Multiple sequence alignment - TraesCS1B01G359600

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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 TraesCS1B01G359600 chr1B 100.000 2232 0 0 1 2232 588515968 588518199 0.000000e+00 4122
1 TraesCS1B01G359600 chr1B 88.288 333 36 1 1 330 657406899 657406567 1.610000e-106 396
2 TraesCS1B01G359600 chr1B 97.630 211 5 0 1979 2189 588526087 588526297 1.630000e-96 363
3 TraesCS1B01G359600 chr1B 86.066 122 15 2 1219 1340 657406296 657406177 1.800000e-26 130
4 TraesCS1B01G359600 chr1D 96.069 1984 69 5 1 1983 435293438 435295413 0.000000e+00 3223
5 TraesCS1B01G359600 chr1D 89.157 332 33 1 2 330 472906750 472906419 5.740000e-111 411
6 TraesCS1B01G359600 chr1D 91.270 252 22 0 633 884 472906401 472906150 5.900000e-91 344
7 TraesCS1B01G359600 chr1D 86.066 122 15 1 1219 1340 472906148 472906029 1.800000e-26 130
8 TraesCS1B01G359600 chr1A 95.235 1364 45 5 1 1362 532796656 532798001 0.000000e+00 2141
9 TraesCS1B01G359600 chr1A 95.142 494 14 1 1356 1839 532806763 532807256 0.000000e+00 771
10 TraesCS1B01G359600 chr1A 88.889 333 34 1 1 330 566636828 566636496 7.420000e-110 407
11 TraesCS1B01G359600 chr1A 96.689 151 5 0 1833 1983 532807381 532807531 3.680000e-63 252
12 TraesCS1B01G359600 chr7D 88.106 908 84 10 1 884 279741307 279740400 0.000000e+00 1057
13 TraesCS1B01G359600 chr7D 87.631 857 70 17 61 884 621644864 621644011 0.000000e+00 963
14 TraesCS1B01G359600 chr7D 85.446 213 23 6 1631 1839 279738693 279738485 4.830000e-52 215
15 TraesCS1B01G359600 chr7D 84.967 153 13 4 1833 1982 279738374 279738229 1.790000e-31 147
16 TraesCS1B01G359600 chr7B 88.106 908 84 9 1 884 253698742 253699649 0.000000e+00 1057
17 TraesCS1B01G359600 chr7B 91.489 564 43 3 322 884 718361506 718362065 0.000000e+00 771
18 TraesCS1B01G359600 chr7B 83.826 507 50 18 1337 1839 744662785 744663263 9.400000e-124 453
19 TraesCS1B01G359600 chr7B 86.385 213 21 6 1631 1839 253701796 253702004 2.230000e-55 226
20 TraesCS1B01G359600 chr7B 84.967 153 13 4 1833 1982 253702115 253702260 1.790000e-31 147
21 TraesCS1B01G359600 chr7A 87.885 908 86 8 1 884 316021023 316021930 0.000000e+00 1046
22 TraesCS1B01G359600 chr7A 87.209 860 71 17 61 884 717086787 717085931 0.000000e+00 942
23 TraesCS1B01G359600 chr7A 90.541 148 11 1 1835 1979 717082916 717082769 2.260000e-45 193
24 TraesCS1B01G359600 chr7A 90.625 128 9 1 1848 1972 735707759 735707632 1.370000e-37 167
25 TraesCS1B01G359600 chr7A 84.967 153 13 4 1833 1982 316024416 316024561 1.790000e-31 147
26 TraesCS1B01G359600 chr5D 84.615 494 50 11 77 545 557181735 557182227 3.360000e-128 468
27 TraesCS1B01G359600 chr5D 90.411 146 12 1 1696 1839 557182827 557182972 8.140000e-45 191
28 TraesCS1B01G359600 chrUn 90.643 342 25 6 883 1219 363863629 363863290 4.370000e-122 448
29 TraesCS1B01G359600 chrUn 88.604 351 24 7 883 1219 430358280 430358628 1.590000e-111 412
30 TraesCS1B01G359600 chrUn 87.464 351 28 9 883 1219 354743915 354743567 7.470000e-105 390
31 TraesCS1B01G359600 chr2D 90.643 342 25 6 883 1219 272805352 272805013 4.370000e-122 448
32 TraesCS1B01G359600 chr2D 90.379 343 24 7 883 1219 196967432 196967093 2.030000e-120 442
33 TraesCS1B01G359600 chr5A 97.590 249 6 0 1984 2232 6718851 6719099 5.700000e-116 427
34 TraesCS1B01G359600 chr5A 97.233 253 6 1 1980 2232 653377689 653377940 5.700000e-116 427
35 TraesCS1B01G359600 chr5A 98.104 211 4 0 1979 2189 6724020 6724230 3.500000e-98 368
36 TraesCS1B01G359600 chr5A 98.104 211 4 0 1979 2189 653382862 653383072 3.500000e-98 368
37 TraesCS1B01G359600 chr4B 88.319 351 25 9 883 1219 151525832 151526180 7.420000e-110 407
38 TraesCS1B01G359600 chr5B 88.012 342 33 7 883 1219 432873047 432873385 4.470000e-107 398
39 TraesCS1B01G359600 chr5B 88.213 263 28 2 1580 1839 709422560 709422298 5.990000e-81 311
40 TraesCS1B01G359600 chr2B 97.788 226 5 0 2007 2232 134568319 134568094 7.470000e-105 390
41 TraesCS1B01G359600 chr2B 99.338 151 1 0 1982 2132 134555760 134555610 7.850000e-70 274
42 TraesCS1B01G359600 chr4A 90.043 231 21 1 1611 1839 605666452 605666682 4.660000e-77 298
43 TraesCS1B01G359600 chr4A 91.579 190 12 4 1364 1551 605666268 605666455 2.200000e-65 259
44 TraesCS1B01G359600 chr4A 81.855 248 24 7 1 248 605665455 605665681 2.930000e-44 189
45 TraesCS1B01G359600 chr4D 78.409 176 27 10 903 1073 509314896 509314727 1.090000e-18 104


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 TraesCS1B01G359600 chr1B 588515968 588518199 2231 False 4122.000000 4122 100.000000 1 2232 1 chr1B.!!$F1 2231
1 TraesCS1B01G359600 chr1B 657406177 657406899 722 True 263.000000 396 87.177000 1 1340 2 chr1B.!!$R1 1339
2 TraesCS1B01G359600 chr1D 435293438 435295413 1975 False 3223.000000 3223 96.069000 1 1983 1 chr1D.!!$F1 1982
3 TraesCS1B01G359600 chr1D 472906029 472906750 721 True 295.000000 411 88.831000 2 1340 3 chr1D.!!$R1 1338
4 TraesCS1B01G359600 chr1A 532796656 532798001 1345 False 2141.000000 2141 95.235000 1 1362 1 chr1A.!!$F1 1361
5 TraesCS1B01G359600 chr1A 532806763 532807531 768 False 511.500000 771 95.915500 1356 1983 2 chr1A.!!$F2 627
6 TraesCS1B01G359600 chr7D 621644011 621644864 853 True 963.000000 963 87.631000 61 884 1 chr7D.!!$R1 823
7 TraesCS1B01G359600 chr7D 279738229 279741307 3078 True 473.000000 1057 86.173000 1 1982 3 chr7D.!!$R2 1981
8 TraesCS1B01G359600 chr7B 718361506 718362065 559 False 771.000000 771 91.489000 322 884 1 chr7B.!!$F1 562
