Multiple sequence alignment - TraesCS2D01G209500

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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 TraesCS2D01G209500 chr2D 100.000 2581 0 0 1 2581 165439237 165436657 0.000000e+00 4767
1 TraesCS2D01G209500 chr2D 92.208 1232 75 10 414 1627 644015509 644014281 0.000000e+00 1724
2 TraesCS2D01G209500 chr2D 93.348 917 49 5 1626 2533 7032741 7033654 0.000000e+00 1345
3 TraesCS2D01G209500 chr5A 91.967 1220 86 9 414 1627 536362167 536363380 0.000000e+00 1700
4 TraesCS2D01G209500 chr2A 91.797 1219 87 10 416 1627 743065571 743066783 0.000000e+00 1685
5 TraesCS2D01G209500 chr2A 90.383 1227 99 11 414 1627 549959904 549958684 0.000000e+00 1594
6 TraesCS2D01G209500 chr2A 87.138 311 24 6 1 301 185345444 185345748 3.180000e-89 339
7 TraesCS2D01G209500 chr7D 91.524 1227 87 11 414 1627 18554230 18553008 0.000000e+00 1674
8 TraesCS2D01G209500 chr5D 91.599 1226 75 19 414 1627 59767193 59765984 0.000000e+00 1668
9 TraesCS2D01G209500 chr7A 90.228 1228 98 12 414 1627 136285149 136286368 0.000000e+00 1583
10 TraesCS2D01G209500 chr7A 90.776 954 65 12 1626 2574 37917952 37918887 0.000000e+00 1253
11 TraesCS2D01G209500 chr7B 89.332 1228 105 11 414 1627 98741742 98742957 0.000000e+00 1519
12 TraesCS2D01G209500 chr1A 89.324 1227 108 16 414 1627 119714783 119715999 0.000000e+00 1519
13 TraesCS2D01G209500 chr1D 92.827 962 56 10 1626 2581 490882874 490883828 0.000000e+00 1382
14 TraesCS2D01G209500 chr2B 92.133 966 55 12 1626 2576 396180724 396179765 0.000000e+00 1343
15 TraesCS2D01G209500 chr2B 91.892 962 60 11 1626 2578 441886314 441887266 0.000000e+00 1328
16 TraesCS2D01G209500 chr6B 91.909 964 58 14 1626 2576 239769601 239770557 0.000000e+00 1330
17 TraesCS2D01G209500 chr6B 91.109 956 72 8 1628 2581 511711503 511710559 0.000000e+00 1282
18 TraesCS2D01G209500 chr5B 91.277 963 58 14 1629 2577 677923485 677922535 0.000000e+00 1290
19 TraesCS2D01G209500 chr3B 89.730 964 85 8 1626 2581 202922537 202923494 0.000000e+00 1219


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 TraesCS2D01G209500 chr2D 165436657 165439237 2580 True 4767 4767 100.000 1 2581 1 chr2D.!!$R1 2580
1 TraesCS2D01G209500 chr2D 644014281 644015509 1228 True 1724 1724 92.208 414 1627 1 chr2D.!!$R2 1213
2 TraesCS2D01G209500 chr2D 7032741 7033654 913 False 1345 1345 93.348 1626 2533 1 chr2D.!!$F1 907
3 TraesCS2D01G209500 chr5A 536362167 536363380 1213 False 1700 1700 91.967 414 1627 1 chr5A.!!$F1 1213
4 TraesCS2D01G209500 chr2A 743065571 743066783 1212 False 1685 1685 91.797 416 1627 1 chr2A.!!$F2 1211
5 TraesCS2D01G209500 chr2A 549958684 549959904 1220 True 1594 1594 90.383 414 1627 1 chr2A.!!$R1 1213
6 TraesCS2D01G209500 chr7D 18553008 18554230 1222 True 1674 1674 91.524 414 1627 1 chr7D.!!$R1 1213
7 TraesCS2D01G209500 chr5D 59765984 59767193 1209 True 1668 1668 91.599 414 1627 1 chr5D.!!$R1 1213
8 TraesCS2D01G209500 chr7A 136285149 136286368 1219 False 1583 1583 90.228 414 1627 1 chr7A.!!$F2 1213
9 TraesCS2D01G209500 chr7A 37917952 37918887 935 False 1253 1253 90.776 1626 2574 1 chr7A.!!$F1 948
10 TraesCS2D01G209500 chr7B 98741742 98742957 1215 False 1519 1519 89.332 414 1627 1 chr7B.!!$F1 1213
11 TraesCS2D01G209500 chr1A 119714783 119715999 1216 False 1519 1519 89.324 414 1627 1 chr1A.!!$F1 1213
12 TraesCS2D01G209500 chr1D 490882874 490883828 954 False 1382 1382 92.827 1626 2581 1 chr1D.!!$F1 955
13 TraesCS2D01G209500 chr2B 396179765 396180724 959 True 1343 1343 92.133 1626 2576 1 chr2B.!!$R1 950
14 TraesCS2D01G209500 chr2B 441886314 441887266 952 False 1328 1328 91.892 1626 2578 1 chr2B.!!$F1 952
15 TraesCS2D01G209500 chr6B 239769601 239770557 956 False 1330 1330 91.909 1626 2576 1 chr6B.!!$F1 950
16 TraesCS2D01G209500 chr6B 511710559 511711503 944 True 1282 1282 91.109 1628 2581 1 chr6B.!!$R1 953
17 TraesCS2D01G209500 chr5B 677922535 677923485 950 True 1290 1290 91.277 1629 2577 1 chr5B.!!$R1 948
18 TraesCS2D01G209500 chr3B 202922537 202923494 957 False 1219 1219 89.730 1626 2581 1 chr3B.!!$F1 955

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
54 55 0.179145 ACGGCTCGTGAGATTAACCG 60.179 55.0 10.15 10.15 43.4 4.44 F
391 392 0.179150 GTGCCTCTCGAGTACAGCTG 60.179 60.0 13.48 13.48 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1174 1218 1.005037 AGCCTCGACGTCATTGCAA 60.005 52.632 17.16 0.0 0.0 4.08 R
2078 2129 0.396435 TCCTCAGGCACGTGTTCATT 59.604 50.000 18.38 0.0 0.0 2.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.330275 GACGGTGCAAGTCGCTTT 58.670 55.556 7.67 0.00 43.06 3.51
21 22 1.204312 GACGGTGCAAGTCGCTTTC 59.796 57.895 7.67 0.00 43.06 2.62
22 23 2.170985 CGGTGCAAGTCGCTTTCG 59.829 61.111 0.00 0.00 43.06 3.46
23 24 2.307309 CGGTGCAAGTCGCTTTCGA 61.307 57.895 0.00 0.00 43.06 3.71
31 32 2.978000 TCGCTTTCGATGAGGGCA 59.022 55.556 8.07 0.00 40.21 5.36
32 33 1.295101 TCGCTTTCGATGAGGGCAA 59.705 52.632 8.07 0.00 40.21 4.52
33 34 0.321210 TCGCTTTCGATGAGGGCAAA 60.321 50.000 8.07 0.00 40.21 3.68
