Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011219.1 Corchorus capsularis cultivar CVL-1 contig11240, 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: 16388
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1605 original size:24 final size:24
Alignment explanation
Indices: 1539--1607 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
1529 GGCTCATTTT
1539 CAGCATCTAAACCAGCATCATTAA
1 CAGCATCTAAACCAGCATCATTAA
* *
1563 CATCAT-TCAAACCAACATCATTAA
1 CAGCATCT-AAACCAGCATCATTAA
**
1587 CAGCATCTAAAATAGCATCAT
1 CAGCATCTAAACCAGCATCAT
1608 GTGGATCATC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
23 1 0.03
24 35 0.95
25 1 0.03
ACGTcount: A:0.43, C:0.28, G:0.06, T:0.23
Consensus pattern (24 bp):
CAGCATCTAAACCAGCATCATTAA
Found at i:7378 original size:18 final size:18
Alignment explanation
Indices: 7355--7393 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
7345 AAGTCTCGGC
7355 CTCATCACCGTAATTAGA
1 CTCATCACCGTAATTAGA
7373 CTCATCACCGTAATTAGA
1 CTCATCACCGTAATTAGA
7391 CTC
1 CTC
7394 TGGTTGATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.28
Consensus pattern (18 bp):
CTCATCACCGTAATTAGA
Found at i:10666 original size:13 final size:13
Alignment explanation
Indices: 10635--10831 Score: 56
Period size: 13 Copynumber: 13.5 Consensus size: 13
10625 TATATGTAAT
*
10635 GAAATTATAATTA
1 GAAATTATATTTA
*
10648 GGAATTATATTTA
1 GAAATTATATTTA
*
10661 TAAATTATATATGTAA
1 GAAATTATAT-T-T-A
*
10677 TGAAA-AATTATTTA
1 -GAAATTA-TATTTA
*
10691 GAAAATAATATTTA
1 G-AAATTATATTTA
* *
10705 TAAAGTATATATGTGAA
1 GAAA-T-TATAT-T-TA
* *
10722 GAAATTATAATCA
1 GAAATTATATTTA
*
10735 GGAATTATATTATAAA
1 GAAATTATATT-T--A
*
10751 TAAATTATATATGTAA
1 GAAATTATAT-T-T-A
10767 TGAAA-TATTATTTA
1 -GAAATTA-TATTTA
10781 GAAATTATATATGTA
1 GAAATTATAT-T-TA
*
10796 TTGAAATTATAATTA
1 --GAAATTATATTTA
*
10811 GAAAATAATATTTA
1 G-AAATTATATTTA
10825 GAAATTA
1 GAAATTA
10832 AAATTTTTTA
Statistics
Matches: 138, Mismatches: 23, Indels: 46
0.67 0.11 0.22
Matches are distributed among these distances:
13 46 0.33
14 28 0.20
15 17 0.12
16 20 0.14
17 27 0.20
ACGTcount: A:0.50, C:0.01, G:0.10, T:0.40
Consensus pattern (13 bp):
GAAATTATATTTA
Found at i:10728 original size:87 final size:89
Alignment explanation
Indices: 10603--10784 Score: 273
Period size: 87 Copynumber: 2.1 Consensus size: 89
10593 AATTATAATG
* *
10603 AGAAAATAATATTTAGAGATGATATATGTAATGAAATTATAATTAGGAATTATATT-T-ATAAAT
1 AGAAAATAATATTTAGAAATGATATATGTAATGAAATTATAATCAGGAATTATATTATAATAAAT
10666 TATATATGTAATGAAAAATTATTT
66 TATATATGTAATGAAAAATTATTT
*
10690 AGAAAATAATATTTATAAA-GTATATATGTGAA-GAAATTATAATCAGGAATTATATTATAAATA
1 AGAAAATAATATTTAGAAATG-ATATATGT-AATGAAATTATAATCAGGAATTATATTAT-AATA
*
10753 AATTATATATGTAATGAAATATTATTT
63 AATTATATATGTAATGAAAAATTATTT
10780 AGAAA
1 AGAAA
10785 TTATATATGT
Statistics
Matches: 86, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
86 1 0.01
87 48 0.56
88 3 0.03
90 34 0.40
ACGTcount: A:0.50, C:0.01, G:0.11, T:0.38
Consensus pattern (89 bp):
AGAAAATAATATTTAGAAATGATATATGTAATGAAATTATAATCAGGAATTATATTATAATAAAT
TATATATGTAATGAAAAATTATTT
Found at i:10777 original size:30 final size:30
Alignment explanation
Indices: 10741--10802 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
10731 ATCAGGAATT
*
10741 ATATTATAAATAAATTATATATGTAATGAA
1 ATATTATAAAGAAATTATATATGTAATGAA
** *
10771 ATATTATTTAGAAATTATATATGTATTGAA
1 ATATTATAAAGAAATTATATATGTAATGAA
10801 AT
1 AT
10803 TATAATTAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (30 bp):
ATATTATAAAGAAATTATATATGTAATGAA
Found at i:10803 original size:17 final size:17
Alignment explanation
Indices: 10752--10806 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
10742 TATTATAAAT
*
10752 AAATTATATATGTAATG
1 AAATTATATATGTATTG
*
10769 AAA-TAT-TAT-T-TAG
1 AAATTATATATGTATTG
10782 AAATTATATATGTATTG
1 AAATTATATATGTATTG
10799 AAATTATA
1 AAATTATA
10807 ATTAGAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 4 0.13
14 4 0.13
15 6 0.19
16 4 0.13
17 13 0.42
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (17 bp):
AAATTATATATGTATTG
Found at i:10812 original size:30 final size:30
Alignment explanation
Indices: 10752--10814 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
10742 TATTATAAAT
*
10752 AAATTATATATGTAATGAAATATTATTTAG
1 AAATTATATATGTAATGAAATATTAATTAG
*
10782 AAATTATATATGTATTGAAAT-TATAATTAG
1 AAATTATATATGTAATGAAATAT-TAATTAG
10812 AAA
1 AAA
10815 ATAATATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (30 bp):
AAATTATATATGTAATGAAATATTAATTAG
Done.