Multiple sequence alignment - TraesCS5B01G487400

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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 TraesCS5B01G487400 chr5B 100.000 4294 0 0 1625 5918 658451145 658455438 0.000000e+00 7930.0
1 TraesCS5B01G487400 chr5B 100.000 1111 0 0 1 1111 658449521 658450631 0.000000e+00 2052.0
2 TraesCS5B01G487400 chr5B 93.939 165 6 2 5412 5573 658464889 658465052 4.580000e-61 246.0
3 TraesCS5B01G487400 chr5D 96.003 2352 69 10 1635 3973 522138600 522140939 0.000000e+00 3799.0
4 TraesCS5B01G487400 chr5D 93.317 1242 53 11 3989 5206 522140908 522142143 0.000000e+00 1807.0
5 TraesCS5B01G487400 chr5D 85.748 842 57 26 294 1107 522137218 522138024 0.000000e+00 832.0
6 TraesCS5B01G487400 chr5D 90.909 363 15 3 5567 5918 522143326 522143681 6.940000e-129 472.0
7 TraesCS5B01G487400 chr5D 88.750 80 3 2 5203 5281 522142247 522142321 6.310000e-15 93.5
8 TraesCS5B01G487400 chr5A 96.579 1491 45 5 2485 3973 650270909 650272395 0.000000e+00 2466.0
9 TraesCS5B01G487400 chr5A 91.209 1365 71 17 3989 5309 650272364 650273723 0.000000e+00 1810.0
10 TraesCS5B01G487400 chr5A 97.212 789 22 0 1625 2413 650269926 650270714 0.000000e+00 1336.0
11 TraesCS5B01G487400 chr5A 91.950 323 15 1 5571 5882 650284429 650284751 5.440000e-120 442.0
12 TraesCS5B01G487400 chr5A 87.906 339 36 5 4974 5309 650283501 650283837 1.550000e-105 394.0
13 TraesCS5B01G487400 chr5A 86.769 325 23 9 5571 5879 650274350 650274670 1.580000e-90 344.0
14 TraesCS5B01G487400 chr5A 86.017 236 19 7 884 1111 650269574 650269803 2.130000e-59 241.0
15 TraesCS5B01G487400 chr5A 87.952 166 11 4 5416 5573 650284224 650284388 2.820000e-43 187.0
16 TraesCS5B01G487400 chr5A 86.585 164 11 8 5412 5572 650274151 650274306 2.840000e-38 171.0
17 TraesCS5B01G487400 chr5A 91.919 99 3 3 179 277 650268996 650269089 3.720000e-27 134.0
18 TraesCS5B01G487400 chr7A 74.843 159 31 7 479 634 19554465 19554313 4.950000e-06 63.9
19 TraesCS5B01G487400 chr7A 95.000 40 1 1 595 633 10956137 10956098 1.780000e-05 62.1
20 TraesCS5B01G487400 chr4B 97.297 37 1 0 9 45 384302018 384301982 4.950000e-06 63.9
21 TraesCS5B01G487400 chr4A 94.595 37 0 2 9 45 168780946 168780980 8.290000e-04 56.5


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 TraesCS5B01G487400 chr5B 658449521 658455438 5917 False 4991.000000 7930 100.000000 1 5918 2 chr5B.!!$F2 5917
1 TraesCS5B01G487400 chr5D 522137218 522143681 6463 False 1400.700000 3799 90.945400 294 5918 5 chr5D.!!$F1 5624
2 TraesCS5B01G487400 chr5A 650268996 650274670 5674 False 928.857143 2466 90.898571 179 5879 7 chr5A.!!$F1 5700
3 TraesCS5B01G487400 chr5A 650283501 650284751 1250 False 341.000000 442 89.269333 4974 5882 3 chr5A.!!$F2 908

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
777 831 0.035881 TCAAAGAGACCCTGCAGCTG 59.964 55.000 10.11 10.11 0.00 4.24 F
854 908 0.178990 GGAAGCAACTCACCACCCTT 60.179 55.000 0.00 0.00 0.00 3.95 F
893 967 0.250338 AAGCACCGAGACTTTGGTCC 60.250 55.000 0.00 0.00 43.05 4.46 F
902 976 0.388263 GACTTTGGTCCGTCTCCGTC 60.388 60.000 0.00 0.00 36.53 4.79 F
1032 1119 0.755698 ATCCGCACTCCTACACCGAT 60.756 55.000 0.00 0.00 0.00 4.18 F
1864 1999 1.153939 CTCGCTCCTCCTCAACGTG 60.154 63.158 0.00 0.00 0.00 4.49 F
2266 2401 2.426023 GTGTTCCTCACGCCCACT 59.574 61.111 0.00 0.00 37.31 4.00 F
3948 4226 1.434188 TTGGAGAAGTCCCTTGCTCA 58.566 50.000 0.00 0.00 43.15 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2266 2401 1.002624 GGCGTCCCCTTTGATGACA 60.003 57.895 0.00 0.00 0.00 3.58 R
2465 2600 2.852449 TCTGCCCCCTCAATTAGACAAT 59.148 45.455 0.00 0.00 0.00 2.71 R
2721 2999 2.884012 TGTTGTGAAACCCTGTATGCAG 59.116 45.455 3.45 3.45 37.33 4.41 R
2722 3000 2.937519 TGTTGTGAAACCCTGTATGCA 58.062 42.857 0.00 0.00 34.36 3.96 R
3057 3335 8.978874 ATCTAATACAATCAACAGGCATAACA 57.021 30.769 0.00 0.00 0.00 2.41 R
3482 3760 2.095768 ACATGTCTGATGGCGTTTTTCG 60.096 45.455 0.00 0.00 43.12 3.46 R
4052 4330 0.667184 GTTTTTCATGCTGCCACCCG 60.667 55.000 0.00 0.00 0.00 5.28 R
5343 5954 0.244994 AAGCTAGAGACCAGCACACG 59.755 55.000 0.00 0.00 41.66 4.49 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
47 48 9.589111 TTTTATTTGGTAAGTCAACAAAAGGTC 57.411 29.630 0.00 0.00 37.60 3.85
48 49 8.528044 TTATTTGGTAAGTCAACAAAAGGTCT 57.472 30.769 0.00 0.00 37.60 3.85
49 50 5.828299 TTGGTAAGTCAACAAAAGGTCTG 57.172 39.130 0.00 0.00 0.00 3.51
50 51 5.105567 TGGTAAGTCAACAAAAGGTCTGA 57.894 39.130 0.00 0.00 0.00 3.27
