Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017277.1 Corchorus olitorius cultivar O-4 contig17310, 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, 1000
Length: 3169
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Found at i:926 original size:8 final size:8
Alignment explanation
Indices: 915--1017 Score: 78
Period size: 8 Copynumber: 13.6 Consensus size: 8
905 AAAAAAAAGT
915 AATAGATA
1 AATAGATA
*
923 AATAAATA
1 AATAGATA
*
931 AATAAATA
1 AATAGATA
*
939 AATAAATA
1 AATAGATA
*
947 AATAGAAA
1 AATAGATA
955 AATA-AGTA
1 AATAGA-TA
963 AA-A-AT-
1 AATAGATA
968 AATAGATA
1 AATAGATA
976 AATA-A-A
1 AATAGATA
982 AA-AGATA
1 AATAGATA
*
989 AATAGGTA
1 AATAGATA
*
997 TATAGAT-
1 AATAGATA
1004 AATAAGATA
1 AAT-AGATA
1013 AATAG
1 AATAG
1018 TTAGGTAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
5 3 0.04
6 6 0.08
7 11 0.14
8 55 0.71
9 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (8 bp):
AATAGATA
Found at i:927 original size:4 final size:4
Alignment explanation
Indices: 915--992 Score: 77
Period size: 4 Copynumber: 19.0 Consensus size: 4
905 AAAAAAAAGT
* *
915 AATA GATA AATA AATA AATA AATA AATA AATA AATA GAA-A AATA AGTA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA -AATA AATA AATA
* * *
963 AAAA TAATA GATA AATA AAAA AGATA AATA
1 AATA -AATA AATA AATA AATA A-ATA AATA
993 GGTATATAGA
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
3 2 0.03
4 50 0.83
5 8 0.13
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:930 original size:12 final size:12
Alignment explanation
Indices: 920--1103 Score: 86
Period size: 12 Copynumber: 16.0 Consensus size: 12
910 AAAGTAATAG
*
920 ATAAATAAATAA
1 ATAAATAGATAA
*
932 ATAAATAAATAA
1 ATAAATAGATAA
*
944 ATAAATAGAAAA
1 ATAAATAGATAA
*
956 ATAAGTA-A-AA
1 ATAAATAGATAA
966 AT-AATAGATAA
1 ATAAATAGATAA
*
977 ATAAAAAAGATAA
1 AT-AAATAGATAA
** * *
990 ATAGGTATATAG
1 ATAAATAGATAA
1002 AT-AATAAGATAA
1 ATAAAT-AGATAA
** *
1014 ATAGTTAGGTAA
1 ATAAATAGATAA
* *
1026 A-AAAAAG-TAG
1 ATAAATAGATAA
1036 AT-AATAG-TAA
1 ATAAATAGATAA
1046 ATAAATAGAT-A
1 ATAAATAGATAA
** * *
1057 ATAGCTAAATTA
1 ATAAATAGATAA
1069 ATAAATA-A-AA
1 ATAAATAGATAA
1079 GCATAAATAG-TAA
1 --ATAAATAGATAA
1092 ATAAATAGATAA
1 ATAAATAGATAA
1104 TAGTTAAATT
Statistics
Matches: 128, Mismatches: 29, Indels: 30
0.68 0.16 0.16
Matches are distributed among these distances:
9 3 0.02
10 17 0.13
11 31 0.24
12 64 0.50
13 13 0.10
ACGTcount: A:0.64, C:0.01, G:0.10, T:0.24
Consensus pattern (12 bp):
ATAAATAGATAA
Found at i:1071 original size:19 final size:19
Alignment explanation
Indices: 1033--1087 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
1023 TAAAAAAAAG
1033 TAGATAATAG-TAAATAAA
1 TAGATAATAGCTAAATAAA
*
1051 TAGATAATAGCTAAATTAA
1 TAGATAATAGCTAAATAAA
* *
1070 TAAATAAAAGCATAAATA
1 TAGATAATAGC-TAAATA
1088 GTAAATAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 10 0.32
19 16 0.52
20 5 0.16
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (19 bp):
TAGATAATAGCTAAATAAA
Found at i:1084 original size:27 final size:27
Alignment explanation
Indices: 925--1140 Score: 99
Period size: 27 Copynumber: 8.0 Consensus size: 27
915 AATAGATAAA
*
925 TAAATAAATAAATAAATAAATAAATAG
1 TAAATAAATAAATAAATAGATAAATAG
* * *
952 AAAAATAAGTAAAAATAATAGATAAATA-
1 -TAAATAAATAAATA-AATAGATAAATAG
** * * *
980 -AAA-AAGATAAATAGGTATATAGATAA
1 TAAATAA-ATAAATAAATAGATAAATAG
** ** * *
1006 TAAGATAAATAGTTAGGTA-AAAAAAAG
1 TAA-ATAAATAAATAAATAGATAAATAG
*
1033 TAGATAATAGTAAATAAATAGAT-AATAG
1 TAAATAA-A-TAAATAAATAGATAAATAG
*
1061 CTAAATTAATAAATAAA-AGCATAAATAG
1 -TAAATAAATAAATAAATAG-ATAAATAG
* * *
1089 TAAATAAATAGAT-AATAGTTAAATTAC
1 TAAATAAATAAATAAATAGATAAA-TAG
1116 TAAATAAA-AATATAAATAG-TAAATA
1 TAAATAAATAA-ATAAATAGATAAATA
1141 AAAAAAAAAT
Statistics
Matches: 142, Mismatches: 30, Indels: 34
0.69 0.15 0.17
Matches are distributed among these distances:
25 10 0.07
26 23 0.16
27 48 0.34
28 42 0.30
29 19 0.13
ACGTcount: A:0.63, C:0.01, G:0.10, T:0.26
Consensus pattern (27 bp):
TAAATAAATAAATAAATAGATAAATAG
Found at i:1089 original size:46 final size:46
Alignment explanation
Indices: 1038--1142 Score: 174
Period size: 46 Copynumber: 2.3 Consensus size: 46
1028 AAAAGTAGAT
*
1038 AATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAAGCATA
1 AATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAAACATA
* * *
1084 AATAGTAAATAAATAGATAATAGTTAAATTACTAAATAAAAATATA
1 AATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAAACATA
1130 AATAGTAAATAAA
1 AATAGTAAATAAA
1143 AAAAAAATCT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.28
Consensus pattern (46 bp):
AATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAAACATA
Found at i:2450 original size:34 final size:35
Alignment explanation
Indices: 2349--2489 Score: 176
Period size: 34 Copynumber: 4.0 Consensus size: 35
2339 TTTTCTTTTG
*
2349 AAGATCAACTCTGATCATCGAAAACTTCTTAAAAAT
1 AAGATCAACTCTGATCATCGAAAACTTCTT-GAAAT
**
2385 AAGATCAACTCTGATCATAAAAAAAACTTCTTGAAAT
1 AAGATCAACTCTGATCAT--CGAAAACTTCTTGAAAT
* * *
2422 AAAATCAACTCTGTTCATC-AAAACTTCTTGAAAC
1 AAGATCAACTCTGATCATCGAAAACTTCTTGAAAT
* *
2456 GAGATCACCTCTGATCATCGAAAACTTCTTGAAA
1 AAGATCAACTCTGATCATCGAAAACTTCTTGAAA
2490 GGTGTAGACA
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
34 29 0.32
35 14 0.15
36 18 0.20
37 20 0.22
38 10 0.11
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (35 bp):
AAGATCAACTCTGATCATCGAAAACTTCTTGAAAT
Done.