Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold950
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: 26288
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Found at i:4146 original size:22 final size:21
Alignment explanation
Indices: 4102--4143 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4092 TAAAAAGTTT
4102 TATATAAAATTAATTATAAAA
1 TATATAAAATTAATTATAAAA
4123 TATATAAATATTAATT-TAAAA
1 TATATAAA-ATTAATTATAAAA
4144 ATAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATATAAAATTAATTATAAAA
Found at i:5864 original size:2 final size:2
Alignment explanation
Indices: 5857--5881 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5847 AGTATAAGTT
5857 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5882 TCTCCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7233 original size:21 final size:21
Alignment explanation
Indices: 7207--7247 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
7197 TGTGCACTTA
7207 AGGAATGAATGAAAATTGTTT
1 AGGAATGAATGAAAATTGTTT
7228 AGGAATGAATGAAAATTGTT
1 AGGAATGAATGAAAATTGTT
7248 CTTAATTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (21 bp):
AGGAATGAATGAAAATTGTTT
Found at i:11658 original size:50 final size:50
Alignment explanation
Indices: 11583--11683 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
11573 TCGTTGAATT
11583 TGTAGTTGCTTCCTTAACTGATATTTTAAAGCCTTGAGAACTGAAAGATA
1 TGTAGTTGCTTCCTTAACTGATATTTTAAAGCCTTGAGAACTGAAAGATA
11633 TGTAGTTGCTTCCTTAACTGATATTTTAAAGCCTTGAGAACTGAAAGATA
1 TGTAGTTGCTTCCTTAACTGATATTTTAAAGCCTTGAGAACTGAAAGATA
11683 T
1 T
11684 AACTGTATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (50 bp):
TGTAGTTGCTTCCTTAACTGATATTTTAAAGCCTTGAGAACTGAAAGATA
Found at i:18181 original size:2 final size:2
Alignment explanation
Indices: 18174--18225 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
18164 TCACACTAAC
* *
18174 AT AT AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18216 AT AT AT AT AT
1 AT AT AT AT AT
18226 GAGTACAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:18833 original size:14 final size:14
Alignment explanation
Indices: 18814--18857 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
18804 ATTATATATT
18814 TATATAAATTTTAA
1 TATATAAATTTTAA
**
18828 TATAT-AATTTATTT
1 TATATAAATTT-TAA
18842 TATATAAATTTTAA
1 TATATAAATTTTAA
18856 TA
1 TA
18858 AATTTATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 5 0.21
14 14 0.58
15 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:18871 original size:28 final size:30
Alignment explanation
Indices: 18803--18871 Score: 101
Period size: 28 Copynumber: 2.4 Consensus size: 30
18793 ATTTAAAAAA
18803 AATTATATATTTATATAAATTTTAATATAT
1 AATTATATATTTATATAAATTTTAATATAT
18833 AATT-TAT-TTTATATAAATTTTAATA-A-
1 AATTATATATTTATATAAATTTTAATATAT
*
18859 ATTTATATATTTA
1 AATTATATATTTA
18872 ATATTTAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
26 3 0.08
27 4 0.11
28 22 0.61
29 3 0.08
30 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
AATTATATATTTATATAAATTTTAATATAT
Found at i:18904 original size:32 final size:33
Alignment explanation
Indices: 18861--18924 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
18851 TTTAATAAAT
18861 TTATATATTTAATATT-TA-ATATTATATTTTAA
1 TTATATATTTAATATTATATA-ATTATATTTTAA
*
18893 TTATATTTTTAATATTATATAATTATATTTTA
1 TTATATATTTAATATTATATAATTATATTTTA
18925 TTTAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.52
33 13 0.45
34 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (33 bp):
TTATATATTTAATATTATATAATTATATTTTAA
Found at i:18907 original size:20 final size:22
Alignment explanation
Indices: 18861--18923 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 22
18851 TTTAATAAAT
* *
18861 TTATATATTTA-ATATTTAATA
1 TTATATAATTATATTTTTAATA
18882 TTATATTTTAATTATATTTTTAATA
1 TTATA---TAATTATATTTTTAATA
18907 TTATATAATTATATTTT
1 TTATATAATTATATTTT
18924 ATTTAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 5 0.14
22 12 0.33
24 5 0.14
25 14 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATATAATTATATTTTTAATA
