Multiple sequence alignment - TraesCS3D01G418200

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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 TraesCS3D01G418200 chr3D 100.000 5089 0 0 1 5089 531042245 531047333 0.000000e+00 9398.0
1 TraesCS3D01G418200 chr3A 95.100 3041 91 20 2067 5089 664684294 664687294 0.000000e+00 4737.0
2 TraesCS3D01G418200 chr3A 92.893 1182 56 18 817 1981 664683118 664684288 0.000000e+00 1692.0
3 TraesCS3D01G418200 chr3A 93.635 597 21 5 3763 4347 664703085 664703676 0.000000e+00 876.0
4 TraesCS3D01G418200 chr3A 94.186 172 7 1 619 790 664682955 664683123 5.050000e-65 259.0
5 TraesCS3D01G418200 chr3B 93.637 3049 102 38 2069 5069 701406205 701409209 0.000000e+00 4471.0
6 TraesCS3D01G418200 chr3B 88.409 1389 88 41 618 1984 701404866 701406203 0.000000e+00 1605.0
7 TraesCS3D01G418200 chr3B 96.809 94 2 1 1984 2076 421670501 421670594 6.820000e-34 156.0
8 TraesCS3D01G418200 chr7D 91.922 619 45 2 1 619 333770448 333769835 0.000000e+00 861.0
9 TraesCS3D01G418200 chr7D 91.115 619 53 1 1 619 131069024 131068408 0.000000e+00 837.0
10 TraesCS3D01G418200 chr7D 90.953 619 54 1 1 619 495438608 495437992 0.000000e+00 832.0
11 TraesCS3D01G418200 chr7D 100.000 30 0 0 1258 1287 234808785 234808756 7.120000e-04 56.5
12 TraesCS3D01G418200 chr4D 91.599 619 50 1 1 619 316433632 316434248 0.000000e+00 854.0
13 TraesCS3D01G418200 chr4D 91.599 619 50 1 1 619 472658159 472657543 0.000000e+00 854.0
14 TraesCS3D01G418200 chr4D 90.953 619 54 1 1 619 71592011 71591395 0.000000e+00 832.0
15 TraesCS3D01G418200 chr4D 90.953 619 53 2 1 619 22505621 22506236 0.000000e+00 830.0
16 TraesCS3D01G418200 chr4D 98.864 88 1 0 1981 2068 437299991 437299904 1.900000e-34 158.0
17 TraesCS3D01G418200 chr2B 91.129 620 52 2 1 619 746381800 746381183 0.000000e+00 837.0
18 TraesCS3D01G418200 chr2D 90.982 621 52 3 1 619 250043946 250044564 0.000000e+00 833.0
19 TraesCS3D01G418200 chr4B 98.889 90 1 0 1983 2072 117191100 117191189 1.470000e-35 161.0
20 TraesCS3D01G418200 chr5D 96.809 94 2 1 1983 2075 502881630 502881723 6.820000e-34 156.0
21 TraesCS3D01G418200 chr5D 92.308 104 7 1 1984 2087 525478256 525478154 4.110000e-31 147.0
22 TraesCS3D01G418200 chr2A 94.231 104 2 4 1966 2069 187514282 187514381 6.820000e-34 156.0
23 TraesCS3D01G418200 chr5B 90.517 116 8 3 1955 2068 13221526 13221640 3.170000e-32 150.0
24 TraesCS3D01G418200 chr1A 92.381 105 4 3 1984 2087 560378198 560378097 4.110000e-31 147.0
25 TraesCS3D01G418200 chr7B 90.351 114 6 5 1976 2086 398380292 398380181 1.480000e-30 145.0
26 TraesCS3D01G418200 chr7B 87.037 54 5 2 1235 1287 210864420 210864368 5.500000e-05 60.2
27 TraesCS3D01G418200 chr7A 100.000 30 0 0 1258 1287 249596456 249596427 7.120000e-04 56.5


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 TraesCS3D01G418200 chr3D 531042245 531047333 5088 False 9398.000000 9398 100.000000 1 5089 1 chr3D.!!$F1 5088
1 TraesCS3D01G418200 chr3A 664682955 664687294 4339 False 2229.333333 4737 94.059667 619 5089 3 chr3A.!!$F2 4470
2 TraesCS3D01G418200 chr3A 664703085 664703676 591 False 876.000000 876 93.635000 3763 4347 1 chr3A.!!$F1 584
3 TraesCS3D01G418200 chr3B 701404866 701409209 4343 False 3038.000000 4471 91.023000 618 5069 2 chr3B.!!$F2 4451
4 TraesCS3D01G418200 chr7D 333769835 333770448 613 True 861.000000 861 91.922000 1 619 1 chr7D.!!$R3 618
5 TraesCS3D01G418200 chr7D 131068408 131069024 616 True 837.000000 837 91.115000 1 619 1 chr7D.!!$R1 618
6 TraesCS3D01G418200 chr7D 495437992 495438608 616 True 832.000000 832 90.953000 1 619 1 chr7D.!!$R4 618
7 TraesCS3D01G418200 chr4D 316433632 316434248 616 False 854.000000 854 91.599000 1 619 1 chr4D.!!$F2 618
8 TraesCS3D01G418200 chr4D 472657543 472658159 616 True 854.000000 854 91.599000 1 619 1 chr4D.!!$R3 618
9 TraesCS3D01G418200 chr4D 71591395 71592011 616 True 832.000000 832 90.953000 1 619 1 chr4D.!!$R1 618
