Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2852
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: 22161
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Found at i:1413 original size:3 final size:3
Alignment explanation
Indices: 1393--1430 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
1383 GTATATGCAT
1393 ATA ATA A-A AT- ATA TATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
1431 TGAAAATACA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.12
3 25 0.78
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3237 original size:13 final size:13
Alignment explanation
Indices: 3219--3253 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3209 AGTTGATTTT
*
3219 TTGAAAATATAAA
1 TTGAAAATAAAAA
*
3232 TTGAAAACAAAAA
1 TTGAAAATAAAAA
3245 TTGAAAATA
1 TTGAAAATA
3254 CCTCAACATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.63, C:0.03, G:0.09, T:0.26
Consensus pattern (13 bp):
TTGAAAATAAAAA
Found at i:3617 original size:14 final size:14
Alignment explanation
Indices: 3598--3632 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3588 AGCTGATTTT
* *
3598 TTGAAAAGTAGGAA
1 TTGAAAAGCAGAAA
3612 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
3626 TTGAAAA
1 TTGAAAA
3633 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.20
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:3805 original size:74 final size:74
Alignment explanation
Indices: 3722--3861 Score: 219
Period size: 74 Copynumber: 1.9 Consensus size: 74
3712 TTGAATAATA
* * *
3722 GAATTTGAAAATACCTC-GACATGTGACCCGAGGCTCAACTCATCTCTTGCAATATGAGTTGATT
1 GAATTTGAAAATACCTCAG-CACGTGACCCAAGGCTCAACTCATCTCTCGCAATATGAGTTGATT
3786 TTGACGAACG
65 TTGACGAACG
* *
3796 GAATTTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCATCTCTCGCAATATGAGTTGATTT
1 GAATTTGAAAATACCTCAGCACGTGACCCAAGGCTCAACTCATCTCTCGCAATATGAGTTGATTT
3861 T
66 T
3862 TGAAAAACAA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
74 59 0.98
75 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (74 bp):
GAATTTGAAAATACCTCAGCACGTGACCCAAGGCTCAACTCATCTCTCGCAATATGAGTTGATTT
TGACGAACG
Found at i:4026 original size:69 final size:69
Alignment explanation
Indices: 3920--4150 Score: 228
Period size: 69 Copynumber: 3.2 Consensus size: 69
3910 AACTTTCTAA
* * * * *
3920 ACATAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATGTGAGTTGATT
1 ACATAAATTAAAAATACCTCAACGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
3985 TTGG
66 TTGG
* * * * *
3989 ACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATT
1 ACATAAATTAAAAATACCTCAACGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-T
*
4054 TTTGAAACA
65 TTTG----G
* * ** *
4063 ACACAGAATTAAAAATACCTCAGCGTGACCTGAGGCTTGACTCACCTCTCGCAATATGAGTTGGT
1 ACATA-AATTAAAAATACCTCAACGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
4128 TTTAGG
65 TTT-GG
4134 ACAGTAAAAATTAAAAA
1 ACA-T--AAATTAAAAA
4151 CAGAATTTGA
Statistics
Matches: 130, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
69 54 0.42
70 5 0.04
71 3 0.02
73 9 0.07
74 9 0.07
75 50 0.38
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.26
Consensus pattern (69 bp):
ACATAAATTAAAAATACCTCAACGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
TTGG
Found at i:4168 original size:14 final size:14
Alignment explanation
Indices: 4149--4175 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4139 AAAAATTAAA
4149 AACAGAATTTGAAT
1 AACAGAATTTGAAT
4163 AACAGAATTTGAA
1 AACAGAATTTGAA
4176 AATACCTCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (14 bp):
AACAGAATTTGAAT
Found at i:16931 original size:3 final size:3
Alignment explanation
Indices: 16912--16948 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
16902 GTATATGCAT
*
16912 ATA ATA AAA ATA TATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
16949 TGAAAATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:18903 original size:89 final size:92
Alignment explanation
Indices: 18718--18932 Score: 228
Period size: 89 Copynumber: 2.4 Consensus size: 92
18708 AGATATTAAA
*
18718 AGGCTCAACTCACCTTTCGCAATATGAGTTGA---TTTTTTGAAAAATATAAATTGAAAACAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAATATAAATTGAAAACAAAA
*
18780 ATTGAAAATACCTCAACATGTGACCTG
66 ATTGAAAATACCTCAACATGAGACCTG
** * * * * *
18807 AAACTCAACTTACCTCTCGCAATATGAGTTGAGTTTTTTTTTG-AAACT-TAATTTGAAAGCAGA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTTGAAAAATATAAATTGAAAACAAA
** * *
18870 TTTTGAAAATACCTC-A-ATGAGTCTTG
65 AATTGAAAATACCTCAACATGAGACCTG
** *
18896 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
18933 GAAAACAGAA
