Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2287
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: 32711
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:13339 original size:12 final size:12
Alignment explanation
Indices: 13322--13349 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
13312 TGTATTTAAG
13322 AAGTTAAAAATT
1 AAGTTAAAAATT
13334 AAGTTAAAAATT
1 AAGTTAAAAATT
13346 AAGT
1 AAGT
13350 CCTACTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (12 bp):
AAGTTAAAAATT
Found at i:21980 original size:18 final size:18
Alignment explanation
Indices: 21957--22034 Score: 86
Period size: 18 Copynumber: 4.4 Consensus size: 18
21947 CAAGGTCACG
**
21957 ATCAATAGCGTCACTATT
1 ATCAATAGCGTCACTAGC
*
21975 ATCAATAGTGTCACTAGC
1 ATCAATAGCGTCACTAGC
* *
21993 ATTAATATCGTCACTAGC
1 ATCAATAGCGTCACTAGC
* *
22011 ATCAATATCGTCAC-ATC
1 ATCAATAGCGTCACTAGC
22028 ATCAATA
1 ATCAATA
22035 TCGATATCAT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
17 9 0.17
18 43 0.83
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (18 bp):
ATCAATAGCGTCACTAGC
Found at i:22045 original size:15 final size:16
Alignment explanation
Indices: 21996--22049 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
21986 CACTAGCATT
*
21996 AATATCGTCACTAGCATC
1 AATATCG-CAC-ATCATC
22014 AATATCGTCACATCATC
1 AATATCG-CACATCATC
*
22031 AATATCG-ATATCATC
1 AATATCGCACATCATC
22046 AATA
1 AATA
22050 AGAAAACCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 11 0.32
17 12 0.35
18 11 0.32
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30
Consensus pattern (16 bp):
AATATCGCACATCATC
Found at i:24445 original size:21 final size:21
Alignment explanation
Indices: 24415--24503 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
24405 CTCACAAAGA
* *
24415 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
24435 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
24456 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
24477 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
24501 AAA
1 AAA
24504 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:24496 original size:24 final size:21
Alignment explanation
Indices: 24415--24483 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
24405 CTCACAAAGA
* * *
24415 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
24435 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
24456 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
24477 AAAAAGA
1 AAAAAGA
24484 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:28640 original size:14 final size:14
Alignment explanation
Indices: 28621--28649 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28611 TGTACAATAT
28621 ATAAGAATTATACG
1 ATAAGAATTATACG
28635 ATAAGAATTATACG
1 ATAAGAATTATACG
28649 A
1 A
28650 ATCCATCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:32539 original size:13 final size:13
Alignment explanation
Indices: 32521--32551 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
32511 CAATGGAGCC
32521 TTAATTTATTAAT
1 TTAATTTATTAAT
32534 TTAATTTATTAAT
1 TTAATTTATTAAT
32547 TTAAT
1 TTAAT
32552 AATTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTAATTTATTAAT
Found at i:32564 original size:14 final size:16
Alignment explanation
Indices: 32522--32567 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 16
32512 AATGGAGCCT
32522 TAATTTATTAA-TT--
1 TAATTTATTAATTTAA
32535 TAATTTATTAATTTAA
1 TAATTTATTAATTTAA
32551 TAATTT-TT-ATTTAA
1 TAATTTATTAATTTAA
32565 TAA
1 TAA
32568 AATAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.37
14 11 0.37
15 2 0.07
16 6 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTATTAATTTAA
Done.