Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2002
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: 11512
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Found at i:4214 original size:29 final size:30
Alignment explanation
Indices: 4172--4233 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
4162 AAATTTACCC
* * *
4172 TTTGGGTTAAAAAAAAAA-GTGGGTTCCAT
1 TTTGGATTAAAAAAAAAACGTGGGGTCAAT
4201 TTTGGATTAAAAAAAAAACGTGGGGTCAAT
1 TTTGGATTAAAAAAAAAACGTGGGGTCAAT
4231 TTT
1 TTT
4234 TGAAAAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (30 bp):
TTTGGATTAAAAAAAAAACGTGGGGTCAAT
Found at i:7897 original size:22 final size:23
Alignment explanation
Indices: 7870--7933 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 23
7860 AGGATTTAAG
7870 TAATAAAATAATTATTTAAAT-T
1 TAATAAAATAATTATTTAAATAT
*
7892 TAATAATAA-AA-TATATAAATAT
1 TAATAA-AATAATTATTTAAATAT
7914 TAATATAAAATAATT-TTTAA
1 T-A-ATAAAATAATTATTTAA
7934 TAATTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
21 8 0.24
22 10 0.29
23 5 0.15
24 10 0.29
25 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATAAAATAATTATTTAAATAT
Found at i:7921 original size:21 final size:21
Alignment explanation
Indices: 7863--7925 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 21
7853 TTGGATTAGG
7863 ATTTAAGTAATAAAATAATTATTTAA
1 ATTTAA-TAATAAAAT-A-TA--TAA
7889 ATTTAATAATAAAATATATAA
1 ATTTAATAATAAAATATATAA
7910 ATATTAAT-ATAAAATA
1 AT-TTAATAATAAAATA
7926 ATTTTTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
21 13 0.36
22 5 0.14
23 2 0.06
24 1 0.03
25 9 0.25
26 6 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTTAATAATAAAATATATAA
Found at i:8233 original size:19 final size:20
Alignment explanation
Indices: 8189--8234 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
8179 ATTATTATAT
* *
8189 TATAATTAATAACATATTTT
1 TATAATTAATAAAATATTTA
*
8209 TTTAATT-ATAAAATATTTA
1 TATAATTAATAAAATATTTA
8228 TATAATT
1 TATAATT
8235 TTTTATTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TATAATTAATAAAATATTTA
Found at i:8522 original size:3 final size:3
Alignment explanation
Indices: 8516--8552 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
8506 AAAATCGATG
8516 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
8553 AATAATAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9377 original size:37 final size:40
Alignment explanation
Indices: 9335--9425 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 40
9325 ACCCAAATTT
*
9335 TAATAAATTTAAA-AA-TTTATATTATTATTTA-AAATAA
1 TAATAAATTTAAATAATTTTATATTAATATTTATAAATAA
*
9372 TAATAAA---AAATAATTTTATATTAATATTTATAAATTA
1 TAATAAATTTAAATAATTTTATATTAATATTTATAAATAA
9409 TAATTAAATTTAAATAA
1 TAA-TAAATTTAAATAA
9426 AATATTCATA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
34 3 0.07
35 2 0.04
36 15 0.33
37 15 0.33
38 4 0.09
41 6 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (40 bp):
TAATAAATTTAAATAATTTTATATTAATATTTATAAATAA
Found at i:10342 original size:28 final size:27
Alignment explanation
Indices: 10310--10369 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
10300 TTTATTTTAA
* * *
10310 AAAATAATATTATTAAGATTTAATATTT
1 AAAATAATATTA-TAAAATTTAAAAATT
**
10338 AAAATTTTATTATAAAATTTAAAAATT
1 AAAATAATATTATAAAATTTAAAAATT
10365 AAAAT
1 AAAAT
10370 GATCAATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (27 bp):
AAAATAATATTATAAAATTTAAAAATT
Found at i:10366 original size:27 final size:28
Alignment explanation
Indices: 10317--10369 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
10307 TAAAAAATAA
* * *
10317 TATTATTAAGATTTAATATTTAAAATTT
1 TATTATTAAAATTTAAAAATTAAAATTT
10345 TATTA-TAAAATTTAAAAATTAAAAT
1 TATTATTAAAATTTAAAAATTAAAAT
10370 GATCAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
TATTATTAAAATTTAAAAATTAAAATTT
Found at i:10987 original size:12 final size:11
Alignment explanation
Indices: 10917--10988 Score: 51
Period size: 11 Copynumber: 6.6 Consensus size: 11
10907 CTTCTGCGAA
10917 TTTTTTAATAT
1 TTTTTTAATAT
*
10928 TCTTTTAATTAT
1 TTTTTTAA-TAT
**
10940 TTTTAAAATAT
1 TTTTTTAATAT
*
10951 ATTATTTAATA-
1 -TTTTTTAATAT
*
10962 ATTTTTAATA-
1 TTTTTTAATAT
*
10972 -TTTTTAATAA
