Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023794.1 Corchorus olitorius cultivar O-4 contig23827, 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: 14988
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Found at i:5512 original size:13 final size:13
Alignment explanation
Indices: 5494--5521 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5484 ATCACAGATT
5494 TGTACGGATCCAA
1 TGTACGGATCCAA
5507 TGTACGGATCCAA
1 TGTACGGATCCAA
5520 TG
1 TG
5522 ATTTAAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (13 bp):
TGTACGGATCCAA
Found at i:6593 original size:15 final size:15
Alignment explanation
Indices: 6561--6594 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6551 GGAATGGTCA
**
6561 TCAACGCCATCCTGC
1 TCAACGCCATCCACC
6576 TCAACGCCATCCACC
1 TCAACGCCATCCACC
6591 TCAA
1 TCAA
6595 GGTATTGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.47, G:0.09, T:0.18
Consensus pattern (15 bp):
TCAACGCCATCCACC
Found at i:7577 original size:20 final size:21
Alignment explanation
Indices: 7535--7577 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
7525 TCCTTTGTTG
7535 ATGATCTCCAATGGGCTTCAA
1 ATGATCTCCAATGGGCTTCAA
* *
7556 ATGATCTCCGAT-GGCTTTAA
1 ATGATCTCCAATGGGCTTCAA
7576 AT
1 AT
7578 TCTTCAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (21 bp):
ATGATCTCCAATGGGCTTCAA
Found at i:11520 original size:21 final size:21
Alignment explanation
Indices: 11493--11581 Score: 144
Period size: 21 Copynumber: 4.2 Consensus size: 21
11483 TGCTAGGAGT
11493 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
* *
11514 ACATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
11535 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
11556 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
11577 TCATT
1 TCATT
11582 AGAATTGCCT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 2 0.03
21 61 0.97
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:12476 original size:28 final size:25
Alignment explanation
Indices: 12434--12486 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
12424 AATCTATCCT
*
12434 TCTATTCATCTATCATCAAGTTTTTCA
1 TCTATTCATCCATCA--AAGTTTTTCA
12461 TCTATCTCATCCATCAAAGTTTTTCA
1 TCTAT-TCATCCATCAAAGTTTTTCA
12487 AATTTTCTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 10 0.42
27 5 0.21
28 9 0.38
ACGTcount: A:0.26, C:0.25, G:0.04, T:0.45
Consensus pattern (25 bp):
TCTATTCATCCATCAAAGTTTTTCA
Found at i:13932 original size:21 final size:21
Alignment explanation
Indices: 13893--13935 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
13883 GGAGTTGCCT
* *
13893 AAGATGCCATTTGATCCATTG
1 AAGATGCCATTAGACCCATTG
*
13914 AAGATGCCATTAGGCCCATTG
1 AAGATGCCATTAGACCCATTG
13935 A
1 A
13936 CAAGGGCAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (21 bp):
AAGATGCCATTAGACCCATTG
Found at i:14919 original size:153 final size:153
Alignment explanation
Indices: 14701--14988 Score: 479
Period size: 153 Copynumber: 1.9 Consensus size: 153
14691 ACATTGCATA
* *
14701 AATCTCACCAAAATGATTATAGTTAGGGCATAAACAATAGAAATAAAGCATTGAGGGTTGCCAAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATAGAAAAAAAGCATTGAGGGTTGCCAAA
* *
14766 TCTAAGACAATTCAAAACAAAACTAATTGGCCCCGATAGGTCCAAAATAACAAGTGTTCCAAATG
66 TCGAAGACAATTCAAAACAAAACTAATGGGCCCCGATAGGTCCAAAATAACAAGTGTTCCAAATG
14831 AGCTAAAAACTTCACAGTAGACT
131 AGCTAAAAACTTCACAGTAGACT
*
14854 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTG-CAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATAGAAA-AAAAGCATTGAGGGTTGCCAA
* * **
14918 ATCGAAGACGATTCAAAGCGGAACTAATGGGCCCCGATAGGTCCAAAATAACAAGTGTTCCAAAT
65 ATCGAAGACAATTCAAAACAAAACTAATGGGCCCCGATAGGTCCAAAATAACAAGTGTTCCAAAT
14983 GAGCTA
130 GAGCTA
Statistics
Matches: 125, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
153 109 0.87
154 16 0.13
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.21
Consensus pattern (153 bp):
AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATAGAAAAAAAGCATTGAGGGTTGCCAAA
TCGAAGACAATTCAAAACAAAACTAATGGGCCCCGATAGGTCCAAAATAACAAGTGTTCCAAATG
AGCTAAAAACTTCACAGTAGACT
Done.