51 52 4.879545 TGGTAAGTCAACAAAAGGTCTGAC 59.120 41.667 0.00 0.00 37.58 3.51
52 53 4.879545 GGTAAGTCAACAAAAGGTCTGACA 59.120 41.667 10.38 0.00 38.69 3.58
53 54 5.007724 GGTAAGTCAACAAAAGGTCTGACAG 59.992 44.000 10.38 0.00 38.69 3.51
54 55 4.222124 AGTCAACAAAAGGTCTGACAGT 57.778 40.909 10.38 0.00 38.69 3.55
55 56 4.589908 AGTCAACAAAAGGTCTGACAGTT 58.410 39.130 10.38 0.00 38.69 3.16
56 57 5.741011 AGTCAACAAAAGGTCTGACAGTTA 58.259 37.500 10.38 0.00 38.69 2.24
57 58 6.177610 AGTCAACAAAAGGTCTGACAGTTAA 58.822 36.000 10.38 0.00 38.69 2.01
58 59 6.316390 AGTCAACAAAAGGTCTGACAGTTAAG 59.684 38.462 10.38 2.70 38.69 1.85
59 60 5.588648 TCAACAAAAGGTCTGACAGTTAAGG 59.411 40.000 10.38 0.22 0.00 2.69
60 61 3.883489 ACAAAAGGTCTGACAGTTAAGGC 59.117 43.478 10.38 0.00 0.00 4.35
61 62 2.457366 AAGGTCTGACAGTTAAGGCG 57.543 50.000 10.38 0.00 0.00 5.52
62 63 1.629043 AGGTCTGACAGTTAAGGCGA 58.371 50.000 10.38 0.00 0.00 5.54
63 64 2.180276 AGGTCTGACAGTTAAGGCGAT 58.820 47.619 10.38 0.00 0.00 4.58
64 65 2.093973 AGGTCTGACAGTTAAGGCGATG 60.094 50.000 10.38 0.00 0.00 3.84
65 66 2.094182 GGTCTGACAGTTAAGGCGATGA 60.094 50.000 10.38 0.00 0.00 2.92
66 67 3.585862 GTCTGACAGTTAAGGCGATGAA 58.414 45.455 2.24 0.00 0.00 2.57
67 68 3.994392 GTCTGACAGTTAAGGCGATGAAA 59.006 43.478 2.24 0.00 0.00 2.69
68 69 4.451096 GTCTGACAGTTAAGGCGATGAAAA 59.549 41.667 2.24 0.00 0.00 2.29
69 70 5.049680 GTCTGACAGTTAAGGCGATGAAAAA 60.050 40.000 2.24 0.00 0.00 1.94
116 117 5.993748 AAAACCCAAAACAAAGAGAGACA 57.006 34.783 0.00 0.00 0.00 3.41
117 118 5.582689 AAACCCAAAACAAAGAGAGACAG 57.417 39.130 0.00 0.00 0.00 3.51
118 119 3.555966 ACCCAAAACAAAGAGAGACAGG 58.444 45.455 0.00 0.00 0.00 4.00
119 120 2.887152 CCCAAAACAAAGAGAGACAGGG 59.113 50.000 0.00 0.00 0.00 4.45
120 121 2.887152 CCAAAACAAAGAGAGACAGGGG 59.113 50.000 0.00 0.00 0.00 4.79
121 122 2.887152 CAAAACAAAGAGAGACAGGGGG 59.113 50.000 0.00 0.00 0.00 5.40
122 123 2.118403 AACAAAGAGAGACAGGGGGA 57.882 50.000 0.00 0.00 0.00 4.81
123 124 2.118403 ACAAAGAGAGACAGGGGGAA 57.882 50.000 0.00 0.00 0.00 3.97
124 125 2.418669 ACAAAGAGAGACAGGGGGAAA 58.581 47.619 0.00 0.00 0.00 3.13
125 126 2.373502 ACAAAGAGAGACAGGGGGAAAG 59.626 50.000 0.00 0.00 0.00 2.62
126 127 2.373502 CAAAGAGAGACAGGGGGAAAGT 59.626 50.000 0.00 0.00 0.00 2.66
127 128 3.562108 AAGAGAGACAGGGGGAAAGTA 57.438 47.619 0.00 0.00 0.00 2.24
128 129 3.786213 AGAGAGACAGGGGGAAAGTAT 57.214 47.619 0.00 0.00 0.00 2.12
129 130 3.379452 AGAGAGACAGGGGGAAAGTATG 58.621 50.000 0.00 0.00 0.00 2.39
130 131 1.840635 AGAGACAGGGGGAAAGTATGC 59.159 52.381 0.00 0.00 0.00 3.14
131 132 1.559682 GAGACAGGGGGAAAGTATGCA 59.440 52.381 0.00 0.00 0.00 3.96
132 133 1.992557 AGACAGGGGGAAAGTATGCAA 59.007 47.619 0.00 0.00 0.00 4.08
133 134 2.025887 AGACAGGGGGAAAGTATGCAAG 60.026 50.000 0.00 0.00 0.00 4.01
134 135 1.005924 ACAGGGGGAAAGTATGCAAGG 59.994 52.381 0.00 0.00 0.00 3.61
135 136 1.284785 CAGGGGGAAAGTATGCAAGGA 59.715 52.381 0.00 0.00 0.00 3.36
136 137 2.091665 CAGGGGGAAAGTATGCAAGGAT 60.092 50.000 0.00 0.00 0.00 3.24
137 138 2.091665 AGGGGGAAAGTATGCAAGGATG 60.092 50.000 0.00 0.00 0.00 3.51
138 139 2.091885 GGGGGAAAGTATGCAAGGATGA 60.092 50.000 0.00 0.00 0.00 2.92
139 140 3.217626 GGGGAAAGTATGCAAGGATGAG 58.782 50.000 0.00 0.00 0.00 2.90
140 141 3.117888 GGGGAAAGTATGCAAGGATGAGA 60.118 47.826 0.00 0.00 0.00 3.27
141 142 4.446889 GGGGAAAGTATGCAAGGATGAGAT 60.447 45.833 0.00 0.00 0.00 2.75
142 143 5.221925 GGGGAAAGTATGCAAGGATGAGATA 60.222 44.000 0.00 0.00 0.00 1.98
143 144 5.936956 GGGAAAGTATGCAAGGATGAGATAG 59.063 44.000 0.00 0.00 0.00 2.08
144 145 6.239714 GGGAAAGTATGCAAGGATGAGATAGA 60.240 42.308 0.00 0.00 0.00 1.98
145 146 6.648725 GGAAAGTATGCAAGGATGAGATAGAC 59.351 42.308 0.00 0.00 0.00 2.59
146 147 5.736951 AGTATGCAAGGATGAGATAGACC 57.263 43.478 0.00 0.00 0.00 3.85
147 148 5.150715 AGTATGCAAGGATGAGATAGACCA 58.849 41.667 0.00 0.00 0.00 4.02
148 149 3.827008 TGCAAGGATGAGATAGACCAC 57.173 47.619 0.00 0.00 0.00 4.16
149 150 3.106827 TGCAAGGATGAGATAGACCACA 58.893 45.455 0.00 0.00 0.00 4.17
150 151 3.713248 TGCAAGGATGAGATAGACCACAT 59.287 43.478 0.00 0.00 0.00 3.21
151 152 4.901250 TGCAAGGATGAGATAGACCACATA 59.099 41.667 0.00 0.00 0.00 2.29
152 153 5.545335 TGCAAGGATGAGATAGACCACATAT 59.455 40.000 0.00 0.00 0.00 1.78
153 154 6.043590 TGCAAGGATGAGATAGACCACATATT 59.956 38.462 0.00 0.00 0.00 1.28
154 155 6.593382 GCAAGGATGAGATAGACCACATATTC 59.407 42.308 0.00 0.00 0.00 1.75
