Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1325
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: 16387
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:3275 original size:4 final size:4
Alignment explanation
Indices: 3266--3292 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3256 GCTGCTGCAT
3266 CTGC CTGC CTGC CTGC CTGC CTGC CTG
1 CTGC CTGC CTGC CTGC CTGC CTGC CTG
3293 GATTGGAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.26, T:0.26
Consensus pattern (4 bp):
CTGC
Found at i:8624 original size:3 final size:3
Alignment explanation
Indices: 8616--8656 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
8606 ATTCAATTGA
8616 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
8657 ATCAAAGGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:11484 original size:2 final size:2
Alignment explanation
Indices: 11465--11506 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
11455 CGTGCGTGCT
*
11465 TG TG TG T- TG TG T- TT TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
11505 TG
1 TG
11507 ATACGGAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (2 bp):
TG
Found at i:13328 original size:26 final size:25
Alignment explanation
Indices: 13260--13339 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 25
13250 ATGATAATAT
* *
13260 ATAAT-TTATATAT-TTTTAATAAA
1 ATAATATTATTTATATTTTATTAAA
*
13283 TTAA-ATTATTT-TATTTTATTAAA
1 ATAATATTATTTATATTTTATTAAA
13306 ATAATATTATTTATATTTATATTTAAA
1 ATAATATTATTTATATTT-TA-TTAAA
13333 A-AATATT
1 ATAATATT
13340 GAGTTAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
22 1 0.02
23 20 0.43
24 7 0.15
25 5 0.11
26 8 0.17
27 6 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATAATATTATTTATATTTTATTAAA
Found at i:13795 original size:92 final size:93
Alignment explanation
Indices: 13633--13812 Score: 281
Period size: 92 Copynumber: 1.9 Consensus size: 93
13623 ATACATGTGG
13633 ATGTATATGTATTTGATATACATCATAAAAGTCAATTTCATAATTTTAAGAAACCTTTTATAATT
1 ATGTATATGTATTTGATATACATCATAAAAGTCAATTTCATAATTTTAAGAAACCTTTTATAATT
*
13698 ACGACG-CCAATCCACCTATGACTTTCA
66 ACGACGCCCAAGCCACCTATGACTTTCA
* * * ** * *
13725 ATGTCTATGTATTTGGTATACATCATTAAAGTCAATTTCATAATTTTAATCAACTTTTTATATTT
1 ATGTATATGTATTTGATATACATCATAAAAGTCAATTTCATAATTTTAAGAAACCTTTTATAATT
13790 ACGACGCCCAAGCCACCTATGAC
66 ACGACGCCCAAGCCACCTATGAC
13813 GTTCCAAAGG
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
92 64 0.81
93 15 0.19
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.38
Consensus pattern (93 bp):
ATGTATATGTATTTGATATACATCATAAAAGTCAATTTCATAATTTTAAGAAACCTTTTATAATT
ACGACGCCCAAGCCACCTATGACTTTCA
Found at i:14645 original size:2 final size:2
Alignment explanation
Indices: 14640--14688 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
14630 TATATATAAT
14640 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
14682 AG AG AG A
1 AG AG AG A
14689 AAGAAAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.