Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008355.1 Hibiscus syriacus cultivar Beakdansim tig00111092_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 983659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:112 original size:17 final size:18
Alignment explanation
Indices: 87--121 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
77 AATTTTTAAT
*
87 ATACTTCTTA-AAAATTC
1 ATACCTCTTATAAAATTC
104 ATACCTCTTATAAAATTC
1 ATACCTCTTATAAAATTC
122 TGTGTTCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (18 bp):
ATACCTCTTATAAAATTC
Found at i:5317 original size:2 final size:2
Alignment explanation
Indices: 5310--5336 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5300 GCTTCTTGAC
5310 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5337 CATGTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5425 original size:2 final size:2
Alignment explanation
Indices: 5418--5446 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5408 GATCTGTAGT
5418 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5447 AACTACACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6709 original size:2 final size:2
Alignment explanation
Indices: 6702--6732 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6692 TACCCTCACT
6702 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6733 CGTTGTAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12084 original size:12 final size:12
Alignment explanation
Indices: 12067--12099 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
12057 TATGAACGAT
12067 AAACAAAGATTA
1 AAACAAAGATTA
12079 AAACAAAGATTA
1 AAACAAAGATTA
12091 AAACAAAGA
1 AAACAAAGA
12100 GAATGTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.70, C:0.09, G:0.09, T:0.12
Consensus pattern (12 bp):
AAACAAAGATTA
Found at i:13966 original size:32 final size:32
Alignment explanation
Indices: 13921--13983 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
13911 AGAAGAGAAT
*
13921 GAAAAAGGGTAAATTACACCATGAGTAATTAG
1 GAAAAAGGATAAATTACACCATGAGTAATTAG
* *
13953 GAAAAATGATAAATTACACCATGAGTCATTA
1 GAAAAAGGATAAATTACACCATGAGTAATTA
13984 AACTTTACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.24
Consensus pattern (32 bp):
GAAAAAGGATAAATTACACCATGAGTAATTAG
Found at i:14148 original size:30 final size:30
Alignment explanation
Indices: 14127--14185 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
14117 AAAATGATTC
* *
14127 AAATGTAAAGTTCAATGAGCAAATTAGAAA
1 AAATGGAAAGTTCAATGAGCAAAATAGAAA
14157 AAATGGAAAGTTCAATGAGCAAAATAGAA
1 AAATGGAAAGTTCAATGAGCAAAATAGAA
14186 GATAGAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.54, C:0.07, G:0.19, T:0.20
Consensus pattern (30 bp):
AAATGGAAAGTTCAATGAGCAAAATAGAAA
Found at i:14671 original size:2 final size:2
Alignment explanation
Indices: 14664--14688 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14654 TAACTATAAT
14664 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
14689 TTGAATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20279 original size:32 final size:32
Alignment explanation
Indices: 20234--20298 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
20224 GGAGAAGAGA
*
20234 AGGAAGAAGGGTAAATTACACCATGAGTCATT
1 AGGAAAAAGGGTAAATTACACCATGAGTCATT
*
20266 AGGAAAAATGGTAAATTACACCATGAGTCATT
1 AGGAAAAAGGGTAAATTACACCATGAGTCATT
20298 A
1 A
20299 AATTTTACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (32 bp):
AGGAAAAAGGGTAAATTACACCATGAGTCATT
Found at i:20845 original size:18 final size:18
Alignment explanation
Indices: 20810--20845 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20800 TTTAATAAAA
* *
20810 AAATTAAAATTATGAATT
1 AAATTAAAATAATAAATT
20828 AAATTAAAATAATAAATT
1 AAATTAAAATAATAAATT
20846 TAAAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AAATTAAAATAATAAATT
Found at i:20921 original size:21 final size:20
Alignment explanation
Indices: 20879--20921 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
20869 AATAACTATA
* * *
20879 AAAAATATCAAATGTAATTT
1 AAAAATATAAAATATAAATT
20899 AAAAATATAAAATCATAAATT
1 AAAAATATAAAAT-ATAAATT
20920 AA
1 AA
20922 TGTTTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAAATATAAAATATAAATT
Found at i:32545 original size:34 final size:34
Alignment explanation
Indices: 32502--32570 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
32492 TTCGTCCTAC
32502 TAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATATGATAGAATTT
*
32536 TAGGATTCAAACTCCTAAAGATATGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATATGATAGAATTT
32570 T
1 T
32571 GCTAGGATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATATGATAGAATTT
Found at i:32927 original size:23 final size:22
Alignment explanation
Indices: 32896--32957 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
32886 CTTTTCTTTT
32896 TTTTCATGTAATATTTTTTTTAC
1 TTTT-ATGTAATATTTTTTTTAC
*
32919 ATTTTATGT-ATTTTCTTTTTTAC
1 -TTTTATGTAATATT-TTTTTTAC
32942 -TTTA-GTATATATTTTT
1 TTTTATGTA-ATATTTTT
32958 ATTTTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 2 0.06
21 7 0.21
22 8 0.24
23 12 0.36
24 4 0.12
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTATGTAATATTTTTTTTAC
Found at i:32954 original size:24 final size:23
Alignment explanation
Indices: 32911--32956 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
32901 ATGTAATATT
*
32911 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
32934 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
32957 TATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:33044 original size:4 final size:4
Alignment explanation
Indices: 33004--33078 Score: 55
Period size: 4 Copynumber: 18.8 Consensus size: 4
32994 TATTATCAAT
* * * * *
33004 TTTA TTAA TTTA TATA TATA TATA TTTA CTTTT TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA
* *
33053 -TT- TTTC TTTA TTTT TTATA TTTA TTT
1 TTTA TTTA TTTA TTTA TT-TA TTTA TTT
33079 TACTTACTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
3 4 0.07
4 48 0.83
5 6 0.10
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:33074 original size:27 final size:27
Alignment explanation
Indices: 33012--33091 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
33002 ATTTTATTAA
* *
33012 TTTATATATATATATATTTACTTTTTT
1 TTTATATTTATTTATATTTACTTTTTT
*
33039 TATT-TATTTATTTAT-TTTTCTTTATTT
1 T-TTATATTTATTTATATTTACTTT-TTT
* *
33066 TTTATATTTATTT-TACTTACTATTTT
1 TTTATATTTATTTATATTTACTTTTTT
33092 ATCTTTGTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
26 13 0.30
27 28 0.65
28 2 0.05
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTATATTTATTTATATTTACTTTTTT
Found at i:33185 original size:15 final size:15
Alignment explanation
Indices: 33167--33196 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33157 TATTTATTTC
33167 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
33182 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
33197 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:35149 original size:18 final size:18
Alignment explanation
Indices: 35126--35165 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
35116 TTCCTTCAAG
35126 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
35144 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
35162 TCTG
1 TCTG
35166 AAAGACTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (18 bp):
TCTGGATTCACATCCACT
Found at i:35699 original size:8 final size:8
Alignment explanation
Indices: 35686--35724 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
35676 GAACATTTCA
*
35686 TGCATTCT
1 TGCATTTT
35694 TGCA-TTT
1 TGCATTTT
35701 TGCATTTT
1 TGCATTTT
*
35709 TGCCTTTT
1 TGCATTTT
35717 TGCATTTT
1 TGCATTTT
35725 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:36865 original size:16 final size:16
Alignment explanation
Indices: 36850--36903 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
36840 AAAAGGCAAA
36850 AAAAAAAAGAAACAAA-
1 AAAAAAAAGAAA-AAAG
*
36866 AAACAAAAGCAAAAAAG
1 AAAAAAAAG-AAAAAAG
*
36883 AACAAAAAGAAAAAAG
1 AAAAAAAAGAAAAAAG
36899 AAAAA
1 AAAAA
36904 GGGACAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 22 0.69
17 10 0.31
ACGTcount: A:0.83, C:0.07, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAG
Found at i:36866 original size:24 final size:22
Alignment explanation
Indices: 36839--36916 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 22
36829 AATCAGAATA
36839 AAAAAGGCAAAAAAAAAAAGAAAC
1 AAAAA-GCAAAAAAAAAAAG-AAC
* *
36863 AAAAAACAAAAGCAAAAAAGAAC
1 AAAAAGCAAAA-AAAAAAAGAAC
*
36886 AAAAAG-AAAAAAGAAAAAGGGAC
1 AAAAAGCAAAAAA-AAAAA-GAAC
36909 AAAAAGCA
1 AAAAAGCA
36917 CATGCAAAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
21 1 0.02
22 9 0.20
23 22 0.49
24 13 0.29
ACGTcount: A:0.77, C:0.09, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAAGCAAAAAAAAAAAGAAC
Found at i:37544 original size:22 final size:22
Alignment explanation
Indices: 37516--37566 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