9 TraesCS1B01G359600 chr7B 253698742 253702260 3518 False 476.666667 1057 86.486000 1 1982 3 chr7B.!!$F3 1981
10 TraesCS1B01G359600 chr7A 316021023 316024561 3538 False 596.500000 1046 86.426000 1 1982 2 chr7A.!!$F1 1981
11 TraesCS1B01G359600 chr7A 717082769 717086787 4018 True 567.500000 942 88.875000 61 1979 2 chr7A.!!$R2 1918
12 TraesCS1B01G359600 chr5D 557181735 557182972 1237 False 329.500000 468 87.513000 77 1839 2 chr5D.!!$F1 1762
13 TraesCS1B01G359600 chr4A 605665455 605666682 1227 False 248.666667 298 87.825667 1 1839 3 chr4A.!!$F1 1838

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
234 238 1.073548 TGCTGCTGCATCTCCACAA 59.926 52.632 14.93 0.0 45.31 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 5556 0.034089 CAAAGCTACAGGGGAAGGGG 60.034 60.0 0.0 0.0 0.0 4.79 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
59 60 2.024414 GGCACAGTTCCAAGAAGTTGT 58.976 47.619 0.00 0.00 30.95 3.32
80 81 1.818060 TGCTGCTGTTGACTTTGTTGT 59.182 42.857 0.00 0.00 0.00 3.32
210 214 6.951971 AGATTATTTGACTGAACTGGTAGCT 58.048 36.000 0.00 0.00 0.00 3.32
234 238 1.073548 TGCTGCTGCATCTCCACAA 59.926 52.632 14.93 0.00 45.31 3.33
404 465 3.244814 GCTCGAGTAATGATTGCACAGAG 59.755 47.826 15.13 2.83 0.00 3.35
586 647 4.362470 AAGATTGCTGCTGCTGGATATA 57.638 40.909 17.00 0.00 40.48 0.86
1090 1153 7.363268 GGAGACTTGCTTCACATTTGGAATTAT 60.363 37.037 0.00 0.00 0.00 1.28
1091 1154 7.318141 AGACTTGCTTCACATTTGGAATTATG 58.682 34.615 0.00 0.00 0.00 1.90
1160 1223 2.285834 CGTCGACATTTGCTGGCTTATC 60.286 50.000 17.16 0.00 0.00 1.75
1167 1230 2.148446 TTGCTGGCTTATCTGGCAAT 57.852 45.000 0.00 0.00 41.92 3.56
1380 1701 5.105146 ACATTTGAGTAGTAGCAAGGAGAGG 60.105 44.000 0.00 0.00 0.00 3.69
1425 1747 8.164070 AGAGTTAAAGATGGTCCAATGTTACTT 58.836 33.333 0.00 0.00 0.00 2.24
1426 1748 8.336801 AGTTAAAGATGGTCCAATGTTACTTC 57.663 34.615 0.00 0.00 0.00 3.01
1439 1761 6.017770 CCAATGTTACTTCAACTTAACGGTCA 60.018 38.462 0.00 0.00 38.05 4.02
1457 1779 2.973224 GTCACAGCATTGCAAACTAACG 59.027 45.455 11.91 0.00 0.00 3.18
1561 1883 1.048601 CCGGCTAATGGGAGAAGCTA 58.951 55.000 0.00 0.00 36.48 3.32
1995 5416 1.125633 ACGGAAGTGTTGTAGGGTGT 58.874 50.000 0.00 0.00 46.97 4.16
1996 5417 1.202604 ACGGAAGTGTTGTAGGGTGTG 60.203 52.381 0.00 0.00 46.97 3.82
1997 5418 1.069513 CGGAAGTGTTGTAGGGTGTGA 59.930 52.381 0.00 0.00 0.00 3.58
1998 5419 2.767505 GGAAGTGTTGTAGGGTGTGAG 58.232 52.381 0.00 0.00 0.00 3.51
1999 5420 2.104281 GGAAGTGTTGTAGGGTGTGAGT 59.896 50.000 0.00 0.00 0.00 3.41
2000 5421 3.433173 GGAAGTGTTGTAGGGTGTGAGTT 60.433 47.826 0.00 0.00 0.00 3.01
2001 5422 4.202284 GGAAGTGTTGTAGGGTGTGAGTTA 60.202 45.833 0.00 0.00 0.00 2.24
2002 5423 4.332428 AGTGTTGTAGGGTGTGAGTTAC 57.668 45.455 0.00 0.00 0.00 2.50
2003 5424 3.707611 AGTGTTGTAGGGTGTGAGTTACA 59.292 43.478 0.00 0.00 36.82 2.41
2004 5425 4.056050 GTGTTGTAGGGTGTGAGTTACAG 58.944 47.826 0.00 0.00 40.69 2.74
2005 5426 3.070446 TGTTGTAGGGTGTGAGTTACAGG 59.930 47.826 0.00 0.00 40.69 4.00
2006 5427 3.247948 TGTAGGGTGTGAGTTACAGGA 57.752 47.619 0.00 0.00 40.69 3.86
2007 5428 3.162666 TGTAGGGTGTGAGTTACAGGAG 58.837 50.000 0.00 0.00 40.69 3.69
2008 5429 2.400467 AGGGTGTGAGTTACAGGAGT 57.600 50.000 0.00 0.00 40.69 3.85
2009 5430 1.971357 AGGGTGTGAGTTACAGGAGTG 59.029 52.381 0.00 0.00 40.69 3.51
2010 5431 1.692519 GGGTGTGAGTTACAGGAGTGT 59.307 52.381 0.00 0.00 40.69 3.55
2011 5432 2.104281 GGGTGTGAGTTACAGGAGTGTT 59.896 50.000 0.00 0.00 40.69 3.32
2012 5433 3.131396 GGTGTGAGTTACAGGAGTGTTG 58.869 50.000 0.00 0.00 40.69 3.33
2013 5434 3.431766 GGTGTGAGTTACAGGAGTGTTGT 60.432 47.826 0.00 0.00 40.69 3.32
2014 5435 4.202182 GGTGTGAGTTACAGGAGTGTTGTA 60.202 45.833 0.00 0.00 40.69 2.41
2015 5436 4.982916 GTGTGAGTTACAGGAGTGTTGTAG 59.017 45.833 0.00 0.00 40.69 2.74
2016 5437 4.038763 TGTGAGTTACAGGAGTGTTGTAGG 59.961 45.833 0.00 0.00 38.19 3.18
2017 5438 3.576982 TGAGTTACAGGAGTGTTGTAGGG 59.423 47.826 0.00 0.00 38.19 3.53
2018 5439 3.577415 GAGTTACAGGAGTGTTGTAGGGT 59.423 47.826 0.00 0.00 38.19 4.34
2019 5440 3.323979 AGTTACAGGAGTGTTGTAGGGTG 59.676 47.826 0.00 0.00 38.19 4.61
2020 5441 1.802553 ACAGGAGTGTTGTAGGGTGT 58.197 50.000 0.00 0.00 30.30 4.16
2021 5442 1.416401 ACAGGAGTGTTGTAGGGTGTG 59.584 52.381 0.00 0.00 30.30 3.82
2022 5443 1.691976 CAGGAGTGTTGTAGGGTGTGA 59.308 52.381 0.00 0.00 0.00 3.58
2023 5444 1.971357 AGGAGTGTTGTAGGGTGTGAG 59.029 52.381 0.00 0.00 0.00 3.51
2024 5445 1.692519 GGAGTGTTGTAGGGTGTGAGT 59.307 52.381 0.00 0.00 0.00 3.41
2025 5446 2.104281 GGAGTGTTGTAGGGTGTGAGTT 59.896 50.000 0.00 0.00 0.00 3.01
2026 5447 3.131396 GAGTGTTGTAGGGTGTGAGTTG 58.869 50.000 0.00 0.00 0.00 3.16
2027 5448 1.602377 GTGTTGTAGGGTGTGAGTTGC 59.398 52.381 0.00 0.00 0.00 4.17
2028 5449 1.210722 TGTTGTAGGGTGTGAGTTGCA 59.789 47.619 0.00 0.00 0.00 4.08
2029 5450 2.294074 GTTGTAGGGTGTGAGTTGCAA 58.706 47.619 0.00 0.00 0.00 4.08
2030 5451 2.685897 GTTGTAGGGTGTGAGTTGCAAA 59.314 45.455 0.00 0.00 0.00 3.68
2031 5452 3.006112 TGTAGGGTGTGAGTTGCAAAA 57.994 42.857 0.00 0.00 0.00 2.44
2032 5453 2.685897 TGTAGGGTGTGAGTTGCAAAAC 59.314 45.455 0.00 0.51 0.00 2.43
2033 5454 1.846007 AGGGTGTGAGTTGCAAAACA 58.154 45.000 0.00 3.54 0.00 2.83
2034 5455 1.750778 AGGGTGTGAGTTGCAAAACAG 59.249 47.619 0.00 0.00 0.00 3.16
2035 5456 1.202405 GGGTGTGAGTTGCAAAACAGG 60.202 52.381 0.00 0.00 0.00 4.00
