Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1835
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: 31080
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Found at i:4368 original size:29 final size:30
Alignment explanation
Indices: 4309--4366 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4299 TCCGAGCATT
*
4309 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* * *
4339 GGGGCAAAATTTTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
4367 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.33
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:4596 original size:13 final size:13
Alignment explanation
Indices: 4578--4609 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4568 TTTCCAGCAA
4578 TTATGAATTTATT
1 TTATGAATTTATT
4591 TTATGAATTTATT
1 TTATGAATTTATT
*
4604 TGATGA
1 TTATGA
4610 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:4817 original size:50 final size:50
Alignment explanation
Indices: 4704--4945 Score: 288
Period size: 50 Copynumber: 4.7 Consensus size: 50
4694 ATTTGGGTAA
* * *
4704 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
4760 AGAGGTCCCTTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
4810 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * * *
4860 AGAGGTCCCCTATAAGACCATGTTTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
4910 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
4946 TTTGGCATGT
Statistics
Matches: 164, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 90 0.55
51 28 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.24
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:4896 original size:100 final size:103
Alignment explanation
Indices: 4704--4953 Score: 346
Period size: 100 Copynumber: 2.4 Consensus size: 103
4694 ATTTGGGTAA
4704 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* * *
4769 TTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
4810 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
*
4872 TAAGACCATGTTTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
4910 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
4954 GTTATTATCA
Statistics
Matches: 131, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 49 0.37
101 39 0.30
105 2 0.02
106 40 0.31
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:15397 original size:3 final size:3
Alignment explanation
Indices: 15391--15437 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
15381 TTTAGCCACT
*
15391 TTA TTA TT- TTG TTTA TT- TTA TTA TTA TTA TTA TTA TTA TTA CTTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
15436 TT
1 TT
15438 TGTTTATGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
2 4 0.10
3 30 0.77
4 5 0.13
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:15996 original size:16 final size:16
Alignment explanation
Indices: 15977--16007 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15967 TACACCCATA
*
15977 TATATGTACATATTTT
1 TATATATACATATTTT
15993 TATATATACATATTT
1 TATATATACATATTT
16008 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
Found at i:18720 original size:28 final size:29
Alignment explanation
Indices: 18689--18744 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
18679 TATTATTATT
*
18689 TATATAAATATATAAATTA-ATTATAAAG
1 TATATAAATAAATAAATTACATTATAAAG
* * *
18717 TATATTATTAAATTAATTACATTATAAA
1 TATATAAATAAATAAATTACATTATAAA
18745 TATTATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (29 bp):
TATATAAATAAATAAATTACATTATAAAG
Found at i:19513 original size:3 final size:3
Alignment explanation
Indices: 19505--19534 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
19495 GTGAGGTAAG
19505 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19535 GAGTGGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:19718 original size:24 final size:25
Alignment explanation
Indices: 19686--19745 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
19676 CGGATTAATT
19686 ATTG-ATTGAAAG-GTGGAAAAA-TG
1 ATTGAATTGAAAGTGT-GAAAAAGTG
19709 ATTGAATTGAAAGTGTGAAAAAGTGTG
1 ATTGAATTGAAAGTGTGAAAAA--GTG
19736 ATTGAATTGA
1 ATTGAATTGA
19746 GAATATATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.12
24 14 0.44
25 2 0.06
27 12 0.38
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.30
Consensus pattern (25 bp):
ATTGAATTGAAAGTGTGAAAAAGTG
Found at i:19948 original size:37 final size:39
Alignment explanation
Indices: 19889--19984 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
19879 CGGATAGATT
* * * *
19889 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
19926 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
19965 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
19985 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:20739 original size:12 final size:12
Alignment explanation
Indices: 20722--20746 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20712 AAATTTTTAT
20722 AAAAAAAAATGA
1 AAAAAAAAATGA
20734 AAAAAAAAATGA
1 AAAAAAAAATGA
20746 A
1 A
20747 GTCATTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAAAAATGA
Done.