Multiple sequence alignment - TraesCS5D01G318100

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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 TraesCS5D01G318100 chr5D 100.000 2837 0 0 1 2837 410954062 410951226 0.000000e+00 5240.0
1 TraesCS5D01G318100 chr5D 91.495 823 60 2 1024 1846 411149415 411148603 0.000000e+00 1123.0
2 TraesCS5D01G318100 chr5D 82.586 781 76 26 173 914 411150204 411149445 3.990000e-178 634.0
3 TraesCS5D01G318100 chr5D 85.143 350 46 3 1134 1483 411225760 411225417 1.250000e-93 353.0
4 TraesCS5D01G318100 chr5D 85.124 121 7 6 2100 2220 411142028 411141919 2.310000e-21 113.0
5 TraesCS5D01G318100 chr5D 94.595 37 2 0 1836 1872 411142678 411142642 1.100000e-04 58.4
6 TraesCS5D01G318100 chr5B 94.029 1658 50 16 342 1973 493481872 493480238 0.000000e+00 2468.0
7 TraesCS5D01G318100 chr5B 91.247 754 66 0 1024 1777 493516802 493516049 0.000000e+00 1027.0
8 TraesCS5D01G318100 chr5B 82.416 745 69 25 163 867 493517587 493516865 6.770000e-166 593.0
9 TraesCS5D01G318100 chr5B 86.118 389 29 15 2059 2425 493480241 493479856 2.050000e-106 396.0
10 TraesCS5D01G318100 chr5B 84.571 350 41 9 1142 1489 492619516 492619854 4.530000e-88 335.0
11 TraesCS5D01G318100 chr5B 83.714 350 51 3 1134 1483 493695441 493695098 2.730000e-85 326.0
12 TraesCS5D01G318100 chr5B 88.000 250 19 4 2507 2756 493478378 493478140 4.630000e-73 285.0
13 TraesCS5D01G318100 chr5B 95.238 126 6 0 163 288 493481994 493481869 1.720000e-47 200.0
14 TraesCS5D01G318100 chr5B 100.000 41 0 0 2100 2140 493514059 493514019 3.030000e-10 76.8
15 TraesCS5D01G318100 chr5A 96.349 986 35 1 989 1973 522883507 522882522 0.000000e+00 1620.0
16 TraesCS5D01G318100 chr5A 91.628 872 65 2 1024 1895 522956863 522956000 0.000000e+00 1199.0
17 TraesCS5D01G318100 chr5A 85.845 438 27 9 2059 2462 522882525 522882089 1.560000e-117 433.0
18 TraesCS5D01G318100 chr5A 84.286 350 49 3 1134 1483 523148706 523148363 1.260000e-88 337.0
19 TraesCS5D01G318100 chr5A 84.507 355 38 10 1142 1489 522066669 522067013 4.530000e-88 335.0
20 TraesCS5D01G318100 chr5A 95.597 159 4 2 358 513 522884185 522884027 4.690000e-63 252.0
21 TraesCS5D01G318100 chr5A 86.809 235 11 2 709 943 522884028 522883814 7.850000e-61 244.0
22 TraesCS5D01G318100 chr6A 93.151 73 3 2 1985 2056 613217698 613217769 3.870000e-19 106.0
23 TraesCS5D01G318100 chr6A 92.105 76 3 3 1983 2057 613190130 613190203 1.390000e-18 104.0
24 TraesCS5D01G318100 chr6A 92.000 75 3 3 1983 2056 613235958 613236030 5.000000e-18 102.0
25 TraesCS5D01G318100 chr6A 90.667 75 5 2 1983 2056 613152825 613152898 6.470000e-17 99.0
26 TraesCS5D01G318100 chr6A 90.789 76 4 3 1983 2056 613170937 613171011 6.470000e-17 99.0
27 TraesCS5D01G318100 chr6D 92.000 75 4 2 1983 2056 466907093 466907166 1.390000e-18 104.0


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 TraesCS5D01G318100 chr5D 410951226 410954062 2836 True 5240.00 5240 100.00000 1 2837 1 chr5D.!!$R1 2836
1 TraesCS5D01G318100 chr5D 411148603 411150204 1601 True 878.50 1123 87.04050 173 1846 2 chr5D.!!$R4 1673
2 TraesCS5D01G318100 chr5B 493478140 493481994 3854 True 837.25 2468 90.84625 163 2756 4 chr5B.!!$R2 2593
3 TraesCS5D01G318100 chr5B 493514019 493517587 3568 True 565.60 1027 91.22100 163 2140 3 chr5B.!!$R3 1977
4 TraesCS5D01G318100 chr5A 522956000 522956863 863 True 1199.00 1199 91.62800 1024 1895 1 chr5A.!!$R1 871
5 TraesCS5D01G318100 chr5A 522882089 522884185 2096 True 637.25 1620 91.15000 358 2462 4 chr5A.!!$R3 2104

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
48 49 0.033504 TTGCCTCAGTCGTTCCTCAC 59.966 55.0 0.0 0.0 0.00 3.51 F
147 148 0.242825 GCCACGAAAAGGTAAAGGCC 59.757 55.0 0.0 0.0 34.71 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 1928 0.385390 GTTGGCACCTGGAACACTTG 59.615 55.0 0.00 0.0 0.0 3.16 R
1972 2387 0.669619 AAAAACCCGTACGCCAAAGG 59.330 50.0 10.49 7.9 0.0 3.11 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
21 22 4.899239 GGCTCGACCTCGCCATGG 62.899 72.222 7.63 7.63 45.59 3.66
22 23 4.148825 GCTCGACCTCGCCATGGT 62.149 66.667 14.67 0.00 41.07 3.55
26 27 2.202756 GACCTCGCCATGGTCGAC 60.203 66.667 22.05 7.13 43.55 4.20
27 28 2.680352 ACCTCGCCATGGTCGACT 60.680 61.111 22.05 10.99 31.03 4.18
28 29 2.105128 CCTCGCCATGGTCGACTC 59.895 66.667 22.05 6.30 32.08 3.36
29 30 2.418910 CCTCGCCATGGTCGACTCT 61.419 63.158 22.05 0.00 32.08 3.24
30 31 1.513158 CTCGCCATGGTCGACTCTT 59.487 57.895 22.05 1.18 32.08 2.85
31 32 0.803768 CTCGCCATGGTCGACTCTTG 60.804 60.000 22.05 12.94 32.08 3.02
32 33 2.456119 CGCCATGGTCGACTCTTGC 61.456 63.158 19.72 12.31 0.00 4.01
33 34 2.109126 GCCATGGTCGACTCTTGCC 61.109 63.158 16.46 0.00 0.00 4.52
34 35 1.599047 CCATGGTCGACTCTTGCCT 59.401 57.895 16.46 0.00 0.00 4.75
35 36 0.460987 CCATGGTCGACTCTTGCCTC 60.461 60.000 16.46 0.00 0.00 4.70
36 37 0.247460 CATGGTCGACTCTTGCCTCA 59.753 55.000 16.46 2.22 0.00 3.86
37 38 0.534412 ATGGTCGACTCTTGCCTCAG 59.466 55.000 16.46 0.00 0.00 3.35
38 39 0.827925 TGGTCGACTCTTGCCTCAGT 60.828 55.000 16.46 0.00 0.00 3.41
39 40 0.109039 GGTCGACTCTTGCCTCAGTC 60.109 60.000 16.46 0.00 36.45 3.51
42 43 3.896317 GACTCTTGCCTCAGTCGTT 57.104 52.632 0.00 0.00 30.15 3.85
43 44 1.704070 GACTCTTGCCTCAGTCGTTC 58.296 55.000 0.00 0.00 30.15 3.95