2036 5457 1.202405 GGTGTGAGTTGCAAAACAGGG 60.202 52.381 0.00 0.00 0.00 4.45
2037 5458 1.748493 GTGTGAGTTGCAAAACAGGGA 59.252 47.619 0.00 0.00 0.00 4.20
2038 5459 2.165437 GTGTGAGTTGCAAAACAGGGAA 59.835 45.455 0.00 0.00 0.00 3.97
2039 5460 2.426738 TGTGAGTTGCAAAACAGGGAAG 59.573 45.455 0.00 0.00 0.00 3.46
2040 5461 2.427095 GTGAGTTGCAAAACAGGGAAGT 59.573 45.455 0.00 0.00 0.00 3.01
2041 5462 2.426738 TGAGTTGCAAAACAGGGAAGTG 59.573 45.455 0.00 0.00 0.00 3.16
2042 5463 2.427095 GAGTTGCAAAACAGGGAAGTGT 59.573 45.455 0.00 0.00 0.00 3.55
2043 5464 2.166254 AGTTGCAAAACAGGGAAGTGTG 59.834 45.455 0.00 0.00 0.00 3.82
2044 5465 2.136298 TGCAAAACAGGGAAGTGTGA 57.864 45.000 0.00 0.00 0.00 3.58
2045 5466 2.451490 TGCAAAACAGGGAAGTGTGAA 58.549 42.857 0.00 0.00 0.00 3.18
2046 5467 2.426738 TGCAAAACAGGGAAGTGTGAAG 59.573 45.455 0.00 0.00 0.00 3.02
2047 5468 2.223805 GCAAAACAGGGAAGTGTGAAGG 60.224 50.000 0.00 0.00 0.00 3.46
2048 5469 2.362077 CAAAACAGGGAAGTGTGAAGGG 59.638 50.000 0.00 0.00 0.00 3.95
2049 5470 1.222567 AACAGGGAAGTGTGAAGGGT 58.777 50.000 0.00 0.00 0.00 4.34
2050 5471 0.765510 ACAGGGAAGTGTGAAGGGTC 59.234 55.000 0.00 0.00 0.00 4.46
2051 5472 0.764890 CAGGGAAGTGTGAAGGGTCA 59.235 55.000 0.00 0.00 0.00 4.02
2052 5473 1.142870 CAGGGAAGTGTGAAGGGTCAA 59.857 52.381 0.00 0.00 34.87 3.18
2053 5474 1.850345 AGGGAAGTGTGAAGGGTCAAA 59.150 47.619 0.00 0.00 34.87 2.69
2054 5475 2.243736 AGGGAAGTGTGAAGGGTCAAAA 59.756 45.455 0.00 0.00 34.87 2.44
2055 5476 3.117131 AGGGAAGTGTGAAGGGTCAAAAT 60.117 43.478 0.00 0.00 34.87 1.82
2056 5477 3.005791 GGGAAGTGTGAAGGGTCAAAATG 59.994 47.826 0.00 0.00 34.87 2.32
2057 5478 3.636764 GGAAGTGTGAAGGGTCAAAATGT 59.363 43.478 0.00 0.00 34.87 2.71
2058 5479 4.825085 GGAAGTGTGAAGGGTCAAAATGTA 59.175 41.667 0.00 0.00 34.87 2.29
2059 5480 5.300792 GGAAGTGTGAAGGGTCAAAATGTAA 59.699 40.000 0.00 0.00 34.87 2.41
2060 5481 6.183360 GGAAGTGTGAAGGGTCAAAATGTAAA 60.183 38.462 0.00 0.00 34.87 2.01
2061 5482 6.976934 AGTGTGAAGGGTCAAAATGTAAAT 57.023 33.333 0.00 0.00 34.87 1.40
2062 5483 6.748132 AGTGTGAAGGGTCAAAATGTAAATG 58.252 36.000 0.00 0.00 34.87 2.32
2063 5484 5.925969 GTGTGAAGGGTCAAAATGTAAATGG 59.074 40.000 0.00 0.00 34.87 3.16
2064 5485 5.835819 TGTGAAGGGTCAAAATGTAAATGGA 59.164 36.000 0.00 0.00 34.87 3.41
2065 5486 6.325028 TGTGAAGGGTCAAAATGTAAATGGAA 59.675 34.615 0.00 0.00 34.87 3.53
2066 5487 6.868339 GTGAAGGGTCAAAATGTAAATGGAAG 59.132 38.462 0.00 0.00 34.87 3.46
2067 5488 6.014669 TGAAGGGTCAAAATGTAAATGGAAGG 60.015 38.462 0.00 0.00 0.00 3.46
2068 5489 5.402630 AGGGTCAAAATGTAAATGGAAGGT 58.597 37.500 0.00 0.00 0.00 3.50
2069 5490 5.245977 AGGGTCAAAATGTAAATGGAAGGTG 59.754 40.000 0.00 0.00 0.00 4.00
2070 5491 5.011635 GGGTCAAAATGTAAATGGAAGGTGT 59.988 40.000 0.00 0.00 0.00 4.16
2071 5492 6.209788 GGGTCAAAATGTAAATGGAAGGTGTA 59.790 38.462 0.00 0.00 0.00 2.90
2072 5493 7.093509 GGGTCAAAATGTAAATGGAAGGTGTAT 60.094 37.037 0.00 0.00 0.00 2.29
2073 5494 8.962679 GGTCAAAATGTAAATGGAAGGTGTATA 58.037 33.333 0.00 0.00 0.00 1.47
2080 5501 9.778741 ATGTAAATGGAAGGTGTATATACTGTG 57.221 33.333 13.89 0.00 0.00 3.66
2081 5502 8.983789 TGTAAATGGAAGGTGTATATACTGTGA 58.016 33.333 13.89 0.00 0.00 3.58
2082 5503 9.477484 GTAAATGGAAGGTGTATATACTGTGAG 57.523 37.037 13.89 0.00 0.00 3.51
2083 5504 6.672266 ATGGAAGGTGTATATACTGTGAGG 57.328 41.667 13.89 0.00 0.00 3.86
2084 5505 5.773091 TGGAAGGTGTATATACTGTGAGGA 58.227 41.667 13.89 0.00 0.00 3.71
2085 5506 5.833667 TGGAAGGTGTATATACTGTGAGGAG 59.166 44.000 13.89 0.00 0.00 3.69
2086 5507 5.244178 GGAAGGTGTATATACTGTGAGGAGG 59.756 48.000 13.89 0.00 0.00 4.30
2087 5508 5.664815 AGGTGTATATACTGTGAGGAGGA 57.335 43.478 13.89 0.00 0.00 3.71
2088 5509 6.027025 AGGTGTATATACTGTGAGGAGGAA 57.973 41.667 13.89 0.00 0.00 3.36
2089 5510 6.625267 AGGTGTATATACTGTGAGGAGGAAT 58.375 40.000 13.89 0.00 0.00 3.01
2090 5511 6.495181 AGGTGTATATACTGTGAGGAGGAATG 59.505 42.308 13.89 0.00 0.00 2.67
2091 5512 6.295349 GGTGTATATACTGTGAGGAGGAATGG 60.295 46.154 13.89 0.00 0.00 3.16
2092 5513 6.493802 GTGTATATACTGTGAGGAGGAATGGA 59.506 42.308 13.89 0.00 0.00 3.41
2093 5514 7.179338 GTGTATATACTGTGAGGAGGAATGGAT 59.821 40.741 13.89 0.00 0.00 3.41
2094 5515 6.865834 ATATACTGTGAGGAGGAATGGATC 57.134 41.667 0.00 0.00 0.00 3.36
2095 5516 1.759445 ACTGTGAGGAGGAATGGATCG 59.241 52.381 0.00 0.00 0.00 3.69
2096 5517 2.034878 CTGTGAGGAGGAATGGATCGA 58.965 52.381 0.00 0.00 0.00 3.59
2097 5518 2.632028 CTGTGAGGAGGAATGGATCGAT 59.368 50.000 0.00 0.00 0.00 3.59
2098 5519 2.366590 TGTGAGGAGGAATGGATCGATG 59.633 50.000 0.54 0.00 0.00 3.84
2099 5520 1.973515 TGAGGAGGAATGGATCGATGG 59.026 52.381 0.54 0.00 0.00 3.51
2100 5521 1.974236 GAGGAGGAATGGATCGATGGT 59.026 52.381 0.54 0.00 0.00 3.55
2101 5522 2.370189 GAGGAGGAATGGATCGATGGTT 59.630 50.000 0.54 0.00 0.00 3.67
2102 5523 2.105477 AGGAGGAATGGATCGATGGTTG 59.895 50.000 0.54 0.00 0.00 3.77
2103 5524 2.104792 GGAGGAATGGATCGATGGTTGA 59.895 50.000 0.54 0.00 0.00 3.18
2104 5525 3.397482 GAGGAATGGATCGATGGTTGAG 58.603 50.000 0.54 0.00 0.00 3.02
2105 5526 3.041211 AGGAATGGATCGATGGTTGAGA 58.959 45.455 0.54 0.00 0.00 3.27
2106 5527 3.649981 AGGAATGGATCGATGGTTGAGAT 59.350 43.478 0.54 0.00 0.00 2.75
2107 5528 4.103785 AGGAATGGATCGATGGTTGAGATT 59.896 41.667 0.54 0.00 0.00 2.40
2108 5529 4.453819 GGAATGGATCGATGGTTGAGATTC 59.546 45.833 0.54 0.02 0.00 2.52
2109 5530 4.970860 ATGGATCGATGGTTGAGATTCT 57.029 40.909 0.54 0.00 0.00 2.40
