Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold842
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: 16851
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Found at i:10570 original size:52 final size:52
Alignment explanation
Indices: 10492--10641 Score: 205
Period size: 52 Copynumber: 2.9 Consensus size: 52
10482 CGAAATATGA
10492 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTAGGC
* * * *
10544 AAATTTGCCTGCATGTATCGATACATT-ATAAAATGTATCGATATATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGA-ATAGTGTATCGATACATCTAGGC
**
10596 AAATTTGCCTGCATGTAATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGT-ATCGATACATTGAAT-AGTGTATCGATACA
10642 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
51 1 0.01
52 63 0.74
53 21 0.25
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTAGGC
Found at i:10648 original size:13 final size:13
Alignment explanation
Indices: 10630--10654 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10620 CAAAGATCAG
10630 TGTATCGATACAA
1 TGTATCGATACAA
10643 TGTATCGATACA
1 TGTATCGATACA
10655 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:11629 original size:51 final size:52
Alignment explanation
Indices: 11497--11707 Score: 199
Period size: 55 Copynumber: 4.2 Consensus size: 52
11487 GAAAAGTGAT
* * * * * * * *
11497 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-G-A
* * *
11551 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
11604 AAAGGTG-CAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* *
11646 AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
11698 AAAGGTGCCA
1 AAAGGTGCCA
11708 CCGACTTGTG
Statistics
Matches: 129, Mismatches: 17, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
42 7 0.05
43 30 0.23
44 1 0.01
45 1 0.01
49 1 0.01
50 1 0.01
51 30 0.23
52 12 0.09
53 6 0.05
54 5 0.04
55 35 0.27
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGA
Found at i:11666 original size:43 final size:42
Alignment explanation
Indices: 11604--11692 Score: 142
Period size: 43 Copynumber: 2.1 Consensus size: 42
11594 TAAAGATGGA
*
11604 AAAGGTGCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
11646 AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTT
1 AAAGGTG-CAATATGCTGATTCAAGGCCAGCTACATTGGACTT
11689 AAAG
1 AAAG
11693 ATGGAAAAGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
42 7 0.16
43 36 0.84
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (42 bp):
AAAGGTGCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:11737 original size:30 final size:29
Alignment explanation
Indices: 11694--11964 Score: 133
Period size: 30 Copynumber: 9.0 Consensus size: 29
11684 GACTTAAAGA
*
11694 TGGAAAA-GGTGCCACCGACTTGTGGGCT
1 TGGAAAAGGGTGCCACTGACTTGTGGGCT
*
11722 TCGGAAAAGGGTGCCACTGATTTGTGGGCT
1 T-GGAAAAGGGTGCCACTGACTTGTGGGCT
* *
11752 TTG--AAGGTTGCCACTGACTTGTGGGCTT
1 TGGAAAAGGGTGCCACTGACTTGTGGGC-T
* *
11780 TTGAAAAGGGTGCCACTAACTTGGTGGG-T
1 TGGAAAAGGGTGCCACTGACTT-GTGGGCT
* ** * * *
11809 TAAAAAGAAAAAAAGTGCTACGGAGTTGTGGTGTGGACTT
1 T-----GGAAAAGGGTGCCACTGA-CT-T-GTG-GG-C-T
* *
11849 TGGAAAA-GATGCCACCGACTTGTGGGCT
1 TGGAAAAGGGTGCCACTGACTTGTGGGCT
* *
11877 TCGAAAAAGGGTGCCACTGATTTGTGGGCT
1 T-GGAAAAGGGTGCCACTGACTTGTGGGCT
* * *
11907 TTG--AAGGTTGCTACTGACTTGTGGGCTT
1 TGGAAAAGGGTGCCACTGACTTGTGGGC-T
** ***
11935 TTAAAAAAAATGCCACTGACTTGTGGGCT
1 TGGAAAAGGGTGCCACTGACTTGTGGGCT
11964 T
1 T
11965 TAAAAAAAAT
Statistics
Matches: 186, Mismatches: 35, Indels: 43
0.70 0.13 0.16
Matches are distributed among these distances:
27 41 0.22
28 10 0.05
29 17 0.09
