Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1704
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: 10514
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Found at i:521 original size:17 final size:16
Alignment explanation
Indices: 484--528 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
474 ATGAAAAATG
**
484 AAAAATAAGAAGTAAA
1 AAAAATAAGAAACAAA
500 AAAAATAAGAAACAAA
1 AAAAATAAGAAACAAA
*
516 AGAAAAAAAGAAA
1 A-AAAATAAGAAA
529 ATTGAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (16 bp):
AAAAATAAGAAACAAA
Found at i:541 original size:10 final size:11
Alignment explanation
Indices: 522--550 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
512 CAAAAGAAAA
522 AAAGAAAATTG
1 AAAGAAAATTG
533 AAA-AAAATTG
1 AAAGAAAATTG
543 AAAGAAAA
1 AAAGAAAA
551 AAAGTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (11 bp):
AAAGAAAATTG
Found at i:3560 original size:22 final size:21
Alignment explanation
Indices: 3527--3567 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3517 TATACAACAG
*
3527 TAATAATGAGATTAATTATTA
1 TAATAATAAGATTAATTATTA
3548 TAATATATAAGATTAATTAT
1 TAATA-ATAAGATTAATTAT
3568 AATGATGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (21 bp):
TAATAATAAGATTAATTATTA
Found at i:6710 original size:16 final size:16
Alignment explanation
Indices: 6689--6721 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6679 ACTCATTCTT
6689 TCTGTTCTTTAAGGTC
1 TCTGTTCTTTAAGGTC
6705 TCTGTTCTTTAAGGTC
1 TCTGTTCTTTAAGGTC
6721 T
1 T
6722 TGACATGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.18, G:0.18, T:0.52
Consensus pattern (16 bp):
TCTGTTCTTTAAGGTC
Found at i:7338 original size:17 final size:17
Alignment explanation
Indices: 7316--7362 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
7306 AAAAAATAAT
7316 TAAAATAAATATAAAAA
1 TAAAATAAATATAAAAA
*
7333 TAAAATAAATATGATAAA
1 TAAAATAAATAT-AAAAA
*
7351 T-ATATAAATATA
1 TAAAATAAATATA
7363 TTTAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 1 0.04
17 21 0.78
18 5 0.19
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
TAAAATAAATATAAAAA
Found at i:7338 original size:26 final size:26
Alignment explanation
Indices: 7308--7360 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
7298 GATTATGTAA
*
7308 AAAATAATTAAAATAAATATAAAAAT
1 AAAATAAATAAAATAAATATAAAAAT
** *
7334 AAAATAAATATGATAAATATATAAAT
1 AAAATAAATAAAATAAATATAAAAAT
7360 A
1 A
7361 TATTTAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (26 bp):
AAAATAAATAAAATAAATATAAAAAT
Found at i:7369 original size:10 final size:8
Alignment explanation
Indices: 7320--7363 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
7310 AATAATTAAA
7320 ATAAATAT
1 ATAAATAT
* *
7328 AAAAATAAA
1 ATAAAT-AT
7337 ATAAATAT
1 ATAAATAT
7345 GATAAATAT
1 -ATAAATAT
7354 ATAAATAT
1 ATAAATAT
7362 AT
1 AT
7364 TTAAATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
8 16 0.53
9 14 0.47
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (8 bp):
ATAAATAT
Found at i:7501 original size:3 final size:3
Alignment explanation
Indices: 7493--7532 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
7483 CGAGATTATA
7493 TTC TTC TTC TTC TTTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC
7533 CGGAATAAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:7982 original size:25 final size:25
Alignment explanation
Indices: 7920--7982 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
7910 TTGGCAAAGG
* * * *
7920 TGCATTTGTATAGGAAAGCAGAAAG
1 TGCATTTGAATATGCAAGCAGAAAC
*
7945 TGCATTTGAATATGCAAGCAGATAC
1 TGCATTTGAATATGCAAGCAGAAAC
*
7970 TGCTTTTGAATAT
1 TGCATTTGAATAT
7983 TATTTATCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (25 bp):
TGCATTTGAATATGCAAGCAGAAAC
Done.