Multiple sequence alignment - TraesCS4D01G282400

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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 TraesCS4D01G282400 chr4D 100.000 3440 0 0 1 3440 453335395 453331956 0.000000e+00 6353.0
1 TraesCS4D01G282400 chr4D 74.121 626 114 39 1728 2329 453333701 453333100 7.480000e-52 215.0
2 TraesCS4D01G282400 chr4B 91.170 1778 101 28 1695 3440 567007790 567006037 0.000000e+00 2362.0
3 TraesCS4D01G282400 chr4B 89.945 1452 74 29 607 1992 567008968 567007523 0.000000e+00 1807.0
4 TraesCS4D01G282400 chr4B 94.702 151 8 0 6 156 567015142 567014992 5.740000e-58 235.0
5 TraesCS4D01G282400 chr4B 89.385 179 16 3 173 348 567009255 567009077 4.470000e-54 222.0
6 TraesCS4D01G282400 chr4B 80.870 230 24 12 1763 1991 567007854 567007644 2.750000e-36 163.0
7 TraesCS4D01G282400 chr4B 84.247 146 11 1 1697 1842 567007602 567007469 7.750000e-27 132.0
8 TraesCS4D01G282400 chr4B 89.000 100 1 3 537 630 567009079 567008984 7.800000e-22 115.0
9 TraesCS4D01G282400 chr4A 85.413 1755 141 61 640 2322 13742289 13744000 0.000000e+00 1716.0
10 TraesCS4D01G282400 chr4A 94.082 828 31 13 2623 3437 13745917 13746739 0.000000e+00 1242.0
11 TraesCS4D01G282400 chr4A 83.598 1006 100 47 1657 2636 13743419 13744385 0.000000e+00 883.0
12 TraesCS4D01G282400 chr4A 75.397 504 86 31 1697 2190 13743591 13744066 3.480000e-50 209.0
13 TraesCS4D01G282400 chr4A 89.167 120 13 0 1889 2008 13743501 13743620 2.140000e-32 150.0
14 TraesCS4D01G282400 chr7A 82.250 400 45 15 2177 2564 717519081 717519466 4.280000e-84 322.0
15 TraesCS4D01G282400 chr7A 91.329 173 12 2 1104 1276 717518738 717518907 2.060000e-57 233.0
16 TraesCS4D01G282400 chr7A 95.238 42 2 0 1284 1325 717518885 717518926 2.220000e-07 67.6


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 TraesCS4D01G282400 chr4D 453331956 453335395 3439 True 3284.000000 6353 87.060500 1 3440 2 chr4D.!!$R1 3439
1 TraesCS4D01G282400 chr4B 567006037 567009255 3218 True 800.166667 2362 87.436167 173 3440 6 chr4B.!!$R2 3267
2 TraesCS4D01G282400 chr4A 13742289 13746739 4450 False 840.000000 1716 85.531400 640 3437 5 chr4A.!!$F1 2797
3 TraesCS4D01G282400 chr7A 717518738 717519466 728 False 207.533333 322 89.605667 1104 2564 3 chr7A.!!$F1 1460

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
29 30 0.032952 TTAACGCACCGAAGCTGAGT 59.967 50.0 0.0 0.0 0.0 3.41 F
45 46 0.179081 GAGTCCCCGCCAATGAGTAC 60.179 60.0 0.0 0.0 0.0 2.73 F
383 387 0.179081 GAATCCGACCACTACCCAGC 60.179 60.0 0.0 0.0 0.0 4.85 F
1341 1437 0.234625 CGTGTCCGTGGTGTTCATTG 59.765 55.0 0.0 0.0 0.0 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 1440 1.143073 ACTCTGACCACCCAAGAAACC 59.857 52.381 0.00 0.0 0.00 3.27 R
2321 2623 0.924090 GTACCCCTGGTTGGCCTTAT 59.076 55.000 3.32 0.0 37.09 1.73 R
2322 2624 1.555477 CGTACCCCTGGTTGGCCTTA 61.555 60.000 3.32 0.0 37.09 2.69 R
2741 4636 0.250793 TCGACATGCCGGTGGTAATT 59.749 50.000 1.90 0.0 0.00 1.40 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
18 19 2.561373 GCACCTGCCTTAACGCAC 59.439 61.111 0.00 0.00 34.35 5.34
19 20 2.978018 GCACCTGCCTTAACGCACC 61.978 63.158 0.00 0.00 34.35 5.01
20 21 2.358247 ACCTGCCTTAACGCACCG 60.358 61.111 0.00 0.00 34.35 4.94
21 22 2.047655 CCTGCCTTAACGCACCGA 60.048 61.111 0.00 0.00 34.35 4.69
22 23 1.669760 CCTGCCTTAACGCACCGAA 60.670 57.895 0.00 0.00 34.35 4.30
23 24 1.635663 CCTGCCTTAACGCACCGAAG 61.636 60.000 0.00 0.00 34.35 3.79
24 25 2.240612 CTGCCTTAACGCACCGAAGC 62.241 60.000 0.00 0.00 34.35 3.86
25 26 2.033194 GCCTTAACGCACCGAAGCT 61.033 57.895 0.00 0.00 0.00 3.74
26 27 1.787847 CCTTAACGCACCGAAGCTG 59.212 57.895 0.00 0.00 0.00 4.24
27 28 0.669318 CCTTAACGCACCGAAGCTGA 60.669 55.000 0.00 0.00 0.00 4.26
28 29 0.716108 CTTAACGCACCGAAGCTGAG 59.284 55.000 0.00 0.00 0.00 3.35
29 30 0.032952 TTAACGCACCGAAGCTGAGT 59.967 50.000 0.00 0.00 0.00 3.41
30 31 0.388134 TAACGCACCGAAGCTGAGTC 60.388 55.000 0.00 0.00 0.00 3.36
31 32 2.811317 CGCACCGAAGCTGAGTCC 60.811 66.667 0.00 0.00 0.00 3.85
32 33 2.435059 GCACCGAAGCTGAGTCCC 60.435 66.667 0.00 0.00 0.00 4.46
33 34 2.266055 CACCGAAGCTGAGTCCCC 59.734 66.667 0.00 0.00 0.00 4.81
34 35 3.382832 ACCGAAGCTGAGTCCCCG 61.383 66.667 0.00 0.00 0.00 5.73
35 36 4.821589 CCGAAGCTGAGTCCCCGC 62.822 72.222 0.00 0.00 0.00 6.13
36 37 4.821589 CGAAGCTGAGTCCCCGCC 62.822 72.222 0.00 0.00 0.00 6.13
37 38 3.706373 GAAGCTGAGTCCCCGCCA 61.706 66.667 0.00 0.00 0.00 5.69
38 39 3.249189 AAGCTGAGTCCCCGCCAA 61.249 61.111 0.00 0.00 0.00 4.52
39 40 2.543067 GAAGCTGAGTCCCCGCCAAT 62.543 60.000 0.00 0.00 0.00 3.16
40 41 2.825836 GCTGAGTCCCCGCCAATG 60.826 66.667 0.00 0.00 0.00 2.82
41 42 2.989639 CTGAGTCCCCGCCAATGA 59.010 61.111 0.00 0.00 0.00 2.57
42 43 1.153289 CTGAGTCCCCGCCAATGAG 60.153 63.158 0.00 0.00 0.00 2.90
43 44 1.903877 CTGAGTCCCCGCCAATGAGT 61.904 60.000 0.00 0.00 0.00 3.41
44 45 0.616395 TGAGTCCCCGCCAATGAGTA 60.616 55.000 0.00 0.00 0.00 2.59
45 46 0.179081 GAGTCCCCGCCAATGAGTAC 60.179 60.000 0.00 0.00 0.00 2.73
46 47 1.520787 GTCCCCGCCAATGAGTACG 60.521 63.158 0.00 0.00 0.00 3.67
