Multiple sequence alignment - TraesCS2D01G012900

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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 TraesCS2D01G012900 chr2D 100.000 8453 0 0 1 8453 6432437 6423985 0.000000e+00 15610.0
1 TraesCS2D01G012900 chr2D 88.105 950 83 20 6730 7652 6280720 6279774 0.000000e+00 1101.0
2 TraesCS2D01G012900 chr2D 82.700 1052 107 27 5701 6729 6281752 6280753 0.000000e+00 865.0
3 TraesCS2D01G012900 chr2D 88.169 710 64 8 4181 4880 6283156 6282457 0.000000e+00 828.0
4 TraesCS2D01G012900 chr2D 85.123 652 47 26 4962 5580 6282460 6281826 9.320000e-174 621.0
5 TraesCS2D01G012900 chr2D 88.667 450 51 0 5900 6349 5917351 5917800 4.460000e-152 549.0
6 TraesCS2D01G012900 chr2D 87.459 303 25 7 2112 2405 6283856 6283558 3.780000e-88 337.0
7 TraesCS2D01G012900 chr2D 94.737 57 1 1 7741 7795 6279731 6279675 4.200000e-13 87.9
8 TraesCS2D01G012900 chr2A 97.323 3026 66 6 3708 6729 4790865 4787851 0.000000e+00 5125.0
9 TraesCS2D01G012900 chr2A 92.208 3478 149 53 291 3708 4794311 4790896 0.000000e+00 4809.0
10 TraesCS2D01G012900 chr2A 95.455 1166 36 6 6730 7882 4787818 4786657 0.000000e+00 1844.0
11 TraesCS2D01G012900 chr2A 89.437 1155 75 15 5308 6442 4745682 4744555 0.000000e+00 1413.0
12 TraesCS2D01G012900 chr2A 87.336 837 71 20 7018 7836 4840828 4841647 0.000000e+00 926.0
13 TraesCS2D01G012900 chr2A 81.105 1249 143 45 3204 4386 4406015 4407236 0.000000e+00 913.0
14 TraesCS2D01G012900 chr2A 92.962 611 38 2 5609 6218 4839483 4840089 0.000000e+00 885.0
15 TraesCS2D01G012900 chr2A 90.385 676 42 10 4914 5580 4838754 4839415 0.000000e+00 867.0
16 TraesCS2D01G012900 chr2A 87.654 729 68 12 7148 7864 4744015 4743297 0.000000e+00 828.0
17 TraesCS2D01G012900 chr2A 91.456 515 44 0 4388 4902 4837975 4838489 0.000000e+00 708.0
18 TraesCS2D01G012900 chr2A 85.397 315 30 6 2103 2405 4760592 4760282 6.370000e-81 313.0
19 TraesCS2D01G012900 chr2A 84.177 316 41 4 7148 7457 4408439 4408751 1.780000e-76 298.0
20 TraesCS2D01G012900 chr2A 85.417 288 12 15 4 291 4795018 4794761 1.080000e-68 272.0
21 TraesCS2D01G012900 chr2A 93.631 157 8 1 6856 7012 4840594 4840748 5.100000e-57 233.0
22 TraesCS2D01G012900 chr2A 75.417 659 67 42 2458 3054 4405159 4405784 1.830000e-56 231.0
23 TraesCS2D01G012900 chr2A 86.869 198 21 2 6535 6729 4744524 4744329 5.140000e-52 217.0
24 TraesCS2D01G012900 chr2A 89.172 157 17 0 6844 7000 4744214 4744058 6.690000e-46 196.0
25 TraesCS2D01G012900 chr2A 95.122 82 3 1 6735 6816 4744292 4744212 2.480000e-25 128.0
26 TraesCS2D01G012900 chr2A 92.500 40 3 0 7735 7774 4786659 4786620 3.300000e-04 58.4
27 TraesCS2D01G012900 chr2B 96.908 2652 66 9 4092 6729 4987035 4989684 0.000000e+00 4429.0
28 TraesCS2D01G012900 chr2B 91.995 2611 119 30 330 2892 4983692 4986260 0.000000e+00 3581.0
29 TraesCS2D01G012900 chr2B 92.506 1788 91 23 4962 6729 69346856 69345092 0.000000e+00 2519.0
30 TraesCS2D01G012900 chr2B 93.907 1477 46 14 6730 8169 4989715 4991184 0.000000e+00 2189.0
31 TraesCS2D01G012900 chr2B 88.815 1663 118 40 6730 8359 69345061 69343434 0.000000e+00 1978.0
32 TraesCS2D01G012900 chr2B 88.026 760 71 18 3793 4537 69347760 69347006 0.000000e+00 881.0
33 TraesCS2D01G012900 chr2B 86.878 724 84 7 3792 4505 5367976 5368698 0.000000e+00 800.0
34 TraesCS2D01G012900 chr2B 98.082 417 6 1 3296 3710 4986266 4986682 0.000000e+00 725.0
35 TraesCS2D01G012900 chr2B 98.165 327 6 0 3708 4034 4986711 4987037 9.520000e-159 571.0
36 TraesCS2D01G012900 chr2B 85.920 348 42 2 4531 4878 5368698 5369038 1.730000e-96 364.0
37 TraesCS2D01G012900 chr2B 88.026 309 27 5 2103 2405 69349062 69348758 2.900000e-94 357.0
38 TraesCS2D01G012900 chr2B 87.248 298 34 3 5908 6202 5442582 5442878 3.780000e-88 337.0
39 TraesCS2D01G012900 chr2B 87.847 288 20 5 8 291 4983341 4983617 2.940000e-84 324.0
40 TraesCS2D01G012900 chr2B 85.619 299 33 6 6114 6403 5369608 5369905 1.070000e-78 305.0
41 TraesCS2D01G012900 chr2B 95.302 149 6 1 3762 3909 5369466 5369614 1.420000e-57 235.0
42 TraesCS2D01G012900 chr2B 91.720 157 13 0 4724 4880 69347009 69346853 1.430000e-52 219.0
43 TraesCS2D01G012900 chr4A 94.145 1059 48 7 5677 6729 693410890 693409840 0.000000e+00 1600.0
44 TraesCS2D01G012900 chr4A 93.100 1058 48 13 6824 7859 693399357 693398303 0.000000e+00 1526.0
45 TraesCS2D01G012900 chr4A 95.876 97 3 1 6730 6826 693409809 693409714 1.140000e-33 156.0
46 TraesCS2D01G012900 chr4B 85.161 465 50 12 5076 5531 580320506 580320052 7.730000e-125 459.0
47 TraesCS2D01G012900 chr4B 83.728 338 49 2 4282 4613 580321149 580320812 1.770000e-81 315.0
48 TraesCS2D01G012900 chr4B 84.590 305 32 8 2106 2405 580322252 580321958 1.070000e-73 289.0
49 TraesCS2D01G012900 chr7A 91.111 90 8 0 6742 6831 288985353 288985442 1.150000e-23 122.0
