Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold856
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: 14447
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:2486 original size:13 final size:14
Alignment explanation
Indices: 2468--2497 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2458 CAAATTCGAA
2468 ATTCTATTTATT-T
1 ATTCTATTTATTCT
2481 ATTCTATTTATTCT
1 ATTCTATTTATTCT
2495 ATT
1 ATT
2498 ATCTATAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTCTATTTATTCT
Found at i:2535 original size:13 final size:13
Alignment explanation
Indices: 2517--2545 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2507 ATCAAATTTT
2517 TATTTTATATCTA
1 TATTTTATATCTA
2530 TATTTTATATCTA
1 TATTTTATATCTA
2543 TAT
1 TAT
2546 ATATTTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTTATATCTA
Found at i:2563 original size:13 final size:13
Alignment explanation
Indices: 2521--2589 Score: 68
Period size: 13 Copynumber: 5.2 Consensus size: 13
2511 AATTTTTATT
* *
2521 TTATATCTATATT
1 TTATTTCTATATA
*
2534 TTATATCTATATA
1 TTATTTCTATATA
2547 -TATTTCTATATA
1 TTATTTCTATATA
*
2559 TTATTTAGACTCTATA
1 TTATTT---CTATATA
2575 TTATTTCTATATA
1 TTATTTCTATATA
2588 TT
1 TT
2590 TAATATATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
12 11 0.23
13 25 0.52
16 12 0.25
ACGTcount: A:0.32, C:0.09, G:0.01, T:0.58
Consensus pattern (13 bp):
TTATTTCTATATA
Found at i:2613 original size:11 final size:11
Alignment explanation
Indices: 2582--2613 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
2572 ATATTATTTC
2582 TATATATTTAA
1 TATATATTTAA
2593 TATATATTTAA
1 TATATATTTAA
2604 TATATATTTA
1 TATATATTTA
2614 TGAGATTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATATTTAA
Found at i:3261 original size:10 final size:10
Alignment explanation
Indices: 3246--3272 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3236 TAATAAAAAT
3246 GAAAATAATA
1 GAAAATAATA
3256 GAAAATAATA
1 GAAAATAATA
3266 GAAAATA
1 GAAAATA
3273 TAGGGCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.19
Consensus pattern (10 bp):
GAAAATAATA
Found at i:6882 original size:14 final size:14
Alignment explanation
Indices: 6863--6895 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
6853 CTTATTATCT
*
6863 TATTATTTAATTTA
1 TATTATCTAATTTA
6877 TATTATCTAATTTA
1 TATTATCTAATTTA
6891 TATTA
1 TATTA
6896 GAATATTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTATCTAATTTA
Found at i:6938 original size:24 final size:20
Alignment explanation
Indices: 6887--6926 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
6877 TATTATCTAA
6887 TTTATATTAGAATATTCATT
1 TTTATATTAGAATATTCATT
6907 TTTATATTAGAATATTCATT
1 TTTATATTAGAATATTCATT
6927 CTATTATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTATATTAGAATATTCATT
Found at i:6963 original size:25 final size:25
Alignment explanation
Indices: 6955--7048 Score: 58
Period size: 23 Copynumber: 3.9 Consensus size: 25
6945 TTCTATTCTA
*
6955 TATTCTATTATAT-TAATA-TATTC
1 TATTCTATTATATATTATATTATTC
*
6978 TATTCTATTA-AT-TCTAT-TAATTC
1 TATTCTATTATATAT-TATATTATTC
* *
7001 TATTATATTAATATATTCTATTCTATT-
1 TATTCTATT-ATATATTATA-T-TATTC
*
7028 AATTCTATTATATA-TATATTA
1 TATTCTATTATATATTATATTA
7049 ATATATATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
22 3 0.05
23 26 0.47
24 2 0.04
25 7 0.13