47 48 1.985662 TCCCCGCCAATGAGTACGT 60.986 57.895 0.00 0.00 0.00 3.57
48 49 1.520787 CCCCGCCAATGAGTACGTC 60.521 63.158 0.00 0.00 0.00 4.34
49 50 1.216977 CCCGCCAATGAGTACGTCA 59.783 57.895 0.00 0.00 40.38 4.35
50 51 1.082117 CCCGCCAATGAGTACGTCAC 61.082 60.000 0.00 0.00 38.28 3.67
51 52 1.082117 CCGCCAATGAGTACGTCACC 61.082 60.000 0.00 0.00 38.28 4.02
52 53 1.410737 CGCCAATGAGTACGTCACCG 61.411 60.000 0.00 0.00 38.28 4.94
53 54 1.082117 GCCAATGAGTACGTCACCGG 61.082 60.000 0.00 0.00 38.28 5.28
54 55 0.528924 CCAATGAGTACGTCACCGGA 59.471 55.000 9.46 0.00 38.28 5.14
55 56 1.136305 CCAATGAGTACGTCACCGGAT 59.864 52.381 9.46 0.00 38.28 4.18
56 57 2.418197 CCAATGAGTACGTCACCGGATT 60.418 50.000 9.46 0.00 38.28 3.01
57 58 3.181484 CCAATGAGTACGTCACCGGATTA 60.181 47.826 9.46 0.00 38.28 1.75
58 59 4.500887 CCAATGAGTACGTCACCGGATTAT 60.501 45.833 9.46 0.00 38.28 1.28
59 60 3.976793 TGAGTACGTCACCGGATTATC 57.023 47.619 9.46 0.00 38.78 1.75
60 61 3.281158 TGAGTACGTCACCGGATTATCA 58.719 45.455 9.46 0.00 38.78 2.15
61 62 3.887110 TGAGTACGTCACCGGATTATCAT 59.113 43.478 9.46 0.00 38.78 2.45
62 63 4.340097 TGAGTACGTCACCGGATTATCATT 59.660 41.667 9.46 0.00 38.78 2.57
63 64 5.163488 TGAGTACGTCACCGGATTATCATTT 60.163 40.000 9.46 0.00 38.78 2.32
64 65 5.047847 AGTACGTCACCGGATTATCATTTG 58.952 41.667 9.46 0.00 38.78 2.32
65 66 4.131649 ACGTCACCGGATTATCATTTGA 57.868 40.909 9.46 0.00 38.78 2.69
66 67 4.509616 ACGTCACCGGATTATCATTTGAA 58.490 39.130 9.46 0.00 38.78 2.69
67 68 4.331717 ACGTCACCGGATTATCATTTGAAC 59.668 41.667 9.46 0.00 38.78 3.18
68 69 4.331443 CGTCACCGGATTATCATTTGAACA 59.669 41.667 9.46 0.00 0.00 3.18
69 70 5.569413 GTCACCGGATTATCATTTGAACAC 58.431 41.667 9.46 0.00 0.00 3.32
70 71 5.123186 GTCACCGGATTATCATTTGAACACA 59.877 40.000 9.46 0.00 0.00 3.72
71 72 5.707764 TCACCGGATTATCATTTGAACACAA 59.292 36.000 9.46 0.00 0.00 3.33
72 73 6.207614 TCACCGGATTATCATTTGAACACAAA 59.792 34.615 9.46 0.00 37.80 2.83
73 74 7.035004 CACCGGATTATCATTTGAACACAAAT 58.965 34.615 9.46 0.00 42.56 2.32
74 75 7.220683 CACCGGATTATCATTTGAACACAAATC 59.779 37.037 9.46 0.00 40.72 2.17
75 76 7.122650 ACCGGATTATCATTTGAACACAAATCT 59.877 33.333 9.46 0.00 40.72 2.40
76 77 8.620416 CCGGATTATCATTTGAACACAAATCTA 58.380 33.333 0.00 0.00 40.72 1.98
113 114 9.993454 TCTTGAATATGAATCTAATGGAGACTG 57.007 33.333 0.00 0.00 36.87 3.51
114 115 8.613060 TTGAATATGAATCTAATGGAGACTGC 57.387 34.615 0.00 0.00 36.87 4.40
115 116 7.738847 TGAATATGAATCTAATGGAGACTGCA 58.261 34.615 0.00 0.00 36.87 4.41
116 117 7.876582 TGAATATGAATCTAATGGAGACTGCAG 59.123 37.037 13.48 13.48 36.87 4.41
117 118 5.627182 ATGAATCTAATGGAGACTGCAGT 57.373 39.130 21.88 21.88 36.87 4.40
118 119 5.426689 TGAATCTAATGGAGACTGCAGTT 57.573 39.130 22.65 11.02 36.87 3.16
119 120 5.181009 TGAATCTAATGGAGACTGCAGTTG 58.819 41.667 22.65 0.46 36.87 3.16
120 121 4.833478 ATCTAATGGAGACTGCAGTTGT 57.167 40.909 22.65 11.85 36.87 3.32
121 122 4.623932 TCTAATGGAGACTGCAGTTGTT 57.376 40.909 22.65 10.03 0.00 2.83
122 123 4.569943 TCTAATGGAGACTGCAGTTGTTC 58.430 43.478 22.65 17.87 0.00 3.18
123 124 2.936919 ATGGAGACTGCAGTTGTTCA 57.063 45.000 22.65 16.63 0.00 3.18
124 125 2.708216 TGGAGACTGCAGTTGTTCAA 57.292 45.000 22.65 10.16 0.00 2.69
125 126 2.997980 TGGAGACTGCAGTTGTTCAAA 58.002 42.857 22.65 8.73 0.00 2.69
126 127 3.351740 TGGAGACTGCAGTTGTTCAAAA 58.648 40.909 22.65 6.50 0.00 2.44
127 128 3.953612 TGGAGACTGCAGTTGTTCAAAAT 59.046 39.130 22.65 0.00 0.00 1.82
128 129 4.402155 TGGAGACTGCAGTTGTTCAAAATT 59.598 37.500 22.65 0.00 0.00 1.82
129 130 5.105392 TGGAGACTGCAGTTGTTCAAAATTT 60.105 36.000 22.65 0.00 0.00 1.82
130 131 5.460091 GGAGACTGCAGTTGTTCAAAATTTC 59.540 40.000 22.65 2.84 0.00 2.17
131 132 5.351458 AGACTGCAGTTGTTCAAAATTTCC 58.649 37.500 22.65 2.36 0.00 3.13
132 133 4.441792 ACTGCAGTTGTTCAAAATTTCCC 58.558 39.130 15.25 0.00 0.00 3.97
133 134 3.802866 TGCAGTTGTTCAAAATTTCCCC 58.197 40.909 0.00 0.00 0.00 4.81
134 135 2.799978 GCAGTTGTTCAAAATTTCCCCG 59.200 45.455 0.00 0.00 0.00 5.73
135 136 2.799978 CAGTTGTTCAAAATTTCCCCGC 59.200 45.455 0.00 0.00 0.00 6.13
136 137 2.139917 GTTGTTCAAAATTTCCCCGCC 58.860 47.619 0.00 0.00 0.00 6.13
137 138 1.414158 TGTTCAAAATTTCCCCGCCA 58.586 45.000 0.00 0.00 0.00 5.69
138 139 1.762957 TGTTCAAAATTTCCCCGCCAA 59.237 42.857 0.00 0.00 0.00 4.52
139 140 2.370189 TGTTCAAAATTTCCCCGCCAAT 59.630 40.909 0.00 0.00 0.00 3.16
140 141 2.741517 GTTCAAAATTTCCCCGCCAATG 59.258 45.455 0.00 0.00 0.00 2.82
141 142 2.251818 TCAAAATTTCCCCGCCAATGA 58.748 42.857 0.00 0.00 0.00 2.57
142 143 2.233431 TCAAAATTTCCCCGCCAATGAG 59.767 45.455 0.00 0.00 0.00 2.90
143 144 1.937191 AAATTTCCCCGCCAATGAGT 58.063 45.000 0.00 0.00 0.00 3.41
144 145 2.818751 AATTTCCCCGCCAATGAGTA 57.181 45.000 0.00 0.00 0.00 2.59
145 146 3.312736 AATTTCCCCGCCAATGAGTAT 57.687 42.857 0.00 0.00 0.00 2.12
146 147 2.051334 TTTCCCCGCCAATGAGTATG 57.949 50.000 0.00 0.00 0.00 2.39
147 148 0.916086 TTCCCCGCCAATGAGTATGT 59.084 50.000 0.00 0.00 0.00 2.29
148 149 0.468226 TCCCCGCCAATGAGTATGTC 59.532 55.000 0.00 0.00 0.00 3.06
149 150 0.180171 CCCCGCCAATGAGTATGTCA 59.820 55.000 0.00 0.00 40.38 3.58
