Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2198
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: 15124
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:943 original size:46 final size:45
Alignment explanation
Indices: 893--1068 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
883 GATGTTGGCA
893 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
939 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
986 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
1032 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1069 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:1048 original size:93 final size:93
Alignment explanation
Indices: 889--1060 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
879 CTAGGATGTT
* *
889 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
954 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
982 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
1047 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
1061 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:6453 original size:46 final size:46
Alignment explanation
Indices: 6400--6561 Score: 182
Period size: 46 Copynumber: 3.5 Consensus size: 46
6390 ATCCGAACTC
* * *
6400 GTTGAGTCCGAATTCACTTATGGATGCGAATGTCTGAACTCGTTGA
1 GTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAGCTCGTTGA
*** * * * * *
6446 GTTGAGTCCGAGTTCGAGAGATGTA-ACTAGGTATCCGAGCTCGTTGA
1 GTTGAGTCCGAGTTC-ACTTATGGATGCGA-ATGTCCGAGCTCGTTGA
* *
6493 GTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGA
1 GTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAGCTCGTTGA
6539 GTTGAGTCCGAGTTCACTTATGG
1 GTTGAGTCCGAGTTCACTTATGG
6562 GCGGGTTACA
Statistics
Matches: 92, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
46 57 0.62
47 35 0.38
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (46 bp):
GTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAGCTCGTTGA
Found at i:12065 original size:45 final size:45
Alignment explanation
Indices: 11965--12091 Score: 147
Period size: 45 Copynumber: 2.9 Consensus size: 45
11955 TTTTCTCAAA
* *
11965 TCACCGGCATT-TCGCCTGTTAGGCTCG-AGGCCCG-ATATCAGT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
12007 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGT-A-T
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA-TCAGT
** * *
12051 CTCACCGGCATTATAGTTTGCTAAGCTCAAAGGCCCGAATA
1 -TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
12092 ATCAAGTCAA
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
42 11 0.15
43 14 0.19
44 8 0.11
45 40 0.54
46 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
Found at i:12469 original size:43 final size:43
Alignment explanation
Indices: 12421--12607 Score: 243
Period size: 43 Copynumber: 4.6 Consensus size: 43
12411 CCGGCATTAC
12421 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
12464 GCCTGCTAGGCACGAA-G-CC---T--GC-T-A--GGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* * * *
12496 GCCTACTTGGCACGAAGGCCCGAATACACATCACCGGTACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
12539 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
12582 GCCTGCTAGGCACGAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
12608 TAATACCAGC
Statistics
Matches: 124, Mismatches: 9, Indels: 22
0.80 0.06 0.14
Matches are distributed among these distances:
32 22 0.18
33 1 0.01
34 3 0.02
35 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 1 0.01
41 3 0.02
42 1 0.01
43 88 0.71
ACGTcount: A:0.29, C:0.33, G:0.26, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:12477 original size:16 final size:16
Alignment explanation
Indices: 12456--12512 Score: 96
Period size: 16 Copynumber: 3.6 Consensus size: 16
12446 ACACATCACC
12456 GGCACGAAGCCTGCTA
1 GGCACGAAGCCTGCTA
12472 GGCACGAAGCCTGCTA
1 GGCACGAAGCCTGCTA
* *
12488 GGCACGAAGCCTACTT
1 GGCACGAAGCCTGCTA
12504 GGCACGAAG
1 GGCACGAAG
12513 GCCCGAATAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.26, C:0.30, G:0.32, T:0.12
Consensus pattern (16 bp):
GGCACGAAGCCTGCTA
Found at i:12654 original size:38 final size:38
Alignment explanation
Indices: 12600--12683 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 38
12590 GGCACGAAGG
* * *
12600 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
12638 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
12676 CCCGAATA
1 CCCGAATA
12684 CACATCAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (38 bp):
CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAA
Done.