Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01003058.1 Corchorus olitorius cultivar O-4 contig03063, 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, 634
Length: 1058
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Found at i:902 original size:14 final size:14
Alignment explanation
Indices: 883--943 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
873 TTATATTTAA
883 TTATATGTCTATTT
1 TTATATGTCTATTT
897 TTATATGTCTATTT
1 TTATATGTCTATTT
* * *
911 TGATTTCATTTATTATTT
1 T--TAT-ATGT-CTATTT
929 TTATATGTCTATTT
1 TTATATGTCTATTT
943 T
1 T
944 GTATTTCATT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
14 21 0.57
15 3 0.08
16 4 0.11
17 3 0.08
18 6 0.16
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (14 bp):
TTATATGTCTATTT
Found at i:931 original size:32 final size:33
Alignment explanation
Indices: 892--963 Score: 137
Period size: 32 Copynumber: 2.2 Consensus size: 33
882 ATTATATGTC
892 TATTTTTATATGTCTATTTTG-ATTTCATTTAT
1 TATTTTTATATGTCTATTTTGTATTTCATTTAT
924 TATTTTTATATGTCTATTTTGTATTTCATTTAT
1 TATTTTTATATGTCTATTTTGTATTTCATTTAT
957 TATTTTT
1 TATTTTT
964 TATTATTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
32 21 0.54
33 18 0.46
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.68
Consensus pattern (33 bp):
TATTTTTATATGTCTATTTTGTATTTCATTTAT
Found at i:962 original size:19 final size:19
Alignment explanation
Indices: 906--967 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 19
896 TTTATATGTC
906 TATTTTG-ATTTCATTTAT
1 TATTTTGTATTTCATTTAT
* *
924 TATTTT-TA--T-ATGT-C
1 TATTTTGTATTTCATTTAT
938 TATTTTGTATTTCATTTAT
1 TATTTTGTATTTCATTTAT
*
957 TATTTTTTATT
1 TATTTTGTATT
968 ATTTTTTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 11
0.67 0.10 0.22
Matches are distributed among these distances:
14 6 0.18
15 5 0.15
16 1 0.03
17 1 0.03
18 10 0.30
19 10 0.30
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (19 bp):
TATTTTGTATTTCATTTAT
Found at i:967 original size:10 final size:10
Alignment explanation
Indices: 952--1058 Score: 75
Period size: 10 Copynumber: 11.2 Consensus size: 10
942 TTGTATTTCA
952 TTTATTATTT
1 TTTATTATTT
962 TTTATTATTT
1 TTTATTATTT
*
972 TTTATTATTG
1 TTTATTATTT
*
982 TCTA-T-TTT
1 TTTATTATTT
* *
990 TGTATT-TCTA
1 TTTATTAT-TT
1000 TTTATTATTT
1 TTTATTATTT
1010 TTTA-TA-TT
1 TTTATTATTT
* *
1018 GTT-CTATTT
1 TTTATTATTT
* *
1027 TGTATT-TCTA
1 TTTATTAT-TT
1037 TTTATTATTT
1 TTTATTATTT
1047 TTTATTATTT
1 TTTATTATTT
1057 TT
1 TT
Statistics
Matches: 75, Mismatches: 14, Indels: 16
0.71 0.13 0.15
Matches are distributed among these distances:
8 11 0.15
9 9 0.12
10 53 0.71
11 2 0.03
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.74
Consensus pattern (10 bp):
TTTATTATTT
Found at i:1004 original size:38 final size:38
Alignment explanation
Indices: 962--1055 Score: 165
Period size: 37 Copynumber: 2.5 Consensus size: 38
952 TTTATTATTT
962 TTTATTATTTTTTATTATTG-TCTATTTTTGTATTTCTA
1 TTTATTATTTTTTATTATTGTTCTA-TTTTGTATTTCTA
1000 TTTATTATTTTTTA-TATTGTTCTATTTTGTATTTCTA
1 TTTATTATTTTTTATTATTGTTCTATTTTGTATTTCTA
1037 TTTATTATTTTTTATTATT
1 TTTATTATTTTTTATTATT
1056 TTT
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
37 32 0.59
38 22 0.41
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (38 bp):
TTTATTATTTTTTATTATTGTTCTATTTTGTATTTCTA
Found at i:1011 original size:47 final size:46
Alignment explanation
Indices: 853--1058 Score: 156
Period size: 46 Copynumber: 4.6 Consensus size: 46
843 AAAAAAAGAA
** * * *
853 TATTTCTATTT-TTCCTTTAATTATATTTAATTATATGTCTATTTT-
1 TATTTCTATTTATTATTTTTATTATTTTTTATTAT-TGTCTATTTTG
*
898 TATATGTCTATTTTGATT-TCATTTATTA-TTTTTA-TA-TGTCTATTTTG
1 TAT-T-TCTA-TTT-ATTAT-TTTTATTATTTTTTATTATTGTCTATTTTG
945 TATTTC-ATTTATTATTTTTTATTATTTTTTATTATTGTCTATTTTTG
1 TATTTCTATTTATTA-TTTTTATTATTTTTTATTATTGTCTA-TTTTG
*
992 TATTTCTATTTATTA-TTTT-TTA-----TATT-GT-TCTATTTTG
1 TATTTCTATTTATTATTTTTATTATTTTTTATTATTGTCTATTTTG
1029 TATTTCTATTTATTATTTTTTATTATTTTT
1 TATTTCTATTTATTA-TTTTTATTATTTTT
Statistics
Matches: 132, Mismatches: 7, Indels: 44
0.72 0.04 0.24
Matches are distributed among these distances:
37 20 0.15
38 4 0.03
39 5 0.04
40 7 0.05
42 3 0.02
43 10 0.08
44 8 0.06
45 10 0.08
46 22 0.17
47 18 0.14
48 13 0.10
49 4 0.03
50 8 0.06
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (46 bp):
TATTTCTATTTATTATTTTTATTATTTTTTATTATTGTCTATTTTG
Found at i:1014 original size:7 final size:7
Alignment explanation
Indices: 951--1057 Score: 58
Period size: 7 Copynumber: 15.0 Consensus size: 7
941 TTTGTATTTC
*
951 ATTTATT
1 ATTTTTT
958 ATTTTTT
1 ATTTTTT
*
965 ATTATTT
1 ATTTTTT
*
972 -TTTATT
1 ATTTTTT
* *
978 ATTGTCT
1 ATTTTTT
985 ATTTTTGT
1 ATTTTT-T
*
993 A-TTTCT
1 ATTTTTT
*
999 ATTTATT
1 ATTTTTT
1006 ATTTTTT
1 ATTTTTT
1013 ATATTGTTCT
1 AT-TT-TT-T
*
1023 ATTTTGT
1 ATTTTTT
*
1030 A-TTTCT
1 ATTTTTT
*
1036 ATTTATT
1 ATTTTTT
1043 ATTTTTT
1 ATTTTTT
1050 ATTATTTT
1 ATT-TTTT
1058 T
Statistics
Matches: 74, Mismatches: 18, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
6 11 0.15
7 47 0.64
8 9 0.12
9 4 0.05
10 3 0.04
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.73
Consensus pattern (7 bp):
ATTTTTT
Done.