Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1007
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: 20128
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Found at i:376 original size:2 final size:2
Alignment explanation
Indices: 369--420 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
359 TTTTCATGGA
*
369 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
411 AT AT AT AT AT
1 AT AT AT AT AT
421 CAAAAGTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:525 original size:5 final size:5
Alignment explanation
Indices: 515--566 Score: 51
Period size: 5 Copynumber: 11.2 Consensus size: 5
505 AATAATTTTA
*
515 AATAT AATAT -AT-T AATAT -ATAT AAAAAT AATAT AATAT -AT-T AATAT
1 AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT AATAT
561 AATAT A
1 AATAT A
567 TTTAAATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
3 2 0.05
4 12 0.31
5 22 0.56
6 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:530 original size:8 final size:9
Alignment explanation
Indices: 516--576 Score: 53
Period size: 8 Copynumber: 7.3 Consensus size: 9
506 ATAATTTTAA
516 ATATAATAT
1 ATATAATAT
525 AT-TAATAT
1 ATATAATAT
533 ATATAA-A-
1 ATATAATAT
540 A-ATAATAT
1 ATATAATAT
*
548 AATATATTA-
1 -ATATAATAT
557 ATATAATAT
1 ATATAATAT
*
566 ATTTAA-AT
1 ATATAATAT
574 ATA
1 ATA
577 ATTAAATGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
6 4 0.10
7 2 0.05
8 20 0.48
9 11 0.26
10 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
ATATAATAT
Found at i:533 original size:13 final size:13
Alignment explanation
Indices: 515--578 Score: 74
Period size: 13 Copynumber: 4.6 Consensus size: 13
505 AATAATTTTA
515 AATATAATATATT
1 AATATAATATATT
* *
528 AATATATATAAAAAT
1 AATATA-AT-ATATT
543 AATATAATATATT
1 AATATAATATATT
556 AATATAATATATTT
1 AATATAATATA-TT
570 AAATATAAT
1 -AATATAAT
579 TAAATGATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
13 20 0.47
14 6 0.14
15 17 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATATAATATATT
Found at i:553 original size:33 final size:33
Alignment explanation
Indices: 515--578 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
505 AATAATTTTA
515 AATATAAT-ATATTAATATATATAAAAATAATAT
1 AATATAATAATA-TAATATATATAAAAATAATAT
* * *
548 AATATATTAATATAATATATTTAAATATAAT
1 AATATAATAATATAATATATATAAAAATAAT
579 TAAATGATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 24 0.89
34 3 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
AATATAATAATATAATATATATAAAAATAATAT
Found at i:554 original size:18 final size:18
Alignment explanation
Indices: 531--566 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
521 ATATATTAAT
531 ATATATAAAAATAATATA
1 ATATATAAAAATAATATA
* *
549 ATATATTAATATAATATA
1 ATATATAAAAATAATATA
567 TTTAAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATATAAAAATAATATA
Found at i:574 original size:28 final size:27
Alignment explanation
Indices: 511--578 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 27
501 ATTCAATAAT
511 TTTAAATATAATATATTAATATATATA
1 TTTAAATATAATATATTAATATATATA
***
538 AAAATAATATAATATATTAATATAATATA
1 TTTA-AATATAATATATTAATAT-ATATA
567 TTTAAATATAAT
1 TTTAAATATAAT
579 TAAATGATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 1 0.03
28 26 0.79
29 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TTTAAATATAATATATTAATATATATA
Found at i:781 original size:2 final size:2
Alignment explanation
Indices: 774--800 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
764 ATGAAAAATG
774 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
801 ATAAAAGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1845 original size:26 final size:26
Alignment explanation
Indices: 1787--1863 Score: 72
Period size: 28 Copynumber: 2.9 Consensus size: 26
1777 CATATGGAAT
*
1787 ATTTATAA-TTTTTTAA-AAATTT-AA
1 ATTTA-AATTTTTTTAATATATTTAAA
1811 ATTTAAAATTTTTTTAATATATTTAAA
1 ATTT-AAATTTTTTTAATATATTTAAA
1838 ATTTAAATATATTTATT-ATATATTTA
1 ATTTAAAT-T-TTT-TTAATATATTTA
1864 CTATAATTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
24 6 0.13
25 9 0.20
26 9 0.20
27 7 0.16
28 12 0.27
29 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTAAATTTTTTTAATATATTTAAA
Found at i:2830 original size:18 final size:19
Alignment explanation
Indices: 2789--2834 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
2779 TATGTAAATG
*
2789 TAAATATAATAAAATTTAT
1 TAAATATAATAAAAATTAT
*
2808 TAAATATATTAAAAATT-T
1 TAAATATAATAAAAATTAT
2826 TAAATATAA
1 TAAATATAA
2835 ATATGATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATATAATAAAAATTAT
Found at i:3851 original size:36 final size:37
Alignment explanation
Indices: 3767--3851 Score: 136
Period size: 37 Copynumber: 2.3 Consensus size: 37
3757 GATTGGCGCC
* *
3767 GCCACCTAAATTCTAACAATCATAGTGGATTGGCATT
1 GCCACCTAAATACTAACAATCATAGTGGATTGGCATA
*
3804 GCCACCCAAATACTAACAATCATAGTGGATTGGCA-A
1 GCCACCTAAATACTAACAATCATAGTGGATTGGCATA
3840 GCCACCTAAATA
1 GCCACCTAAATA
3852 TTACTTGTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 11 0.25
37 33 0.75
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (37 bp):
GCCACCTAAATACTAACAATCATAGTGGATTGGCATA
Found at i:9323 original size:13 final size:13
Alignment explanation
Indices: 9305--9330 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9295 TTTGCTTACA
9305 TTTATTACAAATC
1 TTTATTACAAATC
9318 TTTATTACAAATC
1 TTTATTACAAATC
9331 ACATGCTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTATTACAAATC
Found at i:13660 original size:21 final size:21
Alignment explanation
Indices: 13619--13660 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
13609 ATTTCTATAT
*
13619 TATTATTAAAAAAATATTAAA
1 TATTATTAAAAAAATAATAAA
*
13640 TATTA-TAATAAAATTAATAAA
1 TATTATTAA-AAAAATAATAAA
13661 AATTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TATTATTAAAAAAATAATAAA
Found at i:19971 original size:11 final size:13
Alignment explanation
Indices: 19946--19984 Score: 55
Period size: 11 Copynumber: 3.1 Consensus size: 13
19936 ATAATTATCA
19946 TTTAAAATATATT
1 TTTAAAATATATT
19959 TTTAAAAT-T-TT
1 TTTAAAATATATT
19970 TTTAAAATGATATT
1 TTTAAAAT-ATATT
19984 T
1 T
19985 GTCTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 9 0.39
14 3 0.13
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (13 bp):
TTTAAAATATATT
Done.