Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold811
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: 16876
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Found at i:96 original size:26 final size:26
Alignment explanation
Indices: 67--152 Score: 100
Period size: 27 Copynumber: 3.2 Consensus size: 26
57 TTAAGATGGA
*
67 GTGCCACCGATTTTGGGCTTTAAAGG
1 GTGCCACTGATTTTGGGCTTTAAAGG
*
93 GTGCCACTGATTTGTGGGCTTTGAAGG
1 GTGCCACTGATTT-TGGGCTTTAAAGG
* *
120 TTGCCACTGACTTGTGGGCTTTTAAAGG
1 GTGCCACTGA-TTTTGGGC-TTTAAAGG
*
148 TTGCC
1 GTGCC
153 TGAGTGTGGG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
26 12 0.23
27 26 0.50
28 14 0.27
ACGTcount: A:0.16, C:0.19, G:0.31, T:0.34
Consensus pattern (26 bp):
GTGCCACTGATTTTGGGCTTTAAAGG
Found at i:119 original size:27 final size:29
Alignment explanation
Indices: 67--520 Score: 256
Period size: 29 Copynumber: 16.1 Consensus size: 29
57 TTAAGATGGA
* *
67 GTGCCACCGA-TTTTGGGC-TTT-AAAGG
1 GTGCCACTGACTTGTGGGCTTTTGAAAGG
*
93 GTGCCACTGATTTGTGGGC-TTTG-AAGG
1 GTGCCACTGACTTGTGGGCTTTTGAAAGG
*
120 TTGCCACTGACTTGTGGGCTTTT-AAAGG
1 GTGCCACTGACTTGTGGGCTTTTGAAAGG
* * **
148 TTG-C-CTGA-GTGTGGGCTTTTGAAAAT
1 GTGCCACTGACTTGTGGGCTTTTGAAAGG
*
174 ATGCCACTGACTTGTGGGCTTTTGAACAGG
1 GTGCCACTGACTTGTGGGCTTTTGAA-AGG
*
204 GTGCCACTAACTTGT-GGCTTTT-AAAGG
1 GTGCCACTGACTTGTGGGCTTTTGAAAGG
* **
231 TTGCCACT-ACTTGTGGGCTTTTGAAAAAT
1 GTGCCACTGACTTGTGGGCTTTTG-AAAGG
*
260 ATGCCACTGACTTGTGGGC-TTTGAAAAGG
1 GTGCCACTGACTTGTGGGCTTTTG-AAAGG
* *
289 GTGCCACTAACTTGTGGGC---TGAAA-A
1 GTGCCACTGACTTGTGGGCTTTTGAAAGG
* * * ** *
314 GTG-C-TTAGAGTTGTGAGCTTACAAAAGAAAAAGA
1 GTGCCACT-GACTTGTGGGCTT----TTG--AAAGG
* * * * *
348 GTGCCACGGAGTTGTGGACTTTGGAAA-A
1 GTGCCACTGACTTGTGGGCTTTTGAAAGG
* * **
376 G-ACCACCGACTTGTGGGCTTCGGAAAAGG
1 GTGCCACTGACTTGTGGGCTTTTG-AAAGG
*
405 GTGCCACTGATTTGTGGGC-TTTG-AAGG
1 GTGCCACTGACTTGTGGGCTTTTGAAAGG
* * **
432 TTGCCACTGACTTGTGGGCTTTCGAAAAA
1 GTGCCACTGACTTGTGGGCTTTTGAAAGG
* **
461 ATGCCACTGACTTGTGGGC-TTTGAAAAAA
1 GTGCCACTGACTTGTGGGCTTTTG-AAAGG
* *
490 ATGCCACTGACTTGTGGACTTTTG-AAGG
1 GTGCCACTGACTTGTGGGCTTTTGAAAGG
518 GTG
1 GTG
521 AGGAATGTCT
Statistics
Matches: 340, Mismatches: 55, Indels: 64
0.74 0.12 0.14
Matches are distributed among these distances:
23 1 0.00
24 9 0.03
25 14 0.04
26 27 0.08
27 90 0.26
28 31 0.09
29 105 0.31
30 42 0.12
31 2 0.01
33 3 0.01
34 4 0.01
35 12 0.04
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (29 bp):
GTGCCACTGACTTGTGGGCTTTTGAAAGG
Found at i:166 original size:25 final size:28
Alignment explanation
Indices: 80--308 Score: 177