10 TraesCS3D01G418200 chr4D 22505621 22506236 615 False 830.000000 830 90.953000 1 619 1 chr4D.!!$F1 618
11 TraesCS3D01G418200 chr2B 746381183 746381800 617 True 837.000000 837 91.129000 1 619 1 chr2B.!!$R1 618
12 TraesCS3D01G418200 chr2D 250043946 250044564 618 False 833.000000 833 90.982000 1 619 1 chr2D.!!$F1 618

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
989 993 0.533032 CTCACTTCCCGGGTCTCTTC 59.467 60.000 22.86 0.0 0.00 2.87 F
1198 1227 0.047176 AGAGGAGAGAGAGGGAGGGA 59.953 60.000 0.00 0.0 0.00 4.20 F
1760 1799 0.180171 CTGCCGGTGATGATTACCCA 59.820 55.000 1.90 0.0 34.66 4.51 F
1838 1877 0.530744 TTGGGAGTGTGCGCTACTAG 59.469 55.000 15.98 0.0 0.00 2.57 F
1944 1987 1.066143 GGATCCAAGCAAGGACGAGAA 60.066 52.381 6.95 0.0 41.30 2.87 F
3551 3595 1.533033 TCCAGGGAGAAGCACGTCA 60.533 57.895 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2051 2094 0.635009 TTCTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00 R
2052 2095 0.635009 ATTCTACTCCCTCCGTCCCA 59.365 55.000 0.00 0.00 0.00 4.37 R
3025 3069 1.005924 CCTGACCCCTGCTGGTATTTT 59.994 52.381 9.00 0.00 39.24 1.82 R
3499 3543 1.078143 GCTCTCCATGGTTTCGGCT 60.078 57.895 12.58 0.00 0.00 5.52 R
3872 3916 0.252375 ACCTCCAAAATGGCCATGCT 60.252 50.000 21.63 6.92 37.47 3.79 R
4456 4518 0.105913 AAAAGGCCCGGAAAACCTGA 60.106 50.000 0.73 0.00 32.92 3.86 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
85 88 4.495690 TTTACATGAACCATCATCCCGA 57.504 40.909 0.00 0.00 44.53 5.14
119 122 2.092968 CCAAATAGCTAGTCAGGGCACA 60.093 50.000 0.00 0.00 0.00 4.57
147 150 0.892358 CAGTGACAAGCCCAGCACAT 60.892 55.000 0.00 0.00 33.85 3.21
175 178 2.229792 TCACCTGCAAGCCAACTAAAG 58.770 47.619 0.00 0.00 0.00 1.85
275 278 4.459337 GGGTGTCTAGCTTGTATTGCTTTT 59.541 41.667 0.00 0.00 41.46 2.27
288 291 9.862585 CTTGTATTGCTTTTAATTTGGTCAAAC 57.137 29.630 0.00 0.00 32.51 2.93
308 311 4.148128 ACTGCATCTGCTTAGCTTACAT 57.852 40.909 5.60 0.00 42.66 2.29
462 466 2.688958 GGCTCGTGGACTACTGTAAGAT 59.311 50.000 0.00 0.00 37.43 2.40
470 474 7.013083 TCGTGGACTACTGTAAGATAAGATTCC 59.987 40.741 0.00 0.00 37.43 3.01
494 498 5.278660 CCTTTTAAAGAATGCAGTGTCAGCT 60.279 40.000 6.24 0.00 0.00 4.24
510 514 2.309755 TCAGCTTCCCCACATGATTCTT 59.690 45.455 0.00 0.00 0.00 2.52
528 532 8.109705 TGATTCTTAAGAAACAGCAATGCTAA 57.890 30.769 21.26 0.00 35.45 3.09
553 557 3.701532 AGATAGTCAACGTAGCTCTGC 57.298 47.619 0.00 0.00 0.00 4.26
583 587 1.142060 CCGCATTTCCCCTACACCATA 59.858 52.381 0.00 0.00 0.00 2.74
698 702 3.384532 GCCCCACCTGCCAATGTG 61.385 66.667 0.00 0.00 0.00 3.21
742 746 3.130160 GCAGCCAAAGCCCTCGAG 61.130 66.667 5.13 5.13 41.25 4.04
745 749 1.915769 AGCCAAAGCCCTCGAGTCT 60.916 57.895 12.31 5.13 41.25 3.24
746 750 1.448717 GCCAAAGCCCTCGAGTCTC 60.449 63.158 12.31 0.00 0.00 3.36
747 751 1.893919 GCCAAAGCCCTCGAGTCTCT 61.894 60.000 12.31 2.08 0.00 3.10
823 827 3.900888 GGGACACCCTCACCTTCA 58.099 61.111 0.00 0.00 41.34 3.02
848 852 1.450848 GCTAAACTACCCCGTGGCC 60.451 63.158 0.00 0.00 33.59 5.36
854 858 4.642488 TACCCCGTGGCCCTGTGA 62.642 66.667 0.00 0.00 33.59 3.58
882 886 0.696143 TGTGGGGTCAGGGAGAAACA 60.696 55.000 0.00 0.00 0.00 2.83
989 993 0.533032 CTCACTTCCCGGGTCTCTTC 59.467 60.000 22.86 0.00 0.00 2.87
991 995 2.184579 CTTCCCGGGTCTCTTCGC 59.815 66.667 22.86 0.00 0.00 4.70
992 996 2.283676 TTCCCGGGTCTCTTCGCT 60.284 61.111 22.86 0.00 0.00 4.93
993 997 2.564553 CTTCCCGGGTCTCTTCGCTG 62.565 65.000 22.86 0.00 0.00 5.18
994 998 4.821589 CCCGGGTCTCTTCGCTGC 62.822 72.222 14.18 0.00 0.00 5.25
995 999 4.821589 CCGGGTCTCTTCGCTGCC 62.822 72.222 0.00 0.00 0.00 4.85
1023 1029 2.080693 GTCTCGAGCTGAGTGAGAGAA 58.919 52.381 7.81 0.00 45.46 2.87
1025 1031 3.057876 GTCTCGAGCTGAGTGAGAGAAAA 60.058 47.826 7.81 0.00 45.46 2.29
1026 1032 3.190327 TCTCGAGCTGAGTGAGAGAAAAG 59.810 47.826 7.81 0.00 45.46 2.27
1027 1033 3.149981 TCGAGCTGAGTGAGAGAAAAGA 58.850 45.455 0.00 0.00 0.00 2.52
