Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1732
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: 14791
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Found at i:5157 original size:13 final size:13
Alignment explanation
Indices: 5139--5163 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5129 TGTGTTCTTA
5139 GTATCGATACATT
1 GTATCGATACATT
5152 GTATCGATACAT
1 GTATCGATACAT
5164 AGGCACTATT
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):
GTATCGATACATT
Found at i:7146 original size:25 final size:25
Alignment explanation
Indices: 7113--7162 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
7103 AGAGAAAAAA
*
7113 ATTTTATTAAGAGGGAGTATTAAAT
1 ATTTCATTAAGAGGGAGTATTAAAT
*
7138 ATTTCATTAAGGGGGAGTATTAAAT
1 ATTTCATTAAGAGGGAGTATTAAAT
7163 TGAAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (25 bp):
ATTTCATTAAGAGGGAGTATTAAAT
Found at i:8630 original size:22 final size:22
Alignment explanation
Indices: 8576--8630 Score: 103
Period size: 21 Copynumber: 2.5 Consensus size: 22
8566 CAGTGACTTG
8576 TGAACAGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
8598 TGAA-AGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
8619 TGAACAGTGATG
1 TGAACAGTGATG
8631 AATAGTGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
TGAACAGTGATGTATCGATACA
Found at i:8729 original size:53 final size:53
Alignment explanation
Indices: 8663--8799 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
8653 CTACTACCAA
8663 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* * *
8716 TGTATCGATACATATTGTGTGTATTGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
8769 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
8800 TATGCAATTT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 66 0.85
54 12 0.15
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:8832 original size:20 final size:20
Alignment explanation
Indices: 8769--8839 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
8759 GCCAATGTCC
**
8769 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
8789 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
8809 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
8829 TGTATCGATAC
1 TGTATCGATAC
8840 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:8903 original size:21 final size:21
Alignment explanation
Indices: 8879--8919 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8869 GTCAACCTTG
8879 TGTATTAATATCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
8900 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
8920 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:9182 original size:13 final size:13
Alignment explanation
Indices: 9164--9189 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9154 CACTCCCAGA
9164 TGTATCGATACAT
1 TGTATCGATACAT
9177 TGTATCGATACAT
1 TGTATCGATACAT
9190 GTTTTTTGTA
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:9295 original size:21 final size:20
Alignment explanation
Indices: 9271--9322 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
9261 TGATACATTA
*
9271 TATCGATACATACTTGAATTG
1 TATCGATACATACGT-AATTG
* *
9292 TATCGATACATAGGTATTTG
1 TATCGATACATACGTAATTG
9312 TATCGATACAT
1 TATCGATACAT
9323 TGAGCCTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (20 bp):
TATCGATACATACGTAATTG
Found at i:9854 original size:20 final size:19
Alignment explanation
Indices: 9810--9860 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
9800 GTATCACTGC
* * *
9810 ATTGTATCGATACATGTTC
1 ATTGTATCAATACATGATA
9829 ATTGTATCAATACATGCATA
1 ATTGTATCAATACATG-ATA
9849 ATTGTATCAATA
1 ATTGTATCAATA
9861 TATAAAACTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (19 bp):
ATTGTATCAATACATGATA
Found at i:11525 original size:15 final size:15
Alignment explanation
Indices: 11505--11535 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11495 ATCAAAGATA
11505 ATGATGATAATGATG
1 ATGATGATAATGATG
11520 ATGATGATAATGATG
1 ATGATGATAATGATG
11535 A
1 A
11536 AGTTGACTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (15 bp):
ATGATGATAATGATG
Done.