44 45 0.318762 ACTCTTGCCTCAGTCGTTCC 59.681 55.000 0.00 0.00 0.00 3.62
45 46 0.605589 CTCTTGCCTCAGTCGTTCCT 59.394 55.000 0.00 0.00 0.00 3.36
46 47 0.603569 TCTTGCCTCAGTCGTTCCTC 59.396 55.000 0.00 0.00 0.00 3.71
47 48 0.318441 CTTGCCTCAGTCGTTCCTCA 59.682 55.000 0.00 0.00 0.00 3.86
48 49 0.033504 TTGCCTCAGTCGTTCCTCAC 59.966 55.000 0.00 0.00 0.00 3.51
56 57 4.554163 CGTTCCTCACGTCAGTCC 57.446 61.111 0.00 0.00 44.49 3.85
57 58 1.080705 CGTTCCTCACGTCAGTCCC 60.081 63.158 0.00 0.00 44.49 4.46
58 59 1.080705 GTTCCTCACGTCAGTCCCG 60.081 63.158 0.00 0.00 0.00 5.14
59 60 2.927580 TTCCTCACGTCAGTCCCGC 61.928 63.158 0.00 0.00 0.00 6.13
60 61 4.436998 CCTCACGTCAGTCCCGCC 62.437 72.222 0.00 0.00 0.00 6.13
61 62 3.680786 CTCACGTCAGTCCCGCCA 61.681 66.667 0.00 0.00 0.00 5.69
62 63 2.994995 TCACGTCAGTCCCGCCAT 60.995 61.111 0.00 0.00 0.00 4.40
63 64 2.509336 CACGTCAGTCCCGCCATC 60.509 66.667 0.00 0.00 0.00 3.51
64 65 4.129737 ACGTCAGTCCCGCCATCG 62.130 66.667 0.00 0.00 0.00 3.84
65 66 3.822192 CGTCAGTCCCGCCATCGA 61.822 66.667 0.00 0.00 38.10 3.59
66 67 2.202756 GTCAGTCCCGCCATCGAC 60.203 66.667 0.00 0.00 38.10 4.20
67 68 3.458163 TCAGTCCCGCCATCGACC 61.458 66.667 0.00 0.00 38.10 4.79
68 69 3.461773 CAGTCCCGCCATCGACCT 61.462 66.667 0.00 0.00 38.10 3.85
69 70 3.148279 AGTCCCGCCATCGACCTC 61.148 66.667 0.00 0.00 38.10 3.85
70 71 4.570663 GTCCCGCCATCGACCTCG 62.571 72.222 0.00 0.00 38.10 4.63
72 73 4.873129 CCCGCCATCGACCTCGTG 62.873 72.222 0.00 0.00 40.80 4.35
75 76 4.492160 GCCATCGACCTCGTGCGA 62.492 66.667 0.00 0.00 41.14 5.10
76 77 2.180769 CCATCGACCTCGTGCGAA 59.819 61.111 0.00 0.00 40.20 4.70
77 78 1.874019 CCATCGACCTCGTGCGAAG 60.874 63.158 0.00 0.00 40.20 3.79
93 94 3.511856 CGAAGCAGAAAAGTGACTCAC 57.488 47.619 0.38 0.38 34.10 3.51
94 95 2.866156 CGAAGCAGAAAAGTGACTCACA 59.134 45.455 11.80 0.00 36.74 3.58
127 128 9.520515 AAATTTCTAGAGACCAAAGATTTAGCA 57.479 29.630 0.00 0.00 0.00 3.49
128 129 8.729805 ATTTCTAGAGACCAAAGATTTAGCAG 57.270 34.615 0.00 0.00 0.00 4.24
129 130 5.665459 TCTAGAGACCAAAGATTTAGCAGC 58.335 41.667 0.00 0.00 0.00 5.25
130 131 3.615155 AGAGACCAAAGATTTAGCAGCC 58.385 45.455 0.00 0.00 0.00 4.85
131 132 3.009473 AGAGACCAAAGATTTAGCAGCCA 59.991 43.478 0.00 0.00 0.00 4.75
132 133 3.084786 AGACCAAAGATTTAGCAGCCAC 58.915 45.455 0.00 0.00 0.00 5.01
133 134 1.812571 ACCAAAGATTTAGCAGCCACG 59.187 47.619 0.00 0.00 0.00 4.94
134 135 2.083774 CCAAAGATTTAGCAGCCACGA 58.916 47.619 0.00 0.00 0.00 4.35
135 136 2.487762 CCAAAGATTTAGCAGCCACGAA 59.512 45.455 0.00 0.00 0.00 3.85
136 137 3.057596 CCAAAGATTTAGCAGCCACGAAA 60.058 43.478 0.00 0.00 0.00 3.46
137 138 4.545610 CAAAGATTTAGCAGCCACGAAAA 58.454 39.130 0.00 0.00 0.00 2.29
138 139 4.425577 AAGATTTAGCAGCCACGAAAAG 57.574 40.909 0.00 0.00 0.00 2.27
139 140 2.749621 AGATTTAGCAGCCACGAAAAGG 59.250 45.455 0.00 0.00 0.00 3.11
140 141 1.975660 TTTAGCAGCCACGAAAAGGT 58.024 45.000 0.00 0.00 0.00 3.50
141 142 2.843401 TTAGCAGCCACGAAAAGGTA 57.157 45.000 0.00 0.00 0.00 3.08
142 143 2.843401 TAGCAGCCACGAAAAGGTAA 57.157 45.000 0.00 0.00 0.00 2.85
143 144 1.975660 AGCAGCCACGAAAAGGTAAA 58.024 45.000 0.00 0.00 0.00 2.01
144 145 1.880027 AGCAGCCACGAAAAGGTAAAG 59.120 47.619 0.00 0.00 0.00 1.85
145 146 1.068541 GCAGCCACGAAAAGGTAAAGG 60.069 52.381 0.00 0.00 0.00 3.11
146 147 1.068541 CAGCCACGAAAAGGTAAAGGC 60.069 52.381 0.00 0.00 40.85 4.35
147 148 0.242825 GCCACGAAAAGGTAAAGGCC 59.757 55.000 0.00 0.00 34.71 5.19
148 149 1.611519 CCACGAAAAGGTAAAGGCCA 58.388 50.000 5.01 0.00 0.00 5.36
149 150 2.167662 CCACGAAAAGGTAAAGGCCAT 58.832 47.619 5.01 0.00 0.00 4.40
150 151 2.560981 CCACGAAAAGGTAAAGGCCATT 59.439 45.455 5.01 0.33 0.00 3.16
151 152 3.006430 CCACGAAAAGGTAAAGGCCATTT 59.994 43.478 5.01 5.42 32.84 2.32
152 153 4.502431 CCACGAAAAGGTAAAGGCCATTTT 60.502 41.667 5.01 0.00 30.65 1.82
153 154 5.279056 CCACGAAAAGGTAAAGGCCATTTTA 60.279 40.000 5.01 0.00 30.65 1.52
154 155 5.631929 CACGAAAAGGTAAAGGCCATTTTAC 59.368 40.000 15.88 15.88 40.91 2.01
155 156 5.537295 ACGAAAAGGTAAAGGCCATTTTACT 59.463 36.000 20.85 10.71 41.23 2.24
156 157 6.090783 CGAAAAGGTAAAGGCCATTTTACTC 58.909 40.000 20.85 13.84 41.23 2.59
157 158 5.995565 AAAGGTAAAGGCCATTTTACTCC 57.004 39.130 20.85 10.30 41.23 3.85
158 159 3.617284 AGGTAAAGGCCATTTTACTCCG 58.383 45.455 20.85 0.00 41.23 4.63
159 160 3.009805 AGGTAAAGGCCATTTTACTCCGT 59.990 43.478 20.85 6.91 41.23 4.69
160 161 3.376234 GGTAAAGGCCATTTTACTCCGTC 59.624 47.826 20.85 6.41 41.23 4.79
161 162 1.734163 AAGGCCATTTTACTCCGTCG 58.266 50.000 5.01 0.00 0.00 5.12
180 181 3.805422 GTCGGCCAATTCGATATACAACA 59.195 43.478 2.24 0.00 38.93 3.33
248 256 4.501071 ACAAAAGGTACGCGTATCATTCT 58.499 39.130 29.68 15.49 0.00 2.40
288 369 2.103537 AACGGGATGGGTAACTTTCG 57.896 50.000 0.00 0.00 0.00 3.46
289 370 0.978907 ACGGGATGGGTAACTTTCGT 59.021 50.000 0.00 0.00 0.00 3.85
290 371 1.066645 ACGGGATGGGTAACTTTCGTC 60.067 52.381 0.00 0.00 0.00 4.20
291 372 1.206371 CGGGATGGGTAACTTTCGTCT 59.794 52.381 0.00 0.00 0.00 4.18
292 373 2.629051 GGGATGGGTAACTTTCGTCTG 58.371 52.381 0.00 0.00 0.00 3.51
293 374 2.027469 GGGATGGGTAACTTTCGTCTGT 60.027 50.000 0.00 0.00 0.00 3.41
294 375 3.558533 GGGATGGGTAACTTTCGTCTGTT 60.559 47.826 0.00 0.00 0.00 3.16
295 376 3.683340 GGATGGGTAACTTTCGTCTGTTC 59.317 47.826 0.00 0.00 0.00 3.18
