Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002752.1 Hibiscus syriacus cultivar Beakdansim tig00005669_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: 75055
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:382 original size:25 final size:25
Alignment explanation
Indices: 331--382 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
321 AAAATAAACT
*
331 TAAAAATAATTAAAATAACAAATAA
1 TAAAAATAATTAAAACAACAAATAA
*
356 TAAAAATAGTTAAAACAACCAAA-AA
1 TAAAAATAATTAAAACAA-CAAATAA
381 TA
1 TA
383 TATATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.21
Consensus pattern (25 bp):
TAAAAATAATTAAAACAACAAATAA
Found at i:527 original size:21 final size:22
Alignment explanation
Indices: 501--541 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
491 TCAAATTAAA
501 TAACAGT-AATAAATTAAAAAC
1 TAACAGTGAATAAATTAAAAAC
*
522 TAACAGTGACTAAATTAAAA
1 TAACAGTGAATAAATTAAAA
542 CAAACCAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.59, C:0.10, G:0.07, T:0.24
Consensus pattern (22 bp):
TAACAGTGAATAAATTAAAAAC
Found at i:542 original size:21 final size:20
Alignment explanation
Indices: 493--542 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
483 AACAATGATC
493 AAATT-AAA-TAACAGTAAT
1 AAATTAAAACTAACAGTAAT
*
511 AAATTAAAAACTAACAGTGACT
1 AAATT-AAAACTAACAGT-AAT
533 AAATTAAAAC
1 AAATTAAAAC
543 AAACCAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 5 0.19
20 3 0.11
21 12 0.44
22 7 0.26
ACGTcount: A:0.60, C:0.10, G:0.06, T:0.24
Consensus pattern (20 bp):
AAATTAAAACTAACAGTAAT
Found at i:4788 original size:40 final size:39
Alignment explanation
Indices: 4734--4814 Score: 153
Period size: 40 Copynumber: 2.1 Consensus size: 39
4724 CGCGTAAATA
4734 ATTTCTGGTCTTACTCCTTCCTCTTAAGGATGCTAAGTC
1 ATTTCTGGTCTTACTCCTTCCTCTTAAGGATGCTAAGTC
4773 ATTTCTGGGTCTTACTCCTTCCTCTTAAGGATGCTAAGTC
1 ATTTCT-GGTCTTACTCCTTCCTCTTAAGGATGCTAAGTC
4813 AT
1 AT
4815 AATTTTTGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 6 0.15
40 35 0.85
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.41
Consensus pattern (39 bp):
ATTTCTGGTCTTACTCCTTCCTCTTAAGGATGCTAAGTC
Found at i:6147 original size:75 final size:75
Alignment explanation
Indices: 6024--6174 Score: 293
Period size: 75 Copynumber: 2.0 Consensus size: 75
6014 ATAGCTGATT
*
6024 CTCGAATGCATTCAACTTTAATCTAATGTCTTTATTAATGATGTCATCACGACATAGGATCTCTT
1 CTCGAATACATTCAACTTTAATCTAATGTCTTTATTAATGATGTCATCACGACATAGGATCTCTT
6089 CATACGCGAA
66 CATACGCGAA
6099 CTCGAATACATTCAACTTTAATCTAATGTCTTTATTAATGATGTCATCACGACATAGGATCTCTT
1 CTCGAATACATTCAACTTTAATCTAATGTCTTTATTAATGATGTCATCACGACATAGGATCTCTT
6164 CATACGCGAA
66 CATACGCGAA
6174 C
1 C
6175 CCCAACTCGT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (75 bp):
CTCGAATACATTCAACTTTAATCTAATGTCTTTATTAATGATGTCATCACGACATAGGATCTCTT
CATACGCGAA
Found at i:7165 original size:64 final size:64
Alignment explanation
Indices: 7033--7186 Score: 163
Period size: 64 Copynumber: 2.4 Consensus size: 64
7023 GAAGGTGTAT
* * ** * * *
7033 CGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAAAATAAAAGATCGAATGCAATTAGTGCAT
1 CGATGCACAAGCAGTGCATCGATGCATCTCCATTAAAATAAAACATCGAATACAATTAGTGCAC
* *
7096 CGATGCATAAGGCA-TGCATCGATGCATC-CCATTAATAATAAAACATCGAATACATTTTA-TGC
1 CGATGCACAA-GCAGTGCATCGATGCATCTCCATTAA-AATAAAACATCGAATACA-ATTAGTGC
7158 AC
63 AC
*
7160 CGATGCACAAGTAGTGCATCGATGCAT
1 CGATGCACAAGCAGTGCATCGATGCAT
7187 ACCTTCATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
63 27 0.36
64 45 0.60
65 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (64 bp):
CGATGCACAAGCAGTGCATCGATGCATCTCCATTAAAATAAAACATCGAATACAATTAGTGCAC
Found at i:7602 original size:29 final size:29
Alignment explanation
Indices: 7563--7643 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
7553 TATGTGATAT
7563 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
7593 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
7622 GAGAAATGGCATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
7644 ACATATAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:15968 original size:22 final size:21
Alignment explanation
Indices: 15926--15965 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
15916 GAGTTTATTT
*
15926 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
15947 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
15966 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:23210 original size:64 final size:64
Alignment explanation
Indices: 23142--23298 Score: 151
Period size: 64 Copynumber: 2.5 Consensus size: 64
23132 TTGAAGGTGT
** *
23142 ATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAAGATCGAATGCA-ATTAGT
1 ATCGATGCACAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATATTA-T
23204 GC
63 GC
* * * * *
23206 ATCGATGCATAAGGCA-TGAATCGATGCATCCCATTAATAATAAAACATTGAATGCATTTTATGC
1 ATCGATGCA-CAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
* **
23270 ACCGATGCACAAATAGTGCATCGATGCAT
1 ATCGATGCACAGGTAGTGCATCGATGCAT
23299 ACCTTCATTA
Statistics
Matches: 74, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
63 2 0.03
64 61 0.82
65 11 0.15
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (64 bp):
ATCGATGCACAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