2110 5531 4.760530 TGGATCGATGGTTGAGATTCTT 57.239 40.909 0.54 0.00 0.00 2.52
2111 5532 4.697514 TGGATCGATGGTTGAGATTCTTC 58.302 43.478 0.54 0.00 0.00 2.87
2112 5533 4.061596 GGATCGATGGTTGAGATTCTTCC 58.938 47.826 0.54 0.00 0.00 3.46
2113 5534 4.443457 GGATCGATGGTTGAGATTCTTCCA 60.443 45.833 0.54 8.05 0.00 3.53
2114 5535 4.128925 TCGATGGTTGAGATTCTTCCAG 57.871 45.455 10.37 1.85 0.00 3.86
2115 5536 3.769300 TCGATGGTTGAGATTCTTCCAGA 59.231 43.478 10.37 3.52 0.00 3.86
2116 5537 4.222810 TCGATGGTTGAGATTCTTCCAGAA 59.777 41.667 10.37 0.00 38.78 3.02
2117 5538 4.937620 CGATGGTTGAGATTCTTCCAGAAA 59.062 41.667 10.37 0.00 37.82 2.52
2118 5539 5.587844 CGATGGTTGAGATTCTTCCAGAAAT 59.412 40.000 10.37 0.00 37.82 2.17
2119 5540 6.238320 CGATGGTTGAGATTCTTCCAGAAATC 60.238 42.308 10.37 0.00 37.82 2.17
2120 5541 6.131972 TGGTTGAGATTCTTCCAGAAATCT 57.868 37.500 0.00 0.00 37.82 2.40
2121 5542 6.176183 TGGTTGAGATTCTTCCAGAAATCTC 58.824 40.000 15.00 15.00 37.82 2.75
2122 5543 6.013032 TGGTTGAGATTCTTCCAGAAATCTCT 60.013 38.462 19.94 6.08 37.82 3.10
2123 5544 6.538381 GGTTGAGATTCTTCCAGAAATCTCTC 59.462 42.308 19.94 13.10 37.82 3.20
2124 5545 6.864151 TGAGATTCTTCCAGAAATCTCTCA 57.136 37.500 19.94 14.89 41.68 3.27
2125 5546 7.434927 TGAGATTCTTCCAGAAATCTCTCAT 57.565 36.000 19.94 0.00 40.30 2.90
2126 5547 7.499292 TGAGATTCTTCCAGAAATCTCTCATC 58.501 38.462 19.94 2.14 40.30 2.92
2127 5548 7.345132 TGAGATTCTTCCAGAAATCTCTCATCT 59.655 37.037 19.94 3.79 40.30 2.90
2128 5549 8.093118 AGATTCTTCCAGAAATCTCTCATCTT 57.907 34.615 0.00 0.00 37.82 2.40
2129 5550 8.550585 AGATTCTTCCAGAAATCTCTCATCTTT 58.449 33.333 0.00 0.00 37.82 2.52
2130 5551 9.176460 GATTCTTCCAGAAATCTCTCATCTTTT 57.824 33.333 0.00 0.00 37.82 2.27
2131 5552 8.558973 TTCTTCCAGAAATCTCTCATCTTTTC 57.441 34.615 0.00 0.00 29.99 2.29
2132 5553 7.915930 TCTTCCAGAAATCTCTCATCTTTTCT 58.084 34.615 0.00 0.00 38.58 2.52
2133 5554 8.381636 TCTTCCAGAAATCTCTCATCTTTTCTT 58.618 33.333 0.00 0.00 36.54 2.52
2134 5555 8.558973 TTCCAGAAATCTCTCATCTTTTCTTC 57.441 34.615 0.00 0.00 36.54 2.87
2135 5556 7.108847 TCCAGAAATCTCTCATCTTTTCTTCC 58.891 38.462 0.00 0.00 36.54 3.46
2136 5557 6.318396 CCAGAAATCTCTCATCTTTTCTTCCC 59.682 42.308 0.00 0.00 36.54 3.97
2137 5558 6.318396 CAGAAATCTCTCATCTTTTCTTCCCC 59.682 42.308 0.00 0.00 36.54 4.81
2138 5559 4.787135 ATCTCTCATCTTTTCTTCCCCC 57.213 45.455 0.00 0.00 0.00 5.40
2139 5560 3.808189 TCTCTCATCTTTTCTTCCCCCT 58.192 45.455 0.00 0.00 0.00 4.79
2140 5561 4.179133 TCTCTCATCTTTTCTTCCCCCTT 58.821 43.478 0.00 0.00 0.00 3.95
2141 5562 4.226168 TCTCTCATCTTTTCTTCCCCCTTC 59.774 45.833 0.00 0.00 0.00 3.46
2142 5563 3.267031 TCTCATCTTTTCTTCCCCCTTCC 59.733 47.826 0.00 0.00 0.00 3.46
2143 5564 2.311841 TCATCTTTTCTTCCCCCTTCCC 59.688 50.000 0.00 0.00 0.00 3.97
2144 5565 1.081481 TCTTTTCTTCCCCCTTCCCC 58.919 55.000 0.00 0.00 0.00 4.81
2145 5566 1.084866 CTTTTCTTCCCCCTTCCCCT 58.915 55.000 0.00 0.00 0.00 4.79
2146 5567 0.783850 TTTTCTTCCCCCTTCCCCTG 59.216 55.000 0.00 0.00 0.00 4.45
2147 5568 0.404346 TTTCTTCCCCCTTCCCCTGT 60.404 55.000 0.00 0.00 0.00 4.00
2148 5569 0.499147 TTCTTCCCCCTTCCCCTGTA 59.501 55.000 0.00 0.00 0.00 2.74
2149 5570 0.044244 TCTTCCCCCTTCCCCTGTAG 59.956 60.000 0.00 0.00 0.00 2.74
2150 5571 1.618447 TTCCCCCTTCCCCTGTAGC 60.618 63.158 0.00 0.00 0.00 3.58
2151 5572 2.042930 CCCCCTTCCCCTGTAGCT 59.957 66.667 0.00 0.00 0.00 3.32
2152 5573 1.619669 CCCCCTTCCCCTGTAGCTT 60.620 63.158 0.00 0.00 0.00 3.74
2153 5574 1.214992 CCCCCTTCCCCTGTAGCTTT 61.215 60.000 0.00 0.00 0.00 3.51
2154 5575 0.034089 CCCCTTCCCCTGTAGCTTTG 60.034 60.000 0.00 0.00 0.00 2.77
2155 5576 0.681243 CCCTTCCCCTGTAGCTTTGC 60.681 60.000 0.00 0.00 0.00 3.68
2156 5577 0.329596 CCTTCCCCTGTAGCTTTGCT 59.670 55.000 0.00 0.00 43.41 3.91
2157 5578 1.457346 CTTCCCCTGTAGCTTTGCTG 58.543 55.000 0.00 0.00 40.10 4.41
2158 5579 0.038166 TTCCCCTGTAGCTTTGCTGG 59.962 55.000 0.00 0.00 40.10 4.85
2159 5580 0.840288 TCCCCTGTAGCTTTGCTGGA 60.840 55.000 0.00 0.00 40.10 3.86
2160 5581 0.393537 CCCCTGTAGCTTTGCTGGAG 60.394 60.000 0.00 0.00 40.10 3.86
2161 5582 0.615331 CCCTGTAGCTTTGCTGGAGA 59.385 55.000 0.00 0.00 40.10 3.71
2162 5583 1.003580 CCCTGTAGCTTTGCTGGAGAA 59.996 52.381 0.00 0.00 40.10 2.87
2163 5584 2.354259 CCTGTAGCTTTGCTGGAGAAG 58.646 52.381 0.00 0.00 40.10 2.85
2164 5585 2.289945 CCTGTAGCTTTGCTGGAGAAGT 60.290 50.000 0.00 0.00 40.10 3.01
2165 5586 2.740981 CTGTAGCTTTGCTGGAGAAGTG 59.259 50.000 0.00 0.00 40.10 3.16
2166 5587 2.368548 TGTAGCTTTGCTGGAGAAGTGA 59.631 45.455 0.00 0.00 40.10 3.41
2167 5588 2.181954 AGCTTTGCTGGAGAAGTGAG 57.818 50.000 0.00 0.00 37.57 3.51
2168 5589 1.696336 AGCTTTGCTGGAGAAGTGAGA 59.304 47.619 0.00 0.00 37.57 3.27
2169 5590 2.305343 AGCTTTGCTGGAGAAGTGAGAT 59.695 45.455 0.00 0.00 37.57 2.75
2170 5591 2.677337 GCTTTGCTGGAGAAGTGAGATC 59.323 50.000 0.00 0.00 0.00 2.75
2171 5592 3.867600 GCTTTGCTGGAGAAGTGAGATCA 60.868 47.826 0.00 0.00 0.00 2.92
2172 5593 4.321718 CTTTGCTGGAGAAGTGAGATCAA 58.678 43.478 0.00 0.00 0.00 2.57
2173 5594 3.325293 TGCTGGAGAAGTGAGATCAAC 57.675 47.619 0.00 0.00 0.00 3.18
2174 5595 2.027745 TGCTGGAGAAGTGAGATCAACC 60.028 50.000 0.00 0.00 0.00 3.77
2175 5596 2.027745 GCTGGAGAAGTGAGATCAACCA 60.028 50.000 0.00 0.00 0.00 3.67
2176 5597 3.557898 GCTGGAGAAGTGAGATCAACCAA 60.558 47.826 0.00 0.00 0.00 3.67
2177 5598 4.645535 CTGGAGAAGTGAGATCAACCAAA 58.354 43.478 0.00 0.00 0.00 3.28
