Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006402.1 Kokia drynarioides strain JFW-HI SEQ_120979, 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: 14093
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3441 original size:28 final size:28
Alignment explanation
Indices: 3410--3467 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
3400 GTGCTCCTTT
* * **
3410 TGTTCTATTAAGCATTTTAGTGTTGTTC
1 TGTTCGATTAAGCACTACAGTGTTGTTC
3438 TGTTCGATTAAGCACTACAGTGTTGTTC
1 TGTTCGATTAAGCACTACAGTGTTGTTC
3466 TG
1 TG
3468 ATTTGATAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.19, C:0.14, G:0.21, T:0.47
Consensus pattern (28 bp):
TGTTCGATTAAGCACTACAGTGTTGTTC
Found at i:3484 original size:25 final size:26
Alignment explanation
Indices: 3427--3484 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
3417 TTAAGCATTT
3427 TAGTGTTGTTCTGTTCGATTAAGCAC
1 TAGTGTTGTTCTGTTCGATTAAGCAC
*
3453 TACAGTGTTGTTCTGATTTGA-TAAGCA-
1 T--AGTGTTGTTCTG-TTCGATTAAGCAC
3480 TAGTG
1 TAGTG
3485 ATATTGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 4 0.14
26 1 0.04
27 1 0.04
28 18 0.64
29 4 0.14
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.41
Consensus pattern (26 bp):
TAGTGTTGTTCTGTTCGATTAAGCAC
Found at i:9647 original size:10 final size:10
Alignment explanation
Indices: 9632--9694 Score: 51
Period size: 10 Copynumber: 6.2 Consensus size: 10
9622 TTTTAATTTT
9632 AAAAATTATA
1 AAAAATTATA
9642 AAAAATTATA
1 AAAAATTATA
* *
9652 AAATTTATTTTA
1 AAA--AATTATA
9664 AAAAA-TA-A
1 AAAAATTATA
9672 AAAAATTATTA
1 AAAAATTA-TA
9683 AAGAAA-TATA
1 AA-AAATTATA
9693 AA
1 AA
9695 TTTTTTTATC
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
8 6 0.14
9 3 0.07
10 18 0.42
11 5 0.12
12 11 0.26
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (10 bp):
AAAAATTATA
Found at i:9653 original size:19 final size:18
Alignment explanation
Indices: 9631--9694 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 18
9621 TTTTTAATTT
9631 TAAAAATTATAAAAAATTA
1 TAAAAATTATAAAAAA-TA
*
9650 TAAAATTTATTTTAAAAAATA
1 TAAAA---ATTATAAAAAATA
*
9671 AAAAAATTATTAAAGAAATA
1 TAAAAATTA-TAAA-AAATA
9691 TAAA
1 TAAA
9695 TTTTTTTATC
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
18 3 0.08
19 9 0.25
20 8 0.22
21 6 0.17
22 10 0.28
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
TAAAAATTATAAAAAATA
Found at i:9693 original size:22 final size:21
Alignment explanation
Indices: 9632--9694 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
9622 TTTTAATTTT
*
9632 AAAAATTA-TAAAAAAT-TAT
1 AAAAATTATTAAAAAATATAA
* *
9651 AAAATTTATTTTAAAAA-ATAA
1 AAAAATTA-TTAAAAAATATAA
9672 AAAAATTATTAAAGAAATATAA
1 AAAAATTATTAAA-AAATATAA
9694 A
1 A
9695 TTTTTTTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
19 7 0.21
20 4 0.12
21 18 0.53
22 5 0.15
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAAATTATTAAAAAATATAA
Done.