Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015124.1 Kokia drynarioides strain JFW-HI SEQ_130168, 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: 159680
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 123 characters in sequence are not A, C, G, or T
Found at i:1901 original size:72 final size:72
Alignment explanation
Indices: 1771--1911 Score: 201
Period size: 72 Copynumber: 2.0 Consensus size: 72
1761 TTTTGGTCCG
* * * * * *
1771 ATTCCATTGTCAATAGGGGAGTTATCATCTTTGGAGTTCTTCGATGTTTCGGAAAATCATTTAAG
1 ATTCCATTGTCAATAGGAGAGTTATCATCTTTGAAGTTCTTCGATGTTACAGAAAATCAATTAAA
1836 TGGTCAA
66 TGGTCAA
* * *
1843 ATTCCATTGTCTATAGGAGAGTTATCATCTTTGAAGTTCTTTGATGTTACAGACAATCAATTAAA
1 ATTCCATTGTCAATAGGAGAGTTATCATCTTTGAAGTTCTTCGATGTTACAGAAAATCAATTAAA
1908 TGGT
66 TGGT
1912 ACTGTTCCTC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.38
Consensus pattern (72 bp):
ATTCCATTGTCAATAGGAGAGTTATCATCTTTGAAGTTCTTCGATGTTACAGAAAATCAATTAAA
TGGTCAA
Found at i:5642 original size:27 final size:27
Alignment explanation
Indices: 5585--5642 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
5575 CCTATAGTTT
* * *
5585 ATTTTAATCAATTAATAAATTTTCTTT
1 ATTTTAATCAATTAATAAATTGTATTC
*
5612 ATTTTAATCAATTAAT-TATATGTATTC
1 ATTTTAATCAATTAATAAAT-TGTATTC
5639 ATTT
1 ATTT
5643 CTGCTTCAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (27 bp):
ATTTTAATCAATTAATAAATTGTATTC
Found at i:6632 original size:24 final size:24
Alignment explanation
Indices: 6605--6652 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6595 ACCTGAATTC
*
6605 TTTAAATTTAAAAAAATATAAAAA
1 TTTAAATTTAAAAAAATAAAAAAA
**
6629 TTTAAATTTTTAAAAATAAAAAAA
1 TTTAAATTTAAAAAAATAAAAAAA
6653 CGAGATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
TTTAAATTTAAAAAAATAAAAAAA
Found at i:11696 original size:17 final size:17
Alignment explanation
Indices: 11672--11714 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
11662 TTGAAATTTG
11672 AATTTATTTTAAAATTA
1 AATTTATTTTAAAATTA
* *
11689 AGTTTATTTTAAATTTA
1 AATTTATTTTAAAATTA
11706 AATTTATTT
1 AATTTATTT
11715 ATTTAAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
AATTTATTTTAAAATTA
Found at i:17157 original size:26 final size:26
Alignment explanation
Indices: 17127--17178 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
17117 ATGGAAGCTT
17127 GCCTATCTTCCTTACCATTCGAAGCA
1 GCCTATCTTCCTTACCATTCGAAGCA
17153 GCCTATCTTCCTTACCATTCGAAGCA
1 GCCTATCTTCCTTACCATTCGAAGCA
17179 AACTTATTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.35, G:0.12, T:0.31
Consensus pattern (26 bp):
GCCTATCTTCCTTACCATTCGAAGCA
Found at i:22093 original size:24 final size:26
Alignment explanation
Indices: 22048--22095 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
22038 TTTTCTTCAA
* *
22048 TTTAATAATTTTTAAGTCTTTAATAT
1 TTTAATAATTTTAAAATCTTTAATAT
22074 TTTAA-AATTTTAAAAT-TTTAAT
1 TTTAATAATTTTAAAATCTTTAAT
22096 CTCAAACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 9 0.45
26 5 0.25
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTAATAATTTTAAAATCTTTAATAT
Found at i:31232 original size:29 final size:30
Alignment explanation
Indices: 31200--31256 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
31190 TGATTTAATA
*
31200 TGTAATTGTACACGT-AAATTTTGATTTTG
1 TGTAATTGTACACGTGAAATTTTAATTTTG
* *
31229 TGTAATTTTATACGTGAAATTTTAATTT
1 TGTAATTGTACACGTGAAATTTTAATTT
31257 GATTTAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (30 bp):
TGTAATTGTACACGTGAAATTTTAATTTTG
Found at i:31666 original size:31 final size:31
Alignment explanation
Indices: 31600--31676 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 31
31590 ATGTAATTAT
* *
31600 TTTTAATTTTTATACTTTTGAATTGTTCAAT
1 TTTTAATTTTTATACTTTTGAATTGTTAAAA
*
31631 TTTTAATATTTGTAT-CTTTTTAATT-TTAAAA
1 TTTTAAT-TTT-TATACTTTTGAATTGTTAAAA
* *
31662 TTTTAGTTTTGATAC
1 TTTTAATTTTTATAC
31677 AAAACGGTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
29 2 0.05
30 4 0.11
31 17 0.45
32 12 0.32
33 3 0.08
ACGTcount: A:0.27, C:0.05, G:0.06, T:0.61
Consensus pattern (31 bp):
TTTTAATTTTTATACTTTTGAATTGTTAAAA
Found at i:34277 original size:7 final size:7
Alignment explanation
Indices: 34265--34295 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
34255 TACTATCTCA
34265 CCTAACT
1 CCTAACT
34272 CCTAACT
1 CCTAACT