2178 5599 5.047566 TGGAGAAGTGAGATCAACCAAAA 57.952 39.130 0.00 0.00 0.00 2.44
2179 5600 5.065914 TGGAGAAGTGAGATCAACCAAAAG 58.934 41.667 0.00 0.00 0.00 2.27
2180 5601 4.457257 GGAGAAGTGAGATCAACCAAAAGG 59.543 45.833 0.00 0.00 0.00 3.11
2181 5602 3.823304 AGAAGTGAGATCAACCAAAAGGC 59.177 43.478 0.00 0.00 0.00 4.35
2182 5603 3.515602 AGTGAGATCAACCAAAAGGCT 57.484 42.857 0.00 0.00 0.00 4.58
2183 5604 4.640771 AGTGAGATCAACCAAAAGGCTA 57.359 40.909 0.00 0.00 0.00 3.93
2184 5605 4.583871 AGTGAGATCAACCAAAAGGCTAG 58.416 43.478 0.00 0.00 0.00 3.42
2185 5606 4.287067 AGTGAGATCAACCAAAAGGCTAGA 59.713 41.667 0.00 0.00 0.00 2.43
2186 5607 4.393371 GTGAGATCAACCAAAAGGCTAGAC 59.607 45.833 0.00 0.00 0.00 2.59
2187 5608 4.041567 TGAGATCAACCAAAAGGCTAGACA 59.958 41.667 0.00 0.00 0.00 3.41
2188 5609 4.985538 AGATCAACCAAAAGGCTAGACAA 58.014 39.130 0.00 0.00 0.00 3.18
2189 5610 4.762251 AGATCAACCAAAAGGCTAGACAAC 59.238 41.667 0.00 0.00 0.00 3.32
2190 5611 3.892284 TCAACCAAAAGGCTAGACAACA 58.108 40.909 0.00 0.00 0.00 3.33
2191 5612 4.469657 TCAACCAAAAGGCTAGACAACAT 58.530 39.130 0.00 0.00 0.00 2.71
2192 5613 4.278170 TCAACCAAAAGGCTAGACAACATG 59.722 41.667 0.00 0.00 0.00 3.21
2193 5614 3.157087 ACCAAAAGGCTAGACAACATGG 58.843 45.455 0.00 3.13 0.00 3.66
2194 5615 3.157087 CCAAAAGGCTAGACAACATGGT 58.843 45.455 0.00 0.00 0.00 3.55
2195 5616 3.057315 CCAAAAGGCTAGACAACATGGTG 60.057 47.826 9.83 9.83 0.00 4.17
2196 5617 3.508845 AAAGGCTAGACAACATGGTGT 57.491 42.857 18.31 18.31 0.00 4.16
2197 5618 2.770164 AGGCTAGACAACATGGTGTC 57.230 50.000 32.32 32.32 46.90 3.67
2203 5624 1.882912 GACAACATGGTGTCAGAGCA 58.117 50.000 33.85 0.00 46.00 4.26
2204 5625 2.430465 GACAACATGGTGTCAGAGCAT 58.570 47.619 33.85 2.16 46.00 3.79
2209 5630 1.283347 ATGGTGTCAGAGCATGAGGT 58.717 50.000 0.00 0.00 41.38 3.85
2210 5631 0.322648 TGGTGTCAGAGCATGAGGTG 59.677 55.000 0.00 0.00 39.07 4.00
2211 5632 0.392193 GGTGTCAGAGCATGAGGTGG 60.392 60.000 0.00 0.00 39.07 4.61
2212 5633 0.610174 GTGTCAGAGCATGAGGTGGA 59.390 55.000 0.00 0.00 39.07 4.02
2213 5634 0.900421 TGTCAGAGCATGAGGTGGAG 59.100 55.000 0.00 0.00 39.07 3.86
2214 5635 0.177604 GTCAGAGCATGAGGTGGAGG 59.822 60.000 0.00 0.00 39.07 4.30
2215 5636 1.153208 CAGAGCATGAGGTGGAGGC 60.153 63.158 0.00 0.00 0.00 4.70
2216 5637 2.202987 GAGCATGAGGTGGAGGCG 60.203 66.667 0.00 0.00 0.00 5.52
2217 5638 4.479993 AGCATGAGGTGGAGGCGC 62.480 66.667 0.00 0.00 0.00 6.53
2218 5639 4.479993 GCATGAGGTGGAGGCGCT 62.480 66.667 7.64 0.00 0.00 5.92
2219 5640 2.513204 CATGAGGTGGAGGCGCTG 60.513 66.667 7.64 0.00 0.00 5.18
2220 5641 3.005539 ATGAGGTGGAGGCGCTGT 61.006 61.111 7.64 0.00 0.00 4.40
2221 5642 2.596851 ATGAGGTGGAGGCGCTGTT 61.597 57.895 7.64 0.00 0.00 3.16
2222 5643 2.032681 GAGGTGGAGGCGCTGTTT 59.967 61.111 7.64 0.00 0.00 2.83
2223 5644 2.281761 AGGTGGAGGCGCTGTTTG 60.282 61.111 7.64 0.00 0.00 2.93
2224 5645 2.281484 GGTGGAGGCGCTGTTTGA 60.281 61.111 7.64 0.00 0.00 2.69
2225 5646 2.617274 GGTGGAGGCGCTGTTTGAC 61.617 63.158 7.64 0.00 0.00 3.18
2226 5647 2.281484 TGGAGGCGCTGTTTGACC 60.281 61.111 7.64 1.36 0.00 4.02
2227 5648 3.056328 GGAGGCGCTGTTTGACCC 61.056 66.667 7.64 0.00 0.00 4.46
2228 5649 2.032681 GAGGCGCTGTTTGACCCT 59.967 61.111 7.64 0.00 0.00 4.34
2229 5650 2.032681 AGGCGCTGTTTGACCCTC 59.967 61.111 7.64 0.00 0.00 4.30
2230 5651 3.423154 GGCGCTGTTTGACCCTCG 61.423 66.667 7.64 0.00 0.00 4.63
2231 5652 4.090057 GCGCTGTTTGACCCTCGC 62.090 66.667 0.00 0.00 35.82 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 2.230992 ACAACAAAGTCAACAGCAGCAA 59.769 40.909 0.00 0.00 0.00 3.91
404 465 9.009327 CATAATCAATTGAATTCCGTACAACAC 57.991 33.333 13.09 0.00 0.00 3.32
586 647 3.374058 GCATAATTCACTACTGCAACCGT 59.626 43.478 0.00 0.00 33.13 4.83
803 864 5.209818 TCACTAACATCGGACAGAACTTT 57.790 39.130 0.00 0.00 0.00 2.66
972 1035 3.194755 CCCCCAAAAATTACCTCCTTTCG 59.805 47.826 0.00 0.00 0.00 3.46
1090 1153 4.862902 TCCGATGAAAAATCCTTTTGCA 57.137 36.364 0.00 0.00 42.15 4.08
1091 1154 5.925969 TCTTTCCGATGAAAAATCCTTTTGC 59.074 36.000 0.00 0.00 39.88 3.68
1097 1160 4.944317 AGACCTCTTTCCGATGAAAAATCC 59.056 41.667 0.00 0.00 39.88 3.01
1160 1223 6.422776 ACGTACTCTATTTTTCATTGCCAG 57.577 37.500 0.00 0.00 0.00 4.85
1214 1277 3.091545 GACATCAGCAATTTCCTTCCCA 58.908 45.455 0.00 0.00 0.00 4.37
1333 1648 0.324285 CTGCCTCTCAGCTTTCCACT 59.676 55.000 0.00 0.00 35.78 4.00
1425 1747 2.605837 TGCTGTGACCGTTAAGTTGA 57.394 45.000 0.00 0.00 0.00 3.18
1426 1748 3.554524 CAATGCTGTGACCGTTAAGTTG 58.445 45.455 0.00 0.00 0.00 3.16
1439 1761 1.335872 GGCGTTAGTTTGCAATGCTGT 60.336 47.619 6.82 0.00 37.89 4.40
1561 1883 2.170012 TTCGGTGGCTTATACTCCCT 57.830 50.000 0.00 0.00 0.00 4.20
1670 4949 6.706270 CCAGCAAGGTACCATATACAGTAAAG 59.294 42.308 15.94 0.00 0.00 1.85
1983 5404 3.070446 CCTGTAACTCACACCCTACAACA 59.930 47.826 0.00 0.00 32.33 3.33
1984 5405 3.322828 TCCTGTAACTCACACCCTACAAC 59.677 47.826 0.00 0.00 32.33 3.32
1985 5406 3.576982 CTCCTGTAACTCACACCCTACAA 59.423 47.826 0.00 0.00 32.33 2.41
1986 5407 3.162666 CTCCTGTAACTCACACCCTACA 58.837 50.000 0.00 0.00 32.33 2.74
1987 5408 3.056749 CACTCCTGTAACTCACACCCTAC 60.057 52.174 0.00 0.00 32.33 3.18
1988 5409 3.162666 CACTCCTGTAACTCACACCCTA 58.837 50.000 0.00 0.00 32.33 3.53
1989 5410 1.971357 CACTCCTGTAACTCACACCCT 59.029 52.381 0.00 0.00 32.33 4.34
1990 5411 1.692519 ACACTCCTGTAACTCACACCC 59.307 52.381 0.00 0.00 32.33 4.61
