Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011718.1 Kokia drynarioides strain JFW-HI SEQ_126712, 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: 85946
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 7 characters in sequence are not A, C, G, or T
Found at i:404 original size:13 final size:12
Alignment explanation
Indices: 376--410 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
366 GTGTTATAAA
376 AACTAAGAAATT
1 AACTAAGAAATT
*
388 AACTAAGTAACTT
1 AACTAAG-AAATT
401 AACTAAGAAA
1 AACTAAGAAA
411 AATAAAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.57, C:0.11, G:0.09, T:0.23
Consensus pattern (12 bp):
AACTAAGAAATT
Found at i:1760 original size:22 final size:22
Alignment explanation
Indices: 1734--1778 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1724 TTTTTTAATT
*
1734 TTTAATTA-ATAATTAATAAATA
1 TTTAATTATATAA-TAAAAAATA
1756 TTTAATTATATAATAAAAAATA
1 TTTAATTATATAATAAAAAATA
1778 T
1 T
1779 ATTTTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTAATTATATAATAAAAAATA
Found at i:1863 original size:28 final size:29
Alignment explanation
Indices: 1813--1874 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
1803 AAATATTTTT
* * *
1813 AATTAATAACTTATTTATTTATATATAT-A
1 AATTAATAACATATGTAATTATATA-ATGA
1842 AATTAATAA-ATATGTAATTATATAATGA
1 AATTAATAACATATGTAATTATATAATGA
1870 AATTA
1 AATTA
1875 TATATTTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 2 0.07
28 18 0.62
29 9 0.31
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (29 bp):
AATTAATAACATATGTAATTATATAATGA
Found at i:1929 original size:29 final size:31
Alignment explanation
Indices: 1897--1965 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 31
1887 TTTATCATTG
1897 TGTTAAATATATTTTACTC-TTAT-T-TAATT
1 TGTTAAATATATTTT-CTCTTTATATGTAATT
** *
1926 TGTTTGATATATTTTTTCTTTATATGTAATT
1 TGTTAAATATATTTTCTCTTTATATGTAATT
1957 T-TTAAATAT
1 TGTTAAATAT
1966 TAAATATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.06
29 17 0.53
30 7 0.22
31 6 0.19
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.61
Consensus pattern (31 bp):
TGTTAAATATATTTTCTCTTTATATGTAATT
Found at i:10395 original size:83 final size:83
Alignment explanation
Indices: 10256--10444 Score: 351
Period size: 83 Copynumber: 2.3 Consensus size: 83
10246 TTACCTATGC
*
10256 CTCAAATAAGTCGACTTCGACTCCTTAACAGATGAGGAAATTGTTGCTTTACCAATCACGTTAAA
1 CTCAAATAAGTCGACTTCAACTCCTTAACAGATGAGGAAATTGTTGCTTTACCAATCACGTTAAA
10321 CCTTGTAGAACATAAAGA
66 CCTTGTAGAACATAAAGA
*
10339 CTCAAATAAGTCGACTTCAACTCCTTAACAGATGAGGAAATTGTTGCTTTACCAATCACGTTGAA
1 CTCAAATAAGTCGACTTCAACTCCTTAACAGATGAGGAAATTGTTGCTTTACCAATCACGTTAAA
10404 CCTTGTAGAACATAAAGA
66 CCTTGTAGAACATAAAGA
*
10422 CTCAAATAAGTCGATTTCAACTC
1 CTCAAATAAGTCGACTTCAACTC
10445 ATAAAGACTC
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 103 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (83 bp):
CTCAAATAAGTCGACTTCAACTCCTTAACAGATGAGGAAATTGTTGCTTTACCAATCACGTTAAA
CCTTGTAGAACATAAAGA
Found at i:10450 original size:30 final size:30
Alignment explanation
Indices: 10414--10474 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
10404 CCTTGTAGAA
10414 CATAAAGACTCAAATAAGTCGATTTCAACT
