Multiple sequence alignment - TraesCS5B01G075000

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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 TraesCS5B01G075000 chr5B 100.000 3466 0 0 1 3466 89303921 89307386 0.000000e+00 6401
1 TraesCS5B01G075000 chr5D 94.958 3114 94 24 214 3307 80435997 80439067 0.000000e+00 4822
2 TraesCS5B01G075000 chr5D 97.674 43 1 0 3424 3466 80441364 80441406 1.330000e-09 75
3 TraesCS5B01G075000 chr5A 94.540 2326 69 21 424 2714 76955247 76957549 0.000000e+00 3539
4 TraesCS5B01G075000 chr5A 94.930 572 16 8 2751 3316 76957556 76958120 0.000000e+00 883
5 TraesCS5B01G075000 chr5A 97.674 43 1 0 3424 3466 76958234 76958276 1.330000e-09 75
6 TraesCS5B01G075000 chr1A 95.830 1223 36 6 1229 2449 508205178 508203969 0.000000e+00 1962
7 TraesCS5B01G075000 chr1A 94.703 623 24 2 1554 2175 588667253 588667867 0.000000e+00 959
8 TraesCS5B01G075000 chr2A 95.188 1226 41 8 1229 2449 651807095 651805883 0.000000e+00 1921
9 TraesCS5B01G075000 chr6A 95.045 1231 38 12 1229 2449 558037092 558038309 0.000000e+00 1914
10 TraesCS5B01G075000 chr6A 87.560 209 23 2 10 218 115313780 115313575 4.470000e-59 239
11 TraesCS5B01G075000 chr4B 88.974 653 62 4 1445 2097 580890499 580889857 0.000000e+00 798
12 TraesCS5B01G075000 chr4B 83.913 230 30 5 1 225 115878413 115878640 2.710000e-51 213
13 TraesCS5B01G075000 chr7D 90.232 604 46 4 1494 2097 599758650 599758060 0.000000e+00 776
14 TraesCS5B01G075000 chr1D 90.183 601 45 5 1494 2094 479641819 479642405 0.000000e+00 771
15 TraesCS5B01G075000 chr2D 88.571 210 24 0 1 210 61329293 61329502 4.440000e-64 255
16 TraesCS5B01G075000 chr2D 83.190 232 34 5 1 230 650851502 650851730 1.260000e-49 207
17 TraesCS5B01G075000 chr3D 87.097 217 28 0 1 217 149766685 149766901 2.670000e-61 246
18 TraesCS5B01G075000 chr3D 84.545 220 28 5 1 218 395045040 395045255 2.710000e-51 213
19 TraesCS5B01G075000 chr3A 86.283 226 28 3 1 225 181108177 181107954 3.460000e-60 243
20 TraesCS5B01G075000 chr1B 85.268 224 30 2 1 222 95299962 95300184 9.680000e-56 228
21 TraesCS5B01G075000 chr7A 84.685 222 31 3 1 221 260000807 260001026 5.820000e-53 219


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 TraesCS5B01G075000 chr5B 89303921 89307386 3465 False 6401.0 6401 100.000000 1 3466 1 chr5B.!!$F1 3465
1 TraesCS5B01G075000 chr5D 80435997 80441406 5409 False 2448.5 4822 96.316000 214 3466 2 chr5D.!!$F1 3252
2 TraesCS5B01G075000 chr5A 76955247 76958276 3029 False 1499.0 3539 95.714667 424 3466 3 chr5A.!!$F1 3042
3 TraesCS5B01G075000 chr1A 508203969 508205178 1209 True 1962.0 1962 95.830000 1229 2449 1 chr1A.!!$R1 1220
4 TraesCS5B01G075000 chr1A 588667253 588667867 614 False 959.0 959 94.703000 1554 2175 1 chr1A.!!$F1 621
5 TraesCS5B01G075000 chr2A 651805883 651807095 1212 True 1921.0 1921 95.188000 1229 2449 1 chr2A.!!$R1 1220
6 TraesCS5B01G075000 chr6A 558037092 558038309 1217 False 1914.0 1914 95.045000 1229 2449 1 chr6A.!!$F1 1220
7 TraesCS5B01G075000 chr4B 580889857 580890499 642 True 798.0 798 88.974000 1445 2097 1 chr4B.!!$R1 652
8 TraesCS5B01G075000 chr7D 599758060 599758650 590 True 776.0 776 90.232000 1494 2097 1 chr7D.!!$R1 603
9 TraesCS5B01G075000 chr1D 479641819 479642405 586 False 771.0 771 90.183000 1494 2094 1 chr1D.!!$F1 600

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
74 75 0.038166 GCACCCCTTCATCAAGTGGA 59.962 55.0 0.0 0.0 31.72 4.02 F
95 96 0.456221 AGGAGTAGCGACGGATGTTG 59.544 55.0 0.0 0.0 0.00 3.33 F
957 999 0.458543 ACACATCTCTTAGCACGGCG 60.459 55.0 4.8 4.8 0.00 6.46 F
1577 1619 0.592637 ATGATGTGGTTGTGTGCGTG 59.407 50.0 0.0 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1158 1200 0.173481 GCTGCTCCACGTACTCATCA 59.827 55.0 0.00 0.0 0.0 3.07 R
1159 1201 0.457851 AGCTGCTCCACGTACTCATC 59.542 55.0 0.00 0.0 0.0 2.92 R
2114 2174 0.032813 ACCTTCTCAATGGGGCATGG 60.033 55.0 0.00 0.0 0.0 3.66 R
3073 3157 0.604578 ATCAAGGCCAACACATGCAC 59.395 50.0 5.01 0.0 0.0 4.57 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
23 24 4.914312 TTAGATGTTAGGTTTTCGTGCG 57.086 40.909 0.00 0.00 0.00 5.34
24 25 3.034721 AGATGTTAGGTTTTCGTGCGA 57.965 42.857 0.00 0.00 0.00 5.10
25 26 2.993899 AGATGTTAGGTTTTCGTGCGAG 59.006 45.455 0.00 0.00 0.00 5.03
26 27 1.504359 TGTTAGGTTTTCGTGCGAGG 58.496 50.000 0.00 0.00 0.00 4.63
27 28 1.202557 TGTTAGGTTTTCGTGCGAGGT 60.203 47.619 0.00 0.00 0.00 3.85
28 29 1.458445 GTTAGGTTTTCGTGCGAGGTC 59.542 52.381 0.00 0.00 0.00 3.85
29 30 0.963962 TAGGTTTTCGTGCGAGGTCT 59.036 50.000 0.00 0.00 0.00 3.85
30 31 0.600255 AGGTTTTCGTGCGAGGTCTG 60.600 55.000 0.00 0.00 0.00 3.51
31 32 0.878961 GGTTTTCGTGCGAGGTCTGT 60.879 55.000 0.00 0.00 0.00 3.41
32 33 0.935196 GTTTTCGTGCGAGGTCTGTT 59.065 50.000 0.00 0.00 0.00 3.16
33 34 1.329599 GTTTTCGTGCGAGGTCTGTTT 59.670 47.619 0.00 0.00 0.00 2.83
34 35 0.934496 TTTCGTGCGAGGTCTGTTTG 59.066 50.000 0.00 0.00 0.00 2.93
35 36 0.103390 TTCGTGCGAGGTCTGTTTGA 59.897 50.000 0.00 0.00 0.00 2.69
36 37 0.317160 TCGTGCGAGGTCTGTTTGAT 59.683 50.000 0.00 0.00 0.00 2.57
37 38 1.542472 TCGTGCGAGGTCTGTTTGATA 59.458 47.619 0.00 0.00 0.00 2.15
38 39 2.165641 TCGTGCGAGGTCTGTTTGATAT 59.834 45.455 0.00 0.00 0.00 1.63
39 40 2.930040 CGTGCGAGGTCTGTTTGATATT 59.070 45.455 0.00 0.00 0.00 1.28
40 41 3.370978 CGTGCGAGGTCTGTTTGATATTT 59.629 43.478 0.00 0.00 0.00 1.40
