Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2956
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: 28930
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Found at i:653 original size:48 final size:48
Alignment explanation
Indices: 582--952 Score: 428
Period size: 48 Copynumber: 7.8 Consensus size: 48
572 ACCGTGCTGA
582 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* * * *
630 ATGTGTCTGTGTAAGACCATGTCTGGGACATGACAACTGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* ** *
678 ATGTGCTTGTGTAAGACCATGTCTGGGACATGGCATTAGAGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* * * * ** *
726 ATGTTCTTATGTAAAACCATGTCTAAGACATGGCATCGGCGATGGTAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* * *
774 ATGTGCCTGTTTAAGACCATGTTTGGGATATGGCAT-GAGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCG-GCGATGATAT
* *
822 ATGGGCCTATGTAAGACCATGTCT-GGAGCAT-GCATCGGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGA-CATGGCATCGGCGATGATAT
* * *
869 ATGTGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCGATGATAT
1 ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
* ** *
917 GTG-GATTCATGTAAGACCATGTC-GAGGACATGGCAT
1 ATGTGCCT-GTGTAAGACCATGTCTG-GGACATGGCAT
953 TGATACTTTA
Statistics
Matches: 270, Mismatches: 46, Indels: 14
0.82 0.14 0.04
Matches are distributed among these distances:
47 43 0.16
48 227 0.84
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (48 bp):
ATGTGCCTGTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATAT
Found at i:6919 original size:25 final size:25
Alignment explanation
Indices: 6891--6938 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
6881 TTATATAATG
* * *
6891 AAAATGACTATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
6916 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
6939 GTTTAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:6999 original size:20 final size:20
Alignment explanation
Indices: 6974--7020 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
6964 GTTTTTATAT
6974 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
6994 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
7014 ACATGAT
1 ACATGAT
7021 GTATTCATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:7142 original size:23 final size:24
Alignment explanation
Indices: 7067--7148 Score: 103
Period size: 24 Copynumber: 3.4 Consensus size: 24
7057 AGGAAGTGCA
*
7067 AAAAGGGCTTTTGCCCCAGTTTAAT
1 AAAAGGGC-TTTGCCCCAGTTTATT
* *
7092 AAAAGGGTTTTGCCCCAGTTTATC
1 AAAAGGGCTTTGCCCCAGTTTATT
*
7116 AAAAGGGCATTGCCCCAG-TTATT
1 AAAAGGGCTTTGCCCCAGTTTATT
7139 AAAAGAGGCT
1 AAAAG-GGCT
7149 AGGCCTCCAG
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
23 9 0.18
24 33 0.67
25 7 0.14
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATT
Found at i:15051 original size:20 final size:20
Alignment explanation
Indices: 15026--15072 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
15016 GTTTTGATAT
15026 ACATGAT-TGATATGATATAC
1 ACATGATATG-TATGATATAC
*
15046 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATAC
15066 ACATGAT
1 ACATGAT
15073 GTATTCATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATAC
Found at i:15211 original size:24 final size:25
Alignment explanation
Indices: 15120--15227 Score: 168
Period size: 25 Copynumber: 4.4 Consensus size: 25
15110 AGGAAGAGCA
15120 AAAAGGGCTTTTGCCCCAGTTTATT
1 AAAAGGGCTTTTGCCCCAGTTTATT
*
15145 AAAAGGGCTTTTGCCCTAGTTTATT
1 AAAAGGGCTTTTGCCCCAGTTTATT
15170 AAAAGGGCTTTTGCCCCAGTTTATCT
1 AAAAGGGCTTTTGCCCCAGTTTAT-T
15196 -AAAGGGC-TTTGCCCCAG-TTATT
1 AAAAGGGCTTTTGCCCCAGTTTATT
15218 AAAAGAGGCT
1 AAAAG-GGCT
15228 AGGCCTCCAG
Statistics
Matches: 77, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
22 1 0.01
23 8 0.10
24 13 0.17
25 54 0.70
26 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (25 bp):
AAAAGGGCTTTTGCCCCAGTTTATT
Found at i:24406 original size:46 final size:46
Alignment explanation
Indices: 24356--24531 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
24346 TGGTTGAGCA
24356 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
* *
24402 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGT-AACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAA-T--G
* *
24447 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
* * *
24495 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
24532 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 6 0.05
45 3 0.03
46 63 0.56
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
Found at i:24512 original size:93 final size:93
Alignment explanation
Indices: 24353--24524 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
24343 GGATGGTTGA
* * *
24353 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
24418 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
24446 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
24511 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
24525 CTTATGGGCG
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:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.