34279 CCTAACT
1 CCTAACT
34286 CCTAACT
1 CCTAACT
34293 CCT
1 CCT
34296 GTGATTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.45, G:0.00, T:0.29
Consensus pattern (7 bp):
CCTAACT
Found at i:37574 original size:16 final size:16
Alignment explanation
Indices: 37550--37581 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
37540 TATTCTTCGT
*
37550 CGACGATAGTATTGTC
1 CGACAATAGTATTGTC
37566 CGACAATAGTATTGTC
1 CGACAATAGTATTGTC
37582 TTTGGGGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (16 bp):
CGACAATAGTATTGTC
Found at i:39967 original size:21 final size:22
Alignment explanation
Indices: 39932--39982 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
39922 ATGTGTCATG
39932 AAATGAAACTAAAAT-AAAACC
1 AAATGAAACTAAAATGAAAACC
* * *
39953 AAATGAAAGTTAAATGAAACCC
1 AAATGAAACTAAAATGAAAACC
*
39975 TAATGAAA
1 AAATGAAA
39983 AAAGCAACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.18
Consensus pattern (22 bp):
AAATGAAACTAAAATGAAAACC
Found at i:41971 original size:24 final size:24
Alignment explanation
Indices: 41942--41992 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
41932 AGAAATAATC
*
41942 TTTCAATTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTATTTAATTG
* *
41966 TTTCAATTAAACTTTATTTATTTG
1 TTTCAATTAAACTCTATTTAATTG
41990 TTT
1 TTT
41993 GAGTCAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTAATTG
Found at i:43957 original size:24 final size:24
Alignment explanation
Indices: 43924--43970 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
43914 AGAAATAATC
*
43924 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
43948 TTTCAATTAAACTCTGTTTATTT
1 TTTCAATTAAACTCTGTTTATTT
43971 ACTTGAGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:43983 original size:24 final size:24
Alignment explanation
Indices: 43932--43986 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
43922 TCTTTCAGTT
** *
43932 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTACTTCAATC
* *
43956 AAACTCTGTTTATTTACTTGAGTC
1 AAACTCTGTTTATTTACTTCAATC
43980 AAACTCT
1 AAACTCT
43987 TATTAGTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.47
Consensus pattern (24 bp):
AAACTCTGTTTATTTACTTCAATC
Found at i:45131 original size:25 final size:25
Alignment explanation
Indices: 45081--45132 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
45071 AAGAAAATTA
* **
45081 TTATTTTTTTGTTGCTTTCTTGCTG
1 TTATTTTCTTGTTGCTTTCTCACTG
45106 TTATTTTCTTGTTG-TCTTCTCACTG
1 TTATTTTCTTGTTGCT-TTCTCACTG
45131 TT
1 TT
45133 TTGCTATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.06, C:0.15, G:0.13, T:0.65
Consensus pattern (25 bp):
TTATTTTCTTGTTGCTTTCTCACTG
Found at i:45680 original size:22 final size:23
Alignment explanation
Indices: 45638--45680 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
45628 AAATTAACAA
* *
45638 TAAATCAATAATTATATAATATT
1 TAAATCAATAATAATAAAATATT
45661 TAAAT-AATAATAATAAAATA
1 TAAATCAATAATAATAAAATA
45681 ATAACAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAATCAATAATAATAAAATATT
Found at i:53765 original size:51 final size:51
Alignment explanation
Indices: 53663--53766 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
53653 GAAAAATCTC
* * ***
53663 GACGTGTTTAGAACATAATACATGATAAGTGAGTTAGTAATTGTTGAAAAA
1 GACGTGTTTAGAACATAACACATGATAAGTGAGTTAATAATTACCGAAAAA
* * * *
53714 GACGTGTTTAGAAGATAACATATGATAAGTGAGTTAATAGTTACCGGAAAA
1 GACGTGTTTAGAACATAACACATGATAAGTGAGTTAATAATTACCGAAAAA
53765 GA
1 GA
53767 AAAGAGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (51 bp):
GACGTGTTTAGAACATAACACATGATAAGTGAGTTAATAATTACCGAAAAA
Found at i:72108 original size:17 final size:17
Alignment explanation
Indices: 72082--72125 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
72072 TAGAGAACAT
*
72082 GAATTCATATTTGTTGA
1 GAATTAATATTTGTTGA
72099 GAATTAATATTTGTTGA
1 GAATTAATATTTGTTGA
72116 GAATTAATAT
1 GAATTAATAT
72126 AGAGAGCATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.45
Consensus pattern (17 bp):
GAATTAATATTTGTTGA
Found at i:73971 original size:73 final size:73
Alignment explanation
Indices: 73843--74402 Score: 843
Period size: 73 Copynumber: 7.7 Consensus size: 73
73833 CCCCATTTGT
* * * * *
73843 ACCATTGTCCATTACTGCCGGTGTTGCTCAGCCAACCCCAACTCGGGCTTCTAAAAAGAACAAGC
1 ACCATTGTCCATTGCTGCTGGTGTTGCTCAGCCAACCCCAACTTGAGCTTGTAAAAAGAACAAGC