50 TraesCS2D01G012900 chr7A 90.000 90 9 0 6742 6831 15769567 15769478 5.360000e-22 117.0
51 TraesCS2D01G012900 chr5A 91.111 90 8 0 6742 6831 76188630 76188541 1.150000e-23 122.0


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 TraesCS2D01G012900 chr2D 6423985 6432437 8452 True 15610.000000 15610 100.00000 1 8453 1 chr2D.!!$R1 8452
1 TraesCS2D01G012900 chr2D 6279675 6283856 4181 True 639.983333 1101 87.71550 2112 7795 6 chr2D.!!$R2 5683
2 TraesCS2D01G012900 chr2A 4786620 4795018 8398 True 2421.680000 5125 92.58060 4 7882 5 chr2A.!!$R3 7878
3 TraesCS2D01G012900 chr2A 4837975 4841647 3672 False 723.800000 926 91.15400 4388 7836 5 chr2A.!!$F2 3448
4 TraesCS2D01G012900 chr2A 4743297 4745682 2385 True 556.400000 1413 89.65080 5308 7864 5 chr2A.!!$R2 2556
5 TraesCS2D01G012900 chr2A 4405159 4408751 3592 False 480.666667 913 80.23300 2458 7457 3 chr2A.!!$F1 4999
6 TraesCS2D01G012900 chr2B 4983341 4991184 7843 False 1969.833333 4429 94.48400 8 8169 6 chr2B.!!$F2 8161
7 TraesCS2D01G012900 chr2B 69343434 69349062 5628 True 1190.800000 2519 89.81860 2103 8359 5 chr2B.!!$R1 6256
8 TraesCS2D01G012900 chr2B 5367976 5369905 1929 False 426.000000 800 88.42975 3762 6403 4 chr2B.!!$F3 2641
9 TraesCS2D01G012900 chr4A 693398303 693399357 1054 True 1526.000000 1526 93.10000 6824 7859 1 chr4A.!!$R1 1035
10 TraesCS2D01G012900 chr4A 693409714 693410890 1176 True 878.000000 1600 95.01050 5677 6826 2 chr4A.!!$R2 1149
11 TraesCS2D01G012900 chr4B 580320052 580322252 2200 True 354.333333 459 84.49300 2106 5531 3 chr4B.!!$R1 3425

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
810 1339 0.451383 CAAATTCCAATCTCGCCGCA 59.549 50.000 0.00 0.0 0.00 5.69 F
1431 1962 0.326264 CCACAACTCCTCCTTCCCAG 59.674 60.000 0.00 0.0 0.00 4.45 F
1729 2293 0.250814 TAACCCACAATTTCCGCCGT 60.251 50.000 0.00 0.0 0.00 5.68 F
3199 4012 0.249573 ATGCTTGGTGCTTTGTGTGC 60.250 50.000 0.00 0.0 43.37 4.57 F
3201 4014 1.815196 CTTGGTGCTTTGTGTGCCA 59.185 52.632 0.00 0.0 0.00 4.92 F
5335 6646 3.061831 CAGCTGTTGACTCTGATAAAGCG 59.938 47.826 5.25 0.0 34.65 4.68 F
6191 7667 3.694043 TGTGCTGCTGGTTTCAGTATA 57.306 42.857 0.00 0.0 42.78 1.47 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 2200 0.535335 GGCCTCACATAAGTCGGTGA 59.465 55.000 0.0 0.0 41.44 4.02 R
2902 3652 1.068541 TGGTCAACGACTGATGTCTCG 60.069 52.381 0.0 0.0 40.86 4.04 R
3652 4507 2.303311 AGTTCTTTCTACCTCAGGCACC 59.697 50.000 0.0 0.0 0.00 5.01 R
4670 5608 3.235200 CCCCAATTTGACCCTACAACAA 58.765 45.455 0.0 0.0 0.00 2.83 R
5574 6976 5.163141 TGGATCTCTCCCAGTTCTACTCTAG 60.163 48.000 0.0 0.0 41.29 2.43 R
7011 8639 2.027100 GGACGGAAAGAGGAATGGAGTT 60.027 50.000 0.0 0.0 0.00 3.01 R
8229 9953 0.465287 TCTTGATGCTATGCGGCTGA 59.535 50.000 0.0 0.0 0.00 4.26 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
131 134 1.072489 TGGGTGTGGTTAAATCGCTCA 59.928 47.619 0.00 0.00 0.00 4.26
173 207 8.877864 ATTTTCTTAGGGATGTACATTCAACA 57.122 30.769 16.12 0.00 0.00 3.33
174 208 8.877864 TTTTCTTAGGGATGTACATTCAACAT 57.122 30.769 16.12 5.10 40.23 2.71
175 209 8.877864 TTTCTTAGGGATGTACATTCAACATT 57.122 30.769 16.12 0.00 37.69 2.71
176 210 7.864108 TCTTAGGGATGTACATTCAACATTG 57.136 36.000 16.12 1.43 37.69 2.82
177 211 7.629157 TCTTAGGGATGTACATTCAACATTGA 58.371 34.615 16.12 3.62 37.69 2.57
178 212 8.274322 TCTTAGGGATGTACATTCAACATTGAT 58.726 33.333 16.12 0.00 37.69 2.57
179 213 8.821686 TTAGGGATGTACATTCAACATTGATT 57.178 30.769 16.12 0.00 37.69 2.57
180 214 7.722949 AGGGATGTACATTCAACATTGATTT 57.277 32.000 16.12 0.00 37.69 2.17
181 215 7.775120 AGGGATGTACATTCAACATTGATTTC 58.225 34.615 16.12 0.00 37.69 2.17
182 216 7.616935 AGGGATGTACATTCAACATTGATTTCT 59.383 33.333 16.12 0.00 37.69 2.52
183 217 8.902806 GGGATGTACATTCAACATTGATTTCTA 58.097 33.333 16.12 0.00 37.69 2.10
249 283 8.635765 AATTCTCCAAAAAGTCTGCTTATACA 57.364 30.769 0.00 0.00 33.95 2.29
280 314 9.969001 AGTAAGCTATATAAACCAACCAAAGAA 57.031 29.630 0.00 0.00 0.00 2.52
282 316 8.879427 AAGCTATATAAACCAACCAAAGAAGT 57.121 30.769 0.00 0.00 0.00 3.01
284 318 7.556635 AGCTATATAAACCAACCAAAGAAGTCC 59.443 37.037 0.00 0.00 0.00 3.85
287 321 8.721133 ATATAAACCAACCAAAGAAGTCCTTT 57.279 30.769 0.00 0.00 45.48 3.11
288 322 9.816787 ATATAAACCAACCAAAGAAGTCCTTTA 57.183 29.630 0.00 0.00 42.88 1.85
289 323 6.465439 AAACCAACCAAAGAAGTCCTTTAG 57.535 37.500 0.00 0.00 42.88 1.85
293 776 6.839134 ACCAACCAAAGAAGTCCTTTAGAAAT 59.161 34.615 0.00 0.00 42.88 2.17
298 781 5.984695 AAGAAGTCCTTTAGAAATTGCCC 57.015 39.130 0.00 0.00 0.00 5.36
300 783 2.723273 AGTCCTTTAGAAATTGCCCCG 58.277 47.619 0.00 0.00 0.00 5.73
305 788 4.014406 CCTTTAGAAATTGCCCCGTACTT 58.986 43.478 0.00 0.00 0.00 2.24
308 791 1.633945 AGAAATTGCCCCGTACTTCCT 59.366 47.619 0.00 0.00 0.00 3.36
