Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004012.1 Corchorus capsularis cultivar CVL-1 contig04020, 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, 608
Length: 1014
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Found at i:97 original size:28 final size:26
Alignment explanation
Indices: 49--117 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 26
39 GTATAAGAGA
49 AAAGAAGAGTAA-AAAGTGGTAATCAAT
1 AAAG-AGAGTAAGAAAG-GGTAATCAAT
* *
76 GAAAGAGAGTAAGGAAAGGGTAATTAGT
1 -AAAGAGAGTAA-GAAAGGGTAATCAAT
104 AAA-AGAGTAAGAAA
1 AAAGAGAGTAAGAAA
118 AGAGTAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
25 4 0.11
26 7 0.19
27 10 0.27
28 12 0.32
29 4 0.11
ACGTcount: A:0.55, C:0.01, G:0.28, T:0.16
Consensus pattern (26 bp):
AAAGAGAGTAAGAAAGGGTAATCAAT
Found at i:838 original size:22 final size:22
Alignment explanation
Indices: 803--887 Score: 79
Period size: 21 Copynumber: 3.9 Consensus size: 22
793 TACTGATCAC
*
803 TTTTTACTCTTTACTGATTACTA
1 TTTTTACTC-TTACTAATTACTA
* *
826 TTTTTATTCTTACTAATTACCA
1 TTTTTACTCTTACTAATTACTA
848 TTTGCTT--TC-TACTAATTACTA
1 TTT--TTACTCTTACTAATTACTA
*
869 -TTTTACTCTTACTGATTAC
1 TTTTTACTCTTACTAATTAC
888 CTTTTACTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
18 2 0.04
20 4 0.08
21 20 0.38
22 16 0.31
23 8 0.15
24 2 0.04
ACGTcount: A:0.24, C:0.19, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTTTACTCTTACTAATTACTA
Found at i:901 original size:35 final size:36
Alignment explanation
Indices: 852--969 Score: 130
Period size: 35 Copynumber: 3.0 Consensus size: 36
842 TTACCATTTG
852 CTTTCTACTAATTACTATTTTACTC-TTACTGATTAC
1 CTTT-TACTAATTACTATTTTACTCTTTACTGATTAC
*
888 CTTTTACTGATTACTATTTTACTCTTTACTGATTAC
1 CTTTTACTAATTACTATTTTACTCTTTACTGATTAC
924 CTTCTTACTTTTTACTGATTACTATTTTACTCTTTTACTGATTAC
1 CTT-TTAC----TA---ATTACTATTTTACTC-TTTACTGATTAC
969 C
1 C
970 ATCTTTATTG
Statistics
Matches: 70, Mismatches: 2, Indels: 11
0.84 0.02 0.13
Matches are distributed among these distances:
35 19 0.27
36 18 0.26
37 4 0.06
41 1 0.01
44 15 0.21
45 13 0.19
ACGTcount: A:0.22, C:0.21, G:0.04, T:0.53
Consensus pattern (36 bp):
CTTTTACTAATTACTATTTTACTCTTTACTGATTAC
Found at i:915 original size:22 final size:22
Alignment explanation
Indices: 890--968 Score: 115
Period size: 22 Copynumber: 3.5 Consensus size: 22
880 CTGATTACCT
890 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
* *
912 TTTACTGATTACCT-TCTTACTT
1 TTTACTGATTA-CTATTTTACTC
934 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
956 TTTTACTGATTAC
1 -TTTACTGATTAC
969 CATCTTTATT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
21 2 0.04
22 34 0.68
23 14 0.28
ACGTcount: A:0.22, C:0.19, G:0.05, T:0.54
Consensus pattern (22 bp):
TTTACTGATTACTATTTTACTC
Found at i:943 original size:44 final size:45
Alignment explanation
Indices: 884--974 Score: 157
Period size: 44 Copynumber: 2.0 Consensus size: 45
874 CTCTTACTGA
*
884 TTACCTTTTACTGATTACTATTTTACTC-TTTACTGATTACCTTC
1 TTACCTTTTACTGATTACTATTTTACTCTTTTACTGATTACCATC
*
928 TTACTTTTTACTGATTACTATTTTACTCTTTTACTGATTACCATC
1 TTACCTTTTACTGATTACTATTTTACTCTTTTACTGATTACCATC
973 TT
1 TT
975 TATTGATTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 27 0.61
45 17 0.39
ACGTcount: A:0.21, C:0.21, G:0.04, T:0.54
Consensus pattern (45 bp):
TTACCTTTTACTGATTACTATTTTACTCTTTTACTGATTACCATC
Done.