224 225 1.261480 TTGCGGCATGTAACCCAAAT 58.739 45.000 2.28 0.00 0.00 2.32
230 231 4.061596 CGGCATGTAACCCAAATTTTTGT 58.938 39.130 0.00 0.00 36.45 2.83
249 250 6.939132 TTTGTAGTCAAATAAAACGGGACA 57.061 33.333 0.00 0.00 38.44 4.02
264 265 2.353704 CGGGACAGAGATTGCAGTTGTA 60.354 50.000 0.00 0.00 0.00 2.41
270 271 7.244192 GGACAGAGATTGCAGTTGTATAAAAC 58.756 38.462 0.00 0.00 0.00 2.43
274 275 7.965107 CAGAGATTGCAGTTGTATAAAACTTCC 59.035 37.037 5.50 1.54 38.34 3.46
278 279 4.083565 GCAGTTGTATAAAACTTCCCCCA 58.916 43.478 5.50 0.00 38.34 4.96
327 331 7.946381 AGAAGAGGAGAAAACTCAACTTTTT 57.054 32.000 0.00 0.00 37.43 1.94
335 339 9.196552 GGAGAAAACTCAACTTTTTCATTATGG 57.803 33.333 9.54 0.00 42.86 2.74
340 344 9.533253 AAACTCAACTTTTTCATTATGGAGTTG 57.467 29.630 17.08 17.08 40.88 3.16
341 345 8.463930 ACTCAACTTTTTCATTATGGAGTTGA 57.536 30.769 20.81 20.81 46.11 3.18
343 347 8.463930 TCAACTTTTTCATTATGGAGTTGAGT 57.536 30.769 19.52 6.00 44.51 3.41
344 348 8.912988 TCAACTTTTTCATTATGGAGTTGAGTT 58.087 29.630 19.52 9.91 44.51 3.01
345 349 9.533253 CAACTTTTTCATTATGGAGTTGAGTTT 57.467 29.630 17.72 0.00 43.95 2.66
348 352 9.846248 CTTTTTCATTATGGAGTTGAGTTTAGG 57.154 33.333 0.00 0.00 0.00 2.69
349 353 7.391148 TTTCATTATGGAGTTGAGTTTAGGC 57.609 36.000 0.00 0.00 0.00 3.93
350 354 5.437060 TCATTATGGAGTTGAGTTTAGGCC 58.563 41.667 0.00 0.00 0.00 5.19
351 355 4.919774 TTATGGAGTTGAGTTTAGGCCA 57.080 40.909 5.01 0.00 0.00 5.36
352 356 2.859165 TGGAGTTGAGTTTAGGCCAG 57.141 50.000 5.01 0.00 0.00 4.85
353 357 2.054799 TGGAGTTGAGTTTAGGCCAGT 58.945 47.619 5.01 0.00 0.00 4.00
354 358 2.441750 TGGAGTTGAGTTTAGGCCAGTT 59.558 45.455 5.01 0.00 0.00 3.16
355 359 3.117663 TGGAGTTGAGTTTAGGCCAGTTT 60.118 43.478 5.01 0.00 0.00 2.66
356 360 3.889538 GGAGTTGAGTTTAGGCCAGTTTT 59.110 43.478 5.01 0.00 0.00 2.43
357 361 4.341235 GGAGTTGAGTTTAGGCCAGTTTTT 59.659 41.667 5.01 0.00 0.00 1.94
374 378 1.988293 TTTTTGCCAGAATCCGACCA 58.012 45.000 0.00 0.00 0.00 4.02
375 379 1.243902 TTTTGCCAGAATCCGACCAC 58.756 50.000 0.00 0.00 0.00 4.16
376 380 0.400213 TTTGCCAGAATCCGACCACT 59.600 50.000 0.00 0.00 0.00 4.00
377 381 1.271856 TTGCCAGAATCCGACCACTA 58.728 50.000 0.00 0.00 0.00 2.74
378 382 0.535335 TGCCAGAATCCGACCACTAC 59.465 55.000 0.00 0.00 0.00 2.73
379 383 0.179081 GCCAGAATCCGACCACTACC 60.179 60.000 0.00 0.00 0.00 3.18
380 384 0.464452 CCAGAATCCGACCACTACCC 59.536 60.000 0.00 0.00 0.00 3.69
381 385 1.191535 CAGAATCCGACCACTACCCA 58.808 55.000 0.00 0.00 0.00 4.51
382 386 1.137086 CAGAATCCGACCACTACCCAG 59.863 57.143 0.00 0.00 0.00 4.45
383 387 0.179081 GAATCCGACCACTACCCAGC 60.179 60.000 0.00 0.00 0.00 4.85
384 388 0.617820 AATCCGACCACTACCCAGCT 60.618 55.000 0.00 0.00 0.00 4.24
385 389 0.617820 ATCCGACCACTACCCAGCTT 60.618 55.000 0.00 0.00 0.00 3.74
386 390 1.218316 CCGACCACTACCCAGCTTC 59.782 63.158 0.00 0.00 0.00 3.86
387 391 1.218316 CGACCACTACCCAGCTTCC 59.782 63.158 0.00 0.00 0.00 3.46
388 392 1.258445 CGACCACTACCCAGCTTCCT 61.258 60.000 0.00 0.00 0.00 3.36
389 393 0.537653 GACCACTACCCAGCTTCCTC 59.462 60.000 0.00 0.00 0.00 3.71
390 394 0.910088 ACCACTACCCAGCTTCCTCC 60.910 60.000 0.00 0.00 0.00 4.30
391 395 0.909610 CCACTACCCAGCTTCCTCCA 60.910 60.000 0.00 0.00 0.00 3.86
392 396 0.539051 CACTACCCAGCTTCCTCCAG 59.461 60.000 0.00 0.00 0.00 3.86
393 397 0.413832 ACTACCCAGCTTCCTCCAGA 59.586 55.000 0.00 0.00 0.00 3.86
394 398 1.203313 ACTACCCAGCTTCCTCCAGAA 60.203 52.381 0.00 0.00 0.00 3.02
395 399 2.122768 CTACCCAGCTTCCTCCAGAAT 58.877 52.381 0.00 0.00 32.82 2.40
396 400 0.915364 ACCCAGCTTCCTCCAGAATC 59.085 55.000 0.00 0.00 32.82 2.52
397 401 0.914644 CCCAGCTTCCTCCAGAATCA 59.085 55.000 0.00 0.00 32.82 2.57
398 402 1.407989 CCCAGCTTCCTCCAGAATCAC 60.408 57.143 0.00 0.00 32.82 3.06
399 403 1.558756 CCAGCTTCCTCCAGAATCACT 59.441 52.381 0.00 0.00 32.82 3.41
400 404 2.630158 CAGCTTCCTCCAGAATCACTG 58.370 52.381 0.00 0.00 45.36 3.66
412 416 4.840716 AGAATCACTGAGCCTCATTTCT 57.159 40.909 0.00 0.00 0.00 2.52
413 417 5.176741 AGAATCACTGAGCCTCATTTCTT 57.823 39.130 0.00 0.00 0.00 2.52
414 418 5.568392 AGAATCACTGAGCCTCATTTCTTT 58.432 37.500 0.00 0.00 0.00 2.52
415 419 6.008960 AGAATCACTGAGCCTCATTTCTTTT 58.991 36.000 0.00 0.00 0.00 2.27
416 420 7.170965 AGAATCACTGAGCCTCATTTCTTTTA 58.829 34.615 0.00 0.00 0.00 1.52
417 421 7.833183 AGAATCACTGAGCCTCATTTCTTTTAT 59.167 33.333 0.00 0.00 0.00 1.40
418 422 6.992063 TCACTGAGCCTCATTTCTTTTATC 57.008 37.500 0.00 0.00 0.00 1.75
419 423 6.715280 TCACTGAGCCTCATTTCTTTTATCT 58.285 36.000 0.00 0.00 0.00 1.98
420 424 7.851228 TCACTGAGCCTCATTTCTTTTATCTA 58.149 34.615 0.00 0.00 0.00 1.98
421 425 7.984050 TCACTGAGCCTCATTTCTTTTATCTAG 59.016 37.037 0.00 0.00 0.00 2.43
422 426 7.768120 CACTGAGCCTCATTTCTTTTATCTAGT 59.232 37.037 0.00 0.00 0.00 2.57
423 427 8.325046 ACTGAGCCTCATTTCTTTTATCTAGTT 58.675 33.333 0.00 0.00 0.00 2.24
424 428 9.823647 CTGAGCCTCATTTCTTTTATCTAGTTA 57.176 33.333 0.00 0.00 0.00 2.24
425 429 9.823647 TGAGCCTCATTTCTTTTATCTAGTTAG 57.176 33.333 0.00 0.00 0.00 2.34
426 430 9.267084 GAGCCTCATTTCTTTTATCTAGTTAGG 57.733 37.037 0.00 0.00 0.00 2.69
