Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1859
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: 27128
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Found at i:2338 original size:29 final size:29
Alignment explanation
Indices: 2287--2352 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
2277 TGTATAACTG
* *
2287 AGTGTGCGAGCTTGAAATGCATGGCGCTA
1 AGTGTGCGAGCTTGAAATACATGGCACTA
*
2316 AGTGTGCGAG-TTTAAAGTACATGGCACTA
1 AGTGTGCGAGCTTGAAA-TACATGGCACTA
2345 AGTGTGCG
1 AGTGTGCG
2353 CGGTTGATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 5 0.15
29 28 0.85
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (29 bp):
AGTGTGCGAGCTTGAAATACATGGCACTA
Found at i:9642 original size:29 final size:29
Alignment explanation
Indices: 9605--9674 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
9595 TTGAGAGATT
9605 GCACTGAGTGTGCGAGCTTGAAATGCATG
1 GCACTGAGTGTGCGAGCTTGAAATGCATG
9634 GCACTGAGTGTGCGAGCTTGAAATGCATG
1 GCACTGAGTGTGCGAGCTTGAAATGCATG
9663 G-ACTGA-TGTGCG
1 GCACTGAGTGTGCG
9675 GCTGATGCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 6 0.15
28 5 0.12
29 30 0.73
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.24
Consensus pattern (29 bp):
GCACTGAGTGTGCGAGCTTGAAATGCATG
Found at i:9686 original size:23 final size:28
Alignment explanation
Indices: 9605--9687 Score: 113
Period size: 29 Copynumber: 3.1 Consensus size: 28
9595 TTGAGAGATT
9605 GCACTGAGTGTGCGAGCTTGAAATGCATG
1 GCACTGAGTGTGCGAGCTTG-AATGCATG
9634 GCACTGAGTGTGCGAGCTTGAAATGCATG
1 GCACTGAGTGTGCGAGCTTG-AATGCATG
9663 G-ACTGA-TGTGCG-GC-TG-ATGCATG
1 GCACTGAGTGTGCGAGCTTGAATGCATG
9686 GC
1 GC
9688 GCAGTGTGAG
Statistics
Matches: 53, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.15
25 2 0.04
26 2 0.04
27 6 0.11
28 5 0.09
29 30 0.57
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (28 bp):
GCACTGAGTGTGCGAGCTTGAATGCATG
Found at i:17587 original size:28 final size:29
Alignment explanation
Indices: 17493--17594 Score: 145
Period size: 29 Copynumber: 3.6 Consensus size: 29
17483 GTTGAGAGAT
*
17493 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATGCA
*
17522 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATGCA
* *
17551 TGGCGCTAAGTGTGCGAG-TT-AAAGTACA
1 TGGCACTAAGTGTGCGAGCTTGAAA-TGCA
17579 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
17595 CGGTTGATTA
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
27 3 0.04
28 20 0.29
29 45 0.66
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATGCA
Found at i:24228 original size:29 final size:29
Alignment explanation
Indices: 24191--24322 Score: 194
Period size: 29 Copynumber: 4.6 Consensus size: 29
24181 GTTGAGAGAT
24191 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTGAGTGTGCGAGCTTGAAATGCA
24220 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTGAGTGTGCGAGCTTGAAATGCA
24249 TGGCACTGAGTGTGCGAGCTTGAAATGCA
1 TGGCACTGAGTGTGCGAGCTTGAAATGCA
* * * * *
24278 TGGCGCTAAGTGTGCGAG-TTTAAAGTACG
1 TGGCACTGAGTGTGCGAGCTTGAAA-TGCA
*
24307 TGGCACTAAGTGTGCG
1 TGGCACTGAGTGTGCG
24323 CGGTTGATTA
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
28 5 0.05
29 91 0.95
ACGTcount: A:0.23, C:0.17, G:0.35, T:0.25
Consensus pattern (29 bp):
TGGCACTGAGTGTGCGAGCTTGAAATGCA
Found at i:25589 original size:1 final size:1
Alignment explanation
Indices: 25583--25619 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
25573 GAAAGTAATG
25583 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
25620 GAATGACCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:26502 original size:16 final size:16
Alignment explanation
Indices: 26481--26526 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
26471 GGATGTTATG
26481 GATTTGGGGATTTCAC
1 GATTTGGGGATTTCAC
* *
26497 GATTTGGGAAATTTGAC
1 GATTTGGG-GATTTCAC
*
26514 GAGTTGGGGATTT
1 GATTTGGGGATTT
26527 TAGAAATTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.22, C:0.07, G:0.35, T:0.37
Consensus pattern (16 bp):
GATTTGGGGATTTCAC
Done.