37506 CCCCATCAAT
37516 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
37538 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
37560 CCTTTGA
1 CCTTTGA
37567 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:38473 original size:36 final size:36
Alignment explanation
Indices: 38426--38530 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
38416 GTGCTCACCA
38426 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
*
38462 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * *
38499 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
38531 TAAACATTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 32 0.50
37 32 0.50
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:38520 original size:37 final size:37
Alignment explanation
Indices: 38426--38535 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
38416 GTGCTCACCA
38426 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
38462 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* * *
38499 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
38536 ATTGAAAACA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
36 31 0.46
37 33 0.49
38 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:38693 original size:36 final size:36
Alignment explanation
Indices: 38646--38731 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
38636 ATTGAAAACA
** *
38646 TTTCCCTTGAAATGAATTTTGTCT-CTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCT-TTGAGACAG
38682 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
**
38718 TTTCTATTGAAACA
1 TTTCCCTTGAAACA
38732 TAAACTTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 42 0.95
37 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
Found at i:38749 original size:30 final size:30
Alignment explanation
Indices: 38714--38772 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
38704 CTCCTTTGAG
*
38714 ACAGTTTCTATTGAAACATAAA-CTTTGAAA
1 ACAGTTTCCATTGAAACA-AAATCTTTGAAA
*
38744 ACAGTTTCCCTTGAAACAAAATCTTTGAA
1 ACAGTTTCCATTGAAACAAAATCTTTGAA
38773 TATGTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (30 bp):
ACAGTTTCCATTGAAACAAAATCTTTGAAA
Found at i:38753 original size:102 final size:100
Alignment explanation
Indices: 38444--38759 Score: 508
Period size: 100 Copynumber: 3.1 Consensus size: 100
38434 CTTGAGACAG
* * *
38444 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAA-TAA-TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
38509 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
64 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
38546 TTTCCCTTGAAATAAATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTG
1 TTTCCCTTGAAATAATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTG
*
38611 AGACAATTTCTCTTGAAACATAAACATTGAAAACA
66 AGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
38646 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAATTTTGTCTCCTT
1 TTTCCCTTGAAAT-AA-TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* *
38710 TGAGACAGTTTCTATTGAAACATAAACTTTGAAAACA
64 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
38747 GTTTCCCTTGAAA
1 -TTTCCCTTGAAA
38760 CAAAATCTTT
Statistics
Matches: 201, Mismatches: 10, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
100 94 0.47
101 52 0.26
102 55 0.27
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (100 bp):
TTTCCCTTGAAATAATTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTG
AGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:38847 original size:36 final size:36
Alignment explanation
Indices: 38786--38900 Score: 149
Period size: 37 Copynumber: 3.1 Consensus size: 36
38776 GTTTTACATT
* *
38786 AAACAAATTTCGTCTCTCCTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * * *
38822 AAACAAATTTTGTCTATCTTAAGACATGTTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCTCTTG
*
38859 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
38896 AAACA
1 AAACA
38901 TCAATCCTTG
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
36 23 0.35
37 24 0.36
38 19 0.29
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.38
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:39006 original size:33 final size:33
Alignment explanation
Indices: 38942--39056 Score: 162
Period size: 33 Copynumber: 3.5 Consensus size: 33
38932 CCTTGATACA
38942 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACAC--AAA-AAACCTTTGAAATT
*
38978 GTTTCTCTTGAAACACAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
*
39011 GTTTCTCTTGAAACAC--AAAACCTTTGAGATT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
*
39042 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
39057 AATTTTGTCT
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 27 0.36
33 29 0.39
34 3 0.04
36 16 0.21
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.32
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
Found at i:39103 original size:67 final size:67
Alignment explanation
Indices: 39011--39204 Score: 235
Period size: 67 Copynumber: 2.8 Consensus size: 67
39001 CTTTGAAAAT
*
39011 GTTTCTCTTGAAACACAAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
39076 CA
66 CA
* * * *
39078 GTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCTTTAAAACAAAATTTTTGTCTCCCTTGA
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAAC-AAA-TTTTGTCTCCCTTGA
* *
39143 GGCC
64 GACA
* * * * **
39147 GTTTCTCATGAAACAACATATATCTTTAAGATCGTTTCCCTTGAAATGAATTTTGTCT
1 GTTTCTCTTGAAAC-ACA-AAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCT
39205 TTTTTAAGAC
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
67 40 0.38
68 3 0.03
69 38 0.36
70 5 0.05
71 20 0.19
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.39
Consensus pattern (67 bp):
GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
CA
Found at i:39925 original size:105 final size:103
Alignment explanation
Indices: 39779--40169 Score: 327
Period size: 105 Copynumber: 3.8 Consensus size: 103
39769 ATTTCAACTC
* *
39779 CACGATGGAGGATATCGTGCCACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTG
1 CACGACGGAGGATATCATGCCACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTG
39844 GTTGTCAACGAACAACTTTCCAATTTCAAAGCTGATTTTT
66 GTTGTCAAC-AACAA-TTTCCAATTTCAAAGCTGATTTTT
* * *
39884 CACGACGGAGGATATCATGCTAC-CTATGACAACACAAGTTCAACTTCACAACGAAGGGACGGTT
1 CACGACGGAGGATATCATGCCACTC-AAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
* ** **
39948 GGTTGTCAACAACAATTTCCCAGTTTCAGGGCCAATTTCAACTT
65 GGTTGTCAACAACAATTT-CCAATTTCAAAGCTGATTT----TT
* * * * * *
39992 CAC-AGCGGAGGATAT--TG-GACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCT
1 CACGA-CGGAGGATATCATGCCACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
** ** * * * * **
40053 GACTGTCAACAAACAATTTCGGA--GCCAATCTCA-ACTT
65 GGTTGTCAAC-AACAATTTCCAATTTCAAAGCTGATTTTT
* * * * *
40090 CACAACGAAGGATAT--TG-GACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGGACGGCTG
1 CACGACGGAGGATATCATGCCACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTG
40152 GTTGTCAACAAACAATTT
66 GTTGTCAAC-AACAATTT
40170 TCTGGTTCCA
Statistics
Matches: 235, Mismatches: 41, Indels: 27
0.78 0.14 0.09
Matches are distributed among these distances:
98 70 0.30
99 1 0.00
103 6 0.03
104 20 0.09
105 111 0.47
106 11 0.05
107 1 0.00
108 15 0.06
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (103 bp):
CACGACGGAGGATATCATGCCACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTG
GTTGTCAACAACAATTTCCAATTTCAAAGCTGATTTTT
Found at i:40123 original size:98 final size:98
Alignment explanation
Indices: 39914--40169 Score: 280
Period size: 98 Copynumber: 2.5 Consensus size: 98
39904 TACCTATGAC
* * ** *
39914 AACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAAC-AACAATTTCCCAGTTTCAGG
1 AACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAATTT--C-G-----GA
* * * *
39978 GCCAATTTCAACTTCACAGCGGAGGATATTGGACCCAAGAC
58 GCCAATCTCAACTTCACAACGAAGGATATTGGACCCAAGAA
* * *
40019 AGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCGGAGCCAATCT
1 AACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAATTTCGGAGCCAATCT
* *
40084 CAACTTCACAACGAAGGATATTGGACTCGAGAA
66 CAACTTCACAACGAAGGATATTGGACCCAAGAA
* **
40117 AACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT
1 AACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAATTT
40170 TCTGGTTCCA
Statistics
Matches: 130, Mismatches: 20, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
98 83 0.64
103 1 0.01
104 1 0.01
105 37 0.28
106 8 0.06
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (98 bp):
AACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAATTTCGGAGCCAATCT
CAACTTCACAACGAAGGATATTGGACCCAAGAA
Found at i:40808 original size:34 final size:34
Alignment explanation
Indices: 40765--40889 Score: 120
Period size: 34 Copynumber: 3.8 Consensus size: 34
40755 TTCGTCCTAC
40765 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
40799 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
*