1 CATAAAGACTCAAATAAGTCGATTTCAACT
10444 CATAAAGACTCAAATAAGTCGATTTCAACT
1 CATAAAGACTCAAATAAGTCGATTTCAACT
10474 C
1 C
10475 CTTAATAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (30 bp):
CATAAAGACTCAAATAAGTCGATTTCAACT
Found at i:10529 original size:113 final size:113
Alignment explanation
Indices: 10331--10534 Score: 381
Period size: 113 Copynumber: 1.8 Consensus size: 113
10321 CCTTGTAGAA
*
10331 CATAAAGACTCAAATAAGTCGACTTCAACTCCTTAACAGATGAGGAAATTGTTGCTTTACCAATC
1 CATAAAGACTCAAATAAGTCGACTTCAACTCCTTAACAGATGAGAAAATTGTTGCTTTACCAATC
10396 ACGTTGAACCTTGTAGAACATAAAGACTCAAATAAGTCGATTTCAACT
66 ACGTTGAACCTTGTAGAACATAAAGACTCAAATAAGTCGATTTCAACT
* *
10444 CATAAAGACTCAAATAAGTCGATTTCAACTCCTTAATAGATGAGAAAATTGTTGCTTTACCAATC
1 CATAAAGACTCAAATAAGTCGACTTCAACTCCTTAACAGATGAGAAAATTGTTGCTTTACCAATC
10509 ACGTTGAACCTTGTAGAACATAAAGA
66 ACGTTGAACCTTGTAGAACATAAAGA
10535 TGTCGGTATT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 88 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (113 bp):
CATAAAGACTCAAATAAGTCGACTTCAACTCCTTAACAGATGAGAAAATTGTTGCTTTACCAATC
ACGTTGAACCTTGTAGAACATAAAGACTCAAATAAGTCGATTTCAACT
Found at i:28937 original size:2 final size:2
Alignment explanation
Indices: 28930--28961 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28920 TAGTCTATTC
28930 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
28962 TCCTAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:29598 original size:3 final size:3
Alignment explanation
Indices: 29592--29616 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29582 TTGAAGAAGA
29592 AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG A
29617 AGCCCTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:30946 original size:16 final size:16
Alignment explanation
Indices: 30925--30956 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30915 AATTATGTAA
*
30925 ATATTATTAAAACTAT
1 ATATTAGTAAAACTAT
30941 ATATTAGTAAAACTAT
1 ATATTAGTAAAACTAT
30957 CAAATATCAA
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:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (16 bp):
ATATTAGTAAAACTAT
Found at i:32970 original size:22 final size:22
Alignment explanation
Indices: 32936--32979 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
32926 TAAACGGAAC
32936 TAACAGAAAGTACCA-AAGTACT
1 TAACAGAAAGTA-CATAAGTACT
**
32958 TAACAGAGGGTACATAAGTACT
1 TAACAGAAAGTACATAAGTACT
32980 GGGTAACAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.20
Consensus pattern (22 bp):
TAACAGAAAGTACATAAGTACT
Found at i:33043 original size:25 final size:25
Alignment explanation
Indices: 32983--33066 Score: 115
Period size: 23 Copynumber: 3.5 Consensus size: 25
32973 AAGTACTGGG
32983 TAACAGAGGGCACACGAAGTGCTAA
1 TAACAGAGGGCACACGAAGTGCTAA
33008 T--CAGAGGGCACACGAAGTGCTAA
1 TAACAGAGGGCACACGAAGTGCTAA
33031 TAACAGAGGGCACAC-ACAGTGCT--
1 TAACAGAGGGCACACGA-AGTGCTAA
*
33054 GAACAGAGGGCAC
1 TAACAGAGGGCAC
33067 GAAACATGCT
Statistics
Matches: 55, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
23 35 0.64
24 1 0.02
25 19 0.35
ACGTcount: A:0.37, C:0.23, G:0.30, T:0.11
Consensus pattern (25 bp):
TAACAGAGGGCACACGAAGTGCTAA
Found at i:33076 original size:23 final size:23
