Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_445
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: 71309
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Found at i:6497 original size:93 final size:93
Alignment explanation
Indices: 6382--6551 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 93
6372 CCATAAGCGC
* * *
6382 ACTCAGACTCAACTCAATGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 ACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACG
6447 AGCTCGGATGCCTAGTTACATCTCACGA
66 AGCTCGGATGCCTAGTTACATCTCACGA
* *
6475 ACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTTAACG
1 ACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACG
6540 AGCTCGGATGCC
66 AGCTCGGATGCC
6552 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:6547 original size:46 final size:46
Alignment explanation
Indices: 6372--6547 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
6362 TGTAACCCGC
* * *
6372 CCATAAGCGCACTCAGACTCAACTCAATGAGCTCGGGCATTCGCAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
* * *
6418 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* *
6468 -C-TCA-CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
6511 CCATAAGTGAACTCAGACTCAACTTAACGAGCTCGGA
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGA
6548 TGCCCAAATA
Statistics
Matches: 108, Mismatches: 13, 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 59 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:0.31, G:0.19, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:13985 original size:93 final size:93
Alignment explanation
Indices: 13869--14038 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 93
13859 CCATAAGCGC
* *
13869 ACTCAGACTCAACTCAACAAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 ACTCAGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACG
13934 AGCTCGGATGCCTAGTTACATCTCACGA
66 AGCTCGGATGCCTAGTTACATCTCACGA
* * *
13962 ACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTTAACG
1 ACTCAGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACG
14027 AGCTCGGATGCC
66 AGCTCGGATGCC
14039 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:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (93 bp):
ACTCAGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAACG
AGCTCGGATGCCTAGTTACATCTCACGA
Found at i:14034 original size:46 final size:46
Alignment explanation
Indices: 13859--14034 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
13849 TGTAACCCGC
* * *
13859 CCATAAGCGCACTCAGACTCAACTCAACAAGCTCGGGCATTCGCAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
* * *
13905 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* *
13955 -C-TCA-CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
13998 CCATAAGTGAACTCAGACTCAACTTAACGAGCTCGGA
1 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGA
14035 TGCCCAAATA
Statistics
Matches: 108, Mismatches: 13, 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 59 0.55
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (46 bp):
CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:23452 original size:22 final size:22
Alignment explanation
Indices: 23420--23463 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
23410 CAAGTTGGTT
* * *
23420 TGTAACGCCCCGAGCCCGAGAC
1 TGTAACACCCCAAACCCGAGAC
23442 TGTAACACCCCAAACCCGAGAC
1 TGTAACACCCCAAACCCGAGAC
23464 CGTCGCCGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.41, G:0.20, T:0.09
Consensus pattern (22 bp):
TGTAACACCCCAAACCCGAGAC
Found at i:25041 original size:28 final size:28
Alignment explanation
Indices: 24978--25074 Score: 169
Period size: 28 Copynumber: 3.5 Consensus size: 28
24968 ATATTAAGTC
*
24978 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
25005 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
25033 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
25061 CGCACACTTAGTGC
1 CGCACACTTAGTGC
25075 CGTACAATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 22 0.33
28 45 0.67
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:33233 original size:28 final size:28
Alignment explanation
Indices: 33170--33292 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
33160 ATATTAAGTC
*
33170 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
33197 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
33225 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
33253 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
33282 CGCACACTTAG
1 CGCACACTTAG
33293 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
Found at i:41421 original size:28 final size:28
Alignment explanation
Indices: 41358--41480 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
41348 ATATTAAGTC
*
41358 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
41385 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
