Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1888
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: 19481
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3693 original size:2 final size:2
Alignment explanation
Indices: 3686--3738 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3676 ATCTATCTAC
3686 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
3728 AT AT AT AT AT A
1 AT AT AT AT AT A
3739 AACACCAATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5756 original size:2 final size:2
Alignment explanation
Indices: 5749--5773 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5739 GTATATCTTT
5749 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5774 GTATGTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6796 original size:2 final size:2
Alignment explanation
Indices: 6789--6815 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6779 ATGCAGAACC
6789 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
6816 AATAAAATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7052 original size:20 final size:19
Alignment explanation
Indices: 7001--7052 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
6991 TATATTTATA
*
7001 TAAATTAATTTAATTTAAAAT
1 TAAA-TAATTTTA-TTAAAAT
7022 TAAATAATTTTATTAAAATT
1 TAAATAATTTTATTAAAA-T
*
7042 TTAATAATTTT
1 TAAATAATTTT
7053 TTTATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 6 0.21
20 18 0.64
21 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAAATAATTTTATTAAAAT
Found at i:8801 original size:13 final size:13
Alignment explanation
Indices: 8783--8808 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8773 CAATTTTTTG
8783 TGTATCGATACAT
1 TGTATCGATACAT
8796 TGTATCGATACAT
1 TGTATCGATACAT
8809 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:9498 original size:29 final size:29
Alignment explanation
Indices: 9464--9519 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
9454 CAAATTTGTA
9464 CATTCTCCCCCTTAATAAAGTAATTCACG
1 CATTCTCCCCCTTAATAAAGTAATTCACG
* *
9493 CATTCTCCCCTTTAATCAAGTAATTCA
1 CATTCTCCCCCTTAATAAAGTAATTCA
9520 TATTATAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.34
Consensus pattern (29 bp):
CATTCTCCCCCTTAATAAAGTAATTCACG
Found at i:13396 original size:15 final size:15
Alignment explanation
Indices: 13360--13397 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
13350 TTCATCAATT
* *
13360 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
13375 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
13390 TCATTTTG
1 TCATTTTG
13398 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:17467 original size:12 final size:12
Alignment explanation
Indices: 17450--17474 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17440 ACAATTTTTG
17450 TGTATCGATACA
1 TGTATCGATACA
17462 TGTATCGATACA
1 TGTATCGATACA
17474 T
1 T
17475 TACTTGCTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:17468 original size:31 final size:32
Alignment explanation
Indices: 17430--17493 Score: 96
Period size: 31 Copynumber: 2.0 Consensus size: 32
17420 CGTTAAGCCA
*
17430 ATGTATCGATACAATT-TTTG-TGTATCGATAC
1 ATGTATCGATAC-ATTACTTGCTGTATCGATAC
17461 ATGTATCGATACATTACTTGCTGTATCGATAC
1 ATGTATCGATACATTACTTGCTGTATCGATAC
17493 A
1 A
17494 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 3 0.10
31 15 0.50
32 12 0.40
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (32 bp):
ATGTATCGATACATTACTTGCTGTATCGATAC
Found at i:17556 original size:20 final size:19
Alignment explanation
Indices: 17533--17584 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
17523 ACATCTTTTT
17533 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTG-AA
*
17553 CATGTATCGATACTTTGAA
1 CATGTATCGATACATTGAA
**
17572 TGTGTATCGATAC
1 CATGTATCGATAC
17585 TTTTAAGGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (19 bp):
CATGTATCGATACATTGAA
Found at i:17579 original size:19 final size:20
Alignment explanation
Indices: 17533--17587 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
17523 ACATCTTTTT
*
17533 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
17553 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
**
17572 TGTGTATCGATACTTT
1 CATGTATCGATACTTT
17588 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Done.