Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1069 ID=scaffold_1069-JGI_221_v2.0
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: 3718
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.09
Warning! 2586 characters in sequence are not A, C, G, or T
Found at i:3462 original size:51 final size:51
Alignment explanation
Indices: 3386--3570 Score: 214
Period size: 51 Copynumber: 3.6 Consensus size: 51
3376 AGCTTTTCGG
**
3386 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTATTTATCGA
1 TACACATAGTAGCCTTCACACAGTACTACACATGTGACCATTATTTATCGA
* * * *
3437 TACACGTAGTAGCCTTCACACAGTACTACACACGTG-CTCA-AAGCTTT-TCGG
1 TACACATAGTAGCCTTCACACAGTACTACACATGTGAC-CATTA--TTTATCGA
* ** **
3488 TACACATAGTACCCTTCACTTAGTACTACACATGAAACCATTATTTATCGA
1 TACACATAGTAGCCTTCACACAGTACTACACATGTGACCATTATTTATCGA
*
3539 TACACGTAGTAGCCTTCACACAGTACTACACA
1 TACACATAGTAGCCTTCACACAGTACTACACA
3571 CGTGTTCATC
Statistics
Matches: 109, Mismatches: 19, Indels: 12
0.78 0.14 0.09
Matches are distributed among these distances:
50 5 0.05
51 99 0.91
52 5 0.05
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.29
Consensus pattern (51 bp):
TACACATAGTAGCCTTCACACAGTACTACACATGTGACCATTATTTATCGA
Found at i:3543 original size:102 final size:102
Alignment explanation
Indices: 3367--3574 Score: 389
Period size: 102 Copynumber: 2.0 Consensus size: 102
3357 NNNNNNNNNN
* **
3367 CGTGCTCAAAGCTTTTCGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTATTT
1 CGTGCTCAAAGCTTTTCGGTACACATAGTACCCTTCACTTAGTACTACACATGAAACCATTATTT
3432 ATCGATACACGTAGTAGCCTTCACACAGTACTACACA
66 ATCGATACACGTAGTAGCCTTCACACAGTACTACACA
3469 CGTGCTCAAAGCTTTTCGGTACACATAGTACCCTTCACTTAGTACTACACATGAAACCATTATTT
1 CGTGCTCAAAGCTTTTCGGTACACATAGTACCCTTCACTTAGTACTACACATGAAACCATTATTT
3534 ATCGATACACGTAGTAGCCTTCACACAGTACTACACA
66 ATCGATACACGTAGTAGCCTTCACACAGTACTACACA
3571 CGTG
1 CGTG
3575 TTCATCGACA
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 103 1.00
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (102 bp):
CGTGCTCAAAGCTTTTCGGTACACATAGTACCCTTCACTTAGTACTACACATGAAACCATTATTT
ATCGATACACGTAGTAGCCTTCACACAGTACTACACA
Done.