1029 1035 3.919804 CGAGCTGAGTGAGAGAAAAGAAG 59.080 47.826 0.00 0.00 0.00 2.85
1030 1036 4.320861 CGAGCTGAGTGAGAGAAAAGAAGA 60.321 45.833 0.00 0.00 0.00 2.87
1031 1037 5.138125 AGCTGAGTGAGAGAAAAGAAGAG 57.862 43.478 0.00 0.00 0.00 2.85
1032 1038 4.832266 AGCTGAGTGAGAGAAAAGAAGAGA 59.168 41.667 0.00 0.00 0.00 3.10
1194 1223 1.780309 GGATCAGAGGAGAGAGAGGGA 59.220 57.143 0.00 0.00 0.00 4.20
1197 1226 0.185901 CAGAGGAGAGAGAGGGAGGG 59.814 65.000 0.00 0.00 0.00 4.30
1198 1227 0.047176 AGAGGAGAGAGAGGGAGGGA 59.953 60.000 0.00 0.00 0.00 4.20
1200 1229 0.998945 AGGAGAGAGAGGGAGGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
1201 1230 1.541672 GAGAGAGAGGGAGGGAGGG 59.458 68.421 0.00 0.00 0.00 4.30
1202 1231 0.996762 GAGAGAGAGGGAGGGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
1203 1232 0.998945 AGAGAGAGGGAGGGAGGGAG 60.999 65.000 0.00 0.00 0.00 4.30
1204 1233 2.018086 AGAGAGGGAGGGAGGGAGG 61.018 68.421 0.00 0.00 0.00 4.30
1205 1234 2.204705 AGAGGGAGGGAGGGAGGT 60.205 66.667 0.00 0.00 0.00 3.85
1206 1235 2.041405 GAGGGAGGGAGGGAGGTG 60.041 72.222 0.00 0.00 0.00 4.00
1207 1236 3.700350 AGGGAGGGAGGGAGGTGG 61.700 72.222 0.00 0.00 0.00 4.61
1529 1562 4.162690 CGCCCACCTCCTAGTGCC 62.163 72.222 0.00 0.00 36.38 5.01
1532 1565 2.370445 CCCACCTCCTAGTGCCAGG 61.370 68.421 0.00 0.00 36.38 4.45
1598 1634 1.549203 AATTCCATTTCTGCCTGCGT 58.451 45.000 0.00 0.00 0.00 5.24
1599 1635 1.098050 ATTCCATTTCTGCCTGCGTC 58.902 50.000 0.00 0.00 0.00 5.19
1615 1651 4.357947 TCTGCGTCGTCCCTGTGC 62.358 66.667 0.00 0.00 0.00 4.57
1625 1661 0.387239 GTCCCTGTGCATTTGTTCGC 60.387 55.000 0.00 0.00 0.00 4.70
1626 1662 0.537143 TCCCTGTGCATTTGTTCGCT 60.537 50.000 0.00 0.00 0.00 4.93
1656 1693 3.123621 GCGATTATTGCGGACTGATTAGG 59.876 47.826 0.00 0.00 0.00 2.69
1673 1710 2.956964 GCCAAGATCCGCGTCTCG 60.957 66.667 4.92 0.00 38.08 4.04
1757 1795 1.064060 GTTGCTGCCGGTGATGATTAC 59.936 52.381 1.90 0.00 0.00 1.89
1760 1799 0.180171 CTGCCGGTGATGATTACCCA 59.820 55.000 1.90 0.00 34.66 4.51
1777 1816 6.605963 ATTACCCATAATGCGGCTGATTAGC 61.606 44.000 0.00 0.00 38.14 3.09
1827 1866 2.635915 TGTTAGTAGGTGGTTGGGAGTG 59.364 50.000 0.00 0.00 0.00 3.51
1838 1877 0.530744 TTGGGAGTGTGCGCTACTAG 59.469 55.000 15.98 0.00 0.00 2.57
1944 1987 1.066143 GGATCCAAGCAAGGACGAGAA 60.066 52.381 6.95 0.00 41.30 2.87
1945 1988 2.003301 GATCCAAGCAAGGACGAGAAC 58.997 52.381 0.00 0.00 41.30 3.01
1977 2020 8.854117 AGAAGTTCTCTTTTTCGGTACTAGTTA 58.146 33.333 0.00 0.00 33.64 2.24
1981 2024 8.910666 GTTCTCTTTTTCGGTACTAGTTAGAAC 58.089 37.037 0.00 0.00 33.52 3.01
1983 2026 8.800332 TCTCTTTTTCGGTACTAGTTAGAACAT 58.200 33.333 0.00 0.00 0.00 2.71
1985 2028 9.846248 TCTTTTTCGGTACTAGTTAGAACATAC 57.154 33.333 0.00 0.00 0.00 2.39
1986 2029 9.852091 CTTTTTCGGTACTAGTTAGAACATACT 57.148 33.333 0.00 0.00 0.00 2.12
1987 2030 9.846248 TTTTTCGGTACTAGTTAGAACATACTC 57.154 33.333 0.00 0.00 0.00 2.59
1988 2031 7.559590 TTCGGTACTAGTTAGAACATACTCC 57.440 40.000 0.00 0.00 0.00 3.85
1989 2032 6.058183 TCGGTACTAGTTAGAACATACTCCC 58.942 44.000 0.00 0.00 0.00 4.30
1990 2033 6.060788 CGGTACTAGTTAGAACATACTCCCT 58.939 44.000 0.00 0.00 0.00 4.20
1991 2034 6.204495 CGGTACTAGTTAGAACATACTCCCTC 59.796 46.154 0.00 0.00 0.00 4.30
1992 2035 7.289310 GGTACTAGTTAGAACATACTCCCTCT 58.711 42.308 0.00 0.00 0.00 3.69
1993 2036 7.229106 GGTACTAGTTAGAACATACTCCCTCTG 59.771 44.444 0.00 0.00 0.00 3.35
1994 2037 6.733509 ACTAGTTAGAACATACTCCCTCTGT 58.266 40.000 0.00 0.00 0.00 3.41
1995 2038 6.829811 ACTAGTTAGAACATACTCCCTCTGTC 59.170 42.308 0.00 0.00 0.00 3.51
1996 2039 4.957327 AGTTAGAACATACTCCCTCTGTCC 59.043 45.833 0.00 0.00 0.00 4.02
1997 2040 2.753247 AGAACATACTCCCTCTGTCCC 58.247 52.381 0.00 0.00 0.00 4.46
1998 2041 2.044492 AGAACATACTCCCTCTGTCCCA 59.956 50.000 0.00 0.00 0.00 4.37
1999 2042 2.642171 ACATACTCCCTCTGTCCCAA 57.358 50.000 0.00 0.00 0.00 4.12
