Multiple sequence alignment - TraesCS2D01G263000

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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 TraesCS2D01G263000 chr2D 100.000 4346 0 0 1 4346 320250504 320254849 0.000000e+00 8026.0
1 TraesCS2D01G263000 chr2D 88.830 188 18 3 2746 2931 320252982 320253168 1.220000e-55 228.0
2 TraesCS2D01G263000 chr2D 88.830 188 18 3 2479 2665 320253249 320253434 1.220000e-55 228.0
3 TraesCS2D01G263000 chr2D 92.913 127 9 0 2 128 128471338 128471464 7.420000e-43 185.0
4 TraesCS2D01G263000 chr2D 92.913 127 9 0 2 128 415830049 415829923 7.420000e-43 185.0
5 TraesCS2D01G263000 chr2D 87.407 135 15 2 2 135 49772467 49772334 2.090000e-33 154.0
6 TraesCS2D01G263000 chr2B 88.369 2631 193 55 129 2699 388500555 388503132 0.000000e+00 3059.0
7 TraesCS2D01G263000 chr2B 90.121 1488 71 27 2481 3937 388503134 388504576 0.000000e+00 1864.0
8 TraesCS2D01G263000 chr2B 81.775 417 55 12 2493 2902 388502669 388503071 3.240000e-86 329.0
9 TraesCS2D01G263000 chr2B 91.045 201 18 0 4146 4346 388505364 388505564 5.540000e-69 272.0
10 TraesCS2D01G263000 chr2B 87.685 203 20 4 2748 2946 388503134 388503335 9.400000e-57 231.0
11 TraesCS2D01G263000 chr2B 88.947 190 18 3 2478 2665 388503399 388503587 9.400000e-57 231.0
12 TraesCS2D01G263000 chr2B 98.750 80 1 0 3967 4046 388504568 388504647 4.530000e-30 143.0
13 TraesCS2D01G263000 chr2B 82.558 86 15 0 4257 4342 202901643 202901728 4.660000e-10 76.8
14 TraesCS2D01G263000 chr2A 94.595 1554 68 10 763 2310 410863210 410861667 0.000000e+00 2390.0
15 TraesCS2D01G263000 chr2A 92.826 1157 54 17 2484 3619 410861299 410860151 0.000000e+00 1650.0
16 TraesCS2D01G263000 chr2A 88.642 405 16 4 3762 4157 410860149 410859766 2.370000e-127 466.0
17 TraesCS2D01G263000 chr2A 88.489 278 16 6 2403 2665 410861611 410861335 5.420000e-84 322.0
18 TraesCS2D01G263000 chr2A 87.634 186 20 3 2751 2934 410861299 410861115 3.400000e-51 213.0
19 TraesCS2D01G263000 chr2A 85.787 197 25 3 2478 2673 410861038 410860844 5.700000e-49 206.0
20 TraesCS2D01G263000 chr2A 90.625 128 12 0 4219 4346 410859766 410859639 2.080000e-38 171.0
21 TraesCS2D01G263000 chr2A 77.178 241 44 9 1314 1551 256699738 256699506 3.530000e-26 130.0
22 TraesCS2D01G263000 chr2A 100.000 32 0 0 129 160 578721095 578721126 4.690000e-05 60.2
23 TraesCS2D01G263000 chr5A 90.947 243 22 0 1000 1242 588852153 588852395 1.170000e-85 327.0
24 TraesCS2D01G263000 chr5A 80.565 283 40 13 1274 1551 588852523 588852795 2.050000e-48 204.0
25 TraesCS2D01G263000 chr5D 87.912 273 33 0 1000 1272 468651741 468652013 5.420000e-84 322.0
26 TraesCS2D01G263000 chr5D 79.505 283 43 12 1274 1551 468652137 468652409 2.060000e-43 187.0
27 TraesCS2D01G263000 chr5D 79.918 244 32 13 1314 1551 189931076 189931308 3.480000e-36 163.0
28 TraesCS2D01G263000 chr5D 92.683 41 3 0 4252 4292 245719267 245719307 4.690000e-05 60.2
29 TraesCS2D01G263000 chr5B 90.535 243 23 0 1000 1242 575253007 575253249 5.420000e-84 322.0
30 TraesCS2D01G263000 chr5B 79.505 283 43 12 1274 1551 575253395 575253667 2.060000e-43 187.0
31 TraesCS2D01G263000 chr5B 89.583 48 2 2 129 173 159006136 159006089 1.690000e-04 58.4
32 TraesCS2D01G263000 chr4D 94.697 132 7 0 2 133 251029717 251029586 5.700000e-49 206.0
33 TraesCS2D01G263000 chr4D 100.000 34 0 0 129 162 375621386 375621353 3.630000e-06 63.9
34 TraesCS2D01G263000 chr4D 91.111 45 4 0 129 173 454061200 454061244 1.310000e-05 62.1
35 TraesCS2D01G263000 chr4D 97.143 35 0 1 129 162 94557065 94557099 1.690000e-04 58.4
36 TraesCS2D01G263000 chr4D 94.595 37 1 1 129 165 153265353 153265318 6.070000e-04 56.5
37 TraesCS2D01G263000 chr6D 95.276 127 6 0 2 128 403348816 403348942 7.370000e-48 202.0
38 TraesCS2D01G263000 chr6D 93.701 127 8 0 2 128 320023507 320023381 1.600000e-44 191.0
39 TraesCS2D01G263000 chr3D 93.077 130 7 2 1 128 140588336 140588207 5.740000e-44 189.0
40 TraesCS2D01G263000 chr3D 86.022 93 13 0 4253 4345 547426392 547426300 2.770000e-17 100.0
41 TraesCS2D01G263000 chr1D 92.913 127 9 0 2 128 351393310 351393436 7.420000e-43 185.0
42 TraesCS2D01G263000 chr1D 87.121 132 15 2 2 132 317005362 317005492 9.740000e-32 148.0
43 TraesCS2D01G263000 chr7A 89.474 133 14 0 2 134 90094828 90094960 7.470000e-38 169.0
44 TraesCS2D01G263000 chr4B 90.625 128 10 2 2 128 550366485 550366359 7.470000e-38 169.0
45 TraesCS2D01G263000 chr7B 75.649 308 55 17 1274 1573 493132354 493132059 7.580000e-28 135.0
46 TraesCS2D01G263000 chr6B 97.143 35 1 0 129 163 212422601 212422567 4.690000e-05 60.2
47 TraesCS2D01G263000 chr1A 97.143 35 0 1 129 162 541615626 541615660 1.690000e-04 58.4
48 TraesCS2D01G263000 chr1B 90.698 43 2 2 129 171 322463990 322464030 6.070000e-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 TraesCS2D01G263000 chr2D 320250504 320254849 4345 False 2827.333333 8026 92.553333 1 4346 3 chr2D.!!$F2 4345
1 TraesCS2D01G263000 chr2B 388500555 388505564 5009 False 875.571429 3059 89.527429 129 4346 7 chr2B.!!$F2 4217
2 TraesCS2D01G263000 chr2A 410859639 410863210 3571 True 774.000000 2390 89.799714 763 4346 7 chr2A.!!$R2 3583