155 156 7.526860 GCAAGGATGAGATAGACCACATATTCT 60.527 40.741 0.00 0.00 0.00 2.40
156 157 8.373981 CAAGGATGAGATAGACCACATATTCTT 58.626 37.037 0.00 0.00 0.00 2.52
157 158 9.607333 AAGGATGAGATAGACCACATATTCTTA 57.393 33.333 0.00 0.00 0.00 2.10
158 159 9.030452 AGGATGAGATAGACCACATATTCTTAC 57.970 37.037 0.00 0.00 0.00 2.34
159 160 8.807118 GGATGAGATAGACCACATATTCTTACA 58.193 37.037 0.00 0.00 0.00 2.41
212 213 5.548406 TCCCTTGCTTTAGTCTACAAAGTC 58.452 41.667 0.00 0.00 35.78 3.01
219 220 1.713297 AGTCTACAAAGTCCACCGGT 58.287 50.000 0.00 0.00 0.00 5.28
234 235 3.282021 CACCGGTTTCATCATCTTCCAT 58.718 45.455 2.97 0.00 0.00 3.41
246 247 5.441718 TCATCTTCCATAAAGCCTTGAGT 57.558 39.130 0.00 0.00 34.76 3.41
247 248 5.819991 TCATCTTCCATAAAGCCTTGAGTT 58.180 37.500 0.00 0.00 34.76 3.01
248 249 6.957631 TCATCTTCCATAAAGCCTTGAGTTA 58.042 36.000 0.00 0.00 34.76 2.24
280 281 9.838975 ATTGGTTTCAAATTCAAAACAAAGAAC 57.161 25.926 14.18 1.29 42.29 3.01
281 282 7.811653 TGGTTTCAAATTCAAAACAAAGAACC 58.188 30.769 14.19 0.00 37.16 3.62
282 283 7.663493 TGGTTTCAAATTCAAAACAAAGAACCT 59.337 29.630 14.19 0.00 37.16 3.50
283 284 8.511321 GGTTTCAAATTCAAAACAAAGAACCTT 58.489 29.630 14.19 0.00 37.16 3.50
284 285 9.328721 GTTTCAAATTCAAAACAAAGAACCTTG 57.671 29.630 9.56 0.00 35.83 3.61
285 286 8.614469 TTCAAATTCAAAACAAAGAACCTTGT 57.386 26.923 0.00 0.00 41.31 3.16
286 287 8.027440 TCAAATTCAAAACAAAGAACCTTGTG 57.973 30.769 0.00 0.00 39.47 3.33
287 288 6.421377 AATTCAAAACAAAGAACCTTGTGC 57.579 33.333 0.00 0.00 39.47 4.57
288 289 3.855858 TCAAAACAAAGAACCTTGTGCC 58.144 40.909 0.00 0.00 39.47 5.01
289 290 3.513515 TCAAAACAAAGAACCTTGTGCCT 59.486 39.130 0.00 0.00 39.47 4.75
290 291 4.707448 TCAAAACAAAGAACCTTGTGCCTA 59.293 37.500 0.00 0.00 39.47 3.93
291 292 5.362430 TCAAAACAAAGAACCTTGTGCCTAT 59.638 36.000 0.00 0.00 39.47 2.57
292 293 5.453567 AAACAAAGAACCTTGTGCCTATC 57.546 39.130 0.00 0.00 39.47 2.08
299 300 2.202878 TTGTGCCTATCGCTCGGC 60.203 61.111 0.00 0.00 46.46 5.54
348 349 5.115480 TCATTCCAAAACCAACAAAAGCTC 58.885 37.500 0.00 0.00 0.00 4.09
353 354 5.186021 TCCAAAACCAACAAAAGCTCAGTAA 59.814 36.000 0.00 0.00 0.00 2.24
366 367 9.654663 CAAAAGCTCAGTAAAGTAGTACCTAAT 57.345 33.333 0.00 0.00 0.00 1.73
423 424 9.290483 CATTCATCATCATTTCTTTCAAGAGTG 57.710 33.333 0.00 0.00 36.22 3.51
448 453 8.852894 TGGTACTATCATATAATACTCCCTCCA 58.147 37.037 0.00 0.00 0.00 3.86
591 627 7.834068 AATACCATGACATATCTAATGACGC 57.166 36.000 0.00 0.00 0.00 5.19
645 682 8.437742 TCTTTTATAAAATTGACGACTTCGGAC 58.562 33.333 10.97 0.00 44.95 4.79
650 687 4.663636 AATTGACGACTTCGGACAAATC 57.336 40.909 14.10 0.00 44.95 2.17
654 691 4.482386 TGACGACTTCGGACAAATCTTAG 58.518 43.478 3.30 0.00 44.95 2.18
655 692 4.022589 TGACGACTTCGGACAAATCTTAGT 60.023 41.667 3.30 0.00 44.95 2.24
656 693 5.181811 TGACGACTTCGGACAAATCTTAGTA 59.818 40.000 3.30 0.00 44.95 1.82
657 694 6.127814 TGACGACTTCGGACAAATCTTAGTAT 60.128 38.462 3.30 0.00 44.95 2.12
658 695 7.066163 TGACGACTTCGGACAAATCTTAGTATA 59.934 37.037 3.30 0.00 44.95 1.47
659 696 7.938715 ACGACTTCGGACAAATCTTAGTATAT 58.061 34.615 3.30 0.00 44.95 0.86
660 697 7.861372 ACGACTTCGGACAAATCTTAGTATATG 59.139 37.037 3.30 0.00 44.95 1.78
679 716 3.842007 TGTGAAGTAAAAGGACCCGAA 57.158 42.857 0.00 0.00 0.00 4.30
701 755 7.130269 CGAAGGAGTACTAAAAGTTTGGTTTG 58.870 38.462 0.00 0.00 33.72 2.93
749 803 5.314923 AGTTGCACCATGATGTCATTAAC 57.685 39.130 0.00 0.00 33.61 2.01
773 827 1.704628 TCCAATCAAAGAGACCCTGCA 59.295 47.619 0.00 0.00 0.00 4.41
774 828 2.089980 CCAATCAAAGAGACCCTGCAG 58.910 52.381 6.78 6.78 0.00 4.41
775 829 1.471684 CAATCAAAGAGACCCTGCAGC 59.528 52.381 8.66 0.00 0.00 5.25
776 830 0.990374 ATCAAAGAGACCCTGCAGCT 59.010 50.000 8.66 0.00 0.00 4.24
777 831 0.035881 TCAAAGAGACCCTGCAGCTG 59.964 55.000 10.11 10.11 0.00 4.24
778 832 1.303155 AAAGAGACCCTGCAGCTGC 60.303 57.895 31.89 31.89 42.50 5.25
848 902 1.079503 GTGATCGGAAGCAACTCACC 58.920 55.000 0.00 0.00 32.08 4.02
849 903 0.684535 TGATCGGAAGCAACTCACCA 59.315 50.000 0.00 0.00 0.00 4.17
850 904 1.079503 GATCGGAAGCAACTCACCAC 58.920 55.000 0.00 0.00 0.00 4.16
851 905 0.321653 ATCGGAAGCAACTCACCACC 60.322 55.000 0.00 0.00 0.00 4.61
852 906 1.966451 CGGAAGCAACTCACCACCC 60.966 63.158 0.00 0.00 0.00 4.61
853 907 1.456287 GGAAGCAACTCACCACCCT 59.544 57.895 0.00 0.00 0.00 4.34
854 908 0.178990 GGAAGCAACTCACCACCCTT 60.179 55.000 0.00 0.00 0.00 3.95
855 909 1.239347 GAAGCAACTCACCACCCTTC 58.761 55.000 0.00 0.00 0.00 3.46
856 910 0.178990 AAGCAACTCACCACCCTTCC 60.179 55.000 0.00 0.00 0.00 3.46