2000 2043 2.915869 ACATACTCCCTCTGTCCCAAA 58.084 47.619 0.00 0.00 0.00 3.28
2001 2044 3.256704 ACATACTCCCTCTGTCCCAAAA 58.743 45.455 0.00 0.00 0.00 2.44
2002 2045 3.852578 ACATACTCCCTCTGTCCCAAAAT 59.147 43.478 0.00 0.00 0.00 1.82
2003 2046 5.036916 ACATACTCCCTCTGTCCCAAAATA 58.963 41.667 0.00 0.00 0.00 1.40
2004 2047 5.672194 ACATACTCCCTCTGTCCCAAAATAT 59.328 40.000 0.00 0.00 0.00 1.28
2005 2048 6.849697 ACATACTCCCTCTGTCCCAAAATATA 59.150 38.462 0.00 0.00 0.00 0.86
2006 2049 7.349859 ACATACTCCCTCTGTCCCAAAATATAA 59.650 37.037 0.00 0.00 0.00 0.98
2007 2050 6.253946 ACTCCCTCTGTCCCAAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
2008 2051 5.970640 ACTCCCTCTGTCCCAAAATATAAGA 59.029 40.000 0.00 0.00 0.00 2.10
2009 2052 6.447084 ACTCCCTCTGTCCCAAAATATAAGAA 59.553 38.462 0.00 0.00 0.00 2.52
2010 2053 6.659824 TCCCTCTGTCCCAAAATATAAGAAC 58.340 40.000 0.00 0.00 0.00 3.01
2011 2054 5.527582 CCCTCTGTCCCAAAATATAAGAACG 59.472 44.000 0.00 0.00 0.00 3.95
2012 2055 6.113411 CCTCTGTCCCAAAATATAAGAACGT 58.887 40.000 0.00 0.00 0.00 3.99
2013 2056 6.598064 CCTCTGTCCCAAAATATAAGAACGTT 59.402 38.462 0.00 0.00 0.00 3.99
2014 2057 7.120726 CCTCTGTCCCAAAATATAAGAACGTTT 59.879 37.037 0.46 0.00 0.00 3.60
2015 2058 8.398878 TCTGTCCCAAAATATAAGAACGTTTT 57.601 30.769 0.46 0.00 0.00 2.43
2016 2059 8.852135 TCTGTCCCAAAATATAAGAACGTTTTT 58.148 29.630 9.22 9.22 0.00 1.94
2030 2073 8.707938 AAGAACGTTTTTAACACTACACTAGT 57.292 30.769 0.46 0.00 40.28 2.57
2031 2074 9.801873 AAGAACGTTTTTAACACTACACTAGTA 57.198 29.630 0.46 0.00 37.23 1.82
2032 2075 9.971922 AGAACGTTTTTAACACTACACTAGTAT 57.028 29.630 0.46 0.00 37.23 2.12
2034 2077 9.748708 AACGTTTTTAACACTACACTAGTATCA 57.251 29.630 0.00 0.00 37.23 2.15
2035 2078 9.748708 ACGTTTTTAACACTACACTAGTATCAA 57.251 29.630 0.00 0.00 37.23 2.57
2041 2084 9.748708 TTAACACTACACTAGTATCAAAAACGT 57.251 29.630 0.00 0.00 37.23 3.99
2042 2085 8.652810 AACACTACACTAGTATCAAAAACGTT 57.347 30.769 0.00 0.00 37.23 3.99
2043 2086 8.290663 ACACTACACTAGTATCAAAAACGTTC 57.709 34.615 0.00 0.00 37.23 3.95
2044 2087 8.139989 ACACTACACTAGTATCAAAAACGTTCT 58.860 33.333 0.00 0.00 37.23 3.01
2045 2088 8.975439 CACTACACTAGTATCAAAAACGTTCTT 58.025 33.333 0.00 0.00 37.23 2.52
2058 2101 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
2059 2102 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
2060 2103 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
2061 2104 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
2062 2105 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
2063 2106 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
2064 2107 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
2065 2108 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2111 2154 4.909880 GGTTGTTAGAGTTGTTTCGAATGC 59.090 41.667 0.00 0.00 0.00 3.56
2126 2169 7.112844 TGTTTCGAATGCGTTTATTTTCTTCTG 59.887 33.333 0.00 0.00 38.98 3.02
2326 2369 4.286808 TCTGGACAGAGTTTCATGATTGGA 59.713 41.667 0.00 0.00 32.82 3.53
2455 2499 3.190874 CAGCTCGATTCTTGACCTTACC 58.809 50.000 0.00 0.00 0.00 2.85
2557 2601 2.045524 AGCCTAGATCATGGGAGTGTG 58.954 52.381 0.00 0.00 0.00 3.82
3025 3069 4.889409 ACTTCAAAGATGACTTCAAAGCCA 59.111 37.500 0.00 0.00 34.61 4.75
3069 3113 2.888594 CTCAGCCAATGCAAGGATTTG 58.111 47.619 12.36 1.44 41.13 2.32
3139 3183 7.946776 CAGGGGATTTCAACTCCAGAAATATAT 59.053 37.037 0.00 0.00 43.60 0.86
3148 3192 8.493607 TCAACTCCAGAAATATATGAATCACCA 58.506 33.333 0.00 0.00 0.00 4.17
3235 3279 4.443598 CCAGCTAAGGTTCCCAAGACTATC 60.444 50.000 0.00 0.00 0.00 2.08
3499 3543 3.017442 CGAGGAGGAGACAATGTACTCA 58.983 50.000 12.18 0.00 35.17 3.41
3551 3595 1.533033 TCCAGGGAGAAGCACGTCA 60.533 57.895 0.00 0.00 0.00 4.35
3579 3623 2.613977 GCCAGAGCTGTGTCAACTACAT 60.614 50.000 10.34 0.00 36.82 2.29
3830 3874 2.783135 TGTTCTGATGGTTTGCTCTCC 58.217 47.619 0.00 0.00 0.00 3.71
3832 3876 3.006247 GTTCTGATGGTTTGCTCTCCTC 58.994 50.000 0.00 0.00 0.00 3.71