41 42 4.651994 GTGCGAGGTCTGTTTGATATTTG 58.348 43.478 0.00 0.00 0.00 2.32
42 43 3.689161 TGCGAGGTCTGTTTGATATTTGG 59.311 43.478 0.00 0.00 0.00 3.28
43 44 3.689649 GCGAGGTCTGTTTGATATTTGGT 59.310 43.478 0.00 0.00 0.00 3.67
44 45 4.156008 GCGAGGTCTGTTTGATATTTGGTT 59.844 41.667 0.00 0.00 0.00 3.67
45 46 5.673818 GCGAGGTCTGTTTGATATTTGGTTC 60.674 44.000 0.00 0.00 0.00 3.62
46 47 5.445939 CGAGGTCTGTTTGATATTTGGTTCG 60.446 44.000 0.00 0.00 0.00 3.95
47 48 4.700213 AGGTCTGTTTGATATTTGGTTCGG 59.300 41.667 0.00 0.00 0.00 4.30
48 49 4.698304 GGTCTGTTTGATATTTGGTTCGGA 59.302 41.667 0.00 0.00 0.00 4.55
49 50 5.391629 GGTCTGTTTGATATTTGGTTCGGAC 60.392 44.000 0.00 0.00 0.00 4.79
50 51 5.180492 GTCTGTTTGATATTTGGTTCGGACA 59.820 40.000 0.00 0.00 32.40 4.02
51 52 5.943416 TCTGTTTGATATTTGGTTCGGACAT 59.057 36.000 0.00 0.00 0.00 3.06
52 53 6.432783 TCTGTTTGATATTTGGTTCGGACATT 59.567 34.615 0.00 0.00 0.00 2.71
53 54 6.616947 TGTTTGATATTTGGTTCGGACATTC 58.383 36.000 0.00 0.00 0.00 2.67
54 55 5.478233 TTGATATTTGGTTCGGACATTCG 57.522 39.130 0.00 0.00 0.00 3.34
55 56 3.874543 TGATATTTGGTTCGGACATTCGG 59.125 43.478 0.00 0.00 0.00 4.30
56 57 0.808755 ATTTGGTTCGGACATTCGGC 59.191 50.000 0.00 0.00 0.00 5.54
57 58 0.535328 TTTGGTTCGGACATTCGGCA 60.535 50.000 0.00 0.00 0.00 5.69
58 59 1.231958 TTGGTTCGGACATTCGGCAC 61.232 55.000 0.00 0.00 0.00 5.01
59 60 2.396157 GGTTCGGACATTCGGCACC 61.396 63.158 0.00 0.00 0.00 5.01
60 61 2.046700 TTCGGACATTCGGCACCC 60.047 61.111 0.00 0.00 0.00 4.61
61 62 3.615509 TTCGGACATTCGGCACCCC 62.616 63.158 0.00 0.00 0.00 4.95
62 63 4.096003 CGGACATTCGGCACCCCT 62.096 66.667 0.00 0.00 0.00 4.79
63 64 2.355115 GGACATTCGGCACCCCTT 59.645 61.111 0.00 0.00 0.00 3.95
64 65 1.749258 GGACATTCGGCACCCCTTC 60.749 63.158 0.00 0.00 0.00 3.46
65 66 1.002624 GACATTCGGCACCCCTTCA 60.003 57.895 0.00 0.00 0.00 3.02
66 67 0.394352 GACATTCGGCACCCCTTCAT 60.394 55.000 0.00 0.00 0.00 2.57
67 68 0.394352 ACATTCGGCACCCCTTCATC 60.394 55.000 0.00 0.00 0.00 2.92
68 69 0.394216 CATTCGGCACCCCTTCATCA 60.394 55.000 0.00 0.00 0.00 3.07
69 70 0.331278 ATTCGGCACCCCTTCATCAA 59.669 50.000 0.00 0.00 0.00 2.57
70 71 0.322456 TTCGGCACCCCTTCATCAAG 60.322 55.000 0.00 0.00 0.00 3.02
71 72 1.002134 CGGCACCCCTTCATCAAGT 60.002 57.895 0.00 0.00 0.00 3.16
72 73 1.308069 CGGCACCCCTTCATCAAGTG 61.308 60.000 0.00 0.00 0.00 3.16
73 74 0.967380 GGCACCCCTTCATCAAGTGG 60.967 60.000 0.00 0.00 33.46 4.00
74 75 0.038166 GCACCCCTTCATCAAGTGGA 59.962 55.000 0.00 0.00 31.72 4.02
75 76 1.341383 GCACCCCTTCATCAAGTGGAT 60.341 52.381 0.00 0.00 31.72 3.41
76 77 2.092429 GCACCCCTTCATCAAGTGGATA 60.092 50.000 0.00 0.00 31.72 2.59
77 78 3.813443 CACCCCTTCATCAAGTGGATAG 58.187 50.000 0.00 0.00 31.72 2.08
78 79 2.780010 ACCCCTTCATCAAGTGGATAGG 59.220 50.000 0.00 0.00 31.72 2.57
79 80 3.048600 CCCCTTCATCAAGTGGATAGGA 58.951 50.000 0.00 0.00 33.95 2.94
80 81 3.072184 CCCCTTCATCAAGTGGATAGGAG 59.928 52.174 0.00 0.00 33.95 3.69
81 82 3.713764 CCCTTCATCAAGTGGATAGGAGT 59.286 47.826 0.00 0.00 33.95 3.85
82 83 4.901849 CCCTTCATCAAGTGGATAGGAGTA 59.098 45.833 0.00 0.00 33.95 2.59
83 84 5.011533 CCCTTCATCAAGTGGATAGGAGTAG 59.988 48.000 0.00 0.00 33.95 2.57
84 85 5.510520 CCTTCATCAAGTGGATAGGAGTAGC 60.511 48.000 0.00 0.00 33.95 3.58
85 86 3.570125 TCATCAAGTGGATAGGAGTAGCG 59.430 47.826 0.00 0.00 33.95 4.26
86 87 3.292492 TCAAGTGGATAGGAGTAGCGA 57.708 47.619 0.00 0.00 0.00 4.93
87 88 2.950309 TCAAGTGGATAGGAGTAGCGAC 59.050 50.000 0.00 0.00 0.00 5.19
88 89 1.595466 AGTGGATAGGAGTAGCGACG 58.405 55.000 0.00 0.00 29.37 5.12
89 90 0.592148 GTGGATAGGAGTAGCGACGG 59.408 60.000 0.00 0.00 0.00 4.79
90 91 0.471191 TGGATAGGAGTAGCGACGGA 59.529 55.000 0.00 0.00 0.00 4.69
91 92 1.073444 TGGATAGGAGTAGCGACGGAT 59.927 52.381 0.00 0.00 0.00 4.18
92 93 1.469308 GGATAGGAGTAGCGACGGATG 59.531 57.143 0.00 0.00 0.00 3.51
93 94 2.152830 GATAGGAGTAGCGACGGATGT 58.847 52.381 0.00 0.00 0.00 3.06
94 95 2.048444 TAGGAGTAGCGACGGATGTT 57.952 50.000 0.00 0.00 0.00 2.71
95 96 0.456221 AGGAGTAGCGACGGATGTTG 59.544 55.000 0.00 0.00 0.00 3.33
103 104 1.616620 CGACGGATGTTGCCAAAATG 58.383 50.000 0.00 0.00 0.00 2.32
104 105 1.198867 CGACGGATGTTGCCAAAATGA 59.801 47.619 0.00 0.00 0.00 2.57
105 106 2.159393 CGACGGATGTTGCCAAAATGAT 60.159 45.455 0.00 0.00 0.00 2.45
106 107 3.181397 GACGGATGTTGCCAAAATGATG 58.819 45.455 0.00 0.00 0.00 3.07
107 108 2.094078 ACGGATGTTGCCAAAATGATGG 60.094 45.455 0.00 0.00 43.70 3.51
115 116 2.566952 CCAAAATGATGGCTTCGGAC 57.433 50.000 0.00 0.00 32.78 4.79
116 117 2.094675 CCAAAATGATGGCTTCGGACT 58.905 47.619 0.00 0.00 32.78 3.85
117 118 2.493278 CCAAAATGATGGCTTCGGACTT 59.507 45.455 0.00 0.00 32.78 3.01
118 119 3.694072 CCAAAATGATGGCTTCGGACTTA 59.306 43.478 0.00 0.00 32.78 2.24
119 120 4.438744 CCAAAATGATGGCTTCGGACTTAC 60.439 45.833 0.00 0.00 32.78 2.34
120 121 3.914426 AATGATGGCTTCGGACTTACT 57.086 42.857 0.00 0.00 0.00 2.24
121 122 2.672961 TGATGGCTTCGGACTTACTG 57.327 50.000 0.00 0.00 0.00 2.74
122 123 2.176045 TGATGGCTTCGGACTTACTGA 58.824 47.619 0.00 0.00 0.00 3.41
123 124 2.766263 TGATGGCTTCGGACTTACTGAT 59.234 45.455 0.00 0.00 33.54 2.90
124 125 2.672961 TGGCTTCGGACTTACTGATG 57.327 50.000 0.00 0.00 33.54 3.07
130 131 5.643339 CTTCGGACTTACTGATGCAATAC 57.357 43.478 0.00 0.00 33.54 1.89
131 132 5.339008 TTCGGACTTACTGATGCAATACT 57.661 39.130 0.00 0.00 33.54 2.12