1 TTTTTTAATAT
10982 TTTTTTA
1 TTTTTTA
10989 TTTTTAAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
9 9 0.19
10 8 0.17
11 16 0.33
12 15 0.31
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTTTTAATAT
Found at i:10990 original size:17 final size:18
Alignment explanation
Indices: 10948--11001 Score: 74
Period size: 17 Copynumber: 2.9 Consensus size: 18
10938 ATTTTTAAAA
10948 TATATTATTTAATAATTTT
1 TATATT-TTTAATAATTTT
10967 TAATATTTTTAATAATTTT
1 T-ATATTTTTAATAATTTT
*
10986 T-TATTTTTAAAAATTT
1 TATATTTTTAATAATTT
11002 ATTTTTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
17 14 0.42
19 14 0.42
20 5 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATATTTTTAATAATTTT
Found at i:11001 original size:10 final size:10
Alignment explanation
Indices: 10918--11016 Score: 71
Period size: 10 Copynumber: 9.7 Consensus size: 10
10908 TTCTGCGAAT
*
10918 TTTTTAATAT
1 TTTTTAATAA
*
10928 TCTTTTAATTA
1 T-TTTTAATAA
10939 TTTTTAAAATATA
1 TTTTT--AATA-A
10952 TTATTTAATAA
1 TT-TTTAATAA
10963 TTTTTAAT-A
1 TTTTTAATAA
10972 TTTTTAATAA
1 TTTTTAATAA
10982 TTTTT--T-A
1 TTTTTAATAA
*
10989 TTTTTAAAAA
1 TTTTTAATAA
**
10999 TTTATTTTTAA
1 TTT-TTAATAA
11010 TTTTTAA
1 TTTTTAA
11017 AAGTTAAATG
Statistics
Matches: 70, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
7 6 0.09
8 1 0.01
9 9 0.13
10 23 0.33
11 18 0.26
12 7 0.10
13 3 0.04
14 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:11235 original size:9 final size:9
Alignment explanation
Indices: 11217--11272 Score: 66
Period size: 9 Copynumber: 6.6 Consensus size: 9
11207 AAATAATTTA
11217 TTAA-ATAT
1 TTAATATAT
*
11225 TTATTATAT
1 TTAATATAT
11234 TTAATAT-T
1 TTAATATAT
11242 TTAATAT-T
1 TTAATATAT
11250 TTAATATAT
1 TTAATATAT
11259 TTAACTA-AT
1 TTAA-TATAT
11268 TTAAT
1 TTAAT
11273 TAATTAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
8 20 0.47
9 21 0.49
10 2 0.05
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (9 bp):
TTAATATAT
Found at i:11238 original size:25 final size:25
Alignment explanation
Indices: 11220--11272 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
11210 TAATTTATTA
*
11220 AATA-TTTATTATATTTAATATTTT
1 AATATTTTAATATATTTAATATTTT
*
11244 AATATTTTAATATATTTAACTAATTT
1 AATATTTTAATATATTTAA-TATTTT
11270 AAT
1 AAT
11273 TAATTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 4 0.16
25 13 0.52
26 8 0.32
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
AATATTTTAATATATTTAATATTTT
Found at i:11260 original size:10 final size:8
Alignment explanation
Indices: 11220--11272 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
11210 TAATTTATTA
11220 AATA-TTT
1 AATATTTT
*
11227 ATTATATTT
1 AATAT-TTT
11236 AATATTTT
1 AATATTTT
11244 AATATTTT
1 AATATTTT
11252 AATATATTT
1 AATAT-TTT
*
11261 AACTAATTT
1 AA-TATTTT
11270 AAT
1 AAT
11273 TAATTAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
7 3 0.08
8 17 0.44
9 17 0.44
10 2 0.05
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (8 bp):
AATATTTT
Found at i:11270 original size:18 final size:16
Alignment explanation
Indices: 11178--11272 Score: 59
Period size: 17 Copynumber: 5.5 Consensus size: 16
11168 GATTTAATAA
11178 AATTTAA-ACTTTTAAT
1 AATTTAATA-TTTTAAT
*
11194 CATTTAA-ATTTATAAAT
1 AATTTAATATTT-T-AAT
* *
11211 AATTTATTAAATATTTATT
1 AATTTA--ATAT-TTTAAT
11230 ATATTTAATATTTTAAT
1 A-ATTTAATATTTTAAT
*
11247 ATTTTAATATATTTAACT
1 AATTTAATAT-TTTAA-T
11265 AATTTAAT
1 AATTTAAT
11273 TAATTAAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
15 3 0.05
16 16 0.25
17 19 0.30
18 11 0.17
19 4 0.06
20 8 0.13
21 2 0.03
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
AATTTAATATTTTAAT
Found at i:11276 original size:9 final size:8
Alignment explanation
Indices: 11232--11284 Score: 52
Period size: 8 Copynumber: 6.2 Consensus size: 8
11222 TATTTATTAT
11232 ATTTAATA
1 ATTTAATA
*
11240 TTTTAATA
1 ATTTAATA
*
11248 TTTTAATA
1 ATTTAATA
11256 TATTTAACTA
1 -ATTTAA-TA
11266 ATTTAATTA
1 ATTTAA-TA
*
11275 ATTAAATA
1 ATTTAATA
11283 AT
1 AT
11285 AACAAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
8 19 0.49
9 18 0.46
10 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (8 bp):
ATTTAATA
Done.