*
73908 TTCTCTGC
66 TTTTCTGC
* *
73916 ACCATTGTCCATTGCTGCGGGTGTTTCTCAGCCAACCCCAACTTGAGCTTGTAAAAAGAACAAGC
1 ACCATTGTCCATTGCTGCTGGTGTTGCTCAGCCAACCCCAACTTGAGCTTGTAAAAAGAACAAGC
73981 TTTTCTGC
66 TTTTCTGC
* * * *
73989 ACCATTGTCCATTGCTGCTGATGTTGCTCAGCCAACCCCAATTTGACCTTGTAAAAAGAACGAGC
1 ACCATTGTCCATTGCTGCTGGTGTTGCTCAGCCAACCCCAACTTGAGCTTGTAAAAAGAACAAGC
*
74054 TTTCCTGC
66 TTTTCTGC
* * *
74062 ACCATTGTCCATTGCTGCTGGTGCTGCCCAGCCAACCCCAACTTGAGCTTGTAAAAAGAACAAAC
1 ACCATTGTCCATTGCTGCTGGTGTTGCTCAGCCAACCCCAACTTGAGCTTGTAAAAAGAACAAGC
74127 TTTTCTGC
66 TTTTCTGC
*
74135 ACCATTGTCCATTGCTGCTGATGTTGCTCAGCCAACCCCAA-TTCGAGCTTGTAAAAAGAACAAG
1 ACCATTGTCCATTGCTGCTGGTGTTGCTCAGCCAACCCCAACTT-GAGCTTGTAAAAAGAACAAG
74199 CTTTTCTGC
65 CTTTTCTGC
* * * *
74208 ATCATTGCCCATTGCTGCTGGTGTTTCTCAGCCAAACCCAACTTGAGCTTGTAAAAAGAACAAGC
1 ACCATTGTCCATTGCTGCTGGTGTTGCTCAGCCAACCCCAACTTGAGCTTGTAAAAAGAACAAGC
*
74273 TTTCCTGC
66 TTTTCTGC
* *
74281 ACCATTGTCCATTGCTGCTGGTGCTGCCCAGCCAACCCCAACTTGAGCTTGTAAAAAGAACAAGC
1 ACCATTGTCCATTGCTGCTGGTGTTGCTCAGCCAACCCCAACTTGAGCTTGTAAAAAGAACAAGC
74346 TTTTCTGC
66 TTTTCTGC
* * * * *
74354 ACCGTTGCCCATTGCTGCTGATGTTGCTTAACCAACCCCAACTTGAGCT
1 ACCATTGTCCATTGCTGCTGGTGTTGCTCAGCCAACCCCAACTTGAGCT
74403 GGGGTTAGGA
Statistics
Matches: 439, Mismatches: 46, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
72 2 0.00
73 435 0.99
74 2 0.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (73 bp):
ACCATTGTCCATTGCTGCTGGTGTTGCTCAGCCAACCCCAACTTGAGCTTGTAAAAAGAACAAGC
TTTTCTGC
Found at i:74999 original size:14 final size:14
Alignment explanation
Indices: 74982--75031 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
74972 ATAATTTCTC
74982 TTTTTATATTTTAA
1 TTTTTATATTTTAA
* *
74996 TTTTAATATCTTAA
1 TTTTTATATTTTAA
75010 TATTTTATATTTATAA
1 T-TTTTATATTT-TAA
*
75026 ATTTTA
1 TTTTTA
75032 ATATATTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 13 0.45
15 13 0.45
16 3 0.10
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTATATTTTAA
Found at i:75016 original size:16 final size:16
Alignment explanation
Indices: 74982--75035 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 16
74972 ATAATTTCTC
*
74982 TTTTTATATTT-T-AA
1 TTTTAATATTTATAAA
*
74996 TTTTAATATCTTA-ATA
1 TTTTAATAT-TTATAAA
75012 TTTT-ATATTTATAAA
1 TTTTAATATTTATAAA
75027 TTTTAATAT
1 TTTTAATAT
75036 ATTTGTGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 11 0.34
15 12 0.38
16 9 0.28
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTAATATTTATAAA
Found at i:75910 original size:13 final size:13
Alignment explanation
Indices: 75892--75925 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
75882 TTTGCTCGAT
75892 ATAATTTTTTTAA
1 ATAATTTTTTTAA
75905 ATAATTTTTTTAA
1 ATAATTTTTTTAA
75918 ATAATTTT
1 ATAATTTT
75926 ATTATAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATAATTTTTTTAA
Found at i:76226 original size:2 final size:2
Alignment explanation
Indices: 76219--76243 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
76209 ATTGAATTAT
76219 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
76244 TGAATTATGG
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:84241 original size:87 final size:87
Alignment explanation
Indices: 84085--84291 Score: 306
Period size: 87 Copynumber: 2.4 Consensus size: 87
84075 ACATATCATA
* * * * *
84085 CATAAGTAACATGATATGACTTTCCCTTGCATACGGATTCGATTGTTCAAATCCCAATCGGGGCT
1 CATAAGTAACATGATATGACTTGCCCTTGCATACGGATTCGATTGTTCAAATCACAATAGGGACA
84150 ATTTACTGATTCGTTTACTGAT
66 ATTTACTGATTCGTTTACTGAT
* * * * *
84172 CATAAGTAACATGTTTTGACTTGCCCTTGTATACGGTTTCGATTGTTCATATCACAATAGGGACA
1 CATAAGTAACATGATATGACTTGCCCTTGCATACGGATTCGATTGTTCAAATCACAATAGGGACA
*
84237 ATTTACTGATTTGTTTACTGAT
66 ATTTACTGATTCGTTTACTGAT
*
84259 CATAAGTAACATGGTATGACTTGCCCTTGCATA
1 CATAAGTAACATGATATGACTTGCCCTTGCATA
84292 TCATATGAGT
Statistics
Matches: 106, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 106 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (87 bp):
CATAAGTAACATGATATGACTTGCCCTTGCATACGGATTCGATTGTTCAAATCACAATAGGGACA
ATTTACTGATTCGTTTACTGAT
Found at i:87007 original size:17 final size:16
Alignment explanation
Indices: 86961--87031 Score: 79
Period size: 17 Copynumber: 4.3 Consensus size: 16
86951 ATTTGTTTGG
* * *
86961 ATTTATTGAAAATTGA
1 ATTTATTTAAATTTAA
