Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002200.1 Corchorus olitorius cultivar O-4 contig02200, 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, 650
Length: 1084
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Found at i:804 original size:17 final size:17
Alignment explanation
Indices: 782--880 Score: 58
Period size: 16 Copynumber: 5.6 Consensus size: 17
772 CCAAACAGGA
782 TAAAACCCAACAAGAAT
1 TAAAACCCAACAAGAAT
*
799 TAAAACCCATCATAAAAAGAA-
1 TAAAA-CC--C--AACAAGAAT
* *
820 TAAGACCCAACAACAAT
1 TAAAACCCAACAAGAAT
* * *
837 TGAAACCCAACATGAAAG
1 TAAAACCCAACAAG-AAT
* *
855 TAAAGCCCAAC-AGAAA
1 TAAAACCCAACAAGAAT
871 TAAAACCCAA
1 TAAAACCCAA
881 AATAAAGAGT
Statistics
Matches: 61, Mismatches: 14, Indels: 15
0.68 0.16 0.17
Matches are distributed among these distances:
16 17 0.28
17 16 0.26
18 14 0.23
20 3 0.05
21 4 0.07
22 7 0.11
ACGTcount: A:0.57, C:0.24, G:0.08, T:0.11
Consensus pattern (17 bp):
TAAAACCCAACAAGAAT
Found at i:829 original size:38 final size:38
Alignment explanation
Indices: 781--925 Score: 117
Period size: 38 Copynumber: 4.0 Consensus size: 38
771 ACCAAACAGG
*
781 ATAAAACCCAACAAGAATTAAAACCCATCATAAAAAGA
1 ATAAGACCCAACAAGAATTAAAACCCATCATAAAAAGA
* * * * *
819 ATAAGACCCAACAACAATTGAAACCCAACAT-GAAAGT
1 ATAAGACCCAACAAGAATTAAAACCCATCATAAAAAGA
*
856 A-AAG-CCCAAC-AGAAATAAAACCCA--A-AATAAAGA
1 ATAAGACCCAACAAGAATTAAAACCCATCATAA-AAAGA
* * * *
889 GTAAGGCCCAACAAAAATT-GAACCCATCATATAAAAG
1 ATAAGACCCAACAAGAATTAAAACCCATCATA-AAAAG
926 TAAAGTCTAA
Statistics
Matches: 83, Mismatches: 15, Indels: 18
0.72 0.13 0.16
Matches are distributed among these distances:
32 1 0.01
33 4 0.05
34 14 0.17
35 18 0.22
36 7 0.08
37 6 0.07
38 32 0.39
39 1 0.01
ACGTcount: A:0.56, C:0.22, G:0.10, T:0.12
Consensus pattern (38 bp):
ATAAGACCCAACAAGAATTAAAACCCATCATAAAAAGA
Found at i:865 original size:18 final size:18
Alignment explanation
Indices: 842--901 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 18
832 ACAATTGAAA
842 CCCAACATGAAAGTAAAG
1 CCCAACATGAAAGTAAAG
*
860 CCCAACA-GAAA-TAAAA
1 CCCAACATGAAAGTAAAG
* * *
876 CCCAAAATAAAGAGTAAGG
1 CCCAACATGAA-AGTAAAG
895 CCCAACA
1 CCCAACA
902 AAAATTGAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
16 10 0.30
17 6 0.18
18 8 0.24
19 9 0.27
ACGTcount: A:0.53, C:0.25, G:0.13, T:0.08
Consensus pattern (18 bp):
CCCAACATGAAAGTAAAG
Found at i:892 original size:35 final size:34
Alignment explanation
Indices: 782--930 Score: 100
Period size: 35 Copynumber: 4.1 Consensus size: 34
772 CCAAACAGGA
* * **
782 TAAAACCCAACAAGAATTAAAACCCATCATAAAAAG
1 TAAAGCCCAACAA-AAATAAAACCCAAAAT-AAAAG
* * * * *
818 AATAAGACCCAACAACAATTGAAACCCAACATGAAAG
1 TA-AAG-CCCAACAA-AAATAAAACCCAAAATAAAAG
*
855 TAAAGCCCAACAGAAATAAAACCCAAAATAAAGAG
1 TAAAGCCCAACAAAAATAAAACCCAAAATAAA-AG
* ** *
890 TAAGGCCCAACAAAAATTGAACCCATCATATAAAAG
1 TAAAGCCCAACAAAAATAAAACCCA--AAATAAAAG
926 TAAAG
1 TAAAG
931 TCTAATAAGA
Statistics
Matches: 90, Mismatches: 18, Indels: 10
0.76 0.15 0.08
Matches are distributed among these distances:
34 15 0.17
35 30 0.33
36 10 0.11
37 13 0.14
38 22 0.24
ACGTcount: A:0.56, C:0.21, G:0.10, T:0.13
Consensus pattern (34 bp):
TAAAGCCCAACAAAAATAAAACCCAAAATAAAAG
Found at i:1060 original size:2 final size:2
Alignment explanation
Indices: 1053--1084 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1043 AAACGTAATC
1053 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.