310 793 1.286248 AATTGCCCCGTACTTCCTCT 58.714 50.000 0.00 0.00 0.00 3.69
315 798 1.104630 CCCCGTACTTCCTCTGTCTC 58.895 60.000 0.00 0.00 0.00 3.36
339 822 4.350620 AGTGTCGCAAGCACTCTG 57.649 55.556 0.00 0.00 46.58 3.35
340 823 1.958205 AGTGTCGCAAGCACTCTGC 60.958 57.895 0.00 0.00 46.58 4.26
455 938 2.359531 ACGATCATCGACTTCCCTCTTC 59.640 50.000 15.60 0.00 43.74 2.87
553 1052 0.652592 CTCCATTGAACATCGCGGAC 59.347 55.000 6.13 0.00 0.00 4.79
650 1153 2.296471 AGACGAATTCGGTTGACAGTCT 59.704 45.455 29.79 17.94 44.95 3.24
651 1154 2.662156 GACGAATTCGGTTGACAGTCTC 59.338 50.000 29.79 11.70 44.95 3.36
688 1200 4.828925 GCGGAGAGGCAGACAGGC 62.829 72.222 0.00 0.00 44.61 4.85
810 1339 0.451383 CAAATTCCAATCTCGCCGCA 59.549 50.000 0.00 0.00 0.00 5.69
882 1412 3.089874 CTGAATCCGGCCCCTCCA 61.090 66.667 0.00 0.00 34.01 3.86
1399 1930 2.674220 GCACCTCCTCCTTCCCAGG 61.674 68.421 0.00 0.00 42.50 4.45
1400 1931 1.997874 CACCTCCTCCTTCCCAGGG 60.998 68.421 0.00 0.00 41.25 4.45
1401 1932 2.184631 ACCTCCTCCTTCCCAGGGA 61.185 63.158 3.01 3.01 41.25 4.20
1402 1933 1.690985 CCTCCTCCTTCCCAGGGAC 60.691 68.421 8.12 0.00 41.25 4.46
1403 1934 1.690985 CTCCTCCTTCCCAGGGACC 60.691 68.421 8.12 0.00 41.25 4.46
1404 1935 2.692741 CCTCCTTCCCAGGGACCC 60.693 72.222 8.12 0.59 41.25 4.46
1405 1936 2.456840 CTCCTTCCCAGGGACCCT 59.543 66.667 8.12 7.44 41.25 4.34
1406 1937 1.229984 CTCCTTCCCAGGGACCCTT 60.230 63.158 11.56 0.00 41.25 3.95
1407 1938 1.229853 TCCTTCCCAGGGACCCTTC 60.230 63.158 11.56 0.00 41.25 3.46
1408 1939 2.670148 CCTTCCCAGGGACCCTTCG 61.670 68.421 11.56 3.46 36.36 3.79
1409 1940 2.609610 TTCCCAGGGACCCTTCGG 60.610 66.667 11.56 13.82 0.00 4.30
1420 1951 3.423154 CCTTCGGCGCCACAACTC 61.423 66.667 28.98 0.00 0.00 3.01
1421 1952 3.423154 CTTCGGCGCCACAACTCC 61.423 66.667 28.98 0.00 0.00 3.85
1422 1953 3.883744 CTTCGGCGCCACAACTCCT 62.884 63.158 28.98 0.00 0.00 3.69
1423 1954 3.876589 TTCGGCGCCACAACTCCTC 62.877 63.158 28.98 0.00 0.00 3.71
1425 1956 4.021925 GGCGCCACAACTCCTCCT 62.022 66.667 24.80 0.00 0.00 3.69
1426 1957 2.032681 GCGCCACAACTCCTCCTT 59.967 61.111 0.00 0.00 0.00 3.36
1427 1958 2.035442 GCGCCACAACTCCTCCTTC 61.035 63.158 0.00 0.00 0.00 3.46
1428 1959 1.376037 CGCCACAACTCCTCCTTCC 60.376 63.158 0.00 0.00 0.00 3.46
1429 1960 1.002011 GCCACAACTCCTCCTTCCC 60.002 63.158 0.00 0.00 0.00 3.97
1430 1961 1.779061 GCCACAACTCCTCCTTCCCA 61.779 60.000 0.00 0.00 0.00 4.37
1431 1962 0.326264 CCACAACTCCTCCTTCCCAG 59.674 60.000 0.00 0.00 0.00 4.45
1440 1971 1.307866 TCCTTCCCAGGGACCCATC 60.308 63.158 14.60 0.00 41.25 3.51
1465 1996 3.330720 CACCTCCACCCCAGGGAC 61.331 72.222 7.25 0.00 38.96 4.46
1466 1997 4.677151 ACCTCCACCCCAGGGACC 62.677 72.222 7.25 0.00 38.96 4.46
1468 1999 4.354943 CTCCACCCCAGGGACCCT 62.355 72.222 7.44 7.44 38.96 4.34
1469 2000 3.882670 TCCACCCCAGGGACCCTT 61.883 66.667 11.56 0.00 38.96 3.95
1470 2001 3.339093 CCACCCCAGGGACCCTTC 61.339 72.222 11.56 0.00 38.96 3.46
1471 2002 2.531685 CACCCCAGGGACCCTTCA 60.532 66.667 11.56 0.00 38.96 3.02
1472 2003 2.204151 ACCCCAGGGACCCTTCAG 60.204 66.667 11.56 4.47 38.96 3.02
1473 2004 3.732849 CCCCAGGGACCCTTCAGC 61.733 72.222 11.56 0.00 37.50 4.26
1474 2005 4.101448 CCCAGGGACCCTTCAGCG 62.101 72.222 11.56 0.00 0.00 5.18
1475 2006 4.785453 CCAGGGACCCTTCAGCGC 62.785 72.222 11.56 0.00 0.00 5.92
1476 2007 4.785453 CAGGGACCCTTCAGCGCC 62.785 72.222 11.56 0.00 0.00 6.53
1479 2010 4.021925 GGACCCTTCAGCGCCACT 62.022 66.667 2.29 0.00 0.00 4.00
1480 2011 2.435059 GACCCTTCAGCGCCACTC 60.435 66.667 2.29 0.00 0.00 3.51
1481 2012 3.959991 GACCCTTCAGCGCCACTCC 62.960 68.421 2.29 0.00 0.00 3.85
1482 2013 4.020617 CCCTTCAGCGCCACTCCA 62.021 66.667 2.29 0.00 0.00 3.86
1483 2014 2.032528 CCTTCAGCGCCACTCCAA 59.967 61.111 2.29 0.00 0.00 3.53
1484 2015 2.328099 CCTTCAGCGCCACTCCAAC 61.328 63.158 2.29 0.00 0.00 3.77
1485 2016 2.281484 TTCAGCGCCACTCCAACC 60.281 61.111 2.29 0.00 0.00 3.77
1486 2017 3.842925 TTCAGCGCCACTCCAACCC 62.843 63.158 2.29 0.00 0.00 4.11
1487 2018 4.641645 CAGCGCCACTCCAACCCA 62.642 66.667 2.29 0.00 0.00 4.51
1488 2019 4.335647 AGCGCCACTCCAACCCAG 62.336 66.667 2.29 0.00 0.00 4.45
1490 2021 4.722700 CGCCACTCCAACCCAGGG 62.723 72.222 2.85 2.85 0.00 4.45
1527 2061 2.863988 CCACCCCAGGGACCCTTT 60.864 66.667 11.56 0.00 38.96 3.11
1540 2104 2.906897 CCTTTGGTGCTGTGCCGT 60.907 61.111 0.00 0.00 0.00 5.68
1601 2165 4.742649 TCCGCCGTCAGCTCTCCT 62.743 66.667 0.00 0.00 40.39 3.69
1636 2200 1.004745 CCACAGGGAACACTATGCCTT 59.995 52.381 0.00 0.00 39.41 4.35
1729 2293 0.250814 TAACCCACAATTTCCGCCGT 60.251 50.000 0.00 0.00 0.00 5.68
1730 2294 1.520600 AACCCACAATTTCCGCCGTC 61.521 55.000 0.00 0.00 0.00 4.79
1774 2338 1.973281 CAGAACATGCCACCGCCTT 60.973 57.895 0.00 0.00 0.00 4.35
