Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1328
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: 31035
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Found at i:994 original size:29 final size:29
Alignment explanation
Indices: 960--1033 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
950 TAATCAACCG
*
960 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
989 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
1018 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
1034 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:8117 original size:42 final size:41
Alignment explanation
Indices: 7982--8118 Score: 175
Period size: 42 Copynumber: 3.3 Consensus size: 41
7972 TTGAGATTTA
* *
7982 CGTGTAAGACCATGTCTGGGACATCAGCATCATATCTGATTT
1 CGTGTAAGACCATGTCTGGGACATCGGCATCGTATCTGA-TT
* * * *
8024 CATGTAAGACCATGTCTGCGACATTGGCATCGTATCCGATGT
1 CGTGTAAGACCATGTCTGGGACATCGGCATCGTATCTGAT-T
*
8066 CGTGTAAGACCATGTCTGGGACATCGGCATCGTATCTTATT
1 CGTGTAAGACCATGTCTGGGACATCGGCATCGTATCTGATT
*
8107 CCGTGGAAGACC
1 -CGTGTAAGACC
8119 CCGTTTAGGA
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
41 2 0.02
42 79 0.98
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.28
Consensus pattern (41 bp):
CGTGTAAGACCATGTCTGGGACATCGGCATCGTATCTGATT
Found at i:8137 original size:84 final size:84
Alignment explanation
Indices: 7982--8139 Score: 201
Period size: 84 Copynumber: 1.9 Consensus size: 84
7972 TTGAGATTTA
* * *
7982 CGTGTAAGACCATGTCTGGGACATCAGCATCATATCTGATTTCATGTAAGACCATGTCTGCGACA
1 CGTGTAAGACCATGTCTGGGACATCAGCATCATATCTGATTCCATGGAAGACCACGTCTGCGACA
**
8047 TTGGCATCGTATCCGATGT
66 GAGGCATCGTATCCGATGT
* * * * * *
8066 CGTGTAAGACCATGTCTGGGACATCGGCATCGTATCTTATTCCGTGGAAGACCCCGTTTAG-GAC
1 CGTGTAAGACCATGTCTGGGACATCAGCATCATATCTGATTCCATGGAAGACCACGTCT-GCGAC
8130 AGAGGCATCG
65 AGAGGCATCG
8140 ATACTAAATT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
84 61 0.98
85 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.27
Consensus pattern (84 bp):
CGTGTAAGACCATGTCTGGGACATCAGCATCATATCTGATTCCATGGAAGACCACGTCTGCGACA
GAGGCATCGTATCCGATGT
Found at i:12329 original size:40 final size:40
Alignment explanation
Indices: 12259--12436 Score: 211
Period size: 40 Copynumber: 4.5 Consensus size: 40
12249 AAGCCAAGTA
* * * *
12259 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATA
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCTCAAATG
*
12298 CCTTCGGGACATAGCCCGGATATAGTAACTCG-TACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCT-CAAATG
* *
12338 CCTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCTCAAATG
* * *
12378 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCTCAAATG
12418 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
12437 TTATCATCCA
Statistics
Matches: 123, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
39 14 0.11
40 109 0.89
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCTCAAATG
Found at i:15391 original size:27 final size:26
Alignment explanation
Indices: 15374--15443 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
15364 ATATTAAGTC
15374 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
15401 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
15429 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
15444 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:15437 original size:28 final size:28
Alignment explanation
Indices: 15374--15471 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
15364 ATATTAAGTC
*
15374 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
15401 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
15429 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
15458 CGCACACTTAGTGC
1 CGCACACTTAGTGC
15472 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:23667 original size:27 final size:26
Alignment explanation
Indices: 23650--23719 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
23640 ATATTAAGTC
23650 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
23677 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
23705 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
23720 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:23713 original size:28 final size:28
Alignment explanation
Indices: 23650--23747 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
23640 ATATTAAGTC
*
23650 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
23677 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
23705 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
23734 CGCACACTTAGTGC
1 CGCACACTTAGTGC
23748 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:27492 original size:46 final size:46
Alignment explanation
Indices: 27442--27617 Score: 218
Period size: 46 Copynumber: 3.8 Consensus size: 46
27432 TGATTGAGCA
27442 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
27488 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
27533 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
27581 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
27618 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 8, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 5 0.04
46 61 0.54
47 29 0.26
48 3 0.03
50 5 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:27598 original size:93 final size:93
Alignment explanation
Indices: 27439--27610 Score: 319
Period size: 93 Copynumber: 1.8 Consensus size: 93
27429 GGATGATTGA
27439 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
27504 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
27532 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC-GAACTCGTTGAG
27596 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
27611 CTTATGGGCG
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
92 2 0.03
93 75 0.97
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Done.