Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023040.1 Corchorus olitorius cultivar O-4 contig23073, 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: 3726
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Found at i:649 original size:14 final size:13
Alignment explanation
Indices: 616--645 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
606 GATAAATAGG
616 AAAATAAGTTAAA
1 AAAATAAGTTAAA
*
629 AAAATAATTTAAA
1 AAAATAAGTTAAA
642 AAAA
1 AAAA
646 ATAAATAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
AAAATAAGTTAAA
Found at i:725 original size:15 final size:15
Alignment explanation
Indices: 714--900 Score: 116
Period size: 15 Copynumber: 12.5 Consensus size: 15
704 AATAATAATA
*
714 AATAAATAAATAGAT
1 AATAAATAAATAAAT
* *
729 AATAACTAAATTAAT
1 AATAAATAAATAAAT
744 AAATAAA-AAGATAAAT
1 -AATAAATAA-ATAAAT
* *
760 AGTAAATAAATAGAT
1 AATAAATAAATAAAT
*
775 AAT-AATTAA-AAAT
1 AATAAATAAATAAAT
*
788 AAATAAAT-AGTAAAT
1 -AATAAATAAATAAAT
* *
803 AGTAAATAAATAGAT
1 AATAAATAAATAAAT
* * *
818 AAT-AGT-TACAAAT
1 AATAAATAAATAAAT
*
831 AAATAAATAGATAAAT
1 -AATAAATAAATAAAT
** *
847 GGTAAATAAATAGAT
1 AATAAATAAATAAAT
*
862 AATAAAAAAATAAAT
1 AATAAATAAATAAAT
* *
877 AGTAAATAAATAGAT
1 AATAAATAAATAAAT
892 AAATAAATA
1 -AATAAATA
901 GTGAATAAAT
Statistics
Matches: 127, Mismatches: 34, Indels: 21
0.70 0.19 0.12
Matches are distributed among these distances:
13 7 0.06
14 20 0.16
15 76 0.60
16 24 0.19
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.26
Consensus pattern (15 bp):
AATAAATAAATAAAT
Found at i:732 original size:11 final size:11
Alignment explanation
Indices: 703--918 Score: 136
Period size: 11 Copynumber: 20.1 Consensus size: 11
693 GGTAGCTAAG
703 AAATA-ATAAT
1 AAATAGATAAT
713 AAAT--A-AAT
1 AAATAGATAAT
721 AAATAGATAAT
1 AAATAGATAAT
* *
732 AACTAAATTAAT
1 AAATAGA-TAAT
* *
744 AAATAAAAAGAT
1 AAATAGATA-AT
756 AAATAG-TAAAT
1 AAATAGAT-AAT
767 AAATAGATAAT
1 AAATAGATAAT
* *
778 AATTA-AAAAT
1 AAATAGATAAT
* *
788 AAATAAATAGT
1 AAATAGATAAT
799 AAATAG-TAAAT
1 AAATAGAT-AAT
810 AAATAGATAAT
1 AAATAGATAAT
** *
821 AGTTACA-AAT
1 AAATAGATAAT
*
831 AAATAAATAGAT
1 AAATAGATA-AT
*
843 AAAT-GGTAAAT
1 AAATAGAT-AAT
854 AAATAGATAAT
1 AAATAGATAAT
865 AAA-A-A-AAT
1 AAATAGATAAT
873 AAATAG-TAAAT
1 AAATAGAT-AAT
884 AAATAGATAAAT
1 AAATAGAT-AAT
896 AAATAG-TGAAT
1 AAATAGAT-AAT
907 AAATAGATAAT
1 AAATAGATAAT
918 A
1 A
919 GTTAAAAATG
Statistics
Matches: 163, Mismatches: 23, Indels: 39
0.72 0.10 0.17
Matches are distributed among these distances:
8 13 0.08
9 3 0.02
10 22 0.13
11 84 0.52
12 41 0.25
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.26
Consensus pattern (11 bp):
AAATAGATAAT
Found at i:732 original size:19 final size:19
Alignment explanation
Indices: 703--911 Score: 127
Period size: 19 Copynumber: 11.1 Consensus size: 19
693 GGTAGCTAAG
703 AAATA-ATAATAAATAAAT
1 AAATAGATAATAAATAAAT
*
721 AAATAGATAATAACTAAAT
