Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004912.1 Corchorus capsularis cultivar CVL-1 contig04930, 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: 14602
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1873 original size:67 final size:64
Alignment explanation
Indices: 1768--1896 Score: 231
Period size: 67 Copynumber: 2.0 Consensus size: 64
1758 TAGTTTATTC
1768 TTTTCTTAACTTTTATTTTTATTTACAGCGGCCACTTGGCCAAATGTGTTGAAGGTGTTAGATT
1 TTTTCTTAACTTTTATTTTTATTTACAGCGGCCACTTGGCCAAATGTGTTGAAGGTGTTAGATT
1832 TTTTCTTAACTTTTATTTATTTTATTTACAGCGGCCACTTGGCCAAATGTGTTGAAGGTGTTAGA
1 TTTTCTTAACTTTTA--T-TTTTATTTACAGCGGCCACTTGGCCAAATGTGTTGAAGGTGTTAGA
1897 GGGTATAGCA
Statistics
Matches: 62, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
64 15 0.24
66 1 0.02
67 46 0.74
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (64 bp):
TTTTCTTAACTTTTATTTTTATTTACAGCGGCCACTTGGCCAAATGTGTTGAAGGTGTTAGATT
Found at i:3773 original size:1 final size:1
Alignment explanation
Indices: 3767--3794 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
3757 CACAATTTCC
3767 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
3795 GACTCATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:8028 original size:24 final size:24
Alignment explanation
Indices: 7983--8033 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
7973 TAGATAACGG
**
7983 CAAGTGGATCTTCATGGAAATATC
1 CAAGTGGATCTTCAACGAAATATC
* *
8007 CAAGTTGATCTTCAACGCAATATC
1 CAAGTGGATCTTCAACGAAATATC
8031 CAA
1 CAA
8034 TCTACTTAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (24 bp):
CAAGTGGATCTTCAACGAAATATC
Found at i:8656 original size:151 final size:146
Alignment explanation
Indices: 8383--8680 Score: 488
Period size: 151 Copynumber: 2.0 Consensus size: 146
8373 TCCTAATTCC
* ** *
8383 TTCGAGATCATCTTGGCACTACAACTTTGTAGAAAGCTAGTATAAAAAAAGTAATCAGTAAAATA
1 TTCGAAATCATCTTGAAACTACAACTTTGTAGAAAGCTAGTATAAAAAAAATAATCAGTAAAATA
* *
8448 ATGCTTAGGCAGCAAAACTCTATAAACTGAATTAAAGTATGAAAATTTAACATCAAGCTGTGACA
66 ATGCTTAAGCAGCAAAACTCTATAAACTGAATTAAAGTATGAAAATTTAACAACAAGCTGTGACA
8513 AAGTCTACAAATTTGG
131 AAGTCTACAAATTTGG
8529 TTCGAAATCATCTTGAAACTACAACTTTGTAGAAAGCTAGTATTAAAAAAAATAAAAAATCAGTA
1 TTCGAAATCATCTTGAAACTACAACTTTGTAGAAAGCTAGTA-TAAAAAAAAT----AATCAGTA
8594 AAATAATGCTTAAGCAGCAAAACTCTATAAACTGAATTAAAGTATGAAAATTTAACAACAAGCTG
61 AAATAATGCTTAAGCAGCAAAACTCTATAAACTGAATTAAAGTATGAAAATTTAACAACAAGCTG
*
8659 TGGCAAAGTCTACAAATTTGG
126 TGACAAAGTCTACAAATTTGG
8680 T
1 T
8681 AGTTAATCCA
Statistics
Matches: 140, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
146 39 0.28
147 9 0.06
151 92 0.66
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (146 bp):
TTCGAAATCATCTTGAAACTACAACTTTGTAGAAAGCTAGTATAAAAAAAATAATCAGTAAAATA
ATGCTTAAGCAGCAAAACTCTATAAACTGAATTAAAGTATGAAAATTTAACAACAAGCTGTGACA
AAGTCTACAAATTTGG
Found at i:10983 original size:26 final size:27
Alignment explanation
Indices: 10933--10984 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
10923 CTGATTAATT
*
10933 AAAACACTTGGTACAAACTTCTTCAAAA
1 AAAACACTTGGTACAAAC-TATTCAAAA
10961 AAAACACTTGGTACAAAC-ATTCAA
1 AAAACACTTGGTACAAACTATTCAA
10985 CGATCATGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 5 0.22
28 18 0.78
ACGTcount: A:0.48, C:0.21, G:0.08, T:0.23
Consensus pattern (27 bp):
AAAACACTTGGTACAAACTATTCAAAA
Found at i:13491 original size:21 final size:21
Alignment explanation
Indices: 13465--13505 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13455 GGATTTCCAT
* *
13465 TCAAAGTCCAACAGGAAGGGC
1 TCAAAGCCCAACAAGAAGGGC
13486 TCAAAGCCCAACAAGAAGGG
1 TCAAAGCCCAACAAGAAGGG
13506 TAATACCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.24, G:0.27, T:0.07
Consensus pattern (21 bp):
TCAAAGCCCAACAAGAAGGGC
Found at i:14100 original size:21 final size:21
Alignment explanation
Indices: 14037--14100 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
14027 TTGACATGGT
* *
14037 TTAGGTACTGTACAGATGAGA
1 TTAGATACTGTACATATGAGA
* *
14058 TT--ACACTGTACATATCTA-A
1 TTAGATACTGTACATAT-GAGA
14077 TTAGATACTGTACATATGAGA
1 TTAGATACTGTACATATGAGA
14098 TTA
1 TTA
14101 TTAGAGCAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 13 0.39
20 2 0.06
21 18 0.55
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (21 bp):
TTAGATACTGTACATATGAGA
Found at i:14574 original size:2 final size:2
Alignment explanation
Indices: 14569--14598 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14559 AAACACACAC
14569 AT AT 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
14599 TATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.