Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2893
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: 23937
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:6978 original size:43 final size:45
Alignment explanation
Indices: 6897--7002 Score: 119
Period size: 43 Copynumber: 2.4 Consensus size: 45
6887 AGAACAGAAA
** *
6897 TGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGATAGGAT
1 TGAGCCATGTAAGTCCATATTA-AAATATGGCAATGGAGACAGGAT
* *
6943 TGAGCCATG-AAGTCCATATT-ATATATGGCAATGGAGACAGGAA
1 TGAGCCATGTAAGTCCATATTAAAATATGGCAATGGAGACAGGAT
**
6986 T-ATTCATGTAAGTCCAT
1 TGAGCCATGTAAGTCCAT
7003 GTCAAAGACA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
42 5 0.10
43 27 0.52
45 11 0.21
46 9 0.17
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (45 bp):
TGAGCCATGTAAGTCCATATTAAAATATGGCAATGGAGACAGGAT
Found at i:9696 original size:53 final size:53
Alignment explanation
Indices: 9615--9765 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
9605 CTTACACGGT
* *
9615 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
9670 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
9723 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
9766 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:17165 original size:53 final size:53
Alignment explanation
Indices: 17084--17234 Score: 196
Period size: 53 Copynumber: 2.8 Consensus size: 53
17074 CTTACACGGT
* *
17084 TCACATATCATACCGAAGCCATATCCCAGAC-ATGATCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGATCTTATACGGAATCACATTA
* *
17139 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGATCTTATACGGAATCACATTA
** * *
17192 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGATCTTATACGG
17235 GCACACTTAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 80 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGATCTTATACGGAATCACATTA
Found at i:20275 original size:50 final size:50
Alignment explanation
Indices: 20163--20346 Score: 255
Period size: 50 Copynumber: 3.7 Consensus size: 50
20153 TCTAGACGCA
* *
20163 TAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAATTATCTGGTACACG
** *
20212 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAATTATCTGGTACACG
* * * *
20262 TAGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCT-AA-TTATCTGGTACACG
20313 TAGTAGCCTGCACTTAGTACTACACACGTGACCT
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCT
20347 CACAATAGAT
Statistics
Matches: 118, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
49 32 0.27
50 46 0.39
51 39 0.33
52 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTAATTATCTGGTACACG
Found at i:20323 original size:101 final size:99
Alignment explanation
Indices: 20163--20346 Score: 287
Period size: 101 Copynumber: 1.8 Consensus size: 99
20153 TCTAGACGCA
* * *
20163 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCGGGTACACATAGTAGCCTGCACTTA
20228 GTACTACACACGTGACCTAACCATCTGATACACG
66 GTACTACACACGTGACCTAACCATCTGATACACG
* ** *
20262 TAGTAGCCTGCACTTAGTACTACACACGTGATTGAAGTTATCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCGGGTACACATAGTAGCCTGCACT
20327 TAGTACTACACACGTGACCT
64 TAGTACTACACACGTGACCT
20347 CACAATAGAT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
99 29 0.38
100 2 0.03
101 45 0.59
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCGGGTACACATAGTAGCCTGCACTTA
GTACTACACACGTGACCTAACCATCTGATACACG
Found at i:20510 original size:13 final size:13
Alignment explanation
Indices: 20489--20528 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
20479 GCCACATTTC
*
20489 ATATGATAATAAA
1 ATATAATAATAAA
20502 ATATAATAATAAA
1 ATATAATAATAAA
20515 ATAATAA-AATAAA
1 AT-ATAATAATAAA
20528 A
1 A
20529 GAATCGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 21 0.84
14 4 0.16
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (13 bp):
ATATAATAATAAA
Found at i:22552 original size:30 final size:24
Alignment explanation
Indices: 22483--22532 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
22473 ATAAAATTTC
22483 AATTCAAAATAAACAAGGAAAAAT
1 AATTCAAAATAAACAAGGAAAAAT
22507 AATTCAAAATAAACAAGGAAAAAT
1 AATTCAAAATAAACAAGGAAAAAT
22531 AA
1 AA
22533 ATCATCTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (24 bp):
AATTCAAAATAAACAAGGAAAAAT
Found at i:23748 original size:30 final size:30
Alignment explanation
Indices: 23714--23776 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
23704 AATTATTTTA
23714 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
23744 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
23774 TTG
1 TTG
23777 ATTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Done.