3 TraesCS2D01G263000 chr5A 588852153 588852795 642 False 265.500000 327 85.756000 1000 1551 2 chr5A.!!$F1 551
4 TraesCS2D01G263000 chr5D 468651741 468652409 668 False 254.500000 322 83.708500 1000 1551 2 chr5D.!!$F3 551
5 TraesCS2D01G263000 chr5B 575253007 575253667 660 False 254.500000 322 85.020000 1000 1551 2 chr5B.!!$F1 551

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
40 41 0.030101 TTTCTTTGCCGTCCGCTTTG 59.970 50.000 0.00 0.00 38.78 2.77 F
64 65 0.037790 AGCTGACGACAAAGAGCCTC 60.038 55.000 0.00 0.00 0.00 4.70 F
65 66 0.037790 GCTGACGACAAAGAGCCTCT 60.038 55.000 0.00 0.00 0.00 3.69 F
74 75 0.108585 AAAGAGCCTCTTTGCCGTCA 59.891 50.000 18.60 0.00 44.34 4.35 F
187 188 0.250038 CTCTGTGCCGACCCATATGG 60.250 60.000 15.41 15.41 41.37 2.74 F
1748 1921 1.274728 AGCTTCTCACTGTGTGGCTAG 59.725 52.381 7.79 5.66 33.87 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1472 1640 0.249657 GCAGCCTCAGAACCCTATCG 60.250 60.000 0.0 0.0 0.00 2.92 R
1792 1965 1.663695 ACCTTATTTCATGGCGACCG 58.336 50.000 0.0 0.0 0.00 4.79 R
1981 2157 2.346099 ATTTGCACACGTACAATGGC 57.654 45.000 0.0 0.0 0.00 4.40 R
2068 2244 3.393089 AGTCAGAAGTAGCTGGTTGTG 57.607 47.619 0.0 0.0 36.55 3.33 R
2129 2305 1.124780 TTGGACACGAGGGAACAGAA 58.875 50.000 0.0 0.0 0.00 3.02 R
3708 4170 0.110486 TGGGGAGGTGTGAGCTTTTC 59.890 55.000 0.0 0.0 0.00 2.29 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
27 28 4.018409 GCCATCGGCCCTTTCTTT 57.982 55.556 0.00 0.00 44.06 2.52
28 29 1.512694 GCCATCGGCCCTTTCTTTG 59.487 57.895 0.00 0.00 44.06 2.77
29 30 1.512694 CCATCGGCCCTTTCTTTGC 59.487 57.895 0.00 0.00 0.00 3.68
30 31 1.512694 CATCGGCCCTTTCTTTGCC 59.487 57.895 0.00 0.00 41.85 4.52
33 34 2.962569 GGCCCTTTCTTTGCCGTC 59.037 61.111 0.00 0.00 35.08 4.79
34 35 2.636412 GGCCCTTTCTTTGCCGTCC 61.636 63.158 0.00 0.00 35.08 4.79
35 36 2.978018 GCCCTTTCTTTGCCGTCCG 61.978 63.158 0.00 0.00 0.00 4.79
36 37 2.561373 CCTTTCTTTGCCGTCCGC 59.439 61.111 0.00 0.00 38.31 5.54
37 38 1.966451 CCTTTCTTTGCCGTCCGCT 60.966 57.895 0.00 0.00 38.78 5.52
38 39 1.515521 CCTTTCTTTGCCGTCCGCTT 61.516 55.000 0.00 0.00 38.78 4.68
39 40 0.310854 CTTTCTTTGCCGTCCGCTTT 59.689 50.000 0.00 0.00 38.78 3.51
40 41 0.030101 TTTCTTTGCCGTCCGCTTTG 59.970 50.000 0.00 0.00 38.78 2.77
41 42 1.098712 TTCTTTGCCGTCCGCTTTGT 61.099 50.000 0.00 0.00 38.78 2.83
42 43 1.370414 CTTTGCCGTCCGCTTTGTG 60.370 57.895 0.00 0.00 38.78 3.33
43 44 2.731587 CTTTGCCGTCCGCTTTGTGG 62.732 60.000 0.00 0.00 38.78 4.17
44 45 3.758973 TTGCCGTCCGCTTTGTGGA 62.759 57.895 0.00 0.00 40.17 4.02
45 46 2.975799 GCCGTCCGCTTTGTGGAA 60.976 61.111 1.09 0.00 44.24 3.53
46 47 2.966309 GCCGTCCGCTTTGTGGAAG 61.966 63.158 1.09 3.96 44.24 3.46
55 56 1.581934 CTTTGTGGAAGCTGACGACA 58.418 50.000 5.25 5.25 0.00 4.35
56 57 1.939934 CTTTGTGGAAGCTGACGACAA 59.060 47.619 14.27 14.27 35.07 3.18
57 58 2.031258 TTGTGGAAGCTGACGACAAA 57.969 45.000 15.34 4.33 34.26 2.83
58 59 1.581934 TGTGGAAGCTGACGACAAAG 58.418 50.000 6.56 0.00 0.00 2.77
59 60 1.138069 TGTGGAAGCTGACGACAAAGA 59.862 47.619 6.56 0.00 0.00 2.52
60 61 1.795286 GTGGAAGCTGACGACAAAGAG 59.205 52.381 0.00 0.00 0.00 2.85
61 62 0.793250 GGAAGCTGACGACAAAGAGC 59.207 55.000 0.00 0.00 0.00 4.09
62 63 0.793250 GAAGCTGACGACAAAGAGCC 59.207 55.000 0.00 0.00 0.00 4.70
63 64 0.394565 AAGCTGACGACAAAGAGCCT 59.605 50.000 0.00 0.00 0.00 4.58
64 65 0.037790 AGCTGACGACAAAGAGCCTC 60.038 55.000 0.00 0.00 0.00 4.70
65 66 0.037790 GCTGACGACAAAGAGCCTCT 60.038 55.000 0.00 0.00 0.00 3.69
66 67 1.606737 GCTGACGACAAAGAGCCTCTT 60.607 52.381 0.00 0.00 38.59 2.85
67 68 2.760374 CTGACGACAAAGAGCCTCTTT 58.240 47.619 13.92 13.92 46.75 2.52
73 74 2.934083 AAAGAGCCTCTTTGCCGTC 58.066 52.632 18.60 0.00 44.34 4.79
74 75 0.108585 AAAGAGCCTCTTTGCCGTCA 59.891 50.000 18.60 0.00 44.34 4.35
75 76 0.321122 AAGAGCCTCTTTGCCGTCAG 60.321 55.000 0.00 0.00 31.57 3.51
76 77 2.359230 AGCCTCTTTGCCGTCAGC 60.359 61.111 0.00 0.00 44.14 4.26
77 78 2.359230 GCCTCTTTGCCGTCAGCT 60.359 61.111 0.00 0.00 44.23 4.24
78 79 2.684843 GCCTCTTTGCCGTCAGCTG 61.685 63.158 7.63 7.63 44.23 4.24
79 80 2.037136 CCTCTTTGCCGTCAGCTGG 61.037 63.158 15.13 0.00 44.23 4.85
87 88 2.807045 CGTCAGCTGGCAGACGTC 60.807 66.667 24.83 7.70 46.11 4.34
88 89 2.340078 GTCAGCTGGCAGACGTCA 59.660 61.111 20.86 0.00 0.00 4.35
89 90 1.300931 GTCAGCTGGCAGACGTCAA 60.301 57.895 20.86 0.00 0.00 3.18
90 91 0.880278 GTCAGCTGGCAGACGTCAAA 60.880 55.000 20.86 0.00 0.00 2.69
91 92 0.601046 TCAGCTGGCAGACGTCAAAG 60.601 55.000 20.86 10.08 0.00 2.77
92 93 0.601046 CAGCTGGCAGACGTCAAAGA 60.601 55.000 20.86 0.00 0.00 2.52
93 94 0.601311 AGCTGGCAGACGTCAAAGAC 60.601 55.000 20.86 9.95 0.00 3.01
113 114 1.583054 GTGGCAGACGACAAAGAAGT 58.417 50.000 0.00 0.00 0.00 3.01
114 115 1.261619 GTGGCAGACGACAAAGAAGTG 59.738 52.381 0.00 0.00 0.00 3.16
115 116 0.868406 GGCAGACGACAAAGAAGTGG 59.132 55.000 0.00 0.00 0.00 4.00
116 117 1.540363 GGCAGACGACAAAGAAGTGGA 60.540 52.381 0.00 0.00 0.00 4.02
117 118 2.417719 GCAGACGACAAAGAAGTGGAT 58.582 47.619 0.00 0.00 0.00 3.41