3869 3913 1.665264 AATGAAATGATGGCGCCGCA 61.665 50.000 23.90 22.75 0.00 5.69
3872 3916 2.062361 GAAATGATGGCGCCGCATCA 62.062 55.000 26.31 26.31 41.37 3.07
3995 4052 7.809806 CAGAATGACTTGGACAAATAAAAGGTC 59.190 37.037 0.00 0.00 39.69 3.85
4036 4093 5.069383 TCGACGGAAAAGATAATGGACCATA 59.931 40.000 7.59 0.00 0.00 2.74
4037 4094 5.932303 CGACGGAAAAGATAATGGACCATAT 59.068 40.000 7.59 1.89 0.00 1.78
4087 4144 4.863491 AGCTGTTGAAATGTCATGTGTTC 58.137 39.130 0.00 0.00 32.48 3.18
4341 4402 4.962155 ACTTCAGGTGGACTAAAGAACTG 58.038 43.478 0.00 0.00 0.00 3.16
4444 4506 1.228124 CTGTCAGGTTTTCCGGGCA 60.228 57.895 0.00 0.00 46.57 5.36
4445 4507 1.458486 TGTCAGGTTTTCCGGGCAT 59.542 52.632 0.00 0.00 44.16 4.40
4446 4508 0.693622 TGTCAGGTTTTCCGGGCATA 59.306 50.000 0.00 0.00 44.16 3.14
4447 4509 1.283613 TGTCAGGTTTTCCGGGCATAT 59.716 47.619 0.00 0.00 44.16 1.78
4448 4510 1.676006 GTCAGGTTTTCCGGGCATATG 59.324 52.381 0.00 0.00 46.35 1.78
4450 4512 0.258774 AGGTTTTCCGGGCATATGCT 59.741 50.000 26.12 0.12 46.35 3.79
4452 4514 1.067060 GGTTTTCCGGGCATATGCTTC 59.933 52.381 26.12 17.28 41.70 3.86
4453 4515 1.067060 GTTTTCCGGGCATATGCTTCC 59.933 52.381 26.12 18.51 41.70 3.46
4454 4516 0.550914 TTTCCGGGCATATGCTTCCT 59.449 50.000 26.12 0.00 41.70 3.36
4455 4517 0.179020 TTCCGGGCATATGCTTCCTG 60.179 55.000 26.12 16.05 41.70 3.86
4456 4518 1.149174 CCGGGCATATGCTTCCTGT 59.851 57.895 26.12 0.00 41.70 4.00
4457 4519 0.886490 CCGGGCATATGCTTCCTGTC 60.886 60.000 26.12 8.36 41.70 3.51
4458 4520 0.179048 CGGGCATATGCTTCCTGTCA 60.179 55.000 26.12 0.00 41.70 3.58
4459 4521 1.602311 GGGCATATGCTTCCTGTCAG 58.398 55.000 26.12 0.00 41.70 3.51
4460 4522 1.602311 GGCATATGCTTCCTGTCAGG 58.398 55.000 26.12 13.21 41.70 3.86
4461 4523 1.133976 GGCATATGCTTCCTGTCAGGT 60.134 52.381 26.12 1.39 41.70 4.00
4462 4524 2.648059 GCATATGCTTCCTGTCAGGTT 58.352 47.619 20.64 3.09 35.85 3.50
4463 4525 3.019564 GCATATGCTTCCTGTCAGGTTT 58.980 45.455 20.64 3.41 35.85 3.27
4464 4526 3.445096 GCATATGCTTCCTGTCAGGTTTT 59.555 43.478 20.64 3.74 35.85 2.43
4465 4527 4.439289 GCATATGCTTCCTGTCAGGTTTTC 60.439 45.833 20.64 7.37 35.85 2.29
4466 4528 1.981256 TGCTTCCTGTCAGGTTTTCC 58.019 50.000 18.65 5.08 36.53 3.13
4467 4529 0.875059 GCTTCCTGTCAGGTTTTCCG 59.125 55.000 18.65 3.67 46.35 4.30
4468 4530 1.523758 CTTCCTGTCAGGTTTTCCGG 58.476 55.000 18.65 0.00 46.35 5.14
4504 4566 2.936498 CGGGCTGAATTTCTCGTACAAT 59.064 45.455 0.00 0.00 0.00 2.71
4622 4686 5.839262 TGTCTATGCGTAAAAACAGAGTG 57.161 39.130 0.00 0.00 0.00 3.51
4624 4688 5.176774 TGTCTATGCGTAAAAACAGAGTGTG 59.823 40.000 0.00 0.00 0.00 3.82
4665 4729 0.972471 GAGTTTTCCCCTGCCCCATG 60.972 60.000 0.00 0.00 0.00 3.66
4691 4756 4.511527 TGCAAATGAGGCAAGAAAAACAA 58.488 34.783 0.00 0.00 38.54 2.83
4777 4866 3.426159 GCTTGTGTACGCATAGCATTTGT 60.426 43.478 25.37 0.00 36.10 2.83
4788 4877 5.164158 CGCATAGCATTTGTGTGTTTTTCTC 60.164 40.000 0.00 0.00 0.00 2.87
4980 5070 1.535896 CATGACAGGCAGCATAGCATC 59.464 52.381 0.00 0.00 35.83 3.91
4981 5071 0.542805 TGACAGGCAGCATAGCATCA 59.457 50.000 0.00 0.00 35.83 3.07
4982 5072 1.142262 TGACAGGCAGCATAGCATCAT 59.858 47.619 0.00 0.00 35.83 2.45
5016 5106 6.696411 AGTCTGTCTATCCAAGAACTGAAAG 58.304 40.000 0.00 0.00 35.47 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.754946 TCGGCCTTTCGAATACAAGT 57.245 45.000 0.00 0.00 36.12 3.16
77 80 0.614697 TTCTGGTGCTCTCGGGATGA 60.615 55.000 0.00 0.00 0.00 2.92
85 88 2.943199 GCTATTTGGCTTCTGGTGCTCT 60.943 50.000 0.00 0.00 0.00 4.09
275 278 4.523943 AGCAGATGCAGTTTGACCAAATTA 59.476 37.500 7.68 0.00 45.16 1.40
288 291 6.798315 AATATGTAAGCTAAGCAGATGCAG 57.202 37.500 7.68 0.00 45.16 4.41
329 332 5.329399 TGTACCAAAAACAGGAAGGCATAT 58.671 37.500 0.00 0.00 0.00 1.78
330 333 4.730966 TGTACCAAAAACAGGAAGGCATA 58.269 39.130 0.00 0.00 0.00 3.14
420 424 4.382470 GCCTGACTGTCTCATCATAAGTGT 60.382 45.833 9.51 0.00 0.00 3.55