Alignment explanation
Indices: 32984--33087 Score: 97
Period size: 23 Copynumber: 4.4 Consensus size: 23
32974 AGTACTGGGT
*
32984 AACAGAGGGCACACGA-AGTGCTA
1 AACAGAGGGCACA-AACAGTGCTA
* *
33007 ATCAGAGGGCACACGA-AGTGCTAA
1 AACAGAGGGCACA-AACAGTGCT-A
* *
33031 TAACAGAGGGCACACACAGTGCTG
1 -AACAGAGGGCACAAACAGTGCTA
33055 AACAGAGGGCACGAAACA-TGCTA
1 AACAGAGGGCAC-AAACAGTGCTA
33078 AACAGAGGGC
1 AACAGAGGGC
33088 GCGCTAGTGT
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
23 47 0.66
24 6 0.08
25 18 0.25
ACGTcount: A:0.38, C:0.22, G:0.30, T:0.10
Consensus pattern (23 bp):
AACAGAGGGCACAAACAGTGCTA
Found at i:33077 original size:48 final size:46
Alignment explanation
Indices: 32983--33087 Score: 119
Period size: 48 Copynumber: 2.2 Consensus size: 46
32973 AAGTACTGGG
*
32983 TAACAGAGGGCACACGAAGTGCTAATCAGAGGGCACACGAAGTGCTAA
1 TAACAGAGGGCACACGAAGTGCTAATCAGAGGGCACAC-AAATGCT-A
33031 TAACAGAGGGCACAC-ACAGTGCTGAA-CAGAGGGCACGA-AACATGCTA
1 TAACAGAGGGCACACGA-AGTGCT-AATCAGAGGGCAC-ACAA-ATGCTA
33078 -AACAGAGGGC
1 TAACAGAGGGC
33088 GCGCTAGTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
46 10 0.19
47 4 0.08
48 35 0.67
49 3 0.06
ACGTcount: A:0.38, C:0.22, G:0.30, T:0.10
Consensus pattern (46 bp):
TAACAGAGGGCACACGAAGTGCTAATCAGAGGGCACACAAATGCTA
Found at i:35122 original size:20 final size:22
Alignment explanation
Indices: 35099--35140 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
35089 AATAATTTTT
35099 AATAA-TTTAAT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
35119 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
35141 TAATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
21 6 0.30
22 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:35124 original size:15 final size:15
Alignment explanation
Indices: 35086--35132 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
35076 ATTATAATTT
35086 TAAAATAATTTTTAA
1 TAAAATAATTTTTAA
**
35101 TAATTTAATATTTTAA
1 TAAAATAAT-TTTTAA
35117 -AAAATAA-TTTTAA
1 TAAAATAATTTTTAA
35130 TAA
1 TAA
35133 TTTTAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
13 6 0.23
14 2 0.08
15 12 0.46
16 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAAATAATTTTTAA
Found at i:35141 original size:20 final size:20
Alignment explanation
Indices: 35079--35146 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
35069 GATGATGATT
*
35079 ATAATTTTAAAATAATTTT-TA
1 ATAATTTT--AATAATTTTAAA
35100 ATAA-TTTAAT-ATTTTAAAAA
1 ATAATTTTAATAATTTT--AAA
35120 ATAATTTTAATAATTTTAAA
1 ATAATTTTAATAATTTTAAA
35140 ATAATTT
1 ATAATTT
35147 GCTGACGTGG
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
17 5 0.12
18 3 0.07
20 18 0.44
21 10 0.24
22 5 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAATTTTAATAATTTTAAA
Found at i:37001 original size:29 final size:29
Alignment explanation
Indices: 36968--37056 Score: 97
Period size: 31 Copynumber: 3.0 Consensus size: 29
36958 TTGATTTAAT
36968 GTGCAATTGTATACGTGAACTTTAATTTG
1 GTGCAATTGTATACGTGAACTTTAATTTG
* *
36997 GTGCAATTATATACGTGAGACTCTAATTATG
1 GTGCAATTGTATACGTGA-ACTTTAATT-TG
* * * *
37028 GTTCAAATGTATACTTCAAACTTTAATTT
1 GTGCAATTGTATACGT-GAACTTTAATTT
37057 TGTGTTGATA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