132 133 5.339008 TCGGACTTACTGATGCAATACTT 57.661 39.130 0.00 0.00 0.00 2.24
133 134 5.730550 TCGGACTTACTGATGCAATACTTT 58.269 37.500 0.00 0.00 0.00 2.66
134 135 5.580691 TCGGACTTACTGATGCAATACTTTG 59.419 40.000 0.00 0.00 35.85 2.77
135 136 5.351465 CGGACTTACTGATGCAATACTTTGT 59.649 40.000 0.00 0.00 35.17 2.83
136 137 6.533723 CGGACTTACTGATGCAATACTTTGTA 59.466 38.462 0.00 0.00 35.17 2.41
137 138 7.064134 CGGACTTACTGATGCAATACTTTGTAA 59.936 37.037 0.00 0.00 35.17 2.41
138 139 8.391106 GGACTTACTGATGCAATACTTTGTAAG 58.609 37.037 15.08 15.08 40.48 2.34
139 140 8.268850 ACTTACTGATGCAATACTTTGTAAGG 57.731 34.615 18.13 8.18 39.58 2.69
140 141 7.883311 ACTTACTGATGCAATACTTTGTAAGGT 59.117 33.333 18.13 0.00 39.58 3.50
141 142 8.630054 TTACTGATGCAATACTTTGTAAGGTT 57.370 30.769 0.00 0.00 35.17 3.50
142 143 7.524717 ACTGATGCAATACTTTGTAAGGTTT 57.475 32.000 0.00 0.00 35.17 3.27
143 144 7.951591 ACTGATGCAATACTTTGTAAGGTTTT 58.048 30.769 0.00 0.00 35.17 2.43
144 145 8.421002 ACTGATGCAATACTTTGTAAGGTTTTT 58.579 29.630 0.00 0.00 35.17 1.94
145 146 8.586570 TGATGCAATACTTTGTAAGGTTTTTG 57.413 30.769 0.00 0.00 35.17 2.44
146 147 8.200792 TGATGCAATACTTTGTAAGGTTTTTGT 58.799 29.630 0.00 0.00 35.17 2.83
147 148 7.763172 TGCAATACTTTGTAAGGTTTTTGTG 57.237 32.000 0.00 0.00 35.17 3.33
148 149 7.548097 TGCAATACTTTGTAAGGTTTTTGTGA 58.452 30.769 0.00 0.00 35.17 3.58
149 150 8.035394 TGCAATACTTTGTAAGGTTTTTGTGAA 58.965 29.630 0.00 0.00 35.17 3.18
150 151 9.040939 GCAATACTTTGTAAGGTTTTTGTGAAT 57.959 29.630 0.00 0.00 35.17 2.57
172 173 9.734620 TGAATAGTAAATAAAATGACTGCATGC 57.265 29.630 11.82 11.82 34.26 4.06
173 174 9.734620 GAATAGTAAATAAAATGACTGCATGCA 57.265 29.630 21.29 21.29 34.26 3.96
175 176 9.903682 ATAGTAAATAAAATGACTGCATGCATC 57.096 29.630 22.97 19.75 34.26 3.91
176 177 7.774134 AGTAAATAAAATGACTGCATGCATCA 58.226 30.769 22.97 24.26 34.26 3.07
177 178 8.418662 AGTAAATAAAATGACTGCATGCATCAT 58.581 29.630 26.42 26.42 34.26 2.45
178 179 7.709269 AAATAAAATGACTGCATGCATCATC 57.291 32.000 29.37 23.46 34.26 2.92
179 180 3.728076 AAATGACTGCATGCATCATCC 57.272 42.857 29.37 16.71 34.26 3.51
180 181 2.358322 ATGACTGCATGCATCATCCA 57.642 45.000 26.42 18.51 32.31 3.41
181 182 1.675552 TGACTGCATGCATCATCCAG 58.324 50.000 22.97 10.18 35.90 3.86
182 183 1.210967 TGACTGCATGCATCATCCAGA 59.789 47.619 22.97 1.31 31.82 3.86
183 184 2.158667 TGACTGCATGCATCATCCAGAT 60.159 45.455 22.97 0.00 31.82 2.90
184 185 7.007314 AATGACTGCATGCATCATCCAGATG 62.007 44.000 29.37 16.39 44.48 2.90
195 196 4.526438 TCATCCAGATGTAGAGGTCAGA 57.474 45.455 7.48 0.00 39.72 3.27
196 197 4.468713 TCATCCAGATGTAGAGGTCAGAG 58.531 47.826 7.48 0.00 39.72 3.35
197 198 3.304911 TCCAGATGTAGAGGTCAGAGG 57.695 52.381 0.00 0.00 0.00 3.69
198 199 2.583101 TCCAGATGTAGAGGTCAGAGGT 59.417 50.000 0.00 0.00 0.00 3.85
199 200 2.955660 CCAGATGTAGAGGTCAGAGGTC 59.044 54.545 0.00 0.00 0.00 3.85
200 201 3.625853 CAGATGTAGAGGTCAGAGGTCA 58.374 50.000 0.00 0.00 0.00 4.02
201 202 4.214310 CAGATGTAGAGGTCAGAGGTCAT 58.786 47.826 0.00 0.00 0.00 3.06
202 203 4.278170 CAGATGTAGAGGTCAGAGGTCATC 59.722 50.000 0.00 0.00 0.00 2.92
203 204 3.739401 TGTAGAGGTCAGAGGTCATCA 57.261 47.619 0.00 0.00 0.00 3.07
204 205 4.256983 TGTAGAGGTCAGAGGTCATCAT 57.743 45.455 0.00 0.00 0.00 2.45
205 206 4.211125 TGTAGAGGTCAGAGGTCATCATC 58.789 47.826 0.00 0.00 0.00 2.92
206 207 2.676748 AGAGGTCAGAGGTCATCATCC 58.323 52.381 0.00 0.00 0.00 3.51
207 208 2.247111 AGAGGTCAGAGGTCATCATCCT 59.753 50.000 0.00 0.00 38.09 3.24
208 209 3.037549 GAGGTCAGAGGTCATCATCCTT 58.962 50.000 0.00 0.00 35.20 3.36
209 210 3.454082 GAGGTCAGAGGTCATCATCCTTT 59.546 47.826 0.00 0.00 35.20 3.11
210 211 4.624913 AGGTCAGAGGTCATCATCCTTTA 58.375 43.478 0.00 0.00 35.20 1.85
211 212 5.032846 AGGTCAGAGGTCATCATCCTTTAA 58.967 41.667 0.00 0.00 35.20 1.52
212 213 5.130145 AGGTCAGAGGTCATCATCCTTTAAG 59.870 44.000 0.00 0.00 35.20 1.85
217 218 7.607991 TCAGAGGTCATCATCCTTTAAGAAAAC 59.392 37.037 0.00 0.00 35.20 2.43
296 297 3.337619 GCATGCTGCGTCCATAGG 58.662 61.111 11.37 0.00 31.71 2.57
297 298 2.256591 GCATGCTGCGTCCATAGGG 61.257 63.158 11.37 0.00 31.71 3.53
298 299 1.598962 CATGCTGCGTCCATAGGGG 60.599 63.158 0.00 0.00 38.37 4.79
299 300 2.072487 ATGCTGCGTCCATAGGGGT 61.072 57.895 0.00 0.00 38.11 4.95
300 301 2.203070 GCTGCGTCCATAGGGGTG 60.203 66.667 0.00 0.00 38.11 4.61
301 302 2.731571 GCTGCGTCCATAGGGGTGA 61.732 63.158 0.00 0.00 38.11 4.02
302 303 1.443407 CTGCGTCCATAGGGGTGAG 59.557 63.158 0.00 0.00 38.11 3.51
303 304 1.305802 TGCGTCCATAGGGGTGAGT 60.306 57.895 0.00 0.00 38.11 3.41
304 305 1.144057 GCGTCCATAGGGGTGAGTG 59.856 63.158 0.00 0.00 38.11 3.51
321 322 4.793731 GTGAGTGTAGATGTGTGTATGTCG 59.206 45.833 0.00 0.00 0.00 4.35
326 327 5.631929 GTGTAGATGTGTGTATGTCGTTTCA 59.368 40.000 0.00 0.00 0.00 2.69
327 328 5.861787 TGTAGATGTGTGTATGTCGTTTCAG 59.138 40.000 0.00 0.00 0.00 3.02
328 329 5.134202 AGATGTGTGTATGTCGTTTCAGA 57.866 39.130 0.00 0.00 0.00 3.27
329 330 5.538118 AGATGTGTGTATGTCGTTTCAGAA 58.462 37.500 0.00 0.00 0.00 3.02
330 331 5.989168 AGATGTGTGTATGTCGTTTCAGAAA 59.011 36.000 0.00 0.00 0.00 2.52
331 332 6.481976 AGATGTGTGTATGTCGTTTCAGAAAA 59.518 34.615 0.00 0.00 0.00 2.29
332 333 6.424176 TGTGTGTATGTCGTTTCAGAAAAA 57.576 33.333 0.00 0.00 0.00 1.94
