.307 45.455 0.00 0.00 0.00 2.52
12 13 2.695147 AGCAACCAGGACAAGGAAAAAG 59.305 45.455 0.00 0.00 0.00 2.27
13 14 2.745968 AGCAACCAGGACAAGGAAAAA 58.254 42.857 0.00 0.00 0.00 1.94
14 15 2.452600 AGCAACCAGGACAAGGAAAA 57.547 45.000 0.00 0.00 0.00 2.29
15 16 2.441750 AGTAGCAACCAGGACAAGGAAA 59.558 45.455 0.00 0.00 0.00 3.13
16 17 2.054799 AGTAGCAACCAGGACAAGGAA 58.945 47.619 0.00 0.00 0.00 3.36
17 18 1.729586 AGTAGCAACCAGGACAAGGA 58.270 50.000 0.00 0.00 0.00 3.36
18 19 2.554032 CAAAGTAGCAACCAGGACAAGG 59.446 50.000 0.00 0.00 0.00 3.61
19 20 2.554032 CCAAAGTAGCAACCAGGACAAG 59.446 50.000 0.00 0.00 0.00 3.16
20 21 2.582052 CCAAAGTAGCAACCAGGACAA 58.418 47.619 0.00 0.00 0.00 3.18
21 22 1.202879 CCCAAAGTAGCAACCAGGACA 60.203 52.381 0.00 0.00 0.00 4.02
22 23 1.534729 CCCAAAGTAGCAACCAGGAC 58.465 55.000 0.00 0.00 0.00 3.85
23 24 0.251165 GCCCAAAGTAGCAACCAGGA 60.251 55.000 0.00 0.00 0.00 3.86
24 25 0.539438 TGCCCAAAGTAGCAACCAGG 60.539 55.000 0.00 0.00 35.69 4.45
25 26 1.270550 CTTGCCCAAAGTAGCAACCAG 59.729 52.381 0.00 0.00 43.74 4.00
26 27 1.327303 CTTGCCCAAAGTAGCAACCA 58.673 50.000 0.00 0.00 43.74 3.67
35 36 1.114722 TCCCAGCAACTTGCCCAAAG 61.115 55.000 10.25 0.00 46.52 2.77
36 37 1.075674 TCCCAGCAACTTGCCCAAA 60.076 52.632 10.25 0.00 46.52 3.28
37 38 1.531365 CTCCCAGCAACTTGCCCAA 60.531 57.895 10.25 0.00 46.52 4.12
38 39 2.115910 CTCCCAGCAACTTGCCCA 59.884 61.111 10.25 0.00 46.52 5.36
39 40 2.116125 ACTCCCAGCAACTTGCCC 59.884 61.111 10.25 0.00 46.52 5.36
40 41 2.924105 GCACTCCCAGCAACTTGCC 61.924 63.158 10.25 0.00 46.52 4.52
41 42 1.458639 AAGCACTCCCAGCAACTTGC 61.459 55.000 5.55 5.55 45.46 4.01
42 43 0.595095 GAAGCACTCCCAGCAACTTG 59.405 55.000 0.00 0.00 0.00 3.16
43 44 0.475906 AGAAGCACTCCCAGCAACTT 59.524 50.000 0.00 0.00 0.00 2.66
44 45 0.250640 CAGAAGCACTCCCAGCAACT 60.251 55.000 0.00 0.00 0.00 3.16
45 46 1.860484 GCAGAAGCACTCCCAGCAAC 61.860 60.000 0.00 0.00 41.58 4.17
46 47 1.601759 GCAGAAGCACTCCCAGCAA 60.602 57.895 0.00 0.00 41.58 3.91
47 48 2.033141 GCAGAAGCACTCCCAGCA 59.967 61.111 0.00 0.00 41.58 4.41
48 49 1.744741 GAGCAGAAGCACTCCCAGC 60.745 63.158 0.00 0.00 45.49 4.85
49 50 1.078567 GGAGCAGAAGCACTCCCAG 60.079 63.158 0.00 0.00 45.71 4.45
