Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold747
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: 29227
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Found at i:1632 original size:12 final size:13
Alignment explanation
Indices: 1617--1645 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1607 AGTTTTTTAT
1617 TTTATTTTAT-TA
1 TTTATTTTATATA
1629 TTTATTTTATATA
1 TTTATTTTATATA
1642 TTTA
1 TTTA
1646 CATGTCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTTATATA
Found at i:16974 original size:22 final size:22
Alignment explanation
Indices: 16945--17006 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
16935 TAAAAAAGTC
*
16945 ATAA-TTTTAATTTATATT-AA
1 ATAATTTTTAATTTTTATTAAA
16965 ATAAATTTTTAATTTTTATTAAA
1 AT-AATTTTTAATTTTTATTAAA
16988 ATAATTTTTAATTTTTATT
1 ATAATTTTTAATTTTTATT
17007 TATATTTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
20 2 0.05
21 2 0.05
22 30 0.79
23 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATAATTTTTAATTTTTATTAAA
Found at i:16978 original size:28 final size:27
Alignment explanation
Indices: 16946--17030 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 27
16936 AAAAAAGTCA
16946 TAATTTTAATTTATATTAAATAAATTTT
1 TAATTTT-ATTTATATTAAATAAATTTT
*
16974 TAA--TT-TTTAT-TAAAAT-AATTTT
1 TAATTTTATTTATATTAAATAAATTTT
16996 TAATTTTTATTTATATTTAAATAAATTTT
1 TAA-TTTTATTTATA-TTAAATAAATTTT
17025 TAATTT
1 TAATTT
17031 AGATATAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
22 9 0.19
23 5 0.10
24 5 0.10
25 2 0.04
26 7 0.15
28 11 0.23
29 9 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TAATTTTATTTATATTAAATAAATTTT
Found at i:17000 original size:29 final size:29
Alignment explanation
Indices: 16968--17030 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
16958 ATATTAAATA
*
16968 AATTTTTAATTTTTATTAAAAT-AATTTTT
1 AATTTTT-ATTTATATTAAAATAAATTTTT
*
16997 AATTTTTATTTATATTTAAATAAATTTTT
1 AATTTTTATTTATATTAAAATAAATTTTT
17026 AATTT
1 AATTT
17031 AGATATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 12 0.39
29 19 0.61
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
AATTTTTATTTATATTAAAATAAATTTTT
Found at i:17039 original size:23 final size:22
Alignment explanation
Indices: 16997--17039 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
16987 AATAATTTTT
* *
16997 AATTTTTATTTATATTTAAATA
1 AATTTTTATTTAGATATAAATA
17019 AATTTTTAATTTAGATATAAA
1 AATTTTT-ATTTAGATATAAA
17040 AATATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
AATTTTTATTTAGATATAAATA
Found at i:17062 original size:18 final size:17
Alignment explanation
Indices: 17007--17065 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
16997 AATTTTTATT
*
17007 TATATTTAAAT-AAATT
1 TATATTTAAATAAAATA
*
17023 TTTAATTTAGATATAAAA-A
1 TAT-ATTTA-A-ATAAAATA
17042 TATATTTAAATAAAATGA
1 TATATTTAAATAAAAT-A
17060 TATATT
1 TATATT
17066 AAAAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
16 8 0.24
17 6 0.18
18 13 0.38
19 4 0.12
20 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TATATTTAAATAAAATA
Found at i:17118 original size:21 final size:22
Alignment explanation
Indices: 17077--17118 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17067 AAAATATTTT
*
17077 AATATTTTGAGTATAAAAATAA
1 AATATTTTGAGAATAAAAATAA
*
17099 AATATTTTGA-AATTAAAATA
1 AATATTTTGAGAATAAAAATA
17119 TTGAGAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (22 bp):
AATATTTTGAGAATAAAAATAA
Found at i:25431 original size:27 final size:28
Alignment explanation
Indices: 25376--25436 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
25366 TTCCCTCTAT
* *
25376 TAATTTAATTGCTTTTTTCACATTATTC
1 TAATTTAATTGATTTTATCACATTATTC
* *
25404 TAATTTAA-TGATTTTATCATATTTTTC
1 TAATTTAATTGATTTTATCACATTATTC
*
25431 TCATTT
1 TAATTT
25437 CACAAACCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.26, C:0.11, G:0.03, T:0.59
Consensus pattern (28 bp):
TAATTTAATTGATTTTATCACATTATTC
Done.