34 35 0.179189 CGCTTTCGATGAGGGCAAAC 60.179 55.000 0.00 0.00 38.10 2.93
35 36 0.881118 GCTTTCGATGAGGGCAAACA 59.119 50.000 0.00 0.00 0.00 2.83
36 37 1.401539 GCTTTCGATGAGGGCAAACAC 60.402 52.381 0.00 0.00 0.00 3.32
37 38 0.871722 TTTCGATGAGGGCAAACACG 59.128 50.000 0.00 0.00 0.00 4.49
38 39 0.953471 TTCGATGAGGGCAAACACGG 60.953 55.000 0.00 0.00 0.00 4.94
39 40 2.877691 GATGAGGGCAAACACGGC 59.122 61.111 0.00 0.00 0.00 5.68
40 41 1.675641 GATGAGGGCAAACACGGCT 60.676 57.895 0.00 0.00 0.00 5.52
41 42 1.648467 GATGAGGGCAAACACGGCTC 61.648 60.000 0.00 0.00 0.00 4.70
42 43 3.423154 GAGGGCAAACACGGCTCG 61.423 66.667 0.00 0.00 36.67 5.03
43 44 4.250305 AGGGCAAACACGGCTCGT 62.250 61.111 0.00 0.00 42.36 4.18
53 54 3.735181 ACGGCTCGTGAGATTAACC 57.265 52.632 0.00 0.00 39.18 2.85
54 55 0.179145 ACGGCTCGTGAGATTAACCG 60.179 55.000 10.15 10.15 43.40 4.44
55 56 0.179145 CGGCTCGTGAGATTAACCGT 60.179 55.000 0.00 0.00 40.84 4.83
56 57 1.278238 GGCTCGTGAGATTAACCGTG 58.722 55.000 0.00 0.00 40.84 4.94
57 58 1.403780 GGCTCGTGAGATTAACCGTGT 60.404 52.381 0.00 0.00 40.84 4.49
58 59 1.918609 GCTCGTGAGATTAACCGTGTC 59.081 52.381 0.00 0.00 40.84 3.67
59 60 2.174764 CTCGTGAGATTAACCGTGTCG 58.825 52.381 0.00 0.00 40.84 4.35
60 61 1.135603 TCGTGAGATTAACCGTGTCGG 60.136 52.381 6.64 6.64 44.69 4.79
61 62 4.334606 TCGTGAGATTAACCGTGTCGGG 62.335 54.545 12.71 0.00 43.82 5.14
86 87 2.978010 CGGCGGGTGCTTTGACTT 60.978 61.111 0.00 0.00 42.25 3.01
87 88 2.954611 GGCGGGTGCTTTGACTTC 59.045 61.111 0.00 0.00 42.25 3.01
88 89 2.626780 GGCGGGTGCTTTGACTTCC 61.627 63.158 0.00 0.00 42.25 3.46
89 90 1.600916 GCGGGTGCTTTGACTTCCT 60.601 57.895 0.00 0.00 38.39 3.36
90 91 1.172812 GCGGGTGCTTTGACTTCCTT 61.173 55.000 0.00 0.00 38.39 3.36
91 92 0.593128 CGGGTGCTTTGACTTCCTTG 59.407 55.000 0.00 0.00 0.00 3.61
92 93 0.961753 GGGTGCTTTGACTTCCTTGG 59.038 55.000 0.00 0.00 0.00 3.61
93 94 1.692411 GGTGCTTTGACTTCCTTGGT 58.308 50.000 0.00 0.00 0.00 3.67
94 95 1.609072 GGTGCTTTGACTTCCTTGGTC 59.391 52.381 0.00 0.00 0.00 4.02
95 96 1.264288 GTGCTTTGACTTCCTTGGTCG 59.736 52.381 0.00 0.00 36.58 4.79
96 97 1.134220 TGCTTTGACTTCCTTGGTCGT 60.134 47.619 0.00 0.00 36.58 4.34
97 98 1.947456 GCTTTGACTTCCTTGGTCGTT 59.053 47.619 0.00 0.00 36.58 3.85
98 99 2.357952 GCTTTGACTTCCTTGGTCGTTT 59.642 45.455 0.00 0.00 36.58 3.60
99 100 3.548214 GCTTTGACTTCCTTGGTCGTTTC 60.548 47.826 0.00 0.00 36.58 2.78
100 101 3.553828 TTGACTTCCTTGGTCGTTTCT 57.446 42.857 0.00 0.00 36.58 2.52
101 102 3.107642 TGACTTCCTTGGTCGTTTCTC 57.892 47.619 0.00 0.00 36.58 2.87
102 103 2.059541 GACTTCCTTGGTCGTTTCTCG 58.940 52.381 0.00 0.00 41.41 4.04
103 104 1.411612 ACTTCCTTGGTCGTTTCTCGT 59.588 47.619 0.00 0.00 40.80 4.18
104 105 2.059541 CTTCCTTGGTCGTTTCTCGTC 58.940 52.381 0.00 0.00 40.80 4.20
105 106 0.316204 TCCTTGGTCGTTTCTCGTCC 59.684 55.000 0.00 0.00 45.24 4.79
108 109 2.049802 GGTCGTTTCTCGTCCGCA 60.050 61.111 0.00 0.00 37.89 5.69
109 110 2.087009 GGTCGTTTCTCGTCCGCAG 61.087 63.158 0.00 0.00 37.89 5.18
110 111 2.430244 TCGTTTCTCGTCCGCAGC 60.430 61.111 0.00 0.00 40.80 5.25
111 112 3.479269 CGTTTCTCGTCCGCAGCC 61.479 66.667 0.00 0.00 34.52 4.85
112 113 3.479269 GTTTCTCGTCCGCAGCCG 61.479 66.667 0.00 0.00 0.00 5.52
113 114 3.986006 TTTCTCGTCCGCAGCCGT 61.986 61.111 0.00 0.00 0.00 5.68
114 115 4.717629 TTCTCGTCCGCAGCCGTG 62.718 66.667 0.00 0.00 0.00 4.94
136 137 4.821589 CGCTTCCGAGTCCAGGCC 62.822 72.222 0.00 0.00 36.29 5.19
137 138 4.821589 GCTTCCGAGTCCAGGCCG 62.822 72.222 0.00 0.00 0.00 6.13
138 139 3.068691 CTTCCGAGTCCAGGCCGA 61.069 66.667 0.00 0.00 0.00 5.54
139 140 3.358076 CTTCCGAGTCCAGGCCGAC 62.358 68.421 0.00 0.00 0.00 4.79
142 143 3.691342 CGAGTCCAGGCCGACCAA 61.691 66.667 7.12 0.00 39.06 3.67
143 144 2.266055 GAGTCCAGGCCGACCAAG 59.734 66.667 7.12 0.00 39.06 3.61
144 145 2.203788 AGTCCAGGCCGACCAAGA 60.204 61.111 7.12 0.00 39.06 3.02
145 146 1.827399 GAGTCCAGGCCGACCAAGAA 61.827 60.000 7.12 0.00 39.06 2.52
146 147 1.072505 GTCCAGGCCGACCAAGAAA 59.927 57.895 0.00 0.00 39.06 2.52
147 148 0.955919 GTCCAGGCCGACCAAGAAAG 60.956 60.000 0.00 0.00 39.06 2.62
148 149 2.335712 CCAGGCCGACCAAGAAAGC 61.336 63.158 0.00 0.00 39.06 3.51
149 150 2.358737 AGGCCGACCAAGAAAGCG 60.359 61.111 0.00 0.00 39.06 4.68
150 151 3.431725 GGCCGACCAAGAAAGCGG 61.432 66.667 0.00 0.00 46.14 5.52
152 153 2.358737 CCGACCAAGAAAGCGGCT 60.359 61.111 0.00 0.00 37.08 5.52
153 154 2.680913 CCGACCAAGAAAGCGGCTG 61.681 63.158 1.81 0.00 37.08 4.85
154 155 2.680913 CGACCAAGAAAGCGGCTGG 61.681 63.158 1.81 3.06 0.00 4.85
155 156 2.982744 GACCAAGAAAGCGGCTGGC 61.983 63.158 1.81 0.00 44.05 4.85
156 157 3.752339 CCAAGAAAGCGGCTGGCC 61.752 66.667 1.81 0.00 45.17 5.36
168 169 3.880846 CTGGCCGCGCTTCCATTC 61.881 66.667 16.19 0.00 0.00 2.67
172 173 2.516930 CCGCGCTTCCATTCCCAT 60.517 61.111 5.56 0.00 0.00 4.00
173 174 2.120909 CCGCGCTTCCATTCCCATT 61.121 57.895 5.56 0.00 0.00 3.16
174 175 1.356624 CGCGCTTCCATTCCCATTC 59.643 57.895 5.56 0.00 0.00 2.67
175 176 1.735973 GCGCTTCCATTCCCATTCC 59.264 57.895 0.00 0.00 0.00 3.01