26 6 0.11
27 8 0.15
28 3 0.05
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTCTATTATATATTATATTATTC
Found at i:6965 original size:32 final size:32
Alignment explanation
Indices: 6919--7047 Score: 104
Period size: 32 Copynumber: 3.8 Consensus size: 32
6909 TATATTAGAA
* **
6919 TATTCATTCTATTATATATTCTATTATTCTATTC
1 TATTAATTCTATTATAT-TAATA-TATTCTATTC
6953 TA-T-ATTCTATTATATTAATATATTCTATTCTATTAATTC
1 TATTAATTCTATTATATT-A-ATA---TATTCTA-T---TC
6992 TATTAATTCTATTATATTAATATATTCTATTC
1 TATTAATTCTATTATATTAATATATTCTATTC
7024 TATTAATTCTATTATA-T-ATATATT
1 TATTAATTCTATTATATTAATATATT
7048 AATATATATA
Statistics
Matches: 82, Mismatches: 3, Indels: 24
0.75 0.03 0.22
Matches are distributed among these distances:
30 7 0.09
31 2 0.02
32 30 0.37
33 3 0.04
34 2 0.02
35 8 0.10
36 8 0.10
39 7 0.09
40 2 0.02
41 13 0.16
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (32 bp):
TATTAATTCTATTATATTAATATATTCTATTC
Found at i:6985 original size:23 final size:23
Alignment explanation
Indices: 6955--7028 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
6945 TTCTATTCTA
6955 TATTCTATTATATTAATATATTC
1 TATTCTATTATATTAATATATTC
*
6978 TATTCTATTA-A-T--TCTATT-
1 TATTCTATTATATTAATATATTC
*
6996 AATTCTATTATATTAATATATTC
1 TATTCTATTATATTAATATATTC
7019 TATTCTATTA
1 TATTCTATTA
7029 ATTCTATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 9 0.21
19 6 0.14
20 1 0.02
21 1 0.02
22 6 0.14
23 19 0.45
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTCTATTATATTAATATATTC
Found at i:6993 original size:9 final size:9
Alignment explanation
Indices: 6979--7037 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 9
6969 AATATATTCT
6979 ATTCTATTA
1 ATTCTATTA
6988 ATTCTATTA
1 ATTCTATTA
6997 ATTCTATT-
1 ATTCTATTA
7005 A---TATTA
1 ATTCTATTA
* *
7011 A-TATATTCT
1 ATTCTATT-A
7020 ATTCTATTA
1 ATTCTATTA
7029 ATTCTATTA
1 ATTCTATTA
7038 TATATATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
5 4 0.10
6 1 0.02
8 5 0.12
9 27 0.64
10 5 0.12
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTCTATTA
Found at i:7008 original size:41 final size:41
Alignment explanation
Indices: 6935--7064 Score: 178
Period size: 41 Copynumber: 3.2 Consensus size: 41
6925 TTCTATTATA
6935 TATTCTATT-ATTCTATTCTATATTCTATTATATTAATATATTC
1 TATTCTATTAATTCTA-T-TA-ATTCTATTATATTAATATATTC
6978 TATTCTATTAATTCTATTAATTCTATTATATTAATATATTC
1 TATTCTATTAATTCTATTAATTCTATTATATTAATATATTC
* *
7019 TATTCTATTAATTCTATT-A-TATA-TATATTAATATATATA
1 TATTCTATTAATTCTATTAATTCTATTATATTAATATAT-TC
7058 TATTCTA
1 TATTCTA
7065 ATTTAACTAA
Statistics
Matches: 83, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
38 13 0.16
39 11 0.13
40 1 0.01
41 40 0.48
42 2 0.02
43 10 0.12
44 6 0.07
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (41 bp):
TATTCTATTAATTCTATTAATTCTATTATATTAATATATTC
Found at i:11663 original size:14 final size:14
Alignment explanation
Indices: 11627--11676 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
11617 ACTCGCTTAG
11627 ATATACTTAGTATTTA
1 ATATACTTAGTA--TA
11643 TATATACTTAGTATA
1 -ATATACTTAGTATA
* *
11658 ATATACTAATTATA
1 ATATACTTAGTATA
11672 ATATA
1 ATATA
11677 ATCATTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 17 0.55
15 2 0.06
17 12 0.39
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (14 bp):
ATATACTTAGTATA
Done.