462 466 8.522830 CACTGCATTCTTTAAAAGGGAATCTTA 58.477 33.333 0.00 0.00 34.78 2.10
470 474 4.919754 GCTGACACTGCATTCTTTAAAAGG 59.080 41.667 0.00 0.00 0.00 3.11
494 498 6.310941 TGTTTCTTAAGAATCATGTGGGGAA 58.689 36.000 20.21 0.33 33.54 3.97
528 532 6.697892 GCAGAGCTACGTTGACTATCTTTATT 59.302 38.462 0.00 0.00 0.00 1.40
531 535 4.082190 TGCAGAGCTACGTTGACTATCTTT 60.082 41.667 0.00 0.00 0.00 2.52
553 557 1.133025 GGGAAATGCGGTCATCAACTG 59.867 52.381 0.00 0.00 37.31 3.16
660 664 3.186047 CGCATCCACGTTCCCGTC 61.186 66.667 0.00 0.00 46.28 4.79
698 702 0.796927 GACACGCTTAACTGCCCTTC 59.203 55.000 0.00 0.00 0.00 3.46
741 745 2.509964 GGGGAAGAGAGAGAGAGAGACT 59.490 54.545 0.00 0.00 0.00 3.24
742 746 2.241176 TGGGGAAGAGAGAGAGAGAGAC 59.759 54.545 0.00 0.00 0.00 3.36
745 749 1.286553 GGTGGGGAAGAGAGAGAGAGA 59.713 57.143 0.00 0.00 0.00 3.10
746 750 1.687996 GGGTGGGGAAGAGAGAGAGAG 60.688 61.905 0.00 0.00 0.00 3.20
747 751 0.336737 GGGTGGGGAAGAGAGAGAGA 59.663 60.000 0.00 0.00 0.00 3.10
823 827 0.989602 GGGGTAGTTTAGCTGGTGGT 59.010 55.000 0.00 0.00 0.00 4.16
848 852 2.436417 CCCACAGGTAATTGTCACAGG 58.564 52.381 0.00 0.00 0.00 4.00
870 874 1.463214 TGGGGCTGTTTCTCCCTGA 60.463 57.895 0.00 0.00 42.25 3.86
874 878 2.359975 CGGTGGGGCTGTTTCTCC 60.360 66.667 0.00 0.00 0.00 3.71
876 880 3.175710 ACCGGTGGGGCTGTTTCT 61.176 61.111 6.12 0.00 40.62 2.52
877 881 2.671963 GACCGGTGGGGCTGTTTC 60.672 66.667 14.63 0.00 38.83 2.78
991 995 4.463879 CGAGACAGGGCAGGGCAG 62.464 72.222 0.00 0.00 0.00 4.85
993 997 4.154347 CTCGAGACAGGGCAGGGC 62.154 72.222 6.58 0.00 0.00 5.19
994 998 4.154347 GCTCGAGACAGGGCAGGG 62.154 72.222 18.75 0.00 37.60 4.45
995 999 3.073735 AGCTCGAGACAGGGCAGG 61.074 66.667 18.75 0.00 40.85 4.85
1023 1029 3.268072 CCTTGGGGATTCCTCTCTTCTTT 59.732 47.826 3.76 0.00 36.20 2.52
1025 1031 2.486716 CCTTGGGGATTCCTCTCTTCT 58.513 52.381 3.76 0.00 36.20 2.85
1173 1202 1.498576 CCCTCTCTCTCCTCTGATCCA 59.501 57.143 0.00 0.00 0.00 3.41
1194 1223 4.748798 CTGCCCACCTCCCTCCCT 62.749 72.222 0.00 0.00 0.00 4.20
1197 1226 4.741239 TCCCTGCCCACCTCCCTC 62.741 72.222 0.00 0.00 0.00 4.30
1198 1227 4.748798 CTCCCTGCCCACCTCCCT 62.749 72.222 0.00 0.00 0.00 4.20
1202 1231 4.715130 TACGCTCCCTGCCCACCT 62.715 66.667 0.00 0.00 38.78 4.00
1203 1232 4.468689 GTACGCTCCCTGCCCACC 62.469 72.222 0.00 0.00 38.78 4.61
1204 1233 3.702048 TGTACGCTCCCTGCCCAC 61.702 66.667 0.00 0.00 38.78 4.61
1205 1234 3.702048 GTGTACGCTCCCTGCCCA 61.702 66.667 0.00 0.00 38.78 5.36
1206 1235 4.814294 CGTGTACGCTCCCTGCCC 62.814 72.222 4.67 0.00 38.78 5.36
1219 1248 1.504900 CATCAATGCAGCAGCGTGT 59.495 52.632 0.00 0.00 46.23 4.49
1532 1565 4.610714 GGCGGCTAGGCTGGTAGC 62.611 72.222 15.11 9.53 44.14 3.58
1556 1592 2.352503 AATGCAGCGATTTGGTTCAC 57.647 45.000 0.00 0.00 0.00 3.18
1598 1634 4.357947 GCACAGGGACGACGCAGA 62.358 66.667 4.64 0.00 0.00 4.26
1599 1635 3.939837 ATGCACAGGGACGACGCAG 62.940 63.158 4.64 0.00 34.36 5.18
1615 1651 0.447801 CCGGGAGAAGCGAACAAATG 59.552 55.000 0.00 0.00 0.00 2.32
1625 1661 0.868406 GCAATAATCGCCGGGAGAAG 59.132 55.000 4.11 0.00 0.00 2.85
1626 1662 0.878523 CGCAATAATCGCCGGGAGAA 60.879 55.000 4.11 0.00 0.00 2.87
1656 1693 2.956964 CGAGACGCGGATCTTGGC 60.957 66.667 12.47 0.00 36.03 4.52
1707 1744 0.662970 CCACCAACAACAAATCCGCG 60.663 55.000 0.00 0.00 0.00 6.46
1757 1795 1.470098 GCTAATCAGCCGCATTATGGG 59.530 52.381 2.04 2.04 42.37 4.00
1777 1816 3.829948 CACTAGCAGTTGAATTTGGCTG 58.170 45.455 0.00 0.00 36.10 4.85
1838 1877 5.106197 TGTGATCACCATGATTACAACAAGC 60.106 40.000 22.85 0.00 46.09 4.01
1944 1987 6.766467 ACCGAAAAAGAGAACTTCTATGTTGT 59.234 34.615 0.00 0.00 34.14 3.32
1945 1988 7.190920 ACCGAAAAAGAGAACTTCTATGTTG 57.809 36.000 0.00 0.00 34.14 3.33
1977 2020 2.044492 TGGGACAGAGGGAGTATGTTCT 59.956 50.000 0.00 0.00 27.90 3.01
1981 2024 4.510167 ATTTTGGGACAGAGGGAGTATG 57.490 45.455 0.00 0.00 42.39 2.39
