Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013138.1 Corchorus capsularis cultivar CVL-1 contig13159, 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: 37924
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:1233 original size:14 final size:14
Alignment explanation
Indices: 1196--1238 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
1186 TTTATTACCG
1196 TTTTATT-AAT-AT
1 TTTTATTAAATGAT
1208 GTTTTA-TAAATGAT
1 -TTTTATTAAATGAT
1222 TTTTATTAAATGAT
1 TTTTATTAAATGAT
1236 TTT
1 TTT
1239 GGGTGCAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 1 0.04
13 13 0.48
14 13 0.48
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (14 bp):
TTTTATTAAATGAT
Found at i:4008 original size:11 final size:12
Alignment explanation
Indices: 3987--4013 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3977 ACCGTGTAAA
3987 CCCACCCCCCCC
1 CCCACCCCCCCC
3999 CCCACCCCCCCC
1 CCCACCCCCCCC
4011 CCC
1 CCC
4014 CCAACTTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.93, G:0.00, T:0.00
Consensus pattern (12 bp):
CCCACCCCCCCC
Found at i:7932 original size:2 final size:2
Alignment explanation
Indices: 7925--7956 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7915 CCAAAAATTA
7925 AT 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 AT
7957 TAGATTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15487 original size:42 final size:41
Alignment explanation
Indices: 15412--15497 Score: 145
Period size: 42 Copynumber: 2.1 Consensus size: 41
15402 TTGTAGCAGG
*
15412 AATATGTAAAATCAAATTACTAAGACTCCCCAACCAAAATA
1 AATACGTAAAATCAAATTACTAAGACTCCCCAACCAAAATA
*
15453 AATACGTAAAATCAAATTAATTAAGACTCCCCAACCAAAATA
1 AATACGTAAAATCAAATT-ACTAAGACTCCCCAACCAAAATA
15495 AAT
1 AAT
15498 TATATAAAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
41 17 0.40
42 25 0.60
ACGTcount: A:0.52, C:0.21, G:0.05, T:0.22
Consensus pattern (41 bp):
AATACGTAAAATCAAATTACTAAGACTCCCCAACCAAAATA
Found at i:27851 original size:17 final size:19
Alignment explanation
Indices: 27829--27863 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
27819 AAGAGTTGAG
27829 GAGAAGGG-G-AAAAGAGC
1 GAGAAGGGAGCAAAAGAGC
27846 GAGAAGGGAGCAAAAGAG
1 GAGAAGGGAGCAAAAGAG
27864 ATGACATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.49, C:0.06, G:0.46, T:0.00
Consensus pattern (19 bp):
GAGAAGGGAGCAAAAGAGC
Found at i:31064 original size:16 final size:17
Alignment explanation
Indices: 31039--31081 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
31029 GAAAACTTAC
* *
31039 AATTACAAACAA-ACTT
1 AATTAAAAACAATACTG
31055 AATTAAAAACAATACTG
1 AATTAAAAACAATACTG
31072 AATTTAAAAA
1 AA-TTAAAAA
31082 GATACAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 11 0.48
17 5 0.22
18 7 0.30
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (17 bp):
AATTAAAAACAATACTG
Found at i:35757 original size:18 final size:18
Alignment explanation
Indices: 35729--35779 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
35719 TTTCCTTTAG
35729 TTTTG-TTTTGTTTCGTA
1 TTTTGTTTTTGTTTCGTA
*
35746 TTTTGTTTTTGTTTTTCGTT
1 TTTTGTTTTTG--TTTCGTA
35766 TTTGTGTTTTTGTT
1 TTT-TGTTTTTGTT
35780 AATTTTGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 5 0.17
18 5 0.17
19 2 0.07
20 9 0.31
21 8 0.28
ACGTcount: A:0.02, C:0.04, G:0.18, T:0.76
Consensus pattern (18 bp):
TTTTGTTTTTGTTTCGTA
Found at i:37890 original size:2 final size:2
Alignment explanation
Indices: 37883--37924 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
37873 AAAAGTGTTA
37883 AT AT AT AT AT AT 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 AT AT AT AT AT AT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.