Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_698 ID=scaffold_698-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: 4521
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Found at i:283 original size:88 final size:88
Alignment explanation
Indices: 139--665 Score: 813
Period size: 88 Copynumber: 6.0 Consensus size: 88
129 TAAAACTGGT
* * * * * *
139 GTCTTTGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTATATTCAACCTACTCCACTG
1 GTCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
*
204 CTGCTCAGAGAGACAAGGCTG-G
66 CTGCTCAGGGAGACAAGGCTGAG
* * *
226 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAATATCTGCTATTTTCAACCTACTCCACT
1 -GTCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACT
*
291 ACCGCTCAGGGAGACAAGGCTGAG
65 ACTGCTCAGGGAGACAAGGCTGAG
* ** *
315 ATCTTCGATCTACTTTGCTGCCAATACAGTAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
1 GTCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
* *
380 CTACTCAGGGAGACAAGACTGAG
66 CTGCTCAGGGAGACAAGGCTGAG
* * *
403 GTCTTCGATCTACTTCGCTGCCAATACAGAAAGACAAGATCTGCTATTTTCAACTTACTCCACTA
1 GTCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
468 CTGCTCAGGGAGACAAGGCTGAG
66 CTGCTCAGGGAGACAAGGCTGAG
* * *
491 GTCTTTGATCTACTTCACTGCCAATACAAGAAGACAAGATCTACTATTTTCAACCTACTCCACTA
1 GTCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
556 CTGCTCAGGGAGACAAGGCTGAG
66 CTGCTCAGGGAGACAAGGCTGAG
* *
579 GTCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACATATTCCACTA
1 GTCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
644 CTGCTCAGGGAGACAAGGCTGA
66 CTGCTCAGGGAGACAAGGCTGA
666 AGTTTCACCG
Statistics
Matches: 404, Mismatches: 34, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
88 403 1.00
89 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (88 bp):
GTCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
CTGCTCAGGGAGACAAGGCTGAG
Found at i:658 original size:44 final size:43
Alignment explanation
Indices: 346--660 Score: 111
Period size: 44 Copynumber: 7.2 Consensus size: 43
336 CAATACAGTA
* *
346 AGACAAGATCTGCTATTTTCAACCTACTCCACTACTACTCAGGG
1 AGACAAGATCTGCTATTTTCAA-CTATTCCACTACTGCTCAGGG
*** * * * * *** **
390 AGACAAGA-CTGAGGTCTTCGATCTACTT-CGCTGCCAATACAGAA
1 AGACAAGATCTGCTATTTTC-AACTA-TTCCACTACTGCT-CAGGG
*
434 AGACAAGATCTGCTATTTTCAACTTACTCCACTACTGCTCAGGG
1 AGACAAGATCTGCTATTTTCAAC-TATTCCACTACTGCTCAGGG
* *** * * * *** * *
478 AGACAAG-GCTGAGGTCTTTGATCTACTT-CACTGCCAATACAAGA
1 AGACAAGATCTGCTAT-TTTCAACTA-TTCCACTACTGCT-CAGGG
* *
522 AGACAAGATCTACTATTTTCAACCTACTCCACTACTGCTCAGGG
1 AGACAAGATCTGCTATTTTCAA-CTATTCCACTACTGCTCAGGG
* *** * * * *** *
566 AGACAAG-GCTGAGGTCTTCGATCTACTT-CACTGCCAATACAGGA
1 AGACAAGATCTGCTATTTTC-AACTA-TTCCACTACTGCT-CAGGG
610 AGACAAGATCTGCTATTTTCAACATATTCCACTACTGCTCAGGG
1 AGACAAGATCTGCTATTTTCAAC-TATTCCACTACTGCTCAGGG
654 AGACAAG
1 AGACAAG
661 GCTGAAGTTT
Statistics
Matches: 177, Mismatches: 76, Indels: 36
0.61 0.26 0.12
Matches are distributed among these distances:
43 43 0.24
44 93 0.53
45 41 0.23
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (43 bp):
AGACAAGATCTGCTATTTTCAACTATTCCACTACTGCTCAGGG
Found at i:2428 original size:19 final size:20
Alignment explanation
Indices: 2386--2432 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
2376 TCTTTTCTTC
2386 TTTT-TTTTGTTTTGTTTGT
1 TTTTGTTTTGTTTTGTTTGT
2405 TTTTGTTTTG-TTT-TTTGTT
1 TTTTGTTTTGTTTTGTTTG-T
2424 TTTTGTTTT
1 TTTTGTTTT
2433 TATTTTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.15
19 17 0.65
20 5 0.19
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (20 bp):
TTTTGTTTTGTTTTGTTTGT
Found at i:2441 original size:15 final size:14
Alignment explanation
Indices: 2386--2433 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
2376 TCTTTTCTTC
2386 TTTTTTTTGTTTTG
1 TTTTTTTTGTTTTG
2400 TTTGTTTTTGTTTTG
1 TTT-TTTTTGTTTTG
2415 TTTTTTGTT-TTTTG
1 TTTTTT-TTGTTTTG
2429 TTTTT
1 TTTTT
2434 ATTTTTTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 16 0.50
15 16 0.50
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (14 bp):
TTTTTTTTGTTTTG
Done.