118 119 2.808543 GCAGACGACAAAGAAGTGGATT 59.191 45.455 0.00 0.00 0.00 3.01
119 120 3.120511 GCAGACGACAAAGAAGTGGATTC 60.121 47.826 0.00 0.00 38.28 2.52
120 121 3.433615 CAGACGACAAAGAAGTGGATTCC 59.566 47.826 0.00 0.00 38.84 3.01
121 122 3.071023 AGACGACAAAGAAGTGGATTCCA 59.929 43.478 0.00 0.00 38.84 3.53
122 123 3.403038 ACGACAAAGAAGTGGATTCCAG 58.597 45.455 5.39 0.00 38.84 3.86
123 124 3.181454 ACGACAAAGAAGTGGATTCCAGT 60.181 43.478 5.39 6.40 39.10 4.00
124 125 4.039973 ACGACAAAGAAGTGGATTCCAGTA 59.960 41.667 13.47 0.00 35.94 2.74
125 126 4.627467 CGACAAAGAAGTGGATTCCAGTAG 59.373 45.833 13.47 4.79 35.94 2.57
126 127 5.552178 GACAAAGAAGTGGATTCCAGTAGT 58.448 41.667 13.47 7.60 35.94 2.73
127 128 5.308825 ACAAAGAAGTGGATTCCAGTAGTG 58.691 41.667 13.47 11.02 35.94 2.74
141 142 6.801539 TCCAGTAGTGCAAGAATAAAGTTG 57.198 37.500 0.00 0.00 0.00 3.16
148 149 9.199982 GTAGTGCAAGAATAAAGTTGTGTAGTA 57.800 33.333 0.00 0.00 0.00 1.82
159 160 3.514309 AGTTGTGTAGTAGACATCACCCC 59.486 47.826 10.23 0.00 41.14 4.95
160 161 2.463752 TGTGTAGTAGACATCACCCCC 58.536 52.381 0.00 0.00 41.14 5.40
165 166 1.305802 TAGACATCACCCCCTGCGT 60.306 57.895 0.00 0.00 0.00 5.24
168 169 4.489771 CATCACCCCCTGCGTCCC 62.490 72.222 0.00 0.00 0.00 4.46
176 177 4.767255 CCTGCGTCCCTCTGTGCC 62.767 72.222 0.00 0.00 0.00 5.01
187 188 0.250038 CTCTGTGCCGACCCATATGG 60.250 60.000 15.41 15.41 41.37 2.74
204 205 4.035102 GGCAAAGGGACGCCTCCT 62.035 66.667 1.57 0.00 45.29 3.69
205 206 2.666098 GGCAAAGGGACGCCTCCTA 61.666 63.158 1.57 0.00 45.29 2.94
206 207 1.298667 GCAAAGGGACGCCTCCTAA 59.701 57.895 1.57 0.00 36.68 2.69
312 318 9.631257 AATTCAAAGTTTCCAAAATCTTCCAAT 57.369 25.926 0.00 0.00 0.00 3.16
315 321 9.108284 TCAAAGTTTCCAAAATCTTCCAATTTC 57.892 29.630 0.00 0.00 0.00 2.17
316 322 9.112725 CAAAGTTTCCAAAATCTTCCAATTTCT 57.887 29.630 0.00 0.00 0.00 2.52
409 423 9.224267 TGGTTTTGAAAAATGTTTGAGAAATCA 57.776 25.926 0.00 0.00 0.00 2.57
461 476 7.507733 TCATGAATTTGAAAAATGTTTGGGG 57.492 32.000 0.00 0.00 0.00 4.96
471 486 9.717942 TTGAAAAATGTTTGGGGTTTCATATAG 57.282 29.630 0.00 0.00 37.85 1.31
473 488 9.150348 GAAAAATGTTTGGGGTTTCATATAGTG 57.850 33.333 0.00 0.00 0.00 2.74
482 497 7.353525 TGGGGTTTCATATAGTGTTCATGAAT 58.646 34.615 12.12 0.00 38.21 2.57
535 550 7.927373 GTTTGTGAATTTCAAAAACTGTTTGC 58.073 30.769 27.09 8.59 46.14 3.68
537 552 7.194607 TGTGAATTTCAAAAACTGTTTGCAA 57.805 28.000 6.53 0.00 0.00 4.08
538 553 7.814642 TGTGAATTTCAAAAACTGTTTGCAAT 58.185 26.923 6.53 0.00 29.10 3.56
539 554 8.295288 TGTGAATTTCAAAAACTGTTTGCAATT 58.705 25.926 6.53 8.48 37.73 2.32
546 561 9.950680 TTCAAAAACTGTTTGCAATTGTTTTAA 57.049 22.222 24.43 17.92 39.10 1.52
593 608 9.438228 AATGTTCATGCATTCAATAAAATGTCA 57.562 25.926 0.00 0.00 38.60 3.58
594 609 9.607988 ATGTTCATGCATTCAATAAAATGTCAT 57.392 25.926 0.00 0.00 38.60 3.06
595 610 9.089601 TGTTCATGCATTCAATAAAATGTCATC 57.910 29.630 0.00 0.00 38.60 2.92
596 611 9.089601 GTTCATGCATTCAATAAAATGTCATCA 57.910 29.630 0.00 0.00 38.60 3.07
597 612 9.654663 TTCATGCATTCAATAAAATGTCATCAA 57.345 25.926 0.00 0.00 38.60 2.57
598 613 9.654663 TCATGCATTCAATAAAATGTCATCAAA 57.345 25.926 0.00 0.00 38.60 2.69
601 616 9.269453 TGCATTCAATAAAATGTCATCAAAACA 57.731 25.926 0.00 0.00 38.60 2.83
658 692 7.274447 TCTGAATTTCAAGAAAATGTTTGCCT 58.726 30.769 0.01 0.00 37.64 4.75
667 701 9.388506 TCAAGAAAATGTTTGCCTATTCAAAAA 57.611 25.926 0.00 0.00 37.65 1.94
703 738 5.731599 TCCAAAAATTGTTCACAACATGC 57.268 34.783 0.00 0.00 41.79 4.06
707 742 2.728690 ATTGTTCACAACATGCGCAT 57.271 40.000 19.28 19.28 41.79 4.73
823 858 9.256477 GTACAGCCCATTAAAATTTTATTAGGC 57.744 33.333 23.45 23.45 34.24 3.93
826 861 9.341078 CAGCCCATTAAAATTTTATTAGGCAAT 57.659 29.630 28.25 15.73 35.42 3.56
898 933 2.690840 ACCTCCTGGTCGCCTATAAAT 58.309 47.619 0.00 0.00 44.78 1.40
1152 1190 3.445518 GATGTGCATCTCCGGCGGA 62.446 63.158 29.14 29.14 35.04 5.54
1415 1583 2.421424 CGCCTTATCTTTCTTGCTTGCT 59.579 45.455 0.00 0.00 0.00 3.91
1472 1640 6.851222 TGATCTTTGTCTGACTTCTTGTTC 57.149 37.500 9.51 0.00 0.00 3.18
1585 1754 5.175491 TCAAGGTACGTTTTGTTACATCGAC 59.825 40.000 0.00 5.98 0.00 4.20
1623 1792 6.805271 CACCTCTGAACAAAAATGATGATGAC 59.195 38.462 0.00 0.00 0.00 3.06
1655 1824 7.582352 CATACATATGATTCTTTGGCTCACAG 58.418 38.462 10.38 0.00 35.75 3.66
1675 1848 6.717997 TCACAGTGTTAGATGTAGTTGTCCTA 59.282 38.462 0.00 0.00 0.00 2.94
1707 1880 7.206981 AGTTTGTAGATGTCAACCAGATTTG 57.793 36.000 0.00 0.00 0.00 2.32
1748 1921 1.274728 AGCTTCTCACTGTGTGGCTAG 59.725 52.381 7.79 5.66 33.87 3.42
1792 1965 6.019479 CGAGCTGAAACACAGATTAGGTTATC 60.019 42.308 0.00 0.00 45.71 1.75
1848 2021 4.218417 AGGGTGAAATGCTGAATTGTGTAC 59.782 41.667 0.00 0.00 0.00 2.90
1855 2028 2.935849 TGCTGAATTGTGTACGCCTATG 59.064 45.455 3.51 0.00 0.00 2.23
1867 2040 6.091577 TGTGTACGCCTATGTTACTGATTTTG 59.908 38.462 3.51 0.00 0.00 2.44
1874 2047 7.593273 CGCCTATGTTACTGATTTTGACAAAAA 59.407 33.333 16.85 1.46 39.53 1.94
1876 2049 9.410556 CCTATGTTACTGATTTTGACAAAAAGG 57.589 33.333 16.85 10.88 38.62 3.11