384 385 8.792830 TTCATCATTTTCTTCTACCGAGAAAT 57.207 30.769 0.70 0.00 41.23 2.17
388 389 8.488651 TCATTTTCTTCTACCGAGAAATAACC 57.511 34.615 0.70 0.00 41.23 2.85
401 402 5.334260 CGAGAAATAACCAAAGTTAACCGCA 60.334 40.000 0.88 0.00 41.68 5.69
404 405 7.758495 AGAAATAACCAAAGTTAACCGCATAG 58.242 34.615 0.88 0.00 41.68 2.23
411 412 6.148315 ACCAAAGTTAACCGCATAGTAAACTC 59.852 38.462 0.88 0.00 0.00 3.01
476 478 5.006358 CGTCCTATTTTCCGTATCCAAACTG 59.994 44.000 0.00 0.00 0.00 3.16
576 579 4.878774 GGCTCTATCATCGCCGAG 57.121 61.111 0.00 0.00 33.64 4.63
577 580 1.960612 GGCTCTATCATCGCCGAGT 59.039 57.895 0.00 0.00 33.64 4.18
578 581 1.166129 GGCTCTATCATCGCCGAGTA 58.834 55.000 0.00 0.00 33.64 2.59
579 582 1.540267 GGCTCTATCATCGCCGAGTAA 59.460 52.381 0.00 0.00 33.64 2.24
610 618 4.926860 TGATAAAGTCTTGACACATGCG 57.073 40.909 3.49 0.00 0.00 4.73
652 660 6.525578 TTTAGATTCACTCAGACGTACCAT 57.474 37.500 0.00 0.00 0.00 3.55
696 708 4.258457 TCCCATTTCCCGTTGGATTTAT 57.742 40.909 0.00 0.00 41.40 1.40
725 763 4.389374 CCGTAACTATCCAAGAATGCCAT 58.611 43.478 0.00 0.00 0.00 4.40
738 776 2.908940 GCCATTGGCTAGCGGCAT 60.909 61.111 22.07 6.33 46.69 4.40
745 783 1.026182 TGGCTAGCGGCATGTGAAAG 61.026 55.000 9.00 0.00 44.01 2.62
753 791 1.675714 CGGCATGTGAAAGGAGCAGTA 60.676 52.381 0.00 0.00 0.00 2.74
784 822 7.716612 AGAAGGAAAATTTTGATGAAACGAGT 58.283 30.769 8.47 0.00 0.00 4.18
845 884 0.614415 CTCACTCCCCACTCTGCTCT 60.614 60.000 0.00 0.00 0.00 4.09
915 957 3.041627 GAACGCGGCTCTCTCTCGT 62.042 63.158 12.47 0.00 34.63 4.18
945 987 4.645535 TCTTGCTTAAGCTTGACACATCT 58.354 39.130 26.90 0.00 42.66 2.90
957 999 0.458543 ACACATCTCTTAGCACGGCG 60.459 55.000 4.80 4.80 0.00 6.46
966 1008 1.310216 TTAGCACGGCGAGTCAGCTA 61.310 55.000 16.62 15.24 34.47 3.32
1017 1059 2.851102 ATGCCGGGGATGGAGGAG 60.851 66.667 2.18 0.00 0.00 3.69
1031 1073 2.124403 GGAGGCGGAGGACTACGA 60.124 66.667 8.36 0.00 39.85 3.43
1119 1161 2.159226 CGGCGACCTCTTCTTGTTCTAT 60.159 50.000 0.00 0.00 0.00 1.98
1120 1162 3.190874 GGCGACCTCTTCTTGTTCTATG 58.809 50.000 0.00 0.00 0.00 2.23
1121 1163 3.368531 GGCGACCTCTTCTTGTTCTATGT 60.369 47.826 0.00 0.00 0.00 2.29
1158 1200 2.722487 GACGATGAGGACGGCGAT 59.278 61.111 16.62 0.00 34.93 4.58
1159 1201 1.658717 GACGATGAGGACGGCGATG 60.659 63.158 16.62 0.00 34.93 3.84
1338 1380 1.001158 CCTCGCTCTCCCGATTAGTTC 60.001 57.143 0.00 0.00 36.54 3.01
1341 1383 1.001158 CGCTCTCCCGATTAGTTCCTC 60.001 57.143 0.00 0.00 0.00 3.71
1576 1618 0.874390 GATGATGTGGTTGTGTGCGT 59.126 50.000 0.00 0.00 0.00 5.24
1577 1619 0.592637 ATGATGTGGTTGTGTGCGTG 59.407 50.000 0.00 0.00 0.00 5.34
1578 1620 1.370414 GATGTGGTTGTGTGCGTGC 60.370 57.895 0.00 0.00 0.00 5.34
1579 1621 2.731587 GATGTGGTTGTGTGCGTGCC 62.732 60.000 0.00 0.00 0.00 5.01
1580 1622 3.209097 GTGGTTGTGTGCGTGCCT 61.209 61.111 0.00 0.00 0.00 4.75
1581 1623 2.439338 TGGTTGTGTGCGTGCCTT 60.439 55.556 0.00 0.00 0.00 4.35
1582 1624 2.026014 GGTTGTGTGCGTGCCTTG 59.974 61.111 0.00 0.00 0.00 3.61
1583 1625 2.026014 GTTGTGTGCGTGCCTTGG 59.974 61.111 0.00 0.00 0.00 3.61
1798 1848 1.203287 GTTACGCCCTTCGACTACCTT 59.797 52.381 0.00 0.00 41.67 3.50
2114 2174 5.070981 TCCAAGATGGACAATCTATCTCCAC 59.929 44.000 5.30 0.00 42.78 4.02
2171 2243 9.869757 ACTAAATAAATAACCCTTTTGCATCAC 57.130 29.630 0.00 0.00 0.00 3.06
2174 2246 9.791801 AAATAAATAACCCTTTTGCATCACTTT 57.208 25.926 0.00 0.00 0.00 2.66
2381 2459 9.155975 AGTACATATGATTCTGTTCTTGTTGAC 57.844 33.333 10.38 0.00 0.00 3.18
2396 2474 0.249699 TTGACGATGTTGCCGACACT 60.250 50.000 0.00 0.00 42.04 3.55
2399 2477 2.029288 CGATGTTGCCGACACTGCT 61.029 57.895 0.00 0.00 42.04 4.24
2645 2723 0.323629 TTTGTGAGAGGGGTAAGCGG 59.676 55.000 0.00 0.00 0.00 5.52
2760 2838 4.739793 TGAGAAATTCACCCCAAATCTGT 58.260 39.130 0.00 0.00 0.00 3.41
2775 2853 7.256154 CCCCAAATCTGTACTGTTTTTGGTATT 60.256 37.037 27.37 9.53 42.99 1.89
2800 2878 2.717639 AGTGGTGGATGCCATCTTAC 57.282 50.000 4.41 4.57 41.08 2.34
2960 3043 0.673333 TGCACTGTACTTGCGGATGG 60.673 55.000 13.28 0.00 43.34 3.51
2973 3056 2.439880 TGCGGATGGATGGGTTACATTA 59.560 45.455 0.00 0.00 40.72 1.90
3055 3139 4.227982 TGAGAAATGGGATCAGATTGGTGA 59.772 41.667 0.00 0.00 0.00 4.02
3069 3153 8.628630 TCAGATTGGTGAATTTTGTGTATGTA 57.371 30.769 0.00 0.00 0.00 2.29
3073 3157 8.984891 ATTGGTGAATTTTGTGTATGTATGTG 57.015 30.769 0.00 0.00 0.00 3.21
3125 3213 2.845363 TCTTGATCAGTTCTGCTGCA 57.155 45.000 0.88 0.88 44.66 4.41
3198 3286 3.445987 TCCTTCTCTTCCTCTCCCTTTC 58.554 50.000 0.00 0.00 0.00 2.62
3241 3329 4.606961 ACAACTTTTCCTGTTACATTGCG 58.393 39.130 0.00 0.00 0.00 4.85
3273 3361 1.927487 TGGCACTTGCTTGATTCCAT 58.073 45.000 0.38 0.00 41.70 3.41
3279 3367 4.678574 GCACTTGCTTGATTCCATATTGCA 60.679 41.667 0.00 0.00 38.21 4.08
3280 3368 5.412640 CACTTGCTTGATTCCATATTGCAA 58.587 37.500 0.00 0.00 37.39 4.08
3286 3374 5.544650 CTTGATTCCATATTGCAAATCCCC 58.455 41.667 1.71 0.00 0.00 4.81
3298 3386 5.186256 TGCAAATCCCCTATTAGTGAACA 57.814 39.130 0.00 0.00 0.00 3.18
3307 3395 8.570068 TCCCCTATTAGTGAACAAACAATAAC 57.430 34.615 0.00 0.00 34.17 1.89
3309 3397 8.966868 CCCCTATTAGTGAACAAACAATAACAT 58.033 33.333 0.00 0.00 34.17 2.71
3314 3402 8.932945 TTAGTGAACAAACAATAACATTTGCA 57.067 26.923 0.00 0.00 39.03 4.08
3315 3403 9.539825 TTAGTGAACAAACAATAACATTTGCAT 57.460 25.926 0.00 0.00 39.03 3.96
3336 3424 5.623335 CATAATTGCATTGTTTTGTGCTGG 58.377 37.500 0.00 0.00 41.78 4.85
