Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000087.1 Kokia drynarioides strain JFW-HI SEQ_110713, 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: 47391
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 44 characters in sequence are not A, C, G, or T
Found at i:17245 original size:18 final size:18
Alignment explanation
Indices: 17224--17261 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
17214 TGAATTTTCG
*
17224 AATTTGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
17242 AATTCGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
17260 AA
1 AA
17262 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:23038 original size:27 final size:27
Alignment explanation
Indices: 22994--23048 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
22984 ATTGAATATT
*
22994 AATTAATATGATAGTATG-TTAATGTAA
1 AATTAATATGATACTATGTTTAAT-TAA
* *
23021 AATTAATTTGATCCTATGTTTAATTAA
1 AATTAATATGATACTATGTTTAATTAA
23048 A
1 A
23049 GAACCCAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.44
Consensus pattern (27 bp):
AATTAATATGATACTATGTTTAATTAA
Found at i:23680 original size:19 final size:20
Alignment explanation
Indices: 23645--23685 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
23635 TTTTTAAATC
23645 TATAAAATCAATAATA-TAA
1 TATAAAATCAATAATATTAA
*
23664 TATAAGAAT-AATTATATTAA
1 TATAA-AATCAATAATATTAA
23684 TA
1 TA
23686 AGATTTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
TATAAAATCAATAATATTAA
Found at i:24037 original size:26 final size:26
Alignment explanation
Indices: 23984--24044 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
23974 GATGTTTAGC
* *
23984 TATTATTATTTGATATTCGATAGTTT
1 TATTATTATTTGATATTCAATAATTT
*
24010 TATTATTATTTGAT-TTTAATAATATT
1 TATTATTATTTGATATTCAATAAT-TT
24036 TA-TATTATT
1 TATTATTATT
24045 GTGAATGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.42
26 18 0.58
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.61
Consensus pattern (26 bp):
TATTATTATTTGATATTCAATAATTT
Found at i:24082 original size:18 final size:19
Alignment explanation
Indices: 24037--24090 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
24027 AATAATATTT
*
24037 ATATTATTGTGAATGTAAT
1 ATATTATTGTGAATGTAAA
* * *
24056 TTATCATTGTG-TTGTAAA
1 ATATTATTGTGAATGTAAA
24074 ATATTATTGTGAATGTA
1 ATATTATTGTGAATGTA
24091 GTTTAATAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (19 bp):
ATATTATTGTGAATGTAAA
Found at i:30534 original size:26 final size:26
Alignment explanation
Indices: 30505--30558 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
30495 TTGAACATAG
*
30505 TATAATTAAAAAAATTAAAATTATTA
1 TATAAATAAAAAAATTAAAATTATTA
* * * *
30531 TATAAATATAAAATTTAACATTTTTA
1 TATAAATAAAAAAATTAAAATTATTA
30557 TA
1 TA
30559 GATATAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAAATAAAAAAATTAAAATTATTA
Found at i:39497 original size:18 final size:17
Alignment explanation
Indices: 39465--39498 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39455 TTGTTTATAA
39465 TTTAATAAATTAATTAT
1 TTTAATAAATTAATTAT
*
39482 TTTAAGTAATTTAATTA
1 TTTAA-TAAATTAATTA
39499 AATTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAATAAATTAATTAT
Found at i:44355 original size:15 final size:17
Alignment explanation
Indices: 44335--44381 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
44325 AAAATATTTC
44335 AAACAAT-ATA-ATAAT
1 AAACAATAATATATAAT
44350 AAACAATAATATATAAT
1 AAACAATAATATATAAT
*
44367 AATA-ATTAATATATA
1 AA-ACAATAATATATA
44382 TAACCATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 7 0.25
16 3 0.11
17 17 0.61
18 1 0.04
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
AAACAATAATATATAAT
Found at i:44363 original size:20 final size:19
Alignment explanation
Indices: 44340--44384 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
44330 ATTTCAAACA
44340 ATATAATAATAAACAATAAT
1 ATATAATAATAAACAAT-AT
**
44360 ATATAATAATAATTAATAT
1 ATATAATAATAAACAATAT
44379 ATATAA
1 ATATAA
44385 CCATTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
ATATAATAATAAACAATAT
Found at i:44390 original size:16 final size:17
Alignment explanation
Indices: 44339--44396 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
44329 TATTTCAAAC
44339 AATATAATAATAAACAA-T
1 AATAT-ATAAT-AACAATT
*
44357 AATATATAATAATAATT
1 AATATATAATAACAATT
*
44374 AATATAT-ATAACCATT
1 AATATATAATAACAATT
*
44390 ATTATAT
1 AATATAT
44397 TATAGATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
16 17 0.49
17 13 0.37
18 5 0.14
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
AATATATAATAACAATT
Found at i:44729 original size:3 final size:3
Alignment explanation
Indices: 44716--44748 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
44706 AATTATCAAT
44716 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
44749 ATATTTGCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:45139 original size:6 final size:6
Alignment explanation
Indices: 45118--45155 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
45108 ATCGCCTTTA
45118 AAAAAT ACATAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT A-A-AAAT AAAAAT AAAAAT AAAAAT AAAAAT
45156 TATATAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 23 0.77
7 2 0.07
8 5 0.17
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:45406 original size:32 final size:33
Alignment explanation
Indices: 45339--45413 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 33
45329 TTTTAAATTT
* *
45339 AATATTTTTTGGTGTTTGGATGAATTTATGTAA
1 AATATTTTATGGTGTTTGGATAAATTTATGTAA
* *
45372 AATATTTTATGTTGTTT-GATAAATTTCT-TGAA
1 AATATTTTATGGTGTTTGGATAAATTTATGT-AA
45404 AATATTTTAT
1 AATATTTTAT
45414 AAAAACCATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 1 0.03
32 21 0.57
33 15 0.41
ACGTcount: A:0.31, C:0.01, G:0.15, T:0.53
Consensus pattern (33 bp):
AATATTTTATGGTGTTTGGATAAATTTATGTAA
Found at i:46492 original size:31 final size:31
Alignment explanation
Indices: 46456--46516 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
46446 TATAGGTTCC
46456 GTCTGCAGTGACCAAACCATATCATATATTT
1 GTCTGCAGTGACCAAACCATATCATATATTT
46487 GTCTGCAGTGACCAAACCATATCATATATT
1 GTCTGCAGTGACCAAACCATATCATATATT
46517 AGGCGATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (31 bp):
GTCTGCAGTGACCAAACCATATCATATATTT
Done.