50 51 3.072476 GGAGCAGAAGCACTCCCA 58.928 61.111 0.00 0.00 45.71 4.37
53 54 1.220477 GAGGGGAGCAGAAGCACTC 59.780 63.158 0.00 0.00 45.49 3.51
54 55 0.913451 ATGAGGGGAGCAGAAGCACT 60.913 55.000 0.00 0.00 45.49 4.40
55 56 0.463474 GATGAGGGGAGCAGAAGCAC 60.463 60.000 0.00 0.00 45.49 4.40
56 57 0.911045 TGATGAGGGGAGCAGAAGCA 60.911 55.000 0.00 0.00 45.49 3.91
57 58 0.463474 GTGATGAGGGGAGCAGAAGC 60.463 60.000 0.00 0.00 42.56 3.86
58 59 0.907486 TGTGATGAGGGGAGCAGAAG 59.093 55.000 0.00 0.00 0.00 2.85
59 60 1.003580 GTTGTGATGAGGGGAGCAGAA 59.996 52.381 0.00 0.00 0.00 3.02
60 61 0.615331 GTTGTGATGAGGGGAGCAGA 59.385 55.000 0.00 0.00 0.00 4.26
61 62 0.617413 AGTTGTGATGAGGGGAGCAG 59.383 55.000 0.00 0.00 0.00 4.24
62 63 0.325933 CAGTTGTGATGAGGGGAGCA 59.674 55.000 0.00 0.00 0.00 4.26
63 64 1.028868 GCAGTTGTGATGAGGGGAGC 61.029 60.000 0.00 0.00 0.00 4.70
64 65 0.617413 AGCAGTTGTGATGAGGGGAG 59.383 55.000 0.00 0.00 0.00 4.30
65 66 1.951209 TAGCAGTTGTGATGAGGGGA 58.049 50.000 0.00 0.00 0.00 4.81
66 67 3.209410 GAATAGCAGTTGTGATGAGGGG 58.791 50.000 0.00 0.00 0.00 4.79
67 68 2.868583 CGAATAGCAGTTGTGATGAGGG 59.131 50.000 0.00 0.00 0.00 4.30
68 69 3.785486 TCGAATAGCAGTTGTGATGAGG 58.215 45.455 0.00 0.00 0.00 3.86
69 70 3.801050 CCTCGAATAGCAGTTGTGATGAG 59.199 47.826 0.00 0.00 0.00 2.90
70 71 3.430790 CCCTCGAATAGCAGTTGTGATGA 60.431 47.826 0.00 0.00 0.00 2.92
71 72 2.868583 CCCTCGAATAGCAGTTGTGATG 59.131 50.000 0.00 0.00 0.00 3.07
72 73 2.766263 TCCCTCGAATAGCAGTTGTGAT 59.234 45.455 0.00 0.00 0.00 3.06
73 74 2.094182 GTCCCTCGAATAGCAGTTGTGA 60.094 50.000 0.00 0.00 0.00 3.58
74 75 2.093973 AGTCCCTCGAATAGCAGTTGTG 60.094 50.000 0.00 0.00 0.00 3.33
75 76 2.180276 AGTCCCTCGAATAGCAGTTGT 58.820 47.619 0.00 0.00 0.00 3.32
76 77 2.969628 AGTCCCTCGAATAGCAGTTG 57.030 50.000 0.00 0.00 0.00 3.16
77 78 3.381908 CACTAGTCCCTCGAATAGCAGTT 59.618 47.826 0.00 0.00 39.74 3.16
78 79 2.952978 CACTAGTCCCTCGAATAGCAGT 59.047 50.000 0.00 0.00 39.74 4.40
79 80 2.287909 GCACTAGTCCCTCGAATAGCAG 60.288 54.545 0.00 0.00 39.74 4.24
80 81 1.681793 GCACTAGTCCCTCGAATAGCA 59.318 52.381 0.00 0.00 39.74 3.49
81 82 1.000052 GGCACTAGTCCCTCGAATAGC 60.000 57.143 0.00 0.00 39.74 2.97
82 83 1.614413 GGGCACTAGTCCCTCGAATAG 59.386 57.143 18.19 0.00 41.45 1.73