1 AAATAGATAATAAATAAAT
*
740 TAAT--A-AATAAA-AAGAT
1 AAATAGATAATAAATAA-AT
*
756 AAATAG-TAAATAAATAGAT
1 AAATAGAT-AATAAATAAAT
775 -AATA-ATTAA-AAATAAAT
1 AAATAGA-TAATAAATAAAT
*
792 AAATAG-TAA-ATAGTAAAT
1 AAATAGATAATA-AATAAAT
* *
810 AAATAGATAATAGTTACAAAT
1 AAATAGATAATA--AATAAAT
*
831 AAATAAATAGATAAATGGTAAAT
1 AAATAGATA-ATAAA---TAAAT
*
854 AAATAGATAATAAAAAAAT
1 AAATAGATAATAAATAAAT
*
873 AAATAG-TAAATAAATAGAT
1 AAATAGAT-AATAAATAAAT
* * *
892 AAATAAATAGTGAATAAAT
1 AAATAGATAATAAATAAAT
911 A
1 A
912 GATAATAGTT
Statistics
Matches: 149, Mismatches: 21, Indels: 41
0.71 0.10 0.19
Matches are distributed among these distances:
15 2 0.01
16 10 0.07
17 12 0.08
18 28 0.19
19 60 0.40
20 4 0.03
21 13 0.09
22 8 0.05
23 12 0.08
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.26
Consensus pattern (19 bp):
AAATAGATAATAAATAAAT
Found at i:867 original size:30 final size:31
Alignment explanation
Indices: 703--901 Score: 158
Period size: 31 Copynumber: 6.7 Consensus size: 31
693 GGTAGCTAAG
* * *
703 AAAT-AATA-ATAAATAAATAAATAGATAAT
1 AAATAAATAGATAAATAAATAGATAAATAGT
* *
732 AACTAAATTA-ATAAATAAAAAGATAAATAGT
1 AAATAAA-TAGATAAATAAATAGATAAATAGT
763 AAATAAATAGATAATAATTAAA-A-ATAAATA--
1 AAATAAATAGAT-A-AA-TAAATAGATAAATAGT
793 AATAGTAAATAG-TAAATAAATAGAT-AATAGT
1 AA-A-TAAATAGATAAATAAATAGATAAATAGT
* *
824 ---TACA-A-ATAAATAAATAGATAAATGGT
1 AAATAAATAGATAAATAAATAGATAAATAGT
* *
850 AAATAAATAGAT-AATAAAAAAATAAATAGT
1 AAATAAATAGATAAATAAATAGATAAATAGT
880 AAATAAATAGATAAATAAATAG
1 AAATAAATAGATAAATAAATAG
902 TGAATAAATA
Statistics
Matches: 136, Mismatches: 14, Indels: 38
0.72 0.07 0.20
Matches are distributed among these distances:
25 14 0.10
26 8 0.06
28 4 0.03
29 13 0.10
30 37 0.27
31 38 0.28
32 15 0.11
33 3 0.02
34 4 0.03
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.26
Consensus pattern (31 bp):
AAATAAATAGATAAATAAATAGATAAATAGT
Found at i:911 original size:4 final size:4
Alignment explanation
Indices: 710--900 Score: 109
Period size: 4 Copynumber: 50.0 Consensus size: 4
700 AAGAAATAAT
* * *
710 AATA AATA AATA AATA GAT- AATA ACTA AATT AATA AATA AA-A AGATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A-ATA
* * * *
757 AAT- AGTA AATA AATA GAT- AAT- AATT AA-A AATA AATA AAT- AGTA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
* * * * *
800 AAT- AGTA AATA AATA GAT- AATA GTTACA AATA AATA AATA GATA AAT-
1 AATA AATA AATA AATA AATA AATA --AATA AATA AATA AATA AATA AATA
** * * * *
847 GGTA AATA AATA GAT- AATA AAAA AATA AAT- AGTA AATA AATA GATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
893 AATA AATA
1 AATA AATA
901 GTGAATAAAT
Statistics
Matches: 138, Mismatches: 35, Indels: 28
0.69 0.17 0.14
Matches are distributed among these distances:
3 24 0.17
4 110 0.80
5 2 0.01
6 2 0.01
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:916 original size:19 final size:19
Alignment explanation
Indices: 743--920 Score: 116