176 177 1.738346 GCGCTTCCATTCCCATTCCC 61.738 60.000 0.00 0.00 0.00 3.97
177 178 1.109323 CGCTTCCATTCCCATTCCCC 61.109 60.000 0.00 0.00 0.00 4.81
178 179 0.760567 GCTTCCATTCCCATTCCCCC 60.761 60.000 0.00 0.00 0.00 5.40
210 211 3.446570 CGAAGGCCCCGTACGTCT 61.447 66.667 15.21 3.33 0.00 4.18
211 212 2.493501 GAAGGCCCCGTACGTCTC 59.506 66.667 15.21 1.98 0.00 3.36
212 213 3.073101 AAGGCCCCGTACGTCTCC 61.073 66.667 15.21 11.23 0.00 3.71
215 216 4.185059 GCCCCGTACGTCTCCGAC 62.185 72.222 15.21 0.00 37.88 4.79
276 277 1.443407 CACTAGGTGGCGGATCTGG 59.557 63.158 3.14 0.00 0.00 3.86
277 278 1.762460 ACTAGGTGGCGGATCTGGG 60.762 63.158 3.14 0.00 0.00 4.45
278 279 2.445845 TAGGTGGCGGATCTGGGG 60.446 66.667 3.14 0.00 0.00 4.96
279 280 2.946988 CTAGGTGGCGGATCTGGGGA 62.947 65.000 3.14 0.00 0.00 4.81
280 281 2.946988 TAGGTGGCGGATCTGGGGAG 62.947 65.000 3.14 0.00 0.00 4.30
281 282 4.554036 GTGGCGGATCTGGGGAGC 62.554 72.222 3.14 0.00 0.00 4.70
284 285 3.849951 GCGGATCTGGGGAGCGAA 61.850 66.667 3.14 0.00 0.00 4.70
285 286 2.900273 CGGATCTGGGGAGCGAAA 59.100 61.111 0.00 0.00 0.00 3.46
286 287 1.220749 CGGATCTGGGGAGCGAAAA 59.779 57.895 0.00 0.00 0.00 2.29
287 288 0.811616 CGGATCTGGGGAGCGAAAAG 60.812 60.000 0.00 0.00 0.00 2.27
300 301 2.770532 GCGAAAAGCTATCGTTTGTCC 58.229 47.619 19.30 2.56 44.04 4.02
301 302 2.415512 GCGAAAAGCTATCGTTTGTCCT 59.584 45.455 19.30 0.00 44.04 3.85
302 303 3.615496 GCGAAAAGCTATCGTTTGTCCTA 59.385 43.478 19.30 0.00 44.04 2.94
303 304 4.492085 GCGAAAAGCTATCGTTTGTCCTAC 60.492 45.833 19.30 0.82 44.04 3.18
304 305 4.032558 CGAAAAGCTATCGTTTGTCCTACC 59.967 45.833 12.36 0.00 35.64 3.18
305 306 4.820894 AAAGCTATCGTTTGTCCTACCT 57.179 40.909 0.00 0.00 0.00 3.08
306 307 5.927281 AAAGCTATCGTTTGTCCTACCTA 57.073 39.130 0.00 0.00 0.00 3.08
307 308 6.481434 AAAGCTATCGTTTGTCCTACCTAT 57.519 37.500 0.00 0.00 0.00 2.57
308 309 5.708877 AGCTATCGTTTGTCCTACCTATC 57.291 43.478 0.00 0.00 0.00 2.08
309 310 4.215827 AGCTATCGTTTGTCCTACCTATCG 59.784 45.833 0.00 0.00 0.00 2.92
310 311 4.214971 GCTATCGTTTGTCCTACCTATCGA 59.785 45.833 0.00 0.00 0.00 3.59
311 312 5.106237 GCTATCGTTTGTCCTACCTATCGAT 60.106 44.000 2.16 2.16 39.47 3.59
312 313 4.825546 TCGTTTGTCCTACCTATCGATC 57.174 45.455 0.00 0.00 0.00 3.69
313 314 3.567164 TCGTTTGTCCTACCTATCGATCC 59.433 47.826 0.00 0.00 0.00 3.36
314 315 3.608707 CGTTTGTCCTACCTATCGATCCG 60.609 52.174 0.00 0.00 0.00 4.18
315 316 2.945080 TGTCCTACCTATCGATCCGT 57.055 50.000 0.00 1.40 0.00 4.69
316 317 2.775890 TGTCCTACCTATCGATCCGTC 58.224 52.381 0.00 0.00 0.00 4.79
317 318 2.371179 TGTCCTACCTATCGATCCGTCT 59.629 50.000 0.00 0.00 0.00 4.18
318 319 2.743126 GTCCTACCTATCGATCCGTCTG 59.257 54.545 0.00 0.00 0.00 3.51
319 320 1.469308 CCTACCTATCGATCCGTCTGC 59.531 57.143 0.00 0.00 0.00 4.26
320 321 1.128878 CTACCTATCGATCCGTCTGCG 59.871 57.143 0.00 0.00 37.95 5.18
332 333 2.915738 CGTCTGCGGTTCTACTACTT 57.084 50.000 0.00 0.00 0.00 2.24
334 335 3.678662 CGTCTGCGGTTCTACTACTTAC 58.321 50.000 0.00 0.00 0.00 2.34
335 336 3.678662 GTCTGCGGTTCTACTACTTACG 58.321 50.000 0.00 0.00 0.00 3.18
336 337 3.126000 GTCTGCGGTTCTACTACTTACGT 59.874 47.826 0.00 0.00 0.00 3.57
337 338 3.753272 TCTGCGGTTCTACTACTTACGTT 59.247 43.478 0.00 0.00 0.00 3.99
338 339 3.825308 TGCGGTTCTACTACTTACGTTG 58.175 45.455 0.00 0.00 0.00 4.10
339 340 3.501828 TGCGGTTCTACTACTTACGTTGA 59.498 43.478 0.00 0.00 0.00 3.18
340 341 3.848582 GCGGTTCTACTACTTACGTTGAC 59.151 47.826 0.00 0.00 0.00 3.18
341 342 4.406943 CGGTTCTACTACTTACGTTGACC 58.593 47.826 0.00 0.00 0.00 4.02
342 343 4.672801 CGGTTCTACTACTTACGTTGACCC 60.673 50.000 0.00 0.00 0.00 4.46
343 344 4.460731 GGTTCTACTACTTACGTTGACCCT 59.539 45.833 0.00 0.00 0.00 4.34
344 345 5.047731 GGTTCTACTACTTACGTTGACCCTT 60.048 44.000 0.00 0.00 0.00 3.95
345 346 6.450545 GTTCTACTACTTACGTTGACCCTTT 58.549 40.000 0.00 0.00 0.00 3.11
346 347 6.259550 TCTACTACTTACGTTGACCCTTTC 57.740 41.667 0.00 0.00 0.00 2.62
347 348 4.942761 ACTACTTACGTTGACCCTTTCA 57.057 40.909 0.00 0.00 0.00 2.69
348 349 4.625028 ACTACTTACGTTGACCCTTTCAC 58.375 43.478 0.00 0.00 32.26 3.18
349 350 2.842457 ACTTACGTTGACCCTTTCACC 58.158 47.619 0.00 0.00 32.26 4.02
350 351 1.796459 CTTACGTTGACCCTTTCACCG 59.204 52.381 0.00 0.00 45.20 4.94
351 352 4.449391 CGTTGACCCTTTCACCGT 57.551 55.556 0.00 0.00 35.51 4.83
352 353 2.231820 CGTTGACCCTTTCACCGTC 58.768 57.895 0.00 0.00 35.51 4.79
353 354 0.249741 CGTTGACCCTTTCACCGTCT 60.250 55.000 0.00 0.00 35.51 4.18
354 355 1.000060 CGTTGACCCTTTCACCGTCTA 60.000 52.381 0.00 0.00 35.51 2.59
355 356 2.353406 CGTTGACCCTTTCACCGTCTAT 60.353 50.000 0.00 0.00 35.51 1.98
356 357 3.119388 CGTTGACCCTTTCACCGTCTATA 60.119 47.826 0.00 0.00 35.51 1.31
357 358 4.618927 CGTTGACCCTTTCACCGTCTATAA 60.619 45.833 0.00 0.00 35.51 0.98
358 359 4.460948 TGACCCTTTCACCGTCTATAAC 57.539 45.455 0.00 0.00 0.00 1.89
359 360 4.091549 TGACCCTTTCACCGTCTATAACT 58.908 43.478 0.00 0.00 0.00 2.24
360 361 4.159135 TGACCCTTTCACCGTCTATAACTC 59.841 45.833 0.00 0.00 0.00 3.01
