Multiple sequence alignment - TraesCS7D01G425800

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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 TraesCS7D01G425800 chr7D 100.000 2396 0 0 1 2396 546033782 546031387 0.000000e+00 4425.0
1 TraesCS7D01G425800 chr7D 80.585 479 55 22 793 1263 546039135 546038687 3.820000e-88 335.0
2 TraesCS7D01G425800 chr7B 88.773 1247 88 35 719 1938 590026477 590025256 0.000000e+00 1480.0
3 TraesCS7D01G425800 chr7B 84.043 470 54 12 1932 2394 590011158 590010703 1.320000e-117 433.0
4 TraesCS7D01G425800 chr7B 84.273 337 36 11 318 646 590026900 590026573 1.790000e-81 313.0
5 TraesCS7D01G425800 chr7A 88.394 1189 82 30 604 1760 628706245 628705081 0.000000e+00 1380.0
6 TraesCS7D01G425800 chr7A 85.959 584 62 15 1817 2396 628704937 628704370 7.320000e-170 606.0
7 TraesCS7D01G425800 chr7A 81.163 361 27 21 144 499 628706684 628706360 3.950000e-63 252.0
8 TraesCS7D01G425800 chr7A 83.465 127 16 5 2272 2396 712826435 712826312 1.950000e-21 113.0
9 TraesCS7D01G425800 chr7A 83.621 116 14 5 2272 2385 287243836 287243948 1.170000e-18 104.0
10 TraesCS7D01G425800 chr1B 86.275 153 11 9 2228 2375 189689005 189689152 8.870000e-35 158.0
11 TraesCS7D01G425800 chr3B 85.811 148 13 7 2250 2396 772638842 772638702 1.480000e-32 150.0
12 TraesCS7D01G425800 chr3B 79.577 142 23 6 2039 2176 772639068 772638929 1.960000e-16 97.1
13 TraesCS7D01G425800 chr1D 84.459 148 18 5 2232 2375 125827409 125827555 8.930000e-30 141.0
14 TraesCS7D01G425800 chr2B 85.366 123 13 5 2253 2373 776975386 776975267 3.230000e-24 122.0
15 TraesCS7D01G425800 chr3D 72.400 500 85 29 1917 2378 546822191 546821707 2.520000e-20 110.0
16 TraesCS7D01G425800 chr2D 81.102 127 19 5 2272 2396 175933383 175933260 1.960000e-16 97.1


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 TraesCS7D01G425800 chr7D 546031387 546033782 2395 True 4425.0 4425 100.000 1 2396 1 chr7D.!!$R1 2395
1 TraesCS7D01G425800 chr7B 590025256 590026900 1644 True 896.5 1480 86.523 318 1938 2 chr7B.!!$R2 1620
2 TraesCS7D01G425800 chr7A 628704370 628706684 2314 True 746.0 1380 85.172 144 2396 3 chr7A.!!$R2 2252

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
896 994 0.038166 TCACCCAGCACCATTCCTTC 59.962 55.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 2069 0.035056 ATCAGCAGGCCCACAACTAC 60.035 55.0 0.0 0.0 0.0 2.73 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
32 33 5.837586 GATCTCATCGTAGATTTTCCTGC 57.162 43.478 0.00 0.00 45.12 4.85
33 34 4.060038 TCTCATCGTAGATTTTCCTGCC 57.940 45.455 0.00 0.00 45.12 4.85
34 35 3.706594 TCTCATCGTAGATTTTCCTGCCT 59.293 43.478 0.00 0.00 45.12 4.75
35 36 4.162320 TCTCATCGTAGATTTTCCTGCCTT 59.838 41.667 0.00 0.00 45.12 4.35
36 37 4.191544 TCATCGTAGATTTTCCTGCCTTG 58.808 43.478 0.00 0.00 45.12 3.61
37 38 3.695830 TCGTAGATTTTCCTGCCTTGT 57.304 42.857 0.00 0.00 0.00 3.16
38 39 4.015872 TCGTAGATTTTCCTGCCTTGTT 57.984 40.909 0.00 0.00 0.00 2.83
39 40 4.394729 TCGTAGATTTTCCTGCCTTGTTT 58.605 39.130 0.00 0.00 0.00 2.83
40 41 5.553123 TCGTAGATTTTCCTGCCTTGTTTA 58.447 37.500 0.00 0.00 0.00 2.01
41 42 6.177610 TCGTAGATTTTCCTGCCTTGTTTAT 58.822 36.000 0.00 0.00 0.00 1.40
42 43 6.657541 TCGTAGATTTTCCTGCCTTGTTTATT 59.342 34.615 0.00 0.00 0.00 1.40
43 44 7.825270 TCGTAGATTTTCCTGCCTTGTTTATTA 59.175 33.333 0.00 0.00 0.00 0.98
44 45 7.908601 CGTAGATTTTCCTGCCTTGTTTATTAC 59.091 37.037 0.00 0.00 0.00 1.89
45 46 7.775053 AGATTTTCCTGCCTTGTTTATTACA 57.225 32.000 0.00 0.00 34.12 2.41
46 47 7.830739 AGATTTTCCTGCCTTGTTTATTACAG 58.169 34.615 0.00 0.00 38.19 2.74
47 48 7.669722 AGATTTTCCTGCCTTGTTTATTACAGA 59.330 33.333 0.00 0.00 38.19 3.41
48 49 7.775053 TTTTCCTGCCTTGTTTATTACAGAT 57.225 32.000 0.00 0.00 38.19 2.90
49 50 6.757897 TTCCTGCCTTGTTTATTACAGATG 57.242 37.500 0.00 0.00 38.19 2.90
50 51 4.640201 TCCTGCCTTGTTTATTACAGATGC 59.360 41.667 0.00 0.00 38.19 3.91
51 52 4.398988 CCTGCCTTGTTTATTACAGATGCA 59.601 41.667 0.00 0.00 38.19 3.96
52 53 5.068198 CCTGCCTTGTTTATTACAGATGCAT 59.932 40.000 0.00 0.00 38.19 3.96
53 54 5.893687 TGCCTTGTTTATTACAGATGCATG 58.106 37.500 2.46 0.00 38.19 4.06
54 55 5.163530 TGCCTTGTTTATTACAGATGCATGG 60.164 40.000 2.46 0.00 38.19 3.66
55 56 5.284079 CCTTGTTTATTACAGATGCATGGC 58.716 41.667 2.46 0.00 38.19 4.40
56 57 5.163530 CCTTGTTTATTACAGATGCATGGCA 60.164 40.000 2.46 0.00 39.68 4.92
57 58 5.247507 TGTTTATTACAGATGCATGGCAC 57.752 39.130 2.46 0.00 35.08 5.01
58 59 4.704057 TGTTTATTACAGATGCATGGCACA 59.296 37.500 2.46 0.00 35.08 4.57
59 60 5.392919 TGTTTATTACAGATGCATGGCACAC 60.393 40.000 2.46 0.00 35.08 3.82
60 61 7.524742 TGTTTATTACAGATGCATGGCACACT 61.525 38.462 2.46 0.00 35.08 3.55
61 62 9.224535 TGTTTATTACAGATGCATGGCACACTC 62.225 40.741 2.46 0.00 35.08 3.51
70 71 3.030415 TGGCACACTCTGACTACGA 57.970 52.632 0.00 0.00 0.00 3.43
71 72 1.324383 TGGCACACTCTGACTACGAA 58.676 50.000 0.00 0.00 0.00 3.85
72 73 1.269723 TGGCACACTCTGACTACGAAG 59.730 52.381 0.00 0.00 0.00 3.79
73 74 1.402984 GGCACACTCTGACTACGAAGG 60.403 57.143 0.00 0.00 0.00 3.46
74 75 1.269998 GCACACTCTGACTACGAAGGT 59.730 52.381 0.00 0.00 0.00 3.50
75 76 2.922758 GCACACTCTGACTACGAAGGTG 60.923 54.545 0.00 0.00 0.00 4.00
76 77 1.269998 ACACTCTGACTACGAAGGTGC 59.730 52.381 0.00 0.00 0.00 5.01
