Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014088.1 Corchorus olitorius cultivar O-4 contig14121, 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: 17575
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:424 original size:43 final size:45
Alignment explanation
Indices: 376--465 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 45
366 ATCTTAATAA
*
376 TGGCAATTTTATATA-TTT-TAATAGTGACATAATTAAAATATAT
1 TGGCAATTTTATATATTTTATAATAATGACATAATTAAAATATAT
*
419 TGGCAATTTTATATATTTTAATAATAATGGCATAATTAAAATATAT
1 TGGCAATTTTATATATTTT-ATAATAATGACATAATTAAAATATAT
465 T
1 T
466 TTAATAATGT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
43 15 0.36
44 3 0.07
46 24 0.57
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.44
Consensus pattern (45 bp):
TGGCAATTTTATATATTTTATAATAATGACATAATTAAAATATAT
Found at i:14546 original size:21 final size:21
Alignment explanation
Indices: 14521--14560 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
14511 TTTTTTATTC
14521 AGTTATATATTTATATATAAT
1 AGTTATATATTTATATATAAT
14542 AGTTATATATTTATATATA
1 AGTTATATATTTATATATA
14561 TTCAGATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
AGTTATATATTTATATATAAT
Found at i:15105 original size:4 final size:4
Alignment explanation
Indices: 15090--15121 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
15080 AGTTTTTTTT
*
15090 TTTG TTTA TTTG TTTG TTTG TTTG TTTG TTTG
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTTG
15122 GTACAAGCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.22, T:0.75
Consensus pattern (4 bp):
TTTG
Found at i:16191 original size:25 final size:26
Alignment explanation
Indices: 16130--16191 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 26
16120 GAAAAACATT
16130 CTTTTTGAAAA-TACTTTACCTTGAAA
1 CTTTTTGAAAATTACTTTACCTT-AAA
* * *
16156 ATTCTTG--AATTACTTTTCCTT-AA
1 CTTTTTGAAAATTACTTTACCTTAAA
16179 CTTTTTGAAAATT
1 CTTTTTGAAAATT
16192 GAATAAGAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 7
0.70 0.12 0.17
Matches are distributed among these distances:
23 7 0.25
24 2 0.07
25 14 0.50
26 5 0.18
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (26 bp):
CTTTTTGAAAATTACTTTACCTTAAA
Found at i:16897 original size:18 final size:19
Alignment explanation
Indices: 16876--16914 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
16866 TTCCCCCCTT
16876 TTTTTATTT-TCATCTCCC
1 TTTTTATTTGTCATCTCCC
* *
16894 TTTTTCTTTGTCTTCTCCC
1 TTTTTATTTGTCATCTCCC
16913 TT
1 TT
16915 CTTCTTCCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.05, C:0.28, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTTATTTGTCATCTCCC
Found at i:17377 original size:1 final size:1
Alignment explanation
Indices: 17366--17399 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
17356 AGGTAAGACC
* *
17366 TTTTCTTTTTTTTTTTTTTTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17400 CAGCTTTGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.03, T:0.94
Consensus pattern (1 bp):
T
Done.