29 17 0.35
30 9 0.18
31 22 0.45
32 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.40
Consensus pattern (29 bp):
GTGCAATTGTATACGTGAACTTTAATTTG
Found at i:37143 original size:29 final size:30
Alignment explanation
Indices: 37085--37143 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
37075 GAATTGGATC
* * *
37085 AAATCAAAATTTCATGTATAGAGTTACACA
1 AAATCAAAAGTTCATGTATACAATTACACA
*
37115 AAATC-AAAGTTCATGTATACAATTGCACA
1 AAATCAAAAGTTCATGTATACAATTACACA
37144 TTAAACCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATACAATTACACA
Found at i:52255 original size:24 final size:24
Alignment explanation
Indices: 52220--52355 Score: 173
Period size: 24 Copynumber: 5.7 Consensus size: 24
52210 TATGAAATAA
*
52220 CGTAAACATATATAAGCTGACGAG
1 CGTAAACGTATATAAGCTGACGAG
*
52244 CATAAACGTATATAAGCTGACGAG
1 CGTAAACGTATATAAGCTGACGAG
* ** *
52268 CGTAAACGTGTGCAAGCTGACAAG
1 CGTAAACGTATATAAGCTGACGAG
*
52292 CGTAAACGTATATAAACTGACGAG
1 CGTAAACGTATATAAGCTGACGAG
* **
52316 CGTAAACGTGTGCAAGCTGACGAG
1 CGTAAACGTATATAAGCTGACGAG
*
52340 CGTAAACGTTTATAAG
1 CGTAAACGTATATAAG
52356 TTGTTGTGTA
Statistics
Matches: 93, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 93 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.21
Consensus pattern (24 bp):
CGTAAACGTATATAAGCTGACGAG
Found at i:52298 original size:48 final size:48
Alignment explanation
Indices: 52233--52355 Score: 210
Period size: 48 Copynumber: 2.6 Consensus size: 48
52223 AAACATATAT
*
52233 AAGCTGACGAGCATAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* *
52281 AAGCTGACAAGCGTAAACGTATATAAACTGACGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
*
52329 AAGCTGACGAGCGTAAACGTTTATAAG
1 AAGCTGACGAGCGTAAACGTATATAAG
52356 TTGTTGTGTA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.20
Consensus pattern (48 bp):
AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
Found at i:54818 original size:8 final size:9
Alignment explanation
Indices: 54800--54860 Score: 52
Period size: 10 Copynumber: 6.4 Consensus size: 9
54790 ATTATTTTAG
54800 AAAATTTTT
1 AAAATTTTT
54809 AAAA-TTTT
1 AAAATTTTT
**
54817 AACTTTCTTT
1 AAAATT-TTT
*
54827 ATATATATTTT
1 A-AAAT-TTTT
54838 AAAATTTTT
1 AAAATTTTT
54847 ATAAATTTTT
1 A-AAATTTTT
54857 AAAA
1 AAAA
54861 ATATAAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
8 6 0.14
9 13 0.31
10 16 0.38
11 6 0.14
12 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (9 bp):
AAAATTTTT
Found at i:54849 original size:20 final size:19
Alignment explanation
Indices: 54800--54886 Score: 69
Period size: 18 Copynumber: 4.8 Consensus size: 19
54790 ATTATTTTAG
54800 AAAATTTTTA-AAA-TTTT
1 AAAATTTTTATAAATTTTT
** *
54817 AACTTTCTTTATATATATTTT
1 AAAATT-TTTATAAAT-TTTT
54838 AAAATTTTTATAAATTTTT
1 AAAATTTTTATAAATTTTT
*
54857 AAAA---ATATAAA-TTTT
1 AAAATTTTTATAAATTTTT
*
54872 GAAATTTTTATAAAT
1 AAAATTTTTATAAAT
54887 ATTCTGAATT
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
15 7 0.13
16 6 0.11
17 4 0.08
18 10 0.19
19 10 0.19
20 8 0.15
21 8 0.15
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (19 bp):
AAAATTTTTATAAATTTTT
Found at i:54899 original size:20 final size:18
Alignment explanation
