Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003036.1 Hibiscus syriacus cultivar Beakdansim tig00006317_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: 78458
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:1912 original size:4 final size:4
Alignment explanation
Indices: 1899--1941 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
1889 TTTCCCGTTC
1899 CTTT -TTT CTTT CTTT C-TT CTTT C-TT CTTT C-TT CTTT C-TT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1942 TTCTTCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
3 15 0.44
4 19 0.56
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:1918 original size:7 final size:7
Alignment explanation
Indices: 1903--1946 Score: 72
Period size: 7 Copynumber: 6.3 Consensus size: 7
1893 CCGTTCCTTT
1903 TTTCTTTC
1 TTTC-TTC
1911 TTTCTTC
1 TTTCTTC
1918 TTTCTTC
1 TTTCTTC
1925 TTTCTTC
1 TTTCTTC
1932 TTTCTTC
1 TTTCTTC
1939 TTT-TTC
1 TTTCTTC
1945 TT
1 TT
1947 CTTTTTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 5 0.14
7 27 0.75
8 4 0.11
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTCTTC
Found at i:1958 original size:16 final size:16
Alignment explanation
Indices: 1911--1959 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
1901 TTTTTCTTTC
*
1911 TTTCTTCTTTC-T-TC
1 TTTCTTCTTTCTTATT
*
1925 TTTCTTCTTTCTTCTT
1 TTTCTTCTTTCTTATT
*
1941 TTTCTTCTTTTTTATT
1 TTTCTTCTTTCTTATT
1957 TTT
1 TTT
1960 TATTTTTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 11 0.37
15 1 0.03
16 18 0.60
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTCTTCTTTCTTATT
Found at i:3737 original size:54 final size:53
Alignment explanation
Indices: 3656--4197 Score: 536
Period size: 54 Copynumber: 10.1 Consensus size: 53
3646 AATTTGTGGG
* *
3656 TTGCACACATAGTGCCGAAAC-AGTTATTCATCAACATATGATGAATTCCGTGAA
1 TTGCACACTTAGTG-CGAAACGA-TTATTCATCAACATATGATGAATTCCGTGAT
* * * * *
3710 TTGCACACTTGGTGTCAAAACGATTATTCAGCAACATATGATGAATTACGTGCT
1 TTGCACACTTAGTG-CGAAACGATTATTCATCAACATATGATGAATTCCGTGAT
* * **
3764 TTGCACACTTAGTGCCGAAACGGTTATTCAT-----TATGATGAATTCTGTTCT
1 TTGCACACTTAGTG-CGAAACGATTATTCATCAACATATGATGAATTCCGTGAT
*
3813 TTGCACACTTAGTGCTAAAACGATTATTCATCAACATATGATGAATTCCGT-ACT
1 TTGCACACTTAGTGC-GAAACGATTATTCATCAACATATGATGAATTCCGTGA-T
* * *
3867 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATTATGAATTCCGTGCT
1 TTGCACACTTAGTG-CGAAACGATTATTCATCAACATATGATGAATTCCGTGAT
**
3921 TTGCACACTTAGTGCAGAAACGATTATTCATCAACATATGATGAATTATGT-ACT
1 TTGCACACTTAGTGC-GAAACGATTATTCATCAACATATGATGAATTCCGTGA-T
* * *
3975 TTGCACACGTAATGCTGAAACGGTTATTCATCAACATATGATGAATTCCGT-ACT
1 TTGCACACTTAGTGC-GAAACGATTATTCATCAACATATGATGAATTCCGTGA-T
* * * ** *
4029 TTGCACACTTAGTGTCGAAA-TAGTTATTCATCAACATATGCTAAATTTTGTGCT
1 TTGCACACTTAGTG-CGAAACGA-TTATTCATCAACATATGATGAATTCCGTGAT
* * *
4083 TTGTACACTTAGTGTCGAAAC-ATTTATTCATCAACATATGATGAGTTTCGTGAAT
1 TTGCACACTTAGTG-CGAAACGA-TTATTCATCAACATATGATGAATTCCGTG-AT
* *
4138 TT-CACAGTTAGTACCGAAAC-AGTTATTCATCAACATATGATGAATTCCGT-ACT
1 TTGCACACTTAGT-GCGAAACGA-TTATTCATCAACATATGATGAATTCCGTGA-T
4191 TTGCACA
1 TTGCACA
4198 TTTCTGCCTA
Statistics
Matches: 411, Mismatches: 57, Indels: 40
0.81 0.11 0.08
Matches are distributed among these distances:
48 1 0.00
49 42 0.10
52 1 0.00
53 4 0.01
54 357 0.87
55 6 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (53 bp):
TTGCACACTTAGTGCGAAACGATTATTCATCAACATATGATGAATTCCGTGAT
Found at i:3783 original size:108 final size:107
Alignment explanation
Indices: 3656--4197 Score: 645
Period size: 108 Copynumber: 5.1 Consensus size: 107
3646 AATTTGTGGG
* * * *
3656 TTGCACACATAGTGCCGAAACAGTTATTCATCAACATATGATGAATTCCGTGAATTGCACACTTG
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTTA
* *
3721 GTGTCAAAACGATTATTCAGCAACATATGATGAATTACGTGCT
66 GTG-CAAAACGATTATTCATCAACATATGATGAATTACGTACT
* **
3764 TTGCACACTTAGTGCCGAAACGGTTATTCAT-----TATGATGAATTCTGTTCTTTGCACACTTA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTTA
*
3824 GTGCTAAAACGATTATTCATCAACATATGATGAATTCCGTACT
66 GTGC-AAAACGATTATTCATCAACATATGATGAATTACGTACT
* *
3867 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATTATGAATTCCGTGCTTTGCACACTTA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTTA
*
3932 GTGCAGAAACGATTATTCATCAACATATGATGAATTATGTACT
66 GTGCA-AAACGATTATTCATCAACATATGATGAATTACGTACT
* * *
3975 TTGCACACGTAATGCTGAAACGGTTATTCATCAACATATGATGAATTCCGT-ACTTTGCACACTT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGA-TTTGCACACTT
* * ** *
4039 AGTGTCGAAATA-G-TTATTCATCAACATATGCTAAATTTTGTGCT
65 AGTG-C-AAA-ACGATTATTCATCAACATATGATGAATTACGTACT
* * ** * * *
4083 TTGTACACTTAGTGTCGAAACATTTATTCATCAACATATGATGAGTTTCGTGAATTT-CACAGTT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTG-ATTTGCACACTT
* * *
4147 AGTACCGAAAC-AGTTATTCATCAACATATGATGAATTCCGTACT