40834 GCTAGGATTC--A-----AAAAATAGGATATAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
40863 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
40890 CCACAAGCAC
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 12 0.16
34 39 0.53
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.32
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:41185 original size:23 final size:22
Alignment explanation
Indices: 41154--41215 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
41144 TTTTCTTTTT
41154 TTTTCATGTAATATTTTTTTTAC
1 TTTT-ATGTAATATTTTTTTTAC
*
41177 ATTTTATGT-ATTTTCTTTTTTAC
1 -TTTTATGTAATATT-TTTTTTAC
41200 -TTTA-GTATATATTTTT
1 TTTTATGTA-ATATTTTT
41216 ATTTTTTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 2 0.06
21 7 0.21
22 8 0.24
23 12 0.36
24 4 0.12
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.68
Consensus pattern (22 bp):
TTTTATGTAATATTTTTTTTAC
Found at i:41212 original size:24 final size:23
Alignment explanation
Indices: 41169--41214 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
41159 ATGTAATATT
*
41169 TTTTTTACATTTTATGTATTTTC
1 TTTTTTACATTTTATATATTTTC
41192 TTTTTTAC-TTTAGTATATATTTT
1 TTTTTTACATTT--TATATATTTT
41215 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 8 0.40
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTTACATTTTATATATTTTC
Found at i:41320 original size:34 final size:31
Alignment explanation
Indices: 41281--41341 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
41271 TATATATATA
*
41281 TATATATTTACTT-TTTTTA-TTTTTTTATTT
1 TATATATATA-TTATTTTTACTTTTTTTATTT
41311 TATATATATATTATTTTTACTTTTTTTATTT
1 TATATATATATTATTTTTACTTTTTTTATTT
41342 ATTTGTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 2 0.07
30 15 0.54
31 11 0.39
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (31 bp):
TATATATATATTATTTTTACTTTTTTTATTT
Found at i:41341 original size:39 final size:39
Alignment explanation
Indices: 41211--41407 Score: 149
Period size: 39 Copynumber: 5.0 Consensus size: 39
41201 TTAGTATATA
** * *
41211 TTTTTATTTTTTTAGATTATATATATA-AATATATTA-TT
1 TTTTTATTTTTTTATTTTATATATATATTAT-TTTTACTT
* *
41249 TTTATTATCAGTTTTATTAATTTATATATATATATATATTTACTT
1 TTT-TTAT---TTTT-TTATTTTATATATATAT-TATTTTTACTT
41294 TTTTTATTTTTTTATTTTATATATATATTATTTTTACTT
1 TTTTTATTTTTTTATTTTATATATATATTATTTTTACTT
* * * *
41333 TTTTTATTTATTTGTTTTATTTCTATATT-TTTTT-CTT
1 TTTTTATTTTTTTATTTTATATATATATTATTTTTACTT
*
41370 TTTCTTCTTTTTCTTTATTTT-T-TATAT-TTA-TTTTACTT
1 TTT-TT-ATTTT-TTTATTTTATATATATATTATTTTTACTT
41408 ACTATTTTAT
Statistics
Matches: 131, Mismatches: 15, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
37 12 0.09
38 17 0.13
39 43 0.33
40 23 0.18
41 4 0.03
42 4 0.03
43 14 0.11
44 7 0.05
45 7 0.05
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.70
Consensus pattern (39 bp):
TTTTTATTTTTTTATTTTATATATATATTATTTTTACTT
Found at i:41343 original size:43 final size:43
Alignment explanation
Indices: 41213--41398 Score: 129
Period size: 44 Copynumber: 4.3 Consensus size: 43
41203 AGTATATATT
** * *
41213 TTTATTTTTTTAGATTATATATATA-AATATATTA-TTTTTATTA
1 TTTATTTTTTTATTTTATATATATATTAT-TTTTACTTTTT-TTA
* * * *
41256 -TCAGTTTTATTAATTTATATATATATATATATTTAC---TTTT-
1 TTTA-TTTTTTTATTTTATATATATAT-TATTTTTACTTTTTTTA
41296 TTTATTTTTTTATTTTATATATATATTATTTTTACTTTTTTTA
1 TTTATTTTTTTATTTTATATATATATTATTTTTACTTTTTTTA
* * * *
41339 TTTATTTGTTTTATTTCTATAT-TTTTTTCTTTTT-CTTCTTTTTC
1 TTTATTT-TTTTATTT-TATATATATATTATTTTTACTT-TTTTTA
41383 TTTATTTTTTATATTT
1 TTTATTTTTT-TATTT
41399 ATTTTACTTA
Statistics
Matches: 115, Mismatches: 15, Indels: 25
0.74 0.10 0.16
Matches are distributed among these distances:
39 8 0.07
40 20 0.17
41 4 0.03
42 8 0.07
43 31 0.27
44 37 0.32
45 7 0.06
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (43 bp):
TTTATTTTTTTATTTTATATATATATTATTTTTACTTTTTTTA
Found at i:41397 original size:9 final size:8
Alignment explanation
Indices: 41287--41404 Score: 58
Period size: 9 Copynumber: 13.5 Consensus size: 8
41277 TATATATATA
41287 TTTACTTTT
1 TTTA-TTTT
41296 TTTATTTT
1 TTTATTTT
41304 TTTA-TTT
1 TTTATTTT
* *
41311 TATATATAT
1 TTTAT-TTT
*
41320 ATTATTTT
1 TTTATTTT
*
41328 TACTTTTTTT
1 T--TTATTTT
41338 ATTTATTTGT
1 -TTTATTT-T
*
41348 TTTATTTC
1 TTTATTTT
*
41356 TATATTTT
1 TTTATTTT
*
41364 TTTCTTTT
1 TTTATTTT
*
41372 TCTTCTTTTT
1 T-TT-ATTTT
41382 CTTTATTTT
1 -TTTATTTT
41391 TTATATTTAT
1 TT-TATTT-T
41401 TTTA
1 TTTA
41405 CTTACTATTT
Statistics
Matches: 83, Mismatches: 15, Indels: 22
0.69 0.12 0.18
Matches are distributed among these distances:
7 6 0.07
8 25 0.30
9 34 0.41
10 16 0.19
11 2 0.02
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.76
Consensus pattern (8 bp):
TTTATTTT
Found at i:41509 original size:15 final size:15
Alignment explanation
Indices: 41491--41520 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41481 TATTTATTTC
41491 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
41506 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
41521 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:46469 original size:30 final size:30
Alignment explanation
Indices: 46428--46505 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
46418 TGAAAATTGA
* * *
46428 ATTAAATGGGGATGGGGAAAAATCGTTTAT
1 ATTAAACGGGGACGGGGAAAAACCGTTTAT
* **
46458 GTTAAACGGGGACGGAAAAAAACCGTTTAT
1 ATTAAACGGGGACGGGGAAAAACCGTTTAT
46488 ATTAAACGGGGACGGGGA
1 ATTAAACGGGGACGGGGA
46506 CGGGTTTGGT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.37, C:0.09, G:0.32, T:0.22
Consensus pattern (30 bp):
ATTAAACGGGGACGGGGAAAAACCGTTTAT
Found at i:46611 original size:17 final size:17
Alignment explanation
Indices: 46590--46634 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
46580 TAATTTAAAA
46590 ATATATATATATAATATT
1 ATATATATATATAAT-TT
46608 -TATATAT-T-TAATTT
1 ATATATATATATAATTT
*
46622 AAATATATATATA
1 ATATATATATATA
46635 CCCGGTCCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
14 2 0.09
15 10 0.43
16 2 0.09
17 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATATATATATAATTT
Found at i:46617 original size:36 final size:37
Alignment explanation
Indices: 46549--46634 Score: 124
Period size: 36 Copynumber: 2.4 Consensus size: 37
46539 CCGATAAATA
46549 TTAAAAAT-TAT-TATATATATATTAATAAATTTAAT
1 TTAAAAATATATATATATATATATTAATAAATTTAAT
* *
46584 TTAAAAATATATATATATA-ATATTTATATATTTAAT
1 TTAAAAATATATATATATATATATTAATAAATTTAAT
*
46620 TTAAATATATATATA
1 TTAAAAATATATATA
46635 CCCGGTCCGA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 8 0.17
36 32 0.70
37 6 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
TTAAAAATATATATATATATATATTAATAAATTTAAT
Found at i:46942 original size:4 final size:4
Alignment explanation
Indices: 46933--47024 Score: 70
Period size: 4 Copynumber: 24.5 Consensus size: 4
46923 AAATAATTAT
* * * *
46933 TATA TATA TATA TATA T-TA T-TA -ATA AATT TA-A TTTA AATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
46977 TATA TATA TATA TA-A TATT TATA TATT TA-A TTTA AATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
47023 TA
1 TA
47025 CCCGATCCGA
Statistics
Matches: 68, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
3 12 0.18
4 56 0.82
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:46944 original size:6 final size:6
Alignment explanation
Indices: 46933--47024 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
46923 AAATAATTAT
* * * *
46933 TATATA TATATA TATAT- TAT-TA -ATAAA TTTA-A TTTAAA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
46977 TATATA TATATA TA-ATA TTTATA TATTTA -ATTTA AATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
47023 TA
1 TA
47025 CCCGATCCGA
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
4 3 0.04
5 18 0.25
6 50 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TATATA
Found at i:47005 original size:42 final size:42
Alignment explanation
Indices: 46933--47024 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
46923 AAATAATTAT
*
46933 TATATATATATATATATTATTAATAAATTTAATTTAAATATA
1 TATATATATATATATAATATTAATAAATTTAATTTAAATATA
* *
46975 TATATATATATATATAATATTTATATATTTAATTTAAATATA
1 TATATATATATATATAATATTAATAAATTTAATTTAAATATA
47017 TATATATA
1 TATATATA
47025 CCCGATCCGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (42 bp):
TATATATATATATATAATATTAATAAATTTAATTTAAATATA
Found at i:49173 original size:11 final size:11
Alignment explanation
Indices: 49157--49182 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
49147 CCCAACCCAT
49157 GCTTTATCACA
1 GCTTTATCACA
49168 GCTTTATCACA
1 GCTTTATCACA
49179 GCTT
1 GCTT
49183 AAAAAAATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (11 bp):
GCTTTATCACA
Found at i:50652 original size:20 final size:20
Alignment explanation
Indices: 50629--50680 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
50619 AACGCGATCC
50629 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
50649 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
