Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2537
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: 37885
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Found at i:2521 original size:32 final size:32
Alignment explanation
Indices: 2485--2546 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
2475 AGCTTTTGGT
2485 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
*
2517 TTTTTCGTGTTGTCAAAGAGTTGAACAATG
1 TTTTTCATGTTGTCAAAGAGTTGAACAATG
2547 AAAATAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
Found at i:10730 original size:6 final size:6
Alignment explanation
Indices: 10719--10792 Score: 72
Period size: 6 Copynumber: 13.2 Consensus size: 6
10709 GGGATCACTA
10719 ACTAAT ACTAAT -CTAAT -CT-A- ACTAAT ACTAAT -CTAAT ACTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
*
10762 A-GAAT ACTAAT -CTAAT ACTCTAAT ACTAAT A
1 ACTAAT ACTAAT ACTAAT A--CTAAT ACTAAT A
10793 GAATAGAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
4 3 0.05
5 22 0.38
6 27 0.47
8 6 0.10
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (6 bp):
ACTAAT
Found at i:10736 original size:5 final size:5
Alignment explanation
Indices: 10716--10777 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
10706 GCCGGGATCA
10716 CTAA- CTAAT ACTAAT CTAAT CTAA- CTAAT ACTAAT CTAAT ACTAAT
1 CTAAT CTAAT -CTAAT CTAAT CTAAT CTAAT -CTAAT CTAAT -CTAAT
**
10762 AGAAT ACTAAT CTAAT
1 CTAAT -CTAAT CTAAT
10778 ACTCTAATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
4 8 0.17
5 22 0.46
6 18 0.38
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.34
Consensus pattern (5 bp):
CTAAT
Found at i:10754 original size:11 final size:11
Alignment explanation
Indices: 10715--10791 Score: 94
Period size: 11 Copynumber: 7.5 Consensus size: 11
10705 AGCCGGGATC
10715 ACTAA-CTAAT
1 ACTAATCTAAT
10725 ACTAATCTAAT
1 ACTAATCTAAT
10736 -CTAA-CTAAT
1 ACTAATCTAAT
10745 ACTAATCTAAT
1 ACTAATCTAAT
**
10756 ACTAATAGAAT
1 ACTAATCTAAT
10767 ACTAATCTAAT
1 ACTAATCTAAT
10778 AC---TCTAAT
1 ACTAATCTAAT
10786 ACTAAT
1 ACTAAT
10792 AGAATAGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
8 8 0.14
9 5 0.09
10 13 0.23
11 31 0.54
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (11 bp):
ACTAATCTAAT
Found at i:10770 original size:22 final size:21
Alignment explanation
Indices: 10715--10791 Score: 108
Period size: 20 Copynumber: 3.8 Consensus size: 21
10705 AGCCGGGATC
10715 ACTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
10736 -CTAACTAATACTAATCTAAT
1 ACTAACTAATACTAATCTAAT
10756 ACTAA-TAGAATACTAATCTAAT
1 ACTAACT--AATACTAATCTAAT
10778 ACT--CTAATACTAAT
1 ACTAACTAATACTAAT
10792 AGAATAGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.17
20 21 0.40
21 5 0.10
22 17 0.33
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (21 bp):
ACTAACTAATACTAATCTAAT
Found at i:10806 original size:14 final size:14
Alignment explanation
Indices: 10789--10816 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10779 CTCTAATACT
10789 AATAGAATAGAAAA
1 AATAGAATAGAAAA
10803 AATAGAATAGAAAA
1 AATAGAATAGAAAA
10817 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:19151 original size:18 final size:18
Alignment explanation
Indices: 19072--19165 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
19062 CAAGGTCACG
*
19072 ATCAATAGCGTCACTATC
1 ATCAATATCGTCACTATC
* *
19090 ATCAATAGCGTCACTAGC
1 ATCAATATCGTCACTATC
*
19108 ATCAATATCGTCACTAGC
1 ATCAATATCGTCACTATC
19126 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTATC
19144 ATCAATATCG--A-TATC
1 ATCAATATCGTCACTATC
19159 ATCAATA
1 ATCAATA
19166 AGAAAACCTT
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 61 0.84
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.29
Consensus pattern (18 bp):
ATCAATATCGTCACTATC
Found at i:19152 original size:9 final size:9
Alignment explanation
Indices: 19072--19152 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
19062 CAAGGTCACG
*
19072 ATCAATAGC
1 ATCAATATC
* *
19081 GTCACTATC
1 ATCAATATC
*
19090 ATCAATAGC
1 ATCAATATC
* * *
19099 GTCACTAGC
1 ATCAATATC
19108 ATCAATATC
1 ATCAATATC
* * *
19117 GTCACTAGC
1 ATCAATATC
19126 ATCAATATC
1 ATCAATATC
* *
19135 GTCACTATC
1 ATCAATATC
19144 ATCAATATC
1 ATCAATATC
19153 GATATCATCA
Statistics
Matches: 51, Mismatches: 21, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.28
Consensus pattern (9 bp):
ATCAATATC
Found at i:21555 original size:21 final size:21
Alignment explanation
Indices: 21525--21613 Score: 90
Period size: 21 Copynumber: 4.1 Consensus size: 21
21515 CTCACAAAGA
* *
21525 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTAGAC
* *
21545 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
21566 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTAGAC
*
21587 AAAAAGAAACGAAGTGACTTAGAC
1 AAAAAG--A-GAAGTAACTTAGAC
21611 AAA
1 AAA
21614 TCTTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 6 0.10
21 36 0.62
23 1 0.02
24 15 0.26
ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTAGAC
Found at i:21606 original size:24 final size:21
Alignment explanation
Indices: 21525--21593 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
21515 CTCACAAAGA
* * *
21525 AAAAAG-GAAGTGAGTTAGAC
1 AAAAAGAGAAGTAACTTGGAC
*
21545 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
21566 AAAAAGAGAAGTAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
21587 AAAAAGA
1 AAAAAGA
21594 AACGAAGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 6 0.14
21 37 0.86
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:25770 original size:14 final size:14
Alignment explanation
Indices: 25751--25779 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
25741 TACAATATAT
25751 ATAAGAATTATACG
1 ATAAGAATTATACG
25765 ATAAGAATTATACG
1 ATAAGAATTATACG
25779 A
1 A
25780 ATCCATCTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:28560 original size:13 final size:15
Alignment explanation
Indices: 28535--28574 Score: 66
Period size: 13 Copynumber: 2.8 Consensus size: 15
28525 TATTTTATTA
28535 AATAAATATTAAATT
1 AATAAATATTAAATT
28550 AA-AAA-ATTAAATT
1 AATAAATATTAAATT
28563 AATAAATATTAA
1 AATAAATATTAA
28575 TAAATTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.43
14 6 0.26
15 7 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAAATATTAAATT
Done.