Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2732
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: 7130
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Found at i:2785 original size:52 final size:51
Alignment explanation
Indices: 2705--2823 Score: 202
Period size: 52 Copynumber: 2.3 Consensus size: 51
2695 AAAAGTTGCT
*
2705 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTACC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA-TTACC
* *
2757 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
2808 TGCATGTATCGATACA
1 TGCATGTATCGATACA
2824 AAGCTCAGTG
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
51 20 0.31
52 44 0.69
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (51 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTACC
Found at i:2836 original size:51 final size:52
Alignment explanation
Indices: 2705--2843 Score: 158
Period size: 52 Copynumber: 2.7 Consensus size: 52
2695 AAAAGTTGCT
** *
2705 TGCATGTATCGATAC-ATTTAATAGTGTATCGATACATCTGGGCAAATTTACC
1 TGCATGTATCGATACAAGCT-ACAGTGTATCGATACATCTGGGCAAATTTACC
*** * * *
2757 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-TTGCC
1 TGCATGTATCGATACAAGCTACAGTGTATCGATACATCTGGGCAAATTTACC
2808 TGCATGTATCGATACAAAGCT-CAGTGTATCGATACA
1 TGCATGTATCGATAC-AAGCTACAGTGTATCGATACA
2844 ATGTATCGAT
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
51 32 0.42
52 42 0.55
53 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
TGCATGTATCGATACAAGCTACAGTGTATCGATACATCTGGGCAAATTTACC
Found at i:2850 original size:13 final size:13
Alignment explanation
Indices: 2832--2856 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2822 CAAAGCTCAG
2832 TGTATCGATACAA
1 TGTATCGATACAA
2845 TGTATCGATACA
1 TGTATCGATACA
2857 TTTGAGTAAT
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:2935 original size:13 final size:13
Alignment explanation
Indices: 2917--2941 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2907 TACAAAAAAA
2917 TGTATCGATACAT
1 TGTATCGATACAT
2930 TGTATCGATACA
1 TGTATCGATACA
2942 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3841 original size:52 final size:51
Alignment explanation
Indices: 3709--3919 Score: 186
Period size: 43 Copynumber: 4.2 Consensus size: 51
3699 GAAAAGTGAT
* * * * * * * *
3709 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG-G
* * *
3761 AAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 --AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG
*
3815 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T--
1 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG
* * *
3859 AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTTAAAGATGG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG
3910 AAAGGTGCCA
1 AAAGGTGCCA
3920 CCGATTTGTG
Statistics
Matches: 129, Mismatches: 19, Indels: 21
0.76 0.11 0.12
Matches are distributed among these distances:
43 37 0.29
44 1 0.01
46 1 0.01
49 1 0.01
51 11 0.09
52 32 0.25
53 6 0.05
54 5 0.04
55 35 0.27
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (51 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG
Found at i:4007 original size:28 final size:29
Alignment explanation
Indices: 3939--4078 Score: 187
Period size: 30 Copynumber: 4.9 Consensus size: 29
3929 GGTCTTCGGA
* *
3939 AAAGGGTGCCACTGATTTGTGGGC-TTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG
3967 -AAGGTTGCCACTGACTTGTGGGCTTTT-
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG
3994 AAAGGTTGCCACTGACTTGTGGGCTTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG
**
4023 AAAAATATGCCACTGACTTGTGGGCTTTTG
1 AAAGGT-TGCCACTGACTTGTGGGCTTTTG
* *
4053 AAAAGGGTGCCACTAACTTGTGGGCT
1 -AAAGGTTGCCACTGACTTGTGGGCT
4079 AAAAAGAGTG
Statistics
Matches: 99, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.21
28 30 0.30
29 4 0.04
30 41 0.41
31 3 0.03
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (29 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTTG
Found at i:4014 original size:85 final size:86
Alignment explanation
Indices: 3910--4078 Score: 207
Period size: 85 Copynumber: 2.0 Consensus size: 86
3900 TTAAAGATGG
* * * * * *
3910 AAAGGTGCCACCGATTTGTGGTCTTCGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGGTT
1 AAAGGTGCCACCGACTTGTGGGCTTCGGAAAAAGATGCCACTGACTTGTGGGCTTTTGAAAGGGT
*
3973 GCCACTGACTTGTGGGCTTTT
66 GCCACTAACTTGTGGGCTTTT
* ** *
3994 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
1 AAAGG-TGCCACCGACTTGTGGGCTTCGGAAAAAGATGCCACTGACTTGTGGGCTTTTG-AAAGG
4059 GTGCCACTAACTTGTGGGCT
64 GTGCCACTAACTTGTGGGCT
4079 AAAAAGAGTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
84 5 0.07
85 39 0.56
86 4 0.06
88 22 0.31
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (86 bp):
AAAGGTGCCACCGACTTGTGGGCTTCGGAAAAAGATGCCACTGACTTGTGGGCTTTTGAAAGGGT
GCCACTAACTTGTGGGCTTTT
Found at i:4150 original size:30 final size:30
Alignment explanation
Indices: 4115--4202 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 30
4105 TTACAAAAGA
* * *
4115 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGAGTGCCACCGACTTGTGGGCTTTGG
*
4145 AAAAGA-TGCCACCGACTTGTGGGCTTCGG
1 AAAAGAGTGCCACCGACTTGTGGGCTTTGG
* * *
4174 AAAAGGGTGCCACTGATTTGTGGGCTTTG
1 AAAAGAGTGCCACCGACTTGTGGGCTTTG
4203 AAGGTTGATG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 24 0.49
30 25 0.51
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.25
Consensus pattern (30 bp):
AAAAGAGTGCCACCGACTTGTGGGCTTTGG
Found at i:5647 original size:1 final size:1
Alignment explanation
Indices: 5643--5736 Score: 107
Period size: 1 Copynumber: 94.0 Consensus size: 1
5633 CCGGACCCCC
* * * * *
5643 TTTTTTGTTTTTTTTTGTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * *
5708 TTTTTTCCTTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5737 GGAGGACGCC
Statistics
Matches: 77, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 77 1.00
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.90
Consensus pattern (1 bp):
T
Done.