296 377 2.746269 TGGGTAACTTTCGTCTGTTCG 58.254 47.619 0.00 0.00 0.00 3.95
297 378 2.361757 TGGGTAACTTTCGTCTGTTCGA 59.638 45.455 0.00 0.00 38.08 3.71
298 379 3.006110 TGGGTAACTTTCGTCTGTTCGAT 59.994 43.478 0.00 0.00 39.57 3.59
299 380 3.611549 GGGTAACTTTCGTCTGTTCGATC 59.388 47.826 0.00 0.00 39.57 3.69
300 381 3.300066 GGTAACTTTCGTCTGTTCGATCG 59.700 47.826 9.36 9.36 39.57 3.69
301 382 2.701073 ACTTTCGTCTGTTCGATCGT 57.299 45.000 15.94 0.00 39.57 3.73
302 383 2.316792 ACTTTCGTCTGTTCGATCGTG 58.683 47.619 15.94 4.58 39.57 4.35
303 384 1.057636 TTTCGTCTGTTCGATCGTGC 58.942 50.000 15.94 9.66 39.57 5.34
304 385 1.063412 TTCGTCTGTTCGATCGTGCG 61.063 55.000 15.94 11.25 39.57 5.34
305 386 1.796355 CGTCTGTTCGATCGTGCGT 60.796 57.895 15.94 0.00 0.00 5.24
306 387 1.696644 GTCTGTTCGATCGTGCGTG 59.303 57.895 15.94 6.59 0.00 5.34
307 388 2.086426 TCTGTTCGATCGTGCGTGC 61.086 57.895 15.94 1.23 0.00 5.34
308 389 3.392076 CTGTTCGATCGTGCGTGCG 62.392 63.158 15.94 0.00 0.00 5.34
309 390 4.191485 GTTCGATCGTGCGTGCGG 62.191 66.667 15.94 0.00 0.00 5.69
326 407 4.467084 GGGCCAACCGATCGAGCA 62.467 66.667 18.66 0.00 36.48 4.26
327 408 2.892425 GGCCAACCGATCGAGCAG 60.892 66.667 18.66 1.54 0.00 4.24
328 409 2.892425 GCCAACCGATCGAGCAGG 60.892 66.667 18.66 13.49 0.00 4.85
329 410 2.579201 CCAACCGATCGAGCAGGT 59.421 61.111 18.66 10.65 40.50 4.00
330 411 1.519455 CCAACCGATCGAGCAGGTC 60.519 63.158 18.66 0.00 37.26 3.85
340 421 3.071580 GAGCAGGTCGAATCCCTTG 57.928 57.895 0.00 0.00 0.00 3.61
341 422 0.250513 GAGCAGGTCGAATCCCTTGT 59.749 55.000 0.00 0.00 0.00 3.16
342 423 0.693049 AGCAGGTCGAATCCCTTGTT 59.307 50.000 0.00 0.00 0.00 2.83
343 424 1.073923 AGCAGGTCGAATCCCTTGTTT 59.926 47.619 0.00 0.00 0.00 2.83
344 425 1.468914 GCAGGTCGAATCCCTTGTTTC 59.531 52.381 0.00 0.00 0.00 2.78
356 437 4.090090 TCCCTTGTTTCCTTGTCAAAACA 58.910 39.130 0.00 0.00 42.07 2.83
620 712 3.759086 TCGACTAGAAGCACTGTTCATCT 59.241 43.478 0.00 0.00 0.00 2.90
649 741 1.273154 TGGTGGGGATGAACGTAGGTA 60.273 52.381 0.00 0.00 0.00 3.08
724 816 3.299977 GGAACCCAAACGCCCCAC 61.300 66.667 0.00 0.00 0.00 4.61
742 838 2.885644 CGCCAATCGTCGACCAGG 60.886 66.667 10.58 7.86 0.00 4.45
744 840 1.079405 GCCAATCGTCGACCAGGAA 60.079 57.895 10.58 0.00 0.00 3.36
752 848 2.358737 CGACCAGGAACACCAGCC 60.359 66.667 0.00 0.00 0.00 4.85
835 931 4.828296 CCACCCATCTGCCCTGCC 62.828 72.222 0.00 0.00 0.00 4.85
899 1009 2.227194 CCAACTACCCAACACCTCAAC 58.773 52.381 0.00 0.00 0.00 3.18
922 1032 1.068083 CTCTGCACACCACACTCGT 59.932 57.895 0.00 0.00 0.00 4.18
943 1053 2.559668 TCTACCCAACACGTACCTCAAG 59.440 50.000 0.00 0.00 0.00 3.02
960 1070 2.876219 GCTCAAGCTCAAGCCAGC 59.124 61.111 8.71 0.69 43.38 4.85
967 1077 2.182842 GCTCAAGCCAGCCATACCG 61.183 63.158 0.00 0.00 32.76 4.02
968 1078 2.124736 TCAAGCCAGCCATACCGC 60.125 61.111 0.00 0.00 0.00 5.68
969 1079 3.576356 CAAGCCAGCCATACCGCG 61.576 66.667 0.00 0.00 0.00 6.46
1017 1388 2.481104 GCTCAGCTAGAGTGACCACATC 60.481 54.545 12.71 0.00 46.47 3.06
1020 1391 0.466124 GCTAGAGTGACCACATCCCC 59.534 60.000 0.00 0.00 0.00 4.81
1138 1509 4.927782 GGTGCCTGTGTGGTCGCA 62.928 66.667 0.00 0.00 38.35 5.10
1382 1753 2.281484 GCGTGCCTCAACTTCCCA 60.281 61.111 0.00 0.00 0.00 4.37
1557 1928 3.124921 CCGTGGACAATGCCGACC 61.125 66.667 0.00 0.00 0.00 4.79
1574 1945 1.152777 CCAAGTGTTCCAGGTGCCA 60.153 57.895 0.00 0.00 0.00 4.92
1767 2167 4.440802 GGAGCTACTGATGTCTGTAACCTG 60.441 50.000 0.00 0.00 31.44 4.00
1868 2269 4.032356 ACGTCGACCCGTTTTTCC 57.968 55.556 10.58 0.00 37.96 3.13
1962 2377 4.449743 TCGGTTGAAAAGTAATCGTTCCAG 59.550 41.667 0.00 0.00 33.61 3.86
1974 2389 1.228154 GTTCCAGACGGGTTTGCCT 60.228 57.895 0.00 0.00 38.11 4.75
1975 2390 0.822121 GTTCCAGACGGGTTTGCCTT 60.822 55.000 0.00 0.00 38.11 4.35
1976 2391 0.106419 TTCCAGACGGGTTTGCCTTT 60.106 50.000 0.00 0.00 38.11 3.11
1978 2393 1.659794 CAGACGGGTTTGCCTTTGG 59.340 57.895 0.00 0.00 34.45 3.28
1988 2403 2.670592 GCCTTTGGCGTACGGGTT 60.671 61.111 18.39 0.00 39.62 4.11
1990 2405 1.798234 GCCTTTGGCGTACGGGTTTT 61.798 55.000 18.39 0.00 39.62 2.43
1991 2406 0.669619 CCTTTGGCGTACGGGTTTTT 59.330 50.000 18.39 0.00 0.00 1.94
1992 2407 1.600912 CCTTTGGCGTACGGGTTTTTG 60.601 52.381 18.39 0.00 0.00 2.44
1994 2409 1.959042 TTGGCGTACGGGTTTTTGTA 58.041 45.000 18.39 0.00 0.00 2.41
1996 2411 2.292267 TGGCGTACGGGTTTTTGTAAA 58.708 42.857 18.39 0.00 0.00 2.01
1997 2412 2.684881 TGGCGTACGGGTTTTTGTAAAA 59.315 40.909 18.39 0.00 0.00 1.52
1998 2413 3.042189 GGCGTACGGGTTTTTGTAAAAC 58.958 45.455 18.39 6.50 0.00 2.43
1999 2414 3.488216 GGCGTACGGGTTTTTGTAAAACA 60.488 43.478 18.39 0.00 32.39 2.83
2000 2415 4.289342 GCGTACGGGTTTTTGTAAAACAT 58.711 39.130 18.39 4.82 32.39 2.71
2001 2416 4.739228 GCGTACGGGTTTTTGTAAAACATT 59.261 37.500 18.39 3.57 32.39 2.71
2002 2417 5.108292 GCGTACGGGTTTTTGTAAAACATTC 60.108 40.000 18.39 5.33 32.39 2.67
2008 4043 7.820386 ACGGGTTTTTGTAAAACATTCTTTCTT 59.180 29.630 14.73 0.00 32.39 2.52
2081 4116 4.724399 TGCAGAATGGTTCCAAAGTAAGA 58.276 39.130 0.00 0.00 35.86 2.10
2252 4425 2.783135 TGTTGAAGAATGAGGTGAGGC 58.217 47.619 0.00 0.00 0.00 4.70
2253 4426 1.734465 GTTGAAGAATGAGGTGAGGCG 59.266 52.381 0.00 0.00 0.00 5.52
2289 4489 1.134340 GTATGTCGCCATGGTTGGGTA 60.134 52.381 14.67 0.00 43.84 3.69
