Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold643
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: 23806
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Found at i:5524 original size:19 final size:18
Alignment explanation
Indices: 5500--5567 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
5490 CAGTAGCTGA
5500 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
5519 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
5534 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAA-AC
*
5551 TTATATATCGATACAAA
1 TTATGTATCGATACAAA
5568 TCGTTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 2 0.05
19 26 0.62
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:5540 original size:13 final size:13
Alignment explanation
Indices: 5522--5546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5512 ACAATACTTA
5522 TGTATCGATACAT
1 TGTATCGATACAT
5535 TGTATCGATACA
1 TGTATCGATACA
5547 ACACTTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5541 original size:32 final size:32
Alignment explanation
Indices: 5503--5565 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
5493 TAGCTGATTA
* *
5503 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATATATCGATACAT
5535 TGTATCGATACAACACTTATATATCGATACA
1 TGTATCGATACAACACTTATATATCGATACA
5566 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAACACTTATATATCGATACAT
Found at i:8396 original size:27 final size:28
Alignment explanation
Indices: 8365--8435 Score: 110
Period size: 27 Copynumber: 2.6 Consensus size: 28
8355 TAATATGGAA
*
8365 ATAATTATATAATAAATTTTA-TTTTAT
1 ATAATAATATAATAAATTTTATTTTTAT
8392 ATAATAATAT-ATAAATTTTATTTTTAT
1 ATAATAATATAATAAATTTTATTTTTAT
*
8419 ATAATAATTTAATAAAT
1 ATAATAATATAATAAAT
8436 ATATAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 10 0.25
27 24 0.60
28 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATAATAATATAATAAATTTTATTTTTAT
Found at i:10019 original size:21 final size:20
Alignment explanation
Indices: 9988--10026 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
9978 ATTTTTATTT
9988 TTTAAATTTTTAAGTTTTAC
1 TTTAAATTTTTAAGTTTTAC
*
10008 TTTAAGATTTTTATGTTTT
1 TTTAA-ATTTTTAAGTTTT
10027 TAGATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTAAATTTTTAAGTTTTAC
Found at i:10153 original size:21 final size:22
Alignment explanation
Indices: 10110--10159 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
10100 TGTGAATAAA
*
10110 TTTATTATTAAATTTATAAATT
1 TTTATTATAAAATTTATAAATT
*
10132 TTTATTATAAAATTT-TACATT
1 TTTATTATAAAATTTATAAATT
*
10153 TTCATTA
1 TTTATTA
10160 ACTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATTATAAAATTTATAAATT
Found at i:10621 original size:9 final size:9
Alignment explanation
Indices: 10607--10636 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
10597 ACTCCCAAAT
*
10607 TTCCTCCTC
1 TTCCTCTTC
10616 TTCCTCTTC
1 TTCCTCTTC
10625 TTCCTCTTC
1 TTCCTCTTC
10634 TTC
1 TTC
10637 TTCGTCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (9 bp):
TTCCTCTTC
Found at i:11191 original size:2 final size:2
Alignment explanation
Indices: 11186--11214 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11176 TCTCTCTCTC
11186 TA TA 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 TA TA T
11215 GCACGCACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13900 original size:3 final size:3
Alignment explanation
Indices: 13892--13926 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
13882 GTGTTACCTT
13892 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13927 TGTTAATAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16112 original size:22 final size:22
Alignment explanation
Indices: 16077--16119 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
16067 AAATCTCTTT
** *
16077 TTTTTATTTGAATTCAAATATC
1 TTTTTATTCCAATTAAAATATC
16099 TTTTTATTCCAATTAAAATAT
1 TTTTTATTCCAATTAAAATAT
16120 TAACAATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTTATTCCAATTAAAATATC
Done.