1991 5412 3.131396 CAACACTCCTGTAACTCACACC 58.869 50.000 0.00 0.00 32.33 4.16
1992 5413 3.793559 ACAACACTCCTGTAACTCACAC 58.206 45.455 0.00 0.00 32.33 3.82
1993 5414 4.038763 CCTACAACACTCCTGTAACTCACA 59.961 45.833 0.00 0.00 35.30 3.58
1994 5415 4.557205 CCTACAACACTCCTGTAACTCAC 58.443 47.826 0.00 0.00 0.00 3.51
1995 5416 3.576982 CCCTACAACACTCCTGTAACTCA 59.423 47.826 0.00 0.00 0.00 3.41
1996 5417 3.577415 ACCCTACAACACTCCTGTAACTC 59.423 47.826 0.00 0.00 0.00 3.01
1997 5418 3.323979 CACCCTACAACACTCCTGTAACT 59.676 47.826 0.00 0.00 0.00 2.24
1998 5419 3.070590 ACACCCTACAACACTCCTGTAAC 59.929 47.826 0.00 0.00 0.00 2.50
1999 5420 3.070446 CACACCCTACAACACTCCTGTAA 59.930 47.826 0.00 0.00 0.00 2.41
2000 5421 2.631062 CACACCCTACAACACTCCTGTA 59.369 50.000 0.00 0.00 0.00 2.74
2001 5422 1.416401 CACACCCTACAACACTCCTGT 59.584 52.381 0.00 0.00 0.00 4.00
2002 5423 1.691976 TCACACCCTACAACACTCCTG 59.308 52.381 0.00 0.00 0.00 3.86
2003 5424 1.971357 CTCACACCCTACAACACTCCT 59.029 52.381 0.00 0.00 0.00 3.69
2004 5425 1.692519 ACTCACACCCTACAACACTCC 59.307 52.381 0.00 0.00 0.00 3.85
2005 5426 3.131396 CAACTCACACCCTACAACACTC 58.869 50.000 0.00 0.00 0.00 3.51
2006 5427 2.745152 GCAACTCACACCCTACAACACT 60.745 50.000 0.00 0.00 0.00 3.55
2007 5428 1.602377 GCAACTCACACCCTACAACAC 59.398 52.381 0.00 0.00 0.00 3.32
2008 5429 1.210722 TGCAACTCACACCCTACAACA 59.789 47.619 0.00 0.00 0.00 3.33
2009 5430 1.961793 TGCAACTCACACCCTACAAC 58.038 50.000 0.00 0.00 0.00 3.32
2010 5431 2.719531 TTGCAACTCACACCCTACAA 57.280 45.000 0.00 0.00 0.00 2.41
2011 5432 2.685897 GTTTTGCAACTCACACCCTACA 59.314 45.455 0.00 0.00 0.00 2.74
2012 5433 2.685897 TGTTTTGCAACTCACACCCTAC 59.314 45.455 0.00 0.00 33.58 3.18
2013 5434 2.948979 CTGTTTTGCAACTCACACCCTA 59.051 45.455 0.00 0.00 33.58 3.53
2014 5435 1.750778 CTGTTTTGCAACTCACACCCT 59.249 47.619 0.00 0.00 33.58 4.34
2015 5436 1.202405 CCTGTTTTGCAACTCACACCC 60.202 52.381 0.00 0.00 33.58 4.61
2016 5437 1.202405 CCCTGTTTTGCAACTCACACC 60.202 52.381 0.00 0.00 33.58 4.16
2017 5438 1.748493 TCCCTGTTTTGCAACTCACAC 59.252 47.619 0.00 0.00 33.58 3.82
2018 5439 2.136298 TCCCTGTTTTGCAACTCACA 57.864 45.000 0.00 1.62 33.58 3.58
2019 5440 2.427095 ACTTCCCTGTTTTGCAACTCAC 59.573 45.455 0.00 0.00 33.58 3.51
2020 5441 2.426738 CACTTCCCTGTTTTGCAACTCA 59.573 45.455 0.00 0.13 33.58 3.41
2021 5442 2.427095 ACACTTCCCTGTTTTGCAACTC 59.573 45.455 0.00 0.00 33.58 3.01
2022 5443 2.166254 CACACTTCCCTGTTTTGCAACT 59.834 45.455 0.00 0.00 33.58 3.16
2023 5444 2.165437 TCACACTTCCCTGTTTTGCAAC 59.835 45.455 0.00 0.00 0.00 4.17
2024 5445 2.451490 TCACACTTCCCTGTTTTGCAA 58.549 42.857 0.00 0.00 0.00 4.08
2025 5446 2.136298 TCACACTTCCCTGTTTTGCA 57.864 45.000 0.00 0.00 0.00 4.08
2026 5447 2.223805 CCTTCACACTTCCCTGTTTTGC 60.224 50.000 0.00 0.00 0.00 3.68
2027 5448 2.362077 CCCTTCACACTTCCCTGTTTTG 59.638 50.000 0.00 0.00 0.00 2.44
2028 5449 2.024369 ACCCTTCACACTTCCCTGTTTT 60.024 45.455 0.00 0.00 0.00 2.43
2029 5450 1.569072 ACCCTTCACACTTCCCTGTTT 59.431 47.619 0.00 0.00 0.00 2.83
2030 5451 1.143073 GACCCTTCACACTTCCCTGTT 59.857 52.381 0.00 0.00 0.00 3.16
2031 5452 0.765510 GACCCTTCACACTTCCCTGT 59.234 55.000 0.00 0.00 0.00 4.00
2032 5453 0.764890 TGACCCTTCACACTTCCCTG 59.235 55.000 0.00 0.00 0.00 4.45
2033 5454 1.518367 TTGACCCTTCACACTTCCCT 58.482 50.000 0.00 0.00 0.00 4.20
2034 5455 2.358322 TTTGACCCTTCACACTTCCC 57.642 50.000 0.00 0.00 0.00 3.97
2035 5456 3.636764 ACATTTTGACCCTTCACACTTCC 59.363 43.478 0.00 0.00 0.00 3.46
2036 5457 4.918810 ACATTTTGACCCTTCACACTTC 57.081 40.909 0.00 0.00 0.00 3.01
2037 5458 6.783708 TTTACATTTTGACCCTTCACACTT 57.216 33.333 0.00 0.00 0.00 3.16
2038 5459 6.239289 CCATTTACATTTTGACCCTTCACACT 60.239 38.462 0.00 0.00 0.00 3.55
2039 5460 5.925969 CCATTTACATTTTGACCCTTCACAC 59.074 40.000 0.00 0.00 0.00 3.82
2040 5461 5.835819 TCCATTTACATTTTGACCCTTCACA 59.164 36.000 0.00 0.00 0.00 3.58
2041 5462 6.339587 TCCATTTACATTTTGACCCTTCAC 57.660 37.500 0.00 0.00 0.00 3.18
2042 5463 6.014669 CCTTCCATTTACATTTTGACCCTTCA 60.015 38.462 0.00 0.00 0.00 3.02
2043 5464 6.014584 ACCTTCCATTTACATTTTGACCCTTC 60.015 38.462 0.00 0.00 0.00 3.46
2044 5465 5.843969 ACCTTCCATTTACATTTTGACCCTT 59.156 36.000 0.00 0.00 0.00 3.95
2045 5466 5.245977 CACCTTCCATTTACATTTTGACCCT 59.754 40.000 0.00 0.00 0.00 4.34
2046 5467 5.011635 ACACCTTCCATTTACATTTTGACCC 59.988 40.000 0.00 0.00 0.00 4.46
2047 5468 6.096673 ACACCTTCCATTTACATTTTGACC 57.903 37.500 0.00 0.00 0.00 4.02
2054 5475 9.778741 CACAGTATATACACCTTCCATTTACAT 57.221 33.333 15.18 0.00 0.00 2.29
2055 5476 8.983789 TCACAGTATATACACCTTCCATTTACA 58.016 33.333 15.18 0.00 0.00 2.41
2056 5477 9.477484 CTCACAGTATATACACCTTCCATTTAC 57.523 37.037 15.18 0.00 0.00 2.01
2057 5478 8.647796 CCTCACAGTATATACACCTTCCATTTA 58.352 37.037 15.18 0.00 0.00 1.40
2058 5479 7.347222 TCCTCACAGTATATACACCTTCCATTT 59.653 37.037 15.18 0.00 0.00 2.32
2059 5480 6.844388 TCCTCACAGTATATACACCTTCCATT 59.156 38.462 15.18 0.00 0.00 3.16
2060 5481 6.382087 TCCTCACAGTATATACACCTTCCAT 58.618 40.000 15.18 0.00 0.00 3.41
2061 5482 5.773091 TCCTCACAGTATATACACCTTCCA 58.227 41.667 15.18 0.00 0.00 3.53
2062 5483 5.244178 CCTCCTCACAGTATATACACCTTCC 59.756 48.000 15.18 0.00 0.00 3.46
2063 5484 6.069331 TCCTCCTCACAGTATATACACCTTC 58.931 44.000 15.18 0.00 0.00 3.46
2064 5485 6.027025 TCCTCCTCACAGTATATACACCTT 57.973 41.667 15.18 0.00 0.00 3.50
2065 5486 5.664815 TCCTCCTCACAGTATATACACCT 57.335 43.478 15.18 0.00 0.00 4.00
