Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012044.1 Corchorus capsularis cultivar CVL-1 contig12065, 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: 3923
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.29
Found at i:1748 original size:110 final size:110
Alignment explanation
Indices: 1612--1830 Score: 429
Period size: 110 Copynumber: 2.0 Consensus size: 110
1602 ACTATTGATC
*
1612 ATATTTAGAATTTAGTTAGCATATAGCATCCACAATTTAGCATTTTCACATTAGAATATAAGCAT
1 ATATTTAGAATTTAGTTAGCATATAGCATCCACAATTTAGCATCTTCACATTAGAATATAAGCAT
1677 ACATGGCAACCTTCATTACATCATTCCTAGCATCTCATTACATTA
66 ACATGGCAACCTTCATTACATCATTCCTAGCATCTCATTACATTA
1722 ATATTTAGAATTTAGTTAGCATATAGCATCCACAATTTAGCATCTTCACATTAGAATATAAGCAT
1 ATATTTAGAATTTAGTTAGCATATAGCATCCACAATTTAGCATCTTCACATTAGAATATAAGCAT
1787 ACATGGCAACCTTCATTACATCATTCCTAGCATCTCATTACATT
66 ACATGGCAACCTTCATTACATCATTCCTAGCATCTCATTACATT
1831 TCACTTCACA
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
110 108 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (110 bp):
ATATTTAGAATTTAGTTAGCATATAGCATCCACAATTTAGCATCTTCACATTAGAATATAAGCAT
ACATGGCAACCTTCATTACATCATTCCTAGCATCTCATTACATTA
Found at i:1818 original size:55 final size:55
Alignment explanation
Indices: 1649--1821 Score: 137
Period size: 55 Copynumber: 3.1 Consensus size: 55
1639 ATCCACAATT
*
1649 TAGCATTTTCACATTAGAATATAAGCATACATGGCAACCTTCATTACATCATTCC
1 TAGCATCTTCACATTAGAATATAAGCATACATGGCAACCTTCATTACATCATTCC
* * * ** * * *
1704 TAGCATCTCATTACATT--AATATTTAGAATTTAGTTAGCATA--TAGCA-TCCA-CAATT--
1 TAGCATCT--TCACATTAGAATA-TAAGCA--TACATGGCA-ACCT-TCATTACATC-ATTCC
1759 TAGCATCTTCACATTAGAATATAAGCATACATGGCAACCTTCATTACATCATTCC
1 TAGCATCTTCACATTAGAATATAAGCATACATGGCAACCTTCATTACATCATTCC
1814 TAGCATCT
1 TAGCATCT
1822 CATTACATTT
Statistics
Matches: 85, Mismatches: 17, Indels: 32
0.63 0.13 0.24
Matches are distributed among these distances:
51 1 0.01
52 8 0.09
53 13 0.15
54 5 0.06
55 31 0.36
56 5 0.06
57 13 0.15
58 8 0.09
59 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (55 bp):
TAGCATCTTCACATTAGAATATAAGCATACATGGCAACCTTCATTACATCATTCC
Found at i:3557 original size:22 final size:23
Alignment explanation
Indices: 3529--3602 Score: 86
Period size: 22 Copynumber: 3.4 Consensus size: 23
3519 AGAAAGATGC
*
3529 AATCAGTAAAAG-GTAAAATGGT
1 AATCAGTAAAAGAGTAAAATGAT
*
3551 AATCAGT-AAAGAGTAAAGTGAT
1 AATCAGTAAAAGAGTAAAATGAT
*
3573 AATCAGT-AAAGAGTAATA-GA-
1 AATCAGTAAAAGAGTAAAATGAT
3593 AATCAGTAAA
1 AATCAGTAAA
3603 TCAGTAATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
20 7 0.15
21 8 0.17
22 31 0.67
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.22
Consensus pattern (23 bp):
AATCAGTAAAAGAGTAAAATGAT
Found at i:3649 original size:55 final size:55
Alignment explanation
Indices: 3585--3889 Score: 506
Period size: 55 Copynumber: 5.5 Consensus size: 55
3575 TCAGTAAAGA
* *
3585 GTAATAGAAATCAGTAAATCAGTAATTAAGTGAAAAGCA-ATTAATCAGAGTCAAG
1 GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAG-AGATTAATCAGAGTCAAG
* * *
3640 GTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAGATTAATCAGAGTCAAG
1 GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAG
*
3695 GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAA
1 GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAG
* *
3750 GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATTAGAGTCAAA
1 GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAG
3805 GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAG
1 GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAG
3860 GTAATAGTAATCAGTAAATC-GATAATTAAG
1 GTAATAGTAATCAGTAAATCAG-TAATTAAG
3890 AGTTAAAATG
Statistics
Matches: 240, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
54 2 0.01
55 238 0.99
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (55 bp):
GTAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAG
Found at i:3674 original size:25 final size:25
Alignment explanation
Indices: 3591--3674 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 25
3581 AAGAGTAATA
*
3591 GAAATCAGTAAATCAGTAATTAAGT
1 GAAATCAGTAAATCAATAATTAAGT
* * * *
3616 GAAAAGCAATTAATCAGAGTCAAGGTAA-T
1 G-AAATCAGTAAATCA-A-T-AA-TTAAGT
3645 AGAAATCAGTAAATCAATAATTAAGT
1 -GAAATCAGTAAATCAATAATTAAGT
3671 GAAA
1 GAAA
3675 AGAGATTAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 14
0.65 0.14 0.21
Matches are distributed among these distances:
25 8 0.19
26 14 0.33
27 1 0.02
28 2 0.05
29 14 0.33
30 4 0.09
ACGTcount: A:0.51, C:0.08, G:0.17, T:0.24
Consensus pattern (25 bp):
GAAATCAGTAAATCAATAATTAAGT
Done.