Found at i:23716 original size:29 final size:28
Alignment explanation
Indices: 23677--23757 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 28
23667 TATGTGATAT
23677 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAG-TACATGATCACAA
23707 GAGAAATGACATGAGTTACATGATCACAA
1 GAGAAATGACATGAG-TACATGATCACAA
23736 GAGAAATGACATGAGTACATGA
1 GAGAAATGACATGAGTACATGA
23758 ACATATAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (28 bp):
GAGAAATGACATGAGTACATGATCACAA
Found at i:28785 original size:24 final size:24
Alignment explanation
Indices: 28741--28786 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
28731 ATTTAAGGTA
*
28741 TATTTTATTATATTTAATATTTTG
1 TATTTAATTATATTTAATATTTTG
28765 TATTTAATT-TATTTAAGTATTT
1 TATTTAATTATATTTAA-TATTT
28787 AAATTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TATTTAATTATATTTAATATTTTG
Found at i:28786 original size:17 final size:17
Alignment explanation
Indices: 28764--28801 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
28754 TTAATATTTT
*
28764 GTATTTAATTTATTTAA
1 GTATTTAAATTATTTAA
28781 GTATTTAAATTATTTAA
1 GTATTTAAATTATTTAA
28798 -TATT
1 GTATT
28802 GTATTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (17 bp):
GTATTTAAATTATTTAA
Found at i:34211 original size:21 final size:21
Alignment explanation
Indices: 34185--34229 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
34175 GATTTCTGGG
* *
34185 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
34206 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
34227 CAA
1 CAA
34230 ACGACAGAAT
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:34830 original size:18 final size:18
Alignment explanation
Indices: 34807--34841 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34797 CTAGGAGATT
34807 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
34825 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
34842 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:34927 original size:21 final size:22
Alignment explanation
Indices: 34898--34941 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
34888 GTTGTATGAT
34898 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
34919 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
34941 A
1 A
34942 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:35837 original size:149 final size:149
Alignment explanation
Indices: 35651--35954 Score: 554
Period size: 149 Copynumber: 2.0 Consensus size: 149
35641 GAGTCGAGGG
35651 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
35716 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
35781 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* * *
35800 TCTATGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
35865 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
*
35930 TATGGCACTATGGTGCAAT
131 TATGGCACTACGGTGCAAT
35949 TCTACG
1 TCTACG
35955 GGGCACTTCG
Statistics
Matches: 148, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 148 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:35977 original size:23 final size:23
Alignment explanation
Indices: 35933--35977 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
35923 ATCATTATAT
*
35933 GGCACTATGGTGCAATTCTACGG
1 GGCACTATGGTGCAATTATACGG
*
35956 GGCACT-TCGGTGCATTTATACG
1 GGCACTAT-GGTGCAATTATACG
35978 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (23 bp):
GGCACTATGGTGCAATTATACGG
Found at i:37800 original size:22 final size:22
Alignment explanation
Indices: 37775--37817 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
37765 AATACTGAGA
37775 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
37797 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
37818 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:37823 original size:18 final size:18
Alignment explanation
Indices: 37802--37890 Score: 61
Period size: 18 Copynumber: 5.4 Consensus size: 18
37792 CATATTTTAA
37802 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
* *
37820 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
*
37834 AATAAATCAATCCATACT
1 AATAAATCAATTCATACT
*
37852 AATAAAT-TATT--TA--
1 AATAAATCAATTCATACT
*
37865 AATTAAATCAATCCATACT
1 AA-TAAATCAATTCATACT
37884 AATAAAT
1 AATAAAT
37891 TATTTAAAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 20
0.64 0.11 0.25
Matches are distributed among these distances:
13 2 0.04
14 12 0.23
15 8 0.15
17 9 0.17
18 19 0.37
19 2 0.04
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:37826 original size:22 final size:22
Alignment explanation
Indices: 37777--37825 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
37767 TACTGAGATT
**
37777 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
37799 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
37822 TAAA
1 TAAA
37826 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:37836 original size:32 final size:32
Alignment explanation
Indices: 37797--38102 Score: 254
Period size: 32 Copynumber: 10.7 Consensus size: 32
37787 CAATCCATAT
*
37797 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
37829 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
37861 TTTAAATTAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
37893 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* **
