Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold801
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: 11695
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:3275 original size:7 final size:7
Alignment explanation
Indices: 3225--3276 Score: 52
Period size: 8 Copynumber: 7.1 Consensus size: 7
3215 ATTTTTAAAT
3225 TAATTTA
1 TAATTTA
3232 TAAATTTA
1 T-AATTTA
3240 TAAATTTA
1 T-AATTTA
*
3248 -AATTTT
1 TAATTTA
*
3254 TAATTTT
1 TAATTTA
3261 TAATTTTA
1 TAA-TTTA
3269 TAATTTA
1 TAATTTA
3276 T
1 T
3277 TTATTTATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
6 5 0.12
7 15 0.38
8 20 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TAATTTA
Found at i:3350 original size:18 final size:17
Alignment explanation
Indices: 3327--3362 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
3317 TAATAAAAAT
*
3327 TTTAAATTATTTATTTTA
1 TTTAAATAATTT-TTTTA
3345 TTTAAATAATTTTTTTA
1 TTTAAATAATTTTTTTA
3362 T
1 T
3363 ATTTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTAAATAATTTTTTTA
Found at i:5267 original size:186 final size:190
Alignment explanation
Indices: 4901--5278 Score: 561
Period size: 187 Copynumber: 2.0 Consensus size: 190
4891 ATTTTTTTCT
*
4901 ACTCCTTGAATATTATTTACTTATATAATTTTTTTATTTCCTATAGTCCCTTTATTTATCAAGCA
1 ACTCCTTGAATATTATTTAC-TATATAATTTTTTTATTTCCTACAGTCCCTTTATTTATCAAGCA
* * *
4966 TATGTTTATATAATGTCGGTAAAATTTTTAAATTTAATACGTGAATTTAAAAAATTAACAAGTAT
65 TATGTTTATATAATGTCGGTAAAATTTTTAAATTTAATAAGTAAATTAAAAAAATTAACAAGTAT
5031 TTTTTTGTAATACTAATTTTAAATATTTTTATTATATAATATAAAAATATAAGTCACTTTG
130 TTTTTTGTAATACTAATTTTAAATATTTTTATTATATAATATAAAAATATAAGTCACTTTG
* * * *
5092 ACTCCTTGAATATTA-TTA-TATA-ATTTTTTTTTATTTCCTACATTCCCTTTA-TTATTAAGCC
1 ACTCCTTGAATATTATTTACTATATA-ATTTTTTTATTTCCTACAGTCCCTTTATTTATCAAGCA
* *
5153 TATTTTTATATAATGTCGGTTAAATTTTTAAATTTAATAAGTAAAGTTAAAAAAATTAACAAGTA
65 TATGTTTATATAATGTCGGTAAAATTTTTAAATTTAATAAGTAAA-TTAAAAAAATTAACAAGTA
* * * *
5218 -TTTTTT-TAATATTAATTTTAATTATTTTTATTATATAATATAGAAATATATGTCACTTTG
129 TTTTTTTGTAATACTAATTTTAAATATTTTTATTATATAATATAAAAATATAAGTCACTTTG
5278 A
1 A
5279 TAATTTGCTC
Statistics
Matches: 171, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
186 51 0.30
187 56 0.33
188 46 0.27
190 3 0.02
191 15 0.09
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (190 bp):
ACTCCTTGAATATTATTTACTATATAATTTTTTTATTTCCTACAGTCCCTTTATTTATCAAGCAT
ATGTTTATATAATGTCGGTAAAATTTTTAAATTTAATAAGTAAATTAAAAAAATTAACAAGTATT
TTTTTGTAATACTAATTTTAAATATTTTTATTATATAATATAAAAATATAAGTCACTTTG
Done.