Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1634
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, 875
Length: 1459
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.31
Found at i:85 original size:7 final size:7
Alignment explanation
Indices: 71--225 Score: 62
Period size: 7 Copynumber: 21.1 Consensus size: 7
61 AAAAAGAAAT
71 CCTAAAC
1 CCTAAAC
*
78 CTTAAAC
1 CCTAAAC
85 CCTAAAC
1 CCTAAAC
92 CCTAAAC
1 CCTAAAC
*
99 TC-AATAC
1 CCTAA-AC
*
106 CATAAAC
1 CCTAAAC
113 ACTCGT-AAC
1 -C-C-TAAAC
*
122 CTTAAAAC
1 CCT-AAAC
130 CCATAAAC
1 CC-TAAAC
* *
138 CATAAAA
1 CCTAAAC
**
145 TTTAAAC
1 CCTAAAC
**
152 TTTAAAAC
1 CCT-AAAC
160 CCTAAAC
1 CCTAAAC
*
167 CATAAAC
1 CCTAAAC
* *
174 TCTAAAT
1 CCTAAAC
* *
181 CATAATC
1 CCTAAAC
*
188 CCTAATC
1 CCTAAAC
*
195 CCTAATCC
1 CCTAA-AC
203 CCTAAAC
1 CCTAAAC
210 CCTAAAC
1 CCTAAAC
217 CCATAAAC
1 CC-TAAAC
225 C
1 C
226 TTTACAGTAT
Statistics
Matches: 111, Mismatches: 26, Indels: 21
0.70 0.16 0.13
Matches are distributed among these distances:
6 3 0.03
7 73 0.66
8 30 0.27
9 4 0.04
10 1 0.01
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.22
Consensus pattern (7 bp):
CCTAAAC
Found at i:90 original size:14 final size:14
Alignment explanation
Indices: 71--225 Score: 71
Period size: 14 Copynumber: 10.6 Consensus size: 14
61 AAAAAGAAAT
*
71 CCTAAACCTTAAAC
1 CCTAAACCATAAAC
*
85 CCTAAACCCTAAAC
1 CCTAAACCATAAAC
*
99 TC-AATACCATAAAC
1 CCTAA-ACCATAAAC
*
113 ACTCGT-AACCTTAAAAC
1 -C-C-TAAACCAT-AAAC
*
130 CCATAAACCATAAAA
1 CC-TAAACCATAAAC
** **
145 TTTAAACTTTAAAAC
1 CCTAAACCAT-AAAC
160 CCTAAACCATAAAC
1 CCTAAACCATAAAC
* * *
174 TCTAAATCATAATC
1 CCTAAACCATAAAC
* * *
188 CCTAATCCCTAATCC
1 CCTAAACCATAA-AC
*
203 CCTAAACCCTAAAC
1 CCTAAACCATAAAC
217 CCATAAACC
1 CC-TAAACC
226 TTTACAGTAT
Statistics
Matches: 104, Mismatches: 27, Indels: 19
0.69 0.18 0.13
Matches are distributed among these distances:
13 2 0.02
14 54 0.52
15 32 0.31
16 11 0.11
17 5 0.05
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.22
Consensus pattern (14 bp):
CCTAAACCATAAAC
Found at i:179 original size:29 final size:30
Alignment explanation
Indices: 123--179 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
113 ACTCGTAACC
*
123 TTAAAACCCATAAACCATAAAATTTAAACT
1 TTAAAACCCATAAACCATAAAATCTAAACT
*
153 TTAAAACCC-TAAACCATAAACTCTAAA
1 TTAAAACCCATAAACCATAAAATCTAAA
180 TCATAATCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.25
Consensus pattern (30 bp):
TTAAAACCCATAAACCATAAAATCTAAACT
Found at i:256 original size:7 final size:7
Alignment explanation
Indices: 240--313 Score: 51
Period size: 7 Copynumber: 10.6 Consensus size: 7
230 CAGTATTAAT
*
240 TAAACTC
1 TAAACCC
247 TAAACCC
1 TAAACCC
*
254 TAAAACTC
1 T-AAACCC
*
262 TAGACCC
1 TAAACCC
**
269 TAAACTT
1 TAAACCC
276 TAAACCC
1 TAAACCC
* *
283 CAAACCA
1 TAAACCC
*
290 TAAA-CA
1 TAAACCC
*
296 TACACCC
1 TAAACCC
303 TAAACCC
1 TAAACCC
310 TAAA
1 TAAA
314 TATAAATATT
Statistics
Matches: 50, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
6 5 0.10
7 39 0.78
8 6 0.12
ACGTcount: A:0.46, C:0.34, G:0.01, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:273 original size:14 final size:14
Alignment explanation
Indices: 240--313 Score: 62
Period size: 14 Copynumber: 5.3 Consensus size: 14
230 CAGTATTAAT
240 TAAACTCTAAACCC
1 TAAACTCTAAACCC
*
254 TAAAACTCTAGACCC
1 T-AAACTCTAAACCC
*
269 TAAACTTTAAACCC
1 TAAACTCTAAACCC
* *
283 CAAAC-CATAAA-CA
1 TAAACTC-TAAACCC
* *
296 TACACCCTAAACCC
1 TAAACTCTAAACCC
310 TAAA
1 TAAA
314 TATAAATATT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
13 8 0.17
14 25 0.54
15 13 0.28
ACGTcount: A:0.46, C:0.34, G:0.01, T:0.19
Consensus pattern (14 bp):
TAAACTCTAAACCC
Found at i:401 original size:21 final size:21
Alignment explanation
Indices: 363--410 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
353 TTTAAATCCT
* * *
363 AAACCCTAAACCCCAAACCCC
1 AAACTCTAAACCACAAACCCA
* *
384 AAACTCTAAACCATAAACGCA
1 AAACTCTAAACCACAAACCCA
405 AAACTC
1 AAACTC
411 AAAATTCTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.40, G:0.02, T:0.10
Consensus pattern (21 bp):
AAACTCTAAACCACAAACCCA
Found at i:879 original size:40 final size:39
Alignment explanation
Indices: 770--885 Score: 103
Period size: 40 Copynumber: 2.9 Consensus size: 39
760 TTTCTCAACT
* *
770 TCTTT-GCGGTGTTTTTCGTAAAGCACCGCAAATGT-TTGA
1 TCTTTAGCGGTGTTTTTAG-AAAGCACCGCTAAT-TCTTGA
* ** * *
809 CCTTTAGCGACGTTTTTCATG-ATGCGCCGCTAATTCTTGA
1 TCTTTAGCGGTGTTTTT-A-GAAAGCACCGCTAATTCTTGA
849 TCTTTAGCGGTGTTTTTAGAAAAGCACCGCTAATTCT
1 TCTTTAGCGGTGTTTTTAG-AAAGCACCGCTAATTCT
886 AGGTTTTTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
38 1 0.02
39 6 0.10
40 51 0.86
42 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (39 bp):
TCTTTAGCGGTGTTTTTAGAAAGCACCGCTAATTCTTGA
Done.