83 84 1.700955 GGGCACTAGTCCCTCGAATA 58.299 55.000 18.19 0.00 40.66 1.75
84 85 2.517609 GGGCACTAGTCCCTCGAAT 58.482 57.895 18.19 0.00 40.66 3.34
85 86 4.029472 GGGCACTAGTCCCTCGAA 57.971 61.111 18.19 0.00 40.66 3.71
97 98 4.095036 GCAAGTAAATCTTAGTGAGGGCAC 59.905 45.833 0.00 0.00 38.61 5.01
98 99 4.019321 AGCAAGTAAATCTTAGTGAGGGCA 60.019 41.667 0.00 0.00 34.66 5.36
99 100 4.518249 AGCAAGTAAATCTTAGTGAGGGC 58.482 43.478 0.00 0.00 34.66 5.19
100 101 5.983540 AGAGCAAGTAAATCTTAGTGAGGG 58.016 41.667 0.00 0.00 34.66 4.30
101 102 7.099764 TGAAGAGCAAGTAAATCTTAGTGAGG 58.900 38.462 0.00 0.00 33.53 3.86
102 103 8.031864 TCTGAAGAGCAAGTAAATCTTAGTGAG 58.968 37.037 0.00 0.00 33.53 3.51
103 104 7.815068 GTCTGAAGAGCAAGTAAATCTTAGTGA 59.185 37.037 0.00 0.00 33.53 3.41
104 105 7.064016 GGTCTGAAGAGCAAGTAAATCTTAGTG 59.936 40.741 4.67 0.00 41.81 2.74
105 106 7.038658 AGGTCTGAAGAGCAAGTAAATCTTAGT 60.039 37.037 11.77 0.00 44.42 2.24
106 107 7.277539 CAGGTCTGAAGAGCAAGTAAATCTTAG 59.722 40.741 11.77 0.00 44.42 2.18
107 108 7.099764 CAGGTCTGAAGAGCAAGTAAATCTTA 58.900 38.462 11.77 0.00 44.42 2.10
108 109 5.936956 CAGGTCTGAAGAGCAAGTAAATCTT 59.063 40.000 11.77 0.00 44.42 2.40
109 110 5.012561 ACAGGTCTGAAGAGCAAGTAAATCT 59.987 40.000 11.77 0.00 44.42 2.40
110 111 5.241662 ACAGGTCTGAAGAGCAAGTAAATC 58.758 41.667 11.77 0.00 44.42 2.17
111 112 5.234466 ACAGGTCTGAAGAGCAAGTAAAT 57.766 39.130 11.77 0.00 44.42 1.40
112 113 4.689612 ACAGGTCTGAAGAGCAAGTAAA 57.310 40.909 11.77 0.00 44.42 2.01
113 114 4.345257 AGAACAGGTCTGAAGAGCAAGTAA 59.655 41.667 11.77 0.00 44.42 2.24
114 115 3.898123 AGAACAGGTCTGAAGAGCAAGTA 59.102 43.478 11.77 0.00 44.42 2.24
115 116 2.703007 AGAACAGGTCTGAAGAGCAAGT 59.297 45.455 11.77 6.98 44.42 3.16
116 117 3.399440 AGAACAGGTCTGAAGAGCAAG 57.601 47.619 11.77 6.41 44.42 4.01
126 127 2.826488 AGTGATAGCCAGAACAGGTCT 58.174 47.619 0.00 0.00 36.88 3.85
127 128 3.526534 GAAGTGATAGCCAGAACAGGTC 58.473 50.000 0.00 0.00 0.00 3.85
128 129 2.237392 GGAAGTGATAGCCAGAACAGGT 59.763 50.000 0.00 0.00 0.00 4.00
129 130 2.420687 GGGAAGTGATAGCCAGAACAGG 60.421 54.545 0.00 0.00 0.00 4.00
130 131 2.420687 GGGGAAGTGATAGCCAGAACAG 60.421 54.545 0.00 0.00 0.00 3.16
