Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01004723.1 Corchorus olitorius cultivar O-4 contig04739, 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, 723
Length: 1205
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:968 original size:29 final size:29
Alignment explanation
Indices: 935--1068 Score: 187
Period size: 29 Copynumber: 4.3 Consensus size: 29
925 ACATATAAAA
935 ATATAAAAATATAATGAAATCAAAATGAC
1 ATATAAAAATATAATGAAATCAAAATGAC
964 ATATAAAAATATAATGAAATCAAAATGAC
1 ATATAAAAATATAATGAAATCAAAATGAC
993 ATATAAAAAATATAAAAATATAATGAAATCAAAATGAC
1 ---------ATATAAAAATATAATGAAATCAAAATGAC
1031 ATATAAAAATATAATGAAATCAAAATGAC
1 ATATAAAAATATAATGAAATCAAAATGAC
1060 ATATAAAAA
1 ATATAAAAA
1069 ATGACATATA
Statistics
Matches: 96, Mismatches: 0, Indels: 18
0.84 0.00 0.16
Matches are distributed among these distances:
29 67 0.70
38 29 0.30
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (29 bp):
ATATAAAAATATAATGAAATCAAAATGAC
Found at i:997 original size:21 final size:21
Alignment explanation
Indices: 972--1036 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
962 ACATATAAAA
972 ATATAATGAAATCAAAATGAC
1 ATATAATGAAATCAAAATGAC
*
993 ATATAA-AAAAT-ATAAA--A-
1 ATATAATGAAATCA-AAATGAC
1010 ATATAATGAAATCAAAATGAC
1 ATATAATGAAATCAAAATGAC
1031 ATATAA
1 ATATAA
1037 AAATATAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
17 6 0.17
18 8 0.22
19 2 0.06
20 8 0.22
21 12 0.33
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (21 bp):
ATATAATGAAATCAAAATGAC
Found at i:1014 original size:38 final size:37
Alignment explanation
Indices: 964--1044 Score: 153
Period size: 38 Copynumber: 2.2 Consensus size: 37
954 TCAAAATGAC
964 ATATAAAAATATAATGAAATCAAAATGACATATAAAAA
1 ATATAAAAATATAATGAAATCAAAATGACATAT-AAAA
1002 ATATAAAAATATAATGAAATCAAAATGACATATAAAA
1 ATATAAAAATATAATGAAATCAAAATGACATATAAAA
1039 ATATAA
1 ATATAA
1045 TGAAATCAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 10 0.23
38 33 0.77
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (37 bp):
ATATAAAAATATAATGAAATCAAAATGACATATAAAA
Found at i:1024 original size:67 final size:67
Alignment explanation
Indices: 917--1070 Score: 301
Period size: 67 Copynumber: 2.3 Consensus size: 67
907 CAGAGTCAAT
917 TCAAAATGACATAT-AAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGA
1 TCAAAATGACATATAAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGA
981 AA
66 AA
983 TCAAAATGACATATAAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGA
1 TCAAAATGACATATAAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGA
1048 AA
66 AA
1050 TCAAAATGACATATAAAAAAT
1 TCAAAATGACATATAAAAAAT
1071 GACATATAAT
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
66 14 0.16
67 73 0.84
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (67 bp):
TCAAAATGACATATAAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGA
AA
Found at i:1071 original size:14 final size:14
Alignment explanation
Indices: 1023--1079 Score: 57
Period size: 14 Copynumber: 4.0 Consensus size: 14
1013 TAATGAAATC
1023 AAAATGACATATAA
1 AAAATGACATATAA
1037 AAATAT-A-ATGA-AA
1 AAA-ATGACAT-ATAA
1050 TCAAAATGACATATAA
1 --AAAATGACATATAA
1066 AAAATGACATATAA
1 AAAATGACATATAA
1080 TTAAANATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
13 4 0.11
14 21 0.58
15 7 0.19
16 4 0.11
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (14 bp):
AAAATGACATATAA
Done.