37923 --T--AATAAATCAATCCAT-GTTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
37948 -------TAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
37973 TTTAAAATAAAT---T-AAT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
37995 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
38027 TTTAAAATAAAGC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
38049 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
38081 TTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATCCATAC
38103 AACTGCAATA
Statistics
Matches: 225, Mismatches: 17, Indels: 64
0.74 0.06 0.21
Matches are distributed among these distances:
22 36 0.16
23 8 0.04
24 2 0.01
25 6 0.03
26 23 0.10
27 8 0.04
28 9 0.04
29 1 0.00
30 3 0.01
31 5 0.02
32 124 0.55
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:37988 original size:22 final size:22
Alignment explanation
Indices: 37963--38006 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
37953 CAATCTATAC
37963 TAATAAAT-TATTTAAAATAAAT
1 TAATAAATAT-TTTAAAATAAAT
**
37985 TAATCTATATTTTAAAATAAAT
1 TAATAAATATTTTAAAATAAAT
38007 CAATCCATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATAAATATTTTAAAATAAAT
Found at i:38006 original size:54 final size:54
Alignment explanation
Indices: 37924--38097 Score: 287
Period size: 54 Copynumber: 3.2 Consensus size: 54
37914 CAACTACAAT
* *
37924 AATAAATCAATCCATGTTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
* *
37978 AATAAATTAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
*
38032 AATAAAGCAATCTATATTTTAAAATAAATCAAT-TCATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCT-ATACTAATAAATTATTTAA
38086 AATAAATCAATC
1 AATAAATCAATC
38098 CATACAACTG
Statistics
Matches: 111, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
54 111 1.00
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.37
Consensus pattern (54 bp):
AATAAATCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
Found at i:38093 original size:188 final size:195
Alignment explanation
Indices: 37774--38225 Score: 738
Period size: 188 Copynumber: 2.3 Consensus size: 195
37764 CAATACTGAG
*
37774 ATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAA
1 ATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAA
* *
37839 ATCAATCCATACTAATAAATTATTTAAATTAAATCAATCCATACTAATAAATTATTTAAAATAAA
66 AGCAA--CATACTAAT-AATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
* *
37904 TCAATCCATACAACTACAATAATAAATCAATCCATGTTTTAAAATAAATCAATCTATACTAATAA
128 TCAATCCATACAACTACAATAATAAAGCAATCCATATTTTAAAATAAATCAATCTATACTAATAA
37969 ATT
193 ATT
* *
37972 ATTTAAAATAAATTAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAA
1 ATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAA
*
38037 AGC-A-AT-CT-AT-A-T-TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCA
66 AGCAACATACTAATAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
* *
38095 ATCCATACAACTGCAATAATAAAGCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATT
131 ATCCATACAACTACAATAATAAAGCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATT
38160 ATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAA
1 ATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAA
38225 A
66 A
38226 TAATCTTATT
Statistics
Matches: 242, Mismatches: 12, Indels: 10
0.92 0.05 0.04
Matches are distributed among these distances:
188 169 0.70
189 1 0.00
190 1 0.00
192 2 0.01
193 2 0.01
194 2 0.01
197 1 0.00
198 64 0.26
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (195 bp):
ATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAA
AGCAACATACTAATAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
ATCCATACAACTACAATAATAAAGCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATT
Found at i:38116 original size:134 final size:133
Alignment explanation
Indices: 37986--38230 Score: 445
Period size: 134 Copynumber: 1.8 Consensus size: 133
37976 AAAATAAATT
*
37986 AATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAGCAATCTATATTT
1 AATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAGCAATCCATATTT
*
38051 TAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTGCAATAATA
66 TAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-AATCCATACAACTGCAATAATA
38116 AAGC
130 AAGC
* *
38120 AATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTT
1 AATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAGCAATCCATATTT
38185 TAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAATC
66 TAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAATC
38231 TTATTAAATT
Statistics
Matches: 107, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
133 4 0.04
134 103 0.96
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (133 bp):
AATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAGCAATCCATATTT
TAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAATCCATACAACTGCAATAATAA
AGC
Found at i:38133 original size:80 final size:80
Alignment explanation
Indices: 38032--38181 Score: 284
Period size: 80 Copynumber: 1.9 Consensus size: 80
38022 AATTATTTAA
38032 AATAAAGCAATCTATATTTTAAAATAAATCAAT-TCATACTAATAAATTATTTAAAATAAATCAA
1 AATAAAGCAATCTATATTTTAAAATAAATCAATCT-ATACTAATAAATTATTTAAAATAAATCAA
38096 TCCATACAACTGCAAT
65 TCCATACAACTGCAAT