1877 2050 7.713764 ATGTTACTGATTTTGACAAAAAGGC 57.286 32.000 16.85 10.14 38.62 4.35
1878 2051 6.634805 TGTTACTGATTTTGACAAAAAGGCA 58.365 32.000 16.85 13.56 38.62 4.75
1879 2052 6.756074 TGTTACTGATTTTGACAAAAAGGCAG 59.244 34.615 24.66 24.66 42.04 4.85
1880 2053 5.343307 ACTGATTTTGACAAAAAGGCAGT 57.657 34.783 25.48 25.48 43.15 4.40
1881 2054 5.111293 ACTGATTTTGACAAAAAGGCAGTG 58.889 37.500 27.86 15.70 44.55 3.66
1882 2055 5.083533 TGATTTTGACAAAAAGGCAGTGT 57.916 34.783 16.85 0.00 38.62 3.55
1886 2059 4.734398 TTGACAAAAAGGCAGTGTTCAT 57.266 36.364 0.00 0.00 35.94 2.57
1899 2072 4.869861 GCAGTGTTCATGTTTCCTTTTGTT 59.130 37.500 0.00 0.00 0.00 2.83
1902 2075 6.473455 CAGTGTTCATGTTTCCTTTTGTTCTC 59.527 38.462 0.00 0.00 0.00 2.87
1913 2086 5.084519 TCCTTTTGTTCTCAGCCTAGTAGA 58.915 41.667 0.00 0.00 0.00 2.59
1949 2125 5.010012 CCCTTGTTAAGTGCATTGAGAACTT 59.990 40.000 0.00 0.00 37.82 2.66
1952 2128 7.043192 CCTTGTTAAGTGCATTGAGAACTTTTG 60.043 37.037 0.00 0.00 35.77 2.44
2103 2279 7.840342 ACTTCTGACTAGTCATGCTATTTTG 57.160 36.000 25.35 10.85 39.13 2.44
2116 2292 6.760298 TCATGCTATTTTGTTGACAGCAAAAA 59.240 30.769 26.99 15.23 45.21 1.94
2146 2322 0.966920 TCTTCTGTTCCCTCGTGTCC 59.033 55.000 0.00 0.00 0.00 4.02
2147 2323 0.679505 CTTCTGTTCCCTCGTGTCCA 59.320 55.000 0.00 0.00 0.00 4.02
2226 2402 5.929697 TCTGATTAATCATGGCATTCGTC 57.070 39.130 18.26 0.00 36.02 4.20
2297 2473 7.542130 GGTTATCATCATGTTCTTTTGTTGGTC 59.458 37.037 0.00 0.00 0.00 4.02
2362 2538 1.208052 TGCTACTCTTGATGGGTGCTC 59.792 52.381 0.00 0.00 0.00 4.26
2390 2568 2.093181 TGACCCATAACCACCAAGATCG 60.093 50.000 0.00 0.00 0.00 3.69
2394 2572 1.331756 CATAACCACCAAGATCGCTGC 59.668 52.381 0.00 0.00 0.00 5.25
2397 2575 2.125552 CACCAAGATCGCTGCGGA 60.126 61.111 23.03 9.39 0.00 5.54
2398 2576 2.125512 ACCAAGATCGCTGCGGAC 60.126 61.111 23.03 15.71 0.00 4.79
2405 2583 3.944055 AGATCGCTGCGGACTATTTAT 57.056 42.857 23.03 5.18 0.00 1.40
2406 2584 4.258702 AGATCGCTGCGGACTATTTATT 57.741 40.909 23.03 0.00 0.00 1.40
2407 2585 4.632153 AGATCGCTGCGGACTATTTATTT 58.368 39.130 23.03 0.00 0.00 1.40
2408 2586 5.057149 AGATCGCTGCGGACTATTTATTTT 58.943 37.500 23.03 0.00 0.00 1.82
2497 2704 4.479619 GCACCTGTTTCTCATTCAACATC 58.520 43.478 0.00 0.00 32.50 3.06
2537 2963 5.451103 GCCTGCTCTTTTATTTGATTCTCCC 60.451 44.000 0.00 0.00 0.00 4.30
2544 2970 5.560966 TTTATTTGATTCTCCCGTGCTTC 57.439 39.130 0.00 0.00 0.00 3.86
2744 3171 4.510167 ACTGGGATTGGGTCTCTTAATG 57.490 45.455 0.00 0.00 0.00 1.90
2751 3178 3.806949 TGGGTCTCTTAATGCCTGTTT 57.193 42.857 0.00 0.00 0.00 2.83
2938 3368 8.915654 CATGGCTTGTTTTCTTATTGTTCTAAC 58.084 33.333 0.00 0.00 0.00 2.34
3026 3467 2.428071 GTGCGCTGCTCTTGTTGC 60.428 61.111 9.73 0.00 0.00 4.17
3027 3468 2.901339 TGCGCTGCTCTTGTTGCA 60.901 55.556 9.73 0.00 38.81 4.08
3094 3537 3.449746 TGTTAGGTTCTTGATTGGGGG 57.550 47.619 0.00 0.00 0.00 5.40
3135 3578 1.067199 GAGCGCATGCCTTGAAAACG 61.067 55.000 13.15 0.00 44.31 3.60
3144 3587 6.565811 CGCATGCCTTGAAAACGTATGTATAT 60.566 38.462 13.15 0.00 30.32 0.86
3172 3618 8.801299 TGCAACTAGATGTTATTTGGAAAATGA 58.199 29.630 0.00 0.00 37.07 2.57
3231 3677 1.484653 GAGAAGAGGAAGGAGAAGGCC 59.515 57.143 0.00 0.00 0.00 5.19
3235 3681 0.393673 GAGGAAGGAGAAGGCCAAGC 60.394 60.000 5.01 0.00 0.00 4.01
3288 3734 0.393402 TGCGCATCAAGGCTGAGAAT 60.393 50.000 5.66 0.00 34.23 2.40
3553 4003 4.578516 TCTCCATCATGTTTTTGTTGTCGT 59.421 37.500 0.00 0.00 0.00 4.34
3564 4014 5.728351 TTTTGTTGTCGTCAGGAACTTAG 57.272 39.130 0.00 0.00 34.60 2.18
3568 4018 1.538512 TGTCGTCAGGAACTTAGGACG 59.461 52.381 6.69 6.69 46.54 4.79
3575 4037 0.100861 GGAACTTAGGACGGCTCTCG 59.899 60.000 0.00 0.00 45.88 4.04
3609 4071 1.879380 TGCAAGCGAGTTAAAGCACAT 59.121 42.857 0.00 0.00 35.48 3.21
3627 4089 2.234661 ACATTTGATCCGCTGAGTCTCA 59.765 45.455 1.78 1.78 0.00 3.27
3645 4107 6.631016 AGTCTCAGCGTGATATAAACTGAAA 58.369 36.000 0.00 0.00 36.96 2.69
3672 4134 3.617263 GGCAAACTGAGATTATCGAACGT 59.383 43.478 0.00 0.00 0.00 3.99
3685 4147 7.544566 AGATTATCGAACGTGAAGTAAACATGT 59.455 33.333 0.00 0.00 38.84 3.21
3692 4154 3.660865 GTGAAGTAAACATGTCGGAGGT 58.339 45.455 0.00 0.00 0.00 3.85
3711 4173 2.370281 TTTGCGCCAAACACAAGAAA 57.630 40.000 4.18 0.00 0.00 2.52
3712 4174 2.370281 TTGCGCCAAACACAAGAAAA 57.630 40.000 4.18 0.00 0.00 2.29
3713 4175 1.919918 TGCGCCAAACACAAGAAAAG 58.080 45.000 4.18 0.00 0.00 2.27
3714 4176 0.576798 GCGCCAAACACAAGAAAAGC 59.423 50.000 0.00 0.00 0.00 3.51
3715 4177 1.802508 GCGCCAAACACAAGAAAAGCT 60.803 47.619 0.00 0.00 0.00 3.74
3716 4178 2.119457 CGCCAAACACAAGAAAAGCTC 58.881 47.619 0.00 0.00 0.00 4.09
3717 4179 2.479389 CGCCAAACACAAGAAAAGCTCA 60.479 45.455 0.00 0.00 0.00 4.26
3718 4180 2.860136 GCCAAACACAAGAAAAGCTCAC 59.140 45.455 0.00 0.00 0.00 3.51
3719 4181 3.675775 GCCAAACACAAGAAAAGCTCACA 60.676 43.478 0.00 0.00 0.00 3.58
3720 4182 3.859386 CCAAACACAAGAAAAGCTCACAC 59.141 43.478 0.00 0.00 0.00 3.82
3742 4204 2.512515 CCAGCGCTGCTACCCTTC 60.513 66.667 31.96 0.00 36.40 3.46
3750 4212 0.741915 CTGCTACCCTTCGAGGAGTC 59.258 60.000 0.00 0.00 37.67 3.36