50669 CCAAAATCGCAA
1 CCAGAATCGCAA
50681 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:50761 original size:20 final size:20
Alignment explanation
Indices: 50736--50929 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
50726 GATTTTCCAT
* *
50736 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
50756 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
50776 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
50796 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
50816 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
50836 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
50856 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
50876 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
50897 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
50917 AATCGCAACGCGA
1 AATCGCAACGCGA
50930 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:50781 original size:40 final size:39
Alignment explanation
Indices: 50732--50929 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
50722 TTGCGATTTT
* ** *
50732 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
50770 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
50811 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
50851 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
50890 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
50930 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:50819 original size:60 final size:60
Alignment explanation
Indices: 50736--50928 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
50726 GATTTTCCAT
* ** * *
50736 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
50796 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
50856 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
50917 AATCGCAACGCG
1 AATCGCAACGCG
50929 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:51349 original size:33 final size:33
Alignment explanation
Indices: 51310--51380 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
51300 TTCACTTAGA
*
51310 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
51343 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
51376 TTTCA
1 TTTCA
51381 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:51520 original size:14 final size:14
Alignment explanation
Indices: 51501--51555 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
51491 AGAATGACTG
51501 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
51515 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
51534 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
51548 TCGCAACG
1 TCGCAACG
51556 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:51538 original size:33 final size:33
Alignment explanation
Indices: 51501--51571 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
51491 AGAATGACTG
**
51501 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
51534 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
51567 TCGCA
1 TCGCA
51572 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:51589 original size:19 final size:19
Alignment explanation
Indices: 51567--51664 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
51557 GAAACCAAAA
*
51567 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
51586 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
51600 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
51619 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
51633 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
51652 TCGCGTTGCGATT
1 TCGCGTTGCGATT
51665 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:51608 original size:14 final size:14
Alignment explanation
Indices: 51589--51678 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
51579 TTTCATTTCG
51589 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
51603 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
51622 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
51636 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
51653 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
51669 CGTTGCGATT
1 CGTTGCGATT
51679 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:51614 original size:33 final size:33
Alignment explanation
Indices: 51572--51686 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
51562 CAAAATCGCA
51572 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
51605 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
51638 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
51671 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
51687 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:53611 original size:185 final size:186
Alignment explanation
Indices: 53381--54038 Score: 1293
Period size: 185 Copynumber: 3.5 Consensus size: 186
53371 TAGATTGCTT
*
53381 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
53446 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
53511 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
53566 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
53631 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
53696 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTC-TTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
53751 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
53816 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
53881 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
53937 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54002 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
54039 ATCCATTCAA
Statistics
Matches: 470, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
185 339 0.72
186 131 0.28
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:53695 original size:93 final size:93
Alignment explanation
Indices: 53381--54038 Score: 1293
Period size: 93 Copynumber: 7.1 Consensus size: 93
53371 TAGATTGCTT
*
53381 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
53446 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
53474 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
53538 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
53566 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
53631 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
53659 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
53724 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
53751 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
53816 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
53844 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
53909 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
53937 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54002 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
54030 AGTAAATTT
1 AGTAAATTT
54039 ATCCATTCAA
Statistics
Matches: 562, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.33
93 378 0.67
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:53878 original size:278 final size:278
Alignment explanation
Indices: 53381--54038 Score: 1291
Period size: 278 Copynumber: 2.4 Consensus size: 278
53371 TAGATTGCTT
*
53381 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
53446 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
53511 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
131 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
53576 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
196 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
53641 TTTTGTCTTTTGGTTGAA
261 TTTTGTCTTTTGGTTGAA
53659 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
53724 TTTGTCTTTGTTTTGTC-TTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
53788 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
131 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
53853 GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
195 GTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTT
53918 GTTTTGTCTTTTGGTTGAA
260 GTTTTGTCTTTTGGTTGAA
53937 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
54002 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
54039 ATCCATTCAA
Statistics
Matches: 377, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
277 72 0.19
278 286 0.76
279 19 0.05
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (278 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTG
TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
TTTTGTCTTTTGGTTGAA
Found at i:54122 original size:19 final size:19
Alignment explanation
Indices: 54082--54210 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
54072 TAGTTTACTT
* *
54082 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
54102 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
54121 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
54140 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
54154 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