38112 AATAAAGCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAAGCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
38177 CCATA
66 CCATA
38182 TTTTAAAATA
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
80 68 0.99
81 1 0.01
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (80 bp):
AATAAAGCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTGCAAT
Found at i:38168 original size:32 final size:30
Alignment explanation
Indices: 38129--38249 Score: 120
Period size: 32 Copynumber: 4.3 Consensus size: 30
38119 CAATCTATAT
38129 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCT-TACT-ATAAATTA
38161 TTTAAAATAAATCAATC---C-AT--A-T-
1 TTTAAAATAAATCAATCTTACTATAAATTA
*
38183 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAAT-CTTACT-ATAAATTA
38215 TTTAAAATAAAT-AATCTTA-T-TAAATTA
1 TTTAAAATAAATCAATCTTACTATAAATTA
38242 TTTAAAAT
1 TTTAAAAT
38250 TATTTTAATA
Statistics
Matches: 78, Mismatches: 1, Indels: 25
0.75 0.01 0.24
Matches are distributed among these distances:
22 16 0.21
23 2 0.03
24 1 0.01
26 3 0.04
27 15 0.19
28 3 0.04
29 1 0.01
30 4 0.05
31 4 0.05
32 29 0.37
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (30 bp):
TTTAAAATAAATCAATCTTACTATAAATTA
Found at i:38187 original size:22 final size:22
Alignment explanation
Indices: 38161--38203 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
38151 TAATAAATTA
38161 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
38183 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
38204 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:38212 original size:22 final size:22
Alignment explanation
Indices: 38163--38211 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
38153 ATAAATTATT
**
38163 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
38185 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
38208 TAAA
1 TAAA
38212 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:38226 original size:54 final size:54
Alignment explanation
Indices: 38112--38230 Score: 204
Period size: 54 Copynumber: 2.2 Consensus size: 54
38102 CAACTGCAAT
* * *
38112 AATAAAGCAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
38166 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
38220 AATAAAT-AATC
1 AATAAATCAATC
38231 TTATTAAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
53 4 0.06
54 58 0.94
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:39205 original size:2 final size:2
Alignment explanation
Indices: 39198--39226 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39188 GTAGACTATT
39198 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 T
39227 TCATTTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43424 original size:35 final size:34
Alignment explanation
Indices: 43339--43425 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
43329 ATTTGATATT
*
43339 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
43373 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
43411 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
43426 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:43659 original size:15 final size:15
Alignment explanation
Indices: 43653--43702 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
43643 GTCATCATCG
43653 TCATCGTCGTCGTCA
1 TCATCGTCGTCGTCA
* *
43668 CCATTGTCGTCGTCA
1 TCATCGTCGTCGTCA
*
43683 TCATCGTCGTCGTCG
1 TCATCGTCGTCGTCA
43698 TCATC
1 TCATC
43703 CTGAGCAGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.12, C:0.34, G:0.20, T:0.34
Consensus pattern (15 bp):
TCATCGTCGTCGTCA
Found at i:43663 original size:18 final size:18
Alignment explanation
Indices: 43635--43702 Score: 82
Period size: 18 Copynumber: 3.8 Consensus size: 18
43625 TTCTGACTCC
*
43635 TCGTTGTCGTCATCATCG
1 TCGTCGTCGTCATCATCG
* * * *
43653 TCATCGTCGTCGTCACCA
1 TCGTCGTCGTCATCATCG
*
43671 TTGTCGTCGTCATCATCG
1 TCGTCGTCGTCATCATCG
43689 TCGTCGTCGTCATC
1 TCGTCGTCGTCATC
43703 CTGAGCAGGT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.12, C:0.32, G:0.21, T:0.35
Consensus pattern (18 bp):
TCGTCGTCGTCATCATCG
Found at i:43675 original size:33 final size:33
Alignment explanation
Indices: 43638--43700 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
43628 TGACTCCTCG
*
43638 TTGTCGTCATCATCGTCATCGTCGTCGTCACCA
1 TTGTCGTCATCATCATCATCGTCGTCGTCACCA
* *
43671 TTGTCGTCGTCATCATCGTCGTCGTCGTCA
1 TTGTCGTCATCATCATCATCGTCGTCGTCA
43701 TCCTGAGCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.13, C:0.32, G:0.21, T:0.35
Consensus pattern (33 bp):
TTGTCGTCATCATCATCATCGTCGTCGTCACCA
Found at i:43680 original size:21 final size:21
Alignment explanation
Indices: 43635--43681 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
43625 TTCTGACTCC
* *
43635 TCGTTGTCGTCATCATCGTCA
1 TCGTCGTCGTCACCATCGTCA
* *
43656 TCGTCGTCGTCACCATTGTCG
1 TCGTCGTCGTCACCATCGTCA
43677 TCGTC
1 TCGTC
43682 ATCATCGTCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.32, G:0.21, T:0.36
Consensus pattern (21 bp):
TCGTCGTCGTCACCATCGTCA
Found at i:45698 original size:111 final size:111
Alignment explanation
Indices: 45561--45782 Score: 381
Period size: 111 Copynumber: 2.0 Consensus size: 111
45551 ATTACAAAAA
* *
45561 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