2346 4546 4.099573 TGGGAGAAAAGATCTAGCGTTAGG 59.900 45.833 6.45 0.00 38.96 2.69
2350 4550 0.674534 AAGATCTAGCGTTAGGCCGG 59.325 55.000 6.45 0.00 45.17 6.13
2371 4571 1.410517 GAATGATCTGCGAGGACTCCA 59.589 52.381 0.00 0.00 0.00 3.86
2433 4634 9.529325 GAAAATAGATTTTGTAATAACCCAGGC 57.471 33.333 4.98 0.00 39.86 4.85
2444 4645 2.361610 CCCAGGCCAAATCGCACT 60.362 61.111 5.01 0.00 0.00 4.40
2478 4679 4.641645 CCACCGCTCAACCCTGCA 62.642 66.667 0.00 0.00 0.00 4.41
2479 4680 2.594303 CACCGCTCAACCCTGCAA 60.594 61.111 0.00 0.00 0.00 4.08
2480 4681 1.973281 CACCGCTCAACCCTGCAAT 60.973 57.895 0.00 0.00 0.00 3.56
2481 4682 1.675641 ACCGCTCAACCCTGCAATC 60.676 57.895 0.00 0.00 0.00 2.67
2482 4683 2.409870 CCGCTCAACCCTGCAATCC 61.410 63.158 0.00 0.00 0.00 3.01
2483 4684 2.753966 CGCTCAACCCTGCAATCCG 61.754 63.158 0.00 0.00 0.00 4.18
2487 6056 0.036388 TCAACCCTGCAATCCGACTC 60.036 55.000 0.00 0.00 0.00 3.36
2489 6058 0.620556 AACCCTGCAATCCGACTCAT 59.379 50.000 0.00 0.00 0.00 2.90
2499 6068 4.129737 CGACTCATGGGCGGTCGT 62.130 66.667 16.81 0.00 43.88 4.34
2501 6070 1.740285 GACTCATGGGCGGTCGTAT 59.260 57.895 0.00 0.00 0.00 3.06
2512 6109 0.249322 CGGTCGTATCCATGGTCACC 60.249 60.000 12.58 10.38 0.00 4.02
2520 6117 0.320374 TCCATGGTCACCGTCTTCAC 59.680 55.000 12.58 0.00 0.00 3.18
2531 6128 1.278127 CCGTCTTCACCCATGGTAAGT 59.722 52.381 11.73 0.00 32.11 2.24
2546 6143 6.715264 CCATGGTAAGTTCCATAGGTAAATCC 59.285 42.308 2.57 0.00 45.23 3.01
2547 6144 6.894735 TGGTAAGTTCCATAGGTAAATCCA 57.105 37.500 0.00 0.00 33.76 3.41
2548 6145 7.460214 TGGTAAGTTCCATAGGTAAATCCAT 57.540 36.000 0.00 0.00 33.76 3.41
2549 6146 7.878495 TGGTAAGTTCCATAGGTAAATCCATT 58.122 34.615 0.00 0.00 33.76 3.16
2571 6168 9.871238 CCATTATTAGTCATGGGTAGTGTATAC 57.129 37.037 0.00 0.00 36.96 1.47
2574 6171 9.650714 TTATTAGTCATGGGTAGTGTATACTGT 57.349 33.333 1.82 0.00 37.78 3.55
2576 6173 9.824216 ATTAGTCATGGGTAGTGTATACTGTAT 57.176 33.333 5.53 5.53 37.78 2.29
2578 6175 8.865420 AGTCATGGGTAGTGTATACTGTATAG 57.135 38.462 7.75 0.00 37.78 1.31
2597 6194 0.811616 GGCATAAGGTCCTGCTCGTG 60.812 60.000 0.00 0.00 38.45 4.35
2599 6196 0.179073 CATAAGGTCCTGCTCGTGGG 60.179 60.000 0.00 0.00 0.00 4.61
2615 6212 2.547826 GTGGGTCGCCAGATTAACTAC 58.452 52.381 0.00 0.00 0.00 2.73
2617 6214 2.568062 TGGGTCGCCAGATTAACTACAA 59.432 45.455 0.00 0.00 0.00 2.41
2650 6247 9.702253 TGTTATGTATTTAAATCCCAGCCTAAA 57.298 29.630 3.39 0.00 0.00 1.85
2698 6295 7.222000 ACAGAATAGCTATAGCCTACTTCAC 57.778 40.000 21.17 5.39 43.38 3.18
2705 6302 4.504132 GCCTACTTCACGGCTCAG 57.496 61.111 0.00 0.00 42.98 3.35
2716 6313 1.102978 ACGGCTCAGCACAAAACTTT 58.897 45.000 0.00 0.00 0.00 2.66
2717 6314 1.476488 ACGGCTCAGCACAAAACTTTT 59.524 42.857 0.00 0.00 0.00 2.27
2743 6340 8.533569 TTTCCATAAAAGAACTGGAGAGTTTT 57.466 30.769 0.00 0.00 42.80 2.43
2756 6353 3.503891 GAGAGTTTTGTACGAGAGCTCC 58.496 50.000 10.93 0.68 0.00 4.70
2757 6354 3.158676 AGAGTTTTGTACGAGAGCTCCT 58.841 45.455 10.93 0.00 0.00 3.69
2758 6355 3.057174 AGAGTTTTGTACGAGAGCTCCTG 60.057 47.826 10.93 5.60 0.00 3.86
2759 6356 2.628657 AGTTTTGTACGAGAGCTCCTGT 59.371 45.455 10.93 11.87 0.00 4.00
2760 6357 3.069729 AGTTTTGTACGAGAGCTCCTGTT 59.930 43.478 10.93 0.00 0.00 3.16
2761 6358 3.299340 TTTGTACGAGAGCTCCTGTTC 57.701 47.619 10.93 7.80 0.00 3.18
2762 6359 0.803117 TGTACGAGAGCTCCTGTTCG 59.197 55.000 18.37 18.37 38.88 3.95
2763 6360 0.099082 GTACGAGAGCTCCTGTTCGG 59.901 60.000 22.31 8.73 37.38 4.30
2764 6361 1.654954 TACGAGAGCTCCTGTTCGGC 61.655 60.000 22.31 0.00 37.38 5.54
2765 6362 2.973899 GAGAGCTCCTGTTCGGCA 59.026 61.111 10.93 0.00 0.00 5.69
2766 6363 1.446966 GAGAGCTCCTGTTCGGCAC 60.447 63.158 10.93 0.00 0.00 5.01
2767 6364 1.882989 GAGAGCTCCTGTTCGGCACT 61.883 60.000 10.93 0.00 0.00 4.40
2768 6365 1.446966 GAGCTCCTGTTCGGCACTC 60.447 63.158 0.87 0.00 0.00 3.51
2769 6366 1.882989 GAGCTCCTGTTCGGCACTCT 61.883 60.000 0.87 0.00 33.85 3.24
2770 6367 0.612174 AGCTCCTGTTCGGCACTCTA 60.612 55.000 0.00 0.00 0.00 2.43
2771 6368 0.246635 GCTCCTGTTCGGCACTCTAA 59.753 55.000 0.00 0.00 0.00 2.10
2772 6369 1.737363 GCTCCTGTTCGGCACTCTAAG 60.737 57.143 0.00 0.00 0.00 2.18
2773 6370 0.246635 TCCTGTTCGGCACTCTAAGC 59.753 55.000 0.00 0.00 0.00 3.09
2774 6371 0.037326 CCTGTTCGGCACTCTAAGCA 60.037 55.000 0.00 0.00 0.00 3.91
2775 6372 1.071605 CTGTTCGGCACTCTAAGCAC 58.928 55.000 0.00 0.00 0.00 4.40
2776 6373 0.320421 TGTTCGGCACTCTAAGCACC 60.320 55.000 0.00 0.00 0.00 5.01
2777 6374 0.037232 GTTCGGCACTCTAAGCACCT 60.037 55.000 0.00 0.00 0.00 4.00
2778 6375 0.246635 TTCGGCACTCTAAGCACCTC 59.753 55.000 0.00 0.00 0.00 3.85
2779 6376 0.898326 TCGGCACTCTAAGCACCTCA 60.898 55.000 0.00 0.00 0.00 3.86
2780 6377 0.176680 CGGCACTCTAAGCACCTCAT 59.823 55.000 0.00 0.00 0.00 2.90
2781 6378 1.409064 CGGCACTCTAAGCACCTCATA 59.591 52.381 0.00 0.00 0.00 2.15
2782 6379 2.544694 CGGCACTCTAAGCACCTCATAG 60.545 54.545 0.00 0.00 0.00 2.23
2783 6380 2.478831 GCACTCTAAGCACCTCATAGC 58.521 52.381 0.00 0.00 0.00 2.97
2784 6381 2.736978 CACTCTAAGCACCTCATAGCG 58.263 52.381 0.00 0.00 35.48 4.26
2785 6382 1.683917 ACTCTAAGCACCTCATAGCGG 59.316 52.381 0.00 0.00 35.48 5.52
2786 6383 1.000283 CTCTAAGCACCTCATAGCGGG 60.000 57.143 0.00 0.00 35.48 6.13
2787 6384 0.753262 CTAAGCACCTCATAGCGGGT 59.247 55.000 0.00 0.00 36.07 5.28
