Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007961.1 Kokia drynarioides strain JFW-HI SEQ_122609, 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: 8665
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:934 original size:29 final size:29
Alignment explanation
Indices: 874--934 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
864 TTACAACTAG
* *
874 TAAGAAAATATTATTAATTATTATGATGT
1 TAAGAAAATATTATAAATTATTATAATGT
* *
903 TAAGAGAATATTATCAAATTATT-TAATTT
1 TAAGAAAATATTAT-AAATTATTATAATGT
932 TAA
1 TAA
935 ATAGTTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (29 bp):
TAAGAAAATATTATAAATTATTATAATGT
Found at i:1452 original size:36 final size:36
Alignment explanation
Indices: 1386--1533 Score: 161
Period size: 36 Copynumber: 4.1 Consensus size: 36
1376 TGGAGGTAAG
* * * *
1386 AGACGAGGCCAAAGATCAACCGCGATGTGCACATGA
1 AGACAAGGTCAAAGATCAACCCCGACGTGCACATGA
* * *
1422 AGACAAGGTCGAAGATCAACCCTGACGTGCACGTGA
1 AGACAAGGTCAAAGATCAACCCCGACGTGCACATGA
* * **
1458 AGACGAGGTTAAAGATCAACCCCGACGTGCACGCGA
1 AGACAAGGTCAAAGATCAACCCCGACGTGCACATGA
* * * *
1494 AGACAAGGCCAAAGATCAACCCCAACATGCACAAGA
1 AGACAAGGTCAAAGATCAACCCCGACGTGCACATGA
1530 AGAC
1 AGAC
1534 GGGGCCGAAG
Statistics
Matches: 93, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 93 1.00
ACGTcount: A:0.38, C:0.27, G:0.25, T:0.10
Consensus pattern (36 bp):
AGACAAGGTCAAAGATCAACCCCGACGTGCACATGA
Found at i:1525 original size:72 final size:72
Alignment explanation
Indices: 1386--1546 Score: 187
Period size: 72 Copynumber: 2.2 Consensus size: 72
1376 TGGAGGTAAG
* * * * * ** *
1386 AGACGAGGCCAAAGATCAACCGCGATGTGCACATGAAGACAAGGTCGAAGATCAACCCTGACGTG
1 AGACGAGGCCAAAGATCAACCCCGACGTGCACACGAAGACAAGGCCAAAGATCAACCCCAACATG
**
1451 CACGTGA
66 CACAAGA
** *
1458 AGACGAGGTTAAAGATCAACCCCGACGTGCACGCGAAGACAAGGCCAAAGATCAACCCCAACATG
1 AGACGAGGCCAAAGATCAACCCCGACGTGCACACGAAGACAAGGCCAAAGATCAACCCCAACATG
1523 CACAAGA
66 CACAAGA
* *
1530 AGACGGGGCCGAAGATC
1 AGACGAGGCCAAAGATC
1547 TAGTGGAGTT
Statistics
Matches: 72, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.37, C:0.27, G:0.27, T:0.10
Consensus pattern (72 bp):
AGACGAGGCCAAAGATCAACCCCGACGTGCACACGAAGACAAGGCCAAAGATCAACCCCAACATG
CACAAGA
Found at i:5633 original size:21 final size:21
Alignment explanation
Indices: 5603--5655 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
5593 TACTTGCATT
*
5603 GTATCGGTAGTACCATGATAA
1 GTATCAGTAGTACCATGATAA
5624 GTATCAGTAGTACCATGATAA
1 GTATCAGTAGTACCATGATAA
5645 GTATCAGTAGT
1 GTATCAGTAGT
5656 TTTGTTCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (21 bp):
GTATCAGTAGTACCATGATAA
Found at i:7622 original size:26 final size:26
Alignment explanation
Indices: 7592--7644 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
7582 AAGTTGTAAA
7592 TAAAAAAATTATCTCTAGAG-ATTTTC
1 TAAAAAAA-TATCTCTAGAGAATTTTC
* * *
7618 TAAAATAATCTCTTTAGAGAATTTTC
1 TAAAAAAATATCTCTAGAGAATTTTC
7644 T
1 T
7645 CTTTACAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.42
Consensus pattern (26 bp):
TAAAAAAATATCTCTAGAGAATTTTC
Found at i:7628 original size:23 final size:25
Alignment explanation
Indices: 7596--7644 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
7586 TGTAAATAAA
*
7596 AAAATTATCTC-TAGAG-ATTTTCT
1 AAAATAATCTCTTAGAGAATTTTCT
7619 AAAATAATCTCTTTAGAGAATTTTCT
1 AAAATAATCTC-TTAGAGAATTTTCT
7645 CTTTACAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 10 0.45
25 5 0.23
26 7 0.32
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (25 bp):
AAAATAATCTCTTAGAGAATTTTCT
Found at i:7904 original size:11 final size:11
Alignment explanation
Indices: 7890--7965 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
7880 GATAATCACT
7890 TTAATATTAAA
1 TTAATATTAAA
7901 TTAATA--AAA
1 TTAATATTAAA
*
7910 -TATTATTAAA
1 TTAATATTAAA
*
7920 ATAAGTATTAAA
1 TTAA-TATTAAA
7932 TTAA-ATTTAATA
1 TTAATA-TTAA-A
7944 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
7957 ATAATATTA
1 TTAATATTA
7966 TTTTTGGAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 4 0.08
11 17 0.33
12 15 0.29
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
TTAATATTAAA
Done.