Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2125
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: 75996
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:1934 original size:32 final size:31
Alignment explanation
Indices: 1855--1947 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 31
1845 ACTAAAAAGA
*
1855 TATGTGTATATATGTAATATATATATGCATGGGT
1 TATGT-TATATATAT-A-ATATATATGCATGGGT
*
1889 TATGTTATATATATAATATATATGCTTGGGT
1 TATGTTATATATATAATATATATGCATGGGT
* *
1920 CT-TGATTATATATATCATATATAAGCAT
1 -TATG-TTATATATATAATATATATGCAT
1948 ATATGGGTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
31 17 0.33
32 22 0.42
33 8 0.15
34 5 0.10
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (31 bp):
TATGTTATATATATAATATATATGCATGGGT
Found at i:2957 original size:17 final size:17
Alignment explanation
Indices: 2937--3036 Score: 74
Period size: 17 Copynumber: 5.8 Consensus size: 17
2927 ATTATAGAGT
* *
2937 ATGAACTGTTATTTTGC
1 ATGAACTGTTATTTGGA
* * *
2954 ATGAAATATTATGTGGA
1 ATGAACTGTTATTTGGA
* * **
2971 ATGTAACTATTATGTGTT
1 ATG-AACTGTTATTTGGA
* *
2989 CTGAACTGTTAATTGGA
1 ATGAACTGTTATTTGGA
* *
3006 ATGAACTGTCATTTGGT
1 ATGAACTGTTATTTGGA
3023 ATGAACTGTTATTT
1 ATGAACTGTTATTT
3037 CATATGAAAA
Statistics
Matches: 63, Mismatches: 19, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
17 50 0.79
18 13 0.21
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (17 bp):
ATGAACTGTTATTTGGA
Found at i:3042 original size:17 final size:17
Alignment explanation
Indices: 3006--3044 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2996 GTTAATTGGA
**
3006 ATGAACTGTCATTTGGT
1 ATGAACTGTCATTTCAT
*
3023 ATGAACTGTTATTTCAT
1 ATGAACTGTCATTTCAT
3040 ATGAA
1 ATGAA
3045 AAGATGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (17 bp):
ATGAACTGTCATTTCAT
Found at i:3135 original size:18 final size:18
Alignment explanation
Indices: 3085--3135 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
3075 TTATCTGCGA
* *
3085 ATTTTATGCGAATTACTT
1 ATTTTATGAGAACTACTT
* * *
3103 ATTATATGTGCACTACTT
1 ATTTTATGAGAACTACTT
3121 ATTTTATGAGAACTA
1 ATTTTATGAGAACTA
3136 TTGTGTCGTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (18 bp):
ATTTTATGAGAACTACTT
Found at i:28554 original size:32 final size:31
Alignment explanation
Indices: 28475--28567 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 31
28465 ACTAAAAAGA
*
28475 TATGTGTATATATGTAATATATATATGCATGGGT
1 TATGT-TATATATAT-A-ATATATATGCATGGGT
*
28509 TATGTTATATATATAATATATATGCTTGGGT
1 TATGTTATATATATAATATATATGCATGGGT
* *
28540 CT-TGATTATATATATCATATATAAGCAT
1 -TATG-TTATATATATAATATATATGCAT
28568 ATATGGGTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
31 17 0.33
32 22 0.42
33 8 0.15
34 5 0.10
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (31 bp):
TATGTTATATATATAATATATATGCATGGGT
Found at i:29577 original size:17 final size:17
Alignment explanation
Indices: 29557--29656 Score: 74
Period size: 17 Copynumber: 5.8 Consensus size: 17
29547 ATTATAGAGT
* *
29557 ATGAACTGTTATTTTGC
1 ATGAACTGTTATTTGGA
* * *
29574 ATGAAATATTATGTGGA
1 ATGAACTGTTATTTGGA
* * **
29591 ATGTAACTATTATGTGTT
1 ATG-AACTGTTATTTGGA
* *
29609 CTGAACTGTTAATTGGA
1 ATGAACTGTTATTTGGA
