Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000271.1 Kokia drynarioides strain JFW-HI SEQ_111017, 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: 6892
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:3961 original size:109 final size:108
Alignment explanation
Indices: 3817--4020 Score: 338
Period size: 109 Copynumber: 1.9 Consensus size: 108
3807 ACAAAGAACA
* *
3817 TTTAAGTAGATATTCAATTACTTAGGTTCAAAGAAAAATCATAC-CAAGTACGTTAGGGCACAAT
1 TTTAAATAGATATTCAATTACTTAGGTTCAAAGAAAAATCATACTCAA-TACATTAGGGCACAAT
*
3881 TTCTCGAGTTCCCTAAAATAAAAGAACATTAAACATTTATCGAT
65 TTCTCGAGGTCCCTAAAATAAAAGAACATTAAACATTTATCGAT
*
3925 TTTAAATAGGATATTCAATTACTTAGGTTCAAAGAAAAATCATACTCAATATATTAGGGCACAAT
1 TTTAAATA-GATATTCAATTACTTAGGTTCAAAGAAAAATCATACTCAATACATTAGGGCACAAT
*
3990 TTCTCGAGGTCCCTAAAATAAAAGAATATTA
65 TTCTCGAGGTCCCTAAAATAAAAGAACATTA
4021 CCTTCATTTG
Statistics
Matches: 89, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
108 7 0.08
109 79 0.89
110 3 0.03
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.31
Consensus pattern (108 bp):
TTTAAATAGATATTCAATTACTTAGGTTCAAAGAAAAATCATACTCAATACATTAGGGCACAATT
TCTCGAGGTCCCTAAAATAAAAGAACATTAAACATTTATCGAT
Found at i:4424 original size:41 final size:42
Alignment explanation
Indices: 4354--4434 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
4344 AGATAACAAC
*
4354 AAAATAAAAGGATTAAATTTAAAATGAAAATAAAATAAAAAT
1 AAAATAAAAGGATTAAATTTAAAATGAAAACAAAATAAAAAT
* *
4396 AAAATAAAAGGACTT-AGTTTAAAA-GAAAACAGAATAAAA
1 AAAATAAAAGGA-TTAAATTTAAAATGAAAACAAAATAAAA
4435 GGGCAAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 13 0.37
42 20 0.57
43 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.10, T:0.21
Consensus pattern (42 bp):
AAAATAAAAGGATTAAATTTAAAATGAAAACAAAATAAAAAT
Found at i:4432 original size:30 final size:30
Alignment explanation
Indices: 4398--4454 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
4388 ATAAAAATAA
** *
4398 AATAAAAGGACTTAGTTTAAAAGAAAACAG
1 AATAAAAGGACAAAATTTAAAAGAAAACAG
*
4428 AATAAAAGGGCAAAATTTAAAAGAAAA
1 AATAAAAGGACAAAATTTAAAAGAAAA
4455 ATTTTGAGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.61, C:0.05, G:0.16, T:0.18
Consensus pattern (30 bp):
AATAAAAGGACAAAATTTAAAAGAAAACAG
Found at i:5971 original size:19 final size:19
Alignment explanation
Indices: 5949--5989 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5939 TTTTGTTTTA
5949 TTTGTTTTA-TTTTGGTTGG
1 TTTG-TTTAGTTTTGGTTGG
*
5968 TTTGTTTAGTTTTGTTTGG
1 TTTGTTTAGTTTTGGTTGG
5987 TTT
1 TTT
5990 TGGTTTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.05, C:0.00, G:0.24, T:0.71
Consensus pattern (19 bp):
TTTGTTTAGTTTTGGTTGG
Found at i:6001 original size:5 final size:5
Alignment explanation
Indices: 5939--6008 Score: 54
Period size: 5 Copynumber: 14.2 Consensus size: 5
5929 TGCATATATT
* * * * * *
5939 TTTTG TTTT- ATTTG TTTTA TTTTG -GTTG GTTTG TTTAG TTTTG TTTGG
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
*
5987 TTTTGG TTTTG TTTTA TTTTG T
1 TTTT-G TTTTG TTTTG TTTTG T
6009 ACTACACCTA
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
4 6 0.12
5 38 0.78
6 5 0.10
ACGTcount: A:0.06, C:0.00, G:0.21, T:0.73
Consensus pattern (5 bp):
TTTTG
Found at i:6512 original size:45 final size:45
Alignment explanation
Indices: 6426--6876 Score: 573
Period size: 45 Copynumber: 10.0 Consensus size: 45
6416 TGAGATGGAA
* *
6426 GCTTTAATCTGCCCCTCTGGATTTAGGGGTAAAAGATTGGATGGTG
1 GCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTGGATGGTG
* * * * *
6472 GCTTTAATCAGCCCCTTTTGGTTAGGGGTAAAAGATTGGATGGTA
1 GCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTG
* * *
6517 GCTTCAATCTACCACTCTTGATTAGGGGTGAAAGATTGGATGGTG
1 GCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTG
* * * * * *
6562 GCTTCAACCTACCCCTCTTAACTTAAGGGTAAAAAATTAGATGGTG
1 GCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTGGATGGTG
* * *
6608 GCTTCAATCT-ACCCTCTTGATTAGAGGTAAAAGAGTGGATGGTG
1 GCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTG
* *
6652 GTTTCAATCTTCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTG
1 GCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTG
*
6697 GCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGACGGTG
1 GCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTGGATGGTG
*
6743 GCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGATG
1 GCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTG
* * * * * *
6788 ACTTCAATCTGTCTCTCTTGATTAGTGGAAAAAG-GTGGATGGTG
1 GCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTG
* *
6832 ACTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGTATGGT
1 GCTTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTGGATGGT
6877 CTTCTATTTG
Statistics
Matches: 350, Mismatches: 50, Indels: 10
0.85 0.12 0.02
Matches are distributed among these distances:
44 55 0.16
45 198 0.57
46 97 0.28
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (45 bp):
GCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTG
Done.