3752 4214 1.393487 GCTACCCTTCGAGGAGTCCC 61.393 65.000 5.25 0.00 37.67 4.46
3766 4228 0.108329 AGTCCCGGTCAATAGCAACG 60.108 55.000 0.00 0.00 0.00 4.10
3811 4273 1.205893 GGTTCAGGTGTTTGCCAACAA 59.794 47.619 4.72 0.00 44.72 2.83
3813 4275 2.865551 GTTCAGGTGTTTGCCAACAATG 59.134 45.455 4.72 7.71 44.72 2.82
3814 4276 1.202510 TCAGGTGTTTGCCAACAATGC 60.203 47.619 4.72 0.00 44.72 3.56
3815 4277 0.106521 AGGTGTTTGCCAACAATGCC 59.893 50.000 4.72 2.96 44.72 4.40
3816 4278 0.884259 GGTGTTTGCCAACAATGCCC 60.884 55.000 4.72 0.00 44.72 5.36
3817 4279 0.179062 GTGTTTGCCAACAATGCCCA 60.179 50.000 4.72 0.00 44.72 5.36
3818 4280 0.106335 TGTTTGCCAACAATGCCCAG 59.894 50.000 0.00 0.00 40.10 4.45
3819 4281 1.071128 TTTGCCAACAATGCCCAGC 59.929 52.632 0.00 0.00 35.21 4.85
3820 4282 1.693152 TTTGCCAACAATGCCCAGCA 61.693 50.000 0.00 0.00 44.86 4.41
3821 4283 2.047939 GCCAACAATGCCCAGCAC 60.048 61.111 0.00 0.00 43.04 4.40
3822 4284 2.259204 CCAACAATGCCCAGCACG 59.741 61.111 0.00 0.00 43.04 5.34
3864 4336 4.079253 GGTTTTCTCTGCCCATTTCACTA 58.921 43.478 0.00 0.00 0.00 2.74
3956 4429 5.707242 TGGAGATAATCGTACACAGATCC 57.293 43.478 0.00 0.00 0.00 3.36
3957 4430 4.523173 TGGAGATAATCGTACACAGATCCC 59.477 45.833 0.00 0.00 0.00 3.85
3958 4431 4.767928 GGAGATAATCGTACACAGATCCCT 59.232 45.833 0.00 0.00 0.00 4.20
3959 4432 5.336055 GGAGATAATCGTACACAGATCCCTG 60.336 48.000 0.00 0.00 45.76 4.45
4050 4523 3.080319 GAGCTGCATTCCAGAAACTCTT 58.920 45.455 1.02 0.00 44.64 2.85
4086 4559 2.244695 CATCAAGGGCATGCATGGTAT 58.755 47.619 27.34 4.11 0.00 2.73
4149 4630 8.121305 TGACTGAGTAAATGTATGCCAAAAAT 57.879 30.769 0.00 0.00 0.00 1.82
4171 5295 1.067364 CATGCTGTGCACCTTGTTTGA 59.933 47.619 15.69 0.00 43.04 2.69
4174 5298 2.553602 TGCTGTGCACCTTGTTTGATAG 59.446 45.455 15.69 1.50 31.71 2.08
4182 5306 4.201950 GCACCTTGTTTGATAGCCTACATG 60.202 45.833 0.00 0.00 0.00 3.21
4212 5336 5.417580 TGGCTACATCAGGTAACCAATTTTC 59.582 40.000 0.00 0.00 43.50 2.29
4218 5342 3.141272 TCAGGTAACCAATTTTCCCCTGT 59.859 43.478 0.00 0.00 39.19 4.00
4263 5387 2.308570 TGGCATAACTTGTGATCACCCT 59.691 45.455 22.85 7.27 0.00 4.34
4342 5466 8.924303 AGCTAGTACATAAATGGTAGTTCATCA 58.076 33.333 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.512694 GCAAAGAAAGGGCCGATGG 59.487 57.895 0.00 0.00 0.00 3.51
12 13 1.512694 GGCAAAGAAAGGGCCGATG 59.487 57.895 0.00 0.00 38.04 3.84
13 14 4.018409 GGCAAAGAAAGGGCCGAT 57.982 55.556 0.00 0.00 38.04 4.18
16 17 2.636412 GGACGGCAAAGAAAGGGCC 61.636 63.158 0.00 0.00 44.27 5.80
17 18 2.962569 GGACGGCAAAGAAAGGGC 59.037 61.111 0.00 0.00 0.00 5.19
18 19 2.978018 GCGGACGGCAAAGAAAGGG 61.978 63.158 0.00 0.00 42.87 3.95
19 20 2.561373 GCGGACGGCAAAGAAAGG 59.439 61.111 0.00 0.00 42.87 3.11
28 29 2.966309 CTTCCACAAAGCGGACGGC 61.966 63.158 0.00 0.00 44.05 5.68
29 30 3.253955 CTTCCACAAAGCGGACGG 58.746 61.111 0.00 0.00 30.29 4.79
36 37 1.581934 TGTCGTCAGCTTCCACAAAG 58.418 50.000 0.00 0.00 38.08 2.77
37 38 2.031258 TTGTCGTCAGCTTCCACAAA 57.969 45.000 0.00 0.00 0.00 2.83
38 39 1.939934 CTTTGTCGTCAGCTTCCACAA 59.060 47.619 0.00 0.00 0.00 3.33
39 40 1.138069 TCTTTGTCGTCAGCTTCCACA 59.862 47.619 0.00 0.00 0.00 4.17
40 41 1.795286 CTCTTTGTCGTCAGCTTCCAC 59.205 52.381 0.00 0.00 0.00 4.02
41 42 1.873903 GCTCTTTGTCGTCAGCTTCCA 60.874 52.381 0.00 0.00 0.00 3.53
42 43 0.793250 GCTCTTTGTCGTCAGCTTCC 59.207 55.000 0.00 0.00 0.00 3.46
43 44 0.793250 GGCTCTTTGTCGTCAGCTTC 59.207 55.000 0.00 0.00 0.00 3.86
44 45 0.394565 AGGCTCTTTGTCGTCAGCTT 59.605 50.000 0.00 0.00 0.00 3.74
45 46 0.037790 GAGGCTCTTTGTCGTCAGCT 60.038 55.000 7.40 0.00 0.00 4.24
46 47 0.037790 AGAGGCTCTTTGTCGTCAGC 60.038 55.000 12.24 0.00 0.00 4.26
47 48 2.447244 AAGAGGCTCTTTGTCGTCAG 57.553 50.000 23.76 0.00 31.57 3.51
48 49 2.910688 AAAGAGGCTCTTTGTCGTCA 57.089 45.000 35.03 0.00 44.34 4.35
55 56 0.108585 TGACGGCAAAGAGGCTCTTT 59.891 50.000 31.58 31.58 46.75 2.52
56 57 0.321122 CTGACGGCAAAGAGGCTCTT 60.321 55.000 23.76 23.76 38.59 2.85
57 58 1.294780 CTGACGGCAAAGAGGCTCT 59.705 57.895 12.24 12.24 41.46 4.09
58 59 2.394563 GCTGACGGCAAAGAGGCTC 61.395 63.158 6.34 6.34 41.46 4.70
59 60 2.359230 GCTGACGGCAAAGAGGCT 60.359 61.111 0.00 0.00 41.46 4.58
60 61 2.359230 AGCTGACGGCAAAGAGGC 60.359 61.111 9.39 0.00 44.79 4.70
61 62 2.037136 CCAGCTGACGGCAAAGAGG 61.037 63.158 17.39 0.00 44.79 3.69
62 63 3.571119 CCAGCTGACGGCAAAGAG 58.429 61.111 17.39 0.00 44.79 2.85
71 72 0.880278 TTTGACGTCTGCCAGCTGAC 60.880 55.000 17.39 16.95 40.15 3.51
72 73 0.601046 CTTTGACGTCTGCCAGCTGA 60.601 55.000 17.39 0.00 0.00 4.26
73 74 0.601046 TCTTTGACGTCTGCCAGCTG 60.601 55.000 17.92 6.78 0.00 4.24
74 75 0.601311 GTCTTTGACGTCTGCCAGCT 60.601 55.000 17.92 0.00 0.00 4.24
75 76 1.862806 GTCTTTGACGTCTGCCAGC 59.137 57.895 17.92 0.00 0.00 4.85
85 86 1.853319 CGTCTGCCACGTCTTTGAC 59.147 57.895 0.00 0.00 44.07 3.18
86 87 4.336581 CGTCTGCCACGTCTTTGA 57.663 55.556 0.00 0.00 44.07 2.69
94 95 1.261619 CACTTCTTTGTCGTCTGCCAC 59.738 52.381 0.00 0.00 0.00 5.01
95 96 1.581934 CACTTCTTTGTCGTCTGCCA 58.418 50.000 0.00 0.00 0.00 4.92