Period size: 27 Copynumber: 8.2 Consensus size: 28
70 CCACCGATTT
* **
80 TGGGC-TTTAAAGGGTGCCACTGATTTG
1 TGGGCTTTTAAAGGTTGCCACTGACGTG
* *
107 TGGGC-TTTGAAGGTTGCCACTGACTTG
1 TGGGCTTTTAAAGGTTGCCACTGACGTG
134 TGGGCTTTTAAAGGTTG-C-CTGA-GTG
1 TGGGCTTTTAAAGGTTGCCACTGACGTG
* *
159 TGGGCTTTTGAAA-ATATGCCACTGACTTG
1 TGGGCTTTT-AAAGGT-TGCCACTGACGTG
* * *
188 TGGGCTTTTGAACAGGGTGCCACTAACTTG
1 TGGGCTTTT-AA-AGGTTGCCACTGACGTG
*
218 T-GGCTTTTAAAGGTTGCCACT-ACTTG
1 TGGGCTTTTAAAGGTTGCCACTGACGTG
** *
244 TGGGCTTTTGAAAAATATGCCACTGACTTG
1 TGGGCTTTT-AAAGGT-TGCCACTGACGTG
* * * *
274 TGGGCTTTGAAAAGGGTGCCACTAACTTG
1 TGGGCTTT-TAAAGGTTGCCACTGACGTG
303 TGGGCT
1 TGGGCT
309 GAAAAGTGCT
Statistics
Matches: 171, Mismatches: 18, Indels: 24
0.80 0.08 0.11
Matches are distributed among these distances:
25 12 0.07
26 15 0.09
27 48 0.28
28 20 0.12
29 46 0.27
30 30 0.18
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (28 bp):
TGGGCTTTTAAAGGTTGCCACTGACGTG
Found at i:290 original size:85 final size:82
Alignment explanation
Indices: 94--305 Score: 304
Period size: 85 Copynumber: 2.5 Consensus size: 82
84 CTTTAAAGGG
* * *
94 TGCCACTGATTTGTGGGCTTTG--AAGGTTGCCACTGACTTGTGGGCTTTTAAAGGTTGCCTGAG
1 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGT-GGCTTTTAAAGGTTGCCTGAG
157 TGTGGGCTTTTGAAAATA
65 TGTGGGCTTTTGAAAATA
*
175 TGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGCTTTTAAAGGTTGCCACT-
1 TGCCACTGACTTGTGGGC-TTTGAAAAGGGTGCCACTAACTTGTGGCTTTTAAAGGTTG-C-CTG
*
239 ACTTGTGGGCTTTTGAAAAATA
63 A-GTGTGGGCTTTTG-AAAATA
261 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGG
1 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGG
306 GCTGAAAAGT
Statistics
Matches: 118, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
81 17 0.14
82 4 0.03
83 15 0.13
84 18 0.15
85 40 0.34
86 24 0.20
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.33
Consensus pattern (82 bp):
TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGCTTTTAAAGGTTGCCTGAGT
GTGGGCTTTTGAAAATA
Found at i:312 original size:56 final size:54
Alignment explanation
Indices: 205--313 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 54
195 TTGAACAGGG
* *
205 TGCCACTAACTTGTGGCTTTTAAAGGTTGCCACTACTTGTGGGCTTTTGAAAAATA
1 TGCCACTAACTTGTGGCTTTAAAAGGGTGCCACTACTTGTGGGC--TTGAAAAATA
*
261 TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTAACTTGTGGGC-TGAAAA
1 TGCCACTAACTTGT-GGCTTT-AAAAGGGTGCCACT-ACTTGTGGGCTTGAAAA
314 GTGCTTAGAG
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
56 19 0.40
57 6 0.13
58 12 0.26
59 10 0.21