131 132 1.559682 GGGGAAGTGATAGCCAGAACA 59.440 52.381 0.00 0.00 0.00 3.18
132 133 1.473434 CGGGGAAGTGATAGCCAGAAC 60.473 57.143 0.00 0.00 0.00 3.01
133 134 0.830648 CGGGGAAGTGATAGCCAGAA 59.169 55.000 0.00 0.00 0.00 3.02
134 135 0.325296 ACGGGGAAGTGATAGCCAGA 60.325 55.000 0.00 0.00 0.00 3.86
135 136 0.105039 GACGGGGAAGTGATAGCCAG 59.895 60.000 0.00 0.00 0.00 4.85
136 137 0.325296 AGACGGGGAAGTGATAGCCA 60.325 55.000 0.00 0.00 0.00 4.75
137 138 0.831307 AAGACGGGGAAGTGATAGCC 59.169 55.000 0.00 0.00 0.00 3.93
138 139 1.757699 AGAAGACGGGGAAGTGATAGC 59.242 52.381 0.00 0.00 0.00 2.97
139 140 3.292460 AGAGAAGACGGGGAAGTGATAG 58.708 50.000 0.00 0.00 0.00 2.08
140 141 3.383698 AGAGAAGACGGGGAAGTGATA 57.616 47.619 0.00 0.00 0.00 2.15
141 142 2.239681 AGAGAAGACGGGGAAGTGAT 57.760 50.000 0.00 0.00 0.00 3.06
142 143 2.893215 TAGAGAAGACGGGGAAGTGA 57.107 50.000 0.00 0.00 0.00 3.41
143 144 4.208746 ACTATAGAGAAGACGGGGAAGTG 58.791 47.826 6.78 0.00 0.00 3.16
144 145 4.523168 ACTATAGAGAAGACGGGGAAGT 57.477 45.455 6.78 0.00 0.00 3.01
161 162 1.139058 GAGATGCCCCGACACAACTAT 59.861 52.381 0.00 0.00 0.00 2.12
162 163 0.535335 GAGATGCCCCGACACAACTA 59.465 55.000 0.00 0.00 0.00 2.24
165 166 0.616395 TAGGAGATGCCCCGACACAA 60.616 55.000 0.00 0.00 37.37 3.33
167 168 0.034059 CATAGGAGATGCCCCGACAC 59.966 60.000 0.00 0.00 37.37 3.67
172 173 0.694771 TGATGCATAGGAGATGCCCC 59.305 55.000 0.00 0.26 43.94 5.80
183 184 0.764890 GCAGGGGGTAGTGATGCATA 59.235 55.000 0.00 0.00 36.88 3.14
208 209 2.031012 CACGCTGCAGGGAAGACA 59.969 61.111 34.63 0.00 0.00 3.41
219 220 2.103538 GCATTGCATCCCACGCTG 59.896 61.111 3.15 0.00 0.00 5.18
222 223 0.179156 GTTCTGCATTGCATCCCACG 60.179 55.000 12.53 0.00 38.13 4.94
233 234 1.683011 GCCATGGTAGTGGTTCTGCAT 60.683 52.381 14.67 0.00 41.47 3.96
234 235 0.322456 GCCATGGTAGTGGTTCTGCA 60.322 55.000 14.67 0.00 41.47 4.41
238 239 2.112815 GCGGCCATGGTAGTGGTTC 61.113 63.158 14.67 0.00 41.47 3.62
274 275 0.031616 ACCTCCATCCCTCTCTCCAC 60.032 60.000 0.00 0.00 0.00 4.02
275 276 0.263172 GACCTCCATCCCTCTCTCCA 59.737 60.000 0.00 0.00 0.00 3.86
277 278 1.460273 GCGACCTCCATCCCTCTCTC 61.460 65.000 0.00 0.00 0.00 3.20
278 279 1.456705 GCGACCTCCATCCCTCTCT 60.457 63.158 0.00 0.00 0.00 3.10