96 97 0.868406 CCACTTCTTTGTCGTCTGCC 59.132 55.000 0.00 0.00 0.00 4.85
97 98 1.865865 TCCACTTCTTTGTCGTCTGC 58.134 50.000 0.00 0.00 0.00 4.26
98 99 3.433615 GGAATCCACTTCTTTGTCGTCTG 59.566 47.826 0.00 0.00 34.08 3.51
99 100 3.071023 TGGAATCCACTTCTTTGTCGTCT 59.929 43.478 0.00 0.00 34.08 4.18
100 101 3.399330 TGGAATCCACTTCTTTGTCGTC 58.601 45.455 0.00 0.00 34.08 4.20
101 102 3.181454 ACTGGAATCCACTTCTTTGTCGT 60.181 43.478 0.00 0.00 34.08 4.34
102 103 3.403038 ACTGGAATCCACTTCTTTGTCG 58.597 45.455 0.00 0.00 34.08 4.35
103 104 5.409826 CACTACTGGAATCCACTTCTTTGTC 59.590 44.000 0.00 0.00 34.08 3.18
104 105 5.308825 CACTACTGGAATCCACTTCTTTGT 58.691 41.667 0.00 0.00 34.08 2.83
105 106 4.154918 GCACTACTGGAATCCACTTCTTTG 59.845 45.833 0.00 0.00 34.08 2.77
106 107 4.202461 TGCACTACTGGAATCCACTTCTTT 60.202 41.667 0.00 0.00 34.08 2.52
107 108 3.327757 TGCACTACTGGAATCCACTTCTT 59.672 43.478 0.00 0.00 34.08 2.52
108 109 2.906389 TGCACTACTGGAATCCACTTCT 59.094 45.455 0.00 0.00 34.08 2.85
109 110 3.334583 TGCACTACTGGAATCCACTTC 57.665 47.619 0.00 0.00 0.00 3.01
110 111 3.327757 TCTTGCACTACTGGAATCCACTT 59.672 43.478 0.00 0.00 0.00 3.16
111 112 2.906389 TCTTGCACTACTGGAATCCACT 59.094 45.455 0.00 0.00 0.00 4.00
112 113 3.334583 TCTTGCACTACTGGAATCCAC 57.665 47.619 0.00 0.00 0.00 4.02
113 114 4.574674 ATTCTTGCACTACTGGAATCCA 57.425 40.909 0.48 0.48 0.00 3.41
114 115 6.599638 ACTTTATTCTTGCACTACTGGAATCC 59.400 38.462 0.00 0.00 0.00 3.01
115 116 7.617041 ACTTTATTCTTGCACTACTGGAATC 57.383 36.000 0.00 0.00 0.00 2.52
116 117 7.448469 ACAACTTTATTCTTGCACTACTGGAAT 59.552 33.333 0.00 0.00 0.00 3.01
117 118 6.770785 ACAACTTTATTCTTGCACTACTGGAA 59.229 34.615 0.00 0.00 0.00 3.53
118 119 6.204688 CACAACTTTATTCTTGCACTACTGGA 59.795 38.462 0.00 0.00 0.00 3.86
119 120 6.017109 ACACAACTTTATTCTTGCACTACTGG 60.017 38.462 0.00 0.00 0.00 4.00
120 121 6.959361 ACACAACTTTATTCTTGCACTACTG 58.041 36.000 0.00 0.00 0.00 2.74
121 122 7.931948 ACTACACAACTTTATTCTTGCACTACT 59.068 33.333 0.00 0.00 0.00 2.57
122 123 8.084590 ACTACACAACTTTATTCTTGCACTAC 57.915 34.615 0.00 0.00 0.00 2.73
123 124 9.419297 CTACTACACAACTTTATTCTTGCACTA 57.581 33.333 0.00 0.00 0.00 2.74
124 125 8.148351 TCTACTACACAACTTTATTCTTGCACT 58.852 33.333 0.00 0.00 0.00 4.40
125 126 8.221766 GTCTACTACACAACTTTATTCTTGCAC 58.778 37.037 0.00 0.00 0.00 4.57
126 127 7.929245 TGTCTACTACACAACTTTATTCTTGCA 59.071 33.333 0.00 0.00 31.43 4.08
127 128 8.306680 TGTCTACTACACAACTTTATTCTTGC 57.693 34.615 0.00 0.00 31.43 4.01
141 142 2.431057 CAGGGGGTGATGTCTACTACAC 59.569 54.545 0.00 0.00 42.09 2.90
148 149 2.607750 ACGCAGGGGGTGATGTCT 60.608 61.111 0.00 0.00 0.00 3.41
159 160 4.767255 GGCACAGAGGGACGCAGG 62.767 72.222 0.00 0.00 0.00 4.85
165 166 2.523740 TATGGGTCGGCACAGAGGGA 62.524 60.000 0.00 0.00 0.00 4.20
168 169 0.250038 CCATATGGGTCGGCACAGAG 60.250 60.000 14.52 0.00 0.00 3.35
188 189 0.107165 ATTAGGAGGCGTCCCTTTGC 60.107 55.000 21.60 0.00 45.26 3.68
189 190 2.420058 AATTAGGAGGCGTCCCTTTG 57.580 50.000 21.60 0.00 45.26 2.77
191 192 2.841881 TGTAAATTAGGAGGCGTCCCTT 59.158 45.455 21.60 12.22 45.26 3.95
192 193 2.474112 TGTAAATTAGGAGGCGTCCCT 58.526 47.619 21.60 11.53 45.26 4.20
290 296 9.112725 AGAAATTGGAAGATTTTGGAAACTTTG 57.887 29.630 0.00 0.00 29.21 2.77
291 297 9.685276 AAGAAATTGGAAGATTTTGGAAACTTT 57.315 25.926 0.00 0.00 29.21 2.66
293 299 9.685276 AAAAGAAATTGGAAGATTTTGGAAACT 57.315 25.926 0.00 0.00 29.75 2.66
432 447 9.672086 CAAACATTTTTCAAATTCATGAGCATT 57.328 25.926 0.00 0.00 0.00 3.56
440 455 7.394359 TGAAACCCCAAACATTTTTCAAATTCA 59.606 29.630 0.00 0.00 34.16 2.57
449 464 8.201242 ACACTATATGAAACCCCAAACATTTT 57.799 30.769 0.00 0.00 0.00 1.82
515 530 8.295288 ACAATTGCAAACAGTTTTTGAAATTCA 58.705 25.926 15.07 0.00 42.64 2.57
575 590 9.269453 TGTTTTGATGACATTTTATTGAATGCA 57.731 25.926 0.00 0.00 39.97 3.96
588 603 9.381033 TGAAAACTTTCATTGTTTTGATGACAT 57.619 25.926 8.95 0.00 44.48 3.06
589 604 8.768957 TGAAAACTTTCATTGTTTTGATGACA 57.231 26.923 8.95 0.00 44.48 3.58
633 648 7.274447 AGGCAAACATTTTCTTGAAATTCAGA 58.726 30.769 0.00 0.00 35.79 3.27
667 701 8.791327 ACAATTTTTGGAACTCTTGAACATTT 57.209 26.923 0.00 0.00 34.12 2.32
682 716 4.516359 CGCATGTTGTGAACAATTTTTGG 58.484 39.130 0.00 0.00 45.86 3.28
725 760 3.260884 AGCGGGTCAGTCTCATCTAAAAA 59.739 43.478 0.00 0.00 0.00 1.94
726 761 2.832129 AGCGGGTCAGTCTCATCTAAAA 59.168 45.455 0.00 0.00 0.00 1.52
727 762 2.457598 AGCGGGTCAGTCTCATCTAAA 58.542 47.619 0.00 0.00 0.00 1.85
728 763 2.145397 AGCGGGTCAGTCTCATCTAA 57.855 50.000 0.00 0.00 0.00 2.10
729 764 2.145397 AAGCGGGTCAGTCTCATCTA 57.855 50.000 0.00 0.00 0.00 1.98
730 765 1.205893 GAAAGCGGGTCAGTCTCATCT 59.794 52.381 0.00 0.00 0.00 2.90
731 766 1.205893 AGAAAGCGGGTCAGTCTCATC 59.794 52.381 0.00 0.00 0.00 2.92
732 767 1.270907 AGAAAGCGGGTCAGTCTCAT 58.729 50.000 0.00 0.00 0.00 2.90
733 768 1.919240 TAGAAAGCGGGTCAGTCTCA 58.081 50.000 0.00 0.00 0.00 3.27
734 769 3.528597 ATTAGAAAGCGGGTCAGTCTC 57.471 47.619 0.00 0.00 0.00 3.36
735 770 4.279145 TCTATTAGAAAGCGGGTCAGTCT 58.721 43.478 0.00 0.00 0.00 3.24
