Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004791.1 Kokia drynarioides strain JFW-HI SEQ_118415, 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: 111737
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:209 original size:86 final size:85
Alignment explanation
Indices: 4--316 Score: 463
Period size: 86 Copynumber: 3.7 Consensus size: 85
1 AAG
* * * * *
4 ATTATTATTATATTACAATTTATATAAAATATTGTGTTAATTTGACAATACATTATTTATCAAAT
1 ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTAT-TAAT
* *
69 TTT-CATATTTAAAGT-ATAA-
65 TTTATATATTTAAA-TAAAAAT
* *
88 ATTATTATTATATTACAATTTTTATTATATAATGTGTTGATTTGACAATACATTATTTATTAATT
1 ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTATTAATT
153 TTATATATTTAAATAAAAATT
66 TTATATATTTAAATAAAAA-T
*
174 ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAATACATTATTTATTAATT
1 ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTATTAATT
239 TTATATATTTAAATAAAAAAT
66 TTATATATTTAAAT-AAAAAT
*
260 ATTATTTTTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACA-TATTT
1 ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTT
317 TAAATTTATT
Statistics
Matches: 211, Mismatches: 13, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
83 7 0.03
84 67 0.32
85 5 0.02
86 127 0.60
87 5 0.02
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (85 bp):
ATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTATTAATT
TTATATATTTAAATAAAAAT
Found at i:1954 original size:24 final size:23
Alignment explanation
Indices: 1939--1983 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
1929 TTAAATTTTT
1939 ATTTTCAATTGTAATT-AATTTAAA
1 ATTTTCAA-T-TAATTAAATTTAAA
1963 ATTTTCAATTAATTAAATTTA
1 ATTTTCAATTAATTAAATTTA
1984 TTTATTCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 7 0.35
24 8 0.40
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (23 bp):
ATTTTCAATTAATTAAATTTAAA
Found at i:3882 original size:30 final size:30
Alignment explanation
Indices: 3827--3888 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
3817 AAAAATACCC
*
3827 TTTTTAAAAAATTATCAAATTATGTC-ATT
1 TTTTTAAAAAATTATCAAATCATGTCGATT
*
3856 TTTTTCAAAAAATTA-CGAGATCATGTCGATT
1 TTTTT-AAAAAATTATC-AAATCATGTCGATT
3887 TT
1 TT
3889 ACGAAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 6 0.21
30 17 0.61
31 5 0.18
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (30 bp):
TTTTTAAAAAATTATCAAATCATGTCGATT
Found at i:5034 original size:17 final size:17
Alignment explanation
Indices: 5012--5065 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
5002 AACCTTAAAA
5012 AAAACCTTTCTTTTAAG
1 AAAACCTTTCTTTTAAG
* *
5029 AAAA-C---C-TTAAAA
1 AAAACCTTTCTTTTAAG
5041 AAAACCTTTCTTTTAAG
1 AAAACCTTTCTTTTAAG
5058 AAAACCTT
1 AAAACCTT
5066 AAAACTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
12 8 0.29
13 2 0.07
16 2 0.07
17 16 0.57
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (17 bp):
AAAACCTTTCTTTTAAG
Found at i:5035 original size:29 final size:29
Alignment explanation
Indices: 4993--5069 Score: 154
Period size: 29 Copynumber: 2.7 Consensus size: 29
4983 TTGAGAAAAA
4993 TTTTAAGAAAACCTTAAAAAAAACCTTTC
1 TTTTAAGAAAACCTTAAAAAAAACCTTTC
5022 TTTTAAGAAAACCTTAAAAAAAACCTTTC
1 TTTTAAGAAAACCTTAAAAAAAACCTTTC
5051 TTTTAAGAAAACCTTAAAA
1 TTTTAAGAAAACCTTAAAA
5070 CTTTCAACCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (29 bp):
TTTTAAGAAAACCTTAAAAAAAACCTTTC
Found at i:6641 original size:12 final size:12