295 296 1.153449 TTCATCGACGACCATGGGC 60.153 57.895 18.09 13.46 0.00 5.36
306 307 8.883731 GTCATTCCTTATTCTTTTCTTCATCGA 58.116 33.333 0.00 0.00 0.00 3.59
324 325 9.836179 ATATCCTCTTCATAACTAGTCATTCCT 57.164 33.333 0.00 0.00 0.00 3.36
338 339 5.395103 GCCGCTCATTCTATATCCTCTTCAT 60.395 44.000 0.00 0.00 0.00 2.57
351 352 2.434884 CCACACGCCGCTCATTCT 60.435 61.111 0.00 0.00 0.00 2.40
362 363 1.202722 AGTTTTGGTAGGACCCACACG 60.203 52.381 0.00 0.00 37.50 4.49
369 370 2.303175 TGTGGCAAGTTTTGGTAGGAC 58.697 47.619 0.00 0.00 0.00 3.85
389 390 1.298993 CCACAGCTGAGCTCCACAT 59.701 57.895 23.35 0.00 36.40 3.21
392 393 4.025858 GGCCACAGCTGAGCTCCA 62.026 66.667 23.35 0.00 36.40 3.86
402 403 1.066858 AGTGACATCTTACGGCCACAG 60.067 52.381 2.24 0.00 0.00 3.66
404 405 1.732259 CAAGTGACATCTTACGGCCAC 59.268 52.381 2.24 0.00 0.00 5.01
442 476 3.656045 AAAACGCTTGGCCGGTCG 61.656 61.111 0.00 3.22 0.00 4.79
458 492 3.130819 CATACGGCCGGCTTGCAA 61.131 61.111 31.76 11.52 0.00 4.08
463 497 1.768684 ATGATTCCATACGGCCGGCT 61.769 55.000 31.76 13.62 0.00 5.52
500 534 8.338259 CAGACGGACAGGATATTTAGAAAATTG 58.662 37.037 0.00 0.00 0.00 2.32
513 547 1.188219 ACACAGCAGACGGACAGGAT 61.188 55.000 0.00 0.00 0.00 3.24
515 549 0.532573 ATACACAGCAGACGGACAGG 59.467 55.000 0.00 0.00 0.00 4.00
581 618 2.029470 TCGAATTTCAAACACCATGCCC 60.029 45.455 0.00 0.00 0.00 5.36
610 647 3.799963 CAGGCGTATGCGTATCAGTTTTA 59.200 43.478 4.81 0.00 44.10 1.52
908 951 3.599514 CGCGCAAGAGTTAATTTGTTGAG 59.400 43.478 8.75 2.93 43.02 3.02
975 1019 2.666190 GAGTTGTGCTGCCTCGCA 60.666 61.111 0.00 0.00 37.62 5.10
1066 1110 4.406173 CTCGTGCTGCTCGTCGGT 62.406 66.667 21.39 0.00 0.00 4.69
1219 1263 2.011947 CATGATGTTGATGCAGACGGT 58.988 47.619 0.00 0.00 0.00 4.83
1412 1466 5.473504 ACATAATCGACCTGCTTTGTTTCTT 59.526 36.000 0.00 0.00 0.00 2.52
1485 1539 0.465097 CCGAGTAGGGCGAGGAAGTA 60.465 60.000 0.00 0.00 35.97 2.24
1497 1551 0.393537 ACTGGTACCCGTCCGAGTAG 60.394 60.000 10.07 0.00 0.00 2.57
1515 1569 0.539986 TCTGGCCGTATTTCCTCCAC 59.460 55.000 0.00 0.00 0.00 4.02
1576 1630 4.330894 CAGGAACGCCGAGATATATACGTA 59.669 45.833 0.00 0.00 39.96 3.57
1577 1631 3.126514 CAGGAACGCCGAGATATATACGT 59.873 47.826 0.00 0.00 39.96 3.57