361 362 3.129988 ACCCTTTCACCGTCTATAACTCG 59.870 47.826 0.00 0.00 0.00 4.18
362 363 3.114065 CCTTTCACCGTCTATAACTCGC 58.886 50.000 0.00 0.00 0.00 5.03
363 364 2.857592 TTCACCGTCTATAACTCGCC 57.142 50.000 0.00 0.00 0.00 5.54
364 365 0.659427 TCACCGTCTATAACTCGCCG 59.341 55.000 0.00 0.00 0.00 6.46
365 366 0.379669 CACCGTCTATAACTCGCCGT 59.620 55.000 0.00 0.00 0.00 5.68
366 367 0.379669 ACCGTCTATAACTCGCCGTG 59.620 55.000 0.00 0.00 0.00 4.94
367 368 0.379669 CCGTCTATAACTCGCCGTGT 59.620 55.000 0.00 0.00 0.00 4.49
368 369 1.599071 CCGTCTATAACTCGCCGTGTA 59.401 52.381 0.00 0.00 0.00 2.90
369 370 2.349249 CCGTCTATAACTCGCCGTGTAG 60.349 54.545 0.00 0.00 0.00 2.74
370 371 2.286294 CGTCTATAACTCGCCGTGTAGT 59.714 50.000 0.00 0.00 0.00 2.73
371 372 3.242543 CGTCTATAACTCGCCGTGTAGTT 60.243 47.826 0.00 0.00 39.25 2.24
372 373 4.033684 GTCTATAACTCGCCGTGTAGTTG 58.966 47.826 0.47 0.00 36.62 3.16
373 374 3.691118 TCTATAACTCGCCGTGTAGTTGT 59.309 43.478 0.47 0.00 36.62 3.32
374 375 2.054687 TAACTCGCCGTGTAGTTGTG 57.945 50.000 0.47 0.00 36.62 3.33
375 376 1.219522 AACTCGCCGTGTAGTTGTGC 61.220 55.000 0.00 0.00 34.70 4.57
376 377 2.356553 TCGCCGTGTAGTTGTGCC 60.357 61.111 0.00 0.00 0.00 5.01
377 378 2.357034 CGCCGTGTAGTTGTGCCT 60.357 61.111 0.00 0.00 0.00 4.75
378 379 2.380410 CGCCGTGTAGTTGTGCCTC 61.380 63.158 0.00 0.00 0.00 4.70
379 380 1.004918 GCCGTGTAGTTGTGCCTCT 60.005 57.895 0.00 0.00 0.00 3.69
380 381 1.014564 GCCGTGTAGTTGTGCCTCTC 61.015 60.000 0.00 0.00 0.00 3.20
381 382 0.732880 CCGTGTAGTTGTGCCTCTCG 60.733 60.000 0.00 0.00 0.00 4.04
382 383 0.240145 CGTGTAGTTGTGCCTCTCGA 59.760 55.000 0.00 0.00 0.00 4.04
383 384 1.729472 CGTGTAGTTGTGCCTCTCGAG 60.729 57.143 5.93 5.93 0.00 4.04
384 385 1.269998 GTGTAGTTGTGCCTCTCGAGT 59.730 52.381 13.13 0.00 0.00 4.18
385 386 2.486982 GTGTAGTTGTGCCTCTCGAGTA 59.513 50.000 13.13 0.00 0.00 2.59
386 387 2.486982 TGTAGTTGTGCCTCTCGAGTAC 59.513 50.000 13.13 8.39 0.00 2.73
387 388 1.617322 AGTTGTGCCTCTCGAGTACA 58.383 50.000 13.13 10.79 0.00 2.90
388 389 1.542030 AGTTGTGCCTCTCGAGTACAG 59.458 52.381 13.13 2.20 0.00 2.74
389 390 0.243907 TTGTGCCTCTCGAGTACAGC 59.756 55.000 13.13 11.45 0.00 4.40
390 391 0.609406 TGTGCCTCTCGAGTACAGCT 60.609 55.000 13.13 0.00 0.00 4.24
391 392 0.179150 GTGCCTCTCGAGTACAGCTG 60.179 60.000 13.48 13.48 0.00 4.24
392 393 0.609406 TGCCTCTCGAGTACAGCTGT 60.609 55.000 25.12 25.12 0.00 4.40
393 394 1.339727 TGCCTCTCGAGTACAGCTGTA 60.340 52.381 22.67 22.67 0.00 2.74
394 395 1.332375 GCCTCTCGAGTACAGCTGTAG 59.668 57.143 26.70 16.43 0.00 2.74
395 396 1.332375 CCTCTCGAGTACAGCTGTAGC 59.668 57.143 26.70 19.37 42.49 3.58
396 397 1.332375 CTCTCGAGTACAGCTGTAGCC 59.668 57.143 26.70 18.72 43.38 3.93
397 398 1.065345 TCTCGAGTACAGCTGTAGCCT 60.065 52.381 26.70 20.28 43.38 4.58
398 399 1.064803 CTCGAGTACAGCTGTAGCCTG 59.935 57.143 26.70 16.11 43.38 4.85
399 400 0.811915 CGAGTACAGCTGTAGCCTGT 59.188 55.000 26.70 9.30 43.38 4.00
400 401 2.014857 CGAGTACAGCTGTAGCCTGTA 58.985 52.381 26.70 2.57 43.38 2.74
401 402 2.422479 CGAGTACAGCTGTAGCCTGTAA 59.578 50.000 26.70 1.73 43.38 2.41
402 403 3.487711 CGAGTACAGCTGTAGCCTGTAAG 60.488 52.174 26.70 8.80 43.38 2.34
403 404 2.166664 AGTACAGCTGTAGCCTGTAAGC 59.833 50.000 26.70 11.54 43.38 3.09
404 405 1.270907 ACAGCTGTAGCCTGTAAGCT 58.729 50.000 20.16 0.00 46.70 3.74
405 406 2.457598 ACAGCTGTAGCCTGTAAGCTA 58.542 47.619 20.16 0.00 44.00 3.32
433 434 0.249405 CGTGTTTGGTTGCCTGCATT 60.249 50.000 0.00 0.00 0.00 3.56
438 439 0.828762 TTGGTTGCCTGCATTGAGCT 60.829 50.000 0.00 0.00 45.94 4.09
445 446 1.475280 GCCTGCATTGAGCTCAATCAA 59.525 47.619 33.95 24.16 44.10 2.57
478 479 2.474112 AGGACGAGGCCTATTTGGTTA 58.526 47.619 4.42 0.00 36.22 2.85
483 484 2.169769 CGAGGCCTATTTGGTTACCTGA 59.830 50.000 4.42 0.00 38.35 3.86
490 491 5.163550 GCCTATTTGGTTACCTGATTTCACC 60.164 44.000 2.07 0.00 38.35 4.02
569 570 2.174319 GGATCGGCAGTTTCTCGCC 61.174 63.158 0.00 0.00 45.28 5.54
685 696 1.763546 GCCAGATCTAGCCTCACCCC 61.764 65.000 1.11 0.00 0.00 4.95
720 744 2.912956 TCACCCATAGCCACTTTCTTCT 59.087 45.455 0.00 0.00 0.00 2.85
1174 1218 9.911788 ATCCAAAATCTGAACTACATCTACAAT 57.088 29.630 0.00 0.00 0.00 2.71
1199 1243 3.343788 GACGTCGAGGCTCTGTGGG 62.344 68.421 13.50 0.00 0.00 4.61
1208 1255 0.036388 GGCTCTGTGGGTTCGAATGA 60.036 55.000 0.00 0.00 0.00 2.57
1304 1351 0.991146 TGGAAGAGCAAGTGGCCATA 59.009 50.000 9.72 0.00 46.50 2.74
1310 1357 2.243221 AGAGCAAGTGGCCATATTCCTT 59.757 45.455 9.72 3.78 46.50 3.36
1314 1361 4.141181 AGCAAGTGGCCATATTCCTTCATA 60.141 41.667 9.72 0.00 46.50 2.15
1339 1386 1.922447 TGGCCATAACCAGAGGTTCAT 59.078 47.619 0.00 0.00 43.05 2.57
1371 1418 5.408299 CACAACACGTTTAGGAGATCAATGA 59.592 40.000 0.00 0.00 0.00 2.57
1490 1537 3.080647 CGGAAGCCCAAGATGGTAC 57.919 57.895 0.00 0.00 35.17 3.34
1526 1573 6.540189 AGGTGAGCATTGACAATATACACTTC 59.460 38.462 19.93 11.22 0.00 3.01
1528 1575 7.066284 GGTGAGCATTGACAATATACACTTCTT 59.934 37.037 19.93 0.00 0.00 2.52