2066 5487 6.295349 CCATTCCTCCTCACAGTATATACACC 60.295 46.154 15.18 0.00 0.00 4.16
2067 5488 6.493802 TCCATTCCTCCTCACAGTATATACAC 59.506 42.308 15.18 0.00 0.00 2.90
2068 5489 6.620429 TCCATTCCTCCTCACAGTATATACA 58.380 40.000 15.18 0.00 0.00 2.29
2069 5490 7.415765 CGATCCATTCCTCCTCACAGTATATAC 60.416 44.444 4.60 4.60 0.00 1.47
2070 5491 6.603599 CGATCCATTCCTCCTCACAGTATATA 59.396 42.308 0.00 0.00 0.00 0.86
2071 5492 5.420421 CGATCCATTCCTCCTCACAGTATAT 59.580 44.000 0.00 0.00 0.00 0.86
2072 5493 4.767409 CGATCCATTCCTCCTCACAGTATA 59.233 45.833 0.00 0.00 0.00 1.47
2073 5494 3.576118 CGATCCATTCCTCCTCACAGTAT 59.424 47.826 0.00 0.00 0.00 2.12
2074 5495 2.959030 CGATCCATTCCTCCTCACAGTA 59.041 50.000 0.00 0.00 0.00 2.74
2075 5496 1.759445 CGATCCATTCCTCCTCACAGT 59.241 52.381 0.00 0.00 0.00 3.55
2076 5497 2.034878 TCGATCCATTCCTCCTCACAG 58.965 52.381 0.00 0.00 0.00 3.66
2077 5498 2.159179 TCGATCCATTCCTCCTCACA 57.841 50.000 0.00 0.00 0.00 3.58
2078 5499 2.289320 CCATCGATCCATTCCTCCTCAC 60.289 54.545 0.00 0.00 0.00 3.51
2079 5500 1.973515 CCATCGATCCATTCCTCCTCA 59.026 52.381 0.00 0.00 0.00 3.86
2080 5501 1.974236 ACCATCGATCCATTCCTCCTC 59.026 52.381 0.00 0.00 0.00 3.71
2081 5502 2.105477 CAACCATCGATCCATTCCTCCT 59.895 50.000 0.00 0.00 0.00 3.69
2082 5503 2.104792 TCAACCATCGATCCATTCCTCC 59.895 50.000 0.00 0.00 0.00 4.30
2083 5504 3.070159 TCTCAACCATCGATCCATTCCTC 59.930 47.826 0.00 0.00 0.00 3.71
2084 5505 3.041211 TCTCAACCATCGATCCATTCCT 58.959 45.455 0.00 0.00 0.00 3.36
2085 5506 3.475566 TCTCAACCATCGATCCATTCC 57.524 47.619 0.00 0.00 0.00 3.01
2086 5507 5.303971 AGAATCTCAACCATCGATCCATTC 58.696 41.667 0.00 0.00 0.00 2.67
2087 5508 5.301835 AGAATCTCAACCATCGATCCATT 57.698 39.130 0.00 0.00 0.00 3.16
2088 5509 4.970860 AGAATCTCAACCATCGATCCAT 57.029 40.909 0.00 0.00 0.00 3.41
2089 5510 4.443457 GGAAGAATCTCAACCATCGATCCA 60.443 45.833 0.00 0.00 0.00 3.41
2090 5511 4.061596 GGAAGAATCTCAACCATCGATCC 58.938 47.826 0.00 0.00 0.00 3.36
2091 5512 4.697514 TGGAAGAATCTCAACCATCGATC 58.302 43.478 0.00 0.00 0.00 3.69
2092 5513 4.406972 TCTGGAAGAATCTCAACCATCGAT 59.593 41.667 0.00 0.00 42.31 3.59
2093 5514 3.769300 TCTGGAAGAATCTCAACCATCGA 59.231 43.478 0.00 0.00 42.31 3.59
2094 5515 4.128925 TCTGGAAGAATCTCAACCATCG 57.871 45.455 4.76 0.00 42.31 3.84
2107 5528 7.915930 AGAAAAGATGAGAGATTTCTGGAAGA 58.084 34.615 0.00 0.00 44.68 2.87
2108 5529 8.564509 AAGAAAAGATGAGAGATTTCTGGAAG 57.435 34.615 0.00 0.00 40.28 3.46
2109 5530 7.609532 GGAAGAAAAGATGAGAGATTTCTGGAA 59.390 37.037 0.00 0.00 40.28 3.53
2110 5531 7.108847 GGAAGAAAAGATGAGAGATTTCTGGA 58.891 38.462 0.00 0.00 40.28 3.86
2111 5532 6.318396 GGGAAGAAAAGATGAGAGATTTCTGG 59.682 42.308 0.00 0.00 40.28 3.86
2112 5533 6.318396 GGGGAAGAAAAGATGAGAGATTTCTG 59.682 42.308 0.00 0.00 40.28 3.02
2113 5534 6.422333 GGGGAAGAAAAGATGAGAGATTTCT 58.578 40.000 0.00 0.00 42.30 2.52
2114 5535 5.592282 GGGGGAAGAAAAGATGAGAGATTTC 59.408 44.000 0.00 0.00 33.13 2.17
2115 5536 5.254972 AGGGGGAAGAAAAGATGAGAGATTT 59.745 40.000 0.00 0.00 0.00 2.17
2116 5537 4.792972 AGGGGGAAGAAAAGATGAGAGATT 59.207 41.667 0.00 0.00 0.00 2.40
2117 5538 4.378961 AGGGGGAAGAAAAGATGAGAGAT 58.621 43.478 0.00 0.00 0.00 2.75
2118 5539 3.808189 AGGGGGAAGAAAAGATGAGAGA 58.192 45.455 0.00 0.00 0.00 3.10
2119 5540 4.522114 GAAGGGGGAAGAAAAGATGAGAG 58.478 47.826 0.00 0.00 0.00 3.20
2120 5541 3.267031 GGAAGGGGGAAGAAAAGATGAGA 59.733 47.826 0.00 0.00 0.00 3.27
2121 5542 3.625853 GGAAGGGGGAAGAAAAGATGAG 58.374 50.000 0.00 0.00 0.00 2.90
2122 5543 2.311841 GGGAAGGGGGAAGAAAAGATGA 59.688 50.000 0.00 0.00 0.00 2.92
2123 5544 2.624293 GGGGAAGGGGGAAGAAAAGATG 60.624 54.545 0.00 0.00 0.00 2.90
2124 5545 1.646447 GGGGAAGGGGGAAGAAAAGAT 59.354 52.381 0.00 0.00 0.00 2.40
2125 5546 1.081481 GGGGAAGGGGGAAGAAAAGA 58.919 55.000 0.00 0.00 0.00 2.52
2126 5547 1.084866 AGGGGAAGGGGGAAGAAAAG 58.915 55.000 0.00 0.00 0.00 2.27
2127 5548 0.783850 CAGGGGAAGGGGGAAGAAAA 59.216 55.000 0.00 0.00 0.00 2.29
2128 5549 0.404346 ACAGGGGAAGGGGGAAGAAA 60.404 55.000 0.00 0.00 0.00 2.52
2129 5550 0.499147 TACAGGGGAAGGGGGAAGAA 59.501 55.000 0.00 0.00 0.00 2.52
2130 5551 0.044244 CTACAGGGGAAGGGGGAAGA 59.956 60.000 0.00 0.00 0.00 2.87
2131 5552 1.636769 GCTACAGGGGAAGGGGGAAG 61.637 65.000 0.00 0.00 0.00 3.46
2132 5553 1.618447 GCTACAGGGGAAGGGGGAA 60.618 63.158 0.00 0.00 0.00 3.97
2133 5554 2.042261 GCTACAGGGGAAGGGGGA 59.958 66.667 0.00 0.00 0.00 4.81
2134 5555 1.214992 AAAGCTACAGGGGAAGGGGG 61.215 60.000 0.00 0.00 0.00 5.40
2135 5556 0.034089 CAAAGCTACAGGGGAAGGGG 60.034 60.000 0.00 0.00 0.00 4.79
2136 5557 0.681243 GCAAAGCTACAGGGGAAGGG 60.681 60.000 0.00 0.00 0.00 3.95
2137 5558 0.329596 AGCAAAGCTACAGGGGAAGG 59.670 55.000 0.00 0.00 36.99 3.46
2138 5559 1.457346 CAGCAAAGCTACAGGGGAAG 58.543 55.000 0.00 0.00 36.40 3.46
2139 5560 0.038166 CCAGCAAAGCTACAGGGGAA 59.962 55.000 0.00 0.00 36.40 3.97
2140 5561 0.840288 TCCAGCAAAGCTACAGGGGA 60.840 55.000 0.00 0.00 36.40 4.81
2141 5562 0.393537 CTCCAGCAAAGCTACAGGGG 60.394 60.000 0.00 0.00 36.40 4.79
2142 5563 0.615331 TCTCCAGCAAAGCTACAGGG 59.385 55.000 0.00 0.00 36.40 4.45
2143 5564 2.289945 ACTTCTCCAGCAAAGCTACAGG 60.290 50.000 0.00 0.00 36.40 4.00
2144 5565 2.740981 CACTTCTCCAGCAAAGCTACAG 59.259 50.000 0.00 0.00 36.40 2.74
2145 5566 2.368548 TCACTTCTCCAGCAAAGCTACA 59.631 45.455 0.00 0.00 36.40 2.74
2146 5567 2.999355 CTCACTTCTCCAGCAAAGCTAC 59.001 50.000 0.00 0.00 36.40 3.58
