Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3555
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: 15191
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Found at i:344 original size:19 final size:19
Alignment explanation
Indices: 320--358 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
310 AATTGTACAG
320 CACTAAGTGTGCGATTTGA
1 CACTAAGTGTGCGATTTGA
339 CACTAAGTGTGCGATTTGA
1 CACTAAGTGTGCGATTTGA
358 C
1 C
359 TATGTTGCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (19 bp):
CACTAAGTGTGCGATTTGA
Found at i:377 original size:27 final size:27
Alignment explanation
Indices: 339--514 Score: 201
Period size: 27 Copynumber: 6.5 Consensus size: 27
329 TGCGATTTGA
*
339 CACTAAGTGTGCGATTTGACTATGTTG
1 CACTAAGTGTGCGATTTGACTATGTAG
** *
366 CACTAAGTGTGCGAAATGAATATG-ATG
1 CACTAAGTGTGCGATTTGACTATGTA-G
* * **
393 CACTAAGTGTGCGAATTGACCATGCGG
1 CACTAAGTGTGCGATTTGACTATGTAG
420 CACTAAGTGTGCGAGTTTGACTATGTAG
1 CACTAAGTGTGCGA-TTTGACTATGTAG
* *
448 CACTAAGTGTGCGATTTGATTACGTAG
1 CACTAAGTGTGCGATTTGACTATGTAG
* * *
475 CACTAAGTGTGCGAGTTGATTATATAG
1 CACTAAGTGTGCGATTTGACTATGTAG
*
502 CACTGAGTGTGCG
1 CACTAAGTGTGCG
515 GACTCAATAT
Statistics
Matches: 128, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
CACTAAGTGTGCGATTTGACTATGTAG
Found at i:451 original size:82 final size:81
Alignment explanation
Indices: 339--493 Score: 231
Period size: 82 Copynumber: 1.9 Consensus size: 81
329 TGCGATTTGA
* *
339 CACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGT
1 CACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTGT
403 GCGAATTGACCATGCGG
65 GCGAATTGACCATGCGG
** *
420 CACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGT
1 CACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
*
485 GCGAGTTGA
65 GCGAATTGA
494 TTATATAGCA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 14 0.21
82 51 0.77
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
CACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGTG
CGAATTGACCATGCGG
Found at i:505 original size:82 final size:81
Alignment explanation
Indices: 339--514 Score: 219
Period size: 82 Copynumber: 2.2 Consensus size: 81
329 TGCGATTTGA
* *
339 CACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGTG
1 CACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGTG
* *
404 CGAATTGACCATGCGG
66 CGAATTGACCATACAG
** *
420 CACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGTG
1 CACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAGTG
* ** *
484 TGCGAGTTGATTATATAG
64 TGCGAATTGACCATACAG
*
502 CACTGAGTGTGCG
1 CACTAAGTGTGCG
515 GACTCAATAT
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
81 15 0.19
82 66 0.81
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
CACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGTG
CGAATTGACCATACAG
Found at i:7520 original size:27 final size:27
Alignment explanation
Indices: 7489--7666 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
7479 TAAATTGTAC
7489 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
7516 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
7542 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
7570 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
7598 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
7625 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
7652 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
7667 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:7603 original size:82 final size:81
Alignment explanation
Indices: 7490--7645 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
7480 AAATTGTACA
* *
7490 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
7554 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
7571 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
7636 TGCGAGTTGA
65 TGCGAATTGA
7646 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:7657 original size:82 final size:81
Alignment explanation
Indices: 7486--7666 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
7476 GATTAAATTG
* *
7486 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
7551 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
7567 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
7631 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
7649 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
7667 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.