* *
29626 ATGAACTGTCATTTGGT
1 ATGAACTGTTATTTGGA
29643 ATGAACTGTTATTT
1 ATGAACTGTTATTT
29657 CATATGAAAA
Statistics
Matches: 63, Mismatches: 19, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
17 50 0.79
18 13 0.21
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (17 bp):
ATGAACTGTTATTTGGA
Found at i:29662 original size:17 final size:17
Alignment explanation
Indices: 29626--29664 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
29616 GTTAATTGGA
**
29626 ATGAACTGTCATTTGGT
1 ATGAACTGTCATTTCAT
*
29643 ATGAACTGTTATTTCAT
1 ATGAACTGTCATTTCAT
29660 ATGAA
1 ATGAA
29665 AAGATGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (17 bp):
ATGAACTGTCATTTCAT
Found at i:29755 original size:18 final size:18
Alignment explanation
Indices: 29705--29755 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
29695 TTATCTGCGA
* *
29705 ATTTTATGCGAATTACTT
1 ATTTTATGAGAACTACTT
* * *
29723 ATTATATGTGCACTACTT
1 ATTTTATGAGAACTACTT
29741 ATTTTATGAGAACTA
1 ATTTTATGAGAACTA
29756 TTGTGTCGTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (18 bp):
ATTTTATGAGAACTACTT
Found at i:57708 original size:32 final size:31
Alignment explanation
Indices: 57629--57721 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 31
57619 ACTAAAAAGA
*
57629 TATGTGTATATATGTAATATATATATGCATGGGT
1 TATGT-TATATATAT-A-ATATATATGCATGGGT
*
57663 TATGTTATATATATAATATATATGCTTGGGT
1 TATGTTATATATATAATATATATGCATGGGT
* *
57694 CT-TGATTATATATATCATATATAAGCAT
1 -TATG-TTATATATATAATATATATGCAT
57722 ATATGGGTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
31 17 0.33
32 22 0.42
33 8 0.15
34 5 0.10
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (31 bp):
TATGTTATATATATAATATATATGCATGGGT
Found at i:58731 original size:17 final size:17
Alignment explanation
Indices: 58711--58810 Score: 74
Period size: 17 Copynumber: 5.8 Consensus size: 17
58701 ATTATAGAGT
* *
58711 ATGAACTGTTATTTTGC
1 ATGAACTGTTATTTGGA
* * *
58728 ATGAAATATTATGTGGA
1 ATGAACTGTTATTTGGA
* * **
58745 ATGTAACTATTATGTGTT
1 ATG-AACTGTTATTTGGA
* *
58763 CTGAACTGTTAATTGGA
1 ATGAACTGTTATTTGGA
* *
58780 ATGAACTGTCATTTGGT
1 ATGAACTGTTATTTGGA
58797 ATGAACTGTTATTT
1 ATGAACTGTTATTT
58811 CATATGAAAA
Statistics
Matches: 63, Mismatches: 19, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
17 50 0.79
18 13 0.21
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (17 bp):
ATGAACTGTTATTTGGA
Found at i:58816 original size:17 final size:17
Alignment explanation
Indices: 58780--58818 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
58770 GTTAATTGGA
**
58780 ATGAACTGTCATTTGGT
1 ATGAACTGTCATTTCAT
*
58797 ATGAACTGTTATTTCAT
1 ATGAACTGTCATTTCAT
58814 ATGAA
1 ATGAA
58819 AAGATGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (17 bp):
ATGAACTGTCATTTCAT
Found at i:58909 original size:18 final size:18
Alignment explanation
Indices: 58859--58909 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
58849 TTATCTGCGA
* *
58859 ATTTTATGCGAATTACTT
1 ATTTTATGAGAACTACTT
* * *
58877 ATTATATGTGCACTACTT
1 ATTTTATGAGAACTACTT
58895 ATTTTATGAGAACTA
1 ATTTTATGAGAACTA
58910 TTGTGTCGTA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (18 bp):
ATTTTATGAGAACTACTT
Done.