65 AGT-GCAAAACGA-TTATTCATCAACATATGATGAATTACGTACT
4191 TTGCACA
1 TTGCACA
4198 TTTCTGCCTA
Statistics
Matches: 375, Mismatches: 42, Indels: 34
0.83 0.09 0.08
Matches are distributed among these distances:
102 1 0.00
103 93 0.25
106 1 0.00
107 3 0.01
108 267 0.71
109 7 0.02
110 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (107 bp):
TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTTA
GTGCAAAACGATTATTCATCAACATATGATGAATTACGTACT
Found at i:4038 original size:162 final size:160
Alignment explanation
Indices: 3656--4197 Score: 672
Period size: 162 Copynumber: 3.4 Consensus size: 160
3646 AATTTGTGGG
* *
3656 TTGCACACATAGTGCCGAAACAGTTATTCATCAACATATGATGAATTCCGTGA-ATTGCACACTT
1 TTGCACACGTAGTGCCGAAACAGTTATTCATCAACATATGATGAATTCCGT-ACTTTGCACACTT
* * * *
3720 GGTGTCAAAACGATTATTCAGCAACATATGATGAATTACGTGCTTTGCACACTTAGTGCCGAAAC
65 AGTGTCGAAACGGTTATTCATCAACATATGATGAATTACGTGCTTTGCACACTTAGTG-CGAAAC
* *
3785 GGTTATTCAT-----TATGATGAATTCTGTTCT
129 GATTATTCATCAACATATGATGAATT-TGTACT
* **
3813 TTGCACACTTAGTGCTAAAAC-GATTATTCATCAACATATGATGAATTCCGTACTTTGCACACTT
1 TTGCACACGTAGTGCCGAAACAG-TTATTCATCAACATATGATGAATTCCGTACTTTGCACACTT
* * *
3877 AGTGCCGAAACGGTTATTCATCAACATATTATGAATTCCGTGCTTTGCACACTTAGTGCAGAAAC
65 AGTGTCGAAACGGTTATTCATCAACATATGATGAATTACGTGCTTTGCACACTTAGTGC-GAAAC
3942 GATTATTCATCAACATATGATGAATTATGTACT
129 GATTATTCATCAACATATGATGAATT-TGTACT
* * *
3975 TTGCACACGTAATGCTGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
1 TTGCACACGTAGTGCCGAAACAGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
** * * ** *
4040 GTGTCGAAATAGTTATTCATCAACATATGCTAAATTTTGTGCTTTGTACACTTAGTGTCGAAAC-
66 GTGTCGAAACGGTTATTCATCAACATATGATGAATTACGTGCTTTGCACACTTAGTG-CGAAACG
* *
4104 ATTTATTCATCAACATATGATGAGTTTCGTGAAT
130 A-TTATTCATCAACATATGATGAATTT-GT-ACT
*
4138 TT-CACA-GTTAGTACCGAAACAGTTATTCATCAACATATGATGAATTCCGTACTTTGCACA
1 TTGCACACG-TAGTGCCGAAACAGTTATTCATCAACATATGATGAATTCCGTACTTTGCACA
4198 TTTCTGCCTA
Statistics
Matches: 339, Mismatches: 32, Indels: 23
0.86 0.08 0.06
Matches are distributed among these distances:
156 3 0.01
157 121 0.36
161 3 0.01
162 206 0.61
163 6 0.02
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (160 bp):
TTGCACACGTAGTGCCGAAACAGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTA
GTGTCGAAACGGTTATTCATCAACATATGATGAATTACGTGCTTTGCACACTTAGTGCGAAACGA
TTATTCATCAACATATGATGAATTTGTACT
Found at i:11217 original size:54 final size:54
Alignment explanation
Indices: 10662--11214 Score: 853
Period size: 54 Copynumber: 10.2 Consensus size: 54
10652 ATTCTGTGAG
* * ***
10662 TTGCACACATAGTGTCGAAACGGTTATTCATCAACATATGATGAATTAT-GTTAA
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATT-TCGTGCT
* * *
10716 TTGCACACTTGGTGTCGAAATGGTTATTCATCAACATATGATGAATTTCGTGCT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGCT
10770 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTAT-GTGCT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATT-TCGTGCT
*
10824 TTGCACACTTAGTGACGAAACGGTTATTCATCAACATATGATGAATTTCGTGC-
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGCT
* * * *
10877 TTGTCACACTTAGTGTCGAAATGGTTATTCATCAATATATGATGAATTAT-GTACT
1 TTG-CACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATT-TCGTGCT
*
10932 TTGCACACTTAGTACCGAAACGGTTATTCATCAACATATGATGAATTTCGTGCT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGCT
* *
10986 TTGCACACTTAGTGCCAAAACGGTTATTCATCAACATATGATGAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGCT
* *
11040 TTGCACACTTAGTGTCGAAACGGTTATTCATCAACATATGATGAATTCCGTGCT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGCT
11094 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGCT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGCT
* * *
11148 TTGCACACTTAGTACCGAAACGGTTATTCATCAACATATGATGAATTTTGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGCT
11202 TTGCACACTTAGT
1 TTGCACACTTAGT
11215 ACCTATTTGG
Statistics
Matches: 461, Mismatches: 31, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
53 6 0.01
54 450 0.98
55 5 0.01
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (54 bp):
TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGCT
Found at i:11374 original size:13 final size:13
Alignment explanation
Indices: 11356--11382 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11346 CAAGTACTTT
11356 GCCTTTGCCCTTC
1 GCCTTTGCCCTTC
11369 GCCTTTGCCCTTC
1 GCCTTTGCCCTTC
11382 G
1 G
11383 TTTTTCTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.44, G:0.19, T:0.37
Consensus pattern (13 bp):
GCCTTTGCCCTTC
Found at i:11501 original size:7 final size:7
Alignment explanation
Indices: 11489--11532 Score: 70
Period size: 7 Copynumber: 6.3 Consensus size: 7
11479 TACATTAGTA
11489 TAAACCC
1 TAAACCC
11496 TAAACCC
1 TAAACCC
*
11503 TAAACTC
1 TAAACCC
11510 TAAACCC
