Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1264
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: 21785
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:564 original size:3 final size:3
Alignment explanation
Indices: 556--592 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
546 GATGTAGATG
556 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
593 ACATTGATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:5759 original size:33 final size:33
Alignment explanation
Indices: 5722--5788 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
5712 ATTACGATCA
5722 TAAATTTTATTACGAACATAATTATAAATATTT
1 TAAATTTTATTACGAACATAATTATAAATATTT
5755 TAAATTTTATTACGAACATAATTATAAATATTT
1 TAAATTTTATTACGAACATAATTATAAATATTT
5788 T
1 T
5789 TAATATAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (33 bp):
TAAATTTTATTACGAACATAATTATAAATATTT
Found at i:6372 original size:15 final size:14
Alignment explanation
Indices: 6334--6382 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
6324 ATATTAAAAT
6334 TTAAATATTAAATTTA
1 TTAAATATT--ATTTA
6350 TTAAATATTATTTA
1 TTAAATATTATTTA
6364 TTAAA-A-TATTTA
1 TTAAATATTATTTA
6376 TATAAAT
1 T-TAAAT
6383 TAATTGAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 7 0.23
13 5 0.16
14 10 0.32
16 9 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAAATATTATTTA
Found at i:7385 original size:25 final size:22
Alignment explanation
Indices: 7332--7385 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
7322 GACTTCTGTC
*
7332 AAAAAAATTTTAATTGATGAAA
1 AAAAAAATTTAAATTGATGAAA
*
7354 AATAAAAATTTAAAACTTGATTGTAA
1 AA-AAAAATTT-AAA-TTGA-TGAAA
7380 AAAAAA
1 AAAAAA
7386 TGATAAGGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 2 0.08
23 8 0.31
24 2 0.08
25 8 0.31
26 6 0.23
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (22 bp):
AAAAAAATTTAAATTGATGAAA
Found at i:8523 original size:24 final size:26
Alignment explanation
Indices: 8468--8524 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 26
8458 TTATTTACTT
* *
8468 TTATTTTATTTTTATATAAATATTTA
1 TTATTTTATATTTATATAAATATCTA
**
8494 AAATTTTA-ATTT-TATAAATATCTA
1 TTATTTTATATTTATATAAATATCTA
8518 TTATTTT
1 TTATTTT
8525 TACCATATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 16 0.64
25 3 0.12
26 6 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATTTTATATTTATATAAATATCTA
Found at i:8966 original size:16 final size:15
Alignment explanation
Indices: 8954--9028 Score: 55
Period size: 15 Copynumber: 4.7 Consensus size: 15
8944 TTGAATTATT
8954 TTAAATTTAAATTAA
1 TTAAATTTAAATTAA
8969 TTAAATTTAATATTTAAA
1 TTAAATTTAA-A-TT-AA
8987 TTAATAAAATTTAAATTAA
1 -T--T-AAATTTAAATTAA
* *
9006 TTAAATAT-AA-TAC
1 TTAAATTTAAATTAA
9019 TTAAATTTAA
1 TTAAATTTAA
9029 TGAATTTAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
13 9 0.18
14 3 0.06
15 15 0.31
16 2 0.04
17 2 0.04
18 3 0.06
19 3 0.06
20 2 0.04
21 2 0.04
22 8 0.16
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATTTAAATTAA
Found at i:8974 original size:15 final size:15
Alignment explanation
Indices: 8975--9028 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
8965 TTAATTAAAT
