Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018114.1 Corchorus olitorius cultivar O-4 contig18147, 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, 888
Length: 1480
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Found at i:822 original size:16 final size:16
Alignment explanation
Indices: 789--823 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
779 ATAAAAAAAA
* *
789 AGATAAATAGGTATAG
1 AGATAAATAGATACAG
805 AGATAAATAGATACAG
1 AGATAAATAGATACAG
821 AGA
1 AGA
824 ATAATAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.20
Consensus pattern (16 bp):
AGATAAATAGATACAG
Found at i:892 original size:27 final size:27
Alignment explanation
Indices: 858--957 Score: 94
Period size: 27 Copynumber: 4.0 Consensus size: 27
848 AAAATAATAA
*
858 TAATAAATAAATAGAT-AATAGCTAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
885 TAATAAATAAAAAGATAAATAGT--A-
1 TAATAAATAAAAAGATAAATAGTAAAT
*
909 -AATAAAT----AGAT-AATATTTAAAT
1 TAATAAATAAAAAGATAAATA-GTAAAT
931 TAATAAATAAAAAGATAAATAGTAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
958 AAGTAGATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 22
0.70 0.04 0.26
Matches are distributed among these distances:
18 4 0.07
19 5 0.08
21 1 0.02
23 14 0.24
25 1 0.02
27 25 0.42
28 9 0.15
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (27 bp):
TAATAAATAAAAAGATAAATAGTAAAT
Found at i:984 original size:25 final size:25
Alignment explanation
Indices: 859--1055 Score: 120
Period size: 23 Copynumber: 8.4 Consensus size: 25
849 AAATAATAAT
*
859 AATAAATAAATAGATAATAGCT--A
1 AATAAATAAATAGATAATAGTTAAA
* *
882 AATTAATAAATA-A-AA-AGATAAA
1 AATAAATAAATAGATAATAGTTAAA
* *
904 TAGTAAATAAATAGATAATA-TTTAA
1 -AATAAATAAATAGATAATAGTTAAA
* *
929 ATT-AATAAATA-A-AA-AGATAAA
1 AATAAATAAATAGATAATAGTTAAA
* *
950 TAGTAAATAAGTAGATAATAGTTAAA
1 -AATAAATAAATAGATAATAGTTAAA
*
976 AATAAATAAAAAGATAA-A--T---
1 AATAAATAAATAGATAATAGTTAAA
* *
995 AGTAAATAAATAGATAATAGTTAAG
1 AATAAATAAATAGATAATAGTTAAA
*
1020 AATAAATAAATAGATAGATAGTAAATA
1 AATAAATAAATAGATA-ATAGTTAA-A
*
1047 AATAGATAA
1 AATAAATAA
1056 TAGTAAATAA
Statistics
Matches: 133, Mismatches: 21, Indels: 36
0.70 0.11 0.19
Matches are distributed among these distances:
19 15 0.11
20 5 0.04
21 7 0.05
22 7 0.05
23 36 0.27
24 5 0.04
25 36 0.27
26 14 0.11
27 8 0.06
ACGTcount: A:0.63, C:0.01, G:0.10, T:0.27
Consensus pattern (25 bp):
AATAAATAAATAGATAATAGTTAAA
Found at i:994 original size:12 final size:11
Alignment explanation
Indices: 886--1006 Score: 55
Period size: 11 Copynumber: 10.7 Consensus size: 11
876 TAGCTAAATT
886 AATAAATAAAA
1 AATAAATAAAA
**
897 AGATAAATAGTA
1 A-ATAAATAAAA
* *
909 AATAAATAGAT
1 AATAAATAAAA
** *
920 AATATTTAAATT
1 AATAAATAAA-A
932 AATAAATAAAA
1 AATAAATAAAA
