Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3106
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: 14418
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Found at i:75 original size:15 final size:16
Alignment explanation
Indices: 53--138 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 16
43 AAAAAATATA
53 CCTTCTTTTTTCTT-T
1 CCTTCTTTTTTCTTCT
*
68 CTTTCTTTTTTCCTTCT
1 CCTTCTTTTTT-CTTCT
85 CCTTCTTTTTTCTTCCTT
1 CCTTCTTTTTTCTT-C-T
**
103 CTCTTCTCCTTTCTT-T
1 C-CTTCTTTTTTCTTCT
*
119 CCCTT-TATTTTCTTCT
1 -CCTTCTTTTTTCTTCT
135 CCTT
1 CCTT
139 GCTCCCGAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
15 21 0.36
16 11 0.19
17 13 0.22
18 2 0.03
19 11 0.19
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (16 bp):
CCTTCTTTTTTCTTCT
Found at i:92 original size:25 final size:27
Alignment explanation
Indices: 65--119 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
55 TTCTTTTTTC
**
65 TTTCTTTCTTTTTTC-CTTCTCC-TTC
1 TTTCTTTCTTCCTTCTCTTCTCCTTTC
90 TTT-TTTCTTCCTTCTCTTCTCCTTTC
1 TTTCTTTCTTCCTTCTCTTCTCCTTTC
116 TTTC
1 TTTC
120 CCTTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 9 0.36
25 10 0.40
26 6 0.24
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTCTTTCTTCCTTCTCTTCTCCTTTC
Found at i:102 original size:20 final size:20
Alignment explanation
Indices: 62--109 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
52 ACCTTCTTTT
*
62 TTCT-TTCTTTCTTTTTTCC
1 TTCTCTTCTTTCTTTCTTCC
81 TTCTCCTTCTTT-TTTCTTCC
1 TTCT-CTTCTTTCTTTCTTCC
101 TTCTCTTCT
1 TTCTCTTCT
110 CCTTTCTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 9 0.35
20 11 0.42
21 6 0.23
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
TTCTCTTCTTTCTTTCTTCC
Found at i:113 original size:31 final size:32
Alignment explanation
Indices: 53--113 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
43 AAAAAATATA
* * *
53 CCTTCTTTTTTCTTTCTTTCTTTTTTCCTTCT
1 CCTTCTTTTTTCTTTCCTTCTCTTCTCCTTCT
85 CCTTCTTTTTTC-TTCCTTCTCTTCTCCTT
1 CCTTCTTTTTTCTTTCCTTCTCTTCTCCTT
114 TCTTTCCCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (32 bp):
CCTTCTTTTTTCTTTCCTTCTCTTCTCCTTCT
Found at i:115 original size:19 final size:20
Alignment explanation
Indices: 72--117 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
62 TTCTTTCTTT
* *
72 CTTTTTTCCTTCTCCTTCTT
1 CTTTCTTCCTTCTCCTTCTC
*
92 TTTTCTTCCTTCT-CTTCTC
1 CTTTCTTCCTTCTCCTTCTC
111 CTTTCTT
1 CTTTCTT
118 TCCCTTTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (20 bp):
CTTTCTTCCTTCTCCTTCTC
Found at i:120 original size:20 final size:21
Alignment explanation
Indices: 72--120 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
62 TTCTTTCTTT
*
72 CTTT-TTTCCTTCTCCTTCTT
1 CTTTCTTTCCTTCTCCTTCTC
*
92 TTTTC-TTCCTTCT-CTTCTC
1 CTTTCTTTCCTTCTCCTTCTC
111 CTTTCTTTCC
1 CTTTCTTTCC
121 CTTTATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (21 bp):
CTTTCTTTCCTTCTCCTTCTC
Found at i:981 original size:21 final size:20
Alignment explanation
Indices: 957--999 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
947 TGGGTTGATT
*
957 TTATATATATAATTAGTAGTA
1 TTATATATATAATT-GTAATA
*
978 TTATATTTATAATTGTAATA
1 TTATATATATAATTGTAATA
998 TT
1 TT
1000 CTCAAAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (20 bp):
TTATATATATAATTGTAATA
Found at i:2208 original size:3 final size:3
Alignment explanation
Indices: 2200--2225 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2190 CCAAAATCCT
2200 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2226 GCCATGGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4561 original size:31 final size:32
Alignment explanation
Indices: 4496--4563 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
4486 TATTGTTTTA
* **
4496 AAAAAAAAGAAACAATGTATTTTCTTGCTGAG
1 AAAAAAAAGAAACAACGTATTTTCTTGCCCAG
4528 AAAAAAAA-AAACAACGTATTTTCTT-CACCAG
1 AAAAAAAAGAAACAACGTATTTTCTTGC-CCAG
4559 AAAAA
1 AAAAA
4564 TTGATACTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 23 0.72
32 8 0.25
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.24
Consensus pattern (32 bp):
AAAAAAAAGAAACAACGTATTTTCTTGCCCAG
Done.