Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016777.1 Corchorus olitorius cultivar O-4 contig16810, whole genome shotgun sequence
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: 29495
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3545 original size:23 final size:21
Alignment explanation
Indices: 3499--3582 Score: 62
Period size: 21 Copynumber: 3.9 Consensus size: 21
3489 CCTATGAAAC
* **
3499 ATGAAACTTTGATAACCTAACT
1 ATGAAA-TTTTATAACCTTCCT
**
3521 ATGGGATTTTAATAAACCTTCCT
1 ATGAAATTTT-AT-AACCTTCCT
*
3544 ATGAAATTTTGTAACCTTCCT
1 ATGAAATTTTATAACCTTCCT
*
3565 ATG-ATTTTTGATAACCTT
1 ATGAAATTTT-ATAACCTT
3583 ACTGTGAGAT
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
20 5 0.10
21 22 0.45
22 7 0.14
23 15 0.31
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (21 bp):
ATGAAATTTTATAACCTTCCT
Found at i:3561 original size:21 final size:21
Alignment explanation
Indices: 3535--3597 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
3525 GATTTTAATA
3535 AACCTTCCTATGAAATTTTGT
1 AACCTTCCTATGAAATTTTGT
*
3556 AACCTTCCTATG-ATTTTTGAT
1 AACCTTCCTATGAAATTTTG-T
* * *
3577 AACCTTACTGTGAGATTTTGT
1 AACCTTCCTATGAAATTTTGT
3598 TAATCTCCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 6 0.17
21 24 0.69
22 5 0.14
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.44
Consensus pattern (21 bp):
AACCTTCCTATGAAATTTTGT
Found at i:3581 original size:42 final size:43
Alignment explanation
Indices: 3535--3616 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
3525 GATTTTAATA
* * *
3535 AACCTTCCTATGAAATTTTG-TAACCTTCCTATGATTTTTGAT
1 AACCTTACTATGAAATTTTGTTAACCTCCCTATAATTTTTGAT
* * *
3577 AACCTTACTGTGAGATTTTGTTAATCTCCCTATAATTTTT
1 AACCTTACTATGAAATTTTGTTAACCTCCCTATAATTTTT
3617 TTATACTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
42 17 0.52
43 16 0.48
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (43 bp):
AACCTTACTATGAAATTTTGTTAACCTCCCTATAATTTTTGAT
Found at i:7795 original size:14 final size:15
Alignment explanation
Indices: 7765--7798 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
7755 TTACTTTGCT
7765 TTGTTTTCTAGTTTAA
1 TTGTTTTCTA-TTTAA
7781 TTGTTTTCT-TTTAA
1 TTGTTTTCTATTTAA
7795 TTGT
1 TTGT
7799 GATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
16 9 0.50
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.68
Consensus pattern (15 bp):
TTGTTTTCTATTTAA
Found at i:11194 original size:33 final size:33
Alignment explanation
Indices: 11152--11222 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
11142 TCAACGCCAT
11152 CCGAGCCTCATGCCCGGCTAGGACCGGTCACAC
1 CCGAGCCTCATGCCCGGCTAGGACCGGTCACAC
*
11185 CCGAGCCTCATGCGCGGCTAGGACCGGTCACAC
1 CCGAGCCTCATGCCCGGCTAGGACCGGTCACAC
11218 CCGAG
1 CCGAG
11223 TCAAGTGCCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.18, C:0.41, G:0.30, T:0.11
Consensus pattern (33 bp):
CCGAGCCTCATGCCCGGCTAGGACCGGTCACAC
Found at i:12606 original size:19 final size:18
Alignment explanation
Indices: 12573--12608 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12563 TGGAAATAAT
12573 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
12591 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
12609 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:18768 original size:20 final size:20
Alignment explanation
Indices: 18727--18768 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
18717 CTAGCCTTTA
*
18727 AACTAGAAGAAAAAAACTAG
1 AACTAGAAGAAAAAAACAAG
* *
18747 AACTAGAAGAGAAAAAGAAG
1 AACTAGAAGAAAAAAACAAG
18767 AA
1 AA
18769 AAGAAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.07, G:0.19, T:0.07
Consensus pattern (20 bp):
AACTAGAAGAAAAAAACAAG
Found at i:19396 original size:19 final size:18
Alignment explanation
Indices: 19363--19398 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19353 TGGAAATAAT
19363 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
19381 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
19399 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:27921 original size:15 final size:16
Alignment explanation
Indices: 27890--27924 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
27880 TTACTTTGCT
27890 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
*
27906 TTGTTTTCT-TTTTAA
1 TTGTTTTCTAGTTTAA
27921 TTGT
1 TTGT
27925 GATTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.14, C:0.06, G:0.11, T:0.69
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:28495 original size:2 final size:2
Alignment explanation
Indices: 28482--28513 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
28472 CCATCAATAC
*
28482 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28514 TTACATTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.