77 78 1.269723 CACTCTGACTACGAAGGTGCA 59.730 52.381 0.00 0.00 0.00 4.57
78 79 1.961394 ACTCTGACTACGAAGGTGCAA 59.039 47.619 0.00 0.00 0.00 4.08
79 80 2.364324 ACTCTGACTACGAAGGTGCAAA 59.636 45.455 0.00 0.00 0.00 3.68
80 81 2.731976 CTCTGACTACGAAGGTGCAAAC 59.268 50.000 0.00 0.00 0.00 2.93
81 82 2.364324 TCTGACTACGAAGGTGCAAACT 59.636 45.455 0.00 0.00 0.00 2.66
82 83 2.476619 CTGACTACGAAGGTGCAAACTG 59.523 50.000 0.00 0.00 0.00 3.16
83 84 1.194772 GACTACGAAGGTGCAAACTGC 59.805 52.381 0.00 0.00 45.29 4.40
94 95 1.678360 GCAAACTGCAACTGTCATCG 58.322 50.000 0.00 0.00 44.26 3.84
95 96 1.264020 GCAAACTGCAACTGTCATCGA 59.736 47.619 0.00 0.00 44.26 3.59
96 97 2.663879 GCAAACTGCAACTGTCATCGAG 60.664 50.000 0.00 0.00 44.26 4.04
97 98 2.533266 AACTGCAACTGTCATCGAGT 57.467 45.000 0.00 0.00 0.00 4.18
98 99 2.071688 ACTGCAACTGTCATCGAGTC 57.928 50.000 0.00 0.00 0.00 3.36
99 100 1.337260 ACTGCAACTGTCATCGAGTCC 60.337 52.381 0.00 0.00 0.00 3.85
100 101 0.678950 TGCAACTGTCATCGAGTCCA 59.321 50.000 0.00 0.00 0.00 4.02
101 102 1.069978 TGCAACTGTCATCGAGTCCAA 59.930 47.619 0.00 0.00 0.00 3.53
102 103 2.289631 TGCAACTGTCATCGAGTCCAAT 60.290 45.455 0.00 0.00 0.00 3.16
103 104 2.744202 GCAACTGTCATCGAGTCCAATT 59.256 45.455 0.00 0.00 0.00 2.32
104 105 3.932710 GCAACTGTCATCGAGTCCAATTA 59.067 43.478 0.00 0.00 0.00 1.40
105 106 4.391830 GCAACTGTCATCGAGTCCAATTAA 59.608 41.667 0.00 0.00 0.00 1.40
106 107 5.671329 GCAACTGTCATCGAGTCCAATTAAC 60.671 44.000 0.00 0.00 0.00 2.01
107 108 4.504858 ACTGTCATCGAGTCCAATTAACC 58.495 43.478 0.00 0.00 0.00 2.85
108 109 4.020573 ACTGTCATCGAGTCCAATTAACCA 60.021 41.667 0.00 0.00 0.00 3.67
109 110 4.250464 TGTCATCGAGTCCAATTAACCAC 58.750 43.478 0.00 0.00 0.00 4.16
110 111 3.621715 GTCATCGAGTCCAATTAACCACC 59.378 47.826 0.00 0.00 0.00 4.61
111 112 3.517901 TCATCGAGTCCAATTAACCACCT 59.482 43.478 0.00 0.00 0.00 4.00
112 113 4.019681 TCATCGAGTCCAATTAACCACCTT 60.020 41.667 0.00 0.00 0.00 3.50
113 114 5.188163 TCATCGAGTCCAATTAACCACCTTA 59.812 40.000 0.00 0.00 0.00 2.69
114 115 4.824289 TCGAGTCCAATTAACCACCTTAC 58.176 43.478 0.00 0.00 0.00 2.34
115 116 3.937079 CGAGTCCAATTAACCACCTTACC 59.063 47.826 0.00 0.00 0.00 2.85
116 117 4.267536 GAGTCCAATTAACCACCTTACCC 58.732 47.826 0.00 0.00 0.00 3.69
117 118 3.920841 AGTCCAATTAACCACCTTACCCT 59.079 43.478 0.00 0.00 0.00 4.34
118 119 4.355889 AGTCCAATTAACCACCTTACCCTT 59.644 41.667 0.00 0.00 0.00 3.95
119 120 4.703575 GTCCAATTAACCACCTTACCCTTC 59.296 45.833 0.00 0.00 0.00 3.46
120 121 4.604490 TCCAATTAACCACCTTACCCTTCT 59.396 41.667 0.00 0.00 0.00 2.85
121 122 5.075344 TCCAATTAACCACCTTACCCTTCTT 59.925 40.000 0.00 0.00 0.00 2.52
122 123 5.417894 CCAATTAACCACCTTACCCTTCTTC 59.582 44.000 0.00 0.00 0.00 2.87
123 124 5.853572 ATTAACCACCTTACCCTTCTTCA 57.146 39.130 0.00 0.00 0.00 3.02
124 125 5.853572 TTAACCACCTTACCCTTCTTCAT 57.146 39.130 0.00 0.00 0.00 2.57
125 126 6.956102 TTAACCACCTTACCCTTCTTCATA 57.044 37.500 0.00 0.00 0.00 2.15
126 127 7.519347 TTAACCACCTTACCCTTCTTCATAT 57.481 36.000 0.00 0.00 0.00 1.78
127 128 6.402981 AACCACCTTACCCTTCTTCATATT 57.597 37.500 0.00 0.00 0.00 1.28
128 129 6.402981 ACCACCTTACCCTTCTTCATATTT 57.597 37.500 0.00 0.00 0.00 1.40
129 130 6.800890 ACCACCTTACCCTTCTTCATATTTT 58.199 36.000 0.00 0.00 0.00 1.82
130 131 7.246027 ACCACCTTACCCTTCTTCATATTTTT 58.754 34.615 0.00 0.00 0.00 1.94
131 132 7.396339 ACCACCTTACCCTTCTTCATATTTTTC 59.604 37.037 0.00 0.00 0.00 2.29
132 133 7.615757 CCACCTTACCCTTCTTCATATTTTTCT 59.384 37.037 0.00 0.00 0.00 2.52
133 134 9.025041 CACCTTACCCTTCTTCATATTTTTCTT 57.975 33.333 0.00 0.00 0.00 2.52
134 135 9.601810 ACCTTACCCTTCTTCATATTTTTCTTT 57.398 29.630 0.00 0.00 0.00 2.52
138 139 8.607441 ACCCTTCTTCATATTTTTCTTTTTGC 57.393 30.769 0.00 0.00 0.00 3.68
139 140 7.384932 ACCCTTCTTCATATTTTTCTTTTTGCG 59.615 33.333 0.00 0.00 0.00 4.85
140 141 7.148590 CCCTTCTTCATATTTTTCTTTTTGCGG 60.149 37.037 0.00 0.00 0.00 5.69
141 142 7.148590 CCTTCTTCATATTTTTCTTTTTGCGGG 60.149 37.037 0.00 0.00 0.00 6.13
142 143 6.162777 TCTTCATATTTTTCTTTTTGCGGGG 58.837 36.000 0.00 0.00 0.00 5.73
143 144 5.476091 TCATATTTTTCTTTTTGCGGGGT 57.524 34.783 0.00 0.00 0.00 4.95
144 145 5.859495 TCATATTTTTCTTTTTGCGGGGTT 58.141 33.333 0.00 0.00 0.00 4.11
145 146 5.929415 TCATATTTTTCTTTTTGCGGGGTTC 59.071 36.000 0.00 0.00 0.00 3.62
146 147 3.897141 TTTTTCTTTTTGCGGGGTTCT 57.103 38.095 0.00 0.00 0.00 3.01
147 148 3.897141 TTTTCTTTTTGCGGGGTTCTT 57.103 38.095 0.00 0.00 0.00 2.52
148 149 3.897141 TTTCTTTTTGCGGGGTTCTTT 57.103 38.095 0.00 0.00 0.00 2.52
150 151 2.379972 TCTTTTTGCGGGGTTCTTTCA 58.620 42.857 0.00 0.00 0.00 2.69
153 154 1.253100 TTTGCGGGGTTCTTTCATCC 58.747 50.000 0.00 0.00 0.00 3.51
159 160 2.027192 CGGGGTTCTTTCATCCTCTTCA 60.027 50.000 0.00 0.00 0.00 3.02
163 164 5.767168 GGGGTTCTTTCATCCTCTTCATATG 59.233 44.000 0.00 0.00 0.00 1.78
166 167 7.050377 GGTTCTTTCATCCTCTTCATATGACA 58.950 38.462 4.48 0.00 29.64 3.58
168 169 7.666063 TCTTTCATCCTCTTCATATGACAGA 57.334 36.000 4.48 10.46 35.27 3.41
169 170 7.495901 TCTTTCATCCTCTTCATATGACAGAC 58.504 38.462 4.48 0.00 33.64 3.51
173 174 3.067320 TCCTCTTCATATGACAGACGCAG 59.933 47.826 4.48 0.00 0.00 5.18