45626 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCATATCAACAAAGTGTAGAGATAT
*
45672 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATGTTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
45737 AATTAAAGCGTTAAAATGTTACCATATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCATATCAACAAAGTGTAGAGATAT
45783 ATGATTTCCA
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCATATCAACAAAGTGTAGAGATAT
Found at i:45920 original size:12 final size:10
Alignment explanation
Indices: 45906--45946 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
45896 ACCTTAAAAA
*
45906 GAGAGTATTT
1 GAGAGAATTT
45916 GAGAGAAATTT
1 GAGAG-AATTT
45927 -AGAGAATTT
1 GAGAGAATTT
45936 GAGAGAATTT
1 GAGAGAATTT
45946 G
1 G
45947 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:46144 original size:50 final size:49
Alignment explanation
Indices: 46082--46194 Score: 147
Period size: 50 Copynumber: 2.3 Consensus size: 49
46072 TAGCGCTGAT
* *
46082 CAGGAGGCGCGCTATACCCACGTGGCGCCAGATCACCGTATAT-CGCGGGG
1 CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCA--GTATATACGCGGGG
* * *
46132 CAGGGGGTGCGCTATACCCACGTGGTGCCAAATCAGTATATAGCGCGGTG
1 CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAGTATATA-CGCGGGG
46182 CAGGGGGCGCGCT
1 CAGGGGGCGCGCT
46195 TTCCTACTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
48 6 0.11
50 49 0.89
ACGTcount: A:0.19, C:0.28, G:0.36, T:0.16
Consensus pattern (49 bp):
CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAGTATATACGCGGGG
Found at i:56680 original size:33 final size:33
Alignment explanation
Indices: 56635--56801 Score: 244
Period size: 33 Copynumber: 5.1 Consensus size: 33
56625 CCTCCTCCTC
* *
56635 GTAGGGACGACTATTCTCCTAGAGGAGCAGGAG
1 GTAGGGAAGACTATTCTCCTAGAGGAGCAAGAG
* *
56668 GTAGGGAAGACTATTCTCCTAGAGGAGCTAGTG
1 GTAGGGAAGACTATTCTCCTAGAGGAGCAAGAG
* *
56701 GTAGGGGAGACTTTTCTCCTAGAGGAGCAAGAG
1 GTAGGGAAGACTATTCTCCTAGAGGAGCAAGAG
* *
56734 GCAGGGAAGATTATTCTCCTAGAGGAGCAAGAG
1 GTAGGGAAGACTATTCTCCTAGAGGAGCAAGAG
* *
56767 GCAGGGAAGATTATTCTCCTAGAGGAGCAAGAG
1 GTAGGGAAGACTATTCTCCTAGAGGAGCAAGAG
56800 GT
1 GT
56802 GGTTCTATGG
Statistics
Matches: 121, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 121 1.00
ACGTcount: A:0.29, C:0.16, G:0.35, T:0.20
Consensus pattern (33 bp):
GTAGGGAAGACTATTCTCCTAGAGGAGCAAGAG
Found at i:57500 original size:7 final size:7
Alignment explanation
Indices: 57488--57513 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
57478 CAGAATATGC
57488 AGCTGGA
1 AGCTGGA
57495 AGCTGGA
1 AGCTGGA
57502 AGCTGGA
1 AGCTGGA
57509 AGCTG
1 AGCTG
57514 TAGTCTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.42, T:0.15
Consensus pattern (7 bp):
AGCTGGA
Found at i:60733 original size:33 final size:33
Alignment explanation
Indices: 60623--60907 Score: 134
Period size: 37 Copynumber: 8.1 Consensus size: 33
60613 TACGTATATA
* * *
60623 ATATATAATTTTTAATA-GTTTTTAAAA-TTAT
1 ATATATAATTTTTAAAACATTTTGAAAACTTAT
* *
60654 ATATATAGTTTTAAAAGAAAACATTTTAGAAATA-TATAT
1 ATATATAATTTT----TAAAACATTTT-GAAA-ACT-TAT
60693 AATATATAATTTTTAAAATCATTTTG-AAACTTAT
1 -ATATATAATTTTTAAAA-CATTTTGAAAACTTAT
*
60727 ATATATATAGTTTTTGAAAACATTTTTGAAAACATAT
1 ATATATA-A-TTTTT-AAAACA-TTTTGAAAACTTAT
* *
60764 AT-TATAGTTTTGAAAACATTTTGAAAACATT-T
1 ATATATAATTTTTAAAACATTTTGAAAAC-TTAT
* * *
60796 ATATTATAGTTTTTAAAACGTTTTGGGAAAATTTAT
1 ATA-TATAATTTTTAAAACATTTT--GAAAACTTAT
* ** * *
60832 ATAATCTTTTTTTTTGAAAACATGTTGAAAAAATTCAT
1 AT-AT-ATAATTTTT-AAAACATTTTG-AAAACTT-AT
* * *
60870 ATATTATATAGTTTAAAAACATTTTG-AAATTTAT
1 ATA-TATA-ATTTTTAAAACATTTTGAAAACTTAT
60904 ATAT
1 ATAT
60908 TATATGTTTT
Statistics
Matches: 198, Mismatches: 27, Indels: 56
0.70 0.10 0.20
Matches are distributed among these distances:
31 11 0.06
32 13 0.07
33 15 0.08
34 32 0.16
35 20 0.10
36 32 0.16
37 43 0.22
38 18 0.09
39 3 0.02
40 11 0.06
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (33 bp):
ATATATAATTTTTAAAACATTTTGAAAACTTAT
Found at i:60741 original size:35 final size:35
Alignment explanation
Indices: 60671--60927 Score: 178
Period size: 34 Copynumber: 7.3 Consensus size: 35
60661 GTTTTAAAAG
*
60671 AAAACATTTT-AGAAA-TATATATAATATATAATTTTT
1 AAAACATTTTGA-AAACT-TATAT-ATATATAGTTTTT
60707 AAAATCATTTTG-AAACTTATATATATATAGTTTTT
1 AAAA-CATTTTGAAAACTTATATATATATAGTTTTT
*
60742 GAAAACATTTTTGAAAAC--ATATAT-TATAGTTTTG
1 -AAAACA-TTTTGAAAACTTATATATATATAGTTTTT
60776 AAAACATTTTGAAAACATT-TATAT-TATAGTTTTT
1 AAAACATTTTGAAAAC-TTATATATATATAGTTTTT
* * * **
60810 AAAACGTTTTGGGAAAATTTATATA-ATCTTTTTTTTT
1 AAAACATTTT--GAAAACTTATATATAT-ATAGTTTTT
* * *
60847 GAAAACATGTTGAAAAAATTCATATATTATATAG-TTTA
1 -AAAACATTTTG-AAAACTT-ATATA-TATATAGTTTTT
* *
60885 AAAACATTTTG-AAATTTATATAT-TATATGTTTTG
1 AAAACATTTTGAAAACTTATATATATATA-GTTTTT
*
60919 AAAATATTT
1 AAAACATTT
60928 ATGTATATAT
Statistics
Matches: 181, Mismatches: 19, Indels: 44
0.74 0.08 0.18
Matches are distributed among these distances:
32 14 0.08
33 8 0.04
34 48 0.27
35 27 0.15
36 32 0.18
37 33 0.18
38 16 0.09
39 1 0.01
40 2 0.01
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.46
Consensus pattern (35 bp):
AAAACATTTTGAAAACTTATATATATATAGTTTTT
Found at i:60754 original size:12 final size:12
Alignment explanation
