Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2070
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: 20214
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:2083 original size:21 final size:23
Alignment explanation
Indices: 2030--2085 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
2020 ATATAATTTT
2030 TATATTATA-AAAATTACATAATA
1 TATATTATATAAAATTA-ATAATA
**
2053 TATAAAATATAAAATT-A-AATA
1 TATATTATATAAAATTAATAATA
2074 TATATTATATAA
1 TATATTATATAA
2086 TAGTAAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 14 0.50
22 1 0.04
23 7 0.25
24 6 0.21
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TATATTATATAAAATTAATAATA
Found at i:2092 original size:21 final size:21
Alignment explanation
Indices: 2049--2092 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2039 AAAATTACAT
*
2049 AATATATAAAATATAAAATTA
1 AATATATAAAATATAAAAGTA
** *
2070 AATATATATTATATAATAGTA
1 AATATATAAAATATAAAAGTA
2091 AA
1 AA
2093 ATGACCAGTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AATATATAAAATATAAAAGTA
Found at i:7683 original size:17 final size:17
Alignment explanation
Indices: 7633--7697 Score: 53
Period size: 18 Copynumber: 3.7 Consensus size: 17
7623 AATACTATAA
*
7633 TTATAT-TTAAATTATTT
1 TTATATATT-AATAATTT
*
7650 TT-TATTTTATATAAATTT
1 TTATATATTA-AT-AATTT
7668 TTATATATTAATAATTT
1 TTATATATTAATAATTT
*
7685 ATATTATATTAAT
1 TTA-TATATTAAT
7698 TTTAAAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
16 4 0.10
17 13 0.32
18 17 0.43
19 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATATATTAATAATTT
Found at i:7692 original size:32 final size:33
Alignment explanation
Indices: 7650--7721 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
7640 TAAATTATTT
* * *
7650 TTTATTTTATATAAATTTTTATATATTAATA-A
1 TTTATATTATATAAATTTTAAAATATTAATATA
* *
7682 TTTATATTATATTAATTTTAAAATATTTATATA
1 TTTATATTATATAAATTTTAAAATATTAATATA
7715 TTTATAT
1 TTTATAT
7722 CTTTTATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 26 0.76
33 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (33 bp):
TTTATATTATATAAATTTTAAAATATTAATATA
Found at i:7741 original size:40 final size:42
Alignment explanation
Indices: 7651--7743 Score: 104
Period size: 40 Copynumber: 2.3 Consensus size: 42
7641 AAATTATTTT
* *
7651 TTATTTTATATAAATTTTTATATATTAATAATTTATATTATA
1 TTATTTTTTATAAATATTTATATATTAATAATTTATATTATA
* * *
7693 TTA-ATTTTA-AAATATTTATATATTTAT-ATCTTTTATTA-A
1 TTATTTTTTATAAATATTTATATATTAATAAT-TTATATTATA
7732 TTATTTTTTATA
1 TTATTTTTTATA
7744 TTATATTATC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
39 6 0.14
40 28 0.67
41 5 0.12
42 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (42 bp):
TTATTTTTTATAAATATTTATATATTAATAATTTATATTATA
Found at i:10699 original size:18 final size:18
Alignment explanation
Indices: 10678--10730 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
10668 AGTTATTAAT
10678 TTATATATATTTAAAAAA
1 TTATATATATTTAAAAAA
*
10696 TTATATTTATATT-AAAAA
1 TTATATATAT-TTAAAAAA
* *
10714 TAAAATAT-TTTAAAAAA
1 TTATATATATTTAAAAAA
10731 ATTAAATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 2 0.07
17 6 0.21
18 19 0.66
19 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTATATATATTTAAAAAA
Found at i:11432 original size:34 final size:34
Alignment explanation
Indices: 11386--11514 Score: 98
Period size: 34 Copynumber: 3.4 Consensus size: 34
11376 TATGATATAA
*
11386 ATATATAATATAAAAAATTAAAAATTAAAAAATT
1 ATATATATTATAAAAAATTAAAAATTAAAAAATT
11420 ATATATATTATAATAAAATATAAAAATAATAAAAATATATT
1 ATATATATTATAA-AAAAT-TAAAAAT--T-AAAA-A-ATT
* *
11461 AATATTTATTAATTATAAATAATTAATATATT-AAAAATT
1 -ATA--TA-T-ATTATAAAAAATTAA-AAATTAAAAAATT
11500 ATATATATCTATAAA
1 ATATATAT-TATAAA
11515 TATACGATAA
Statistics
Matches: 78, Mismatches: 3, Indels: 27
0.72 0.03 0.25
Matches are distributed among these distances:
34 14 0.18
35 12 0.15
36 9 0.12
38 4 0.05
39 7 0.09
40 2 0.03
41 6 0.08
42 3 0.04
43 1 0.01
44 5 0.06
45 8 0.10
46 7 0.09
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (34 bp):
ATATATATTATAAAAAATTAAAAATTAAAAAATT
Found at i:11480 original size:25 final size:26
Alignment explanation
Indices: 11452--11507 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
11442 AAAATAATAA
**
11452 AAATATATTAATAT-TTATTAATTAT
1 AAATATATTAATATATTAAAAATTAT
11477 AAATA-ATTAATATATTAAAAATTAT
1 AAATATATTAATATATTAAAAATTAT
*
11502 ATATAT
1 AAATAT
11508 CTATAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATATATTAATATATTAAAAATTAT
Found at i:11505 original size:16 final size:16
Alignment explanation
Indices: 11396--11507 Score: 58
Period size: 15 Copynumber: 7.0 Consensus size: 16
11386 ATATATAATA
* *
11396 TAAAAAATTAA-AAAT
1 TAAATAATTAATATAT
*
11411 TAAAAAATTATATATAT
1 TAAATAATTA-ATATAT
11428 TATAATAA--AATATA-
1 TA-AATAATTAATATAT
* *
11442 AAAATAATAAAAATATAT
1 TAAATAAT--TAATATAT
*
11460 TAATATTTATTAAT-TA-
1 TAA-A-TAATTAATATAT
11476 TAAATAATTAATATAT
1 TAAATAATTAATATAT
11492 TAAA-AATTATATATAT
1 TAAATAATTA-ATATAT
11508 CTATAAATAT
Statistics
Matches: 77, Mismatches: 7, Indels: 25
0.71 0.06 0.23
Matches are distributed among these distances:
13 5 0.06
14 8 0.10
15 23 0.30
16 15 0.19
17 13 0.17
18 9 0.12
19 1 0.01
20 3 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATAATTAATATAT
Found at i:11894 original size:19 final size:19
Alignment explanation
Indices: 11839--11894 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
11829 TAAAATAAAA
*
11839 TATATAAATATATTAAAATT
1 TATATAAATATA-TAATATT
* *
11859 TAT-TGAATATAAAAATATT
1 TATATAAATAT-ATAATATT
*
11878 TGTATAAATATATAATA
1 TATATAAATATATAATA
11895 ATAATTATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (19 bp):
TATATAAATATATAATATT
Found at i:16179 original size:17 final size:18
Alignment explanation
Indices: 16165--16198 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16155 TTATATTATA
16165 TAAAAA-TAAAAATTAAT
1 TAAAAATTAAAAATTAAT
16182 TAAAAATTAAAAATTAA
1 TAAAAATTAAAAATTAA
16199 AATTGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAATTAAAAATTAAT
Done.