Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021215.1 Corchorus olitorius cultivar O-4 contig21248, 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: 12978
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Found at i:1333 original size:35 final size:35
Alignment explanation
Indices: 1288--1753 Score: 513
Period size: 35 Copynumber: 13.0 Consensus size: 35
1278 ATCAATATGA
* *
1288 AGATCAACTCTGATCATCGAAAACTTCTTGGAATA
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
** *
1323 AGATCAACTCTGATCATAAAAAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCAT--CGAAAACTTCTTGAAATG
**
1360 AGATCAACTCTGATCATATAAAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATC--AT--CGAAAACTTCTTGAAATG
* *
1399 AGATCAACTCTGATCAACGAAAAC-TCTTTGAAACG
1 AGATCAACTCTGATCATCGAAAACTTC-TTGAAATG
*
1434 AGATCAACTCTAATCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
* * *
1469 AGATCAACTCTGACCAT-AAAAACATCTTGAAAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTG-AAATG
** * *
1504 AGATCAACTCTGATCATAAAAAACTTCCTGAAAGG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
* *
1539 AGATCAACTCTGATCACCGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
*
1574 AGATCAACTCTGATCATCGAAAACTTCTTGAAATA
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
* ** *
1609 AGATCAACTCTAATCATAAAAAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCAT--CGAAAACTTCTTGAAATG
* **
1646 ACATCAACTCTGATCATATAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATC--ATCGAAAACTTCTTGAAATG
* * * *
1683 AGATCAACCCTGATCAACGAAAACTCCTTGAAACG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
* *
1718 AGATCAACTCTGGTCATCGAAAACTTCTTGGAATG
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
1753 A
1 A
1754 CCGCACTGGA
Statistics
Matches: 369, Mismatches: 50, Indels: 24
0.83 0.11 0.05
Matches are distributed among these distances:
34 12 0.03
35 221 0.60
36 12 0.03
37 86 0.23
39 38 0.10
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (35 bp):
AGATCAACTCTGATCATCGAAAACTTCTTGAAATG
Found at i:1724 original size:144 final size:144
Alignment explanation
Indices: 1288--1747 Score: 723
Period size: 144 Copynumber: 3.2 Consensus size: 144
1278 ATCAATATGA
*
1288 AGATCAACTCTGATCATCGAAAACTTCTTGGAATAAGATCAACTCTGATCATAAAAAAAACTTCT
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATAAGATCAACTCTGATCATAAAAAAAACTTCT
1353 TGAAAGGAGATCAACTCTGATCATATAAAAAAAACTTCTTGAAATGAGATCAACTCTGATCAACG
66 TGAAAGGAGATCAACTCTGATCATAT--AAAAAACTTCTTGAAATGAGATCAACTCTGATCAACG
*
1418 AAAACTCTTTGAAACG
129 AAAACTCCTTGAAACG
* * * *
1434 AGATCAACTCTAATCATCGAAAACTTCTTGAAATGAGATCAACTCTGACCAT---AAAAACATCT
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATAAGATCAACTCTGATCATAAAAAAAACTTCT
* * * *
1496 TGAAAATGAGATCAACTCTGATC--ATAAAAAACTTCCTGAAAGGAGATCAACTCTGATCACCGA
66 TG-AAAGGAGATCAACTCTGATCATATAAAAAACTTCTTGAAATGAGATCAACTCTGATCAACGA
*
1559 AAACTTCTTGAAACG
130 AAACTCCTTGAAACG
*
1574 AGATCAACTCTGATCATCGAAAACTTCTTGAAATAAGATCAACTCTAATCATAAAAAAAACTTCT
1 AGATCAACTCTGATCATCGAAAACTTCTTGAAATAAGATCAACTCTGATCATAAAAAAAACTTCT
* *
1639 TGAAAGGACATCAACTCTGATCATATAAAAAACTTCTTGAAATGAGATCAACCCTGATCAACGAA
66 TGAAAGGAGATCAACTCTGATCATATAAAAAACTTCTTGAAATGAGATCAACTCTGATCAACGAA
1704 AACTCCTTGAAACG
131 AACTCCTTGAAACG
*
1718 AGATCAACTCTGGTCATCGAAAACTTCTTG
1 AGATCAACTCTGATCATCGAAAACTTCTTG
1748 GAATGACCGC
Statistics
Matches: 284, Mismatches: 24, Indels: 14
0.88 0.07 0.04
Matches are distributed among these distances:
140 96 0.34
142 20 0.07
143 22 0.08
144 98 0.35
146 48 0.17
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (144 bp):
AGATCAACTCTGATCATCGAAAACTTCTTGAAATAAGATCAACTCTGATCATAAAAAAAACTTCT
TGAAAGGAGATCAACTCTGATCATATAAAAAACTTCTTGAAATGAGATCAACTCTGATCAACGAA
AACTCCTTGAAACG
Found at i:1800 original size:54 final size:54
Alignment explanation
Indices: 1718--1934 Score: 326
Period size: 54 Copynumber: 4.0 Consensus size: 54
1708 CCTTGAAACG
** *
1718 AGATCAACTCTGGTCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
1 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
* *
1772 AGATCAACTCTGACCATTGGAAACTTCTTGGAATGACCGCACTGGATCATCTCA
1 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
* * * * * **
1826 GGATCAACTCTAACCATTGAAGACTTCTTAGAATGACGGCACCAGATCATCTGA
1 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
1880 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
1 AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
1934 A
1 A
1935 CACCTGTTTC
Statistics
Matches: 142, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 142 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (54 bp):
AGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGA
Found at i:10063 original size:21 final size:21
Alignment explanation
Indices: 10007--10063 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
9997 TTTATAACAC
* *
10007 CTTGTTCCCGCCTCATCTCTT
1 CTTGTGCCTGCCTCATCTCTT
* ** * *
10028 CTTGCGAATGTCTCATTTCTT
1 CTTGTGCCTGCCTCATCTCTT
10049 CTTGTGCCTGCCTCA
1 CTTGTGCCTGCCTCA
10064 GATGTTGGAC
Statistics
Matches: 25, Mismatches: 11, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.09, C:0.35, G:0.14, T:0.42
Consensus pattern (21 bp):
CTTGTGCCTGCCTCATCTCTT
Done.