Period size: 18 Copynumber: 10.1 Consensus size: 19
733 ACTAAATTAA
*
743 TAAATAAAAAGATAAATAG
1 TAAATAAATAGATAAATAG
*
762 TAAATAAATAGAT-AATAA
1 TAAATAAATAGATAAATAG
* *
780 TTAA-AAATAAATAAATAG
1 TAAATAAATAGATAAATAG
* *
798 TAAAT-AGTAAATAAATAG
1 TAAATAAATAGATAAATAG
*
816 ---AT-AATAGTTACAA-A-
1 TAAATAAATAGATA-AATAG
*
830 TAAATAAATAGATAAATGG
1 TAAATAAATAGATAAATAG
*
849 TAAATAAATAGAT-AATAAA
1 TAAATAAATAGATAAAT-AG
*
868 AAAATAAATAG-T-AA-A-
1 TAAATAAATAGATAAATAG
* *
883 TAAATAGATAAATAAATAG
1 TAAATAAATAGATAAATAG
*
902 TGAATAAATAGAT-AATAG
1 TAAATAAATAGATAAATAG
920 T
1 T
921 TAAAAATGTA
Statistics
Matches: 124, Mismatches: 21, Indels: 29
0.71 0.12 0.17
Matches are distributed among these distances:
15 16 0.13
16 4 0.03
17 13 0.10
18 46 0.37
19 45 0.36
ACGTcount: A:0.63, C:0.01, G:0.10, T:0.26
Consensus pattern (19 bp):
TAAATAAATAGATAAATAG
Found at i:980 original size:15 final size:15
Alignment explanation
Indices: 703--982 Score: 95
Period size: 15 Copynumber: 18.4 Consensus size: 15
693 GGTAGCTAAG
*
703 AAAT-AATAATAAAT
1 AAATAAATAGTAAAT
717 AAATAAATAG-ATAAT
1 AAATAAATAGTA-AAT
* *
732 AACTAAATTAATAAAT
1 AAATAAA-TAGTAAAT
748 AAAAAGATAAATAGTAAAT
1 ---AA-ATAAATAGTAAAT
* *
767 AAATAGATAAT-AAT
1 AAATAAATAGTAAAT
* *
781 TAA-AAATAAATAAAT
1 AAATAAAT-AGTAAAT
*
796 -AGTAAATAGTAAAT
1 AAATAAATAGTAAAT
* *
810 AAATAGATAATAGT-TAC
1 AAAT--A-AATAGTAAAT
827 AAAT-AA-A-TAAAT
1 AAATAAATAGTAAAT
* *
839 AGATAAATGGTAAAT
1 AAATAAATAGTAAAT
* * *
854 AAATAGATAATAAAA
1 AAATAAATAGTAAAT
869 AAATAAATAGTAAAT
1 AAATAAATAGTAAAT
* *
884 AAATAGATAAATAAAT
1 AAATAAAT-AGTAAAT
900 AGTGAATAAATAGATAATAGT
1 A---AATAAATAG-TAA-A-T
* *
921 TAA-AAAT-GTAAAAA
1 AAATAAATAGT-AAAT
935 AAATAAA-A-TAAAAT
1 AAATAAATAGT-AAAT
* *
949 AAA-AAA-AGGAAAA
1 AAATAAATAGTAAAT
962 AAATAAATAGTAAAT
1 AAATAAATAGTAAAT
977 AAATAA
1 AAATAA
983 TAAAAAAAAT
Statistics
Matches: 196, Mismatches: 38, Indels: 63
0.66 0.13 0.21
Matches are distributed among these distances:
11 1 0.01
12 5 0.03
13 17 0.09
14 33 0.17
15 79 0.40
16 17 0.09
17 11 0.06
18 9 0.05
19 18 0.09
20 5 0.03
21 1 0.01
ACGTcount: A:0.67, C:0.01, G:0.08, T:0.25
Consensus pattern (15 bp):
AAATAAATAGTAAAT
Found at i:988 original size:27 final size:27
Alignment explanation
Indices: 880--992 Score: 76
Period size: 27 Copynumber: 4.1 Consensus size: 27
870 AATAAATAGT
*
880 AAATAAATAGATAAATAAATAGTGAATAAA
1 AAATAAATAG-TAAATAAATAAT-AA-AAA
* * *
910 TAGAT-AATAGTTAA-AAAT-GTAAAAA
1 -AAATAAATAGTAAATAAATAATAAAAA
*
935 AAATAAA-A-TAAAATAAA-AAAAGGAAAA
1 AAATAAATAGT-AAATAAATAATA--AAAA
962 AAATAAATAGTAAATAAATAATAAAAA
1 AAATAAATAGTAAATAAATAATAAAAA
989 AAAT
1 AAAT
993 CTTTTTGGTC
Statistics
Matches: 66, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
23 1 0.02
24 6 0.09
25 9 0.14
26 2 0.03
27 21 0.32
28 12 0.18
29 7 0.11
30 5 0.08
31 3 0.05
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (27 bp):
AAATAAATAGTAAATAAATAATAAAAA
Done.