Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002242.1 Corchorus capsularis cultivar CVL-1 contig02248, 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, 690
Length: 1150
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:926 original size:30 final size:30
Alignment explanation
Indices: 892--1137 Score: 197
Period size: 30 Copynumber: 7.4 Consensus size: 30
882 TTTGATTTCA
892 TTCTATTTCATTATATGGTATTACATAATT
1 TTCTATTTCATTATATGGTATTACATAATT
922 TTCTATTTCATTATATGGTATTACATAATT
1 TTCTATTTCATTATATGGTATTACATAATT
**
952 TTCTATTTCATTATATGGTATTATGTAATT
1 TTCTATTTCATTATATGGTATTACATAATT
* *
982 TTGATTTCATTCTATGTTCATTATATGGTATTACATAATT
1 TT-CTAT--TTC-A--TT-A-T--ATGGTATTACATAATT
*
1022 TTGATTTCATTCTATTTCATTATATGGTATTACATAATT
1 T---TC------TATTTCATTATATGGTATTACATAATT
1061 TTCTATGTTCATTATATGGTATTACATAATTT
1 TTCTAT-TTCATTATATGGTATTACATAA-TT
*
1093 CAATTCTATGTTCATTATATGATATTACATAATT
1 ---TTCTAT-TTCATTATATGGTATTACATAATT
*
1127 TT-GATTTCATT
1 TTCTATTTCATT
1138 CTATTTCATT
Statistics
Matches: 181, Mismatches: 11, Indels: 49
0.75 0.05 0.20
Matches are distributed among these distances:
29 6 0.03
30 65 0.36
31 26 0.14
32 2 0.01
33 3 0.02
34 3 0.02
35 28 0.15
36 3 0.02
37 1 0.01
38 1 0.01
39 17 0.09
40 15 0.08
41 1 0.01
42 1 0.01
43 3 0.02
45 1 0.01
46 3 0.02
48 2 0.01
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (30 bp):
TTCTATTTCATTATATGGTATTACATAATT
Found at i:973 original size:15 final size:15
Alignment explanation
Indices: 895--973 Score: 68
Period size: 15 Copynumber: 5.3 Consensus size: 15
885 GATTTCATTC
895 TATTTCATTATATGG
1 TATTTCATTATATGG
* * * **
910 TATTACATAATTTTC
1 TATTTCATTATATGG
925 TATTTCATTATATGG
1 TATTTCATTATATGG
* * * **
940 TATTACATAATTTTC
1 TATTTCATTATATGG
955 TATTTCATTATATGG
1 TATTTCATTATATGG
970 TATT
1 TATT
974 ATGTAATTTT
Statistics
Matches: 44, Mismatches: 20, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.54
Consensus pattern (15 bp):
TATTTCATTATATGG
Found at i:1002 original size:40 final size:39
Alignment explanation
Indices: 952--1150 Score: 237
Period size: 40 Copynumber: 5.4 Consensus size: 39
942 TTACATAATT
**
952 TTCTATTTCATTATATGGTATTATGTAATTTTGATTTCA
1 TTCTATTTCATTATATGGTATTACATAATTTTGATTTCA
991 TTCTATGTTCATTATATGGTATTACATAATTTTGATTTCA
1 TTCTAT-TTCATTATATGGTATTACATAATTTTGATTTCA
1031 TTCTATTTCATTATATGGTATTACAT-A-----A-TT--
1 TTCTATTTCATTATATGGTATTACATAATTTTGATTTCA
*
1061 TTCTATGTTCATTATATGGTATTACATAA-TTTCA----A
1 TTCTAT-TTCATTATATGGTATTACATAATTTTGATTTCA
*
1096 TTCTATGTTCATTATATGATATTACATAATTTTGATTTCA
1 TTCTAT-TTCATTATATGGTATTACATAATTTTGATTTCA
1136 TTCTATTTCATTATA
1 TTCTATTTCATTATA
Statistics
Matches: 143, Mismatches: 4, Indels: 26
0.83 0.02 0.15
Matches are distributed among these distances:
30 6 0.04
31 20 0.14
32 3 0.02
33 1 0.01
35 28 0.20
36 5 0.03
38 1 0.01
39 35 0.24
40 44 0.31
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (39 bp):