2801 6398 3.741476 GGGTGCTGGCGCTCAAAG 61.741 66.667 7.64 1.15 36.97 2.77
2802 6399 4.410743 GGTGCTGGCGCTCAAAGC 62.411 66.667 7.64 12.39 38.02 3.51
2810 6407 4.394712 CGCTCAAAGCCGAGGGGT 62.395 66.667 4.97 0.00 41.09 4.95
2811 6408 2.436824 GCTCAAAGCCGAGGGGTC 60.437 66.667 0.00 0.00 34.48 4.46
2812 6409 3.068881 CTCAAAGCCGAGGGGTCA 58.931 61.111 0.00 0.00 34.97 4.02
2813 6410 1.604378 CTCAAAGCCGAGGGGTCAT 59.396 57.895 0.00 0.00 34.97 3.06
2814 6411 0.745845 CTCAAAGCCGAGGGGTCATG 60.746 60.000 0.00 0.00 34.97 3.07
2815 6412 1.750399 CAAAGCCGAGGGGTCATGG 60.750 63.158 0.00 0.00 34.97 3.66
2816 6413 2.983879 AAAGCCGAGGGGTCATGGG 61.984 63.158 0.00 0.00 34.97 4.00
2825 6422 4.864334 GGTCATGGGCCGGCTCAG 62.864 72.222 35.67 25.13 0.00 3.35
2826 6423 4.101448 GTCATGGGCCGGCTCAGT 62.101 66.667 35.67 19.78 0.00 3.41
2827 6424 4.100084 TCATGGGCCGGCTCAGTG 62.100 66.667 35.67 29.01 0.00 3.66
2828 6425 4.100084 CATGGGCCGGCTCAGTGA 62.100 66.667 35.67 11.61 0.00 3.41
2829 6426 3.329889 ATGGGCCGGCTCAGTGAA 61.330 61.111 35.67 11.14 0.00 3.18
2830 6427 3.628646 ATGGGCCGGCTCAGTGAAC 62.629 63.158 35.67 11.13 0.00 3.18
2832 6429 4.681978 GGCCGGCTCAGTGAACGT 62.682 66.667 28.56 0.00 0.00 3.99
2833 6430 3.414700 GCCGGCTCAGTGAACGTG 61.415 66.667 22.15 7.98 0.00 4.49
2834 6431 2.338620 CCGGCTCAGTGAACGTGA 59.661 61.111 13.73 0.00 0.00 4.35
2835 6432 1.734477 CCGGCTCAGTGAACGTGAG 60.734 63.158 13.73 0.00 43.77 3.51
2836 6433 1.734477 CGGCTCAGTGAACGTGAGG 60.734 63.158 8.33 0.00 41.60 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.148825 ACCATGGCGAGGTCGAGC 62.149 66.667 13.04 6.48 43.02 5.03
6 7 2.105128 GACCATGGCGAGGTCGAG 59.895 66.667 13.04 0.00 45.35 4.04
10 11 2.680352 AGTCGACCATGGCGAGGT 60.680 61.111 25.06 15.78 43.46 3.85
11 12 1.949847 AAGAGTCGACCATGGCGAGG 61.950 60.000 25.06 8.25 38.59 4.63
12 13 0.803768 CAAGAGTCGACCATGGCGAG 60.804 60.000 25.06 12.31 38.59 5.03
13 14 1.215382 CAAGAGTCGACCATGGCGA 59.785 57.895 22.05 22.05 35.08 5.54
14 15 2.456119 GCAAGAGTCGACCATGGCG 61.456 63.158 13.04 16.58 0.00 5.69
15 16 2.109126 GGCAAGAGTCGACCATGGC 61.109 63.158 13.04 16.64 0.00 4.40
16 17 0.460987 GAGGCAAGAGTCGACCATGG 60.461 60.000 13.01 11.19 0.00 3.66
17 18 0.247460 TGAGGCAAGAGTCGACCATG 59.753 55.000 13.01 10.08 0.00 3.66
18 19 0.534412 CTGAGGCAAGAGTCGACCAT 59.466 55.000 13.01 0.00 0.00 3.55
19 20 0.827925 ACTGAGGCAAGAGTCGACCA 60.828 55.000 13.01 0.00 0.00 4.02
20 21 0.109039 GACTGAGGCAAGAGTCGACC 60.109 60.000 13.01 3.77 29.86 4.79
21 22 3.410098 GACTGAGGCAAGAGTCGAC 57.590 57.895 7.70 7.70 29.86 4.20
24 25 1.670380 GGAACGACTGAGGCAAGAGTC 60.670 57.143 0.00 0.00 36.10 3.36
25 26 0.318762 GGAACGACTGAGGCAAGAGT 59.681 55.000 0.00 0.00 0.00 3.24
26 27 0.605589 AGGAACGACTGAGGCAAGAG 59.394 55.000 0.00 0.00 0.00 2.85
27 28 0.603569 GAGGAACGACTGAGGCAAGA 59.396 55.000 0.00 0.00 0.00 3.02
28 29 0.318441 TGAGGAACGACTGAGGCAAG 59.682 55.000 0.00 0.00 0.00 4.01
29 30 0.033504 GTGAGGAACGACTGAGGCAA 59.966 55.000 0.00 0.00 0.00 4.52
30 31 1.666011 GTGAGGAACGACTGAGGCA 59.334 57.895 0.00 0.00 0.00 4.75
31 32 4.580835 GTGAGGAACGACTGAGGC 57.419 61.111 0.00 0.00 0.00 4.70
40 41 1.080705 CGGGACTGACGTGAGGAAC 60.081 63.158 7.04 0.00 0.00 3.62
41 42 2.927580 GCGGGACTGACGTGAGGAA 61.928 63.158 7.04 0.00 0.00 3.36
42 43 3.371063 GCGGGACTGACGTGAGGA 61.371 66.667 7.04 0.00 0.00 3.71
43 44 4.436998 GGCGGGACTGACGTGAGG 62.437 72.222 7.04 0.00 0.00 3.86
44 45 2.890847 GATGGCGGGACTGACGTGAG 62.891 65.000 0.00 0.00 0.00 3.51
45 46 2.994995 ATGGCGGGACTGACGTGA 60.995 61.111 0.00 0.00 0.00 4.35
46 47 2.509336 GATGGCGGGACTGACGTG 60.509 66.667 0.00 0.00 0.00 4.49
47 48 4.129737 CGATGGCGGGACTGACGT 62.130 66.667 0.00 0.00 0.00 4.34
48 49 3.822192 TCGATGGCGGGACTGACG 61.822 66.667 0.00 0.00 38.28 4.35
49 50 2.202756 GTCGATGGCGGGACTGAC 60.203 66.667 0.00 0.00 38.28 3.51
50 51 3.458163 GGTCGATGGCGGGACTGA 61.458 66.667 0.00 0.00 38.28 3.41
51 52 3.432051 GAGGTCGATGGCGGGACTG 62.432 68.421 0.00 0.00 38.28 3.51
52 53 3.148279 GAGGTCGATGGCGGGACT 61.148 66.667 0.00 0.00 38.28 3.85
53 54 4.570663 CGAGGTCGATGGCGGGAC 62.571 72.222 0.00 0.00 43.02 4.46
55 56 4.873129 CACGAGGTCGATGGCGGG 62.873 72.222 6.35 0.98 43.02 6.13
58 59 3.982372 TTCGCACGAGGTCGATGGC 62.982 63.158 6.35 5.96 43.02 4.40
59 60 1.874019 CTTCGCACGAGGTCGATGG 60.874 63.158 6.35 0.00 43.02 3.51
60 61 2.508891 GCTTCGCACGAGGTCGATG 61.509 63.158 6.35 2.32 43.02 3.84
61 62 2.202623 GCTTCGCACGAGGTCGAT 60.203 61.111 6.35 0.00 43.02 3.59
62 63 3.610791 CTGCTTCGCACGAGGTCGA 62.611 63.158 6.35 0.00 43.39 4.20
63 64 3.175240 CTGCTTCGCACGAGGTCG 61.175 66.667 4.07 0.00 46.33 4.79
64 65 0.944311 TTTCTGCTTCGCACGAGGTC 60.944 55.000 4.07 0.00 33.79 3.85
65 66 0.531974 TTTTCTGCTTCGCACGAGGT 60.532 50.000 4.07 0.00 33.79 3.85
66 67 0.164647 CTTTTCTGCTTCGCACGAGG 59.835 55.000 0.00 0.00 33.79 4.63
67 68 0.861837 ACTTTTCTGCTTCGCACGAG 59.138 50.000 0.00 0.00 33.79 4.18
68 69 0.581529 CACTTTTCTGCTTCGCACGA 59.418 50.000 0.00 0.00 33.79 4.35
69 70 0.581529 TCACTTTTCTGCTTCGCACG 59.418 50.000 0.00 0.00 33.79 5.34
70 71 1.599542 AGTCACTTTTCTGCTTCGCAC 59.400 47.619 0.00 0.00 33.79 5.34
71 72 1.867233 GAGTCACTTTTCTGCTTCGCA 59.133 47.619 0.00 0.00 36.92 5.10
72 73 1.867233 TGAGTCACTTTTCTGCTTCGC 59.133 47.619 0.00 0.00 0.00 4.70