1572 1619 6.201226 TGTTCAATTTGAGCACTAACACAA 57.799 33.333 11.37 0.00 32.63 3.33
1591 1638 2.642139 AGCTTGTGATGCCATTTTCG 57.358 45.000 0.00 0.00 0.00 3.46
1806 1853 3.307762 GGCAAGTTCTACCTTGGAGATGT 60.308 47.826 3.39 0.00 41.70 3.06
1824 1871 1.097547 GTTGGCTATGCATGTCGGCT 61.098 55.000 10.16 0.00 34.04 5.52
1924 1975 6.315642 CACATGAGCTGTTTAATCTCAGACAT 59.684 38.462 0.00 7.81 39.82 3.06
1927 1978 6.705302 TGAGCTGTTTAATCTCAGACATTCT 58.295 36.000 0.00 0.00 33.42 2.40
1928 1979 7.164122 TGAGCTGTTTAATCTCAGACATTCTT 58.836 34.615 0.00 0.00 33.42 2.52
1966 2017 0.998145 AGAGGGCATTTGGAGCTCTT 59.002 50.000 14.64 0.00 44.35 2.85
1975 2026 6.058183 GGCATTTGGAGCTCTTAAGAATAGA 58.942 40.000 14.64 0.00 0.00 1.98
2078 2129 1.564348 GGATCCTTCAGTGGGGCTTTA 59.436 52.381 3.84 0.00 0.00 1.85
2182 2234 3.949113 ACGCTTGGAAGAACAAAAGGTTA 59.051 39.130 0.00 0.00 40.63 2.85
2190 2242 5.128171 GGAAGAACAAAAGGTTAAAGTGGGT 59.872 40.000 0.00 0.00 40.63 4.51
2222 2274 2.159099 TGGCTTAATAGAGGTCAGTGCG 60.159 50.000 0.00 0.00 0.00 5.34
2223 2275 2.100916 GGCTTAATAGAGGTCAGTGCGA 59.899 50.000 0.00 0.00 0.00 5.10
2224 2276 3.243907 GGCTTAATAGAGGTCAGTGCGAT 60.244 47.826 0.00 0.00 0.00 4.58
2233 2285 4.160439 AGAGGTCAGTGCGATATTTGAAGA 59.840 41.667 0.00 0.00 0.00 2.87
2281 2357 5.681179 GCAGAAGAAGAGGAAGATCTGGTAC 60.681 48.000 0.00 0.00 35.87 3.34
2284 2360 4.689062 AGAAGAGGAAGATCTGGTACCAA 58.311 43.478 17.11 7.62 0.00 3.67
2394 2480 4.935205 TGTTTAACTAGCTGGCACTACATG 59.065 41.667 0.00 0.00 0.00 3.21
2395 2481 4.819105 TTAACTAGCTGGCACTACATGT 57.181 40.909 2.69 2.69 0.00 3.21
2396 2482 3.703001 AACTAGCTGGCACTACATGTT 57.297 42.857 2.30 0.00 0.00 2.71
2397 2483 3.703001 ACTAGCTGGCACTACATGTTT 57.297 42.857 2.30 0.00 0.00 2.83
2398 2484 4.819105 ACTAGCTGGCACTACATGTTTA 57.181 40.909 2.30 0.00 0.00 2.01
2399 2485 4.759782 ACTAGCTGGCACTACATGTTTAG 58.240 43.478 2.30 0.00 0.00 1.85
2400 2486 3.981071 AGCTGGCACTACATGTTTAGA 57.019 42.857 2.30 0.00 0.00 2.10
2401 2487 4.494091 AGCTGGCACTACATGTTTAGAT 57.506 40.909 2.30 0.00 0.00 1.98
2410 2496 6.073276 GCACTACATGTTTAGATTGTGTGTGA 60.073 38.462 2.30 0.00 34.29 3.58
2495 2581 4.154015 GTCATATGTGCGCCTAATGCAATA 59.846 41.667 4.18 0.00 45.23 1.90
2500 2586 0.882927 GCGCCTAATGCAATACGGGA 60.883 55.000 0.00 0.00 41.33 5.14
2543 2629 3.411446 TGGTTGTCTCATGCAACTAAGG 58.589 45.455 12.51 0.00 43.93 2.69
2578 2665 2.684881 CCAAACTATGTGCATCTGGGTC 59.315 50.000 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.179189 GTTTGCCCTCATCGAAAGCG 60.179 55.000 0.00 0.00 39.35 4.68
16 17 0.881118 TGTTTGCCCTCATCGAAAGC 59.119 50.000 0.00 0.00 0.00 3.51
17 18 1.135972 CGTGTTTGCCCTCATCGAAAG 60.136 52.381 0.00 0.00 0.00 2.62
18 19 0.871722 CGTGTTTGCCCTCATCGAAA 59.128 50.000 0.00 0.00 0.00 3.46
19 20 0.953471 CCGTGTTTGCCCTCATCGAA 60.953 55.000 0.00 0.00 0.00 3.71
20 21 1.375396 CCGTGTTTGCCCTCATCGA 60.375 57.895 0.00 0.00 0.00 3.59
21 22 3.039202 GCCGTGTTTGCCCTCATCG 62.039 63.158 0.00 0.00 0.00 3.84
22 23 1.648467 GAGCCGTGTTTGCCCTCATC 61.648 60.000 0.00 0.00 0.00 2.92
23 24 1.675641 GAGCCGTGTTTGCCCTCAT 60.676 57.895 0.00 0.00 0.00 2.90
24 25 2.281484 GAGCCGTGTTTGCCCTCA 60.281 61.111 0.00 0.00 0.00 3.86
25 26 3.423154 CGAGCCGTGTTTGCCCTC 61.423 66.667 0.00 0.00 0.00 4.30
26 27 4.250305 ACGAGCCGTGTTTGCCCT 62.250 61.111 0.00 0.00 39.18 5.19
35 36 0.179145 CGGTTAATCTCACGAGCCGT 60.179 55.000 0.00 0.00 42.36 5.68
36 37 0.179145 ACGGTTAATCTCACGAGCCG 60.179 55.000 8.06 8.06 42.86 5.52
37 38 1.278238 CACGGTTAATCTCACGAGCC 58.722 55.000 0.00 0.00 0.00 4.70
38 39 1.918609 GACACGGTTAATCTCACGAGC 59.081 52.381 0.00 0.00 0.00 5.03
39 40 2.174764 CGACACGGTTAATCTCACGAG 58.825 52.381 0.00 0.00 0.00 4.18
40 41 1.135603 CCGACACGGTTAATCTCACGA 60.136 52.381 1.80 0.00 42.73 4.35
41 42 1.265568 CCGACACGGTTAATCTCACG 58.734 55.000 1.80 0.00 42.73 4.35
42 43 1.636988 CCCGACACGGTTAATCTCAC 58.363 55.000 9.28 0.00 46.80 3.51
43 44 0.108520 GCCCGACACGGTTAATCTCA 60.109 55.000 9.28 0.00 46.80 3.27
44 45 0.175073 AGCCCGACACGGTTAATCTC 59.825 55.000 9.28 0.00 46.80 2.75
45 46 0.611714 AAGCCCGACACGGTTAATCT 59.388 50.000 9.28 0.00 46.80 2.40
46 47 0.725117 CAAGCCCGACACGGTTAATC 59.275 55.000 9.28 0.00 46.80 1.75
47 48 0.675522 CCAAGCCCGACACGGTTAAT 60.676 55.000 9.28 0.00 46.80 1.40
48 49 1.301874 CCAAGCCCGACACGGTTAA 60.302 57.895 9.28 0.00 46.80 2.01
49 50 2.344500 CCAAGCCCGACACGGTTA 59.656 61.111 9.28 0.00 46.80 2.85
50 51 4.636435 CCCAAGCCCGACACGGTT 62.636 66.667 9.28 0.00 46.80 4.44
69 70 2.966309 GAAGTCAAAGCACCCGCCG 61.966 63.158 0.00 0.00 39.83 6.46
70 71 2.626780 GGAAGTCAAAGCACCCGCC 61.627 63.158 0.00 0.00 39.83 6.13
71 72 1.172812 AAGGAAGTCAAAGCACCCGC 61.173 55.000 0.00 0.00 38.99 6.13
72 73 0.593128 CAAGGAAGTCAAAGCACCCG 59.407 55.000 0.00 0.00 0.00 5.28
73 74 0.961753 CCAAGGAAGTCAAAGCACCC 59.038 55.000 0.00 0.00 0.00 4.61
74 75 1.609072 GACCAAGGAAGTCAAAGCACC 59.391 52.381 0.00 0.00 34.27 5.01
75 76 1.264288 CGACCAAGGAAGTCAAAGCAC 59.736 52.381 0.00 0.00 33.70 4.40