1797 2361 1.386057 GGGGCCACCTTCCTCCTAT 60.386 63.158 4.39 0.00 36.80 2.57
1850 2414 2.512515 GATGGGCACGCTCCAGAC 60.513 66.667 5.64 0.41 37.75 3.51
2016 2580 1.139095 GAGGTACTTCCGGCTGACG 59.861 63.158 0.00 0.00 41.55 4.35
2128 2692 7.562135 TGATGGGGTAATGAACTCTACTTTAC 58.438 38.462 0.00 0.00 0.00 2.01
2686 3415 6.916360 TCCTGATTAGCTTTGAAAATGGTT 57.084 33.333 0.00 0.00 33.55 3.67
2929 3679 1.148310 CAGTCGTTGACCATCACACC 58.852 55.000 0.00 0.00 32.18 4.16
2937 3687 2.150390 TGACCATCACACCAAATGTCG 58.850 47.619 0.00 0.00 40.64 4.35
3004 3756 0.677288 TGTGATTATACCGAGGCCCG 59.323 55.000 0.00 2.20 38.18 6.13
3081 3871 4.748102 TCTTAGTTCAAGCTTAACCACGTG 59.252 41.667 9.08 9.08 33.94 4.49
3194 4007 4.025480 GTCAAAGAAATGCTTGGTGCTTTG 60.025 41.667 0.00 0.00 41.94 2.77
3199 4012 0.249573 ATGCTTGGTGCTTTGTGTGC 60.250 50.000 0.00 0.00 43.37 4.57
3201 4014 1.815196 CTTGGTGCTTTGTGTGCCA 59.185 52.632 0.00 0.00 0.00 4.92
3266 4115 8.760980 ACTTACACTCTTAGATAGAATGAGCT 57.239 34.615 0.00 0.00 33.82 4.09
3406 4258 9.953565 TTAGAAGCTATGTTACTTATTTGGTGT 57.046 29.630 0.00 0.00 0.00 4.16
3758 4653 5.083821 AGCACCCTTTTCCTTGCTAAAATA 58.916 37.500 0.00 0.00 43.51 1.40
3760 4655 5.812127 GCACCCTTTTCCTTGCTAAAATATG 59.188 40.000 0.00 0.00 32.00 1.78
4057 4957 5.773176 TCATTGACGATGTAGATTAGGGCTA 59.227 40.000 2.54 0.00 37.06 3.93
4585 5500 5.183904 GCATTCATGGTTATGGTAAGATCCC 59.816 44.000 0.00 0.00 34.97 3.85
4920 5858 8.494433 TGATATAGCTTCCTTAGGTGACAATTT 58.506 33.333 0.00 0.00 35.80 1.82
4931 5869 4.023291 AGGTGACAATTTGTTGACAACCT 58.977 39.130 15.59 9.08 35.47 3.50
5335 6646 3.061831 CAGCTGTTGACTCTGATAAAGCG 59.938 47.826 5.25 0.00 34.65 4.68
5574 6976 5.440610 AGATCCATGAATAGGGTTTGTCAC 58.559 41.667 0.00 0.00 0.00 3.67
5868 7310 6.183360 GCTAGAATCGGTTAGTACTAGATCGG 60.183 46.154 16.14 10.28 32.00 4.18
5875 7317 5.303971 GGTTAGTACTAGATCGGTGCTCTA 58.696 45.833 13.43 7.16 32.38 2.43
6191 7667 3.694043 TGTGCTGCTGGTTTCAGTATA 57.306 42.857 0.00 0.00 42.78 1.47
6585 8099 7.582667 AAAATGGGCAGAACCAGTATATAAC 57.417 36.000 0.00 0.00 45.20 1.89
6614 8129 5.740290 AACTGGCTAGTCTGCTTAGTTAA 57.260 39.130 2.06 0.00 37.97 2.01
7015 8643 2.094130 CCTGACCTCGGGACTTAAACTC 60.094 54.545 0.00 0.00 45.36 3.01
7035 8663 2.642807 TCCATTCCTCTTTCCGTCCTTT 59.357 45.455 0.00 0.00 0.00 3.11
7281 8942 3.244700 ACTTCATGGCAGTACAAAGAGCT 60.245 43.478 0.00 0.00 0.00 4.09
7471 9137 3.309682 GTGATGATGTACGGTGGATGTTG 59.690 47.826 0.00 0.00 0.00 3.33
7588 9267 2.233676 CCGTGCTCTACCATATGCCATA 59.766 50.000 0.00 0.00 0.00 2.74
7682 9363 7.691050 GTGATTATTTTTCGTACCGAGAAAAGG 59.309 37.037 6.46 0.00 44.91 3.11
7683 9364 7.603404 TGATTATTTTTCGTACCGAGAAAAGGA 59.397 33.333 6.46 0.00 44.91 3.36
7686 9367 6.710692 TTTTTCGTACCGAGAAAAGGATAC 57.289 37.500 7.07 0.00 44.91 2.24
8005 9727 0.999406 CTGTATTTGTGCCGAGACCG 59.001 55.000 0.00 0.00 0.00 4.79
8193 9916 5.720371 ATTATTACAAAACTGGCAGTGCA 57.280 34.783 22.83 1.78 0.00 4.57
8196 9919 2.228138 ACAAAACTGGCAGTGCAATG 57.772 45.000 22.83 18.57 0.00 2.82
8199 9922 3.573538 ACAAAACTGGCAGTGCAATGATA 59.426 39.130 22.83 4.40 0.00 2.15
8200 9923 4.039004 ACAAAACTGGCAGTGCAATGATAA 59.961 37.500 22.83 0.77 0.00 1.75
8201 9924 5.172934 CAAAACTGGCAGTGCAATGATAAT 58.827 37.500 22.83 0.00 0.00 1.28
8202 9925 4.644103 AACTGGCAGTGCAATGATAATC 57.356 40.909 22.83 0.00 0.00 1.75
8204 9927 3.881688 ACTGGCAGTGCAATGATAATCTC 59.118 43.478 21.37 0.00 0.00 2.75
8205 9928 3.881089 CTGGCAGTGCAATGATAATCTCA 59.119 43.478 20.00 0.00 38.53 3.27
8211 9934 7.076362 GCAGTGCAATGATAATCTCATAACAG 58.924 38.462 20.00 0.00 44.03 3.16
8234 9960 4.153835 GCATGAGCTCATAAATAGTCAGCC 59.846 45.833 28.27 6.30 37.91 4.85
8243 9969 2.847327 AATAGTCAGCCGCATAGCAT 57.153 45.000 0.00 0.00 34.23 3.79
8244 9970 2.376808 ATAGTCAGCCGCATAGCATC 57.623 50.000 0.00 0.00 34.23 3.91
8246 9972 0.178767 AGTCAGCCGCATAGCATCAA 59.821 50.000 0.00 0.00 34.23 2.57
8265 9991 6.925165 GCATCAAGAAAGTTTTTCATGAAGGA 59.075 34.615 8.41 0.00 0.00 3.36
8266 9992 7.439056 GCATCAAGAAAGTTTTTCATGAAGGAA 59.561 33.333 8.41 5.34 0.00 3.36
8268 9994 8.066612 TCAAGAAAGTTTTTCATGAAGGAAGT 57.933 30.769 8.41 7.98 0.00 3.01
8269 9995 9.184523 TCAAGAAAGTTTTTCATGAAGGAAGTA 57.815 29.630 8.41 0.00 0.00 2.24
8272 9998 7.998964 AGAAAGTTTTTCATGAAGGAAGTAGGA 59.001 33.333 8.41 0.00 0.00 2.94
8273 9999 8.712228 AAAGTTTTTCATGAAGGAAGTAGGAT 57.288 30.769 8.41 0.00 0.00 3.24
8274 10000 7.693969 AGTTTTTCATGAAGGAAGTAGGATG 57.306 36.000 8.41 0.00 0.00 3.51
8275 10001 6.660949 AGTTTTTCATGAAGGAAGTAGGATGG 59.339 38.462 8.41 0.00 0.00 3.51
8276 10002 5.779241 TTTCATGAAGGAAGTAGGATGGT 57.221 39.130 8.41 0.00 0.00 3.55
8277 10003 4.760530 TCATGAAGGAAGTAGGATGGTG 57.239 45.455 0.00 0.00 0.00 4.17
8278 10004 3.118261 TCATGAAGGAAGTAGGATGGTGC 60.118 47.826 0.00 0.00 0.00 5.01
