Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013560.1 Corchorus capsularis cultivar CVL-1 contig13581, 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: 24698
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1130 original size:3 final size:3
Alignment explanation
Indices: 1122--1153 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1112 AGATATATAT
1122 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1154 GAGAGGCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2537 original size:5 final size:5
Alignment explanation
Indices: 2527--2552 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2517 AAAAAAACGC
2527 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
2553 GACTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:5113 original size:20 final size:20
Alignment explanation
Indices: 5088--5128 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5078 ACAAATGAGA
5088 GGGTGCAATCAACTAAATCT
1 GGGTGCAATCAACTAAATCT
5108 GGGTGCAATCAACTAAATCT
1 GGGTGCAATCAACTAAATCT
5128 G
1 G
5129 CTTCAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
GGGTGCAATCAACTAAATCT
Found at i:13243 original size:14 final size:13
Alignment explanation
Indices: 13220--13277 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
13210 TAATGCACCC
13220 AAAACATTTAATA
1 AAAACATTTAATA
13233 AAAATCATTT-ATA
1 AAAA-CATTTAATA
*
13246 AAAACACTTTATTA
1 AAAACA-TTTAATA
* *
13260 AAAATA-GTAATA
1 AAAACATTTAATA
13272 AAAACA
1 AAAACA
13278 AGTCCCTCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 11 0.30
13 14 0.38
14 12 0.32
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.29
Consensus pattern (13 bp):
AAAACATTTAATA
Found at i:13272 original size:26 final size:26
Alignment explanation
Indices: 13220--13277 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
13210 TAATGCACCC
* *
13220 AAAACATTTAATAAAAATCATTTATA
1 AAAACATTTAATAAAAATCAGTAATA
*
13246 AAAACACTTTATTAAAAAT-AGTAATA
1 AAAACA-TTTAATAAAAATCAGTAATA
13272 AAAACA
1 AAAACA
13278 AGTCCCTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.29
Consensus pattern (26 bp):
AAAACATTTAATAAAAATCAGTAATA
Found at i:19237 original size:30 final size:32
Alignment explanation
Indices: 19202--19260 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 32
19192 TTTCTTCCAG
19202 TTTTCTGAGTCTTTT-CC-TTCCCCTTTTTCC
1 TTTTCTGAGTCTTTTCCCTTTCCCCTTTTTCC
***
19232 TTTTCTTCTTCTTTTCCCTTTCCCCTTTT
1 TTTTCTGAGTCTTTTCCCTTTCCCCTTTT
19261 CTCTTTCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.50
31 2 0.08
32 10 0.42
ACGTcount: A:0.02, C:0.34, G:0.03, T:0.61
Consensus pattern (32 bp):
TTTTCTGAGTCTTTTCCCTTTCCCCTTTTTCC
Found at i:23002 original size:19 final size:18
Alignment explanation
Indices: 22978--23014 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
22968 GAAGTTCGTG
*
22978 TTTGAAGATAATTTGAAGA
1 TTTGAAGACAA-TTGAAGA
22997 TTTGAAGACAATTGAAGA
1 TTTGAAGACAATTGAAGA
23015 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.32
Consensus pattern (18 bp):
TTTGAAGACAATTGAAGA
Found at i:24346 original size:6 final size:6
Alignment explanation
Indices: 24335--24365 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
24325 ATAATTGCCA
24335 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
24366 CTTTGCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Done.