Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_744
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: 48076
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:19443 original size:23 final size:23
Alignment explanation
Indices: 19413--19458 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
19403 ATTTATTTAG
19413 TTACTTTGTTTAAAATCTTAGTT
1 TTACTTTGTTTAAAATCTTAGTT
19436 TTACTTTGTTTAAAATCTTAGTT
1 TTACTTTGTTTAAAATCTTAGTT
19459 CTTAATCACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (23 bp):
TTACTTTGTTTAAAATCTTAGTT
Found at i:23514 original size:22 final size:22
Alignment explanation
Indices: 23486--23529 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
23476 ACTTAAGGTA
23486 CTTAACCACTATGTCATTCCAC
1 CTTAACCACTATGTCATTCCAC
23508 CTTAACCACTATGTCATTCCAC
1 CTTAACCACTATGTCATTCCAC
23530 TTACTTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.36, G:0.05, T:0.32
Consensus pattern (22 bp):
CTTAACCACTATGTCATTCCAC
Found at i:27321 original size:48 final size:47
Alignment explanation
Indices: 27266--27536 Score: 229
Period size: 48 Copynumber: 5.7 Consensus size: 47
27256 GGTGAATTGT
* * *
27266 CGATGCCATGTTCCAAACATGGTCTTACACCGGCTCACATGTTGAGGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCAT-TTGAGGC
* * * *
27314 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATAATGTGGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCAT-TTGAGGC
* * * * * ** ***
27362 CGATACCATGTCCCAAACATTGTCTTACACTAGCGCACATATCAATAT
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCAT-TTGAGGC
* * **
27410 CGATGCCATATCCCAAACATGGTCTTACATTGGCTCTCATTAT-ATTTC
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATT-TGA-GGC
* * * * * *
27458 CAATGCCATGTTCCAAACATGGTCTTACATTGGCTCTTATATCATGGC
1 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATTTGA-GGC
*
27506 CGATGCCATGTCCCAGACATGGTCTTACACT
1 CGATGCCATGTCCCAAACATGGTCTTACACT
27537 AGTGCACATA
Statistics
Matches: 177, Mismatches: 43, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
47 3 0.02
48 174 0.98
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (47 bp):
CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATTTGAGGC
Found at i:27435 original size:96 final size:96
Alignment explanation
Indices: 27271--27536 Score: 268
Period size: 96 Copynumber: 2.8 Consensus size: 96
27261 ATTGTCGATG
* ** * *
27271 CCATGTTCCAAACATGGTCTTACACCGGCTCACATGT--TGAGGCCGATGCCATGTCCCAGACAT
1 CCATGTCCCAAACATGGTCTTACACTAGCGCACATATCATGA--CCGATGCCATGTCCCAGACAT
* * *
27334 GGTCTTACACTGGCTTTCATAATGTGGCCGATA
64 GGTCTTACACTGGCTCTCATAATATGGCCAATA
* * * *
27367 CCATGTCCCAAACATTGTCTTACACTAGCGCACATATCAAT-ATCGATGCCATATCCCAAACATG
1 CCATGTCCCAAACATGGTCTTACACTAGCGCACATATC-ATGACCGATGCCATGTCCCAGACATG
* * ** *
27431 GTCTTACATTGGCTCTCATTATATTTCCAATG
65 GTCTTACACTGGCTCTCATAATATGGCCAATA
* * * * ** *
27463 CCATGTTCCAAACATGGTCTTACATTGGCTCTTATATCATGGCCGATGCCATGTCCCAGACATGG
1 CCATGTCCCAAACATGGTCTTACACTAGCGCACATATCATGACCGATGCCATGTCCCAGACATGG
27528 TCTTACACT
66 TCTTACACT
27537 AGTGCACATA
Statistics
Matches: 137, Mismatches: 29, Indels: 8
0.79 0.17 0.05
Matches are distributed among these distances:
95 2 0.01
96 133 0.97
98 1 0.01
99 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (96 bp):
CCATGTCCCAAACATGGTCTTACACTAGCGCACATATCATGACCGATGCCATGTCCCAGACATGG
TCTTACACTGGCTCTCATAATATGGCCAATA
Found at i:33881 original size:27 final size:26
Alignment explanation
Indices: 33846--34026 Score: 157
Period size: 27 Copynumber: 6.7 Consensus size: 26
33836 AGACCTTGGA