86977 ATTTATTTAAATTTAA
1 ATTTATTTAAATTTAA
*
86993 GTTTATTTGAAATTTAA
1 ATTTATTT-AAATTTAA
*
87010 ATTTATTATAAAATTAA
1 ATTTATT-TAAATTTAA
87027 ATTTA
1 ATTTA
87032 GAAAATCCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
16 20 0.43
17 26 0.55
18 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.51
Consensus pattern (16 bp):
ATTTATTTAAATTTAA
Found at i:87085 original size:15 final size:15
Alignment explanation
Indices: 87065--87123 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
87055 AACAAAGTAT
87065 AAATGACCCAATTAC
1 AAATGACCCAATTAC
* *
87080 AAATGAGCCAAGTAC
1 AAATGACCCAATTAC
*
87095 AAATTGCCCCCAATTAC
1 AAA-TG-ACCCAATTAC
*
87112 AAATGGCCCAAT
1 AAATGACCCAAT
87124 GGCCTAAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 22 0.61
16 4 0.11
17 10 0.28
ACGTcount: A:0.42, C:0.27, G:0.12, T:0.19
Consensus pattern (15 bp):
AAATGACCCAATTAC
Found at i:87112 original size:17 final size:17
Alignment explanation
Indices: 87087--87120 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
87077 TACAAATGAG
*
87087 CCAAGTACAAATTGCCC
1 CCAAGTACAAATGGCCC
*
87104 CCAATTACAAATGGCCC
1 CCAAGTACAAATGGCCC
87121 AATGGCCTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.35, G:0.12, T:0.18
Consensus pattern (17 bp):
CCAAGTACAAATGGCCC
Found at i:87791 original size:22 final size:21
Alignment explanation
Indices: 87765--87814 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
87755 TTTAATAATA
* *
87765 TTAATAATAATAAA-CA-TTT
1 TTAATAATAATAAATAACGTT
87784 TTAATAATAATAAATAACGTT
1 TTAATAATAATAAATAACGTT
87805 TTAATAATAA
1 TTAATAATAA
87815 AAAAAGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 14 0.52
20 1 0.04
21 12 0.44
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAATAATAATAAATAACGTT
Found at i:88872 original size:30 final size:29
Alignment explanation
Indices: 88836--89157 Score: 350
Period size: 30 Copynumber: 10.9 Consensus size: 29
88826 CCTCGAGGGT
*
88836 CCCTAAACTATCCAAAAGTTCCATTTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAC
*
88866 CCCTAAACTTTCAAAAA-TCCTATTTTTAAC
1 CCCTAAACTTCCAAAAATTCC-ATTTTT-AC
* * *
88896 TCCGAAACTTCCAAAATTTCCATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
*
88925 CCCTAAACTTCCAAAAA-TCATATTTTTGAC
1 CCCTAAACTTCCAAAAATTC-CATTTTT-AC
*
88955 CCTTAAACTATCCAAAAATTCCA-TTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAC
*
88984 CCCTAAACTTCCGAAAA-TCCTATTTTTGAC
1 CCCTAAACTTCCAAAAATTCC-ATTTTT-AC
* *
89014 CTCGAAACTTCCAAAAATTCCA-TTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
*
89042 CCCTAAACTTCCAAAAATCCCATTTTTGAC
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* *
89072 CCCGAAACTTCCAAAAATTCCATTTTTAG
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
*
89101 CCCTGAACTTCCAAAAATTCCATTTTTGA-
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* *
89130 CACTGAAACTTTCAAAAATTACCATTTT
1 CCCT-AAACTTCCAAAAATT-CCATTTT
89158 ACCTCTGGAT
Statistics
Matches: 248, Mismatches: 28, Indels: 31
0.81 0.09 0.10
Matches are distributed among these distances:
27 3 0.01
28 34 0.14
29 85 0.34
30 102 0.41
31 22 0.09
32 2 0.01
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAC
Found at i:88940 original size:59 final size:58
Alignment explanation
Indices: 88840--89224 Score: 428
Period size: 59 Copynumber: 6.6 Consensus size: 58
88830 GAGGGTCCCT
* * *
88840 AAACTATCCAAAAGTTCCATTTTTACCCCTAAACTTTCAAAAATCCTATTTTTAACTCCG
1 AAACT-TCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCTATTTTTGAC-CCG
* * *
88900 AAACTTCCAAAATTTCCATTTTTACCCCTAAACTTCCAAAAATCATATTTTTGACCCTT
1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCTATTTTTGACCC-G
*
88959 AAACTATCCAAAAATTCCA-TTTTACCCCTAAACTTCCGAAAATCCTATTTTTGACCTCG
1 AAACT-TCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCTATTTTTGACC-CG
*
89018 AAACTTCCAAAAATTCCA-TTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCTATTTTTGA-CCCG
* * *
89076 AAACTTCCAAAAATTCCATTTTTAGCCCTGAACTTCCAAAAATTCC-ATTTTTGACACTG
1 AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAA-TCCTATTTTTGAC-CCG
* * ** *
89135 AAACTTTCAAAAATTACCA-TTTTACCTCTGGA-TGTCCAAAAACTCC-ATTTTCGACCTCG
1 AAACTTCCAAAAATT-CCATTTTTACCCCTAAACT-TCCAAAAA-TCCTATTTTTGACC-CG
*
89194 AAAC-TCTC-AAAATTACC-CTTTTACCCCTAAA
1 AAACTTC-CAAAAATT-CCATTTTTACCCCTAAA
89225 TGTTTAAATT
Statistics