857 911 1.062488 AGCAACTCACCACCCTTCCT 61.062 55.000 0.00 0.00 0.00 3.36
880 954 1.215014 GGTTTCGCAGCAAAAGCACC 61.215 55.000 3.06 0.00 34.93 5.01
889 963 1.334869 AGCAAAAGCACCGAGACTTTG 59.665 47.619 0.00 0.00 36.28 2.77
892 966 1.594331 AAAGCACCGAGACTTTGGTC 58.406 50.000 0.00 0.00 39.19 4.02
893 967 0.250338 AAGCACCGAGACTTTGGTCC 60.250 55.000 0.00 0.00 43.05 4.46
894 968 2.027625 GCACCGAGACTTTGGTCCG 61.028 63.158 0.00 0.00 43.05 4.79
895 969 1.366366 CACCGAGACTTTGGTCCGT 59.634 57.895 0.00 0.00 43.05 4.69
896 970 0.666577 CACCGAGACTTTGGTCCGTC 60.667 60.000 0.00 0.00 43.05 4.79
902 976 0.388263 GACTTTGGTCCGTCTCCGTC 60.388 60.000 0.00 0.00 36.53 4.79
1032 1119 0.755698 ATCCGCACTCCTACACCGAT 60.756 55.000 0.00 0.00 0.00 4.18
1864 1999 1.153939 CTCGCTCCTCCTCAACGTG 60.154 63.158 0.00 0.00 0.00 4.49
2266 2401 2.426023 GTGTTCCTCACGCCCACT 59.574 61.111 0.00 0.00 37.31 4.00
2356 2491 3.966665 ACCTCATCACCAACAAAACCAAT 59.033 39.130 0.00 0.00 0.00 3.16
2382 2517 4.565652 GGACTTCTGGCTAAATGAGGTGAA 60.566 45.833 0.00 0.00 0.00 3.18
2465 2600 6.939132 TCGAATTTACCAAAACACCTGTTA 57.061 33.333 0.00 0.00 37.25 2.41
2604 2882 4.021102 AGTTGGAATCTCAATCAACCGT 57.979 40.909 0.00 0.00 39.98 4.83
2638 2916 7.864108 TTATTCAACCAGGACTCATTGTATG 57.136 36.000 0.00 0.00 0.00 2.39
2647 2925 5.923114 CAGGACTCATTGTATGGTAGATTCG 59.077 44.000 0.00 0.00 0.00 3.34
2705 2983 6.524734 TCACACATTCAACTAGAACTGTCAT 58.475 36.000 0.00 0.00 39.49 3.06
2716 2994 9.469807 CAACTAGAACTGTCATGGTAATATCTC 57.530 37.037 0.00 0.00 0.00 2.75
2721 2999 9.606631 AGAACTGTCATGGTAATATCTCTTTTC 57.393 33.333 0.00 0.00 0.00 2.29
2722 3000 9.606631 GAACTGTCATGGTAATATCTCTTTTCT 57.393 33.333 0.00 0.00 0.00 2.52
3057 3335 4.643334 TGACTAACTGTGACTGTGTACTGT 59.357 41.667 0.00 0.00 0.00 3.55
3201 3479 5.663456 CCAATGTACCTGGGATTGAAAATG 58.337 41.667 13.78 0.00 30.03 2.32
3386 3664 6.014925 GGGAGCTTTACTTGGAAAATTTACCA 60.015 38.462 0.00 0.00 0.00 3.25
3441 3719 7.701539 ATTGGCAATACTCTGTTTTGATACA 57.298 32.000 11.81 0.00 28.57 2.29
3454 3732 7.665145 TCTGTTTTGATACATCATCCAGTTTCA 59.335 33.333 10.52 0.00 36.56 2.69
3503 3781 2.095768 CGAAAAACGCCATCAGACATGT 60.096 45.455 0.00 0.00 34.51 3.21
3561 3839 4.601019 AGTCAGTTGTTGAAGCATTTTCG 58.399 39.130 0.00 0.00 37.61 3.46
3621 3899 7.497249 CCAGTTAGAATAGATTGTTCCTCCTTG 59.503 40.741 0.00 0.00 0.00 3.61
3624 3902 5.039645 AGAATAGATTGTTCCTCCTTGGGA 58.960 41.667 0.00 0.00 36.20 4.37
3650 3928 7.633789 ACCAGAGATAACCTATTTGTTGTCAT 58.366 34.615 0.00 0.00 38.41 3.06
3860 4138 9.454859 AGAACCAGATTCTCCTTATAAGTTTTG 57.545 33.333 11.50 0.00 44.99 2.44
3943 4221 2.643304 GGGTACTTTGGAGAAGTCCCTT 59.357 50.000 14.09 0.00 43.15 3.95
3944 4222 3.559384 GGGTACTTTGGAGAAGTCCCTTG 60.559 52.174 14.09 0.00 43.15 3.61
3945 4223 2.278332 ACTTTGGAGAAGTCCCTTGC 57.722 50.000 0.00 0.00 43.15 4.01
3946 4224 1.777272 ACTTTGGAGAAGTCCCTTGCT 59.223 47.619 0.00 0.00 43.15 3.91
3947 4225 2.224646 ACTTTGGAGAAGTCCCTTGCTC 60.225 50.000 0.00 0.00 43.15 4.26
3948 4226 1.434188 TTGGAGAAGTCCCTTGCTCA 58.566 50.000 0.00 0.00 43.15 4.26
3949 4227 1.661463 TGGAGAAGTCCCTTGCTCAT 58.339 50.000 0.00 0.00 43.15 2.90
3950 4228 1.556911 TGGAGAAGTCCCTTGCTCATC 59.443 52.381 0.00 0.00 43.15 2.92
3951 4229 1.556911 GGAGAAGTCCCTTGCTCATCA 59.443 52.381 0.00 0.00 36.76 3.07
3952 4230 2.172293 GGAGAAGTCCCTTGCTCATCAT 59.828 50.000 0.00 0.00 36.76 2.45
3953 4231 3.389329 GGAGAAGTCCCTTGCTCATCATA 59.611 47.826 0.00 0.00 36.76 2.15
3954 4232 4.041444 GGAGAAGTCCCTTGCTCATCATAT 59.959 45.833 0.00 0.00 36.76 1.78
3955 4233 5.247110 GGAGAAGTCCCTTGCTCATCATATA 59.753 44.000 0.00 0.00 36.76 0.86
3956 4234 6.070309 GGAGAAGTCCCTTGCTCATCATATAT 60.070 42.308 0.00 0.00 36.76 0.86
3957 4235 7.124901 GGAGAAGTCCCTTGCTCATCATATATA 59.875 40.741 0.00 0.00 36.76 0.86
3958 4236 8.621126 AGAAGTCCCTTGCTCATCATATATAT 57.379 34.615 0.00 0.00 0.00 0.86
3959 4237 9.720874 AGAAGTCCCTTGCTCATCATATATATA 57.279 33.333 0.00 0.00 0.00 0.86
4161 4440 5.003804 AGGTTGCGTCAATTAATTGAGACT 58.996 37.500 27.26 16.63 46.44 3.24
4214 4493 6.318648 TGATACTGAAGCAGTTGTTTCAAGTT 59.681 34.615 11.61 3.67 42.59 2.66
4229 4508 3.087031 TCAAGTTACGGAGGGAGTAGTG 58.913 50.000 0.00 0.00 0.00 2.74
4541 4859 2.166270 GACAAGAGCTTGGCTTCCG 58.834 57.895 14.14 0.00 44.96 4.30
4612 4931 5.650543 ACTGATTTTTATCGCCATTTGTCC 58.349 37.500 0.00 0.00 0.00 4.02
4706 5025 0.105964 TTCCTCCAGCTAGCGATCCT 60.106 55.000 9.55 0.00 0.00 3.24