73 74 2.866156 TGTGAGTCACTTTTCTGCTTCG 59.134 45.455 23.29 0.00 35.11 3.79
74 75 4.202578 GTGTGAGTCACTTTTCTGCTTC 57.797 45.455 23.29 0.00 43.13 3.86
82 83 9.178758 AGAAATTTTTCTAGTGTGAGTCACTTT 57.821 29.630 23.29 13.75 45.39 2.66
83 84 8.738645 AGAAATTTTTCTAGTGTGAGTCACTT 57.261 30.769 23.29 14.08 45.39 3.16
101 102 9.520515 TGCTAAATCTTTGGTCTCTAGAAATTT 57.479 29.630 0.00 0.00 0.00 1.82
102 103 9.171877 CTGCTAAATCTTTGGTCTCTAGAAATT 57.828 33.333 0.00 0.00 0.00 1.82
103 104 7.281999 GCTGCTAAATCTTTGGTCTCTAGAAAT 59.718 37.037 0.00 0.00 0.00 2.17
104 105 6.595716 GCTGCTAAATCTTTGGTCTCTAGAAA 59.404 38.462 0.00 0.00 0.00 2.52
105 106 6.109359 GCTGCTAAATCTTTGGTCTCTAGAA 58.891 40.000 0.00 0.00 0.00 2.10
106 107 5.395768 GGCTGCTAAATCTTTGGTCTCTAGA 60.396 44.000 0.00 0.00 0.00 2.43
107 108 4.813697 GGCTGCTAAATCTTTGGTCTCTAG 59.186 45.833 0.00 0.00 0.00 2.43
108 109 4.225042 TGGCTGCTAAATCTTTGGTCTCTA 59.775 41.667 0.00 0.00 0.00 2.43
109 110 3.009473 TGGCTGCTAAATCTTTGGTCTCT 59.991 43.478 0.00 0.00 0.00 3.10
110 111 3.127721 GTGGCTGCTAAATCTTTGGTCTC 59.872 47.826 0.00 0.00 0.00 3.36
111 112 3.084786 GTGGCTGCTAAATCTTTGGTCT 58.915 45.455 0.00 0.00 0.00 3.85
112 113 2.159517 CGTGGCTGCTAAATCTTTGGTC 60.160 50.000 0.00 0.00 0.00 4.02
113 114 1.812571 CGTGGCTGCTAAATCTTTGGT 59.187 47.619 0.00 0.00 0.00 3.67
114 115 2.083774 TCGTGGCTGCTAAATCTTTGG 58.916 47.619 0.00 0.00 0.00 3.28
115 116 3.829886 TTCGTGGCTGCTAAATCTTTG 57.170 42.857 0.00 0.00 0.00 2.77
116 117 4.321230 CCTTTTCGTGGCTGCTAAATCTTT 60.321 41.667 0.00 0.00 0.00 2.52
117 118 3.191371 CCTTTTCGTGGCTGCTAAATCTT 59.809 43.478 0.00 0.00 0.00 2.40
118 119 2.749621 CCTTTTCGTGGCTGCTAAATCT 59.250 45.455 0.00 0.00 0.00 2.40
119 120 2.488153 ACCTTTTCGTGGCTGCTAAATC 59.512 45.455 0.00 0.00 0.00 2.17
120 121 2.514803 ACCTTTTCGTGGCTGCTAAAT 58.485 42.857 0.00 0.00 0.00 1.40
121 122 1.975660 ACCTTTTCGTGGCTGCTAAA 58.024 45.000 0.00 0.00 0.00 1.85
122 123 2.843401 TACCTTTTCGTGGCTGCTAA 57.157 45.000 0.00 0.00 0.00 3.09
123 124 2.843401 TTACCTTTTCGTGGCTGCTA 57.157 45.000 0.00 0.00 0.00 3.49
124 125 1.880027 CTTTACCTTTTCGTGGCTGCT 59.120 47.619 0.00 0.00 0.00 4.24
125 126 1.068541 CCTTTACCTTTTCGTGGCTGC 60.069 52.381 0.00 0.00 0.00 5.25
126 127 1.068541 GCCTTTACCTTTTCGTGGCTG 60.069 52.381 0.00 0.00 36.32 4.85
127 128 1.244816 GCCTTTACCTTTTCGTGGCT 58.755 50.000 0.00 0.00 36.32 4.75
128 129 0.242825 GGCCTTTACCTTTTCGTGGC 59.757 55.000 0.00 0.00 38.28 5.01
129 130 1.611519 TGGCCTTTACCTTTTCGTGG 58.388 50.000 3.32 0.00 0.00 4.94
130 131 3.934457 AATGGCCTTTACCTTTTCGTG 57.066 42.857 3.32 0.00 0.00 4.35
131 132 4.948341 AAAATGGCCTTTACCTTTTCGT 57.052 36.364 3.32 0.00 36.38 3.85
132 133 6.020971 AGTAAAATGGCCTTTACCTTTTCG 57.979 37.500 19.03 0.00 40.97 3.46
133 134 6.395629 GGAGTAAAATGGCCTTTACCTTTTC 58.604 40.000 19.03 12.27 40.97 2.29
134 135 5.047590 CGGAGTAAAATGGCCTTTACCTTTT 60.048 40.000 19.03 10.98 40.97 2.27
135 136 4.461431 CGGAGTAAAATGGCCTTTACCTTT 59.539 41.667 19.03 7.41 40.97 3.11
136 137 4.014406 CGGAGTAAAATGGCCTTTACCTT 58.986 43.478 19.03 7.71 40.97 3.50
137 138 3.009805 ACGGAGTAAAATGGCCTTTACCT 59.990 43.478 19.03 9.56 41.94 3.08
138 139 3.349927 ACGGAGTAAAATGGCCTTTACC 58.650 45.455 19.03 12.67 41.94 2.85
154 155 0.031585 TATCGAATTGGCCGACGGAG 59.968 55.000 20.50 0.00 38.97 4.63
155 156 0.677288 ATATCGAATTGGCCGACGGA 59.323 50.000 20.50 0.00 38.97 4.69
156 157 1.990563 GTATATCGAATTGGCCGACGG 59.009 52.381 10.29 10.29 38.97 4.79
157 158 2.668250 TGTATATCGAATTGGCCGACG 58.332 47.619 0.00 0.00 38.97 5.12
158 159 3.805422 TGTTGTATATCGAATTGGCCGAC 59.195 43.478 0.00 0.00 38.97 4.79
159 160 3.805422 GTGTTGTATATCGAATTGGCCGA 59.195 43.478 0.00 0.00 40.53 5.54
160 161 3.558006 TGTGTTGTATATCGAATTGGCCG 59.442 43.478 0.00 0.00 0.00 6.13
161 162 5.493133 TTGTGTTGTATATCGAATTGGCC 57.507 39.130 0.00 0.00 0.00 5.36
180 181 6.569179 AAGTGTGTTGTAGACTTGTTTTGT 57.431 33.333 0.00 0.00 40.97 2.83
204 211 1.797537 GATTGCTTTGTGCGGCGAC 60.798 57.895 12.98 6.82 46.63 5.19
248 256 1.673920 TCTGCTGCGTGATACGTGATA 59.326 47.619 0.00 0.00 44.73 2.15
288 369 1.696644 CACGCACGATCGAACAGAC 59.303 57.895 24.34 3.08 0.00 3.51
289 370 2.086426 GCACGCACGATCGAACAGA 61.086 57.895 24.34 0.00 0.00 3.41
290 371 2.391821 GCACGCACGATCGAACAG 59.608 61.111 24.34 12.12 0.00 3.16
291 372 3.466260 CGCACGCACGATCGAACA 61.466 61.111 24.34 0.00 34.06 3.18
292 373 4.191485 CCGCACGCACGATCGAAC 62.191 66.667 24.34 12.02 34.06 3.95
309 390 4.467084 TGCTCGATCGGTTGGCCC 62.467 66.667 16.41 0.00 0.00 5.80
310 391 2.892425 CTGCTCGATCGGTTGGCC 60.892 66.667 16.41 0.00 0.00 5.36
311 392 2.892425 CCTGCTCGATCGGTTGGC 60.892 66.667 16.41 14.46 0.00 4.52
312 393 1.519455 GACCTGCTCGATCGGTTGG 60.519 63.158 16.41 14.32 0.00 3.77
313 394 1.874019 CGACCTGCTCGATCGGTTG 60.874 63.158 16.41 4.81 46.14 3.77
314 395 2.044555 TCGACCTGCTCGATCGGTT 61.045 57.895 16.41 0.00 46.75 4.44
315 396 2.437895 TCGACCTGCTCGATCGGT 60.438 61.111 16.41 4.26 46.75 4.69
321 402 0.807667 CAAGGGATTCGACCTGCTCG 60.808 60.000 0.00 0.00 44.44 5.03
322 403 0.250513 ACAAGGGATTCGACCTGCTC 59.749 55.000 0.00 0.00 38.63 4.26
323 404 0.693049 AACAAGGGATTCGACCTGCT 59.307 50.000 0.00 0.00 38.63 4.24
324 405 1.468914 GAAACAAGGGATTCGACCTGC 59.531 52.381 0.00 0.00 38.63 4.85