8975 TTAATATTTAAATTAA
1 TTAA-ATTTAAATTAA
*
8991 TAAAATTTAAATTAA
1 TTAAATTTAAATTAA
* *
9006 TTAAATAT-AA-TAC
1 TTAAATTTAAATTAA
9019 TTAAATTTAA
1 TTAAATTTAA
9029 TGAATTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 9 0.28
14 3 0.09
15 17 0.53
16 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAAATTTAAATTAA
Found at i:8976 original size:22 final size:22
Alignment explanation
Indices: 8951--9081 Score: 83
Period size: 22 Copynumber: 5.7 Consensus size: 22
8941 AATTTGAATT
8951 ATTTTAAATTTAAATTAATTAA
1 ATTTTAAATTTAAATTAATTAA
8973 A-TTTAATATTTAAATTAA-TAA
1 ATTTTAA-ATTTAAATTAATTAA
* *
8994 AATTTAAA-TT-AATTAAATATA
1 ATTTTAAATTTAAATTAATTA-A
* *
9015 ATACTTAAATTT-AATGAATTTAA
1 AT-TTTAAATTTAAATTAA-TTAA
* *
9038 TTATTTTAAGTTTAAATTATTTAAA
1 --ATTTTAAATTTAAATTAATT-AA
9063 ATCATTTCAAATTTAAATT
1 AT--TTT-AAATTTAAATT
9082 TATCGATTTC
Statistics
Matches: 86, Mismatches: 9, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
19 6 0.07
20 4 0.05
21 12 0.14
22 22 0.26
23 10 0.12
24 11 0.13
25 11 0.13
26 10 0.12
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTTAAATTTAAATTAATTAA
Found at i:9037 original size:28 final size:25
Alignment explanation
Indices: 8957--9062 Score: 75
Period size: 24 Copynumber: 4.3 Consensus size: 25
8947 AATTATTTTA
8957 AATTTAAATT-A-ATTAAATTTAAT
1 AATTTAAATTAATATTAAATTTAAT
8980 -ATTTAAATTAATA--AAATTTAAATT
1 AATTTAAATTAATATTAAATTT-AA-T
9004 AA-TTAAATATAATACTTAAATTTAAT
1 AATTTAAAT-TAATA-TTAAATTTAAT
* *
9030 GAATTT-AATT-ATTTTAAGTTTAAAT
1 -AATTTAAATTAATATTAAATTT-AAT
*
9055 TATTTAAA
1 AATTTAAA
9063 ATCATTTCAA
Statistics
Matches: 67, Mismatches: 3, Indels: 24
0.71 0.03 0.26
Matches are distributed among these distances:
22 15 0.22
23 3 0.04
24 19 0.28
25 13 0.19
26 2 0.03
27 7 0.10
28 8 0.12
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (25 bp):
AATTTAAATTAATATTAAATTTAAT
Found at i:11014 original size:2 final size:2
Alignment explanation
Indices: 11009--11036 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10999 TGTTCCATAC
11009 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
11037 TTAAGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14052 original size:19 final size:19
Alignment explanation
Indices: 14012--14053 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
14002 ATTAATGTAA
*
14012 AAATAATATTTAAATATTT
1 AAATAATATTTAAATATAT
*
14031 AAATATTATTATAAATA-AT
1 AAATAATATT-TAAATATAT
14050 AAAT
1 AAAT
14054 TAAATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATAATATTTAAATATAT
Found at i:18155 original size:2 final size:2
Alignment explanation
Indices: 18148--18198 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
18138 AATTCTTGCA
18148 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
18190 AG AG AG AG A
1 AG AG AG AG A
18199 ATAGGATTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19154 original size:14 final size:14
Alignment explanation
Indices: 19099--19196 Score: 78
Period size: 14 Copynumber: 7.1 Consensus size: 14
19089 TGTTAGGTAA
19099 CTGTGTCAAAAGTAC
1 CTGTGTC-AAAGTAC
* *
19114 CTGTG-CTAAAATGC
1 CTGTGTC-AAAGTAC
* *
19128 CTATATC-AAGTAC