Matches: 288, Mismatches: 25, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
58 91 0.32
59 173 0.60
60 24 0.08
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.33
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCTATTTTTGACCCG
Found at i:89205 original size:30 final size:30
Alignment explanation
Indices: 88840--89198 Score: 286
Period size: 30 Copynumber: 12.2 Consensus size: 30
88830 GAGGGTCCCT
* * *
88840 AAACTATCCAAAAGTTCCATTTTT-ACCCCT
1 AAACT-TCCAAAAATTCCATTTTTGACCTCG
* *
88870 AAACTTTCAAAAA-TCCTATTTTT-AACTCCG
1 AAACTTCCAAAAATTCC-ATTTTTGACCT-CG
* * *
88900 AAACTTCCAAAATTTCCATTTTT-ACCCCT
1 AAACTTCCAAAAATTCCATTTTTGACCTCG
* *
88929 AAACTTCCAAAAA-TCATATTTTTGACC-CTT
1 AAACTTCCAAAAATTC-CATTTTTGACCTC-G
* *
88959 AAACTATCCAAAAATTCCA-TTTT-ACCCCT
1 AAACT-TCCAAAAATTCCATTTTTGACCTCG
*
88988 AAACTTCCGAAAA-TCCTATTTTTGACCTCG
1 AAACTTCCAAAAATTCC-ATTTTTGACCTCG
* *
89018 AAACTTCCAAAAATTCCA-TTTT-ACCCCT
1 AAACTTCCAAAAATTCCATTTTTGACCTCG
* *
89046 AAACTTCCAAAAATCCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCATTTTTGACCTCG
*
89076 AAACTTCCAAAAATTCCATTTTTAGCCCT-G
1 AAACTTCCAAAAATTCCATTTTT-GACCTCG
89106 -AACTTCCAAAAATTCCATTTTTGACACT-G
1 AAACTTCCAAAAATTCCATTTTTGAC-CTCG
*
89135 AAACTTTCAAAAATTACCA-TTTT-ACCTCTG
1 AAACTTCCAAAAATT-CCATTTTTGACCTC-G
* * *
89165 -GA-TGTCCAAAAACTCCATTTTCGACCTCG
1 AAACT-TCCAAAAATTCCATTTTTGACCTCG
89194 AAACT
1 AAACT
89199 CTCAAAATTA
Statistics
Matches: 272, Mismatches: 31, Indels: 51
0.77 0.09 0.14
Matches are distributed among these distances:
27 3 0.01
28 42 0.15
29 95 0.35
30 108 0.40
31 22 0.08
32 2 0.01
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTGACCTCG
Found at i:89244 original size:176 final size:176
Alignment explanation
Indices: 88840--89224 Score: 494
Period size: 176 Copynumber: 2.2 Consensus size: 176
88830 GAGGGTCCCT
* * * *
88840 AAACTATCCAAAAGTTCCATTTTTACCCCTAAACTTTCAAAAATCCTATTTTTAACTCCGAAACT
1 AAACT-TCCAAAAATTCCA-TTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCGAAACT
* * * *
88905 TCCAAAATTTCCATTTTTACCCCTAAACTTCCAAAAATCATATTTTTGACCCTTAAACTATCCAA
64 TCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCACATTTTTGACACTGAAACTATCCAA
* *
88970 AAATTCCATTTTACCCCTAAACTTCCGAAAATCCTATTTTTGACCTCG
129 AAATTCCATTTTACCCCTAAACTTCCAAAAATCCTATTTTCGACCTCG
*
89018 AAACTTCCAAAAATTCCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTC
1 AAACTTCCAAAAATTCCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCGAAACTTC
* * *
89083 CAAAAATTCCATTTTTAGCCCTGAACTTCCAAAAATTC-CATTTTTGACACTGAAACT-TTCAAA
66 CAAAAATTCCATTTTTACCCCTAAACTTCCAAAAA-TCACATTTTTGACACTGAAACTATCCAAA
* **
89146 AATTACCATTTTACCTCTGGA-TGTCCAAAAACTCC-ATTTTCGACCTCG
130 AATT-CCATTTTACCCCTAAACT-TCCAAAAA-TCCTATTTTCGACCTCG
*
89194 AAAC-TCTC-AAAATTACCCTTTTACCCCTAAA
1 AAACTTC-CAAAAATT-CCATTTTACCCCTAAA
89225 TGTTTAAATT
Statistics
Matches: 183, Mismatches: 18, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
175 18 0.10
176 143 0.78
177 17 0.09
178 5 0.03
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.33
Consensus pattern (176 bp):
AAACTTCCAAAAATTCCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCCCGAAACTTC
CAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCACATTTTTGACACTGAAACTATCCAAAA
ATTCCATTTTACCCCTAAACTTCCAAAAATCCTATTTTCGACCTCG
Found at i:94032 original size:17 final size:18
Alignment explanation
Indices: 94012--94045 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
94002 TTCTTCTTCT
94012 ATTTTTTAAT-ATTTATA
1 ATTTTTTAATAATTTATA
94029 ATTTTTTAATAATTTAT
1 ATTTTTTAATAATTTAT
94046 TTAATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTTTAATAATTTATA
Found at i:94621 original size:29 final size:29
Alignment explanation
Indices: 94571--94642 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
94561 TTAAGTTAAT
* *
94571 AAATAATAAAATTATATTTTAATCT-TCTAA
1 AAATAAT-AAATTTTAATTTAAT-TATCTAA
*
94601 AAATAATAAATTTTAATTTAATTATTTAA
1 AAATAATAAATTTTAATTTAATTATCTAA
94630 AAATAATAAATTT
1 AAATAATAAATTT
94643 GGTTCTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.03
29 30 0.79
30 7 0.18
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (29 bp):
AAATAATAAATTTTAATTTAATTATCTAA
Found at i:98449 original size:14 final size:14
Alignment explanation
Indices: 98430--98456 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