325 406 2.084546 GGAAACAAGGGATTCGACCTG 58.915 52.381 0.00 0.00 38.63 4.00
326 407 1.985895 AGGAAACAAGGGATTCGACCT 59.014 47.619 0.00 0.00 40.96 3.85
327 408 2.488153 CAAGGAAACAAGGGATTCGACC 59.512 50.000 0.00 0.00 0.00 4.79
328 409 3.146847 ACAAGGAAACAAGGGATTCGAC 58.853 45.455 0.00 0.00 0.00 4.20
329 410 3.181449 TGACAAGGAAACAAGGGATTCGA 60.181 43.478 0.00 0.00 0.00 3.71
330 411 3.146066 TGACAAGGAAACAAGGGATTCG 58.854 45.455 0.00 0.00 0.00 3.34
331 412 5.529581 TTTGACAAGGAAACAAGGGATTC 57.470 39.130 0.00 0.00 0.00 2.52
332 413 5.188751 TGTTTTGACAAGGAAACAAGGGATT 59.811 36.000 2.19 0.00 41.33 3.01
333 414 4.714308 TGTTTTGACAAGGAAACAAGGGAT 59.286 37.500 2.19 0.00 41.33 3.85
334 415 4.090090 TGTTTTGACAAGGAAACAAGGGA 58.910 39.130 2.19 0.00 41.33 4.20
335 416 4.464069 TGTTTTGACAAGGAAACAAGGG 57.536 40.909 2.19 0.00 41.33 3.95
336 417 4.810491 CCATGTTTTGACAAGGAAACAAGG 59.190 41.667 9.78 9.78 45.55 3.61
337 418 5.418676 ACCATGTTTTGACAAGGAAACAAG 58.581 37.500 7.70 4.39 45.55 3.16
338 419 5.047021 TGACCATGTTTTGACAAGGAAACAA 60.047 36.000 7.70 0.00 45.55 2.83
339 420 4.464244 TGACCATGTTTTGACAAGGAAACA 59.536 37.500 7.70 6.42 46.21 2.83
340 421 4.803613 GTGACCATGTTTTGACAAGGAAAC 59.196 41.667 7.70 2.50 36.53 2.78
341 422 4.464244 TGTGACCATGTTTTGACAAGGAAA 59.536 37.500 7.70 0.00 33.18 3.13
342 423 4.019858 TGTGACCATGTTTTGACAAGGAA 58.980 39.130 7.70 0.00 33.18 3.36
343 424 3.625853 TGTGACCATGTTTTGACAAGGA 58.374 40.909 7.70 0.00 33.18 3.36
344 425 4.300803 CATGTGACCATGTTTTGACAAGG 58.699 43.478 0.00 0.00 42.92 3.61
356 437 2.811410 ACAAGATTGGCATGTGACCAT 58.189 42.857 0.00 0.00 36.96 3.55
649 741 0.312416 CGCAGCTAAGCTCCGTCTAT 59.688 55.000 0.00 0.00 34.88 1.98
724 816 2.885644 CTGGTCGACGATTGGCGG 60.886 66.667 8.73 0.00 46.49 6.13
742 838 3.429410 GCCTGATATTTTGGCTGGTGTTC 60.429 47.826 7.15 0.00 43.05 3.18
744 840 2.102578 GCCTGATATTTTGGCTGGTGT 58.897 47.619 7.15 0.00 43.05 4.16
899 1009 1.153188 TGTGGTGTGCAGAGTGTGG 60.153 57.895 0.00 0.00 0.00 4.17
922 1032 2.291209 TGAGGTACGTGTTGGGTAGA 57.709 50.000 0.00 0.00 0.00 2.59
943 1053 2.698763 GGCTGGCTTGAGCTTGAGC 61.699 63.158 12.41 12.41 41.70 4.26
1020 1391 2.892425 GAGTGCCGATCGCTTGGG 60.892 66.667 10.32 0.00 38.78 4.12
1328 1699 2.202987 CCGAGCAGGGTGAGCATC 60.203 66.667 0.00 0.00 35.97 3.91
1557 1928 0.385390 GTTGGCACCTGGAACACTTG 59.615 55.000 0.00 0.00 0.00 3.16
1619 1990 1.847798 CGTCCAGGTCCATTTCCCCA 61.848 60.000 0.00 0.00 0.00 4.96
1868 2269 6.306397 TGATCGACGATTCAAACAAAGAATG 58.694 36.000 12.40 0.00 35.93 2.67
1971 2386 1.798234 AAAACCCGTACGCCAAAGGC 61.798 55.000 10.49 0.00 46.75 4.35
1972 2387 0.669619 AAAAACCCGTACGCCAAAGG 59.330 50.000 10.49 7.90 0.00 3.11
1974 2389 1.101331 ACAAAAACCCGTACGCCAAA 58.899 45.000 10.49 0.00 0.00 3.28
1975 2390 1.959042 TACAAAAACCCGTACGCCAA 58.041 45.000 10.49 0.00 0.00 4.52
1976 2391 1.959042 TTACAAAAACCCGTACGCCA 58.041 45.000 10.49 0.00 0.00 5.69
1978 2393 3.689346 TGTTTTACAAAAACCCGTACGC 58.311 40.909 10.49 0.00 0.00 4.42
1979 2394 6.200808 AGAATGTTTTACAAAAACCCGTACG 58.799 36.000 8.69 8.69 0.00 3.67
1980 2395 7.990541 AAGAATGTTTTACAAAAACCCGTAC 57.009 32.000 11.56 0.00 0.00 3.67
1982 2397 7.324935 AGAAAGAATGTTTTACAAAAACCCGT 58.675 30.769 11.56 0.00 0.00 5.28
1983 2398 7.764695 AGAAAGAATGTTTTACAAAAACCCG 57.235 32.000 11.56 0.00 0.00 5.28
1984 2399 8.609176 GGAAGAAAGAATGTTTTACAAAAACCC 58.391 33.333 11.56 3.24 0.00 4.11
1985 2400 9.378551 AGGAAGAAAGAATGTTTTACAAAAACC 57.621 29.630 11.56 0.00 0.00 3.27
2056 4091 3.299503 ACTTTGGAACCATTCTGCAACT 58.700 40.909 0.00 0.00 0.00 3.16
2057 4092 3.733443 ACTTTGGAACCATTCTGCAAC 57.267 42.857 0.00 0.00 0.00 4.17
2252 4425 2.036958 TACCACATCTTTGGCATCCG 57.963 50.000 0.00 0.00 40.77 4.18
2253 4426 3.290710 ACATACCACATCTTTGGCATCC 58.709 45.455 0.00 0.00 40.77 3.51
2289 4489 9.368416 TCTAGCACTGTAGTATCAAAATATCCT 57.632 33.333 0.00 0.00 0.00 3.24
2346 4546 1.958205 CTCGCAGATCATTCCCGGC 60.958 63.158 0.00 0.00 33.89 6.13
2350 4550 1.270041 GGAGTCCTCGCAGATCATTCC 60.270 57.143 0.41 0.00 33.89 3.01
2371 4571 3.902881 AGCAAATCTCTCTCGGAACAT 57.097 42.857 0.00 0.00 0.00 2.71
2427 4628 2.361610 AGTGCGATTTGGCCTGGG 60.362 61.111 3.32 0.00 0.00 4.45
2433 4634 1.089920 CCCTTCAGAGTGCGATTTGG 58.910 55.000 0.00 0.00 0.00 3.28
2444 4645 4.500265 GCTTTGCCACCCTTCAGA 57.500 55.556 0.00 0.00 0.00 3.27
2462 4663 1.926511 GATTGCAGGGTTGAGCGGTG 61.927 60.000 0.00 0.00 0.00 4.94
2463 4664 1.675641 GATTGCAGGGTTGAGCGGT 60.676 57.895 0.00 0.00 0.00 5.68
2465 4666 2.753966 CGGATTGCAGGGTTGAGCG 61.754 63.158 0.00 0.00 0.00 5.03
2467 4668 0.036010 AGTCGGATTGCAGGGTTGAG 60.036 55.000 0.00 0.00 0.00 3.02
2468 4669 0.036388 GAGTCGGATTGCAGGGTTGA 60.036 55.000 0.00 0.00 0.00 3.18
2469 4670 0.321564 TGAGTCGGATTGCAGGGTTG 60.322 55.000 0.00 0.00 0.00 3.77
2470 4671 0.620556 ATGAGTCGGATTGCAGGGTT 59.379 50.000 0.00 0.00 0.00 4.11
2471 4672 0.107508 CATGAGTCGGATTGCAGGGT 60.108 55.000 0.00 0.00 0.00 4.34
2472 4673 0.816825 CCATGAGTCGGATTGCAGGG 60.817 60.000 0.00 0.00 0.00 4.45
2473 4674 0.816825 CCCATGAGTCGGATTGCAGG 60.817 60.000 0.00 0.00 0.00 4.85
2475 4676 1.451927 GCCCATGAGTCGGATTGCA 60.452 57.895 0.00 0.00 0.00 4.08
2477 4678 1.889105 CCGCCCATGAGTCGGATTG 60.889 63.158 12.79 0.00 45.53 2.67