3337 3425 1.950828 TTGCATTGTTTTGTGCTGGG 58.049 45.000 0.00 0.00 41.78 4.45
3338 3426 0.829333 TGCATTGTTTTGTGCTGGGT 59.171 45.000 0.00 0.00 41.78 4.51
3339 3427 1.209019 TGCATTGTTTTGTGCTGGGTT 59.791 42.857 0.00 0.00 41.78 4.11
3340 3428 2.287769 GCATTGTTTTGTGCTGGGTTT 58.712 42.857 0.00 0.00 38.30 3.27
3341 3429 2.287644 GCATTGTTTTGTGCTGGGTTTC 59.712 45.455 0.00 0.00 38.30 2.78
3355 5584 4.142838 GCTGGGTTTCATTGCATTTAAAGC 60.143 41.667 8.29 8.29 0.00 3.51
3377 5659 8.668510 AAGCAATGTAGTAGAAGATTATGTGG 57.331 34.615 0.00 0.00 0.00 4.17
3379 5661 8.267894 AGCAATGTAGTAGAAGATTATGTGGTT 58.732 33.333 0.00 0.00 0.00 3.67
3382 5664 7.843490 TGTAGTAGAAGATTATGTGGTTTGC 57.157 36.000 0.00 0.00 0.00 3.68
3387 5669 6.655078 AGAAGATTATGTGGTTTGCAAAGT 57.345 33.333 13.26 0.00 0.00 2.66
3395 5677 5.243426 TGTGGTTTGCAAAGTAAGTTCTC 57.757 39.130 13.26 0.00 0.00 2.87
3399 5681 4.524749 GTTTGCAAAGTAAGTTCTCGTCC 58.475 43.478 13.26 0.00 0.00 4.79
3409 5691 3.516981 AGTTCTCGTCCACATGATCAG 57.483 47.619 0.00 0.00 0.00 2.90
3410 5692 2.828520 AGTTCTCGTCCACATGATCAGT 59.171 45.455 0.00 0.00 0.00 3.41
3411 5693 4.017126 AGTTCTCGTCCACATGATCAGTA 58.983 43.478 0.00 0.00 0.00 2.74
3412 5694 4.462834 AGTTCTCGTCCACATGATCAGTAA 59.537 41.667 0.00 0.00 0.00 2.24
3413 5695 4.639135 TCTCGTCCACATGATCAGTAAG 57.361 45.455 0.00 0.00 0.00 2.34
3414 5696 4.017126 TCTCGTCCACATGATCAGTAAGT 58.983 43.478 0.00 0.00 0.00 2.24
3415 5697 5.190677 TCTCGTCCACATGATCAGTAAGTA 58.809 41.667 0.00 0.00 0.00 2.24
3416 5698 5.066117 TCTCGTCCACATGATCAGTAAGTAC 59.934 44.000 0.00 0.00 0.00 2.73
3417 5699 4.097437 TCGTCCACATGATCAGTAAGTACC 59.903 45.833 0.00 0.00 0.00 3.34
3418 5700 4.098044 CGTCCACATGATCAGTAAGTACCT 59.902 45.833 0.00 0.00 0.00 3.08
3419 5701 5.298527 CGTCCACATGATCAGTAAGTACCTA 59.701 44.000 0.00 0.00 0.00 3.08
3420 5702 6.183360 CGTCCACATGATCAGTAAGTACCTAA 60.183 42.308 0.00 0.00 0.00 2.69
3421 5703 7.203910 GTCCACATGATCAGTAAGTACCTAAG 58.796 42.308 0.00 0.00 0.00 2.18
3422 5704 6.323996 TCCACATGATCAGTAAGTACCTAAGG 59.676 42.308 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.119588 TCGCACGAAAACCTAACATCTAAAG 59.880 40.000 0.00 0.00 0.00 1.85
1 2 4.989797 TCGCACGAAAACCTAACATCTAAA 59.010 37.500 0.00 0.00 0.00 1.85
2 3 4.558178 TCGCACGAAAACCTAACATCTAA 58.442 39.130 0.00 0.00 0.00 2.10
3 4 4.171005 CTCGCACGAAAACCTAACATCTA 58.829 43.478 0.00 0.00 0.00 1.98
4 5 2.993899 CTCGCACGAAAACCTAACATCT 59.006 45.455 0.00 0.00 0.00 2.90
5 6 2.093783 CCTCGCACGAAAACCTAACATC 59.906 50.000 0.00 0.00 0.00 3.06
6 7 2.073816 CCTCGCACGAAAACCTAACAT 58.926 47.619 0.00 0.00 0.00 2.71
7 8 1.202557 ACCTCGCACGAAAACCTAACA 60.203 47.619 0.00 0.00 0.00 2.41
8 9 1.458445 GACCTCGCACGAAAACCTAAC 59.542 52.381 0.00 0.00 0.00 2.34
9 10 1.342174 AGACCTCGCACGAAAACCTAA 59.658 47.619 0.00 0.00 0.00 2.69
10 11 0.963962 AGACCTCGCACGAAAACCTA 59.036 50.000 0.00 0.00 0.00 3.08
11 12 0.600255 CAGACCTCGCACGAAAACCT 60.600 55.000 0.00 0.00 0.00 3.50
12 13 0.878961 ACAGACCTCGCACGAAAACC 60.879 55.000 0.00 0.00 0.00 3.27
13 14 0.935196 AACAGACCTCGCACGAAAAC 59.065 50.000 0.00 0.00 0.00 2.43
14 15 1.329292 CAAACAGACCTCGCACGAAAA 59.671 47.619 0.00 0.00 0.00 2.29
15 16 0.934496 CAAACAGACCTCGCACGAAA 59.066 50.000 0.00 0.00 0.00 3.46
16 17 0.103390 TCAAACAGACCTCGCACGAA 59.897 50.000 0.00 0.00 0.00 3.85
17 18 0.317160 ATCAAACAGACCTCGCACGA 59.683 50.000 0.00 0.00 0.00 4.35
18 19 1.990799 TATCAAACAGACCTCGCACG 58.009 50.000 0.00 0.00 0.00 5.34
19 20 4.437390 CCAAATATCAAACAGACCTCGCAC 60.437 45.833 0.00 0.00 0.00 5.34
20 21 3.689161 CCAAATATCAAACAGACCTCGCA 59.311 43.478 0.00 0.00 0.00 5.10
21 22 3.689649 ACCAAATATCAAACAGACCTCGC 59.310 43.478 0.00 0.00 0.00 5.03
22 23 5.445939 CGAACCAAATATCAAACAGACCTCG 60.446 44.000 0.00 0.00 0.00 4.63
23 24 5.163754 CCGAACCAAATATCAAACAGACCTC 60.164 44.000 0.00 0.00 0.00 3.85
24 25 4.700213 CCGAACCAAATATCAAACAGACCT 59.300 41.667 0.00 0.00 0.00 3.85
25 26 4.698304 TCCGAACCAAATATCAAACAGACC 59.302 41.667 0.00 0.00 0.00 3.85
26 27 5.180492 TGTCCGAACCAAATATCAAACAGAC 59.820 40.000 0.00 0.00 0.00 3.51
27 28 5.309638 TGTCCGAACCAAATATCAAACAGA 58.690 37.500 0.00 0.00 0.00 3.41
28 29 5.621197 TGTCCGAACCAAATATCAAACAG 57.379 39.130 0.00 0.00 0.00 3.16
29 30 6.582677 AATGTCCGAACCAAATATCAAACA 57.417 33.333 0.00 0.00 0.00 2.83
30 31 5.737290 CGAATGTCCGAACCAAATATCAAAC 59.263 40.000 0.00 0.00 0.00 2.93
31 32 5.163703 CCGAATGTCCGAACCAAATATCAAA 60.164 40.000 0.00 0.00 0.00 2.69
32 33 4.334203 CCGAATGTCCGAACCAAATATCAA 59.666 41.667 0.00 0.00 0.00 2.57
33 34 3.874543 CCGAATGTCCGAACCAAATATCA 59.125 43.478 0.00 0.00 0.00 2.15
34 35 3.303791 GCCGAATGTCCGAACCAAATATC 60.304 47.826 0.00 0.00 0.00 1.63
35 36 2.616842 GCCGAATGTCCGAACCAAATAT 59.383 45.455 0.00 0.00 0.00 1.28
36 37 2.011222 GCCGAATGTCCGAACCAAATA 58.989 47.619 0.00 0.00 0.00 1.40
37 38 0.808755 GCCGAATGTCCGAACCAAAT 59.191 50.000 0.00 0.00 0.00 2.32
38 39 0.535328 TGCCGAATGTCCGAACCAAA 60.535 50.000 0.00 0.00 0.00 3.28
39 40 1.071642 TGCCGAATGTCCGAACCAA 59.928 52.632 0.00 0.00 0.00 3.67
40 41 1.669760 GTGCCGAATGTCCGAACCA 60.670 57.895 0.00 0.00 0.00 3.67
41 42 2.396157 GGTGCCGAATGTCCGAACC 61.396 63.158 0.00 0.00 0.00 3.62
42 43 2.396157 GGGTGCCGAATGTCCGAAC 61.396 63.158 0.00 0.00 0.00 3.95
43 44 2.046700 GGGTGCCGAATGTCCGAA 60.047 61.111 0.00 0.00 0.00 4.30