1 TAAACCC
*
11517 TAAAGCC
1 TAAACCC
11524 TAAACCC
1 TAAACCC
11531 TA
1 TA
11533 TTTGATCTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.43, C:0.36, G:0.02, T:0.18
Consensus pattern (7 bp):
TAAACCC
Found at i:15864 original size:12 final size:13
Alignment explanation
Indices: 15819--15863 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
15809 CGCCCCGATT
*
15819 ACCCGATTATCCG
1 ACCCGATTACCCG
*
15832 CCCCGATTACCCG
1 ACCCGATTACCCG
15845 ACCCGA-TACCCG
1 ACCCGATTACCCG
15857 ACCCGAT
1 ACCCGAT
15864 AAATATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 12 0.43
13 16 0.57
ACGTcount: A:0.22, C:0.47, G:0.16, T:0.16
Consensus pattern (13 bp):
ACCCGATTACCCG
Found at i:15937 original size:19 final size:19
Alignment explanation
Indices: 15913--15952 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
15903 AATAAATTTA
15913 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
15932 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
15951 AT
1 AT
15953 ATATACCCGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:15999 original size:12 final size:12
Alignment explanation
Indices: 15975--16008 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
15965 CGATTCCCAG
15975 CCCAATA-CCGA
1 CCCAATACCCGA
15986 CCCAATACCCGA
1 CCCAATACCCGA
15998 CCCAATACCCG
1 CCCAATACCCG
16009 TTTAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.32, C:0.50, G:0.09, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:16582 original size:20 final size:20
Alignment explanation
Indices: 16532--16586 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
16522 CCTAAAATAA
* * *
16532 TAAAAAAATATTATTTTTAT
1 TAAAAAAATAATAATTTAAT
16552 TCAATAAAAATAATAATTTAAT
1 T-AA-AAAAATAATAATTTAAT
16574 TAAAAAAATAATA
1 TAAAAAAATAATA
16587 TATAAAGAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 11 0.37
21 4 0.13
22 15 0.50
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAAAATAATAATTTAAT
Found at i:19439 original size:20 final size:20
Alignment explanation
Indices: 19400--19440 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19390 AAAAATATTT
* * *
19400 TTAATTTATAAATTATTTAC
1 TTAATTTAAAAATAAATTAC
19420 TTAATTTAAAAATAAATTAC
1 TTAATTTAAAAATAAATTAC
19440 T
1 T
19441 ATCCATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAATTTAAAAATAAATTAC
Found at i:20737 original size:23 final size:23
Alignment explanation
Indices: 20711--20760 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
20701 GAAGAACAAT
20711 ATTTACAAAAATAAAG-AAATAAA
1 ATTT-CAAAAATAAAGAAAATAAA
* *
20734 ATTTTAAAAATAAGGAAAATAAA
1 ATTTCAAAAATAAAGAAAATAAA
20757 ATTT
1 ATTT
20761 TATTATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (23 bp):
ATTTCAAAAATAAAGAAAATAAA
Found at i:20742 original size:22 final size:23
Alignment explanation
Indices: 20717--20762 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
20707 CAATATTTAC
20717 AAAAATAAAG-AAATAAAATTTT
1 AAAAATAAAGAAAATAAAATTTT
*
20739 AAAAATAAGGAAAATAAAATTTT
1 AAAAATAAAGAAAATAAAATTTT
20762 A
1 A
20763 TTATTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (23 bp):
AAAAATAAAGAAAATAAAATTTT
Found at i:21578 original size:87 final size:88
Alignment explanation
Indices: 21486--21716 Score: 317
Period size: 87 Copynumber: 2.6 Consensus size: 88
21476 TTGCATAAGG
** *
21486 TTGAGTCTTTATACTTCAATATTGAATATAATCTTTATATGCTGACTCGGATAATATGGAGTCC-
1 TTGAGTCTTTATACTTCAATATTGAATATAATCTTTATATGCTGAAACAGATAATATGGAG-CCA
*
21550 TATACATAC-ACCCATGTATAAGAC
65 TATACAT-CTACCCATATATAAGAC
* *
21574 -TGAGTCTTTATACTTCAATATTGAATATAACCTTTATATGTTGAAACAGATAATATGGAGCCAT
1 TTGAGTCTTTATACTTCAATATTGAATATAATCTTTATATGCTGAAACAGATAATATGGAGCCAT
* *
21638 GTACATCTACCCCTATATAAGAC
66 ATACATCTACCCATATATAAGAC
* *
21661 TTTGAGTCTTTATACTTCAATATTGAATATGATCTTTAAATGCTG-AACAGATAATA
1 -TTGAGTCTTTATACTTCAATATTGAATATAATCTTTATATGCTGAAACAGATAATA
21717 AATTAGTAAA
Statistics
Matches: 127, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
86 3 0.02
87 74 0.58
88 11 0.09
89 39 0.31
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (88 bp):
TTGAGTCTTTATACTTCAATATTGAATATAATCTTTATATGCTGAAACAGATAATATGGAGCCAT
ATACATCTACCCATATATAAGAC
Found at i:23709 original size:37 final size:37
Alignment explanation
Indices: 23633--23710 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
23623 TTTTTATATT
*
23633 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATAAA
* * *
23670 TTTAATTTTTTAAATAAAA-TATATAAATGTTATAAAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-AAA
23707 TTTA
1 TTTA
23711 TAATATTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
36 13 0.36
37 23 0.64
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATAAA
Found at i:23732 original size:18 final size:17
Alignment explanation