190 191 3.560068 ACGCAGTTAACAAAGAGGACAAG 59.440 43.478 8.61 0.00 37.78 3.16
215 216 2.034066 ACCATGTTCCTGCGTGGG 59.966 61.111 8.87 0.00 46.89 4.61
229 230 0.250727 CGTGGGTGTGGAAGGTGAAT 60.251 55.000 0.00 0.00 0.00 2.57
231 232 1.073923 GTGGGTGTGGAAGGTGAATCT 59.926 52.381 0.00 0.00 0.00 2.40
235 236 1.808945 GTGTGGAAGGTGAATCTGCAG 59.191 52.381 7.63 7.63 0.00 4.41
238 244 3.149196 GTGGAAGGTGAATCTGCAGAAA 58.851 45.455 22.50 6.77 0.00 2.52
251 257 8.579006 TGAATCTGCAGAAAACATATTTTGACT 58.421 29.630 22.50 0.00 38.17 3.41
257 263 8.629158 TGCAGAAAACATATTTTGACTACACTT 58.371 29.630 0.00 0.00 38.17 3.16
258 264 8.905702 GCAGAAAACATATTTTGACTACACTTG 58.094 33.333 0.00 0.00 38.17 3.16
282 288 1.758280 ACATACTTGATTCGGCCGGTA 59.242 47.619 27.83 18.35 0.00 4.02
287 293 2.081462 CTTGATTCGGCCGGTAAAAGT 58.919 47.619 27.83 0.86 0.00 2.66
288 294 1.444836 TGATTCGGCCGGTAAAAGTG 58.555 50.000 27.83 0.00 0.00 3.16
289 295 1.002201 TGATTCGGCCGGTAAAAGTGA 59.998 47.619 27.83 0.00 0.00 3.41
290 296 1.664151 GATTCGGCCGGTAAAAGTGAG 59.336 52.381 27.83 0.00 0.00 3.51
291 297 0.952010 TTCGGCCGGTAAAAGTGAGC 60.952 55.000 27.83 0.00 0.00 4.26
293 299 1.231958 CGGCCGGTAAAAGTGAGCAA 61.232 55.000 20.10 0.00 0.00 3.91
311 317 4.328231 CGGCGCCGATCGATCAGA 62.328 66.667 44.86 0.00 42.83 3.27
312 318 2.429907 GGCGCCGATCGATCAGAG 60.430 66.667 24.40 16.21 41.67 3.35
313 319 2.639853 GCGCCGATCGATCAGAGA 59.360 61.111 24.40 0.00 41.67 3.10
314 320 1.211449 GCGCCGATCGATCAGAGAT 59.789 57.895 24.40 0.00 41.67 2.75
315 321 0.796491 GCGCCGATCGATCAGAGATC 60.796 60.000 24.40 5.13 41.67 2.75
330 336 5.800296 TCAGAGATCGGTGTTTAATTTCCA 58.200 37.500 0.00 0.00 0.00 3.53
334 340 3.926821 TCGGTGTTTAATTTCCAAGCC 57.073 42.857 0.00 0.00 0.00 4.35
335 341 3.492337 TCGGTGTTTAATTTCCAAGCCT 58.508 40.909 0.00 0.00 0.00 4.58
336 342 3.504520 TCGGTGTTTAATTTCCAAGCCTC 59.495 43.478 0.00 0.00 0.00 4.70
337 343 3.254657 CGGTGTTTAATTTCCAAGCCTCA 59.745 43.478 0.00 0.00 0.00 3.86
373 379 2.462456 AGACACACATGATTGCGAGT 57.538 45.000 0.00 0.00 0.00 4.18
393 406 5.106157 CGAGTTTAAGAAATGCATTCCCTGT 60.106 40.000 13.38 0.00 38.94 4.00
395 408 7.361713 CGAGTTTAAGAAATGCATTCCCTGTAA 60.362 37.037 13.38 10.73 38.94 2.41
456 470 2.627699 CAAGGCAGAAAAGGGTTTAGCA 59.372 45.455 0.00 0.00 32.31 3.49
576 626 5.224441 TCATTAAGTAGATTAGCACCCCCT 58.776 41.667 0.00 0.00 0.00 4.79
578 628 7.023120 TCATTAAGTAGATTAGCACCCCCTAT 58.977 38.462 0.00 0.00 0.00 2.57
579 629 6.681729 TTAAGTAGATTAGCACCCCCTATG 57.318 41.667 0.00 0.00 0.00 2.23
615 665 3.134081 CACCAGGATAGTGTATCGGGTTT 59.866 47.826 0.00 0.00 39.81 3.27
633 683 0.969149 TTGGATCGCTCAGTGTCAGT 59.031 50.000 0.00 0.00 0.00 3.41
642 692 2.675423 AGTGTCAGTAGCGCCCGA 60.675 61.111 2.29 0.00 0.00 5.14
643 693 2.260434 GTGTCAGTAGCGCCCGAA 59.740 61.111 2.29 0.00 0.00 4.30
663 713 3.311143 ACCGGGGACCTGTTAACGTTC 62.311 57.143 2.82 0.00 46.02 3.95
689 739 6.149308 TGAATGAATGTTTACGCTGTCAGATT 59.851 34.615 3.32 0.00 0.00 2.40
692 742 5.348724 TGAATGTTTACGCTGTCAGATTCTC 59.651 40.000 3.32 0.00 0.00 2.87
705 755 3.810310 AGATTCTCATCTGAACCGACC 57.190 47.619 0.00 0.00 38.44 4.79
706 756 2.432510 AGATTCTCATCTGAACCGACCC 59.567 50.000 0.00 0.00 38.44 4.46
707 757 1.938585 TTCTCATCTGAACCGACCCT 58.061 50.000 0.00 0.00 0.00 4.34
709 759 1.186200 CTCATCTGAACCGACCCTGA 58.814 55.000 0.00 0.00 0.00 3.86
710 760 1.759445 CTCATCTGAACCGACCCTGAT 59.241 52.381 0.00 0.00 0.00 2.90
711 761 1.757118 TCATCTGAACCGACCCTGATC 59.243 52.381 0.00 0.00 0.00 2.92
712 762 1.123928 ATCTGAACCGACCCTGATCC 58.876 55.000 0.00 0.00 0.00 3.36
713 763 0.252057 TCTGAACCGACCCTGATCCA 60.252 55.000 0.00 0.00 0.00 3.41
714 764 0.176680 CTGAACCGACCCTGATCCAG 59.823 60.000 0.00 0.00 0.00 3.86
781 862 6.128363 CCATCGTATACTAAGCGATCACACTA 60.128 42.308 0.56 0.00 42.48 2.74
782 863 6.220579 TCGTATACTAAGCGATCACACTAC 57.779 41.667 0.56 0.00 0.00 2.73
783 864 5.987953 TCGTATACTAAGCGATCACACTACT 59.012 40.000 0.56 0.00 0.00 2.57
842 924 1.125633 ACGTTAACTCCACCACCACT 58.874 50.000 3.71 0.00 0.00 4.00
868 950 0.598680 CGATCCTTGCTCCGATCCAC 60.599 60.000 0.00 0.00 32.83 4.02
869 951 0.250081 GATCCTTGCTCCGATCCACC 60.250 60.000 0.00 0.00 30.64 4.61
884 979 2.854032 ACCCCACACCTCACCCAG 60.854 66.667 0.00 0.00 0.00 4.45
885 980 4.351054 CCCCACACCTCACCCAGC 62.351 72.222 0.00 0.00 0.00 4.85
889 984 2.772191 ACACCTCACCCAGCACCA 60.772 61.111 0.00 0.00 0.00 4.17
892 990 0.962356 CACCTCACCCAGCACCATTC 60.962 60.000 0.00 0.00 0.00 2.67
893 991 1.379044 CCTCACCCAGCACCATTCC 60.379 63.158 0.00 0.00 0.00 3.01
894 992 1.687612 CTCACCCAGCACCATTCCT 59.312 57.895 0.00 0.00 0.00 3.36
895 993 0.038744 CTCACCCAGCACCATTCCTT 59.961 55.000 0.00 0.00 0.00 3.36
896 994 0.038166 TCACCCAGCACCATTCCTTC 59.962 55.000 0.00 0.00 0.00 3.46
897 995 0.967380 CACCCAGCACCATTCCTTCC 60.967 60.000 0.00 0.00 0.00 3.46
898 996 1.142688 ACCCAGCACCATTCCTTCCT 61.143 55.000 0.00 0.00 0.00 3.36
899 997 0.394899 CCCAGCACCATTCCTTCCTC 60.395 60.000 0.00 0.00 0.00 3.71
923 1021 0.532862 CCTTCCTCGTTGCACACTGT 60.533 55.000 0.00 0.00 0.00 3.55
1048 1158 2.266627 GCTGCTGCTGCTCCTGTTT 61.267 57.895 22.10 0.00 40.48 2.83
1051 1161 0.179009 TGCTGCTGCTCCTGTTTCTT 60.179 50.000 17.00 0.00 40.48 2.52
