Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007414.1 Corchorus olitorius cultivar O-4 contig07439, 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, 868
Length: 1447
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Found at i:966 original size:20 final size:20
Alignment explanation
Indices: 933--977 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
923 GTTTCATTTT
933 ATTTAGACTTATAATGTATC
1 ATTTAGACTTATAATGTATC
953 ATTTA-ACTTAATAATGTATC
1 ATTTAGACTT-ATAATGTATC
973 ATTTA
1 ATTTA
978 TATAATCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.47
Consensus pattern (20 bp):
ATTTAGACTTATAATGTATC
Found at i:1049 original size:2 final size:2
Alignment explanation
Indices: 1044--1154 Score: 51
Period size: 2 Copynumber: 60.0 Consensus size: 2
1034 TAAATAATAC
* * *
1044 AT AT AT AA AT -T AT AT AT AC AT AT AT AA AT -T AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
1083 AT AA AT AG AA AT -T AT AT -T AA AT -T AT AT A- AT AT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1120 AT AT AA AT CT AT TT AT A- AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1155 GAATTGAATC
Statistics
Matches: 78, Mismatches: 22, Indels: 18
0.66 0.19 0.15
Matches are distributed among these distances:
1 9 0.12
2 69 0.88
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1064 original size:19 final size:18
Alignment explanation
Indices: 1044--1154 Score: 84
Period size: 19 Copynumber: 5.9 Consensus size: 18
1034 TAAATAATAC
1044 ATATATAAATTATATATA
1 ATATATAAATTATATATA
1062 CATATATAAATTATATAATA
1 -ATATATAAATTATAT-ATA
*
1082 TATAAATAGAAATTATAT-TA
1 -AT--ATATAAATTATATATA
* * *
1102 A-AT-TATATAATATAAA
1 ATATATAAATTATATATA
*
1118 ATATATAAATCTATTTATA
1 ATATATAAAT-TATATATA
*
1137 ATATATATAAATATATAT
1 ATATATA-AATTATATAT
1155 GAATTGAATC
Statistics
Matches: 72, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
15 7 0.10
16 4 0.06
17 2 0.03
18 4 0.06
19 34 0.47
20 9 0.12
22 12 0.17
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (18 bp):
ATATATAAATTATATATA
Found at i:1081 original size:39 final size:37
Alignment explanation
Indices: 1037--1153 Score: 98
Period size: 37 Copynumber: 3.1 Consensus size: 37
1027 AAAAATGTAA
1037 ATAATACATATATAAATTATATATACATATATAAATTAT
1 ATAATA-ATATATAAATTATATATA-ATATATAAATTAT
* * *
1076 ATAATATATAAATAGAAATTATAT-TAA-AT-TATATAAT
1 ATAATA-AT--ATATAAATTATATATAATATATAAATTAT
* *
1113 ATAA-AATATATAAATCTATTTATAATATATATAAATAT
1 ATAATAATATATAAAT-TATATATAATATATA-AATTAT
1151 ATA
1 ATA
1154 TGAATTGAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
33 7 0.11
34 4 0.06
35 5 0.08
36 3 0.05
37 12 0.19
38 8 0.13
39 9 0.15
40 2 0.03
41 12 0.19
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (37 bp):
ATAATAATATATAAATTATATATAATATATAAATTAT
Found at i:1097 original size:41 final size:39
Alignment explanation
Indices: 1050--1127 Score: 104
Period size: 39 Copynumber: 1.9 Consensus size: 39
1040 ATACATATAT
* *
1050 AAATTATATATACA-TATATAAATTATATAATATATAAATAG
1 AAATTATAT-TAAATTATAT-AA-TATAAAATATATAAATAG
1091 AAATTATATTAAATTATATAATATAAAATATATAAAT
1 AAATTATATTAAATTATATAATATAAAATATATAAAT
1128 CTATTTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 15 0.44
40 5 0.15
41 14 0.41
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (39 bp):
AAATTATATTAAATTATATAATATAAAATATATAAATAG
Found at i:1109 original size:32 final size:34
Alignment explanation
Indices: 1063--1153 Score: 107
Period size: 32 Copynumber: 2.6 Consensus size: 34
1053 TTATATATAC
1063 ATATATAAATTATATAATATATAA-ATAGAAAT-T
1 ATAT-TAAATTATATAATATATAATATAGAAATCT
* *
1096 ATATTAAATTATATAATATAAAATATATAAATCT
1 ATATTAAATTATATAATATATAATATAGAAATCT
1130 AT-TTATAATATATATAAATATATA
1 ATATTA-AAT-TATAT-AATATATA
1154 TGAATTGAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
32 18 0.36
33 14 0.28
34 6 0.12
35 5 0.10
36 7 0.14
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (34 bp):
ATATTAAATTATATAATATATAATATAGAAATCT
Done.