Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_796 ID=scaffold_796-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: 3724
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.40
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:188 original size:19 final size:20
Alignment explanation
Indices: 164--203 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
154 CAATTGTTTT
164 AAAA-TTAA-ATAAGTTTAAA
1 AAAATTTAATATAA-TTTAAA
183 AAAATTTAATATAATTTAAA
1 AAAATTTAATATAATTTAAA
203 A
1 A
204 TTTTAAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 11 0.58
21 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
AAAATTTAATATAATTTAAA
Found at i:1765 original size:15 final size:15
Alignment explanation
Indices: 1745--1782 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
1735 AAACGAAATA
1745 GATATCCCAAAAAGG
1 GATATCCCAAAAAGG
1760 GATATCCCAAAAAGG
1 GATATCCCAAAAAGG
1775 GATATCCC
1 GATATCCC
1783 GGTCCGGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (15 bp):
GATATCCCAAAAAGG
Found at i:3406 original size:7 final size:7
Alignment explanation
Indices: 3394--3724 Score: 80
Period size: 7 Copynumber: 46.3 Consensus size: 7
3384 TCTCTACTTT
3394 GTTTGGG
1 GTTTGGG
3401 GTTTGGG
1 GTTTGGG
*
3408 GTTCTAGG
1 GTT-TGGG
* *
3416 GTTGTAGA
1 GTT-TGGG
*
3424 GTTT--A
1 GTTTGGG
3429 GTTTGGG
1 GTTTGGG
**
3436 GTGGGGG
1 GTTTGGG
*
3443 GATTGGG
1 GTTTGGG
3450 GTTTGGG
1 GTTTGGG
3457 GTTTTGGG
1 G-TTTGGG
**
3465 GTTATATG
1 GTT-TGGG
* *
3473 GTTTTGA
1 GTTTGGG
*
3480 GATTGGG
1 GTTTGGG
3487 GTTTGGG
1 GTTTGGG
*
3494 TTTTAGGG
1 GTTT-GGG
*
3502 ATTTAGGG
1 GTTT-GGG
* *
3510 TTTTAGG
1 GTTTGGG
* *
3517 GTTTTGA
1 GTTTGGG
*
3524 GTTTAGG
1 GTTTGGG
**
3531 GTTTATG
1 GTTTGGG
*
3538 GTTTGGA
1 GTTTGGG
*
3545 GTTT-TG
1 GTTTGGG
*
3551 GTTTTGG
1 GTTTGGG
* **
3558 GTGTAAG
1 GTTTGGG
*
3565 ATTTGGG
1 GTTTGGG
* *
3572 GTATCGG
1 GTTTGGG
*
3579 GTTTTGG
1 GTTTGGG
*
3586 GTTTTGG
1 GTTTGGG
*
3593 GTTT-AG
1 GTTTGGG
* *
3599 GTAAT-AG
1 GT-TTGGG
*
3606 GTTGGGG
1 GTTTGGG
*
3613 GTGTGGG
1 GTTTGGG
*
3620 GGTTGGG
1 GTTTGGG
*
3627 GGTTGGG
1 GTTTGGG
*
3634 GGTT-GG
1 GTTTGGG
3640 GTTTAGGG
1 GTTT-GGG
* *
3648 TTTTAGG
1 GTTTGGG
3655 GTTTGGG
1 GTTTGGG
*
3662 GGTTGGG
1 GTTTGGG
3669 GTTTTAGGG
1 G-TTT-GGG
* *
3678 TTTTAGG
1 GTTTGGG
3685 GTTTGGGG
1 GTTT-GGG
3693 GTTTTGGGG
1 G-TTT-GGG
*
3702 GTTTAGG
1 GTTTGGG
*
3709 GTTTAGG
1 GTTTGGG
3716 GTTTGGG
1 GTTTGGG
3723 GT
1 GT
Statistics
Matches: 240, Mismatches: 69, Indels: 30
0.71 0.20 0.09
Matches are distributed among these distances:
5 5 0.02
6 12 0.05
7 159 0.66