76 77 1.134220 ACGACCAAGGAAGTCAAAGCA 60.134 47.619 0.00 0.00 33.70 3.91
77 78 1.594331 ACGACCAAGGAAGTCAAAGC 58.406 50.000 0.00 0.00 33.70 3.51
78 79 3.877508 AGAAACGACCAAGGAAGTCAAAG 59.122 43.478 0.00 0.00 33.70 2.77
79 80 3.875134 GAGAAACGACCAAGGAAGTCAAA 59.125 43.478 0.00 0.00 33.70 2.69
80 81 3.463944 GAGAAACGACCAAGGAAGTCAA 58.536 45.455 0.00 0.00 33.70 3.18
81 82 2.545113 CGAGAAACGACCAAGGAAGTCA 60.545 50.000 0.00 0.00 45.77 3.41
82 83 2.059541 CGAGAAACGACCAAGGAAGTC 58.940 52.381 0.00 0.00 45.77 3.01
83 84 1.411612 ACGAGAAACGACCAAGGAAGT 59.588 47.619 0.00 0.00 45.77 3.01
84 85 2.059541 GACGAGAAACGACCAAGGAAG 58.940 52.381 0.00 0.00 45.77 3.46
85 86 2.144482 GACGAGAAACGACCAAGGAA 57.856 50.000 0.00 0.00 45.77 3.36
86 87 3.879912 GACGAGAAACGACCAAGGA 57.120 52.632 0.00 0.00 45.77 3.36
92 93 2.717809 GCTGCGGACGAGAAACGAC 61.718 63.158 0.00 0.00 45.77 4.34
93 94 2.430244 GCTGCGGACGAGAAACGA 60.430 61.111 0.00 0.00 45.77 3.85
119 120 4.821589 GGCCTGGACTCGGAAGCG 62.822 72.222 0.00 0.00 0.00 4.68
120 121 4.821589 CGGCCTGGACTCGGAAGC 62.822 72.222 0.00 0.00 0.00 3.86
121 122 3.068691 TCGGCCTGGACTCGGAAG 61.069 66.667 0.00 0.00 0.00 3.46
122 123 3.379445 GTCGGCCTGGACTCGGAA 61.379 66.667 0.00 0.00 34.09 4.30
125 126 3.649277 CTTGGTCGGCCTGGACTCG 62.649 68.421 7.97 0.00 37.12 4.18
126 127 1.827399 TTCTTGGTCGGCCTGGACTC 61.827 60.000 7.97 2.52 37.12 3.36
127 128 1.415672 TTTCTTGGTCGGCCTGGACT 61.416 55.000 7.97 0.00 37.12 3.85
128 129 0.955919 CTTTCTTGGTCGGCCTGGAC 60.956 60.000 7.97 0.88 36.18 4.02
129 130 1.374947 CTTTCTTGGTCGGCCTGGA 59.625 57.895 7.97 1.99 35.27 3.86
130 131 2.335712 GCTTTCTTGGTCGGCCTGG 61.336 63.158 7.97 0.00 35.27 4.45
131 132 2.680913 CGCTTTCTTGGTCGGCCTG 61.681 63.158 7.97 0.00 35.27 4.85
132 133 2.358737 CGCTTTCTTGGTCGGCCT 60.359 61.111 7.97 0.00 35.27 5.19
133 134 3.431725 CCGCTTTCTTGGTCGGCC 61.432 66.667 0.00 0.00 35.20 6.13
135 136 2.358737 AGCCGCTTTCTTGGTCGG 60.359 61.111 0.00 0.00 44.29 4.79
136 137 2.680913 CCAGCCGCTTTCTTGGTCG 61.681 63.158 0.00 0.00 0.00 4.79
137 138 2.982744 GCCAGCCGCTTTCTTGGTC 61.983 63.158 0.00 0.00 0.00 4.02
138 139 2.985847 GCCAGCCGCTTTCTTGGT 60.986 61.111 0.00 0.00 0.00 3.67
139 140 3.752339 GGCCAGCCGCTTTCTTGG 61.752 66.667 0.00 0.00 37.74 3.61
151 152 3.880846 GAATGGAAGCGCGGCCAG 61.881 66.667 24.56 0.00 37.64 4.85
155 156 2.063541 GAATGGGAATGGAAGCGCGG 62.064 60.000 8.83 0.00 0.00 6.46
156 157 1.356624 GAATGGGAATGGAAGCGCG 59.643 57.895 0.00 0.00 0.00 6.86
157 158 1.735973 GGAATGGGAATGGAAGCGC 59.264 57.895 0.00 0.00 0.00 5.92
158 159 1.109323 GGGGAATGGGAATGGAAGCG 61.109 60.000 0.00 0.00 0.00 4.68
159 160 0.760567 GGGGGAATGGGAATGGAAGC 60.761 60.000 0.00 0.00 0.00 3.86
160 161 3.539338 GGGGGAATGGGAATGGAAG 57.461 57.895 0.00 0.00 0.00 3.46
193 194 3.407046 GAGACGTACGGGGCCTTCG 62.407 68.421 21.06 15.43 0.00 3.79
194 195 2.493501 GAGACGTACGGGGCCTTC 59.506 66.667 21.06 6.71 0.00 3.46
195 196 3.073101 GGAGACGTACGGGGCCTT 61.073 66.667 21.06 0.00 0.00 4.35
258 259 1.443407 CCAGATCCGCCACCTAGTG 59.557 63.158 0.00 0.00 0.00 2.74
259 260 1.762460 CCCAGATCCGCCACCTAGT 60.762 63.158 0.00 0.00 0.00 2.57
260 261 2.511452 CCCCAGATCCGCCACCTAG 61.511 68.421 0.00 0.00 0.00 3.02
261 262 2.445845 CCCCAGATCCGCCACCTA 60.446 66.667 0.00 0.00 0.00 3.08
262 263 4.414956 TCCCCAGATCCGCCACCT 62.415 66.667 0.00 0.00 0.00 4.00
263 264 3.866582 CTCCCCAGATCCGCCACC 61.867 72.222 0.00 0.00 0.00 4.61
264 265 4.554036 GCTCCCCAGATCCGCCAC 62.554 72.222 0.00 0.00 0.00 5.01
267 268 2.869503 TTTTCGCTCCCCAGATCCGC 62.870 60.000 0.00 0.00 0.00 5.54
268 269 0.811616 CTTTTCGCTCCCCAGATCCG 60.812 60.000 0.00 0.00 0.00 4.18
269 270 1.098129 GCTTTTCGCTCCCCAGATCC 61.098 60.000 0.00 0.00 35.14 3.36
270 271 2.398803 GCTTTTCGCTCCCCAGATC 58.601 57.895 0.00 0.00 35.14 2.75
271 272 4.645809 GCTTTTCGCTCCCCAGAT 57.354 55.556 0.00 0.00 35.14 2.90
280 281 2.415512 AGGACAAACGATAGCTTTTCGC 59.584 45.455 16.07 2.84 40.19 4.70
281 282 4.032558 GGTAGGACAAACGATAGCTTTTCG 59.967 45.833 14.93 14.93 42.20 3.46
282 283 5.176592 AGGTAGGACAAACGATAGCTTTTC 58.823 41.667 0.00 0.00 42.67 2.29
283 284 5.161943 AGGTAGGACAAACGATAGCTTTT 57.838 39.130 0.00 0.00 42.67 2.27
284 285 4.820894 AGGTAGGACAAACGATAGCTTT 57.179 40.909 0.00 0.00 42.67 3.51
285 286 5.278364 CGATAGGTAGGACAAACGATAGCTT 60.278 44.000 0.00 0.00 42.67 3.74
286 287 4.215827 CGATAGGTAGGACAAACGATAGCT 59.784 45.833 0.00 0.00 42.67 3.32
287 288 4.214971 TCGATAGGTAGGACAAACGATAGC 59.785 45.833 0.00 0.00 42.67 2.97
288 289 5.936686 TCGATAGGTAGGACAAACGATAG 57.063 43.478 0.00 0.00 46.19 2.08
289 290 5.413833 GGATCGATAGGTAGGACAAACGATA 59.586 44.000 0.00 0.00 38.88 2.92
290 291 4.217983 GGATCGATAGGTAGGACAAACGAT 59.782 45.833 0.00 0.00 40.87 3.73
291 292 3.567164 GGATCGATAGGTAGGACAAACGA 59.433 47.826 0.00 0.00 0.00 3.85
292 293 3.608707 CGGATCGATAGGTAGGACAAACG 60.609 52.174 0.00 0.00 0.00 3.60
293 294 3.317430 ACGGATCGATAGGTAGGACAAAC 59.683 47.826 0.00 0.00 0.00 2.93
294 295 3.559069 ACGGATCGATAGGTAGGACAAA 58.441 45.455 0.00 0.00 0.00 2.83