1053 1163 1.466558 GCTGCTGCTCCTGTTTCTTAC 59.533 52.381 8.53 0.00 36.03 2.34
1296 1418 3.643595 TACCATGTGCCTGGCTGCC 62.644 63.158 21.03 12.87 40.15 4.85
1314 1436 1.583495 CCTGCTCGTCTCGTGGTGTA 61.583 60.000 0.00 0.00 0.00 2.90
1383 1505 1.048160 TAGATGGCCACGGAGCATCA 61.048 55.000 8.16 0.00 36.25 3.07
1384 1506 1.228063 GATGGCCACGGAGCATCAT 60.228 57.895 8.16 0.00 36.25 2.45
1385 1507 1.228063 ATGGCCACGGAGCATCATC 60.228 57.895 8.16 0.00 36.25 2.92
1431 1553 6.014156 AGGGATAGGAATTAAGAATGGAGACG 60.014 42.308 0.00 0.00 0.00 4.18
1436 1558 4.807304 GGAATTAAGAATGGAGACGCGTAA 59.193 41.667 13.97 0.00 0.00 3.18
1437 1559 5.276726 GGAATTAAGAATGGAGACGCGTAAC 60.277 44.000 13.97 9.40 0.00 2.50
1470 1592 1.132453 CTTAGGATCGATCGGCGCATA 59.868 52.381 18.81 4.29 40.61 3.14
1588 1714 1.623811 TGGGAGTAACAGCTGGTTCTC 59.376 52.381 25.62 25.62 40.96 2.87
1637 1768 5.385198 AGCTGTTCCTTTGTTGGATTTAGA 58.615 37.500 0.00 0.00 35.83 2.10
1639 1770 6.015940 AGCTGTTCCTTTGTTGGATTTAGAAG 60.016 38.462 0.00 0.00 35.83 2.85
1658 1789 9.681062 TTTAGAAGGCTGCTGTAATATAACTTT 57.319 29.630 4.87 0.00 0.00 2.66
1707 1838 7.659652 ACTAGTCTCTTCTTTTGATTTTCGG 57.340 36.000 0.00 0.00 0.00 4.30
1755 1886 3.437049 AGCTAACTGATCTTCGCCAAAAC 59.563 43.478 0.00 0.00 0.00 2.43
1772 1989 6.183360 CGCCAAAACAATAAGTTGGTTGAAAA 60.183 34.615 9.10 0.00 44.24 2.29
1811 2041 7.492344 TGGCAAAGAAAAGAAGAAGTGAAAATC 59.508 33.333 0.00 0.00 0.00 2.17
1860 2090 2.677524 TTGTGGGCCTGCTGATGC 60.678 61.111 4.53 0.00 40.20 3.91
1880 2110 3.882888 TGCCAAAATATCTAGGCCGAAAG 59.117 43.478 0.00 0.00 46.45 2.62
1946 2176 2.878991 CCGACGCTCGCGAAATGA 60.879 61.111 18.98 0.00 42.83 2.57
1955 2185 1.660607 CTCGCGAAATGAGCAGCTTTA 59.339 47.619 11.33 0.00 34.19 1.85
1977 2207 0.600557 TAAAGGTGGTGCGCAAATGG 59.399 50.000 14.00 0.00 0.00 3.16
1999 2229 4.918201 GCCCTATTCGCAGGCGCT 62.918 66.667 7.64 1.34 36.84 5.92
2035 2267 7.732222 AAAAATAATATTGCTCCCAACCTCA 57.268 32.000 0.00 0.00 32.95 3.86
2037 2269 3.737559 AATATTGCTCCCAACCTCACA 57.262 42.857 0.00 0.00 32.95 3.58
2064 2296 2.605101 TAGCGACGCTAGCTAGCCG 61.605 63.158 34.27 31.40 46.34 5.52
2066 2298 2.249896 CGACGCTAGCTAGCCGAG 59.750 66.667 34.27 24.43 46.34 4.63
2091 2323 1.398390 GGACTAAGCACGGCTGAAATG 59.602 52.381 0.00 0.00 39.62 2.32
2141 2373 1.542881 TGGGAGATCCGGGGGTTTT 60.543 57.895 0.00 0.00 38.76 2.43
2146 2378 1.004394 GAGATCCGGGGGTTTTCAACT 59.996 52.381 0.00 0.00 0.00 3.16
2167 2399 9.277783 TCAACTTTTTCAACATTTCTTGGAAAA 57.722 25.926 0.00 0.00 36.61 2.29
2179 2411 7.632721 CATTTCTTGGAAAAATGTGGACAAAG 58.367 34.615 0.00 0.00 38.64 2.77
2183 2415 6.816140 TCTTGGAAAAATGTGGACAAAGTTTC 59.184 34.615 0.00 0.00 0.00 2.78
2188 2420 9.157104 GGAAAAATGTGGACAAAGTTTCTTAAA 57.843 29.630 10.52 0.00 30.92 1.52
2193 2425 9.665719 AATGTGGACAAAGTTTCTTAAAAATGT 57.334 25.926 0.00 0.00 0.00 2.71
2194 2426 8.472683 TGTGGACAAAGTTTCTTAAAAATGTG 57.527 30.769 0.00 0.00 34.56 3.21
2197 2429 9.145865 TGGACAAAGTTTCTTAAAAATGTGAAC 57.854 29.630 0.00 0.00 32.62 3.18
2198 2430 8.318167 GGACAAAGTTTCTTAAAAATGTGAACG 58.682 33.333 0.00 0.00 32.62 3.95
2223 2455 9.130312 CGGTTTGGAAATCGTAAATAAAATTCA 57.870 29.630 0.00 0.00 37.71 2.57
2256 2488 8.846452 TTTGTGAAAACGTTTAACAAATTTCG 57.154 26.923 31.12 0.00 34.59 3.46
2257 2489 7.792383 TGTGAAAACGTTTAACAAATTTCGA 57.208 28.000 20.91 2.48 31.23 3.71
2258 2490 8.224169 TGTGAAAACGTTTAACAAATTTCGAA 57.776 26.923 20.91 0.00 31.23 3.71
2267 2499 9.656834 CGTTTAACAAATTTCGAATATTTGAGC 57.343 29.630 30.57 19.22 42.72 4.26
2285 2517 8.665643 ATTTGAGCAATTTTTCTGAAATGTGA 57.334 26.923 3.31 0.00 27.83 3.58
2287 2519 7.467557 TGAGCAATTTTTCTGAAATGTGAAC 57.532 32.000 3.31 2.39 0.00 3.18
2340 2572 8.380644 CACACTGAACATTTTCTTAGTATACCG 58.619 37.037 0.00 0.00 32.36 4.02
2345 2577 8.928733 TGAACATTTTCTTAGTATACCGTGAAC 58.071 33.333 0.00 0.00 32.36 3.18
2346 2578 8.836268 AACATTTTCTTAGTATACCGTGAACA 57.164 30.769 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.688413 GGCAGGAAAATCTACGATGAGATC 59.312 45.833 0.00 0.00 35.01 2.75
11 12 4.346418 AGGCAGGAAAATCTACGATGAGAT 59.654 41.667 0.00 0.00 37.81 2.75
12 13 3.706594 AGGCAGGAAAATCTACGATGAGA 59.293 43.478 0.00 0.00 0.00 3.27
13 14 4.065321 AGGCAGGAAAATCTACGATGAG 57.935 45.455 0.00 0.00 0.00 2.90
14 15 4.191544 CAAGGCAGGAAAATCTACGATGA 58.808 43.478 0.00 0.00 0.00 2.92
15 16 3.941483 ACAAGGCAGGAAAATCTACGATG 59.059 43.478 0.00 0.00 0.00 3.84
16 17 4.222124 ACAAGGCAGGAAAATCTACGAT 57.778 40.909 0.00 0.00 0.00 3.73
17 18 3.695830 ACAAGGCAGGAAAATCTACGA 57.304 42.857 0.00 0.00 0.00 3.43
18 19 4.766404 AAACAAGGCAGGAAAATCTACG 57.234 40.909 0.00 0.00 0.00 3.51
19 20 8.736244 TGTAATAAACAAGGCAGGAAAATCTAC 58.264 33.333 0.00 0.00 34.29 2.59
20 21 8.871629 TGTAATAAACAAGGCAGGAAAATCTA 57.128 30.769 0.00 0.00 34.29 1.98
21 22 7.669722 TCTGTAATAAACAAGGCAGGAAAATCT 59.330 33.333 0.00 0.00 37.74 2.40
22 23 7.826690 TCTGTAATAAACAAGGCAGGAAAATC 58.173 34.615 0.00 0.00 37.74 2.17
23 24 7.775053 TCTGTAATAAACAAGGCAGGAAAAT 57.225 32.000 0.00 0.00 37.74 1.82
24 25 7.601856 CATCTGTAATAAACAAGGCAGGAAAA 58.398 34.615 0.00 0.00 37.74 2.29
25 26 6.350110 GCATCTGTAATAAACAAGGCAGGAAA 60.350 38.462 0.00 0.00 37.74 3.13