Indices: 60737--60761 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60727 ATATATATAG
60737 TTTTTGAAAACA
1 TTTTTGAAAACA
60749 TTTTTGAAAACA
1 TTTTTGAAAACA
60761 T
1 T
60762 ATATTATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:60764 original size:71 final size:71
Alignment explanation
Indices: 60618--60819 Score: 199
Period size: 71 Copynumber: 2.9 Consensus size: 71
60608 GAAACTACGT
* * *
60618 ATATAATATATAATTTTT--AAT-AGTTTTTAAA-ATTATATATATAGTTTTAAAAGAAAACATT
1 ATATAATATATAATTTTTAAAATCA-TTTTGAAACTTTATATATATAGTTTT---TGAAAACATT
*
60679 TTAGAAATAT
62 TTAGAAATAC
*
60689 ATATAATATATAATTTTTAAAATCATTTTGAAACTTATATATATATAGTTTTTGAAAACATTTTT
1 ATATAATATATAATTTTTAAAATCATTTTGAAACTT-TATATATATAGTTTTTGAAAACATTTTA
60754 GAAA-AC
65 GAAATAC
* * *
60760 ATAT-AT-TATAGTTTTGAAAA-CATTTTGAAAACATTTATAT-TATAGTTTTT-AAAACGTTTT
1 ATATAATATATAATTTTTAAAATCATTTTG-AAAC-TTTATATATATAGTTTTTGAAAACATTTT
60820 GGGAAAATTT
Statistics
Matches: 116, Mismatches: 8, Indels: 18
0.82 0.06 0.13
Matches are distributed among these distances:
67 9 0.08
68 17 0.15
69 21 0.18
70 4 0.03
71 23 0.20
72 15 0.13
73 10 0.09
74 2 0.02
75 15 0.13
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (71 bp):
ATATAATATATAATTTTTAAAATCATTTTGAAACTTTATATATATAGTTTTTGAAAACATTTTAG
AAATAC
Found at i:60787 original size:11 final size:11
Alignment explanation
Indices: 60771--60795 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
60761 TATATTATAG
60771 TTTTGAAAACA
1 TTTTGAAAACA
60782 TTTTGAAAACA
1 TTTTGAAAACA
60793 TTT
1 TTT
60796 ATATTATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:60900 original size:72 final size:71
Alignment explanation
Indices: 60771--60906 Score: 170
Period size: 72 Copynumber: 1.9 Consensus size: 71
60761 TATATTATAG
* * * *
60771 TTTTGAAAACATTTTGAAAACATTTATATTATAGTTTTTAAAACGTTTTGGGAAAATTTATATAA
1 TTTTGAAAACATGTTGAAAAAATTTATATTATAGTTTTAAAAACATTTT-GGAAAATTTATATAA
60836 TCTTTTT
65 TCTTTTT
60843 TTTTGAAAACATGTTGAAAAAATTCATATATTATA-TAGTTTAAAAACATTTT-G-AAATTTATA
1 TTTTGAAAACATGTTGAAAAAATT--TATATTATAGT--TTTAAAAACATTTTGGAAAATTTATA
60905 TA
62 TA
60907 TTATATGTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
72 33 0.59
73 2 0.04
74 9 0.16
75 12 0.21
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (71 bp):
TTTTGAAAACATGTTGAAAAAATTTATATTATAGTTTTAAAAACATTTTGGAAAATTTATATAAT
CTTTTT
Found at i:60934 original size:23 final size:23
Alignment explanation
Indices: 60891--60935 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
60881 TTTAAAAACA
*
60891 TTTTGAAATTTATATATTATATG
1 TTTTGAAATATATATATTATATG
*
60914 TTTTGAAA-ATATTTATGTATAT
1 TTTTGAAATATATATAT-TATAT
60936 ATATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (23 bp):
TTTTGAAATATATATATTATATG
Found at i:60957 original size:5 final size:5
Alignment explanation
Indices: 60941--60981 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
60931 TATATATATA
60941 TTATT ATTATT TTATT TTATTT TTATT TTA-T TTATT TTATT
1 TTATT -TTATT TTATT TTA-TT TTATT TTATT TTATT TTATT
60982 GTTTTGGTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.12
5 19 0.58
6 10 0.30
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:60960 original size:16 final size:14
Alignment explanation
Indices: 60941--60981 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 14
60931 TATATATATA
60941 TTATTATTATTTTATT
1 TTATT-TTATTTTA-T
60957 TTATTTTTATTTTAT
1 TTA-TTTTATTTTAT
60972 TTATTTTATT
1 TTATTTTATT
60982 GTTTTGGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.29
15 4 0.17
16 11 0.46
17 2 0.08
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTATTTTATTTTAT
Found at i:60964 original size:11 final size:10
Alignment explanation
Indices: 60941--60981 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 10
60931 TATATATATA
60941 TTATTATTATT
1 TTATT-TTATT
60952 TTATTTTATTT
1 TTATTTTA-TT
60963 TTATTTTA-T
1 TTATTTTATT
60972 TTATTTTATT
1 TTATTTTATT
60982 GTTTTGGTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.32
10 4 0.14
11 15 0.54
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
TTATTTTATT
Found at i:62146 original size:24 final size:24
Alignment explanation
Indices: 62101--62146 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
62091 ATTTTATCTT
* *
62101 TATTTTTTTATTTTACTTTTTAAA
1 TATTTTTTTATTTAACTCTTTAAA
62125 TATTTTTTTAATTTAAC-CTTTA
1 TATTTTTTT-ATTTAACTCTTTA
62147 TTATTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTTTTTTATTTAACTCTTTAAA
Found at i:62198 original size:19 final size:19
Alignment explanation
Indices: 62143--62203 Score: 52
Period size: 22 Copynumber: 3.0 Consensus size: 19
62133 TAATTTAACC
62143 TTTATTATTATTTATTATTTCT
1 TTTA-TATT-TTTATTATTT-T
* *
62165 TTCTTTCATTATTATTATTTT
1 TT-TAT-ATTTTTATTATTTT
62186 TTTATATTTTTATT-TTTT
1 TTTATATTTTTATTATTTT
62204 AGCATTTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 4 0.12
19 8 0.24
20 2 0.06
21 3 0.09
22 12 0.36
23 4 0.12
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTATATTTTTATTATTTT
Found at i:67557 original size:164 final size:164
Alignment explanation
Indices: 67315--67958 Score: 927
Period size: 164 Copynumber: 3.9 Consensus size: 164
67305 ACCTGCCACC
67315 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
*
67380 AAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
