Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1084
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: 8400
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1499 original size:2 final size:2
Alignment explanation
Indices: 1494--1524 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1484 TCTCTCTCTC
1494 TA TA TA 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 TA TA TA T
1525 TTCCCCCGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1777 original size:22 final size:21
Alignment explanation
Indices: 1745--1825 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 21
1735 AATATGTATA
*
1745 TTAAATTTATTATTTTAATATT
1 TTAAATATATTATTTT-ATATT
1767 TTAAATATATT-TTATTATA--
1 TTAAATATATTATT-TTATATT
* *
1786 CTAAAAATATTATTTTATATTT
1 TTAAATATATTATTTTATA-TT
1808 ATTAAATATATATATTTT
1 -TTAAATATAT-TATTTT
1826 TACATCATGT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
19 14 0.30
20 2 0.04
21 5 0.11
22 12 0.26
23 8 0.17
24 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAAATATATTATTTTATATT
Found at i:1823 original size:24 final size:23
Alignment explanation
Indices: 1771--1825 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
1761 AATATTTTAA
1771 ATATATTTTATTATACTAAAAAT
1 ATATATTTTATTATACTAAAAAT
* * *
1794 AT-TATTTTATATTTATTAAATAT
1 ATATATTTTAT-TATACTAAAAAT
1817 ATATATTTT
1 ATATATTTT
1826 TACATCATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.30
23 13 0.48
24 6 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATATTTTATTATACTAAAAAT
Found at i:3121 original size:2 final size:2
Alignment explanation
Indices: 3109--3140 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3099 CCCTCCCTCC
*
3109 CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3141 GGTAATGCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:5514 original size:14 final size:14
Alignment explanation
Indices: 5497--5534 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
5487 GTATAGGGTG
*
5497 AAAAAGAAAAACGA
1 AAAAAGAAAAACCA
5511 AAAAA-AAACAACCA
1 AAAAAGAAA-AACCA
5525 AAAAAGAAAA
1 AAAAAGAAAA
5535 GAAAAAGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 3 0.14
14 15 0.71
15 3 0.14
ACGTcount: A:0.82, C:0.11, G:0.08, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAACCA
Found at i:6840 original size:54 final size:53
Alignment explanation
Indices: 6781--6886 Score: 160
Period size: 54 Copynumber: 2.0 Consensus size: 53
6771 TAAAAATTTC
6781 TAGTGAATCTAATAAAGAAGGGGAAA-CACACGGCAATATATGCAATCTGCATTG
1 TAGTGAATCTAATAAAGAAGGGGAAAGCACAC--CAATATATGCAATCTGCATTG
* *
6835 TAGTGAATCTAATAAAGCAGGGGAAATGCACACCAATATATGGAATCTGCAT
1 TAGTGAATCTAATAAAGAAGGGGAAA-GCACACCAATATATGCAATCTGCAT
6887 CCTTAGTAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
54 43 0.90
56 5 0.10
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.23
Consensus pattern (53 bp):
TAGTGAATCTAATAAAGAAGGGGAAAGCACACCAATATATGCAATCTGCATTG
Found at i:8166 original size:17 final size:17
Alignment explanation
Indices: 8116--8166 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
8106 TTTAGACTTA
8116 TAAAAATATA-AAAATAT
1 TAAAAATATATAAAAT-T
*
8133 TAAATAAT-TATATAATT
1 TAAA-AATATATAAAATT
*
8150 TAAAAATACATAAAATT
1 TAAAAATATATAAAATT
8167 AAATAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 3 0.11
17 18 0.64
18 7 0.25
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAATATATAAAATT
Found at i:8195 original size:31 final size:32
Alignment explanation
Indices: 8116--8218 Score: 86
Period size: 31 Copynumber: 3.2 Consensus size: 32
8106 TTTAGACTTA
* *
8116 TAAAAATATA-AAAATATTAAATAATTATATAATT
1 TAAAAATACATAAAA-ATTAAATAA-AAT-TAATT
8150 TAAAAATACAT-AAAATTAAATAAAATTAATT
1 TAAAAATACATAAAAATTAAATAAAATTAATT
* ** * * *
8181 TAAAGATATTTAAAAATTAATTAAATTTAA-A
1 TAAAAATACATAAAAATTAAATAAAATTAATT
8212 TAAAAAT
1 TAAAAAT
8219 CTTTAAAACT
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
31 19 0.33
32 18 0.31
33 9 0.16
34 12 0.21
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (32 bp):
TAAAAATACATAAAAATTAAATAAAATTAATT
Found at i:8215 original size:21 final size:22
Alignment explanation
Indices: 8160--8218 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
8150 TAAAAATACA
8160 TAAAATTAAAT-AAAATTAATT
1 TAAAATTAAATAAAAATTAATT
**
8181 TAAAGA-TATTTAAAAATTAA-T
1 TAAA-ATTAAATAAAAATTAATT
*
8202 TAAATTTAAATAAAAAT
1 TAAAATTAAATAAAAAT
8219 CTTTAAAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
21 21 0.70
22 9 0.30
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
TAAAATTAAATAAAAATTAATT
Found at i:8224 original size:31 final size:32
Alignment explanation
Indices: 8161--8231 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
8151 AAAAATACAT
* *
8161 AAAATTAAATAAAATTAATTTAAAGATATTTA
1 AAAATTAAATAAAATTAAATAAAAGATATTTA
* * *
8193 AAAATTAATTAAATTTAAATAAAA-ATCTTTA
1 AAAATTAAATAAAATTAAATAAAAGATATTTA
*
8224 AAACTTAA
1 AAAATTAA
8232 CTATTTTCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (32 bp):
AAAATTAAATAAAATTAAATAAAAGATATTTA
Done.