26 27 5.125417 GCATCTGTAATAAACAAGGCAGGAA 59.875 40.000 0.00 0.00 37.74 3.36
27 28 4.640201 GCATCTGTAATAAACAAGGCAGGA 59.360 41.667 0.00 0.00 37.74 3.86
28 29 4.398988 TGCATCTGTAATAAACAAGGCAGG 59.601 41.667 0.00 0.00 37.74 4.85
29 30 5.565592 TGCATCTGTAATAAACAAGGCAG 57.434 39.130 0.00 0.00 37.74 4.85
30 31 5.163530 CCATGCATCTGTAATAAACAAGGCA 60.164 40.000 0.00 0.00 38.90 4.75
31 32 5.284079 CCATGCATCTGTAATAAACAAGGC 58.716 41.667 0.00 0.00 37.74 4.35
32 33 5.163530 TGCCATGCATCTGTAATAAACAAGG 60.164 40.000 0.00 0.00 33.13 3.61
33 34 5.745294 GTGCCATGCATCTGTAATAAACAAG 59.255 40.000 0.00 0.00 41.91 3.16
34 35 5.184671 TGTGCCATGCATCTGTAATAAACAA 59.815 36.000 0.00 0.00 41.91 2.83
35 36 4.704057 TGTGCCATGCATCTGTAATAAACA 59.296 37.500 0.00 0.00 41.91 2.83
36 37 5.036737 GTGTGCCATGCATCTGTAATAAAC 58.963 41.667 0.00 0.00 41.91 2.01
37 38 4.949238 AGTGTGCCATGCATCTGTAATAAA 59.051 37.500 0.00 0.00 41.91 1.40
38 39 4.525996 AGTGTGCCATGCATCTGTAATAA 58.474 39.130 0.00 0.00 41.91 1.40
39 40 4.129380 GAGTGTGCCATGCATCTGTAATA 58.871 43.478 0.00 0.00 41.91 0.98
40 41 2.947652 GAGTGTGCCATGCATCTGTAAT 59.052 45.455 0.00 0.00 41.91 1.89
41 42 2.026915 AGAGTGTGCCATGCATCTGTAA 60.027 45.455 0.00 0.00 41.91 2.41
42 43 1.556451 AGAGTGTGCCATGCATCTGTA 59.444 47.619 0.00 0.00 41.91 2.74
43 44 0.327259 AGAGTGTGCCATGCATCTGT 59.673 50.000 0.00 0.00 41.91 3.41
44 45 0.733150 CAGAGTGTGCCATGCATCTG 59.267 55.000 0.00 0.00 41.91 2.90
45 46 0.616891 TCAGAGTGTGCCATGCATCT 59.383 50.000 0.00 0.00 41.91 2.90
46 47 0.731417 GTCAGAGTGTGCCATGCATC 59.269 55.000 0.00 0.00 41.91 3.91
47 48 0.327259 AGTCAGAGTGTGCCATGCAT 59.673 50.000 0.00 0.00 41.91 3.96
48 49 0.975887 TAGTCAGAGTGTGCCATGCA 59.024 50.000 0.00 0.00 35.60 3.96
49 50 1.363744 GTAGTCAGAGTGTGCCATGC 58.636 55.000 0.00 0.00 0.00 4.06
50 51 1.202348 TCGTAGTCAGAGTGTGCCATG 59.798 52.381 0.00 0.00 0.00 3.66
51 52 1.545841 TCGTAGTCAGAGTGTGCCAT 58.454 50.000 0.00 0.00 0.00 4.40
52 53 1.269723 CTTCGTAGTCAGAGTGTGCCA 59.730 52.381 0.00 0.00 0.00 4.92
53 54 1.402984 CCTTCGTAGTCAGAGTGTGCC 60.403 57.143 0.00 0.00 0.00 5.01
54 55 1.269998 ACCTTCGTAGTCAGAGTGTGC 59.730 52.381 0.00 0.00 0.00 4.57
55 56 2.922758 GCACCTTCGTAGTCAGAGTGTG 60.923 54.545 0.00 0.00 0.00 3.82
56 57 1.269998 GCACCTTCGTAGTCAGAGTGT 59.730 52.381 0.00 0.00 0.00 3.55
57 58 1.269723 TGCACCTTCGTAGTCAGAGTG 59.730 52.381 0.00 0.00 0.00 3.51
58 59 1.617322 TGCACCTTCGTAGTCAGAGT 58.383 50.000 0.00 0.00 0.00 3.24
59 60 2.724977 TTGCACCTTCGTAGTCAGAG 57.275 50.000 0.00 0.00 0.00 3.35
60 61 2.364324 AGTTTGCACCTTCGTAGTCAGA 59.636 45.455 0.00 0.00 0.00 3.27
61 62 2.476619 CAGTTTGCACCTTCGTAGTCAG 59.523 50.000 0.00 0.00 0.00 3.51
62 63 2.479837 CAGTTTGCACCTTCGTAGTCA 58.520 47.619 0.00 0.00 0.00 3.41
63 64 1.194772 GCAGTTTGCACCTTCGTAGTC 59.805 52.381 0.00 0.00 44.26 2.59
64 65 1.226746 GCAGTTTGCACCTTCGTAGT 58.773 50.000 0.00 0.00 44.26 2.73
75 76 1.264020 TCGATGACAGTTGCAGTTTGC 59.736 47.619 0.00 0.00 45.29 3.68
76 77 2.545526 ACTCGATGACAGTTGCAGTTTG 59.454 45.455 0.00 0.00 0.00 2.93
77 78 2.802816 GACTCGATGACAGTTGCAGTTT 59.197 45.455 0.00 0.00 0.00 2.66
78 79 2.408050 GACTCGATGACAGTTGCAGTT 58.592 47.619 0.00 0.00 0.00 3.16
79 80 1.337260 GGACTCGATGACAGTTGCAGT 60.337 52.381 0.00 0.00 0.00 4.40
80 81 1.337167 TGGACTCGATGACAGTTGCAG 60.337 52.381 0.00 0.00 0.00 4.41
81 82 0.678950 TGGACTCGATGACAGTTGCA 59.321 50.000 0.00 0.00 0.00 4.08
82 83 1.795768 TTGGACTCGATGACAGTTGC 58.204 50.000 0.00 0.00 0.00 4.17
83 84 5.163854 GGTTAATTGGACTCGATGACAGTTG 60.164 44.000 0.00 0.00 0.00 3.16
84 85 4.935808 GGTTAATTGGACTCGATGACAGTT 59.064 41.667 0.00 0.00 0.00 3.16
85 86 4.020573 TGGTTAATTGGACTCGATGACAGT 60.021 41.667 0.00 0.00 0.00 3.55
86 87 4.330074 GTGGTTAATTGGACTCGATGACAG 59.670 45.833 0.00 0.00 0.00 3.51
87 88 4.250464 GTGGTTAATTGGACTCGATGACA 58.750 43.478 0.00 0.00 0.00 3.58
88 89 3.621715 GGTGGTTAATTGGACTCGATGAC 59.378 47.826 0.00 0.00 0.00 3.06
89 90 3.517901 AGGTGGTTAATTGGACTCGATGA 59.482 43.478 0.00 0.00 0.00 2.92
90 91 3.873910 AGGTGGTTAATTGGACTCGATG 58.126 45.455 0.00 0.00 0.00 3.84
91 92 4.569719 AAGGTGGTTAATTGGACTCGAT 57.430 40.909 0.00 0.00 0.00 3.59
92 93 4.322953 GGTAAGGTGGTTAATTGGACTCGA 60.323 45.833 0.00 0.00 0.00 4.04
93 94 3.937079 GGTAAGGTGGTTAATTGGACTCG 59.063 47.826 0.00 0.00 0.00 4.18
94 95 4.018688 AGGGTAAGGTGGTTAATTGGACTC 60.019 45.833 0.00 0.00 0.00 3.36
95 96 3.920841 AGGGTAAGGTGGTTAATTGGACT 59.079 43.478 0.00 0.00 0.00 3.85
96 97 4.311520 AGGGTAAGGTGGTTAATTGGAC 57.688 45.455 0.00 0.00 0.00 4.02
97 98 4.604490 AGAAGGGTAAGGTGGTTAATTGGA 59.396 41.667 0.00 0.00 0.00 3.53
98 99 4.930696 AGAAGGGTAAGGTGGTTAATTGG 58.069 43.478 0.00 0.00 0.00 3.16
99 100 6.007703 TGAAGAAGGGTAAGGTGGTTAATTG 58.992 40.000 0.00 0.00 0.00 2.32
100 101 6.208840 TGAAGAAGGGTAAGGTGGTTAATT 57.791 37.500 0.00 0.00 0.00 1.40
101 102 5.853572 TGAAGAAGGGTAAGGTGGTTAAT 57.146 39.130 0.00 0.00 0.00 1.40
102 103 5.853572 ATGAAGAAGGGTAAGGTGGTTAA 57.146 39.130 0.00 0.00 0.00 2.01
103 104 7.519347 AATATGAAGAAGGGTAAGGTGGTTA 57.481 36.000 0.00 0.00 0.00 2.85
104 105 6.402981 AATATGAAGAAGGGTAAGGTGGTT 57.597 37.500 0.00 0.00 0.00 3.67
105 106 6.402981 AAATATGAAGAAGGGTAAGGTGGT 57.597 37.500 0.00 0.00 0.00 4.16
