Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold977
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: 29675
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Found at i:455 original size:53 final size:56
Alignment explanation
Indices: 388--509 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 56
378 ATATATTAGT
* * *
388 CCGCACACTCAGTGCTATATAATC-AACT-CACACTTAGTGCTATATAA-TCAAAC
1 CCGCACACTTAGTGCTACATAATCAAACTCCACACTTAGTGCTATACAATTCAAAC
* * *
441 TCGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTGTACAATTTAAAC
1 CCGCACACTTAGTGCTACATAATCAAACTC-CACACTTAGTGCTATACAATTCAAAC
498 CCGCACACTTAG
1 CCGCACACTTAG
510 CGCCAATTCA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
53 21 0.36
54 4 0.07
56 17 0.29
57 16 0.28
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.26
Consensus pattern (56 bp):
CCGCACACTTAGTGCTACATAATCAAACTCCACACTTAGTGCTATACAATTCAAAC
Found at i:456 original size:28 final size:28
Alignment explanation
Indices: 389--509 Score: 158
Period size: 28 Copynumber: 4.4 Consensus size: 28
379 TATATTAGTC
*
389 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
416 --CACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
442 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
470 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
499 CGCACACTTAG
1 CGCACACTTAG
510 CGCCAATTCA
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
25 20 0.24
26 4 0.05
28 43 0.52
29 16 0.19
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:8735 original size:28 final size:28
Alignment explanation
Indices: 8672--8794 Score: 167
Period size: 28 Copynumber: 4.4 Consensus size: 28
8662 ATATTAAGTC
*
8672 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
8699 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
8727 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
8755 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
8784 CGCACACTTAG
1 CGCACACTTAG
8795 CGCCAATCTC
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
27 21 0.25
28 48 0.56
29 16 0.19
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:12185 original size:56 final size:50
Alignment explanation
Indices: 12056--12193 Score: 143
Period size: 50 Copynumber: 2.6 Consensus size: 50
12046 ATCGGTGCCC
*
12056 ATGCCATGTCCTAGACATGGTCTTACAG-GGGACCTCTCATCTCAGTACCA
1 ATGCCATGTCCTAGACATGGTCTTAC-GTGGGACCTCTCATCTCAATACCA
* * *
12106 ACGCCATGTCCTAGACATAGTCTTACGTGGGACCTCTCATAACCTCAATAATGCGA
1 ATGCCATGTCCTAGACATGGTCTTACGTGGGACCTCTCAT---CTCAAT-A--CCA
* * *
12162 ATGCCATGTCCCAAACATGGTCTTACATGGGA
1 ATGCCATGTCCTAGACATGGTCTTACGTGGGA
12194 TCTCATTCCC
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
49 1 0.01
50 36 0.50
53 5 0.07
54 1 0.01
56 29 0.40
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (50 bp):
ATGCCATGTCCTAGACATGGTCTTACGTGGGACCTCTCATCTCAATACCA
Found at i:14215 original size:34 final size:34
Alignment explanation
Indices: 14139--14217 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
14129 ATCATAATGC
**
14139 CAGTAATCAGTAGGGCCTTTGCCCAATTTCAGTAA
1 CAGT-ATCAGTAGGGCCTTTGCCCAATAACAGTAA
* * *
14174 TAGTATCAGTAGGGCC-TTGGCCTATAACAGTAA
1 CAGTATCAGTAGGGCCTTTGCCCAATAACAGTAA
14207 CAGATATCAGT
1 CAG-TATCAGT
14218 CATGCAGTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
33 15 0.41
34 19 0.51
35 3 0.08
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (34 bp):
CAGTATCAGTAGGGCCTTTGCCCAATAACAGTAA
Found at i:14698 original size:27 final size:27
Alignment explanation
Indices: 14681--14827 Score: 213
Period size: 27 Copynumber: 5.4 Consensus size: 27
14671 TATAACAGTG
* *
14681 ATTTTACCCTATGGGGGTATTTTGATT
1 ATTTTACCCTATGGGGGTATTTCGATC
*
14708 ATTTTACCCTATGGAGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGATC
14735 ATTTTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGATC
* * *
14762 ATTTTATCCTATGGGGGTATTTCGGTT
1 ATTTTACCCTATGGGGGTATTTCGATC
* *
14789 ATTTTACACTATAGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGATC
*
14816 ATTTTATCCTAT
1 ATTTTACCCTAT
14828 TTTGGGGTCT
Statistics
Matches: 106, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 106 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGATC
Found at i:15095 original size:19 final size:19
Alignment explanation
Indices: 15059--15114 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
15049 GTGTAAGGCC
*
15059 CACGAGCCCATTT-AGCCCA
1 CACG-GCCCATTTCGGCCCA
15078 CACGGCCCATTTCGGCCCA
1 CACGGCCCATTTCGGCCCA
*
15097 -ACGTGGCCCATTACGGCC
1 CAC--GGCCCATTTCGGCC
15115 TAAGCCCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 10 0.31
19 9 0.28
20 13 0.41
ACGTcount: A:0.20, C:0.43, G:0.21, T:0.16
Consensus pattern (19 bp):
CACGGCCCATTTCGGCCCA
Found at i:18210 original size:27 final size:27
Alignment explanation
Indices: 18180--18237 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
18170 TCATCTCCTA
*
18180 GGGGCATAAT-AGTGATTTTACTCTATG
1 GGGGCAT-ATCAGTCATTTTACTCTATG
* * *
18207 GGGGTATTTCGGTCATTTTACTCTATG
1 GGGGCATATCAGTCATTTTACTCTATG
18234 GGGG
1 GGGG
18238 TTTTTTGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.19, C:0.12, G:0.31, T:0.38
Consensus pattern (27 bp):
GGGGCATATCAGTCATTTTACTCTATG
Found at i:18238 original size:27 final size:27
Alignment explanation
Indices: 18194--18307 Score: 131
Period size: 27 Copynumber: 4.2 Consensus size: 27
18184 CATAATAGTG
18194 ATTTTACTCTATGGGGGTATTTCGGTC
1 ATTTTACTCTATGGGGGTATTTCGGTC
* * *
18221 ATTTTACTCTATGGGGGTTTTTTGGTT
1 ATTTTACTCTATGGGGGTATTTCGGTC
* *
18248 ATTTTA-TCCTATGGGGATATTTTGGTC
1 ATTTTACT-CTATGGGGGTATTTCGGTC
* ** *
18275 ATTTTACCCTATAAGGGTATTTCGATC
1 ATTTTACTCTATGGGGGTATTTCGGTC
18302 ATTTTA
1 ATTTTA
18308 TCCTATTTTG
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
26 1 0.01
27 72 0.99
ACGTcount: A:0.18, C:0.12, G:0.21, T:0.48
Consensus pattern (27 bp):
ATTTTACTCTATGGGGGTATTTCGGTC
Found at i:18590 original size:20 final size:20
Alignment explanation
Indices: 18565--18602 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18555 TTAGCCCACA
*
18565 TGGCCCATTTCGGCCTAACG
1 TGGCCCATTACGGCCTAACG
18585 TGGCCCATTACGGCCTAA
1 TGGCCCATTACGGCCTAA
18603 GCCCATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.34, G:0.24, T:0.24
Consensus pattern (20 bp):
TGGCCCATTACGGCCTAACG
Found at i:21740 original size:27 final size:27
Alignment explanation
Indices: 21710--21887 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
21700 ATATTGAGTC
* * * *
21710 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
21737 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
21764 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
21792 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
21819 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
21846 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
21873 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
21888 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:21849 original size:82 final size:81
Alignment explanation
Indices: 21731--21886 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
21721 TGCTATATAA
* *
21731 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
21796 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
21813 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
21877 CACTTAGTGC
65 CACTTAGTGC
21887 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
Done.