Alignment explanation
Indices: 6624--6649 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6614 AACTATCAAC
6624 TTATATTAATTT
1 TTATATTAATTT
6636 TTATATTAATTT
1 TTATATTAATTT
6648 TT
1 TT
6650 TAGGGTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATATTAATTT
Found at i:14180 original size:2 final size:2
Alignment explanation
Indices: 14169--14207 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
14159 AATTATTAAA
14169 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14208 TCATATTAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:14890 original size:19 final size:20
Alignment explanation
Indices: 14862--14900 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
14852 AAAGAAAATC
14862 AAAATAATTT-TCAAAAATTT
1 AAAATAATTTAT-AAAAATTT
14882 AAAAT-ATTTATAAAAATTT
1 AAAATAATTTATAAAAATTT
14901 TAGAAACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATAATTTATAAAAATTT
Found at i:23671 original size:22 final size:21
Alignment explanation
Indices: 23639--23695 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
23629 TTTACCTTTG
23639 TTTTTTATTATTTTACTATCA
1 TTTTTTATTATTTTACTATCA
* * *
23660 TTTTGTTATTATATTATTATTA
1 TTTT-TTATTATTTTACTATCA
*
23682 TATTATTATTATTT
1 T-TTTTTATTATTT
23696 AGATATTACA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 4 0.14
22 23 0.79
23 2 0.07
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTTTATTATTTTACTATCA
Found at i:23679 original size:11 final size:11
Alignment explanation
Indices: 23665--23693 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
23655 TATCATTTTG
23665 TTATTATATTA
1 TTATTATATTA
23676 TTATTATATTA
1 TTATTATATTA
23687 TTATTAT
1 TTATTAT
23694 TTAGATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATTATATTA
Found at i:23703 original size:33 final size:34
Alignment explanation
Indices: 23643--23725 Score: 89
Period size: 33 Copynumber: 2.5 Consensus size: 34
23633 CCTTTGTTTT
* * * * * *
23643 TTATTATTTTACTATCATTTTGTTATTATAT-TA
1 TTATTATTTTATTATTATTTAGATATTACATAAA
*
23676 TTATTATATTATTATTATTTAGATATTACATAAA
1 TTATTATTTTATTATTATTTAGATATTACATAAA
23710 TT-TTATTTTATTATTA
1 TTATTATTTTATTATTA
23726 ATTTTGTTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 38 0.93
34 3 0.07
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (34 bp):
TTATTATTTTATTATTATTTAGATATTACATAAA
Found at i:25067 original size:36 final size:36
Alignment explanation
Indices: 25027--25098 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
25017 GATAATATTT
*
25027 TTTATTTATAGATATAAGTGGGTTATTCTATTCTAA
1 TTTATTTATAGATATAAGTGAGTTATTCTATTCTAA
*
25063 TTTATTTATAGATATAAGTGAGTTATTCTGTTCTAA
1 TTTATTTATAGATATAAGTGAGTTATTCTATTCTAA
25099 ACTTAACACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.50
Consensus pattern (36 bp):
TTTATTTATAGATATAAGTGAGTTATTCTATTCTAA
Found at i:26980 original size:16 final size:16
Alignment explanation
Indices: 26961--27028 Score: 50
Period size: 16 Copynumber: 4.2 Consensus size: 16
26951 TTGGATTCAA
26961 AATTTTATTATTTTAT
1 AATTTTATTATTTTAT
* **
26977 AATTATATTAAATTAT
1 AATTTTATTATTTTAT
* *
26993 -ATTTTAATTATTTCAA
1 AATTTT-ATTATTTTAT
27009 ATATATTTATT-TTTTAT
1 A-AT-TTTATTATTTTAT
27026 AAT
1 AAT
27029 ATATAATAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
15 4 0.11
16 21 0.55
17 5 0.13
18 5 0.13
19 3 0.08
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTATTATTTTAT
Found at i:26992 original size:21 final size:20
Alignment explanation
Indices: 26967--27016 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
26957 TCAAAATTTT
26967 ATTATTTTATAATTATATT-AA
1 ATTATTTT-TAATTAT-TTCAA
26988 ATTATATTTTAATTATTTCAA
1 ATTAT-TTTTAATTATTTCAA
27009 ATATATTT
1 AT-TATTT
27017 ATTTTTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 2 0.08
21 18 0.69
22 6 0.23
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTATTTTTAATTATTTCAA
Found at i:36872 original size:2 final size:2
Alignment explanation
Indices: 36860--36915 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
36850 GTTAATAACC
*
36860 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36902 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
36916 AACTCATGTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:46426 original size:18 final size:18
Alignment explanation
Indices: 46405--46441 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
46395 TTTTACATGG
46405 TATTGATGTTCCCGCTAA
1 TATTGATGTTCCCGCTAA
46423 TATTGATGTTCCCGCTAA
1 TATTGATGTTCCCGCTAA
46441 T
1 T
46442 GGTTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (18 bp):
TATTGATGTTCCCGCTAA
Found at i:51968 original size:26 final size:26
Alignment explanation
Indices: 51934--51996 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
51924 AATAAACAAT
* * *
51934 TTAATTATATTTTAAT-ATAATTATTA
1 TTAAATATAATTTAATAATAA-TAATA
51960 TTAAATATAATTTAATAATAATAATA
1 TTAAATATAATTTAATAATAATAATA
*
51986 TTAAATTTAAT
1 TTAAATATAAT
51997 AATTTTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 28 0.88
27 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TTAAATATAATTTAATAATAATAATA
Found at i:52005 original size:58 final size:61
Alignment explanation
Indices: 51896--52013 Score: 170
Period size: 61 Copynumber: 2.0 Consensus size: 61
51886 ATTTTTGTTG
*
51896 TTATTAAATATAATTTAATAAAAATGAAAATAAACAATTTAATTATATTTTAATATAATTA
1 TTATTAAATATAATTTAATAAAAATGAAAATAAACAATTTAATAATATTTTAATATAATTA
* * * *
51957 TTATTAAATATAATTTAATAATAAT-AATAT-TA-AATTTAATAATTTTTTAATATAATT
1 TTATTAAATATAATTTAATAAAAATGAAAATAAACAATTTAATAATATTTTAATATAATT
52014 GTTTTTATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
58 23 0.44
59 1 0.02
60 4 0.08
61 24 0.46
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.47
Consensus pattern (61 bp):
TTATTAAATATAATTTAATAAAAATGAAAATAAACAATTTAATAATATTTTAATATAATTA
Found at i:52309 original size:53 final size:54
Alignment explanation
Indices: 52252--52367 Score: 141
Period size: 53 Copynumber: 2.2 Consensus size: 54
52242 ACCATGTACC
*
52252 CACACCCGTG-CGTCA-GCCCATGTGTAAGCCCATGTTCCCTAGAA-CAATATACA
1 CACACCCGTGACG-CACGCCCATGTGTAAGCCCATGTGCCCTA-AAGCAATATACA
* * *
52305 CACA-CCTTGACGCACGCCCATGTGTCAGCCCGTGTGCCCTAAAGCAATATACA
1 CACACCCGTGACGCACGCCCATGTGTAAGCCCATGTGCCCTAAAGCAATATACA
*
52358 CACGCCCGTG
1 CACACCCGTG
52368 TGCCTCAGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
52 8 0.15
53 41 0.77
54 4 0.08
ACGTcount: A:0.26, C:0.36, G:0.19, T:0.19
Consensus pattern (54 bp):
CACACCCGTGACGCACGCCCATGTGTAAGCCCATGTGCCCTAAAGCAATATACA
Found at i:61944 original size:19 final size:19
Alignment explanation
Indices: 61920--61966 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
61910 ATTTGAATTT
61920 GTGAAGAGAGAAAATACCA
1 GTGAAGAGAGAAAATACCA
61939 GTGAAGAGAGAAAATACCA
1 GTGAAGAGAGAAAATACCA
*
61958 ATGAAGAGA
1 GTGAAGAGA
