Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_520
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: 63235
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:539 original size:4 final size:4
Alignment explanation
Indices: 532--558 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
522 TAATTTAATC
532 TCTG TCTG TCTG TCTG TCTG TCTG TCT
1 TCTG TCTG TCTG TCTG TCTG TCTG TCT
559 CTCTCTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.22, T:0.52
Consensus pattern (4 bp):
TCTG
Found at i:4991 original size:20 final size:20
Alignment explanation
Indices: 4968--5035 Score: 61
Period size: 19 Copynumber: 3.4 Consensus size: 20
4958 TTAAATTTTA
*
4968 TTTAAAAAGTAATTACAAAT
1 TTTAAAAAGTAATTAAAAAT
*
4988 TTT-AAAAG-AATATATAAA-
1 TTTAAAAAGTAAT-TAAAAAT
*
5006 TTTAAAAAATATATTAAAAAT
1 TTTAAAAAGTA-ATTAAAAAT
5027 ATTTAAAAA
1 -TTTAAAAA
5036 CTATAGGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
18 6 0.15
19 14 0.36
20 9 0.23
21 2 0.05
22 8 0.21
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (20 bp):
TTTAAAAAGTAATTAAAAAT
Found at i:8144 original size:2 final size:2
Alignment explanation
Indices: 8139--8170 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
8129 TTTTTGGGTC
*
8139 CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
8171 TTTTAGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:10503 original size:26 final size:27
Alignment explanation
Indices: 10474--10539 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 27
10464 AATATTTATA
*
10474 TTATATTATTTTAATATTTAATAAT-T
1 TTATATTATTTTAATATATAATAATCT
* *
10500 TTATA-TATTTT-TTATATAATTATCT
1 TTATATTATTTTAATATATAATAATCT
*
10525 TAATATTATTTTAAT
1 TTATATTATTTTAAT
10540 GTTTGTGTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 9 0.28
25 11 0.34
26 11 0.34
27 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
TTATATTATTTTAATATATAATAATCT
Found at i:20804 original size:31 final size:31
Alignment explanation
Indices: 20768--20848 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
20758 AGACCCCAAA
*
20768 AAGTTTAAGTACTAACTTAAGAAAAAGTGTC
1 AAGTTTAAGTACTAAATTAAGAAAAAGTGTC
** *
20799 AAGTTT-AGATACTAAATTTGGAAAATGTGTC
1 AAGTTTAAG-TACTAAATTAAGAAAAAGTGTC
* *
20830 AAGTTCAGGTACTAAATTA
1 AAGTTTAAGTACTAAATTA
20849 GATCAAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
30 2 0.05
31 38 0.93
32 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (31 bp):
AAGTTTAAGTACTAAATTAAGAAAAAGTGTC
Found at i:20899 original size:88 final size:90
Alignment explanation
Indices: 20737--20900 Score: 215
Period size: 88 Copynumber: 1.8 Consensus size: 90
20727 AGAAAAAAGA
* * * * *
20737 GTCAAGTTCAGTTACCAAATTAGACCCCAAAAAGTTTAAGTACTAACTTAAGAAAAAGTGTCAAG
1 GTCAAGTTCAGGTACCAAATTAGACCCAAAAAAATTTAAGTACTAAATTAAGAAAAAGTATCAAG
* *
20802 TTTAGATACTAAATTTGGAAAATGT
66 TTCAAATACTAAATTTGGAAAATGT
* * * *
20827 GTCAAGTTCAGGTACTAAATTAGA-TCAAAAAAATTTAGGTACTAAATT-AGAAAAATTATCAAG
1 GTCAAGTTCAGGTACCAAATTAGACCCAAAAAAATTTAAGTACTAAATTAAGAAAAAGTATCAAG
20890 TTCAAATACTA
66 TTCAAATACTA
20901 TATGTTATAT
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
