Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023503.1 Corchorus olitorius cultivar O-4 contig23536, 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: 6886
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:678 original size:24 final size:24
Alignment explanation
Indices: 651--699 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
641 ATGTATTTTG
651 TTATTATCTTAATGACAATTTCTC
1 TTATTATCTTAATGACAATTTCTC
675 TTATTATCTTAATGACAATTTCTC
1 TTATTATCTTAATGACAATTTCTC
699 T
1 T
700 CTGTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (24 bp):
TTATTATCTTAATGACAATTTCTC
Found at i:965 original size:21 final size:21
Alignment explanation
Indices: 941--980 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
931 TTAACTTCCG
941 TCTAAAATATCT-GCTACGGTC
1 TCTAAAATAT-TAGCTACGGTC
*
962 TCTAGAATATTAGCTACGG
1 TCTAAAATATTAGCTACGG
981 GTTTGGTCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (21 bp):
TCTAAAATATTAGCTACGGTC
Found at i:2558 original size:29 final size:30
Alignment explanation
Indices: 2503--2578 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 30
2493 GATTTTGGTT
* * *
2503 AAGTGCGGGTTGTGCACTTGTGTTTG-TTC
1 AAGTGTGGGTTGTGCACTTGCGATTGTTTC
*
2532 AAGTGTGGGTTGTGCACTTGCGATTGTTTT
1 AAGTGTGGGTTGTGCACTTGCGATTGTTTC
*
2562 GAGTGTGGGTT-TGCACT
1 AAGTGTGGGTTGTGCACT
2579 CGTTCAAAGC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 29 0.71
30 12 0.29
ACGTcount: A:0.12, C:0.12, G:0.36, T:0.41
Consensus pattern (30 bp):
AAGTGTGGGTTGTGCACTTGCGATTGTTTC
Found at i:4497 original size:2 final size:2
Alignment explanation
Indices: 4485--4526 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
4475 CCTTTGTCAC
*
4485 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
4526 A
1 A
4527 GGAATTTGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4758 original size:43 final size:42
Alignment explanation
Indices: 4618--4946 Score: 418
Period size: 43 Copynumber: 7.8 Consensus size: 42
4608 TAAGGAGAAA
4618 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAG
1 TGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAG
* *
4661 ATGCCTCTGTGTTATATATGTGTTTGGGGACTTTG-ATATA-AA
1 -TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAG
4703 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
1 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* * * *
4745 TTACCCCAGTGTTATATATGTGTTTGGGGACTTTG-ATATAGA-
1 -TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAG
* *
4787 TGCCTCTGTGTTATATATGTATTTGAGGACTTTGTAGTAGAG
1 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
* * *
4829 TTGCCCCTATGTTATATATGTGTTTGGGGACTTTG-ATATAGA-
1 -TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAG
*
4871 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGG
1 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGA-G
* *
4914 TGCCCCTGTGTTATATATGTGTTTGGGGACTTT
1 TGCCTCTGTGTTATATATGTGTTTGAGGACTTT
4947 TTGGCTATTG
Statistics
Matches: 248, Mismatches: 25, Indels: 25
0.83 0.08 0.08
Matches are distributed among these distances:
41 104 0.42
42 8 0.03
43 107 0.43
44 29 0.12
ACGTcount: A:0.21, C:0.11, G:0.25, T:0.43
Consensus pattern (42 bp):
TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAG
Found at i:4776 original size:84 final size:84
Alignment explanation
Indices: 4615--4946 Score: 540
Period size: 84 Copynumber: 3.9 Consensus size: 84
4605 CCATAAGGAG
* * *
4615 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGATGCCTCTGTGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGTTGCCCCAGTGTTATATAT
4680 GTGTTTGGGGACTTTGATAT
65 GTGTTTGGGGACTTTGATAT
*
4700 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTACCCCAGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCAGTGTTATATATG
4765 TGTTTGGGGACTTTGATAT
66 TGTTTGGGGACTTTGATAT
* * *
4784 AGATGCCTCTGTGTTATATATGTATTTGAGGACTTTGTAGTAGAGTTGCCCCTA-TGTTATATAT
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCC-AGTGTTATATAT
4848 GTGTTTGGGGACTTTGATAT
65 GTGTTTGGGGACTTTGATAT
* * * *
4868 AGATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAGGTGCCCCTGTGTTATATATG
1 AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCAGTGTTATATATG
4933 TGTTTGGGGACTTT
66 TGTTTGGGGACTTT
4947 TTGGCTATTG
Statistics
Matches: 232, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
84 198 0.85
85 34 0.15
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (84 bp):
AAATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGTTGCCCCAGTGTTATATATG
TGTTTGGGGACTTTGATAT
Done.