1983 2026 7.136885 TCTTATATTTTGGGACAGAGGGAGTA 58.863 38.462 0.00 0.00 42.39 2.59
1985 2028 6.500589 TCTTATATTTTGGGACAGAGGGAG 57.499 41.667 0.00 0.00 42.39 4.30
1986 2029 6.631766 CGTTCTTATATTTTGGGACAGAGGGA 60.632 42.308 0.00 0.00 42.39 4.20
1987 2030 5.527582 CGTTCTTATATTTTGGGACAGAGGG 59.472 44.000 0.00 0.00 42.39 4.30
1988 2031 6.113411 ACGTTCTTATATTTTGGGACAGAGG 58.887 40.000 0.00 0.00 42.39 3.69
1989 2032 7.611213 AACGTTCTTATATTTTGGGACAGAG 57.389 36.000 0.00 0.00 42.39 3.35
1990 2033 7.989416 AAACGTTCTTATATTTTGGGACAGA 57.011 32.000 0.00 0.00 42.39 3.41
2004 2047 9.801873 ACTAGTGTAGTGTTAAAAACGTTCTTA 57.198 29.630 0.00 0.00 37.69 2.10
2005 2048 8.707938 ACTAGTGTAGTGTTAAAAACGTTCTT 57.292 30.769 0.00 0.00 37.69 2.52
2006 2049 9.971922 ATACTAGTGTAGTGTTAAAAACGTTCT 57.028 29.630 5.39 0.00 39.81 3.01
2008 2051 9.748708 TGATACTAGTGTAGTGTTAAAAACGTT 57.251 29.630 5.39 0.00 39.81 3.99
2009 2052 9.748708 TTGATACTAGTGTAGTGTTAAAAACGT 57.251 29.630 5.39 0.00 39.81 3.99
2015 2058 9.748708 ACGTTTTTGATACTAGTGTAGTGTTAA 57.251 29.630 5.39 0.00 39.81 2.01
2016 2059 9.748708 AACGTTTTTGATACTAGTGTAGTGTTA 57.251 29.630 5.39 0.00 39.81 2.41
2017 2060 8.652810 AACGTTTTTGATACTAGTGTAGTGTT 57.347 30.769 5.39 0.00 39.81 3.32
2018 2061 8.139989 AGAACGTTTTTGATACTAGTGTAGTGT 58.860 33.333 5.39 0.00 39.81 3.55
2019 2062 8.516811 AGAACGTTTTTGATACTAGTGTAGTG 57.483 34.615 5.39 0.00 39.81 2.74
2032 2075 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
2033 2076 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
2034 2077 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
2035 2078 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
2036 2079 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
2037 2080 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
2038 2081 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
2039 2082 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
2040 2083 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
2041 2084 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
2042 2085 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2043 2086 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2044 2087 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2045 2088 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2046 2089 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2047 2090 3.659195 TCTACTCCCTCCGTCCCATAATA 59.341 47.826 0.00 0.00 0.00 0.98
2048 2091 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
2049 2092 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
2050 2093 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
2051 2094 0.635009 TTCTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00
2052 2095 0.635009 ATTCTACTCCCTCCGTCCCA 59.365 55.000 0.00 0.00 0.00 4.37
2053 2096 1.790818 AATTCTACTCCCTCCGTCCC 58.209 55.000 0.00 0.00 0.00 4.46
2054 2097 4.344390 ACATTAATTCTACTCCCTCCGTCC 59.656 45.833 0.00 0.00 0.00 4.79
2055 2098 5.068723 TCACATTAATTCTACTCCCTCCGTC 59.931 44.000 0.00 0.00 0.00 4.79
2056 2099 4.960469 TCACATTAATTCTACTCCCTCCGT 59.040 41.667 0.00 0.00 0.00 4.69
2057 2100 5.531122 TCACATTAATTCTACTCCCTCCG 57.469 43.478 0.00 0.00 0.00 4.63
2058 2101 8.624776 CAAAATCACATTAATTCTACTCCCTCC 58.375 37.037 0.00 0.00 0.00 4.30
2059 2102 8.131731 GCAAAATCACATTAATTCTACTCCCTC 58.868 37.037 0.00 0.00 0.00 4.30
2060 2103 7.201732 CGCAAAATCACATTAATTCTACTCCCT 60.202 37.037 0.00 0.00 0.00 4.20
2061 2104 6.912591 CGCAAAATCACATTAATTCTACTCCC 59.087 38.462 0.00 0.00 0.00 4.30
2062 2105 6.414987 GCGCAAAATCACATTAATTCTACTCC 59.585 38.462 0.30 0.00 0.00 3.85
2063 2106 6.139169 CGCGCAAAATCACATTAATTCTACTC 59.861 38.462 8.75 0.00 0.00 2.59
2064 2107 5.965334 CGCGCAAAATCACATTAATTCTACT 59.035 36.000 8.75 0.00 0.00 2.57
2065 2108 5.171337 CCGCGCAAAATCACATTAATTCTAC 59.829 40.000 8.75 0.00 0.00 2.59
