Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014786.1 Corchorus capsularis cultivar CVL-1 contig14807, 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: 14849
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:1608 original size:31 final size:32
Alignment explanation
Indices: 1573--1653 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 32
1563 CCTAATTGAT
**
1573 TATATCCTTAATTGCTTGAAAT-CGAAAACGA
1 TATATCCTTAATTGCTTGAAATAAAAAAACGA
* *
1604 TATATCCTTAATTGCTTGAAATAAAAAAATGT
1 TATATCCTTAATTGCTTGAAATAAAAAAACGA
*
1636 TATATACTTAATTGCTTG
1 TATATCCTTAATTGCTTG
1654 GGGCAGCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 22 0.50
32 22 0.50
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.38
Consensus pattern (32 bp):
TATATCCTTAATTGCTTGAAATAAAAAAACGA
Found at i:2671 original size:2 final size:2
Alignment explanation
Indices: 2664--2700 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2654 TCAATTTAGG
* *
2664 AT AT AT AT AT AT AT AT AT AT TT AT AA AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2701 ACGTTTGCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4731 original size:17 final size:18
Alignment explanation
Indices: 4709--4749 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
4699 TTACGTTTCC
4709 TATTTGTTATA-CTATAG
1 TATTTGTTATATCTATAG
*
4726 TATTTG-TATATGTATAG
1 TATTTGTTATATCTATAG
4743 TATTTGT
1 TATTTGT
4750 ATTTCCTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.56
Consensus pattern (18 bp):
TATTTGTTATATCTATAG
Found at i:10076 original size:21 final size:21
Alignment explanation
Indices: 10050--10093 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
10040 AAAAACTGAA
10050 TTGCTAAACACCGCCCCATTT
1 TTGCTAAACACCGCCCCATTT
** *
10071 TTGCTATTCACCGCCCTATTT
1 TTGCTAAACACCGCCCCATTT
10092 TT
1 TT
10094 TACGCTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.34, G:0.09, T:0.39
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCATTT
Found at i:10483 original size:32 final size:32
Alignment explanation
Indices: 10407--10499 Score: 123
Period size: 32 Copynumber: 2.9 Consensus size: 32
10397 ATTTTGGTCT
** **
10407 AGCCGCCCCACCAGGGTGGCCTGCCGTGGCAA
1 AGCCGCCCCATGAGGGCAGCCTGCCGTGGCAA
10439 AGCCGCCCCATGAGGGCAGCCTGCCGTGGCAA
1 AGCCGCCCCATGAGGGCAGCCTGCCGTGGCAA
* * *
10471 AGCCGCCTCATGAGGGCGGCTTGCCGTGG
1 AGCCGCCCCATGAGGGCAGCCTGCCGTGG
10500 TCGTGGTGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.15, C:0.37, G:0.37, T:0.12
Consensus pattern (32 bp):
AGCCGCCCCATGAGGGCAGCCTGCCGTGGCAA
Found at i:11193 original size:24 final size:23
Alignment explanation
Indices: 11157--11201 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
11147 AAAAAAATCA
*
11157 ATTTTTCTGTTTTTTTAAAGAACC
1 ATTTTTCT-CTTTTTTAAAGAACC
*
11181 ATTTTTTTCTTTTTTAAAGAA
1 ATTTTTCTCTTTTTTAAAGAA
11202 GAAAATGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.27, C:0.09, G:0.07, T:0.58
Consensus pattern (23 bp):
ATTTTTCTCTTTTTTAAAGAACC
Found at i:11837 original size:16 final size:16
Alignment explanation
Indices: 11816--11854 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
11806 CAATTTTTTT
11816 TTTTTTTTAAAAAATA
1 TTTTTTTTAAAAAATA
*
11832 TTTTTTTTGAAAAATA
1 TTTTTTTTAAAAAATA
11848 TTTTTTT
1 TTTTTTT
11855 AATCAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TTTTTTTTAAAAAATA
Found at i:11862 original size:17 final size:16
Alignment explanation
Indices: 11817--11863 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
11807 AATTTTTTTT
11817 TTTTTTTAA-AAAATA
1 TTTTTTTAATAAAATA
*
11832 TTTTTTTTGA-AAAATA
1 -TTTTTTTAATAAAATA
11848 TTTTTTTAATCAAAAT
1 TTTTTTTAAT-AAAAT
11864 GTATGACGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 8 0.30
16 14 0.52
17 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTTTTTAATAAAATA
Found at i:13716 original size:2 final size:2
Alignment explanation
Indices: 13709--13743 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
13699 ATTAAAAATA
*
13709 AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13744 ATGAAAAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14781 original size:17 final size:17
Alignment explanation
Indices: 14759--14796 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
14749 CCATGAAAAA
14759 TTATTAATTTATAGAGG
1 TTATTAATTTATAGAGG
*
14776 TTATTAATTTATCGAGG
1 TTATTAATTTATAGAGG
14793 TTAT
1 TTAT
14797 ACTGTAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.50
Consensus pattern (17 bp):
TTATTAATTTATAGAGG
Done.