61967 ATGATAAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.53, C:0.09, G:0.28, T:0.11
Consensus pattern (19 bp):
GTGAAGAGAGAAAATACCA
Found at i:64845 original size:29 final size:30
Alignment explanation
Indices: 64776--64845 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
64766 ATGATTGATC
**
64776 AACGTAATAATGAAAGGTTATTTTAAAAAA
1 AACGTAATAATGAAAGACTATTTTAAAAAA
* * * *
64806 AACCTAGTAATGGAAGACTATTTT-TAAAA
1 AACGTAATAATGAAAGACTATTTTAAAAAA
64835 AACGTAATAAT
1 AACGTAATAAT
64846 TATAAGAATT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (30 bp):
AACGTAATAATGAAAGACTATTTTAAAAAA
Found at i:69746 original size:22 final size:21
Alignment explanation
Indices: 69721--69761 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
69711 ATAAAAGAAA
*
69721 ATTAGGATAAATATTTATTTCT
1 ATTAGAATAAAT-TTTATTTCT
*
69743 ATTAGAATTAATTTTATTT
1 ATTAGAATAAATTTTATTT
69762 TAAAAATCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (21 bp):
ATTAGAATAAATTTTATTTCT
Found at i:69937 original size:21 final size:21
Alignment explanation
Indices: 69891--69944 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
69881 AAATTGGTTT
* *
69891 TTCCTCTAAAAATTCAAATTTT
1 TTCCTATAAAAATT-AAATTTA
69913 TTCCTATAAAAATT-AATGTTA
1 TTCCTATAAAAATTAAAT-TTA
69934 TTCCATATAAA
1 TTCC-TATAAA
69945 CCCCCCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 3 0.11
21 6 0.21
22 19 0.68
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.43
Consensus pattern (21 bp):
TTCCTATAAAAATTAAATTTA
Found at i:71210 original size:53 final size:53
Alignment explanation
Indices: 71060--71217 Score: 142
Period size: 54 Copynumber: 2.9 Consensus size: 53
71050 CCATGGCAAG
* * * *
71060 TGAAGACCATATCGTGTAAGACTTAGTAC-GGGACTACGACATCATATGGGGAAA
1 TGAAGACCATATCGTGTAAGACCTAGT-CTGGGACTATGGCATCATAT-GGAAAA
* * * ** *
71114 -GAAAATCCATATAGTGTAAGGCCTAGTCATATTG-TTATGGCATCATATGGAAAA
1 TGAAGA-CCATATCGTGTAAGACCTAGTC-T-GGGACTATGGCATCATATGGAAAA
* *
71168 TGAAGACCACATCGTGTAAGACCTAGTCTGGGACTATGGCATCATGTGGA
1 TGAAGACCATATCGTGTAAGACCTAGTCTGGGACTATGGCATCATATGGA
71218 TATATGTATA
Statistics
Matches: 80, Mismatches: 18, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
52 1 0.01
53 21 0.26
54 42 0.52
55 15 0.19
56 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (53 bp):
TGAAGACCATATCGTGTAAGACCTAGTCTGGGACTATGGCATCATATGGAAAA
Found at i:75941 original size:3 final size:3
Alignment explanation
Indices: 75933--75966 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
75923 AAGGAGCATG
*
75933 AGA AGA AGA GGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
75967 TCTTGTTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:83008 original size:4 final size:4
Alignment explanation
Indices: 82999--83052 Score: 72
Period size: 4 Copynumber: 13.5 Consensus size: 4
82989 ATAACTTTGA
* * * *
82999 TATT TATT TATA TATT TATT TATT TATT TACT TACT TATT TATG TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
83047 TATT TA
1 TATT TA
83053 CATCGTAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (4 bp):
TATT
Found at i:84416 original size:37 final size:37
Alignment explanation
Indices: 84366--84447 Score: 155
Period size: 37 Copynumber: 2.2 Consensus size: 37
84356 GTAATCAATA
*
84366 AAGTATTGTATGAATAAGTCACTAACCTTGCTTTTCG
1 AAGTATTGTATGAATAAGTCACTAACCTCGCTTTTCG
84403 AAGTATTGTATGAATAAGTCACTAACCTCGCTTTTCG
1 AAGTATTGTATGAATAAGTCACTAACCTCGCTTTTCG
84440 AAGTATTG
1 AAGTATTG
