Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024833.1 Corchorus olitorius cultivar O-4 contig24866, 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: 5721
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Found at i:2890 original size:276 final size:272
Alignment explanation
Indices: 2397--2917 Score: 846
Period size: 276 Copynumber: 1.9 Consensus size: 272
2387 TATTTAATGT
* * *
2397 TCAAAACTATTCCCTAAGGAGACACATGTCGACCCTTTAACCATAACCCTGCATGTGCAGTCTGC
1 TCAAAACTATTCCCTAAGGAGACACATGTCAACCCTTTAACCATAACCATGCATATGCAGTCTGC
* * *
2462 TAAACTTCACTAATGGTGGATAAGATAATTTTCCTTAAAAAATATATACTAAAAAGACACATGTC
66 TAAACTTCACTAACGGTGGATAAAATAATTTTCCTTAAAAAATATACACTAAAAAGACACATGTC
* *
2527 AATCCTTTAACCCCGTTTGTACAATCTAATAGTAAACTACACTAATAGTGGATGTGATAATTTTA
131 AAACCTTTAACCCCGTTTATACAATCTAATAGTAAACTACACTAATAGTGGATGTGATAATTTTA
* *
2592 CTTTTTGTAATAACCATAAACACTTTTAGGTTTAATTTAAGTAACATTATTATGGCTTTTTACTT
196 CTTTTCGTAATAACCATAAACACTTTTAAG--T--TTTAAGTAACATTATTATGGCTTTTTACTT
2657 AATTAATGTTCAAAAA
257 AATTAATGTTCAAAAA
* **
2673 TCAAAACTATTCCCTAAGG-GTATACATGTCAACCCTTTAACTGTAACCATGCATATGCAGTCTG
1 TCAAAACTATTCCCTAAGGAG-ACACATGTCAACCCTTTAACCATAACCATGCATATGCAGTCTG
*
2737 CTAAACTTCACTAACGGTGGATAAAATATTTTTCCTTAAAAAATATACACTAAAAAGACACATGT
65 CTAAACTTCACTAACGGTGGATAAAATAATTTTCCTTAAAAAATATACACTAAAAAGACACATGT
* *
2802 CAAACTTTTAACCCCGTTTATACAATCTAATAGTAAACTACACTGATAGTGGATGTGATAATTTT
130 CAAACCTTTAACCCCGTTTATACAATCTAATAGTAAACTACACTAATAGTGGATGTGATAATTTT
2867 ACTTTTCGTAATAACCATAAACACTTTTAAGTTTTAAGTAACATTATTATG
195 ACTTTTCGTAATAACCATAAACACTTTTAAGTTTTAAGTAACATTATTATG
2918 ACAAAACTTT
Statistics
Matches: 228, Mismatches: 16, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
272 19 0.08
274 1 0.00
275 1 0.00
276 207 0.91
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (272 bp):
TCAAAACTATTCCCTAAGGAGACACATGTCAACCCTTTAACCATAACCATGCATATGCAGTCTGC
TAAACTTCACTAACGGTGGATAAAATAATTTTCCTTAAAAAATATACACTAAAAAGACACATGTC
AAACCTTTAACCCCGTTTATACAATCTAATAGTAAACTACACTAATAGTGGATGTGATAATTTTA
CTTTTCGTAATAACCATAAACACTTTTAAGTTTTAAGTAACATTATTATGGCTTTTTACTTAATT
AATGTTCAAAAA
Found at i:5225 original size:108 final size:108
Alignment explanation
Indices: 5012--5228 Score: 407
Period size: 108 Copynumber: 2.0 Consensus size: 108
5002 ATTATTTTAG
5012 ACTTTTTTAATATGGAAATAAAATCTGACTGGATAGATTACATATTAACCTTTAAAAATATAATT
1 ACTTTTTTAATATGGAAATAAAATCTGACTGGATAGATTACATATTAACCTTTAAAAATATAATT
5077 AAAATTTTAAAATTTAAAAGGGTATTTTAGATATTTCAGGTCA
66 AAAATTTTAAAATTTAAAAGGGTATTTTAGATATTTCAGGTCA
**
5120 ACTTTTTTAATATGGAAATAAAATCTGGTTGGATAGATTACATATTAACCTTTAAAAATATAATT
1 ACTTTTTTAATATGGAAATAAAATCTGACTGGATAGATTACATATTAACCTTTAAAAATATAATT
*
5185 AAAATTTTAAAATTTAATAGGGTATTTTAGATATTTCAGGTCA
66 AAAATTTTAAAATTTAAAAGGGTATTTTAGATATTTCAGGTCA
5228 A
1 A
5229 GGTTTTTGAA
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 106 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.40
Consensus pattern (108 bp):
ACTTTTTTAATATGGAAATAAAATCTGACTGGATAGATTACATATTAACCTTTAAAAATATAATT
AAAATTTTAAAATTTAAAAGGGTATTTTAGATATTTCAGGTCA
Found at i:5697 original size:2 final size:2
Alignment explanation
Indices: 5690--5721 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5680 AAAAACCATG
5690 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.