**
943 AGATAAATAGTA
1 A-ATAAATAAAA
* * *
955 AATAAGTAGAT
1 AATAAATAAAA
* *
966 AAT-AGTTAAA
1 AATAAATAAAA
976 AATAAATAAAA
1 AATAAATAAAA
**
987 AGATAAATAGTA
1 A-ATAAATAAAA
999 AATAAATA
1 AATAAATA
1007 GATAATAGTT
Statistics
Matches: 83, Mismatches: 22, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
10 7 0.08
11 40 0.48
12 36 0.43
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.26
Consensus pattern (11 bp):
AATAAATAAAA
Found at i:995 original size:44 final size:44
Alignment explanation
Indices: 856--1074 Score: 312
Period size: 44 Copynumber: 4.9 Consensus size: 44
846 AAAAAATAAT
* *
856 AATAATAAATAAATAGATAATAGCTAAATTAATAAATAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAAA--AATAAATAAAAAGATA
*
902 AATAGTAAATAAATAGATAATATTTAAATTAATAAATAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAAA--AATAAATAAAAAGATA
*
948 AATAGTAAATAAGTAGATAATAGTTAAAAATAAATAAAAAGATA
1 AATAGTAAATAAATAGATAATAGTTAAAAATAAATAAAAAGATA
* *
992 AATAGTAAATAAATAGATAATAGTTAAGAATAAATAAATAGATA
1 AATAGTAAATAAATAGATAATAGTTAAAAATAAATAAAAAGATA
* * *
1036 GATAGTAAATAAATAGATAATAGTAAATAAATAGATAAA
1 AATAGTAAATAAATAGATAATAGTTAA-AAATAAATAAA
1075 TAGTTAAAAA
Statistics
Matches: 160, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
44 82 0.51
45 9 0.06
46 69 0.43
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (44 bp):
AATAGTAAATAAATAGATAATAGTTAAAAATAAATAAAAAGATA
Found at i:1029 original size:29 final size:28
Alignment explanation
Indices: 859--1098 Score: 78
Period size: 27 Copynumber: 8.5 Consensus size: 28
849 AAATAATAAT
* *
859 AATAAATAAATAGATAATAGCT-AAATT
1 AATAAATAAATAGATAATAGTTAAAATA
*
886 AATAAATAAAAAGATAAATAG-T-AAATA
1 AATAAATAAATAGAT-AATAGTTAAAATA
* **
913 AATAGAT-AATATTTAA-A-TTAATAAATA
1 AATAAATAAATAGATAATAGTT-A-AAATA
* * *
940 AA-AAGATAAATAGTAAATAAGTAGATAATAGTT
1 AATAA-ATAAATAG---ATAA-TAGTTAA-AATA
*
973 AA-AAATAAATA-A-AA-AGATAAATAGTA
1 AATAAATAAATAGATAATAGTTAAA-A-TA
999 AATAAAT----AGATAATAGTTAAGAATA
1 AATAAATAAATAGATAATAGTTAA-AATA
* * * *
1024 AATAAATAGATAGATAGTAAATAAATAGATA
1 AATAAATAAATAGATAAT-AGTTAA-A-ATA
*
1055 ATAGTAAATAAATAGATAAATAGTTAAAAAA
1 A-A-TAAATAAATAGAT-AATAGTTAAAATA
1086 AATAAATAAATAG
1 AATAAATAAATAG
1099 TGAATAAATA
Statistics
Matches: 159, Mismatches: 24, Indels: 58
0.66 0.10 0.24
Matches are distributed among these distances:
23 1 0.01
24 4 0.03
25 19 0.12
26 14 0.09
27 41 0.26
28 10 0.06
29 17 0.11
30 6 0.04
31 10 0.06
32 10 0.06
33 24 0.15
34 3 0.02
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (28 bp):
AATAAATAAATAGATAATAGTTAAAATA
Found at i:1107 original size:62 final size:63
Alignment explanation
Indices: 976--1109 Score: 193
Period size: 62 Copynumber: 2.1 Consensus size: 63
966 AATAGTTAAA
* *
