Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011355.1 Kokia drynarioides strain JFW-HI SEQ_126335, 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: 25138
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Found at i:1641 original size:24 final size:25
Alignment explanation
Indices: 1614--1672 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
1604 TTACTCACCG
*
1614 CGCACCGTTTCACTA-AACCTCAAA
1 CGCACCGTTTCACTAGAACCCCAAA
*
1638 CGCACCGTTTCACTAGACCCCCAAA
1 CGCACCGTTTCACTAGAACCCCAAA
1663 CGCACCGTTT
1 CGCACCGTTT
1673 TGAACACAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 15 0.47
25 17 0.53
ACGTcount: A:0.27, C:0.41, G:0.12, T:0.20
Consensus pattern (25 bp):
CGCACCGTTTCACTAGAACCCCAAA
Found at i:12559 original size:31 final size:31
Alignment explanation
Indices: 12523--12581 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
12513 TTTTTTATTC
12523 AATTTGGTACTCAAACTTGACACTTTTTCCT
1 AATTTGGTACTCAAACTTGACACTTTTTCCT
* *
12554 AATTTGGTACTTAAATTTGACACTTTTT
1 AATTTGGTACTCAAACTTGACACTTTTT
12582 TTTTTTGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (31 bp):
AATTTGGTACTCAAACTTGACACTTTTTCCT
Found at i:12870 original size:31 final size:29
Alignment explanation
Indices: 12830--12981 Score: 116
Period size: 29 Copynumber: 5.0 Consensus size: 29
12820 CTAAAAAAGC
12830 TTAGGTACCAAATTAGGAAAAAATGCCAAGT
1 TTAGGTACCAAATT-GGAAAAAATG-CAAGT
*
12861 TCAGGTACCAAATTGGATCCAAAAA---AAGT
1 TTAGGTACCAAATTGGA---AAAAATGCAAGT
*
12890 TTAGGTACCAAATTGGGAAAAAGTGTCAAGT
1 TTAGGTACCAAATT-GGAAAAAATG-CAAGT
* *
12921 TTAGGTACCAAATTGGATCAAAAA--AAAAT
1 TTAGGTACCAAATTGGA--AAAAATGCAAGT
**
12950 TTAGGTACCAAATTAAAAAAAAGTGTCAAGT
1 TTAGGTACCAAATTGGAAAAAA-TG-CAAGT
12981 T
1 T
12982 CAAGTACTAA
Statistics
Matches: 97, Mismatches: 10, Indels: 28
0.72 0.07 0.21
Matches are distributed among these distances:
27 9 0.09
29 35 0.36
30 9 0.09
31 35 0.36
32 4 0.04
33 5 0.05
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.24
Consensus pattern (29 bp):
TTAGGTACCAAATTGGAAAAAATGCAAGT
Found at i:12901 original size:60 final size:60
Alignment explanation
Indices: 12804--12993 Score: 249
Period size: 60 Copynumber: 3.2 Consensus size: 60
12794 TAATAAATTT
* * * *
12804 AGGTACCAAATTGAAT-CTAAAAAAGCTTAGGTACCAAATTAGGAAAAAATGCCAAGTTC
1 AGGTACCAAATTGGATCCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTC
* * *
12863 AGGTACCAAATTGGATCCAAAAAAAGTTTAGGTACCAAATTGGGAAAAAGTGTCAAGTTT
1 AGGTACCAAATTGGATCCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTC
* * *
12923 AGGTACCAAATTGGATCAAAAAAAAATTTAGGTACCAAATTA-AAAAAAAGTGTCAAGTTC
1 AGGTACCAAATTGGATCCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAA-TGTCAAGTTC
* *
12983 AAGTACTAAAT
1 AGGTACCAAAT
12994 ATTATATTAA
Statistics
Matches: 114, Mismatches: 15, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
59 20 0.18
60 94 0.82
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.24
Consensus pattern (60 bp):
AGGTACCAAATTGGATCCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTC
Found at i:15390 original size:50 final size:50
Alignment explanation
Indices: 15315--15414 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
15305 AGTTTATTCG
*
15315 GATGTTTGTGAATTAAATAGAACTCTAACAAGAGGTGGAAAATGATATTT
1 GATGTTTGTGAATTAAATAGAACTCTAACAAGAGGTAGAAAATGATATTT
*
15365 GATGTTTGTGAATTAAATGGAACTCTAACAAGAGGTAGAAAATGATATTT
1 GATGTTTGTGAATTAAATAGAACTCTAACAAGAGGTAGAAAATGATATTT
15415 TATCACTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (50 bp):
GATGTTTGTGAATTAAATAGAACTCTAACAAGAGGTAGAAAATGATATTT
Found at i:17072 original size:18 final size:18
Alignment explanation
Indices: 17049--17085 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17039 ACAATTCATA
17049 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
17067 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
17085 T
1 T
17086 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:17840 original size:9 final size:9
Alignment explanation
Indices: 17828--17852 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
17818 CTTCTATTCC
17828 TTCTTTTGT
1 TTCTTTTGT
17837 TTCTTTTGT
1 TTCTTTTGT
17846 TTCTTTT
1 TTCTTTT
17853 CTTTATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (9 bp):
TTCTTTTGT
Done.