8283 10009 4.206244 AGGAAGTAGGATGGTGCTCTAT 57.794 45.455 0.00 0.00 0.00 1.98
8292 10018 3.688553 GGTGCTCTATGCCTACACC 57.311 57.895 0.00 0.00 43.57 4.16
8293 10019 1.123928 GGTGCTCTATGCCTACACCT 58.876 55.000 3.28 0.00 45.86 4.00
8304 10030 1.742761 CCTACACCTGGCATGTGAAG 58.257 55.000 26.36 12.06 37.18 3.02
8306 10032 2.625737 CTACACCTGGCATGTGAAGAG 58.374 52.381 26.36 16.38 37.18 2.85
8307 10033 0.767375 ACACCTGGCATGTGAAGAGT 59.233 50.000 26.36 3.76 37.18 3.24
8309 10035 0.767375 ACCTGGCATGTGAAGAGTGT 59.233 50.000 0.00 0.00 0.00 3.55
8310 10036 1.162698 CCTGGCATGTGAAGAGTGTG 58.837 55.000 0.00 0.00 0.00 3.82
8320 10046 1.546029 TGAAGAGTGTGTGGAGATCCG 59.454 52.381 0.00 0.00 39.43 4.18
8321 10047 0.247736 AAGAGTGTGTGGAGATCCGC 59.752 55.000 5.45 5.45 46.40 5.54
8331 10057 1.226888 GAGATCCGCCGCGTAGTTT 60.227 57.895 12.58 0.00 0.00 2.66
8341 10067 1.423845 GCGTAGTTTGGCACATCGG 59.576 57.895 0.00 0.00 39.30 4.18
8371 10097 4.634133 GCACGTCGACGGTGTGGA 62.634 66.667 37.89 0.00 44.95 4.02
8372 10098 2.257371 CACGTCGACGGTGTGGAT 59.743 61.111 37.89 15.71 44.95 3.41
8373 10099 1.503091 CACGTCGACGGTGTGGATA 59.497 57.895 37.89 0.00 44.95 2.59
8374 10100 0.522705 CACGTCGACGGTGTGGATAG 60.523 60.000 37.89 14.26 44.95 2.08
8375 10101 1.063649 CGTCGACGGTGTGGATAGG 59.936 63.158 29.70 0.00 35.37 2.57
8376 10102 1.436336 GTCGACGGTGTGGATAGGG 59.564 63.158 0.00 0.00 0.00 3.53
8377 10103 2.106332 CGACGGTGTGGATAGGGC 59.894 66.667 0.00 0.00 0.00 5.19
8378 10104 2.504519 GACGGTGTGGATAGGGCC 59.495 66.667 0.00 0.00 0.00 5.80
8379 10105 3.441011 GACGGTGTGGATAGGGCCG 62.441 68.421 0.00 0.00 46.83 6.13
8380 10106 4.910585 CGGTGTGGATAGGGCCGC 62.911 72.222 0.00 0.00 38.91 6.53
8381 10107 4.910585 GGTGTGGATAGGGCCGCG 62.911 72.222 0.00 0.00 41.34 6.46
8384 10110 4.971125 GTGGATAGGGCCGCGCTC 62.971 72.222 14.03 0.45 0.00 5.03
8387 10113 4.671569 GATAGGGCCGCGCTCCTG 62.672 72.222 23.03 2.03 32.93 3.86
8411 10137 3.787001 CGGAGGAGGGTTGGGCTC 61.787 72.222 0.00 0.00 0.00 4.70
8412 10138 3.412408 GGAGGAGGGTTGGGCTCC 61.412 72.222 0.00 0.00 37.53 4.70
8413 10139 3.787001 GAGGAGGGTTGGGCTCCG 61.787 72.222 0.00 0.00 41.82 4.63
8425 10151 4.329545 GCTCCGGCTGTGGGTTGA 62.330 66.667 0.00 0.00 35.22 3.18
8426 10152 2.046892 CTCCGGCTGTGGGTTGAG 60.047 66.667 0.00 0.00 0.00 3.02
8427 10153 4.329545 TCCGGCTGTGGGTTGAGC 62.330 66.667 0.00 0.00 34.23 4.26
8428 10154 4.335647 CCGGCTGTGGGTTGAGCT 62.336 66.667 0.00 0.00 35.42 4.09
8429 10155 2.743928 CGGCTGTGGGTTGAGCTC 60.744 66.667 6.82 6.82 35.42 4.09
8430 10156 2.753029 GGCTGTGGGTTGAGCTCT 59.247 61.111 16.19 0.00 35.42 4.09
8431 10157 1.673665 GGCTGTGGGTTGAGCTCTG 60.674 63.158 16.19 0.00 35.42 3.35
8432 10158 1.673665 GCTGTGGGTTGAGCTCTGG 60.674 63.158 16.19 0.00 32.12 3.86
8433 10159 1.673665 CTGTGGGTTGAGCTCTGGC 60.674 63.158 16.19 4.80 39.06 4.85
8443 10169 2.749441 GCTCTGGCTGAGGGTTGC 60.749 66.667 20.97 5.30 42.87 4.17
8444 10170 2.752358 CTCTGGCTGAGGGTTGCA 59.248 61.111 13.11 0.00 39.08 4.08
8445 10171 1.376942 CTCTGGCTGAGGGTTGCAG 60.377 63.158 13.11 0.00 39.08 4.41
8446 10172 2.121992 CTCTGGCTGAGGGTTGCAGT 62.122 60.000 13.11 0.00 39.08 4.40
8447 10173 1.970114 CTGGCTGAGGGTTGCAGTG 60.970 63.158 0.00 0.00 35.81 3.66
8448 10174 3.368571 GGCTGAGGGTTGCAGTGC 61.369 66.667 8.58 8.58 35.81 4.40
8449 10175 2.595463 GCTGAGGGTTGCAGTGCA 60.595 61.111 15.37 15.37 35.81 4.57
8450 10176 1.975407 GCTGAGGGTTGCAGTGCAT 60.975 57.895 20.50 3.05 38.76 3.96
8451 10177 1.930908 GCTGAGGGTTGCAGTGCATC 61.931 60.000 20.50 18.16 38.76 3.91
8452 10178 0.607217 CTGAGGGTTGCAGTGCATCA 60.607 55.000 20.50 17.93 38.76 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.568007 TGCAACAACTCTTTGTATGTCCC 59.432 43.478 0.00 0.00 45.69 4.46
1 2 4.515191 TCTGCAACAACTCTTTGTATGTCC 59.485 41.667 0.00 0.00 45.69 4.02
2 3 5.237344 AGTCTGCAACAACTCTTTGTATGTC 59.763 40.000 0.00 0.00 45.69 3.06
6 7 5.233476 CGTAAGTCTGCAACAACTCTTTGTA 59.767 40.000 0.00 0.00 45.69 2.41
127 130 9.321590 GAAAATAAATTTGAAAGTGCATTGAGC 57.678 29.630 0.00 0.00 45.96 4.26
167 201 9.187996 TGCATTCCTATAGAAATCAATGTTGAA 57.812 29.630 0.00 0.00 37.21 2.69
168 202 8.623903 GTGCATTCCTATAGAAATCAATGTTGA 58.376 33.333 0.00 0.00 38.21 3.18
169 203 8.627403 AGTGCATTCCTATAGAAATCAATGTTG 58.373 33.333 0.00 0.00 38.21 3.33
170 204 8.757982 AGTGCATTCCTATAGAAATCAATGTT 57.242 30.769 0.00 0.00 38.21 2.71
171 205 8.757982 AAGTGCATTCCTATAGAAATCAATGT 57.242 30.769 0.00 0.00 38.21 2.71
180 214 8.786898 GCAATGATAAAAGTGCATTCCTATAGA 58.213 33.333 0.00 0.00 36.97 1.98
181 215 8.790718 AGCAATGATAAAAGTGCATTCCTATAG 58.209 33.333 0.00 0.00 39.50 1.31
182 216 8.696043 AGCAATGATAAAAGTGCATTCCTATA 57.304 30.769 0.00 0.00 39.50 1.31