Indices: 23683--23733 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
23673 AATTTTTTAA
*
23683 ATAAAATATATAAATGTT
1 ATAAAATATAT-AATATT
*
23701 ATAAAATTTATAATATT
1 ATAAAATATATAATATT
23718 ATACAAATATATAATA
1 ATA-AAATATATAATA
23734 AGGACAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 8 0.28
18 21 0.72
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
ATAAAATATATAATATT
Found at i:24130 original size:27 final size:27
Alignment explanation
Indices: 24100--24152 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
24090 CAATAGTTAT
24100 GTTAATTATGATTTTGAAAAATATAAC
1 GTTAATTATGATTTTGAAAAATATAAC
24127 GTTAATTATGATTTTGAAAAATATAA
1 GTTAATTATGATTTTGAAAAATATAA
24153 TTGAGTGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.42
Consensus pattern (27 bp):
GTTAATTATGATTTTGAAAAATATAAC
Found at i:28164 original size:8 final size:8
Alignment explanation
Indices: 28151--28176 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
28141 TTATTATAAT
28151 TAGATATA
1 TAGATATA
28159 TAGATATA
1 TAGATATA
28167 TAGATATA
1 TAGATATA
28175 TA
1 TA
28177 CAAACCAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (8 bp):
TAGATATA
Found at i:31271 original size:28 final size:28
Alignment explanation
Indices: 31231--31298 Score: 136
Period size: 28 Copynumber: 2.4 Consensus size: 28
31221 GTATCCTTTG
31231 GTCATAAGTCTTTATACCTTTCTATTGA
1 GTCATAAGTCTTTATACCTTTCTATTGA
31259 GTCATAAGTCTTTATACCTTTCTATTGA
1 GTCATAAGTCTTTATACCTTTCTATTGA
31287 GTCATAAGTCTT
1 GTCATAAGTCTT
31299 ATATTTTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.46
Consensus pattern (28 bp):
GTCATAAGTCTTTATACCTTTCTATTGA
Found at i:33581 original size:23 final size:24
Alignment explanation
Indices: 33553--33606 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
33543 TATTAAAAAC
33553 AATAAATGAAATAA-AA-TTTTAA
1 AATAAATGAAATAACAACTTTTAA
* *
33575 TAATAAAAGAGATAACAACTTTTAA
1 -AATAAATGAAATAACAACTTTTAA
33600 AATAAAT
1 AATAAAT
33607 ATAATTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 12 0.46
24 8 0.31
25 6 0.23
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.30
Consensus pattern (24 bp):
AATAAATGAAATAACAACTTTTAA
Found at i:34103 original size:15 final size:16
Alignment explanation
Indices: 34083--34121 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
34073 AATTAAAAAA
34083 ATATATATAAT-ATTT
1 ATATATATAATAATTT
34098 ATATATAT-ATAATTT
1 ATATATATAATAATTT
*
34113 AAATATATA
1 ATATATATA
34122 CCCGGCCCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 19 0.90
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATATATAATAATTT
Found at i:34118 original size:17 final size:17
Alignment explanation
Indices: 34083--34121 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
34073 AATTAAAAAA
*
34083 ATATATATAATATTTAT
1 ATATATATAATATTAAT
34100 ATATATATAAT-TTAA-
1 ATATATATAATATTAAT
34115 ATATATA
1 ATATATA
34122 CCCGGCCCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 3 0.14
17 11 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATATAATATTAAT
Found at i:35050 original size:20 final size:21
Alignment explanation
Indices: 34960--35098 Score: 67
Period size: 20 Copynumber: 6.9 Consensus size: 21
34950 GCGAAATCCG
* * *
34960 AATTCGAGTTGCAAATTTGAA
1 AATTCGTGTTGCGAATTCGAA
* * * *
34981 AACT-GAGTTACGAATTTGATA
1 AATTCGTGTTGCGAATTCGA-A
* *
35002 AATTCGT-TTGCGAAAT-GTA
1 AATTCGTGTTGCGAATTCGAA
*
35021 AATTCTTGTTGCGAATTCGAA
1 AATTCGTGTTGCGAATTCGAA
** *
35042 AATT-GTGTTGTTAATTTG-A
1 AATTCGTGTTGCGAATTCGAA
**
35061 CTTTCGTGTTGCGAATTCG-A
1 AATTCGTGTTGCGAATTCGAA
**
35081 AA-TCGAATTGCGAATTCG
1 AATTCGTGTTGCGAATTCG
35099 TTGGTTATTT
Statistics
Matches: 89, Mismatches: 24, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
19 24 0.27
20 44 0.49
21 20 0.22
22 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (21 bp):
AATTCGTGTTGCGAATTCGAA
Found at i:52643 original size:19 final size:18
Alignment explanation
Indices: 52585--52644 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 18
52575 CTTGAATTTT
52585 TTTTATCTCACTTGAGACA
1 TTTT-TCTCACTTGAGACA
* *
52604 TTTTTCT--CTTAAAACAAA
1 TTTTTCTCACTTGAGAC--A
52622 TTTTGTCTCACTTGAGACA
1 TTTT-TCTCACTTGAGACA
52641 TTTT
1 TTTT
52645 CCTTCGGAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 6 0.19
18 8 0.25
19 12 0.38
21 6 0.19
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.47
Consensus pattern (18 bp):
TTTTTCTCACTTGAGACA
Found at i:52725 original size:38 final size:38
Alignment explanation
Indices: 52673--52746 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 38
52663 CCAAAAAAAT
*
52673 TCTTAAAAGCAAATTTTGTCTCACTTGAGACATTTTTC
1 TCTTAAAAGCAAATTTCGTCTCACTTGAGACATTTTTC
*
52711 TCTTAAAA-CAAAATTTCGTCTCACTTGAGATATTTT
1 TCTTAAAAGC-AAATTTCGTCTCACTTGAGACATTTT
52747 CCTTCGAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (38 bp):
