Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3603
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: 40352
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:14747 original size:15 final size:15
Alignment explanation
Indices: 14729--14757 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
14719 AAAACTAACT
14729 TTTTTTTTTCACAAA
1 TTTTTTTTTCACAAA
14744 TTTTTTTTTCACAA
1 TTTTTTTTTCACAA
14758 CTTGATATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTTTTTCACAAA
Found at i:14817 original size:11 final size:11
Alignment explanation
Indices: 14793--14833 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
14783 GAATGGAAAT
**
14793 ATTTTTTTTGA
1 ATTTTTTTCAA
14804 ATTTTTTTCAA
1 ATTTTTTTCAA
14815 ATTTTTGTTCAA
1 ATTTTT-TTCAA
14827 ATTTTTT
1 ATTTTTT
14834 CGAAGAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (11 bp):
ATTTTTTTCAA
Found at i:14820 original size:12 final size:12
Alignment explanation
Indices: 14793--14833 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
14783 GAATGGAAAT
*
14793 ATTTTTTTT-GA
1 ATTTTTTTTCAA
14804 A-TTTTTTTCAA
1 ATTTTTTTTCAA
*
14815 ATTTTTGTTCAA
1 ATTTTTTTTCAA
14827 ATTTTTT
1 ATTTTTT
14834 CGAAGAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
10 7 0.28
11 3 0.12
12 15 0.60
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (12 bp):
ATTTTTTTTCAA
Found at i:22124 original size:30 final size:30
Alignment explanation
Indices: 22088--22160 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
22078 ACAAAGGAAA
22088 AAGAAAATCAAGATTCACTTTCTTGTTTTC
1 AAGAAAATCAAGATTCACTTTCTTGTTTTC
*
22118 AAGAAAATCAAGATTCACTTTCTTGTTTTT
1 AAGAAAATCAAGATTCACTTTCTTGTTTTC
22148 AAGAAAATCAAGA
1 AAGAAAATCAAGA
22161 AACCGAATCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.36
Consensus pattern (30 bp):
AAGAAAATCAAGATTCACTTTCTTGTTTTC
Found at i:24996 original size:20 final size:21
Alignment explanation
Indices: 24971--25012 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
24961 AACTAAAGTA
24971 AGCTAAAAATGAGCTG-ATTG
1 AGCTAAAAATGAGCTGAATTG
*
24991 AGCTAAAATTGAGCTGAATTG
1 AGCTAAAAATGAGCTGAATTG
25012 A
1 A
25013 ACTCGATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (21 bp):
AGCTAAAAATGAGCTGAATTG
Found at i:27868 original size:14 final size:14
Alignment explanation
Indices: 27837--27881 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
27827 TTCAAAACTT
**
27837 TTTTTTTGAATTCC
1 TTTTTTTGAATTTA
27851 TTTTTTTGAATTTA
1 TTTTTTTGAATTTA
* *
27865 TTTTTTTAAATATA
1 TTTTTTTGAATTTA
27879 TTT
1 TTT
27882 CAATACAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (14 bp):
TTTTTTTGAATTTA
Found at i:29374 original size:10 final size:11
Alignment explanation
Indices: 29348--29376 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29338 AGACGAGCTC
29348 ATTGAGCTAAG
1 ATTGAGCTAAG
29359 ATTGAGCTAA-
1 ATTGAGCTAAG
29369 ATTGAGCT
1 ATTGAGCT
29377 TAACCAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (11 bp):
ATTGAGCTAAG
Found at i:29933 original size:20 final size:20
Alignment explanation
Indices: 29887--29933 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
29877 AGCTCGTTTC
* *
29887 CAGCTCAGTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
29907 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
29927 CAGCTCA
1 CAGCTCA
29934 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.15, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:33268 original size:26 final size:27
Alignment explanation
Indices: 33206--33273 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
33196 ATATTGAGTC
* *
33206 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
33233 CGCACACTTAGTGCTACGTAATCAA-T
1 CGCACACTTAGTGCTACATAATCAACT
33259 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
33274 GTACAATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
26 16 0.42
27 22 0.58
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:38712 original size:20 final size:21
Alignment explanation
Indices: 38689--38730 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
38679 AAACTAAAGT
38689 AGCTAAAAATGAGCTG-ATTG
1 AGCTAAAAATGAGCTGAATTG
*
38709 AGCTAAAATTGAGCTGAATTG
1 AGCTAAAAATGAGCTGAATTG
38730 A
1 A
38731 ACTCGATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (21 bp):
AGCTAAAAATGAGCTGAATTG
Done.