183 217 7.592885 AGCAATGATAAAAGTGCATTCCTAT 57.407 32.000 0.00 0.00 39.50 2.57
184 218 8.518430 TTAGCAATGATAAAAGTGCATTCCTA 57.482 30.769 0.00 0.00 39.50 2.94
185 219 5.927281 AGCAATGATAAAAGTGCATTCCT 57.073 34.783 0.00 0.00 39.50 3.36
186 220 7.922278 TCATTAGCAATGATAAAAGTGCATTCC 59.078 33.333 0.00 0.00 42.69 3.01
187 221 8.861033 TCATTAGCAATGATAAAAGTGCATTC 57.139 30.769 0.00 0.00 42.69 2.67
188 222 8.689061 TCTCATTAGCAATGATAAAAGTGCATT 58.311 29.630 10.62 0.00 46.10 3.56
189 223 8.229253 TCTCATTAGCAATGATAAAAGTGCAT 57.771 30.769 10.62 0.00 46.10 3.96
218 252 6.918022 AGCAGACTTTTTGGAGAATTAAAACG 59.082 34.615 0.00 0.00 0.00 3.60
278 312 3.128764 CGGGGCAATTTCTAAAGGACTTC 59.871 47.826 0.00 0.00 0.00 3.01
280 314 2.041216 ACGGGGCAATTTCTAAAGGACT 59.959 45.455 0.00 0.00 0.00 3.85
281 315 2.443416 ACGGGGCAATTTCTAAAGGAC 58.557 47.619 0.00 0.00 0.00 3.85
282 316 2.891191 ACGGGGCAATTTCTAAAGGA 57.109 45.000 0.00 0.00 0.00 3.36
284 318 4.095932 GGAAGTACGGGGCAATTTCTAAAG 59.904 45.833 0.00 0.00 0.00 1.85
287 321 2.841881 AGGAAGTACGGGGCAATTTCTA 59.158 45.455 0.00 0.00 0.00 2.10
288 322 1.633945 AGGAAGTACGGGGCAATTTCT 59.366 47.619 0.00 0.00 0.00 2.52
289 323 2.014857 GAGGAAGTACGGGGCAATTTC 58.985 52.381 0.00 0.00 0.00 2.17
293 776 0.834687 ACAGAGGAAGTACGGGGCAA 60.835 55.000 0.00 0.00 0.00 4.52
298 781 3.936372 TTTGAGACAGAGGAAGTACGG 57.064 47.619 0.00 0.00 0.00 4.02
300 783 6.422400 CACTTCTTTTGAGACAGAGGAAGTAC 59.578 42.308 15.21 0.00 39.51 2.73
305 788 4.499865 CGACACTTCTTTTGAGACAGAGGA 60.500 45.833 0.00 0.00 0.00 3.71
308 791 3.123804 GCGACACTTCTTTTGAGACAGA 58.876 45.455 0.00 0.00 0.00 3.41
310 793 2.899976 TGCGACACTTCTTTTGAGACA 58.100 42.857 0.00 0.00 0.00 3.41
315 798 2.111756 GTGCTTGCGACACTTCTTTTG 58.888 47.619 0.00 0.00 35.12 2.44
365 848 6.753180 TGGTAATAATGCTTTGTGCTTTCAA 58.247 32.000 0.00 0.00 43.37 2.69
375 858 5.127031 GGTGGACACATGGTAATAATGCTTT 59.873 40.000 4.69 0.00 0.00 3.51
455 938 2.588877 GACGACGATGCCATGGGG 60.589 66.667 15.13 0.00 37.18 4.96
533 1032 1.089481 TCCGCGATGTTCAATGGAGC 61.089 55.000 8.23 0.00 0.00 4.70
615 1114 5.330792 CGAATTCGTCTGAAAACACAAAAGC 60.331 40.000 19.67 0.00 37.71 3.51
616 1115 5.171337 CCGAATTCGTCTGAAAACACAAAAG 59.829 40.000 25.10 1.13 37.71 2.27
628 1127 2.404215 ACTGTCAACCGAATTCGTCTG 58.596 47.619 25.10 20.23 37.74 3.51
650 1153 2.032302 CCGTGTCAAATTCCGTTTGTGA 59.968 45.455 1.05 0.00 45.87 3.58
651 1154 2.380660 CCGTGTCAAATTCCGTTTGTG 58.619 47.619 1.05 0.00 45.87 3.33
692 1204 3.691342 TGTCTCGCTTCGGTGGGG 61.691 66.667 0.00 0.00 0.00 4.96
745 1257 3.918566 TCCGAATAGAATACAGGTGGGA 58.081 45.455 0.00 0.00 0.00 4.37
968 1499 1.068333 CCTGCGGAATTCACAACAAGG 60.068 52.381 7.93 1.60 0.00 3.61
1404 1935 3.423154 GGAGTTGTGGCGCCGAAG 61.423 66.667 23.90 0.00 0.00 3.79
1405 1936 3.876589 GAGGAGTTGTGGCGCCGAA 62.877 63.158 23.90 14.66 33.40 4.30
1406 1937 4.373116 GAGGAGTTGTGGCGCCGA 62.373 66.667 23.90 8.13 33.40 5.54
1408 1939 3.553095 AAGGAGGAGTTGTGGCGCC 62.553 63.158 22.73 22.73 0.00 6.53
1409 1940 2.032681 AAGGAGGAGTTGTGGCGC 59.967 61.111 0.00 0.00 0.00 6.53
1410 1941 1.376037 GGAAGGAGGAGTTGTGGCG 60.376 63.158 0.00 0.00 0.00 5.69
1411 1942 1.002011 GGGAAGGAGGAGTTGTGGC 60.002 63.158 0.00 0.00 0.00 5.01
1412 1943 0.326264 CTGGGAAGGAGGAGTTGTGG 59.674 60.000 0.00 0.00 0.00 4.17
1413 1944 0.326264 CCTGGGAAGGAGGAGTTGTG 59.674 60.000 0.00 0.00 31.48 3.33
1414 1945 0.842467 CCCTGGGAAGGAGGAGTTGT 60.842 60.000 7.01 0.00 31.48 3.32
1415 1946 0.547712 TCCCTGGGAAGGAGGAGTTG 60.548 60.000 14.48 0.00 31.48 3.16
1416 1947 0.547954 GTCCCTGGGAAGGAGGAGTT 60.548 60.000 19.06 0.00 32.84 3.01
1417 1948 1.081277 GTCCCTGGGAAGGAGGAGT 59.919 63.158 19.06 0.00 32.84 3.85
1418 1949 1.690985 GGTCCCTGGGAAGGAGGAG 60.691 68.421 19.06 0.00 32.84 3.69
1419 1950 2.454941 GGTCCCTGGGAAGGAGGA 59.545 66.667 19.06 0.00 32.84 3.71
1420 1951 2.692741 GGGTCCCTGGGAAGGAGG 60.693 72.222 19.06 0.00 32.84 4.30
1421 1952 1.308216 ATGGGTCCCTGGGAAGGAG 60.308 63.158 19.06 0.00 32.84 3.69
1422 1953 1.307866 GATGGGTCCCTGGGAAGGA 60.308 63.158 19.06 3.99 31.38 3.36
1423 1954 2.746375 CGATGGGTCCCTGGGAAGG 61.746 68.421 19.06 0.00 31.38 3.46
1424 1955 2.746375 CCGATGGGTCCCTGGGAAG 61.746 68.421 19.06 4.92 31.38 3.46
1425 1956 2.690881 CCGATGGGTCCCTGGGAA 60.691 66.667 19.06 1.73 31.38 3.97
1464 1995 4.021925 GGAGTGGCGCTGAAGGGT 62.022 66.667 4.71 0.00 0.00 4.34
1465 1996 3.551496 TTGGAGTGGCGCTGAAGGG 62.551 63.158 4.71 0.00 0.00 3.95
1466 1997 2.032528 TTGGAGTGGCGCTGAAGG 59.967 61.111 4.71 0.00 0.00 3.46
1467 1998 2.328099 GGTTGGAGTGGCGCTGAAG 61.328 63.158 4.71 0.00 0.00 3.02
1468 1999 2.281484 GGTTGGAGTGGCGCTGAA 60.281 61.111 4.71 0.00 0.00 3.02
1469 2000 4.329545 GGGTTGGAGTGGCGCTGA 62.330 66.667 4.71 0.00 0.00 4.26