TCTTAAAAGCAAATTTCGTCTCACTTGAGACATTTTTC
Found at i:52757 original size:37 final size:39
Alignment explanation
Indices: 52673--52765 Score: 113
Period size: 38 Copynumber: 2.5 Consensus size: 39
52663 CCAAAAAAAT
* *
52673 TCTTAAAA-GCAAATTTTGTCTCACTTGAGACATTTTTC
1 TCTTAAAACACAAATTTCGTCTCACTTGAGACATTTTTC
*
52711 TCTTAAAACA-AAATTTCGTCTCACTTGAGATA-TTTTC
1 TCTTAAAACACAAATTTCGTCTCACTTGAGACATTTTTC
*
52748 -CTTCGAAACACAAATTTC
1 TCTT-AAAACACAAATTTC
52766 AAAGTTGTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
36 3 0.06
37 10 0.21
38 35 0.73
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (39 bp):
TCTTAAAACACAAATTTCGTCTCACTTGAGACATTTTTC
Found at i:52763 original size:38 final size:36
Alignment explanation
Indices: 52674--52831 Score: 111
Period size: 38 Copynumber: 4.4 Consensus size: 36
52664 CAAAAAAATT
* *
52674 CTTAAA-AGCAAATTTTGTCTCACTTGAGACATTTTTC
1 CTTAAACA-CAAATTTCGTCTCACTTGAGATA-TTTTC
52711 TCTTAAA-ACAAAATTTCGTCTCACTTGAGATATTTTC
1 -CTTAAACAC-AAATTTCGTCTCACTTGAGATATTTTC
** *
52748 CTTCGAAACACAAA-TT--TCAAAGTT--G-T-TTTT-
1 CTT--AAACACAAATTTCGTCTCACTTGAGATATTTTC
* *
52778 CTTAAAAACAAATTTCATCTCACTTGAGATATTTTC
1 CTTAAACACAAATTTCGTCTCACTTGAGATATTTTC
52814 CTTCAGAACACAAATTTC
1 CTT-A-AACACAAATTTC
52832 AAAGTTCTTT
Statistics
Matches: 96, Mismatches: 10, Indels: 28
0.72 0.07 0.21
Matches are distributed among these distances:
28 8 0.08
29 2 0.02
30 3 0.03
31 9 0.09
32 1 0.01
33 2 0.02
34 1 0.01
35 9 0.09
36 6 0.06
37 9 0.09
38 44 0.46
39 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.39
Consensus pattern (36 bp):
CTTAAACACAAATTTCGTCTCACTTGAGATATTTTC
Found at i:52784 original size:66 final size:67
Alignment explanation
Indices: 52706--52842 Score: 217
Period size: 66 Copynumber: 2.1 Consensus size: 67
52696 CTTGAGACAT
*
52706 TTTTCTCTT-AAAACAAAATTTCGTCTCACTTGAGATATTTTCCTTC-GAAACACAAATTTCAAA
1 TTTTCTCTTAAAAAC-AAATTTCATCTCACTTGAGATATTTTCCTTCAG-AACACAAATTTCAAA
*
52769 GTTG
64 GTTC
52773 TTTT-TCTTAAAAACAAATTTCATCTCACTTGAGATATTTTCCTTCAGAACACAAATTTCAAAGT
1 TTTTCTCTTAAAAACAAATTTCATCTCACTTGAGATATTTTCCTTCAGAACACAAATTTCAAAGT
52837 TC
66 TC
52839 TTTT
1 TTTT
52843 ACTTGAACCA
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
66 56 0.85
67 10 0.15
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (67 bp):
TTTTCTCTTAAAAACAAATTTCATCTCACTTGAGATATTTTCCTTCAGAACACAAATTTCAAAGT
TC
Found at i:52889 original size:168 final size:168
Alignment explanation
Indices: 52604--52907 Score: 384
Period size: 168 Copynumber: 1.8 Consensus size: 168
52594 ACTTGAGACA
* ** * *
52604 TTTTTCTCTTAAAACAAATTTTGTCTCACTTGAGACATTTTCCTTCGGAACATAAATTTCCAAAA
1 TTTTTCTCTAAAAACAAATTTCATCTCACTTGAGACATTTTCCTTCAGAACACAAATTTCCAAAA
* * * *
52669 AAATTCTTAAAAGCAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAA-ATTTCGTCTC
66 AAATTCTTAAAACCAAATTTTGTCTCACATGAGACATATTTCTCTCAAAACAAACA--TCGTCTC
52733 ACTTGAGATATTTTCCTTCGAAACACAAATTTCAAAGTTG
129 ACTTGAGATATTTTCCTTCGAAACACAAATTTCAAAGTTG
* *
52773 TTTTTCT-TAAAAACAAATTTCATCTCACTTGAGATATTTTCCTTCAGAACACAAATTT-CAAAG
1 TTTTTCTCTAAAAACAAATTTCATCTCACTTGAGACATTTTCCTTCAGAACACAAATTTCCAAAA
*** * *
52836 TTCTT-TTACTTGAACCAAATTTTGTCTCGCATGAGACA-ATTTCTCTCAAAACAAACATCGTCT
66 AAATTCTTA---AAACCAAATTTTGTCTCACATGAGACATATTTCTCTCAAAACAAACATCGTCT
52899 CACTTGAGA
128 CACTTGAGA
52908 CATTCTCCCA
Statistics
Matches: 115, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
166 3 0.03
167 21 0.18
168 60 0.52
169 31 0.27
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.38
Consensus pattern (168 bp):
TTTTTCTCTAAAAACAAATTTCATCTCACTTGAGACATTTTCCTTCAGAACACAAATTTCCAAAA
AAATTCTTAAAACCAAATTTTGTCTCACATGAGACATATTTCTCTCAAAACAAACATCGTCTCAC
TTGAGATATTTTCCTTCGAAACACAAATTTCAAAGTTG
Found at i:53023 original size:38 final size:36
Alignment explanation
Indices: 52973--53111 Score: 134
Period size: 36 Copynumber: 3.8 Consensus size: 36
52963 TTTCTCTAAA
* * *
52973 AAAACGAATTTTGTCTCACTTGATACATTTTCTTCTC
1 AAAACAAATTTTGTCTCACTTGAGACAGTTTC-TCTC
* *
53010 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAA-TTTTGTCTCACTTGAGACAGTTTCTCTC
* * * * *
53047 GAAACAAATTTTATCTCCCTTGAGACAGTTTCCCTT
1 AAAACAAATTTTGTCTCACTTGAGACAGTTTCTCTC
* * * *
53083 GAAACAAATTTTGACTCCCTTAAGACAGT
1 AAAACAAATTTTGTCTCACTTGAGACAGT
53112 CTCCCTTGAG
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
36 51 0.57
37 17 0.19
38 21 0.24
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCACTTGAGACAGTTTCTCTC
Found at i:53071 original size:36 final size:36
Alignment explanation
Indices: 53011--53120 Score: 150
Period size: 36 Copynumber: 3.0 Consensus size: 36
53001 TTTCTTCTCA
* * *
53011 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAA-TTTTATCTCCCTTGAGACAGTTTCCCTTG
53048 AAACAAATTTTATCTCCCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTATCTCCCTTGAGACAGTTTCCCTTG
* *
53084 AAACAAATTTTGA-CTCCCTTAAGACAGTCTCCCTTG
1 AAACAAATTTT-ATCTCCCTTGAGACAGTTTCCCTTG
53120 A
1 A
53121 GACAGTTTTC
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
36 59 0.88
37 8 0.12
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (36 bp):
AAACAAATTTTATCTCCCTTGAGACAGTTTCCCTTG
Found at i:53177 original size:15 final size:15
Alignment explanation
Indices: 53153--53228 Score: 53
Period size: 15 Copynumber: 4.7 Consensus size: 15
53143 TTTTGTCTTT
53153 CTTGAGACAATTTCC
1 CTTGAGACAATTTCC
*
53168 CTTGAAACAAATTTTGTCTCC
1 CTTGAGAC-AA---T-T-TCC
* *
53189 CTTGAGACAGTCTCC
1 CTTGAGACAATTTCC
*
53204 CTTGAGACATTTTCC
1 CTTGAGACAATTTCC
*
53219 CTTGAAACAA
1 CTTGAGACAA
53229 ATTTTGTCTC
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
15 31 0.66
16 2 0.04
17 1 0.02
19 1 0.02
20 2 0.04
21 10 0.21
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (15 bp):
CTTGAGACAATTTCC
Found at i:53183 original size:36 final size:37
Alignment explanation
Indices: 53110--53208 Score: 146
Period size: 37 Copynumber: 2.7 Consensus size: 37
53100 CCTTAAGACA
*
53110 GTCTCCCTTGAGACAGTTTTCCTTGAAACAAAGTTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTT
** *
53147 GTCTTTCTTGAGACAATTTCCCTTGAAACAAA-TTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTT
*
53183 GTCTCCCTTGAGACAGTCTCCCTTGA
1 GTCTCCCTTGAGACAGTTTCCCTTGA
53209 GACATTTTCC
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
36 26 0.48
37 28 0.52
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.37
Consensus pattern (37 bp):
GTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTT
Found at i:53218 original size:51 final size:51
Alignment explanation
Indices: 53153--53259 Score: 178
Period size: 51 Copynumber: 2.1 Consensus size: 51
53143 TTTTGTCTTT
*
53153 CTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTCTCC
1 CTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCATTGAGACAGTCTCC
* * *
53204 CTTGAGACATTTTCCCTTGAAACAAATTTTGTCTCCATTGAGACGGTTTCC
1 CTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCATTGAGACAGTCTCC
53255 CTTGA
1 CTTGA
53260 AACAGAATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (51 bp):
CTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCATTGAGACAGTCTCC
Found at i:53238 original size:36 final size:36
Alignment explanation
Indices: 53198--53304 Score: 115
Period size: 36 Copynumber: 2.9 Consensus size: 36
53188 CCTTGAGACA
*
53198 GTCTCCCTTGAGACATTTTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
* *
53234 GTCTCCATTGAGACGGTTTCCCTTGAAACAGAATATTTT
1 GTCTCCCTTGAGACAGTTTCCCTTGAAAC--AA-ATTTT
* * * * *
53273 ATCTCGCTTGAGATAGTTTCGCTCGAAACAAA
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAA
53305 ATATTTTTAG
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
36 27 0.47
37 2 0.03
38 2 0.03
39 27 0.47
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (36 bp):
GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTT
Found at i:53238 original size:124 final size:125
Alignment explanation
Indices: 52974--53304 Score: 320
Period size: 124 Copynumber: 2.6 Consensus size: 125
52964 TTCTCTAAAA
* * **
52974 AAACGAATTTTGTCTCACTTGATACA-TTTTCTTCTCAAAACAAAGTTTTGTCTCTCTTGAGACA
1 AAAC-AATTTTGTCTCCCTTGAGACAGTTTTC--CTTGAAACAAAGTTTTGTCTCTCTTGAGACA
* * *
53038 GTTTCTCTTGAAACAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGACTCCCT
63 ATTTCCCTTGAAACAAATTTTATCTCCCTTGAGACAGTCTCCCTTGAAAC-AATTTT-A-TCCCT
53103 T
125 T
*
53104 AAGAC-A----GTCTCCCTTGAGACAGTTTTCCTTGAAACAAAGTTTTGTCTTTCTTGAGACAAT
1 AA-ACAATTTTGTCTCCCTTGAGACAGTTTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAAT
* *
53164 TTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTCTCCCTTGAGAC-A-TTT-TCCCTT
65 TTCCCTTGAAACAAATTTTATCTCCCTTGAGACAGTCTCCCTTGAAACAATTTTATCCCTT
* * * * * * *
53222 GAAACAAATTTTGTCTCCATTGAGACGGTTTCCCTTGAAACAGAATATTTTATCTCGCTTGAGAT
1 -AAAC-AATTTTGTCTCCCTTGAGACAGTTTTCCTTGAAACA-AA-GTTTTGTCTCTCTTGAGAC
* * *
53287 AGTTTCGCTCGAAACAAA
62 AATTTCCCTTGAAACAAA
53305 ATATTTTTAG
Statistics
Matches: 169, Mismatches: 21, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
118 8 0.05
119 2 0.01
120 1 0.01
121 3 0.02
122 1 0.01
124 100 0.59
125 15 0.09
126 34 0.20
129 1 0.01
130 2 0.01
131 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (125 bp):
AAACAATTTTGTCTCCCTTGAGACAGTTTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAATT
TCCCTTGAAACAAATTTTATCTCCCTTGAGACAGTCTCCCTTGAAACAATTTTATCCCTT
Found at i:53284 original size:39 final size:37
Alignment explanation
Indices: 53203--53311 Score: 114
Period size: 39 Copynumber: 2.9 Consensus size: 37
53193 AGACAGTCTC
* *
53203 CCTTGAGACATTTTCCCTTGAAAC-AA-ATTTTGTCT
1 CCTTGAGACAGTTTCCCTTGAAACAAATATTTTATCT
*
