Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015130.1 Kokia drynarioides strain JFW-HI SEQ_130174, 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: 63067
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:16465 original size:26 final size:26
Alignment explanation
Indices: 16436--16487 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
16426 CGCCGTCCGA
16436 TTTGAGCTTGTTGATACGCCGACAAT
1 TTTGAGCTTGTTGATACGCCGACAAT
*
16462 TTTGGGCTTGTTGATACGCCGACAAT
1 TTTGAGCTTGTTGATACGCCGACAAT
16488 ATATCGCGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (26 bp):
TTTGAGCTTGTTGATACGCCGACAAT
Found at i:21883 original size:21 final size:20
Alignment explanation
Indices: 21859--21899 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
21849 TTTATATATA
21859 TTCTTATAAAAATATGTTTTT
1 TTCTTATAAAAA-ATGTTTTT
* *
21880 TTCTTCTACAAAATGTTTTT
1 TTCTTATAAAAAATGTTTTT
21900 ATTAATAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (20 bp):
TTCTTATAAAAAATGTTTTT
Found at i:23337 original size:9 final size:9
Alignment explanation
Indices: 23323--23357 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
23313 GACATTTTTA
23323 AATTAAAAT
1 AATTAAAAT
23332 AATTAAATAT
1 AATTAAA-AT
*
23342 AATTAAATT
1 AATTAAAAT
23351 AATTAAA
1 AATTAAA
23358 CTAAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
AATTAAAAT
Found at i:24202 original size:9 final size:10
Alignment explanation
Indices: 24178--24202 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
24168 TATAAACTTA
24178 TAAAAAATAT
1 TAAAAAATAT
24188 TAAAAAATAT
1 TAAAAAATAT
24198 TAAAA
1 TAAAA
24203 CTTATAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:24537 original size:12 final size:12
Alignment explanation
Indices: 24522--24554 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
24512 ATTGTTTTGG
*
24522 TTTTTCTTT-TT
1 TTTTTTTTTCTT
24533 TTTTTTTTTCTT
1 TTTTTTTTTCTT
24545 TTTTTTTTTC
1 TTTTTTTTTC
24555 AGATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:24540 original size:15 final size:15
Alignment explanation
Indices: 24522--24553 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
24512 ATTGTTTTGG
24522 TTTTTCTTTTTTTTT
1 TTTTTCTTTTTTTTT
24537 TTTTTCTTTTTTTTT
1 TTTTTCTTTTTTTTT
24552 TT
1 TT
24554 CAGATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (15 bp):
TTTTTCTTTTTTTTT
Found at i:41540 original size:14 final size:14
Alignment explanation
Indices: 41521--41556 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
41511 TTGTTTGATT
41521 GAAAATGACTTTCG
1 GAAAATGACTTTCG
* *
41535 GAAAATGATTTTTG
1 GAAAATGACTTTCG
41549 GAAAATGA
1 GAAAATGA
41557 ATTACTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (14 bp):
GAAAATGACTTTCG
Found at i:41828 original size:22 final size:22
Alignment explanation
Indices: 41796--41839 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
41786 ATATATTAAT
41796 AATCATACCTAATTAGCTGATG
1 AATCATACCTAATTAGCTGATG
* *
41818 AATCATGCCTAGTTAGCTGATG
1 AATCATACCTAATTAGCTGATG
41840 CTTAGTACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (22 bp):
AATCATACCTAATTAGCTGATG
Found at i:45131 original size:45 final size:45
Alignment explanation
Indices: 45081--45172 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
45071 ATATTTAATT
45081 TTGGTAGTTAAGTTTTTTGGCAAGAATAATACTTAAATTATTAAA
1 TTGGTAGTTAAGTTTTTTGGCAAGAATAATACTTAAATTATTAAA
45126 TTGGTAGTTAAGTTTTTTGGCAAGAATAATACTTAAATTATTAAA
1 TTGGTAGTTAAGTTTTTTGGCAAGAATAATACTTAAATTATTAAA
45171 TT
1 TT
45173 TATCTTAGCG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.43
Consensus pattern (45 bp):
TTGGTAGTTAAGTTTTTTGGCAAGAATAATACTTAAATTATTAAA
Found at i:46108 original size:21 final size:20
Alignment explanation
Indices: 46059--46104 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
46049 AAAGAACTTA
46059 TTTTATGTTGATCTGTAAATAT
1 TTTTATGTTGATC--TAAATAT
46081 TTTTATGTTGATC-AAATTAT
1 TTTTATGTTGATCTAAA-TAT
46101 TTTT
1 TTTT
46105 TATGAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.13
20 7 0.30
22 13 0.57
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.59
Consensus pattern (20 bp):
TTTTATGTTGATCTAAATAT
Found at i:57809 original size:26 final size:24
Alignment explanation
Indices: 57780--57830 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
57770 ATTAATTATT
*
57780 TAAACTAATTAATAATAATATAAAAA
1 TAAACAAATT-AT-ATAATATAAAAA
* *
57806 TAAAGAAATTATATTATATAAAAA
1 TAAACAAATTATATAATATAAAAA
57830 T
1 T
57831 TTAAAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 12 0.55
25 2 0.09
26 8 0.36
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAACAAATTATATAATATAAAAA
Found at i:61531 original size:30 final size:31
Alignment explanation
Indices: 61470--61531 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
61460 TAATAGATAA
* *
61470 AAATTAATAAAAGGATTAATTTATATGTTTTT
1 AAATAAATAAAA-GATTAATTTATATATTTTT
*
61502 AAATAAATAAAA-ATTAATTTATTTATTTTT
1 AAATAAATAAAAGATTAATTTATATATTTTT
61532 TTAGTAATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 16 0.59
32 11 0.41
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (31 bp):
AAATAAATAAAAGATTAATTTATATATTTTT
Done.