Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001572.1 Kokia drynarioides strain JFW-HI SEQ_113176, 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: 8996
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Found at i:3623 original size:53 final size:53
Alignment explanation
Indices: 3543--3649 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
3533 TTGACAATAA
3543 ATTATATCAAACAATGAACTAATCTTTGGACTAACTTATTGCTCACGTAAAAT
1 ATTATATCAAACAATGAACTAATCTTTGGACTAACTTATTGCTCACGTAAAAT
3596 ATTATATCAAACAATGAACTAATCTTTGGACTAACTTATTGCTCACGTAAAAT
1 ATTATATCAAACAATGAACTAATCTTTGGACTAACTTATTGCTCACGTAAAAT
3649 A
1 A
3650 CCTTATAATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (53 bp):
ATTATATCAAACAATGAACTAATCTTTGGACTAACTTATTGCTCACGTAAAAT
Found at i:4576 original size:2 final size:2
Alignment explanation
Indices: 4571--4598 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4561 TTTTTTATTA
4571 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4599 GTCAAAGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6454 original size:20 final size:21
Alignment explanation
Indices: 6420--6467 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
6410 TTTTTTAAAA
6420 TTTTTAAATAATTTA-AATATT
1 TTTTTAAATAATTTAGAA-ATT
* *
6441 TTTTTAAA-ATTTTAGAAGTT
1 TTTTTAAATAATTTAGAAATT
6461 TTTTTAA
1 TTTTTAA
6468 TTTTGTACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
TTTTTAAATAATTTAGAAATT
Found at i:7704 original size:43 final size:41
Alignment explanation
Indices: 7606--7736 Score: 140
Period size: 43 Copynumber: 3.1 Consensus size: 41
7596 ACGTCACTAT
* * * *
7606 AGAACATCGTCTTTCGCGGCGCTTTTCCAAAAACACCGCTAA
1 AGAACAT-GTCTTTAGCGACGCTTTTCCACAAACGCCGCTAA
* *
7648 AG-ACATTGTCTTTAGCGACGCTTATCTCACAAACGCCGTTAA
1 AGAACA-TGTCTTTAGCGACGCTTTTC-CACAAACGCCGCTAA
7690 AGAACATGATCTTTAGC-AGCGCTTTTCCCACAAACGCCGCTAA
1 AGAACATG-TCTTTAGCGA-CGCTTTT-CCACAAACGCCGCTAA
7733 AGAA
1 AGAA
7737 ACGCCGCTAA
Statistics
Matches: 75, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
41 19 0.25
42 20 0.27
43 35 0.47
44 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (41 bp):
AGAACATGTCTTTAGCGACGCTTTTCCACAAACGCCGCTAA
Found at i:7740 original size:14 final size:14
Alignment explanation
Indices: 7721--7750 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
7711 CTTTTCCCAC
7721 AAACGCCGCTAAAG
1 AAACGCCGCTAAAG
7735 AAACGCCGCTAAAG
1 AAACGCCGCTAAAG
7749 AA
1 AA
7751 CATGATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.27, G:0.20, T:0.07
Consensus pattern (14 bp):
AAACGCCGCTAAAG
Found at i:7769 original size:57 final size:57
Alignment explanation
Indices: 7678--7793 Score: 196
Period size: 57 Copynumber: 2.0 Consensus size: 57
7668 CTTATCTCAC
* *
7678 AAACGCCGTTAAAGAACATGATCTTTAGCAGCGCTTTTCCCACAAACGCCGCTAAAG
1 AAACGCCGCTAAAGAACATGATCTTTAGCAGCGCTTTTCCAACAAACGCCGCTAAAG
* *
7735 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCAACAAATGCCGCTAAAG
1 AAACGCCGCTAAAGAACATGATCTTTAGCAGCGCTTTTCCAACAAACGCCGCTAAAG
7792 AA
1 AA
7794 CATGGTCTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (57 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCAGCGCTTTTCCAACAAACGCCGCTAAAG
Found at i:7780 original size:100 final size:100
Alignment explanation
Indices: 7636--7836 Score: 264
Period size: 100 Copynumber: 2.0 Consensus size: 100
7626 GCTTTTCCAA
*
7636 AAACACCGCTAAAGACATTGTCTTTAGCGACGCTTATCTCACAAACGCCGTTAAAGAACATGATC
1 AAACACCGCTAAAGACATTGTCTTTAGCGACGCTTATCTCACAAACGCCGCTAAAGAACATGATC
* *
7701 TTTAGCAGCGCT-TTTCCCACAAACGCCGCTAAAG
66 TTTAGCAGCGCTCATTCCCACAAACACCGCTAAAG
* * * *
7735 AAACGCCGCTAAAGAACA-TGATCTTTAGCGGCGCTTTTC-CAACAAATGCCGCTAAAGAACATG
1 AAACACCGCTAAAG-ACATTG-TCTTTAGCGACGCTTATCTC-ACAAACGCCGCTAAAGAACATG
* * *
7798 GTCTTTAGCGGCGCTCATTCCCGCAAACACCGCTAAAG
63 ATCTTTAGCAGCGCTCATTCCCACAAACACCGCTAAAG
7836 A
1 A
7837 CCATGGTCTT
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
99 16 0.18
100 52 0.59
101 20 0.23
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (100 bp):
AAACACCGCTAAAGACATTGTCTTTAGCGACGCTTATCTCACAAACGCCGCTAAAGAACATGATC
TTTAGCAGCGCTCATTCCCACAAACACCGCTAAAG
Found at i:7842 original size:44 final size:43
Alignment explanation
Indices: 7735--7891 Score: 206
Period size: 43 Copynumber: 3.6 Consensus size: 43
7725 GCCGCTAAAG
* **
7735 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCAAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCGC
* *
7778 AAATGCCGCTAAAGAACATGGTCTTTAGCGGCGCTCATTCCCGC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCT-TTTCCCGC
* * * *
7822 AAACACCGCTAAAGACCATGGTCTTTAACGGCACTTTTCCCGC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCGC
* *
7865 AAACGCCGTTAAAGACCATGGTCTTTA
1 AAACGCCGCTAAAGAACATGGTCTTTA
7892 ATGGCATTTT
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
43 65 0.65
44 35 0.35
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCGC
Found at i:7892 original size:43 final size:43
Alignment explanation
Indices: 7735--7919 Score: 199
Period size: 43 Copynumber: 4.3 Consensus size: 43
7725 GCCGCTAAAG
* * * *
7735 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCAAC
1 AAACGCCGCTAAAGAACATGGTCTTTAACGGCACTTTTCCCAC
* * * * *
7778 AAATGCCGCTAAAGAACATGGTCTTTAGCGGCGCTCATTCCCGC
1 AAACGCCGCTAAAGAACATGGTCTTTAACGGCACT-TTTCCCAC
* * *
7822 AAACACCGCTAAAGACCATGGTCTTTAACGGCACTTTTCCCGC
1 AAACGCCGCTAAAGAACATGGTCTTTAACGGCACTTTTCCCAC
* * * * *
7865 AAACGCCGTTAAAGACCATGGTCTTTAATGGCATTTTTCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAACGGCACTTTTCCCAC
*
7908 AAACGCCACTAA
1 AAACGCCGCTAA
7920 TATTAACAAA
Statistics
Matches: 122, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
43 87 0.71
44 35 0.29
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAACGGCACTTTTCCCAC
Done.