Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007574.1 Kokia drynarioides strain JFW-HI SEQ_122202, 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: 13219
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3595 original size:15 final size:15
Alignment explanation
Indices: 3575--3680 Score: 50
Period size: 15 Copynumber: 7.5 Consensus size: 15
3565 AAATATGATT
3575 TAAAAGAGTTTTAAA
1 TAAAAGAGTTTTAAA
*
3590 TAAAAGA----TAAT
1 TAAAAGAGTTTTAAA
* *
3601 TAAATAGAATTTTAAG
1 TAAA-AGAGTTTTAAA
*
3617 TAAAAGAGTTTTAGA
1 TAAAAGAGTTTTAAA
*
3632 TAAATA-A----TAAT
1 TAAA-AGAGTTTTAAA
* * *
3643 TAAAATAGAATTTAAT
1 TAAAAGAG-TTTTAAA
3659 TAAAAGAGTTTTAAA
1 TAAAAGAGTTTTAAA
3674 TAAAAGA
1 TAAAAGA
3681 TAATTTATCA
Statistics
Matches: 69, Mismatches: 10, Indels: 24
0.67 0.10 0.23
Matches are distributed among these distances:
10 1 0.01
11 14 0.20
12 3 0.04
15 32 0.46
16 19 0.28
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (15 bp):
TAAAAGAGTTTTAAA
Found at i:3628 original size:42 final size:42
Alignment explanation
Indices: 3575--3685 Score: 172
Period size: 42 Copynumber: 2.6 Consensus size: 42
3565 AAATATGATT
3575 TAAAAGAGTTTTAAATAAAAGATAATT-AAATAGAATTTTAAG
1 TAAAAGAGTTTTAAATAAAAGATAATTAAAATAGAA-TTTAAG
* *
3617 TAAAAGAGTTTTAGATAAATA-ATAATTAAAATAGAATTTAAT
1 TAAAAGAGTTTTAAATAAA-AGATAATTAAAATAGAATTTAAG
3659 TAAAAGAGTTTTAAATAAAAGATAATT
1 TAAAAGAGTTTTAAATAAAAGATAATT
3686 TATCAGAAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
41 1 0.02
42 53 0.84
43 9 0.14
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (42 bp):
TAAAAGAGTTTTAAATAAAAGATAATTAAAATAGAATTTAAG
Found at i:5977 original size:15 final size:16
Alignment explanation
Indices: 5945--5982 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5935 TCAAGATAGA
*
5945 ATTTTGAATTCATTTG
1 ATTTTGAATTCATATG
5961 ATTTTGAA-TCATATG
1 ATTTTGAATTCATATG
5976 ATATTTG
1 AT-TTTG
5983 TAAATCTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (16 bp):
ATTTTGAATTCATATG
Found at i:12598 original size:24 final size:24
Alignment explanation
Indices: 12533--13177 Score: 398
Period size: 24 Copynumber: 26.9 Consensus size: 24
12523 GCATTTACTG
* *
12533 TCGTCAGCTTGCACACGTTTATAG-
1 TCGTCAGCTTGCATACGTTTA-CGC
* ** *
12557 TCGCCAGCTTATATACATTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
* * * * *
12581 TCGTCAACTTGCACACATTTAAGG
1 TCGTCAGCTTGCATACGTTTACGC
* * ** *
12605 TCATCAACTTATATAC-TTTATGC
1 TCGTCAGCTTGCATACGTTTACGC
* * *
12628 TCGTCAGCTTGCACACATTTACGA
1 TCGTCAGCTTGCATACGTTTACGC
* *
12652 TCGTCAACATAT-C-TACATTTACGC
1 TCGTCAGC-T-TGCATACGTTTACGC
* * **
12676 TCGTCAGCTTGCACACATTTACAT
1 TCGTCAGCTTGCATACGTTTACGC
** *
12700 TCGTCAGCTTAAATACATTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
* ** *
12724 TCATCAGCTTATATATGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
* *
12748 TCGTCAACTTGCACACGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
** *
12772 TCGTCAGCTTATATATGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
* *
12796 TCGTCAACTTGCACACGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
**
12820 TCGTCAGCTTATATACGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
* * * *
12844 TCGTTAGCTTGCACACGTTTATGG
1 TCGTCAGCTTGCATACGTTTACGC
**
12868 TCGTCAGCTTATATACGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
* * *
12892 TCGTCAGCTTGCTTATGTTTACAC
1 TCGTCAGCTTGCATACGTTTACGC
* **
12916 TTGTCAGCTTATATACGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
** *
12940 TCGTCAATTTGCACACGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
** *
12964 TCGTCAATTTGCACACGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
* ** * *
12988 TCATCAGCTTATATATGTTTATGC
1 TCGTCAGCTTGCATACGTTTACGC
* * * *
13012 TCGTCAACTTGCACACATTTACAC
1 TCGTCAGCTTGCATACGTTTACGC
* ** * *
13036 TCGTCAGCATATATACATTTATGC
1 TCGTCAGCTTGCATACGTTTACGC
* ** * *
13060 TCGTCAACTTATATATGTTTATGC
1 TCGTCAGCTTGCATACGTTTACGC
* * * * *
13084 TCATCAGCTTGCACATGATTATGC
1 TCGTCAGCTTGCATACGTTTACGC
* ** * *
13108 TTGTCAGCTTATATATGTTTACAC
1 TCGTCAGCTTGCATACGTTTACGC
* *
13132 TCATCAGCTTGCACACGTTTACGC
1 TCGTCAGCTTGCATACGTTTACGC
* **
13156 TCGTCAGCCTATATACGTTTAC
1 TCGTCAGCTTGCATACGTTTAC
13178 CTTAATTAAC
Statistics
Matches: 470, Mismatches: 145, Indels: 12
0.75 0.23 0.02
Matches are distributed among these distances:
22 1 0.00
23 19 0.04
24 447 0.95
25 2 0.00
26 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (24 bp):
TCGTCAGCTTGCATACGTTTACGC
Found at i:12745 original size:48 final size:48
Alignment explanation
Indices: 12669--13177 Score: 478
Period size: 48 Copynumber: 10.6 Consensus size: 48
12659 CATATCTACA
** * * ** ** * *
12669 TTTACGCTCGTCAGCTTGCACACATTTACATTCGTCAGCTTAAATACA
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* * *
12717 TTTACGCTCATCAGCTTATATATGTTTACGCTCGTCAACTTGCACACG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* *
12765 TTTACGCTCGTCAGCTTATATATGTTTACGCTCGTCAACTTGCACACG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
*
12813 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTTAGCTTGCACACG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* * ** *
12861 TTTATGGTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCTTATG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* * **
12909 TTTACACTTGTCAGCTTATATACGTTTACGCTCGTCAATTTGCACACG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
** ** * * ** * *
12957 TTTACGCTCGTCAATTTGCACACGTTTACGCTCATCAGCTTATATATG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* * ** * * * * ** * *
13005 TTTATGCTCGTCAACTTGCACACATTTACACTCGTCAGCATATATACA
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* * * * * *
13053 TTTATGCTCGTCAACTTATATATGTTTATGCTCATCAGCTTGCACATG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* * * * * *
13101 ATTATGCTTGTCAGCTTATATATGTTTACACTCATCAGCTTGCACACG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
*
13149 TTTACGCTCGTCAGCCTATATACGTTTAC
1 TTTACGCTCGTCAGCTTATATACGTTTAC
13178 CTTAATTAAC
Statistics
Matches: 382, Mismatches: 79, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 382 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (48 bp):
TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
Done.