1 CTGTGTCAAAGTAC
*
19141 CTATGTCAAAGTAC
1 CTGTGTCAAAGTAC
* *
19155 TTGTGTCAAAGT-G
1 CTGTGTCAAAGTAC
*
19168 CTGTG-CCAAGTAC
1 CTGTGTCAAAGTAC
19181 CTGTGTCAAAGTAC
1 CTGTGTCAAAGTAC
19195 CT
1 CT
19197 ACGCCAGGCA
Statistics
Matches: 64, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
12 5 0.08
13 19 0.30
14 34 0.53
15 6 0.09
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (14 bp):
CTGTGTCAAAGTAC
Found at i:19228 original size:14 final size:14
Alignment explanation
Indices: 19135--19232 Score: 76
Period size: 14 Copynumber: 7.2 Consensus size: 14
19125 TGCCTATATC
* *
19135 AAGTACCTATGTCA
1 AAGTACCTGTGCCA
* *
19149 AAGTACTTGTGTCA
1 AAGTACCTGTGCCA
*
19163 AAGT-GCTGTGCC-
1 AAGTACCTGTGCCA
*
19175 AAGTACCTGTGTCA
1 AAGTACCTGTGCCA
**
19189 AAGTACCTACGCC-
1 AAGTACCTGTGCCA
* * *
19202 AGGCACTTGTGCCA
1 AAGTACCTGTGCCA
19216 AAGTACCTGTGCCA
1 AAGTACCTGTGCCA
19230 AAG
1 AAG
19233 AGTATTATGG
Statistics
Matches: 63, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
12 4 0.06
13 19 0.30
14 40 0.63
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (14 bp):
AAGTACCTGTGCCA
Found at i:19229 original size:27 final size:27
Alignment explanation
Indices: 19135--19230 Score: 86
Period size: 27 Copynumber: 3.6 Consensus size: 27
19125 TGCCTATATC
* * *
19135 AAGTACCTATGTCAAAGTACTTGTGTCA
1 AAGTACCTGTG-CCAAGCACTTGTGTCA
* * *
19163 AAGT-GCTGTGCCAAGTACCTGTGTCA
1 AAGTACCTGTGCCAAGCACTTGTGTCA
** * *
19189 AAGTACCTACGCCAGGCACTTGTGCCA
1 AAGTACCTGTGCCAAGCACTTGTGTCA
19216 AAGTACCTGTGCCAA
1 AAGTACCTGTGCCAA
19231 AGAGTATTAT
Statistics
Matches: 53, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
26 18 0.34
27 31 0.58
28 4 0.08
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (27 bp):
AAGTACCTGTGCCAAGCACTTGTGTCA
Found at i:19798 original size:14 final size:14
Alignment explanation
Indices: 19781--19819 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 14
19771 CCCACGAGGC
19781 ATTATCCGTAAGGT
1 ATTATCCGTAAGGT
19795 ATTATTCACTGTAAGGT
1 ATTA-TC-C-GTAAGGT
19812 ATTATCCG
1 ATTATCCG
19820 CGAGATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.23
15 3 0.14
16 3 0.14
17 11 0.50
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (14 bp):
ATTATCCGTAAGGT
Found at i:20403 original size:22 final size:20
Alignment explanation
Indices: 20375--20414 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
20365 TGCAATACGA
20375 ATTTTTTAAACAACAATAATAT
1 ATTTTTTAAA-AA-AATAATAT
20397 ATTTTTTAAAAAAATAAT
1 ATTTTTTAAAAAAATAAT
20415 CAATTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
22 10 0.56
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTTTTTAAAAAAATAATAT
Found at i:20420 original size:20 final size:21
Alignment explanation
Indices: 20374--20420 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 21
20364 ATGCAATACG
20374 AATTTTTTAAACAACAATAAT
1 AATTTTTTAAACAACAATAAT
20395 ATATTTTTTAAA-AA-AATAAT
1 A-ATTTTTTAAACAACAATAAT
20415 CAATTT
1 -AATTT
20421 AATATATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 10 0.42
21 4 0.17
22 10 0.42
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTTTTTAAACAACAATAAT
Done.