33846 TTGTAAAATTATCGAAATACCCCCGAT
1 TTGTAAAATTA-CGAAATACCCCCGAT
*
33873 TTGTAAAATTACTGAAATACCCTCGAT
1 TTGTAAAATTAC-GAAATACCCCCGAT
* *
33900 TTGTAAAATTGATGAAATACCCTCGAT
1 TTGTAAAATT-ACGAAATACCCCCGAT
* ** *
33927 TTTTAAAATTACCGAAATACCCCTAAA
1 TTGTAAAATTA-CGAAATACCCCCGAT
* * *
33954 TTGTAAAATTACAGAAGTATCCTCAGA-
1 TTGTAAAATTAC-GAAATA-CCCCCGAT
* * *
33981 TTGTAAAATTAACTAAATACCCCTGGT
1 TTGTAAAATT-ACGAAATACCCCCGAT
*
34008 TTGTGAAATTACTGAAATA
1 TTGTAAAATTAC-GAAATA
34027 TCCTTGTAGT
Statistics
Matches: 126, Mismatches: 20, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
26 9 0.07
27 110 0.87
28 7 0.06
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (26 bp):
TTGTAAAATTACGAAATACCCCCGAT
Found at i:34017 original size:81 final size:81
Alignment explanation
Indices: 33846--34026 Score: 206
Period size: 81 Copynumber: 2.2 Consensus size: 81
33836 AGACCTTGGA
* * * * *
33846 TTGTAAAATTATCGAAATACCCCCGATTTGTAAAATTACTGAAATACCCTCGATTTGTAAAATTG
1 TTGTAAAATTACCGAAATACCCCCAAATTGTAAAATTACAGAAATACCCTCGATTTGTAAAATTA
33911 ATGAAATACCCTCGAT
66 ATGAAATACCCTCGAT
* * * *
33927 TTTTAAAATTACCGAAATACCCCTAAATTGTAAAATTACAGAAGTATCCTCAGA-TTGTAAAATT
1 TTGTAAAATTACCGAAATACCCCCAAATTGTAAAATTACAGAAATACCCTC-GATTTGTAAAATT
*
33991 AACT-AAATACCC-CTGGT
65 AA-TGAAATACCCTC-GAT
* *
34008 TTGTGAAATTACTGAAATA
1 TTGTAAAATTACCGAAATA
34027 TCCTTGTAGT
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
80 1 0.01
81 80 0.95
82 3 0.04
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (81 bp):
TTGTAAAATTACCGAAATACCCCCAAATTGTAAAATTACAGAAATACCCTCGATTTGTAAAATTA
ATGAAATACCCTCGAT
Found at i:34044 original size:27 final size:27
Alignment explanation
Indices: 34013--34103 Score: 103
Period size: 27 Copynumber: 3.3 Consensus size: 27
34003 CTGGTTTGTG
34013 AAATTACTGAAATATCCTTGTAGTGTA
1 AAATTACTGAAATATCCTTGTAGTGTA
* * * *
34040 CAATTACCGAAGTA-CCATTATAGTGTA
1 AAATTACTGAAATATCC-TTGTAGTGTA
*
34067 AAATTACTGAAATATCCCTTGTAGGGTA
1 AAATTACTGAAATAT-CCTTGTAGTGTA
*
34095 AAATGACTG
1 AAATTACTG
34104 TTTTGCCCTT
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
26 2 0.04
27 31 0.61
28 16 0.31
29 2 0.04
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (27 bp):
AAATTACTGAAATATCCTTGTAGTGTA
Found at i:40820 original size:79 final size:82
Alignment explanation
Indices: 40709--40893 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 82
40699 GCTACTCGTT
* * *
40709 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* * *
40772 GGATTTAGTAAC-TCGCG
65 GGATATAGTAACTTAGCA
* **
40789 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
40852 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
40869 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40894 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.60
80 33 0.37
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:40893 original size:40 final size:40
Alignment explanation
Indices: 40690--40893 Score: 220
Period size: 40 Copynumber: 5.1 Consensus size: 40
40680 CGGAATTTAA
** *
40690 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
40730 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40770 CCGGATTTAGTAACTCGCGCAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
40809 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
40849 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
40889 CCGGA
1 CCGGA
40894 CATCATTCAA
Statistics
Matches: 137, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 91 0.66
41 12 0.09
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.