98420 AGATAAGACA
98430 AAATATATACTAAC
1 AAATATATACTAAC
98444 AAATATATACTAA
1 AAATATATACTAA
98457 ATTTAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATATATACTAAC
Found at i:106886 original size:21 final size:23
Alignment explanation
Indices: 106861--106908 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
106851 AACTTGTTAC
*
106861 TTTTTGCTGCTG-TTT-TCATTG
1 TTTTTGATGCTGTTTTGTCATTG
*
106882 TTTTTGATGTTGTTTTGTCATTG
1 TTTTTGATGCTGTTTTGTCATTG
106905 TTTT
1 TTTT
106909 GTTGTCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 3 0.13
23 10 0.43
ACGTcount: A:0.06, C:0.08, G:0.19, T:0.67
Consensus pattern (23 bp):
TTTTTGATGCTGTTTTGTCATTG
Found at i:107748 original size:3 final size:3
Alignment explanation
Indices: 107740--107766 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
107730 ACAACTCTAT
107740 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
107767 ATCAAGTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:108217 original size:9 final size:8
Alignment explanation
Indices: 108194--108235 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
108184 ATAGTAAAAA
108194 TATAATTT
1 TATAATTT
108202 TATAATTT
1 TATAATTT
108210 TAATAA-TT
1 T-ATAATTT
*
108218 TATATTTT
1 TATAATTT
108226 TATAATTT
1 TATAATTT
108234 TA
1 TA
108236 AAAAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 3 0.10
8 23 0.77
9 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATAATTT
Found at i:108235 original size:16 final size:17
Alignment explanation
Indices: 108194--108235 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
108184 ATAGTAAAAA
108194 TATAATTTTATAATTTT
1 TATAATTTTATAATTTT
*
108211 AATAA-TTTAT-ATTTT
1 TATAATTTTATAATTTT
108226 TATAATTTTA
1 TATAATTTTA
108236 AAAAATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 9 0.41
16 9 0.41
17 4 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATAATTTTATAATTTT
Found at i:110999 original size:35 final size:35
Alignment explanation
Indices: 110950--111021 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
110940 TATTACTTAG
110950 TTTTTTTTTCTTGATGTAATGTCTTTTATTCGGAT
1 TTTTTTTTTCTTGATGTAATGTCTTTTATTCGGAT
*
110985 TTTTTTTTTTTTGATGTAATGTCTTTTATTCGGAT
1 TTTTTTTTTCTTGATGTAATGTCTTTTATTCGGAT
111020 TT
1 TT
111022 AGGTAAGAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.65
Consensus pattern (35 bp):
TTTTTTTTTCTTGATGTAATGTCTTTTATTCGGAT
Found at i:111757 original size:19 final size:18
Alignment explanation
Indices: 111718--111758 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
111708 AAAAATGAGA
*
111718 AAATTTAAAAATATATAT
1 AAATTTAAAAATAGATAT
*
111736 AAATTTGAAAAATAGATTT
1 AAATTT-AAAAATAGATAT
111755 AAAT
1 AAAT
111759 AAAATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (18 bp):
AAATTTAAAAATAGATAT
Found at i:117317 original size:21 final size:22
Alignment explanation
Indices: 117291--117333 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
117281 TTCAATTTTA
*
117291 AAAATA-TAAAAATTTATTATT
1 AAAATATTAAAAAGTTATTATT
*
117312 AAAATATTCAAAAGTTATTATT
1 AAAATATTAAAAAGTTATTATT
117334 CAAGTCATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AAAATATTAAAAAGTTATTATT
Found at i:118280 original size:8 final size:8
Alignment explanation
Indices: 118267--118293 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
118257 TTCTCAAAAT
118267 ATTTAATA
1 ATTTAATA
118275 ATTTAATA
1 ATTTAATA
118283 ATTTAATA
1 ATTTAATA
118291 ATT
1 ATT
118294 GAGAATCGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
ATTTAATA
Found at i:121890 original size:20 final size:20
Alignment explanation
Indices: 121867--121907 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
121857 TTGATTGGAT
121867 TAAATAAAT-TATTAAAAAAA
1 TAAA-AAATATATTAAAAAAA
121887 TAAAAAATATATTAAAAAAA
1 TAAAAAATATATTAAAAAAA
121907 T
1 T
121908 TAATTTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAAAATATATTAAAAAAA
Found at i:128631 original size:2 final size:2
Alignment explanation
Indices: 128624--128704 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
128614 TCTTTCCTTT
128624 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
128666 TA TA TA 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 TA TA TA T
128705 NNNNNNNNNN
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:128762 original size:2 final size:2