Indices: 54801--54899 Score: 64
Period size: 18 Copynumber: 5.4 Consensus size: 18
54791 TTATTTTAGA
54801 AAATTTTTA-AAATTTT-
1 AAATTTTTATAAATTTTG
* *
54817 AACTTTCTTTATATATATTTTA
1 AA-ATT-TTTATA-A-ATTTTG
*
54839 AAATTTTTATAAATTTTT
1 AAATTTTTATAAATTTTG
**
54857 AAA--AATATAAATTTTG
1 AAATTTTTATAAATTTTG
54873 AAATTTTTATAAATATTCTG
1 AAATTTTTATAAAT-TT-TG
54893 -AATTTTT
1 AAATTTTT
54900 GAAAATTATT
Statistics
Matches: 65, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
16 15 0.23
17 2 0.03
18 19 0.29
19 11 0.17
20 9 0.14
21 7 0.11
22 2 0.03
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (18 bp):
AAATTTTTATAAATTTTG
Found at i:55493 original size:22 final size:21
Alignment explanation
Indices: 55468--55511 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
55458 TAATTTTAAA
*
55468 ATTTATATTTACATATAAATAT
1 ATTTATATGTACATAT-AATAT
*
55490 ATTTATATGTATATATAATAT
1 ATTTATATGTACATATAATAT
55511 A
1 A
55512 GAATTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTTATATGTACATATAATAT
Found at i:55520 original size:28 final size:26
Alignment explanation
Indices: 55470--55546 Score: 66
Period size: 28 Copynumber: 2.8 Consensus size: 26
55460 ATTTTAAAAT
* *
55470 TTATATTTACATATAAATATATTTATA
1 TTATATATA-ATATAAATTTATTTATA
*
55497 TGTATATATAATATAGAATTTATTTTTA
1 T-TATATATAATATA-AATTTATTTATA
* *
55525 TCA-AAATAATATATAATTTATT
1 TTATATATAATATA-AATTTATT
55547 AAGAAATTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
26 17 0.40
27 7 0.17
28 18 0.43
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (26 bp):
TTATATATAATATAAATTTATTTATA
Found at i:61994 original size:22 final size:22
Alignment explanation
Indices: 61969--62013 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
61959 GTAATAGCGT
**
61969 GCAACAGTAACAGCGGTGTGCG
1 GCAACAGTAACAGCAATGTGCG
*
61991 GCAACGGTAACAGCAATGTGCG
1 GCAACAGTAACAGCAATGTGCG
62013 G
1 G
62014 TAGCAACGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.22, G:0.36, T:0.13
Consensus pattern (22 bp):
GCAACAGTAACAGCAATGTGCG
Found at i:65827 original size:30 final size:30
Alignment explanation
Indices: 65793--65855 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
65783 ATAATTTTTT
65793 AAGAAAGATTCAAATTTATTGATTCACATG
1 AAGAAAGATTCAAATTTATTGATTCACATG
65823 AAGAAAGATTCAAATTTATTGATTCACATG
1 AAGAAAGATTCAAATTTATTGATTCACATG
65853 AAG
1 AAG
65856 CCCCTAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (30 bp):
AAGAAAGATTCAAATTTATTGATTCACATG
Found at i:66006 original size:64 final size:64
Alignment explanation
Indices: 65908--66027 Score: 231
Period size: 64 Copynumber: 1.9 Consensus size: 64
65898 ACATTAAAAA
*
65908 AAAAAAAATCTTAAAAGAGTATTACACTTTTGATTGAGTTAGAAAAATCAATAAATTCAGAATT
1 AAAAAAAATCTTAAAAGAGTATTACACTTTTGATTGAGTAAGAAAAATCAATAAATTCAGAATT
65972 AAAAAAAATCTTAAAAGAGTATTACACTTTTGATTGAGTAAGAAAAATCAATAAAT
1 AAAAAAAATCTTAAAAGAGTATTACACTTTTGATTGAGTAAGAAAAATCAATAAAT
66028 CAAAACCAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (64 bp):
AAAAAAAATCTTAAAAGAGTATTACACTTTTGATTGAGTAAGAAAAATCAATAAATTCAGAATT
Found at i:72534 original size:29 final size:30
Alignment explanation
Indices: 72502--72741 Score: 173
Period size: 30 Copynumber: 8.1 Consensus size: 30
