Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013424.1 Kokia drynarioides strain JFW-HI SEQ_128450, 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: 56203
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 115 characters in sequence are not A, C, G, or T
Found at i:10436 original size:29 final size:30
Alignment explanation
Indices: 10402--10460 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
10392 TATGGTTTAA
10402 TGTGTAATTGTATACATG-AATTTTAATTT
1 TGTGTAATTGTATACATGAAATTTTAATTT
* *
10431 TGTGTAATTTTATACATGAAATTTTGATTT
1 TGTGTAATTGTATACATGAAATTTTAATTT
10461 GATCCAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (30 bp):
TGTGTAATTGTATACATGAAATTTTAATTT
Found at i:12270 original size:134 final size:136
Alignment explanation
Indices: 12132--12401 Score: 372
Period size: 137 Copynumber: 2.0 Consensus size: 136
12122 TTCAGATGTT
* **
12132 AAAGATAAACAAA-ATTGCAAACAATAATCACAAATCTT-AAAATCT-CGAAAAAATTAATGTTT
1 AAAGATAAACAAAGA-TGCAAACAATAATCACAAA-CTTAAAAATCTCCAAAAAAATTAATACTT
* * **
12194 ATAATTTAT-AAATCAAAATGAAAATAT-ATAAATTTT-AAAATTATATACCAATTTTTATTTTA
64 ATAATCTATAAAATCAAAATGAAAAT-TGAT-AATTTTAAAAATTATAAACCAATTTTTAAGTTA
12256 ATATCAAATA
127 ATATCAAATA
*
12266 AAAGATAAACAAAGATGCTAACAATAATCACAAACTTCAAAAATCTCCAAAAAAATTAATACTTA
1 AAAGATAAACAAAGATGCAAACAATAATCACAAACTT-AAAAATCTCCAAAAAAATTAATACTTA
*
12331 TAATCTATAAAATCAAAATGAAAATTGATAATTTTAAAAATTATAAATCAATTTTTAAGTTAATA
65 TAATCTATAAAATCAAAATGAAAATTGATAATTTTAAAAATTATAAACCAATTTTTAAGTTAATA
12396 TCAAAT
130 TCAAAT
12402 CGATTGTATC
Statistics
Matches: 120, Mismatches: 9, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
133 3 0.03
134 31 0.26
135 8 0.07
136 29 0.24
137 49 0.41
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.32
Consensus pattern (136 bp):
AAAGATAAACAAAGATGCAAACAATAATCACAAACTTAAAAATCTCCAAAAAAATTAATACTTAT
AATCTATAAAATCAAAATGAAAATTGATAATTTTAAAAATTATAAACCAATTTTTAAGTTAATAT
CAAATA
Found at i:20785 original size:2 final size:2
Alignment explanation
Indices: 20780--20821 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
20770 TCTTGATATA
* *
20780 TG TG TG TG TG TG TG TG TG TG TG TT TG TG TT TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
20822 CTAGAGTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (2 bp):
TG
Found at i:43038 original size:25 final size:25
Alignment explanation
Indices: 42977--43038 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
42967 AAATTTATTA
* *
42977 TATAATAAAATTTTTATTTTGATATG
1 TATAAT-ATATTTTTATTTTAATATG
* *
43003 TTTTATATATTTTTATTTTAATATG
1 TATAATATATTTTTATTTTAATATG
*
43028 TATAATTTATT
1 TATAATATATT
43039 ATCTTCATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (25 bp):
TATAATATATTTTTATTTTAATATG
Found at i:43517 original size:14 final size:14
Alignment explanation
Indices: 43494--43528 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
43484 TACAATATCT
43494 AAATAATAACAACA
1 AAATAATAACAACA
*
43508 AAATAGTAACAACA
1 AAATAATAACAACA
*
43522 TAATAAT
1 AAATAAT
43529 GAAATGACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (14 bp):
AAATAATAACAACA
Found at i:44570 original size:20 final size:20
Alignment explanation
Indices: 44544--44597 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
44534 ATCGATGCAA
44544 AATAAATAATTAAAATTTATT
1 AATAAATAATTAAAA-TTATT
*
44565 -ATAAATAA-TATAATTATT
1 AATAAATAATTAAAATTATT
44583 AATAAAGTAATTAAA
1 AATAAA-TAATTAAA
44598 TAAATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 5 0.18
19 9 0.32
20 11 0.39
21 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
AATAAATAATTAAAATTATT
Found at i:55415 original size:11 final size:11
Alignment explanation
Indices: 55377--55415 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
55367 AAATAACAGT
55377 AAAAACAATAA
1 AAAAACAATAA
*
55388 GAAAACAATAA
1 AAAAACAATAA
*
55399 CCAAAACAATAA
1 -AAAAACAATAA
55411 AAAAA
1 AAAAA
55416 GTACTAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.77, C:0.13, G:0.03, T:0.08
Consensus pattern (11 bp):
AAAAACAATAA
Found at i:55424 original size:20 final size:21
Alignment explanation
Indices: 55378--55436 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
55368 AATAACAGTA
55378 AAAACAATAAGAAAACAATAACC
1 AAAACAATAA-AAAA-AATAACC
* *
55401 AAAACAATAAAAAAAGT-ACT
1 AAAACAATAAAAAAAATAACC
*
55421 AAAACAGTAAAAAAAA
1 AAAACAATAAAAAAAA
55437 ACAACACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 16 0.50
21 2 0.06
22 4 0.12
23 10 0.31
ACGTcount: A:0.73, C:0.12, G:0.05, T:0.10
Consensus pattern (21 bp):
AAAACAATAAAAAAAATAACC
Found at i:55448 original size:34 final size:33
Alignment explanation
Indices: 55401--55482 Score: 101
Period size: 34 Copynumber: 2.5 Consensus size: 33
55391 AACAATAACC
* * **
55401 AAAACAATAAAAAAAGTACTAAAACAGTAAAAA
1 AAAACAACAAAAAAAGCAAAAAAACAGTAAAAA
55434 AAAACAACACAAAAAAGCAAAAAAACAGTAAAAA
1 AAAACAACA-AAAAAAGCAAAAAAACAGTAAAAA
* *
55468 AAAGCACCAAAAAAA
1 AAAACAACAAAAAAA
55483 CAATATAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 14 0.33
34 28 0.67
ACGTcount: A:0.74, C:0.13, G:0.06, T:0.06
Consensus pattern (33 bp):
AAAACAACAAAAAAAGCAAAAAAACAGTAAAAA
Found at i:55466 original size:18 final size:16
Alignment explanation
Indices: 55421--55470 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
55411 AAAAAGTACT
55421 AAAACAGTAAAAAAAA
1 AAAACAGTAAAAAAAA
* **
55437 ACAACACAAAAAAGCAAA
1 AAAACAGTAAAAA--AAA
55455 AAAACAGTAAAAAAAA
1 AAAACAGTAAAAAAAA
55471 GCACCAAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
16 13 0.50
18 13 0.50
ACGTcount: A:0.78, C:0.12, G:0.06, T:0.04
Consensus pattern (16 bp):
AAAACAGTAAAAAAAA
Done.