Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1461
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: 12782
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Found at i:582 original size:12 final size:13
Alignment explanation
Indices: 554--586 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
544 TTTATTTCTT
554 TTCTCCATCTACC
1 TTCTCCATCTACC
*
567 TTCTCC-TCTTCC
1 TTCTCCATCTACC
579 TTCTCCAT
1 TTCTCCAT
587 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:1675 original size:28 final size:28
Alignment explanation
Indices: 1643--1707 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
1633 ATTTACTAGA
*
1643 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
1671 ATACCCCTATGTGTGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
1699 ATACCCCTA
1 ATACCCCTA
1708 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:1870 original size:27 final size:28
Alignment explanation
Indices: 1812--1901 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
1802 AGGAAGCGTC
*
1812 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* **
1840 CTGGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
1867 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
1896 CTGGTG
1 CTGGTG
1902 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:1912 original size:29 final size:28
Alignment explanation
Indices: 1822--1912 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
1812 CTGGTGGCTA
* * *
1822 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
1850 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
1877 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
1906 TGTCACA
1 TGCCACA
1913 TTTTCTGTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
27 23 0.44
28 14 0.27
29 15 0.29
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:1920 original size:55 final size:56
Alignment explanation
Indices: 1812--1926 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
1802 AGGAAGCGTC
* * *
1812 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
1867 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
1923 CTGG
1 CTGG
1927 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:3000 original size:11 final size:10
Alignment explanation
Indices: 2972--3005 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2962 AGCCTGTAAG
2972 TATTCTGAAT
1 TATTCTGAAT
*
2982 TTTTCTGAAT
1 TATTCTGAAT
2992 ATATTCTGAAT
1 -TATTCTGAAT
3003 TAT
1 TAT
3006 CTGTCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:8445 original size:23 final size:23
Alignment explanation
Indices: 8415--8461 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
8405 GTGTGTAACT
8415 GACACCCTTTCATAGGCTAGATC
1 GACACCCTTTCATAGGCTAGATC
8438 GACACCCTTTCATAGGCTAGATC
1 GACACCCTTTCATAGGCTAGATC
8461 G
1 G
8462 GCAAAAGCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (23 bp):
GACACCCTTTCATAGGCTAGATC
Found at i:8804 original size:28 final size:29
Alignment explanation
Indices: 8747--8808 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
8737 AACTAGAATA
*
8747 CCCTATGTATGCAAAATTACCATTATTAC
1 CCCTATGTATGCAAAATGACCATTATTAC
* **
8776 CCCTATGTGTGCAAAATGACTTTTA-TAC
1 CCCTATGTATGCAAAATGACCATTATTAC
8804 CCCTA
1 CCCTA
8809 GGGTTAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.34
Consensus pattern (29 bp):
CCCTATGTATGCAAAATGACCATTATTAC
Found at i:8955 original size:28 final size:28
Alignment explanation
Indices: 8914--8994 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
8904 AGGAAGCGTC
8914 CTGGTGGCTA-TGCCACAAATTATCTG-TT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTTT
* **
8942 CTGGTGGCCCTGCCACGTATATCTGTTT
1 CTGGTGGCACTGCCACAAATATCTGTTT
8970 CTGGTGGCACTGCCACAAAATATCT
1 CTGGTGGCACTGCCAC-AAATATCT
8995 ATATATAGTG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
27 6 0.14
28 32 0.73
29 6 0.14
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAATATCTGTTT
Found at i:9134 original size:14 final size:15
Alignment explanation
Indices: 9107--9137 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
9097 TGAAAGGATG
9107 GTATGGGTGGTGTAT
1 GTATGGGTGGTGTAT
9122 GTATGGG-GGTGTAT
1 GTATGGGTGGTGTAT
9136 GT
1 GT
9138 GGTTGGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.13, C:0.00, G:0.48, T:0.39
Consensus pattern (15 bp):
GTATGGGTGGTGTAT
Found at i:12297 original size:45 final size:45
Alignment explanation
Indices: 12248--12420 Score: 185
Period size: 45 Copynumber: 3.8 Consensus size: 45
12238 TGGTTGAGCA
12248 TCCGAACTCGTTGAGTTGAGTCCGAG-TCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAATG
* *
12293 TCCGAACTCGTTGAGTTGAGTCCGAGTT--CGA-GAGATG-TAACTAG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATG-GATGCGAA-T-G
* * *
12337 GCATCGAGCTCATTGAGTTGAGTCCGAGTTCACTATGGATGCGAATG
1 TC--CGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAATG
* *
12384 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGG
12421 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 9, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
42 3 0.03
43 6 0.06
44 3 0.03
45 54 0.50
46 30 0.28
47 2 0.02
48 7 0.06
49 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAATG
Done.