Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold632
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: 15640
ACGTcount: A:0.21, C:0.13, G:0.12, T:0.25
Warning! 4482 characters in sequence are not A, C, G, or T
Found at i:2660 original size:70 final size:70
Alignment explanation
Indices: 2554--2855 Score: 262
Period size: 70 Copynumber: 4.4 Consensus size: 70
2544 AGCTCCCAGC
* ** *
2554 TGTACTCTTAAGGCTCGCTGATTTAATATCATGGCCTCCAAAATAGTTAGTGTGAGCTCAAGCTC
1 TGTACTCTTAAGGCTCGCTGATTCAATATCGCGGCCTCCAAAATAGTTAGCGTGAGCTCAAGCTC
2619 TCAAT
66 TCAAT
** *
2624 TGTACTCTTAAGGCTCATTGATTCAATATCGCGGCCTCCAAAATTGTTAGC---A---CAAG--C
1 TGTACTCTTAAGGCTCGCTGATTCAATATCGCGGCCTCCAAAATAGTTAGCGTGAGCTCAAGCTC
2681 TCAAGT
66 TCAA-T
* * * * * * ***
2687 TGTACCCTTAAGGCTTGCTAATTCAATATTGCGGCCTCTAAAATTGTTAGCACAAGCTCAAGCTC
1 TGTACTCTTAAGGCTCGCTGATTCAATATCGCGGCCTCCAAAATAGTTAGCGTGAGCTCAAGCTC
* *
2752 CCAAC
66 TCAAT
* * * * * *
2757 TGTACTCTTAAGGCTCGTTGATTCAATATCGCAGCCCCCAAAACAGTTACCGGGAGCTCAAGCTG
1 TGTACTCTTAAGGCTCGCTGATTCAATATCGCGGCCTCCAAAATAGTTAGCGTGAGCTCAAGCT-
**
2822 C-CAGC
65 CTCAAT
* * *
2827 TATATTCTTAAGGCTCGCTAATTCAATAT
1 TGTACTCTTAAGGCTCGCTGATTCAATAT
2856 TACGAAGTTG
Statistics
Matches: 187, Mismatches: 35, Indels: 20
0.77 0.14 0.08
Matches are distributed among these distances:
62 5 0.03
63 45 0.24
64 4 0.02
66 1 0.01
67 1 0.01
69 4 0.02
70 122 0.65
71 5 0.03
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (70 bp):
TGTACTCTTAAGGCTCGCTGATTCAATATCGCGGCCTCCAAAATAGTTAGCGTGAGCTCAAGCTC
TCAAT
Found at i:2712 original size:63 final size:63
Alignment explanation
Indices: 2618--2748 Score: 192
Period size: 63 Copynumber: 2.1 Consensus size: 63
2608 AGCTCAAGCT
* * *
2618 CTCAA-TTGTACTCTTAAGGCTCATTGATTCAATATCGCGGCCTCCAAAATTGTTAGCACAAG
1 CTCAAGTTGTACCCTTAAGGCTCACTAATTCAATATCGCGGCCTCCAAAATTGTTAGCACAAG
** * *
2680 CTCAAGTTGTACCCTTAAGGCTTGCTAATTCAATATTGCGGCCTCTAAAATTGTTAGCACAAG
1 CTCAAGTTGTACCCTTAAGGCTCACTAATTCAATATCGCGGCCTCCAAAATTGTTAGCACAAG
2743 CTCAAG
1 CTCAAG
2749 CTCCCAACTG
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
62 5 0.08
63 56 0.92
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (63 bp):
CTCAAGTTGTACCCTTAAGGCTCACTAATTCAATATCGCGGCCTCCAAAATTGTTAGCACAAG
Found at i:9309 original size:14 final size:14
Alignment explanation
Indices: 9252--9311 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
9242 TAAAACATTC
9252 AAAC-AAGTAATT-
1 AAACTAAGTAATTA
* *
9264 AAGCTATAGGAATTA
1 AAACTA-AGTAATTA
*
9279 AAACATAATTAAATTA
1 AAAC-TAAGT-AATTA
9295 AAACTAAGTAATTA
1 AAACTAAGTAATTA
9309 AAA
1 AAA
9312 TATCTAAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
12 3 0.08
13 1 0.03
14 14 0.38
15 8 0.22
16 11 0.30
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.27
Consensus pattern (14 bp):
AAACTAAGTAATTA
Found at i:10775 original size:96 final size:96
Alignment explanation
Indices: 10611--10802 Score: 384
Period size: 96 Copynumber: 2.0 Consensus size: 96
10601 CGATTAATGC
10611 ATGGTATGATTGTGCAACTCTGTGAACCGTGTGAACCTTTTCAAATACCTACTTGTGATGATTAC
1 ATGGTATGATTGTGCAACTCTGTGAACCGTGTGAACCTTTTCAAATACCTACTTGTGATGATTAC
10676 GTTTACCATTTGATTTATTACTCGTGATTTA
66 GTTTACCATTTGATTTATTACTCGTGATTTA
10707 ATGGTATGATTGTGCAACTCTGTGAACCGTGTGAACCTTTTCAAATACCTACTTGTGATGATTAC
1 ATGGTATGATTGTGCAACTCTGTGAACCGTGTGAACCTTTTCAAATACCTACTTGTGATGATTAC
10772 GTTTACCATTTGATTTATTACTCGTGATTTA
66 GTTTACCATTTGATTTATTACTCGTGATTTA
10803 TTCATGGTTT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.41
Consensus pattern (96 bp):
ATGGTATGATTGTGCAACTCTGTGAACCGTGTGAACCTTTTCAAATACCTACTTGTGATGATTAC
GTTTACCATTTGATTTATTACTCGTGATTTA
Found at i:12446 original size:22 final size:22
Alignment explanation
Indices: 12392--12447 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
12382 TACCAGTAAC
12392 CAGAATGGCTAAGAGCCATAAA
1 CAGAATGGCTAAGAGCCATAAA
* *
12414 CA-AGATAGCTATA-AGCTATAAA
1 CAGA-ATGGCTA-AGAGCCATAAA
12436 CAGAATGGCTAA
1 CAGAATGGCTAA
12448 AANNNNNNNN
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
21 2 0.07
22 24 0.86
23 2 0.07
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.18
Consensus pattern (22 bp):
CAGAATGGCTAAGAGCCATAAA
Done.