Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2748
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: 13361
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:859 original size:20 final size:20
Alignment explanation
Indices: 836--889 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
826 AGTTTTTCCC
*
836 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
856 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
876 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
890 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:871 original size:30 final size:30
Alignment explanation
Indices: 836--909 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
826 AGTTTTTCCC
836 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
866 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
896 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
910 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:899 original size:20 final size:20
Alignment explanation
Indices: 836--900 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
826 AGTTTTTCCC
* * * *
836 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
856 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
875 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
896 AGCTC
1 AGCTC
901 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:3627 original size:6 final size:6
Alignment explanation
Indices: 3618--3736 Score: 82
Period size: 6 Copynumber: 19.7 Consensus size: 6
3608 GAAAGAGATT
* ** *
3618 GAAAAA G-AAAA -AAAAA G-AAAA CAAAAA GAAAAA GAAATT GCAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
** ** * * *
3663 GAAAAA GAAATC GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA GAAAATT
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A
3714 GAAAAA GAAAAA GAAAAAA GAAA
1 GAAAAA GAAAAA G-AAAAA GAAA
3737 TTGAAAGAGA
Statistics
Matches: 84, Mismatches: 22, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
5 12 0.14
6 55 0.65
7 13 0.15
8 4 0.05
ACGTcount: A:0.74, C:0.03, G:0.18, T:0.06
Consensus pattern (6 bp):
GAAAAA
Found at i:3643 original size:11 final size:10
Alignment explanation
Indices: 3619--3650 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
3609 AAAGAGATTG
3619 AAAAAGAAAA
1 AAAAAGAAAA
3629 AAAAAGAAAA
1 AAAAAGAAAA
3639 CAAAAAGAAAA
1 -AAAAAGAAAA
3650 A
1 A
3651 GAAATTGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:3780 original size:33 final size:32
Alignment explanation
Indices: 3739--3800 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
3729 AAAAGAAATT
3739 GAAAGAGAG-CTTGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTT-AAAAGAAA-CAAGTGAAAAA
*
3772 GAAAGAGAGTCTTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTTAAAAGAAACAAGTGAA
3801 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 7 0.26
33 17 0.63
34 3 0.11
ACGTcount: A:0.55, C:0.06, G:0.26, T:0.13
Consensus pattern (32 bp):
GAAAGAGAGTCTTAAAAGAAACAAGTGAAAAA
Found at i:5599 original size:20 final size:20
Alignment explanation
Indices: 5576--5629 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
5566 AGTTTTTCCC
*
5576 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
5596 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
5616 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
5630 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:5611 original size:30 final size:30
Alignment explanation
Indices: 5576--5649 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
5566 AGTTTTTCCC
5576 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
5606 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
5636 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
5650 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:5639 original size:20 final size:20
Alignment explanation
Indices: 5576--5640 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
5566 AGTTTTTCCC
* * * *
5576 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
5596 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
5615 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
5636 AGCTC
1 AGCTC
5641 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:10432 original size:23 final size:22
Alignment explanation
Indices: 10381--10432 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
10371 CCTCGTCTTT
*
10381 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
10403 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
10426 TTCTTTT
1 TTCTTTT
10433 TCAATTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:10441 original size:12 final size:12
Alignment explanation
Indices: 10390--10444 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
10380 TTTCTTTTGT
10390 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
10403 -TCATTTTC-TC
1 TTCTTTTTCAAC
10413 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
*
10426 TTCTTTTTCAAT
1 TTCTTTTTCAAC
10438 TTCTTTT
1 TTCTTTT
10445 CTGTTTCACA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 1 0.03
11 4 0.12
12 22 0.65
13 7 0.21
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:10451 original size:17 final size:18
Alignment explanation
Indices: 10426--10463 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
10416 TTTCTTCAAC
* *
10426 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
10443 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
10461 TTC
1 TTC
10464 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Done.