427 431 8.993424 AGCCTCATTTCTTTTATCTAGTTAGGA 58.007 33.333 0.00 0.00 0.00 2.94
428 432 9.785982 GCCTCATTTCTTTTATCTAGTTAGGAT 57.214 33.333 0.00 0.00 0.00 3.24
477 481 8.815565 AAAAAGGCTTAAAAATTCTGGGAAAA 57.184 26.923 0.00 0.00 0.00 2.29
478 482 8.450578 AAAAGGCTTAAAAATTCTGGGAAAAG 57.549 30.769 0.00 0.00 0.00 2.27
479 483 5.551233 AGGCTTAAAAATTCTGGGAAAAGC 58.449 37.500 0.00 0.00 37.85 3.51
480 484 5.307976 AGGCTTAAAAATTCTGGGAAAAGCT 59.692 36.000 11.05 0.00 38.46 3.74
481 485 5.409520 GGCTTAAAAATTCTGGGAAAAGCTG 59.590 40.000 11.05 0.00 38.46 4.24
482 486 6.223120 GCTTAAAAATTCTGGGAAAAGCTGA 58.777 36.000 0.00 0.00 36.16 4.26
483 487 6.367149 GCTTAAAAATTCTGGGAAAAGCTGAG 59.633 38.462 0.00 0.00 36.16 3.35
484 488 5.876651 AAAAATTCTGGGAAAAGCTGAGT 57.123 34.783 0.00 0.00 0.00 3.41
485 489 6.976934 AAAAATTCTGGGAAAAGCTGAGTA 57.023 33.333 0.00 0.00 0.00 2.59
486 490 6.976934 AAAATTCTGGGAAAAGCTGAGTAA 57.023 33.333 0.00 0.00 0.00 2.24
487 491 6.581171 AAATTCTGGGAAAAGCTGAGTAAG 57.419 37.500 0.00 0.00 0.00 2.34
488 492 3.703001 TCTGGGAAAAGCTGAGTAAGG 57.297 47.619 0.00 0.00 0.00 2.69
489 493 2.305927 TCTGGGAAAAGCTGAGTAAGGG 59.694 50.000 0.00 0.00 0.00 3.95
490 494 2.040412 CTGGGAAAAGCTGAGTAAGGGT 59.960 50.000 0.00 0.00 0.00 4.34
491 495 2.445525 TGGGAAAAGCTGAGTAAGGGTT 59.554 45.455 0.00 0.00 0.00 4.11
492 496 2.820197 GGGAAAAGCTGAGTAAGGGTTG 59.180 50.000 0.00 0.00 0.00 3.77
493 497 2.820197 GGAAAAGCTGAGTAAGGGTTGG 59.180 50.000 0.00 0.00 0.00 3.77
494 498 3.497942 GGAAAAGCTGAGTAAGGGTTGGA 60.498 47.826 0.00 0.00 0.00 3.53
495 499 4.336280 GAAAAGCTGAGTAAGGGTTGGAT 58.664 43.478 0.00 0.00 0.00 3.41
496 500 4.388577 AAAGCTGAGTAAGGGTTGGATT 57.611 40.909 0.00 0.00 0.00 3.01
497 501 3.636153 AGCTGAGTAAGGGTTGGATTC 57.364 47.619 0.00 0.00 0.00 2.52
498 502 3.185455 AGCTGAGTAAGGGTTGGATTCT 58.815 45.455 0.00 0.00 0.00 2.40
499 503 3.589288 AGCTGAGTAAGGGTTGGATTCTT 59.411 43.478 0.00 0.00 0.00 2.52
500 504 3.691609 GCTGAGTAAGGGTTGGATTCTTG 59.308 47.826 0.00 0.00 0.00 3.02
501 505 4.265073 CTGAGTAAGGGTTGGATTCTTGG 58.735 47.826 0.00 0.00 0.00 3.61
502 506 3.913799 TGAGTAAGGGTTGGATTCTTGGA 59.086 43.478 0.00 0.00 0.00 3.53
503 507 4.352595 TGAGTAAGGGTTGGATTCTTGGAA 59.647 41.667 0.00 0.00 0.00 3.53
504 508 5.163034 TGAGTAAGGGTTGGATTCTTGGAAA 60.163 40.000 0.00 0.00 0.00 3.13
505 509 5.711698 AGTAAGGGTTGGATTCTTGGAAAA 58.288 37.500 0.00 0.00 0.00 2.29
506 510 6.322931 AGTAAGGGTTGGATTCTTGGAAAAT 58.677 36.000 0.00 0.00 0.00 1.82
507 511 5.745312 AAGGGTTGGATTCTTGGAAAATC 57.255 39.130 0.00 0.00 33.29 2.17
513 517 3.981212 GGATTCTTGGAAAATCCCCAGA 58.019 45.455 3.93 0.00 44.28 3.86
514 518 4.550669 GGATTCTTGGAAAATCCCCAGAT 58.449 43.478 3.93 0.00 44.28 2.90
515 519 4.964897 GGATTCTTGGAAAATCCCCAGATT 59.035 41.667 3.93 0.00 44.28 2.40
516 520 5.069648 GGATTCTTGGAAAATCCCCAGATTC 59.930 44.000 3.93 0.00 44.28 2.52
517 521 4.953781 TCTTGGAAAATCCCCAGATTCT 57.046 40.909 0.00 0.00 42.03 2.40
518 522 6.401537 TTCTTGGAAAATCCCCAGATTCTA 57.598 37.500 0.00 0.00 42.03 2.10
519 523 6.006275 TCTTGGAAAATCCCCAGATTCTAG 57.994 41.667 0.00 0.00 42.03 2.43
520 524 5.731187 TCTTGGAAAATCCCCAGATTCTAGA 59.269 40.000 0.00 0.00 42.03 2.43
521 525 6.217487 TCTTGGAAAATCCCCAGATTCTAGAA 59.783 38.462 7.82 7.82 42.03 2.10
522 526 6.401537 TGGAAAATCCCCAGATTCTAGAAA 57.598 37.500 9.71 0.00 42.03 2.52
523 527 6.799827 TGGAAAATCCCCAGATTCTAGAAAA 58.200 36.000 9.71 0.00 42.03 2.29
524 528 7.245292 TGGAAAATCCCCAGATTCTAGAAAAA 58.755 34.615 9.71 0.00 42.03 1.94
558 562 4.405671 ATGCGTGCTGCTGAGCCT 62.406 61.111 0.23 0.00 45.57 4.58
562 566 2.281345 GTGCTGCTGAGCCTGTGT 60.281 61.111 0.23 0.00 45.57 3.72
563 567 2.281276 TGCTGCTGAGCCTGTGTG 60.281 61.111 0.23 0.00 45.57 3.82
564 568 2.281345 GCTGCTGAGCCTGTGTGT 60.281 61.111 0.23 0.00 39.57 3.72
565 569 2.614446 GCTGCTGAGCCTGTGTGTG 61.614 63.158 0.23 0.00 39.57 3.82
735 793 2.765807 AGAGCCATCACCTCCCGG 60.766 66.667 0.00 0.00 0.00 5.73
736 794 2.764128 GAGCCATCACCTCCCGGA 60.764 66.667 0.73 0.00 0.00 5.14
763 822 3.705638 CTGCGTGTGTGCCGACTG 61.706 66.667 0.00 0.00 0.00 3.51
797 864 3.056458 CTACGTGGCCACCTCACA 58.944 61.111 29.95 9.58 35.03 3.58
878 950 2.360980 CCGCCCCATAAAACCCCA 59.639 61.111 0.00 0.00 0.00 4.96
917 989 2.959030 CCGATCACTCCTACTGATTCCA 59.041 50.000 0.00 0.00 0.00 3.53
923 995 2.363680 ACTCCTACTGATTCCATCGCAG 59.636 50.000 0.00 0.00 35.81 5.18
962 1034 0.383231 AAAGCACACAAGCAGCTGAC 59.617 50.000 20.43 9.11 38.86 3.51
991 1063 2.541556 GTTCTAGCTCGGGACAATCAC 58.458 52.381 0.00 0.00 0.00 3.06
1158 1233 1.604915 GGGCAAGGAGGAAGAGTCC 59.395 63.158 0.00 0.00 45.35 3.85
1341 1437 0.234625 CGTGTCCGTGGTGTTCATTG 59.765 55.000 0.00 0.00 0.00 2.82
1344 1440 1.673400 TGTCCGTGGTGTTCATTGTTG 59.327 47.619 0.00 0.00 0.00 3.33
1345 1441 1.001815 GTCCGTGGTGTTCATTGTTGG 60.002 52.381 0.00 0.00 0.00 3.77
1351 1447 4.676723 CGTGGTGTTCATTGTTGGTTTCTT 60.677 41.667 0.00 0.00 0.00 2.52
1353 1449 4.119136 GGTGTTCATTGTTGGTTTCTTGG 58.881 43.478 0.00 0.00 0.00 3.61
1360 1456 1.006043 TGTTGGTTTCTTGGGTGGTCA 59.994 47.619 0.00 0.00 0.00 4.02
