Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1553
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: 13766
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Found at i:1892 original size:15 final size:15
Alignment explanation
Indices: 1872--1901 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1862 AATTTTAAGA
*
1872 TTAATTAAGTTTAAT
1 TTAATTAAATTTAAT
1887 TTAATTAAATTTAAT
1 TTAATTAAATTTAAT
1902 GTTTGAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TTAATTAAATTTAAT
Found at i:1905 original size:22 final size:21
Alignment explanation
Indices: 1876--1920 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1866 TTAAGATTAA
1876 TTAAGTTT-AATTTAATTAAAT
1 TTAAGTTTGAATTT-ATTAAAT
*
1897 TTAATGTTTGAGTTTATTAAAT
1 TTAA-GTTTGAATTTATTAAAT
1919 TT
1 TT
1921 GATCATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 13 0.62
23 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTAAGTTTGAATTTATTAAAT
Found at i:2069 original size:16 final size:16
Alignment explanation
Indices: 1964--2072 Score: 62
Period size: 16 Copynumber: 6.8 Consensus size: 16
1954 ATTTCAAGAC
*
1964 TTAGATTATTTTG-AT
1 TTAGATCATTTTGAAT
* * *
1979 TTTGAATTATTTTGAGT
1 TTAG-ATCATTTTGAAT
* *
1996 TTAAATCATTTTAAAT
1 TTAGATCATTTTGAAT
**
2012 TTA-ATTCATTTCAAAT
1 TTAGA-TCATTTTGAAT
*
2028 TGAGAGTCATTTTGAAT
1 TTAGA-TCATTTTGAAT
* *
2045 TAATG-TCATTTTGAGT
1 TTA-GATCATTTTGAAT
2061 TTAGATCATTTT
1 TTAGATCATTTT
2073 TAGGTTTTTT
Statistics
Matches: 73, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
15 5 0.07
16 52 0.71
17 15 0.21
18 1 0.01
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (16 bp):
TTAGATCATTTTGAAT
Found at i:8001 original size:3 final size:3
Alignment explanation
Indices: 7993--8025 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
7983 TAAAGATCTA
7993 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
8026 TTGTGAGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:9900 original size:16 final size:16
Alignment explanation
Indices: 9857--9913 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
9847 TTAAAAAATT
9857 TAAT-TTATA-TAAAA
1 TAATATTATATTAAAA
* *
9871 TAATATAAAATTAAAA
1 TAATATTATATTAAAA
*
9887 TAATATTATTTTAAAA
1 TAATATTATATTAAAA
9903 TAAGTATTATA
1 TAA-TATTATA
9914 AGTAATATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 4 0.12
15 3 0.09
16 21 0.62
17 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
TAATATTATATTAAAA
Found at i:12822 original size:17 final size:17
Alignment explanation
Indices: 12780--12814 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
12770 TTTCAACATA
*
12780 AAAAAGAAAAAAAAAAG
1 AAAAAGAAGAAAAAAAG
12797 AAAAAGAAGAAAAAAAG
1 AAAAAGAAGAAAAAAAG
12814 A
1 A
12815 GGAAGAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAGAAGAAAAAAAG
Found at i:13058 original size:14 final size:15
Alignment explanation
Indices: 13039--13071 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
13029 ATTTTTTTTA
13039 ATTTTAAG-AATAAT
1 ATTTTAAGCAATAAT
*
13053 ATTTTACGCAATAAT
1 ATTTTAAGCAATAAT
13068 ATTT
1 ATTT
13072 ATTTAGGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (15 bp):
ATTTTAAGCAATAAT
Found at i:13444 original size:7 final size:7
Alignment explanation
Indices: 13429--13462 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
13419 AAATTATTAA
*
13429 TAAATTT
1 TAAAATT
13436 TAAAATT
1 TAAAATT
13443 TAAAATT
1 TAAAATT
13450 TAAAATTT
1 TAAAA-TT
13458 TAAAA
1 TAAAA
13463 AAATTTATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAAAATT
Done.