Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_295 ID=scaffold_295-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: 8603
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:2698 original size:132 final size:132
Alignment explanation
Indices: 2503--3013 Score: 873
Period size: 132 Copynumber: 3.9 Consensus size: 132
2493 GTAACTTCAA
* * * *
2503 GGAGATAAGAA-TACTGGCTTCAGTATACTCCACTGTAACCTCAGGGAGGTAAAATCTGTCATCT
1 GGAGAT-AGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCT
* * *
2567 TCGATCTACTCCACTACTG-TCTAGGGAGATAAAATTTGTAATCTTCAATCTATTCCACTGTTGC
65 TTGATCTGCTCCACTACTGCT-TAGGGAGATAAAATCTGTAATCTTCAATCTATTCCACTGTTGC
*
2631 ACAG
129 CCAG
2635 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
*
2700 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCC
66 TGATCTGCTCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCAATCTATTCCACTGTTGCCC
2765 AG
131 AG
*
2767 GGAGATAGAATTACTGACTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
2832 TGATCTGCTCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCAATCTATTCCACTGTTGCCC
66 TGATCTGCTCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCAATCTATTCCACTGTTGCCC
*
2897 TG
131 AG
*
2899 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTT
1 GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
*
2964 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCT
66 TGATCTGCTCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCAATCT
3014 GTTTCGCTGT
Statistics
Matches: 362, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
131 4 0.01
132 357 0.99
133 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (132 bp):
GGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTT
TGATCTGCTCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCAATCTATTCCACTGTTGCCC
AG
Found at i:2902 original size:44 final size:44
Alignment explanation
Indices: 2528--3013 Score: 234
Period size: 44 Copynumber: 11.0 Consensus size: 44
2518 GGCTTCAGTA
** * * *
2528 TACTCCACTGTAACCTCAGGGAGGTAAAATCTGTCATCTTCGATC
1 TACTCCACTGTTGCC-CAGGGAGATAAAATCTGTAATCTTCAATC
** * * *
2573 TACTCCACTACTGTCTAGGGAGATAAAATTTGTAATCTTCAATC
1 TACTCCACTGTTGCCCAGGGAGATAAAATCTGTAATCTTCAATC
* * * * *
2617 TATTCCACTGTTGCACAGGGAGATAGAATTACTG---GCTTCAATG
1 TACTCCACTGTTGCCCAGGGAGATA-AAAT-CTGTAATCTTCAATC
** * * ** **
2660 TACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTTGATC
1 TACTCCACTGTTGCC-CAGGGAGATAAAATCTGTAATCTTCAATC
* ** ** *
2705 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
1 TACTCCACTGTTGCCCAGGGAGATAAAATCTGTAATCTTCAATC
* * *
2749 TATTCCACTGTTGCCCAGGGAGATAGAATTACTG--A-CTTCAATG
1 TACTCCACTGTTGCCCAGGGAGATA-AAAT-CTGTAATCTTCAATC
** * * ** **
2792 TACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTTGATC
1 TACTCCACTGTTGCC-CAGGGAGATAAAATCTGTAATCTTCAATC
* ** **
2837 TGCTCCACTACTGCTTAGGGAGATAAAATCTGTAATCTTCAATC
1 TACTCCACTGTTGCCCAGGGAGATAAAATCTGTAATCTTCAATC
* * * * *
2881 TATTCCACTGTTGCCCTGGGAGATAGAATTACTG---GCTTCAATG
1 TACTCCACTGTTGCCCAGGGAGATA-AAAT-CTGTAATCTTCAATC
** * **** **
2924 TACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATC
1 TACTCCACTGTTGCC-CAGGGAGATAAAATCTGTAATCTTCAATC
* ** ** *
2969 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATC
1 TACTCCACTGTTGCCCAGGGAGATAAAATCTGTAATCTTCAATC
3013 T
1 T
3014 GTTTCGCTGT
Statistics
Matches: 310, Mismatches: 113, Indels: 37
0.67 0.25 0.08
Matches are distributed among these distances:
42 5 0.02
43 65 0.21
44 172 0.55
45 60 0.19
46 8 0.03
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
TACTCCACTGTTGCCCAGGGAGATAAAATCTGTAATCTTCAATC
Found at i:3165 original size:88 final size:88
Alignment explanation
Indices: 3044--3237 Score: 309
Period size: 88 Copynumber: 2.2 Consensus size: 88
3034 AGGCAAGATT
* * * *
3044 CTGAGGGAGGCAAGAC-TTTATTTTCGATCTGCTTCGCTGTCGATGCAGGAAGTCAAGATTTGCT
1 CTGAGGGAGGCAAGGCTTTTATTTTCGATCTGCTTCGCAGTCGATACAGGAAGGCAAGATTTGCT
* *
3108 ATCTTTAACTTACTCTACTGCAA
66 ATCTTTAACTTACTCCACTACAA
*
3131 CTGACGGAGGCAAGGCTTTTATTTTCGATCTGCTTCGCAGTCGATACAGGAAGGCAAGATTTGCT
1 CTGAGGGAGGCAAGGCTTTTATTTTCGATCTGCTTCGCAGTCGATACAGGAAGGCAAGATTTGCT
*
3196 ATCTTTAACTTGCTCCACTACAA
66 ATCTTTAACTTACTCCACTACAA
3219 CTGAGGGAGGCAAGGCTTT
1 CTGAGGGAGGCAAGGCTTT
3238 ATAATTTCAC
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
87 14 0.14
88 83 0.86
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (88 bp):
CTGAGGGAGGCAAGGCTTTTATTTTCGATCTGCTTCGCAGTCGATACAGGAAGGCAAGATTTGCT
ATCTTTAACTTACTCCACTACAA
Found at i:5484 original size:19 final size:19
Alignment explanation
Indices: 5460--5499 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5450 GGTTTGGCAG
5460 AAAAAATCCAAAAGAATGA
1 AAAAAATCCAAAAGAATGA
**
5479 AAAAAATCGTAAAGAATGA
1 AAAAAATCCAAAAGAATGA
5498 AA
1 AA
5500 TAACATTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.68, C:0.07, G:0.12, T:0.12
Consensus pattern (19 bp):
AAAAAATCCAAAAGAATGA
Found at i:7452 original size:13 final size:13
Alignment explanation
Indices: 7434--7459 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7424 TGTTCAATTT
7434 TTTACTAGAAAAC
1 TTTACTAGAAAAC
7447 TTTACTAGAAAAC
1 TTTACTAGAAAAC
7460 AAATCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Done.