8 53 0.22
9 11 0.05
ACGTcount: A:0.09, C:0.01, G:0.47, T:0.43
Consensus pattern (7 bp):
GTTTGGG
Found at i:3485 original size:22 final size:21
Alignment explanation
Indices: 3463--3541 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 21
3453 TGGGGTTTTG
* *
3463 GGGTTATATGGTTTTGAGATTG
1 GGGTT-TAGGGTTTTGAGATTA
*
3485 GGGTTT-GGGTTTTAGGGATTTA
1 GGGTTTAGGGTTTT-GAGA-TTA
*
3507 GGGTTTTAGGGTTTTGAGTTTA
1 GGG-TTTAGGGTTTTGAGATTA
*
3529 GGGTTTATGGTTT
1 GGGTTTAGGGTTT
3542 GGAGTTTTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
20 6 0.13
21 13 0.28
22 16 0.34
23 5 0.11
24 7 0.15
ACGTcount: A:0.14, C:0.00, G:0.38, T:0.48
Consensus pattern (21 bp):
GGGTTTAGGGTTTTGAGATTA
Found at i:3511 original size:44 final size:44
Alignment explanation
Indices: 3440--3534 Score: 109
Period size: 44 Copynumber: 2.2 Consensus size: 44
3430 TTTGGGGTGG
* * * * *
3440 GGGGATTGGGGTTTGGGGTTTTGGGGTTATATGGTTTTGAGATT
1 GGGGTTTGGGGTTTAGGGATTTAGGGTTATAGGGTTTTGAGATT
* * *
3484 GGGGTTTGGGTTTTAGGGATTTAGGGTTTTAGGGTTTTGAGTTT
1 GGGGTTTGGGGTTTAGGGATTTAGGGTTATAGGGTTTTGAGATT
*
3528 AGGGTTT
1 GGGGTTT
3535 ATGGTTTGGA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.12, C:0.00, G:0.43, T:0.45
Consensus pattern (44 bp):
GGGGTTTGGGGTTTAGGGATTTAGGGTTATAGGGTTTTGAGATT
Found at i:3652 original size:8 final size:8
Alignment explanation
Indices: 3641--3719 Score: 74
Period size: 8 Copynumber: 10.2 Consensus size: 8
3631 GGGGGTTGGG
3641 TTTAGGGT
1 TTTAGGGT
3649 TTTAGGG-
1 TTTAGGGT
*
3656 TTT-GGGG
1 TTTAGGGT
* *
3663 GTTGGGGT
1 TTTAGGGT
3671 TTTAGGGT
1 TTTAGGGT
3679 TTTAGGGT
1 TTTAGGGT
**
3687 TTGGGGGT
1 TTTAGGGT
* *
3695 TTTGGGGG
1 TTTAGGGT
3703 TTTAGGG-
1 TTTAGGGT
3710 TTTAGGGT
1 TTTAGGGT
3718 TT
1 TT
3720 GGGGT
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
6 3 0.05
7 12 0.20
8 44 0.75
ACGTcount: A:0.08, C:0.00, G:0.47, T:0.46
Consensus pattern (8 bp):
TTTAGGGT
Found at i:3677 original size:30 final size:29
Alignment explanation
Indices: 3629--3723 Score: 140
Period size: 30 Copynumber: 3.2 Consensus size: 29
3619 GGGTTGGGGG
3629 TTGGGGGTT-GGGTTTAGGGTTTTAGGGT
1 TTGGGGGTTGGGGTTTAGGGTTTTAGGGT
3657 TTGGGGGTTGGGGTTTTAGGGTTTTAGGGT
1 TTGGGGGTTGGGG-TTTAGGGTTTTAGGGT
3687 TTGGGGGTTTTGGGGGTTTAGGG-TTTAGGGT
1 TTGGGGG--TT-GGGGTTTAGGGTTTTAGGGT
3718 TTGGGG
1 TTGGGG
3724 T
Statistics
Matches: 62, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.15
29 3 0.05
30 23 0.37
31 14 0.23
32 9 0.15
33 4 0.06
ACGTcount: A:0.06, C:0.00, G:0.52, T:0.42
Consensus pattern (29 bp):
TTGGGGGTTGGGGTTTAGGGTTTTAGGGT
Done.