736 771 4.338682 TCTCTATTAGAAAGCGGGTCAGTC 59.661 45.833 0.00 0.00 0.00 3.51
737 772 4.098196 GTCTCTATTAGAAAGCGGGTCAGT 59.902 45.833 0.00 0.00 35.47 3.41
738 773 4.098044 TGTCTCTATTAGAAAGCGGGTCAG 59.902 45.833 0.00 0.00 35.47 3.51
739 774 4.021229 TGTCTCTATTAGAAAGCGGGTCA 58.979 43.478 0.00 0.00 35.47 4.02
740 775 4.650754 TGTCTCTATTAGAAAGCGGGTC 57.349 45.455 0.00 0.00 35.47 4.46
741 776 4.649674 TCATGTCTCTATTAGAAAGCGGGT 59.350 41.667 0.00 0.00 35.47 5.28
742 777 4.985409 GTCATGTCTCTATTAGAAAGCGGG 59.015 45.833 0.00 0.00 35.47 6.13
743 778 5.592054 TGTCATGTCTCTATTAGAAAGCGG 58.408 41.667 0.00 0.00 35.47 5.52
744 779 8.079203 ACTATGTCATGTCTCTATTAGAAAGCG 58.921 37.037 0.00 0.00 35.47 4.68
823 858 6.151648 TCTCAAAAGAACAATAGGCCTCATTG 59.848 38.462 22.83 22.83 38.95 2.82
826 861 5.241403 TCTCAAAAGAACAATAGGCCTCA 57.759 39.130 9.68 0.00 0.00 3.86
898 933 5.484715 CAGGAAGACGTTAGGGTTTATGAA 58.515 41.667 0.00 0.00 0.00 2.57
1113 1151 3.515316 CTCGCACCGGACAACCACT 62.515 63.158 9.46 0.00 35.59 4.00
1119 1157 2.362503 ATCTCCTCGCACCGGACA 60.363 61.111 9.46 0.00 0.00 4.02
1152 1190 1.924731 TCATCTTCTGACGGACCAGT 58.075 50.000 0.00 0.00 35.71 4.00
1472 1640 0.249657 GCAGCCTCAGAACCCTATCG 60.250 60.000 0.00 0.00 0.00 2.92
1623 1792 7.019418 CCAAAGAATCATATGTATGCATCACG 58.981 38.462 0.19 0.00 36.58 4.35
1655 1824 6.127140 ACCCATAGGACAACTACATCTAACAC 60.127 42.308 0.00 0.00 33.70 3.32
1675 1848 6.433093 GGTTGACATCTACAAACTAAACCCAT 59.567 38.462 0.00 0.00 32.92 4.00
1748 1921 4.558860 GCTCGACAGCAATTAATTTTGACC 59.441 41.667 13.66 6.54 46.06 4.02
1782 1955 2.631062 TCATGGCGACCGATAACCTAAT 59.369 45.455 0.00 0.00 0.00 1.73
1792 1965 1.663695 ACCTTATTTCATGGCGACCG 58.336 50.000 0.00 0.00 0.00 4.79
1848 2021 5.794687 TGTCAAAATCAGTAACATAGGCG 57.205 39.130 0.00 0.00 0.00 5.52
1855 2028 6.756542 ACTGCCTTTTTGTCAAAATCAGTAAC 59.243 34.615 24.34 10.69 40.32 2.50
1867 2040 4.045636 ACATGAACACTGCCTTTTTGTC 57.954 40.909 0.00 0.00 0.00 3.18
1874 2047 2.664402 AGGAAACATGAACACTGCCT 57.336 45.000 0.00 0.00 0.00 4.75
1876 2049 4.432712 ACAAAAGGAAACATGAACACTGC 58.567 39.130 0.00 0.00 0.00 4.40
1877 2050 6.332630 AGAACAAAAGGAAACATGAACACTG 58.667 36.000 0.00 0.00 0.00 3.66
1878 2051 6.152661 TGAGAACAAAAGGAAACATGAACACT 59.847 34.615 0.00 0.00 0.00 3.55
1879 2052 6.329496 TGAGAACAAAAGGAAACATGAACAC 58.671 36.000 0.00 0.00 0.00 3.32
1880 2053 6.522625 TGAGAACAAAAGGAAACATGAACA 57.477 33.333 0.00 0.00 0.00 3.18
1881 2054 5.460091 GCTGAGAACAAAAGGAAACATGAAC 59.540 40.000 0.00 0.00 0.00 3.18
1882 2055 5.451798 GGCTGAGAACAAAAGGAAACATGAA 60.452 40.000 0.00 0.00 0.00 2.57
1886 2059 3.631250 AGGCTGAGAACAAAAGGAAACA 58.369 40.909 0.00 0.00 0.00 2.83
1899 2072 5.066913 TGATGGAATCTACTAGGCTGAGA 57.933 43.478 0.00 0.00 45.81 3.27
1902 2075 5.510520 GGAACTGATGGAATCTACTAGGCTG 60.511 48.000 0.00 0.00 45.81 4.85
1913 2086 5.711976 CACTTAACAAGGGAACTGATGGAAT 59.288 40.000 0.00 0.00 42.68 3.01
1981 2157 2.346099 ATTTGCACACGTACAATGGC 57.654 45.000 0.00 0.00 0.00 4.40
1983 2159 4.914504 TGCTAAATTTGCACACGTACAATG 59.085 37.500 0.00 0.00 35.31 2.82
1984 2160 5.114785 TGCTAAATTTGCACACGTACAAT 57.885 34.783 0.00 0.00 35.31 2.71
1986 2162 4.214332 TCATGCTAAATTTGCACACGTACA 59.786 37.500 14.67 0.00 43.59 2.90
1987 2163 4.553429 GTCATGCTAAATTTGCACACGTAC 59.447 41.667 14.67 7.59 43.59 3.67
1988 2164 4.454161 AGTCATGCTAAATTTGCACACGTA 59.546 37.500 14.67 1.20 43.59 3.57
1990 2166 3.605056 CAGTCATGCTAAATTTGCACACG 59.395 43.478 14.67 8.73 43.59 4.49
2068 2244 3.393089 AGTCAGAAGTAGCTGGTTGTG 57.607 47.619 0.00 0.00 36.55 3.33
2116 2292 8.101419 ACGAGGGAACAGAAGAATTAAAATAGT 58.899 33.333 0.00 0.00 0.00 2.12
2129 2305 1.124780 TTGGACACGAGGGAACAGAA 58.875 50.000 0.00 0.00 0.00 3.02
2147 2323 9.860898 GGCTAAAAGAAAAACATGTCTATCATT 57.139 29.630 0.00 0.00 34.09 2.57
2194 2370 8.520351 TGCCATGATTAATCAGAAATCATCATC 58.480 33.333 21.97 3.54 46.25 2.92
2223 2399 1.364721 TACAATGGAATGTGGCGACG 58.635 50.000 0.00 0.00 34.75 5.12
2226 2402 4.336433 AGAATCTTACAATGGAATGTGGCG 59.664 41.667 0.00 0.00 34.75 5.69
2297 2473 8.218338 AGGCATATCATTAAAACACAAGAGAG 57.782 34.615 0.00 0.00 0.00 3.20
2333 2509 9.725019 CACCCATCAAGAGTAGCAATTATTATA 57.275 33.333 0.00 0.00 0.00 0.98
2334 2510 7.175641 GCACCCATCAAGAGTAGCAATTATTAT 59.824 37.037 0.00 0.00 0.00 1.28
2340 2516 2.240667 AGCACCCATCAAGAGTAGCAAT 59.759 45.455 0.00 0.00 0.00 3.56
2362 2538 2.107366 GTGGTTATGGGTCAATTGGGG 58.893 52.381 5.42 0.00 0.00 4.96
2367 2543 4.536765 GATCTTGGTGGTTATGGGTCAAT 58.463 43.478 0.00 0.00 0.00 2.57
2422 2616 8.020819 TCAAATAATTGAAACGAACTAGCCAAG 58.979 33.333 0.00 0.00 42.47 3.61
2459 2654 6.909550 ACAGGTGCCAAAGTTTTATGATTA 57.090 33.333 0.00 0.00 0.00 1.75
2518 2944 5.355350 AGCACGGGAGAATCAAATAAAAGAG 59.645 40.000 0.00 0.00 36.25 2.85
2525 2951 3.012518 CTGAAGCACGGGAGAATCAAAT 58.987 45.455 0.00 0.00 36.25 2.32
2702 3128 8.778358 CCCAGTTCTATGATTTGCTATCTTTAC 58.222 37.037 0.00 0.00 0.00 2.01
2703 3129 8.713971 TCCCAGTTCTATGATTTGCTATCTTTA 58.286 33.333 0.00 0.00 0.00 1.85
2704 3130 7.577303 TCCCAGTTCTATGATTTGCTATCTTT 58.423 34.615 0.00 0.00 0.00 2.52