TTCTATTTCATTATATGGTATTACATAATTTTGATTTCA
Found at i:1003 original size:70 final size:69
Alignment explanation
Indices: 922--1150 Score: 241
Period size: 70 Copynumber: 3.2 Consensus size: 69
912 TTACATAATT
* *
922 TTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATATGGTATTATGTAATTTTGAT
1 TTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATATGATATTATATAATTTTGAT
987 TTCA
66 TTCA
* * * ** *
991 TTCTATGTTCATTATATGGTATTACATAATTTT-GATTTCATTCTAT-TTCATTATATGGTATTA
1 TTCTAT-TTCATTATATGGTATTACATAATTTTCTATTTCATTATATGAT-ATTATATAAT-TTT
*
1054 CATAATT--
63 GAT--TTCA
*
1061 TTCTATGTTCATTATATGGTATTACATAATTTCAATTCTATGTTCATTATATGATATTACATAAT
1 TTCTAT-TTCATTATATGGTATTACATAA-TT---TTCTAT-TTCATTATATGATATTATATAAT
1126 TTTGATTTCA
60 TTTGATTTCA
1136 TTCTATTTCATTATA
1 TTCTATTTCATTATA
Statistics
Matches: 130, Mismatches: 16, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
68 1 0.01
69 24 0.18
70 59 0.45
71 2 0.02
72 2 0.02
73 2 0.02
74 11 0.08
75 12 0.09
76 16 0.12
77 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (69 bp):
TTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATATGATATTATATAATTTTGAT
TTCA
Found at i:1073 original size:31 final size:31
Alignment explanation
Indices: 1031--1128 Score: 144
Period size: 35 Copynumber: 3.1 Consensus size: 31
1021 TTTGATTTCA
1031 TTCTAT-TTCATTATATGGTATTACATAATT
1 TTCTATGTTCATTATATGGTATTACATAATT
1061 TTCTATGTTCATTATATGGTATTACATAATTT
1 TTCTATGTTCATTATATGGTATTACATAA-TT
*
1093 CAATTCTATGTTCATTATATGATATTACATAATT
1 ---TTCTATGTTCATTATATGGTATTACATAATT
1127 TT
1 TT
1129 GATTTCATTC
Statistics
Matches: 62, Mismatches: 1, Indels: 9
0.86 0.01 0.12
Matches are distributed among these distances:
30 6 0.10
31 24 0.39
32 2 0.03
34 2 0.03
35 28 0.45
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (31 bp):
TTCTATGTTCATTATATGGTATTACATAATT
Found at i:1131 original size:105 final size:106
Alignment explanation
Indices: 922--1150 Score: 372
Period size: 105 Copynumber: 2.1 Consensus size: 106
912 TTACATAATT
** *
922 TTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATATGGTATTATGTAATTTTGAT
1 TTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATATGGTATTACATAATTTTCA-
*
987 TTCATTCTATGTTCATTATATGGTATTACATAATTTTGATTTCA
65 -T-ATTCTATGTTCATTATATGATATTACATAATTTTGATTTCA
1031 TTCTATTTCATTATATGGTATTACATAATTTTCTATGTTCATTATATGGTATTACATAA-TTTCA
1 TTCTATTTCATTATATGGTATTACATAATTTTCTAT-TTCATTATATGGTATTACATAATTTTCA
1095 -ATTCTATGTTCATTATATGATATTACATAATTTTGATTTCA
65 TATTCTATGTTCATTATATGATATTACATAATTTTGATTTCA
1136 TTCTATTTCATTATA
1 TTCTATTTCATTATA
Statistics
Matches: 115, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
105 55 0.48
109 40 0.35
110 20 0.17
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (106 bp):
TTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATATGGTATTACATAATTTTCAT
ATTCTATGTTCATTATATGATATTACATAATTTTGATTTCA
Done.