Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1040
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: 40025
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Found at i:3654 original size:40 final size:42
Alignment explanation
Indices: 3559--3665 Score: 109
Period size: 41 Copynumber: 2.7 Consensus size: 42
3549 TATTCGAATG
* * *
3559 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGAACT
1 ATATCCGGGCTAAGATCCCGAAGGCATTCGTGCGAGGTG-ACT
* * *
3601 ATA-CCGGACTAAGAT-CCTAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCCGAAGGCATTCGTGCGAGGTGACT
3640 ATATCCGGGCTAAGA-CCCGAA-GCATT
1 ATATCCGGGCTAAGATCCCGAAGGCATT
3666 TTGTGCTAGC
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
39 10 0.19
40 14 0.26
41 26 0.48
42 4 0.07
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (42 bp):
ATATCCGGGCTAAGATCCCGAAGGCATTCGTGCGAGGTGACT
Found at i:3706 original size:37 final size:37
Alignment explanation
Indices: 3638--3766 Score: 179
Period size: 38 Copynumber: 3.4 Consensus size: 37
3628 GTGCGAGTTG
*
3638 CTATATCCGGGCTAAGACCCGAAGCATTTTGTGCTAGCA
1 CTATATCCGGGCTAA-AACCGAAGCA-TTTGTGCTAGCA
3677 -TATATCCGGGCTAAAACCGAAGGCATTTGTGCTAGCA
1 CTATATCCGGGCTAAAACCGAA-GCATTTGTGCTAGCA
* *
3714 TTATATCCGGGCTAAAACCGAAGTATTTGTGCTAGCGA
1 CTATATCCGGGCTAAAACCGAAGCATTTGTGCTAGC-A
*
3752 CTATATCTGGGCTAA
1 CTATATCCGGGCTAA
3767 GTCCTAAAGG
Statistics
Matches: 83, Mismatches: 4, Indels: 7
0.88 0.04 0.07
Matches are distributed among these distances:
37 31 0.37
38 52 0.63
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (37 bp):
CTATATCCGGGCTAAAACCGAAGCATTTGTGCTAGCA
Found at i:3786 original size:76 final size:76
Alignment explanation
Indices: 3639--3787 Score: 187
Period size: 76 Copynumber: 2.0 Consensus size: 76
3629 TGCGAGTTGC
* *
3639 TATATCCGGGCTAAGACCCGAAGCATTTTGTGCTAGCATATATCCGGGCTAAAACCGAAGGCATT
1 TATATCCGGGCTAAGAACCGAAGCATTTTGTGCTAGCATATATCCGGGCTAAAACCAAAGGCATT
*
3704 TGTGCTAGCAT
66 TATGCTAGCAT
* * **
3715 TATATCCGGGCTAA-AACCGAAGTA-TTTGTGCTAGCGACTATATCTGGGCTAAGTCCTAAAGG-
1 TATATCCGGGCTAAGAACCGAAGCATTTTGTGCTAGC-A-TATATCCGGGCTAAAACC-AAAGGC
3777 ATTTATGCTAG
63 ATTTATGCTAG
3788 TGACCACATC
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
74 11 0.17
75 9 0.14
76 39 0.62
77 4 0.06
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (76 bp):
TATATCCGGGCTAAGAACCGAAGCATTTTGTGCTAGCATATATCCGGGCTAAAACCAAAGGCATT
TATGCTAGCAT
Found at i:14717 original size:103 final size:104
Alignment explanation
Indices: 14501--14722 Score: 270
Period size: 103 Copynumber: 2.2 Consensus size: 104
14491 TTGCTACTGG
14501 CCAA-AAAGTATCGATACCTTTTTGGCCAAGTATCAATATGTTTTGAATTACCAATACCCCCTCT
1 CCAACAAAGTATCGATACCTTTTTGGCCAAGTATCAATATGTTTTGAATTACCAATACCCCCTCT
* * * * * *
14565 TAAAAACGATACCAAAATGGTAGTCTGTTTTTCACAAAC
66 TAAAAACGATACCAAAATAGCAGTCTATTTCTCAAAAAA
* * * * * *
14604 CCTACTAAGTACCGATACC-TTTTGGTCAAGTATCAATAT-TTTCTGAATTATCGATACCCCCTC
1 CCAACAAAGTATCGATACCTTTTTGGCCAAGTATCAATATGTTT-TGAATTACCAATACCCCCTC
** * *
14667 TTAAAAGTGATACCAAAATAGCATTTTATTTCTCAAAAAA
65 TTAAAAACGATACCAAAATAGCAGTCTATTTCTCAAAAAA
14707 CCAACAAAGTATCGAT
1 CCAACAAAGTATCGAT
14723 TCGATACCGA
Statistics
Matches: 98, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
102 3 0.03
103 83 0.85
104 12 0.12
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.32
Consensus pattern (104 bp):
CCAACAAAGTATCGATACCTTTTTGGCCAAGTATCAATATGTTTTGAATTACCAATACCCCCTCT
TAAAAACGATACCAAAATAGCAGTCTATTTCTCAAAAAA
Found at i:15010 original size:14 final size:14
Alignment explanation
Indices: 14993--15029 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
14983 GAAAGCACTT
14993 TCAAGCAAAAATCA
1 TCAAGCAAAAATCA
15007 TCAAGCAAAAATCA
1 TCAAGCAAAAATCA
*
15021 TCAATCAAA
1 TCAAGCAAA
15030 CAACCTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.57, C:0.22, G:0.05, T:0.16
Consensus pattern (14 bp):
TCAAGCAAAAATCA
Found at i:35629 original size:29 final size:29
Alignment explanation
Indices: 35589--35662 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
35579 ATGTCGCTGG
* *
35589 GCCTAACGGGCCATATAAATGTGACTTG-
1 GCCTAATGGGCCATATAAAGGTGACTTGC
* * * *
35617 GTCCTAGTGGGCCATGTACAGGTGATTTGC
1 G-CCTAATGGGCCATATAAAGGTGACTTGC
35647 GCCTAATGGGCCATAT
1 GCCTAATGGGCCATAT
35663 GAATATGATT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 1 0.03
29 34 0.94
30 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (29 bp):
GCCTAATGGGCCATATAAAGGTGACTTGC
Found at i:35885 original size:57 final size:57
Alignment explanation
Indices: 35797--35910 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
35787 GTTATAGGGT
35797 TAAGGTGTGGCAACGGGTATAGGCATGTCTAGGATTGGATCTAGGGAGAGCTTGGTA
1 TAAGGTGTGGCAACGGGTATAGGCATGTCTAGGATTGGATCTAGGGAGAGCTTGGTA
35854 TAAGGTGTGGCAACGGGTATAGGCATGTCTAGGATTGGATCTAGGGAGAGCTTGGTA
1 TAAGGTGTGGCAACGGGTATAGGCATGTCTAGGATTGGATCTAGGGAGAGCTTGGTA
35911 CTTAAGCGGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.25, C:0.11, G:0.39, T:0.26
Consensus pattern (57 bp):
TAAGGTGTGGCAACGGGTATAGGCATGTCTAGGATTGGATCTAGGGAGAGCTTGGTA
Done.