Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold790
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: 18634
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:4084 original size:20 final size:20
Alignment explanation
Indices: 4037--4111 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
4027 AAAAAGACAT
*
4037 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
4056 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
4077 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
4097 AATGTATCGATACAT
1 AATGTATCGATACAT
4112 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:4105 original size:40 final size:39
Alignment explanation
Indices: 4034--4111 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
4024 GGTAAAAAGA
* *
4034 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
4073 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
4112 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:8312 original size:21 final size:23
Alignment explanation
Indices: 8288--8351 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 23
8278 AATTAGAGGA
8288 AAAATGAATGAGTTAG-AAAA-G
1 AAAATGAATGAGTTAGCAAAATG
8309 AAAA-GAAATGAGTT-GCAAAATG
1 AAAATG-AATGAGTTAGCAAAATG
8331 AAAATG-ATGAGTTAGCTAAAA
1 AAAATGAATGAGTTAGC-AAAA
8352 AAAATAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
20 2 0.05
21 23 0.62
22 7 0.19
23 5 0.14
ACGTcount: A:0.55, C:0.03, G:0.22, T:0.20
Consensus pattern (23 bp):
AAAATGAATGAGTTAGCAAAATG
Found at i:11181 original size:13 final size:13
Alignment explanation
Indices: 11163--11187 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11153 ATTTTGCTTA
11163 GTATCGATACATT
1 GTATCGATACATT
11176 GTATCGATACAT
1 GTATCGATACAT
11188 AAAACTGGCA
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:11237 original size:10 final size:10
Alignment explanation
Indices: 11218--11258 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
11208 CTCATTTTTT
11218 TCACTGTTCA
1 TCACTGTTCA
*
11228 TCACTATTCA
1 TCACTGTTCA
11238 TCACTGTTCA
1 TCACTGTTCA
* *
11248 CCACTGCTCA
1 TCACTGTTCA
11258 T
1 T
11259 GTATCGATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.22, C:0.34, G:0.07, T:0.37
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:11314 original size:52 final size:52
Alignment explanation
Indices: 11236--11342 Score: 169
Period size: 52 Copynumber: 2.1 Consensus size: 52
11226 CATCACTATT
* * *
11236 CATCACTGTTCACCACTGCTCATGTATCGATATATTGTGAATAGTATCGATA
1 CATCACTGTTCACCACTACTCATGTATCGATACATTATGAATAGTATCGATA
* *
11288 CATCACTGTTCATCACTACTTATGTATCGATACATTATGAATAGTATCGATA
1 CATCACTGTTCACCACTACTCATGTATCGATACATTATGAATAGTATCGATA
11340 CAT
1 CAT
11343 TGAGTCCAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (52 bp):
CATCACTGTTCACCACTACTCATGTATCGATACATTATGAATAGTATCGATA
Found at i:14709 original size:33 final size:33
Alignment explanation
Indices: 14667--14729 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
14657 TTAAAAGCAA
14667 TGTATCGATACAAT-TCATCATGTATCGATATAT
1 TGTATCGATACAATGT-ATCATGTATCGATATAT
*
14700 TGTATCGATACAATGTGTCATGTATCGATA
1 TGTATCGATACAATGTATCATGTATCGATA
14730 CAAACAGTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (33 bp):
TGTATCGATACAATGTATCATGTATCGATATAT
Found at i:15478 original size:23 final size:22
Alignment explanation
Indices: 15447--15489 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
15437 ATACATGTAA
15447 AAATAAATTTAATAAAATAAATG
1 AAATAAATTTAAT-AAATAAATG
* *
15470 AAATTAATTTTATAAATAAA
1 AAATAAATTTAATAAATAAA
15490 AAAATCATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AAATAAATTTAATAAATAAATG
Found at i:15642 original size:21 final size:22
Alignment explanation
Indices: 15599--15648 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
15589 TATTTTAATT
15599 TTTTTAAATTTAATTAAATATTA
1 TTTTTAAATTTAATT-AATATTA
15622 TTTTTAAATTTAATT-ATATTA
1 TTTTTAAATTTAATTAATATTA
*
15643 TATTTA
1 TTTTTA
15649 TAGTATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 11 0.42
23 15 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTTAAATTTAATTAATATTA
Found at i:15749 original size:19 final size:19
Alignment explanation
Indices: 15727--15766 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
15717 AAATTATTTT
15727 AATTAATTAAAATATCATA
1 AATTAATTAAAATATCATA
* * *
15746 AATTATTTTAAGTATCATA
1 AATTAATTAAAATATCATA
15765 AA
1 AA
15767 ATATATGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (19 bp):
AATTAATTAAAATATCATA
Found at i:15865 original size:21 final size:20
Alignment explanation
Indices: 15848--15887 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
15838 AAGAATTTTT
15848 TATTATTATAATATAATTATTA
1 TATT-TTATAATA-AATTATTA
15870 TATTTTATAATAAATTAT
1 TATTTTATAATAAATTAT
15888 ATAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 8 0.44
22 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTTATAATAAATTATTA
Found at i:16331 original size:24 final size:23
Alignment explanation
Indices: 16289--16333 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
16279 CCTTGTGTAT
* *
16289 TAAAAAAAATATAAGTTTTAATC
1 TAAAAAAAATAAAACTTTTAATC
16312 TAAAAAAAATAAATACTTTTAA
1 TAAAAAAAATAAA-ACTTTTAA
16334 AAAATGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAAAAAAATAAAACTTTTAATC
Done.