Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023400.1 Corchorus olitorius cultivar O-4 contig23433, 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: 2996
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Found at i:9 original size:4 final size:4
Alignment explanation
Indices: 1--37 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
38 TGCTTAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:846 original size:33 final size:33
Alignment explanation
Indices: 809--871 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
799 GCCACGCGCG
809 GGTCGCGACC-GAGCCATGGTCAGGTCGCGATTC
1 GGTCGCGACCGGA-CCATGGTCAGGTCGCGATTC
*
842 GGTCGGGACCGGACCATGGTCAGGTCGCGA
1 GGTCGCGACCGGACCATGGTCAGGTCGCGA
872 CCCGCCTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.16, C:0.29, G:0.40, T:0.16
Consensus pattern (33 bp):
GGTCGCGACCGGACCATGGTCAGGTCGCGATTC
Found at i:1326 original size:19 final size:19
Alignment explanation
Indices: 1302--1341 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1292 TTTGATATTT
*
1302 AAACTCTCAAAACTTCTTC
1 AAACTCTCAAAACTACTTC
**
1321 AAACTCTTTAAACTACTTC
1 AAACTCTCAAAACTACTTC
1340 AA
1 AA
1342 GAACATCATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.33
Consensus pattern (19 bp):
AAACTCTCAAAACTACTTC
Found at i:1672 original size:14 final size:14
Alignment explanation
Indices: 1640--1777 Score: 63
Period size: 14 Copynumber: 10.0 Consensus size: 14
1630 ATTTAATTAA
*
1640 AATTAATTATTCTT
1 AATTAATTATTATT
1654 AATTAATTATTAATT
1 AATTAATTATT-ATT
*
1669 -ATTAATTTTTATTT
1 AATTAATTATTA-TT
*
1683 AGTT-ATT-TTATT
1 AATTAATTATTATT
* * * *
1695 ATTTGACTATAATT
1 AATTAATTATTATT
* *
1709 AATTATTTACTA-T
1 AATTAATTATTATT
*
1722 AATTATTTATTATTGT
1 AATTAATTATTA-T-T
*
1738 AATTAATTATAATT
1 AATTAATTATTATT
* * * *
1752 -TTTATTTACTA-G
1 AATTAATTATTATT
1764 AATTAATTATTATT
1 AATTAATTATTATT
1778 TTTTATTTAG
Statistics
Matches: 90, Mismatches: 24, Indels: 20
0.67 0.18 0.15
Matches are distributed among these distances:
12 5 0.06
13 33 0.37
14 36 0.40
15 5 0.06
16 11 0.12
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (14 bp):
AATTAATTATTATT
Found at i:1680 original size:17 final size:18
Alignment explanation
Indices: 1652--1757 Score: 67
Period size: 18 Copynumber: 5.7 Consensus size: 18
1642 TTAATTATTC
*
1652 TTAATTAATTATTAATTA
1 TTAATTATTTATTAATTA
*
1670 TTAATT-TTTATTTAGTTA
1 TTAATTATTTA-TTAATTA
* * *
1688 TTTTATTATTTGACT-ATAA
1 -TTAATTATTT-ATTAATTA
1707 TTAATTATTTACTATAATTA
1 TTAATTATTTA-T-TAATTA
*
1727 TTTATTATTGTAATTAATTA
1 TTAATTATT-T-ATTAATTA
1747 -TAATT-TTTATT
1 TTAATTATTTATT
1758 TACTAGAATT
Statistics
Matches: 68, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
16 3 0.04
17 5 0.07
18 23 0.34
19 12 0.18
20 21 0.31
21 3 0.04
22 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (18 bp):
TTAATTATTTATTAATTA
Found at i:1750 original size:26 final size:25
Alignment explanation
Indices: 1719--1780 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
1709 AATTATTTAC
*
1719 TATAATTATTTATTA-TTGTAATTAAT
1 TATAATT-TTTATTACTAG-AATTAAT
1745 TATAATTTTTATTTACTAGAATTAAT
1 TATAATTTTTA-TTACTAGAATTAAT
*
1771 TATTATTTTT
1 TATAATTTTT
1781 TATTTAGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 4 0.12
26 26 0.81
27 2 0.06
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (25 bp):
TATAATTTTTATTACTAGAATTAAT
Done.