Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008763.1 Kokia drynarioides strain JFW-HI SEQ_123446, 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: 4887
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Found at i:3471 original size:60 final size:58
Alignment explanation
Indices: 3332--3504 Score: 213
Period size: 58 Copynumber: 2.9 Consensus size: 58
3322 TTAATATAAT
* ** *
3332 ATTTGATACTTGAACTTGATACATTTTCCTAATTTGGTACCTACACTTTTTTTACTCA
1 ATTTGATACTTGAACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTTACTCA
* *
3390 ATTTGGTACTTGAACTTGACATTTTTTCCTAATTTGGTATCTAAACTTTTTTTGGAC-CTA
1 ATTTGATACTTGAACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTT--ACTC-A
* * * *
3450 ATTTGATGCTTAAACTTGACATTTTTTTCCTAATTTGGTACCTAAGCTTATTTTA
1 ATTTGATACTTGAACTTGACA-TTTTTTCCTAATTTGGTACCTAAACTTTTTTTA
3505 GATTCAATTT
Statistics
Matches: 99, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
58 47 0.47
59 2 0.02
60 21 0.21
61 29 0.29
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (58 bp):
ATTTGATACTTGAACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTTACTCA
Found at i:3514 original size:61 final size:56
Alignment explanation
Indices: 3332--3524 Score: 179
Period size: 58 Copynumber: 3.2 Consensus size: 56
3322 TTAATATAAT
* * ** *
3332 ATTTGATACTTGAACTTGATACATTTTCCTAATTTGGTACCTACACTTTTTTTACTCA
1 ATTTGATACTTAAACTTGACATTTTTTCCTAATTTGGTACCTA-ACTTTTTTGA-TCA
* * * *
3390 ATTTGGTACTTGAACTTGACATTTTTTCCTAATTTGGTATCTAAACTTTTTTTGGACCTA
1 ATTTGATACTTAAACTTGACATTTTTTCCTAATTTGGTACCT-AAC-TTTTTT-GATC-A
*
3450 ATTTGATGCTTAAACTTGACATTTTTTTCCTAATTTGGTACCTAAGCTTATTTTAGATTCA
1 ATTTGATACTTAAACTTGACA-TTTTTTCCTAATTTGGTACCTAA-CTT-TTTT-GA-TCA
* *
3511 ATTTGGTACCTAAA
1 ATTTGATACTTAAA
3525 TTTATTAAAT
Statistics
Matches: 111, Mismatches: 16, Indels: 13
0.79 0.11 0.09
Matches are distributed among these distances:
58 39 0.35
59 8 0.07
60 24 0.22
61 39 0.35
62 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (56 bp):
ATTTGATACTTAAACTTGACATTTTTTCCTAATTTGGTACCTAACTTTTTTGATCA
Found at i:3724 original size:60 final size:60
Alignment explanation
Indices: 3661--3772 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
3651 ATTAATATTA
* *
3661 AAAAAGATTATGTACCAAATT-AAGAAAAAGAGTCAAGTTCAGATACCAAATTGGACCTC
1 AAAAAGATTAAGTACCAAATTAAAAAAAAAGAGTCAAGTTCAGATACCAAATTGGACCTC
* * * * *
3720 AAAAAGTTTAAGTACCAACTTAAAAAAAAAGTGTCAAGTTTAGGTACCAAATT
1 AAAAAGATTAAGTACCAAATTAAAAAAAAAGAGTCAAGTTCAGATACCAAATT
3773 AAAAAAAATG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 18 0.40
60 27 0.60
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.24
Consensus pattern (60 bp):
AAAAAGATTAAGTACCAAATTAAAAAAAAAGAGTCAAGTTCAGATACCAAATTGGACCTC
Found at i:3779 original size:30 final size:31
Alignment explanation
Indices: 3723--3790 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 31
3713 GGACCTCAAA
*
3723 AAGTTTAAGTACCAACTTAAAAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAA-TGTC
*
3755 AAGTTTAGGTACCAAATT-AAAAAAAATGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAATGTC
3785 AAGTTT
1 AAGTTT
3791 GAGAACTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 10 0.29
31 8 0.24
32 16 0.47
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAAATGTC
Found at i:3802 original size:30 final size:31
Alignment explanation
Indices: 3723--3803 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 31
3713 GGACCTCAAA
* * *
3723 AAGTTTAAGTACCAACTTAAAAAAAAAGTGTC
1 AAGTTTAGGAACCAAATT-AAAAAAAAGTGTC
*
3755 AAGTTTAGGTACCAAATTAAAAAAAA-TGTC
1 AAGTTTAGGAACCAAATTAAAAAAAAGTGTC
*
3785 AAGTTT-GAGAACTAAATTA
1 AAGTTTAG-GAACCAAATTA
3804 GATCAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 1 0.02
30 19 0.43
31 8 0.18
32 16 0.36
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (31 bp):
AAGTTTAGGAACCAAATTAAAAAAAAGTGTC
Found at i:4838 original size:20 final size:20
Alignment explanation
Indices: 4813--4864 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
4803 ATTAATTATT
*
4813 TGTAAAATCTAATTTAAATA
1 TGTAAAATATAATTTAAATA
* *
4833 TGTAAATTATATTTTAAATA
1 TGTAAAATATAATTTAAATA
4853 T-TAAAATATAAT
1 TGTAAAATATAAT
4865 CATTACAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (20 bp):
TGTAAAATATAATTTAAATA
Done.