976 AATAAATAAAAAGATAAATAGTAAATAAATAGATAATAGTTAAGAATAAATAAATAGATAGAT
1 AATAAATAAAAAGATAAATAGTAAATAAATAGATAATAGTTAAGAAAAAATAAATAAATAGAT
* *
1039 AGTAAATAAATAGAT-AATAGTAAATAAATAGATAAATAGTTAA-AAAAAATAAATAAATAG-T
1 AATAAATAAAAAGATAAATAGTAAATAAATAGAT-AATAGTTAAGAAAAAATAAATAAATAGAT
1100 GAATAAATAA
1 -AATAAATAA
1110 TAAAAAAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
61 1 0.02
62 41 0.64
63 22 0.34
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.25
Consensus pattern (63 bp):
AATAAATAAAAAGATAAATAGTAAATAAATAGATAATAGTTAAGAAAAAATAAATAAATAGAT
Found at i:1109 original size:4 final size:4
Alignment explanation
Indices: 859--1097 Score: 86
Period size: 4 Copynumber: 60.0 Consensus size: 4
849 AAATAATAAT
* ** *
859 AATA AATA AATA GAT- AATA GCTA AATT AATA AATA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
* * ** *
905 AGTA AATA AATA GAT- AATA TTTA AATT AATA AATA AA-A AGATA AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
* * * * *
951 AGTA AATA AGTA GATA ATAGTT AA-A AATA AATA AA-A AGATA AAT- AGTA
1 AATA AATA AATA AATA A-A-TA AATA AATA AATA AATA A-ATA AATA AATA
* * * * * *
999 AATA AATA GATA ATAGTT AA-G AATA AATA AATA GATA GAT- AGTA AATA
1 AATA AATA AATA A-A-TA AATA AATA AATA AATA AATA AATA AATA AATA
* * ** *
1047 AATA GATA ATAGTA AATA AATA GATA AATA GTTAA AAAA AATA AATA AATA
1 AATA AATA A-A-TA AATA AATA AATA AATA AAT-A AATA AATA AATA AATA
1098 GTGAATAAAT
Statistics
Matches: 167, Mismatches: 47, Indels: 42
0.65 0.18 0.16
Matches are distributed among these distances:
3 21 0.13
4 126 0.75
5 13 0.08
6 7 0.04
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:1113 original size:18 final size:19
Alignment explanation
Indices: 874--1113 Score: 183
Period size: 19 Copynumber: 12.5 Consensus size: 19
864 ATAAATAGAT
* *
874 AATAGCTAAATTAATAAATA
1 AATAGATAAA-TAGTAAATA
*
894 AAAAGATAAATAGTAAATA
1 AATAGATAAATAGTAAATA
* *
913 AATAGAT-AATATTTAAATT
1 AATAGATAAATA-GTAAATA
* *
932 AATAAATAAA-A--AGATA
1 AATAGATAAATAGTAAATA
*
948 AATAG-TAAATAAGTAGAT-
1 AATAGATAAAT-AGTAAATA
* *
966 AATAGTTAAA-AATAAATA
1 AATAGATAAATAGTAAATA
*
984 AAAAGATAAATAGTAAATA
1 AATAGATAAATAGTAAATA
1003 AATAGATAATAGTTAAGAATAAATA
1 AATAGATAA-A--T-AG--TAAATA
*
1028 AATAGATAGATAGTAAATA
1 AATAGATAAATAGTAAATA
1047 AATAGAT-AATAGTAAATA
1 AATAGATAAATAGTAAATA
*
1065 AATAGATAAATAGTTAAAAAA
1 AATAGATAAATAG-T-AAATA
* *
1086 AATAAATAAATAGTGAATA
1 AATAGATAAATAGTAAATA
1105 AATA-ATAAA
1 AATAGATAAA
1114 AAAAATCTTT
Statistics
Matches: 180, Mismatches: 22, Indels: 38
0.75 0.09 0.16
Matches are distributed among these distances:
15 4 0.02
16 7 0.04
17 6 0.03
18 39 0.22
19 74 0.41
20 13 0.07
21 18 0.10
22 2 0.01
23 2 0.01
24 1 0.01
25 14 0.08
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (19 bp):
AATAGATAAATAGTAAATA
Done.