53238 CCATTGAGACGGTTTCCCTTGAAACAGAATATTTTATCT
1 CC-TTGAGACAGTTTCCCTTGAAACA-AATATTTTATCT
* * *
53277 CGCTTGAGATAGTTTCGCTCGAAACAAAATATTTT
1 C-CTTGAGACAGTTTCCCTTGAAAC-AAATATTTT
53312 TAGAAACTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
35 2 0.03
36 20 0.33
38 2 0.03
39 35 0.57
40 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (37 bp):
CCTTGAGACAGTTTCCCTTGAAACAAATATTTTATCT
Found at i:53401 original size:52 final size:52
Alignment explanation
Indices: 53313--53503 Score: 235
Period size: 52 Copynumber: 3.7 Consensus size: 52
53303 AAATATTTTT
*
53313 AGAAACTAAGTC-AGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAA
1 AGAAACTAAGCCTA-ATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTT-AA
* * *
53366 AGAAGCTAAGCCTAATTTT-AGGGGTTTCTTAATGTTTTGAAATGAATTTCAA
1 AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTT-AA
* * * **
53418 AGAAATTAAGCCTAAGTTTT-ATGGATTTCTTGATGTTTTCAAATGAATTTTT
1 AGAAACTAAGCCTAA-TTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTAA
*
53470 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGAT
1 AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGAT
53504 AATTATTTTC
Statistics
Matches: 118, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
51 4 0.03
52 68 0.58
53 45 0.38
54 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (52 bp):
AGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTAA
Found at i:61894 original size:13 final size:12
Alignment explanation
Indices: 61873--61902 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
61863 CCCACTTTGT
61873 AAAAAAAAAAGA
1 AAAAAAAAAAGA
61885 AAAAAGAAAAAGA
1 AAAAA-AAAAAGA
61898 AAAAA
1 AAAAA
61903 TGAAGCTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:62175 original size:20 final size:20
Alignment explanation
Indices: 62150--62192 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
62140 TCTAAAAGCC
*
62150 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
62170 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
62190 CAT
1 CAT
62193 GTGGTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:64247 original size:22 final size:22
Alignment explanation
Indices: 64222--64290 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 22
64212 AGTTCATAAT
64222 GAGAAGAACTCATCTGATAAGA
1 GAGAAGAACTCATCTGATAAGA
* *
64244 GAGAAGAAGT--TC--ATAA-T
1 GAGAAGAACTCATCTGATAAGA
64261 GAGAAGAACTCATCTGATAAGA
1 GAGAAGAACTCATCTGATAAGA
64283 GAGAAGAA
1 GAGAAGAA
64291 GTTCTTAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
17 9 0.24
18 4 0.11
19 2 0.05
20 2 0.05
21 4 0.11
22 17 0.45
ACGTcount: A:0.48, C:0.10, G:0.25, T:0.17
Consensus pattern (22 bp):
GAGAAGAACTCATCTGATAAGA
Found at i:64266 original size:39 final size:39
Alignment explanation
Indices: 64212--64343 Score: 202
Period size: 39 Copynumber: 3.5 Consensus size: 39
64202 TCCAATGGAG
64212 AGTTCATAATGAGAAGAACTCATCTGATAAGAGAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTGATAAGAGAGAAGA
64251 AGTTCATAATGAGAAGAACTCATCTGATAAGAGAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTGATAAGAGAGAAGA
* *
64290 AGTTCTTAATGAGAAGAACTCGTCCT-A-AAG-GAG-A-A
1 AGTTCATAATGAGAAGAACTCAT-CTGATAAGAGAGAAGA
64325 AGTTCATAATGAGAAGAAC
1 AGTTCATAATGAGAAGAAC
64344 ATGTTCCTTG
Statistics
Matches: 89, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
35 19 0.21
36 1 0.01
37 3 0.03
38 3 0.03
39 61 0.69
40 2 0.02
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (39 bp):
AGTTCATAATGAGAAGAACTCATCTGATAAGAGAGAAGA
Found at i:64479 original size:105 final size:105
Alignment explanation
Indices: 64284--64555 Score: 377
Period size: 105 Copynumber: 2.6 Consensus size: 105
64274 CTGATAAGAG
* * *
64284 AGAAGAAGTTCTTAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAAGAACATGTT
1 AGAAG-AGTTCATAATGAGAAGAACTCGTCTTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTT
* *
64349 CCTTGTAAATCCACCCCAGAGGGAGGTGAATCAACATTTCC
65 CCTTGTAAATCCACCCCAGAAGGAGGTGAACCAACATTTCC
*
64390 AGAAGAGTTCATAATGAGAAGAACTCGTCTTAAAGGAGAAAGTTCATAATGAAAAGAACTTGTTC
1 AGAAGAGTTCATAATGAGAAGAACTCGTCTTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTC
* ** * * *
64455 CTT-TCAAATCCATCGTATAAGGAGGTGAACCAATATTTTC
66 CTTGT-AAATCCACCCCAGAAGGAGGTGAACCAACATTTCC
* *
64495 AGAAGAGTTCATAATGAGAAGAACT-ATCCTTAAAGGAGGAAGTTCATAATGAGAAGAACTT
1 AGAAGAGTTCATAATGAGAAGAACTCGT-CTTAAAGGAGAAAGTTCATAATGAGAAGAACTT
64556 ACTCAACTTT
Statistics
Matches: 149, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
104 2 0.01
105 142 0.95
106 5 0.03
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.25
Consensus pattern (105 bp):
AGAAGAGTTCATAATGAGAAGAACTCGTCTTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTC
CTTGTAAATCCACCCCAGAAGGAGGTGAACCAACATTTCC
Found at i:64628 original size:42 final size:43
Alignment explanation
