Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2963
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: 43670
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Found at i:5788 original size:40 final size:39
Alignment explanation
Indices: 5744--5968 Score: 281
Period size: 40 Copynumber: 5.7 Consensus size: 39
5734 GCCACTAGCT
*
5744 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
*
5784 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* *
5823 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * *
5863 CAAACGCCTTCGGGAATTAGCCCGGATATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * ** * *
5903 CGAATGCCTTCGGGACTTAGCCCGGAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
5943 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
5969 TATCATCCGA
Statistics
Matches: 165, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
39 40 0.24
40 125 0.76
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:17933 original size:93 final size:93
Alignment explanation
Indices: 17818--17987 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 93
17808 CCATAAGTGC
* * *
17818 ACTCAGACTCAACTCAATGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 ACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACG
17883 AGCTCGGATGCCTAGTTACATCTCACGA
66 AGCTCGGATGCCTAGTTACATCTCACGA
* *
17911 ACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTTAACG
1 ACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACG
17976 AGCTCGGATGCC
66 AGCTCGGATGCC
17988 CAAATATCCT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (93 bp):
ACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACG
AGCTCGGATGCCTAGTTACATCTCACGA
Found at i:17983 original size:46 final size:46
Alignment explanation
Indices: 17808--17983 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
17798 TGTAACCCGC
* * *
17808 CCATAAGTGCACTCAGACTCAACTCAATGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
17854 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* * *
17904 -C-TCA-CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
*
17947 CCATAAGTGAACTCAGACTCAACTTAACGAGCTCGGA
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGA
17984 TGCCCAAATA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 60 0.55
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:25419 original size:93 final size:93
Alignment explanation
Indices: 25307--25476 Score: 304
Period size: 93 Copynumber: 1.8 Consensus size: 93
25297 CCATAAGTGC
* *
25307 ACTCAGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 ACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACG
25372 AGCTCGGATGCCTAGTTACATCTCACGA
66 AGCTCGGATGCCTAGTTACATCTCACGA
* *
25400 ACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTTAACG
1 ACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACG
25465 AGCTCGGATGCC
66 AGCTCGGATGCC
25477 CAAATATCCT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.20
Consensus pattern (93 bp):
ACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACG
AGCTCGGATGCCTAGTTACATCTCACGA
Found at i:25472 original size:46 final size:46
Alignment explanation
Indices: 25297--25472 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
25287 TGTAACCCGC
* *
25297 CCATAAGTGCACTCAGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
25343 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* * *
25393 -C-TCA-CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
*
25436 CCATAAGTGAACTCAGACTCAACTTAACGAGCTCGGA
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGA
25473 TGCCCAAATA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:34901 original size:22 final size:22
Alignment explanation
Indices: 34869--34912 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
34859 CAAGTTGGTT
* *
34869 TGTAACGCCCCGAGCCCGAGAC
1 TGTAACACCCCGAACCCGAGAC
34891 TGTAACACCCCGAACCCGAGAC
1 TGTAACACCCCGAACCCGAGAC
34913 CGTCGCCGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.41, G:0.23, T:0.09
Consensus pattern (22 bp):
TGTAACACCCCGAACCCGAGAC
Found at i:36491 original size:28 final size:28
Alignment explanation
Indices: 36428--36550 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
36418 ATATTAAGTC
*
36428 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
36455 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
36483 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
36511 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
36540 CGCACACTTAG
1 CGCACACTTAG
36551 CGCCAATCTC
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.25
28 49 0.56
29 16 0.18
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Done.