44 45 4.090588 GGGGTGCCGAATGTCCGA 62.091 66.667 0.00 0.00 0.00 4.55
45 46 3.622060 AAGGGGTGCCGAATGTCCG 62.622 63.158 0.00 0.00 0.00 4.79
46 47 1.749258 GAAGGGGTGCCGAATGTCC 60.749 63.158 0.00 0.00 0.00 4.02
47 48 0.394352 ATGAAGGGGTGCCGAATGTC 60.394 55.000 0.00 0.00 0.00 3.06
48 49 0.394352 GATGAAGGGGTGCCGAATGT 60.394 55.000 0.00 0.00 0.00 2.71
49 50 0.394216 TGATGAAGGGGTGCCGAATG 60.394 55.000 0.00 0.00 0.00 2.67
50 51 0.331278 TTGATGAAGGGGTGCCGAAT 59.669 50.000 0.00 0.00 0.00 3.34
51 52 0.322456 CTTGATGAAGGGGTGCCGAA 60.322 55.000 0.00 0.00 0.00 4.30
52 53 1.299648 CTTGATGAAGGGGTGCCGA 59.700 57.895 0.00 0.00 0.00 5.54
53 54 1.002134 ACTTGATGAAGGGGTGCCG 60.002 57.895 0.00 0.00 32.95 5.69
54 55 0.967380 CCACTTGATGAAGGGGTGCC 60.967 60.000 4.81 0.00 46.61 5.01
55 56 2.571548 CCACTTGATGAAGGGGTGC 58.428 57.895 4.81 0.00 46.61 5.01
59 60 3.713764 ACTCCTATCCACTTGATGAAGGG 59.286 47.826 0.00 0.00 34.76 3.95
60 61 5.510520 GCTACTCCTATCCACTTGATGAAGG 60.511 48.000 0.00 0.00 34.76 3.46
61 62 5.537188 GCTACTCCTATCCACTTGATGAAG 58.463 45.833 0.00 0.00 34.76 3.02
62 63 4.038042 CGCTACTCCTATCCACTTGATGAA 59.962 45.833 0.00 0.00 34.76 2.57
63 64 3.570125 CGCTACTCCTATCCACTTGATGA 59.430 47.826 0.00 0.00 34.76 2.92
64 65 3.570125 TCGCTACTCCTATCCACTTGATG 59.430 47.826 0.00 0.00 34.76 3.07
65 66 3.570550 GTCGCTACTCCTATCCACTTGAT 59.429 47.826 0.00 0.00 37.49 2.57
66 67 2.950309 GTCGCTACTCCTATCCACTTGA 59.050 50.000 0.00 0.00 0.00 3.02
67 68 2.287069 CGTCGCTACTCCTATCCACTTG 60.287 54.545 0.00 0.00 0.00 3.16
68 69 1.948145 CGTCGCTACTCCTATCCACTT 59.052 52.381 0.00 0.00 0.00 3.16
69 70 1.595466 CGTCGCTACTCCTATCCACT 58.405 55.000 0.00 0.00 0.00 4.00
70 71 0.592148 CCGTCGCTACTCCTATCCAC 59.408 60.000 0.00 0.00 0.00 4.02
71 72 0.471191 TCCGTCGCTACTCCTATCCA 59.529 55.000 0.00 0.00 0.00 3.41
72 73 1.469308 CATCCGTCGCTACTCCTATCC 59.531 57.143 0.00 0.00 0.00 2.59
73 74 2.152830 ACATCCGTCGCTACTCCTATC 58.847 52.381 0.00 0.00 0.00 2.08
74 75 2.273538 ACATCCGTCGCTACTCCTAT 57.726 50.000 0.00 0.00 0.00 2.57
75 76 1.674441 CAACATCCGTCGCTACTCCTA 59.326 52.381 0.00 0.00 0.00 2.94
76 77 0.456221 CAACATCCGTCGCTACTCCT 59.544 55.000 0.00 0.00 0.00 3.69
77 78 1.146358 GCAACATCCGTCGCTACTCC 61.146 60.000 0.00 0.00 0.00 3.85
78 79 1.146358 GGCAACATCCGTCGCTACTC 61.146 60.000 0.00 0.00 0.00 2.59
79 80 1.153628 GGCAACATCCGTCGCTACT 60.154 57.895 0.00 0.00 0.00 2.57
80 81 1.447140 TGGCAACATCCGTCGCTAC 60.447 57.895 0.00 0.00 46.17 3.58
81 82 2.974717 TGGCAACATCCGTCGCTA 59.025 55.556 0.00 0.00 46.17 4.26
96 97 2.094675 AGTCCGAAGCCATCATTTTGG 58.905 47.619 0.00 0.00 39.94 3.28
97 98 3.855689 AAGTCCGAAGCCATCATTTTG 57.144 42.857 0.00 0.00 0.00 2.44
98 99 4.396166 CAGTAAGTCCGAAGCCATCATTTT 59.604 41.667 0.00 0.00 0.00 1.82
99 100 3.941483 CAGTAAGTCCGAAGCCATCATTT 59.059 43.478 0.00 0.00 0.00 2.32
100 101 3.197766 TCAGTAAGTCCGAAGCCATCATT 59.802 43.478 0.00 0.00 0.00 2.57
101 102 2.766263 TCAGTAAGTCCGAAGCCATCAT 59.234 45.455 0.00 0.00 0.00 2.45
102 103 2.176045 TCAGTAAGTCCGAAGCCATCA 58.824 47.619 0.00 0.00 0.00 3.07
103 104 2.961526 TCAGTAAGTCCGAAGCCATC 57.038 50.000 0.00 0.00 0.00 3.51
104 105 2.743183 GCATCAGTAAGTCCGAAGCCAT 60.743 50.000 0.00 0.00 0.00 4.40
105 106 1.405526 GCATCAGTAAGTCCGAAGCCA 60.406 52.381 0.00 0.00 0.00 4.75
106 107 1.291132 GCATCAGTAAGTCCGAAGCC 58.709 55.000 0.00 0.00 0.00 4.35
107 108 2.010145 TGCATCAGTAAGTCCGAAGC 57.990 50.000 0.00 0.00 0.00 3.86
108 109 5.352284 AGTATTGCATCAGTAAGTCCGAAG 58.648 41.667 0.00 0.00 0.00 3.79
109 110 5.339008 AGTATTGCATCAGTAAGTCCGAA 57.661 39.130 0.00 0.00 0.00 4.30
110 111 5.339008 AAGTATTGCATCAGTAAGTCCGA 57.661 39.130 0.00 0.00 0.00 4.55
111 112 5.351465 ACAAAGTATTGCATCAGTAAGTCCG 59.649 40.000 0.00 0.00 40.34 4.79
112 113 6.743575 ACAAAGTATTGCATCAGTAAGTCC 57.256 37.500 0.00 0.00 40.34 3.85
113 114 8.391106 CCTTACAAAGTATTGCATCAGTAAGTC 58.609 37.037 0.00 0.00 40.34 3.01
114 115 7.883311 ACCTTACAAAGTATTGCATCAGTAAGT 59.117 33.333 0.00 2.68 40.34 2.24
115 116 8.268850 ACCTTACAAAGTATTGCATCAGTAAG 57.731 34.615 0.00 0.00 40.34 2.34
116 117 8.630054 AACCTTACAAAGTATTGCATCAGTAA 57.370 30.769 0.00 0.00 40.34 2.24
117 118 8.630054 AAACCTTACAAAGTATTGCATCAGTA 57.370 30.769 0.00 0.00 40.34 2.74
118 119 7.524717 AAACCTTACAAAGTATTGCATCAGT 57.475 32.000 0.00 0.00 40.34 3.41
119 120 8.702438 CAAAAACCTTACAAAGTATTGCATCAG 58.298 33.333 0.00 0.00 40.34 2.90
120 121 8.200792 ACAAAAACCTTACAAAGTATTGCATCA 58.799 29.630 0.00 0.00 40.34 3.07
121 122 8.487176 CACAAAAACCTTACAAAGTATTGCATC 58.513 33.333 0.00 0.00 40.34 3.91
122 123 8.200792 TCACAAAAACCTTACAAAGTATTGCAT 58.799 29.630 0.00 0.00 40.34 3.96
123 124 7.548097 TCACAAAAACCTTACAAAGTATTGCA 58.452 30.769 0.00 0.00 40.34 4.08
124 125 7.995463 TCACAAAAACCTTACAAAGTATTGC 57.005 32.000 0.00 0.00 40.34 3.56
146 147 9.734620 GCATGCAGTCATTTTATTTACTATTCA 57.265 29.630 14.21 0.00 0.00 2.57
147 148 9.734620 TGCATGCAGTCATTTTATTTACTATTC 57.265 29.630 18.46 0.00 0.00 1.75
149 150 9.903682 GATGCATGCAGTCATTTTATTTACTAT 57.096 29.630 26.69 1.61 0.00 2.12
150 151 8.901793 TGATGCATGCAGTCATTTTATTTACTA 58.098 29.630 26.69 0.00 0.00 1.82
151 152 7.774134 TGATGCATGCAGTCATTTTATTTACT 58.226 30.769 26.69 2.43 0.00 2.24
152 153 7.990541 TGATGCATGCAGTCATTTTATTTAC 57.009 32.000 26.69 0.00 0.00 2.01