30 75 0.40
31 8 0.04
32 1 0.01
33 1 0.01
34 18 0.10
35 6 0.03
36 5 0.03
37 2 0.01
40 2 0.01
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (29 bp):
TGGAAAAGGGTGCCACTGACTTGTGGGCT
Found at i:11922 original size:27 final size:27
Alignment explanation
Indices: 11858--11935 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
11848 TTGGAAAAGA
* *
11858 TGCCACCGACTTGTGGGCTTCGAAAAAGGG
1 TGCCACTGACTTGTGGGCTTTG---AAGGG
* *
11888 TGCCACTGATTTGTGGGCTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTGAAGGG
*
11915 TGCTACTGACTTGTGGGCTTT
1 TGCCACTGACTTGTGGGCTTT
11936 TAAAAAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 23 0.55
30 19 0.45
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.32
Consensus pattern (27 bp):
TGCCACTGACTTGTGGGCTTTGAAGGG
Found at i:11965 original size:30 final size:30
Alignment explanation
Indices: 11919--11997 Score: 124
Period size: 29 Copynumber: 2.6 Consensus size: 30
11909 GAAGGTTGCT
11919 ACTGACTTGTGGGCTTTTAAAAAAAATGCC
1 ACTGACTTGTGGGCTTTTAAAAAAAATGCC
11949 ACTGACTTGTGGGC-TTTAAAAAAAATGCC
1 ACTGACTTGTGGGCTTTTAAAAAAAATGCC
*
11978 ACTACGACTTGTGGACTTTT
1 ACT--GACTTGTGGGCTTTT
11998 GAAGGGTGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
29 18 0.40
30 14 0.31
31 10 0.22
32 3 0.07
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (30 bp):
ACTGACTTGTGGGCTTTTAAAAAAAATGCC
Found at i:13430 original size:1 final size:1
Alignment explanation
Indices: 13426--13556 Score: 91
Period size: 1 Copynumber: 131.0 Consensus size: 1
13416 CCGGACCCCC
* * * * * * * * *
13426 TTTTTTGTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTGTTTTTTTTTGTTTTTTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** ** * * * * * *
13491 TTTCATTTTTTTCATTTTTTTTGTGTTTGTTTTTTTTTTGTTTTTTTTTGTTTTTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13556 T
1 T
13557 GGAGGACGCC
Statistics
Matches: 94, Mismatches: 36, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 94 1.00
ACGTcount: A:0.03, C:0.02, G:0.10, T:0.85
Consensus pattern (1 bp):
T
Found at i:13456 original size:10 final size:10
Alignment explanation
Indices: 13427--13548 Score: 117
Period size: 10 Copynumber: 11.8 Consensus size: 10
13417 CGGACCCCCT
13427 TTTTTGTTTTG
1 TTTTT-TTTTG
13438 TTTGTTTTTT-
1 TTT-TTTTTTG
*
13448 TATTGTTTTTG
1 T-TTTTTTTTG
13459 -TTTTTTTTG
1 TTTTTTTTTG
13468 TTTTTTTTTG
1 TTTTTTTTTG
13478 TTTTTTTTTG
1 TTTTTTTTTG
13488 TTTTTTCATTT-
1 TTTTTT--TTTG
13499 TTTTCATTTTT-
1 TTTT--TTTTTG
* *
13510 TTTGTGTTTG
1 TTTTTTTTTG
13520 TTTTTTTTTTG
1 -TTTTTTTTTG
13531 TTTTTTTTTG
1 TTTTTTTTTG
13541 TTTTTTTT
1 TTTTTTTT
13549 ATTTTTTTGG
Statistics
Matches: 95, Mismatches: 6, Indels: 21
0.78 0.05 0.17
Matches are distributed among these distances:
9 12 0.13
10 49 0.52
11 27 0.28
12 5 0.05
13 2 0.02
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:13553 original size:26 final size:25
Alignment explanation
Indices: 13427--13555 Score: 143
Period size: 25 Copynumber: 5.0 Consensus size: 25
13417 CGGACCCCCT
* *
13427 TTTTTGTTTTGTTTGTTTTTTTATTG
1 TTTTT-TTTTGTTTTTTTTTTTTTTG
*
13453 TTTTTGTTTT-TTTTGTTTTTTTTTG
1 TTTTT-TTTTGTTTTTTTTTTTTTTG
**
13478 TTTTTTTTTGTTTTTTCATTTTTTTCA
1 TTTTTTTTTGTTTTTT--TTTTTTTTG
*
13505 TTTTTTTTGTGTTTGTTTTTTTTTTG
1 TTTTTTTT-TGTTTTTTTTTTTTTTG
13531 TTTTTTTTTGTTTTTTTTATTTTTT
1 TTTTTTTTTGTTTTTTTT-TTTTTT
13556 TGGAGGACGC
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
24 4 0.05
25 31 0.35
26 31 0.35
27 15 0.17
28 7 0.08
ACGTcount: A:0.03, C:0.02, G:0.10, T:0.85
Consensus pattern (25 bp):
TTTTTTTTTGTTTTTTTTTTTTTTG
Done.