1578 1632 3.126514 ACAGGAACGCCGAGATATATACG 59.873 47.826 0.00 5.23 39.96 3.06
1579 1633 4.698583 ACAGGAACGCCGAGATATATAC 57.301 45.455 0.00 0.00 39.96 1.47
1618 1672 7.382488 ACTCATCATCCGTCGATTAATTAGTTG 59.618 37.037 0.00 0.00 0.00 3.16
1631 1685 4.052159 ACTCAATCACTCATCATCCGTC 57.948 45.455 0.00 0.00 0.00 4.79
1649 1703 1.661112 GTTAGAGCGACATGGCAACTC 59.339 52.381 10.05 10.05 34.64 3.01
1677 1733 8.988546 TGGCTATAATTTTTAGGAGCATGTTA 57.011 30.769 0.00 0.00 0.00 2.41
1701 1757 2.345641 CAGCGTCACGATCTAAACCTTG 59.654 50.000 0.00 0.00 0.00 3.61
1722 1778 2.327244 CCGTACGCGCTCTCTACC 59.673 66.667 10.49 0.00 36.67 3.18
1749 1805 4.483476 ACCTAATCTTGCACGTGTTTTC 57.517 40.909 18.38 0.09 0.00 2.29
1752 1808 3.472652 TGAACCTAATCTTGCACGTGTT 58.527 40.909 18.38 5.47 0.00 3.32
1753 1809 3.120321 TGAACCTAATCTTGCACGTGT 57.880 42.857 18.38 0.00 0.00 4.49
1754 1810 4.154015 TGAATGAACCTAATCTTGCACGTG 59.846 41.667 12.28 12.28 0.00 4.49
1776 1832 0.378257 CGTGGCCATCCGAAAATCTG 59.622 55.000 9.72 0.00 34.14 2.90
1777 1833 1.376609 GCGTGGCCATCCGAAAATCT 61.377 55.000 19.07 0.00 34.14 2.40
1778 1834 1.064134 GCGTGGCCATCCGAAAATC 59.936 57.895 19.07 0.00 34.14 2.17
1779 1835 2.760159 CGCGTGGCCATCCGAAAAT 61.760 57.895 19.07 0.00 34.14 1.82
1780 1836 3.427425 CGCGTGGCCATCCGAAAA 61.427 61.111 19.07 0.00 34.14 2.29
1781 1837 3.673956 ATCGCGTGGCCATCCGAAA 62.674 57.895 27.11 12.29 33.10 3.46
1782 1838 4.155733 ATCGCGTGGCCATCCGAA 62.156 61.111 27.11 12.60 33.10 4.30
1783 1839 4.889856 CATCGCGTGGCCATCCGA 62.890 66.667 26.06 26.06 34.14 4.55
1902 1974 1.227350 CCGATCGGCTGCTCATCAA 60.227 57.895 23.37 0.00 0.00 2.57
1924 1996 4.265056 GCCGTGTGGGGAACTGGT 62.265 66.667 0.00 0.00 35.78 4.00
1967 2073 1.177401 CGAGTGGACACATCTCTCCA 58.823 55.000 5.14 0.00 33.95 3.86
1968 2074 1.464734 TCGAGTGGACACATCTCTCC 58.535 55.000 5.14 0.00 0.00 3.71
1969 2075 3.443037 CATTCGAGTGGACACATCTCTC 58.557 50.000 5.14 0.00 0.00 3.20
1970 2076 2.167281 CCATTCGAGTGGACACATCTCT 59.833 50.000 21.68 0.00 42.02 3.10
1971 2077 2.166459 TCCATTCGAGTGGACACATCTC 59.834 50.000 24.40 0.00 43.20 2.75
1972 2078 2.179427 TCCATTCGAGTGGACACATCT 58.821 47.619 24.40 0.00 43.20 2.90
1973 2079 2.672961 TCCATTCGAGTGGACACATC 57.327 50.000 24.40 0.00 43.20 3.06