84448 ATTTAACAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (37 bp):
AAGTATTGTATGAATAAGTCACTAACCTCGCTTTTCG
Found at i:85836 original size:16 final size:15
Alignment explanation
Indices: 85805--85843 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
85795 TACCGAAAAA
85805 AGAAAACAAAATAAT
1 AGAAAACAAAATAAT
*
85820 AGAAAATAAATATAAT
1 AGAAAACAAA-ATAAT
85836 ATGAAAAC
1 A-GAAAAC
85844 GATATAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 9 0.45
16 6 0.30
17 5 0.25
ACGTcount: A:0.69, C:0.05, G:0.08, T:0.18
Consensus pattern (15 bp):
AGAAAACAAAATAAT
Found at i:86332 original size:12 final size:12
Alignment explanation
Indices: 86317--86359 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
86307 AAATGCATAA
86317 AAAAATAACAAC
1 AAAAATAACAAC
*
86329 AAAAATAACAGC
1 AAAAATAACAAC
* *
86341 AAAAACAATAAC
1 AAAAATAACAAC
*
86353 CAAAATA
1 AAAAATA
86360 GTAGCAAAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.72, C:0.16, G:0.02, T:0.09
Consensus pattern (12 bp):
AAAAATAACAAC
Found at i:86344 original size:24 final size:24
Alignment explanation
Indices: 86317--86380 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
86307 AAATGCATAA
*
86317 AAAAATAACAACAAAAATAACAGC
1 AAAAACAACAACAAAAATAACAGC
* * **
86341 AAAAACAATAACCAAAATAGTAGC
1 AAAAACAACAACAAAAATAACAGC
* *
86365 AAAAGCAACACCAAAA
1 AAAAACAACAACAAAA
86381 CAATAAAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.67, C:0.19, G:0.06, T:0.08
Consensus pattern (24 bp):
AAAAACAACAACAAAAATAACAGC
Found at i:88701 original size:24 final size:25
Alignment explanation
Indices: 88674--88727 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
88664 ACTTGACATC
88674 ATCTTCCTCCTCCT-CATCATC-CTT
1 ATCTTCC-CCTCCTGCATCATCACTT
*
88698 ATCTTCCCCTGCTGCATCATCACTT
1 ATCTTCCCCTCCTGCATCATCACTT
*
88723 CTCTT
1 ATCTT
88728 TCTCTTAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 5 0.19
24 14 0.54
25 7 0.27
ACGTcount: A:0.13, C:0.43, G:0.04, T:0.41
Consensus pattern (25 bp):
ATCTTCCCCTCCTGCATCATCACTT
Found at i:90534 original size:6 final size:6
Alignment explanation
Indices: 90511--90595 Score: 64
Period size: 6 Copynumber: 14.2 Consensus size: 6
90501 TCATTATCTA
* * * * *
90511 CCTCTT CCTCCT CTTCAT CCTCAT CCTCAT CCTCAT CATCAT CATCAT
1 CCTCAT CCTCAT CCTCAT CCTCAT CCTCAT CCTCAT CCTCAT CCTCAT
* * * * *
90559 CATCAT CCTC-T ACCCCAT CTTCCT CCTCAT CATCAT C
1 CCTCAT CCTCAT -CCTCAT CCTCAT CCTCAT CCTCAT C
90596 ACTATCCACA
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
5 1 0.02
6 62 0.97
7 1 0.02
ACGTcount: A:0.18, C:0.47, G:0.00, T:0.35
Consensus pattern (6 bp):
CCTCAT
Found at i:90551 original size:3 final size:3
Alignment explanation
Indices: 90525--90565 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
90515 TTCCTCCTCT
* * *
90525 TCA TCC TCA TCC TCA TCC TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
90566 CTCTACCCCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:90939 original size:18 final size:18
Alignment explanation
Indices: 90912--90946 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
90902 ATCATCCTCA
*
90912 TCCTCATCCTCTTCATCT
1 TCCTCATCCTCCTCATCT
*
90930 TCCTCTTCCTCCTCATC
1 TCCTCATCCTCCTCATC
90947 ATCCGATTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.49, G:0.00, T:0.43
Consensus pattern (18 bp):
TCCTCATCCTCCTCATCT
Found at i:96430 original size:35 final size:35
Alignment explanation