Statistics
Matches: 103, Mismatches: 19, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
88 4 0.04
89 62 0.60
90 1 0.01
91 25 0.24
92 4 0.04
93 7 0.07
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (92 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAATATAAATTGAAAACAAAA
ATTGAAAATACCTCAACATGAGACCTG
Found at i:18948 original size:72 final size:71
Alignment explanation
Indices: 18858--19008 Score: 171
Period size: 72 Copynumber: 2.1 Consensus size: 71
18848 TGAAACTTAA
* ** * * * *
18858 TTTGAAAGCAGATTTTGAAAAT-ACCTCAATGAGTCTTGAGGCTCAACTCA-TTTCTCGCAATAT
1 TTTGAAAACAGAAATTG-AAATGACCTCAACGAGACCTGAGGCTCAACTCACCTT-TCGCAATAT
*
18921 GAGTTGAAT
64 GAGCTG-AT
*
18930 TTTGAAAACAGAAATTGAAATGACCTCAACGTGACCTGAGGCTCAACTCACCTTTCGCAATATGA
1 TTTGAAAACAGAAATTGAAATGACCTCAACGAGACCTGAGGCTCAACTCACCTTTCGCAATATGA
18995 GCTGAT
66 GCTGAT
*
19001 TTTAAAAA
1 TTTGAAAA
19009 AGTAGAAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
71 13 0.19
72 52 0.78
73 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (71 bp):
TTTGAAAACAGAAATTGAAATGACCTCAACGAGACCTGAGGCTCAACTCACCTTTCGCAATATGA
GCTGAT
Found at i:19156 original size:14 final size:14
Alignment explanation
Indices: 19137--19171 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
19127 AGCTGATTTT
* *
19137 TTGAAAAGTAGGAA
1 TTGAAAAGCAGAAA
19151 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
19165 TTGAAAA
1 TTGAAAA
19172 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.20
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:19344 original size:74 final size:74
Alignment explanation
Indices: 19261--19400 Score: 219
Period size: 74 Copynumber: 1.9 Consensus size: 74
19251 TTGAATAATA
* * *
19261 GAATTTGAAAATACCTC-GACATGTGACCCGAGGCTCAACTCATCTCTTGCAATATGAGTTGATT
1 GAATTTGAAAATACCTCAG-CACGTGACCCAAGGCTCAACTCATCTCTCGCAATATGAGTTGATT
19325 TTGACGAACG
65 TTGACGAACG
* *
19335 GAATTTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCATCTCTCGCAATATGAGTTGATTT
1 GAATTTGAAAATACCTCAGCACGTGACCCAAGGCTCAACTCATCTCTCGCAATATGAGTTGATTT
19400 T
66 T
19401 TGAAAAACAA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
74 59 0.98
75 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (74 bp):
GAATTTGAAAATACCTCAGCACGTGACCCAAGGCTCAACTCATCTCTCGCAATATGAGTTGATTT
TGACGAACG
Found at i:19565 original size:69 final size:70
Alignment explanation
Indices: 19462--19688 Score: 231
Period size: 69 Copynumber: 3.2 Consensus size: 70
19452 TTTCTAAACA
* * * * *
19462 TAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATGTGAGTTGATTTTG
1 TAAATTAAAAATACCTCAACGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG
19527 GACA-
66 GACAC
* * * * *
19531 TAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTT
1 TAAATTAAAAATACCTCAACGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT
*
19596 GAAACAAC
65 G-GAC-AC
* * ** *
19604 AAGAATTAAAAATACCTCAGCGTGACCTGAGGCTTGACTCACCTCTCGCAATATGAGTTGGTTTT
1 TA-AATTAAAAATACCTCAACGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
*
19669 AGGACAG
65 -GGACAC
19676 TAAAAATTAAAAA
1 T--AAATTAAAAA
19689 CAGAATTTGA
Statistics
Matches: 127, Mismatches: 23, Indels: 12
0.78 0.14 0.07
Matches are distributed among these distances:
69 51 0.40
70 5 0.04
71 2 0.02
72 2 0.02
73 16 0.13
74 51 0.40
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (70 bp):
TAAATTAAAAATACCTCAACGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG
GACAC
Found at i:19706 original size:14 final size:14
Alignment explanation
Indices: 19687--19713 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19677 AAAAATTAAA
19687 AACAGAATTTGAAT
1 AACAGAATTTGAAT
19701 AACAGAATTTGAA
1 AACAGAATTTGAA
19714 AATACCTCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (14 bp):
AACAGAATTTGAAT
Found at i:19830 original size:72 final size:75
Alignment explanation
Indices: 19694--19838 Score: 208
Period size: 72 Copynumber: 2.0 Consensus size: 75
19684 AAAAACAGAA
* * *
19694 TTTGAATAACAGAATTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCATCTCTTGCAATA
1 TTTGAATAACAGAAATTGAAAATACCTCGACACGTGACCCGAGGCTCAACTCATCTCTAGCAATA
19759 TGAGTTGAAT
66 TGAGTTGAAT
* *
19769 TTTGAA-AACAGAAATTGAAATTACCTC-A-ACGTGACCTGAGGCTCAACTCA-CTTCTAGCAAT
1 TTTGAATAACAGAAATTGAAAATACCTCGACACGTGACCCGAGGCTCAACTCATC-TCTAGCAAT
19830 ATGAGTTGA
65 ATGAGTTGA
19839 TTCTTTCAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
71 1 0.02
72 37 0.58
73 1 0.02
74 19 0.30
75 6 0.09
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (75 bp):
TTTGAATAACAGAAATTGAAAATACCTCGACACGTGACCCGAGGCTCAACTCATCTCTAGCAATA
TGAGTTGAAT
Done.