Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1964
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: 9586
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Found at i:841 original size:13 final size:13
Alignment explanation
Indices: 823--850 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
813 ATACAAAGAT
823 CAATGTATCGATA
1 CAATGTATCGATA
836 CAATGTATCGATA
1 CAATGTATCGATA
849 CA
1 CA
851 TTGAGTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:847 original size:33 final size:33
Alignment explanation
Indices: 805--870 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
795 AAATTCCCAG
805 ATGTATCGATACAAAGA-TCAATGTATCGATACA
1 ATGTATCGATACAAAGAGT-AATGTATCGATACA
**
838 ATGTATCGATACATTGAGTAATGTATCGATACA
1 ATGTATCGATACAAAGAGTAATGTATCGATACA
871 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGAGTAATGTATCGATACA
Found at i:925 original size:19 final size:19
Alignment explanation
Indices: 901--957 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
891 TAGTATACAT
901 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
920 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
933 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
952 TGTATC
1 TGTATC
958 AATTCAGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.28
14 1 0.03
16 6 0.19
18 1 0.03
19 15 0.47
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:931 original size:32 final size:32
Alignment explanation
Indices: 895--957 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
885 GCTTTGTAGT
895 ATACATTGTATCGATACAACACTTATGTATCG
1 ATACATTGTATCGATACAACACTTATGTATCG
927 ATACATTGTATCGATACAACACTTATGTATC
1 ATACATTGTATCGATACAACACTTATGTATC
958 AATTCAGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (32 bp):
ATACATTGTATCGATACAACACTTATGTATCG
Found at i:938 original size:13 final size:13
Alignment explanation
Indices: 920--944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
910 ACAACACTTA
920 TGTATCGATACAT
1 TGTATCGATACAT
933 TGTATCGATACA
1 TGTATCGATACA
945 ACACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1815 original size:10 final size:10
Alignment explanation
Indices: 1800--1863 Score: 62
Period size: 10 Copynumber: 6.5 Consensus size: 10
1790 CTTTGCACTC
1800 TTTTTTTGTG
1 TTTTTTTGTG
*
1810 TTTTTTTGTT
1 TTTTTTTGTG
*
1820 TTTGTTATTTTG
1 TTT-TT-TTGTG
*
1832 TTTTTTTTTG
1 TTTTTTTGTG
1842 -TTTTTT-T-
1 TTTTTTTGTG
1849 TTTTTTTGTG
1 TTTTTTTGTG
1859 TTTTT
1 TTTTT
1864 ACTTATGAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
8 7 0.15
9 7 0.15
10 22 0.48
11 4 0.09
12 6 0.13
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (10 bp):
TTTTTTTGTG
Found at i:1819 original size:8 final size:8
Alignment explanation
Indices: 1801--1863 Score: 67
Period size: 8 Copynumber: 7.8 Consensus size: 8
1791 TTTGCACTCT
1801 TTTTTTGTG
1 TTTTTT-TG
1810 TTTTTTTG
1 TTTTTTTG
*
1818 TTTTTGTTA
1 TTTTT-TTG
*
1827 TTTTGTT-
1 TTTTTTTG
1834 TTTTTTTG
1 TTTTTTTG
1842 TTTTTTT-
1 TTTTTTTG
1849 TTTTTTTG
1 TTTTTTTG
1857 TGTTTTT
1 T-TTTTT
1864 ACTTATGAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
7 13 0.28
8 17 0.36
9 17 0.36
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.86
Consensus pattern (8 bp):
TTTTTTTG
Found at i:1830 original size:14 final size:14
Alignment explanation
Indices: 1803--1836 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1793 TGCACTCTTT
*
1803 TTTTGTGTTTTTTTG
1 TTTT-TGTTATTTTG
1818 TTTTTGTTATTTTG
1 TTTTTGTTATTTTG
1832 TTTTT
1 TTTTT
1837 TTTTGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (14 bp):
TTTTTGTTATTTTG
Found at i:1854 original size:24 final size:25
Alignment explanation
Indices: 1800--1863 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
1790 CTTTGCACTC
1800 TTTTTTTGTGTTTTTTTG-TTTTTG
1 TTTTTTTGTGTTTTTTTGTTTTTTG
* * *
1824 TTATTTTGTTTTTTTTTGTTTTTTT
1 TTTTTTTGTGTTTTTTTGTTTTTTG
1849 TTTTTTTGTGTTTTT
1 TTTTTTTGTGTTTTT
1864 ACTTATGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 16 0.47
25 18 0.53
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (25 bp):
TTTTTTTGTGTTTTTTTGTTTTTTG
Found at i:6644 original size:27 final size:29
Alignment explanation
Indices: 6610--6681 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
6600 AGTTGAAAAT
*
6610 GGGTTGGAGTGTCCCCTC-G-GAGGAATG
1 GGGTTGGAGTGTCCCCTCAGAGAGGAATA
6637 GGGTTGGAGTGTCCCCTCAGAGAGGAATA
1 GGGTTGGAGTGTCCCCTCAGAGAGGAATA
*
6666 GGGTTAGAGTGTCCCC
1 GGGTTGGAGTGTCCCC
6682 GATGAATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 18 0.44
28 1 0.02
29 22 0.54
ACGTcount: A:0.18, C:0.19, G:0.40, T:0.22
Consensus pattern (29 bp):
GGGTTGGAGTGTCCCCTCAGAGAGGAATA
Found at i:7879 original size:32 final size:33
Alignment explanation
Indices: 7838--7901 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
7828 TAGCCAAACT
*
7838 TGTATCGATACACAAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
*
7870 TGTATCGATATACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
7902 TTGGTTTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Done.