1980 2086 6.978343 TTTACTTTGTATCCATTCGAGTGG 57.022 37.500 20.32 20.32 40.76 4.00
1981 2087 6.961554 GCTTTTACTTTGTATCCATTCGAGTG 59.038 38.462 0.04 0.04 0.00 3.51
1982 2088 6.093633 GGCTTTTACTTTGTATCCATTCGAGT 59.906 38.462 0.00 0.00 0.00 4.18
1983 2089 6.093495 TGGCTTTTACTTTGTATCCATTCGAG 59.907 38.462 0.00 0.00 0.00 4.04
1984 2090 5.941058 TGGCTTTTACTTTGTATCCATTCGA 59.059 36.000 0.00 0.00 0.00 3.71
1985 2091 6.128007 ACTGGCTTTTACTTTGTATCCATTCG 60.128 38.462 0.00 0.00 0.00 3.34
1986 2092 7.158099 ACTGGCTTTTACTTTGTATCCATTC 57.842 36.000 0.00 0.00 0.00 2.67
1987 2093 7.539034 AACTGGCTTTTACTTTGTATCCATT 57.461 32.000 0.00 0.00 0.00 3.16
1988 2094 7.539034 AAACTGGCTTTTACTTTGTATCCAT 57.461 32.000 0.00 0.00 0.00 3.41
1989 2095 6.969993 AAACTGGCTTTTACTTTGTATCCA 57.030 33.333 0.00 0.00 0.00 3.41
1990 2096 7.430441 TCAAAACTGGCTTTTACTTTGTATCC 58.570 34.615 0.00 0.00 30.39 2.59
1991 2097 8.915654 CATCAAAACTGGCTTTTACTTTGTATC 58.084 33.333 0.00 0.00 30.39 2.24
1992 2098 7.384932 GCATCAAAACTGGCTTTTACTTTGTAT 59.615 33.333 0.00 0.00 30.39 2.29
1993 2099 6.699642 GCATCAAAACTGGCTTTTACTTTGTA 59.300 34.615 0.00 0.00 30.39 2.41
1994 2100 5.523552 GCATCAAAACTGGCTTTTACTTTGT 59.476 36.000 0.00 0.00 30.39 2.83
1995 2101 5.754890 AGCATCAAAACTGGCTTTTACTTTG 59.245 36.000 0.00 0.00 31.34 2.77
1996 2102 5.754890 CAGCATCAAAACTGGCTTTTACTTT 59.245 36.000 0.00 0.00 33.60 2.66
1997 2103 5.068987 TCAGCATCAAAACTGGCTTTTACTT 59.931 36.000 0.00 0.00 33.60 2.24
2044 2151 3.146847 GGTTGGTCGAGAAAACATTCCT 58.853 45.455 7.01 0.00 0.00 3.36
2045 2152 2.882137 TGGTTGGTCGAGAAAACATTCC 59.118 45.455 7.01 0.00 0.00 3.01
2057 2164 3.574614 GGATGAAAATTGTGGTTGGTCG 58.425 45.455 0.00 0.00 0.00 4.79
2063 2170 4.901250 ACTTTCAGGGATGAAAATTGTGGT 59.099 37.500 5.08 0.00 37.35 4.16
2077 2215 3.794138 GCCACAAAACGTAACTTTCAGGG 60.794 47.826 0.00 0.00 0.00 4.45
2135 2274 4.494484 CTGTTCGTTCACTATGATGGTGA 58.506 43.478 7.59 7.59 41.23 4.02
2137 2276 3.369471 CCCTGTTCGTTCACTATGATGGT 60.369 47.826 0.00 0.00 0.00 3.55
2138 2277 3.198068 CCCTGTTCGTTCACTATGATGG 58.802 50.000 0.00 0.00 0.00 3.51
2139 2278 3.861840 ACCCTGTTCGTTCACTATGATG 58.138 45.455 0.00 0.00 0.00 3.07
