Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3676
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: 46035
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:9735 original size:50 final size:47
Alignment explanation
Indices: 9613--9741 Score: 163
Period size: 47 Copynumber: 2.7 Consensus size: 47
9603 TATAATGCTA
* *
9613 ATGCCATGTCCCAGACATGGTCTTACACAGGCTCATCCATCAAGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTCATCCATCAAGTCG
*
9660 ATGCCATGTCCCAGACATGGTCTTACACTGACTC-TCACAT-ATCCGTGCAG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTCATC-CATCA--AGT-C-G
*
9710 ATGTCATGTCCCAGACATGGTCTTACACTGAC
1 ATGCCATGTCCCAGACATGGTCTTACACTGAC
9742 ACATGTTGTA
Statistics
Matches: 73, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
46 3 0.04
47 35 0.48
48 2 0.03
49 1 0.01
50 32 0.44
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (47 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGACTCATCCATCAAGTCG
Found at i:9767 original size:45 final size:47
Alignment explanation
Indices: 9617--9782 Score: 139
Period size: 50 Copynumber: 3.5 Consensus size: 47
9607 ATGCTAATGC
* * * * *
9617 CATGTCCCAGACATGGTCTTACACAGGCTCATC-CATCAAGT-C-GATGC
1 CATGTCCCAGACATGGTCTTACACTGAC-CA-CATATC-CGTGCAGATGT
9664 CATGTCCCAGACATGGTCTTACACTGACTCTCACATATCCGTGCAGATGT
1 CATGTCCCAGACATGGTCTTACACTGA--C-CACATATCCGTGCAGATGT
* * *
9714 CATGTCCCAGACATGGTCTTACACTGA-CACATGT-TGTAGCCGATG-
1 CATGTCCCAGACATGGTCTTACACTGACCACATATCCGT-GCAGATGT
*
9759 CTTGTCCCAGACAT-GTCTTACACT
1 CATGTCCCAGACATGGTCTTACACT
9783 AGCTCTCAGC
Statistics
Matches: 104, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
44 10 0.10
45 15 0.14
46 12 0.12
47 25 0.24
48 3 0.03
49 8 0.08
50 31 0.30
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (47 bp):
CATGTCCCAGACATGGTCTTACACTGACCACATATCCGTGCAGATGT
Found at i:12914 original size:16 final size:16
Alignment explanation
Indices: 12893--12927 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12883 CCTTTCGACT
* *
12893 TTTCGGCTTTTTGGTA
1 TTTCGGCATTTTGGCA
12909 TTTCGGCATTTTGGCA
1 TTTCGGCATTTTGGCA
12925 TTT
1 TTT
12928 ACCGACCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.14, G:0.23, T:0.54
Consensus pattern (16 bp):
TTTCGGCATTTTGGCA
Found at i:13737 original size:24 final size:24
Alignment explanation
Indices: 13709--13775 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
13699 CTCCTTAAAT
* *
13709 CTCTCCATAAATCACTCCTTGATT
1 CTCTCCATAAATCACTCCATGATA
* *
13733 TTCTCC-TAATATCTCTCCATGATA
1 CTCTCCATAA-ATCACTCCATGATA
*
13757 CACTCCATAAATCACTCCA
1 CTCTCCATAAATCACTCCA
13776 ACCTCCCATT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
23 3 0.09
24 28 0.82
25 3 0.09
ACGTcount: A:0.28, C:0.34, G:0.03, T:0.34
Consensus pattern (24 bp):
CTCTCCATAAATCACTCCATGATA
Found at i:20887 original size:6 final size:6
Alignment explanation
Indices: 20865--20937 Score: 60
Period size: 6 Copynumber: 12.3 Consensus size: 6
20855 TTCAAAATAG
* * * *
20865 AAAAAT AAAACT CAAAAT AAAAAT -AAAAT AAAAGAA AAAAAC AAAAA-
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA-AT AAAAAT AAAAAT
* * *
20912 AAACAT AAACAT AAACAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
20938 TCGGACTCAA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
5 9 0.16
6 42 0.75
7 5 0.09
ACGTcount: A:0.78, C:0.08, G:0.01, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:20897 original size:29 final size:30
Alignment explanation