1364 1460 1.143073 GGTTTCTTGGGTGGTCAGAGT 59.857 52.381 0.00 0.00 0.00 3.24
1366 1462 1.801242 TTCTTGGGTGGTCAGAGTGA 58.199 50.000 0.00 0.00 0.00 3.41
1367 1463 1.048601 TCTTGGGTGGTCAGAGTGAC 58.951 55.000 0.00 0.00 46.23 3.67
1368 1464 1.051812 CTTGGGTGGTCAGAGTGACT 58.948 55.000 6.99 0.00 46.19 3.41
1369 1465 0.758734 TTGGGTGGTCAGAGTGACTG 59.241 55.000 6.99 0.00 46.19 3.51
1378 1481 3.448093 TCAGAGTGACTGGAGTCTGAT 57.552 47.619 8.24 0.00 44.18 2.90
1379 1482 3.087781 TCAGAGTGACTGGAGTCTGATG 58.912 50.000 8.24 2.90 44.18 3.07
1393 1515 4.898320 AGTCTGATGCTGATTTGTGTGTA 58.102 39.130 0.00 0.00 0.00 2.90
1543 1668 2.261671 GCGAGGCGTCCAAGAAGA 59.738 61.111 0.00 0.00 0.00 2.87
1573 1698 2.704572 CTAAGCACAAGACCAAGGAGG 58.295 52.381 0.00 0.00 45.67 4.30
1635 1760 3.640407 TCGAAGCAGGGCAAGGCT 61.640 61.111 0.00 0.00 43.46 4.58
1648 1773 1.680249 GCAAGGCTAAGGTTGAGGAGG 60.680 57.143 0.00 0.00 0.00 4.30
1659 1784 3.717294 GAGGAGGCGGCCAAGGAA 61.717 66.667 23.09 0.00 0.00 3.36
2498 2837 7.434897 GCTTTACATGAATGTTTTCAGTGTTCA 59.565 33.333 0.00 0.00 44.75 3.18
2543 2885 8.322906 TGTTCCTTCTTGTACAATAATGTGAG 57.677 34.615 9.13 0.00 40.84 3.51
2544 2886 8.154203 TGTTCCTTCTTGTACAATAATGTGAGA 58.846 33.333 9.13 0.00 40.84 3.27
2572 2914 0.534412 AGAGAACCCTGCACGATCAG 59.466 55.000 0.00 0.00 0.00 2.90
2575 2917 1.078759 GAACCCTGCACGATCAGACG 61.079 60.000 9.58 0.00 36.19 4.18
2580 2922 1.670087 CCTGCACGATCAGACGAGTTT 60.670 52.381 9.58 0.00 36.19 2.66
2631 4519 9.933723 ATCTTTTTACAAATTTGATCCTTCTGG 57.066 29.630 24.64 6.35 0.00 3.86
2674 4562 5.772521 TCTTTTACTCAAAATTGGAGCTGC 58.227 37.500 0.00 0.00 35.79 5.25
2741 4636 6.899393 AATTGGAAAGAGCTGAATTACACA 57.101 33.333 0.00 0.00 0.00 3.72
2772 4667 4.098055 GGCATGTCGACGATGATAGTAT 57.902 45.455 23.42 3.40 0.00 2.12
2773 4668 5.231265 GGCATGTCGACGATGATAGTATA 57.769 43.478 23.42 0.12 0.00 1.47
2840 4736 3.055891 AGCATTTCCCAAATTCTTTCCCG 60.056 43.478 0.00 0.00 0.00 5.14
2873 4769 0.389817 CGCGGGAACTGATTCAGACA 60.390 55.000 20.33 0.00 36.46 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.561373 GTGCGTTAAGGCAGGTGC 59.439 61.111 22.31 7.80 44.93 5.01
2 3 2.677003 CGGTGCGTTAAGGCAGGTG 61.677 63.158 22.31 11.56 44.93 4.00
3 4 2.358247 CGGTGCGTTAAGGCAGGT 60.358 61.111 22.31 0.00 44.93 4.00
4 5 1.635663 CTTCGGTGCGTTAAGGCAGG 61.636 60.000 22.31 16.75 44.93 4.85
5 6 1.787847 CTTCGGTGCGTTAAGGCAG 59.212 57.895 22.31 12.33 44.93 4.85
6 7 2.322081 GCTTCGGTGCGTTAAGGCA 61.322 57.895 18.37 18.37 41.45 4.75
7 8 2.033194 AGCTTCGGTGCGTTAAGGC 61.033 57.895 13.14 13.14 38.13 4.35
8 9 0.669318 TCAGCTTCGGTGCGTTAAGG 60.669 55.000 0.00 0.00 38.13 2.69
9 10 0.716108 CTCAGCTTCGGTGCGTTAAG 59.284 55.000 0.00 0.00 38.13 1.85
10 11 0.032952 ACTCAGCTTCGGTGCGTTAA 59.967 50.000 0.00 0.00 38.13 2.01
11 12 0.388134 GACTCAGCTTCGGTGCGTTA 60.388 55.000 0.00 0.00 38.13 3.18
12 13 1.664965 GACTCAGCTTCGGTGCGTT 60.665 57.895 0.00 0.00 38.13 4.84
13 14 2.049063 GACTCAGCTTCGGTGCGT 60.049 61.111 0.00 0.00 38.13 5.24
14 15 2.811317 GGACTCAGCTTCGGTGCG 60.811 66.667 0.00 0.00 38.13 5.34
15 16 2.435059 GGGACTCAGCTTCGGTGC 60.435 66.667 0.00 0.00 0.00 5.01
16 17 2.266055 GGGGACTCAGCTTCGGTG 59.734 66.667 0.00 0.00 0.00 4.94
17 18 3.382832 CGGGGACTCAGCTTCGGT 61.383 66.667 0.00 0.00 0.00 4.69
18 19 4.821589 GCGGGGACTCAGCTTCGG 62.822 72.222 0.00 0.00 0.00 4.30
19 20 4.821589 GGCGGGGACTCAGCTTCG 62.822 72.222 0.00 0.00 0.00 3.79
20 21 2.543067 ATTGGCGGGGACTCAGCTTC 62.543 60.000 0.00 0.00 0.00 3.86
21 22 2.606587 ATTGGCGGGGACTCAGCTT 61.607 57.895 0.00 0.00 0.00 3.74
22 23 3.011517 ATTGGCGGGGACTCAGCT 61.012 61.111 0.00 0.00 0.00 4.24
23 24 2.825836 CATTGGCGGGGACTCAGC 60.826 66.667 0.00 0.00 0.00 4.26
24 25 1.153289 CTCATTGGCGGGGACTCAG 60.153 63.158 0.00 0.00 0.00 3.35
25 26 0.616395 TACTCATTGGCGGGGACTCA 60.616 55.000 0.00 0.00 0.00 3.41
26 27 0.179081 GTACTCATTGGCGGGGACTC 60.179 60.000 0.00 0.00 0.00 3.36
27 28 1.905512 GTACTCATTGGCGGGGACT 59.094 57.895 0.00 0.00 0.00 3.85
28 29 1.520787 CGTACTCATTGGCGGGGAC 60.521 63.158 0.00 0.00 0.00 4.46
29 30 1.952102 GACGTACTCATTGGCGGGGA 61.952 60.000 0.00 0.00 0.00 4.81
30 31 1.520787 GACGTACTCATTGGCGGGG 60.521 63.158 0.00 0.00 0.00 5.73
31 32 1.082117 GTGACGTACTCATTGGCGGG 61.082 60.000 0.00 0.00 0.00 6.13
32 33 1.082117 GGTGACGTACTCATTGGCGG 61.082 60.000 0.00 0.00 0.00 6.13
33 34 2.369870 GGTGACGTACTCATTGGCG 58.630 57.895 0.00 0.00 0.00 5.69
46 47 5.123186 TGTGTTCAAATGATAATCCGGTGAC 59.877 40.000 0.00 0.00 0.00 3.67
47 48 5.249420 TGTGTTCAAATGATAATCCGGTGA 58.751 37.500 0.00 0.00 0.00 4.02
48 49 5.559427 TGTGTTCAAATGATAATCCGGTG 57.441 39.130 0.00 0.00 0.00 4.94
49 50 6.582677 TTTGTGTTCAAATGATAATCCGGT 57.417 33.333 0.00 0.00 38.44 5.28
87 88 9.993454 CAGTCTCCATTAGATTCATATTCAAGA 57.007 33.333 0.00 0.00 36.36 3.02
88 89 8.719648 GCAGTCTCCATTAGATTCATATTCAAG 58.280 37.037 0.00 0.00 36.36 3.02
89 90 8.212995 TGCAGTCTCCATTAGATTCATATTCAA 58.787 33.333 0.00 0.00 36.36 2.69
90 91 7.738847 TGCAGTCTCCATTAGATTCATATTCA 58.261 34.615 0.00 0.00 36.36 2.57
91 92 7.877097 ACTGCAGTCTCCATTAGATTCATATTC 59.123 37.037 15.25 0.00 36.36 1.75
