Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2778
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: 15733
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:2443 original size:34 final size:35
Alignment explanation
Indices: 2400--2468 Score: 113
Period size: 34 Copynumber: 2.0 Consensus size: 35
2390 ACATACATAG
*
2400 TTTTTATTCCTCATTTCTGTTGG-GTTTTCACACA
1 TTTTTATTCCTCATTCCTGTTGGAGTTTTCACACA
*
2434 TTTTTATTCCTCATTCCTGTTGGATTTTTCACACA
1 TTTTTATTCCTCATTCCTGTTGGAGTTTTCACACA
2469 GGAAGAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 22 0.69
35 10 0.31
ACGTcount: A:0.16, C:0.22, G:0.10, T:0.52
Consensus pattern (35 bp):
TTTTTATTCCTCATTCCTGTTGGAGTTTTCACACA
Found at i:3448 original size:30 final size:30
Alignment explanation
Indices: 3412--3473 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
3402 CTTTTCATTA
*
3412 TTCATATTTCATAACACTGGGCCGAAGCCT
1 TTCATATTTCATAACACTAGGCCGAAGCCT
**
3442 TTCATATTTCATATTACTAGGCCGAAGCCT
1 TTCATATTTCATAACACTAGGCCGAAGCCT
3472 TT
1 TT
3474 ACTGTAACCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (30 bp):
TTCATATTTCATAACACTAGGCCGAAGCCT
Found at i:3724 original size:24 final size:24
Alignment explanation
Indices: 3680--3760 Score: 128
Period size: 24 Copynumber: 3.4 Consensus size: 24
3670 TGGAGAGCCT
*
3680 AGCCTCTTTTAATAACT-GGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
3704 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
3728 AGCCCTTTAAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
3752 AGCCCTTTT
1 AGCCCTTTT
3761 GCACTTCCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
23 12 0.23
24 41 0.77
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:3832 original size:20 final size:20
Alignment explanation
Indices: 3809--3875 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
3799 TTTATGAAAC
3809 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
3829 ATCATGTGCATAGCATACAT
1 ATCATGTGCATATCATACAT
*
3849 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
3869 ACCATGT
1 ATCATGT
3876 TTACTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:6534 original size:41 final size:41
Alignment explanation
Indices: 6368--6523 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
6358 TTTATCGTTA
* * * *
6368 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
6409 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
6450 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
6491 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
6524 AAGAGCCGGT
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 102 0.95
42 2 0.02
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:6794 original size:33 final size:33
Alignment explanation
Indices: 6738--6835 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
6728 ATAGATATGT
*
6738 ATATATATATATGT-TGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
*
6770 ATATATTTATGTGTATGCATTCGGCATAGGTGA
1 ATATATATATGTGTATGCATTCGGCATAGGTGA
* * *
6803 AAATAAGTGTATGTATCTATGCATTCGGCATAG
1 ATAT-A-TATATG--TGTATGCATTCGGCATAG
6836 ATGGGTATAG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 21 0.38
34 1 0.02
35 5 0.09
37 17 0.30
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (33 bp):
ATATATATATGTGTATGCATTCGGCATAGGTGA
Found at i:14151 original size:41 final size:41
Alignment explanation
Indices: 14010--14140 Score: 214
Period size: 41 Copynumber: 3.2 Consensus size: 41
14000 TTACTTACGT
14010 TAGCA-GCTTAATGCCGGTGA-A-ATTATTCAGACTATAAGTC
1 TAGCAGGCTTAATGCCGGTGACACA-T-TTCAGACTATAAGTC
14050 TAGCAGGCTTAATGCCGGTGACACATTTCAGACTATAAGTC
1 TAGCAGGCTTAATGCCGGTGACACATTTCAGACTATAAGTC
*
14091 TAGCAGGCTTAATGCCGGTGACACATTTCGGACTATAAGTC
1 TAGCAGGCTTAATGCCGGTGACACATTTCAGACTATAAGTC
14132 TAGCAGGCT
1 TAGCAGGCT
14141 AAGAGCCGGT
Statistics
Matches: 87, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
40 5 0.06
41 79 0.91
42 2 0.02
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGACACATTTCAGACTATAAGTC
Found at i:14411 original size:33 final size:32
Alignment explanation
Indices: 14355--14418 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
14345 ATAGATATGT
14355 ATATATATATATGTTGCATTCGGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
14387 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
14419 AAATAAGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Done.