Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013901.1 Corchorus capsularis cultivar CVL-1 contig13922, 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: 46123
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3928 original size:143 final size:144
Alignment explanation
Indices: 3743--4015 Score: 487
Period size: 143 Copynumber: 1.9 Consensus size: 144
3733 CGAAATTCGA
*
3743 AGTGATATTTATTCATCATTGTAATTAGTTAGAAACTGTACTTTTTATTGGATCTGAGTATTTAA
1 AGTGATATTTATTCATCACTGTAATTAGTTAGAAACTGTACTTTTTATTGGATCTGAGTATTTAA
*
3808 TTTAGGAGTTAGTGTGTTA-TTTTTATTAGAAAGTGAAGTTGAATTTTATCTTTCGAAATTTGAA
66 TTTAGGAGTTAGTGTGTTATTTTTTATTAGAAAGTGAAGTTGAATTTTATCTTTCGAAAGTTGAA
3872 GTTCTGAAGTTGAC
131 GTTCTGAAGTTGAC
*
3886 AGTGATATTTATTCATTACTGTAATTAGTTAGAAAC-GATACTTTTTATTGGATCTGAGTATTTA
1 AGTGATATTTATTCATCACTGTAATTAGTTAGAAACTG-TACTTTTTATTGGATCTGAGTATTTA
*
3950 ATTTAGGAGTTAGTGTGTTATTTTTTATTAGAAAGTGAAGTTGAATTTTATTTTTCGAAAGTTGA
65 ATTTAGGAGTTAGTGTGTTATTTTTTATTAGAAAGTGAAGTTGAATTTTATCTTTCGAAAGTTGA
4015 A
130 A
4016 CTTGACAATG
Statistics
Matches: 124, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
142 1 0.01
143 80 0.65
144 43 0.35
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.46
Consensus pattern (144 bp):
AGTGATATTTATTCATCACTGTAATTAGTTAGAAACTGTACTTTTTATTGGATCTGAGTATTTAA
TTTAGGAGTTAGTGTGTTATTTTTTATTAGAAAGTGAAGTTGAATTTTATCTTTCGAAAGTTGAA
GTTCTGAAGTTGAC
Found at i:8234 original size:21 final size:20
Alignment explanation
Indices: 8208--8246 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
8198 ATCATGCAGG
8208 AAAAAAGAAAAAGAGAGAAAA
1 AAAAAAGAAAAAGA-AGAAAA
*
8229 AAAAAAGAAGAAGAAGAA
1 AAAAAAGAAAAAGAAGAA
8247 GAAGGAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAAGAAGAAAA
Found at i:12690 original size:41 final size:41
Alignment explanation
Indices: 12633--12717 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
12623 GTGACTTAGG
12633 TTTGATACTGATCTAGGAAGTTTAAAGATTTTGCTTGAGCA
1 TTTGATACTGATCTAGGAAGTTTAAAGATTTTGCTTGAGCA
12674 TTTGATACTGATCTAGGAAGTTTAAAGATTTTGCTTGAGCA
1 TTTGATACTGATCTAGGAAGTTTAAAGATTTTGCTTGAGCA
12715 TTT
1 TTT
12718 TTCTACTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.41
Consensus pattern (41 bp):
TTTGATACTGATCTAGGAAGTTTAAAGATTTTGCTTGAGCA
Found at i:29950 original size:12 final size:12
Alignment explanation
Indices: 29935--29964 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
29925 CATTTTGTAA
29935 GTAATTTATTAT
1 GTAATTTATTAT
29947 GTAATTTATTAT
1 GTAATTTATTAT
29959 GTAATT
1 GTAATT
29965 GGTTTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (12 bp):
GTAATTTATTAT
Found at i:34329 original size:2 final size:2
Alignment explanation
Indices: 34322--34347 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34312 AGCCTTTTAA
34322 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
34348 TTCTTTAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35899 original size:2 final size:2
Alignment explanation
Indices: 35892--35920 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
35882 TTAATTTTTA
35892 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35921 TTAAGCAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:39995 original size:2 final size:2
Alignment explanation
Indices: 39988--40018 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39978 AGTGTATGAG
39988 AT AT AT AT AT AT 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 A
40019 AACTGAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.