54173 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
54187 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
54206 TCGCA
1 TCGCA
54211 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:54161 original size:33 final size:32
Alignment explanation
Indices: 54118--54210 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
54108 CGCGAAACCA
**
54118 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
54150 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
54183 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
54211 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:54208 original size:52 final size:52
Alignment explanation
Indices: 54082--54210 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
54072 TAGTTTACTT
**
54082 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
54134 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
54187 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
54211 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:54758 original size:20 final size:20
Alignment explanation
Indices: 54730--55078 Score: 427
Period size: 20 Copynumber: 17.4 Consensus size: 20
54720 AAATTTCAGT
* * * *
54730 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
54750 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
54770 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
54790 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
54810 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
54830 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
54850 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
54870 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
54890 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
54910 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
54930 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
54950 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
54970 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
54990 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
55010 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
55030 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
55050 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
55070 GTTGCGATT
1 GTTGCGATT
55079 ATGGAAAATC
Statistics
Matches: 291, Mismatches: 30, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.02
20 281 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:56285 original size:16 final size:16
Alignment explanation
Indices: 56262--56304 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
56252 AAAGAAAAAG
*
56262 AAAAATAAATAAATTA
1 AAAAATAAATAAACTA
*
56278 ATAAATAAATAAACTA
1 AAAAATAAATAAACTA
56294 AAAAGATAAAT
1 AAAA-ATAAAT
56305 TGAAAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (16 bp):
AAAAATAAATAAACTA
Found at i:56426 original size:16 final size:15
Alignment explanation
Indices: 56405--56472 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 15
56395 AATTTAAGGC
*
56405 AAATAAGATGAAAATA
1 AAATAA-ATAAAAATA
56421 AAATAAATAAAAATA
1 AAATAAATAAAAATA
*
56436 ATAATAAATATACTAATA
1 A-AATAAATA-A-AAATA
56454 AATATGAAAT-AAAATA
1 AA-AT-AAATAAAAATA
56470 AAA
1 AAA
56473 AAACAACATG
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
15 10 0.23
16 20 0.45
17 3 0.07
18 7 0.16
19 4 0.09
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (15 bp):
AAATAAATAAAAATA
Found at i:56456 original size:12 final size:12
Alignment explanation
Indices: 56416--56470 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
56406 AATAAGATGA
*
56416 AAATAAAATAAAT
1 AAATATAAT-AAT
*
56429 AAAAATAATAAT
1 AAATATAATAAT
*
56441 AAATATACTAAT
1 AAATATAATAAT
*
56453 AAATATGA-AAT
1 AAATATAATAAT
56464 AAA-ATAA
1 AAATATAA
56471 AAAAACAACA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
10 3 0.09
11 6 0.17
12 19 0.54
13 7 0.20
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (12 bp):
AAATATAATAAT
Found at i:57738 original size:18 final size:18
Alignment explanation
Indices: 57715--57753 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
57705 CCATAAAACA
*
57715 GAATAAA-TGAAATTAAAT
1 GAATAAAGTG-AATAAAAT
57733 GAATAAAGTGAATAAAAT
1 GAATAAAGTGAATAAAAT
57751 GAA
1 GAA
57754 AAGAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (18 bp):
GAATAAAGTGAATAAAAT
Found at i:57764 original size:27 final size:27
Alignment explanation
Indices: 57715--57766 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
57705 CCATAAAACA
**
57715 GAATAAATGAAATTAAATGAATAAAGT
1 GAATAAATGAAAAGAAATGAATAAAGT
57742 GAATAAAATGAAAAGAAAT-AATAAA
1 GAAT-AAATGAAAAGAAATGAATAAA
57767 AATACTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.21
Consensus pattern (27 bp):
GAATAAATGAAAAGAAATGAATAAAGT
Found at i:57908 original size:33 final size:31
Alignment explanation
Indices: 57865--57932 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 31
57855 ACTATATACC
57865 ATATAGTTTTCAAAAATGA-TTTTAAAAATATT
1 ATATAGTTTTCAAAAAT-ATTTTTAAAAATA-T
* *
57897 ATATGAGTTTTCCAAAATATTTTTAAAACTAT
1 ATAT-AGTTTTCAAAAATATTTTTAAAAATAT
57929 ATAT
1 ATAT
57933 TATATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (31 bp):
ATATAGTTTTCAAAAATATTTTTAAAAATAT
Found at i:58023 original size:35 final size:35
Alignment explanation
Indices: 57979--58061 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 35
57969 TATACATTAT
57979 ATTTTCAAAATGATTTCAAAA-ATATA-TGTTATATA
1 ATTTTCAAAATG-TTTCAAAATATATATTG-TATATA
*
58014 ATTTTCAAAATGTTTTAAAACTTATATATTGTATATA
1 ATTTTCAAAATGTTTCAAAA--TATATATTGTATATA
58051 AGTTTTCAAAA
1 A-TTTTCAAAA
58062 ACGTTTTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
34 7 0.17
35 12 0.29
37 12 0.29
38 11 0.26
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (35 bp):
ATTTTCAAAATGTTTCAAAATATATATTGTATATA
Found at i:58068 original size:110 final size:110
Alignment explanation
Indices: 57866--58068 Score: 256
Period size: 110 Copynumber: 1.8 Consensus size: 110
57856 CTATATACCA
* * *
57866 TATAGTTTTCAAAAATGATTTTAAAAATATTATATGAGTTTTCCAAAATATTTTTAAAACTATAT
1 TATAGTTTTCAAAAATGATTTAAAAAATATTATATGAATTTTCCAAAATAGTTTTAAAACTATAT
*
57931 ATTATATAAAATTTTCAAAAAATGTTTTTACTTTAAACTATACAT
66 ATTATATAAAATTTTCAAAAAACGTTTTTACTTTAAACTATACAT
57976 TATA-TTTTC-AAAATGATTTCAAAAATATATGTTATAT-AATTTT-CAAAAT-GTTTTAAAACT
1 TATAGTTTTCAAAAATGATTT-AAAAA-ATA--TTATATGAATTTTCCAAAATAGTTTTAAAAC-
* *
58036 TATATATTGTATATAAGTTTTC-AAAAACGTTTT
61 TATATATTATATA-AAATTTTCAAAAAACGTTTT
58069 AAAAGAACTA
Statistics
Matches: 81, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
108 10 0.12
109 18 0.22
110 35 0.43
111 12 0.15
112 6 0.07
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (110 bp):
TATAGTTTTCAAAAATGATTTAAAAAATATTATATGAATTTTCCAAAATAGTTTTAAAACTATAT
ATTATATAAAATTTTCAAAAAACGTTTTTACTTTAAACTATACAT
Found at i:58072 original size:39 final size:37
Alignment explanation
Indices: 58000--58072 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 37
57990 GATTTCAAAA
*
58000 ATATATGTTATATAATTTTCAAAATGTTTTAAAACTT
1 ATATATGTTATATAATTTTCAAAACGTTTTAAAACTT
58037 ATATAT-TGTATATAAGTTTTCAAAAACGTTTTAAAA
1 ATATATGT-TATATAA-TTTTC-AAAACGTTTTAAAA
58073 GAACTATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 1 0.03
37 13 0.41
38 5 0.16
39 13 0.41
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (37 bp):
ATATATGTTATATAATTTTCAAAACGTTTTAAAACTT
Found at i:58081 original size:39 final size:37
Alignment explanation
Indices: 57999--58095 Score: 99
Period size: 39 Copynumber: 2.5 Consensus size: 37
57989 TGATTTCAAA
* *
57999 AATATATGT-TATATAATTTTCAAAATGTTTTAAAACT
1 AATATAT-TATATATAATTTTCAAAACGTTTTAAAACG
* *
58036 TATATATTGTATATAAGTTTTCAAAAACGTTTTAAAA-G
1 AATATATTATATATAA-TTTTC-AAAACGTTTTAAAACG
58074 AACTATATTATATATATATTTT
1 AA-TATATTATATATA-ATTTT
58096 TGGAAACCGT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
36 1 0.02
37 13 0.26
38 6 0.12
39 29 0.58
40 1 0.02
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (37 bp):
AATATATTATATATAATTTTCAAAACGTTTTAAAACG
Found at i:58920 original size:84 final size:84
Alignment explanation
Indices: 58780--59457 Score: 747
Period size: 84 Copynumber: 8.2 Consensus size: 84
58770 TTGAATATAA
* * * *
58780 TCGAACTCGAAGGTC--TT--TAGCAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
58841 GCCTTGGAGCTGAGCGGAG
66 GCCTTGGAGCTGAGCGGAG
** * * * *
58860 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
58925 GCCTTGGAGCTGAGCGGAG
66 GCCTTGGAGCTGAGCGGAG
* * * * * ** *
58944 TCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTATTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
59009 GCCTTGGAGCTGAGCAGAG
66 GCCTTGGAGCTGAGCGGAG
* * ** *
59028 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTGTATTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
59093 GCCTTGGAGCTGAGCAGAG
66 GCCTTGGAGCTGAGCGGAG
*
59112 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
** * *
59177 GCCCCCGAAGCTGAGTGTGA-
66 G-CCTTGGAGCTGAGCG-GAG
