Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold405
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: 28418
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Found at i:1850 original size:79 final size:81
Alignment explanation
Indices: 1714--1898 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
1704 TTGAATGATG
* *
1714 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
1778 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
1793 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
1855 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
1873 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1899 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:1912 original size:40 final size:40
Alignment explanation
Indices: 1715--1898 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
1705 TGAATGATGT
* * * *
1715 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
1755 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
1795 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
1833 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
1874 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
1899 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:1920 original size:79 final size:79
Alignment explanation
Indices: 1767--1931 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
1757 GGACTAAGAT
* * **
1767 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
1832 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
1846 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
1909 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
1925 CCGAAGG
1 CCGAAGG
1932 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:9741 original size:29 final size:29
Alignment explanation
Indices: 9678--9745 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
9668 TAATCAACCA
9678 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
9707 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
9736 CGCACACTTA
1 CGCACACTTA
9746 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:9886 original size:29 final size:30
Alignment explanation
Indices: 9847--9925 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
9837 CTTAATAATC
9847 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
9877 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
9906 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
9926 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:17878 original size:29 final size:29
Alignment explanation
Indices: 17815--17882 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
17805 TAATCAACCA
17815 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
17844 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
17873 CGCACACTTA
1 CGCACACTTA
17883 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:18023 original size:29 final size:30
Alignment explanation
Indices: 17984--18062 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
17974 CTTAATAATC
17984 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
18014 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
18043 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
18063 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:26031 original size:29 final size:29
Alignment explanation
Indices: 25968--26035 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
25958 TAATCAACCA
25968 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
25997 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
26026 CGCACACTTA
1 CGCACACTTA
26036 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:26176 original size:29 final size:30
Alignment explanation
Indices: 26137--26215 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
26127 CTTAATAATC
26137 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
26167 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
26196 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
26216 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Done.