Alignment explanation
Indices: 128755--128797 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
128745 NNNNNNNNNN
128755 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
128797 T
1 T
128798 TATTCATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:133226 original size:2 final size:2
Alignment explanation
Indices: 133219--133246 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
133209 CTTTTATCAT
133219 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
133247 CAGAGAGAGA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:136489 original size:28 final size:29
Alignment explanation
Indices: 136438--136520 Score: 96
Period size: 28 Copynumber: 2.8 Consensus size: 29
136428 CAGAAGGTCC
* * *
136438 TCAAACTCTTTAAAAATCATATTTTGACCT
1 TCAAACT-TCTAAAAATTACATTTTGACCT
*
136468 T-AAATTTCTAAAAATTACATTTTGACCT
1 TCAAACTTCTAAAAATTACATTTTGACCT
*
136496 TCGAACTTCTCAAAAATTACATTTT
1 TCAAACTTCT-AAAAATTACATTTT
136521 TCCCATTAGC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 20 0.44
29 10 0.22
30 15 0.33
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.41
Consensus pattern (29 bp):
TCAAACTTCTAAAAATTACATTTTGACCT
Found at i:136607 original size:29 final size:28
Alignment explanation
Indices: 136472--136754 Score: 107
Period size: 29 Copynumber: 9.6 Consensus size: 28
136462 TGACCTTAAA
136472 TTTCTAAAAATTACATTTTGA-CCTTCGAAC
1 TTTC-AAAAATTACATTTT-ACCCTT-GAAC
* *
136502 TTCTCAAAAATTACATTTTTCCCATT-AGC
1 TT-TCAAAAATTACATTTTACCC-TTGAAC
* * **
136531 -TTCCAAAATTACCGTTTTAACCC-CAAAC
1 TTTCAAAAATTA-CATTTT-ACCCTTGAAC
* * *
136559 TTTTCCAAAATCACACTTTTTCCCTTGAAC
1 -TTTCAAAAATTACA-TTTTACCCTTGAAC
*
136589 TTTCAAAAATTACCATTTTTTACCC-CGAAC
1 TTTCAAAAATTA-CA--TTTTACCCTTGAAC
* *
136619 TTTTCAAAAATTACCATTTTACCAC-CGGA-
1 -TTTCAAAAATTA-CATTTTACC-CTTGAAC
* * * *
136648 TGTCCAAAAATCATATTTTTGA-CTTTGAAC
1 T-TTCAAAAATTACA-TTTT-ACCCTTGAAC
*
136678 TTTCCAAAAATTATTATTTTACCCTTGAAC
1 TTT-CAAAAATTA-CATTTTACCCTTGAAC
* * * *
136708 ATTAAAAAATTACCATTTTACCC-TCAAA
1 TTTCAAAAATTA-CATTTTACCCTTGAAC
*
136736 TGTCCAAAAATTACATTTT
1 T-TTCAAAAATTACATTTT
136755 TGACCCCAAA
Statistics
Matches: 194, Mismatches: 36, Indels: 48
0.70 0.13 0.17
Matches are distributed among these distances:
27 9 0.05
28 19 0.10
29 70 0.36
30 68 0.35
31 28 0.14
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (28 bp):
TTTCAAAAATTACATTTTACCCTTGAAC
Found at i:136627 original size:31 final size:31
Alignment explanation
Indices: 136535--136638 Score: 108
Period size: 30 Copynumber: 3.5 Consensus size: 31
136525 ATTAGCTTCC
* * * *
136535 AAAATTACC-GTTTTAACCCCAAACTTTTCC
1 AAAATTACCATTTTTTACCCCGAACTTTTCA
* * *
136565 AAAATCA-CACTTTTT-CCCTTGAAC-TTTCA
1 AAAATTACCATTTTTTACCC-CGAACTTTTCA
136594 AAAATTACCATTTTTTACCCCGAACTTTTCA
1 AAAATTACCATTTTTTACCCCGAACTTTTCA
136625 AAAATTACCATTTT
1 AAAATTACCATTTT
136639 ACCACCGGAT
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
29 14 0.23
30 24 0.40
31 22 0.37
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.38
Consensus pattern (31 bp):
AAAATTACCATTTTTTACCCCGAACTTTTCA
Found at i:136627 original size:59 final size:57
Alignment explanation
Indices: 136441--136627 Score: 148
Period size: 58 Copynumber: 3.2 Consensus size: 57
136431 AAGGTCCTCA
* * ** * * *
136441 AACTCTTTAAAAATCATATTTTGACC-TTAAATTTCTAAAAATTA-CATTTTGACCTTCG
1 AACT-TTTCAAAATCACATTTTTCCCATTAACTTTC-AAAAATTACCATTTTAACC-CCG
* * * * * *
136499 AACTTCTCAAAAATTACATTTTTCCCATTAGC-TTCCAAAATTACCGTTTTAACCCCA
1 AACTTTTC-AAAATCACATTTTTCCCATTAACTTTCAAAAATTACCATTTTAACCCCG
*
136556 AACTTTTCCAAAATCACACTTTTTCCC-TTGAACTTTCAAAAATTACCATTTTTTACCCCG
1 AACTTTT-CAAAATCACA-TTTTTCCCATT-AACTTTCAAAAATTACCA-TTTTAACCCCG
136616 AACTTTTCAAAA
1 AACTTTTCAAAA
136628 ATTACCATTT
Statistics
Matches: 101, Mismatches: 20, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
57 26 0.26
58 39 0.39
59 20 0.20
60 16 0.16
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (57 bp):
AACTTTTCAAAATCACATTTTTCCCATTAACTTTCAAAAATTACCATTTTAACCCCG
Found at i:136667 original size:88 final size:88
Alignment explanation
Indices: 136535--136759 Score: 221
Period size: 88 Copynumber: 2.5 Consensus size: 88
136525 ATTAGCTTCC
* * *
136535 AAAATTACCGTTTTAACCC-CAAACTTTTCC-AAAATCACACTTTTT-CCCTTGAACTTT-CAAA
