Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016425.1 Corchorus capsularis cultivar CVL-1 contig16446, 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: 33541
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:892 original size:2 final size:2
Alignment explanation
Indices: 885--914 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
875 CTAATTAATA
885 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
915 TCAATGTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1902 original size:2 final size:2
Alignment explanation
Indices: 1895--1924 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1885 AATTAGAACC
1895 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1925 AGGTATAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7738 original size:18 final size:19
Alignment explanation
Indices: 7699--7739 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
7689 TAGATAAATA
*
7699 TAGTGAGGCTTTGGGCCAT
1 TAGTGAGGCTTTGGACCAT
7718 TAGTG-GGCTTCTGGACC-T
1 TAGTGAGGCTT-TGGACCAT
7736 TAGT
1 TAGT
7740 AGCTAGTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.15, C:0.17, G:0.34, T:0.34
Consensus pattern (19 bp):
TAGTGAGGCTTTGGACCAT
Found at i:20943 original size:6 final size:6
Alignment explanation
Indices: 20932--20973 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
20922 GACCTATCCT
* *
20932 CGTCCC CGTCCC CGTCTC CGTCCC CGTCTC CGTCCC CGTCCC
1 CGTCCC CGTCCC CGTCCC CGTCCC CGTCCC CGTCCC CGTCCC
20974 TATCCCCGGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.62, G:0.17, T:0.21
Consensus pattern (6 bp):
CGTCCC
Found at i:21312 original size:14 final size:15
Alignment explanation
Indices: 21293--21325 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
21283 TAATTTGTAA
21293 ATTAGTAAATAT-TT
1 ATTAGTAAATATATT
*
21307 ATTAGTATATATATT
1 ATTAGTAAATATATT
21322 ATTA
1 ATTA
21326 TTTATTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
ATTAGTAAATATATT
Found at i:21423 original size:2 final size:2
Alignment explanation
Indices: 21418--21445 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21408 ACACACACAC
21418 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
21446 TTCGGGGCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23513 original size:13 final size:13
Alignment explanation
Indices: 23495--23519 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23485 TGTTGTTATT
23495 TTGTAGATCTAAG
1 TTGTAGATCTAAG
23508 TTGTAGATCTAA
1 TTGTAGATCTAA
23520 AACGAAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGTAGATCTAAG
Found at i:24600 original size:46 final size:46
Alignment explanation
Indices: 24533--24628 Score: 183
Period size: 46 Copynumber: 2.1 Consensus size: 46
24523 CGATTGTAGT
24533 CTAATGTTCCATTGACAAATGTACAATTATGTAACCTCATTTTTCG
1 CTAATGTTCCATTGACAAATGTACAATTATGTAACCTCATTTTTCG
*
24579 CTAATGTTTCATTGACAAATGTACAATTATGTAACCTCATTTTTCG
1 CTAATGTTCCATTGACAAATGTACAATTATGTAACCTCATTTTTCG
24625 CTAA
1 CTAA
24629 ATGGAAATTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (46 bp):
CTAATGTTCCATTGACAAATGTACAATTATGTAACCTCATTTTTCG
Found at i:24639 original size:46 final size:46
Alignment explanation
Indices: 24543--24639 Score: 151
Period size: 46 Copynumber: 2.1 Consensus size: 46
24533 CTAATGTTCC
***
24543 ATTGACAAATGTACAATTATGTAACCTCATTTTTCGCTAATGTTTC
1 ATTGACAAATGTACAATTATGTAACCTCATTTTTCGCTAATGTGAA
24589 ATTGACAAATGTACAATTATGTAACCTCATTTTTCGCTAAATG-GAA
1 ATTGACAAATGTACAATTATGTAACCTCATTTTTCGCT-AATGTGAA
24635 ATTGA
1 ATTGA
24640 ATGTGATTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 43 0.91
47 4 0.09
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (46 bp):
ATTGACAAATGTACAATTATGTAACCTCATTTTTCGCTAATGTGAA
Found at i:24756 original size:15 final size:15
Alignment explanation
Indices: 24736--24765 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24726 GTAAACACTA
*
24736 CTGAAATTCATCTGC
1 CTGAAATACATCTGC
24751 CTGAAATACATCTGC
1 CTGAAATACATCTGC
24766 TTGAGCTCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (15 bp):
CTGAAATACATCTGC
Done.