Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023613.1 Corchorus olitorius cultivar O-4 contig23646, 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: 5062
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:1808 original size:44 final size:43
Alignment explanation
Indices: 1732--1851 Score: 100
Period size: 42 Copynumber: 2.8 Consensus size: 43
1722 ATCTCCGTTG
* * * ** *
1732 ATATTTGTT-ATACATCCTTCATGCATGGTCCATGTCTTTTTAT
1 ATATATGTTCATACATACATCATGCATTATCCATGTC-CTTTAT
* *
1775 ATATATGTTCATACATTCATCATGCATTATCCAT-TCCTTTGT
1 ATATATGTTCATACATACATCATGCATTATCCATGTCCTTTAT
* * * **
1817 ACATAGGTTCATGCATAGGTCATGCATTATCCATG
1 ATATATGTTCATACATACATCATGCATTATCCATG
1852 CATTACTACA
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
42 32 0.52
43 10 0.16
44 20 0.32
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.42
Consensus pattern (43 bp):
ATATATGTTCATACATACATCATGCATTATCCATGTCCTTTAT
Found at i:3354 original size:12 final size:12
Alignment explanation
Indices: 3337--3375 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
3327 TCACTTCATC
3337 AAATTCAAATCA
1 AAATTCAAATCA
*
3349 AAATTCAAATTA
1 AAATTCAAATCA
*
3361 AAGTTCAAATCA
1 AAATTCAAATCA
3373 AAA
1 AAA
3376 GTGAATCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.26
Consensus pattern (12 bp):
AAATTCAAATCA
Found at i:3754 original size:7 final size:7
Alignment explanation
Indices: 3742--3812 Score: 142
Period size: 7 Copynumber: 10.1 Consensus size: 7
3732 AAAGAAAGAG
3742 AAATGAA
1 AAATGAA
3749 AAATGAA
1 AAATGAA
3756 AAATGAA
1 AAATGAA
3763 AAATGAA
1 AAATGAA
3770 AAATGAA
1 AAATGAA
3777 AAATGAA
1 AAATGAA
3784 AAATGAA
1 AAATGAA
3791 AAATGAA
1 AAATGAA
3798 AAATGAA
1 AAATGAA
3805 AAATGAA
1 AAATGAA
3812 A
1 A
3813 TGAAAAAATG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 64 1.00
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAATGAA
Found at i:3820 original size:21 final size:21
Alignment explanation
Indices: 3742--3820 Score: 117
Period size: 21 Copynumber: 3.9 Consensus size: 21
3732 AAAGAAAGAG
*
3742 AAATGAAAAATGAAAAATGAA
1 AAATGAAAAATGAAAAAAGAA
*
3763 AAATGAAAAATGAAAAATGAA
1 AAATGAAAAATGAAAAAAGAA
*
3784 AAATGAAAAATGAAAAATGAA
1 AAATGAAAAATGAAAAAAGAA
3805 AAATGAAA--TGAAAAAA
1 AAATGAAAAATGAAAAAA
3821 TGTTGAAAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
19 7 0.12
21 50 0.88
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (21 bp):
AAATGAAAAATGAAAAAAGAA
Found at i:4871 original size:35 final size:35
Alignment explanation
Indices: 4825--5062 Score: 351
Period size: 35 Copynumber: 6.9 Consensus size: 35
4815 ATTACCATCT
*
4825 TCCAGATGACTCAGTGTAGCATCTTCAAAATTGAA
1 TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
*
4860 TCCAGATGACTCGGTGCAGCATCTTCAAAATTGAA
1 TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
*
4895 -CTCAGATGACTCGGTGTAGCATCTTCAAAGTTG--
1 TC-CAGATGACTCGGTGTAGCATCTTCAAAATTGAA
4928 TCCAAAGATGACTCGGTGTAGCATCTTCAAAATT-AA
1 TCC--AGATGACTCGGTGTAGCATCTTCAAAATTGAA
* *
4964 TCCAGATGACTCGGTGCAACATCTTCAAAATTGAA
1 TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
*
4999 TCCAGATGACTCGGTGCAGCATCTTCAAAATTGAA
1 TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
*
5034 TCC-GATGACTCGGTGTAACATCTTCAAAA
1 TCCAGATGACTCGGTGTAGCATCTTCAAAA
Statistics
Matches: 186, Mismatches: 10, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
33 1 0.01
34 53 0.28
35 129 0.69
36 3 0.02
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (35 bp):
TCCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
Found at i:5006 original size:69 final size:70
Alignment explanation
Indices: 4825--5062 Score: 360
Period size: 69 Copynumber: 3.4 Consensus size: 70
4815 ATTACCATCT
* *
4825 TCCAGATGACTCAGTGTAGCATCTTCAAAATTGAATCCAGATGACTCGGTGCAGCATCTTCAAAA
1 TCCAGATGACTCGGTGTAACATCTTCAAAATTGAATCCAGATGACTCGGTGCAGCATCTTCAAAA
4890 TTGAA
66 TTGAA
* * *
4895 -CTCAGATGACTCGGTGTAGCATCTTCAAAGTTG--TCCAAAGATGACTCGGTGTAGCATCTTCA
1 TC-CAGATGACTCGGTGTAACATCTTCAAAATTGAATCC--AGATGACTCGGTGCAGCATCTTCA
4957 AAATT-AA
63 AAATTGAA
*
4964 TCCAGATGACTCGGTGCAACATCTTCAAAATTGAATCCAGATGACTCGGTGCAGCATCTTCAAAA
1 TCCAGATGACTCGGTGTAACATCTTCAAAATTGAATCCAGATGACTCGGTGCAGCATCTTCAAAA
5029 TTGAA
66 TTGAA
5034 TCC-GATGACTCGGTGTAACATCTTCAAAA
1 TCCAGATGACTCGGTGTAACATCTTCAAAA
Statistics
Matches: 153, Mismatches: 8, Indels: 15
0.87 0.05 0.09
Matches are distributed among these distances:
68 3 0.02
69 84 0.55
70 63 0.41
71 3 0.02
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (70 bp):
TCCAGATGACTCGGTGTAACATCTTCAAAATTGAATCCAGATGACTCGGTGCAGCATCTTCAAAA
TTGAA
Done.