72492 TTTTGAACAC
*
72502 TTCGAGGTAAAAAATGGAATCTTTGG-AAG
1 TTCGAGGTAAAAAATGGAATTTTTGGAAAG
*
72531 TTCGGGGGT--AAAATGGTAATTTTT-GAGAAG
1 TTC-GAGGTAAAAAATGG-AATTTTTGGA-AAG
* *
72561 TTCGAGGTCAAAAATGGAATTTTTGG-ATG
1 TTCGAGGTAAAAAATGGAATTTTTGGAAAG
*
72590 TTCGAGGGT--AAAAT-GATAGTTTTTGGAAAA
1 TTCGA-GGTAAAAAATGGA-A-TTTTTGGAAAG
* * * *
72620 TTCGGGGTCAAAATTGGAA-TTATGGAAAG
1 TTCGAGGTAAAAAATGGAATTTTTGGAAAG
* *
72649 TTTCGGAGGTAAAAAATGTAATTTTTGGAAAA
1 -TTC-GAGGTAAAAAATGGAATTTTTGGAAAG
* * *
72681 TTCAAGGTTAAAAATAGAA--TTTGGAAAG
1 TTCGAGGTAAAAAATGGAATTTTTGGAAAG
72709 TTCGAGGGTAAAAATAT--AATTTTTGGAAAG
1 TTCGA-GGTAAAAA-ATGGAATTTTTGGAAAG
72739 TTC
1 TTC
72742 AAGGACCTTC
Statistics
Matches: 167, Mismatches: 23, Indels: 41
0.72 0.10 0.18
Matches are distributed among these distances:
27 2 0.01
28 28 0.17
29 45 0.27
30 54 0.32
31 28 0.17
32 10 0.06
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (30 bp):
TTCGAGGTAAAAAATGGAATTTTTGGAAAG
Found at i:72555 original size:59 final size:59
Alignment explanation
Indices: 72502--72737 Score: 234
Period size: 59 Copynumber: 4.0 Consensus size: 59
72492 TTTTGAACAC
* * *
72502 TTCGAGGTAAAAAATGGAATCTTTGG-AAGTTCGGGGGTAAAATGGTAATTTTT-GAGAAG
1 TTCGAGGTCAAAAATGGAAT-TTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGA-AAA
* * *
72561 TTCGAGGTCAAAAATGGAATTTTTGG-ATGTTCGAGGGTAAAATGATAGTTTTTGGAAAA
1 TTCGAGGTCAAAAATGGAA-TTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAA
* * *
72620 TTCGGGGTCAAAATTGGAATTATGGAAAGTTTCG-GAGGTAAAAAAT-GTAATTTTTGGAAAA
1 TTCGAGGTCAAAAATGGAATTTTGGAAAG-TTCGAG-GGT--AAAATGGTAATTTTTGGAAAA
* * * *
72681 TTCAAGGTTAAAAATAGAA-TTTGGAAAGTTCGAGGGTAAAAAT-ATAATTTTTGGAAA
1 TTCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT-AAAATGGTAATTTTTGGAAA
72738 GTTCAAGGAC
Statistics
Matches: 150, Mismatches: 19, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
58 24 0.16
59 75 0.50
60 19 0.13
61 27 0.18
62 5 0.03
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (59 bp):
TTCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAA
Found at i:73862 original size:3 final size:3
Alignment explanation
Indices: 73856--73887 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
73846 AAAAAAAAAG
73856 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
73888 AAATTAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:74685 original size:6 final size:6
Alignment explanation
Indices: 74674--74734 Score: 56
Period size: 6 Copynumber: 10.0 Consensus size: 6
74664 TATTTCAAAT
*
74674 TTTAAA TTTAAA -ATAAA TTTAAA CTTAATAAA TTTAAA TTTATAA --TAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA -TT--TAAA TTTAAA TTTA-AA TTTAAA
74723 TTTAAA TTTAAA
1 TTTAAA TTTAAA
74735 ATAATTCTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
4 2 0.04
5 6 0.13
6 28 0.61
7 4 0.09
8 2 0.04
9 4 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:74696 original size:17 final size:17
Alignment explanation
Indices: 74674--74762 Score: 112
Period size: 17 Copynumber: 5.4 Consensus size: 17
74664 TATTTCAAAT
74674 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
74691 TTTAAACTT--AATAAA
1 TTTAAATTTAAAATAAA
*
74706 TTTAAATTTATAATAAA
1 TTTAAATTTAAAATAAA