* ** * *
59197 TCGAACTTGGGGGTC--TT--TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
59258 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGGAG
* * * * * * *
59277 TCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTAT
1 TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * *
59341 GCCCTTGAAGCTGAGTGTAA
66 G-CCTTGGAGCTGAGCGGAG
* * * *
59361 TCGAACT-TAAGGGTC--TT--TGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATG
1 TCGAACTCGAA-GGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
*
59421 TGCCTTGGAGCTGAGCGTAG
65 TGCCTTGGAGCTGAGCGGAG
59441 TCGAACTCGAAGGTCTT
1 TCGAACTCGAAGGTCTT
59458 AGTGGCAGGT
Statistics
Matches: 509, Mismatches: 74, Indels: 28
0.83 0.12 0.05
Matches are distributed among these distances:
79 1 0.00
80 64 0.13
81 82 0.16
82 2 0.00
83 42 0.08
84 294 0.58
85 22 0.04
86 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTTGGTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
GCCTTGGAGCTGAGCGGAG
Found at i:62865 original size:18 final size:19
Alignment explanation
Indices: 62825--62869 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
62815 AGTTAATGTG
*
62825 AATGCAGAGAAAATAATAA
1 AATGCAAAGAAAATAATAA
62844 AATGCAAAGAAAATAA-AA
1 AATGCAAAGAAAATAATAA
62862 AATGCAAA
1 AATGCAAA
62870 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (19 bp):
AATGCAAAGAAAATAATAA
Found at i:64601 original size:14 final size:14
Alignment explanation
Indices: 64564--64601 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
64554 AAAAACATTA
*
64564 AATACAAAAA-AAT
1 AATAAAAAAATAAT
64577 AATAAAAAAATAAT
1 AATAAAAAAATAAT
*
64591 AATAATAAAAT
1 AATAAAAAAAT
64602 TAACTAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (14 bp):
AATAAAAAAATAAT
Found at i:64799 original size:16 final size:15
Alignment explanation
Indices: 64778--64845 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 15
64768 AATTTAAGGC
*
64778 AAATAAGATGAAAATA
1 AAATAA-ATAAAAATA
64794 AAATAAATAAAAATA
1 AAATAAATAAAAATA
*
64809 ATAATAAATATACTAATA
1 A-AATAAATA-A-AAATA
64827 AATATGAAAT-AAAATA
1 AA-AT-AAATAAAAATA
64843 AAA
1 AAA
64846 AAAAAACAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
15 10 0.23
16 20 0.45
17 3 0.07
18 7 0.16
19 4 0.09
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (15 bp):
AAATAAATAAAAATA
Found at i:64829 original size:12 final size:12
Alignment explanation
Indices: 64789--64843 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
64779 AATAAGATGA
*
64789 AAATAAAATAAAT
1 AAATATAAT-AAT
*
64802 AAAAATAATAAT
1 AAATATAATAAT
*
64814 AAATATACTAAT
1 AAATATAATAAT
*
64826 AAATATGA-AAT
1 AAATATAATAAT
64837 AAA-ATAA
1 AAATATAA
64844 AAAAAAAACA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
10 3 0.09
11 6 0.17
12 19 0.54
13 7 0.20
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (12 bp):
AAATATAATAAT
Found at i:66113 original size:18 final size:18
Alignment explanation
Indices: 66090--66128 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
66080 CCATAAAACA
*
66090 GAATAAA-TGAAATTAAAT
1 GAATAAAGTG-AATAAAAT
66108 GAATAAAGTGAATAAAAT
1 GAATAAAGTGAATAAAAT
66126 GAA
1 GAA
66129 AAGAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (18 bp):
GAATAAAGTGAATAAAAT
Found at i:66139 original size:27 final size:27
Alignment explanation
Indices: 66090--66141 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
66080 CCATAAAACA
**
66090 GAATAAATGAAATTAAATGAATAAAGT
1 GAATAAATGAAAAGAAATGAATAAAGT
66117 GAATAAAATGAAAAGAAAT-AATAAA
1 GAAT-AAATGAAAAGAAATGAATAAA
66142 ATACTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.21
Consensus pattern (27 bp):
GAATAAATGAAAAGAAATGAATAAAGT
Found at i:66203 original size:29 final size:30
Alignment explanation
Indices: 66168--66231 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
66158 AGACTATATA
* *
66168 ATATATATCTCAAAAAATATTTT-TAAACT
1 ATATATATATCAAAAAATATTTTCAAAACT
** *
66197 ATATATATATTTAAAAATGTTTTCAAAACT
1 ATATATATATCAAAAAATATTTTCAAAACT
66227 ATATA
1 ATATA
66232 CCATATAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (30 bp):
ATATATATATCAAAAAATATTTTCAAAACT
Found at i:66277 original size:33 final size:31
Alignment explanation
Indices: 66180--66301 Score: 90
Period size: 33 Copynumber: 3.8 Consensus size: 31
66170 ATATATCTCA
*
66180 AAAAATATTTTT-AAACTATATATA-TATTT-
1 AAAAATATTTTTAAAAATATATATAGT-TTTC
* *
66209 AAAAATGTTTTCAAAACTATATACCATATAGTTTTC
1 AAAAATATTTTTAAAA--ATAT---ATATAGTTTTC
66245 AAAAATGA-TTTTAAAAATATTATATGAGTTTTC
1 AAAAAT-ATTTTTAAAAATA-TATAT-AGTTTTC
* *
66278 CAAAATATTTTTAAAACTATATAT
1 AAAAATATTTTTAAAAATATATAT
66302 TATATAAAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 21
0.73 0.07 0.21
Matches are distributed among these distances:
29 10 0.14
30 3 0.04
32 13 0.18
33 22 0.30
34 3 0.04
35 9 0.12
36 14 0.19
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (31 bp):
AAAAATATTTTTAAAAATATATATAGTTTTC
Found at i:66392 original size:35 final size:35
Alignment explanation
Indices: 66348--66430 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 35
66338 TATACATTAT
66348 ATTTTCAAAATGATTTCAAAA-ATATA-TGTTATATA
1 ATTTTCAAAATG-TTTCAAAATATATATTG-TATATA
*
66383 ATTTTCAAAATGTTTTAAAACTTATATATTGTATATA
1 ATTTTCAAAATGTTTCAAAA--TATATATTGTATATA
66420 AGTTTTCAAAA
1 A-TTTTCAAAA
66431 ACGTTTTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
34 7 0.17
35 12 0.29
37 12 0.29
38 11 0.26
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (35 bp):
ATTTTCAAAATGTTTCAAAATATATATTGTATATA
Found at i:66437 original size:110 final size:110
Alignment explanation
Indices: 66235--66437 Score: 256
Period size: 110 Copynumber: 1.8 Consensus size: 110
66225 CTATATACCA
* * *
66235 TATAGTTTTCAAAAATGATTTTAAAAATATTATATGAGTTTTCCAAAATATTTTTAAAACTATAT
1 TATAGTTTTCAAAAATGATTTAAAAAATATTATATGAATTTTCCAAAATAGTTTTAAAACTATAT
*
66300 ATTATATAAAATTTTCAAAAAATGTTTTTAGTTTAAACTATACAT
66 ATTATATAAAATTTTCAAAAAACGTTTTTAGTTTAAACTATACAT
66345 TATA-TTTTC-AAAATGATTTCAAAAATATATGTTATAT-AATTTT-CAAAAT-GTTTTAAAACT
1 TATAGTTTTCAAAAATGATTT-AAAAA-ATA--TTATATGAATTTTCCAAAATAGTTTTAAAAC-
* *
66405 TATATATTGTATATAAGTTTTC-AAAAACGTTTT
61 TATATATTATATA-AAATTTTCAAAAAACGTTTT
66438 AAAAGAACTA
Statistics
Matches: 81, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
108 10 0.12
109 18 0.22
110 35 0.43
111 12 0.15
112 6 0.07
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (110 bp):
TATAGTTTTCAAAAATGATTTAAAAAATATTATATGAATTTTCCAAAATAGTTTTAAAACTATAT
ATTATATAAAATTTTCAAAAAACGTTTTTAGTTTAAACTATACAT
Found at i:66441 original size:39 final size:37
Alignment explanation
Indices: 66369--66441 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 37
66359 GATTTCAAAA
*
66369 ATATATGTTATATAATTTTCAAAATGTTTTAAAACTT
1 ATATATGTTATATAATTTTCAAAACGTTTTAAAACTT
66406 ATATAT-TGTATATAAGTTTTCAAAAACGTTTTAAAA
1 ATATATGT-TATATAA-TTTTC-AAAACGTTTTAAAA
66442 GAACTATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 1 0.03
37 13 0.41
38 5 0.16
39 13 0.41
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (37 bp):
ATATATGTTATATAATTTTCAAAACGTTTTAAAACTT
Found at i:66450 original size:39 final size:37
Alignment explanation
Indices: 66368--66464 Score: 99
Period size: 39 Copynumber: 2.5 Consensus size: 37
66358 TGATTTCAAA
* *
66368 AATATATGT-TATATAATTTTCAAAATGTTTTAAAACT
1 AATATAT-TATATATAATTTTCAAAACGTTTTAAAACG
* *
66405 TATATATTGTATATAAGTTTTCAAAAACGTTTTAAAA-G
1 AATATATTATATATAA-TTTTC-AAAACGTTTTAAAACG
66443 AACTATATTATATATATATTTT
1 AA-TATATTATATATA-ATTTT
66465 TGGAAACCGT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
36 1 0.02
37 13 0.26
38 6 0.12
39 29 0.58
40 1 0.02
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (37 bp):
AATATATTATATATAATTTTCAAAACGTTTTAAAACG
Found at i:67835 original size:20 final size:19
Alignment explanation
Indices: 67797--67837 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
67787 AACTTTAAAA
*
67797 TAATGATTTGAGCATAATT
1 TAATGATTTGAACATAATT
*
67816 TAATGATTTAGAATATAATT
1 TAATGATTT-GAACATAATT
67836 TA
1 TA
67838 CTTTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.44
Consensus pattern (19 bp):
TAATGATTTGAACATAATT
Found at i:67853 original size:17 final size:18
Alignment explanation
Indices: 67831--67865 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
67821 ATTTAGAATA
67831 TAATTTACTTTTT-TTTT
1 TAATTTACTTTTTCTTTT
*
67848 TAATTTCCTTTTTCTTTT
1 TAATTTACTTTTTCTTTT
67866 CCTTCACTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.74
Consensus pattern (18 bp):
TAATTTACTTTTTCTTTT
Found at i:76831 original size:222 final size:222
Alignment explanation
Indices: 76445--76857 Score: 718
Period size: 222 Copynumber: 1.9 Consensus size: 222
76435 CCAGGTCCAA
**
76445 CTTGTGTAGTTGGGACTATGAAATCATAACATTGTTTAGTGAACTAAATTTATACTCTTCATGTG
1 CTTGTGTAGTTGGGACTATGAAATCATAACATTGTTTAGTGAACTAAATTTATACTCTTCACATG
* * *
76510 TTGTATATTCTGTGAATTTCGCACGAGTTTGGGAATTATATTTAAACGTTCTCTTCTTTTCTTAG
66 TTGTATATTCTGTGAATTTCGCACGAGTTTGGAAATTATATTTAAACATTCTCTTCATTTCTTAG