92 93 7.743749 ACTGCAGTCTCCATTAGATTCATATT 58.256 34.615 15.25 0.00 36.36 1.28
93 94 7.313740 ACTGCAGTCTCCATTAGATTCATAT 57.686 36.000 15.25 0.00 36.36 1.78
94 95 6.737720 ACTGCAGTCTCCATTAGATTCATA 57.262 37.500 15.25 0.00 36.36 2.15
95 96 5.627182 ACTGCAGTCTCCATTAGATTCAT 57.373 39.130 15.25 0.00 36.36 2.57
96 97 5.181009 CAACTGCAGTCTCCATTAGATTCA 58.819 41.667 21.95 0.00 36.36 2.57
97 98 5.181748 ACAACTGCAGTCTCCATTAGATTC 58.818 41.667 21.95 0.00 36.36 2.52
98 99 5.171339 ACAACTGCAGTCTCCATTAGATT 57.829 39.130 21.95 0.00 36.36 2.40
99 100 4.833478 ACAACTGCAGTCTCCATTAGAT 57.167 40.909 21.95 0.00 36.36 1.98
100 101 4.040339 TGAACAACTGCAGTCTCCATTAGA 59.960 41.667 21.95 0.00 0.00 2.10
101 102 4.318332 TGAACAACTGCAGTCTCCATTAG 58.682 43.478 21.95 5.51 0.00 1.73
102 103 4.350368 TGAACAACTGCAGTCTCCATTA 57.650 40.909 21.95 0.88 0.00 1.90
103 104 3.213206 TGAACAACTGCAGTCTCCATT 57.787 42.857 21.95 10.07 0.00 3.16
104 105 2.936919 TGAACAACTGCAGTCTCCAT 57.063 45.000 21.95 0.00 0.00 3.41
105 106 2.708216 TTGAACAACTGCAGTCTCCA 57.292 45.000 21.95 12.90 0.00 3.86
106 107 4.574599 ATTTTGAACAACTGCAGTCTCC 57.425 40.909 21.95 10.39 0.00 3.71
107 108 5.460091 GGAAATTTTGAACAACTGCAGTCTC 59.540 40.000 21.95 16.94 0.00 3.36
108 109 5.351458 GGAAATTTTGAACAACTGCAGTCT 58.649 37.500 21.95 7.86 0.00 3.24
109 110 4.507756 GGGAAATTTTGAACAACTGCAGTC 59.492 41.667 21.95 8.17 0.00 3.51
110 111 4.441792 GGGAAATTTTGAACAACTGCAGT 58.558 39.130 15.25 15.25 0.00 4.40
111 112 3.809279 GGGGAAATTTTGAACAACTGCAG 59.191 43.478 13.48 13.48 0.00 4.41
112 113 3.739519 CGGGGAAATTTTGAACAACTGCA 60.740 43.478 0.00 0.00 0.00 4.41
113 114 2.799978 CGGGGAAATTTTGAACAACTGC 59.200 45.455 0.00 0.00 0.00 4.40
114 115 2.799978 GCGGGGAAATTTTGAACAACTG 59.200 45.455 0.00 0.00 0.00 3.16
115 116 2.224185 GGCGGGGAAATTTTGAACAACT 60.224 45.455 0.00 0.00 0.00 3.16
116 117 2.139917 GGCGGGGAAATTTTGAACAAC 58.860 47.619 0.00 0.00 0.00 3.32
117 118 1.762957 TGGCGGGGAAATTTTGAACAA 59.237 42.857 0.00 0.00 0.00 2.83
118 119 1.414158 TGGCGGGGAAATTTTGAACA 58.586 45.000 0.00 0.00 0.00 3.18
119 120 2.535012 TTGGCGGGGAAATTTTGAAC 57.465 45.000 0.00 0.00 0.00 3.18
120 121 2.634940 TCATTGGCGGGGAAATTTTGAA 59.365 40.909 0.00 0.00 0.00 2.69
121 122 2.233431 CTCATTGGCGGGGAAATTTTGA 59.767 45.455 0.00 0.00 0.00 2.69
122 123 2.028203 ACTCATTGGCGGGGAAATTTTG 60.028 45.455 0.00 0.00 0.00 2.44
123 124 2.256306 ACTCATTGGCGGGGAAATTTT 58.744 42.857 0.00 0.00 0.00 1.82
124 125 1.937191 ACTCATTGGCGGGGAAATTT 58.063 45.000 0.00 0.00 0.00 1.82
125 126 2.818751 TACTCATTGGCGGGGAAATT 57.181 45.000 0.00 0.00 0.00 1.82
126 127 2.091885 ACATACTCATTGGCGGGGAAAT 60.092 45.455 0.00 0.00 0.00 2.17
127 128 1.283613 ACATACTCATTGGCGGGGAAA 59.716 47.619 0.00 0.00 0.00 3.13
128 129 0.916086 ACATACTCATTGGCGGGGAA 59.084 50.000 0.00 0.00 0.00 3.97
129 130 0.468226 GACATACTCATTGGCGGGGA 59.532 55.000 0.00 0.00 0.00 4.81
130 131 0.180171 TGACATACTCATTGGCGGGG 59.820 55.000 0.00 0.00 0.00 5.73
131 132 2.260844 ATGACATACTCATTGGCGGG 57.739 50.000 0.00 0.00 35.99 6.13
187 188 6.540551 TGCCGCAAAAAGTACATCATTAGATA 59.459 34.615 0.00 0.00 31.88 1.98
194 195 2.556189 ACATGCCGCAAAAAGTACATCA 59.444 40.909 0.00 0.00 0.00 3.07
208 209 4.061596 ACAAAAATTTGGGTTACATGCCG 58.938 39.130 10.38 0.00 42.34 5.69
224 225 7.769220 TGTCCCGTTTTATTTGACTACAAAAA 58.231 30.769 0.00 0.00 46.77 1.94
230 231 6.349243 TCTCTGTCCCGTTTTATTTGACTA 57.651 37.500 0.00 0.00 0.00 2.59
238 239 3.244422 ACTGCAATCTCTGTCCCGTTTTA 60.244 43.478 0.00 0.00 0.00 1.52
249 250 7.121315 GGGAAGTTTTATACAACTGCAATCTCT 59.879 37.037 11.14 0.00 37.07 3.10
264 265 5.464069 ACTCTTTTGTGGGGGAAGTTTTAT 58.536 37.500 0.00 0.00 0.00 1.40
270 271 3.790089 ACTACTCTTTTGTGGGGGAAG 57.210 47.619 0.00 0.00 0.00 3.46
274 275 6.702716 TTAAACAACTACTCTTTTGTGGGG 57.297 37.500 0.00 0.00 36.08 4.96
327 331 5.045213 TGGCCTAAACTCAACTCCATAATGA 60.045 40.000 3.32 0.00 0.00 2.57
333 337 2.054799 ACTGGCCTAAACTCAACTCCA 58.945 47.619 3.32 0.00 0.00 3.86
335 339 5.515797 AAAAACTGGCCTAAACTCAACTC 57.484 39.130 3.32 0.00 0.00 3.01
355 359 1.611491 GTGGTCGGATTCTGGCAAAAA 59.389 47.619 0.00 0.00 0.00 1.94
356 360 1.202879 AGTGGTCGGATTCTGGCAAAA 60.203 47.619 0.00 0.00 0.00 2.44
357 361 0.400213 AGTGGTCGGATTCTGGCAAA 59.600 50.000 0.00 0.00 0.00 3.68
358 362 1.066430 GTAGTGGTCGGATTCTGGCAA 60.066 52.381 0.00 0.00 0.00 4.52
359 363 0.535335 GTAGTGGTCGGATTCTGGCA 59.465 55.000 0.00 0.00 0.00 4.92
360 364 0.179081 GGTAGTGGTCGGATTCTGGC 60.179 60.000 0.00 0.00 0.00 4.85
361 365 0.464452 GGGTAGTGGTCGGATTCTGG 59.536 60.000 0.00 0.00 0.00 3.86
362 366 1.137086 CTGGGTAGTGGTCGGATTCTG 59.863 57.143 0.00 0.00 0.00 3.02
363 367 1.486211 CTGGGTAGTGGTCGGATTCT 58.514 55.000 0.00 0.00 0.00 2.40
364 368 0.179081 GCTGGGTAGTGGTCGGATTC 60.179 60.000 0.00 0.00 0.00 2.52
365 369 0.617820 AGCTGGGTAGTGGTCGGATT 60.618 55.000 0.00 0.00 0.00 3.01
366 370 0.617820 AAGCTGGGTAGTGGTCGGAT 60.618 55.000 0.00 0.00 0.00 4.18
367 371 1.229082 AAGCTGGGTAGTGGTCGGA 60.229 57.895 0.00 0.00 0.00 4.55