Found at i:18911 original size:14 final size:14
Alignment explanation
Indices: 18875--18912 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
18865 ATATTTAATA
18875 TTTAATATTATA-T
1 TTTAATATTATATT
18888 TTT-A-ATTATATT
1 TTTAATATTATATT
18900 TTTAATATTATAT
1 TTTAATATTATAT
18913 AATTATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 6 0.27
12 5 0.23
13 4 0.18
14 7 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTAATATTATATT
Found at i:18928 original size:25 final size:26
Alignment explanation
Indices: 18864--18935 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 26
18854 AATAAATTTA
18864 TATATTTAATATTTAATATTATATTTTAAT
1 TATATTT--TATTTAATATTATA--TTAAT
18894 TATA--TT-TTTAATATTATA-TAAT
1 TATATTTTATTTAATATTATATTAAT
*
18916 TATATTTTATTTAAAATTAT
1 TATATTTTATTTAATATTAT
18936 CGTATCTAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
22 8 0.21
24 2 0.05
25 22 0.58
26 1 0.03
28 1 0.03
30 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TATATTTTATTTAATATTATATTAAT
Found at i:19177 original size:17 final size:17
Alignment explanation
Indices: 19132--19205 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 17
19122 ATTTATTAAT
*
19132 TTTATATTAAAAATTATA
1 TTTATATTAAATA-TATA
*
19150 TTATTAAATTAAATATATA
1 -T-TTATATTAAATATATA
* *
19169 TTTTTATTAATTATA-A
1 TTTATATTAAATATATA
* *
19185 ATTATATTAAATATTTA
1 TTTATATTAAATATATA
19202 TTTA
1 TTTA
19206 ATTTATTAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
16 12 0.28
17 15 0.35
18 1 0.02
19 5 0.12
20 10 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTATATTAAATATATA
Found at i:19177 original size:22 final size:22
Alignment explanation
Indices: 19150--19192 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
19140 AAAAATTATA
19150 TTATTAAAT-TAAATATATATTT
1 TTATTAAATATAAAT-TATATTT
*
19172 TTATTAATTATAAATTATATT
1 TTATTAAATATAAATTATATT
19193 AAATATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTATTAAATATAAATTATATTT
Found at i:19201 original size:27 final size:27
Alignment explanation
Indices: 19107--19208 Score: 68
Period size: 28 Copynumber: 3.8 Consensus size: 27
19097 TTTGTAATAA
* * **
19107 TATATTTAAATATTGATTTATTA-ATTT
1 TATA-TTAAATATTTATTAATTATAAAT
*
19134 TATATTAAA-AATTA-T-ATTATTAAAT
1 TATATTAAATATTTATTAATTA-TAAAT
* * *
19159 TAAATATATATTTTTATTAATTATAAAT
1 TATAT-TAAATATTTATTAATTATAAAT
19187 TATATTAAATATTTATTTAATT
1 TATATTAAATATTTA-TTAATT
19209 TATTAAATAA
Statistics
Matches: 57, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
23 4 0.07
24 1 0.02
25 9 0.16
26 8 0.14
27 15 0.26
28 16 0.28
29 4 0.07
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
TATATTAAATATTTATTAATTATAAAT
Found at i:19688 original size:1 final size:1
Alignment explanation
Indices: 19648--19678 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
19638 GCAAGTCAAG
19648 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
19679 CACACTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:21090 original size:79 final size:80
Alignment explanation
Indices: 20935--21095 Score: 297
Period size: 79 Copynumber: 2.0 Consensus size: 80
20925 CTTACGTGTT
20935 TTCTGCATGCCTTTGCTCTTTACTTTTTTTTTTCTTTTTTTTTTTTTAGGAATTAGTCTCGTGAA
1 TTCTGCATGCCTTTGCTCTTTACTTTTTTTTTTCTTTTTTTTTTTTTAGGAATTAGTCTCGTGAA
*
21000 TGATATTTTAGGTCA
66 TGATATATTAGGTCA
*
21015 TTCTGCATGCCTTTGCTCTTTACTTTTTTTTTTC-TTTTTTTTTTTTGGGAATTAGTCTCGTGAA
1 TTCTGCATGCCTTTGCTCTTTACTTTTTTTTTTCTTTTTTTTTTTTTAGGAATTAGTCTCGTGAA
21079 TGATATATTAGGTCA
66 TGATATATTAGGTCA
21094 TT
1 TT
21096 ACAGGGTTCT
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
79 45 0.57
80 34 0.43
ACGTcount: A:0.15, C:0.14, G:0.14, T:0.57
Consensus pattern (80 bp):
TTCTGCATGCCTTTGCTCTTTACTTTTTTTTTTCTTTTTTTTTTTTTAGGAATTAGTCTCGTGAA
TGATATATTAGGTCA
Found at i:25125 original size:1 final size:1
Alignment explanation
Indices: 25119--25165 Score: 94
Period size: 1 Copynumber: 47.0 Consensus size: 1
25109 GTTTCACCCT
25119 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
25166 GCCTTTTTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Done.