295 296 3.144506 GACGGATCGATAGGTAGGACAA 58.855 50.000 0.00 0.00 0.00 3.18
296 297 2.371179 AGACGGATCGATAGGTAGGACA 59.629 50.000 0.00 0.00 0.00 4.02
297 298 2.743126 CAGACGGATCGATAGGTAGGAC 59.257 54.545 0.00 0.00 0.00 3.85
298 299 2.874861 GCAGACGGATCGATAGGTAGGA 60.875 54.545 0.00 0.00 0.00 2.94
299 300 1.469308 GCAGACGGATCGATAGGTAGG 59.531 57.143 0.00 0.00 0.00 3.18
300 301 1.128878 CGCAGACGGATCGATAGGTAG 59.871 57.143 0.00 0.00 34.97 3.18
301 302 1.154197 CGCAGACGGATCGATAGGTA 58.846 55.000 0.00 0.00 34.97 3.08
302 303 1.950007 CGCAGACGGATCGATAGGT 59.050 57.895 0.00 0.00 34.97 3.08
303 304 4.849336 CGCAGACGGATCGATAGG 57.151 61.111 0.00 0.00 34.97 2.57
313 314 2.915738 AAGTAGTAGAACCGCAGACG 57.084 50.000 0.00 0.00 39.67 4.18
314 315 3.678662 CGTAAGTAGTAGAACCGCAGAC 58.321 50.000 0.00 0.00 0.00 3.51
335 336 2.825861 TAGACGGTGAAAGGGTCAAC 57.174 50.000 0.00 0.00 40.94 3.18
336 337 4.529377 AGTTATAGACGGTGAAAGGGTCAA 59.471 41.667 0.00 0.00 38.23 3.18
337 338 4.091549 AGTTATAGACGGTGAAAGGGTCA 58.908 43.478 0.00 0.00 33.18 4.02
338 339 4.680702 GAGTTATAGACGGTGAAAGGGTC 58.319 47.826 0.00 0.00 0.00 4.46
339 340 3.129988 CGAGTTATAGACGGTGAAAGGGT 59.870 47.826 0.00 0.00 0.00 4.34
340 341 3.703420 CGAGTTATAGACGGTGAAAGGG 58.297 50.000 0.00 0.00 0.00 3.95
341 342 3.114065 GCGAGTTATAGACGGTGAAAGG 58.886 50.000 0.00 0.00 0.00 3.11
342 343 3.114065 GGCGAGTTATAGACGGTGAAAG 58.886 50.000 0.00 0.00 0.00 2.62
343 344 2.478370 CGGCGAGTTATAGACGGTGAAA 60.478 50.000 0.00 0.00 34.81 2.69
344 345 1.064505 CGGCGAGTTATAGACGGTGAA 59.935 52.381 0.00 0.00 34.81 3.18
345 346 0.659427 CGGCGAGTTATAGACGGTGA 59.341 55.000 0.00 0.00 34.81 4.02
346 347 0.379669 ACGGCGAGTTATAGACGGTG 59.620 55.000 16.62 0.00 44.33 4.94
347 348 0.379669 CACGGCGAGTTATAGACGGT 59.620 55.000 16.62 0.00 44.33 4.83
348 349 0.379669 ACACGGCGAGTTATAGACGG 59.620 55.000 16.62 0.00 44.33 4.79
349 350 2.286294 ACTACACGGCGAGTTATAGACG 59.714 50.000 16.62 0.00 45.74 4.18
350 351 3.959573 ACTACACGGCGAGTTATAGAC 57.040 47.619 16.62 0.00 0.00 2.59
351 352 3.691118 ACAACTACACGGCGAGTTATAGA 59.309 43.478 16.62 0.00 34.13 1.98
352 353 3.789756 CACAACTACACGGCGAGTTATAG 59.210 47.826 16.62 9.17 34.13 1.31
353 354 3.761657 CACAACTACACGGCGAGTTATA 58.238 45.455 16.62 0.00 34.13 0.98
354 355 2.602878 CACAACTACACGGCGAGTTAT 58.397 47.619 16.62 0.00 34.13 1.89
355 356 1.931709 GCACAACTACACGGCGAGTTA 60.932 52.381 16.62 0.00 34.13 2.24
356 357 1.219522 GCACAACTACACGGCGAGTT 61.220 55.000 16.62 10.62 36.31 3.01
357 358 1.663702 GCACAACTACACGGCGAGT 60.664 57.895 16.62 15.91 0.00 4.18
358 359 2.380410 GGCACAACTACACGGCGAG 61.380 63.158 16.62 8.85 0.00 5.03
359 360 2.356553 GGCACAACTACACGGCGA 60.357 61.111 16.62 0.00 0.00 5.54
360 361 2.357034 AGGCACAACTACACGGCG 60.357 61.111 4.80 4.80 0.00 6.46
361 362 1.004918 AGAGGCACAACTACACGGC 60.005 57.895 0.00 0.00 0.00 5.68
362 363 0.732880 CGAGAGGCACAACTACACGG 60.733 60.000 0.00 0.00 0.00 4.94
363 364 0.240145 TCGAGAGGCACAACTACACG 59.760 55.000 0.00 0.00 0.00 4.49
364 365 1.269998 ACTCGAGAGGCACAACTACAC 59.730 52.381 21.68 0.00 0.00 2.90
365 366 1.617322 ACTCGAGAGGCACAACTACA 58.383 50.000 21.68 0.00 0.00 2.74
366 367 2.486982 TGTACTCGAGAGGCACAACTAC 59.513 50.000 21.68 8.20 0.00 2.73
367 368 2.747989 CTGTACTCGAGAGGCACAACTA 59.252 50.000 21.68 0.00 30.58 2.24
368 369 1.542030 CTGTACTCGAGAGGCACAACT 59.458 52.381 21.68 0.00 30.58 3.16
369 370 1.983972 CTGTACTCGAGAGGCACAAC 58.016 55.000 21.68 5.84 30.58 3.32
370 371 0.243907 GCTGTACTCGAGAGGCACAA 59.756 55.000 21.68 0.00 30.58 3.33
371 372 0.609406 AGCTGTACTCGAGAGGCACA 60.609 55.000 21.68 15.11 0.00 4.57
372 373 0.179150 CAGCTGTACTCGAGAGGCAC 60.179 60.000 21.68 11.35 0.00 5.01
373 374 0.609406 ACAGCTGTACTCGAGAGGCA 60.609 55.000 20.16 13.08 0.00 4.75
374 375 1.332375 CTACAGCTGTACTCGAGAGGC 59.668 57.143 22.67 16.03 0.00 4.70
375 376 1.332375 GCTACAGCTGTACTCGAGAGG 59.668 57.143 22.67 11.32 38.21 3.69
376 377 1.332375 GGCTACAGCTGTACTCGAGAG 59.668 57.143 22.67 13.82 41.70 3.20
377 378 1.065345 AGGCTACAGCTGTACTCGAGA 60.065 52.381 22.67 2.54 41.70 4.04
378 379 1.064803 CAGGCTACAGCTGTACTCGAG 59.935 57.143 22.67 15.28 41.70 4.04
379 380 1.095600 CAGGCTACAGCTGTACTCGA 58.904 55.000 22.67 4.14 41.70 4.04
380 381 0.811915 ACAGGCTACAGCTGTACTCG 59.188 55.000 22.67 14.16 41.70 4.18
381 382 3.735514 GCTTACAGGCTACAGCTGTACTC 60.736 52.174 22.67 16.29 41.70 2.59
382 383 2.166664 GCTTACAGGCTACAGCTGTACT 59.833 50.000 22.67 15.96 41.70 2.73
383 384 2.166664 AGCTTACAGGCTACAGCTGTAC 59.833 50.000 22.67 17.78 41.17 2.90
384 385 2.457598 AGCTTACAGGCTACAGCTGTA 58.542 47.619 24.63 24.63 41.17 2.74
385 386 1.270907 AGCTTACAGGCTACAGCTGT 58.729 50.000 25.12 25.12 41.17 4.40
392 393 4.454847 CGCTAGTATGTAGCTTACAGGCTA 59.545 45.833 0.00 1.43 42.77 3.93
393 394 3.253677 CGCTAGTATGTAGCTTACAGGCT 59.746 47.826 0.00 0.00 42.77 4.58
394 395 3.004524 ACGCTAGTATGTAGCTTACAGGC 59.995 47.826 0.00 0.00 42.77 4.85
