Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold711
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: 9081
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.31
Warning! 220 characters in sequence are not A, C, G, or T
Found at i:5678 original size:74 final size:74
Alignment explanation
Indices: 5087--5677 Score: 1067
Period size: 74 Copynumber: 8.0 Consensus size: 74
5077 TTACTTGAAA
* *
5087 GTACACCACAATATATTTGTATATTATACATGGAATAATGAGACTCTACTCACATTCCTGACCAC
1 GTACACTACAATATATTTGTATATTATATATGGAATAATGAGACTCTACTCACATTCCTGACCAC
5152 CAGATGATG
66 CAGATGATG
5161 GTACACTACAATATATTTGTATATTATATATGGAATAATGAGACTCTACTCACATTCCTGACCAC
1 GTACACTACAATATATTTGTATATTATATATGGAATAATGAGACTCTACTCACATTCCTGACCAC
5226 CAGATGATG
66 CAGATGATG
5235 GTACACTACAATATATTTGTATATTATATATGGAATAATGAGACTCTACTCACATTCCTGACCAC
1 GTACACTACAATATATTTGTATATTATATATGGAATAATGAGACTCTACTCACATTCCTGACCAC
5300 CAGATGATG
66 CAGATGATG
5309 GTACACTACAATATATTTGTATATTATATATGGAATAATGAGACTCTACTCACATTCCTGACCAC
1 GTACACTACAATATATTTGTATATTATATATGGAATAATGAGACTCTACTCACATTCCTGACCAC
5374 CAGATGATG
66 CAGATGATG
5383 GTACACTACAATATATTTGTATATTATATATGGAATAATGAGACTCTACTCACATTCCTGACCAC
1 GTACACTACAATATATTTGTATATTATATATGGAATAATGAGACTCTACTCACATTCCTGACCAC
5448 CAGATGATG
66 CAGATGATG
** * ***
5457 GTACACTACAATATATTTGTATAAAACA-AAAAAATTAATGAGACTCTACTCACATTCCTGACCA
1 GTACACTACAATATATTTGTATATTATATATGGAA-TAATGAGACTCTACTCACATTCCTGACCA
5521 CCAGATGATG
65 CCAGATGATG
5531 GTACACTACAATATATTTGTATATTATATATGGAATAATGAGACTCTACTCACATTCCTGACCAC
1 GTACACTACAATATATTTGTATATTATATATGGAATAATGAGACTCTACTCACATTCCTGACCAC
*
5596 CAGATGATA
66 CAGATGATG
* *
5605 ATACACTACAATATATTTGTATATTATATATGGAATAATAAGACTCTACTCACATTCCTGACCAC
1 GTACACTACAATATATTTGTATATTATATATGGAATAATGAGACTCTACTCACATTCCTGACCAC
5670 CAGATGAT
66 CAGATGAT
5678 AGATTTTGTT
Statistics
Matches: 498, Mismatches: 17, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
73 3 0.01
74 492 0.99
75 3 0.01
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (74 bp):
GTACACTACAATATATTTGTATATTATATATGGAATAATGAGACTCTACTCACATTCCTGACCAC
CAGATGATG
Found at i:6682 original size:32 final size:32
Alignment explanation
Indices: 6645--6739 Score: 120
Period size: 32 Copynumber: 3.0 Consensus size: 32
6635 CCATAAGTAC
6645 AGTAATATGATTGGCACAAAGCCATCAGTAGT
1 AGTAATATGATTGGCACAAAGCCATCAGTAGT
* *
6677 AGTAATATGATTGGCACACAGCCTAT-AGTAAT
1 AGTAATATGATTGGCACAAAGCC-ATCAGTAGT
* ** *
6709 GGTAATATGATCCGCACAAAGCCGTCAGTAG
1 AGTAATATGATTGGCACAAAGCCATCAGTAG
6740 CATCGCAACA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
31 1 0.02
32 50 0.94
33 2 0.04
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (32 bp):
AGTAATATGATTGGCACAAAGCCATCAGTAGT
Found at i:6790 original size:26 final size:26
Alignment explanation
Indices: 6754--6806 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
6744 GCAACAGAGT
*
6754 TGCCAACAATAGTACCGTAGCAAAGC
1 TGCCAAAAATAGTACCGTAGCAAAGC
6780 TGCCAAAAATAGTACCGTAGCAAAGC
1 TGCCAAAAATAGTACCGTAGCAAAGC
6806 T
1 T
6807 ACCAGTAACA
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:0.40, C:0.25, G:0.19, T:0.17
Consensus pattern (26 bp):
TGCCAAAAATAGTACCGTAGCAAAGC
Found at i:6956 original size:24 final size:24
Alignment explanation
Indices: 6924--6993 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
6914 GTCATACAAT
*
6924 TCACAGACAAATCAGTCATTTACA
1 TCACAGACAAATCAATCATTTACA
* * *
6948 TCTCGGACAAATCAATCACTTACA
1 TCACAGACAAATCAATCATTTACA
*
6972 TCACAGATAAATCAATCATTTA
1 TCACAGACAAATCAATCATTTA
6994 ACCTCGAGGG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (24 bp):
TCACAGACAAATCAATCATTTACA
Found at i:7113 original size:27 final size:27
Alignment explanation
Indices: 7073--7136 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
7063 CAATCAACGG
* *
7073 TCATTTTACCCTACAGAGGCATTGCGA
1 TCATTTTACACTACAGAGGCATTACGA
*
7100 TCATTTTACACTACAGGGGCATTACGA
1 TCATTTTACACTACAGAGGCATTACGA
7127 TCATTTTACA
1 TCATTTTACA
7137 AATATTGAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (27 bp):
TCATTTTACACTACAGAGGCATTACGA
Done.