Indices: 20865--20934 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
20855 TTCAAAATAG
**
20865 AAAAATAAAACTCAAAATAAAA-ATAAA-AT
1 AAAAATAAAAAACAAAA-AAAACATAAACAT
20894 AAAAGA-AAAAAACAAAAAAAACATAAACAT
1 AAAA-ATAAAAAACAAAAAAAACATAAACAT
*
20924 AAACATAAAAA
1 AAAAATAAAAA
20935 TAATCGGACT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 4 0.12
29 19 0.56
30 11 0.32
ACGTcount: A:0.79, C:0.09, G:0.01, T:0.11
Consensus pattern (30 bp):
AAAAATAAAAAACAAAAAAAACATAAACAT
Found at i:33428 original size:20 final size:18
Alignment explanation
Indices: 33368--33450 Score: 64
Period size: 18 Copynumber: 4.4 Consensus size: 18
33358 AATAATGACT
33368 AAATAAATAATAAGA-AAA
1 AAAT-AATAATAAGAGAAA
*
33386 CAATAATAATAAGAGAAA
1 AAATAATAATAAGAGAAA
*
33404 AAATAATAGACTAAGAGTAA
1 AAATAATA-A-TAAGAGAAA
*
33424 TAATAGA-AATAAG-GAAA
1 AAATA-ATAATAAGAGAAA
33441 TAAATTAATA
1 -AAA-TAATA
33451 GATAGAAGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
17 13 0.25
18 20 0.38
19 5 0.10
20 13 0.25
21 1 0.02
ACGTcount: A:0.66, C:0.02, G:0.11, T:0.20
Consensus pattern (18 bp):
AAATAATAATAAGAGAAA
Found at i:38345 original size:189 final size:189
Alignment explanation
Indices: 38025--38404 Score: 715
Period size: 189 Copynumber: 2.0 Consensus size: 189
38015 AAAACAATAT
*
38025 TACAAAAATAACACAATCTAGCTTTATTTAACTGGCATATAACCAATTTTAATATCTTATAACAG
1 TACAAAAATAACACAATCTAGCTTTATTTAACTGACATATAACCAATTTTAATATCTTATAACAG
*
38090 AATTGCTAATCACACAATAAGTTTTCAATATAGAAACTAAATATTTGAAACATACTATTTAAATA
66 AATTGCTAATCACACAATAAGTTTTCAATATAGAAAATAAATATTTGAAACATACTATTTAAATA
*
38155 TGCTACACTATGTAACAATGTTGTCTTTCTTTAATACTATACACGCATAAAACTTTTCA
131 TGCTACACTATGTAACAATGTTGTCTTTCTTTAATACTATACACACATAAAACTTTTCA
38214 TACAAAAATAACACAATCTAGCTTTATTTAACTGACATATAACCAATTTTAATATCTTATAACAG
1 TACAAAAATAACACAATCTAGCTTTATTTAACTGACATATAACCAATTTTAATATCTTATAACAG
*
38279 AATTGCTAATCACACAATAAGTTTTCAATATAGAAAATGAATATTTGAAACATACTATTTAAATA
66 AATTGCTAATCACACAATAAGTTTTCAATATAGAAAATAAATATTTGAAACATACTATTTAAATA
*
38344 TGCTACACTCTGTAACAATGTTGTCTTTCTTTAATACTATACACACATAAAACTTTTCA
131 TGCTACACTATGTAACAATGTTGTCTTTCTTTAATACTATACACACATAAAACTTTTCA
38403 TA
1 TA
38405 GTATCTAATC
Statistics
Matches: 186, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
189 186 1.00
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.36
Consensus pattern (189 bp):
TACAAAAATAACACAATCTAGCTTTATTTAACTGACATATAACCAATTTTAATATCTTATAACAG
AATTGCTAATCACACAATAAGTTTTCAATATAGAAAATAAATATTTGAAACATACTATTTAAATA
TGCTACACTATGTAACAATGTTGTCTTTCTTTAATACTATACACACATAAAACTTTTCA
Found at i:43174 original size:40 final size:39
Alignment explanation
Indices: 43130--43281 Score: 170
Period size: 40 Copynumber: 3.9 Consensus size: 39
43120 GAATATAGCT
* *
43130 ACTCGCTCAAATGCCTTCGGGACATAGCTCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGC-CGGTTATAGTA
* * *
43170 ACTCGCACCAATGCCTTCGGGACTTAGCCCAGATT-TGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAG-CC-GGTTATAGTA
*
43210 ACTCGCACAAATGCCTTCGGGACTTAGCCGG-AATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCGGTTA-TAGTA
43249 A-TCGCAC-AATGCCTTCGGGACTT-GCCTGGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCC-GGTTAT
43282 CACCGAATAT
Statistics
Matches: 96, Mismatches: 10, Indels: 15
0.79 0.08 0.12
Matches are distributed among these distances:
36 3 0.03
37 19 0.20
38 8 0.08
39 7 0.07
40 55 0.57
41 4 0.04
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (39 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCGGTTATAGTA
Done.