Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold7903.1
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: 5895
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Found at i:102 original size:19 final size:18
Alignment explanation
Indices: 80--119 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
70 TGAATAAAAC
80 TTATCTATCC-AAATAAGAT
1 TTATCTA-CCTAAATAA-AT
99 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
117 TTA
1 TTA
120 AAATATATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:3842 original size:43 final size:44
Alignment explanation
Indices: 3781--3873 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 44
3771 TCCTAATTGG
3781 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
* *
3824 GAAAATAGTTCCCTTATTCTAGTAAACTACTAAAAGATAAAATA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
3868 -AAAATA
1 GAAAATA
3874 TTTCTAGAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.52, C:0.14, G:0.06, T:0.28
Consensus pattern (44 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
Found at i:3917 original size:19 final size:18
Alignment explanation
Indices: 3895--3934 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
3885 TGAATAAAAC
3895 TTATCTAACC-AAATAAGAT
1 TTATCT-ACCTAAATAA-AT
3914 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
3932 TTA
1 TTA
3935 AAATATATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.38
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:4471 original size:49 final size:49
Alignment explanation
Indices: 4399--4495 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
4389 TCCCTCACAG
4399 CTCCAAGCCCACTATGGTTGGGGATTTCCTACGTGGATGAAAATAAAAT
1 CTCCAAGCCCACTATGGTTGGGGATTTCCTACGTGGATGAAAATAAAAT
*
4448 CTCCAAGCCCACTATGGTTGGGGATTTCCTGCGTGGATGAAAATAAAA
1 CTCCAAGCCCACTATGGTTGGGGATTTCCTACGTGGATGAAAATAAAA
4496 GGGGTGAGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (49 bp):
CTCCAAGCCCACTATGGTTGGGGATTTCCTACGTGGATGAAAATAAAAT
Found at i:4630 original size:32 final size:34
Alignment explanation
Indices: 4594--4658 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
4584 TGACAGTGGT
*
4594 ACTGGACCAGAG-CCCTT-TTCAGATTACAATAA
1 ACTGGACCAGAGCCCCTTATTCAGATAACAATAA
* **
4626 ACTGGGCCTTAGCCCCTTATTCAGATAACAATA
1 ACTGGACCAGAGCCCCTTATTCAGATAACAATA
4659 TGGCCCATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 9 0.33
33 5 0.19
34 13 0.48
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (34 bp):
ACTGGACCAGAGCCCCTTATTCAGATAACAATAA
Found at i:4939 original size:25 final size:25
Alignment explanation
Indices: 4911--4993 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 25
4901 ATCCAAATCC
4911 CATGCATCAGATAATAACAACATGG
1 CATGCATCAGATAATAACAACATGG
* * *
4936 CATGCAGT-AAATACAATATC-CCA-GG
1 CATGCA-TCAGAT--AATAACAACATGG
4961 CCCATGCATCAGATAATAACAACATGG
1 --CATGCATCAGATAATAACAACATGG
4988 CATGCA
1 CATGCA
4994 GTAAATAACA
Statistics
Matches: 44, Mismatches: 6, Indels: 16
0.67 0.09 0.24
Matches are distributed among these distances:
25 22 0.50
26 6 0.14
27 16 0.36
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (25 bp):
CATGCATCAGATAATAACAACATGG
Found at i:5001 original size:25 final size:25
Alignment explanation
Indices: 4921--5006 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 25
4911 CATGCATCAG
4921 ATAATAACAACATGGCATGCAGTAA
1 ATAATAACAACATGGCATGCAGTAA
* * *
4946 ATACAATATC-CCA-GGCCCATGCA-TCAG
1 AT--AATAACAACATGG--CATGCAGT-AA
4973 ATAATAACAACATGGCATGCAGTAA
1 ATAATAACAACATGGCATGCAGTAA
*
4998 ATAACAACA
1 ATAATAACA
5007 GTCAAACATG
Statistics
Matches: 46, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
25 24 0.52
26 6 0.13
27 16 0.35
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.19
Consensus pattern (25 bp):
ATAATAACAACATGGCATGCAGTAA
Done.