Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2624
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: 25073
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:1678 original size:37 final size:39
Alignment explanation
Indices: 1587--1766 Score: 210
Period size: 40 Copynumber: 4.7 Consensus size: 39
1577 TTGAATGATG
* * * *
1587 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA
1626 TCC-GG-TAAGAT-CCGAAGGCATTTGTGCGAG-TACTAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
*
1662 TTCGGGTTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AA
1701 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
* * *
1741 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
1767 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 8, Indels: 17
0.83 0.05 0.11
Matches are distributed among these distances:
36 6 0.05
37 35 0.28
38 18 0.15
39 16 0.13
40 49 0.40
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:1784 original size:80 final size:76
Alignment explanation
Indices: 1624--1799 Score: 196
Period size: 80 Copynumber: 2.3 Consensus size: 76
1614 CTAAGTGACC
** *
1624 AATCCGG-TAAGAT-CCGAAGGCATTTGTGCGAGTACTAATTCGGGTTAAGCCCGAAGGCATTTG
1 AATCCGGTTAA-ATCCCGAAGGCATTTGTGCGAGTACTAAACCGGGCTAAGCCCGAAGGCATTTG
**
1687 TGCGAGTTACTA
65 AACGAGTTACTA
* *
1699 AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCAT
1 AATCC-GGTTAAATCCCGAAGGCATTTGTGCGAG-TACTA-AACCGGGCTAAG-CCCGAAGGCAT
1764 TTGAACGAG-TAGCTA
62 TTGAACGAGTTA-CTA
* *
1779 TATCCGGTTAAATTCCGAAGG
1 AATCCGGTTAAATCCCGAAGG
1800 TACGTGATTT
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
75 5 0.06
76 3 0.04
77 22 0.26
78 5 0.06
79 24 0.29
80 25 0.30
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (76 bp):
AATCCGGTTAAATCCCGAAGGCATTTGTGCGAGTACTAAACCGGGCTAAGCCCGAAGGCATTTGA
ACGAGTTACTA
Found at i:9664 original size:40 final size:40
Alignment explanation
Indices: 9512--9657 Score: 197
Period size: 40 Copynumber: 3.6 Consensus size: 40
9502 TTGAATGATG
* * * *
9512 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
9552 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
9592 TCCGGGTTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
9633 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
9658 AACGAGTAGC
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 87 0.91
41 9 0.09
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:9664 original size:80 final size:80
Alignment explanation
Indices: 9512--9680 Score: 193
Period size: 80 Copynumber: 2.1 Consensus size: 80
9502 TTGAATGATG
* * *
9512 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCAAAGGCTTTGTGCTAAGTGACCAAATCCGGGCTAAGTCCCGAAGGCATTT
**
9577 GTGCGAGTTA-CTAAA
66 GAACGAG-TAGCTAAA
* * * *
9592 TCCGGGTTAAGTCCCAAAGGCATTTGTGC-GAGTTACTATAA-CCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCAAAGGC-TTTGTGCTAAGTGACCA-AATCCGGGCTAAGTCCCGAAGGCAT
*
9655 TTGAACGAGTAGCTATA
64 TTGAACGAGTAGCTAAA
9672 TCC-GGTTAA
1 TCCGGGTTAA
9681 ATTCCGAAGG
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
79 8 0.11
80 59 0.78
81 9 0.12
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCAAAGGCTTTGTGCTAAGTGACCAAATCCGGGCTAAGTCCCGAAGGCATTT
GAACGAGTAGCTAAA
Found at i:18694 original size:40 final size:39
Alignment explanation
Indices: 18639--18871 Score: 315
Period size: 40 Copynumber: 5.9 Consensus size: 39
18629 GGATATAGCT
* * *
18639 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT-TAGTA
* *
18679 ACTCGCACAATTGCCTTCGGGACTTAGCCCAGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCC-GGTTTAGTA
18719 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTTAGTA
18759 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTTAGTA
** *
18799 ACTCGCACAAATGCCTTCGGGACTT-GCCCGGAACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTTAGTA
* * *
18838 ACTAGCGCAGATGCCTTCGGGACTTAGCCCGGTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT
18872 ATCATCCAAA
Statistics
Matches: 175, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
39 34 0.19
40 138 0.79
41 3 0.02
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTTAGTA
Found at i:20290 original size:29 final size:29
Alignment explanation
Indices: 20248--20309 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
20238 ATTTTTCCTA
20248 ACATATATCACTAACATAACATGTTTGTG
1 ACATATATCACTAACATAACATGTTTGTG
20277 ACATATATCACTAACATAACATGTTTGTG
1 ACATATATCACTAACATAACATGTTTGTG
20306 ACAT
1 ACAT
20310 GTTTCCACCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.34
Consensus pattern (29 bp):
ACATATATCACTAACATAACATGTTTGTG
Done.