41413 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
41441 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
41470 CGCACACTTAG
1 CGCACACTTAG
41481 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
Found at i:49607 original size:28 final size:28
Alignment explanation
Indices: 49544--49666 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
49534 ATATTAAGTC
*
49544 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
49571 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
49599 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
49627 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
49656 CGCACACTTAG
1 CGCACACTTAG
49667 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
Found at i:54836 original size:40 final size:40
Alignment explanation
Indices: 54792--55023 Score: 283
Period size: 40 Copynumber: 5.8 Consensus size: 40
54782 GGATATAGCT
* * *
54792 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
*
54832 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATT-TAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA
*
54872 ACTCGCACAAATGCCTTCGAGACTTAGCCCGGATT-TAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA
* * *
54912 ACTCGCACAAATGCCTTCGGG-TTTGGCCCGGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* * *
54951 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATAGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTA
* *
54991 ACTTAGCACAAAAGCCTTCGGGACTTAGCCCGG
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGG
55024 ATATCATTCG
Statistics
Matches: 169, Mismatches: 17, Indels: 11
0.86 0.09 0.06
Matches are distributed among these distances:
38 3 0.02
39 31 0.18
40 107 0.63
41 25 0.15
42 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:54913 original size:80 final size:79
Alignment explanation
Indices: 54780--55027 Score: 313
Period size: 80 Copynumber: 3.1 Consensus size: 79
54770 TGGAATTTAA
* * * *
54780 CCGGATATAGCT-ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGAGTAACTCGCACAAT
1 CCGGATATAG-TAACTCGCACAAATGCCTTC-GGACTTAGCCCGGATT-TAGTAACTCGCACAAA
54843 TGCCTTCGGGACTTAGC
63 TGCCTTCGGGACTTAGC
*
54860 CCGGATTTAGTAACTCGCACAAATGCCTTCGAGACTTAGCCCGGATTTAGTAACTCGCACAAATG
1 CCGGATATAGTAACTCGCACAAATGCCTTCG-GACTTAGCCCGGATTTAGTAACTCGCACAAATG
* *
54925 CCTTCGGG-TTTGGC
65 CCTTCGGGACTTAGC
* * * * *
54939 CCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAAA
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCACAAAT
55004 GCCTTCGGGACTTAGC
64 GCCTTCGGGACTTAGC
55020 CCGGATAT
1 CCGGATAT
55028 CATTCGAATA
Statistics
Matches: 147, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
78 2 0.01
79 53 0.36
80 78 0.53
81 14 0.10
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (79 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
CTTCGGGACTTAGC
Found at i:62963 original size:40 final size:40
Alignment explanation
Indices: 62919--63150 Score: 283
Period size: 40 Copynumber: 5.8 Consensus size: 40
62909 GGATATAGCT
* * *
62919 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
*
62959 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATT-TAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA
62999 ACTCGCACAAATGCCTTC-GGACTTAGCCCGGATT-TAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTATAGTA
** * *
63038 ACTCGCACAAATGCCTTCGGGTTTTGGCCCGGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* * *
63078 ACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATAGTC
1 ACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTA
* *
63118 ACTTAGCACAAAAGCCTTCGGGACTTAGCCCGG
1 AC-TCGCACAAATGCCTTCGGGACTTAGCCCGG
63151 ATATCATTCG
Statistics
Matches: 169, Mismatches: 17, Indels: 11
0.86 0.09 0.06
Matches are distributed among these distances:
39 42 0.25
40 99 0.59
41 25 0.15
42 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:63053 original size:79 final size:79
Alignment explanation
Indices: 62907--63154 Score: 320
Period size: 79 Copynumber: 3.1 Consensus size: 79
62897 TGGAATTTAA
* * * *
62907 CCGGATATAGCT-ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGAGTAACTCGCACAAT
1 CCGGATATAG-TAACTCGCACAAATGCCTTC-GGACTTAGCCCGGATT-TAGTAACTCGCACAAA
62970 TGCCTTCGGGACTTAGC
63 TGCCTTCGGGACTTAGC
*
62987 CCGGATTTAGTAACTCGCACAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
** *
63052 CTTCGGGTTTTGGC
66 CTTCGGGACTTAGC
* * * * *
63066 CCGGATATAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAAA
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCACAAAT
63131 GCCTTCGGGACTTAGC
64 GCCTTCGGGACTTAGC
63147 CCGGATAT
1 CCGGATAT
63155 CATTCGAATA
Statistics
Matches: 147, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
79 73 0.50
80 45 0.31
81 29 0.20
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (79 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAATGC
CTTCGGGACTTAGC
Done.