1 AAAATTACCATTTT-ACCCTCAAA--TGTCCAAAAATCACA-TTTTTGACCTTGAACTTTCCAAA
* *
136596 AATTACCATT-TTTTACCC-CGAACTTTTCA
62 AATT---ATTATTTTACCCTCGAAC-ATTAA
** * *
136625 AAAATTACCATTTTACCAC-CGGATGTCCAAAAATCATATTTTTGACTTTGAACTTTCCAAAAAT
1 AAAATTACCATTTTACC-CTCAAATGTCCAAAAATCACATTTTTGACCTTGAACTTTCCAAAAAT
*
136689 TATTATTTTACCCTTGAACATTAA
65 TATTATTTTACCCTCGAACATTAA
*
136713 AAAATTACCATTTTACCCTCAAATGTCCAAAAATTACATTTTTGACC
1 AAAATTACCATTTTACCCTCAAATGTCCAAAAATCACATTTTTGACC
136760 CCAAACTTTT
Statistics
Matches: 113, Mismatches: 15, Indels: 16
0.78 0.10 0.11
Matches are distributed among these distances:
87 4 0.04
88 60 0.53
89 25 0.22
90 24 0.21
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (88 bp):
AAAATTACCATTTTACCCTCAAATGTCCAAAAATCACATTTTTGACCTTGAACTTTCCAAAAATT
ATTATTTTACCCTCGAACATTAA
Found at i:136789 original size:88 final size:86
Alignment explanation
Indices: 136624--136841 Score: 211
Period size: 88 Copynumber: 2.5 Consensus size: 86
136614 CGAACTTTTC
* * ****
136624 AAAAATTACCATTTTACCACCGGATGTCCAAAAATCATATTTTTGACTTTGAACTTTCCAAAAAT
1 AAAAATTACCATTTTACC-CC-GATGTCCAAAAATTACATTTTTGACCCCAAACTTTCCAAAAAT
** ** *** *
136689 TATTATTTTACCCTTGAACATTA
64 TACCATCGTACCCAAAAACATCA
* * *
136712 AAAAATTACCATTTTACCCTCAAATGTCCAAAAATTACATTTTTGACCCCAAACTTTTCAAATAT
1 AAAAATTACCATTTTACCC-C-GATGTCCAAAAATTACATTTTTGACCCCAAACTTTCCAAAAAT
*
136777 TACCATCGTACCCAAAAACATCC
64 TACCATCGTACCCAAAAACATCA
* *
136800 AAAAATTACCGTTTTACCCCGGTGTCCAAAAATTACTATTTT
1 AAAAATTACCATTTTACCCCGATGTCCAAAAATTAC-ATTTT
136842 ACCCCCGGGT
Statistics
Matches: 106, Mismatches: 22, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
86 14 0.13
87 7 0.07
88 85 0.80
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (86 bp):
AAAAATTACCATTTTACCCCGATGTCCAAAAATTACATTTTTGACCCCAAACTTTCCAAAAATTA
CCATCGTACCCAAAAACATCA
Found at i:136834 original size:27 final size:29
Alignment explanation
Indices: 136797--136869 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 29
136787 CCCAAAAACA
136797 TCCAAAAATTACCGTTTTA-CCCC-GGTG
1 TCCAAAAATTACCGTTTTACCCCCGGGTG
**
136824 TCCAAAAATTACTATTTTACCCCCGGGTG
1 TCCAAAAATTACCGTTTTACCCCCGGGTG
* *
136853 TCCTAAAATCA-CGTTTT
1 TCCAAAAATTACCGTTTT
136870 TCATCACGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 17 0.45
28 8 0.21
29 13 0.34
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.33
Consensus pattern (29 bp):
TCCAAAAATTACCGTTTTACCCCCGGGTG
Found at i:151897 original size:15 final size:15
Alignment explanation
Indices: 151879--151911 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
151869 ATCCACTGTT
151879 TCATCATCATCAGCA
1 TCATCATCATCAGCA
151894 TCATCATCATCAGCA
1 TCATCATCATCAGCA
151909 TCA
1 TCA
151912 GACTCATCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.06, T:0.27
Consensus pattern (15 bp):
TCATCATCATCAGCA
Found at i:151918 original size:15 final size:15
Alignment explanation
Indices: 151883--151921 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
151873 ACTGTTTCAT
*
151883 CATCATCAGCATCAT
1 CATCATCAGCATCAA
151898 CATCATCAGCATCAGA
1 CATCATCAGCATCA-A
151914 C-TCATCAG
1 CATCATCAG
151922 ACTCTTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 21 0.95
16 1 0.05
ACGTcount: A:0.33, C:0.33, G:0.10, T:0.23
Consensus pattern (15 bp):
CATCATCAGCATCAA
Found at i:154635 original size:31 final size:31
Alignment explanation
Indices: 154597--154852 Score: 512
Period size: 31 Copynumber: 8.3 Consensus size: 31
154587 TTTTATTTTA
154597 TATTCAATTACAATTTCATTCTAAATTAAAC
1 TATTCAATTACAATTTCATTCTAAATTAAAC
154628 TATTCAATTACAATTTCATTCTAAATTAAAC
1 TATTCAATTACAATTTCATTCTAAATTAAAC
154659 TATTCAATTACAATTTCATTCTAAATTAAAC
1 TATTCAATTACAATTTCATTCTAAATTAAAC
154690 TATTCAATTACAATTTCATTCTAAATTAAAC
1 TATTCAATTACAATTTCATTCTAAATTAAAC
154721 TATTCAATTACAATTTCATTCTAAATTAAAC
1 TATTCAATTACAATTTCATTCTAAATTAAAC
154752 TATTCAATTACAATTTCATTCTAAATTAAAC
1 TATTCAATTACAATTTCATTCTAAATTAAAC
154783 TATTCAATTACAATTTCATTCTAAATTAAAC
1 TATTCAATTACAATTTCATTCTAAATTAAAC
154814 TATTCAATTACAATTTCATTCTAAATTAAAC
1 TATTCAATTACAATTTCATTCTAAATTAAAC
154845 TATTCAAT
1 TATTCAAT
154853 AATACCTTAT
Statistics
Matches: 225, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 225 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (31 bp):
TATTCAATTACAATTTCATTCTAAATTAAAC
Done.