395 396 4.036498 ACACGCTAGTATGTAGCTTACAGG 59.964 45.833 0.00 0.00 42.77 4.00
396 397 5.171147 ACACGCTAGTATGTAGCTTACAG 57.829 43.478 0.00 0.00 42.77 2.74
397 398 5.571784 AACACGCTAGTATGTAGCTTACA 57.428 39.130 0.00 0.00 43.80 2.41
398 399 5.231568 CCAAACACGCTAGTATGTAGCTTAC 59.768 44.000 0.00 0.00 38.35 2.34
399 400 5.105635 ACCAAACACGCTAGTATGTAGCTTA 60.106 40.000 0.00 0.00 38.35 3.09
400 401 4.181578 CCAAACACGCTAGTATGTAGCTT 58.818 43.478 0.00 0.00 38.35 3.74
401 402 3.194968 ACCAAACACGCTAGTATGTAGCT 59.805 43.478 0.00 0.00 38.35 3.32
402 403 3.518590 ACCAAACACGCTAGTATGTAGC 58.481 45.455 1.98 0.00 37.21 3.58
403 404 4.201685 GCAACCAAACACGCTAGTATGTAG 60.202 45.833 1.98 0.00 0.00 2.74
404 405 3.680937 GCAACCAAACACGCTAGTATGTA 59.319 43.478 1.98 0.00 0.00 2.29
405 406 2.482721 GCAACCAAACACGCTAGTATGT 59.517 45.455 0.00 0.00 0.00 2.29
406 407 2.159572 GGCAACCAAACACGCTAGTATG 60.160 50.000 0.00 0.00 0.00 2.39
407 408 2.081462 GGCAACCAAACACGCTAGTAT 58.919 47.619 0.00 0.00 0.00 2.12
408 409 1.071071 AGGCAACCAAACACGCTAGTA 59.929 47.619 0.00 0.00 37.17 1.82
409 410 0.179029 AGGCAACCAAACACGCTAGT 60.179 50.000 0.00 0.00 37.17 2.57
410 411 0.238289 CAGGCAACCAAACACGCTAG 59.762 55.000 0.00 0.00 37.17 3.42
411 412 1.791103 GCAGGCAACCAAACACGCTA 61.791 55.000 0.00 0.00 37.17 4.26
412 413 3.119193 CAGGCAACCAAACACGCT 58.881 55.556 0.00 0.00 37.17 5.07
433 434 1.941209 GCGTGGACTTGATTGAGCTCA 60.941 52.381 13.74 13.74 0.00 4.26
438 439 1.375396 CCCGCGTGGACTTGATTGA 60.375 57.895 18.79 0.00 37.49 2.57
445 446 3.692406 GTCCTTCCCGCGTGGACT 61.692 66.667 18.79 0.00 45.11 3.85
462 463 2.169769 TCAGGTAACCAAATAGGCCTCG 59.830 50.000 9.68 0.00 43.14 4.63
478 479 0.893727 GCCCAACGGTGAAATCAGGT 60.894 55.000 0.00 0.00 0.00 4.00
483 484 2.275380 GCAGGCCCAACGGTGAAAT 61.275 57.895 0.00 0.00 0.00 2.17
685 696 2.467880 TGGGTGAGCTAGTAGAAAGGG 58.532 52.381 0.00 0.00 0.00 3.95
696 713 0.995024 AAAGTGGCTATGGGTGAGCT 59.005 50.000 0.00 0.00 39.98 4.09
720 744 1.255667 GCCGGTGGTGAGGAAGTAGA 61.256 60.000 1.90 0.00 0.00 2.59
745 769 0.585357 GCGCAGATCTGAAATCGCAT 59.415 50.000 28.91 0.00 37.94 4.73
908 947 0.919710 CTAACAAAGGAGGGAGGGGG 59.080 60.000 0.00 0.00 0.00 5.40
1174 1218 1.005037 AGCCTCGACGTCATTGCAA 60.005 52.632 17.16 0.00 0.00 4.08
1199 1243 4.128554 TGACGCTCTTTTTCATTCGAAC 57.871 40.909 0.00 0.00 0.00 3.95
1208 1255 2.288395 CCTGGCAAATGACGCTCTTTTT 60.288 45.455 0.00 0.00 0.00 1.94
1304 1351 6.041979 GGTTATGGCCAACAATATGAAGGAAT 59.958 38.462 10.96 0.00 0.00 3.01
1310 1357 5.122707 TCTGGTTATGGCCAACAATATGA 57.877 39.130 10.96 0.00 38.18 2.15
1314 1361 2.042979 ACCTCTGGTTATGGCCAACAAT 59.957 45.455 10.96 0.00 38.18 2.71
1339 1386 3.562141 CCTAAACGTGTTGTGAATGACCA 59.438 43.478 0.00 0.00 0.00 4.02
1371 1418 5.128008 GCTTGAAGTACCTAGAGATGGTCTT 59.872 44.000 0.00 0.00 38.88 3.01
1490 1537 2.787473 TGCTCACCTTGAAGTATGGG 57.213 50.000 0.00 0.00 0.00 4.00
1526 1573 7.879070 ACAATACAAGCATATCAAGCCATAAG 58.121 34.615 0.00 0.00 0.00 1.73
1528 1575 7.501892 TGAACAATACAAGCATATCAAGCCATA 59.498 33.333 0.00 0.00 0.00 2.74
1572 1619 1.203052 CCGAAAATGGCATCACAAGCT 59.797 47.619 0.00 0.00 0.00 3.74
1591 1638 3.724624 TTGCCCCAATGCAATCCC 58.275 55.556 0.00 0.00 45.77 3.85
1723 1770 2.932614 ACTGAGAATGTTAGCGTCATGC 59.067 45.455 0.00 0.00 46.98 4.06
1724 1771 4.032217 GTCACTGAGAATGTTAGCGTCATG 59.968 45.833 0.00 0.00 0.00 3.07
1729 1776 2.346847 GCTGTCACTGAGAATGTTAGCG 59.653 50.000 0.00 0.00 0.00 4.26
1806 1853 1.096967 CAGCCGACATGCATAGCCAA 61.097 55.000 0.00 0.00 0.00 4.52
1924 1975 6.041637 TCTCAACAGTTACTCTAAGGCAAGAA 59.958 38.462 0.00 0.00 0.00 2.52
1927 1978 5.279506 CCTCTCAACAGTTACTCTAAGGCAA 60.280 44.000 0.00 0.00 0.00 4.52
1928 1979 4.220821 CCTCTCAACAGTTACTCTAAGGCA 59.779 45.833 0.00 0.00 0.00 4.75
1975 2026 5.133322 TGGCTTCTGATCCAGGATCTTAAAT 59.867 40.000 26.94 0.00 39.56 1.40
2078 2129 0.396435 TCCTCAGGCACGTGTTCATT 59.604 50.000 18.38 0.00 0.00 2.57
2182 2234 2.555227 CCACATTGCCTCTACCCACTTT 60.555 50.000 0.00 0.00 0.00 2.66
2190 2242 5.221722 CCTCTATTAAGCCACATTGCCTCTA 60.222 44.000 0.00 0.00 0.00 2.43
2233 2285 5.559148 TCTGCTTCTTCTTCTTCCTCTTT 57.441 39.130 0.00 0.00 0.00 2.52
2281 2357 3.374058 GGATAGTTCATCGGTGTTGTTGG 59.626 47.826 0.00 0.00 34.12 3.77
2284 2360 2.093128 GGGGATAGTTCATCGGTGTTGT 60.093 50.000 0.00 0.00 34.12 3.32
2360 2436 6.215845 CAGCTAGTTAAACAAATGGCAGTTT 58.784 36.000 0.00 2.90 40.68 2.66
2366 2442 4.218417 AGTGCCAGCTAGTTAAACAAATGG 59.782 41.667 0.00 0.00 0.00 3.16
2394 2480 7.364522 TGAGCTTATCACACACAATCTAAAC 57.635 36.000 0.00 0.00 31.12 2.01
2410 2496 6.868622 CACTTCTAACTAGTGGTGAGCTTAT 58.131 40.000 0.00 0.00 39.42 1.73
2495 2581 1.888638 CCGACGTTTGGTTTCCCGT 60.889 57.895 0.00 0.00 36.04 5.28
2500 2586 1.461559 TTTGACCCGACGTTTGGTTT 58.538 45.000 10.81 0.00 34.20 3.27
2510 2596 2.882137 GAGACAACCATTTTTGACCCGA 59.118 45.455 0.00 0.00 0.00 5.14
2543 2629 5.646360 ACATAGTTTGGTTGCCTACATGTAC 59.354 40.000 0.08 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.