Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002242.1 Corchorus olitorius cultivar O-4 contig02242, 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, 668
Length: 1114
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.28
Found at i:686 original size:27 final size:26
Alignment explanation
Indices: 656--905 Score: 401
Period size: 27 Copynumber: 9.3 Consensus size: 26
646 TTAAAAAAAG
656 CGATGATACCAATACTCTTACTAATAC
1 CGATGATACCAATACT-TTACTAATAC
*
683 CGATGATACCAATACTTTATTAATAC
1 CGATGATACCAATACTTTACTAATAC
*
709 CGATGATACCGATACTTATACTAATAC
1 CGATGATACCAATACTT-TACTAATAC
*
736 CGATGATACCGATACTTATACTAATAC
1 CGATGATACCAATACTT-TACTAATAC
763 CGATGATACCAATACTTTACTAATAC
1 CGATGATACCAATACTTTACTAATAC
789 CGATGATACCAATACTTTTACTAATAC
1 CGATGATACCAATAC-TTTACTAATAC
816 CGATGATACCAATACTTTTACTAATAC
1 CGATGATACCAATAC-TTTACTAATAC
843 CGATGATACCAATACTCTTACTAATAC
1 CGATGATACCAATACT-TTACTAATAC
*
870 CGATGATACCAATACTTTTATTAATAC
1 CGATGATACCAATAC-TTTACTAATAC
897 CGATGATAC
1 CGATGATAC
906 TGATAATACC
Statistics
Matches: 214, Mismatches: 5, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
26 50 0.23
27 163 0.76
28 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (26 bp):
CGATGATACCAATACTTTACTAATAC
Found at i:774 original size:80 final size:79
Alignment explanation
Indices: 656--905 Score: 419
Period size: 80 Copynumber: 3.1 Consensus size: 79
646 TTAAAAAAAG
* *
656 CGATGATACCAATACTCTTACTAATACCGATGATACCAATACTTTATTAATACCGATGATACCGA
1 CGATGATACCAATACT-TTACTAATACCGATGATACCAATACTTTACTAATACCGATGATACCAA
*
721 TACTTATACTAATAC
65 TACTTTTACTAATAC
*
736 CGATGATACCGATACTTATACTAATACCGATGATACCAATACTTTACTAATACCGATGATACCAA
1 CGATGATACCAATACTT-TACTAATACCGATGATACCAATACTTTACTAATACCGATGATACCAA
801 TACTTTTACTAATAC
65 TACTTTTACTAATAC
816 CGATGATACCAATACTTTTACTAATACCGATGATACCAATACTCTTACTAATACCGATGATACCA
1 CGATGATACCAATAC-TTTACTAATACCGATGATACCAATACT-TTACTAATACCGATGATACCA
*
881 ATACTTTTATTAATAC
64 ATACTTTTACTAATAC
897 CGATGATAC
1 CGATGATAC
906 TGATAATACC
Statistics
Matches: 161, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
79 1 0.01
80 113 0.70
81 47 0.29
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (79 bp):
CGATGATACCAATACTTTACTAATACCGATGATACCAATACTTTACTAATACCGATGATACCAAT
ACTTTTACTAATAC
Found at i:831 original size:107 final size:106
Alignment explanation
Indices: 656--905 Score: 412
Period size: 107 Copynumber: 2.3 Consensus size: 106
646 TTAAAAAAAG
* *
656 CGATGATACCAATACTCTTACTAATACCGATGATACCAATACTTTATTAATACCGATGATACCGA
1 CGATGATACCAATACT-TTACTAATACCGATGATACCAATACTTTACTAATACCGATGATACCAA
*
721 TACTTATACTAATACCGATGATACCGATACT-TATACTAATAC
65 TACTTATACTAATACCGATGATACCAATACTCT-TACTAATAC
763 CGATGATACCAATACTTTACTAATACCGATGATACCAATACTTTTACTAATACCGATGATACCAA
1 CGATGATACCAATACTTTACTAATACCGATGATACCAATAC-TTTACTAATACCGATGATACCAA
*
828 TACTTTTACTAATACCGATGATACCAATACTCTTACTAATAC
65 TACTTATACTAATACCGATGATACCAATACTCTTACTAATAC
*
870 CGATGATACCAATACTTTTATTAATACCGATGATAC
1 CGATGATACCAATAC-TTTACTAATACCGATGATAC
906 TGATAATACC
Statistics
Matches: 135, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
106 25 0.19
107 90 0.67
108 20 0.15
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (106 bp):
CGATGATACCAATACTTTACTAATACCGATGATACCAATACTTTACTAATACCGATGATACCAAT
ACTTATACTAATACCGATGATACCAATACTCTTACTAATAC
Found at i:932 original size:21 final size:21
Alignment explanation
Indices: 906--954 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
896 CCGATGATAC
*
906 TGATAATACCAATAATCCTAA
1 TGATAATACCAAGAATCCTAA
927 TGATAATACCAAGAATCCTAA
1 TGATAATACCAAGAATCCTAA
*
948 AGATAAT
1 TGATAAT
955 GATGATGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.27
Consensus pattern (21 bp):
TGATAATACCAAGAATCCTAA
Found at i:954 original size:27 final size:27
Alignment explanation
Indices: 924--986 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
914 CCAATAATCC
924 TAATGATAAT-ACCAAGAATCCTAAAGA
1 TAATGATAATGA-CAAGAATCCTAAAGA
* *
951 TAATGATGATGACAAGAATCCTAATGA
1 TAATGATAATGACAAGAATCCTAAAGA
978 TAATGATAA
1 TAATGATAA
987 ACTAGAGGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.25
Consensus pattern (27 bp):
TAATGATAATGACAAGAATCCTAAAGA
Done.