4710 5029 0.395724 TCCAGCTAGCGATCCTCACA 60.396 55.000 9.55 0.00 0.00 3.58
4776 5095 3.013648 AGGTGGGAAGGATGAAGTACCTA 59.986 47.826 0.00 0.00 35.66 3.08
4797 5116 2.492090 CCGCTCTACAGCTCGCTT 59.508 61.111 0.00 0.00 44.40 4.68
4863 5182 0.836400 TCTCGGAGGCCCAAGAGTTT 60.836 55.000 15.70 0.00 32.90 2.66
4941 5260 4.211125 TGAGTTGAAGCCACATTTTACCA 58.789 39.130 0.00 0.00 0.00 3.25
5010 5330 4.335315 TCGCTCATTTCTTCCGCATAAAAT 59.665 37.500 0.00 0.00 0.00 1.82
5038 5358 1.908340 CTCCTGGAGCTGACCTTGGG 61.908 65.000 11.42 0.00 0.00 4.12
5044 5366 1.272147 GGAGCTGACCTTGGGTGAAAT 60.272 52.381 0.00 0.00 35.25 2.17
5082 5404 3.061295 GTGATGTGTTATGTGAGACTGCG 59.939 47.826 0.00 0.00 0.00 5.18
5159 5481 4.067896 CAATATCCTGTGGTGATACTGCC 58.932 47.826 0.00 0.00 0.00 4.85
5162 5484 1.915489 TCCTGTGGTGATACTGCCATT 59.085 47.619 0.00 0.00 37.09 3.16
5163 5485 2.019249 CCTGTGGTGATACTGCCATTG 58.981 52.381 0.00 0.00 37.09 2.82
5172 5494 5.294552 GGTGATACTGCCATTGTCTCTTAAC 59.705 44.000 0.00 0.00 0.00 2.01
5192 5514 3.883441 CGGTCATCGTCTTTTAACTCG 57.117 47.619 0.00 0.00 0.00 4.18
5206 5633 9.095065 GTCTTTTAACTCGAATCTGGCTTATAA 57.905 33.333 0.00 0.00 0.00 0.98
5239 5669 1.167851 GTGCCTGTGCTTTGCTATGA 58.832 50.000 0.00 0.00 38.71 2.15
5246 5681 4.397103 CCTGTGCTTTGCTATGAAATGAGA 59.603 41.667 0.00 0.00 0.00 3.27
5306 5917 1.480954 TCTTGATGCGGTTCTAGGGAC 59.519 52.381 0.00 0.00 0.00 4.46
5311 5922 2.901042 CGGTTCTAGGGACTGGGC 59.099 66.667 0.00 0.00 41.52 5.36
5323 5934 1.689273 GGACTGGGCGAGAAGATATGT 59.311 52.381 2.65 0.00 0.00 2.29
5335 5946 5.106277 CGAGAAGATATGTCAGCCGGTTATA 60.106 44.000 1.90 0.00 0.00 0.98
5343 5954 2.032924 GTCAGCCGGTTATACAAATGGC 59.967 50.000 1.90 0.00 42.76 4.40
5344 5955 1.002900 CAGCCGGTTATACAAATGGCG 60.003 52.381 1.90 0.00 46.85 5.69
5346 5957 1.268335 GCCGGTTATACAAATGGCGTG 60.268 52.381 1.90 0.00 32.14 5.34
5349 5960 2.789779 CGGTTATACAAATGGCGTGTGC 60.790 50.000 0.00 0.00 41.71 4.57
5350 5961 2.422127 GGTTATACAAATGGCGTGTGCT 59.578 45.455 0.00 0.00 42.25 4.40
5351 5962 3.425404 GTTATACAAATGGCGTGTGCTG 58.575 45.455 0.00 0.00 42.25 4.41
5353 5964 0.536233 TACAAATGGCGTGTGCTGGT 60.536 50.000 0.00 0.00 42.25 4.00
5354 5965 1.081242 CAAATGGCGTGTGCTGGTC 60.081 57.895 0.00 0.00 42.25 4.02
5355 5966 1.228245 AAATGGCGTGTGCTGGTCT 60.228 52.632 0.00 0.00 42.25 3.85
5356 5967 1.237285 AAATGGCGTGTGCTGGTCTC 61.237 55.000 0.00 0.00 42.25 3.36
5380 6180 2.224079 GCTTATTGCGCTGCTTGCTATA 59.776 45.455 9.73 0.00 40.11 1.31
5386 6186 1.334419 GCGCTGCTTGCTATACAATGG 60.334 52.381 0.00 0.00 37.72 3.16
5413 6218 5.477637 TGAATGGTCTGAAAATGCTTGATGA 59.522 36.000 0.00 0.00 0.00 2.92
5414 6219 4.771590 TGGTCTGAAAATGCTTGATGAC 57.228 40.909 0.00 0.00 0.00 3.06
5450 6643 4.380841 AGCATGCTGACCACAATAAATG 57.619 40.909 21.98 0.00 0.00 2.32
5515 6834 4.012374 CCTTATGACAGGCAGTTTGTGAT 58.988 43.478 0.00 0.00 0.00 3.06
5560 6886 7.665559 TGTTCCCAAGATAATAACTGCCATATC 59.334 37.037 0.00 0.00 0.00 1.63
5593 7014 4.377760 TTCCTCGCCTCCTCCCGT 62.378 66.667 0.00 0.00 0.00 5.28
5699 7131 2.956987 GCGATGCAGCCAAACAGT 59.043 55.556 0.00 0.00 0.00 3.55
5722 7154 1.415659 CTGAGGCCCTCTCCTGTAATG 59.584 57.143 12.94 0.00 41.76 1.90
5816 7252 7.181569 ACAGTTTGTTGGGGAATAATTATGG 57.818 36.000 0.00 0.00 0.00 2.74
5855 7291 4.341366 AGAGGTTGAAAATGGCAAAAGG 57.659 40.909 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.589111 GACCTTTTGTTGACTTACCAAATAAAA 57.411 29.630 0.00 0.00 0.00 1.52
22 23 8.973182 AGACCTTTTGTTGACTTACCAAATAAA 58.027 29.630 0.00 0.00 0.00 1.40
23 24 8.410141 CAGACCTTTTGTTGACTTACCAAATAA 58.590 33.333 0.00 0.00 0.00 1.40
24 25 7.776030 TCAGACCTTTTGTTGACTTACCAAATA 59.224 33.333 0.00 0.00 0.00 1.40
25 26 6.605594 TCAGACCTTTTGTTGACTTACCAAAT 59.394 34.615 0.00 0.00 0.00 2.32
26 27 5.946972 TCAGACCTTTTGTTGACTTACCAAA 59.053 36.000 0.00 0.00 0.00 3.28
27 28 5.355910 GTCAGACCTTTTGTTGACTTACCAA 59.644 40.000 0.00 0.00 37.53 3.67
28 29 4.879545 GTCAGACCTTTTGTTGACTTACCA 59.120 41.667 0.00 0.00 37.53 3.25
29 30 4.879545 TGTCAGACCTTTTGTTGACTTACC 59.120 41.667 0.00 0.00 40.36 2.85
30 31 5.585047 ACTGTCAGACCTTTTGTTGACTTAC 59.415 40.000 6.91 0.00 40.36 2.34
31 32 5.741011 ACTGTCAGACCTTTTGTTGACTTA 58.259 37.500 6.91 0.00 40.36 2.24
32 33 4.589908 ACTGTCAGACCTTTTGTTGACTT 58.410 39.130 6.91 0.00 40.36 3.01
33 34 4.222124 ACTGTCAGACCTTTTGTTGACT 57.778 40.909 6.91 0.00 40.36 3.41
34 35 4.965119 AACTGTCAGACCTTTTGTTGAC 57.035 40.909 6.91 0.00 40.17 3.18