Indices: 64564--64646 Score: 116
Period size: 42 Copynumber: 1.9 Consensus size: 43
64554 TTACTCAACT
*
64564 TTTTGCTCGATTCTATCACATAAGGAGTTA-GATCAGCATCATCG
1 TTTTGCTCGA-TCCATCACATAAGGAG-TAGGATCAGCATCATCG
*
64608 TTTTGCTCG-TCCATCACATAAGGAGTAGGATCGGCATCA
1 TTTTGCTCGATCCATCACATAAGGAGTAGGATCAGCATCA
64647 CTATTGGAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
41 2 0.06
42 25 0.69
44 9 0.25
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (43 bp):
TTTTGCTCGATCCATCACATAAGGAGTAGGATCAGCATCATCG
Found at i:68755 original size:17 final size:17
Alignment explanation
Indices: 68731--68776 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
68721 TATTATTATT
68731 TTTC-CTGTATTGTTCA
1 TTTCACTGTATTGTTCA
* *
68747 TTTCACTGTACTGTTCC
1 TTTCACTGTATTGTTCA
68764 TTTCTA-TGTATTG
1 TTTC-ACTGTATTG
68777 AATTTTTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 4 0.16
17 20 0.80
18 1 0.04
ACGTcount: A:0.13, C:0.20, G:0.13, T:0.54
Consensus pattern (17 bp):
TTTCACTGTATTGTTCA
Found at i:69039 original size:65 final size:65
Alignment explanation
Indices: 68970--69219 Score: 383
Period size: 65 Copynumber: 3.8 Consensus size: 65
68960 GATCTTTGCA
* *
68970 GTATTCAATTATCACTCCACCTCATGCACCACAAAGTTACATGAGTCATATGAGTGATATGTAAT
1 GTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTAAT
* * * *
69035 GTATTCAATTATCACTCCACCTCATGCACCACAAAGGTATATGAGTCATATGAGTGATCTGTACT
1 GTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTAAT
* * * * * *
69100 GTATTCAATTATCACTCTACCCCATGTACTAAAAAGATACATGAGTCATATGAGTGATATGTATT
1 GTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTAAT
*
69165 GTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTTATATGAGT
1 GTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGT
69220 AATCTGTACT
Statistics
Matches: 166, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 166 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (65 bp):
GTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTAAT
Found at i:69191 original size:130 final size:130
Alignment explanation
Indices: 68951--69229 Score: 425
Period size: 130 Copynumber: 2.2 Consensus size: 130
68941 TACTCGAGTC
* * * * * *
68951 TCAT-TGAGTGATCTTTGCAGTATTCAATTATCACTCCACCTCATGCACCACAAAGTTACATGAG
1 TCATATGAGTGATCTGTACTGTATTCAATTATCACTCCACCCCATGCACCAAAAAGATACATGAG
* *
69015 TCATATGAGTGATATGTAATGTATTCAATTATCACTCCACCTCATGCACCACAAAGGTATATGAG
66 TCATATGAGTGATATGTAATGTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAG
* * *
69080 TCATATGAGTGATCTGTACTGTATTCAATTATCACTCTACCCCATGTACTAAAAAGATACATGAG
1 TCATATGAGTGATCTGTACTGTATTCAATTATCACTCCACCCCATGCACCAAAAAGATACATGAG
*
69145 TCATATGAGTGATATGTATTGTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAG
66 TCATATGAGTGATATGTAATGTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAG
* *
69210 TTATATGAGTAATCTGTACT
1 TCATATGAGTGATCTGTACT
69230 TGTTCACTCT
Statistics
Matches: 135, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
129 4 0.03
130 131 0.97
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (130 bp):
TCATATGAGTGATCTGTACTGTATTCAATTATCACTCCACCCCATGCACCAAAAAGATACATGAG
TCATATGAGTGATATGTAATGTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAG
Found at i:73053 original size:20 final size:20
Alignment explanation
Indices: 73024--73072 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
73014 ACCACAGAAA
*
73024 TTTATAATTTTTTTTTTATAT
1 TTTAT-ATTTTTTTCTTATAT
*
73045 TTTATATTTTTTTCTTGTAT
1 TTTATATTTTTTTCTTATAT
*
73065 TTTTTATT
1 TTTATATT
73073 AATAATATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTATATTTTTTTCTTATAT
Found at i:73828 original size:15 final size:15
Alignment explanation
Indices: 73771--73851 Score: 58
Period size: 15 Copynumber: 5.5 Consensus size: 15
73761 AAGTATCTTA
73771 TTAAA-ATAAATTAAT
1 TTAAATATAAATT-AT
* *
73786 TT-ATTATCAATTAT
1 TTAAATATAAATTAT
* **
73800 TAAAATATGTATTAT
1 TTAAATATAAATTAT
73815 TTAAATATAAATTAT
1 TTAAATATAAATTAT
** * *
73830 GCAAACATAAATTGT
1 TTAAATATAAATTAT
73845 TTAAATA
1 TTAAATA
73852 AATTAAAATT
Statistics
Matches: 48, Mismatches: 16, Indels: 4
0.71 0.24 0.06
Matches are distributed among these distances:
14 4 0.08
15 44 0.92
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (15 bp):
TTAAATATAAATTAT
Found at i:76720 original size:16 final size:16
Alignment explanation
Indices: 76680--76728 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
76670 ATTCTGAACA
76680 AATAT-TATATT-TT-
1 AATATCTATATTATTC
76693 AATTATCATATATTATTC
1 AA-TATC-TATATTATTC
76711 AATATCTATATTA-TC
1 AATATCTATATTATTC
76726 AAT
1 AAT
76729 TTGATCTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.06
14 3 0.10
15 5 0.16
16 13 0.42
17 6 0.19
18 2 0.06
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (16 bp):
AATATCTATATTATTC
Done.