2111 2154 6.735130 ACCTTTCCACAGAAGAAAATAAACG 58.265 36.000 0.00 0.00 33.06 3.60
2126 2169 3.958147 TCCCTGAAGAAAAACCTTTCCAC 59.042 43.478 0.00 0.00 41.72 4.02
2455 2499 2.609459 GGCAGAATCAACACCGACTATG 59.391 50.000 0.00 0.00 0.00 2.23
2557 2601 2.438795 TGCCCCAGCAGGTAAACC 59.561 61.111 0.00 0.00 46.52 3.27
2608 2652 1.086696 CCGTGCCAATCACTACCTTG 58.913 55.000 0.00 0.00 43.46 3.61
2611 2655 2.870411 GTTATCCGTGCCAATCACTACC 59.130 50.000 0.00 0.00 43.46 3.18
3025 3069 1.005924 CCTGACCCCTGCTGGTATTTT 59.994 52.381 9.00 0.00 39.24 1.82
3069 3113 3.285484 ACCAGAGGATTTGCATCATGAC 58.715 45.455 0.00 0.00 0.00 3.06
3148 3192 1.985895 CCCTGACAAGAACTACCCCTT 59.014 52.381 0.00 0.00 0.00 3.95
3235 3279 2.859165 TCAAGGGCAGTGGTAGAAAG 57.141 50.000 0.00 0.00 0.00 2.62
3298 3342 2.654385 TCTGGATGGATTCCTGGGTTTT 59.346 45.455 3.95 0.00 45.68 2.43
3499 3543 1.078143 GCTCTCCATGGTTTCGGCT 60.078 57.895 12.58 0.00 0.00 5.52
3568 3612 2.028112 GCTCCACCTGATGTAGTTGACA 60.028 50.000 0.00 0.00 43.97 3.58
3608 3652 1.539827 CAAGGTCCCGGTTTGAATCAC 59.460 52.381 0.00 0.00 0.00 3.06
3818 3862 4.706842 AAACTAAGAGGAGAGCAAACCA 57.293 40.909 0.00 0.00 0.00 3.67
3869 3913 1.760613 CTCCAAAATGGCCATGCTGAT 59.239 47.619 21.63 0.00 37.47 2.90
3872 3916 0.252375 ACCTCCAAAATGGCCATGCT 60.252 50.000 21.63 6.92 37.47 3.79
3995 4052 6.025280 TCCGTCGAACTTTTCTTTTTCTTTG 58.975 36.000 0.00 0.00 0.00 2.77
4036 4093 3.116356 TGACACCTCCATCCAGGGTATAT 60.116 47.826 0.00 0.00 37.96 0.86
4037 4094 2.248950 TGACACCTCCATCCAGGGTATA 59.751 50.000 0.00 0.00 37.96 1.47
4087 4144 0.665670 CCAGACTGTCTGCACACGAG 60.666 60.000 28.14 11.92 42.98 4.18
4308 4369 5.964477 AGTCCACCTGAAGTTCTAATCCATA 59.036 40.000 4.17 0.00 0.00 2.74
4341 4402 2.489722 GGGTGAAAGAATCTCACTTGGC 59.510 50.000 3.24 0.00 42.38 4.52
4444 4506 4.273318 GGAAAACCTGACAGGAAGCATAT 58.727 43.478 28.56 0.00 37.67 1.78
4445 4507 3.686016 GGAAAACCTGACAGGAAGCATA 58.314 45.455 28.56 0.00 37.67 3.14
4446 4508 2.519013 GGAAAACCTGACAGGAAGCAT 58.481 47.619 28.56 8.91 37.67 3.79
4447 4509 1.813862 CGGAAAACCTGACAGGAAGCA 60.814 52.381 28.56 0.00 37.67 3.91
4448 4510 0.875059 CGGAAAACCTGACAGGAAGC 59.125 55.000 28.56 13.10 37.67 3.86
4450 4512 0.109723 CCCGGAAAACCTGACAGGAA 59.890 55.000 28.56 0.00 37.67 3.36
4452 4514 1.971695 GCCCGGAAAACCTGACAGG 60.972 63.158 20.45 20.45 42.49 4.00
4453 4515 1.971695 GGCCCGGAAAACCTGACAG 60.972 63.158 0.73 0.00 0.00 3.51
4454 4516 2.002018 AAGGCCCGGAAAACCTGACA 62.002 55.000 0.73 0.00 32.92 3.58
4455 4517 0.826256 AAAGGCCCGGAAAACCTGAC 60.826 55.000 0.73 0.00 32.92 3.51
4456 4518 0.105913 AAAAGGCCCGGAAAACCTGA 60.106 50.000 0.73 0.00 32.92 3.86
4457 4519 0.756294 AAAAAGGCCCGGAAAACCTG 59.244 50.000 0.73 0.00 32.92 4.00
4458 4520 3.233953 AAAAAGGCCCGGAAAACCT 57.766 47.368 0.73 0.28 34.45 3.50
4504 4566 4.961435 TCATATCAGCAACGCAAATCAA 57.039 36.364 0.00 0.00 0.00 2.57
4636 4700 1.968493 GGGGAAAACTCCTTTTGACCC 59.032 52.381 0.00 0.00 40.85 4.46
4638 4702 2.035961 GCAGGGGAAAACTCCTTTTGAC 59.964 50.000 0.00 0.00 29.21 3.18
4665 4729 3.581024 TTCTTGCCTCATTTGCATGAC 57.419 42.857 0.00 0.00 41.03 3.06
4691 4756 1.095228 CGCTGTGAACAGTTGGGTGT 61.095 55.000 11.87 0.00 45.45 4.16
4777 4866 3.601435 TGTGAACGGAGAGAAAAACACA 58.399 40.909 0.00 0.00 35.24 3.72
4788 4877 3.257393 CCTCAGAAATCTGTGAACGGAG 58.743 50.000 12.71 1.22 44.12 4.63
4806 4895 3.147629 CATTTCTCAGCCATGATCCCTC 58.852 50.000 0.00 0.00 34.12 4.30
4980 5070 2.045524 AGACAGACTAGGGGATGCATG 58.954 52.381 2.46 0.00 0.00 4.06
4981 5071 2.485966 AGACAGACTAGGGGATGCAT 57.514 50.000 0.00 0.00 0.00 3.96
4982 5072 3.501349 GATAGACAGACTAGGGGATGCA 58.499 50.000 0.00 0.00 34.35 3.96
5016 5106 3.514309 TCTGGCTAAGTTCAAGGGACTAC 59.486 47.826 0.00 0.00 38.49 2.73
5024 5114 5.483685 TTAGCTTCTCTGGCTAAGTTCAA 57.516 39.130 0.00 0.00 44.21 2.69


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

AutoCloner maintained by Alex Coulton.