35 36 5.588648 CCTTAACTGTCAGACCTTTTGTTGA 59.411 40.000 6.91 0.00 0.00 3.18
36 37 5.733373 GCCTTAACTGTCAGACCTTTTGTTG 60.733 44.000 6.91 0.00 0.00 3.33
37 38 4.338400 GCCTTAACTGTCAGACCTTTTGTT 59.662 41.667 6.91 0.00 0.00 2.83
38 39 3.883489 GCCTTAACTGTCAGACCTTTTGT 59.117 43.478 6.91 0.00 0.00 2.83
39 40 3.058914 CGCCTTAACTGTCAGACCTTTTG 60.059 47.826 6.91 0.00 0.00 2.44
40 41 3.139077 CGCCTTAACTGTCAGACCTTTT 58.861 45.455 6.91 0.00 0.00 2.27
41 42 2.367567 TCGCCTTAACTGTCAGACCTTT 59.632 45.455 6.91 0.00 0.00 3.11
42 43 1.968493 TCGCCTTAACTGTCAGACCTT 59.032 47.619 6.91 0.00 0.00 3.50
43 44 1.629043 TCGCCTTAACTGTCAGACCT 58.371 50.000 6.91 0.00 0.00 3.85
44 45 2.094182 TCATCGCCTTAACTGTCAGACC 60.094 50.000 6.91 0.00 0.00 3.85
45 46 3.232213 TCATCGCCTTAACTGTCAGAC 57.768 47.619 6.91 0.00 0.00 3.51
46 47 3.953712 TTCATCGCCTTAACTGTCAGA 57.046 42.857 6.91 0.00 0.00 3.27
47 48 5.356882 TTTTTCATCGCCTTAACTGTCAG 57.643 39.130 0.00 0.00 0.00 3.51
93 94 6.353404 TGTCTCTCTTTGTTTTGGGTTTTT 57.647 33.333 0.00 0.00 0.00 1.94
94 95 5.105351 CCTGTCTCTCTTTGTTTTGGGTTTT 60.105 40.000 0.00 0.00 0.00 2.43
95 96 4.402474 CCTGTCTCTCTTTGTTTTGGGTTT 59.598 41.667 0.00 0.00 0.00 3.27
96 97 3.954258 CCTGTCTCTCTTTGTTTTGGGTT 59.046 43.478 0.00 0.00 0.00 4.11
97 98 3.555966 CCTGTCTCTCTTTGTTTTGGGT 58.444 45.455 0.00 0.00 0.00 4.51
98 99 2.887152 CCCTGTCTCTCTTTGTTTTGGG 59.113 50.000 0.00 0.00 0.00 4.12
99 100 2.887152 CCCCTGTCTCTCTTTGTTTTGG 59.113 50.000 0.00 0.00 0.00 3.28
100 101 2.887152 CCCCCTGTCTCTCTTTGTTTTG 59.113 50.000 0.00 0.00 0.00 2.44
101 102 2.783510 TCCCCCTGTCTCTCTTTGTTTT 59.216 45.455 0.00 0.00 0.00 2.43
102 103 2.418669 TCCCCCTGTCTCTCTTTGTTT 58.581 47.619 0.00 0.00 0.00 2.83
103 104 2.118403 TCCCCCTGTCTCTCTTTGTT 57.882 50.000 0.00 0.00 0.00 2.83
104 105 2.118403 TTCCCCCTGTCTCTCTTTGT 57.882 50.000 0.00 0.00 0.00 2.83
105 106 2.373502 ACTTTCCCCCTGTCTCTCTTTG 59.626 50.000 0.00 0.00 0.00 2.77
106 107 2.707554 ACTTTCCCCCTGTCTCTCTTT 58.292 47.619 0.00 0.00 0.00 2.52
107 108 2.424684 ACTTTCCCCCTGTCTCTCTT 57.575 50.000 0.00 0.00 0.00 2.85
108 109 3.379452 CATACTTTCCCCCTGTCTCTCT 58.621 50.000 0.00 0.00 0.00 3.10
109 110 2.158885 GCATACTTTCCCCCTGTCTCTC 60.159 54.545 0.00 0.00 0.00 3.20
110 111 1.840635 GCATACTTTCCCCCTGTCTCT 59.159 52.381 0.00 0.00 0.00 3.10
111 112 1.559682 TGCATACTTTCCCCCTGTCTC 59.440 52.381 0.00 0.00 0.00 3.36
112 113 1.668826 TGCATACTTTCCCCCTGTCT 58.331 50.000 0.00 0.00 0.00 3.41
113 114 2.369394 CTTGCATACTTTCCCCCTGTC 58.631 52.381 0.00 0.00 0.00 3.51
114 115 1.005924 CCTTGCATACTTTCCCCCTGT 59.994 52.381 0.00 0.00 0.00 4.00
115 116 1.284785 TCCTTGCATACTTTCCCCCTG 59.715 52.381 0.00 0.00 0.00 4.45
116 117 1.681229 TCCTTGCATACTTTCCCCCT 58.319 50.000 0.00 0.00 0.00 4.79
117 118 2.091885 TCATCCTTGCATACTTTCCCCC 60.092 50.000 0.00 0.00 0.00 5.40
118 119 3.117888 TCTCATCCTTGCATACTTTCCCC 60.118 47.826 0.00 0.00 0.00 4.81
119 120 4.156455 TCTCATCCTTGCATACTTTCCC 57.844 45.455 0.00 0.00 0.00 3.97
120 121 6.648725 GTCTATCTCATCCTTGCATACTTTCC 59.351 42.308 0.00 0.00 0.00 3.13
121 122 6.648725 GGTCTATCTCATCCTTGCATACTTTC 59.351 42.308 0.00 0.00 0.00 2.62
122 123 6.100279 TGGTCTATCTCATCCTTGCATACTTT 59.900 38.462 0.00 0.00 0.00 2.66
123 124 5.604231 TGGTCTATCTCATCCTTGCATACTT 59.396 40.000 0.00 0.00 0.00 2.24
124 125 5.011533 GTGGTCTATCTCATCCTTGCATACT 59.988 44.000 0.00 0.00 0.00 2.12
125 126 5.221521 TGTGGTCTATCTCATCCTTGCATAC 60.222 44.000 0.00 0.00 0.00 2.39
126 127 4.901250 TGTGGTCTATCTCATCCTTGCATA 59.099 41.667 0.00 0.00 0.00 3.14
127 128 3.713248 TGTGGTCTATCTCATCCTTGCAT 59.287 43.478 0.00 0.00 0.00 3.96
128 129 3.106827 TGTGGTCTATCTCATCCTTGCA 58.893 45.455 0.00 0.00 0.00 4.08
129 130 3.827008 TGTGGTCTATCTCATCCTTGC 57.173 47.619 0.00 0.00 0.00 4.01
130 131 7.905265 AGAATATGTGGTCTATCTCATCCTTG 58.095 38.462 0.00 0.00 0.00 3.61
131 132 8.503428 AAGAATATGTGGTCTATCTCATCCTT 57.497 34.615 0.00 0.00 0.00 3.36
132 133 9.030452 GTAAGAATATGTGGTCTATCTCATCCT 57.970 37.037 0.00 0.00 0.00 3.24
133 134 8.807118 TGTAAGAATATGTGGTCTATCTCATCC 58.193 37.037 0.00 0.00 0.00 3.51
185 186 7.854710 ACTTTGTAGACTAAAGCAAGGGAACTT 60.855 37.037 0.00 0.00 43.37 2.66
186 187 6.409349 ACTTTGTAGACTAAAGCAAGGGAACT 60.409 38.462 0.00 0.00 39.53 3.01
187 188 5.763698 ACTTTGTAGACTAAAGCAAGGGAAC 59.236 40.000 0.00 0.00 38.41 3.62
212 213 2.017049 GGAAGATGATGAAACCGGTGG 58.983 52.381 8.52 0.00 0.00 4.61
