Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024754.1 Corchorus olitorius cultivar O-4 contig24787, 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: 21586
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:1431 original size:15 final size:16
Alignment explanation
Indices: 1411--1440 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1401 TTTTTATAAA
1411 AATTTGA-AAACAAAC
1 AATTTGAGAAACAAAC
1426 AATTTGAGAAACAAA
1 AATTTGAGAAACAAA
1441 ATGACCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.20
Consensus pattern (16 bp):
AATTTGAGAAACAAAC
Found at i:7825 original size:30 final size:30
Alignment explanation
Indices: 7762--7842 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
7752 GCTAAATACC
*
7762 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTTGGGA
*
7793 CAAAATAATCTCTTATGTTTT-TTTTCGGGA
1 CAAAATAATCCCTTATGTTTTCTTTT-GGGA
* *
7823 CAAATTAATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
7843 CAAAAATGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 4 0.09
30 21 0.48
31 19 0.43
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTTGGGA
Found at i:8000 original size:31 final size:31
Alignment explanation
Indices: 7965--8060 Score: 138
Period size: 31 Copynumber: 3.1 Consensus size: 31
7955 CAAGGACTGA
* *
7965 TTTGTCCCAAAAGAAAAACATACGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGACTTT
7996 TTTGTCCCAAAAGAAAAACATAAGGGACTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGACTTT
* * * *
8027 TTTGTCACAAAAGAAAAATATAAGAGAATTT
1 TTTGTCCCAAAAGAAAAACATAAGGGACTTT
8058 TTT
1 TTT
8061 TAGTATTTAG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGGACTTT
Found at i:8797 original size:125 final size:125
Alignment explanation
Indices: 8663--8900 Score: 311
Period size: 125 Copynumber: 1.9 Consensus size: 125
8653 CTTATTTTTC
* * **
8663 AAATATATTTTTTAAAT-ACCATT-TTTAAATTTTTACAATTTTACTCAATTAAAAACTCTATTT
1 AAATATATTTCTTAAATGA-CATTATTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTT
*
8726 TTATTTAATCAAA-TCTAATATATTTATAACTATTTTATTTTTACCATTTTACTATTTTAATT
65 TT-TTTAATCAAATTC-AATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
* * ** *
8788 AAATATATTTCTTAAATGACATTATTTAAACTTTTACAGTTTTATTTTACCAAAAATTCTATTTT
1 AAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTT
* * *
8853 TTTTAATTAAATTCAATATTTTTATAATTATTTTATCTTTACCATTTT
66 TTTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTT
8901 TTTTAGGGAA
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
125 60 0.62
126 37 0.38
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.53
Consensus pattern (125 bp):
AAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTT
TTTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
Found at i:8864 original size:20 final size:21
Alignment explanation
Indices: 8841--8882 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
8831 ATTTTACCAA
* *
8841 AAATTCTAT-TTTTTTTAATT
1 AAATTCAATATTTTTATAATT
8861 AAATTCAATATTTTTATAATT
1 AAATTCAATATTTTTATAATT
8882 A
1 A
8883 TTTTATCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATTCAATATTTTTATAATT
Found at i:9124 original size:32 final size:32
Alignment explanation
Indices: 9057--9151 Score: 151
Period size: 31 Copynumber: 3.1 Consensus size: 32
9047 ACTAAATACT
* *
9057 AAAAAAATCCCTAATGTTTTTCTTTTGAGAC-
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGACA
9088 AAAAAAATCCCTTATGTTTTTCTTTTGGGACA
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGACA
9120 AAAAAAATCCCTTATGTTTTT-TTTT-GGACA
1 AAAAAAATCCCTTATGTTTTTCTTTTGGGACA
9150 AA
1 AA
9152 TTAGTCCATT
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
30 7 0.11
31 33 0.54
32 21 0.34
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (32 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGGGACA
Found at i:10225 original size:2 final size:2
Alignment explanation
Indices: 10218--10256 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
10208 ATAATTACTC
* * *
10218 AT AT AT AT AT AT AT AT TT AT AT AT AT TT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10257 GGATTTATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.