Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold989
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: 3583
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Found at i:3389 original size:32 final size:32
Alignment explanation
Indices: 3344--3422 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
3334 GGGATATCCT
* * *
3344 ATTCCACGGATATCTCGGTTTAGG-TTTATTCC
1 ATTCCATGCATATCCCGGTTT-GGATTTATTCC
*
3376 ATTCCATGCATATCCCGGTTTGGATTTATTCT
1 ATTCCATGCATATCCCGGTTTGGATTTATTCC
*
3408 ATTCCTTGCATATCC
1 ATTCCATGCATATCC
3423 TGGCTTGGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
31 2 0.05
32 39 0.95
ACGTcount: A:0.19, C:0.24, G:0.15, T:0.42
Consensus pattern (32 bp):
ATTCCATGCATATCCCGGTTTGGATTTATTCC
Found at i:3442 original size:8 final size:8
Alignment explanation
Indices: 3429--3563 Score: 76
Period size: 7 Copynumber: 18.2 Consensus size: 8
3419 ATCCTGGCTT
3429 GGGTTTAG
1 GGGTTTAG
*
3437 GGGTTTAT
1 GGGTTTAG
* *
3445 TGTTTTAG
1 GGGTTTAG
*
3453 GGGTTTAT
1 GGGTTTAG
*
3461 CGGTTT-G
1 GGGTTTAG
*
3468 GGGGTTA-
1 GGGTTTAG
3475 GGGTTT-G
1 GGGTTTAG
3482 GGGTTTA-
1 GGGTTTAG
*
3489 GGGTTT-T
1 GGGTTTAG
3496 GGGTTTAG
1 GGGTTTAG
*
3504 GGG-TTCG
1 GGGTTTAG
3511 GGG-TT-G
1 GGGTTTAG
*
3517 GGGGTT-G
1 GGGTTTAG
3524 GGGTTTAG
1 GGGTTTAG
*
3532 GGTTTTA-
1 GGGTTTAG
* *
3539 AGG-TTGG
1 GGGTTTAG
3546 GGGTTTAG
1 GGGTTTAG
*
3554 GGTTTTAG
1 GGGTTTAG
3562 GG
1 GG
3564 TTGGGGGTTG
Statistics
Matches: 96, Mismatches: 22, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
6 6 0.06
7 46 0.48
8 44 0.46
ACGTcount: A:0.09, C:0.01, G:0.48, T:0.41
Consensus pattern (8 bp):
GGGTTTAG
Found at i:3471 original size:16 final size:16
Alignment explanation
Indices: 3430--3473 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
3420 TCCTGGCTTG
*
3430 GGTTTAGGGGTTTATT
1 GGTTTAGGGGTTTATC
*
3446 GTTTTAGGGGTTTATC
1 GGTTTAGGGGTTTATC
*
3462 GGTTTGGGGGTT
1 GGTTTAGGGGTT
3474 AGGGTTTGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.09, C:0.02, G:0.41, T:0.48
Consensus pattern (16 bp):
GGTTTAGGGGTTTATC
Found at i:3487 original size:7 final size:7
Alignment explanation
Indices: 3462--3583 Score: 86
Period size: 7 Copynumber: 17.3 Consensus size: 7
3452 GGGGTTTATC
3462 GGTTTGG
1 GGTTTGG
* *
3469 GGGTTAG
1 GGTTTGG
3476 GGTTTGG
1 GGTTTGG
*
3483 GGTTTAG
1 GGTTTGG
*
3490 GGTTTTG
1 GGTTTGG
3497 GGTTTAGG
1 GGTTT-GG
*
3505 GGTTCGG
1 GGTTTGG
3512 GG-TTGG
1 GGTTTGG
*
3518 GGGTTGG
1 GGTTTGG
3525 GGTTTAGG
1 GGTTT-GG
* **
3533 GTTTTAA
1 GGTTTGG
*
3540 GGTTGGG
1 GGTTTGG
3547 GGTTTAGG
1 GGTTT-GG
* *
3555 GTTTTAG
1 GGTTTGG
3562 GG-TTGG
1 GGTTTGG
*
3568 GGGTTGG
1 GGTTTGG
3575 GGTTTGG
1 GGTTTGG
3582 GG
1 GG
Statistics
Matches: 87, Mismatches: 23, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
6 10 0.11
7 60 0.69
8 17 0.20
ACGTcount: A:0.07, C:0.01, G:0.54, T:0.39
Consensus pattern (7 bp):
GGTTTGG
Found at i:3566 original size:22 final size:22
Alignment explanation
Indices: 3472--3572 Score: 109
Period size: 22 Copynumber: 4.7 Consensus size: 22
3462 GGTTTGGGGG
*
3472 TTAGGGTTTGGGGTTTAGGGTT
1 TTAGGGTTGGGGGTTTAGGGTT
* * *
3494 TT-GGGTTTAGGGG-TTCGGGGT
1 TTAGGG-TTGGGGGTTTAGGGTT
**
3515 TGGGGGTT-GGGGTTTAGGGTT
1 TTAGGGTTGGGGGTTTAGGGTT
*
3536 TTAAGGTTGGGGGTTTAGGGTT
1 TTAGGGTTGGGGGTTTAGGGTT
3558 TTAGGGTTGGGGGTT
1 TTAGGGTTGGGGGTT
3573 GGGGTTTGGG
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
20 4 0.06
21 23 0.35
22 38 0.58
ACGTcount: A:0.08, C:0.01, G:0.50, T:0.41
Consensus pattern (22 bp):
TTAGGGTTGGGGGTTTAGGGTT
Done.