74723 TTTAAATTTAAAAT-AA
1 TTTAAATTTAAAATAAA
* *
74739 TTCTAAACTTAGAATAAA
1 TT-TAAATTTAAAATAAA
74757 TTTAAA
1 TTTAAA
74763 ATAAAGATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
15 14 0.22
16 4 0.06
17 41 0.65
18 4 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:75315 original size:49 final size:49
Alignment explanation
Indices: 75262--75695 Score: 276
Period size: 49 Copynumber: 8.9 Consensus size: 49
75252 AGGTTTGCCA
* * *
75262 TTGCGACTCAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCTG
1 TTGCGACTTAAACCTTTCCCTTTATGTCTTCGTGGTACTGGATTCGCCG
* * * * * *
75311 TTGCGGCTTAAATCTTTCCCTTCATG-CTTCTGAGGTACAAGG-TTCGCCA
1 TTGCGACTTAAACCTTTCCCTTTATGTCTTC-GTGGTAC-TGGATTCGCCG
* * * * * *
75360 TTGTGACTTAAACCCTTCCCTTTATATCTTCTTGTTACTGGATTCGCTG
1 TTGCGACTTAAACCTTTCCCTTTATGTCTTCGTGGTACTGGATTCGCCG
* * * * * * *
75409 TTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTA-TAAGG-TTCACCA
1 TTGCGACTTAAACCTTTCCCTTTATGTCTTCGTGGTACT--GGATTCGCCG
* * *
75458 TTGCGACTTAAACCTTTCCCTTTGTATCTTCATGGTACTGGATTCGCCG
1 TTGCGACTTAAACCTTTCCCTTTATGTCTTCGTGGTACTGGATTCGCCG
* * * * * * * *
75507 TTACGGCTCAAATCTTTCCCTTCATG-CTTCTGAGGTACAAGG-TTCGCTG
1 TTGCGACTTAAACCTTTCCCTTTATGTCTTC-GTGGTAC-TGGATTCGCCG
** * * ** * * *
75556 TTGTAACTTAAATGC-TTCTCTCCATATCTTCGTCGTACTAGATTCGCCG
1 TTGCGACTTAAA-CCTTTCCCTTTATGTCTTCGTGGTACTGGATTCGCCG
* * * * *
75605 TTGCGGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTA-TAAGG-TTCGCCA
1 TTGCGACTTAAACCTTTCCCTTTATGTCTTC-GTGGTACT--GGATTCGCCG
*
75654 TTGCGACTTAAACCTTTCCCTTTATATCTTCGTGGTACTGGA
1 TTGCGACTTAAACCTTTCCCTTTATGTCTTCGTGGTACTGGA
75696 ACCTGTAGAA
Statistics
Matches: 280, Mismatches: 85, Indels: 40
0.69 0.21 0.10
Matches are distributed among these distances:
48 20 0.07
49 240 0.86
50 20 0.07
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.38
Consensus pattern (49 bp):
TTGCGACTTAAACCTTTCCCTTTATGTCTTCGTGGTACTGGATTCGCCG
Found at i:75373 original size:98 final size:98
Alignment explanation
Indices: 75196--75695 Score: 657
Period size: 98 Copynumber: 5.1 Consensus size: 98
75186 TCAATTTGCA
** * * *
75196 TGGTACTAAATTCGTCGTTGCGGCTTAAAAT-TTTCCTTTCATGCTTCTGAGGTATAAGGTTTGC
1 TGGTACTGGATTCGCCGTTGCGGCTT-AAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTCGC
* * *
75260 CATTGCGACTCAAACCTTTCCCTTTGTGTCTTCG
65 CATTGCGACTTAAACCTTTCCCTTTATATCTTCG
* *
75294 TGGTACTGGATTCGCTGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTCGCC
* * *
75359 ATTGTGACTTAAACCCTTCCCTTTATATCTTCT
66 ATTGCGACTTAAACCTTTCCCTTTATATCTTCG
* * *
75392 TGTTACTGGATTCGCTGTTGCGGCTTAAATCTTTCCCTTCATGTCTT-TGAGGTATAAGGTTCAC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-CTTCTGAGGTATAAGGTTCGC
* *
75456 CATTGCGACTTAAACCTTTCCCTTTGTATCTTCA
65 CATTGCGACTTAAACCTTTCCCTTTATATCTTCG
* * * *
75490 TGGTACTGGATTCGCCGTTACGGCTCAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCT
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTCGCC
* ** * * **
75555 GTTGTAACTTAAATGC-TTCTCTCCATATCTTCG
66 ATTGCGACTTAAA-CCTTTCCCTTTATATCTTCG
* *
75588 TCGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG-TCTCTGAGGTATAAGGTTCGC
1 TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCT-TCTGAGGTATAAGGTTCGC