368 372 1.218316 GAAGCTGGGTAGTGGTCGG 59.782 63.158 0.00 0.00 0.00 4.79
369 373 1.218316 GGAAGCTGGGTAGTGGTCG 59.782 63.158 0.00 0.00 0.00 4.79
370 374 0.537653 GAGGAAGCTGGGTAGTGGTC 59.462 60.000 0.00 0.00 0.00 4.02
371 375 0.910088 GGAGGAAGCTGGGTAGTGGT 60.910 60.000 0.00 0.00 0.00 4.16
372 376 0.909610 TGGAGGAAGCTGGGTAGTGG 60.910 60.000 0.00 0.00 0.00 4.00
373 377 0.539051 CTGGAGGAAGCTGGGTAGTG 59.461 60.000 0.00 0.00 0.00 2.74
374 378 0.413832 TCTGGAGGAAGCTGGGTAGT 59.586 55.000 0.00 0.00 0.00 2.73
375 379 1.573108 TTCTGGAGGAAGCTGGGTAG 58.427 55.000 0.00 0.00 0.00 3.18
376 380 2.119495 GATTCTGGAGGAAGCTGGGTA 58.881 52.381 0.00 0.00 37.37 3.69
377 381 0.915364 GATTCTGGAGGAAGCTGGGT 59.085 55.000 0.00 0.00 37.37 4.51
378 382 0.914644 TGATTCTGGAGGAAGCTGGG 59.085 55.000 0.00 0.00 40.60 4.45
379 383 1.558756 AGTGATTCTGGAGGAAGCTGG 59.441 52.381 0.00 0.00 40.60 4.85
380 384 2.235650 TCAGTGATTCTGGAGGAAGCTG 59.764 50.000 0.00 0.00 43.76 4.24
381 385 2.500910 CTCAGTGATTCTGGAGGAAGCT 59.499 50.000 0.00 0.00 43.76 3.74
382 386 2.903798 CTCAGTGATTCTGGAGGAAGC 58.096 52.381 0.00 0.00 43.76 3.86
383 387 2.419851 GGCTCAGTGATTCTGGAGGAAG 60.420 54.545 0.00 0.00 43.76 3.46
384 388 1.556911 GGCTCAGTGATTCTGGAGGAA 59.443 52.381 0.00 0.00 43.76 3.36
385 389 1.198713 GGCTCAGTGATTCTGGAGGA 58.801 55.000 0.00 0.00 43.76 3.71
386 390 1.138661 GAGGCTCAGTGATTCTGGAGG 59.861 57.143 10.25 0.00 43.76 4.30
387 391 1.829849 TGAGGCTCAGTGATTCTGGAG 59.170 52.381 14.43 0.00 43.76 3.86
388 392 1.942776 TGAGGCTCAGTGATTCTGGA 58.057 50.000 14.43 0.00 43.76 3.86
389 393 3.278668 AATGAGGCTCAGTGATTCTGG 57.721 47.619 23.24 0.00 43.76 3.86
390 394 4.515361 AGAAATGAGGCTCAGTGATTCTG 58.485 43.478 23.24 0.00 44.85 3.02
391 395 4.840716 AGAAATGAGGCTCAGTGATTCT 57.159 40.909 23.24 22.36 0.00 2.40
392 396 5.893897 AAAGAAATGAGGCTCAGTGATTC 57.106 39.130 23.24 20.77 0.00 2.52
393 397 7.833183 AGATAAAAGAAATGAGGCTCAGTGATT 59.167 33.333 23.24 15.04 0.00 2.57
394 398 7.344913 AGATAAAAGAAATGAGGCTCAGTGAT 58.655 34.615 23.24 9.72 0.00 3.06
395 399 6.715280 AGATAAAAGAAATGAGGCTCAGTGA 58.285 36.000 23.24 0.00 0.00 3.41
396 400 6.998968 AGATAAAAGAAATGAGGCTCAGTG 57.001 37.500 23.24 0.00 0.00 3.66
397 401 7.856415 ACTAGATAAAAGAAATGAGGCTCAGT 58.144 34.615 23.24 18.18 0.00 3.41
398 402 8.729805 AACTAGATAAAAGAAATGAGGCTCAG 57.270 34.615 23.24 6.23 0.00 3.35
399 403 9.823647 CTAACTAGATAAAAGAAATGAGGCTCA 57.176 33.333 21.19 21.19 0.00 4.26
400 404 9.267084 CCTAACTAGATAAAAGAAATGAGGCTC 57.733 37.037 7.79 7.79 0.00 4.70
401 405 8.993424 TCCTAACTAGATAAAAGAAATGAGGCT 58.007 33.333 0.00 0.00 0.00 4.58
402 406 9.785982 ATCCTAACTAGATAAAAGAAATGAGGC 57.214 33.333 0.00 0.00 0.00 4.70
452 456 8.815565 TTTTCCCAGAATTTTTAAGCCTTTTT 57.184 26.923 0.00 0.00 0.00 1.94
453 457 7.013274 GCTTTTCCCAGAATTTTTAAGCCTTTT 59.987 33.333 0.00 0.00 32.70 2.27
454 458 6.486657 GCTTTTCCCAGAATTTTTAAGCCTTT 59.513 34.615 0.00 0.00 32.70 3.11
455 459 5.997746 GCTTTTCCCAGAATTTTTAAGCCTT 59.002 36.000 0.00 0.00 32.70 4.35
456 460 5.307976 AGCTTTTCCCAGAATTTTTAAGCCT 59.692 36.000 0.00 0.00 37.94 4.58
457 461 5.409520 CAGCTTTTCCCAGAATTTTTAAGCC 59.590 40.000 0.00 0.00 37.94 4.35
458 462 6.223120 TCAGCTTTTCCCAGAATTTTTAAGC 58.777 36.000 0.00 0.00 37.58 3.09
459 463 7.436933 ACTCAGCTTTTCCCAGAATTTTTAAG 58.563 34.615 0.00 0.00 0.00 1.85
460 464 7.360113 ACTCAGCTTTTCCCAGAATTTTTAA 57.640 32.000 0.00 0.00 0.00 1.52
461 465 6.976934 ACTCAGCTTTTCCCAGAATTTTTA 57.023 33.333 0.00 0.00 0.00 1.52
462 466 5.876651 ACTCAGCTTTTCCCAGAATTTTT 57.123 34.783 0.00 0.00 0.00 1.94
463 467 6.015095 CCTTACTCAGCTTTTCCCAGAATTTT 60.015 38.462 0.00 0.00 0.00 1.82
464 468 5.478332 CCTTACTCAGCTTTTCCCAGAATTT 59.522 40.000 0.00 0.00 0.00 1.82
465 469 5.012893 CCTTACTCAGCTTTTCCCAGAATT 58.987 41.667 0.00 0.00 0.00 2.17
466 470 4.568592 CCCTTACTCAGCTTTTCCCAGAAT 60.569 45.833 0.00 0.00 0.00 2.40
467 471 3.244911 CCCTTACTCAGCTTTTCCCAGAA 60.245 47.826 0.00 0.00 0.00 3.02
468 472 2.305927 CCCTTACTCAGCTTTTCCCAGA 59.694 50.000 0.00 0.00 0.00 3.86
469 473 2.040412 ACCCTTACTCAGCTTTTCCCAG 59.960 50.000 0.00 0.00 0.00 4.45
470 474 2.062636 ACCCTTACTCAGCTTTTCCCA 58.937 47.619 0.00 0.00 0.00 4.37
471 475 2.820197 CAACCCTTACTCAGCTTTTCCC 59.180 50.000 0.00 0.00 0.00 3.97
472 476 2.820197 CCAACCCTTACTCAGCTTTTCC 59.180 50.000 0.00 0.00 0.00 3.13
473 477 3.751518 TCCAACCCTTACTCAGCTTTTC 58.248 45.455 0.00 0.00 0.00 2.29
474 478 3.876309 TCCAACCCTTACTCAGCTTTT 57.124 42.857 0.00 0.00 0.00 2.27
475 479 4.043435 AGAATCCAACCCTTACTCAGCTTT 59.957 41.667 0.00 0.00 0.00 3.51
476 480 3.589288 AGAATCCAACCCTTACTCAGCTT 59.411 43.478 0.00 0.00 0.00 3.74
477 481 3.185455 AGAATCCAACCCTTACTCAGCT 58.815 45.455 0.00 0.00 0.00 4.24
478 482 3.636153 AGAATCCAACCCTTACTCAGC 57.364 47.619 0.00 0.00 0.00 4.26
479 483 4.019321 TCCAAGAATCCAACCCTTACTCAG 60.019 45.833 0.00 0.00 0.00 3.35
480 484 3.913799 TCCAAGAATCCAACCCTTACTCA 59.086 43.478 0.00 0.00 0.00 3.41
481 485 4.569719 TCCAAGAATCCAACCCTTACTC 57.430 45.455 0.00 0.00 0.00 2.59
482 486 5.333566 TTTCCAAGAATCCAACCCTTACT 57.666 39.130 0.00 0.00 0.00 2.24
