Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2379
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: 10296
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.30
Found at i:1772 original size:25 final size:25
Alignment explanation
Indices: 1739--1786 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1729 AATGTGAAAG
*
1739 GGGGTTGCTATGTGCTGATTCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCGA
1764 GGGGTTGCTAAGTGCTGATTCCC
1 GGGGTTGCTAAGTGCTGATTCCC
1787 CGGTTCATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.21, G:0.35, T:0.31
Consensus pattern (25 bp):
GGGGTTGCTAAGTGCTGATTCCCGA
Found at i:1837 original size:102 final size:103
Alignment explanation
Indices: 1661--1889 Score: 372
Period size: 102 Copynumber: 2.2 Consensus size: 103
1651 TGTATATAAA
** * *
1661 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
1726 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
* *
1763 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
1827 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
1867 AGGGGTTGCTAAGTGCTGATTCC
1 AGGGGTTGCTAAGTGCTGATTCC
1890 ATTCATTGGT
Statistics
Matches: 118, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
102 90 0.76
103 1 0.01
104 27 0.23
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.32
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:1958 original size:26 final size:26
Alignment explanation
Indices: 1922--1974 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1912 TGAAATGAAA
*
1922 AGGGGTTGCTATGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
1948 AGGGGTTGCTAAGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
1974 A
1 A
1975 TTCAGTGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.23, G:0.34, T:0.28
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCTGATTCCCCG
Found at i:4538 original size:32 final size:30
Alignment explanation
Indices: 4498--4560 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 30
4488 AAGTCAGTGG
4498 TAAAAGTGTGATGAAAGATGCAGCTGGAGGA
1 TAAAAGTGTGATGAAAGATGCAGCT-GAGGA
4529 TAAAGAGTGTGATGAAAGATGCAGCTGAGGA
1 TAAA-AGTGTGATGAAAGATGCAGCTGAGGA
4560 T
1 T
4561 CAGAAATTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 10 0.32
32 21 0.68
ACGTcount: A:0.38, C:0.06, G:0.35, T:0.21
Consensus pattern (30 bp):
TAAAAGTGTGATGAAAGATGCAGCTGAGGA
Found at i:4785 original size:20 final size:20
Alignment explanation
Indices: 4760--4797 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4750 TATGTAGTTA
4760 AAGTATCAAATCCATTAGGC
1 AAGTATCAAATCCATTAGGC
4780 AAGTATCAAATCCATTAG
1 AAGTATCAAATCCATTAG
4798 TATGTCTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (20 bp):
AAGTATCAAATCCATTAGGC
Found at i:8867 original size:24 final size:25
Alignment explanation
Indices: 8825--8874 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
8815 ATGTGAAAAG
8825 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGC-ATGTGCTGATTCCCCGA
8851 GGGGTTGC-TGTGCTGATTCCCCGA
1 GGGGTTGCATGTGCTGATTCCCCGA
8875 TTCATTGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 16 0.67
26 8 0.33
ACGTcount: A:0.10, C:0.24, G:0.36, T:0.30
Consensus pattern (25 bp):
GGGGTTGCATGTGCTGATTCCCCGA
Found at i:8924 original size:102 final size:102
Alignment explanation
Indices: 8748--9108 Score: 567
Period size: 102 Copynumber: 3.6 Consensus size: 102
8738 TTGTATATAA
* *
8748 AGGGGTTGCTGTGTGCTGATT-CCCGATTCATGGTGGTGCTATGTGCGTGATCCACCATATCTTT
1 AGGGGTTGCT-AGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
8812 GAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCG
65 GAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCG
*
8850 AGGGGTTGCT-GTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGTGATCCACCATATCTTT
1 AGGGGTTGCTAGTGCTGATTCCCCGATTCA-TGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
8914 GAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCG
65 GAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCG
8952 AGGGGTTGCTAAGTGCTGATTCCCCG-TTCATTGGTGGTG--AAGTGCGAT-ATCC-CCATATCT
1 AGGGGTTGCT-AGTGCTGATTCCCCGATTCA-TGGTGGTGCTAAGTGCG-TGATCCACCATATCT
9012 TTGAAATGTG-AAAGGGGGTTGCTATGTGCTGATTCCCCG
63 TTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCG
* *
9051 AGGGGTTGCTAAGTGCTGATTCCCCGATTCACGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCT-AGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCA
9109 ATAACGGTTA
Statistics
Matches: 246, Mismatches: 3, Indels: 20
0.91 0.01 0.07
Matches are distributed among these distances:
99 62 0.25
100 31 0.13
101 30 0.12
102 96 0.39
103 13 0.05
104 14 0.06
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.31
Consensus pattern (102 bp):
AGGGGTTGCTAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTTG
AAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:8962 original size:26 final size:26
Alignment explanation
Indices: 8927--8977 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
8917 ATGTGAAAAG
*
8927 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
8953 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
8978 TTCATTGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:9061 original size:26 final size:26
Alignment explanation
Indices: 9026--9077 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
9016 AATGTGAAAG
*
9026 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
9052 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
9078 TTCACGGTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Done.