106 107 7.615757 AGAAAAATATGAAGAAGGGTAAGGTGG 59.384 37.037 0.00 0.00 0.00 4.61
107 108 8.581253 AGAAAAATATGAAGAAGGGTAAGGTG 57.419 34.615 0.00 0.00 0.00 4.00
108 109 9.601810 AAAGAAAAATATGAAGAAGGGTAAGGT 57.398 29.630 0.00 0.00 0.00 3.50
112 113 9.705290 GCAAAAAGAAAAATATGAAGAAGGGTA 57.295 29.630 0.00 0.00 0.00 3.69
113 114 7.384932 CGCAAAAAGAAAAATATGAAGAAGGGT 59.615 33.333 0.00 0.00 0.00 4.34
114 115 7.148590 CCGCAAAAAGAAAAATATGAAGAAGGG 60.149 37.037 0.00 0.00 0.00 3.95
115 116 7.148590 CCCGCAAAAAGAAAAATATGAAGAAGG 60.149 37.037 0.00 0.00 0.00 3.46
116 117 7.148590 CCCCGCAAAAAGAAAAATATGAAGAAG 60.149 37.037 0.00 0.00 0.00 2.85
117 118 6.648725 CCCCGCAAAAAGAAAAATATGAAGAA 59.351 34.615 0.00 0.00 0.00 2.52
118 119 6.162777 CCCCGCAAAAAGAAAAATATGAAGA 58.837 36.000 0.00 0.00 0.00 2.87
119 120 5.931724 ACCCCGCAAAAAGAAAAATATGAAG 59.068 36.000 0.00 0.00 0.00 3.02
120 121 5.859495 ACCCCGCAAAAAGAAAAATATGAA 58.141 33.333 0.00 0.00 0.00 2.57
121 122 5.476091 ACCCCGCAAAAAGAAAAATATGA 57.524 34.783 0.00 0.00 0.00 2.15
122 123 5.931724 AGAACCCCGCAAAAAGAAAAATATG 59.068 36.000 0.00 0.00 0.00 1.78
123 124 6.109156 AGAACCCCGCAAAAAGAAAAATAT 57.891 33.333 0.00 0.00 0.00 1.28
124 125 5.538849 AGAACCCCGCAAAAAGAAAAATA 57.461 34.783 0.00 0.00 0.00 1.40
125 126 4.415881 AGAACCCCGCAAAAAGAAAAAT 57.584 36.364 0.00 0.00 0.00 1.82
126 127 3.897141 AGAACCCCGCAAAAAGAAAAA 57.103 38.095 0.00 0.00 0.00 1.94
127 128 3.897141 AAGAACCCCGCAAAAAGAAAA 57.103 38.095 0.00 0.00 0.00 2.29
128 129 3.195825 TGAAAGAACCCCGCAAAAAGAAA 59.804 39.130 0.00 0.00 0.00 2.52
129 130 2.761208 TGAAAGAACCCCGCAAAAAGAA 59.239 40.909 0.00 0.00 0.00 2.52
130 131 2.379972 TGAAAGAACCCCGCAAAAAGA 58.620 42.857 0.00 0.00 0.00 2.52
131 132 2.880963 TGAAAGAACCCCGCAAAAAG 57.119 45.000 0.00 0.00 0.00 2.27
132 133 2.036604 GGATGAAAGAACCCCGCAAAAA 59.963 45.455 0.00 0.00 0.00 1.94
133 134 1.616374 GGATGAAAGAACCCCGCAAAA 59.384 47.619 0.00 0.00 0.00 2.44
134 135 1.203001 AGGATGAAAGAACCCCGCAAA 60.203 47.619 0.00 0.00 0.00 3.68
135 136 0.404040 AGGATGAAAGAACCCCGCAA 59.596 50.000 0.00 0.00 0.00 4.85
136 137 0.035439 GAGGATGAAAGAACCCCGCA 60.035 55.000 0.00 0.00 0.00 5.69
137 138 0.253327 AGAGGATGAAAGAACCCCGC 59.747 55.000 0.00 0.00 0.00 6.13
138 139 2.027192 TGAAGAGGATGAAAGAACCCCG 60.027 50.000 0.00 0.00 0.00 5.73
139 140 3.721087 TGAAGAGGATGAAAGAACCCC 57.279 47.619 0.00 0.00 0.00 4.95
140 141 6.484977 GTCATATGAAGAGGATGAAAGAACCC 59.515 42.308 7.07 0.00 31.62 4.11
141 142 7.050377 TGTCATATGAAGAGGATGAAAGAACC 58.950 38.462 7.07 0.00 31.62 3.62
142 143 7.984050 TCTGTCATATGAAGAGGATGAAAGAAC 59.016 37.037 7.07 0.00 39.78 3.01
143 144 7.984050 GTCTGTCATATGAAGAGGATGAAAGAA 59.016 37.037 7.07 0.00 42.74 2.52
144 145 7.495901 GTCTGTCATATGAAGAGGATGAAAGA 58.504 38.462 7.07 0.77 40.22 2.52
145 146 6.420306 CGTCTGTCATATGAAGAGGATGAAAG 59.580 42.308 20.82 0.00 36.60 2.62
146 147 6.276091 CGTCTGTCATATGAAGAGGATGAAA 58.724 40.000 20.82 1.26 31.62 2.69
147 148 5.737349 GCGTCTGTCATATGAAGAGGATGAA 60.737 44.000 25.24 5.24 31.62 2.57
148 149 4.261783 GCGTCTGTCATATGAAGAGGATGA 60.262 45.833 25.24 10.33 0.00 2.92
150 151 3.638627 TGCGTCTGTCATATGAAGAGGAT 59.361 43.478 25.24 0.00 0.00 3.24
153 154 4.039151 ACTGCGTCTGTCATATGAAGAG 57.961 45.455 7.07 6.82 0.00 2.85
159 160 6.163476 TCTTTGTTAACTGCGTCTGTCATAT 58.837 36.000 7.22 0.00 0.00 1.78
163 164 3.184581 CCTCTTTGTTAACTGCGTCTGTC 59.815 47.826 7.22 0.00 0.00 3.51
166 167 3.181469 TGTCCTCTTTGTTAACTGCGTCT 60.181 43.478 7.22 0.00 0.00 4.18
168 169 3.188159 TGTCCTCTTTGTTAACTGCGT 57.812 42.857 7.22 0.00 0.00 5.24
169 170 3.807622 TCTTGTCCTCTTTGTTAACTGCG 59.192 43.478 7.22 0.00 0.00 5.18
173 174 8.017946 GTGATTGATCTTGTCCTCTTTGTTAAC 58.982 37.037 0.00 0.00 0.00 2.01
183 184 4.581309 ACATGGTGATTGATCTTGTCCT 57.419 40.909 0.00 0.00 0.00 3.85
187 188 4.439700 GCAGGAACATGGTGATTGATCTTG 60.440 45.833 0.00 0.00 0.00 3.02
190 191 2.032550 CGCAGGAACATGGTGATTGATC 59.967 50.000 0.00 0.00 0.00 2.92
214 215 1.168714 GCAGATTCACCTTCCACACC 58.831 55.000 0.00 0.00 0.00 4.16
215 216 1.808945 CTGCAGATTCACCTTCCACAC 59.191 52.381 8.42 0.00 0.00 3.82
229 230 8.289618 GTGTAGTCAAAATATGTTTTCTGCAGA 58.710 33.333 13.74 13.74 35.41 4.26
231 232 8.165239 AGTGTAGTCAAAATATGTTTTCTGCA 57.835 30.769 0.00 0.98 35.41 4.41
251 257 7.223971 GCCGAATCAAGTATGTATTCAAGTGTA 59.776 37.037 0.00 0.00 31.37 2.90
257 263 4.055360 CGGCCGAATCAAGTATGTATTCA 58.945 43.478 24.07 0.00 31.37 2.57
258 264 3.432252 CCGGCCGAATCAAGTATGTATTC 59.568 47.826 30.73 0.00 0.00 1.75
259 265 3.181458 ACCGGCCGAATCAAGTATGTATT 60.181 43.478 30.73 0.00 0.00 1.89
260 266 2.367567 ACCGGCCGAATCAAGTATGTAT 59.632 45.455 30.73 0.00 0.00 2.29
261 267 1.758280 ACCGGCCGAATCAAGTATGTA 59.242 47.619 30.73 0.00 0.00 2.29
262 268 0.539986 ACCGGCCGAATCAAGTATGT 59.460 50.000 30.73 8.86 0.00 2.29
263 269 2.519377 TACCGGCCGAATCAAGTATG 57.481 50.000 30.73 8.09 0.00 2.39
264 270 3.547054 TTTACCGGCCGAATCAAGTAT 57.453 42.857 30.73 2.38 0.00 2.12
265 271 3.264104 CTTTTACCGGCCGAATCAAGTA 58.736 45.455 30.73 16.39 0.00 2.24
266 272 2.081462 CTTTTACCGGCCGAATCAAGT 58.919 47.619 30.73 17.57 0.00 3.16
267 273 2.081462 ACTTTTACCGGCCGAATCAAG 58.919 47.619 30.73 23.49 0.00 3.02