483 487 6.605471 ATTTTCCAAGAATCCAACCCTTAC 57.395 37.500 0.00 0.00 0.00 2.34
484 488 6.850752 GATTTTCCAAGAATCCAACCCTTA 57.149 37.500 0.00 0.00 0.00 2.69
485 489 5.745312 GATTTTCCAAGAATCCAACCCTT 57.255 39.130 0.00 0.00 0.00 3.95
493 497 5.896106 AGAATCTGGGGATTTTCCAAGAATC 59.104 40.000 0.00 0.00 41.68 2.52
494 498 5.846868 AGAATCTGGGGATTTTCCAAGAAT 58.153 37.500 0.00 0.00 41.68 2.40
495 499 5.275263 AGAATCTGGGGATTTTCCAAGAA 57.725 39.130 0.00 0.00 41.68 2.52
496 500 4.953781 AGAATCTGGGGATTTTCCAAGA 57.046 40.909 0.00 0.00 41.68 3.02
497 501 6.006275 TCTAGAATCTGGGGATTTTCCAAG 57.994 41.667 0.00 0.00 41.68 3.61
498 502 6.401537 TTCTAGAATCTGGGGATTTTCCAA 57.598 37.500 0.00 0.00 41.68 3.53
499 503 6.401537 TTTCTAGAATCTGGGGATTTTCCA 57.598 37.500 5.89 0.00 41.68 3.53
500 504 7.718334 TTTTTCTAGAATCTGGGGATTTTCC 57.282 36.000 5.89 0.00 41.68 3.13
524 528 2.171003 GCATGACTAGGCCCAGTTTTT 58.829 47.619 4.96 0.00 0.00 1.94
525 529 1.839424 GCATGACTAGGCCCAGTTTT 58.161 50.000 4.96 0.00 0.00 2.43
526 530 0.392998 CGCATGACTAGGCCCAGTTT 60.393 55.000 4.96 0.00 0.00 2.66
527 531 1.221840 CGCATGACTAGGCCCAGTT 59.778 57.895 4.96 0.00 0.00 3.16
528 532 1.990060 ACGCATGACTAGGCCCAGT 60.990 57.895 2.43 2.43 0.00 4.00
529 533 1.522355 CACGCATGACTAGGCCCAG 60.522 63.158 0.00 0.00 0.00 4.45
532 536 2.176273 CAGCACGCATGACTAGGCC 61.176 63.158 0.00 0.00 0.00 5.19
535 539 0.459063 TCAGCAGCACGCATGACTAG 60.459 55.000 0.00 0.00 46.13 2.57
558 562 1.520564 GCAGTCGACCACACACACA 60.521 57.895 13.01 0.00 0.00 3.72
562 566 0.249447 CTTGAGCAGTCGACCACACA 60.249 55.000 13.01 6.70 0.00 3.72
563 567 0.032130 TCTTGAGCAGTCGACCACAC 59.968 55.000 13.01 3.89 0.00 3.82
564 568 0.315251 CTCTTGAGCAGTCGACCACA 59.685 55.000 13.01 4.75 0.00 4.17
565 569 0.598562 TCTCTTGAGCAGTCGACCAC 59.401 55.000 13.01 4.43 0.00 4.16
735 793 1.815421 ACACGCAGCCATCGGAATC 60.815 57.895 0.00 0.00 0.00 2.52
736 794 2.108514 CACACGCAGCCATCGGAAT 61.109 57.895 0.00 0.00 0.00 3.01
763 822 0.378257 TAGCCGATACACGTCGTTCC 59.622 55.000 0.00 0.00 39.89 3.62
878 950 1.518302 GGTTTGGGTTTTGTGGCGT 59.482 52.632 0.00 0.00 0.00 5.68
917 989 1.411977 CTCTGAATGGAGGACTGCGAT 59.588 52.381 0.00 0.00 0.00 4.58
923 995 1.086634 GCGTGCTCTGAATGGAGGAC 61.087 60.000 6.15 6.15 46.43 3.85
962 1034 1.405821 CCGAGCTAGAACCTAGTGTGG 59.594 57.143 0.00 0.00 0.00 4.17
1272 1347 2.432628 GCGGACTTGACGGTCTGG 60.433 66.667 9.88 4.72 41.45 3.86
1338 1434 2.698274 GACCACCCAAGAAACCAACAAT 59.302 45.455 0.00 0.00 0.00 2.71
1341 1437 1.681264 CTGACCACCCAAGAAACCAAC 59.319 52.381 0.00 0.00 0.00 3.77
1344 1440 1.143073 ACTCTGACCACCCAAGAAACC 59.857 52.381 0.00 0.00 0.00 3.27
1345 1441 2.158813 TCACTCTGACCACCCAAGAAAC 60.159 50.000 0.00 0.00 0.00 2.78
1366 1462 3.008813 ACAAATCAGCATCAGACTCCAGT 59.991 43.478 0.00 0.00 0.00 4.00
1367 1463 3.374367 CACAAATCAGCATCAGACTCCAG 59.626 47.826 0.00 0.00 0.00 3.86
1368 1464 3.244665 ACACAAATCAGCATCAGACTCCA 60.245 43.478 0.00 0.00 0.00 3.86
1369 1465 3.126514 CACACAAATCAGCATCAGACTCC 59.873 47.826 0.00 0.00 0.00 3.85
1378 1481 4.058124 GTCTCTGTACACACAAATCAGCA 58.942 43.478 0.00 0.00 33.22 4.41
1379 1482 3.121944 CGTCTCTGTACACACAAATCAGC 59.878 47.826 0.00 0.00 33.22 4.26
1393 1515 2.681778 CTGCCTCCCCGTCTCTGT 60.682 66.667 0.00 0.00 0.00 3.41
1543 1668 2.111999 TTGTGCTTAGCCTGCTCCGT 62.112 55.000 0.29 0.00 0.00 4.69
1635 1760 2.666098 GGCCGCCTCCTCAACCTTA 61.666 63.158 0.71 0.00 0.00 2.69
1659 1784 1.838073 CGTACCCCTGTCCAGCCTTT 61.838 60.000 0.00 0.00 0.00 3.11
1665 1790 1.676635 CGTCTCGTACCCCTGTCCA 60.677 63.158 0.00 0.00 0.00 4.02
2321 2623 0.924090 GTACCCCTGGTTGGCCTTAT 59.076 55.000 3.32 0.00 37.09 1.73
2322 2624 1.555477 CGTACCCCTGGTTGGCCTTA 61.555 60.000 3.32 0.00 37.09 2.69
2468 2803 9.630098 CACTGAAAACATTCATGTAAAGCTATT 57.370 29.630 0.00 0.00 40.80 1.73
2477 2816 5.273170 CGTGAACACTGAAAACATTCATGT 58.727 37.500 3.51 0.00 44.20 3.21
2522 2864 6.878923 TGGTCTCACATTATTGTACAAGAAGG 59.121 38.462 22.06 22.06 33.76 3.46
2543 2885 2.159028 GCAGGGTTCTCTACAGATGGTC 60.159 54.545 0.00 0.00 0.00 4.02
2544 2886 1.834263 GCAGGGTTCTCTACAGATGGT 59.166 52.381 0.00 0.00 0.00 3.55
2572 2914 9.249844 CAACAAAATTTTCAAAAGAAACTCGTC 57.750 29.630 0.00 0.00 0.00 4.20
2575 2917 9.541724 GGACAACAAAATTTTCAAAAGAAACTC 57.458 29.630 0.00 0.00 0.00 3.01
2580 2922 8.839310 TTCAGGACAACAAAATTTTCAAAAGA 57.161 26.923 0.00 0.00 0.00 2.52
2591 2933 9.712305 TTTGTAAAAAGATTCAGGACAACAAAA 57.288 25.926 0.00 0.00 32.11 2.44
2631 4519 4.925068 AGATTCAGGCGCACAATAAAATC 58.075 39.130 10.83 8.10 0.00 2.17
2674 4562 1.721389 CGTCCTGTTGTTCATCAGTCG 59.279 52.381 9.17 9.25 0.00 4.18
2733 4628 3.422796 TGCCGGTGGTAATTGTGTAATT 58.577 40.909 1.90 0.00 39.69 1.40
2741 4636 0.250793 TCGACATGCCGGTGGTAATT 59.749 50.000 1.90 0.00 0.00 1.40
2773 4668 9.807921 TTTGAAAAGGAAGGTAAGATAAGATGT 57.192 29.630 0.00 0.00 0.00 3.06
2840 4736 2.615618 CGCGCTCTGTTCGTATGC 59.384 61.111 5.56 0.00 0.00 3.14
2873 4769 2.985456 CTGGAAGCTCCGCTCCTT 59.015 61.111 3.88 0.00 40.17 3.36


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

AutoCloner maintained by Alex Coulton.