Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020273.1 Corchorus olitorius cultivar O-4 contig20306, 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: 6697
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Found at i:1906 original size:21 final size:21
Alignment explanation
Indices: 1881--1963 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
1871 TATCTTAGAT
1881 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
1902 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
1923 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
1945 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
1964 TTACTAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:1914 original size:25 final size:25
Alignment explanation
Indices: 1883--1931 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1873 TCTTAGATAT
*
1883 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
1908 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
1932 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:2248 original size:26 final size:26
Alignment explanation
Indices: 2219--2274 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
2209 AAATTTAGTT
* *
2219 ACCTCACATTCTTAGAATTTTTACTA
1 ACCTCACATTCTTACAAATTTTACTA
** *
2245 ACCTTGCATTCTTACAAATTTTAGTA
1 ACCTCACATTCTTACAAATTTTACTA
2271 ACCT
1 ACCT
2275 TTCATCAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.41
Consensus pattern (26 bp):
ACCTCACATTCTTACAAATTTTACTA
Found at i:2275 original size:26 final size:26
Alignment explanation
Indices: 2225--2275 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2215 AGTTACCTCA
* *
2225 CATTCTTAGAATTTTTACTAACCTTG
1 CATTCTTACAAATTTTACTAACCTTG
*
2251 CATTCTTACAAATTTTAGTAACCTT
1 CATTCTTACAAATTTTACTAACCTT
2276 TCATCAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.45
Consensus pattern (26 bp):
CATTCTTACAAATTTTACTAACCTTG
Found at i:3362 original size:37 final size:38
Alignment explanation
Indices: 3297--3375 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 38
3287 TTTATATATT
* * *
3297 TGATCAACATACATGTTTTTTCATATAGACATAACTTTA
1 TGATCAACA-ACATGTCTTTCCAAATAGACATAACTTTA
3336 TGATCAAC-ACATGTCTTTCCAAATAGACATAACTTTA
1 TGATCAACAACATGTCTTTCCAAATAGACATAACTTTA
3373 TGA
1 TGA
3376 ATAATTATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 29 0.78
39 8 0.22
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.37
Consensus pattern (38 bp):
TGATCAACAACATGTCTTTCCAAATAGACATAACTTTA
Found at i:6592 original size:31 final size:31
Alignment explanation
Indices: 6555--6687 Score: 266
Period size: 31 Copynumber: 4.3 Consensus size: 31
6545 ATTATATATA
6555 GCGGCGTTTCCATTTGAAACGCCGCTAAGTG
1 GCGGCGTTTCCATTTGAAACGCCGCTAAGTG
6586 GCGGCGTTTCCATTTGAAACGCCGCTAAGTG
1 GCGGCGTTTCCATTTGAAACGCCGCTAAGTG
6617 GCGGCGTTTCCATTTGAAACGCCGCTAAGTG
1 GCGGCGTTTCCATTTGAAACGCCGCTAAGTG
6648 GCGGCGTTTCCATTTGAAACGCCGCTAAGTG
1 GCGGCGTTTCCATTTGAAACGCCGCTAAGTG
6679 GCGGCGTTT
1 GCGGCGTTT
6688 ATGCTCTAAA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 102 1.00
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.26
Consensus pattern (31 bp):
GCGGCGTTTCCATTTGAAACGCCGCTAAGTG
Done.