2721 3148 4.569719 TTAAGAGACCCAATCCCAGTTC 57.430 45.455 0.00 0.00 0.00 3.01
2744 3171 7.145932 AGTCAAATGTTACATAGAAACAGGC 57.854 36.000 0.00 0.00 40.00 4.85
2751 3178 7.759489 AAAGCCAAGTCAAATGTTACATAGA 57.241 32.000 0.00 0.00 0.00 1.98
2938 3368 9.925268 TTTTCTAAAACGAACTAGCTAACAAAG 57.075 29.630 0.00 0.00 0.00 2.77
2978 3410 8.655651 TCTAACATCATTACGATATGTGCAAA 57.344 30.769 0.00 0.00 34.20 3.68
3026 3467 7.980662 TCAATGGCCATTAACTATTGAAATGTG 59.019 33.333 30.19 13.08 35.51 3.21
3027 3468 7.981225 GTCAATGGCCATTAACTATTGAAATGT 59.019 33.333 30.19 0.00 38.87 2.71
3094 3537 8.420189 CGCTCAAATCAAGAATTAAAAACAGTC 58.580 33.333 0.00 0.00 0.00 3.51
3144 3587 7.994425 TTTCCAAATAACATCTAGTTGCAGA 57.006 32.000 0.51 0.00 41.50 4.26
3172 3618 7.201821 CCAGTTTAAACAAAAGAGGTGATGAGT 60.202 37.037 20.06 0.00 0.00 3.41
3251 3697 1.152368 AGCTTGGCCAGTTGCTTCT 59.848 52.632 19.79 3.74 40.92 2.85
3274 3720 1.390565 GCAGCATTCTCAGCCTTGAT 58.609 50.000 0.00 0.00 31.68 2.57
3288 3734 2.999648 AGCTTCTCCTCGGCAGCA 61.000 61.111 0.00 0.00 34.49 4.41
3367 3813 4.403432 CCACCATTATCCAGCAAAACAGAT 59.597 41.667 0.00 0.00 0.00 2.90
3553 4003 1.183549 GAGCCGTCCTAAGTTCCTGA 58.816 55.000 0.00 0.00 0.00 3.86
3609 4071 2.662006 CTGAGACTCAGCGGATCAAA 57.338 50.000 19.25 0.00 37.72 2.69
3627 4089 6.183360 GCCTCTTTTTCAGTTTATATCACGCT 60.183 38.462 0.00 0.00 0.00 5.07
3640 4102 5.702349 ATCTCAGTTTGCCTCTTTTTCAG 57.298 39.130 0.00 0.00 0.00 3.02
3645 4107 5.734720 TCGATAATCTCAGTTTGCCTCTTT 58.265 37.500 0.00 0.00 0.00 2.52
3672 4134 4.345859 AACCTCCGACATGTTTACTTCA 57.654 40.909 0.00 0.00 0.00 3.02
3685 4147 2.203224 TTTGGCGCAAACCTCCGA 60.203 55.556 10.83 0.00 0.00 4.55
3692 4154 2.370281 TTTCTTGTGTTTGGCGCAAA 57.630 40.000 10.83 0.00 45.63 3.68
3706 4168 1.202940 GGGGAGGTGTGAGCTTTTCTT 60.203 52.381 0.00 0.00 0.00 2.52
3707 4169 0.402121 GGGGAGGTGTGAGCTTTTCT 59.598 55.000 0.00 0.00 0.00 2.52
3708 4170 0.110486 TGGGGAGGTGTGAGCTTTTC 59.890 55.000 0.00 0.00 0.00 2.29
3709 4171 0.111253 CTGGGGAGGTGTGAGCTTTT 59.889 55.000 0.00 0.00 0.00 2.27
3710 4172 1.763770 CTGGGGAGGTGTGAGCTTT 59.236 57.895 0.00 0.00 0.00 3.51
3711 4173 2.900106 GCTGGGGAGGTGTGAGCTT 61.900 63.158 0.00 0.00 0.00 3.74
3712 4174 3.325753 GCTGGGGAGGTGTGAGCT 61.326 66.667 0.00 0.00 0.00 4.09
3713 4175 4.767255 CGCTGGGGAGGTGTGAGC 62.767 72.222 0.00 0.00 0.00 4.26
3714 4176 4.767255 GCGCTGGGGAGGTGTGAG 62.767 72.222 0.00 0.00 0.00 3.51
3720 4182 4.537433 GTAGCAGCGCTGGGGAGG 62.537 72.222 36.47 12.81 40.10 4.30
3742 4204 0.669077 CTATTGACCGGGACTCCTCG 59.331 60.000 6.32 0.00 0.00 4.63
3750 4212 2.012937 TAACGTTGCTATTGACCGGG 57.987 50.000 11.99 0.00 0.00 5.73
3752 4214 4.593597 ACAATAACGTTGCTATTGACCG 57.406 40.909 22.73 3.49 38.50 4.79
3766 4228 7.255001 CCGGTATGGGTGAAGATAAACAATAAC 60.255 40.741 0.00 0.00 0.00 1.89
3814 4276 1.875963 CTTAAACTGCCGTGCTGGG 59.124 57.895 7.46 0.00 38.63 4.45
3815 4277 1.210155 GCTTAAACTGCCGTGCTGG 59.790 57.895 7.46 0.00 42.50 4.85
3816 4278 0.310543 TTGCTTAAACTGCCGTGCTG 59.689 50.000 2.15 2.15 0.00 4.41
3817 4279 1.001378 CTTTGCTTAAACTGCCGTGCT 60.001 47.619 0.00 0.00 0.00 4.40
3818 4280 1.001815 TCTTTGCTTAAACTGCCGTGC 60.002 47.619 0.00 0.00 0.00 5.34
3819 4281 2.650608 GTCTTTGCTTAAACTGCCGTG 58.349 47.619 0.00 0.00 0.00 4.94
3820 4282 1.263217 CGTCTTTGCTTAAACTGCCGT 59.737 47.619 0.00 0.00 0.00 5.68
3821 4283 1.529438 TCGTCTTTGCTTAAACTGCCG 59.471 47.619 0.00 0.00 0.00 5.69
3822 4284 2.095718 CCTCGTCTTTGCTTAAACTGCC 60.096 50.000 0.00 0.00 0.00 4.85
3864 4336 3.018149 GAGGTGTTCGATCCTCTGTACT 58.982 50.000 18.40 0.00 44.68 2.73
3956 4429 0.523072 CCCAAATGTTCAGCGACAGG 59.477 55.000 0.00 0.00 32.19 4.00
3957 4430 0.109597 GCCCAAATGTTCAGCGACAG 60.110 55.000 0.00 0.00 32.19 3.51
3958 4431 1.523154 GGCCCAAATGTTCAGCGACA 61.523 55.000 0.00 0.00 0.00 4.35
3959 4432 1.212751 GGCCCAAATGTTCAGCGAC 59.787 57.895 0.00 0.00 0.00 5.19
3960 4433 0.611618 ATGGCCCAAATGTTCAGCGA 60.612 50.000 0.00 0.00 0.00 4.93
3961 4434 0.179129 GATGGCCCAAATGTTCAGCG 60.179 55.000 0.00 0.00 0.00 5.18
3962 4435 0.896923 TGATGGCCCAAATGTTCAGC 59.103 50.000 0.00 0.00 0.00 4.26
3963 4436 2.449464 TCTGATGGCCCAAATGTTCAG 58.551 47.619 0.00 5.14 33.55 3.02
3964 4437 2.601240 TCTGATGGCCCAAATGTTCA 57.399 45.000 0.00 0.00 0.00 3.18
3965 4438 5.537674 AGATATTCTGATGGCCCAAATGTTC 59.462 40.000 0.00 0.00 0.00 3.18
4050 4523 3.126225 TGCATTGCTCGCATGCGA 61.126 55.556 37.69 37.69 46.87 5.10
4157 5281 2.162681 AGGCTATCAAACAAGGTGCAC 58.837 47.619 8.80 8.80 0.00 4.57
4182 5306 1.123928 ACCTGATGTAGCCAGCCTAC 58.876 55.000 0.00 0.00 45.44 3.18
4193 5317 4.093743 GGGGAAAATTGGTTACCTGATGT 58.906 43.478 2.07 0.00 0.00 3.06
4212 5336 1.120795 ATGCCACCAAACAACAGGGG 61.121 55.000 0.00 0.00 0.00 4.79
4218 5342 0.529337 CAACGCATGCCACCAAACAA 60.529 50.000 13.15 0.00 0.00 2.83
4246 5370 5.940470 GTGAGAAAGGGTGATCACAAGTTAT 59.060 40.000 26.47 13.59 41.32 1.89
4287 5411 6.070897 TGAAATGATGTTTTGATCGTGTGT 57.929 33.333 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.