Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3259
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: 40419
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:9238 original size:46 final size:46
Alignment explanation
Indices: 9185--9278 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
9175 CAAAGAAAAG
*
9185 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
9231 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
9277 AC
1 AC
9279 GCCACACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 45 0.98
47 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:13629 original size:23 final size:22
Alignment explanation
Indices: 13577--13629 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
13567 TTCACGTCAT
*
13577 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
13599 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
13622 TTTCTTTT
1 TTTCTTTT
13630 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:15960 original size:11 final size:11
Alignment explanation
Indices: 15944--15977 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
15934 TAGTAGTTTC
15944 TTCAAAAAAAA
1 TTCAAAAAAAA
15955 TTCAAAAAAAAA
1 TTC-AAAAAAAA
15967 TTCAAAAAAAA
1 TTCAAAAAAAA
15978 ATTGGTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:15964 original size:12 final size:12
Alignment explanation
Indices: 15947--15980 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
15937 TAGTTTCTTC
15947 AAAAAAAATTCA
1 AAAAAAAATTCA
15959 AAAAAAAATTCA
1 AAAAAAAATTCA
15971 AAAAAAAATT
1 AAAAAAAATT
15981 GGTTTCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:16037 original size:15 final size:15
Alignment explanation
Indices: 16017--16071 Score: 101
Period size: 15 Copynumber: 3.6 Consensus size: 15
16007 GATATCAAGT
16017 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
16032 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
16047 TGAAAAAAAAATTTCG
1 TGAAAAAAAAA-TTCG
16063 TGAAAAAAA
1 TGAAAAAAA
16072 GAAGAAGCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
15 26 0.67
16 13 0.33
ACGTcount: A:0.62, C:0.05, G:0.13, T:0.20
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:16040 original size:16 final size:16
Alignment explanation
Indices: 16019--16071 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
16009 TATCAAGTTG
16019 AAAAAAAAATTCGTG-
1 AAAAAAAAATTCGTGA
16034 AAAAAAAAATTCGTGA
1 AAAAAAAAATTCGTGA
*
16050 AAAAAAAATTTCGTGA
1 AAAAAAAAATTCGTGA
16066 AAAAAA
1 AAAAAA
16072 GAAGAAGCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
15 15 0.42
16 21 0.58
ACGTcount: A:0.64, C:0.06, G:0.11, T:0.19
Consensus pattern (16 bp):
AAAAAAAAATTCGTGA
Found at i:23504 original size:13 final size:13
Alignment explanation
Indices: 23486--23512 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23476 TACCTGAAAG
23486 AAATTTAATTCAT
1 AAATTTAATTCAT
23499 AAATTTAATTCAT
1 AAATTTAATTCAT
23512 A
1 A
23513 TTAGGACACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTTAATTCAT
Found at i:30519 original size:23 final size:22
Alignment explanation
Indices: 30467--30519 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
30457 TCCACGTCTT
*
30467 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
30489 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
30512 TTTCTTTT
1 TTTCTTTT
30520 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:39007 original size:23 final size:21
Alignment explanation
Indices: 38980--39029 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
38970 TGGCAAACAT
*
38980 AAAAACATCATATAAAATAAAAA
1 AAAAACA-CA-ATAAAACAAAAA
* *
39003 AAAAATACAATAAAACAACAA
1 AAAAACACAATAAAACAAAAA
39024 AAAAAC
1 AAAAAC
39030 TAATAAACTC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.65
22 2 0.09
23 6 0.26
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (21 bp):
AAAAACACAATAAAACAAAAA
Done.