1470 2001 4.641645 TGGGTTGGAGTGGCGCTG 62.642 66.667 4.71 0.00 0.00 5.18
1471 2002 4.335647 CTGGGTTGGAGTGGCGCT 62.336 66.667 7.64 0.00 0.00 5.92
1473 2004 4.722700 CCCTGGGTTGGAGTGGCG 62.723 72.222 3.97 0.00 0.00 5.69
1474 2005 3.256960 TCCCTGGGTTGGAGTGGC 61.257 66.667 13.56 0.00 0.00 5.01
1475 2006 2.757077 GTCCCTGGGTTGGAGTGG 59.243 66.667 13.56 0.00 30.98 4.00
1476 2007 2.757077 GGTCCCTGGGTTGGAGTG 59.243 66.667 13.56 0.00 30.98 3.51
1477 2008 2.531942 GGGTCCCTGGGTTGGAGT 60.532 66.667 13.56 0.00 30.98 3.85
1478 2009 1.852626 AAGGGTCCCTGGGTTGGAG 60.853 63.158 12.53 0.00 32.13 3.86
1479 2010 1.850755 GAAGGGTCCCTGGGTTGGA 60.851 63.158 12.53 0.00 32.13 3.53
1480 2011 2.763902 GAAGGGTCCCTGGGTTGG 59.236 66.667 12.53 0.00 32.13 3.77
1481 2012 2.351276 CGAAGGGTCCCTGGGTTG 59.649 66.667 12.53 0.00 32.13 3.77
1503 2034 4.329545 CCCTGGGGTGGACGTGTG 62.330 72.222 4.27 0.00 0.00 3.82
1504 2035 4.567597 TCCCTGGGGTGGACGTGT 62.568 66.667 14.00 0.00 36.47 4.49
1527 2061 4.961511 GACGACGGCACAGCACCA 62.962 66.667 0.00 0.00 0.00 4.17
1530 2064 3.145422 TTGAGACGACGGCACAGCA 62.145 57.895 2.19 0.00 0.00 4.41
1533 2067 2.338620 CCTTGAGACGACGGCACA 59.661 61.111 2.19 0.00 0.00 4.57
1535 2069 4.373116 GGCCTTGAGACGACGGCA 62.373 66.667 2.19 0.00 44.23 5.69
1540 2104 0.250727 CCAAAAGGGCCTTGAGACGA 60.251 55.000 21.72 0.00 0.00 4.20
1561 2125 0.535102 CGAAAAGGTGGAGGTGCTGT 60.535 55.000 0.00 0.00 0.00 4.40
1601 2165 2.848679 TGGGAGACTGTGGCTGCA 60.849 61.111 0.50 0.00 0.00 4.41
1636 2200 0.535335 GGCCTCACATAAGTCGGTGA 59.465 55.000 0.00 0.00 41.44 4.02
1729 2293 1.673009 GTTGAAACGATGGCCGGGA 60.673 57.895 2.18 0.00 43.93 5.14
1730 2294 1.922135 CTGTTGAAACGATGGCCGGG 61.922 60.000 2.18 0.00 43.93 5.73
1774 2338 3.346734 GGAAGGTGGCCCCATGGA 61.347 66.667 15.22 0.00 34.66 3.41
1797 2361 3.587498 AGGATATGCTGGCTGGTTACTA 58.413 45.455 0.00 0.00 0.00 1.82
1938 2502 0.676184 GCTCCTCATCGCCATACAGA 59.324 55.000 0.00 0.00 0.00 3.41
2016 2580 1.520787 CGCCGGAATAGTGTGGGTC 60.521 63.158 5.05 0.00 0.00 4.46
2642 3369 6.429078 CAGGAATCAAGACAAAACATCTCTCA 59.571 38.462 0.00 0.00 0.00 3.27
2643 3370 6.652481 TCAGGAATCAAGACAAAACATCTCTC 59.348 38.462 0.00 0.00 0.00 3.20
2902 3652 1.068541 TGGTCAACGACTGATGTCTCG 60.069 52.381 0.00 0.00 40.86 4.04
2929 3679 2.350772 GCACCTTCTGGAACGACATTTG 60.351 50.000 0.00 0.00 37.04 2.32
2974 3724 6.046593 TCGGTATAATCACAATGTCCAACTC 58.953 40.000 0.00 0.00 0.00 3.01
2978 3728 4.742440 GCCTCGGTATAATCACAATGTCCA 60.742 45.833 0.00 0.00 0.00 4.02
2982 3732 3.074412 GGGCCTCGGTATAATCACAATG 58.926 50.000 0.84 0.00 0.00 2.82
3004 3756 3.764237 TGTGTAACAGGTCCTCTTTCC 57.236 47.619 0.00 0.00 45.67 3.13
3057 3845 4.748600 ACGTGGTTAAGCTTGAACTAAGAC 59.251 41.667 9.86 0.00 38.76 3.01
3116 3906 9.569122 GGCCCACTTAATCTTTATTCTAATGTA 57.431 33.333 0.00 0.00 0.00 2.29
3199 4012 5.047377 GGGGCATATACAATGGTATTTGTGG 60.047 44.000 11.09 0.00 39.60 4.17
3201 4014 5.083821 GGGGGCATATACAATGGTATTTGT 58.916 41.667 11.09 0.00 39.60 2.83
3254 4103 6.702282 GGGTACAAGTGTAAGCTCATTCTATC 59.298 42.308 0.00 0.00 31.52 2.08
3266 4115 6.358991 AGCTAACTTTTGGGTACAAGTGTAA 58.641 36.000 0.00 0.00 37.97 2.41
3652 4507 2.303311 AGTTCTTTCTACCTCAGGCACC 59.697 50.000 0.00 0.00 0.00 5.01
3758 4653 4.666512 ACTGCAGAAAAGGGAACATACAT 58.333 39.130 23.35 0.00 0.00 2.29
3760 4655 4.082733 GGAACTGCAGAAAAGGGAACATAC 60.083 45.833 23.35 0.00 0.00 2.39
4585 5500 8.545420 ACGCGTACTTCAATAATAAACCATTAG 58.455 33.333 11.67 0.00 32.61 1.73
4670 5608 3.235200 CCCCAATTTGACCCTACAACAA 58.765 45.455 0.00 0.00 0.00 2.83
5574 6976 5.163141 TGGATCTCTCCCAGTTCTACTCTAG 60.163 48.000 0.00 0.00 41.29 2.43
5868 7310 5.428253 TGACATTTATGAAGGGTAGAGCAC 58.572 41.667 0.00 0.00 0.00 4.40
6191 7667 3.285484 CCTTCTTGCAGGCAGTATCATT 58.715 45.455 0.00 0.00 0.00 2.57
6585 8099 4.319177 AGCAGACTAGCCAGTTTAACTTG 58.681 43.478 0.00 0.00 34.21 3.16
6597 8112 5.349809 ACCGAATTAACTAAGCAGACTAGC 58.650 41.667 0.00 0.00 0.00 3.42
6614 8129 5.382664 AATGGGTTGAGGTAATACCGAAT 57.617 39.130 3.47 0.00 44.90 3.34
7002 8556 3.197983 AGAGGAATGGAGTTTAAGTCCCG 59.802 47.826 15.47 0.00 36.88 5.14
7011 8639 2.027100 GGACGGAAAGAGGAATGGAGTT 60.027 50.000 0.00 0.00 0.00 3.01
7015 8643 2.789409 AAGGACGGAAAGAGGAATGG 57.211 50.000 0.00 0.00 0.00 3.16
7079 8716 9.520515 ACATACTAAAAAGGAGAAATGTCATGT 57.479 29.630 0.00 0.00 0.00 3.21
7281 8942 2.688214 CGAAGAATCCCTCTCCCTCAGA 60.688 54.545 0.00 0.00 31.02 3.27
7471 9137 9.605955 AGTTTACACAAAAACAAAAATTTCTGC 57.394 25.926 0.00 0.00 40.97 4.26
7588 9267 2.345244 AGCGCTGCTGCTAACAGT 59.655 55.556 10.39 0.00 45.14 3.55
7671 9352 2.567615 AGCTGTGTATCCTTTTCTCGGT 59.432 45.455 0.00 0.00 0.00 4.69
7682 9363 4.188247 TCTGGTACAACAGCTGTGTATC 57.812 45.455 22.49 22.45 39.20 2.24