2140 2279 4.253685 CAACCCTGTTCGTTCACTATGAT 58.746 43.478 0.00 0.00 0.00 2.45
2142 2281 2.742053 CCAACCCTGTTCGTTCACTATG 59.258 50.000 0.00 0.00 0.00 2.23
2143 2282 2.290071 CCCAACCCTGTTCGTTCACTAT 60.290 50.000 0.00 0.00 0.00 2.12
2144 2283 1.071071 CCCAACCCTGTTCGTTCACTA 59.929 52.381 0.00 0.00 0.00 2.74
2146 2285 0.464916 ACCCAACCCTGTTCGTTCAC 60.465 55.000 0.00 0.00 0.00 3.18
2147 2286 0.179040 GACCCAACCCTGTTCGTTCA 60.179 55.000 0.00 0.00 0.00 3.18
2149 2288 1.227734 CGACCCAACCCTGTTCGTT 60.228 57.895 0.00 0.00 0.00 3.85
2150 2289 1.974973 AACGACCCAACCCTGTTCGT 61.975 55.000 0.00 0.00 39.70 3.85
2151 2290 0.033781 TAACGACCCAACCCTGTTCG 59.966 55.000 0.00 0.00 34.11 3.95
2152 2291 1.875514 GTTAACGACCCAACCCTGTTC 59.124 52.381 0.00 0.00 0.00 3.18
2153 2292 1.811176 CGTTAACGACCCAACCCTGTT 60.811 52.381 23.35 0.00 43.02 3.16
2154 2293 0.249996 CGTTAACGACCCAACCCTGT 60.250 55.000 23.35 0.00 43.02 4.00
2155 2294 0.033781 TCGTTAACGACCCAACCCTG 59.966 55.000 26.00 0.00 44.22 4.45
2156 2295 2.439837 TCGTTAACGACCCAACCCT 58.560 52.632 26.00 0.00 44.22 4.34
2171 2310 9.319143 ACTAATACTACTACTACGTCAAATCGT 57.681 33.333 0.00 0.00 45.97 3.73
2246 2385 3.615614 CTTGAGAGCAATTATTCAGCGC 58.384 45.455 0.00 0.00 32.68 5.92
2327 2476 8.446394 TCCAGCAGGACTATTAGTATTAGTAGT 58.554 37.037 0.00 0.81 39.61 2.73
2825 3243 1.063764 GACGTATCGAGCGAAAGACCT 59.936 52.381 17.16 0.00 0.00 3.85
2967 3385 9.416794 GAAACTCAATCTACATATCATCGACAT 57.583 33.333 0.00 0.00 0.00 3.06
3030 3462 2.802414 GGTGTGCCGTCGTCGTAC 60.802 66.667 0.71 0.94 35.01 3.67
3321 3766 6.627087 ATGAGAACACCTCTGAGGAAAATA 57.373 37.500 29.71 9.91 42.44 1.40
3357 3802 2.877168 CTGAATGCAGTAGGGATGAAGC 59.123 50.000 0.00 0.00 37.37 3.86
3528 3983 1.808945 CTCCATTGTGTGCTTGGTCTC 59.191 52.381 0.00 0.00 0.00 3.36
3636 4092 6.824305 ATTGCATTTTTAGTGTGCTCTAGT 57.176 33.333 0.00 0.00 39.52 2.57
3637 4093 9.065871 GTTTATTGCATTTTTAGTGTGCTCTAG 57.934 33.333 0.00 0.00 39.52 2.43
3818 4276 9.703892 TTTGTTTCAATCGGATATTCAAAACAT 57.296 25.926 12.70 0.00 35.87 2.71
3862 4320 8.008513 TCTTGGACTAAACGAGCTATTCTAAT 57.991 34.615 0.00 0.00 0.00 1.73
3873 4331 4.448210 ACTTTTGCTCTTGGACTAAACGA 58.552 39.130 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.