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (54 bp):
TGCCACTAACTTGTGGCTTTAAAAGGGTGCCACTACTTGTGGGCTTGAAAAATA
Found at i:1951 original size:1 final size:1
Alignment explanation
Indices: 1947--2046 Score: 119
Period size: 1 Copynumber: 100.0 Consensus size: 1
1937 CCGGACCCCC
* * * * * *
1947 TTTTTTTGTTTTGTTTGTTTTTTTTGTTTTTGTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
2012 TTTTTTGTTTTTTTTTTGTTGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2047 GGAGGACGCC
Statistics
Matches: 81, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 81 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:1969 original size:19 final size:18
Alignment explanation
Indices: 1947--2045 Score: 134
Period size: 18 Copynumber: 5.7 Consensus size: 18
1937 CCGGACCCCC
*
1947 TTTTTTTGTTTTGTTTGT
1 TTTTTTTTTTTTGTTTGT
1965 TTTTTTTGTTTTTGTTT-T
1 TTTTTTT-TTTTTGTTTGT
*
1983 TTTTTTTTTTTTTTTTGT
1 TTTTTTTTTTTTGTTTGT
2001 TTTTTTTTTTTT-TTT-T
1 TTTTTTTTTTTTGTTTGT
*
2017 TGTTTTTTTTTTG-TTGT
1 TTTTTTTTTTTTGTTTGT
2034 TTTTTTTTTTTT
1 TTTTTTTTTTTT
2046 TGGAGGACGC
Statistics
Matches: 73, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
16 14 0.19
17 23 0.32
18 28 0.38
19 8 0.11
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (18 bp):
TTTTTTTTTTTTGTTTGT
Found at i:1978 original size:15 final size:14
Alignment explanation
Indices: 1948--2045 Score: 137
Period size: 14 Copynumber: 6.9 Consensus size: 14
1938 CGGACCCCCT
1948 TTTTTTGTTTTGTTTG
1 TTTTTT-TTTT-TTTG
1964 TTTTTTTTGTTTTTG
1 TTTTTTTT-TTTTTG
1979 TTTTTTTTTTTTT-
1 TTTTTTTTTTTTTG
*
1992 TTTTTTTGTTTTT-
1 TTTTTTTTTTTTTG
2005 TTTTTTTTTTTTTG
1 TTTTTTTTTTTTTG
*
2019 TTTTTTTTTTGTTG
1 TTTTTTTTTTTTTG
2033 TTTTTTTTTTTTT
1 TTTTTTTTTTTTT
2046 TGGAGGACGC
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
13 24 0.32
14 30 0.39
15 14 0.18
16 8 0.11
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (14 bp):
TTTTTTTTTTTTTG
Found at i:1993 original size:40 final size:38
Alignment explanation
Indices: 1947--2046 Score: 141
Period size: 38 Copynumber: 2.6 Consensus size: 38
1937 CCGGACCCCC
1947 TTTTTTTGTTTTGTTTGTTTTTTTTGTTTTTGTT-TTTTTT
1 TTTTTTTGTTTTGTTT-TTTTTTTT-TTTTT-TTGTTTTTT
*
1987 TTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTGTTTTTT
1 TTTTTTTGTTTTGTTTTTTTTTTTTTTTTTTGTTTTTT
*
2025 TTTTGTTGTTTT-TTTTTTTTTT
1 TTTTTTTGTTTTGTTTTTTTTTT
2047 GGAGGACGCC
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
37 12 0.21
38 21 0.38
39 8 0.14
40 15 0.27
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (38 bp):
TTTTTTTGTTTTGTTTTTTTTTTTTTTTTTTGTTTTTT
Done.