Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2523
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: 24076
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Found at i:4181 original size:40 final size:40
Alignment explanation
Indices: 4137--4323 Score: 293
Period size: 40 Copynumber: 4.7 Consensus size: 40
4127 CCAACCCAAT
* * ** *
4137 TGCCTTCGGGATTTAGCCCGGATGTAACAACCAGCACAAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
* * *
4177 TGCCTTCGGAACTTAACCCGGGAATAGCAACCAGCACGAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
4217 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
4257 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
1 TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
*
4297 TGCCTTCGGGACTTAACCCGGATATAA
1 TGCCTTCGGGACTTAACCCGGAAATAA
4324 TCCTCAATTG
Statistics
Matches: 135, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 135 1.00
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAA
Found at i:7426 original size:31 final size:32
Alignment explanation
Indices: 7385--7445 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
7375 CCTTTACATA
*
7385 TTTCATATTTCATAACACTGGGCC-AAGCCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCCT
**
7416 TTTCAAATTTCATATTACTGGGCCGAAGCC
1 TTTCAAATTTCATAACACTGGGCCGAAGCC
7446 TTTACTGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (32 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCCT
Found at i:7693 original size:24 final size:24
Alignment explanation
Indices: 7642--7759 Score: 161
Period size: 23 Copynumber: 5.0 Consensus size: 24
7632 GCTTTATCAT
*
7642 ATAACTGGAGGC-TTAGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
7667 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
7691 ATAATTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
7714 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
7737 ATAACTAGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
7760 TCACTTCCTC
Statistics
Matches: 85, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 44 0.52
24 29 0.34
25 12 0.14
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:7835 original size:20 final size:20
Alignment explanation
Indices: 7810--7848 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
7800 TATGAATACA
7810 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
7830 TCATGTGCATATCATACAT
1 TCATGTGCATATCATACAT
7849 ACCATGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATG
Found at i:7854 original size:20 final size:20
Alignment explanation
Indices: 7811--7855 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
7801 ATGAATACAT
**
7811 CATGTGCATATCATACATGT
1 CATGTGCATATCATACATAC
7831 CATGTGCATATCATACATAC
1 CATGTGCATATCATACATAC
7851 CATGT
1 CATGT
7856 TTATCAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTGCATATCATACATAC
Found at i:10231 original size:28 final size:29
Alignment explanation
Indices: 10199--10263 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
10189 ATACATGTGA
10199 CATGT-TATAAGATGA-TATAGCTTCGGGC
1 CATGTATATAAGATGAGT-TAGCTTCGGGC
** *
10227 CATGTATATTGGATGAGTTGGCTTCGGGC
1 CATGTATATAAGATGAGTTAGCTTCGGGC
10256 CATG-ATAT
1 CATGTATAT
10264 TAGCACTTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 9 0.28
29 22 0.69
30 1 0.03
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.34
Consensus pattern (29 bp):
CATGTATATAAGATGAGTTAGCTTCGGGC
Found at i:10852 original size:21 final size:20
Alignment explanation
Indices: 10827--10879 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 20
10817 TTGGCTTGGA
10827 TGTTAATATTAATATGTGCT
1 TGTTAATATTAATATGTGCT
*
10847 TAGTTATTA-TAA-ATG-GCT
1 T-GTTAATATTAATATGTGCT
10865 TGTTAAT-TT-ATATGT
1 TGTTAATATTAATATGT
10880 TTTGATTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
16 1 0.04
17 9 0.33
18 4 0.15
19 3 0.11
20 4 0.15
21 6 0.22
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.51
Consensus pattern (20 bp):
TGTTAATATTAATATGTGCT
Found at i:16315 original size:22 final size:22
Alignment explanation
Indices: 16287--16329 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
16277 TTTAGCAACA
16287 ATGGATATGAGTGAATCATGCG
1 ATGGATATGAGTGAATCATGCG
16309 ATGGATATGAGTGAATCATGC
1 ATGGATATGAGTGAATCATGC
16330 AAATCATCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (22 bp):
ATGGATATGAGTGAATCATGCG
Found at i:17719 original size:27 final size:27
Alignment explanation
Indices: 17702--17879 Score: 133
Period size: 27 Copynumber: 6.6 Consensus size: 27
17692 ATATTAAGTC
17702 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *
17729 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
* * *
17757 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTCAGTGCTATATAATCAACT
* *** ** *
17784 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTCAGTGCTATATAATCAACT
* * **
17811 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTCAGTGCTAT-ATAATCAACT
* * * * *
17838 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTCAGTGCTATATAATCAACT
*
17865 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
17880 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 104 0.79
28 27 0.21
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:17841 original size:54 final size:54
Alignment explanation
Indices: 17702--17878 Score: 214
Period size: 54 Copynumber: 3.3 Consensus size: 54
17692 ATATTAAGTC
* * *
17702 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAA-T
* ** * *
17757 CGCACACTTAGTGC-TACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* **
17811 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
17865 CGCACACTTAGTGC
1 CGCACACTTAGTGC
17879 TGTACAATTT
Statistics
Matches: 105, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
53 1 0.01
54 60 0.57
55 44 0.42
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:17868 original size:81 final size:82
Alignment explanation
Indices: 17723--17878 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
17713 TGCTATATAA
* *
17723 TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
17788 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
17805 TCAATTCGCACACTTAGTGC-ATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
17868 ACACTTAGTGC
65 ACACTTAGTGC
17879 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 42 0.63
82 25 0.37
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Done.