Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3026
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: 35019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7058 original size:3 final size:3
Alignment explanation
Indices: 7028--7066 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
7018 AATTAAAAGG
* * *
7028 ATA ATA ACA ATA ATG ATA ATA GTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
7067 GGACTAGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:8208 original size:27 final size:27
Alignment explanation
Indices: 8168--8263 Score: 176
Period size: 27 Copynumber: 3.6 Consensus size: 27
8158 GTTTTTTGTT
*
8168 TTGGGTT-TTGGGCTGAGGGTAGGCTA
1 TTGGGTTATTGGGCTAAGGGTAGGCTA
8194 TTGGGTTATTGGGCTAAGGGTAGGCTA
1 TTGGGTTATTGGGCTAAGGGTAGGCTA
8221 TTGGGTTATTGGGCTAAGGGTAGGCTA
1 TTGGGTTATTGGGCTAAGGGTAGGCTA
8248 TTGGGTTATTGGGCTA
1 TTGGGTTATTGGGCTA
8264 GTGGTTCTGA
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
26 7 0.10
27 61 0.90
ACGTcount: A:0.16, C:0.07, G:0.42, T:0.35
Consensus pattern (27 bp):
TTGGGTTATTGGGCTAAGGGTAGGCTA
Found at i:9103 original size:20 final size:20
Alignment explanation
Indices: 9057--9103 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
9047 CGATTTCAAT
9057 TAAATAAATTACTAAAAATAA
1 TAAA-AAATTACTAAAAATAA
* *
9078 TTAAAAATTA-TAAAAACTGA
1 TAAAAAATTACTAAAAA-TAA
9098 TAAAAA
1 TAAAAA
9104 TTTAAATTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 6 0.27
20 13 0.59
21 3 0.14
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (20 bp):
TAAAAAATTACTAAAAATAA
Found at i:12988 original size:19 final size:19
Alignment explanation
Indices: 12964--13003 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12954 AAAACACAAA
12964 AAAAAAAAACTTTTCTAAC
1 AAAAAAAAACTTTTCTAAC
* * *
12983 AAAAAAATATTTTTTTAAC
1 AAAAAAAAACTTTTCTAAC
13002 AA
1 AA
13004 TTTTCCCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAAAAAACTTTTCTAAC
Found at i:15013 original size:28 final size:29
Alignment explanation
Indices: 14956--15014 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
14946 TTGTTATGGA
*
14956 TTTAGTGTTTGTTTTCTAATTTTATTATT
1 TTTAGTGTTTGTTTTCTAATTTTATAATT
* *
14985 TTTAGT-TTTTTTTTTTAATTTTGA-AATT
1 TTTAGTGTTTGTTTTCTAATTTT-ATAATT
15013 TT
1 TT
15015 AGACTCAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.19, C:0.02, G:0.08, T:0.71
Consensus pattern (29 bp):
TTTAGTGTTTGTTTTCTAATTTTATAATT
Found at i:29396 original size:3 final size:3
Alignment explanation
Indices: 29390--29433 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
29380 TTTAGCCACT
*
29390 TTA TTA TT- TTG TTTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29434 CCTATTTGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
2 4 0.11
3 31 0.84
4 2 0.05
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:29994 original size:16 final size:16
Alignment explanation
Indices: 29975--30005 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29965 TACACCCATA
*
29975 TATATGTACATATTTT
1 TATATATACATATTTT
29991 TATATATACATATTT
1 TATATATACATATTT
30006 ATCGTTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATATACATATTTT
Done.