Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_105 ID=scaffold_105-JGI_221_v2.0
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: 13545
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Found at i:1668 original size:44 final size:44
Alignment explanation
Indices: 1616--2033 Score: 359
Period size: 44 Copynumber: 9.5 Consensus size: 44
1606 CTACCAAAAT
* * * *
1616 AGGAAGACAGGACCTACTATCTTCGATCTACTTCATGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATAC
* * * * *
1660 ATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCA-CGCCAATAC
* *
1705 GGGAAGACAAGATCTGC-ATCTTCGATCTACTACACGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATAC
* * * * *
1748 ATGAAGACAAGATCTGCTTTCTTCGATCTACTTTGC-CACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTAC-TT-CACGCCAATAC
* * *
1793 AGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATAC
* * *
1836 AGGAAGACAGGACCTGCTATCCTCGATCTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATAC
* * * * * * **
1880 ATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCTACCAGTTT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATAC
* * * * *
1925 GGGAAGACAAGAAT-TGC-ACCTTCGATCCACTTC-CTACCAATAT
1 AGGAAGACAAG-ATCTGCTATCTTCGATCTACTTCAC-GCCAATAC
* *
1968 AGGAAAACAGGATCTGC-ATTCTTCGATCTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTA-TCTTCGATCTACTTCACGCCAATAC
*
2012 ATGAAGACAAGATCTGC-ATCTT
1 AGGAAGACAAGATCTGCTATCTT
2034 TTATGACTTC
Statistics
Matches: 300, Mismatches: 62, Indels: 25
0.78 0.16 0.06
Matches are distributed among these distances:
42 4 0.01
43 69 0.23
44 164 0.55
45 60 0.20
46 3 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (44 bp):
AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATAC
Found at i:1750 original size:88 final size:88
Alignment explanation
Indices: 1608--2033 Score: 423
Period size: 88 Copynumber: 4.8 Consensus size: 88
1598 TCCACTTCCT
* * * * *
1608 ACCAAAATAGGAAGACAGGACCTACTATCTTCGATCTACTTCATGCCAATACATGAAGACAAGAT
1 ACCAATATAGGAAGACAAGATCTGC-ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
*
1673 CTGCTTTCTTCGATCTACTTCACC
65 CTGCTATCTTCGATCTACTTCACC
* * *
1697 ACCAGTATGGGAAGACAAGATCTGCATCTTCGATCTACTACACGCCAATACATGAAGACAAGATC
1 ACCAATATAGGAAGACAAGATCTGCATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATC
* **
1762 TGCTTTCTTCGATCTACTTTGCC
66 TGCTATCTTCGATCTACTTCACC
* * * * * * *
1785 ACCAGTATAGGAAGACAAGATCTGCATCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGAC
1 ACCAATATAGGAAGACAAGATCTGCATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGAT
*
1849 CTGCTATCCTCGATCTACTTCA-C
65 CTGCTATCTTCGATCTACTTCACC
* * * * * * * * ****
1872 GCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCTACCAGTTTGGGAAGACAAGA
1 ACCAATATAGGAAGACAAGATCTGC-ATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAG-
* * *
1937 AT-TGC-ACCTTCGATCCACTTC-CT
63 ATCTGCTATCTTCGATCTACTTCACC
* *
1960 ACCAATATAGGAAAACAGGATCTGCATTCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
1 ACCAATATAGGAAGACAAGATCTGCA-TCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
2025 CTGC-ATCTT
65 CTGCTATCTT
2034 TTATGACTTC
Statistics
Matches: 277, Mismatches: 53, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
86 2 0.01
87 42 0.15
88 193 0.70
89 39 0.14
90 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (88 bp):
ACCAATATAGGAAGACAAGATCTGCATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATC
TGCTATCTTCGATCTACTTCACC
Found at i:1862 original size:132 final size:131
Alignment explanation
Indices: 1662--2028 Score: 538
Period size: 132 Copynumber: 2.8 Consensus size: 131
1652 GCCAATACAT
* * * * * *
1662 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTT
1 GAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGATCTGCATCTT
* *
1727 CGATCTACTACACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTTGCCACCAGTA
64 CGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTA
1792 TAG
129 TAG
* *
1795 GAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCCTC
1 GAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATCTGC-ATCTTC
* * *
1860 GATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCTACCAGTTT
65 GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTAT
*
1925 GG
130 AG
* *
1927 GAAGACAAGAAT-TGCACCTTCGATCCACTTCCTACCAATATAGGAAAACAGGATCTGCATTCTT
1 GAAGACAAG-ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATCTGCA-TCTT
1991 CGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
64 CGATCTACTTCACGCCAATACATGAAGACAAGATCTGC
2029 ATCTTTTATG
Statistics
Matches: 212, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
131 23 0.11
132 172 0.81
133 17 0.08
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (131 bp):
GAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATCTGCATCTTCG
ATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATA
G
Found at i:1984 original size:220 final size:219
Alignment explanation
Indices: 1597--2033 Score: 628
Period size: 220 Copynumber: 2.0 Consensus size: 219
1587 CTATTTTTCA
* *
1597 ATCCACTTCCTACCAAAATAGGAAGACAGGACCTACTATCTTCGATCTACTTCATGCCAATACAT
1 ATCCACTTCCTACCAAAATAGGAAGACAGGACCTACTATCCTCGATCTACTTCACGCCAATACAT
* *
1662 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCACCTT
* * * * * *
1727 CGATCTACTACACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTTGC-CACCAGT
131 CGATCCACTACACACCAATACAGGAAAACAAGATCTGCATTCTTCGATCTAC-TT-CACACCAAT
*
1791 ATAGGAAGACAAGATCTGCATCTTCG
194 ACAGGAAGACAAGATCTGCATCTTCG
* *
1817 ATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCCTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAAAATAGGAAGACAGGACCTACTATCCTCGATCTACTTCACGCCAATACAT
* * *
1882 GAAGACAAGATCTACTTTCTTCGATCTACTTCGCTACCAGTTTGGGAAGACAAGAAT-TGCACCT
66 GAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAG-ATCTGCACCT
* * * *
1946 TCGATCCACTTC-CTACCAATATAGGAAAACAGGATCTGCATTCTTCGATCTACTTCACGCCAAT
130 TCGATCCACTACAC-ACCAATACAGGAAAACAAGATCTGCATTCTTCGATCTACTTCACACCAAT
*
2010 ACATGAAGACAAGATCTGCATCTT
194 ACAGGAAGACAAGATCTGCATCTT
2034 TTATGACTTC
Statistics
Matches: 193, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
218 1 0.01
219 30 0.16
220 160 0.83
221 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (219 bp):
ATCCACTTCCTACCAAAATAGGAAGACAGGACCTACTATCCTCGATCTACTTCACGCCAATACAT
GAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCACCTT
CGATCCACTACACACCAATACAGGAAAACAAGATCTGCATTCTTCGATCTACTTCACACCAATAC
AGGAAGACAAGATCTGCATCTTCG
Done.