2478 4679 2.311688 GACCGCCCATGAGTCGGATT 62.312 60.000 21.28 5.51 45.53 3.01
2479 4680 2.764128 ACCGCCCATGAGTCGGAT 60.764 61.111 21.28 7.84 45.53 4.18
2480 4681 3.458163 GACCGCCCATGAGTCGGA 61.458 66.667 21.28 0.00 45.53 4.55
2483 4684 0.318784 GATACGACCGCCCATGAGTC 60.319 60.000 0.00 0.00 0.00 3.36
2487 6056 0.950555 CATGGATACGACCGCCCATG 60.951 60.000 17.70 17.70 46.64 3.66
2489 6058 2.802724 CCATGGATACGACCGCCCA 61.803 63.158 5.56 0.00 42.51 5.36
2494 6063 0.249322 CGGTGACCATGGATACGACC 60.249 60.000 21.47 14.39 42.51 4.79
2499 6068 2.167693 GTGAAGACGGTGACCATGGATA 59.832 50.000 21.47 3.31 0.00 2.59
2501 6070 0.320374 GTGAAGACGGTGACCATGGA 59.680 55.000 21.47 0.00 0.00 3.41
2512 6109 2.762535 ACTTACCATGGGTGAAGACG 57.237 50.000 22.95 5.35 36.19 4.18
2548 6145 9.650714 ACAGTATACACTACCCATGACTAATAA 57.349 33.333 5.50 0.00 32.21 1.40
2558 6155 5.955944 TGCCTATACAGTATACACTACCCA 58.044 41.667 5.50 0.00 32.21 4.51
2571 6168 3.580458 AGCAGGACCTTATGCCTATACAG 59.420 47.826 0.00 0.00 43.60 2.74
2572 6169 3.578716 GAGCAGGACCTTATGCCTATACA 59.421 47.826 0.00 0.00 43.60 2.29
2573 6170 3.367498 CGAGCAGGACCTTATGCCTATAC 60.367 52.174 0.00 0.00 43.60 1.47
2574 6171 2.826128 CGAGCAGGACCTTATGCCTATA 59.174 50.000 0.00 0.00 43.60 1.31
2575 6172 1.620819 CGAGCAGGACCTTATGCCTAT 59.379 52.381 0.00 0.00 43.60 2.57
2576 6173 1.040646 CGAGCAGGACCTTATGCCTA 58.959 55.000 0.00 0.00 43.60 3.93
2577 6174 0.978146 ACGAGCAGGACCTTATGCCT 60.978 55.000 0.00 0.00 43.60 4.75
2578 6175 0.811616 CACGAGCAGGACCTTATGCC 60.812 60.000 0.00 0.00 43.60 4.40
2597 6194 2.973694 TGTAGTTAATCTGGCGACCC 57.026 50.000 0.00 0.00 0.00 4.46
2599 6196 5.041940 CCTACTTGTAGTTAATCTGGCGAC 58.958 45.833 6.99 0.00 0.00 5.19
2650 6247 6.374417 ACTGGACTGTATTGGTTCACTAAT 57.626 37.500 0.00 0.00 0.00 1.73
2652 6249 5.776208 TGTACTGGACTGTATTGGTTCACTA 59.224 40.000 0.00 0.00 0.00 2.74
2698 6295 2.208326 AAAAGTTTTGTGCTGAGCCG 57.792 45.000 0.23 0.00 0.00 5.52
2716 6313 8.533569 AACTCTCCAGTTCTTTTATGGAAAAA 57.466 30.769 0.00 0.00 42.40 1.94
2717 6314 8.533569 AAACTCTCCAGTTCTTTTATGGAAAA 57.466 30.769 0.00 0.00 42.45 2.29
2723 6320 7.929785 TCGTACAAAACTCTCCAGTTCTTTTAT 59.070 33.333 0.00 0.00 42.45 1.40
2731 6328 3.305471 GCTCTCGTACAAAACTCTCCAGT 60.305 47.826 0.00 0.00 0.00 4.00
2733 6330 2.891580 AGCTCTCGTACAAAACTCTCCA 59.108 45.455 0.00 0.00 0.00 3.86
2734 6331 3.503891 GAGCTCTCGTACAAAACTCTCC 58.496 50.000 6.43 0.00 0.00 3.71
2743 6340 0.803117 CGAACAGGAGCTCTCGTACA 59.197 55.000 14.64 0.00 0.00 2.90
2756 6353 1.071605 GTGCTTAGAGTGCCGAACAG 58.928 55.000 0.00 0.00 0.00 3.16
2757 6354 0.320421 GGTGCTTAGAGTGCCGAACA 60.320 55.000 0.00 0.00 0.00 3.18
2758 6355 0.037232 AGGTGCTTAGAGTGCCGAAC 60.037 55.000 0.00 0.00 0.00 3.95
2759 6356 0.246635 GAGGTGCTTAGAGTGCCGAA 59.753 55.000 0.00 0.00 0.00 4.30
2760 6357 0.898326 TGAGGTGCTTAGAGTGCCGA 60.898 55.000 0.00 0.00 0.00 5.54
2761 6358 0.176680 ATGAGGTGCTTAGAGTGCCG 59.823 55.000 0.00 0.00 0.00 5.69
2762 6359 2.804933 GCTATGAGGTGCTTAGAGTGCC 60.805 54.545 0.00 0.00 0.00 5.01
2763 6360 2.478831 GCTATGAGGTGCTTAGAGTGC 58.521 52.381 0.00 0.00 0.00 4.40
2764 6361 2.544694 CCGCTATGAGGTGCTTAGAGTG 60.545 54.545 0.00 0.00 0.00 3.51
2765 6362 1.683917 CCGCTATGAGGTGCTTAGAGT 59.316 52.381 0.00 0.00 0.00 3.24
2766 6363 1.000283 CCCGCTATGAGGTGCTTAGAG 60.000 57.143 0.00 0.00 0.00 2.43
2767 6364 1.040646 CCCGCTATGAGGTGCTTAGA 58.959 55.000 0.00 0.00 0.00 2.10
2768 6365 0.753262 ACCCGCTATGAGGTGCTTAG 59.247 55.000 0.00 0.00 34.20 2.18
2769 6366 0.464036 CACCCGCTATGAGGTGCTTA 59.536 55.000 0.00 0.00 46.55 3.09
2770 6367 1.221840 CACCCGCTATGAGGTGCTT 59.778 57.895 0.00 0.00 46.55 3.91
2771 6368 2.903357 CACCCGCTATGAGGTGCT 59.097 61.111 0.00 0.00 46.55 4.40
2786 6383 4.410743 GGCTTTGAGCGCCAGCAC 62.411 66.667 17.24 6.17 46.77 4.40
2793 6390 4.394712 ACCCCTCGGCTTTGAGCG 62.395 66.667 0.00 0.00 43.62 5.03
2794 6391 2.436824 GACCCCTCGGCTTTGAGC 60.437 66.667 0.00 0.00 41.46 4.26
2795 6392 0.745845 CATGACCCCTCGGCTTTGAG 60.746 60.000 0.00 0.00 35.70 3.02
2796 6393 1.299648 CATGACCCCTCGGCTTTGA 59.700 57.895 0.00 0.00 0.00 2.69
2797 6394 1.750399 CCATGACCCCTCGGCTTTG 60.750 63.158 0.00 0.00 0.00 2.77
2798 6395 2.677228 CCATGACCCCTCGGCTTT 59.323 61.111 0.00 0.00 0.00 3.51
2799 6396 3.411517 CCCATGACCCCTCGGCTT 61.412 66.667 0.00 0.00 0.00 4.35
2808 6405 4.864334 CTGAGCCGGCCCATGACC 62.864 72.222 26.15 4.28 0.00 4.02
2809 6406 4.101448 ACTGAGCCGGCCCATGAC 62.101 66.667 26.15 8.57 0.00 3.06
2810 6407 4.100084 CACTGAGCCGGCCCATGA 62.100 66.667 26.15 0.00 0.00 3.07
2811 6408 3.626996 TTCACTGAGCCGGCCCATG 62.627 63.158 26.15 17.46 0.00 3.66
2812 6409 3.329889 TTCACTGAGCCGGCCCAT 61.330 61.111 26.15 3.93 0.00 4.00
2813 6410 4.329545 GTTCACTGAGCCGGCCCA 62.330 66.667 26.15 18.76 0.00 5.36
2815 6412 4.681978 ACGTTCACTGAGCCGGCC 62.682 66.667 26.15 15.80 0.00 6.13
2816 6413 3.414700 CACGTTCACTGAGCCGGC 61.415 66.667 21.89 21.89 0.00 6.13
2817 6414 1.734477 CTCACGTTCACTGAGCCGG 60.734 63.158 0.00 0.00 0.00 6.13
2818 6415 1.734477 CCTCACGTTCACTGAGCCG 60.734 63.158 0.00 0.14 34.84 5.52
2819 6416 4.268687 CCTCACGTTCACTGAGCC 57.731 61.111 0.00 0.00 34.84 4.70


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

AutoCloner maintained by Alex Coulton.