66 AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
*
67445 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGAA
131 CATAACTCAAGGCAAGAAGGGTTATCTGTTAGAA
* *
67479 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
* *
67544 AAGAGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
66 AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
* *
67609 CATAACTCAAGGCTAGAAGGGTTATCTGTTAGCA
131 CATAACTCAAGGCAAGAAGGGTTATCTGTTAGAA
*
67643 AAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
* * * * *
67708 AAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACGCTCAGCTTCGAGAGCGCAT--CATTTGC
66 AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTC-A-AGGGCATAACATTTAC
* * **
67771 AGCATAACTTAAGTCAAGAAGGGTTATCTGCCA-ATCA
129 AGCATAACTCAAGGCAAGAAGGGTTATCTGTTAGA--A
* * * *
67808 AAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCAAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
* * * * * * *
67873 AAGGGCCATCTGCCAAAGACTCC-CGAGTTCAATTACACTCAACTTCGAGGTCATATCATTTACA
66 AAGGGCTATCTGCCAAAGAC-CCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACA
* * *
67937 ACATAGCTCATGGCAAGAAGGG
130 GCATAACTCAAGGCAAGAAGGG
67959 CTATTTGTCA
Statistics
Matches: 437, Mismatches: 36, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
163 5 0.01
164 299 0.68
165 125 0.29
166 8 0.02
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (164 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAG
AAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAG
CATAACTCAAGGCAAGAAGGGTTATCTGTTAGAA
Found at i:67871 original size:84 final size:81
Alignment explanation
Indices: 67296--67892 Score: 603
Period size: 81 Copynumber: 7.3 Consensus size: 81
67286 GCTCAAGGCC
* *
67296 AGAAGGGCTACCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
1 AGAAGGGCTATCTG-CACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
*
67361 CAGAATAGCTTAAGTCG
65 CAGCATAGCTTAAGTCG
* * * * * *
67378 AGAAGGGCTATCTGC-CAAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATAACATTT
1 AGAAGGGCTATCTGCACAAAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTT
* * * * *
67441 ACAGCATAACTCAAGGCT
64 GCAGCATAGCTTAAGTCG
* * * *
67459 AGAAGGGTTATCTGTTAGAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGCTATCTG-CA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
*
67524 GCAGTATAGCTTAAGTCG
64 GCAGCATAGCTTAAGTCG
* * * * * * *
67542 AGAAGAGCTATCTGC-CAAAGACCCTT-AAGTTCGATTACACTCAGCTTCAAGGGCATAACATTT
1 AGAAGGGCTATCTGCACAAAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTT
* * * * *
67605 ACAGCATAACTCAAGGCT
64 GCAGCATAGCTTAAGTCG
* * *
67623 AGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGCTATCTG-CA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
*
67688 GCAGAATAGCTTAAGTCG
64 GCAGCATAGCTTAAGTCG
** * * * *
67706 AGAAGGGCTATCTGC-CAAAGACCCCCGAGTTCGATTACGCTCAGCTTCGAGAGCGCATCATTTG
1 AGAAGGGCTATCTGCACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAG-GCACATCATTTG
* *
67770 CAGCATAACTTAAGTCA
65 CAGCATAGCTTAAGTCG
* * *
67787 AGAAGGGTTATCTGCCAATCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGCTATCTG-C-A-CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
67852 TGCAGCATAGCTTAAGTCA
63 TGCAGCATAGCTTAAGTCG
*
67871 AGAAGGGCCATCTGC-CAAAGAC
1 AGAAGGGCTATCTGCACAAAGAC
67893 TCCCGAGTTC
Statistics
Matches: 414, Mismatches: 84, Indels: 36
0.78 0.16 0.07
Matches are distributed among these distances:
80 87 0.21
81 116 0.28
82 14 0.03
83 78 0.19
84 89 0.21
85 30 0.07
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (81 bp):
AGAAGGGCTATCTGCACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGC
AGCATAGCTTAAGTCG
Found at i:68645 original size:73 final size:71
Alignment explanation
Indices: 68558--68852 Score: 216
Period size: 72 Copynumber: 4.2 Consensus size: 71
68548 TGAAACTACG
*
68558 TATATAATATATAATTTTT-AAT-AGTTTTTAAAA-TTATATAATATATAGTTTTAAAAGAAAAC
1 TATATAATATATAATTTTTAAATCA-TTTTGAAAACTTATAT-ATATATAGTTTT---AGAAAAC
68620 ATTTTAGAAAA
61 ATTTTAGAAAA
*
68631 TATATAATATATAATTTTTAAAATCATTTTGAAAACTTATATATATATAGTTTTTGAAAACATTT
1 TATATAATATATAATTTTT-AAATCATTTTGAAAACTTATATATATATAGTTTTAGAAAACATTT
*
68696 TTGAAAA
65 TAGAAAA
* * * * * * **
68703 CATAT-AT-TATAGTTTTGAAAACATTTTGAAAAC--ATTTATATATAGTTTT-TAAAATGTTTT
1 TATATAATATATAATTTTTAAATCATTTTGAAAACTTATATATATATAGTTTTAGAAAACATTTT
*
68763 GGGAAAA
66 -AGAAAA
* * * ** * * * *
68770 TTTATAATCTTTTTTTTTTGAAAACATGTTGAAAAATTCATATTTATATAG-TTTA-AAAACATT
1 TATATAATATATAATTTTT-AAATCATTTTGAAAACTT-ATATATATATAGTTTTAGAAAACATT
*
68833 TT-GAAATT
64 TTAGAAA-A
*
68841 TATATATTATAT
1 TATATAATATAT
68853 GTTTTTGAAA
Statistics
Matches: 180, Mismatches: 29, Indels: 28
0.76 0.12 0.12
Matches are distributed among these distances:
66 8 0.04
67 23 0.13
68 2 0.01
69 21 0.12
70 26 0.14
71 10 0.06
72 31 0.17
73 29 0.16
75 23 0.13
76 7 0.04
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (71 bp):
TATATAATATATAATTTTTAAATCATTTTGAAAACTTATATATATATAGTTTTAGAAAACATTTT
AGAAAA
Found at i:68677 original size:36 final size:36
Alignment explanation
Indices: 68544--68757 Score: 173
Period size: 34 Copynumber: 6.0 Consensus size: 36
68534 ATATATACAT
*
68544 ATTTTGAAACTACGTATATAATATATAATTTTT--AAT-
1 ATTTTGAAA--AC-TATATAATATATAGTTTTTAAAATC