268 274 1.807742 CACTTTTACCGGCCGAATCAA 59.192 47.619 30.73 13.05 0.00 2.57
269 275 1.002201 TCACTTTTACCGGCCGAATCA 59.998 47.619 30.73 4.57 0.00 2.57
282 288 2.331451 GCGCCGTTGCTCACTTTT 59.669 55.556 0.00 0.00 34.43 2.27
291 297 3.692367 GATCGATCGGCGCCGTTG 61.692 66.667 44.16 32.84 40.61 4.10
293 299 4.630785 CTGATCGATCGGCGCCGT 62.631 66.667 44.16 32.33 40.61 5.68
301 307 3.634568 AACACCGATCTCTGATCGATC 57.365 47.619 25.41 18.72 43.59 3.69
302 308 5.515797 TTAAACACCGATCTCTGATCGAT 57.484 39.130 25.41 10.82 43.59 3.59
303 309 4.976224 TTAAACACCGATCTCTGATCGA 57.024 40.909 25.41 7.01 43.59 3.59
304 310 6.292381 GGAAATTAAACACCGATCTCTGATCG 60.292 42.308 19.28 19.28 40.86 3.69
305 311 6.538742 TGGAAATTAAACACCGATCTCTGATC 59.461 38.462 0.00 0.00 0.00 2.92
306 312 6.414732 TGGAAATTAAACACCGATCTCTGAT 58.585 36.000 0.00 0.00 0.00 2.90
307 313 5.800296 TGGAAATTAAACACCGATCTCTGA 58.200 37.500 0.00 0.00 0.00 3.27
308 314 6.494893 TTGGAAATTAAACACCGATCTCTG 57.505 37.500 0.00 0.00 0.00 3.35
309 315 5.123979 GCTTGGAAATTAAACACCGATCTCT 59.876 40.000 0.00 0.00 0.00 3.10
310 316 5.332707 GCTTGGAAATTAAACACCGATCTC 58.667 41.667 0.00 0.00 0.00 2.75
311 317 4.157840 GGCTTGGAAATTAAACACCGATCT 59.842 41.667 0.00 0.00 0.00 2.75
312 318 4.157840 AGGCTTGGAAATTAAACACCGATC 59.842 41.667 0.00 0.00 0.00 3.69
313 319 4.086457 AGGCTTGGAAATTAAACACCGAT 58.914 39.130 0.00 0.00 0.00 4.18
314 320 3.492337 AGGCTTGGAAATTAAACACCGA 58.508 40.909 0.00 0.00 0.00 4.69
315 321 3.254657 TGAGGCTTGGAAATTAAACACCG 59.745 43.478 0.00 0.00 0.00 4.94
316 322 4.864704 TGAGGCTTGGAAATTAAACACC 57.135 40.909 0.00 0.00 0.00 4.16
330 336 0.179000 GGGATCACGTGATGAGGCTT 59.821 55.000 34.48 10.79 41.91 4.35
334 340 1.592669 GCCGGGATCACGTGATGAG 60.593 63.158 34.48 22.69 41.91 2.90
335 341 1.893919 TTGCCGGGATCACGTGATGA 61.894 55.000 34.48 6.86 43.13 2.92
336 342 1.431488 CTTGCCGGGATCACGTGATG 61.431 60.000 34.48 20.67 34.37 3.07
337 343 1.153369 CTTGCCGGGATCACGTGAT 60.153 57.895 30.37 30.37 37.51 3.06
373 379 6.951198 TCCTTACAGGGAATGCATTTCTTAAA 59.049 34.615 17.29 7.07 35.59 1.52
393 406 3.140623 GCGTTTAGTGGTTGGTTCCTTA 58.859 45.455 0.00 0.00 0.00 2.69
395 408 1.142262 AGCGTTTAGTGGTTGGTTCCT 59.858 47.619 0.00 0.00 0.00 3.36
456 470 0.951040 GCTGCGCCTTTGACTGTACT 60.951 55.000 4.18 0.00 0.00 2.73
491 505 4.759693 ACCAAATTGTCTAATCTGCGTGAA 59.240 37.500 0.00 0.00 0.00 3.18
551 601 5.763698 GGGGGTGCTAATCTACTTAATGAAC 59.236 44.000 0.00 0.00 0.00 3.18
597 647 3.649843 TCCAAACCCGATACACTATCCT 58.350 45.455 0.00 0.00 31.43 3.24
598 648 4.566987 GATCCAAACCCGATACACTATCC 58.433 47.826 0.00 0.00 31.43 2.59
600 650 3.554337 GCGATCCAAACCCGATACACTAT 60.554 47.826 0.00 0.00 0.00 2.12
601 651 2.223876 GCGATCCAAACCCGATACACTA 60.224 50.000 0.00 0.00 0.00 2.74
602 652 1.472728 GCGATCCAAACCCGATACACT 60.473 52.381 0.00 0.00 0.00 3.55
615 665 1.745653 CTACTGACACTGAGCGATCCA 59.254 52.381 0.00 0.00 0.00 3.41
642 692 1.372307 CGTTAACAGGTCCCCGGTT 59.628 57.895 6.39 4.30 43.65 4.44
643 693 1.410050 AACGTTAACAGGTCCCCGGT 61.410 55.000 0.00 0.00 32.35 5.28
663 713 5.120674 TCTGACAGCGTAAACATTCATTCAG 59.879 40.000 0.00 0.00 0.00 3.02
689 739 1.186200 CAGGGTCGGTTCAGATGAGA 58.814 55.000 0.00 0.00 0.00 3.27
692 742 1.202580 GGATCAGGGTCGGTTCAGATG 60.203 57.143 0.00 0.00 0.00 2.90
706 756 2.435693 GGGTCGGGTCCTGGATCAG 61.436 68.421 9.58 4.85 0.00 2.90
707 757 2.365105 GGGTCGGGTCCTGGATCA 60.365 66.667 9.58 0.00 0.00 2.92
781 862 0.687354 CCACTGGCAGGTTACTCAGT 59.313 55.000 20.34 0.00 40.62 3.41
782 863 0.976641 TCCACTGGCAGGTTACTCAG 59.023 55.000 20.34 0.00 0.00 3.35
783 864 1.429930 TTCCACTGGCAGGTTACTCA 58.570 50.000 20.34 0.00 0.00 3.41
842 924 1.115467 GGAGCAAGGATCGAGGAGAA 58.885 55.000 0.00 0.00 0.00 2.87
868 950 4.351054 GCTGGGTGAGGTGTGGGG 62.351 72.222 0.00 0.00 0.00 4.96
869 951 3.569210 TGCTGGGTGAGGTGTGGG 61.569 66.667 0.00 0.00 0.00 4.61
884 979 0.332972 AAGGGAGGAAGGAATGGTGC 59.667 55.000 0.00 0.00 0.00 5.01
885 980 1.064389 GGAAGGGAGGAAGGAATGGTG 60.064 57.143 0.00 0.00 0.00 4.17
889 984 2.209758 GGAAGGAAGGGAGGAAGGAAT 58.790 52.381 0.00 0.00 0.00 3.01
892 990 1.208706 GAGGAAGGAAGGGAGGAAGG 58.791 60.000 0.00 0.00 0.00 3.46
893 991 0.827368 CGAGGAAGGAAGGGAGGAAG 59.173 60.000 0.00 0.00 0.00 3.46
894 992 0.116541 ACGAGGAAGGAAGGGAGGAA 59.883 55.000 0.00 0.00 0.00 3.36
895 993 0.116541 AACGAGGAAGGAAGGGAGGA 59.883 55.000 0.00 0.00 0.00 3.71
896 994 0.250513 CAACGAGGAAGGAAGGGAGG 59.749 60.000 0.00 0.00 0.00 4.30
897 995 0.391793 GCAACGAGGAAGGAAGGGAG 60.392 60.000 0.00 0.00 0.00 4.30
898 996 1.125093 TGCAACGAGGAAGGAAGGGA 61.125 55.000 0.00 0.00 0.00 4.20
899 997 0.955919 GTGCAACGAGGAAGGAAGGG 60.956 60.000 0.00 0.00 0.00 3.95
923 1021 2.304761 GGTGTGGTATGTTCTTCTGGGA 59.695 50.000 0.00 0.00 0.00 4.37
1051 1161 1.440850 CGCCAACGACGACGAAGTA 60.441 57.895 15.32 0.00 42.41 2.24
1053 1163 4.117372 GCGCCAACGACGACGAAG 62.117 66.667 15.32 5.56 43.93 3.79
1234 1356 3.701040 CCTTTTATCTGTTGTGGATGGGG 59.299 47.826 0.00 0.00 0.00 4.96
1296 1418 0.454620 GTACACCACGAGACGAGCAG 60.455 60.000 0.00 0.00 0.00 4.24
1314 1436 1.000955 CAAGCTTACTCAGACCACCGT 59.999 52.381 0.00 0.00 0.00 4.83