88 22 0.35
89 19 0.30
90 22 0.35
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (90 bp):
GTCAAGTTCAGGTACCAAATTAGACCCAAAAAAATTTAAGTACTAAATTAAGAAAAAGTATCAAG
TTCAAATACTAAATTTGGAAAATGT
Found at i:21426 original size:18 final size:18
Alignment explanation
Indices: 21403--21437 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21393 TAATACTTTT
*
21403 AAATAAAATCTTTTTAAG
1 AAATAAAATATTTTTAAG
*
21421 AAATAAACTATTTTTAA
1 AAATAAAATATTTTTAA
21438 TTAAAGAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (18 bp):
AAATAAAATATTTTTAAG
Found at i:28813 original size:21 final size:19
Alignment explanation
Indices: 28770--28816 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
28760 AATTTAAAAT
*
28770 TTAAATTTTTTTAATCGAA
1 TTAAATTTTTTTAACCGAA
*
28789 TTAAATTTTATTTAACCTTAA
1 TTAAATTTT-TTTAACC-GAA
28810 TTAAATT
1 TTAAATT
28817 AAAGATGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.38
20 6 0.25
21 9 0.38
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (19 bp):
TTAAATTTTTTTAACCGAA
Found at i:33913 original size:23 final size:20
Alignment explanation
Indices: 33870--33919 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 20
33860 TAAAATTATC
33870 AATTTTATTATTTTAATTAA
1 AATTTTATTATTTTAATTAA
* *
33890 AGTTTTATTTGATTTTTATATAA
1 AATTTTA-TT-ATTTTAAT-TAA
33913 AATTTTA
1 AATTTTA
33920 ATAAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 2 0.08
22 7 0.29
23 9 0.38
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
AATTTTATTATTTTAATTAA
Found at i:34560 original size:37 final size:35
Alignment explanation
Indices: 34505--34573 Score: 86
Period size: 37 Copynumber: 1.9 Consensus size: 35
34495 CCACATCAAG
* *
34505 ATAATTTTTTATTTATATTTATATTTA-TATTTTTA
1 ATAATTTTTTAATTATA-TTATAATTATTATTTTTA
34540 ATAATTTAATTTAATTATATTATAATTATTATTT
1 ATAATTT--TTTAATTATATTATAATTATTATTT
34574 AATGCTCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 7 0.24
36 8 0.28
37 14 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (35 bp):
ATAATTTTTTAATTATATTATAATTATTATTTTTA
Found at i:36132 original size:16 final size:18
Alignment explanation
Indices: 36101--36133 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
36091 TTATTATATT
36101 ATTTTATAATTTAATAAA
1 ATTTTATAATTTAATAAA
36119 ATTTTA-AA-TTAATAA
1 ATTTTATAATTTAATAA
36134 TCACATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTTTATAATTTAATAAA
Found at i:45041 original size:77 final size:77
Alignment explanation
Indices: 44914--45067 Score: 272
Period size: 77 Copynumber: 2.0 Consensus size: 77
44904 CAGTAGAATC
44914 AACAATAATAAGGATAGACGATGTAAGGACAATCAGAACTCAAAAGTGGTCAAGTCTGACGTCAC
1 AACAATAATAAGGATAGACGATGTAAGGACAATCAGAACTCAAAAGTGGTCAAGTCTGACGTCAC
44979 TTAACATTCAGT
66 TTAACATTCAGT
* * * *
44991 AACAATAATAAGGATAGCCGATGTAATGACAATCAGAACTCAATAGTGGTCGAGTCTGACGTCAC
1 AACAATAATAAGGATAGACGATGTAAGGACAATCAGAACTCAAAAGTGGTCAAGTCTGACGTCAC
45056 TTAACATTCAGT
66 TTAACATTCAGT
45068 CTGCTTGGTT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (77 bp):
AACAATAATAAGGATAGACGATGTAAGGACAATCAGAACTCAAAAGTGGTCAAGTCTGACGTCAC
TTAACATTCAGT
Done.