* * * *
68580 AGTTTTTAAAATTATATAATATATAGTTTTAAAAGAAAAC
1 A-TTTTGAAAACTATATAATATATAGTTTT--TA-AAATC
*
68620 ATTTTAGAAAA-TATATAATATATAATTTTTAAAATC
1 ATTTT-GAAAACTATATAATATATAGTTTTTAAAATC
68656 ATTTTGAAAACT-TATATATATATAGTTTTTGAAAA-C
1 ATTTTGAAAACTATATA-ATATATAGTTTTT-AAAATC
*
68692 ATTTTTGAAAAC-ATAT-AT-TATAGTTTTGAAAA-C
1 A-TTTTGAAAACTATATAATATATAGTTTTTAAAATC
*
68725 ATTTTGAAAAC-AT-TTATATATAGTTTTTAAAAT
1 ATTTTGAAAACTATATAATATATAGTTTTTAAAAT
68758 GTTTTGGGAA
Statistics
Matches: 150, Mismatches: 12, Indels: 34
0.77 0.06 0.17
Matches are distributed among these distances:
31 1 0.01
32 14 0.09
33 19 0.13
34 26 0.17
35 12 0.08
36 25 0.17
37 25 0.17
39 23 0.15
40 5 0.03
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (36 bp):
ATTTTGAAAACTATATAATATATAGTTTTTAAAATC
Found at i:68698 original size:12 final size:12
Alignment explanation
Indices: 68681--68705 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
68671 ATATATATAG
68681 TTTTTGAAAACA
1 TTTTTGAAAACA
68693 TTTTTGAAAACA
1 TTTTTGAAAACA
68705 T
1 T
68706 ATATTATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:68719 original size:33 final size:33
Alignment explanation
Indices: 68614--68756 Score: 171
Period size: 33 Copynumber: 4.2 Consensus size: 33
68604 AGTTTTAAAA
* *
68614 GAAAACATTTTAGAAAATATATAATATATAATTTT
1 GAAAACATTTT-GAAAACATAT-ATATATAGTTTT
*
68649 TAAAATCATTTTGAAAACTTATATATATATAGTTTTT
1 GAAAA-CATTTTGAAAAC--ATATATATATAG-TTTT
68686 GAAAACATTTTTGAAAACATATAT-TATAGTTTT
1 GAAAACA-TTTTGAAAACATATATATATAGTTTT
*
68719 GAAAACATTTTGAAAACATTTATATATAGTTTT
1 GAAAACATTTTGAAAACATATATATATAGTTTT
*
68752 TAAAA
1 GAAAA
68757 TGTTTTGGGA
Statistics
Matches: 96, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
32 15 0.16
33 24 0.25
34 5 0.05
35 15 0.16
36 15 0.16
37 22 0.23
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (33 bp):
GAAAACATTTTGAAAACATATATATATAGTTTT
Found at i:68731 original size:11 final size:11
Alignment explanation
Indices: 68715--68739 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
68705 TATATTATAG
68715 TTTTGAAAACA
1 TTTTGAAAACA
68726 TTTTGAAAACA
1 TTTTGAAAACA
68737 TTT
1 TTT
68740 ATATATAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:68773 original size:33 final size:32
Alignment explanation
Indices: 68615--68775 Score: 126
Period size: 33 Copynumber: 4.7 Consensus size: 32
68605 GTTTTAAAAG
* *
68615 AAAACATTTTAGAAAATATATAATATATAATTTTT
1 AAAACATTTTGGAAAAT-T-T-ATATATAGTTTTT
68650 AAAATCATTTT-GAAAACTTATATATATATAGTTTTT
1 AAAA-CATTTTGGAAAA--T-T-TATATATAGTTTTT
* ** *
68686 GAAAACATTTTTGAAAACATATATTATAGTTTTG
1 -AAAACATTTTGGAAAATTTATA-TATAGTTTTT
*
68720 AAAACATTTTGAAAACATTTATATATAGTTTTT
1 AAAACATTTTGGAAA-ATTTATATATAGTTTTT
**
68753 AAAATGTTTTGGGAAAATTTATA
1 AAAACATTTT-GGAAAATTTATA
68776 ATCTTTTTTT
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
33 41 0.39
34 18 0.17
35 9 0.08
36 24 0.23
37 14 0.13
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.43
Consensus pattern (32 bp):
AAAACATTTTGGAAAATTTATATATAGTTTTT
Found at i:68875 original size:24 final size:24
Alignment explanation
Indices: 68831--68876 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
68821 TTTAAAAACA
*
68831 TTTTGAAATTTATATATTATATGT
1 TTTTGAAATATATATATTATATGT
*
68855 TTTTGAAA-ATATTTATGTATAT
1 TTTTGAAATATATATAT-TATAT
68877 ATATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTTGAAATATATATATTATATGT
Found at i:68898 original size:11 final size:11
Alignment explanation
Indices: 68885--68926 Score: 75
Period size: 11 Copynumber: 3.7 Consensus size: 11
68875 ATATATATTA
68885 TTTATTATTTAT
1 TTTATT-TTTAT
68897 TTTATTTTTAT
1 TTTATTTTTAT
68908 TTTATTTTTAT
1 TTTATTTTTAT
68919 TTTATTTT
1 TTTATTTT
68927 ATTGTTTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 24 0.80
12 6 0.20
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:68901 original size:16 final size:17
Alignment explanation
Indices: 68882--68929 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
68872 TATATATATA
68882 TTATTTATTA-TTTA-TT
1 TTATTT-TTATTTTATTT
68898 TTATTTTTATTTTATTT
1 TTATTTTTATTTTATTT
68915 TTA-TTTTATTTTATT
1 TTATTTTTATTTTATT
68930 GTTTTGGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.10
16 22 0.73
17 5 0.17
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTATTTTTATTTTATTT
Found at i:68902 original size:5 final size:5
Alignment explanation
Indices: 68892--68929 Score: 58
Period size: 5 Copynumber: 7.2 Consensus size: 5
68882 TTATTTATTA
68892 TTTAT TTTATT TTTAT TTTATT TTTAT TTTAT TTTAT T
1 TTTAT TTTA-T TTTAT TTTA-T TTTAT TTTAT TTTAT T
68930 GTTTTGGTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 21 0.68
6 10 0.32
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:70075 original size:23 final size:23
Alignment explanation
Indices: 70048--70106 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
70038 ATTTTATCTT
* *
70048 TATTTTTTTATTTTACTTTTTAA
1 TATTTTTTTATTTAACCTTTTAA
*
70071 TATTTTTTTAATTTAACCTTTTAT
1 TATTTTTTT-ATTTAACCTTTTAA
*
70095 TATTATTTTATT
1 TATTTTTTTATT
70107 ATTTCTTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 12 0.39
24 19 0.61
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (23 bp):
TATTTTTTTATTTAACCTTTTAA
Done.