1316 1438 2.841442 ACAAGCTTACTCAGACCACC 57.159 50.000 0.00 0.00 0.00 4.61
1383 1505 1.065854 GTGTGCCCTCACTGCTTAGAT 60.066 52.381 0.00 0.00 43.49 1.98
1384 1506 0.321671 GTGTGCCCTCACTGCTTAGA 59.678 55.000 0.00 0.00 43.49 2.10
1385 1507 0.035317 TGTGTGCCCTCACTGCTTAG 59.965 55.000 2.69 0.00 43.49 2.18
1431 1553 0.595310 GCTCGATCCTCCAGTTACGC 60.595 60.000 0.00 0.00 0.00 4.42
1436 1558 1.215673 TCCTAAGCTCGATCCTCCAGT 59.784 52.381 0.00 0.00 0.00 4.00
1437 1559 1.988293 TCCTAAGCTCGATCCTCCAG 58.012 55.000 0.00 0.00 0.00 3.86
1464 1586 2.014128 AGGGTTTACACACATATGCGC 58.986 47.619 0.00 0.00 0.00 6.09
1470 1592 7.334858 ACAAAATTGAAAGGGTTTACACACAT 58.665 30.769 0.00 0.00 0.00 3.21
1554 1676 5.472478 TGTTACTCCCATATGACTAGCTACG 59.528 44.000 3.65 0.00 0.00 3.51
1555 1677 6.570764 GCTGTTACTCCCATATGACTAGCTAC 60.571 46.154 3.65 1.79 0.00 3.58
1566 1692 3.450904 AGAACCAGCTGTTACTCCCATA 58.549 45.455 13.81 0.00 37.29 2.74
1588 1714 2.586425 ACAAGTGACAACATGAAGGGG 58.414 47.619 0.00 0.00 0.00 4.79
1637 1768 7.066284 CAGACAAAGTTATATTACAGCAGCCTT 59.934 37.037 0.00 0.00 0.00 4.35
1639 1770 6.316390 ACAGACAAAGTTATATTACAGCAGCC 59.684 38.462 0.00 0.00 0.00 4.85
1658 1789 0.105224 CCGTGTACCACCAACAGACA 59.895 55.000 0.00 0.00 0.00 3.41
1675 1806 6.479001 TCAAAAGAAGAGACTAGTTTGTTCCG 59.521 38.462 16.80 6.52 0.00 4.30
1707 1838 1.026718 AGGCCGCAATGCAGAACTAC 61.027 55.000 5.91 0.00 0.00 2.73
1778 1995 9.013229 ACTTCTTCTTTTCTTTGCCAAAATTTT 57.987 25.926 0.00 0.00 0.00 1.82
1780 1997 7.823799 TCACTTCTTCTTTTCTTTGCCAAAATT 59.176 29.630 0.00 0.00 0.00 1.82
1783 2000 6.279513 TCACTTCTTCTTTTCTTTGCCAAA 57.720 33.333 0.00 0.00 0.00 3.28
1786 2003 7.042456 GGATTTTCACTTCTTCTTTTCTTTGCC 60.042 37.037 0.00 0.00 0.00 4.52
1821 2051 6.093082 ACAACTACGCTTTCTTTTTGTGTACT 59.907 34.615 0.00 0.00 0.00 2.73
1822 2052 6.193959 CACAACTACGCTTTCTTTTTGTGTAC 59.806 38.462 0.00 0.00 38.23 2.90
1824 2054 5.092781 CACAACTACGCTTTCTTTTTGTGT 58.907 37.500 0.00 0.00 38.23 3.72
1825 2055 4.499040 CCACAACTACGCTTTCTTTTTGTG 59.501 41.667 0.00 0.00 41.19 3.33
1837 2067 3.431725 GCAGGCCCACAACTACGC 61.432 66.667 0.00 0.00 0.00 4.42
1839 2069 0.035056 ATCAGCAGGCCCACAACTAC 60.035 55.000 0.00 0.00 0.00 2.73
1860 2090 4.714632 TCCTTTCGGCCTAGATATTTTGG 58.285 43.478 0.00 0.00 0.00 3.28
1880 2110 4.696899 AATAGGCGTTTTGTAGCTTTCC 57.303 40.909 0.00 0.00 0.00 3.13
1929 2159 2.849966 CTCATTTCGCGAGCGTCGG 61.850 63.158 17.24 6.18 40.84 4.79
1950 2180 1.130561 CGCACCACCTTTAGCTAAAGC 59.869 52.381 32.21 22.47 40.93 3.51
1955 2185 0.821711 TTTGCGCACCACCTTTAGCT 60.822 50.000 11.12 0.00 0.00 3.32
1977 2207 2.280186 CTGCGAATAGGGCCGGTC 60.280 66.667 1.90 0.00 0.00 4.79
2019 2251 3.355378 CATTGTGAGGTTGGGAGCAATA 58.645 45.455 0.00 0.00 0.00 1.90
2059 2291 1.818522 GCTTAGTCCCTAGCTCGGCTA 60.819 57.143 0.00 5.64 40.44 3.93
2064 2296 0.386113 CCGTGCTTAGTCCCTAGCTC 59.614 60.000 0.00 0.00 0.00 4.09
2066 2298 1.227292 GCCGTGCTTAGTCCCTAGC 60.227 63.158 0.00 0.00 0.00 3.42
2072 2304 1.202076 GCATTTCAGCCGTGCTTAGTC 60.202 52.381 0.00 0.00 36.40 2.59
2094 2326 5.628134 AGTTGTTACTTTTAAGCATAGCGC 58.372 37.500 0.00 0.00 42.91 5.92
2105 2337 8.762481 ATCTCCCACTTTTAGTTGTTACTTTT 57.238 30.769 0.00 0.00 35.78 2.27
2141 2373 8.839310 TTTCCAAGAAATGTTGAAAAAGTTGA 57.161 26.923 0.00 0.00 0.00 3.18
2167 2399 9.665719 ACATTTTTAAGAAACTTTGTCCACATT 57.334 25.926 0.00 0.00 0.00 2.71
2173 2405 8.318167 CCGTTCACATTTTTAAGAAACTTTGTC 58.682 33.333 0.00 0.00 0.00 3.18
2179 2411 7.275999 TCCAAACCGTTCACATTTTTAAGAAAC 59.724 33.333 0.00 0.00 0.00 2.78
2183 2415 7.527084 TTTCCAAACCGTTCACATTTTTAAG 57.473 32.000 0.00 0.00 0.00 1.85
2188 2420 4.202070 ACGATTTCCAAACCGTTCACATTT 60.202 37.500 0.00 0.00 30.41 2.32
2189 2421 3.316868 ACGATTTCCAAACCGTTCACATT 59.683 39.130 0.00 0.00 30.41 2.71
2190 2422 2.882137 ACGATTTCCAAACCGTTCACAT 59.118 40.909 0.00 0.00 30.41 3.21
2191 2423 2.290464 ACGATTTCCAAACCGTTCACA 58.710 42.857 0.00 0.00 30.41 3.58
2192 2424 4.471157 TTACGATTTCCAAACCGTTCAC 57.529 40.909 0.00 0.00 36.58 3.18
2193 2425 5.692613 ATTTACGATTTCCAAACCGTTCA 57.307 34.783 0.00 0.00 36.58 3.18
2194 2426 8.504812 TTTTATTTACGATTTCCAAACCGTTC 57.495 30.769 0.00 0.00 36.58 3.95
2197 2429 9.130312 TGAATTTTATTTACGATTTCCAAACCG 57.870 29.630 0.00 0.00 0.00 4.44
2252 2484 9.689976 TCAGAAAAATTGCTCAAATATTCGAAA 57.310 25.926 0.00 0.00 32.99 3.46
2253 2485 9.689976 TTCAGAAAAATTGCTCAAATATTCGAA 57.310 25.926 0.00 0.00 32.99 3.71
2254 2486 9.689976 TTTCAGAAAAATTGCTCAAATATTCGA 57.310 25.926 0.00 0.00 32.99 3.71
2260 2492 8.665643 TCACATTTCAGAAAAATTGCTCAAAT 57.334 26.923 0.00 0.00 0.00 2.32
2261 2493 8.389603 GTTCACATTTCAGAAAAATTGCTCAAA 58.610 29.630 0.00 0.00 0.00 2.69
2263 2495 7.040494 TGTTCACATTTCAGAAAAATTGCTCA 58.960 30.769 0.00 0.00 0.00 4.26
2264 2496 7.467557 TGTTCACATTTCAGAAAAATTGCTC 57.532 32.000 0.00 0.00 0.00 4.26
2265 2497 7.846644 TTGTTCACATTTCAGAAAAATTGCT 57.153 28.000 0.00 0.00 0.00 3.91
2266 2498 9.505995 AAATTGTTCACATTTCAGAAAAATTGC 57.494 25.926 0.00 0.00 39.52 3.56
2316 2548 8.380644 CACGGTATACTAAGAAAATGTTCAGTG 58.619 37.037 2.25 0.00 36.09 3.66
2320 2552 8.928733 TGTTCACGGTATACTAAGAAAATGTTC 58.071 33.333 2.25 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.