Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001733.1 Kokia drynarioides strain JFW-HI SEQ_113438, whole genome shotgun sequence
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: 4676
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.35
Found at i:3335 original size:33 final size:32
Alignment explanation
Indices: 3298--3368 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 32
3288 ATTATATTAT
* * *
3298 TGTTTTGATGTTTTTTTTTGCTGTTTTGGTTGC
1 TGTTTTGATGTTGTTTTTTACTATTTTGG-TGC
3331 TGTTTTGATGTTGTTTTTTACTATTTTGGTGC
1 TGTTTTGATGTTGTTTTTTACTATTTTGGTGC
*
3363 TTTTTT
1 TGTTTT
3369 TTACTGCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 8 0.24
33 26 0.76
ACGTcount: A:0.06, C:0.06, G:0.21, T:0.68
Consensus pattern (32 bp):
TGTTTTGATGTTGTTTTTTACTATTTTGGTGC
Found at i:3368 original size:21 final size:20
Alignment explanation
Indices: 3334--3390 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
3324 TGGTTGCTGT
* *
3334 TTTGATGTTGTTTTTTACTAT
1 TTTGGTGTT-TTTTTTACTAC
*
3355 TTTGGTGCTTTTTTTTACTGC
1 TTTGGTG-TTTTTTTTACTAC
3376 TTTGGTGTTATTTTT
1 TTTGGTGTT-TTTTT
3391 GCTGTTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.09, C:0.07, G:0.18, T:0.67
Consensus pattern (20 bp):
TTTGGTGTTTTTTTTACTAC
Found at i:3405 original size:21 final size:20
Alignment explanation
Indices: 3381--3447 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 20
3371 ACTGCTTTGG
*
3381 TGTTATTTTTGCTGTTGTTTTTGT
1 TGTT-TTTTTGCTG-T-TATTT-T
*
3405 TGTTGTTTTTGTTGTTATTTT
1 TGTT-TTTTTGCTGTTATTTT
*
3426 TGTTGTTTTGCTGTTATTTT
1 TGTTTTTTTGCTGTTATTTT
3446 TG
1 TG
3448 CTGCTATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
20 16 0.42
21 5 0.13
22 4 0.11
23 1 0.03
24 12 0.32
ACGTcount: A:0.04, C:0.03, G:0.21, T:0.72
Consensus pattern (20 bp):
TGTTTTTTTGCTGTTATTTT
Found at i:3435 original size:44 final size:44
Alignment explanation
Indices: 3387--3490 Score: 136
Period size: 44 Copynumber: 2.4 Consensus size: 44
3377 TTGGTGTTAT
* * * * * *
3387 TTTTGCTGTTGTTTTTGTTGTTGTTTTTGTTGTTATTTTTGTTG
1 TTTTGCTGTTATTTTTGCTGCTATTTTGGTTGTTATTTTAGTTG
3431 TTTTGCTGTTATTTTTGCTGCTATTTTGGTTGTTATTTTAGTTG
1 TTTTGCTGTTATTTTTGCTGCTATTTTGGTTGTTATTTTAGTTG
* *
3475 TTTGGATGTTATTTTT
1 TTTTGCTGTTATTTTT
3491 ATTCGTTTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.07, C:0.04, G:0.21, T:0.68
Consensus pattern (44 bp):
TTTTGCTGTTATTTTTGCTGCTATTTTGGTTGTTATTTTAGTTG
Found at i:3440 original size:20 final size:20
Alignment explanation
Indices: 3393--3490 Score: 90
Period size: 20 Copynumber: 4.7 Consensus size: 20
3383 TTATTTTTGC
3393 TGTTGTT-TTTGTTGTTGTTTT
1 TGTTGTTATTT-TTGTTG-TTT
3414 TGTTGTTATTTTTGTTGTTT
1 TGTTGTTATTTTTGTTGTTT
* *
3434 TGCTGTTATTTTTGCTGCTATTT
1 TGTTGTTATTTTTG-T--TGTTT
*
3457 TGGTTGTTATTTTAGTTGTTT
1 T-GTTGTTATTTTTGTTGTTT
* *
3478 GGATGTTATTTTT
1 TGTTGTTATTTTT
3491 ATTCGTTTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
20 26 0.41
21 18 0.28
22 3 0.05
23 6 0.09
24 11 0.17
ACGTcount: A:0.07, C:0.03, G:0.21, T:0.68
Consensus pattern (20 bp):
TGTTGTTATTTTTGTTGTTT
Found at i:3446 original size:32 final size:32
Alignment explanation
Indices: 3393--3464 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
3383 TTATTTTTGC
* * * *
3393 TGTTGTTTTTGTTGTTGTTTTTGTTGTTATTTT
1 TGTTG-TTTTGCTGTTATTTTTGCTGCTATTTT
3426 TGTTGTTTTGCTGTTATTTTTGCTGCTATTTT
1 TGTTGTTTTGCTGTTATTTTTGCTGCTATTTT
*
3458 GGTTGTT
1 TGTTGTT
3465 ATTTTAGTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 29 0.85
33 5 0.15
ACGTcount: A:0.04, C:0.04, G:0.22, T:0.69
Consensus pattern (32 bp):
TGTTGTTTTGCTGTTATTTTTGCTGCTATTTT
Found at i:3474 original size:12 final size:12
Alignment explanation
Indices: 3376--3476 Score: 93
Period size: 12 Copynumber: 8.8 Consensus size: 12
3366 TTTTTACTGC
*
3376 TTTGGTGTTATT
1 TTTGTTGTTATT
* *
3388 TTTGCTGTTGTT
1 TTTGTTGTTATT
*
3400 TTTGTTGTTGTT
1 TTTGTTGTTATT
3412 TTTGTTGTTATT
1 TTTGTTGTTATT
3424 TTTGTTG----T
1 TTTGTTGTTATT
*
3432 TTTGCTGTTATT
1 TTTGTTGTTATT
* *
3444 TTTGCTGCTATT
1 TTTGTTGTTATT
*
3456 TTGGTTGTTATT
1 TTTGTTGTTATT
*
3468 TTAGTTGTT
1 TTTGTTGTT
3477 TGGATGTTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
8 7 0.09
12 68 0.91
ACGTcount: A:0.06, C:0.04, G:0.22, T:0.68
Consensus pattern (12 bp):
TTTGTTGTTATT
Found at i:3633 original size:15 final size:16
Alignment explanation
Indices: 3603--3640 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3593 AATATAAAAA
3603 AAATTTAATGTATTTT
1 AAATTTAATGTATTTT
*
3619 AAATTT-ATTTATTTT
1 AAATTTAATGTATTTT
3634 AATATTT
1 AA-ATTT
3641 GTTTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
AAATTTAATGTATTTT
Done.