Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015084.1 Kokia drynarioides strain JFW-HI SEQ_130128, 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: 42996
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Found at i:10312 original size:23 final size:22
Alignment explanation
Indices: 10270--10318 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
10260 AGAAATCTAA
*
10270 TTTATTTAAACTTTACTTTTAT
1 TTTATTTAAACTGTACTTTTAT
10292 TTTATTTTACAACTGTA-TTTTAT
1 TTTA-TTTA-AACTGTACTTTTAT
10315 TTTA
1 TTTA
10319 ACAAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 14 0.58
24 6 0.25
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTATTTAAACTGTACTTTTAT
Found at i:10491 original size:71 final size:71
Alignment explanation
Indices: 10375--10516 Score: 284
Period size: 71 Copynumber: 2.0 Consensus size: 71
10365 ATGAAGGGAG
10375 ACTGCAAAGGAATTTTGGAGATAAAAGAAGACAAGAAACCGAGTATAAATTTACATACATTGCTT
1 ACTGCAAAGGAATTTTGGAGATAAAAGAAGACAAGAAACCGAGTATAAATTTACATACATTGCTT
10440 AGAACT
66 AGAACT
10446 ACTGCAAAGGAATTTTGGAGATAAAAGAAGACAAGAAACCGAGTATAAATTTACATACATTGCTT
1 ACTGCAAAGGAATTTTGGAGATAAAAGAAGACAAGAAACCGAGTATAAATTTACATACATTGCTT
10511 AGAACT
66 AGAACT
10517 GGGGCAGGCA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (71 bp):
ACTGCAAAGGAATTTTGGAGATAAAAGAAGACAAGAAACCGAGTATAAATTTACATACATTGCTT
AGAACT
Found at i:16235 original size:21 final size:19
Alignment explanation
Indices: 16211--16264 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
16201 ATGTTATGTA
*
16211 TATATTAAAGTAATATTAATT
1 TATATTAAA-TAAAATTAA-T
*
16232 TATATTATAATAAAATTCAT
1 TATATTA-AATAAAATTAAT
16252 TATATT-AATAAAA
1 TATATTAAATAAAA
16265 AGAAAAGGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 7 0.23
20 7 0.23
21 14 0.47
22 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
TATATTAAATAAAATTAAT
Found at i:18090 original size:15 final size:15
Alignment explanation
Indices: 18070--18099 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18060 AGTAAATTTC
18070 ATGGTTTGGTTTATG
1 ATGGTTTGGTTTATG
18085 ATGGTTTGGTTTATG
1 ATGGTTTGGTTTATG
18100 TTATCAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.53
Consensus pattern (15 bp):
ATGGTTTGGTTTATG
Found at i:29604 original size:9 final size:10
Alignment explanation
Indices: 29583--29608 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
29573 GGACATTTCC
29583 AAAATATTAA
1 AAAATATTAA
29593 AAAATATTAA
1 AAAATATTAA
29603 AAAATA
1 AAAATA
29609 AATTTTAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAATATTAA
Found at i:36807 original size:30 final size:30
Alignment explanation
Indices: 36746--36836 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 30
36736 TAATAATTAG
* * *
36746 AATATACAGGAAATTAGAAA-AAAAATTAA
1 AATATAAAGGAAATTAGAAATTAAATTTAA
* *
36775 AATATAGAGGAAATTGGAAATTAAATTTAA
1 AATATAAAGGAAATTAGAAATTAAATTTAA
* * *
36805 AATAAAAACGAAATTACAAATTAAATTTAA
1 AATATAAAGGAAATTAGAAATTAAATTTAA
36835 AA
1 AA
36837 AGTAAACGGA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
29 18 0.35
30 34 0.65
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.25
Consensus pattern (30 bp):
AATATAAAGGAAATTAGAAATTAAATTTAA
Found at i:39421 original size:86 final size:86
Alignment explanation
Indices: 39273--39830 Score: 790
Period size: 86 Copynumber: 6.5 Consensus size: 86
39263 ATTTAAAATA
39273 TGATAAAAATTGTAATATAATAATAATAATAGTTTTTATTTAAATATATAAAATTAATAAATAAT
1 TGATAAAAATTGTAATATAATAATAAT-A-A-TTTTTATTTAAATATATAAAATTAATAAATAAT
*
39338 ATATTGTCAAATCAACACATTATT
63 GTATTGTCAAATCAACACATTATT
*
39362 TGATAAAAATTATAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATGTA
*
39427 TTATCAAATCAACACATTATT
66 TTGTCAAATCAACACATTATT
* *
39448 TGATAAAAATTGCAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATGTA
39513 TTGTCAAATCAACACATTATT
66 TTGTCAAATCAACACATTATT
* **
39534 TTATAAAAATTGTAATATAATAATAATCTTTTTTATTTAAATATATAAAATTAATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATGTA
* *
39599 TTGTTAAATCAACATATTATT
66 TTGTCAAATCAACACATTATT
* * *
39620 TGATAAAAATTGTAATATTATAATAATAATTTTTATTTAAATAT-TTAAGTTAATTAAATAATGT
1 TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAA-TAAATAATGT
*
39684 GTTGTCAAATCAACACATTATT
65 ATTGTCAAATCAACACATTATT
* * * *
39706 TGATAAAAATTG-----TAAT-ATAATAATTTGTACTTTAAATATGA-AAATTTGATAAATAATA
1 TGATAAAAATTGTAATATAATAATAATAATTTTTA-TTTAAATAT-ATAAAATTAATAAATAATG
* *
39764 TATTGTCAAATTAACACAATATT
64 TATTGTCAAATCAACACATTATT
* **
39787 TGATATAAATTGTAATATAATAATAATCTTTTTTTATTTAAATA
1 TGATAAAAATTGTAATATAATAATAAT-AATTTTTATTTAAATA
39831 ATGTTAAATT
Statistics
Matches: 422, Mismatches: 36, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
80 12 0.03
81 51 0.12
82 5 0.01
85 7 0.02
86 301 0.71
87 14 0.03
88 6 0.01
89 26 0.06
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (86 bp):
TGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATGTA
TTGTCAAATCAACACATTATT
Done.