76575 TCAAACTGTATCTTGTTAAGAGGGAATGGCTCAGGTAGCATCTAAAGGTTTAATTTCATGTCATC
131 TCAAACTGTATCTTGTTAAGAGGGAATGGCTCAGGTAGCATCTAAAGGTTTAATTTCATGTCATC
76640 TGTGGGATAGCTAAAATAGTATTCTAG
196 TGTGGGATAGCTAAAATAGTATTCTAG
* * *
76667 CTTGTGTAGTTGGGACTATGAAATGATATCATTGTTTAGTGAACTAGATTTATACTCTTCACATG
1 CTTGTGTAGTTGGGACTATGAAATCATAACATTGTTTAGTGAACTAAATTTATACTCTTCACATG
*
76732 TTGTATATTCTGTGAATTTCGCATGAGTTTGGAAATTATATTTAAACATTCTCTTCATTTCTTAG
66 TTGTATATTCTGTGAATTTCGCACGAGTTTGGAAATTATATTTAAACATTCTCTTCATTTCTTAG
* * *
76797 TTAAATTGTATCTTGTTAAGAGGGAATGGCTCAGGTAGCATCTAAATGTTTAATTTCATGT
131 TCAAACTGTATCTTGTTAAGAGGGAATGGCTCAGGTAGCATCTAAAGGTTTAATTTCATGT
76858 TGTGTAACAC
Statistics
Matches: 179, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
222 179 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (222 bp):
CTTGTGTAGTTGGGACTATGAAATCATAACATTGTTTAGTGAACTAAATTTATACTCTTCACATG
TTGTATATTCTGTGAATTTCGCACGAGTTTGGAAATTATATTTAAACATTCTCTTCATTTCTTAG
TCAAACTGTATCTTGTTAAGAGGGAATGGCTCAGGTAGCATCTAAAGGTTTAATTTCATGTCATC
TGTGGGATAGCTAAAATAGTATTCTAG
Found at i:93343 original size:21 final size:20
Alignment explanation
Indices: 93319--93360 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 20
93309 TGATAAAAAA
93319 TTATTTAAAATATTATTATTT
1 TTATTTAAAATATTATT-TTT
93340 TTATTTAAAATATTATTTTT
1 TTATTTAAAATATTATTTTT
93360 T
1 T
93361 AATATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTTAAAATATTATTTTT
Found at i:94012 original size:30 final size:30
Alignment explanation
Indices: 93897--94013 Score: 128
Period size: 31 Copynumber: 3.8 Consensus size: 30
93887 AGATACTTAT
* *
93897 ATAAAAAATGAATACTTTAAGTATTTATTTT-
1 ATAAAAAA--AATAATTTAAGTACTTATTTTG
*
93928 AAAAAAAAAATAATTTAAGTACTTATTTTG
1 ATAAAAAAAATAATTTAAGTACTTATTTTG
* * * *
93958 ATTAAAACAATAATCATAAATACTTATTTTG
1 ATAAAAAAAATAAT-TTAAGTACTTATTTTG
*
93989 ATAAAAAAAATAATTTATGTACTTA
1 ATAAAAAAAATAATTTAAGTACTTA
94014 AATTAAATAA
Statistics
Matches: 71, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
29 19 0.27
30 19 0.27
31 33 0.46
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (30 bp):
ATAAAAAAAATAATTTAAGTACTTATTTTG
Found at i:109027 original size:3 final size:3
Alignment explanation
Indices: 109019--109047 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
109009 GTTTCTCTTT
109019 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
109048 ACAAACTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:112141 original size:10 final size:10
Alignment explanation
Indices: 112128--112154 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
112118 TTTTTATTTT
112128 TTTCATAAAA
1 TTTCATAAAA
112138 TTTCATAAAA
1 TTTCATAAAA
112148 TTTCATA
1 TTTCATA
112155 TTCTTGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTCATAAAA
Found at i:113870 original size:10 final size:10
Alignment explanation
Indices: 113857--113899 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 10
113847 ACAATAAATG
113857 AACATAAACA
1 AACATAAACA
113867 AACATAAATGAACA
1 AACAT--A--AACA
113881 AACATAAACA
1 AACATAAACA
113891 AACATAAAC
1 AACATAAAC
113900 CACAACAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 18 0.62
12 2 0.07
14 9 0.31
ACGTcount: A:0.67, C:0.19, G:0.02, T:0.12
Consensus pattern (10 bp):
AACATAAACA
Found at i:114124 original size:14 final size:14
Alignment explanation
Indices: 114083--114125 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
114073 AGACTGGGCT
*
114083 AAACATAAATGAAT
1 AAACATAAATGAAC
*
114097 AAACATAAACGAAC
1 AAACATAAATGAAC
* *
114111 GAACATGAATGAAC
1 AAACATAAATGAAC
114125 A
1 A
114126 TAAATGAACG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.60, C:0.14, G:0.12, T:0.14
Consensus pattern (14 bp):
AAACATAAATGAAC
Found at i:114125 original size:24 final size:24
Alignment explanation
Indices: 114091--114140 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
114081 CTAAACATAA
114091 ATGAATAAACATAAACGAACGAAC
1 ATGAATAAACATAAACGAACGAAC
* * *
114115 ATGAATGAACATAAATGAACGGAC
1 ATGAATAAACATAAACGAACGAAC
114139 AT
1 AT
114141 ATTATCAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.14, G:0.16, T:0.16
Consensus pattern (24 bp):
ATGAATAAACATAAACGAACGAAC
Found at i:115183 original size:16 final size:18
Alignment explanation
Indices: 115152--115184 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
115142 TCTAAAAAAC
115152 TTAAAATTACTATATATT
1 TTAAAATTACTATATATT
115170 TTAAAA-TA-TATATAT
1 TTAAAATTACTATATAT
115185 GTATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAAATTACTATATATT
Found at i:115486 original size:2 final size:2
Alignment explanation
Indices: 115479--115511 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
115469 ATTTTTCCTT
115479 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
115512 TAATTTTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:115541 original size:12 final size:11
Alignment explanation
Indices: 115514--115540 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
115504 ATATATATTA
115514 ATTTTCTAATT
1 ATTTTCTAATT
115525 ATTTTCTAATT
1 ATTTTCTAATT
115536 ATTTT
1 ATTTT
115541 TAACGATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTCTAATT
Found at i:116938 original size:2 final size:2
Alignment explanation
Indices: 116931--116958 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
116921 GTGGATTCTC
116931 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
116959 CCGCTTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:120930 original size:20 final size:20
Alignment explanation
Indices: 120905--120960 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 20
120895 TATGCAGGGA
120905 TATCGATACTCGAGG-TCTAG
1 TATCGATACTCGAGGCT-TAG
120925 TATCGATACTCGGAGGCTTAG
1 TATCGATACTC-GAGGCTTAG
120946 TATCGATACT-GAGGC
1 TATCGATACTCGAGGC
120961 ATTTTTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.15
20 11 0.32
21 17 0.50
22 1 0.03
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.29
Consensus pattern (20 bp):
TATCGATACTCGAGGCTTAG
Found at i:123832 original size:26 final size:27
Alignment explanation
Indices: 123787--123843 Score: 98
Period size: 26 Copynumber: 2.1 Consensus size: 27
123777 TAATTTCATT
*
123787 CATAAAGAGTATTTTGATAATTTAACA
1 CATAAAGAGTATTTTAATAATTTAACA
123814 CATAAA-AGTATTTTAATAATTTAACA
1 CATAAAGAGTATTTTAATAATTTAACA
123840 CATA
1 CATA
123844 TGCAAGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 23 0.79
27 6 0.21
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (27 bp):
CATAAAGAGTATTTTAATAATTTAACA
Found at i:124810 original size:17 final size:18
Alignment explanation
Indices: 124778--124811 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
124768 CCATACTTGA
*
124778 TTAAATATTTAATATTTT
1 TTAAATATTAAATATTTT
124796 TTAAAT-TTAAATATTT
1 TTAAATATTAAATATTT
124812 ATTTTTACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAAATATTAAATATTTT
Found at i:128113 original size:46 final size:46
Alignment explanation
Indices: 128024--128113 Score: 103
Period size: 46 Copynumber: 2.0 Consensus size: 46
128014 TAGTACCTAA
* * * * *
128024 AAATAAATACATAATTATATTGGTGAAAATATGTTTTAATATTTTT
1 AAATAAATAAATAATTATATTGATAAAAATATATTTAAATATTTTT
128070 AAATAAATAAATAATTA-A-TGATAAAAATATATATTAAATTATTT
1 AAATAAATAAATAATTATATTGATAAAAATATAT-TTAAA-TATTT
128114 GTGTACATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
44 11 0.30
45 5 0.14
46 21 0.57
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.42
Consensus pattern (46 bp):
AAATAAATAAATAATTATATTGATAAAAATATATTTAAATATTTTT
Found at i:130956 original size:21 final size:21
Alignment explanation
Indices: 130932--130976 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
130922 AAATGACCGG
* *
130932 ATTAACATAATAATTTAGGTA
1 ATTAACAGAAAAATTTAGGTA
*
130953 ATTACCAGAAAAATTTAGGTA
1 ATTAACAGAAAAATTTAGGTA
130974 ATT
1 ATT
130977 TCTACCGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.36
Consensus pattern (21 bp):
ATTAACAGAAAAATTTAGGTA
Found at i:132090 original size:29 final size:29
Alignment explanation
Indices: 132058--132117 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
132048 TGGTAATAAT
* * *
132058 AAATTAAAGGGCTAAAACAGAAAAATAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
* *
132087 AAATTAAAAGACTAAAATAGCAAAACAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
132116 AA
1 AA
132118 CGTAGGGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.65, C:0.08, G:0.13, T:0.13
Consensus pattern (29 bp):
AAATTAAAAGACTAAAACAGAAAAACAGA
Found at i:133731 original size:3 final size:3
Alignment explanation
Indices: 133712--133760 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
133702 ATGTAAAATG
*
133712 TAA TAT TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
133758 TAA
1 TAA
133761 CGATAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:134103 original size:43 final size:43
Alignment explanation
Indices: 134047--134250 Score: 148