219 220 6.891361 TCAAGGCTTTATGGAAGATGATGAAA 59.109 34.615 0.00 0.00 37.57 2.69
316 317 6.887368 GTTGGTTTTGGAATGATTAAGCAAC 58.113 36.000 14.02 14.02 44.53 4.17
366 367 7.695480 TGGCTGCAACTTGTTTAAGATAATA 57.305 32.000 0.50 0.00 37.36 0.98
423 424 9.357161 CTGGAGGGAGTATTATATGATAGTACC 57.643 40.741 13.56 13.56 36.53 3.34
448 453 6.591935 TCTTATATGCGGAATGAAAAGGTCT 58.408 36.000 0.00 0.00 0.00 3.85
589 625 6.958752 TCAACATTTACAATACGAAATCAGCG 59.041 34.615 0.00 0.00 0.00 5.18
590 626 8.841444 ATCAACATTTACAATACGAAATCAGC 57.159 30.769 0.00 0.00 0.00 4.26
633 670 4.483311 ACTAAGATTTGTCCGAAGTCGTC 58.517 43.478 0.00 0.00 37.74 4.20
634 671 4.516365 ACTAAGATTTGTCCGAAGTCGT 57.484 40.909 0.00 0.00 37.74 4.34
635 672 7.861372 ACATATACTAAGATTTGTCCGAAGTCG 59.139 37.037 0.00 0.00 39.44 4.18
650 687 9.543783 GGGTCCTTTTACTTCACATATACTAAG 57.456 37.037 0.00 0.00 0.00 2.18
654 691 6.576185 TCGGGTCCTTTTACTTCACATATAC 58.424 40.000 0.00 0.00 0.00 1.47
655 692 6.795144 TCGGGTCCTTTTACTTCACATATA 57.205 37.500 0.00 0.00 0.00 0.86
656 693 5.687166 TCGGGTCCTTTTACTTCACATAT 57.313 39.130 0.00 0.00 0.00 1.78
657 694 5.484715 CTTCGGGTCCTTTTACTTCACATA 58.515 41.667 0.00 0.00 0.00 2.29
658 695 4.324267 CTTCGGGTCCTTTTACTTCACAT 58.676 43.478 0.00 0.00 0.00 3.21
659 696 3.495453 CCTTCGGGTCCTTTTACTTCACA 60.495 47.826 0.00 0.00 0.00 3.58
660 697 3.072211 CCTTCGGGTCCTTTTACTTCAC 58.928 50.000 0.00 0.00 0.00 3.18
679 716 5.889289 TGCAAACCAAACTTTTAGTACTCCT 59.111 36.000 0.00 0.00 0.00 3.69
701 755 2.352715 GGTGTAGGAAATTGCAGGTTGC 60.353 50.000 0.00 0.00 45.29 4.17
709 763 2.159382 ACTTGCCGGTGTAGGAAATTG 58.841 47.619 1.90 0.00 0.00 2.32
749 803 3.698040 CAGGGTCTCTTTGATTGGAATGG 59.302 47.826 0.00 0.00 0.00 3.16
777 831 0.681175 AAAGATGGGGTGCAACTTGC 59.319 50.000 0.00 6.82 45.29 4.01
778 832 2.548493 CCAAAAGATGGGGTGCAACTTG 60.548 50.000 0.00 0.00 46.27 3.16
856 910 1.791103 TTTTGCTGCGAAACCGGGAG 61.791 55.000 10.93 0.00 0.00 4.30
857 911 1.791103 CTTTTGCTGCGAAACCGGGA 61.791 55.000 10.93 0.00 0.00 5.14
916 990 2.757077 GGGGTTGGGTCTGGTCTG 59.243 66.667 0.00 0.00 0.00 3.51
917 991 2.928396 CGGGGTTGGGTCTGGTCT 60.928 66.667 0.00 0.00 0.00 3.85
952 1035 1.850755 GACTGGGGAGGGTTTGGGA 60.851 63.158 0.00 0.00 0.00 4.37
1831 1966 2.202743 GAGTAGGTGATGCGCGCA 60.203 61.111 38.27 38.27 0.00 6.09
2127 2262 2.758327 CCATGTCCTCGACCCCGA 60.758 66.667 0.00 0.00 43.35 5.14
2266 2401 1.002624 GGCGTCCCCTTTGATGACA 60.003 57.895 0.00 0.00 0.00 3.58
2356 2491 3.198635 CCTCATTTAGCCAGAAGTCCTCA 59.801 47.826 0.00 0.00 0.00 3.86
2382 2517 3.290710 AGCACACATGAGGACAAAAAGT 58.709 40.909 0.00 0.00 0.00 2.66
2416 2551 9.504708 AATTCCATTTGCACATAAGATCAAAAA 57.495 25.926 0.00 0.00 32.97 1.94
2417 2552 9.153721 GAATTCCATTTGCACATAAGATCAAAA 57.846 29.630 0.00 0.00 32.97 2.44
2418 2553 7.488792 CGAATTCCATTTGCACATAAGATCAAA 59.511 33.333 0.00 0.00 33.64 2.69
2419 2554 6.974048 CGAATTCCATTTGCACATAAGATCAA 59.026 34.615 0.00 0.00 0.00 2.57
2420 2555 6.318396 TCGAATTCCATTTGCACATAAGATCA 59.682 34.615 0.00 0.00 0.00 2.92
2421 2556 6.728200 TCGAATTCCATTTGCACATAAGATC 58.272 36.000 0.00 0.00 0.00 2.75
2465 2600 2.852449 TCTGCCCCCTCAATTAGACAAT 59.148 45.455 0.00 0.00 0.00 2.71
2602 2880 7.325097 GTCCTGGTTGAATAAAATTGTAACACG 59.675 37.037 0.00 0.00 0.00 4.49
2604 2882 8.472007 AGTCCTGGTTGAATAAAATTGTAACA 57.528 30.769 0.00 0.00 0.00 2.41
2705 2983 7.933577 CCTGTATGCAGAAAAGAGATATTACCA 59.066 37.037 12.93 0.00 45.28 3.25
2716 2994 4.278170 TGTGAAACCCTGTATGCAGAAAAG 59.722 41.667 12.93 0.86 39.95 2.27
2719 2997 3.500448 TGTGAAACCCTGTATGCAGAA 57.500 42.857 12.93 0.00 39.95 3.02
2720 2998 3.146066 GTTGTGAAACCCTGTATGCAGA 58.854 45.455 12.93 0.00 39.95 4.26
2721 2999 2.884012 TGTTGTGAAACCCTGTATGCAG 59.116 45.455 3.45 3.45 37.33 4.41
2722 3000 2.937519 TGTTGTGAAACCCTGTATGCA 58.062 42.857 0.00 0.00 34.36 3.96
3057 3335 8.978874 ATCTAATACAATCAACAGGCATAACA 57.021 30.769 0.00 0.00 0.00 2.41
3386 3664 3.504906 CCTGTGATGCTTCAACATCTGTT 59.495 43.478 3.51 0.00 45.51 3.16
3441 3719 9.995003 GAGATAGACTATTTGAAACTGGATGAT 57.005 33.333 0.00 0.00 0.00 2.45
3482 3760 2.095768 ACATGTCTGATGGCGTTTTTCG 60.096 45.455 0.00 0.00 43.12 3.46
3621 3899 6.002653 ACAAATAGGTTATCTCTGGTTCCC 57.997 41.667 0.00 0.00 0.00 3.97
3624 3902 7.458397 TGACAACAAATAGGTTATCTCTGGTT 58.542 34.615 0.00 0.00 0.00 3.67
3772 4050 7.816640 TGCTTCTTCCACTAATTTCAATGTAC 58.183 34.615 0.00 0.00 0.00 2.90
3853 4131 7.381789 ACCCAACCCATTATAAACAAAACTT 57.618 32.000 0.00 0.00 0.00 2.66
