Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold643
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: 14204
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.33
Warning! 1029 characters in sequence are not A, C, G, or T
Found at i:4176 original size:5 final size:5
Alignment explanation
Indices: 4166--4244 Score: 67
Period size: 5 Copynumber: 15.6 Consensus size: 5
4156 AAAAAAATAT
* *
4166 TATTA TATTA TAGTAA TGATTA TGTT- T-TTA TATTA TATTA TTATTA
1 TATTA TATTA TA-TTA T-ATTA TATTA TATTA TATTA TATTA -TATTA
4212 -A-TA TATTA TATTA TATTA TATATA TATATA TAT
1 TATTA TATTA TATTA TATTA TAT-TA TAT-TA TAT
4245 ATCTNNNNNN
Statistics
Matches: 63, Mismatches: 3, Indels: 15
0.78 0.04 0.19
Matches are distributed among these distances:
3 4 0.06
4 4 0.06
5 32 0.51
6 22 0.35
7 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:4218 original size:19 final size:19
Alignment explanation
Indices: 4194--4246 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
4184 ATTATGTTTT
4194 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
4213 TATATTATATTATATTATA
1 TATATTATATTATATTATA
4232 TATA-TATATATATAT
1 TATATTATAT-TATAT
4247 CTNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.31
19 22 0.69
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:4233 original size:2 final size:2
Alignment explanation
Indices: 4194--4246 Score: 50
Period size: 2 Copynumber: 30.5 Consensus size: 2
4184 ATTATGTTTT
4194 TA TA T- TA TA T- TA T- TA T- TA -A TA TA T- TA TA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4228 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
4247 CTNNNNNNNN
Statistics
Matches: 43, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
1 8 0.19
2 35 0.81
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:8407 original size:17 final size:17
Alignment explanation
Indices: 8349--8407 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
8339 AGCTAATTTT
*
8349 AAAATGAAAATTTTAAAG
1 AAAATG-AAATTTTAAAA
* *
8367 AAACT-AAA-ATTAAATA
1 AAAATGAAATTTTAAA-A
*
8383 AAATTGAAATTTTAAAA
1 AAAATGAAATTTTAAAA
8400 AAAATGAA
1 AAAATGAA
8408 CAATAAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
15 5 0.16
16 7 0.22
17 11 0.34
18 9 0.28
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (17 bp):
AAAATGAAATTTTAAAA
Found at i:9379 original size:15 final size:15
Alignment explanation
Indices: 9361--9390 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9351 ATTTCGATTT
9361 AGTTAATACTAATTC
1 AGTTAATACTAATTC
9376 AGTTAATACTAATTC
1 AGTTAATACTAATTC
9391 GATTTGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (15 bp):
AGTTAATACTAATTC
Done.