75652 CATTGCGACTTAAACCTTTCCCTTTATATCTTCG
65 CATTGCGACTTAAACCTTTCCCTTTATATCTTCG
75686 TGGTACTGGA
1 TGGTACTGGA
75696 ACCTGTAGAA
Statistics
Matches: 345, Mismatches: 51, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
97 9 0.03
98 332 0.96
99 4 0.01
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (98 bp):
TGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTCGCC
ATTGCGACTTAAACCTTTCCCTTTATATCTTCG
Found at i:75546 original size:196 final size:196
Alignment explanation
Indices: 75198--75695 Score: 732
Period size: 196 Copynumber: 2.5 Consensus size: 196
75188 AATTTGCATG
* * * *
75198 GTACTAAATTCGTCGTTGCGGCTTAAAAT-TTTCCTTTCATG-CTTCTGAGGTATAAGGTTTGCC
1 GTACTAGATTCGCCGTTGCGGCTT-AAATCTTTCCCTTCATGTCTT-TGAGGTATAAGGTTCGCC
* * * * *
75261 ATTGCGACTCAAACCTTTCCCTTTGTGTCTTCGTGGTACTGGATTCGCTGTTGCGGCTTAAATCT
64 ATTGCGACTTAAACCTTTCCCTTTGTATCTTCGTGGTACTGGATTCGCCGTTACGGCTCAAATCT
* **
75326 TTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGTGACTTAAACCCTTCCCTTTATATCTTC
129 TTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGTAACTTAAACCCTTCCCTCCATATCTTC
*
75391 -TT
194 GTC
* * *
75393 GTTACTGGATTCGCTGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCACCA
1 G-TACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCGCCA
*
75458 TTGCGACTTAAACCTTTCCCTTTGTATCTTCATGGTACTGGATTCGCCGTTACGGCTCAAATCTT
65 TTGCGACTTAAACCTTTCCCTTTGTATCTTCGTGGTACTGGATTCGCCGTTACGGCTCAAATCTT
** ** *
75523 TCCCTTCATGCTTCTGAGGTACAAGGTTCGCTGTTGTAACTTAAATGCTTCTCTCCATATCTTCG
130 TCCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGTAACTTAAACCCTTCCCTCCATATCTTCG
75588 TC
195 TC
*
75590 GTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCAT
1 GTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCGCCAT
*
75655 TGCGACTTAAACCTTTCCCTTTATATCTTCGTGGTACTGGA
66 TGCGACTTAAACCTTTCCCTTTGTATCTTCGTGGTACTGGA
75696 ACCTGTAGAA
Statistics
Matches: 271, Mismatches: 28, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
195 5 0.02
196 261 0.96
197 5 0.02
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (196 bp):
GTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCGCCAT
TGCGACTTAAACCTTTCCCTTTGTATCTTCGTGGTACTGGATTCGCCGTTACGGCTCAAATCTTT
CCCTTCATGCTTCTGAGGTACAAGGTTCGCCATTGTAACTTAAACCCTTCCCTCCATATCTTCGT
C
Found at i:83683 original size:18 final size:18
Alignment explanation
Indices: 83648--83685 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
83638 TGTTGTTCGG
**
83648 AAAATATTTTTGGGATAA
1 AAAATATTTTTGAAATAA
83666 AAAATATTTTTGAAATAA
1 AAAATATTTTTGAAATAA
83684 AA
1 AA
83686 TATTGGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (18 bp):
AAAATATTTTTGAAATAA
Found at i:83685 original size:16 final size:16
Alignment explanation
Indices: 83648--83707 Score: 52
Period size: 15 Copynumber: 3.7 Consensus size: 16
83638 TGTTGTTCGG
83648 AAAATATTTTTGGGATAA-
1 AAAATATTTTT--GA-AAT
83666 AAAATATTTTTGAAAT
1 AAAATATTTTTGAAAT
**
83682 AAAATATTGGT-AAAT
1 AAAATATTTTTGAAAT
*
83697 AAAGTATTTTT
1 AAAATATTTTT
83708 TAAGTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
15 14 0.39
16 11 0.31
18 11 0.31
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.42
Consensus pattern (16 bp):
AAAATATTTTTGAAAT
Done.