Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1809
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: 27372
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5125 original size:53 final size:53
Alignment explanation
Indices: 5045--5150 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
5035 GTTCGCCAAA
*
5045 CCCTTAACATTTAGATGAAAGATGATGAGAGCCAAAGGACCAATATTTTTCAT
1 CCCTTAACATTCAGATGAAAGATGATGAGAGCCAAAGGACCAATATTTTTCAT
5098 CCCTTAACATTCAGATGAAAGATGATGAGAGCCAAAGGACCAATATTTTTCAT
1 CCCTTAACATTCAGATGAAAGATGATGAGAGCCAAAGGACCAATATTTTTCAT
5151 TCTCGGTGTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (53 bp):
CCCTTAACATTCAGATGAAAGATGATGAGAGCCAAAGGACCAATATTTTTCAT
Found at i:6368 original size:46 final size:46
Alignment explanation
Indices: 6315--6408 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
6305 CAAAGAAAAG
*
6315 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
6361 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
6407 AC
1 AC
6409 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:7074 original size:21 final size:23
Alignment explanation
Indices: 7029--7075 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
7019 TCACCTGCAA
* *
7029 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
7052 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
7073 TAA
1 TAA
7076 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:14561 original size:21 final size:23
Alignment explanation
Indices: 14516--14562 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
14506 TCACCTGCAA
* *
14516 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
14539 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
14560 TAA
1 TAA
14563 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:19920 original size:16 final size:16
Alignment explanation
Indices: 19899--19935 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
19889 TAGCTTCTTC
19899 TTTTTTTCACGAATTT
1 TTTTTTTCACGAATTT
19915 TTTTTTTCACGAATTT
1 TTTTTTTCACGAATTT
19931 TTTTT
1 TTTTT
19936 CAACTTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.16, C:0.11, G:0.05, T:0.68
Consensus pattern (16 bp):
TTTTTTTCACGAATTT
Found at i:19993 original size:12 final size:12
Alignment explanation
Indices: 19976--20022 Score: 78
Period size: 12 Copynumber: 3.9 Consensus size: 12
19966 TGGAAACCAA
19976 TTTTTTTTGAAT
1 TTTTTTTTGAAT
19988 TTTTTTTTGAA-
1 TTTTTTTTGAAT
19999 TTTTTTTTGAAAT
1 TTTTTTTTG-AAT
20012 TTTTTTTTGAA
1 TTTTTTTTGAA
20023 GAAACTACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 9 0.27
12 15 0.45
13 9 0.27
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:20012 original size:24 final size:23
Alignment explanation
Indices: 19974--20022 Score: 89
Period size: 24 Copynumber: 2.1 Consensus size: 23
19964 AATGGAAACC
19974 AATTTTTTTTGAATTTTTTTTTG
1 AATTTTTTTTGAATTTTTTTTTG
19997 AATTTTTTTTGAAATTTTTTTTTG
1 AATTTTTTTTG-AATTTTTTTTTG
20021 AA
1 AA
20023 GAAACTACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (23 bp):
AATTTTTTTTGAATTTTTTTTTG
Found at i:20197 original size:20 final size:20
Alignment explanation
Indices: 20151--20197 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
20141 AGCTCGTTTC
*
20151 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
20171 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
20191 CAGCTCA
1 CAGCTCA
20198 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:22882 original size:48 final size:47
Alignment explanation
Indices: 22803--22908 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
22793 GAGTGTCATG
*
22803 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
22851 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
22899 GAAAAAGAAA
1 GAAAAAGAAA
22909 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:24620 original size:20 final size:20
Alignment explanation
Indices: 24574--24620 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
24564 AGCTCGTTTC
*
24574 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
24594 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
24614 CAGCTCA
1 CAGCTCA
24621 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:26936 original size:21 final size:23
Alignment explanation
Indices: 26891--26937 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
26881 TCACCTGCAA
* *
26891 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
26914 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
26935 TAA
1 TAA
26938 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Done.