Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2774
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: 64788
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Found at i:7894 original size:27 final size:27
Alignment explanation
Indices: 7861--8010 Score: 239
Period size: 27 Copynumber: 5.6 Consensus size: 27
7851 TAAATTGTGC
*
7861 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
7888 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
7916 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
7943 AGCACTAAGTGTGCGAGTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
* *
7970 AGCACTAAGTGTGCGAGTT-ATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
7996 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
8011 GACTTAATAA
Statistics
Matches: 118, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
26 20 0.17
27 71 0.60
28 27 0.23
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:7902 original size:55 final size:54
Alignment explanation
Indices: 7841--8010 Score: 204
Period size: 55 Copynumber: 3.1 Consensus size: 54
7831 TTGGCGCTAC
*
7841 GTGTGCG-GTTTAAATTGTGCAGCACTAAGTGTGCGAATTGACTATGTAGCACTAA
1 GTGTGCGAGTTT-AATTGTG-AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAA
*
7896 GTGTGCGAGTTTGACTATGT-AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAA
1 GTGTGCGAGTTT-AAT-TGTGAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAA
* * * * *
7951 GTGTGCGAG-TTGATTATGTAGCACTAAGTGTGCGAGTT-ATTATATAGCACTGA
1 GTGTGCGAGTTTAATTGTG-AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAA
8004 GTGTGCG
1 GTGTGCG
8011 GACTTAATAA
Statistics
Matches: 102, Mismatches: 9, Indels: 10
0.84 0.07 0.08
Matches are distributed among these distances:
52 2 0.02
53 20 0.20
54 21 0.21
55 50 0.49
56 6 0.06
57 3 0.03
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (54 bp):
GTGTGCGAGTTTAATTGTGAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAA
Found at i:25107 original size:23 final size:23
Alignment explanation
Indices: 25077--25124 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
25067 ACCTACAAAC
25077 AGTTTTATGAATTTTTTCTAAAT
1 AGTTTTATGAATTTTTTCTAAAT
25100 AGTTTTATGAATTTTTTCTAAAT
1 AGTTTTATGAATTTTTTCTAAAT
25123 AG
1 AG
25125 CCCTTATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.54
Consensus pattern (23 bp):
AGTTTTATGAATTTTTTCTAAAT
Found at i:39362 original size:39 final size:39
Alignment explanation
Indices: 39319--39396 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
39309 AAAGTATGTA
*
39319 TCTTAGAGCTAAACTAGGAAGATGCCATGATCTTTATAT
1 TCTTAGAGCTAAACTAGGAAGATGCCATGATCTTAATAT
*
39358 TCTTAGAGCTAAACTAGGATGATGCCATGATCTTAATAT
1 TCTTAGAGCTAAACTAGGAAGATGCCATGATCTTAATAT
39397 GATAAGAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (39 bp):
TCTTAGAGCTAAACTAGGAAGATGCCATGATCTTAATAT
Found at i:48902 original size:21 final size:21
Alignment explanation
Indices: 48878--48933 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
48868 GTTAACTACC
48878 TAATGGTCATGGAAAGGCCTA
1 TAATGGTCATGGAAAGGCCTA
48899 TAATGGTCATGGAAAGGCCTA
1 TAATGGTCATGGAAAGGCCTA
48920 TAATGGTCATGGAA
1 TAATGGTCATGGAA
48934 CTATAGTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (21 bp):
TAATGGTCATGGAAAGGCCTA
Found at i:51995 original size:8 final size:8
Alignment explanation
Indices: 51982--52006 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
51972 TTATCAGCTC
51982 TTATTATT
1 TTATTATT
51990 TTATTATT
1 TTATTATT
51998 TTATTATT
1 TTATTATT
52006 T
1 T
52007 CAAATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATTATT
Found at i:63834 original size:14 final size:15
Alignment explanation
Indices: 63817--63849 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
63807 GAAGTGATGA
63817 AAAATTAAAAAAA-G
1 AAAATTAAAAAAAGG
63831 AAAATTAAAAAAAGG
1 AAAATTAAAAAAAGG
63846 AAAA
1 AAAA
63850 AATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAATTAAAAAAAGG
Done.