153 154 7.868922 GGATGATGCATGCAGTCATTTTATTTA 59.131 33.333 29.63 10.81 33.03 1.40
154 155 6.704493 GGATGATGCATGCAGTCATTTTATTT 59.296 34.615 29.63 16.95 33.03 1.40
155 156 6.183360 TGGATGATGCATGCAGTCATTTTATT 60.183 34.615 29.63 17.44 37.28 1.40
156 157 5.303333 TGGATGATGCATGCAGTCATTTTAT 59.697 36.000 29.63 16.39 37.28 1.40
157 158 4.645588 TGGATGATGCATGCAGTCATTTTA 59.354 37.500 29.63 21.27 37.28 1.52
158 159 3.449377 TGGATGATGCATGCAGTCATTTT 59.551 39.130 29.63 18.42 37.28 1.82
159 160 3.028130 TGGATGATGCATGCAGTCATTT 58.972 40.909 29.63 18.91 37.28 2.32
160 161 2.661718 TGGATGATGCATGCAGTCATT 58.338 42.857 29.63 16.07 37.28 2.57
161 162 2.358322 TGGATGATGCATGCAGTCAT 57.642 45.000 29.54 29.54 37.28 3.06
162 163 3.886324 TGGATGATGCATGCAGTCA 57.114 47.368 26.69 25.65 37.28 3.41
173 174 5.072129 TCTGACCTCTACATCTGGATGAT 57.928 43.478 16.27 4.72 41.20 2.45
174 175 4.468713 CTCTGACCTCTACATCTGGATGA 58.531 47.826 16.27 1.27 41.20 2.92
175 176 3.573538 CCTCTGACCTCTACATCTGGATG 59.426 52.174 8.81 8.81 44.15 3.51
176 177 3.206412 ACCTCTGACCTCTACATCTGGAT 59.794 47.826 0.00 0.00 0.00 3.41
177 178 2.583101 ACCTCTGACCTCTACATCTGGA 59.417 50.000 0.00 0.00 0.00 3.86
178 179 2.955660 GACCTCTGACCTCTACATCTGG 59.044 54.545 0.00 0.00 0.00 3.86
179 180 3.625853 TGACCTCTGACCTCTACATCTG 58.374 50.000 0.00 0.00 0.00 2.90
180 181 4.079500 TGATGACCTCTGACCTCTACATCT 60.080 45.833 0.00 0.00 35.45 2.90
181 182 4.211125 TGATGACCTCTGACCTCTACATC 58.789 47.826 0.00 0.00 35.13 3.06
182 183 4.256983 TGATGACCTCTGACCTCTACAT 57.743 45.455 0.00 0.00 0.00 2.29
183 184 3.739401 TGATGACCTCTGACCTCTACA 57.261 47.619 0.00 0.00 0.00 2.74
184 185 3.572255 GGATGATGACCTCTGACCTCTAC 59.428 52.174 0.00 0.00 0.00 2.59
185 186 3.465210 AGGATGATGACCTCTGACCTCTA 59.535 47.826 0.00 0.00 31.43 2.43
186 187 2.247111 AGGATGATGACCTCTGACCTCT 59.753 50.000 0.00 0.00 31.43 3.69
187 188 2.676748 AGGATGATGACCTCTGACCTC 58.323 52.381 0.00 0.00 31.43 3.85
188 189 2.864885 AGGATGATGACCTCTGACCT 57.135 50.000 0.00 0.00 31.43 3.85
189 190 3.922171 AAAGGATGATGACCTCTGACC 57.078 47.619 0.00 0.00 36.67 4.02
190 191 6.227298 TCTTAAAGGATGATGACCTCTGAC 57.773 41.667 0.00 0.00 36.67 3.51
191 192 6.874278 TTCTTAAAGGATGATGACCTCTGA 57.126 37.500 0.00 0.00 36.67 3.27
192 193 7.391554 TGTTTTCTTAAAGGATGATGACCTCTG 59.608 37.037 0.00 0.00 36.67 3.35
193 194 7.461749 TGTTTTCTTAAAGGATGATGACCTCT 58.538 34.615 0.00 0.00 36.67 3.69
194 195 7.687941 TGTTTTCTTAAAGGATGATGACCTC 57.312 36.000 0.00 0.00 36.67 3.85
195 196 8.360390 GTTTGTTTTCTTAAAGGATGATGACCT 58.640 33.333 0.00 0.00 39.69 3.85
196 197 8.141268 TGTTTGTTTTCTTAAAGGATGATGACC 58.859 33.333 0.00 0.00 0.00 4.02
197 198 9.528018 TTGTTTGTTTTCTTAAAGGATGATGAC 57.472 29.630 0.00 0.00 0.00 3.06
200 201 9.883142 TGTTTGTTTGTTTTCTTAAAGGATGAT 57.117 25.926 0.00 0.00 0.00 2.45
201 202 9.145865 GTGTTTGTTTGTTTTCTTAAAGGATGA 57.854 29.630 0.00 0.00 0.00 2.92
202 203 8.930760 TGTGTTTGTTTGTTTTCTTAAAGGATG 58.069 29.630 0.00 0.00 0.00 3.51
203 204 9.495572 TTGTGTTTGTTTGTTTTCTTAAAGGAT 57.504 25.926 0.00 0.00 0.00 3.24
204 205 8.766151 GTTGTGTTTGTTTGTTTTCTTAAAGGA 58.234 29.630 0.00 0.00 0.00 3.36
205 206 8.552034 TGTTGTGTTTGTTTGTTTTCTTAAAGG 58.448 29.630 0.00 0.00 0.00 3.11
206 207 9.922305 TTGTTGTGTTTGTTTGTTTTCTTAAAG 57.078 25.926 0.00 0.00 0.00 1.85
211 212 9.429359 TCATATTGTTGTGTTTGTTTGTTTTCT 57.571 25.926 0.00 0.00 0.00 2.52
217 218 8.320295 GTCACTTCATATTGTTGTGTTTGTTTG 58.680 33.333 0.00 0.00 0.00 2.93
233 234 7.554118 GGATTCTTGAATTCCAGTCACTTCATA 59.446 37.037 2.27 0.00 0.00 2.15
293 294 3.096852 CACACATCTACACTCACCCCTA 58.903 50.000 0.00 0.00 0.00 3.53
294 295 1.902508 CACACATCTACACTCACCCCT 59.097 52.381 0.00 0.00 0.00 4.79
295 296 1.623811 ACACACATCTACACTCACCCC 59.376 52.381 0.00 0.00 0.00 4.95
296 297 4.081642 ACATACACACATCTACACTCACCC 60.082 45.833 0.00 0.00 0.00 4.61
297 298 5.073311 ACATACACACATCTACACTCACC 57.927 43.478 0.00 0.00 0.00 4.02
298 299 4.793731 CGACATACACACATCTACACTCAC 59.206 45.833 0.00 0.00 0.00 3.51
299 300 4.457949 ACGACATACACACATCTACACTCA 59.542 41.667 0.00 0.00 0.00 3.41
300 301 4.982999 ACGACATACACACATCTACACTC 58.017 43.478 0.00 0.00 0.00 3.51
301 302 5.386958 AACGACATACACACATCTACACT 57.613 39.130 0.00 0.00 0.00 3.55
302 303 5.631929 TGAAACGACATACACACATCTACAC 59.368 40.000 0.00 0.00 0.00 2.90
303 304 5.774630 TGAAACGACATACACACATCTACA 58.225 37.500 0.00 0.00 0.00 2.74
304 305 6.090783 TCTGAAACGACATACACACATCTAC 58.909 40.000 0.00 0.00 0.00 2.59
365 366 8.857694 TTGGTTATTTCTCGGTAGAAGAAAAT 57.142 30.769 2.75 0.00 42.60 1.82
384 385 7.661027 AGTTTACTATGCGGTTAACTTTGGTTA 59.339 33.333 5.42 0.00 36.19 2.85
388 389 6.238508 CGAGTTTACTATGCGGTTAACTTTG 58.761 40.000 5.42 0.00 38.58 2.77
404 405 8.103924 TCGTATTTCGAATTTTAGCGAGTTTAC 58.896 33.333 0.00 0.00 45.98 2.01
437 438 9.750882 GAAAATAGGACGAAAACAACTATGTAC 57.249 33.333 0.00 0.00 39.40 2.90
447 449 5.581874 TGGATACGGAAAATAGGACGAAAAC 59.418 40.000 0.00 0.00 42.51 2.43
575 578 7.766736 AGACTTTATCAAGGGGGTATTTACT 57.233 36.000 0.00 0.00 33.82 2.24
576 579 8.050930 TCAAGACTTTATCAAGGGGGTATTTAC 58.949 37.037 0.00 0.00 33.82 2.01
577 580 8.050930 GTCAAGACTTTATCAAGGGGGTATTTA 58.949 37.037 0.00 0.00 33.82 1.40
578 581 6.890268 GTCAAGACTTTATCAAGGGGGTATTT 59.110 38.462 0.00 0.00 33.82 1.40