2147 5568 2.899900 TCTCACTTCTCCAGCAAAGCTA 59.100 45.455 0.00 0.00 36.40 3.32
2148 5569 1.696336 TCTCACTTCTCCAGCAAAGCT 59.304 47.619 0.00 0.00 40.77 3.74
2149 5570 2.175878 TCTCACTTCTCCAGCAAAGC 57.824 50.000 0.00 0.00 0.00 3.51
2150 5571 3.935315 TGATCTCACTTCTCCAGCAAAG 58.065 45.455 0.00 0.00 0.00 2.77
2151 5572 4.067896 GTTGATCTCACTTCTCCAGCAAA 58.932 43.478 0.00 0.00 0.00 3.68
2152 5573 3.557898 GGTTGATCTCACTTCTCCAGCAA 60.558 47.826 0.00 0.00 0.00 3.91
2153 5574 2.027745 GGTTGATCTCACTTCTCCAGCA 60.028 50.000 0.00 0.00 0.00 4.41
2154 5575 2.027745 TGGTTGATCTCACTTCTCCAGC 60.028 50.000 0.00 0.00 0.00 4.85
2155 5576 3.969287 TGGTTGATCTCACTTCTCCAG 57.031 47.619 0.00 0.00 0.00 3.86
2156 5577 4.705110 TTTGGTTGATCTCACTTCTCCA 57.295 40.909 0.00 0.00 0.00 3.86
2157 5578 4.457257 CCTTTTGGTTGATCTCACTTCTCC 59.543 45.833 0.00 0.00 34.07 3.71
2158 5579 4.083057 GCCTTTTGGTTGATCTCACTTCTC 60.083 45.833 0.00 0.00 42.99 2.87
2159 5580 3.823304 GCCTTTTGGTTGATCTCACTTCT 59.177 43.478 0.00 0.00 42.99 2.85
2160 5581 3.823304 AGCCTTTTGGTTGATCTCACTTC 59.177 43.478 0.00 0.00 42.99 3.01
2161 5582 3.837355 AGCCTTTTGGTTGATCTCACTT 58.163 40.909 0.00 0.00 42.99 3.16
2162 5583 3.515602 AGCCTTTTGGTTGATCTCACT 57.484 42.857 0.00 0.00 42.99 3.41
2163 5584 4.393371 GTCTAGCCTTTTGGTTGATCTCAC 59.607 45.833 0.00 0.00 42.99 3.51
2164 5585 4.041567 TGTCTAGCCTTTTGGTTGATCTCA 59.958 41.667 0.00 0.00 42.99 3.27
2165 5586 4.579869 TGTCTAGCCTTTTGGTTGATCTC 58.420 43.478 0.00 0.00 42.99 2.75
2166 5587 4.640771 TGTCTAGCCTTTTGGTTGATCT 57.359 40.909 0.00 0.00 42.99 2.75
2167 5588 4.518970 TGTTGTCTAGCCTTTTGGTTGATC 59.481 41.667 0.00 0.00 42.99 2.92
2168 5589 4.469657 TGTTGTCTAGCCTTTTGGTTGAT 58.530 39.130 0.00 0.00 42.99 2.57
2169 5590 3.892284 TGTTGTCTAGCCTTTTGGTTGA 58.108 40.909 0.00 0.00 42.99 3.18
2170 5591 4.549458 CATGTTGTCTAGCCTTTTGGTTG 58.451 43.478 0.00 0.00 42.99 3.77
2171 5592 3.573967 CCATGTTGTCTAGCCTTTTGGTT 59.426 43.478 0.00 0.00 42.99 3.67
2172 5593 3.157087 CCATGTTGTCTAGCCTTTTGGT 58.843 45.455 0.00 0.00 42.99 3.67
2173 5594 3.057315 CACCATGTTGTCTAGCCTTTTGG 60.057 47.826 0.00 0.00 44.18 3.28
2174 5595 3.569701 ACACCATGTTGTCTAGCCTTTTG 59.430 43.478 0.00 0.00 0.00 2.44
2175 5596 3.821033 GACACCATGTTGTCTAGCCTTTT 59.179 43.478 15.53 0.00 42.36 2.27
2176 5597 3.181445 TGACACCATGTTGTCTAGCCTTT 60.181 43.478 22.08 0.00 45.34 3.11
2177 5598 2.371841 TGACACCATGTTGTCTAGCCTT 59.628 45.455 22.08 0.00 45.34 4.35
2178 5599 1.977854 TGACACCATGTTGTCTAGCCT 59.022 47.619 22.08 0.00 45.34 4.58
2179 5600 2.028112 TCTGACACCATGTTGTCTAGCC 60.028 50.000 22.08 0.00 45.34 3.93
2180 5601 3.257393 CTCTGACACCATGTTGTCTAGC 58.743 50.000 22.08 0.00 45.34 3.42
2181 5602 3.257393 GCTCTGACACCATGTTGTCTAG 58.743 50.000 22.08 18.96 45.34 2.43
2182 5603 2.632512 TGCTCTGACACCATGTTGTCTA 59.367 45.455 22.08 10.88 45.34 2.59
2183 5604 1.417517 TGCTCTGACACCATGTTGTCT 59.582 47.619 22.08 0.00 45.34 3.41
2184 5605 1.882912 TGCTCTGACACCATGTTGTC 58.117 50.000 15.90 15.90 45.34 3.18
2185 5606 2.156917 CATGCTCTGACACCATGTTGT 58.843 47.619 0.00 0.00 33.46 3.32
2186 5607 2.418976 CTCATGCTCTGACACCATGTTG 59.581 50.000 0.00 0.00 37.99 3.33
2187 5608 2.617276 CCTCATGCTCTGACACCATGTT 60.617 50.000 0.00 0.00 37.99 2.71
2188 5609 1.065636 CCTCATGCTCTGACACCATGT 60.066 52.381 0.00 0.00 37.99 3.21
2189 5610 1.065636 ACCTCATGCTCTGACACCATG 60.066 52.381 0.00 0.00 38.10 3.66
2190 5611 1.065636 CACCTCATGCTCTGACACCAT 60.066 52.381 0.00 0.00 0.00 3.55
2191 5612 0.322648 CACCTCATGCTCTGACACCA 59.677 55.000 0.00 0.00 0.00 4.17
2192 5613 0.392193 CCACCTCATGCTCTGACACC 60.392 60.000 0.00 0.00 0.00 4.16
2193 5614 0.610174 TCCACCTCATGCTCTGACAC 59.390 55.000 0.00 0.00 0.00 3.67
2194 5615 0.900421 CTCCACCTCATGCTCTGACA 59.100 55.000 0.00 0.00 0.00 3.58
2195 5616 0.177604 CCTCCACCTCATGCTCTGAC 59.822 60.000 0.00 0.00 0.00 3.51
2196 5617 1.620739 GCCTCCACCTCATGCTCTGA 61.621 60.000 0.00 0.00 0.00 3.27
2197 5618 1.153208 GCCTCCACCTCATGCTCTG 60.153 63.158 0.00 0.00 0.00 3.35
2198 5619 2.729479 CGCCTCCACCTCATGCTCT 61.729 63.158 0.00 0.00 0.00 4.09
2199 5620 2.202987 CGCCTCCACCTCATGCTC 60.203 66.667 0.00 0.00 0.00 4.26
2200 5621 4.479993 GCGCCTCCACCTCATGCT 62.480 66.667 0.00 0.00 0.00 3.79
2201 5622 4.479993 AGCGCCTCCACCTCATGC 62.480 66.667 2.29 0.00 0.00 4.06
2202 5623 2.513204 CAGCGCCTCCACCTCATG 60.513 66.667 2.29 0.00 0.00 3.07
2203 5624 2.129555 AAACAGCGCCTCCACCTCAT 62.130 55.000 2.29 0.00 0.00 2.90
2204 5625 2.818169 AAACAGCGCCTCCACCTCA 61.818 57.895 2.29 0.00 0.00 3.86
2205 5626 2.032681 AAACAGCGCCTCCACCTC 59.967 61.111 2.29 0.00 0.00 3.85
2206 5627 2.281761 CAAACAGCGCCTCCACCT 60.282 61.111 2.29 0.00 0.00 4.00
2207 5628 2.281484 TCAAACAGCGCCTCCACC 60.281 61.111 2.29 0.00 0.00 4.61
2208 5629 2.617274 GGTCAAACAGCGCCTCCAC 61.617 63.158 2.29 0.00 0.00 4.02
2209 5630 2.281484 GGTCAAACAGCGCCTCCA 60.281 61.111 2.29 0.00 0.00 3.86
2210 5631 3.056328 GGGTCAAACAGCGCCTCC 61.056 66.667 2.29 0.00 0.00 4.30
2211 5632 2.032681 AGGGTCAAACAGCGCCTC 59.967 61.111 2.29 0.00 0.00 4.70
2212 5633 2.032681 GAGGGTCAAACAGCGCCT 59.967 61.111 2.29 0.00 0.00 5.52
2213 5634 3.423154 CGAGGGTCAAACAGCGCC 61.423 66.667 2.29 0.00 0.00 6.53
2214 5635 4.090057 GCGAGGGTCAAACAGCGC 62.090 66.667 0.00 0.00 37.60 5.92


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

AutoCloner maintained by Alex Coulton.