3860 4138 6.888088 ACAAGTCTACCCAACCCATTATAAAC 59.112 38.462 0.00 0.00 0.00 2.01
4033 4311 7.149973 CCACCCGACGATTCTATAATAGAAAA 58.850 38.462 0.00 0.00 46.81 2.29
4052 4330 0.667184 GTTTTTCATGCTGCCACCCG 60.667 55.000 0.00 0.00 0.00 5.28
4161 4440 7.510675 AATTGAGAAACTATTACTCCCTCCA 57.489 36.000 0.00 0.00 0.00 3.86
4214 4493 3.350833 GAACTTCACTACTCCCTCCGTA 58.649 50.000 0.00 0.00 0.00 4.02
4229 4508 3.704800 AGCTAAAGAGGGTGGAACTTC 57.295 47.619 0.00 0.00 36.74 3.01
4450 4763 7.609760 TGCAGTAACTGAAAACCACATATAG 57.390 36.000 0.00 0.00 32.44 1.31
4520 4838 1.609208 GAAGCCAAGCTCTTGTCCAA 58.391 50.000 8.60 0.00 38.25 3.53
4579 4897 9.997482 TGGCGATAAAAATCAGTTAATCTTAAC 57.003 29.630 4.95 4.95 42.50 2.01
4612 4931 5.606348 AGAGCAGTAACCTGGATAGAAAG 57.394 43.478 0.00 0.00 39.22 2.62
4706 5025 0.250295 GTAACACCTGCAGCCTGTGA 60.250 55.000 23.18 11.12 34.18 3.58
4710 5029 0.764890 TGAAGTAACACCTGCAGCCT 59.235 50.000 8.66 0.00 0.00 4.58
4809 5128 1.753368 GCATCTTCTCCTCCTCCCCG 61.753 65.000 0.00 0.00 0.00 5.73
4863 5182 2.799452 GCGGGCTATCGGGTGGTAA 61.799 63.158 0.00 0.00 0.00 2.85
4902 5221 3.341823 ACTCAACTAGCCATGCTTCAAG 58.658 45.455 0.00 0.00 40.44 3.02
4941 5260 5.022787 AGATGTTCTCTCTACTTCAGGCTT 58.977 41.667 0.00 0.00 0.00 4.35
5010 5330 3.957497 GTCAGCTCCAGGAGAGAGATAAA 59.043 47.826 21.89 0.00 46.50 1.40
5038 5358 4.515567 ACGGAAGGAAGTTCAGAATTTCAC 59.484 41.667 17.55 8.92 36.82 3.18
5044 5366 3.071023 ACATCACGGAAGGAAGTTCAGAA 59.929 43.478 5.01 0.00 36.82 3.02
5082 5404 4.634443 AGGGTCAGAATAAATTACGCACAC 59.366 41.667 0.00 0.00 0.00 3.82
5123 5445 4.999950 CAGGATATTGTTATCAGGAGGCAC 59.000 45.833 0.00 0.00 36.68 5.01
5159 5481 4.761910 CGATGACCGTTAAGAGACAATG 57.238 45.455 0.00 0.00 0.00 2.82
5172 5494 3.495193 TCGAGTTAAAAGACGATGACCG 58.505 45.455 0.00 0.00 45.44 4.79
5189 5511 9.781834 CTACTCTATTTATAAGCCAGATTCGAG 57.218 37.037 0.00 0.00 0.00 4.04
5192 5514 9.712305 TTGCTACTCTATTTATAAGCCAGATTC 57.288 33.333 0.00 0.00 0.00 2.52
5206 5633 4.194640 CACAGGCACATTGCTACTCTATT 58.805 43.478 0.00 0.00 44.28 1.73
5212 5642 0.883833 AAGCACAGGCACATTGCTAC 59.116 50.000 2.24 0.00 45.92 3.58
5239 5669 6.821616 ACTGATAACATCCTCCTCTCATTT 57.178 37.500 0.00 0.00 0.00 2.32
5246 5681 5.273208 ACACACTACTGATAACATCCTCCT 58.727 41.667 0.00 0.00 0.00 3.69
5281 5716 2.839486 AGAACCGCATCAAGAAGACA 57.161 45.000 0.00 0.00 0.00 3.41
5306 5917 2.865670 GCTGACATATCTTCTCGCCCAG 60.866 54.545 0.00 0.00 0.00 4.45
5311 5922 1.338337 ACCGGCTGACATATCTTCTCG 59.662 52.381 0.00 0.00 0.00 4.04
5323 5934 2.294074 GCCATTTGTATAACCGGCTGA 58.706 47.619 0.00 0.00 36.58 4.26
5335 5946 1.795170 GACCAGCACACGCCATTTGT 61.795 55.000 0.00 0.00 39.83 2.83
5343 5954 0.244994 AAGCTAGAGACCAGCACACG 59.755 55.000 0.00 0.00 41.66 4.49
5344 5955 3.810310 ATAAGCTAGAGACCAGCACAC 57.190 47.619 0.00 0.00 41.66 3.82
5346 5957 2.869192 GCAATAAGCTAGAGACCAGCAC 59.131 50.000 0.00 0.00 41.66 4.40
5349 5960 2.131183 GCGCAATAAGCTAGAGACCAG 58.869 52.381 0.30 0.00 42.61 4.00
5350 5961 1.757118 AGCGCAATAAGCTAGAGACCA 59.243 47.619 11.47 0.00 44.05 4.02
5351 5962 2.131183 CAGCGCAATAAGCTAGAGACC 58.869 52.381 11.47 0.00 44.06 3.85
5353 5964 1.410517 AGCAGCGCAATAAGCTAGAGA 59.589 47.619 11.47 0.00 44.06 3.10
5354 5965 1.863267 AGCAGCGCAATAAGCTAGAG 58.137 50.000 11.47 0.00 44.06 2.43
5355 5966 1.935873 CAAGCAGCGCAATAAGCTAGA 59.064 47.619 11.47 0.00 44.06 2.43
5356 5967 1.596464 GCAAGCAGCGCAATAAGCTAG 60.596 52.381 11.47 0.00 44.06 3.42
5380 6180 3.090210 TCAGACCATTCATGCCATTGT 57.910 42.857 0.00 0.00 0.00 2.71
5386 6186 4.119442 AGCATTTTCAGACCATTCATGC 57.881 40.909 0.00 0.00 36.59 4.06
5450 6643 9.657121 GCTTCTATGTGCACTTTCTATTTATTC 57.343 33.333 19.41 0.00 0.00 1.75
5465 6663 2.103941 AGCCCTTCTAGCTTCTATGTGC 59.896 50.000 0.00 0.00 37.24 4.57
5501 6818 3.434641 CACACTCTATCACAAACTGCCTG 59.565 47.826 0.00 0.00 0.00 4.85
5515 6834 1.833630 CATCAGGAAGGCCACACTCTA 59.166 52.381 5.01 0.00 36.29 2.43
5560 6886 3.627577 CGAGGAAGAACAAACATATGGGG 59.372 47.826 7.80 0.00 0.00 4.96
5611 7032 2.482333 CGACGAGGCGAGGAAGGAT 61.482 63.158 0.00 0.00 0.00 3.24
5699 7131 1.075674 CAGGAGAGGGCCTCAGCTA 60.076 63.158 33.86 0.00 43.76 3.32
5704 7136 1.794714 TCATTACAGGAGAGGGCCTC 58.205 55.000 26.42 26.42 41.22 4.70
5722 7154 2.681848 CTGATCTGTTGATGGTGGCTTC 59.318 50.000 0.00 0.00 32.19 3.86
5816 7252 3.616379 CCTCTTCTCGTTGCTCATTTCTC 59.384 47.826 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.