579 582 6.011981 TGTCAAGACTTTATCAAGGGGGTATT 60.012 38.462 1.53 0.00 33.82 1.89
652 660 4.215109 TGAGATGAGATTCATGGGTACGA 58.785 43.478 0.00 0.00 37.20 3.43
696 708 1.694844 TGGATAGTTACGGCGATGGA 58.305 50.000 16.62 0.00 0.00 3.41
725 763 0.607762 TTTCACATGCCGCTAGCCAA 60.608 50.000 9.66 0.00 42.71 4.52
784 822 4.108570 TCCTCCCTTCTATTTAAGTGCCA 58.891 43.478 0.00 0.00 0.00 4.92
910 952 3.143675 GCAAGAAGCATGGACGAGA 57.856 52.632 0.00 0.00 44.79 4.04
945 987 1.506718 CTGACTCGCCGTGCTAAGA 59.493 57.895 0.00 0.00 0.00 2.10
966 1008 0.884704 CGTTACTGCAACCAGCCAGT 60.885 55.000 0.00 0.00 43.02 4.00
1017 1059 2.821688 CGACTCGTAGTCCTCCGCC 61.822 68.421 8.73 0.00 42.12 6.13
1158 1200 0.173481 GCTGCTCCACGTACTCATCA 59.827 55.000 0.00 0.00 0.00 3.07
1159 1201 0.457851 AGCTGCTCCACGTACTCATC 59.542 55.000 0.00 0.00 0.00 2.92
1341 1383 3.390017 CGATCGATGCTCGCACCG 61.390 66.667 10.26 0.00 40.21 4.94
1576 1618 4.666253 GCCCTCTGCACCAAGGCA 62.666 66.667 7.28 0.00 43.32 4.75
1798 1848 2.364317 CGGGAGGAGAAGCAGGGA 60.364 66.667 0.00 0.00 0.00 4.20
2114 2174 0.032813 ACCTTCTCAATGGGGCATGG 60.033 55.000 0.00 0.00 0.00 3.66
2163 2235 8.510243 ACATTACTATGATCAAAGTGATGCAA 57.490 30.769 0.00 0.00 41.14 4.08
2164 2236 8.510243 AACATTACTATGATCAAAGTGATGCA 57.490 30.769 0.00 0.00 41.14 3.96
2165 2237 9.443283 GAAACATTACTATGATCAAAGTGATGC 57.557 33.333 0.00 0.00 41.14 3.91
2381 2459 2.029288 AGCAGTGTCGGCAACATCG 61.029 57.895 0.00 0.00 40.80 3.84
2645 2723 1.576356 CAGCCCTTATCTTCGCTCAC 58.424 55.000 0.00 0.00 0.00 3.51
2651 2729 0.839946 TCAGCCCAGCCCTTATCTTC 59.160 55.000 0.00 0.00 0.00 2.87
2775 2853 1.227102 GGCATCCACCACTATGGCA 59.773 57.895 0.00 0.00 45.31 4.92
2800 2878 2.675767 GCATCTCACCATATGCAACG 57.324 50.000 0.00 0.00 46.19 4.10
2960 3043 6.811253 TGTCACAAACTAATGTAACCCATC 57.189 37.500 0.00 0.00 31.75 3.51
2973 3056 3.490348 CCCAAGGAGATTGTCACAAACT 58.510 45.455 0.00 0.00 37.17 2.66
3055 3139 7.328982 CACATGCACACATACATACACAAAATT 59.671 33.333 0.00 0.00 33.67 1.82
3069 3153 0.828762 AGGCCAACACATGCACACAT 60.829 50.000 5.01 0.00 36.79 3.21
3073 3157 0.604578 ATCAAGGCCAACACATGCAC 59.395 50.000 5.01 0.00 0.00 4.57
3125 3213 0.672342 CTGAAAAACCTGCAGCTGCT 59.328 50.000 36.61 17.15 42.66 4.24
3198 3286 4.121317 GTCTTGGATTCTCATCTCTGCAG 58.879 47.826 7.63 7.63 0.00 4.41
3241 3329 1.251251 AGTGCCATTCAAAGCTGGTC 58.749 50.000 0.00 0.00 34.86 4.02
3255 3343 4.365723 CAATATGGAATCAAGCAAGTGCC 58.634 43.478 0.00 0.00 43.38 5.01
3273 3361 7.350382 TGTTCACTAATAGGGGATTTGCAATA 58.650 34.615 0.00 0.00 0.00 1.90
3279 3367 8.664669 ATTGTTTGTTCACTAATAGGGGATTT 57.335 30.769 0.00 0.00 0.00 2.17
3280 3368 9.762381 TTATTGTTTGTTCACTAATAGGGGATT 57.238 29.630 0.00 0.00 0.00 3.01
3314 3402 4.696402 CCCAGCACAAAACAATGCAATTAT 59.304 37.500 0.00 0.00 44.59 1.28
3315 3403 4.063689 CCCAGCACAAAACAATGCAATTA 58.936 39.130 0.00 0.00 44.59 1.40
3316 3404 2.879646 CCCAGCACAAAACAATGCAATT 59.120 40.909 0.00 0.00 44.59 2.32
3318 3406 1.209019 ACCCAGCACAAAACAATGCAA 59.791 42.857 0.00 0.00 44.59 4.08
3319 3407 0.829333 ACCCAGCACAAAACAATGCA 59.171 45.000 0.00 0.00 44.59 3.96
3321 3409 3.529533 TGAAACCCAGCACAAAACAATG 58.470 40.909 0.00 0.00 0.00 2.82
3322 3410 3.902881 TGAAACCCAGCACAAAACAAT 57.097 38.095 0.00 0.00 0.00 2.71
3323 3411 3.902881 ATGAAACCCAGCACAAAACAA 57.097 38.095 0.00 0.00 0.00 2.83
3324 3412 3.529533 CAATGAAACCCAGCACAAAACA 58.470 40.909 0.00 0.00 0.00 2.83
3326 3414 2.093288 TGCAATGAAACCCAGCACAAAA 60.093 40.909 0.00 0.00 0.00 2.44
3327 3415 1.483827 TGCAATGAAACCCAGCACAAA 59.516 42.857 0.00 0.00 0.00 2.83
3328 3416 1.117994 TGCAATGAAACCCAGCACAA 58.882 45.000 0.00 0.00 0.00 3.33
3329 3417 1.340088 ATGCAATGAAACCCAGCACA 58.660 45.000 0.00 0.00 38.12 4.57
3330 3418 2.460757 AATGCAATGAAACCCAGCAC 57.539 45.000 0.00 0.00 38.12 4.40
3331 3419 4.613925 TTAAATGCAATGAAACCCAGCA 57.386 36.364 0.00 0.00 39.79 4.41
3332 3420 4.142838 GCTTTAAATGCAATGAAACCCAGC 60.143 41.667 0.00 0.00 0.00 4.85
3333 3421 4.996122 TGCTTTAAATGCAATGAAACCCAG 59.004 37.500 9.09 0.00 37.51 4.45
3334 3422 4.965814 TGCTTTAAATGCAATGAAACCCA 58.034 34.783 9.09 0.00 37.51 4.51
3365 5594 8.082242 ACTTACTTTGCAAACCACATAATCTTC 58.918 33.333 8.05 0.00 0.00 2.87
3377 5659 4.034742 TGGACGAGAACTTACTTTGCAAAC 59.965 41.667 8.05 0.00 0.00 2.93
3379 5661 3.558418 GTGGACGAGAACTTACTTTGCAA 59.442 43.478 0.00 0.00 0.00 4.08
3381 5663 3.128349 TGTGGACGAGAACTTACTTTGC 58.872 45.455 0.00 0.00 0.00 3.68
3382 5664 4.988540 TCATGTGGACGAGAACTTACTTTG 59.011 41.667 0.00 0.00 0.00 2.77
3387 5669 4.462834 ACTGATCATGTGGACGAGAACTTA 59.537 41.667 0.00 0.00 0.00 2.24
3395 5677 4.098044 AGGTACTTACTGATCATGTGGACG 59.902 45.833 0.00 0.00 27.25 4.79
3399 5681 6.516718 CCCTTAGGTACTTACTGATCATGTG 58.483 44.000 0.00 0.00 41.75 3.21
3416 5698 5.063880 GGATGCAATGTACTTACCCTTAGG 58.936 45.833 0.00 0.00 40.04 2.69
3417 5699 5.930135 AGGATGCAATGTACTTACCCTTAG 58.070 41.667 0.00 0.00 0.00 2.18
3418 5700 5.968676 AGGATGCAATGTACTTACCCTTA 57.031 39.130 0.00 0.00 0.00 2.69
3419 5701 4.862641 AGGATGCAATGTACTTACCCTT 57.137 40.909 0.00 0.00 0.00 3.95
3420 5702 4.862641 AAGGATGCAATGTACTTACCCT 57.137 40.909 0.00 0.00 0.00 4.34
3421 5703 5.914898 AAAAGGATGCAATGTACTTACCC 57.085 39.130 0.00 0.00 0.00 3.69
3422 5704 6.687604 ACAAAAAGGATGCAATGTACTTACC 58.312 36.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.