Period size: 43 Copynumber: 4.7 Consensus size: 43
134037 TTAGGTGATA
* *
134047 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTGTCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTATGGTTG
* ** *
134090 ACACGGCTCCTACGTGATGAGGAGATCTGG---TCTGGGGAATG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTATGG-TTG
* * * ** ** * *
134131 GCACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCT-ATGGT--TG
* *
134177 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCCATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTATGGTTG
* *
134220 ACACGACTCCTACGTGATGAGGAGATCTGGT
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGT
134251 CTGGGAATGA
Statistics
Matches: 125, Mismatches: 26, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
40 5 0.04
41 28 0.22
42 2 0.02
43 53 0.42
44 3 0.02
45 6 0.05
46 27 0.22
47 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.25
Consensus pattern (43 bp):
ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTATGGTTG
Found at i:134164 original size:130 final size:129
Alignment explanation
Indices: 134010--134297 Score: 450
Period size: 130 Copynumber: 2.2 Consensus size: 129
134000 ACACTTCTCC
*
134010 TACGTGATGAAGAGTTCTTGGCCATCTTTAGGTGATAACACGGTTCCTACGTGATGAGGACGGCT
1 TACGTGATGAAGAGTTC-TGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCT
* * * *
134075 GGTTGTCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGAATGGCACGGCTC
65 GGTTATCCATGGTTGACACGACTCCTACGTGATGAGGAGATCTGGTCT-GGGAATGACACGGCTC
134140 A
129 A
*
134141 TACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTG
1 TACGTGATGAAGAGTTCTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTG
* *
134206 GTTATCCATGGTTGACACGACTCCTACGTGATGAGGAGATCTGGTCTGGGAATGACACGGTTCC
66 GTTATCCATGGTTGACACGACTCCTACGTGATGAGGAGATCTGGTCTGGGAATGACACGGCTCA
* * * *
134270 TATGTGATGAGGACTACTGGCCATCTTA
1 TACGTGATGAAGAGTTCTGGCCATCTTA
134298 GGAATAATGG
Statistics
Matches: 144, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
129 37 0.26
130 90 0.62
131 17 0.12
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (129 bp):
TACGTGATGAAGAGTTCTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTG
GTTATCCATGGTTGACACGACTCCTACGTGATGAGGAGATCTGGTCTGGGAATGACACGGCTCA
Found at i:134612 original size:35 final size:36
Alignment explanation
Indices: 134561--134640 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 36
134551 TGAGACAAAA
* * **
134561 TTTGTTTTTAAGGGAAAC-GTTCTCAAAGAT-GTTTAT
1 TTTG-TTTCAAGGGAAACAGAT-TCAAAGATGGTAAAT
134597 TTTGTTTCAAGGGAAACAGATTCAAAGATGGTAAAT
1 TTTGTTTCAAGGGAAACAGATTCAAAGATGGTAAAT
134633 TTTGTTTC
1 TTTGTTTC
134641 CAAAGAAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 20 0.53
36 18 0.47
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACAGATTCAAAGATGGTAAAT
Found at i:134943 original size:15 final size:15
Alignment explanation
Indices: 134899--134943 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
134889 AAGATGATCT
* *
134899 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAC
134914 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
*
134929 TGTTTCAAGTGAAAC
1 TGTTTCAAGAGAAAC
134944 GACTCAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (15 bp):
TGTTTCAAGAGAAAC
Found at i:135087 original size:40 final size:40
Alignment explanation
Indices: 135038--135117 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
135028 GTTTTAATAA
*
135038 AAACAATCTCCAAGGTGGGTAGTTTT-AAAAGAAATTGTCT
1 AAACAATCTCAAAGGTGGGTA-TTTTCAAAAGAAATTGTCT
* * *
135078 AAACGATCTCAAATGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
135118 CGAGAGACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (40 bp):
AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
Found at i:135170 original size:62 final size:63
Alignment explanation
Indices: 135099--135222 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 63
135089 AATGTGGGTA
* * *
135099 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATT
* * * *
135161 TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAATAGACTCAAAGAT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
135223 GGATTACATC
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
62 17 0.31
63 37 0.69
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (63 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATT
Found at i:135501 original size:37 final size:37
Alignment explanation
Indices: 135455--135580 Score: 110
Period size: 37 Copynumber: 3.6 Consensus size: 37
135445 GAAACAGATT
*
135455 CAAAGATTTTTTTTCAAAAGAAGTTATCTTAAGAGAGA
1 CAAAGATTTTGTTTCAAAAGAA-TTATCTTAAGAGAGA
* * **
135493 CAAA-ATTTTGCTTCCAAAGAA--A-C---A-A-ACT
1 CAAAGATTTTGTTTCAAAAGAATTATCTTAAGAGAGA
135521 CAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAAGA-TTTTGTTTCAAAAG-AATTATCTTAAGAGAGA
135560 CAAA-ATTTTGTTTCAAAAGAA
1 CAAAGATTTTGTTTCAAAAGAA
135581 ACAAACTCAA
Statistics
Matches: 68, Mismatches: 9, Indels: 24
0.67 0.09 0.24
Matches are distributed among these distances:
28 5 0.07
29 2 0.03
30 13 0.19
31 2 0.03
33 2 0.03
34 2 0.03
36 2 0.03
37 29 0.43
38 6 0.09
39 5 0.07
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (37 bp):
CAAAGATTTTGTTTCAAAAGAATTATCTTAAGAGAGA
Found at i:135552 original size:67 final size:67
Alignment explanation
Indices: 135444--135640 Score: 299
Period size: 67 Copynumber: 3.0 Consensus size: 67
135434 TCATTTTAAG
* * * *
135444 AGAAACAGATTCAAAGATTTTT-TTTCAAAAGAAGTTATCTTAAGAGAGACAAAATTTTGCTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGCTTCA
135508 AA
66 AA
*
135510 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGCTTCA
135575 AA
66 AA
* * * *
135577 AGAAACAAACTCAAAGATTTTTGTTTCAAAA-AAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGCTTCA
135641 GACTCAGAGA
Statistics
Matches: 122, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
66 50 0.41
67 72 0.59
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (67 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGCTTCA
AA
Found at i:135718 original size:27 final size:28
Alignment explanation
Indices: 135688--135838 Score: 166
Period size: 29 Copynumber: 5.4 Consensus size: 28
135678 CAAAACTTTG
* * *
135688 TTTCAAAATAAATAGACTCAAAGA-TTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
* *
135715 TTTCAAACGAAAC-AAGTCAAAGATTTT
1 TTTCAAAAGAAACAAACTCAAAGATTTT
* *
135742 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTT
*
135771 TATTCAAAAGGAACAAACTCAAAGA-TTT
1 T-TTCAAAAGAAACAAACTCAAAGATTTT
*
135799 TTTCAAGAGGAAA-AAACTCAAAGATTTT
1 TTTCAA-AAGAAACAAACTCAAAGATTTT
135827 TTTCAAAAGAAA
1 TTTCAAAAGAAA
135839 TTGTCTTTAA
Statistics
Matches: 106, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
26 8 0.08
27 35 0.33
28 27 0.25
29 36 0.34
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (28 bp):
TTTCAAAAGAAACAAACTCAAAGATTTT
Found at i:135776 original size:29 final size:28
Alignment explanation
Indices: 135703--135835 Score: 173
Period size: 29 Copynumber: 4.8 Consensus size: 28
135693 AAATAAATAG
* *
135703 ACTCAAAGA-TTTTTTCAAACGAAAC-A
1 ACTCAAAGATTTTTTTCAAAAGGAACAA
*
135729 AGTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTT-TTCAAAAGGAACAA
*
135758 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTT-TTCAAAAGGAACAA
* *
135787 ACTCAAAGA-TTTTTTCAAGAGGAAAAA
1 ACTCAAAGATTTTTTTCAAAAGGAACAA
135814 ACTCAAAGATTTTTTTCAAAAG
1 ACTCAAAGATTTTTTTCAAAAG
135836 AAATTGTCTT
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
26 8 0.09
27 25 0.27
28 25 0.27
29 36 0.38
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (28 bp):
ACTCAAAGATTTTTTTCAAAAGGAACAA
Found at i:136161 original size:36 final size:36
Alignment explanation
Indices: 136077--136180 Score: 106
Period size: 36 Copynumber: 3.0 Consensus size: 36
136067 GAGAAAATGA
* * * *
136077 TGTCTCAAGCGAGACGAGATTTG-CTTTA-AGATAC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAC
* ** *
136111 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAC
*
136147 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
136181 ACGATCTCAA
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
34 18 0.32
35 10 0.18
36 28 0.50
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAC
Found at i:136189 original size:36 final size:36
Alignment explanation
Indices: 136078--136196 Score: 102
Period size: 36 Copynumber: 3.4 Consensus size: 36
136068 AGAAAATGAT
* * * *
136078 GTCTCAAGCGAGACGAGATTTG-CTTTA-AG-ATAC
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
** **
136111 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 -GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
*
136148 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
*
136183 GATCTCAAGTGAGA
1 G-TCTCAAGCGAGA
136197 TCAACTTTGT
Statistics
Matches: 67, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
34 18 0.27
35 11 0.16
36 37 0.55
37 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.29
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAAC
Done.