Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold707
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: 7559
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Found at i:295 original size:18 final size:19
Alignment explanation
Indices: 267--302 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
257 GCTTTGTGGT
267 TTTTATTTATTTTATAAAA
1 TTTTATTTATTTTATAAAA
*
286 TTTT-TTTATTTTTTAAA
1 TTTTATTTATTTTATAAA
303 TAAATAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTATTTATTTTATAAAA
Found at i:1648 original size:16 final size:17
Alignment explanation
Indices: 1611--1651 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1601 TATGATCTAA
*
1611 ATATATAATAATTTATT
1 ATATATAATAAATTATT
*
1628 A-ATATATTAAATT-TT
1 ATATATAATAAATTATT
1643 ATATATAAT
1 ATATATAAT
1652 TATAATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 3 0.15
16 16 0.80
17 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATATAATAAATTATT
Found at i:1661 original size:13 final size:13
Alignment explanation
Indices: 1627--1678 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
1617 AATAATTTAT
*
1627 TAATATATTAAATT
1 TAATATA-TAAATA
* *
1641 TTATATATAATTA
1 TAATATATAAATA
1654 TAATATATAAATA
1 TAATATATAAATA
*
1667 TATACATATAAA
1 TA-ATATATAAA
1679 CTTGAATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
13 17 0.55
14 14 0.45
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATATATAAATA
Found at i:1675 original size:27 final size:28
Alignment explanation
Indices: 1599--1677 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 28
1589 AATTGATAAA
*
1599 AATATGATCTAAATATATAATA-ATTTATT
1 AATAT-AT-TAAATATATAATATAATTATT
*
1628 AATATATTAAAT-TTTATATATAATTA-T
1 AATATATTAAATATATA-ATATAATTATT
1655 AATATA-TAAATATATACATATAA
1 AATATATTAAATATATA-ATATAA
1678 ACTTGAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
26 8 0.19
27 24 0.56
28 6 0.14
29 5 0.12
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (28 bp):
AATATATTAAATATATAATATAATTATT
Found at i:3144 original size:20 final size:20
Alignment explanation
Indices: 3094--3132 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3084 ATCTAAATAC
*
3094 ATTAAAATTTATATTAAATT
1 ATTAAATTTTATATTAAATT
3114 ATTAAATTTTATA-TAAATT
1 ATTAAATTTTATATTAAATT
3133 TATAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTAAATTTTATATTAAATT
Found at i:5631 original size:20 final size:20
Alignment explanation
Indices: 5606--5646 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5596 ACAGATAAAA
5606 TTATAT-AAAGTAAAATATTC
1 TTATATCAAA-TAAAATATTC
*
5626 TTATATCACATAAAATATTC
1 TTATATCAAATAAAATATTC
5646 T
1 T
5647 CTCTCAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (20 bp):
TTATATCAAATAAAATATTC
Found at i:6497 original size:21 final size:22
Alignment explanation
Indices: 6472--6513 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
6462 TTTATCATTA
6472 TTTTAAATA-ATATTAAAATTT
1 TTTTAAATATATATTAAAATTT
*
6493 TTTTAAATATATTTTAAAATT
1 TTTTAAATATATATTAAAATT
6514 AAATAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTAAATATATATTAAAATTT
Found at i:6782 original size:24 final size:24
Alignment explanation
Indices: 6710--6785 Score: 68
Period size: 24 Copynumber: 3.1 Consensus size: 24
6700 AATTTTATTA
* **
6710 ATTTAAATTAAATTAATTAATTATT
1 ATTTAAATTTAATTAAAAAATT-TT
6735 A-TTAAA--TAATTAAAAAATATTTTT
1 ATTTAAATTTAATT-AAAAA-A-TTTT
6759 ATTTAAATTTAATTAAAAAATTTT
1 ATTTAAATTTAATTAAAAAATTTT
6783 ATT
1 ATT
6786 AAAAAATTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
22 4 0.10
23 3 0.07
24 16 0.38
25 9 0.21
26 5 0.12
27 5 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTTAAATTTAATTAAAAAATTTT
Found at i:6799 original size:12 final size:13
Alignment explanation
Indices: 6763--6801 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
6753 ATTTTTATTT
*
6763 AAATTTAATTAAA
1 AAATTTTATTAAA
6776 AAATTTTATTAAA
1 AAATTTTATTAAA
6789 AAATTTT-TTAAA
1 AAATTTTATTAAA
6801 A
1 A
6802 TTTTTAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 6 0.24
13 19 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTTTATTAAA
Found at i:7050 original size:6 final size:6
Alignment explanation
Indices: 7039--7074 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
7029 CTTATAGCCC
*
7039 CTATGG CTATGG CTATGG CTATGG CAATGG CTATGG
1 CTATGG CTATGG CTATGG CTATGG CTATGG CTATGG
7075 GGGGATTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (6 bp):
CTATGG
Found at i:7433 original size:17 final size:17
Alignment explanation
Indices: 7390--7439 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
7380 AAAAATATTA
7390 AATTTAATAAATTAATTT
1 AATTTAA-AAATTAATTT
* *
7408 AAGTAAAAAATTAATTT
1 AATTTAAAAATTAATTT
*
7425 TATTTAAAAA-TAATT
1 AATTTAAAAATTAATT
7440 GAATCTTGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 5 0.19
17 17 0.63
18 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AATTTAAAAATTAATTT
Found at i:7515 original size:20 final size:19
Alignment explanation
Indices: 7490--7535 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
7480 TCATATCATT
7490 TTTAATTAATAATATATATA
1 TTTAATTAATAATATAT-TA
* *
7510 TTTAATTATTTATATATTA
1 TTTAATTAATAATATATTA
*
7529 TTAAATT
1 TTTAATT
7536 TATATCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAATTAATAATATATTA
Done.