Indices: 96384--96453 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
96374 TCGAGAAAAC
*
96384 CTCCATGAGGGAGGACCCAAAGGAAATCTTTATTA
1 CTCCATGAGGGAGGACCCAAAGGAAACCTTTATTA
96419 CTCCATGAGGGAGGACCCAAAGGAAACCTTTATTA
1 CTCCATGAGGGAGGACCCAAAGGAAACCTTTATTA
96454 TGTCGAGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (35 bp):
CTCCATGAGGGAGGACCCAAAGGAAACCTTTATTA
Found at i:97925 original size:28 final size:28
Alignment explanation
Indices: 97892--97967 Score: 73
Period size: 31 Copynumber: 2.6 Consensus size: 28
97882 ATAAATAAGA
97892 ATATTATATT-ATTTTCAAATTAATAAAT
1 ATATTATATTAATTTT-AAATTAATAAAT
* *
97920 ATATTATTTTCAAGATTTTTAATTAATAAAT
1 ATATTATATT--A-ATTTTAAATTAATAAAT
*
97951 ATATTATTTTCAATTTT
1 ATATTATATT-AATTTT
97968 TTATTTTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 9 0.22
29 5 0.12
30 1 0.02
31 21 0.51
32 5 0.12
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (28 bp):
ATATTATATTAATTTTAAATTAATAAAT
Found at i:98671 original size:16 final size:14
Alignment explanation
Indices: 98639--98668 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
98629 AAAACCACAA
98639 ATTTTTTTTTAAAT
1 ATTTTTTTTTAAAT
*
98653 ATTTTTTTTTGAAT
1 ATTTTTTTTTAAAT
98667 AT
1 AT
98669 ATTAATATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
ATTTTTTTTTAAAT
Found at i:104191 original size:19 final size:19
Alignment explanation
Indices: 104169--104218 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
104159 TTTTCTGAAA
104169 TTAAAATAAATTATATTAT
1 TTAAAATAAATTATATTAT
* *
104188 TTAAAGAT-AATTTTTTTAT
1 TTAAA-ATAAATTATATTAT
*
104207 TTTAAA-AAATTA
1 TTAAAATAAATTA
104219 ATAAAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 5 0.20
19 18 0.72
20 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
TTAAAATAAATTATATTAT
Found at i:104950 original size:102 final size:102
Alignment explanation
Indices: 104814--105012 Score: 380
Period size: 102 Copynumber: 2.0 Consensus size: 102
104804 TGAAAGTTAG
* *
104814 AAAACTTATGAGGAGAGTTATAAATATAATGTTTTGTAGGTTACAAACATGGTGAGTTAAAAAAA
1 AAAACTTATGAGGAGAGTTACAAACATAATGTTTTGTAGGTTACAAACATGGTGAGTTAAAAAAA
104879 ATTAAAACAAATAAAACTATGTAACTGCCTTTGAAAC
66 ATTAAAACAAATAAAACTATGTAACTGCCTTTGAAAC
104916 AAAACTTATGAGGAGAGTTACAAACATAATGTTTTGTAGGTTACAAACATGGTGAGTTAAAAAAA
1 AAAACTTATGAGGAGAGTTACAAACATAATGTTTTGTAGGTTACAAACATGGTGAGTTAAAAAAA
104981 ATTAAAACAAATAAAACTATGTAACTGCCTTT
66 ATTAAAACAAATAAAACTATGTAACTGCCTTT
105013 AAAATATTAA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 95 1.00
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.29
Consensus pattern (102 bp):
AAAACTTATGAGGAGAGTTACAAACATAATGTTTTGTAGGTTACAAACATGGTGAGTTAAAAAAA
ATTAAAACAAATAAAACTATGTAACTGCCTTTGAAAC
Found at i:106609 original size:18 final size:21
Alignment explanation
Indices: 106578--106621 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
106568 AAAGATGTAA
*
106578 ATTTTGGAATTTTTATAAA-T
1 ATTTTGGAATTTTTAAAAATT
106598 ATTTT-GAA-TTTTAAAAATT
1 ATTTTGGAATTTTTAAAAATT
106617 ATTTT
1 ATTTT
106622 AAAATTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 9 0.41
20 5 0.23
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
ATTTTGGAATTTTTAAAAATT
Found at i:111718 original size:2 final size:2
Alignment explanation
Indices: 111713--111737 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
111703 TTCTTTTCTT
111713 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.