7683 9364 4.617253 TTCTGGTACAACAGCTGTGTAT 57.383 40.909 22.49 11.50 39.20 2.29
7686 9367 4.997395 ACTTATTCTGGTACAACAGCTGTG 59.003 41.667 22.49 16.62 39.20 3.66
8005 9727 4.312443 TGTGGTCAAAATCGACTAGAACC 58.688 43.478 0.00 0.00 36.12 3.62
8169 9892 6.616947 TGCACTGCCAGTTTTGTAATAATAC 58.383 36.000 0.00 0.00 0.00 1.89
8170 9893 6.825944 TGCACTGCCAGTTTTGTAATAATA 57.174 33.333 0.00 0.00 0.00 0.98
8171 9894 5.720371 TGCACTGCCAGTTTTGTAATAAT 57.280 34.783 0.00 0.00 0.00 1.28
8172 9895 5.521906 TTGCACTGCCAGTTTTGTAATAA 57.478 34.783 0.00 0.00 0.00 1.40
8186 9909 6.962686 TGTTATGAGATTATCATTGCACTGC 58.037 36.000 0.00 0.00 46.97 4.40
8187 9910 7.076362 GCTGTTATGAGATTATCATTGCACTG 58.924 38.462 0.00 0.00 46.97 3.66
8188 9911 6.769341 TGCTGTTATGAGATTATCATTGCACT 59.231 34.615 0.00 0.00 46.97 4.40
8211 9934 4.153835 GGCTGACTATTTATGAGCTCATGC 59.846 45.833 34.48 25.05 37.15 4.06
8228 9952 0.585357 CTTGATGCTATGCGGCTGAC 59.415 55.000 0.00 0.00 0.00 3.51
8229 9953 0.465287 TCTTGATGCTATGCGGCTGA 59.535 50.000 0.00 0.00 0.00 4.26
8230 9954 1.302366 TTCTTGATGCTATGCGGCTG 58.698 50.000 0.00 0.00 0.00 4.85
8234 9960 5.858049 TGAAAAACTTTCTTGATGCTATGCG 59.142 36.000 1.22 0.00 0.00 4.73
8243 9969 8.066612 ACTTCCTTCATGAAAAACTTTCTTGA 57.933 30.769 9.88 11.54 32.86 3.02
8244 9970 9.455847 CTACTTCCTTCATGAAAAACTTTCTTG 57.544 33.333 9.88 8.11 0.00 3.02
8246 9972 7.998964 TCCTACTTCCTTCATGAAAAACTTTCT 59.001 33.333 9.88 0.00 0.00 2.52
8265 9991 3.760580 GCATAGAGCACCATCCTACTT 57.239 47.619 0.00 0.00 44.79 2.24
8277 10003 3.997672 CCAGGTGTAGGCATAGAGC 57.002 57.895 0.00 0.00 44.65 4.09
8292 10018 1.534163 CACACACTCTTCACATGCCAG 59.466 52.381 0.00 0.00 0.00 4.85
8293 10019 1.596603 CACACACTCTTCACATGCCA 58.403 50.000 0.00 0.00 0.00 4.92
8300 10026 1.546029 CGGATCTCCACACACTCTTCA 59.454 52.381 0.00 0.00 35.14 3.02
8304 10030 1.153549 GGCGGATCTCCACACACTC 60.154 63.158 0.00 0.00 35.14 3.51
8306 10032 2.509336 CGGCGGATCTCCACACAC 60.509 66.667 0.00 0.00 35.14 3.82
8307 10033 4.451150 GCGGCGGATCTCCACACA 62.451 66.667 9.78 0.00 35.14 3.72
8310 10036 3.825833 CTACGCGGCGGATCTCCAC 62.826 68.421 27.37 0.00 35.14 4.02
8320 10046 2.577763 GATGTGCCAAACTACGCGGC 62.578 60.000 12.47 2.03 46.43 6.53
8321 10047 1.423845 GATGTGCCAAACTACGCGG 59.576 57.895 12.47 0.00 0.00 6.46
8356 10082 1.651240 CCTATCCACACCGTCGACGT 61.651 60.000 33.49 20.15 37.74 4.34
8359 10085 2.420568 GCCCTATCCACACCGTCGA 61.421 63.158 0.00 0.00 0.00 4.20
8360 10086 2.106332 GCCCTATCCACACCGTCG 59.894 66.667 0.00 0.00 0.00 5.12
8361 10087 2.504519 GGCCCTATCCACACCGTC 59.495 66.667 0.00 0.00 0.00 4.79
8362 10088 3.467226 CGGCCCTATCCACACCGT 61.467 66.667 0.00 0.00 39.05 4.83
8363 10089 4.910585 GCGGCCCTATCCACACCG 62.911 72.222 0.00 0.00 46.50 4.94
8364 10090 4.910585 CGCGGCCCTATCCACACC 62.911 72.222 0.00 0.00 0.00 4.16
8367 10093 4.971125 GAGCGCGGCCCTATCCAC 62.971 72.222 8.83 0.00 0.00 4.02
8370 10096 4.671569 CAGGAGCGCGGCCCTATC 62.672 72.222 17.09 0.36 30.36 2.08
8394 10120 3.787001 GAGCCCAACCCTCCTCCG 61.787 72.222 0.00 0.00 0.00 4.63
8395 10121 3.412408 GGAGCCCAACCCTCCTCC 61.412 72.222 0.33 0.00 44.40 4.30
8396 10122 3.787001 CGGAGCCCAACCCTCCTC 61.787 72.222 5.96 0.00 45.37 3.71
8408 10134 4.329545 TCAACCCACAGCCGGAGC 62.330 66.667 5.05 0.00 40.32 4.70
8409 10135 2.046892 CTCAACCCACAGCCGGAG 60.047 66.667 5.05 0.00 0.00 4.63
8410 10136 4.329545 GCTCAACCCACAGCCGGA 62.330 66.667 5.05 0.00 0.00 5.14
8411 10137 4.335647 AGCTCAACCCACAGCCGG 62.336 66.667 0.00 0.00 36.17 6.13
8412 10138 2.743928 GAGCTCAACCCACAGCCG 60.744 66.667 9.40 0.00 36.17 5.52
8413 10139 1.673665 CAGAGCTCAACCCACAGCC 60.674 63.158 17.77 0.00 36.17 4.85
8414 10140 1.673665 CCAGAGCTCAACCCACAGC 60.674 63.158 17.77 0.00 35.73 4.40
8415 10141 1.673665 GCCAGAGCTCAACCCACAG 60.674 63.158 17.77 0.00 35.50 3.66
8416 10142 2.431683 GCCAGAGCTCAACCCACA 59.568 61.111 17.77 0.00 35.50 4.17
8426 10152 2.749441 GCAACCCTCAGCCAGAGC 60.749 66.667 0.00 0.00 43.31 4.09
8427 10153 1.376942 CTGCAACCCTCAGCCAGAG 60.377 63.158 0.00 0.00 44.31 3.35
8428 10154 2.149383 ACTGCAACCCTCAGCCAGA 61.149 57.895 0.00 0.00 35.04 3.86
8429 10155 1.970114 CACTGCAACCCTCAGCCAG 60.970 63.158 0.00 0.00 35.04 4.85
8430 10156 2.113774 CACTGCAACCCTCAGCCA 59.886 61.111 0.00 0.00 35.04 4.75
8431 10157 3.368571 GCACTGCAACCCTCAGCC 61.369 66.667 0.00 0.00 35.04 4.85
8432 10158 1.930908 GATGCACTGCAACCCTCAGC 61.931 60.000 8.03 0.00 43.62 4.26
8433 10159 0.607217 TGATGCACTGCAACCCTCAG 60.607 55.000 8.03 0.00 43.62 3.35
8434 10160 1.455412 TGATGCACTGCAACCCTCA 59.545 52.632 8.03 4.35 43.62 3.86
8435 10161 4.402851 TGATGCACTGCAACCCTC 57.597 55.556 8.03 1.48 43.62 4.30


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

AutoCloner maintained by Alex Coulton.