Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020419.1 Corchorus olitorius cultivar O-4 contig20452, 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: 2465
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Found at i:1227 original size:2 final size:2
Alignment explanation
Indices: 1215--1255 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1205 CCTTTGTCAC
*
1215 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT 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
1256 GGGAATTTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1412 original size:43 final size:42
Alignment explanation
Indices: 1365--1694 Score: 391
Period size: 41 Copynumber: 7.8 Consensus size: 42
1355 ATAAGGAGAA
1365 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-AATAGAG
*
1408 ATGCC-CTTGTGTTATATATGTGTTTGGGGACTTTGATATA-A-
1 ATGCCTC-TGTGTTATATATGTGTTTGAGGACTTTGA-ATAGAG
* *
1449 ATGTCTTTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-AATAGAG
* * * * *
1492 TTGCCCCTATGTTATATATGTGTTTGGGGACTTTG-ATATAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAG
*
1533 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-AATAGAG
* * * *
1576 GTGCCCCTGTGTTATATATGTGTTTGGGGAC-TTGAATATAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAG
* * *
1617 GTGCTTCTGTGTTATATATGTGTTTGAGAACTTTTGGAATAGAG
1 ATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTT-GAATAGAG
* * *
1661 ATGCCCCTGTGTTATATATGTATTTGGGGACTTT
1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTT
1695 TGCTTATTGG
Statistics
Matches: 245, Mismatches: 31, Indels: 22
0.82 0.10 0.07
Matches are distributed among these distances:
41 103 0.42
42 8 0.03
43 102 0.42
44 32 0.13
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.43
Consensus pattern (42 bp):
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGAATAGAG
Found at i:1459 original size:41 final size:41
Alignment explanation
Indices: 1363--1694 Score: 332
Period size: 43 Copynumber: 7.9 Consensus size: 41
1353 CCATAAGGAG
*
1363 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-TAAT
1 AAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGAT-AT
* *
1404 AGAGATGCCCTTGTGTTATATATGTGTTTGGGGACTTTGATAT
1 A-A-ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGATAT
* **
1447 AAATGTCTTTGTGTTATATATGTGTTTGAGGACTTTG-TAAT
1 AAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGAT-AT
* * *
1488 AGAGTTGCCCCTATGTTATATATGTGTTTGGGGACTTTGATAT
1 A-A-ATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGATAT
* *
1531 AGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG-TAAT
1 AAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGAT-AT
*
1572 AAAGGTGCCCCTGTGTTATATATGTGTTTGGGGAC-TTGAATAT
1 AAA--TGCCCCTGTGTTATATATGTGTTTGAGGACTTTG-ATAT
** ** *
1615 AGGTGCTTCTGTGTTATATATGTGTTTGAGAACTTTTGGA-AT
1 AAATGCCCCTGTGTTATATATGTGTTTGAGGAC-TTT-GATAT
* *
1657 AGAGATGCCCCTGTGTTATATATGTATTTGGGGACTTT
1 A-A-ATGCCCCTGTGTTATATATGTGTTTGAGGACTTT
1695 TGCTTATTGG
Statistics
Matches: 241, Mismatches: 33, Indels: 32
0.79 0.11 0.10
Matches are distributed among these distances:
40 2 0.01
41 97 0.40
42 9 0.04
43 104 0.43
44 29 0.12
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.43
Consensus pattern (41 bp):
AAATGCCCCTGTGTTATATATGTGTTTGAGGACTTTGATAT
Found at i:1477 original size:84 final size:84
Alignment explanation
Indices: 1363--1694 Score: 513
Period size: 84 Copynumber: 3.9 Consensus size: 84
1353 CCATAAGGAG
*
1363 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCTTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
1428 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
* * * *
1447 AAATGTCTTTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCTATGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
1512 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
* * *
1531 AGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
1596 TGTTTGGGGAC-TTGAATAT
66 TGTTTGGGGACTTTG-ATAT
** * * *
1615 AGGTGCTTCTGTGTTATATATGTGTTTGAGAACTTTTGGAATAGAGATGCCCCTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGATGCCCCTGTGTTATATAT
*
1680 GTATTTGGGGACTTT
65 GTGTTTGGGGACTTT
1695 TGCTTATTGG
Statistics
Matches: 227, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
83 3 0.01
84 183 0.81
85 39 0.17
86 2 0.01
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.43
Consensus pattern (84 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATG
TGTTTGGGGACTTTGATAT
Done.