Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6124.1
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: 13849
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:1503 original size:11 final size:12
Alignment explanation
Indices: 1471--1501 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1461 TTGAGAGAAC
1471 TTGAAAAAGCCT
1 TTGAAAAAGCCT
1483 TTGAAAAAGCCT
1 TTGAAAAAGCCT
1495 TTGAAAA
1 TTGAAAA
1502 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:6187 original size:13 final size:13
Alignment explanation
Indices: 6169--6194 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6159 ACCTGAAAGC
6169 AATTTAATTCATA
1 AATTTAATTCATA
6182 AATTTAATTCATA
1 AATTTAATTCATA
6195 TTAGGACACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:6609 original size:20 final size:21
Alignment explanation
Indices: 6584--6622 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
6574 TCAAACAAGC
6584 AAATGAGCTCAA-TGAGCTGG
1 AAATGAGCTCAATTGAGCTGG
*
6604 AAATGAGCTGAATTGAGCT
1 AAATGAGCTCAATTGAGCT
6623 CAACGAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATGAGCTCAATTGAGCTGG
Found at i:7897 original size:17 final size:17
Alignment explanation
Indices: 7877--7930 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
7867 CTTCACTCGT
7877 TTTCTTTTCAAACTCTC
1 TTTCTTTTCAAACTCTC
*
7894 TTTCTTTTTCAATCTCAT-
1 TTTC-TTTTCAAACTC-TC
7912 TTTGCTTTTC--ACTCTC
1 TTT-CTTTTCAAACTCTC
7928 TTT
1 TTT
7931 TGTTTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 1 0.03
16 6 0.19
17 4 0.13
18 18 0.58
19 2 0.06
ACGTcount: A:0.13, C:0.26, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTCTTTTCAAACTCTC
Found at i:7920 original size:18 final size:18
Alignment explanation
Indices: 7899--7950 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
7889 CTCTCTTTCT
7899 TTTTCAATCTCATTTTGC
1 TTTTCAATCTCATTTTGC
* *
7917 TTTTCACTCTC-TTTTGT
1 TTTTCAATCTCATTTTGC
*
7934 TTTTGAAATCTCATTTT
1 TTTT-CAATCTCATTTT
7951 CATATTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 9 0.32
18 15 0.54
19 4 0.14
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (18 bp):
TTTTCAATCTCATTTTGC
Found at i:7964 original size:6 final size:6
Alignment explanation
Indices: 7955--8053 Score: 74
Period size: 6 Copynumber: 16.0 Consensus size: 6
7945 CATTTTCATA
* * * **
7955 TTTTTC TTTTTC AATTTTC TTTTCTTC ATTTTC TTTTTC TCTCAC TTTTTC
1 TTTTTC TTTTTC -TTTTTC -TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC
* * **
8006 GTTTTC TTTTTC TTTTT- TGTTTTC TTTTTC TTCTTC ACTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTTC
8054 GAATTCATTA
Statistics
Matches: 70, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
5 1 0.01
6 56 0.80
7 10 0.14
8 3 0.04
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTTTC
Found at i:9535 original size:13 final size:13
Alignment explanation
Indices: 9517--9541 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9507 GTATTGATCA
9517 TGTGTTCACACCT
1 TGTGTTCACACCT
9530 TGTGTTCACACC
1 TGTGTTCACACC
9542 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:10690 original size:8 final size:8
Alignment explanation
Indices: 10679--10712 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
10669 TTTTTACTTT
10679 TTTTTTTA
1 TTTTTTTA
10687 TTTTTTTCGA
1 TTTTTTT--A
10697 TTTTTTTA
1 TTTTTTTA
10705 TTTTTTTA
1 TTTTTTTA
10713 ATCACTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (8 bp):
TTTTTTTA
Found at i:10840 original size:42 final size:42
Alignment explanation
Indices: 10792--10875 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
10782 GCGATCTCGG
* **
10792 TTTAGTAGTTGAGTCCGAGTCGTTT-GATTCCCGATCGTAAAC
1 TTTAGTAGTCGAACCCGAGTCGTTTAG-TTCCCGATCGTAAAC
*
10834 TTTAGTAGTCGAACCCGAGTCGTTTAGTTCTCGATCGTAAAC
1 TTTAGTAGTCGAACCCGAGTCGTTTAGTTCCCGATCGTAAAC
10876 GAAGAAGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 36 0.97
43 1 0.03
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
TTTAGTAGTCGAACCCGAGTCGTTTAGTTCCCGATCGTAAAC
Found at i:11080 original size:21 final size:21
Alignment explanation
Indices: 11054--11116 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
11044 TTGGTATTTG
11054 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
11075 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
11096 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
11117 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:11332 original size:46 final size:48
Alignment explanation
Indices: 11265--11357 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 48
11255 GTGAACGCCA
*
11265 CACTCGGGTTTAAGGAGTGATAAGTTCG-GA-AAAGACTCGGAAAGAT
1 CACTCGGGTTTAAGGAGTGATAAGTTCGAAAGAAAGACTCGGAAAGAT
*
11311 CACTCGGGTTTAGGGAGTGATAAGTTCGAAAGAAAGACTCGGAAAGA
1 CACTCGGGTTTAAGGAGTGATAAGTTCGAAAGAAAGACTCGGAAAGA
11358 CGCCACTAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
46 27 0.63
47 1 0.02
48 15 0.35
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.20
Consensus pattern (48 bp):
CACTCGGGTTTAAGGAGTGATAAGTTCGAAAGAAAGACTCGGAAAGAT
Found at i:12484 original size:22 final size:22
Alignment explanation
Indices: 12454--12497 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
12444 TTTGGTATTT
12454 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
12476 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
12498 TGATTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Done.