Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2205
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: 28979
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Found at i:77 original size:16 final size:16
Alignment explanation
Indices: 52--90 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
42 GAAATACAGG
*
52 TTATGGCTAGCAGGGC-
1 TTATGCCTAGCA-GGCT
68 TTATGCCTAGCAGGCT
1 TTATGCCTAGCAGGCT
84 TTATGCC
1 TTATGCC
91 AGTGATTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (16 bp):
TTATGCCTAGCAGGCT
Found at i:7601 original size:27 final size:27
Alignment explanation
Indices: 7571--7748 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
7561 ATATTGAGTC
* * * *
7571 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
7598 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
7625 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
7653 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
7680 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
7707 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
7734 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
7749 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:7710 original size:82 final size:81
Alignment explanation
Indices: 7592--7747 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
7582 TGCTATATAA
* *
7592 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
7657 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
7674 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
7738 CACTTAGTGC
65 CACTTAGTGC
7748 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:15785 original size:27 final size:27
Alignment explanation
Indices: 15755--15932 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
15745 ATATTGAGTC
* * * *
15755 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
15782 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
15809 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
15837 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
15864 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
15891 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
15918 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
15933 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:15894 original size:82 final size:81
Alignment explanation
Indices: 15776--15931 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
15766 TGCTATATAA
* *
15776 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
15841 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
15858 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
15922 CACTTAGTGC
65 CACTTAGTGC
15932 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:23869 original size:26 final size:26
Alignment explanation
Indices: 23828--24003 Score: 124
Period size: 27 Copynumber: 6.5 Consensus size: 26
23818 GATATTAGTC
*
23828 CGCACACTCAGTGCTATATAATCAACGT
1 CGCACACT-AGTGCTACATAATCAAC-T
* *
23856 -GCACACTAGTGCTACGTAATCAAAT
1 CGCACACTAGTGCTACATAATCAACT
*
23881 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACAC-TAGTGCTACATAATCAACT
** ** *
23908 CGCACACTTAGTCGCCGCATGGTCAATT
1 CGCACAC-TAGT-GCTACATAATCAACT
**
23936 CGCACACTTAGTGC-ATCAT-ATCATTT
1 CGCACAC-TAGTGCTA-CATAATCAACT
* * *
23962 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACAC-TAGTGCTACATAATCAACT
23989 CGCACACTTAGTGCT
1 CGCACAC-TAGTGCT
24004 GTACAATTAA
Statistics
Matches: 125, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
25 1 0.01
26 42 0.34
27 59 0.47
28 23 0.18
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (26 bp):
CGCACACTAGTGCTACATAATCAACT
Found at i:23913 original size:53 final size:53
Alignment explanation
Indices: 23828--24003 Score: 187
Period size: 53 Copynumber: 3.3 Consensus size: 53
23818 GATATTAGTC
* * * * *
23828 CGCACACTCAGTGCTATATAATCAACGT-GCACAC-TAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACAT-ATCAAC-TCGCACACTTAGTGCAACATAGTCAAAT
** * *
23881 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTCGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATA-TCAACTCGCACACTTAGT-GCAACATAGTCAAAT
**
23936 CGCACACTTAGTGC-ATCATATCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATATCAACTCGCACACTTAGTGCAACATAGTCAAAT
23989 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
24004 GTACAATTAA
Statistics
Matches: 103, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
52 2 0.02
53 53 0.51
54 21 0.20
55 27 0.26
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (53 bp):
CGCACACTTAGTGCTACATATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Done.