Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3206
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: 19750
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Found at i:6083 original size:18 final size:18
Alignment explanation
Indices: 6060--6101 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
6050 TCTCCATCTC
*
6060 AATTTCCGTCATTT-ATTT
1 AATTT-CGTAATTTAATTT
6078 AATTTCGTAATTTCAATTT
1 AATTTCGTAATTT-AATTT
6097 AATTT
1 AATTT
6102 AAATACTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 7 0.33
18 5 0.24
19 9 0.43
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.55
Consensus pattern (18 bp):
AATTTCGTAATTTAATTT
Found at i:6786 original size:17 final size:18
Alignment explanation
Indices: 6764--6798 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
6754 AAAAAATAAA
6764 AATAAAATATATA-AATT
1 AATAAAATATATATAATT
6781 AATAAAATATATATAATT
1 AATAAAATATATATAATT
6799 TTTTTCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAAATATATATAATT
Found at i:12118 original size:23 final size:23
Alignment explanation
Indices: 12088--12135 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
12078 AAATCAAAGA
12088 AAAATGACTAGGGACTTGAAATT
1 AAAATGACTAGGGACTTGAAATT
12111 AAAATGACTAGGGACTTGAAATT
1 AAAATGACTAGGGACTTGAAATT
12134 AA
1 AA
12136 GGTCAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (23 bp):
AAAATGACTAGGGACTTGAAATT
Found at i:12709 original size:16 final size:16
Alignment explanation
Indices: 12683--12721 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 16
12673 TATTATTTTA
12683 AAAATTTTAAAATATAT
1 AAAA-TTTAAAATATAT
12700 AAAATTTAAAATATAT
1 AAAATTTAAAATATAT
12716 ATAAAT
1 A-AAAT
12722 AATAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTTAAAATATAT
Found at i:12715 original size:18 final size:17
Alignment explanation
Indices: 12683--12720 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
12673 TATTATTTTA
*
12683 AAAATTTTAAAATATAT
1 AAAATTTAAAAATATAT
12700 AAAATTTAAAATATATAT
1 AAAATTTAAAA-ATATAT
12718 AAA
1 AAA
12721 TAATAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATTTAAAAATATAT
Found at i:12727 original size:18 final size:16
Alignment explanation
Indices: 12690--12728 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
12680 TTAAAAATTT
*
12690 TAAAATATATAAAATT
1 TAAAATATATAAAATA
12706 TAAAATATATATAAATAA
1 TAAAATATATA-AAAT-A
12724 TAAAA
1 TAAAA
12729 AAATGTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAATATATAAAATA
Found at i:17543 original size:14 final size:14
Alignment explanation
Indices: 17526--17561 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
17516 ATGGTTTTCA
*
17526 GAAAATGATTTCTG
1 GAAAATAATTTCTG
17540 GAAAATAATTTCTG
1 GAAAATAATTTCTG
17554 GAAAATAA
1 GAAAATAA
17562 CTTACTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.31
Consensus pattern (14 bp):
GAAAATAATTTCTG
Found at i:18247 original size:13 final size:13
Alignment explanation
Indices: 18229--18261 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
18219 ATAATTGTAA
*
18229 TAAATATTATTAT
1 TAAATATTAATAT
18242 TAAATA-TAATAT
1 TAAATATTAATAT
18254 TAAATATT
1 TAAATATT
18262 TTCAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATATTAATAT
Found at i:18299 original size:12 final size:11
Alignment explanation
Indices: 18236--18311 Score: 59
Period size: 11 Copynumber: 7.0 Consensus size: 11
18226 TAATAAATAT
18236 TATTATTAAATA
1 TATTATTAAA-A
*
18248 TAATATT-AAA
1 TATTATTAAAA
*
18258 TATT-TT-CAA
1 TATTATTAAAA
* *
18267 TAATATGAAGAA
1 TATTATTAA-AA
18279 TATTATTAAAA
1 TATTATTAAAA
*
18290 TATTATTTAAA
1 TATTATTAAAA
*
18301 TTTTATTAAAA
1 TATTATTAAAA
18312 AAATAAATAT
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
9 7 0.14
10 5 0.10
11 23 0.46
12 15 0.30
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (11 bp):
TATTATTAAAA
Found at i:18354 original size:23 final size:23
Alignment explanation
Indices: 18311--18355 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
18301 TTTTATTAAA
*
18311 AAAATAAATATTAAATAATTATT
1 AAAATAAAAATTAAATAATTATT
* *
18334 AAAATAAAAATTATATTATTAT
1 AAAATAAAAATTAAATAATTAT
18356 ATCATAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAATAAAAATTAAATAATTATT
Done.